From c0703e675c1db693e7f531068902bda50772f8fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Jan 2019 13:38:23 +0100 Subject: [PATCH 0001/9987] adding easyconfigs: STAR-CCM+-13.04.011.eb --- .../s/STAR-CCM+/STAR-CCM+-13.04.011.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-13.04.011.eb diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-13.04.011.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-13.04.011.eb new file mode 100644 index 00000000000..d8bd830cd11 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-13.04.011.eb @@ -0,0 +1,15 @@ +name = 'STAR-CCM+' +version = '13.04.011' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a complete multidisciplinary platform for the simulation of products and + designs operating under real-world conditions.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['STAR-CCM+%(version)s_01_linux-x86_64-r8.tar.gz'] +checksums = ['aa1e41a2dbfc939612b2c2f1aa121558ff5213067757705722d01c1ee2de0b65'] + +dependencies = [('Java', '1.8')] + +moduleclass = 'cae' From 0c0d1cf10f521654dd675619f7f51851542f8f87 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 22 Jan 2019 16:47:31 +0200 Subject: [PATCH 0002/9987] adding easyconfigs: Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb --- ...ree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb new file mode 100644 index 00000000000..560ec3fc001 --- /dev/null +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' +name = 'Embree' +version = "3.4.0" + +homepage = 'https://embree.github.io/' +description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" + +toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.3.0'} + +source_urls = ['https://github.com/embree/embree/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [] + +builddependencies = [('CMake', '3.11.4')] + +dependencies = [ + ('ispc', '1.10.0'), + ('tbb', '2018.1.163'), +] + +configopts = '-DEMBREE_TUTORIALS=OFF ' + +moduleclass = 'vis' From 3a9544975460d9bc726c3e430326a396e19cc9df Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Thu, 24 Jan 2019 11:04:39 +0200 Subject: [PATCH 0003/9987] added checksum and changed to available easyconfig-dependencies --- ....4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..19f13449e6a --- /dev/null +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' +name = 'Embree' +version = '3.4.0' + +gccver = '6.4.0' +binutilsver = '2.28' +gccsuff = '-GCC-%s' % (gccver) + +homepage = 'https://embree.github.io/' +description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" + +toolchain = {'name': 'iccifort', 'version': '2018.1.163%s-%s' % (gccsuff,binutilsver)} + +source_urls = ['https://github.com/embree/embree/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['22229f19332d4fd08eb3bf60198211bda674f51632b977c9d7fd09531e09dd8d'] + +builddependencies = [('CMake', '3.11.4','-GCCcore-%s' % gccver),] + +dependencies = [ + ('ispc', '1.10.0'), + ('tbb', '2018_U5','-GCCcore-%s' % gccver), +] + +configopts = '-DEMBREE_TUTORIALS=OFF ' + +moduleclass = 'vis' From 1a849ed22a7fd032557b9f7c8cb9d2c8875e3f9c Mon Sep 17 00:00:00 2001 From: Andreas Henkel Date: Thu, 24 Jan 2019 11:04:35 +0100 Subject: [PATCH 0004/9987] Delete Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb --- ...ree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb deleted file mode 100644 index 560ec3fc001..00000000000 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'CMakeMake' -name = 'Embree' -version = "3.4.0" - -homepage = 'https://embree.github.io/' -description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" - -toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.3.0'} - -source_urls = ['https://github.com/embree/embree/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = [] - -builddependencies = [('CMake', '3.11.4')] - -dependencies = [ - ('ispc', '1.10.0'), - ('tbb', '2018.1.163'), -] - -configopts = '-DEMBREE_TUTORIALS=OFF ' - -moduleclass = 'vis' From 75800d4c3c8b677f43474e822ba32bd2df7c6325 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Jan 2019 15:36:42 +0100 Subject: [PATCH 0005/9987] Calcam v2.1.0 for Python/3.6.4-intel-2018a --- .../Calcam-2.1.0-intel-2018a-Python-3.6.4.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..10926635e02 --- /dev/null +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Calcam' +version = '2.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://euratom-software.github.io/calcam' + +description = """Calcam is a Python package providing tools for spatial calibration + of cameras, i.e. determining the mapping between pixel coordinates in an image and + real-world 3D sight lines & coordinates.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/euratom-software/calcam/archive'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'download_filename': 'v%(version)s.tar.gz', # provided source tarball is not versioned... +}] +checksums = ['8348545719209650ac62ed8c77087ec6e42df77995ead59f3b2e035da962a679'] + +dependencies = [ + ('Python', '3.6.4'), + ('matplotlib', '2.1.2', '-Python-%(pyver)s'), + ('OpenCV', '3.4.1', '-Python-%(pyver)s'), + ('PyQt5', '5.9.2', '-Python-%(pyver)s'), + ('VTK', '8.1.0', '-Python-%(pyver)s'), +] + +download_dep_fail = True + +preinstallopts = 'echo n |' + +sanity_check_paths = { + 'files': ['bin/calcam'], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' From e76c2911c0844f1e522300bf237816b189477ca5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Jan 2019 18:36:47 +0100 Subject: [PATCH 0006/9987] Calcam v2.1.0 for Python/2.7.14-intel-2018a --- .../Calcam-2.1.0-intel-2018a-Python-2.7.14.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..2078324412c --- /dev/null +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Calcam' +version = '2.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://euratom-software.github.io/calcam' + +description = """Calcam is a Python package providing tools for spatial calibration + of cameras, i.e. determining the mapping between pixel coordinates in an image and + real-world 3D sight lines & coordinates.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/euratom-software/calcam/archive'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'download_filename': 'v%(version)s.tar.gz', # provided source tarball is not versioned... +}] +checksums = ['8348545719209650ac62ed8c77087ec6e42df77995ead59f3b2e035da962a679'] + +dependencies = [ + ('Python', '2.7.14'), + ('matplotlib', '2.1.2', '-Python-%(pyver)s'), + ('OpenCV', '3.4.1', '-Python-%(pyver)s'), + ('PyQt5', '5.9.2', '-Python-%(pyver)s'), + ('VTK', '8.1.0', '-Python-%(pyver)s'), +] + +download_dep_fail = True + +preinstallopts = 'echo n |' + +sanity_check_paths = { + 'files': ['bin/calcam'], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' From d6904e810a1c2e7401890df79f727c382c6ce57d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Jan 2019 18:59:55 +0100 Subject: [PATCH 0007/9987] OpenCV v3.4.1 for Python/2.7.14 on intel/2018a --- .../OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..e017af4d366 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,46 @@ +name = 'OpenCV' +version = '3.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [ + 'https://github.com/Itseez/opencv/archive/', + # the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake + 'https://raw.githubusercontent.com/Itseez/opencv_3rdparty/dfe3162c237af211e98b8960018b564bc209261d/ippicv', +] +sources = [ + '%(version)s.zip', + {'filename': 'ippicv_2017u3_lnx_intel64_general_20170822.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '24bda432eaace9e992322dcc3d30144cefa5314c2424d4aa02e5fe3fa9dd17bd', # 3.4.1.zip + # ippicv_2017u3_lnx_intel64_general_20170822.tgz + '9a4b14a24d31768c3ead0720f27d55dcf80723b5ba1cd8903bed1fd69f1b9e2e', +] + +builddependencies = [ + ('CMake', '3.10.2'), +] + +dependencies = [ + ('Python', '2.7.14'), + ('zlib', '1.2.11'), + ('FFmpeg', '3.4.2'), + ('libjpeg-turbo', '1.5.3'), + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), + ('JasPer', '2.0.14'), + ('Java', '1.8.0_162', '', True), + ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('GLib', '2.54.3'), + ('GTK+', '2.24.32'), +] + +moduleclass = 'vis' From 9cc6d66fc553c667499223912ea213a7045fca9a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Jan 2019 19:01:39 +0100 Subject: [PATCH 0008/9987] PyQt5 v5.9.2 for Python/2.7.14 on intel/2018a --- .../PyQt5-5.9.2-intel-2018a-Python-2.7.14.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..68fd5bf4ffd --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.9.2-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt5' +version = '5.9.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-%(version)s'] +sources = ['%(name)s_gpl-%(version)s.tar.gz'] +checksums = ['c190dac598c97b0113ca5e7a37c71c623f02d1d713088addfacac4acfa4b8394'] + +dependencies = [ + ('Python', '2.7.14'), + ('SIP', '4.19.8', versionsuffix), + ('Qt5', '5.10.1'), +] + +configopts = "configure.py --confirm-license --verbose" +configopts += " --destdir=%(installdir)s/lib/python%(pyshortver)s/site-packages --bindir=%(installdir)s/bin" +configopts += " --designer-plugindir=%(installdir)s/plugins/designer --qml-plugindir=%(installdir)s/plugins/PyQt5" +configopts += " --no-sip-files --no-stubs " + +options = {'modulename': '%(name)s'} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_PLUGIN_PATH': 'plugins', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'vis' From 6bcd154a657d90b272e588742df01afb61eb98d6 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 25 Jan 2019 08:39:24 +0100 Subject: [PATCH 0009/9987] SIP v4.19.8 for Python/2.7.14-intel-2018a --- .../SIP-4.19.8-intel-2018a-Python-2.7.14.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2018a-Python-2.7.14.eb new file mode 100644 index 00000000000..35357ae851c --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.19.8-intel-2018a-Python-2.7.14.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.19.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7eaf7a2ea7d4d38a56dd6d2506574464bddf7cf284c960801679942377c297bc'] + +dependencies = [('Python', '2.7.14')] + +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %(installdir)s/lib/python%(pyshortver)s/site-packages" + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%%(pyshortver)s/site-packages/%s' % x + for x in ['sip.%s' % SHLIB_EXT, 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' From 3692b57052b981f9dcaec345b9dd36ce157ad744 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 2 Feb 2019 19:09:29 +0100 Subject: [PATCH 0010/9987] Use pip to install Calcam v2.1.0 with Python/2.7.14 and Python/3.6.4 --- .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb | 2 ++ .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb index 2078324412c..d15eb614ace 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb @@ -27,6 +27,8 @@ dependencies = [ ('VTK', '8.1.0', '-Python-%(pyver)s'), ] +use_pip = True + download_dep_fail = True preinstallopts = 'echo n |' diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb index 10926635e02..78fed5ee963 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb @@ -27,6 +27,8 @@ dependencies = [ ('VTK', '8.1.0', '-Python-%(pyver)s'), ] +use_pip = True + download_dep_fail = True preinstallopts = 'echo n |' From cf6e06b286bc0ad30ccc6f2fe1e5a1a4656313bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Feb 2019 10:14:50 +0100 Subject: [PATCH 0011/9987] {bio}[intel/2018b] atropos v1.1.21 w/ Python 3.6.6 (+ deps) --- ...atropos-1.1.21-intel-2018b-Python-3.6.6.eb | 78 +++++++++++++++++++ .../NGS/NGS-2.9.3-intel-2018b-Python-3.6.6.eb | 40 ++++++++++ .../NGS-2.9.3_fix-python-install-prefix.patch | 13 ++++ .../Pysam-0.15.1-intel-2018b-Python-3.6.6.eb | 38 +++++++++ 4 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/n/NGS/NGS-2.9.3-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/n/NGS/NGS-2.9.3_fix-python-install-prefix.patch create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..440192d5efc --- /dev/null +++ b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'atropos' +version = '1.1.21' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://atropos.readthedocs.io' +description = "Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. " + +toolchain = {'name': 'intel', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('Pysam', '0.15.1', versionsuffix), + ('pytest', '3.8.2', versionsuffix), + ('NGS', '2.9.3', versionsuffix), # required for srastream +] + +#use_pip = True + +exts_list = [ + ('python-utils', '2.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-utils/'], + 'checksums': ['34aaf26b39b0b86628008f2ae0ac001b30e7986a8d303b61e1357dfcdad4f6d3'], + }), + ('progressbar2', '3.39.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/progressbar2/'], + 'checksums': ['6eb5135b987caca4212d2c7abc2923d4ad5ba18bb34ccbe7044b3628f52efc2c'], + 'modulename': 'progressbar', + }), + ('tqdm', '4.31.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tqdm/'], + 'checksums': ['e22977e3ebe961f72362f6ddfb9197cc531c9737aaf5f607ef09740c849ecd05'], + }), + ('bz2file', '0.98', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file/'], + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('screed', '1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/screed/'], + 'checksums': ['5db69f8c413a984ade62eb8344a6eb2be26555d74be86d38512673c1cf621b91'], + }), + ('khmer', '2.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/khmer/'], + 'checksums': ['a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24'], + }), + ('MarkupSafe', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], + }), + ('Jinja2', '2.10', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], + }), + ('pokrok', '0.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pokrok'], + 'checksums': ['cfe7956602d8bbc142a07bcb259e0d1d939f96d7b074e00dceea3cb5e39244e8'], + }), + ('xphyle', '4.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/x/xphyle/'], + 'checksums': ['b744723a3c88d81318c7291c32682b8715a046f70d0a1db729bda783fd5e08bd'], + }), + ('srastream', '0.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/srastream/'], + 'checksums': ['7f2cfd76ae988349ad5407a952cd4c133ae5dff7cf12c76072c53d82b50c2634'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/a/atropos/'], + 'checksums': ['8178af467734b299960edae15d8835a2228ba0cc1b718af436c7d86041fbd4ec'], + }), +] + +sanity_check_paths = { + 'files': ['bin/atropos'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.9.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NGS/NGS-2.9.3-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..410071ff7cb --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-2.9.3-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'NGS' +version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from + Next Generation Sequencing.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/ncbi/ngs/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['NGS-%(version)s_fix-python-install-prefix.patch'] +checksums = [ + 'd16cdf340f4c66e449cc490a222e54e9074cd15fe0938cb75b951a72985f757d', # 2.9.3.tar.gz + '72df59433ff1ad64e8313c6ed85286bcd25570eaef28c74ad5239fcaa9de8875', # NGS-2.9.3_fix-python-install-prefix.patch +] + +dependencies = [('Python', '3.6.6')] + +# override default of using $HOME/ncbi-outdir +configopts = "--build-prefix=%(builddir)s/ncbi-outdir" + +buildopts = 'CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-sdk && ' +buildopts += 'make CC="$CC -c" CPP="$CXX" CP="$CXX -c" -C ngs-python' + +installopts = "-C ngs-sdk && make install -C ngs-python" + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib64/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-adapt-c++.a', 'lib64/libngs-c++.a'], + 'dirs': ['include/ngs', 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.9.3_fix-python-install-prefix.patch b/easybuild/easyconfigs/n/NGS/NGS-2.9.3_fix-python-install-prefix.patch new file mode 100644 index 00000000000..92b99ee5e44 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-2.9.3_fix-python-install-prefix.patch @@ -0,0 +1,13 @@ +fix installation prefix for installing NGS Python bindings +author: Kenneth Hoste (HPC-UGent) +--- ngs-2.9.3/ngs-python/Makefile.python.orig 2019-02-12 09:33:55.145471383 +0100 ++++ ngs-2.9.3/ngs-python/Makefile.python 2019-02-12 09:34:09.145729890 +0100 +@@ -85,7 +85,7 @@ + + else + @ echo "Installing ngs package..." +- @ python setup.py -q install --user ++ @ python setup.py -q install --prefix $(INST_PYTHONDIR) + endif + + ifneq (, $(NGS_LIBDIR)) diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..d8ccf82a7a9 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.15.1-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Erich Birngruber +# Gregor Mendel Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.15.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'intel', 'version': '2018b'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['12221285af17e32b8f3fed033f90c6177a798afe41420eb5c3352d4e18ee12ed'] + +dependencies = [ + ('Python', '3.6.6'), + ('ncurses', '6.1'), + ('cURL', '7.60.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 9db07ad6cfc3cf2cae72a71065f6be2fe71611c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Feb 2019 11:40:58 +0100 Subject: [PATCH 0012/9987] use pip to install atropos --- .../a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb index 440192d5efc..487026ab37c 100644 --- a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb @@ -16,7 +16,7 @@ dependencies = [ ('NGS', '2.9.3', versionsuffix), # required for srastream ] -#use_pip = True +use_pip = True exts_list = [ ('python-utils', '2.3.0', { From 9ef18507280d8b6168c643a97fca0d1cde8f1e8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Feb 2019 10:47:56 +0100 Subject: [PATCH 0013/9987] adding easyconfigs: CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb, SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb --- .../CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb | 45 +++++++++++++++++++ ...iteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb | 22 +++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..f3d00fec42d --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb @@ -0,0 +1,45 @@ +easyblock = "PythonPackage" + +name = 'CVXOPT' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['CVXOPT-1.2.1-fix-setup-py.patch'] +checksums = [ + 'ea62a2a1b8e2db3a6ae44ac394f58e4620149af226c250c6f2b18739b48cfc21', # cvxopt-1.2.3.tar.gz + '85d8475098895e9af45f330489a712b5b944489c5fb4a6c67f59bef8fed4303d', # CVXOPT-1.2.1-fix-setup-py.patch +] + +dependencies = [ + ('Python', '3.6.6'), + ('SuiteSparse', '5.1.2', '-METIS-5.1.0'), + ('GSL', '2.5'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' +preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' + +installopts = ' --no-binary cvxopt' + +postinstallcmds = ['nosetests'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb new file mode 100644 index 00000000000..7b5db09357a --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.1.2-intel-2018b-METIS-5.1.0.eb @@ -0,0 +1,22 @@ +name = 'SuiteSparse' +version = '5.1.2' +metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % metis_ver + +homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4ec8d344bd8e95b898132ddffd7ee93bfbb2c1224925d11bab844b08f9b4c3b7'] + +dependencies = [('METIS', metis_ver)] + +parallel = 1 + +prebuildopts = "sed -i 's/-openmp/-fopenmp/g' SuiteSparse_config/SuiteSparse_config.mk && " + +moduleclass = 'numlib' From 92c07fa70c3c48731574c78a79d4b66226c7aadd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Feb 2019 11:00:53 +0100 Subject: [PATCH 0014/9987] allow different dep variants for NGS (different language bindings) --- test/easyconfigs/easyconfigs.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c0129534add..2184e800ecf 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -175,6 +175,8 @@ def check_dep_vars(dep, dep_vars): # 'guilty' until proven 'innocent' res = False + version_regex = re.compile('^version: (?P[^;]+);') + # filter out binutils with empty versionsuffix which is used to build toolchain compiler if dep == 'binutils' and len(dep_vars) > 1: empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')] @@ -185,10 +187,17 @@ def check_dep_vars(dep, dep_vars): elif dep == 'HTSlib' and len(dep_vars) > 1: for key, ecs in dep_vars.items(): # filter out HTSlib variants that are only used as dependency for BCFtools with same version - htslib_ver = re.search('^version: (?P[^;]+);', key).group('ver') + htslib_ver = version_regex.search(key).group('version') if all(ec.startswith('BCFtools-%s-' % htslib_ver) for ec in ecs): dep_vars.pop(key) + # multiple variants of NGS is OK, as long as they only differ by versionsuffix (same version) + # to allow for different language bindings (Java, Python 2, Python 3, ...) + elif dep == 'NGS' and len(dep_vars) > 1: + ngs_vers = [version_regex.search(key).group('version') for key in dep_vars] + if len(ngs_vers) == 1: + dep_vars.pop(key) + # filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains elif dep in ['FFTW', 'imkl']: serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] @@ -199,7 +208,7 @@ def check_dep_vars(dep, dep_vars): # as long as that's indicated by the versionsuffix elif dep in ['Boost', 'R'] and len(dep_vars) > 1: for key in dep_vars.keys(): - dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') + dep_ver = version_regex.search(key).group('version') # filter out dep version if all easyconfig filenames using it include specific dep version if all(re.search('-%s-%s' % (dep, dep_ver), v) for v in dep_vars[key]): dep_vars.pop(key) From 214a2aa94017481e5eb716de975b0d4dac178731 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Thu, 14 Feb 2019 16:31:58 +0100 Subject: [PATCH 0015/9987] adding easyconfigs: G-PhoCS-1.2.3-GCCcore-6.4.0.eb --- .../g/G-PhoCS/G-PhoCS-1.2.3-GCCcore-6.4.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..2ad11df7a60 --- /dev/null +++ b/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-GCCcore-6.4.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'G-PhoCS' +version = '1.2.3' + +homepage = 'http://compgen.cshl.edu/GPhoCS/' + +description = """G-PhoCS is a software package for inferring ancestral population sizes, population divergence +times, and migration rates from individual genome sequences. G-PhoCS accepts as input a set of multiple sequence +alignments from separate neutrally evolving loci along the genome. Parameter inference is done in a Bayesian manner, +using a Markov Chain Monte Carlo (MCMC) to jointly sample model parameters and genealogies at the input loci. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://compgen.cshl.edu/GPhoCS/downloads/'] +sources = ['GPhoCS-%(version)s.tar.gz'] +checksums = ['e3854591f68b2111d5095f64221007456ae7a601bf760a21bd00ca5c21273776'] + +builddependencies = [ + ('binutils', '2.28'), +] + +parallel = 1 + +prebuildopts = 'sed -i "/^CC=.*/d" Makefile && ' + +files_to_copy = [(['bin/readTrace', 'bin/G-PhoCS-1-2-3'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/readTrace', 'bin/G-PhoCS-1-2-3'], + 'dirs': [], +} + +moduleclass = 'tools' From ae9dd187a8b91b9b556c242c0d3df5d101af3fad Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 19 Feb 2019 15:37:15 +0100 Subject: [PATCH 0016/9987] Switch to icc for better perf. --- ....3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..e9a53b66b6f --- /dev/null +++ b/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'G-PhoCS' +version = '1.2.3' + +homepage = 'http://compgen.cshl.edu/GPhoCS/' + +description = """G-PhoCS is a software package for inferring ancestral population sizes, population divergence +times, and migration rates from individual genome sequences. G-PhoCS accepts as input a set of multiple sequence +alignments from separate neutrally evolving loci along the genome. Parameter inference is done in a Bayesian manner, +using a Markov Chain Monte Carlo (MCMC) to jointly sample model parameters and genealogies at the input loci. +""" + +toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} + +source_urls = ['http://compgen.cshl.edu/GPhoCS/downloads/'] +sources = ['GPhoCS-%(version)s.tar.gz'] +checksums = ['e3854591f68b2111d5095f64221007456ae7a601bf760a21bd00ca5c21273776'] + +parallel = 1 + +prebuildopts = 'sed -i "/^CC=.*/d" Makefile && ' + +files_to_copy = [(['bin/readTrace', 'bin/G-PhoCS-1-2-3'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/readTrace', 'bin/G-PhoCS-1-2-3'], + 'dirs': [], +} + +moduleclass = 'tools' From ed8cddbc5a0fd6848b95ead8e9e42826b8fc6893 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 19 Feb 2019 15:47:14 +0100 Subject: [PATCH 0017/9987] Remove GCCcore version, fix module class --- .../g/G-PhoCS/G-PhoCS-1.2.3-GCCcore-6.4.0.eb | 35 ------------------- ....3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- 2 files changed, 1 insertion(+), 36 deletions(-) delete mode 100644 easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-GCCcore-6.4.0.eb deleted file mode 100644 index 2ad11df7a60..00000000000 --- a/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-GCCcore-6.4.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'MakeCp' - -name = 'G-PhoCS' -version = '1.2.3' - -homepage = 'http://compgen.cshl.edu/GPhoCS/' - -description = """G-PhoCS is a software package for inferring ancestral population sizes, population divergence -times, and migration rates from individual genome sequences. G-PhoCS accepts as input a set of multiple sequence -alignments from separate neutrally evolving loci along the genome. Parameter inference is done in a Bayesian manner, -using a Markov Chain Monte Carlo (MCMC) to jointly sample model parameters and genealogies at the input loci. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = ['http://compgen.cshl.edu/GPhoCS/downloads/'] -sources = ['GPhoCS-%(version)s.tar.gz'] -checksums = ['e3854591f68b2111d5095f64221007456ae7a601bf760a21bd00ca5c21273776'] - -builddependencies = [ - ('binutils', '2.28'), -] - -parallel = 1 - -prebuildopts = 'sed -i "/^CC=.*/d" Makefile && ' - -files_to_copy = [(['bin/readTrace', 'bin/G-PhoCS-1-2-3'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/readTrace', 'bin/G-PhoCS-1-2-3'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index e9a53b66b6f..29d461af0fd 100644 --- a/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -28,4 +28,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'bio' From 7684c08c7ccfeffe7be0500a4288022db5cffe50 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 12 Mar 2019 09:57:00 +0200 Subject: [PATCH 0018/9987] update --- ....4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 10 +++---- easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb | 27 +++++++++++++++++++ 2 files changed, 32 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 19f13449e6a..9ba7175fd0d 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -1,6 +1,6 @@ easyblock = 'CMakeMake' name = 'Embree' -version = '3.4.0' +version = "3.4.0" gccver = '6.4.0' binutilsver = '2.28' @@ -9,17 +9,17 @@ gccsuff = '-GCC-%s' % (gccver) homepage = 'https://embree.github.io/' description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" -toolchain = {'name': 'iccifort', 'version': '2018.1.163%s-%s' % (gccsuff,binutilsver)} +toolchain = {'name': 'iccifort', 'version': '2018.1.163%s-%s' % (gccsuff, binutilsver)} source_urls = ['https://github.com/embree/embree/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['22229f19332d4fd08eb3bf60198211bda674f51632b977c9d7fd09531e09dd8d'] -builddependencies = [('CMake', '3.11.4','-GCCcore-%s' % gccver),] +builddependencies = [('CMake', '3.11.4')] dependencies = [ - ('ispc', '1.10.0'), - ('tbb', '2018_U5','-GCCcore-%s' % gccver), + ('ispc', '1.10.0'), + ('tbb', '2018_U5', '-GCCcore-%s' % gccver), ] configopts = '-DEMBREE_TUTORIALS=OFF ' diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb new file mode 100644 index 00000000000..82c7a63390c --- /dev/null +++ b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'ispc' +version = '1.10.0' + +homepage = 'http://ispc.github.io/ , https://github.com/ispc/ispc/' +description = """Intel SPMD Program Compilers; An open-source compiler for high-performance + SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, + with extensions for 'single program, multiple data' (SPMD) programming. + Under the SPMD model, the programmer writes a program that generally appears + to be a regular serial program, though the execution model is actually that + a number of program instances execute in parallel on the hardware.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['ispc-v%(version)s-linux.tar.gz'] +source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] +checksums = ['453211ade91c33826f4facb1336114831adbd35196d016e09d589a6ad8699aa3'] + +sanity_check_paths = { + 'files': ["bin/ispc"], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'compiler' From 28d3bcf046b234a39590bd013a6b89433ed982e3 Mon Sep 17 00:00:00 2001 From: "\"Andreas \"" Date: Tue, 12 Mar 2019 12:39:00 +0200 Subject: [PATCH 0019/9987] update --- .../Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 9ba7175fd0d..76d37e5201a 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -18,8 +18,8 @@ checksums = ['22229f19332d4fd08eb3bf60198211bda674f51632b977c9d7fd09531e09dd8d'] builddependencies = [('CMake', '3.11.4')] dependencies = [ - ('ispc', '1.10.0'), - ('tbb', '2018_U5', '-GCCcore-%s' % gccver), + ('ispc', '1.10.0', '', True), + ('tbb', '2018_U5', '', ('GCCcore', gccver)), ] configopts = '-DEMBREE_TUTORIALS=OFF ' From 2ad87f5cb39e8b3405a92bb46ed57e4f26f1cf4a Mon Sep 17 00:00:00 2001 From: Andreas Henkel Date: Tue, 12 Mar 2019 15:47:08 +0100 Subject: [PATCH 0020/9987] Update Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb Rearrange description --- .../Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 76d37e5201a..8d9da0f977c 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -7,7 +7,13 @@ binutilsver = '2.28' gccsuff = '-GCC-%s' % (gccver) homepage = 'https://embree.github.io/' -description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. The target users of Intel® Embree are graphics application engineers who want to improve the performance of their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" +description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. +The target users of Intel® Embree are graphics application engineers who want to improve the performance of +their photo-realistic rendering application by leveraging Embree's performance-optimized ray tracing kernels. +The kernels are optimized for the latest Intel® processors with support for SSE, AVX, AVX2, and AVX-512 instructions. +Intel® Embree supports runtime code selection to choose the traversal and build algorithms that best matches +the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit +from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" toolchain = {'name': 'iccifort', 'version': '2018.1.163%s-%s' % (gccsuff, binutilsver)} From ec74e6b46d1292d693f70d8ba2c17280edcba7c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 22 Mar 2019 14:01:48 +0100 Subject: [PATCH 0021/9987] update homepage and source_urls --- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb | 4 ++-- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb | 4 ++-- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb | 4 ++-- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb index 47d9f67b516..6c83c0b51ab 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb @@ -11,13 +11,13 @@ easyblock = 'MakeCp' name = 'GLIMMER' version = '3.02b' -homepage = 'http://www.cbcb.umd.edu/software/%(namelower)s/' +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['http://www.cbcb.umd.edu/software/glimmer'] +source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] buildopts = '-C ./src' diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb index 8e1a574fde6..a8932d6d6a3 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb @@ -12,13 +12,13 @@ easyblock = 'MakeCp' name = 'GLIMMER' version = '3.02b' -homepage = 'http://www.cbcb.umd.edu/software/%(namelower)s/' +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://www.cbcb.umd.edu/software/%(namelower)s'] +source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%(namelower)s302b.tar.gz'] checksums = ['a531f83b6162064539bebedbef5bec6b99df32b5d2877ba4431d2fa93faa78a3'] diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb index 9224bccf7f9..7b9af0a1d22 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb @@ -11,13 +11,13 @@ easyblock = 'MakeCp' name = "GLIMMER" version = "3.02b" -homepage = 'http://www.cbcb.umd.edu/software/glimmer/' +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://www.cbcb.umd.edu/software/glimmer'] +source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] buildopts = '-C ./src' diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb index 90a24de0cf2..e7f8082104e 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb @@ -11,13 +11,13 @@ easyblock = 'MakeCp' name = "GLIMMER" version = "3.02b" -homepage = 'http://www.cbcb.umd.edu/software/glimmer/' +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://www.cbcb.umd.edu/software/glimmer'] +source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] buildopts = '-C ./src' From 5d2be2c1dd8adb8f26fc7c18e9e59579518b5876 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 22 Mar 2019 20:47:35 +0100 Subject: [PATCH 0022/9987] Add checksums --- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb | 1 + easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb | 2 +- easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb | 1 + easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb | 1 + 4 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb index 6c83c0b51ab..59dcbaec249 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb @@ -19,6 +19,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] +checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = '-C ./src' diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb index a8932d6d6a3..1c389bd393d 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb @@ -20,7 +20,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%(namelower)s302b.tar.gz'] -checksums = ['a531f83b6162064539bebedbef5bec6b99df32b5d2877ba4431d2fa93faa78a3'] +checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = "-C ./src" diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb index 7b9af0a1d22..da9c09fd6d5 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb @@ -19,6 +19,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] +checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = '-C ./src' diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb index e7f8082104e..49bd7675820 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb @@ -19,6 +19,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] +checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = '-C ./src' From a5d711adf8dc1aea92b6b98564650d69fae9f6fc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 9 May 2019 18:17:40 +0200 Subject: [PATCH 0023/9987] Improve comments in Calcam v2.1.0 EB files regarding use of preinstallopts --- .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb | 2 ++ .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb index d15eb614ace..ba8db2d6ade 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb @@ -31,6 +31,8 @@ use_pip = True download_dep_fail = True +# Pip asks whether an update from Calcam 1.x data representation to Calcam 2 is desired. +# The following line answers "n" to this question and skips the conversion. preinstallopts = 'echo n |' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb index 78fed5ee963..193dc5501b8 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb @@ -31,6 +31,8 @@ use_pip = True download_dep_fail = True +# Pip asks whether an update from Calcam 1.x data representation to Calcam 2 is desired. +# The following line answers "n" to this question and skips the conversion. preinstallopts = 'echo n |' sanity_check_paths = { From 839e4676f1a5619de380b36e42c5d536dc4a3be1 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 29 May 2019 21:12:53 +0200 Subject: [PATCH 0024/9987] adding easyconfigs: CrystFEL-0.8.0-intel-2019a.eb, CrystFEL-0.8.0-foss-2019a.eb --- .../c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb | 46 +++++++++++++++++++ .../c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb | 46 +++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb create mode 100644 easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb diff --git a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb new file mode 100644 index 00000000000..05afe734900 --- /dev/null +++ b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'CrystFEL' +version = '0.8.0' + +homepage = 'http://www.desy.de/~twhite/crystfel/' +description = """CrystFEL is a suite of programs for processing diffraction data acquired "serially" in a "snapshot" +manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser +source.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['http://www.desy.de/~twhite/crystfel/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.13.3'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('HDF5', '1.10.5'), + ('GSL', '2.5'), + ('LibTIFF', '4.0.10'), + ('ncurses', '6.1'), + ('GLib', '2.60.1'), + ('GTK+', '3.24.8'), + ('cairo', '1.16.0'), + ('Gdk-Pixbuf', '2.38.1'), + ('FFTW', '3.3.8'), + ('util-linux', '2.33'), + ('zlib', '1.2.11'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib64/libcrystfel.%s' % SHLIB_EXT] + + ['bin/' + b for b in ['ambigator', 'cell_explorer', 'check_hkl', 'compare_hkl', 'geoptimiser', + 'get_hkl', 'hdfsee', 'indexamajig', 'list_events', 'make_pixelmap', 'partialator', + 'partial_sim', 'pattern_sim', 'process_hkl', 'render_hkl', 'whirligig']], + 'dirs': ['share/doc/crystfel/scripts/'] +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb new file mode 100644 index 00000000000..8ec16f8b822 --- /dev/null +++ b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'CrystFEL' +version = '0.8.0' + +homepage = 'http://www.desy.de/~twhite/crystfel/' +description = """CrystFEL is a suite of programs for processing diffraction data acquired "serially" in a "snapshot" +manner, such as when using the technique of Serial Femtosecond Crystallography (SFX) with a free-electron laser +source.""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = ['http://www.desy.de/~twhite/crystfel/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.13.3'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('HDF5', '1.10.5'), + ('GSL', '2.5'), + ('LibTIFF', '4.0.10'), + ('ncurses', '6.1'), + ('GLib', '2.60.1'), + ('GTK+', '3.24.8'), + ('cairo', '1.16.0'), + ('Gdk-Pixbuf', '2.38.1'), + ('FFTW', '3.3.8'), + ('util-linux', '2.33'), + ('zlib', '1.2.11'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib64/libcrystfel.%s' % SHLIB_EXT] + + ['bin/' + b for b in ['ambigator', 'cell_explorer', 'check_hkl', 'compare_hkl', 'geoptimiser', + 'get_hkl', 'hdfsee', 'indexamajig', 'list_events', 'make_pixelmap', 'partialator', + 'partial_sim', 'pattern_sim', 'process_hkl', 'render_hkl', 'whirligig']], + 'dirs': ['share/doc/crystfel/scripts/'] +} + + +moduleclass = 'vis' From 0810423fa78221bad3194f84143c64db38cbfbce Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 3 Jun 2019 18:16:37 +0200 Subject: [PATCH 0025/9987] Add build type and checksums --- easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb | 3 +++ easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb index 05afe734900..1164c652609 100644 --- a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb +++ b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2019a'} source_urls = ['http://www.desy.de/~twhite/crystfel/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['6139b818079a16aa4da90344d4f413810e741c321013a1d6980c01f5d79c7b3a'] builddependencies = [ ('CMake', '3.13.3'), @@ -32,6 +33,8 @@ dependencies = [ ('zlib', '1.2.11'), ] +configopts = '-DCMAKE_BUILD_TYPE=Release' + separate_build_dir = True sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb index 8ec16f8b822..e899a7cc6fd 100644 --- a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb +++ b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2019a'} source_urls = ['http://www.desy.de/~twhite/crystfel/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['6139b818079a16aa4da90344d4f413810e741c321013a1d6980c01f5d79c7b3a'] builddependencies = [ ('CMake', '3.13.3'), @@ -32,6 +33,8 @@ dependencies = [ ('zlib', '1.2.11'), ] +configopts = '-DCMAKE_BUILD_TYPE=Release' + separate_build_dir = True sanity_check_paths = { From abb1a21a347106c4a715ac9ad36bc1d12c44dbc1 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Tue, 4 Jun 2019 17:33:37 +0200 Subject: [PATCH 0026/9987] Run test suite --- easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb | 2 ++ easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb index 1164c652609..5ef66f2d34d 100644 --- a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb +++ b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb @@ -37,6 +37,8 @@ configopts = '-DCMAKE_BUILD_TYPE=Release' separate_build_dir = True +runtest = 'test' + sanity_check_paths = { 'files': ['lib64/libcrystfel.%s' % SHLIB_EXT] + ['bin/' + b for b in ['ambigator', 'cell_explorer', 'check_hkl', 'compare_hkl', 'geoptimiser', diff --git a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb index e899a7cc6fd..4d48b784031 100644 --- a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb +++ b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb @@ -37,6 +37,8 @@ configopts = '-DCMAKE_BUILD_TYPE=Release' separate_build_dir = True +runtest = 'test' + sanity_check_paths = { 'files': ['lib64/libcrystfel.%s' % SHLIB_EXT] + ['bin/' + b for b in ['ambigator', 'cell_explorer', 'check_hkl', 'compare_hkl', 'geoptimiser', From 3b7344076d3a3d21fdebb071855c591a86f23e38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Jun 2019 20:48:44 +0200 Subject: [PATCH 0027/9987] adding easyconfigs: PRISMS-PF-2.1.1-foss-2019a.eb, p4est-2.2-foss-2019a.eb, deal.II-9.1.1-foss-2019a.eb --- .../d/deal.II/deal.II-9.1.1-foss-2019a.eb | 45 ++++++++++++++++++ .../p/PRISMS-PF/PRISMS-PF-2.1.1-foss-2019a.eb | 33 +++++++++++++ .../p/p4est/p4est-2.2-foss-2019a.eb | 47 +++++++++++++++++++ 3 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb create mode 100644 easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.1.1-foss-2019a.eb create mode 100644 easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb diff --git a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb new file mode 100644 index 00000000000..e4990e2bda0 --- /dev/null +++ b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'deal.II' +version = '9.1.1' + +homepage = 'https://www.dealii.org' +description = """deal.II is a C++ program library targeted at the computational solution of + partial differential equations using adaptive finite elements.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/dealii/dealii/releases/download/v%(version)s/'] +sources = ['dealii-%(version)s.tar.gz'] +checksums = ['fc5b483f7fe58dfeb52d05054011280f115498e337af3e085bf272fd1fd81276'] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [ + ('Boost', '1.70.0'), + ('GSL', '2.5'), + ('HDF5', '1.10.5'), + ('METIS', '5.1.0'), + ('netCDF', '4.6.2'), + ('p4est', '2.2'), + ('PETSc', '3.11.1'), + ('zlib', '1.2.11'), +] + +configopts = "-DCMAKE_BUILD_TYPE=Release " +configopts += "-DDEAL_II_WITH_LAPACK=ON -DDEAL_II_WITH_MPI=ON " +configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_METIS=ON -DMETIS_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_NETCDF=ON -DNETCDF_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=$EBROOTP4EST" +configopts += "-DDEAL_II_WITH_PETSC=ON -DPETSC_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_ZLIB=ON -DZLIB_DIR=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libdeal_II.%s' % SHLIB_EXT], + 'dirs': ['include/deal.II', 'lib/cmake', 'lib/pkgconfig', 'share/deal.II'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.1.1-foss-2019a.eb b/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.1.1-foss-2019a.eb new file mode 100644 index 00000000000..5e30567763c --- /dev/null +++ b/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.1.1-foss-2019a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMakeCp' + +name = 'PRISMS-PF' +version = '2.1.1' + +homepage = 'https://prisms-center.github.io/phaseField' +description = """PRISMS-PF is a powerful, massively parallel finite element code for conducting phase field and + other related simulations of microstructural evolution.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/prisms-center/phaseField/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd76b105d28791c5be5e624cacca9db4c453fbba26727c829ef3f0810f02fffe'] + +builddependencies = [('CMake', '3.13.3')] + +dependencies = [ + ('p4est', '2.2'), + ('deal.II', '9.1.1'), +] + +configopts = "-DCMAKE_PREFIX_PATH=$EBROOTDEALII" +buildopts = 'release' + +files_to_copy = ['applications', 'include', (['libprisms_pf*.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libprisms_pf.a', 'lib/libprisms_pf_debug.a'], + 'dirs': ['applications', 'include'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb new file mode 100644 index 00000000000..c2d29a78764 --- /dev/null +++ b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'p4est' +version = '2.2' + +homepage = 'http://www.p4est.org' +description = """p4est is a C library to manage a collection (a forest) of multiple +connected adaptive quadtrees or octrees in parallel.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +# disable architecture-specific optimisations to fix failing sc_test_dmatrix test +# cfr. https://github.com/cburstedde/libsc/issues/15 +toolchainopts = {'openmp': True, 'usempi': True, 'optarch': False} + +source_urls = [ + 'https://github.com/cburstedde/p4est/archive', + 'https://github.com/cburstedde/libsc/archive/', +] +sources = [ + 'v%(version)s.tar.gz', + {'download_filename': '5282025.tar.gz', 'filename': 'libsc-2.2.tar.gz'}, +] +checksums = ['7df0e9a161b6ea680324dfdbc0ffc6e0d0a6c9c9b0ea5b37c973e71a054226c2'] + +dependencies = [ + ('zlib', '1.2.11'), + ('METIS', '5.1.0') +] + +builddependencies = [ + ('Autotools', '20180311') +] + +preconfigopts = "rmdir sc && mv %(builddir)s/libsc-* sc && " +preconfigopts += "echo '%(version)s' >> .tarball-version && ./bootstrap && " +configopts = "--enable-openmp --enable-mpi --with-metis " +configopts += "--with-blas=$EBROOTOPENBLAS/lib/libopenblas.a --with-lapack=$EBROOTOPENBLAS/lib/libopenblas.a" + +runtest = 'check VERBOSE=1' + +sanity_check_paths = { + 'files': ['bin/p4est_simple', 'bin/p4est_step1', 'bin/p4est_step2', 'bin/p4est_step3', 'bin/p4est_step4', + 'lib/libp4est-%%(version)s.%s' % SHLIB_EXT, 'lib/libp4est.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' From ac65f13da7670951c049b6eac451039588e3383f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Jun 2019 22:35:01 +0200 Subject: [PATCH 0028/9987] add missing checksum in p4est easyconfig --- easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb index c2d29a78764..99c7f47225b 100644 --- a/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb +++ b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb @@ -20,7 +20,10 @@ sources = [ 'v%(version)s.tar.gz', {'download_filename': '5282025.tar.gz', 'filename': 'libsc-2.2.tar.gz'}, ] -checksums = ['7df0e9a161b6ea680324dfdbc0ffc6e0d0a6c9c9b0ea5b37c973e71a054226c2'] +checksums = [ + '7df0e9a161b6ea680324dfdbc0ffc6e0d0a6c9c9b0ea5b37c973e71a054226c2', # v2.2.tar.gz + 'c32682c7542ecf2c115150bf79c7b9ac379cb6396179878575d7b228cc0295c5', # libsc-2.2.tar.gz +] dependencies = [ ('zlib', '1.2.11'), From dcec385971c6c04092b703ba57c6424a503dd593 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Tue, 16 Jul 2019 15:01:21 +0200 Subject: [PATCH 0029/9987] AptaSUITE and JavaFX for deps --- .../a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb | 43 +++++++++++++++++++ .../JavaFX/JavaFX-11.0.2_linux-x64_bin-sdk.eb | 27 ++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb create mode 100644 easybuild/easyconfigs/j/JavaFX/JavaFX-11.0.2_linux-x64_bin-sdk.eb diff --git a/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb b/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb new file mode 100644 index 00000000000..c3dfdefa0a3 --- /dev/null +++ b/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'AptaSUITE' +version = '0.9.4' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://drivenbyentropy.github.io/' +description = """ A full-featured bioinformatics software collection for the + comprehensive analysis of aptamers in HT-SELEX experiments """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/drivenbyentropy/aptasuite/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.zip'] +checksums = ['e7b86ddccac38ce11e620d65129654a6f8a2cfe5105c092baa12c8d6e643abc3'] + +dependencies = [ + ('Java', '11'), + ('JavaFX', '11.0.2', '_linux-x64_bin-sdk'), +] + +modaliases = { + 'aptasuite-gui': 'java -Dprism.order=sw --module-path ${EBROOTJAVAFX}/lib ' + + '--add-modules javafx.controls,javafx.fxml -jar ${EBROOTAPTASUITE}/aptasuite-%(version)s.jar', + # split in two lines to make travis happy (line length below 120 characters) +} + +sanity_check_paths = { + 'files': ['aptasuite-%(version)s.jar'], + 'dirs': [] +} + +modloadmsg = """ +To execute on command line run: java -jar ${EBROOTAPTASUITE}/aptasuite-%(version)s.jar +To open graphical interface run: aptasuite-gui +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/JavaFX/JavaFX-11.0.2_linux-x64_bin-sdk.eb b/easybuild/easyconfigs/j/JavaFX/JavaFX-11.0.2_linux-x64_bin-sdk.eb new file mode 100644 index 00000000000..b5926bf9dfa --- /dev/null +++ b/easybuild/easyconfigs/j/JavaFX/JavaFX-11.0.2_linux-x64_bin-sdk.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'JavaFX' +version = '11.0.2' +versionsuffix = '_linux-x64_bin-sdk' + +homepage = 'https://openjfx.io/' +description = """ OpenJFX is an open source, next generation client application platform for desktop, + mobile and embedded systems built on Java """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://download2.gluonhq.com/openjfx/%(version)s/'] +sources = ['openjfx-%(version)s%(versionsuffix)s.zip'] +checksums = ['40ef06cd50ea535d45403d9c44e9cb405b631c547734b5b50a6cb7b222293f97'] + +sanity_check_paths = { + 'files': ['lib/javafx.base.jar', 'lib/libfxplugins.so'], + 'dirs': [] +} + +moduleclass = 'lang' From 52c97f7539f1563abe68a9a0bc0354615c9d5681 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 17 Jul 2019 11:52:08 +0200 Subject: [PATCH 0030/9987] use a symlink in install dir in postinstallcmds --- .../easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb b/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb index c3dfdefa0a3..ab2ce358038 100644 --- a/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb +++ b/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb @@ -24,19 +24,21 @@ dependencies = [ ('JavaFX', '11.0.2', '_linux-x64_bin-sdk'), ] +postinstallcmds = ["cd %(installdir)s && ln -s aptasuite-%(version)s.jar aptasuite.jar"] + modaliases = { 'aptasuite-gui': 'java -Dprism.order=sw --module-path ${EBROOTJAVAFX}/lib ' + - '--add-modules javafx.controls,javafx.fxml -jar ${EBROOTAPTASUITE}/aptasuite-%(version)s.jar', + '--add-modules javafx.controls,javafx.fxml -jar ${EBROOTAPTASUITE}/aptasuite.jar', # split in two lines to make travis happy (line length below 120 characters) } sanity_check_paths = { - 'files': ['aptasuite-%(version)s.jar'], + 'files': ['aptasuite-%(version)s.jar', 'aptasuite.jar'], 'dirs': [] } modloadmsg = """ -To execute on command line run: java -jar ${EBROOTAPTASUITE}/aptasuite-%(version)s.jar +To execute on command line run: java -jar ${EBROOTAPTASUITE}/aptasuite.jar To open graphical interface run: aptasuite-gui """ From a354f8da300cd82a62563a945cfb7ed795c56e51 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 17 Jul 2019 11:52:39 +0200 Subject: [PATCH 0031/9987] style fix --- easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb b/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb index ab2ce358038..84060f3c3eb 100644 --- a/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb +++ b/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb @@ -39,7 +39,7 @@ sanity_check_paths = { modloadmsg = """ To execute on command line run: java -jar ${EBROOTAPTASUITE}/aptasuite.jar -To open graphical interface run: aptasuite-gui +To launch the graphical interface run: aptasuite-gui """ moduleclass = 'bio' From 32d1a38c07d6b1e8f95d967812f4c179552fa249 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Aug 2019 19:40:20 +0200 Subject: [PATCH 0032/9987] adding easyconfigs: FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb --- .../FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb | 133 ++++++++++++++++++ 1 file changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..bf9ea65a71c --- /dev/null +++ b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,133 @@ +easyblock = 'PythonBundle' + +name = 'FMRIprep' +version = '1.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://fmriprep.readthedocs.io' +description = """FMRIprep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is + designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan + acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive + error and output reporting.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), + ('FSL', '5.0.11', versionsuffix), + ('ANTs', '2.3.1', versionsuffix), + ('AFNI', '18.3.00', versionsuffix), + ('C3D', '1.0.0', '', True), + ('FreeSurfer', '6.0.1', '-centos6_x86_64', True), + ('ICA-AROMA', '0.4.4-beta', versionsuffix), + ('Seaborn', '0.9.0', versionsuffix), + ('PyYAML', '3.13', versionsuffix), + ('scikit-learn', '0.20.0', versionsuffix), + ('scikit-image', '0.14.1', versionsuffix), + ('Nipype', '1.1.3', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('versioneer', '0.18', { + 'checksums': ['ead1f78168150011189521b479d3a0dd2f55c94f5b07747b484fd693c3fbf335'], + }), + ('indexed_gzip', '0.8.10', { + 'checksums': ['37957f14e70125d3e1bcb5ed83e7bca3a00212f4411e4f9af22cc2a626778616'], + }), + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + ('statsmodels', '0.10.1', { + 'checksums': ['320659a80f916c2edf9dfbe83512d9004bb562b72eedb7d9374562038697fa10'], + }), + ('svgutils', '0.3.1', { + 'checksums': ['cd52474765fd460ad2389947f77589de96142f6f0ce3f61e08ccfabeac2ff8af'], + }), + ('nilearn', '0.5.2', { + 'checksums': ['18b763d641e6903bdf8512e0ec5cdc14133fb4679e9a15648415e9be62c81b56'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.10.1', { + 'checksums': ['065c4f02ebe7f7cf559e49ee5a95fb800a9e4528727aec6f24402a5374c65013'], + }), + ('tqdm', '4.33.0', { + 'checksums': ['1dc82f87a8726602fa7177a091b5e8691d6523138a8f7acd08e58088f51e389f'], + }), + ('prov', '1.5.3', { + 'checksums': ['a0c951107eafd508d5a26caa54863dc11fee3da86778db2a559d32450d2030a9'], + }), + ('neurdflib', '5.0.0.post1', { + 'modulename': 'rdflib', + 'checksums': ['65ef138f7a20f646b5257d312e14c624a83abdac4df234e5edcc77dc63bef5e1'], + }), + ('num2words', '0.5.10', { + 'checksums': ['37cd4f60678f7e1045cdc3adf6acf93c8b41bf732da860f97d301f04e611cc57'], + }), + ('bids-validator', '1.2.4', { + 'checksums': ['cf456428219c7985c13e462380bff31453c6694532f67ca47fd89b19620d77d7'], + }), + ('SQLAlchemy', '1.3.6', { + 'checksums': ['217e7fc52199a05851eee9b6a0883190743c4fb9c8ac4313ccfceaffd852b0ff'], + }), + ('nipype', '1.2.0', { + 'checksums': ['a5b5afbfec522686a0ac7826b6cfd82496f4ef48f6c48afb602225b0aa7b5f25'], + }), + ('nitime', '0.8.1', { + 'checksums': ['269eae522f613c9ca8c3d62b66074a76b40d9484f468b4b8525f7c9342e96341'], + }), + ('grabbit', '0.2.6', { + 'checksums': ['134fdad2d079693f8836f1074241d01ba5ed38f768c26279a3fe39afb6757f5b'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('appdirs', '1.4.3', { + 'checksums': ['9e5896d1372858f8dd3344faf4e5014d21849c756c8d5701f78f8a103b372d92'], + }), + ('rply', '0.7.7', { + 'checksums': ['4d6d25703efd28fb3d5707f7b3bd4fe66c306159a5c25af10ba26d206a66d00d'], + }), + ('citeproc-py', '0.4.0', { + 'modulename': 'citeproc', + 'checksums': ['ed513dbc76f782b5e98126d6bebbd1284841fcf199ec9dda552e2bce864adadf'], + }), + ('duecredit', '0.7.0', { + 'checksums': ['8a13be317afcf56bdccba6a5d3d82c2f4e3509ffa1aff47d61c1a91e6d454010'], + }), + ('tedana', '0.0.7', { + 'checksums': ['9f541bdf9ecd06b883e3bb2a753987279aabe7b7a55651a59916a798a6578c81'], + }), + ('pybids', '0.7.1', { + 'modulename': 'bids', + 'checksums': ['a4725f691e9fa05294338b049d2babc623a6feb718d2607a8c56146537e309b4'], + }), + ('templateflow', '0.3.0', { + 'checksums': ['14830702c293e870a69fdefca2928618179cdbb631ce84a99522aa859a1f4205'], + }), + ('niworkflows', '0.9.6', { + 'checksums': ['07275844f5e830562109acca7340f971b98e4a22e7938d8d5aceb2cb5891049c'], + }), + ('smriprep', '0.2.4', { + 'checksums': ['3bd2fbdf4ba9037d698eae06957c69bad2f15de5b20b84ee8b71bdaf35c27e1e'], + }), + (name, version, { + 'source_tmpl': 'fmriprep-%(version)s.tar.gz', + 'checksums': ['ed25582ce739afbd1887954303c5fe3e648eb1e7d18de017ceff0ff3f6e24d4d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/fmriprep'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 77eebd589af653a60757ff9467260b7600f5145f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Aug 2019 15:47:54 +0200 Subject: [PATCH 0033/9987] add patch for niworkflows extension in FMRIprep 1.4.1 easyconfig to fix Bus Error --- .../FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb | 6 +++++- .../FMRIprep/niworkflows-0.9.6_fix-bus-error.patch | 14 ++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/FMRIprep/niworkflows-0.9.6_fix-bus-error.patch diff --git a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb index bf9ea65a71c..a1d620134f1 100644 --- a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb @@ -114,7 +114,11 @@ exts_list = [ 'checksums': ['14830702c293e870a69fdefca2928618179cdbb631ce84a99522aa859a1f4205'], }), ('niworkflows', '0.9.6', { - 'checksums': ['07275844f5e830562109acca7340f971b98e4a22e7938d8d5aceb2cb5891049c'], + 'patches': ['niworkflows-%(version)s_fix-bus-error.patch'], + 'checksums': [ + '07275844f5e830562109acca7340f971b98e4a22e7938d8d5aceb2cb5891049c', # niworkflows-0.9.6.tar.gz + 'd42ea11f54b4be75e68764a3bb74e6d202e60e4e6b174ded217fe18acb439133', # niworkflows-0.9.6_fix-bus-error.patch + ], }), ('smriprep', '0.2.4', { 'checksums': ['3bd2fbdf4ba9037d698eae06957c69bad2f15de5b20b84ee8b71bdaf35c27e1e'], diff --git a/easybuild/easyconfigs/f/FMRIprep/niworkflows-0.9.6_fix-bus-error.patch b/easybuild/easyconfigs/f/FMRIprep/niworkflows-0.9.6_fix-bus-error.patch new file mode 100644 index 00000000000..601483e30e5 --- /dev/null +++ b/easybuild/easyconfigs/f/FMRIprep/niworkflows-0.9.6_fix-bus-error.patch @@ -0,0 +1,14 @@ +fix for "Bus Error" +see https://neurostars.org/t/bus-error-fmriprep/4641 and https://github.com/poldracklab/niworkflows/pull/378 +diff -ru niworkflows-0.9.6.orig/niworkflows/interfaces/itk.py niworkflows-0.9.6/niworkflows/interfaces/itk.py +--- niworkflows-0.9.6.orig/niworkflows/interfaces/itk.py 2019-07-09 08:30:30.000000000 +0200 ++++ niworkflows-0.9.6/niworkflows/interfaces/itk.py 2019-08-28 15:41:11.602201555 +0200 +@@ -262,7 +262,7 @@ + runtime = xfm.run().runtime + + if copy_dtype: +- nii = nb.load(out_file) ++ nii = nb.load(out_file, mmap=False) + in_dtype = nb.load(in_file).get_data_dtype() + + # Overwrite only iff dtypes don't match From 0a814d53c03c3ed8b3f69eb535e46ac786007b69 Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 9 Sep 2019 12:41:03 +0200 Subject: [PATCH 0034/9987] adding easyconfigs: beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb, MrBayes-3.2.7a-iimpi-2019a.eb --- ....2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 29 +++++++++++++++++++ .../m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb | 22 ++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb create mode 100644 easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..41775d36646 --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '3.1.2' +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'iccifort', 'version': '2019.1.144-GCC-8.2.0-2.31.1'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] + +dependencies = [('Java', '1.8', '', True)] + +builddependencies = [('Autotools', '20180311')] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile + for includefile in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % libfile + for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb new file mode 100644 index 00000000000..49a07435889 --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb @@ -0,0 +1,22 @@ +block = 'ConfigureMake' +name = 'MrBayes' +version = '3.2.7a' + +homepage = 'https://nbisweden.github.io/MrBayes/' +description = "MrBayes is a program for the Bayesian estimation of phylogeny." + +toolchain = {'name': 'iimpi', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/NBISweden/MrBayes/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3eed2e3b1d9e46f265b6067a502a89732b6f430585d258b886e008e846ecc5c6'] + +dependencies = [ + ('beagle-lib', '3.1.2'), + ('libreadline', '8.0'), +] + +configopts = '--with-beagle --with-mpi' + +moduleclass = 'bio' From 1d135fcace3bd5c058798bf46a1c9bcdffeb7c2a Mon Sep 17 00:00:00 2001 From: Mikael OEhman Date: Mon, 9 Sep 2019 20:43:54 +0200 Subject: [PATCH 0035/9987] Fix travis checks --- ...agle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 8 ++++---- .../easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb | 5 +++++ 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 41775d36646..c0440d924f1 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -19,10 +19,10 @@ builddependencies = [('Autotools', '20180311')] preconfigopts = "./autogen.sh && " sanity_check_paths = { - 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile - for includefile in ["beagle.h", "platform.h"]] + - ["lib/libhmsbeagle%s.so" % libfile - for libfile in ["-cpu", "-cpu-sse", "-jni", ""]], + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % x + for x in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.so" % x + for x in ["-cpu", "-cpu-sse", "-jni", ""]], 'dirs': [] } diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb index 49a07435889..efe6e616e1d 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb @@ -19,4 +19,9 @@ dependencies = [ configopts = '--with-beagle --with-mpi' +sanity_check_paths = { + 'files': ['bin/mb'], + 'dirs': [] +} + moduleclass = 'bio' From f049d982d919cdc524e660bd4f0da027ddbea00d Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 9 Sep 2019 21:39:47 +0200 Subject: [PATCH 0036/9987] make beagle-lib match GCC variant --- ...agle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index c0440d924f1..ce1ff6795f0 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -12,17 +12,15 @@ source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '11', '', True)] builddependencies = [('Autotools', '20180311')] preconfigopts = "./autogen.sh && " sanity_check_paths = { - 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % x - for x in ["beagle.h", "platform.h"]] + - ["lib/libhmsbeagle%s.so" % x - for x in ["-cpu", "-cpu-sse", "-jni", ""]], + 'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % x for x in ["beagle.h", "platform.h"]] + + ["lib/libhmsbeagle%s.%s" % (x, SHLIB_EXT) for x in ["-cpu", "-cpu-sse", "-jni", ""]], 'dirs': [] } From aa31011b0ab9702da84ac1c3aae6184f50de0746 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 10 Sep 2019 09:27:40 +0200 Subject: [PATCH 0037/9987] fix typo, add pkg-config build dep --- easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb index efe6e616e1d..77812adf58f 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb @@ -1,4 +1,4 @@ -block = 'ConfigureMake' +easyblock = 'ConfigureMake' name = 'MrBayes' version = '3.2.7a' @@ -12,6 +12,8 @@ source_urls = ['https://github.com/NBISweden/MrBayes/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['3eed2e3b1d9e46f265b6067a502a89732b6f430585d258b886e008e846ecc5c6'] +builddependencies = [('pkg-config', '0.29.2')] + dependencies = [ ('beagle-lib', '3.1.2'), ('libreadline', '8.0'), From 09a97924af2a6cb48bed44f43d27a87c24c1659f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 25 Sep 2019 10:01:58 +0200 Subject: [PATCH 0038/9987] added ragoo easyconfig and deps --- ...ervaltree-3.0.2-foss-2018b-Python-3.6.6.eb | 30 ++++++++++++++++ .../m/minimap2/minimap2-2.17-foss-2018b.eb | 34 ++++++++++++++++++ .../RaGOO-1.11-foss-2018b-Python-3.6.6.eb | 36 +++++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb create mode 100644 easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..ca15abe5443 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'intervaltree' +version = '3.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/chaimleib/intervaltree' +description = 'A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment' + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/chaimleib/intervaltree/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e8ab75b66077f2e5fb85ac56cb6df834689edb048d38601d53d8867cce3b77d1'] + +dependencies = [ + ('Python', '3.6.6'), +] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/intervaltree-%(version)s-py%(pyshortver)s.egg'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb new file mode 100644 index 00000000000..59e42b8bb3f --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'MakeCp' + +name = 'minimap2' +version = "2.17" + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['b68ac8882d33cc63e9e3246775062aeb159b6990ff7f38099172c3fe6f8a2742'] + +files_to_copy = [(['%(name)s'], 'bin'), 'LICENSE.txt', 'NEWS.md', 'README.md', (['%(name)s.1'], 'share/man/man1')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..a76297e3b5a --- /dev/null +++ b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "PythonPackage" + +name = 'RaGOO' +version = '1.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/malonge/RaGOO' +description = 'A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome' + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/malonge/RaGOO/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a14ea39d4542989609d09b2f33fc59c5003f5b14bfac53f6eca15a367e95082a'] + +dependencies = [ + ('Python', '3.6.6'), + ('minimap2', '2.17'), + ('intervaltree', '3.0.2', '-Python-%(pyver)s'), + # numpy dependency is provided by the python module +] + +sanity_check_paths = { + 'files': ['bin/ragoo.py'], + 'dirs': [], +} + +# workaround for the python sanity check trying to do 'import ragoo' +options = {'modulename': 'os'} + +moduleclass = 'bio' From 8e41adb313882d1b42ca222bf65236745665251e Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 23 Oct 2019 23:51:03 -0500 Subject: [PATCH 0039/9987] adding easyconfigs: ImageJ-1.52q.eb --- .../easyconfigs/i/ImageJ/ImageJ-1.52q.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb new file mode 100644 index 00000000000..6d9dde6fd6a --- /dev/null +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb @@ -0,0 +1,41 @@ +easyblock = 'PackedBinary' + +name = 'ImageJ' +version = '1.52q' + +homepage = 'https://imagej.nih.gov/ij' +description = "Image Processing and Analysis in Java" + +toolchain = SYSTEM + +source_urls = [ + 'https://imagej.nih.gov/ij/download/src/', + # 'http://www.mecourse.com/landinig/software/', # old/broken + 'https://beardatashare.bham.ac.uk/getlink/fiLUS55SmtWwJKijDRbwqv9p/' +] +sources = [ + 'ij%(version_major)s%(version_minor)s-src.zip', + 'morphology.zip', +] +checksums = [ + '2181455c75b630b9fbc11f838fe76ab490ac6d41e4aa39fcc467155847deae0e', # ij152q-src.zip + '5701de853d2b5f606f2cf0f1d3db72767b6a432bf2123a656cff06e979852079', # morphology.zip +] + +dependencies = [ + ('Java', '1.8'), +] + +builddependencies = [('ant', '1.10.1', '-Java-%(javaver)s')] + +install_cmd = "cd source && ant build && cp ij.jar %(installdir)s && " +install_cmd += "mkdir -p %(installdir)s/plugins && cp -a %(builddir)s/Morphology/* %(installdir)s/plugins/" + +sanity_check_paths = { + 'files': ['ij.jar'], + 'dirs': ['plugins'], +} + +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dij1.plugins.dir=$EBROOTIMAGE/plugins'\n" + +moduleclass = 'tools' From 4309e1addcd4798a7f57f19502e0e1df727dcb74 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 24 Oct 2019 15:31:57 -0500 Subject: [PATCH 0040/9987] fix second EBROOT var for classpath in load message --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb index 6d9dde6fd6a..cf9283fae93 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb @@ -36,6 +36,6 @@ sanity_check_paths = { 'dirs': ['plugins'], } -modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dij1.plugins.dir=$EBROOTIMAGE/plugins'\n" +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dij1.plugins.dir=$EBROOTIMAGEJ/plugins'\n" moduleclass = 'tools' From bd893cb1d9a7998d7f355ca1c7b15e34e6778fe9 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 25 Oct 2019 21:28:33 -0500 Subject: [PATCH 0041/9987] more cleanups given testing input --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb index cf9283fae93..6b0b3efd0b5 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb @@ -36,6 +36,6 @@ sanity_check_paths = { 'dirs': ['plugins'], } -modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dij1.plugins.dir=$EBROOTIMAGEJ/plugins'\n" +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dij1.plugins.dir=$EBROOTIMAGEJ'\n" moduleclass = 'tools' From 4512f91792f90e3c92b7fc9e879c568229e21acb Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sat, 26 Oct 2019 09:56:52 -0500 Subject: [PATCH 0042/9987] should be -ijpath and not -Dij1.plugins.dir= --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb index 6b0b3efd0b5..895e0a3c4b5 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb @@ -36,6 +36,6 @@ sanity_check_paths = { 'dirs': ['plugins'], } -modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dij1.plugins.dir=$EBROOTIMAGEJ'\n" +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -ijpath $EBROOTIMAGEJ'\n" moduleclass = 'tools' From 9495e06192e2bdc33639b075bcfa110c413a3a5d Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 10 Nov 2019 08:15:30 -0500 Subject: [PATCH 0043/9987] add Java versionsuffix --- .../i/ImageJ/ImageJ-1.52q-Java-1.8.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb new file mode 100644 index 00000000000..0166dc74439 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb @@ -0,0 +1,42 @@ +easyblock = 'PackedBinary' + +name = 'ImageJ' +version = '1.52q' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://imagej.nih.gov/ij' +description = "Image Processing and Analysis in Java" + +toolchain = SYSTEM + +source_urls = [ + 'https://imagej.nih.gov/ij/download/src/', + # 'http://www.mecourse.com/landinig/software/', # old/broken + 'https://beardatashare.bham.ac.uk/getlink/fiLUS55SmtWwJKijDRbwqv9p/' +] +sources = [ + 'ij%(version_major)s%(version_minor)s-src.zip', + 'morphology.zip', +] +checksums = [ + '2181455c75b630b9fbc11f838fe76ab490ac6d41e4aa39fcc467155847deae0e', # ij152q-src.zip + '5701de853d2b5f606f2cf0f1d3db72767b6a432bf2123a656cff06e979852079', # morphology.zip +] + +dependencies = [ + ('Java', '1.8'), +] + +builddependencies = [('ant', '1.10.1', '-Java-%(javaver)s')] + +install_cmd = "cd source && ant build && cp ij.jar %(installdir)s && " +install_cmd += "mkdir -p %(installdir)s/plugins && cp -a %(builddir)s/Morphology/* %(installdir)s/plugins/" + +sanity_check_paths = { + 'files': ['ij.jar'], + 'dirs': ['plugins'], +} + +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -ijpath $EBROOTIMAGEJ'\n" + +moduleclass = 'tools' From f5e725f147a3f35ba691687ebdaa2d4237ff422f Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 10 Nov 2019 07:18:31 -0600 Subject: [PATCH 0044/9987] Delete ImageJ-1.52q.eb --- .../easyconfigs/i/ImageJ/ImageJ-1.52q.eb | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb deleted file mode 100644 index 895e0a3c4b5..00000000000 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'ImageJ' -version = '1.52q' - -homepage = 'https://imagej.nih.gov/ij' -description = "Image Processing and Analysis in Java" - -toolchain = SYSTEM - -source_urls = [ - 'https://imagej.nih.gov/ij/download/src/', - # 'http://www.mecourse.com/landinig/software/', # old/broken - 'https://beardatashare.bham.ac.uk/getlink/fiLUS55SmtWwJKijDRbwqv9p/' -] -sources = [ - 'ij%(version_major)s%(version_minor)s-src.zip', - 'morphology.zip', -] -checksums = [ - '2181455c75b630b9fbc11f838fe76ab490ac6d41e4aa39fcc467155847deae0e', # ij152q-src.zip - '5701de853d2b5f606f2cf0f1d3db72767b6a432bf2123a656cff06e979852079', # morphology.zip -] - -dependencies = [ - ('Java', '1.8'), -] - -builddependencies = [('ant', '1.10.1', '-Java-%(javaver)s')] - -install_cmd = "cd source && ant build && cp ij.jar %(installdir)s && " -install_cmd += "mkdir -p %(installdir)s/plugins && cp -a %(builddir)s/Morphology/* %(installdir)s/plugins/" - -sanity_check_paths = { - 'files': ['ij.jar'], - 'dirs': ['plugins'], -} - -modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -ijpath $EBROOTIMAGEJ'\n" - -moduleclass = 'tools' From 95431e3b720e3bd2f489c42ad331e98581b1a381 Mon Sep 17 00:00:00 2001 From: adm_seren Date: Tue, 12 Nov 2019 16:36:06 +0200 Subject: [PATCH 0045/9987] adding easyconfigs: 3d-dna-180922-foss-2019a-Python-2.7.15.eb, LASTZ-1.02.00-GCCcore-8.2.0.eb --- .../3d-dna-180922-foss-2019a-Python-2.7.15.eb | 33 +++++++++++++++++++ .../l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb | 28 ++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..e3fbb217c74 --- /dev/null +++ b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = '3d-dna' +version = '180922' +versionsuffix = '-Python-%(pyver)s' +local_githash = '529ccf46599825b3047e58a69091d599e9858a19' + +homepage = 'https://github.com/theaidenlab/3d-dna' +description = """3D de novo assembly (3D DNA) pipeline""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = ['https://github.com/theaidenlab/%(name)s/archive'] +sources = ['%s.zip' % local_githash] +checksums = ['348c3e019ea29e47382eb2d85228a56bc11b316c130afabae016ad8e7d7640ca'] + +dependencies = [ + ('Python', '2.7.15'), + ('LASTZ', '1.02.00'), + ('Java', '1.8', '', True), + ('parallel', '20190622'), +] + +modextrapaths = {'PATH': '.'} + +postinstallcmds = ['chmod 755 %(installdir)s/*.sh'] + +sanity_check_paths = { + 'files': ['run-asm-pipeline.sh', 'run-asm-pipeline-post-review.sh'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..a183ee2b5d3 --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'LASTZ' +version = '1.02.00' + +homepage = 'http://www.bx.psu.edu/~rsharris/lastz/' +description = """ LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle + sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS + sequencing technologies such as Roche 454. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] + +patches = ['LASTZ-%(version)s_Makefile.patch'] + +skipsteps = ['configure'] + +installopts = 'installDir=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/lastz', 'bin/lastz_D'], + 'dirs': [], +} + +moduleclass = 'bio' From 2bed34d72cc9265912f1afba8efadd0fecb554e5 Mon Sep 17 00:00:00 2001 From: adm_seren Date: Wed, 27 Nov 2019 12:51:09 +0200 Subject: [PATCH 0046/9987] Fix reviewers comments --- ...-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb | 33 +++++++++++++++++++ .../l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb | 9 +++-- 2 files changed, 40 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb new file mode 100644 index 00000000000..56b6f12cab2 --- /dev/null +++ b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = '3d-dna' +version = '180922' +versionsuffix = '-Python-%(pyver)s' +local_githash = '529ccf46599825b3047e58a69091d599e9858a19' + +homepage = 'https://github.com/theaidenlab/3d-dna' +description = """3D de novo assembly (3D DNA) pipeline""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +source_urls = ['https://github.com/theaidenlab/%(name)s/archive'] +sources = ['%s.zip' % local_githash] +checksums = ['348c3e019ea29e47382eb2d85228a56bc11b316c130afabae016ad8e7d7640ca'] + +dependencies = [ + ('Python', '2.7.15'), + ('LASTZ', '1.02.00'), + ('Java', '1.11', '', True), + ('parallel', '20190622'), +] + +modextrapaths = {'PATH': '.'} + +postinstallcmds = ['chmod 755 %(installdir)s/*.sh'] + +sanity_check_paths = { + 'files': ['run-asm-pipeline.sh', 'run-asm-pipeline-post-review.sh'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb index a183ee2b5d3..e7411dd51bf 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb @@ -11,10 +11,15 @@ description = """ LASTZ is a program for aligning DNA sequences, a pairwise alig toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] - +sources = [SOURCELOWER_TAR_GZ] patches = ['LASTZ-%(version)s_Makefile.patch'] +checksums = [ + '054515f27fdf9392f3d2e84ca421103b5e5575ba7a1979addf3c277212114a21', # lastz-1.02.00.tar.gz + '9bdceb84925cff083546c5f5165f27f850dbdd43fa0eda8b4f34f3cc0ecb3b6a', # LASTZ-1.02.00_Makefile.patch +] + +builddependencies = [('binutils', '2.31.1')] skipsteps = ['configure'] From d8cc15596c183e44258bccfefe3aa2b25265b5b2 Mon Sep 17 00:00:00 2001 From: adm_seren Date: Wed, 27 Nov 2019 17:55:21 +0200 Subject: [PATCH 0047/9987] Fix http check --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb index e7411dd51bf..8c54f783628 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb @@ -11,7 +11,7 @@ description = """ LASTZ is a program for aligning DNA sequences, a pairwise alig toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['http://www.bx.psu.edu/miller_lab/dist/'] +source_urls = ['https://www.bx.psu.edu/miller_lab/dist/'] sources = [SOURCELOWER_TAR_GZ] patches = ['LASTZ-%(version)s_Makefile.patch'] checksums = [ From 6851ab446d16656886d4e2d110bcf8b87a71577a Mon Sep 17 00:00:00 2001 From: adm_seren Date: Wed, 27 Nov 2019 19:16:15 +0200 Subject: [PATCH 0048/9987] Fix http check --- easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb index 8c54f783628..ba661013128 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.02.00-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'LASTZ' version = '1.02.00' -homepage = 'http://www.bx.psu.edu/~rsharris/lastz/' +homepage = 'https://www.bx.psu.edu/~rsharris/lastz/' description = """ LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. From 62a0aae0f4f71b15888c9e6b335e066f4fa852c5 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 1 Dec 2019 19:45:46 -0500 Subject: [PATCH 0049/9987] version morphology.zuo --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb index 0166dc74439..1518619044e 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb @@ -11,16 +11,16 @@ toolchain = SYSTEM source_urls = [ 'https://imagej.nih.gov/ij/download/src/', - # 'http://www.mecourse.com/landinig/software/', # old/broken - 'https://beardatashare.bham.ac.uk/getlink/fiLUS55SmtWwJKijDRbwqv9p/' + 'https://beardatashare.bham.ac.uk/dl/fiLUS55SmtWwJKijDRbwqv9p/', ] sources = [ 'ij%(version_major)s%(version_minor)s-src.zip', - 'morphology.zip', + # datestamp is determined by most recent file in zipball + {'download_filename': 'morphology.zip', 'filename': 'morphology-20190912.zip'}, ] checksums = [ '2181455c75b630b9fbc11f838fe76ab490ac6d41e4aa39fcc467155847deae0e', # ij152q-src.zip - '5701de853d2b5f606f2cf0f1d3db72767b6a432bf2123a656cff06e979852079', # morphology.zip + '5701de853d2b5f606f2cf0f1d3db72767b6a432bf2123a656cff06e979852079', # morphology-20190912.zip ] dependencies = [ From e709fbd3beec49c5f273f2529247470f1f4471f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Dec 2019 16:43:01 +0100 Subject: [PATCH 0050/9987] adding easyconfigs: CuCLARK-1.1-fosscuda-2019b.eb and patches: CuCLARK-1.1_fix-shfl.patch --- .../c/CuCLARK/CuCLARK-1.1-fosscuda-2019b.eb | 36 +++++++++++++++++++ .../c/CuCLARK/CuCLARK-1.1_fix-shfl.patch | 15 ++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/c/CuCLARK/CuCLARK-1.1-fosscuda-2019b.eb create mode 100644 easybuild/easyconfigs/c/CuCLARK/CuCLARK-1.1_fix-shfl.patch diff --git a/easybuild/easyconfigs/c/CuCLARK/CuCLARK-1.1-fosscuda-2019b.eb b/easybuild/easyconfigs/c/CuCLARK/CuCLARK-1.1-fosscuda-2019b.eb new file mode 100644 index 00000000000..65f0a8979dc --- /dev/null +++ b/easybuild/easyconfigs/c/CuCLARK/CuCLARK-1.1-fosscuda-2019b.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'CuCLARK' +version = '1.1' + +homepage = 'https://github.com/Funatiq/cuclark' +description = "Metagenomic classifier for CUDA-enabled GPUs" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://github.com/Funatiq/cuclark/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['CuCLARK-%(version)s_fix-shfl.patch'] +checksums = [ + 'fd27082aa851f43ac65d8d57918e0c928eab7941c4d2e058993b9fbfdaa4d060', # v1.1.tar.gz + 'f2dc781168613395ed8803a37ab635d438e68d4e2e6569d5078e9fd2a92a9b66', # CuCLARK-1.1_fix-shfl.patch +] + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" ' +# can't use compute_70, must use compute_60 arch because deprecated __ballot() is used +buildopts += 'NVCCFLAGS="-gencode arch=compute_60,code=sm_70 -O2"' + +local_binaries = ['cuCLARK', 'cuCLARK-l', 'getAccssnTaxID', 'getfilesToTaxNodes', 'getTargetsDef'] +local_scripts = ['classify_metagenome.sh', 'clean.sh', 'download_data.sh', 'download_taxondata.sh', + 'make_metadata.sh', 'resetCustomDB.sh', 'updateTaxonomy.sh', 'set_targets.sh'] + +files_to_copy = [(['exe/*'] + local_scripts, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries + local_scripts], + 'dirs': [], +} + +sanity_check_commands = ["cuCLARK --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CuCLARK/CuCLARK-1.1_fix-shfl.patch b/easybuild/easyconfigs/c/CuCLARK/CuCLARK-1.1_fix-shfl.patch new file mode 100644 index 00000000000..00e6899dd95 --- /dev/null +++ b/easybuild/easyconfigs/c/CuCLARK/CuCLARK-1.1_fix-shfl.patch @@ -0,0 +1,15 @@ +replace use of deprecated/no longer supported in recent CUDA compute capabilities (7.0 & up) __shfl with __shfl_sync +see also https://docs.nvidia.com/cuda/cuda-c-programming-guide/index.html#warp-shuffle-functions + +author: Kenneth Hoste (HPC-UGent) +--- cuclark-1.1/src/CuClarkDB.cu.orig 2017-01-04 10:35:20.000000000 +0100 ++++ cuclark-1.1/src/CuClarkDB.cu 2019-12-09 17:02:51.982293942 +0100 +@@ -1218,7 +1218,7 @@ + #endif + sharedResultRow[0+wid*(pitch/sizeof(RESULTS))] = total; + } +- total = __shfl(total, warpSize-1); // get total from last lane ++ total = __shfl_sync(0xFFFFFFFF, total, warpSize-1); // get total from last lane + } + + From a4ea10ee7585150d052576bca0dab0274ce346a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jan 2020 13:26:21 +0100 Subject: [PATCH 0051/9987] adding easyconfigs: OpenMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb --- ...penMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..be94dc54b60 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,66 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['OpenMM-%(version)s_fix-Doxygen.patch'] +checksums = [ + 'e8102b68133e6dcf7fcf29bc76a11ea54f30af71d8a7705aec0aee957ebe3a6d', # 7.4.1.tar.gz + '99d59e3106d9c9f9fbce3c3161117a37b2699e1dc09bc2a75619e0d880f29708', # OpenMM-7.4.1_fix-Doxygen.patch +] + +builddependencies = [ + ('CMake', '3.15.3'), + ('Doxygen', '1.8.16'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('SWIG', '4.0.1'), +] + +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" +runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)\'" """ + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} +modextravars = { + 'OPENMM_CUDA_COMPILER': 'nvcc', +} + +moduleclass = 'bio' From 6db6b0f7903bb47dce783aa0c914bf3c9d6504cf Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Fri, 10 Jan 2020 12:46:44 -0500 Subject: [PATCH 0052/9987] adding easyconfigs: ARTS-2.2.64-gompi-2019a.eb --- .../a/ARTS/ARTS-2.2.64-gompi-2019a.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb diff --git a/easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb b/easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb new file mode 100644 index 00000000000..7d197a651e6 --- /dev/null +++ b/easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb @@ -0,0 +1,54 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'CMakeMake' + +name = 'ARTS' +version = '2.2.64' + +homepage = 'http://www.radiativetransfer.org/' + +description = """ + ARTS is a radiative transfer model for the millimeter and sub-millimeter + spectral range. There are a number of models mostly developed explicitly + for the different sensors. +""" + +toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'opt': True, 'cstd': 'gnu++98', 'openmp': True} + +source_urls = ['http://www.radiativetransfer.org/misc/download/stable/2.2/'] +sources = [ + SOURCELOWER_TAR_GZ, + '%(namelower)s-xml-data-2.2.5.tar.gz', +] +checksums = [ + 'e33308b0c9d7697fa885a865f18e8c6ec5feddafc815df907c2905bd150d0b01', + '6a4e15ebd5c718e46f41c2e7d7d1462578c008fd96e78f4d8cc59e366b91c795', +] + +builddependencies = [ + ('CMake', '3.13.3'), + ('Doxygen', '1.8.15'), +] + +dependencies = [ + ('netCDF', '4.6.2'), + ('netCDF-C++4', '4.3.0'), +] + +separate_build_dir = True + +configopts = """\ + -DENABLE_FORTRAN=1\ + -DARTS_XML_DATA_PATH=../arts-xml-data-2.2.5\ + -DNETCDF_INCLUDE_DIR=$EBROOTNETCDF/include\ + -DNETCDF_LIBRARY=$EBROOTNETCDF/lib64/libnetcdf.so\ + -DNETCDFXX_LIBRARY=$EBROOTNETCDFMINCPLUSPLUS4/lib/libnetcdf_c++4.so\ +""" + +sanity_check_paths = { + 'dirs': ['bin', 'share/arts/controlfiles/artscomponents'], + 'files': ['bin/arts'], +} + +moduleclass = 'phys' From 6b9c68a9284afd135ed3c14ba87bf25400d8d307 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 14 Jan 2020 09:25:44 -0500 Subject: [PATCH 0053/9987] adding easyconfigs: AutoDock-4.2.6-GCCcore-8.3.0.eb, AutoGrid-4.2.6-GCCcore-8.3.0.eb --- .../AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb | 30 +++++++++++++++++++ .../AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb | 30 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..ae4948bdffc --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb @@ -0,0 +1,30 @@ +# Currently there is not an EasyBlock to unify AutoDock and AutoGrid so this is a happy medium until then +easyblock = 'ConfigureMake' + +name = 'AutoDock' +version = '4.2.6' + +homepage = 'http://autodock.scripps.edu/' + +description = """ + AutoDock is a suite of automated docking tools. It is designed to + predict how small molecules, such as substrates or drug candidates, bind to + a receptor of known 3D structure. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [' https://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/'] +sources = ['%(namelower)ssuite-%(version)s-src.tar.gz'] +checksums = ['4b24ce4baf216a5e1a6a79bb664eeed684aed17cede64ff0061aa1bcc17874c4'] + +builddependencies = [('binutils', '2.32')] + +start_dir = 'autodock' + +sanity_check_paths = { + 'files': ["bin/autodock4"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..ca8ac8a7376 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb @@ -0,0 +1,30 @@ +# Currently there is not an EasyBlock to unify AutoDock and AutoGrid so this is a happy medium until then +easyblock = 'ConfigureMake' + +name = 'AutoGrid' +version = '4.2.6' + +homepage = 'http://autodock.scripps.edu/' + +description = """ + AutoDock is a suite of automated docking tools. It is designed to + predict how small molecules, such as substrates or drug candidates, bind to + a receptor of known 3D structure. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/'] +sources = ['autodocksuite-%(version)s-src.tar.gz'] +checksums = ['4b24ce4baf216a5e1a6a79bb664eeed684aed17cede64ff0061aa1bcc17874c4'] + +builddependencies = [('binutils', '2.32')] + +start_dir = 'autogrid' + +sanity_check_paths = { + 'files': ["bin/autogrid4"], + 'dirs': [] +} + +moduleclass = 'tools' From 31a99957231d8e182ec19e4e071e2cf0397730c7 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 14 Jan 2020 10:14:46 -0500 Subject: [PATCH 0054/9987] s/http:/https:/ --- .../easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb index ae4948bdffc..4033cdfaf6a 100644 --- a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb @@ -4,7 +4,7 @@ easyblock = 'ConfigureMake' name = 'AutoDock' version = '4.2.6' -homepage = 'http://autodock.scripps.edu/' +homepage = 'https://autodock.scripps.edu/' description = """ AutoDock is a suite of automated docking tools. It is designed to diff --git a/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb index ca8ac8a7376..73f2a7a7985 100644 --- a/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb @@ -4,7 +4,7 @@ easyblock = 'ConfigureMake' name = 'AutoGrid' version = '4.2.6' -homepage = 'http://autodock.scripps.edu/' +homepage = 'https://autodock.scripps.edu/' description = """ AutoDock is a suite of automated docking tools. It is designed to From 25ee55cb51299a6f13f5004b63f82f4429eb8f69 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Tue, 14 Jan 2020 19:53:29 -0500 Subject: [PATCH 0055/9987] fix source_urls --- .../easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb index 4033cdfaf6a..efaf7902dcb 100644 --- a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb @@ -14,7 +14,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [' https://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/'] +source_urls = ['https://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/'] sources = ['%(namelower)ssuite-%(version)s-src.tar.gz'] checksums = ['4b24ce4baf216a5e1a6a79bb664eeed684aed17cede64ff0061aa1bcc17874c4'] From 5d5e8035174a8690c0aec99660f13bb87210fec6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Jan 2020 14:52:56 +0200 Subject: [PATCH 0056/9987] netMHC-4.0a: fix postinstallcmds and clarify download instructions --- easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb | 24 ++++++++++--------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb b/easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb index 5cf8e1384e9..db306984cd5 100644 --- a/easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb +++ b/easybuild/easyconfigs/n/netMHC/netMHC-4.0a.eb @@ -3,15 +3,14 @@ easyblock = 'Tarball' name = 'netMHC' version = '4.0a' -homepage = 'http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC' -description = """ NetMHC 4.0 software predicts binding of peptides to a number of different - HLA alleles using artificial neural networks (ANN). """ +homepage = 'https://www.cbs.dtu.dk/services/NetMHC/' +description = """NetMHC 4.0 predicts binding of peptides to a number of different + HLA alleles using artificial neural networks (ANN).""" toolchain = SYSTEM -# netMHC is proprietary software, but free for academcs -# see: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC -source_urls = ['http://www.cbs.dtu.dk/services/NetMHC-4.0'] +# netMHC is proprietary software, but free for academics. +# It can be requested at https://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC sources = [ { 'filename': '%(name)s-%(version)s.Linux.tar.gz', @@ -27,18 +26,21 @@ checksums = [ 'f3fb6d77ec11bc51de963e96fd75a0622f5098a2d1e37d750afa3709d5b876d1', # netMHC-4.0a-data.tar.gz ] +keepsymlinks = True + postinstallcmds = [ - 'sed -i -e "s|setenv[[:space:]]NMHOME.*|setenv NMHOME \$EBROOTNETMHC|" %(installdir)s/netMHC', - 'sed -i -e "s|setenv[[:space:]]TMPDIR.*|setenv TMPDIR /tmp|" %(installdir)s/netMHC', + "sed -i -e 's|setenv[[:space:]]NMHOME.*|setenv NMHOME $EBROOTNETMHC|' %(installdir)s/netMHC", + "sed -i -e 's|setenv[[:space:]]*TMPDIR.*|setenv TMPDIR /tmp|' %(installdir)s/netMHC", + "chmod -R +rX %(installdir)s", ] -modextrapaths = {'PATH': ''} - sanity_check_paths = { 'files': ['netMHC', 'Linux_x86_64/bin/netMHC'], - 'dirs': [], + 'dirs': ['data'], } sanity_check_commands = ['netMHC -h'] +modextrapaths = {'PATH': ''} + moduleclass = 'bio' From f997ba8b7c2c153a8e8c8481ef7218b85c2048c7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Jan 2020 16:24:56 +0200 Subject: [PATCH 0057/9987] netMHCpan-4.0a: fix postinstallcmds and clarify download instructions --- .../easyconfigs/n/netMHCpan/netMHCpan-4.0a.eb | 27 ++++++++++--------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/n/netMHCpan/netMHCpan-4.0a.eb b/easybuild/easyconfigs/n/netMHCpan/netMHCpan-4.0a.eb index 7cda16cb513..1515b7f4e1a 100644 --- a/easybuild/easyconfigs/n/netMHCpan/netMHCpan-4.0a.eb +++ b/easybuild/easyconfigs/n/netMHCpan/netMHCpan-4.0a.eb @@ -3,24 +3,22 @@ easyblock = 'Tarball' name = 'netMHCpan' version = '4.0a' -homepage = 'http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan' -description = """ The NetMHCpan software predicts binding of peptides to any known MHC - molecule using artificial neural networks (ANNs). """ +homepage = 'https://www.cbs.dtu.dk/services/NetMHCpan/' +description = """The NetMHCpan software predicts binding of peptides to any known MHC + molecule using artificial neural networks (ANNs).""" toolchain = SYSTEM -# netMHCpan is proprietary software, but free for academcs -# see: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan -source_urls = ['http://www.cbs.dtu.dk/services/NetMHCpan-4.0'] +# netMHCpan is proprietary software, but free for academics. +# It can be requested at https://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan sources = [ { 'filename': '%(name)s-%(version)s.Linux.tar.gz', - 'extract_cmd': 'tar --strip-components=1 -xzf %s && chmod -R +rX *', + 'extract_cmd': 'tar --strip-components=1 -xzf %s', }, { 'download_filename': 'data.Linux.tar.gz', 'filename': '%(name)s-%(version)s-data.Linux.tar.gz', - 'extract_cmd': 'tar -xzf %s -C Linux_x86_64 && chmod -R +rX Linux_x86_64/data' }, ] @@ -29,18 +27,21 @@ checksums = [ 'c2a4c9263af448f1a46e63f7c068194fd5bbfa0413413c741cf92d88e6a76b06', # netMHCpan-4.0a-data.Linux.tar.gz ] +keepsymlinks = True + postinstallcmds = [ - 'sed -i -e "s|setenv[[:space:]]NMHOME.*|setenv NMHOME \$EBROOTNETMHCPAN|" %(installdir)s/netMHCpan', - 'sed -i -e "s|setenv[[:space:]]TMPDIR.*|setenv TMPDIR /tmp|" %(installdir)s/netMHCpan', + "sed -i -e 's|setenv[[:space:]]NMHOME.*|setenv NMHOME $EBROOTNETMHCPAN|' %(installdir)s/netMHCpan", + "sed -i -e 's|setenv[[:space:]]*TMPDIR.*|setenv TMPDIR /tmp|' %(installdir)s/netMHCpan", + "chmod -R +rX %(installdir)s", ] -modextrapaths = {'PATH': ''} - sanity_check_paths = { 'files': ['netMHCpan', 'Linux_x86_64/bin/netMHCpan'], - 'dirs': [], + 'dirs': ['data'], } sanity_check_commands = ['netMHCpan -h'] +modextrapaths = {'PATH': ''} + moduleclass = 'bio' From f4899fc7a75c055b2dfbbec3978012b1956d2db2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Jan 2020 16:36:07 +0200 Subject: [PATCH 0058/9987] adding easyconfigs: netMHCII-2.3.eb --- .../easyconfigs/n/netMHCII/netMHCII-2.3.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/n/netMHCII/netMHCII-2.3.eb diff --git a/easybuild/easyconfigs/n/netMHCII/netMHCII-2.3.eb b/easybuild/easyconfigs/n/netMHCII/netMHCII-2.3.eb new file mode 100644 index 00000000000..0729f2f8382 --- /dev/null +++ b/easybuild/easyconfigs/n/netMHCII/netMHCII-2.3.eb @@ -0,0 +1,49 @@ +easyblock = 'Tarball' + +name = 'netMHCII' +version = '2.3' + +homepage = 'https://www.cbs.dtu.dk/services/NetMHCII/' +description = """NetMHCII 2.3 server predicts binding of peptides to HLA-DR, + HLA-DQ, HLA-DP and mouse MHC class II alleles using articial neuron networks. + Predictions can be obtained for 25 HLA-DR alleles, 20 HLA-DQ, 9 HLA-DP, and + 7 mouse H2 class II alleles.""" + +toolchain = SYSTEM + +# netMHCII is proprietary software, but free for academics. +# It can be requested at https://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCII +sources = [ + { + 'filename': '%(name)s-%(version)s.Linux.tar.gz', + 'extract_cmd': 'tar --strip-components=1 -xzf %s', + }, + { + 'download_filename': 'data.Linux.tar.gz', + 'filename': '%(name)s-%(version)s-data.Linux.tar.gz', + }, +] +checksums = [ + '8b184b2463b93bbcbb93a7351c6c0bae12d82c7827c451ebc5153b257dd0be86', # netMHCII-2.3.Linux.tar.gz + '6bf8af9e2e89d96b8fe9a2752164606417c4583872bdc2e81637f6668dee30a0', # netMHCII-2.3-data.Linux.tar.gz +] + +keepsymlinks = True + +postinstallcmds = [ + "sed -i -e 's|setenv[[:space:]]NMHOME.*|setenv NMHOME $EBROOTNETMHCII|' %(installdir)s/netMHCII-%(version)s", + "sed -i -e 's|setenv[[:space:]]*TMPDIR.*|setenv TMPDIR $TMPDIR|' %(installdir)s/netMHCII-%(version)s", + "cd %(installdir)s && ln -s netMHCII-2.3 netMHCII", + "chmod -R +rX %(installdir)s", +] + +sanity_check_paths = { + 'files': ['netMHCII-%(version)s', 'Linux_x86_64/bin/netMHCII'], + 'dirs': ['data'], +} + +sanity_check_commands = ['netMHCII-%(version)s -h'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From a789ce941cd132ce1c9e97c0fe45fb6c6a06dfe5 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Thu, 30 Jan 2020 12:47:55 +0100 Subject: [PATCH 0059/9987] Add CPU/GPU builds for GROMACS/2019.4 with PLUMED/2.5.4 --- .../GROMACS-2019.4-foss-2019b-PLUMED-2.5.4.eb | 58 ++++++++++++++++++ ...MACS-2019.4-fosscuda-2019b-PLUMED-2.5.4.eb | 60 +++++++++++++++++++ .../GROMACS/GROMACS-2019.4-fosscuda-2019b.eb | 54 +++++++++++++++++ .../PLUMED-2.5.4-foss-2019b-Python-3.7.4.eb | 57 ++++++++++++++++++ ...LUMED-2.5.4-fosscuda-2019b-Python-3.7.4.eb | 57 ++++++++++++++++++ 5 files changed, 286 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b-PLUMED-2.5.4.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-fosscuda-2019b-PLUMED-2.5.4.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-fosscuda-2019b.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.4-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.4-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b-PLUMED-2.5.4.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b-PLUMED-2.5.4.eb new file mode 100644 index 00000000000..582265358ee --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-foss-2019b-PLUMED-2.5.4.eb @@ -0,0 +1,58 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * J. Sassmannshausen (Crick HPC team) +# * Lars Viklund +# License:: MIT/GPL +# + +name = 'GROMACS' +version = '2019.4' +local_plum_ver = '2.5.4' +versionsuffix = '-PLUMED-%s' % local_plum_ver + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a CPU only build, containing both MPI and threadMPI builds. +""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch', +] +checksums = [ + 'ba4366eedfc8a1dbf6bddcef190be8cd75de53691133f305a7f9c296e5ca1867', # gromacs-2019.4.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch + '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06', +] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +dependencies = [ + ('PLUMED', local_plum_ver, '-Python-3.7.4'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-fosscuda-2019b-PLUMED-2.5.4.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-fosscuda-2019b-PLUMED-2.5.4.eb new file mode 100644 index 00000000000..c7f4b27ddd7 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-fosscuda-2019b-PLUMED-2.5.4.eb @@ -0,0 +1,60 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Lars Viklund +# License:: MIT/GPL +# 2019.3 version +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# + +name = 'GROMACS' +version = '2019.4' +local_plum_ver = '2.5.4' +versionsuffix = '-PLUMED-%s' % local_plum_ver + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. +""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', +] +checksums = [ + 'ba4366eedfc8a1dbf6bddcef190be8cd75de53691133f305a7f9c296e5ca1867', # gromacs-2019.4.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', +] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +dependencies = [ + ('PLUMED', local_plum_ver, '-Python-3.7.4'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-fosscuda-2019b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-fosscuda-2019b.eb new file mode 100644 index 00000000000..23d4e624864 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.4-fosscuda-2019b.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Lars Viklund +# License:: MIT/GPL +# 2019.3 version +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# + +name = 'GROMACS' +version = '2019.4' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. +""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', +] +checksums = [ + 'ba4366eedfc8a1dbf6bddcef190be8cd75de53691133f305a7f9c296e5ca1867', # gromacs-2019.4.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', +] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.4-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..3da44632a6d --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.4-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,57 @@ +# by Ward Poelmans +# updated by Lars Viklund + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.5.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['12eda9c533f765a33425215fa1e6ea05d8763d29bad0dae637a38e5c83d4ce17'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('libmatheval', '1.1.11'), + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# requires to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.4-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.4-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..1c7b2104a89 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.5.4-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,57 @@ +# by Ward Poelmans +# updated by Lars Viklund + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.5.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['12eda9c533f765a33425215fa1e6ea05d8763d29bad0dae637a38e5c83d4ce17'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.6'), + ('libmatheval', '1.1.11'), + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# requires to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From 3fa92057084179505479650b57100918449fefd5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Mar 2020 12:09:28 +0100 Subject: [PATCH 0060/9987] adding easyconfigs: elastix-5.0.0-foss-2019b-Python-3.7.4.eb --- .../elastix-5.0.0-foss-2019b-Python-3.7.4.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/e/elastix/elastix-5.0.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/e/elastix/elastix-5.0.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/e/elastix/elastix-5.0.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..23b0095b86f --- /dev/null +++ b/easybuild/easyconfigs/e/elastix/elastix-5.0.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'elastix' +version = '5.0.0' +versionsuffix = '-Python-3.7.4' + +homepage = 'http://elastix.isi.uu.nl/' +description = " elastix: a toolbox for rigid and nonrigid registration of images. " + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/SuperElastix/elastix/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a377ae0307231bf70c474e87ebbf07d649faca211febf1c1d981a2039fcfcd0e'] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('ITK', '5.0.1', versionsuffix), +] + +configopts = '-DCMAKE_BUILD_TYPE=Release ' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/elastix', 'bin/transformix'], + 'dirs': ['include', 'lib'] +} + +moduleclass = 'vis' From 9e19d95fb6c942601e97a3a1765f96ec47dee44d Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 6 Apr 2020 11:19:40 +0000 Subject: [PATCH 0061/9987] tabix-0-2-6 updated to foss-2019b tool chain --- .../t/tabix/tabix-0.2.6-foss-2019b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb new file mode 100644 index 00000000000..ea06aa33c78 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb @@ -0,0 +1,36 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' From db681884a57a65a7ded1c970bb35d1f3853bb4b2 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 6 Apr 2020 11:49:40 +0000 Subject: [PATCH 0062/9987] Checksum added --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb index ea06aa33c78..72de4243f37 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'foss', 'version': '2019b'} source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] sources = [SOURCE_TAR_BZ2] +checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73'] dependencies = [('zlib', '1.2.11')] From 3ff59076902be491bfe662f12e51100ec38e202b Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 6 Apr 2020 12:51:00 +0000 Subject: [PATCH 0063/9987] URL changed to https --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb index 72de4243f37..1606e872263 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb @@ -12,7 +12,7 @@ description = """ Generic indexer for TAB-delimited genome position files """ toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')] sources = [SOURCE_TAR_BZ2] checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73'] From 2580aa1553932bc65ca53d71cc4e72c01e1054c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Apr 2020 12:52:58 +0200 Subject: [PATCH 0064/9987] adding easyconfigs: Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb --- ...ychopper-2.3.1-intel-2019b-Python-3.7.4.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..6912c2271d7 --- /dev/null +++ b/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'Pychopper' +version = '2.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nanoporetech/pychopper' +description = "A tool to identify, orient, trim and rescue full length cDNA reads." + +toolchain = {'name': 'intel', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # for pandas + ('matplotlib', '3.1.1', versionsuffix), + ('Biopython', '1.75', versionsuffix), + ('parasail', '2.4.1'), + ('Seaborn', '0.10.0', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('edlib', '1.3.8.post1', { + 'checksums': ['81bc688e8fc69d657a6b5067e104a0924b0217b7ab54547155278935d09346e0'], + }), + ('parasail', '1.2', { + 'checksums': ['6ceef978e7d06293c38c9824f76557f3d7e137cb05487be31bf89286f7a8201e'], + }), + ('sphinx_rtd_theme', '0.4.3', { + 'checksums': ['728607e34d60456d736cc7991fd236afb828b21b82f956c5ea75f94c8414040a'], + }), + ('tqdm', '4.45.0', { + 'checksums': ['00339634a22c10a7a22476ee946bbde2dbe48d042ded784e4d88e0236eca5d81'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/nanoporetech/pychopper/archive'], + 'checksums': ['ef92553c27a068baf18794a802c79fcc85554df4c9eec9da5e2e017dd6827e0a'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 3c1508cb9cec1d6174c62cada8dfbffd2f086fa1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Apr 2020 11:02:02 +0200 Subject: [PATCH 0065/9987] adding easyconfigs: FLUENT-2019R3.eb --- easybuild/easyconfigs/f/FLUENT/FLUENT-2019R3.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLUENT/FLUENT-2019R3.eb diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-2019R3.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-2019R3.eb new file mode 100644 index 00000000000..3528e38c2e3 --- /dev/null +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-2019R3.eb @@ -0,0 +1,17 @@ +name = 'FLUENT' +version = '2019R3' + +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' +description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed +to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from +air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, +from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" + +toolchain = SYSTEM + +sources = ['FLUIDS_%(version)s_LINX64.tar'] +checksums = ['4c28dfc789a86a5ed1122f62ba08ec7e399743b1542d7b0742f7da523ea45acd'] + +subdir_version = '195' + +moduleclass = 'cae' From 2795c880bd2910f1289f125b0b31b7ead25b2502 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 16 Apr 2020 22:15:04 +0100 Subject: [PATCH 0066/9987] adding easyconfigs: ABAQUS-2020.eb --- easybuild/easyconfigs/a/ABAQUS/ABAQUS-2020.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABAQUS/ABAQUS-2020.eb diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2020.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2020.eb new file mode 100644 index 00000000000..5f3a77e2f8c --- /dev/null +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2020.eb @@ -0,0 +1,24 @@ +name = 'ABAQUS' +version = '2020' + +homepage = 'http://www.simulia.com/products/abaqus_fea.html' +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" + +toolchain = SYSTEM + +sources = [ + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-4.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-4.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-4.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-4.tar', +] + +checksums = [ + '583da4cb732b7cf479eb437a3f6ff76e91771c0fa6dd020e5a21c6c498357157', # 2020.AM_SIM_Abaqus_Extend.AllOS.1-4.tar + '3c0a028fc8c4ce2eb633eb0c4aa1d590de7214b093193e48b9a212d185d03ae6', # 2020.AM_SIM_Abaqus_Extend.AllOS.2-4.tar + '376c6285a8ba258a9beedb801bc6846b1536e472fc252492f77174c3afd3119f', # 2020.AM_SIM_Abaqus_Extend.AllOS.3-4.tar + '76cfff12bd6dd8a4c52fde58af3e42c7e1a1f92c3294e5d48d4e112bc51e7d0c', # 2020.AM_SIM_Abaqus_Extend.AllOS.4-4.tar +] + +moduleclass = 'cae' From 711295b8dec414616635e5816865ef7f4527ca54 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 16 Apr 2020 22:29:49 +0100 Subject: [PATCH 0067/9987] New URL --- easybuild/easyconfigs/a/ABAQUS/ABAQUS-2020.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2020.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2020.eb index 5f3a77e2f8c..a17777c85b0 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2020.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2020.eb @@ -1,7 +1,7 @@ name = 'ABAQUS' version = '2020' -homepage = 'http://www.simulia.com/products/abaqus_fea.html' +homepage = 'https://www.3ds.com/products-services/simulia/products/abaqus/' description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.""" From 144716a55be6f91fb4391c0cc29495a72e907fac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Apr 2020 13:35:48 +0200 Subject: [PATCH 0068/9987] adding easyconfigs: Stacks-2.53-iccifort-2019.5.281.eb --- .../Stacks/Stacks-2.53-iccifort-2019.5.281.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..0f660b7c780 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '2.53' + +homepage = 'http://catchenlab.life.illinois.edu/stacks' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee1efceaeeeb7a39f0c2e804ad7c0a003094db28c9101120c38ddb02846e90fd'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks', + 'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks', + 'bin/tsv2bam', 'bin/ustacks'], + 'dirs': [], +} + +moduleclass = 'bio' From e3ec482a382aba8e58955b0ac2600739ff4626e3 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 1 Jun 2020 15:54:29 +0200 Subject: [PATCH 0069/9987] adding easyconfigs: numba-0.49.1-foss-2020a-Python-3.8.2.eb, LLVM-8.0.1-GCCcore-9.3.0.eb --- .../l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb | 45 +++++++++++++++++ .../numba-0.49.1-foss-2020a-Python-3.8.2.eb | 50 +++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..b39d56ac18c --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '8.0.1' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s'] +sources = ['llvm-%(version)s.src.tar.xz'] +checksums = ['44787a6d02f7140f145e2250d56c9f849334e11f9ae379827510ed72f12b75e7'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), + ('Python', '3.8.2'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=ON ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +separate_build_dir = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..ea12473895c --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.49.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('LLVM', '8.0.1'), +] + +use_pip = True + +exts_list = [ + ('llvmlite', '0.32.1', { + 'patches': ['llvmlite-0.30.0_fix-ffi-Makefile.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'checksums': [ + '41262a47b8cbba5a09203b15b65fbdf11192f92aa226c81e99115acdee8f3b8d', # llvmlite-0.32.1.tar.gz + # llvmlite-0.30.0_fix-ffi-Makefile.patch + '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', + ], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + 'checksums': ['89e1ad8215918036b0ffc53501888d44ed44c1f2cb09a9e047d06af5cd7e7a5a'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' From 776e29481f0f4db09cd9dcb4a5497a465789e027 Mon Sep 17 00:00:00 2001 From: sassy Date: Sat, 13 Jun 2020 23:20:35 +0000 Subject: [PATCH 0070/9987] New EC for version 1.9.1 and download URL changed for both versions --- .../FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 46 +++++++++++++++++++ .../FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 46 +++++++++++++++++++ .../f/FLANN/cmake-flann-1.8.4.patch | 23 ++++++++++ .../f/FLANN/cmake-flann-1.9.1.patch | 21 +++++++++ 4 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch create mode 100644 easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..bf9a0af1ea8 --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'FLANN' +version = '1.8.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/mariusmuja/flann/' +description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/mariusmuja/flann/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = [ + 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz + '491b1ead0bd4167d1d3e59cecb188cc54cb1ee854179b9571a68ab02f934bcb6', # cmake-flann-1.8.4.patch' +] + +builddependencies = [('CMake', '3.16.4')] +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-3.8.2'), +] + +separate_build_dir = True + +patches = ['cmake-flann-1.8.4.patch'] + +preconfigopts = 'touch %(builddir)s/flann-%(version)s/src/cpp/empty.cpp && ' +configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" + +modextrapaths = {'PYTHONPATH': ['share/flann/python']} + +sanity_check_paths = { + 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', + 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], + 'dirs': ['include/flann', 'lib/pkgconfig', 'share/doc/flann', 'share/flann/python'], +} +sanity_check_commands = [('python', '-c "import pyflann"')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..4f8590bfeb0 --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'FLANN' +version = '1.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/mariusmuja/flann/' +description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/mariusmuja/flann/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = [ + 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz + '14218e775a8de5197bad1afa470e66e53a8a850b5a7ae2c0d2e840727030a7a2', # cmake-flann-1.9.1.patch +] + +builddependencies = [('CMake', '3.16.4')] +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-3.8.2'), +] + +separate_build_dir = True + +patches = ['cmake-flann-1.9.1.patch'] + +preconfigopts = 'touch %(builddir)s/flann-%(version)s/src/cpp/empty.cpp && ' +configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" + +modextrapaths = {'PYTHONPATH': ['share/flann/python']} + +sanity_check_paths = { + 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', + 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], + 'dirs': ['include/flann', 'lib/pkgconfig', 'share/flann/python'], +} +sanity_check_commands = [('python', '-c "import pyflann"')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch new file mode 100644 index 00000000000..e06e7f70eed --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch @@ -0,0 +1,23 @@ +diff -Nru flann-1.8.4.orig/src/cpp/CMakeLists.txt flann-1.8.4/src/cpp/CMakeLists.txt +--- flann-1.8.4.orig/src/cpp/CMakeLists.txt 2013-01-24 17:54:36.000000000 +0000 ++++ flann-1.8.4/src/cpp/CMakeLists.txt 2020-06-12 22:23:14.032194077 +0000 +@@ -29,7 +29,7 @@ + endif() + + if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) +- add_library(flann_cpp SHARED "") ++ add_library(flann_cpp SHARED empty.cpp) + set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) + target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) + +@@ -83,7 +83,7 @@ + set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) + + if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) +- add_library(flann SHARED "") ++ add_library(flann SHARED empty.cpp) + set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) + target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) + else() + + diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch new file mode 100644 index 00000000000..ae411342b6e --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch @@ -0,0 +1,21 @@ +diff -Nru flann-1.9.1.orig/src/cpp/CMakeLists.txt flann-1.9.1/src/cpp/CMakeLists.txt +--- flann-1.9.1.orig/src/cpp/CMakeLists.txt 2016-08-04 23:20:50.000000000 +0000 ++++ flann-1.9.1/src/cpp/CMakeLists.txt 2020-06-13 20:56:59.634970091 +0000 +@@ -29,7 +29,7 @@ + endif() + + if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) +- add_library(flann_cpp SHARED "") ++ add_library(flann_cpp SHARED empty.cpp) + set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) + target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) + +@@ -83,7 +83,7 @@ + set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) + + if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) +- add_library(flann SHARED "") ++ add_library(flann SHARED empty.cpp) + set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) + target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) + else() From 9b7629fce074a1b5e9a8b2be781fe521e31b8b31 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 14 Jun 2020 13:38:05 +0000 Subject: [PATCH 0071/9987] Style corrected --- .../f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index 4f8590bfeb0..952488f148e 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -23,8 +23,8 @@ checksums = [ builddependencies = [('CMake', '3.16.4')] dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', '-Python-3.8.2'), + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-3.8.2'), ] separate_build_dir = True From ab24b2379cebbce0e9dd21f6631f3518adc9e21d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 17 Jun 2020 00:42:42 +0200 Subject: [PATCH 0072/9987] adding easyconfigs: MrBayes-3.2.7a-foss-2020a.eb --- .../m/MrBayes/MrBayes-3.2.7a-foss-2020a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-foss-2020a.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-foss-2020a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-foss-2020a.eb new file mode 100644 index 00000000000..8affddc7c40 --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-foss-2020a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'MrBayes' +version = '3.2.7a' + +homepage = 'http://mrbayes.csit.fsu.edu' +description = "MrBayes is a program for the Bayesian estimation of phylogeny." + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +github_account = 'NBISweden' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3eed2e3b1d9e46f265b6067a502a89732b6f430585d258b886e008e846ecc5c6'] + +builddependencies = [ + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('beagle-lib', '3.1.2'), + ('libreadline', '8.0'), +] + +configopts = "--with-mpi=yes" + +sanity_check_paths = { + 'files': ['bin/mb'], + 'dirs': ['share/doc', 'share/examples'], +} + + +moduleclass = 'bio' From 48530e8525d8af4f30de98d47adfdce1f79a1d07 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 6 Jul 2020 18:03:54 +0200 Subject: [PATCH 0073/9987] Code Saturne from JSC --- .../Code_Saturne-6.1.1-gpsmkl-2019a.1.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb diff --git a/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb b/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb new file mode 100644 index 00000000000..53c5c098a0b --- /dev/null +++ b/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb @@ -0,0 +1,56 @@ +# easyconfig file for Code_Saturne +# author: Metin Cakircali (Juelich Supercomputing Centre) +name = 'Code_Saturne' +version = '6.1.1' + +# extra option for the SLURM batch system +slurm = True + +homepage = 'https://www.code-saturne.org' +description = """Code_Saturne solves the Navier-Stokes equations +for 2D, 2D-axisymmetric and 3D flows, steady or unsteady, +laminar or turbulent, incompressible or weakly dilatable, +isothermal or not, with scalars transport if required. + +Code_Saturne %(version)s%(versionsuffix)s is installed in +$EBROOTCODE_SATURNE +""" +site_contacts = 'a.strube@fz-juelich.de' + +toolchain = {'name': 'gpsmkl', 'version': '2019a.1'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +sources = [{ + 'source_urls': ['https://github.com/code-saturne/code_saturne/archive/'], + 'filename': 'v%(version)s.tar.gz' +}] + +builddependencies = [ + ('Autotools', '20180311'), + ('gettext', '0.19.8.1'), + ('Bison', '3.3.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('Python', '3.6.8'), + ('PyQt5', '5.11.3', '-Python-%(pyver)s'), + ('HDF5', '1.10.5'), + ('MED', '4.0.0'), + ('CGNS', '4.1.1'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '6.0.6'), + ('ParaView', '5.6.0', '-Python-%(pyver)s', ('gpsmkl', '2019a.1')), +] + +# better to configure these dependents explicitly +configopts = ['--with-med=$EBROOTMED --with-cgns=$EBROOTCGNS \ + --with-metis=$EBROOTPARMETIS --with-scotch=$EBROOTSCOTCH'] + +parallel = 48 + +modloadmsg = "To benefit from shell completion for %(name)s commands and\n" +modloadmsg += "options, you may also source a bash completion file by;\n" +modloadmsg += ". $CS_BASH\n" + +moduleclass = 'cae' From e14d534992fe3b8a63b462b1a5f252a1b6428626 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 6 Jul 2020 21:09:19 +0000 Subject: [PATCH 0074/9987] Patch files updated --- .../FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 3 +-- .../FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 3 +-- .../f/FLANN/cmake-flann-1.8.4.patch | 18 +++++++++++------- .../f/FLANN/cmake-flann-1.9.1.patch | 16 +++++++++++----- 4 files changed, 24 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index bf9a0af1ea8..ff188f43291 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -18,7 +18,7 @@ source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] checksums = [ 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz - '491b1ead0bd4167d1d3e59cecb188cc54cb1ee854179b9571a68ab02f934bcb6', # cmake-flann-1.8.4.patch' + '662e5972487a6616cbca36ac9459bcc3ca773ed781564ed2532d9792d97c2897', # cmake-flann-1.8.4.patch' ] builddependencies = [('CMake', '3.16.4')] @@ -31,7 +31,6 @@ separate_build_dir = True patches = ['cmake-flann-1.8.4.patch'] -preconfigopts = 'touch %(builddir)s/flann-%(version)s/src/cpp/empty.cpp && ' configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index 952488f148e..1dad550d3d0 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -18,7 +18,7 @@ source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] checksums = [ 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz - '14218e775a8de5197bad1afa470e66e53a8a850b5a7ae2c0d2e840727030a7a2', # cmake-flann-1.9.1.patch + '479068a9f1c745780a7fbf55e6ba02011d5a6ca0a917ce0d4e11367c14a8cf78', # cmake-flann-1.9.1.patch ] builddependencies = [('CMake', '3.16.4')] @@ -31,7 +31,6 @@ separate_build_dir = True patches = ['cmake-flann-1.9.1.patch'] -preconfigopts = 'touch %(builddir)s/flann-%(version)s/src/cpp/empty.cpp && ' configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch index e06e7f70eed..db8f515db34 100644 --- a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch +++ b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch @@ -1,7 +1,10 @@ -diff -Nru flann-1.8.4.orig/src/cpp/CMakeLists.txt flann-1.8.4/src/cpp/CMakeLists.txt ---- flann-1.8.4.orig/src/cpp/CMakeLists.txt 2013-01-24 17:54:36.000000000 +0000 -+++ flann-1.8.4/src/cpp/CMakeLists.txt 2020-06-12 22:23:14.032194077 +0000 -@@ -29,7 +29,7 @@ +# Flann fails to build with newer versions of CMake, see: +# https://stackoverflow.com/questions/50763621/building-flann-with-cmake-fails +diff --git a/flann-1.8.4.orig/src/cpp/CMakeLists.txt b/flann-1.8.4/src/cpp/CMakeLists.txt +index 78a204a..d9b5777 100644 +--- a/flann-1.8.4.orig/src/cpp/CMakeLists.txt ++++ b/flann-1.8.4/src/cpp/CMakeLists.txt +@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB) endif() if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) @@ -10,7 +13,7 @@ diff -Nru flann-1.8.4.orig/src/cpp/CMakeLists.txt flann-1.8.4/src/cpp/CMakeLists set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) -@@ -83,7 +83,7 @@ +@@ -83,7 +83,7 @@ if (BUILD_C_BINDINGS) set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) @@ -19,5 +22,6 @@ diff -Nru flann-1.8.4.orig/src/cpp/CMakeLists.txt flann-1.8.4/src/cpp/CMakeLists set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) else() - - +diff --git a/flann-1.8.4/src/cpp/empty.cpp b/flann-1.8.4/src/cpp/empty.cpp +new file mode 100644 +index 0000000..e69de29 diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch index ae411342b6e..4f3c2fd45f9 100644 --- a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch +++ b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch @@ -1,7 +1,10 @@ -diff -Nru flann-1.9.1.orig/src/cpp/CMakeLists.txt flann-1.9.1/src/cpp/CMakeLists.txt ---- flann-1.9.1.orig/src/cpp/CMakeLists.txt 2016-08-04 23:20:50.000000000 +0000 -+++ flann-1.9.1/src/cpp/CMakeLists.txt 2020-06-13 20:56:59.634970091 +0000 -@@ -29,7 +29,7 @@ +# Flann fails to build with newer versions of CMake, see: +# https://stackoverflow.com/questions/50763621/building-flann-with-cmake-fails +diff --git a/flann-1.9.1.orig/src/cpp/CMakeLists.txt b/flann-1.9.1/src/cpp/CMakeLists.txt +index 49c53f0..0976e41 100644 +--- a/flann-1.9.1.orig/src/cpp/CMakeLists.txt ++++ b/flann-1.9.1/src/cpp/CMakeLists.txt +@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB) endif() if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) @@ -10,7 +13,7 @@ diff -Nru flann-1.9.1.orig/src/cpp/CMakeLists.txt flann-1.9.1/src/cpp/CMakeLists set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) -@@ -83,7 +83,7 @@ +@@ -83,7 +83,7 @@ if (BUILD_C_BINDINGS) set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) @@ -19,3 +22,6 @@ diff -Nru flann-1.9.1.orig/src/cpp/CMakeLists.txt flann-1.9.1/src/cpp/CMakeLists set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) else() +diff --git a/flann-1.9.1/src/cpp/empty.cpp b/flann-1.9.1/src/cpp/empty.cpp +new file mode 100644 +index 0000000..e69de29 From 8e87416d80f9e095c14718940a04b98d173fba26 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 6 Jul 2020 21:29:37 +0000 Subject: [PATCH 0075/9987] Patch files name updated --- .../easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 2 +- .../{cmake-flann-1.8.4.patch => FLANN-1.8.4_fix-cmake.patch} | 0 .../easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 2 +- .../{cmake-flann-1.9.1.patch => FLANN-1.9.1_fix-cmake.patch} | 0 4 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/f/FLANN/{cmake-flann-1.8.4.patch => FLANN-1.8.4_fix-cmake.patch} (100%) rename easybuild/easyconfigs/f/FLANN/{cmake-flann-1.9.1.patch => FLANN-1.9.1_fix-cmake.patch} (100%) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index ff188f43291..438121d4c3d 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -29,7 +29,7 @@ dependencies = [ separate_build_dir = True -patches = ['cmake-flann-1.8.4.patch'] +patches = ['%(name)s-%(version)s_fix-cmake.patch'] configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch similarity index 100% rename from easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch rename to easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index 1dad550d3d0..aaef2f96e6a 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -29,7 +29,7 @@ dependencies = [ separate_build_dir = True -patches = ['cmake-flann-1.9.1.patch'] +patches = ['%(name)s-%(version)s_fix-cmake.patch'] configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1_fix-cmake.patch similarity index 100% rename from easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch rename to easybuild/easyconfigs/f/FLANN/FLANN-1.9.1_fix-cmake.patch From 7442860a6727cf365816520e6501fdf31dc3f205 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 7 Jul 2020 18:30:05 +0200 Subject: [PATCH 0076/9987] numba v0.50.0 with LLVM v9.0.1 for foss/2020a --- .../l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb | 45 ------------------- ...> numba-0.50.0-foss-2020a-Python-3.8.2.eb} | 10 ++--- 2 files changed, 5 insertions(+), 50 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb rename easybuild/easyconfigs/n/numba/{numba-0.49.1-foss-2020a-Python-3.8.2.eb => numba-0.50.0-foss-2020a-Python-3.8.2.eb} (82%) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb deleted file mode 100644 index b39d56ac18c..00000000000 --- a/easybuild/easyconfigs/l/LLVM/LLVM-8.0.1-GCCcore-9.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'LLVM' -version = '8.0.1' - -homepage = "https://llvm.org/" -description = """The LLVM Core libraries provide a modern source- and target-independent - optimizer, along with code generation support for many popular CPUs - (as well as some less common ones!) These libraries are built around a well - specified code representation known as the LLVM intermediate representation - ("LLVM IR"). The LLVM Core libraries are well documented, and it is - particularly easy to invent your own language (or port an existing compiler) - to use LLVM as an optimizer and code generator.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'cstd': 'gnu++11'} - -source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s'] -sources = ['llvm-%(version)s.src.tar.xz'] -checksums = ['44787a6d02f7140f145e2250d56c9f849334e11f9ae379827510ed72f12b75e7'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), - ('Python', '3.8.2'), -] - -dependencies = [ - ('ncurses', '6.2'), - ('zlib', '1.2.11'), -] - -configopts = '-DBUILD_SHARED_LIBS=ON ' -# required to install extra tools in bin/ -configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=ON ' -configopts += '-DCMAKE_BUILD_TYPE=Release ' - -sanity_check_paths = { - 'files': ['bin/llvm-ar', 'bin/FileCheck'], - 'dirs': ['include/llvm', 'include/llvm-c'], -} - -separate_build_dir = True - -moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb similarity index 82% rename from easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb rename to easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb index ea12473895c..0ee44b6c216 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.49.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'numba' -version = '0.49.1' +version = '0.50.0' versionsuffix = '-Python-%(pyver)s' homepage = 'https://numba.pydata.org/' @@ -17,24 +17,24 @@ toolchainopts = {'pic': True} dependencies = [ ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', versionsuffix), - ('LLVM', '8.0.1'), + ('LLVM', '9.0.1'), ] use_pip = True exts_list = [ - ('llvmlite', '0.32.1', { + ('llvmlite', '0.33.0', { 'patches': ['llvmlite-0.30.0_fix-ffi-Makefile.patch'], 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], 'checksums': [ - '41262a47b8cbba5a09203b15b65fbdf11192f92aa226c81e99115acdee8f3b8d', # llvmlite-0.32.1.tar.gz + '9c8aae96f7fba10d9ac864b443d1e8c7ee4765c31569a2b201b3d0b67d8fc596', # llvmlite-0.33.0.tar.gz # llvmlite-0.30.0_fix-ffi-Makefile.patch '672aba7b753dcfe5cb07c731bf1ec8bde1de148d4e0e2d10f6be81fb17f34bbc', ], }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], - 'checksums': ['89e1ad8215918036b0ffc53501888d44ed44c1f2cb09a9e047d06af5cd7e7a5a'], + 'checksums': ['c9e5752821530694294db41ee19a4b00e5826c689821907f6c2ece9a02756b29'], }), ] From 365aceb7c4464c1e103e4148b7edb0b83620715d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 9 Jul 2020 13:22:04 +0000 Subject: [PATCH 0077/9987] adding easyconfigs: PheWeb-1.1.20-foss-2019b-Python-3.7.4.eb --- .../PheWeb-1.1.20-foss-2019b-Python-3.7.4.eb | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/p/PheWeb/PheWeb-1.1.20-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/PheWeb/PheWeb-1.1.20-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PheWeb/PheWeb-1.1.20-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..32260ebf77c --- /dev/null +++ b/easybuild/easyconfigs/p/PheWeb/PheWeb-1.1.20-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,85 @@ +easyblock = 'PythonBundle' + +name = 'PheWeb' +version = '1.1.20' +versionsuffix = '-Python-%(pyver)s' + + +homepage = 'https://github.com/statgen/pheweb' +description = """A tool for building PheWAS websites from association files""" + +toolchain = {'name': 'foss', 'version': '2019b'} + + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('Pysam', '0.15.3'), + ('openpyxl', '3.0.3', versionsuffix, ('GCCcore', '8.3.0')), + ('Flask', '1.1.2', versionsuffix, ('GCCcore', '8.3.0')), + ('tqdm', '4.41.1'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('Brotli', '1.0.7', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['0538dc1744fd17c314d2adc409ea7d1b779783b89fd95bcfb0c2acc93a6ea5a7'], + }), + ('Flask-Compress', '1.5.0', { + 'checksums': ['f367b2b46003dd62be34f7fb1379938032656dca56377a9bc90e7188e4289a7c'], + }), + ('Flask-Login', '0.5.0', { + 'checksums': ['6d33aef15b5bcead780acc339464aae8a6e28f13c90d8b1cf9de8b549d1c0b4b'], + }), + ('rauth', '0.7.3', { + 'checksums': ['524cdbc1c28560eacfc9a9d40c59525eb8d00fdf07fbad86107ea24411477b0a'], + }), + ('marisa-trie', '0.7.5', { + 'checksums': ['c73bc25d868e8c4ea7aa7f1e19892db07bba2463351269b05340ccfa06eb2baf'], + }), + ('sortedcontainers', '2.2.2', { + 'checksums': ['4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba'], + }), + ('intervaltree', '3.0.2', { + 'checksums': ['cb4f61c81dcb4fea6c09903f3599015a83c9bdad1f0bbd232495e6681e19e273'], + }), + ('requests', '2.24.0', { + 'checksums': ['b3559a131db72c33ee969480840fff4bb6dd111de7dd27c8ee1f820f4f00231b'], + }), + ('gunicorn', '20.0.4', { + 'checksums': ['1904bb2b8a43658807108d59c3f3d56c2b6121a701161de0ddf9ad140073c626'], + }), + ('boltons', '19.1.0', { + 'checksums': ['c32b2d121331a9bc7c220050d4273f3aa359b7569cb4794188e71524603113dc'], + }), + ('blist', '1.3.6', { + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('wget', '3.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['35e630eca2aa50ce998b9b1a127bb26b30dfee573702782aa982f875e3f16061'], + }), + ('greenlet', '0.4.16', { + 'checksums': ['6e06eac722676797e8fce4adb8ad3dc57a1bb3adfb0dd3fdf8306c055a38456c'], + }), + ('zope.event', '4.4', { + 'checksums': ['69c27debad9bdacd9ce9b735dad382142281ac770c4a432b533d6d65c4614bcf'], + }), + ('zope.interface', '5.1.0', { + 'checksums': ['40e4c42bd27ed3c11b2c983fecfb03356fae1209de10686d03c02c8696a1d90e'], + }), + ('gevent', '1.5.0', { + 'checksums': ['b2814258e3b3fb32786bb73af271ad31f51e1ac01f33b37426b66cb8491b4c29'], + }), + (name, version, { + 'checksums': ['98cc12c0cecb115b8db351bc3903ab047431e0f1c15bd8249a7270e60e61e85b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 5a274a5531caee2cff2d33f65795bcd8ece61e17 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 10 Jul 2020 11:39:41 +0000 Subject: [PATCH 0078/9987] adding easyconfigs: axel-2.17.9-GCCcore-8.3.0.eb --- .../a/axel/axel-2.17.9-GCCcore-8.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..6774d2e6f9e --- /dev/null +++ b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'axel' +version = '2.17.9' + +github_account = "axel-download-accelerator" +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """Lightweight CLI download accelerator """ + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/%(github_account)s/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +checksums = ['d50dfbc59cb04fa70fb8d414579259c3eefe2a87aab52611309feeec9acb851a'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ["bin/axel"], + 'dirs': [""], +} + +moduleclass = 'tools' From eef020f6bea525f2054d2400c88cf50c02e7da35 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 10 Jul 2020 11:55:49 +0000 Subject: [PATCH 0079/9987] Add missing deps --- .../easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb index 6774d2e6f9e..65dd62c1c53 100644 --- a/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb @@ -14,13 +14,19 @@ source_urls = ['https://github.com/%(github_account)s/%(name)s/releases/download sources = [SOURCE_TAR_BZ2] checksums = ['d50dfbc59cb04fa70fb8d414579259c3eefe2a87aab52611309feeec9acb851a'] -builddependencies = [('binutils', '2.32')] +builddependencies = [ + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), + ('gettext', '0.20.1'), +] -dependencies = [('zlib', '1.2.11')] +dependencies = [('OpenSSL', '1.1.1d')] sanity_check_paths = { 'files': ["bin/axel"], 'dirs': [""], } +sanity_check_commands = [True, ('%(name)s', '--version')] + moduleclass = 'tools' From 27b391ac0a899c2a483137f1ed14696be80efff9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 10 Jul 2020 16:54:58 +0000 Subject: [PATCH 0080/9987] Fix bad indentation --- easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb index 65dd62c1c53..28b86b3e619 100644 --- a/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb @@ -15,9 +15,9 @@ sources = [SOURCE_TAR_BZ2] checksums = ['d50dfbc59cb04fa70fb8d414579259c3eefe2a87aab52611309feeec9acb851a'] builddependencies = [ - ('binutils', '2.32'), - ('pkg-config', '0.29.2'), - ('gettext', '0.20.1'), + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), + ('gettext', '0.20.1'), ] dependencies = [('OpenSSL', '1.1.1d')] From 9ab80d0fced7bf06e21b0bbc3291b154e635cc9c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 13 Jul 2020 11:48:09 +0000 Subject: [PATCH 0081/9987] Add GCCcore/9.3.0 version of axel --- .../a/axel/axel-2.17.9-GCCcore-9.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..dbbbd372428 --- /dev/null +++ b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-9.3.0.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'axel' +version = '2.17.9' + +github_account = "axel-download-accelerator" +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """Lightweight CLI download accelerator """ + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/%(github_account)s/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +checksums = ['d50dfbc59cb04fa70fb8d414579259c3eefe2a87aab52611309feeec9acb851a'] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), + ('gettext', '0.20.1'), +] + +dependencies = [('OpenSSL', '1.1.1e')] + +sanity_check_paths = { + 'files': ["bin/axel"], + 'dirs': [""], +} + +sanity_check_commands = [True, ('%(name)s', '--version')] + +moduleclass = 'tools' From bd7527c85e256c9e9030a25c8d6adde01ba1b409 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 13 Jul 2020 17:13:57 +0200 Subject: [PATCH 0082/9987] Triangle/1.6 for GCCcore/9.3.0 --- .../t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..0967ef1c173 --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'Triangle' +version = '1.6' + +homepage = 'http://www.cs.cmu.edu/~quake/triangle.html' +description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, + conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. + The latter can be generated with no small or large angles, + and are thus suitable for finite element analysis.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/voronoi/'] +sources = ['%(namelower)s.zip'] +checksums = [ + '1766327add038495fa3499e9b7cc642179229750f7201b94f8e1b7bee76f8480', # triangle.zip + '38fc1395c2392f627068b669275c30da0c25b1a6db8ed8b80d6bf05a98971568', # Triangle-1.6_makefile.patch +] + +patches = ['%(name)s-%(version)s_makefile.patch'] + +builddependencies = [('binutils', '2.34')] + +buildopts = 'triangle trilibrary' + +files_to_copy = [ + (['triangle', 'tricall'], 'bin'), + (['triangle.h'], 'include'), + (['libtriangle.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], + 'dirs': [] +} + +moduleclass = 'numlib' From 86aee4cfe7b4111bd7fc8ccad6c9a85ac45bcf36 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 16 Jul 2020 20:35:43 +0200 Subject: [PATCH 0083/9987] Triangle v1.6 for GCCcore/9.3.0: http --> https --- .../easyconfigs/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb index 0967ef1c173..a1773acd90b 100644 --- a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'MakeCp' name = 'Triangle' version = '1.6' -homepage = 'http://www.cs.cmu.edu/~quake/triangle.html' +homepage = 'https://www.cs.cmu.edu/~quake/triangle.html' description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. The latter can be generated with no small or large angles, @@ -12,7 +12,7 @@ description = """Triangle generates exact Delaunay triangulations, constrained D toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.netlib.org/voronoi/'] +source_urls = ['https://www.netlib.org/voronoi/'] sources = ['%(namelower)s.zip'] checksums = [ '1766327add038495fa3499e9b7cc642179229750f7201b94f8e1b7bee76f8480', # triangle.zip From 741f5ccbdf0ad67a8ae4cda4ea30ec7730eb5a7b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 16 Jul 2020 21:27:40 +0200 Subject: [PATCH 0084/9987] numba v0.50.1 for foss/2020a and Python/3.8.2 --- ...ython-3.8.2.eb => numba-0.50.1-foss-2020a-Python-3.8.2.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/n/numba/{numba-0.50.0-foss-2020a-Python-3.8.2.eb => numba-0.50.1-foss-2020a-Python-3.8.2.eb} (92%) diff --git a/easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb similarity index 92% rename from easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb rename to easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb index 0ee44b6c216..13cfcdf1e7f 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.50.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'numba' -version = '0.50.0' +version = '0.50.1' versionsuffix = '-Python-%(pyver)s' homepage = 'https://numba.pydata.org/' @@ -34,7 +34,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], - 'checksums': ['c9e5752821530694294db41ee19a4b00e5826c689821907f6c2ece9a02756b29'], + 'checksums': ['89e81b51b880f9b18c82b7095beaccc6856fcf84ba29c4f0ced42e4e5748a3a7'], }), ] From 46da040cf547a7621339063981d29d48d4c2b0bf Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 17 Jul 2020 11:43:31 +0200 Subject: [PATCH 0085/9987] numba v0.50.1 for foss/2020a and Python/3.8.2: Add sanity_pip_check --- .../easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb index 13cfcdf1e7f..e5b096d734b 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb @@ -21,6 +21,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_list = [ ('llvmlite', '0.33.0', { From d230e9b41e111a349f48507a07571b0912262be6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Aug 2020 16:14:55 +0200 Subject: [PATCH 0086/9987] adding easyconfigs: fastp-0.20.1-iccifort-2020.1.217.eb --- .../fastp/fastp-0.20.1-iccifort-2020.1.217.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb b/easybuild/easyconfigs/f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb new file mode 100644 index 00000000000..a29e2ae4bff --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.20.1' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'iccifort', 'version': '2020.1.217'} + +source_urls = ['https://github.com/OpenGene/fastp/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e1b663717850bed7cb560c0c540e9a05dd9448ec76978faaf853a6959fd5b1b3'] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'dirs': [], + 'files': ['bin/fastp'], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' From 089665735542fcc1403eb923e8a91e23d0336380 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 27 Aug 2020 22:22:38 -0500 Subject: [PATCH 0087/9987] adding easyconfigs: bbFTP-3.2.1.eb, bbFTP-3.2.1-GCCcore-9.3.0.eb --- .../b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb | 42 ++++++++++++++++++ easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb | 43 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..6546cadf635 --- /dev/null +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'bbFTP' +version = '3.2.1' + +homepage = 'https://software.in2p3.fr/bbftp/' + +description = """bbFTP is a file transfer software. It implements its own transfer protocol, + which is optimized for large files (larger than 2GB) and secure as it does not read the + password in a file and encrypts the connection information. bbFTP main features are: + * Encoded username and password at connection * SSH and Certificate authentication modules + * Multi-stream transfer * Big windows as defined in RFC1323 * On-the-fly data compression + * Automatic retry * Customizable time-outs * Transfer simulation + * AFS authentication integration * RFIO interface""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [homepage + 'dist'] +sources = ['%s-client-%s.tar.gz' % (name.lower(), version)] +checksums = ['4000009804d90926ad3c0e770099874084fb49013e8b0770b82678462304456d'] + +start_dir = 'bbftpc' + +builddependencies = [('binutils', '2.34')] +dependencies = [('zlib', '1.2.11')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/bbftp'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb new file mode 100644 index 00000000000..d7a35d651e5 --- /dev/null +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'bbFTP' +version = '3.2.1' + +homepage = 'https://software.in2p3.fr/bbftp/' + +description = """bbFTP is a file transfer software. It implements its own transfer protocol, + which is optimized for large files (larger than 2GB) and secure as it does not read the + password in a file and encrypts the connection information. bbFTP main features are: + * Encoded username and password at connection * SSH and Certificate authentication modules + * Multi-stream transfer * Big windows as defined in RFC1323 * On-the-fly data compression + * Automatic retry * Customizable time-outs * Transfer simulation + * AFS authentication integration * RFIO interface""" + +toolchain = SYSTEM + +source_urls = [homepage + 'dist'] +sources = ['%s-client-%s.tar.gz' % (name.lower(), version)] +checksums = ['4000009804d90926ad3c0e770099874084fb49013e8b0770b82678462304456d'] + +start_dir = 'bbftpc' + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), + ('zlib-devel', 'zlib1g-dev'), +] + +sanity_check_paths = { + 'files': ['bin/bbftp'], + 'dirs': [] +} + +moduleclass = 'tools' From bb39049fc727a6c75669a8dd32039689659d6646 Mon Sep 17 00:00:00 2001 From: gmatteo Date: Tue, 1 Sep 2020 21:02:10 +0200 Subject: [PATCH 0088/9987] Add initial version of eb file --- .../a/ABINIT/ABINIT-9.1.0-foss-2019b.eb | 54 +++++++++++++++++++ .../a/ABINIT/ABINIT-9.1.0-intel-2019b.eb | 48 +++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb new file mode 100644 index 00000000000..dc2060c22dc --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb @@ -0,0 +1,54 @@ +# +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.0.4' + +homepage = 'https://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +#checksums = ['82e8d071088ab8dc1b3a24380e30b68c544685678314df1213180b449c84ca65'] + +dependencies = [ + ('libxc', '4.3.4'), + ('HDF5', '1.10.5'), + ('netCDF', '4.7.1'), + ('netCDF-Fortran', '4.5.2'), +] + +# ensure mpi and intel toolchain +configopts = '--with-mpi="yes" --enable-openmp="no" ' +configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="-L${EBROOTOPENBLAS}/lib -lopenblas" ' + +# fftw3 support +configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4. Use nc-config and nf-config to get installation directory +configopts += 'with_netcdf="`nc-config --prefix`" ' +configopts += 'with_netcdf_fortran="`nf-config --prefix`" ' +configopts += 'with_hdf5="${EBROOTHDF5}" ' + +#configopts += 'FCFLAGS_EXTRA="-free-line-length-none" ' +#configopts += 'FCFLAGS_FREEFORM="-free-line-length-none" ' +#configopts += 'FCFLAGS="-g -O2 --free-line-length-none" ' +configopts += 'FCFLAGS="${FCFLAGS} --free-line-length-none" ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb new file mode 100644 index 00000000000..2fade0f1318 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb @@ -0,0 +1,48 @@ +# +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.0.4' + +homepage = 'https://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" + +toolchain = {'name': 'iimpi', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +#checksums = ['82e8d071088ab8dc1b3a24380e30b68c544685678314df1213180b449c84ca65'] + +dependencies = [ + ("imkl", "2019.5.281"), + ('libxc', '4.3.4'), + ('HDF5', '1.10.5'), + ('netCDF', '4.7.1'), + ('netCDF-Fortran', '4.5.2'), +] + +# ensure mpi and intel toolchain +configopts = '--with-mpi="yes" --enable-openmp="no" ' +configopts += '--with-linalg-flavor=mkl ' +configopts += '--with-fft-flavor=dfti ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4. Use nc-config and nf-config to get installation directory +configopts += 'with_netcdf="`nc-config --prefix`" ' +configopts += 'with_netcdf_fortran="`nf-config --prefix`" ' +configopts += 'with_hdf5="${EBROOTHDF5}" ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' From 7f1f3401fa91b0386637c70df46fe3bdd958948a Mon Sep 17 00:00:00 2001 From: gmatteo Date: Wed, 2 Sep 2020 01:24:42 +0200 Subject: [PATCH 0089/9987] Add tests --- .../a/ABINIT/ABINIT-9.1.0-foss-2019b.eb | 29 ++++++++++++------- .../a/ABINIT/ABINIT-9.1.0-intel-2019b.eb | 25 ++++++++++++---- 2 files changed, 38 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb index dc2060c22dc..31b29b5b7a1 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb @@ -19,33 +19,42 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('libxc', '4.3.4'), - ('HDF5', '1.10.5'), - ('netCDF', '4.7.1'), + #('HDF5', '1.10.5'), + #('netCDF', '4.7.1'), ('netCDF-Fortran', '4.5.2'), ] -# ensure mpi and intel toolchain +# Ensure MPI. configopts = '--with-mpi="yes" --enable-openmp="no" ' + +# BLAS/Lapack configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="-L${EBROOTOPENBLAS}/lib -lopenblas" ' -# fftw3 support +# FFTW3 support configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" ' # libxc support configopts += '--with-libxc=${EBROOTLIBXC} ' -# hdf5/netcdf4. Use nc-config and nf-config to get installation directory -configopts += 'with_netcdf="`nc-config --prefix`" ' -configopts += 'with_netcdf_fortran="`nf-config --prefix`" ' +# hdf5/netcdf4. +configopts += 'with_netcdf="${EBROOTNETCDF}" ' +configopts += 'with_netcdf_fortran="${EBROOTNETCDFMINFORTRAN}" ' configopts += 'with_hdf5="${EBROOTHDF5}" ' -#configopts += 'FCFLAGS_EXTRA="-free-line-length-none" ' -#configopts += 'FCFLAGS_FREEFORM="-free-line-length-none" ' -#configopts += 'FCFLAGS="-g -O2 --free-line-length-none" ' +# make sure --free-line-length-none is added to FCFLAGS configopts += 'FCFLAGS="${FCFLAGS} --free-line-length-none" ' runtest = 'check' +tests = [ + "make test_fast", + "make test_v1", + "make test_v5", + "make test_libxc", + "./tests/runtests.py v1 -j2", + "./tests/runtests.py paral mpiio -j1 -n4 -o1", +] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb index 2fade0f1318..867afd90085 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb @@ -20,26 +20,39 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ("imkl", "2019.5.281"), ('libxc', '4.3.4'), - ('HDF5', '1.10.5'), - ('netCDF', '4.7.1'), + #('HDF5', '1.10.5'), + #('netCDF', '4.7.1'), ('netCDF-Fortran', '4.5.2'), ] -# ensure mpi and intel toolchain +# Ensure MPI. configopts = '--with-mpi="yes" --enable-openmp="no" ' + +# BLAS/Lapack from MKL configopts += '--with-linalg-flavor=mkl ' + +# FFTW from MKL configopts += '--with-fft-flavor=dfti ' # libxc support configopts += '--with-libxc=${EBROOTLIBXC} ' -# hdf5/netcdf4. Use nc-config and nf-config to get installation directory -configopts += 'with_netcdf="`nc-config --prefix`" ' -configopts += 'with_netcdf_fortran="`nf-config --prefix`" ' +# hdf5/netcdf4. +configopts += 'with_netcdf="${EBROOTNETCDF}" ' +configopts += 'with_netcdf_fortran="${EBROOTNETCDFMINFORTRAN}" ' configopts += 'with_hdf5="${EBROOTHDF5}" ' runtest = 'check' +tests = [ + "make test_fast", + "make test_v1", + "make test_v5", + "make test_libxc", + "./tests/runtests.py v1 -j2", + "./tests/runtests.py paral mpiio -j1 -n4 -o1", +] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], From d23e2426392e22ca15aaf4680435651fbb85cebd Mon Sep 17 00:00:00 2001 From: rs7wz Date: Fri, 4 Sep 2020 18:13:41 -0400 Subject: [PATCH 0090/9987] required to add MIT license --- .../a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..cc6fecdbffa --- /dev/null +++ b/easybuild/easyconfigs/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb @@ -0,0 +1,68 @@ +# Copyright (c) 2020 The Rector and Visitors of the University of Virginia +# +# Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated +# documentation files (the "Software"), to deal in the Software without restriction, including without +# limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the +# Software, and to permit persons to whom the Software is furnished to do so, subject to the following +# conditions: +# +# The above copyright notice and this permission notice shall be included in all copies or substantial portions +# of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED +# TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL +# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF +# CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. +# +# Ruoshi Sun +# Research Computing, University of Virginia +# 2020-05-24 + +easyblock = 'ConfigureMake' + +name = 'ATAT' +version = '3.36' + +homepage = 'https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/' +description = """ +The Alloy-Theoretic Automated Toolkit (ATAT) is a generic name that refers to a collection of alloy theory tools +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['http://alum.mit.edu/www/avdw/%(namelower)s'] +sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '_')] +checksums = ['e829da5b714a012b5fc456d1060cfdb784642a8c0cbb702d409497b65466ee39'] + +builddependencies = [ + ('binutils', '2.34') +] + +skipsteps = ['configure'] + +local_bindir = '%(builddir)s/%(namelower)s/bin' + +prebuildopts = 'mkdir -p %s && ' % local_bindir +buildopts = 'BINDIR=%s' % local_bindir + +local_install1 = 'make -C src BINDIR=%s install && ' % local_bindir +local_install2 = 'make -C glue/jobctrl BINDIR=%s install && ' % local_bindir +local_install3 = 'make -C glue/vasp BINDIR=%s install' % local_bindir + +install_cmd = local_install1 + local_install2 + local_install3 + +local_to_copy = ['bin', 'data', 'doc', 'examples', 'glue', 'license.txt'] + +postinstallcmds = [ + 'cp -r %%(builddir)s/%%(namelower)s/%s %%(installdir)s' % x for x in local_to_copy +] + +sanity_check_paths = { + 'files': ['bin/maps'], + 'dirs': local_to_copy[:-1] +} + +modloadmsg = "First-time users please run:\necho set atatdir=$EBROOTATAT > $HOME/.atat.rc\n" + +moduleclass = 'chem' From 80a57c3904a997dc87f232179dedeb719b3b2348 Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Mon, 7 Sep 2020 11:24:15 +0200 Subject: [PATCH 0091/9987] adding easyconfigs: Bazel-0.29.1-GCCcore-9.3.0.eb --- .../b/Bazel/Bazel-0.29.1-GCCcore-9.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..8acaf9676d9 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +name = 'Bazel' +version = '0.29.1' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = [ + 'Bazel-%(version)s_fix-gold-flag.patch', + 'Bazel-%(version)s_fix-zip-d-on-power.patch', +] +checksums = [ + '872a52cff208676e1169b3e1cae71b1fe572c4109cbd66eab107d8607c378de5', # bazel-0.29.1-dist.zip + '99928d0902beeaf962a8ad14db8432f8e5114645e3caf64c7ee2fa136c31609f', # Bazel-0.29.1_fix-gold-flag.patch + '0089567af6a991084d5628a8b6fa92b68402ff4b7a0ef8fa944e629e7be63b93', # Bazel-0.29.1_fix-zip-d-on-power.patch +] + +builddependencies = [ + ('binutils', '2.34'), + ('Python', '3.8.2'), + ('Zip', '3.0'), +] +dependencies = [('Java', '1.8', '', True)] + +moduleclass = 'devel' From d2880c412f576ea775ae33d29c5d052bca753247 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Sep 2020 15:54:49 +0200 Subject: [PATCH 0092/9987] adding easyconfigs: pyiron-0.3.0-intel-2020a-Python-3.8.2.eb --- .../pyiron-0.3.0-intel-2020a-Python-3.8.2.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..84124a4b951 --- /dev/null +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,88 @@ +easyblock = 'PythonBundle' + +name = 'pyiron' +version = '0.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pyiron/pyiron' +description = "An integrated development environment (IDE) for computational materials science." + +toolchain = {'name': 'intel', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('matplotlib', '3.2.1', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + ('PyYAML', '5.3'), + ('phonopy', '2.7.1', versionsuffix), + ('spglib-python', '1.16.0', versionsuffix), + ('ASE', '3.20.1', versionsuffix), + ('numexpr', '2.7.1', versionsuffix), + ('PyTables', '3.6.1', versionsuffix), + ('nglview', '2.7.7', versionsuffix), + ('tqdm', '4.47.0'), + ('molmod', '1.4.5', versionsuffix), + ('scikit-learn', '0.23.1', versionsuffix), + ('yaff', '1.6.0', versionsuffix), + ('TAMkin', '1.2.6', versionsuffix), + ('QuickFF', '2.2.4', versionsuffix), +] + +check_ldshared = True +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('h5io', '0.1.2', { + 'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'], + }), + ('defusedxml', '0.6.0', { + 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], + }), + ('pysqa', '0.0.11', { + 'checksums': ['b1a1995ac8b83b86046cef8b72cda962c5fdbf480c6dbba906a467a5dd1d3c81'], + }), + ('SQLAlchemy', '1.3.19', { + 'checksums': ['3bba2e9fbedb0511769780fe1d63007081008c5c2d7d715e91858c94dbaa260e'], + }), + ('dill', '0.3.2', { + 'source_tmpl': 'dill-%(version)s.zip', + 'checksums': ['6e12da0d8e49c220e8d6e97ee8882002e624f1160289ce85ec2cc0a5246b3a2e'], + }), + ('smmap', '3.0.4', { + 'checksums': ['9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24'], + }), + ('gitdb', '4.0.5', { + 'checksums': ['c9e1f2d0db7ddb9a704c2a0217be31214e91a4fe1dea1efad19ae42ba0c285c9'], + }), + ('GitPython', '3.1.8', { + 'checksums': ['080bf8e2cf1a2b907634761c2eaefbe83b69930c94c66ad11b65a8252959f912'], + 'modulename': 'git', + }), + ('colorama', '0.4.3', { + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), + ('pyfiglet', '0.8.post1', { + 'checksums': ['c6c2321755d09267b438ec7b936825a4910fec696292139e664ca8670e103639'], + }), + ('mendeleev', '0.6.0', { + 'checksums': ['944d185e81f158e48dd394b011e6c14acb612c2ffbc3c32c4aa490cd5b4f65dd'], + }), + ('pyfileindex', '0.0.4', { + 'checksums': ['bbfbfc9372f810587917ab1a88bebb8de44d32a1210bbd436c5b88447d97dfd2'], + }), + ('seekpath', '2.0.1', { + 'checksums': ['188513ee187fbbace49066a29ecea9bbd351f23da3bea33d507d0f590856b082'], + }), + (name, version, { + 'checksums': ['6d49899c2dbec4b80299c227b04dceb9211a668c49e9d80a621448b69bb2ac65'], + # import pyiron triggers interactive configuration setup, so we disable it + 'modulename': False, + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From f09fc14de3e6ea15cfa568fd38cb8a82d8939a34 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 9 Sep 2020 11:24:55 -0500 Subject: [PATCH 0093/9987] add OpenSSL 1.1.0 patch --- .../b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb | 6 +- easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb | 6 +- .../b/bbFTP/bbFTP-3.2.1_fix-openssl-1.1.patch | 85 +++++++++++++++++++ 3 files changed, 95 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1_fix-openssl-1.1.patch diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb index 6546cadf635..f9fbe576f84 100644 --- a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb @@ -26,7 +26,11 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = [homepage + 'dist'] sources = ['%s-client-%s.tar.gz' % (name.lower(), version)] -checksums = ['4000009804d90926ad3c0e770099874084fb49013e8b0770b82678462304456d'] +patches = ['%(name)s-%(version)s_fix-openssl-1.1.patch'] +checksums = [ + '4000009804d90926ad3c0e770099874084fb49013e8b0770b82678462304456d', # bbftp-client-3.2.1.tar.gz + 'de8f23637a5d7b6874372c1e989fb3d7aaca6457312272021799354ee50eeb06', # bbFTP-3.2.1_fix-openssl-1.1.patch +] start_dir = 'bbftpc' diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb index d7a35d651e5..b3cd1205071 100644 --- a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb @@ -26,7 +26,11 @@ toolchain = SYSTEM source_urls = [homepage + 'dist'] sources = ['%s-client-%s.tar.gz' % (name.lower(), version)] -checksums = ['4000009804d90926ad3c0e770099874084fb49013e8b0770b82678462304456d'] +patches = ['%(name)s-%(version)s_fix-openssl-1.1.patch'] +checksums = [ + '4000009804d90926ad3c0e770099874084fb49013e8b0770b82678462304456d', # bbftp-client-3.2.1.tar.gz + 'de8f23637a5d7b6874372c1e989fb3d7aaca6457312272021799354ee50eeb06', # bbFTP-3.2.1_fix-openssl-1.1.patch +] start_dir = 'bbftpc' diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1_fix-openssl-1.1.patch b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1_fix-openssl-1.1.patch new file mode 100644 index 00000000000..886eec9acd2 --- /dev/null +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1_fix-openssl-1.1.patch @@ -0,0 +1,85 @@ +OpenSSL 1.1.0 makes all structs opaque and introduces accessors for +members like RSA's key and exponent. + +This patch branches on OpenSSL version and either accesses the members +directly or uses their accessor. + +Author: Lars Viklund +diff -ru bbftp-client-3.2.1.orig/bbftpc/connecttoserver.c bbftp-client-3.2.1/bbftpc/connecttoserver.c +--- bbftp-client-3.2.1.orig/bbftpc/connecttoserver.c 2013-02-07 11:42:46.000000000 +0100 ++++ bbftp-client-3.2.1/bbftpc/connecttoserver.c 2020-09-01 12:47:32.197158831 +0200 +@@ -516,6 +516,8 @@ + + #ifdef WITH_SSL + RSA *hisrsa ; ++ BIGNUM *hisrsa_n; ++ BIGNUM *hisrsa_e; + int lenrsa ; + #endif + /* +@@ -629,13 +631,13 @@ + /* + ** Getting BIGNUM structures to store the key and exponent + */ +- if ( (hisrsa->n = BN_new()) == NULL) { ++ if ( (hisrsa_n = BN_new()) == NULL) { + free(readbuffer) ; + close(tmpctrlsock) ; + printmessage(stderr,CASE_ERROR,56,timestamp,"Error reading encrypted message : %s (%s)\n","getting BIGNUM",(char *) ERR_error_string(ERR_get_error(),NULL)) ; + return -1 ; + } +- if ( (hisrsa->e = BN_new()) == NULL) { ++ if ( (hisrsa_e = BN_new()) == NULL) { + free(readbuffer) ; + close(tmpctrlsock) ; + printmessage(stderr,CASE_ERROR,56,timestamp,"Error reading encrypted message : %s (%s)\n","getting BIGNUM",(char *) ERR_error_string(ERR_get_error(),NULL)) ; +@@ -644,18 +646,24 @@ + /* + ** Copy the key and exponent received + */ +- if ( BN_mpi2bn(pubkey,lenkey,hisrsa->n) == NULL ) { ++ if ( BN_mpi2bn(pubkey,lenkey,hisrsa_n) == NULL ) { + free(readbuffer) ; + close(tmpctrlsock) ; + printmessage(stderr,CASE_ERROR,56,timestamp,"Error reading encrypted message : %s (%s)\n","copying pubkey",(char *) ERR_error_string(ERR_get_error(),NULL)) ; + return -1 ; + } +- if ( BN_mpi2bn(pubexponent,lenexpo,hisrsa->e) == NULL ) { ++ if ( BN_mpi2bn(pubexponent,lenexpo,hisrsa_e) == NULL ) { + free(readbuffer) ; + close(tmpctrlsock) ; + printmessage(stderr,CASE_ERROR,56,timestamp,"Error reading encrypted message : %s (%s)\n","copying pubexponent",(char *) ERR_error_string(ERR_get_error(),NULL)) ; + return -1 ; + } ++ #if OPENSSL_VERSION_NUMBER < 0x10100000L ++ hisrsa->n = hisrsa_n; ++ hisrsa->e = hisrsa_e; ++#else ++ RSA_set0_key(hisrsa, hisrsa_n, hisrsa_e, NULL); ++#endif + lenrsa = RSA_size(hisrsa) ; + + if (strlen(username) > lenrsa - 41 ) { +diff -ru bbftp-client-3.2.1.orig/bbftpc/treatcommand.c bbftp-client-3.2.1/bbftpc/treatcommand.c +--- bbftp-client-3.2.1.orig/bbftpc/treatcommand.c 2013-02-07 11:42:46.000000000 +0100 ++++ bbftp-client-3.2.1/bbftpc/treatcommand.c 2020-09-01 12:50:07.447302930 +0200 +@@ -38,6 +38,7 @@ + #include + #include + #include ++#include + #include + #if HAVE_STRING_H + # include +@@ -49,6 +50,11 @@ + #include + #include + ++int bbftp_dir(char *remotefile, int *errcode); ++int bbftp_rm(char *filename, int *errcode); ++int bbftp_stat(char *filename, int *errcode); ++int bbftp_statfs(char *filename, int *errcode); ++ + extern int timestamp; + extern int globaltrymax; + extern int myexitcode; From e2c20d72053dfd2d2d36c6845d585fa8c6c3806e Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Wed, 9 Sep 2020 18:59:44 +0000 Subject: [PATCH 0094/9987] adding easyconfigs: QuantumESPRESSO-6.6-intel-2020a.eb --- .../QuantumESPRESSO-6.6-intel-2020a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb new file mode 100644 index 00000000000..e121b620371 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb @@ -0,0 +1,43 @@ +name = 'QuantumESPRESSO' +version = '6.6' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes + for electronic-structure calculations and materials modeling at the nanoscale. + It is based on density-functional theory, plane waves, and pseudopotentials + (both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s/', + 'https://github.com/dceresoli/qe-gipaw/archive/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + # to be uncommented once qe-gipaw-6.6 is released + # {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + 'de6996b9f1bf480bcd0166d24e918f5ff3c8fdb710f59f781bc9d33819280eb5', # qe-6.6-ReleasePack.tgz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.10.6'), + ('ELPA', '2020.05.001'), + ('libxc', '4.3.4'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built +buildopts = 'all gwl xspectra couple epw w90' # gipaw + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' From ac246899f0c71351a61a4c76b6c619ef70a11b85 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Sep 2020 13:18:33 +0200 Subject: [PATCH 0095/9987] use https in homepage for p4est --- easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb index 99c7f47225b..20a5323912e 100644 --- a/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb +++ b/easybuild/easyconfigs/p/p4est/p4est-2.2-foss-2019a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'p4est' version = '2.2' -homepage = 'http://www.p4est.org' +homepage = 'https://www.p4est.org' description = """p4est is a C library to manage a collection (a forest) of multiple connected adaptive quadtrees or octrees in parallel.""" From 2548bacdf12cbfe7d62f79699497180513814c28 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Sep 2020 13:20:46 +0200 Subject: [PATCH 0096/9987] fix PETSc dep in deal.II easyconfig --- easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb index e4990e2bda0..06af00f0bdd 100644 --- a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb +++ b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-foss-2019a.eb @@ -22,7 +22,7 @@ dependencies = [ ('METIS', '5.1.0'), ('netCDF', '4.6.2'), ('p4est', '2.2'), - ('PETSc', '3.11.1'), + ('PETSc', '3.11.1', '-Python-3.7.2'), ('zlib', '1.2.11'), ] From fdf32b3730d0639830644de62a373a02d5f7c5b7 Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Thu, 24 Sep 2020 23:22:27 +0200 Subject: [PATCH 0097/9987] adding easyconfigs: OpenFOAM-v2006-intel-2020a.eb --- .../o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb new file mode 100644 index 00000000000..aa7c52b3734 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb @@ -0,0 +1,41 @@ +name = 'OpenFOAM' +version = 'v2006' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + 'OpenFOAM-%(version)s-cleanup.patch', + 'OpenFOAM-v1906-wmake-ompi.patch', +] +checksums = [ + '30c6376d6f403985fc2ab381d364522d1420dd58a42cb270d2ad86f8af227edc', # OpenFOAM-v2006.tgz + 'cb3c6d26569cf11d22941963acb9741238fe829f21b452506a51a71b5c42ae84', # OpenFOAM-v2006-cleanup.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +dependencies = [ + ('libreadline', '8.0'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.9'), + ('CGAL', '4.14.3', '-Python-3.8.2'), + ('ParaView', '5.8.0', '-Python-3.8.2-mpi'), +] + +builddependencies = [ + ('Bison', '3.5.3'), + ('CMake', '3.16.4'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' From bd81b88aea2be3d196caf50cb577a16f202bc955 Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Fri, 25 Sep 2020 15:08:31 +0200 Subject: [PATCH 0098/9987] adding easyconfigs: libctl-4.0.0-intel-2020a.eb --- .../l/libctl/libctl-4.0.0-intel-2020a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb diff --git a/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb b/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb new file mode 100644 index 00000000000..bc10d5e8882 --- /dev/null +++ b/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'libctl' +version = '4.0.0' + +homepage = 'https://github.com/stevengj/libctl' +description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/stevengj/libctl/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b0f46ed29acd13be542a4988d7f0604b10869d6b4c41916c539dc99711fb5458'] + +dependencies = [('Guile', '2.2.4')] + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +moduleclass = 'chem' From aff07e4ca111a7f8ff26426aad9d3f85c22f31ea Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Fri, 25 Sep 2020 15:21:54 +0200 Subject: [PATCH 0099/9987] Added checks --- easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb b/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb index bc10d5e8882..847a07cf640 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb @@ -18,4 +18,9 @@ dependencies = [('Guile', '2.2.4')] # fix for guile-config being broken because shebang line contains full path to bin/guile configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib'] +} + moduleclass = 'chem' From 203529e64dc7c3384d363fa1d2724bdfe35067ab Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Fri, 25 Sep 2020 15:25:12 +0200 Subject: [PATCH 0100/9987] adding easyconfigs: Meep-1.4.3-intel-2020a.eb --- .../m/Meep/Meep-1.4.3-intel-2020a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb new file mode 100644 index 00000000000..6ba80a1738f --- /dev/null +++ b/easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Meep' +version = '1.4.3' + +homepage = 'https://github.com/stevengj/meep' +description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package + developed at MIT to model electromagnetic systems.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = ['https://github.com/stevengj/meep/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Meep-1.3_version-string-without-spaces.patch'] +checksums = [ + '1105b369c3f7f4aae0de62e933e49f4e3c94b8031a7eb39e2ee315d4cea46b02', # meep-1.4.3.tar.gz + '9d1ade5d656ab20feb18661a06a73aa9a36e1e583b98a630b7810ca7ffc91af6', # Meep-1.3_version-string-without-spaces.patch +] + +dependencies = [ + ('Harminv', '1.4.1'), + ('HDF5', '1.10.6'), + ('libctl', '4.0.0'), + ('GSL', '2.6'), + ('FFTW', '3.3.8'), + ('Guile', '2.2.4'), +] + +configopts = "--with-pic --with-mpi --with-blas=mkl_em64t --with-lapack=mkl_em64t --without-gcc-arch " +configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib'] +} + +moduleclass = 'phys' From 4d0be53c6f95b5adc2d0b18862ac183421215396 Mon Sep 17 00:00:00 2001 From: gmatteo Date: Wed, 30 Sep 2020 23:48:16 +0200 Subject: [PATCH 0101/9987] Comment tests section --- .../a/ABINIT/ABINIT-9.1.0-foss-2019b.eb | 22 +++++++++---------- .../a/ABINIT/ABINIT-9.1.0-intel-2019b.eb | 20 ++++++++--------- 2 files changed, 19 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb index 31b29b5b7a1..a584ddfa8ea 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb @@ -19,12 +19,10 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ('libxc', '4.3.4'), - #('HDF5', '1.10.5'), - #('netCDF', '4.7.1'), ('netCDF-Fortran', '4.5.2'), ] -# Ensure MPI. +# Ensure MPI. configopts = '--with-mpi="yes" --enable-openmp="no" ' # BLAS/Lapack @@ -36,7 +34,7 @@ configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lff # libxc support configopts += '--with-libxc=${EBROOTLIBXC} ' -# hdf5/netcdf4. +# hdf5/netcdf4. configopts += 'with_netcdf="${EBROOTNETCDF}" ' configopts += 'with_netcdf_fortran="${EBROOTNETCDFMINFORTRAN}" ' configopts += 'with_hdf5="${EBROOTHDF5}" ' @@ -46,14 +44,14 @@ configopts += 'FCFLAGS="${FCFLAGS} --free-line-length-none" ' runtest = 'check' -tests = [ - "make test_fast", - "make test_v1", - "make test_v5", - "make test_libxc", - "./tests/runtests.py v1 -j2", - "./tests/runtests.py paral mpiio -j1 -n4 -o1", -] +#tests = [ +# "make test_fast", +# "make test_v1", +# "make test_v5", +# "make test_libxc", +# "./tests/runtests.py v1 -j2", +# "./tests/runtests.py paral mpiio -j1 -n4 -o1", +#] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb index 867afd90085..136951794b0 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb @@ -20,12 +20,10 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [ ("imkl", "2019.5.281"), ('libxc', '4.3.4'), - #('HDF5', '1.10.5'), - #('netCDF', '4.7.1'), ('netCDF-Fortran', '4.5.2'), ] -# Ensure MPI. +# Ensure MPI. configopts = '--with-mpi="yes" --enable-openmp="no" ' # BLAS/Lapack from MKL @@ -44,14 +42,14 @@ configopts += 'with_hdf5="${EBROOTHDF5}" ' runtest = 'check' -tests = [ - "make test_fast", - "make test_v1", - "make test_v5", - "make test_libxc", - "./tests/runtests.py v1 -j2", - "./tests/runtests.py paral mpiio -j1 -n4 -o1", -] +#tests = [ +# "make test_fast", +# "make test_v1", +# "make test_v5", +# "make test_libxc", +# "./tests/runtests.py v1 -j2", +# "./tests/runtests.py paral mpiio -j1 -n4 -o1", +#] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], From a6b45173b97d1c221486a7225ec1850fa2b40914 Mon Sep 17 00:00:00 2001 From: gmatteo Date: Thu, 1 Oct 2020 01:01:57 +0200 Subject: [PATCH 0102/9987] Use stable 9.2.1 version --- ....0-foss-2019b.eb => ABINIT-9.2.1-foss-2019b.eb} | 13 +++++++++---- ...-intel-2019b.eb => ABINIT-9.2.1-intel-2019b.eb} | 14 ++++++++++---- 2 files changed, 19 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/a/ABINIT/{ABINIT-9.1.0-foss-2019b.eb => ABINIT-9.2.1-foss-2019b.eb} (78%) rename easybuild/easyconfigs/a/ABINIT/{ABINIT-9.1.0-intel-2019b.eb => ABINIT-9.2.1-intel-2019b.eb} (73%) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb similarity index 78% rename from easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb rename to easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb index a584ddfa8ea..d0cc8cc0a7a 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-foss-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb @@ -2,18 +2,23 @@ easyblock = 'ConfigureMake' name = 'ABINIT' -version = '9.0.4' +version = '9.2.1' homepage = 'https://www.abinit.org/' description = """ABINIT is a package whose main program allows one to find the total energy, - charge density and electronic structure of systems made of electrons and nuclei (molecules - and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'usempi': True, 'pic': True} -source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +# Fetch tarball from github repo. +#https://github.com/abinit/abinit/archive/9.2.1.tar.gz +source_urls = ['https://github.com/abinit/abinit/archive/'] +# +#source_urls = ['https://www.abinit.org/sites/default/files/packages/'] + sources = [SOURCELOWER_TAR_GZ] #checksums = ['82e8d071088ab8dc1b3a24380e30b68c544685678314df1213180b449c84ca65'] diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb similarity index 73% rename from easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb rename to easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb index 136951794b0..effcb868f18 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.1.0-intel-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb @@ -6,14 +6,19 @@ version = '9.0.4' homepage = 'https://www.abinit.org/' description = """ABINIT is a package whose main program allows one to find the total energy, - charge density and electronic structure of systems made of electrons and nuclei (molecules - and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" toolchain = {'name': 'iimpi', 'version': '2019b'} toolchainopts = {'usempi': True, 'pic': True} -source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +# Fetch tarball from github repo. +#https://github.com/abinit/abinit/archive/9.2.1.tar.gz +source_urls = ['https://github.com/abinit/abinit/archive/'] +# +#source_urls = ['https://www.abinit.org/sites/default/files/packages/'] + sources = [SOURCELOWER_TAR_GZ] #checksums = ['82e8d071088ab8dc1b3a24380e30b68c544685678314df1213180b449c84ca65'] @@ -23,8 +28,9 @@ dependencies = [ ('netCDF-Fortran', '4.5.2'), ] -# Ensure MPI. +# Ensure MPI with intel wrappers. configopts = '--with-mpi="yes" --enable-openmp="no" ' +configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' # BLAS/Lapack from MKL configopts += '--with-linalg-flavor=mkl ' From c0a2c9c9133b3b8f3157a204ffc76379542563c8 Mon Sep 17 00:00:00 2001 From: gmatteo Date: Thu, 1 Oct 2020 03:12:19 +0200 Subject: [PATCH 0103/9987] update checksums and versions --- .../a/ABINIT/ABINIT-9.2.1-foss-2019b.eb | 24 ++++++------------- .../a/ABINIT/ABINIT-9.2.1-intel-2019b.eb | 24 ++++++------------- 2 files changed, 14 insertions(+), 34 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb index d0cc8cc0a7a..42b1bf52dbf 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb @@ -13,14 +13,9 @@ description = """ABINIT is a package whose main program allows one to find the t toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'usempi': True, 'pic': True} -# Fetch tarball from github repo. -#https://github.com/abinit/abinit/archive/9.2.1.tar.gz -source_urls = ['https://github.com/abinit/abinit/archive/'] -# -#source_urls = ['https://www.abinit.org/sites/default/files/packages/'] - +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] sources = [SOURCELOWER_TAR_GZ] -#checksums = ['82e8d071088ab8dc1b3a24380e30b68c544685678314df1213180b449c84ca65'] +checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0'] dependencies = [ ('libxc', '4.3.4'), @@ -47,16 +42,11 @@ configopts += 'with_hdf5="${EBROOTHDF5}" ' # make sure --free-line-length-none is added to FCFLAGS configopts += 'FCFLAGS="${FCFLAGS} --free-line-length-none" ' -runtest = 'check' - -#tests = [ -# "make test_fast", -# "make test_v1", -# "make test_v5", -# "make test_libxc", -# "./tests/runtests.py v1 -j2", -# "./tests/runtests.py paral mpiio -j1 -n4 -o1", -#] +# `make check` is just executing some basic unit tests. +# In principle, one should run `make tests_v1`` to have some basic validation +# but it seems it's not possible to execute abinit at the end of the build +# due to missing dynamic libs (e.g. libxc) +runtest = "check" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb index effcb868f18..6bd75c66b9e 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'ABINIT' -version = '9.0.4' +version = '9.2.1' homepage = 'https://www.abinit.org/' description = """ABINIT is a package whose main program allows one to find the total energy, @@ -13,14 +13,9 @@ description = """ABINIT is a package whose main program allows one to find the t toolchain = {'name': 'iimpi', 'version': '2019b'} toolchainopts = {'usempi': True, 'pic': True} -# Fetch tarball from github repo. -#https://github.com/abinit/abinit/archive/9.2.1.tar.gz -source_urls = ['https://github.com/abinit/abinit/archive/'] -# -#source_urls = ['https://www.abinit.org/sites/default/files/packages/'] - +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] sources = [SOURCELOWER_TAR_GZ] -#checksums = ['82e8d071088ab8dc1b3a24380e30b68c544685678314df1213180b449c84ca65'] +checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0'] dependencies = [ ("imkl", "2019.5.281"), @@ -46,17 +41,12 @@ configopts += 'with_netcdf="${EBROOTNETCDF}" ' configopts += 'with_netcdf_fortran="${EBROOTNETCDFMINFORTRAN}" ' configopts += 'with_hdf5="${EBROOTHDF5}" ' +# `make check` is just executing some basic unit tests. +# In principle, one should run `make tests_v1`` to have some basic validation +# but it seems it's not possible to execute abinit at the end of the build +# due to missing dynamic libs (e.g. libxc) runtest = 'check' -#tests = [ -# "make test_fast", -# "make test_v1", -# "make test_v5", -# "make test_libxc", -# "./tests/runtests.py v1 -j2", -# "./tests/runtests.py paral mpiio -j1 -n4 -o1", -#] - sanity_check_paths = { 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], 'dirs': ['lib/pkgconfig'], From fd0d6459fc4dddb17aa37a092cd3f9a5da64d674 Mon Sep 17 00:00:00 2001 From: gmatteo Date: Thu, 1 Oct 2020 04:42:57 +0200 Subject: [PATCH 0104/9987] Rename file as ABINIT-9.2.1-iimpi-2019b.eb --- .../{ABINIT-9.2.1-intel-2019b.eb => ABINIT-9.2.1-iimpi-2019b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/ABINIT/{ABINIT-9.2.1-intel-2019b.eb => ABINIT-9.2.1-iimpi-2019b.eb} (100%) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb similarity index 100% rename from easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb rename to easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb From 7c99b6a42b5255472f1ea5d21cf19aec77f15502 Mon Sep 17 00:00:00 2001 From: gmatteo Date: Thu, 1 Oct 2020 05:25:35 +0200 Subject: [PATCH 0105/9987] Make styletests.py happy --- easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb | 4 ++-- easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb index 42b1bf52dbf..8b083ceb2b2 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb @@ -44,9 +44,9 @@ configopts += 'FCFLAGS="${FCFLAGS} --free-line-length-none" ' # `make check` is just executing some basic unit tests. # In principle, one should run `make tests_v1`` to have some basic validation -# but it seems it's not possible to execute abinit at the end of the build +# but it seems it's not possible to execute abinit at the end of the build # due to missing dynamic libs (e.g. libxc) -runtest = "check" +runtest = "check" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb index 6bd75c66b9e..edcf0b65eee 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb @@ -43,7 +43,7 @@ configopts += 'with_hdf5="${EBROOTHDF5}" ' # `make check` is just executing some basic unit tests. # In principle, one should run `make tests_v1`` to have some basic validation -# but it seems it's not possible to execute abinit at the end of the build +# but it seems it's not possible to execute abinit at the end of the build # due to missing dynamic libs (e.g. libxc) runtest = 'check' From 391693f4a6d8698c0251bc2a7775529b08ce59fa Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 26 Oct 2020 16:49:13 +0100 Subject: [PATCH 0106/9987] fix LAMMPS-3Mar2020-intel installations on AMD CPUs --- ...MPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb | 2 ++ ...MPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb | 6 +++++- .../lammps-stable_3Mar2020_intel_ebflag.patch | 14 ++++++++++++++ 3 files changed, 21 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index a0a8ee53589..572b35ddbfe 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -25,9 +25,11 @@ sources = [ 'stable_%(version)s.tar.gz', {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] +patches = ['lammps-stable_3Mar2020_intel_ebflag.patch'] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py + '491a2da88f37960e0d9013bd28108bf3c6952733ab2664ea7395acfb2e7ccdf9', # lammps-stable_3Mar2020_intel_ebflag.patch ] local_source_dir_name = '%(namelower)s-%(version)s' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb index 9c903f6b9de..3752cd44de5 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb @@ -25,11 +25,15 @@ sources = [ 'stable_%(version)s.tar.gz', {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] -patches = ['LAMMPS-3Mar2020_fix-docs-build.patch'] +patches = [ + 'LAMMPS-3Mar2020_fix-docs-build.patch', + 'lammps-stable_3Mar2020_intel_ebflag.patch', +] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch + '491a2da88f37960e0d9013bd28108bf3c6952733ab2664ea7395acfb2e7ccdf9', # lammps-stable_3Mar2020_intel_ebflag.patch ] local_source_dir_name = '%(namelower)s-%(version)s' diff --git a/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch b/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch new file mode 100644 index 00000000000..1156b6a7c3b --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch @@ -0,0 +1,14 @@ +# remove hard coded -xHost flag for intel compilers (useful on AMD systems, as -xHost may lead to mmx/sse code) +# OCT 26th 2020 by B. Hajgato (UGent) +diff -ru lammps-stable_3Mar2020.orig/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi lammps-stable_3Mar2020/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi +--- lammps-stable_3Mar2020.orig/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi 2020-10-26 16:41:59.900088648 +0100 +@@ -7,7 +7,7 @@ + # specify flags and libraries needed for your compiler + + CC = mpiicpc -std=c++11 +-OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \ ++OPTFLAGS = ${EBVAROPTFLAGS} -fp-model fast=2 -no-prec-div -qoverride-limits \ + -qopt-zmm-usage=high + CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \ + -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \ From 5dfd1a192d81bff102c83e5067f977d60797bc2c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 27 Oct 2020 09:02:22 +0100 Subject: [PATCH 0107/9987] fix cmake -xHost --- ...AMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb | 2 +- ...AMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb | 4 +++- .../LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch | 12 ++++++++++++ 3 files changed, 16 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index 572b35ddbfe..fd0612cf229 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -29,7 +29,7 @@ patches = ['lammps-stable_3Mar2020_intel_ebflag.patch'] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py - '491a2da88f37960e0d9013bd28108bf3c6952733ab2664ea7395acfb2e7ccdf9', # lammps-stable_3Mar2020_intel_ebflag.patch + '3b04681bf8d5c60818a197905f68c83e477ef41824278ebc05d437ecac6d5c0a', # lammps-stable_3Mar2020_intel_ebflag.patch ] local_source_dir_name = '%(namelower)s-%(version)s' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb index 3752cd44de5..e9360befb8c 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb @@ -33,7 +33,7 @@ checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch - '491a2da88f37960e0d9013bd28108bf3c6952733ab2664ea7395acfb2e7ccdf9', # lammps-stable_3Mar2020_intel_ebflag.patch + '3b04681bf8d5c60818a197905f68c83e477ef41824278ebc05d437ecac6d5c0a', # lammps-stable_3Mar2020_intel_ebflag.patch ] local_source_dir_name = '%(namelower)s-%(version)s' @@ -106,6 +106,8 @@ user_packages = [ 'SCAFACOS', 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF' ] +maxparallel = 1 + enhance_sanity_check = True # run short test case to make sure installation doesn't produce blatently incorrect results; diff --git a/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch b/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch index 1156b6a7c3b..51cc9e246a6 100644 --- a/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch +++ b/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch @@ -1,5 +1,17 @@ # remove hard coded -xHost flag for intel compilers (useful on AMD systems, as -xHost may lead to mmx/sse code) # OCT 26th 2020 by B. Hajgato (UGent) +diff -ru lammps-stable_3Mar2020.orig/cmake/Modules/Packages/USER-INTEL.cmake lammps-stable_3Mar2020/cmake/Modules/Packages/USER-INTEL.cmake +--- lammps-stable_3Mar2020.orig/cmake/Modules/Packages/USER-INTEL.cmake 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/cmake/Modules/Packages/USER-INTEL.cmake 2020-10-27 08:54:15.816960998 +0100 +@@ -77,7 +77,7 @@ + if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512") + else() +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost") ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ") + endif() + include(CheckCXXCompilerFlag) + foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict) diff -ru lammps-stable_3Mar2020.orig/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi lammps-stable_3Mar2020/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi --- lammps-stable_3Mar2020.orig/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi 2020-03-03 16:27:12.000000000 +0100 +++ lammps-stable_3Mar2020/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi 2020-10-26 16:41:59.900088648 +0100 From 38ffb9a148172a60bf911ed7fae63bfb0f6bf8ce Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 27 Oct 2020 09:12:12 +0100 Subject: [PATCH 0108/9987] remove maxparallel --- .../l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb index e9360befb8c..03571e9e23b 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb @@ -106,8 +106,6 @@ user_packages = [ 'SCAFACOS', 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF' ] -maxparallel = 1 - enhance_sanity_check = True # run short test case to make sure installation doesn't produce blatently incorrect results; From 7f08cd28925b41e0f1bb304a0bec8474f6571b93 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Nov 2020 16:28:16 +0100 Subject: [PATCH 0109/9987] adding easyconfigs: meshalyzer-20200308-foss-2020a-Python-3.8.2.eb --- ...alyzer-20200308-foss-2020a-Python-3.8.2.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..14a294f9343 --- /dev/null +++ b/easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'meshalyzer' +local_commit = 'b1ab66863a293768cd23b444f16efe00d0acef4e' +version = '20200308' # datestamp of commit +versionsuffix = '-Python-3.8.2' + +homepage = 'https://git.opencarp.org/openCARP/meshalyzer' +description = "Graphical program for display time dependent data on 3D finite elment meshes" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://git.opencarp.org/openCARP/meshalyzer/-/archive/%s' % local_commit] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = ['meshalyzer-2.0_fix-VTK-linking.patch'] +checksums = [ + 'b1df0be12d377a4e12e0d1f2cd17820b9d5cc3a5a813a17d187ee72adf5a8500', # meshalyzer-20200308.tar.gz + '23f55c2290ea9b62440bdf8e0c1006116438beb7c4b7065b8cf136387a537e0f', # meshalyzer-2.0_fix-VTK-linking.patch +] + +local_vtk_majmin_ver = '8.2' +dependencies = [ + ('libpng', '1.6.37'), + ('FLTK', '1.3.5'), + ('glew', '2.1.0'), + ('freeglut', '3.2.1'), + ('HDF5', '1.10.6'), + ('VTK', '%s.0' % local_vtk_majmin_ver, versionsuffix), +] + +buildopts = 'HDF5_ROOT=$EBROOTHDF5 LIB_EXT=".so" ' +buildopts += 'VTK_INCDIR=$EBROOTVTK/include/vtk-%s/ VTK_LIBDIR=$EBROOTVTK/lib' % local_vtk_majmin_ver + +files_to_copy = [(['meshalyzer'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/meshalyzer'], + 'dirs': [], +} + +sanity_check_commands = ["meshalyzer --help"] + +moduleclass = 'vis' From 1e236970528bc116ecb9c224b55ccb951854296a Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 12 Nov 2020 19:58:49 +0200 Subject: [PATCH 0110/9987] adding easyconfigs: Schrodinger-2020-4.eb --- .../s/Schrodinger/Schrodinger-2020-4.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Schrodinger/Schrodinger-2020-4.eb diff --git a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2020-4.eb b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2020-4.eb new file mode 100644 index 00000000000..d917544ea19 --- /dev/null +++ b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2020-4.eb @@ -0,0 +1,31 @@ +easyblock='PackedBinary' + +name = 'Schrodinger' +version = '2020-4' + +homepage = 'https://www.schrodinger.com/' +description = """ Schrodinger aims to provide integrated software solutions and services + that truly meet its customers needs. We want to empower researchers around the world to + achieve their goals of improving human health and quality of life through advanced computational + techniques that transform the way chemists design compounds and materials. """ + +toolchain = SYSTEM + +# Download from schrodinger.com +sources = ['%(name)s_Suites_%(version)s_Linux-x86_64.tar'] +checksums = ['15c44c5e16a6c2ac75883ddb66f41a8e90465dbb8ecaa5709f4e7071712f74e8'] + +install_cmd = 'cd %(builddir)s/%(name)s_Suites_%(version)s_Linux-x86_64 && ' +install_cmd += './INSTALL -d . -s %(installdir)s -k /usr/tmp -t %(installdir)s/thirdparty -b *' + +sanity_check_paths = { + 'files': ['desmond','maestro'], + 'dirs': [], +} + +modextravars = { + 'SCHROD_LICENSE_FILE': '$HOME/.schrodinger_license', + 'SCHRODINGER': '%(installdir)s', +} + +moduleclass = 'bio' From f6c1ce3fea33b9ea3f3e7003be05c2569d4635bf Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 12 Nov 2020 20:49:40 +0200 Subject: [PATCH 0111/9987] fix style --- easybuild/easyconfigs/s/Schrodinger/Schrodinger-2020-4.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2020-4.eb b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2020-4.eb index d917544ea19..7053eefa580 100644 --- a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2020-4.eb +++ b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2020-4.eb @@ -1,4 +1,4 @@ -easyblock='PackedBinary' +easyblock = 'PackedBinary' name = 'Schrodinger' version = '2020-4' @@ -19,7 +19,7 @@ install_cmd = 'cd %(builddir)s/%(name)s_Suites_%(version)s_Linux-x86_64 && ' install_cmd += './INSTALL -d . -s %(installdir)s -k /usr/tmp -t %(installdir)s/thirdparty -b *' sanity_check_paths = { - 'files': ['desmond','maestro'], + 'files': ['desmond', 'maestro'], 'dirs': [], } From 5eaffd31113a8b10255606d55b2d0fc3ec98ccea Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 23 Nov 2020 11:55:30 +0100 Subject: [PATCH 0112/9987] {chem}[foss/2020a] CP2K {5,7}.1 --- .../easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb | 45 +++++++++++++++++++ .../easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb | 35 +++++++++++++++ .../l/Libint/Libint-1.1.6-foss-2020a.eb | 32 +++++++++++++ .../l/libxc/libxc-3.0.1-foss-2020a.eb | 33 ++++++++++++++ 4 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020a.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020a.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb new file mode 100644 index 00000000000..7b10457c3c3 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb @@ -0,0 +1,45 @@ +name = 'CP2K' +version = '5.1' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] +checksums = [ + 'e23613b593354fa82e0b8410e17d94c607a0b8c6d9b5d843528403ab09904412', # cp2k-5.1.tar.bz2 + '02475cbe24c8d4ba27037c826adf8a534cad634c3c4e02c21d743f5284516bda', # CP2K-2.4.0-fix_compile_date_lastsvn.patch +] + +dependencies = [ + ('Libint', '1.1.6'), + ('libxc', '3.0.1'), + ('libxsmm', '1.16.1'), + ('FFTW', '3.3.8'), + ('PLUMED', '2.6.0', '-Python-3.8.2'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.5.3'), +] + +# values to use here are +1 those used for building Libint +# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT +extradflags = "-D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5" + +# regression test reports failures +ignore_regtest_fails = True + +modextrapaths = {'OMP_NUM_THREADS': '1'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb new file mode 100644 index 00000000000..80e88ecded1 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb @@ -0,0 +1,35 @@ +name = 'CP2K' +version = '7.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ccd711a09a426145440e666310dd01cc5772ab103493c4ae6a3470898cd0addb'] + +dependencies = [ + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '4.3.4'), + ('libxsmm', '1.16.1'), + ('PLUMED', '2.6.0', '-Python-3.8.2'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.5.3'), +] + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +modextrapaths = {'OMP_NUM_THREADS': '1'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020a.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020a.eb new file mode 100644 index 00000000000..97a00710a0c --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020a.eb @@ -0,0 +1,32 @@ +name = 'Libint' +version = '1.1.6' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/evaleev/libint/archive/'] +sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] +checksums = ['f201b0c621df678cfe8bdf3990796b8976ff194aba357ae398f2f29b0e2985a6'] + +builddependencies = [('Autotools', '20180311')] + +preconfigopts = "aclocal -I lib/autoconf && libtoolize && autoconf && " + +# these are important for CP2K +# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT +configopts = "--with-libint-max-am=5 --with-libderiv-max-am1=4 " + +configopts += " --enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020a.eb new file mode 100644 index 00000000000..3e2c8e7575a --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '3.0.1' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] +checksums = [ + '836692f2ab60ec3aca0cca105ed5d0baa7d182be07cc9d0daa7b80ee1362caf7', # libxc-3.0.1.tar.gz + '27338d9f63ce33386a6241e7bd8edde66ac8684d103acf0e6cbb5bde011730b9', # libxc-3.0_no-longdouble.patch +] + +configopts = '--enable-static --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' From 078fb5fa0d36c7eae11c5c11c918f89b88532b49 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 23 Nov 2020 12:19:56 +0100 Subject: [PATCH 0113/9987] http -> https --- easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb index 7b10457c3c3..d82c1306962 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb @@ -1,7 +1,7 @@ name = 'CP2K' version = '5.1' -homepage = 'http://www.cp2k.org/' +homepage = 'https://www.cp2k.org/' description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and From 82423df3f94866716b54575553c3be3eb62ffe48 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 24 Nov 2020 07:43:02 +0100 Subject: [PATCH 0114/9987] modextrapaths -> modextravars --- easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb | 2 +- easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb index d82c1306962..56b25d79ac2 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb @@ -40,6 +40,6 @@ extradflags = "-D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5" # regression test reports failures ignore_regtest_fails = True -modextrapaths = {'OMP_NUM_THREADS': '1'} +modextravars = {'OMP_NUM_THREADS': '1'} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb index 80e88ecded1..99521683c61 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb @@ -30,6 +30,6 @@ builddependencies = [ # we're assuming those are OK to ignore... ignore_regtest_fails = True -modextrapaths = {'OMP_NUM_THREADS': '1'} +modextravars = {'OMP_NUM_THREADS': '1'} moduleclass = 'chem' From 25114bd3453a65affac4efe21775cca22860c862 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 11 Dec 2020 12:36:23 +1050 Subject: [PATCH 0115/9987] adding easyconfigs: ANGEL-3.0-foss-2019a-Python-3.7.2.eb --- .../ANGEL-3.0-foss-2019a-Python-3.7.2.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..23a199adbb3 --- /dev/null +++ b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'ANGEL' +version = '3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/PacificBiosciences/ANGEL' +description = """ANGEL: Robust Open Reading Frame prediction""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PacificBiosciences/ANGEL/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a0319553055d3dfc84a4f732ed246c180c23ee9c397810c96acd7940721ae57d'] + +dependencies = [ + ('Python', '3.7.2'), + ('Biopython', '1.73'), + ('scikit-learn', '0.20.3'), +] + +bin_files = [ + 'dumb_predict.py', + 'angel_make_training_set.py', + 'angel_train.py', + 'angel_predict.py', + 'angel_compare_files.py', +] + +skipsteps = ['sanitycheck'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in bin_files], + 'dirs': [''], +} + +moduleclass = 'bio' From e66edaf1e0c4480a96f22014d9d339c83a99bcaa Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 11 Dec 2020 14:40:31 +1050 Subject: [PATCH 0116/9987] local var sync --- .../easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb index 23a199adbb3..8cdb56bc1c7 100644 --- a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb @@ -30,7 +30,7 @@ dependencies = [ ('scikit-learn', '0.20.3'), ] -bin_files = [ +local_bin_files = [ 'dumb_predict.py', 'angel_make_training_set.py', 'angel_train.py', @@ -41,7 +41,7 @@ bin_files = [ skipsteps = ['sanitycheck'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in bin_files], + 'files': ['bin/%s' % x for x in local_bin_files], 'dirs': [''], } From 10d3980b1438c5edc3825ed14b18e7162bfed917 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 17 Dec 2020 10:24:19 +1050 Subject: [PATCH 0117/9987] sanity_check + --- .../easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb index 8cdb56bc1c7..37a86c26221 100644 --- a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb @@ -35,10 +35,10 @@ local_bin_files = [ 'angel_make_training_set.py', 'angel_train.py', 'angel_predict.py', - 'angel_compare_files.py', + 'angel_compare_files.py' ] -skipsteps = ['sanitycheck'] +options = {'modulename': False} sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bin_files], From 7d3b6fddf0b98de7189ac66761b880fe8a894eb6 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 17 Dec 2020 10:46:37 +1050 Subject: [PATCH 0118/9987] prereqs + --- .../easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb index 37a86c26221..7bb4ef20c12 100644 --- a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb @@ -30,6 +30,10 @@ dependencies = [ ('scikit-learn', '0.20.3'), ] +download_dep_fail = True + +use_pip = False + local_bin_files = [ 'dumb_predict.py', 'angel_make_training_set.py', From f502d39d3b3b45ef457f77c63d8a24bda7975314 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 22 Dec 2020 10:38:31 +0100 Subject: [PATCH 0119/9987] remove OMP_NUM_THREADS=1 --- easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb | 6 +++++- easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb index 56b25d79ac2..b169375381f 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020a.eb @@ -40,6 +40,10 @@ extradflags = "-D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5" # regression test reports failures ignore_regtest_fails = True -modextravars = {'OMP_NUM_THREADS': '1'} +# You might want to set OMP_NUM_THREADS, otherwise OpenBLAS will start (by default) +# the number of accessible CPUcores OpenMP threads. Since it is a MPI only version (popt), +# the performance will be copletely bad, as on N CPU cores N^2 threads will run. +# intel toolchain versions do not have this problem. YOU HAVE BEEN WARNED! +# modextravars = {'OMP_NUM_THREADS': '1'} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb index 99521683c61..dc411a994fa 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-7.1-foss-2020a.eb @@ -30,6 +30,10 @@ builddependencies = [ # we're assuming those are OK to ignore... ignore_regtest_fails = True -modextravars = {'OMP_NUM_THREADS': '1'} +# You might want to set OMP_NUM_THREADS, otherwise OpenBLAS will start (by default) +# the number of accessible CPUcores OpenMP threads. Since it is a MPI only version (popt), +# the performance will be copletely bad, as on N CPU cores N^2 threads will run. +# intel toolchain versions do not have this problem. YOU HAVE BEEN WARNED! +# modextravars = {'OMP_NUM_THREADS': '1'} moduleclass = 'chem' From 1d82dc821cb3855b9073fcd1ad48a8e66f597046 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Dec 2020 14:35:27 +0100 Subject: [PATCH 0120/9987] add -Java-1.8 versionsuffix for Bazel 0.29.1 with GCCcore/9.3.0 --- ...1-GCCcore-9.3.0.eb => Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/b/Bazel/{Bazel-0.29.1-GCCcore-9.3.0.eb => Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb} (96%) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb similarity index 96% rename from easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0.eb rename to easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb index 8acaf9676d9..0387b85aec6 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb @@ -1,5 +1,6 @@ name = 'Bazel' version = '0.29.1' +versionsuffix = '-Java-%(javaver)s' homepage = 'https://bazel.io/' description = """Bazel is a build tool that builds code quickly and reliably. From 7b36bca7fbe01e5afff3d96be79e8ca6c97c44d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Jan 2021 14:23:00 +0100 Subject: [PATCH 0121/9987] enable use_pip and sanity_pip_check in ANGEL easyconfig --- .../a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb index 7bb4ef20c12..2c7340a7bec 100644 --- a/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/a/ANGEL/ANGEL-3.0-foss-2019a-Python-3.7.2.eb @@ -31,8 +31,7 @@ dependencies = [ ] download_dep_fail = True - -use_pip = False +use_pip = True local_bin_files = [ 'dumb_predict.py', @@ -46,7 +45,9 @@ options = {'modulename': False} sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bin_files], - 'dirs': [''], + 'dirs': [], } +sanity_pip_check = True + moduleclass = 'bio' From 07fc2729f741d6ee56cb6f52b644689072f0a3a2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 11 Jan 2021 17:38:26 +0200 Subject: [PATCH 0122/9987] adding easyconfigs: Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb and patches: Gurobi-9.0.1_use-eb-python-gurobi-shell.patch --- ...Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb | 37 +++++++++++++++++++ ...obi-9.0.1_use-eb-python-gurobi-shell.patch | 18 +++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1_use-eb-python-gurobi-shell.patch diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..40cefa76807 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,37 @@ +name = 'Gurobi' +version = '9.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +patches = ['%(name)s-%(version)s_use-eb-python-gurobi-shell.patch'] +checksums = [ + '17e2facda111180eee61eeded0b8716230bbe09faa7c61356dc79f002ff86cb7', # gurobi9.0.1_linux64.tar.gz + 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01', # Gurobi-9.0.1_use-eb-python-gurobi-shell.patch +] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('Python', '3.8.2'), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python3.7'] + +license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' + +modloadmsg = 'Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh`\n' +modloadmsg += 'Gurobi Python Interface can be loaded in Python %(pyver)s with "import gurobipy"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1_use-eb-python-gurobi-shell.patch b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1_use-eb-python-gurobi-shell.patch new file mode 100644 index 00000000000..29910369535 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1_use-eb-python-gurobi-shell.patch @@ -0,0 +1,18 @@ +Use the Python environement from EB in the Guroby Python shell +autho: Alex Domingo (Vrije Universiteit Brussel) +--- a/bin/gurobi.sh 2020-01-29 00:56:47.000000000 +0100 ++++ b/bin/gurobi.sh 2021-01-11 16:07:28.180329000 +0100 +@@ -7,11 +7,6 @@ + echo + fi + +-PATH=$GUROBI_HOME/bin:$PATH;export PATH +-LD_LIBRARY_PATH=$GUROBI_HOME/lib:$LD_LIBRARY_PATH;export LD_LIBRARY_PATH +-PYTHONHOME=$GUROBI_HOME;export PYTHONHOME +-PYTHONPATH=$GUROBI_HOME:$PYTHONPATH;export PYTHONPATH ++PYTHONSTARTUP=$EBROOTGUROBI/lib/gurobi.py;export PYTHONSTARTUP + +-PYTHONSTARTUP=$PYTHONHOME/lib/gurobi.py;export PYTHONSTARTUP +- +-$PYTHONHOME/bin/python3.7 "$@" ++$EBROOTPYTHON/bin/python "$@" From a580c4fe10a6c786f4ac857fcf0a51fd637328ea Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 11 Jan 2021 18:29:46 +0200 Subject: [PATCH 0123/9987] fix quoting of modloadmsg in Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb --- .../g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb index 40cefa76807..fbf05bd573f 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -31,7 +31,8 @@ postinstallcmds = ['rm %(installdir)s/bin/python3.7'] license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' -modloadmsg = 'Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh`\n' -modloadmsg += 'Gurobi Python Interface can be loaded in Python %(pyver)s with "import gurobipy"' +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" moduleclass = 'math' From 309ef2b03d07e2348cf56769304ba3a0612dc763 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 17 Jan 2021 17:23:24 +0200 Subject: [PATCH 0124/9987] remove any bundled python in Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb --- .../g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb index fbf05bd573f..302ab9d01a0 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.0.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -27,7 +27,7 @@ dependencies = [ ] # remove bundled Python interpreter in favour of the dependency in EB -postinstallcmds = ['rm %(installdir)s/bin/python3.7'] +postinstallcmds = ['rm %(installdir)s/bin/python*'] license_file = HOME + '/licenses/%(name)s/%(namelower)s.lic' From fc8f54fc4ca85200898ef4833cf5738d4a61291a Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 29 Jan 2021 13:32:35 +0000 Subject: [PATCH 0125/9987] [esl] fdict update to 0.8.0 and foss 2020b --- .../f/fdict/fdict-0.8.0-GCC-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..d4ec2b5be50 --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ + A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. + """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +files_to_copy = [(['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), (['settings.bash'], 'bin')] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['bin'], +} + +moduleclass = 'data' From af87c6a5e199676eee55fd7864f10d8444bb8847 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 29 Jan 2021 13:11:38 +0000 Subject: [PATCH 0126/9987] [esl] update flook to version 0.8.1 and foss2020b --- .../f/flook/flook-0.8.1-GCC-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb new file mode 100644 index 00000000000..6b9f747a77f --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """ + The fortran-Lua-hook library. + """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +checksums = ['beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'] + +dependencies = [('libreadline', '8.0')] + +buildopts = ' liball ' +parallel = 1 + +files_to_copy = [(['libflookall.a', 'libflook.a'], 'lib'), (['flook.mod'], 'include')] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' From 90315933084435f015e83aed5b1a7e6eed778496 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Feb 2021 21:05:42 +0100 Subject: [PATCH 0127/9987] {bio}[foss/2020b] OrthoFinder v2.5.2, FastME v2.1.6.1, MCL v14.137, ... w/ Python 3.8.6 --- .../d/DIAMOND/DIAMOND-2.0.6-GCC-10.2.0.eb | 26 +++++++++++ .../f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb | 32 ++++++++++++++ .../m/MCL/MCL-14.137-GCCcore-10.2.0.eb | 41 +++++++++++++++++ .../m/MMseqs2/MMseqs2-12-113e3-gompi-2020b.eb | 36 +++++++++++++++ .../OrthoFinder-2.5.2-foss-2020b.eb | 44 +++++++++++++++++++ 5 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.6-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-12-113e3-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.6-GCC-10.2.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.6-GCC-10.2.0.eb new file mode 100644 index 00000000000..de62849aa4b --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.6-GCC-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.0.6' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/bbuchfink/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4231f6ed75191fc9757f22b60f9068f4b4412918bf2e8c37367880d189667f80'] + +builddependencies = [ + ('CMake', '3.18.4') +] +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["diamond help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb new file mode 100644 index 00000000000..4d4476d1104 --- /dev/null +++ b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FastME' +version = '2.1.6.1' + +homepage = 'http://www.atgc-montpellier.fr/fastme/' +description = "FastME: a comprehensive, accurate and fast distance-based phylogeny inference program." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://gite.lirmm.fr/atgc/FastME/-/archive/v%(version)s/'] +sources = ['FastME-v%(version)s.tar.gz'] +checksums = ['fae0609576873cb137ad4f63529b3ccba8f747b857c23c7870236aba440076ca'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +# install-sh, missing, config.sub, depcomp scripts included in source tarball are symlinks into /usr/share/... +local_scripts = "config.sub depcomp install-sh missing" +preconfigopts = "rm %s && " % local_scripts +preconfigopts += "for x in %s; do ln -s $EBROOTAUTOMAKE/share/automake-*/$x; done && " % local_scripts + +sanity_check_paths = { + 'files': ['bin/fastme'], + 'dirs': [] +} + +sanity_check_commands = ["fastme --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9aaca698b9d --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '14.137' + +homepage = 'https://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://micans.org/%(namelower)s/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +patches = ['%(name)s-%(version)s_fixperl.patch'] +checksums = [ + 'b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497', # mcl-14-137.tar.gz + '46988a287b2ee400a54fa485176d043b2a2d6589b6257cc6cf9c21689ea3842d', # MCL-14.137_fixperl.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Perl', '5.32.0'), +] + +preconfigopts = 'export CFLAGS="$CFLAGS -fcommon" && ' +configopts = '--enable-blast ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['clm', 'clmformat', 'clxdo', 'mcl', 'mclblastline', 'mclcm', 'mclpipeline', 'mcx', + 'mcxarray', 'mcxassemble', 'mcxdeblast', 'mcxdump', 'mcxi', 'mcxload', 'mcxmap', + 'mcxrand', 'mcxsubs']], + 'dirs': ['share'] +} + +sanity_check_commands = ["mcl --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-12-113e3-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-12-113e3-gompi-2020b.eb new file mode 100644 index 00000000000..5137ffe33fa --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-12-113e3-gompi-2020b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'MMseqs2' +version = '12-113e3' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['81fa0d77eab9d74b429567da00aa7ec2d46049537ce469595d7356b6d8b5458a'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [('bzip2', '1.0.8')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE' + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb new file mode 100644 index 00000000000..ff9a4ad647a --- /dev/null +++ b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonPackage' + +name = 'OrthoFinder' +version = '2.5.2' + +homepage = 'https://github.com/davidemms/OrthoFinder' +description = "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'davidemms' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e85c1fb920179655bf1611b6c0cb17efdf1fd26caf07667ae7eefe05be3fbc35'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('BLAST+', '2.11.0'), + ('DIAMOND', '2.0.6'), + ('FastME', '2.1.6.1'), + ('MCL', '14.137'), + ('MMseqs2', '12-113e3'), +] + +download_dep_fail = True +use_pip = True + +# see https://github.com/davidemms/OrthoFinder/pull/500 +preinstallopts = 'sed -i "s/ExampleDataset/ExampleData/g" setup.py && ' + +options = {'modulename': 'scripts_of'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['convert_orthofinder_tree_ids', 'make_ultrametric', 'orthofinder', + 'primary_transcript']], + 'dirs': ['ExampleData', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["orthofinder --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From c07529e84a39d2edbd117b342683db90478fd26a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Feb 2021 10:55:15 +0100 Subject: [PATCH 0128/9987] use autoreconf rather than symlinking Automake scripts for FastME --- easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb index 4d4476d1104..7b8029d3783 100644 --- a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb @@ -17,10 +17,7 @@ builddependencies = [ ('Autotools', '20200321'), ] -# install-sh, missing, config.sub, depcomp scripts included in source tarball are symlinks into /usr/share/... -local_scripts = "config.sub depcomp install-sh missing" -preconfigopts = "rm %s && " % local_scripts -preconfigopts += "for x in %s; do ln -s $EBROOTAUTOMAKE/share/automake-*/$x; done && " % local_scripts +preconfigopts = "autoreconf -if && " sanity_check_paths = { 'files': ['bin/fastme'], From 838bb6d50e1079b26e09fac854783770a6686b3d Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 9 Feb 2021 10:18:49 +0100 Subject: [PATCH 0129/9987] adding easyconfigs: cromwell-56-Java-11.eb --- .../c/cromwell/cromwell-56-Java-11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb diff --git a/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb b/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb new file mode 100644 index 00000000000..b4f1c18430c --- /dev/null +++ b/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb @@ -0,0 +1,34 @@ +easyblock = 'JAR' + +name = 'cromwell' +version = '56' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://cromwell.readthedocs.io/' +description = """Cromwell is a Workflow Management System geared towards scientific workflows.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/broadinstitute/%(name)s/releases/download/%(version)s/'] +sources = [ + { + 'download_filename': '%(name)s-%(version)s.jar', + 'filename': '%(name)s.jar', + }, + { + 'download_filename': 'womtool-%(version)s.jar', + 'filename': 'womtool.jar', + }, +] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'womtool.jar'], + 'dirs': [], +} + +modloadmsg = "To execute %(name)s, run: java -jar $EBROOTCROMWELL/%(name)s.jar" +modloadmsg += "\nTo execute womtool, run: java -jar $EBROOTCROMWELL/womtool.jar" + +moduleclass = 'bio' From e53936c01a012dc8d6ac08bd6ca654a2e7533641 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 9 Feb 2021 10:37:39 +0100 Subject: [PATCH 0130/9987] add checksums --- easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb b/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb index b4f1c18430c..7e167fc41e1 100644 --- a/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb +++ b/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb @@ -20,6 +20,10 @@ sources = [ 'filename': 'womtool.jar', }, ] +checksums = [ + '955502419cfec2a687ea56f7f4a433b395af09c9a078e60a5676c7ad56c3965d', # cromwell.jar + '0f561c0d387412715f1f688ad5ae7cd4d8af3dc8d68c69ae9fc35ecae4f481c6', # womtool.jar +] dependencies = [('Java', '11')] From fc10190a05440301453c6b2975809c2f6c30e51c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Feb 2021 10:38:36 +0100 Subject: [PATCH 0131/9987] add missing gnuplot dependency for OpenFOAM v2006 with intel/2020a --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb index aa7c52b3734..2770a91bb5d 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb @@ -30,6 +30,7 @@ dependencies = [ ('SCOTCH', '6.0.9'), ('CGAL', '4.14.3', '-Python-3.8.2'), ('ParaView', '5.8.0', '-Python-3.8.2-mpi'), + ('gnuplot', '5.2.8'), ] builddependencies = [ From 276145537cc2042b8bd498df73aab1c06964395a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Feb 2021 21:09:15 +0100 Subject: [PATCH 0132/9987] add patch file to fix compilation of setAlphaField utility in OpenFOAM v2006 with intel/2020a --- .../o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb | 3 + ...-v2006_fix-setAlphaField-compilation.patch | 81 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006_fix-setAlphaField-compilation.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb index 2770a91bb5d..0ca9926c885 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb @@ -15,11 +15,14 @@ sources = [SOURCE_TGZ] patches = [ 'OpenFOAM-%(version)s-cleanup.patch', 'OpenFOAM-v1906-wmake-ompi.patch', + 'OpenFOAM-%(version)s_fix-setAlphaField-compilation.patch', ] checksums = [ '30c6376d6f403985fc2ab381d364522d1420dd58a42cb270d2ad86f8af227edc', # OpenFOAM-v2006.tgz 'cb3c6d26569cf11d22941963acb9741238fe829f21b452506a51a71b5c42ae84', # OpenFOAM-v2006-cleanup.patch '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch + # OpenFOAM-v2006_fix-setAlphaField-compilation.patch + 'ce7ed531f75ca9ee404963736d8140df62d766bdfeeba469777f1bf44b5aa8bc', ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006_fix-setAlphaField-compilation.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006_fix-setAlphaField-compilation.patch new file mode 100644 index 00000000000..1a099c53c4e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2006_fix-setAlphaField-compilation.patch @@ -0,0 +1,81 @@ +fix compilation error for setAlphaField with intel/2020a +obtained via https://develop.openfoam.com/Development/openfoam/-/commit/719d3f77bea23bbdb9c530ee2dde09383f03bc71.patch + +From 719d3f77bea23bbdb9c530ee2dde09383f03bc71 Mon Sep 17 00:00:00 2001 +From: Mark Olesen +Date: Tue, 1 Sep 2020 09:32:13 +0200 +Subject: [PATCH] COMP: Intel compiler bug with inheriting constructors (fixes + #1821) + +- the compiler reports + + Internal error loop: assertion failed: + find_seq_in_lookup_table: seq_number not found + (shared/cfe/edgcpfe/il.c, line 4118) + + Seems to be the same as the bug report + https://community.intel.com/t5/Intel-C-Compiler/Internal-error-loop-assertion-failed-find-seq-in-lookup-table/td-p/1087603 + +This _should_ be fixed in icc 17.0 update 1, but appears to have +struck here as well. + +- workaround: explicitly construct member elements. +--- + .../cylinder/cylinderImplicitFunction.C | 13 ++++++------- + .../implicitFunctions/sin/sinImplicitFunction.C | 16 +++++++--------- + 2 files changed, 13 insertions(+), 16 deletions(-) + +diff --git a/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/cylinder/cylinderImplicitFunction.C b/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/cylinder/cylinderImplicitFunction.C +index 909087e473..1c68b7fef2 100644 +--- a/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/cylinder/cylinderImplicitFunction.C ++++ b/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/cylinder/cylinderImplicitFunction.C +@@ -69,13 +69,12 @@ Foam::implicitFunctions::cylinderImplicitFunction::cylinderImplicitFunction + const dictionary& dict + ) + : +- cylinderImplicitFunction +- ( +- dict.get("origin"), +- dict.get("radius"), +- dict.getOrDefault("scale", 1), +- dict.get("direction") +- ) ++ // __INTEL_COMPILER bug with inheriting constructors?? (issue #1821) ++ origin_(dict.get("origin")), ++ radius_(dict.get("radius")), ++ scale_(dict.getOrDefault("scale", 1)), ++ direction_(dict.get("direction").normalise()), ++ project_(tensor::I - direction_*direction_) // outer product + {} + + +diff --git a/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/sin/sinImplicitFunction.C b/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/sin/sinImplicitFunction.C +index a193d2b663..4256baad94 100644 +--- a/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/sin/sinImplicitFunction.C ++++ b/applications/utilities/preProcessing/setAlphaField/alphaFieldFunctions/implicitFunctions/sin/sinImplicitFunction.C +@@ -72,15 +72,13 @@ Foam::implicitFunctions::sinImplicitFunction::sinImplicitFunction + const dictionary& dict + ) + : +- sinImplicitFunction +- ( +- dict.get("period"), +- dict.getOrDefault("phase", 0), +- dict.get("amplitude"), +- dict.get("direction"), +- dict.get("up"), +- dict.get("origin") +- ) ++ // __INTEL_COMPILER bug with inheriting constructors?? (issue #1821) ++ period_(dict.get("period")), ++ phase_(dict.getOrDefault("phase", 0)), ++ amplitude_(dict.get("amplitude")), ++ up_(dict.get("up").normalise()), ++ direction_(dict.get("direction").normalise()), ++ origin_(dict.get("origin")) + {} + + +-- +GitLab + From 9793c8e9df09ed10f3be7098016fc2990b69a0cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Feb 2021 18:37:35 +0100 Subject: [PATCH 0133/9987] adding easyconfigs: SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb and patches: SqueezeMeta-1.0.0_fix-hardcoding.patch --- ...eezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb | 82 +++++++++++++++++++ .../SqueezeMeta-1.0.0_fix-hardcoding.patch | 63 ++++++++++++++ 2 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb create mode 100644 easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0_fix-hardcoding.patch diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb new file mode 100644 index 00000000000..700c3b31af3 --- /dev/null +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb @@ -0,0 +1,82 @@ +easyblock = 'Tarball' + +name = 'SqueezeMeta' +version = '1.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jtamames/SqueezeMeta' +description = """SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, + covering all steps of the analysis.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/jtamames/SqueezeMeta/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['SqueezeMeta-%(version)s_fix-hardcoding.patch'] +checksums = [ + '35fa45246fa3580e7ab00644176f719151465aa0ed5f0023d30075668baefb11', # v1.0.0.tar.gz + '5fe6b721669d022a1d891472d64061f217791ff8efd1642d34a03de18a21d677', # SqueezeMeta-1.0.0_fix-hardcoding.patch +] + +dependencies = [ + ('Perl', '5.28.0'), # provides XML::Parser + ('XML-LibXML', '2.0132', '-Perl-%(perlver)s'), + ('Python', '2.7.15'), + ('matplotlib', '2.2.3', versionsuffix), + ('Pysam', '0.15.1', versionsuffix), + ('R', '3.5.1', versionsuffix), + ('BLAST+', '2.7.1'), + ('BWA', '0.7.17'), + #('barrnap', '0.9'), + ('CD-HIT', '4.6.8'), + ('CheckM', '1.0.13', versionsuffix), + ('DAS_Tool', '1.1.1', '-R-%(rver)s-Python-%(pyver)s'), # depends on prodigal & pullseq + ('DIAMOND', '0.9.22'), + ('MEGAHIT', '1.1.4', versionsuffix), + ('minimap2', '2.13'), + ('Java', '1.8', '', True), + ('RDP-Classifier', '2.12', '-Java-%(javaver)s', True), + ('MetaBAT', '2.12.1', versionsuffix), + ('MinPath', '1.4', versionsuffix), # depends on GPLK (which provides glpsol) + ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), + ('Trimmomatic', '0.38', '-Java-%(javaver)s', True), + ('AMOS', '3.1.0'), + ('MaxBin', '2.2.6', '-Perl-%(perlver)s'), + ('SPAdes', '3.13.0'), + ('Bowtie2', '2.3.4.2'), + ('canu', '1.8', '-Perl-%(perlver)s'), + ('HMMER', '3.2.1'), + ('MUMmer', '4.0.0beta2'), + ('pplacer', '1.1.alpha19', '', True), + ('Short-Pair', '20170125', versionsuffix), + ('SAMtools', '1.9'), + ('CompareM', '0.0.23', versionsuffix), +] + +keepsymlinks = True + +postinstallcmds = [ + # backup patched barrnap + "cp %(installdir)s/bin/barrnap %(builddir)s/", + # remove vendored tools that are include as dependencies + "rm -r %(installdir)s/bin/*", + "cp %(builddir)s/barrnap %(installdir)s/bin/", + # fix shebang in Perl scripts + "sed -i 's@#!/usr/bin/perl@#!/usr/bin/env perl@g' %(installdir)s/scripts/*.pl", + # also install SQMtools R library + "mkdir %(installdir)s/R && R CMD INSTALL lib/SQMtools --library=%(installdir)s/R/ --no-clean-on-error", +] + +sanity_check_paths = { + 'files': ['scripts/SqueezeMeta.pl'], + 'dirs': ['scripts/preparing_databases'], +} + +sanity_check_commands = ["""echo 'library("SQMtools")' | R -q --no-save"""] + +modextrapaths = { + 'PATH': 'scripts', + 'R_LIBS': 'R', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0_fix-hardcoding.patch b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0_fix-hardcoding.patch new file mode 100644 index 00000000000..eb762a4a11a --- /dev/null +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0_fix-hardcoding.patch @@ -0,0 +1,63 @@ +fix hardcoded paths, rely on specified dependencies via $PATH and $EBROOT* +author: Kenneth Hoste (HPC-UGent) +--- SqueezeMeta-1.0.0/scripts/SqueezeMeta_conf_original.pl.orig 2019-11-26 11:48:35.838688703 +0100 ++++ SqueezeMeta-1.0.0/scripts/SqueezeMeta_conf_original.pl 2019-11-26 11:52:57.253843644 +0100 +@@ -80,25 +80,25 @@ + + #-- External software + +-$metabat_soft="$installpath/bin/metabat2"; +-$maxbin_soft="$installpath/bin/MaxBin/run_MaxBin.pl"; +-$spades_soft="$installpath/bin/SPAdes/spades.py"; +-$barrnap_soft="$installpath/bin/barrnap"; +-$rdpclassifier_soft="java -jar $installpath/bin/classifier.jar"; +-$bowtie2_build_soft="$installpath/bin/bowtie2/bowtie2-build"; +-$bowtie2_x_soft="$installpath/bin/bowtie2/bowtie2"; +-$bwa_soft = "$installpath/bin/bwa"; +-$minimap2_soft = "$installpath/bin/minimap2"; +-$diamond_soft="$installpath/bin/diamond"; +-$hmmer_soft="$installpath/bin/hmmer/hmmsearch"; +-$megahit_soft="$installpath/bin/megahit/megahit"; +-$prinseq_soft="$installpath/bin/prinseq-lite.pl"; +-$prodigal_soft="$installpath/bin/prodigal"; +-$cdhit_soft="$installpath/bin/cd-hit-est"; +-$toamos_soft="$installpath/bin/AMOS/toAmos"; +-$minimus2_soft="$installpath/bin/AMOS/minimus2"; +-$checkm_soft="$installpath/bin/checkm"; +-$minpath_soft="python $installpath/bin/MinPath1.4.py"; +-$canu_soft="$installpath/bin/canu/canu"; +-$trimmomatic_soft="java -jar $installpath/bin/trimmomatic-0.38.jar"; +-$dastool_soft="$installpath/bin/DAS_Tool/DAS_Tool"; ++$metabat_soft="metabat2"; ++$maxbin_soft="$ENV{'EBROOTMAXBIN'}/run_MaxBin.pl"; ++$spades_soft="spades.py"; ++$barrnap_soft="barrnap"; ++$rdpclassifier_soft="java -jar $ENV{'EBROOTRDPMINCLASSIFIER'}/dist/classifier.jar"; ++$bowtie2_build_soft="bowtie2-build"; ++$bowtie2_x_soft="bowtie2"; ++$bwa_soft = "bwa"; ++$minimap2_soft = "minimap2"; ++$diamond_soft="diamond"; ++$hmmer_soft="hmmsearch"; ++$megahit_soft="megahit"; ++$prinseq_soft="prinseq-lite.pl"; ++$prodigal_soft="prodigal"; ++$cdhit_soft="cd-hit-est"; ++$toamos_soft="AMOS/toAmos"; ++$minimus2_soft="AMOS/minimus2"; ++$checkm_soft="checkm"; ++$minpath_soft="MinPath$ENV{'EBVERSIONMINPATH'}.py"; ++$canu_soft="canu"; +++$trimmomatic_soft="java -jar $ENV{'EBROOTTRIMMOMATIC'}/trimmomatic-$ENV{'EBVERSIONTRIMMOMATIC'}.jar"; +++$dastool_soft="DAS_Tool"; +--- SqueezeMeta-1.0.0/utils/sqm_hmm_reads.pl.orig 2019-11-26 11:53:35.804013957 +0100 ++++ SqueezeMeta-1.0.0/utils/sqm_hmm_reads.pl 2019-11-26 11:54:08.748159508 +0100 +@@ -15,7 +15,7 @@ + + use File::Basename; + my $utilsdir = dirname(__FILE__); +-my $shortpair_soft = "$utilsdir/../bin/Short-Pair/Short-Pair.py"; ++my $shortpair_soft = "Short-Pair.py"; + + my($numthreads,$pair1,$pair2,$pfam,$outfile,$dietext,$tempfile1,$tempfile2,$hel); + From 8ab209e4081bc3d0575e8d257b4e4de58a722d84 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 16:56:30 +0100 Subject: [PATCH 0134/9987] adding easyconfigs: PyRETIS-2.5.0-intel-2020b-Python-3.8.6.eb, PyRETIS-2.5.0-foss-2020b-Python-3.8.6.eb --- .../PyRETIS-2.5.0-foss-2020b-Python-3.8.6.eb | 45 +++++++++++++++++++ .../PyRETIS-2.5.0-intel-2020b-Python-3.8.6.eb | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b-Python-3.8.6.eb create mode 100644 easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..1e403a1e407 --- /dev/null +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'PyRETIS' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pyretis.org' +description = """PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based + on transition interface sampling and replica exchange transition interface sampling.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('MDTraj', '1.9.5'), + ('PyTables', '3.6.1'), + ('tqdm', '4.56.2'), +] + +use_pip = True + +exts_list = [ + ('colorama', '0.4.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + (name, version, { + 'source_tmpl': 'pyretis-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyretis'], + 'checksums': ['b4b842a83f39e97a9bbf2d9797f53823b9e741b479b5a6744aeb42daf1c7ad2b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyretisanalyse', 'bin/pyretisrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pyretisanalyse --help", + "pyretisrun --help", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..259e2fbac31 --- /dev/null +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b-Python-3.8.6.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'PyRETIS' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pyretis.org' +description = """PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based + on transition interface sampling and replica exchange transition interface sampling.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('MDTraj', '1.9.5'), + ('PyTables', '3.6.1'), + ('tqdm', '4.56.2'), +] + +use_pip = True + +exts_list = [ + ('colorama', '0.4.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + (name, version, { + 'source_tmpl': 'pyretis-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyretis'], + 'checksums': ['b4b842a83f39e97a9bbf2d9797f53823b9e741b479b5a6744aeb42daf1c7ad2b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyretisanalyse', 'bin/pyretisrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pyretisanalyse --help", + "pyretisrun --help", +] + +moduleclass = 'chem' From 2ee6650abc9d6c44bbe3365214607f565058143b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 17:06:14 +0100 Subject: [PATCH 0135/9987] adding easyconfigs: parallel-fastq-dump-0.6.6-GCCcore-9.3.0.eb --- ...parallel-fastq-dump-0.6.6-GCCcore-9.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..f030de09913 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'parallel-fastq-dump' +version = '0.6.6' + +homepage = 'https://github.com/rvalieris/parallel-fastq-dump' +description = "parallel fastq-dump wrapper" +docurls = ["https://github.com/rvalieris/parallel-fastq-dump"] + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +# https://github.com/rvalieris/parallel-fastq-dump/archive/ +github_account = 'rvalieris' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['38a3db72e4f87b8ca2412147a5938372098df15e839c78cddc8a7bfa3dd35b64'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('Python', '3.8.2'), + ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', True) +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + "files": ["bin/parallel-fastq-dump"], + "dirs": ["lib/python%(pyshortver)s/site-packages"], +} + +# This package doesn't produce importable module, only executable script. +options = {'modulename': False} + +sanity_check_commands = ["parallel-fastq-dump --version"] + +moduleclass = "bio" From 18c9754bec71f51789a457d0de68704659ceb651 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 17:13:15 +0100 Subject: [PATCH 0136/9987] add missing Python versionsuffix for parallel-fastq-dump 0.6.6 --- ...b => parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/p/parallel-fastq-dump/{parallel-fastq-dump-0.6.6-GCCcore-9.3.0.eb => parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb} (96%) diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb similarity index 96% rename from easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0.eb rename to easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb index f030de09913..646b5f3b343 100644 --- a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb @@ -5,6 +5,7 @@ easyblock = 'PythonPackage' name = 'parallel-fastq-dump' version = '0.6.6' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/rvalieris/parallel-fastq-dump' description = "parallel fastq-dump wrapper" From 7a943e557d2b90c1573fc9c9497c295812d0726a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Feb 2021 17:15:47 +0100 Subject: [PATCH 0137/9987] drop Python versionsuffix for PyRETIS with */2020b --- ....0-foss-2020b-Python-3.8.6.eb => PyRETIS-2.5.0-foss-2020b.eb} | 1 - ...-intel-2020b-Python-3.8.6.eb => PyRETIS-2.5.0-intel-2020b.eb} | 1 - 2 files changed, 2 deletions(-) rename easybuild/easyconfigs/p/PyRETIS/{PyRETIS-2.5.0-foss-2020b-Python-3.8.6.eb => PyRETIS-2.5.0-foss-2020b.eb} (97%) rename easybuild/easyconfigs/p/PyRETIS/{PyRETIS-2.5.0-intel-2020b-Python-3.8.6.eb => PyRETIS-2.5.0-intel-2020b.eb} (97%) diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb similarity index 97% rename from easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b-Python-3.8.6.eb rename to easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb index 1e403a1e407..223cac29600 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b-Python-3.8.6.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonBundle' name = 'PyRETIS' version = '2.5.0' -versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.pyretis.org' description = """PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb similarity index 97% rename from easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b-Python-3.8.6.eb rename to easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb index 259e2fbac31..73df2b8f6b0 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b-Python-3.8.6.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonBundle' name = 'PyRETIS' version = '2.5.0' -versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.pyretis.org' description = """PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based From b1514ccb81a9f9b3a363e1519d579b23a4bc1354 Mon Sep 17 00:00:00 2001 From: patbel-pwr Date: Thu, 25 Feb 2021 21:54:18 +0100 Subject: [PATCH 0138/9987] Fix build error on old GCC --- .../b/Bison/Bison-3.7.1-old_gcc_fix.patch | 20 +++++++++++++++++++ easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb | 5 +++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.7.1-old_gcc_fix.patch diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.1-old_gcc_fix.patch b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-old_gcc_fix.patch new file mode 100644 index 00000000000..94e39a6c22e --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-old_gcc_fix.patch @@ -0,0 +1,20 @@ +--- src/parse-simulation.c.orig 2020-08-02 07:59:31.000000000 +0200 ++++ src/parse-simulation.c 2021-02-24 11:12:02.385501723 +0100 +@@ -28,7 +28,7 @@ + #include "lssi.h" + #include "nullable.h" + +-typedef struct parse_state ++struct parse_state + { + // Path of state-items the parser has traversed. + struct si_chunk +@@ -58,7 +58,7 @@ + // Causes chunk contents to be freed when the reference count is + // one. Used when only the chunk metadata will be needed. + bool free_contents_early; +-} parse_state; ++} ; + + + static void diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb index c3cedc9436e..f056aaf8422 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb @@ -21,6 +21,11 @@ builddependencies = [ ('M4', '1.4.18'), ] +# Uncomment if you encounter "error: redefinition of typedef 'parse_state'" during build +#patches = [ +# 'Bison-3.7.1-old_gcc_fix.patch' +#] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], 'dirs': [], From 54e76b186df18bb21d6d87dc40a2dc6d52ee2367 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Feb 2021 12:05:28 +0100 Subject: [PATCH 0139/9987] adding easyconfigs: TopHat-2.1.2-gompi-2020a.eb, TopHat-2.1.2-iimpi-2020a.eb --- .../t/TopHat/TopHat-2.1.2-gompi-2020a.eb | 47 +++++++++++++++++++ .../t/TopHat/TopHat-2.1.2-iimpi-2020a.eb | 47 +++++++++++++++++++ 2 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iimpi-2020a.eb diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-gompi-2020a.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-gompi-2020a.eb new file mode 100644 index 00000000000..c6f8cd70110 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-gompi-2020a.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.2' + +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' +description = "TopHat is a fast splice junction mapper for RNA-Seq reads." + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'cstd': 'gnu++98', 'pic': True} + +github_account = 'infphilo' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] + +patches = ['%(namelower)s-2.0.13-zlib.patch'] + +checksums = [ + '15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1', # v2.1.2.tar.gz + 'a33075c2affda995ddbd250933dbcaf94f68768b1eebead58a69705fc40306ef', # tophat-2.0.13-zlib.patch +] + +builddependencies = [('Autotools', '20180311')] + +dependencies = [ + ('Boost', '1.72.0'), + ('zlib', '1.2.11'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iimpi-2020a.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iimpi-2020a.eb new file mode 100644 index 00000000000..33584a2546e --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iimpi-2020a.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.2' + +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' +description = "TopHat is a fast splice junction mapper for RNA-Seq reads." + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'cstd': 'gnu++98', 'pic': True} + +github_account = 'infphilo' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] + +patches = ['%(namelower)s-2.0.13-zlib.patch'] + +checksums = [ + '15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1', # v2.1.2.tar.gz + 'a33075c2affda995ddbd250933dbcaf94f68768b1eebead58a69705fc40306ef', # tophat-2.0.13-zlib.patch +] + +builddependencies = [('Autotools', '20180311')] + +dependencies = [ + ('Boost', '1.72.0'), + ('zlib', '1.2.11'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 08453cc6a6ee08e4629ed7005b8d92a6ddf450b1 Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 26 Feb 2021 14:36:24 +0000 Subject: [PATCH 0140/9987] Changed foss-2018b to GCCcore-8.3.0, added GCCcore-10.2.0 as that is latest --- .../t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb | 45 +++++++++++++++++++ ...-2019b.eb => tabix-0.2.6-GCCcore-8.3.0.eb} | 10 ++++- 2 files changed, 54 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb rename easybuild/easyconfigs/t/tabix/{tabix-0.2.6-foss-2019b.eb => tabix-0.2.6-GCCcore-8.3.0.eb} (72%) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..442eed6ab0c --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Jens Timmerman, Ghent University +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# updated to newer toolchain + +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] +checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-8.3.0.eb similarity index 72% rename from easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb rename to easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-8.3.0.eb index 1606e872263..7ac739b5ddd 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2019b.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-8.3.0.eb @@ -1,6 +1,12 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Jens Timmerman, Ghent University # Contribution from the NIHR Biomedical Research Centre # Guy's and St Thomas' NHS Foundation Trust and King's College London # uploaded by J. Sassmannshausen +# updated to newer toolchain easyblock = 'MakeCp' @@ -10,12 +16,14 @@ version = '0.2.6' homepage = 'http://samtools.sourceforge.net' description = """ Generic indexer for TAB-delimited genome position files """ -toolchain = {'name': 'foss', 'version': '2019b'} +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')] sources = [SOURCE_TAR_BZ2] checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73'] +builddependencies = [('binutils', '2.32')] + dependencies = [('zlib', '1.2.11')] buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' From 99391f573a80a8b37bd66779d750513893af5f62 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 2 Mar 2021 13:08:20 +0000 Subject: [PATCH 0141/9987] New EC for libcotp and libbaseencode created --- .../libbaseencode-1.0.11-GCCcore-10.2.0.eb | 34 ++++++++++++++++++ .../l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c277c47c1fd --- /dev/null +++ b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'libbaseencode' +version = '1.0.11' + +homepage = 'https://github.com/paolostivanin/libbaseencode' +description = """Library written in C for encoding and decoding +data using base32 or base64 according to RFC-4648""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/paolostivanin/libbaseencode/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['645329236992ee85f05569475da2af0f0d81aaccd4aebc8d0b8603e54a320935'] # v1.0.11.tar.gz + +builddependencies = [ + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), +] + +parallel = 1 + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libbaseencode.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..bb91a4503b4 --- /dev/null +++ b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'libcotp' +version = '1.2.3' + +homepage = 'https://github.com/paolostivanin/libcotp' +description = """C library that generates TOTP and HOTP according to RFC-6238""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/paolostivanin/libcotp/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f122aea37337cdfcdaa1ce979ecfb5177ad7dcb273caf2d6056820f1dbf92e93'] # v1.2.3.tar.gz + +builddependencies = [ + ('CMake', '3.18.4'), + ('libgcrypt', '1.9.2'), + ('libbaseencode', '1.0.11'), + ('pkg-config', '0.29.2'), +] + +parallel = 1 + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libcotp.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'lib' From 6033353a1a2e52ce65cd34aa5954982e7202028e Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 2 Mar 2021 14:44:21 +0000 Subject: [PATCH 0142/9987] Binutils added --- .../l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb index c277c47c1fd..694e34a5a2a 100644 --- a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb @@ -20,6 +20,7 @@ checksums = ['645329236992ee85f05569475da2af0f0d81aaccd4aebc8d0b8603e54a320935'] builddependencies = [ ('CMake', '3.18.4'), ('pkg-config', '0.29.2'), + ('binutils', '2.35'), ] parallel = 1 diff --git a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb index bb91a4503b4..5fd70b9bace 100644 --- a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('libgcrypt', '1.9.2'), ('libbaseencode', '1.0.11'), ('pkg-config', '0.29.2'), + ('binutils', '2.35'), ] parallel = 1 From ee99eecd6502214e5a680e26c0a53d578ad0bb12 Mon Sep 17 00:00:00 2001 From: hrn Date: Wed, 3 Mar 2021 11:05:53 +0100 Subject: [PATCH 0143/9987] adding easyconfigs: FSL-6.0.4-foss-2019b-Python-3.7.4.eb and patches: FSL-6.0.4_Makefile_fixes.patch, FSL-6.0.4_disable_cuda.patch, FSL-6.0.4_build_fixes.patch --- .../FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb | 75 ++++++ .../f/FSL/FSL-6.0.4_Makefile_fixes.patch | 250 ++++++++++++++++++ .../f/FSL/FSL-6.0.4_build_fixes.patch | 30 +++ .../f/FSL/FSL-6.0.4_disable_cuda.patch | 16 ++ 4 files changed, 371 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.4_Makefile_fixes.patch create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.4_build_fixes.patch create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.4_disable_cuda.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..67bcb389db5 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,75 @@ +# This build still relies on the following libraries (or part of them) shipped with FSL: +# GDCHART, libprob, libcprob, cprob, newran, newmat +# Attempts to use externally built libraries failed. Worth trying again in the future... +# +# Added fslpy 3.5.3, which provides tools like imcp and imglob + +name = 'FSL' +version = '6.0.4' +versionsuffix = '-Python-3.7.4' + +homepage = 'https://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://www.fmrib.ox.ac.uk/fsldownloads/'] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] +patches = [ + 'FSL-6.0.4_Makefile_fixes.patch', + 'FSL-6.0.4_disable_cuda.patch', + 'FSL-6.0.4_build_fixes.patch', + 'FSL-6.0.2_Build_extras.patch', + 'FSL-6.0.1_Melodic-use-ifstream-good.patch', + 'FSL-6.0.1_Fix_fsl_exec_script.patch', +] +checksums = [ + '58b88f38e080b05d70724d57342f58e1baf56e2bd3b98506a72b4446cad5033e', # fsl-6.0.4-sources.tar.gz + '43217e86e715a149ec27dfad471383e8f142863aa6f3f943ab4db379bc851055', # FSL-6.0.4_Makefile_fixes.patch + '6b81e6f45edb43cc2a008f5760610fb0812e3666ffd6e208f283388d35e530cf', # FSL-6.0.4_disable_cuda.patch + '1bc83cfeffff21a68db47b6929e94634fc8aaf3db8e276e160e3f468f0889000', # FSL-6.0.4_build_fixes.patch + '168157f07818e7dfd04c222916e663e9d21db84b4b86df5b79bab56e3bf8ccf5', # FSL-6.0.2_Build_extras.patch + 'c07644fbd89cf9c70db5a1a8f4f2918ab5daeb60cdf0ce4ee2b91f8ae48173fa', # FSL-6.0.1_Melodic-use-ifstream-good.patch + 'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef', # FSL-6.0.1_Fix_fsl_exec_script.patch +] + +dependencies = [ + ('Python', '3.7.4'), + ('Boost', '1.71.0'), + ('libgd', '2.2.5'), + ('libxml2', '2.9.9'), + ('libxml++', '2.40.1'), + ('SQLite', '3.29.0'), + ('libpng', '1.6.37'), + ('Tk', '8.6.9'), + ('NLopt', '2.6.1'), + ('freeglut', '3.2.1'), + ('expat', '2.2.7'), + ('zlib', '1.2.11'), + ('VTK', '8.2.0', versionsuffix), + ('GSL', '2.6'), + ('Qwt', '6.1.4'), +] + +modextrapaths = {'PYTHONPATH': ['fsl/lib/python%(pyshortver)s/site-packages']} + +# The executable file 'imcp' is a part of fslpy +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('fslpy', '3.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/f/fslpy/'], + 'checksums': ['f80ef8b7b49f475bfb71946619d33c118a7cbbe106c72f7777aaf14d9e261530'], + 'installopts': '--prefix=%(installdir)s/fsl', + }), +] + +modextravars = { + 'FSLOUTPUTTYPE': 'NIFTI_GZ', + 'FSLMULTIFILEQUIT': 'TRUE', + 'FSLTCLSH': 'tclsh', + 'FSLWISH': 'wish8.6' +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.4_Makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.4_Makefile_fixes.patch new file mode 100644 index 00000000000..486ecbd3377 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.4_Makefile_fixes.patch @@ -0,0 +1,250 @@ +Fix the Makefile to use libraries built with EB instead of the ones +shipped with the code. +Also: invoke the system's tclsh, instead of the one shipped with fsl +Author: Caspar van Leeuwen (SURFsara) +diff -Nru fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk +--- fsl.orig/config/buildSettings.mk 2020-06-19 15:48:02.000000000 +0200 ++++ fsl/config/buildSettings.mk 2021-02-24 11:44:50.000000000 +0100 +@@ -18,7 +18,7 @@ + CHMOD = /bin/chmod + MKDIR = /bin/mkdir + INSTALL = install -p +-TCLSH = ${FSLDIR}/bin/fsltclsh ++TCLSH = tclsh + DEPENDFLAGS = -MM + MACHDBGFLAGS = -g + ##################################################################### +@@ -33,17 +33,17 @@ + LIB_CEPHES = ${FSLEXTLIB} + INC_CEPHES = ${FSLEXTINC}/cephes + # GD library +-LIB_GD = ${FSLEXTLIB} +-INC_GD = ${FSLEXTINC} ++LIB_GD = ${EBROOTLIBGD}/lib ++INC_GD = ${EBROOTLIBGD}/include + # GDC library + LIB_GDC = ${FSLEXTLIB} + INC_GDC = ${FSLEXTINC}/libgdc + # GSL library +-LIB_GSL = ${FSLEXTLIB} +-INC_GSL = ${FSLEXTINC}/gsl ++LIB_GSL = ${EBROOTGSL}/lib ++INC_GSL = ${EBROOTGSL}/include + # PNG library +-LIB_PNG = ${FSLEXTLIB} +-INC_PNG = ${FSLEXTINC} ++LIB_PNG = ${EBROOTLIBPNG}/lib ++INC_PNG = ${EBROOTLIBPNG}/include + # PROB library + # This is now for legacy support only + LIB_PROB = ${FSLEXTLIB} +@@ -55,21 +55,21 @@ + LIB_NEWRAN = ${FSLEXTLIB} + INC_NEWRAN = ${FSLEXTINC}/newran + # BOOST library +-BOOSTDIR = ${FSLEXTINC}/boost +-LIB_BOOST = ${BOOSTDIR} +-INC_BOOST = ${BOOSTDIR} ++BOOSTDIR = ${EBROOTBOOST} ++LIB_BOOST = ${BOOSTDIR}/lib ++INC_BOOST = ${BOOSTDIR}/include + # QWT library +-QWTDIR = /usr/local/qwt ++QWTDIR = ${EBROOTQWT} + INC_QWT = ${QWTDIR}/include + LIB_QWT = ${QWTDIR}/lib + # FFTW3 library +-LIB_FFTW3 = ${FSLEXTLIB} +-INC_FFTW3 = ${FSLEXTINC}/fftw3 ++LIB_FFTW3 = ${EBROOTFFTW}/lib ++INC_FFTW3 = ${EBROOTFFTW}/include + # LIBXML2 library +-INC_XML2 = ${FSLEXTINC}/libxml2 ++INC_XML2 = ${EBROOTLIBXML2}/include + # LIBXML++ library +-INC_XML++ = ${FSLEXTINC}/libxml++-2.6 +-INC_XML++CONF = ${FSLEXTLIB}/libxml++-2.6/include ++INC_XML++ = ${EBROOTLIBXMLPLUSPLUS}/include/libxml++-2.6 ++INC_XML++CONF = ${EBROOTLIBXMLPLUSPLUS}/lib/libxml++-2.6/include + # NEWMAT library/armadillo + INC_NEWMAT = ${FSLEXTINC}/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD + ##################################################################### +@@ -127,16 +127,16 @@ + ##################################################################### + ifeq ($(SYSTYPE), Linux) + ############### System Vars ##################################### +-CC = gcc +-CXX = c++ +-CXX11 = c++ ++CC := ${CC} ++CXX := ${CXX} ++CXX11 := ${CXX} -std=c++11 + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + ARCHFLAGS = -m64 + ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib' + PARALLELFLAGS = -fopenmp +-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS} +-GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long ++OPTFLAGS := ${OPTFLAGS} ${ARCHFLAGS} ++GNU_ANSI_FLAGS = -Wall -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn + ANSI_FLAGS = ${GNU_ANSI_FLAGS} + RANLIB = echo +@@ -144,7 +144,7 @@ + # CUDA development environment + CUDAVER := $(or $(CUDAVER),9.1) + #$(info $$CUDAVER is [${CUDAVER}]) +-CUDA_INSTALLATION = /opt/cuda-${CUDAVER} ++CUDA_INSTALLATION := ${EBROOTCUDA} + ifdef SINGULARITY_NAME + CUDA_INSTALLATION = /usr/local/cuda-${CUDAVER} + endif +@@ -158,16 +158,16 @@ + NVCC = ${CUDA_INSTALLATION}/bin/nvcc + ############### External Libs ##################################### + # ZLIB library +-LIB_ZLIB = ${FSLEXTLIB} +-INC_ZLIB = ${FSLEXTINC} ++LIB_ZLIB = ${EBROOTZLIB}/lib ++INC_ZLIB = ${EBROOTZLIB}/include + # QT library +-QTDIR = /usr/lib/qt3 ++QTDIR = ${EBROOTQT} + LIB_QT = ${QTDIR}/lib + INC_QT = ${QTDIR}/include + # VTK library +-VTKDIR_INC = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/include/vtk-7.0 +-VTKDIR_LIB = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/lib +-VTKSUFFIX = -7.0 ++VTKDIR_INC = ${EBROOTVTK}/include/vtk-`echo ${EBVERSIONVTK} | cut -f1-2 -d.` ++VTKDIR_LIB = ${EBROOTVTK}/lib ++VTKSUFFIX = -`echo ${EBVERSIONVTK} | cut -f1-2 -d.` + # openblas + LIB_NEWMAT = ${FSLEXTLIB} -lopenblas + # get and then parse gcc version to run context specific builds +diff -Nru fsl.orig/config/common/vars.mk fsl/config/common/vars.mk +--- fsl.orig/config/common/vars.mk 2020-06-19 15:48:02.000000000 +0200 ++++ fsl/config/common/vars.mk 2021-02-24 11:12:18.000000000 +0100 +@@ -24,14 +24,14 @@ + USRCFLAGS = + USRCXXFLAGS = + +-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ++LDFLAGS = ${EBVARLDFLAGS} ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} + +-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ++AccumulatedIncFlags = ${EBVARCPPFLAGS} -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} + +-CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ ++CFLAGS = ${EBVARCFLAGS} ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ + ${AccumulatedIncFlags} + +-CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ ++CXXFLAGS = ${EBVARCXXFLAGS} ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ + ${AccumulatedIncFlags} + + HFILES = *.h +diff -Nru fsl.orig/etc/fslconf/fsl.csh fsl/etc/fslconf/fsl.csh +--- fsl.orig/etc/fslconf/fsl.csh 2019-11-26 14:56:10.000000000 +0100 ++++ fsl/etc/fslconf/fsl.csh 2021-02-24 09:58:49.000000000 +0100 +@@ -25,8 +25,8 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-setenv FSLTCLSH $FSLDIR/bin/fsltclsh +-setenv FSLWISH $FSLDIR/bin/fslwish ++setenv FSLTCLSH tclsh ++setenv FSLWISH wish + + # The following variables are used for running code in parallel across + # several machines ( i.e. for FDT ) +diff -Nru fsl.orig/etc/fslconf/fsl-devel.sh fsl/etc/fslconf/fsl-devel.sh +--- fsl.orig/etc/fslconf/fsl-devel.sh 2019-11-26 14:56:10.000000000 +0100 ++++ fsl/etc/fslconf/fsl-devel.sh 2021-02-24 09:59:22.000000000 +0100 +@@ -26,8 +26,8 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-FSLTCLSH=$FSLDIR/bin/fsltclsh +-FSLWISH=$FSLDIR/bin/fslwish ++FSLTCLSH=tclsh ++FSLWISH=wish + + export FSLTCLSH FSLWISH + +diff -Nru fsl.orig/etc/fslconf/fsl.sh fsl/etc/fslconf/fsl.sh +--- fsl.orig/etc/fslconf/fsl.sh 2019-11-26 14:56:10.000000000 +0100 ++++ fsl/etc/fslconf/fsl.sh 2021-02-24 09:59:46.000000000 +0100 +@@ -26,8 +26,8 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-FSLTCLSH=$FSLDIR/bin/fsltclsh +-FSLWISH=$FSLDIR/bin/fslwish ++FSLTCLSH=tclsh ++FSLWISH=wish + + export FSLTCLSH FSLWISH + +diff -Nru fsl.orig/src/film/Makefile fsl/src/film/Makefile +--- fsl.orig/src/film/Makefile 2020-07-15 11:54:04.000000000 +0200 ++++ fsl/src/film/Makefile 2021-02-24 10:01:51.000000000 +0100 +@@ -28,7 +28,7 @@ + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} ftoz.o ${LIBS} + + film_gls:${OBJS} film_gls.o +- ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -l giftiio ++ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -lgiftiio + + film_gls_res:${OBJS} film_gls_res.o + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls_res.o ${LIBS} +diff -Nru fsl.orig/src/fslsurface/Makefile fsl/src/fslsurface/Makefile +--- fsl.orig/src/fslsurface/Makefile 2014-12-16 15:52:05.000000000 +0100 ++++ fsl/src/fslsurface/Makefile 2021-02-24 13:46:49.000000000 +0100 +@@ -37,7 +37,7 @@ + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} + + +-LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass ++LIBS=-lgiftiio -lexpat -lfirst_lib -lmeshclass -lglapi + + APPLY_ZLIB = -DHAVE_ZLIB + +diff -Nru fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile +--- fsl.orig/src/libmeshutils/Makefile 2014-12-16 15:20:18.000000000 +0100 ++++ fsl/src/libmeshutils/Makefile 2021-02-24 10:05:09.000000000 +0100 +@@ -3,7 +3,7 @@ + + PROJNAME = meshUtils + +-LD_LIBRARY_PATH=${FSLDIR}/lib ++#LD_LIBRARY_PATH=${FSLDIR}/lib + + USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} + USRLDFLAGS = -L${LIB_PROB} -L${LIB_NEWMAT} -L${LIB_ZLIB} +diff -Nru fsl.orig/src/mist/Makefile fsl/src/mist/Makefile +--- fsl.orig/src/mist/Makefile 2019-01-07 15:22:09.000000000 +0100 ++++ fsl/src/mist/Makefile 2021-02-24 10:07:34.000000000 +0100 +@@ -1,16 +1,16 @@ + include ${FSLCONFDIR}/default.mk + +-NLOPT_INC = ${FSLEXTINC} +-NLOPT_LIB = ${FSLEXTLIB} +-SQLITE_INC = ${FSLEXTINC}/libsqlite +-SQLITE_LIB = ${FSLEXTLIB} ++NLOPT_INC = ${EBROOTNLOPT}/include ++NLOPT_LIB = ${EBROOTNLOPT}/lib ++SQLITE_INC = ${EBROOTSQLITE}/include ++SQLITE_LIB = ${EBROOTSQLITE}/lib + + PROJNAME = mist + + XFILES = mist/mist + SCRIPTS = bin/mist_1_train bin/mist_2_fit bin/mist_FA_reg bin/mist_display bin/mist_mesh_utils + +-USRCXXFLAGS = -std=c++11 ++USRCXXFLAGS = -std=c++11 -DBOOST_LOG_DYN_LINK + USRINCFLAGS = -I${FSLDIR}/include/newimage -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_GDC} -I${INC_GD} -I${SQLITE_INC} -I${NLOPT_INC} -I${VTKDIR_INC} -Icommon + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_ZLIB} -L${LIB_BOOST} -L${LIB_GDC} -L${LIB_GD} -L${NLOPT_LIB} -L${VTKDIR_LIB} + diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.4_build_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.4_build_fixes.patch new file mode 100644 index 00000000000..87f47c8a180 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.4_build_fixes.patch @@ -0,0 +1,30 @@ +The master project 'ptx2' produces an error during compilation: +tractvolsx.h:311:29: error: call of overloaded ‘round(float)’ is ambiguous +It has therefore been disabled. +Also: EasyBuild creates the site-packages directory for the python +package 'fslpy' in the wrong place, so it must be created in the fsl +directory, before 'fslpy' is installed. 'fslpy' provides the tools +imglob and imcp, which would otherwise have to be provided by the conda +script fslpython. These tools *must* be in the fsl/bin directory. +Author: Henrik R. Nagel (NTNU) +diff -Nru fsl.orig/build fsl/build +--- fsl.orig/build 2020-06-29 17:30:36.000000000 +0200 ++++ fsl/build 2021-02-26 17:30:26.000000000 +0100 +@@ -114,7 +114,6 @@ + nma \ + oxford_asl \ + possum \ +- ptx2 \ + qboot \ + randomise \ + relax \ +@@ -165,4 +164,9 @@ + else + echo "Build failed to build all projects."; + fi ++ ++# Create the site-packages directory for fslpy ++mkdir -p lib/python3.7/site-packages ++ln -s lib lib64 ++ + exit $finalStatus diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.4_disable_cuda.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.4_disable_cuda.patch new file mode 100644 index 00000000000..837ac06229b --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.4_disable_cuda.patch @@ -0,0 +1,16 @@ +CUDA must now be disabled explicitly. +Author: Henrik R. Nagel (NTNU) +diff -Nru fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk +--- fsl.orig/config/buildSettings.mk 2020-06-19 15:48:02.000000000 +0200 ++++ fsl/config/buildSettings.mk 2021-02-25 18:27:52.000000000 +0100 +@@ -182,8 +182,8 @@ + #$(info GCC PAT VER $(GCCPAT)) + #Project specific variables + EDDYBUILDPARAMETERS = "cuda=1 CUDAVER=8.0" "cuda=1 CUDAVER=9.1" "cpu=1" +-fdt_MASTERBUILD = COMPILE_GPU = 1 +-ptx2_MASTERBUILD = COMPILE_GPU = 1 ++fdt_MASTERBUILD = COMPILE_GPU = 0 ++ptx2_MASTERBUILD = COMPILE_GPU = 0 + define newline + + From 21bf295042656420d56fa7a30d6b4f295d34c35d Mon Sep 17 00:00:00 2001 From: hrn Date: Wed, 3 Mar 2021 14:55:51 +0100 Subject: [PATCH 0144/9987] Added h5py dependency --- .../easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb index 67bcb389db5..da03b0def1a 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb @@ -50,12 +50,15 @@ dependencies = [ ('VTK', '8.2.0', versionsuffix), ('GSL', '2.6'), ('Qwt', '6.1.4'), + ('h5py', '2.10.0', versionsuffix), ] modextrapaths = {'PYTHONPATH': ['fsl/lib/python%(pyshortver)s/site-packages']} -# The executable file 'imcp' is a part of fslpy +# The executable files 'imglob' and 'imcp' come from fslpy exts_defaultclass = 'PythonPackage' +exts_download_dep_fail = True +exts_default_options = {'use_pip': True} exts_list = [ ('fslpy', '3.5.3', { From 3e0d4bff9b57c4fa50b40bfa0b976ec119898d88 Mon Sep 17 00:00:00 2001 From: hrn Date: Wed, 3 Mar 2021 17:54:11 +0100 Subject: [PATCH 0145/9987] Fixed syntax --- .../easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb index da03b0def1a..f61773e90bd 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.4-foss-2019b-Python-3.7.4.eb @@ -57,8 +57,10 @@ modextrapaths = {'PYTHONPATH': ['fsl/lib/python%(pyshortver)s/site-packages']} # The executable files 'imglob' and 'imcp' come from fslpy exts_defaultclass = 'PythonPackage' -exts_download_dep_fail = True -exts_default_options = {'use_pip': True} +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} exts_list = [ ('fslpy', '3.5.3', { From f36c897b397fcc3f3139e9ffe0e6f114677adc58 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Mar 2021 18:53:31 +0000 Subject: [PATCH 0146/9987] Addressed the suggested changes, merged 2 patch file into one --- .../FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 6 ++--- .../f/FLANN/FLANN-1.8.4_fix-cmake.patch | 27 ------------------- .../FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 5 ++-- ..._fix-cmake.patch => FLANN-fix-cmake.patch} | 11 +++++--- 4 files changed, 13 insertions(+), 36 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch rename easybuild/easyconfigs/f/FLANN/{FLANN-1.9.1_fix-cmake.patch => FLANN-fix-cmake.patch} (74%) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index 438121d4c3d..38bb91aac90 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -16,9 +16,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-fix-cmake.patch'] + checksums = [ 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz - '662e5972487a6616cbca36ac9459bcc3ca773ed781564ed2532d9792d97c2897', # cmake-flann-1.8.4.patch' + '0ab2575d78c27f7b4f42b69261a181a4d92f09baf391d6f386fc4b7f2380c33b', # FLANN-fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] @@ -29,8 +31,6 @@ dependencies = [ separate_build_dir = True -patches = ['%(name)s-%(version)s_fix-cmake.patch'] - configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch deleted file mode 100644 index db8f515db34..00000000000 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch +++ /dev/null @@ -1,27 +0,0 @@ -# Flann fails to build with newer versions of CMake, see: -# https://stackoverflow.com/questions/50763621/building-flann-with-cmake-fails -diff --git a/flann-1.8.4.orig/src/cpp/CMakeLists.txt b/flann-1.8.4/src/cpp/CMakeLists.txt -index 78a204a..d9b5777 100644 ---- a/flann-1.8.4.orig/src/cpp/CMakeLists.txt -+++ b/flann-1.8.4/src/cpp/CMakeLists.txt -@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB) - endif() - - if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) -- add_library(flann_cpp SHARED "") -+ add_library(flann_cpp SHARED empty.cpp) - set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) - target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) - -@@ -83,7 +83,7 @@ if (BUILD_C_BINDINGS) - set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) - - if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) -- add_library(flann SHARED "") -+ add_library(flann SHARED empty.cpp) - set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) - target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) - else() -diff --git a/flann-1.8.4/src/cpp/empty.cpp b/flann-1.8.4/src/cpp/empty.cpp -new file mode 100644 -index 0000000..e69de29 diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index aaef2f96e6a..b1d818c4301 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -16,9 +16,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-fix-cmake.patch'] + checksums = [ 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz - '479068a9f1c745780a7fbf55e6ba02011d5a6ca0a917ce0d4e11367c14a8cf78', # cmake-flann-1.9.1.patch + '0ab2575d78c27f7b4f42b69261a181a4d92f09baf391d6f386fc4b7f2380c33b', # FLANN-fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] @@ -29,7 +31,6 @@ dependencies = [ separate_build_dir = True -patches = ['%(name)s-%(version)s_fix-cmake.patch'] configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1_fix-cmake.patch b/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch similarity index 74% rename from easybuild/easyconfigs/f/FLANN/FLANN-1.9.1_fix-cmake.patch rename to easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch index 4f3c2fd45f9..78ff18ab065 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1_fix-cmake.patch +++ b/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch @@ -1,9 +1,12 @@ # Flann fails to build with newer versions of CMake, see: # https://stackoverflow.com/questions/50763621/building-flann-with-cmake-fails -diff --git a/flann-1.9.1.orig/src/cpp/CMakeLists.txt b/flann-1.9.1/src/cpp/CMakeLists.txt +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt index 49c53f0..0976e41 100644 ---- a/flann-1.9.1.orig/src/cpp/CMakeLists.txt -+++ b/flann-1.9.1/src/cpp/CMakeLists.txt +--- a/src/cpp/CMakeLists.txt ++++ b/src/cpp/CMakeLists.txt @@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB) endif() @@ -22,6 +25,6 @@ index 49c53f0..0976e41 100644 set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) else() -diff --git a/flann-1.9.1/src/cpp/empty.cpp b/flann-1.9.1/src/cpp/empty.cpp +diff --git a/src/cpp/empty.cpp b/flann-1.9.1/src/cpp/empty.cpp new file mode 100644 index 0000000..e69de29 From ad95d3bd6cc9330aa7878b1c8711dac6f7541651 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Mar 2021 18:56:50 +0000 Subject: [PATCH 0147/9987] Corrected patch-file --- easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch b/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch index 78ff18ab065..a1932dfb573 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch +++ b/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch @@ -25,6 +25,6 @@ index 49c53f0..0976e41 100644 set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) else() -diff --git a/src/cpp/empty.cpp b/flann-1.9.1/src/cpp/empty.cpp +diff --git a/src/cpp/empty.cpp b/src/cpp/empty.cpp new file mode 100644 index 0000000..e69de29 From c6a7159a23fe2652c5a9d6cb382704a9c49073d4 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Mar 2021 22:42:46 +0000 Subject: [PATCH 0148/9987] Corrected wrong builddep. and swapped lib over to include in sanity checks --- .../libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb | 2 +- .../l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb | 9 ++++++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb index 694e34a5a2a..2823fc58971 100644 --- a/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libbaseencode/libbaseencode-1.0.11-GCCcore-10.2.0.eb @@ -29,7 +29,7 @@ separate_build_dir = True sanity_check_paths = { 'files': ['lib/libbaseencode.%s' % SHLIB_EXT], - 'dirs': ['lib'], + 'dirs': ['include'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb index 5fd70b9bace..c2da1b819dd 100644 --- a/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libcotp/libcotp-1.2.3-GCCcore-10.2.0.eb @@ -18,19 +18,22 @@ checksums = ['f122aea37337cdfcdaa1ce979ecfb5177ad7dcb273caf2d6056820f1dbf92e93'] builddependencies = [ ('CMake', '3.18.4'), - ('libgcrypt', '1.9.2'), - ('libbaseencode', '1.0.11'), ('pkg-config', '0.29.2'), ('binutils', '2.35'), ] +dependencies = [ + ('libgcrypt', '1.9.2'), + ('libbaseencode', '1.0.11'), +] + parallel = 1 separate_build_dir = True sanity_check_paths = { 'files': ['lib/libcotp.%s' % SHLIB_EXT], - 'dirs': ['lib'], + 'dirs': ['include'], } moduleclass = 'lib' From 21ea1b000045f21575d9cf599ed0133456783856 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Mar 2021 23:12:35 +0000 Subject: [PATCH 0149/9987] Checksum updated in EC files --- .../easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index 38bb91aac90..e13b4bfa6cc 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -20,7 +20,7 @@ patches = ['%(name)s-fix-cmake.patch'] checksums = [ 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz - '0ab2575d78c27f7b4f42b69261a181a4d92f09baf391d6f386fc4b7f2380c33b', # FLANN-fix-cmake.patch + '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index b1d818c4301..35ecc703705 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -20,7 +20,7 @@ patches = ['%(name)s-fix-cmake.patch'] checksums = [ 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz - '0ab2575d78c27f7b4f42b69261a181a4d92f09baf391d6f386fc4b7f2380c33b', # FLANN-fix-cmake.patch + '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] From 9f3845074e2fd33358f27891cc329737b308c208 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 29 Jan 2021 14:39:36 +0000 Subject: [PATCH 0150/9987] [esl] update lipspio to 0.2.4 and gcc 10.2.0 --- .../l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb new file mode 100644 index 00000000000..93bb74df602 --- /dev/null +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpspio' +version = '0.2.4' + +homepage = 'https://gitlab.e-cam2020.eu/esl/pspio/' +description = """libpspio is a library to read and write pseudopotentials in multiple formats.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://gitlab.e-cam2020.eu/esl/pspio/uploads/7efa924be97bd46354237ca3fb89495e/'] +checksums = ['740861617e1feb50a9e00609769b12d8'] + +configopts = ' --enable-gsl --enable-fortran ' + +dependencies = [('GSL', '2.6')] + +sanity_check_paths = { + 'files': ['include/pspiof_m.mod', 'include/pspio.h'] + [('lib/libpspiof.a', 'lib64/libpspiof.a')], + 'dirs': [], +} + +moduleclass = 'phys' From 34a8f948f53cd2c931ab14eed42636333c57dad1 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 29 Jan 2021 13:47:47 +0000 Subject: [PATCH 0151/9987] [esl] add libfdf --- .../l/libfdf/libfdf-0.2.2-foss-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b.eb new file mode 100644 index 00000000000..b3aa3054822 --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' + +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': False} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +preconfigopts = 'unset MPIFC && unset MPICC && ' +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', ('lib/libfdf.a', 'lib64/libfdf.a')], + 'dirs': ['include'], +} + +moduleclass = 'data' From e49abd1841c7f113b88efb6d61c256d19ed7778f Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 22 Mar 2021 21:03:59 +0000 Subject: [PATCH 0152/9987] Name of patchfile changed as requested --- .../f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 4 ++-- .../{FLANN-fix-cmake.patch => FLANN-1.8.4_fix-cmake.patch} | 0 .../f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/f/FLANN/{FLANN-fix-cmake.patch => FLANN-1.8.4_fix-cmake.patch} (100%) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index e13b4bfa6cc..6bae6453023 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -16,11 +16,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-fix-cmake.patch'] +patches = ['%(name)s-%(version)s_fix-cmake.patch'] checksums = [ 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz - '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-fix-cmake.patch + '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-1.8.4_fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch similarity index 100% rename from easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch rename to easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index 35ecc703705..a8e0f8d3ec0 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -16,11 +16,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-fix-cmake.patch'] +patches = ['%(name)s-1.8.4_fix-cmake.patch'] checksums = [ 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz - '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-fix-cmake.patch + '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-1.8.4_fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] From f6a4cfb682d04b4832c525e56e9df8eedf10d789 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Mar 2021 18:34:04 +0100 Subject: [PATCH 0153/9987] adding easyconfigs: segemehl-0.3.4-iccifort-2020.4.304.eb --- .../segemehl-0.3.4-iccifort-2020.4.304.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..7a0308a476a --- /dev/null +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = "segemehl" +version = "0.3.4" + +homepage = 'https://www.bioinf.uni-leipzig.de/Software/segemehl/' +description = """segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping + and split read mapping.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] + +dependencies = [ + ('HTSlib', '1.11'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +buildopts = 'all' + +files_to_copy = [(["haarz.x", "segemehl.x"], "bin")] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["haarz.x", "segemehl.x"]], + 'dirs': [] +} + +moduleclass = 'bio' From fba0e0e4f715e490b0a6faa028f419428d39a5c4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 09:45:29 +0200 Subject: [PATCH 0154/9987] adding easyconfigs: IMOD-4.11.0.eb --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb | 47 +++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb new file mode 100644 index 00000000000..15db60b3649 --- /dev/null +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb @@ -0,0 +1,47 @@ +# Thomas Hoffmann, EMBL, Heidelberg, structures-it@embl.de, 2021/3; +# based on generic Binary instead of imod.py easyblock. +name = 'IMOD' +version = '4.11.0' +easyblock = 'Binary' + + +homepage = 'https://bio3d.colorado.edu/imod/' +description = """IMOD is a set of image processing, modeling and display +programs used for tomographic reconstruction and for 3D reconstruction of EM +serial sections and optical sections. The package contains tools for assembling +and aligning data within multiple types and sizes of image stacks, viewing 3-D +data from any orientation, and modeling and display of the image files. IMOD +was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim +Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" + +toolchain = {'name': 'system', 'version': 'system'} + +source_urls = ['http://bio3d.colorado.edu/ftp/latestIMOD/RHEL7-64_CUDA8.0/'] +sources = [ + { + 'filename': '%(namelower)s_%(version)s.sh', + 'download_filename': '%(namelower)s_%(version)s_RHEL7-64_CUDA8.0.sh' + } +] +checksums = ['748101eaa5f2ce6f206fb0c888d3095df8a700f4f9c4a931a656a97fe4bc197e'] + +install_cmd = ' ./%(namelower)s_%(version)s.sh ' +installopts = '-dir %(installdir)s -script %(installdir)s -name tmpinst -skip -yes' +postinstallcmds = ['mv %(installdir)s/tmpinst/* %(installdir)s && rm -rf %(installdir)s/tmpinst'] +dependencies = [ + ('Java', '11.0.2'), +] +modextravars = { + 'IMOD_DIR': "%(installdir)s", + 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', + 'IMOD_QTLIBDIR': '%(installdir)s/qtlib', + 'IMOD_JAVADIR': '$JAVA_HOME', + 'FOR_DISABLE_STACK_TRACE': '1', +} +modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.' +# Observed problems with alias on a tcl based module system. Use bin/subm python +# script instead. +# modaliases = { +# 'subm': 'submfg $* &' +# } +moduleclass = 'vis' From b6ee41506d545dc465fed885f18269dada9cae5e Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 12:00:49 +0200 Subject: [PATCH 0155/9987] added sanity check paths --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb index 15db60b3649..12edf685034 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb @@ -39,9 +39,14 @@ modextravars = { 'FOR_DISABLE_STACK_TRACE': '1', } modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.' -# Observed problems with alias on a tcl based module system. Use bin/subm python -# script instead. +# Observed problems with alias on a tcl based module system. Use bin/subm python script instead. # modaliases = { # 'subm': 'submfg $* &' # } +sanity_check_paths = { + 'files': ['VERSION'], + 'dirs': ['bin', 'lib', 'com', 'autodoc', 'qtlib', 'pylib', 'Plugins', 'man', 'SystemTemplate'], +} + + moduleclass = 'vis' From d4ebb5c0c4b7467583e2a1e4772ae8756c14686e Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 12:23:37 +0200 Subject: [PATCH 0156/9987] fix source_urls --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb index 12edf685034..aa3ab5acc4e 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb @@ -16,7 +16,7 @@ Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" toolchain = {'name': 'system', 'version': 'system'} -source_urls = ['http://bio3d.colorado.edu/ftp/latestIMOD/RHEL7-64_CUDA8.0/'] +source_urls = ['https://bio3d.colorado.edu/imod/AMD64-RHEL5/'] sources = [ { 'filename': '%(namelower)s_%(version)s.sh', From ab804dca8ed6c29778db4ad89128b7d4ee7b6e07 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 1 Apr 2021 14:27:09 +0200 Subject: [PATCH 0157/9987] add 4.11.5 --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb | 52 +++++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb new file mode 100644 index 00000000000..f84a59fccc0 --- /dev/null +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb @@ -0,0 +1,52 @@ +# Thomas Hoffmann, EMBL, Heidelberg, structures-it@embl.de, 2021/4; +# based on generic Binary instead of imod.py easyblock. +name = 'IMOD' +version = '4.11.5' +easyblock = 'Binary' + + +homepage = 'https://bio3d.colorado.edu/imod/' +description = """IMOD is a set of image processing, modeling and display +programs used for tomographic reconstruction and for 3D reconstruction of EM +serial sections and optical sections. The package contains tools for assembling +and aligning data within multiple types and sizes of image stacks, viewing 3-D +data from any orientation, and modeling and display of the image files. IMOD +was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim +Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" + +toolchain = {'name': 'system', 'version': 'system'} + +source_urls = ['https://bio3d.colorado.edu/imod/AMD64-RHEL5/'] +sources = [ + { + 'filename': '%(namelower)s_%(version)s.sh', + 'download_filename': '%(namelower)s_%(version)s_RHEL7-64_CUDA10.1.sh' + } +] +checksums = ['d1791322e5970bf1e4d11ca703be1a96aee385671f8da56a2502441a9402024a'] + +install_cmd = ' ./%(namelower)s_%(version)s.sh ' +installopts = '-dir %(installdir)s -script %(installdir)s -name tmpinst -skip -yes' +postinstallcmds = ['mv %(installdir)s/tmpinst/* %(installdir)s && rm -rf %(installdir)s/tmpinst'] +dependencies = [ + ('Java', '11.0.2'), +] +modextravars = { + 'IMOD_DIR': "%(installdir)s", + 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', + 'IMOD_QTLIBDIR': '%(installdir)s/qtlib', + 'IMOD_JAVADIR': '$JAVA_HOME', + 'FOR_DISABLE_STACK_TRACE': '1', +} +modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.' +# Observed problems with alias on a tcl based module system. Use bin/subm python script instead. +# modaliases = { +# 'subm': 'submfg $* &' +# } +sanity_check_paths = { + 'files': ['VERSION'], + 'dirs': ['bin', 'lib', 'com', 'autodoc', 'qtlib', 'pylib', 'Plugins', 'man', 'SystemTemplate'], +} + + +moduleclass = 'vis' From f681fb1cf42b1881a21ba1786f99170eabd28b98 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 6 Apr 2021 12:53:08 +0200 Subject: [PATCH 0158/9987] toolchain SYSTEM; Python3 dependency --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb | 8 +++++++- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb | 7 ++++++- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb index aa3ab5acc4e..11516244f7b 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb @@ -14,7 +14,7 @@ data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" -toolchain = {'name': 'system', 'version': 'system'} +toolchain = SYSTEM source_urls = ['https://bio3d.colorado.edu/imod/AMD64-RHEL5/'] sources = [ @@ -31,6 +31,12 @@ postinstallcmds = ['mv %(installdir)s/tmpinst/* %(installdir)s && rm -rf %(insta dependencies = [ ('Java', '11.0.2'), ] +multi_deps = { + 'Python': [ + '3.8.6-GCCcore-10.2.0', + '3.8.2-GCCcore-9.3.0', + '3.7.4-GCCcore-8.3.0']} + modextravars = { 'IMOD_DIR': "%(installdir)s", 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb index f84a59fccc0..743058e88e7 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb @@ -14,7 +14,7 @@ data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" -toolchain = {'name': 'system', 'version': 'system'} +toolchain = SYSTEM source_urls = ['https://bio3d.colorado.edu/imod/AMD64-RHEL5/'] sources = [ @@ -31,6 +31,11 @@ postinstallcmds = ['mv %(installdir)s/tmpinst/* %(installdir)s && rm -rf %(insta dependencies = [ ('Java', '11.0.2'), ] +multi_deps = { + 'Python': [ + '3.8.6-GCCcore-10.2.0', + '3.8.2-GCCcore-9.3.0', + '3.7.4-GCCcore-8.3.0']} modextravars = { 'IMOD_DIR': "%(installdir)s", 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', From 24ea0b15007e29eddb9443847ff42f9417957b20 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 8 Apr 2021 15:11:07 +0200 Subject: [PATCH 0159/9987] add ECs for build from source on foss(cuda)/2020b --- .../i/IMOD/IMOD-4.11.5-foss-2020b.eb | 80 ++++++++++++++++ .../i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 92 +++++++++++++++++++ 2 files changed, 172 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb new file mode 100644 index 00000000000..ed59ad6eb9b --- /dev/null +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -0,0 +1,80 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04 +easyblock = 'ConfigureMake' + +name = 'IMOD' +version = '4.11.5' + +homepage = 'https://bio3d.colorado.edu/imod/' +description = """IMOD is a set of image processing, modeling and display +programs used for tomographic reconstruction and for 3D reconstruction of EM +serial sections and optical sections. The package contains tools for assembling +and aligning data within multiple types and sizes of image stacks, viewing 3-D +data from any orientation, and modeling and display of the image files. IMOD +was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim +Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +sources = [SOURCE_TAR_GZ] +# mercurial repository +# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD +# get lunch +# cd IMOD +# hg update -r IMOD_4-11-5 +# cd .. +# tar czf IMOD-4.11.5.tar.gz IMOD + + +dependencies = [ + ('LibTIFF', '4.1.0'), + ('Qt5', '5.14.2'), + ('Java', '13.0.2', '', True), + ('HDF5', '1.10.7'), + ('Python', '3.8.6'), +] + +# modify all qmake pro files in order to pass CFLAGS +local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&" + +# exports required for configure and build +local_exports = 'export QTDIR=$EBROOTQT5 &&' +local_exports += 'export HDF5_DIR=$EBROOTHDF5 &&' +local_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&' +# readw_or_imod.f and others with gfortran10: +# Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2)) +# => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0. +local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&' # required for gfortran10 + +preconfigopts = local_exports +preconfigopts += local_qmake_pass_cflags + +# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. +# CFLAGs are passed with -flags. +configure_cmd = './setup ' +configure_cmd += '-flags "$CFLAGS" ' # inject CFLAGS +configure_cmd += '-i %(installdir)s ' # set installdir +configure_cmd += ' #' # avoid passing unknown arg --prefix + +prebuildopts = local_exports + +# create some missing directories required for installation process: +preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&' + +modextravars = { + 'IMOD_DIR': "%(installdir)s", + 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', + 'IMOD_JAVADIR': '$JAVA_HOME', + 'FOR_DISABLE_STACK_TRACE': '1', +} +modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.' +# Observed problems with alias on a tcl based module system. Use bin/subm python script instead. +# modaliases = { +# 'subm': 'submfg $* &' +# } +sanity_check_paths = { + 'files': ['VERSION', 'bin/subm'], + 'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb new file mode 100644 index 00000000000..d8a23a6cc5f --- /dev/null +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -0,0 +1,92 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04 +easyblock = 'ConfigureMake' + +name = 'IMOD' +version = '4.11.5' + +homepage = 'https://bio3d.colorado.edu/imod/' +description = """IMOD is a set of image processing, modeling and display +programs used for tomographic reconstruction and for 3D reconstruction of EM +serial sections and optical sections. The package contains tools for assembling +and aligning data within multiple types and sizes of image stacks, viewing 3-D +data from any orientation, and modeling and display of the image files. IMOD +was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim +Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] + +sources = [SOURCE_TAR_GZ] +# mercurial repository +# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD +# get lunch +# cd IMOD +# hg update -r IMOD_4-11-5 +# cd .. +# tar czf IMOD-4.11.5.tar.gz IMOD + + +dependencies = [ + ('LibTIFF', '4.1.0'), + ('Qt5', '5.14.2'), + ('Java', '13.0.2', '', True), + ('HDF5', '1.10.7'), + ('Python', '3.8.6'), +] + +# replace hardcoded CUDA compute capabilitites in machines/rhlinux. +local_cuda_replace = 'echo %(cuda_cc_space_sep)s|sed "s/\\.//g"|' +local_cuda_replace += ' awk \'{' +local_cuda_replace += ' printf "-arch sm_"$1; ' +local_cuda_replace += ' for (i=1;i<=NF; i++){printf(" -gencode=arch=compute_%s,code=sm_%s",$i,$i) } ' +local_cuda_replace += ' }\'' +local_cudaarch_sed = 'sed -i "s/-arch sm_35/`' + local_cuda_replace + '`/g" machines/rhlinux &&' + +# modify all qmake pro files in order to pass CFLAGS +local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&" + +# exports required for configure and build +local_exports = 'export QTDIR=$EBROOTQT5 &&' +local_exports += 'export HDF5_DIR=$EBROOTHDF5 &&' +local_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&' +local_exports += 'export CUDA_DIR=$CUDA_HOME &&' +# readw_or_imod.f and others with gfortran10: +# Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2)) +# => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0. +local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&' # required for gfortran10 + +preconfigopts = local_exports +preconfigopts += local_cudaarch_sed +preconfigopts += local_qmake_pass_cflags + +# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. +# CFLAGs are passed with -flags. +configure_cmd = './setup ' +configure_cmd += '-flags "$CFLAGS" ' # inject CFLAGS +configure_cmd += '-i %(installdir)s ' # set installdir +configure_cmd += ' #' # avoid passing unknown arg --prefix + +prebuildopts = local_exports + +# create some missing directories required for installation process: +preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&' + +modextravars = { + 'IMOD_DIR': "%(installdir)s", + 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', + 'IMOD_JAVADIR': '$JAVA_HOME', + 'FOR_DISABLE_STACK_TRACE': '1', +} +modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.' +# Observed problems with alias on a tcl based module system. Use bin/subm python script instead. +# modaliases = { +# 'subm': 'submfg $* &' +# } +sanity_check_paths = { + 'files': ['VERSION', 'bin/subm'], + 'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'], +} + +moduleclass = 'vis' From c24eae97425c07f33b522cb96a99578acf15d6a3 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 8 Apr 2021 16:05:36 +0200 Subject: [PATCH 0160/9987] add checksums. downgrade dependency Java to 11. --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb | 4 +++- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index ed59ad6eb9b..1758cf4d8a7 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -17,6 +17,8 @@ toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCE_TAR_GZ] +checksums = ['5c50f1457134fe5113b95e0939d3181b948d211f25d9a05ad2b4ec0f23251c79'] + # mercurial repository # hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD # get lunch @@ -29,7 +31,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('LibTIFF', '4.1.0'), ('Qt5', '5.14.2'), - ('Java', '13.0.2', '', True), + ('Java', '11', '', True), ('HDF5', '1.10.7'), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index d8a23a6cc5f..803e0308fe5 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -19,6 +19,8 @@ toolchainopts = {'pic': True, 'openmp': True} cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] sources = [SOURCE_TAR_GZ] +checksums = ['5c50f1457134fe5113b95e0939d3181b948d211f25d9a05ad2b4ec0f23251c79'] + # mercurial repository # hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD # get lunch @@ -31,7 +33,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('LibTIFF', '4.1.0'), ('Qt5', '5.14.2'), - ('Java', '13.0.2', '', True), + ('Java', '11', '', True), ('HDF5', '1.10.7'), ('Python', '3.8.6'), ] From 380dc45074e9d280e086735f7bb6a7efe83f32b9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Apr 2021 19:50:07 +0200 Subject: [PATCH 0161/9987] adding easyconfigs: WPS-4.2-foss-2020b-dmpar.eb, WRF-4.2.2-foss-2020b-dmpar.eb and patches: WPS-4.2_netCDF-Fortran_seperate_path.patch, WPS-4.2_GCC-10-allow-argument-mismatch.patch, WRF-4.2.2_netCDF-Fortran_separate_path.patch --- .../w/WPS/WPS-4.2-foss-2020b-dmpar.eb | 40 +++ ...S-4.2_GCC-10-allow-argument-mismatch.patch | 49 ++++ ...WPS-4.2_netCDF-Fortran_seperate_path.patch | 90 ++++++ .../w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb | 43 +++ ...F-4.2.2_netCDF-Fortran_separate_path.patch | 262 ++++++++++++++++++ 5 files changed, 484 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.2-foss-2020b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.2_GCC-10-allow-argument-mismatch.patch create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.2_netCDF-Fortran_seperate_path.patch create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.2.2_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.2-foss-2020b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.2-foss-2020b-dmpar.eb new file mode 100644 index 00000000000..7161c17020c --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.2-foss-2020b-dmpar.eb @@ -0,0 +1,40 @@ +name = 'WPS' +version = '4.2' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WPS-%(version)s_netCDF-Fortran_seperate_path.patch', + 'WPS-%(version)s_GCC-10-allow-argument-mismatch.patch', +] +checksums = [ + '3e175d033355d3e7638be75bc7c0bc0de6da299ebd175a9bbc1b7a121acd0168', # v4.2.tar.gz + '25359a9abfc6a4afc2f7b9624727eeea47d1a6421b99dbc8dd9b54a37d378ae5', # WPS-4.2_netCDF-Fortran_seperate_path.patch + 'c195d82e189780631b8c31110199b09a52e447b47fe2dd31d86dc86846a61148', # WPS-4.2_GCC-10-allow-argument-mismatch.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +builddependencies = [ + ('Perl', '5.32.0'), +] + +dependencies = [ + ('WRF', '4.2.2', versionsuffix), + ('JasPer', '2.0.24'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.2_GCC-10-allow-argument-mismatch.patch b/easybuild/easyconfigs/w/WPS/WPS-4.2_GCC-10-allow-argument-mismatch.patch new file mode 100644 index 00000000000..057ef629107 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.2_GCC-10-allow-argument-mismatch.patch @@ -0,0 +1,49 @@ +see https://github.com/wrf-model/WRF/issues/1250 and https://github.com/wrf-model/WRF/pull/1251 + +diff -ru WPS-4.2.orig/arch/configure.defaults WPS-4.2/arch/configure.defaults +--- WPS-4.2.orig/arch/configure.defaults 2020-04-23 21:31:06.000000000 +0200 ++++ WPS-4.2/arch/configure.defaults 2021-04-14 18:50:05.340985134 +0200 +@@ -157,8 +157,8 @@ + FC = CONFIGURE_FC + CC = CONFIGURE_CC + LD = $(FC) +-FFLAGS = -ffree-form -O -fconvert=big-endian -frecord-marker=4 +-F77FLAGS = -ffixed-form -O -fconvert=big-endian -frecord-marker=4 ++FFLAGS = -ffree-form -O -fconvert=big-endian -frecord-marker=4 -fallow-argument-mismatch -fallow-invalid-boz ++F77FLAGS = -ffixed-form -O -fconvert=big-endian -frecord-marker=4 -fallow-argument-mismatch -fallow-invalid-boz + FCSUFFIX = + FNGFLAGS = $(FFLAGS) + LDFLAGS = +@@ -180,8 +180,8 @@ + FC = CONFIGURE_FC + CC = CONFIGURE_CC + LD = $(FC) +-FFLAGS = -ffree-form -O -fconvert=big-endian -frecord-marker=4 +-F77FLAGS = -ffixed-form -O -fconvert=big-endian -frecord-marker=4 ++FFLAGS = -ffree-form -O -fconvert=big-endian -frecord-marker=4 -fallow-argument-mismatch -fallow-invalid-boz ++F77FLAGS = -ffixed-form -O -fconvert=big-endian -frecord-marker=4 -fallow-argument-mismatch -fallow-invalid-boz + FCSUFFIX = + FNGFLAGS = $(FFLAGS) + LDFLAGS = +@@ -450,8 +450,8 @@ + FC = CONFIGURE_FC + CC = CONFIGURE_CC + LD = $(FC) +-FFLAGS = -ffree-form -O -fconvert=big-endian -frecord-marker=4 +-F77FLAGS = -ffixed-form -O -fconvert=big-endian -frecord-marker=4 ++FFLAGS = -ffree-form -O -fconvert=big-endian -frecord-marker=4 -fallow-argument-mismatch -fallow-invalid-boz ++F77FLAGS = -ffixed-form -O -fconvert=big-endian -frecord-marker=4 -fallow-argument-mismatch -fallow-invalid-boz + FCSUFFIX = + FNGFLAGS = $(FFLAGS) + LDFLAGS = +@@ -475,8 +475,8 @@ + FC = CONFIGURE_FC + CC = CONFIGURE_CC + LD = $(FC) +-FFLAGS = -ffree-form -O -fconvert=big-endian -frecord-marker=4 +-F77FLAGS = -ffixed-form -O -fconvert=big-endian -frecord-marker=4 ++FFLAGS = -ffree-form -O -fconvert=big-endian -frecord-marker=4 -fallow-argument-mismatch -fallow-invalid-boz ++F77FLAGS = -ffixed-form -O -fconvert=big-endian -frecord-marker=4 -fallow-argument-mismatch -fallow-invalid-boz + FCSUFFIX = + FNGFLAGS = $(FFLAGS) + # For a WRF OpenMP build, add the gomp library for WPS diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.2_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.2_netCDF-Fortran_seperate_path.patch new file mode 100644 index 00000000000..c4bd7bc75f9 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.2_netCDF-Fortran_seperate_path.patch @@ -0,0 +1,90 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since 2013; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain +# +# updated for WPS v4.1 by Kenneth Hoste (HPC-UGent) +# updated for WPS v4.2 by Åke Sandgren (HPC2N) + +diff -ru WPS-4.2.orig/arch/Config.pl WPS-4.2/arch/Config.pl +--- WPS-4.2.orig/arch/Config.pl 2020-04-23 21:31:06.000000000 +0200 ++++ WPS-4.2/arch/Config.pl 2021-04-14 13:11:31.470659452 +0200 +@@ -41,6 +41,7 @@ + if(substr( $ARGV[0], 1, 8 ) eq "netcdff=") + { + $sw_netcdff_lib = substr( $ARGV[0], 9); ++ $sw_netcdff_lib =~ s/!/ /g ; + } + if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") + { +diff -ru WPS-4.2.orig/arch/preamble WPS-4.2/arch/preamble +--- WPS-4.2.orig/arch/preamble 2020-04-23 21:31:06.000000000 +0200 ++++ WPS-4.2/arch/preamble 2021-04-14 13:11:31.470659452 +0200 +@@ -39,7 +39,7 @@ + -I$(WRF_DIR)/external/io_grib1 \ + -I$(WRF_DIR)/external/io_int \ + -I$(WRF_DIR)/inc \ +- -I$(NETCDF)/include ++ -I$(NETCDF)/include -I$(NETCDFF)/include + + WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ + -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ +diff -ru WPS-4.2.orig/configure WPS-4.2/configure +--- WPS-4.2.orig/configure 2020-04-23 21:31:06.000000000 +0200 ++++ WPS-4.2/configure 2021-04-14 13:11:31.470659452 +0200 +@@ -119,9 +119,14 @@ + echo "Will use NETCDF in dir: $NETCDF" + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available +- NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then +- NETCDFF="-lnetcdff" ++ USENETCDFF=" " ++ # for netCDF 4.2 and greater, the Fortran library is a seperate install ++ if [ -z "$NETCDFF" ] ++ then ++ NETCDFF=$NETCDF ++ fi ++ if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-lnetcdff" + fi + else + echo "Will configure for use without NetCDF" +@@ -190,7 +195,7 @@ + fi + + # Found perl, so proceed with configuration +-perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$NETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir ++perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$USENETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir + + + #Checking cross-compiling capability for some particular environment +@@ -356,9 +361,9 @@ + end program + EOF + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -lnetcdf $USENETCDFF > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + ./fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then +diff -ru WPS-4.2.orig/util/src/Makefile WPS-4.2/util/src/Makefile +--- WPS-4.2.orig/util/src/Makefile 2020-04-23 21:31:06.000000000 +0200 ++++ WPS-4.2/util/src/Makefile 2021-04-14 13:11:31.470659452 +0200 +@@ -41,11 +41,11 @@ + write_met_module.o misc_definitions_module.o met_data_module.o + $(SFC) $(LDFLAGS) -o $@ elev_angle.o cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o met_data_module.o \ +- -L$(NETCDF)/lib -I$(NETCDF)/include -lnetcdf ++ -L$(NETCDFF)/lib -I$(NETCDFF)/include -lnetcdff + + elev_angle.o: elev_angle.F cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o +- $(SFC) -c elev_angle.F -I$(NETCDF)/include ++ $(SFC) -c elev_angle.F -I$(NETCDFF)/include + + calc_ecmwf_p.exe: calc_ecmwf_p.o cio.o module_debug.o module_stringutil.o gridinfo_module.o read_met_module.o \ + write_met_module.o module_date_pack.o misc_definitions_module.o met_data_module.o constants_module.o diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb new file mode 100644 index 00000000000..20b645cfdbc --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.2.2-foss-2020b-dmpar.eb @@ -0,0 +1,43 @@ +name = 'WRF' +version = '4.2.2' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', +] +checksums = [ + '7be2968c67c2175cd40b57118d9732eda5fdb0828edaa25baf57cc289da1a9b8', # v4.2.2.tar.gz + 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + 'fcc0d0c9604a1aba83b665594e945fb8f3b79ecb9f69df3f2874e273a40ce3d9', # WRF-4.2.2_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20200321'), + ('tcsh', '6.22.03'), + ('time', '1.9'), + ('Perl', '5.32.0'), +] + +dependencies = [ + ('JasPer', '2.0.24'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.2.2_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.2.2_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..e081a75bb3d --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.2.2_netCDF-Fortran_separate_path.patch @@ -0,0 +1,262 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since WRF3.5; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain +# +# Adapted to WRF 4.2.2 by Åke Sandgren (HPC2N) + +diff -ru WRF-4.2.2.orig/arch/Config.pl WRF-4.2.2/arch/Config.pl +--- WRF-4.2.2.orig/arch/Config.pl 2021-01-15 18:21:58.000000000 +0100 ++++ WRF-4.2.2/arch/Config.pl 2021-04-14 13:45:56.203965507 +0200 +@@ -8,6 +8,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; # for netCDF 4.2 and greater, Fortran lib might be in a different path + $sw_pnetcdf_path = "" ; + $sw_hdf5_path=""; + $sw_phdf5_path=""; +@@ -90,6 +91,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -117,6 +122,7 @@ + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { + $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -443,6 +449,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ; + $_ =~ s/CONFIGURE_PHDF5_PATH/$sw_phdf5_path/g ; +@@ -489,7 +496,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +diff -ru WRF-4.2.2.orig/arch/configure.defaults WRF-4.2.2/arch/configure.defaults +--- WRF-4.2.2.orig/arch/configure.defaults 2021-01-15 18:21:58.000000000 +0100 ++++ WRF-4.2.2/arch/configure.defaults 2021-04-14 13:45:56.203965507 +0200 +@@ -1602,6 +1602,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +diff -ru WRF-4.2.2.orig/arch/conf_tokens WRF-4.2.2/arch/conf_tokens +--- WRF-4.2.2.orig/arch/conf_tokens 2021-01-15 18:21:58.000000000 +0100 ++++ WRF-4.2.2/arch/conf_tokens 2021-04-14 13:45:56.207965495 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDFF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -ru WRF-4.2.2.orig/arch/postamble WRF-4.2.2/arch/postamble +--- WRF-4.2.2.orig/arch/postamble 2021-01-15 18:21:58.000000000 +0100 ++++ WRF-4.2.2/arch/postamble 2021-04-14 13:45:56.207965495 +0200 +@@ -52,7 +52,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/wrftladj \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ +- -I$(NETCDFPATH)/include \ ++ -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include \ + CONFIGURE_RTTOV_INC + REGISTRY = Registry + CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE +@@ -62,6 +62,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + RTTOVPATH = CONFIGURE_RTTOV_PATH +@@ -93,13 +94,13 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_pnf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \ +- make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ ++ make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ + FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_grib_share : +diff -ru WRF-4.2.2.orig/configure WRF-4.2.2/configure +--- WRF-4.2.2.orig/configure 2021-01-15 18:21:58.000000000 +0100 ++++ WRF-4.2.2/configure 2021-04-14 13:45:56.207965495 +0200 +@@ -183,9 +183,13 @@ + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then + USENETCDFF="-lnetcdff" + else +- USENETCDFF=" " ++ if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++ else ++ USENETCDFF=" " ++ fi + fi +- if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib/libnetcdf.dll.a" ] ; then ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" -o -f "$NETCDF/lib/libnetcdf.dll.a" ] ; then + USENETCDF="-lnetcdf" + else + USENETCDF=" " +@@ -552,7 +556,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -634,14 +638,14 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +diff -ru WRF-4.2.2.orig/external/io_netcdf/makefile WRF-4.2.2/external/io_netcdf/makefile +--- WRF-4.2.2.orig/external/io_netcdf/makefile 2021-01-15 18:21:58.000000000 +0100 ++++ WRF-4.2.2/external/io_netcdf/makefile 2021-04-14 13:45:56.207965495 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so -o -f $(NETCDFPATH)/lib/libnetcdff.dll.a \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib64/libnetcdff.a -o -f $(NETCDFFPATH)/lib64/libnetcdff.so -o -f $(NETCDFPATH)/lib/libnetcdff.dll.a \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -ru WRF-4.2.2.orig/external/io_pnetcdf/Makefile WRF-4.2.2/external/io_pnetcdf/Makefile +--- WRF-4.2.2.orig/external/io_pnetcdf/Makefile 2021-01-15 18:21:58.000000000 +0100 ++++ WRF-4.2.2/external/io_pnetcdf/Makefile 2021-04-14 13:45:56.207965495 +0200 +@@ -9,8 +9,8 @@ + ext_pnc_put_var_td.code \ + ext_pnc_put_var_ti.code \ + transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = -L$(NETCDFPATH)/lib -lpnetcdf ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = -L$(NETCDFFPATH)/lib -lpnetcdf + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -25,15 +25,15 @@ + $(RANLIB) libwrfio_pnf.a + + wrf_io.o: wrf_io.F90 $(CODE) +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f + $(FC) $(FFLAGS) -c wrf_io.f + + module_wrfsi_static.o: module_wrfsi_static.F90 +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f + $(FC) $(FFLAGS) -c module_wrfsi_static.f + + field_routines.o: field_routines.F90 wrf_io.o +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f + $(FC) $(FFLAGS) -c field_routines.f + + superclean: +diff -ru WRF-4.2.2.orig/Makefile WRF-4.2.2/Makefile +--- WRF-4.2.2.orig/Makefile 2021-01-15 18:21:58.000000000 +0100 ++++ WRF-4.2.2/Makefile 2021-04-14 13:45:56.207965495 +0200 +@@ -976,7 +976,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \ + FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ +@@ -1106,7 +1106,7 @@ + + # rule used by configure to test if this will compile with netcdf4 + nc4_test: +- @cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib $(USENETCDF) ; cd .. ++ @cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 $(USENETCDF) ; cd .. + + # rule used by configure to test if Fortran 2003 IEEE signaling is available + fortran_2003_ieee_test: From 3ae4f7cf5545a80aef3bc98768a7654d266aa46f Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 15 Apr 2021 11:24:55 +0200 Subject: [PATCH 0162/9987] Delete IMOD-4.11.5.eb build from source should be the preferred way --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb | 57 --------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb deleted file mode 100644 index 743058e88e7..00000000000 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5.eb +++ /dev/null @@ -1,57 +0,0 @@ -# Thomas Hoffmann, EMBL, Heidelberg, structures-it@embl.de, 2021/4; -# based on generic Binary instead of imod.py easyblock. -name = 'IMOD' -version = '4.11.5' -easyblock = 'Binary' - - -homepage = 'https://bio3d.colorado.edu/imod/' -description = """IMOD is a set of image processing, modeling and display -programs used for tomographic reconstruction and for 3D reconstruction of EM -serial sections and optical sections. The package contains tools for assembling -and aligning data within multiple types and sizes of image stacks, viewing 3-D -data from any orientation, and modeling and display of the image files. IMOD -was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim -Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" - -toolchain = SYSTEM - -source_urls = ['https://bio3d.colorado.edu/imod/AMD64-RHEL5/'] -sources = [ - { - 'filename': '%(namelower)s_%(version)s.sh', - 'download_filename': '%(namelower)s_%(version)s_RHEL7-64_CUDA10.1.sh' - } -] -checksums = ['d1791322e5970bf1e4d11ca703be1a96aee385671f8da56a2502441a9402024a'] - -install_cmd = ' ./%(namelower)s_%(version)s.sh ' -installopts = '-dir %(installdir)s -script %(installdir)s -name tmpinst -skip -yes' -postinstallcmds = ['mv %(installdir)s/tmpinst/* %(installdir)s && rm -rf %(installdir)s/tmpinst'] -dependencies = [ - ('Java', '11.0.2'), -] -multi_deps = { - 'Python': [ - '3.8.6-GCCcore-10.2.0', - '3.8.2-GCCcore-9.3.0', - '3.7.4-GCCcore-8.3.0']} -modextravars = { - 'IMOD_DIR': "%(installdir)s", - 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', - 'IMOD_QTLIBDIR': '%(installdir)s/qtlib', - 'IMOD_JAVADIR': '$JAVA_HOME', - 'FOR_DISABLE_STACK_TRACE': '1', -} -modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.' -# Observed problems with alias on a tcl based module system. Use bin/subm python script instead. -# modaliases = { -# 'subm': 'submfg $* &' -# } -sanity_check_paths = { - 'files': ['VERSION'], - 'dirs': ['bin', 'lib', 'com', 'autodoc', 'qtlib', 'pylib', 'Plugins', 'man', 'SystemTemplate'], -} - - -moduleclass = 'vis' From d12fa8dc421e02e0b7b7fd80207f25ef558e08da Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 15 Apr 2021 11:25:13 +0200 Subject: [PATCH 0163/9987] Delete IMOD-4.11.0.eb build from source should be the preferred way --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb | 58 --------------------- 1 file changed, 58 deletions(-) delete mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb deleted file mode 100644 index 11516244f7b..00000000000 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.0.eb +++ /dev/null @@ -1,58 +0,0 @@ -# Thomas Hoffmann, EMBL, Heidelberg, structures-it@embl.de, 2021/3; -# based on generic Binary instead of imod.py easyblock. -name = 'IMOD' -version = '4.11.0' -easyblock = 'Binary' - - -homepage = 'https://bio3d.colorado.edu/imod/' -description = """IMOD is a set of image processing, modeling and display -programs used for tomographic reconstruction and for 3D reconstruction of EM -serial sections and optical sections. The package contains tools for assembling -and aligning data within multiple types and sizes of image stacks, viewing 3-D -data from any orientation, and modeling and display of the image files. IMOD -was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim -Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" - -toolchain = SYSTEM - -source_urls = ['https://bio3d.colorado.edu/imod/AMD64-RHEL5/'] -sources = [ - { - 'filename': '%(namelower)s_%(version)s.sh', - 'download_filename': '%(namelower)s_%(version)s_RHEL7-64_CUDA8.0.sh' - } -] -checksums = ['748101eaa5f2ce6f206fb0c888d3095df8a700f4f9c4a931a656a97fe4bc197e'] - -install_cmd = ' ./%(namelower)s_%(version)s.sh ' -installopts = '-dir %(installdir)s -script %(installdir)s -name tmpinst -skip -yes' -postinstallcmds = ['mv %(installdir)s/tmpinst/* %(installdir)s && rm -rf %(installdir)s/tmpinst'] -dependencies = [ - ('Java', '11.0.2'), -] -multi_deps = { - 'Python': [ - '3.8.6-GCCcore-10.2.0', - '3.8.2-GCCcore-9.3.0', - '3.7.4-GCCcore-8.3.0']} - -modextravars = { - 'IMOD_DIR': "%(installdir)s", - 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', - 'IMOD_QTLIBDIR': '%(installdir)s/qtlib', - 'IMOD_JAVADIR': '$JAVA_HOME', - 'FOR_DISABLE_STACK_TRACE': '1', -} -modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.' -# Observed problems with alias on a tcl based module system. Use bin/subm python script instead. -# modaliases = { -# 'subm': 'submfg $* &' -# } -sanity_check_paths = { - 'files': ['VERSION'], - 'dirs': ['bin', 'lib', 'com', 'autodoc', 'qtlib', 'pylib', 'Plugins', 'man', 'SystemTemplate'], -} - - -moduleclass = 'vis' From 3ed726abf7246777f0bb58109875bba8829a5688 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Apr 2021 11:20:45 +0200 Subject: [PATCH 0164/9987] {chem}[intel/2020b] WIEN2k v19.2, DFT-D3 v3.2.0 --- .../DFT-D3-3.2.0-iccifort-2020.4.304.eb | 34 ++++++++++++++ .../w/WIEN2k/WIEN2k-19.2-intel-2020b.eb | 45 +++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..113163554cd --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'DFT-D3' +version = '3.2.0' + +homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical + quantum chemical methods.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3'] +sources = [{'download_filename': 'dftd3.tgz', 'filename': SOURCELOWER_TGZ}] +checksums = ['d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59'] + +# Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version +# numbering. Also, the authors are prone (alas) to stealth upgrades, so that two +# tarballs with the same version number can have different checksums. For this +# reason, it is suggested to manually download and rename the tarball. The +# checksum may also need updating from time to time. +# Checksum last updated: 20 September 2018 +# Date tarball was reported to have been modified: 14 June 2016 +prebuildopts = "sed -i 's/OSTYPE=LINUXL/OSTYPE=LINUXI/' Makefile && " + +files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/dftd3'], + 'dirs': [], +} + +sanity_check_commands = ["dftd3"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb new file mode 100644 index 00000000000..5e5f66e861c --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-19.2-intel-2020b.eb @@ -0,0 +1,45 @@ +name = 'WIEN2k' +version = '19.2' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['f28c0bc94f813b805f8204a43b487cc4f8cf0e7f1595206eb8c0dbd423a436de'] + +dependencies = [ + ('DFT-D3', '3.2.0'), + ('ELPA', '2020.11.001'), + ('FFTW', '3.3.8'), + ('libxc', '4.3.4'), +] + +osdependencies = [('glibc-static', 'libc6-dev')] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1', r'^:ENE.*-1248.14']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.*total forces', + ]), +] + +moduleclass = 'chem' From 689e7650e05b9ca7e5e56c475d48a0082d4dc576 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 21 Apr 2021 15:50:29 -0700 Subject: [PATCH 0165/9987] {devel}[foss/2020b] Spark 3.1.1 --- .../s/Spark/Spark-3.1.1-foss-2020b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb new file mode 100644 index 00000000000..ba34f767b68 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -0,0 +1,53 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'Tarball' + +name = 'Spark' +version = '3.1.1' + +homepage = 'https://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' +] +sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] +checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] + +dependencies = [ + ('Python', '3.8.6'), + ('Java', '11', '', True), + # ('Hadoop', '2.10.0', '-native'), + ('Arrow', '0.17.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('py4j', '0.10.9.2', { + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], + 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyspark', 'bin/spark-shell'], + 'dirs': ['python'] +} + +sanity_check_commands = [ + "pyspark -h", + "python -c 'import pyspark'", +] + +modextrapaths = {'PYTHONPATH': ['python', 'lib/python%(pyshortver)s/site-packages']} + +modextravars = {'SPARK_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 0c4a3876d978c63d07a40cce30f259edce464391 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 21 Apr 2021 17:53:07 -0700 Subject: [PATCH 0166/9987] non Cuda foss Arrow --- .../a/Arrow/Arrow-0.17.1-foss-2020b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb new file mode 100644 index 00000000000..e4c0d64a274 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '0.17.1' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'http://apache.belnet.be/arrow/arrow-%(version)s/', + 'https://www-eu.apache.org/dist/arrow/arrow-%(version)s/', +] +sources = ['apache-arrow-%(version)s.tar.gz'] +patches = ['Arrow-0.16.0_fix-intel.patch'] +checksums = [ + 'cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2', # apache-arrow-0.17.1.tar.gz + '7c1569087f93959a0dfc163d80e5f542edb4d7ed0b9d71a2a05b4081211ad2b9', # Arrow-0.16.0_fix-intel.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Autotools', '20200321'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('pkg-config', '0.29.2'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11',), # for numpy + ('Boost', '1.74.0'), +] + +separate_build_dir = True +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/python/development.html +configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' From c2127bf85dde516f3418a2484e23da49f6ae5e60 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Mon, 3 May 2021 18:20:40 +0200 Subject: [PATCH 0167/9987] adding easyconfigs: Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb, DFT-D4-3.2.0-intel-2019b.eb --- .../d/DFT-D4/DFT-D4-3.2.0-intel-2019b.eb | 25 +++++++++++++ ...Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb | 35 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b.eb create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b.eb new file mode 100644 index 00000000000..3326480052c --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b.eb @@ -0,0 +1,25 @@ +easyblock = 'MesonNinja' + +name = 'DFT-D4' +version = '3.2.0' + +homepage = 'https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4' +description = """Generally Applicable Atomic-Charge Dependent London Dispersion Correction.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = ['https://github.com/dftd4/dftd4/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9874db9e2329519db258dd75ee7ce7c97947f975b00087ba5fdf9a28741088f1'] + +builddependencies = [ + ('Ninja', '1.9.0'), + ('Meson', '0.58.0', '-Python-3.7.4'), +] + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.a', 'lib/libdftd4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..31bf8a63634 --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.58.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f4820df0bc969c99019fd4af8ca5f136ee94c63d8a5ad67e7eb73bdbc9182fdd'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('Python', '3.7.4'), + ('Ninja', '1.9.0'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From a08442aaa733b2d16ee1265af2c9e28ca90e90c6 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Mon, 3 May 2021 18:48:17 +0200 Subject: [PATCH 0168/9987] Add python support --- ...2019b.eb => DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb} | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/d/DFT-D4/{DFT-D4-3.2.0-intel-2019b.eb => DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb} (81%) diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb similarity index 81% rename from easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b.eb rename to easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb index 3326480052c..fa5771c508f 100644 --- a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b.eb +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb @@ -2,6 +2,7 @@ easyblock = 'MesonNinja' name = 'DFT-D4' version = '3.2.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4' description = """Generally Applicable Atomic-Charge Dependent London Dispersion Correction.""" @@ -14,9 +15,15 @@ checksums = ['9874db9e2329519db258dd75ee7ce7c97947f975b00087ba5fdf9a28741088f1'] builddependencies = [ ('Ninja', '1.9.0'), - ('Meson', '0.58.0', '-Python-3.7.4'), + ('Meson', '0.58.0', versionsuffix), ] +dependencies = [ + ('Python', '3.7.4'), +] + +buildopts = '-Dpython=true' + sanity_check_paths = { 'files': ['bin/dftd4', 'lib/libdftd4.a', 'lib/libdftd4.%s' % SHLIB_EXT], 'dirs': [], From 9876f5138f606c1644fd03172355012ceb3992bb Mon Sep 17 00:00:00 2001 From: c3-builder Date: Mon, 3 May 2021 19:03:14 +0200 Subject: [PATCH 0169/9987] Add python support --- .../d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb index fa5771c508f..ad6a9dbd676 100644 --- a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb @@ -22,7 +22,7 @@ dependencies = [ ('Python', '3.7.4'), ] -buildopts = '-Dpython=true' +configopts = '-Dpython=true' sanity_check_paths = { 'files': ['bin/dftd4', 'lib/libdftd4.a', 'lib/libdftd4.%s' % SHLIB_EXT], From 6064d95e7320d73505c3ce5308165ea481dcd168 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 3 May 2021 19:40:08 +0200 Subject: [PATCH 0170/9987] add sanity_pip_check --- .../m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb index 31bf8a63634..6ba9f6a7b73 100644 --- a/easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -24,6 +24,7 @@ dependencies = [ download_dep_fail = True use_pip = True +sanity_pip_check = True options = {'modulename': 'mesonbuild'} From aa9ee57f85a33d947a7cfb6a97cf2504c7eae53c Mon Sep 17 00:00:00 2001 From: c3-builder Date: Mon, 3 May 2021 19:57:58 +0200 Subject: [PATCH 0171/9987] Add sanity check command --- .../d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb index ad6a9dbd676..d1bffb80a7e 100644 --- a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb @@ -29,4 +29,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["dftd4 --version"] + moduleclass = 'chem' From 272f5294fed562dfa4a57e1eb8e640fcba39b0d8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 5 May 2021 10:00:19 +0100 Subject: [PATCH 0172/9987] adding easyconfigs: GEMMA-0.98.4-foss-2020a.eb --- .../g/GEMMA/GEMMA-0.98.4-foss-2020a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb new file mode 100644 index 00000000000..07b7575ea1d --- /dev/null +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'GEMMA' +version = '0.98.4' + +homepage = 'https://github.com/genetics-statistics/GEMMA' +description = "Genome-wide Efficient Mixed Model Association" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/genetics-statistics/GEMMA/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4f57a045d3289afaf31f818bf411ac46c5ee6f78ff8c9c4117963ca54e0bb9f0'] + +builddependencies = [ + ('Eigen', '3.3.7', '', True), +] + +dependencies = [ + ('GSL', '2.6'), + ('zlib', '1.2.11') +] + +files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES.md", "scripts", "VERSION"] + +sanity_check_commands = ["cd %(builddir)s/%(name)s-%(version)s/ && ./run_tests.sh"] + +sanity_check_paths = { + 'files': ["bin/gemma"], + 'dirs': [] +} + +moduleclass = 'bio' From c48c31f0b8698bb9a10a298f655640a3bb118d96 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 5 May 2021 14:28:35 +0100 Subject: [PATCH 0173/9987] Update easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb index 07b7575ea1d..4b770c6f4d4 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['4f57a045d3289afaf31f818bf411ac46c5ee6f78ff8c9c4117963ca54e0bb9f0'] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7'), ] dependencies = [ From fc59466d4fef23fad4bdcb5e96fe7d3fe2fbb70e Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 12 Mar 2021 14:21:01 +0100 Subject: [PATCH 0174/9987] Add libGridXC-0.9.6-foss-2020b and libGridXC-0.9.6-intel-2020b. --- .../l/libGridXC/libGridXC-0.9.6-foss-2020b.eb | 34 +++++++++++++++++++ .../libGridXC/libGridXC-0.9.6-intel-2020b.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-intel-2020b.eb diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-foss-2020b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-foss-2020b.eb new file mode 100644 index 00000000000..fa93050e3db --- /dev/null +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libGridXC' +version = '0.9.6' + +homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' +description = """A library to compute the exchange and correlation energy + and potential in spherical (i.e. atoms) or periodic systems.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/uploads/e6e4ec1e3ec648a45b3613e724c7be04'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee513eeb08b631e2efaaea62e73d85b6fbf204da85963be785915802e5497463'] + +local_common_configopts = "--enable-static --enable-shared --enable-multiconfig --with-libxc" + +configopts = [ + local_common_configopts + " --without-mpi", + local_common_configopts + " CC=$MPICC FC=$MPIFC CXX=$MPICXX --with-mpi", +] + +dependencies = [('libxc', '4.3.4')] + +sanity_check_paths = { + 'files': + ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], + 'dirs': ['include'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-intel-2020b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-intel-2020b.eb new file mode 100644 index 00000000000..1a3bbd7bb92 --- /dev/null +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-intel-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libGridXC' +version = '0.9.6' + +homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' +description = """A library to compute the exchange and correlation energy + and potential in spherical (i.e. atoms) or periodic systems.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/uploads/e6e4ec1e3ec648a45b3613e724c7be04'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee513eeb08b631e2efaaea62e73d85b6fbf204da85963be785915802e5497463'] + +local_common_configopts = "--enable-static --enable-shared --enable-multiconfig --with-libxc" + +configopts = [ + local_common_configopts + " --without-mpi", + local_common_configopts + " CC=$MPICC FC=$MPIFC CXX=$MPICXX --with-mpi", +] + +dependencies = [('libxc', '4.3.4')] + +sanity_check_paths = { + 'files': + ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], + 'dirs': ['include'], +} + +moduleclass = 'phys' From 4b1e1c35694cb933ca787acde05893a4272db92b Mon Sep 17 00:00:00 2001 From: c3-builder Date: Fri, 7 May 2021 18:42:41 +0200 Subject: [PATCH 0175/9987] adding easyconfigs: h5py-2.10.0-foss-2019b-serial-Python-3.7.4.eb --- ...y-2.10.0-foss-2019b-serial-Python-3.7.4.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-serial-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-serial-Python-3.7.4.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-serial-Python-3.7.4.eb new file mode 100644 index 00000000000..971bdbe30d3 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-serial-Python-3.7.4.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.10.0' +versionsuffix = '-serial-Python-%(pyver)s' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': False} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['h5py-%(version)s_avoid-mpi-init.patch'] +checksums = [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch +] + +builddependencies = [('pkgconfig', '1.5.1', '-Python-%(pyver)s')] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', '-Python-%(pyver)s'), + ('HDF5', '1.10.5', '-serial'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = 'HDF5_MPI=OFF HDF5_DIR="$EBROOTHDF5" ' + +moduleclass = 'data' From bb248e58a79f01f3d9a78c1c85306483fffabe4c Mon Sep 17 00:00:00 2001 From: c3-builder Date: Fri, 7 May 2021 20:04:04 +0200 Subject: [PATCH 0176/9987] Drop source_urls --- .../h/h5py/h5py-2.10.0-foss-2019b-serial-Python-3.7.4.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-serial-Python-3.7.4.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-serial-Python-3.7.4.eb index 971bdbe30d3..baf227005b5 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-serial-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2019b-serial-Python-3.7.4.eb @@ -12,7 +12,6 @@ description = """HDF5 for Python (h5py) is a general-purpose Python interface to toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'usempi': False} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['h5py-%(version)s_avoid-mpi-init.patch'] checksums = [ From 26ef446d45cc567bd6fabea1af675ae7b6ac66df Mon Sep 17 00:00:00 2001 From: c3-builder Date: Tue, 11 May 2021 00:25:37 +0200 Subject: [PATCH 0177/9987] Add patch to simplify include path --- .../DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb | 8 ++++-- .../DFT-D4-3.2.0-remove_module_id.patch | 26 +++++++++++++++++++ 2 files changed, 32 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-remove_module_id.patch diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb index d1bffb80a7e..5dbd6861084 100644 --- a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'intel', 'version': '2019b'} source_urls = ['https://github.com/dftd4/dftd4/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] -checksums = ['9874db9e2329519db258dd75ee7ce7c97947f975b00087ba5fdf9a28741088f1'] +patches = ['DFT-D4-%(version)s-remove_module_id.patch'] +checksums = [ + '9874db9e2329519db258dd75ee7ce7c97947f975b00087ba5fdf9a28741088f1', # v3.2.0.tar.gz + '8c3c81338cb57972580e4cf3db307aa2e44b8b3f6d1ba7ae24fa9d807490a93b', # DFT-D4-3.2.0-remove_module_id.patch +] builddependencies = [ ('Ninja', '1.9.0'), @@ -25,7 +29,7 @@ dependencies = [ configopts = '-Dpython=true' sanity_check_paths = { - 'files': ['bin/dftd4', 'lib/libdftd4.a', 'lib/libdftd4.%s' % SHLIB_EXT], + 'files': ['bin/dftd4', 'lib/libdftd4.a', 'lib/libdftd4.%s' % SHLIB_EXT, 'include/dftd4.mod'], 'dirs': [], } diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-remove_module_id.patch b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-remove_module_id.patch new file mode 100644 index 00000000000..85a7da6cd06 --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-remove_module_id.patch @@ -0,0 +1,26 @@ +# The separate mod directory isn't helpful for a EB install since we install a unique version per compiler anyway. +# The pkg-config file can just include one path anyway +# so separating out the (compiler specific) mod files won't help either way. +# Author: mikael.ohman@chalmers.se +--- meson.build.orig 2021-05-10 23:11:21.509151845 +0200 ++++ meson.build 2021-05-10 23:32:55.890484048 +0200 +@@ -79,17 +79,16 @@ + dftd4_header, + ) + +- module_id = meson.project_name() / fc_id + '-' + fc.version() + meson.add_install_script( + find_program(files('config'/'install-mod.py')), +- get_option('includedir') / module_id, ++ get_option('includedir'), + ) + + pkg = import('pkgconfig') + pkg.generate( + dftd4_lib, + description: 'Generally Applicable Atomic-Charge Dependent London Dispersion Correction', +- subdirs: ['', module_id], ++ subdirs: [''], + ) + + asciidoc = find_program('asciidoctor', required: false) From c720efd33f532e0dcdc68690ce31ac5a45a0bad3 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 12 May 2021 10:43:44 +0200 Subject: [PATCH 0178/9987] Adding scikit-image into intelcuda-2020b --- .../b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb | 39 ++++++++++ .../d/dask/dask-2021.2.0-intelcuda-2020b.eb | 73 +++++++++++++++++++ .../networkx/networkx-2.5-intelcuda-2020b.eb | 24 ++++++ .../PyWavelets-1.1.1-intelcuda-2020b.eb | 25 +++++++ .../scikit-image-0.18.1-intelcuda-2020b.eb | 48 ++++++++++++ 5 files changed, 209 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb new file mode 100644 index 00000000000..513e9f6b2fc --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.2.3-intelcuda-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.2.3' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('Pillow', '8.0.1'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), +] + +use_pip = True + +exts_list = [ + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + (name, version, { + 'checksums': ['c4a3f97afe5f525019dd58ee8c4e3d43f53fe1b1ac264ccaae9b02c07b2abc17'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb new file mode 100644 index 00000000000..b012d3c6604 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2021.2.0-intelcuda-2020b.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2021.2.0' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('SciPy-bundle', '2020.11'), + ('bokeh', '2.2.3'), +] + +use_pip = True + +exts_list = [ + ('fsspec', '0.8.7', { + 'checksums': ['4b11557a90ac637089b10afa4c77adf42080c0696f6f2771c41ce92d73c41432'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('locket', '0.2.1', { + 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], + }), + ('partd', '1.1.0', { + 'checksums': ['6e258bf0810701407ad1410d63d1a15cfd7b773fd9efe555dac6bb82cc8832b0'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '2.0.0', { + 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + (name, version, { + 'checksums': ['e7054b8d685205e95c789900ae87d6174550180cbe38a3cb1142e10c73004c22'], + }), + ('distributed', version, { + 'checksums': ['9150b99b2c28e7c238c486b117154abd545c6990080d084aaff02f803f86f75e'], + }), + ('dask-mpi', '2.21.0', { + 'checksums': ['76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.7.2', { + 'checksums': ['1767f4146b2663d9d2eaef62b882a86e1df0bccdb8ae68ae3e5e546aa6796d35'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb new file mode 100644 index 00000000000..d6967a10d78 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5-intelcuda-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.5' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7978955423fbc9639c10498878be59caf99b44dc304c2286162fd24b458c1602'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb new file mode 100644 index 00000000000..5dda1d53259 --- /dev/null +++ b/easybuild/easyconfigs/p/PyWavelets/PyWavelets-1.1.1-intelcuda-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'PyWavelets' +version = '1.1.1' + +homepage = 'https://pywavelets.readthedocs.io' +description = "PyWavelets is open source wavelet transform software for Python." + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'pywt'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb new file mode 100644 index 00000000000..3169f709e70 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.18.1' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'intelcuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('Pillow', '8.0.1'), + ('networkx', '2.5'), + ('dask', '2021.2.0'), + ('PyWavelets', '1.1.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('imageio', '2.9.0', { + 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.3.0', { + 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], + }), + ('tifffile', '2021.2.1', { + 'checksums': ['6793787742e18cf2116bc65e17c51cd9c14cd27a4a6033a8ddd5bf801a637615'], + }), + (name, version, { + 'modulename': 'skimage', + 'patches': ['scikit-image-%(version)s_fix-README-cache-perms.patch'], + 'preinstallopts': "sed -i 's/-fopenmp//g' setup.py && ", + 'checksums': [ + 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz + # scikit-image-0.18.1_fix-README-cache-perms.patch + '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', + ], + }), +] + +moduleclass = 'vis' From bc74a5a79ee79ed0e62639285c73cecea29b9cf5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 12 May 2021 11:21:42 +0200 Subject: [PATCH 0179/9987] adding easyconfigs: OSPRay-2.5.0.eb --- .../easyconfigs/o/OSPRay/OSPRay-2.5.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSPRay/OSPRay-2.5.0.eb diff --git a/easybuild/easyconfigs/o/OSPRay/OSPRay-2.5.0.eb b/easybuild/easyconfigs/o/OSPRay/OSPRay-2.5.0.eb new file mode 100644 index 00000000000..ea6780a19fe --- /dev/null +++ b/easybuild/easyconfigs/o/OSPRay/OSPRay-2.5.0.eb @@ -0,0 +1,21 @@ +easyblock = 'Tarball' + +name = 'OSPRay' +version = '2.5.0' + +homepage = 'https://www.ospray.org' +description = "Open, Scalable, and Portable Ray Tracing Engine" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s/%(name)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.x86_64.linux.tar.gz'] +checksums = ['0ac452d085fdd4e1c953c09766274c8c4f33d21f043d04a0c4d9ff81c0c8fcb7'] + +sanity_check_paths = { + 'files': ['bin/ospConvertRawToAMR', 'include/ospray/ospray.h', + 'include/ospray/version.h', 'lib/libospray.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/ospray', 'lib64/cmake', 'doc'], +} + +moduleclass = 'vis' From 6bbfe017266826cc504bae467b8b66bf33d41025 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 13 May 2021 16:36:47 +0100 Subject: [PATCH 0180/9987] adding easyconfigs: freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb and patches: freebayes-1.3.5_find-external-libs.patch, freebayes-1.3.5_fix-includes.patch, freebayes-1.3.5_install-libs-headers.patch --- .../freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb | 57 ++++++ .../freebayes-1.3.5_find-external-libs.patch | 49 +++++ .../freebayes-1.3.5_fix-includes.patch | 169 ++++++++++++++++++ ...freebayes-1.3.5_install-libs-headers.patch | 74 ++++++++ 4 files changed, 349 insertions(+) create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_find-external-libs.patch create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-includes.patch create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_install-libs-headers.patch diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..880e529e029 --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb @@ -0,0 +1,57 @@ +easyblock = 'MesonNinja' + +name = 'freebayes' +version = '1.3.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://github.com/ekg/freebayes' +description = """FreeBayes is a Bayesian genetic variant detector designed to find small + polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and + deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and + substitution events) smaller than the length of a short-read sequencing alignment. +""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +github_account = name +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-1.3.5_find-external-libs.patch', + '%(name)s-1.3.5_fix-includes.patch', + '%(name)s-1.3.5_install-libs-headers.patch', +] +checksums = [ + 'af195a8c54b742d01af5a7e1fd1781a89290d726b310216c83e78c650d7aee49', # v1.3.5.tar.gz + '1e7142d5328c4b9334a680e9bc5a16ef726afb6ae8592679494e33933805cdb0', # freebayes-1.3.5_find-external-libs.patch + '2dfc1d0c1d111c11e827d66fd716946555e09283f9183ebf07552d7a1297efa9', # freebayes-1.3.5_fix-includes.patch + 'be4b513828d5ee34be785be32002a97de1ab0246efffd55d4868098a07a76c96', # freebayes-1.3.5_install-libs-headers.patch +] + +builddependencies = [ + ('CMake', '3.16.4'), + ('Meson', '0.55.1', versionsuffix), + ('Ninja', '1.10.0'), + ('pkgconfig', '1.5.1', versionsuffix), +] + +dependencies = [ + ('Python', '3.8.2'), + ('SAMtools', '1.11'), + ('parallel', '20200522'), + ('intervaltree', '0.1'), + ('libffi', '3.3'), + ('SeqLib', '1.2.0'), + ('vcflib', '1.0.2', versionsuffix), + ('VCFtools', '0.1.16'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/bamleftalign', 'scripts/%(name)s-parallel'], + 'dirs': ['bin', 'scripts'], +} +sanity_check_commands = ["%(name)s -h"] + +modextrapaths = {'PATH': ['scripts']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_find-external-libs.patch b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_find-external-libs.patch new file mode 100644 index 00000000000..8a7b8f0fe3d --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_find-external-libs.patch @@ -0,0 +1,49 @@ +diff -Nru freebayes-1.3.5.orig/meson.build freebayes-1.3.5/meson.build +--- freebayes-1.3.5.orig/meson.build 2021-05-13 15:56:53.000000000 +0100 ++++ freebayes-1.3.5/meson.build 2021-05-13 16:00:25.000000000 +0100 +@@ -16,10 +16,12 @@ + lzma_dep = dependency('liblzma') + thread_dep = dependency('threads') + +-htslib_dep = dependency('htslib', required : false) +-tabixpp_dep = cc.find_library('tabixpp', required : false) +-vcflib_dep = dependency('libvcflib', required : false) +-seqlib_dep = dependency('libseqlib', required : false) ++htslib_dep = dependency('htslib', required : true) ++tabixpp_dep = cc.find_library('tabixpp', required : true) ++vcflib_dep = cc.find_library('libvcflib', required : true) ++seqlib_dep = cc.find_library('libseqlib', required : true) ++fastahack_dep = cc.find_library('libfastahack', required : true) ++sw_dep = cc.find_library('libsw', required : true) + + # for setting a warning_level on the external code in custom_* targets below + warn_quiet = ['warning_level=0'] +@@ -191,7 +193,7 @@ + include_directories : incdir, + cpp_args : extra_cpp_args, + dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep, +- vcflib_dep, seqlib_dep], ++ vcflib_dep, seqlib_dep, fastahack_dep, sw_dep], + install : false, + ) + +@@ -200,7 +202,8 @@ + include_directories : incdir, + cpp_args : extra_cpp_args, + dependencies: [zlib_dep, lzma_dep, thread_dep, +- htslib_dep, tabixpp_dep, vcflib_dep, seqlib_dep], ++ htslib_dep, tabixpp_dep, vcflib_dep, seqlib_dep, ++ fastahack_dep, sw_dep], + link_with : freebayes_lib, + install: true + ) +@@ -210,7 +213,8 @@ + include_directories : incdir, + cpp_args : extra_cpp_args, + dependencies: [zlib_dep, lzma_dep, thread_dep, +- htslib_dep, vcflib_dep, seqlib_dep], ++ htslib_dep, vcflib_dep, seqlib_dep, fastahack_dep, ++ sw_dep], + link_with : freebayes_lib, + install: true + ) diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-includes.patch b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-includes.patch new file mode 100644 index 00000000000..31a8c01600f --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-includes.patch @@ -0,0 +1,169 @@ +diff -Nru freebayes-1.3.5/src/Allele.cpp freebayes-1.3.5b/src/Allele.cpp +--- freebayes-1.3.5/src/Allele.cpp 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/Allele.cpp 2021-05-13 16:26:23.000000000 +0100 +@@ -1,5 +1,5 @@ + #include "Allele.h" +-#include "multichoose.h" ++#include "multichoose/multichoose.h" + #include "TryCatch.h" + + +diff -Nru freebayes-1.3.5/src/AlleleParser.cpp freebayes-1.3.5b/src/AlleleParser.cpp +--- freebayes-1.3.5/src/AlleleParser.cpp 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/AlleleParser.cpp 2021-05-13 16:26:24.000000000 +0100 +@@ -1,9 +1,9 @@ + #include "AlleleParser.h" +-#include "multichoose.h" // includes generic functions, so it must be included here ++#include "multichoose/multichoose.h" // includes generic functions, so it must be included here + // otherwise we will get a linker error + // see: http://stackoverflow.com/questions/36039/templates-spread-across-multiple-files + // http://www.cplusplus.com/doc/tutorial/templates/ "Templates and Multi-file projects" +-#include "multipermute.h" ++#include "multichoose/multipermute.h" + #include "Logging.h" + + using namespace std; +diff -Nru freebayes-1.3.5/src/AlleleParser.h freebayes-1.3.5b/src/AlleleParser.h +--- freebayes-1.3.5/src/AlleleParser.h 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/AlleleParser.h 2021-05-13 16:26:24.000000000 +0100 +@@ -13,7 +13,7 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + #include // XXX workaround for a missing include in vcflib's join.h + #include "join.h" + +diff -Nru freebayes-1.3.5/src/BedReader.cpp freebayes-1.3.5b/src/BedReader.cpp +--- freebayes-1.3.5/src/BedReader.cpp 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/BedReader.cpp 2021-05-13 16:26:23.000000000 +0100 +@@ -7,10 +7,10 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + #include "Utility.h" + #include "BedReader.h" +-#include "../intervaltree/IntervalTree.h" ++#include "intervaltree/IntervalTree.h" + + using namespace std; + +diff -Nru freebayes-1.3.5/src/BedReader.h freebayes-1.3.5b/src/BedReader.h +--- freebayes-1.3.5/src/BedReader.h 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/BedReader.h 2021-05-13 16:26:23.000000000 +0100 +@@ -9,8 +9,8 @@ + #include + #include + #include +-#include "../intervaltree/IntervalTree.h" +-#include "split.h" ++#include "intervaltree/IntervalTree.h" ++#include "fastahack/split.h" + + using namespace std; + +diff -Nru freebayes-1.3.5/src/Bias.h freebayes-1.3.5b/src/Bias.h +--- freebayes-1.3.5/src/Bias.h 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/Bias.h 2021-05-13 16:26:24.000000000 +0100 +@@ -7,7 +7,7 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + + using namespace std; + +diff -Nru freebayes-1.3.5/src/CNV.h freebayes-1.3.5b/src/CNV.h +--- freebayes-1.3.5/src/CNV.h 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/CNV.h 2021-05-13 16:26:24.000000000 +0100 +@@ -10,7 +10,7 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + + using namespace std; + +diff -Nru freebayes-1.3.5/src/Contamination.h freebayes-1.3.5b/src/Contamination.h +--- freebayes-1.3.5/src/Contamination.h 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/Contamination.h 2021-05-13 16:26:24.000000000 +0100 +@@ -8,7 +8,7 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + + using namespace std; + +diff -Nru freebayes-1.3.5/src/DataLikelihood.cpp freebayes-1.3.5b/src/DataLikelihood.cpp +--- freebayes-1.3.5/src/DataLikelihood.cpp 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/DataLikelihood.cpp 2021-05-13 16:26:24.000000000 +0100 +@@ -1,6 +1,6 @@ + #include "DataLikelihood.h" +-#include "multichoose.h" +-#include "multipermute.h" ++#include "multichoose/multichoose.h" ++#include "multichoose/multipermute.h" + #include "Logging.h" + + long double +diff -Nru freebayes-1.3.5/src/FBFasta.h freebayes-1.3.5b/src/FBFasta.h +--- freebayes-1.3.5/src/FBFasta.h 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/FBFasta.h 2021-05-13 16:26:24.000000000 +0100 +@@ -16,10 +16,10 @@ + #include + #include + #include +-#include "LargeFileSupport.h" ++#include "fastahack/LargeFileSupport.h" + #include "Utility.h" + #include +-#include "split.h" ++#include "fastahack/split.h" + #include + #include + #include +diff -Nru freebayes-1.3.5/src/freebayes.cpp freebayes-1.3.5b/src/freebayes.cpp +--- freebayes-1.3.5/src/freebayes.cpp 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/freebayes.cpp 2021-05-13 16:26:23.000000000 +0100 +@@ -30,8 +30,8 @@ + #include "Utility.h" + #include "SegfaultHandler.h" + +-#include "multichoose.h" +-#include "multipermute.h" ++#include "multichoose/multichoose.h" ++#include "multichoose/multipermute.h" + + #include "Genotype.h" + #include "DataLikelihood.h" +diff -Nru freebayes-1.3.5/src/Genotype.cpp freebayes-1.3.5b/src/Genotype.cpp +--- freebayes-1.3.5/src/Genotype.cpp 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/Genotype.cpp 2021-05-13 16:26:23.000000000 +0100 +@@ -1,6 +1,6 @@ + #include "Genotype.h" +-#include "multichoose.h" +-#include "multipermute.h" ++#include "multichoose/multichoose.h" ++#include "multichoose/multipermute.h" + + + vector Genotype::uniqueAlleles(void) { +diff -Nru freebayes-1.3.5/src/Parameters.h freebayes-1.3.5b/src/Parameters.h +--- freebayes-1.3.5/src/Parameters.h 2021-02-10 09:21:07.000000000 +0000 ++++ freebayes-1.3.5b/src/Parameters.h 2021-05-13 16:26:24.000000000 +0100 +@@ -9,7 +9,7 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + #include "version_git.h" + #include "Utility.h" + diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_install-libs-headers.patch b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_install-libs-headers.patch new file mode 100644 index 00000000000..ef0082386c2 --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_install-libs-headers.patch @@ -0,0 +1,74 @@ +diff -Nru freebayes-1.3.5b/meson.build freebayes-1.3.5c/meson.build +--- freebayes-1.3.5b/meson.build 2021-05-13 16:00:36.000000000 +0100 ++++ freebayes-1.3.5c/meson.build 2021-05-13 16:22:17.000000000 +0100 +@@ -173,6 +173,38 @@ + freebayes_src = files('src/freebayes.cpp') + bamleftalign_src = files('src/bamleftalign.cpp') + ++# FreeBayes headers ++freebayes_headers = files( ++ 'src/Allele.h', ++ 'src/AlleleParser.h', ++ 'src/BedReader.h', ++ 'src/Bias.h', ++ 'src/CNV.h', ++ 'src/Contamination.h', ++ 'src/DataLikelihood.h', ++ 'src/Dirichlet.h', ++ 'src/Ewens.h', ++ 'src/FBFasta.h', ++ 'src/Genotype.h', ++ 'src/IndelAllele.h', ++ 'src/LeftAlign.h', ++ 'src/Logging.h', ++ 'src/Marginals.h', ++ 'src/Multinomial.h', ++ 'src/NonCall.h', ++ 'src/Parameters.h', ++ 'src/Product.h', ++ 'src/Result.h', ++ 'src/ResultData.h', ++ 'src/Sample.h', ++ 'src/SegfaultHandler.h', ++ 'src/Sum.h', ++ 'src/TryCatch.h', ++ 'src/Utility.h', ++ 'src/version_git.h', ++ ) ++ ++ + # Include paths + incdir = include_directories( + 'src', +@@ -188,15 +220,29 @@ + ) + + freebayes_lib = static_library( +- 'freebayes_common', ++ 'freebayes', + freebayes_common_src, + include_directories : incdir, + cpp_args : extra_cpp_args, + dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep, + vcflib_dep, seqlib_dep, fastahack_dep, sw_dep], +- install : false, ++ install : true, + ) + ++freebayes_slib = shared_library( ++ 'freebayes', ++ freebayes_common_src, ++ include_directories : incdir, ++ cpp_args : extra_cpp_args, ++ dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep, ++ vcflib_dep, seqlib_dep, fastahack_dep, sw_dep], ++ install : true ++ ) ++ ++install_headers(freebayes_headers, subdir : 'freebayes') ++ ++install_subdir('scripts', install_dir : '') ++ + executable('freebayes', + freebayes_src, + include_directories : incdir, From 9b8e3a35146a35f6459a05f154807d2ca437b3b2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 14 May 2021 12:30:56 +0100 Subject: [PATCH 0181/9987] Add description, author to patches and update checksums --- .../freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb | 10 ++++++---- .../freebayes/freebayes-1.3.5_find-external-libs.patch | 3 +++ .../f/freebayes/freebayes-1.3.5_fix-includes.patch | 2 ++ .../freebayes-1.3.5_install-libs-headers.patch | 4 ++++ 4 files changed, 15 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb index 880e529e029..32a031a8418 100644 --- a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-9.3.0-Python-3.8.2.eb @@ -1,10 +1,12 @@ +# Author: Jasper Grimm (UoY) + easyblock = 'MesonNinja' name = 'freebayes' version = '1.3.5' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://github.com/ekg/freebayes' +homepage = 'https://github.com/ekg/freebayes' description = """FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and @@ -23,9 +25,9 @@ patches = [ ] checksums = [ 'af195a8c54b742d01af5a7e1fd1781a89290d726b310216c83e78c650d7aee49', # v1.3.5.tar.gz - '1e7142d5328c4b9334a680e9bc5a16ef726afb6ae8592679494e33933805cdb0', # freebayes-1.3.5_find-external-libs.patch - '2dfc1d0c1d111c11e827d66fd716946555e09283f9183ebf07552d7a1297efa9', # freebayes-1.3.5_fix-includes.patch - 'be4b513828d5ee34be785be32002a97de1ab0246efffd55d4868098a07a76c96', # freebayes-1.3.5_install-libs-headers.patch + '68b62f532fb658cbee20aa0a9d19a4f5ab942f64510753bc01eb44006bad15dc', # freebayes-1.3.5_find-external-libs.patch + '4c6c74b30bf3b2f04b8a50bbdef26e74f6e2412f3efbd81512226e557c2a53d1', # freebayes-1.3.5_fix-includes.patch + '9a30129ea9457cfd49234b5b4cca0b3f9ac64765f122632f8eb9a1295ee6cb13', # freebayes-1.3.5_install-libs-headers.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_find-external-libs.patch b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_find-external-libs.patch index 8a7b8f0fe3d..41e9c926767 100644 --- a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_find-external-libs.patch +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_find-external-libs.patch @@ -1,3 +1,6 @@ +Created by Jasper Grimm (UoY) +Switch to cc.find_library to search for libraries in LD_LIBRARY_PATH +Add dependencies on fastahack, smithwaterman diff -Nru freebayes-1.3.5.orig/meson.build freebayes-1.3.5/meson.build --- freebayes-1.3.5.orig/meson.build 2021-05-13 15:56:53.000000000 +0100 +++ freebayes-1.3.5/meson.build 2021-05-13 16:00:25.000000000 +0100 diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-includes.patch b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-includes.patch index 31a8c01600f..7e8d4afc8ae 100644 --- a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-includes.patch +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-includes.patch @@ -1,3 +1,5 @@ +Created by Jasper Grimm (UoY) +Patch include statements to match installed include hierarchy diff -Nru freebayes-1.3.5/src/Allele.cpp freebayes-1.3.5b/src/Allele.cpp --- freebayes-1.3.5/src/Allele.cpp 2021-02-10 09:21:07.000000000 +0000 +++ freebayes-1.3.5b/src/Allele.cpp 2021-05-13 16:26:23.000000000 +0100 diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_install-libs-headers.patch b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_install-libs-headers.patch index ef0082386c2..c1a34e2432b 100644 --- a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_install-libs-headers.patch +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_install-libs-headers.patch @@ -1,3 +1,7 @@ +Created by Jasper Grimm (UoY) +Install header files and scripts +Rename static lib to freebayes, and set install to True +Add target to build shared library diff -Nru freebayes-1.3.5b/meson.build freebayes-1.3.5c/meson.build --- freebayes-1.3.5b/meson.build 2021-05-13 16:00:36.000000000 +0100 +++ freebayes-1.3.5c/meson.build 2021-05-13 16:22:17.000000000 +0100 From 8645bed3c014675b577cc72d4b469f25e947a2d6 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 14 May 2021 14:08:12 +0200 Subject: [PATCH 0182/9987] Use gompi and iimpi toolchains instead of foss and intel. --- ...ridXC-0.9.6-foss-2020b.eb => libGridXC-0.9.6-gompi-2020b.eb} | 2 +- ...idXC-0.9.6-intel-2020b.eb => libGridXC-0.9.6-iimpi-2020b.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/l/libGridXC/{libGridXC-0.9.6-foss-2020b.eb => libGridXC-0.9.6-gompi-2020b.eb} (95%) rename easybuild/easyconfigs/l/libGridXC/{libGridXC-0.9.6-intel-2020b.eb => libGridXC-0.9.6-iimpi-2020b.eb} (95%) diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-foss-2020b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb similarity index 95% rename from easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-foss-2020b.eb rename to easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb index fa93050e3db..a46d4f4f179 100644 --- a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb @@ -7,7 +7,7 @@ homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' description = """A library to compute the exchange and correlation energy and potential in spherical (i.e. atoms) or periodic systems.""" -toolchain = {'name': 'foss', 'version': '2020b'} +toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'usempi': True, 'opt': True} source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/uploads/e6e4ec1e3ec648a45b3613e724c7be04'] diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-intel-2020b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb similarity index 95% rename from easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-intel-2020b.eb rename to easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb index 1a3bbd7bb92..3c9d3dbdceb 100644 --- a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb @@ -7,7 +7,7 @@ homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' description = """A library to compute the exchange and correlation energy and potential in spherical (i.e. atoms) or periodic systems.""" -toolchain = {'name': 'intel', 'version': '2020b'} +toolchain = {'name': 'iimpi', 'version': '2020b'} toolchainopts = {'usempi': True, 'opt': True} source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/uploads/e6e4ec1e3ec648a45b3613e724c7be04'] From ea1a2135205155a1ad16ade10727af7bca431ad6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 18 May 2021 09:52:04 +0100 Subject: [PATCH 0183/9987] adding easyconfigs: SortMeRNA-2.1-foss-2020a.eb --- .../s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb diff --git a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb new file mode 100644 index 00000000000..049e4c237bc --- /dev/null +++ b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb @@ -0,0 +1,34 @@ +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# # +easyblock = 'ConfigureMake' + +name = 'SortMeRNA' +version = '2.1' + +homepage = 'http://bioinfo.lifl.fr/RNA/sortmerna/' +description = "SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads." + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/biocore/%(namelower)s/archive/'] +sources = ['%(version)s.tar.gz'] +# Patch for double includes of header files in Makefile.in +patches = ['%(name)s-%(version)s_Makefile.in.patch'] + + +sanity_check_paths = { + 'files': ['bin/indexdb_rna', 'bin/%(namelower)s'], + 'dirs': ['include', '%(namelower)s'], +} + +moduleclass = 'bio' From 3d2f420397dc0d69e72b76c0b3bea37c87f3b9d9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 18 May 2021 12:34:19 +0100 Subject: [PATCH 0184/9987] adding easyconfigs: Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb --- ...py-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb new file mode 100644 index 00000000000..80c71362ead --- /dev/null +++ b/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb @@ -0,0 +1,60 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'CmdCp' + +name = 'Snippy' +version = '4.6.0' +local_pyversuffix = '-Python-%(pyver)s' +local_javaversuffix= '-Java-%(javaver)s' +versionsuffix = local_javaversuffix + local_pyversuffix + +homepage = 'https://github.com/tseemann/snippy' +description = """Snippy finds SNPs between a haploid reference genome and your NGS sequence + reads. It will find both substitutions (snps) and insertions/deletions (indels). + Rapid haploid variant calling and core genome alignment.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +github_account = 'tseemann' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['7264e3819e249387effd3eba170ff49404b1cf7347dfa25944866f5aeb6b11c3'] + +dependencies = [ + ('Java', '13', '', True), + ('Python', '3.8.2'), + ('Perl', '5.30.2'), + ('BioPerl', '1.7.7'), + ('any2fasta', '0.4.2'), + ('BWA', '0.7.17'), + ('BCFtools', '1.10.2'), + ('BEDTools', '2.29.2'), + ('freebayes', '1.3.5', local_pyversuffix), + ('minimap2', '2.17'), + ('parallel', '20200522'), + ('samclip', '0.4.0'), + ('SAMtools', '1.11'), + ('SeqLib', '1.2.0'), + ('seqtk', '1.3'), + ('snp-sites', '2.5.1'), + ('snpEff', '5.0', versionsuffix), + ('vcflib', '1.0.2', local_pyversuffix), + ('vt', '0.57721'), +] + +skipsteps = ['configure', 'build'] + +pretestopts = "cd test && " +runtest = '' + +files_to_copy = ['bin', 'etc', 'perl5', 'LICENSE', 'README.md'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'etc/snpeff.config'], + 'dirs': [], +} +sanity_check_commands = ["%(namelower)s --check"] + +modextrapaths = {'PERL5LIB': 'perl5/%(name)s'} + +moduleclass = 'bio' From a02f0bd8731b9cd803069abaee7fdfb4f058fbdc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 May 2021 13:43:16 +0200 Subject: [PATCH 0185/9987] adding easyconfigs: antiSMASH-5.2.0-foss-2020b.eb, GlimmerHMM-3.0.4c-GCC-10.2.0.eb, HMMER2-2.3.2-GCC-10.2.0.eb, MUSCLE-3.8.1551-GCC-10.2.0.eb and patches: antiSMASH-5.2.0_Biopython-1.78.patch --- .../a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb | 91 ++++ .../antiSMASH-5.2.0_Biopython-1.78.patch | 470 ++++++++++++++++++ .../GlimmerHMM-3.0.4c-GCC-10.2.0.eb | 45 ++ .../h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb | 27 + .../m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb | 30 ++ 5 files changed, 663 insertions(+) create mode 100644 easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0_Biopython-1.78.patch create mode 100644 easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb new file mode 100644 index 00000000000..57fe702e6cf --- /dev/null +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb @@ -0,0 +1,91 @@ +easyblock = 'PythonBundle' + +name = 'antiSMASH' +version = '5.2.0' + +homepage = 'https://github.com/antismash/antismash' +description = """antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary + metabolite biosynthesis gene clusters in bacterial and fungal genomes.""" + +docurls = ['https://docs.antismash.secondarymetabolites.org'] + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('DIAMOND', '2.0.7'), + ('FastTree', '2.1.11'), + ('GlimmerHMM', '3.0.4c'), + ('HMMER2', '2.3.2'), + ('HMMER', '3.3.2'), + ('MUSCLE', '3.8.1551'), + ('BLAST+', '2.11.0'), + ('prodigal', '2.6.3'), + ('Biopython', '1.78'), + ('matplotlib', '3.3.3'), + ('scikit-learn', '0.23.2'), +] + +# install MEME as a component in this installation, +# since antiSMASH requires very specific old version +# see https://docs.antismash.secondarymetabolites.org/install/#full-manual-install +components = [ + ('MEME', '4.11.2', { + 'source_urls': ['http://meme-suite.org/meme-software/%(version)s/'], + 'sources': ['meme_%(version)s_2.tar.gz'], + 'checksums': ['377238c2a9dda64e01ffae8ecdbc1492c100df9b0f84132d50c1cf2f68921b22'], + 'easyblock': 'ConfigureMake', + 'start_dir': 'meme_%(version)s', + 'buildopts': 'CFLAGS="$CFLAGS -std=gnu89 -DUNIX -D__USE_FIXED_PROTOTYPES__ -fcommon"', + }), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('helperlibs', '0.2.1', { + 'checksums': ['4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732'], + }), + ('pysvg-py3', '0.2.2.post3', { + 'modulename': 'pysvg', + 'checksums': ['a1183aa5d89871298c11f25d28640edc3798b6ed1e2b2a95c30d35985d6431d0'], + }), + ('bcbio-gff', '0.6.6', { + 'modulename': 'BCBio.GFF', + 'checksums': ['74c6920c91ca18ed9cb872e9471c0be442dad143d8176345917eb1fefc86bc37'], + }), + ('pyScss', '1.3.7', { + 'modulename': 'scss', + 'checksums': ['f1df571569021a23941a538eb154405dde80bed35dc1ea7c5f3e18e0144746bf'], + }), + (name, version, { + 'source_urls': ['https://github.com/antismash/antismash/archive/'], + 'source_tmpl': '%s.tar.gz' % '-'.join(version.split('.')), + 'patches': ['antiSMASH-%(version)s_Biopython-1.78.patch'], + 'checksums': [ + 'a6fae892e46fd945701dda4640d07467e2d0ab37913d29da403127833bc77291', # 5-2-0.tar.gz + '4ca5d671085761c5f86719603fa3bbd0e82b7b52deefe8cac6eb4a3973825f16', # antiSMASH-5.2.0_Biopython-1.78.patch + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/antismash', 'bin/meme'], + 'dirs': [], +} + +sanity_check_commands = [ + # 'meme -h' exits with non-zero exit status, so use 'grep' to check for pattern + "meme -h 2>&1 | grep 'Usage:[ \t]*meme'", + "antismash --version", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0_Biopython-1.78.patch b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0_Biopython-1.78.patch new file mode 100644 index 00000000000..ab977c49987 --- /dev/null +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0_Biopython-1.78.patch @@ -0,0 +1,470 @@ +see https://github.com/antismash/antismash/pull/310 + +From 94eaa1570bd7a2be9e24238234ccd33ab08270c2 Mon Sep 17 00:00:00 2001 +From: Simon Shaw +Date: Tue, 29 Sep 2020 17:01:37 +0200 +Subject: [PATCH 1/2] chore: handle biopython's removal of Alphabet in 1.78 and + update + +--- + antismash/common/record_processing.py | 24 ++------------ + antismash/common/secmet/features/region.py | 3 ++ + .../secmet/features/test/test_region.py | 5 ++- + antismash/common/secmet/record.py | 32 +++++++++++++++---- + .../secmet/test/test_circular_conversion.py | 11 ++++--- + antismash/common/secmet/test/test_secmet.py | 20 ++++++++++-- + antismash/common/serialiser.py | 15 +++------ + antismash/common/test/helpers.py | 4 +-- + .../common/test/test_record_processing.py | 17 ---------- + .../modules/pfam2go/test/test_pfam2go.py | 3 +- + antismash/modules/tta/test/test_tta.py | 3 +- + setup.py | 2 +- + 12 files changed, 67 insertions(+), 72 deletions(-) + +diff --git a/antismash/common/record_processing.py b/antismash/common/record_processing.py +index 0ab8ef89..489d2b95 100644 +--- a/antismash/common/record_processing.py ++++ b/antismash/common/record_processing.py +@@ -7,10 +7,9 @@ + import functools + import logging + import re +-from typing import Any, Callable, List, Set, Tuple, Union ++from typing import Any, Callable, List, Set, Tuple + import warnings + +-import Bio + from Bio.Seq import Seq, UnknownSeq + from Bio.SeqRecord import SeqRecord + from helperlibs.bio import seqio +@@ -97,7 +96,7 @@ def parse_input_sequence(filename: str, taxon: str = "bacteria", minimum_length: + raise AntismashInputError("all input records smaller than minimum length (%d)" % minimum_length) + + for record in records: +- if isinstance(record.seq.alphabet, Bio.Alphabet.ProteinAlphabet) or not is_nucl_seq(record.seq): ++ if not Record.is_nucleotide_sequence(record.seq): + raise AntismashInputError("protein records are not supported: %s" % record.id) + + # before conversion to secmet records, trim if required +@@ -356,8 +355,6 @@ def pre_process_sequences(sequences: List[Record], options: ConfigType, genefind + sequences = [sanitise_sequence(sequences[0])] + else: + sequences = parallel_function(sanitise_sequence, ([record] for record in sequences)) +- for sequence in sequences: +- sequence.seq.alphabet = Bio.Alphabet.generic_dna + + for record in sequences: + if record.skip or not record.seq: +@@ -413,7 +410,7 @@ def sanitise_sequence(record: Record) -> Record: + has_real_content = True + else: + sanitised.append("N") +- record.seq = Seq("".join(sanitised), alphabet=record.seq.alphabet) ++ record.seq = Seq("".join(sanitised)) + if not has_real_content: + record.skip = "contains no sequence" + return record +@@ -446,21 +443,6 @@ def trim_sequence(record: SeqRecord, start: int, end: int) -> SeqRecord: + return new + + +-def is_nucl_seq(sequence: Union[Seq, str]) -> bool: +- """ Determines if a sequence is a nucleotide sequence based on content. +- +- Arguments: +- sequence: the sequence to check, either a string or Bio.Seq +- +- Returns: +- True if more than 80% of characters are nucleotide bases +- """ +- other = str(sequence).lower() +- for char in "acgtn": +- other = other.replace(char, "") +- return len(other) < 0.2 * len(sequence) +- +- + def records_contain_shotgun_scaffolds(records: List[Record]) -> bool: + """ Check if given records contain a WGS master record or supercontig record + +diff --git a/antismash/common/secmet/features/region.py b/antismash/common/secmet/features/region.py +index 79f8f9a2..f0af7a52 100644 +--- a/antismash/common/secmet/features/region.py ++++ b/antismash/common/secmet/features/region.py +@@ -162,6 +162,9 @@ def write_to_genbank(self, filename: str = None, directory: str = None, record: + cluster_record.annotations["taxonomy"] = record.annotations.get("taxonomy", []) + cluster_record.annotations["data_file_division"] = record.annotations.get("data_file_division", 'UNK') + cluster_record.annotations["comment"] = record.annotations.get("comment", '') ++ # biopython does not persist the molecule_type annotation in slices, ++ # despite it being required for output to the genbank format ++ cluster_record.annotations["molecule_type"] = record.annotations["molecule_type"] + + # update the antiSMASH annotation to include some cluster details + comment_end_marker = "##antiSMASH-Data-END" +diff --git a/antismash/common/secmet/features/test/test_region.py b/antismash/common/secmet/features/test/test_region.py +index 0d34046a..364fc2a5 100644 +--- a/antismash/common/secmet/features/test/test_region.py ++++ b/antismash/common/secmet/features/test/test_region.py +@@ -7,7 +7,6 @@ + from tempfile import NamedTemporaryFile + import unittest + +-from Bio.Alphabet import generic_dna + from Bio.Seq import Seq + from helperlibs.bio import seqio + +@@ -138,7 +137,7 @@ def test_probabilities(self): + assert Region(candidate_clusters=candidates, subregions=subs).probabilities == [0.1, 0.7] + + def test_genbank(self): +- dummy_record = Record(Seq("A"*100, generic_dna)) ++ dummy_record = Record(Seq("A"*100)) + clusters = [create_protocluster(3, 20, "prodA"), + create_protocluster(25, 41, "prodB")] + for cluster in clusters: +@@ -164,7 +163,7 @@ def test_genbank(self): + assert new.probabilities == region.probabilities + + def test_prepeptide_adjustment(self): +- dummy_record = Record(Seq("A"*400, generic_dna)) ++ dummy_record = Record(Seq("A"*400)) + subregion = DummySubRegion(start=100, end=300) + dummy_record.add_subregion(subregion) + region = Region(subregions=[subregion]) +diff --git a/antismash/common/secmet/record.py b/antismash/common/secmet/record.py +index 95e63725..a177b789 100644 +--- a/antismash/common/secmet/record.py ++++ b/antismash/common/secmet/record.py +@@ -16,7 +16,7 @@ + import logging + from typing import Any, Dict, List, Optional, Sequence, Type, Tuple, Union, cast + +-from Bio import Alphabet, SeqIO ++from Bio import SeqIO + from Bio.Seq import Seq + from Bio.SeqFeature import SeqFeature, FeatureLocation, CompoundLocation + from Bio.SeqRecord import SeqRecord +@@ -467,6 +467,8 @@ def to_biopython(self) -> SeqRecord: + bio_features: List[SeqFeature] = [] + for feature in sorted(features): + bio_features.extend(feature.to_biopython()) ++ if "molecule_type" not in self._record.annotations: ++ self._record.annotations["molecule_type"] = "DNA" + return SeqRecord(self.seq, id=self._record.id, name=self._record.name, + description=self._record.description, + dbxrefs=self.dbxrefs, features=bio_features, +@@ -653,9 +655,10 @@ def from_biopython(seq_record: SeqRecord, taxon: str) -> "Record": + postponed_features[kind.FEATURE_TYPE] = (kind, []) + + assert isinstance(seq_record, SeqRecord), type(seq_record) +- if seq_record.seq and isinstance(seq_record.seq, Seq): +- if isinstance(seq_record.seq.alphabet, Alphabet.ProteinAlphabet): +- raise SecmetInvalidInputError("protein records are not supported") ++ if seq_record.annotations.get("molecule_type", "DNA") != "DNA": ++ raise SecmetInvalidInputError("protein records are not supported") ++ if seq_record.seq and not Record.is_nucleotide_sequence(seq_record.seq): ++ raise SecmetInvalidInputError("protein records are not supported") + transl_table = 1 # standard + if str(taxon) == "bacteria": + transl_table = 11 # bacterial, archea, plant plastid code +@@ -831,11 +834,11 @@ def get_aa_translation_from_location(self, location: FeatureLocation, + string_version = str(seq) + for invalid in "*BJOUZ": + string_version = string_version.replace(invalid, "X") +- seq = Seq(string_version, Alphabet.generic_protein) + + if "-" in str(seq): +- seq = Seq(str(seq).replace("-", ""), Alphabet.generic_protein) +- return seq ++ seq = Seq(str(seq).replace("-", "")) ++ ++ return Seq(string_version) + + def get_cds_features_within_regions(self) -> List[CDSFeature]: # pylint: disable=invalid-name + """ Returns all CDS features in the record that are located within a +@@ -958,3 +961,18 @@ def strip_antismash_annotations(self) -> None: + # clean up antiSMASH annotations in CDS features + for feature in self.get_cds_features(): + feature.strip_antismash_annotations() ++ ++ @staticmethod ++ def is_nucleotide_sequence(sequence: Union[Seq, str]) -> bool: ++ """ Determines if a sequence is a nucleotide sequence based on content. ++ ++ Arguments: ++ sequence: the sequence to check, either a string or Bio.Seq ++ ++ Returns: ++ True if more than 80% of characters are nucleotide bases ++ """ ++ other = str(sequence).lower() ++ for char in "acgtn": ++ other = other.replace(char, "") ++ return len(other) < 0.2 * len(sequence) +diff --git a/antismash/common/secmet/test/test_circular_conversion.py b/antismash/common/secmet/test/test_circular_conversion.py +index e001480b..1619d425 100644 +--- a/antismash/common/secmet/test/test_circular_conversion.py ++++ b/antismash/common/secmet/test/test_circular_conversion.py +@@ -6,7 +6,7 @@ + + import unittest + +-from Bio.Seq import UnknownSeq ++from Bio.Seq import Seq + from Bio.SeqFeature import SeqFeature + from Bio.SeqRecord import SeqRecord + +@@ -16,7 +16,7 @@ + + class TestBridgeConversion(unittest.TestCase): + def setUp(self): +- self.seqrec = SeqRecord(UnknownSeq(21)) ++ self.seqrec = SeqRecord(Seq("A"*21)) + loc = CompoundLocation([FeatureLocation(12, 15, strand=1), + FeatureLocation(18, 21, strand=1), + FeatureLocation(0, 3, strand=1), +@@ -25,6 +25,7 @@ def setUp(self): + self.seqcds = SeqFeature(loc, type="CDS") + self.seqgene = SeqFeature(loc, type="gene") + self.seqrec.annotations["topology"] = "circular" ++ self.seqrec.annotations["molecule_type"] = "DNA" + + def test_bridge_in_linear_record(self): + self.seqrec.annotations["topology"] = "linear" +@@ -110,7 +111,7 @@ def test_gene_with_no_id(self): + + class TestSingleLower(TestBridgeConversion): + def setUp(self): +- self.seqrec = SeqRecord(UnknownSeq(21)) ++ self.seqrec = SeqRecord(Seq("A"*21)) + loc = CompoundLocation([FeatureLocation(12, 15, strand=1), + FeatureLocation(18, 21, strand=1), + FeatureLocation(0, 9, strand=1)], +@@ -122,7 +123,7 @@ def setUp(self): + + class TestSingleUpper(TestBridgeConversion): + def setUp(self): +- self.seqrec = SeqRecord(UnknownSeq(21)) ++ self.seqrec = SeqRecord(Seq("A"*21)) + loc = CompoundLocation([FeatureLocation(12, 21, strand=1), + FeatureLocation(0, 3, strand=1), + FeatureLocation(6, 9, strand=1)], +@@ -133,7 +134,7 @@ def setUp(self): + + class TestSingleBoth(TestBridgeConversion): + def setUp(self): +- self.seqrec = SeqRecord(UnknownSeq(21)) ++ self.seqrec = SeqRecord(Seq("A"*21)) + loc = CompoundLocation([FeatureLocation(12, 21, strand=1), + FeatureLocation(0, 9, strand=1)], + operator="join") +diff --git a/antismash/common/secmet/test/test_secmet.py b/antismash/common/secmet/test/test_secmet.py +index d802d6fd..65ac7b2c 100644 +--- a/antismash/common/secmet/test/test_secmet.py ++++ b/antismash/common/secmet/test/test_secmet.py +@@ -8,7 +8,6 @@ + import unittest + + import Bio.SeqIO +-from Bio.Alphabet.IUPAC import IUPACProtein + from Bio.Seq import Seq + from Bio.SeqFeature import FeatureLocation, SeqFeature + +@@ -78,7 +77,7 @@ def test_protein_sequences_caught(self): + assert isinstance(before.seq, Seq) + Record.from_biopython(before, taxon="bacteria") + +- before.seq = Seq("AAAA", IUPACProtein()) ++ before.annotations["molecule_type"] = "protein" + with self.assertRaisesRegex(ValueError, "protein records are not supported"): + Record.from_biopython(before, taxon="bacteria") + +@@ -789,3 +788,20 @@ def test_nonoverlapping_location(self): + cds = CDSFeature(FeatureLocation(12, 18, 1), locus_tag="test", protein_id="prot", translation="MA") + with self.assertRaisesRegex(ValueError, "same name for mapping"): + record.add_cds_feature(cds) ++ ++ ++class TestIsNuclSeq(unittest.TestCase): ++ def test_seq(self): ++ # > 20% ++ for seq in ["AGTC", "AGCTFC", "agtcfc", "AGTCFCT"]: ++ assert Record.is_nucleotide_sequence(Seq(seq)) ++ # edge case == 20% should be failure ++ assert not Record.is_nucleotide_sequence(Seq("AGFTC")) ++ # and less than 20% ++ assert not Record.is_nucleotide_sequence(Seq("AGFTCF")) ++ ++ def test_str(self): ++ for seq in ["AGTC", "AGCTFC", "agtcfc", "AGTCFCT"]: ++ assert Record.is_nucleotide_sequence(seq) ++ assert not Record.is_nucleotide_sequence("AGFTC") ++ assert not Record.is_nucleotide_sequence("AGFTCF") +diff --git a/antismash/common/serialiser.py b/antismash/common/serialiser.py +index a9ca198d..9436b60b 100644 +--- a/antismash/common/serialiser.py ++++ b/antismash/common/serialiser.py +@@ -10,8 +10,6 @@ + import logging + from typing import Any, Dict, IO, List, Union + +-import Bio.Alphabet +-import Bio.Alphabet.IUPAC + from Bio.Seq import Seq + from Bio.SeqFeature import SeqFeature, Reference + from Bio.SeqRecord import SeqRecord +@@ -179,8 +177,10 @@ def rebuild_references(annotations: Dict) -> Dict[str, List[Reference]]: + + def sequence_to_json(sequence: Seq) -> Dict[str, str]: + """ Constructs a JSON object that represents a Seq sequence """ +- return {"data": str(sequence), +- "alphabet": str(sequence.alphabet).rsplit('()')[0]} # DNA() -> DNA ++ return { ++ "data": str(sequence), ++ "alphabet": "DNA", # for compatibility, removable on schema version change ++ } + + + def sequence_from_json(data: Union[str, Dict]) -> Seq: +@@ -188,12 +188,7 @@ def sequence_from_json(data: Union[str, Dict]) -> Seq: + if isinstance(data, str): + data = json.loads(data) + assert isinstance(data, dict) +- alphabet = data["alphabet"] +- if "IUPAC" in alphabet: +- alphabet_class = getattr(Bio.Alphabet.IUPAC, alphabet) +- else: +- alphabet_class = getattr(Bio.Alphabet, alphabet) +- return Seq(data["data"], alphabet=alphabet_class()) ++ return Seq(data["data"]) + + + def feature_to_json(feature: SeqFeature) -> Dict[str, Any]: +diff --git a/antismash/common/test/helpers.py b/antismash/common/test/helpers.py +index 315c8fcc..66ff2a63 100644 +--- a/antismash/common/test/helpers.py ++++ b/antismash/common/test/helpers.py +@@ -13,7 +13,6 @@ + + import os + +-from Bio.Seq import Seq + from helperlibs.wrappers.io import TemporaryDirectory + + import antismash +@@ -46,8 +45,9 @@ def get_simple_options(module, args): + + class DummyRecord(Record): + "class for generating a Record like data structure" +- def __init__(self, features=None, seq='FAKESEQ', taxon='bacteria'): ++ def __init__(self, features=None, seq='AGCTACGT', taxon='bacteria'): + super().__init__(seq, transl_table=11 if taxon == 'bacteria' else 1) ++# self.annotations["molecule_type"] = "DNA" + if features: + for feature in features: + self.add_feature(feature) +diff --git a/antismash/common/test/test_record_processing.py b/antismash/common/test/test_record_processing.py +index 3deac06c..3f4c9852 100644 +--- a/antismash/common/test/test_record_processing.py ++++ b/antismash/common/test/test_record_processing.py +@@ -154,23 +154,6 @@ def test_no_change(self): + assert new.seq == self.record.seq + + +-class TestIsNuclSeq(unittest.TestCase): +- def test_seq(self): +- # > 20% +- for seq in ["AGTC", "AGCTFC", "agtcfc", "AGTCFCT"]: +- assert record_processing.is_nucl_seq(Seq(seq)) +- # edge case == 20% should be failure +- assert not record_processing.is_nucl_seq(Seq("AGFTC")) +- # and less than 20% +- assert not record_processing.is_nucl_seq(Seq("AGFTCF")) +- +- def test_str(self): +- for seq in ["AGTC", "AGCTFC", "agtcfc", "AGTCFCT"]: +- assert record_processing.is_nucl_seq(seq) +- assert not record_processing.is_nucl_seq("AGFTC") +- assert not record_processing.is_nucl_seq("AGFTCF") +- +- + class TestPreprocessRecords(unittest.TestCase): + def setUp(self): + class DummyModule: +diff --git a/antismash/modules/pfam2go/test/test_pfam2go.py b/antismash/modules/pfam2go/test/test_pfam2go.py +index 8f772dd6..03b80839 100644 +--- a/antismash/modules/pfam2go/test/test_pfam2go.py ++++ b/antismash/modules/pfam2go/test/test_pfam2go.py +@@ -8,7 +8,6 @@ + + from typing import Dict + +-from Bio.Alphabet import generic_dna + from Bio.Seq import Seq + from Bio.SeqFeature import FeatureLocation + +@@ -97,7 +96,7 @@ def test_get_gos(self): + + def test_blank_records(self): + blank_no_pfams = DummyRecord() +- blank_no_ids = Record(Seq("ATGTTATGAGGGTCATAACAT", generic_dna)) ++ blank_no_ids = Record(Seq("ATGTTATGAGGGTCATAACAT")) + fake_pfam = DummyPFAMDomain(identifier="PF00000") + blank_no_ids.add_pfam_domain(fake_pfam) + +diff --git a/antismash/modules/tta/test/test_tta.py b/antismash/modules/tta/test/test_tta.py +index e03f9fc5..eb27d548 100644 +--- a/antismash/modules/tta/test/test_tta.py ++++ b/antismash/modules/tta/test/test_tta.py +@@ -7,7 +7,6 @@ + from argparse import Namespace + import unittest + +-from Bio.Alphabet import generic_dna + from Bio.Seq import Seq + from Bio.SeqFeature import SeqFeature, FeatureLocation + +@@ -19,7 +18,7 @@ + class TtaTest(unittest.TestCase): + def setUp(self): + # locations: VVV VVV +- record = Record(Seq("ATGTTATGAGGGTCATAACAT", generic_dna)) ++ record = Record(Seq("ATGTTATGAGGGTCATAACAT")) + + record.add_cds_feature(DummyCDS(0, 9, strand=1)) + record.add_cds_feature(DummyCDS(12, 21, strand=-1)) +diff --git a/setup.py b/setup.py +index cba1f338..b0b02341 100644 +--- a/setup.py ++++ b/setup.py +@@ -16,7 +16,7 @@ def read(fname): + + install_requires = [ + 'numpy', +- 'biopython >=1.71,<1.77', ++ 'biopython >=1.78', + 'helperlibs', + 'jinja2', + 'joblib', + +From 98dbffe5a726444bdf9b24c8f8664533a3d450eb Mon Sep 17 00:00:00 2001 +From: Simon Shaw +Date: Tue, 27 Oct 2020 10:01:59 +0100 +Subject: [PATCH 2/2] chore: bump minimum python version to 3.7 + +--- + setup.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/setup.py b/setup.py +index b0b02341..c7709966 100644 +--- a/setup.py ++++ b/setup.py +@@ -95,7 +95,7 @@ def run_tests(self): + + setup( + name="antismash", +- python_requires='>=3.5', ++ python_requires='>=3.7', + version=read_version(), + packages=find_packages(exclude=["*.tests", "*.tests.*", "tests.*", "tests"]), + package_data={ diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb new file mode 100644 index 00000000000..947e4cda9a7 --- /dev/null +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GlimmerHMM' +version = '3.0.4c' + +homepage = 'https://ccb.jhu.edu/software/glimmerhmm' +description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. + Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally + it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted + from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] +sources = [SOURCE_TAR_GZ] +checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] + +start_dir = 'sources' + +# make sure -O0 is not used as compiler option +prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && " + +# also build in 'train' subdirectory to overwrite pre-compiled binaries +buildopts = "&& cd ../train && make" + +local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp', + 'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP', + 'scoreSTOP2', 'splicescore', 'trainGlimmerHMM'] +files_to_copy = [ + (['sources/%(namelower)s'], 'bin'), + (['train/%s' % x for x in local_train_files], 'bin'), + 'trained_dir', 'README', 'train/readme.train', +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['trained_dir'], +} + +sanity_check_commands = [('%(namelower)s -h')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb new file mode 100644 index 00000000000..496d7c1314c --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'HMMER2' +version = '2.3.2' + +homepage = 'http://hmmer.org' +description = """HMMER is used for searching sequence databases for sequence homologs, + and for making sequence alignments.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://eddylab.org/software/hmmer'] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4'] + +postinstallcmds = ["cd %(installdir)s/bin && for cmd in $(ls); do mv ${cmd} ${cmd}2; done"] + +local_cmd_suffixes = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'index', 'pfam', 'search'] + +sanity_check_paths = { + 'files': ['bin/hmm%s2' % x for x in local_cmd_suffixes], + 'dirs': ['man'], +} + +sanity_check_commands = ["hmm%s2 -h" % x for x in local_cmd_suffixes] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb new file mode 100644 index 00000000000..75cf15432a6 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = "3.8.1551" + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.drive5.com/muscle/'] +sources = ['%(namelower)s_src_%(version)s.tar.gz'] +checksums = ['c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e'] + +# use correct compiler flags + +# don't use -static when linking, since that implies requiring glibc-static to be installed +buildopts = 'CFLAGS="$CXXFLAGS" LDLIBS="-lm"' + +files_to_copy = [(["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/%(namelower)s"], + 'dirs': [], +} + +moduleclass = 'bio' From cacc2959d453481845a3c0e91c704933f1b5d218 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 18 May 2021 13:50:27 +0200 Subject: [PATCH 0186/9987] adding easyconfigs: Nipype-1.6.0-foss-2020b.eb --- .../n/Nipype/Nipype-1.6.0-foss-2020b.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb new file mode 100644 index 00000000000..b4ace4a2053 --- /dev/null +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb @@ -0,0 +1,87 @@ +easyblock = 'PythonBundle' + +name = 'Nipype' +version = '1.6.0' + +homepage = 'https://nipype.readthedocs.io' +description = """Nipype is a Python project that provides a uniform interface to existing neuroimaging software and + facilitates interaction between these packages within a single workflow.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('lxml', '4.6.2'), + ('networkx', '2.5'), + ('NiBabel', '3.2.1'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('traits', '6.2.0', { + 'checksums': ['16fa1518b0778fd53bf0547e6a562b1787bf68c8f6b7995a13bd1902529fdb0c'], + }), + ('pydot', '1.4.2', { + 'checksums': ['248081a39bcb56784deb018977e428605c1c758f10897a339fce1dd728ff007d'], + }), + ('pydotplus', '2.0.2', { + 'checksums': ['91e85e9ee9b85d2391ead7d635e3d9c7f5f44fd60a60e59b13e2403fa66505c4'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('isodate', '0.6.0', { + 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], + }), + ('rdflib', '5.0.0', { + 'checksums': ['78149dd49d385efec3b3adfbd61c87afaf1281c30d3fcaf1b323b34f603fb155'], + }), + ('prov', '2.0.0', { + 'checksums': ['b6438f2195ecb9f6e8279b58971e02bc51814599b5d5383366eef91d867422ee'], + }), + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + ('pytest-forked', '1.3.0', { + 'modulename': 'pytest_forked', + 'checksums': ['6aa9ac7e00ad1a539c41bec6d21011332de671e938c7637378ec9710204e37ca'], + }), + ('apipkg', '1.5', { + 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], + }), + ('execnet', '1.8.0', { + 'checksums': ['b73c5565e517f24b62dea8a5ceac178c661c4309d3aa0c3e420856c072c411b4'], + }), + ('pytest-xdist', '2.2.1', { + 'modulename': 'xdist', + 'checksums': ['718887296892f92683f6a51f25a3ae584993b06f7076ce1e1fd482e59a8220a2'], + }), + ('ci-info', '0.2.0', { + 'checksums': ['dd70632c977feb8797b1e633507166b64ad5f57183cebb2b0ea56934abba4616'], + }), + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], + }), + ('etelemetry', '0.2.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3e304ea9070902e6367282369cb8eaae05f4beef9313820053cc03f611bd1e29'], + }), + ('nipype', version, { + 'preinstallopts': "sed -i'' 's/.*neurdflib.*//g' nipype/info.py && ", + 'checksums': ['bc56ce63f74c9a9a23c6edeaf77631377e8ad2bea928c898cc89527a47f101cf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/nipypecli'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import nipype.interfaces'"] + +sanity_pip_check = True + +moduleclass = 'vis' From de17db005227572403b54af721a5f508d09c753c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 19 May 2021 09:57:38 +0100 Subject: [PATCH 0187/9987] Add missing checksum --- .../easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb index 049e4c237bc..6164b5dac92 100644 --- a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb +++ b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb @@ -24,7 +24,10 @@ source_urls = ['https://github.com/biocore/%(namelower)s/archive/'] sources = ['%(version)s.tar.gz'] # Patch for double includes of header files in Makefile.in patches = ['%(name)s-%(version)s_Makefile.in.patch'] - +checksums = [ + '44a3b29570e339da235acc00a35cde18f4fff03b7087b0fa8100f6c3826385d5', # 2.1.tar.gz + '0137ee3d4c583f3c4a4b18aadd1029e8a9cf0ff1748d364d993b82482777d4d5', # SortMeRNA-2.1_Makefile.in.patch +] sanity_check_paths = { 'files': ['bin/indexdb_rna', 'bin/%(namelower)s'], From 88d33b345fc467e06a6d18b7617c1df937f9a718 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 19 May 2021 13:15:53 +0100 Subject: [PATCH 0188/9987] Use https for homepage --- easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb index 6164b5dac92..3aac61c0081 100644 --- a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb +++ b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'SortMeRNA' version = '2.1' -homepage = 'http://bioinfo.lifl.fr/RNA/sortmerna/' +homepage = 'https://bioinfo.lifl.fr/RNA/sortmerna/' description = "SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads." toolchain = {'name': 'foss', 'version': '2020a'} From beac104fbfb6a6d2c785c30aa0ae3465909705c5 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 21 May 2021 14:52:44 +0950 Subject: [PATCH 0189/9987] adding easyconfigs: MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb --- ...MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..5f5569489c8 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,52 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# Software License:: MIT +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'MetaPhlAn' +version = '3.0.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/biobakery/MetaPhlAn' +description = """MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data """ + +source_urls = ['https://github.com/biobakery/MetaPhlAn/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['de965469e4f93e3dd5c9e2dac8914f7debd242c196f343cd7cefd8c7faddd33c'] + +toolchain = {'name':'foss', 'version':'2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Perl', '5.30.2'), + ('Bowtie2', '2.4.1'), + ('SAMtools', '1.10'), + ('BLAST', '2.11.0', '-Linux_x86_64', True), + ('MAFFT', '7.470', '-with-extensions'), + ('RAxML', '8.2.12', '-hybrid-avx2'), + ('DIAMOND', '2.0.4'), + ('trimAl', '1.4.1'), + ('FastTree', '2.1.11'), +] + +modextrapaths = { + 'PATH': 'bin', +} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']], + 'dirs': ['bin', 'lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': 'metaphlan'} + +moduleclass = 'bio' From 8afa13565408a3a9683c848d36b984b5a9121c51 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 21 May 2021 16:00:36 +0950 Subject: [PATCH 0190/9987] Syntax fix --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index 5f5569489c8..7824b57fa65 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -15,13 +15,14 @@ version = '3.0.9' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/biobakery/MetaPhlAn' -description = """MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data """ +description = """MetaPhlAn is a computational tool for profiling the composition + of microbial communities from metagenomic shotgun sequencing data """ source_urls = ['https://github.com/biobakery/MetaPhlAn/archive'] sources = ['%(version)s.tar.gz'] checksums = ['de965469e4f93e3dd5c9e2dac8914f7debd242c196f343cd7cefd8c7faddd33c'] -toolchain = {'name':'foss', 'version':'2020a'} +toolchain = {'name': 'foss', 'version': '2020a'} dependencies = [ ('Python', '3.8.2'), From 160966ddf4bc2b075025febaf75531bd84798d3c Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Sat, 22 May 2021 18:41:38 +0950 Subject: [PATCH 0191/9987] lib PATH + --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index 7824b57fa65..6bba4f19e22 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -39,7 +39,8 @@ dependencies = [ ] modextrapaths = { - 'PATH': 'bin', + 'LIBRARY_PATH': 'lib', + 'LD_LIBRARY_PATH': 'lib' } sanity_check_paths = { From 96d41982ace2f56b89d7fc76de4cca38eb9feb20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 May 2021 16:06:11 +0200 Subject: [PATCH 0192/9987] {lang}[intel/2021.03] SciPy-bundle v2021.05 w/ Python 3.9.5 (WIP) --- .../SciPy-bundle-2021.05-intel-2021.03.eb | 65 +++ ...-1.20.3_disable-broken-override-test.patch | 13 + ...pu-feature-detection-intel-compilers.patch | 530 ++++++++++++++++++ 3 files changed, 608 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021.03.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_disable-broken-override-test.patch create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021.03.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021.03.eb new file mode 100644 index 00000000000..63b4ab5a7ea --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021.03.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2021.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intel', 'version': '2021.03'} +toolchainopts = {'pic': True, 'lowopt': True, 'strict': True} + +builddependencies = [('hypothesis', '6.13.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('pybind11', '2.6.2'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.20.3', { + 'patches': [ + 'numpy-1.18.2-mkl.patch', + 'numpy-1.20.3_disable-broken-override-test.patch', + 'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch', + ], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': [ + 'e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69', # numpy-1.20.3.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + # numpy-1.20.3_disable-broken-override-test.patch + '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', + # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch + '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046', + ], + }), + ('scipy', '1.6.3', { + 'checksums': ['a75b014d3294fce26852a9d04ea27b5671d86736beb34acdfc05859246260707'], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('numexpr', '2.7.3', { + 'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '1.2.4', { + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'checksums': ['649ecab692fade3cbfcf967ff936496b0cfba0af00a55dfaacd82bdda5cb2279'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_disable-broken-override-test.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_disable-broken-override-test.patch new file mode 100644 index 00000000000..4abd30fce6a --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_disable-broken-override-test.patch @@ -0,0 +1,13 @@ +skip broken test, see https://github.com/numpy/numpy/issues/16769 +author: Kenneth Hoste (HPC-UGent) +--- numpy-1.20.3/numpy/distutils/tests/test_system_info.py.orig 2021-05-09 12:38:00.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/tests/test_system_info.py 2021-05-26 09:49:48.966125918 +0200 +@@ -254,7 +254,7 @@ + finally: + os.chdir(previousDir) + +- def test_overrides(self): ++ def ignored_test_overrides(self): + previousDir = os.getcwd() + cfg = os.path.join(self._dir1, 'site.cfg') + shutil.copy(self._sitecfg, cfg) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch new file mode 100644 index 00000000000..142059b827a --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch @@ -0,0 +1,530 @@ +see https://github.com/numpy/numpy/issues/19084 + https://github.com/numpy/numpy/pull/19098 + +diff -ru numpy-1.20.3.orig/numpy/distutils/ccompiler_opt.py numpy-1.20.3/numpy/distutils/ccompiler_opt.py +--- numpy-1.20.3.orig/numpy/distutils/ccompiler_opt.py 2021-05-09 12:38:00.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/ccompiler_opt.py 2021-05-26 08:50:31.482607838 +0200 +@@ -552,7 +552,7 @@ + sources, extra_postargs=flags, **kwargs + ) + +- def dist_test(self, source, flags): ++ def dist_test(self, source, flags, macros=[]): + """Return True if 'CCompiler.compile()' able to compile + a source file with certain flags. + """ +@@ -569,7 +569,7 @@ + test = False + try: + self.dist_compile( +- [source], flags, output_dir=self.conf_tmp_path ++ [source], flags, macros=macros, output_dir=self.conf_tmp_path + ) + test = True + except CompileError as e: +@@ -1163,20 +1163,23 @@ + + self.feature_is_cached = True + +- def feature_names(self, names=None, force_flags=None): ++ def feature_names(self, names=None, force_flags=None, macros=[]): + """ + Returns a set of CPU feature names that supported by platform and the **C** compiler. + + Parameters + ---------- +- 'names': sequence or None, optional ++ names: sequence or None, optional + Specify certain CPU features to test it against the **C** compiler. + if None(default), it will test all current supported features. + **Note**: feature names must be in upper-case. + +- 'force_flags': list or None, optional +- If None(default), default compiler flags for every CPU feature will be used +- during the test. ++ force_flags: list or None, optional ++ If None(default), default compiler flags for every CPU feature will ++ be used during the test. ++ ++ macros : list of tuples, optional ++ A list of C macro definitions. + """ + assert( + names is None or ( +@@ -1189,7 +1192,9 @@ + names = self.feature_supported.keys() + supported_names = set() + for f in names: +- if self.feature_is_supported(f, force_flags=force_flags): ++ if self.feature_is_supported( ++ f, force_flags=force_flags, macros=macros ++ ): + supported_names.add(f) + return supported_names + +@@ -1424,20 +1429,23 @@ + return self.cc_normalize_flags(flags) + + @_Cache.me +- def feature_test(self, name, force_flags=None): ++ def feature_test(self, name, force_flags=None, macros=[]): + """ + Test a certain CPU feature against the compiler through its own + check file. + + Parameters + ---------- +- 'name': str ++ name: str + Supported CPU feature name. + +- 'force_flags': list or None, optional ++ force_flags: list or None, optional + If None(default), the returned flags from `feature_flags()` + will be used. +- """ ++ ++ macros : list of tuples, optional ++ A list of C macro definitions. ++ """ + if force_flags is None: + force_flags = self.feature_flags(name) + +@@ -1453,24 +1461,29 @@ + if not os.path.exists(test_path): + self.dist_fatal("feature test file is not exist", test_path) + +- test = self.dist_test(test_path, force_flags + self.cc_flags["werror"]) ++ test = self.dist_test( ++ test_path, force_flags + self.cc_flags["werror"], macros ++ ) + if not test: + self.dist_log("testing failed", stderr=True) + return test + + @_Cache.me +- def feature_is_supported(self, name, force_flags=None): ++ def feature_is_supported(self, name, force_flags=None, macros=[]): + """ + Check if a certain CPU feature is supported by the platform and compiler. + + Parameters + ---------- +- 'name': str ++ name: str + CPU feature name in uppercase. + +- 'force_flags': list or None, optional +- If None(default), default compiler flags for every CPU feature will be used +- during test. ++ force_flags: list or None, optional ++ If None(default), default compiler flags for every CPU feature will ++ be used during test. ++ ++ macros : list of tuples, optional ++ A list of C macro definitions. + """ + assert(name.isupper()) + assert(force_flags is None or isinstance(force_flags, list)) +@@ -1478,9 +1491,9 @@ + supported = name in self.feature_supported + if supported: + for impl in self.feature_implies(name): +- if not self.feature_test(impl, force_flags): ++ if not self.feature_test(impl, force_flags, macros=macros): + return False +- if not self.feature_test(name, force_flags): ++ if not self.feature_test(name, force_flags, macros=macros): + return False + return supported + +@@ -1803,7 +1816,9 @@ + self.dist_fatal(arg_name, + "native option isn't supported by the compiler" + ) +- features_to = self.feature_names(force_flags=native) ++ features_to = self.feature_names( ++ force_flags=native, macros=[("DETECT_FEATURES", 1)] ++ ) + elif TOK == "MAX": + features_to = self.feature_supported.keys() + elif TOK == "MIN": +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx2.c numpy-1.20.3/numpy/distutils/checks/cpu_avx2.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx2.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_avx2.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __AVX2__ ++ #error "HOST/ARCH doesn't support AVX2" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512cd.c numpy-1.20.3/numpy/distutils/checks/cpu_avx512cd.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512cd.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_avx512cd.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __AVX512CD__ ++ #error "HOST/ARCH doesn't support AVX512CD" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_clx.c numpy-1.20.3/numpy/distutils/checks/cpu_avx512_clx.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_clx.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_avx512_clx.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __AVX512VNNI__ ++ #error "HOST/ARCH doesn't support CascadeLake AVX512 features" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_cnl.c numpy-1.20.3/numpy/distutils/checks/cpu_avx512_cnl.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_cnl.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_avx512_cnl.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #if !defined(__AVX512VBMI__) || !defined(__AVX512IFMA__) ++ #error "HOST/ARCH doesn't support CannonLake AVX512 features" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512f.c numpy-1.20.3/numpy/distutils/checks/cpu_avx512f.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512f.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_avx512f.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __AVX512F__ ++ #error "HOST/ARCH doesn't support AVX512F" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_icl.c numpy-1.20.3/numpy/distutils/checks/cpu_avx512_icl.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_icl.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_avx512_icl.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #if !defined(__AVX512VPOPCNTDQ__) || !defined(__AVX512BITALG__) || !defined(__AVX512VPOPCNTDQ__) ++ #error "HOST/ARCH doesn't support IceLake AVX512 features" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_knl.c numpy-1.20.3/numpy/distutils/checks/cpu_avx512_knl.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_knl.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_avx512_knl.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #if !defined(__AVX512ER__) || !defined(__AVX512PF__) ++ #error "HOST/ARCH doesn't support Knights Landing AVX512 features" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_knm.c numpy-1.20.3/numpy/distutils/checks/cpu_avx512_knm.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_knm.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_avx512_knm.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #if !defined(__AVX5124FMAPS__) || !defined(__AVX5124VNNIW__) || !defined(__AVX512VPOPCNTDQ__) ++ #error "HOST/ARCH doesn't support Knights Mill AVX512 features" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_skx.c numpy-1.20.3/numpy/distutils/checks/cpu_avx512_skx.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx512_skx.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_avx512_skx.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #if !defined(__AVX512VL__) || !defined(__AVX512BW__) || !defined(__AVX512DQ__) ++ #error "HOST/ARCH doesn't support SkyLake AVX512 features" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx.c numpy-1.20.3/numpy/distutils/checks/cpu_avx.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_avx.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_avx.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __AVX__ ++ #error "HOST/ARCH doesn't support AVX" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_f16c.c numpy-1.20.3/numpy/distutils/checks/cpu_f16c.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_f16c.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_f16c.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __F16C__ ++ #error "HOST/ARCH doesn't support F16C" ++ #endif ++#endif ++ + #include + #include + +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_fma3.c numpy-1.20.3/numpy/distutils/checks/cpu_fma3.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_fma3.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_fma3.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #if !defined(__FMA__) && !defined(__AVX2__) ++ #error "HOST/ARCH doesn't support FMA3" ++ #endif ++#endif ++ + #include + #include + +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_popcnt.c numpy-1.20.3/numpy/distutils/checks/cpu_popcnt.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_popcnt.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_popcnt.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env vr `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #if !defined(__SSE4_2__) && !defined(__POPCNT__) ++ #error "HOST/ARCH doesn't support POPCNT" ++ #endif ++#endif ++ + #ifdef _MSC_VER + #include + #else +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_sse2.c numpy-1.20.3/numpy/distutils/checks/cpu_sse2.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_sse2.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_sse2.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __SSE2__ ++ #error "HOST/ARCH doesn't support SSE2" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_sse3.c numpy-1.20.3/numpy/distutils/checks/cpu_sse3.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_sse3.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_sse3.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __SSE3__ ++ #error "HOST/ARCH doesn't support SSE3" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_sse41.c numpy-1.20.3/numpy/distutils/checks/cpu_sse41.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_sse41.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_sse41.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __SSE4_1__ ++ #error "HOST/ARCH doesn't support SSE41" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_sse42.c numpy-1.20.3/numpy/distutils/checks/cpu_sse42.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_sse42.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_sse42.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __SSE4_2__ ++ #error "HOST/ARCH doesn't support SSE42" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_sse.c numpy-1.20.3/numpy/distutils/checks/cpu_sse.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_sse.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_sse.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __SSE__ ++ #error "HOST/ARCH doesn't support SSE" ++ #endif ++#endif ++ + #include + + int main(void) +diff -ru numpy-1.20.3.orig/numpy/distutils/checks/cpu_ssse3.c numpy-1.20.3/numpy/distutils/checks/cpu_ssse3.c +--- numpy-1.20.3.orig/numpy/distutils/checks/cpu_ssse3.c 2021-05-08 20:35:28.000000000 +0200 ++++ numpy-1.20.3/numpy/distutils/checks/cpu_ssse3.c 2021-05-26 08:50:31.482607838 +0200 +@@ -1,3 +1,16 @@ ++#if defined(DETECT_FEATURES) && defined(__INTEL_COMPILER) ++ /* ++ * Unlike GCC and CLANG, Intel Compiler exposes all supported intrinsics, ++ * whether or not the build options for those features are specified. ++ * Therefore, we must test #definitions of CPU features when option native/host ++ * is enabled via `--cpu-baseline` or through env var `CFLAGS` otherwise ++ * the test will be broken and leads to enable all possible features. ++ */ ++ #ifndef __SSSE3__ ++ #error "HOST/ARCH doesn't support SSSE3" ++ #endif ++#endif ++ + #include + + int main(void) From 0f762c1d8482bb7f0f5b8fb3639a1ba7222d16c6 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 28 May 2021 11:44:58 +0950 Subject: [PATCH 0193/9987] MAFFT ver downgrade to 7.453 --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index 6bba4f19e22..d42e309a208 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -31,7 +31,7 @@ dependencies = [ ('Bowtie2', '2.4.1'), ('SAMtools', '1.10'), ('BLAST', '2.11.0', '-Linux_x86_64', True), - ('MAFFT', '7.470', '-with-extensions'), + ('MAFFT', '7.453 53 53 53 53 ', '-with-extensions'), ('RAxML', '8.2.12', '-hybrid-avx2'), ('DIAMOND', '2.0.4'), ('trimAl', '1.4.1'), From 5dbf3125e17486b0b568ff87949f7f1b9a9bdc85 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 28 May 2021 12:01:07 +0950 Subject: [PATCH 0194/9987] MAFFT ver typo fix --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index d42e309a208..c617510fa38 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -31,7 +31,7 @@ dependencies = [ ('Bowtie2', '2.4.1'), ('SAMtools', '1.10'), ('BLAST', '2.11.0', '-Linux_x86_64', True), - ('MAFFT', '7.453 53 53 53 53 ', '-with-extensions'), + ('MAFFT', '7.453', '-with-extensions'), ('RAxML', '8.2.12', '-hybrid-avx2'), ('DIAMOND', '2.0.4'), ('trimAl', '1.4.1'), From 9687dc5ab3907862c67da6863e85cfbf223ea43c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 May 2021 09:39:39 +0200 Subject: [PATCH 0195/9987] adding easyconfigs: Boost-1.76.0-GCC-10.3.0.eb, Boost-1.76.0-intel-compilers-2021.2.0.eb --- .../b/Boost/Boost-1.76.0-GCC-10.3.0.eb | 29 +++++++++++++++++++ .../Boost-1.76.0-intel-compilers-2021.2.0.eb | 28 ++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..650eee3178d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb @@ -0,0 +1,29 @@ +## +# Authors:: Denis Kristak +## +name = 'Boost' +version = '1.76.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['7bd7ddceec1a1dfdcbdb3e609b60d01739c38390a5f956385a12f3122049f0ca'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, enable threading support +boost_mpi = False +boost_multi_thread = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..9839c3bf6aa --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb @@ -0,0 +1,28 @@ +name = 'Boost' +version = '1.76.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} +# add C++ compiler option as workaround for "error: no instance of constructor .* matches the argument list" errors +#toolchainopts = {'pic': True, 'extra_cxxflags': '-DBOOST_ASIO_USE_TS_EXECUTOR_AS_DEFAULT=1'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['7bd7ddceec1a1dfdcbdb3e609b60d01739c38390a5f956385a12f3122049f0ca'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, enable threading support +boost_mpi = False +boost_multi_thread = True + +moduleclass = 'devel' From 2ccfa92ce54f2f465fef2ac9c981e2585e2706fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 May 2021 09:51:29 +0200 Subject: [PATCH 0196/9987] remove commented out toolchainopts in Boost 1.76.0 easyconfig using intel-compilers toolchain --- .../b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb index 9839c3bf6aa..1c1f2bb6389 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb @@ -5,8 +5,6 @@ homepage = 'https://www.boost.org/' description = """Boost provides free peer-reviewed portable C++ source libraries.""" toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} -# add C++ compiler option as workaround for "error: no instance of constructor .* matches the argument list" errors -#toolchainopts = {'pic': True, 'extra_cxxflags': '-DBOOST_ASIO_USE_TS_EXECUTOR_AS_DEFAULT=1'} toolchainopts = {'pic': True} source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] From 1dfc81719e8294fd93a131fa89485599ff6a73fb Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 3 Jun 2021 16:41:41 +0950 Subject: [PATCH 0197/9987] pip + dep settings turned on --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index c617510fa38..d49afd6c48a 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -38,6 +38,10 @@ dependencies = [ ('FastTree', '2.1.11'), ] +use_pip = True +sanity_pip_check = True +download_dep_fail = True + modextrapaths = { 'LIBRARY_PATH': 'lib', 'LD_LIBRARY_PATH': 'lib' From fcc4568e6060e80a6e70b1af5e47c951950f9e9a Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 4 Jun 2021 20:11:59 +0950 Subject: [PATCH 0198/9987] adding easyconfigs: libplinkio-0.9.8-GCCcore-8.3.0.eb --- .../libplinkio-0.9.8-GCCcore-8.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..076825ebcc6 --- /dev/null +++ b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb @@ -0,0 +1,37 @@ +## +# This easyconfig is contributed by DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: BSD +# +# Notes:: +## + +easyblock = 'CMakeMake' + +name = 'libplinkio' +version = '0.9.8' + +homepage = "https://github.com/mfranberg/libplinkio" +description = """A small C and Python library for reading PLINK genotype files.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/mfranberg/%(namelower)s/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['de54dd4789b2da9b937a1f445dc6976153211dc35b4376a4cf561ad2ee861075'] + +builddependencies = [ + ('CMake', '3.15.3'), + ('binutils', '2.32'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/%(name)s.so'], + 'dirs': ['lib', 'include'], +} + +moduleclass = 'lib' From fc8e277b34876d18bea8756d8057a438826de4b5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 4 Jun 2021 15:58:25 +0100 Subject: [PATCH 0199/9987] adding easyconfigs: R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb, ncdf4-1.17-foss-2021a-R-4.1.0.eb --- .../n/ncdf4/ncdf4-1.17-foss-2021a-R-4.1.0.eb | 29 + ...le-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 1063 +++++++++++++++++ 2 files changed, 1092 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2021a-R-4.1.0.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..8a4f0dec1a2 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.17-foss-2021a-R-4.1.0.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.17' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/%(name)s' +description = "ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['db95c4729d3187d1a56dfd019958216f442be6221bd15e23cd597e6129219af6'] + +dependencies = [ + ('R', '4.1.0'), + ('netCDF', '4.8.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..f0887fb1855 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -0,0 +1,1063 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.13' +versionsuffix = '-R-%(rver)s' + +local_biocver = version + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('R', '4.1.0'), + ('Boost', '1.76.0'), # for mzR + ('GSL', '2.7'), # for flowClust + ('HDF5', '1.10.7'), # for rhdf5 + ('ncdf4', '1.17', versionsuffix), # for mzR +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.13/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.13/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.13/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on 3rd June 2021 +exts_list = [ + ('BiocGenerics', '0.38.0', { + 'checksums': ['a692fe68256578fc1beb60630cfd45ffc3b003ad36801dce8970c4e9eba767cf'], + }), + ('Biobase', '2.52.0', { + 'checksums': ['79abe91af6c5c133582fd08d2035f65034ad90eae5b81b74fa147e6010e2e8e9'], + }), + ('S4Vectors', '0.30.0', { + 'checksums': ['98dce0f9a5f92419e6fa5ce4237e1b352c964b2ad4fd5afddbf108055eedbb6c'], + }), + ('IRanges', '2.26.0', { + 'checksums': ['7d1e8fcbd1f9fc9005765e216418d819775452a77e48a59b80347eb93047f237'], + }), + ('GenomeInfoDbData', '1.2.6', { + 'checksums': ['09209adea5f0ea69535b27710b191f2679f83ccc0bd4342a4d91a9dcf0f91f31'], + }), + ('GenomeInfoDb', '1.28.0', { + 'checksums': ['c36427b5689db58cb1489e6e6c0fd5ce1244ad6fb2d4bf1a7334e579a03e4d72'], + }), + ('zlibbioc', '1.38.0', { + 'checksums': ['3702d30db5ddb22ea2907f533509894b9b50a3d7e50dedfcf761fe29825b65b7'], + }), + ('XVector', '0.32.0', { + 'checksums': ['192b8175d836bf574254cf163580cc7f18fc6c3eb49f7136a057ab98da2383b3'], + }), + ('Biostrings', '2.60.0', { + 'checksums': ['fe0b28157ea2e11700f2b920f76d89d7f8199276a4a19e6478875070b9812d76'], + }), + ('KEGGREST', '1.32.0', { + 'checksums': ['8d5daf8823a1b906fb2222a0d0db947d06cffe728641278af5f18f0d441b6194'], + }), + ('AnnotationDbi', '1.54.0', { + 'checksums': ['f06a5df46a902a0fe7462ac4f2dddaa356a5729f85ec997bd6f01a85e381ff84'], + }), + ('GenomicRanges', '1.44.0', { + 'checksums': ['1da88df1a1bf9aa97ffc46fa70ccc329fa773e743e49f0e0b06ad2c65933ace3'], + }), + ('BiocParallel', '1.26.0', { + 'checksums': ['401297f6ea653be0272a8b3d6b656110b7bef269e132cfe373baf62e557b849f'], + }), + ('Rhtslib', '1.24.0', { + 'checksums': ['8e66aeaa25f3a1f87ec9fafcc54381664d55c0b7738029a260318982d27e9729'], + }), + ('Rsamtools', '2.8.0', { + 'checksums': ['05ab1ef36e9f5d3b4583929d5c461bc863aed9674fea0267edf58ebe5681302b'], + }), + ('MatrixGenerics', '1.4.0', { + 'checksums': ['ba88596471c750d3ec07f0f4ab359dc60dfcbb5e2d8f60a175bc88a0695203f7'], + }), + ('DelayedArray', '0.18.0', { + 'checksums': ['59e2f53c97ccac0f74015bbb50ba576da4afec615b1a9df0b6ece3268c10c370'], + }), + ('SummarizedExperiment', '1.22.0', { + 'checksums': ['2f58077942686218a01ef5645a41516a71eea7f666450a2b32713d69662cd79a'], + }), + ('GenomicAlignments', '1.28.0', { + 'checksums': ['e242de78aab5ba1d8f1d4f72801b5915cdaef544f017305fb709c12941083803'], + }), + ('ShortRead', '1.50.0', { + 'checksums': ['e372bcda18598826a445fc3116f7b226689e63fc717e680b0bbb40c306b7117f'], + }), + ('graph', '1.70.0', { + 'checksums': ['aa6701bad9af248cd4174e0874472244daa9f01e4d636ccd7c84cfd2500afac4'], + }), + ('affyio', '1.62.0', { + 'checksums': 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['6cad635fe196a739bfb9839e6c6d1690ff4036a8f1af2ec15f28382ba806cc43'], + }), + ('qvalue', '2.24.0', { + 'checksums': ['f55a09483db70a4cdcb26979daebb92d1711f9655fd98a883b1906e89c555a77'], + }), + ('impute', '1.66.0', { + 'checksums': ['33341ffd43051d3521b59d60c5ddc475453bfcc65b6bd61aa5b06f55c49ef95e'], + }), + ('shinyFiles', '0.9.0', { + 'checksums': ['51ad2aad61bcae22fb2c48a79d02bf6f86e36ffc49a3b64e26a76d133a955167'], + }), + ('samr', '3.0', { + 'checksums': ['25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506'], + }), + ('DEGseq', '1.46.0', { + 'checksums': ['0a06703453f1c666a7251504ab739540746f7f122a83fcf4af9e4b865eab1216'], + }), + ('hgu133plus2.db', '3.13.0', { + 'checksums': ['ddde58e777a8341536a664c7d4be874a2f395f8aaa019c1f738462a8ce74cc44'], + }), + ('illuminaio', '0.34.0', { + 'checksums': ['69d3e7e790256dc871f54cba8ee2b83e3db643f79747d55bf584ebbfec88c0eb'], + }), + ('BiocIO', '1.2.0', { + 'checksums': ['f09625df03bbbe07ab8d7172696408bd8075e0ff2ee3db228c783a43fbb57c6a'], + }), + ('restfulr', '0.0.13', { + 'checksums': ['7b59f5887aaf02f46a80617f4d1e0ffd4e11e4840e9e2fbd486a9a9c7f2d64b6'], + }), + ('rtracklayer', '1.52.0', { + 'checksums': ['1b3e9e8cd3ea7e6d13ea1dbcdfe1d7aeda0c459946bbdaae4f4d6acac0032c46'], + }), + ('filelock', '1.0.2', { + 'checksums': ['ac2915950789b16c43a625a2b8dab6ba423588db4a7d0daa75b74518b82b1403'], + }), + ('BiocFileCache', '2.0.0', { + 'checksums': ['bb77b8e8de8df4e9a65abd459b45a8d44bc894308d6aad1e1e43cca52a24af7a'], + }), + ('biomaRt', '2.48.0', { + 'checksums': ['a5383f391a7bf5fb8078582d803e0ccf50e8e7fd0a5a6acbf1c16f3c4cfb14c1'], + }), + ('GenomicFeatures', '1.44.0', { + 'checksums': ['cf915a63b5154e5704a15fe46a922954b3f43d66fd183b57174767c7dcb6f478'], + }), + ('bumphunter', '1.34.0', { + 'checksums': ['5b604e753c1e387a704cc468bcb133ccedd33bf5d0c54e3a0819a3e8f8462372'], + }), + ('multtest', '2.48.0', { + 'checksums': ['2a718469c69022ff762badfcb5abe5ca665b86223049b12e0c613f4ac92e21f2'], + }), + ('scrime', '1.3.5', { + 'checksums': ['5d97d3e57d8eb30709340fe572746029fd139456d7a955421c4e3aa75d825578'], + }), + ('siggenes', '1.66.0', { + 'checksums': ['0e528edd7c95b4d82785c2a2ce24e1f660122c9171675784f197b95284036a53'], + }), + ('DynDoc', '1.70.0', { + 'checksums': ['9074872276017c04e5e7a2f5651ac4d9255156b236877cf7d04ab6415c1ed322'], + }), + ('NOISeq', '2.36.0', { + 'checksums': ['3f4ac4e23c6634ba01908500a0adff2af3cc830b6450c5e73c553f2f760ba5a1'], + }), + ('Rgraphviz', '2.36.0', { + 'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'], + 'checksums': [ + '1a519beb85f931224d0afa5545724c2d302f5dfde7716259316191fc76c01d34', # Rgraphviz_2.36.0.tar.gz + # Rgraphviz-2.28.0_fno-tree-vectorize.patch + '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9', + ], + }), + ('RNASeqPower', '1.32.0', { + 'checksums': ['0ad4cdd72d29d6b8be00d504ba6b01f44c5550b38c7747f019e8469de5f97d9e'], + }), + ('annotate', '1.70.0', { + 'checksums': ['e7eb71f67dbfd5813cd68485f452e2619a461024ed03bedae1ba18c84d2ade8e'], + }), + ('GSEABase', '1.54.0', { + 'checksums': ['7618e77120ce9531d019b00f71363b1be6fc3b105818d12daee9e83afd9c8624'], + }), + ('genefilter', '1.74.0', { + 'checksums': ['13138f8cac1da15fdc59b4e98a67152e3158edfb69b9a22759895db068bdc937'], + }), + ('Category', '2.58.0', { + 'checksums': ['3d9ceceef4222a0c44a4df716f249b4b0b70530500dfa2580d856104cfbae638'], + }), + ('GOstats', '2.58.0', { + 'checksums': ['8aa767c4626261001fa5b81418867d21f5a477bbc98fb98d13f9b98a8de75a4a'], + }), + ('BSgenome', '1.60.0', { + 'checksums': ['968504723d9933e561bac5da87d5c29e20bba8f623ff05aeb0393495aed611ca'], + }), + ('VariantAnnotation', '1.38.0', { + 'checksums': ['301b906e144e33d85582242e9147de5fd2c0e4099193dd80357a0d8524003931'], + }), + ('interactiveDisplayBase', '1.30.0', { + 'checksums': ['3b0abd6aee0ced9b7301791d62b21984504f5ba9e0427ea4598f6afa6ace2f03'], + }), + ('BiocVersion', '3.13.1', { + 'checksums': ['d1ad6a280ce314ff5b1b9e8daec9c41de6369a3fa1a3be7ee092ddf0c8435c67'], + }), + ('AnnotationHub', '3.0.0', { + 'checksums': ['97327df6693358d402b47e3ee39eb098268fc5e00a63a94327f8c8b3dd3827dd'], + }), + ('AnnotationFilter', '1.16.0', { + 'checksums': ['4a03a9a0af23e168c62bab17d0625731d3922755727123a296839e6d9494291d'], + }), + ('ProtGenerics', '1.24.0', { + 'checksums': ['d899a98099bea1abdf4c1a4ec31b0cb8b52a519df7c4fe0a17e820c12c9ae9b0'], + }), + ('ensembldb', '2.16.0', { + 'checksums': ['b209df28bbd45e89bfeac41e2ae6f40b5bd2acfdcdfd1e71a3f512da7f151580'], + }), + ('biovizBase', '1.40.0', { + 'checksums': ['43f008722d6ce1cf4ea644a9f5bc33074e7f55330e13092ec40ab6f7c6f35e92'], + }), + ('OrganismDbi', '1.34.0', { + 'checksums': ['b14f6ba963b20c4a73a8d9bc7da345babedf54e307f8b427898c37c8da650c5d'], + }), + ('ggbio', '1.40.0', { + 'checksums': ['9d46bb3f1b875979e49cfed9a30033daad1b74d082bd77ea9ed93f9e99ea6d4c'], + }), + ('geneplotter', '1.70.0', { + 'checksums': ['9fb47280dad9e486f1d36aa3e043e39881f7fe07cb05ed272f2efaa11c2d08b4'], + }), + ('DESeq2', '1.32.0', { + 'checksums': ['5f4d52e371d358ea047070398cde5b41ffd1f711562a298e5c60ab232bcf2b64'], + }), + ('ReportingTools', '2.32.0', { + 'checksums': ['b2d6367a073a0368154133042f4bb9246f5527fd2f29fe7aeba131ceb5fbdc6c'], + }), + ('Glimma', '2.2.0', { + 'checksums': ['4a43a2a97bb13ea14dfb0f70862c54a1ca10707a5c92497a68f5d7c82b465337'], + }), + ('affycoretools', '1.64.0', { + 'checksums': ['b0e569d8ff3c4662f0a068140301ce759d1c68d18338c87b0b768e7c7530a8b7'], + }), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', { + 'checksums': ['063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9'], + }), + ('Homo.sapiens', '1.3.1', { + 'checksums': ['014809fc6ef6410be8dc1094c9cb083719f20d999065ae4bf388855be0913b94'], + }), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.3', { + 'checksums': ['5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a'], + }), + ('AgiMicroRna', '2.42.0', { + 'checksums': ['bd7cd8e18591bc41cc5af8602ba6b8efb4e2fdda788f6cf6c5a02801de758760'], + }), + ('geneLenDataBase', '1.28.0', { + 'checksums': ['1f6678274dfa387baf27fb462f979ab18bf7d6131ae0d5c9fc791b6a36505134'], + }), + ('goseq', '1.44.0', { + 'checksums': ['1ac4737eafe357060310233258cabdbdfdeb3aea55878c4aca6865d2b5ee191f'], + }), + ('KEGGgraph', '1.52.0', { + 'checksums': ['1ad3699b4b271b9f233f7c11ac8b4a28281e77bc58d6f084fc73e40f0bbcad7f'], + }), + ('GEOquery', '2.60.0', { + 'checksums': ['5581713a5588f18d24e32d27d63d5753f6209c696af66137b2a50dd0d86a134a'], + }), + ('RSpectra', '0.16-0', { + 'checksums': ['aaf1cfc9ffe3a4c6684247899924e1c18306971dfef4bae1dc596a2fb42a64a9'], + }), + ('rARPACK', '0.11-0', { + 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], + }), + ('mixOmics', '6.16.0', { + 'checksums': ['3ca32e2a7c940828f82aaddd967372357d0fccaecaed780d1b782387732e31c3'], + }), + ('Rhdf5lib', '1.14.0', { + 'checksums': ['07d9c6bc5bc52c38ff6437853518940d37824e71c72b8dc5a21d926f49abf8fa'], + }), + ('rhdf5filters', '1.4.0', { + 'patches': ['rhdf5filters-1.2.0_fix-configure-aarch64.patch'], + 'checksums': [ + 'ec2dd94273dfec06f95d52366990fa18e4dc85d2cfb8d548bc9a295188067b8c', # rhdf5filters_1.4.0.tar.gz + # rhdf5filters-1.2.0_fix-configure-aarch64.patch + '01d00415dcf41d7ca331b69ef7b3d99834719474ef1da8f66a540d027e24da5b', + ], + }), + ('rhdf5', '2.36.0', { + 'checksums': ['7f2adc8e8755fdf7ff0ea55fdf98ae3ed85eb406787440152a22b3e473e2b3a8'], + }), + ('HDF5Array', '1.20.0', { + 'checksums': ['2cef8fc8bba194afa0b84707bb699c29477ae84aa01cb478e78be2f2e985289c'], + }), + ('sparseMatrixStats', '1.4.0', { + 'checksums': ['99d9998a829984c1d9fc2e99abb461749b0d95d052a667a970f6e2e95abb9a46'], + }), + ('DelayedMatrixStats', '1.14.0', { + 'checksums': ['135f3a0618d7f84bb183311eb68430251ab1fdadaaf0eb46199514567f46260b'], + }), + ('minfi', '1.38.0', { + 'checksums': ['b24a9485c3c76875b3463fc585bc874a402f9d7e5cdd7ba7e0cbfcbceffd34a1'], + }), + ('FDb.InfiniumMethylation.hg19', '2.2.0', { + 'checksums': ['605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f'], + }), + ('methylumi', '2.38.0', { + 'checksums': ['121f4fea4b220b11d7d1bbd1078d76adc1ec5e0564f20af9435d6b220acb81a4'], + }), + ('lumi', '2.44.0', { + 'checksums': ['02408f60eb6f389956d3810e1083c3452334d0d8a1b8754065dd5af79bec4d62'], + }), + ('widgetTools', '1.70.0', { + 'checksums': ['62b531a17e4333b66c47d9f94bffd77bffeb282ac57cd89f55247ae7df7ddda0'], + }), + ('tkWidgets', '1.70.0', { + 'checksums': ['c9d28b42a8b8ff08320476b5869c738ba9f86ddba7197057d5e978aca75da25e'], + }), + ('Mfuzz', '2.52.0', { + 'checksums': ['cb9301d13f8db26ef3035e2ffa2cc875b4636133610b5a4bbc19dbc287a5525a'], + }), + ('admisc', '0.15', { + 'checksums': ['27b7ce48026ec2b28b85870b07ad2d338488f39eb879e9a4bfadb7c78793d549'], + }), + ('venn', '1.10', { + 'checksums': ['65422a158cdc8581182d3d326e448e43ecc3764501a5dab1ccac1234b4f961e4'], + }), + ('maSigPro', '1.64.0', { + 'checksums': ['78055e87db33bff8fd507f189d6cf17207ffcc5c4f32bc3e5d55a3deee695ea4'], + }), + ('SPIA', '2.44.0', { + 'checksums': ['09f121cb778c71579fb516fa0a0f4b0fefdc4aeb5d6cb968ef2a15a63572fa6a'], + }), + ('Gviz', '1.36.1', { + 'checksums': ['e5dd779dc1149450a7e17d88ff8dd177f134ee2046ba06717ecd8c77c19192d6'], + }), + ('cummeRbund', '2.34.0', { + 'checksums': ['5d6aae3fc5a3e7f40be40739bc9dfa6b7ad985984699d60f637a355af3ae7bab'], + }), + ('GenomicFiles', '1.28.0', { + 'checksums': ['7e84594e8a76a173153fa1d482ba0200a3b7c83bb7b3ee0ba78a197e2a0990de'], + }), + ('derfinderHelper', '1.26.0', { + 'checksums': ['abfcbc154acb38363d9f70bb8916cbff0b9feaeac6c918f1a157d3d19deeadf0'], + }), + ('derfinder', '1.26.0', { + 'checksums': ['5b1054ce0d5e68e67b8b0bc7c67b79e774eaa1d2e736d7fab3d012ccfea81faf'], + }), + ('polyester', '1.28.0', { + 'checksums': ['c059e37a9ea0c9edadc213ec0874eec84e05adde9fbc0ebb08134841dcb9f038'], + }), + ('Rsubread', '2.6.1', { + 'checksums': ['c8fc4d32e0cf77bf05736edc1f9775eb2e69ad8251c937db07234138fb5ef700'], + }), + ('pcaMethods', '1.84.0', { + 'checksums': ['65556f989400c46ba0d85f24150bfee49f9012742e86269848be1d446cd798b1'], + }), + ('marray', '1.70.0', { + 'checksums': ['a628561c453d1afb50445bd2743af627939383f81f86616180476c7f31ccf572'], + }), + ('CGHbase', '1.52.0', { + 'checksums': ['4421e120d31622297f7f19151352e3b294e772be75b295da4933a0c4379907dd'], + }), + ('Wrench', '1.10.0', { + 'checksums': ['40ef65d4d7edb92cd1e88dfe4c6902e3b9866f6c1d4ba91560d967e515ae5a7b'], + }), + ('lpsymphony', '1.20.0', { + 'checksums': ['f6433dac3e6e7012f0c9dd873004e9bc0f30b15e4323cfe93fdaa35fee58842b'], + }), + ('IHW', '1.20.0', { + 'checksums': ['dc51f14ae444c419b93ad81fc6c7ba4c6d75640b5c9832e7cb767daf901a692c'], + }), + ('metagenomeSeq', '1.34.0', { + 'checksums': ['67a83c151b536b067568f7773964dbfd9d00f31fe2a2b47eb6d663258ce7dd23'], + }), + ('gdsfmt', '1.28.0', { + 'checksums': ['7e5326e82dfd589c2f79c345683f82d08867628b3c5bb0e4c44aedd3766c3885'], + }), + ('SNPRelate', '1.26.0', { + 'checksums': ['6a4d410903b8cefb3dbf3f7ab7e88c5ac226081c89f1df96d54c421704d27a54'], + }), + ('biomformat', '1.20.0', { + 'checksums': ['c96bd41b5afd0a0b9027a7f485a3d136958bf7b90dd47961d4b7aededa84faf1'], + }), + ('phyloseq', '1.36.0', { + 'checksums': ['f112e646382558fda90ecc7b4af770c42bfdb1463c82f5a6a4695bd701d84fa4'], + }), + ('NADA', '1.6-1.1', { + 'checksums': ['670ff6595ba074ed0a930b7a09624d5ef20616379a20e768c1a7b37332aee44a'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('zCompositions', '1.3.4', { + 'checksums': ['ae22c86fe92368a26265933f42eecc518b9b69e7d9b698bc31bfaabfc3c48e95'], + }), + ('RcppZiggurat', '0.1.6', { + 'checksums': ['9c78255ca476c945c05a564d1e4da363de714d890e0e27f3b252fd73c50eed71'], + }), + ('Rfast', '2.0.3', { + 'checksums': ['25bc8c4028c021c7135bd86812265d2cf190bc07b3a412c4406f126c22adb0ae'], + }), + ('ALDEx2', '1.24.0', { + 'checksums': ['14181f57035004dbfad33c509109037862c26b951a90b2a6e3ba57677418e29d'], + }), + ('dada2', '1.20.0', { + 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], + 'checksums': [ + '85242fcf2c2f273d72a08869128f2e85d388c709531c1523c241ece8bb9d69f1', # dada2_1.20.0.tar.gz + # dada2-1.16.0-remove-sse-on-aarch64.patch + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + ], + }), + ('LEA', '3.4.0', { + 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], + 'checksums': [ + 'ca58096dd7bcd104044314b50ed304ccb82af1adbd6f7aaf0c3cb04a0b56eb82', # LEA_3.4.0.tar.gz + # LEA-3.0.0_support_aarch64_and_ppc64le.patch + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', + ], + }), + ('tximport', '1.20.0', { + 'checksums': ['2e0ab41a6e025acbb51e5681b470e10d91cc2c6f84f6a99f52c25dfd41f6e246'], + }), + ('SingleCellExperiment', '1.14.1', { + 'checksums': ['ffe10077c9617c469f5fb02cdf484f04d9ab10e9a7f1d73a714803ad41878daf'], + }), + ('beachmat', '2.8.0', { + 'checksums': ['0629aacb6631f5ed548f8c45da62d2bbf2ad7d011913db54f01a79b214d4e69a'], + }), + ('RcppAnnoy', '0.0.18', { + 'checksums': ['e4e7ddf071109b47b4fdf285db6d2155618ed73da829c30d8e64fc778e63c858'], + }), + ('RcppHNSW', '0.3.0', { + 'checksums': ['a0eb4eea65e28ba31e8306a1856f7e617a192bd448b148f88abe99181cbde007'], + }), + ('BiocNeighbors', '1.10.0', { + 'checksums': ['fbe400f8214c4d51c953c1e56b00967b03322507090dd47f4f374a8e426c5132'], + }), + ('rsvd', '1.0.5', { + 'checksums': ['e40686b869acd4f71fdb1e8e7a6c64cd6792fc9d52a78f9e559a7176ab84e21e'], + }), + ('ScaledMatrix', '1.0.0', { + 'checksums': ['06a8606f0ed6129d2bf6237c3fc00767e01635acce57c4ca5e1d2b1ef87626c9'], + }), + ('BiocSingular', '1.8.0', { + 'checksums': ['372b86f6cfc7bb087cfdcbcb7310cc80c432c17bdaa2145ad425b2f2077b1dd0'], + }), + ('scuttle', '1.2.0', { + 'checksums': ['e56b29639a1fa1702c4e96c2210f6eb98c56ae5485917654a8e2172b4a7db5ef'], + }), + ('scater', '1.20.0', { + 'checksums': ['450eb0ea7e768571c5047b8d6d1f9454483b664d894453160f247a57415bf766'], + }), + ('sitmo', '2.0.1', { + 'checksums': ['0c90d357af334d5c99c8956739dc12623ddd87dda5efa59f4a43f7393c87ed2a'], + }), + ('dqrng', '0.3.0', { + 'checksums': ['4beeabfe245ce7196b07369f2a7d277cb08869ad8b45a22c6354c4cc70a39abb'], + }), + ('bluster', '1.2.1', { + 'checksums': ['8f1aebbdd967cb85395194ca56650ddf6196a7ed2ddcbb009eb942ca77691f89'], + }), + ('metapod', '1.0.0', { + 'checksums': ['9b426dae5ef4c289ff5eb02cfdce7fe6e5d9112af101f81571d93fd44ce66cc1'], + }), + ('scran', '1.20.1', { + 'checksums': ['c039eae54a46a8c4b8eb035b6a5854b240d7bf6031a6331f42f826feacb99f46'], + }), + ('SC3', '1.20.0', { + 'checksums': ['9c421a02000f3687b1fe146b92a82d01148ba4f6143012d68f264b54bd2f3d32'], + }), + ('ComplexHeatmap', '2.8.0', { + 'checksums': ['2e102de57cbfb17b40276353eea88870c35b37281a99f7ecce4dda207535894a'], + }), + ('GENIE3', '1.14.0', { + 'checksums': ['2bd011e127b845bde1f8ec90521da831915dca7ae8ae6b47759c14f3d96fa4ec'], + }), + ('dupRadar', '1.22.0', { + 'checksums': ['ca4ece6a714bbbbf5daa62cd78cc3cfefd09eec7be946ccab058e4937295bdbf'], + }), + ('DNAcopy', '1.66.0', { + 'checksums': ['8d30c9b6475bcf954327aa97981551756cabd730e7752a5a384230e34840f855'], + }), + ('sva', '3.40.0', { + 'checksums': ['51ce2d1875715e5efeee98ed371ee730489728218d88d00f5cea6ad79667538a'], + }), + ('ballgown', '2.24.0', { + 'checksums': ['211eccb48e3356885dba01c29e2897296ab8cc789439a5081651fde72ef9c839'], + }), + ('DropletUtils', '1.12.1', { + 'checksums': ['298f644106103ad3efd64c34251af81544e38dbd28e0cb8f40e20548fccacf77'], + }), + ('DeconRNASeq', '1.34.0', { + 'checksums': ['e480ec254f26aedc439681faec66ebcf6ad00322786be31c72c2c4dd02093b04'], + }), + ('GSVA', '1.40.0', { + 'checksums': ['0207a189c2fadc3d3d953ce96f673861d5ec06fc8f8ca55e4b5eb334adff4d0d'], + }), + ('PureCN', '1.22.1', { + 'checksums': ['b953c53df361a1ef7ae23d3259628d5edb7b74078174a6b35efff1fa35ba851d'], + }), + ('globaltest', '5.46.0', { + 'checksums': ['3f0ae9b34de6e3daec896ed7583141e056186f45a5fc12957b86251af11429b9'], + }), + ('GlobalAncova', '4.10.0', { + 'checksums': ['320f1a7f36458d67a78eed6f5d7e700f7f34ef90c71cb5e2351df949bb53debc'], + }), + ('vsn', '3.60.0', { + 'checksums': ['5beb0d330a78e30430813344ef934012b34decd068598dcc18e8a33d07bcf75a'], + }), + ('mzID', '1.30.0', { + 'checksums': ['dabf9cca3d3b6bb3a4a8696def386af1be5fd3d898dab0b014c014d5b3335ef3'], + }), + ('mzR', '2.26.0', { + 'patches': ['mzR-2.22.0_use-external-boost.patch'], + 'checksums': [ + '772601b6e053df5a5eef85b98da1b7a5b411b2cfde73496276d9f70cb6ddbdd4', # mzR_2.26.0.tar.gz + '8b5ba4f0c4efbbab9b4801d7da3fb04a490a5d95af1cefb489f209afa4d14fb4', # mzR-2.22.0_use-external-boost.patch + ], + }), + ('MsCoreUtils', '1.4.0', { + 'checksums': ['a8dd139e14777e69851cdf50d8a787d5b6ad90db82b419aad1d2eb6dc451e88d'], + }), + ('MSnbase', '2.18.0', { + 'checksums': ['79d2d4e80984fbbe813c7c1fc576a4df2e4b318bc97938410567bd6fe409fafc'], + }), + ('MassSpecWavelet', '1.58.0', { + 'checksums': ['1f988dbae5037454be066829753aa58b0a38eb757033a07bb278fbf0a21643b3'], + }), + ('xcms', '3.14.0', { + 'checksums': ['9dcff26777cd5a9b9b87450dd8faa5391b2891236b995875985186ff261547bb'], + }), + ('CAMERA', '1.48.0', { + 'checksums': ['bed3d65914791907c604184312eb3d3819d8870ca3f6ca123a7735a9ab3e4688'], + }), + ('fgsea', '1.18.0', { + 'checksums': ['2d3d63bb30a735ae5138fe1fae68a05fbe0dbcc32bcd45ca3efb756b887f0dd6'], + }), + ('GWASExactHW', '1.01', { + 'checksums': ['e850ed40fbf14b02eb3798603cfb111fe3718bb69d74c0ff4cb6f679209a15a7'], + }), + ('quantsmooth', '1.58.0', { + 'checksums': ['7d9008700c0ae754d10d71d68d2819bf3bc83b0aeffb37da78c76c73239c005b'], + }), + ('GWASTools', '1.38.0', { + 'checksums': ['f759070b907b9c320cbfdd61705aea1bc5be5b60d2678c9c9fc1982728cc462b'], + }), + ('SeqArray', '1.32.0', { + 'checksums': ['016f523104bb07ca67fd7aac59bb754b246c531a20ca1d3ff72b9c6770918c5a'], + }), + ('SeqVarTools', '1.30.0', { + 'checksums': ['c7775c0c5db8ca644971d3c0b2bca0ef5705617354b1af160e41158e6e3735ae'], + }), + ('GENESIS', '2.22.0', { + 'checksums': ['a76a60d6d4deb6203fa3e0895f6519c259d08251320a71033dcd31c7edbc62de'], + }), + ('MLInterfaces', '1.72.0', { + 'checksums': ['eb669bf5d39a19d906cc2637537bd32f06203036254d15a56f10bbddf8d9ff46'], + }), + ('pRoloc', '1.32.0', { + 'checksums': ['b758b1d6a8e99de46b71629cbdd8212303b878f4198cb1a8efa4affbdf34dd24'], + }), + ('pRolocdata', '1.30.0', { + 'checksums': ['91482fb61a75ce87ee7a351b1676edac8d539d685d8e3aac465b744055afa8bd'], + }), + ('fresh', '0.2.0', { + 'checksums': ['a92db254ae88e8371efac44efe2cf1f5be7cce62291fdf994ebd68c14dad079d'], + }), + ('waiter', '0.2.1', { + 'checksums': ['85b9efef4d396698ba300e1f20f151ed5dc351e2391653d8eccbdd5bb77ead15'], + }), + ('shinydashboardPlus', '2.0.1', { + 'checksums': ['5b25b510b151a78e25ec679a8abf37ee1d21ca49e437fd0538f5eaa39bce78cd'], + }), + ('shinyhelper', '0.3.2', { + 'checksums': ['f7ed62543ab4d05a34b69a9183517a09e93e1b2da85b113282de0f9982db90b0'], + }), + ('shinyWidgets', '0.6.0', { + 'checksums': ['764a4876b4466dc10b85b43a91fe01359533b1b5dc1e177ca3d86918fe2e0f90'], + }), + ('pRolocGUI', '2.2.0', { + 'checksums': ['b6309ec2f9a0004e21adc277b164211d93bdc80d2bc31579e437a715d28e8f3f'], + }), + ('EBImage', '4.34.0', { + 'checksums': ['03221ccab083dc65ac2eece74e01e307b5201b141096ff9935a68d545eef6cfc'], + }), + ('GenomicScores', '2.4.0', { + 'checksums': ['dc74b41ca5e3f05c325cafb461112f28b1615dd392f2448e7cf164209d4009ad'], + }), + ('BSgenome.Mmusculus.UCSC.mm10', '1.4.0', { + 'checksums': ['6e2eb3bce208cc7766f0e0ef1e14465289d5463b34d94c9a9279256545b5408b'], + }), + ('TxDb.Mmusculus.UCSC.mm10.knownGene', '3.10.0', { + 'checksums': ['696281749d01737c94894564d62093433045bc007a4528cc3d94f205edb54977'], + }), + ('regioneR', '1.24.0', { + 'checksums': ['54dbf1302eacd1fee259dad6a20b688b9730d10e2335f0b4ebfe1acac657ff77'], + }), + ('InteractionSet', '1.20.0', { + 'checksums': ['ab1b458afdadbfc1b4b6e96a245901d754f9ceafed5a170e09f6185b658b9d0c'], + }), + ('ChIPpeakAnno', '3.26.0', { + 'checksums': ['f30d7eff4a1653fe96ace7f5e16f155e8cce011ccdd622f3c5e273b272d3d5f2'], + }), + ('seqLogo', '1.58.0', { + 'checksums': ['9755621d3a8725356573c63b40a98e1bdb9ff650bdec089ccb6b190683d4a388'], + }), + ('rGADEM', '2.40.0', { + 'checksums': ['f54b126363bd2b46ba9f56d3626a2efb9a25dac87b0048a69971168b255cb915'], + }), + ('MotifDb', '1.34.0', { + 'checksums': ['7f2c8123ef0cbe7e12ce4670139cf3bdd5e96b14ccf95fd25b98055ecb7b9511'], + }), + ('motifStack', '1.36.0', { + 'checksums': ['f78da2a47c8d8aa045d1be2da456fddd16e849677684547d34641f5e2722c37a'], + }), + ('ATACseqQC', '1.16.0', { + 'checksums': ['b4cfc602a77aa6fc69567af995fdcda3770d9d6f2e5a1fd4952e7f09671f0f99'], + }), + ('ResidualMatrix', '1.2.0', { + 'checksums': ['3becaaa3d668e4a64852b140118e6fc7b212d74c074d76ba554602ae5250fb5c'], + }), + ('batchelor', '1.8.0', { + 'checksums': ['0a474dc558f73c26ad096e6f31a42d956fb916d334151d18ad75d4713901a2f6'], + }), + ('gsmoothr', '0.1.7', { + 'checksums': ['b75ffd2a4a0f357762e02e46e355b45cc90ea637830f0a1b01f216bb4541e903'], + }), + ('Ringo', '1.56.0', { + 'checksums': ['5de0e1baaf497b10fc5f496a881b3349abe6606b4d13dc6a28daf54e02dc51fb'], + }), + ('R.devices', '2.17.0', { + 'checksums': ['c2d4b12949e0faab414c9f7575e39ee9dbf50ea12d858143df529f15ea365fb6'], + }), + ('R.filesets', '2.14.0', { + 'checksums': ['707dd7c099aeadbecebbd2ba57e6400405aa44487c641f3729ce06c4c642bb23'], + }), + ('aroma.light', '3.22.0', { + 'checksums': ['c50f8be7d7b6bafca440fdd54c957ac0c288904fd69115e996f13274033578fb'], + }), + ('PSCBS', '0.65.0', { + 'checksums': ['3365065d5375c599eb024bfff12c5f6b10a6b1a4fe4ba6f200f7e83618dd399a'], + }), + ('aroma.core', '3.2.2', { + 'checksums': ['35e0312e403a1894da036afac12d1d727c937e666d7eb400bfe4018b21244855'], + }), + ('R.huge', '0.9.0', { + 'checksums': ['f12d113a965603cfdbbb46e1a57331d267916235555b22f2bbc06caa302ae58e'], + }), + ('aroma.apd', '0.6.0', { + 'checksums': ['87513774baeed8e1d43f819e615c85278aef748ebc842f1ee50686c3392e37d1'], + }), + ('aroma.affymetrix', '3.2.0', { + 'checksums': ['d279cf13cf6ed8369cfdf6682ace12924379bad578003453449aa1ccec31b0a7'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('Repitools', '1.38.0', { + 'checksums': ['7464394ebd039cd1d57e242ddb71bf02fa35a6d0dc9aafae04c834e021c36a50'], + }), + ('BSgenome.Hsapiens.UCSC.hg38', '1.4.3', { + 'checksums': ['c29911ca93935e3b9aa6a67e894337dc2ad707405da1500c9898bd0578519ecc'], + }), + ('MEDIPS', '1.44.0', { + 'checksums': ['3128cdc286275faffc792c4a6cf08562cad072be6b9c8595d52353f06151a750'], + }), + ('RProtoBufLib', '2.4.0', { + 'checksums': ['cb2e6eba5fabea2f3ecc9a97ae25d54f2b5ad14ed08381a83db612af4ed2cdc3'], + }), + ('cytolib', '2.4.0', { + 'checksums': ['db92fc4dc0f0e8546f692b07eb1c1ab12f568705e46b87bf6b6844b039fe8772'], + }), + ('flowCore', '2.4.0', { + 'checksums': ['cc92e084d693928e034bcda4f844eb9545589b5fc6c77637ac3d8f12fb5cb78f'], + }), + ('mutoss', '0.1-12', { + 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], + }), + ('mathjaxr', '1.4-0', { + 'checksums': ['ba57378236d593a39c5839054adc5473526de0c8f05b7eeb87c99438496ddc67'], + }), + ('metap', '1.4', { + 'checksums': ['5fac23d823d0ad4eebc3f97620364e25f7b41f8d0c3579f6c09ec059940b85a5'], + }), + ('uwot', '0.1.10', { + 'checksums': ['6ee1b6027bce679cd5a35f647f516a5b327632234bcf323c7f3d5b5e10807d23'], + }), + ('scattermore', '0.7', { + 'checksums': ['f36280197b8476314d6ce81a51c4ae737180b180204043d2937bc25bf3a5dfa2'], + }), + ('sctransform', '0.3.2', { + 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], + }), + ('SeuratObject', '4.0.1', { + 'checksums': ['c90596cc11d623ab95ffb408f085e024402e060ad517d6970e8a9877fa8e623c'], + }), + ('Seurat', '4.0.2', { + 'checksums': ['cfc2db402f85581585bd477f06a07afcb5fc04121fd1049e83c0cade88f43cac'], + }), + ('ALL', '1.34.0', { + 'checksums': ['6c376f3360bbb0aad4b5aad9655cb95d2f9d33a1abd2ba4533bee803988d8b63'], + }), + ('ConsensusClusterPlus', '1.56.0', { + 'checksums': ['0b496182208b41928caeea4cc05f0d66e20bceed8f815aa5d2996f6f41c97698'], + }), + ('flowViz', '1.56.0', { + 'checksums': ['3b30dc5b6ade5880afd3127643314f3b2f86d6ec35ef07e72ff70aee7927a09f'], + }), + ('ncdfFlow', '2.38.0', { + 'checksums': ['c0d9ec37b275e98f717f6ac063a594358a23a4e77bbdca4fb6369bed2c46a8d2'], + }), + ('aws.signature', '0.6.0', { + 'checksums': ['f7fe4f686979be21e5a8ba7ae11f0fade4f5aaf4e98063b5349ee0962dbb9496'], + }), + ('aws.s3', '0.3.21', { + 'checksums': ['bd21054ab63555d294e7465dcb6c86f107db52ba841aeac5bdf4d00af0674c8c'], + }), + ('flowWorkspace', '4.4.0', { + 'checksums': ['a933b1526f9090218ed0394e71541bed1cff73b07fadb6c11febf1cd9a5838a9'], + }), + ('ash', '1.0-15', { + 'checksums': ['8b0a7bc39dd0ce2172f09edc5b5e029347d041a4d508bbff3f3fd6f69450c2ab'], + }), + ('hdrcde', '3.4', { + 'checksums': ['4341c6a021da46dcae3b1ef6d580e84dcf625c2b2139f537d0c26ec90899149b'], + }), + ('rainbow', '3.6', { + 'checksums': ['63d1246f88a498f3db0321b46a552163631b288a25b24400935db41326636e87'], + }), + ('fds', '1.8', { + 'checksums': ['203a5e7671e542dcb83d4c75d0f4012aaebc32d54f94657afaf9e71e99dd0489'], + }), + ('fda', '5.1.9', { + 'checksums': ['c8bdf4bd285100c4c7ee89bb67df96dbf1132c1cf2c9ee85c59cad52b696597a'], + }), + ('flowStats', '4.4.0', { + 'checksums': ['a60b93ea5f06f1b225f5e945918f9210b8f789ffa08d0f0e13a55658f1a925fb'], + }), + ('flowClust', '3.30.0', { + 'installopts': "--configure-args='--with-gsl=${EBROOTGSL} 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['b01c8fd81e4c4d766606e546482482d07ebe9e46e12538a1661bc685a2aca26a'], + }), + ('SCANVIS', '1.6.0', { + 'checksums': ['d8aa379f1274ef4f52078c9ad72cb9045a0e32fbb984226d0e9ef3010b8429d6'], + }), + ('EnsDb.Hsapiens.v86', '2.99.0', { + 'checksums': ['552c07bcc2a1420089d4330deafaeb5303e03d0fa75c96b78075dfd67eeee7be'], + }), + ('agricolae', '1.3-3', { + 'checksums': ['e9b16317f7f97c8af5d5edcf414ff209114bfc76329e06701fffc279eaa21f8e'], + }), + ('bookdown', '0.22', { + 'checksums': ['1fe466484e0ef8d413180bede8b89ec1399e40efa672c72c096ef06a46e50049'], + }), + ('BiocStyle', '2.20.0', { + 'checksums': ['3f781f49bbf593f9bcb5487d8552627871a03debd2c287570487093586875f18'], + }), + ('estimability', '1.3', { + 'checksums': ['a33179c5fbd6a1a623d90cb6f1743148f92c09429fac466867f3ea70946a2e32'], + }), + ('emmeans', '1.6.1', { + 'checksums': ['94e35de9d97ae07fdeafa89d1c861ab66d891479d35d4406376546e10c0e500b'], + }), + ('ggdendro', '0.1.22', { + 'checksums': ['f0a65f3498c1abc3076df0fb56364b63bdf5d212d8931f85bcc6997510916b6a'], + }), + ('pmp', '1.4.0', { + 'checksums': ['20fccc9ace7fbb0f5375240fcb2c69587f60c33e6ec685f89c092f013c71cbd1'], + }), + ('MultiDataSet', '1.20.0', { + 'checksums': ['d235d69b02b55850cb6545d2bad1d3bbfc77472386edc63bcea0f8fa3a20d3c3'], + }), + ('ropls', '1.24.0', { + 'checksums': ['abcc7dba829c34c4ca74b7b5fb798c88130e5281da176d59fb5852cf7d9b29c9'], + }), + ('ontologyIndex', '2.7', { + 'checksums': ['33f4918cafb983635f9f831553daf15e10103dc375475e170f104a8eaf0e7048'], + }), + ('struct', '1.4.0', { + 'checksums': ['4bf66c88e905e8fead7c46453c9987653b940fd83e3545097b42411f1746c625'], + }), + ('ggthemes', '4.2.4', { + 'checksums': ['7b35168cf5b68f6f52dd533a1b345ec87e09d1a85ca68e8dc5377cdf95718567'], + }), + ('structToolbox', '1.4.0', { + 'checksums': ['59b8d36e55e81e5db4100aad91d43e5606fdb4037074685b40f20f1102b41c77'], + }), + ('EnsDb.Hsapiens.v75', '2.99.0', { + 'checksums': ['2c59f95959f344b2a3eaa65a00086b01a420823e30b0810fc81e49b08dcba64b'], + }), + ('ggseqlogo', '0.1', { + 'checksums': ['c14f145a982597f32264b37a5f2645206a0bee30dd2584a25cb8e3dc2f9b068f'], + }), + ('sparsesvd', '0.2', { + 'checksums': ['1a1f54d6b0dca6ae83e3f729a1895c91c58bfe55427dacc50ddb0d2c5d32a9f6'], + }), + ('docopt', '0.7.1', { + 'checksums': ['9f473887e4607e9b21fd4ab02e802858d0ac2ca6dad9e357a9d884a47fe4b0ff'], + }), + ('qlcMatrix', '0.9.7', { + 'checksums': ['1ef5e0350cfbdb07fca761fc7251584d39d3da2958ea813498b467e4f7661347'], + }), + ('Signac', '1.2.1', { + 'checksums': ['626e976bef3f4647dbbb7adf2a0d4d650c4b24827f3e09f5f8a9e6fe0dda4bde'], + }), + ('poweRlaw', '0.70.6', { + 'checksums': ['efc091449c5c6494c1c13c85a8eb95625d1c55ffffebe86c7ea16e4abbafa191'], + }), + ('CNEr', '1.28.0', { + 'checksums': ['533c7a3053e6b3de8d8e52f7d80cbc06941ec5d2898165cb6d49cc539d7e808f'], + }), + ('DirichletMultinomial', '1.34.0', { + 'checksums': ['546be33fee6b05291ca9fee856538125f259ba7750f91db091df510006907546'], + }), + ('TFMPvalue', '0.0.8', { + 'checksums': ['6d052529f7b59d0384edc097f724f70468013777b6adf4c63e61a359029d3841'], + }), + ('TFBSTools', '1.30.0', { + 'checksums': ['596d30e5ca511035ca0c5a89af83292e6408f680bba50f146548646fc5966fab'], + }), + ('motifmatchr', '1.14.0', { + 'checksums': ['75594c5591aebbdb9d9f15d35c653118e518d2791160dd6ff8926c4a6e1b2eee'], + }), + ('extraDistr', '1.9.1', { + 'checksums': ['9990348c4dbc611684fcb58ab8db7e856dfde1c9c86ffb7705f4b3dff6b2d7bf'], + }), + ('PRROC', '1.3.1', { + 'checksums': ['479118ce47c527bc97fb58d531a31cabc094d9843d62f16922009dc62e8248d4'], + }), + ('TSP', '1.1-10', { + 'checksums': ['44979f16803806419a94a6b0daeac812f4e7bd52d2fff11561fd4bbc41353b7c'], + }), + ('qap', '0.1-1', { + 'checksums': ['60bd564bb0e6325de44351af33870177d84b1c00ded142a2efb12a16a20d4d34'], + }), + ('seriation', '1.2-9', { + 'checksums': ['8b9279caf60755377ee9023971bff33634f7bb9c055d4ebb493b648512b09dbe'], + }), + ('egg', '0.4.5', { + 'checksums': ['15c8ba7cf2676eb0460de7e5dfbc89fc3175ac22a8869cfd44d66d156fd6c7bb'], + }), + ('heatmaply', '1.2.1', { + 'checksums': ['2dddf6741eaaa49c1354b7092ded5ac6d06df9d6accd879c16c6731bed745743'], + }), + ('OUTRIDER', '1.10.0', { + 'checksums': ['4180041609e3668232155df1ce3658735d2825ca2116e4e13ce687c112176cef'], + }), + ('FRASER', '1.4.0', { + 'checksums': ['5205d8623ce0e5629a49aa092e4aa3350fc5d1a4575130400b1e61115f56cb0d'], + }), + ('GenABEL.data', '1.0.0', { + 'checksums': ['2c28d5df63ae13545cf7aea6ce5f22ae1bbb58219fdaed6c1d5d5affc072c65c'], + }), + ('GenABEL', '1.8-0', { + 'checksums': ['434fc806b918738ec67171a37a47099d1706332819317e368fe0ccb8f149a469'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' From a55f661c1a502932f90e300ae62bc14cdbf1d3e2 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 4 Jun 2021 16:26:11 +0100 Subject: [PATCH 0200/9987] remove local_biocver --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index f0887fb1855..16de0f1236c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -4,8 +4,6 @@ name = 'R-bundle-Bioconductor' version = '3.13' versionsuffix = '-R-%(rver)s' -local_biocver = version - homepage = 'https://bioconductor.org' description = """Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.""" From d56fcaff2817f087ed80c3a0c88510d63b8d91c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Jun 2021 17:28:14 +0200 Subject: [PATCH 0201/9987] adding easyconfigs: harmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb --- ...rmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/h/harmony/harmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/h/harmony/harmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/h/harmony/harmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb new file mode 100644 index 00000000000..4bb25703763 --- /dev/null +++ b/easybuild/easyconfigs/h/harmony/harmony-0.1.0-20210528-foss-2020b-R-4.0.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'harmony' +local_commit = '2586afd' +# see DESCRIPTION to determine version, +# but also take date of last commit into account (since version isn't always bumped) +version = '0.1.0-20210528' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://portals.broadinstitute.org/harmony' +description = "Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/immunogenomics/harmony/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['55c4aaa3cef0c06216a2a51946fb4ed7b189967e34c88bb0dfa53c4d52135d2f'] + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'data' From 1dcccaba60cb67aae7afe70a1975507e51d711cc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 4 Jun 2021 19:55:44 +0100 Subject: [PATCH 0202/9987] patch no longer needed --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index 16de0f1236c..913d192cece 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -331,12 +331,7 @@ exts_list = [ 'checksums': ['07d9c6bc5bc52c38ff6437853518940d37824e71c72b8dc5a21d926f49abf8fa'], }), ('rhdf5filters', '1.4.0', { - 'patches': ['rhdf5filters-1.2.0_fix-configure-aarch64.patch'], - 'checksums': [ - 'ec2dd94273dfec06f95d52366990fa18e4dc85d2cfb8d548bc9a295188067b8c', # rhdf5filters_1.4.0.tar.gz - # rhdf5filters-1.2.0_fix-configure-aarch64.patch - '01d00415dcf41d7ca331b69ef7b3d99834719474ef1da8f66a540d027e24da5b', - ], + 'checksums': ['ec2dd94273dfec06f95d52366990fa18e4dc85d2cfb8d548bc9a295188067b8c'], }), ('rhdf5', '2.36.0', { 'checksums': ['7f2adc8e8755fdf7ff0ea55fdf98ae3ed85eb406787440152a22b3e473e2b3a8'], From fa8753ca8e1fcf07d0594c4feb09054491134d0e Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sat, 5 Jun 2021 08:27:50 +0200 Subject: [PATCH 0203/9987] adding easyconfigs: Extrae-3.8.3-gompi-2021a.eb, libdwarf-20210305-GCCcore-10.3.0.eb, libelf-0.8.13-GCCcore-10.3.0.eb --- .../e/Extrae/Extrae-3.8.3-gompi-2021a.eb | 33 ++++++++++++++++++ .../libdwarf-20210305-GCCcore-10.3.0.eb | 34 +++++++++++++++++++ .../l/libelf/libelf-0.8.13-GCCcore-10.3.0.eb | 29 ++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb new file mode 100644 index 00000000000..a58b66ffa82 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +name = 'Extrae' +version = '3.8.3' + +homepage = 'https://www.bsc.es/computer-sciences/performance-tools' +description = """Extrae is the core instrumentation package developed by +the Performance Tools group at BSC. Extrae is capable of instrumenting +applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 +using different instrumentation approaches. The information gathered by +Extrae typically includes timestamped events of runtime calls, +performance counters and source code references. Besides, Extrae +provides its own API to allow the user to manually instrument his or her +application.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] +checksums = ['32a3d6b01da2c9b8d177d91307d4c04c6db0923ca1d63bfb32768a172af7943b'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.76.0'), + ('libunwind', '1.5.0'), + ('libxml2', '2.9.10'), + ('libdwarf', '20210305'), + ('PAPI', '6.0.0.1'), +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4d501a86e34 --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '20210305' + +homepage = 'https://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.prevanders.net'] +sources = [SOURCE_TAR_GZ] +checksums = ['b86bef41725326d13ee3e7e45b929e0ca97b639e93cc1a9214c90a1774fa1c1a'] + +builddependencies = [ + ('binutils', '2.36.1'), +] +dependencies = [ + ('libelf', '0.8.13'), +] + +configopts = "--enable-shared " + +sanity_check_paths = { + 'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..155b9c5bd4e --- /dev/null +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'libelf' +version = '0.8.13' + +homepage = 'https://sourceware.org/elfutils' +description = """libelf is a free ELF object file access library""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://fossies.org/linux/misc/old/'] +sources = [SOURCE_TAR_GZ] +checksums = ['591a9b4ec81c1f2042a97aa60564e0cb79d041c52faa7416acb38bc95bd2c76d'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +modextrapaths = {'CPATH': 'include/libelf'} + +sanity_check_paths = { + 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf/libelf.h'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'devel' From 5f65729c942ad56658764167cd2681773a8e47c2 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 5 Jun 2021 12:41:37 +0100 Subject: [PATCH 0204/9987] fix build of RProtoBufLib --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index 913d192cece..e0f03a51ff3 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -714,7 +714,12 @@ exts_list = [ 'checksums': ['3128cdc286275faffc792c4a6cf08562cad072be6b9c8595d52353f06151a750'], }), ('RProtoBufLib', '2.4.0', { - 'checksums': ['cb2e6eba5fabea2f3ecc9a97ae25d54f2b5ad14ed08381a83db612af4ed2cdc3'], + 'patches': ['%(name)s-%(version)s_fix-protobuf-build.patch'], + 'checksums': [ + 'cb2e6eba5fabea2f3ecc9a97ae25d54f2b5ad14ed08381a83db612af4ed2cdc3', # RProtoBufLib_2.4.0.tar.gz + # RProtoBufLib-2.4.0_fix-protobuf-build.patch + '379e0227b22ee027de3ab22be9667f358de7d176f74aba598e5a3cbf41dc99a3', + ], }), ('cytolib', '2.4.0', { 'checksums': ['db92fc4dc0f0e8546f692b07eb1c1ab12f568705e46b87bf6b6844b039fe8772'], From 505858f3483038627dfad7d9d5322b483fbe04a8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 5 Jun 2021 12:43:45 +0100 Subject: [PATCH 0205/9987] add patch for RProtoBufLib --- ...ProtoBufLib-2.4.0_fix-protobuf-build.patch | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/RProtoBufLib-2.4.0_fix-protobuf-build.patch diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/RProtoBufLib-2.4.0_fix-protobuf-build.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/RProtoBufLib-2.4.0_fix-protobuf-build.patch new file mode 100644 index 00000000000..037f9f5bc50 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/RProtoBufLib-2.4.0_fix-protobuf-build.patch @@ -0,0 +1,41 @@ +Replace the protobuf map files so that the required symbols are extern "C++" +Fix from https://github.com/protocolbuffers/protobuf/issues/5144#issuecomment-688723405 + +Add extra path to includes. + +Patch by Simon Branford (University of Birmingham) +--- RProtoBufLib/configure.orig 2021-06-05 10:58:25.972255000 +0100 ++++ RProtoBufLib/configure 2021-06-05 11:08:16.635526105 +0100 +@@ -2867,6 +2867,23 @@ + gzip -dc ${PBTGZNAME} | tar -xf - + fi; + ++mapfiles="libprotoc.map libprotobuf-lite.map libprotobuf.map" ++for mapfile in ${mapfiles}; do ++ cat << EOF > protobuf-3.13.0/src/${mapfile} ++{ ++ global: ++ extern "C++" { ++ *google*; ++ }; ++ scc_info_*; ++ descriptor_table_*; ++ ++ local: ++ *; ++}; ++EOF ++done ++ + #run this bootstrap script to update all the gnu auto build files (e.g. automake symlinked fils (e.g. ./compile), alocal.m4,etc... ) + cd ${BASEPBNAME} + #./autogen.sh +--- RProtoBufLib/src/Makevars.in.orig 2021-06-05 11:58:07.587850000 +0100 ++++ RProtoBufLib/src/Makevars.in 2021-06-05 11:58:57.608744000 +0100 +@@ -1,5 +1,5 @@ + CXX_STD = CXX11 +-PKG_CPPFLAGS =-I../inst/include/ -I@PBBUILD@/include/ ++PKG_CPPFLAGS =-I../inst/include/ -I@PBBUILD@/include/ -I@PBBUILD@/src + #expose headers in installed package include folder + USER_INCLUDE = ${R_PACKAGE_DIR}/include + USER_LIB_DIR = ${R_PACKAGE_DIR}/lib${R_ARCH}/ From f0862d77807f79aaa8e35fedde5608e13eb7b8c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Jun 2021 14:39:32 +0200 Subject: [PATCH 0206/9987] add commented out post-install commands to download antiSMASH databases --- .../a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb index 57fe702e6cf..a0c8a90bc51 100644 --- a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb @@ -46,8 +46,6 @@ components = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('helperlibs', '0.2.1', { 'checksums': ['4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732'], @@ -72,12 +70,25 @@ exts_list = [ 'a6fae892e46fd945701dda4640d07467e2d0ab37913d29da403127833bc77291', # 5-2-0.tar.gz '4ca5d671085761c5f86719603fa3bbd0e82b7b52deefe8cac6eb4a3973825f16', # antiSMASH-5.2.0_Biopython-1.78.patch ], + # use http mirrors for ftp URLs + 'preinstallopts': "sed -i 's/ftp:/http:/g' antismash/download_databases.py && ", + # run additional commands to download databases and check prerequisites, + # which creates some missing .pkl files (which requires the databases); + # this is not done by default because the resulting installation is pretty big (~18GB) + # 'postinstallcmds': [ + # "download-antismash-databases", + # # check prerequisites, which also creates some missing .pkl files in the installation... + # "antismash --check-prereqs", + # ], }), ] sanity_check_paths = { 'files': ['bin/antismash', 'bin/meme'], - 'dirs': [], + 'dirs': [ + # antismash/databases subdirectory is only populated when postinstallcmds above are commented out + # 'lib/python%(pyshortver)s/site-packages/antismash/databases', + ], } sanity_check_commands = [ From 803eb240d25b7a96fd21379cb5184a166e616a75 Mon Sep 17 00:00:00 2001 From: Martin Lueders Date: Wed, 9 Jun 2021 09:55:00 +0200 Subject: [PATCH 0207/9987] easyconfigs for libmbd added --- .../l/libmbd/libmbd-0.10.4-foss-2020b.eb | 45 +++++++++++++++++++ .../l/libmbd/libmbd-0.10.4-foss-2021a.eb | 45 +++++++++++++++++++ .../l/libmbd/libmbd-0.10.4-intel-2020b.eb | 45 +++++++++++++++++++ .../l/libmbd/libmbd-0.10.4-intel-2021a.eb | 45 +++++++++++++++++++ 4 files changed, 180 insertions(+) create mode 100644 easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb create mode 100644 easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb create mode 100644 easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb new file mode 100644 index 00000000000..057ee5f7d9e --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.10.4' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] + +builddependencies = [ + ('CMake', '3.18.4') +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.so'] + + ['lib64/libmbd.so'], + 'dirs': ['include', 'lib/cmake/mbd'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb new file mode 100644 index 00000000000..ab04682265c --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.10.4' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] + +builddependencies = [ + ('CMake', '3.20.1') +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.so'] + + ['lib64/libmbd.so'], + 'dirs': ['include', 'lib/cmake/mbd'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb new file mode 100644 index 00000000000..2785d0ed46e --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.10.4' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] + +builddependencies = [ + ('CMake', '3.18.4') +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.so'] + + ['lib64/libmbd.so'], + 'dirs': ['include', 'lib/cmake/mbd'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb new file mode 100644 index 00000000000..ee732fec796 --- /dev/null +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libmbd' +version = '0.10.4' + +homepage = 'https://libmbd.github.io/index.html' +description = """ +Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: + + - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. +""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] + +builddependencies = [ + ('CMake', '3.20.1') +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmbd.so'] + + ['lib64/libmbd.so'], + 'dirs': ['include', 'lib/cmake/mbd'], +} + +moduleclass = 'chem' From 88cba514a5a5dab6c65a7f34386c726d030f886f Mon Sep 17 00:00:00 2001 From: Martin Lueders Date: Wed, 9 Jun 2021 10:25:16 +0200 Subject: [PATCH 0208/9987] fixed line length issue --- .../l/libmbd/libmbd-0.10.4-foss-2020b.eb | 15 ++++++++++----- .../l/libmbd/libmbd-0.10.4-foss-2021a.eb | 15 ++++++++++----- .../l/libmbd/libmbd-0.10.4-intel-2020b.eb | 15 ++++++++++----- .../l/libmbd/libmbd-0.10.4-intel-2021a.eb | 15 ++++++++++----- 4 files changed, 40 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb index 057ee5f7d9e..149f34fc779 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -7,11 +7,16 @@ homepage = 'https://libmbd.github.io/index.html' description = """ Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. - -The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. """ toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb index ab04682265c..5ca94201575 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb @@ -7,11 +7,16 @@ homepage = 'https://libmbd.github.io/index.html' description = """ Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. - -The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. """ toolchain = {'name': 'foss', 'version': '2021a'} diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb index 2785d0ed46e..32d0079345c 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb @@ -7,11 +7,16 @@ homepage = 'https://libmbd.github.io/index.html' description = """ Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. - -The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. """ toolchain = {'name': 'intel', 'version': '2020b'} diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb index ee732fec796..2528a42bc11 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb @@ -7,11 +7,16 @@ homepage = 'https://libmbd.github.io/index.html' description = """ Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. - -The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd. + - The Fortran implementation is the reference, most advanced implementation, with support for analytical + gradients and distributed parallelism, and additional functionality beyond the MBD method itself. + It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings + to the C API are provided. + - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. + - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine + learning applications with MBD. + +The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the +Python package called Pymbd. """ toolchain = {'name': 'intel', 'version': '2021a'} From 6b864d0ea50348b1d919160aff9b3016eff11471 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Jun 2021 16:17:09 +0200 Subject: [PATCH 0209/9987] update to intel/2021a --- ....05-intel-2021.03.eb => SciPy-bundle-2021.05-intel-2021a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/SciPy-bundle/{SciPy-bundle-2021.05-intel-2021.03.eb => SciPy-bundle-2021.05-intel-2021a.eb} (97%) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021.03.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb similarity index 97% rename from easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021.03.eb rename to easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb index 63b4ab5a7ea..7065c3550d1 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021.03.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb @@ -6,7 +6,7 @@ version = '2021.05' homepage = 'https://python.org/' description = "Bundle of Python packages for scientific software" -toolchain = {'name': 'intel', 'version': '2021.03'} +toolchain = {'name': 'intel', 'version': '2021a'} toolchainopts = {'pic': True, 'lowopt': True, 'strict': True} builddependencies = [('hypothesis', '6.13.1')] From 7e6a2cc7d415d7fdd022bf0342ff96fcba1970b0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 11 Jun 2021 11:42:53 +0200 Subject: [PATCH 0210/9987] adding easyconfigs: ABINIT-9.4.2-intel-2021a.eb --- .../a/ABINIT/ABINIT-9.4.2-intel-2021a.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-intel-2021a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-intel-2021a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-intel-2021a.eb new file mode 100644 index 00000000000..f0a1e44d90f --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-intel-2021a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.4.2' + +homepage = 'https://www.abinit.org/' +description = """ +ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of +systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using +pseudopotentials and a planewave or wavelet basis. +""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d40886f5c8b138bb4aa1ca05da23388eb70a682790cfe5020ecce4db1b1a76bc'] + +builddependencies = [ + ('Python', '3.9.5'), +] +dependencies = [ + ('libxc', '5.1.4'), + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), + ('HDF5', '1.10.7'), + ('Wannier90', '3.1.0'), +] + +# Ensure MPI with intel wrappers. +configopts = '--with-mpi="yes" ' +configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# Enable OpenMP +configopts += '--enable-openmp="yes" ' + +# BLAS/Lapack from MKL +configopts += '--with-linalg-flavor=mkl ' + +# FFTW from MKL +configopts += '--with-fft-flavor=dfti ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# Enable double precision for GW calculations +configopts += '--enable-gw-dpc ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' From 3b01220ace12a60e745b1073bd9c3cdc462dd3ee Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 11 Jun 2021 14:29:18 +0100 Subject: [PATCH 0211/9987] adding easyconfigs: RepeatModeler-2.0.2a-foss-2020b.eb --- .../RepeatModeler-2.0.2a-foss-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb new file mode 100644 index 00000000000..44ec3867afc --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb @@ -0,0 +1,40 @@ +# Author: Jasper Grimm (UoY) + +name = 'RepeatModeler' +version = '2.0.2a' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatModeler is a de novo transposable element (TE) family identification and modeling package. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://www.repeatmasker.org/RepeatModeler'] +sources = ['RepeatModeler-%(version)s.tar.gz'] +checksums = ['8a9d69c8d7afbfb07f8bb6560c5f2fd35e61e5e7ccd01361e4f9a63f4ef3e50c'] + +dependencies = [ + ('Perl', '5.32.0'), + ('TRF', '4.09.1'), + ('RMBlast', '2.11.0'), + ('RepeatMasker', '4.1.2-p1'), + ('RepeatScout', '1.0.6'), + ('RECON', '1.08'), + ('Kent_tools', '411'), + ('CD-HIT', '4.8.1'), + # Optional (required for LTR pipeline): + ('MAFFT', '7.475', '-with-extensions'), + ('GenomeTools', '1.6.1'), # for LTRHarvest + ('LTR_retriever', '2.9.0'), + ('NINJA', '0.97-cluster_only'), +] + +exts_defaultclass = 'PerlModule' +exts_list = [ + ('Devel::Size', '0.83', { + 'source_tmpl': 'Devel-Size-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['757a67e0aa59ae103ea5ca092cbecc025644ebdc326731688ffab6f8823ef4b3'], + }), +] + +moduleclass = 'bio' From 2f5807fe2fa618ae328a4bb05a022bce902f4fac Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Sun, 13 Jun 2021 00:39:46 +0950 Subject: [PATCH 0212/9987] dep issue fix with pip --- ...MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 19 ++----------------- 1 file changed, 2 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index d49afd6c48a..f484f3c9d9b 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -27,25 +27,12 @@ toolchain = {'name': 'foss', 'version': '2020a'} dependencies = [ ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', versionsuffix), - ('Perl', '5.30.2'), - ('Bowtie2', '2.4.1'), - ('SAMtools', '1.10'), - ('BLAST', '2.11.0', '-Linux_x86_64', True), - ('MAFFT', '7.453', '-with-extensions'), - ('RAxML', '8.2.12', '-hybrid-avx2'), - ('DIAMOND', '2.0.4'), - ('trimAl', '1.4.1'), - ('FastTree', '2.1.11'), ] use_pip = True +use_pip_for_deps = True sanity_pip_check = True -download_dep_fail = True - -modextrapaths = { - 'LIBRARY_PATH': 'lib', - 'LD_LIBRARY_PATH': 'lib' -} +download_dep_fail = False sanity_check_paths = { 'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']], @@ -53,6 +40,4 @@ sanity_check_paths = { } sanity_check_commands = [('%(namelower)s', '-h')] -options = {'modulename': 'metaphlan'} - moduleclass = 'bio' From c49ebefc18cb2c9eda0cae4c91397f21a3151bf0 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 14 Jun 2021 13:18:17 +0200 Subject: [PATCH 0213/9987] adding easyconfigs: naturalsort-0.1.3-foss-2020b.eb, pysamstats-1.1.2-foss-2020b.eb, Excel-Writer-XLSX-1.09-foss-2020b.eb --- .../Excel-Writer-XLSX-1.09-foss-2020b.eb | 24 +++++++++++++++ .../naturalsort-0.1.3-foss-2020b.eb | 24 +++++++++++++++ .../pysamstats/pysamstats-1.1.2-foss-2020b.eb | 30 +++++++++++++++++++ 3 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb create mode 100644 easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb new file mode 100644 index 00000000000..134d149bbcc --- /dev/null +++ b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PerlModule' + +name = 'Excel-Writer-XLSX' +version = '1.09' + +homepage = 'https://metacpan.org/pod/Excel::Writer::XLSX' +description = """The Excel::Writer::XLSX module can be used to create an Excel file in the 2007+ XLSX format. +Multiple worksheets can be added to a workbook and formatting can be applied to cells. Text, numbers, and formulas +can be written to the cells.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['d679c6ac19e93c32ab77594c793e41b948c7bb3873b600e70ad637d093dca187'] + +dependencies = [ + ('Perl', '5.32.0'), + ('Archive-Zip', '1.68'), +] + +options = {'modulename': 'Excel::Writer::XLSX'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb b/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb new file mode 100644 index 00000000000..44c1ff9c316 --- /dev/null +++ b/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'RPackage' + +name = 'naturalsort' +version = '0.1.3' + +homepage = 'https://github.com/kos59125/naturalsort/' +description = """The package provides functions related to human natural ordering.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['http://cran.r-project.org/src/contrib/'] +sources = ['%s_%s.tar.gz' % (name, version)] +checksums = ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'] + +dependencies = [ + ('R', '4.0.3'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['naturalsort'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb new file mode 100644 index 00000000000..6233dc44ab7 --- /dev/null +++ b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'pysamstats' +version = '1.1.2' + +homepage = 'https://github.com/alimanfoo/pysamstats' +description = """A Python utility for calculating statistics +against genome positions based on sequence alignments from a SAM or BAM file.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d8b41934fdc700552d689f473860c64525a88600460344d0cac2095424750c6'] + +use_pip = True + +dependencies = [ + ('Python', '3.8.6'), + ('Pysam', '0.16.0.1'), + ('SciPy-bundle', '2020.11'), + ('PyTables', '3.6.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.8/site-packages'], +} + +moduleclass = 'bio' From af9d99981a18eb99db833be6da122ffd34a82cba Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 14 Jun 2021 13:38:26 +0200 Subject: [PATCH 0214/9987] less strict requirements of pysamstats --- .../easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb index 6233dc44ab7..1211730884c 100644 --- a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb @@ -9,11 +9,13 @@ against genome positions based on sequence alignments from a SAM or BAM file.""" toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['6d8b41934fdc700552d689f473860c64525a88600460344d0cac2095424750c6'] use_pip = True +download_dep_fail = True + +preinstallopts = "sed -i -e 's/ (<0.16)//g' setup.py && " dependencies = [ ('Python', '3.8.6'), @@ -22,6 +24,7 @@ dependencies = [ ('PyTables', '3.6.1'), ] +sanity_pip_check = True sanity_check_paths = { 'files': [], 'dirs': ['lib/python3.8/site-packages'], From c39a53a2e430f05a36bc6e8c620afdb18a2fc8fd Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 14 Jun 2021 15:37:41 +0200 Subject: [PATCH 0215/9987] repaired source file name --- .../Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb index 134d149bbcc..d259f3941ac 100644 --- a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb +++ b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb @@ -11,7 +11,7 @@ can be written to the cells.""" toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://cpan.metacpan.org/authors/id/J/JM/JMCNAMARA/'] -sources = ['%(name)s-v%(version)s.tar.gz'] +sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['d679c6ac19e93c32ab77594c793e41b948c7bb3873b600e70ad637d093dca187'] dependencies = [ @@ -21,4 +21,9 @@ dependencies = [ options = {'modulename': 'Excel::Writer::XLSX'} +sanity_check_paths = { + 'files': ['bin/extract_vba'], + 'dirs': ['lib', 'bin'], +} + moduleclass = 'tools' From a91aa340553f69513e67462d9e98a226ea888df3 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 14 Jun 2021 16:06:00 +0200 Subject: [PATCH 0216/9987] changed http to https --- .../easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb b/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb index 44c1ff9c316..d56aff73a49 100644 --- a/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb @@ -8,7 +8,7 @@ description = """The package provides functions related to human natural orderin toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = ['http://cran.r-project.org/src/contrib/'] +source_urls = ['https://cran.r-project.org/src/contrib/'] sources = ['%s_%s.tar.gz' % (name, version)] checksums = ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'] From 941968dc6bc782df13693ce5102e214c38c3b18b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 15 Jun 2021 10:50:30 +0200 Subject: [PATCH 0217/9987] adding easyconfigs: molecularGSM-20190826-intel-2020b.eb and patches: molecularGSM-20190826_fix_ase_test.patch, molecularGSM-20190826_fix_intel.patch --- .../molecularGSM-20190826-intel-2020b.eb | 63 +++ .../molecularGSM-20190826_fix_ase_test.patch | 14 + .../molecularGSM-20190826_fix_intel.patch | 532 ++++++++++++++++++ 3 files changed, 609 insertions(+) create mode 100644 easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb create mode 100644 easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826_fix_ase_test.patch create mode 100644 easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826_fix_intel.patch diff --git a/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb new file mode 100644 index 00000000000..e7ef463af93 --- /dev/null +++ b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'molecularGSM' +version = '20190826' +_commit_moleculargsm = '02ae717' +_commit_tribits = '5308a8e' + +homepage = 'https://github.com/ZimmermanGroup/molecularGSM' +description = """Code for single-ended and double-ended molecular GSM. +The growing string method is a reaction path and transition state finding method developed in c++.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'debug': True, 'noopt': True, 'extra_cxxflags': '-traceback', 'optarch': False} + +sources = [ + { + 'source_urls': ['https://github.com/ZimmermanGroup/molecularGSM/archive/'], + 'download_filename': '%s.tar.gz' % _commit_moleculargsm, + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/TriBITSPub/TriBITS/archive'], + 'download_filename': '%s.tar.gz' % _commit_tribits, + 'filename': 'TriBITS-%s.tar.gz' % _commit_tribits, + 'extract_cmd': 'tar -xzf %s -C %(name)s-* && cd %(name)s-* && mv TriBITS-* TriBITS', + }, +] +patches = [ + 'molecularGSM-20190826_fix_intel.patch', + 'molecularGSM-20190826_fix_ase_test.patch', +] +checksums = [ + '7bb7fd30d4220f720c25a0c6f761eba2b62f94b3be91b15eb536e49778245afc', # molecularGSM-20190826.tar.gz + '121c3885f8b8d2080a299db7f3f527520c985671280e69cb7beb00cd9e9f3e00', # TriBITS-5308a8e.tar.gz + '64b81dec0380db1d350c6ab33d10acb4364ad929544596025e6c7dfea6144a70', # molecularGSM-20190826_fix_intel.patch + '13b4f207af96749a118dee66a5b1fa9606c65c4c39b1b9981edfe713b46dd9c5', # molecularGSM-20190826_fix_ase_test.patch +] + +builddependencies = [('CMake', '3.18.4')] + +# parallel = 1 + +configopts = [ + # '', # default is MOPAC + # '-DGSM_ENABLE_QCHEM=1', + # '-DGSM_ENABLE_QCHEM_SF=1', + # '-DGSM_ENABLE_ORCA=1', + '-DGSM_ENABLE_GAUSSIAN=1', + # '-DGSM_ENABLE_MOLPRO=1', + # '-DGSM_ENABLE_ASE=1', +] + +install_cmd = 'mkdir -p %(installdir)s/bin && cp -a GSM/*.exe %(installdir)s/bin/' + +# _bins = ['ase', 'gaussian', 'molpro', 'mopac', 'orca', 'qchem', 'qchem_sf'] +_bins = ['gaussian'] + +sanity_check_paths = { + 'files': ['bin/gsm.%s.exe' % x for x in _bins], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826_fix_ase_test.patch b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826_fix_ase_test.patch new file mode 100644 index 00000000000..60b57bf2d5e --- /dev/null +++ b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826_fix_ase_test.patch @@ -0,0 +1,14 @@ +Remove missing test for ASE +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur molecularGSM-02ae717e8f3b3bdfb4fe778c04db61d39194f746.orig/TEST/CMakeLists.txt molecularGSM-02ae717e8f3b3bdfb4fe778c04db61d39194f746/TEST/CMakeLists.txt +--- molecularGSM-02ae717e8f3b3bdfb4fe778c04db61d39194f746.orig/TEST/CMakeLists.txt 2019-08-26 19:05:31.000000000 +0200 ++++ molecularGSM-02ae717e8f3b3bdfb4fe778c04db61d39194f746/TEST/CMakeLists.txt 2021-03-30 12:11:41.946968000 +0200 +@@ -78,7 +78,7 @@ + #GFSTRINGQ_TEST(methanolFormaldehydeHydTransfer/orca/de-gsm methanol) + elseif(GSM_ENABLE_ASE) + MESSAGE(STATUS "ASE is enabled.") +- GFSTRINGQ_TEST(dielsAlder/ase/de-gsm diels) ++ #GFSTRINGQ_TEST(dielsAlder/ase/de-gsm diels) + elseif(GSM_ENABLE_TURBOMOLE) + MESSAGE(STATUS "TURBOMOLE is enabled.") + GFSTRINGQ_TEST(dielsAlder/turbomole/de-gsm-wrapper diels-w-wrapper) diff --git a/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826_fix_intel.patch b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826_fix_intel.patch new file mode 100644 index 00000000000..e0b8e9111d3 --- /dev/null +++ b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826_fix_intel.patch @@ -0,0 +1,532 @@ +Fix source for building with intel compilers +Source: https://github.com/ZimmermanGroup/molecularGSM/files/4912332/patchfile-GSM.txt +--- GSM/ase.cpp.org 2020-07-09 08:31:35.425473399 +0200 ++++ GSM/ase.cpp 2020-07-09 08:51:59.209752687 +0200 +@@ -130,7 +130,7 @@ + string line; + bool success = true; + +- success=getline(gradfile, line); ++ success=static_cast(getline(gradfile, line)); + double V = -1 * atof(line.c_str()) / 27.2114; + //printf(" found E: %7.5f \n",V); + +@@ -142,7 +142,7 @@ + grad[3*i+0] = grad[3*i+1] = grad[3*i+2] = 1.; + break; + } +- success=getline(gradfile, line); ++ success=static_cast(getline(gradfile, line)); + //cout << "RR " << line << endl; + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t[]"); +--- GSM/bmat.cpp.org 2020-07-09 08:31:35.426473390 +0200 ++++ GSM/bmat.cpp 2020-07-09 08:53:45.562819591 +0200 +@@ -4683,7 +4683,7 @@ + int found = 0; + while(!hessfile.eof()) + { +- success = getline(hessfile,line); ++ success = static_cast(getline(hessfile,line)); + if (line.find("Hessian of the SCF Energy")!=string::npos) + { + found = 1; +@@ -4698,7 +4698,7 @@ + while(!hessfile.eof() && found) + { + nf++; +- success = getline(hessfile,line); ++ success = static_cast(getline(hessfile,line)); + //cout << " RR0: " << line << endl; + for (int j=0;j(getline(hesspfile, line)); + //cout << " RR: " << line << endl; + int length=StringTools::cleanstring(line); + tok_line = StringTools::tokenize(line, " \t"); + natomsf = atoi(tok_line[1].c_str()); + +- success=getline(hesspfile, line); ++ success=static_cast(getline(hesspfile, line)); + //cout << " RR: " << line << endl; + length=StringTools::cleanstring(line); + tok_line = StringTools::tokenize(line, " \t"); +@@ -4855,7 +4855,7 @@ + + for (int i=0;i(getline(hesspfile, line)); + length=StringTools::cleanstring(line); + if (length<1) break; + tok_line = StringTools::tokenize(line, " \t"); +--- GSM/gaussian.cpp.org 2020-07-09 08:31:35.426473390 +0200 ++++ GSM/gaussian.cpp 2020-07-09 08:56:34.787334572 +0200 +@@ -141,7 +141,7 @@ + int done = 0; + while (!gradfile.eof() && done<2) + { +- success=getline(gradfile, line); ++ success=static_cast(getline(gradfile, line)); + if (line.find("SCF Energy")!=string::npos) + { + //cout << " RRe: " << line << endl; +@@ -155,7 +155,7 @@ + int ngf = 0; + while (ngf<3*natoms) + { +- success=getline(gradfile, line); ++ success=static_cast(getline(gradfile, line)); + tok_line = StringTools::tokenize(line, " \t"); + int lsize = tok_line.size(); + for (int j=0;j(getline(infile, line)); + nstates0 = atoi(line.c_str()); + + infile.close(); +@@ -425,7 +425,7 @@ + bool success=true; + while (!infile.eof()) + { +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + if (success) + hf_lines0[nhf++] = line; + } +@@ -462,7 +462,7 @@ + int nf = 0; + while (!infile.eof()) + { +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + vector tok_line = StringTools::tokenize(line, " "); + //cout << "RR0: " << line << endl; fflush(stdout); + +@@ -690,7 +690,7 @@ + int nf = 0; + while (!infile.eof()) + { +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + vector tok_line = StringTools::tokenize(line, " "); + if (tok_line.size()>3) + { +--- GSM/gstring.cpp.org 2020-07-09 08:31:35.429473364 +0200 ++++ GSM/gstring.cpp 2020-07-09 08:56:34.817334309 +0200 +@@ -1284,14 +1284,14 @@ + + string line; + bool success=true; +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + if (success){ + int length=StringTools::cleanstring(line); + natoms=atoi(line.c_str()); + } + cout <<" -The number of atoms is: " << natoms << endl; + +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + vector tok_line0 = StringTools::tokenize(line, " \t"); + CHARGE = 0; + if (tok_line0.size()>0) +@@ -1308,7 +1308,7 @@ + + cout <<" -Reading the atomic names..."; + for (int i=0;i(getline(infile, line)); + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); + anames[i]=tok_line[0]; +@@ -1345,8 +1345,8 @@ + for (int i=0;i<2;i++) + { + if (isSSM && i==1) break; +- success=getline(infile, line); +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); ++ success=static_cast(getline(infile, line)); + for (int j=0;j(getline(infile, line)); + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); + // cout << " i: " << i << " string: " << line << endl; +@@ -5997,7 +5997,7 @@ + + string line; + bool success=true; +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + if (success) + { + int length=StringTools::cleanstring(line); +@@ -6013,8 +6013,8 @@ + for (int i=0;i0) +- success=getline(infile, line); +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); ++ success=static_cast(getline(infile, line)); + if (infile.eof()) + { + printf(" end of restart.xyz reached \n"); +@@ -6026,7 +6026,7 @@ + + for (int j=0;j(getline(infile, line)); + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); + // cout << " i: " << i << " string: " << line << endl; +--- GSM/icoord.cpp.org 2020-07-09 08:31:35.430473355 +0200 ++++ GSM/icoord.cpp 2020-07-09 08:56:34.827334221 +0200 +@@ -1866,14 +1866,14 @@ + + string line; + bool success=true; +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + if (success){ + int length=StringTools::cleanstring(line); + natoms=atoi(line.c_str()); + } + cout <<" natoms: " << natoms << endl; + +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + // if (success){ + // comment=line; + // } +@@ -1885,7 +1885,7 @@ + + //cout <<" -Reading the atomic names..."; + for (int i=0;i(getline(infile, line)); + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); + anames[i]=tok_line[0]; +@@ -1911,10 +1911,10 @@ + + + // for (int i=1;i<=2;i++){ +- success=getline(infile, line); +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); ++ success=static_cast(getline(infile, line)); + for (int j=0;j(getline(infile, line)); + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); + coords[3*j+0]=atof(tok_line[1].c_str()); +@@ -1973,10 +1973,10 @@ + string line; + bool success=true; + int type = 1; +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + while (!infile.eof()) + { +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + //cout << "RR0: " << line << endl; + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); +@@ -1993,7 +1993,7 @@ + + for (int i=0;i(getline(infile, line)); + //cout << "RR: " << line << endl; + length=StringTools::cleanstring(line); + tok_line = StringTools::tokenize(line, " \t"); +@@ -2015,7 +2015,7 @@ + + for (int i=0;i(getline(infile, line)); + //cout << "RR: " << line << endl; + length=StringTools::cleanstring(line); + tok_line = StringTools::tokenize(line, " \t"); +@@ -2038,7 +2038,7 @@ + + for (int i=0;i(getline(infile, line)); + //cout << "RR: " << line << endl; + length=StringTools::cleanstring(line); + tok_line = StringTools::tokenize(line, " \t"); +--- GSM/knnr.cpp.org 2020-07-09 08:31:35.430473355 +0200 ++++ GSM/knnr.cpp 2020-07-09 08:58:27.384346467 +0200 +@@ -1118,7 +1118,7 @@ + bool success=true; + while (!infile.eof()) + { +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + //cout << "RR: " << line << endl; + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); +@@ -1148,10 +1148,10 @@ + string line; + bool success=true; + int type = 1; +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + while (!infile.eof()) + { +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + //cout << "RR0: " << line << endl; + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); +@@ -1166,7 +1166,7 @@ + + for (int i=0;i(getline(infile, line)); + //cout << "RR: " << line << endl; + length=StringTools::cleanstring(line); + tok_line = StringTools::tokenize(line, " \t"); +@@ -1186,7 +1186,7 @@ + + for (int i=0;i(getline(infile, line)); + //cout << "RR: " << line << endl; + length=StringTools::cleanstring(line); + tok_line = StringTools::tokenize(line, " \t"); +@@ -1207,7 +1207,7 @@ + + for (int i=0;i(getline(infile, line)); + //cout << "RR: " << line << endl; + length=StringTools::cleanstring(line); + tok_line = StringTools::tokenize(line, " \t"); +@@ -1253,18 +1253,18 @@ + + string line; + bool success=true; +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + if (success){ + int length=StringTools::cleanstring(line); + //natoms=atoi(line.c_str()); + } + //printf(" natoms: %i \n",natoms); + +- success=getline(infile, line); ++ success=static_cast(getline(infile, line)); + + for (int i=0;i(getline(infile, line)); + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); + anames[i]=tok_line[0]; +@@ -1337,8 +1337,8 @@ + int done = 0; + while(!infile.eof() && !done) + { +- success = getline(infile,line); +- success = getline(infile,line); ++ success = static_cast(getline(infile,line)); ++ success = static_cast(getline(infile,line)); + + //cout << " RR: " << line << endl; fflush(stdout); + int length=StringTools::cleanstring(line); +@@ -1432,9 +1432,9 @@ + int done = 0; + while(!infile.eof() && !done) + { +- success = getline(infile,line); ++ success = static_cast(getline(infile,line)); + //cout << "RR0: " << line << endl; +- success = getline(infile,line); ++ success = static_cast(getline(infile,line)); + //cout << "RR0: " << line << endl; + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); +--- GSM/molpro.cpp.org 2020-07-09 08:31:35.431473346 +0200 ++++ GSM/molpro.cpp 2020-07-09 08:56:34.841334098 +0200 +@@ -318,7 +318,7 @@ + int found = 0; + while(!outfilei.eof()) + { +- success=getline(outfilei, line); ++ success=static_cast(getline(outfilei, line)); + if (line.find("MCSCF STATE 1.1 Energy")!=string::npos) + { + //cout << " found: " << line << endl; +@@ -481,11 +481,11 @@ + + string line; + bool success=true; +- success=getline(outfilei, line); ++ success=static_cast(getline(outfilei, line)); + int cont = 0; + while(!outfilei.eof()) + { +- success=getline(outfilei, line); ++ success=static_cast(getline(outfilei, line)); + if (line.find("SA-MC GRADIENT FOR STATE")!=string::npos) + { + //cout << " found: " << line << endl; +@@ -511,7 +511,7 @@ + if (cont) + for (int i=0;i(getline(outfilei, line)); + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); + //cout << " RR: " << line << endl; +@@ -557,11 +557,11 @@ + + string line; + bool success=true; +- success=getline(outfilei, line); ++ success=static_cast(getline(outfilei, line)); + int cont = 0; + while(!outfilei.eof()) + { +- success=getline(outfilei, line); ++ success=static_cast(getline(outfilei, line)); + if (line.find("SA-MC NACME FOR STATES")!=string::npos) + { + //cout << " found: " << line << endl; +@@ -576,7 +576,7 @@ + if (cont) + for (int i=0;i(getline(outfilei, line)); + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); + //cout << " RR: " << line << endl; +--- GSM/orca.cpp.org 2020-07-09 08:31:35.431473346 +0200 ++++ GSM/orca.cpp 2020-07-09 08:56:34.846334054 +0200 +@@ -138,7 +138,7 @@ + int done = 0; + while (!gradfile.eof() && done<2) + { +- success=getline(gradfile, line); ++ success=static_cast(getline(gradfile, line)); + if (line.find("Total Energy")!=string::npos) + { + //cout << " RRe: " << line << endl; fflush(stdout); +@@ -148,12 +148,12 @@ + } + if (line.find("CARTESIAN GRADIENT")!=string::npos) + { +- success=getline(gradfile, line); +- success=getline(gradfile, line); ++ success=static_cast(getline(gradfile, line)); ++ success=static_cast(getline(gradfile, line)); + //cout << " RR0g: " << line << endl; + for (int j=0;j(getline(gradfile, line)); + //cout << " RRg: " << line << endl; + tok_line = StringTools::tokenize(line, " \t"); + for (int k=0;k<3;k++) +--- GSM/qchem.cpp.org 2020-07-09 08:31:35.432473337 +0200 ++++ GSM/qchem.cpp 2020-07-09 08:56:34.852334001 +0200 +@@ -430,9 +430,9 @@ + bool success = true; + //cout << "reading gradient... " << endl; + +- success=getline(gradfile, line); +- success=getline(gradfile, line); +- success=getline(gradfile, line); ++ success=static_cast(getline(gradfile, line)); ++ success=static_cast(getline(gradfile, line)); ++ success=static_cast(getline(gradfile, line)); + + for (int i=0;i(getline(gradfile, line)); + //cout << "RR " << line << endl; + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); +--- GSM/qchemsf.cpp.org 2020-07-09 08:31:35.432473337 +0200 ++++ GSM/qchemsf.cpp 2020-07-09 08:56:34.857333958 +0200 +@@ -349,7 +349,7 @@ + int wg = 0; + while (!gradfile.eof()) + { +- success=getline(gradfile, line); ++ success=static_cast(getline(gradfile, line)); + if (line.find("GSM-formatted gradient")!=string::npos) + { + double* gradn = grad1; +@@ -360,7 +360,7 @@ + + for (int i=0;i(getline(gradfile, line)); + //cout << "RR " << line << endl; + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); +--- GSM/turbomole.cpp.org 2020-07-09 08:31:35.432473337 +0200 ++++ GSM/turbomole.cpp 2020-07-09 08:56:34.863333905 +0200 +@@ -458,9 +458,9 @@ + bool success = true; + cout << "reading gradient from... " << file.c_str() << endl; + +- success=getline(gradfile, line); +- success=getline(gradfile, line); +- success=getline(gradfile, line); ++ success=static_cast(getline(gradfile, line)); ++ success=static_cast(getline(gradfile, line)); ++ success=static_cast(getline(gradfile, line)); + + //for (int i=0;i(getline(gradfile, line)); + // cout << "RR " << line << endl; + int length=StringTools::cleanstring(line); + vector tok_line = StringTools::tokenize(line, " \t"); From 0071bfa5d5f53684e5e25c6f22b89498bb0f8f8e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 15 Jun 2021 11:01:26 +0200 Subject: [PATCH 0218/9987] adding easyconfigs: AIMAll-19.10.12-intel-2020b-linux_64bit.eb --- ...AIMAll-19.10.12-intel-2020b-linux_64bit.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb diff --git a/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb b/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb new file mode 100644 index 00000000000..92c08277777 --- /dev/null +++ b/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb @@ -0,0 +1,39 @@ +easyblock = 'Tarball' + +name = 'AIMAll' +version = '19.10.12' +versionsuffix = '-linux_64bit' + +homepage = 'http://aim.tkgristmill.com' +description = """ +AIMAll is an easy to use, accurate, reliable and efficient quantum chemistry software package for performing +comprehensive, quantitative and visual QTAIM analyses of molecular systems - starting from molecular wavefunction +data.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +# download sources from http://aim.tkgristmill.com/download/download.html (requires login) +# to run in professional mode, add required license files to the main AIMAll directory +sources = [ + {'filename': 'aimall_%s_linux_64bit.tar.gz' % version.replace('.', '_'), + 'extract_cmd': 'tar -xzf %s --strip-components=1'}, + # {'filename': 'license_file_b.lslicb', 'extract_cmd': 'cp %s .'}, + # {'filename': 'license_file_a.lslica', 'extract_cmd': 'cp %s .'}, +] +checksums = [ + 'bf369ec8dd829c23a954b1c405edc7d8a01034d106cabc9c332bf7c4c177a54c', # aimall_19_10_12_linux_64bit.tar.gz +] + +buildininstalldir = True +skipsteps = ['install'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['bin/%s.exe' % x for x in ['aimext', 'aimint', 'aimqb', 'aimstudio', 'aimsum', 'aimutil']], + 'dirs': [], +} + +sanity_check_commands = ['aimqb.ish -nogui -help'] + +moduleclass = 'chem' From bf369b0c5f0e5f9443d9769a706000c09b8686cd Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 15 Jun 2021 12:33:28 +0200 Subject: [PATCH 0219/9987] adding easyconfigs: AMS-2020.102-iimpi-2020b-intelmpi.eb --- .../AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb diff --git a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb new file mode 100644 index 00000000000..0e032547e34 --- /dev/null +++ b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'AMS' +version = '2020.102' +versionsuffix = '-intelmpi' + +homepage = 'https://www.scm.com/amsterdam-modeling-suite/' +description = """ +The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for computational chemistry and materials +science, from quantum mechanics to fluid thermodynamics. +""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} + +sources = ['ams%(version)s.pc64_linux.intelmpi.bin.tgz'] +checksums = ['8a68eef268d7eb53ea1e10f66a48a8280f4dadae585999096ba1c246e88989db'] + +dependencies = [('libGLU', '9.0.1')] + +keepsymlinks = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +modextrapaths = { + 'AMSHOME': '', + 'AMSBIN': 'bin', + 'AMSRESOURCES': 'atomicdata', +} + +modloadmsg = """These environment variables need to be defined before using AMS: + * $SCMLICENSE: path to AMS license file + * $SCM_TMPDIR: path to user scratch directory +""" + +moduleclass = 'chem' From b7acc596770bf7c72c42e5c2e1c685ab8d7e755a Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 15 Jun 2021 13:36:36 +0200 Subject: [PATCH 0220/9987] adding easyconfigs: networkx-2.5.1-foss-2021a.eb and patches: networkx-2.5.1_pin_decorator.patch --- .../n/networkx/networkx-2.5.1-foss-2021a.eb | 32 +++++++++++++++++++ .../networkx-2.5.1_pin_decorator.patch | 19 +++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.5.1_pin_decorator.patch diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb new file mode 100644 index 00000000000..1cb8435b164 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb @@ -0,0 +1,32 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.5.1' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +patches = ['networkx-2.5.1_pin_decorator.patch'] +checksums = [ + '109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a', # networkx-2.5.1.tar.gz + # networkx-2.5.1_pin_decorator.patch + '5399a682ee52cafb601e800711058a9aed2e1a20e60d26c0b428461dd76a2246', +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5.1_pin_decorator.patch b/easybuild/easyconfigs/n/networkx/networkx-2.5.1_pin_decorator.patch new file mode 100644 index 00000000000..2ff8c846283 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5.1_pin_decorator.patch @@ -0,0 +1,19 @@ +From caffb25cae8c6fa783db1489136ae41bbd17fd23 Mon Sep 17 00:00:00 2001 +From: Ross Barnowski +Date: Tue, 18 May 2021 10:52:23 -0700 +Subject: [PATCH] Pin upper bound on decorator for 2.6 release. + +--- + requirements/default.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/requirements/default.txt b/requirements/default.txt +index 9cdb86317d..5c78e7c125 100644 +--- a/requirements/default.txt ++++ b/requirements/default.txt +@@ -1,4 +1,4 @@ +-decorator>=5.0.7 ++decorator>=5.0.7,<6 + numpy>=1.19; platform_python_implementation!='PyPy' and python_version<'3.10' + scipy>=1.5,!=1.6.1; platform_python_implementation!='PyPy' and python_version<'3.10' + matplotlib>=3.3; platform_python_implementation!='PyPy' and python_version<'3.10' From a9662facced8d6af7173bb1d4f5c8675c10f0b19 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 15 Jun 2021 15:10:50 +0200 Subject: [PATCH 0221/9987] changes according to review --- .../crispr-dav/crispr-dav-2.3.4-foss-2020b.eb | 39 +++++++++++++++++++ .../Excel-Writer-XLSX-1.09-foss-2020b.eb | 3 ++ .../naturalsort-0.1.3-foss-2020b.eb | 2 +- .../pysamstats/pysamstats-1.1.2-foss-2020b.eb | 5 +-- 4 files changed, 44 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb new file mode 100644 index 00000000000..f451b6554f0 --- /dev/null +++ b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'Binary' + +name = 'crispr-dav' +version = '2.3.4' + +homepage = 'https://github.com/pinetree1/crispr-dav/' +description = """CRISPR-DAV is a pipeline to analyze +amplicon-based NGS data of CRISPR clones in a high throughput manner.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/pinetree1/crispr-dav/archive/'] +sources = ['v%(version)s.tar.gz'] + +extract_sources = True + +dependencies = [ + ('R', '4.0.3'), + ('Perl', '5.32.0'), + ('NGS', '2.10.9'), + ('Pysam', '0.16.0.1'), + ('Excel-Writer-XLSX', '1.09'), + ('naturalsort', '0.1.3'), + ('pysamstats', '1.1.2'), +] + +# exts_defaultclass = 'PythonPackage' +# exts_list = [ +# ('pysamstats', '1.1.2', { +# 'source_urls': ['https://pypi.python.org/packages/source/p/pysamstats/'], +# }), +# ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['Modules', 'Examples', 'Rscripts'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb index d259f3941ac..c5eb8676cc9 100644 --- a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb +++ b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb @@ -26,4 +26,7 @@ sanity_check_paths = { 'dirs': ['lib', 'bin'], } +sanity_check_commands = ['extract_vba --help 2>&1 | grep "This utility is used to extract the VBA project binary from an Excel"'] + + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb b/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb index d56aff73a49..b5b5ae7f56b 100644 --- a/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb @@ -9,7 +9,7 @@ description = """The package provides functions related to human natural orderin toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://cran.r-project.org/src/contrib/'] -sources = ['%s_%s.tar.gz' % (name, version)] +sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'] dependencies = [ diff --git a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb index 1211730884c..b0cebf283a5 100644 --- a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb @@ -15,6 +15,7 @@ checksums = ['6d8b41934fdc700552d689f473860c64525a88600460344d0cac2095424750c6'] use_pip = True download_dep_fail = True +# acceptance of pysam>0.16 preinstallopts = "sed -i -e 's/ (<0.16)//g' setup.py && " dependencies = [ @@ -25,9 +26,5 @@ dependencies = [ ] sanity_pip_check = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python3.8/site-packages'], -} moduleclass = 'bio' From 69c6bdb3cea5c9ec991be5759fd20dd2e551670f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 15 Jun 2021 17:19:19 +0200 Subject: [PATCH 0222/9987] WIP removing hardcoded paths --- .../crispr-dav/crispr-dav-2.3.4-foss-2020b.eb | 9 +- ...av-2.3.4-foss2020b_remove_hardcoding.patch | 169 ++++++++++++++++++ 2 files changed, 171 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch diff --git a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb index f451b6554f0..086d38d4f44 100644 --- a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb @@ -14,6 +14,8 @@ sources = ['v%(version)s.tar.gz'] extract_sources = True +patches = ['crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch'] + dependencies = [ ('R', '4.0.3'), ('Perl', '5.32.0'), @@ -24,13 +26,6 @@ dependencies = [ ('pysamstats', '1.1.2'), ] -# exts_defaultclass = 'PythonPackage' -# exts_list = [ -# ('pysamstats', '1.1.2', { -# 'source_urls': ['https://pypi.python.org/packages/source/p/pysamstats/'], -# }), -# ] - sanity_check_paths = { 'files': [], 'dirs': ['Modules', 'Examples', 'Rscripts'], diff --git a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch new file mode 100644 index 00000000000..6130b838bdd --- /dev/null +++ b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch @@ -0,0 +1,169 @@ +diff -ruN crispr-dav-2.3.4_orig/conf.txt crispr-dav-2.3.4/conf.txt +--- crispr-dav-2.3.4_orig/conf.txt 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/conf.txt 2021-06-15 15:42:22.658826437 +0200 +@@ -9,40 +9,40 @@ + ## Absolute path must be used for genome files when a samplesheet is used to prepare run.sh. + + [genomex] +-ref_fasta = /bfx/app/crispr-dav/Examples/example1/genome/genomex.fa +-bwa_idx = /bfx/app/crispr-dav/Examples/example1/genome/genomex.fa +-refGene = /bfx/app/crispr-dav/Examples/example1/genome/refgenex.txt ++# ref_fasta = /bfx/app/crispr-dav/Examples/example1/genome/genomex.fa ++# bwa_idx = /bfx/app/crispr-dav/Examples/example1/genome/genomex.fa ++# refGene = /bfx/app/crispr-dav/Examples/example1/genome/refgenex.txt + + [hg38] +-ref_fasta = /bfx/genome/hg38/hg38.fa +-bwa_idx = /bfx/genome/hg38/hg38.fa +-refGene = /bfx/genome/hg38/hg38_UCSCrefGene.txt ++# ref_fasta = /bfx/genome/hg38/hg38.fa ++# bwa_idx = /bfx/genome/hg38/hg38.fa ++# refGene = /bfx/genome/hg38/hg38_UCSCrefGene.txt + + [hg19] +-ref_fasta = /bfx/genome/hg19/hg19.fa +-bwa_idx = /bfx/genome/hg19/hg19.fa +-refGene = /bfx/genome/hg19/UCSCrefGene.txt ++# ref_fasta = /bfx/genome/hg19/hg19.fa ++# bwa_idx = /bfx/genome/hg19/hg19.fa ++# refGene = /bfx/genome/hg19/UCSCrefGene.txt + + [mm10] +-ref_fasta = /bfx/genome/mm10/mm10.fa +-bwa_idx = /bfx/genome/mm10/mm10.fa +-refGene = /bfx/genome/mm10/mm10_UCSCrefGene.txt ++# ref_fasta = /bfx/genome/mm10/mm10.fa ++# bwa_idx = /bfx/genome/mm10/mm10.fa ++# refGene = /bfx/genome/mm10/mm10_UCSCrefGene.txt + + [rn6] +-ref_fasta = /bfx/genome/rn6/rn6.fa +-bwa_idx = /bfx/genome/rn6/rn6.fa +-refGene = /bfx/genome/rn6/rn6_UCSCrefGene.txt ++# ref_fasta = /bfx/genome/rn6/rn6.fa ++# bwa_idx = /bfx/genome/rn6/rn6.fa ++# refGene = /bfx/genome/rn6/rn6_UCSCrefGene.txt + + [canFam3] +-ref_fasta = /bfx/genome/canFam3/canFam3.fa +-bwa_idx = /bfx/genome/canFam3/canFam3.fa +-refGene = /bfx/genome/canFam3/canFam3_UCSCrefGene.txt ++# ref_fasta = /bfx/genome/canFam3/canFam3.fa ++# bwa_idx = /bfx/genome/canFam3/canFam3.fa ++# refGene = /bfx/genome/canFam3/canFam3_UCSCrefGene.txt + + + [criGri1] +-ref_fasta = /bfx/genome/criGri1/criGri1.fa +-bwa_idx = /bfx/genome/criGri1/criGri1.fa +-refGene = /bfx/genome/criGri1/criGri1_UCSCrefGene.txt ++# ref_fasta = /bfx/genome/criGri1/criGri1.fa ++# bwa_idx = /bfx/genome/criGri1/criGri1.fa ++vrefGene = /bfx/genome/criGri1/criGri1_UCSCrefGene.txt + + ## Required tools + +@@ -52,30 +52,30 @@ + # For others, if path is not provided, it must be accessible + # in your environment + +-abra = /bfx/app/bin/abra-0.97-SNAPSHOT-jar-with-dependencies.jar ++# abra = /bfx/app/bin/abra-0.97-SNAPSHOT-jar-with-dependencies.jar + + # Path to prinseq-lite.pl. Make sure prinseq path is executable. +-prinseq = /bfx/app/bin/prinseq-lite.pl ++# prinseq = /bfx/app/bin/prinseq-lite.pl + + # bwa (e.g. 0.7.15) must support bwa mem -M, and be searchable in environment variable PATH + + # samtools +-samtools = /bfx/app/bin/samtools ++# samtools = /bfx/app/bin/samtools + + # Path of flash. By default use flash in PATH. +-flash = /bfx/app/bin/flash2 ++# flash = /bfx/app/bin/flash2 + + # bedtools (e.g. v2.25) must support: bedtools intersect -F +-bedtools = /bfx/app/bin/bedtools ++# bedtools = /bfx/app/bin/bedtools + + # java must be 1.7 or later +-java = /usr/bin/java ++# java = /usr/bin/java + + # pysamstats +-pysamstats = /bfx/app/bin/pysamstats ++# pysamstats = /bfx/app/bin/pysamstats + + # R must have ggplot2, reshape2, and naturalsort packages +-rscript = /bfx/app/bin/Rscript ++# rscript = /bfx/app/bin/Rscript + + ## Filtering parameters + +diff -ruN crispr-dav-2.3.4_orig/Examples/example1/conf.txt crispr-dav-2.3.4/Examples/example1/conf.txt +--- crispr-dav-2.3.4_orig/Examples/example1/conf.txt 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Examples/example1/conf.txt 2021-06-15 15:31:29.165679076 +0200 +@@ -21,30 +21,30 @@ + # For others, if path is not provided, it must be accessible + # in your environment + +-abra = /bfx/app/bin/abra-0.97-SNAPSHOT-jar-with-dependencies.jar ++# abra = /bfx/app/bin/abra-0.97-SNAPSHOT-jar-with-dependencies.jar + + # Path to prinseq-lite.pl. Make sure prinseq path is executable. +-prinseq = /bfx/app/bin/prinseq-lite.pl ++# prinseq = /bfx/app/bin/prinseq-lite.pl + + # bwa (e.g. 0.7.15) must support bwa mem -M, and be searchable in environment variable PATH + + # samtools +-samtools = /bfx/app/bin/samtools ++# samtools = /bfx/app/bin/samtools + + # Path of flash. By default use flash in PATH. +-flash = /bfx/app/bin/flash2 ++# flash = /bfx/app/bin/flash2 + + # bedtools (e.g. v2.25) must support: bedtools intersect -F +-bedtools = /bfx/app/bin/bedtools ++# bedtools = /bfx/app/bin/bedtools + + # java must be 1.7 or later +-java = /usr/bin/java ++# java = /usr/bin/java + + # pysamstats +-pysamstats = /bfx/app/bin/pysamstats ++# pysamstats = /bfx/app/bin/pysamstats + + # R must have ggplot2, reshape2, and naturalsort packages +-rscript = /bfx/app/bin/Rscript ++# rscript = /bfx/app/bin/Rscript + + ## Filtering parameters + +diff -ruN crispr-dav-2.3.4_orig/Examples/example1/run.sh crispr-dav-2.3.4/Examples/example1/run.sh +--- crispr-dav-2.3.4_orig/Examples/example1/run.sh 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Examples/example1/run.sh 2021-06-15 15:36:58.854366160 +0200 +@@ -4,6 +4,7 @@ + + ## If there is problem loading Perl modules., set PERL5LIB accordingly. + #export PERL5LIB=$HOME/perlmod/lib/perl5:$PERL5LIB +-../../crispr.pl --conf conf.txt --region amplicon.bed --crispr site.bed \ ++ ++$EBROOTCRISPRMINDAV/crispr.pl --conf conf.txt --region amplicon.bed --crispr site.bed \ + --sitemap sample.site --fastqmap fastq.list --genome genomex + +diff -ruN crispr-dav-2.3.4_orig/Examples/example2/run.sh crispr-dav-2.3.4/Examples/example2/run.sh +--- crispr-dav-2.3.4_orig/Examples/example2/run.sh 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Examples/example2/run.sh 2021-06-15 15:29:03.089257825 +0200 +@@ -5,6 +5,6 @@ + ## If there is problem loading Perl modules., set PERL5LIB accordingly. + #export PERL5LIB=$HOME/perlmod/lib/perl5:$PERL5LIB + +-../../crispr.pl --conf conf.txt --amp_fasta amp.fa --crispr site.bed \ ++$EBROOTCRISPRMINDAV/Examples/example2/crispr.pl --conf conf.txt --amp_fasta amp.fa --crispr site.bed \ + --sitemap sample.site --fastqmap fastq.list --codon_start 1 + From ca430810d3cd0047d269e146f09ab1caf8e19701 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 16 Jun 2021 12:31:26 +0200 Subject: [PATCH 0223/9987] adding easyconfigs: Libint-2.6.0-GCC-10.3.0-lmax-6-cp2k.eb --- .../Libint-2.6.0-GCC-10.3.0-lmax-6-cp2k.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.3.0-lmax-6-cp2k.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.3.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.3.0-lmax-6-cp2k.eb new file mode 100644 index 00000000000..3944c683f1d --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-10.3.0-lmax-6-cp2k.eb @@ -0,0 +1,52 @@ +## +# Author: Robert Mijakovic +## +name = 'Libint' +version = '2.6.0' +local_lmax = 6 +# custom configuration, to be used as dependency for CP2K +versionsuffix = '-lmax-%s-cp2k' % local_lmax + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/evaleev/libint/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch', + 'Libint-2.6.0_remove-test-eri.patch', +] +checksums = [ + '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz + # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch + 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', + # Libint-2.6.0_remove-test-eri.patch + 'e47868901250078adeb35b80ab866ba8063ad9756881d1b557cb925334df653b', +] + +builddependencies = [ + ('Autotools', '20210128'), + ('GMP', '6.2.1'), + ('Boost', '1.76.0'), + ('Eigen', '3.3.9'), + ('Python', '3.9.5'), +] + +# configure options as required by CP2K, +# see Jenkinsfile in https://github.com/cp2k/libint-cp2k +local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) +local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) + +libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax +libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am +libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--enable-generic-code --disable-unrolling' + +with_fortran = True + +moduleclass = 'chem' From a34d38c6e06ba3d1591e9ad87ba4ee56a95299a7 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 16 Jun 2021 14:51:45 +0200 Subject: [PATCH 0224/9987] adding easyconfigs: CP2K-8.2-foss-2021a.eb --- .../easyconfigs/c/CP2K/CP2K-8.2-foss-2021a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-8.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-8.2-foss-2021a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-8.2-foss-2021a.eb new file mode 100644 index 00000000000..ba96f807c90 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-8.2-foss-2021a.eb @@ -0,0 +1,39 @@ +## +# Author: Robert Mijakovic +## +name = 'CP2K' +version = '8.2' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2e24768720efed1a5a4a58e83e2aca502cd8b95544c21695eb0de71ed652f20a'] + +dependencies = [ + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '5.1.5'), + ('libxsmm', '1.16.1'), + ('FFTW', '3.3.9'), + ('PLUMED', '2.6.3'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.6'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' From 65a83445086aa3380a36b2895919ae6747b979a7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 17 Jun 2021 15:30:18 +0200 Subject: [PATCH 0225/9987] adding easyconfig: SNAP-ESA-8.0-Java-1.8.0_292-OpenJDK.eb --- .../SNAP-ESA-8.0-Java-1.8.0_292-OpenJDK.eb | 71 +++++++++++++++++++ .../s/SNAP-ESA/SNAP-ESA-8.0-response.varfile | 15 ++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.0_292-OpenJDK.eb create mode 100644 easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-response.varfile diff --git a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.0_292-OpenJDK.eb b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.0_292-OpenJDK.eb new file mode 100644 index 00000000000..dd992f6d9ea --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.0_292-OpenJDK.eb @@ -0,0 +1,71 @@ +easyblock = 'Binary' + +name = 'SNAP-ESA' +version = '8.0' +versionsuffix = '-Java-%(javaver)s-OpenJDK' + +homepage = 'https://step.esa.int/main/toolboxes/snap/' +description = """ +The Sentinel Application Platform (SNAP) is a common architecture for all +Sentinel Toolboxes being jointly developed by Brockmann Consult, SkyWatch and +C-S. +The SNAP architecture is ideal for Earth Observation processing and analysis +due to the following technological innovations: Extensibility, Portability, +Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory +Management, and a Graph Processing Framework.""" + +toolchain = SYSTEM + +local_installer = 'esa-snap_all_unix_%s.sh' % version.replace('.', '_') +local_varfile = '%(name)s-%(version)s-response.varfile' + +source_urls = [ + 'https://download.esa.int/step/snap/%(version)s/installers', + 'https://step.esa.int/downloads/%(version)s/installers', +] +sources = [local_installer] +patches = [(local_varfile, '.')] +checksums = [ + 'b49d6795f55bbe9ecb46f9c289ac245626243d3fcd32211b47a54b26b508798e', # esa-snap_all_unix_8_0.sh + '5ea98e3376bb3df52b9c4c99ab4986015296b815021e16486b58e4aad58e21a4', # SNAP-ESA-8.0-response.varfile +] + +# The installation is executed with the bundled JRE 1.8.0_242 (Zulu) +# at runtime we switch it to AdoptOpenJDK, which is known to be more reliable for SNAP-ESA +dependencies = [ + ('Java', '1.8.0_292', '-OpenJDK'), +] + +install_cmd = "INSTALL4J_TEMP='%(builddir)s' " +install_cmd += "bash %s -dir '%%(installdir)s'" % local_installer +install_cmd += " -q -varfile '%s'" % local_varfile + +postinstallcmds = [ + # set paths + 'sed -i "s|jdkhome.*|jdkhome=$JAVA_HOME|" %(installdir)s/etc/snap.conf', + 'sed -i "s|#snap.home.*|snap.home=%(installdir)s|" %(installdir)s/etc/snap.properties', + # remove default maximum memory allocation pool + 'sed -i "s|-J-Xmx[0-9G]* ||" %(installdir)s/etc/snap.conf', + # disable update checks + "echo 'snap.versionCheck.interval=NEVER' >> %(installdir)s/etc/snap.properties", + "sed -i 's|dpiaware=false|& -J-Dplugin.manager.check.interval=NEVER|' %(installdir)s/etc/snap.conf", + # (optional) update all modules to latest version + # the update command is buggy and it hangs after doing the update, kill it whenever it prints "updates=0" + # see issue https://senbox.atlassian.net/browse/SNAP-927 + # ('LOG="$(mktemp -d)/snap-update.log"; mkfifo $LOG; trap "rm -f $LOG" EXIT;' + # 'SNAPCMD="%(installdir)s/bin/snap --nosplash --nogui --userdir "%(builddir)s/snap" --modules --update-all";' + # '$SNAPCMD 2>&1 > $LOG & SNAPPID=$!;' + # 'while read line; do echo "$line"; [ "$line" = "updates=0" ] && kill $SNAPPID; done < $LOG;'), +] + +sanity_check_paths = { + 'files': ['bin/snap', 'bin/gpt'], + 'dirs': ['probavbox', 'rstb', 's1tbx', 's2tbx', 's3tbx', 'smos', 'snap'], +} + +sanity_check_commands = [ + "snap --nosplash --nogui --modules --list", + "gpt -h", +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-response.varfile b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-response.varfile new file mode 100644 index 00000000000..e5b052bbfce --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-response.varfile @@ -0,0 +1,15 @@ +# install4j response file for ESA SNAP 8.0 +deleteSnapDir=DESKTOP +executeLauncherWithPythonAction$Boolean=false +forcePython$Boolean=true +pythonExecutable=python +sys.adminRights$Boolean=false +sys.component.3109$Boolean=true +sys.component.RSTB$Boolean=true +sys.component.S1TBX$Boolean=true +sys.component.S2TBX$Boolean=true +sys.component.S3TBX$Boolean=true +sys.component.SMOS$Boolean=true +sys.component.SNAP$Boolean=true +sys.languageId=en +sys.programGroupDisabled$Boolean=true From 0beda8f7f40772f593c9307dc91b59dcee28a130 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 17 Jun 2021 15:30:42 +0200 Subject: [PATCH 0226/9987] adding easyconfigs: SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb --- ....0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb new file mode 100644 index 00000000000..f8fcca9c9be --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'SNAP-ESA-python' +version = '8.0' +local_javasuffix = '-Java-%(javaver)s-OpenJDK' +versionsuffix = local_javasuffix + '-Python-%(pyver)s' + +homepage = 'https://step.esa.int/main/toolboxes/snap/' +description = "Python interface to the Sentinel Application Platform (SNAP) API" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Java', '1.8.0_292', '-OpenJDK', True), + ('SNAP-ESA', version, local_javasuffix, True), + ('Python', '2.7.18'), +] + +local_pysite = 'lib/python%(pyshortver)s/site-packages' +local_pyinstalldir = '%%(installdir)s/%s' % local_pysite + +postinstallcmds = [ + # Install snappy from SNAP-ESA + # snappy-conf is buggy and it hangs after doing the installation of snappy, + # start snappy-conf in a new SID and kill all processes of its PGID + # whenever it prints the final line starting with "or copy" + "mkdir -p %s" % local_pyinstalldir, + ('LOG="$(mktemp -d)/snappy-conf.log"; mkfifo $LOG; trap "rm -f $LOG" EXIT;' + 'setsid snappy-conf $EBROOTPYTHON/bin/python %s 2>&1 > $LOG & CONFPID=$!;' + 'while read line; do echo "$line"; [ -z "${line##or copy*}" ] && kill -- -$CONFPID; done < $LOG;') + % local_pyinstalldir, +] + +sanity_check_paths = { + 'files': [], + 'dirs': [local_pysite], +} + +sanity_check_commands = ["python -c 'import snappy'"] + +modextrapaths = {'PYTHONPATH': [local_pysite]} + +local_javaopts = " -Dsnap.pythonExecutable=python" +local_javaopts += " -Dsnap.pythonModuleDir=%s" % local_pyinstalldir + +modluafooter = 'setenv("JAVA_TOOL_OPTIONS", os.getenv("JAVA_TOOL_OPTIONS").."%s")' % local_javaopts + +moduleclass = 'geo' From d28d6954e77fd481405cdad2dbf1fb792d4d2a30 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 18 Jun 2021 00:38:29 +0950 Subject: [PATCH 0227/9987] adding easyconfigs: RAPSearch2-2.24-GCC-9.3.0.eb --- .../r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb new file mode 100644 index 00000000000..80948486498 --- /dev/null +++ b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb @@ -0,0 +1,38 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU GPLv1 +# +# Notes:: +## + +easyblock = 'CmdCp' + +name = 'RAPSearch2' +version = '2.24' + +homepage = 'https://omics.informatics.indiana.edu/mg/RAPSearch2' +description = """ +RAPSearch stands for Reduced Alphabet based Protein similarity Search +""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://sourceforge.net/projects/rapsearch2/files'] +sources = ['%(name)s.24_64bits.tar.gz'] +checksums = ['85db4573f4c768b6c3c73bb44ff2611ba48dc6c8d188feb40f44bf7c55de36ce'] + +install_cmd = './install' + +skipsteps = ['configure', 'build'] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ('rapsearch', 'prerapsearch')], + 'dirs': [], +} + +moduleclass = 'bio' From b7a5095eca5ece3eb1684587ff5dfd230d1c241f Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 18 Jun 2021 13:29:28 +0950 Subject: [PATCH 0228/9987] adding easyconfigs: biom-format-2.1.10-foss-2020a-Python-3.8.2.eb --- ...m-format-2.1.10-foss-2020a-Python-3.8.2.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..504fc231858 --- /dev/null +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,49 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Revised BSD +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'biom-format' +version = '2.1.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://biom-format.org' +description = """ +The BIOM file format (canonically pronounced biome) is designed to be + a general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth Microbiome + Project and is a Genomics Standards Consortium supported project. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://files.pythonhosted.org/packages/2b/8f/\ + ef865d43a06dd3d1b09808fbd129074e64127fa8db0b93b5e0cf1d1a50de'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('h5py', '2.10.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/biom'], + 'dirs': ['lib'], +} + +options = {'modulename': 'biom'} + +moduleclass = 'bio' From 3e8d1f3b189070ddf09ae51a06c76486340c89a7 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 18 Jun 2021 14:58:30 +0950 Subject: [PATCH 0229/9987] pip_sanity enabled --- ...-format-2.1.10-gompi-2020a-Python-3.8.2.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-gompi-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-gompi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-gompi-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..280f24c8124 --- /dev/null +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-gompi-2020a-Python-3.8.2.eb @@ -0,0 +1,50 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Revised BSD +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'biom-format' +version = '2.1.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://biom-format.org' +description = """ +The BIOM file format (canonically pronounced biome) is designed to be + a general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth Microbiome + Project and is a Genomics Standards Consortium supported project. +""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://files.pythonhosted.org/packages/2b/8f/\ + ef865d43a06dd3d1b09808fbd129074e64127fa8db0b93b5e0cf1d1a50de'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('h5py', '2.10.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/biom'], + 'dirs': ['lib'], +} + +options = {'modulename': 'biom'} + +moduleclass = 'bio' From e2131d2b7b9ec3e85c741dc2a61da7f094d14561 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 18 Jun 2021 20:52:30 +0950 Subject: [PATCH 0230/9987] dep stack change --- ...m-format-2.1.10-foss-2020a-Python-3.8.2.eb | 49 ------------------- 1 file changed, 49 deletions(-) delete mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 504fc231858..00000000000 --- a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,49 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Revised BSD -# -# Notes:: -## - -easyblock = 'PythonPackage' - -name = 'biom-format' -version = '2.1.10' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://biom-format.org' -description = """ -The BIOM file format (canonically pronounced biome) is designed to be - a general-use format for representing biological sample by observation - contingency tables. BIOM is a recognized standard for the Earth Microbiome - Project and is a Genomics Standards Consortium supported project. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://files.pythonhosted.org/packages/2b/8f/\ - ef865d43a06dd3d1b09808fbd129074e64127fa8db0b93b5e0cf1d1a50de'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('h5py', '2.10.0', versionsuffix), -] - -download_dep_fail = True -use_pip = True - -sanity_check_paths = { - 'files': ['bin/biom'], - 'dirs': ['lib'], -} - -options = {'modulename': 'biom'} - -moduleclass = 'bio' From 256e60626a3958b539a28b32a78ecaeee6d5af7d Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 18 Jun 2021 21:03:49 +0950 Subject: [PATCH 0231/9987] dep stack change --- ...m-format-2.1.10-foss-2020a-Python-3.8.2.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..bf3d7ad875e --- /dev/null +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,50 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Revised BSD +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'biom-format' +version = '2.1.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://biom-format.org' +description = """ +The BIOM file format (canonically pronounced biome) is designed to be + a general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth Microbiome + Project and is a Genomics Standards Consortium supported project. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://files.pythonhosted.org/packages/2b/8f/\ + ef865d43a06dd3d1b09808fbd129074e64127fa8db0b93b5e0cf1d1a50de'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('h5py', '2.10.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/biom'], + 'dirs': ['lib'], +} + +options = {'modulename': 'biom'} + +moduleclass = 'bio' From 4b5cd1fdf16b1b5d15e243dca8b9faa362b29549 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 18 Jun 2021 21:04:48 +0950 Subject: [PATCH 0232/9987] dep stack change --- ...m-format-2.1.10-foss-2020a-Python-3.8.2.eb | 50 ------------------- 1 file changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index bf3d7ad875e..00000000000 --- a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,50 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Revised BSD -# -# Notes:: -## - -easyblock = 'PythonPackage' - -name = 'biom-format' -version = '2.1.10' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://biom-format.org' -description = """ -The BIOM file format (canonically pronounced biome) is designed to be - a general-use format for representing biological sample by observation - contingency tables. BIOM is a recognized standard for the Earth Microbiome - Project and is a Genomics Standards Consortium supported project. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://files.pythonhosted.org/packages/2b/8f/\ - ef865d43a06dd3d1b09808fbd129074e64127fa8db0b93b5e0cf1d1a50de'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('h5py', '2.10.0', versionsuffix), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/biom'], - 'dirs': ['lib'], -} - -options = {'modulename': 'biom'} - -moduleclass = 'bio' From 6cdd35387ada2dafa0f34157490be40ed0af57ab Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 18 Jun 2021 21:08:58 +0950 Subject: [PATCH 0233/9987] dep stack change --- ...m-format-2.1.10-foss-2020a-Python-3.8.2.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..bf3d7ad875e --- /dev/null +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,50 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Revised BSD +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'biom-format' +version = '2.1.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://biom-format.org' +description = """ +The BIOM file format (canonically pronounced biome) is designed to be + a general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth Microbiome + Project and is a Genomics Standards Consortium supported project. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://files.pythonhosted.org/packages/2b/8f/\ + ef865d43a06dd3d1b09808fbd129074e64127fa8db0b93b5e0cf1d1a50de'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('h5py', '2.10.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/biom'], + 'dirs': ['lib'], +} + +options = {'modulename': 'biom'} + +moduleclass = 'bio' From ea8bd3d3409469b150f606ba5ef81ff3d022ed2b Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 18 Jun 2021 21:10:19 +0950 Subject: [PATCH 0234/9987] dep stack change --- ...m-format-2.1.10-foss-2020a-Python-3.8.2.eb | 50 ------------------- 1 file changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index bf3d7ad875e..00000000000 --- a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,50 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Revised BSD -# -# Notes:: -## - -easyblock = 'PythonPackage' - -name = 'biom-format' -version = '2.1.10' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://biom-format.org' -description = """ -The BIOM file format (canonically pronounced biome) is designed to be - a general-use format for representing biological sample by observation - contingency tables. BIOM is a recognized standard for the Earth Microbiome - Project and is a Genomics Standards Consortium supported project. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://files.pythonhosted.org/packages/2b/8f/\ - ef865d43a06dd3d1b09808fbd129074e64127fa8db0b93b5e0cf1d1a50de'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('h5py', '2.10.0', versionsuffix), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/biom'], - 'dirs': ['lib'], -} - -options = {'modulename': 'biom'} - -moduleclass = 'bio' From b3ceead735dce3be7d61f25bf00f5cf722d348b3 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 18 Jun 2021 21:11:20 +0950 Subject: [PATCH 0235/9987] dep stack change --- ...m-format-2.1.10-foss-2020a-Python-3.8.2.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..bf3d7ad875e --- /dev/null +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,50 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Revised BSD +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'biom-format' +version = '2.1.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://biom-format.org' +description = """ +The BIOM file format (canonically pronounced biome) is designed to be + a general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth Microbiome + Project and is a Genomics Standards Consortium supported project. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://files.pythonhosted.org/packages/2b/8f/\ + ef865d43a06dd3d1b09808fbd129074e64127fa8db0b93b5e0cf1d1a50de'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('h5py', '2.10.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/biom'], + 'dirs': ['lib'], +} + +options = {'modulename': 'biom'} + +moduleclass = 'bio' From 5d2d85b40c9827a5df61fccf80e33a2c7bf97aac Mon Sep 17 00:00:00 2001 From: manifest Date: Fri, 18 Jun 2021 20:52:03 +0930 Subject: [PATCH 0236/9987] Delete biom-format-2.1.10-gompi-2020a-Python-3.8.2.eb rm `gompi` stack --- ...-format-2.1.10-gompi-2020a-Python-3.8.2.eb | 50 ------------------- 1 file changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-gompi-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-gompi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-gompi-2020a-Python-3.8.2.eb deleted file mode 100644 index 280f24c8124..00000000000 --- a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-gompi-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,50 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Revised BSD -# -# Notes:: -## - -easyblock = 'PythonPackage' - -name = 'biom-format' -version = '2.1.10' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://biom-format.org' -description = """ -The BIOM file format (canonically pronounced biome) is designed to be - a general-use format for representing biological sample by observation - contingency tables. BIOM is a recognized standard for the Earth Microbiome - Project and is a Genomics Standards Consortium supported project. -""" - -toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://files.pythonhosted.org/packages/2b/8f/\ - ef865d43a06dd3d1b09808fbd129074e64127fa8db0b93b5e0cf1d1a50de'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('h5py', '2.10.0', versionsuffix), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/biom'], - 'dirs': ['lib'], -} - -options = {'modulename': 'biom'} - -moduleclass = 'bio' From 850430dd9f06b2352f680f9b9f9870f33ceab3e0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Jun 2021 21:27:26 +0200 Subject: [PATCH 0237/9987] update easyconfigs ABINIT-9.4.2-intel-2021a.eb: use libxc 5.1.5 --- easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-intel-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-intel-2021a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-intel-2021a.eb index f0a1e44d90f..2c65450d26f 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-intel-2021a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-intel-2021a.eb @@ -21,7 +21,7 @@ builddependencies = [ ('Python', '3.9.5'), ] dependencies = [ - ('libxc', '5.1.4'), + ('libxc', '5.1.5'), ('netCDF', '4.8.0'), ('netCDF-Fortran', '4.5.3'), ('HDF5', '1.10.7'), From e87dbabe0b3f0379f4d4c6005303c8eb74b505ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 19 Jun 2021 09:34:05 +0200 Subject: [PATCH 0238/9987] {vis}[GCC/10.3.0] GIMP v2.10.24 --- .../b/babl/babl-0.1.86-GCCcore-10.3.0.eb | 32 ++++++++++ .../g/GEGL/GEGL-0.4.30-GCCcore-10.3.0.eb | 38 ++++++++++++ .../g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb | 50 ++++++++++++++++ .../glib-networking-2.68.1-GCCcore-10.3.0.eb | 34 +++++++++++ .../JSON-GLib-1.6.2-GCCcore-10.3.0.eb | 39 ++++++++++++ .../j/json-c/json-c-0.15-GCCcore-10.3.0.eb | 30 ++++++++++ .../libmypaint-1.6.1-GCCcore-10.3.0.eb | 49 +++++++++++++++ .../librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb | 37 ++++++++++++ .../poppler/poppler-21.06.1-GCCcore-10.3.0.eb | 59 +++++++++++++++++++ 9 files changed, 368 insertions(+) create mode 100644 easybuild/easyconfigs/b/babl/babl-0.1.86-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/GEGL/GEGL-0.4.30-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/glib-networking/glib-networking-2.68.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/j/JSON-GLib/JSON-GLib-1.6.2-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libmypaint/libmypaint-1.6.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/babl/babl-0.1.86-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/babl/babl-0.1.86-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..21bbe05b74f --- /dev/null +++ b/easybuild/easyconfigs/b/babl/babl-0.1.86-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'babl' +version = '0.1.86' + +homepage = 'https://www.gegl.org/babl' +description = "babl is pixel encoding and color space conversion engine in C" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://download.gimp.org/pub/babl/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['0b3f595159ad1b216cd729c0504c3a5f6cf780c641f4dc63fc164f3c0382c8f0'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GObject-Introspection', '1.68.0'), + ('LittleCMS', '2.12'), +] + +sanity_check_paths = { + 'files': ['lib/libbabl-%%(version_major_minor)s.%s' % SHLIB_EXT, 'lib/pkgconfig/babl.pc'], + 'dirs': ['include/babl-%(version_major_minor)s/babl', 'lib/babl-%(version_major_minor)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GEGL/GEGL-0.4.30-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GEGL/GEGL-0.4.30-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..a2f4f7da5a1 --- /dev/null +++ b/easybuild/easyconfigs/g/GEGL/GEGL-0.4.30-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MesonNinja' + +name = 'GEGL' +version = '0.4.30' + +homepage = 'https://www.gegl.org' +description = """GEGL (Generic Graphics Library) is a data flow based image processing framework, + providing floating point processing and non-destructive image processing capabilities to + GNU Image Manipulation Program (GIMP) and other projects.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://download.gimp.org/pub/gegl/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c112782cf4096969e23217ccdfabe42284e35d5435ff0c43d40e4c70faeca8dd'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('babl', '0.1.86'), + ('JSON-GLib', '1.6.2'), + ('libpng', '1.6.37'), + ('cairo', '1.16.0'), +] + +sanity_check_paths = { + 'files': ['bin/gegl', 'lib/libgegl-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/gegl-%(version_major_minor)s', 'lib/pkgconfig', 'share'], +} + +sanity_check_commands = ["gegl --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb new file mode 100644 index 00000000000..121f12f483d --- /dev/null +++ b/easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'GIMP' +version = '2.10.24' + +homepage = 'https://www.gimp.org' +description = "GIMP is a cross-platform image editor available for GNU/Linux, OS X, Windows and more operating systems." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://download.gimp.org/mirror/pub/gimp/v%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['bd1bb762368c0dd3175cf05006812dd676949c3707e21f4e6857435cb435989e'] + +builddependencies = [ + ('intltool', '0.51.0'), +] + +dependencies = [ + ('GTK+', '2.24.33'), + ('Gdk-Pixbuf', '2.42.6'), + ('babl', '0.1.86'), + ('GEGL', '0.4.30'), + ('ATK', '2.36.0'), + ('Pango', '1.48.5'), + ('HarfBuzz', '2.6.7'), + ('LibTIFF', '4.2.0'), + ('libjpeg-turbo', '2.0.6'), + ('libmypaint', '1.6.1'), + ('LittleCMS', '2.12'), + ('glib-networking', '2.68.1'), + ('JSON-GLib', '1.6.2'), + ('gexiv2', '0.12.2'), + ('librsvg', '2.51.2'), + ('poppler', '21.06.1'), +] + +configopts = "--disable-python" + +sanity_check_paths = { + 'files': ['bin/gimp', 'bin/gimp-console', 'lib/libgimp-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['etc/gimp', 'include/gimp-%(version_major)s.0', 'libexec', 'share'], +} + +sanity_check_commands = [ + "gimp --version", + "gimp-console --help", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.68.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.68.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..692e5b0ce68 --- /dev/null +++ b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.68.1-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +name = 'glib-networking' +version = '2.68.1' + +homepage = 'https://gitlab.gnome.org/GNOME/glib-networking' +description = "Network extensions for GLib" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/glib-networking/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['42fa5a90f92d4376e32ae029b7cd29c4710dce9fce70be3e2d03eccb6790913a'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.68.2'), + ('GnuTLS', '3.7.2'), +] + +sanity_check_paths = { + 'files': ['lib/gio/modules/libgiognutls.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'GIO_EXTRA_MODULES': 'lib/gio/modules'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/JSON-GLib/JSON-GLib-1.6.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JSON-GLib/JSON-GLib-1.6.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..9c8b4312ad7 --- /dev/null +++ b/easybuild/easyconfigs/j/JSON-GLib/JSON-GLib-1.6.2-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'JSON-GLib' +version = '1.6.2' + +homepage = 'https://wiki.gnome.org/Projects/JsonGlib' +description = """JSON-GLib implements a full JSON parser and generator using GLib and GObject, + and integrates JSON with GLib data types.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://download.gnome.org/sources/json-glib/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['a33d66c6d038bda46b910c6c6d59c4e15db014e363dc997a0414c2e07d134f24'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.68.2'), + ('GObject-Introspection', '1.68.0'), +] + +sanity_check_paths = { + 'files': ['bin/json-glib-format', 'bin/json-glib-validate', + 'lib/libjson-glib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['include/json-glib-%(version_major)s.0/json-glib', 'lib/pkgconfig', 'share'], +} + +sanity_check_commands = [ + "json-glib-format --help", + "json-glib-validate --help", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..195c011df45 --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.15' +local_suff = '-20200726' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['4ba9a090a42cf1e12b84c64e4464bb6fb893666841d5843cc5bef90774028882'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmypaint/libmypaint-1.6.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libmypaint/libmypaint-1.6.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..20f19a2a1d5 --- /dev/null +++ b/easybuild/easyconfigs/l/libmypaint/libmypaint-1.6.1-GCCcore-10.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'libmypaint' +version = '1.6.1' + +homepage = 'https://github.com/mypaint/libmypaint' +description = """libmypaint, a.k.a. "brushlib", is a library for making brushstrokes which is used by MyPaint + and other projects""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('intltool', '0.51.0'), +] + +dependencies = [ + ('json-c', '0.15'), + ('GObject-Introspection', '1.68.0'), + ('GLib', '2.68.2'), + ('babl', '0.1.86'), + ('GEGL', '0.4.30'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_XZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': ['https://github.com/mypaint/libmypaint/releases/download/v%(version)s/'], + 'checksums': ['741754f293f6b7668f941506da07cd7725629a793108bb31633fb6c3eae5315f'], + 'configopts': "--enable-gegl", + }), + ('mypaint-brushes', '1.3.1', { + 'source_urls': ['https://github.com/mypaint/mypaint-brushes/releases/download/v%(version)s/'], + 'checksums': ['fef66ffc241b7c5cd29e9c518e933c739618cb51c4ed4d745bf648a1afc3fe70'], + }), +] + +sanity_check_paths = { + 'files': ['lib/libmypaint.%s' % SHLIB_EXT, 'lib/libmypaint-gegl.%s' % SHLIB_EXT], + 'dirs': ['include/libmypaint', 'include/libmypaint-gegl', 'lib/pkgconfig', 'share/mypaint-data/1.0/brushes'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6c22d273cfc --- /dev/null +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'librsvg' +version = '2.51.2' + +homepage = 'https://wiki.gnome.org/Projects/LibRsvg' +description = "Librsvg is a library to render SVG files using cairo." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['6b80840ef3e4724624e715398bb4470fa68368943cdbd507e681708bbe32b289'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Rust', '1.52.1'), +] + +dependencies = [ + ('cairo', '1.16.0'), + ('freetype', '2.10.4'), + ('Gdk-Pixbuf', '2.42.6'), + ('HarfBuzz', '2.6.7'), + ('Pango', '1.48.5'), + ('GObject-Introspection', '1.68.0'), +] + +sanity_check_paths = { + 'files': ['bin/rsvg-convert', 'lib/librsvg-%(version_major)s.a', 'lib/librsvg-%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/librsvg-%(version_major)s.0.pc'], + 'dirs': ['include/librsvg-%(version_major)s.0/librsvg', 'share'], +} + +sanity_check_commands = ["rsvg-convert --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c7eef98ae3b --- /dev/null +++ b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'poppler' +version = '21.06.1' + +homepage = 'https://poppler.freedesktop.org' +description = "Poppler is a PDF rendering library" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('freetype', '2.10.4'), + ('fontconfig', '2.13.93'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('NSS', '3.65'), + ('LibTIFF', '4.2.0'), + ('Qt5', '5.15.2'), + #('Boost', '1.76.0'), + ('cairo', '1.16.0'), + ('OpenJPEG', '2.4.0'), + ('zlib', '1.2.11'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['86b09e5a02de40081a3916ef8711c5128eaf4b1fc59d5f87d0ec66f04f595db4'], + 'configopts': "-DENABLE_BOOST=OFF", + }), + ('poppler-data', '0.4.10', { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['6e2fcef66ec8c44625f94292ccf8af9f1d918b410d5aa69c274ce67387967b30'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdfinfo', 'lib/libpoppler.%s' % SHLIB_EXT, 'lib/libpoppler-cpp.%s' % SHLIB_EXT, + 'lib/libpoppler-glib.%s' % SHLIB_EXT, 'lib/libpoppler-qt5.%s' % SHLIB_EXT], + 'dirs': ['include/poppler', 'lib/pkgconfig', 'share'], +} + +sanity_check_commands = ["pdfinfo --help"] + +moduleclass = 'lib' From 38f69e2828cb036bab275aff87b66599184283e2 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 19 Jun 2021 14:43:57 +0100 Subject: [PATCH 0239/9987] adding easyconfigs: Hypre-2.21.0-fosscuda-2020b.eb and patches: Hypre-2.21.0_use-c++14-for-nvcc.patch --- .../h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb | 25 +++++++++++++++++++ .../Hypre-2.21.0_use-c++14-for-nvcc.patch | 13 ++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.21.0_use-c++14-for-nvcc.patch diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..de1ee211cf6 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-fosscuda-2020b.eb @@ -0,0 +1,25 @@ +name = 'Hypre' +version = '2.21.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_use-c++14-for-nvcc.patch'] +checksums = [ + 'e380f914fe7efe22afc44cdf553255410dc8a02a15b2e5ebd279ba88817feaf5', # v2.21.0.tar.gz + 'e7914139e0a8b8804f22d75b135a1457849558bc57800b7845fea0f318b76bff', # Hypre-2.21.0_use-c++14-for-nvcc.patch +] + +start_dir = 'src' + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0_use-c++14-for-nvcc.patch b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0_use-c++14-for-nvcc.patch new file mode 100644 index 00000000000..7c25fd7f5ca --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0_use-c++14-for-nvcc.patch @@ -0,0 +1,13 @@ +Change only the CUDA compliation to use c++14 +Patch by Simon Branford (University of Birmingham) +--- src/configure.orig 2021-06-19 12:44:05.690180000 +0100 ++++ src/configure 2021-06-19 12:44:19.303311554 +0100 +@@ -8886,7 +8886,7 @@ + + if test "$hypre_user_chose_cuflags" = "no" + then +- CUFLAGS="-lineinfo -expt-extended-lambda -dc -std=c++11 --x cu" ++ CUFLAGS="-lineinfo -expt-extended-lambda -dc -std=c++14 --x cu" + if test "$hypre_using_debug" = "yes" + then + CUFLAGS="-g -O0 ${CUFLAGS}" From 065f00c81cfca7937ad4e8509d42dea90c29bf57 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 21 Jun 2021 12:12:49 +0100 Subject: [PATCH 0240/9987] Bump to SeuratObject to 4.0.2 and Seurat to 4.0.3 --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index e0f03a51ff3..7365b86e9c3 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -745,11 +745,11 @@ exts_list = [ ('sctransform', '0.3.2', { 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], }), - ('SeuratObject', '4.0.1', { - 'checksums': ['c90596cc11d623ab95ffb408f085e024402e060ad517d6970e8a9877fa8e623c'], + ('SeuratObject', '4.0.2', { + 'checksums': ['64ee97a221ccaa0bbdc1890da9d3e9cf5b3b9fab037095cfb757db5bbb69cb1c'], }), - ('Seurat', '4.0.2', { - 'checksums': ['cfc2db402f85581585bd477f06a07afcb5fc04121fd1049e83c0cade88f43cac'], + ('Seurat', '4.0.3', { + 'checksums': ['75d98696d0cee22eac5154ac26ef94accde5a5b0a140f3bdd60265322d9edfc9'], }), ('ALL', '1.34.0', { 'checksums': ['6c376f3360bbb0aad4b5aad9655cb95d2f9d33a1abd2ba4533bee803988d8b63'], From d7692884bd16e6e7fa21751b8279894c6e2fc87a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Jun 2021 18:22:08 +0200 Subject: [PATCH 0241/9987] fix draft stuff --- .../molecularGSM-20190826-intel-2020b.eb | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb index e7ef463af93..ce073ff0933 100644 --- a/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb +++ b/easybuild/easyconfigs/m/molecularGSM/molecularGSM-20190826-intel-2020b.eb @@ -38,22 +38,19 @@ checksums = [ builddependencies = [('CMake', '3.18.4')] -# parallel = 1 - configopts = [ - # '', # default is MOPAC - # '-DGSM_ENABLE_QCHEM=1', - # '-DGSM_ENABLE_QCHEM_SF=1', - # '-DGSM_ENABLE_ORCA=1', + '', # default is MOPAC + '-DGSM_ENABLE_QCHEM=1', + '-DGSM_ENABLE_QCHEM_SF=1', + '-DGSM_ENABLE_ORCA=1', '-DGSM_ENABLE_GAUSSIAN=1', - # '-DGSM_ENABLE_MOLPRO=1', - # '-DGSM_ENABLE_ASE=1', + '-DGSM_ENABLE_MOLPRO=1', + '-DGSM_ENABLE_ASE=1', ] install_cmd = 'mkdir -p %(installdir)s/bin && cp -a GSM/*.exe %(installdir)s/bin/' -# _bins = ['ase', 'gaussian', 'molpro', 'mopac', 'orca', 'qchem', 'qchem_sf'] -_bins = ['gaussian'] +_bins = ['ase', 'gaussian', 'molpro', 'mopac', 'orca', 'qchem', 'qchem_sf'] sanity_check_paths = { 'files': ['bin/gsm.%s.exe' % x for x in _bins], From 1175731bbd16dc068140955662bddbe5ebda1155 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 21 Jun 2021 18:31:29 +0200 Subject: [PATCH 0242/9987] adding easyconfigs: PETSc-3.14.4-intel-2020b.eb --- .../p/PETSc/PETSc-3.14.4-intel-2020b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-intel-2020b.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-intel-2020b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-intel-2020b.eb new file mode 100644 index 00000000000..5e792a3e974 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.14.4-intel-2020b.eb @@ -0,0 +1,47 @@ +name = 'PETSc' +version = '3.14.4' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] +checksums = [ + '2fb431434b91e054cc3a176f7cb008951088243b5dcb3efc8eec8ce589a2658e', # petsc-3.14.4.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Boost', '1.74.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('MUMPS', '5.3.5', '-metis'), + ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('Hypre', '2.20.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' From 43839a0862e75a5c96a2dadace52ac2ffcbe8d9c Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Tue, 22 Jun 2021 12:06:40 +0200 Subject: [PATCH 0243/9987] adding easyconfigs: HDF-EOS-2.20-GCCcore-10.2.0.eb, HDF-EOS-2.20-GCCcore-10.2.0.eb, h4toh5-2.2.3-gompi-2020b.eb --- .../h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ .../h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb | 29 ++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb diff --git a/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6f42eeb5aaa --- /dev/null +++ b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'HDF-EOS' +version = '2.20' + +homepage = 'https://hdfeos.org/' +description = """HDF-EOS libraries are software libraries built on HDF libraries. + It supports three data structures for remote sensing data: Grid, Point and Swath.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos/latest_release/', + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos/previous_releases/', +] + +sources = ['%(name)s%(version)sv1.00.tar.Z'] + +checksums = ['cb0f900d2732ab01e51284d6c9e90d0e852d61bba9bce3b43af0430ab5414903'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('HDF', '4.2.15'), + ('Szip', '2.1.1'), +] + +preconfigopts = 'export CC="$EBROOTHDF/bin/h4cc -Df2cFortran" && ' + +configopts = "--with-szlib=$EBROOTSZIP --enable-install-include" + +sanity_check_paths = { + 'files': ['include/HdfEosDef.h', 'include/HDFEOSVersion.h', 'lib/libGctp.a', 'lib/libhdfeos.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb new file mode 100644 index 00000000000..8e8e8c7f705 --- /dev/null +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.3-gompi-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'h4toh5' +version = '2.2.3' + +homepage = 'http://www.hdfgroup.org/h4toh5/' +description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, + as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/tools/%s/src' % name] +sources = ['h4h5tools-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['ba167d9e5ec1f9014a95e3f5d0621f814caa6e83508e235ce60cfd315e3a9d3f'] + +dependencies = [ + ('HDF', '4.2.15'), + ('HDF5', '1.10.7'), + ('HDF-EOS', '2.20'), +] + +configopts = "CC=$EBROOTHDF/bin/h4cc --with-hdf5=$EBROOTHDF5 --with-hdfeos2=$EBROOTHDFMINEOS " + +sanity_check_paths = { + 'files': ['bin/h4toh5', 'bin/h5toh4', 'include/h4toh5.h', 'lib/libh4toh5.a'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'data' From 5dda442d5a09686313bb350cbd7b5daf34a69d4b Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Tue, 22 Jun 2021 12:18:51 +0200 Subject: [PATCH 0244/9987] added HDF-EOS5-1.16-gompi-2020b.eb --- .../h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb diff --git a/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb new file mode 100644 index 00000000000..20f1019fff2 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'HDF-EOS5' +version = '1.16' + +homepage = 'https://hdfeos.org/' +description = """HDF-EOS libraries are software libraries built on HDF libraries. + It supports three data structures for remote sensing data: Grid, Point and Swath.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos5/latest_release/', + 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos5/previous_releases/', +] + +sources = ['%(name)s.%(version)s.tar.Z'] + +checksums = ['7054de24b90b6d9533329ef8dc89912c5227c83fb447792103279364e13dd452'] + +dependencies = [ + ('HDF5', '1.10.7'), + ('Szip', '2.1.1'), +] + +preconfigopts = 'export CC="$EBROOTHDF5/bin/h5pcc -Df2cFortran" && ' + +configopts = "--with-szlib=$EBROOTSZIP --enable-install-include" + +sanity_check_paths = { + 'files': ['include/HE5_HdfEosDef.h', 'include/HE5_GctpFunc.h', 'lib/libGctp.a', 'lib/libhe5_hdfeos.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' From c0ec90b056b4ccf22a334423ec90bd831af6ee15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Jun 2021 17:03:46 +0200 Subject: [PATCH 0245/9987] use correct HarfBuzz version as dependency for GIMP --- easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb | 2 +- .../easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb index 121f12f483d..6948840be8f 100644 --- a/easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('GEGL', '0.4.30'), ('ATK', '2.36.0'), ('Pango', '1.48.5'), - ('HarfBuzz', '2.6.7'), + ('HarfBuzz', '2.8.1'), ('LibTIFF', '4.2.0'), ('libjpeg-turbo', '2.0.6'), ('libmypaint', '1.6.1'), diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb index 6c22d273cfc..eb5dff78218 100644 --- a/easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('cairo', '1.16.0'), ('freetype', '2.10.4'), ('Gdk-Pixbuf', '2.42.6'), - ('HarfBuzz', '2.6.7'), + ('HarfBuzz', '2.8.1'), ('Pango', '1.48.5'), ('GObject-Introspection', '1.68.0'), ] From 70c84c0d3d4dd58a2c47853ff5453c152387ebdd Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 22 Jun 2021 18:38:33 +0100 Subject: [PATCH 0246/9987] adding easyconfigs: PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb, imageio-2.9.0-fosscuda-2020b.eb --- .../i/imageio/imageio-2.9.0-fosscuda-2020b.eb | 26 ++++++++++ ...ch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb | 51 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..a67dbeea4c2 --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.9.0' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb new file mode 100644 index 00000000000..380a99eee47 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb @@ -0,0 +1,51 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'PyTorch3D' +version = '0.4.0' +local_pytorch_version = '1.8.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = "https://pytorch3d.org/" +description = """PyTorch3D is FAIR's library of reusable components for deep learning with 3D data.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('tqdm', '4.60.0'), + ('PyTorch', local_pytorch_version), + ('imageio', '2.9.0'), + ('IPython', '7.18.1'), + ('torchvision', '0.9.1', versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('portalocker', '2.3.0', { + 'checksums': ['4e913d807aa6598c320e8a50c50e2ee0602bc45240b485e3f8bc06f13060084c'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('yacs', '0.1.8', { + 'checksums': ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'], + }), + ('iopath', '0.1.8', { + 'source_tmpl': '%(namelower)s-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['e11029c30ee77616b3efd82888aa80941d12afcc5940c2ef57e04a8e93a10f9f'], + }), + ('fvcore', '0.1.5.post20210617', { + 'checksums': ['1f1fb91b82166f85ed0f7da8906e87688de9e1b4879b478dc3969d93d24f0379'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/facebookresearch/%(namelower)s/archive'], + 'checksums': ['6f33c45c8b698b068ff267287ad490dc2f8f48ad2f486175438b0426575e391a'], + }), +] + +moduleclass = 'tools' From 6002d30c4613f4f0262ccc909e761a38cd6bb54e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 23 Jun 2021 13:01:18 +0100 Subject: [PATCH 0247/9987] use the correct tqdm version --- .../p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb index 380a99eee47..9be26b1a985 100644 --- a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ('PyTorch', local_pytorch_version), ('imageio', '2.9.0'), ('IPython', '7.18.1'), From 8ac653864e0789ed23e82d2f9cb18a8c2be49049 Mon Sep 17 00:00:00 2001 From: Diego Lasa Date: Wed, 23 Jun 2021 15:26:49 +0200 Subject: [PATCH 0248/9987] adding easyconfigs: PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb --- ...CMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..3fb0888f0eb --- /dev/null +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'PCMSolver' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pcmsolver.readthedocs.org' +description = """An API for the Polarizable Continuum Model.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +# we have to disable use of -march=native to ensure a correct build on recent Intel systems +# see also https://github.com/PCMSolver/pcmsolver/issues/159 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d1ef6bdc268a2e719b36c85125c3543df7a26e1a738daf4483f4ded0c76f5b60'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Eigen', '3.3.8', '', ('GCCcore', '10.2.0')), +] + +dependencies = [ + ('Python', '3.8.6'), + ('zlib', '1.2.11'), + ('Boost', '1.74.0'), +] + +configopts = '-DEIGEN3_ROOT=$EBROOTEIGEN ' + +# The spherical test fails regardless of how it is compiled. +# Instead of patching the tests to skip it just don't run the tests for now. +# runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/run_pcm', 'lib/libpcm.a', 'lib/libpcm.%s' % SHLIB_EXT], + 'dirs': ['include/PCMSolver'] +} + +moduleclass = 'chem' From 5443b568485ede9a67a7787f26af43c3e074ce62 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 23 Jun 2021 15:37:39 +0200 Subject: [PATCH 0249/9987] functional crispr-dav --- .../a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb | 48 +++ .../crispr-dav/crispr-dav-2.3.4-foss-2020b.eb | 27 +- ...av-2.3.4-foss2020b_remove_hardcoding.patch | 281 ++++++++---------- .../f/FLASH/FLASH-2.2.00-foss-2020b.eb | 28 ++ .../PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb | 99 ++++++ 5 files changed, 319 insertions(+), 164 deletions(-) create mode 100644 easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb new file mode 100644 index 00000000000..734e544fc9f --- /dev/null +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'ABRA2' +version = '2.23' + +homepage = 'https://github.com/mozack/abra2' +description = "Assembly Based ReAligner" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/mozack/abra2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ABRA2-2.22_fix-Makefile.patch'] +checksums = [ + '3993f66a493070ee49df2865b6786a45a0cf6c379bae83e94b8339abbe673289', # v2.23.tar.gz + '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch +] + +builddependencies = [('Maven', '3.6.3', '', True)] + +dependencies = [ + ('Java', '11', '', True), + ('BWA', '0.7.17'), +] + +parallel = 1 + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' +buildopts += '&& make standalone CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +files_to_copy = [ + (['abra'], 'bin'), + (['target/libAbra.%s' % SHLIB_EXT], 'lib'), + 'target/abra2-%(version)s-jar-with-dependencies.jar', +] + +postinstallcmds = ["cd %(installdir)s && mv abra2-%(version)s-jar-with-dependencies.jar abra2-%(version)s.jar"] + +sanity_check_paths = { + 'files': ['abra2-%(version)s.jar', 'bin/abra', 'lib/libAbra.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextravars = { + "LC_ALL": "en_US.UTF-8", +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb index 086d38d4f44..8adecc04755 100644 --- a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb @@ -1,4 +1,4 @@ -easyblock = 'Binary' +easyblock = 'EB_crisprdav' name = 'crispr-dav' version = '2.3.4' @@ -11,11 +11,15 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/pinetree1/crispr-dav/archive/'] sources = ['v%(version)s.tar.gz'] +patches = ['crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch'] +checksums = [ + '49975cd48bdbf31fe5a9e2aaa3f5ed85d3cc6f65a422ee3aa8daed890159d2ae', # v2.3.4.tar.gz + # crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch + 'a06414a1cf00be359cea46a36133fc312f948f50c2e4bc9043d2e83f3a011e97', +] extract_sources = True -patches = ['crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch'] - dependencies = [ ('R', '4.0.3'), ('Perl', '5.32.0'), @@ -24,11 +28,28 @@ dependencies = [ ('Excel-Writer-XLSX', '1.09'), ('naturalsort', '0.1.3'), ('pysamstats', '1.1.2'), + ('ABRA2', '2.23'), + ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), + ('SAMtools', '1.12'), + ('BEDTools', '2.30.0'), + ('FLASH', '2.2.00'), ] +postinstallcmds = ' mkdir bin && ln -s crispr.pl bin/crispr.pl && chmod +x bin/crispr.pl ' + +modextrapaths = {'PATH': ['bin/']} + sanity_check_paths = { 'files': [], 'dirs': ['Modules', 'Examples', 'Rscripts'], } +sanity_check_commands = [("""crispr.pl --conf $EBROOTCRISPRMINDAV/Examples/example1/conf.txt \ + --region $EBROOTCRISPRMINDAV/Examples/example1/amplicon.bed \ + --crispr $EBROOTCRISPRMINDAV/Examples/example1/site.bed \ + --sitemap $EBROOTCRISPRMINDAV/Examples/example1/sample.site \ + --fastqmap $EBROOTCRISPRMINDAV/Examples/example1/fastq.list \ + --genome genomex 2>&1 | grep 'Generated HTML report for GENEX_CR1'""", ''), + ("crispr.pl --help 2>&1 | grep 'Usage: '", '')] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch index 6130b838bdd..5fd3b89e92c 100644 --- a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch +++ b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch @@ -1,169 +1,128 @@ -diff -ruN crispr-dav-2.3.4_orig/conf.txt crispr-dav-2.3.4/conf.txt ---- crispr-dav-2.3.4_orig/conf.txt 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/conf.txt 2021-06-15 15:42:22.658826437 +0200 -@@ -9,40 +9,40 @@ - ## Absolute path must be used for genome files when a samplesheet is used to prepare run.sh. - - [genomex] --ref_fasta = /bfx/app/crispr-dav/Examples/example1/genome/genomex.fa --bwa_idx = /bfx/app/crispr-dav/Examples/example1/genome/genomex.fa --refGene = /bfx/app/crispr-dav/Examples/example1/genome/refgenex.txt -+# ref_fasta = /bfx/app/crispr-dav/Examples/example1/genome/genomex.fa -+# bwa_idx = /bfx/app/crispr-dav/Examples/example1/genome/genomex.fa -+# refGene = /bfx/app/crispr-dav/Examples/example1/genome/refgenex.txt - - [hg38] --ref_fasta = /bfx/genome/hg38/hg38.fa --bwa_idx = /bfx/genome/hg38/hg38.fa --refGene = /bfx/genome/hg38/hg38_UCSCrefGene.txt -+# ref_fasta = /bfx/genome/hg38/hg38.fa -+# bwa_idx = /bfx/genome/hg38/hg38.fa -+# refGene = /bfx/genome/hg38/hg38_UCSCrefGene.txt - - [hg19] --ref_fasta = /bfx/genome/hg19/hg19.fa --bwa_idx = /bfx/genome/hg19/hg19.fa --refGene = /bfx/genome/hg19/UCSCrefGene.txt -+# ref_fasta = /bfx/genome/hg19/hg19.fa -+# bwa_idx = /bfx/genome/hg19/hg19.fa -+# refGene = /bfx/genome/hg19/UCSCrefGene.txt - - [mm10] --ref_fasta = /bfx/genome/mm10/mm10.fa --bwa_idx = /bfx/genome/mm10/mm10.fa --refGene = /bfx/genome/mm10/mm10_UCSCrefGene.txt -+# ref_fasta = /bfx/genome/mm10/mm10.fa -+# bwa_idx = /bfx/genome/mm10/mm10.fa -+# refGene = /bfx/genome/mm10/mm10_UCSCrefGene.txt - - [rn6] --ref_fasta = /bfx/genome/rn6/rn6.fa --bwa_idx = /bfx/genome/rn6/rn6.fa --refGene = /bfx/genome/rn6/rn6_UCSCrefGene.txt -+# ref_fasta = /bfx/genome/rn6/rn6.fa -+# bwa_idx = /bfx/genome/rn6/rn6.fa -+# refGene = /bfx/genome/rn6/rn6_UCSCrefGene.txt - - [canFam3] --ref_fasta = /bfx/genome/canFam3/canFam3.fa --bwa_idx = /bfx/genome/canFam3/canFam3.fa --refGene = /bfx/genome/canFam3/canFam3_UCSCrefGene.txt -+# ref_fasta = /bfx/genome/canFam3/canFam3.fa -+# bwa_idx = /bfx/genome/canFam3/canFam3.fa -+# refGene = /bfx/genome/canFam3/canFam3_UCSCrefGene.txt - - - [criGri1] --ref_fasta = /bfx/genome/criGri1/criGri1.fa --bwa_idx = /bfx/genome/criGri1/criGri1.fa --refGene = /bfx/genome/criGri1/criGri1_UCSCrefGene.txt -+# ref_fasta = /bfx/genome/criGri1/criGri1.fa -+# bwa_idx = /bfx/genome/criGri1/criGri1.fa -+vrefGene = /bfx/genome/criGri1/criGri1_UCSCrefGene.txt - - ## Required tools - -@@ -52,30 +52,30 @@ - # For others, if path is not provided, it must be accessible - # in your environment - --abra = /bfx/app/bin/abra-0.97-SNAPSHOT-jar-with-dependencies.jar -+# abra = /bfx/app/bin/abra-0.97-SNAPSHOT-jar-with-dependencies.jar - - # Path to prinseq-lite.pl. Make sure prinseq path is executable. --prinseq = /bfx/app/bin/prinseq-lite.pl -+# prinseq = /bfx/app/bin/prinseq-lite.pl - - # bwa (e.g. 0.7.15) must support bwa mem -M, and be searchable in environment variable PATH - - # samtools --samtools = /bfx/app/bin/samtools -+# samtools = /bfx/app/bin/samtools - - # Path of flash. By default use flash in PATH. --flash = /bfx/app/bin/flash2 -+# flash = /bfx/app/bin/flash2 - - # bedtools (e.g. v2.25) must support: bedtools intersect -F --bedtools = /bfx/app/bin/bedtools -+# bedtools = /bfx/app/bin/bedtools - - # java must be 1.7 or later --java = /usr/bin/java -+# java = /usr/bin/java - - # pysamstats --pysamstats = /bfx/app/bin/pysamstats -+# pysamstats = /bfx/app/bin/pysamstats - - # R must have ggplot2, reshape2, and naturalsort packages --rscript = /bfx/app/bin/Rscript -+# rscript = /bfx/app/bin/Rscript - - ## Filtering parameters - -diff -ruN crispr-dav-2.3.4_orig/Examples/example1/conf.txt crispr-dav-2.3.4/Examples/example1/conf.txt ---- crispr-dav-2.3.4_orig/Examples/example1/conf.txt 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Examples/example1/conf.txt 2021-06-15 15:31:29.165679076 +0200 -@@ -21,30 +21,30 @@ - # For others, if path is not provided, it must be accessible - # in your environment - --abra = /bfx/app/bin/abra-0.97-SNAPSHOT-jar-with-dependencies.jar -+# abra = /bfx/app/bin/abra-0.97-SNAPSHOT-jar-with-dependencies.jar - - # Path to prinseq-lite.pl. Make sure prinseq path is executable. --prinseq = /bfx/app/bin/prinseq-lite.pl -+# prinseq = /bfx/app/bin/prinseq-lite.pl - - # bwa (e.g. 0.7.15) must support bwa mem -M, and be searchable in environment variable PATH - - # samtools --samtools = /bfx/app/bin/samtools -+# samtools = /bfx/app/bin/samtools - - # Path of flash. By default use flash in PATH. --flash = /bfx/app/bin/flash2 -+# flash = /bfx/app/bin/flash2 - - # bedtools (e.g. v2.25) must support: bedtools intersect -F --bedtools = /bfx/app/bin/bedtools -+# bedtools = /bfx/app/bin/bedtools - - # java must be 1.7 or later --java = /usr/bin/java -+# java = /usr/bin/java - - # pysamstats --pysamstats = /bfx/app/bin/pysamstats -+# pysamstats = /bfx/app/bin/pysamstats - - # R must have ggplot2, reshape2, and naturalsort packages --rscript = /bfx/app/bin/Rscript -+# rscript = /bfx/app/bin/Rscript - - ## Filtering parameters - +# changing example command to contain absolute paths + tabs escaping + changing plotting type to cairo diff -ruN crispr-dav-2.3.4_orig/Examples/example1/run.sh crispr-dav-2.3.4/Examples/example1/run.sh --- crispr-dav-2.3.4_orig/Examples/example1/run.sh 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Examples/example1/run.sh 2021-06-15 15:36:58.854366160 +0200 ++++ crispr-dav-2.3.4/Examples/example1/run.sh 2021-06-22 12:57:41.700453098 +0200 @@ -4,6 +4,7 @@ ## If there is problem loading Perl modules., set PERL5LIB accordingly. #export PERL5LIB=$HOME/perlmod/lib/perl5:$PERL5LIB -../../crispr.pl --conf conf.txt --region amplicon.bed --crispr site.bed \ +- --sitemap sample.site --fastqmap fastq.list --genome genomex + -+$EBROOTCRISPRMINDAV/crispr.pl --conf conf.txt --region amplicon.bed --crispr site.bed \ - --sitemap sample.site --fastqmap fastq.list --genome genomex - -diff -ruN crispr-dav-2.3.4_orig/Examples/example2/run.sh crispr-dav-2.3.4/Examples/example2/run.sh ---- crispr-dav-2.3.4_orig/Examples/example2/run.sh 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Examples/example2/run.sh 2021-06-15 15:29:03.089257825 +0200 -@@ -5,6 +5,6 @@ - ## If there is problem loading Perl modules., set PERL5LIB accordingly. - #export PERL5LIB=$HOME/perlmod/lib/perl5:$PERL5LIB - --../../crispr.pl --conf conf.txt --amp_fasta amp.fa --crispr site.bed \ -+$EBROOTCRISPRMINDAV/Examples/example2/crispr.pl --conf conf.txt --amp_fasta amp.fa --crispr site.bed \ - --sitemap sample.site --fastqmap fastq.list --codon_start 1 - ++$EBROOTCRISPRMINDAV/crispr.pl --conf $EBROOTCRISPRMINDAV/Examples/example1/conf.txt --region $EBROOTCRISPRMINDAV/Examples/example1/amplicon.bed --crispr $EBROOTCRISPRMINDAV/Examples/example1/site.bed \ ++ --sitemap $EBROOTCRISPRMINDAV/Examples/example1/sample.site --fastqmap $EBROOTCRISPRMINDAV/Examples/example1/fastq.list --genome genomex --verbose 1 + +diff -ruN crispr-dav-2.3.4_orig/Modules/NGS.pm crispr-dav-2.3.4/Modules/NGS.pm +--- crispr-dav-2.3.4_orig/Modules/NGS.pm 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Modules/NGS.pm 2021-06-21 17:37:39.381993860 +0200 +@@ -296,7 +296,7 @@ + my $cmd = "$self->{bwa} mem"; + $cmd .= " $h{param}" if $h{param}; + if ( $h{id} && $h{sm} ) { +- $cmd .= " -R \'\@RG\tID:$h{id}\tSM:$h{sm}\tPL:$h{pl}\'"; ++ $cmd .= " -R \'\@RG\\tID:$h{id}\\tSM:$h{sm}\\tPL:$h{pl}\'"; + } + $cmd .= " $h{idxbase} $h{read1_inf}"; + $cmd .= " $h{read2_inf}" if -f $h{read2_inf}; +@@ -558,7 +558,7 @@ + # file is already indexed. + my $cmd = "rm -rf $workdir && mkdir -p $workdir" . + " && $self->{java} -Djava.io.tmpdir=$tmpdir -jar $h{abra} --threads 2" . +- " --ref $h{ref_fasta} --targets $h{target_bed} --working $workdir" . ++ " --ref $h{ref_fasta} --targets $h{target_bed} --tmpdir $workdir" . + " --in $h{bam_inf} --out $h{bam_outf}"; + + if ($h{single}) { +diff -ruN crispr-dav-2.3.4_orig/Rscripts/allele.R crispr-dav-2.3.4/Rscripts/allele.R +--- crispr-dav-2.3.4_orig/Rscripts/allele.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/allele.R 2021-06-22 13:13:45.868418215 +0200 +@@ -114,7 +114,7 @@ + } else { + h<-400 + w<- ifelse(n>40, 13*n, h*1.25) +- png(filename=outfile, height=h, width=w) ++ png(filename=outfile, type='cairo', height=h, width=w) + } + + on.exit(dev.off()) +diff -ruN crispr-dav-2.3.4_orig/Rscripts/amplicon.R crispr-dav-2.3.4/Rscripts/amplicon.R +--- crispr-dav-2.3.4_orig/Rscripts/amplicon.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/amplicon.R 2021-06-22 13:13:45.868418215 +0200 +@@ -111,7 +111,7 @@ + if ( high_res ) { + tiff(filename=outfile, width=5, height=4, units='in', res=1200) + } else { +- png(filename=outfile, width=500, height=400) ++ png(filename=outfile, type='cairo', width=500, height=400) + } + on.exit(dev.off()) + print(p) +diff -ruN crispr-dav-2.3.4_orig/Rscripts/hdr.R crispr-dav-2.3.4/Rscripts/hdr.R +--- crispr-dav-2.3.4_orig/Rscripts/hdr.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/hdr.R 2021-06-22 13:13:45.868418215 +0200 +@@ -102,7 +102,7 @@ + h<-400 + barspace=60 + w<- ifelse( n*barspace10, 50*n, h) +- png(filename=imgfile, height=h, width=w) ++ png(filename=imgfile, type='cairo', height=h, width=w) + } + + on.exit(dev.off()) +diff -ruN crispr-dav-2.3.4_orig/Rscripts/read_chr.R crispr-dav-2.3.4/Rscripts/read_chr.R +--- crispr-dav-2.3.4_orig/Rscripts/read_chr.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/read_chr.R 2021-06-22 13:13:45.868418215 +0200 +@@ -72,7 +72,7 @@ + w<-ifelse(n>5, 100*n, 550) + max_w=1000 + w <- ifelse(w>max_w, max_w, w) +- png(filename=outfile, height=h, width=w) ++ png(filename=outfile, type='cairo', height=h, width=w) + } + + print(p) +diff -ruN crispr-dav-2.3.4_orig/Rscripts/read_stats.R crispr-dav-2.3.4/Rscripts/read_stats.R +--- crispr-dav-2.3.4_orig/Rscripts/read_stats.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/read_stats.R 2021-06-22 13:13:45.868418215 +0200 +@@ -69,7 +69,7 @@ + } else { + h<-400 + w<- ifelse(n>10, 50*n, h) +- png(filename=outfile, height=h, width=w) ++ png(filename=outfile, type='cairo', height=h, width=w) + } + + p <- ggplot(dat.m, aes(x=Sample, y=value, fill=variable)) + +diff -ruN crispr-dav-2.3.4_orig/Rscripts/snp.R crispr-dav-2.3.4/Rscripts/snp.R +--- crispr-dav-2.3.4_orig/Rscripts/snp.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/snp.R 2021-06-22 13:13:45.868418215 +0200 +@@ -76,7 +76,7 @@ + if ( high_res ) { + tiff(filename=outfile, width=5, height=4, units='in', res=1200) + } else { +- png(filename=outfile, width=500, height=400) ++ png(filename=outfile, type='cairo', width=500, height=400) + } + print(p) + invisible(dev.off()) +@@ -182,7 +182,7 @@ + wt <- 600 + } + ht <- 400 +- png(filename=outfile, width=wt, height=ht) ++ png(filename=outfile, type='cairo', width=wt, height=ht) + } + + print(p) diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb new file mode 100644 index 00000000000..da47c15d06e --- /dev/null +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'FLASH' +version = '2.2.00' + +homepage = 'https://ccb.jhu.edu/software/FLASH/' +description = """FLASH (Fast Length Adjustment of SHort reads) is a very fast +and accurate software tool to merge paired-end reads from next-generation +sequencing experiments. FLASH is designed to merge pairs of reads when the +original DNA fragments are shorter than twice the length of reads. The +resulting longer reads can significantly improve genome assemblies. They can +also improve transcriptome assembly when FLASH is used to merge RNA-seq data. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/dstreett/FLASH2/archive/'] +sources = ['%(version)s.zip'] +checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] + +files_to_copy = [(['flash2'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/flash2'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb new file mode 100644 index 00000000000..c7576441aed --- /dev/null +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb @@ -0,0 +1,99 @@ +# author: Denis Kristak + +easyblock = 'Tarball' + +name = 'PRINSEQ' +version = '0.20.4' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://prinseq.sourceforge.net' +description = """A bioinformatics tool to PRe-process and show INformation of SEQuence data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/'] +sources = ['%(namelower)s-lite-%(version)s.tar.gz'] +checksums = ['9b5e0dce3b7f02f09e1cc7e8a2dd77c0b133e5e35529d570ee901f53ebfeb56f'] + +dependencies = [ + ('Perl', '5.32.0'), + ('cairo', '1.16.0'), +] + +# these are the perl libraries dependencies +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::Depends', '0.8001', { + 'source_tmpl': 'ExtUtils-Depends-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['673c4387e7896c1a216099c1fbb3faaa7763d7f5f95a1a56a60a2a2906c131c5'], + }), + ('ExtUtils::PkgConfig', '1.16', { + 'source_tmpl': 'ExtUtils-PkgConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e'], + }), + ('Pod::Usage', '2.0', { + 'source_tmpl': 'Pod-Usage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + 'checksums': ['530943a9ac3ba00404d7be8ee8572f30f6db9de123cd725af3647333a87d4fea'], + }), + ('Cairo', '1.109', { + 'source_tmpl': 'Cairo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['8219736e401c2311da5f515775de43fd87e6384b504da36a192f2b217643077f'], + }), + ('Statistics::PCA', '0.0.1', { + 'source_tmpl': 'Statistics-PCA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSTH/'], + 'checksums': ['f8adb10b00232123d103a5b49161ad46370f47fe0f752e5462a4dc15f9d46bc4'], + }), + ('MIME::Base64', '3.15', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + 'checksums': ['7f863566a6a9cb93eda93beadb77d9aa04b9304d769cea3bb921b9a91b3a1eb9'], + }), + ('Math::Cephes::Matrix', '0.5305', { + 'source_tmpl': 'Math-Cephes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['561a800a4822e748d2befc366baa4b21e879a40cc00c22293c7b8736caeb83a1'], + }), + ('Math::MatrixReal', '2.13', { + 'source_tmpl': 'Math-MatrixReal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LETO/'], + 'checksums': ['4f9fa1a46dd34d2225de461d9a4ed86932cdd821c121fa501a15a6d4302fb4b2'], + }), + ('Text::SimpleTable', '2.07', { + 'source_tmpl': 'Text-SimpleTable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRAMBERG/'], + 'checksums': ['256d3f38764e96333158b14ab18257b92f3155c60d658cafb80389f72f4619ed'], + }), + ('Contextual::Return', '0.2.1', { + 'source_tmpl': 'Contextual-Return-v%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'], + 'checksums': ['17a1ed1043a2abe123920894d6023709e834de66ef766be86e4cfbb96b1dd16c'], + }), +] + +# this is the script which relies in many extra Perl libraries so we verify it's working fine +sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl'] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +postinstallcmds = [ + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", + "chmod +x %(installdir)s/*.pl", +] + +sanity_check_paths = { + 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], + 'dirs': [] +} + + +moduleclass = 'bio' From b3ea244575262d6ab1c7ed22d454af6895e40de3 Mon Sep 17 00:00:00 2001 From: manifest Date: Thu, 24 Jun 2021 15:39:50 +0930 Subject: [PATCH 0250/9987] URL fix --- .../b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb index bf3d7ad875e..aedfd4b2c42 100644 --- a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.10-foss-2020a-Python-3.8.2.eb @@ -25,8 +25,6 @@ The BIOM file format (canonically pronounced biome) is designed to be toolchain = {'name': 'foss', 'version': '2020a'} toolchainopts = {'usempi': True} -source_urls = ['https://files.pythonhosted.org/packages/2b/8f/\ - ef865d43a06dd3d1b09808fbd129074e64127fa8db0b93b5e0cf1d1a50de'] sources = [SOURCELOWER_TAR_GZ] checksums = ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'] From 27165fa55ad4474fd28f977ec20c73538ba17b90 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 25 Jun 2021 17:35:55 +0950 Subject: [PATCH 0251/9987] easyblock change --- .../r/RAPSearch2/RAPSearch2-2.24.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb diff --git a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb new file mode 100644 index 00000000000..679405c3428 --- /dev/null +++ b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb @@ -0,0 +1,38 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU GPLv1 +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'RAPSearch2' +version = '2.24' + +homepage = 'https://omics.informatics.indiana.edu/mg/RAPSearch2' +description = """ +RAPSearch stands for Reduced Alphabet based Protein similarity Search +""" + +toolchain = {'name': 'system', 'version': 'system'} + +source_urls = ['https://sourceforge.net/projects/rapsearch2/files'] +sources = ['%(name)s.24_64bits.tar.gz'] +checksums = ['85db4573f4c768b6c3c73bb44ff2611ba48dc6c8d188feb40f44bf7c55de36ce'] + +skipsteps = ['configure'] +build_cmd = './install' +parallel = 1 + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ('rapsearch', 'prerapsearch')], + 'dirs': [], +} + +moduleclass = 'bio' From 0e144592d4bef142a5866344b79399d2378ae2bf Mon Sep 17 00:00:00 2001 From: manifest Date: Fri, 25 Jun 2021 17:17:06 +0930 Subject: [PATCH 0252/9987] Delete RAPSearch2-2.24-GCC-9.3.0.eb Change to lagacy toolchange for compilation. --- .../r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb deleted file mode 100644 index 80948486498..00000000000 --- a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: GNU GPLv1 -# -# Notes:: -## - -easyblock = 'CmdCp' - -name = 'RAPSearch2' -version = '2.24' - -homepage = 'https://omics.informatics.indiana.edu/mg/RAPSearch2' -description = """ -RAPSearch stands for Reduced Alphabet based Protein similarity Search -""" - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://sourceforge.net/projects/rapsearch2/files'] -sources = ['%(name)s.24_64bits.tar.gz'] -checksums = ['85db4573f4c768b6c3c73bb44ff2611ba48dc6c8d188feb40f44bf7c55de36ce'] - -install_cmd = './install' - -skipsteps = ['configure', 'build'] - -files_to_copy = ['bin'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ('rapsearch', 'prerapsearch')], - 'dirs': [], -} - -moduleclass = 'bio' From f59f3736cffeb56a45f6fdc7fd92beb39cca50ee Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 25 Jun 2021 11:24:38 +0200 Subject: [PATCH 0253/9987] networkx: removes the patch --- .../n/networkx/networkx-2.5.1-foss-2021a.eb | 6 +----- .../networkx-2.5.1_pin_decorator.patch | 19 ------------------- 2 files changed, 1 insertion(+), 24 deletions(-) delete mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.5.1_pin_decorator.patch diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb index 1cb8435b164..dfdec9b4e9c 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb @@ -14,11 +14,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} sources = [SOURCE_TAR_GZ] patches = ['networkx-2.5.1_pin_decorator.patch'] -checksums = [ - '109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a', # networkx-2.5.1.tar.gz - # networkx-2.5.1_pin_decorator.patch - '5399a682ee52cafb601e800711058a9aed2e1a20e60d26c0b428461dd76a2246', -] +checksums = ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'] dependencies = [ ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5.1_pin_decorator.patch b/easybuild/easyconfigs/n/networkx/networkx-2.5.1_pin_decorator.patch deleted file mode 100644 index 2ff8c846283..00000000000 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5.1_pin_decorator.patch +++ /dev/null @@ -1,19 +0,0 @@ -From caffb25cae8c6fa783db1489136ae41bbd17fd23 Mon Sep 17 00:00:00 2001 -From: Ross Barnowski -Date: Tue, 18 May 2021 10:52:23 -0700 -Subject: [PATCH] Pin upper bound on decorator for 2.6 release. - ---- - requirements/default.txt | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/requirements/default.txt b/requirements/default.txt -index 9cdb86317d..5c78e7c125 100644 ---- a/requirements/default.txt -+++ b/requirements/default.txt -@@ -1,4 +1,4 @@ --decorator>=5.0.7 -+decorator>=5.0.7,<6 - numpy>=1.19; platform_python_implementation!='PyPy' and python_version<'3.10' - scipy>=1.5,!=1.6.1; platform_python_implementation!='PyPy' and python_version<'3.10' - matplotlib>=3.3; platform_python_implementation!='PyPy' and python_version<'3.10' From f087cca2f4d5b69e875cb6339ce59036290b6d06 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 25 Jun 2021 13:32:24 +0200 Subject: [PATCH 0254/9987] networkx: removes the patch --- easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb index dfdec9b4e9c..c5f6189ee9d 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb @@ -13,7 +13,6 @@ and study of the structure, dynamics, and functions of complex networks.""" toolchain = {'name': 'foss', 'version': '2021a'} sources = [SOURCE_TAR_GZ] -patches = ['networkx-2.5.1_pin_decorator.patch'] checksums = ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'] dependencies = [ From 2b7ba73e5556602a2bd4a1754d5e79f1a5b3863a Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 25 Jun 2021 17:55:38 +0200 Subject: [PATCH 0255/9987] adding easyconfigs: ASE-3.22.0-foss-2020b.eb, ASE-3.22.0-intel-2020b.eb, GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb, GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb --- .../a/ASE/ASE-3.22.0-foss-2020b.eb | 66 +++++++++++++++++ .../a/ASE/ASE-3.22.0-intel-2020b.eb | 70 +++++++++++++++++++ .../GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb | 49 +++++++++++++ .../GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb | 52 ++++++++++++++ 4 files changed, 237 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb new file mode 100644 index 00000000000..ccc42711101 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.3.3'), + ('spglib-python', '1.16.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '2.0.1', { + 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], + }), + ('Jinja2', '3.0.1', { + 'checksums': ['703f484b47a6af502e743c9122595cc812b0271f661722403114f71a79d0f5a4'], + }), + ('Werkzeug', '2.0.1', { + 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('itsdangerous', '2.0.1', { + 'checksums': ['9e724d68fc22902a1435351f84c3fb8623f303fffcc566a4cb952df8c572cff0'], + }), + ('Flask', '1.1.2', { + 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], + }), + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['e60259c7b50867b1cb817caf938fcc1ed383702413df6d2e1afe7ea07f65acee'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb new file mode 100644 index 00000000000..fa2e15624a3 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.3.3'), + ('spglib-python', '1.16.0'), +] + +use_pip = True +sanity_pip_check = True + +# required because we're building Python packages (MarkupSafe, +# ase-ext) using Intel compilers on top of Python built with GCC. +check_ldshared = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '2.0.1', { + 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], + }), + ('Jinja2', '3.0.1', { + 'checksums': ['703f484b47a6af502e743c9122595cc812b0271f661722403114f71a79d0f5a4'], + }), + ('Werkzeug', '2.0.1', { + 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('itsdangerous', '2.0.1', { + 'checksums': ['9e724d68fc22902a1435351f84c3fb8623f303fffcc566a4cb952df8c572cff0'], + }), + ('Flask', '1.1.2', { + 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], + }), + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['e60259c7b50867b1cb817caf938fcc1ed383702413df6d2e1afe7ea07f65acee'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb new file mode 100644 index 00000000000..f2b603dd335 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb @@ -0,0 +1,49 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '21.6.0' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('libxc', '4.3.4'), + ('libvdwxc', '0.4.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb new file mode 100644 index 00000000000..362e25c7825 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -0,0 +1,52 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '21.6.0' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', +] + +# The intel version is not built with libvdwxc support, as that library is incompatible with MKL. +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('libxc', '4.3.4'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC. +check_ldshared = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' From bd864bb80a42bba1085283c4af05452af8f56aa8 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 25 Jun 2021 18:54:37 +0200 Subject: [PATCH 0256/9987] Style fix: remove superfluous pypi.org source specification. --- easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb | 2 -- easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb index ccc42711101..70498c9207a 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '2.0.1', { 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb index fa2e15624a3..09a4e223837 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb @@ -27,8 +27,6 @@ sanity_pip_check = True # ase-ext) using Intel compilers on top of Python built with GCC. check_ldshared = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('MarkupSafe', '2.0.1', { 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], From 8552d470c7ee4b20b2ddc3e828c4027f309ff088 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sun, 27 Jun 2021 11:07:21 +0200 Subject: [PATCH 0257/9987] networkx: returns the patch :) --- .../n/networkx/networkx-2.5.1-foss-2021a.eb | 6 +++++- .../n/networkx/networkx-2.5.1_decorator.patch | 21 +++++++++++++++++++ 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb index c5f6189ee9d..0dac68fbfbe 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb @@ -13,7 +13,11 @@ and study of the structure, dynamics, and functions of complex networks.""" toolchain = {'name': 'foss', 'version': '2021a'} sources = [SOURCE_TAR_GZ] -checksums = ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'] +patches = ['%(name)s-%(version)s_decorator.patch'] +checksums = [ + '109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a', # + '85001802a7d8fe3244b83ce0e0f8c9066708c8d2b3e20fad023dfe3b06954d1e', # networkx-2.5.1_decorator.patch +] dependencies = [ ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch b/easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch new file mode 100644 index 00000000000..ba828792c79 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch @@ -0,0 +1,21 @@ +diff -Naur networkx-2.5.1.orig/networkx.egg-info/requires.txt networkx-2.5.1/networkx.egg-info/requires.txt +--- networkx-2.5.1.orig/networkx.egg-info/requires.txt 2021-04-04 00:20:57.000000000 +0200 ++++ networkx-2.5.1/networkx.egg-info/requires.txt 2021-06-27 10:48:45.453840000 +0200 +@@ -1,4 +1,4 @@ +-decorator<5,>=4.3 ++decorator>=5.0.7,<6 + + [all] + numpy +diff -Naur networkx-2.5.1.orig/setup.py networkx-2.5.1/setup.py +--- networkx-2.5.1.orig/setup.py 2021-04-04 00:01:13.000000000 +0200 ++++ networkx-2.5.1/setup.py 2021-06-27 11:02:45.537344000 +0200 +@@ -124,7 +124,7 @@ + "networkx.utils": ["tests/*.py"], + } + +-install_requires = ["decorator>=4.3,<5"] ++install_requires = ["decorator>=5.0.7,<6"] + extras_require = { + "all": [ + "numpy", From 12a64c5ebaa92b2a7f261de359eb34d133db5792 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sun, 27 Jun 2021 11:24:14 +0200 Subject: [PATCH 0258/9987] networkx: fixes formatting issues :) --- .../easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb index 0dac68fbfbe..9cd40fabe2b 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb @@ -15,8 +15,9 @@ toolchain = {'name': 'foss', 'version': '2021a'} sources = [SOURCE_TAR_GZ] patches = ['%(name)s-%(version)s_decorator.patch'] checksums = [ - '109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a', # - '85001802a7d8fe3244b83ce0e0f8c9066708c8d2b3e20fad023dfe3b06954d1e', # networkx-2.5.1_decorator.patch + '109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a', # networkx-2.5.1.tar.gz + # networkx-2.5.1_decorator.patch + '85001802a7d8fe3244b83ce0e0f8c9066708c8d2b3e20fad023dfe3b06954d1e', ] dependencies = [ From 767a96e503f0a9497382552865649661af9cfa59 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sun, 27 Jun 2021 17:02:52 +0200 Subject: [PATCH 0259/9987] adding easyconfigs: itac-2021.2.0.eb --- easybuild/easyconfigs/i/itac/itac-2021.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/itac/itac-2021.2.0.eb diff --git a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb new file mode 100644 index 00000000000..b95225dd483 --- /dev/null +++ b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb @@ -0,0 +1,25 @@ +## +# Author: Robert Mijakovic +## +name = 'itac' +version = '2021.2.0' + +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' +description = """The Intel Trace Collector is a low-overhead tracing library that performs + event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application + activities gathered by the Intel Trace Collector through graphical displays. """ + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17686/'] +sources = ['l_itac_oneapi_p_%(version)s.152_offline.sh'] +checksums = ['dca9d1cb2b77c43496009e191916e0d37c2e6606c228e37c11091778d038dd90'] + +dontcreateinstalldir = True + +preferredmpi = 'impi5' + +# license file +# license_file = HOME + '/licenses/intel/license.lic' + +moduleclass = 'tools' From b9d0b33a82bb439e7049a725b84348b740a0138d Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sun, 27 Jun 2021 20:24:50 +0200 Subject: [PATCH 0260/9987] adding easyconfigs: PETSc-3.15.1-foss-2021a.eb --- .../p/PETSc/PETSc-3.15.1-foss-2021a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-foss-2021a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-foss-2021a.eb new file mode 100644 index 00000000000..6515cea646b --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-foss-2021a.eb @@ -0,0 +1,50 @@ +## +# Author: Robert Mijakovic +## +name = 'PETSc' +version = '3.15.1' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] +checksums = [ + 'c0ac6566e69d1d70b431e07e7598e9de95e84891c2452db1367c846b75109deb', # petsc-3.15.1.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch +] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Boost', '1.76.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('MUMPS', '5.4.0', '-metis'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('Hypre', '2.21.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' From b42f57979388b87b24a1f826ce5b0fa0111ef6fb Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sun, 27 Jun 2021 20:34:40 +0200 Subject: [PATCH 0261/9987] adding easyconfigs: OpenFOAM-v2106-foss-2021a.eb --- .../o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb new file mode 100644 index 00000000000..2f640516ac7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb @@ -0,0 +1,45 @@ +## +# Author: Robert Mijakovic +## +name = 'OpenFOAM' +version = 'v2106' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2012-cleanup.patch', 1), + 'OpenFOAM-v1906-wmake-ompi.patch', +] +checksums = [ + 'e765881451d8d15ce33caa28850cdcc4534b8c4590e08ee6011bcafd11216940', # OpenFOAM-v2106.tgz + 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +dependencies = [ + ('libreadline', '8.1'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('CGAL', '5.2.2'), + ('ParaView', '5.9.1', '-mpi'), + ('gnuplot', '5.4.2'), +] + +builddependencies = [ + ('Bison', '3.7.6'), + ('CMake', '3.20.1'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' From 47f6b47ad74c8fea84b2fe771a7bf541f17d9f21 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 28 Jun 2021 12:13:30 +0200 Subject: [PATCH 0262/9987] Depend on the Flask module instead of duplicating it. --- .../a/ASE/ASE-3.22.0-foss-2020b.eb | 23 +++---------------- .../a/ASE/ASE-3.22.0-intel-2020b.eb | 23 +++---------------- 2 files changed, 6 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb index 70498c9207a..87ef103fc63 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-foss-2020b.eb @@ -15,33 +15,16 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('Tkinter', '%(pyver)s'), + ('Flask', '1.1.2'), ('matplotlib', '3.3.3'), - ('spglib-python', '1.16.0'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional ] use_pip = True sanity_pip_check = True exts_list = [ - ('MarkupSafe', '2.0.1', { - 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], - }), - ('Jinja2', '3.0.1', { - 'checksums': ['703f484b47a6af502e743c9122595cc812b0271f661722403114f71a79d0f5a4'], - }), - ('Werkzeug', '2.0.1', { - 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], - }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('itsdangerous', '2.0.1', { - 'checksums': ['9e724d68fc22902a1435351f84c3fb8623f303fffcc566a4cb952df8c572cff0'], - }), - ('Flask', '1.1.2', { - 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], - }), ('pytest-mock', '3.6.1', { 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], }), diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb index 09a4e223837..a31426b7e1f 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb @@ -15,9 +15,10 @@ toolchain = {'name': 'intel', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('Tkinter', '%(pyver)s'), + ('Flask', '1.1.2'), ('matplotlib', '3.3.3'), - ('spglib-python', '1.16.0'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional ] use_pip = True @@ -28,24 +29,6 @@ sanity_pip_check = True check_ldshared = True exts_list = [ - ('MarkupSafe', '2.0.1', { - 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], - }), - ('Jinja2', '3.0.1', { - 'checksums': ['703f484b47a6af502e743c9122595cc812b0271f661722403114f71a79d0f5a4'], - }), - ('Werkzeug', '2.0.1', { - 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], - }), - ('click', '7.1.2', { - 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], - }), - ('itsdangerous', '2.0.1', { - 'checksums': ['9e724d68fc22902a1435351f84c3fb8623f303fffcc566a4cb952df8c572cff0'], - }), - ('Flask', '1.1.2', { - 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], - }), ('pytest-mock', '3.6.1', { 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], }), From d1f81ebe89d99d4b15a56abdd03a3d3f0daef6ff Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 28 Jun 2021 13:47:21 +0200 Subject: [PATCH 0263/9987] adding easyconfigs: ParaView-5.9.1-foss-2021a-mpi.eb --- .../ParaView/ParaView-5.9.1-foss-2021a-mpi.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb new file mode 100644 index 00000000000..ec60fd29f59 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb @@ -0,0 +1,63 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.9.1' +versionsuffix = '-mpi' + +homepage = "https://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +#source_urls = ['https://gitlab.kitware.com/paraview/paraview/-/archive/v%(version)s'] +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] +#sources = ["%(namelower)s-v%(version)s.tar.gz"] +checksums = ['efbcba00ba38c23d0ada1bde7144a8745caa308d9e1f94a4a71d8af63732266f'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('XZ', '5.2.5'), + ('HDF5', '1.10.7'), + ('netCDF', '4.8.0'), + ('libGLU', '9.0.1'), + ('X11', '20210518'), + ('Mesa', '21.1.1'), + ('Qt5', '5.15.2'), + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.2'), + ('Szip', '2.1.1'), +] + +builddependencies = [('CMake', '3.20.1')] + +separate_build_dir = True + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include' +configopts += '-DVTK_OPENGL_HAS_OSMESA=ON ' + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': ['lib64/python%(pyshortver)s/site-packages', 'lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' From 974e09c4ae1fd8f3099f1de08fef96a51ee5b8a1 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 28 Jun 2021 14:02:15 +0200 Subject: [PATCH 0264/9987] flash2 should be accessible via `flash` cmd --- easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb index da47c15d06e..858caac9c7b 100644 --- a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb @@ -20,8 +20,9 @@ checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] files_to_copy = [(['flash2'], 'bin')] +postinstallcmds = ['ln -s %(installdir)s/bin/flash2 %(installdir)s/bin/flash'] sanity_check_paths = { - 'files': ['bin/flash2'], + 'files': ['bin/flash2', 'bin/flash'], 'dirs': [], } From 51b0b2a3500ff56a7455e1c7dbd9992620438de2 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 28 Jun 2021 14:05:36 +0200 Subject: [PATCH 0265/9987] adding easyconfigs: CRISPResso2-2.1.2-foss-2020b.eb --- .../CRISPResso2-2.1.2-foss-2020b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb new file mode 100644 index 00000000000..82b4d8fd290 --- /dev/null +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'CRISPResso2' +version = '2.1.2' + +homepage = 'https://github.com/pinellolab/CRISPResso2/' +description = """CRISPResso2 is a software pipeline designed to enable rapid and +intuitive interpretation of genome editing experiments.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/pinellolab/CRISPResso2/archive/'] +sources = ['v%(version)s.tar.gz'] + +sources = [ + {'source_urls': ['https://github.com/pinellolab/CRISPResso2/archive/'], + 'filename': 'v%(version)s.tar.gz'}, + {'source_urls': ['https://crispresso.pinellolab.partners.org/static/demo/'], + 'filename': 'base_editor.fastq.gz', 'extract_cmd': 'cp %s %(builddir)s'}] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', '-Python-%(pyver)s'), + ('matplotlib', '2.2.5', '-Python-%(pyver)s'), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('FLASH', '2.2.00'), + ('SAMtools', '1.12'), + ('Bowtie2', '2.4.2'), + ('Seaborn', '0.9.1', '-Python-%(pyver)s'), +] +download_dep_fail = True +use_pip = True +options = {'modulename': False} + +local_seq_str = 'GGCCCCAGTGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTAC' +local_seq_str += 'AAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATG' +local_seq_str += 'GGGAGGACATCGATGTCACCTCCAATGACTAGGGTGG' +sanity_check_commands = [('CRISPResso -h'), + ("""CRISPResso --fastq_r1 %%(builddir)s/base_editor.fastq.gz --amplicon_seq %s \ + --guide_seq GAGTCCGAGCAGAAGAAGAA --quantification_window_size 10 \ + --quantification_window_center -10 --base_editor_output""" % local_seq_str)] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} + +moduleclass = 'bio' From a997fcad5436ecce670e68ac03cd8be923695542 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 28 Jun 2021 15:46:14 +0200 Subject: [PATCH 0266/9987] allowing pip check, removing strict dependency requirements --- .../CRISPResso2-2.1.2-foss-2020b.eb | 13 +++++++++--- ...-2.1.2-foss-2020b_remove_strict_deps.patch | 21 +++++++++++++++++++ 2 files changed, 31 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb index 82b4d8fd290..6a6003f6062 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb @@ -1,3 +1,5 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak easyblock = 'PythonPackage' name = 'CRISPResso2' @@ -9,14 +11,18 @@ intuitive interpretation of genome editing experiments.""" toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = ['https://github.com/pinellolab/CRISPResso2/archive/'] -sources = ['v%(version)s.tar.gz'] - sources = [ {'source_urls': ['https://github.com/pinellolab/CRISPResso2/archive/'], 'filename': 'v%(version)s.tar.gz'}, {'source_urls': ['https://crispresso.pinellolab.partners.org/static/demo/'], 'filename': 'base_editor.fastq.gz', 'extract_cmd': 'cp %s %(builddir)s'}] +patches = ['CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch'] +checksums = [ + '29dfaaa65f66225faee4887376ea6b524355332fc6f7ca4d07bb7d63596ef5e6', # v2.1.2.tar.gz + '371aad07a164721188deaa80ca7589f5cd4b871119d90d55a984c6d9c8d31c7a', # base_editor.fastq.gz + # CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch + '4168c02c4e26b08a39b3102bf63170860afe5c2c7e283d0ecc7fd9bb262ef4a3', +] dependencies = [ ('Java', '11', '', True), @@ -32,6 +38,7 @@ dependencies = [ download_dep_fail = True use_pip = True options = {'modulename': False} +sanity_pip_check = True local_seq_str = 'GGCCCCAGTGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTAC' local_seq_str += 'AAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATG' diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch new file mode 100644 index 00000000000..737fe007644 --- /dev/null +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch @@ -0,0 +1,21 @@ +# unimportantly strict dependency version requirements +diff -ruN "CRISPResso2-2.1.2 copy/setup.py" CRISPResso2-2.1.2/setup.py +--- "CRISPResso2-2.1.2 copy/setup.py" 2021-06-28 15:30:43.197061000 +0200 ++++ CRISPResso2-2.1.2/setup.py 2021-06-28 15:36:03.124070000 +0200 +@@ -89,12 +89,12 @@ + 'Programming Language :: Cython', + ], + install_requires=[ +- 'pandas>=0.15,<=0.24', +- 'matplotlib>=1.3.1,<=2.2.3', ++ 'pandas>=0.15', ++ 'matplotlib>=1.3.1', + 'argparse>=1.3,<=1.4', + 'seaborn>0.7.1,<0.10', +- 'jinja2==2.10', +- 'scipy==1.1.0', ++ 'jinja2>=2.10', ++ 'scipy>=1.1.0', + 'numpy>=1.9,<=1.16.6', + 'kiwisolver<1.2', + 'pyparsing<3', From 1542be0105d32496699dd77cfe8253bf86facaf4 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 28 Jun 2021 15:51:57 +0200 Subject: [PATCH 0267/9987] OpenFOAM: dependency --- .../c/CGAL/CGAL-5.2.2-gompi-2021a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-5.2.2-gompi-2021a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.2.2-gompi-2021a.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.2.2-gompi-2021a.eb new file mode 100644 index 00000000000..8d104249daf --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.2.2-gompi-2021a.eb @@ -0,0 +1,38 @@ +name = 'CGAL' +version = '5.2.2' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['80b05049d20dc0e346f33037b6f87f69eb0b4407a3e27ffc10f7c71d45c05f7a'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Eigen', '3.3.9'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.9.5'), + ('Boost', '1.76.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('Mesa', '21.1.1'), + ('libGLU', '9.0.1'), + ('Qt5', '5.15.2'), +] + +configopts = "-DCGAL_HEADER_ONLY=OFF " +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' From 2a3f08f49266ddf3bcff139743e7dbdde8d25213 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 28 Jun 2021 15:56:13 +0200 Subject: [PATCH 0268/9987] ParaView: Fixes comments and generalizes the EB a bit. --- .../p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb index ec60fd29f59..008c13ccf43 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb @@ -14,10 +14,8 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True, 'usempi': True} local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' -#source_urls = ['https://gitlab.kitware.com/paraview/paraview/-/archive/v%(version)s'] source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] -sources = ["ParaView-v%(version)s.tar.gz"] -#sources = ["%(namelower)s-v%(version)s.tar.gz"] +sources = ["%(name)s-v%(version)s.tar.gz"] checksums = ['efbcba00ba38c23d0ada1bde7144a8745caa308d9e1f94a4a71d8af63732266f'] dependencies = [ @@ -52,11 +50,11 @@ configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include' configopts += '-DVTK_OPENGL_HAS_OSMESA=ON ' sanity_check_paths = { - 'files': ['bin/paraview', 'bin/pvpython'], - 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], + 'files': ['bin/%(namelower)s', 'bin/pvpython'], + 'dirs': ['include/%(namelower)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ['python -c "import paraview"'] +sanity_check_commands = ['python -c "import %(namelower)s"'] modextrapaths = {'PYTHONPATH': ['lib64/python%(pyshortver)s/site-packages', 'lib/python%(pyshortver)s/site-packages']} From 7b2a024eb15d9ecf86fb10f4efd1c6dd871fc417 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 28 Jun 2021 16:20:03 +0200 Subject: [PATCH 0269/9987] OpenFOAM: Adds missing dependencies. --- .../c/CGAL/CGAL-5.2.2-gompi-2021a.eb | 3 ++ .../g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb | 49 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.2.2-gompi-2021a.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.2.2-gompi-2021a.eb index 8d104249daf..a3c0f97b487 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-5.2.2-gompi-2021a.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.2.2-gompi-2021a.eb @@ -1,3 +1,6 @@ +## +# Author: Robert Mijakovic +## name = 'CGAL' version = '5.2.2' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..a959fffd999 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb @@ -0,0 +1,49 @@ +## +# Authors:: Fotis Georgatos +# Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.4.2' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['e57c75e1318133951d32a83bcdc4aff17fed28722c4e71f2305cfc2ae1cae7ba'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), + ('Autotools', '20210128'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('cairo', '1.16.0'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('libgd', '2.3.1'), + ('Pango', '1.48.0'), + ('libcerf', '1.15'), + ('X11', '20210518'), + ('Qt5', '5.15.2'), + ('Lua', '5.4.3'), +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' From f9e7578be0bb950af92cc344b744b609fcc579ad Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 28 Jun 2021 16:40:59 +0200 Subject: [PATCH 0270/9987] OpenFOAM: Adds missing dependencies. --- .../g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb | 2 +- .../l/Lua/Lua-5.4.3-GCCcore-10.3.0.eb | 31 ++++++++++++++++ .../l/libcerf/libcerf-1.15-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ 3 files changed, 69 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.4.3-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.15-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb index a959fffd999..671ca91a4a2 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-10.3.0.eb @@ -28,7 +28,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.6'), ('libpng', '1.6.37'), ('libgd', '2.3.1'), - ('Pango', '1.48.0'), + ('Pango', '1.48.5'), ('libcerf', '1.15'), ('X11', '20210518'), ('Qt5', '5.15.2'), diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.4.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.4.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e91223f8c5c --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.4.3-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +## +# Author: Robert Mijakovic +## +name = 'Lua' +version = '5.4.3' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f8612276169e3bfcbcfb8f226195bfc6e466fe13042f1076cbde92b7ec96bbfb'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('libreadline', '8.1'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.15-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.15-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f701c6f094e --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.15-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '1.15' + +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['a5d45475e08d431267fd29d6af987a9dd9b6792578ec3feb466d4d21f2844868'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('Perl', '5.32.1'), # required for pod2html +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From 9aa08062c3df69651dc49f1b6378463cf1366e9c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Jun 2021 22:28:22 +0200 Subject: [PATCH 0271/9987] add missing space in configopts for ParaView 5.9.1 easyconfig --- .../easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb index 008c13ccf43..f5929112fe1 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb @@ -46,7 +46,7 @@ configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' # OpenGL & Mesa configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT -configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' configopts += '-DVTK_OPENGL_HAS_OSMESA=ON ' sanity_check_paths = { From 973d8aac727b165d6ace22c78683a8f9038b8e6b Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 29 Jun 2021 10:29:06 +0200 Subject: [PATCH 0272/9987] adding versionsuffix --- ...SPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb new file mode 100644 index 00000000000..5c267480b25 --- /dev/null +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'CRISPResso2' +version = '2.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pinellolab/CRISPResso2/' +description = """CRISPResso2 is a software pipeline designed to enable rapid and +intuitive interpretation of genome editing experiments.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [ + {'source_urls': ['https://github.com/pinellolab/CRISPResso2/archive/'], + 'filename': 'v%(version)s.tar.gz'}, + {'source_urls': ['https://crispresso.pinellolab.partners.org/static/demo/'], + 'filename': 'base_editor.fastq.gz', 'extract_cmd': 'cp %s %(builddir)s'}] +patches = ['CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch'] +checksums = [ + '29dfaaa65f66225faee4887376ea6b524355332fc6f7ca4d07bb7d63596ef5e6', # v2.1.2.tar.gz + '371aad07a164721188deaa80ca7589f5cd4b871119d90d55a984c6d9c8d31c7a', # base_editor.fastq.gz + # CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch + '87e4515d87c5e70fa65a8216a950dca5876948821ef5132a993102c168ece66a', +] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', '-Python-%(pyver)s'), + ('matplotlib', '2.2.5', '-Python-%(pyver)s'), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('FLASH', '2.2.00'), + ('SAMtools', '1.12'), + ('Bowtie2', '2.4.2'), + ('Seaborn', '0.9.1', '-Python-%(pyver)s'), +] +download_dep_fail = True +use_pip = True +options = {'modulename': False} +sanity_pip_check = True + +local_seq_str = 'GGCCCCAGTGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTAC' +local_seq_str += 'AAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATG' +local_seq_str += 'GGGAGGACATCGATGTCACCTCCAATGACTAGGGTGG' +sanity_check_commands = [('CRISPResso -h'), + ("""CRISPResso --fastq_r1 %%(builddir)s/base_editor.fastq.gz --amplicon_seq %s \ + --guide_seq GAGTCCGAGCAGAAGAAGAA --quantification_window_size 10 \ + --quantification_window_center -10 --base_editor_output""" % local_seq_str)] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} + +moduleclass = 'bio' From b4794d3fcfd7835e5e4533c9c8699b8355f46c71 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 29 Jun 2021 10:33:54 +0200 Subject: [PATCH 0273/9987] Delete CRISPResso2-2.1.2-foss-2020b.eb replaced by version with `versionsuffix` --- .../CRISPResso2-2.1.2-foss-2020b.eb | 53 ------------------- 1 file changed, 53 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb deleted file mode 100644 index 6a6003f6062..00000000000 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b.eb +++ /dev/null @@ -1,53 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'PythonPackage' - -name = 'CRISPResso2' -version = '2.1.2' - -homepage = 'https://github.com/pinellolab/CRISPResso2/' -description = """CRISPResso2 is a software pipeline designed to enable rapid and -intuitive interpretation of genome editing experiments.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -sources = [ - {'source_urls': ['https://github.com/pinellolab/CRISPResso2/archive/'], - 'filename': 'v%(version)s.tar.gz'}, - {'source_urls': ['https://crispresso.pinellolab.partners.org/static/demo/'], - 'filename': 'base_editor.fastq.gz', 'extract_cmd': 'cp %s %(builddir)s'}] -patches = ['CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch'] -checksums = [ - '29dfaaa65f66225faee4887376ea6b524355332fc6f7ca4d07bb7d63596ef5e6', # v2.1.2.tar.gz - '371aad07a164721188deaa80ca7589f5cd4b871119d90d55a984c6d9c8d31c7a', # base_editor.fastq.gz - # CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch - '4168c02c4e26b08a39b3102bf63170860afe5c2c7e283d0ecc7fd9bb262ef4a3', -] - -dependencies = [ - ('Java', '11', '', True), - ('Python', '2.7.18'), - ('SciPy-bundle', '2020.11', '-Python-%(pyver)s'), - ('matplotlib', '2.2.5', '-Python-%(pyver)s'), - ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), - ('FLASH', '2.2.00'), - ('SAMtools', '1.12'), - ('Bowtie2', '2.4.2'), - ('Seaborn', '0.9.1', '-Python-%(pyver)s'), -] -download_dep_fail = True -use_pip = True -options = {'modulename': False} -sanity_pip_check = True - -local_seq_str = 'GGCCCCAGTGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTAC' -local_seq_str += 'AAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATG' -local_seq_str += 'GGGAGGACATCGATGTCACCTCCAATGACTAGGGTGG' -sanity_check_commands = [('CRISPResso -h'), - ("""CRISPResso --fastq_r1 %%(builddir)s/base_editor.fastq.gz --amplicon_seq %s \ - --guide_seq GAGTCCGAGCAGAAGAAGAA --quantification_window_size 10 \ - --quantification_window_center -10 --base_editor_output""" % local_seq_str)] - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} - -moduleclass = 'bio' From f1b3cecfe9e4c88754971432168447ab51e6e934 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 29 Jun 2021 11:17:09 +0200 Subject: [PATCH 0274/9987] commented patch --- .../CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch index 737fe007644..d6733f0f0ce 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch @@ -1,4 +1,5 @@ # unimportantly strict dependency version requirements +# Author: Denis Kristak diff -ruN "CRISPResso2-2.1.2 copy/setup.py" CRISPResso2-2.1.2/setup.py --- "CRISPResso2-2.1.2 copy/setup.py" 2021-06-28 15:30:43.197061000 +0200 +++ CRISPResso2-2.1.2/setup.py 2021-06-28 15:36:03.124070000 +0200 From c06d427146daf512debcbb67c23febf38afde0a1 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 29 Jun 2021 14:21:14 +0200 Subject: [PATCH 0275/9987] review changes --- .../CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 34 +++++ ...av-2.3.4-foss2020b_remove_hardcoding.patch | 129 ++++++++++++++++++ 2 files changed, 163 insertions(+) create mode 100644 easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb new file mode 100644 index 00000000000..d6b5db719a7 --- /dev/null +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -0,0 +1,34 @@ +name = 'CRISPR-DAV' +version = '2.3.4' + +homepage = 'https://github.com/pinetree1/crispr-dav/' +description = """CRISPR-DAV is a pipeline to analyze +amplicon-based NGS data of CRISPR clones in a high throughput manner.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/pinetree1/crispr-dav/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch'] +checksums = [ + '49975cd48bdbf31fe5a9e2aaa3f5ed85d3cc6f65a422ee3aa8daed890159d2ae', # v2.3.4.tar.gz + # crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch + '41475a09754d65cc2c88d4161be6eacdfc98242bccbe49778c4f1f74210a6cb2', +] + +dependencies = [ + ('R', '4.0.3'), + ('Perl', '5.32.0'), + ('NGS', '2.10.9'), + ('Pysam', '0.16.0.1'), + ('Excel-Writer-XLSX', '1.09'), + ('naturalsort', '0.1.3'), + ('pysamstats', '1.1.2'), + ('ABRA2', '2.23'), + ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), + ('SAMtools', '1.12'), + ('BEDTools', '2.30.0'), + ('FLASH', '2.2.00'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch b/easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch new file mode 100644 index 00000000000..c8d1e981e7d --- /dev/null +++ b/easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch @@ -0,0 +1,129 @@ +# author: Denis Kristak (INUITS) +# changing example command to contain absolute paths + tabs escaping + changing plotting type to cairo +diff -ruN crispr-dav-2.3.4_orig/Examples/example1/run.sh crispr-dav-2.3.4/Examples/example1/run.sh +--- crispr-dav-2.3.4_orig/Examples/example1/run.sh 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Examples/example1/run.sh 2021-06-22 12:57:41.700453098 +0200 +@@ -4,6 +4,7 @@ + + ## If there is problem loading Perl modules., set PERL5LIB accordingly. + #export PERL5LIB=$HOME/perlmod/lib/perl5:$PERL5LIB +-../../crispr.pl --conf conf.txt --region amplicon.bed --crispr site.bed \ +- --sitemap sample.site --fastqmap fastq.list --genome genomex ++ ++$EBROOTCRISPRMINDAV/crispr.pl --conf $EBROOTCRISPRMINDAV/Examples/example1/conf.txt --region $EBROOTCRISPRMINDAV/Examples/example1/amplicon.bed --crispr $EBROOTCRISPRMINDAV/Examples/example1/site.bed \ ++ --sitemap $EBROOTCRISPRMINDAV/Examples/example1/sample.site --fastqmap $EBROOTCRISPRMINDAV/Examples/example1/fastq.list --genome genomex --verbose 1 + +diff -ruN crispr-dav-2.3.4_orig/Modules/NGS.pm crispr-dav-2.3.4/Modules/NGS.pm +--- crispr-dav-2.3.4_orig/Modules/NGS.pm 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Modules/NGS.pm 2021-06-21 17:37:39.381993860 +0200 +@@ -296,7 +296,7 @@ + my $cmd = "$self->{bwa} mem"; + $cmd .= " $h{param}" if $h{param}; + if ( $h{id} && $h{sm} ) { +- $cmd .= " -R \'\@RG\tID:$h{id}\tSM:$h{sm}\tPL:$h{pl}\'"; ++ $cmd .= " -R \'\@RG\\tID:$h{id}\\tSM:$h{sm}\\tPL:$h{pl}\'"; + } + $cmd .= " $h{idxbase} $h{read1_inf}"; + $cmd .= " $h{read2_inf}" if -f $h{read2_inf}; +@@ -558,7 +558,7 @@ + # file is already indexed. + my $cmd = "rm -rf $workdir && mkdir -p $workdir" . + " && $self->{java} -Djava.io.tmpdir=$tmpdir -jar $h{abra} --threads 2" . +- " --ref $h{ref_fasta} --targets $h{target_bed} --working $workdir" . ++ " --ref $h{ref_fasta} --targets $h{target_bed} --tmpdir $workdir" . + " --in $h{bam_inf} --out $h{bam_outf}"; + + if ($h{single}) { +diff -ruN crispr-dav-2.3.4_orig/Rscripts/allele.R crispr-dav-2.3.4/Rscripts/allele.R +--- crispr-dav-2.3.4_orig/Rscripts/allele.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/allele.R 2021-06-22 13:13:45.868418215 +0200 +@@ -114,7 +114,7 @@ + } else { + h<-400 + w<- ifelse(n>40, 13*n, h*1.25) +- png(filename=outfile, height=h, width=w) ++ png(filename=outfile, type='cairo', height=h, width=w) + } + + on.exit(dev.off()) +diff -ruN crispr-dav-2.3.4_orig/Rscripts/amplicon.R crispr-dav-2.3.4/Rscripts/amplicon.R +--- crispr-dav-2.3.4_orig/Rscripts/amplicon.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/amplicon.R 2021-06-22 13:13:45.868418215 +0200 +@@ -111,7 +111,7 @@ + if ( high_res ) { + tiff(filename=outfile, width=5, height=4, units='in', res=1200) + } else { +- png(filename=outfile, width=500, height=400) ++ png(filename=outfile, type='cairo', width=500, height=400) + } + on.exit(dev.off()) + print(p) +diff -ruN crispr-dav-2.3.4_orig/Rscripts/hdr.R crispr-dav-2.3.4/Rscripts/hdr.R +--- crispr-dav-2.3.4_orig/Rscripts/hdr.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/hdr.R 2021-06-22 13:13:45.868418215 +0200 +@@ -102,7 +102,7 @@ + h<-400 + barspace=60 + w<- ifelse( n*barspace10, 50*n, h) +- png(filename=imgfile, height=h, width=w) ++ png(filename=imgfile, type='cairo', height=h, width=w) + } + + on.exit(dev.off()) +diff -ruN crispr-dav-2.3.4_orig/Rscripts/read_chr.R crispr-dav-2.3.4/Rscripts/read_chr.R +--- crispr-dav-2.3.4_orig/Rscripts/read_chr.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/read_chr.R 2021-06-22 13:13:45.868418215 +0200 +@@ -72,7 +72,7 @@ + w<-ifelse(n>5, 100*n, 550) + max_w=1000 + w <- ifelse(w>max_w, max_w, w) +- png(filename=outfile, height=h, width=w) ++ png(filename=outfile, type='cairo', height=h, width=w) + } + + print(p) +diff -ruN crispr-dav-2.3.4_orig/Rscripts/read_stats.R crispr-dav-2.3.4/Rscripts/read_stats.R +--- crispr-dav-2.3.4_orig/Rscripts/read_stats.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/read_stats.R 2021-06-22 13:13:45.868418215 +0200 +@@ -69,7 +69,7 @@ + } else { + h<-400 + w<- ifelse(n>10, 50*n, h) +- png(filename=outfile, height=h, width=w) ++ png(filename=outfile, type='cairo', height=h, width=w) + } + + p <- ggplot(dat.m, aes(x=Sample, y=value, fill=variable)) + +diff -ruN crispr-dav-2.3.4_orig/Rscripts/snp.R crispr-dav-2.3.4/Rscripts/snp.R +--- crispr-dav-2.3.4_orig/Rscripts/snp.R 2019-07-26 21:15:08.000000000 +0200 ++++ crispr-dav-2.3.4/Rscripts/snp.R 2021-06-22 13:13:45.868418215 +0200 +@@ -76,7 +76,7 @@ + if ( high_res ) { + tiff(filename=outfile, width=5, height=4, units='in', res=1200) + } else { +- png(filename=outfile, width=500, height=400) ++ png(filename=outfile, type='cairo', width=500, height=400) + } + print(p) + invisible(dev.off()) +@@ -182,7 +182,7 @@ + wt <- 600 + } + ht <- 400 +- png(filename=outfile, width=wt, height=ht) ++ png(filename=outfile, type='cairo', width=wt, height=ht) + } + + print(p) From eb48f968d870222a011958c24d7cca3a7c033d02 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Jun 2021 14:41:47 +0200 Subject: [PATCH 0276/9987] adding easyconfigs: OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb --- ...enchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..a58ef89181a --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.7.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TGZ] + +dependencies = [ + ('CUDAcore', '11.3.1', '', True), + ('UCX-CUDA', '1.10.0', versionsuffix), +] + +configopts = 'CC="$MPICC" CXX="$MPICC"' +configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From b2f5110276a31587e83d44dbc5770e54eb7ccf53 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 29 Jun 2021 15:46:49 +0200 Subject: [PATCH 0277/9987] Disables X to let configure step for OpenGL work --- .../easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb index f5929112fe1..a6ebb81f419 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb @@ -45,6 +45,7 @@ configopts += '-DPARAVIEW_USE_PYTHON=ON ' configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' # OpenGL & Mesa +configopts += '-DVTK_USE_X:BOOL=OFF ' configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' configopts += '-DVTK_OPENGL_HAS_OSMESA=ON ' From 2819c7801123bff564efaa6b893d08a4ebfad26f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Jun 2021 17:07:46 +0200 Subject: [PATCH 0278/9987] Fix checksum, config statement --- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb index a58ef89181a..fa684c6a3e8 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] +checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] dependencies = [ ('CUDAcore', '11.3.1', '', True), @@ -18,7 +19,7 @@ dependencies = [ ] configopts = 'CC="$MPICC" CXX="$MPICC"' -configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' +configopts += ' --enable-cuda --with-cuda=$EBROOTCUDACORE' local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] modextrapaths = {'PATH': local_benchmark_dirs} From b4d94f8f4c2196a3a5d2c2160f3fc43a4d417b2f Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 30 Jun 2021 14:51:33 +0200 Subject: [PATCH 0279/9987] adding easyconfigs: CUDAcore-11.4.0.eb, CUDA-11.4.0-GCC-10.3.0.eb --- .../c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb | 20 ++++++++++++ .../easyconfigs/c/CUDAcore/CUDAcore-11.4.0.eb | 31 +++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..4f3b65f368c --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb @@ -0,0 +1,20 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Bundle' +name = 'CUDA' +version = '11.4.0' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +dependencies = [('CUDAcore', version, '', True)] + +altroot = 'CUDAcore' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.0.eb b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.0.eb new file mode 100644 index 00000000000..e5e87706325 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.0.eb @@ -0,0 +1,31 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'EB_CUDA' + +name = 'CUDAcore' +version = '11.4.0' +local_nv_version = '470.42.01' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + 'd219db30f7415a115a4ea22bdbb5984b0a18f7f891cad6074c5da45d223aaa4b', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '6eb2fd0d9d5bc39fb243b5e1789ff827f325d098cd1fbb828a0499552b9544cc', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'f0c8e80d98a601ddca031b6764459984366008c7d3847e7c7f99b36bd4438e3c' + } +] + +moduleclass = 'system' From 0d0d4fbefa4681829f10592165e587f0062646c2 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 30 Jun 2021 16:48:37 +0100 Subject: [PATCH 0280/9987] linting --- .../s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb index 80c71362ead..fd94307bacb 100644 --- a/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb @@ -5,7 +5,7 @@ easyblock = 'CmdCp' name = 'Snippy' version = '4.6.0' local_pyversuffix = '-Python-%(pyver)s' -local_javaversuffix= '-Java-%(javaver)s' +local_javaversuffix = '-Java-%(javaver)s' versionsuffix = local_javaversuffix + local_pyversuffix homepage = 'https://github.com/tseemann/snippy' From 1c4b21aed1fe158f2dd7cf2848c6f453ce009576 Mon Sep 17 00:00:00 2001 From: manifest Date: Thu, 1 Jul 2021 09:41:28 +0930 Subject: [PATCH 0281/9987] Update easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb Co-authored-by: Adam Huffman --- easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb index 679405c3428..38c5a263b4c 100644 --- a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb +++ b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb @@ -18,7 +18,7 @@ description = """ RAPSearch stands for Reduced Alphabet based Protein similarity Search """ -toolchain = {'name': 'system', 'version': 'system'} +toolchain = SYSTEM source_urls = ['https://sourceforge.net/projects/rapsearch2/files'] sources = ['%(name)s.24_64bits.tar.gz'] From 4782eb9d761d9e48f0b4a711528ff72776b3e23e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 1 Jul 2021 11:39:47 +0200 Subject: [PATCH 0282/9987] changes from review --- ...SPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 25 ++++++++++++------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb index 5c267480b25..571c2db3c06 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -16,13 +16,11 @@ sources = [ {'source_urls': ['https://github.com/pinellolab/CRISPResso2/archive/'], 'filename': 'v%(version)s.tar.gz'}, {'source_urls': ['https://crispresso.pinellolab.partners.org/static/demo/'], - 'filename': 'base_editor.fastq.gz', 'extract_cmd': 'cp %s %(builddir)s'}] -patches = ['CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch'] + 'filename': 'base_editor_v%(version)s.fastq.gz', 'download_filename': 'base_editor.fastq.gz', + 'extract_cmd': 'cp %s %(builddir)s'}] checksums = [ '29dfaaa65f66225faee4887376ea6b524355332fc6f7ca4d07bb7d63596ef5e6', # v2.1.2.tar.gz - '371aad07a164721188deaa80ca7589f5cd4b871119d90d55a984c6d9c8d31c7a', # base_editor.fastq.gz - # CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch - '87e4515d87c5e70fa65a8216a950dca5876948821ef5132a993102c168ece66a', + '371aad07a164721188deaa80ca7589f5cd4b871119d90d55a984c6d9c8d31c7a', # base_editor_v2.1.2.fastq.gz ] dependencies = [ @@ -41,13 +39,22 @@ use_pip = True options = {'modulename': False} sanity_pip_check = True +# strip out too strict version requirements for dependencies +preinstallopts = "sed -i 's/,<=[0-9]*//g' setup.py && sed -i 's/==/>=/g' setup.py && " + +# this is an example command from: +# https://github.com/pinellolab/CRISPResso2#example-run-base-editing-experiment local_seq_str = 'GGCCCCAGTGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTAC' local_seq_str += 'AAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATG' local_seq_str += 'GGGAGGACATCGATGTCACCTCCAATGACTAGGGTGG' -sanity_check_commands = [('CRISPResso -h'), - ("""CRISPResso --fastq_r1 %%(builddir)s/base_editor.fastq.gz --amplicon_seq %s \ - --guide_seq GAGTCCGAGCAGAAGAAGAA --quantification_window_size 10 \ - --quantification_window_center -10 --base_editor_output""" % local_seq_str)] +local_test_cmd = "CRISPResso --fastq_r1 %(builddir)s/base_editor_v%(version)s.fastq.gz " +local_test_cmd += "--amplicon_seq %s " % local_seq_str +local_test_cmd += "--guide_seq GAGTCCGAGCAGAAGAAGAA --quantification_window_size 10 " +local_test_cmd += "--quantification_window_center -10 --base_editor_output" +sanity_check_commands = [ + "CRISPResso -h", + local_test_cmd, +] modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} From 4d084ac0b8ac7130f96f786ab957a9eb60e7d7bd Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 2 Jul 2021 12:36:35 +0200 Subject: [PATCH 0283/9987] TF 1.13.1 needs some repolishing --- ...ensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb | 11 ++++++++++- .../TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch | 14 ++++++++++++++ .../TensorFlow-1.13.1_icu_sha_changed.patch | 14 ++++++++++++++ 3 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_icu_sha_changed.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb index 574f0ddf817..c9bd2e79ba2 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb @@ -24,8 +24,11 @@ dependencies = [ ('NCCL', '2.4.2'), ] +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} use_pip = True -sanity_pip_check = True exts_list = [ ('protobuf-python', '3.6.1', { @@ -94,6 +97,8 @@ exts_list = [ 'TensorFlow-1.13.1_dont_expand_cuda_cudnn_path.patch', 'TensorFlow-1.13.1_fix_protobuf_problem.patch', 'TensorFlow-1.13.1_fix_cudalib_version_for_cuda10.1.patch', + 'TensorFlow-1.13.1_icu_sha_changed.patch', + 'TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch', ], 'checksums': [ '7cd19978e6bc7edc2c847bce19f95515a742b34ea5e28e4389dade35348f58ed', # v1.13.1.tar.gz @@ -107,6 +112,10 @@ exts_list = [ 'd2fab1497078a2980a68adeea4d0f8719be5bef03741ea4775163745a1e52d40', # TensorFlow-1.13.1_fix_cudalib_version_for_cuda10.1.patch '176237dc2736d99d343f7a086503f9c724e7747f9289884302a010e5dff2dd1b', + # TensorFlow-1.13.1_icu_sha_changed.patch + '4b3a82464298000e67d99ab1a38f554b520a9b15e63e4c8e1b7a5f1ec34cdafc', + # TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch + '4fb1234cd548f91ee131ac72017007ec5ebf962362d5eae8511721400e76a057', ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch new file mode 100644 index 00000000000..9e51e5994a9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch @@ -0,0 +1,14 @@ +# cloud is still imported despite tensorflow bulit with nogcp. See: +# https://github.com/tensorflow/tensorflow/issues/29617 +diff -ru tensorflow-1.13.1.orig/tensorflow/contrib/__init__.py tensorflow-1.13.1/tensorflow/contrib/__init__.py +--- tensorflow-1.13.1.orig/tensorflow/contrib/__init__.py 2019-02-25 21:37:04.000000000 +0100 ++++ tensorflow-1.13.1/tensorflow/contrib/__init__.py 2021-07-02 10:19:17.276767786 +0200 +@@ -26,8 +26,6 @@ + from tensorflow.contrib import batching + from tensorflow.contrib import bayesflow + from tensorflow.contrib import checkpoint +-if os.name != "nt": +- from tensorflow.contrib import cloud + from tensorflow.contrib import cluster_resolver + from tensorflow.contrib import coder + from tensorflow.contrib import compiler diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_icu_sha_changed.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_icu_sha_changed.patch new file mode 100644 index 00000000000..46eb41ffe14 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_icu_sha_changed.patch @@ -0,0 +1,14 @@ +# ICU SHA256 changed upstream see: +# https://github.com/tensorflow/tensorflow/issues/24135 +diff -ru tensorflow-1.13.1.orig/third_party/icu/workspace.bzl tensorflow-1.13.1/third_party/icu/workspace.bzl +--- tensorflow-1.13.1.orig/third_party/icu/workspace.bzl 2019-02-25 21:37:04.000000000 +0100 ++++ tensorflow-1.13.1/third_party/icu/workspace.bzl 2021-07-01 23:02:32.266223519 +0200 +@@ -11,7 +11,7 @@ + third_party_http_archive( + name = "icu", + strip_prefix = "icu-release-62-1", +- sha256 = "e15ffd84606323cbad5515bf9ecdf8061cc3bf80fb883b9e6aa162e485aa9761", ++ sha256 = "86b85fbf1b251d7a658de86ce5a0c8f34151027cc60b01e1b76f167379acf181", + urls = [ + "https://mirror.bazel.build/github.com/unicode-org/icu/archive/release-62-1.tar.gz", + "https://github.com/unicode-org/icu/archive/release-62-1.tar.gz", From 3584a37b144a04cdbf518099f520ad235fc329f3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 2 Jul 2021 12:44:41 +0200 Subject: [PATCH 0284/9987] TF 1.13.1 needs some repolishing v2 --- .../TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb index c9bd2e79ba2..29354c720af 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb @@ -24,11 +24,8 @@ dependencies = [ ('NCCL', '2.4.2'), ] -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'sanity_pip_check': True, -} use_pip = True +sanity_pip_check = True exts_list = [ ('protobuf-python', '3.6.1', { From 1214ae43d55aba299a4304e3645e865a3de166c7 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 2 Jul 2021 16:18:08 +0100 Subject: [PATCH 0285/9987] Apply suggestions from code review --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index 7365b86e9c3..d5850118826 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -899,9 +899,6 @@ exts_list = [ ('ccdata', '1.18.0', { 'checksums': ['de24c7205723067599de8b7dbec3c8488c9fcf8cbac7948966a82c22bab4ea6d'], }), - ('xgboost', '1.4.1.1', { - 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], - }), ('lsa', '0.73.2', { 'checksums': ['cb0017bbda9b0eb1d05b451e0f557d02f789f65b2f8bf005606b63a3708e63a8'], }), From 066f655704ac8d4d87d78d54bfdfa17cdda3ce07 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 3 Jul 2021 04:21:49 +0200 Subject: [PATCH 0286/9987] adding easyconfigs: configurable-http-proxy-4.4.0-GCCcore-10.3.0.eb, nodejs-14.17.2-GCCcore-10.3.0.eb, JupyterHub-1.4.1-GCCcore-10.3.0.eb --- ...gurable-http-proxy-4.4.0-GCCcore-10.3.0.eb | 33 +++++ .../JupyterHub-1.4.1-GCCcore-10.3.0.eb | 116 ++++++++++++++++++ .../n/nodejs/nodejs-14.17.2-GCCcore-10.3.0.eb | 42 +++++++ 3 files changed, 191 insertions(+) create mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.4.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-14.17.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.4.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..9af97e3a882 --- /dev/null +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.4.0-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'Binary' + +name = 'configurable-http-proxy' +version = '4.4.0' + +homepage = 'https://github.com/jupyterhub/configurable-http-proxy' +description = """HTTP proxy for node.js including a REST API for updating the routing table. + Developed as a part of the Jupyter Hub multi-user server.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = { + ('binutils', '2.36.1'), +} + +dependencies = [ + ('nodejs', '14.17.2'), +] + +source_urls = ['https://github.com/jupyterhub/configurable-http-proxy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a4a53ad766f3a00250e9c2454c97ab2ecd6e0153e4f8800e2be4c3a0ebe6a18f'] + +install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz' + +sanity_check_paths = { + 'files': ['bin/configurable-http-proxy'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..455a2d9bee3 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb @@ -0,0 +1,116 @@ +easyblock = 'PythonBundle' + +name = 'JupyterHub' +version = '1.4.1' + +homepage = 'https://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed + for centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = { + ('binutils', '2.36.1'), +} + +dependencies = [ + ('Python', '3.9.5'), + ('IPython', '7.25.0'), + ('Mako', '1.1.4'), + ('configurable-http-proxy', '4.4.0'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +use_pip = True + +exts_list = [ + ('certipy', '0.1.3', { + 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], + }), + ('pamela', '1.0.0', { + 'checksums': ['65c9389bef7d1bb0b168813b6be21964df32016923aac7515bdf05366acbab6c'], + }), + ('SQLAlchemy', '1.4.20', { + 'checksums': ['38ee3a266afef2978e82824650457f70c5d74ec0cadec1b10fe5ed6f038eb5d0'], + }), + ('alembic', '1.6.5', { + 'checksums': ['a21fedebb3fb8f6bbbba51a11114f08c78709377051384c9c5ead5705ee93a51'], + }), + ('oauthlib', '3.1.1', { + 'checksums': ['8f0215fcc533dd8dd1bee6f4c412d4f0cd7297307d43ac61666389e3bc3198a3'], + }), + ('pyOpenSSL', '20.0.1', { + 'modulename': 'OpenSSL', + 'checksums': ['4c231c759543ba02560fcd2480c48dcec4dae34c9da7d3747c508227e0624b51'], + }), + ('python-json-logger', '2.0.1', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['f26eea7898db40609563bed0a7ca11af12e2a79858632706d835a0f961b7d398'], + }), + ('ruamel.yaml', '0.16.12', { + 'checksums': ['076cc0bc34f1966d920a49f18b52b6ad559fbe656a0748e3535cf7b3f29ebf9e'], + }), + ('ruamel.yaml.clib', '0.2.4', { + 'modulename': False, + 'checksums': ['f997f13fd94e37e8b7d7dbe759088bb428adc6570da06b64a913d932d891ac8d'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('jupyter-telemetry', '0.1.0', { + 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', + 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], + }), + ('jupyterhub', version, { + 'checksums': ['ee1b0718a4db8e0b339796e3e50b704ca6822ab22a7435289dbb5932f65b5199'], + }), + ('batchspawner', '1.1.0', { + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/jupyterhub/batchspawner/archive/']}], + 'checksums': ['11fe187844e311531597cde841660b4d949f1131726d3701c57ba6080ba15c1a'], + }), + ('jupyterhub-systemdspawner', '0.15.0', { + 'modulename': 'systemdspawner', + 'checksums': ['b6e2d981657aa5d3794abb89b1650d056524158a3d0f0f706007cae9b6dbeb2b'], + }), + ('jupyterhub-simplespawner', '0.1', { + 'modulename': 'simplespawner', + 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], + }), + ('ldap3', '2.9', { + 'checksums': ['18c3ee656a6775b9b0d60f7c6c5b094d878d1d90fc03d56731039f0a4b546a91'], + }), + ('jupyterhub-ldapauthenticator', '1.3.2', { + 'modulename': 'ldapauthenticator', + 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], + }), + ('PyJWT', '2.1.0', { + 'modulename': 'jwt', + 'checksums': ['fba44e7898bbca160a2b2b501f492824fc8382485d3a6f11ba5d0c1937ce6130'], + }), + ('jupyterhub-jwtauthenticator-v2', '2.0.3', { + 'modulename': 'jwtauthenticator', + 'checksums': ['b94b6dff8246250904c5ee511da3f062680eb657dabe766d75993cbe72747d41'], + }), + ('onetimepass', '1.0.1', { + 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], + }), + ('jupyterhub-nativeauthenticator', '0.0.7', { + 'modulename': 'nativeauthenticator', + 'checksums': ['e8c690746e16ec57b9e2d09c7942e0c8ae39cbc993c1cd5fd14e5a140dd64720'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/jupyterhub'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], +} + +sanity_pip_check = True + +sanity_check_commands = ['jupyterhub --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..7152fd81ed8 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.2-GCCcore-10.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '14.17.2' # LTS on 2020-07-03 +local_libversion = '83' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://%(name)s.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['03bea54a68c6fa8b520c273a1dc80f2fdbf80ddc9c303200d2eeaf25bd7e62fa'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), +] + +configopts = [ + '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library + '--shared --with-intl=none', # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +postinstallcmds = [ + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'dirs': ['lib/node_modules', 'include/node'] +} + +moduleclass = 'lang' From 5e4278b0226b83062ba6704f4b7c22e3c1cfd825 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 3 Jul 2021 15:54:56 +0200 Subject: [PATCH 0287/9987] MUMPS/5.3.5, SuiteSparse/5.8.1 and Hypre/2.20.0 for intel/2020b --- .../h/Hypre/Hypre-2.20.0-intel-2020b.eb | 18 ++++++++++++ .../m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb | 27 +++++++++++++++++ ...iteSparse-5.8.1-intel-2020b-METIS-5.1.0.eb | 29 +++++++++++++++++++ 3 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2020b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-intel-2020b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-intel-2020b.eb new file mode 100644 index 00000000000..6b3ba1660ed --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.20.0-intel-2020b.eb @@ -0,0 +1,18 @@ +name = 'Hypre' +version = '2.20.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5be77b28ddf945c92cde4b52a272d16fb5e9a7dc05e714fc5765948cba802c01'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb new file mode 100644 index 00000000000..162fb38b82c --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb @@ -0,0 +1,27 @@ +name = 'MUMPS' +version = '5.3.5' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4'] + +dependencies = [ + ('SCOTCH', '6.1.0'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2020b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2020b-METIS-5.1.0.eb new file mode 100644 index 00000000000..d26467a833a --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2020b-METIS-5.1.0.eb @@ -0,0 +1,29 @@ +name = 'SuiteSparse' +version = '5.8.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['06726e471fbaa55f792578f9b4ab282ea9d008cf39ddcc3b42b73400acddef40'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From b9bd78f77961b557416ebb44ebd393911741de1a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jul 2021 02:49:45 +0200 Subject: [PATCH 0288/9987] Use proper openssl dep --- .../j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb index 455a2d9bee3..9f04b1629f4 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb @@ -18,10 +18,9 @@ dependencies = [ ('IPython', '7.25.0'), ('Mako', '1.1.4'), ('configurable-http-proxy', '4.4.0'), + ('OpenSSL', '1.1', '', True), ] -osdependencies = [OS_PKG_OPENSSL_DEV] - use_pip = True exts_list = [ From 50be52cf8c7a48362695d42372fa846caa32ac01 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jul 2021 15:49:47 +0200 Subject: [PATCH 0289/9987] Fix extension list --- .../j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb index 9f04b1629f4..459a67aa17e 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb @@ -30,6 +30,9 @@ exts_list = [ ('pamela', '1.0.0', { 'checksums': ['65c9389bef7d1bb0b168813b6be21964df32016923aac7515bdf05366acbab6c'], }), + ('greenlet', '1.1.0', { + 'checksums': ['c87df8ae3f01ffb4483c796fe1b15232ce2b219f0b18126948616224d3f658ee'], + }), ('SQLAlchemy', '1.4.20', { 'checksums': ['38ee3a266afef2978e82824650457f70c5d74ec0cadec1b10fe5ed6f038eb5d0'], }), @@ -47,8 +50,8 @@ exts_list = [ 'modulename': 'pythonjsonlogger', 'checksums': ['f26eea7898db40609563bed0a7ca11af12e2a79858632706d835a0f961b7d398'], }), - ('ruamel.yaml', '0.16.12', { - 'checksums': ['076cc0bc34f1966d920a49f18b52b6ad559fbe656a0748e3535cf7b3f29ebf9e'], + ('ruamel.yaml', '0.17.10', { + 'checksums': ['106bc8d6dc6a0ff7c9196a47570432036f41d556b779c6b4e618085f57e39e67'], }), ('ruamel.yaml.clib', '0.2.4', { 'modulename': False, From fcd9901f55807010fd0bfc69057b5f9f97b829f4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jul 2021 16:01:49 +0200 Subject: [PATCH 0290/9987] Remove unnecssary source url for batchspawner --- .../easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb index 459a67aa17e..5669d88511b 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb @@ -69,7 +69,6 @@ exts_list = [ 'checksums': ['ee1b0718a4db8e0b339796e3e50b704ca6822ab22a7435289dbb5932f65b5199'], }), ('batchspawner', '1.1.0', { - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://github.com/jupyterhub/batchspawner/archive/']}], 'checksums': ['11fe187844e311531597cde841660b4d949f1131726d3701c57ba6080ba15c1a'], }), ('jupyterhub-systemdspawner', '0.15.0', { From d30e6440dcacf4da876537e63fcffea83308e020 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 5 Jul 2021 08:59:23 +0100 Subject: [PATCH 0291/9987] adding easyconfigs: Control-FREEC-11.6-GCC-10.2.0.eb --- .../Control-FREEC-11.6-GCC-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb b/easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb new file mode 100644 index 00000000000..f705159c83d --- /dev/null +++ b/easybuild/easyconfigs/c/Control-FREEC/Control-FREEC-11.6-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'Control-FREEC' +version = '11.6' + +homepage = 'https://github.com/BoevaLab/FREEC' +description = """Copy number and genotype annotation from whole +genome and whole exome sequencing data.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/BoevaLab/FREEC/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['36564f86a01236e720cf412780e87eb24f224470f5bae45a99edb2d4a3cd1734'] + +build_cmd = "cd src && make all" + +files_to_copy = ['src/freec', 'scripts', 'data', 'README.md'] + +sanity_check_paths = { + 'dirs': [''], + 'files': ['freec'], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 006821bfa9a0fff6120c246a4198b3d7a01dcd74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 6 Jul 2021 09:47:32 +0200 Subject: [PATCH 0292/9987] adding easyconfigs: fumi_tools-0.18.2-foss-2018b-Python-3.6.6.eb --- ...mi_tools-0.18.2-foss-2018b-Python-3.6.6.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..e5dde653607 --- /dev/null +++ b/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'fumi_tools' +version = '0.18.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools' +description = """This tool is intended to deduplicate UMIs from single-end and paired-end + sequencing data. Reads are considered identical when their UMIs have the same sequence, + they have the same length and map at the same position.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools/uploads/bff8865d9eeaaa27849dd580aa2a9dd1/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3570890e232f4a1862541c08d5755f11a12cf8972e2ee7461adc270ba4a220f1'] + +builddependencies = [('CMake', '3.12.1')] + +dependencies = [ + ('Python', '3.6.6'), + ('pigz', '2.4'), + ('zlib', '1.2.11'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ["%(name)s -h"] + +moduleclass = 'bio' From fd09da3a34cc91ef2836aabe26502fee7fb7c728 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 6 Jul 2021 09:58:46 +0200 Subject: [PATCH 0293/9987] TF 1.13.1 needs some repolishing v3 --- ...Flow-1.13.1-fosscuda-2019a-Python-3.7.2.eb | 2 +- .../TensorFlow-1.13.1_icu_sha_changed.patch | 26 ++++++++++++------- 2 files changed, 17 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb index 29354c720af..6890ac7968f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-fosscuda-2019a-Python-3.7.2.eb @@ -110,7 +110,7 @@ exts_list = [ # TensorFlow-1.13.1_fix_cudalib_version_for_cuda10.1.patch '176237dc2736d99d343f7a086503f9c724e7747f9289884302a010e5dff2dd1b', # TensorFlow-1.13.1_icu_sha_changed.patch - '4b3a82464298000e67d99ab1a38f554b520a9b15e63e4c8e1b7a5f1ec34cdafc', + '936611ef1baf213a430d2706459dd0274a088472c3b2657173f450e2d4d72e0f', # TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch '4fb1234cd548f91ee131ac72017007ec5ebf962362d5eae8511721400e76a057', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_icu_sha_changed.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_icu_sha_changed.patch index 46eb41ffe14..77762f389b2 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_icu_sha_changed.patch +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1_icu_sha_changed.patch @@ -1,14 +1,20 @@ -# ICU SHA256 changed upstream see: -# https://github.com/tensorflow/tensorflow/issues/24135 +# bazel expect Git LSF resolved sources +# And that only provided by the new URL. +# additionally we need the original (wrong mirror) url as well: +# ERROR: Analysis of target '//tensorflow/tools/pip_package:build_pip_package' failed; build aborted: no such package +# '@icu//': tf_http_archive(urls) must have redundant URLs. +# The mirror.bazel.build URL must be present and it must come first. +# Even if you don't have permission to mirror the file, please put the correctly formatted mirror URL there anyway, +# because someone will come along shortly thereafter and mirror the file. diff -ru tensorflow-1.13.1.orig/third_party/icu/workspace.bzl tensorflow-1.13.1/third_party/icu/workspace.bzl --- tensorflow-1.13.1.orig/third_party/icu/workspace.bzl 2019-02-25 21:37:04.000000000 +0100 -+++ tensorflow-1.13.1/third_party/icu/workspace.bzl 2021-07-01 23:02:32.266223519 +0200 -@@ -11,7 +11,7 @@ - third_party_http_archive( - name = "icu", - strip_prefix = "icu-release-62-1", -- sha256 = "e15ffd84606323cbad5515bf9ecdf8061cc3bf80fb883b9e6aa162e485aa9761", -+ sha256 = "86b85fbf1b251d7a658de86ce5a0c8f34151027cc60b01e1b76f167379acf181", ++++ tensorflow-1.13.1/third_party/icu/workspace.bzl 2021-07-06 09:31:01.496253109 +0200 +@@ -14,7 +14,7 @@ + sha256 = "e15ffd84606323cbad5515bf9ecdf8061cc3bf80fb883b9e6aa162e485aa9761", urls = [ "https://mirror.bazel.build/github.com/unicode-org/icu/archive/release-62-1.tar.gz", - "https://github.com/unicode-org/icu/archive/release-62-1.tar.gz", +- "https://github.com/unicode-org/icu/archive/release-62-1.tar.gz", ++ "http://mirror.tensorflow.org/github.com/unicode-org/icu/archive/release-62-1.tar.gz", + ], + build_file = "//third_party/icu:BUILD.bazel", + system_build_file = "//third_party/icu:BUILD.system", From 501b7e18fb613b38848eb6afde890c0b7e52f587 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 6 Jul 2021 10:03:21 +0200 Subject: [PATCH 0294/9987] CUDA 11.4.0 is removed --- .../c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb | 20 ------------------- 1 file changed, 20 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb deleted file mode 100644 index 4f3b65f368c..00000000000 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.4.0-GCC-10.3.0.eb +++ /dev/null @@ -1,20 +0,0 @@ -## -# Author: Robert Mijakovic -## -easyblock = 'Bundle' -name = 'CUDA' -version = '11.4.0' - -homepage = 'https://developer.nvidia.com/cuda-toolkit' -description = """CUDA (formerly Compute Unified Device Architecture) is a parallel - computing platform and programming model created by NVIDIA and implemented by the - graphics processing units (GPUs) that they produce. CUDA gives developers access - to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" - -toolchain = {'name': 'GCC', 'version': '10.3.0'} - -dependencies = [('CUDAcore', version, '', True)] - -altroot = 'CUDAcore' - -moduleclass = 'system' From ff7b7a62e284ab8bd9d3baa681e845c7fe3b8fd2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 6 Jul 2021 11:15:48 +0200 Subject: [PATCH 0295/9987] adding easyconfigs: ORCA-5.0.0-gompi-2021a.eb, ORCA-5.0.0-gompi-2021a-static.eb --- .../o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb | 30 +++++++++++++++++++ .../o/ORCA/ORCA-5.0.0-gompi-2021a.eb | 22 ++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb new file mode 100644 index 00000000000..b8e0ff3f174 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb @@ -0,0 +1,30 @@ +name = 'ORCA' +version = '5.0.0' +versionsuffix = '-static' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +# Static binaries of ORCA dynamically linking to OpenMPI +sources = ['%%(namelower)s_%s_linux_x86-64_openmpi411_part%s.tar.xz' % (version.replace('.', '_'), p) + for p in range(1, 5)] +checksums = [ + # orca_5_0_0_linux_x86-64_openmpi411_part1.tar.xz + '4ada3b343701e6a37c3f9f50fa3514396dcad4c8d7d625e170e77e3bd3864758', + # orca_5_0_0_linux_x86-64_openmpi411_part2.tar.xz + 'd7a7148632b1a0323b1b9ed317b504d914e58802181e63280bd1136159ab974c', + # orca_5_0_0_linux_x86-64_openmpi411_part3.tar.xz + '1503585466416a6c1a662ad8dad23b3b4f923a41a5821894ca8542d9dcf7ea91', + # orca_5_0_0_linux_x86-64_openmpi411_part4.tar.xz + '2af59dda79023581d9f5e287e4d455935514d1ef04f6d966c2523575dccb40d2', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a.eb new file mode 100644 index 00000000000..2db15bd998b --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a.eb @@ -0,0 +1,22 @@ +name = 'ORCA' +version = '5.0.0' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +# ORCA binaries (mostly) dynamically linked (it has SCALAPACK, OpenBLAS embedded) +sources = ['%%(namelower)s_%s_linux_x86-64_shared_openmpi411.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_5_0_0_linux_x86-64_shared_openmpi411.tar.xz + '4e6dc3fca2f1bc1f98af60413fe1dd13baa7aa3b2e197754c40826167d2bcf56', +] + +moduleclass = 'chem' From d81f7f36dcb6e5a1d3367559c00f2b41d1d1eb12 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 6 Jul 2021 12:33:12 +0200 Subject: [PATCH 0296/9987] use orca easyblock in easyconfigs of ORCA v4.x --- .../o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb | 14 -------------- .../easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb | 14 -------------- .../easyconfigs/o/ORCA/ORCA-4.1.0-OpenMPI-3.1.3.eb | 14 -------------- .../easyconfigs/o/ORCA/ORCA-4.2.0-gompi-2019b.eb | 14 -------------- .../easyconfigs/o/ORCA/ORCA-4.2.1-gompi-2019b.eb | 14 -------------- 5 files changed, 70 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb index 079ce0d9410..7f30132c7c5 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb @@ -1,5 +1,3 @@ -easyblock = "PackedBinary" - name = "ORCA" version = '4.0.0.2' local_ompi_ver = '2.0.2' @@ -23,16 +21,4 @@ checksums = ['a5b8ecdd3d004af4bc8190c986f34e11'] dependencies = [('OpenMPI', local_ompi_ver, '-GCC-6.3.0-2.27')] -sanity_check_paths = { - 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] for y in ['', '_mpi']] + - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', - 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + - ['orca'], - 'dirs': [], -} - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb index 1e2409dadb5..5b85eff3902 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.1-OpenMPI-2.0.2.eb @@ -1,5 +1,3 @@ -easyblock = "PackedBinary" - name = "ORCA" version = '4.0.1' @@ -24,16 +22,4 @@ checksums = ['6644b95fdb16e117b870fd9e5cea8b4f829f1547d5df4e87d52ef08e3f1ee310'] dependencies = [('OpenMPI', local_ompi_ver, '-GCC-6.3.0-2.27')] -sanity_check_paths = { - 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cleanup', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] for y in ['', '_mpi']] + - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', - 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + - ['orca'], - 'dirs': [], -} - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.1.0-OpenMPI-3.1.3.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.1.0-OpenMPI-3.1.3.eb index 0b39e8e12ed..c2ab79ef64d 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.1.0-OpenMPI-3.1.3.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.1.0-OpenMPI-3.1.3.eb @@ -1,5 +1,3 @@ -easyblock = "PackedBinary" - name = "ORCA" version = '4.1.0' @@ -23,16 +21,4 @@ checksums = ['d54df169f3e61d0692d08a6cbd59ea81123772fad2e3766e785d9e14a0cc90d5'] dependencies = [('OpenMPI', local_ompi_ver, '-GCC-8.2.0-2.31.1')] -sanity_check_paths = { - 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] for y in ['', '_mpi']] + - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', - 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + - ['orca'], - 'dirs': [], -} - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.2.0-gompi-2019b.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.2.0-gompi-2019b.eb index 0ce3bd39b77..b29d6fdc97b 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.2.0-gompi-2019b.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.2.0-gompi-2019b.eb @@ -1,5 +1,3 @@ -easyblock = "PackedBinary" - name = "ORCA" version = '4.2.0' @@ -16,16 +14,4 @@ toolchain = {'name': 'gompi', 'version': '2019b'} sources = ['%%(namelower)s_%s_linux_x86-64_openmpi314.tar.xz' % version.replace('.', '_')] checksums = ['29a3699f79638dcbe6404a6735a1e0a41391f2faf0d24a803330fa89b95b57a1'] -sanity_check_paths = { - 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] for y in ['', '_mpi']] + - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', - 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + - ['orca'], - 'dirs': [], -} - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-gompi-2019b.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-gompi-2019b.eb index 49892b30f36..fbd04e70094 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-gompi-2019b.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.2.1-gompi-2019b.eb @@ -1,5 +1,3 @@ -easyblock = "PackedBinary" - name = "ORCA" version = '4.2.1' @@ -16,16 +14,4 @@ toolchain = {'name': 'gompi', 'version': '2019b'} sources = ['%%(namelower)s_%s_linux_x86-64_openmpi314.tar.xz' % version.replace('.', '_')] checksums = ['a1ff07bb01ac81ce9a4d6637fef77c12d0ec45354cebc72245c4e0d1620af956'] -sanity_check_paths = { - 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cpscf', - 'eprnmr', 'gtoint', 'mdci', 'mp2', 'mrci', 'pc', - 'rocis', 'scf', 'scfgrad', 'soc'] for y in ['', '_mpi']] + - ['orca_%s' % x for x in ['2mkl', 'asa', 'chelpg', 'ciprep', 'eca', 'ecplib', - 'euler', 'fci', 'fitpes', 'gstep', 'loc', 'mapspc', - 'md', 'mergefrag', 'ndoint', 'numfreq', 'plot', - 'pltvib', 'pop', 'rel', 'vib', 'vpot']] + - ['orca'], - 'dirs': [], -} - moduleclass = 'chem' From 735b2813669ba719a8bb40d94fbab961daf7bda0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Jul 2021 12:34:00 +0200 Subject: [PATCH 0297/9987] remove Python 2.6 from list of supported Python versions in setup.py --- setup.py | 1 - 1 file changed, 1 deletion(-) diff --git a/setup.py b/setup.py index fbbf8c4e026..e382efdb250 100644 --- a/setup.py +++ b/setup.py @@ -93,7 +93,6 @@ def get_data_files(): "Intended Audience :: System Administrators", "License :: OSI Approved :: GNU General Public License v2 (GPLv2)", "Operating System :: POSIX :: Linux", - "Programming Language :: Python :: 2.6", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", From 45ca7a7837461c2b9799a983c47fca697aca7224 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Jul 2021 14:40:05 +0200 Subject: [PATCH 0298/9987] Add variants of NCCL and magma as well --- .../magma-2.6.0-foss-2021a-CUDA-11.3.1.eb | 42 +++++++++++++++++++ .../NCCL-2.9.9-GCCcore-10.3.0-CUDA-11.3.1.eb | 23 ++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-GCCcore-10.3.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..47d1210e771 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,42 @@ +easyblock = "CMakeMake" + +name = 'magma' +version = '2.6.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/magma/downloads/'] +sources = [SOURCE_TAR_GZ] +patches = ['magma-2.5.4_allow-all-sms.patch'] +checksums = [ + '50cdd384f44f06a34469e7125f8b2ffae13c1975d373c3f1510d91be2b7638ec', # magma-2.6.0.tar.gz + '4e47ecc080ff761866f179c9b383b8930e4daa2fcee1c2a48db585fc50531561', # magma-2.5.4_allow-all-sms.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('CUDAcore', '11.3.1', '', True), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0'] +# make sure both static and shared libs are built +configopts = [ + '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') +] + +sanity_check_paths = { + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-GCCcore-10.3.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..35fc34249b3 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -0,0 +1,23 @@ +name = 'NCCL' +version = '2.9.9' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['01629a1bdadbadb2828e26023ba7685bbc07678468cb7df63cc96460f5337e08'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('CUDAcore', '11.3.1', '', True), + ('UCX-CUDA', '1.10.0', versionsuffix), +] + +moduleclass = 'lib' From 60e5336fe71d6bcdc3c03ec02528b6345d995f86 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 6 Jul 2021 14:46:32 +0100 Subject: [PATCH 0299/9987] adding easyconfigs: LADR-2009-11A-GCCcore-10.2.0.eb --- .../l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..e7a9e16bb55 --- /dev/null +++ b/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'LADR' +version = '2009-11A' + +homepage = 'https://www.cs.unm.edu/~mccune/mace4/download' +description = """Prover9, Mace4, and several related programs come packaged in + a system called LADR (Library for Automated Deduction Research). +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.cs.unm.edu/~mccune/mace4/download'] +sources = [SOURCE_TAR_GZ] +checksums = ['c32bed5807000c0b7161c276e50d9ca0af0cb248df2c1affb2f6fc02471b51d0'] + +dependencies = [('binutils', '2.35')] + +# parallel build fails +parallel = 1 + +buildopts = "all" + +runtest = "test1 && make test2 && make test3" + +files_to_copy = [(['manpages/*.1'], 'share/man/man1'), 'bin', 'Changelog', 'COPYING'] + +sanity_check_paths = { + 'files': ['bin/mace4', 'bin/prover9', 'bin/prover9-mace4'], + 'dirs': ['share'], +} + +sanity_check_commands = [("prover9 -h 2>&1 | grep 'Usage: prover9 \[-h\] \[-x\] \[-p\] \[-t \] \[-f \]'", '')] + +moduleclass = 'math' From ed261589e59a956bb4cebb2976c856e0400011ab Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 6 Jul 2021 14:48:28 +0100 Subject: [PATCH 0300/9987] adding easyconfigs: Vampire-4.5.1-GCCcore-10.2.0.eb --- .../v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..edb6a8fe3b1 --- /dev/null +++ b/easybuild/easyconfigs/v/Vampire/Vampire-4.5.1-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'CMakeMakeCp' + +name = 'Vampire' +version = '4.5.1' + +homepage = 'https://vprover.github.io/' +description = "The Vampire Theorem Prover." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'vprover' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['f7bf491a2576a7fc6551eabf37763b2b6ffd36e87ad660ff191dcd88a8969ae7'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [('Z3', '4.8.10')] + +configopts = '-DZ3_DIR="$EBROOTZ3/lib64/cmake/z3"' + +files_to_copy = ['bin', 'scripts', 'LICENCE', 'README.md'] + +postinstallcmds = ["cd %(installdir)s/bin && ln -sf vampire_z3_Release vampire"] + +sanity_check_paths = { + 'files': ['bin/vampire_z3_Release', 'bin/vampire'], + 'dirs': ['scripts'], +} + +sanity_check_commands = [ + "%(namelower)s --help", + "%(namelower)s --show_options on", +] + +moduleclass = 'math' From 60807fd014d07160a76d0e6c503605615be498f8 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 6 Jul 2021 17:51:53 +0200 Subject: [PATCH 0301/9987] adding easyconfigs: freud-analysis-2.6.2-foss-2020b.eb --- .../freud-analysis-2.6.2-foss-2020b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb new file mode 100644 index 00000000000..877385766cc --- /dev/null +++ b/easybuild/easyconfigs/f/freud-analysis/freud-analysis-2.6.2-foss-2020b.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'freud-analysis' +version = '2.6.2' + +homepage = 'https://github.com/glotzerlab/freud' +description = """The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories +obtained from molecular dynamics or Monte Carlo simulations. High performance, parallelized C++ is used to compute +standard tools such as radial distribution functions, correlation functions, order parameters, and clusters, as well as +original analysis methods including potentials of mean force and torque (PMFTs) and local environment matching. The +freud library supports many input formats and outputs NumPy arrays, enabling integration with the scientific Python +ecosystem for many typical materials science workflows.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('CMake', '3.18.4'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('tbb', '2020.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('rowan', '1.3.0.post1', { + 'source_urls': ['https://pypi.python.org/packages/source/r/rowan'], + 'checksums': ['8f1d0e3279f80c6ae1ee68a90955301853b5586f64e42ba4c27d85504d525e4f'], + }), + (name, version, { + 'modulename': 'freud', + 'source_urls': ['https://pypi.python.org/packages/source/f/freud-analysis'], + 'checksums': ['1cc1b95a8a386e0ac7162246b42be800cfdaf335684a614aae02841aa4df6614'], + }), +] + +moduleclass = 'vis' From bb72a85bfaacb4f5b5628963d74dd7d621e4ff6c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Jul 2021 17:56:57 +0200 Subject: [PATCH 0302/9987] Fix magma patch --- .../magma-2.6.0-foss-2021a-CUDA-11.3.1.eb | 4 +- .../m/magma/magma-2.6.0_allow-all-sms.patch | 230 ++++++++++++++++++ 2 files changed, 232 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb index 47d1210e771..b8977cb73d5 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -13,10 +13,10 @@ toolchainopts = {'pic': True, 'openmp': True} source_urls = ['https://icl.cs.utk.edu/projectsfiles/magma/downloads/'] sources = [SOURCE_TAR_GZ] -patches = ['magma-2.5.4_allow-all-sms.patch'] +patches = ['magma-2.6.0_allow-all-sms.patch'] checksums = [ '50cdd384f44f06a34469e7125f8b2ffae13c1975d373c3f1510d91be2b7638ec', # magma-2.6.0.tar.gz - '4e47ecc080ff761866f179c9b383b8930e4daa2fcee1c2a48db585fc50531561', # magma-2.5.4_allow-all-sms.patch + '6dbe0f5fe1a9f39dce9e081d98df86ab60577509b41255a99b69842c3bd77d35', # magma-2.6.0_allow-all-sms.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch b/easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch new file mode 100644 index 00000000000..2508e51a40f --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch @@ -0,0 +1,230 @@ +This allows to process any sm_xx passed to GPU_TARGET. Previously some were silently ignored +See https://bitbucket.org/icl/magma/issues/32/list-of-whitelisted-sm_-values-for-cuda-is +and https://bitbucket.org/icl/magma/pull-requests/5 + +Author: Alexander Grund (TU Dresden) +Updated to 2.6.0: micketeer@gmail.com + +--- CMakeLists.txt.orig 2021-07-06 17:02:37.125227748 +0200 ++++ CMakeLists.txt 2021-07-06 17:40:06.597705725 +0200 +@@ -124,14 +124,6 @@ + #message( STATUS " CUDA_CUBLAS_LIBRARIES: ${CUDA_CUBLAS_LIBRARIES}" ) + include_directories( ${CUDA_INCLUDE_DIRS} ) + +- # NVCC options for the different cards +- # sm_xx is binary, compute_xx is PTX for forward compatability +- # MIN_ARCH is lowest requested version +- # NV_SM accumulates sm_xx for all requested versions +- # NV_COMP is compute_xx for highest requested version +- set( NV_SM "" ) +- set( NV_COMP "" ) +- + set(CUDA_SEPARABLE_COMPILATION ON) + + # nvcc >= 6.5 supports -std=c++11, so propagate CXXFLAGS to NVCCFLAGS. +@@ -140,168 +132,44 @@ + ## set( CUDA_PROPAGATE_HOST_FLAGS OFF ) + ##endif() + +- if (GPU_TARGET MATCHES Fermi) +- set( GPU_TARGET "${GPU_TARGET} sm_20" ) +- endif() +- +- if (GPU_TARGET MATCHES Kepler) +- set( GPU_TARGET "${GPU_TARGET} sm_30 sm_35 sm_37" ) +- endif() +- +- if (GPU_TARGET MATCHES Maxwell) +- set( GPU_TARGET "${GPU_TARGET} sm_50" ) +- endif() +- +- if (GPU_TARGET MATCHES Pascal) +- set( GPU_TARGET "${GPU_TARGET} sm_60" ) +- endif() +- +- if (GPU_TARGET MATCHES Volta) +- set( GPU_TARGET "${GPU_TARGET} sm_70" ) +- endif() +- +- if (GPU_TARGET MATCHES Turing) +- set( GPU_TARGET "${GPU_TARGET} sm_75" ) +- endif() +- +- if (GPU_TARGET MATCHES Ampere) +- set( GPU_TARGET "${GPU_TARGET} sm_80" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_20) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 200 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_20,code=sm_20 ) +- set( NV_COMP -gencode arch=compute_20,code=compute_20 ) +- message( STATUS " compile for CUDA arch 2.0 (Fermi)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_30) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 300 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_30,code=sm_30 ) +- set( NV_COMP -gencode arch=compute_30,code=compute_30 ) +- message( STATUS " compile for CUDA arch 3.0 (Kepler)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_35) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 300 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_35,code=sm_35 ) +- set( NV_COMP -gencode arch=compute_35,code=compute_35 ) +- message( STATUS " compile for CUDA arch 3.5 (Kepler)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_37) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 300 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_37,code=sm_37 ) +- set( NV_COMP -gencode arch=compute_37,code=compute_37 ) +- message( STATUS " compile for CUDA arch 3.7 (Kepler)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_50) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 500 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_50,code=sm_50 ) +- set( NV_COMP -gencode arch=compute_50,code=compute_50 ) +- message( STATUS " compile for CUDA arch 5.0 (Maxwell)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_52) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 520 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_52,code=sm_52 ) +- set( NV_COMP -gencode arch=compute_52,code=compute_52 ) +- message( STATUS " compile for CUDA arch 5.2 (Maxwell)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_53) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 530 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_53,code=sm_53 ) +- set( NV_COMP -gencode arch=compute_53,code=compute_53 ) +- message( STATUS " compile for CUDA arch 5.3 (Maxwell)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_60) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 600 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_60,code=sm_60 ) +- set( NV_COMP -gencode arch=compute_60,code=compute_60 ) +- message( STATUS " compile for CUDA arch 6.0 (Pascal)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_61) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 610 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_61,code=sm_61 ) +- set( NV_COMP -gencode arch=compute_61,code=compute_61 ) +- message( STATUS " compile for CUDA arch 6.1 (Pascal)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_62) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 620 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_62,code=sm_62 ) +- set( NV_COMP -gencode arch=compute_62,code=compute_62 ) +- message( STATUS " compile for CUDA arch 6.2 (Pascal)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_70) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 700 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_70,code=sm_70 ) +- set( NV_COMP -gencode arch=compute_70,code=compute_70 ) +- message( STATUS " compile for CUDA arch 7.0 (Volta)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_71) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 710 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_71,code=sm_71 ) +- set( NV_COMP -gencode arch=compute_71,code=compute_71 ) +- message( STATUS " compile for CUDA arch 7.1 (Volta)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_75) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 750 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_75,code=sm_75 ) +- set( NV_COMP -gencode arch=compute_75,code=compute_75 ) +- message( STATUS " compile for CUDA arch 7.5 (Turing)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_80) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 800 ) +- endif() +- set( NV_SM ${NV_SM} -gencode arch=compute_80,code=sm_80 ) +- set( NV_COMP -gencode arch=compute_80,code=compute_80 ) +- message( STATUS " compile for CUDA arch 8.0 (Ampere)" ) +- endif() +- +- if (NOT MIN_ARCH) +- message( FATAL_ERROR "GPU_TARGET must contain one or more of Fermi, Kepler, Maxwell, Pascal, Volta, Turing, Ampere, or valid sm_[0-9][0-9]" ) +- endif() ++ # NVCC options for the different cards ++ # sm_xx is binary, compute_xx is PTX for forward compatability ++ # MIN_SM/MAX_SM is lowest/highest requested version ++ # NV_SM accumulates sm_xx for all requested versions ++ # NV_COMP is compute_xx for highest requested version ++ set( MIN_SM 99 ) ++ set( MAX_SM 0 ) ++ set( NV_SM "" ) ++ set( NV_COMP "" ) + +- set( CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} -Xcompiler -fPIC ${NV_SM} ${NV_COMP} ${FORTRAN_CONVENTION} ) +- #add_definitions( "-DMAGMA_HAVE_CUDA -DMAGMA_CUDA_ARCH_MIN=${MIN_ARCH}" ) +- set(MAGMA_HAVE_CUDA "1") +- set(MAGMA_CUDA_ARCH_MIN "${MIN_ARCH}") ++ string( REGEX MATCHALL "sm_[0-9][0-9]" sms "${GPU_TARGET}" ) ++ list( SORT sms ) # To make output easier to reason about ++ foreach (sm IN LISTS sms) ++ string( REPLACE "sm_" "" sm "${sm}") # Remove sm_ prefix ++ if (sm LESS MIN_SM) ++ set( MIN_SM "${sm}" ) ++ endif() ++ if (sm GREATER MAX_SM) ++ set( MAX_SM "${sm}" ) ++ endif() ++ list( APPEND NV_SM -gencode arch=compute_${sm},code=sm_${sm} ) ++ string( REGEX REPLACE "([0-9])([0-9])" "\\1.\\2" cuda_arch "${sm}" ) ++ message( STATUS " compile for CUDA arch ${cuda_arch}" ) ++ endforeach() ++ ++ if (NOT NV_SM) ++ message( FATAL_ERROR ++ "GPU_TARGET must contain one or more of " ++ "Fermi, Kepler, Maxwell, Pascal, Volta, Turing, Ampere, or valid sm_[0-9][0-9]" ++ "Was: ${GPU_TARGET}" ) ++ endif() ++ ++ set( MIN_ARCH ${MIN_SM}0 ) ++ set( NV_COMP -gencode arch=compute_${MAX_SM},code=compute_${MAX_SM} ) ++ ++ list( APPEND CUDA_NVCC_FLAGS -Xcompiler -fPIC ${NV_SM} ${NV_COMP} ${FORTRAN_CONVENTION} ) ++ add_definitions( -DMIN_CUDA_ARCH=${MIN_ARCH} ) ++ add_definitions( -DMAGMA_HAVE_CUDA=1 ) + message( STATUS "Define -DMAGMA_HAVE_CUDA -DMAGMA_CUDA_ARCH_MIN=${MIN_ARCH}" ) + else() + message( STATUS "Could not find CUDA" ) From 554ce1e2a39731cd6cf52c8d5fef07a97d3ba3b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Jul 2021 20:47:48 +0200 Subject: [PATCH 0303/9987] Fix checksum --- .../easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb index 5669d88511b..3457f1b8086 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb @@ -69,7 +69,7 @@ exts_list = [ 'checksums': ['ee1b0718a4db8e0b339796e3e50b704ca6822ab22a7435289dbb5932f65b5199'], }), ('batchspawner', '1.1.0', { - 'checksums': ['11fe187844e311531597cde841660b4d949f1131726d3701c57ba6080ba15c1a'], + 'checksums': ['9bae72f7c1bd9bb11aa58ecc3bc9fae5475a10fdd92dc0c0d67fa7eb95c9dd3a'], }), ('jupyterhub-systemdspawner', '0.15.0', { 'modulename': 'systemdspawner', From 47e80238470c078eb14e9514ec37d2441677ff82 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Jul 2021 20:50:34 +0200 Subject: [PATCH 0304/9987] adding easyconfigs: SDL2-2.0.14-GCCcore-10.3.0.eb --- .../s/SDL2/SDL2-2.0.14-GCCcore-10.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.14-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.14-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.14-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6ac0cdf4ba7 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.14-GCCcore-10.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.14' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d8215b571a581be1332d2106f8036fcb03d12a70bae01e20f424976d275432bc'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('X11', '20210518'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 645c274cec29df2aa6626b4ee06a41e22a9f2a1c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Jul 2021 20:57:53 +0200 Subject: [PATCH 0305/9987] adding easyconfigs: file-5.40-GCCcore-10.3.0.eb --- .../f/file/file-5.40-GCCcore-10.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.40-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/file/file-5.40-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/file/file-5.40-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..62934d6d447 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.40-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.40' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['167321f43c148a553f68a0ea7f579821ef3b11c27b8cbe158e4df897e4a5dd57'] + +builddependencies = [ + ('Autotools', '20210128'), + ('binutils', '2.36.1'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From 18e802c1a6474b6250b741b0e3f3655831302a37 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Jul 2021 22:23:40 +0200 Subject: [PATCH 0306/9987] adding easyconfigs: GTK+-3.24.29-GCCcore-10.3.0.eb, at-spi2-core-2.40.2-GCCcore-10.3.0.eb, at-spi2-atk-2.38.0-GCCcore-10.3.0.eb --- .../at-spi2-atk-2.38.0-GCCcore-10.3.0.eb | 37 ++++++++++ .../at-spi2-core-2.40.2-GCCcore-10.3.0.eb | 39 +++++++++++ .../g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb | 69 +++++++++++++++++++ 3 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4460a40f2da --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.68.2'), + ('DBus', '1.13.18'), + ('at-spi2-core', '2.40.2'), + ('libxml2', '2.9.10'), + ('ATK', '2.36.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8abec6ada60 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.40.2' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['44dc17af943b0fd196c61c1e03b6c166960385cae96ccb5e95bdefffb6849f98'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.68.2'), + ('DBus', '1.13.18'), + ('X11', '20210518'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..2a8e7038914 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb @@ -0,0 +1,69 @@ +easyblock = 'Bundle' + +name = 'GTK+' +version = '3.24.29' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('cairo', '1.16.0'), + ('Perl', '5.32.1'), +] + +dependencies = [ + ('ATK', '2.36.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.5'), + ('libepoxy', '1.5.8'), + ('X11', '20210518'), + ('FriBidi', '1.0.10'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '3.38.0', { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97'], + }), + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['5d864d248357a2251545b3387b35942de5f66e4c66013f0962eb5cb6f8dae2b1'], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' From 69c95c3e47091e6c72d21e315ca500ae02875996 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Jul 2021 23:46:14 +0200 Subject: [PATCH 0307/9987] adding easyconfigs: ack-3.5.0-GCCcore-10.3.0.eb, Archive-Zip-1.68-GCCcore-10.3.0.eb, Blosc-1.21.0-GCCcore-10.3.0.eb, bpytop-1.0.67-GCCcore-10.3.0.eb, jemalloc-5.2.1-GCCcore-10.3.0.eb, json-c-0.15-GCCcore-10.3.0.eb, libpsl-0.21.1-GCCcore-10.3.0.eb, lxml-4.6.3-GCCcore-10.3.0.eb, Qhull-2020.2-GCCcore-10.3.0.eb, time-1.9-GCCcore-10.3.0.eb, tqdm-4.61.1-GCCcore-10.3.0.eb, Xerces-C++-3.2.3-GCCcore-10.3.0.eb, XlsxWriter-1.4.4-GCCcore-10.3.0.eb, YACS-0.1.8-GCCcore-10.3.0.eb, libxslt-1.1.34-GCCcore-10.3.0.eb --- .../Archive-Zip-1.68-GCCcore-10.3.0.eb | 32 +++++++++++++++ .../a/ack/ack-3.5.0-GCCcore-10.3.0.eb | 25 ++++++++++++ .../b/Blosc/Blosc-1.21.0-GCCcore-10.3.0.eb | 28 +++++++++++++ .../b/bpytop/bpytop-1.0.67-GCCcore-10.3.0.eb | 26 ++++++++++++ .../jemalloc/jemalloc-5.2.1-GCCcore-10.3.0.eb | 37 +++++++++++++++++ .../j/json-c/json-c-0.15-GCCcore-10.3.0.eb | 30 ++++++++++++++ .../l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb | 27 +++++++++++++ .../libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb | 31 ++++++++++++++ .../l/lxml/lxml-4.6.3-GCCcore-10.3.0.eb | 26 ++++++++++++ .../q/Qhull/Qhull-2020.2-GCCcore-10.3.0.eb | 40 +++++++++++++++++++ .../t/time/time-1.9-GCCcore-10.3.0.eb | 27 +++++++++++++ .../t/tqdm/tqdm-4.61.1-GCCcore-10.3.0.eb | 22 ++++++++++ .../Xerces-C++-3.2.3-GCCcore-10.3.0.eb | 39 ++++++++++++++++++ .../XlsxWriter-1.4.4-GCCcore-10.3.0.eb | 34 ++++++++++++++++ .../y/YACS/YACS-0.1.8-GCCcore-10.3.0.eb | 31 ++++++++++++++ 15 files changed, 455 insertions(+) create mode 100644 easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/a/ack/ack-3.5.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/b/bpytop/bpytop-1.0.67-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/lxml/lxml-4.6.3-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/t/time/time-1.9-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/t/tqdm/tqdm-4.61.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.4-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..127fd3128c0 --- /dev/null +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Archive-Zip' +version = '1.68' + +homepage = 'https://metacpan.org/pod/Archive::Zip' +description = "Provide an interface to ZIP archive files." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Perl', '5.32.1'), + ('UnZip', '6.0'), + ('Zip', '3.0'), +] + +options = {'modulename': 'Archive::Zip'} + +sanity_check_paths = { + 'files': ['bin/crc32'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/ack/ack-3.5.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/ack/ack-3.5.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e827bcccd48 --- /dev/null +++ b/easybuild/easyconfigs/a/ack/ack-3.5.0-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PerlModule' + +name = 'ack' +version = '3.5.0' + +homepage = 'https://beyondgrep.com' +description = "ack is a tool like grep, optimized for programmers" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['66053e884e803387a02ddee0d68abf2a10239fab654364dab33287309a725521'] + +builddependencies = [('binutils', '2.36.1')] +dependencies = [('Perl', '5.32.1')] + +options = {'modulename': 'App::Ack'} + +sanity_check_paths = { + 'files': ['bin/ack', 'lib/perl5/site_perl/%(perlver)s/App/Ack.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/App/Ack'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..5ba5c8fa001 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.21.0' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b0ef4fda82a1d9cbd11e0f4b9685abf14372db51703c595ecd4d76001a8b342d'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/bpytop/bpytop-1.0.67-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bpytop/bpytop-1.0.67-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..eda98b63f44 --- /dev/null +++ b/easybuild/easyconfigs/b/bpytop/bpytop-1.0.67-GCCcore-10.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'bpytop' +version = '1.0.67' + +homepage = 'https://github.com/aristocratos/bpytop/' +description = """Resource monitor that shows usage and stats for processor, memory, disks, network and processes.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/aristocratos/bpytop/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3f0267bd40a58016b5ac81ed6424f1c8d953b33a537546b22dd1a2b01b07a97'] + +dependencies = [('Python', '3.9.5')] + +postinstallcmds = ['mv %(installdir)s/bpytop.py %(installdir)s/bpytop'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['bpytop'], + 'dirs': ['themes'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..721378bfdb6 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.2.1' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ed51b0b37098af4ca6ed31c22324635263f8ad6471889e0592a9c0dba9136aea'] + +builddependencies = [ + ('Autotools', '20210128'), + ('binutils', '2.36.1'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..195c011df45 --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.15' +local_suff = '-20200726' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['4ba9a090a42cf1e12b84c64e4464bb6fb893666841d5843cc5bef90774028882'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..58d836e0aab --- /dev/null +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libpsl' +version = '0.21.1' + +homepage = 'https://rockdaboot.github.io/libpsl' +description = "C library for the Public Suffix List" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/rockdaboot/%(name)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ac6ce1e1fbd4d0254c4ddb9d37f1fa99dec83619c1253328155206b896210d4c'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('libtool', '2.4.6'), + ('Autotools', '20210128'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['bin/psl', 'lib/libpsl.a'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1fd2e54ea8a --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.34' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), +] + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.6.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.6.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..9a20f6dd000 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-4.6.3-GCCcore-10.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '4.6.3' + +homepage = 'https://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['39b78571b3b30645ac77b95f7c69d1bffc4cf8c3b157c435a34da72e78c82468'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c69c792e71d --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1678e6ee5de --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'https://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] + +builddependencies = [('binutils', '2.36.1')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.61.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.61.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..20ac2e2854e --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.61.1-GCCcore-10.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.61.1' + +homepage = "https://github.com/tqdm/tqdm" +description = """A fast, extensible progress bar for Python and CLI""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['24be966933e942be5f074c29755a95b315c69a91f839a29139bf26ffffe2d3fd'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..61fdfbcc7ca --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Xerces-C++' +version = '3.2.3' + +homepage = 'https://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['fb96fc49b1fb892d1e64e53a6ada8accf6f0e6d30ce0937956ec68d39bd72c7e'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('cURL', '7.76.0'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/XInclude', + 'include/xercesc/xinclude/XIncludeUtils.hpp', + 'lib/libxerces-c-3.2.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4e93958da08 --- /dev/null +++ b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-1.4.4-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'XlsxWriter' +version = '1.4.4' + +homepage = 'https://xlsxwriter.readthedocs.io/' +description = "A Python module for creating Excel XLSX files" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['791567acccc485ba76e0b84bccced2651981171de5b47d541520416f2f9f93e3'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/vba_extract.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['vba_extract.py --help'] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1f348953b0a --- /dev/null +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'YACS' +version = '0.1.8' + +homepage = "https://github.com/rbgirshick/yacs" +description = """YACS was created as a lightweight library to define and +manage system configurations, such as those commonly found in software +designed for scientific experimentation. These "configurations" +typically cover concepts like hyperparameters used in training a machine +learning model or configurable model hyperparameters, such as the depth +of a convolutional neural network.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'lib' From e83a64fcb471871ac30f9e4f3be0c8fc4c99d776 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 7 Jul 2021 02:33:22 +0200 Subject: [PATCH 0308/9987] adding easyconfigs: MariaDB-connector-c-3.2.2-GCCcore-10.3.0.eb, PostgreSQL-13.3-GCCcore-10.3.0.eb --- ...ariaDB-connector-c-3.2.2-GCCcore-10.3.0.eb | 34 +++++++++++++++ .../PostgreSQL-13.3-GCCcore-10.3.0.eb | 43 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.2.2-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.2.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ae581382571 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB-connector-c/MariaDB-connector-c-3.2.2-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB-connector-c' +version = '3.2.2' + +homepage = 'https://downloads.mariadb.org/connector-c/' +description = "MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/MariaDB/mariadb-connector-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f8360a801794cf261fe24934c92164196f87e60faa6792d2f24cf9338f56655d'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +# don't use gold linker, leads to error: "invalid use of VERSION in input file" +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd'" + +sanity_check_paths = { + 'files': ['lib/mariadb/libmariadbclient.a', 'lib/mariadb/libmariadb.%s' % SHLIB_EXT], + 'dirs': ['include/mariadb'], +} + +modextrapaths = { + 'CPATH': ['include/mariadb'], + 'LD_LIBRARY_PATH': ['lib/mariadb'], + 'LIBRARY_PATH': ['lib/mariadb'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8fcf51f7cc2 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '13.3' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3386a40736332aceb055c7c9012ecc665188536d874d967fcc5a33e7992f8080'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('Perl', '5.32.1'), + ('Python', '3.9.5'), +] + +dependencies = [ + ('libreadline', '8.1'), + ('zlib', '1.2.11'), + ('OpenSSL', '1.1', '', True), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' From 515a6146a2db80051acd7e3a7ba59e716a276511 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 7 Jul 2021 02:37:20 +0200 Subject: [PATCH 0309/9987] Fix checksum --- .../easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb index 8fcf51f7cc2..bbe63ecc522 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['3386a40736332aceb055c7c9012ecc665188536d874d967fcc5a33e7992f8080'] +checksums = ['0b54a8a68dbfaf5dcddd89eb3922740143df50fbea02fefda8de743d8af99516'] builddependencies = [ ('binutils', '2.36.1'), From 501fba83ab93172d4d9fe0e6b68189852586e74d Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Wed, 7 Jul 2021 12:47:35 +0200 Subject: [PATCH 0310/9987] adding easyconfigs: Armadillo-10.5.3-foss-2020b.eb --- .../Armadillo/Armadillo-10.5.3-foss-2020b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-10.5.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-10.5.3-foss-2020b.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-10.5.3-foss-2020b.eb new file mode 100644 index 00000000000..8bc6b53c4de --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-10.5.3-foss-2020b.eb @@ -0,0 +1,24 @@ +name = 'Armadillo' +version = "10.5.3" + +homepage = 'http://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = [ + 'e6c51d8d52a6f78b9c6459f6986135093e0ee705a674307110f6175f2cd5ee37', +] + +dependencies = [ + ('Boost', '1.74.0'), + ('arpack-ng', '3.8.0'), +] + +builddependencies = [('CMake', '3.18.4')] + +moduleclass = 'numlib' From 8a6ac582ce6a3610d699a60d2d676141f958f45d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 7 Jul 2021 12:53:52 +0200 Subject: [PATCH 0311/9987] adding easyconfigs: goatools-1.1.6-foss-2020b.eb --- .../g/goatools/goatools-1.1.6-foss-2020b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb b/easybuild/easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb new file mode 100644 index 00000000000..579601d7989 --- /dev/null +++ b/easybuild/easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb @@ -0,0 +1,65 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'goatools' +version = '1.1.6' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2020b'} + +# extra downloaded files are needed acc. to docs: https://github.com/tanghaibao/goatools#installation +sources = [ + {'source_urls': ['https://github.com/tanghaibao/goatools/archive/'], + 'filename': 'v%(version)s.tar.gz'}, + {'source_urls': ['http://geneontology.org/ontology/'], + 'filename': 'go-basic.obo', 'extract_cmd': 'cp %s %(builddir)s'}, + {'source_urls': ['http://www.geneontology.org/ontology/subsets/'], + 'filename': 'goslim_generic.obo', 'extract_cmd': 'cp %s %(builddir)s'}] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('XlsxWriter', '1.4.0'), + ('statsmodels', '0.12.1'), + ('pydot', '1.4.2'), +] + +preinstallopts = "sed -i 's/==[0-9]*.[0-9]*.[0-9]*//g' requirements.txt && " +# wget was here only to download some src files which we download via sources +preinstallopts += "sed -i 's/wget//g' requirements.txt && " + +local_go_path = "%(installdir)s/bin/goafiles" + + +local_data_dir = '%(builddir)s/%(name)s-%(version)s/data/*' +# copy downloaded GOA files into dedicated folder for user and to bin/ for sanity_check +postinstallcmds = ["mkdir %s" % local_go_path, + "cp %%(builddir)s/go-basic.obo %s" % local_go_path, + "cp %%(builddir)s/goslim_generic.obo %s" % local_go_path, + "cp %(builddir)s/go-basic.obo %(installdir)s/bin/", + "cp %(builddir)s/goslim_generic.obo %(installdir)s/bin/", + "mkdir %%(installdir)s/bin/data && cp -r %s %%(installdir)s/bin/data" % local_data_dir] + +# making sure user knows about downloaded files +modextravars = {'GOAFILES': local_go_path} +modloadmsg = """\n GOATOOLS: Downloaded files from "geneontology.org" are accessible in a directory behind a variable \ +$GOAFILES.\n You need to have them in a directory from which you run goatools commands.""" + +use_pip = True + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['bin/data'], +} + +# example from https://github.com/tanghaibao/goatools#find-go-enrichment-of-genes-under-study +local_cmd = "cd %(installdir)s/bin && find_enrichment.py --pval=0.05\ + --indent data/study data/population data/association && cd -" +sanity_check_commands = [local_cmd] + +sanity_pip_check = True + +moduleclass = 'bio' From 5fd320d206c9424b80e189d6f2e12cc14fe02ed7 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 7 Jul 2021 13:13:27 +0200 Subject: [PATCH 0312/9987] checksums --- .../easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb b/easybuild/easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb index 579601d7989..ff75c3edb88 100644 --- a/easybuild/easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb +++ b/easybuild/easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb @@ -18,6 +18,11 @@ sources = [ 'filename': 'go-basic.obo', 'extract_cmd': 'cp %s %(builddir)s'}, {'source_urls': ['http://www.geneontology.org/ontology/subsets/'], 'filename': 'goslim_generic.obo', 'extract_cmd': 'cp %s %(builddir)s'}] +checksums = [ + '41222308c2bc34eefd3292326a61bc215bd32831b4b2652eff00b1b8e3fcf8c6', # v1.1.6.tar.gz + '57bd37b4301a7a6be65da033c8e812698e62fd0f12a30e18cf9e3cfeed238702', # go-basic.obo + '161ccdabf702faee796335939858772703f5e05a2ccb0400a4cab481f41136d9', # goslim_generic.obo +] dependencies = [ ('Python', '3.8.6'), @@ -26,6 +31,7 @@ dependencies = [ ('statsmodels', '0.12.1'), ('pydot', '1.4.2'), ] +download_dep_fail = True preinstallopts = "sed -i 's/==[0-9]*.[0-9]*.[0-9]*//g' requirements.txt && " # wget was here only to download some src files which we download via sources From 6a0deb6aa7909c4379d48a62750d5bdcdd85ca80 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 7 Jul 2021 13:36:19 +0200 Subject: [PATCH 0313/9987] {math}[foss/2021a] lavaan 0.6-9 /w R-4.1.0 --- .../lavaan/lavaan-0.6-9-foss-2021a-R-4.1.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/lavaan/lavaan-0.6-9-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/l/lavaan/lavaan-0.6-9-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/l/lavaan/lavaan-0.6-9-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..beee4bf467b --- /dev/null +++ b/easybuild/easyconfigs/l/lavaan/lavaan-0.6-9-foss-2021a-R-4.1.0.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'lavaan' +version = '0.6-9' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/%(name)s' +description = """Fit a variety of latent variable models, including confirmatory factor analysis, structural + equation modeling and latent growth curve models.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['d404c4eb40686534f9c05f24f908cd954041f66d1072caea4a3adfa83a5f108a'] + +dependencies = [('R', '4.1.0')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lavaan'], +} + +moduleclass = 'math' From 8a2a4aac87ce52bb39e068f6fd1fe289a0471a78 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 7 Jul 2021 14:28:18 +0200 Subject: [PATCH 0314/9987] adding easyconfigs: PyQt5-5.15.4-GCCcore-10.3.0.eb --- .../p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb | 91 +++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e06fa986624 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb @@ -0,0 +1,91 @@ +easyblock = 'PythonBundle' + +name = 'PyQt5' +version = '5.15.4' + +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.36.1')] +dependencies = [ + ('Python', '3.9.5'), + ('Qt5', '5.15.2'), +] + +default_easyblock = 'PythonPackage' + +use_pip = True + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_sipver = '6.1.1' +components = [ + ('SIP', local_sipver, { + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['52d25af2fcd764c4e15cc9cd1350bdb0e63f52dfa2aa3c5e7679af7fde9f7e20'], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + ('PyQt-builder', '1.10.1', { + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['967b0c7bac0331597e9f8c5b336660f173a9896830b721d6d025e14bde647e17'], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + ('PyQt5_sip', '12.9.0', { + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + (name, version, { + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], + 'easyblock': 'Binary', + 'start_dir': '%(name)s-%(version)s', + 'skipsteps': ['configure', 'build'], + 'install_cmd': local_setup_env + local_pyqt5_sip_install, + }), + ('PyQtWebEngine', version, { + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['cedc28f54165f4b8067652145aec7f732a17eadf6736835852868cf76119cc19'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip5 --help", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' From c8dd94dbb4caa34fa8e3d947e33157f4aca592ce Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 7 Jul 2021 15:11:57 +0200 Subject: [PATCH 0315/9987] {bio}[GCCcore 10.3.0] InterProScan 5.52-86.0 --- .../InterProScan-5.52-86.0-GCCcore-10.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..770592cc670 --- /dev/null +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'Tarball' + +name = 'InterProScan' +version = '5.52-86.0' + +homepage = 'https://www.ebi.ac.uk/interpro/' +description = """InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines + different protein signature recognition methods into one resource.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +# from my location, the ftp download is 30x faster than http/https +source_urls = [ + 'ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/%(version)s/', + 'ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/data', +] +sources = [ + '%(namelower)s-%(version)s-64-bit.tar.gz', + # note: unpacked this is ~30GB, mostly 5 *.hmm files + # this data can also be provided in another location, which can be specified in interproscan.properties + # see https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload#2-installing-panther-models + 'panther-data-15.0.tar.gz', +] +checksums = [ + '50a03c47fb16c669c265e99ba05c4a8558b82047f713c9945f362d3d4be6069a', # interproscan-5.52-86.0-64-bit.tar.gz + '5907c661546cfac7e796e317ff41023f8c44e8481193b7f1f7457ffe315350d3', # panther-data-15.0.tar.gz +] + +dependencies = [ + ('Java', '11', '', True), + ('Perl', '5.32.1'), + ('libgd', '2.3.1'), + ('Python', '3.9.5'), +] + +postinstallcmds = ["cp -a %(builddir)s/panther %(installdir)s/data"] + +sanity_check_paths = { + 'files': ['interproscan-%(version_major)s.jar', 'interproscan.sh', 'interproscan.properties'], + 'dirs': ['bin', 'lib', 'data/panther/15.0'], +} + +sanity_check_commands = ['interproscan.sh'] + +# also include top install directory in $PATH, to make interproscan.sh available +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 6c3ab7eaff5573d9bb234f364aa79aa765df8b19 Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 7 Jul 2021 15:43:25 +0200 Subject: [PATCH 0316/9987] adding easyconfigs: XML-Parser-2.46-GCCcore-10.3.0-Perl-5.32.1.eb --- ...-Parser-2.46-GCCcore-10.3.0-Perl-5.32.1.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-10.3.0-Perl-5.32.1.eb diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-10.3.0-Perl-5.32.1.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-10.3.0-Perl-5.32.1.eb new file mode 100644 index 00000000000..afa1cbf2c33 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-10.3.0-Perl-5.32.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.46' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://search.cpan.org/~toddr/XML-Parser-2.46/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d331332491c51cccfb4cb94ffc44f9cd73378e618498d4a37df9e043661c515d'] + +builddependencies = [ + ('binutils', '2.36.1') +] + +dependencies = [ + ('Perl', '5.32.1'), + ('expat', '2.2.9') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML'], +} + +moduleclass = 'data' From 20ba3998f6bb202da4a8e01e2e29e23855e33697 Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 7 Jul 2021 15:49:57 +0200 Subject: [PATCH 0317/9987] adding easyconfigs: Elk-7.2.42-foss-2021a.eb --- .../e/Elk/Elk-7.2.42-foss-2021a.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/e/Elk/Elk-7.2.42-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/Elk/Elk-7.2.42-foss-2021a.eb b/easybuild/easyconfigs/e/Elk/Elk-7.2.42-foss-2021a.eb new file mode 100644 index 00000000000..bed8499fc6b --- /dev/null +++ b/easybuild/easyconfigs/e/Elk/Elk-7.2.42-foss-2021a.eb @@ -0,0 +1,62 @@ +easyblock = 'MakeCp' + +name = 'Elk' +version = '7.2.42' + +homepage = 'http://elk.sourceforge.net/' +description = """An all-electron full-potential linearised +augmented-plane wave (FP-LAPW) code with many advanced features. Written +originally at Karl-Franzens-Universität Graz as a milestone of the +EXCITING EU Research and Training Network, the code is designed to be as +simple as possible so that new developments in the field of density +functional theory (DFT) can be added quickly and reliably. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True, 'opt': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TGZ] +checksums = ['73f03776dbf9b2147bfcc5b7c062af5befa0944608f6fc4b6a1e590615400fc6'] + +dependencies = [ + ('libxc', '5.1.5'), + ('Wannier90', '3.1.0'), +] + + +# make.inc file is generated interactively by "setup" command, creating it here +prebuildopts = 'echo "F90_OPTS = -std=legacy $FFLAGS" > make.inc && ' +prebuildopts += 'echo "F77_OPTS = -std=legacy $FFLAGS" >> make.inc && ' +prebuildopts += 'echo "LIB_LPK = $LIBLAPACK" >> make.inc && ' +prebuildopts += 'echo "LIB_FFT = $LIBFFT" >> make.inc && ' +prebuildopts += 'echo "LIB_W90 = -lwannier" >> make.inc && ' +prebuildopts += 'echo "LIB_libxc = -lxcf90 -lxc" >> make.inc && ' +prebuildopts += 'echo "SRC_libxc = libxcf90.f90 libxcifc.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_FFT = zfftifc_fftw.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_OBLAS = oblas_stub.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_BLIS = blis_stub.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_MKL = mkl_stub.f90" >> make.inc && ' + +buildopts = 'all' + +runtest = 'test' + +parallel = 1 + +files_to_copy = [( + [ + 'src/elk', 'src/spacegroup/spacegroup', 'src/eos/eos', + 'utilities/elk-bands/elk-bands', 'utilities/elk-optics/elk-optics.py', + 'utilities/wien2k-elk/se.pl' + ], 'bin' +)] + +sanity_check_paths = { + 'files': ['bin/elk', 'bin/spacegroup', 'bin/eos'], + 'dirs': [] +} + +sanity_check_commands = ["elk | grep '^Elk code version %(version)s'"] + +moduleclass = 'phys' From 78cc8e04b3fbb90b90c1fca49b2e6a747abaeb12 Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 7 Jul 2021 16:34:26 +0200 Subject: [PATCH 0318/9987] adding easyconfigs: Shapely-1.8a1-GCC-10.3.0.eb --- .../s/Shapely/Shapely-1.8a1-GCC-10.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.3.0.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.3.0.eb new file mode 100644 index 00000000000..21fb4ee9b52 --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '1.8a1' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a748ab74c187060264e7ce838aaac30eead2a791bbea8cc3ab1dfc3cc0b4d067'] + +dependencies = [ + ('Python', '3.9.5'), + ('GEOS', '3.9.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From 64fd9cf88166c25f524e260cbc2e6e6a7187fb55 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Jul 2021 16:34:47 +0200 Subject: [PATCH 0319/9987] Fix PyQt 5.15.1 ECs --- .../p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb | 11 ++++++----- .../PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb | 11 ++++++----- 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb index d50e24ff287..2fc24f0a12a 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'Bundle' name = 'PyQt5' version = '5.15.1' @@ -18,8 +18,6 @@ dependencies = [ default_easyblock = 'PythonPackage' -use_pip = True - local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " @@ -34,6 +32,7 @@ local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/si local_sipver = '5.4.0' components = [ ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], 'start_dir': 'sip-%s' % local_sipver, @@ -41,18 +40,21 @@ components = [ 'options': {'modulename': 'PyQt5.sip'}, }), ('PyQt-builder', '1.5.0', { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.8.1', { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], 'easyblock': 'Binary', @@ -61,6 +63,7 @@ components = [ 'install_cmd': local_setup_env + local_pyqt5_sip_install, }), ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], 'easyblock': 'ConfigureMakePythonPackage', @@ -71,8 +74,6 @@ components = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb index 1005bfa8e3e..2122c835fca 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'Bundle' name = 'PyQt5' version = '5.15.1' @@ -19,8 +19,6 @@ dependencies = [ default_easyblock = 'PythonPackage' -use_pip = True - local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " @@ -35,6 +33,7 @@ local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/si local_sipver = '5.4.0' components = [ ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], 'start_dir': 'sip-%s' % local_sipver, @@ -42,18 +41,21 @@ components = [ 'options': {'modulename': 'PyQt5.sip'}, }), ('PyQt-builder', '1.5.0', { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.8.1', { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], 'easyblock': 'Binary', @@ -62,6 +64,7 @@ components = [ 'install_cmd': local_setup_env + local_pyqt5_sip_install, }), ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], 'easyblock': 'ConfigureMakePythonPackage', @@ -72,8 +75,6 @@ components = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From cad750945528eee3f114a61ead83e1539f8d857a Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 7 Jul 2021 17:10:47 +0200 Subject: [PATCH 0320/9987] adding easyconfigs: archspec-0.1.2-GCCcore-10.2.0.eb --- .../archspec/archspec-0.1.2-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..06b4ffb6c8f --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.1.2' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = ['archspec-%(version)s-py2.py3-none-any.whl'] +checksums = ['71aef85b8114c357723b0ea455cba9a2bf567400dce25b0ee7f96eb4f1405d37'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +sanity_pip_check = True + +moduleclass = 'tools' From adaa3980a8be0abac4826d7badc3b88d1ea613c7 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 7 Jul 2021 17:12:06 +0200 Subject: [PATCH 0321/9987] adding easyconfigs: Voro++-0.4.6-GCCcore-10.2.0.eb --- .../v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6eb09719067 --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] +builddependencies = [('binutils', '2.35')] + + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +moduleclass = 'math' From f7429526aef1111efe1dc328d50343d0993c3b6e Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Wed, 7 Jul 2021 17:24:11 +0200 Subject: [PATCH 0322/9987] Update Matlab Runtime Compiler to 8.4 for FreeSurfer 7 --- .../f/FreeSurfer/FreeSurfer-7.1.1-centos6_x86_64.eb | 13 ++++++++----- .../f/FreeSurfer/FreeSurfer-7.1.1-centos7_x86_64.eb | 13 ++++++++----- .../f/FreeSurfer/FreeSurfer-7.1.1-centos8_x86_64.eb | 11 ++++++----- 3 files changed, 22 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos6_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos6_x86_64.eb index 0bb1d8a557f..6012cc86501 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos6_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos6_x86_64.eb @@ -12,17 +12,20 @@ source_urls = [ 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' ] + +# Fresurfer > v7 uses MCR 8.4 (R2014b) +# https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime sources = [ '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', - 'runtime2012bLinux.tar.gz' + 'runtime2014bLinux.tar.gz' ] + checksums = [ - # freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz - '4026a5d5df41fd5a82a1b8c43a011cf0da4a0055737822e6b011fdb1370284a3', - '3ef4231d566fca45436eda03ae3bb93ffa7af0974a48112348c0d76c62b5fa64', # runtime2012bLinux.tar.gz + '4026a5d5df41fd5a82a1b8c43a011cf0da4a0055737822e6b011fdb1370284a3', # freesurfer-linux-centos6_x86_64-7.1.1.tar.gz + '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz ] -postinstallcmds = ['cp -a %(builddir)s/MCRv80/ %(installdir)s'] +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] license_text = """email@example.com 00000 diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos7_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos7_x86_64.eb index 10dfb815724..23b4136ad44 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos7_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos7_x86_64.eb @@ -12,17 +12,20 @@ source_urls = [ 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' ] + +# Fresurfer > v7 uses MCR 8.4 (R2014b) +# https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime sources = [ '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', - 'runtime2012bLinux.tar.gz' + 'runtime2014bLinux.tar.gz' ] + checksums = [ - # freesurfer-Linux-centos7_x86_64-stable-pub-v7.1.1.tar.gz - '6098b166fee8644f44f9ec88f3ffe88d05f2bc033cca60443e99e3e56f2e166b', - '3ef4231d566fca45436eda03ae3bb93ffa7af0974a48112348c0d76c62b5fa64', # runtime2012bLinux.tar.gz + '6098b166fee8644f44f9ec88f3ffe88d05f2bc033cca60443e99e3e56f2e166b', # freesurfer-linux-centos7_x86_64-7.1.1.tar.gz + '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz ] -postinstallcmds = ['cp -a %(builddir)s/MCRv80/ %(installdir)s'] +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] license_text = """email@example.com 00000 diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos8_x86_64.eb index 5b67471c76d..53008321d1a 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos8_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos8_x86_64.eb @@ -14,15 +14,16 @@ source_urls = [ ] sources = [ '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', - 'runtime2012bLinux.tar.gz' + 'runtime2014bLinux.tar.gz' ] checksums = [ - # freesurfer-Linux-centoss86_x86_64-stable-pub-v7.1.1.tar.gz - '6098b166fee8644f44f9ec88f3ffe88d05f2bc033cca60443e99e3e56f2e166b', - '3ef4231d566fca45436eda03ae3bb93ffa7af0974a48112348c0d76c62b5fa64', # runtime2012bLinux.tar.gz + '6098b166fee8644f44f9ec88f3ffe88d05f2bc033cca60443e99e3e56f2e166b', # freesurfer-linux-centos8_x86_64-7.1.1.tar.gz + '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz ] -postinstallcmds = ['cp -a %(builddir)s/MCRv80/ %(installdir)s'] +# Fresurfer > v7 uses MCR 8.4 (R2014b) +# https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] license_text = """email@example.com 00000 From 02727d89ed05c66a9bbbb490ca28f40b92f090ca Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 7 Jul 2021 17:42:01 +0200 Subject: [PATCH 0323/9987] interproscan.sh exists with -1 --- .../i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb index 770592cc670..92ba3725ea5 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb @@ -40,8 +40,6 @@ sanity_check_paths = { 'dirs': ['bin', 'lib', 'data/panther/15.0'], } -sanity_check_commands = ['interproscan.sh'] - # also include top install directory in $PATH, to make interproscan.sh available modextrapaths = {'PATH': ''} From 2662ffe4d2d8c3a70ebe2a748945b2d197d751a5 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Wed, 7 Jul 2021 17:48:24 +0200 Subject: [PATCH 0324/9987] Added BEDTools and BamTools for GCC-10.3.0 --- .../b/BEDTools/BEDTools-2.30.0-GCC-10.3.0.eb | 43 +++++++++++++++++++ .../b/BamTools/BamTools-2.5.2-GCC-10.3.0.eb | 19 ++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..fac1fd2b962 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-10.3.0.eb @@ -0,0 +1,43 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.30.0' + +homepage = "https://bedtools.readthedocs.io/" +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8'] + +builddependencies = [('Python', '3.9.5')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-10.3.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..aa6e988100d --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-10.3.0.eb @@ -0,0 +1,19 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +name = 'BamTools' +version = '2.5.2' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8'] + +builddependencies = [('CMake', '3.20.1')] + +moduleclass = 'bio' From 8949bad105f2fadda1c276d4ccb981995f77a257 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 7 Jul 2021 17:58:59 +0200 Subject: [PATCH 0325/9987] adding easyconfigs: ScaFaCoS-1.0.1-foss-2020b.eb --- .../s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb new file mode 100644 index 00000000000..c7c6f359dfa --- /dev/null +++ b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2020b.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'ScaFaCoS' +version = '1.0.1' + +homepage = 'http://www.scafacos.de/' +description = """ScaFaCoS is a library of scalable fast coulomb solvers.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '2b125f313795c81b0e87eb920082e91addf94c17444f9486d979e691aaded99b', # scafacos-1.0.1.tar.gz +] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GMP', '6.2.0'), + ('GSL', '2.6'), +] + +preconfigopts = 'unset F77 && ' + +configopts = 'FCFLAGS="-fallow-argument-mismatch $FCFLAGS" ' +configopts += '--enable-shared --enable-static --disable-doc ' +# tell it where to find provided FFTW +configopts += '--without-internal-fftw --with-fftw3-includedir=$EBROOTFFTW/include --with-fftw3-libdir=$EBROOTFFTW/lib ' +# only include the solvers supported for LAMMPS +# (for p2nfft we need an additonal dependency) +configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' + +sanity_check_paths = { + 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], + 'dirs': [], +} + +moduleclass = 'math' From 2fb858314a1b5698f6d4ce224554b9068a7e07db Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 7 Jul 2021 18:25:54 +0200 Subject: [PATCH 0326/9987] adding easyconfigs: patchelf-0.12-GCCcore-10.3.0.eb --- .../patchelf/patchelf-0.12-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.12-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.12-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.12-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d68d496f127 --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.12-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.12' + +homepage = 'https://github.com/NixOS/patchelf' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['3dca33fb862213b3541350e1da262249959595903f559eae0fbc68966e9c3f56'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +moduleclass = 'tools' From bd2219987612cc3822981a1f7c160702d276fd82 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Wed, 7 Jul 2021 18:40:40 +0200 Subject: [PATCH 0327/9987] Added Samtools --- .../b/BCFtools/BCFtools-1.12-GCC-10.3.0.eb | 38 +++++++++++++++++++ .../h/HTSlib/HTSlib-1.12-GCC-10.3.0.eb | 37 ++++++++++++++++++ .../s/SAMtools/SAMtools-1.12-GCC-10.3.0.eb | 35 +++++++++++++++++ 3 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.12-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.3.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.3.0.eb new file mode 100644 index 00000000000..b2e9741d569 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.12-GCC-10.3.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.12' + +homepage = 'https://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7a0e6532b1495b9254e38c6698d955e5176c1ee08b760dfea2235ee161a024f5'] + +dependencies = [ + ('zlib', '1.2.11'), + ('HTSlib', '1.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('GSL', '2.7'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['libexec/bcftools'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.12-GCC-10.3.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.12-GCC-10.3.0.eb new file mode 100644 index 00000000000..c84cf566142 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.12-GCC-10.3.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.12' + +homepage = "https://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2280141b46e953ba4ae01b98335a84f8e6ccbdb6d5cdbab7f70ee4f7e3b6f4ca'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.76.0'), +] + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.3.0.eb new file mode 100644 index 00000000000..913d5ae11bf --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.12-GCC-10.3.0.eb @@ -0,0 +1,35 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +## + +name = 'SAMtools' +version = '1.12' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6da3770563b1c545ca8bdf78cf535e6d1753d6383983c7929245d5dba2902dcb'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.76.0'), +] + +moduleclass = 'bio' From 08a337beb53e0116fea9b1e841febc4b77f63063 Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 7 Jul 2021 19:03:34 +0200 Subject: [PATCH 0328/9987] adding easyconfigs: PRSice-2.3.3-GCCcore-10.3.0.eb --- .../p/PRSice/PRSice-2.3.3-GCCcore-10.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRSice/PRSice-2.3.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ebbf3203a91 --- /dev/null +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.3-GCCcore-10.3.0.eb @@ -0,0 +1,36 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMakeCp' + +name = 'PRSice' +version = '2.3.3' + +homepage = 'https://www.prsice.info/' +description = """PRSice (pronounced 'precise') is a Polygenic Risk +Score software for calculating, applying, evaluating and +plotting the results of polygenic risk scores (PRS) analyses.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/choishingwan/PRSice/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['99cac1fdff727b652969ca50be32c1aebf5393c17c2df0a1a745ce6991b69eab'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), + ('Eigen', '3.3.9'), +] + +files_to_copy = [(['bin/PRSice'], 'bin'), "README.md", "LICENSE"] + +sanity_check_paths = { + 'files': ['bin/PRSice'], + 'dirs': [], +} + +sanity_check_commands = ["PRSice --help"] + +moduleclass = 'bio' From 3fe28502451cffc549fb66496fafed807f28e91d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 7 Jul 2021 22:14:27 +0200 Subject: [PATCH 0329/9987] adding easyconfigs: Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb --- .../Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..07c0c7e731c --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '8.2.0' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d966a27bd027d960c62ce5593858b4bf3e98ea44b9f7684a4486086b6f0ea3aa'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.2.0'), + ('freetype', '2.10.4') +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From ef046f83d0b8e87fc1bd40715fc85cb43cfceec7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 7 Jul 2021 22:44:43 +0200 Subject: [PATCH 0330/9987] Revert to bundle --- .../p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb index e06fa986624..6050db2ac53 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'Bundle' name = 'PyQt5' version = '5.15.4' @@ -18,8 +18,6 @@ dependencies = [ default_easyblock = 'PythonPackage' -use_pip = True - local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " @@ -34,6 +32,7 @@ local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/si local_sipver = '6.1.1' components = [ ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['52d25af2fcd764c4e15cc9cd1350bdb0e63f52dfa2aa3c5e7679af7fde9f7e20'], 'start_dir': 'sip-%s' % local_sipver, @@ -41,18 +40,21 @@ components = [ 'options': {'modulename': 'PyQt5.sip'}, }), ('PyQt-builder', '1.10.1', { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['967b0c7bac0331597e9f8c5b336660f173a9896830b721d6d025e14bde647e17'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.9.0', { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], 'easyblock': 'Binary', @@ -61,6 +63,7 @@ components = [ 'install_cmd': local_setup_env + local_pyqt5_sip_install, }), ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['cedc28f54165f4b8067652145aec7f732a17eadf6736835852868cf76119cc19'], 'easyblock': 'ConfigureMakePythonPackage', @@ -71,8 +74,6 @@ components = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From a1bf6673cd283849de48ea6706fa5c477adb5859 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 8 Jul 2021 01:37:42 +0200 Subject: [PATCH 0331/9987] Fix checksum --- easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb index 2a8e7038914..3ffbb8ae74b 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb @@ -50,7 +50,7 @@ components = [ }), (name, version, { 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['5d864d248357a2251545b3387b35942de5f66e4c66013f0962eb5cb6f8dae2b1'], + 'checksums': ['f57ec4ade8f15cab0c23a80dcaee85b876e70a8823d9105f067ce335a8268caa'], 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", }), ] From 81465b489271210808ef6e49dea1bd2d67ff4c72 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 8 Jul 2021 02:18:07 +0200 Subject: [PATCH 0332/9987] Drop sip back to 5 version --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb index 6050db2ac53..54c02ccf191 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb @@ -29,12 +29,12 @@ local_pyqtweb_configopts += "--no-stubs --no-dist-info" local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -local_sipver = '6.1.1' +local_sipver = '5.5.0' components = [ ('SIP', local_sipver, { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['52d25af2fcd764c4e15cc9cd1350bdb0e63f52dfa2aa3c5e7679af7fde9f7e20'], + 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], 'start_dir': 'sip-%s' % local_sipver, 'use_pip': True, 'options': {'modulename': 'PyQt5.sip'}, From 7ed96d33a66bd42644e5b9eaad31a20ef9bb25ea Mon Sep 17 00:00:00 2001 From: Max Voit Date: Thu, 8 Jul 2021 08:10:21 +0200 Subject: [PATCH 0333/9987] fix the libxml2 dependency (like #13030) which was broken due to #11065 --- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb index ea56b033afc..a164b3b0354 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb @@ -20,6 +20,10 @@ checksums = [ '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch ] +builddependencies = [ + ('pkg-config', '0.29.2'), +] + dependencies = [ ('Python', '3.8.6'), ('netCDF', '4.7.4'), From fd63940d1cbf5c68cba8926e8d0333f6e1b8df7c Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Thu, 8 Jul 2021 12:21:49 +0200 Subject: [PATCH 0334/9987] fix download link --- .../h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb | 10 ++++------ .../h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb | 10 ++++------ 2 files changed, 8 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb index 6f42eeb5aaa..801944ccbed 100644 --- a/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/HDF-EOS/HDF-EOS-2.20-GCCcore-10.2.0.eb @@ -10,13 +10,11 @@ description = """HDF-EOS libraries are software libraries built on HDF libraries toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos/latest_release/', - 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos/previous_releases/', +source_urls = ['https://git.earthdata.nasa.gov/rest/git-lfs/storage/DAS/hdfeos/'] +sources = [ + {'download_filename': 'cb0f900d2732ab01e51284d6c9e90d0e852d61bba9bce3b43af0430ab5414903', + 'filename': '%(name)s%(version)sv1.00.tar.Z'} ] - -sources = ['%(name)s%(version)sv1.00.tar.Z'] - checksums = ['cb0f900d2732ab01e51284d6c9e90d0e852d61bba9bce3b43af0430ab5414903'] builddependencies = [ diff --git a/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb index 20f1019fff2..49eb02b40fd 100644 --- a/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HDF-EOS5/HDF-EOS5-1.16-gompi-2020b.eb @@ -10,13 +10,11 @@ description = """HDF-EOS libraries are software libraries built on HDF libraries toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = [ - 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos5/latest_release/', - 'https://observer.gsfc.nasa.gov/ftp/edhs/hdfeos5/previous_releases/', +source_urls = ['https://git.earthdata.nasa.gov/rest/git-lfs/storage/DAS/hdfeos5/'] +sources = [ + {'download_filename': '7054de24b90b6d9533329ef8dc89912c5227c83fb447792103279364e13dd452', + 'filename': '%(name)s.%(version)s.tar.Z'} ] - -sources = ['%(name)s.%(version)s.tar.Z'] - checksums = ['7054de24b90b6d9533329ef8dc89912c5227c83fb447792103279364e13dd452'] dependencies = [ From e10fc0165a66156ef838370d1a5298f30f12361e Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 8 Jul 2021 12:28:06 +0200 Subject: [PATCH 0335/9987] adding easyconfigs: Anaconda3-2021.05.eb --- .../a/Anaconda3/Anaconda3-2021.05.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.05.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.05.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.05.eb new file mode 100644 index 00000000000..e9548a7fc7f --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.05.eb @@ -0,0 +1,28 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, 2019.10, 2020.2, 2020.11 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2021.05' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +sources = ['%(name)s-%(version)s-Linux-%(arch)s.sh'] + +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': '2751ab3d678ff0277ae80f9e8a74f218cfc70fe9a9cdc7bb1c137d7e47e33d53', + '%(name)s-%(version)s-Linux-ppc64le.sh': '097064807a9adae3f91fc4c5852cd90df2b77fc96505929bb25bf558f1eef76f', + } +] + +moduleclass = 'lang' From f5cc34dccfd6a6c77c58c2d6c226cb25a9fb471b Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 8 Jul 2021 13:14:13 +0200 Subject: [PATCH 0336/9987] adding easyconfigs: netCDF-C++4-4.3.1-gompi-2021a.eb --- .../netCDF-C++4-4.3.1-gompi-2021a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2021a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2021a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2021a.eb new file mode 100644 index 00000000000..c64526eb80a --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2021a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.8.0')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' From febe7e18d5962e624559fdbace71a9987ad1a451 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 8 Jul 2021 13:40:15 +0200 Subject: [PATCH 0337/9987] adding easyconfigs: MDAnalysis-1.1.1-foss-2020b.eb --- .../MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb new file mode 100644 index 00000000000..fb11a6330fc --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb @@ -0,0 +1,51 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '1.1.1' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Biopython', '1.78'), + ('networkx', '2.5'), + ('tqdm', '4.60.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('GridDataFormats', '0.5.0', { + 'modulename': 'gridData', + 'checksums': ['f317ed60708de22d1b2a76ce89a00f722d903291b1055ff1018d441870c39d69'], + }), + ('gsd', '2.4.2', { + 'checksums': ['fa2ed62da3eb2cbfea02a22dadc1d84e80c16d874535de4bace6941c6d805851'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('mmtf-python', '1.1.2', { + 'modulename': 'mmtf', + 'checksums': ['a5caa7fcd2c1eaa16638b5b1da2d3276cbd3ed3513f0c2322957912003b6a8df'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + (name, version, { + 'modulename': 'MDAnalysis', + 'checksums': ['edfd5a8ac6cbaa8d02f505ac3e68d5a1866644a2d392a8f20e279c43e0886253'], + }), +] + +moduleclass = 'bio' From b598d4f698109fb4f4c598ebc4cbd8ec86392c1e Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 8 Jul 2021 15:09:17 +0200 Subject: [PATCH 0338/9987] adding easyconfigs: intel-compilers-2021.3.0.eb --- .../intel-compilers-2021.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb new file mode 100644 index 00000000000..efcc5a7498b --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.3.0.eb @@ -0,0 +1,35 @@ +## +# Author: Robert Mijakovic +## +name = 'intel-compilers' +version = '2021.3.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17928/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3168_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17959/'], + 'filename': 'l_fortran-compiler_p_%(version)s.3168_offline.sh', + }, +] +checksums = [ + # l_dpcpp-cpp-compiler_p_2021.3.0.3168_offline.sh + 'f848d81b7cabc76c2841c9757abb2290921efd7b82491d830605f5785600e7a1', + 'c4553f7e707be8e8e196f625e4e7fbc8eff5474f64ab85fc7146b5ed53ebc87c', # l_fortran-compiler_p_2021.3.0.3168_offline.sh +] + +local_gccver = '10.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.36.1', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' From 88d2380035fccaed8c144bc2ebf53cbc2697950a Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 8 Jul 2021 16:14:52 +0200 Subject: [PATCH 0339/9987] adding easyconfigs: imkl-2021.3.0-gompi-2021a.eb --- .../i/imkl/imkl-2021.3.0-gompi-2021a.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb new file mode 100644 index 00000000000..07a876f213e --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.3.0-gompi-2021a.eb @@ -0,0 +1,17 @@ +## +# Author: Robert Mijakovic +## +name = 'imkl' +version = '2021.3.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17901'] +sources = ['l_onemkl_p_%(version)s.520_offline.sh'] +checksums = ['a06e1cdbfd8becc63440b473b153659885f25a6e3c4dcb2907ad9cd0c3ad59ce'] + +moduleclass = 'numlib' From d1bf2c2ec269d91dee3ab45d8744378881366c89 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 8 Jul 2021 16:20:29 +0200 Subject: [PATCH 0340/9987] adding easyconfigs: STAR-2.7.9a-GCC-10.3.0.eb --- .../s/STAR/STAR-2.7.9a-GCC-10.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-10.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-10.3.0.eb new file mode 100644 index 00000000000..a30aeb95848 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-10.3.0.eb @@ -0,0 +1,41 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.9a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ff52c9d6daaa9fb7261efa3aa49ef6ce5262aa089b0762a3cbc751e81321050e'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/STAR', 'bin/STARlong'], + 'dirs': [], +} + +moduleclass = 'bio' From 6c4598000f6917dc3ea1dd5c86f49b4d28385ef2 Mon Sep 17 00:00:00 2001 From: Theofilos Manitaras Date: Thu, 8 Jul 2021 16:34:12 +0200 Subject: [PATCH 0341/9987] {devel}[system] ReFrame v3.6.3 --- .../easyconfigs/r/ReFrame/ReFrame-3.6.3.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb new file mode 100644 index 00000000000..8a23c82c0ef --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.6.3' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.1.2', { + 'use_pip': False, + 'checksums': ['eb5df6b9ab0af50fe1098a52fd439b04730b6e066887ff7497357b9ebd19f79b'], + }), + ('setuptools', '53.0.0', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['1b18ef17d74ba97ac9c0e4b4265f123f07a8ae85d9cd093949fa056d3eeeead5'], + }), + ('reframe', version, { + 'prebuildopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], + 'use_pip': False, + 'checksums': ['3616478c886c89385385d04f5bce625a690eec6bdca603cd5ac3a6f443168ac2'], + }), +] + +postinstallcmds = [ + 'cp -r tutorials %(installdir)s', + 'mkdir -p %(installdir)s/share/man/man1 %(installdir)s/share/man/man8', + 'cp docs/man/man1/reframe.1 %(installdir)s/share/man/man1', + 'cp docs/man/man8/reframe.settings.8 %(installdir)s/share/man/man8', + 'cp -r share/completions %(installdir)s/share/completions' +] + +sanity_check_paths = { + 'files': ['bin/reframe', 'share/man/man1/reframe.1', + 'share/man/man8/reframe.settings.8', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['lib', 'tutorials', 'external'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions +modextrapaths = { + 'PATH': 'bin', + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From f3f4a1308f309c8ad14585fb406beee4dd8882ed Mon Sep 17 00:00:00 2001 From: Theofilos Manitaras Date: Thu, 8 Jul 2021 16:48:18 +0200 Subject: [PATCH 0342/9987] Split string in multiple lines to conform with formatting --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb index 8a23c82c0ef..a3f94b9c0c7 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb @@ -25,7 +25,8 @@ exts_list = [ 'checksums': ['1b18ef17d74ba97ac9c0e4b4265f123f07a8ae85d9cd093949fa056d3eeeead5'], }), ('reframe', version, { - 'prebuildopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'prebuildopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], 'use_pip': False, From a05e9ddfc11adffb0fcd6368a88f02efabfbc42b Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 8 Jul 2021 18:16:37 +0200 Subject: [PATCH 0343/9987] adding easyconfigs: impi-2021.3.0-intel-compilers-2021.3.0.eb --- .../impi-2021.3.0-intel-compilers-2021.3.0.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb diff --git a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb new file mode 100644 index 00000000000..1575cd8bb2b --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb @@ -0,0 +1,19 @@ +## +# Author: Robert Mijakovic +## +name = 'impi' +version = '2021.3.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2021.3.0'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls= ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17947/'], +sources = ['l_mpi_oneapi_p_%(version)s.294_offline.sh'] +checksums = ['04c48f864ee4c723b1b4ca62f2bea8c04d5d7e3de19171fd62b17868bc79bc36'], + +dependencies = [('UCX', '1.10.0')] + +moduleclass = 'mpi' From bbc1fd2805ea98123ea13880014a931eca42ab4d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 9 Jul 2021 09:23:36 +0200 Subject: [PATCH 0344/9987] {bio}[foss/2021a] scVelo 0.2.3 w/ deps --- .../b/Blosc/Blosc-1.21.0-GCCcore-10.3.0.eb | 28 ++++++ .../p/PyTables/PyTables-3.6.1-foss-2021a.eb | 48 ++++++++++ .../s/scVelo/scVelo-0.2.3-foss-2021a.eb | 87 +++++++++++++++++++ .../s/scVelo/umap-learn-0.4.6_numba.patch | 17 ++++ .../t/tqdm/tqdm-4.61.2-GCCcore-10.3.0.eb | 22 +++++ 5 files changed, 202 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/scVelo/scVelo-0.2.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/scVelo/umap-learn-0.4.6_numba.patch create mode 100644 easybuild/easyconfigs/t/tqdm/tqdm-4.61.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..5ba5c8fa001 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.0-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.21.0' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b0ef4fda82a1d9cbd11e0f4b9685abf14372db51703c595ecd4d76001a8b342d'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021a.eb new file mode 100644 index 00000000000..98fe7e3027f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.6.1' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-fix-libs.patch'] +checksums = [ + '4cea86bab5bcb5423a07c7951b8c65e24b674e0dcec0e448d434829eff5f18d0', # v3.6.1.tar.gz + '8df2a6379a9e4a941cb939ed1257a7d6105792d9c5e9dd0abd4bba3ece767c3a', # PyTables-3.6.1-fix-libs.patch +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # provides numexpr + ('HDF5', '1.10.7'), + ('LZO', '2.10'), + ('Blosc', '1.21.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.2.3-foss-2021a.eb b/easybuild/easyconfigs/s/scVelo/scVelo-0.2.3-foss-2021a.eb new file mode 100644 index 00000000000..f6eb1923bb9 --- /dev/null +++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.2.3-foss-2021a.eb @@ -0,0 +1,87 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'scVelo' +version = '0.2.3' + +homepage = "https://scvelo.org" +description = """scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using + dynamical modeling.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-learn', '0.24.2'), + ('h5py', '3.2.1'), + ('matplotlib', '3.4.2'), + ('networkx', '2.5.1'), + ('numba', '0.53.1'), + ('PyTables', '3.6.1'), + ('statsmodels', '0.12.2'), + ('libpng', '1.6.37'), + ('freetype', '2.10.4'), + ('Tkinter', '%(pyver)s'), + ('tqdm', '4.61.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('numpy-groupies', '0.9.13', { + 'modulename': 'numpy_groupies', + 'source_tmpl': 'numpy_groupies-%(version)s.tar.gz', + 'checksums': ['7b17b291322353f07c51598512d077e3731da0a048cfa8f738f3460d1ef0658d'], + }), + ('seaborn', '0.11.1', { + 'checksums': ['44e78eaed937c5a87fc7a892c329a7cc091060b67ebd1d0d306b446a74ba01ad'], + }), + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('get_version', '3.2', { + 'use_pip': False, + 'checksums': ['b01a7d84d60a4839d035375151ae03b9ee902baa503effb0cf8ccd6d4d79aa1d'], + }), + ('legacy-api-wrap', '1.2', { + 'use_pip': False, + 'checksums': ['034a44612da7e9943d3964363a98937ab54d55e3301075374abe0d521eb8101b'], + }), + ('loompy', '3.0.6', { + 'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'], + }), + ('xlrd', '1.2.0', { + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('anndata', '0.7.6', { + 'checksums': ['a3cc67bba9a4cd4b5984aec64c4f577c2d5a4695f4064027f8e6a9dac1f508b2'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.4', { + 'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'], + }), + ('scanpy', '1.8.1', { + 'checksums': ['1b8603a868d783bd6c18c8db763a450153feefc8daed862c440749790d47c654'], + }), + ('umap-learn', '0.4.6', { + 'modulename': 'umap', + 'patches': ['umap-learn-0.4.6_numba.patch'], + 'checksums': [ + '4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3', # umap-learn-0.4.6.tar.gz + '068573a9c422c4232223220cee527dc2580e6fcc6cc3f72f5fd7888319eb90d9', # umap-learn-0.53.1_numba.patch + ], + }), + (name, version, { + 'modulename': 'scvelo', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['5ec3fd5c2cae4d19bbe5a8afb50957c515cb75ff5455765aa0b652c95e7ea9de'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scVelo/umap-learn-0.4.6_numba.patch b/easybuild/easyconfigs/s/scVelo/umap-learn-0.4.6_numba.patch new file mode 100644 index 00000000000..dc0ff3090c3 --- /dev/null +++ b/easybuild/easyconfigs/s/scVelo/umap-learn-0.4.6_numba.patch @@ -0,0 +1,17 @@ +# https://github.com/lmcinnes/umap/commit/1412b49fddf5c9b948fa57f40ba3973137578ac2 +# It seems like previous Numba versions (up to 0.51.2 or 0.52.0) may have +# worked 'by accident'. When running umap against a recent +# development version of Numba. +diff --git a/umap/layouts.py b/umap/layouts.py +index ebb9e8e2..c3d79fc7 100644 +--- a/umap/layouts.py ++++ b/umap/layouts.py +@@ -33,7 +33,7 @@ def clip(val): + locals={ + "result": numba.types.float32, + "diff": numba.types.float32, +- "dim": numba.types.int32, ++ "dim": numba.types.intp, + }, + ) + def rdist(x, y): diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.61.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.61.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..85685e62ab8 --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.61.2-GCCcore-10.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.61.2' + +homepage = "https://github.com/tqdm/tqdm" +description = """A fast, extensible progress bar for Python and CLI""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8bb94db0d4468fea27d004a0f1d1c02da3cdedc00fe491c0de986b76a04d6b0a'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' From a06a039879690080414b47af79f87a95dea27aac Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 9 Jul 2021 09:44:16 +0200 Subject: [PATCH 0345/9987] fix comments --- easybuild/easyconfigs/s/scVelo/scVelo-0.2.3-foss-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.2.3-foss-2021a.eb b/easybuild/easyconfigs/s/scVelo/scVelo-0.2.3-foss-2021a.eb index f6eb1923bb9..9e1449eca87 100644 --- a/easybuild/easyconfigs/s/scVelo/scVelo-0.2.3-foss-2021a.eb +++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.2.3-foss-2021a.eb @@ -1,4 +1,3 @@ -# This easyconfig was created by the BEAR Software team at the University of Birmingham. easyblock = 'PythonBundle' name = 'scVelo' @@ -54,6 +53,7 @@ exts_list = [ ('loompy', '3.0.6', { 'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'], }), + # anndata 0.7.6 needs xlrd<2.0 ('xlrd', '1.2.0', { 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], }), @@ -69,6 +69,7 @@ exts_list = [ ('scanpy', '1.8.1', { 'checksums': ['1b8603a868d783bd6c18c8db763a450153feefc8daed862c440749790d47c654'], }), + # scvelo 0.2.3 requires umap-learn<0.5,>=0.3.10 ('umap-learn', '0.4.6', { 'modulename': 'umap', 'patches': ['umap-learn-0.4.6_numba.patch'], From dcf61ab9f00748046bbbffb3705a2092fb3e3e32 Mon Sep 17 00:00:00 2001 From: spottho1 Date: Fri, 9 Jul 2021 10:32:00 +0200 Subject: [PATCH 0346/9987] Add Python-3.9.5-bare to builddependencies as required by LLVM --- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb index a4cedb1f126..9ca755b64e9 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb @@ -16,6 +16,7 @@ checksums = ['3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98'] builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), + ('Python', '3.9.5', '-bare'), ] dependencies = [ From 3a21f557bb0ea879f533569a3343b9c7397c241a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 9 Jul 2021 10:44:02 +0200 Subject: [PATCH 0347/9987] add missing deps --- .../n/numba/numba-0.53.1-foss-2021a.eb | 51 +++++++++++++++++++ .../statsmodels-0.12.2-foss-2021a.eb | 29 +++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2021a.eb b/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2021a.eb new file mode 100644 index 00000000000..949917c9cd1 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.53.1-foss-2021a.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.53.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('LLVM', '11.1.0'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + +exts_list = [ + ('llvmlite', '0.36.0', { + 'patches': ['llvmlite-0.36.0_fix-LLVM-11.patch'], + 'preinstallopts': local_llvmlite_preinstallopts, + 'checksums': [ + '765128fdf5f149ed0b889ffbe2b05eb1717f8e20a5c87fa2b4018fbcce0fcfc9', # llvmlite-0.36.0.tar.gz + '17ebf3e8eaea2dd820bf4e089983d5743656613eb6313c1ffed30c58e8d66be4', # llvmlite-0.36.0_fix-LLVM-11.patch + ], + }), + (name, version, { + 'checksums': ['9cd4e5216acdc66c4e9dab2dfd22ddb5bef151185c070d4a3cd8e78638aff5b0'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["numba --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.2-foss-2021a.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.2-foss-2021a.eb new file mode 100644 index 00000000000..ab15e8a67cf --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.12.2-foss-2021a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.12.2' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + (name, version, { + 'checksums': ['8ad7a7ae7cdd929095684118e3b05836c0ccb08b6a01fe984159475d174a1b10'], + }), +] + +moduleclass = 'math' From ad6216ffee5fb1294ef355e72d21d0841bc60d18 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Jul 2021 11:53:46 +0200 Subject: [PATCH 0348/9987] Fix order of cffi in Python ECs --- easybuild/easyconfigs/p/Python/Python-3.6.3-foss-2017b.eb | 6 +++--- .../easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.3-foss-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.3-foss-2017b.eb index 971a41dc778..21619609a88 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.3-foss-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.3-foss-2017b.eb @@ -128,15 +128,15 @@ exts_list = [ ('pycparser', '2.19', { 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), + ('cffi', '1.11.5', { + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), ('cryptography', '2.1.1', { 'checksums': ['2699ed21e1f73dd1bdb7b0b22a517295de07809d535b23e200dd22166037fe6f'], }), ('pyasn1', '0.4.3', { 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), - ('cffi', '1.11.5', { - 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], - }), ('PyNaCl', '1.2.1', { 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb index 4ba48e9fbda..6fb51065a60 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.3-fosscuda-2017b.eb @@ -128,15 +128,15 @@ exts_list = [ ('pycparser', '2.19', { 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), + ('cffi', '1.11.5', { + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), ('cryptography', '2.1.1', { 'checksums': ['2699ed21e1f73dd1bdb7b0b22a517295de07809d535b23e200dd22166037fe6f'], }), ('pyasn1', '0.4.3', { 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), - ('cffi', '1.11.5', { - 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], - }), ('PyNaCl', '1.2.1', { 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', From 431161646b051b4b98638dd51755ecba1f649a3a Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 9 Jul 2021 11:59:21 +0200 Subject: [PATCH 0349/9987] adding easyconfigs: LLVM-12.0.1-GCCcore-10.3.0.eb --- .../l/LLVM/LLVM-12.0.1-GCCcore-10.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..dac180c1c97 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-10.3.0.eb @@ -0,0 +1,43 @@ +## +# Author: Robert Mijakovic +## +name = 'LLVM' +version = '12.0.1' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = ['llvm-%(version)s.src.tar.xz'] +checksums = ['7d9a8405f557cefc5a21bf5672af73903b64749d9bc3a50322239f56f34ffddf'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('Python', '3.9.5'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' From d7e8ea405358e06d7b84c8aab99565463f5c41df Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Jul 2021 11:59:56 +0200 Subject: [PATCH 0350/9987] Add more faulty ECs --- easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2017b.eb | 6 +++--- easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2017b.eb | 6 +++--- .../easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2017b.eb index 7bfa572ace5..feb2f81b6b7 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.2-intel-2017b.eb @@ -132,15 +132,15 @@ exts_list = [ ('pycparser', '2.19', { 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), + ('cffi', '1.11.5', { + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), ('cryptography', '2.0.3', { 'checksums': ['d04bb2425086c3fe86f7bc48915290b13e798497839fbb18ab7f6dffcf98cc3a'], }), ('pyasn1', '0.4.3', { 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), - ('cffi', '1.11.5', { - 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], - }), ('PyNaCl', '1.2.1', { 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2017b.eb index 3fb4a2f7fb9..9800d4ce806 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.3-intel-2017b.eb @@ -136,15 +136,15 @@ exts_list = [ ('pycparser', '2.19', { 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), + ('cffi', '1.11.5', { + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), ('cryptography', '2.1.1', { 'checksums': ['2699ed21e1f73dd1bdb7b0b22a517295de07809d535b23e200dd22166037fe6f'], }), ('pyasn1', '0.4.3', { 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), - ('cffi', '1.11.5', { - 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], - }), ('PyNaCl', '1.2.1', { 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', diff --git a/easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb b/easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb index b9fbee6941a..9b9457942e0 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.6.3-intelcuda-2017b.eb @@ -136,15 +136,15 @@ exts_list = [ ('pycparser', '2.19', { 'checksums': ['a988718abfad80b6b157acce7bf130a30876d27603738ac39f140993246b25b3'], }), + ('cffi', '1.11.5', { + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), ('cryptography', '2.1.1', { 'checksums': ['2699ed21e1f73dd1bdb7b0b22a517295de07809d535b23e200dd22166037fe6f'], }), ('pyasn1', '0.4.3', { 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), - ('cffi', '1.11.5', { - 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], - }), ('PyNaCl', '1.2.1', { 'checksums': ['e0d38fa0a75f65f556fb912f2c6790d1fa29b7dd27a1d9cc5591b281321eaaa9'], 'modulename': 'nacl', From 2d3310de5864141b7ef60cda58c0d0d723ed1a09 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Fri, 9 Jul 2021 12:44:48 +0200 Subject: [PATCH 0351/9987] Added CDO for gompi-2021a --- .../c/CDO/CDO-1.9.10-gompi-2021a.eb | 33 ++++++++++++++ .../e/ecCodes/ecCodes-2.22.1-gompi-2021a.eb | 44 +++++++++++++++++++ .../y/YAXT/YAXT-0.9.1-gompi-2021a.eb | 23 ++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.22.1-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2021a.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2021a.eb new file mode 100644 index 00000000000..fa60a7e3964 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2021a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.9.10' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/24638/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cc39c89bbb481d7b3945a06c56a8492047235f46ac363c4f0d980fccdde6677e'] + +dependencies = [ + ('HDF5', '1.10.7'), + ('netCDF', '4.8.0'), + ('YAXT', '0.9.1'), + ('ecCodes', '2.22.1'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES" + +# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && " + +sanity_check_paths = { + 'files': ['bin/cdo'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.22.1-gompi-2021a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.22.1-gompi-2021a.eb new file mode 100644 index 00000000000..df77163295c --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.22.1-gompi-2021a.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.22.1' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': False, 'openmp': True} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['75c7ee96469bb30b0c8f7edbdc4429ece4415897969f75c36173545242bc9e85'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('netCDF', '4.8.0'), + ('JasPer', '2.0.28'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +# Python bindings are now provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON " +configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " +configopts += "-DENABLE_ECCODES_OMP_THREADS=ON" + +local_exes = ['%s_%s' % (a, b) + for a in ['bufr', 'grib', 'gts', 'metar'] + for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] +local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + + ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb new file mode 100644 index 00000000000..58474ef9a1a --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.9.1' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.dkrz.de/redmine/attachments/download/506/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c87ec59e29b3e4965ce2f8e614bd7f1597012b89af0fda4242f2eef06460794c'] + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' From 5a34ce7b97c6067f5a164a9edb493e0fe5dde720 Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 9 Jul 2021 13:23:51 +0200 Subject: [PATCH 0352/9987] adding easyconfigs: PnetCDF-1.12.2-gompi-2021a.eb --- .../p/PnetCDF/PnetCDF-1.12.2-gompi-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompi-2021a.eb diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompi-2021a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompi-2021a.eb new file mode 100644 index 00000000000..06a342628c6 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-gompi-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = "1.12.2" + +homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://parallel-netcdf.github.io/Release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ef1411875b07955f519a5b03278c31e566976357ddfc74c2493a1076e7d7c74'] + +builddependencies = [ + ('Autotools', '20210128'), + ('Perl', '5.32.1'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' From 7730e6a73863419688de8daf4b99b7c2a75dee1f Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 9 Jul 2021 14:37:39 +0200 Subject: [PATCH 0353/9987] adding easyconfigs: Advisor-2021.2.0.eb --- .../easyconfigs/a/Advisor/Advisor-2021.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb new file mode 100644 index 00000000000..2a7de357e47 --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.2.0.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'Advisor' +version = '2021.2.0' + +homepage = 'https://software.intel.com/intel-advisor-xe' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17730/'] +sources = ['l_oneapi_advisor_p_%(version)s.189_offline.sh'] +checksums = ['9d9e9aa11819e6422f732de0e29e70a164e576254504857713cfec90b6b78664'] + +dontcreateinstalldir = True + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/advisor'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'perf' From 04ac89bf141161bec3805063209593bc883f1b69 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 9 Jul 2021 19:54:57 +0200 Subject: [PATCH 0354/9987] {numlib}[foss/2021a] petsc4py/3.14.0 SLEPc/3.15.1 slepc4py/3.15.1 --- .../p/petsc4py/petsc4py-3.15.0-foss-2021a.eb | 26 +++++++++++++++++++ .../s/SLEPc/SLEPc-3.15.1-foss-2021a.eb | 21 +++++++++++++++ .../s/slepc4py/slepc4py-3.15.1-foss-2021a.eb | 26 +++++++++++++++++++ 3 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/p/petsc4py/petsc4py-3.15.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/SLEPc/SLEPc-3.15.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/slepc4py/slepc4py-3.15.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.15.0-foss-2021a.eb b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.15.0-foss-2021a.eb new file mode 100644 index 00000000000..d92f71f87e9 --- /dev/null +++ b/easybuild/easyconfigs/p/petsc4py/petsc4py-3.15.0-foss-2021a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'petsc4py' +version = '3.15.0' + +homepage = 'https://bitbucket.org/petsc/petsc4py' +description = "petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation." + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['fe744bd9c92557f0a38027f19a419b6e6765a982f531d02e620c79eb1a97bae7'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PETSc', '3.15.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from petsc4py import PETSc'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.15.1-foss-2021a.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.15.1-foss-2021a.eb new file mode 100644 index 00000000000..295fc89a7c2 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.15.1-foss-2021a.eb @@ -0,0 +1,21 @@ +name = 'SLEPc' +version = '3.15.1' + +homepage = 'https://www.grycap.upv.es/slepc/' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://slepc.upv.es/download/distrib'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9c7c3a45f0d9df51decf357abe090ef05114c38a69b7836386a19a96fb203aea'] + +dependencies = [('PETSc', '3.15.1')] + +petsc_arch = 'installed-arch-linux2-c-opt' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/slepc4py/slepc4py-3.15.1-foss-2021a.eb b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.15.1-foss-2021a.eb new file mode 100644 index 00000000000..97a3f207909 --- /dev/null +++ b/easybuild/easyconfigs/s/slepc4py/slepc4py-3.15.1-foss-2021a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'slepc4py' +version = '3.15.1' + +homepage = 'https://bitbucket.org/slepc/slepc4py' +description = "Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations." + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['bcdab6d2101ae00e189f4b33072805358cee2dda806a6b6a8e3c2f1b9f619dfd'] + +dependencies = [ + ('Python', '3.9.5'), + ('SLEPc', '3.15.1'), + ('petsc4py', '3.15.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from slepc4py import SLEPc'"] + +moduleclass = 'tools' From 5a8d9448188506b3e322287fcae5b1a42f702dd5 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 9 Jul 2021 20:55:43 +0200 Subject: [PATCH 0355/9987] {bio}[foss/2021a] CellRank 1.4.0 --- .../c/CellRank/CellRank-1.4.0-foss-2021a.eb | 67 +++++++++++++++++++ .../c/CellRank/cellrank-1.4.0_numba.patch | 30 +++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellRank/CellRank-1.4.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/c/CellRank/cellrank-1.4.0_numba.patch diff --git a/easybuild/easyconfigs/c/CellRank/CellRank-1.4.0-foss-2021a.eb b/easybuild/easyconfigs/c/CellRank/CellRank-1.4.0-foss-2021a.eb new file mode 100644 index 00000000000..00b992b9580 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/CellRank-1.4.0-foss-2021a.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'CellRank' +version = '1.4.0' + +homepage = 'https://cellrank.readthedocs.io/en/stable/' +description = """CellRank is a toolkit to uncover cellular dynamics based on + Markov state modeling of single-cell data. It contains two main modules: +kernels compute cell-cell transition probabilities and estimators generate +hypothesis based on these. """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PETSc', '3.15.1'), + ('petsc4py', '3.15.0'), + ('SLEPc', '3.15.1'), + ('slepc4py', '3.15.1'), + ('scikit-learn', '0.24.2'), + ('scVelo', '0.2.3'), + ('typing-extensions', '3.10.0.0'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('python-utils', '2.5.6', { + 'checksums': ['352d5b1febeebf9b3cdb9f3c87a3b26ef22d3c9e274a8ec1e7048ecd2fac4349'], + }), + ('progressbar2', '3.53.1', { + 'modulename': 'progressbar', + 'checksums': ['ef72be284e7f2b61ac0894b44165926f13f5d995b2bf3cd8a8dedc6224b255a7'], + }), + ('pygam', '0.8.0', { + 'checksums': ['5cae01aea8b2fede72a6da0aba1490213af54b3476745666af26bbe700479166'], + }), + ('joblib', '1.0.1', { + 'checksums': ['9c17567692206d2f3fb9ecf5e991084254fe631665c450b443761c4186a613f7'], + }), + ('pygpcca', '1.0.2', { + 'checksums': ['a383636461698f6cda9a9e5678f9efb98ca2f8367b942221bc6d27f119f9be75'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + (name, version, { + 'modulename': 'cellrank', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'patches': ['cellrank-1.4.0_numba.patch'], + 'use_pip_extras': 'krylov', + 'checksums': [ + '957fd9b135ad7c1a43ff34c071cab4ee9290dfbcd663792d59eb544581f24634', # cellrank-1.4.0.tar.gz + '891579d404682efdc0fe938f6e72734a107790c56e805c60e959631d8836b3e1', # cellrank-1.4.0_numba.patch + ], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import cellrank as cr'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRank/cellrank-1.4.0_numba.patch b/easybuild/easyconfigs/c/CellRank/cellrank-1.4.0_numba.patch new file mode 100644 index 00000000000..d30d0aa5b4b --- /dev/null +++ b/easybuild/easyconfigs/c/CellRank/cellrank-1.4.0_numba.patch @@ -0,0 +1,30 @@ +# numba <0.53.0 restriction were made due to the bug in umap-learn, see: +# https://github.com/theislab/cellrank/commit/e5c6191ac50401ecda5c46ff5e9e92a86d6f3769#diff-2c9c11d26b09b8afde329980309d967121543a456e4592c76886a20b5cf56c90L8-L9 +# Since this fixed in scVelo-0.2.3-foss-2021a.eb, see: +# https://github.com/easybuilders/easybuild-easyconfigs/pull/13398/files#diff-db270fae41d98bc2f577480759252029490fb0d9518d59b8fd3b0f13b0e2b820R1-R17 +# This limit can be safely fifted +# July 7th 2021 by B. Hajgato (UGent) +diff -ru cellrank-1.4.0.orig/cellrank.egg-info/requires.txt cellrank-1.4.0/cellrank.egg-info/requires.txt +--- cellrank-1.4.0.orig/cellrank.egg-info/requires.txt 2021-06-30 17:48:49.000000000 +0200 ++++ cellrank-1.4.0/cellrank.egg-info/requires.txt 2021-07-09 20:15:21.756925337 +0200 +@@ -2,7 +2,7 @@ + joblib>=0.13.1 + matplotlib>=3.3.0 + networkx>=2.2 +-numba<0.53.0,>=0.51.0 ++numba>=0.51.0 + numpy>=1.2.0 + pandas>=1.2.0 + pygam>=0.8.0 +diff -ru cellrank-1.4.0.orig/requirements.txt cellrank-1.4.0/requirements.txt +--- cellrank-1.4.0.orig/requirements.txt 2021-06-30 17:48:33.000000000 +0200 ++++ cellrank-1.4.0/requirements.txt 2021-07-09 20:15:32.333795389 +0200 +@@ -2,7 +2,7 @@ + joblib>=0.13.1 + matplotlib>=3.3.0 + networkx>=2.2 +-numba>=0.51.0,<0.53.0 ++numba>=0.51.0 + numpy>=1.2.0 + pandas>=1.2.0 + pygam>=0.8.0 From 1bc8c00cffc56e174861ae805104ac59dd58fe8e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 9 Jul 2021 21:09:01 +0200 Subject: [PATCH 0356/9987] remove download_dep_fail --- easybuild/easyconfigs/c/CellRank/CellRank-1.4.0-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CellRank/CellRank-1.4.0-foss-2021a.eb b/easybuild/easyconfigs/c/CellRank/CellRank-1.4.0-foss-2021a.eb index 00b992b9580..c9d9078d5eb 100644 --- a/easybuild/easyconfigs/c/CellRank/CellRank-1.4.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/CellRank/CellRank-1.4.0-foss-2021a.eb @@ -22,7 +22,6 @@ dependencies = [ ('typing-extensions', '3.10.0.0'), ] -download_dep_fail = True use_pip = True exts_list = [ From ae871462ff574ed5385e1e9e62a5cf99e1ca17f3 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sat, 10 Jul 2021 10:23:12 +0200 Subject: [PATCH 0357/9987] MDAnalysis: tqdm is adapted to foss 2020b requirements --- .../easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb index fb11a6330fc..62cbd2a4191 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-1.1.1-foss-2020b.eb @@ -18,7 +18,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('Biopython', '1.78'), ('networkx', '2.5'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ] use_pip = True From dc30c406c6f03c3c892cd0d4570fcd786f2f2257 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sat, 10 Jul 2021 19:23:04 +0200 Subject: [PATCH 0358/9987] networkx, foss-2021a: bumps version to 2.6.1 --- .../matplotlib/matplotlib-3.4.2-foss-2021a.eb | 54 +++++++++++++++++++ ...-2021a.eb => networkx-2.6.1-foss-2021a.eb} | 12 ++--- 2 files changed, 59 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb rename easybuild/easyconfigs/n/networkx/{networkx-2.5.1-foss-2021a.eb => networkx-2.6.1-foss-2021a.eb} (67%) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb new file mode 100644 index 00000000000..18ceae7ed0f --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.4.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('libpng', '1.6.37'), + ('freetype', '2.10.4'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.1', { + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'checksums': ['d8d994cefdff9aaba45166eb3de4f5211adb4accac85cbf97137e98f26ea0219'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/n/networkx/networkx-2.6.1-foss-2021a.eb similarity index 67% rename from easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb rename to easybuild/easyconfigs/n/networkx/networkx-2.6.1-foss-2021a.eb index 9cd40fabe2b..6d3159169d0 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.6.1-foss-2021a.eb @@ -4,7 +4,7 @@ easyblock = 'PythonPackage' name = 'networkx' -version = '2.5.1' +version = '2.6.1' homepage = 'https://pypi.python.org/pypi/networkx' description = """NetworkX is a Python package for the creation, manipulation, @@ -13,16 +13,14 @@ and study of the structure, dynamics, and functions of complex networks.""" toolchain = {'name': 'foss', 'version': '2021a'} sources = [SOURCE_TAR_GZ] -patches = ['%(name)s-%(version)s_decorator.patch'] -checksums = [ - '109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a', # networkx-2.5.1.tar.gz - # networkx-2.5.1_decorator.patch - '85001802a7d8fe3244b83ce0e0f8c9066708c8d2b3e20fad023dfe3b06954d1e', -] +checksums = ['bf4cb807d1bccf1593c7d0742d9127d9e04e021867299082658b0fc3907924e8'] + +#patches = ['%(name)s-%(version)s_decorator.patch'] dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), # required for numpy, scipy, ... + ('matplotlib', '3.4.2'), ] use_pip = True From 5501c64911b803e03ed9a4b05d0ff3c536d6cf47 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sat, 10 Jul 2021 19:24:44 +0200 Subject: [PATCH 0359/9987] Delete networkx-2.5.1_decorator.patch --- .../n/networkx/networkx-2.5.1_decorator.patch | 21 ------------------- 1 file changed, 21 deletions(-) delete mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch b/easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch deleted file mode 100644 index ba828792c79..00000000000 --- a/easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -Naur networkx-2.5.1.orig/networkx.egg-info/requires.txt networkx-2.5.1/networkx.egg-info/requires.txt ---- networkx-2.5.1.orig/networkx.egg-info/requires.txt 2021-04-04 00:20:57.000000000 +0200 -+++ networkx-2.5.1/networkx.egg-info/requires.txt 2021-06-27 10:48:45.453840000 +0200 -@@ -1,4 +1,4 @@ --decorator<5,>=4.3 -+decorator>=5.0.7,<6 - - [all] - numpy -diff -Naur networkx-2.5.1.orig/setup.py networkx-2.5.1/setup.py ---- networkx-2.5.1.orig/setup.py 2021-04-04 00:01:13.000000000 +0200 -+++ networkx-2.5.1/setup.py 2021-06-27 11:02:45.537344000 +0200 -@@ -124,7 +124,7 @@ - "networkx.utils": ["tests/*.py"], - } - --install_requires = ["decorator>=4.3,<5"] -+install_requires = ["decorator>=5.0.7,<6"] - extras_require = { - "all": [ - "numpy", From 95638fe65d422f25d42de75bfb7c929de8638c20 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sat, 10 Jul 2021 19:41:22 +0200 Subject: [PATCH 0360/9987] networkx: remove the comment --- easybuild/easyconfigs/n/networkx/networkx-2.6.1-foss-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.6.1-foss-2021a.eb b/easybuild/easyconfigs/n/networkx/networkx-2.6.1-foss-2021a.eb index 6d3159169d0..babff3abde7 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.6.1-foss-2021a.eb @@ -15,8 +15,6 @@ toolchain = {'name': 'foss', 'version': '2021a'} sources = [SOURCE_TAR_GZ] checksums = ['bf4cb807d1bccf1593c7d0742d9127d9e04e021867299082658b0fc3907924e8'] -#patches = ['%(name)s-%(version)s_decorator.patch'] - dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), # required for numpy, scipy, ... From b9993a9d7951db1c1ee833609c63848951db9a53 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 11 Jul 2021 00:40:00 +0200 Subject: [PATCH 0361/9987] Fix incorrect define name in updated patch --- .../easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb index b8977cb73d5..8ca69511fe5 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -16,7 +16,7 @@ sources = [SOURCE_TAR_GZ] patches = ['magma-2.6.0_allow-all-sms.patch'] checksums = [ '50cdd384f44f06a34469e7125f8b2ffae13c1975d373c3f1510d91be2b7638ec', # magma-2.6.0.tar.gz - '6dbe0f5fe1a9f39dce9e081d98df86ab60577509b41255a99b69842c3bd77d35', # magma-2.6.0_allow-all-sms.patch + '9a0571c63756391d99da5dca3fe45d23e89ffdbbc62ca99db4dab10e77158daa', # magma-2.6.0_allow-all-sms.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch b/easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch index 2508e51a40f..1c2dc1aee21 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch +++ b/easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch @@ -6,7 +6,7 @@ Author: Alexander Grund (TU Dresden) Updated to 2.6.0: micketeer@gmail.com --- CMakeLists.txt.orig 2021-07-06 17:02:37.125227748 +0200 -+++ CMakeLists.txt 2021-07-06 17:40:06.597705725 +0200 ++++ CMakeLists.txt 2021-07-06 18:43:13.400804473 +0200 @@ -124,14 +124,6 @@ #message( STATUS " CUDA_CUBLAS_LIBRARIES: ${CUDA_CUBLAS_LIBRARIES}" ) include_directories( ${CUDA_INCLUDE_DIRS} ) @@ -223,8 +223,8 @@ Updated to 2.6.0: micketeer@gmail.com + set( NV_COMP -gencode arch=compute_${MAX_SM},code=compute_${MAX_SM} ) + + list( APPEND CUDA_NVCC_FLAGS -Xcompiler -fPIC ${NV_SM} ${NV_COMP} ${FORTRAN_CONVENTION} ) -+ add_definitions( -DMIN_CUDA_ARCH=${MIN_ARCH} ) + add_definitions( -DMAGMA_HAVE_CUDA=1 ) ++ add_definitions( -DMAGMA_CUDA_ARCH_MIN=${MIN_ARCH} ) message( STATUS "Define -DMAGMA_HAVE_CUDA -DMAGMA_CUDA_ARCH_MIN=${MIN_ARCH}" ) else() message( STATUS "Could not find CUDA" ) From c0961867b971e35e5da84eaae818db7b521a3b1c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 11 Jul 2021 00:42:25 +0200 Subject: [PATCH 0362/9987] Update NCCL version --- ...DA-11.3.1.eb => NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/n/NCCL/{NCCL-2.9.9-GCCcore-10.3.0-CUDA-11.3.1.eb => NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb} (85%) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb similarity index 85% rename from easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-GCCcore-10.3.0-CUDA-11.3.1.eb rename to easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb index 35fc34249b3..d24e1b214b6 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -1,5 +1,5 @@ name = 'NCCL' -version = '2.9.9' +version = '2.10.3' versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://developer.nvidia.com/nccl' @@ -11,7 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['01629a1bdadbadb2828e26023ba7685bbc07678468cb7df63cc96460f5337e08'] +checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] builddependencies = [('binutils', '2.36.1')] From d0546114ad3c453652df6439a3d602c440e8d8f2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 11 Jul 2021 02:26:18 +0200 Subject: [PATCH 0363/9987] use orcaarch template in ORCA v5.0.0 easyconfigs --- .../easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb | 5 +++-- easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb index b8e0ff3f174..b370a8dccea 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb @@ -13,8 +13,9 @@ effects.""" toolchain = {'name': 'gompi', 'version': '2021a'} -# Static binaries of ORCA dynamically linking to OpenMPI -sources = ['%%(namelower)s_%s_linux_x86-64_openmpi411_part%s.tar.xz' % (version.replace('.', '_'), p) +# Static build of ORCA: download from https://orcaforum.kofo.mpg.de +# OpenMPI is dynamically linked +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_openmpi411_part%s.tar.xz' % (version.replace('.', '_'), p) for p in range(1, 5)] checksums = [ # orca_5_0_0_linux_x86-64_openmpi411_part1.tar.xz diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a.eb index 2db15bd998b..43698faa090 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a.eb @@ -12,8 +12,9 @@ effects.""" toolchain = {'name': 'gompi', 'version': '2021a'} -# ORCA binaries (mostly) dynamically linked (it has SCALAPACK, OpenBLAS embedded) -sources = ['%%(namelower)s_%s_linux_x86-64_shared_openmpi411.tar.xz' % version.replace('.', '_')] +# Shared build of ORCA: download from https://orcaforum.kofo.mpg.de +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi411.tar.xz' % version.replace('.', '_')] checksums = [ # orca_5_0_0_linux_x86-64_shared_openmpi411.tar.xz '4e6dc3fca2f1bc1f98af60413fe1dd13baa7aa3b2e197754c40826167d2bcf56', From 739967ef3fcb02e28fad10fd29cff396784d2368 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 11 Jul 2021 13:33:46 +0100 Subject: [PATCH 0364/9987] patch out __asm__ use in ctffind to avoid build failure on ppc64le --- .../c/ctffind/ctffind-4.1.14-foss-2019b.eb | 6 +++++- .../c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb | 6 +++++- .../c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb | 6 +++++- .../c/ctffind/ctffind-4.1.14_asm-fix.patch | 17 +++++++++++++++++ 4 files changed, 32 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_asm-fix.patch diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb index 9d4f7394fad..33e59b6b429 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb @@ -18,7 +18,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5'] +patches = ['%(name)s-%(version)s_asm-fix.patch'] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb index 0df2cde3c70..4a09018d4d9 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb @@ -18,7 +18,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5'] +patches = ['%(name)s-%(version)s_asm-fix.patch'] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb index e011de44edf..234319daa15 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb @@ -18,7 +18,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5'] +patches = ['%(name)s-%(version)s_asm-fix.patch'] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_asm-fix.patch b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_asm-fix.patch new file mode 100644 index 00000000000..073e3e5f372 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_asm-fix.patch @@ -0,0 +1,17 @@ +Only use __asm__ on x86 - see https://grigoriefflab.umassmed.edu/comment/1703#comment-1703 +Patch added by Simon Branford (University of Birmingham) +--- src/core/matrix.cpp.orig 2021-07-10 19:11:51.226608000 +0100 ++++ src/core/matrix.cpp 2021-07-10 19:12:09.421456198 +0100 +@@ -4,7 +4,11 @@ + // think i got it from a book i had about game programming in c.. it's probably slower than what the compiler would do these days. + + #define AL_PI 3.14159265358979323846 +-#define _AL_SINCOS(x, s, c) __asm__ ("fsincos" : "=t" (c), "=u" (s) : "0" (x)) ++#if defined(__i386__) || defined(__x86_64__) ++#define _AL_SINCOS(x, s, c) __asm__ ("fsincos" : "=t" (c), "=u" (s) : "0" (x)) ++#else ++#define _AL_SINCOS(x, s, c) s = sinf(x); c = cosf(x); ++#endif + #define FLOATSINCOS(x, s, c) _AL_SINCOS((x) * AL_PI / 128.0, s ,c) + + #define MAKE_ROTATION_f(x, y, z) \ From 8afaa0243177e12f642f5b8f3324f04e793107c6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 11 Jul 2021 13:43:50 +0100 Subject: [PATCH 0365/9987] Disable building man pages in Gdk-Pixbuf --- .../easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb | 2 +- .../easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.2-GCCcore-8.3.0.eb | 2 +- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb index a394b340004..6358948ab16 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.1-GCCcore-8.2.0.eb @@ -38,7 +38,7 @@ dependencies = [ ] configopts = "--buildtype=release --default-library=both " -configopts += "-Dgio_sniffing=false -Dgir=true " +configopts += "-Dgio_sniffing=false -Dgir=true -Dman=false " sanity_check_paths = { 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.2-GCCcore-8.3.0.eb index f9a6e400916..de84656767c 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.2-GCCcore-8.3.0.eb @@ -38,7 +38,7 @@ dependencies = [ ] configopts = "--buildtype=release --default-library=both " -configopts += "-Dgio_sniffing=false -Dgir=true " +configopts += "-Dgio_sniffing=false -Dgir=true -Dman=false " sanity_check_paths = { 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb index 2d4114f9681..84d05664734 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb @@ -34,7 +34,7 @@ dependencies = [ ] configopts = "--buildtype=release --default-library=both " -configopts += "-Dgio_sniffing=false -Dgir=true " +configopts += "-Dgio_sniffing=false -Dgir=true -Dman=false " sanity_check_paths = { 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb index 933fe2247c5..a7901baed20 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-9.3.0.eb @@ -36,7 +36,7 @@ dependencies = [ ] configopts = "--buildtype=release --default-library=both " -configopts += "-Dgio_sniffing=false -Dgir=true " +configopts += "-Dgio_sniffing=false -Dgir=true -Dman=false " sanity_check_paths = { 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], From 81840587735f8816efdbf0bbb37bb9435805943e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 11 Jul 2021 20:29:32 +0200 Subject: [PATCH 0366/9987] adding easyconfigs: gpustat-0.6.0-GCCcore-10.3.0.eb --- .../g/gpustat/gpustat-0.6.0-GCCcore-10.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8c5a4eb5125 --- /dev/null +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'gpustat' +version = '0.6.0' + +homepage = 'https://github.com/wookayin/gpustat' +description = 'dstat-like utilization monitor for NVIDIA GPUs' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +# This software works directly against the nvidia drivers and doesn't require CUDA. +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True + +exts_list = [ + ('blessings', '1.7', { + 'checksums': ['98e5854d805f50a5b58ac2333411b0482516a8210f23f43308baeb58d77c157d'], + }), + ('nvidia-ml-py3', '7.352.0', { + 'modulename': 'pynvml', + 'checksums': ['390f02919ee9d73fe63a98c73101061a6b37fa694a793abf56673320f1f51277'], + }), + (name, version, { + 'checksums': ['f69135080b2668b662822633312c2180002c10111597af9631bb02e042755b6c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gpustat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gpustat --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From 592db62c8f52847d4435ce0cbd07ced34f2eb1d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 11 Jul 2021 20:44:18 +0200 Subject: [PATCH 0367/9987] add binutils builddep --- easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-GCCcore-10.3.0.eb index 8c5a4eb5125..6b59c0217ec 100644 --- a/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/gpustat/gpustat-0.6.0-GCCcore-10.3.0.eb @@ -8,6 +8,8 @@ description = 'dstat-like utilization monitor for NVIDIA GPUs' toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +builddependencies = [('binutils', '2.36.1')] + # This software works directly against the nvidia drivers and doesn't require CUDA. dependencies = [ ('Python', '3.9.5'), From 1e925488066468c4279d9a62d8afd16c7635ccde Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 11 Jul 2021 21:39:59 +0200 Subject: [PATCH 0368/9987] adding easyconfigs: wxWidgets-3.1.5-GCC-10.3.0.eb, GST-plugins-base-1.18.4-GCC-10.3.0.eb, GStreamer-1.18.4-GCC-10.3.0.eb, jbigkit-2.1-GCCcore-10.3.0.eb --- .../GST-plugins-base-1.18.4-GCC-10.3.0.eb | 43 ++++++++++++ .../GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb | 44 ++++++++++++ .../j/jbigkit/jbigkit-2.1-GCCcore-10.3.0.eb | 46 ++++++++++++ .../w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb | 70 +++++++++++++++++++ 4 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..e6f5b7d514d --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-base' +version = '1.18.4' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['29e53229a84d01d722f6f6db13087231cdf6113dd85c25746b9b58c3d68e8323'] + +builddependencies = [ + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('Bison', '3.7.6'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('GLib', '2.68.2'), + ('GTK+', '3.24.29'), + ('GStreamer', '1.18.4'), + ('Gdk-Pixbuf', '2.42.6'), + ('X11', '20210518'), + ('Mesa', '21.1.1'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..f782b1ed825 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GStreamer' +version = '1.18.4' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] + +builddependencies = [ + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('GMP', '6.2.1'), + ('GSL', '2.7'), + ('GLib', '2.68.2'), + ('GTK+', '3.24.29'), + ('libunwind', '1.4.0'), +] + +configopts = '-Dlibdw=disabled ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..cad518c7e6f --- /dev/null +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'jbigkit' +version = '2.1' + +homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' + +description = """JBIG-KIT is a software implementation of the JBIG1 data + compression standard (ITU-T T.82), which was designed for bi-level image + data, such as scanned documents.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_libpath.patch', + '%(name)s-%(version)s_shlib.patch', +] +checksums = [ + 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932', # jbigkit-2.1.tar.gz + '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce', # jbigkit-2.1_libpath.patch + '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696', # jbigkit-2.1_shlib.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +files_to_copy = [ + (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), + (['libjbig/jbig85.h', 'libjbig/jbig.h'], 'include'), + (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libjbig85.a', 'lib/libjbig.a', + 'bin/pbmtojbg', 'bin/jbgtopbm', + 'include/jbig.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb new file mode 100644 index 00000000000..435e094bea0 --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb @@ -0,0 +1,70 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.1.5' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/wxWidgets/wxWidgets/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e8fd5f9fbff864562aa4d9c094f898c97f5e1274c90f25beb0bfd5cb61319dea'] + +builddependencies = [ + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('Python', '3.9.5'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.2.0'), + ('expat', '2.2.9'), + ('GTK+', '3.24.29'), + ('X11', '20210518'), + ('Mesa', '21.1.1'), + ('libGLU', '9.0.1'), + ('SDL2', '2.0.14'), + ('cairo', '1.16.0'), + ('GST-plugins-base', '1.18.4'), + ('GLib', '2.68.2'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webkit --disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From f44bf3a5fd303f566ee73ee9bcce9074e745a787 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 12 Jul 2021 11:13:29 +0200 Subject: [PATCH 0369/9987] adding easyconfigs: lwgrp-1.0.3-gompi-2020b.eb --- .../l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb diff --git a/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb new file mode 100644 index 00000000000..10d0197ebdb --- /dev/null +++ b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.3-gompi-2020b.eb @@ -0,0 +1,36 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'lwgrp' +version = '1.0.3' + +homepage = 'https://github.com/LLNL/lwgrp' +description = """The light-weight group library defines data structures and collective operations to +group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators +when the overhead of communicator creation is too costly. For example, certain sorting algorithms +recursively divide processes into subgroups as the sort algorithm progresses. These groups may be +different with each invocation, so that it is inefficient to create and destroy communicators during +the sort routine.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['650ab50d53f9af94d1c0dc0f8feb17b6692a8e1f01f9b6effafbb8a822f10eb7'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['share/%(name)s'], +} + +moduleclass = 'lib' From 0391d62358ae466ea09d8da7e2a2f28240ee80a2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Jul 2021 14:50:19 +0200 Subject: [PATCH 0370/9987] adding easyconfigs: Java-16.0.1.eb, Java-16.eb --- easybuild/easyconfigs/j/Java/Java-16.0.1.eb | 14 ++++++++++++++ easybuild/easyconfigs/j/Java/Java-16.eb | 18 ++++++++++++++++++ 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-16.0.1.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-16.eb diff --git a/easybuild/easyconfigs/j/Java/Java-16.0.1.eb b/easybuild/easyconfigs/j/Java/Java-16.0.1.eb new file mode 100644 index 00000000000..1f0671733fc --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-16.0.1.eb @@ -0,0 +1,14 @@ +name = 'Java' +version = '16.0.1' + +homepage = 'https://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +source_urls = ['https://download.java.net/java/GA/jdk16.0.1/7147401fd7354114ac51ef3e1328291f/9/GPL'] +sources = ['openjdk-%(version)s_linux-x64_bin.tar.gz'] +checksums = ['b1198ffffb7d26a3fdedc0fa599f60a0d12aa60da1714b56c1defbce95d8b235'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-16.eb b/easybuild/easyconfigs/j/Java/Java-16.eb new file mode 100644 index 00000000000..96c7eba892f --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-16.eb @@ -0,0 +1,18 @@ +# Contribution from the Crick HPC team / UL HPC Team +# uploaded by J. Sassmannshausen +# updated to version 202 + +easyblock = 'ModuleRC' + +name = 'Java' +version = '16' + +homepage = 'https://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +dependencies = [('Java', '%(version)s.0.1')] + +moduleclass = 'lang' From 94971e040a87511aaff1f6e4482dcc2e6951a917 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Jul 2021 15:02:23 +0200 Subject: [PATCH 0371/9987] Add ARM version --- easybuild/easyconfigs/j/Java/Java-16.0.1.eb | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/Java/Java-16.0.1.eb b/easybuild/easyconfigs/j/Java/Java-16.0.1.eb index 1f0671733fc..02f8adce5e5 100644 --- a/easybuild/easyconfigs/j/Java/Java-16.0.1.eb +++ b/easybuild/easyconfigs/j/Java/Java-16.0.1.eb @@ -7,8 +7,17 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM +local_tarball_tmpl = 'openjdk-%%(version)s_linux-%s_bin.tar.gz' + source_urls = ['https://download.java.net/java/GA/jdk16.0.1/7147401fd7354114ac51ef3e1328291f/9/GPL'] -sources = ['openjdk-%(version)s_linux-x64_bin.tar.gz'] -checksums = ['b1198ffffb7d26a3fdedc0fa599f60a0d12aa60da1714b56c1defbce95d8b235'] +sources = [local_tarball_tmpl % '%(jdkarch)s'] +checksums = [ + { + local_tarball_tmpl % 'x64': + 'b1198ffffb7d26a3fdedc0fa599f60a0d12aa60da1714b56c1defbce95d8b235', + local_tarball_tmpl % 'aarch64': + '602b005074777df2a0b4306e20152a6446803edd87ccbab95b2f313c4d9be6ba', + } +] moduleclass = 'lang' From b95808d7d9bbaa5bb306abaf5836270d359f07da Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Jul 2021 16:44:58 +0200 Subject: [PATCH 0372/9987] Remove comment --- easybuild/easyconfigs/j/Java/Java-16.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/j/Java/Java-16.eb b/easybuild/easyconfigs/j/Java/Java-16.eb index 96c7eba892f..6501276ce44 100644 --- a/easybuild/easyconfigs/j/Java/Java-16.eb +++ b/easybuild/easyconfigs/j/Java/Java-16.eb @@ -1,7 +1,3 @@ -# Contribution from the Crick HPC team / UL HPC Team -# uploaded by J. Sassmannshausen -# updated to version 202 - easyblock = 'ModuleRC' name = 'Java' From f0f1b2e55c99aedce2a27806a6eae27e1a1a2254 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 13 Jul 2021 09:40:14 +0200 Subject: [PATCH 0373/9987] {bio}[gompi/2020b] barrnap --- .../b/barrnap/barrnap-0.9-gompi-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2020b.eb diff --git a/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2020b.eb b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2020b.eb new file mode 100644 index 00000000000..42ca6abb5ed --- /dev/null +++ b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'barrnap' +version = '0.9' + +homepage = 'https://github.com/tseemann/barrnap' +description = "Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes." + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://github.com/tseemann/barrnap/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['36c27cd4350531d98b3b2fb7d294a2d35c15b7365771476456d7873ba33cce15'] + +dependencies = [ + ('Perl', '5.32.0'), + ('HMMER', '3.3.2'), + ('BEDTools', '2.30.0'), +] + +sanity_check_paths = { + 'files': ['bin/barrnap'], + 'dirs': [], +} + +sanity_check_commands = ["barrnap --help"] + +moduleclass = 'bio' From da5639ff546518f8d74a64f1dc39f0cec71eee60 Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Tue, 13 Jul 2021 10:23:12 +0200 Subject: [PATCH 0374/9987] Clarify that MCR and FreeSurfer versions are linked --- .../f/FreeSurfer/FreeSurfer-7.1.1-centos6_x86_64.eb | 3 ++- .../f/FreeSurfer/FreeSurfer-7.1.1-centos7_x86_64.eb | 3 ++- .../f/FreeSurfer/FreeSurfer-7.1.1-centos8_x86_64.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos6_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos6_x86_64.eb index 6012cc86501..3ff7305bc66 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos6_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos6_x86_64.eb @@ -13,7 +13,8 @@ source_urls = [ 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' ] -# Fresurfer > v7 uses MCR 8.4 (R2014b) +# The FreeSurfer and MCR versions are linked. Fresurfer > v7 uses MCR 8.4 (R2014b). +# Please check the documentation for the latest linked versions: # https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime sources = [ '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos7_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos7_x86_64.eb index 23b4136ad44..e0c851d4607 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos7_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos7_x86_64.eb @@ -13,7 +13,8 @@ source_urls = [ 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' ] -# Fresurfer > v7 uses MCR 8.4 (R2014b) +# The FreeSurfer and MCR versions are linked. Fresurfer > v7 uses MCR 8.4 (R2014b). +# Please check the documentation for the latest linked versions: # https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime sources = [ '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos8_x86_64.eb index 53008321d1a..0d0830a6309 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos8_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.1.1-centos8_x86_64.eb @@ -21,7 +21,8 @@ checksums = [ '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz ] -# Fresurfer > v7 uses MCR 8.4 (R2014b) +# The FreeSurfer and MCR versions are linked. Fresurfer > v7 uses MCR 8.4 (R2014b). +# Please check the documentation for the latest linked versions: # https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] From 1316c60d548ee4b7473d0ee09f80fb30ce994260 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 13 Jul 2021 11:06:08 +0200 Subject: [PATCH 0375/9987] prokka needs Bio-Search-hmmer, but it is not part of BioPerl>1.7.3 --- .../Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb | 28 +++++++++++++++++++ .../p/prokka/prokka-1.14.5-gompi-2020b.eb | 1 + 2 files changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb new file mode 100644 index 00000000000..ae7154fd3d3 --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.32.0'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/auto'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb index 28077ad116d..0ba029a4f1a 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb @@ -23,6 +23,7 @@ dependencies = [ ('BioPerl', '1.7.8'), ('BLAST+', '2.11.0'), ('Java', '11', '', True), + ('Bio-SearchIO-hmmer', '1.7.3'), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', From d5097fc56bc0f0c00d3e47fef90cc6e53e9b2b8f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 13 Jul 2021 11:36:09 +0200 Subject: [PATCH 0376/9987] {bio}[{foss,fosscuda}/2020b] mhcnuggets 2.3 --- .../m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb | 28 +++++++++++++++++++ .../mhcnuggets-2.3-fosscuda-2020b.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb new file mode 100644 index 00000000000..25f8d885bda --- /dev/null +++ b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'mhcnuggets' +version = '2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/KarchinLab/mhcnuggets' +description = 'MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II.' + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'KarchinLab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5b0a8771e851e5d47c5f06c5b4a4ace218660c837b5bb527d8fa087d6dd55906'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('Keras', '2.4.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb new file mode 100644 index 00000000000..4da712bc5dd --- /dev/null +++ b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'mhcnuggets' +version = '2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/KarchinLab/mhcnuggets' +description = 'MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II.' + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +github_account = 'KarchinLab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5b0a8771e851e5d47c5f06c5b4a4ace218660c837b5bb527d8fa087d6dd55906'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('Keras', '2.4.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 3715e8a2c6c0931c87f38b4e5713ce14a23f9cae Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 13 Jul 2021 11:52:14 +0200 Subject: [PATCH 0377/9987] adding easyconfigs: OpenBLAS-0.3.16-GCC-10.3.0.eb --- .../o/OpenBLAS/OpenBLAS-0.3.16-GCC-10.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.16-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.16-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.16-GCC-10.3.0.eb new file mode 100644 index 00000000000..b8fe20b165c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.16-GCC-10.3.0.eb @@ -0,0 +1,28 @@ +name = 'OpenBLAS' +version = '0.3.16' + +homepage = 'https://xianyi.github.com/OpenBLAS/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), +] +checksums = [ + 'fa19263c5732af46d40d3adeec0b2c77951b67687e670fb6ba52ea3950460d79', # v0.3.16.tar.gz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From 83ad65a4676ea9146e950cbec873a6fdd4bd1b2a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 13 Jul 2021 12:02:28 +0200 Subject: [PATCH 0378/9987] remove versionsuffix --- easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb | 1 - .../easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb index 25f8d885bda..e03e3bf7310 100644 --- a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-foss-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonPackage' name = 'mhcnuggets' version = '2.3' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/KarchinLab/mhcnuggets' description = 'MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II.' diff --git a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb index 4da712bc5dd..7bca8c2f08c 100644 --- a/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/mhcnuggets/mhcnuggets-2.3-fosscuda-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonPackage' name = 'mhcnuggets' version = '2.3' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/KarchinLab/mhcnuggets' description = 'MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II.' From b2b28ec8fedac09d1715df8d0b470db75e35ed5f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 13 Jul 2021 12:44:14 +0200 Subject: [PATCH 0379/9987] Add 1 more --- easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb index 016bc5c4749..d26f4fc3ad2 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb @@ -97,6 +97,9 @@ exts_list = [ ('ecdsa', '0.13', { 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), + ('cffi', '1.11.5', { + 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], + }), ('cryptography', '1.4', { 'checksums': ['bb149540ed90c4b2171bf694fe6991d6331bc149ae623c8ff419324f4222d128'], }), From 20bb47aa92591d1536ce10cd42751d285ccd60ba Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 13 Jul 2021 13:29:05 +0200 Subject: [PATCH 0380/9987] Add pycparser --- easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb index d26f4fc3ad2..1218aa2108d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb @@ -97,6 +97,9 @@ exts_list = [ ('ecdsa', '0.13', { 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), + ('pycparser', '2.18', { + 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], + }), ('cffi', '1.11.5', { 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), From 629aff5c6c1d80ee7305d610bc366baf99b68c0d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 13 Jul 2021 13:32:58 +0200 Subject: [PATCH 0381/9987] Move archive files to correct folder --- .../__archive__/{__archive__/i => i/ictce}/ictce-5.2.0.eb | 0 .../__archive__/{__archive__/i => i/ictce}/ictce-5.3.0.eb | 0 .../__archive__/{__archive__/i => i/ictce}/ictce-5.4.0.eb | 0 .../__archive__/{__archive__/i => i/ictce}/ictce-5.5.0.eb | 0 .../__archive__/{__archive__/i => i/ictce}/ictce-6.1.5.eb | 0 .../__archive__/{__archive__/i => i/ictce}/ictce-6.2.5.eb | 0 .../__archive__/{__archive__/i => i/ictce}/ictce-7.1.2.eb | 0 .../__archive__/{__archive__/i => i/ictce}/ictce-7.3.5.eb | 0 .../__archive__/{__archive__/i => i/intel}/intel-2014.06.eb | 0 .../__archive__/{__archive__/i => i/intel}/intel-2014.10.eb | 0 .../__archive__/{__archive__/i => i/intel}/intel-2014.11.eb | 0 .../__archive__/{__archive__/i => i/intel}/intel-2014b.eb | 0 .../__archive__/{__archive__/i => i/intel}/intel-2015.02.eb | 0 .../__archive__/{__archive__/i => i/intel}/intel-2015.08.eb | 0 .../__archive__/{__archive__/i => i/intel}/intel-2015a.eb | 0 .../__archive__/{__archive__/i => i/intel}/intel-2015b.eb | 0 16 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/__archive__/{__archive__/i => i/ictce}/ictce-5.2.0.eb (100%) rename easybuild/easyconfigs/__archive__/{__archive__/i => i/ictce}/ictce-5.3.0.eb (100%) rename easybuild/easyconfigs/__archive__/{__archive__/i => i/ictce}/ictce-5.4.0.eb (100%) rename easybuild/easyconfigs/__archive__/{__archive__/i => i/ictce}/ictce-5.5.0.eb (100%) rename easybuild/easyconfigs/__archive__/{__archive__/i => i/ictce}/ictce-6.1.5.eb (100%) rename easybuild/easyconfigs/__archive__/{__archive__/i => i/ictce}/ictce-6.2.5.eb (100%) rename easybuild/easyconfigs/__archive__/{__archive__/i => i/ictce}/ictce-7.1.2.eb (100%) rename easybuild/easyconfigs/__archive__/{__archive__/i => i/ictce}/ictce-7.3.5.eb (100%) rename easybuild/easyconfigs/__archive__/{__archive__/i => i/intel}/intel-2014.06.eb (100%) rename 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a/easybuild/easyconfigs/__archive__/__archive__/i/ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/i/ictce/ictce-5.3.0.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/ictce-5.3.0.eb rename to easybuild/easyconfigs/__archive__/i/ictce/ictce-5.3.0.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/ictce-5.4.0.eb b/easybuild/easyconfigs/__archive__/i/ictce/ictce-5.4.0.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/ictce-5.4.0.eb rename to easybuild/easyconfigs/__archive__/i/ictce/ictce-5.4.0.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/ictce-5.5.0.eb b/easybuild/easyconfigs/__archive__/i/ictce/ictce-5.5.0.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/ictce-5.5.0.eb rename to easybuild/easyconfigs/__archive__/i/ictce/ictce-5.5.0.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/ictce-6.1.5.eb b/easybuild/easyconfigs/__archive__/i/ictce/ictce-6.1.5.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/ictce-6.1.5.eb rename to easybuild/easyconfigs/__archive__/i/ictce/ictce-6.1.5.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/ictce-6.2.5.eb b/easybuild/easyconfigs/__archive__/i/ictce/ictce-6.2.5.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/ictce-6.2.5.eb rename to easybuild/easyconfigs/__archive__/i/ictce/ictce-6.2.5.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/ictce-7.1.2.eb b/easybuild/easyconfigs/__archive__/i/ictce/ictce-7.1.2.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/ictce-7.1.2.eb rename to easybuild/easyconfigs/__archive__/i/ictce/ictce-7.1.2.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/ictce-7.3.5.eb b/easybuild/easyconfigs/__archive__/i/ictce/ictce-7.3.5.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/ictce-7.3.5.eb rename to easybuild/easyconfigs/__archive__/i/ictce/ictce-7.3.5.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/intel-2014.06.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2014.06.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/intel-2014.06.eb rename to easybuild/easyconfigs/__archive__/i/intel/intel-2014.06.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/intel-2014.10.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2014.10.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/intel-2014.10.eb rename to easybuild/easyconfigs/__archive__/i/intel/intel-2014.10.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/intel-2014.11.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2014.11.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/intel-2014.11.eb rename to easybuild/easyconfigs/__archive__/i/intel/intel-2014.11.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/intel-2014b.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2014b.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/intel-2014b.eb rename to easybuild/easyconfigs/__archive__/i/intel/intel-2014b.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/intel-2015.02.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2015.02.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/intel-2015.02.eb rename to easybuild/easyconfigs/__archive__/i/intel/intel-2015.02.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/intel-2015.08.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2015.08.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/intel-2015.08.eb rename to easybuild/easyconfigs/__archive__/i/intel/intel-2015.08.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/intel-2015a.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2015a.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/intel-2015a.eb rename to easybuild/easyconfigs/__archive__/i/intel/intel-2015a.eb diff --git a/easybuild/easyconfigs/__archive__/__archive__/i/intel-2015b.eb b/easybuild/easyconfigs/__archive__/i/intel/intel-2015b.eb similarity index 100% rename from easybuild/easyconfigs/__archive__/__archive__/i/intel-2015b.eb rename to easybuild/easyconfigs/__archive__/i/intel/intel-2015b.eb From cce9599c2e4e76e7d5b0b94d68e66b33e08c9e48 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 13 Jul 2021 14:59:11 +0200 Subject: [PATCH 0382/9987] impi: removes commas after source and checksums --- .../i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb index 1575cd8bb2b..a46849c0a36 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb @@ -10,9 +10,9 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.3.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls= ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17947/'], +source_urls= ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17947/'] sources = ['l_mpi_oneapi_p_%(version)s.294_offline.sh'] -checksums = ['04c48f864ee4c723b1b4ca62f2bea8c04d5d7e3de19171fd62b17868bc79bc36'], +checksums = ['04c48f864ee4c723b1b4ca62f2bea8c04d5d7e3de19171fd62b17868bc79bc36'] dependencies = [('UCX', '1.10.0')] From c883c5bd53c05af70a60b921ca55c4221aae6fd6 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 13 Jul 2021 15:09:04 +0200 Subject: [PATCH 0383/9987] LLVM: depends on Python 3.9.5 bare --- easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-10.3.0.eb index dac180c1c97..6a81e472cdf 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-10.3.0.eb @@ -23,7 +23,7 @@ checksums = ['7d9a8405f557cefc5a21bf5672af73903b64749d9bc3a50322239f56f34ffddf'] builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), - ('Python', '3.9.5'), + ('Python', '3.9.5', '-bare'), ] dependencies = [ From 221357400dc81b7a1fe223ec540dc1ef0927a0a2 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 13 Jul 2021 15:14:36 +0200 Subject: [PATCH 0384/9987] impi: fixes source_urls --- .../i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb index a46849c0a36..8a736821926 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.3.0-intel-compilers-2021.3.0.eb @@ -10,7 +10,7 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2021.3.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls= ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17947/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17947'] sources = ['l_mpi_oneapi_p_%(version)s.294_offline.sh'] checksums = ['04c48f864ee4c723b1b4ca62f2bea8c04d5d7e3de19171fd62b17868bc79bc36'] From 35ff772e904a6ddbd7d03347d68f21f4d0a7e7dc Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 13 Jul 2021 15:27:40 +0200 Subject: [PATCH 0385/9987] adding easyconfigs: CubeLib-4.6-GCCcore-10.3.0.eb --- .../c/CubeLib/CubeLib-4.6-GCCcore-10.3.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..2e0efc2fe08 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.6-GCCcore-10.3.0.eb @@ -0,0 +1,56 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.6' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '36eaffa7688db8b9304c9e48ca5dc4edc2cb66538aaf48657b9b5ccd7979385b', # cubelib-4.4.4.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' From edd3cddb842fadac4b62bb54c079da41a4a97989 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 13 Jul 2021 15:45:52 +0200 Subject: [PATCH 0386/9987] adding easyconfigs: CubeWriter-4.6-GCCcore-10.3.0.eb, OPARI2-2.0.6-GCCcore-10.3.0.eb, PDT-3.25-GCCcore-10.3.0.eb --- .../CubeWriter-4.6-GCCcore-10.3.0.eb | 55 +++++++++++++++++++ .../o/OPARI2/OPARI2-2.0.6-GCCcore-10.3.0.eb | 44 +++++++++++++++ .../p/PDT/PDT-3.25-GCCcore-10.3.0.eb | 37 +++++++++++++ 3 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b75e6eab177 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.6-GCCcore-10.3.0.eb @@ -0,0 +1,55 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.6' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = [ + '99fe58ce7ab13061ebfbc360aedaecc28099a30636c5269a42c0cbaf57149aa8', # cubew-4.6.tar.gz +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..0c43647cc7f --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-10.3.0.eb @@ -0,0 +1,44 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.6' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['55972289ce66080bb48622110c3189a36e88a12917635f049b37685b9d3bbcb0'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..da323b46cc2 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +checksums = ['1037628d854edfeded3d847150d3e8fbd3774e8146407ce32f5021c80f6299be'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + + +moduleclass = 'perf' From 5e2cca4c0fcdae6a0f8587d598c6b1b434c811e0 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Tue, 13 Jul 2021 15:01:15 +0100 Subject: [PATCH 0387/9987] Suppress h5py's dependency management By default h5py's setup.py has a setup_requires for the minimum supported version of numpy (older then the one in SciPy-bundle, in some cases) based on the python interpretor version, resulting in pip attempting to fetch it during the install phase. As the dependency is already managed through easy_build, and h5py's install_requires is for any version newer than the minimum version, this change suppresses the setup_requires (using the mechanism provided by h2py for "downstream packgers - e.g. Linux distros"). --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb index 140b138358a..ed2fe2ae898 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb @@ -26,6 +26,6 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 65742d329c73b6d646261c41467f26741420a2bc Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Tue, 13 Jul 2021 15:06:09 +0100 Subject: [PATCH 0388/9987] Suppress h5py's dependency management By default h5py's setup.py has a setup_requires for the minimum supported version of numpy (older then the one in SciPy-bundle, in some cases) based on the python interpretor version, resulting in pip attempting to fetch it during the install phase. As the dependency is already managed through easy_build, and h5py's install_requires is for any version newer than the minimum version, this change suppresses the setup_requires (using the mechanism provided by h2py for "downstream packgers - e.g. Linux distros"). --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb index 59473c4bdbf..0124eaaa1e0 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb @@ -26,6 +26,6 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 8e62cc9759956e288186d233ff848fd81ad9b911 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Tue, 13 Jul 2021 15:06:31 +0100 Subject: [PATCH 0389/9987] Suppress h5py's dependency management By default h5py's setup.py has a setup_requires for the minimum supported version of numpy (older then the one in SciPy-bundle, in some cases) based on the python interpretor version, resulting in pip attempting to fetch it during the install phase. As the dependency is already managed through easy_build, and h5py's install_requires is for any version newer than the minimum version, this change suppresses the setup_requires (using the mechanism provided by h2py for "downstream packgers - e.g. Linux distros"). --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb index 591338dd644..7e0797f278a 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb @@ -26,6 +26,6 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From a10aaac559fdeaa0ee20229e8bea8139904bc19c Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Tue, 13 Jul 2021 15:07:04 +0100 Subject: [PATCH 0390/9987] Suppress h5py's dependency management By default h5py's setup.py has a setup_requires for the minimum supported version of numpy (older then the one in SciPy-bundle, in some cases) based on the python interpretor version, resulting in pip attempting to fetch it during the install phase. As the dependency is already managed through easy_build, and h5py's install_requires is for any version newer than the minimum version, this change suppresses the setup_requires (using the mechanism provided by h2py for "downstream packgers - e.g. Linux distros"). --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb index f6bb27ac98f..e53dea9b4bf 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb @@ -26,6 +26,6 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From c8e518d39f9b8592388ebc0db94bf258001680ca Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 13 Jul 2021 16:17:26 +0200 Subject: [PATCH 0391/9987] adding easyconfigs: OTF2-2.3-GCCcore-10.3.0.eb, SIONlib-1.7.6-GCCcore-10.3.0-tools.eb --- .../o/OTF2/OTF2-2.3-GCCcore-10.3.0.eb | 50 ++++++++++++++++++ .../SIONlib-1.7.6-GCCcore-10.3.0-tools.eb | 51 +++++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.3.0-tools.eb diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..65c554940e8 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.3-GCCcore-10.3.0.eb @@ -0,0 +1,50 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '2.3' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['36957428d37c40d35b6b45208f050fb5cfe23c54e874189778a24b0e9219c7e3'] + +builddependencies = [ + ('binutils', '2.36.1'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.6', '-tools'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.3.0-tools.eb new file mode 100644 index 00000000000..445daf66eb4 --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.6-GCCcore-10.3.0-tools.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.6' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +checksums = ['2c220390ef63d001f8ab02c380087187ea02ad2bfc5956e05ecaa0725a6f9942'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' From e6aafb5669233fc361a491f36006f00db9188e9a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 13 Jul 2021 16:23:52 +0200 Subject: [PATCH 0392/9987] Add more missing deps --- .../p/Python/Python-2.7.12-foss-2016b.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb index 1218aa2108d..cc5f634a3ea 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb @@ -97,6 +97,19 @@ exts_list = [ ('ecdsa', '0.13', { 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), + ('ipaddress', '1.0.22', { + 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], + }), + ('asn1crypto', '0.24.0', { + 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], + }), + ('idna', '2.7', { + 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], + }), ('pycparser', '2.18', { 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), @@ -106,6 +119,9 @@ exts_list = [ ('cryptography', '1.4', { 'checksums': ['bb149540ed90c4b2171bf694fe6991d6331bc149ae623c8ff419324f4222d128'], }), + ('pyasn1', '0.4.3', { + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), ('paramiko', '2.0.1', { 'checksums': ['261afe9246c2494e50bbeab55e50934348e91d1189803123459e0c81cda70fac'], }), From eb812ed2f02a36dc06d8886314cff75dac5d18fb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 13 Jul 2021 17:08:44 +0200 Subject: [PATCH 0393/9987] Fix dep order --- easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb index cc5f634a3ea..c0e04d1e1e3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb @@ -116,12 +116,12 @@ exts_list = [ ('cffi', '1.11.5', { 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), - ('cryptography', '1.4', { - 'checksums': ['bb149540ed90c4b2171bf694fe6991d6331bc149ae623c8ff419324f4222d128'], - }), ('pyasn1', '0.4.3', { 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], }), + ('cryptography', '1.4', { + 'checksums': ['bb149540ed90c4b2171bf694fe6991d6331bc149ae623c8ff419324f4222d128'], + }), ('paramiko', '2.0.1', { 'checksums': ['261afe9246c2494e50bbeab55e50934348e91d1189803123459e0c81cda70fac'], }), From 5321ca6fd9497f5b3da82e49937911d448c8c298 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 13 Jul 2021 18:04:33 +0200 Subject: [PATCH 0394/9987] adding easyconfigs: dtcmp-1.1.2-gompi-2020b.eb --- .../d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb diff --git a/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb new file mode 100644 index 00000000000..e2c9c89b8c0 --- /dev/null +++ b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.2-gompi-2020b.eb @@ -0,0 +1,39 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'dtcmp' +version = '1.1.2' + +homepage = 'https://github.com/LLNL/dtcmp' +description = """The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined +comparison operations to compare the values of two items which can be arbitrary MPI datatypes. +Using these comparison operations, the library provides various routines for manipulating data, +which may be distributed over the processes of an MPI communicator.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['2187897220ef6cf1be753110adcd1b78571eb8f9386d90a835b79a3f9c60f18a'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('lwgrp', '1.0.3'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-lwgrp=$EBROOTLWGRP' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT, 'share/%(name)s/README.md'], + 'dirs': [] +} + +moduleclass = 'lib' From c31a97820c0f54d62bfb620d53080a98dd414a34 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:34:35 +0100 Subject: [PATCH 0395/9987] Suppress h5py's dependency management By default h5py's setup.py has a setup_requires for the minimum supported version of numpy (older then the one in SciPy-bundle, in some cases) based on the python interpretor version, resulting in pip attempting to fetch it during the install phase. As the dependency is already managed through easy_build, and h5py's install_requires is for any version newer than the minimum version, this change suppresses the setup_requires (using the mechanism provided by h2py for "downstream packgers - e.g. Linux distros"). --- easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb index 36656ead5b2..3c0f9795669 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb @@ -26,6 +26,9 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 714a0ac46bc77e79f5c45599c461dbd2b14168c3 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:35:01 +0100 Subject: [PATCH 0396/9987] Comment explaining H5PY_SETUP_REQUIRES=0 --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb index ed2fe2ae898..b072b43d3b8 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb @@ -26,6 +26,9 @@ use_pip = True sanity_pip_check = True download_dep_fail = True +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 057d5e73c45543f294c57e158ce92a657daa7d9c Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:35:29 +0100 Subject: [PATCH 0397/9987] Comment explaining H5PY_SETUP_REQUIRES=0 --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb index 0124eaaa1e0..4110e34cc9c 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb @@ -26,6 +26,9 @@ use_pip = True sanity_pip_check = True download_dep_fail = True +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From dd3564e8f631434bd0a750f8242e4d9ae6d963d3 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:35:48 +0100 Subject: [PATCH 0398/9987] Comment explaining H5PY_SETUP_REQUIRES=0 --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb index 7e0797f278a..039b2bc3ae8 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb @@ -26,6 +26,9 @@ use_pip = True sanity_pip_check = True download_dep_fail = True +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 4ea010f12d544a79c9331592c6cced6a1ee09c4b Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:36:06 +0100 Subject: [PATCH 0399/9987] Comment explaining H5PY_SETUP_REQUIRES=0 --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb index e53dea9b4bf..87ef29ddce5 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb @@ -26,6 +26,9 @@ use_pip = True sanity_pip_check = True download_dep_fail = True +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' moduleclass = 'data' From 963bcae0ed807a3191c628fdac0b7815f0ff5692 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:38:11 +0100 Subject: [PATCH 0400/9987] Missing word in comment --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb index b072b43d3b8..3d235989290 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-foss-2020b.eb @@ -27,7 +27,7 @@ sanity_pip_check = True download_dep_fail = True # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 -# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# without this environment variable, pip will fetch the minimum numpy version h5py supports during intall, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' From 23c4d1854aa987fb3e65184cc55c872dff46f078 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:38:35 +0100 Subject: [PATCH 0401/9987] Missing word in comment --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb index 4110e34cc9c..2ccf55fe6a1 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-fosscuda-2020b.eb @@ -27,7 +27,7 @@ sanity_pip_check = True download_dep_fail = True # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 -# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' From 64c35dca135be0d168d98a314ca5af96e3b8a1bb Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:38:56 +0100 Subject: [PATCH 0402/9987] Missing word in comment --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb index 039b2bc3ae8..ab4a302e173 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intel-2020b.eb @@ -27,7 +27,7 @@ sanity_pip_check = True download_dep_fail = True # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 -# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' From de8db70c4c8827a31eb6242cdd920d1daf105f18 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:39:14 +0100 Subject: [PATCH 0403/9987] Missing word in comment --- easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb index 87ef29ddce5..f8dce1b3d79 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.1.0-intelcuda-2020b.eb @@ -27,7 +27,7 @@ sanity_pip_check = True download_dep_fail = True # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 -# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' From 29252c70d1c1305e591de8eec7066fb9b45769a5 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 14 Jul 2021 09:39:31 +0100 Subject: [PATCH 0404/9987] Missing word in comment --- easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb index 3c0f9795669..744dfd6903e 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-foss-2021a.eb @@ -27,7 +27,7 @@ sanity_pip_check = True download_dep_fail = True # h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 -# without this environment variable, pip will fetch the minimum version h5py supports during intall, +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, # even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' From ddd6de4d4a484fee90e01decc9ae7456b3b64482 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 14 Jul 2021 11:34:50 +0200 Subject: [PATCH 0405/9987] networkx 2.5.1 foss 2021a: resurrects 2.5.1 version --- ...-2021a.eb => networkx-2.5.1-foss-2021a.eb} | 10 ++++++--- .../n/networkx/networkx-2.5.1_decorator.patch | 21 +++++++++++++++++++ 2 files changed, 28 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/n/networkx/{networkx-2.6.1-foss-2021a.eb => networkx-2.5.1-foss-2021a.eb} (67%) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.6.1-foss-2021a.eb b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb similarity index 67% rename from easybuild/easyconfigs/n/networkx/networkx-2.6.1-foss-2021a.eb rename to easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb index babff3abde7..9cd40fabe2b 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-2.6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5.1-foss-2021a.eb @@ -4,7 +4,7 @@ easyblock = 'PythonPackage' name = 'networkx' -version = '2.6.1' +version = '2.5.1' homepage = 'https://pypi.python.org/pypi/networkx' description = """NetworkX is a Python package for the creation, manipulation, @@ -13,12 +13,16 @@ and study of the structure, dynamics, and functions of complex networks.""" toolchain = {'name': 'foss', 'version': '2021a'} sources = [SOURCE_TAR_GZ] -checksums = ['bf4cb807d1bccf1593c7d0742d9127d9e04e021867299082658b0fc3907924e8'] +patches = ['%(name)s-%(version)s_decorator.patch'] +checksums = [ + '109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a', # networkx-2.5.1.tar.gz + # networkx-2.5.1_decorator.patch + '85001802a7d8fe3244b83ce0e0f8c9066708c8d2b3e20fad023dfe3b06954d1e', +] dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), # required for numpy, scipy, ... - ('matplotlib', '3.4.2'), ] use_pip = True diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch b/easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch new file mode 100644 index 00000000000..ba828792c79 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.5.1_decorator.patch @@ -0,0 +1,21 @@ +diff -Naur networkx-2.5.1.orig/networkx.egg-info/requires.txt networkx-2.5.1/networkx.egg-info/requires.txt +--- networkx-2.5.1.orig/networkx.egg-info/requires.txt 2021-04-04 00:20:57.000000000 +0200 ++++ networkx-2.5.1/networkx.egg-info/requires.txt 2021-06-27 10:48:45.453840000 +0200 +@@ -1,4 +1,4 @@ +-decorator<5,>=4.3 ++decorator>=5.0.7,<6 + + [all] + numpy +diff -Naur networkx-2.5.1.orig/setup.py networkx-2.5.1/setup.py +--- networkx-2.5.1.orig/setup.py 2021-04-04 00:01:13.000000000 +0200 ++++ networkx-2.5.1/setup.py 2021-06-27 11:02:45.537344000 +0200 +@@ -124,7 +124,7 @@ + "networkx.utils": ["tests/*.py"], + } + +-install_requires = ["decorator>=4.3,<5"] ++install_requires = ["decorator>=5.0.7,<6"] + extras_require = { + "all": [ + "numpy", From 998f1e8b401da04b09950f292596438d653c37de Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 14 Jul 2021 13:17:31 +0200 Subject: [PATCH 0406/9987] adding easyconfigs: Biopython-1.79-foss-2021a.eb --- .../b/Biopython/Biopython-1.79-foss-2021a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021a.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021a.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021a.eb new file mode 100644 index 00000000000..bc0859cd2c7 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021a.eb @@ -0,0 +1,45 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.79' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['edb07eac99d3b8abd7ba56ff4bedec9263f76dfc3c3f450e7d2e2bcdecf8559b'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From f1c72d772fb2b0241b4431a2a84d9b4948df3fd4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 14 Jul 2021 14:20:44 +0200 Subject: [PATCH 0407/9987] Fix compile failure in Qt5 --- .../easyconfigs/q/Qt5/Qt5-5.8.0-foss-2017b.eb | 8 +- ...x-template-compile-failure-in-webkit.patch | 91 +++++++++++++++++++ 2 files changed, 98 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.8.0_fix-template-compile-failure-in-webkit.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-foss-2017b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-foss-2017b.eb index 1b0221b68f9..073d60e48ae 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-foss-2017b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0-foss-2017b.eb @@ -14,7 +14,13 @@ source_urls = [ 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', ] sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] -checksums = ['0f4c54386d3dbac0606a936a7145cebb7b94b0ca2d29bc001ea49642984824b6'] +patches = ['Qt5-5.8.0_fix-template-compile-failure-in-webkit.patch'] +checksums = [ + # qt-everywhere-opensource-src-5.8.0.tar.xz + '0f4c54386d3dbac0606a936a7145cebb7b94b0ca2d29bc001ea49642984824b6', + # Qt5-5.8.0_fix-template-compile-failure-in-webkit.patch + '76b98cea1b4e3422e50e22c4ab040b4b4f2004433ba1f46e53ae710664186d25', +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0_fix-template-compile-failure-in-webkit.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0_fix-template-compile-failure-in-webkit.patch new file mode 100644 index 00000000000..c9653b097a8 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.8.0_fix-template-compile-failure-in-webkit.patch @@ -0,0 +1,91 @@ +Fix a compile failure due to missing template code +Taken from https://bugs.chromium.org/p/chromium/issues/detail?id=593980 + +diff --git i/qtwebengine/src/3rdparty/chromium/third_party/WebKit/Source/core/css/resolver/StyleBuilderConverter.cpp w/qtwebengine/src/3rdparty/chromium/third_party/WebKit/Source/core/css/resolver/StyleBuilderConverter.cpp +index fd34261..bc3a58a 100644 +--- i/qtwebengine/src/3rdparty/chromium/third_party/WebKit/Source/core/css/resolver/StyleBuilderConverter.cpp ++++ w/qtwebengine/src/3rdparty/chromium/third_party/WebKit/Source/core/css/resolver/StyleBuilderConverter.cpp +@@ -638,35 +638,6 @@ StyleMotionRotation StyleBuilderConverter::convertMotionRotation(const CSSValue& + return result; + } + +-template +-Length StyleBuilderConverter::convertPositionLength(StyleResolverState& state, const CSSValue& value) +-{ +- if (value.isValuePair()) { +- const CSSValuePair& pair = toCSSValuePair(value); +- Length length = StyleBuilderConverter::convertLength(state, pair.second()); +- if (toCSSPrimitiveValue(pair.first()).getValueID() == cssValueFor0) +- return length; +- ASSERT(toCSSPrimitiveValue(pair.first()).getValueID() == cssValueFor100); +- return length.subtractFromOneHundredPercent(); +- } +- +- const CSSPrimitiveValue& primitiveValue = toCSSPrimitiveValue(value); +- if (primitiveValue.isValueID()) { +- switch (primitiveValue.getValueID()) { +- case cssValueFor0: +- return Length(0, Percent); +- case cssValueFor100: +- return Length(100, Percent); +- case CSSValueCenter: +- return Length(50, Percent); +- default: +- ASSERT_NOT_REACHED(); +- } +- } +- +- return StyleBuilderConverter::convertLength(state, primitiveValue); +-} +- + LengthPoint StyleBuilderConverter::convertPosition(StyleResolverState& state, const CSSValue& value) + { + const CSSValuePair& pair = toCSSValuePair(value); +diff --git i/qtwebengine/src/3rdparty/chromium/third_party/WebKit/Source/core/css/resolver/StyleBuilderConverter.h w/qtwebengine/src/3rdparty/chromium/third_party/WebKit/Source/core/css/resolver/StyleBuilderConverter.h +index 22fd808..9075bcc 100644 +--- i/qtwebengine/src/3rdparty/chromium/third_party/WebKit/Source/core/css/resolver/StyleBuilderConverter.h ++++ w/qtwebengine/src/3rdparty/chromium/third_party/WebKit/Source/core/css/resolver/StyleBuilderConverter.h +@@ -30,6 +30,7 @@ + #include "core/css/CSSStringValue.h" + #include "core/css/CSSValue.h" + #include "core/css/CSSValueList.h" ++#include "core/css/CSSValuePair.h" + #include "core/css/resolver/StyleResolverState.h" + #include "core/style/QuotesData.h" + #include "core/style/ShadowList.h" +@@ -118,6 +119,35 @@ T StyleBuilderConverter::convertComputedLength(StyleResolverState& state, const + return toCSSPrimitiveValue(value).computeLength(state.cssToLengthConversionData()); + } + ++template ++Length StyleBuilderConverter::convertPositionLength(StyleResolverState& state, const CSSValue& value) ++{ ++ if (value.isValuePair()) { ++ const CSSValuePair& pair = toCSSValuePair(value); ++ Length length = StyleBuilderConverter::convertLength(state, pair.second()); ++ if (toCSSPrimitiveValue(pair.first()).getValueID() == cssValueFor0) ++ return length; ++ ASSERT(toCSSPrimitiveValue(pair.first()).getValueID() == cssValueFor100); ++ return length.subtractFromOneHundredPercent(); ++ } ++ ++ const CSSPrimitiveValue& primitiveValue = toCSSPrimitiveValue(value); ++ if (primitiveValue.isValueID()) { ++ switch (primitiveValue.getValueID()) { ++ case cssValueFor0: ++ return Length(0, Percent); ++ case cssValueFor100: ++ return Length(100, Percent); ++ case CSSValueCenter: ++ return Length(50, Percent); ++ default: ++ ASSERT_NOT_REACHED(); ++ } ++ } ++ ++ return StyleBuilderConverter::convertLength(state, primitiveValue); ++} ++ + template + T StyleBuilderConverter::convertFlags(StyleResolverState& state, const CSSValue& value) + { From aa4b63061e6e2d37f25a4d433350491b26c4c321 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 14 Jul 2021 18:49:57 +0200 Subject: [PATCH 0408/9987] adding easyconfigs: libcircle-0.3-gompi-2020b.eb --- .../l/libcircle/libcircle-0.3-gompi-2020b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020b.eb diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020b.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020b.eb new file mode 100644 index 00000000000..7044e9c9fe6 --- /dev/null +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020b.eb @@ -0,0 +1,37 @@ +## +# Authors: +# * Petar Forai +# * Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'libcircle' +version = '0.3' + +homepage = 'https://github.com/hpc/libcircle/' + +description = """ + An API to provide an efficient distributed queue on a cluster. libcircle is an + API for distributing embarrassingly parallel workloads using self-stabilization. +""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://github.com/hpc/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' From 6887c0372876ccf675936d5153cc15f168d14cef Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 14 Jul 2021 19:05:12 +0200 Subject: [PATCH 0409/9987] avoid downloading and building freetype and qhull for matplotlib 3.4.2 --- .../m/matplotlib/matplotlib-3.4.2-foss-2021a.eb | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb index 6f49ab3c3f6..b8e89a53178 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb @@ -21,11 +21,19 @@ dependencies = [ ('freetype', '2.10.4'), ('Tkinter', '%(pyver)s'), ('Pillow', '8.2.0'), + ('Qhull', '2020.2') ] use_pip = True sanity_pip_check = True +# use system freetype and qhull to avoid that matplotlib downloads and builds its own copies +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' setup.cfg.template >setup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:" +_include_path += "$EBROOTQHULL/include/libqhull:${CPLUS_INCLUDE_PATH} && " + exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', @@ -38,8 +46,7 @@ exts_list = [ 'checksums': ['950a199911a8d94683a6b10321f9345d5a3a8433ec58b217ace979e18f16e248'], }), (name, version, { - 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", - 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': _fix_setup + _include_path, 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': ['d8d994cefdff9aaba45166eb3de4f5211adb4accac85cbf97137e98f26ea0219'], }), From e8fdc39ef667bc58da7c0ebf60e576914b37b1eb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 14 Jul 2021 20:20:45 +0200 Subject: [PATCH 0410/9987] Remove Panter data (as it part of the bundle) and index hmmer files --- .../InterProScan-5.52-86.0-GCCcore-10.3.0.eb | 19 +++++++------------ 1 file changed, 7 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb index 92ba3725ea5..951552ca5a1 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb @@ -14,17 +14,8 @@ source_urls = [ 'ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/%(version)s/', 'ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/data', ] -sources = [ - '%(namelower)s-%(version)s-64-bit.tar.gz', - # note: unpacked this is ~30GB, mostly 5 *.hmm files - # this data can also be provided in another location, which can be specified in interproscan.properties - # see https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload#2-installing-panther-models - 'panther-data-15.0.tar.gz', -] -checksums = [ - '50a03c47fb16c669c265e99ba05c4a8558b82047f713c9945f362d3d4be6069a', # interproscan-5.52-86.0-64-bit.tar.gz - '5907c661546cfac7e796e317ff41023f8c44e8481193b7f1f7457ffe315350d3', # panther-data-15.0.tar.gz -] +sources = ['%(namelower)s-%(version)s-64-bit.tar.gz'] +checksums = ['50a03c47fb16c669c265e99ba05c4a8558b82047f713c9945f362d3d4be6069a'] dependencies = [ ('Java', '11', '', True), @@ -33,7 +24,11 @@ dependencies = [ ('Python', '3.9.5'), ] -postinstallcmds = ["cp -a %(builddir)s/panther %(installdir)s/data"] +postinstallcmds = [ + "cd %(installdir)s && python initial_setup.py", + "cd %(installdir)s && ./interproscan.sh -b %(builddir)s/output -i test_all_appl.fasta -f tsv -dp", + "cd %(installdir)s && ./interproscan.sh -b %(builddir)s/output -i test_all_appl.fasta -f tsv", +] sanity_check_paths = { 'files': ['interproscan-%(version_major)s.jar', 'interproscan.sh', 'interproscan.properties'], From 17262564e3bef01fd265e561d9ac29d3f900adac Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 14 Jul 2021 20:27:07 +0200 Subject: [PATCH 0411/9987] remove platform spec subdir from sanity check --- .../b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb index ae7154fd3d3..b740298019d 100644 --- a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb @@ -22,7 +22,7 @@ options = {'modulename': 'Bio::SearchIO::hmmer3'} sanity_check_paths = { 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/auto'], + 'dirs': [''], } moduleclass = 'bio' From 54f9a4f136165a1e86f0831a615e6b378d8e4e93 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 14 Jul 2021 20:28:37 +0200 Subject: [PATCH 0412/9987] remove platform spec subdir from sanity check v2 --- .../b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb index b740298019d..124e6f88759 100644 --- a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.2.0.eb @@ -22,7 +22,7 @@ options = {'modulename': 'Bio::SearchIO::hmmer3'} sanity_check_paths = { 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], - 'dirs': [''], + 'dirs': [], } moduleclass = 'bio' From 8df8360d8d18e619c93a795f33be269d323e2433 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 14 Jul 2021 21:11:10 +0100 Subject: [PATCH 0413/9987] Apply suggestions from code review Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb | 1 + .../b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb | 3 +++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb index 650eee3178d..cb7ea91130e 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('ICU', '69.1'), ] configopts = '--without-libraries=python,mpi' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb index 1c1f2bb6389..eb74a78b452 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb @@ -15,8 +15,11 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('ICU', '69.1'), ] +preconfigopts = 'sed -i "s/-static//g" tools/build/src/engine/build.sh && ' + configopts = '--without-libraries=python,mpi' # disable MPI, enable threading support From 17bc21268410a8abc8395e45ce6648e0d8430ee4 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 14 Jul 2021 21:25:45 +0100 Subject: [PATCH 0414/9987] tagged_layout --- easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb | 4 ++-- .../b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb index cb7ea91130e..a6d9755bb2d 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb @@ -23,8 +23,8 @@ dependencies = [ configopts = '--without-libraries=python,mpi' -# disable MPI, enable threading support +# disable MPI, build Boost libraries with tagged layout boost_mpi = False -boost_multi_thread = True +tagged_layout = True moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb index eb74a78b452..4cb0ac3840c 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb @@ -22,8 +22,8 @@ preconfigopts = 'sed -i "s/-static//g" tools/build/src/engine/build.sh && ' configopts = '--without-libraries=python,mpi' -# disable MPI, enable threading support +# disable MPI, build Boost libraries with tagged layout boost_mpi = False -boost_multi_thread = True +tagged_layout = True moduleclass = 'devel' From 2c9cfab8bc0b36cd70da02724f74b83d2f990a3a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 15 Jul 2021 00:05:18 +0200 Subject: [PATCH 0415/9987] {chem}[intel/2021a] OpenMolcas 21.06 --- .../GlobalArrays-5.8-intel-2021a.eb | 30 ++++++++++++ .../OpenMolcas-21.06-intel-2021a.eb | 48 +++++++++++++++++++ .../OpenMolcas-21.06_mcpdft_deps.patch | 14 ++++++ 3 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-intel-2021a.eb create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06_mcpdft_deps.patch diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb new file mode 100644 index 00000000000..958448a2e21 --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.8' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['64df7d1ea4053d24d84ca361e67a6f51c7b17ed7d626cb18a9fbc759f4a078ac'] + +configopts = ' --with-mpi --enable-i8' +configopts += ' --with-blas8="-L$EBROOTIMKL/mkl/latest/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack8="L${MKLROOT}/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' + +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + +# use IB network +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', + 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-intel-2021a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-intel-2021a.eb new file mode 100644 index 00000000000..ebefff700b7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-intel-2021a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'OpenMolcas' +version = '21.06' + +homepage = "https://gitlab.com/Molcas/OpenMolcas" +description = "OpenMolcas is a quantum chemistry software package" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] +sources = ["OpenMolcas-v%(version)s.tar.gz"] +patches = ['OpenMolcas-21.06_mcpdft_deps.patch'] +checksums = [ + '54cf989c1e0fcb7e8927f0c64fe356b300bf3537e4868356eea47105a8a06e3a', # OpenMolcas-v21.06.tar.gz + '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a', # OpenMolcas-21.06_mcpdft_deps.patch +] + +dependencies = [ + ('GlobalArrays', '5.8'), + ('HDF5', '1.10.7'), + ('Python', '3.9.5'), +] + +builddependencies = [('CMake', '3.20.1')] + +separate_build_dir = True + +preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' +configopts = '-DLINALG=MKL -DMKLROOT=$EBROOTIMKL/mkl/latest ' +configopts += '-DMPI=ON -DOPENMP=ON -DGA=ON ' +configopts += '-DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON' + +modextrapaths = {'PATH': ''} +modextravars = { + 'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', +} + +sanity_check_paths = { + 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, + 'sbin/help_basis', 'pymolcas'], + 'dirs': ['data/', 'basis_library/'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06_mcpdft_deps.patch b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06_mcpdft_deps.patch new file mode 100644 index 00000000000..4b6cce49e7a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06_mcpdft_deps.patch @@ -0,0 +1,14 @@ +# mcpdft has a rasscf dependency +# July 14th 2021 by B. Hajgato (UGent) +--- OpenMolcas-v21.06/CMakeLists.txt.orig 2021-06-09 11:56:51.000000000 +0200 ++++ OpenMolcas-v21.06/CMakeLists.txt 2021-07-14 22:57:35.247625196 +0200 +@@ -2652,6 +2652,9 @@ + + # set program dependencies of super modules + # (note dependencies are not recursive with object libraries, so child dependencies must be explicit) ++set (mcpdft_deplibs ++ rasscf ++) + set (casvb_deplibs + rasscf + ) From f08c7f7278fb374c8e82b7f52a092a76aacc236d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 15 Jul 2021 04:07:38 +0200 Subject: [PATCH 0416/9987] fix long line --- .../easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb index 958448a2e21..3dcdc976fbb 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb @@ -15,7 +15,8 @@ checksums = ['64df7d1ea4053d24d84ca361e67a6f51c7b17ed7d626cb18a9fbc759f4a078ac'] configopts = ' --with-mpi --enable-i8' configopts += ' --with-blas8="-L$EBROOTIMKL/mkl/latest/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' -configopts += ' --with-scalapack8="L${MKLROOT}/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' +configopts += ' --with-scalapack8="L${MKLROOT}/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' # select armci network as (Comex) MPI-1 two-sided configopts += ' --with-mpi-ts' From 13b0c360c15d4408f619a37010edf947a5c8c511 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 15 Jul 2021 11:40:08 +0200 Subject: [PATCH 0417/9987] fix comment and remove unnecessary include path --- .../easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb index b8e89a53178..85becc1cab4 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb @@ -27,12 +27,11 @@ dependencies = [ use_pip = True sanity_pip_check = True -# use system freetype and qhull to avoid that matplotlib downloads and builds its own copies +# avoid that matplotlib downloads and builds its own copies of freetype and qhull _fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " _fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' setup.cfg.template >setup.cfg && " -_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:" -_include_path += "$EBROOTQHULL/include/libqhull:${CPLUS_INCLUDE_PATH} && " +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " exts_list = [ ('Cycler', '0.10.0', { From dffca2cf41c5e77e29625348852e5a85da8605d9 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 15 Jul 2021 10:50:43 +0100 Subject: [PATCH 0418/9987] Update easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index d5850118826..3d6caf654e3 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -714,7 +714,7 @@ exts_list = [ 'checksums': ['3128cdc286275faffc792c4a6cf08562cad072be6b9c8595d52353f06151a750'], }), ('RProtoBufLib', '2.4.0', { - 'patches': ['%(name)s-%(version)s_fix-protobuf-build.patch'], + 'patches': ['RProtoBufLib-2.4.0_fix-protobuf-build.patch'], 'checksums': [ 'cb2e6eba5fabea2f3ecc9a97ae25d54f2b5ad14ed08381a83db612af4ed2cdc3', # RProtoBufLib_2.4.0.tar.gz # RProtoBufLib-2.4.0_fix-protobuf-build.patch From 2dafcedb7c859af3346a4d0a29f4328d145d35cb Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 15 Jul 2021 10:57:50 +0100 Subject: [PATCH 0419/9987] update FlowSorted.Blood.EPIC --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index 3d6caf654e3..2455d799e21 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -857,8 +857,8 @@ exts_list = [ ('SingleR', '1.6.1', { 'checksums': ['d66d4c355edf6278616b5164528e651cb3e012aa5c505b49dfe6b53090b51198'], }), - ('FlowSorted.Blood.EPIC', '1.10.0', { - 'checksums': ['1464f4e956c83e137c1d8c4733d654fb722705c889aa46cb9edddb64eebc4ee9'], + ('FlowSorted.Blood.EPIC', '1.10.1', { + 'checksums': ['7e791e844585b0deca8a879f2c1283cc93590e137441b38ce9f6620ccf68ccb3'], }), ('FlowSorted.CordBloodCombined.450k', '1.8.0', { 'checksums': ['b7c78d61f6f2dd823027207bb0ca07b9a4e24c0be12690bb0c46f2852abb7f1d'], From 621f17b48f3099ecd4f86a971877fe94798ef873 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Thu, 15 Jul 2021 12:11:04 +0200 Subject: [PATCH 0420/9987] Updated VCFtools --- .../v/VCFtools/VCFtools-0.1.16-GCC-10.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.3.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.3.0.eb new file mode 100644 index 00000000000..0d2e4a43fd6 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Perl', '5.32.1'), + ('HTSlib', '1.12'), + ('zlib', '1.2.11'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' From 027d5f2cf6e92a0df8e997e8bbe6eb8716fd1538 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 15 Jul 2021 12:26:52 +0100 Subject: [PATCH 0421/9987] adding easyconfigs: bitarray-1.5.3-GCC-8.3.0-Python-2.7.16.eb --- .../bitarray-1.5.3-GCC-8.3.0-Python-2.7.16.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/b/bitarray/bitarray-1.5.3-GCC-8.3.0-Python-2.7.16.eb diff --git a/easybuild/easyconfigs/b/bitarray/bitarray-1.5.3-GCC-8.3.0-Python-2.7.16.eb b/easybuild/easyconfigs/b/bitarray/bitarray-1.5.3-GCC-8.3.0-Python-2.7.16.eb new file mode 100644 index 00000000000..d350eb0674e --- /dev/null +++ b/easybuild/easyconfigs/b/bitarray/bitarray-1.5.3-GCC-8.3.0-Python-2.7.16.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'bitarray' +version = '1.5.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ilanschnell/bitarray' +description = "bitarray provides an object type which efficiently represents an array of booleans" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['567631fc922b1c2c528c376795f18dcc0604d18702e0b8b50e8e35f0474214a5'] + +dependencies = [('Python', '2.7.16')] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'data' From 836025b6dc652890cc2d46656d5c9d2cfd2898c9 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 15 Jul 2021 12:45:19 +0100 Subject: [PATCH 0422/9987] alt checksum for ccdata --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index 2455d799e21..49d5dc62a7c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -897,7 +897,8 @@ exts_list = [ 'checksums': ['3480b9cf9b73240630dba3fa29bde1546324e7c62f26da3107fce34f5ff67e58'], }), ('ccdata', '1.18.0', { - 'checksums': ['de24c7205723067599de8b7dbec3c8488c9fcf8cbac7948966a82c22bab4ea6d'], + 'checksums': [('de24c7205723067599de8b7dbec3c8488c9fcf8cbac7948966a82c22bab4ea6d' + '48c5b1c054972b5ad720e3cb3ad9fe02b0a9fe39590681450c2dbadecaea1e95')], }), ('lsa', '0.73.2', { 'checksums': ['cb0017bbda9b0eb1d05b451e0f557d02f789f65b2f8bf005606b63a3708e63a8'], From 704e43dda3b3d3c0df440c37c5c793bfe9da80cf Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 15 Jul 2021 12:46:28 +0100 Subject: [PATCH 0423/9987] fix typo --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index 49d5dc62a7c..05c3d062d71 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -897,7 +897,7 @@ exts_list = [ 'checksums': ['3480b9cf9b73240630dba3fa29bde1546324e7c62f26da3107fce34f5ff67e58'], }), ('ccdata', '1.18.0', { - 'checksums': [('de24c7205723067599de8b7dbec3c8488c9fcf8cbac7948966a82c22bab4ea6d' + 'checksums': [('de24c7205723067599de8b7dbec3c8488c9fcf8cbac7948966a82c22bab4ea6d', '48c5b1c054972b5ad720e3cb3ad9fe02b0a9fe39590681450c2dbadecaea1e95')], }), ('lsa', '0.73.2', { From 041be70f9451e0028fe5f996327225f45e09b589 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 15 Jul 2021 13:49:15 +0200 Subject: [PATCH 0424/9987] adding easyconfigs: Score-P-7.0-gompi-2021a.eb --- .../s/Score-P/Score-P-7.0-gompi-2021a.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2021a.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2021a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2021a.eb new file mode 100644 index 00000000000..5276c7c689e --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2021a.eb @@ -0,0 +1,59 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '7.0' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['68f24a68eb6f94eaecf500e17448f566031946deab74f2cba072ee8368af0996'] + +dependencies = [ + ('CubeLib', '4.6'), + ('CubeWriter', '4.6'), + ('libunwind', '1.5.0'), + ('OPARI2', '2.0.6'), + ('OTF2', '2.3'), + # Hardware counter support (optional): + ('PAPI', '6.0.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 1cda603b4eaa51acb1e5ae5b9a4d8f562b71fc5f Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 15 Jul 2021 13:59:59 +0200 Subject: [PATCH 0425/9987] adding easyconfigs: torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb --- ...text-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb new file mode 100644 index 00000000000..05a3968437b --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.9.1-fosscuda-2020b-PyTorch-1.8.1.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.9.1' +local_pytorch_version = '1.8.1' +local_python_suffix = '-Python-%(pyver)s' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +# The tarball of the final v0.9.1 release is labelled as a release candidate +# see https://github.com/pytorch/text/releases/tag/v0.9.1-rc1 +local_tarball_version = '%(version)s-rc1' + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = ['v%s.tar.gz' % local_tarball_version] +checksums = ['336397dfae5587e5dbdd2235020acb86f46af36c1c75b47186c67d0b19acee12'] + +builddependencies = [ + ('RE2', '2021-06-01'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SentencePiece', '0.1.96'), + ('tqdm', '4.56.2'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.1.5'), +] + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/BuildExtension/d' setup.py &&" + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From f27259b0b543dcd93ab2615ca1b0a0b807a58bfd Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 15 Jul 2021 15:28:25 +0200 Subject: [PATCH 0426/9987] adding easyconfigs: Scalasca-2.6-gompic-2020b.eb --- .../s/Scalasca/Scalasca-2.6-gompic-2020b.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompic-2020b.eb diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompic-2020b.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompic-2020b.eb new file mode 100644 index 00000000000..6896e705ca5 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompic-2020b.eb @@ -0,0 +1,52 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Scalasca' +version = '2.6' + +homepage = 'https://www.scalasca.org/' +description = """ + Scalasca is a software tool that supports the performance optimization of + parallel programs by measuring and analyzing their runtime behavior. The + analysis identifies potential performance bottlenecks -- in particular + those concerning communication and synchronization -- and offers guidance + in exploring their causes. +""" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b3f9cb1d58f3e25090a39da777bae8ca2769fd10cbd6dfb9a4887d873ee2441e'] + +builddependencies = [ + ('CubeWriter', '4.6'), +] + +dependencies = [ + ('CubeGUI', '4.6'), + ('CubeLib', '4.6'), + ('OTF2', '2.3'), + ('Score-P', '7.0'), +] + +sanity_check_paths = { + 'files': ['bin/scalasca', 'lib/libpearl.replay.a'], + 'dirs': [], +} + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scalasca/patterns'} + +moduleclass = 'perf' From 1b505cee30c27d3b8351dc8c935f198b7707c5c0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 15 Jul 2021 16:10:09 +0200 Subject: [PATCH 0427/9987] remove tests from postinstall and instruct proscan utils not to use affinity --- .../InterProScan-5.52-86.0-GCCcore-10.3.0.eb | 12 +++++----- ...InterProScan-5.52_proscan_noaffinity.patch | 24 +++++++++++++++++++ 2 files changed, 30 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/i/InterProScan/InterProScan-5.52_proscan_noaffinity.patch diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb index 951552ca5a1..dca22cac5f6 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb @@ -15,7 +15,11 @@ source_urls = [ 'ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/data', ] sources = ['%(namelower)s-%(version)s-64-bit.tar.gz'] -checksums = ['50a03c47fb16c669c265e99ba05c4a8558b82047f713c9945f362d3d4be6069a'] +patches = ['InterProScan-5.52_proscan_noaffinity.patch'] +checksums = [ + '50a03c47fb16c669c265e99ba05c4a8558b82047f713c9945f362d3d4be6069a', # interproscan-5.52-86.0-64-bit.tar.gz + 'ee73b11cf4b9187f784055445f9db5623a9affe33ba41aa755143ea4594bf011', # InterProScan-5.52_proscan_noaffinity.patch +] dependencies = [ ('Java', '11', '', True), @@ -24,11 +28,7 @@ dependencies = [ ('Python', '3.9.5'), ] -postinstallcmds = [ - "cd %(installdir)s && python initial_setup.py", - "cd %(installdir)s && ./interproscan.sh -b %(builddir)s/output -i test_all_appl.fasta -f tsv -dp", - "cd %(installdir)s && ./interproscan.sh -b %(builddir)s/output -i test_all_appl.fasta -f tsv", -] +postinstallcmds = ["cd %(installdir)s && python initial_setup.py"] sanity_check_paths = { 'files': ['interproscan-%(version_major)s.jar', 'interproscan.sh', 'interproscan.properties'], diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52_proscan_noaffinity.patch b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52_proscan_noaffinity.patch new file mode 100644 index 00000000000..7d604e8246a --- /dev/null +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52_proscan_noaffinity.patch @@ -0,0 +1,24 @@ +# Do not use affinity (as it already should be set by the queue system) with proscan utils +# July 15th 2021 by B. Hajgato (UGent) +--- interproscan-5.52-86.0/bin/prosite/ps_scan.pl.org 2021-06-02 16:33:37.000000000 +0200 ++++ interproscan-5.52-86.0/bin/prosite/ps_scan.pl 2021-07-15 16:00:51.589475628 +0200 +@@ -1730,7 +1730,7 @@ + if ($level_arg eq 0) { # yes default scan l=0 is internally run at -1 (so that postprocessing could consider weak matches) + $level_arg = -1; + } +- @pre_command = $use_pfscan_v3 ? "$PFSCAN --matrix-only -o4 -L$level_arg $PROSITE" : "$PFSCAN -flxz -v -C$level_arg"; ++ @pre_command = $use_pfscan_v3 ? "$PFSCAN --no-affinity --matrix-only -o4 -L$level_arg $PROSITE" : "$PFSCAN -flxz -v -C$level_arg"; + @post_command = $use_pfscan_v3 ? "" : $PROSITE; + } + my $out; +--- interproscan-5.52-86.0/bin/prosite/runprosite.py.org 2021-06-02 16:33:37.000000000 +0200 ++++ interproscan-5.52-86.0/bin/prosite/runprosite.py 2021-07-15 16:00:25.908539401 +0200 +@@ -43,7 +43,7 @@ + binary_command = arg_list[4] + binary_switches = arg_list[5:] + +- pfsearch_cmd_switches = ' '.join(binary_switches) ++ pfsearch_cmd_switches = ' '.join(['--no-affinity'] + binary_switches) + #print pfsearch_cmd + + #print (binary_switches) From 48365ebb0dc3808f346ea272afe505452444926f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 15 Jul 2021 22:04:43 +0200 Subject: [PATCH 0428/9987] update easyconfig: OpenBLAS-0.3.17-GCC-10.3.0.eb --- ...LAS-0.3.16-GCC-10.3.0.eb => OpenBLAS-0.3.17-GCC-10.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/o/OpenBLAS/{OpenBLAS-0.3.16-GCC-10.3.0.eb => OpenBLAS-0.3.17-GCC-10.3.0.eb} (88%) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.16-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb similarity index 88% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.16-GCC-10.3.0.eb rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb index b8fe20b165c..6feee08faf6 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.16-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb @@ -1,5 +1,5 @@ name = 'OpenBLAS' -version = '0.3.16' +version = '0.3.17' homepage = 'https://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." @@ -17,7 +17,7 @@ patches = [ ('timing.tgz', '.'), ] checksums = [ - 'fa19263c5732af46d40d3adeec0b2c77951b67687e670fb6ba52ea3950460d79', # v0.3.16.tar.gz + 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f', # v0.3.17.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz ] From e062139c3424c3ad467291d3d703e75d2e1649d8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 16 Jul 2021 13:56:04 +0100 Subject: [PATCH 0429/9987] Add PCAmatchR to recent R --- .../easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 ++ .../easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 ++ .../easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 ++ .../easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 ++ .../easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 28 ++++++++----------- .../easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 ++ .../easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 3 ++ 7 files changed, 30 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 42178857455..ba996e728c3 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2882,6 +2882,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index d988cd20cce..e745b17b3ee 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2892,6 +2892,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 1f05e7f1af3..b221d6c94b9 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2918,6 +2918,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index f56ea3e03bf..be354b8bf2d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2923,6 +2923,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index b6cddf6beef..417a6fa52c6 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -770,7 +770,7 @@ exts_list = [ ('memoise', '2.0.0', { 'checksums': ['ff9ae3a1a95ad6271d98e6eca016768b790e44bd613356b8e86b685aefd9ecaf'], }), - ('bit64', '4.0.5', { + ('bit64', version, { 'checksums': ['25df6826ea5e93241c4874cad4fa8dadc87a40f4ff74c9107aa12a9e033e1578'], }), ('blob', '1.2.1', { @@ -1740,7 +1740,7 @@ exts_list = [ 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], 'checksums': [ 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz - '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch ], }), ('diveRsity', '1.9.90', { @@ -2160,8 +2160,7 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', - 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], + 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], @@ -2222,13 +2221,12 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.1', { 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], @@ -2342,8 +2340,7 @@ exts_list = [ 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], }), ('rda', '1.0.2-2.1', { - 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', - 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], }), ('sampling', '2.9', { 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], @@ -2442,9 +2439,9 @@ exts_list = [ 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], }), ('V8', '3.4.0', { - 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], - 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], }), ('rstan', '2.21.2', { 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], @@ -2696,13 +2693,9 @@ exts_list = [ 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), ('gWidgets2tcltk', '1.0-6', { - 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" - 'preinstallopts': "xvfb-run ", - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... 'modulename': False, + 'preinstallopts': "xvfb-run ", + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], }), ('mgsub', '1.7.2', { 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], @@ -2927,6 +2920,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index ad61d8b44d6..8262ab1509e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2938,6 +2938,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index c3e0f54a993..3926d455cbf 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -2960,6 +2960,9 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), ] moduleclass = 'lang' From 0f74eef298178a99c6379cb8c12f9b4bd3a86376 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 16 Jul 2021 14:21:50 +0100 Subject: [PATCH 0430/9987] Include recent changes to R-4.0.5 --- .../easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 27 ++++++++++++------- 1 file changed, 17 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 417a6fa52c6..2492b2ca6c1 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -770,7 +770,7 @@ exts_list = [ ('memoise', '2.0.0', { 'checksums': ['ff9ae3a1a95ad6271d98e6eca016768b790e44bd613356b8e86b685aefd9ecaf'], }), - ('bit64', version, { + ('bit64', '4.0.5', { 'checksums': ['25df6826ea5e93241c4874cad4fa8dadc87a40f4ff74c9107aa12a9e033e1578'], }), ('blob', '1.2.1', { @@ -1740,7 +1740,7 @@ exts_list = [ 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], 'checksums': [ 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz - '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch + '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch, ], }), ('diveRsity', '1.9.90', { @@ -2160,7 +2160,8 @@ exts_list = [ 'checksums': ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'], }), ('mvabund', '4.1.9', { - 'checksums': ['60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6'], + 'checksums': [('60d09af4b82fe4945ef0b5aeb85aee2741ccc8a7b3cea26eecef4cf914787ea6', + 'fa48c1cabe3a5bed35b0f31b02f55d9f15e57b3945cf3f407ddc9d3c9e29bb30')], }), ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], @@ -2221,12 +2222,13 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.1', { 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], @@ -2340,7 +2342,8 @@ exts_list = [ 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.9', { 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], @@ -2439,9 +2442,9 @@ exts_list = [ 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], }), ('V8', '3.4.0', { - 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', - 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", 'checksums': ['f5c8a2a03cc1be9f504f47711a0fcd1b962745139c9fb2a10fbd79c4ae103fbd'], + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', }), ('rstan', '2.21.2', { 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], @@ -2693,9 +2696,13 @@ exts_list = [ 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), ('gWidgets2tcltk', '1.0-6', { - 'modulename': False, - 'preinstallopts': "xvfb-run ", 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, }), ('mgsub', '1.7.2', { 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], @@ -2920,7 +2927,7 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), - ('PCAmatchR', '0.3.0', { + ('PCAmatchR', '0.3.0', { 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], }), ] From 25a0b553e540e88ea1bd73f4560d38f400f5ab20 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 16 Jul 2021 14:50:38 +0100 Subject: [PATCH 0431/9987] Fix bad indent in R-4.0.5 --- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 2492b2ca6c1..d80f499a0b0 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2927,7 +2927,7 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), - ('PCAmatchR', '0.3.0', { + ('PCAmatchR', '0.3.0', { 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], }), ] From ffe8e37433add6b6ba80f352d97cb843becb0e70 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 16 Jul 2021 15:46:02 +0200 Subject: [PATCH 0432/9987] Avoid dependency on system GTK+ in GTK+ themes --- .../g/GTK+/GTK+-3.24.13-GCCcore-8.3.0.eb | 19 +++++++++++++------ .../g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb | 19 +++++++++++++------ .../g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb | 19 +++++++++++++------ .../g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb | 19 +++++++++++++------ ...-theme-3.34.3_disable-svg-conversion.patch | 16 ++++++++++++++++ 5 files changed, 68 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/g/GTK+/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.13-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.13-GCCcore-8.3.0.eb index 7d7e14c196c..6b3ef66990e 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.13-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.13-GCCcore-8.3.0.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} builddependencies = [ ('binutils', '2.32'), + ('Autotools', '20180311'), ('GObject-Introspection', '1.63.1', '-Python-3.7.4'), ('gettext', '0.20.1'), ('pkg-config', '0.29.2'), @@ -40,18 +41,24 @@ default_component_specs = { } components = [ + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['4c775c38cf1e3c534ef0ca52ca6c7a890fe169981af66141c713e054e68930a9'], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], }), ('adwaita-icon-theme', '3.34.3', { + 'preconfigopts': 'autoreconf -f -i && ', 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['e7c2d8c259125d5f35ec09522b88c8fe7ecf625224ab0811213ef0a95d90b908'], - }), - (name, version, { - 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['4c775c38cf1e3c534ef0ca52ca6c7a890fe169981af66141c713e054e68930a9'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + 'e7c2d8c259125d5f35ec09522b88c8fe7ecf625224ab0811213ef0a95d90b908', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], }), ] diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb index 0fac0e6076c..9397344d1d9 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} builddependencies = [ ('binutils', '2.34'), + ('Autotools', '20180311'), ('GObject-Introspection', '1.64.0', '-Python-3.8.2'), ('gettext', '0.20.1'), ('pkg-config', '0.29.2'), @@ -40,18 +41,24 @@ default_component_specs = { } components = [ + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['f210255b221cb0f0db3e7b21399983b715c9dda6eb1e5c2f7fdf38f4f1b6bac0'], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], }), ('adwaita-icon-theme', '3.36.0', { + 'preconfigopts': 'autoreconf -f -i && ', 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['1a172112b6da482d3be3de6a0c1c1762886e61e12b4315ae1aae9b69da1ed518'], - }), - (name, version, { - 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['f210255b221cb0f0db3e7b21399983b715c9dda6eb1e5c2f7fdf38f4f1b6bac0'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '1a172112b6da482d3be3de6a0c1c1762886e61e12b4315ae1aae9b69da1ed518', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], }), ] diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb index daf5522a2c4..9eaad73eab7 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} builddependencies = [ ('binutils', '2.35'), + ('Autotools', '20200321'), ('GObject-Introspection', '1.66.1'), ('gettext', '0.21'), ('pkg-config', '0.29.2'), @@ -40,18 +41,24 @@ default_component_specs = { } components = [ + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['5d864d248357a2251545b3387b35942de5f66e4c66013f0962eb5cb6f8dae2b1'], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], }), ('adwaita-icon-theme', '3.38.0', { + 'preconfigopts': 'autoreconf -f -i && ', 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97'], - }), - (name, version, { - 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['5d864d248357a2251545b3387b35942de5f66e4c66013f0962eb5cb6f8dae2b1'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], }), ] diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb index 3ffbb8ae74b..bf8d243b92b 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} builddependencies = [ ('binutils', '2.36.1'), + ('Autotools', '20210128'), ('GObject-Introspection', '1.68.0'), ('gettext', '0.21'), ('pkg-config', '0.29.2'), @@ -40,18 +41,24 @@ default_component_specs = { } components = [ + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['f57ec4ade8f15cab0c23a80dcaee85b876e70a8823d9105f067ce335a8268caa'], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], }), ('adwaita-icon-theme', '3.38.0', { + 'preconfigopts': 'autoreconf -f -i && ', 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97'], - }), - (name, version, { - 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['f57ec4ade8f15cab0c23a80dcaee85b876e70a8823d9105f067ce335a8268caa'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], }), ] diff --git a/easybuild/easyconfigs/g/GTK+/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch b/easybuild/easyconfigs/g/GTK+/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch new file mode 100644 index 00000000000..bf0b97f9489 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch @@ -0,0 +1,16 @@ +As we don't have SVG support we disable the search for the converter. + +Author: Alexander Grund (TU Dresden) + +diff -aur a/configure.ac b/configure.ac +--- a/configure.ac 2021-07-16 15:16:15.774630738 +0200 ++++ b/configure.ac 2021-07-16 15:15:10.138814059 +0200 +@@ -49,7 +49,7 @@ + AM_CONDITIONAL(ALLOW_RENDERING, test "x$allow_rendering" = "xyes") + + symbolic_encode_sizes="16x16 24x24 32x32 48x48 64x64 96x96" +-AC_PATH_PROG([GTK_ENCODE_SYMBOLIC_SVG], [gtk-encode-symbolic-svg], [false]) ++GTK_ENCODE_SYMBOLIC_SVG="false" + if test "x$GTK_ENCODE_SYMBOLIC_SVG" = "xfalse"; then + symbolic_encode_sizes="" + fi From 7ac15a69dd8536dfbf5adcdaaba02143f2b92fd0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 16 Jul 2021 16:33:15 +0200 Subject: [PATCH 0433/9987] {bio}[foss/2020b] Qualimap 2.2.1 --- .../Qualimap-2.2.1-foss-2020b-R-4.0.3.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb new file mode 100644 index 00000000000..4b25f9686c6 --- /dev/null +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'Qualimap' +version = '2.2.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://qualimap.bioinfo.cipf.es/' +description = """Qualimap 2 is a platform-independent application written in Java and R that provides both + a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of + alignment sequencing data and its derivatives like feature counts.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads/'] +sources = ['qualimap_v%(version)s.zip'] +checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] + +dependencies = [ + ('Java', '11', '', True), + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', versionsuffix), +] + +sanity_check_paths = { + 'files': ['qualimap'], + 'dirs': [], +} + +sanity_check_commands = ["qualimap --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 5c4ac4b40ef25ff5fdc83e8127382a5206b1826a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 16 Jul 2021 21:19:26 +0200 Subject: [PATCH 0434/9987] Add hal9001 module to R v4 --- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 6 ++++++ 9 files changed, 54 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 525775e4f02..a5752479d37 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -2705,6 +2705,12 @@ exts_list = [ ('sensemakr', '0.1.3', { 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb index a2e481d0822..e3624b70a79 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb @@ -2713,6 +2713,12 @@ exts_list = [ ('sensemakr', '0.1.3', { 'checksums': ['2eccda4ac3752266779d9c8ae87154c9fbaf0f73e0a768692a836a29ceaeffdd'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 42178857455..79690927e5d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2882,6 +2882,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index d988cd20cce..115fc7be076 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2892,6 +2892,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 1f05e7f1af3..8723c64f4ed 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2918,6 +2918,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index f56ea3e03bf..bfe7e126652 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2923,6 +2923,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index b6cddf6beef..2e7c4556976 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2927,6 +2927,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index ad61d8b44d6..3ea4c22b463 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2938,6 +2938,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index c3e0f54a993..7a86c5808e9 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -2960,6 +2960,12 @@ exts_list = [ ('neuralnet', '1.44.2', { 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), + ('origami', '1.0.3', { + 'checksums': ['43d33c47d66a08f84cb4914497a5ebea9dd0937151f47f41c3947e4a6d4b900c'], + }), + ('hal9001', '0.2.7', { + 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], + }), ] moduleclass = 'lang' From 21cf7062ccd7542c1ca190288db3a9dfeac6b0c8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 16 Jul 2021 21:35:08 +0200 Subject: [PATCH 0435/9987] remove dupliacte memoise from R-4.0.0-foss-2020a --- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index a5752479d37..e4788de50ef 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -2594,9 +2594,6 @@ exts_list = [ ('gWidgets2', '1.0-8', { 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), - ('memoise', '1.1.0', { - 'checksums': ['b276f9452a26aeb79e12dd7227fcc8712832781a42f92d70e86040da0573980c'], - }), ('gWidgets2tcltk', '1.0-6', { 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], # need to run installation via xvfb-run to avoid problems on headless systems: From 1c1e779c0e2e13156666257df5125a7af6d0e11c Mon Sep 17 00:00:00 2001 From: Sassy Date: Sat, 17 Jul 2021 21:05:36 +0000 Subject: [PATCH 0436/9987] OpenMM update to 7.5.1 required for alphafold --- .../o/OpenMM/OpenMM-7.5.1-foss-2020b.eb | 58 ++++++++++++++++ .../o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb | 66 +++++++++++++++++++ .../OpenMM-7.5.1_fix_path_to_nvcc.patch | 15 +++++ 3 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_path_to_nvcc.patch diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb new file mode 100644 index 00000000000..15672d73428 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2020b.eb @@ -0,0 +1,58 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.1' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +separate_build_dir = True + +dependencies = [ + ('FFTW', '3.3.8'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SWIG', '4.0.2'), +] + +runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb new file mode 100644 index 00000000000..5f6aeae351d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb @@ -0,0 +1,66 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.1' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_path_to_nvcc.patch'] +checksums = [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # 7.5.1.tar.gz + '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SWIG', '4.0.2'), +] + +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_path_to_nvcc.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_path_to_nvcc.patch new file mode 100644 index 00000000000..6749338995b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_path_to_nvcc.patch @@ -0,0 +1,15 @@ +Make sure OpenMM does use it's stupid hardcoded path to nvcc. + +Åke Sandgren, 2021-04-15 +diff -ru openmm-7.5.0.orig/platforms/cuda/src/CudaPlatform.cpp openmm-7.5.0/platforms/cuda/src/CudaPlatform.cpp +--- openmm-7.5.0.orig/platforms/cuda/src/CudaPlatform.cpp 2020-11-25 06:39:09.000000000 +0100 ++++ openmm-7.5.0/platforms/cuda/src/CudaPlatform.cpp 2021-04-15 14:36:46.293660324 +0200 +@@ -136,7 +136,7 @@ + setPropertyDefaultValue(CudaTempDirectory(), string(getenv("TEMP"))); + #else + char* compiler = getenv("OPENMM_CUDA_COMPILER"); +- string nvcc = (compiler == NULL ? "/usr/local/cuda/bin/nvcc" : string(compiler)); ++ string nvcc = (compiler == NULL ? "nvcc" : string(compiler)); + setPropertyDefaultValue(CudaCompiler(), nvcc); + char* tmpdir = getenv("TMPDIR"); + string tmp = (tmpdir == NULL ? string(P_tmpdir) : string(tmpdir)); From aca90cf2565dcd0c63f6e1180ca2a140fcfb16d8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 19 Jul 2021 00:59:09 +0200 Subject: [PATCH 0437/9987] adding easyconfigs: Highway-0.12.2-GCCcore-10.3.0.eb, Brotli-1.0.9-GCCcore-10.3.0.eb, libjxl-0.3.7-GCCcore-10.3.0.eb --- .../b/Brotli/Brotli-1.0.9-GCCcore-10.3.0.eb | 36 ++++++++++ .../Highway/Highway-0.12.2-GCCcore-10.3.0.eb | 29 +++++++++ .../l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb | 65 +++++++++++++++++++ 3 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b5eb9cab797 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' +name = 'Brotli' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brotli-%(version)s_pc_link_flags.patch'] +checksums = [ + 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz + '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch +] + +separate_build_dir = True + +dependencies = [('binutils', '2.36.1')] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..fc9bed83d0f --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'Highway' +version = '0.12.2' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e1d47ce510429fdcf31f41697ca74fb0dcd59d933196e531a86d51751a56f4cc'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b6455b3d42f --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'libjxl' +version = '0.3.7' +local_lodepng_version = "48e5364" +local_skcms_version = "6437475" + +homepage = 'https://github.com/libjxl/libjxl' + +description = """JPEG XL image format reference implementation""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'optarch': False} # optarch causes some test failures + +github_account = 'libjxl' +source_urls = [GITHUB_SOURCE] +sources = [ + 'v%(version)s.tar.gz', + {'filename': 'lodepng-%s.tar.gz' % local_lodepng_version, + 'download_filename': local_lodepng_version, + 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], + 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, + {'filename': 'skcms-%s.tar.gz' % local_skcms_version, + 'download_filename': '%s.tar.gz' % local_skcms_version, + 'source_urls': ['https://skia.googlesource.com/skcms/+archive/'], + 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/skcms --strip-components=0 -xf %s'}, + +] +patches = ['libjxl-%(version)s_openexr-3.0_compat.patch'] +checksums = [ + '8318a5d1ce82e5683a52512b6f242d2b33a1191e89fc76f7c0ead0a1d60f6c60', # v0.3.7.tar.gz + 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz + '1be9a0e16cdd1d2749c8111b862c496100ec959d2efaea7996eee86ef796fddd', # skcms-6437475.tar.gz + 'b5bf92b8eb8f41e7cedce1b43ea3fe7a9407d3cc0e29bb2afec652cabe084cee', # libjxl-0.3.7_openexr-3.0_compat.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('googletest', '1.11.0'), + ('pkg-config', '0.29.2'), + ('Highway', '0.12.2'), # Highway only has a static library +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('giflib', '5.2.1'), + ('libwebp', '1.2.0'), + ('OpenEXR', '3.0.1'), + ('gperftools', '2.9.1'), +] + +configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 7419074a55e83217105fa0ba727b796cea297a1b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 19 Jul 2021 16:30:50 +0200 Subject: [PATCH 0438/9987] Fix Python 2.7.13 packages --- .../p/Python/Python-2.7.13-foss-2017a.eb | 29 +++++++++++++++++-- .../p/Python/Python-2.7.13-intel-2017a.eb | 29 +++++++++++++++++-- 2 files changed, 52 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb index 8b83e77fb18..8586d43d2b3 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-foss-2017a.eb @@ -98,21 +98,44 @@ exts_list = [ ('ecdsa', '0.13', { 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), + ('ipaddress', '1.0.22', { + 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], + }), + ('asn1crypto', '0.24.0', { + 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], + }), + ('idna', '2.7', { + 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], + }), ('pycparser', '2.18', { 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), + ('pyasn1', '0.4.3', { + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), + ('pyparsing', '2.2.0', { + 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], + }), + ('attrs', '19.1.0', { + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], + 'modulename': 'attr', + }), + ('packaging', '19.1', { + 'checksums': ['c491ca87294da7cc01902edbe30a5bc6c4c28172b5138ab4e4aa1b9d7bfaeafe'], + }), ('cryptography', '1.8.1', { 'checksums': ['323524312bb467565ebca7e50c8ae5e9674e544951d28a2904a50012a8828190'], }), ('paramiko', '2.1.2', { 'checksums': ['5fae49bed35e2e3d45c4f7b0db2d38b9ca626312d91119b3991d0ecf8125e310'], }), - ('pyparsing', '2.2.0', { - 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], - }), ('netifaces', '0.10.5', { 'checksums': ['59d8ad52dd3116fcb6635e175751b250dc783fb011adba539558bd764e5d628b'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb index 73b08e8b434..229b0bf80d8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.13-intel-2017a.eb @@ -98,21 +98,44 @@ exts_list = [ ('ecdsa', '0.13', { 'checksums': ['64cf1ee26d1cde3c73c6d7d107f835fed7c6a2904aef9eac223d57ad800c43fa'], }), + ('ipaddress', '1.0.22', { + 'checksums': ['b146c751ea45cad6188dd6cf2d9b757f6f4f8d6ffb96a023e6f2e26eea02a72c'], + }), + ('asn1crypto', '0.24.0', { + 'checksums': ['9d5c20441baf0cb60a4ac34cc447c6c189024b6b4c6cd7877034f4965c464e49'], + }), + ('idna', '2.7', { + 'checksums': ['684a38a6f903c1d71d6d5fac066b58d7768af4de2b832e426ec79c30daa94a16'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'checksums': ['8ad8c4783bf61ded74527bffb48ed9b54166685e4230386a9ed9b1279e2df5b1'], + }), ('pycparser', '2.18', { 'checksums': ['99a8ca03e29851d96616ad0404b4aad7d9ee16f25c9f9708a11faf2810f7b226'], }), ('cffi', '1.11.5', { 'checksums': ['e90f17980e6ab0f3c2f3730e56d1fe9bcba1891eeea58966e89d352492cc74f4'], }), + ('pyasn1', '0.4.3', { + 'checksums': ['fb81622d8f3509f0026b0683fe90fea27be7284d3826a5f2edf97f69151ab0fc'], + }), + ('pyparsing', '2.2.0', { + 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], + }), + ('attrs', '19.1.0', { + 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], + 'modulename': 'attr', + }), + ('packaging', '19.1', { + 'checksums': ['c491ca87294da7cc01902edbe30a5bc6c4c28172b5138ab4e4aa1b9d7bfaeafe'], + }), ('cryptography', '1.8.1', { 'checksums': ['323524312bb467565ebca7e50c8ae5e9674e544951d28a2904a50012a8828190'], }), ('paramiko', '2.1.2', { 'checksums': ['5fae49bed35e2e3d45c4f7b0db2d38b9ca626312d91119b3991d0ecf8125e310'], }), - ('pyparsing', '2.2.0', { - 'checksums': ['0832bcf47acd283788593e7a0f542407bd9550a55a8a8435214a1960e04bcb04'], - }), ('netifaces', '0.10.5', { 'checksums': ['59d8ad52dd3116fcb6635e175751b250dc783fb011adba539558bd764e5d628b'], }), From e0c20407964b96e7f46fb7f9b6cb977701db81d4 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 19 Jul 2021 16:12:09 +0000 Subject: [PATCH 0439/9987] hhsuite-3.3.0 needed for alphafold created --- .../h/hhsuite/hhsuite-3.3.0-foss-2020b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/hhsuite/hhsuite-3.3.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/hhsuite/hhsuite-3.3.0-foss-2020b.eb b/easybuild/easyconfigs/h/hhsuite/hhsuite-3.3.0-foss-2020b.eb new file mode 100644 index 00000000000..6b846a56c79 --- /dev/null +++ b/easybuild/easyconfigs/h/hhsuite/hhsuite-3.3.0-foss-2020b.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'hhsuite' +version = '3.3.0' + +homepage = 'https://github.com/soedinglab/hh-suite' +description = """The HH-suite is an open-source software package +for sensitive protein sequence searching based on the pairwise +alignment of hidden Markov models (HMMs).""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +separate_build_dir = True + +_binaries = [ + 'hhalign', 'hhalign_mpi', 'hhalign_omp', + 'hhblits', 'hhblits_mpi', 'hhblits_omp', + 'hhmake', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries], + 'dirs': ['data', 'scripts', ] +} + +moduleclass = 'bio' From 359b365e8074c49c5dcef81faf76845b8f259b0c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 20 Jul 2021 11:19:37 +0200 Subject: [PATCH 0440/9987] fix codestyle in ORCA-5.0.0-gompi-2021a-static.eb --- easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb index b370a8dccea..b36de4fdcd2 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.0-gompi-2021a-static.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'gompi', 'version': '2021a'} # Static build of ORCA: download from https://orcaforum.kofo.mpg.de # OpenMPI is dynamically linked sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_openmpi411_part%s.tar.xz' % (version.replace('.', '_'), p) - for p in range(1, 5)] + for p in range(1, 5)] checksums = [ # orca_5_0_0_linux_x86-64_openmpi411_part1.tar.xz '4ada3b343701e6a37c3f9f50fa3514396dcad4c8d7d625e170e77e3bd3864758', From 61c38d6fda808a1297d1331edcd0334315ce39f0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 20 Jul 2021 11:22:36 +0200 Subject: [PATCH 0441/9987] update MD5 checksum to SHA256 in ORCA-4.0.0.2-OpenMPI-2.0.2.eb --- easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb index 7f30132c7c5..30376ba2e68 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-4.0.0.2-OpenMPI-2.0.2.eb @@ -17,7 +17,7 @@ sources = [ '%%(namelower)s_%s_linux_x86-64_openmpi%s.tbz' % (version.replace('.', '_'), local_ompi_ver.replace('.', '')), ] -checksums = ['a5b8ecdd3d004af4bc8190c986f34e11'] +checksums = ['be2e42a8f75d4a7761959a134cc9e60f69c6a65f46121a8f00c7ebad028770c9'] dependencies = [('OpenMPI', local_ompi_ver, '-GCC-6.3.0-2.27')] From 60a0531ba3d050a2993eb6cd57b99a41a6c3f413 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 20 Jul 2021 16:55:31 +0200 Subject: [PATCH 0442/9987] Add TensorFlow patch to fix crash on shutdown --- .../TensorFlow-2.5.0-fosscuda-2020b.eb | 3 +++ ...nsorFlow-2.5.0_fix-crash-on-shutdown.patch | 20 +++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-crash-on-shutdown.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 5e6c23ac575..bafbef6444f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -163,6 +163,7 @@ exts_list = [ 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', ], 'checksums': [ @@ -187,6 +188,8 @@ exts_list = [ '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_fix-crash-on-shutdown.patch + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-crash-on-shutdown.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-crash-on-shutdown.patch new file mode 100644 index 00000000000..18021a240ab --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-crash-on-shutdown.patch @@ -0,0 +1,20 @@ +Releasing and reaquiring the GIL during Python shutdown is not possible and leads to force termination. +Remove that. +See https://github.com/tensorflow/tensorflow/issues/50853 + +Author: Alexander Grund + +diff --git a/tensorflow/python/client/tf_session_wrapper.cc b/tensorflow/python/client/tf_session_wrapper.cc +index 306381347c7..1208aa2ce61 100644 +--- a/tensorflow/python/client/tf_session_wrapper.cc ++++ b/tensorflow/python/client/tf_session_wrapper.cc +@@ -557,8 +557,7 @@ PYBIND11_MODULE(_pywrap_tf_session, m) { + + m.def("TF_NewGraph", TF_NewGraph, py::return_value_policy::reference, + py::call_guard()); +- m.def("TF_DeleteGraph", TF_DeleteGraph, +- py::call_guard()); ++ m.def("TF_DeleteGraph", TF_DeleteGraph); + + m.def("TF_GraphGetOpDef", + [](TF_Graph* graph, const char* op_name, TF_Buffer* output_op_def) { From c61c14b90380341fd22b771bcb9946df03f6d6e2 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 20 Jul 2021 15:29:24 +0000 Subject: [PATCH 0443/9987] kalign2 v2.04 and v3.3.1 required for alphahelix created --- .../k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ .../k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb | 32 +++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..df1a6862142 --- /dev/null +++ b/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'kalign2' +version = '2.0.4' + +homepage = '' +description = "Kalign is a fast multiple sequence alignment program for biological sequences." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://msa.sbc.su.se/downloads/kalign/'] +sources = ['current.tar.gz'] +checksums = ['8cf20ac4e1807dc642e7ffba8f42a117313beccaee4f87c5555d53a2eeac4cbb'] # current.tar.gz + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Autoconf', '2.69'), +] + +configure_cmd_prefix = "autoreconf -vfi && " + +install_cmd = "mkdir %(installdir)s/bin && cp kalign %(installdir)s/bin" + +sanity_check_paths = { + 'files': ['bin/kalign'], + 'dirs': [''], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..90a26ddeb45 --- /dev/null +++ b/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'kalign2' +version = '3.3.1' + +homepage = '' +description = "Kalign is a fast multiple sequence alignment program for biological sequences." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7f10acf9a3fa15deabbc0304e7c14efa25cea39108318c9f02b47257de2d7390'] # 3.3.1.tar.gz + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Autoconf', '2.69'), +] + +configure_cmd_prefix = "autoreconf -vfi && " + +sanity_check_paths = { + 'files': ['bin/kchaos', 'bin/kalign'], + 'dirs': [''], +} + +moduleclass = 'bio' From dcc7fcece3378c90cf54032f56ecc5fd1288b624 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 20 Jul 2021 13:55:09 +0200 Subject: [PATCH 0444/9987] adding easyconfigs: PySide2-5.14.2.3-GCCcore-10.2.0.eb --- .../PySide2-5.14.2.3-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..dcc75de0c8d --- /dev/null +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PySide2' +version = '5.14.2.3' + +homepage = "https://pypi.python.org/pypi/%(name)s/" +description = """PySide2 is the official Python module from the Qt for Python project, + which provides access to the complete Qt 5.12+ framework.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://download.qt.io/official_releases/QtForPython/%(namelower)s/%(name)s-%(version)s-src/'] +sources = ['pyside-setup-opensource-src-%(version)s.tar.xz'] +checksums = ['032de309505c78ba52c225aaf5fd717b8d87ae863aa7cee8ba58ba6141c59022'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Sphinx', '3.5.2'), + ('Clang', '11.0.1'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Qt5', '5.14.2'), +] + +preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' +prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' +preinstallopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' + +options = {'modulename': 'PySide2'} + +moduleclass = 'devel' From 3eb8b629a73382a15fd6a200bd97513caec38754 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 21 Jul 2021 02:09:10 +0200 Subject: [PATCH 0445/9987] Add patch --- .../b/Brotli/Brotli-1.0.9_pc_link_flags.patch | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.0.9_pc_link_flags.patch diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9_pc_link_flags.patch b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9_pc_link_flags.patch new file mode 100644 index 00000000000..b61b0651ff1 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9_pc_link_flags.patch @@ -0,0 +1,35 @@ +# Removes old -R flag from link line, as it's not supported un newer compilers. +# Just leave it up to the user if they want to rpath or not. +# Author: micketeer@gmail.com +diff -ru scripts.orig/libbrotlicommon.pc.in scripts/libbrotlicommon.pc.in +--- scripts.orig/libbrotlicommon.pc.in 2021-07-12 21:37:48.253345970 +0200 ++++ scripts/libbrotlicommon.pc.in 2021-07-12 21:38:14.466282849 +0200 +@@ -7,5 +7,5 @@ + URL: https://github.com/google/brotli + Description: Brotli common dictionary library + Version: @PACKAGE_VERSION@ +-Libs: -L${libdir} -R${libdir} -lbrotlicommon ++Libs: -L${libdir} -lbrotlicommon + Cflags: -I${includedir} +diff -ru scripts.orig/libbrotlidec.pc.in scripts/libbrotlidec.pc.in +--- scripts.orig/libbrotlidec.pc.in 2021-07-12 21:37:48.252345973 +0200 ++++ scripts/libbrotlidec.pc.in 2021-07-12 21:38:00.008317664 +0200 +@@ -7,6 +7,6 @@ + URL: https://github.com/google/brotli + Description: Brotli decoder library + Version: @PACKAGE_VERSION@ +-Libs: -L${libdir} -R${libdir} -lbrotlidec ++Libs: -L${libdir} -lbrotlidec + Requires.private: libbrotlicommon >= 1.0.2 + Cflags: -I${includedir} +diff -ru scripts.orig/libbrotlienc.pc.in scripts/libbrotlienc.pc.in +--- scripts.orig/libbrotlienc.pc.in 2021-07-12 21:37:48.252345973 +0200 ++++ scripts/libbrotlienc.pc.in 2021-07-12 21:38:07.535299541 +0200 +@@ -7,6 +7,6 @@ + URL: https://github.com/google/brotli + Description: Brotli encoder library + Version: @PACKAGE_VERSION@ +-Libs: -L${libdir} -R${libdir} -lbrotlienc ++Libs: -L${libdir} -lbrotlienc + Requires.private: libbrotlicommon >= 1.0.2 + Cflags: -I${includedir} From 05d2b82779f209e00199920a8d5a11c3b55e3e16 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 21 Jul 2021 11:13:21 +0200 Subject: [PATCH 0446/9987] adding easyconfigs: Julia-1.6.2-linux-x86_64.eb --- .../j/Julia/Julia-1.6.2-linux-x86_64.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.6.2-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.2-linux-x86_64.eb new file mode 100644 index 00000000000..d6cc2f24346 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.2-linux-x86_64.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.6.2' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['3eb4b5775b0df1ad38f6c409e989501ab445c95bcb01ab02bd60f5bd1e823240'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.so'], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lang' From c4206afcb17c61d033d14f8569a6a6c71291f3c7 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 21 Jul 2021 15:08:45 +0200 Subject: [PATCH 0447/9987] adding easyconfigs: Go-1.16.6.eb --- easybuild/easyconfigs/g/Go/Go-1.16.6.eb | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.16.6.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.16.6.eb b/easybuild/easyconfigs/g/Go/Go-1.16.6.eb new file mode 100644 index 00000000000..f0fc4a279e7 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.16.6.eb @@ -0,0 +1,25 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Tarball' + +name = 'Go' +version = '1.16.6' + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] +sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] +checksums = ['be333ef18b3016e9d7cb7b1ff1fdb0cac800ca0be4cf2290fe613b3d069dfe0d'] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +modextravars = {'GOROOT': '%(installdir)s'} +moduleclass = 'compiler' From 52da28279e50fd9e5e3d56ad5a1df602e5fec81e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 21 Jul 2021 15:23:41 +0200 Subject: [PATCH 0448/9987] Explicitly specify use of pip and pip sanity checking for PySide2 --- .../easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb index dcc75de0c8d..3ec394a440c 100644 --- a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -24,6 +24,9 @@ dependencies = [ ('Qt5', '5.14.2'), ] +use_pip = True +sanity_pip_check = True + preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' preinstallopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' From 22d3da58a39c01c2766a6237792f304a200fcb57 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 21 Jul 2021 15:40:11 +0200 Subject: [PATCH 0449/9987] Explicitly prevent downloading pip dependencies for PySide2 --- .../easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb index 3ec394a440c..f69741b3eed 100644 --- a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -26,6 +26,7 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' From 71dc9fd2e70ac66f6efca0af2e5740d084afd740 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 21 Jul 2021 18:17:03 +0200 Subject: [PATCH 0450/9987] adding easyconfigs: Spack-0.16.2.eb --- easybuild/easyconfigs/s/Spack/Spack-0.16.2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spack/Spack-0.16.2.eb diff --git a/easybuild/easyconfigs/s/Spack/Spack-0.16.2.eb b/easybuild/easyconfigs/s/Spack/Spack-0.16.2.eb new file mode 100644 index 00000000000..ee2085e032f --- /dev/null +++ b/easybuild/easyconfigs/s/Spack/Spack-0.16.2.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'Spack' +version = '0.16.2' + +homepage = 'https://spack.io/' +description = """Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific + software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, + and all of these builds can coexist on the same machine.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/spack/spack/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ed3e5d479732b0ba82489435b4e0f9088571604e789f7ab9bc5ce89030793350'] + +sanity_check_paths = { + 'files': ['bin/spack'], + 'dirs': ['etc/spack/defaults', 'lib/spack', 'share/spack', 'var/spack'], +} + +sanity_check_commands = [ + "spack list", + "spack versions gcc", +] + +moduleclass = 'devel' From b2f3a6f9e4a19a57a4baad224e55f7b966af9b40 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 21 Jul 2021 19:22:41 +0200 Subject: [PATCH 0451/9987] Another patch --- .../libjxl-0.3.7_openexr-3.0_compat.patch | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_openexr-3.0_compat.patch diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_openexr-3.0_compat.patch b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_openexr-3.0_compat.patch new file mode 100644 index 00000000000..0b29f2041c3 --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_openexr-3.0_compat.patch @@ -0,0 +1,28 @@ +# Compatibility with OpenEXR 3.0 series. +# Taken from https://gitlab.com/wg1/jpeg-xl/-/issues/238 + +diff -urN a/lib/extras/codec_exr.cc b/lib/extras/codec_exr.cc +--- a/lib/extras/codec_exr.cc 2021-03-29 20:31:10.000000000 +0900 ++++ b/lib/extras/codec_exr.cc 2021-05-02 16:14:52.532445954 +0900 +@@ -90,8 +90,8 @@ + return pos_ < bytes_.size(); + } + +- OpenEXR::Int64 tellg() override { return pos_; } +- void seekg(const OpenEXR::Int64 pos) override { ++ uint64_t tellg() override { return pos_; } ++ void seekg(const uint64_t pos) override { + JXL_ASSERT(pos + 1 <= bytes_.size()); + pos_ = pos; + } +@@ -115,8 +115,8 @@ + pos_ += n; + } + +- OpenEXR::Int64 tellp() override { return pos_; } +- void seekp(const OpenEXR::Int64 pos) override { ++ uint64_t tellp() override { return pos_; } ++ void seekp(const uint64_t pos) override { + if (bytes_.size() + 1 < pos) { + bytes_.resize(pos - 1); + } From 7dc93b3d2e1922b30ed7f5d3d2c90556490a3788 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 22 Jul 2021 07:59:42 +0200 Subject: [PATCH 0452/9987] adding easyconfigs: StringTie-2.1.7-GCC-10.3.0.eb --- .../s/StringTie/StringTie-2.1.7-GCC-10.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-2.1.7-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.1.7-GCC-10.3.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.1.7-GCC-10.3.0.eb new file mode 100644 index 00000000000..1343bdd7d03 --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.1.7-GCC-10.3.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '2.1.7' + +homepage = 'https://ccb.jhu.edu/software/stringtie/' +description = 'StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c75f3ba616e710c502c4550c5a0edf189a95a6916b52658a265b511e0d29496c'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +# the test script downloads some test data from the internet +buildopts = 'release && ./run_tests.sh' + +files_to_copy = [ + (['%(namelower)s', 'prepDE.py'], 'bin'), + 'README.md', + 'LICENSE' +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 0461497a469e9baf86cafe661ea0247a3b8d2607 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 22 Jul 2021 08:46:47 +0200 Subject: [PATCH 0453/9987] adding easyconfigs: PEAR-0.9.11-GCC-10.3.0.eb --- .../p/PEAR/PEAR-0.9.11-GCC-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-10.3.0.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-10.3.0.eb new file mode 100644 index 00000000000..6850da15eba --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'PEAR' +version = '0.9.11' + +homepage = 'https://cme.h-its.org/exelixis/web/software/%(namelower)s/' +description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. + It is fully parallelized and can run with as low as just a few kilobytes of memory.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +# Needs manual download via web-form, +# https://www.h-its.org/en/research/sco/software/#NextGenerationSequencingSequenceAnalysis +sources = ['%(namelower)s-src-%(version)s.tar.gz'] +checksums = ['94f4a1835cd75ec6fab83405c2545ddba6b6bb1644579222e9cc2ad57a59d654'] + +builddependencies = [('Autotools', '20210128')] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +preconfigopts = 'aclocal && autoconf && automake --add-missing && ' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From b0ef87ec56a3d9f29c7cc8e74c02ac75ffb73ed6 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 22 Jul 2021 12:04:34 +0200 Subject: [PATCH 0454/9987] adding easyconfigs: libdeflate-1.7-GCCcore-10.2.0.eb, libRmath-4.1.0-GCCcore-10.2.0.eb, LIBSVM-3.25-GCCcore-10.2.0.eb, TCLAP-1.2.4-GCCcore-10.2.0.eb, vt-0.57721-GCC-10.2.0.eb and patches: vt-0.57721_avoid-implicit-conversion.patch, vt-0.57721_fail-on-test-error.patch, vt-0.57721_fix-Rmath-includes.patch, vt-0.57721_update_htsutils.patch, vt-0.57721_use-external-libs.patch --- .../l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb | 38 ++++ .../libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb | 53 ++++++ .../libdeflate-1.7-GCCcore-10.2.0.eb | 38 ++++ .../t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb | 32 ++++ .../easyconfigs/v/vt/vt-0.57721-GCC-10.2.0.eb | 72 ++++++++ .../v/vt/vt-0.57721_update_htsutils.patch | 168 ++++++++++++++++++ 6 files changed, 401 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/v/vt/vt-0.57721_update_htsutils.patch diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..54bac051fb8 --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM' +version = '3.25' + +homepage = 'https://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression + (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'cjlin1' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%s.tar.gz' % version.replace('.', '')] +patches = ['LIBSVM-3.23_shared_lib.patch'] +checksums = [ + '1f587ec0df6fd422dfe50f942f8836ac179b0723b768fe9d2fabdfd1601a0963', # v325.tar.gz + 'c0ede89365949644f5d7f11382a3f176fd76317c7f5ae5769226ff7c3a801fe6', # LIBSVM-3.23_shared_lib.patch +] + +dependencies = [('binutils', '2.35')] + +local_bins = ['svm-%s' % x for x in ['predict', 'scale', 'train']] + +files_to_copy = [ + (local_bins, 'bin'), + (['svm.o'], 'lib'), + (['libsvm*'], 'lib'), + (['svm.h'], 'include/libsvm'), + 'tools' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + ['lib/libsvm.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..1f09fb058ea --- /dev/null +++ b/easybuild/easyconfigs/l/libRmath/libRmath-4.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# Updated: Denis Kristak (INUITS) +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'libRmath' +version = '4.1.0' + +homepage = 'https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library' +description = """The routines supporting the distribution and special functions in R and a few others are declared + in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = ['R-%(version)s.tar.gz'] +checksums = ['e8e68959d7282ca147360fc9644ada9bd161bab781bab14d33b8999a95182781'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('cURL', '7.72.0'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('PCRE2', '10.35'), +] + +parallel = 1 + +start_dir = 'src/nmath/standalone' + +preconfigopts = 'cd %(builddir)s/R-%(version)s && ' +configopts = '--with-readline=no --with-recommended-packages=no --with-x=no' + +postinstallcmds = ["cp -r %(builddir)s/R-%(version)s/src/include/R_ext %(installdir)s/include/"] + +runtest = 'check' + +sanity_check_paths = { + 'files': ["lib/libRmath.%s" % SHLIB_EXT, "lib/libRmath.a", + "lib/pkgconfig/libRmath.pc", + "include/Rmath.h"], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c517a5b337e --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'libdeflate' +version = '1.7' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a5e6a0a9ab69f40f0f59332106532ca76918977a974e7004977a9498e3f11350'] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b2e44cb235d --- /dev/null +++ b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.4-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'TCLAP' +version = '1.2.4' + +homepage = 'http://tclap.sourceforge.net/' +description = """TCLAP is a small, flexible library that provides a simple interface for defining and accessing +command line arguments. It was intially inspired by the user friendly CLAP libary.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['634c5b59dbb1ccbc9d6a5f6de494a257e29a3f59dcb6fc30445ff39b45188574'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "autoreconf -i -f && " + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/tclap/CmdLine.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.2.0.eb new file mode 100644 index 00000000000..f5b37df4b68 --- /dev/null +++ b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.2.0.eb @@ -0,0 +1,72 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) + +easyblock = 'MakeCp' + +name = 'vt' +version = '0.57721' + +homepage = 'https://genome.sph.umich.edu/wiki/Vt' +description = """A tool set for short variant discovery in genetic sequence data.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'atks' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-0.57721_use-external-libs.patch', + '%(name)s-0.57721_fix-Rmath-includes.patch', + '%(name)s-0.57721_avoid-implicit-conversion.patch', + '%(name)s-0.57721_fail-on-test-error.patch', + '%(name)s-0.57721_update_htsutils.patch', +] +checksums = [ + '8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17', # 0.57721.tar.gz + '5a31713ae7c5febf850eec294dbba45b6b240d832cb94bdfe9ee695fd13e45bb', # vt-0.57721_use-external-libs.patch + '663525f5180a66d8817f271a69de1884576e2414d46b7ba93029d78f71d5b14c', # vt-0.57721_fix-Rmath-includes.patch + '56d874d5c7d488761f25afb4ee3717c88dfd959ed76efb75a8531b8428d30ccd', # vt-0.57721_avoid-implicit-conversion.patch + '4146282eb6ec852485f5a16e647da9c3b210450ceb5519b9b4a98bc52124469a', # vt-0.57721_fail-on-test-error.patch + '1c170b7ba2a4d392830f64392075ff75bbbc29137fe9f2922aeb7345e2ab6298', # vt-0.57721_update_htsutils.patch +] + +# checksums = [ +# '8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17', # 0.57721.tar.gz +# '5a31713ae7c5febf850eec294dbba45b6b240d832cb94bdfe9ee695fd13e45bb', # vt-0.57721_use-external-libs.patch +# '663525f5180a66d8817f271a69de1884576e2414d46b7ba93029d78f71d5b14c', # vt-0.57721_fix-Rmath-includes.patch +# '56d874d5c7d488761f25afb4ee3717c88dfd959ed76efb75a8531b8428d30ccd', # vt-0.57721_avoid-implicit-conversion.patch +# 'ba2cfc24a88a4291b2da634db49e18199c379eb95d3b3acac59556bc68c292df', # vt-0.57721_update-faidx.patch +# '4146282eb6ec852485f5a16e647da9c3b210450ceb5519b9b4a98bc52124469a', # vt-0.57721_fail-on-test-error.patch +# ] + +builddependencies = [ + ('binutils', '2.35'), + ('TCLAP', '1.2.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.72.0'), + ('PCRE', '8.44'), + ('PCRE2', '10.35'), + ('libdeflate', '1.7'), + ('libRmath', '4.1.0'), + ('LIBSVM', '3.25'), + ('HTSlib', '1.12'), +] + +runtest = 'test' + +files_to_copy = [ + (['vt'], 'bin'), + (['*.h'], 'include/vt'), + 'test', 'README.md', 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/vt'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vt/vt-0.57721_update_htsutils.patch b/easybuild/easyconfigs/v/vt/vt-0.57721_update_htsutils.patch new file mode 100644 index 00000000000..59f6400f926 --- /dev/null +++ b/easybuild/easyconfigs/v/vt/vt-0.57721_update_htsutils.patch @@ -0,0 +1,168 @@ +diff -ruN vt-0.57721_orig/hts_utils.cpp vt-0.57721/hts_utils.cpp +--- vt-0.57721_orig/hts_utils.cpp 2018-05-09 02:33:23.000000000 +0200 ++++ vt-0.57721/hts_utils.cpp 2021-07-14 14:19:04.897424632 +0200 +@@ -1,17 +1,13 @@ + /* The MIT License +- + Copyright (c) 2013 Adrian Tan +- + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: +- + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. +- + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +@@ -40,36 +36,13 @@ + */ + char *faidx_fetch_uc_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len) + { +- int l; +- char c; +- khiter_t iter; +- faidx1_t val; +- char *seq=NULL; +- +- // Adjust position +- iter = kh_get(s, fai->hash, c_name); +- if(iter == kh_end(fai->hash)) return 0; +- val = kh_value(fai->hash, iter); +- if(p_end_i < p_beg_i) p_beg_i = p_end_i; +- if(p_beg_i < 0) p_beg_i = 0; +- else if(val.len <= p_beg_i) p_beg_i = val.len - 1; +- if(p_end_i < 0) p_end_i = 0; +- else if(val.len <= p_end_i) p_end_i = val.len - 1; +- +- // Now retrieve the sequence +- int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET); +- if ( ret<0 ) +- { +- *len = -1; +- fprintf(stderr, "[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n"); +- return NULL; +- } +- l = 0; +- seq = (char*)malloc(p_end_i - p_beg_i + 2); +- while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1) +- if (isgraph(c)) seq[l++] = toupper(c); +- seq[l] = '\0'; +- *len = l; ++ char* seq = faidx_fetch_seq(fai, c_name, p_beg_i, p_end_i, len); ++ ++ for (int32_t i=0; i<*len; ++i) ++ { ++ if (isgraph(seq[i])) seq[i] = toupper(seq[i]); ++ } ++ + return seq; + } + +@@ -330,7 +303,7 @@ + kputw(bam_cigar_oplen(cigar[i]), &str); + char* stop; + uint32_t len = strtol(str.s, &stop, 10); +- assert(stop); ++ //assert(stop); + + if (op=='M') + { +@@ -425,7 +398,11 @@ + */ + void bcf_hdr_print(bcf_hdr_t *h) + { +- if ( h->dirty ) bcf_hdr_sync(h); ++ if (h->dirty && bcf_hdr_sync(h)<0) ++ { ++ fprintf(stderr, "[%s:%d %s] Cannot update header\n", __FILE__, __LINE__, __FUNCTION__); ++ exit(1); ++ } + kstring_t htxt = {0,0,0}; + bcf_hdr_format(h, 0, &htxt); + std::cerr << htxt.s; +diff -ruN vt-0.57721_orig/hts_utils.h vt-0.57721/hts_utils.h +--- vt-0.57721_orig/hts_utils.h 2018-05-09 02:33:23.000000000 +0200 ++++ vt-0.57721/hts_utils.h 2021-07-14 14:18:46.925356770 +0200 +@@ -1,17 +1,13 @@ + /* The MIT License +- + Copyright (c) 2013 Adrian Tan +- + Permission is hereby granted, free of charge, to any person obtaining a copy + of this software and associated documentation files (the "Software"), to deal + in the Software without restriction, including without limitation the rights + to use, copy, modify, merge, publish, distribute, sublicense, and/or sell + copies of the Software, and to permit persons to whom the Software is + furnished to do so, subject to the following conditions: +- + The above copyright notice and this permission notice shall be included in + all copies or substantial portions of the Software. +- + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +@@ -47,13 +43,6 @@ + + KHASH_MAP_INIT_STR(s, faidx1_t) + +-struct __faidx_t { +- BGZF *bgzf; +- int n, m; +- char **name; +- khash_t(s) *hash; +-}; +- + /** + * An alternate sequence fetcher for upper case sequence. + */ +@@ -118,12 +107,12 @@ + /** + * Gets the 1 based start position of the first mapped base in the read. + */ +-#define bam_get_pos1(s) ((s)->core.pos + 1) ++#define bam_get_pos1(s) ((int32_t)(s)->core.pos + 1) + + /** + * Gets the 0 based start position of the first mapped base in the read. + */ +-#define bam_get_pos0(s) ((s)->core.pos) ++#define bam_get_pos0(s) ((int32_t)(s)->core.pos) + + /** + * Gets the end position of the last mapped base in the read. +@@ -451,7 +440,7 @@ + /** + * Get 0-based position + */ +-#define bcf_get_pos0(v) ((v)->pos) ++#define bcf_get_pos0(v) ((int32_t)(v)->pos) + + /** + * Set 0-based position +@@ -461,12 +450,12 @@ + /** + * Get 1-based position + */ +-#define bcf_get_pos1(v) ((v)->pos+1) ++#define bcf_get_pos1(v) ((int32_t)(v)->pos+1) + + /** + * Get 1-based end position + */ +-#define bcf_get_end1(v) ((v)->pos + strlen((v)->d.allele[0])) ++#define bcf_get_end1(v) ((int32_t)(v)->pos + strlen((v)->d.allele[0])) + + /** + * Set 1-based position +@@ -648,4 +637,4 @@ + */ + void notice(const char * msg, ...); + +-#endif ++#endif +\ No newline at end of file From 44679070d172d812f798c13da8a3cc11ec74bd5a Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 22 Jul 2021 12:11:51 +0200 Subject: [PATCH 0455/9987] adding easyconfigs: vcflib-1.0.2-GCC-10.2.0.eb, fsom-20141119-GCCcore-10.2.0.eb, intervaltree-0.1-GCCcore-10.2.0.eb, fastahack-1.0.0-GCCcore-10.2.0.eb and patches: vcflib-1.0.2_use-external-deps.patch, fsom-20141119_build-libs.patch, fsom-20141119_fix-abs-overload.patch, fastahack-1.0.0_build-libs.patch --- .../fastahack-1.0.0-GCCcore-10.2.0.eb | 32 ++++++++++ .../f/fsom/fsom-20141119-GCCcore-10.2.0.eb | 34 +++++++++++ .../intervaltree-0.1-GCCcore-10.2.0.eb | 32 ++++++++++ .../v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 60 +++++++++++++++++++ 4 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..73aaa73c4a0 --- /dev/null +++ b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'fastahack' +version = '1.0.0' + +homepage = 'https://github.com/ekg/fastahack' +description = """Utilities for indexing and sequence extraction from FASTA files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.0.0_build-libs.patch'] +checksums = [ + 'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae', # v1.0.0.tar.gz + '7f804486c6bafd9b1572cb5f86ff28dbebb4d6da551bde1091d6ff8f82748bf4', # fastahack-1.0.0_build-libs.patch +] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfastahack.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..eac8d686cd6 --- /dev/null +++ b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'fsom' +version = '20141119' +local_commit = 'a6ef318' + +homepage = 'https://github.com/ekg/fsom' +description = """A tiny C library for managing SOM (Self-Organizing Maps) neural networks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = [ + '%(name)s-20141119_build-libs.patch', + '%(name)s-20141119_fix-abs-overload.patch' +] + + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfsom.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..bdf771c0994 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'intervaltree' +version = '0.1' + +homepage = 'https://github.com/ekg/intervaltree' +description = """An interval tree can be used to efficiently find a set of numeric intervals + overlapping or containing another interval. This library provides a basic implementation of an + interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307'] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +preinstallopts = 'DESTDIR="" PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/interval_tree_test', 'include/intervaltree/IntervalTree.h'], + 'dirs': [], +} +sanity_check_commands = ["interval_tree_test"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb new file mode 100644 index 00000000000..1b77b9cb61a --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -0,0 +1,60 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.2' +# versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/vcflib/vcflib' +description = """vcflib provides methods to manipulate and interpret sequence variation as it can be + described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended + to concisely describe reference-indexed genetic variations between individuals.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['vcflib-1.0.2_use-external-deps.patch'] +checksums = [ + 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz + '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.12'), + ('tabixpp', '1.1.0'), + ('intervaltree', '0.1'), + ('fastahack', '1.0.0'), + ('filevercmp', '20191210'), + ('fsom', '20141119'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), +] + +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f -regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" +preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" +preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" +preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" +preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " + +sanity_check_paths = { + 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["vcfremap"] + +moduleclass = 'bio' From 396f4d09cd5fc17fe92bdc78c6c67f4e79e2f899 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 22 Jul 2021 12:17:42 +0200 Subject: [PATCH 0456/9987] adding easyconfigs: any2fasta-0.4.2-GCCcore-10.2.0.eb, filevercmp-20191210-GCCcore-10.2.0.eb, freebayes-1.3.5-GCC-10.2.0.eb, multichoose-1.0.3-GCCcore-10.2.0.eb, samclip-0.4.0-GCCcore-10.2.0.eb and patches: filevercmp-20191210_build-libs.patch --- .../any2fasta-0.4.2-GCCcore-10.2.0.eb | 34 ++++++++ .../filevercmp-20191210-GCCcore-10.2.0.eb | 30 +++++++ .../filevercmp-20191210_build-libs.patch | 87 +++++++++++++++++++ .../f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb | 43 +++++++++ .../multichoose-1.0.3-GCCcore-10.2.0.eb | 26 ++++++ .../s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb | 27 ++++++ 6 files changed, 247 insertions(+) create mode 100644 easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..4b16b010fe9 --- /dev/null +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'any2fasta' +version = '0.4.2' + +homepage = 'https://github.com/tseemann/any2fasta' +description = "Convert various sequence formats to FASTA" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# https://github.com/tseemann/any2fasta +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] + +dependencies = [('Perl', '5.32.0')] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['any2fasta'], + 'dirs': [], +} + +sanity_check_commands = [ + 'any2fasta -h', + 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..2ce8759f9a6 --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'filevercmp' +version = '20191210' +local_commit = 'df20dcc' + +homepage = 'https://github.com/ekg/filevercmp' +description = """filevercmp function as in sort --version-sort.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20191210_build-libs.patch'] + + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'DESTDIR="" PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch new file mode 100644 index 00000000000..791f1b231ab --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch @@ -0,0 +1,87 @@ +diff -ruN filevercmp-master_orig/Makefile filevercmp-master/Makefile +--- filevercmp-master_orig/Makefile 2019-12-10 10:58:23.000000000 +0100 ++++ filevercmp-master/Makefile 2021-07-13 16:35:15.738330513 +0200 +@@ -4,18 +4,69 @@ + + OBJS= main.o filevercmp.o + +-all: filevercmp ++# Use ?= to allow overriding from the env or command-line, e.g. ++# ++# make CXXFLAGS="-O3 -fPIC" install ++# ++# Package managers will override many of these variables automatically, so ++# this is aimed at making it easy to create packages (Debian packages, ++# FreeBSD ports, MacPorts, pkgsrc, etc.) ++ ++CC ?= cc ++CFLAGS ?= -O -g #-m64 #-arch ppc ++ ++PREFIX ?= /usr/local ++STRIP ?= strip ++INSTALL ?= install -c ++MKDIR ?= mkdir -p ++AR ?= ar ++ARFLAGS ?= rs ++ ++BIN = filevercmp ++LIB = libfilevercmp.a ++SOVERSION = 0 ++SLIB = libfilevercmp.so ++OBJS = filevercmp.o ++ ++LIBDIR = $(DESTDIR)$(PREFIX)/lib ++BINDIR = $(DESTDIR)$(PREFIX)/bin ++INCDIR = $(DESTDIR)$(PREFIX)/include/filevercmp ++ ++.SUFFIXES:.c .o .pico .so ++ ++.c.o: ++ $(CC) $(CFLAGS) -I. -c -o $@ $< ++ ++.c.pico: ++ $(CC) $(CFLAGS) -I. -fPIC -c -o $@ $< ++ ++all: $(BIN) $(SLIB) $(LIB) ++ ++$(LIB): $(OBJS) ++ $(AR) $(ARFLAGS) $@ $^ ++ ++$(SLIB): $(OBJS:.o=.pico) ++ $(CC) -shared -Wl,-soname,$(SLIB).$(SOVERSION) $(LDFLAGS) -o $@ $^ $(LIBS) ++ ln -sf $@ $(SLIB).$(SOVERSION) ++ ++$(BIN): $(OBJS) main.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) ++ ++install: all ++ $(MKDIR) $(BINDIR) ++ $(MKDIR) $(LIBDIR) ++ $(MKDIR) $(INCDIR) ++ $(INSTALL) $(BIN) $(BINDIR) ++ $(INSTALL) *.h $(INCDIR) ++ $(INSTALL) $(LIB) $(SLIB) $(SLIB).$(SOVERSION) $(LIBDIR) ++ ++install-strip: install ++ $(STRIP) $(BINDIR)/$(BIN) $(LIBDIR)/$(LIB) ++ ++cleanlocal: ++ rm -rf $(BIN) $(LIB) $(SLIB) $(OBJS) $(DESTDIR) ++ rm -fr gmon.out *.o a.out *.dSYM $(BIN) *~ *.a tabix.aux tabix.log \ ++ tabix.pdf *.class libtabix.*.dylib ++ cd htslib && $(MAKE) clean + +-clean: +- rm -f filevercmp ${OBJS} +- +-.PHONY: all clean +- +-filevercmp.o: filevercmp.c filevercmp.h +- $(CC) $(CPPFLAGS) $(CFLAGS) -c filevercmp.c +- +-main.o: main.c filevercmp.h +- $(CC) $(CPPFLAGS) $(CFLAGS) -c main.c +- +-filevercmp: ${OBJS} +- $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) -o filevercmp ${OBJS} ++clean: cleanlocal-recur diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb new file mode 100644 index 00000000000..4f981788db9 --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'freebayes' +version = '1.3.5' + +homepage = 'https://github.com/freebayes/freebayes' +description = "Bayesian haplotype-based genetic polymorphism discovery and genotyping." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/freebayes', + 'repo_name': 'freebayes', + 'tag': 'v1.3.5', + 'recursive': True, + }, +}] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), +] + +dependencies = [ + ('parallel', '20210322'), + ('VCFtools', '0.1.16'), +] + +configopts = "--buildtype debug" + +postinstallcmds = ['cp %(builddir)s/freebayes/scripts/* %(installdir)s/'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['bin/freebayes', 'bin/bamleftalign', 'freebayes-parallel'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..423504cb402 --- /dev/null +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'multichoose' +version = '1.0.3' + +homepage = 'https://github.com/ekg/multichoose' +description = """generate multiset combinations (n multichoose k).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877'] + +builddependencies = [('binutils', '2.35')] + +local_bins = [name, 'multipermute'] +files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/multichoose')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..52eb3f5c232 --- /dev/null +++ b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'samclip' +version = '0.4.0' + +homepage = 'https://github.com/tseemann/samclip' +description = """Filter SAM file for soft and hard clipped alignments.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127'] + +dependencies = [('Perl', '5.32.0')] + +sanity_check_paths = { + 'files': [name], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From a599f408b1a58d2d35cf25678f28b3ac00e599b0 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 22 Jul 2021 12:26:36 +0200 Subject: [PATCH 0457/9987] update --- .../smithwaterman-20160702-GCCcore-10.2.0.eb | 34 +++++++++++++ .../s/snippy/snippy-4.6.0-GCC-10.2.0.eb | 49 +++++++++++++++++++ .../snp-sites-2.5.1-GCCcore-10.2.0.eb | 37 ++++++++++++++ .../w/wgsim/wgsim-20111017-GCC-10.2.0.eb | 32 ++++++++++++ .../w/wgsim/wgsim-20111017_add_makefile.patch | 9 ++++ 5 files changed, 161 insertions(+) create mode 100644 easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/w/wgsim/wgsim-20111017_add_makefile.patch diff --git a/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..65ec48867c8 --- /dev/null +++ b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'smithwaterman' +version = '20160702' +local_commit = '2610e25' + +homepage = 'https://github.com/ekg/smithwaterman' +description = """smith-waterman-gotoh alignment algorithm.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20160702_build-shared-lib.patch'] +checksums = [ + '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8', # 2610e25.tar.gz + '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582', # smithwaterman-20160702_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..b27c7c54550 --- /dev/null +++ b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'Tarball' + +name = 'snippy' +version = '4.6.0' + +homepage = 'https://github.com/tseemann/snippy' +description = "Rapid haploid variant calling and core genome alignment" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/tseemann/snippy/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7264e3819e249387effd3eba170ff49404b1cf7347dfa25944866f5aeb6b11c3'] + +dependencies = [ + ('Perl', '5.32.0'), + ('BioPerl', '1.7.8'), + ('BWA', '0.7.17'), + ('BCFtools', '1.12'), + ('BEDTools', '2.30.0'), + ('SAMtools', '1.11'), + ('parallel', '20210322'), + ('minimap2', '2.18'), + ('vcflib', '1.0.2'), + ('vt', '0.57721'), + ('snpEff', '5.0', '-Java-13', True), + ('samclip', '0.4.0'), + ('seqtk', '1.3'), + ('snp-sites', '2.5.1'), + ('any2fasta', '0.4.2'), + ('wgsim', '20111017'), + ('freebayes', '1.3.5'), # todo freebayes-parallel +] + +# remove included binaries for required dependencies +postinstallcmds = ["rm -r %(installdir)s/binaries"] + +sanity_check_paths = { + 'files': ['bin/snippy', 'perl5/Snippy/Version.pm'], + 'dirs': ['etc'], +} + +sanity_check_commands = [ + "snippy --version", + "snippy --check", + "snippy --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d21942b0531 --- /dev/null +++ b/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'snp-sites' +version = '2.5.1' + +homepage = 'https://sanger-pathogens.github.io/snp-sites/' +description = """Finds SNP sites from a multi-FASTA alignment file.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'sanger-pathogens' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['913f79302e5d3127aea382756abc9ffeb05e26ce00022f43a6ea16a55cdd7a7e'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), + ('binutils', '2.35'), + ('Check', '0.15.2'), +] + +dependencies = [('zlib', '1.2.11')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/snp-sites'], + 'dirs': [], +} +sanity_check_commands = ["snp-sites -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb new file mode 100644 index 00000000000..de520d35fab --- /dev/null +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'wgsim' +version = '20111017' +local_commit = 'a12da3375ff3b51a5594d4b6fa35591173ecc229' + +homepage = 'https://github.com/lh3/wgsim/' +description = """Wgsim is a small tool for simulating sequence reads from a reference genome.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = [ + ('wgsim-%(version)s_add_makefile.patch', 1) +] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +files_to_copy = [(["wgsim"], 'bin')] + +sanity_check_commands = [("%(name)s -h 2>&1 | grep 'Program: wgsim (short read simulator)'")] + +sanity_check_paths = { + 'files': ['bin/wgsim'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017_add_makefile.patch b/easybuild/easyconfigs/w/wgsim/wgsim-20111017_add_makefile.patch new file mode 100644 index 00000000000..635f3c569ea --- /dev/null +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017_add_makefile.patch @@ -0,0 +1,9 @@ +diff -ruN wgsim-master_orig/Makefile wgsim-master/Makefile +--- wgsim-master_orig/Makefile 1970-01-01 01:00:00.000000000 +0100 ++++ wgsim-master/Makefile 2021-07-16 11:35:20.997347480 +0200 +@@ -0,0 +1,5 @@ ++CC=gcc ++CFLAGS=-g -O2 -Wall ++ ++install: ++ $(CC) $(CFLAGS) -o wgsim -lz -lm wgsim.c From b9cd82734b23234f38eac29d30a13ac85dc05fad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 22 Jul 2021 13:51:00 +0200 Subject: [PATCH 0458/9987] adding easyconfigs: ncdu-1.16-GCC-10.3.0.eb --- .../n/ncdu/ncdu-1.16-GCC-10.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdu/ncdu-1.16-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.16-GCC-10.3.0.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.16-GCC-10.3.0.eb new file mode 100644 index 00000000000..3ed4021b2c5 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.16-GCC-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ncdu' +version = '1.16' + +homepage = 'https://dev.yorhel.nl/ncdu' +description = """Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a + remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular + desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like + environment with ncurses installed.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://dev.yorhel.nl/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2b915752a183fae014b5e5b1f0a135b4b408de7488c716e325217c2513980fd4'] + +dependencies = [('ncurses', '6.2')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' From 605ddd331ee2669ef58a43598f435159b7019e50 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 22 Jul 2021 14:03:07 +0200 Subject: [PATCH 0459/9987] Optimise PySide2/5.14.2.3 EB file --- .../p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb index f69741b3eed..4d1fe0c1f1e 100644 --- a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -14,8 +14,8 @@ sources = ['pyside-setup-opensource-src-%(version)s.tar.xz'] checksums = ['032de309505c78ba52c225aaf5fd717b8d87ae863aa7cee8ba58ba6141c59022'] builddependencies = [ + ('binutils', '2.35'), ('CMake', '3.18.4'), - ('Sphinx', '3.5.2'), ('Clang', '11.0.1'), ] @@ -24,13 +24,17 @@ dependencies = [ ('Qt5', '5.14.2'), ] -use_pip = True +use_pip = False sanity_pip_check = True download_dep_fail = True preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' + prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' +buildcmd = 'build --parallel=16' + preinstallopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' +install_target = 'install --parallel=16' options = {'modulename': 'PySide2'} From 34c0a184aab84750757897c874c77d082166ed2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 22 Jul 2021 14:34:26 +0200 Subject: [PATCH 0460/9987] adding easyconfigs: KronaTools-2.8-GCC-10.3.0.eb --- .../k/KronaTools/KronaTools-2.8-GCC-10.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCC-10.3.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCC-10.3.0.eb new file mode 100644 index 00000000000..ed750ec4e87 --- /dev/null +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8-GCC-10.3.0.eb @@ -0,0 +1,41 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# this is a bug fix to make sure the symlinks in bin are not getting destroyed +# by Easybuild when it is tidying up +# This build also links updateTaxonomy.sh and updateAccessions.sh in the bin folder +# so users can install their own Taxonomy database + +easyblock = 'Tarball' + +name = 'KronaTools' +version = '2.8' + +homepage = 'https://github.com/marbl/Krona/wiki/KronaTools' +description = """Krona Tools is a set of scripts to create Krona charts from +several Bioinformatics tools as well as from text and XML files.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['56efc028b6226a1aea8ec4e9f049836b07d4833e7e4d5b9189118ed51a47c9c0'] + +dependencies = [('Perl', '5.32.1')] + +postinstallcmds = [ + "cd %(installdir)s && ./install.pl --prefix=%(installdir)s;", + "cd %(installdir)s/bin && ln -s ../updateAccessions.sh . && ln -s ../updateTaxonomy.sh .", +] + +sanity_check_paths = { + 'files': ['bin/ktClassifyBLAST', 'bin/ktImportBLAST', 'bin/ktImportTaxonomy', + 'bin/updateAccessions.sh', 'bin/updateTaxonomy.sh'], + 'dirs': ['data', 'img', 'scripts'], +} + +sanity_check_commands = [ + "updateAccessions.sh --help", + "ktImportText", +] + +moduleclass = 'bio' From f732d8868243a298f3a2a7442863dbf00ecefcf8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 22 Jul 2021 14:57:12 +0200 Subject: [PATCH 0461/9987] adding easyconfigs: DIAMOND-2.0.11-GCC-10.3.0.eb --- .../d/DIAMOND/DIAMOND-2.0.11-GCC-10.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.11-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.11-GCC-10.3.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.11-GCC-10.3.0.eb new file mode 100644 index 00000000000..516ab46667d --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.11-GCC-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.0.11' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'bbuchfink' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['41f3197aaafff9c42763fb7658b67f730ebc6dd3c0533c9c3d54bd3166e93f24'] + +separate_build_dir = True + +builddependencies = [ + ('CMake', '3.20.1') +] +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["%(namelower)s help"] + +moduleclass = 'bio' From 03538a591bac0363d01f8c1279516779e927ca92 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 22 Jul 2021 16:53:07 +0200 Subject: [PATCH 0462/9987] Don't resolve symlinks on copy --- easybuild/easyconfigs/s/Spack/Spack-0.16.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Spack/Spack-0.16.2.eb b/easybuild/easyconfigs/s/Spack/Spack-0.16.2.eb index ee2085e032f..7264da653c2 100644 --- a/easybuild/easyconfigs/s/Spack/Spack-0.16.2.eb +++ b/easybuild/easyconfigs/s/Spack/Spack-0.16.2.eb @@ -14,6 +14,8 @@ source_urls = ['https://github.com/spack/spack/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['ed3e5d479732b0ba82489435b4e0f9088571604e789f7ab9bc5ce89030793350'] +keepsymlinks = True + sanity_check_paths = { 'files': ['bin/spack'], 'dirs': ['etc/spack/defaults', 'lib/spack', 'share/spack', 'var/spack'], From 616f5ca80092578e97df3c720e418122942fb1a9 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 22 Jul 2021 17:05:10 +0200 Subject: [PATCH 0463/9987] Julia: fixes SHLIB specifier --- easybuild/easyconfigs/j/Julia/Julia-1.6.2-linux-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.2-linux-x86_64.eb index d6cc2f24346..164cc65c5ed 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.2-linux-x86_64.eb @@ -22,7 +22,7 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['3eb4b5775b0df1ad38f6c409e989501ab445c95bcb01ab02bd60f5bd1e823240'] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.so'], + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] } From 201b0ba3095ba143fc12d227b2bf9480c936e26f Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 22 Jul 2021 15:13:54 +0000 Subject: [PATCH 0464/9987] minimap2 bumped to 2.20 --- .../minimap2/minimap2-2.20-GCCcore-10.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..2966ea397c4 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# Big Data Institute, University of Oxford +# Updated to 2.20 +# J. Sassmannshausen / GSTT + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.20' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['f9eff90a7f14f999df93dff6ed4e3428277edbbd6bda6bdb1800e8d57c9135e3'] + +builddependencies = [('binutils', '2.36.1')] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = ["minimap2 --help"] + +moduleclass = 'bio' From 41b8a8873b5d574e6ba19606c11cb9f5984f0bbc Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 22 Jul 2021 18:00:25 +0200 Subject: [PATCH 0465/9987] adding easyconfigs: VTune-2021.6.0.eb --- .../easyconfigs/v/VTune/VTune-2021.6.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb new file mode 100644 index 00000000000..fa93be8f89a --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +name = 'VTune' +version = '2021.6.0' + +homepage = 'https://software.intel.com/en-us/vtune' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18012/'] +sources = ['l_oneapi_vtune_p_%(version)s.411_offline.sh'] +checksums = ['6b1df7da713337aa665bcc6ff23e4a006695b5bfaf71dffd305cbadca2e5560c'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'tools' From 46136ed5ac59d014afb25bcc15beb2ae02d177f1 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 22 Jul 2021 13:46:46 -0700 Subject: [PATCH 0466/9987] BAli-Phy 3.6.0 --- .../easyconfigs/b/BAli-Phy/BAli-Phy-3.6.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/BAli-Phy/BAli-Phy-3.6.0.eb diff --git a/easybuild/easyconfigs/b/BAli-Phy/BAli-Phy-3.6.0.eb b/easybuild/easyconfigs/b/BAli-Phy/BAli-Phy-3.6.0.eb new file mode 100644 index 00000000000..5218aca79e5 --- /dev/null +++ b/easybuild/easyconfigs/b/BAli-Phy/BAli-Phy-3.6.0.eb @@ -0,0 +1,28 @@ +# # +# This is a contribution from Fred Hutch +# Authors:: John Dey jfdey@fredhutch.org +# # + +easyblock = 'Tarball' + +name = 'BAli-Phy' +version = '3.6.0' + +homepage = 'http://www.bali-phy.org/' +description = """BAli-Phy estimates multiple sequence alignments and evolutionary trees from DNA, amino acid, +or codon sequences.""" + +toolchain = SYSTEM + +source_urls = ['http://www.bali-phy.org/files'] +sources = ['%(namelower)s-%(version)s-linux64.tar.gz'] +checksums = ['c50816938b295a962153fff4ad5790aa4bdc46adb1b8c5ae1e9e30dc0d7a8d07'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['bin', 'lib', 'share'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' From 85f766b524b4830a4be83ec63113a3d15fc95dfb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 22 Jul 2021 23:04:20 +0200 Subject: [PATCH 0467/9987] Fix checksum --- easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb index b6455b3d42f..c82f2f1b6cd 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb @@ -30,7 +30,7 @@ patches = ['libjxl-%(version)s_openexr-3.0_compat.patch'] checksums = [ '8318a5d1ce82e5683a52512b6f242d2b33a1191e89fc76f7c0ead0a1d60f6c60', # v0.3.7.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz - '1be9a0e16cdd1d2749c8111b862c496100ec959d2efaea7996eee86ef796fddd', # skcms-6437475.tar.gz + '2430124e244cb3cd29059215545a17bed4b772e4550317acc755393b8c5e6580', # skcms-6437475.tar.gz 'b5bf92b8eb8f41e7cedce1b43ea3fe7a9407d3cc0e29bb2afec652cabe084cee', # libjxl-0.3.7_openexr-3.0_compat.patch ] From 6243dfdcc11aa593d6d4057c5023d421f9e43b68 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 22 Jul 2021 16:05:21 -0700 Subject: [PATCH 0468/9987] Metal 2020.05.05 --- .../m/Metal/Metal-2020-05-05-foss-2020b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/Metal/Metal-2020-05-05-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-foss-2020b.eb b/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-foss-2020b.eb new file mode 100644 index 00000000000..b2d08a31a35 --- /dev/null +++ b/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'Metal' +version = '2020-05-05' + +homepage = 'http://csg.sph.umich.edu/abecasis/Metal/' +description = """Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large + datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/statgen/METAL/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['0ffa2419ca2ab43766e7e6e8c97822c8ce1f5b6233fb5f992d1b1be1955fede7'] + +builddependencies = [('CMake', '3.18.4')] +dependencies = [('zlib', '1.2.11')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin && ' + + 'cp %(builddir)s/easybuild_obj/bin/metal %(installdir)s/bin' +] + +sanity_check_paths = { + 'files': ['bin/metal'], + 'dirs': [''], +} + +sanity_check_commands = ['%(namelower)s /dev/null'] + +moduleclass = 'bio' From 6253284e8122eb350cde03470a1e31e01709e65c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 23 Jul 2021 07:19:25 +0200 Subject: [PATCH 0469/9987] adding easyconfigs: GffCompare-0.12.2-GCC-10.3.0.eb --- .../GffCompare-0.12.2-GCC-10.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.2-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..b1e07dea5d7 --- /dev/null +++ b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.2-GCC-10.3.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GffCompare' +version = '0.12.2' + +# Some docs also at GitHub site - this is referred to as canonical +homepage = 'https://ccb.jhu.edu/software/stringtie/gffcompare.shtml' +description = """GffCompare provides classification and reference annotation mapping and + matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +# Switched to GitHub sources owing to SSL error at original download site +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6d1419aabe2bb7dae474a4ddf4559de4d1002b9455d6b2af1e0b59b0639af0bd'] + +buildopts = " release" + +files_to_copy = ['%(namelower)s', 'LICENSE', 'README.md'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s -v'] + +moduleclass = 'bio' From d5b94b99d7dfa0985d34b59190bb613a59c6f286 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 23 Jul 2021 08:00:37 +0200 Subject: [PATCH 0470/9987] adding easyconfigs: gffread-0.12.6-GCC-10.3.0.eb --- .../g/gffread/gffread-0.12.6-GCC-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/gffread/gffread-0.12.6-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.6-GCC-10.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.6-GCC-10.3.0.eb new file mode 100644 index 00000000000..70beac3c1a3 --- /dev/null +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.6-GCC-10.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'MakeCp' + +name = 'gffread' +version = '0.12.6' + +homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' +description = """GFF/GTF parsing utility providing format conversions, +region filtering, FASTA sequence extraction and more.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/stringtie/dl/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1c558151f668d6f6fa20be9abb42ad224889855681f6e816b0ad681d85a5ce1b'] + +buildopts = " release" + +files_to_copy = ['%(name)s', 'LICENSE'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s '] + +moduleclass = 'bio' From 370c3d8b2bde88ccdf204449f9dd8fb46b73b98b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 23 Jul 2021 08:30:04 +0200 Subject: [PATCH 0471/9987] adding easyconfigs: Bowtie2-2.4.4-GCC-10.3.0.eb --- .../b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..ce1402a0d0f --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp + +name = 'Bowtie2' +version = '2.4.4' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From 667ad103756e2023d29409c5fc8adfa734d81b36 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 23 Jul 2021 10:20:28 +0200 Subject: [PATCH 0472/9987] adding easyconfigs: Arb-2.19.0-GCC-10.3.0.eb, FLINT-2.7.1-GCC-10.3.0.eb --- .../a/Arb/Arb-2.19.0-GCC-10.3.0.eb | 35 +++++++++++++++++++ .../f/FLINT/FLINT-2.7.1-GCC-10.3.0.eb | 32 +++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arb/Arb-2.19.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.7.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.19.0-GCC-10.3.0.eb b/easybuild/easyconfigs/a/Arb/Arb-2.19.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..4b931759ff0 --- /dev/null +++ b/easybuild/easyconfigs/a/Arb/Arb-2.19.0-GCC-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Arb' +version = '2.19.0' + +homepage = 'https://arblib.org/' + +description = """Arb is a C library for arbitrary-precision interval arithmetic. + It has full support for both real and complex numbers. The library is thread-safe, + portable, and extensively tested.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +github_account = 'fredrik-johansson' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['0aec6b492b6e9a543bdb3287a91f976951e2ba74fd4de942e692e21f7edbcf13'] + +dependencies = [ + ('FLINT', '2.7.1'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), +] + +configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.7.1-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.7.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..0901acccbca --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.7.1-GCC-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'FLINT' +version = '2.7.1' + +homepage = 'https://www.flintlib.org/' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.flintlib.org'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['186e2fd9ab67df8a05b122fb018269b382e4babcdb17353c4be1fe364dca481e'] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), +] + +configopts = '--with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'math' From fcad51d3ae1a5fbeb99c588fca8fff90b6d63e34 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 23 Jul 2021 10:46:57 +0200 Subject: [PATCH 0473/9987] adding easyconfigs: Arriba-2.1.0-GCC-10.3.0.eb --- .../a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..2277c6288da --- /dev/null +++ b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'Arriba' +version = '2.1.0' + +homepage = 'https://github.com/suhrig/arriba' +description = """Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. + It was developed for the use in a clinical research setting. Therefore, short runtimes and high + sensitivity were important design criteria.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +github_account = 'suhrig' +source_urls = ['https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] +checksums = ['21c46121e00cf84ad471b2b22fca722d37e55bbdf9e7118978dc250754a264bb'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('STAR', '2.7.9a'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +postinstallcmds = ['mkdir %(installdir)s/database'] +files_to_copy = ['%(namelower)s', 'documentation', 'download_references.sh', 'draw_fusions.R', 'LICENSE', + 'README.md', 'run_%(namelower)s.sh'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [('%(namelower)s', '-h')] + +moduleclass = 'bio' From 813b5847314b34ec1179b748cc3c94639095ca59 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 23 Jul 2021 11:35:41 +0200 Subject: [PATCH 0474/9987] added checksums --- .../easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb index eac8d686cd6..a298d8f0994 100644 --- a/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.2.0.eb @@ -17,7 +17,11 @@ patches = [ '%(name)s-20141119_build-libs.patch', '%(name)s-20141119_fix-abs-overload.patch' ] - +checksums = [ + '832ec7d0aff53e04fdb8bbaa5be2177de362afac6ed58a59a97abb7eef29cb60', # a6ef318.tar.gz + 'a6349a6462473f011260074eca6ad9826e3c6aeb20674b696c5848d10610cdd7', # fsom-20141119_build-libs.patch + '54dd6ae76033535fe1b0231142d8bd41a815950dc3fd269dc321f698d4973639', # fsom-20141119_fix-abs-overload.patch +] builddependencies = [('binutils', '2.35')] From a1a8d10ce3222d45e0b16ceea9bbdb34675554a6 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 23 Jul 2021 11:36:44 +0200 Subject: [PATCH 0475/9987] added checksums --- .../f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb | 5 ++++- .../easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb | 1 + 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb index 2ce8759f9a6..a1ba056e298 100644 --- a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb @@ -14,7 +14,10 @@ github_account = 'ekg' source_urls = [GITHUB_SOURCE] sources = ['%s.tar.gz' % local_commit] patches = ['%(name)s-20191210_build-libs.patch'] - +checksums = [ + '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz + 'f0145a1590b555288d5c4560a58bf6976a7605ef949f9071d45e7afb815b540c', # filevercmp-20191210_build-libs.patch +] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb index 4f981788db9..7889e193d7a 100644 --- a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb @@ -17,6 +17,7 @@ sources = [{ 'recursive': True, }, }] +checksums = ['b614a44cb53a164ab8579d75c8eb6fc17415a502628aeeb12b42218893a10278'] builddependencies = [ ('binutils', '2.35'), From 9b41ecf134f392ddef914754c394a02f01bd282a Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 23 Jul 2021 11:38:44 +0200 Subject: [PATCH 0476/9987] added checksums --- easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb index de520d35fab..f7361ba8bbc 100644 --- a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb @@ -15,6 +15,10 @@ sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_TAR patches = [ ('wgsim-%(version)s_add_makefile.patch', 1) ] +checksums = [ + 'e1e6bff5c084e4494023505206ae3e0b0f5a315c9f7390b2f347c370c7f36533', # wgsim-20111017.tar.gz + '81b61c6cceaa4a05e9ee12976dede0df1639f9504ded11e7099cbd1f932c6c9d', # wgsim-20111017_add_makefile.patch +] dependencies = [('zlib', '1.2.11')] From c5d245849b7664a2847306d26bfba779f8f65cbc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 23 Jul 2021 12:17:14 +0200 Subject: [PATCH 0477/9987] Remove unnecessary comment --- .../easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb index 3dcdc976fbb..322946d8896 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb @@ -21,7 +21,6 @@ configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread # select armci network as (Comex) MPI-1 two-sided configopts += ' --with-mpi-ts' -# use IB network sanity_check_paths = { 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libcomex.a', 'lib/libga.a'], From f34d21d6eabfa323cbbe896994723728adab5e2a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 23 Jul 2021 13:03:51 +0200 Subject: [PATCH 0478/9987] add CMake to builddependencies, remove configopts --- easybuild/easyconfigs/f/FLINT/FLINT-2.7.1-GCC-10.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.7.1-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.7.1-GCC-10.3.0.eb index 0901acccbca..6d6372b49bb 100644 --- a/easybuild/easyconfigs/f/FLINT/FLINT-2.7.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.7.1-GCC-10.3.0.eb @@ -17,12 +17,16 @@ source_urls = ['https://www.flintlib.org'] sources = [SOURCELOWER_TAR_GZ] checksums = ['186e2fd9ab67df8a05b122fb018269b382e4babcdb17353c4be1fe364dca481e'] +builddependencies = [ + ('CMake', '3.20.1'), +] + dependencies = [ ('GMP', '6.2.1'), ('MPFR', '4.1.0'), ] -configopts = '--with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR' +separate_build_dir = True sanity_check_paths = { 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], From 46fd0ad9fbe83e3f84253643d9eaf88c1bc3dead Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 23 Jul 2021 14:38:00 +0200 Subject: [PATCH 0479/9987] adding easyconfigs: AOCC-3.1.0-GCCcore-10.2.0.eb, AOCC-3.1.0-GCCcore-10.3.0.eb --- .../a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ .../a/AOCC/AOCC-3.1.0-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..3d7d1d725ea --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +name = 'AOCC' +version = '3.1.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['1948104a430506fe5e445c0c796d6956109e7cc9fc0a1e32c9f1285cfd566d0c'] + +clangversion = '12.0.0' + +dependencies = [ + ('binutils', '2.35'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..841088e8643 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +name = 'AOCC' +version = '3.1.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['1948104a430506fe5e445c0c796d6956109e7cc9fc0a1e32c9f1285cfd566d0c'] + +clangversion = '12.0.0' + +dependencies = [ + ('binutils', '2.36.1'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), +] + +moduleclass = 'compiler' From 0fbbe13236219b3bf83c956ef78f6846ac4173c6 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 23 Jul 2021 16:10:36 +0200 Subject: [PATCH 0480/9987] adding easyconfigs: NVHPC-21.7.eb --- easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb | 74 +++++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb new file mode 100644 index 00000000000..5d73e9ea97f --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb @@ -0,0 +1,74 @@ +## +# Author: Robert Mijakovic +## +name = 'NVHPC' +version = '21.7' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +# By downloading, you accept the HPC SDK Software License Agreement (https://docs.nvidia.com/hpc-sdk/eula/index.html) +accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +local_tarball_tmpl = 'nvhpc_2021_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + '73eb3513845b59645f118b1e313472f54519dc252d5f5c32a05df2a2a8a19878', + local_tarball_tmpl % 'ppc64le': + '37ea23b5a9c696fb3fdb82855643afc4e02aea618102ec801206441f10fc9fba', + local_tarball_tmpl % 'x86_64': + '49d6e23492d131474698cf12971722d42e13a54a4eddec382e66e1053b4ac902', + } +] + +local_gccver = '10.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.35', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.13', '', ('GCCcore', local_gccver)) +] + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/21.7/cuda/) +# for NVHPC 21.7, those are: 11.4, 11.0, 10.2; +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '11.4' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDAcore as a dependency, for example +# dependencies = [('CUDAcore', '11.4.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From 0188ac0cc8b5a141ab2a7fc63b9b73024af4bf78 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 23 Jul 2021 16:29:36 +0200 Subject: [PATCH 0481/9987] NVHPC: updates dependencies --- easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb index 5d73e9ea97f..d996db615a5 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb @@ -28,9 +28,9 @@ checksums = [ local_gccver = '10.3.0' dependencies = [ ('GCCcore', local_gccver), - ('binutils', '2.35', '', ('GCCcore', local_gccver)), + ('binutils', '2.36.1', '', ('GCCcore', local_gccver)), # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails - ('numactl', '2.0.13', '', ('GCCcore', local_gccver)) + ('numactl', '2.0.14', '', ('GCCcore', local_gccver)) ] # specify default CUDA version that should be used by NVHPC From 7926df39e45f6fc5c85013718fcdcd2ddff86f53 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 23 Jul 2021 17:40:06 +0200 Subject: [PATCH 0482/9987] adding easyconfigs: BLIS-3.0.1-GCCcore-10.3.0-amd.eb --- .../b/BLIS/BLIS-3.0.1-GCCcore-10.3.0-amd.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.3.0-amd.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.3.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.3.0-amd.eb new file mode 100644 index 00000000000..7a8a7f4e2e7 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.3.0-amd.eb @@ -0,0 +1,41 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '3.0.1' +versionsuffix = '-amd' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' +description = """AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/amd/blis/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), + ('Perl', '5.32.1'), +] + +# Build Serial and multithreaded library +configopts = ['--enable-cblas --enable-shared CC="$CC" auto', + '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto'] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT, + 'lib/libblis-mt.a', 'lib/libblis-mt.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' From a770562278dc9842fcea203d0d452cd29fda6574 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 23 Jul 2021 18:21:22 +0200 Subject: [PATCH 0483/9987] adding easyconfigs: HDF5-1.12.1-gompi-2021a.eb --- .../h/HDF5/HDF5-1.12.1-gompi-2021a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021a.eb new file mode 100644 index 00000000000..05f4456f763 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021a.eb @@ -0,0 +1,24 @@ +## +# Author: Robert Mijakovic +## +name = 'HDF5' +version = '1.12.1' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['79c66ff67e666665369396e9c90b32e238e501f345afd2234186bfb8331081ca'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From 2c71b639ce80cdd6eb24b477a40d913ab88efeb5 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 23 Jul 2021 18:52:27 +0200 Subject: [PATCH 0484/9987] adding easyconfigs: cuDNN-8.2.2.26-CUDA-11.4.0.eb --- .../c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.0.eb new file mode 100644 index 00000000000..0f8aaee850c --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.0.eb @@ -0,0 +1,41 @@ +## +# Author: Robert Mijakovic +## + +name = 'cuDNN' +version = '8.2.2.26' +local_cuda_version = '11.4.0' +local_cuda_version_majmin = '.'.join(local_cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] +local_tarball_tmpl = '-'.join(['%%(namelower)s', local_cuda_version_majmin, 'linux', '%s', 'v%%(version)s.tgz']) +sources = [local_tarball_tmpl % '%(cudnnarch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64sbsa': + 'e240d45d79eecb2257fcb8a219324f19d8e2d6e145fbd035a38d267580d65e9a', + local_tarball_tmpl % 'ppc64le': + 'b11b9e515a86978dc21ab50a7d2320bfb505cbce9dffa25480225c597c682b43', + local_tarball_tmpl % 'x64': + 'fbc631ce19688e87d7d2420403b20db97885b17f718f0f51d7e9fc0905d86e07', + } +] + +dependencies = [('CUDAcore', local_cuda_version)] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From 3574eff49ca769df384a548351f13f185ab55ed1 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 23 Jul 2021 18:19:23 +0100 Subject: [PATCH 0485/9987] adding easyconfigs: GDCM-3.0.8-GCCcore-9.3.0.eb, GDCM-3.0.8-GCCcore-10.2.0.eb --- .../g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ .../g/GDCM/GDCM-3.0.8-GCCcore-9.3.0.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9386c090914 --- /dev/null +++ b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'GDCM' +version = '3.0.8' + +homepage = 'https://sourceforge.net/projects/gdcm' +description = "Grassroots DICOM: Cross-platform DICOM implementation" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['33077958ec2fb43361cd4e2889dc901cc4d45c30b7f134950fc57ecd4f0637e1'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = "-DGDCM_BUILD_DOCBOOK_MANPAGES=0" + +sanity_check_paths = { + 'files': ['lib/libgdcmCommon.a', 'lib/libgdcmDICT.a'], + 'dirs': ['include/gdcm-%(version_major_minor)s', 'lib/gdcm-%(version_major_minor)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..044e0a80dc9 --- /dev/null +++ b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.8-GCCcore-9.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'GDCM' +version = '3.0.8' + +homepage = 'https://sourceforge.net/projects/gdcm' +description = "Grassroots DICOM: Cross-platform DICOM implementation" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['33077958ec2fb43361cd4e2889dc901cc4d45c30b7f134950fc57ecd4f0637e1'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +configopts = "-DGDCM_BUILD_DOCBOOK_MANPAGES=0" + +sanity_check_paths = { + 'files': ['lib/libgdcmCommon.a', 'lib/libgdcmDICT.a'], + 'dirs': ['include/gdcm-%(version_major_minor)s', 'lib/gdcm-%(version_major_minor)s'], +} + +moduleclass = 'tools' From a1e3f21d5e4e6a7c974167ef353fb9d4f6c30c20 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 23 Jul 2021 12:32:03 -0700 Subject: [PATCH 0486/9987] {bio}[GCC/10.2.0] Jellyfish 2.3.0 --- .../j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..116f07001d5 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.3.0' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e195b7cf7ba42a90e5e112c0ed27894cd7ac864476dc5fb45ab169f5b930ea5a'] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, +# they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' From 99ff37394e04dfa1639dbd0ca8fbf865a77f3c71 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 23 Jul 2021 14:51:26 -0700 Subject: [PATCH 0487/9987] moved down to GCC --- .../m/Metal/Metal-2020-05-05-GCC-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb b/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb new file mode 100644 index 00000000000..67bd18df244 --- /dev/null +++ b/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'Metal' +version = '2020-05-05' + +homepage = 'http://csg.sph.umich.edu/abecasis/Metal/' +description = """Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large + datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/statgen/METAL/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['0ffa2419ca2ab43766e7e6e8c97822c8ce1f5b6233fb5f992d1b1be1955fede7'] + +builddependencies = [('CMake', '3.18.4')] +dependencies = [('zlib', '1.2.11')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin && ' + + 'cp %(builddir)s/easybuild_obj/bin/metal %(installdir)s/bin' +] + +sanity_check_paths = { + 'files': ['bin/metal'], + 'dirs': [''], +} + +sanity_check_commands = ['%(namelower)s /dev/null'] + +moduleclass = 'bio' From 6b03447d0748da32a775315a8549c85a264818b8 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Jul 2021 10:57:36 +0100 Subject: [PATCH 0488/9987] adding easyconfigs: FBPIC-0.20.3-fosscuda-2020b.eb, pyFFTW-0.12.0-fosscuda-2020b.eb --- .../f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb | 40 +++++++++++++++++++ .../p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb | 24 +++++++++++ 2 files changed, 64 insertions(+) create mode 100755 easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb create mode 100755 easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb new file mode 100755 index 00000000000..03490cd20dc --- /dev/null +++ b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb @@ -0,0 +1,40 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'FBPIC' +version = '0.20.3' + +homepage = "https://fbpic.github.io/" +description = """FBPIC (Fourier-Bessel Particle-In-Cell) is a Particle-In-Cell (PIC) code for relativistic plasma + physics. It is especially well-suited for physical simulations of laser-wakefield acceleration and + plasma-wakefield acceleration.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('CuPy', '8.5.0'), + ('h5py', '3.1.0'), + ('numba', '0.53.1'), + ('pyFFTW', '0.12.0'), + ('SciPy-bundle', '2020.11'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('picmistandard', '0.0.14', { + 'checksums': ['8f83b25b281fc0309a0c4f75c7605afd5fa0ef4df3b3ac115069478c119bc8c3'], + }), + ('periodictable', '1.6.0', { + 'checksums': ['52e925220005c20e97601e7b04ad6cebc271680947ab9adcbb1a796ddbaa0f23'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'use_pip_extras': 'picmi', + 'checksums': ['967d7f087861679467eab31d4b3b12e823a539b1161a1b5f9054e3578a7e000f'], + }), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb new file mode 100755 index 00000000000..6572216ac3e --- /dev/null +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pyFFTW' +version = '0.12.0' + +homepage = 'https://github.com/pyFFTW/pyFFTW' +description = """A pythonic wrapper around FFTW, the FFT library, presenting a unified interface + for all the supported transforms.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['60988e823ca75808a26fd79d88dbae1de3699e72a293f812aa4534f8a0a58cb0'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('FFTW', '3.3.8'), +] + +download_dep_fail = True +use_pip = True + +moduleclass = 'lib' From 83c69aba6726bb1ed3589961efd35ff460b69747 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Jul 2021 11:07:31 +0100 Subject: [PATCH 0489/9987] enable sanity_pip_check in pyFFTW --- easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb index 6572216ac3e..bff68e67027 100755 --- a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-fosscuda-2020b.eb @@ -20,5 +20,6 @@ dependencies = [ download_dep_fail = True use_pip = True +sanity_pip_check = True moduleclass = 'lib' From 6b0d3274aefa87ce2622e9d714ab6815adcdb7b1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Jul 2021 11:19:15 +0100 Subject: [PATCH 0490/9987] numba multi-variant deps --- easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb index 03490cd20dc..676751bc2c6 100755 --- a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb @@ -15,7 +15,7 @@ dependencies = [ ('Python', '3.8.6'), ('CuPy', '8.5.0'), ('h5py', '3.1.0'), - ('numba', '0.53.1'), + ('numba', '0.52.0'), ('pyFFTW', '0.12.0'), ('SciPy-bundle', '2020.11'), ] From 15c32c53b75c35a068086f0a43ee70565e621ad0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Jul 2021 11:28:27 +0100 Subject: [PATCH 0491/9987] revert numba change in FBPIC --- easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb index 676751bc2c6..03490cd20dc 100755 --- a/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/f/FBPIC/FBPIC-0.20.3-fosscuda-2020b.eb @@ -15,7 +15,7 @@ dependencies = [ ('Python', '3.8.6'), ('CuPy', '8.5.0'), ('h5py', '3.1.0'), - ('numba', '0.52.0'), + ('numba', '0.53.1'), ('pyFFTW', '0.12.0'), ('SciPy-bundle', '2020.11'), ] From 2c03fdb84f0343fdb04f73b6d68cb6c364f43b00 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 24 Jul 2021 11:34:32 +0100 Subject: [PATCH 0492/9987] add numba multi-variant deps exception --- test/easyconfigs/easyconfigs.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4a937e0793d..0ebeafe64d4 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -444,6 +444,13 @@ def check_dep_vars(self, gen, dep, dep_vars): ], # rampart requires nodejs > 10, artic-ncov2019 requires rampart 'nodejs': [('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13'])], + # some software depends on an older numba; + # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy + 'numba': [ + (r'0\.52\.0', ], [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', + r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', + r'umap-learn-0\.4\.6-']), + ], # OPERA requires SAMtools 0.x 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], From cd4ce182ddca9c7acc52ab3aef888f57472067a8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 24 Jul 2021 11:38:13 +0100 Subject: [PATCH 0493/9987] remove mistype --- test/easyconfigs/easyconfigs.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0ebeafe64d4..12f639a2d9b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -447,9 +447,9 @@ def check_dep_vars(self, gen, dep, dep_vars): # some software depends on an older numba; # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy 'numba': [ - (r'0\.52\.0', ], [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', - r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', - r'umap-learn-0\.4\.6-']), + (r'0\.52\.0', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', + r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', + r'umap-learn-0\.4\.6-']), ], # OPERA requires SAMtools 0.x 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', From 32348116a3af631ec9448669940dcd81e681882d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 24 Jul 2021 12:32:35 +0100 Subject: [PATCH 0494/9987] allow for non-x86_64 in postinstallcmds for CuPy --- easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb index 498590b96ea..7a92cacfd67 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb @@ -24,7 +24,7 @@ exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} postinstallcmds = [ # req for sanity check on build nodes without libcuda.so. # will be removed my patched __init__.py at sanity check import. - 'cp $EBROOTCUDA/./targets/x86_64-linux/lib/stubs/libcuda.* %(installdir)s/lib && ls %(installdir)s/lib' + 'cp $EBROOTCUDA/./targets/*-linux/lib/stubs/libcuda.* %(installdir)s/lib && ls %(installdir)s/lib' ] exts_list = [ ('fastrlock', '0.5', { From 68db7386839cbfada33456c32e40f8999e037828 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 26 Jul 2021 07:50:02 +0200 Subject: [PATCH 0495/9987] shorten first line of files_to_copy --- easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb index 2277c6288da..c775fc48a12 100644 --- a/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb @@ -26,8 +26,8 @@ dependencies = [ ] postinstallcmds = ['mkdir %(installdir)s/database'] -files_to_copy = ['%(namelower)s', 'documentation', 'download_references.sh', 'draw_fusions.R', 'LICENSE', - 'README.md', 'run_%(namelower)s.sh'] +files_to_copy = ['%(namelower)s', 'documentation', 'download_references.sh', 'draw_fusions.R', + 'LICENSE', 'README.md', 'run_%(namelower)s.sh'] modextrapaths = {'PATH': ''} From e9086af228eaae01f74a6b532109a54788b3b7fd Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 26 Jul 2021 10:55:56 +0200 Subject: [PATCH 0496/9987] AOCC: Adds EULA --- easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.3.0.eb index 841088e8643..afdcf87cd4b 100644 --- a/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.3.0.eb @@ -11,6 +11,8 @@ description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0 # already specified as the toolchain. toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +# By downloading, you accept the AOCC Compiler EULA (https://developer.amd.com/aocc-compiler-eula/) +# accept_eula = True source_urls = ['http://developer.amd.com/wordpress/media/files/'] sources = ['aocc-compiler-%(version)s.tar'] checksums = ['1948104a430506fe5e445c0c796d6956109e7cc9fc0a1e32c9f1285cfd566d0c'] From 1cbf01144c696ca147ccb5483a80da11a36c8e10 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 26 Jul 2021 10:57:43 +0200 Subject: [PATCH 0497/9987] AOCC: Adds EULA --- easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb index 3d7d1d725ea..de0d6d8e54a 100644 --- a/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-10.2.0.eb @@ -11,6 +11,8 @@ description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0 # already specified as the toolchain. toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +# By downloading, you accept the AOCC Compiler EULA (https://developer.amd.com/aocc-compiler-eula/) +# accept_eula = True source_urls = ['http://developer.amd.com/wordpress/media/files/'] sources = ['aocc-compiler-%(version)s.tar'] checksums = ['1948104a430506fe5e445c0c796d6956109e7cc9fc0a1e32c9f1285cfd566d0c'] From 490ad571e53b165a486b24a5942b46bcd80db1a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 26 Jul 2021 11:34:43 +0200 Subject: [PATCH 0498/9987] use github for source_urls and switch to version 0.12.7 --- ...ad-0.12.6-GCC-10.3.0.eb => gffread-0.12.7-GCC-10.3.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/gffread/{gffread-0.12.6-GCC-10.3.0.eb => gffread-0.12.7-GCC-10.3.0.eb} (77%) diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.6-GCC-10.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb similarity index 77% rename from easybuild/easyconfigs/g/gffread/gffread-0.12.6-GCC-10.3.0.eb rename to easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb index 70beac3c1a3..24ecba45d8d 100644 --- a/easybuild/easyconfigs/g/gffread/gffread-0.12.6-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'gffread' -version = '0.12.6' +version = '0.12.7' homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' description = """GFF/GTF parsing utility providing format conversions, @@ -11,9 +11,9 @@ region filtering, FASTA sequence extraction and more.""" toolchain = {'name': 'GCC', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://ccb.jhu.edu/software/stringtie/dl/'] +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['1c558151f668d6f6fa20be9abb42ad224889855681f6e816b0ad681d85a5ce1b'] +checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] buildopts = " release" From e456fbac56dc5cbca45ca3b893ebefc0f4726396 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 26 Jul 2021 14:38:15 +0200 Subject: [PATCH 0499/9987] adding easyconfigs: Subread-2.0.3-GCC-10.3.0.eb --- .../s/Subread/Subread-2.0.3-GCC-10.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-10.3.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..fc8c40d5c2b --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-10.3.0.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'MakeCp' + +name = 'Subread' +version = '2.0.3' + +# HTTPS is not valid +homepage = 'http://%(namelower)s.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] + +checksums = ['56cef3a2f914d432713069d5c282f48831c3a1ecc89432ad5580caa322a5f56b'] + +start_dir = 'src' + +prebuildopts = "sed -i 's/-mtune=core2//g' Makefile.Linux && " +prebuildopts += "sed -i 's/-mtune=core2//g' longread-one/Makefile && " + +buildopts = " -f Makefile.Linux" + +files_to_copy = ['bin'] + +local_binaries_list = [ + 'exactSNP', 'featureCounts', 'subindel', 'subjunc', 'sublong', 'subread-align', 'subread-buildindex', +] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_binaries_list], + 'dirs': ['bin/utilities'], +} + +sanity_check_commands = [ + 'cd %(builddir)s/%(namelower)s-%(version)s-source/test && bash test_all.sh' +] + +moduleclass = 'bio' From 70dd80b53c81566e1e33bea8647c09213b4c5a92 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 26 Jul 2021 16:38:26 +0200 Subject: [PATCH 0500/9987] adding easyconfigs: TRAVIS-Analyzer-210521-GCC-10.3.0.eb --- .../TRAVIS-Analyzer-210521-GCC-10.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/t/TRAVIS-Analyzer/TRAVIS-Analyzer-210521-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/t/TRAVIS-Analyzer/TRAVIS-Analyzer-210521-GCC-10.3.0.eb b/easybuild/easyconfigs/t/TRAVIS-Analyzer/TRAVIS-Analyzer-210521-GCC-10.3.0.eb new file mode 100644 index 00000000000..ff2075570cb --- /dev/null +++ b/easybuild/easyconfigs/t/TRAVIS-Analyzer/TRAVIS-Analyzer-210521-GCC-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'TRAVIS-Analyzer' +version = '210521' + +homepage = 'http://www.travis-analyzer.de/' +description = """ +TRAVIS is a free tool for analyzing and visualizing trajectories from all kinds +of Molecular Dynamics or Monte Carlo simulations.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'cstd': 'c++14'} + +source_urls = ['http://www.travis-analyzer.de/files'] +sources = ['travis-src-%(version)s.tar.gz'] +checksums = ['f085071c467957b79275f2a64325a465579e310833f827cf2333811f681f4330'] + +# use CFLAGS from EB +prebuildopts = "sed -i 's/^CFLAGS .*14/CFLAGS := $(CFLAGS)/' Makefile && " +prebuildopts += "CXX=${CXX}" + +local_exe = 'travis' +files_to_copy = [ + (['exe/%s' % local_exe], 'bin'), + (['README', 'travis-quickstart.pdf'], 'share'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % local_exe], + 'dirs': ['share'] +} + +sanity_check_commands = [('%s' % local_exe, '-help')] + +moduleclass = 'chem' From 0e8b62b62d60e829c498590b54b8fcbbc24c0381 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 26 Jul 2021 16:39:09 +0200 Subject: [PATCH 0501/9987] adding easyconfigs: snakemake-6.6.1-foss-2021a.eb and patches: snakemake-6.6.1_fix_jobs.patch --- .../s/snakemake/snakemake-6.6.1-foss-2021a.eb | 75 +++++++++++++++++++ .../snakemake/snakemake-6.6.1_fix_jobs.patch | 16 ++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-6.6.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-6.6.1_fix_jobs.patch diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-6.6.1-foss-2021a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-6.6.1-foss-2021a.eb new file mode 100644 index 00000000000..071e9f0e9a6 --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-6.6.1-foss-2021a.eb @@ -0,0 +1,75 @@ +easyblock = 'PythonBundle' + +name = 'snakemake' +version = '6.6.1' + +homepage = 'https://snakemake.readthedocs.io' +description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('GitPython', '3.1.18'), + ('IPython', '7.25.0'), +] + +use_pip = True +sanity_pip_check = True + +# snakemake-6.6.1_fix_jobs.patch is needed for clusters that do not support copying the full env into the batch job +exts_list = [ + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('ratelimiter', '1.2.0.post0', { + 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], + }), + ('ConfigArgParse', '1.5.1', { + 'checksums': ['371f46577e76ec71a183b88378f36dd09f4b946f60fe60712f411b020f26b812'], + }), + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('toposort', '1.6', { + 'checksums': ['a7428f56ef844f5055bb9e9e44b343983773ae6dce0fe5b101e08e27ffbd50ac'], + }), + ('amply', '0.1.4', { + 'checksums': ['cb12dcb49d16b168c02be128a1527ecde50211e4bd94af76ff4e67707f5a2d38'], + }), + ('PuLP', '2.4', { + 'checksums': ['b2aff10989b3692e3a59301a0cb0acddeb25dcea378f8804c86007075eae55b5'], + }), + ('smart_open', '4.2.0', { + 'checksums': ['d9f5a0f173ccb9bbae528db5a3804f57145815774f77ef755b9b0f3b4b2a9dcb'], + }), + ('connection_pool', '0.0.3', { + 'checksums': ['bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc'], + }), + ('stopit', '1.1.2', { + 'checksums': ['f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d'], + }), + (name, version, { + 'patches': ['snakemake-%(version)s_fix_jobs.patch'], + 'checksums': [ + '91637a801342f3bc349c033b284fef7c0201b4e5e29d5650cb6c7f69096d4184', # snakemake-6.6.1.tar.gz + '916875eaf4869c65b93098e362b8676cf55c6e37067a54b191f34b13e06c37e3', # snakemake-6.6.1_fix_jobs.patch + ], + }), +] + +# SNAKEMAKE_LOAD_MODULE is needed for snakemake-6.6.1_fix_jobs.patch to work +# local_snakemake_load is the command for loading this module (here: default EB module naming scheme) +local_snakemake_load = 'module load %(module_name)s' +modextravars = {'SNAKEMAKE_LOAD_MODULE': local_snakemake_load} + +sanity_check_paths = { + 'files': ['bin/snakemake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], +} + +sanity_check_commands = ['snakemake --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-6.6.1_fix_jobs.patch b/easybuild/easyconfigs/s/snakemake/snakemake-6.6.1_fix_jobs.patch new file mode 100644 index 00000000000..503ea396a65 --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-6.6.1_fix_jobs.patch @@ -0,0 +1,16 @@ +Load the snakemake module before running in job script, with added environment variable SNAKEMAKE_LOAD_MODULE, +and always use the python executable defined by the environment. +This patch is for clusters that don't support exporting the full environment into the batch job. +Author: Samuel Moors (Vrije Universiteit Brussel) +--- snakemake/executors/__init__.py.orig 2021-07-26 11:52:00.645527272 +0200 ++++ snakemake/executors/__init__.py 2021-07-26 13:51:35.838445917 +0200 +@@ -682,7 +682,8 @@ + "{envvars} " "cd {workflow.workdir_init} && " + if assume_shared_fs + else "", +- "{sys.executable} " if assume_shared_fs else "python ", ++ os.getenv('SNAKEMAKE_LOAD_MODULE', ':') + ' && ', ++ "python ", + "-m snakemake {target} --snakefile {snakefile} ", + "--force --cores {cores} --keep-target-files --keep-remote --max-inventory-time 0 ", + "{waitfiles_parameter:u} --latency-wait {latency_wait} ", From 1728325fb667d9752c31be599c9d4052719e46a8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 26 Jul 2021 16:39:56 +0200 Subject: [PATCH 0502/9987] adding easyconfigs: DROP-1.1.0-foss-2020b-R-4.0.3.eb --- .../d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb new file mode 100644 index 00000000000..014ae7c311e --- /dev/null +++ b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'DROP' +version = '1.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://gagneurlab-drop.readthedocs.io' +description = "Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('R', '4.0.3'), + ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), + ('tMAE', '1.0.0', '-R-%(rver)s'), + ('Java', '11', '', True), + ('GATK', '4.2.0.0', '-Java-%(javaver)s'), + ('Graphviz', '2.47.0', '-Java-%(javaver)s'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('snakemake', '6.1.0'), + ('wget', '1.20.3'), + ('HTSlib', '1.11'), # for tabix + ('SAMtools', '1.11'), + ('BCFtools', '1.11'), + ('Pandoc', '2.13', '', True), +] + +exts_list = [ + ('wbuild', '1.8.0', { + 'checksums': ['3088d3fcbc71106464f20e3546a73df400dc03d17f11e70bdb15d35d7e6c5a7e'], + }), + ('click-log', '0.3.2', { + 'checksums': ['16fd1ca3fc6b16c98cea63acf1ab474ea8e676849dc669d86afafb0ed7003124'], + }), + ('graphviz', '0.17', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['ef6e2c5deb9cdcc0c7eece1d89625fd07b0f2208ea2bcb483520907ddf8b4e12'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('about', '5.2', { + 'checksums': ['4a318ad1dcf6e9355b8ae18195c707d26413782b57ac5c740cc696b44350c959'], + }), + ('plumbum', '1.7.0', { + 'checksums': ['317744342c755319907c773cc87c3a30adaa3a41b0d34c0ce02d9d1904922dce'], + }), + ('pandoc', version, { + 'checksums': ['374f1791151b084e7aac17feeadf43b0c08f0ed39c666a907040f4ee18016b73'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/gagneurlab/drop/archive'], + 'checksums': ['705693610480aa319cec51c2c3118a8f96d2a781c85f9f1d7393e3cd3408d253'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/drop'], + 'dirs': [], +} + +sanity_check_commands = ['drop --help'] + +moduleclass = 'bio' From f19d604e1f20fa0016ad3358a6dd73063a547ac5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 26 Jul 2021 17:22:59 +0200 Subject: [PATCH 0503/9987] comment out patch for snakemake-6.6.1-foss-2021a.eb --- .../easyconfigs/s/snakemake/snakemake-6.6.1-foss-2021a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-6.6.1-foss-2021a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-6.6.1-foss-2021a.eb index 071e9f0e9a6..cf2f4ba5d4d 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-6.6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-6.6.1-foss-2021a.eb @@ -52,18 +52,18 @@ exts_list = [ 'checksums': ['f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d'], }), (name, version, { - 'patches': ['snakemake-%(version)s_fix_jobs.patch'], + # 'patches': ['snakemake-%(version)s_fix_jobs.patch'], 'checksums': [ '91637a801342f3bc349c033b284fef7c0201b4e5e29d5650cb6c7f69096d4184', # snakemake-6.6.1.tar.gz - '916875eaf4869c65b93098e362b8676cf55c6e37067a54b191f34b13e06c37e3', # snakemake-6.6.1_fix_jobs.patch + # '916875eaf4869c65b93098e362b8676cf55c6e37067a54b191f34b13e06c37e3', # snakemake-6.6.1_fix_jobs.patch ], }), ] # SNAKEMAKE_LOAD_MODULE is needed for snakemake-6.6.1_fix_jobs.patch to work # local_snakemake_load is the command for loading this module (here: default EB module naming scheme) -local_snakemake_load = 'module load %(module_name)s' -modextravars = {'SNAKEMAKE_LOAD_MODULE': local_snakemake_load} +# local_snakemake_load = 'module load %(module_name)s' +# modextravars = {'SNAKEMAKE_LOAD_MODULE': local_snakemake_load} sanity_check_paths = { 'files': ['bin/snakemake'], From 5710d6a8938e63ce626708032c1360fb893c208f Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 26 Jul 2021 18:16:42 +0000 Subject: [PATCH 0504/9987] adding easyconfigs: iomkl-2021a.eb, iompi-2021a.eb, imkl-2021.2.0-iompi-2021a.eb --- .../i/imkl/imkl-2021.2.0-iompi-2021a.eb | 14 ++++++++++++++ easybuild/easyconfigs/i/iomkl/iomkl-2021a.eb | 18 ++++++++++++++++++ easybuild/easyconfigs/i/iompi/iompi-2021a.eb | 18 ++++++++++++++++++ 3 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb create mode 100644 easybuild/easyconfigs/i/iomkl/iomkl-2021a.eb create mode 100644 easybuild/easyconfigs/i/iompi/iompi-2021a.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb new file mode 100644 index 00000000000..60282631f05 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.2.0-iompi-2021a.eb @@ -0,0 +1,14 @@ +name = 'imkl' +version = '2021.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iompi', 'version': '2021a'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/17757/'] +sources = ['l_onemkl_p_%(version)s.296_offline.sh'] +checksums = ['816e9df26ff331d6c0751b86ed5f7d243f9f172e76f14e83b32bf4d1d619dbae'] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2021a.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2021a.eb new file mode 100644 index 00000000000..1bfdccc4bbf --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2021a.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'iomkl' +version = '2021a' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2021.2.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('OpenMPI', '4.1.1', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2021a.eb b/easybuild/easyconfigs/i/iompi/iompi-2021a.eb new file mode 100644 index 00000000000..844e9e075d5 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2021a.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iompi' +version = '2021a' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2021.2.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('OpenMPI', '4.1.1', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' From 3926f7fe8c57aa0fd99219141b197f8f82940489 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 27 Jul 2021 07:51:37 +0200 Subject: [PATCH 0505/9987] adding easyconfigs: segemehl-0.3.4-GCC-10.3.0.eb --- .../s/segemehl/segemehl-0.3.4-GCC-10.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.3.0.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..38fb0cbe9c3 --- /dev/null +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'segemehl' +version = '0.3.4' + +homepage = 'https://www.bioinf.uni-leipzig.de/Software/segemehl/' +description = """segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping + and split read mapping.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://www.bioinf.uni-leipzig.de/Software/%(name)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('HTSlib', '1.12'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +buildopts = 'all' + +files_to_copy = [(["haarz.x", "%(name)s.x"], "bin")] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["haarz.x", "%(name)s.x"]], + 'dirs': [] +} + +moduleclass = 'bio' From 6bf71b556fee143e93734fe13b345e7100d88603 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 27 Jul 2021 09:20:21 +0200 Subject: [PATCH 0506/9987] adding easyconfigs: preseq-3.1.2-GCC-10.3.0.eb --- .../p/preseq/preseq-3.1.2-GCC-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/preseq/preseq-3.1.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/p/preseq/preseq-3.1.2-GCC-10.3.0.eb b/easybuild/easyconfigs/p/preseq/preseq-3.1.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..2d8165add8e --- /dev/null +++ b/easybuild/easyconfigs/p/preseq/preseq-3.1.2-GCC-10.3.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'preseq' +version = '3.1.2' + +homepage = 'https://smithlabresearch.org/software/preseq' +description = "Software for predicting library complexity and genome coverage in high-throughput sequencing." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/smithlabcode/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['ed5176eb638e709bd22c0a43cedae5a2a3fcece40f6c130c509fbce6a59fa788'] + +dependencies = [ + ('GSL', '2.7'), + ('HTSlib', '1.12'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-hts CPPFLAGS="-I$EBROOTHTSLIB/include" LDFLAGS="-L$EBROOTHTSLIB/lib"' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(name)s', 'to-mr']], + 'dirs': [], +} + +sanity_check_commands = [('%(name)s')] + +moduleclass = 'bio' From 31ff741e0778860b17a20811fbf5a35b8a5dfaaf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 27 Jul 2021 11:09:38 +0200 Subject: [PATCH 0507/9987] adding easyconfigs: ORCA-5.0.1-gompi-2021a.eb, ORCA-5.0.1-gompi-2021a-static.eb --- .../o/ORCA/ORCA-5.0.1-gompi-2021a-static.eb | 31 +++++++++++++++++++ .../o/ORCA/ORCA-5.0.1-gompi-2021a.eb | 23 ++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.1-gompi-2021a-static.eb create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.1-gompi-2021a.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.1-gompi-2021a-static.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.1-gompi-2021a-static.eb new file mode 100644 index 00000000000..3fbaf0af9b6 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.1-gompi-2021a-static.eb @@ -0,0 +1,31 @@ +name = 'ORCA' +version = '5.0.1' +versionsuffix = '-static' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +# Static build of ORCA: download from https://orcaforum.kofo.mpg.de +# OpenMPI is dynamically linked +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_openmpi411_part%s.tar.xz' % (version.replace('.', '_'), p) + for p in range(1, 5)] +checksums = [ + # orca_5_0_1_linux_x86-64_openmpi411_part1.tar.xz + '251b6f6bb570e3755254cdc7c14b464c21a474ad8c287c83fdbdb940532d078b', + # orca_5_0_1_linux_x86-64_openmpi411_part2.tar.xz + 'f24818809b4dee4dc52c9578d7698b0cae299ea0c90ec6fd62d04c776f7f0c29', + # orca_5_0_1_linux_x86-64_openmpi411_part3.tar.xz + '44353ce99734095fc0e69f873d90b2c0950019d21fc3cc8a4c052b014936cc74', + # orca_5_0_1_linux_x86-64_openmpi411_part4.tar.xz + '170f64766571e43a5d9823761d1daa21b4a48382b484280147a6094f3dc3d868', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.1-gompi-2021a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.1-gompi-2021a.eb new file mode 100644 index 00000000000..26153cab8cc --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.1-gompi-2021a.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '5.0.1' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +# Shared build of ORCA: download from https://orcaforum.kofo.mpg.de +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi411.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_5_0_1_linux_x86-64_shared_openmpi411.tar.xz + '84199af6931de9be261685f7f1d6d63b47eed8512ce1f2f93ca5356fed1cbae8', +] + +moduleclass = 'chem' From 6cc34d6177c9f960372044cfb518fdc97e813ad4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 27 Jul 2021 11:36:08 +0200 Subject: [PATCH 0508/9987] adding easyconfigs: HMMER-3.3.2-gompi-2021a.eb --- .../h/HMMER/HMMER-3.3.2-gompi-2021a.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021a.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021a.eb new file mode 100644 index 00000000000..7d4fadc98a4 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021a.eb @@ -0,0 +1,68 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = [ + 'http://eddylab.org/software/%(namelower)s/', + 'http://eddylab.org/software/%(namelower)s%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] + +builddependencies = [('Python', '3.9.5')] + +configopts = '--enable-mpi' + +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From 29db091ad02541b23736e7738b48287d9d9e0ca4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 27 Jul 2021 11:19:33 +0100 Subject: [PATCH 0509/9987] adding easyconfigs: QTLtools-1.3.1-foss-2020b.eb --- .../q/QTLtools/QTLtools-1.3.1-foss-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb new file mode 100644 index 00000000000..12a9ff928b4 --- /dev/null +++ b/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb @@ -0,0 +1,43 @@ +# Easyconfig for QTLtools +# Author: Caspar van Leeuwen +# SURFsara, Amsterdam, The Netherlands + +easyblock = 'MakeCp' + +name = 'QTLtools' +version = '1.3.1' + +homepage = "https://qtltools.github.io/qtltools/" +description = """QTLtools is a tool set for molecular QTL discovery and analysis. +It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) +in few easy-to-perform steps.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://qtltools.github.io/qtltools/binaries/'] +sources = ['QTLtools_%(version)s_source.tar.gz'] +checksums = ['8d812145a210fe96ae31590423a0eab6bf9e3f46b33a62c8b04b0d428bcfed8d'] + +dependencies = [ + ('GSL', '2.6'), + ('bzip2', '1.0.8'), + ('Boost', '1.74.0'), + ('Rmath', '4.0.4'), + ('HTSlib', '1.12'), + ('imkl', '2020.4.304'), +] + +# Overwrite CXX, CXXFLAG, LIB_FLAGS and LIB_FILES build options from the default makefile +# since the default makefile uses hard-coded compiler & library paths +buildopts = 'CXX="$CXX -std=c++0x" CXXFLAG="$CXXFLAGS" LIB_FILES="" ' +buildopts += 'LIB_FLAGS="-lz -lgsl -lmkl -lbz2 -lm -lpthread -lRmath -lhts -lboost_iostreams -lboost_program_options"' +buildopts += ' RMATH_INC=$EBROOTRMAT/include HTSLD_INC=$EBROOTHTSLIB/include BOOST_INC=$EBROOTBOOST/include' + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/QTLtools'], + 'dirs': [] +} + +moduleclass = 'bio' From 6bbfa02f8f8ad3fa51523ec6b57596f9f1e879dc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 27 Jul 2021 11:33:09 +0100 Subject: [PATCH 0510/9987] Use the older HTSlib for 2020b in common with other ECs --- easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb index 12a9ff928b4..e71d8260809 100644 --- a/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QTLtools/QTLtools-1.3.1-foss-2020b.eb @@ -23,7 +23,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('Boost', '1.74.0'), ('Rmath', '4.0.4'), - ('HTSlib', '1.12'), + ('HTSlib', '1.11'), ('imkl', '2020.4.304'), ] From 861ee0ae580c17e4af55f028b2ebf3b55fda0a5a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 27 Jul 2021 12:53:41 +0200 Subject: [PATCH 0511/9987] Bump magma version --- ...DA-11.3.1.eb => magma-2.6.1-foss-2021a-CUDA-11.3.1.eb} | 8 ++++---- ...llow-all-sms.patch => magma-2.6.1_allow-all-sms.patch} | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/magma/{magma-2.6.0-foss-2021a-CUDA-11.3.1.eb => magma-2.6.1-foss-2021a-CUDA-11.3.1.eb} (80%) rename easybuild/easyconfigs/m/magma/{magma-2.6.0_allow-all-sms.patch => magma-2.6.1_allow-all-sms.patch} (99%) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb similarity index 80% rename from easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb rename to easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb index 8ca69511fe5..be9537ac8bb 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb @@ -1,7 +1,7 @@ easyblock = "CMakeMake" name = 'magma' -version = '2.6.0' +version = '2.6.1' versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://icl.cs.utk.edu/magma/' @@ -13,10 +13,10 @@ toolchainopts = {'pic': True, 'openmp': True} source_urls = ['https://icl.cs.utk.edu/projectsfiles/magma/downloads/'] sources = [SOURCE_TAR_GZ] -patches = ['magma-2.6.0_allow-all-sms.patch'] +patches = ['magma-%(version)s_allow-all-sms.patch'] checksums = [ - '50cdd384f44f06a34469e7125f8b2ffae13c1975d373c3f1510d91be2b7638ec', # magma-2.6.0.tar.gz - '9a0571c63756391d99da5dca3fe45d23e89ffdbbc62ca99db4dab10e77158daa', # magma-2.6.0_allow-all-sms.patch + '6cd83808c6e8bc7a44028e05112b3ab4e579bcc73202ed14733f66661127e213', # magma-2.6.1.tar.gz + 'b89285bac007b68e88e3b5ddbb7f94dbc8a9d77590e58c352e477574d8dca738', # magma-2.6.1_allow-all-sms.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch b/easybuild/easyconfigs/m/magma/magma-2.6.1_allow-all-sms.patch similarity index 99% rename from easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch rename to easybuild/easyconfigs/m/magma/magma-2.6.1_allow-all-sms.patch index 1c2dc1aee21..5f077c673a6 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.0_allow-all-sms.patch +++ b/easybuild/easyconfigs/m/magma/magma-2.6.1_allow-all-sms.patch @@ -3,7 +3,7 @@ See https://bitbucket.org/icl/magma/issues/32/list-of-whitelisted-sm_-values-for and https://bitbucket.org/icl/magma/pull-requests/5 Author: Alexander Grund (TU Dresden) -Updated to 2.6.0: micketeer@gmail.com +Updated to 2.6.1: micketeer@gmail.com --- CMakeLists.txt.orig 2021-07-06 17:02:37.125227748 +0200 +++ CMakeLists.txt 2021-07-06 18:43:13.400804473 +0200 From bb1cc82edbb0bdb43e1085650a3d87b7f49a7660 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 27 Jul 2021 13:24:50 +0200 Subject: [PATCH 0512/9987] changed version for PDT 3.25.1 --- ...{PDT-3.25-GCCcore-10.3.0.eb => PDT-3.25.1-GCCcore-10.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/PDT/{PDT-3.25-GCCcore-10.3.0.eb => PDT-3.25.1-GCCcore-10.3.0.eb} (98%) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-10.3.0.eb similarity index 98% rename from easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-10.3.0.eb index da323b46cc2..ba0c227ba84 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.25-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-10.3.0.eb @@ -11,7 +11,7 @@ # # name = 'PDT' -version = '3.25' +version = '3.25.1' homepage = 'https://www.cs.uoregon.edu/research/pdt/' description = """ From 00c2c5545f0a3deb40bc4e2ab1b0bcb5d2dbd21f Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 27 Jul 2021 11:31:29 +0000 Subject: [PATCH 0513/9987] {mpi}[intel-compilers/2021.2.0] OpenMPI v4.1.1 --- .../OpenMPI-4.1.1-intel-compilers-2021.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..9a44bea237d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb @@ -0,0 +1,40 @@ +## +# Author: Robert Mijakovic +## +name = 'OpenMPI' +version = '4.1.1' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch'] +checksums = [ + 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 + # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch + 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.4.1'), + ('libevent', '2.1.12'), + ('UCX', '1.10.0'), + ('libfabric', '1.12.1'), + ('PMIx', '3.2.3'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From 671be3320b8638a4423ab4fb1bf5b74600ca9145 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 27 Jul 2021 11:35:24 +0000 Subject: [PATCH 0514/9987] Sync OpenMPI 4.1.1 with patch from develop --- .../o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb index 9a44bea237d..6d64daf9054 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb @@ -11,11 +11,16 @@ toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch'] +patches = [ + 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', + 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' +] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', + # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch + '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', ] builddependencies = [ From 010822b971c4c2d3448a955b92bd43ade6fe201a Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 27 Jul 2021 13:50:17 +0200 Subject: [PATCH 0515/9987] fixed check sum for 3.25.1 --- easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-10.3.0.eb index ba0c227ba84..616d76a254c 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-10.3.0.eb @@ -27,7 +27,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['http://tau.uoregon.edu/pdt_releases/'] sources = ['pdtoolkit-%(version)s.tar.gz'] -checksums = ['1037628d854edfeded3d847150d3e8fbd3774e8146407ce32f5021c80f6299be'] +checksums = ['0b6f8a6b8769c181b2ae6cae7298f04b8e3e3d68066f598ed24574e19500bc97'] builddependencies = [ ('binutils', '2.36.1'), From c415eda1332fd7e9514944441e0cb2166d3c1f65 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 27 Jul 2021 15:58:54 +0200 Subject: [PATCH 0516/9987] adding easyconfigs: BLIS-3.0.1-GCCcore-10.2.0-amd.eb --- .../b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb new file mode 100644 index 00000000000..58742db0fc1 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb @@ -0,0 +1,41 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '3.0.1' +versionsuffix = '-amd' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' +description = """AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/amd/blis/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +# Build Serial and multithreaded library +configopts = ['--enable-cblas --enable-shared CC="$CC" auto', + '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto'] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT, + 'lib/libblis-mt.a', 'lib/libblis-mt.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' From 76000bf15d4de3199e48ec20acd80d779467d760 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 27 Jul 2021 16:47:47 +0200 Subject: [PATCH 0517/9987] adding easyconfigs: arpack-ng-3.8.0-foss-2021a.eb --- .../a/arpack-ng/arpack-ng-3.8.0-foss-2021a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021a.eb new file mode 100644 index 00000000000..0382ae7ae84 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021a.eb @@ -0,0 +1,38 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = "3.8.0" + +homepage = 'https://github.com/opencollab/arpack-ng' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'opencollab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['ada5aeb3878874383307239c9235b716a8a170c6d096a6625bfd529844df003d'] + +builddependencies = [ + ('Autotools', '20210128'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Eigen', '3.3.9') +] + +preconfigopts = "sh bootstrap && " +configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib64/libarpack.la", "lib64/libarpack.%s" % SHLIB_EXT, + "lib64/libparpack.la", "lib64/libparpack.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'numlib' From 7ae98c00514b2fd67a0bc7e58148fe07f180646c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 27 Jul 2021 17:08:46 +0200 Subject: [PATCH 0518/9987] adding easyconfigs: mimalloc-1.7.2-GCCcore-10.3.0.eb --- .../mimalloc/mimalloc-1.7.2-GCCcore-10.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..0c7871b8989 --- /dev/null +++ b/easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'mimalloc' +version = '1.7.2' + +homepage = 'https://microsoft.github.io/mimalloc/' +description = """mimalloc is a general purpose allocator with excellent performance characteristics.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'microsoft' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b1912e354565a4b698410f7583c0f83934a6dbb3ade54ab7ddcb1569320936bd'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['lib/mimalloc-%(version_major_minor)s/libmimalloc.a', 'lib/libmimalloc.%s' % SHLIB_EXT], + 'dirs': ['include/mimalloc-%(version_major_minor)s'], +} + +runtest = 'test' + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libmimalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' From 2f397c10f5ca84eb127074525ffc72bb5c22488d Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 27 Jul 2021 13:27:40 -0700 Subject: [PATCH 0519/9987] remove foss --- .../m/Metal/Metal-2020-05-05-foss-2020b.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/m/Metal/Metal-2020-05-05-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-foss-2020b.eb b/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-foss-2020b.eb deleted file mode 100644 index b2d08a31a35..00000000000 --- a/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-foss-2020b.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Metal' -version = '2020-05-05' - -homepage = 'http://csg.sph.umich.edu/abecasis/Metal/' -description = """Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large - datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://github.com/statgen/METAL/archive/refs/tags'] -sources = ['%(version)s.tar.gz'] -checksums = ['0ffa2419ca2ab43766e7e6e8c97822c8ce1f5b6233fb5f992d1b1be1955fede7'] - -builddependencies = [('CMake', '3.18.4')] -dependencies = [('zlib', '1.2.11')] - -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=Release' - -postinstallcmds = [ - 'mkdir -p %(installdir)s/bin && ' + - 'cp %(builddir)s/easybuild_obj/bin/metal %(installdir)s/bin' -] - -sanity_check_paths = { - 'files': ['bin/metal'], - 'dirs': [''], -} - -sanity_check_commands = ['%(namelower)s /dev/null'] - -moduleclass = 'bio' From 2cca164c7cbf91ab458e7dca80c0dd2220285790 Mon Sep 17 00:00:00 2001 From: "benjamin.czaja" Date: Wed, 28 Jul 2021 11:02:49 +0200 Subject: [PATCH 0520/9987] Adding easyconfigs: Paraver-4.9.2-foss-2021a.eb, wxWidgets-3.1.4-GCC-10.3.0.eb, GST-plugins-base-1.18.4-GCC-10.3.0.eb, GStreamer-1.18.4-GCC-10.3.0.eb --- .../GST-plugins-base-1.18.4-GCC-10.3.0.eb | 38 +++++++++++ .../GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb | 43 +++++++++++++ .../p/Paraver/Paraver-4.9.2-foss-2021a.eb | 21 ++++++ .../w/wxWidgets/wxWidgets-3.1.4-GCC-10.3.0.eb | 64 +++++++++++++++++++ 4 files changed, 166 insertions(+) create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..f50410c2fe1 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-base' +version = '1.18.4' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['29e53229a84d01d722f6f6db13087231cdf6113dd85c25746b9b58c3d68e8323'] +builddependencies = [ + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('Bison', '3.7.6'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('GLib', '2.68.2'), + ('GTK+', '3.24.29'), + ('GStreamer', '1.18.4'), + ('Gdk-Pixbuf', '2.42.6'), + ('X11', '20210518'), + ('Mesa', '21.1.1'), +] +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} +moduleclass = 'vis' \ No newline at end of file diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..fbd4142bb19 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GStreamer' +version = '1.18.4' + +homepage = 'https://gstreamer.freedesktop.org/' + +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] + +builddependencies = [ + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('GMP', '6.2.1'), + ('GSL', '2.7'), + ('GLib', '2.68.2'), + ('GTK+', '3.24.29'), + ('libunwind', '1.4.0'), +] + +configopts = '-Dlibdw=disabled ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} +moduleclass = 'vis' \ No newline at end of file diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb new file mode 100644 index 00000000000..0f380e95d98 --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb @@ -0,0 +1,21 @@ +name = 'Paraver' +version = '4.9.2' + +homepage = 'https://tools.bsc.es/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://ftp.tools.bsc.es/wxparaver/'] +sources = ['wxparaver-%(version)s-src.tar.bz2'] +checksums = ['83289584040bcedf8cab1b2ae3545191c8bdef0e11ab62b06e54cbf111f2127a'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.76.0'), + ('wxWidgets', '3.1.5'), +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..caeb0b8eaed --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.3.0.eb @@ -0,0 +1,64 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.1.5' + +homepage = 'https://www.wxwidgets.org' + +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/wxWidgets/wxWidgets/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e8fd5f9fbff864562aa4d9c094f898c97f5e1274c90f25beb0bfd5cb61319dea'] + +builddependencies = [ + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('Python', '3.9.5'), +] +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.2.0'), + ('expat', '2.2.9'), + ('GTK+', '3.24.29'), + ('X11', '20210518'), + ('Mesa', '21.1.1'), + ('libGLU', '9.0.1'), + ('SDL2', '2.0.14'), + ('cairo', '1.16.0'), + ('GST-plugins-base', '1.18.4'), + ('GLib', '2.68.2'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} +moduleclass = 'vis' \ No newline at end of file From 5f1de6683624227c7e15402b65635c8fd2ae0f88 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 28 Jul 2021 12:19:50 +0200 Subject: [PATCH 0521/9987] Drop config flag --- easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb index 435e094bea0..4867d22fcd0 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb @@ -56,7 +56,7 @@ configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' configopts += '--enable-mediactrl --enable-display --enable-geometry ' configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' configopts += '--enable-autoidman --with-sdl ' -configopts += '--disable-webkit --disable-webview --disable-webviewwebkit ' +configopts += '--disable-webview --disable-webviewwebkit ' configopts += '--disable-tests ' From e15e97679b91b1ac97ab8076c051fd5c45765c94 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 28 Jul 2021 13:14:03 +0200 Subject: [PATCH 0522/9987] Update easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-10.3.0.eb Co-authored-by: Alex Domingo --- .../easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-10.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-10.3.0.eb index 0c7871b8989..f54a56ff07b 100644 --- a/easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-10.3.0.eb @@ -25,8 +25,8 @@ sanity_check_paths = { runtest = 'test' -# jemalloc can be used via $LD_PRELOAD, but we don't enable this by -# default, you need to opt-in to it +# mimalloc is a drop-in replacement for malloc and can be used in other programs without code changes, +# but we don't enable this by default, you need to opt-in by setting $LD_PRELOAD as follows # modextrapaths = {'LD_PRELOAD': ['lib/libmimalloc.%s' % SHLIB_EXT]} moduleclass = 'lib' From 5f93b9d99205b6220b6226b32a75d0b8cf699d9b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 21 Jul 2021 15:16:26 +0200 Subject: [PATCH 0523/9987] adding easyconfigs: VisPy-0.6.6-foss-2020b.eb, VisPy-0.6.6-intel-2020b.eb --- .../v/VisPy/VisPy-0.6.6-foss-2020b.eb | 34 +++++++++++++++++++ .../v/VisPy/VisPy-0.6.6-intel-2020b.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb create mode 100644 easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb diff --git a/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb new file mode 100644 index 00000000000..8bdc452acc6 --- /dev/null +++ b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'VisPy' +version = '0.6.6' + +homepage = 'https://vispy.org' +description = """VisPy is a high-performance interactive 2D/3D data visualization library + leveraging the computational power of modern Graphics Processing Units (GPUs) through the + OpenGL library to display very large datasets.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyQt5', '5.15.1'), +] + +use_pip = True + +exts_list = [ + ('freetype_py', '2.2.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-2.2.0.zip'], + 'checksums': ['cf43716bc5246cd54a64b2238b942e8dc80b79eda92f814c720286fa6fab387a'], + }), + ('vispy', version, { + 'checksums': ['6f3c4d00be9e6761c046d520a86693d78a0925d47eeb2fc095e95dac776f74ee'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb new file mode 100644 index 00000000000..6ae981a0217 --- /dev/null +++ b/easybuild/easyconfigs/v/VisPy/VisPy-0.6.6-intel-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'VisPy' +version = '0.6.6' + +homepage = 'https://vispy.org' +description = """VisPy is a high-performance interactive 2D/3D data visualization library + leveraging the computational power of modern Graphics Processing Units (GPUs) through the + OpenGL library to display very large datasets.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyQt5', '5.15.1'), +] + +use_pip = True + +exts_list = [ + ('freetype_py', '2.2.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-2.2.0.zip'], + 'checksums': ['cf43716bc5246cd54a64b2238b942e8dc80b79eda92f814c720286fa6fab387a'], + }), + ('vispy', version, { + 'checksums': ['6f3c4d00be9e6761c046d520a86693d78a0925d47eeb2fc095e95dac776f74ee'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From c68721dcd0d830fa919f173797d4c9111142139c Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 28 Jul 2021 20:49:50 +0000 Subject: [PATCH 0524/9987] Missing URL for homepage added --- easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb index df1a6862142..c7645d9ed33 100644 --- a/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb @@ -7,7 +7,7 @@ easyblock = 'ConfigureMake' name = 'kalign2' version = '2.0.4' -homepage = '' +homepage = 'https://msa.sbc.su.se/cgi-bin/msa.cgi' description = "Kalign is a fast multiple sequence alignment program for biological sequences." toolchain = {'name': 'GCCcore', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb index 90a26ddeb45..efbe208f5b6 100644 --- a/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb @@ -7,7 +7,7 @@ easyblock = 'ConfigureMake' name = 'kalign2' version = '3.3.1' -homepage = '' +homepage = 'https://github.com/TimoLassmann/kalign' description = "Kalign is a fast multiple sequence alignment program for biological sequences." toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From d98d762a76ca20e8a7e9ddf3606905489db59bc8 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 28 Jul 2021 21:02:44 +0000 Subject: [PATCH 0525/9987] Surplus autoreconf removed for kalign-2.04, both versions surpluse ticks removed --- .../easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb | 4 +--- .../easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb index c7645d9ed33..84dfafa171b 100644 --- a/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb @@ -22,13 +22,11 @@ dependencies = [ ('Autoconf', '2.69'), ] -configure_cmd_prefix = "autoreconf -vfi && " - install_cmd = "mkdir %(installdir)s/bin && cp kalign %(installdir)s/bin" sanity_check_paths = { 'files': ['bin/kalign'], - 'dirs': [''], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb index efbe208f5b6..2e19a2c48d5 100644 --- a/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb @@ -26,7 +26,7 @@ configure_cmd_prefix = "autoreconf -vfi && " sanity_check_paths = { 'files': ['bin/kchaos', 'bin/kalign'], - 'dirs': [''], + 'dirs': [], } moduleclass = 'bio' From ff31cc701bcd782ba20cb2ae145f8de164e60314 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 28 Jul 2021 21:33:56 +0000 Subject: [PATCH 0526/9987] Sanity check corrected --- .../easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb index 2966ea397c4..5fc4e7155b5 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb @@ -41,6 +41,9 @@ sanity_check_paths = { 'dirs': ['include'] } -sanity_check_commands = ["minimap2 --help"] +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] moduleclass = 'bio' From 7104a003acea5c941fbfd440992750768b02058d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 28 Jul 2021 23:35:06 +0200 Subject: [PATCH 0527/9987] disable default EULA acceptance in n/NVHPC/NVHPC-21.5.eb --- easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb index 722a853a9a9..236a16334b5 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb @@ -9,8 +9,9 @@ description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK ( toolchain = SYSTEM -# By downloading, you accept the HPC SDK Software License Agreement (https://docs.nvidia.com/hpc-sdk/eula/index.html) -accept_eula = True +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] local_tarball_tmpl = 'nvhpc_2021_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' sources = [local_tarball_tmpl % '%(arch)s'] From dc075d2a4e0b2891a6bb506d58787d63459854d4 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 29 Jul 2021 07:52:34 +0200 Subject: [PATCH 0528/9987] Update easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb index d996db615a5..4b6b2fbe1a2 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb @@ -9,8 +9,9 @@ description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK ( toolchain = SYSTEM -# By downloading, you accept the HPC SDK Software License Agreement (https://docs.nvidia.com/hpc-sdk/eula/index.html) -accept_eula = True +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] local_tarball_tmpl = 'nvhpc_2021_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' sources = [local_tarball_tmpl % '%(arch)s'] From 81f4c5aed408eb794ccdb3c1bee6f7e048621daa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 29 Jul 2021 09:48:19 +0200 Subject: [PATCH 0529/9987] adding easyconfigs: fumi_tools-0.18.2-GCC-10.3.0.eb --- .../fumi_tools-0.18.2-GCC-10.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-10.3.0.eb b/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..3c43c02915c --- /dev/null +++ b/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'fumi_tools' +version = '0.18.2' + +homepage = 'https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools' +description = """This tool is intended to deduplicate UMIs from single-end and paired-end + sequencing data. Reads are considered identical when their UMIs have the same sequence, + they have the same length and map at the same position.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://ccb-gitlab.cs.uni-saarland.de/tobias/%(name)s/uploads/bff8865d9eeaaa27849dd580aa2a9dd1/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3570890e232f4a1862541c08d5755f11a12cf8972e2ee7461adc270ba4a220f1'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('pigz', '2.6'), + ('zlib', '1.2.11'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ["%(name)s -h"] + +moduleclass = 'bio' From c1606548b644dcfbe3c81b703478519e17fa4011 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 29 Jul 2021 10:08:48 +0200 Subject: [PATCH 0530/9987] adding easyconfigs: FASTX-Toolkit-0.0.14-GCC-10.3.0.eb --- .../FASTX-Toolkit-0.0.14-GCC-10.3.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-10.3.0.eb new file mode 100644 index 00000000000..be52bdfb220 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-10.3.0.eb @@ -0,0 +1,63 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'Bundle' + +name = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +default_easyblock = 'ConfigureMake' + +components = [ + ('libgtextutils', '0.7', { + 'source_urls': ['https://github.com/agordon/libgtextutils/releases/download/%(version)s/'], + 'sources': [SOURCE_TAR_GZ], + 'patches': ['libgtextutils-%(version)s_fix-bool.patch'], + 'checksums': [ + '792e0ea3c96ffe3ad65617a104b7dc50684932bc96d2adab501c952fd65c3e4a', # libgtextutils-0.7.tar.gz + 'bb16a4fd86c2eb12215d8780b09f0898771a73e53889a015e2351f2d737c9a00', # libgtextutils-0.7_fix-bool.patch + ], + 'start_dir': 'libgtextutils-%(version)s', + }), + (name, version, { + 'source_urls': ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'], + 'sources': ['fastx_toolkit-%(version)s.tar.bz2'], + 'checksums': ['9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806'], + 'start_dir': 'fastx_toolkit-%(version)s', + 'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ", + 'configopts': 'CXXFLAGS="$CXXFLAGS -Wno-implicit-fallthrough"', + }), +] + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']] + + ['lib/libgtextutils.%s' % SHLIB_EXT, 'lib/libgtextutils.a'], + 'dirs': [] +} + +moduleclass = 'bio' From dd00fc6b3753b8400019d1654c499f73a87b9902 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 29 Jul 2021 10:27:27 +0200 Subject: [PATCH 0531/9987] adding easyconfigs: fastq-tools-0.8.3-GCC-10.3.0.eb --- .../fastq-tools-0.8.3-GCC-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastq-tools/fastq-tools-0.8.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/fastq-tools/fastq-tools-0.8.3-GCC-10.3.0.eb b/easybuild/easyconfigs/f/fastq-tools/fastq-tools-0.8.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..169e3d2d6b2 --- /dev/null +++ b/easybuild/easyconfigs/f/fastq-tools/fastq-tools-0.8.3-GCC-10.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'fastq-tools' +version = '0.8.3' + +homepage = 'https://homes.cs.washington.edu/~dcjones/%(name)s/' +description = """This package provides a number of small and efficient programs to perform + common tasks with high throughput sequencing data in the FASTQ format. All of the programs + work with typical FASTQ files as well as gzipped FASTQ files.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +github_account = 'dcjones' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = ['0cd7436e81129090e707f69695682df80623b06448d95df483e572c61ddf538e'] + +builddependencies = [('Autotools', '20210128')] + +dependencies = [ + ('PCRE', '8.44'), + ('zlib', '1.2.11'), +] + +# unsetting LIBS is needed because configure script can't handle it properly if it is already defined +preconfigopts = './autogen.sh && unset LIBS && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['fastq-grep', 'fastq-kmers', 'fastq-match', 'fastq-qscale', + 'fastq-qual', 'fastq-qualadj', 'fastq-sample', 'fastq-sort', + 'fastq-uniq']], + 'dirs': ['share/man/man1'], +} + +moduleclass = 'bio' From 6e9fcdfd2e3af8b2fa8d7283948d8d541d145e2d Mon Sep 17 00:00:00 2001 From: benczaja Date: Thu, 29 Jul 2021 11:37:52 +0200 Subject: [PATCH 0532/9987] removed files for PR 13413 --- .../GST-plugins-base-1.18.4-GCC-10.3.0.eb | 38 ----------- .../GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb | 43 ------------- .../w/wxWidgets/wxWidgets-3.1.4-GCC-10.3.0.eb | 64 ------------------- 3 files changed, 145 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb delete mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb delete mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb deleted file mode 100644 index f50410c2fe1..00000000000 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'GST-plugins-base' -version = '1.18.4' - -homepage = 'https://gstreamer.freedesktop.org/' -description = """GStreamer is a library for constructing graphs of media-handling - components. The applications it supports range from simple - Ogg/Vorbis playback, audio/video streaming to complex audio - (mixing) and video (non-linear editing) processing.""" - -toolchain = {'name': 'GCC', 'version': '10.3.0'} -source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['29e53229a84d01d722f6f6db13087231cdf6113dd85c25746b9b58c3d68e8323'] -builddependencies = [ - ('Meson', '0.58.0'), - ('Ninja', '1.10.2'), - ('GObject-Introspection', '1.68.0'), - ('gettext', '0.21'), - ('pkg-config', '0.29.2'), - ('Bison', '3.7.6'), -] -dependencies = [ - ('zlib', '1.2.11'), - ('GLib', '2.68.2'), - ('GTK+', '3.24.29'), - ('GStreamer', '1.18.4'), - ('Gdk-Pixbuf', '2.42.6'), - ('X11', '20210518'), - ('Mesa', '21.1.1'), -] -sanity_check_paths = { - 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + - ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], - 'dirs': ['include', 'share'] -} -moduleclass = 'vis' \ No newline at end of file diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb deleted file mode 100644 index fbd4142bb19..00000000000 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'GStreamer' -version = '1.18.4' - -homepage = 'https://gstreamer.freedesktop.org/' - -description = """GStreamer is a library for constructing graphs of media-handling - components. The applications it supports range from simple - Ogg/Vorbis playback, audio/video streaming to complex audio - (mixing) and video (non-linear editing) processing.""" - -toolchain = {'name': 'GCC', 'version': '10.3.0'} - -source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] - -builddependencies = [ - ('Meson', '0.58.0'), - ('Ninja', '1.10.2'), - ('Bison', '3.7.6'), - ('flex', '2.6.4'), - ('GObject-Introspection', '1.68.0'), - ('gettext', '0.21'), - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('zlib', '1.2.11'), - ('GMP', '6.2.1'), - ('GSL', '2.7'), - ('GLib', '2.68.2'), - ('GTK+', '3.24.29'), - ('libunwind', '1.4.0'), -] - -configopts = '-Dlibdw=disabled ' - -sanity_check_paths = { - 'files': [], - 'dirs': ['include', 'share', 'libexec'], -} -moduleclass = 'vis' \ No newline at end of file diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.3.0.eb deleted file mode 100644 index caeb0b8eaed..00000000000 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.4-GCC-10.3.0.eb +++ /dev/null @@ -1,64 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'wxWidgets' -version = '3.1.5' - -homepage = 'https://www.wxwidgets.org' - -description = """wxWidgets is a C++ library that lets developers create -applications for Windows, Mac OS X, Linux and other platforms with a -single code base. It has popular language bindings for Python, Perl, -Ruby and many other languages, and unlike other cross-platform toolkits, -wxWidgets gives applications a truly native look and feel because it -uses the platform's native API rather than emulating the GUI.""" - -toolchain = {'name': 'GCC', 'version': '10.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/wxWidgets/wxWidgets/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['e8fd5f9fbff864562aa4d9c094f898c97f5e1274c90f25beb0bfd5cb61319dea'] - -builddependencies = [ - ('gettext', '0.21'), - ('pkg-config', '0.29.2'), - ('Python', '3.9.5'), -] -dependencies = [ - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.6'), - ('XZ', '5.2.5'), - ('jbigkit', '2.1'), - ('LibTIFF', '4.2.0'), - ('expat', '2.2.9'), - ('GTK+', '3.24.29'), - ('X11', '20210518'), - ('Mesa', '21.1.1'), - ('libGLU', '9.0.1'), - ('SDL2', '2.0.14'), - ('cairo', '1.16.0'), - ('GST-plugins-base', '1.18.4'), - ('GLib', '2.68.2'), -] - -local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' -preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext -configopts = '--enable-intl --enable-ipv6 ' -# Options required by wxPython -configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' -# Note: the configure step might claim to find OpenGL headers in -# /usr/include, but it will still use the ones from the Mesa dependency above -configopts += '--with-opengl ' -configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' -configopts += '--enable-mediactrl --enable-display --enable-geometry ' -configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' -configopts += '--enable-autoidman --with-sdl ' -configopts += '--disable-webview --disable-webviewwebkit ' -configopts += '--disable-tests ' -prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext -sanity_check_paths = { - 'files': ['bin/wx-config', 'bin/wxrc'], - 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], -} -moduleclass = 'vis' \ No newline at end of file From 4eff7737193db965cbcddb1a46b0af947439aae1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 29 Jul 2021 10:55:49 +0100 Subject: [PATCH 0533/9987] adding easyconfigs: OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb, HPL-2.3-iomkl-2021a.eb --- .../easyconfigs/h/HPL/HPL-2.3-iomkl-2021a.eb | 21 ++++++++++++++++ .../OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb | 24 +++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-iomkl-2021a.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-iomkl-2021a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-iomkl-2021a.eb new file mode 100644 index 00000000000..bb523b79659 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-iomkl-2021a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'iomkl', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb new file mode 100644 index 00000000000..b6b6cf0d108 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.7.1' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iompi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TGZ] +checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From a8d278c4e92e83589066e1d57f4811b59ee4bf7c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 29 Jul 2021 14:07:10 +0200 Subject: [PATCH 0534/9987] adding easyconfigs: AdapterRemoval-2.3.2-GCC-10.3.0.eb --- .../AdapterRemoval-2.3.2-GCC-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.3.0.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..b56f2a5062e --- /dev/null +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'AdapterRemoval' +version = '2.3.2' + +homepage = 'https://github.com/MikkelSchubert/adapterremoval' +description = """AdapterRemoval searches for and removes remnant adapter sequences + from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases + from the 3' end of reads following adapter removal.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +github_account = 'MikkelSchubert' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ded7e08fb64e1b19f5c3de623de276d9cbb657a52b23a844ff74576d1b4f8d4'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] +} + +sanity_check_commands = [('%(name)s', '--version')] + +moduleclass = 'bio' From d107184ed19f18c2d61b0423f3bb0e6284812f66 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 29 Jul 2021 14:41:06 +0200 Subject: [PATCH 0535/9987] {bio}[foss/2020b] nanopolish 0.13.3 --- .../nanopolish-0.13.3-foss-2020b.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb new file mode 100644 index 00000000000..ffba642eb45 --- /dev/null +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb @@ -0,0 +1,52 @@ +easyblock = 'MakeCp' + +name = 'nanopolish' +version = '0.13.3' + +homepage = 'https://github.com/jts/nanopolish' +description = "Software package for signal-level analysis of Oxford Nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://github.com/jts/nanopolish/archive/', + 'https://github.com/mateidavid/fast5/archive/', +] +sources = [ + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'download_filename': 'v0.6.5.tar.gz', 'filename': 'fast5-v0.6.5.tar.gz'}, +] +checksums = [ + 'eac02b7db76f223375e246fa361a0a4fbf74021b9094573e5324fd7f75743d55', # nanopolish-0.13.3.tar.gz + 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz +] + +builddependencies = [('Eigen', '3.3.7', '', True)] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.8.6'), + ('Biopython', '1.78'), + ('Pysam', '0.16.0.1'), + ('HDF5', '1.10.7'), + ('HTSlib', '1.11'), + ('minimap2', '2.18'), +] + +prebuildopts = "rmdir fast5 && ln -s %(builddir)s/fast5-*/ fast5 && " +buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall" + +runtest = 'test ' + buildopts + +files_to_copy = [(['nanopolish'], 'bin'), 'scripts'] + +postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"] + +sanity_check_paths = { + 'files': ['bin/nanopolish'], + 'dirs': ['scripts'], +} + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From 2979a882e3c45e351f5b7b3b6e1d6786f7baf578 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 29 Jul 2021 16:31:41 +0100 Subject: [PATCH 0536/9987] adding easyconfigs: Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb and patches: Qt5Webkit-5.212.0-alpha4_bison3.7.patch --- ...Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb | 56 +++++++++++++++++++ .../Qt5Webkit-5.212.0-alpha4_bison3.7.patch | 46 +++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_bison3.7.patch diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0fff752203f --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb @@ -0,0 +1,56 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeNinja' + +name = 'Qt5Webkit' +# Qt5 > 5.9 required at least version 5.212.0 +# At the time of writing the latest version was 5.212.0-alpha3 +version = '5.212.0-alpha4' + +homepage = 'https://github.com/qt/qtwebkit' +description = "Qt Port of WebKit. WebKit is an open source web browser engine." +docurls = ['https://github.com/qt/qtwebkit/blob/dev/README'] + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/qtwebkit/qtwebkit/releases/download/qtwebkit-%(version)s/'] +sources = ['qtwebkit-%(version)s.tar.xz'] +patches = ['%(name)s-%(version)s_bison3.7.patch'] +checksums = [ + '9ca126da9273664dd23a3ccd0c9bebceb7bb534bddd743db31caf6a5a6d4a9e6', # qtwebkit-5.212.0-alpha4.tar.xz + '34f37b53ee0bc31c63ce85ebd1ae95543a8ba28483e387b20efd50574bd813be', # Qt5Webkit-5.212.0-alpha4_bison3.7.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.10.1'), + ('Python', '3.8.6'), + ('Ruby', '2.7.2'), +] + +dependencies = [ + ('Qt5', '5.14.2'), + ('zlib', '1.2.11'), + ('SQLite', '3.33.0'), + ('ICU', '67.1'), + ('libxslt', '1.1.34'), + ('libjpeg-turbo', '2.0.5'), +] + +configopts = "-G Ninja -DPORT=Qt -DCMAKE_BUILD_TYPE=Release -DUSE_LIBHYPHEN=OFF -DUSE_GSTREAMER=OFF " + +sanity_check_paths = { + 'files': [ + 'lib64/libQt5WebKit.%s' % SHLIB_EXT, + 'lib64/libQt5WebKitWidgets.%s' % SHLIB_EXT, + ], + 'dirs': ['include/QtWebKit', 'include/QtWebKitWidgets'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_bison3.7.patch b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_bison3.7.patch new file mode 100644 index 00000000000..13dd68182af --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_bison3.7.patch @@ -0,0 +1,46 @@ +From d92b11fea65364fefa700249bd3340e0cd4c5b31 Mon Sep 17 00:00:00 2001 +From: Dmitry Shachnev +Date: Tue, 4 Aug 2020 21:04:06 +0300 +Subject: [PATCH] Let Bison generate the header directly, to fix build with + Bison 3.7 + +Starting with Bison 3.7, the generated C++ file #include's the header +by default, instead of duplicating it. So we should not delete it. + +Remove the code to add #ifdef guards to the header, since Bison adds +them itself since version 2.6.3. +--- + Source/WebCore/css/makegrammar.pl | 21 +-------------------- + 1 file changed, 1 insertion(+), 20 deletions(-) + +diff --git a/Source/WebCore/css/makegrammar.pl b/Source/WebCore/css/makegrammar.pl +index 5d63b08102eb5..9435701c70612 100644 +--- a/Source/WebCore/css/makegrammar.pl ++++ b/Source/WebCore/css/makegrammar.pl +@@ -73,25 +73,6 @@ + } + + my $fileBase = File::Spec->join($outputDir, $filename); +-my @bisonCommand = ($bison, "-d", "-p", $symbolsPrefix, $grammarFilePath, "-o", "$fileBase.cpp"); ++my @bisonCommand = ($bison, "--defines=$fileBase.h", "-p", $symbolsPrefix, $grammarFilePath, "-o", "$fileBase.cpp"); + push @bisonCommand, "--no-lines" if $^O eq "MSWin32"; # Work around bug in bison >= 3.0 on Windows where it puts backslashes into #line directives. + system(@bisonCommand) == 0 or die; +- +-open HEADER, ">$fileBase.h" or die; +-print HEADER << "EOF"; +-#ifndef CSSGRAMMAR_H +-#define CSSGRAMMAR_H +-EOF +- +-open HPP, "<$fileBase.cpp.h" or open HPP, "<$fileBase.hpp" or die; +-while () { +- print HEADER; +-} +-close HPP; +- +-print HEADER "#endif\n"; +-close HEADER; +- +-unlink("$fileBase.cpp.h"); +-unlink("$fileBase.hpp"); +- From c61bd0e594cfd2c803bd2194987bd5c4c6da875e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 30 Jul 2021 00:03:32 +0200 Subject: [PATCH 0537/9987] put gffread executable into bin --- .../g/gffread/gffread-0.12.7-GCC-10.3.0.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb index 24ecba45d8d..0b1607a0ada 100644 --- a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb @@ -17,15 +17,16 @@ checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] buildopts = " release" -files_to_copy = ['%(name)s', 'LICENSE'] - -modextrapaths = {'PATH': ''} +files_to_copy = [ + (['%(name)s'], 'bin'), + 'LICENSE', +] sanity_check_paths = { - 'files': ['%(name)s'], + 'files': ['bin/%(name)s'], 'dirs': [] } -sanity_check_commands = ['%(name)s '] +sanity_check_commands = ['%(name)s'] moduleclass = 'bio' From 0eb3e5ea4c9e39375afb7b93e470ed23b185156e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 30 Jul 2021 00:35:06 +0200 Subject: [PATCH 0538/9987] use CMakeMakeCp easyblock in Metal v2020-05-05 --- .../m/Metal/Metal-2020-05-05-GCC-10.2.0.eb | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb b/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb index 67bd18df244..5d713d8d117 100644 --- a/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/Metal/Metal-2020-05-05-GCC-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakeMakeCp' name = 'Metal' version = '2020-05-05' @@ -16,20 +16,13 @@ checksums = ['0ffa2419ca2ab43766e7e6e8c97822c8ce1f5b6233fb5f992d1b1be1955fede7'] builddependencies = [('CMake', '3.18.4')] dependencies = [('zlib', '1.2.11')] -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=Release' - -postinstallcmds = [ - 'mkdir -p %(installdir)s/bin && ' + - 'cp %(builddir)s/easybuild_obj/bin/metal %(installdir)s/bin' -] +files_to_copy = [(['metal/metal'], 'bin')] sanity_check_paths = { 'files': ['bin/metal'], 'dirs': [''], } -sanity_check_commands = ['%(namelower)s /dev/null'] +sanity_check_commands = ['%(namelower)s'] moduleclass = 'bio' From aaea69b3459d367250d8a52431a8ebcd594f0839 Mon Sep 17 00:00:00 2001 From: benczaja Date: Fri, 30 Jul 2021 09:32:15 +0200 Subject: [PATCH 0539/9987] removing Paraver --- .../p/Paraver/Paraver-4.9.2-foss-2021a.eb | 21 ------------------- 1 file changed, 21 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb deleted file mode 100644 index 0f380e95d98..00000000000 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'Paraver' -version = '4.9.2' - -homepage = 'https://tools.bsc.es/paraver' -description = """A very powerful performance visualization and analysis tool based on - traces that can be used to analyse any information that is expressed on its input trace format. - Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -source_urls = ['https://ftp.tools.bsc.es/wxparaver/'] -sources = ['wxparaver-%(version)s-src.tar.bz2'] -checksums = ['83289584040bcedf8cab1b2ae3545191c8bdef0e11ab62b06e54cbf111f2127a'] - -dependencies = [ - ('zlib', '1.2.11'), - ('Boost', '1.76.0'), - ('wxWidgets', '3.1.5'), -] - -moduleclass = 'perf' From 1e08bfce39eef7b0bb04a4e32616fb27333a51f3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 30 Jul 2021 09:16:35 +0100 Subject: [PATCH 0540/9987] adding easyconfigs: velocyto-0.17.17-foss-2021a.eb, Pysam-0.16.0.1-GCC-10.3.0.eb --- .../p/Pysam/Pysam-0.16.0.1-GCC-10.3.0.eb | 38 +++++++++++++++ .../v/velocyto/velocyto-0.17.17-foss-2021a.eb | 47 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..4198d10d48c --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-10.3.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Erich Birngruber +# Gregor Mendel Institute + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.16.0.1' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a61e98e299fa93ba121aab521081282b61bc978bb9052d33b26b38f8fe15573e'] + +dependencies = [ + ('Python', '3.9.5'), + ('ncurses', '6.2'), + ('cURL', '7.76.0'), + ('XZ', '5.2.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2021a.eb b/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2021a.eb new file mode 100644 index 00000000000..17e2ba963fb --- /dev/null +++ b/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'velocyto' +version = '0.17.17' + +homepage = 'https://velocyto.org/velocyto.py/' +description = "Velocyto is a library for the analysis of RNA velocity." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('numba', '0.53.1'), + ('scikit-learn', '0.24.2'), + ('h5py', '3.2.1'), + ('Pysam', '0.16.0.1'), + +] + +use_pip = True + +exts_list = [ + ('numpy_groupies', '0.9.13', { + 'checksums': ['7b17b291322353f07c51598512d077e3731da0a048cfa8f738f3460d1ef0658d'], + }), + ('loompy', '3.0.6', { + 'checksums': ['58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46'], + }), + (name, version, { + 'checksums': ['1ad65fc53292ce1970a70bc742d73491b370038e0b0065761303e787bf7ffe39'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/velocyto'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'velocyto', +] + +moduleclass = 'bio' From b1b8683f99e0f673eedda6b4cd33986db66f0912 Mon Sep 17 00:00:00 2001 From: benczaja Date: Fri, 30 Jul 2021 10:35:25 +0200 Subject: [PATCH 0541/9987] {perf}[foss/2021a] Paraver v4.9.2 --- .../p/Paraver/Paraver-4.9.2-foss-2021a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb new file mode 100644 index 00000000000..0f380e95d98 --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.9.2-foss-2021a.eb @@ -0,0 +1,21 @@ +name = 'Paraver' +version = '4.9.2' + +homepage = 'https://tools.bsc.es/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://ftp.tools.bsc.es/wxparaver/'] +sources = ['wxparaver-%(version)s-src.tar.bz2'] +checksums = ['83289584040bcedf8cab1b2ae3545191c8bdef0e11ab62b06e54cbf111f2127a'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.76.0'), + ('wxWidgets', '3.1.5'), +] + +moduleclass = 'perf' From d2ac91f53bb53ce12cfb4ae4c5970f92057d0c2d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 30 Jul 2021 13:47:37 +0200 Subject: [PATCH 0542/9987] Switch to lcms2 --- .../l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb | 17 ++++---- .../libjxl/libjxl-0.3.7_external_lcms2.patch | 40 +++++++++++++++++++ 2 files changed, 48 insertions(+), 9 deletions(-) create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_external_lcms2.patch diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb index c82f2f1b6cd..c7eb007cae2 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libjxl' version = '0.3.7' local_lodepng_version = "48e5364" -local_skcms_version = "6437475" +#local_skcms_version = "6437475" homepage = 'https://github.com/libjxl/libjxl' @@ -20,18 +20,16 @@ sources = [ 'download_filename': local_lodepng_version, 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, - {'filename': 'skcms-%s.tar.gz' % local_skcms_version, - 'download_filename': '%s.tar.gz' % local_skcms_version, - 'source_urls': ['https://skia.googlesource.com/skcms/+archive/'], - 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/skcms --strip-components=0 -xf %s'}, - ] -patches = ['libjxl-%(version)s_openexr-3.0_compat.patch'] +patches = [ + 'libjxl-%(version)s_openexr-3.0_compat.patch', + 'libjxl-%(version)s_external_lcms2.patch', +] checksums = [ '8318a5d1ce82e5683a52512b6f242d2b33a1191e89fc76f7c0ead0a1d60f6c60', # v0.3.7.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz - '2430124e244cb3cd29059215545a17bed4b772e4550317acc755393b8c5e6580', # skcms-6437475.tar.gz 'b5bf92b8eb8f41e7cedce1b43ea3fe7a9407d3cc0e29bb2afec652cabe084cee', # libjxl-0.3.7_openexr-3.0_compat.patch + '9e6decaf6be74eeccfd5728df175930b4be33de6cbdf9e1816f68cb4b718fa1b', # libjxl-0.3.7_external_lcms2.patch ] builddependencies = [ @@ -43,6 +41,7 @@ builddependencies = [ ] dependencies = [ + ('LittleCMS', '2.12'), ('Brotli', '1.0.9'), ('libjpeg-turbo', '2.0.6'), ('libpng', '1.6.37'), @@ -53,7 +52,7 @@ dependencies = [ ('gperftools', '2.9.1'), ] -configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF' +configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF' runtest = "test" diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_external_lcms2.patch b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_external_lcms2.patch new file mode 100644 index 00000000000..a2aa4c95aff --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_external_lcms2.patch @@ -0,0 +1,40 @@ +# Add external linking to lcms2 +# Author: micketeer@gmail.com +--- third_party/CMakeLists.txt.orig 2021-07-27 23:27:44.236251072 +0200 ++++ third_party/CMakeLists.txt 2021-07-27 23:28:34.219135611 +0200 +@@ -195,14 +195,14 @@ + configure_file("${CMAKE_CURRENT_SOURCE_DIR}/skcms/LICENSE" + ${PROJECT_BINARY_DIR}/LICENSE.skcms COPYONLY) + endif () +-if (JPEGXL_ENABLE_VIEWERS OR NOT JPEGXL_ENABLE_SKCMS) +- if( NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/lcms/.git" ) +- message(SEND_ERROR "Please run git submodule update --init") +- endif() +- include(lcms2.cmake) +- configure_file("${CMAKE_CURRENT_SOURCE_DIR}/lcms/COPYING" +- ${PROJECT_BINARY_DIR}/LICENSE.lcms COPYONLY) +-endif() ++#if (JPEGXL_ENABLE_VIEWERS OR NOT JPEGXL_ENABLE_SKCMS) ++# if( NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/lcms/.git" ) ++# message(SEND_ERROR "Please run git submodule update --init") ++# endif() ++# include(lcms2.cmake) ++# configure_file("${CMAKE_CURRENT_SOURCE_DIR}/lcms/COPYING" ++# ${PROJECT_BINARY_DIR}/LICENSE.lcms COPYONLY) ++#endif() + + # sjpeg + if (JPEGXL_ENABLE_SJPEG) +--- lib/jxl.cmake.orig 2021-07-27 23:29:41.173980148 +0200 ++++ lib/jxl.cmake 2021-07-30 13:36:44.745536958 +0200 +@@ -352,12 +352,6 @@ + $ + ) + else () +- target_include_directories(jxl_enc-obj PRIVATE +- $ +- ) +- target_include_directories(jxl_dec-obj PRIVATE +- $ +- ) + endif () From 63c430fc6d8b88b638290987b06007457bd5790e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 30 Jul 2021 14:03:15 +0200 Subject: [PATCH 0543/9987] Remove old code --- easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb index c7eb007cae2..b0a69f2ad40 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb @@ -3,7 +3,6 @@ easyblock = 'CMakeMake' name = 'libjxl' version = '0.3.7' local_lodepng_version = "48e5364" -#local_skcms_version = "6437475" homepage = 'https://github.com/libjxl/libjxl' From 9054ad71b9c71e7f3d546b5a60de83c0149eaf01 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 30 Jul 2021 15:38:47 +0100 Subject: [PATCH 0544/9987] Rename NINJA to TWL-NINJA to avoid nameclash --- .../TWL-NINJA/TWL-NINJA-0.97-cluster_only-GCC-10.2.0.eb} | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/{n/NINJA/NINJA-0.97-cluster_only-GCC-10.2.0.eb => t/TWL-NINJA/TWL-NINJA-0.97-cluster_only-GCC-10.2.0.eb} (74%) diff --git a/easybuild/easyconfigs/n/NINJA/NINJA-0.97-cluster_only-GCC-10.2.0.eb b/easybuild/easyconfigs/t/TWL-NINJA/TWL-NINJA-0.97-cluster_only-GCC-10.2.0.eb similarity index 74% rename from easybuild/easyconfigs/n/NINJA/NINJA-0.97-cluster_only-GCC-10.2.0.eb rename to easybuild/easyconfigs/t/TWL-NINJA/TWL-NINJA-0.97-cluster_only-GCC-10.2.0.eb index 62d086e7a85..7a2314cce73 100644 --- a/easybuild/easyconfigs/n/NINJA/NINJA-0.97-cluster_only-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/t/TWL-NINJA/TWL-NINJA-0.97-cluster_only-GCC-10.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' -name = 'NINJA' +name = 'TWL-NINJA' version = '0.97-cluster_only' homepage = 'https://github.com/TravisWheelerLab/NINJA' @@ -11,15 +11,14 @@ description = "Nearly Infinite Neighbor Joining Application." toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'cstd': 'gnu++11', 'openmp': True, 'opt': True} -github_account = 'TravisWheelerLab' -source_urls = [GITHUB_SOURCE] +source_urls = ['https://github.com/TravisWheelerLab/NINJA/archive'] sources = ['%(version)s.tar.gz'] checksums = ['b9b948c698efc3838e63817f732ead35c08debe1c0ae36b5c74df7d26ca4c4b6'] -start_dir = name +start_dir = 'NINJA' buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' -files_to_copy = [(['%(name)s/Ninja'], 'bin'), 'NINJA/README', 'README.md', 'LICENSE'] +files_to_copy = [(['NINJA/Ninja'], 'bin'), 'NINJA/README', 'README.md', 'LICENSE'] sanity_check_paths = { 'files': ['bin/Ninja'], From 0de1fd6cb4f6f0cc30056c71b1143d6ea7d77889 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 30 Jul 2021 15:44:49 +0100 Subject: [PATCH 0545/9987] use renamed TWL-NINJA NINJA renamed to TWL-NINJA in #13529 --- .../r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb index 44ec3867afc..97c902e910b 100644 --- a/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.2a-foss-2020b.eb @@ -25,7 +25,7 @@ dependencies = [ ('MAFFT', '7.475', '-with-extensions'), ('GenomeTools', '1.6.1'), # for LTRHarvest ('LTR_retriever', '2.9.0'), - ('NINJA', '0.97-cluster_only'), + ('TWL-NINJA', '0.97-cluster_only'), ] exts_defaultclass = 'PerlModule' From 02974406aa8f3bc55aa37b226e0731716517bb31 Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 30 Jul 2021 15:05:39 +0000 Subject: [PATCH 0546/9987] Some suggested tidy up, name changed to kalign, current.tar.gz renamed to kalign-2.0.4.tar.gz --- .../k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb | 28 ++++++++++++++++ .../k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb | 32 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..dd1f62fb098 --- /dev/null +++ b/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'Kalign' +version = '2.0.4' + +homepage = 'https://msa.sbc.su.se/cgi-bin/msa.cgi' +description = "Kalign is a fast multiple sequence alignment program for biological sequences." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://msa.sbc.su.se/downloads/kalign/'] +sources = [{'filename': SOURCELOWER_TAR_GZ, 'download_filename': 'current.tar.gz'}] +checksums = ['8cf20ac4e1807dc642e7ffba8f42a117313beccaee4f87c5555d53a2eeac4cbb'] # kalign.tar.gz + +builddependencies = [('binutils', '2.35')] + +install_cmd = "mkdir %(installdir)s/bin && cp kalign %(installdir)s/bin" + +sanity_check_paths = { + 'files': ['bin/kalign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..61e06fe1570 --- /dev/null +++ b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'Kalign' +version = '3.3.1' + +homepage = 'https://github.com/TimoLassmann/kalign' +description = "Kalign is a fast multiple sequence alignment program for biological sequences." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7f10acf9a3fa15deabbc0304e7c14efa25cea39108318c9f02b47257de2d7390'] # 3.3.1.tar.gz + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Autotools', '20200321'), +] + +configure_cmd_prefix = "autoreconf -vfi && " + +sanity_check_paths = { + 'files': ['bin/kchaos', 'bin/kalign'], + 'dirs': [], +} + +moduleclass = 'bio' From afecc0ede93251ace7df948db7444e324585de98 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 30 Jul 2021 17:54:57 +0200 Subject: [PATCH 0547/9987] adding easyconfigs: binutils-2.37.eb, GCCcore-11.2.0.eb, zlib-1.2.11-GCCcore-11.2.0.eb, help2man-1.48.3-GCCcore-11.2.0.eb, M4-1.4.19-GCCcore-11.2.0.eb, Bison-3.7.6-GCCcore-11.2.0.eb, flex-2.6.4-GCCcore-11.2.0.eb, binutils-2.37-GCCcore-11.2.0.eb, GCC-11.2.0.eb --- .../b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb | 28 +++++++++ .../binutils/binutils-2.37-GCCcore-11.2.0.eb | 31 ++++++++++ .../easyconfigs/b/binutils/binutils-2.37.eb | 26 ++++++++ .../f/flex/flex-2.6.4-GCCcore-11.2.0.eb | 34 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-11.2.0.eb | 22 +++++++ .../easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 62 +++++++++++++++++++ .../help2man-1.48.3-GCCcore-11.2.0.eb | 25 ++++++++ .../m/M4/M4-1.4.19-GCCcore-11.2.0.eb | 29 +++++++++ .../z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb | 26 ++++++++ 9 files changed, 283 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.37.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c272626ed8f --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.7.6' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['69dc0bb46ea8fc307d4ca1e0b61c8c355eb207d0b0c69f4f8462328e74d7b9ea'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.37', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2f25a58407b --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.37' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c44968b97cd86499efbc4b4ab7d98471f673e5414c554ef54afa930062dbbfcb'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.11'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.37.eb b/easybuild/easyconfigs/b/binutils/binutils-2.37.eb new file mode 100644 index 00000000000..b0741dccfc4 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.37.eb @@ -0,0 +1,26 @@ +name = 'binutils' +version = '2.37' + +homepage = 'https://directory.fsf.org/project/binutils/' + +description = "binutils: GNU binary utilities" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c44968b97cd86499efbc4b4ab7d98471f673e5414c554ef54afa930062dbbfcb'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.11'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ad0b3d96faa --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.7.6'), + ('help2man', '1.48.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.36.1', '', True), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-11.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-11.2.0.eb new file mode 100644 index 00000000000..e3841d432c7 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-11.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '11.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', '2.37', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0adf0fee9ca --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '11.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.1.0.tar.bz2', + 'mpc-1.2.1.tar.gz', + 'isl-0.24.tar.bz2', + 'newlib-4.1.0.tar.gz', + {'download_filename': 'd0524fb.tar.gz', 'filename': 'nvptx-tools-20210115.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + 'f0837f1bf8244a5cc23bd96ff6366712a791cfae01df8e25b137698aca26efc1', # gcc-11.2.0.tar.gz + 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 + 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 + '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz + 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 + 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz + '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch + '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.37'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..dd03b0d33f5 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.48.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['8361ff3c643fbd391064e97e5f54592ca28b880eaffbf566a68e0ad800d1a8ac'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.37', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0f426d46de5 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.37', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a7d80d3c9c2 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.11' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.37', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 9c2a36cd1f088609a886a536345988a475683110 Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 30 Jul 2021 16:23:09 +0000 Subject: [PATCH 0548/9987] Name changed as suggestd to HH-suite, minor tidy up --- .../HH-suite-3.3.0-foss-2020b.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/h/{hhsuite/hhsuite-3.3.0-foss-2020b.eb => HH-suite/HH-suite-3.3.0-foss-2020b.eb} (95%) diff --git a/easybuild/easyconfigs/h/hhsuite/hhsuite-3.3.0-foss-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-foss-2020b.eb similarity index 95% rename from easybuild/easyconfigs/h/hhsuite/hhsuite-3.3.0-foss-2020b.eb rename to easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-foss-2020b.eb index 6b846a56c79..4152735bd5e 100644 --- a/easybuild/easyconfigs/h/hhsuite/hhsuite-3.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-foss-2020b.eb @@ -6,7 +6,7 @@ easyblock = 'CMakeMake' -name = 'hhsuite' +name = 'HH-suite' version = '3.3.0' homepage = 'https://github.com/soedinglab/hh-suite' @@ -36,7 +36,7 @@ _binaries = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in _binaries], - 'dirs': ['data', 'scripts', ] + 'dirs': ['data', 'scripts'] } moduleclass = 'bio' From 1bfb1ec3f9cf14972f3c8458d4ba86347c99079f Mon Sep 17 00:00:00 2001 From: satishskamath Date: Fri, 30 Jul 2021 18:42:49 +0200 Subject: [PATCH 0549/9987] adding easyconfigs: MPICH-3.3.2-GCC-10.3.0.eb --- .../m/MPICH/MPICH-3.3.2-GCC-10.3.0.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..e445bdd0573 --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.3.0.eb @@ -0,0 +1,16 @@ +name = 'MPICH' +version = '3.3.2' + +homepage = 'https://www.mpich.org/' +description = """MPICH is a high-performance and widely portable implementation +of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://www.mpich.org/static/tarballs/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4bfaf8837a54771d3e4922c84071ef80ffebddbb6971a006038d91ee7ef959b9'] + +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" ' + +moduleclass = 'mpi' From 8bd1f51cdb2a1dada35893ccfc856329c69109a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 30 Jul 2021 19:03:34 +0200 Subject: [PATCH 0550/9987] adding easyconfigs: CVXOPT-1.2.6-foss-2021a.eb --- .../c/CVXOPT/CVXOPT-1.2.6-foss-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2021a.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2021a.eb new file mode 100644 index 00000000000..5452340e79c --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.6-foss-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'CVXOPT' +version = '1.2.6' + +homepage = 'https://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['CVXOPT-1.2.1-fix-setup-py.patch'] +checksums = [ + 'a4c433706fd0ad9d47e7f222773a7f7601766fb8e74b633524b3c3fce29aa73e', # cvxopt-1.2.6.tar.gz + '85d8475098895e9af45f330489a712b5b944489c5fb4a6c67f59bef8fed4303d', # CVXOPT-1.2.1-fix-setup-py.patch +] + +dependencies = [ + ('Python', '3.9.5'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('GSL', '2.7'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' +preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' + +installopts = ' --no-binary cvxopt' + +sanity_check_commands = ['cd %(builddir)s/%(namelower)s-%(version)s && nosetests'] + +moduleclass = 'math' From 1bff9f45b6c3c72c8b3c3a7b239911fdb4a88524 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 30 Jul 2021 19:15:53 +0200 Subject: [PATCH 0551/9987] Update easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb index ad0b3d96faa..bd40de3b73d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.6'), ('help2man', '1.48.3'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.37', '', True), ] dependencies = [ From 3e706cb1a006ece38415410dec392130d6d04f7f Mon Sep 17 00:00:00 2001 From: satishskamath Date: Fri, 30 Jul 2021 19:29:11 +0200 Subject: [PATCH 0552/9987] Updating to 3.4.2 from the 3.3.2 as per the review in PR. --- .../m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..7b5485410ac --- /dev/null +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb @@ -0,0 +1,16 @@ +name = 'MPICH' +version = '3.4.2' + +homepage = 'https://www.mpich.org/' +description = """MPICH is a high-performance and widely portable implementation +of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://www.mpich.org/static/tarballs/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c19bea8b84e8d74cca5f047e82b147ff3fba096144270e3911ad623d6c587bf'] + +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" ' + +moduleclass = 'mpi' From ab69fc0917122b514d4a941fb8822145a16b1599 Mon Sep 17 00:00:00 2001 From: satishskamath Date: Fri, 30 Jul 2021 19:45:05 +0200 Subject: [PATCH 0553/9987] Removing file MPICH-3.3.2-GCC-10.3.0.eb --- .../m/MPICH/MPICH-3.3.2-GCC-10.3.0.eb | 16 ---------------- 1 file changed, 16 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.3.0.eb deleted file mode 100644 index e445bdd0573..00000000000 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.3.2-GCC-10.3.0.eb +++ /dev/null @@ -1,16 +0,0 @@ -name = 'MPICH' -version = '3.3.2' - -homepage = 'https://www.mpich.org/' -description = """MPICH is a high-performance and widely portable implementation -of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3).""" - -toolchain = {'name': 'GCC', 'version': '10.3.0'} - -source_urls = ['https://www.mpich.org/static/tarballs/%(version)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['4bfaf8837a54771d3e4922c84071ef80ffebddbb6971a006038d91ee7ef959b9'] - -configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" ' - -moduleclass = 'mpi' From e9c34c02f5ec01bd1aa2efaecc74886e6328afbe Mon Sep 17 00:00:00 2001 From: satishskamath Date: Fri, 30 Jul 2021 21:30:49 +0200 Subject: [PATCH 0554/9987] Adding a preferred network library UCX for ch4. --- easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb index 7b5485410ac..cd909925ba1 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb @@ -11,6 +11,6 @@ source_urls = ['https://www.mpich.org/static/tarballs/%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['5c19bea8b84e8d74cca5f047e82b147ff3fba096144270e3911ad623d6c587bf'] -configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" ' +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" --with-devices=ch4:ucx' moduleclass = 'mpi' From c23be117796710a063a72e132a2fa90ea1c13c86 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 31 Jul 2021 02:04:25 +0200 Subject: [PATCH 0555/9987] remove leftover comment in vcflib-1.0.2-GCC-10.2.0.eb --- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 1b77b9cb61a..734f106ab15 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -4,7 +4,6 @@ easyblock = 'CMakeMake' name = 'vcflib' version = '1.0.2' -# versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/vcflib/vcflib' description = """vcflib provides methods to manipulate and interpret sequence variation as it can be From 7fbf815dd5dddaf2776baa62b82a38db839a3ced Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 31 Jul 2021 02:09:38 +0200 Subject: [PATCH 0556/9987] adding easyconfig filevercmp-20191210-GCCcore-10.2.0.eb --- .../filevercmp-20191210-GCCcore-10.2.0.eb | 33 +++++++ .../filevercmp-20191210_build-libs.patch | 90 +++++++++++++++++++ 2 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a1ba056e298 --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'filevercmp' +version = '20191210' +local_commit = 'df20dcc' + +homepage = 'https://github.com/ekg/filevercmp' +description = """filevercmp function as in sort --version-sort.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20191210_build-libs.patch'] +checksums = [ + '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz + 'f0145a1590b555288d5c4560a58bf6976a7605ef949f9071d45e7afb815b540c', # filevercmp-20191210_build-libs.patch +] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'DESTDIR="" PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch new file mode 100644 index 00000000000..49fde8b526a --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch @@ -0,0 +1,90 @@ +# Patch to build static and dynamic libraries. Based on PR by outpaddling: +# https://github.com/ekg/filevercmp/pull/2 +# Updated: Denis Kristak (INUITS) +diff -ruN filevercmp-master_orig/Makefile filevercmp-master/Makefile +--- filevercmp-master_orig/Makefile 2019-12-10 10:58:23.000000000 +0100 ++++ filevercmp-master/Makefile 2021-07-13 16:35:15.738330513 +0200 +@@ -4,18 +4,69 @@ + + OBJS= main.o filevercmp.o + +-all: filevercmp ++# Use ?= to allow overriding from the env or command-line, e.g. ++# ++# make CXXFLAGS="-O3 -fPIC" install ++# ++# Package managers will override many of these variables automatically, so ++# this is aimed at making it easy to create packages (Debian packages, ++# FreeBSD ports, MacPorts, pkgsrc, etc.) ++ ++CC ?= cc ++CFLAGS ?= -O -g #-m64 #-arch ppc ++ ++PREFIX ?= /usr/local ++STRIP ?= strip ++INSTALL ?= install -c ++MKDIR ?= mkdir -p ++AR ?= ar ++ARFLAGS ?= rs ++ ++BIN = filevercmp ++LIB = libfilevercmp.a ++SOVERSION = 0 ++SLIB = libfilevercmp.so ++OBJS = filevercmp.o ++ ++LIBDIR = $(DESTDIR)$(PREFIX)/lib ++BINDIR = $(DESTDIR)$(PREFIX)/bin ++INCDIR = $(DESTDIR)$(PREFIX)/include/filevercmp ++ ++.SUFFIXES:.c .o .pico .so ++ ++.c.o: ++ $(CC) $(CFLAGS) -I. -c -o $@ $< ++ ++.c.pico: ++ $(CC) $(CFLAGS) -I. -fPIC -c -o $@ $< ++ ++all: $(BIN) $(SLIB) $(LIB) ++ ++$(LIB): $(OBJS) ++ $(AR) $(ARFLAGS) $@ $^ ++ ++$(SLIB): $(OBJS:.o=.pico) ++ $(CC) -shared -Wl,-soname,$(SLIB).$(SOVERSION) $(LDFLAGS) -o $@ $^ $(LIBS) ++ ln -sf $@ $(SLIB).$(SOVERSION) ++ ++$(BIN): $(OBJS) main.c ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) ++ ++install: all ++ $(MKDIR) $(BINDIR) ++ $(MKDIR) $(LIBDIR) ++ $(MKDIR) $(INCDIR) ++ $(INSTALL) $(BIN) $(BINDIR) ++ $(INSTALL) *.h $(INCDIR) ++ $(INSTALL) $(LIB) $(SLIB) $(SLIB).$(SOVERSION) $(LIBDIR) ++ ++install-strip: install ++ $(STRIP) $(BINDIR)/$(BIN) $(LIBDIR)/$(LIB) ++ ++cleanlocal: ++ rm -rf $(BIN) $(LIB) $(SLIB) $(OBJS) $(DESTDIR) ++ rm -fr gmon.out *.o a.out *.dSYM $(BIN) *~ *.a tabix.aux tabix.log \ ++ tabix.pdf *.class libtabix.*.dylib ++ cd htslib && $(MAKE) clean + +-clean: +- rm -f filevercmp ${OBJS} +- +-.PHONY: all clean +- +-filevercmp.o: filevercmp.c filevercmp.h +- $(CC) $(CPPFLAGS) $(CFLAGS) -c filevercmp.c +- +-main.o: main.c filevercmp.h +- $(CC) $(CPPFLAGS) $(CFLAGS) -c main.c +- +-filevercmp: ${OBJS} +- $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) -o filevercmp ${OBJS} ++clean: cleanlocal-recur From 1bde72b3b6811107ad76e8fadccef6b167268f52 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 31 Jul 2021 02:11:06 +0200 Subject: [PATCH 0557/9987] adding easyconfig multichoose-1.0.3-GCCcore-10.2.0.eb --- .../multichoose-1.0.3-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..423504cb402 --- /dev/null +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'multichoose' +version = '1.0.3' + +homepage = 'https://github.com/ekg/multichoose' +description = """generate multiset combinations (n multichoose k).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877'] + +builddependencies = [('binutils', '2.35')] + +local_bins = [name, 'multipermute'] +files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/multichoose')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +moduleclass = 'bio' From 60d85de386eb8b012279494b2e16548f6f3ec4cf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 31 Jul 2021 02:11:53 +0200 Subject: [PATCH 0558/9987] adding easyconfig smithwaterman-20160702-GCCcore-10.2.0.eb --- .../smithwaterman-20160702-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..65ec48867c8 --- /dev/null +++ b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'smithwaterman' +version = '20160702' +local_commit = '2610e25' + +homepage = 'https://github.com/ekg/smithwaterman' +description = """smith-waterman-gotoh alignment algorithm.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20160702_build-shared-lib.patch'] +checksums = [ + '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8', # 2610e25.tar.gz + '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582', # smithwaterman-20160702_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' From 21ff54d7aabeacdd27298e709e2d3782018503b8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 31 Jul 2021 02:23:33 +0200 Subject: [PATCH 0559/9987] update checksum of filevercmp-20191210_build-libs.patch --- .../f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb index a1ba056e298..5aafc945508 100644 --- a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ sources = ['%s.tar.gz' % local_commit] patches = ['%(name)s-20191210_build-libs.patch'] checksums = [ '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz - 'f0145a1590b555288d5c4560a58bf6976a7605ef949f9071d45e7afb815b540c', # filevercmp-20191210_build-libs.patch + '051438f76dd04219abfb283f61101c04d748407031e180b7ae3841344416ec4f', # filevercmp-20191210_build-libs.patch ] builddependencies = [('binutils', '2.35')] From 0f0a2a8f95591218a24ee0eb8ec2ed48072e783e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 31 Jul 2021 19:49:44 +0200 Subject: [PATCH 0560/9987] adding easyconfigs: Quandl-3.6.1-foss-2021a.eb --- .../q/Quandl/Quandl-3.6.1-foss-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2021a.eb b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2021a.eb new file mode 100644 index 00000000000..29644c9c84b --- /dev/null +++ b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'Quandl' +version = '3.6.1' + +homepage = 'https://pypi.python.org/pypi/Quandl' +description = "A Python library for Quandl’s RESTful API." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('inflection', '0.5.1', { + 'checksums': ['1a29730d366e996aaacffb2f1f1cb9593dc38e2ddd30c91250c6dde09ea9b417'], + }), + ('more-itertools', '8.8.0', { + 'checksums': ['83f0308e05477c68f56ea3a888172c78ed5d5b3c282addb67508e7ba6c8f813a'], + }), + ('pyOpenSSL', '20.0.1', { + 'modulename': 'OpenSSL', + 'checksums': ['4c231c759543ba02560fcd2480c48dcec4dae34c9da7d3747c508227e0624b51'], + }), + ('ndg-httpsclient', '0.5.1', { + 'modulename': 'ndg', + 'source_tmpl': 'ndg_httpsclient-%(version)s.tar.gz', + 'checksums': ['d72faed0376ab039736c2ba12e30695e2788c4aa569c9c3e3d72131de2592210'], + }), + (name, version, { + 'checksums': ['84414e5f8e870a9c8a9392e9dc639d50e839c5f5e07737a09bb57dd8b14b264b'], + }), +] + +moduleclass = 'tools' From 5f9bd166eb901fbe8f6ad742da8abf255f9d3d98 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 1 Aug 2021 00:07:49 +0200 Subject: [PATCH 0561/9987] add missing dependencies and fix build of freebayes-1.3.5-GCC-10.2.0.eb --- .../f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb | 50 +++++++++++++------ .../freebayes-1.3.5_fix-meson-build.patch | 33 ++++++++++++ 2 files changed, 68 insertions(+), 15 deletions(-) create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-meson-build.patch diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb index 7889e193d7a..f57fb4074be 100644 --- a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5-GCC-10.2.0.eb @@ -8,37 +8,57 @@ description = "Bayesian haplotype-based genetic polymorphism discovery and genot toolchain = {'name': 'GCC', 'version': '10.2.0'} -sources = [{ - 'filename': SOURCE_TAR_GZ, - 'git_config': { - 'url': 'https://github.com/freebayes', - 'repo_name': 'freebayes', - 'tag': 'v1.3.5', - 'recursive': True, - }, -}] -checksums = ['b614a44cb53a164ab8579d75c8eb6fc17415a502628aeeb12b42218893a10278'] +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['freebayes-1.3.5_fix-meson-build.patch'] +checksums = [ + 'af195a8c54b742d01af5a7e1fd1781a89290d726b310216c83e78c650d7aee49', # v1.3.5.tar.gz + 'c408bda1092d6f72d14eb22ab842e12ba27f52be35d82e3a33506e64e04077d8', # freebayes-1.3.5_fix-meson-build.patch +] builddependencies = [ ('binutils', '2.35'), + ('CMake', '3.18.4'), ('Meson', '0.55.3'), ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), ] dependencies = [ ('parallel', '20210322'), ('VCFtools', '0.1.16'), + ('vcflib', '1.0.2'), + ('SeqLib', '1.2.0'), + ('fastahack', '1.0.0'), + ('intervaltree', '0.1'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), ] -configopts = "--buildtype debug" +# freebayes expects intervaltree headers in its source directory +local_intervaltree_path = '%(builddir)s/%(name)s-%(version)s/intervaltree' +preconfigopts = "mv %(i)s %(i)s.orig && " % {'i': local_intervaltree_path} +preconfigopts += "ln -s $EBROOTINTERVALTREE/include/intervaltree %(i)s && " % {'i': local_intervaltree_path} +# workaround for direct includes of multichoose headers +preconfigopts += 'CPPFLAGS="-I${EBROOTMULTICHOOSE}/include/multichoose ${CPPFLAGS}" ' +# add missing linker flags for fastahack and smithwaterman +preconfigopts += 'LDFLAGS="-lsw -lfastahack ${LDFLAGS}"' -postinstallcmds = ['cp %(builddir)s/freebayes/scripts/* %(installdir)s/'] +configopts = "--buildtype release" -modextrapaths = {'PATH': ['']} +postinstallcmds = [ + # add extra scripts + "cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s/", + # only make freebayes-parallel directly executable + "cd %(installdir)s/bin && ln -s ../scripts/freebayes-parallel", +] sanity_check_paths = { - 'files': ['bin/freebayes', 'bin/bamleftalign', 'freebayes-parallel'], - 'dirs': [], + 'files': ['bin/freebayes', 'bin/bamleftalign', 'bin/freebayes-parallel'], + 'dirs': ['scripts'], } +sanity_check_commands = ["freebayes --help"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-meson-build.patch b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-meson-build.patch new file mode 100644 index 00000000000..f3df628718e --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.5_fix-meson-build.patch @@ -0,0 +1,33 @@ +fix discovery of vcflib and SeqLib from external libraries +author: Alex Domingo (Vrije Universiteit Brussel) +--- a/meson.build 2021-02-10 10:21:07.000000000 +0100 ++++ b/meson.build 2021-07-31 18:10:17.491193000 +0200 +@@ -18,8 +18,8 @@ + + htslib_dep = dependency('htslib', required : false) + tabixpp_dep = cc.find_library('tabixpp', required : false) +-vcflib_dep = dependency('libvcflib', required : false) +-seqlib_dep = dependency('libseqlib', required : false) ++vcflib_dep = cc.find_library('libvcflib', required : false) ++seqlib_dep = cc.find_library('libseqlib', required : false) + + # for setting a warning_level on the external code in custom_* targets below + warn_quiet = ['warning_level=0'] +@@ -113,6 +113,8 @@ + override_options : warn_quiet) + vcflib_dep = declare_dependency(link_with : vcflib_lib, + include_directories : vcflib_inc) ++else ++ vcflib_inc = [] + endif + + +@@ -138,6 +140,8 @@ + override_options : warn_quiet) + seqlib_dep = declare_dependency(link_with : seqlib_lib, + include_directories : seqlib_inc) ++else ++ seqlib_inc = [] + endif + + From a6c159426afd273239fb3076a847a51210a91ef5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 1 Aug 2021 00:09:10 +0200 Subject: [PATCH 0562/9987] upgrade dependency on HTSlib to v1.12 --- easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb index 04dec16e82e..faf8ac86078 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ dependencies = [ ('Perl', '5.32.0'), - ('HTSlib', '1.11'), + ('HTSlib', '1.12'), ('zlib', '1.2.11'), ] From 2745a013f32f22cf5d29a6abc578fb68ee69aa50 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 1 Aug 2021 00:10:25 +0200 Subject: [PATCH 0563/9987] adding easyconfigs: SeqLib-1.2.0-GCC-10.2.0.eb, fermi-lite-20190320-GCCcore-10.2.0.eb, SSW-1.1-GCCcore-10.2.0.eb --- .../fermi-lite-20190320-GCCcore-10.2.0.eb | 46 +++++++++++++++++ .../s/SSW/SSW-1.1-GCCcore-10.2.0.eb | 48 ++++++++++++++++++ .../s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb | 49 +++++++++++++++++++ 3 files changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..5f7b29effc1 --- /dev/null +++ b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'fermi-lite' +version = '20190320' +local_commit = 'b499514' + +homepage = 'https://github.com/lh3/fermi-lite' +description = """Standalone C library for assembling Illumina short reads in small regions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = [ + '%(name)s-20190320_avoid-bwa-namespace-conflict.patch', + '%(name)s-20190320_build-shared-lib.patch', +] +checksums = [ + 'ea1230e298b8e7193a996b5aceeff7fea44ef00852b0b87d4fcb504bdca0e712', # b499514.tar.gz + # fermi-lite-20190320_avoid-bwa-namespace-conflict.patch + '27600733f1cea8b1d1503b1a67b9d41526e907c1b6321313ff51194e166c1842', + '43398559fbb3910d6d3d1a41af3fb16bf8f26bd7cc34176dfc9a068a551c3f50', # fermi-lite-20190320_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +prebuildopts = 'CFLAGS="$CFLAGS -fcommon"' + +files_to_copy = [ + (['fml-asm'], 'bin'), + (['*.a', '*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/fml'), + 'test', +] + +sanity_check_paths = { + 'files': ['bin/fml-asm', 'lib/libfml.a', 'lib/libfml.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..915ce0d1e95 --- /dev/null +++ b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'SSW' +version = '1.1' + +homepage = 'https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library' +description = """SSW is a fast implementation of the Smith-Waterman algorithm, which uses the + Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the + instruction level. SSW library provides an API that can be flexibly used by programs written in + C, C++ and other languages. We also provide a software that can do protein and genome alignment + directly. Current version of our implementation is ~50 times faster than an ordinary + Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path + (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and + location heuristically. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1_build-cpp-lib.patch'] +checksums = [ + 'cdbc20740daeb188ed39413ea5ff9ae4cf72c4d7ccff1d2de2cac0446d64d99f', # v1.1.tar.gz + 'fe0d1f536ecd526dda8879b2f41b62c3c82b39d236f023ee735c1c18d584f06a', # SSW-1.1_build-cpp-lib.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +start_dir = 'src' + +buildopts = 'default' + +files_to_copy = [ + (['ssw_test'], 'bin'), + (['*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/ssw'), +] + +sanity_check_paths = { + 'files': ['bin/ssw_test', 'lib/libssw.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..507c2fec11f --- /dev/null +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb @@ -0,0 +1,49 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'SeqLib' +version = '1.2.0' + +homepage = 'https://github.com/walaj/SeqLib' +description = """C++ interface to HTSlib, BWA-MEM and Fermi.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +github_account = 'walaj' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version_major_minor)s.0_avoid-bwa-fml-namespace-conflict.patch', + '%(name)s-%(version_major_minor)s.0_use-external-deps.patch', +] +checksums = [ + '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz + # SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch + '9be9229bcf34db8e4bd1fd49614bb55d84c12df263ca7174980f7f4b1bd63da9', + '8a90edf72f95a52c61e4aed62a9a951bbd56f7c668dec326f2d3836f76b0f71d', # SeqLib-1.2.0_use-external-deps.patch +] + +builddependencies = [('Autotools', '20200321')] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), + ('JsonCpp', '1.9.4'), + ('BWA', '0.7.17'), + ('HTSlib', '1.12'), + ('fermi-lite', '20190320'), + ('SSW', '1.1'), + ('PCRE', '8.44'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/seqtools', 'lib/libseqlib.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["seqtools"] + +moduleclass = 'bio' From eec1a39cd19903bd9c7b26808f91d7acb54f2ef7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 1 Aug 2021 00:36:01 +0200 Subject: [PATCH 0564/9987] removing easyconfigs from PR: any2fasta-0.4.2-GCCcore-10.2.0.eb, samclip-0.4.0-GCCcore-10.2.0.eb, filevercmp-20191210-GCCcore-10.2.0.eb --- .../any2fasta-0.4.2-GCCcore-10.2.0.eb | 34 -------- .../filevercmp-20191210-GCCcore-10.2.0.eb | 33 ------- .../filevercmp-20191210_build-libs.patch | 87 ------------------- .../s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb | 27 ------ 4 files changed, 181 deletions(-) delete mode 100644 easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch delete mode 100644 easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb deleted file mode 100644 index 4b16b010fe9..00000000000 --- a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'Tarball' - -name = 'any2fasta' -version = '0.4.2' - -homepage = 'https://github.com/tseemann/any2fasta' -description = "Convert various sequence formats to FASTA" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -# https://github.com/tseemann/any2fasta -github_account = 'tseemann' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.zip'] -checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] - -dependencies = [('Perl', '5.32.0')] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['any2fasta'], - 'dirs': [], -} - -sanity_check_commands = [ - 'any2fasta -h', - 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb deleted file mode 100644 index a1ba056e298..00000000000 --- a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.2.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -# Updated: Denis Kristak (INUITS) -easyblock = 'ConfigureMake' - -name = 'filevercmp' -version = '20191210' -local_commit = 'df20dcc' - -homepage = 'https://github.com/ekg/filevercmp' -description = """filevercmp function as in sort --version-sort.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -github_account = 'ekg' -source_urls = [GITHUB_SOURCE] -sources = ['%s.tar.gz' % local_commit] -patches = ['%(name)s-20191210_build-libs.patch'] -checksums = [ - '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz - 'f0145a1590b555288d5c4560a58bf6976a7605ef949f9071d45e7afb815b540c', # filevercmp-20191210_build-libs.patch -] - -builddependencies = [('binutils', '2.35')] - -skipsteps = ['configure'] - -installopts = 'DESTDIR="" PREFIX=%(installdir)s ' - -sanity_check_paths = { - 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch deleted file mode 100644 index 791f1b231ab..00000000000 --- a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210_build-libs.patch +++ /dev/null @@ -1,87 +0,0 @@ -diff -ruN filevercmp-master_orig/Makefile filevercmp-master/Makefile ---- filevercmp-master_orig/Makefile 2019-12-10 10:58:23.000000000 +0100 -+++ filevercmp-master/Makefile 2021-07-13 16:35:15.738330513 +0200 -@@ -4,18 +4,69 @@ - - OBJS= main.o filevercmp.o - --all: filevercmp -+# Use ?= to allow overriding from the env or command-line, e.g. -+# -+# make CXXFLAGS="-O3 -fPIC" install -+# -+# Package managers will override many of these variables automatically, so -+# this is aimed at making it easy to create packages (Debian packages, -+# FreeBSD ports, MacPorts, pkgsrc, etc.) -+ -+CC ?= cc -+CFLAGS ?= -O -g #-m64 #-arch ppc -+ -+PREFIX ?= /usr/local -+STRIP ?= strip -+INSTALL ?= install -c -+MKDIR ?= mkdir -p -+AR ?= ar -+ARFLAGS ?= rs -+ -+BIN = filevercmp -+LIB = libfilevercmp.a -+SOVERSION = 0 -+SLIB = libfilevercmp.so -+OBJS = filevercmp.o -+ -+LIBDIR = $(DESTDIR)$(PREFIX)/lib -+BINDIR = $(DESTDIR)$(PREFIX)/bin -+INCDIR = $(DESTDIR)$(PREFIX)/include/filevercmp -+ -+.SUFFIXES:.c .o .pico .so -+ -+.c.o: -+ $(CC) $(CFLAGS) -I. -c -o $@ $< -+ -+.c.pico: -+ $(CC) $(CFLAGS) -I. -fPIC -c -o $@ $< -+ -+all: $(BIN) $(SLIB) $(LIB) -+ -+$(LIB): $(OBJS) -+ $(AR) $(ARFLAGS) $@ $^ -+ -+$(SLIB): $(OBJS:.o=.pico) -+ $(CC) -shared -Wl,-soname,$(SLIB).$(SOVERSION) $(LDFLAGS) -o $@ $^ $(LIBS) -+ ln -sf $@ $(SLIB).$(SOVERSION) -+ -+$(BIN): $(OBJS) main.c -+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) -+ -+install: all -+ $(MKDIR) $(BINDIR) -+ $(MKDIR) $(LIBDIR) -+ $(MKDIR) $(INCDIR) -+ $(INSTALL) $(BIN) $(BINDIR) -+ $(INSTALL) *.h $(INCDIR) -+ $(INSTALL) $(LIB) $(SLIB) $(SLIB).$(SOVERSION) $(LIBDIR) -+ -+install-strip: install -+ $(STRIP) $(BINDIR)/$(BIN) $(LIBDIR)/$(LIB) -+ -+cleanlocal: -+ rm -rf $(BIN) $(LIB) $(SLIB) $(OBJS) $(DESTDIR) -+ rm -fr gmon.out *.o a.out *.dSYM $(BIN) *~ *.a tabix.aux tabix.log \ -+ tabix.pdf *.class libtabix.*.dylib -+ cd htslib && $(MAKE) clean - --clean: -- rm -f filevercmp ${OBJS} -- --.PHONY: all clean -- --filevercmp.o: filevercmp.c filevercmp.h -- $(CC) $(CPPFLAGS) $(CFLAGS) -c filevercmp.c -- --main.o: main.c filevercmp.h -- $(CC) $(CPPFLAGS) $(CFLAGS) -c main.c -- --filevercmp: ${OBJS} -- $(CC) $(LDFLAGS) $(CPPFLAGS) $(CFLAGS) -o filevercmp ${OBJS} -+clean: cleanlocal-recur diff --git a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb deleted file mode 100644 index 52eb3f5c232..00000000000 --- a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'Tarball' - -name = 'samclip' -version = '0.4.0' - -homepage = 'https://github.com/tseemann/samclip' -description = """Filter SAM file for soft and hard clipped alignments.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -github_account = 'tseemann' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127'] - -dependencies = [('Perl', '5.32.0')] - -sanity_check_paths = { - 'files': [name], - 'dirs': [], -} - -sanity_check_commands = ["%(name)s --help"] - -modextrapaths = {'PATH': ''} - -moduleclass = 'bio' From 1df7d9bb90aab00f40e15872def6b8ae3515cf8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 1 Aug 2021 14:52:17 +0200 Subject: [PATCH 0565/9987] Update easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2021a.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2021a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2021a.eb b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2021a.eb index 29644c9c84b..4192107f244 100644 --- a/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/q/Quandl/Quandl-3.6.1-foss-2021a.eb @@ -20,9 +20,6 @@ exts_list = [ ('inflection', '0.5.1', { 'checksums': ['1a29730d366e996aaacffb2f1f1cb9593dc38e2ddd30c91250c6dde09ea9b417'], }), - ('more-itertools', '8.8.0', { - 'checksums': ['83f0308e05477c68f56ea3a888172c78ed5d5b3c282addb67508e7ba6c8f813a'], - }), ('pyOpenSSL', '20.0.1', { 'modulename': 'OpenSSL', 'checksums': ['4c231c759543ba02560fcd2480c48dcec4dae34c9da7d3747c508227e0624b51'], From 356062fda1ee17870ff7f294fe3282ab4fe207a9 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 2 Aug 2021 10:03:30 +0200 Subject: [PATCH 0566/9987] moving samclip and anytofasta to final (SNIPPY) PR --- .../any2fasta-0.4.2-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ .../s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb | 30 ++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..1ba03ee6136 --- /dev/null +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Author: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'any2fasta' +version = '0.4.2' + +homepage = 'https://github.com/tseemann/any2fasta' +description = "Convert various sequence formats to FASTA" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# https://github.com/tseemann/any2fasta +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] + +dependencies = [('Perl', '5.32.0')] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['any2fasta'], + 'dirs': [], +} + +sanity_check_commands = [ + 'any2fasta -h', + 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..372ab575da8 --- /dev/null +++ b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# Author: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'samclip' +version = '0.4.0' + +homepage = 'https://github.com/tseemann/samclip' +description = """Filter SAM file for soft and hard clipped alignments.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127'] + +dependencies = [('Perl', '5.32.0')] + +sanity_check_paths = { + 'files': [name], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From cff88c474a1e32d06f36264a9e480f4692fb0bf5 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 2 Aug 2021 11:26:44 +0200 Subject: [PATCH 0567/9987] add VBZ compress capability (for fast5 files) --- .../nanopolish-0.13.3-foss-2020b.eb | 1 + .../vbz_compression-1.0.1-gompi-2020b.eb | 39 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb index ffba642eb45..d0a19258d2e 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb @@ -31,6 +31,7 @@ dependencies = [ ('HDF5', '1.10.7'), ('HTSlib', '1.11'), ('minimap2', '2.18'), + ('vbz_compression', '1.0.1'), ] prebuildopts = "rmdir fast5 && ln -s %(builddir)s/fast5-*/ fast5 && " diff --git a/easybuild/easyconfigs/v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb b/easybuild/easyconfigs/v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb new file mode 100644 index 00000000000..6772b10a852 --- /dev/null +++ b/easybuild/easyconfigs/v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'vbz_compression' +version = '1.0.1' + +homepage = 'https://github.com/nanoporetech/vbz_compression' +description = "VBZ HDF5 plugin for nanopolish" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = [ + 'https://github.com/nanoporetech/vbz_compression/archive', + 'https://github.com/lemire/streamvbyte/archive', +] +sources = [ + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'download_filename': 'v0.4.1.tar.gz', 'filename': 'stramvbyte-v0.4.1.tar.gz'}, +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('HDF5', '1.10.7'), + ('zstd', '1.4.5'), +] + +preconfigopts = "rmdir %(builddir)s/vbz_compression*/third_party/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte-* %(builddir)s/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte %(builddir)s/vbz_compression*/third_party/. && " +configopts = "-DENABLE_CONAN=OFF -DENABLE_PERF_TESTING=OFF -DENABLE_PYTHON=OFF " + +sanity_check_paths = { + 'files': ['hdf5/lib/plugin/libvbz_hdf_plugin.so'], + 'dirs': [], +} + +modextrapaths = {'HDF5_PLUGIN_PATH': 'hdf5/lib/plugin/'} + +moduleclass = 'lib' From 7a537411031dc7f797a33342a530a84dd579c8b8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 2 Aug 2021 11:36:09 +0200 Subject: [PATCH 0568/9987] Add checksums --- .../v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb b/easybuild/easyconfigs/v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb index 6772b10a852..f7a05eaa8d9 100644 --- a/easybuild/easyconfigs/v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb +++ b/easybuild/easyconfigs/v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb @@ -14,7 +14,11 @@ source_urls = [ ] sources = [ {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, - {'download_filename': 'v0.4.1.tar.gz', 'filename': 'stramvbyte-v0.4.1.tar.gz'}, + {'download_filename': 'v0.4.1.tar.gz', 'filename': 'streamvbyte-v0.4.1.tar.gz'}, +] +checksums = [ + '3c140fb4f60f8451db68768457c59b10aadba4c33f1b1a1eadb4439345b68192', # vbz_compression-1.0.1.tar.gz + '4c4e53134a60b0b06816d3faa7dcde28c3e5e8a656dd415d16d80ae6e3d39fcc', # streamvbyte-v0.4.1.tar.gz ] builddependencies = [('CMake', '3.18.4')] From 94148435b86a51cbe5eb208a1cbe1842bcc07ac2 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Mon, 2 Aug 2021 12:27:37 +0200 Subject: [PATCH 0569/9987] Added PLUMED for 2021a --- .../p/PLUMED/PLUMED-2.7.2-foss-2021a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb new file mode 100644 index 00000000000..ba5e629146f --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.7.2' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['6069bc134f74cb15dd63e27e3587a15a31a9ddd9e7eebdd717da898f31512645'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.7'), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Boost', '1.76.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From 2017508aa8498ab158344ec538199c4b43c75412 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 2 Aug 2021 10:36:08 +0000 Subject: [PATCH 0570/9987] pkg-config build dependency added --- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb index 9ca755b64e9..11974f2841f 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb @@ -17,6 +17,7 @@ builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('Python', '3.9.5', '-bare'), + ('pkg-config', '0.29.2'), ] dependencies = [ From c2ee8abd5591912536eae30b9f36c396132cddef Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 2 Aug 2021 13:33:51 +0200 Subject: [PATCH 0571/9987] vbz_c -> VBZ_C and use SHLIB_EXT --- .../n/nanopolish/nanopolish-0.13.3-foss-2020b.eb | 2 +- .../VBZ_Compression-1.0.1-gompi-2020b.eb} | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/v/{vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb => VBZ_Compression/VBZ_Compression-1.0.1-gompi-2020b.eb} (86%) diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb index d0a19258d2e..84295cb17e0 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb @@ -31,7 +31,7 @@ dependencies = [ ('HDF5', '1.10.7'), ('HTSlib', '1.11'), ('minimap2', '2.18'), - ('vbz_compression', '1.0.1'), + ('VBZ_Compression', '1.0.1'), ] prebuildopts = "rmdir fast5 && ln -s %(builddir)s/fast5-*/ fast5 && " diff --git a/easybuild/easyconfigs/v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb b/easybuild/easyconfigs/v/VBZ_Compression/VBZ_Compression-1.0.1-gompi-2020b.eb similarity index 86% rename from easybuild/easyconfigs/v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb rename to easybuild/easyconfigs/v/VBZ_Compression/VBZ_Compression-1.0.1-gompi-2020b.eb index f7a05eaa8d9..ff411c5d178 100644 --- a/easybuild/easyconfigs/v/vbz_compression/vbz_compression-1.0.1-gompi-2020b.eb +++ b/easybuild/easyconfigs/v/VBZ_Compression/VBZ_Compression-1.0.1-gompi-2020b.eb @@ -1,10 +1,10 @@ easyblock = 'CMakeMake' -name = 'vbz_compression' +name = 'VBZ_Compression' version = '1.0.1' homepage = 'https://github.com/nanoporetech/vbz_compression' -description = "VBZ HDF5 plugin for nanopolish" +description = "VBZ compression HDF5 plugin for nanopolish" toolchain = {'name': 'gompi', 'version': '2020b'} @@ -17,7 +17,7 @@ sources = [ {'download_filename': 'v0.4.1.tar.gz', 'filename': 'streamvbyte-v0.4.1.tar.gz'}, ] checksums = [ - '3c140fb4f60f8451db68768457c59b10aadba4c33f1b1a1eadb4439345b68192', # vbz_compression-1.0.1.tar.gz + '3c140fb4f60f8451db68768457c59b10aadba4c33f1b1a1eadb4439345b68192', # VBZ_Compression-1.0.1.tar.gz '4c4e53134a60b0b06816d3faa7dcde28c3e5e8a656dd415d16d80ae6e3d39fcc', # streamvbyte-v0.4.1.tar.gz ] @@ -34,7 +34,7 @@ preconfigopts += "mv %(builddir)s/streamvbyte %(builddir)s/vbz_compression*/thir configopts = "-DENABLE_CONAN=OFF -DENABLE_PERF_TESTING=OFF -DENABLE_PYTHON=OFF " sanity_check_paths = { - 'files': ['hdf5/lib/plugin/libvbz_hdf_plugin.so'], + 'files': ['hdf5/lib/plugin/libvbz_hdf_plugin.%s' % SHLIB_EXT], 'dirs': [], } From 5a8e03c643b7844a31099b96d9784e0954c3ef46 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 2 Aug 2021 11:49:11 +0000 Subject: [PATCH 0572/9987] Header corrected, toolchain downgraded to gompi, sanity check improved by adding more relevant files, toolchainoptions removed --- ...2020b.eb => HH-suite-3.3.0-gompi-2020b.eb} | 20 ++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/h/HH-suite/{HH-suite-3.3.0-foss-2020b.eb => HH-suite-3.3.0-gompi-2020b.eb} (65%) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-foss-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb similarity index 65% rename from easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-foss-2020b.eb rename to easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index 4152735bd5e..d59bb692b10 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -1,7 +1,17 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Updated to use gompi-2020b toolchain: # Contribution from the NIHR Biomedical Research Centre # Guy's and St Thomas' NHS Foundation Trust and King's College London -# Based on STAR-2.7.7a-GCC-10.2.0.eb # uploaded by J. Sassmannshausen easyblock = 'CMakeMake' @@ -14,8 +24,7 @@ description = """The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).""" -toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'opt': True} +toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] sources = ['v%(version)s.tar.gz'] @@ -31,7 +40,8 @@ separate_build_dir = True _binaries = [ 'hhalign', 'hhalign_mpi', 'hhalign_omp', 'hhblits', 'hhblits_mpi', 'hhblits_omp', - 'hhmake', + 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp', + 'hhmake', 'hhfilter', 'hhconsensus', ] sanity_check_paths = { From 3e49870ecc926934da72dc6541298093f774252b Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 2 Aug 2021 12:01:00 +0000 Subject: [PATCH 0573/9987] Forgot to remove old files when switching names --- .../k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb | 32 ------------------- .../k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb | 32 ------------------- 2 files changed, 64 deletions(-) delete mode 100644 easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb deleted file mode 100644 index 84dfafa171b..00000000000 --- a/easybuild/easyconfigs/k/kalign2/kalign2-2.0.4-GCCcore-10.2.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen - -easyblock = 'ConfigureMake' - -name = 'kalign2' -version = '2.0.4' - -homepage = 'https://msa.sbc.su.se/cgi-bin/msa.cgi' -description = "Kalign is a fast multiple sequence alignment program for biological sequences." - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = ['http://msa.sbc.su.se/downloads/kalign/'] -sources = ['current.tar.gz'] -checksums = ['8cf20ac4e1807dc642e7ffba8f42a117313beccaee4f87c5555d53a2eeac4cbb'] # current.tar.gz - -builddependencies = [('binutils', '2.35')] - -dependencies = [ - ('Autoconf', '2.69'), -] - -install_cmd = "mkdir %(installdir)s/bin && cp kalign %(installdir)s/bin" - -sanity_check_paths = { - 'files': ['bin/kalign'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb deleted file mode 100644 index 2e19a2c48d5..00000000000 --- a/easybuild/easyconfigs/k/kalign2/kalign2-3.3.1-GCCcore-10.2.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen - -easyblock = 'ConfigureMake' - -name = 'kalign2' -version = '3.3.1' - -homepage = 'https://github.com/TimoLassmann/kalign' -description = "Kalign is a fast multiple sequence alignment program for biological sequences." - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['7f10acf9a3fa15deabbc0304e7c14efa25cea39108318c9f02b47257de2d7390'] # 3.3.1.tar.gz - -builddependencies = [('binutils', '2.35')] - -dependencies = [ - ('Autoconf', '2.69'), -] - -configure_cmd_prefix = "autoreconf -vfi && " - -sanity_check_paths = { - 'files': ['bin/kchaos', 'bin/kalign'], - 'dirs': [], -} - -moduleclass = 'bio' From 4a90fa16ef6f7292367682dc41e8a5bc1c3af243 Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Mon, 2 Aug 2021 09:25:34 -0400 Subject: [PATCH 0574/9987] Fix p7zip path issues (Issue #13540) --- .../p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb index 7da7616f42f..14596aee0f6 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb @@ -22,12 +22,19 @@ prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' files_to_copy = [ - (['bin/7z', 'bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), - (['bin/7z.%s' % SHLIB_EXT, 'bin/Codecs'], 'libexec'), + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.%s' % SHLIB_EXT, 'bin/Codecs'], 'libexec'), # 7z requires 7z.so plugin in same directory +] + +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + "echo '#!/bin/sh\n%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask ] sanity_check_paths = { - 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z.%s' % SHLIB_EXT], + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.%s' % SHLIB_EXT], 'dirs': ['libexec/Codecs'], } From 419fdd2c001980c66badb0b22d2898f673a1524b Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Mon, 2 Aug 2021 09:34:32 -0400 Subject: [PATCH 0575/9987] add changes to latest version --- .../p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb index 6d18ac44dc4..c5f1bfce6ff 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb @@ -22,12 +22,19 @@ prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' files_to_copy = [ - (['bin/7z', 'bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), - (['bin/7z.%s' % SHLIB_EXT, 'bin/Codecs'], 'libexec'), + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.%s' % SHLIB_EXT, 'bin/Codecs'], 'libexec'), # 7z requires 7z.so plugin in same directory +] + +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + "echo '#!/bin/sh\n%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask ] sanity_check_paths = { - 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z.%s' % SHLIB_EXT], + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.%s' % SHLIB_EXT], 'dirs': ['libexec/Codecs'], } From 6f65aa3b9e3f2a710202af08152e887dd4e30f19 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 2 Aug 2021 17:05:25 +0200 Subject: [PATCH 0576/9987] VBZ_C -> VBZ-C --- .../easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb | 2 +- .../VBZ-Compression-1.0.1-gompi-2020b.eb} | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/v/{VBZ_Compression/VBZ_Compression-1.0.1-gompi-2020b.eb => VBZ-Compression/VBZ-Compression-1.0.1-gompi-2020b.eb} (95%) diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb index 84295cb17e0..d7aeb4c75de 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb @@ -31,7 +31,7 @@ dependencies = [ ('HDF5', '1.10.7'), ('HTSlib', '1.11'), ('minimap2', '2.18'), - ('VBZ_Compression', '1.0.1'), + ('VBZ-Compression', '1.0.1'), ] prebuildopts = "rmdir fast5 && ln -s %(builddir)s/fast5-*/ fast5 && " diff --git a/easybuild/easyconfigs/v/VBZ_Compression/VBZ_Compression-1.0.1-gompi-2020b.eb b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.1-gompi-2020b.eb similarity index 95% rename from easybuild/easyconfigs/v/VBZ_Compression/VBZ_Compression-1.0.1-gompi-2020b.eb rename to easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.1-gompi-2020b.eb index ff411c5d178..09c6e077ce4 100644 --- a/easybuild/easyconfigs/v/VBZ_Compression/VBZ_Compression-1.0.1-gompi-2020b.eb +++ b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.1-gompi-2020b.eb @@ -1,6 +1,6 @@ easyblock = 'CMakeMake' -name = 'VBZ_Compression' +name = 'VBZ-Compression' version = '1.0.1' homepage = 'https://github.com/nanoporetech/vbz_compression' @@ -17,7 +17,7 @@ sources = [ {'download_filename': 'v0.4.1.tar.gz', 'filename': 'streamvbyte-v0.4.1.tar.gz'}, ] checksums = [ - '3c140fb4f60f8451db68768457c59b10aadba4c33f1b1a1eadb4439345b68192', # VBZ_Compression-1.0.1.tar.gz + '3c140fb4f60f8451db68768457c59b10aadba4c33f1b1a1eadb4439345b68192', # VBZ-Compression-1.0.1.tar.gz '4c4e53134a60b0b06816d3faa7dcde28c3e5e8a656dd415d16d80ae6e3d39fcc', # streamvbyte-v0.4.1.tar.gz ] From 5a70004432c12799c216c22aa15fb5e6e02fb428 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Aug 2021 18:11:45 +0200 Subject: [PATCH 0577/9987] add cobalt extension for recent R 4.0.x and 4.1.0 easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 3 +++ 7 files changed, 21 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 8e1e2c5b932..df5788a6eb9 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2891,6 +2891,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index cb0dff7a4df..2154e87ccb2 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2901,6 +2901,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 9b77a35e2f1..3d0bffd5021 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2927,6 +2927,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index dec33c7779b..e7e51b34c74 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2932,6 +2932,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index e0d0501d058..8a52c5c7c87 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2936,6 +2936,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 4a7563f2d6d..d60bd6ae026 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2947,6 +2947,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index 0bb5fc2a96d..eb0de773448 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -2969,6 +2969,9 @@ exts_list = [ ('hal9001', '0.2.7', { 'checksums': ['6facafa87179c7efb34d4acb3746198bb4c123f749fd784c8aab1021b8d77941'], }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), ] moduleclass = 'lang' From 3f6f56458bfefec670b3e8fda57a54aa65c8406e Mon Sep 17 00:00:00 2001 From: satishskamath Date: Mon, 2 Aug 2021 19:04:22 +0200 Subject: [PATCH 0578/9987] Adding the UCX path --with-ucx= and UCX as dependency. --- easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb index cd909925ba1..5fd1606a57d 100644 --- a/easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/MPICH/MPICH-3.4.2-GCC-10.3.0.eb @@ -11,6 +11,10 @@ source_urls = ['https://www.mpich.org/static/tarballs/%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['5c19bea8b84e8d74cca5f047e82b147ff3fba096144270e3911ad623d6c587bf'] -configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" --with-devices=ch4:ucx' +configopts = 'FFLAGS="-w -fallow-argument-mismatch -O2" --with-devices=ch4:ucx --with-ucx=$EBROOTUCX' + +dependencies = [ + ('UCX', '1.10.0'), +] moduleclass = 'mpi' From fec351552d82dac15c97eb839e90f0b4447e5170 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 2 Aug 2021 18:01:38 +0000 Subject: [PATCH 0579/9987] Patch file removed, patch version set to 7.5.0 in OpenMM-7.5.1-fosscuda-2020b.eb --- .../o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb | 2 +- .../o/OpenMM/OpenMM-7.5.1_fix_path_to_nvcc.patch | 15 --------------- 2 files changed, 1 insertion(+), 16 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_path_to_nvcc.patch diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb index 5f6aeae351d..439ac033415 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-fosscuda-2020b.eb @@ -18,7 +18,7 @@ toolchainopts = {'opt': True} source_urls = ['https://github.com/openmm/openmm/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix_path_to_nvcc.patch'] +patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] checksums = [ 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # 7.5.1.tar.gz '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_path_to_nvcc.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_path_to_nvcc.patch deleted file mode 100644 index 6749338995b..00000000000 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_path_to_nvcc.patch +++ /dev/null @@ -1,15 +0,0 @@ -Make sure OpenMM does use it's stupid hardcoded path to nvcc. - -Åke Sandgren, 2021-04-15 -diff -ru openmm-7.5.0.orig/platforms/cuda/src/CudaPlatform.cpp openmm-7.5.0/platforms/cuda/src/CudaPlatform.cpp ---- openmm-7.5.0.orig/platforms/cuda/src/CudaPlatform.cpp 2020-11-25 06:39:09.000000000 +0100 -+++ openmm-7.5.0/platforms/cuda/src/CudaPlatform.cpp 2021-04-15 14:36:46.293660324 +0200 -@@ -136,7 +136,7 @@ - setPropertyDefaultValue(CudaTempDirectory(), string(getenv("TEMP"))); - #else - char* compiler = getenv("OPENMM_CUDA_COMPILER"); -- string nvcc = (compiler == NULL ? "/usr/local/cuda/bin/nvcc" : string(compiler)); -+ string nvcc = (compiler == NULL ? "nvcc" : string(compiler)); - setPropertyDefaultValue(CudaCompiler(), nvcc); - char* tmpdir = getenv("TMPDIR"); - string tmp = (tmpdir == NULL ? string(P_tmpdir) : string(tmpdir)); From a410ca06b45a0a1ddac5965d2c81591a8267eb3e Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Tue, 3 Aug 2021 12:29:19 +1000 Subject: [PATCH 0580/9987] Create almosthere-2.0.2-GCCcore-10.2.0.eb Update to new major release and new GCC --- .../almosthere-2.0.2-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..70063cf416c --- /dev/null +++ b/easybuild/easyconfigs/a/almosthere/almosthere-2.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'almosthere' +version = '2.0.2' + +homepage = 'https://github.com/horta/almosthere' +description = """Progress indicator C library. +ATHR is a simple yet powerful progress indicator library that works on Windows, +Linux, and macOS. It is non-blocking as the progress update is done via a +dedicated, lightweight thread, as to not impair the performance of the calling program.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'horta' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b50ff32f5f1aa213589c81118e7312bd5e0f5a3d0a72ace499595a1f0bbff42f'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libathr.a', 'lib/libathr.%s' % SHLIB_EXT, 'include/athr/athr.h'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'tools' From 535889619e01e5997357503f6b54c42f02481038 Mon Sep 17 00:00:00 2001 From: jedokaplan Date: Tue, 3 Aug 2021 14:20:26 +0800 Subject: [PATCH 0581/9987] adding easyconfigs: PyQt5-5.15.4-GCCcore-10.2.0.eb --- .../p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb | 99 +++++++++++++++++++ 1 file changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b04ed87846e --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb @@ -0,0 +1,99 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.4' + +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.35')] +dependencies = [ + ('Python', '3.8.6'), + ('Qt5', '5.14.2'), + ('Qt5Webkit', '5.212.0-alpha4') +] + +default_easyblock = 'PythonPackage' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +local_sipver = '5.5.0' + +components = [ + ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + + ('PyQt-builder', '1.10.3', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['6ade47445b7d8c08eb96e91ebda5f8b3494b3e7a9da2be343b9d0704419cb5c7'], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + + ('PyQt5_sip', '12.9.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], + 'easyblock': 'Binary', + 'start_dir': '%(name)s-%(version)s', + 'skipsteps': ['configure', 'build'], + 'install_cmd': local_setup_env + local_pyqt5_sip_install, + }), + + ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['cedc28f54165f4b8067652145aec7f732a17eadf6736835852868cf76119cc19'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip-wheel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip-wheel --help", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' From b48861b2a8a4768bc64fc88493b32d64d1131141 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Tue, 3 Aug 2021 16:40:32 +1000 Subject: [PATCH 0582/9987] Create bgen-4.1.3-GCCcore-10.2.0.eb New major version, new toolchain, new sanity checks. --- .../b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..460afd5c0d0 --- /dev/null +++ b/easybuild/easyconfigs/b/bgen/bgen-4.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'bgen' +version = '4.1.3' + +homepage = 'https://github.com/limix/bgen' +description = "A BGEN file format reader. It fully supports the BGEN format specifications 1.2 and 1.3." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'limix' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7e2da4831b631cb18e16bbe2b645f08c9b325fb4eb2f53615fcdeec2a75bbd35'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('zstd', '1.4.5'), + ('almosthere', '2.0.2'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libbgen.a', 'include/bgen/bgen.h'], + 'dirs': [], +} + +moduleclass = 'bio' From ad8c8801743064c0e150ae943e75dde9e1d580b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Aug 2021 10:15:31 +0200 Subject: [PATCH 0583/9987] add CBPS extension for recent R 4.0.x and 4.1.0 easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 3 +++ 7 files changed, 21 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index df5788a6eb9..9eb85d1c0d7 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2894,6 +2894,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 2154e87ccb2..2b8973c8469 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2904,6 +2904,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 3d0bffd5021..cf3cce38242 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2930,6 +2930,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index e7e51b34c74..99facf4817f 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2935,6 +2935,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 8a52c5c7c87..f9a6bf36299 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2939,6 +2939,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index d60bd6ae026..ef355408f91 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2950,6 +2950,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index eb0de773448..33b82fa2331 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -2972,6 +2972,9 @@ exts_list = [ ('cobalt', '4.3.1', { 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), ] moduleclass = 'lang' From 950fbda08c2cb368eb65e245391e74ef0850fb4d Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Tue, 3 Aug 2021 11:12:25 +0200 Subject: [PATCH 0584/9987] patch so that MaxBin2 uses the EB provided Perl and not the system Perl --- .../easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb | 6 +++++- .../m/MaxBin/MaxBin-2.2.7_fix_perl_shebang.patch | 8 ++++++++ 2 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7_fix_perl_shebang.patch diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb index 65c321a1695..523aa09a5ec 100644 --- a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e'] +patches = ['MaxBin-2.2.7_fix_perl_shebang.patch'] +checksums = [ + 'cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e', # src + 'f966952e7bb910b24687001c89dd1667318346911db964438b8e726ca3415913', # MaxBin-2.2.7_fix_perl_shebang.patch +] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7_fix_perl_shebang.patch b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7_fix_perl_shebang.patch new file mode 100644 index 00000000000..508c60e0313 --- /dev/null +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7_fix_perl_shebang.patch @@ -0,0 +1,8 @@ +--- run_MaxBin.pl_orig 2021-08-02 10:08:36.990459000 +0200 ++++ run_MaxBin.pl 2021-08-02 10:09:31.675685960 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + use strict; + use Cwd; + use LWP::Simple; From 714e6b8f7cf31eb93b4628e2e8fc80e1b87dce99 Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 3 Aug 2021 16:12:15 +0200 Subject: [PATCH 0585/9987] adding easyconfigs: archspec-0.1.2-GCCcore-10.3.0.eb --- .../archspec/archspec-0.1.2-GCCcore-10.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f1e3fc9518f --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.2-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.1.2' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = ['archspec-%(version)s-py2.py3-none-any.whl'] +checksums = ['71aef85b8114c357723b0ea455cba9a2bf567400dce25b0ee7f96eb4f1405d37'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +sanity_pip_check = True + +moduleclass = 'tools' From 10d4258e0369924e7004ae8822ebe19afa5f4558 Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 3 Aug 2021 16:14:32 +0200 Subject: [PATCH 0586/9987] adding easyconfigs: Voro++-0.4.6-GCCcore-10.3.0.eb --- .../v/Voro++/Voro++-0.4.6-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..cb1a8cb8417 --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] +builddependencies = [('binutils', '2.36.1')] + + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +moduleclass = 'math' From 838c030741a3f6a4562460b796d3c82f7b0990ef Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 3 Aug 2021 16:16:36 +0200 Subject: [PATCH 0587/9987] adding easyconfigs: kim-api-2.2.1-GCCcore-10.3.0.eb --- .../k/kim-api/kim-api-2.2.1-GCCcore-10.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..910fef02a8c --- /dev/null +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'kim-api' +version = '2.2.1' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +KIM is an API and OpenKIM is a collection of interatomic models (potentials) for +atomistic simulations. This is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild only installs the API, the models can be installed with the +package openkim-models, or the user can install them manually by running + kim-api-collections-management install user MODELNAME +or + kim-api-collections-management install user OpenKIM +to install them all. + """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://s3.openkim.org/kim-api/'] +sources = ['%(name)s-%(version)s.txz'] +checksums = ['1d5a12928f7e885ebe74759222091e48a7e46f77e98d9147e26638c955efbc8e'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('CMake', '3.20.1'), # Also needed to install models, thus not just a builddependency. +] + +parallel = 1 +separate_build_dir = True +build_type = 'Release' + +modextravars = { + 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' +} + +sanity_check_paths = { + 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'chem' From 341d6d2cdc30014421e22b2b8c48d4fb393581ae Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Tue, 3 Aug 2021 16:18:03 +0200 Subject: [PATCH 0588/9987] Updated molmod --- .../m/molmod/molmod-1.4.8-foss-2021a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021a.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021a.eb new file mode 100644 index 00000000000..0f4bb6c8b8e --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = [ + '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8', # molmod-1.4.8.tar.gz +] + +dependencies = [ + ('Python', '3.9.5'), + ('matplotlib', '3.4.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; pytest -ra" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From 75b4a1367afc59ee688d4d537ad3498ed3e6400c Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 3 Aug 2021 16:18:11 +0200 Subject: [PATCH 0589/9987] adding easyconfigs: ScaFaCoS-1.0.1-foss-2021a.eb --- .../s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2021a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2021a.eb b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2021a.eb new file mode 100644 index 00000000000..c5dbaccdf6c --- /dev/null +++ b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2021a.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'ScaFaCoS' +version = '1.0.1' + +homepage = 'http://www.scafacos.de/' +description = """ScaFaCoS is a library of scalable fast coulomb solvers.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '2b125f313795c81b0e87eb920082e91addf94c17444f9486d979e691aaded99b', # scafacos-1.0.1.tar.gz +] + +builddependencies = [ + ('Autotools', '20210128'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('GSL', '2.7'), +] + +preconfigopts = 'unset F77 && ' + +configopts = 'FCFLAGS="-fallow-argument-mismatch $FCFLAGS" ' +configopts += '--enable-shared --enable-static --disable-doc ' +# tell it where to find provided FFTW +configopts += '--without-internal-fftw --with-fftw3-includedir=$EBROOTFFTW/include --with-fftw3-libdir=$EBROOTFFTW/lib ' +# only include the solvers supported for LAMMPS +# (for p2nfft we need an additonal dependency) +configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' + +sanity_check_paths = { + 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], + 'dirs': [], +} + +moduleclass = 'math' From c2d0552d44bb698d4186ee879757c60ce8da90c2 Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Tue, 3 Aug 2021 11:08:13 -0400 Subject: [PATCH 0590/9987] add sanity check to address path issue --- easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb index 14596aee0f6..d0abc3db272 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb @@ -41,6 +41,7 @@ sanity_check_paths = { sanity_check_commands = [ '7z --help', '7z x || test $? -gt 0', + "! 7z i | grep -q \"Can't load\"", ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb index c5f1bfce6ff..c00944a79d3 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb @@ -41,6 +41,7 @@ sanity_check_paths = { sanity_check_commands = [ '7z --help', '7z x || test $? -gt 0', + "! 7z i | grep -q \"Can't load\"", ] moduleclass = 'tools' From 155d58dbdb4e623c11aa944709c1fd43a7056aba Mon Sep 17 00:00:00 2001 From: Justin Krometis Date: Tue, 3 Aug 2021 11:38:34 -0400 Subject: [PATCH 0591/9987] add spaces to fix parsing issue --- easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb index d0abc3db272..8c1b293c372 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb @@ -41,7 +41,7 @@ sanity_check_paths = { sanity_check_commands = [ '7z --help', '7z x || test $? -gt 0', - "! 7z i | grep -q \"Can't load\"", + "! 7z i | grep -q \"Can't load\" ", ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb index c00944a79d3..3239c13051d 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb @@ -41,7 +41,7 @@ sanity_check_paths = { sanity_check_commands = [ '7z --help', '7z x || test $? -gt 0', - "! 7z i | grep -q \"Can't load\"", + "! 7z i | grep -q \"Can't load\" ", ] moduleclass = 'tools' From 541c6f0f33b24e906e232d99dd3bba73dd15b847 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 3 Aug 2021 20:49:19 +0200 Subject: [PATCH 0592/9987] adding easyconfigs: libarchive-3.5.1-GCCcore-11.2.0.eb, XZ-5.2.5-GCCcore-11.2.0.eb --- .../libarchive-3.5.1-GCCcore-11.2.0.eb | 29 +++++++++++++ .../x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..692cfb34323 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.5.1' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['9015d109ec00bb9ae1a384b172bf2fc1dff41e2c66e5a9eeddf933af9db37f5a'] + +builddependencies = [ + ('binutils', '2.37'), + ('XZ', '5.2.5'), + ('OpenSSL', '1.1', '', True), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0ff1f6a50bc --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.5' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['XZ-5.2.2_compat-libs.patch'] +checksums = [ + '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 + '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch +] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.21', '', True), + ('binutils', '2.37'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' From 5290d5f849c6068f9a47e85c809ff29c97276ab9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 3 Aug 2021 20:52:39 +0200 Subject: [PATCH 0593/9987] adding easyconfigs: cURL-7.76.0-GCCcore-11.2.0.eb --- .../c/cURL/cURL-7.76.0-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1615413cf86 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.76.0' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ed936c0b02c06d42cf84b39dd12bb14b62d77c7c4e875ade022280df5dcc81d7'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('OpenSSL', '1.1', '', True), +] + +configopts = '--with-zlib' +# configopts += '--with-ssl=$EBROOTOPENSSL' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' From 18ce733689f2b8be62332921c04a8cfe668b18da Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 3 Aug 2021 20:58:09 +0200 Subject: [PATCH 0594/9987] update easyconfig to cURL 7.78.0 --- ...L-7.76.0-GCCcore-11.2.0.eb => cURL-7.78.0-GCCcore-11.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/cURL/{cURL-7.76.0-GCCcore-11.2.0.eb => cURL-7.78.0-GCCcore-11.2.0.eb} (98%) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb similarity index 98% rename from easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb index 1615413cf86..f740091af75 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'cURL' -version = '7.76.0' +version = '7.78.0' homepage = 'https://curl.haxx.se' From d0551d2f9ddc26d553eb0ca0107fb6c9b4939070 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 3 Aug 2021 21:09:20 +0200 Subject: [PATCH 0595/9987] update easyconfig cURL-7.78.0-GCCcore-11.2.0.eb: add --with-ssl configopts --- easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb index f740091af75..e66d05453ca 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb @@ -30,8 +30,8 @@ dependencies = [ ('OpenSSL', '1.1', '', True), ] -configopts = '--with-zlib' -# configopts += '--with-ssl=$EBROOTOPENSSL' +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} From 3b9b601088c1ef57c552d257c8ccc1c62a912cb9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 3 Aug 2021 21:11:58 +0200 Subject: [PATCH 0596/9987] adding easyconfigs: PCRE-8.45-GCCcore-11.2.0.eb, PCRE2-10.37-GCCcore-11.2.0.eb --- .../p/PCRE/PCRE-8.45-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ .../p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb | 28 ++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b20423ccc52 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.45' + +homepage = 'https://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.pcre.org/pub/pcre/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4e6ce03e0336e8b4a3d6c2b70b1c5e18590a5673a98186da90d4f33c23defc09'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +configopts = """\ + --enable-utf\ + --enable-unicode-properties\ + --enable-pcre16\ + --enable-pcre32\ +""" + +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..257c390e0b9 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.37' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.sourceforge.net/pcre'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e214c0c40a97b8a5c2b4ae88a3aa8a93e6f2e45c6b3534ddac351f26548577'] + +builddependencies = [('binutils', '2.37')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' From 21517bf897bb270128cc36a12da22c879a4c1cc9 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 3 Aug 2021 19:22:33 +0000 Subject: [PATCH 0597/9987] Moved Autotools to builddep --- .../easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb index 61e06fe1570..aeeec32aa8e 100644 --- a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.2.0.eb @@ -16,9 +16,8 @@ source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['7f10acf9a3fa15deabbc0304e7c14efa25cea39108318c9f02b47257de2d7390'] # 3.3.1.tar.gz -builddependencies = [('binutils', '2.35')] - -dependencies = [ +builddependencies = [ + ('binutils', '2.35'), ('Autotools', '20200321'), ] From b7673182a9e05f60e08b075131d8598a00321761 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 3 Aug 2021 21:26:18 +0200 Subject: [PATCH 0598/9987] adding easyconfigs: CMake-3.21.1-GCCcore-11.2.0.eb, ncurses-6.2-GCCcore-11.2.0.eb, pkg-config-0.29.2-GCCcore-11.2.0.eb --- .../c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb | 30 ++++++++++++++ .../n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ .../pkg-config-0.29.2-GCCcore-11.2.0.eb | 34 +++++++++++++++ 3 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..60e004e5627 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.21.1' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fac3915171d4dff25913975d712f76e69aef44bf738ba7b976793a458b4cfed4'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.78.0'), + ('libarchive', '3.5.1'), + ('OpenSSL', '1.1', '', True), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a977bf74971 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.2' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] + +builddependencies = [('binutils', '2.37')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +configopts = [ + # default build + local_common_configopts, + # the UTF-8 enabled version (ncursesw) + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +local_libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a3f62fffa54 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [('binutils', '2.37')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' From 9c77b6100bc4fb88239f0aae8338754a12d5d636 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 3 Aug 2021 21:40:09 +0200 Subject: [PATCH 0599/9987] adding easyconfigs: zstd-1.5.0-GCCcore-11.2.0.eb, gzip-1.10-GCCcore-11.2.0.eb, LZO-2.10-GCCcore-11.2.0.eb, libzip-1.7.3-GCCcore-11.2.0.eb, lz4-1.9.3-GCCcore-11.2.0.eb, p7zip-17.04-GCCcore-11.2.0.eb, pigz-2.6-GCCcore-11.2.0.eb, Szip-2.1.1-GCCcore-11.2.0.eb, UnZip-6.0-GCCcore-11.2.0.eb, Zip-3.0-GCCcore-11.2.0.eb --- .../g/gzip/gzip-1.10-GCCcore-11.2.0.eb | 24 +++++++++ .../l/LZO/LZO-2.10-GCCcore-11.2.0.eb | 27 ++++++++++ .../l/libzip/libzip-1.7.3-GCCcore-11.2.0.eb | 32 ++++++++++++ .../l/lz4/lz4-1.9.3-GCCcore-11.2.0.eb | 30 +++++++++++ .../p/p7zip/p7zip-17.04-GCCcore-11.2.0.eb | 47 +++++++++++++++++ .../p/pigz/pigz-2.6-GCCcore-11.2.0.eb | 45 ++++++++++++++++ .../s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb | 29 +++++++++++ .../u/UnZip/UnZip-6.0-GCCcore-11.2.0.eb | 52 +++++++++++++++++++ .../z/Zip/Zip-3.0-GCCcore-11.2.0.eb | 40 ++++++++++++++ .../z/zstd/zstd-1.5.0-GCCcore-11.2.0.eb | 41 +++++++++++++++ 10 files changed, 367 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libzip/libzip-1.7.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.5.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..633d7f7791b --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.10' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c91f74430bf7bc20402e1f657d0b252cb80aa66ba333a25704512af346633c68'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9434b4e9093 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.37')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.7.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.7.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..76e25cf8b7e --- /dev/null +++ b/easybuild/easyconfigs/l/libzip/libzip-1.7.3-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libzip' +version = '1.7.3' + +homepage = 'https://libzip.org/' +description = "libzip is a C library for reading, creating, and modifying zip archives." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/nih-at/libzip/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c0a086901dfc8bda0fb8695f2d3c8050ed140b7899536b9348bcc72b47b2f307'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': [ + 'bin/zipcmp', + 'bin/zipmerge', + 'bin/ziptool', + 'lib64/libzip.%s' % SHLIB_EXT, + ], + 'dirs': ['include', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..09b7377077b --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.3-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.3' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['030644df4611007ff7dc962d981f390361e6c97a34e5cbc393ddfbe019ffe2c1'] + +builddependencies = [('binutils', '2.37')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ac2df0865b0 --- /dev/null +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '17.04' + +homepage = 'https://github.com/jinfeihan57/p7zip/' +description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of +7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'jinfeihan57' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ea029a2e21d2d6ad0a156f6679bd66836204aa78148a4c5e498fe682e77127ef'] + +builddependencies = [ + ('binutils', '2.37'), +] + +prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" +buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' + +files_to_copy = [ + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.%s' % SHLIB_EXT, 'bin/Codecs'], 'libexec'), # 7z requires 7z.so plugin in same directory +] + +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + "echo '#!/bin/sh\n%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask +] + +sanity_check_paths = { + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.%s' % SHLIB_EXT], + 'dirs': ['libexec/Codecs'], +} + +sanity_check_commands = [ + '7z --help', + '7z x || test $? -gt 0', + "! 7z i | grep -q \"Can't load\" ", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2670597f6ad --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.6-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.6' + +homepage = 'https://zlib.net/pigz/' + +description = """ + pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. pigz was written by Mark Adler, and + uses the zlib and pthread libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + 'https://zlib.net/pigz/', + 'https://zlib.net/pigz/fossils/', +] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + '2eed7b0d7449d1d70903f2a62cd6005d262eb3a8c9e98687bc8cbb5809db2a7d', # pigz-2.6.tar.gz + '7e37175714d43c946373d07c522ec98a77c0f8572a9d448f759c41f6f060275d', # pigz-2.6_makefile.patch +] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ['bin/pigz', 'bin/unpigz'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b2d223898c7 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.37'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..60bf6654f0c --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-11.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' +buildopts += 'LF2="$LDFLAGS" ' +# Note: CF is multiple lines +buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' +buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' +buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f376553d7a0 --- /dev/null +++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Zip' +version = '3.0' + +homepage = 'http://www.info-zip.org/Zip.html' +description = """Zip is a compression and file packaging/archive utility. +Although highly compatible both with PKWARE's PKZIP and PKUNZIP +utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives +have been portability and other-than-MSDOS functionality""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] + +builddependencies = [ + ('binutils', '2.37'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' +buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' +buildopts += 'generic_gcc' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["zip --version"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..422d044f3d9 --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.5.0' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5194fbfa781fcf45b98c5e849651aa7b3b0a008c6b72d4a0db760f3002291e94'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('XZ', '5.2.5'), + ('lz4', '1.9.3'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From efe840c045e8014eb3ebd8f9c07340b752f40e4d Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 3 Aug 2021 21:44:23 +0200 Subject: [PATCH 0600/9987] update zstd-1.5.0-GCCcore-11.2.0.eb: Checksum --- easybuild/easyconfigs/z/zstd/zstd-1.5.0-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.0-GCCcore-11.2.0.eb index 422d044f3d9..39a21b894e7 100644 --- a/easybuild/easyconfigs/z/zstd/zstd-1.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.0-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} github_account = 'facebook' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['5194fbfa781fcf45b98c5e849651aa7b3b0a008c6b72d4a0db760f3002291e94'] +checksums = ['0d9ade222c64e912d6957b11c923e214e2e010a18f39bec102f572e693ba2867'] builddependencies = [ ('binutils', '2.37'), From f7c1231fdd0b5841467be5340463c084f60fecc5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Aug 2021 21:36:41 +0200 Subject: [PATCH 0601/9987] add SBdecomp extension for recent R 4.0.x and 4.1.0 easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 3 +++ 7 files changed, 21 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 9eb85d1c0d7..3f73cf6e804 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2897,6 +2897,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 2b8973c8469..25bfe941168 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2907,6 +2907,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index cf3cce38242..600336ef2ae 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2933,6 +2933,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 99facf4817f..6410c41672c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2938,6 +2938,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index f9a6bf36299..9d7859add85 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2942,6 +2942,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index ef355408f91..044bfdd2951 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2953,6 +2953,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index 33b82fa2331..1fa9d01d249 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -2975,6 +2975,9 @@ exts_list = [ ('CBPS', '0.22', { 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), ] moduleclass = 'lang' From e968d992fe9a5515a09bf3fee7fcea6834ed04cf Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 3 Aug 2021 21:50:15 +0200 Subject: [PATCH 0602/9987] adding easyconfigs: libgcrypt-1.9.3-GCCcore-11.2.0.eb, libgpg-error-1.42-GCCcore-11.2.0.eb --- .../libgcrypt-1.9.3-GCCcore-11.2.0.eb | 24 +++++++++++++++++++ .../libgpg-error-1.42-GCCcore-11.2.0.eb | 22 +++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.42-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1ece41de6a0 --- /dev/null +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.9.3-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libgcrypt' +version = '1.9.3' + +homepage = 'https://gnupg.org/related_software/libgcrypt/index.html' +description = """Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['97ebe4f94e2f7e35b752194ce15a0f3c66324e0ff6af26659bbfb5ff2ec328fd'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('libgpg-error', '1.42')] + +sanity_check_paths = { + 'files': ['bin/libgcrypt-config', 'include/gcrypt.h', 'lib/libgcrypt.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.42-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.42-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f99fc6535c9 --- /dev/null +++ b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.42-GCCcore-11.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libgpg-error' +version = '1.42' + +homepage = 'https://gnupg.org/related_software/libgpg-error/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['fc07e70f6c615f8c4f590a8e37a9b8dd2e2ca1e9408f8e60459c67452b925e23'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/gpg-error-config', 'include/gpg-error.h', 'lib/libgpg-error.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From 0165b7b7269d22bd73242ebfb810b6d939c6aed0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Aug 2021 22:09:19 +0200 Subject: [PATCH 0603/9987] adding easyconfigs: horton-2.1.1-intel-2020a-Python-2.7.18.eb, h5py-2.10.0-intel-2020a-Python-2.7.18.eb --- .../h5py-2.10.0-intel-2020a-Python-2.7.18.eb | 36 ++++++++ .../horton-2.1.1-intel-2020a-Python-2.7.18.eb | 92 +++++++++++++++++++ 2 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb new file mode 100644 index 00000000000..461b8f274f1 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['h5py-%(version)s_avoid-mpi-init.patch'] +checksums = [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch +] + +#builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('HDF5', '1.10.6'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb new file mode 100644 index 00000000000..523a43d128f --- /dev/null +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb @@ -0,0 +1,92 @@ +easyblock = 'Bundle' + +name = 'horton' +version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://theochem.github.io/horton' +description = """HORTON is a Helpful Open-source Research TOol for N-fermion systems, written + primarily in the Python programming language. (HORTON is named after the helpful + pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON + is to provide a platform for testing new ideas on the quantum many-body problem + at a reasonable computational cost. Although HORTON is primarily designed to be + a quantum-chemistry program, it can perform computations involving model + Hamiltonians, and could be extended for computations in nuclear physics.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +dependencies = [ + ('Python', '2.7.18'), + ('h5py', '2.10.0', versionsuffix), + ('matplotlib', '2.2.5', versionsuffix), +] + +local_horton_prebuildopts = ' '.join([ + 'BLAS_EXTRA_COMPILE_ARGS=-DMKL_ILP64:-I${MKLROOT}/include', + 'BLAS_LIBRARY_DIRS=${MKLROOT}/lib/intel64', + 'BLAS_LIBRARIES=mkl_intel_ilp64:mkl_core:mkl_sequential:pthread:m:mkl_def', + 'LIBRARY_PATH=%(installdir)s/lib:$LIBRARY_PATH', +]) + +# Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc +local_horton_runtest = ' '.join([ + 'export MATPLOTLIBRC=$PWD;', + 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', + '%s python setup.py build_ext -i; ' % local_horton_prebuildopts, + 'nosetests -v', +]) + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +# Horton 2.1.1 requires very specific versions of libxc (2.2.2) and Libint (2.0.3), +# so we install these as components along with Horton itself +components = [ + ('Libint', '2.0.3', { + 'toolchainopts': {'pic': True}, + 'source_urls': ['http://downloads.sourceforge.net/project/libint/libint-for-mpqc'], + 'sources': ['libint-%(version)s-stable.tgz'], + 'checksums': ['5d4944ed6e60b08d05b4e396b10dc7deee7968895984f4892fd17159780f5b02'], + 'start_dir': 'libint-%(version)s-stable', + 'easyblock': 'EB_Libint', + }), + ('libxc', '2.2.2', { + 'easyblock': 'ConfigureMake', + # Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. + # Tests also fail with Intel Compilers on Haswell when optarch is enabled. + 'toolchainopts': {'lowopt': True, 'optarch': False}, + 'source_urls': ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'], + 'checksums': ['6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642'], + 'configopts': 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran', + 'parallel': 1, + 'runtest': 'check', + }), + (name, version, { + 'source_urls': ['https://github.com/theochem/horton/releases/download/%(version)s'], + 'checksums': ['4b3f87920d881030ba80f097326a744de2cfee5316aa4499cc9a6501f64b5060'], + 'easyblock': 'PythonPackage', + 'download_dep_fail': True, + 'use_pip': False, + 'prebuildopts': local_horton_prebuildopts, + 'runtest': local_horton_runtest, + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['include/xc.h', 'lib/libint2.a', 'lib/libint2.%s' % SHLIB_EXT] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['bin', 'include/horton', 'include/libint2', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import horton'", + "horton-esp-fit.py --version", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From 18ffbff3e64685c51ffd7466de9bf2bad3239f6a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 3 Aug 2021 22:29:47 +0200 Subject: [PATCH 0604/9987] adding easyconfigs: Perl.bare-5.34.0-GCCcore-11.2.0.eb, makeinfo-6.8-GCCcore-11.2.0-minimal.eb, expat-2.4.1-GCCcore-11.2.0.eb, ncurses-6.2-GCCcore-11.2.0.eb, libreadline-8.1-GCCcore-11.2.0.eb, groff-1.22.4-GCCcore-11.2.0.eb, DB-18.1.40-GCCcore-11.2.0.eb, Perl-5.34.0-GCCcore-11.2.0.eb --- .../d/DB/DB-18.1.40-GCCcore-11.2.0.eb | 33 + .../e/expat/expat-2.4.1-GCCcore-11.2.0.eb | 33 + .../g/groff/groff-1.22.4-GCCcore-11.2.0.eb | 26 + .../libreadline-8.1-GCCcore-11.2.0.eb | 41 + .../makeinfo-6.8-GCCcore-11.2.0-minimal.eb | 35 + .../n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb | 41 + .../Perl.bare-5.34.0-GCCcore-11.2.0.eb | 27 + .../p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 1777 +++++++++++++++++ 8 files changed, 2013 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.4.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0-minimal.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/Perl.bare/Perl.bare-5.34.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..94dd6b092b5 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('OpenSSL', '1.1', '', True)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.4.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.4.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..061388ea159 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.4.1-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.4.1' + +homepage = 'https://libexpat.github.io' + +description = """ + Expat is an XML parser library written in C. It is a stream-oriented parser + in which an application registers handlers for things the parser might find + in the XML document (like start tags) +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_TAR_BZ2] +checksums = ['2f9b6a580b94577b150a7d5617ad4643a4301a6616ff459307df3e225bcfbf40'] + +builddependencies = [('binutils', '2.37')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..454c00e43bb --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.22.4' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] + +builddependencies = [ + ('binutils', '2.37'), + ('makeinfo', '6.8', '-minimal'), +] + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c609a5ccc7e --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.1' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['f8ceb4ee131e3232226a17f51b164afc46cd0b9e6cef344be87c65962cb82b02'] + +builddependencies = [ + ('binutils', '2.37'), +] +dependencies = [ + ('ncurses', '6.2'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0-minimal.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0-minimal.eb new file mode 100644 index 00000000000..79d4c64db52 --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0-minimal.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '6.8' +versionsuffix = '-minimal' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project. + +This is a minimal build with very basic functionality. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['8eb753ed28bca21f8f56c1a180362aed789229bd62fff58bf8368e9beb59fec4'] + +builddependencies = [ + ('binutils', '2.37'), +] +dependencies = [ + ('Perl.bare', '5.34.0'), +] + +configopts = '--disable-perl-xs --disable-perl-api-texi-build --disable-pod-simple-texinfo-tests ' + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a977bf74971 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.2' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] + +builddependencies = [('binutils', '2.37')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +configopts = [ + # default build + local_common_configopts, + # the UTF-8 enabled version (ncursesw) + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +local_libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Perl.bare/Perl.bare-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl.bare/Perl.bare-5.34.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..cdf0e62f1f3 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl.bare/Perl.bare-5.34.0-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Perl' + +name = 'Perl.bare' +version = '5.34.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +This is a minimal build without any modules. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = ['perl-%(version)s.tar.gz'] +checksums = ['551efc818b968b05216024fb0b727ef2ad4c100f8cb6b43fab615fa78ae5be9a'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a02d680ca3b --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -0,0 +1,1777 @@ +easyblock = 'Bundle' + +name = 'Perl' +version = '5.34.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['03b693901cd8ae807231b1787798cf1f2e0b8a56218d07b7da44f784a7caeb2c'] + +builddependencies = [ + ('binutils', '2.37'), + ('groff', '1.22.4'), +] + +dependencies = [ + ('Perl.bare', version), + ('zlib', '1.2.11'), # for Net::SSLeay + ('expat', '2.4.1'), # for XML::Parser + ('ncurses', '6.2'), # for Term::ReadLine::Gnu + ('libreadline', '8.1'), # for Term::ReadLine::Gnu + ('DB', '18.1.40'), # for DB_File + ('OpenSSL', '1.1', '', True), # required for Net::SSLeay +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +# !! order of extensions is important !! +# extensions updated on Aug 3rd 2021 +exts_list = [ + ('Config::General', '2.63', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], + }), + ('File::Listing', '6.14', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['15b3a4871e23164a36f226381b74d450af41f12cc94985f592a669fcac7b48ff'], + }), + ('ExtUtils::InstallPaths', '0.012', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], + }), + ('Test::Harness', '3.42', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['0fd90d4efea82d6e262e6933759e85d27cbcfa4091b14bf4042ae20bab528e53'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Test::Fatal', '0.016', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7283d430f2ba2030b8cd979ae3039d3f1b2ec3dde1a11ca6ae09f992a66f788f'], + }), + ('Test::Warnings', '0.031', { + 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'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293'], + }), + ('Meta::Builder', '0.004', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['acb499aa7206eb9db21eb85357a74521bfe3bdae4a6416d50a7c75b939cf56fe'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['4bd70d6ca76f6f6ba7e4c618d4ac93b8593a58f1233ccbe18b10f5f204f1d4e4'], + }), + ('Getopt::Long', '2.52', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + 'checksums': ['9dc7a7c373353d5c05efae548e7b123aa8a31d1f506eb8dbbec8f0dca77705fa'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['bd697dd62aaf26d118e9f0a0813429deb1c544e4501559879b61fcbdfe99fe46'], + }), + ('Mouse', 'v2.5.10', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SK/SKAJI'], + 'checksums': ['ce8dc23946153a467ff09765167ee2590f5c502120f48a2d9441733f39aa32ee'], + }), + ('Test::Version', '2.09', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['9ce1dd2897a5f30e1b7f8966ec66f57d8d8f280f605f28c7ca221fa79aca38e0'], + }), + ('DBIx::Admin::TableInfo', '3.04', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['b9625992683b97378bea0947773f50e3c9f81974048b84f4c3422cae7e6082f4'], + }), + ('Net::HTTP', '6.21', { + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['375aa35b76be99f06464089174d66ac76f78ce83a5c92a907bbfab18b099eec4'], + }), + ('Test::Deep', '1.130', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['4064f494f5f62587d0ae501ca439105821ee5846c687dc6503233f55300a7c56'], + }), + ('Test::Warn', '0.36', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + 'checksums': ['ecbca346d379cef8d3c0e4ac0c8eb3b2613d737ffaaeae52271c38d7bf3c6cda'], + }), + ('MRO::Compat', '0.13', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['8a2c3b6ccc19328d5579d02a7d91285e2afd85d801f49d423a8eb16f323da4f8'], + }), + ('Moo', '2.005004', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['e3030b80bd554a66f6b3c27fd53b1b5909d12af05c4c11ece9a58f8d1e478928'], + }), + ('Clone::Choose', '0.010', { + 'source_tmpl': 'Clone-Choose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'], + 'checksums': ['5623481f58cee8edb96cd202aad0df5622d427e5f748b253851dfd62e5123632'], + }), + ('Hash::Merge', '0.302', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'], + 'checksums': ['ae0522f76539608b61dde14670e79677e0f391036832f70a21f31adde2538644'], + }), + ('SQL::Abstract', '2.000001', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSTROUT'], + 'checksums': ['35a642662c349420d44be6e0ef7d8765ea743eb12ad14399aa3a232bb94e6e9a'], + }), + ('HTML::Form', '6.07', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['7daa8c7eaff4005501c3431c8bf478d58bbee7b836f863581aa14afe1b4b6227'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['83293737e803b43112830443fb5208ec5208a2e6ea512ed54ef8e4dd2b880827'], + }), + ('IPC::Run', '20200505.0', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['816ebf217fa0df99c583d73c0acc6ced78ac773787c664c75cbf140bb7e4c901'], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c'], + }), + ('File::Remove', '1.60', { + 'source_tmpl': 'File-Remove-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['e86e2a40ffedc6d5697d071503fd6ba14a5f9b8220af3af022110d8e724f8ca6'], + }), + ('YAML::Tiny', '1.73', { + 'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['bc315fa12e8f1e3ee5e2f430d90b708a5dc7e47c867dba8dce3a6b8fbe257744'], + }), + ('Module::Install', '1.19', { + 'source_tmpl': 'Module-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['1a53a78ddf3ab9e3c03fc5e354b436319a944cba4281baf0b904fa932a13011b'], + }), + ('Config::Tiny', '2.26', { + 'source_tmpl': 'Config-Tiny-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['83b53291baec7884fbdfeb2a231297202df266cac58638b895ce25ec877dcf5f'], + }), + ('Test::ClassAPI', '1.07', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['30e9dbfc5e0cc2ee14eae8f3465a908a710daecbd0a3ebdb2888fc4504fa18aa'], + }), + ('Test::Most', '0.37', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + 'checksums': ['533370141eb9f18cf4ac380f6ded2ab57802a6e184008a80fd2304bfcc474fc7'], + }), + ('Class::Accessor', '0.51', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['bf12a3e5de5a2c6e8a447b364f4f5a050bf74624c56e315022ae7992ff2f411c'], + }), + ('Test::Differences', '0.68', { + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': ['c88dbbb48b934b069284874f33abbaaa438aa31204aa3fa73bfc2f4aeac878da'], + }), + ('HTTP::Tiny', '0.078', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['ddbdaa2fb511339fa621a80021bf1b9733fddafc4fe0245f26c8b92171ef9387'], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['1d743ada482b5c9871d894966e87d4c20edc96931bb949fb2638b000ddd6684b'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['68c1dac2187421f0eb7abf71452a06f190181b8fc4b28ededf5b90296fb943cc'], + }), + ('Date::Language', '2.33', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['c0b69c4b039de6f501b0d9f13ec58c86b040c1f7e9b27ef249651c143d605eb2'], + }), + ('version', '0.9929', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['5056ed481ada4e0fa497096d4091b18658f214d862e1ed164edf10bc6b39c8b0'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'checksums': ['865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': ['ea844b9686c94d666d9d444321d764490b2cde2f985c4165b4c2c77665caedc4'], + }), + ('Sub::Name', '0.26', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['2d2f2d697d516c89547e7c4307f1e79441641cae2c7395e7319b306d390df105'], + }), + ('Time::Piece', '1.3401', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + 'checksums': ['4b55b7bb0eab45cf239a54dfead277dfa06121a43e63b3fce0853aecfdb04c27'], + }), + ('Digest::HMAC', '1.04', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARODLAND'], + 'checksums': ['d6bc8156aa275c44d794b7c18f44cdac4a58140245c959e6b19b2c3838b08ed4'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016'], + }), + ('MIME::Lite', '3.033', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['f1235866482b67f00858b3edaa4ff4cf909ef900f1d15d889948bf9c03a591e0'], + }), + ('Crypt::Rijndael', '1.16', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['6540085e3804b82a6f0752c1122cf78cadd221990136dd6fd4c097d056c84d40'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['dc49408964fd8b7963859c92e013f0b9f92f74be5a7c2a78e3996279827c10b3'], + }), + ('Canary::Stability', '2013', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a5c91c62cf95fcb868f60eab5c832908f6905221013fea2bce3ff57046d7b6ea'], + }), + ('AnyEvent', '7.17', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['50beea689c098fe4aaeb83806c40b9fe7f946d5769acf99f849f099091a4b985'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['76cb824a27b6b4e560409fcf6fd5b3bfbbd38b72f1f3d37ed0b54bd9c0baeade'], + }), + ('Data::UUID', '1.226', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['093d57ffa0d411a94bafafae495697db26f5c9d0277198fe3f7cf2be22996453'], + }), + ('Test::Pod', '1.52', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['60a8dbcc60168bf1daa5cc2350236df9343e9878f4ab9830970a5dde6fe8e5fc'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['1177027025ecb09ee64d9f9f255615c04db5e14f7536c344af632032eb887b0f'], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7b29c45add19d3d5084b751f7ba89a8e40479a446ce21cfd9cc741e558332a00'], + }), + ('XML::Tiny', '2.07', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': ['ce39fcb53e0fe9f1cbcd86ddf152e1db48566266b70ec0769ef364eeabdd8941'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['adb17dac9e36cd011f5243881c9739417fd102fce760f8de4e9be4c7131108e2'], + }), + ('HTML::Tree', '5.07', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': 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['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['fc3dad06cb2e6fc86a2f2abc5b5491d9da328ca3e6b6306559c224521db174da'], + }), + ('ExtUtils::ParseXS', '3.35', { + 'source_tmpl': 'ExtUtils-ParseXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['41def0511278a2a8ba9afa25ccab45b0453f75e7fd774e8644b5f9a57cc4ee1c'], + }), + ('Pod::Man', '4.14', { + 'source_tmpl': 'podlators-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRA'], + 'checksums': ['7af1c41de34b2e4dbff700a29d7387549c2b6cf16142214450c924707ddb0f82'], + }), + ('Mozilla::CA', '20200520', { + 'source_tmpl': 'Mozilla-CA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABH'], + 'checksums': ['b3ca0002310bf24a16c0d5920bdea97a2f46e77e7be3e7377e850d033387c726'], + }), + ('Test::More', '1.302186', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['9a03bda5ec420aea9692b650437f4d5b574fa505fdd7ff60cdb5f3ec034106ff'], + }), + ('Test::RequiresInternet', '0.05', { + 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN'], + 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], + }), + ('LWP::Protocol::https', '6.10', { + 'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['cecfc31fe2d4fc854cac47fce13d3a502e8fdfe60c5bc1c09535743185f2a86c'], + }), + ('Module::Load', '0.36', { + 'source_tmpl': 'Module-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['d825020ac00b220e89f9524e24d838f9438b072fcae8c91938e4026677bef6e0'], + }), + ('Module::Load::Conditional', '0.74', { + 'source_tmpl': 'Module-Load-Conditional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['54c354a9393820f1ebc2a095da084ea0392dcbccb0cb38a187a71831cc60a730'], + }), + ('parent', '0.238', { + 'source_tmpl': 'parent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['38f58fdef3e28a194c9c8d0dc5d02672faf93c069f40c5bcb1fabeadbbc4d2d1'], + }), + ('Net::Domain', '3.13', { + 'source_tmpl': 'libnet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['5a35fb1f2d4aa291680eb1af38899fab453c22c28e71f7c7bd3747b5a3db348c'], + }), + ('Scalar::Util', '1.56', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['15b8537d40fb3e6dae64b2e7e983c47a99b2c20816a180bb9c868b787a12ab5b'], + }), + ('Text::ParseWords', '3.30', { + 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': ['85e0238179dd43997e58c66bd51611182bc7d533505029a2db0d3232edaff5e8'], + }), + ('Encode', '3.11', { + 'source_tmpl': 'Encode-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], + 'checksums': ['ed063d01d01a140a3a3ec0aeba2f2b4849a35c18ca96ac231a5d7c7d54d17b5b'], + }), + ('constant', '1.33', { + 'source_tmpl': 'constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], + }), + ('Data::Dumper', '2.183', { + 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], + }), + ('Cwd', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('MIME::Base64', '3.16', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['77f73d6f7aeb8d33be08b0d8c2617f9b6c77fb7fc45422d507ca8bafe4246017'], + }), + ('ExtUtils::CppGuess', '0.23', { + 'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['ff629178321a1e591b83f809712593eae4408a413aa448654bce59b156f24153'], + }), + ('XSLoader', '0.24', { + 'source_tmpl': 'XSLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'], + 'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], + }), + ('AutoLoader', '5.74', { + 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], + }), + ('URI::Escape', '5.09', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['03e63ada499d2645c435a57551f041f3943970492baa3b3338246dab6f1fae0a'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], + 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], + }), + ('MCE::Mutex', '1.874', { + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], + 'checksums': ['d809e3018475115ad7eccb8bef49bde3bf3e75abbbcd80564728bbcfab86d3d0'], + }), + ('Text::CSV_XS', '1.46', { + 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['27e39f0d5f2322aaf78ff90eb1221f3cbed1d4c514d0956bda19407fcb98bed6'], + }), + ('DBD::CSV', '0.58', { + 'source_tmpl': 'DBD-CSV-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['6c26f710453b14d7b3cf5f3e1697e8ddaa48c0a66f5d811f4394bd8c32f287ef'], + }), + ('Array::Transpose', '0.06', { + 'source_tmpl': 'Array-Transpose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'], + 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], + }), + ('Config::Simple', '4.58', { + 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], + 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], + }), + ('Business::ISBN', '3.006', { + 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['c1fefe68354ffb80cdbd24303ebe684b3b6828df3d5f09b429a09fc4f0919c9a'], + }), + ('Business::ISBN::Data', '20210112.006', { + 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['98c2cfb266b5fdd016989abaa471d9dd4c1d593c508a6f01f66d184d5fee8bae'], + }), + ('common::sense', '3.75', { + 'source_tmpl': 'common-sense-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], + }), + ('IO::Compress::Bzip2', '2.102', { + 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['d6fa7f9a5beee446452a0fbc43589a0c73fe7e925c075b98628b018048dc72a4'], + }), + ('JSON::XS', '4.03', { + 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], + }), + ('List::MoreUtils::XS', '0.430', { + 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], + }), + ('Authen::NTLM', '1.09', { + 'source_tmpl': 'NTLM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'], + 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('XML::SAX::Expat', '0.51', { + 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN'], + 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], + }), + ('Inline', '0.86', { + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], + }), +] + +moduleclass = 'lang' From 304d9f586b12b588aba5cb90f361bf64faca13a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 3 Aug 2021 22:57:27 +0200 Subject: [PATCH 0605/9987] Drop sources from bundle --- easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index a02d680ca3b..61b60ebc057 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -9,10 +9,6 @@ description = """Larry Wall's Practical Extraction and Report Language""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['03b693901cd8ae807231b1787798cf1f2e0b8a56218d07b7da44f784a7caeb2c'] - builddependencies = [ ('binutils', '2.37'), ('groff', '1.22.4'), From e81e2d192fb4c43f49cbf0c40b2d49ce101062fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 3 Aug 2021 23:25:14 +0200 Subject: [PATCH 0606/9987] Fix checksums --- .../p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 98 +++++++++---------- 1 file changed, 48 insertions(+), 50 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 61b60ebc057..d630f424b0c 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -98,7 +98,7 @@ exts_list = [ ('Test::Warnings', '0.031', { 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['89a4947ddf1564ae01122275584433d7f6c4370370bcf3768922d796956ae24f'], + 'checksums': ['1e542909fef305e45563e9878ea1c3b0c7cef1b28bb7ae07eba2e1efabec477b'], }), ('File::ShareDir', '1.118', { 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', @@ -113,7 +113,7 @@ exts_list = [ ('DateTime::Locale', '1.32', { 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['c7224c7e51dce4dd9ba80d8857cd4c3b72137653da34d3ba3c3a3c20cbf438b8'], + 'checksums': ['78eabec73d13e1a23b0afcd1b05e84e3196258b98d1bbfafbad90d47db9c6679'], }), ('DateTime::TimeZone', '2.47', { 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', @@ -213,9 +213,8 @@ exts_list = [ ('Archive::Extract', '0.88', { 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], - 'checksums': ['9acd09cdb8e8cf0b6d08210a3b80342300c89a359855319bf6b00c14c4aab687'], + 'checksums': ['cffcf135cd0622287d3b02154f7d6716495449fcaed03966621948e25ea5f742'], }), - ('DBIx::Simple', '1.37', { 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], @@ -289,7 +288,7 @@ exts_list = [ ('MIME::Types', '2.21', { 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], - 'checksums': ['3e71099b92bfdbd8ef9f0643d7160201c4176053276bcf7e074cf5734ea9f8f1'], + 'checksums': ['0086454aec7144ddcaf842ec88e01d7fc27a61091454eb8f6f8afd568da68dd7'], }), ('File::Copy::Recursive', '0.45', { 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', @@ -402,15 +401,15 @@ exts_list = [ 'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'], }), ('Net::SSLeay', '1.90', { + 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", 'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'], 'checksums': ['f8696cfaca98234679efeedc288a9398fcf77176f1f515dbc589ada7c650dc93'], - 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", }), ('IO::Socket::SSL', '2.071', { 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], - 'checksums': ['876fe09763e7a474519431aff248cb1f1abaf070d6bdc791f60bf9abe781cd3b'], + 'checksums': ['40da40948ecc9c787ed39c95715872679eebfd54243721174993a2003e32ab0a'], }), ('Fennec::Lite', '0.004', { 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', @@ -555,12 +554,12 @@ exts_list = [ ('Test::Differences', '0.68', { 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], - 'checksums': ['c88dbbb48b934b069284874f33abbaaa438aa31204aa3fa73bfc2f4aeac878da'], + 'checksums': ['e68547206cb099a2594165ca0adc99fc12adb97c7f02a1222f62961fd775e270'], }), ('HTTP::Tiny', '0.078', { 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], - 'checksums': ['ddbdaa2fb511339fa621a80021bf1b9733fddafc4fe0245f26c8b92171ef9387'], + 'checksums': ['6d150215b0177bef1ff4f0d9a42abecc08507872e09417b01e6b57092d2e48c2'], }), ('Package::DeprecationManager', '0.17', { 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', @@ -620,7 +619,7 @@ exts_list = [ ('MIME::Lite', '3.033', { 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['f1235866482b67f00858b3edaa4ff4cf909ef900f1d15d889948bf9c03a591e0'], + 'checksums': ['78a279f1d2e242551c347ef97a13fc675766602cb84c2a80c569400f4f368bab'], }), ('Crypt::Rijndael', '1.16', { 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', @@ -700,7 +699,7 @@ exts_list = [ ('Term::UI', '0.48', { 'source_tmpl': 'Term-UI-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], - 'checksums': ['91946c80d7f4aab0ca4bfedc3bbe0a75b37cab1a29bd7bca3b3b7456d417e9a6'], + 'checksums': ['1e1e300a62b932acd7511c31c6b59efd92b0aab8eaac863a6c0121a4c246dd34'], }), ('Net::SNMP', 'v6.0.1', { 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', @@ -730,7 +729,7 @@ exts_list = [ ('LWP::Simple', '6.55', { 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['9cbb7c688416a20c1aba9a32568504af1143ced58b572c502a1b2fb8a500f535'], + 'checksums': ['c1d0d3a44a039b136ebac7336f576e3f5c232347e8221abd69ceb4108e85c920'], }), ('Time::Piece::MySQL', '0.06', { 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', @@ -764,8 +763,8 @@ exts_list = [ }), ('Test::NoWarnings', '1.06', { 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], - 'checksums': ['638a57658cb119af1fe5b15e73d47c2544dcfef84af0c6b1b2e97f08202b686c'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['c2dc51143b7eb63231210e27df20d2c8393772e0a333547ec8b7a205ed62f737'], }), ('Crypt::DES', '2.07', { 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', @@ -810,9 +809,8 @@ exts_list = [ ('Sub::Exporter', '0.988', { 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['543cb2e803ab913d44272c7da6a70bb62c19e467f3b12aaac4c9523259b083d6'], + 'checksums': ['23324887d6c590f145702f077d8ca42f1b2f26a3b76f08d66c2c1e21e606040c'], }), - ('Class::Load::XS', '0.10', { 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], @@ -850,8 +848,8 @@ exts_list = [ }), ('Class::Data::Inheritable', '0.09', { 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], - 'checksums': ['9967feceea15227e442ec818723163eb6d73b8947e31f16ab806f6e2391af14a'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSHERER'], + 'checksums': ['44088d6e90712e187b8a5b050ca5b1c70efe2baa32ae123e9bd8f59f29f06e4d'], }), ('Text::Balanced', '2.04', { 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', @@ -871,7 +869,7 @@ exts_list = [ ('File::Which', '1.27', { 'source_tmpl': 'File-Which-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], - 'checksums': ['7c5414dd6d5c61cb992fdd257aefe52f9a80bf55158cd5ec17469199d0b12eef'], + 'checksums': ['3201f1a60e3f16484082e6045c896842261fc345de9fb2e620fd2a2c7af3a93a'], }), ('Email::Date::Format', '1.005', { 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', @@ -891,7 +889,7 @@ exts_list = [ ('Text::CSV', '2.01', { 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], - 'checksums': ['8ccbd9195805222d995844114d0e595bb24ce188f85284dbf256080311cbb2c2'], + 'checksums': ['2a90a5eea3f22c40b87932a929621680609ab5f6b874a77c4134c8a04eb8e74b'], }), ('Test::Output', '1.033', { 'source_tmpl': 'Test-Output-%(version)s.tar.gz', @@ -916,7 +914,7 @@ exts_list = [ ('List::AllUtils', '0.19', { 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['b7c4bf80090b281c4a1560c76a1a819094c3a1294302f77afb8c60ca4862ecf9'], + 'checksums': ['30a8146ab21a7787b8c56d5829cf9a7f2b15276d3b3fca07336ac38d3002ffbc'], }), ('UNIVERSAL::moniker', '0.08', { 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', @@ -926,7 +924,7 @@ exts_list = [ ('Exception::Class', '1.45', { 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['33f3fbf8b138d3b04ea4ec0ba83fb0df6ba898806bcf4ef393d4cafc1a23ee0d'], + 'checksums': ['5482a77ef027ca1f9f39e1f48c558356e954936fc8fbbdee6c811c512701b249'], }), ('File::CheckTree', '4.42', { 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', @@ -951,7 +949,7 @@ exts_list = [ ('HTTP::Request', '6.33', { 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['f4417970679e08f6deb0609009aa9515dee0c8d91dbadd6b86a26e2b8e0d6341'], + 'checksums': ['23b967f71b852cb209ec92a1af6bac89a141dff1650d69824d29a345c1eceef7'], }), ('XML::Twig', '3.52', { 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', @@ -1116,7 +1114,7 @@ exts_list = [ ('Data::OptList', '0.112', { 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['366117cb2966473f2559f2f4575ff6ae69e84c69a0f30a0773e1b51a457ef5c3'], + 'checksums': ['62c60ccaae88d5339ae36bcc8940b03388cf84adbf27828b1f8b300307103bab'], }), ('Package::Constants', '0.06', { 'source_tmpl': 'Package-Constants-%(version)s.tar.gz', @@ -1161,7 +1159,7 @@ exts_list = [ ('PDF::API2', '2.041', { 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], - 'checksums': ['4925f109f47bb6bdd6deb8cf37db4f2e39aa6cdc51991d1d8008b4312ed1935a'], + 'checksums': ['cfa47682471ed4e0c56be92aac2864ef26e6c521723c34e29706d875b6e58537'], }), ('Devel::CheckLib', '1.14', { 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', @@ -1171,7 +1169,7 @@ exts_list = [ ('SVG', '2.86', { 'source_tmpl': 'SVG-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], - 'checksums': ['159ec81f3236175957c9a4e911cb0e3715dc5b658144c8a5418b772768a1477c'], + 'checksums': ['72c6eb6f86bb2c330280f9f3d342bb2673ad5da22d1f44fba3e04cfb5d30a67b'], }), ('Statistics::Basic', '1.6611', { 'source_tmpl': 'Statistics-Basic-%(version)s.tar.gz', @@ -1216,7 +1214,7 @@ exts_list = [ ('Graph', '0.9722', { 'source_tmpl': 'Graph-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], - 'checksums': ['70ed685529a7baa2a4731553f1a959b5536e337cdf1f4241f5fefbff705ca3f3'], + 'checksums': ['c113633833f3a1bef8fa8eb96680be36d00e41ef404bddd7fc0bb98703e28d4d'], }), ('Graph::ReadWrite', '2.10', { 'source_tmpl': 'Graph-ReadWrite-%(version)s.tar.gz', @@ -1231,7 +1229,7 @@ exts_list = [ ('Devel::OverloadInfo', '0.007', { 'source_tmpl': 'Devel-OverloadInfo-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], - 'checksums': ['8bfde2ffa47c9946f8adc8cfc445c2f97b8d1cdd678111bee9f444e82f7aa6e7'], + 'checksums': ['21a184163b90f91f06ffc7f5de0b968356546ae9b400a9d75c573c958c246222'], }), ('Sub::Identify', '0.14', { 'source_tmpl': 'Sub-Identify-%(version)s.tar.gz', @@ -1256,7 +1254,7 @@ exts_list = [ ('App::Cmd', '0.334', { 'source_tmpl': 'App-Cmd-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['3ba1aa7890f2354501e4977cc5367cd6c462ef7b702d381d9923f7df6ec258f6'], + 'checksums': ['22e31e0f8f7b8c4303ad62b0ab1f941fcf598ca6e3a146b7e482e5870d6d58d3'], }), ('Path::Tiny', '0.118', { 'source_tmpl': 'Path-Tiny-%(version)s.tar.gz', @@ -1331,7 +1329,7 @@ exts_list = [ ('Log::Dispatchouli', '2.023', { 'source_tmpl': 'Log-Dispatchouli-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['2a2a4176adafb85a1eb9c9dc389052919e8c2c9df99aaba538c06b8da964a5df'], + 'checksums': ['c4ac41b9729b71439682b34dd2772b040b5adb9e1a611d30322c01f4608e0cf2'], }), ('Data::Section', '0.200007', { 'source_tmpl': 'Data-Section-%(version)s.tar.gz', @@ -1340,13 +1338,13 @@ exts_list = [ }), ('Software::License', '0.104001', { 'source_tmpl': 'Software-License-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['eb45ea602d75006683789fbba57a01c0a1f7037371de95ea54b91577535d1789'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['51386fdee57de4d38187ad3ffd7c5482431123bbf883f7abc28e0929fb46c387'], }), ('MooseX::SetOnce', '0.201', { 'source_tmpl': 'MooseX-SetOnce-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['cbed06b7fcd353f0d99bf80a87c1c0b581160697231b3ad9a608da231ba2b659'], + 'checksums': ['f55734d9823cab6c77cace28406e6deafa16071d2f574d5c394060def1c07c87'], }), ('Term::Encoding', '0.03', { 'source_tmpl': 'Term-Encoding-%(version)s.tar.gz', @@ -1361,7 +1359,7 @@ exts_list = [ ('Throwable', '1.000', { 'source_tmpl': 'Throwable-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['9987d0deb5bddd352a6330cefbe932f882e36dd8c8a4564bcfd372dc396b8fa0'], + 'checksums': ['023aac67baad5b7bcdc08dc858ea5e6a8ddb0e291d15dd6d24818cdd702d318f'], }), ('Sub::Quote', '2.006006', { 'source_tmpl': 'Sub-Quote-%(version)s.tar.gz', @@ -1396,12 +1394,12 @@ exts_list = [ ('Mixin::Linewise::Readers', '0.110', { 'source_tmpl': 'Mixin-Linewise-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['7df20678474c0973930a472b0c55e3f8e85b7790b68ab18ef618f9c453c8aef2'], + 'checksums': ['a7f120b7aa82dfb1a5ad1aa11abd33232b26a2b09c654e649e97a3c2128b1d8b'], }), ('Config::INI', '0.027', { 'source_tmpl': 'Config-INI-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['628bf76d5b91f89dde22d4813ec033026ebf71b772bb61ccda909da00c869732'], + 'checksums': ['12eb8b7d43ab13db443b3c7110c8b70a264c19f78ff06ab8823e11f86a4f330e'], }), ('String::Truncate', '1.100602', { 'source_tmpl': 'String-Truncate-%(version)s.tar.gz', @@ -1411,7 +1409,7 @@ exts_list = [ ('Pod::Eventual', '0.094002', { 'source_tmpl': 'Pod-Eventual-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['be9fb8910b108e5d1a66f002b659ad22576e88d779b703dff9d15122c3f80834'], + 'checksums': ['80194f3fe66dd8bd91282eb3610f5c7cac8dc5a0cd51a81c4d56a9ec18fea2bc'], }), ('Pod::Elemental', '0.103005', { 'source_tmpl': 'Pod-Elemental-%(version)s.tar.gz', @@ -1421,12 +1419,12 @@ exts_list = [ ('Pod::Weaver', '4.018', { 'source_tmpl': 'Pod-Weaver-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['ec6dc6fe1df3d61f14242323092ad7c5542587f30365acaedcd8cca62de442a4'], + 'checksums': ['8ca92ec948974023194197c058e33a98ad00a88561f5bf7fe672329227a910b7'], }), ('Dist::Zilla', '6.024', { 'source_tmpl': 'Dist-Zilla-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['5c8d30ce33ac8b5e937e6f83fcfa779e7225ca149951ee5c9bc2c3af3c2b6fee'], + 'checksums': ['f063a6839c145a3aafcf0d8d9ec5519601d0c0f61d0174aed424297f65b928a8'], }), ('XML::RegExp', '0.04', { 'source_tmpl': 'XML-RegExp-%(version)s.tar.gz', @@ -1440,8 +1438,8 @@ exts_list = [ }), ('Data::Dump', '1.25', { 'source_tmpl': 'Data-Dump-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], - 'checksums': ['af53b05ef1387b4cab4427e6789179283e4f0da8cf036e8db516ddb344512b65'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': ['a4aa6e0ddbf39d5ad49bddfe0f89d9da864e3bc00f627125d1bc580472f53fbd'], }), ('File::Next', '1.18', { 'source_tmpl': 'File-Next-%(version)s.tar.gz', @@ -1491,7 +1489,7 @@ exts_list = [ ('Term::ReadLine::Gnu', '1.42', { 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], - 'checksums': ['3bd31a998a9c14748ee553aed3e6b888ec47ff57c07fc5beafb04a38a72f0078'], + 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], }), ('ExtUtils::MakeMaker', '7.62', { 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', @@ -1506,7 +1504,7 @@ exts_list = [ ('Module::CoreList', '5.20210723', { 'source_tmpl': 'Module-CoreList-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], - 'checksums': ['0d4e2d6c59cf80e9163227364cd3ab14050d232093144f6226e961999cf0144b'], + 'checksums': ['509ec984dca1325ef73b2676624f785f56c9ec1d4f1dfdd8c02aa75d37a48e39'], }), ('Module::Metadata', '1.000037', { 'source_tmpl': 'Module-Metadata-%(version)s.tar.gz', @@ -1566,12 +1564,12 @@ exts_list = [ ('Pod::Simple', '3.43', { 'source_tmpl': 'Pod-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KH/KHW'], - 'checksums': ['a9fceb2e0318e3786525e6bf205e3e143f0cf3622740819cab5f058e657e8ac5'], + 'checksums': ['65abe3f5363fa4cdc108f5ad9ce5ce91e7a39186a1b297bb7a06fa1b0f45d377'], }), ('Socket', '2.032', { 'source_tmpl': 'Socket-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], - 'checksums': ['c7bc60af60c1cce36fb83866ac8108a3d937c50e62493240d858df0eb6f4bcd2'], + 'checksums': ['20ecb6ad469f4a13c5c7a891abfa12a3cecfdeccc7140ad57b05be12815dd517'], }), ('Time::Local', '1.30', { 'source_tmpl': 'Time-Local-%(version)s.tar.gz', @@ -1601,7 +1599,7 @@ exts_list = [ ('Test::More', '1.302186', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], - 'checksums': ['9a03bda5ec420aea9692b650437f4d5b574fa505fdd7ff60cdb5f3ec034106ff'], + 'checksums': ['2895c8da7c3fe632e5714c7cc548705202cdbf3afcbc0e929bc5e6a5172265d4'], }), ('Test::RequiresInternet', '0.05', { 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', @@ -1646,7 +1644,7 @@ exts_list = [ ('Encode', '3.11', { 'source_tmpl': 'Encode-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], - 'checksums': ['ed063d01d01a140a3a3ec0aeba2f2b4849a35c18ca96ac231a5d7c7d54d17b5b'], + 'checksums': ['47e05cefb550ef039808564e6181a22dbf2e50d0475f8eb9de63f9d9f4912e7c'], }), ('constant', '1.33', { 'source_tmpl': 'constant-%(version)s.tar.gz', @@ -1655,8 +1653,8 @@ exts_list = [ }), ('Data::Dumper', '2.183', { 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], - 'checksums': ['697608b39330988e519131be667ff47168aaaaf99f06bd2095d5b46ad05d76fa'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['e42736890b7dae1b37818d9c5efa1f1fdc52dec04f446a33a4819bf1d4ab5ad3'], }), ('Cwd', '3.75', { 'source_tmpl': 'PathTools-%(version)s.tar.gz', @@ -1671,7 +1669,7 @@ exts_list = [ ('ExtUtils::CppGuess', '0.23', { 'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], - 'checksums': ['ff629178321a1e591b83f809712593eae4408a413aa448654bce59b156f24153'], + 'checksums': ['f96c48984eb6d8efb7d933b34f361d0c8b38335e3e5382e9aeccc0aa519a002c'], }), ('XSLoader', '0.24', { 'source_tmpl': 'XSLoader-%(version)s.tar.gz', From bc101e490ba0ad840db2adadfb1611ec6866d5b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 3 Aug 2021 23:34:49 +0200 Subject: [PATCH 0607/9987] Include modextrapaths --- easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index d630f424b0c..ee40720ad7f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1768,4 +1768,8 @@ exts_list = [ }), ] +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + moduleclass = 'lang' From a37e88eb51a9d8aa9906872aa1c1e796853be10f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 3 Aug 2021 23:50:53 +0200 Subject: [PATCH 0608/9987] adding easyconfigs: giflib-5.2.1-GCCcore-11.2.0.eb, JasPer-2.0.33-GCCcore-11.2.0.eb, LibTIFF-4.3.0-GCCcore-11.2.0.eb, libjpeg-turbo-2.0.6-GCCcore-11.2.0.eb, libpng-1.6.37-GCCcore-11.2.0.eb, libwebp-1.2.0-GCCcore-11.2.0.eb, NASM-2.15.05-GCCcore-11.2.0.eb, OpenEXR-3.1.1-GCCcore-11.2.0.eb, OpenJPEG-2.4.0-GCCcore-11.2.0.eb, x264-20210613-GCCcore-11.2.0.eb, x265-3.5-GCCcore-11.2.0.eb, Yasm-1.3.0-GCCcore-11.2.0.eb --- .../g/giflib/giflib-5.2.1-GCCcore-11.2.0.eb | 28 +++++++++++ .../j/JasPer/JasPer-2.0.33-GCCcore-11.2.0.eb | 36 ++++++++++++++ .../l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb | 32 +++++++++++++ .../libjpeg-turbo-2.0.6-GCCcore-11.2.0.eb | 42 ++++++++++++++++ .../l/libpng/libpng-1.6.37-GCCcore-11.2.0.eb | 31 ++++++++++++ .../l/libwebp/libwebp-1.2.0-GCCcore-11.2.0.eb | 36 ++++++++++++++ .../n/NASM/NASM-2.15.05-GCCcore-11.2.0.eb | 25 ++++++++++ .../o/OpenEXR/OpenEXR-3.1.1-GCCcore-11.2.0.eb | 31 ++++++++++++ .../OpenJPEG/OpenJPEG-2.4.0-GCCcore-11.2.0.eb | 48 +++++++++++++++++++ .../x/x264/x264-20210613-GCCcore-11.2.0.eb | 34 +++++++++++++ .../x/x265/x265-3.5-GCCcore-11.2.0.eb | 33 +++++++++++++ .../y/Yasm/Yasm-1.3.0-GCCcore-11.2.0.eb | 23 +++++++++ 12 files changed, 399 insertions(+) create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.33-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.2.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..340aaeaf312 --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.1' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.33-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.33-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a3a9a8e799c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.33-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.33' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['38b8f74565ee9e7fec44657e69adb5c9b2a966ca5947ced5717cde18a7d2eca6'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d6c6f6e6216 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.3.0' + +homepage = 'https://libtiff.maptools.org/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.osgeo.org/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['0e46e5acb087ce7d1ac53cf4f56a09b221537fc86dfc5daaad1c2e89e1b37ac8'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6') +] + +configopts = " --enable-ld-version-script " + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..35de4049393 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.6-GCCcore-11.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.0.6' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d74b92ac33b0e3657123ddcf6728788c90dc84dcb6a52013d758af3c4af481bb'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('binutils', '2.37'), +] + +dependencies = [ + ('NASM', '2.15.05'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..87ca63dc4d1 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.37' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['daeb2620d829575513e35fecc83f0d3791a620b9b93d800b763542ece9390fb4'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('zlib', '1.2.11')] + +local_majminver = ''.join(version.split('.')[:2]) + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..89ff37dc673 --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.0-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.2.0' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2fc8bbde9f97f2ab403c0224fb9ca62b2e6852cbc519e91ceaa7c153ffd88a0c'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('giflib', '5.2.1'), +] + +configopts = "--enable-libwebpmux" + +sanity_check_paths = { + 'files': ['include/webp/%s' % f for f in ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h']] + + ['lib/lib%s.a' % l for l in ['webp', 'webpdemux', 'webpmux']] + + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['webp', 'webpdemux', 'webpmux']], + 'dirs': ['lib/'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..31ceb59091f --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.15.05' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['3c4b8339e5ab54b1bcb2316101f8985a5da50a3f9e504d43fa6f35668bee2fd0'] + +builddependencies = [ + ('binutils', '2.37'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6e9e8261d52 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.1-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.1' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/openexr/openexr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['045254e201c0f87d1d1a4b2b5815c4ae54845af2e6ec0ab88e979b5fdb30a86e'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in + ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil']] + + ['bin/exr%s' % x for x in + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr']], + 'dirs': ['include/OpenEXR', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..3646fa1dbc1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-11.2.0.eb @@ -0,0 +1,48 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchenson Cancer Research Center Seattle WA +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.4.0' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/openjpeg/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8702ba68b442657f11aaeb2b338443ca8d5fb95b0d845757968a7be31ef7f16d'] + +separate_build_dir = True + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1') +] + +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0') +] + +sanity_check_paths = { + 'files': ['bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..69e6f112ded --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +local_commit = '5db6aa6c' +version = '20210613' + +homepage = 'https://www.videolan.org/developers/x264.html' + +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://code.videolan.org/videolan/x264/-/archive/%s/' % local_commit] +sources = [{'download_filename': 'x264-%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['88b8f738e420bcb1dcc6ef27e13d10261dbcddd047712a31867a946a265eec4d'] + +builddependencies = [ + ('binutils', '2.37'), + ('NASM', '2.15.05'), +] + +configopts = " --enable-shared --enable-static" + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', + 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8b337e94692 --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.5' + +homepage = 'https://x265.org/' + +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://bitbucket.org/multicoreware/x265_git/downloads/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['e70a3335cacacbba0b3a20ec6fecd6783932288ebc8163ad74bcc9606477cae8'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Yasm', '1.3.0'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4d56392bf0c --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'https://www.tortall.net/projects/yasm/' + +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.tortall.net/projects/yasm/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' From 6e008eabee07f4ad0335a13c8e1bb00674f2bdb0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 3 Aug 2021 23:56:24 +0200 Subject: [PATCH 0609/9987] update easyconfig x264-20210613-GCCcore-11.2.0.eb: checksum --- easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb index 69e6f112ded..c51d6bdacf0 100644 --- a/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://code.videolan.org/videolan/x264/-/archive/%s/' % local_commit] sources = [{'download_filename': 'x264-%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['88b8f738e420bcb1dcc6ef27e13d10261dbcddd047712a31867a946a265eec4d'] +checksums = ['9b5543a5f114f4c6905a2319ea4c2063d6ebd2db209b41642086df3c1f7b6f50'] builddependencies = [ ('binutils', '2.37'), From d8992ded7a9b7e226a4d964520db2b7caaf0c4c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 4 Aug 2021 00:04:14 +0200 Subject: [PATCH 0610/9987] Avoid using perlver --- easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index ee40720ad7f..6def18ddee8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1768,8 +1768,9 @@ exts_list = [ }), ] +# Can't use perlver because the template isn't resolved while we are building extensions modextrapaths = { - 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', + 'PERL5LIB': 'lib/perl5/site_perl/%s/' % version, } moduleclass = 'lang' From f042437b48d9b595c2d680d98b96a26fe7366fe0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 4 Aug 2021 00:07:34 +0200 Subject: [PATCH 0611/9987] adding easyconfigs: libtool-2.4.6-GCCcore-11.2.0.eb, Autoconf-2.71-GCCcore-11.2.0.eb, Automake-1.16.4-GCCcore-11.2.0.eb, Autotools-20210726-GCCcore-11.2.0.eb --- .../Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ .../Automake-1.16.4-GCCcore-11.2.0.eb | 32 +++++++++++++++ .../Autotools-20210726-GCCcore-11.2.0.eb | 24 +++++++++++ .../l/libtool/libtool-2.4.6-GCCcore-11.2.0.eb | 32 +++++++++++++++ 4 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.4-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20210726-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a6216388c38 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.71' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] + +builddependencies = [ + ('binutils', '2.37'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl.bare', '5.34.0'), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a47580d9afd --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.4-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.4' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8a0f0be7aaae2efa3a68482af28e5872d8830b9813a6a932a2571eac63ca1794'] + +builddependencies = [ + ('binutils', '2.37'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.34.0'), +] + +dependencies = [ + ('Autoconf', '2.71'), +] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20210726-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20210726-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..121721f98d8 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20210726-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20210726' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Autoconf', '2.71'), # 20210128 + ('Automake', '1.16.4'), # 20210726 + ('libtool', '2.4.6'), # 20150215 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4869984ed3b --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' From 37caf8310829890ee1095072e7d1d819e1fc2d05 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 00:15:34 +0200 Subject: [PATCH 0612/9987] adding easyconfigs: fontconfig-2.13.94-GCCcore-11.2.0.eb, freetype-2.11.0-GCCcore-11.2.0.eb, gperf-3.1-GCCcore-11.2.0.eb, util-linux-2.37-GCCcore-11.2.0.eb --- .../fontconfig-2.13.94-GCCcore-11.2.0.eb | 39 ++++++++++++++++++ .../freetype-2.11.0-GCCcore-11.2.0.eb | 40 ++++++++++++++++++ .../g/gperf/gperf-3.1-GCCcore-11.2.0.eb | 31 ++++++++++++++ .../util-linux-2.37-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ 4 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.94-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.11.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.37-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.94-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.94-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0a0da831671 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.94-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.13.94' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['246d1640a7e54fba697b28e4445f4d9eb63dda1b511d19986249368ee7191882'] + +builddependencies = [ + ('binutils', '2.37'), + ('gperf', '3.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('expat', '2.4.1'), + ('freetype', '2.11.0'), + ('util-linux', '2.37'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.11.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.11.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..3f312567b39 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.11.0-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +name = 'freetype' +version = '2.11.0' + +homepage = 'https://www.freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + GNU_SAVANNAH_SOURCE, + SOURCEFORGE_SOURCE, +] +sources = [SOURCE_TAR_GZ] +checksums = ['a45c6b403413abd5706f3582f04c8339d26397c4304b78fa552f2215df64101f'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0f33857f082 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'https://www.gnu.org/software/gperf/' +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.37'), +] + + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.37-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.37-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0d322000ab6 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.37-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.37' + +homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['faa8b46d080faa6f32c57da81eda871e38e1e27ba4e9b61cb2589334671aba50'] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' From a619d58825b59ba2a471e366d6de5244e08e3fae Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 00:24:53 +0200 Subject: [PATCH 0613/9987] update easyconfig: OpenJPEG-2.4.0-GCCcore-11.2.0.eb --- .../easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-11.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-11.2.0.eb index 3646fa1dbc1..ad834747cdd 100644 --- a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.4.0-GCCcore-11.2.0.eb @@ -1,8 +1,3 @@ -# easybuild easyconfig -# -# John Dey jfdey@fredhutch.org -# -# Fred Hutchenson Cancer Research Center Seattle WA easyblock = 'CMakeMake' name = 'OpenJPEG' From e76ca13732a985928101b3d1e1b2ce7ac7f1a0cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 4 Aug 2021 00:35:46 +0200 Subject: [PATCH 0614/9987] Add missing zlib dependency to libarchive --- .../l/libarchive/libarchive-3.4.0-GCCcore-8.2.0.eb | 4 ++++ .../l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb | 4 ++++ .../l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb | 4 ++++ .../l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb | 4 ++++ .../l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb | 4 ++++ .../l/libarchive/libarchive-3.5.1-GCCcore-8.3.0.eb | 4 ++++ 6 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.0-GCCcore-8.2.0.eb index a670e2affb6..747cbbb1639 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.0-GCCcore-8.2.0.eb @@ -19,6 +19,10 @@ checksums = ['8643d50ed40c759f5412a3af4e353cffbce4fdf3b5cf321cb72cacf06b2d825e'] builddependencies = [ ('binutils', '2.31.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), ('XZ', '5.2.4'), ] diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb index 5a9350da514..c60d93c060f 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb @@ -19,6 +19,10 @@ checksums = ['b60d58d12632ecf1e8fad7316dc82c6b9738a35625746b47ecdcaf4aed176176'] builddependencies = [ ('binutils', '2.34'), +] + +dependencies = [ + ('zlib', '1.2.11'), ('XZ', '5.2.5'), ] diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb index 8c373a125e9..7214c3ae947 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb @@ -19,6 +19,10 @@ checksums = ['ee1e749213c108cb60d53147f18c31a73d6717d7e3d2481c157e1b34c881ea39'] builddependencies = [ ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), ('XZ', '5.2.5'), ] diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb index f366494c3d8..9f8743b3091 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb @@ -20,6 +20,10 @@ checksums = ['9015d109ec00bb9ae1a384b172bf2fc1dff41e2c66e5a9eeddf933af9db37f5a'] builddependencies = [ ('binutils', '2.36.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), ('XZ', '5.2.5'), ('OpenSSL', '1.1', '', True), ] diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb index 692cfb34323..a5bba4c08fc 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb @@ -17,6 +17,10 @@ checksums = ['9015d109ec00bb9ae1a384b172bf2fc1dff41e2c66e5a9eeddf933af9db37f5a'] builddependencies = [ ('binutils', '2.37'), +] + +dependencies = [ + ('zlib', '1.2.11'), ('XZ', '5.2.5'), ('OpenSSL', '1.1', '', True), ] diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-8.3.0.eb index 85bd90476f0..e0c3efaa076 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-8.3.0.eb @@ -22,6 +22,10 @@ osdependencies = [OS_PKG_OPENSSL_DEV] builddependencies = [ ('binutils', '2.32'), +] + +dependencies = [ + ('zlib', '1.2.11'), ('XZ', '5.2.4'), ] From 7ec2ef1279752b6d2eaf53b32313e6c318ee4a11 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 00:40:33 +0200 Subject: [PATCH 0615/9987] adding easyconfigs: OpenBLAS-0.3.17-GCC-11.2.0.eb --- .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb new file mode 100644 index 00000000000..d4c2a7327e9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +name = 'OpenBLAS' +version = '0.3.17' + +homepage = 'http://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), +] +checksums = [ + 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f', # v0.3.17.tar.gz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From 187ce44b781fe875a3584606d328e48c79358467 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 4 Aug 2021 00:43:56 +0200 Subject: [PATCH 0616/9987] Fix pkgconfig version in patch for bzip 1.0.8 --- .../b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb | 4 +-- .../b/bzip2/bzip2-1.0.8-GCCcore-10.3.0.eb | 4 +-- .../b/bzip2/bzip2-1.0.8-GCCcore-11.2.0.eb | 28 ++++++++++++++++ .../b/bzip2/bzip2-1.0.8-GCCcore-8.3.0.eb | 4 +-- .../b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb | 4 +-- .../b/bzip2/bzip2-1.0.8-pkgconfig.patch | 33 +++++++++++++++++++ 6 files changed, 69 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-pkgconfig.patch diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb index ec886cad08b..4e0873a1c5d 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb @@ -14,10 +14,10 @@ toolchainopts = {'pic': True} source_urls = ['https://sourceware.org/pub/%(name)s/'] sources = [SOURCE_TAR_GZ] -patches = ['bzip2-1.0.6-pkgconfig.patch'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] checksums = [ 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz - '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.3.0.eb index 663f7b87fda..70db2ca4a15 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.3.0.eb @@ -14,10 +14,10 @@ toolchainopts = {'pic': True} source_urls = ['https://sourceware.org/pub/%(name)s/'] sources = [SOURCE_TAR_GZ] -patches = ['bzip2-1.0.6-pkgconfig.patch'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] checksums = [ 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz - '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d0f221c2d33 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.37'), +] + + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-8.3.0.eb index 268d5bc0ef1..3768ad723a1 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-8.3.0.eb @@ -15,10 +15,10 @@ toolchainopts = {'pic': True} source_urls = ['https://sourceware.org/pub/bzip2/'] sources = [SOURCE_TAR_GZ] -patches = ['bzip2-1.0.6-pkgconfig.patch'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] checksums = [ 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz - '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch ] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb index 188fa77e175..b39d3a5e236 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-9.3.0.eb @@ -14,10 +14,10 @@ toolchainopts = {'pic': True} source_urls = ['https://sourceware.org/pub/%(name)s/'] sources = [SOURCE_TAR_GZ] -patches = ['bzip2-1.0.6-pkgconfig.patch'] +patches = ['bzip2-%(version)s-pkgconfig.patch'] checksums = [ 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz - '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-pkgconfig.patch b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-pkgconfig.patch new file mode 100644 index 00000000000..ab8d7041506 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-pkgconfig.patch @@ -0,0 +1,33 @@ +#- Adds a pkgconfig/bzip2.pc file +# +# author: Jiri Furst +# inspired by OpenSUSE patch by Stanislav Brabec , see +# http://ftp.suse.com/pub/people/sbrabec/bzip2/ +diff -Nau bzip2-1.0.8.orig/bzip2.pc.in bzip2-1.0.6/bzip2.pc.in +--- bzip2-1.0.8.orig/bzip2.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ bzip2-1.0.8/bzip2.pc.in 2019-05-01 11:47:29.795517973 +0200 +@@ -0,0 +1,11 @@ ++exec_prefix=${prefix} ++bindir=${exec_prefix}/bin ++libdir=${exec_prefix}/lib ++includedir=${prefix}/include ++ ++Name: bzip2 ++Description: Lossless, block-sorting data compression ++Version: 1.0.8 ++Libs: -L${libdir} -lbz2 ++Cflags: -I${includedir} ++ +diff -Nau bzip2-1.0.8.orig/Makefile bzip2-1.0.6/Makefile +--- bzip2-1.0.8.orig/Makefile 2019-05-01 11:28:04.788206974 +0200 ++++ bzip2-1.0.8/Makefile 2019-05-01 11:46:20.911324226 +0200 +@@ -107,6 +107,9 @@ + echo ".so man1/bzgrep.1" > $(PREFIX)/man/man1/bzfgrep.1 + echo ".so man1/bzmore.1" > $(PREFIX)/man/man1/bzless.1 + echo ".so man1/bzdiff.1" > $(PREFIX)/man/man1/bzcmp.1 ++ if ( test ! -d $(PREFIX)/lib/pkgconfig ) ; then mkdir -p $(PREFIX)/lib/pkgconfig ; fi ++ echo "prefix=$(PREFIX)" > $(PREFIX)/lib/pkgconfig/bzip2.pc ++ cat bzip2.pc.in >> $(PREFIX)/lib/pkgconfig/bzip2.pc + + clean: + rm -f *.o libbz2.a bzip2 bzip2recover \ From d9ebe1d92b9b2450f000c838ae34ade040555dd8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 4 Aug 2021 03:05:07 +0200 Subject: [PATCH 0617/9987] adding easyconfigs: CUDAcore-11.4.1.eb --- .../easyconfigs/c/CUDAcore/CUDAcore-11.4.1.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.1.eb diff --git a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.1.eb b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.1.eb new file mode 100644 index 00000000000..d615b89734c --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.1.eb @@ -0,0 +1,28 @@ +easyblock = 'EB_CUDA' + +name = 'CUDAcore' +version = '11.4.1' +local_nv_version = '470.57.02' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + 'dd6c339a719989d2518f5d54eeac1ed707d0673f8664ba0c4d4b2af7c3ba0005', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'dd92ca04f76ad938da3480e2901c0e52dbff6028ada63c09071ed9e3055dc361', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'i8efa725a41dfd3c0c0f453c2dd535d149154102bf2b791718859417b4f84f922', + } +] + +moduleclass = 'system' From fef96d9e341c8b88c489fb8698f23c7bb0d3f784 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 4 Aug 2021 07:11:23 +0200 Subject: [PATCH 0618/9987] adding easyconfigs: bioawk-1.0-GCC-10.3.0.eb --- .../b/bioawk/bioawk-1.0-GCC-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/bioawk/bioawk-1.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/bioawk/bioawk-1.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/bioawk/bioawk-1.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..f4892ce9594 --- /dev/null +++ b/easybuild/easyconfigs/b/bioawk/bioawk-1.0-GCC-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'bioawk' +version = '1.0' + +homepage = 'https://github.com/lh3/bioawk' +description = """ Bioawk is an extension to Brian Kernighan's awk, + adding the support of several common biological data formats, + including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. """ + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5cbef3f39b085daba45510ff450afcf943cfdfdd483a546c8a509d3075ff51b5'] + +builddependencies = [('Bison', '3.7.6')] +dependencies = [('zlib', '1.2.11')] + +parallel = 1 + +files_to_copy = [([name], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 377e1528797eaaf85fc074c9f4705695a2732c67 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Wed, 4 Aug 2021 15:30:31 +1000 Subject: [PATCH 0619/9987] Create CharLS-2.2.0-GCCcore-10.2.0.eb New minor version, new GCCcore --- .../c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..afad4ef3564 --- /dev/null +++ b/easybuild/easyconfigs/c/CharLS/CharLS-2.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CharLS' +version = '2.2.0' + +homepage = 'https://github.com/team-charls/charls' +description = """CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image +compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 +compression ratios.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/team-charls/charls/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e1d7dd70cd9d6d46de5abbf22278dc8169707995a21e8bf705f5746c04c76891'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libcharls.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 36c140ceb37a9d3b4b6173c63b2772fa4c755612 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 4 Aug 2021 08:00:02 +0200 Subject: [PATCH 0620/9987] adding easyconfigs: ClustalW2-2.1-GCC-10.3.0.eb --- .../c/ClustalW2/ClustalW2-2.1-GCC-10.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-10.3.0.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..0d1f3dbfbda --- /dev/null +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'ClustalW2' +version = '2.1' + +homepage = 'https://www.ebi.ac.uk/Tools/msa/clustalw2/' +description = """ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.clustal.org/download/%(version)s'] +sources = ['clustalw-%(version)s.tar.gz'] +checksums = ['e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' From d07d9ac634d9596e1a64471ece2f698d4112002c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 11:20:26 +0200 Subject: [PATCH 0621/9987] update easyconfig OpenBLAS-0.3.17-GCC-11.2.0.eb: disable vectorize --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index d4c2a7327e9..a024a86ae82 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -5,6 +5,7 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble From 537ed62bb7474920ec5b5e8bb52a192138a8a92b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 4 Aug 2021 11:35:49 +0200 Subject: [PATCH 0622/9987] adding easyconfigs: coverage-5.5-GCCcore-10.2.0.eb --- .../c/coverage/coverage-5.5-GCCcore-10.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b619a1c1c2c --- /dev/null +++ b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'coverage' +version = '5.5' + +homepage = 'https://coverage.readthedocs.io' +description = """ Coverage.py is a tool for measuring code coverage of Python programs. + It monitors your program, noting which parts of the code have been executed, + then analyzes the source to identify code that could have been executed but was not. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ebe78fe9a0e874362175b02371bdfbee64d8edc42a044253ddf4ee7d3c15212c'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True + +sanity_check_paths = { + 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'tools' From def9e7a8e047e0107c385559cf8a4a5ef93f5405 Mon Sep 17 00:00:00 2001 From: Tom Strempel <37880275+tstrempel@users.noreply.github.com> Date: Wed, 4 Aug 2021 12:52:09 +0200 Subject: [PATCH 0623/9987] Delete MaxBin-2.2.7_fix_perl_shebang.patch --- .../m/MaxBin/MaxBin-2.2.7_fix_perl_shebang.patch | 8 -------- 1 file changed, 8 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7_fix_perl_shebang.patch diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7_fix_perl_shebang.patch b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7_fix_perl_shebang.patch deleted file mode 100644 index 508c60e0313..00000000000 --- a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7_fix_perl_shebang.patch +++ /dev/null @@ -1,8 +0,0 @@ ---- run_MaxBin.pl_orig 2021-08-02 10:08:36.990459000 +0200 -+++ run_MaxBin.pl 2021-08-02 10:09:31.675685960 +0200 -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - use strict; - use Cwd; - use LWP::Simple; From e770691eecca2df7b10dd39e1b0d65bb2eaf6a20 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Wed, 4 Aug 2021 12:53:17 +0200 Subject: [PATCH 0624/9987] use fix_perl_shebang for function --- .../easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb index 523aa09a5ec..535fd62d214 100644 --- a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2020b.eb @@ -12,11 +12,7 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['MaxBin-2.2.7_fix_perl_shebang.patch'] -checksums = [ - 'cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e', # src - 'f966952e7bb910b24687001c89dd1667318346911db964438b8e726ca3415913', # MaxBin-2.2.7_fix_perl_shebang.patch -] +checksums = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e'] builddependencies = [('binutils', '2.35')] @@ -32,6 +28,8 @@ prebuildopts = "cd src && " files_to_copy = ['*'] +fix_perl_shebang_for = ['run_MaxBin.pl'] + sanity_check_paths = { 'files': ['run_MaxBin.pl', 'src/MaxBin'], 'dirs': [], From 8edfb420db7435cb9f7aa3986c7fd39396c88ec0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 13:23:32 +0200 Subject: [PATCH 0625/9987] update easyconfig OpenBLAS-0.3.17-GCC-11.2.0.eb: add a comment to explain why we disable vectorize --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index a024a86ae82..e68ba4eae8f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -5,6 +5,8 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} +# need to build with -fno-tree-vectorize due to precision errors with GCC 11.2.0 +# cfr. https://github.com/easybuilders/easybuild-easyconfigs/pull/13580 toolchainopts = {'vectorize': False} source_urls = [ From d9e5d04d58a20f2f22560069b8917c56fd7518ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Aug 2021 14:27:40 +0200 Subject: [PATCH 0626/9987] remove commented out pkgconfig build dep in h5py easyconfig using Python 2.7.18 --- .../easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb index 461b8f274f1..0f90a6b7b59 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-intel-2020a-Python-2.7.18.eb @@ -19,8 +19,6 @@ checksums = [ '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch ] -#builddependencies = [('pkgconfig', '1.5.1', versionsuffix)] - dependencies = [ ('Python', '2.7.18'), ('SciPy-bundle', '2020.03', versionsuffix), From 01583cdfbc2c17ca83b6830db13ad92dc1abe20a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Aug 2021 14:28:01 +0200 Subject: [PATCH 0627/9987] define $MPLBACKEND rather than using $MATPLOTLIBRC in horton easyconfig --- .../h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb index 523a43d128f..26358925ae1 100644 --- a/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb +++ b/easybuild/easyconfigs/h/horton/horton-2.1.1-intel-2020a-Python-2.7.18.eb @@ -30,8 +30,7 @@ local_horton_prebuildopts = ' '.join([ # Avoid need for X11 in tests by specifying "backend: agg" in matplotlibrc local_horton_runtest = ' '.join([ - 'export MATPLOTLIBRC=$PWD;', - 'echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc;', + 'export MPLBACKEND=agg;', '%s python setup.py build_ext -i; ' % local_horton_prebuildopts, 'nosetests -v', ]) From e6556f851d64ff577ee43fadd3b68bdff30c61c3 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 21:38:38 +0200 Subject: [PATCH 0628/9987] adding easyconfigs: GLPK-5.0-GCCcore-11.2.0.eb, GMP-6.2.1-GCCcore-11.2.0.eb, ISL-0.24-GCCcore-11.2.0.eb, MPC-1.2.1-GCCcore-11.2.0.eb, MPFR-4.1.0-GCCcore-11.2.0.eb, nettle-3.7.3-GCCcore-11.2.0.eb --- .../g/GLPK/GLPK-5.0-GCCcore-11.2.0.eb | 31 ++++++++++++++ .../g/GMP/GMP-6.2.1-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ .../i/ISL/ISL-0.24-GCCcore-11.2.0.eb | 23 +++++++++++ .../m/MPC/MPC-1.2.1-GCCcore-11.2.0.eb | 35 ++++++++++++++++ .../m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb | 39 ++++++++++++++++++ .../n/nettle/nettle-3.7.3-GCCcore-11.2.0.eb | 38 ++++++++++++++++++ 6 files changed, 206 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.7.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..13994a3781c --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '5.0' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a1013eebb50f728fc601bdd833b0b2870333c3b3e5a816eeba921d95bec6f15'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('GMP', '6.2.1')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e2a92bee0a6 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.2.1' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +# copy libgmp.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b440df6aef7 --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.24' + +homepage = 'http://isl.gforge.inria.fr/' +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://isl.gforge.inria.fr/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['043105cc544f416b48736fff8caf077fb0663a717d06b1113f16e391ac99ebad'] + +builddependencies = [('binutils', '2.37')] +dependencies = [('GMP', '6.2.1')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..167126ce659 --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.2.1' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..cf964266691 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '4.1.0' + +homepage = 'https://www.mpfr.org' + +description = """ + The MPFR library is a C library for multiple-precision floating-point + computations with correct rounding. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +runtest = 'check' + +# copy libmpfr.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a src/.libs/libmpfr.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.7.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.7.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..101eaedd47c --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.7.3-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.7.3' + +homepage = 'https://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['661f5eb03f048a3b924c3a8ad2515d4068e40f67e774e8a26827658007e3bcf0'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = '--disable-openssl ' # openssl is just used for the nettle-openssl example and requires openssl 1.1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' From 9f3f97ec0a832b51a334af69f9d66d08a34156b2 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 21:42:34 +0200 Subject: [PATCH 0629/9987] adding easyconfigs: Tcl-8.6.11-GCCcore-11.2.0.eb --- .../t/Tcl/Tcl-8.6.11-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.11-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.11-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.11-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..164554cf266 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.11-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.11' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['8c0486668586672c5693d7d95817cb05a18c5ecca2f40e2836b9578064088258'] + +builddependencies = [ + ('binutils', '2.37'), +] +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' From f52ba531a89bd32322211630a5a675b9c001c4e0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 21:46:54 +0200 Subject: [PATCH 0630/9987] adding easyconfigs: LMDB-0.9.29-GCCcore-11.2.0.eb --- .../l/LMDB/LMDB-0.9.29-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8ed7a0228ea --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.29' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['22054926b426c66d8f2bc22071365df6e35f3aacf19ad943bc6167d4cae3bebb'] + +builddependencies = [('binutils', '2.37')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'], 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From d65cca0b82bf1c058a641ccbe62e73f7a0d9f78b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 21:49:38 +0200 Subject: [PATCH 0631/9987] adding easyconfigs: libpci-3.7.0-GCCcore-11.2.0.eb --- .../l/libpci/libpci-3.7.0-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpci/libpci-3.7.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libpci/libpci-3.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libpci/libpci-3.7.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5d64a4ed2d1 --- /dev/null +++ b/easybuild/easyconfigs/l/libpci/libpci-3.7.0-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libpci' +version = '3.7.0' + +homepage = 'https://github.com/pciutils/pciutils' +description = "Library for portable access to PCI bus configuration registers from PCI Utils." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pciutils/pciutils/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-install-lib-symlinks.patch'] +checksums = [ + 'ea768aa0187ba349391c6c157445ecc2b42e7d671fc1ce8c53ff5ef513f1e2ab', # v3.7.0.tar.gz + '4f078fcfe76b79d82a7b428afcfe866aab94c9e4bd52d0bf41c57a4ef47d124c', # libpci-3.7.0_fix-install-lib-symlinks.patch +] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +skipsteps = ['configure'] + +buildopts = "PREFIX=%(installdir)s SHARED=yes ZLIB=yes" + +# only install the library and header files +install_cmd = "make install-lib" +installopts = buildopts + +sanity_check_paths = { + 'files': ['lib/libpci.%s' % SHLIB_EXT], + 'dirs': ['include/pci', 'lib/pkgconfig'], +} + +moduleclass = 'system' From 56e72365d517925d2a90c61cbf6c10a36b9f374e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 21:52:29 +0200 Subject: [PATCH 0632/9987] adding easyconfigs: libffi-3.4.2-GCCcore-11.2.0.eb --- .../l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d30e1b0f774 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.2' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'ftp://sourceware.org/pub/%(name)s/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/%(name)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['540fb721619a6aba3bdeef7d940d8e9e0e6d2c193595bc243241b77ff9e93620'] + +builddependencies = [ + ('binutils', '2.37'), +] + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From b959b5113d6dde1bf867948f1f2a4ea1e1477fe3 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 21:57:09 +0200 Subject: [PATCH 0633/9987] adding easyconfigs: Doxygen-1.9.1-GCCcore-11.2.0.eb, libiconv-1.16-GCCcore-11.2.0.eb --- .../d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ .../libiconv/libiconv-1.16-GCCcore-11.2.0.eb | 23 +++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..394f61d368a --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +name = 'Doxygen' +version = '1.9.1' + +homepage = 'https://www.doxygen.org' +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['67aeae1be4e1565519898f46f1f7092f1973cce8a767e93101ee0111717091d1'] + +builddependencies = [ + ('binutils', '2.37'), + ('Bison', '3.7.6'), + ('CMake', '3.21.1'), + ('flex', '2.6.4'), + ('pkg-config', '0.29.2'), +] +dependencies = [('libiconv', '1.16')] + +configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c306c634ed6 --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.16-GCCcore-11.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.16' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e6a1b1b589654277ee790cce3734f07876ac4ccfaecbee8afa0b649cf529cc04'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' From b2a5fd91b80f3b00f11803d0d159222d31f2eee9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:05:10 +0200 Subject: [PATCH 0634/9987] update easyconfig libffi-3.4.2-GCCcore-11.2.0.eb: update source_urls --- .../easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb index d30e1b0f774..81d0e8fb36b 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb @@ -11,10 +11,7 @@ description = """The libffi library provides a portable, high level programming toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'ftp://sourceware.org/pub/%(name)s/', - 'https://www.mirrorservice.org/sites/sourceware.org/pub/%(name)s/', -] +source_urls = ['https://github.com/libffi/libffi/releases/download/v3.4.2/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['540fb721619a6aba3bdeef7d940d8e9e0e6d2c193595bc243241b77ff9e93620'] From cc8bcad18e7f61bf10ad97595f969c58aa9441a0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:13:53 +0200 Subject: [PATCH 0635/9987] adding easyconfigs: make-4.3-GCCcore-11.2.0.eb, imake-1.0.8-GCCcore-11.2.0.eb, xproto-7.0.31-GCCcore-11.2.0.eb --- .../i/imake/imake-1.0.8-GCCcore-11.2.0.eb | 29 +++++++++++++++++++ .../m/make/make-4.3-GCCcore-11.2.0.eb | 29 +++++++++++++++++++ .../x/xproto/xproto-7.0.31-GCCcore-11.2.0.eb | 29 +++++++++++++++++++ 3 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..94027a521e9 --- /dev/null +++ b/easybuild/easyconfigs/i/imake/imake-1.0.8-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'imake' +version = '1.0.8' + +homepage = 'https://www.x.org/' +description = """imake is a Makefile-generator that is intended to make it +easier to develop software portably for multiple systems.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://artfiles.org/x.org/pub/individual/util/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8178a09bfef33ad5f61cb5cb62283df7d3a5682f014507d2e7cfd922485a5c00'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('xproto', '7.0.31'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ccmakedep', 'cleanlinks', 'imake', + 'makeg', 'mergelib', 'mkdirhier', + 'mkhtmlindex', 'revpath', 'xmkmf']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5d2384a414d --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.3' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e05fdde47c5f7ca45cb697e973894ff4f5d79e13b750ed57d7b66d8defc78e19'] + +builddependencies = [('binutils', '2.37')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6d58d849344 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = 'https://www.freedesktop.org/wiki/Software/xlibs' +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] + +builddependencies = [ + ('binutils', '2.37'), + ('xorg-macros', '1.19.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' From 34c908d865bdd6e7d98cd135dc17cf43e28a68a8 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:16:02 +0200 Subject: [PATCH 0636/9987] adding easyconfigs: Eigen-3.3.9-GCCcore-11.2.0.eb --- .../e/Eigen/Eigen-3.3.9-GCCcore-11.2.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0b4155d9416 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-11.2.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.3.9' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['0fa5cafe78f66d2b501b43016858070d52ba47bd9b1016b0165a7b8e04675677'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.37'), # to make CMake compiler health check pass on old systems + ('CMake', '3.21.1'), +] + +moduleclass = 'math' From 7d2f0fa4229699c0ef81ee4f7e4fceedeba5f0a0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:18:48 +0200 Subject: [PATCH 0637/9987] adding easyconfigs: libgit2-1.1.1-GCCcore-11.2.0.eb --- .../l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..63f2b8b0aca --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.1.1' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'libgit2' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['13a525373f64c711a00a058514d890d1512080265f98e0935ab279393f21a620'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('PCRE', '8.44'), + ('OpenSSL', '1.1', '', True), +] + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], + 'dirs': [] +} + +moduleclass = 'devel' From 2cb21cc3ce40b48e290ff891c2dce7d4acedd913 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:21:29 +0200 Subject: [PATCH 0638/9987] update easyconfig libgit2-1.1.1-GCCcore-11.2.0.eb: update deps --- .../easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb index 63f2b8b0aca..085a5fb9f66 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb @@ -16,13 +16,13 @@ sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_G checksums = ['13a525373f64c711a00a058514d890d1512080265f98e0935ab279393f21a620'] builddependencies = [ - ('binutils', '2.36.1'), - ('CMake', '3.20.1'), + ('binutils', '2.37'), + ('CMake', '3.21.1'), ('pkg-config', '0.29.2'), ] dependencies = [ - ('PCRE', '8.44'), + ('PCRE', '8.45'), ('OpenSSL', '1.1', '', True), ] From 2fc101dde3b2293f44477c1d1e19bf095600780a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:23:57 +0200 Subject: [PATCH 0639/9987] adding easyconfigs: NLopt-2.7.0-GCCcore-11.2.0.eb --- .../n/NLopt/NLopt-2.7.0-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.7.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5d5877cfd0e --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.0-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.7.0' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b881cc2a5face5139f1c5a30caf26b7d3cb43d69d5e423c9d78392f99844499f'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('binutils', '2.37'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' From 4d2e5c5810362c5d71bb0508d1d16af3289ad673 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:27:11 +0200 Subject: [PATCH 0640/9987] adding easyconfigs: double-conversion-3.1.5-GCCcore-11.2.0.eb --- .../double-conversion-3.1.5-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a1ba9120b64 --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.1.5' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a63ecb93182134ba4293fd5f22d6e08ca417caafa244afaa751cbfddf6415b13'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +separate_build_dir = True + +build_type = 'Release' + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a', + '-DBUILD_SHARED_LIBS=ON' +] + +sanity_check_paths = { + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 9922414b4f78a13218b75ceb8f6146962f617f02 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:30:57 +0200 Subject: [PATCH 0641/9987] adding easyconfigs: SQLite-3.36-GCCcore-11.2.0.eb --- .../s/SQLite/SQLite-3.36-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.36-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.36-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.36-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f299b6d7623 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.36-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.36' +local_filename_version = '3360000' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2021/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['bd90c3eb96bee996206b83be7065c9ce19aef38c3f4fb53073ada0d0b69bbce3'] + +builddependencies = [ + ('binutils', '2.37'), +] +dependencies = [ + ('libreadline', '8.1'), + ('Tcl', '8.6.11'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' From d321026f015ba2f2008a77a1426723d66de4f236 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:34:52 +0200 Subject: [PATCH 0642/9987] adding easyconfigs: libunwind-1.5.0-GCCcore-11.2.0.eb --- .../libunwind-1.5.0-GCCcore-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.5.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..69be1059ae2 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.5.0' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['libunwind-1.3.1_fix_ppc64_fpreg_t.patch'] +checksums = [ + '90337653d92d4a13de590781371c604f9031cdb50520366aa1e3a91e1efb1017', # libunwind-1.5.0.tar.gz + '61a507eec7ece286b06be698c742f0016d8c605eaeedf34f451cf1d0e510ec86', # libunwind-1.3.1_fix_ppc64_fpreg_t.patch +] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('XZ', '5.2.5'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd -fno-common" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' From 5e0a139a521a022d2b545e320155697b8909b855 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:43:12 +0200 Subject: [PATCH 0643/9987] adding easyconfigs: libpciaccess-0.16-GCCcore-11.2.0.eb --- .../libpciaccess-0.16-GCCcore-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..56d0c9048de --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.16' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['84413553994aef0070cf420050aa5c0a51b1956b404920e21b81e96db6a61a27'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('xorg-macros', '1.19.3'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' From fa77d695c5926701e75fc7e616b233bc7dfd62d0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:46:10 +0200 Subject: [PATCH 0644/9987] adding easyconfigs: DBus-1.13.18-GCCcore-11.2.0.eb --- .../d/DBus/DBus-1.13.18-GCCcore-11.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..3591a25194f --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-11.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.13.18' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['8078f5c25e34ab907ce06905d969dc8ef0ccbec367e1e1707c7ecf8460f4254e'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('expat', '2.4.1'), +] + +configopts = '--without-systemdsystemunitdir' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' From 5d561f2b1767bc1ea476a182ce9192136561ee53 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:47:25 +0200 Subject: [PATCH 0645/9987] adding easyconfigs: libyaml-0.2.5-GCCcore-11.2.0.eb --- .../l/libyaml/libyaml-0.2.5-GCCcore-11.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..87d72c1f725 --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.5' + +homepage = 'https://pyyaml.org/wiki/LibYAML' + +description = """LibYAML is a YAML parser and emitter written in C.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://pyyaml.org/download/libyaml/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['c642ae9b75fee120b2d96c712538bd2cf283228d2337df2cf2988e3c02678ef4'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.%s" % SHLIB_EXT], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From 2c9d221379fa6ae61217531fcb00df26768fb031 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:51:17 +0200 Subject: [PATCH 0646/9987] adding easyconfigs: pixman-0.40.0-GCCcore-11.2.0.eb --- .../p/pixman/pixman-0.40.0-GCCcore-11.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..913df957af3 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.40.0' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6d200dec3740d9ec4ec8d1180e25779c00bc749f94278c8b9021f5534db223fc'] + +builddependencies = [ + ('binutils', '2.37'), +] + + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From e2b29761ceac7fe0a9a374ee8426dcbb20f45db0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:55:56 +0200 Subject: [PATCH 0647/9987] adding easyconfigs: libidn-1.38-GCCcore-11.2.0.eb, libidn2-2.3.2-GCCcore-11.2.0.eb --- .../l/libidn/libidn-1.38-GCCcore-11.2.0.eb | 22 +++++++++++++++++ .../l/libidn2/libidn2-2.3.2-GCCcore-11.2.0.eb | 24 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.38-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.38-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.38-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9f391db409b --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.38-GCCcore-11.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.38' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['de00b840f757cd3bb14dd9a20d5936473235ddcba06d4bc2da804654b8bbf0f6'] + +builddependencies = [('binutils', '2.36.1')] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e1f1bdca274 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libidn2' +version = '2.3.2' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = """Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libidn/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['76940cd4e778e8093579a9d195b25fff5e936e9dc6242068528b437a76764f91'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/idn2', 'lib/libidn2.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["idn2 --help"] + +moduleclass = 'lib' From 936aff7d119e3819164b924df3478bbf4fb0dec5 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 22:57:22 +0200 Subject: [PATCH 0648/9987] update easyconfig libidn-1.38-GCCcore-11.2.0.eb: update deps --- easybuild/easyconfigs/l/libidn/libidn-1.38-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.38-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.38-GCCcore-11.2.0.eb index 9f391db409b..769eff5a612 100644 --- a/easybuild/easyconfigs/l/libidn/libidn-1.38-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libidn/libidn-1.38-GCCcore-11.2.0.eb @@ -13,7 +13,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['de00b840f757cd3bb14dd9a20d5936473235ddcba06d4bc2da804654b8bbf0f6'] -builddependencies = [('binutils', '2.36.1')] +builddependencies = [('binutils', '2.37')] sanity_check_paths = { 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], From 10d02c636e849bbfca1e7ceadcbcce1800232a25 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 4 Aug 2021 23:07:37 +0200 Subject: [PATCH 0649/9987] adding easyconfig: xorg-macros-1.19.3-GCCcore-11.2.0.eb --- .../xorg-macros-1.19.3-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..88c72ddb8b7 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.3' + +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['8205d210a580da0938f5ce4392a96b60cf1d9a5f792eaa1474fa4c1977aef4d0'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From 94f2cede1acaebae00a294b6ef5204a20a0be19c Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Thu, 5 Aug 2021 14:13:28 +1000 Subject: [PATCH 0650/9987] Create FreeImage-3.18.0-GCCcore-10.2.0.eb Update to GCCcore 10.2.0 and binutils 2.35 --- .../FreeImage-3.18.0-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6953a03bafa --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FreeImage' +version = '3.18.0' + +homepage = 'http://freeimage.sourceforge.net' +description = """FreeImage is an Open Source library project for developers who would like to support popular graphics +image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to +use, fast, multithreading safe.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(name)s%s.zip' % ''.join(version.split('.'))] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip + '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # FreeImage-3.18.0-fix-makefile.patch +] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +buildopts = ['', '-f Makefile.fip'] +installopts = [ + 'INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib', + '-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib' +] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['include/FreeImage.h', 'include/FreeImagePlus.h', 'lib/libfreeimage.a', 'lib/libfreeimage.%s' % SHLIB_EXT, + 'lib/libfreeimageplus.a', 'lib/libfreeimageplus.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' From 38be65b9a1aec679bbc679232d878f334be641f9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 09:04:38 +0200 Subject: [PATCH 0651/9987] Fix DIRAC build with high compiler optimiztations --- ...AC-19.0-intel-2020a-Python-2.7.18-int64.eb | 10 +-- ...9.0-intel-2020a-Python-2.7.18-mpi-int64.eb | 10 +-- .../DIRAC/DIRAC-19.0_use_easybuild_opts.patch | 70 +++++++++++++++++++ .../DIRAC-19.0_use_easybuild_opts_intel.patch | 33 --------- 4 files changed, 76 insertions(+), 47 deletions(-) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts.patch delete mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts_intel.patch diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb index c938fbf458e..82a95e63297 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb @@ -15,14 +15,14 @@ sources = ['DIRAC-%(version)s-Source.tar.gz'] patches = [ '%(name)s-%(version)s_remove-broken-tests-intel.patch', '%(name)s-%(version)s_fix-bss_energy_test.patch', - '%(name)s-%(version)s_use_easybuild_opts_intel.patch', + '%(name)s-%(version)s_use_easybuild_opts.patch', '%(name)s-%(version)s_fix_test_path.patch', ] checksums = [ 'f0e3610bdd1fbcff90cdfb4cf3fd7582a4762f533af7d635c4bc4d114f402c32', # DIRAC-19.0-Source.tar.gz 'cb0e07097499fe59180d79a5db9ee883b9c83e16dcc6210fd945072c3a54c8a4', # DIRAC-19.0_remove-broken-tests-intel.patch 'e66be847d87ccfda23687de31a3a7c8d71c97b0accd290cf7ade4b4184f1fb93', # DIRAC-19.0_fix-bss_energy_test.patch - '666a9053d6c1287ee7aa471d18436133931959b3eacb7619d5197dbfb4e0c1fe', # DIRAC-19.0_use_easybuild_opts_intel.patch + '150b293250f1ca476a1d268534a236e06dbf5960d25c2a09f6d3f5e82c043316', # DIRAC-19.0_use_easybuild_opts.patch '527680cab911a8c7a52347d7ace516a497b725043537a6274670a1aaa97bfb0f', # DIRAC-19.0_fix_test_path.patch ] @@ -30,10 +30,7 @@ builddependencies = [('CMake', '3.16.4')] dependencies = [('Python', '2.7.18')] -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DENABLE_BLAS=off ' +configopts = '-DENABLE_BLAS=off ' configopts += '-DENABLE_LAPACK=off ' configopts += '-DMKL_FLAG=off ' configopts += '-DBLAS_LANG=Fortran ' @@ -47,7 +44,6 @@ configopts += '-DENABLE_RUNTIMECHECK=False ' configopts += '-DENABLE_64BIT_INTEGERS=True ' configopts += '-DEXPLICIT_LIBS="${LIBLAPACK_MT}" ' configopts += '-DENABLE_PCMSOLVER=OFF ' -configopts += '-G"Unix Makefiles" ' parallel = 1 diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb index bdb2729a3aa..f8abf1845ff 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb @@ -15,7 +15,7 @@ sources = ['DIRAC-%(version)s-Source.tar.gz'] patches = [ '%(name)s-%(version)s_remove-broken-tests-intel.patch', '%(name)s-%(version)s_fix-bss_energy_test.patch', - '%(name)s-%(version)s_use_easybuild_opts_intel.patch', + '%(name)s-%(version)s_use_easybuild_opts.patch', '%(name)s-%(version)s_fix_test_path.patch', '%(name)s-%(version)s_fix_mpi_tests.patch', ] @@ -23,7 +23,7 @@ checksums = [ 'f0e3610bdd1fbcff90cdfb4cf3fd7582a4762f533af7d635c4bc4d114f402c32', # DIRAC-19.0-Source.tar.gz 'cb0e07097499fe59180d79a5db9ee883b9c83e16dcc6210fd945072c3a54c8a4', # DIRAC-19.0_remove-broken-tests-intel.patch 'e66be847d87ccfda23687de31a3a7c8d71c97b0accd290cf7ade4b4184f1fb93', # DIRAC-19.0_fix-bss_energy_test.patch - '666a9053d6c1287ee7aa471d18436133931959b3eacb7619d5197dbfb4e0c1fe', # DIRAC-19.0_use_easybuild_opts_intel.patch + '150b293250f1ca476a1d268534a236e06dbf5960d25c2a09f6d3f5e82c043316', # DIRAC-19.0_use_easybuild_opts.patch '527680cab911a8c7a52347d7ace516a497b725043537a6274670a1aaa97bfb0f', # DIRAC-19.0_fix_test_path.patch 'ccc26fc320f0967211b6390244b1fa359ba5d0294071d5d2cb9e36b4652a52b2', # DIRAC-19.0_fix_mpi_tests.patch ] @@ -32,10 +32,7 @@ builddependencies = [('CMake', '3.16.4')] dependencies = [('Python', '2.7.18')] -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DENABLE_BLAS=off ' +configopts = '-DENABLE_BLAS=off ' configopts += '-DENABLE_LAPACK=off ' configopts += '-DMKL_FLAG=off ' configopts += '-DBLAS_LANG=Fortran ' @@ -49,7 +46,6 @@ configopts += '-DENABLE_RUNTIMECHECK=False ' configopts += '-DENABLE_64BIT_INTEGERS=True ' configopts += '-DEXPLICIT_LIBS="${LIBSCALAPACK_MT}" ' configopts += '-DENABLE_PCMSOLVER=OFF ' -configopts += '-G"Unix Makefiles" ' parallel = 1 diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts.patch b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts.patch new file mode 100644 index 00000000000..e7e16b65880 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts.patch @@ -0,0 +1,70 @@ +# Take EasyBuild compiler flags for C, C++, and Fortran +# OCT 5th, 2020 by B. Hajgato (UGent) +# Updated by Alexander Grund (TU Dresden) +diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.C.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.C.cmake +--- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.C.cmake 2021-08-04 17:42:21.340186361 +0200 ++++ DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.C.cmake 2021-08-04 17:53:53.657008099 +0200 +@@ -3,7 +3,5 @@ + message(STATUS "Added gcc -maix64 flag due to IBM AIX XL Fortran and integer*8") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -maix64 ") + endif() +- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g") +- set(CMAKE_C_FLAGS_RELEASE "-O2 -Wno-unused") +- set(CMAKE_C_FLAGS_DEBUG "-O0") ++ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unused") + endif() +diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.CXX.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.CXX.cmake +--- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.CXX.cmake 2021-08-04 17:42:21.340186361 +0200 ++++ DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.CXX.cmake 2021-08-04 17:53:53.657008099 +0200 +@@ -1,5 +1,4 @@ + if(CMAKE_CXX_COMPILER_ID MATCHES GNU) +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -Wno-unknown-pragmas -Wno-sign-compare -Woverloaded-virtual -Wwrite-strings -Wno-unused") +- set(CMAKE_CXX_FLAGS_RELEASE "-Ofast -march=native -DNDEBUG -Wno-unused") +- set(CMAKE_CXX_FLAGS_DEBUG "-O0 -DDEBUG") ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-unknown-pragmas -Wno-sign-compare -Woverloaded-virtual -Wwrite-strings -Wno-unused") ++ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DDEBUG") + endif() +diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.Fortran.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.Fortran.cmake +--- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/GNU.Fortran.cmake 2021-08-04 17:42:21.340186361 +0200 ++++ DIRAC-19.0-Source/cmake/custom/compiler_flags/GNU.Fortran.cmake 2021-08-04 17:53:53.657008099 +0200 +@@ -4,7 +4,6 @@ + set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -maix64") + message(STATUS "Added gfortran -maix64 flag due to IBM AIX and integer*8") + endif() +- set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -funroll-all-loops -w") +- set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS} -O0 -fbounds-check -finit-real=nan -finit-integer=-9999 -Wall") +- #set(CMAKE_Fortran_FLAGS_DEBUG "-O0") ++ set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -funroll-all-loops -w") ++ set(CMAKE_Fortran_FLAGS_DEBUG "${CMAKE_Fortran_FLAGS} -fbounds-check -finit-real=nan -finit-integer=-9999 -Wall") + endif() +diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.C.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.C.cmake +--- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.C.cmake 2021-08-04 17:42:21.340186361 +0200 ++++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.C.cmake 2021-08-04 17:53:53.657008099 +0200 +@@ -1,5 +1,3 @@ + if(CMAKE_C_COMPILER_ID MATCHES Intel) +- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -wd981 -wd279 -wd383 -wd1572 -wd177") +- set(CMAKE_C_FLAGS_RELEASE "-O2") +- set(CMAKE_C_FLAGS_DEBUG "-O0") ++ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -wd981 -wd279 -wd383 -wd1572 -wd177") + endif() +diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.CXX.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.CXX.cmake +--- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.CXX.cmake 2021-08-04 17:42:21.340186361 +0200 ++++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.CXX.cmake 2021-08-04 17:53:53.657008099 +0200 +@@ -1,5 +1,4 @@ + if(CMAKE_CXX_COMPILER_ID MATCHES Intel) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unknown-pragmas") +- set(CMAKE_CXX_FLAGS_RELEASE "-debug -O3 -DNDEBUG") +- set(CMAKE_CXX_FLAGS_DEBUG "-O0 -debug -DDEBUG") ++ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DDEBUG") + endif() +diff -ur DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.Fortran.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.Fortran.cmake +--- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.Fortran.cmake 2021-08-04 17:42:21.340186361 +0200 ++++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.Fortran.cmake 2021-08-04 17:53:53.657008099 +0200 +@@ -1,5 +1,4 @@ + if(CMAKE_Fortran_COMPILER_ID MATCHES Intel) +- set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -w -assume byterecl -g -traceback -DVAR_IFORT") +- set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -ip") +- set(CMAKE_Fortran_FLAGS_DEBUG "-O0") ++ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -w -assume byterecl -DVAR_IFORT") ++ set(CMAKE_Fortran_FLAGS_RELEASE "${CMAKE_Fortran_FLAGS_RELEASE} -ip") + endif() diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts_intel.patch b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts_intel.patch deleted file mode 100644 index d0cd900f24c..00000000000 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts_intel.patch +++ /dev/null @@ -1,33 +0,0 @@ -# Take EasyBuild compiler flags for C, C++, and Fortran -# OCT 5th, 2020 by B. Hajgato (UGent) -diff -ru DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.C.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.C.cmake ---- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.C.cmake 2019-12-12 17:26:15.000000000 +0100 -+++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.C.cmake 2020-10-07 19:53:57.517988580 +0200 -@@ -1,5 +1,5 @@ - if(CMAKE_C_COMPILER_ID MATCHES Intel) -- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -wd981 -wd279 -wd383 -wd1572 -wd177") -+ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -wd981 -wd279 -wd383 -wd1572 -wd177") - set(CMAKE_C_FLAGS_RELEASE "-O2") - set(CMAKE_C_FLAGS_DEBUG "-O0") - endif() -diff -ru DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.CXX.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.CXX.cmake ---- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.CXX.cmake 2019-12-12 17:26:15.000000000 +0100 -+++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.CXX.cmake 2020-10-07 19:54:10.338306645 +0200 -@@ -1,5 +1,5 @@ - if(CMAKE_CXX_COMPILER_ID MATCHES Intel) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unknown-pragmas") -- set(CMAKE_CXX_FLAGS_RELEASE "-debug -O3 -DNDEBUG") -+ set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG") - set(CMAKE_CXX_FLAGS_DEBUG "-O0 -debug -DDEBUG") - endif() -diff -ru DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.Fortran.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.Fortran.cmake ---- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.Fortran.cmake 2019-12-12 17:26:15.000000000 +0100 -+++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.Fortran.cmake 2020-10-07 19:55:34.670398011 +0200 -@@ -1,5 +1,5 @@ - if(CMAKE_Fortran_COMPILER_ID MATCHES Intel) -- set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -w -assume byterecl -g -traceback -DVAR_IFORT") -- set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -ip") -+ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -w -assume byterecl -DVAR_IFORT") -+ set(CMAKE_Fortran_FLAGS_RELEASE " ") - set(CMAKE_Fortran_FLAGS_DEBUG "-O0") - endif() From e256ac3a7d96ce53c42f939d1709f52e139f7c8c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 09:52:07 +0200 Subject: [PATCH 0652/9987] CLHEP: Remove superflous configopts and add sanity-checks/checksums --- .../easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb | 10 ++++++++-- .../easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb | 10 ++++++++-- .../easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb | 10 ++++++++-- .../easyconfigs/c/CLHEP/CLHEP-2.3.4.3-foss-2017b.eb | 7 ++++++- .../easyconfigs/c/CLHEP/CLHEP-2.3.4.3-intel-2017b.eb | 7 ++++++- .../easyconfigs/c/CLHEP/CLHEP-2.4.0.0-intel-2017b.eb | 7 ++++++- .../easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb | 7 ++++++- .../easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2018b.eb | 7 ++++++- .../easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb | 7 ++++++- .../easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2018b.eb | 7 ++++++- 10 files changed, 66 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb index 0e16a666125..441fffa6cb6 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2016a.eb @@ -11,13 +11,19 @@ description = """The CLHEP project is intended to be a set of HEP-specific found toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] +sources = [SOURCELOWER_TGZ] +checksums = ['5d3e45b39a861731fe3a532bb1426353bf62b54c7b90ecf268827e50f925642b'] builddependencies = [('CMake', '3.4.3')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb index fb7adb464b2..f156e273921 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.8-intel-2016a.eb @@ -11,13 +11,19 @@ description = """The CLHEP project is intended to be a set of HEP-specific found toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] +sources = [SOURCELOWER_TGZ] +checksums = ['f735e236b1f023ba7399269733b2e84eaed4de615081555b1ab3af25a1e92112'] builddependencies = [('CMake', '3.4.3')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb index 0c5534a7378..f2fbfc307d4 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.1.1-intel-2016a.eb @@ -11,13 +11,19 @@ description = """The CLHEP project is intended to be a set of HEP-specific found toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -sources = [SOURCELOWER_TGZ] source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] +sources = [SOURCELOWER_TGZ] +checksums = ['0e2b170df99176feb0aa4f20ea3b33463193c086682749790c5b9b79388d0ff4'] builddependencies = [('CMake', '3.4.3')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-foss-2017b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-foss-2017b.eb index 6f8910ad70e..63abfef5a29 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-foss-2017b.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-foss-2017b.eb @@ -19,6 +19,11 @@ builddependencies = [('CMake', '3.9.5')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-intel-2017b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-intel-2017b.eb index 6ee2fced2e1..32ec1348ceb 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-intel-2017b.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.3.4.3-intel-2017b.eb @@ -19,6 +19,11 @@ builddependencies = [('CMake', '3.9.5')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.0.0-intel-2017b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.0.0-intel-2017b.eb index 2c616de6d7f..45d0a5b234d 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.0.0-intel-2017b.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.0.0-intel-2017b.eb @@ -19,6 +19,11 @@ builddependencies = [('CMake', '3.10.0')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb index 21fe05f6d94..4cb4607a061 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2017b.eb @@ -19,6 +19,11 @@ builddependencies = [('CMake', '3.10.0')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2018b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2018b.eb index 053e43549ef..0c75cafccd2 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2018b.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-foss-2018b.eb @@ -19,6 +19,11 @@ builddependencies = [('CMake', '3.12.1')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb index 92485e9ac0e..60fd1abce1d 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2017b.eb @@ -19,6 +19,11 @@ builddependencies = [('CMake', '3.10.0')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2018b.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2018b.eb index 323ba4ee22b..17a3cf55a43 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2018b.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.1.0-intel-2018b.eb @@ -19,6 +19,11 @@ builddependencies = [('CMake', '3.12.1')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] moduleclass = 'numlib' From fea74e4be3a0d1d29978d4704d3437d24e900dea Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 10:02:06 +0200 Subject: [PATCH 0653/9987] Arrow: Remove superflous CMAKE_BUILD_TYPE --- .../a/Arrow/Arrow-0.12.0-foss-2018b-Python-2.7.15.eb | 2 +- .../a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb | 2 +- .../a/Arrow/Arrow-0.12.0-intel-2018b-Python-3.6.6.eb | 2 +- .../a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb | 2 +- .../a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb | 2 +- .../a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 2 +- .../a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 2 +- .../a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb | 6 ++++-- 10 files changed, 13 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-foss-2018b-Python-2.7.15.eb index 11d2da152e0..cd12d541a58 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-foss-2018b-Python-2.7.15.eb @@ -32,7 +32,7 @@ separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DCMAKE_INSTALL_LIBDIR=lib" +configopts = "-DARROW_PYTHON=on -DCMAKE_INSTALL_LIBDIR=lib" exts_defaultclass = 'PythonPackage' exts_default_options = { diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb index 81cb0dcd22c..3c7aa8f68bb 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-2.7.15.eb @@ -32,7 +32,7 @@ separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DCMAKE_INSTALL_LIBDIR=lib" +configopts = "-DARROW_PYTHON=on -DCMAKE_INSTALL_LIBDIR=lib" exts_defaultclass = 'PythonPackage' exts_default_options = { diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-3.6.6.eb index 8e32cce73bf..f0765af582b 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.12.0-intel-2018b-Python-3.6.6.eb @@ -32,7 +32,7 @@ separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DCMAKE_INSTALL_LIBDIR=lib" +configopts = "-DARROW_PYTHON=on -DCMAKE_INSTALL_LIBDIR=lib" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb index df20932272c..77e68e14b2e 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb @@ -33,7 +33,7 @@ separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=on -DCMAKE_INSTALL_LIBDIR=lib" +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=on -DCMAKE_INSTALL_LIBDIR=lib" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb index 4f5877dfda8..fa3efdcbe4b 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb @@ -37,7 +37,7 @@ separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" # also install Python bindings diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb index d5dace22be7..d503e7f9046 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb @@ -39,7 +39,7 @@ separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" # also install Python bindings diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 5ab6551adb8..8fbcaf84689 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -40,7 +40,7 @@ separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" # also install Python bindings diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb index 1988ecab002..f1476481258 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb @@ -37,7 +37,7 @@ separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" # also install Python bindings diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index d5c0491c4cb..ee3c0441109 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -36,7 +36,7 @@ separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" # also install Python bindings diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb index 75ad9458c57..293e630bae8 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.7.1-intel-2017b-Python-3.6.3.eb @@ -9,8 +9,8 @@ description = """Apache Arrow is a cross-language development platform for in-me toolchain = {'name': 'intel', 'version': '2017b'} -sources = ['apache-arrow-%(version)s.tar.gz'] source_urls = ['https://github.com/apache/arrow/archive/'] +sources = ['apache-arrow-%(version)s.tar.gz'] checksums = ['22667b9d3f4d36c2060d5ade8c904c528325ea4ffcea2e71671013addcd033af'] dependencies = [ @@ -22,7 +22,7 @@ dependencies = [ builddependencies = [('CMake', '3.9.5')] preconfigopts = "ZLIB_HOME=$EBROOTZLIB" -configopts = "-DARROW_PYTHON=ON -DARROW_PLASMA=ON -DARROW_BUILD_TESTS=ON -DCMAKE_BUILD_TYPE=Release" +configopts = "-DARROW_PYTHON=ON -DARROW_PLASMA=ON -DARROW_BUILD_TESTS=ON" start_dir = 'cpp' separate_build_dir = True @@ -30,6 +30,7 @@ separate_build_dir = True exts_defaultclass = 'PythonPackage' exts_default_options = { 'download_dep_fail': True, + 'use_pip': True } exts_list = [ @@ -38,6 +39,7 @@ exts_list = [ 'source_tmpl': sources[0], 'buildcmd': 'build_ext', 'buildopts': '--with-plasma --inplace --build-type=release', + 'checksums': ['22667b9d3f4d36c2060d5ade8c904c528325ea4ffcea2e71671013addcd033af'], }), ] From 7fdb7b0fea21dfc662be142b72fa39556289233a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 10:06:46 +0200 Subject: [PATCH 0654/9987] Update Hypre URLs and checksums (moved) --- easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-foss-2019a.eb | 5 +++-- easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-intel-2019a.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-foss-2019a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-foss-2019a.eb index e31136e3c07..97250fc49df 100644 --- a/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-foss-2019a.eb +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-foss-2019a.eb @@ -9,9 +9,10 @@ description = """Hypre is a library for solving large, sparse linear systems of toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'pic': True} -source_urls = ['https://github.com/LLNL/hypre/archive/'] +source_urls = ['https://github.com/hypre-space/hypre/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['58d215146e1c7c2c11be4cb1eac0d1663a45584efbe5f603205d8c4766b7579f'] +checksums = [('58d215146e1c7c2c11be4cb1eac0d1663a45584efbe5f603205d8c4766b7579f', + '50d0c0c86b4baad227aa9bdfda4297acafc64c3c7256c27351f8bae1ae6f2402')] start_dir = 'src' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-intel-2019a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-intel-2019a.eb index 759501b07d9..d50fa6f5bb0 100644 --- a/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-intel-2019a.eb +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.15.1-intel-2019a.eb @@ -9,9 +9,10 @@ description = """Hypre is a library for solving large, sparse linear systems of toolchain = {'name': 'intel', 'version': '2019a'} toolchainopts = {'pic': True} -source_urls = ['https://github.com/LLNL/hypre/archive/'] +source_urls = ['https://github.com/hypre-space/hypre/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['58d215146e1c7c2c11be4cb1eac0d1663a45584efbe5f603205d8c4766b7579f'] +checksums = [('58d215146e1c7c2c11be4cb1eac0d1663a45584efbe5f603205d8c4766b7579f', + '50d0c0c86b4baad227aa9bdfda4297acafc64c3c7256c27351f8bae1ae6f2402')] start_dir = 'src' From a4e6993b8952c883f86bea301bff1427921834f6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 10:10:45 +0200 Subject: [PATCH 0655/9987] Add new Mesa URLs to 2017b ECs --- easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-foss-2017b.eb | 1 + easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb | 2 ++ 2 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-foss-2017b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-foss-2017b.eb index 236bd17749a..543ff867b1d 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-foss-2017b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-foss-2017b.eb @@ -20,6 +20,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'optarch': False} source_urls = [ + 'https://archive.mesa3d.org/older-versions/%(version_major)s.x/', 'https://mesa.freedesktop.org/archive/', 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb index 62cc87c9103..0b66164c7ca 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.2.5-fosscuda-2017b.eb @@ -23,9 +23,11 @@ toolchain = {'name': 'fosscuda', 'version': '2017b'} toolchainopts = {'optarch': False} source_urls = [ + 'https://archive.mesa3d.org/older-versions/%(version_major)s.x/', 'https://mesa.freedesktop.org/archive/', 'https://mesa.freedesktop.org/archive/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] From 76f342e15d1ea5c32127b5b4579ce908b2a3a0bf Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 10:19:06 +0200 Subject: [PATCH 0656/9987] ITK: Use system-deps, drop CMakeBuildType, fix URL and build --- .../ITK-4.12.2-foss-2016b-Python-2.7.12.eb | 19 +- .../ITK/ITK-4.12.2_update-download-URLs.patch | 211 ++++++++++++++++++ .../ITK-4.13.0-foss-2018a-Python-2.7.14.eb | 19 +- .../ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb | 19 +- .../ITK/ITK-4.13.0_update-download-URLs.patch | 151 +++++++++++++ .../ITK-4.13.1-foss-2018a-Python-2.7.14.eb | 12 +- .../ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb | 12 +- .../ITK-4.13.1-foss-2018b-Python-2.7.15.eb | 12 +- .../ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb | 12 +- .../ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb | 17 +- .../ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb | 17 +- .../ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb | 14 +- 12 files changed, 466 insertions(+), 49 deletions(-) create mode 100644 easybuild/easyconfigs/i/ITK/ITK-4.12.2_update-download-URLs.patch create mode 100644 easybuild/easyconfigs/i/ITK/ITK-4.13.0_update-download-URLs.patch diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb index f3fc7b1e120..1f8b31e8d93 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb @@ -14,7 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/InsightSoftwareConsortium/ITK/releases/download/v%(version)s/'] sources = ['InsightToolkit-%(version)s.tar.gz'] -checksums = ['8ba2183111723c4405af80724c60d07484c2bff8120ee4cef543bb726d07855e'] +patches = ['ITK-4.12.2_update-download-URLs.patch'] +checksums = [ + '8ba2183111723c4405af80724c60d07484c2bff8120ee4cef543bb726d07855e', # InsightToolkit-4.12.2.tar.gz + '73f8588b4a0c7595c654ecebb1030158a27d1b18c2a461560d6b188b5f89102d', # ITK-4.12.2_update-download-URLs.patch +] builddependencies = [ ('CMake', '3.7.1'), @@ -30,10 +34,17 @@ dependencies = [ ('X11', '20160819') ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DITK_WRAP_PYTHON=ON ' -configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON ' +local_sys_deps = ['HDF5', 'SWIG'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DITK_WRAP_PYTHON=ON ' +configopts += '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +configopts += ' '.join(local_sys_cmake) +# Don't depend on MPICXX (which makes linking to ITK painful) +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' +prebuildopts = "export LC_ALL=C && " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " separate_build_dir = True @@ -42,7 +53,7 @@ modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', - 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkhdf5.a', + 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkjpeg-%(version_major_minor)s.a', 'lib/libitkpng-%(version_major_minor)s.a'], 'dirs': ['include/ITK-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages', diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.12.2_update-download-URLs.patch b/easybuild/easyconfigs/i/ITK/ITK-4.12.2_update-download-URLs.patch new file mode 100644 index 00000000000..fcda0ce99c0 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-4.12.2_update-download-URLs.patch @@ -0,0 +1,211 @@ +From 716fe079a6fad64f63f1166c7cb1565acef982ee Mon Sep 17 00:00:00 2001 +From: Matt McCormick +Date: Wed, 6 Jun 2018 11:32:18 -0400 +Subject: [PATCH] BUG: Migrate midas3.kitware.com to data.kitware.com + +midas3.kitware.com is deprecated. + +Change-Id: Iba445e27b6c0f136cc6c5a361c088075dfa1facb + + +Backported to 4.12.2 +Author (backport): Alexander Grund (TU Dresden) + +diff --git a/CMake/ITKExternalData.cmake b/CMake/ITKExternalData.cmake +index a97d725922..4e2dcd2965 100644 +--- a/CMake/ITKExternalData.cmake ++++ b/CMake/ITKExternalData.cmake +@@ -37,9 +37,6 @@ if(NOT ITK_FORBID_DOWNLOADS) + # Data published on Girder + "https://data.kitware.com:443/api/v1/file/hashsum/%(algo)/%(hash)/download" + +- # Data published on MIDAS +- "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=%(hash)&algorithm=%(algo)" +- + # Data published by developers using git-gerrit-push. + "https://itk.org/files/ExternalData/%(algo)/%(hash)" + +diff --git a/CMake/itkExternal_FFTW.cmake b/CMake/itkExternal_FFTW.cmake +index 7b44f0d68c..bcfae61c2e 100644 +--- a/CMake/itkExternal_FFTW.cmake ++++ b/CMake/itkExternal_FFTW.cmake +@@ -82,15 +82,15 @@ else() + endif() + + set(_fftw_target_version 3.3.4) +- set(_fftw_url_md5 "2edab8c06b24feeb3b82bbb3ebf3e7b3") +- set(_fftw_url "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${_fftw_url_md5}&name=fftw-${_fftw_target_version}.tar.gz") ++ set(_fftw_url_hash "1ee2c7bec3657f6846e63c6dfa71410563830d2b951966bf0123bd8f4f2f5d6b50f13b76d9a7b0eae70e44856f829ca6ceb3d080bb01649d1572c9f3f68e8eb1") ++ set(_fftw_url "https://data.kitware.com/api/v1/file/hashsum/sha512/${_fftw_url_hash}/download") + + if(ITK_USE_FFTWF) + itk_download_attempt_check(FFTW) + ExternalProject_add(fftwf + PREFIX fftwf + URL "${_fftw_url}" +- URL_MD5 "${_fftw_url_md5}" ++ URL_HASH SHA512="${_fftw_url_hash}" + DOWNLOAD_NAME "fftw-${_fftw_target_version}.tar.gz" + CONFIGURE_COMMAND + env +@@ -118,7 +118,7 @@ else() + ExternalProject_add(fftwd + PREFIX fftwd + URL "${_fftw_url}" +- URL_MD5 "${_fftw_url_md5}" ++ URL_HASH SHA512="${_fftw_url_hash}" + DOWNLOAD_NAME "fftw-${_fftw_target_version}.tar.gz" + CONFIGURE_COMMAND + env +diff --git a/Utilities/Maintenance/JREUpdate.py b/Utilities/Maintenance/JREUpdate.py +index 09bb5d37f2..2026ec7a7d 100755 +--- a/Utilities/Maintenance/JREUpdate.py ++++ b/Utilities/Maintenance/JREUpdate.py +@@ -10,8 +10,8 @@ plugin "just works". + The Fiji fellows maintain Git repositories that tracks the OpenJDK JRE. + Here we clone that repository and create the JRE tarball from it. + +-Currently, the tarball needs to be uploaded manually to midas3.kitware.com. +-In the future, pydas can be used for automatic upload. ++Currently, the tarball needs to be uploaded manually to data.kitware.com. ++In the future, the Python girder client can be used for automatic upload. + """ + + from __future__ import print_function +diff --git a/Utilities/Maintenance/SourceTarball.bash b/Utilities/Maintenance/SourceTarball.bash +index 1c0335674e..221d88813b 100755 +--- a/Utilities/Maintenance/SourceTarball.bash ++++ b/Utilities/Maintenance/SourceTarball.bash +@@ -57,7 +57,7 @@ download_object() { + algo="$1" ; hash="$2" ; path="$3" + mkdir -p $(dirname "$path") && + if wget "https://www.itk.org/files/ExternalData/$algo/$hash" -O "$path.tmp$$" 1>&2 || \ +- wget "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${hash}&algorithm=${algo}" -O "$path.tmp$$" 1>&2; then ++ wget "https://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&checksum=${hash}&algorithm=${algo}" -O "$path.tmp$$" 1>&2; then + mv "$path.tmp$$" "$path" + else + rm -f "$path.tmp$$" +diff --git a/Wrapping/Generators/CastXML/CMakeLists.txt b/Wrapping/Generators/CastXML/CMakeLists.txt +index f15d0cce01..f4f698b78a 100644 +--- a/Wrapping/Generators/CastXML/CMakeLists.txt ++++ b/Wrapping/Generators/CastXML/CMakeLists.txt +@@ -25,23 +25,22 @@ else() + # If 64 bit Linux build host, use the CastXML binary + if(CMAKE_HOST_SYSTEM_NAME MATCHES "Linux" AND CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64") + +- set(_castxml_hash 48d812ca105d7aa10fdc2d16678f7388) +- set(_castxml_url "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${_castxml_hash}&name=castxml-linux.tar.gz") ++ set(_castxml_hash 1e0f51ab98592ac9934bb1c93040fd473519a02d1e3ce0090443f4f3566eb8354eb3e5bd04a2c91d832d33d0d712363c508bd2304da34db9963787890808ec9e) ++ set(_castxml_url "https://data.kitware.com/api/v1/file/hashsum/sha512/${_castxml_hash}/download") + set(_download_castxml_binaries 1) + + # If 64 bit Windows build host, use the CastXML binary + elseif(CMAKE_HOST_SYSTEM_NAME MATCHES "Windows" AND CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "AMD64") + +- set(_castxml_hash dd0cf24fd9d9a06ed49189f11e72c9f0) +- set(_castxml_url https://midas3.kitware.com/midas/download/bitstream/460537/castxml-windows.zip) +- set(_castxml_url "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${_castxml_hash}&name=castxml-windows.zip") ++ set(_castxml_hash 1c379ea91f4c0d9b8127d841edee7c415fdde40665a2a3682aef22def75bd1cea99d26bb3b1b243e61e976d78233ed12a2614236e76206d1ae083583f4bc17ea) ++ set(_castxml_url "https://data.kitware.com/api/v1/file/hashsum/sha512/${_castxml_hash}/download") + set(_download_castxml_binaries 1) + + # If 64 bit Mac OS X build host ( >= 10.9, Mavericks), use the CastXML binary + elseif(CMAKE_HOST_SYSTEM_NAME MATCHES "Darwin" AND CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64" AND (NOT CMAKE_HOST_SYSTEM_VERSION VERSION_LESS "13.0.0")) + +- set(_castxml_hash 5de72fb4970513f805457db9a2c4e6a3) +- set(_castxml_url "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${_castxml_hash}&name=castxml-macosx.tar.gz") ++ set(_castxml_hash 2fa32cd083ed901499774eb34249c70c2d32a93c55e27dbb62f5ec3c7386ab6745dbbad78c653a0909b05b5d965839ec31ad9fca294cc0b7af9dfc15e2a7e063) ++ set(_castxml_url "https://data.kitware.com/api/v1/file/hashsum/sha512/${_castxml_hash}/download") + set(_download_castxml_binaries 1) + + endif() +@@ -53,7 +52,7 @@ else() + endif() + ExternalProject_Add(castxml + URL ${_castxml_url} +- URL_MD5 ${_castxml_hash} ++ URL_HASH SHA512=${_castxml_hash} + CONFIGURE_COMMAND "" + BUILD_COMMAND "" + INSTALL_COMMAND "${CMAKE_COMMAND}" -E copy_directory "${CMAKE_CURRENT_BINARY_DIR}/castxml-prefix/src/castxml" "${CMAKE_CURRENT_BINARY_DIR}/castxml" +@@ -98,9 +97,10 @@ else() + itk_download_attempt_check(Clang) + endif() + set(llvm_version 3.7.0) ++ set(llvm_hash 57b5ded48d777f10f26963a4) + ExternalProject_Add(llvm +- URL https://midas3.kitware.com/midas/download/bitstream/457222/llvm-${llvm_version}.src.tar.gz +- URL_MD5 255939e1ba0a40d687a683e41323baca ++ URL "https://data.kitware.com/api/v1/file/${llvm_hash}/download" ++ URL_HASH MD5=${llvm_hash} + SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/llvm-${llvm_version} + CMAKE_ARGS -Wno-dev + CMAKE_GENERATOR "${CMAKE_GENERATOR}" +@@ -113,12 +113,13 @@ else() + -DLLVM_INCLUDE_DOCS:BOOL=OFF + INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/llvm + ) ++ set(clang_hash 57b5dec48d777f10f2696395) + ExternalProject_Add(clang + # This is the upstream source code repackages in a .tar.gz for + # compatibility with older CMake. Also the tests/ and doc/ directories + # are removed to remove symlink files and save space. +- URL https://midas3.kitware.com/midas/download/bitstream/457221/cfe-${llvm_version}.src.tar.gz +- URL_MD5 d4290cab76f44be2d38631f819b8c2ec ++ URL "https://data.kitware.com/api/v1/file/${clang_hash}/download" ++ URL_HASH_MD5=${clang_hash} + DEPENDS llvm + SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/cfe-${llvm_version} + CMAKE_ARGS -Wno-dev +diff --git a/Wrapping/Generators/SwigInterface/CMakeLists.txt b/Wrapping/Generators/SwigInterface/CMakeLists.txt +index b92cf8cb83..cd27f7a41b 100644 +--- a/Wrapping/Generators/SwigInterface/CMakeLists.txt ++++ b/Wrapping/Generators/SwigInterface/CMakeLists.txt +@@ -24,8 +24,8 @@ mark_as_advanced(ITK_USE_SYSTEM_SWIG) + set(swig_version_min 3.0.0) + + set(ITK_SWIG_VERSION 3.0.12) +-set(swig_md5 "82133dfa7bba75ff9ad98a7046be687c") +-set(swigwin_md5 "a49524dad2c91ae1920974e7062bfc93") ++set(swig_hash "85605bd98bf2b56f5bfca23ae23d76d764d76a174b05836c8686825e912d6326c370e9cf2134c0bf4f425560be103b16bf9c9d075077f52e713a69082616e906") ++set(swigwin_hash "90734503b9c3cd54c3351182d116d100fdcb379fe2e4a510264f81f1e07d5035c778416c665b1fbeeeea56e8aec55af27c53c7f4b082ff54d4fc3a6c0cd382a8") + + if(WIN32) + set(swig_ep "${CMAKE_CURRENT_BINARY_DIR}/swigwin-${ITK_SWIG_VERSION}/swig.exe") +@@ -68,8 +68,8 @@ else() + itk_download_attempt_check(SWIG) + endif() + ExternalProject_Add(swig +- URL "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${swigwin_md5}&name=swigwin-${ITK_SWIG_VERSION}.zip" +- URL_MD5 ${swigwin_md5} ++ URL "https://data.kitware.com/api/v1/file/hashsum/sha512/${swigwin_hash}/download" ++ URL_HASH SHA512=${swigwin_hash} + SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/swigwin-${SWIG_VERSION} + CONFIGURE_COMMAND "" + BUILD_COMMAND "" +@@ -141,11 +141,10 @@ else() + install + ) + endif() +- set(pcre_md5 890c808122bd90f398e6bc40ec862102) +- set(pcre_version 8.40) ++ set(pcre_hash f919957ce6e1f52b5579faa7fccfe192944884dc56ad831ebb3e3787f752fe2f14567fe302d884fa86900018e92b758e4589406f7e8d7af1baa2a1d6add40865) + ExternalProject_Add(PCRE +- URL "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${pcre_md5}&name=pcre-${pcre_version}.tar.gz" +- URL_MD5 ${pcre_md5} ++ URL "https://data.kitware.com/api/v1/file/hashsum/sha512/${pcre_hash}/download" ++ URL_HASH SHA512=${pcre_hash} + CONFIGURE_COMMAND + ${pcre_env} + ../PCRE/configure +@@ -245,8 +244,8 @@ message(STATUS \"Swig configure successfully completed.\") + endif() + + ExternalProject_Add(swig +- URL "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${swig_md5}&name=swig-${ITK_SWIG_VERSION}.tar.gz" +- URL_MD5 ${swig_md5} ++ URL "https://data.kitware.com/api/v1/file/hashsum/sha512/${swig_hash}/download" ++ URL_HASH SHA512=${swig_hash} + CONFIGURE_COMMAND + ${extra_swig_configure_env} ${CMAKE_COMMAND} -P "${_swig_configure_script}" + ${extra_external_project_commands} diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb index c983270e9ea..b6a25b25c4e 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb @@ -14,7 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/InsightSoftwareConsortium/ITK/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['37122d65b89699df33f34e0859f1e7adf5a6222060dc1c47383ff7aa4531223a'] +patches = ['ITK-4.13.0_update-download-URLs.patch'] +checksums = [ + '37122d65b89699df33f34e0859f1e7adf5a6222060dc1c47383ff7aa4531223a', # v4.13.0.tar.gz + 'a05c883634077de177af09f166bad7cfcd73bfebec671394299a08a55e109bc0', # ITK-4.13.0_update-download-URLs.patch +] builddependencies = [ ('CMake', '3.10.2'), @@ -30,10 +34,17 @@ dependencies = [ ('X11', '20180131') ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DITK_WRAP_PYTHON=ON ' -configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON ' +local_sys_deps = ['HDF5', 'SWIG'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DITK_WRAP_PYTHON=ON ' +configopts += '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +configopts += ' '.join(local_sys_cmake) +# Don't depend on MPICXX (which makes linking to ITK painful) +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' +prebuildopts = "export LC_ALL=C && " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " separate_build_dir = True @@ -42,7 +53,7 @@ modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', - 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkhdf5.a', + 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkjpeg-%(version_major_minor)s.a', 'lib/libitkpng-%(version_major_minor)s.a'], 'dirs': ['include/ITK-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages', diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb index 31bc442fec8..ff2ea437903 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb @@ -14,7 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/InsightSoftwareConsortium/ITK/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['37122d65b89699df33f34e0859f1e7adf5a6222060dc1c47383ff7aa4531223a'] +patches = ['ITK-4.13.0_update-download-URLs.patch'] +checksums = [ + '37122d65b89699df33f34e0859f1e7adf5a6222060dc1c47383ff7aa4531223a', # v4.13.0.tar.gz + 'a05c883634077de177af09f166bad7cfcd73bfebec671394299a08a55e109bc0', # ITK-4.13.0_update-download-URLs.patch +] builddependencies = [ ('CMake', '3.10.2'), @@ -30,10 +34,17 @@ dependencies = [ ('X11', '20180131') ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DITK_WRAP_PYTHON=ON ' -configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON ' +local_sys_deps = ['HDF5', 'SWIG'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DITK_WRAP_PYTHON=ON ' +configopts += '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +configopts += ' '.join(local_sys_cmake) +# Don't depend on MPICXX (which makes linking to ITK painful) +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' +prebuildopts = "export LC_ALL=C && " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " separate_build_dir = True @@ -42,7 +53,7 @@ modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', - 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkhdf5.a', + 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkjpeg-%(version_major_minor)s.a', 'lib/libitkpng-%(version_major_minor)s.a'], 'dirs': ['include/ITK-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages', diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.0_update-download-URLs.patch b/easybuild/easyconfigs/i/ITK/ITK-4.13.0_update-download-URLs.patch new file mode 100644 index 00000000000..ab20a7f7fd4 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.0_update-download-URLs.patch @@ -0,0 +1,151 @@ +From 716fe079a6fad64f63f1166c7cb1565acef982ee Mon Sep 17 00:00:00 2001 +From: Matt McCormick +Date: Wed, 6 Jun 2018 11:32:18 -0400 +Subject: [PATCH] BUG: Migrate midas3.kitware.com to data.kitware.com + +midas3.kitware.com is deprecated. + +Change-Id: Iba445e27b6c0f136cc6c5a361c088075dfa1facb +--- + CMake/ITKExternalData.cmake | 3 --- + CMake/itkExternal_FFTW.cmake | 8 +++--- + Documentation/Release.md | 2 +- + Utilities/Maintenance/JREUpdate.py | 4 +-- + Utilities/Maintenance/SourceTarball.bash | 2 +- + Wrapping/Generators/CastXML/CMakeLists.txt | 27 +++++++++---------- + .../Generators/SwigInterface/CMakeLists.txt | 19 +++++++------ + 7 files changed, 30 insertions(+), 35 deletions(-) + +diff --git a/CMake/ITKExternalData.cmake b/CMake/ITKExternalData.cmake +index a97d725922c..4e2dcd29651 100644 +--- a/CMake/ITKExternalData.cmake ++++ b/CMake/ITKExternalData.cmake +@@ -37,9 +37,6 @@ if(NOT ITK_FORBID_DOWNLOADS) + # Data published on Girder + "https://data.kitware.com:443/api/v1/file/hashsum/%(algo)/%(hash)/download" + +- # Data published on MIDAS +- "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=%(hash)&algorithm=%(algo)" +- + # Data published by developers using git-gerrit-push. + "https://itk.org/files/ExternalData/%(algo)/%(hash)" + +diff --git a/CMake/itkExternal_FFTW.cmake b/CMake/itkExternal_FFTW.cmake +index 7b44f0d68cb..bcfae61c2ec 100644 +--- a/CMake/itkExternal_FFTW.cmake ++++ b/CMake/itkExternal_FFTW.cmake +@@ -82,15 +82,15 @@ else() + endif() + + set(_fftw_target_version 3.3.4) +- set(_fftw_url_md5 "2edab8c06b24feeb3b82bbb3ebf3e7b3") +- set(_fftw_url "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${_fftw_url_md5}&name=fftw-${_fftw_target_version}.tar.gz") ++ set(_fftw_url_hash "1ee2c7bec3657f6846e63c6dfa71410563830d2b951966bf0123bd8f4f2f5d6b50f13b76d9a7b0eae70e44856f829ca6ceb3d080bb01649d1572c9f3f68e8eb1") ++ set(_fftw_url "https://data.kitware.com/api/v1/file/hashsum/sha512/${_fftw_url_hash}/download") + + if(ITK_USE_FFTWF) + itk_download_attempt_check(FFTW) + ExternalProject_add(fftwf + PREFIX fftwf + URL "${_fftw_url}" +- URL_MD5 "${_fftw_url_md5}" ++ URL_HASH SHA512="${_fftw_url_hash}" + DOWNLOAD_NAME "fftw-${_fftw_target_version}.tar.gz" + CONFIGURE_COMMAND + env +@@ -118,7 +118,7 @@ else() + ExternalProject_add(fftwd + PREFIX fftwd + URL "${_fftw_url}" +- URL_MD5 "${_fftw_url_md5}" ++ URL_HASH SHA512="${_fftw_url_hash}" + DOWNLOAD_NAME "fftw-${_fftw_target_version}.tar.gz" + CONFIGURE_COMMAND + env +diff --git a/Utilities/Maintenance/SourceTarball.bash b/Utilities/Maintenance/SourceTarball.bash +index 1c0335674e2..221d88813bc 100755 +--- a/Utilities/Maintenance/SourceTarball.bash ++++ b/Utilities/Maintenance/SourceTarball.bash +@@ -57,7 +57,7 @@ download_object() { + algo="$1" ; hash="$2" ; path="$3" + mkdir -p $(dirname "$path") && + if wget "https://www.itk.org/files/ExternalData/$algo/$hash" -O "$path.tmp$$" 1>&2 || \ +- wget "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${hash}&algorithm=${algo}" -O "$path.tmp$$" 1>&2; then ++ wget "https://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&checksum=${hash}&algorithm=${algo}" -O "$path.tmp$$" 1>&2; then + mv "$path.tmp$$" "$path" + else + rm -f "$path.tmp$$" +diff --git a/Wrapping/Generators/CastXML/CMakeLists.txt b/Wrapping/Generators/CastXML/CMakeLists.txt +index f0254b2f4e6..efa83e0325f 100644 +--- a/Wrapping/Generators/CastXML/CMakeLists.txt ++++ b/Wrapping/Generators/CastXML/CMakeLists.txt +@@ -25,23 +25,22 @@ else() + # If 64 bit Linux build host, use the CastXML binary + if(CMAKE_HOST_SYSTEM_NAME MATCHES "Linux" AND CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64") + +- set(_castxml_hash 84c2851a4df419b5834114bbfafa8d3e) +- set(_castxml_url "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${_castxml_hash}&name=castxml-linux.tar.gz") ++ set(_castxml_hash 1e0f51ab98592ac9934bb1c93040fd473519a02d1e3ce0090443f4f3566eb8354eb3e5bd04a2c91d832d33d0d712363c508bd2304da34db9963787890808ec9e) ++ set(_castxml_url "https://data.kitware.com/api/v1/file/hashsum/sha512/${_castxml_hash}/download") + set(_download_castxml_binaries 1) + + # If 64 bit Windows build host, use the CastXML binary + elseif(CMAKE_HOST_SYSTEM_NAME MATCHES "Windows" AND CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "AMD64") + +- set(_castxml_hash b862fcc384b496c0d9a39dea0386454a) +- set(_castxml_url https://midas3.kitware.com/midas/download/bitstream/460537/castxml-windows.zip) +- set(_castxml_url "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${_castxml_hash}&name=castxml-windows.zip") ++ set(_castxml_hash 1c379ea91f4c0d9b8127d841edee7c415fdde40665a2a3682aef22def75bd1cea99d26bb3b1b243e61e976d78233ed12a2614236e76206d1ae083583f4bc17ea) ++ set(_castxml_url "https://data.kitware.com/api/v1/file/hashsum/sha512/${_castxml_hash}/download") + set(_download_castxml_binaries 1) + + # If 64 bit Mac OS X build host ( >= 10.9, Mavericks), use the CastXML binary + elseif(CMAKE_HOST_SYSTEM_NAME MATCHES "Darwin" AND CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64" AND (NOT CMAKE_HOST_SYSTEM_VERSION VERSION_LESS "13.0.0")) + +- set(_castxml_hash e784aa985f59f57f4d71339bd60e27a8) +- set(_castxml_url "https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${_castxml_hash}&name=castxml-macosx.tar.gz") ++ set(_castxml_hash 2fa32cd083ed901499774eb34249c70c2d32a93c55e27dbb62f5ec3c7386ab6745dbbad78c653a0909b05b5d965839ec31ad9fca294cc0b7af9dfc15e2a7e063) ++ set(_castxml_url "https://data.kitware.com/api/v1/file/hashsum/sha512/${_castxml_hash}/download") + set(_download_castxml_binaries 1) + + endif() +@@ -53,7 +52,7 @@ else() + endif() + ExternalProject_Add(castxml + URL ${_castxml_url} +- URL_MD5 ${_castxml_hash} ++ URL_HASH SHA512=${_castxml_hash} + CONFIGURE_COMMAND "" + BUILD_COMMAND "" + INSTALL_COMMAND "${CMAKE_COMMAND}" -E copy_directory "${CMAKE_CURRENT_BINARY_DIR}/castxml-prefix/src/castxml" "${CMAKE_CURRENT_BINARY_DIR}/castxml" +@@ -98,10 +97,10 @@ else() + itk_download_attempt_check(Clang) + endif() + set(llvm_version 5.0.0) +- set(llvm_md5 e3782305ff4a60ad9bbc3a926425786f) ++ set(llvm_hash a65412cb45c73f73fcdef8016d3538114c1d0d1c6a5ed030a20e5049a6582b7926f184f2a3c065550e92e8ac27743bbf1a87b76be85949c0114d0320264018bd) + ExternalProject_Add(llvm +- URL https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${llvm_md5}&name=llvm-${llvm_version}.src.tar.gz +- URL_MD5 ${llvm_md5} ++ URL "https://data.kitware.com/api/v1/file/hashsum/sha512/${llvm_hash}/download" ++ URL_HASH SHA512=${llvm_hash} + SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/llvm-${llvm_version} + CMAKE_ARGS -Wno-dev + CMAKE_GENERATOR "${CMAKE_GENERATOR}" +@@ -115,13 +114,13 @@ else() + -DLLVM_INCLUDE_DOCS:BOOL=OFF + INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/llvm + ) +- set(clang_md5 79eddb9b1f6e6ee8e9eeff1245d3f359) ++ set(clang_hash f4d46cb0e76b84d8270da7bc62927c6c3acfa42cf9982012842f5e56b4b846ca4fc6ddb1ed6370cc5b6cd224c0dc420a7f3550d867855c23bcc20a3a3ee2d1bc) + ExternalProject_Add(clang + # This is the upstream source code repackages in a .tar.gz for + # compatibility with older CMake. Also the tests/ and doc/ directories + # are removed to remove symlink files and save space. +- URL https://midas3.kitware.com/midas/api/rest?method=midas.bitstream.download&checksum=${clang_md5}&name=cfe-${llvm_version}.src.tar.gz +- URL_MD5 ${clang_md5} ++ URL "https://data.kitware.com/api/v1/file/hashsum/sha512/${clang_hash}/download" ++ URL_HASH SHA512=${clang_hash} + DEPENDS llvm + SOURCE_DIR ${CMAKE_CURRENT_BINARY_DIR}/cfe-${llvm_version} + CMAKE_ARGS -Wno-dev diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb index aabbde17e3a..555fee43bb0 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb @@ -30,9 +30,15 @@ dependencies = [ ('X11', '20180131') ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DITK_WRAP_PYTHON=ON ' -configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON ' +local_sys_deps = ['HDF5', 'SWIG'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DITK_WRAP_PYTHON=ON ' +configopts += '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +configopts += ' '.join(local_sys_cmake) +# Don't depend on MPICXX (which makes linking to ITK painful) +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " @@ -42,7 +48,7 @@ modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', - 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkhdf5.a', + 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkjpeg-%(version_major_minor)s.a', 'lib/libitkpng-%(version_major_minor)s.a'], 'dirs': ['include/ITK-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages', diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb index c1cdf667eb3..b7300beac4d 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb @@ -30,9 +30,15 @@ dependencies = [ ('X11', '20180131') ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DITK_WRAP_PYTHON=ON ' -configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON ' +local_sys_deps = ['HDF5', 'SWIG'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DITK_WRAP_PYTHON=ON ' +configopts += '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +configopts += ' '.join(local_sys_cmake) +# Don't depend on MPICXX (which makes linking to ITK painful) +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " @@ -42,7 +48,7 @@ modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', - 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkhdf5.a', + 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkjpeg-%(version_major_minor)s.a', 'lib/libitkpng-%(version_major_minor)s.a'], 'dirs': ['include/ITK-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages', diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb index fd19870d6e2..4357de2d400 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb @@ -30,9 +30,15 @@ dependencies = [ ('X11', '20180604') ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DITK_WRAP_PYTHON=ON ' -configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON ' +local_sys_deps = ['HDF5', 'SWIG'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DITK_WRAP_PYTHON=ON ' +configopts += '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +configopts += ' '.join(local_sys_cmake) +# Don't depend on MPICXX (which makes linking to ITK painful) +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " @@ -42,7 +48,7 @@ modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', - 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkhdf5.a', + 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkjpeg-%(version_major_minor)s.a', 'lib/libitkpng-%(version_major_minor)s.a'], 'dirs': ['include/ITK-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages', diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb index 2a3d5f3e9f5..e7c39f1cca9 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb @@ -30,9 +30,15 @@ dependencies = [ ('X11', '20180604') ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DITK_WRAP_PYTHON=ON ' -configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON ' +local_sys_deps = ['HDF5', 'SWIG'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DITK_WRAP_PYTHON=ON ' +configopts += '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +configopts += ' '.join(local_sys_cmake) +# Don't depend on MPICXX (which makes linking to ITK painful) +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " @@ -42,7 +48,7 @@ modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', - 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkhdf5.a', + 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkjpeg-%(version_major_minor)s.a', 'lib/libitkpng-%(version_major_minor)s.a'], 'dirs': ['include/ITK-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages', diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb index 2a71979fdb2..a9c09084622 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb @@ -46,19 +46,16 @@ dependencies = [ separate_build_dir = True +local_sys_deps = ['EIGEN', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'SWIG', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + preconfigopts = 'Eigen3_DIR=$EBROOTEIGEN ' -configopts = '-DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' configopts += '-DITK_WRAP_PYTHON=ON -DITK_LEGACY_SILENT=ON ' -configopts += '-DITK_USE_SYSTEM_SWIG=ON -DITK_USE_SYSTEM_EIGEN=ON -DITK_USE_SYSTEM_HDF5=ON ' -configopts += '-DITK_USE_SYSTEM_JPEG=ON -DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' -configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib64/libjpeg.%s ' % SHLIB_EXT -configopts += '-DITK_USE_SYSTEM_PNG=ON -DPNG_PNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' -configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT -configopts += '-DITK_USE_SYSTEM_TIFF=ON -DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' -configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT -configopts += '-DITK_USE_SYSTEM_ZLIB=ON -DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' -configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +configopts += ' '.join(local_sys_cmake) +# Don't depend on MPICXX (which makes linking to ITK painful) +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb index 4ecc1f13527..443239f5b85 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb @@ -46,19 +46,16 @@ dependencies = [ separate_build_dir = True +local_sys_deps = ['EIGEN', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'SWIG', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + preconfigopts = 'Eigen3_DIR=$EBROOTEIGEN ' -configopts = '-DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' configopts += '-DITK_WRAP_PYTHON=ON -DITK_LEGACY_SILENT=ON ' -configopts += '-DITK_USE_SYSTEM_SWIG=ON -DITK_USE_SYSTEM_EIGEN=ON -DITK_USE_SYSTEM_HDF5=ON ' -configopts += '-DITK_USE_SYSTEM_JPEG=ON -DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include ' -configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib*/libjpeg.%s ' % SHLIB_EXT -configopts += '-DITK_USE_SYSTEM_PNG=ON -DPNG_PNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' -configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.%s ' % SHLIB_EXT -configopts += '-DITK_USE_SYSTEM_TIFF=ON -DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' -configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s ' % SHLIB_EXT -configopts += '-DITK_USE_SYSTEM_ZLIB=ON -DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' -configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +configopts += ' '.join(local_sys_cmake) +# Don't depend on MPICXX (which makes linking to ITK painful) +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' prebuildopts = "LC_ALL=C " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb index c9b063e7075..22d9b08b31e 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb @@ -30,19 +30,23 @@ dependencies = [ ('X11', '20180604') ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DITK_WRAP_PYTHON=ON ' -configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON ' +local_sys_deps = ['HDF5', 'SWIG'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DITK_WRAP_PYTHON=ON ' +configopts += '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +configopts += ' '.join(local_sys_cmake) -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +prebuildopts = "LC_ALL=C " -separate_build_dir = True +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', - 'lib/libITKVtkGlue-%(version_major)s.0.a', 'lib/libitkhdf5.a', + 'lib/libITKVtkGlue-%(version_major)s.0.a', 'lib/libitkjpeg-%(version_major)s.0.a', 'lib/libitkpng-%(version_major)s.0.a'], 'dirs': ['include/ITK-%(version_major)s.0', 'lib/python%(pyshortver)s/site-packages', From 4298c418c0c3e02c96c8f8b9649fe1f323c4c995 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 10:38:20 +0200 Subject: [PATCH 0657/9987] MMseqs2: Use build_type instead of configopts --- easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb | 2 +- easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-gompi-2019b.eb | 2 +- easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-iimpi-2019b.eb | 2 +- easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb | 2 +- easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb | 1 - easybuild/easyconfigs/m/MMseqs2/MMseqs2-5-9375b-intel-2018a.eb | 2 +- easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb | 2 +- 7 files changed, 6 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb index 818052dcf9d..ff98ddc348f 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb @@ -21,7 +21,7 @@ separate_build_dir = True builddependencies = [('CMake', '3.4.3')] -configopts = '-DCMAKE_BUILD_TYPE=RELEASE' +build_type = 'RELEASE' dependencies = [ ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-gompi-2019b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-gompi-2019b.eb index 77d564b2bc8..0deebfba285 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-gompi-2019b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-gompi-2019b.eb @@ -22,7 +22,7 @@ builddependencies = [('CMake', '3.15.3')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=RELEASE' +build_type = 'RELEASE' sanity_check_paths = { 'files': ['bin/mmseqs'], diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-iimpi-2019b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-iimpi-2019b.eb index ce11764bfb4..c0e0588511d 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-iimpi-2019b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-iimpi-2019b.eb @@ -20,7 +20,7 @@ builddependencies = [('CMake', '3.15.3')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=RELEASE' +build_type = 'RELEASE' sanity_check_paths = { 'files': ['bin/mmseqs'], diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb index 668c50a0754..c53106f4e18 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb @@ -26,7 +26,7 @@ builddependencies = [('CMake', '3.15.3')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=RELEASE' +build_type = 'RELEASE' sanity_check_paths = { 'files': ['bin/mmseqs'], diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb index 876e969d182..2ea322fa298 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb @@ -19,7 +19,6 @@ dependencies = [('bzip2', '1.0.8')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=RELEASE' sanity_check_paths = { 'files': ['bin/mmseqs'], diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-5-9375b-intel-2018a.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-5-9375b-intel-2018a.eb index ad123863b1a..41b7ac2e421 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-5-9375b-intel-2018a.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-5-9375b-intel-2018a.eb @@ -16,7 +16,7 @@ builddependencies = [('CMake', '3.10.2')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=RELEASE' +build_type = 'RELEASE' sanity_check_paths = { 'files': ['bin/mmseqs'], diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb index aa1307b0c4e..051d3e33a52 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb @@ -16,7 +16,7 @@ builddependencies = [('CMake', '3.12.1')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=RELEASE' +build_type = 'RELEASE' sanity_check_paths = { 'files': ['bin/mmseqs'], From b4144a99e75bda9c6c397dc07451f208908c11fa Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 10:56:20 +0200 Subject: [PATCH 0658/9987] MMseqs2: Remove superflous cfg option --- easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb | 2 -- .../easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-gompi-2019b.eb | 2 -- .../easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-iimpi-2019b.eb | 2 -- .../easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb | 2 -- .../easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb | 3 --- easybuild/easyconfigs/m/MMseqs2/MMseqs2-5-9375b-intel-2018a.eb | 2 -- easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb | 2 -- 7 files changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb index ff98ddc348f..a6533f3fb00 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-1-c7a89-foss-2016b.eb @@ -17,8 +17,6 @@ source_urls = ['https://github.com/soedinglab/MMseqs2/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['e756a0e5cb3aa8e1e5a5b834a58ae955d9594be1806f0f32800427c55f3a45d5'] -separate_build_dir = True - builddependencies = [('CMake', '3.4.3')] build_type = 'RELEASE' diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-gompi-2019b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-gompi-2019b.eb index 0deebfba285..c61306b9936 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-gompi-2019b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-gompi-2019b.eb @@ -20,8 +20,6 @@ checksums = ['62415e545706adc6e9e6689d34902f405ab5e5c67c8c7562bdd9dd4da2088697'] builddependencies = [('CMake', '3.15.3')] -separate_build_dir = True - build_type = 'RELEASE' sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-iimpi-2019b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-iimpi-2019b.eb index c0e0588511d..46da7624b74 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-iimpi-2019b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-10-6d92c-iimpi-2019b.eb @@ -18,8 +18,6 @@ checksums = [ builddependencies = [('CMake', '3.15.3')] -separate_build_dir = True - build_type = 'RELEASE' sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb index c53106f4e18..2ab31a38aa8 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb @@ -24,8 +24,6 @@ checksums = [ builddependencies = [('CMake', '3.15.3')] -separate_build_dir = True - build_type = 'RELEASE' sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb index 2ea322fa298..0e1cf8f454a 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2020b.eb @@ -17,9 +17,6 @@ builddependencies = [('CMake', '3.18.4')] dependencies = [('bzip2', '1.0.8')] -separate_build_dir = True - - sanity_check_paths = { 'files': ['bin/mmseqs'], 'dirs': [], diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-5-9375b-intel-2018a.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-5-9375b-intel-2018a.eb index 41b7ac2e421..cff65efb666 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-5-9375b-intel-2018a.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-5-9375b-intel-2018a.eb @@ -14,8 +14,6 @@ checksums = ['3f2905b01ab61d2ce0c30acbf53ed7eb3b36171da748d327da5edcbf1472bf59'] builddependencies = [('CMake', '3.10.2')] -separate_build_dir = True - build_type = 'RELEASE' sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb index 051d3e33a52..540dabdb605 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-8-fac81-intel-2018b.eb @@ -14,8 +14,6 @@ checksums = ['035d1c9a5fcfae50bc2d201f177722bd79d95d3ba32342972baa7b142b52aa82'] builddependencies = [('CMake', '3.12.1')] -separate_build_dir = True - build_type = 'RELEASE' sanity_check_paths = { From fe77982104da6aab9494807dc489df8b32b264b8 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 5 Aug 2021 11:03:03 +0200 Subject: [PATCH 0659/9987] adding easyconfigs: jax-0.2.18-foss-2020b.eb --- .../j/jax/jax-0.2.18-foss-2020b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb new file mode 100644 index 00000000000..532849a2ad4 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'jax' +version = '0.2.18' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and +more""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +# source_urls = [PYPI_SOURCE] +# sources = [SOURCE_TAR_GZ] + +source_urls = ['https://github.com/google/jax/archive/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = [ + 'jax-0.2.18-correct_libraries.patch', +] + +preinstallopts = 'python3 build/build.py --output_user_root=%(builddir)s --bazel_path="$EBROOTBAZEL/bin/bazel" && ' +preinstallopts += 'pip install dist/*.whl && ' + +dependencies = [ + ('Python', '3.8.6'), + ('Bazel', '3.7.2'), + ('SciPy-bundle', '2020.11'), + ('Cython', '0.29.22'), + # ('TensorFlow', '2.5.0'), do we need this? +] + +use_pip = True + + +moduleclass = 'tools' From 0ae1b5937720d5bd4a26a0f8086ca4ed7d0c08a9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 11:04:04 +0200 Subject: [PATCH 0660/9987] OpenCV: Avoid using system GTK+3 and remove CMAKE_BUILD_TYPE --- .../easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb | 8 +++++--- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 4 ++-- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 3 +-- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 3 +-- .../o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb | 3 +-- .../o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb | 3 +-- .../o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb | 3 +-- .../o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb | 3 +-- 11 files changed, 19 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb index eaf3b0adfec..70e5bf517cc 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb @@ -13,8 +13,11 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://github.com/Itseez/opencv/archive/'] sources = ['%(version)s.zip'] - patches = ['OpenCV-2.4.9_with_IPP.patch'] +checksums = [ + '2a7e47da87b9119be922f010a1059539e96130c242f4d38e2dbb445ccbeccbc1', # 2.4.12.zip + '420a55405e638623c7d606828489955d4186b5c22ba9bcfd49f4937bbb62b31c', # OpenCV-2.4.9_with_IPP.patch +] builddependencies = [ ('CMake', '3.5.2'), @@ -36,8 +39,7 @@ dependencies = [ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts = '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index 73c03c05319..71a179c34f1 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -49,8 +49,7 @@ dependencies = [ local_ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (local_ippicv_dir, local_ippicv_dir) -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts = '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT @@ -66,6 +65,7 @@ configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +configopts += '-DWITH_GTK_2_X=ON' local_startdir = '%(builddir)s/%(namelower)s-%(version)s' postinstallcmds = ["cp %s/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %%(installdir)s/lib" diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index fae2abfc2d0..c983e1fdf0b 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -47,8 +47,7 @@ dependencies = [ local_ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts = "mkdir -p %s && cp -a ../*.tgz %s && " % (local_ippicv_dir, local_ippicv_dir) -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts = '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT @@ -64,6 +63,7 @@ configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +configopts += '-DWITH_GTK_2_X=ON' local_startdir = '%(builddir)s/%(namelower)s-%(version)s' postinstallcmds = ["cp %s/3rdparty/ippicv/unpack/ippicv_lnx/lib/intel64/libippicv.* %%(installdir)s/lib" diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index a266b897122..1ea167eadfc 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -50,8 +50,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' local_ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts += "mkdir -p %s && cp -a ../*.tgz %s && " % (local_ippicv_dir, local_ippicv_dir) -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts = '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index bc59e66067d..554cb1cb273 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -51,8 +51,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' local_ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts += "mkdir -p %s && cp -a ../*.tgz %s && " % (local_ippicv_dir, local_ippicv_dir) -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts = '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb index 771550ead62..204d5064bea 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb @@ -50,8 +50,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' local_ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts += "mkdir -p %s && cp -a ../*.tgz %s && " % (local_ippicv_dir, local_ippicv_dir) -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts = '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT @@ -67,6 +66,7 @@ configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +configopts += '-DWITH_GTK_2_X=ON' postinstallcmds = ["cp 3rdparty/ippicv/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb index f57bbe5c0a2..6727d4e58da 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb @@ -50,8 +50,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' local_ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts += "mkdir -p %s && cp -a ../*.tgz %s && " % (local_ippicv_dir, local_ippicv_dir) -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts = '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT @@ -67,6 +66,7 @@ configopts += '-DJASPER_INCLUDE_DIR=$EBROOTJASPER/include ' configopts += '-DWITH_IPP=ON ' configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' configopts += '-DWITH_CUDA=OFF ' +configopts += '-DWITH_GTK_2_X=ON' postinstallcmds = ["cp 3rdparty/ippicv/ippicv_lnx/lib/intel64/libippicv.* %(installdir)s/lib"] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb index 839f277cf51..750d74b0485 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb @@ -52,8 +52,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' local_ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts += "mkdir -p %s && cp -a ../*.tgz %s && " % (local_ippicv_dir, local_ippicv_dir) -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts = '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb index cf822b74fe2..6d11e2ff77d 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb @@ -52,8 +52,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' local_ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts += "mkdir -p %s && cp -a ../*.tgz %s && " % (local_ippicv_dir, local_ippicv_dir) -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts = '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb index c5efd9cb14c..293945598e4 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb @@ -50,8 +50,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' local_ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts += "mkdir -p %s && cp -a ../*.tgz %s && " % (local_ippicv_dir, local_ippicv_dir) -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts = '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb index 042fd87ce1b..7c0fdad4b14 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb @@ -50,8 +50,7 @@ preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' local_ippicv_dir = '3rdparty/ippicv/downloads/linux-808b791a6eac9ed78d32a7666804320e/' preconfigopts += "mkdir -p %s && cp -a ../*.tgz %s && " % (local_ippicv_dir, local_ippicv_dir) -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts = '-DBUILD_PYTHON_SUPPORT=ON ' configopts += '-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages ' configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s ' % SHLIB_EXT From 9a1e5a301948614756b18d32a4ca5a101ab4f9ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Aug 2021 11:05:26 +0200 Subject: [PATCH 0661/9987] use $MKLROOT to specify Intel MKL prefix in OpenMolcas easyconfig --- .../easyconfigs/o/OpenMolcas/OpenMolcas-21.06-intel-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-intel-2021a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-intel-2021a.eb index ebefff700b7..bc3c48de829 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-intel-2021a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-intel-2021a.eb @@ -28,7 +28,7 @@ builddependencies = [('CMake', '3.20.1')] separate_build_dir = True preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' -configopts = '-DLINALG=MKL -DMKLROOT=$EBROOTIMKL/mkl/latest ' +configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' configopts += '-DMPI=ON -DOPENMP=ON -DGA=ON ' configopts += '-DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON' From e325630215373a5386b03b2280afab4f513bd9e9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 11:08:05 +0200 Subject: [PATCH 0662/9987] Avoid MPICXX dependency in SimpleElastics ITK --- .../SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb index 7a9bf4502a2..03165ec8f41 100644 --- a/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb @@ -35,7 +35,7 @@ dependencies = [ default_easyblock = 'CMakeMake' -local_itk_configopts = "-DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=OFF -DBUILD_TESTING=OFF " +local_itk_configopts = "-DBUILD_SHARED_LIBS=OFF -DBUILD_TESTING=OFF " local_itk_configopts += "-DITK_WRAP_PYTHON=OFF -DModule_ITKReview=ON " local_itk_configopts += "-DITK_USE_SYSTEM_SWIG=ON -DITK_USE_SYSTEM_EIGEN=ON -DITK_USE_SYSTEM_HDF5=ON " local_itk_configopts += "-DITK_USE_SYSTEM_JPEG=ON -DJPEG_INCLUDE_DIR=$EBROOTLIBJPEGMINTURBO/include " @@ -46,11 +46,13 @@ local_itk_configopts += "-DITK_USE_SYSTEM_TIFF=ON -DTIFF_INCLUDE_DIR=$EBROOTLIBT local_itk_configopts += "-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.%s " % SHLIB_EXT local_itk_configopts += "-DITK_USE_SYSTEM_ZLIB=ON -DZLIB_INCLUDE_DIR=$EBROOTZLIB/include " local_itk_configopts += "-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.%s " % SHLIB_EXT +# Don't depend on MPICXX (which makes linking to ITK painful) +local_itk_configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' -local_elastix_configopts = "-DCMAKE_BUILD_TYPE=Release -DELASTIX_BUILD_EXECUTABLE=OFF " +local_elastix_configopts = "-DELASTIX_BUILD_EXECUTABLE=OFF " local_elastix_configopts += "-DITK_DIR=%%(builddir)s/ITK-%s/easybuild_obj/" % local_itk_ver -local_simpleelastix_configopts = "-DCMAKE_BUILD_TYPE=ON -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF " +local_simpleelastix_configopts = "-DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF " local_simpleelastix_configopts += '-DCMAKE_C_FLAGS="$CFLAGS -fpermissive" -DCMAKE_CXX_FLAGS="$CXXFLAGS -fpermissive" ' local_simpleelastix_configopts += "-DITK_DIR=%%(builddir)s/ITK-%s/easybuild_obj/ " % local_itk_ver local_simpleelastix_configopts += "-DElastix_DIR=%%(builddir)s/elastix-%s/easybuild_obj/ " % local_elastix_ver From f3e3c7c99271b36a681c69768e6dfe22ffbe09d7 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 5 Aug 2021 11:11:21 +0200 Subject: [PATCH 0663/9987] adding jax patch --- .../j/jax/jax-0.2.18-correct_libraries.patch | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch new file mode 100644 index 00000000000..9fe87443594 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch @@ -0,0 +1,63 @@ +diff -ruN jax_orig/build/build.py jax/build/build.py +--- jax_orig/build/build.py 2021-07-30 10:18:43.599233082 +0200 ++++ jax/build/build.py 2021-08-02 15:58:09.654165000 +0200 +@@ -41,7 +41,7 @@ + else: + from distutils.spawn import find_executable as which + # pylint: enable=g-import-not-at-top +- ++use_default_shell_env = True + + def is_windows(): + return sys.platform.startswith("win32") +Binary files jax_orig/.git/index and jax/.git/index differ +diff -ruN jax_orig/jaxlib/jax.bzl jax/jaxlib/jax.bzl +--- jax_orig/jaxlib/jax.bzl 2021-07-30 10:18:47.211049000 +0200 ++++ jax/jaxlib/jax.bzl 2021-08-02 10:39:41.567268000 +0200 +@@ -30,3 +30,4 @@ + if_rocm_is_configured = _if_rocm_is_configured + flatbuffer_cc_library = _flatbuffer_cc_library + flatbuffer_py_library = _flatbuffer_py_library ++use_default_shell_env = True +diff -ruN jax_orig/jaxlib/lapack.pyx jax/jaxlib/lapack.pyx +--- jax_orig/jaxlib/lapack.pyx 2021-07-30 10:18:47.214725015 +0200 ++++ jax/jaxlib/lapack.pyx 2021-07-30 10:23:25.084607000 +0200 +@@ -49,6 +49,7 @@ + + cdef int _int32_max = 0x7FFFFFFF; + ++use_default_shell_env = True + + cdef register_cpu_custom_call_target(fn_name, void* fn): + cdef const char* name = "xla._CUSTOM_CALL_TARGET" +diff -ruN jax_orig/WORKSPACE jax/WORKSPACE +--- jax_orig/WORKSPACE 2021-07-30 10:18:43.503078000 +0200 ++++ jax/WORKSPACE 2021-08-03 18:13:58.627602000 +0200 +@@ -7,17 +7,24 @@ + # and update the sha256 with the result. + http_archive( + name = "org_tensorflow", +- sha256 = "de22145c9dc51b3ed9399dbee2ab681f094f09e5213d6819451da500f163a14b", ++ # sha256 = "de22145c9dc51b3ed9399dbee2ab681f094f09e5213d6819451da500f163a14b", + strip_prefix = "tensorflow-8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532", + urls = [ + "https://github.com/tensorflow/tensorflow/archive/8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532.tar.gz", + ], ++ patch_cmds=['sed -i -e "s|arguments = \[args\],|arguments = \[args\],\\n\\tuse_default_shell_env = True,|" third_party/mlir/tblgen.bzl'] + ) + +-# For development, one can use a local TF repository instead. ++# # For development, one can use a local TF repository instead. + # local_repository( + # name = "org_tensorflow", +-# path = "tensorflow", ++# path = "/apps/gent/CO7/skylake-ib/software/TensorFlow/2.5.0-foss-2020b", ++# ) ++# new_local_repository( ++# name = "org_tensorflow", ++# path = "/apps/gent/CO7/skylake-ib/software/TensorFlow/2.5.0-foss-2020b/lib/python3.8/site-packages/tensorflow/", ++# # build_file = "org_tensorflow.BUILD", ++ + # ) + + load("//third_party/pocketfft:workspace.bzl", pocketfft = "repo") From 98f804da649863ca6d41f2f6a27e354ea852667e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 5 Aug 2021 11:21:02 +0200 Subject: [PATCH 0664/9987] LLVM: Remove CMAKE_BUILD_TYPE --- easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb | 2 +- easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb | 6 ++++-- easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb | 2 +- easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb | 2 +- easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb | 2 +- easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017a.eb | 1 - easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017b.eb | 1 - easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-foss-2017b.eb | 1 - easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-fosscuda-2017b.eb | 1 - easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intel-2017b.eb | 1 - easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intelcuda-2017b.eb | 1 - easybuild/easyconfigs/l/LLVM/LLVM-5.0.1-GCCcore-6.4.0.eb | 1 - 12 files changed, 8 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb index c67faef292c..e3a624c70b3 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-foss-2016b.eb @@ -17,6 +17,7 @@ toolchainopts = {'cstd': 'gnu++11'} source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] +checksums = ['66c73179da42cee1386371641241f79ded250e117a79f571bbd69e56daa48948'] builddependencies = [ ('CMake', '3.6.1'), @@ -31,7 +32,6 @@ dependencies = [ configopts = "-DBUILD_SHARED_LIBS=ON " # required to install extra tools in bin/ configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=1 " -configopts += "-DCMAKE_BUILD_TYPE=Release " sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb index 7252e90e8be..37c35fb33e0 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.0-intel-2016b.eb @@ -17,8 +17,11 @@ toolchainopts = {'cstd': 'gnu++11'} source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] - patches = ['LLVM-3.9.0-intel-fix-loop.patch'] +checksums = [ + '66c73179da42cee1386371641241f79ded250e117a79f571bbd69e56daa48948', # llvm-3.9.0.src.tar.xz + '8c15c2888b3c4700cad030af4c0ccfbc086b1541859116a36ed810ad8547192a', # LLVM-3.9.0-intel-fix-loop.patch +] builddependencies = [ ('CMake', '3.6.1'), @@ -33,7 +36,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' # required to install extra tools in bin/ configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=1 " -configopts += "-DCMAKE_BUILD_TYPE=Release " sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb index 741ddda8b5d..e5601c17ae7 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.9.1-foss-2017a.eb @@ -17,6 +17,7 @@ toolchainopts = {'cstd': 'gnu++11'} source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] +checksums = ['1fd90354b9cf19232e8f168faf2220e79be555df3aa743242700879e8fd329ee'] builddependencies = [ ('CMake', '3.7.2'), @@ -31,7 +32,6 @@ dependencies = [ configopts = "-DBUILD_SHARED_LIBS=ON " # required to install extra tools in bin/ configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=1 " -configopts += "-DCMAKE_BUILD_TYPE=Release " sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb index 80c6f388ec5..57ffd380f8a 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-foss-2017a.eb @@ -17,6 +17,7 @@ toolchainopts = {'cstd': 'gnu++11'} source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] +checksums = ['8d10511df96e73b8ff9e7abbfb4d4d432edbdbe965f1f4f07afaf370b8a533be'] builddependencies = [ ('CMake', '3.7.2'), @@ -31,7 +32,6 @@ dependencies = [ configopts = "-DBUILD_SHARED_LIBS=ON " # required to install extra tools in bin/ configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=1 " -configopts += "-DCMAKE_BUILD_TYPE=Release " sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb index 0122c286a5e..db6643e8f6b 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.0-intel-2017a.eb @@ -17,6 +17,7 @@ toolchainopts = {'cstd': 'gnu++11'} source_urls = ["http://llvm.org/releases/%(version)s"] sources = ["llvm-%(version)s.src.tar.xz"] +checksums = ['8d10511df96e73b8ff9e7abbfb4d4d432edbdbe965f1f4f07afaf370b8a533be'] builddependencies = [ ('CMake', '3.7.2'), @@ -31,7 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' # required to install extra tools in bin/ configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=1 " -configopts += "-DCMAKE_BUILD_TYPE=Release " sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017a.eb index 9787394f8fb..b88b7b77deb 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017a.eb @@ -32,7 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' # required to install extra tools in bin/ configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=1 " -configopts += "-DCMAKE_BUILD_TYPE=Release " sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017b.eb index 0803920d392..d730299b86b 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-4.0.1-intel-2017b.eb @@ -32,7 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' # required to install extra tools in bin/ configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=1 " -configopts += '-DCMAKE_BUILD_TYPE=Release ' sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-foss-2017b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-foss-2017b.eb index 353f40d8fbb..92fb3075a67 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-foss-2017b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-foss-2017b.eb @@ -32,7 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' # required to install extra tools in bin/ configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=ON ' -configopts += '-DCMAKE_BUILD_TYPE=Release ' sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-fosscuda-2017b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-fosscuda-2017b.eb index ef87d251b82..cb000e66209 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-fosscuda-2017b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-fosscuda-2017b.eb @@ -32,7 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' # required to install extra tools in bin/ configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=ON ' -configopts += '-DCMAKE_BUILD_TYPE=Release ' sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intel-2017b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intel-2017b.eb index e4e7c04f11d..96fe79a1ce5 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intel-2017b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intel-2017b.eb @@ -32,7 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' # required to install extra tools in bin/ configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=1 " -configopts += "-DCMAKE_BUILD_TYPE=Release " sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intelcuda-2017b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intelcuda-2017b.eb index 38fcfaf3b0b..2c059a786c1 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intelcuda-2017b.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.0-intelcuda-2017b.eb @@ -32,7 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON -DCMAKE_EXE_LINKER_FLAGS="$LDFLAGS -shared-intel" ' # required to install extra tools in bin/ configopts += "-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=1 " -configopts += "-DCMAKE_BUILD_TYPE=Release " sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.1-GCCcore-6.4.0.eb index e1fbd9619ac..47096a65443 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-5.0.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-5.0.1-GCCcore-6.4.0.eb @@ -33,7 +33,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' # required to install extra tools in bin/ configopts += '-DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD=X86 -DLLVM_ENABLE_ZLIB=ON -DLLVM_ENABLE_RTTI=ON ' -configopts += '-DCMAKE_BUILD_TYPE=Release ' sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], From 4339d942bd1b261158a31235ac276c7810a4cbb3 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 5 Aug 2021 11:38:20 +0200 Subject: [PATCH 0665/9987] tmp dir prefix --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 532849a2ad4..280b9092adc 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -18,7 +18,9 @@ patches = [ 'jax-0.2.18-correct_libraries.patch', ] -preinstallopts = 'python3 build/build.py --output_user_root=%(builddir)s --bazel_path="$EBROOTBAZEL/bin/bazel" && ' +preinstallopts = 'python3 build/build.py +preinstallopts += '--bazel_startup_options="--output_user_root=%(builddir)s" ' +preinstallopts += ' --bazel_path="$EBROOTBAZEL/bin/bazel" && ' preinstallopts += 'pip install dist/*.whl && ' dependencies = [ From 49092477fab560487f1c341d60edb03481d0428f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 5 Aug 2021 11:44:57 +0200 Subject: [PATCH 0666/9987] removed unnecessary code --- .../j/jax/jax-0.2.18-correct_libraries.patch | 50 +++---------------- 1 file changed, 6 insertions(+), 44 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch index 9fe87443594..ec229a50638 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch @@ -1,39 +1,8 @@ -diff -ruN jax_orig/build/build.py jax/build/build.py ---- jax_orig/build/build.py 2021-07-30 10:18:43.599233082 +0200 -+++ jax/build/build.py 2021-08-02 15:58:09.654165000 +0200 -@@ -41,7 +41,7 @@ - else: - from distutils.spawn import find_executable as which - # pylint: enable=g-import-not-at-top -- -+use_default_shell_env = True - - def is_windows(): - return sys.platform.startswith("win32") Binary files jax_orig/.git/index and jax/.git/index differ -diff -ruN jax_orig/jaxlib/jax.bzl jax/jaxlib/jax.bzl ---- jax_orig/jaxlib/jax.bzl 2021-07-30 10:18:47.211049000 +0200 -+++ jax/jaxlib/jax.bzl 2021-08-02 10:39:41.567268000 +0200 -@@ -30,3 +30,4 @@ - if_rocm_is_configured = _if_rocm_is_configured - flatbuffer_cc_library = _flatbuffer_cc_library - flatbuffer_py_library = _flatbuffer_py_library -+use_default_shell_env = True -diff -ruN jax_orig/jaxlib/lapack.pyx jax/jaxlib/lapack.pyx ---- jax_orig/jaxlib/lapack.pyx 2021-07-30 10:18:47.214725015 +0200 -+++ jax/jaxlib/lapack.pyx 2021-07-30 10:23:25.084607000 +0200 -@@ -49,6 +49,7 @@ - - cdef int _int32_max = 0x7FFFFFFF; - -+use_default_shell_env = True - - cdef register_cpu_custom_call_target(fn_name, void* fn): - cdef const char* name = "xla._CUSTOM_CALL_TARGET" diff -ruN jax_orig/WORKSPACE jax/WORKSPACE --- jax_orig/WORKSPACE 2021-07-30 10:18:43.503078000 +0200 -+++ jax/WORKSPACE 2021-08-03 18:13:58.627602000 +0200 -@@ -7,17 +7,24 @@ ++++ jax/WORKSPACE 2021-08-05 11:44:13.187308000 +0200 +@@ -7,18 +7,14 @@ # and update the sha256 with the result. http_archive( name = "org_tensorflow", @@ -47,17 +16,10 @@ diff -ruN jax_orig/WORKSPACE jax/WORKSPACE ) -# For development, one can use a local TF repository instead. -+# # For development, one can use a local TF repository instead. - # local_repository( - # name = "org_tensorflow", +-# local_repository( +-# name = "org_tensorflow", -# path = "tensorflow", -+# path = "/apps/gent/CO7/skylake-ib/software/TensorFlow/2.5.0-foss-2020b", -+# ) -+# new_local_repository( -+# name = "org_tensorflow", -+# path = "/apps/gent/CO7/skylake-ib/software/TensorFlow/2.5.0-foss-2020b/lib/python3.8/site-packages/tensorflow/", -+# # build_file = "org_tensorflow.BUILD", -+ - # ) +-# ) load("//third_party/pocketfft:workspace.bzl", pocketfft = "repo") + pocketfft() From 56b1d48e4a1ff333ea21c29b66c63e5aee4cd58e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 5 Aug 2021 11:47:02 +0200 Subject: [PATCH 0667/9987] patch comment --- easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch index ec229a50638..23ad1156e6b 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch @@ -1,3 +1,4 @@ +solving bug in jaxlib's tensorflow dependency by providing it with correct env variables Binary files jax_orig/.git/index and jax/.git/index differ diff -ruN jax_orig/WORKSPACE jax/WORKSPACE --- jax_orig/WORKSPACE 2021-07-30 10:18:43.503078000 +0200 From 40672c6576d3c3a165f6e90ccee00a0f6d1ad7dd Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 5 Aug 2021 11:48:34 +0200 Subject: [PATCH 0668/9987] patch cleanup --- .../j/jax/jax-0.2.18-correct_libraries.patch | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch index 23ad1156e6b..76b94b95f97 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch @@ -2,14 +2,8 @@ solving bug in jaxlib's tensorflow dependency by providing it with correct env v Binary files jax_orig/.git/index and jax/.git/index differ diff -ruN jax_orig/WORKSPACE jax/WORKSPACE --- jax_orig/WORKSPACE 2021-07-30 10:18:43.503078000 +0200 -+++ jax/WORKSPACE 2021-08-05 11:44:13.187308000 +0200 -@@ -7,18 +7,14 @@ - # and update the sha256 with the result. - http_archive( - name = "org_tensorflow", -- sha256 = "de22145c9dc51b3ed9399dbee2ab681f094f09e5213d6819451da500f163a14b", -+ # sha256 = "de22145c9dc51b3ed9399dbee2ab681f094f09e5213d6819451da500f163a14b", - strip_prefix = "tensorflow-8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532", ++++ jax/WORKSPACE 2021-08-05 11:48:00.882688000 +0200 +@@ -12,13 +12,9 @@ urls = [ "https://github.com/tensorflow/tensorflow/archive/8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532.tar.gz", ], From 5a4705985c5212257117e931ac537f97a5c0c5a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Aug 2021 11:50:42 +0200 Subject: [PATCH 0669/9987] consistently use $MKLROOT in GlobalArrays easyconfig --- .../g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb index 322946d8896..7959aad80fa 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb @@ -14,8 +14,8 @@ sources = ['v%(version)s/ga-%(version)s.tar.gz'] checksums = ['64df7d1ea4053d24d84ca361e67a6f51c7b17ed7d626cb18a9fbc759f4a078ac'] configopts = ' --with-mpi --enable-i8' -configopts += ' --with-blas8="-L$EBROOTIMKL/mkl/latest/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' -configopts += ' --with-scalapack8="L${MKLROOT}/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += ' --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' # select armci network as (Comex) MPI-1 two-sided From 04ddadd1e358007bbcef59c882060fec456418d5 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 5 Aug 2021 12:30:13 +0200 Subject: [PATCH 0670/9987] cleanup --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 280b9092adc..9840c5651de 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -9,16 +9,13 @@ more""" toolchain = {'name': 'foss', 'version': '2020b'} -# source_urls = [PYPI_SOURCE] -# sources = [SOURCE_TAR_GZ] - source_urls = ['https://github.com/google/jax/archive/'] sources = ['%(name)s-v%(version)s.tar.gz'] patches = [ 'jax-0.2.18-correct_libraries.patch', ] -preinstallopts = 'python3 build/build.py +preinstallopts = 'python3 build/build.py ' preinstallopts += '--bazel_startup_options="--output_user_root=%(builddir)s" ' preinstallopts += ' --bazel_path="$EBROOTBAZEL/bin/bazel" && ' preinstallopts += 'pip install dist/*.whl && ' @@ -28,7 +25,6 @@ dependencies = [ ('Bazel', '3.7.2'), ('SciPy-bundle', '2020.11'), ('Cython', '0.29.22'), - # ('TensorFlow', '2.5.0'), do we need this? ] use_pip = True From 66f5d57db130e00be47d4a9620143041e29909a2 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 5 Aug 2021 14:16:09 +0200 Subject: [PATCH 0671/9987] {numlib}[GCC/11.2.0] OpenBLAS v0.3.17: Workaround for error in C/ZBLAS3 tests with GCC11 --- .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 6 +- ...nd-gcc11-miscompiling-C-ZBLAS3-tests.patch | 101 ++++++++++++++++++ 2 files changed, 104 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index e68ba4eae8f..4892d464d85 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -5,9 +5,6 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} -# need to build with -fno-tree-vectorize due to precision errors with GCC 11.2.0 -# cfr. https://github.com/easybuilders/easybuild-easyconfigs/pull/13580 -toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -18,11 +15,14 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + '%(name)s-%(version)s_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch', ] checksums = [ 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f', # v0.3.17.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.17_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch + 'ea76320bc047eff1bf2a2f50c1c19acb4fd6d2b8a5bf81a4dce73145a2a5cfcb', ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch new file mode 100644 index 00000000000..224c38daf54 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch @@ -0,0 +1,101 @@ +https://github.com/xianyi/OpenBLAS/pull/3329 +From cbc41973fde6137bc42c34de64a41b5a82b597c0 Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Fri, 30 Jul 2021 14:20:12 +0200 +Subject: [PATCH 1/4] Disable gfortran tree vectorizer to avoid gcc11+ + miscompilation at O3 + +--- + ctest/CMakeLists.txt | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/ctest/CMakeLists.txt b/ctest/CMakeLists.txt +index 17f29fe693..f785d3f90d 100644 +--- a/ctest/CMakeLists.txt ++++ b/ctest/CMakeLists.txt +@@ -4,6 +4,9 @@ include_directories(${PROJECT_BINARY_DIR}) + enable_language(Fortran) + + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DADD${BU} -DCBLAS") ++if (CMAKE_Fortran_COMPILER_ID STREQUAL GNU) ++ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fno-tree-vectorize") ++endif() + + if(WIN32) + FILE(WRITE ${CMAKE_CURRENT_BINARY_DIR}/test_cblas_helper.ps1 + +From b4f4ed378b2343b0af8b1235838feef4f6c8c51c Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Fri, 30 Jul 2021 14:21:08 +0200 +Subject: [PATCH 2/4] Disable gfortran tree vectorizer to avoid gcc11+ + miscompilation at O3 + +--- + test/CMakeLists.txt | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt +index d338242ff8..e4ee8b28b8 100644 +--- a/test/CMakeLists.txt ++++ b/test/CMakeLists.txt +@@ -2,6 +2,10 @@ include_directories(${PROJECT_SOURCE_DIR}) + include_directories(${PROJECT_BINARY_DIR}) + + enable_language(Fortran) ++if (CMAKE_Fortran_COMPILER_ID STREQUAL GNU) ++ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fno-tree-vectorize") ++endif() ++ + + if (BUILD_SINGLE) + list( APPEND OpenBLAS_Tests sblat1 sblat2 sblat3) + +From e78fbe46541dedcf39eb0362e69b1de6f7808642 Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Fri, 30 Jul 2021 14:44:54 +0200 +Subject: [PATCH 3/4] Disable gfortran tree vectorizer to avoid gcc11+ + miscompilation at O3 + +--- + ctest/Makefile | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/ctest/Makefile b/ctest/Makefile +index 15c83a9079..c5e1094da0 100644 +--- a/ctest/Makefile ++++ b/ctest/Makefile +@@ -6,6 +6,9 @@ TOPDIR = .. + include $(TOPDIR)/Makefile.system + + override CFLAGS += -DADD$(BU) -DCBLAS ++ifeq ($(F_COMPILER),GFORTRAN) ++ override FFLAGS += -fno-tree-vectorize ++endif + override TARGET_ARCH= + override TARGET_MACH= + + +From 5dc6aa74f05cc6c4405be195461fa5afc2c03888 Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Fri, 30 Jul 2021 14:46:19 +0200 +Subject: [PATCH 4/4] Disable gfortran tree vectorizer to avoid gcc11+ + miscompilation at O3 + +--- + test/Makefile | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/test/Makefile b/test/Makefile +index 6c5f041c28..923f1537c2 100644 +--- a/test/Makefile ++++ b/test/Makefile +@@ -1,6 +1,8 @@ + TOPDIR = .. + include ../Makefile.system +- ++ifeq ($(F_COMPILER),GFORTRAN) ++ override FFLAGS += -fno-tree-vectorize ++endif + + ifeq ($(NOFORTRAN),1) + all :: From 0379bcfc639fe45eb4fcffe91772788b6372be3e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 5 Aug 2021 14:28:23 +0200 Subject: [PATCH 0672/9987] Drop makeinfo minimal, perl bare --- .../g/groff/groff-1.22.4-GCCcore-11.2.0.eb | 3 +- .../makeinfo-6.8-GCCcore-11.2.0-minimal.eb | 35 ------------------- .../Perl.bare-5.34.0-GCCcore-11.2.0.eb | 27 -------------- .../p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 15 +++----- 4 files changed, 6 insertions(+), 74 deletions(-) delete mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0-minimal.eb delete mode 100644 easybuild/easyconfigs/p/Perl.bare/Perl.bare-5.34.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.2.0.eb index 454c00e43bb..ddc36e9736c 100644 --- a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.2.0.eb @@ -15,9 +15,10 @@ checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] builddependencies = [ ('binutils', '2.37'), - ('makeinfo', '6.8', '-minimal'), ] +configopts = '--with-doc=no' + sanity_check_paths = { 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], 'dirs': ['lib/groff', 'share'], diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0-minimal.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0-minimal.eb deleted file mode 100644 index 79d4c64db52..00000000000 --- a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0-minimal.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'makeinfo' -version = '6.8' -versionsuffix = '-minimal' - -homepage = 'https://www.gnu.org/software/texinfo/' -description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project. - -This is a minimal build with very basic functionality. Should only be used for build dependencies. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] -sources = ['texinfo-%(version)s.tar.xz'] -checksums = ['8eb753ed28bca21f8f56c1a180362aed789229bd62fff58bf8368e9beb59fec4'] - -builddependencies = [ - ('binutils', '2.37'), -] -dependencies = [ - ('Perl.bare', '5.34.0'), -] - -configopts = '--disable-perl-xs --disable-perl-api-texi-build --disable-pod-simple-texinfo-tests ' - -sanity_check_paths = { - 'files': ['bin/makeinfo'], - 'dirs': ['share'], -} - -sanity_check_commands = ["makeinfo --help"] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Perl.bare/Perl.bare-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl.bare/Perl.bare-5.34.0-GCCcore-11.2.0.eb deleted file mode 100644 index cdf0e62f1f3..00000000000 --- a/easybuild/easyconfigs/p/Perl.bare/Perl.bare-5.34.0-GCCcore-11.2.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'EB_Perl' - -name = 'Perl.bare' -version = '5.34.0' - -homepage = 'https://www.perl.org/' -description = """Larry Wall's Practical Extraction and Report Language - -This is a minimal build without any modules. Should only be used for build dependencies. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] -sources = ['perl-%(version)s.tar.gz'] -checksums = ['551efc818b968b05216024fb0b727ef2ad4c100f8cb6b43fab615fa78ae5be9a'] - -builddependencies = [ - ('binutils', '2.37'), -] - -dependencies = [ - ('zlib', '1.2.11'), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 6def18ddee8..c43e89bf8e1 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1,5 +1,3 @@ -easyblock = 'Bundle' - name = 'Perl' version = '5.34.0' @@ -9,13 +7,16 @@ description = """Larry Wall's Practical Extraction and Report Language""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = ['perl-%(version)s.tar.gz'] +checksums = ['551efc818b968b05216024fb0b727ef2ad4c100f8cb6b43fab615fa78ae5be9a'] + builddependencies = [ ('binutils', '2.37'), ('groff', '1.22.4'), ] dependencies = [ - ('Perl.bare', version), ('zlib', '1.2.11'), # for Net::SSLeay ('expat', '2.4.1'), # for XML::Parser ('ncurses', '6.2'), # for Term::ReadLine::Gnu @@ -24,9 +25,6 @@ dependencies = [ ('OpenSSL', '1.1', '', True), # required for Net::SSLeay ] -exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") - # !! order of extensions is important !! # extensions updated on Aug 3rd 2021 exts_list = [ @@ -1768,9 +1766,4 @@ exts_list = [ }), ] -# Can't use perlver because the template isn't resolved while we are building extensions -modextrapaths = { - 'PERL5LIB': 'lib/perl5/site_perl/%s/' % version, -} - moduleclass = 'lang' From aeec0f915e5a0b5852bc8a41c694e3df36a34960 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Aug 2021 16:53:31 +0200 Subject: [PATCH 0673/9987] adding easyconfigs: IRkernel-1.2-foss-2021a-R-4.1.0.eb --- .../IRkernel-1.2-foss-2021a-R-4.1.0.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..4f72aab2b80 --- /dev/null +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb @@ -0,0 +1,68 @@ +easyblock = 'Bundle' + +name = 'IRkernel' +version = '1.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://irkernel.github.io' +description = """The R kernel for the 'Jupyter' environment executes R code + which the front-end (Jupyter Notebook or other front-ends) submits to the + kernel via the network.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('R', '4.1.0'), + ('Python', '3.9.5'), + ('IPython', '7.25.0'), + ('ZeroMQ', '4.3.4'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.rstudio.com/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('repr', '1.1.3', { + 'checksums': ['531b43d413b51cbc96e3b9162493c975d9395bb9532e500ad51cd99b36a53562'], + }), + ('IRdisplay', '1.0', { + 'checksums': ['8967ec58656ede561d20ab07dd9ef27de088c0ea099e325242b3860a63964b96'], + }), + ('pbdZMQ', '0.3-5', { + 'checksums': ['4d8088b3365d612a661f0078bcba50357cb3a7ec04a699348b4312fd6fd811ed'], + }), + (name, version, { + 'checksums': ['5fb4dbdb741d05043120a8be0eb73f054b607d9854f314bd79cfec08d219ff91'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +# IPython notebook looks for the json kernel file in kernels/IRkernel +# We start the kernel with default bitmapType 'cairo'. This is a more sensible default +# for headless nodes. See https://github.com/IRkernel/IRkernel/issues/388 +local_kerneldir = '%(installdir)s/IRkernel' +postinstallcmds = [ + 'mkdir -p %s/kernels/ir' % local_kerneldir, + 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir), + ('sed -i \'s/"IRkernel::main()"/"options(bitmapType=\\x27cairo\\x27); IRkernel::main()"/g\'' + ' %s/kernels/ir/kernel.json') % local_kerneldir +] + +modextravars = {'JUPYTER_PATH': local_kerneldir} + +sanity_check_paths = { + 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], + 'dirs': [name], +} + +moduleclass = 'tools' From 23c2f1319384a9f5f8ee85ad3dff11f61c65cf83 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 5 Aug 2021 16:54:23 +0200 Subject: [PATCH 0674/9987] Update easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 9840c5651de..65a504e561b 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -17,7 +17,7 @@ patches = [ preinstallopts = 'python3 build/build.py ' preinstallopts += '--bazel_startup_options="--output_user_root=%(builddir)s" ' -preinstallopts += ' --bazel_path="$EBROOTBAZEL/bin/bazel" && ' +preinstallopts += '--bazel_options=--subcommands --bazel_options=--jobs=1 --bazel_options=--action_env=PYTHONPATH --bazel_options=--action_env=EBPYTHONPREFIXES && ' preinstallopts += 'pip install dist/*.whl && ' dependencies = [ From af41b436fae8017231581e23f63f700ca536cf5f Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 5 Aug 2021 16:54:28 +0200 Subject: [PATCH 0675/9987] Update easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 65a504e561b..97c3d23c939 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -28,6 +28,8 @@ dependencies = [ ] use_pip = True +download_dep_fail = True +sanity_pip_check = True moduleclass = 'tools' From 09fe906ff8ccd34f6ad38c9cdc5773e7712c66aa Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 5 Aug 2021 16:55:54 +0200 Subject: [PATCH 0676/9987] Update easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 97c3d23c939..5bfe4bdd4d7 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -15,7 +15,7 @@ patches = [ 'jax-0.2.18-correct_libraries.patch', ] -preinstallopts = 'python3 build/build.py ' +preinstallopts = 'python build/build.py ' preinstallopts += '--bazel_startup_options="--output_user_root=%(builddir)s" ' preinstallopts += '--bazel_options=--subcommands --bazel_options=--jobs=1 --bazel_options=--action_env=PYTHONPATH --bazel_options=--action_env=EBPYTHONPREFIXES && ' preinstallopts += 'pip install dist/*.whl && ' From bd3383d9a673fba768179c169f847e3ada1de5f8 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 5 Aug 2021 17:03:49 +0200 Subject: [PATCH 0677/9987] Update easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 5bfe4bdd4d7..b6cd028938c 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -18,7 +18,7 @@ patches = [ preinstallopts = 'python build/build.py ' preinstallopts += '--bazel_startup_options="--output_user_root=%(builddir)s" ' preinstallopts += '--bazel_options=--subcommands --bazel_options=--jobs=1 --bazel_options=--action_env=PYTHONPATH --bazel_options=--action_env=EBPYTHONPREFIXES && ' -preinstallopts += 'pip install dist/*.whl && ' +preinstallopts += 'pip install --prefix %(installdir)s dist/*.whl && ' dependencies = [ ('Python', '3.8.6'), From c0658bf2f34bfd575af49f3957d6e945d1874980 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 5 Aug 2021 15:50:46 +0000 Subject: [PATCH 0678/9987] Add upstream GCC patch to avoid spurious FPE on avx512 (affects UCX) --- .../easyconfigs/g/GCCcore/GCCcore-10.1.0.eb | 2 ++ .../easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 2 ++ .../easyconfigs/g/GCCcore/GCCcore-10.3.0.eb | 2 ++ .../easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 2 ++ .../easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 2 ++ .../easyconfigs/g/GCCcore/GCCcore-9.1.0.eb | 2 ++ .../easyconfigs/g/GCCcore/GCCcore-9.2.0.eb | 2 ++ .../easyconfigs/g/GCCcore/GCCcore-9.3.0.eb | 2 ++ .../easyconfigs/g/GCCcore/GCCcore-9.4.0.eb | 2 ++ ...core-9.x-11.x_fix-unsigned-fpe-traps.patch | 33 +++++++++++++++++++ 10 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb index bc096d39ad9..ae0206847fd 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb @@ -28,6 +28,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', ] checksums = [ '954057239c89d25bc7a62bfbceb58026363ad74f079c63fdba27f95abbf60900', # gcc-10.1.0.tar.gz @@ -37,6 +38,7 @@ checksums = [ '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 65f6fc7c6cd..4ce3d1f4b94 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -36,6 +36,7 @@ patches = [ 'GCCcore-10.2.0_fix-has-include-Fortran.patch', 'GCCcore-10.2.0_fix-ice-on-arm.patch', 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', ] checksums = [ '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d', # gcc-10.2.0.tar.gz @@ -52,6 +53,7 @@ checksums = [ '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278', # GCCcore-10.2.0_fix-ice-on-arm.patch # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962', + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb index abac9ee3662..8e9a76ab85b 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb @@ -34,6 +34,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.3.0_nvptx_sm_35_default.patch', 'gcc-10.3.0_fix-ice-in-tsubst.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', ] checksums = [ '8fcf994811ad4e5c7ac908e8cf62af2c1982319e5551f62ae72016064dacdf16', # gcc-10.3.0.tar.gz @@ -47,6 +48,7 @@ checksums = [ '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch '74e6e019458aa2feb36ae3c45f45e164725ca5edd66f4fe9f873c8ee78c35717', # gcc-10.3.0_fix-ice-in-tsubst.patch + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index 3b4548535a2..f4578a964af 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -32,6 +32,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', ] checksums = [ 'e7abb1b4cb58aaa67c5eb49d98e89d13363b8e258ac2b5b105c197b441c09f85', # gcc-11.1.0.tar.gz @@ -43,6 +44,7 @@ checksums = [ '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb index 0adf0fee9ca..4946587aea8 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -32,6 +32,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', ] checksums = [ 'f0837f1bf8244a5cc23bd96ff6366712a791cfae01df8e25b137698aca26efc1', # gcc-11.2.0.tar.gz @@ -43,6 +44,7 @@ checksums = [ '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb index 2b1aa9b12a7..4fe5df40dbc 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb @@ -28,6 +28,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-8.3.0_fix-xsmin-ppc.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', ] checksums = [ 'be303f7a8292982a35381489f5a9178603cbe9a4715ee4fa4a815d6bcd2b658d', # gcc-9.1.0.tar.gz @@ -37,6 +38,7 @@ checksums = [ 'd18ca11f8ad1a39ab6d03d3dcb3365ab416720fcb65b42d69f34f51bf0a0e859', # isl-0.21.tar.bz2 '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch 'bea1bce8f50ea6d51b038309eb61dec00a8681fb653d211c539be80f184609a3', # GCCcore-8.3.0_fix-xsmin-ppc.patch + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb index 5c1a4628db7..839d68ee7d3 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb @@ -31,6 +31,7 @@ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-8.3.0_fix-xsmin-ppc.patch', 'GCCcore-9.2.0-fix-glibc-2.31-libsanitizer.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', ] checksums = [ 'a931a750d6feadacbeecb321d73925cd5ebb6dfa7eff0802984af3aef63759f4', # gcc-9.2.0.tar.gz @@ -42,6 +43,7 @@ checksums = [ 'bea1bce8f50ea6d51b038309eb61dec00a8681fb653d211c539be80f184609a3', # GCCcore-8.3.0_fix-xsmin-ppc.patch # GCCcore-9.2.0-fix-glibc-2.31-libsanitizer.patch '459006b69e19ffdc3102ad78b81c124741faaac4c42b6117365314d908cb506f', + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb index a0037cc1561..a0bb5a12552 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-%(version)s_gmp-c99.patch', 'GCCcore-%(version)s_vect_broadcasts_masmintel.patch', 'GCCcore-%(version)s_nvptx_sm_35_default.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', ] checksums = [ '5258a9b6afe9463c2e56b9e8355b1a4bee125ca828b8078f910303bc2ef91fa6', # gcc-9.3.0.tar.gz @@ -49,6 +50,7 @@ checksums = [ '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch 'a32ac9c7d999a8b91bf93dba6a9d81b6ff58b3c89c425ff76090cbc90076685c', # GCCcore-9.3.0_vect_broadcasts_masmintel.patch '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb index 814431d3215..aec0247b17e 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb @@ -32,6 +32,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', ] checksums = [ '07ea650894cde75ab0f7cfbee0e69832c8a789b01efa2de3bfba7569338e24cb', # gcc-9.4.0.tar.gz @@ -43,6 +44,7 @@ checksums = [ '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch new file mode 100644 index 00000000000..411f035218c --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch @@ -0,0 +1,33 @@ +From 99b520f031c0e491d7e170916df11dd645d60617 Mon Sep 17 00:00:00 2001 +From: Andrew Pinski +Date: Thu, 29 Jul 2021 19:48:46 -0700 +Subject: [PATCH] Fix PR 101683: FP exceptions for float->unsigned + +Just like the old bug PR9651, unsigned_fix rtl should +also be handled as a trapping instruction. + +OK? Bootstrapped and tested on x86_64-linux-gnu with no regressions. + +gcc/ChangeLog: + + PR rtl-optimization/101683 + * rtlanal.c (may_trap_p_1): Handle UNSIGNED_FIX. +--- + gcc/rtlanal.c | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/gcc/rtlanal.c b/gcc/rtlanal.c +index 3b8d88afd4d..f7f3acb75db 100644 +--- a/gcc/rtlanal.c ++++ b/gcc/rtlanal.c +@@ -3261,6 +3261,7 @@ may_trap_p_1 (const_rtx x, unsigned flags) + break; + + case FIX: ++ case UNSIGNED_FIX: + /* Conversion of floating point might trap. */ + if (flag_trapping_math && HONOR_NANS (XEXP (x, 0))) + return 1; +-- +2.27.0 + From 6a5d2b5cf3a950c26cbae07a756b7c24c7a0e21d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Aug 2021 17:52:42 +0200 Subject: [PATCH 0679/9987] rename goatools to GOATOOLS (to use official software name) --- .../GOATOOLS-1.1.6-foss-2020b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/g/{goatools/goatools-1.1.6-foss-2020b.eb => GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb} (99%) diff --git a/easybuild/easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb similarity index 99% rename from easybuild/easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb rename to easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb index ff75c3edb88..fd0085761c9 100644 --- a/easybuild/easyconfigs/g/goatools/goatools-1.1.6-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb @@ -2,7 +2,7 @@ # Author: Denis Kristak easyblock = 'PythonPackage' -name = 'goatools' +name = 'GOATOOLS' version = '1.1.6' homepage = 'https://github.com/tanghaibao/goatools' From f6513d37f2d960c6e2295aa806038f195c1dbd90 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 5 Aug 2021 16:41:20 +0000 Subject: [PATCH 0680/9987] Perl shebang changed to /usr/bin/env perl, all Perl and Python scripts included in check --- .../HH-suite-3.3.0-gompi-2020b-Perl-5.32.0.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b-Perl-5.32.0.eb diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b-Perl-5.32.0.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b-Perl-5.32.0.eb new file mode 100644 index 00000000000..3d4582c6be2 --- /dev/null +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b-Perl-5.32.0.eb @@ -0,0 +1,72 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Updated to use gompi-2020b toolchain: +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'HH-suite' +version = '3.3.0' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://github.com/soedinglab/hh-suite' +description = """The HH-suite is an open-source software package +for sensitive protein sequence searching based on the pairwise +alignment of hidden Markov models (HMMs).""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Perl', '5.32.0'), +] + +separate_build_dir = True + +_binaries = [ + 'hhalign', 'hhalign_mpi', 'hhalign_omp', + 'hhblits', 'hhblits_mpi', 'hhblits_omp', + 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp', + 'hhmake', 'hhfilter', 'hhconsensus', +] + +_scriptfiles = [ + 'a3m.py', 'check_a3m.py', 'cif2fasta.py', 'ffindex.py', 'get_a3m_size.py', + 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', +] + +_perlfiles = [ + 'addss.pl', 'create_profile_from_hmmer.pl', 'hhmakemodel.pl', + 'mergeali.pl', 'multithread.pl', 'pdb2fasta.pl', 'pdbfilter.pl', + 'reformat.pl', 'renumberpdb.pl', 'splitfasta.pl', +] + +fix_perl_shebang_for = ['scripts/%s' % z for z in _perlfiles] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + ['scripts/%s' % y for y in _scriptfiles], + 'dirs': ['data', 'scripts'] +} + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From a5e005d65d7409ebcb246c01f53495437e2161c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Aug 2021 18:41:38 +0200 Subject: [PATCH 0681/9987] don't include unversioned go-basic.odo and goslin_generic.odo files in GOATOOLS installation --- .../g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb | 53 ++++++------------- 1 file changed, 17 insertions(+), 36 deletions(-) diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb index fd0085761c9..18701693a49 100644 --- a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.1.6-foss-2020b.eb @@ -10,19 +10,11 @@ description = "A Python library for Gene Ontology analyses" toolchain = {'name': 'foss', 'version': '2020b'} -# extra downloaded files are needed acc. to docs: https://github.com/tanghaibao/goatools#installation -sources = [ - {'source_urls': ['https://github.com/tanghaibao/goatools/archive/'], - 'filename': 'v%(version)s.tar.gz'}, - {'source_urls': ['http://geneontology.org/ontology/'], - 'filename': 'go-basic.obo', 'extract_cmd': 'cp %s %(builddir)s'}, - {'source_urls': ['http://www.geneontology.org/ontology/subsets/'], - 'filename': 'goslim_generic.obo', 'extract_cmd': 'cp %s %(builddir)s'}] -checksums = [ - '41222308c2bc34eefd3292326a61bc215bd32831b4b2652eff00b1b8e3fcf8c6', # v1.1.6.tar.gz - '57bd37b4301a7a6be65da033c8e812698e62fd0f12a30e18cf9e3cfeed238702', # go-basic.obo - '161ccdabf702faee796335939858772703f5e05a2ccb0400a4cab481f41136d9', # goslim_generic.obo -] +source_urls = ['https://github.com/tanghaibao/goatools/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['41222308c2bc34eefd3292326a61bc215bd32831b4b2652eff00b1b8e3fcf8c6'] + +builddependencies = [('cURL', '7.72.0')] dependencies = [ ('Python', '3.8.6'), @@ -31,40 +23,29 @@ dependencies = [ ('statsmodels', '0.12.1'), ('pydot', '1.4.2'), ] + download_dep_fail = True +use_pip = True preinstallopts = "sed -i 's/==[0-9]*.[0-9]*.[0-9]*//g' requirements.txt && " # wget was here only to download some src files which we download via sources preinstallopts += "sed -i 's/wget//g' requirements.txt && " -local_go_path = "%(installdir)s/bin/goafiles" - - -local_data_dir = '%(builddir)s/%(name)s-%(version)s/data/*' -# copy downloaded GOA files into dedicated folder for user and to bin/ for sanity_check -postinstallcmds = ["mkdir %s" % local_go_path, - "cp %%(builddir)s/go-basic.obo %s" % local_go_path, - "cp %%(builddir)s/goslim_generic.obo %s" % local_go_path, - "cp %(builddir)s/go-basic.obo %(installdir)s/bin/", - "cp %(builddir)s/goslim_generic.obo %(installdir)s/bin/", - "mkdir %%(installdir)s/bin/data && cp -r %s %%(installdir)s/bin/data" % local_data_dir] - -# making sure user knows about downloaded files -modextravars = {'GOAFILES': local_go_path} -modloadmsg = """\n GOATOOLS: Downloaded files from "geneontology.org" are accessible in a directory behind a variable \ -$GOAFILES.\n You need to have them in a directory from which you run goatools commands.""" - -use_pip = True +local_data_dir = '%(builddir)s/%(namelower)s-%(version)s/data/*' +postinstallcmds = ["mkdir %%(installdir)s/data && cp -r %s %%(installdir)s/data" % local_data_dir] sanity_check_paths = { 'files': ['bin/find_enrichment.py'], - 'dirs': ['bin/data'], + 'dirs': ['data'], } -# example from https://github.com/tanghaibao/goatools#find-go-enrichment-of-genes-under-study -local_cmd = "cd %(installdir)s/bin && find_enrichment.py --pval=0.05\ - --indent data/study data/population data/association && cd -" -sanity_check_commands = [local_cmd] +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] sanity_pip_check = True From cf32c94389cba5c4c916482cd51c6eb8b6fd59c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 5 Aug 2021 20:39:00 +0200 Subject: [PATCH 0682/9987] Update easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index c43e89bf8e1..0192140b141 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -198,10 +198,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], 'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'], }), - ('DBD::SQLite', '1.66', { + ('DBD::SQLite', '1.70', { 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], - 'checksums': ['89e75dff9f66c273e0e459d51f151f88960eb7d82e2821e6902f18688ba592fe'], + 'checksums': ['40fd8ddf539e0e773a7a4e6d376794c3301459f9ab0050978bdcf97113dafe3e'], }), ('Math::Bezier', '0.01', { 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', From 2083ce10dc49d0c9d36a3de0776942d989188375 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 5 Aug 2021 20:39:08 +0200 Subject: [PATCH 0683/9987] Update easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 0192140b141..48668be4e1e 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -228,10 +228,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], }), - ('Test::Simple', '1.302183', { + ('Test::Simple', '1.302186', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], - 'checksums': ['9a03bda5ec420aea9692b650437f4d5b574fa505fdd7ff60cdb5f3ec034106ff'], + 'checksums': ['2895c8da7c3fe632e5714c7cc548705202cdbf3afcbc0e929bc5e6a5172265d4'], }), ('Set::Scalar', '1.29', { 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', From 55067732dfe9d1393b57a380c36e975f435c2cef Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 5 Aug 2021 19:51:24 +0100 Subject: [PATCH 0684/9987] adding easyconfigs: snappy-1.1.9-GCCcore-11.2.0.eb and patches: snappy-1.1.9_inline-functions.patch --- .../s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb | 35 ++++++++++ .../snappy-1.1.9_inline-functions.patch | 67 +++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.9_inline-functions.patch diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..14a20951cb0 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.9' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_inline-functions.patch'] +checksums = [ + '75c1fbb3d618dd3a0483bff0e26d0a92b495bbe5059c8b4f1c962b478b6e06e7', # 1.1.9.tar.gz + 'ad79190b274df5ddabf14eddd2bb0d9a091ee7d44e4afde89febf9a8f783fdce', # snappy-1.1.9_inline-functions.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [''] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.9_inline-functions.patch b/easybuild/easyconfigs/s/snappy/snappy-1.1.9_inline-functions.patch new file mode 100644 index 00000000000..3fd38154287 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.9_inline-functions.patch @@ -0,0 +1,67 @@ +From 0c716d435abe65250100c2caea0e5126ac4e14bd Mon Sep 17 00:00:00 2001 +From: "Georgi D. Sotirov" +Date: Wed, 5 May 2021 14:16:46 +0300 +Subject: [PATCH] Add inline with SNAPPY_ATTRIBUTE_ALWAYS_INLINE + +Add inline with SNAPPY_ATTRIBUTE_ALWAYS_INLINE on AdvanceToNextTag to +fix the following compilation errors and a warning with GCC: + +[ 2%] Building CXX object CMakeFiles/snappy.dir/snappy.cc.o +/usr/bin/c++ -DHAVE_CONFIG_H -Dsnappy_EXPORTS +-I/tmp/snappy-1.1.9/build -I/tmp/snappy-1.1.9 -O3 +-march=i586 -mtune=i686 -Wall -Wextra -fno-exceptions -fno-rtti -O3 +-DNDEBUG -fPIC -std=c++11 -o CMakeFiles/snappy.dir/snappy.cc.o -c +/tmp/snappy-1.1.9/snappy.cc +/tmp/snappy-1.1.9/snappy.cc:1017:8: warning: always_inline +function might not be inlinable [-Wattributes] + size_t AdvanceToNextTag(const uint8_t** ip_p, size_t* tag) { + ^ +/tmp/snappy-1.1.9/snappy.cc: In function 'std::pair snappy::DecompressBranchless(const uint8_t*, const +uint8_t*, ptrdiff_t, T, ptrdiff_t) [with T = char*; uint8_t = unsigned +char; ptrdiff_t = int]': +/tmp/snappy-1.1.9/snappy.cc:1017:8: error: inlining failed in +call to always_inline 'size_t snappy::AdvanceToNextTag(const uint8_t**, +size_t*)': function body can be overwritten at link time +/tmp/snappy-1.1.9/snappy.cc:1097:53: error: called from here + size_t tag_type = AdvanceToNextTag(&ip, &tag); + ^ +/tmp/snappy-1.1.9/snappy.cc:1017:8: error: inlining failed in +call to always_inline 'size_t snappy::AdvanceToNextTag(const uint8_t**, +size_t*)': function body can be overwritten at link time + size_t AdvanceToNextTag(const uint8_t** ip_p, size_t* tag) { + ^ +/tmp/snappy-1.1.9/snappy.cc:1097:53: error: called from here + size_t tag_type = AdvanceToNextTag(&ip, &tag); + ^ +/tmp/snappy-1.1.9/snappy.cc:1017:8: error: inlining failed in +call to always_inline 'size_t snappy::AdvanceToNextTag(const uint8_t**, +size_t*)': function body can be overwritten at link time + size_t AdvanceToNextTag(const uint8_t** ip_p, size_t* tag) { + ^ +/tmp/snappy-1.1.9/snappy.cc:1097:53: error: called from here + size_t tag_type = AdvanceToNextTag(&ip, &tag); + ^ +CMakeFiles/snappy.dir/build.make:137: recipe for target +'CMakeFiles/snappy.dir/snappy.cc.o' failed + +Just like with other functions using SNAPPY_ATTRIBUTE_ALWAYS_INLINE +macro (i.e. __attribute__((always_inline)) ) it is necessary to use C++ +inline specifier. +--- + snappy.cc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/snappy.cc b/snappy.cc +index 79dc0e8d..51157be2 100644 +--- a/snappy.cc ++++ b/snappy.cc +@@ -1014,7 +1014,7 @@ void MemMove(ptrdiff_t dst, const void* src, size_t size) { + } + + SNAPPY_ATTRIBUTE_ALWAYS_INLINE +-size_t AdvanceToNextTag(const uint8_t** ip_p, size_t* tag) { ++inline size_t AdvanceToNextTag(const uint8_t** ip_p, size_t* tag) { + const uint8_t*& ip = *ip_p; + // This section is crucial for the throughput of the decompression loop. + // The latency of an iteration is fundamentally constrained by the From d9565f6b2fc9da86690197bccb640507bfeda514 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 5 Aug 2021 19:39:25 +0000 Subject: [PATCH 0685/9987] Perl suffix and separate_build_dir = True removed --- .../HH-suite-3.3.0-gompi-2020b-Perl-5.32.0.eb | 72 ------------------- .../h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 23 +++++- 2 files changed, 20 insertions(+), 75 deletions(-) delete mode 100644 easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b-Perl-5.32.0.eb diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b-Perl-5.32.0.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b-Perl-5.32.0.eb deleted file mode 100644 index 3d4582c6be2..00000000000 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b-Perl-5.32.0.eb +++ /dev/null @@ -1,72 +0,0 @@ -## -# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -## -# Updated to use gompi-2020b toolchain: -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# uploaded by J. Sassmannshausen - -easyblock = 'CMakeMake' - -name = 'HH-suite' -version = '3.3.0' -versionsuffix = '-Perl-%(perlver)s' - -homepage = 'https://github.com/soedinglab/hh-suite' -description = """The HH-suite is an open-source software package -for sensitive protein sequence searching based on the pairwise -alignment of hidden Markov models (HMMs).""" - -toolchain = {'name': 'gompi', 'version': '2020b'} - -source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] - -builddependencies = [ - ('CMake', '3.18.4'), -] - -dependencies = [ - ('Perl', '5.32.0'), -] - -separate_build_dir = True - -_binaries = [ - 'hhalign', 'hhalign_mpi', 'hhalign_omp', - 'hhblits', 'hhblits_mpi', 'hhblits_omp', - 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp', - 'hhmake', 'hhfilter', 'hhconsensus', -] - -_scriptfiles = [ - 'a3m.py', 'check_a3m.py', 'cif2fasta.py', 'ffindex.py', 'get_a3m_size.py', - 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', -] - -_perlfiles = [ - 'addss.pl', 'create_profile_from_hmmer.pl', 'hhmakemodel.pl', - 'mergeali.pl', 'multithread.pl', 'pdb2fasta.pl', 'pdbfilter.pl', - 'reformat.pl', 'renumberpdb.pl', 'splitfasta.pl', -] - -fix_perl_shebang_for = ['scripts/%s' % z for z in _perlfiles] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in _binaries] + - ['scripts/%s' % y for y in _scriptfiles], - 'dirs': ['data', 'scripts'] -} - -modextrapaths = {'PATH': 'scripts'} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index d59bb692b10..6e6f5b7ed60 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -32,10 +32,11 @@ checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] builddependencies = [ ('CMake', '3.18.4'), - ('Doxygen', '1.8.20'), ] -separate_build_dir = True +dependencies = [ + ('Perl', '5.32.0'), +] _binaries = [ 'hhalign', 'hhalign_mpi', 'hhalign_omp', @@ -44,9 +45,25 @@ _binaries = [ 'hhmake', 'hhfilter', 'hhconsensus', ] +_scriptfiles = [ + 'a3m.py', 'check_a3m.py', 'cif2fasta.py', 'ffindex.py', 'get_a3m_size.py', + 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', +] + +_perlfiles = [ + 'addss.pl', 'create_profile_from_hmmer.pl', 'hhmakemodel.pl', + 'mergeali.pl', 'multithread.pl', 'pdb2fasta.pl', 'pdbfilter.pl', + 'reformat.pl', 'renumberpdb.pl', 'splitfasta.pl', +] + +fix_perl_shebang_for = ['scripts/%s' % z for z in _perlfiles] + sanity_check_paths = { - 'files': ['bin/%s' % x for x in _binaries], + 'files': ['bin/%s' % x for x in _binaries] + + ['scripts/%s' % y for y in _scriptfiles], 'dirs': ['data', 'scripts'] } +modextrapaths = {'PATH': 'scripts'} + moduleclass = 'bio' From c20fac1d36b2f247ddfb5500057f52931ec80a14 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 5 Aug 2021 20:45:46 +0100 Subject: [PATCH 0686/9987] style --- easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb index 14a20951cb0..a98a6f1158f 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb @@ -29,7 +29,7 @@ configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] sanity_check_paths = { 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], - 'dirs': [''] + 'dirs': [] } moduleclass = 'lib' From 67618f24aea56465cef538eb3e3c64a670813464 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 5 Aug 2021 22:05:23 +0200 Subject: [PATCH 0687/9987] Update easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb Co-authored-by: SebastianAchilles --- .../easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb index a6216388c38..3af406badc2 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('binutils', '2.37'), # non-standard Perl modules are required, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 - ('Perl.bare', '5.34.0'), + ('Perl', '5.34.0'), ] dependencies = [ From 545609a7ce8af06312ffad989dd1731bc8f3d730 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 5 Aug 2021 22:50:12 +0200 Subject: [PATCH 0688/9987] update easyconfig ISL-0.24-GCCcore-11.2.0.eb: checksum --- easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.2.0.eb index b440df6aef7..6138d673f70 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.2.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['http://isl.gforge.inria.fr/'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['043105cc544f416b48736fff8caf077fb0663a717d06b1113f16e391ac99ebad'] +checksums = ['fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'] builddependencies = [('binutils', '2.37')] dependencies = [('GMP', '6.2.1')] From 0ac9769fe77189ed7d39c213dd9a83d3d35f665c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 6 Aug 2021 00:43:17 +0200 Subject: [PATCH 0689/9987] adding easyconfigs: SymEngine-0.7.0-GCC-10.3.0.eb --- .../s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..367c8509159 --- /dev/null +++ b/easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'SymEngine' +version = '0.7.0' + +homepage = 'https://github.com/symengine/symengine' +description = "SymEngine is a standalone fast C++ symbolic manipulation library" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'cstd': 'c++17', 'vectorize': True} + +source_urls = ['https://github.com/symengine/symengine/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8b865bb72b71539d9cd2488a0468c6c3ea90cc606062a7880c3ff5af6abd74b1'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), + ('LLVM', '11.1.0'), + ('gperftools', '2.9.1'), +] + +local_opts = '-DWITH_MPFR=yes -DWITH_MPC=yes -DWITH_LLVM=yes -DWITH_BFD=yes -DWITH_TCMALLOC=yes' +configopts = [local_opts + ' -DBUILD_SHARED_LIBS=OFF', local_opts + ' -DBUILD_SHARED_LIBS=ON'] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib64/libsymengine.a', 'lib64/libsymengine.%s' % SHLIB_EXT], + 'dirs': ['include/symengine/'] +} + +moduleclass = 'lib' From 8484da32b63732c8483db3bdcab18783014434c9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Aug 2021 01:20:01 +0200 Subject: [PATCH 0690/9987] adding easyconfigs: Python-3.9.6-GCCcore-11.2.0.eb, Python-3.9.6-GCCcore-11.2.0-bare.eb, Rust-1.54.0-GCCcore-11.2.0.eb --- .../Python-3.9.6-GCCcore-11.2.0-bare.eb | 34 ++ .../p/Python/Python-3.9.6-GCCcore-11.2.0.eb | 463 ++++++++++++++++++ .../r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb | 47 ++ 3 files changed, 544 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb new file mode 100644 index 00000000000..e5fe2be7e2e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb @@ -0,0 +1,34 @@ +name = 'Python' +version = '3.9.6' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['d0a35182e19e416fc8eae25a3dcd4d02d4997333e4ad1f2eee6010aadc3fe866'] + +builddependencies = [ + ('UnZip', '6.0'), +] + +dependencies = [ + ('binutils', '2.37'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('SQLite', '3.36'), + ('XZ', '5.2.5'), + ('libffi', '3.4.2'), + ('OpenSSL', '1.1', '', True), +] + +install_pip = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4e8449701f6 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb @@ -0,0 +1,463 @@ +name = 'Python' +version = '3.9.6' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['d0a35182e19e416fc8eae25a3dcd4d02d4997333e4ad1f2eee6010aadc3fe866'] + +builddependencies = [ + ('UnZip', '6.0'), + ('Rust', '1.54.0'), # required for setuptools-rust, which is needed for cryptography +] + +dependencies = [ + ('binutils', '2.37'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('SQLite', '3.36'), + ('XZ', '5.2.5'), + ('GMP', '6.2.1'), # required for pycrypto + ('libffi', '3.4.2'), + ('OpenSSL', '1.1', '', True), +] + +install_pip = True + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 06 August 2021 +exts_list = [ + ('wheel', '0.36.2', { + 'checksums': ['e11eefd162658ea59a60a0f6c7d493a7190ea4b9a85e335b33489d9f17e0245e'], + }), + ('setuptools', '57.4.0', { + 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], + }), + ('pip', '21.2.2', { + 'checksums': ['38e9250dfb0d7fa842492bede9259d4b3289a936ce454f7c58f059f28a94c01d'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('blist', '1.3.6', { + 'patches': ['Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch'], + 'checksums': [ + '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3', # blist-1.3.6.tar.gz + # Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch + '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0', + ], + }), + ('paycheck', '1.0.2', { + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '5.6.0', { + 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], + }), + ('Cython', '0.29.24', { + 'checksums': ['cdf04d07c3600860e8c2ebaad4e8f52ac3feb212453c1764a49ac08c827e8443'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('setuptools_scm', '6.0.1', { + 'checksums': ['d1925a69cb07e9b29416a275b9fadb009a23c148ace905b2fb220649a6c18e92'], + }), + ('python-dateutil', '2.8.2', { + 'modulename': 'dateutil', + 'checksums': ['0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86'], + }), + ('decorator', '5.0.9', { + 'checksums': ['72ecfba4320a893c53f9706bebb2d55c270c1e51a28789361aa93e4a21319ed5'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], + 'checksums': [ + 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz + # pycrypto-2.6.1_remove-usr-include.patch + '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e', + ], + }), + ('ecdsa', '0.17.0', { + 'checksums': ['b9f500bb439e4153d0330610f5d26baaf18d17b8ced1bc54410d189385ea68aa'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.4.0', { + 'checksums': ['f4f6e119474e58e04a2b1af817eb585b4fd72bdd89b998624712b5c99be7641c'], + }), + ('idna', '3.2', { + 'checksums': ['467fbad99067910785144ce333826c71fb0e63a425657295239737f7ecd125f3'], + }), + ('pycparser', '2.20', { + 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], + }), + ('cffi', '1.14.6', { + 'checksums': ['c9a875ce9d7fe32887784274dd533c57909b7b1dcadcc128a2ac21331a9765dd'], + }), + ('semantic_version', '2.8.5', { + 'checksums': ['d2cb2de0558762934679b9a104e82eca7af448c9f4974d1f3eeccff651df8a54'], + }), + ('setuptools-rust', '0.12.1', { + 'checksums': ['647009e924f0ae439c7f3e0141a184a69ad247ecb9044c511dabde232d3d570e'], + }), + ('cryptography', '3.4.7', { + 'checksums': ['3d10de8116d25649631977cb37da6cbdd2d6fa0e0281d014a5b7d337255ca713'], + # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, + # see https://github.com/rust-lang/cargo/issues/6652 + 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", + }), + ('pyasn1', '0.4.8', { + 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], + }), + ('PyNaCl', '1.4.0', { + 'modulename': 'nacl', + 'checksums': ['54e9a2c849c742006516ad56a88f5c74bf2ce92c9f67435187c3c5953b346505'], + }), + ('bcrypt', '3.2.0', { + 'checksums': ['5b93c1726e50a93a033c36e5ca7fdcd29a5c7395af50a6892f5d9e7c6cfbfb29'], + }), + ('paramiko', '2.7.2', { + 'checksums': ['7f36f4ba2c0d81d219f4595e35f70d56cc94f9ac40a6acdf51d6ca210ce65035'], + }), + ('pyparsing', '2.4.7', { + 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], + }), + ('netifaces', '0.11.0', { + 'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'], + }), + ('netaddr', '0.8.0', { + 'checksums': ['d6cc57c7a07b1d9d2e917aa8b36ae8ce61c35ba3fcd1b83ca31c5a0ee2b5a243'], + }), + ('mock', '4.0.3', { + 'checksums': ['7d3fbbde18228f4ff2f1f119a45cdffa458b4c0dee32eb4d2bb2f82554bac7bc'], + }), + ('pytz', '2021.1', { + 'checksums': ['83a4a90894bf38e243cf052c8b58f381bfe9a7a483f6a9cab140bc7f702ac4da'], + }), + ('bitstring', '3.1.9', { + 'checksums': ['a5848a3f63111785224dca8bb4c0a75b62ecdef56a042c8d6be74b16f7e860e7'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.2', { + 'source_tmpl': 'distlib-%(version)s.zip', + 'checksums': ['106fef6dc37dd8c0e2c0a60d3fca3e77460a48907f335fa28420463a6f799736'], + }), + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], + }), + ('zipp', '3.5.0', { + 'checksums': ['f5812b1e007e48cff63449a5e9f4e7ebea716b4111f9c4f9a645f91d579bf0c4'], + }), + ('typing_extensions', '3.10.0.0', { + 'checksums': ['50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342'], + }), + ('importlib_metadata', '4.6.3', { + 'checksums': ['0645585859e9a6689c523927a5032f2ba5919f1f7d0e84bd4533312320de1ff9'], + }), + ('backports.entry_points_selectable', '1.1.0', { + 'checksums': ['988468260ec1c196dab6ae1149260e2f5472c9110334e5d51adcb77867361f6a'], + }), + ('platformdirs', '2.2.0', { + 'checksums': ['632daad3ab546bd8e6af0537d09805cec458dce201bccfe23012df73332e181e'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.6', { + 'checksums': ['7d8bcb5555003cdf4a8d2872c538faa3a0f5d20630cb360e518ca3b981795e5f'], + }), + ('importlib_resources', '5.2.2', { + 'checksums': ['a65882a4d0fe5fbf702273456ba2ce74fe44892c25e42e057aca526b702a6d4b'], + }), + ('virtualenv', '20.7.0', { + 'checksums': ['97066a978431ec096d163e72771df5357c5c898ffdd587048f45e0aecc228094'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '1.0.1', { + 'checksums': ['9c17567692206d2f3fb9ecf5e991084254fe631665c450b443761c4186a613f7'], + }), + ('chardet', '4.0.0', { + 'checksums': ['0d6f53a15db4120f2b08c94f11e7d93d2c911ee118b6b30a04ec3ee8310179fa'], + }), + ('certifi', '2021.5.30', { + 'checksums': ['2bbf76fd432960138b3ef6dda3dde0544f27cbf8546c458e60baf371917ba9ee'], + }), + ('urllib3', '1.26.6', { + 'checksums': ['f57b4c16c62fa2760b7e3d97c35b255512fb6b59a259730f36ba32ce9f8e342f'], + }), + ('charset-normalizer', '2.0.4', { + 'checksums': ['f23667ebe1084be45f6ae0538e4a5a865206544097e4e8bbcacf42cd02a348f3'], + }), + ('requests', '2.26.0', { + 'checksums': ['b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7'], + }), + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('py_expression_eval', '0.3.13', { + 'checksums': ['6e7d59d391d54a034609ce66b820e7dd68c757672d166dcc514bf7abf15ba57e'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('ujson', '4.0.2', { + 'checksums': ['c615a9e9e378a7383b756b7e7a73c38b22aeb8967a8bfbffd4741f7ffd043c4d'], + }), + ('atomicwrites', '1.4.0', { + 'checksums': ['ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a'], + }), + ('py', '1.10.0', { + 'checksums': ['21b81bda15b66ef5e1a777a21c4dcd9c20ad3efd0b3f817e7a809035269e1bd3'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('more-itertools', '8.8.0', { + 'checksums': ['83f0308e05477c68f56ea3a888172c78ed5d5b3c282addb67508e7ba6c8f813a'], + }), + ('attrs', '21.2.0', { + 'modulename': 'attr', + 'checksums': ['ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb'], + }), + ('backports.functools_lru_cache', '1.6.4', { + 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], + }), + ('wcwidth', '0.2.5', { + 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], + }), + ('iniconfig', '1.1.1', { + 'checksums': ['bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32'], + }), + ('packaging', '20.9', { + 'checksums': ['5b327ac1320dc863dca72f4514ecc086f31186744b84a230374cc1fd776feae5'], + }), + ('colorama', '0.4.4', { + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + ('pytest', '6.2.4', { + 'checksums': ['50bcad0a0b9c5a72c8e4e7c9855a3ad496ca6a881a3641b4260605450772c54b'], + }), + ('MarkupSafe', '2.0.1', { + 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], + }), + ('Jinja2', '3.0.1', { + 'checksums': ['703f484b47a6af502e743c9122595cc812b0271f661722403114f71a79d0f5a4'], + }), + ('sphinxcontrib-serializinghtml', '1.1.5', { + 'modulename': 'sphinxcontrib.serializinghtml', + 'checksums': ['aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952'], + }), + ('sphinxcontrib-websupport', '1.2.4', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['4edf0223a0685a7c485ae5a156b6f529ba1ee481a1417817935b20bde1956232'], + }), + ('Pygments', '2.9.0', { + 'checksums': ['a18f47b506a429f6f4b9df81bb02beab9ca21d0a5fee38ed15aef65f0545519f'], + }), + ('imagesize', '1.2.0', { + 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], + }), + ('docutils', '0.17.1', { + 'checksums': ['686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125'], + }), + ('snowballstemmer', '2.1.0', { + 'checksums': ['e997baa4f2e9139951b6f4c631bad912dfd3c792467e2f03d7239464af90e914'], + }), + ('alabaster', '0.7.12', { + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('sphinxcontrib-applehelp', '1.0.2', { + 'modulename': 'sphinxcontrib.applehelp', + 'checksums': ['a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58'], + }), + ('sphinxcontrib-devhelp', '1.0.2', { + 'modulename': 'sphinxcontrib.devhelp', + 'checksums': ['ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4'], + }), + ('sphinxcontrib-htmlhelp', '2.0.0', { + 'modulename': 'sphinxcontrib.htmlhelp', + 'checksums': ['f5f8bb2d0d629f398bf47d0d69c07bc13b65f75a81ad9e2f71a63d4b7a2f6db2'], + }), + ('sphinxcontrib-jsmath', '1.0.1', { + 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}), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('flit-core', '3.3.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': ['b1404accffd6504b5f24eeca9ec5d3c877f828d16825348ba81515fa084bd5f0'], + }), + ('zipfile36', '0.1.3', { + 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], + }), + ('flit', '3.3.0', { + 'checksums': ['65fbe22aaa7f880b776b20814bd80b0afbf91d1f95b17235b608aa256325ce57'], + }), + ('regex', '2021.8.3', { + 'checksums': ['8935937dad2c9b369c3d932b0edbc52a62647c2afb2fafc0c280f14a8bf56a6a'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('pylev', '1.4.0', { + 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], + }), + ('pastel', '0.2.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], + }), + ('crashtest', '0.3.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], + }), + ('clikit', '0.6.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], + }), + ('jeepney', '0.7.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['1b5a0ea5c0e7b166b2f5895b91a08c14de8915afda4407fb5022a195224958ac'], + }), + ('SecretStorage', '3.3.1', { + 'checksums': ['fd666c51a6bf200643495a04abb261f83229dcb6fd8472ec393df7ffc8b6f195'], + }), + ('keyring', '21.2.0', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['197fd5903901030ef7b82fe247f43cfed2c157a28e7747d1cfcf4bc5e699dd03'], + }), + ('keyrings.alt', '4.1.0', { + 'modulename': False, + 'checksums': ['52ccb61d6f16c10f32f30d38cceef7811ed48e086d73e3bae86f0854352c4ab2'], + }), + ('tomlkit', '0.7.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['173ad840fa5d2aac140528ca1933c29791b79a374a0861a80347f42ec9328117'], + }), + ('shellingham', '1.4.0', { + 'checksums': ['4855c2458d6904829bd34c299f11fdeed7cfefbf8a2c522e4caea6cd76b3171e'], + }), + ('requests-toolbelt', '0.9.1', { + 'checksums': ['968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0'], + }), + ('pyrsistent', '0.18.0', { + 'checksums': ['773c781216f8c2900b42a7b638d5b517bb134ae1acbebe4d1e8f1f41ea60eb4b'], + }), + ('pkginfo', '1.7.1', { + 'checksums': ['e7432f81d08adec7297633191bbf0bd47faf13cd8724c3a13250e51d542635bd'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('simplejson', '3.17.3', { + 'checksums': ['da72a452bcf4349fc467a12b54ab0e63e654a571cacc44084826d52bde12b6ee'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('cleo', '0.8.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('CacheControl', '0.12.6', { + 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.0.3', { + 'modulename': 'poetry.core', + 'checksums': ['2315c928249fc3207801a81868b64c66273077b26c8d8da465dccf8f488c90c5'], + }), + ('glob2', '0.7', { + 'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'], + }), + ('poetry', '1.1.7', { + 'checksums': ['3833c7b22411b8393e8e594fede94f0ef7a5260c19f51e272cce76512cffe6c8'], + }), + ('fsspec', '2021.7.0', { + 'checksums': ['792ebd3b54de0b30f1ce73f0ba0a8bcc864724f2d9f248cb8d0ece47db0cbde8'], + }), + ('threadpoolctl', '2.2.0', { + 'checksums': ['86d4b6801456d780e94681d155779058759eaef3c3564758b17b6c99db5f81cb'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a03a5a29908 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.54.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +checksums = ['ac8511633e9b5a65ad030a1a2e5bdaa841fdfe3132f2baaa52cc04e71c6c6976'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Python', '3.9.6', '-bare'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' From 8ec38695fefd8c7889759d538b758e386841f8fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 6 Aug 2021 01:35:27 +0200 Subject: [PATCH 0691/9987] adding easyconfigs: libevent-2.1.12-GCCcore-11.2.0.eb, numactl-2.0.14-GCCcore-11.2.0.eb, UCX-1.11.0-GCCcore-11.2.0.eb, libfabric-1.13.0-GCCcore-11.2.0.eb, hwloc-2.5.0-GCCcore-11.2.0.eb --- .../h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb | 48 ++++++++++++++ .../libevent-2.1.12-GCCcore-11.2.0.eb | 38 +++++++++++ .../libfabric-1.13.0-GCCcore-11.2.0.eb | 63 +++++++++++++++++++ .../numactl/numactl-2.0.14-GCCcore-11.2.0.eb | 34 ++++++++++ .../u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb | 50 +++++++++++++++ 5 files changed, 233 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.14-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8f1e093450f --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.5.0' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +# need to build with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake +# cfr. https://github.com/open-mpi/hwloc/issues/315 +toolchainopts = {'vectorize': False} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['38aa8102faec302791f6b4f0d23960a3ffa25af3af6af006c64dbecac23f852c'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('numactl', '2.0.14'), + ('libxml2', '2.9.10'), + ('libpciaccess', '0.16'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ce86a4e932c --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('OpenSSL', '1.1', '', True), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9fa99b0363d --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.13.0' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +# The psm3 provider (enabled by default) requires an AVX capable system to run +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'ofiwg' +source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +patches = [ + '%(name)s-1.12.1_disable-psm3-avx-config.patch', +] +checksums = [ + '0c68264ae18de5c31857724c754023351614330bd61a50b40cef2b5e8f63ab28', # libfabric-1.13.0.tar.bz2 + # libfabric-1.12.1_disable-psm3-avx-config.patch + '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('numactl', '2.0.14'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# Regenerate build files +preconfigopts = "autoreconf -f -i &&" + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) +configopts += "--disable-usnic " + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.14-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.14-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c2ebf71aad0 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.14-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.14' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1ee27abd07ff6ba140aaf9bc6379b37825e54496e01d6f7343330cf1a4487035'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..847d1c18e3b --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.11.0' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = ['UCX-1.10.0-dynamic_modules.patch'] +checksums = [ + 'b7189b69fe0e16e3c03784ef674e45687a9c520750bd74a45125c460ede37647', # ucx-1.11.0.tar.gz + '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.11'), + ('numactl', '2.0.14'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From b53c9e9564611782ea3d2676afac4afee8366da8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 6 Aug 2021 02:01:50 +0200 Subject: [PATCH 0692/9987] Add libxml2 --- .../libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c0fa3931030 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.10' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lib' From cfc57b7a122db093ddf323cbf2232e108e4ede9b Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Fri, 6 Aug 2021 14:04:24 +1000 Subject: [PATCH 0693/9987] Create gflags-2.2.2-GCCcore-10.2.0.eb New compiler, binutils, CMake --- .../g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..958caa83e61 --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' From 8eee456e6cda3e00ce76f9342d1bf8ca47fca2d3 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Fri, 6 Aug 2021 14:14:11 +1000 Subject: [PATCH 0694/9987] Create glog-0.5.0-GCCcore-10.2.0.eb Update version, toolchain, builddependencies, dependencies --- .../g/glog/glog-0.5.0-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/glog/glog-0.5.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/glog/glog-0.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/glog/glog-0.5.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d6dded49867 --- /dev/null +++ b/easybuild/easyconfigs/g/glog/glog-0.5.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'glog' +version = '0.5.0' + +homepage = 'https://github.com/google/glog' +description = "A C++ implementation of the Google logging module." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/google/glog/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['eede71f28371bf39aa69b45de23b329d37214016e2055269b3b5e7cfd40b59f5'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('gflags', '2.2.2'), + ('libunwind', '1.4.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['include/glog/logging.h', 'include/glog/raw_logging.h', 'lib/libglog.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From 30df81956c6cda51332d341f16ff2c5adc1d2c68 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Aug 2021 12:12:13 +0200 Subject: [PATCH 0695/9987] adding easyconfigs: HPCG-3.1-foss-2021a.eb, HPCG-3.1-intel-2021a.eb --- .../easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb | 17 +++++++++++++++++ .../easyconfigs/h/HPCG/HPCG-3.1-intel-2021a.eb | 17 +++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021a.eb diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb new file mode 100644 index 00000000000..b70f6793470 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb @@ -0,0 +1,17 @@ +name = 'HPCG' +version = '3.1' + +homepage = 'https://software.sandia.gov/hpcg' +description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than + the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://www.hpcg-benchmark.org/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4'] + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021a.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021a.eb new file mode 100644 index 00000000000..a57e12821ab --- /dev/null +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021a.eb @@ -0,0 +1,17 @@ +name = 'HPCG' +version = '3.1' + +homepage = 'https://software.sandia.gov/hpcg' +description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than + the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://www.hpcg-benchmark.org/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4'] + +runtest = True + +moduleclass = 'math' From 4aff8e2fa0ab631e63a96fcd4e39a0821178479b Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Fri, 6 Aug 2021 12:13:57 +0200 Subject: [PATCH 0696/9987] Added WRF-4.3 --- .../t/tcsh/tcsh-6.22.04-GCCcore-10.3.0.eb | 43 +++ .../w/WRF/WRF-4.3-foss-2021a-dmpar.eb | 43 +++ ...WRF-4.3_netCDF-Fortran_separate_path.patch | 254 ++++++++++++++++++ 3 files changed, 340 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.22.04-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.3_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.04-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.04-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..06843271545 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.04-GCCcore-10.3.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.22.04' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['eb16356243218c32f39e07258d72bf8b21e62ce94bb0e8a95e318b151397e231'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('ncurses', '6.2')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb new file mode 100644 index 00000000000..b91d211c638 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb @@ -0,0 +1,43 @@ +name = 'WRF' +version = '4.3' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ +# 'WRF_parallel_build_fix.patch', + 'WRF-4.3_netCDF-Fortran_separate_path.patch', +] +checksums = [ + '68109070e3e6b3106257f738c0e69e774816589bf3a0cedaf66dd15f99ad63b5', # v4.3.tar.gz +# 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + '7007c1caa019da76baa157bebd1886a3d152feaf2f71c1675687a1874c7514e3', # WRF-4.3_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20210128'), + ('tcsh', '6.22.04'), + ('time', '1.9'), + ('Perl', '5.32.1'), +] + +dependencies = [ + ('JasPer', '2.0.28'), + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.3_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.3_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..adc51a233bd --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.3_netCDF-Fortran_separate_path.patch @@ -0,0 +1,254 @@ +diff -Nru WRF-4.3.orig/arch/Config.pl WRF-4.3/arch/Config.pl +--- WRF-4.3.orig/arch/Config.pl 2021-08-04 15:09:59.634194394 +0200 ++++ WRF-4.3/arch/Config.pl 2021-08-05 11:14:34.614153019 +0200 +@@ -8,6 +8,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; # for netCDF 4.2 and greater, Fortran lib might be in a different path + $sw_pnetcdf_path = "" ; + $sw_hdf5_path=""; + $sw_phdf5_path=""; +@@ -91,6 +92,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -118,6 +123,7 @@ + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { + $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -458,6 +464,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ; + $_ =~ s/CONFIGURE_PHDF5_PATH/$sw_phdf5_path/g ; +@@ -504,7 +511,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +diff -Nru WRF-4.3.orig/arch/configure.defaults WRF-4.3/arch/configure.defaults +--- WRF-4.3.orig/arch/configure.defaults 2021-08-04 15:09:59.603194629 +0200 ++++ WRF-4.3/arch/configure.defaults 2021-08-05 11:23:16.835203445 +0200 +@@ -1602,6 +1602,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +diff -Nru WRF-4.3.orig/arch/conf_tokens WRF-4.3/arch/conf_tokens +--- WRF-4.3.orig/arch/conf_tokens 2021-08-04 15:09:59.624194471 +0200 ++++ WRF-4.3/arch/conf_tokens 2021-08-05 11:23:57.889893151 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDFF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -Nru WRF-4.3.orig/arch/postamble WRF-4.3/arch/postamble +--- WRF-4.3.orig/arch/postamble 2021-08-04 15:09:59.629194433 +0200 ++++ WRF-4.3/arch/postamble 2021-08-05 11:28:36.010792236 +0200 +@@ -52,6 +52,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/wrftladj \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ ++ -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include \ + -I$(NETCDFPATH)/include \ + CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC + REGISTRY = Registry +@@ -62,6 +63,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + RTTOVPATH = CONFIGURE_RTTOV_PATH +@@ -93,13 +95,13 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_pnf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \ +- make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ ++ make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ + FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_grib_share : +diff -Nru WRF-4.3.orig/configure WRF-4.3/configure +--- WRF-4.3.orig/configure 2021-08-04 15:10:11.719102875 +0200 ++++ WRF-4.3/configure 2021-08-05 11:34:41.078036732 +0200 +@@ -183,9 +183,13 @@ + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then + USENETCDFF="-lnetcdff" + else +- USENETCDFF=" " ++ if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++ else ++ USENETCDFF=" " ++ fi + fi +- if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib/libnetcdf.dll.a" ] ; then ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then + USENETCDF="-lnetcdf" + else + USENETCDF=" " +@@ -552,7 +556,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -634,14 +638,14 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +diff -Nru WRF-4.3.orig/external/io_netcdf/makefile WRF-4.3/external/io_netcdf/makefile +--- WRF-4.3.orig/external/io_netcdf/makefile 2021-08-04 15:10:07.298136355 +0200 ++++ WRF-4.3/external/io_netcdf/makefile 2021-08-05 11:36:26.046244872 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so -o -f $(NETCDFPATH)/lib/libnetcdff.dll.a \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib64/libnetcdff.a -o -f $(NETCDFFPATH)/lib64/libnetcdff.so \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -Nru WRF-4.3.orig/external/io_pnetcdf/Makefile WRF-4.3/external/io_pnetcdf/Makefile +--- WRF-4.3.orig/external/io_pnetcdf/Makefile 2021-08-04 15:10:05.733148207 +0200 ++++ WRF-4.3/external/io_pnetcdf/Makefile 2021-08-05 11:37:34.441729005 +0200 +@@ -9,8 +9,8 @@ + ext_pnc_put_var_td.code \ + ext_pnc_put_var_ti.code \ + transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = -L$(NETCDFPATH)/lib -lpnetcdf ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = -L$(NETCDFFPATH)/lib -lpnetcdf + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -25,15 +25,15 @@ + $(RANLIB) libwrfio_pnf.a + + wrf_io.o: wrf_io.F90 $(CODE) +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f + $(FC) $(FFLAGS) -c wrf_io.f + + module_wrfsi_static.o: module_wrfsi_static.F90 +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f + $(FC) $(FFLAGS) -c module_wrfsi_static.f + + field_routines.o: field_routines.F90 wrf_io.o +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f + $(FC) $(FFLAGS) -c field_routines.f + + superclean: +diff -Nru WRF-4.3.orig/Makefile WRF-4.3/Makefile +--- WRF-4.3.orig/Makefile 2021-08-04 15:10:04.526157349 +0200 ++++ WRF-4.3/Makefile 2021-08-05 11:38:25.538343676 +0200 +@@ -1003,7 +1003,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \ + FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ +@@ -1133,7 +1133,7 @@ + + # rule used by configure to test if this will compile with netcdf4 + nc4_test: +- @cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib $(USENETCDF) ; cd .. ++ @cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 $(USENETCDF) ; cd .. + + # rule used by configure to test if Fortran 2003 IEEE signaling is available + fortran_2003_ieee_test: From b169a40969b242325e77ba10ca74d4fb2020f2bb Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Fri, 6 Aug 2021 12:30:56 +0200 Subject: [PATCH 0697/9987] Removed redundant patch --- easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb index b91d211c638..6d423a181a1 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb @@ -14,12 +14,10 @@ toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 source_urls = ['https://github.com/wrf-model/WRF/archive/'] sources = ['v%(version)s.tar.gz'] patches = [ -# 'WRF_parallel_build_fix.patch', 'WRF-4.3_netCDF-Fortran_separate_path.patch', ] checksums = [ '68109070e3e6b3106257f738c0e69e774816589bf3a0cedaf66dd15f99ad63b5', # v4.3.tar.gz -# 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch '7007c1caa019da76baa157bebd1886a3d152feaf2f71c1675687a1874c7514e3', # WRF-4.3_netCDF-Fortran_separate_path.patch ] From ea472a11d195434e43d192222958776efafe26c6 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 6 Aug 2021 12:42:47 +0200 Subject: [PATCH 0698/9987] adding easyconfigs: ctffind-4.1.14-foss-2021a.eb --- .../c/ctffind/ctffind-4.1.14-foss-2021a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a.eb new file mode 100644 index 00000000000..2b1b7ab23a2 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_asm-fix.patch'] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.2.0'), + ('GSL', '2.7'), + ('wxWidgets', '3.1.5'), + ('CUDAcore', '11.3.1', '', True), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From e1ef7855fe753423dde6c13ac5c6bad5142e3feb Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Aug 2021 12:44:18 +0200 Subject: [PATCH 0699/9987] update easyconfig HPCG-3.1-foss-2021a.eb: add patch --- .../easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb | 8 +++++++ ...o-be-explicitly-designated-as-shared.patch | 24 +++++++++++++++++++ 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPCG/HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb index b70f6793470..a0f81a48140 100644 --- a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb @@ -10,7 +10,15 @@ toolchainopts = {'usempi': True, 'openmp': True} source_urls = ['http://www.hpcg-benchmark.org/downloads'] sources = [SOURCELOWER_TAR_GZ] +# Newer compilers require loop's upper-bound variable to be +# explicitly designated as private/shared/firstprivate/lastprivate +patches = ['HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch'] checksums = ['33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4'] +checksums = [ + '33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4', # hpcg-3.1.tar.gz + # HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch + '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482', +] runtest = True diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch b/easybuild/easyconfigs/h/HPCG/HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch new file mode 100644 index 00000000000..704cd4c73ee --- /dev/null +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch @@ -0,0 +1,24 @@ +From e9e0b7e6cae23e1f30dd983c2ce2d3bd34d56f75 Mon Sep 17 00:00:00 2001 +From: Piotr Luszczek +Date: Mon, 17 Feb 2020 12:04:33 -0500 +Subject: [PATCH] Add missing variable designation, fixes issue #64 + +Newer compilers (GCC 9.2) require loop's upper-bound variable to be +explicitly designated as private/shared/firstprivate/lastprivate +--- + src/ComputeResidual.cpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/ComputeResidual.cpp b/src/ComputeResidual.cpp +index afc57c6..2e9498b 100644 +--- a/src/ComputeResidual.cpp ++++ b/src/ComputeResidual.cpp +@@ -53,7 +53,7 @@ int ComputeResidual(const local_int_t n, const Vector & v1, const Vector & v2, d + double local_residual = 0.0; + + #ifndef HPCG_NO_OPENMP +- #pragma omp parallel default(none) shared(local_residual, v1v, v2v) ++ #pragma omp parallel default(none) shared(n, local_residual, v1v, v2v) + { + double threadlocal_residual = 0.0; + #pragma omp for From f2ab284b9779eb45089ff44fd8ba6125cde673c8 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 6 Aug 2021 12:47:44 +0200 Subject: [PATCH 0700/9987] renamed file --- .../ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..2b1b7ab23a2 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_asm-fix.patch'] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.2.0'), + ('GSL', '2.7'), + ('wxWidgets', '3.1.5'), + ('CUDAcore', '11.3.1', '', True), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From ec593a1caf872bf547dd5daeda0fe16857a19d7c Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Fri, 6 Aug 2021 12:50:18 +0200 Subject: [PATCH 0701/9987] Delete ctffind-4.1.14-foss-2021a.eb git deleted file with incorrect name scheme. --- .../c/ctffind/ctffind-4.1.14-foss-2021a.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a.eb deleted file mode 100644 index 2b1b7ab23a2..00000000000 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a.eb +++ /dev/null @@ -1,45 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# -# Author: Ake Sandgren, HPC2N, Umea University - -easyblock = 'ConfigureMake' - -name = 'ctffind' -version = '4.1.14' - -homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' -description = """Program for finding CTFs of electron micrographs.""" - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'openmp': True} - -source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_asm-fix.patch'] -checksums = [ - 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz - 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch -] - -dependencies = [ - ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.6'), - ('LibTIFF', '4.2.0'), - ('GSL', '2.7'), - ('wxWidgets', '3.1.5'), - ('CUDAcore', '11.3.1', '', True), -] - -configopts = '--enable-openmp ' - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/ctffind'], - 'dirs': [], -} - -moduleclass = 'bio' From f820355bff27d49fc6198777a603e73b634f8c10 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Aug 2021 12:58:57 +0200 Subject: [PATCH 0702/9987] update easyconfig HPCG-3.1-foss-2021a.eb: update checksums --- easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb index a0f81a48140..766a6e714c7 100644 --- a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021a.eb @@ -13,7 +13,6 @@ sources = [SOURCELOWER_TAR_GZ] # Newer compilers require loop's upper-bound variable to be # explicitly designated as private/shared/firstprivate/lastprivate patches = ['HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch'] -checksums = ['33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4'] checksums = [ '33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4', # hpcg-3.1.tar.gz # HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch From c47cea8cce9fe10a1dbcb109baa5b1059db42501 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 6 Aug 2021 13:08:33 +0200 Subject: [PATCH 0703/9987] Implement locale workaround for all ITK ECs --- .../easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb | 2 -- .../easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb | 2 -- .../easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb | 5 +++-- .../easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb | 5 +++-- .../easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb | 5 +++-- .../easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb | 5 +++-- .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb | 5 +++-- .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb | 4 ++-- .../easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb | 1 + .../easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb | 1 + easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb | 1 + .../i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb | 1 + easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb | 1 + 13 files changed, 22 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb index b6a25b25c4e..ffccf345a71 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb @@ -47,8 +47,6 @@ configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' prebuildopts = "export LC_ALL=C && " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -separate_build_dir = True - modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb index ff2ea437903..674ff273f1c 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb @@ -47,8 +47,6 @@ configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' prebuildopts = "export LC_ALL=C && " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -separate_build_dir = True - modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb index 555fee43bb0..65fdf6aa19b 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb @@ -40,9 +40,10 @@ configopts += ' '.join(local_sys_cmake) # Don't depend on MPICXX (which makes linking to ITK painful) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 +prebuildopts = "LC_ALL=C " -separate_build_dir = True +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb index b7300beac4d..20dbdbd99ef 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb @@ -40,9 +40,10 @@ configopts += ' '.join(local_sys_cmake) # Don't depend on MPICXX (which makes linking to ITK painful) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 +prebuildopts = "LC_ALL=C " -separate_build_dir = True +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb index 4357de2d400..d7e58e8d38b 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb @@ -40,9 +40,10 @@ configopts += ' '.join(local_sys_cmake) # Don't depend on MPICXX (which makes linking to ITK painful) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 +prebuildopts = "LC_ALL=C " -separate_build_dir = True +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb index e7c39f1cca9..c21771fabdd 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb @@ -40,9 +40,10 @@ configopts += ' '.join(local_sys_cmake) # Don't depend on MPICXX (which makes linking to ITK painful) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 +prebuildopts = "LC_ALL=C " -separate_build_dir = True +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb index a9c09084622..ce4e65388fe 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb @@ -44,8 +44,6 @@ dependencies = [ ('LibTIFF', '4.0.10'), ] -separate_build_dir = True - local_sys_deps = ['EIGEN', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'SWIG', 'ZLIB'] local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] @@ -57,6 +55,9 @@ configopts += ' '.join(local_sys_cmake) # Don't depend on MPICXX (which makes linking to ITK painful) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 +prebuildopts = "LC_ALL=C " + preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb index 443239f5b85..296c41e3a10 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb @@ -44,8 +44,6 @@ dependencies = [ ('LibTIFF', '4.0.10'), ] -separate_build_dir = True - local_sys_deps = ['EIGEN', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'SWIG', 'ZLIB'] local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] @@ -57,7 +55,9 @@ configopts += ' '.join(local_sys_cmake) # Don't depend on MPICXX (which makes linking to ITK painful) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " + preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb index 22d9b08b31e..c1c7e6c3323 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb @@ -38,6 +38,7 @@ configopts += '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' configopts += ' '.join(local_sys_cmake) +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb index 8827c4fb24f..7090bc154cf 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb @@ -52,6 +52,7 @@ configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' configopts += '-DITK_WRAP_PYTHON=ON ' configopts += ' '.join(local_sys_cmake) +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb index afeb4c9c2cf..ce6769a5718 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb @@ -48,6 +48,7 @@ configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK configopts += ' '.join(local_sys_cmake) +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb index be676ecd362..1a24fe1e84f 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb @@ -53,6 +53,7 @@ configopts += '-DITK_WRAP_PYTHON=ON ' configopts += '-DITK_USE_CUFFTW=ON ' configopts += ' '.join(local_sys_cmake) +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb index ab7b2e46867..4a8a99ad07a 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb @@ -49,6 +49,7 @@ configopts += '-DITK_USE_CUFFTW:BOOL=ON ' configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK configopts += ' '.join(local_sys_cmake) +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', From 06a919dcac311187e4a4f7a3b2e241706638234f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 6 Aug 2021 13:11:33 +0200 Subject: [PATCH 0704/9987] Use build_share_libs option --- .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb | 4 +++- .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb | 4 +++- .../easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb | 4 +++- easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb | 4 +++- .../i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb | 4 +++- easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb | 4 +++- 6 files changed, 18 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb index ce4e65388fe..c59648df84a 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb @@ -48,13 +48,15 @@ local_sys_deps = ['EIGEN', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'SWIG', 'ZLIB'] local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] preconfigopts = 'Eigen3_DIR=$EBROOTEIGEN ' -configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_TESTING=OFF ' configopts += '-DITK_WRAP_PYTHON=ON -DITK_LEGACY_SILENT=ON ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' configopts += ' '.join(local_sys_cmake) # Don't depend on MPICXX (which makes linking to ITK painful) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' +build_shared_libs = True + # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb index 296c41e3a10..37a8b30a8dc 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb @@ -48,13 +48,15 @@ local_sys_deps = ['EIGEN', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'SWIG', 'ZLIB'] local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] preconfigopts = 'Eigen3_DIR=$EBROOTEIGEN ' -configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_TESTING=OFF ' configopts += '-DITK_WRAP_PYTHON=ON -DITK_LEGACY_SILENT=ON ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' configopts += ' '.join(local_sys_cmake) # Don't depend on MPICXX (which makes linking to ITK painful) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' +build_shared_libs = True + # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb index 7090bc154cf..594e71ea6bf 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb @@ -47,11 +47,13 @@ dependencies = [ local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'SWIG', 'ZLIB'] local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] -configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' configopts += '-DITK_WRAP_PYTHON=ON ' configopts += ' '.join(local_sys_cmake) +build_shared_libs = True + # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb index ce6769a5718..99e21b1056b 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb @@ -42,12 +42,14 @@ dependencies = [ local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] -configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK configopts += ' '.join(local_sys_cmake) +build_shared_libs = True + # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb index 1a24fe1e84f..d18a6d07e82 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb @@ -47,12 +47,14 @@ dependencies = [ local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'SWIG', 'ZLIB'] local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] -configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' configopts += '-DITK_WRAP_PYTHON=ON ' configopts += '-DITK_USE_CUFFTW=ON ' configopts += ' '.join(local_sys_cmake) +build_shared_libs = True + # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb index 4a8a99ad07a..53edcf1b8d1 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb @@ -42,13 +42,15 @@ dependencies = [ local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] -configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' configopts += '-DITK_USE_CUFFTW:BOOL=ON ' configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK configopts += ' '.join(local_sys_cmake) +build_shared_libs = True + # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " From 006b15fa10029a54ef75100dc79f039b1cc6915b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 6 Aug 2021 13:14:17 +0200 Subject: [PATCH 0705/9987] Fix invalid local variable --- .../easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb | 2 +- .../easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb index 594e71ea6bf..becaaa8025f 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb @@ -63,7 +63,7 @@ local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF sanity_check_paths = { 'files': ['bin/itkTestDriver'] + - ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (i, SHLIB_EXT) for i in local_lib_names], 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], } diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb index 99e21b1056b..93e38ad421c 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a.eb @@ -58,7 +58,7 @@ local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF sanity_check_paths = { 'files': ['bin/itkTestDriver'] + - ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (i, SHLIB_EXT) for i in local_lib_names], 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], } diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb index d18a6d07e82..eac8435fd26 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb @@ -64,7 +64,7 @@ local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF sanity_check_paths = { 'files': ['bin/itkTestDriver'] + - ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (i, SHLIB_EXT) for i in local_lib_names], 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], } diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb index 53edcf1b8d1..e4cfb4c1e83 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a.eb @@ -59,7 +59,7 @@ local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF sanity_check_paths = { 'files': ['bin/itkTestDriver'] + - ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (i, SHLIB_EXT) for i in local_lib_names], 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], } From 2a73f3d66b017403d193538af4a2efaf9df75c6e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 6 Aug 2021 13:20:22 +0200 Subject: [PATCH 0706/9987] Switch to CMakePythonPackage --- .../i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb | 7 +------ .../i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb | 7 +------ .../i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb | 7 +------ .../i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb | 7 +------ .../i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb | 7 +------ .../i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb | 7 +------ .../i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb | 7 +------ .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb | 7 +------ .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb | 7 +------ .../i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb | 7 +------ .../easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb | 7 +------ .../i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb | 7 +------ 12 files changed, 12 insertions(+), 72 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb index 1f8b31e8d93..b67bc22298a 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '4.12.2' @@ -45,12 +45,9 @@ configopts += ' '.join(local_sys_cmake) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' prebuildopts = "export LC_ALL=C && " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " separate_build_dir = True -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/itkTestDriver', 'lib/libITKVtkGlue-%(version_major_minor)s.a', @@ -60,6 +57,4 @@ sanity_check_paths = { 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb index ffccf345a71..1e29ff00718 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '4.13.0' @@ -45,9 +45,6 @@ configopts += ' '.join(local_sys_cmake) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' prebuildopts = "export LC_ALL=C && " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', @@ -58,6 +55,4 @@ sanity_check_paths = { 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb index 674ff273f1c..0ddd6eb72da 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '4.13.0' @@ -45,9 +45,6 @@ configopts += ' '.join(local_sys_cmake) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' prebuildopts = "export LC_ALL=C && " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', @@ -58,6 +55,4 @@ sanity_check_paths = { 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb index 65fdf6aa19b..e2252497704 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '4.13.1' @@ -43,9 +43,6 @@ configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', @@ -56,6 +53,4 @@ sanity_check_paths = { 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb index 20dbdbd99ef..30809b9a4fe 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '4.13.1' @@ -43,9 +43,6 @@ configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', @@ -56,6 +53,4 @@ sanity_check_paths = { 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb index d7e58e8d38b..b064c81e876 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '4.13.1' @@ -43,9 +43,6 @@ configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', @@ -56,6 +53,4 @@ sanity_check_paths = { 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb index c21771fabdd..4a275d06bf5 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '4.13.1' @@ -43,9 +43,6 @@ configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', @@ -56,6 +53,4 @@ sanity_check_paths = { 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb index c59648df84a..3a236d912fd 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb @@ -7,7 +7,7 @@ # Vrije Universiteit Brussel (VUB) # Vanderbilt University # -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '5.0.1' @@ -60,7 +60,6 @@ build_shared_libs = True # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " sanity_check_paths = { 'files': ['bin/itkTestDriver', @@ -74,8 +73,4 @@ sanity_check_paths = { 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb index 37a8b30a8dc..b7df120055d 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb @@ -7,7 +7,7 @@ # Vrije Universiteit Brussel (VUB) # Vanderbilt University # -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '5.0.1' @@ -60,7 +60,6 @@ build_shared_libs = True # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " sanity_check_paths = { 'files': ['bin/itkTestDriver', @@ -74,8 +73,4 @@ sanity_check_paths = { 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb index c1c7e6c3323..4c4055172af 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '5.0b01' @@ -41,9 +41,6 @@ configopts += ' '.join(local_sys_cmake) # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['bin/itkTestDriver', @@ -54,6 +51,4 @@ sanity_check_paths = { 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb index becaaa8025f..ff966362678 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb @@ -2,7 +2,7 @@ # Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University # Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) # -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '5.1.2' @@ -57,7 +57,6 @@ build_shared_libs = True # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', 'ITKReview', 'ITKVTK', 'ITKVtkGlue'] @@ -67,8 +66,4 @@ sanity_check_paths = { 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'data' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb index eac8435fd26..2452214456e 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb @@ -2,7 +2,7 @@ # Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University # Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) # -easyblock = 'CMakeMake' +easyblock = 'CMakePythonPackage' name = 'ITK' version = '5.1.2' @@ -58,7 +58,6 @@ build_shared_libs = True # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', 'ITKReview', 'ITKVTK', 'ITKVtkGlue'] @@ -68,8 +67,4 @@ sanity_check_paths = { 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], } -sanity_check_commands = [('python', "-c 'import %(namelower)s'")] - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'data' From 8750eae17a090b114844a7b8c2f328696cbeac89 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 6 Aug 2021 13:27:26 +0200 Subject: [PATCH 0707/9987] adding easyconfigs: openstackclient-5.5.0-GCCcore-10.2.0.eb --- .../openstackclient-5.5.0-GCCcore-10.2.0.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..3237cb7dc75 --- /dev/null +++ b/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb @@ -0,0 +1,88 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/08 +easyblock = 'PythonBundle' + +name = 'openstackclient' +version = '5.5.0' + +homepage = 'https://docs.openstack.org/python-openstackclient/latest/' +description = """OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the +command set for Compute, Identity, Image, Network, Object Store and Block +Storage APIs together in a single shell with a uniform command structure.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), +] +builddependencies = [('binutils', '2.35')] +exts_download_dep_fail = True +exts_default_options = { + 'use_pip': True, + 'source_urls': [PYPI_SOURCE] +} +exts_list = [ + ('pbr', '5.6.0', { + 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], + }), + ('osc-lib', '2.4.1', { + 'checksums': ['257ef0cda902664605a850a858172306acb2b08b0e7e32d7a5b4f12dc6bc56c5'], + }), + ('keystoneauth1', '4.3.1', { + 'checksums': ['93605430a6d1424f31659bc5685e9dc1be9a6254e88c99f00cffc0a60c648a64'], + }), + ('debtcollector', '2.2.0', { + 'checksums': ['787981f4d235841bf6eb0467e23057fb1ac7ee24047c32028a8498b9128b6829'], + }), + ('oslo.i18n', '5.0.1', { + 'modulename': 'oslo_i18n', + 'checksums': ['3484b71e30f75c437523302d1151c291caf4098928269ceec65ce535456e035b'], + }), + ('oslo.utils', '4.9.2', { + 'modulename': 'oslo_utils', + 'checksums': ['20db285734ff6c3b50d5a6afcb2790ade0c7ba02fbc876feed43733f2c41a5c9'], + }), + ('oslo.serialization', '4.1.0', { + 'modulename': 'oslo_serialization', + 'checksums': ['cecc7794df806c85cb70dbd6c2b3af19bc68047ad29e3c6442be90a0a4de5379'], + }), + ('oslo.config', '8.7.1', { + 'modulename': 'oslo_config', + 'checksums': ['a0c346d778cdc8870ab945e438bea251b5f45fae05d6d99dfe4953cca2277b60'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('iso-8601', '0.3.1', { + 'modulename': 'iso8601', + 'checksums': ['afc2bca0f002f817c2e597312dcaa0280306845d85939b4219f069319d075405'], + }), + ('python-novaclient', '17.5.0', { + 'modulename': 'novaclient', + 'checksums': ['7aa0fe9a74b1336e56c2f7965f14e04bad29dbfbd7ba41dcb7b364f94c9bee7f'], + }), + ('python-keystoneclient', '4.2.0', { + 'modulename': 'keystoneclient', + 'checksums': ['0248426e483b95de395086482c077d48e45990d3b1a3e334b2ec8b2e108f5a8a'], + }), + ('python-cinderclient', '8.0.0', { + 'modulename': 'cinderclient', + 'checksums': ['4ced8c562064ab73f757d91d26846faaf1fc1c82f1fee5597e24df3d1ffcf116'], + }), + ('python-openstackclient', version, { + 'modulename': 'openstackclient', + 'checksums': ['8d40491374172f9375ce1642ac2230b1cbb5a564320edbcc2a9ebe857fd9a880'], + }), +] + +enhance_sanity_check = True +sanity_check_commands = ['openstack -h'] + +sanity_check_paths = { + 'files': ['bin/openstack'], + 'dirs': ["bin", 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' From dd27d694d7cb1fafd244f44d758df3e95329ebd1 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 6 Aug 2021 13:33:19 +0200 Subject: [PATCH 0708/9987] Remove trailing whitespace --- .../easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb | 2 +- .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb | 2 +- .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb index b67bc22298a..6aa6b68da04 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb @@ -6,7 +6,7 @@ versionsuffix = '-Python-%(pyver)s' homepage = 'https://itk.org' description = """Insight Segmentation and Registration Toolkit (ITK) provides - an extensive suite of software tools for registering and segmenting + an extensive suite of software tools for registering and segmenting multidimensional imaging data.""" toolchain = {'name': 'foss', 'version': '2016b'} diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb index 3a236d912fd..c5e843c3655 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb @@ -1,6 +1,6 @@ # # Alex Domingo and Fenglai Liu -# +# # alex.domingo.toro@vub.be # fenglai@accre.vanderbilt.edu # diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb index b7df120055d..7dfe7995198 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb @@ -1,6 +1,6 @@ # # Alex Domingo and Fenglai Liu -# +# # alex.domingo.toro@vub.be # fenglai@accre.vanderbilt.edu # From 030b9a6cd3aefaaa06121902c4aab3b14f214b69 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 6 Aug 2021 13:55:42 +0200 Subject: [PATCH 0709/9987] added CUDA suffix --- .../c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb index 2b1b7ab23a2..d89f83d545c 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb @@ -9,6 +9,8 @@ easyblock = 'ConfigureMake' name = 'ctffind' version = '4.1.14' +local_cudaversion = '11.3.1' +versionsuffix = '-CUDA-%s' % local_cudaversion homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' description = """Program for finding CTFs of electron micrographs.""" @@ -30,7 +32,7 @@ dependencies = [ ('LibTIFF', '4.2.0'), ('GSL', '2.7'), ('wxWidgets', '3.1.5'), - ('CUDAcore', '11.3.1', '', True), + ('CUDAcore', local_cudaversion, '', True), ] configopts = '--enable-openmp ' From e134e063c196b52083d13086c1b802de2be4723c Mon Sep 17 00:00:00 2001 From: satishskamath Date: Fri, 6 Aug 2021 14:22:11 +0200 Subject: [PATCH 0710/9987] There is a patch included which is needed when symbolic links are used for paths to QT5 libraries. The path may be a symbolic link to the actual paths on different nodes and the paths generated by qmake are the actual paths which are textually different. The original code in the patch tries to manipulate the qtlib paths generated by qmake (the actual paths) using the symlink path (in ) which results in wrong library paths for QT in the makefile. This has been remedied using readlink. --- .../c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb | 59 +++++++++++++++++++ .../CubeGUI-4.6_qtlibs_symlink_realpath.patch | 12 ++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6_qtlibs_symlink_realpath.patch diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e9e59e11134 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb @@ -0,0 +1,59 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeGUI' +version = '4.6' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube graphical report explorer. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['CubeGUI-4.6_qtlibs_symlink_realpath.patch'] +checksums = [ + '1871c6736121d94a22314cb5daa8f3cbb978b58bfe54f677c4c9c9693757d0c5', # cubegui-4.6.tar.gz + 'ffb6b3cb02ffe6401505fcbe6d71cf4f46ecfe1f93e2ac8eaacf51da1010a5a5', # CubeGUI-4.6_qtlibs_symlink_realpath.patch +] + +configopts = [ + "--with-qt=$EBROOTQT5" +] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.36.1'), + ('CubeLib', '4.6'), +] + +dependencies = [ + ('Qt5', '5.15.2'), +] + +sanity_check_paths = { + 'files': ['bin/cube', 'bin/cubegui-config', + 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], + 'dirs': ['include/cubegui', 'lib/cube-plugins'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6_qtlibs_symlink_realpath.patch b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6_qtlibs_symlink_realpath.patch new file mode 100644 index 00000000000..e7f67012c48 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6_qtlibs_symlink_realpath.patch @@ -0,0 +1,12 @@ +diff -Nru cubegui-4.6_orig/build-config/m4/autotroll.m4 cubegui-4.6/build-config/m4/autotroll.m4 +--- cubegui-4.6_orig/build-config/m4/autotroll.m4 2021-08-06 13:03:13.758365694 +0200 ++++ cubegui-4.6/build-config/m4/autotroll.m4 2021-08-06 13:06:18.972956958 +0200 +@@ -741,7 +741,7 @@ + ]) + AS_IF([ test "x$LIBPATH" != "x" ], # perform correction only if one has found .so libraries instead of -lXXXX + [ +- at_cv_env_QT_LIBS="-L$LIBPATH "`echo $at_cv_env_QT_LIBS | sed "s,.so , ,g;s,.a , ,g;s,$LIBPATH/lib,-l,g"` ++ at_cv_env_QT_LIBS="-L$LIBPATH "`echo $at_cv_env_QT_LIBS | sed "s,.so , ,g;s,.a , ,g;s,$(readlink -m $LIBPATH)/lib,-l,g"` + echo "Fixed libraries are: $at_cv_env_QT_LIBS" + ]) + AC_SUBST([QT_LIBS], [$at_cv_env_QT_LIBS]) From 1ff8e36951f22dc129f8c42b3f92fbf6c4d9e4d3 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 6 Aug 2021 14:31:31 +0200 Subject: [PATCH 0711/9987] removed download_dep_fail and source_urls --- .../openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb index 3237cb7dc75..0aa753259f6 100644 --- a/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb @@ -15,10 +15,9 @@ dependencies = [ ('PyYAML', '5.3.1'), ] builddependencies = [('binutils', '2.35')] -exts_download_dep_fail = True + exts_default_options = { 'use_pip': True, - 'source_urls': [PYPI_SOURCE] } exts_list = [ ('pbr', '5.6.0', { @@ -76,7 +75,7 @@ exts_list = [ 'checksums': ['8d40491374172f9375ce1642ac2230b1cbb5a564320edbcc2a9ebe857fd9a880'], }), ] - +sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] From 8fc88b684caf6fbbd11b98fa9c89e3e7650d7940 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 6 Aug 2021 14:55:05 +0200 Subject: [PATCH 0712/9987] Remove last separate_build_dir setting and add missing comments --- .../easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb | 3 +-- .../easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb | 1 + .../easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb | 1 + .../easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb | 1 - .../easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb | 1 - .../easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb | 1 - .../easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb | 1 - .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb | 1 - .../easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb | 1 - .../easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb | 1 - .../easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb | 2 -- .../easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb | 2 -- 12 files changed, 3 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb index 6aa6b68da04..6b3e12cf9ee 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.12.2-foss-2016b-Python-2.7.12.eb @@ -44,10 +44,9 @@ configopts += ' '.join(local_sys_cmake) # Don't depend on MPICXX (which makes linking to ITK painful) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "export LC_ALL=C && " -separate_build_dir = True - sanity_check_paths = { 'files': ['bin/itkTestDriver', 'lib/libITKVtkGlue-%(version_major_minor)s.a', diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb index 1e29ff00718..9a879ce0860 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-2.7.14.eb @@ -44,6 +44,7 @@ configopts += ' '.join(local_sys_cmake) # Don't depend on MPICXX (which makes linking to ITK painful) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "export LC_ALL=C && " sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb index 0ddd6eb72da..5cf0c0a4a9d 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.0-foss-2018a-Python-3.6.4.eb @@ -44,6 +44,7 @@ configopts += ' '.join(local_sys_cmake) # Don't depend on MPICXX (which makes linking to ITK painful) configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "export LC_ALL=C && " sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb index e2252497704..faeb777f5e9 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-2.7.14.eb @@ -43,7 +43,6 @@ configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " - sanity_check_paths = { 'files': ['bin/itkTestDriver', 'lib/libITKVtkGlue-%(version_major_minor)s.a', diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb index 30809b9a4fe..db5f2054718 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018a-Python-3.6.4.eb @@ -43,7 +43,6 @@ configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " - sanity_check_paths = { 'files': ['bin/itkTestDriver', 'lib/libITKVtkGlue-%(version_major_minor)s.a', diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb index b064c81e876..6266d444fad 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-2.7.15.eb @@ -43,7 +43,6 @@ configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " - sanity_check_paths = { 'files': ['bin/itkTestDriver', 'lib/libITKVtkGlue-%(version_major_minor)s.a', diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb index 4a275d06bf5..b2247978c7f 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2018b-Python-3.6.6.eb @@ -43,7 +43,6 @@ configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " - sanity_check_paths = { 'files': ['bin/itkTestDriver', 'lib/libITKVtkGlue-%(version_major_minor)s.a', diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb index c5e843c3655..62e178a70de 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb @@ -60,7 +60,6 @@ build_shared_libs = True # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " - sanity_check_paths = { 'files': ['bin/itkTestDriver', 'lib/libITKCommon-%%(version_major)s.0.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb index 7dfe7995198..091109392a2 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb @@ -60,7 +60,6 @@ build_shared_libs = True # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " - sanity_check_paths = { 'files': ['bin/itkTestDriver', 'lib/libITKCommon-%%(version_major)s.0.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb index 4c4055172af..5ffe31bd951 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0b01-foss-2018b-Python-3.6.6.eb @@ -41,7 +41,6 @@ configopts += ' '.join(local_sys_cmake) # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " - sanity_check_paths = { 'files': ['bin/itkTestDriver', 'lib/libITKVtkGlue-%(version_major)s.0.a', diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb index ff966362678..1f129fdda19 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-foss-2020a-Python-3.8.2.eb @@ -16,7 +16,6 @@ description = """Insight Segmentation and Registration Toolkit (ITK) provides toolchain = {'name': 'foss', 'version': '2020a'} toolchainopts = {'pic': True, 'cstd': 'c++11'} - source_urls = ['https://github.com/InsightSoftwareConsortium/ITK/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_fix_wrap_vtkglue.patch'] @@ -57,7 +56,6 @@ build_shared_libs = True # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " - local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', 'ITKReview', 'ITKVTK', 'ITKVtkGlue'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb index 2452214456e..ce90113f564 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.1.2-fosscuda-2020a-Python-3.8.2.eb @@ -16,7 +16,6 @@ description = """Insight Segmentation and Registration Toolkit (ITK) provides toolchain = {'name': 'fosscuda', 'version': '2020a'} toolchainopts = {'pic': True, 'cstd': 'c++11'} - source_urls = ['https://github.com/InsightSoftwareConsortium/ITK/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_fix_wrap_vtkglue.patch'] @@ -58,7 +57,6 @@ build_shared_libs = True # See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 prebuildopts = "LC_ALL=C " - local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', 'ITKReview', 'ITKVTK', 'ITKVtkGlue'] sanity_check_paths = { From 536be9f5cc4a6fcc433291066223d427820a2629 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Aug 2021 15:03:56 +0200 Subject: [PATCH 0713/9987] adding easyconfigs: MiXCR-3.0.13-Java-11.eb --- .../m/MiXCR/MiXCR-3.0.13-Java-11.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-11.eb diff --git a/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-11.eb b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-11.eb new file mode 100644 index 00000000000..f6c889767ac --- /dev/null +++ b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-11.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'MiXCR' +version = '3.0.13' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://milaboratory.com/software/mixcr' +description = """MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires +from any type of sequencing data.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/milaboratory/mixcr/releases/download/v%(version)s/'] +sources = [SOURCELOWER_ZIP] +checksums = ['f0b32efadf6dae95819cd90cf49978e48797fc9f2685af1fd282a47d3f9fda08'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['mixcr', 'mixcr.jar'], + 'dirs': ['libraries'], +} + +sanity_check_commands = ["mixcr help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 0a3ccd3a0e3bdea3ee04a05902ceab13702dd578 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 6 Aug 2021 16:26:45 +0200 Subject: [PATCH 0714/9987] Improvements to SymEngine easyconfig --- .../easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb index 367c8509159..714a0b11fbf 100644 --- a/easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb @@ -22,11 +22,13 @@ dependencies = [ ('MPFR', '4.1.0'), ('MPC', '1.2.1'), ('LLVM', '11.1.0'), + ('FLINT', '2.7.1'), ('gperftools', '2.9.1'), ] -local_opts = '-DWITH_MPFR=yes -DWITH_MPC=yes -DWITH_LLVM=yes -DWITH_BFD=yes -DWITH_TCMALLOC=yes' -configopts = [local_opts + ' -DBUILD_SHARED_LIBS=OFF', local_opts + ' -DBUILD_SHARED_LIBS=ON'] +local_opts = '-DWITH_OPENMP=ON -DWITH_SYMENGINE_RCP=ON -DWITH_COTIRE=OFF ' +local_opts += '-DWITH_MPFR=ON -DWITH_MPC=ON -DWITH_LLVM=ON -DWITH_BFD=ON -DWITH_TCMALLOC=ON -DWITH_FLINT=ON ' +configopts = [local_opts + '-DBUILD_SHARED_LIBS=OFF', local_opts + '-DBUILD_SHARED_LIBS=ON'] runtest = 'test' From 373b002268884a15fa43b133f5f189ce57ec0b39 Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Fri, 6 Aug 2021 16:39:43 +0200 Subject: [PATCH 0715/9987] Update easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb index d89f83d545c..4953c0486fe 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb @@ -9,8 +9,7 @@ easyblock = 'ConfigureMake' name = 'ctffind' version = '4.1.14' -local_cudaversion = '11.3.1' -versionsuffix = '-CUDA-%s' % local_cudaversion +versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' description = """Program for finding CTFs of electron micrographs.""" From 5574d20f86714ba10e67c0f19338df22e20dacfe Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Fri, 6 Aug 2021 16:39:52 +0200 Subject: [PATCH 0716/9987] Update easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb index 4953c0486fe..cf2a0d71b0f 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb @@ -31,7 +31,7 @@ dependencies = [ ('LibTIFF', '4.2.0'), ('GSL', '2.7'), ('wxWidgets', '3.1.5'), - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', '11.3.1', '', True), ] configopts = '--enable-openmp ' From f17b06a9ad36a6277787d5d8f2e2da76dd72da7d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 6 Aug 2021 16:19:04 +0100 Subject: [PATCH 0717/9987] adding easyconfigs: CREST-2.11-intel-2021a.eb and patches: CREST-2.11_fix-install-targets.patch --- .../c/CREST/CREST-2.11-intel-2021a.eb | 36 +++++ .../CREST-2.11_fix-install-targets.patch | 143 ++++++++++++++++++ 2 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/c/CREST/CREST-2.11-intel-2021a.eb create mode 100644 easybuild/easyconfigs/c/CREST/CREST-2.11_fix-install-targets.patch diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.11-intel-2021a.eb b/easybuild/easyconfigs/c/CREST/CREST-2.11-intel-2021a.eb new file mode 100644 index 00000000000..26beb63a046 --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.11-intel-2021a.eb @@ -0,0 +1,36 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'CMakeMake' + +name = 'CREST' +version = '2.11' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-2.11_fix-install-targets.patch'] +checksums = [ + 'e6d9154b6e22a88709203945fa24f1ecccb5d5a5906111c225ad5749125252f4', # v2.11.tar.gz + 'ce397bf4ab607b6b711018cacb32033d7916f59fa419d6dc67f286f8a0ea045a', # CREST-2.11_fix-install-targets.patch +] + +builddependencies = [('CMake', '3.20.1')] + +sanity_check_paths = { + 'files': ['bin/%s' % name.lower()], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.11_fix-install-targets.patch b/easybuild/easyconfigs/c/CREST/CREST-2.11_fix-install-targets.patch new file mode 100644 index 00000000000..69f3d7b648d --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.11_fix-install-targets.patch @@ -0,0 +1,143 @@ +From d55d6715893ad950cda29a2c7272b15e6ce76bc3 Mon Sep 17 00:00:00 2001 +From: Sebastian Ehlert <28669218+awvwgk@users.noreply.github.com> +Date: Mon, 1 Feb 2021 18:55:07 +0100 +Subject: [PATCH] Add testing with Intel oneAPI (#29) + +- builds crest with Intel oneAPI classic compilers using meson +- installs xtb from selected release in testing environment +- runs example 0 to check for basic functionality +--- + .github/workflows/build.yml | 86 +++++++++++++++++++++++++++++++++++++ + CMakeLists.txt | 10 ++--- + meson.build | 10 ++--- + 3 files changed, 96 insertions(+), 10 deletions(-) + create mode 100644 .github/workflows/build.yml + +diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml +new file mode 100644 +index 0000000..a6564dc +--- /dev/null ++++ b/.github/workflows/build.yml +@@ -0,0 +1,86 @@ ++name: CI ++on: [push, pull_request] ++ ++env: ++ BUILD_DIR: _build ++ XTB_VERSION: 6.4.0 ++ ++jobs: ++ intel-meson-build: ++ runs-on: ${{ matrix.os }} ++ strategy: ++ fail-fast: false ++ matrix: ++ os: [ubuntu-20.04] ++ fc: [ifort] ++ cc: [icc] ++ env: ++ FC: ${{ matrix.fc }} ++ CC: ${{ matrix.cc }} ++ APT_PACKAGES: >- ++ intel-oneapi-compiler-fortran ++ intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic ++ intel-oneapi-mkl ++ intel-oneapi-mkl-devel ++ ++ steps: ++ - name: Checkout code ++ uses: actions/checkout@v2 ++ ++ - name: Setup Python ++ uses: actions/setup-python@v1 ++ with: ++ python-version: 3.x ++ ++ - name: Add Intel repository ++ if: contains(matrix.os, 'ubuntu') ++ run: | ++ wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB ++ sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB ++ rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB ++ echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list ++ sudo apt-get update ++ ++ - name: Install Intel oneAPI compiler ++ if: contains(matrix.os, 'ubuntu') ++ run: | ++ sudo apt-get install ${{ env.APT_PACKAGES }} ++ source /opt/intel/oneapi/setvars.sh ++ printenv >> $GITHUB_ENV ++ ++ - name: Install meson ++ run: pip3 install meson==0.55.3 ninja ++ ++ - name: Configure meson build ++ run: meson setup ${{ env.BUILD_DIR }} --prefix=/ -Dfortran_args=-qopenmp ++ ++ - name: Build project ++ run: ninja -C ${{ env.BUILD_DIR }} ++ ++ - name: Install package ++ run: | ++ meson install -C ${{ env.BUILD_DIR }} --no-rebuild ++ env: ++ DESTDIR: ${{ env.PWD }}/_dist ++ ++ - name: Add crest to path ++ run: | ++ echo ${{ env.PWD }}/_dist/bin >> $GITHUB_PATH ++ ++ - name: Download xtb ++ uses: i3h/download-release-asset@v1 ++ with: ++ owner: grimme-lab ++ repo: xtb ++ tag: v${{ env.XTB_VERSION }} ++ file: '/xtb-\d+\.tar\.xz/' ++ ++ - name: Add xtb to path ++ run: | ++ tar xvf xtb-*.tar.xz ++ echo ${{ env.PWD }}/xtb-${{ env.XTB_VERSION }}/bin >> $GITHUB_PATH ++ ++ - name: Run example 0 ++ run: | ++ bash run.sh ++ working-directory: examples/expl-0 +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 0a4b9b1..82f57fd 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -74,8 +74,8 @@ install( + ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}" + ) + +-install( +- PROGRAMS +- "${CMAKE_CURRENT_SOURCE_DIR}/combi-scripts/crest_combi" +- DESTINATION "${CMAKE_INSTALL_BINDIR}" +-) ++# install( ++# PROGRAMS ++# "${CMAKE_CURRENT_SOURCE_DIR}/combi-scripts/crest_combi" ++# DESTINATION "${CMAKE_INSTALL_BINDIR}" ++# ) +diff --git a/meson.build b/meson.build +index 4c83b7d..c9dbc12 100644 +--- a/meson.build ++++ b/meson.build +@@ -41,8 +41,8 @@ crest_exe = executable( + link_language: 'fortran', + ) + +-install_data( +- files('combi-scripts/crest_combi'), +- install_dir: get_option('bindir'), +- install_mode: 'rwxr--r--', +-) ++# install_data( ++# files('combi-scripts/crest_combi'), ++# install_dir: get_option('bindir'), ++# install_mode: 'rwxr--r--', ++# ) From 4f1bb83d5c83d23891cbedcd1ffe498cbd548b56 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 6 Aug 2021 16:22:10 +0100 Subject: [PATCH 0718/9987] adding easyconfigs: xTB-6.4.1-intel-2021a.eb --- .../x/xTB/xTB-6.4.1-intel-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb diff --git a/easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb b/easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb new file mode 100644 index 00000000000..5a512b5638f --- /dev/null +++ b/easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb @@ -0,0 +1,40 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MesonNinja' + +name = 'xTB' +version = '6.4.1' + +homepage = 'https://xtb-docs.readthedocs.io' +description = "Semiempirical Extended Tight-Binding Program Package." + +toolchain = {'name': 'intel', 'version': '2021a'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +configopts = "-Dla_backend='mkl-rt' --buildtype release " + +runtest = 'meson' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' + +sanity_check_paths = { + 'files': ['bin/xtb', 'include/xtb/xtb.h'] + ['lib/libxtb.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = ["xtb --help"] + +modextrapaths = { + 'XTBHOME': '', + 'XTBPATH': '', +} + +moduleclass = 'chem' From 8e651068d55af3b0c2458c1710c8580e585e6d2a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 6 Aug 2021 16:24:04 +0100 Subject: [PATCH 0719/9987] adding easyconfigs: QCxMS-5.0.3.eb --- easybuild/easyconfigs/q/QCxMS/QCxMS-5.0.3.eb | 30 ++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/q/QCxMS/QCxMS-5.0.3.eb diff --git a/easybuild/easyconfigs/q/QCxMS/QCxMS-5.0.3.eb b/easybuild/easyconfigs/q/QCxMS/QCxMS-5.0.3.eb new file mode 100644 index 00000000000..34a912daa3d --- /dev/null +++ b/easybuild/easyconfigs/q/QCxMS/QCxMS-5.0.3.eb @@ -0,0 +1,30 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'Tarball' + +name = 'QCxMS' +version = '5.0.3' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html' +description = """QCxMS is a quantum chemical based program to calculate electron ionization (EI) + and collision induced dissociation (CID) mass spectra using Born-Oppenheimer Molecular Dynamics + (BO-MD). It is the successor of the QCEIMS program, in which the EI part is exchanged to x to + account for the greater general applicibility of the program. +""" + +toolchain = SYSTEM + +# current release does not include source code +source_urls = ['https://github.com/qcxms/QCxMS/releases/download/v.5.0.3'] +sources = ['%(name)s.v%(version)s.tar.xz'] +checksums = ['9afffbc9f16d860bea939d9d569a91067f6c4292b89d3603e4d08f53ae23b954'] + +local_bins = ['pqcxms', 'qcxms', 'q-batch', 'getres'] # 5.0.3 doesn't include 'plotms' +preinstall_cmd = "mkdir bin && mv %s bin" % " ".join(local_bins) + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +moduleclass = 'chem' From cf6d6584c658a76b5a2bbea35e6f3b7d180f9c7d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 6 Aug 2021 17:42:21 +0200 Subject: [PATCH 0720/9987] missing exts --- .../openstackclient-5.5.0-GCCcore-10.2.0.eb | 52 +++++++++++++++++-- 1 file changed, 49 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb index 0aa753259f6..441ba8a8bc7 100644 --- a/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb @@ -23,6 +23,52 @@ exts_list = [ ('pbr', '5.6.0', { 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('cmd2', '2.1.2', { + 'checksums': ['25dbb2e9847aaa686a8a21e84e3d101db8b79f5cb992e044fc54210ab8c0ad41'], + }), + ('charset-normalizer', '2.0.4', { + 'checksums': ['f23667ebe1084be45f6ae0538e4a5a865206544097e4e8bbcacf42cd02a348f3'], + }), + ('jsonpointer', '2.1', { + 'checksums': ['5a34b698db1eb79ceac454159d3f7c12a451a91f6334a4f638454327b7a89962'], + }), + ('cliff', '3.8.0', { + 'checksums': ['8dd215d0a84c9a3ab2fa2aa700849f4e7b786639f66caa0ad4108c85dca95a7c'], + }), + ('openstacksdk', '0.58.0', { + 'modulename': 'openstack', + 'checksums': ['d8368d1728f686114213d22cc8e3eef71629fae1424b2ad2c5d22a7b9a04a278'], + }), + ('stevedore', '3.3.0', { + 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], + }), + ('dogpile.cache', '1.1.3', { + 'checksums': ['6f0bcf97c73bfec1a7bf14e5a248488cee00c2d494bf63f3789ea6d95a57c1cf'], + }), + ('prettytable', '0.7.2', { + 'checksums': ['2d5460dc9db74a32bcc8f9f67de68b2c4f4d2f01fa3bd518764c69156d9cacd9'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + ('jsonpatch', '1.32', { + 'checksums': ['b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + ('os-service-types', '1.7.0', { + 'checksums': ['31800299a82239363995b91f1ebf9106ac7758542a1e4ef6dc737a5932878c6c'], + }), + ('requestsexceptions', '1.4.0', { + 'checksums': ['b095cbc77618f066d459a02b137b020c37da9f46d9b057704019c9f77dba3065'], + }), + ('requests', '2.26.0', { + 'checksums': ['b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7'], + }), ('osc-lib', '2.4.1', { 'checksums': ['257ef0cda902664605a850a858172306acb2b08b0e7e32d7a5b4f12dc6bc56c5'], }), @@ -54,9 +100,8 @@ exts_list = [ ('wrapt', '1.12.1', { 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], }), - ('iso-8601', '0.3.1', { - 'modulename': 'iso8601', - 'checksums': ['afc2bca0f002f817c2e597312dcaa0280306845d85939b4219f069319d075405'], + ('iso8601', '0.1.16', { + 'checksums': ['36532f77cc800594e8f16641edae7f1baf7932f05d8e508545b95fc53c6dc85b'], }), ('python-novaclient', '17.5.0', { 'modulename': 'novaclient', @@ -75,6 +120,7 @@ exts_list = [ 'checksums': ['8d40491374172f9375ce1642ac2230b1cbb5a564320edbcc2a9ebe857fd9a880'], }), ] + sanity_pip_check = True enhance_sanity_check = True sanity_check_commands = ['openstack -h'] From b5ebd5125b11fc8b87254cf28e0485d15ccb7479 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 6 Aug 2021 19:49:56 +0200 Subject: [PATCH 0721/9987] using snippys prebuilt snpEff binary --- easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb index b27c7c54550..5f23968bf19 100644 --- a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb @@ -23,17 +23,15 @@ dependencies = [ ('minimap2', '2.18'), ('vcflib', '1.0.2'), ('vt', '0.57721'), - ('snpEff', '5.0', '-Java-13', True), ('samclip', '0.4.0'), ('seqtk', '1.3'), ('snp-sites', '2.5.1'), ('any2fasta', '0.4.2'), ('wgsim', '20111017'), - ('freebayes', '1.3.5'), # todo freebayes-parallel + ('freebayes', '1.3.5') ] -# remove included binaries for required dependencies -postinstallcmds = ["rm -r %(installdir)s/binaries"] +modextrapaths = {'PATH': 'binaries/noarch'} sanity_check_paths = { 'files': ['bin/snippy', 'perl5/Snippy/Version.pm'], From 536451dc683cb9ca5dfa14850b46aca28c02d416 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Aug 2021 23:12:13 +0200 Subject: [PATCH 0722/9987] update checksum of wgsim v20111017 --- easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb index f7361ba8bbc..fc3409253c1 100644 --- a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb @@ -16,7 +16,7 @@ patches = [ ('wgsim-%(version)s_add_makefile.patch', 1) ] checksums = [ - 'e1e6bff5c084e4494023505206ae3e0b0f5a315c9f7390b2f347c370c7f36533', # wgsim-20111017.tar.gz + '1180fdd1d66691da5634e8c98b78c4742d0faf10042f35c2d17d26844d550f1c', # wgsim-20111017.tar.gz '81b61c6cceaa4a05e9ee12976dede0df1639f9504ded11e7099cbd1f932c6c9d', # wgsim-20111017_add_makefile.patch ] From 74fa096adbdf29e6f5d847ff37efc7c62bedae2d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Aug 2021 23:26:29 +0200 Subject: [PATCH 0723/9987] use CmdCp easyblock for wgsim v20111017 --- .../w/wgsim/wgsim-20111017-GCC-10.2.0.eb | 26 ++++++++----------- .../w/wgsim/wgsim-20111017_add_makefile.patch | 9 ------- 2 files changed, 11 insertions(+), 24 deletions(-) delete mode 100644 easybuild/easyconfigs/w/wgsim/wgsim-20111017_add_makefile.patch diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb index fc3409253c1..718a1bb0cb5 100644 --- a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb @@ -1,36 +1,32 @@ -easyblock = 'MakeCp' +easyblock = 'CmdCp' name = 'wgsim' version = '20111017' local_commit = 'a12da3375ff3b51a5594d4b6fa35591173ecc229' homepage = 'https://github.com/lh3/wgsim/' -description = """Wgsim is a small tool for simulating sequence reads from a reference genome.""" +description = "Wgsim is a small tool for simulating sequence reads from a reference genome." toolchain = {'name': 'GCC', 'version': '10.2.0'} github_account = 'lh3' source_urls = [GITHUB_SOURCE] -sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = [ - ('wgsim-%(version)s_add_makefile.patch', 1) -] -checksums = [ - '1180fdd1d66691da5634e8c98b78c4742d0faf10042f35c2d17d26844d550f1c', # wgsim-20111017.tar.gz - '81b61c6cceaa4a05e9ee12976dede0df1639f9504ded11e7099cbd1f932c6c9d', # wgsim-20111017_add_makefile.patch -] - -dependencies = [('zlib', '1.2.11')] +sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_ZIP}] +checksums = ['1180fdd1d66691da5634e8c98b78c4742d0faf10042f35c2d17d26844d550f1c'] -buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' +dependencies = [ + ('zlib', '1.2.11'), +] -files_to_copy = [(["wgsim"], 'bin')] +cmds_map = [('.*', "$CC $CFLAGS -o %(name)s %(name)s.c $LDFLAGS -lz -lm")] -sanity_check_commands = [("%(name)s -h 2>&1 | grep 'Program: wgsim (short read simulator)'")] +files_to_copy = [(['wgsim'], 'bin')] sanity_check_paths = { 'files': ['bin/wgsim'], 'dirs': [], } +sanity_check_commands = ["wgsim -h 2>&1 | grep 'Program: wgsim (short read simulator)'"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017_add_makefile.patch b/easybuild/easyconfigs/w/wgsim/wgsim-20111017_add_makefile.patch deleted file mode 100644 index 635f3c569ea..00000000000 --- a/easybuild/easyconfigs/w/wgsim/wgsim-20111017_add_makefile.patch +++ /dev/null @@ -1,9 +0,0 @@ -diff -ruN wgsim-master_orig/Makefile wgsim-master/Makefile ---- wgsim-master_orig/Makefile 1970-01-01 01:00:00.000000000 +0100 -+++ wgsim-master/Makefile 2021-07-16 11:35:20.997347480 +0200 -@@ -0,0 +1,5 @@ -+CC=gcc -+CFLAGS=-g -O2 -Wall -+ -+install: -+ $(CC) $(CFLAGS) -o wgsim -lz -lm wgsim.c From 59f8fc2ebec4f3ebcbf4fd2115ae30b4bcceebe2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Aug 2021 23:28:03 +0200 Subject: [PATCH 0724/9987] add wgsim_eval.pl to installation of wgsim --- easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb index 718a1bb0cb5..4fc09775ac6 100644 --- a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-10.2.0.eb @@ -16,14 +16,15 @@ checksums = ['1180fdd1d66691da5634e8c98b78c4742d0faf10042f35c2d17d26844d550f1c'] dependencies = [ ('zlib', '1.2.11'), + ('Perl', '5.32.0'), ] cmds_map = [('.*', "$CC $CFLAGS -o %(name)s %(name)s.c $LDFLAGS -lz -lm")] -files_to_copy = [(['wgsim'], 'bin')] +files_to_copy = [(['wgsim', 'wgsim_eval.pl'], 'bin')] sanity_check_paths = { - 'files': ['bin/wgsim'], + 'files': ['bin/wgsim', 'bin/wgsim_eval.pl'], 'dirs': [], } From ff6cf25f1a8187b976a076a4e7e963fd19356d4e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Aug 2021 23:29:33 +0200 Subject: [PATCH 0725/9987] restore original attribution in any2fasta v0.4.2 --- .../easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb index 1ba03ee6136..52f84450815 100644 --- a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.2.0.eb @@ -1,4 +1,5 @@ -# Author: Denis Kristak (INUITS) +# Author: Pavel Grochal (INUITS) +# Updated by: Denis Kristak (INUITS) # License: GPLv2 easyblock = 'Tarball' From 23dad1152a20b1ce3fe65472df4b48fdd266135f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 6 Aug 2021 23:55:35 +0200 Subject: [PATCH 0726/9987] add dependency on snpEff v5.0e to snippy v4.6.0 --- .../s/snippy/snippy-4.6.0-GCC-10.2.0.eb | 5 ++- .../snpEff-5.0e-GCCcore-10.2.0-Java-13.eb | 35 +++++++++++++++++++ 2 files changed, 37 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb diff --git a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb index 5f23968bf19..ac4d831cb43 100644 --- a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-10.2.0.eb @@ -26,16 +26,15 @@ dependencies = [ ('samclip', '0.4.0'), ('seqtk', '1.3'), ('snp-sites', '2.5.1'), + ('snpEff', '5.0e', '-Java-13'), ('any2fasta', '0.4.2'), ('wgsim', '20111017'), ('freebayes', '1.3.5') ] -modextrapaths = {'PATH': 'binaries/noarch'} - sanity_check_paths = { 'files': ['bin/snippy', 'perl5/Snippy/Version.pm'], - 'dirs': ['etc'], + 'dirs': ['etc', 'test'], } sanity_check_commands = [ diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb new file mode 100644 index 00000000000..cfde903143c --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.0e' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d'] + +dependencies = [ + ('Java', '13', '', True), + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From 47372ae619dbd1e680312932de226aa0d0abf7ac Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 7 Aug 2021 12:42:41 +0200 Subject: [PATCH 0727/9987] Filter out HDF5 with -serial versionsuffix --- test/easyconfigs/easyconfigs.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4d07a767be5..f66b8d23d89 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -247,6 +247,12 @@ def check_dep_vars(self, gen, dep, dep_vars): if len(bl_vsuff_vars) == 1: dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bl_vsuff_vars[0]) + # filter out HDF5 with -serial versionsuffix which is used in HDF5 for Python (h5py) + if dep in ['HDF5']: + serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] + if len(serial_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) + # for some dependencies, we allow exceptions for software that depends on a particular version, # as long as that's indicated by the versionsuffix if dep in ['ASE', 'Boost', 'Java', 'Lua', 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] and len(dep_vars) > 1: From 63a01980904c3596012c33242f56e989a2a161a7 Mon Sep 17 00:00:00 2001 From: Sassy Date: Sat, 7 Aug 2021 11:46:05 +0000 Subject: [PATCH 0728/9987] gofasta v0.0.5 created --- .../easyconfigs/g/gofasta/gofasta-0.0.5.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb diff --git a/easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb b/easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb new file mode 100644 index 00000000000..51bd3dea3e2 --- /dev/null +++ b/easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb @@ -0,0 +1,26 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'GoPackage' + +name = 'gofasta' +version = '0.0.5' + +homepage = 'https://github.com/cov-ert/gofasta' +description = """Some functions for dealing with alignments, +developed to handle SARS-CoV-2 data as part of the COG-UK project.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cov-ert/gofasta/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2d66f1bfd68cc673b4991634eedda14faf5f8c3e6ca578b18d68b3763a45606b'] + +builddependencies = [ + ('Go', '1.16.5'), +] + +# options = {'modulename': 'absl'} + +moduleclass = 'bio' From 5eccdc16d82564bcb30be9a396f75721fa9879ec Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Sat, 7 Aug 2021 14:30:29 +0100 Subject: [PATCH 0729/9987] Add checksum --- easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb b/easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb index 5a512b5638f..cf9d7725cde 100644 --- a/easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb +++ b/easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'intel', 'version': '2021a'} github_account = 'grimme-lab' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] +checksums = ['cd7b6ec9b7963012ce71220a70773641f0d9e06e0691750a25b83e823510d1d7'] builddependencies = [ ('Meson', '0.58.0'), From e28c90a4277766a1c337d2410b11906bba542b1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 7 Aug 2021 19:04:04 +0200 Subject: [PATCH 0730/9987] adding easyconfigs: SymEngine-python-0.7.2-GCC-10.3.0.eb --- .../SymEngine-python-0.7.2-GCC-10.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..363edbd9592 --- /dev/null +++ b/easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'SymEngine-python' +version = '0.7.2' + +homepage = 'https://github.com/symengine/symengine.py' +description = "Python wrappers to the C++ library SymEngine, a fast C++ symbolic manipulation library." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/symengine/symengine.py/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('SymEngine', '0.7.0'), + ('Python', '3.9.5'), +] + +options = {'modulename': 'symengine'} + +moduleclass = 'lib' From 5e82d47191508810c38fce04ffd8bd775e3e6d80 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 7 Aug 2021 19:37:37 +0200 Subject: [PATCH 0731/9987] adding easyconfigs: FORD-6.1.1-GCCcore-10.2.0.eb --- .../f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..f51c81c9289 --- /dev/null +++ b/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'FORD' +version = '6.1.1' + +homepage = 'https://github.com/Fortran-FOSS-Programmers/ford/wiki' +description = 'FORD is an automatic documentation generator for modern Fortran programs' + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Graphviz', '2.47.0', '-Java-11'), + ('BeautifulSoup', '4.9.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('graphviz', '0.17', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['ef6e2c5deb9cdcc0c7eece1d89625fd07b0f2208ea2bcb483520907ddf8b4e12'], + }), + ('MarkupSafe', '2.0.1', { + 'checksums': ['594c67807fb16238b30c44bdf74f36c02cdf22d1c8cda91ef8a0ed8dabf5620a'], + }), + ('Jinja2', '3.0.1', { + 'checksums': ['703f484b47a6af502e743c9122595cc812b0271f661722403114f71a79d0f5a4'], + }), + ('Pygments', '2.9.0', { + 'checksums': ['a18f47b506a429f6f4b9df81bb02beab9ca21d0a5fee38ed15aef65f0545519f'], + }), + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('markdown-include', '0.6.0', { + 'checksums': ['6f5d680e36f7780c7f0f61dca53ca581bd50d1b56137ddcd6353efafa0c3e4a2'], + }), + ('md-environ', '0.1.0', { + 'checksums': ['fe3c2a255af523d6f522831c699336cd71f9d543714067d93206ed35836f1793'], + }), + ('toposort', '1.6', { + 'checksums': ['a7428f56ef844f5055bb9e9e44b343983773ae6dce0fe5b101e08e27ffbd50ac'], + }), + ('tqdm', '4.62.0', { + 'checksums': ['3642d483b558eec80d3c831e23953582c34d7e4540db86d9e5ed9dad238dabc6'], + }), + (name, version, { + 'checksums': ['6c107316ecee48f174316f0deffa9e6407dabca414845b9fa66f4313341da9ac'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ford'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' From ac40897383d01bff96b0e846c39244076c1b970e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 7 Aug 2021 19:46:19 +0200 Subject: [PATCH 0732/9987] Tidy up EB file for coverage v5.5 for GCCcore/10.2.0 --- easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb index b619a1c1c2c..441df135abb 100644 --- a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb @@ -10,7 +10,6 @@ description = """ Coverage.py is a tool for measuring code coverage of Python pr toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['ebe78fe9a0e874362175b02371bdfbee64d8edc42a044253ddf4ee7d3c15212c'] @@ -23,6 +22,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], From 66eb400488d06944f6e999414a96259662349b32 Mon Sep 17 00:00:00 2001 From: Sassy Date: Sat, 7 Aug 2021 20:31:23 +0000 Subject: [PATCH 0733/9987] Surpluse modulename removed --- easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb b/easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb index 51bd3dea3e2..9a431e5392a 100644 --- a/easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb +++ b/easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb @@ -21,6 +21,4 @@ builddependencies = [ ('Go', '1.16.5'), ] -# options = {'modulename': 'absl'} - moduleclass = 'bio' From 5523207fe0d97df3b227c713e7bdcb3309cd807a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 7 Aug 2021 22:35:35 +0200 Subject: [PATCH 0734/9987] adding easyconfigs: Meson-0.58.2-GCCcore-11.2.0.eb, Ninja-1.10.2-GCCcore-11.2.0.eb --- .../m/Meson/Meson-0.58.2-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ .../n/Ninja/Ninja-1.10.2-GCCcore-11.2.0.eb | 31 +++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.58.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.58.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-0.58.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7557cb24d0a --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.58.2-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.58.2' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7634ec32955d3f897d623b88e9d2988451035f43d73c17a29caf767387baedb7'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Ninja', '1.10.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d8bb11e06ba --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.10.2' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ce35865411f0490368a8fc383f29071de6690cbadc27704734978221f25e2bed'] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +sanity_check_commands = ["ninja --version"] + +moduleclass = 'tools' From 8bfed531c5aa9bcbd595f0ad67a3182ba5cd511f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 7 Aug 2021 23:23:16 +0200 Subject: [PATCH 0735/9987] adding easyconfigs: gettext-0.21-GCCcore-11.2.0.eb, intltool-0.51.0-GCCcore-11.2.0.eb, X11-20210802-GCCcore-11.2.0.eb --- .../g/gettext/gettext-0.21-GCCcore-11.2.0.eb | 32 +++ .../intltool-0.51.0-GCCcore-11.2.0.eb | 35 +++ .../x/X11/X11-20210802-GCCcore-11.2.0.eb | 210 ++++++++++++++++++ 3 files changed, 277 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7d329d1be72 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c77d0da3102aec9c07f43671e60611ebff89a996ef159497ce8e59d075786b12'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2d693a38180 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Perl', '5.34.0'), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +sanity_check_commands = ["intltool-merge --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..259c0017c55 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb @@ -0,0 +1,210 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20210802' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('Bison', '3.7.6'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('intltool', '0.51.0'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.13.94'), + ('freetype', '2.11.0'), + ('zlib', '1.2.11'), + ('xorg-macros', '1.19.3'), + ('libpciaccess', '0.16'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libpthread-stubs', '0.4', { # 2017-03-14 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('xorgproto', '2021.4.99.2', { # 2021-05-30 + 'checksums': ['179531d0a797eb464076bd8a1a698ea9c1cba4e67fcac65cc73758dd2712d892'], + }), + ('libXau', '1.0.9', { # 2019-02-10 + 'checksums': ['1f123d8304b082ad63a9e89376400a3b1d4c29e67e3ea07b3f659cccca690eea'], + }), + ('libXdmcp', '1.1.3', { # 2019-03-16 + 'checksums': ['2ef9653d32e09d1bf1b837d0e0311024979653fe755ad3aaada8db1aa6ea180c'], + }), + ('xcb-proto', '1.14.1', { # 2020-10-08 + 'checksums': ['85cd21e9d9fbc341d0dbf11eace98d55d7db89fda724b0e598855fcddf0944fd'], + }), + ('libxcb', '1.14', { # 2020-02-22 + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2c7fcddd1da34d9b238c9caeda20d3bd7486456fc50b3cc6567185dbd5b0ad02'], + }), + ('xtrans', '1.4.0', { # 2019-03-16 + 'checksums': ['48ed850ce772fef1b44ca23639b0a57e38884045ed2cbb18ab137ef33ec713f9'], + }), + ('libxkbcommon', '1.3.0', { # 2021-05-01 + 'easyblock': 'MesonNinja', + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'checksums': ['7b09e098ea69bc3054f0c57a9a25fda571c4df22398811606e32b5fffeb75e7b'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.7.2', { # 2021-06-06 + 'checksums': ['2c26ccd08f43a6214de89110554fbe97c71692eeb7e7d4829f3004ae6fafd2c0'], + }), + ('libXext', '1.3.4', { # 2019-03-16 + 'checksums': ['8ef0789f282826661ff40a8eef22430378516ac580167da35cc948be9041aac1'], + }), + ('libFS', '1.0.8', { # 2019-03-10 + 'checksums': ['e3da723257f4f4c0c629aec402e0a36fbec66a9418f70d24a159cb0470ec83d2'], + }), + ('libICE', '1.0.10', { # 2019-07-14 + 'checksums': ['1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d'], + }), + ('libSM', '1.2.3', { # 2018-10-10 + 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], + }), + ('libXScrnSaver', '1.2.3', { # 2018-07-05 + 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], + }), + ('libXt', '1.2.1', { # 2021-01-24 + 'checksums': ['6da1bfa9dd0ed87430a5ce95b129485086394df308998ebe34d98e378e3dfb33'], + }), + ('libXmu', '1.1.3', { # 2019-03-16 + 'checksums': ['5bd9d4ed1ceaac9ea023d86bf1c1632cd3b172dce4a193a72a94e1d9df87a62e'], + }), + ('libXpm', '3.5.13', { # 2019-12-13 + 'checksums': ['e3dfb0fb8c1f127432f2a498c7856b37ce78a61e8da73f1aab165a73dd97ad00'], + }), + ('libXaw', '1.0.14', { # 2021-03-27 + 'checksums': ['59cfed2712cc80bbfe62dd1aacf24f58d74a76dd08329a922077b134a8d8048f'], + }), + ('libXfixes', '6.0.0', { # 2021-05-11 + 'checksums': ['82045da5625350838390c9440598b90d69c882c324ca92f73af9f0e992cb57c7'], + }), + ('libXcomposite', '0.4.5', { # 2019-03-11 + 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], + }), + ('libXrender', '0.9.10', { # 2016-10-04 + 'checksums': ['770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf'], + }), + ('libXcursor', '1.2.0', { # 2019-03-11 + 'checksums': ['ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8'], + }), + ('libXdamage', '1.1.5', { # 2019-03-11 + 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], + }), + ('libfontenc', '1.1.4', { # 2019-02-20 + 'checksums': ['895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.5', { # 2021-08-02 + 'checksums': ['d7544aa35ea67a87840ff0b1bd15130b102e473de3611b7d78604ba635fd6d94'], + }), + ('libXft', '2.3.4', { # 2021-08-02 + 'checksums': ['1eca71bec9cb483165ce1ab94f5cd3036269f5268651df6a2d99c4a7ab644d79'], + }), + ('libXi', '1.7.99.2', { # 2021-06-01 + 'checksums': ['991d212bb9583b1dbe429e2c8fc510fcab3c820b3d7fba07e1e8b9fefcf9ac76'], + }), + ('libXinerama', '1.1.4', { # 2018-07-05 + 'checksums': ['64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18'], + }), + ('libXrandr', '1.5.2', { # 2019-03-16 + 'checksums': ['3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e'], + }), + ('libXres', '1.2.1', { # 2021-03-31 + 'checksums': ['918fb33c3897b389a1fbb51571c5c04c6b297058df286d8b48faa5af85e88bcc'], + }), + ('libXtst', '1.2.3', { # 2016-10-04 + 'checksums': ['a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2'], + }), + ('libXv', '1.0.11', { # 2016-10-04 + 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], + }), + ('libXvMC', '1.0.12', { # 2019-09-24 + 'checksums': ['024c9ec4f001f037eeca501ee724c7e51cf287eb69ced8c6126e16e7fa9864b5'], + }), + ('libXxf86dga', '1.1.5', { # 2019-03-16 + 'checksums': ['715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69'], + }), + ('libXxf86vm', '1.1.4', { # 2015-02-24 + 'checksums': ['5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99'], + }), + ('libdmx', '1.1.4', { # 2018-05-14 + 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], + }), + ('libxkbfile', '1.1.0', { # 2019-03-16 + 'checksums': ['2a92adda3992aa7cbad758ef0b8dfeaedebb49338b772c64ddf369d78c1c51d3'], + }), + ('libxshmfence', '1.3', { # 2018-02-26 + 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], + }), + ('xcb-util', '0.4.0', { # 2014-10-15 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.0', { # 2014-10-15 + 'checksums': ['cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42'], + }), + ('xcb-util-keysyms', '0.4.0', { # 2014-10-01 + 'checksums': ['0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96'], + }), + ('xcb-util-renderutil', '0.3.9', { # 2014-06-13 + 'checksums': ['55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5'], + }), + ('xcb-util-wm', '0.4.1', { # 2014-02-19 + 'checksums': ['038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334'], + }), + ('xcb-util-cursor', '0.1.3', { # 2016-05-12 + 'checksums': ['a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8'], + }), + ('xkeyboard-config', '2.33', { # 2021-06-08 + 'checksums': ['112df68e1150e8da421bc0abe79eebeacca16a91e54e1877cb39fc878d17b365'], + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.3', { # 2015-02-21 + 'checksums': ['f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c'], + }), + ('xbitmaps', '1.1.2', { # 2018-03-10 + 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' From 465b765f3d7ee699fa5a7f498049bd542c86f8f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 8 Aug 2021 00:10:01 +0200 Subject: [PATCH 0736/9987] Checksum --- .../s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb index 363edbd9592..4f02d6c4d5f 100644 --- a/easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://github.com/symengine/symengine.py/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] +checksums = ['2147e4bc6b616482dc86f332c7009a6a39de0b66c8f4acebc9ad10b5415b4e53'] builddependencies = [ ('CMake', '3.20.1'), From 09ee2b9ea2a2e4dd180a2bf5d4f895a94b371982 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 8 Aug 2021 00:24:34 +0200 Subject: [PATCH 0737/9987] Add psm3 version patch --- .../l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb | 2 ++ .../l/libfabric/libfabric-1.13.0_psm3-version.patch | 6 ++++++ 2 files changed, 8 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.13.0_psm3-version.patch diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb index 9fa99b0363d..ac417b1a711 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb @@ -19,10 +19,12 @@ github_account = 'ofiwg' source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] sources = [SOURCE_TAR_BZ2] patches = [ + '%(name)s-%(version)s_psm3-version.patch', '%(name)s-1.12.1_disable-psm3-avx-config.patch', ] checksums = [ '0c68264ae18de5c31857724c754023351614330bd61a50b40cef2b5e8f63ab28', # libfabric-1.13.0.tar.bz2 + 'f357a60f9cfd054469fef46f560531aa53ded3b7708c313b73d9bfdcb89bf24d', # libfabric-1.13.0_psm3-version.patch # libfabric-1.12.1_disable-psm3-avx-config.patch '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', ] diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0_psm3-version.patch b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0_psm3-version.patch new file mode 100644 index 00000000000..ac17f51a610 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0_psm3-version.patch @@ -0,0 +1,6 @@ +Add version file which if missing breaks when rebuilding the configure script. +Author: micketeer@gmail.com per request of Simon Branford +--- prov/psm3/VERSION.orig 1970-01-01 01:00:00.000000000 +0100 ++++ prov/psm3/VERSION 2021-08-08 00:19:07.634693856 +0200 +@@ -0,0 +1 @@ ++3_1_0_0 From 4ca4f0f8320f138daccac2f43012e4433b42c76b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 8 Aug 2021 00:43:29 +0200 Subject: [PATCH 0738/9987] Fix patchlevel --- .../l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb index ac417b1a711..a161943044c 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb @@ -19,15 +19,9 @@ github_account = 'ofiwg' source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] sources = [SOURCE_TAR_BZ2] patches = [ - '%(name)s-%(version)s_psm3-version.patch', + ('%(name)s-%(version)s_psm3-version.patch', 0), '%(name)s-1.12.1_disable-psm3-avx-config.patch', ] -checksums = [ - '0c68264ae18de5c31857724c754023351614330bd61a50b40cef2b5e8f63ab28', # libfabric-1.13.0.tar.bz2 - 'f357a60f9cfd054469fef46f560531aa53ded3b7708c313b73d9bfdcb89bf24d', # libfabric-1.13.0_psm3-version.patch - # libfabric-1.12.1_disable-psm3-avx-config.patch - '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', -] builddependencies = [ ('binutils', '2.37'), From 186fc4c135b649382a8c74e29a73cff464fbe9d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 8 Aug 2021 00:54:06 +0200 Subject: [PATCH 0739/9987] Add all the required pythonpackage stuff that I still don't understand why it isn't the default --- .../s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb index 4f02d6c4d5f..8b401bfe906 100644 --- a/easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/SymEngine-python/SymEngine-python-0.7.2-GCC-10.3.0.eb @@ -21,6 +21,10 @@ dependencies = [ ('Python', '3.9.5'), ] +use_pip = True +download_dep_fail = True +sanity_pip_check = True + options = {'modulename': 'symengine'} moduleclass = 'lib' From 62e5a8f7806d4048c2f1b5dd3721a984c460d48c Mon Sep 17 00:00:00 2001 From: Sassy Date: Sun, 8 Aug 2021 10:36:03 +0000 Subject: [PATCH 0740/9987] Sanity checks added --- easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb b/easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb index 9a431e5392a..ed65ae508e8 100644 --- a/easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb +++ b/easybuild/easyconfigs/g/gofasta/gofasta-0.0.5.eb @@ -21,4 +21,11 @@ builddependencies = [ ('Go', '1.16.5'), ] +sanity_check_commands = ['gofasta -h'] + +sanity_check_paths = { + 'files': ['bin/gofasta'], + 'dirs': [], +} + moduleclass = 'bio' From a59303d1813bf111e9f14ef23e5e506a076596bc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 8 Aug 2021 21:21:18 +0200 Subject: [PATCH 0741/9987] Update easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb Co-authored-by: SebastianAchilles --- .../l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb index a161943044c..bb2faf1ae40 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.0-GCCcore-11.2.0.eb @@ -22,6 +22,12 @@ patches = [ ('%(name)s-%(version)s_psm3-version.patch', 0), '%(name)s-1.12.1_disable-psm3-avx-config.patch', ] +checksums = [ + '0c68264ae18de5c31857724c754023351614330bd61a50b40cef2b5e8f63ab28', # libfabric-1.13.0.tar.bz2 + 'f357a60f9cfd054469fef46f560531aa53ded3b7708c313b73d9bfdcb89bf24d', # libfabric-1.13.0_psm3-version.patch + # libfabric-1.12.1_disable-psm3-avx-config.patch + '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', +] builddependencies = [ ('binutils', '2.37'), From 70294bdf2fae0db0020e734b6eab50c52f57a147 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Mon, 9 Aug 2021 09:38:26 +0200 Subject: [PATCH 0742/9987] using GCC toolchain instead of foss --- .../ctffind-4.1.14-GCC-10.3.0-CUDA-11.3.1.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-GCC-10.3.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-GCC-10.3.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..5b3acc57bbb --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-GCC-10.3.0-CUDA-11.3.1.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_asm-fix.patch'] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.2.0'), + ('GSL', '2.7'), + ('wxWidgets', '3.1.5'), + ('CUDAcore', '11.3.1', '', True), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From 7ed537406eacb6ba1f1c1f4f5ed026272f98f44e Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Mon, 9 Aug 2021 09:43:21 +0200 Subject: [PATCH 0743/9987] Delete ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb --- .../ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb | 46 ------------------- 1 file changed, 46 deletions(-) delete mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb deleted file mode 100644 index cf2a0d71b0f..00000000000 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb +++ /dev/null @@ -1,46 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# -# Author: Ake Sandgren, HPC2N, Umea University - -easyblock = 'ConfigureMake' - -name = 'ctffind' -version = '4.1.14' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' -description = """Program for finding CTFs of electron micrographs.""" - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'openmp': True} - -source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_asm-fix.patch'] -checksums = [ - 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz - 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch -] - -dependencies = [ - ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.6'), - ('LibTIFF', '4.2.0'), - ('GSL', '2.7'), - ('wxWidgets', '3.1.5'), - ('CUDAcore', '11.3.1', '', True), -] - -configopts = '--enable-openmp ' - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/ctffind'], - 'dirs': [], -} - -moduleclass = 'bio' From 68026df851e54ea16be4a1dc8abfac473a635b17 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 9 Aug 2021 09:46:52 +0200 Subject: [PATCH 0744/9987] Update and rename openstackclient-5.5.0-GCCcore-10.2.0.eb to OpenStackClient-5.5.0-GCCcore-10.2.0.eb rename to OpenStackClient --- ...CCcore-10.2.0.eb => OpenStackClient-5.5.0-GCCcore-10.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/o/openstackclient/{openstackclient-5.5.0-GCCcore-10.2.0.eb => OpenStackClient-5.5.0-GCCcore-10.2.0.eb} (99%) diff --git a/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb similarity index 99% rename from easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb rename to easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb index 441ba8a8bc7..b013362d2e5 100644 --- a/easybuild/easyconfigs/o/openstackclient/openstackclient-5.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -1,7 +1,7 @@ # Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/08 easyblock = 'PythonBundle' -name = 'openstackclient' +name = 'OpenStackClient' version = '5.5.0' homepage = 'https://docs.openstack.org/python-openstackclient/latest/' From bcd9726e47278e9e963334461403509bf163f128 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Mon, 9 Aug 2021 09:49:32 +0200 Subject: [PATCH 0745/9987] Added description to the patch --- easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb | 2 +- .../w/WRF/WRF-4.3_netCDF-Fortran_separate_path.patch | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb index 6d423a181a1..6ada7b5e843 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.3-foss-2021a-dmpar.eb @@ -18,7 +18,7 @@ patches = [ ] checksums = [ '68109070e3e6b3106257f738c0e69e774816589bf3a0cedaf66dd15f99ad63b5', # v4.3.tar.gz - '7007c1caa019da76baa157bebd1886a3d152feaf2f71c1675687a1874c7514e3', # WRF-4.3_netCDF-Fortran_separate_path.patch + '8171e1721eca9b32f39d9ca71848cb181bf65b5487d682dd36c237ed2597dfca', # WRF-4.3_netCDF-Fortran_separate_path.patch ] # csh is used by WRF install scripts diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.3_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.3_netCDF-Fortran_separate_path.patch index adc51a233bd..5053c7e3410 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.3_netCDF-Fortran_separate_path.patch +++ b/easybuild/easyconfigs/w/WRF/WRF-4.3_netCDF-Fortran_separate_path.patch @@ -1,3 +1,9 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since WRF3.5; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain +# Adapted by @maxim-masterov for WRF-v4.3 + diff -Nru WRF-4.3.orig/arch/Config.pl WRF-4.3/arch/Config.pl --- WRF-4.3.orig/arch/Config.pl 2021-08-04 15:09:59.634194394 +0200 +++ WRF-4.3/arch/Config.pl 2021-08-05 11:14:34.614153019 +0200 From 1c7db782e47e82f0c900be533beae1a8dfd8c5bf Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 9 Aug 2021 10:20:30 +0200 Subject: [PATCH 0746/9987] rename to OpenStackClient --- .../OpenStackClient-5.5.0-GCCcore-10.2.0.eb | 133 ++++++++++++++++++ 1 file changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b013362d2e5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb @@ -0,0 +1,133 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/08 +easyblock = 'PythonBundle' + +name = 'OpenStackClient' +version = '5.5.0' + +homepage = 'https://docs.openstack.org/python-openstackclient/latest/' +description = """OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the +command set for Compute, Identity, Image, Network, Object Store and Block +Storage APIs together in a single shell with a uniform command structure.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), +] +builddependencies = [('binutils', '2.35')] + +exts_default_options = { + 'use_pip': True, +} +exts_list = [ + ('pbr', '5.6.0', { + 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('cmd2', '2.1.2', { + 'checksums': ['25dbb2e9847aaa686a8a21e84e3d101db8b79f5cb992e044fc54210ab8c0ad41'], + }), + ('charset-normalizer', '2.0.4', { + 'checksums': ['f23667ebe1084be45f6ae0538e4a5a865206544097e4e8bbcacf42cd02a348f3'], + }), + ('jsonpointer', '2.1', { + 'checksums': ['5a34b698db1eb79ceac454159d3f7c12a451a91f6334a4f638454327b7a89962'], + }), + ('cliff', '3.8.0', { + 'checksums': ['8dd215d0a84c9a3ab2fa2aa700849f4e7b786639f66caa0ad4108c85dca95a7c'], + }), + ('openstacksdk', '0.58.0', { + 'modulename': 'openstack', + 'checksums': ['d8368d1728f686114213d22cc8e3eef71629fae1424b2ad2c5d22a7b9a04a278'], + }), + ('stevedore', '3.3.0', { + 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], + }), + ('dogpile.cache', '1.1.3', { + 'checksums': ['6f0bcf97c73bfec1a7bf14e5a248488cee00c2d494bf63f3789ea6d95a57c1cf'], + }), + ('prettytable', '0.7.2', { + 'checksums': ['2d5460dc9db74a32bcc8f9f67de68b2c4f4d2f01fa3bd518764c69156d9cacd9'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + ('jsonpatch', '1.32', { + 'checksums': ['b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + ('os-service-types', '1.7.0', { + 'checksums': ['31800299a82239363995b91f1ebf9106ac7758542a1e4ef6dc737a5932878c6c'], + }), + ('requestsexceptions', '1.4.0', { + 'checksums': ['b095cbc77618f066d459a02b137b020c37da9f46d9b057704019c9f77dba3065'], + }), + ('requests', '2.26.0', { + 'checksums': ['b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7'], + }), + ('osc-lib', '2.4.1', { + 'checksums': ['257ef0cda902664605a850a858172306acb2b08b0e7e32d7a5b4f12dc6bc56c5'], + }), + ('keystoneauth1', '4.3.1', { + 'checksums': ['93605430a6d1424f31659bc5685e9dc1be9a6254e88c99f00cffc0a60c648a64'], + }), + ('debtcollector', '2.2.0', { + 'checksums': ['787981f4d235841bf6eb0467e23057fb1ac7ee24047c32028a8498b9128b6829'], + }), + ('oslo.i18n', '5.0.1', { + 'modulename': 'oslo_i18n', + 'checksums': ['3484b71e30f75c437523302d1151c291caf4098928269ceec65ce535456e035b'], + }), + ('oslo.utils', '4.9.2', { + 'modulename': 'oslo_utils', + 'checksums': ['20db285734ff6c3b50d5a6afcb2790ade0c7ba02fbc876feed43733f2c41a5c9'], + }), + ('oslo.serialization', '4.1.0', { + 'modulename': 'oslo_serialization', + 'checksums': ['cecc7794df806c85cb70dbd6c2b3af19bc68047ad29e3c6442be90a0a4de5379'], + }), + ('oslo.config', '8.7.1', { + 'modulename': 'oslo_config', + 'checksums': ['a0c346d778cdc8870ab945e438bea251b5f45fae05d6d99dfe4953cca2277b60'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('iso8601', '0.1.16', { + 'checksums': ['36532f77cc800594e8f16641edae7f1baf7932f05d8e508545b95fc53c6dc85b'], + }), + ('python-novaclient', '17.5.0', { + 'modulename': 'novaclient', + 'checksums': ['7aa0fe9a74b1336e56c2f7965f14e04bad29dbfbd7ba41dcb7b364f94c9bee7f'], + }), + ('python-keystoneclient', '4.2.0', { + 'modulename': 'keystoneclient', + 'checksums': ['0248426e483b95de395086482c077d48e45990d3b1a3e334b2ec8b2e108f5a8a'], + }), + ('python-cinderclient', '8.0.0', { + 'modulename': 'cinderclient', + 'checksums': ['4ced8c562064ab73f757d91d26846faaf1fc1c82f1fee5597e24df3d1ffcf116'], + }), + ('python-openstackclient', version, { + 'modulename': 'openstackclient', + 'checksums': ['8d40491374172f9375ce1642ac2230b1cbb5a564320edbcc2a9ebe857fd9a880'], + }), +] + +sanity_pip_check = True +enhance_sanity_check = True +sanity_check_commands = ['openstack -h'] + +sanity_check_paths = { + 'files': ['bin/openstack'], + 'dirs': ["bin", 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' From 41f3e2e1983894ea1fba9c62bdebf019d7f34dd2 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 9 Aug 2021 10:22:52 +0200 Subject: [PATCH 0747/9987] Delete easybuild/easyconfigs/o/openstackclient directory --- .../OpenStackClient-5.5.0-GCCcore-10.2.0.eb | 133 ------------------ 1 file changed, 133 deletions(-) delete mode 100644 easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb deleted file mode 100644 index b013362d2e5..00000000000 --- a/easybuild/easyconfigs/o/openstackclient/OpenStackClient-5.5.0-GCCcore-10.2.0.eb +++ /dev/null @@ -1,133 +0,0 @@ -# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/08 -easyblock = 'PythonBundle' - -name = 'OpenStackClient' -version = '5.5.0' - -homepage = 'https://docs.openstack.org/python-openstackclient/latest/' -description = """OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the -command set for Compute, Identity, Image, Network, Object Store and Block -Storage APIs together in a single shell with a uniform command structure.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -dependencies = [ - ('Python', '3.8.6'), - ('PyYAML', '5.3.1'), -] -builddependencies = [('binutils', '2.35')] - -exts_default_options = { - 'use_pip': True, -} -exts_list = [ - ('pbr', '5.6.0', { - 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], - }), - ('pyperclip', '1.8.2', { - 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], - }), - ('cmd2', '2.1.2', { - 'checksums': ['25dbb2e9847aaa686a8a21e84e3d101db8b79f5cb992e044fc54210ab8c0ad41'], - }), - ('charset-normalizer', '2.0.4', { - 'checksums': ['f23667ebe1084be45f6ae0538e4a5a865206544097e4e8bbcacf42cd02a348f3'], - }), - ('jsonpointer', '2.1', { - 'checksums': ['5a34b698db1eb79ceac454159d3f7c12a451a91f6334a4f638454327b7a89962'], - }), - ('cliff', '3.8.0', { - 'checksums': ['8dd215d0a84c9a3ab2fa2aa700849f4e7b786639f66caa0ad4108c85dca95a7c'], - }), - ('openstacksdk', '0.58.0', { - 'modulename': 'openstack', - 'checksums': ['d8368d1728f686114213d22cc8e3eef71629fae1424b2ad2c5d22a7b9a04a278'], - }), - ('stevedore', '3.3.0', { - 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], - }), - ('dogpile.cache', '1.1.3', { - 'checksums': ['6f0bcf97c73bfec1a7bf14e5a248488cee00c2d494bf63f3789ea6d95a57c1cf'], - }), - ('prettytable', '0.7.2', { - 'checksums': ['2d5460dc9db74a32bcc8f9f67de68b2c4f4d2f01fa3bd518764c69156d9cacd9'], - }), - ('jmespath', '0.10.0', { - 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], - }), - ('jsonpatch', '1.32', { - 'checksums': ['b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2'], - }), - ('munch', '2.5.0', { - 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], - }), - ('os-service-types', '1.7.0', { - 'checksums': ['31800299a82239363995b91f1ebf9106ac7758542a1e4ef6dc737a5932878c6c'], - }), - ('requestsexceptions', '1.4.0', { - 'checksums': ['b095cbc77618f066d459a02b137b020c37da9f46d9b057704019c9f77dba3065'], - }), - ('requests', '2.26.0', { - 'checksums': ['b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7'], - }), - ('osc-lib', '2.4.1', { - 'checksums': ['257ef0cda902664605a850a858172306acb2b08b0e7e32d7a5b4f12dc6bc56c5'], - }), - ('keystoneauth1', '4.3.1', { - 'checksums': ['93605430a6d1424f31659bc5685e9dc1be9a6254e88c99f00cffc0a60c648a64'], - }), - ('debtcollector', '2.2.0', { - 'checksums': ['787981f4d235841bf6eb0467e23057fb1ac7ee24047c32028a8498b9128b6829'], - }), - ('oslo.i18n', '5.0.1', { - 'modulename': 'oslo_i18n', - 'checksums': ['3484b71e30f75c437523302d1151c291caf4098928269ceec65ce535456e035b'], - }), - ('oslo.utils', '4.9.2', { - 'modulename': 'oslo_utils', - 'checksums': ['20db285734ff6c3b50d5a6afcb2790ade0c7ba02fbc876feed43733f2c41a5c9'], - }), - ('oslo.serialization', '4.1.0', { - 'modulename': 'oslo_serialization', - 'checksums': ['cecc7794df806c85cb70dbd6c2b3af19bc68047ad29e3c6442be90a0a4de5379'], - }), - ('oslo.config', '8.7.1', { - 'modulename': 'oslo_config', - 'checksums': ['a0c346d778cdc8870ab945e438bea251b5f45fae05d6d99dfe4953cca2277b60'], - }), - ('rfc3986', '1.5.0', { - 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('iso8601', '0.1.16', { - 'checksums': ['36532f77cc800594e8f16641edae7f1baf7932f05d8e508545b95fc53c6dc85b'], - }), - ('python-novaclient', '17.5.0', { - 'modulename': 'novaclient', - 'checksums': ['7aa0fe9a74b1336e56c2f7965f14e04bad29dbfbd7ba41dcb7b364f94c9bee7f'], - }), - ('python-keystoneclient', '4.2.0', { - 'modulename': 'keystoneclient', - 'checksums': ['0248426e483b95de395086482c077d48e45990d3b1a3e334b2ec8b2e108f5a8a'], - }), - ('python-cinderclient', '8.0.0', { - 'modulename': 'cinderclient', - 'checksums': ['4ced8c562064ab73f757d91d26846faaf1fc1c82f1fee5597e24df3d1ffcf116'], - }), - ('python-openstackclient', version, { - 'modulename': 'openstackclient', - 'checksums': ['8d40491374172f9375ce1642ac2230b1cbb5a564320edbcc2a9ebe857fd9a880'], - }), -] - -sanity_pip_check = True -enhance_sanity_check = True -sanity_check_commands = ['openstack -h'] - -sanity_check_paths = { - 'files': ['bin/openstack'], - 'dirs': ["bin", 'lib/python%(pyshortver)s/site-packages'] -} - -moduleclass = 'tools' From 82a963ab7eb3b52a7fcebdcc3caf51c97b9184cc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 9 Aug 2021 10:12:20 +0100 Subject: [PATCH 0748/9987] Create the symlinks in the lib folder for ncurses --- easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 4 ++-- easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb | 4 ++-- easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 6d21e403d3d..f17cb5fb125 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -32,8 +32,8 @@ buildopts = 'CFLAGS="-O2 -fPIC"' # Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS postinstallcmds = [ - "ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.so", - "ln -s %(installdir)s/lib/libncurses.a %(installdir)s/lib/libtinfo.a" + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" ] local_libs = ["form", "menu", "ncurses", "panel"] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb index 4f72ab2ce53..9e75f70cd1d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb @@ -28,8 +28,8 @@ buildopts = 'CFLAGS="-O2 -fPIC"' # Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS postinstallcmds = [ - "ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.so", - "ln -s %(installdir)s/lib/libncurses.a %(installdir)s/lib/libtinfo.a" + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" ] local_libs = ["form", "menu", "ncurses", "panel"] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb index 83b361eff08..5df1d2c1038 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb @@ -28,8 +28,8 @@ buildopts = 'CFLAGS="-O2 -fPIC"' # Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS postinstallcmds = [ - "ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.so", - "ln -s %(installdir)s/lib/libncurses.a %(installdir)s/lib/libtinfo.a" + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" ] local_libs = ["form", "menu", "ncurses", "panel"] From 99c6db49de8d9f8aa751c15592e15f6a4651b427 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Aug 2021 11:22:25 +0200 Subject: [PATCH 0749/9987] {perf}[gompi/2021a] DistributedStream v20210628 --- .../DistributedStream-20210628-gompi-2021a.eb | 34 +++++++++++++++++++ .../m/Mini-XML/Mini-XML-3.2-GCCcore-10.3.0.eb | 23 +++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/d/DistributedStream/DistributedStream-20210628-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/d/DistributedStream/DistributedStream-20210628-gompi-2021a.eb b/easybuild/easyconfigs/d/DistributedStream/DistributedStream-20210628-gompi-2021a.eb new file mode 100644 index 00000000000..1cf2cdb1e44 --- /dev/null +++ b/easybuild/easyconfigs/d/DistributedStream/DistributedStream-20210628-gompi-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'DistributedStream' +version = '20210628' +local_commit = '998f747' + +homepage = 'https://github.com/adrianjhpc/DistributedStream' +description = """A MPI distributed stream benchmark, useful to identifying nodes with poor memory performance and +characterising memory bandwidth variation over systems.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/adrianjhpc/DistributedStream/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['af44b702ac9a5a66deed58f77c19a7a7398d7ff19b871a1bb11e295360408f9b'] + +dependencies = [('Mini-XML', '3.2')] + +start_dir = 'src' + +prebuildopts = 'sed -i "s/-O3/$CFLAGS/g" Makefile && ' +buildopts = 'CC="$CC" MXMLINC="-I$EBROOTMINIMINXML/include" MXMLLIB="-L$EBROOTMINIMINXML/lib -lmxml"' + +files_to_copy = [(['src/distributed_streams'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/distributed_streams'], + 'dirs': [], +} + +sanity_check_commands = ["distributed_streams"] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..fddac248df7 --- /dev/null +++ b/easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.2-GCCcore-10.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Mini-XML' +version = '3.2' + +homepage = 'https://www.msweet.org/mxml' +description = """Mini-XML is a small XML parsing library that you can use to read XML data files or strings in your + application without requiring large non-standard libraries""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/michaelrsweet/mxml/releases/download/v%(version)s/'] +sources = ['mxml-%(version)s.tar.gz'] +checksums = ['b894f6c64964f2e77902564c17ba00f5d077a7a24054e7c1937903b0bd42c974'] + +builddependencies = [('binutils', '2.36.1')] + +sanity_check_paths = { + 'files': ['include/mxml.h', 'lib/libmxml.a', 'lib/libmxml.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +moduleclass = 'lib' From f1cbbf1b8a15231e9bfcaf2780a71e40e0dba601 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 9 Aug 2021 10:35:44 +0100 Subject: [PATCH 0750/9987] Create libtinfo symlinks in ncurses 6.2 --- easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb | 6 ++++++ .../easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb | 6 ++++++ .../easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb | 6 ++++++ .../easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb | 6 ++++++ .../easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb | 6 ++++++ 5 files changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb index b037cf0613a..816870478e9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb @@ -28,6 +28,12 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb index a3839f21819..5044d91b4c5 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -28,6 +28,12 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb index 5d3035e81f4..07bfbcd9e14 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb @@ -28,6 +28,12 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb index a977bf74971..61c14fe5a04 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb @@ -28,6 +28,12 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb index d1e45e0229f..18dcd5668cf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb @@ -28,6 +28,12 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", From 3a790418240c9dda8a6c7d374b9a5539d3e8f82d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 9 Aug 2021 10:50:33 +0100 Subject: [PATCH 0751/9987] create libtinfo symlinks in easyconfigs for ncurses 6.1 --- .../easyconfigs/n/ncurses/ncurses-6.1-GCCcore-6.4.0.eb | 6 ++++++ .../easyconfigs/n/ncurses/ncurses-6.1-GCCcore-7.2.0.eb | 6 ++++++ .../easyconfigs/n/ncurses/ncurses-6.1-GCCcore-7.3.0.eb | 6 ++++++ .../easyconfigs/n/ncurses/ncurses-6.1-GCCcore-8.2.0.eb | 6 ++++++ .../easyconfigs/n/ncurses/ncurses-6.1-GCCcore-8.3.0.eb | 6 ++++++ 5 files changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-6.4.0.eb index ff37c7f6918..93a437fad05 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-6.4.0.eb @@ -31,6 +31,12 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-7.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-7.2.0.eb index 8c1a19f160b..7fc906c280e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-7.2.0.eb @@ -31,6 +31,12 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-7.3.0.eb index 93201754b8f..2f48f5d2ebc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-7.3.0.eb @@ -31,6 +31,12 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-8.2.0.eb index 2840ef6bd35..fbdcb82ccda 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-8.2.0.eb @@ -31,6 +31,12 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-8.3.0.eb index b86f5af72f8..eb7ec1bd18e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1-GCCcore-8.3.0.eb @@ -29,6 +29,12 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", From a485b66b9983da4e77dadb5fd8533fd9363f6f7d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Aug 2021 12:42:29 +0200 Subject: [PATCH 0752/9987] fix Boost dependency for poppler --- .../easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb index c7eef98ae3b..2654fe98e59 100644 --- a/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('NSS', '3.65'), ('LibTIFF', '4.2.0'), ('Qt5', '5.15.2'), - #('Boost', '1.76.0'), + ('Boost', '1.76.0'), ('cairo', '1.16.0'), ('OpenJPEG', '2.4.0'), ('zlib', '1.2.11'), From dcfa6227fb455b673a1a0da5ff18fac3eafa0315 Mon Sep 17 00:00:00 2001 From: satishskamath Date: Mon, 9 Aug 2021 14:43:35 +0200 Subject: [PATCH 0753/9987] Added a autoreconf command in the preconfigopts since an m4 file modified after applying patch. --- .../easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb index e9e59e11134..6f6e00c7207 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb @@ -36,9 +36,7 @@ checksums = [ 'ffb6b3cb02ffe6401505fcbe6d71cf4f46ecfe1f93e2ac8eaacf51da1010a5a5', # CubeGUI-4.6_qtlibs_symlink_realpath.patch ] -configopts = [ - "--with-qt=$EBROOTQT5" -] +preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' builddependencies = [ # use same binutils version that was used when building GCCcore @@ -50,6 +48,10 @@ dependencies = [ ('Qt5', '5.15.2'), ] +configopts = [ + "--with-qt=$EBROOTQT5" +] + sanity_check_paths = { 'files': ['bin/cube', 'bin/cubegui-config', 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], From af280f5ecacd59c5dc4d3c60fe58529411e7f469 Mon Sep 17 00:00:00 2001 From: satishskamath Date: Mon, 9 Aug 2021 15:01:28 +0200 Subject: [PATCH 0754/9987] Extra space removed, style check passes now. --- easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb index 6f6e00c7207..fb9320b75ea 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb @@ -36,7 +36,7 @@ checksums = [ 'ffb6b3cb02ffe6401505fcbe6d71cf4f46ecfe1f93e2ac8eaacf51da1010a5a5', # CubeGUI-4.6_qtlibs_symlink_realpath.patch ] -preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' +preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' builddependencies = [ # use same binutils version that was used when building GCCcore From 66c87138162486fd420ef92228946b6b8c628ff7 Mon Sep 17 00:00:00 2001 From: satishskamath Date: Mon, 9 Aug 2021 15:13:19 +0200 Subject: [PATCH 0755/9987] Added author information and description as a comment in the patch and updated checksums in the config file. --- easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb | 2 +- .../c/CubeGUI/CubeGUI-4.6_qtlibs_symlink_realpath.patch | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb index fb9320b75ea..76c9562ade8 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb @@ -33,7 +33,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['CubeGUI-4.6_qtlibs_symlink_realpath.patch'] checksums = [ '1871c6736121d94a22314cb5daa8f3cbb978b58bfe54f677c4c9c9693757d0c5', # cubegui-4.6.tar.gz - 'ffb6b3cb02ffe6401505fcbe6d71cf4f46ecfe1f93e2ac8eaacf51da1010a5a5', # CubeGUI-4.6_qtlibs_symlink_realpath.patch + '0b382346251b82792393e44103ddb44f9b1665dd3c652670171a0833984e8987', # CubeGUI-4.6_qtlibs_symlink_realpath.patch ] preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6_qtlibs_symlink_realpath.patch b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6_qtlibs_symlink_realpath.patch index e7f67012c48..b8181ef7e74 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6_qtlibs_symlink_realpath.patch +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6_qtlibs_symlink_realpath.patch @@ -1,3 +1,7 @@ +# Author: Satish Kamath (email: satishs.kamath@gmail.com) +# The path may be a symbolic link to the actual paths on different nodes and the paths generated by qmake are the actual paths which are textually different. +# The original code in the patch tries to manipulate the qtlib paths generated by qmake (the actual paths) using the symlink path (in $LIBPATH) +# which results in wrong library paths for QT in the makefile. This has been remedied using readlink. diff -Nru cubegui-4.6_orig/build-config/m4/autotroll.m4 cubegui-4.6/build-config/m4/autotroll.m4 --- cubegui-4.6_orig/build-config/m4/autotroll.m4 2021-08-06 13:03:13.758365694 +0200 +++ cubegui-4.6/build-config/m4/autotroll.m4 2021-08-06 13:06:18.972956958 +0200 From 217991abc1c1afa245396e6beba1cc48d2ecf781 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Aug 2021 15:15:06 +0200 Subject: [PATCH 0756/9987] use GCC toolchain for poppler 21.06.1 because of Boost dependency --- ....06.1-GCCcore-10.3.0.eb => poppler-21.06.1-GCC-10.3.0.eb} | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/poppler/{poppler-21.06.1-GCCcore-10.3.0.eb => poppler-21.06.1-GCC-10.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.3.0.eb similarity index 92% rename from easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.3.0.eb index 2654fe98e59..2c00a04e7d0 100644 --- a/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.3.0.eb @@ -6,10 +6,9 @@ version = '21.06.1' homepage = 'https://poppler.freedesktop.org' description = "Poppler is a PDF rendering library" -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchain = {'name': 'GCC', 'version': '10.3.0'} builddependencies = [ - ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('pkg-config', '0.29.2'), ] @@ -39,7 +38,7 @@ components = [ 'source_urls': ['https://poppler.freedesktop.org/'], 'sources': [SOURCE_TAR_XZ], 'checksums': ['86b09e5a02de40081a3916ef8711c5128eaf4b1fc59d5f87d0ec66f04f595db4'], - 'configopts': "-DENABLE_BOOST=OFF", + 'configopts': "-DENABLE_BOOST=ON", }), ('poppler-data', '0.4.10', { 'source_urls': ['https://poppler.freedesktop.org/'], From d10c7c7c6755c618c19e2fdd7ddd094eeb89c519 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Aug 2021 15:36:34 +0200 Subject: [PATCH 0757/9987] use tagged version 1.0 of DistributedStreams --- ...gompi-2021a.eb => DistributedStream-1.0-gompi-2021a.eb} | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/d/DistributedStream/{DistributedStream-20210628-gompi-2021a.eb => DistributedStream-1.0-gompi-2021a.eb} (80%) diff --git a/easybuild/easyconfigs/d/DistributedStream/DistributedStream-20210628-gompi-2021a.eb b/easybuild/easyconfigs/d/DistributedStream/DistributedStream-1.0-gompi-2021a.eb similarity index 80% rename from easybuild/easyconfigs/d/DistributedStream/DistributedStream-20210628-gompi-2021a.eb rename to easybuild/easyconfigs/d/DistributedStream/DistributedStream-1.0-gompi-2021a.eb index 1cf2cdb1e44..44a190e1357 100644 --- a/easybuild/easyconfigs/d/DistributedStream/DistributedStream-20210628-gompi-2021a.eb +++ b/easybuild/easyconfigs/d/DistributedStream/DistributedStream-1.0-gompi-2021a.eb @@ -1,8 +1,7 @@ easyblock = 'MakeCp' name = 'DistributedStream' -version = '20210628' -local_commit = '998f747' +version = '1.0' homepage = 'https://github.com/adrianjhpc/DistributedStream' description = """A MPI distributed stream benchmark, useful to identifying nodes with poor memory performance and @@ -12,8 +11,8 @@ toolchain = {'name': 'gompi', 'version': '2021a'} toolchainopts = {'usempi': True} source_urls = ['https://github.com/adrianjhpc/DistributedStream/archive/'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['af44b702ac9a5a66deed58f77c19a7a7398d7ff19b871a1bb11e295360408f9b'] +sources = ['%(version)s.tar.gz'] +checksums = ['5eec87a3edf91620d70876ff6f1801ddc3f72317bf2639cbdeaa25052549dbbf'] dependencies = [('Mini-XML', '3.2')] From 2bd7b9772604907c9385afd3e9af988a168765e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Aug 2021 15:55:50 +0200 Subject: [PATCH 0758/9987] disable GdkPixbuf loader in librsvg 2.51.2 easyconfig --- .../easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb index eb5dff78218..0c434e7143d 100644 --- a/easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.51.2-GCCcore-10.3.0.eb @@ -26,6 +26,9 @@ dependencies = [ ('GObject-Introspection', '1.68.0'), ] +# don't GdkPixbuf loader (which gets added to the Gdk-Pixbuf installation directory) +configopts = "--disable-pixbuf-loader" + sanity_check_paths = { 'files': ['bin/rsvg-convert', 'lib/librsvg-%(version_major)s.a', 'lib/librsvg-%%(version_major)s.%s' % SHLIB_EXT, 'lib/pkgconfig/librsvg-%(version_major)s.0.pc'], From edd174811551c1fc81aa3216b05dc4fbb32f93bf Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 9 Aug 2021 16:13:20 +0200 Subject: [PATCH 0759/9987] adding easyconfigs: torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb, torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb --- ...orchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb | 32 +++++++++++++++++++ ...info-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb create mode 100644 easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb diff --git a/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb new file mode 100644 index 00000000000..0ba85a72a58 --- /dev/null +++ b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-foss-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'torchinfo' +version = '1.5.2' +local_pytorch_version = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/TylerYep/torchinfo' +description = """" +Torchinfo provides information complementary to what is provided by print(your_model) in PyTorch, similar to +Tensorflow's model.summary() API to view the visualization of the model, which is helpful while debugging your network. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'TylerYep' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['25f076ab469f29a63dee5a048d39edf0f7a809a5d9e640dccd4174a349ea0143'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', local_pytorch_version), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb new file mode 100644 index 00000000000..1b2083358fb --- /dev/null +++ b/easybuild/easyconfigs/t/torchinfo/torchinfo-1.5.2-fosscuda-2020b-PyTorch-1.7.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'torchinfo' +version = '1.5.2' +local_pytorch_version = '1.7.1' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/TylerYep/torchinfo' +description = """" +Torchinfo provides information complementary to what is provided by print(your_model) in PyTorch, similar to +Tensorflow's model.summary() API to view the visualization of the model, which is helpful while debugging your network. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +github_account = 'TylerYep' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['25f076ab469f29a63dee5a048d39edf0f7a809a5d9e640dccd4174a349ea0143'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', local_pytorch_version), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From e2561ec97622ffed90b7f5bbbf3098e67ff90479 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 9 Aug 2021 15:59:21 +0100 Subject: [PATCH 0760/9987] adding easyconfigs: ISA-L-2.30.0-GCCcore-10.3.0.eb, python-isal-0.11.0-GCCcore-10.3.0.eb --- .../i/ISA-L/ISA-L-2.30.0-GCCcore-10.3.0.eb | 46 +++++++++++++++++++ .../python-isal-0.11.0-GCCcore-10.3.0.eb | 35 ++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..943166392af --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.30.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['bcf592c04fdfa19e723d2adf53d3e0f4efd5b956bb618fed54a1108d76a6eb56'] + +builddependencies = [ + ('Autotools', '20210128'), + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [('NASM', '2.15.05')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +_bins = ['bin/igzip'] +_includes = ['include/%(namelower)s.h'] +_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test', 'types']] +_libs = ['lib/libisal.%s' % l for l in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': _bins + _includes + _libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..512fada81bf --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '0.11.0' +_modname = 'isal' + +homepage = 'https://github.com/pycompression/python-isal' +description = """Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'pycompression' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3959ce30f1043ae591bc9d6ee9edb5781c09cc15c69dd5361517d29b56327260'] + +dependencies = [ + ('Python', '3.9.5'), + ('ISA-L', '2.30.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' +installopts = '--no-binary isal' + +options = {'modulename': _modname} + +moduleclass = 'lib' From 3cf6d0e6ed9c5640bc2562c7f49c865f63d9de35 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 9 Aug 2021 16:00:46 +0100 Subject: [PATCH 0761/9987] adding easyconfigs: cutadapt-3.4-GCCcore-10.3.0-Python-3.9.5.eb --- ...utadapt-3.4-GCCcore-10.3.0-Python-3.9.5.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0-Python-3.9.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0-Python-3.9.5.eb new file mode 100644 index 00000000000..c4aab508a65 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0-Python-3.9.5.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '3.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('python-isal', '0.11.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + ('dnaio', '0.5.1', { + 'checksums': ['c68ecffbf653dfe122f1c10fb8d7c5957ad68acc5c9035c66f81eba1a591d31c'], + }), + (name, version, { + 'checksums': ['eb8d52d45a7d38bd3ddc901eb397599bca8716a20d39e2b1feeb20242352dab2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cutadapt --help", "cutadapt --version"] + +moduleclass = 'bio' From 13f7a9bb1ebb04ff6e8c271003990a3020c480e4 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 9 Aug 2021 16:04:09 +0100 Subject: [PATCH 0762/9987] Remove versionsuffix --- .../c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4a74f24cfe2 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb @@ -0,0 +1,52 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '3.4' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('python-isal', '0.11.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + ('dnaio', '0.5.1', { + 'checksums': ['c68ecffbf653dfe122f1c10fb8d7c5957ad68acc5c9035c66f81eba1a591d31c'], + }), + (name, version, { + 'checksums': ['eb8d52d45a7d38bd3ddc901eb397599bca8716a20d39e2b1feeb20242352dab2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cutadapt --help", "cutadapt --version"] + +moduleclass = 'bio' From 5b696e83e345ece2d2c9f4cd4f23de8e2a81a7f0 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Mon, 9 Aug 2021 16:04:56 +0100 Subject: [PATCH 0763/9987] remove versionsuffixed EC --- ...utadapt-3.4-GCCcore-10.3.0-Python-3.9.5.eb | 53 ------------------- 1 file changed, 53 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0-Python-3.9.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0-Python-3.9.5.eb deleted file mode 100644 index c4aab508a65..00000000000 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0-Python-3.9.5.eb +++ /dev/null @@ -1,53 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics (SIB) -# Biozentrum - University of Basel -# Modified by: Adam Huffman, Jonas Demeulemeester -# The Francis Crick Institute -# Modified by: Albert Bogdanowicz -# Institute of Biochemistry and Biophysics PAS -# Modified by: Jasper Grimm -# University of York - -easyblock = 'PythonBundle' - -name = 'cutadapt' -version = '3.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' -description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and - other types of unwanted sequence from your high-throughput sequencing reads.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -builddependencies = [('binutils', '2.36.1')] - -dependencies = [ - ('Python', '3.9.5'), - ('python-isal', '0.11.0'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('xopen', '1.1.0', { - 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], - }), - ('dnaio', '0.5.1', { - 'checksums': ['c68ecffbf653dfe122f1c10fb8d7c5957ad68acc5c9035c66f81eba1a591d31c'], - }), - (name, version, { - 'checksums': ['eb8d52d45a7d38bd3ddc901eb397599bca8716a20d39e2b1feeb20242352dab2'], - }), -] - -sanity_check_paths = { - 'files': ['bin/cutadapt'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["cutadapt --help", "cutadapt --version"] - -moduleclass = 'bio' From 3b4ea21542ae26e814033a7520b68b00fbbc9ef0 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Mon, 9 Aug 2021 16:14:53 +0100 Subject: [PATCH 0764/9987] add binutils build dep to python-isal --- .../p/python-isal/python-isal-0.11.0-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.3.0.eb index 512fada81bf..9a5313be404 100644 --- a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.3.0.eb @@ -18,6 +18,8 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['3959ce30f1043ae591bc9d6ee9edb5781c09cc15c69dd5361517d29b56327260'] +builddependencies = [('binutils', '2.36.1')] + dependencies = [ ('Python', '3.9.5'), ('ISA-L', '2.30.0'), From e35e07f9a0f0092a0c727d32abc40a9b74c237aa Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 9 Aug 2021 16:45:22 +0100 Subject: [PATCH 0765/9987] functions without return should be declared as void in ctffind --- .../c/ctffind/ctffind-4.1.14-foss-2019b.eb | 6 +++- .../ctffind/ctffind-4.1.14-fosscuda-2019b.eb | 6 +++- .../ctffind/ctffind-4.1.14-fosscuda-2020b.eb | 6 +++- .../ctffind-4.1.14_void-functions.patch | 36 +++++++++++++++++++ 4 files changed, 51 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_void-functions.patch diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb index 33e59b6b429..6311b4f1128 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb @@ -18,10 +18,14 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_asm-fix.patch'] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] checksums = [ 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb index 4a09018d4d9..2a4f2638a2e 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb @@ -18,10 +18,14 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_asm-fix.patch'] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] checksums = [ 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb index 234319daa15..978e186cf1c 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb @@ -18,10 +18,14 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_asm-fix.patch'] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] checksums = [ 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_void-functions.patch b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_void-functions.patch new file mode 100644 index 00000000000..1ac0eb8913d --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_void-functions.patch @@ -0,0 +1,36 @@ +Change functions with no return from bool to void to prevent a segfault (https://grigoriefflab.umassmed.edu/comment/1696#comment-1696) +Patch added to EasyBuild by Simon Branford (University of Birmingham) +--- src/programs/ctffind/ctffind.cpp.orig 2021-08-09 16:18:25.313802000 +0100 ++++ src/programs/ctffind/ctffind.cpp 2021-08-09 16:19:52.881232575 +0100 +@@ -267,11 +267,11 @@ + float FindRotationalAlignmentBetweenTwoStacksOfImages(Image *self, Image *other_image, int number_of_images, float search_half_range, float search_step_size, float minimum_radius, float maximum_radius); + void ComputeImagesWithNumberOfExtremaAndCTFValues(CTF *ctf, Image *number_of_extrema, Image *ctf_values); + int ReturnSpectrumBinNumber(int number_of_bins, float number_of_extrema_profile[], Image *number_of_extrema, long address, Image *ctf_values, float ctf_values_profile[]); +-bool ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_renormalized[], float number_of_extrema_profile[], float ctf_values_profile[]); ++void ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_renormalized[], float number_of_extrema_profile[], float ctf_values_profile[]); + void ComputeEquiPhaseAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Curve *epa_pre_max, Curve *epa_post_max); + void OverlayCTF( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins_in_1d_spectra, double spatial_frequency[], double rotational_average_astig[], float number_of_extrema_profile[], float ctf_values_profile[], Curve *equiphase_average_pre_max, Curve *equiphase_average_post_max); + void ComputeFRCBetween1DSpectrumAndFit( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[], double frc[], double frc_sigma[], int first_fit_bin); +-bool RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ); ++void RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ); + void Renormalize1DSpectrumForFRC( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[]); + float ReturnAzimuthToUseFor1DPlots(CTF *ctf); + +@@ -2419,7 +2419,7 @@ + + // Rescale the spectrum and its 1D rotational avereage so that the peaks and troughs are at 0.0 and 1.0. The location of peaks and troughs are worked out + // by parsing the suppilied 1D average_fit array +-bool RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ) ++void RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ) + { + MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated"); + MyDebugAssertTrue(number_of_bins > 1,"Bad number of bins: %i\n",number_of_bins); +@@ -2762,7 +2762,7 @@ + } + + // +-bool ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_rank[], float number_of_extrema_profile[], float ctf_values_profile[]) ++void ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_rank[], float number_of_extrema_profile[], float ctf_values_profile[]) + { + MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated"); + MyDebugAssertTrue(number_of_extrema->is_in_memory,"Number of extrema image not allocated"); From 8fae4b9895578d42404688f1f91ac56b5345a1ec Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 9 Aug 2021 17:11:27 +0100 Subject: [PATCH 0766/9987] adding easyconfigs: RSeQC-4.0.0-foss-2021a.eb, bx-python-0.8.11-foss-2021a.eb, pyBigWig-0.3.18-foss-2021a.eb --- .../bx-python/bx-python-0.8.11-foss-2021a.eb | 34 +++++++++++++ .../p/pyBigWig/pyBigWig-0.3.18-foss-2021a.eb | 31 +++++++++++ .../r/RSeQC/RSeQC-4.0.0-foss-2021a.eb | 51 +++++++++++++++++++ 3 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/b/bx-python/bx-python-0.8.11-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2021a.eb create mode 100644 easybuild/easyconfigs/r/RSeQC/RSeQC-4.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.11-foss-2021a.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.11-foss-2021a.eb new file mode 100644 index 00000000000..551f81355bb --- /dev/null +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.11-foss-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'bx-python' +version = '0.8.11' + +homepage = 'https://github.com/bxlab/bx-python' +description = """The bx-python project is a Python library and associated set of scripts to allow for rapid + implementation of genome scale analyses.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('LZO', '2.10'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True + +exts_list = [ + ('python-lzo', '1.12', { + 'modulename': 'lzo', + 'preinstallopts': "export PREFIX=$EBROOTLZO && ", + 'checksums': ['97a8e46825e8f1abd84c2a3372bc09adae9745a5be5d3af2692cd850dac35345'], + }), + (name, version, { + 'modulename': 'bx', + 'checksums': ['7f26c2a5516b999f4330887f2b126608b4d96ed0f1de6e62ee59f3d066586974'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2021a.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2021a.eb new file mode 100644 index 00000000000..083d379028f --- /dev/null +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2021a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pyBigWig' +version = '0.3.18' + +github_account = 'deeptools' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """A python extension, written in C, for quick access to bigBed + files and access to and creation of bigWig files.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['552564d8ce8720a8ae70ed5e5534617fb0cab306b666468d1c61b6d389b8a10c'] + +dependencies = [ + ('Python', '3.9.5'), + ('cURL', '7.76.0'), + ('NSS', '3.65'), # provides libfreebl3 + ('SciPy-bundle', '2021.05'), # optional, for numpy support +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-4.0.0-foss-2021a.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-4.0.0-foss-2021a.eb new file mode 100644 index 00000000000..2ac51d287d5 --- /dev/null +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-4.0.0-foss-2021a.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'RSeQC' +version = '4.0.0' + +homepage = 'http://rseqc.sourceforge.net/' +description = """RSeQC provides a number of useful modules that can + comprehensively evaluate high throughput sequence data especially RNA-seq + data. Some basic modules quickly inspect sequence quality, nucleotide + composition bias, PCR bias and GC bias, while RNA-seq specific modules + evaluate sequencing saturation, mapped reads distribution, coverage + uniformity, strand specificity, transcript level RNA integrity etc.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5b44932bad669c6d9190c5c111d181e868fb40077ed20c16c0881f67fbcc669b'] + +dependencies = [ + ('Python', '3.9.5'), + ('Pysam', '0.16.0.1'), + ('bx-python', '0.8.11'), + ('pyBigWig', '0.3.18'), +] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +options = {'modulename': 'qcmodule'} + +sanity_check_paths = { + 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', 'bin/split_paired_bam.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + 'bam_stat.py --help', + 'overlay_bigwig.py --help', + 'split_bam.py --help', +] + +sanity_pip_check = True + +moduleclass = 'bio' From c055b031f6db0b2003866a383ca878df8fb3f566 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 9 Aug 2021 19:11:04 +0200 Subject: [PATCH 0767/9987] adding easyconfigs: UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb, GDRCopy-2.3-GCCcore-11.2.0.eb --- .../g/GDRCopy/GDRCopy-2.3-GCCcore-11.2.0.eb | 52 +++++++++++++++++++ ...-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb | 42 +++++++++++++++ 2 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7074317643e --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.3' + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +# This easyconfig only installs the library of GDRCopy. Please keep in mind +# that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] + +local_envopts = "prefix=%(installdir)s" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib %s" % local_envopts +install_cmd = "make lib_install" +installopts = local_envopts + +sanity_check_paths = { + 'files': ['lib/libgdrapi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb new file mode 100644 index 00000000000..773ca78734f --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -0,0 +1,42 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.11.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['ucx-%(version)s.tar.gz'] +patches = [ + '%(name)s-1.10.0_link_against_existing_UCX_libs.patch', +] +checksums = [ + 'b7189b69fe0e16e3c03784ef674e45687a9c520750bd74a45125c460ede37647', # ucx-1.11.0.tar.gz + # UCX-CUDA-1.10.0_link_against_existing_UCX_libs.patch + '794cb5b6476ca3aca6e0156b19e833696c816e3e4b874ad4d0b3b6a7a9c14e1b', +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('UCX', version), + ('CUDAcore', '11.4.1', '', True), + ('GDRCopy', '2.3'), +] + +moduleclass = 'lib' From b3bb7e63ccb81b2f8c2570ebfd8e1f7cc591ee89 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 9 Aug 2021 19:30:00 +0200 Subject: [PATCH 0768/9987] Update patch --- ...-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb | 6 +- ....11.0_link_against_existing_UCX_libs.patch | 66 +++++++++++++++++++ 2 files changed, 69 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb index 773ca78734f..cd0cd5581fa 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -18,12 +18,12 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['ucx-%(version)s.tar.gz'] patches = [ - '%(name)s-1.10.0_link_against_existing_UCX_libs.patch', + '%(name)s-%(version)s_link_against_existing_UCX_libs.patch', ] checksums = [ 'b7189b69fe0e16e3c03784ef674e45687a9c520750bd74a45125c460ede37647', # ucx-1.11.0.tar.gz - # UCX-CUDA-1.10.0_link_against_existing_UCX_libs.patch - '794cb5b6476ca3aca6e0156b19e833696c816e3e4b874ad4d0b3b6a7a9c14e1b', + # UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch + 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3', ] builddependencies = [ diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch new file mode 100644 index 00000000000..765d880238e --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch @@ -0,0 +1,66 @@ +Make CUDA/ROCm plugins link against the existing ucs/ucm/uct libraries. + +Åke Sandgren, Mikael Öhman 2021-08-09 +diff -ru ucx-1.11.0.orig/configure.ac ucx-1.11.0/configure.ac +--- ucx-1.11.0.orig/configure.ac 2021-06-26 02:05:59.632558898 +0200 ++++ ucx-1.11.0/configure.ac 2021-06-26 02:08:39.330081752 +0200 +@@ -29,13 +29,13 @@ + AC_GNU_SOURCE + AC_CONFIG_HEADERS([config.h]) + +-AC_CHECK_PROG(GITBIN, git, yes) +-AS_IF([test x"${GITBIN}" = x"yes"], +- [# remove preceding "refs/heads/" (11 characters) for symbolic ref +- AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) +- AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], +- [AC_SUBST(SCM_BRANCH, "") +- AC_SUBST(SCM_VERSION, "0000000")]) ++#AC_CHECK_PROG(GITBIN, git, yes) ++#AS_IF([test x"${GITBIN}" = x"yes"], ++# [# remove preceding "refs/heads/" (11 characters) for symbolic ref ++# AC_SUBST(SCM_BRANCH, esyscmd([sh -c 'git symbolic-ref --quiet HEAD | sed "s/^.\{11\}//"'])) ++# AC_SUBST(SCM_VERSION, esyscmd([sh -c 'git rev-parse --short=7 HEAD']))], ++# [AC_SUBST(SCM_BRANCH, "") ++# AC_SUBST(SCM_VERSION, "0000000")]) + + AH_TOP([ + #ifndef UCX_CONFIG_H +diff -ru ucx-1.11.0.orig/src/ucm/cuda/Makefile.am ucx-1.11.0/src/ucm/cuda/Makefile.am +--- ucx-1.11.0.orig/src/ucm/cuda/Makefile.am 2021-08-09 19:14:56.904346018 +0200 ++++ ucx-1.11.0/src/ucm/cuda/Makefile.am 2021-08-09 19:15:22.472286262 +0200 +@@ -9,7 +9,7 @@ + module_LTLIBRARIES = libucm_cuda.la + libucm_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libucm_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) +-libucm_cuda_la_LIBADD = ../libucm.la $(CUDA_LIBS) ++libucm_cuda_la_LIBADD = -lucm $(CUDA_LIBS) + libucm_cuda_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(patsubst %, -Xlinker %, $(CUDA_LDFLAGS)) \ + -version-info $(SOVERSION) +diff -ru ucx-1.11.0.orig/src/uct/cuda/Makefile.am ucx-1.11.0/src/uct/cuda/Makefile.am +--- ucx-1.11.0.orig/src/uct/cuda/gdr_copy/Makefile.am 2021-08-09 19:16:59.146060323 +0200 ++++ ucx-1.11.0/src/uct/cuda/gdr_copy/Makefile.am 2021-08-09 19:17:27.915993083 +0200 +@@ -10,7 +10,7 @@ + libuct_cuda_gdrcopy_la_CFLAGS = $(BASE_CFLAGS) + libuct_cuda_gdrcopy_la_LDFLAGS = $(CUDA_LDFLAGS) $(GDR_COPY_LDFLAGS) \ + -version-info $(SOVERSION) +-libuct_cuda_gdrcopy_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ ++libuct_cuda_gdrcopy_la_LIBADD = -lucs \ + $(top_builddir)/src/uct/cuda/libuct_cuda.la \ + $(CUDA_LIBS) + +diff -ru ucx-1.11.0.orig/src/uct/cuda/gdr_copy/Makefile.am ucx-1.11.0/src/uct/cuda/gdr_copy/Makefile.am +--- ucx-1.11.0.orig/src/uct/cuda/Makefile.am 2021-08-09 19:16:06.472183427 +0200 ++++ ucx-1.11.0/src/uct/cuda/Makefile.am 2021-08-09 19:16:38.201109272 +0200 +@@ -11,8 +11,8 @@ + libuct_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) + libuct_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) + libuct_cuda_la_LDFLAGS = $(CUDA_LDFLAGS) -version-info $(SOVERSION) +-libuct_cuda_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la \ ++libuct_cuda_la_LIBADD = -lucs \ ++ -luct \ + $(CUDA_LIBS) + + noinst_HEADERS = \ + From 7768b1feb2aaa91b8014ed43c75fa3ae764c625f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 9 Aug 2021 19:40:34 +0200 Subject: [PATCH 0769/9987] adding easyconfigs: OpenMPI-4.1.1-GCC-11.2.0.eb, PMIx-4.1.0-GCCcore-11.2.0.eb --- .../o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 42 +++++++++++++++++ .../p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..a702b3a699e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -0,0 +1,42 @@ +name = 'OpenMPI' +version = '4.1.1' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', + 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' +] +checksums = [ + 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 + # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch + 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', + # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch + '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.5.0'), + ('libevent', '2.1.12'), + ('UCX', '1.11.0'), + ('libfabric', '1.13.0'), + ('PMIx', '4.1.0'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f28081b4d11 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '4.1.0' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['145f05a6c621bfb3fc434776b615d7e6d53260cc9ba340a01f55b383e07c842e'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.2.11'), + ('hwloc', '2.5.0'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' From d8e04da700e82e0f22fb6fa47c482b394a96d3c2 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Tue, 10 Aug 2021 11:59:54 +1000 Subject: [PATCH 0770/9987] Create libffcall-2.4-GCCcore-10.2.0.eb New version, new compiler, new binutils --- .../libffcall/libffcall-2.4-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..60a3b0255b4 --- /dev/null +++ b/easybuild/easyconfigs/l/libffcall/libffcall-2.4-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libffcall' +version = '2.4' + +homepage = 'https://www.gnu.org/software/libffcall/' + +description = """ + GNU Libffcall is a collection of four libraries which can be used to build + foreign function call interfaces in embedded interpreters +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8ef69921dbdc06bc5bb90513622637a7b83a71f31f5ba377be9d8fd8f57912c2'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['include/avcall.h', 'include/callback.h', 'include/trampoline.h', + 'include/vacall.h', 'lib/libavcall.a', 'lib/libcallback.a', + 'lib/libtrampoline.a', 'lib/libvacall.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'lib' From 743374d7300d211f74f4145325755c60b0d629ee Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 10 Aug 2021 09:28:04 +0200 Subject: [PATCH 0771/9987] using foss instead of GCC because of dep. on FFTW --- ...-CUDA-11.3.1.eb => ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/ctffind/{ctffind-4.1.14-GCC-10.3.0-CUDA-11.3.1.eb => ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb} (96%) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb similarity index 96% rename from easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-GCC-10.3.0-CUDA-11.3.1.eb rename to easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb index 5b3acc57bbb..cf2a0d71b0f 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb @@ -14,7 +14,7 @@ versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' description = """Program for finding CTFs of electron micrographs.""" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] From e32fb2e4f1eba603765b4deeeaa65fbc353f109a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 9 Aug 2021 16:45:22 +0100 Subject: [PATCH 0772/9987] functions without return should be declared as void in ctffind --- .../c/ctffind/ctffind-4.1.14-foss-2019b.eb | 6 +++- .../ctffind/ctffind-4.1.14-fosscuda-2019b.eb | 6 +++- .../ctffind/ctffind-4.1.14-fosscuda-2020b.eb | 6 +++- .../ctffind-4.1.14_void-functions.patch | 36 +++++++++++++++++++ 4 files changed, 51 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_void-functions.patch diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb index 33e59b6b429..6311b4f1128 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2019b.eb @@ -18,10 +18,14 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_asm-fix.patch'] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] checksums = [ 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb index 4a09018d4d9..2a4f2638a2e 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2019b.eb @@ -18,10 +18,14 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_asm-fix.patch'] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] checksums = [ 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb index 234319daa15..978e186cf1c 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-fosscuda-2020b.eb @@ -18,10 +18,14 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_asm-fix.patch'] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] checksums = [ 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_void-functions.patch b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_void-functions.patch new file mode 100644 index 00000000000..1ac0eb8913d --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14_void-functions.patch @@ -0,0 +1,36 @@ +Change functions with no return from bool to void to prevent a segfault (https://grigoriefflab.umassmed.edu/comment/1696#comment-1696) +Patch added to EasyBuild by Simon Branford (University of Birmingham) +--- src/programs/ctffind/ctffind.cpp.orig 2021-08-09 16:18:25.313802000 +0100 ++++ src/programs/ctffind/ctffind.cpp 2021-08-09 16:19:52.881232575 +0100 +@@ -267,11 +267,11 @@ + float FindRotationalAlignmentBetweenTwoStacksOfImages(Image *self, Image *other_image, int number_of_images, float search_half_range, float search_step_size, float minimum_radius, float maximum_radius); + void ComputeImagesWithNumberOfExtremaAndCTFValues(CTF *ctf, Image *number_of_extrema, Image *ctf_values); + int ReturnSpectrumBinNumber(int number_of_bins, float number_of_extrema_profile[], Image *number_of_extrema, long address, Image *ctf_values, float ctf_values_profile[]); +-bool ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_renormalized[], float number_of_extrema_profile[], float ctf_values_profile[]); ++void ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_renormalized[], float number_of_extrema_profile[], float ctf_values_profile[]); + void ComputeEquiPhaseAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Curve *epa_pre_max, Curve *epa_post_max); + void OverlayCTF( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins_in_1d_spectra, double spatial_frequency[], double rotational_average_astig[], float number_of_extrema_profile[], float ctf_values_profile[], Curve *equiphase_average_pre_max, Curve *equiphase_average_post_max); + void ComputeFRCBetween1DSpectrumAndFit( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[], double frc[], double frc_sigma[], int first_fit_bin); +-bool RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ); ++void RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ); + void Renormalize1DSpectrumForFRC( int number_of_bins, double average[], double fit[], float number_of_extrema_profile[]); + float ReturnAzimuthToUseFor1DPlots(CTF *ctf); + +@@ -2419,7 +2419,7 @@ + + // Rescale the spectrum and its 1D rotational avereage so that the peaks and troughs are at 0.0 and 1.0. The location of peaks and troughs are worked out + // by parsing the suppilied 1D average_fit array +-bool RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ) ++void RescaleSpectrumAndRotationalAverage( Image *spectrum, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], float number_of_extrema_profile[], float ctf_values_profile[], int last_bin_without_aliasing, int last_bin_with_good_fit ) + { + MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated"); + MyDebugAssertTrue(number_of_bins > 1,"Bad number of bins: %i\n",number_of_bins); +@@ -2762,7 +2762,7 @@ + } + + // +-bool ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_rank[], float number_of_extrema_profile[], float ctf_values_profile[]) ++void ComputeRotationalAverageOfPowerSpectrum( Image *spectrum, CTF *ctf, Image *number_of_extrema, Image *ctf_values, int number_of_bins, double spatial_frequency[], double average[], double average_fit[], double average_rank[], float number_of_extrema_profile[], float ctf_values_profile[]) + { + MyDebugAssertTrue(spectrum->is_in_memory, "Spectrum memory not allocated"); + MyDebugAssertTrue(number_of_extrema->is_in_memory,"Number of extrema image not allocated"); From afda908d198266803b7fd384762a467b33823dca Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 10 Aug 2021 09:38:44 +0200 Subject: [PATCH 0773/9987] applied void-functions patch --- .../c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb index cf2a0d71b0f..8a560eca003 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb @@ -19,10 +19,14 @@ toolchainopts = {'openmp': True} source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_asm-fix.patch'] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] checksums = [ 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch ] dependencies = [ From ca314f2db78359b69b41c712be982c3f2c7bf59d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 10 Aug 2021 11:16:51 +0200 Subject: [PATCH 0774/9987] remove separate_build_dir Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-10.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-10.3.0.eb b/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-10.3.0.eb index 3c43c02915c..5605691648e 100644 --- a/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-10.3.0.eb @@ -24,8 +24,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -separate_build_dir = True - sanity_check_paths = { 'files': ['bin/%(name)s'], 'dirs': [] From b7908e58d8f10d4113a0bfbe1c63ac168d70f929 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 Aug 2021 11:44:25 +0200 Subject: [PATCH 0775/9987] Add download_dep_file = True to coverage/5.5 for GCCcore/10.2.0 --- easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb index 441df135abb..9d69f0f5eb8 100644 --- a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.2.0.eb @@ -23,6 +23,7 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True sanity_check_paths = { 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], From c5240aab8e0d823ea28de070bf427472f21652c7 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 10 Aug 2021 11:49:01 +0200 Subject: [PATCH 0776/9987] BeautifulSoup v4.9.3 for GCCcore/10.2.0 --- .../BeautifulSoup-4.9.3-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..7d8438a884b --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.9.3-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.9.3' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35') +] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.2.1', { + 'checksums': ['052774848f448cf19c7e959adf5566904d525f33a3f8b6ba6f6f8f26ec7de0cc'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['84729e322ad1d5b4d25f805bfa05b902dd96450f43842c4e99067d5e1369eb25'], + }), +] + +moduleclass = 'data' From 877fcbf24a9e972b8ae95832e8fa342afcd4782e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 12:26:00 +0200 Subject: [PATCH 0777/9987] adding easyconfigs: Pyomo-6.0.1-foss-2021a.eb --- .../p/Pyomo/Pyomo-6.0.1-foss-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2021a.eb new file mode 100644 index 00000000000..280f7d96ba1 --- /dev/null +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Pyomo' +version = '6.0.1' + +homepage = 'https://www.pyomo.org/' +description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization + capabilities for formulating and analyzing optimization models. """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [('Python', '3.9.5')] + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('PyUtilib', '6.0.0', { + 'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'], + }), + (name, version, { + 'checksums': ['4b27bc917b12a6011e7eb3442a54619f0f42f1087d4defa14b903dd985fdbe7c'], + }), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_commands = ['pyomo -h'] + +moduleclass = 'math' From 94af34a35da8232386a6add27380b0bd2bbef006 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 12:33:54 +0200 Subject: [PATCH 0778/9987] adding easyconfigs: PyPSA-0.17.1-foss-2021a.eb --- .../p/PyPSA/PyPSA-0.17.1-foss-2021a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2021a.eb new file mode 100644 index 00000000000..f66b994f932 --- /dev/null +++ b/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2021a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyPSA' +version = '0.17.1' + +homepage = 'https://pypsa.readthedocs.io/' +description = """PyPSA is an open source toolbox for simulating and optimising modern power systems that include +features such as conventional generators with unit commitment, variable wind and solar generation, storage units, +coupling to other energy sectors, and mixed alternating and direct current networks. PyPSA is designed to scale +well with large networks and long time series.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'PyPSA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['47811fc24b2daf663a2bb86749235e03e9988c7604a4d7fea48fbc8d9b4431c9'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('networkx', '2.5.1'), + ('PyTables', '3.6.1'), + ('Pyomo', '6.0.1'), + ('netCDF', '4.8.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'phys' From 51c93ef6f085486bc05b54c03b3620ee690cacc8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 12:36:29 +0200 Subject: [PATCH 0779/9987] Drop download_dep_fail --- easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2021a.eb index 280f7d96ba1..d3869bc4a6d 100644 --- a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2021a.eb @@ -27,7 +27,6 @@ exts_list = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True sanity_check_commands = ['pyomo -h'] From 154e1824f9ff3501f32f0d6045fa0b0c4938b1fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Aug 2021 12:41:37 +0200 Subject: [PATCH 0780/9987] add lwgeom extension to R 4.1.0 easyconfig --- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index 1fa9d01d249..e6a51010b23 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -2978,6 +2978,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('lwgeom', '0.2-7', { + 'checksums': ['b34c155f3d7c4535ef3d02e3381b05a57990d19b3b1ec09a7458c101f8fafae1'], + }), ] moduleclass = 'lang' From c27d2a3933c46120f5ae00d00593abea526a6dbb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 13:37:12 +0200 Subject: [PATCH 0781/9987] Update easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb index f28081b4d11..d36693b0c91 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb @@ -34,6 +34,7 @@ dependencies = [ configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' configopts += ' --with-hwloc=$EBROOTHWLOC' configopts += ' --enable-pmix-binaries' +configopts += ' --disable-man-pages' buildopts = 'V=1' From 5694512c492d6b7992ea09114f759342e4085c14 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Tue, 10 Aug 2021 13:50:14 +0200 Subject: [PATCH 0782/9987] adding easyconfigs: RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb --- .../RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb new file mode 100644 index 00000000000..a853e77a979 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2020b-hybrid-avx2.eb @@ -0,0 +1,38 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.12' +versionsuffix = '-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105'] + +buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +moduleclass = 'bio' From b4cfde2d7342ecd228ca1d99ec45ca74393421ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 14:30:27 +0200 Subject: [PATCH 0783/9987] adding easyconfigs: libsodium-1.0.18-GCCcore-11.2.0.eb, OpenPGM-5.2.122-GCCcore-11.2.0.eb, ZeroMQ-4.3.4-GCCcore-11.2.0.eb, IPython-7.26.0-GCCcore-11.2.0.eb --- .../IPython/IPython-7.26.0-GCCcore-11.2.0.eb | 163 ++++++++++++++++++ .../libsodium-1.0.18-GCCcore-11.2.0.eb | 33 ++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-11.2.0.eb | 45 +++++ .../z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.2.0.eb | 38 ++++ 4 files changed, 279 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..86c05a433f2 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb @@ -0,0 +1,163 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '7.26.0' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('ZeroMQ', '4.3.4'), +] + +use_pip = True + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['0cff04bb042800129348701f7bd68a430a844e8fb193979c08f6c99f28bb735e'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '3.0.19', { + 'checksums': ['08360ee3a3148bdb5163621709ee322ec34fc4375099afa4bbf751e9b7b7fa4f'], + }), + ('traitlets', '5.0.5', { + 'checksums': ['178f4ce988f69189f7e523337a3e11d91c786ded9360174a3d9ca83e79bc5396'], + }), + ('parso', '0.8.2', { + 'checksums': ['12b83492c6239ce32ff5eed6d3639d6a536170723c6f3f1506869f1ace413398'], + }), + ('jedi', '0.18.0', { + 'checksums': ['92550a404bad8afed881a137ec9a461fed49eca661414be45059329614ed0707'], + }), + ('testpath', '0.5.0', { + 'use_pip': False, + 'checksums': ['1acf7a0bcd3004ae8357409fc33751e16d37ccc650921da1094a86581ad1e417'], + }), + ('Send2Trash', '1.8.0', { + 'checksums': ['d2c24762fd3759860a0aff155e45871447ea58d2be6bdd39b5c8f966a0c99c2d'], + }), + ('bleach', '4.0.0', { + 'checksums': ['ffa9221c6ac29399cc50fcc33473366edd0cf8d5e2cbbbb63296dc327fb67cc8'], + }), + ('pandocfilters', '1.4.3', { + 'checksums': ['bc63fbb50534b4b1f8ebe1860889289e8af94a23bff7445259592df25a3906eb'], + }), + ('pyzmq', '22.2.1', { + 'modulename': 'zmq', + 'checksums': ['6d18c76676771fd891ca8e0e68da0bbfb88e30129835c0ade748016adb3b6242'], + }), + ('entrypoints', '0.3', { + 'use_pip': False, + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('jupyter_core', '4.7.1', { + 'checksums': ['79025cb3225efcd36847d0840f3fc672c0abd7afd0de83ba8a1d3837619122b4'], + }), + ('nbformat', '5.1.3', { + 'checksums': ['b516788ad70771c6250977c1374fcca6edebe6126fd2adb5a69aa5c2356fd1c8'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('nest_asyncio', '1.5.1', { + 'checksums': ['afc5a1c515210a23c461932765691ad39e8eba6551c055ac8d5546e69250d0aa'], + }), + ('nbclient', '0.5.3', { + 'checksums': ['db17271330c68c8c88d46d72349e24c147bb6f34ec82d8481a8f025c4d26589c'], + }), + ('nbconvert', '6.1.0', { + 'checksums': ['d22a8ff202644d31db254d24d52c3a96c82156623fcd7c7f987bba2612303ec9'], + }), + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('terminado', '0.10.1', { + 'checksums': ['89d5dac2f4e2b39758a0ff9a3b643707c95a020a6df36e70583b88297cd59cbe'], + }), + ('jupyter_client', '6.1.12', { + 'checksums': ['c4bca1d0846186ca8be97f4d2fa6d2bae889cce4892a167ffa1ba6bd1f73e782'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('ipykernel', '6.0.3', { + 'checksums': ['0df34a78c7e1422800d6078cde65ccdcdb859597046c338c759db4dbc535c58f'], + }), + ('prometheus_client', '0.11.0', { + 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], + }), + ('ipywidgets', '7.6.3', { + 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.10.4', { + 'checksums': ['589db027cb85a92612f9bcfaeecaa8a9072ac8a4bddaf827f648664258e587c4'], + }), + ('jupyterlab_widgets', '1.0.0', { + 'checksums': ['5c1a29a84d3069208cb506b10609175b249b6486d6b1cbae8fcde2a11584fb78'], + }), + ('argon2-cffi', '20.1.0', { + 'modulename': 'argon2', + 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], + }), + ('notebook', '6.4.0', { + 'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + ('matplotlib-inline', '0.1.2', { + 'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'], + }), + ('debugpy', '1.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['84ff51b8b5c847d5421324ca419db1eec813a4dd2bbf19dbbbe132e2ab2b2fc6'], + }), +] + +modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/IPython', + 'share/jupyter' + ], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "NOSE_EXCLUDE='system_interrupt' iptest", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7b5cad31e15 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.37'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1aff357627c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + 'OpenPGM-5.2.122-pkgconfig_includes.patch', + 'OpenPGM-5.2.122-python3-compliant.patch' +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c649a3d7be3 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.4' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.37'), +] + +configopts = '--with-pic --with-pgm --with-libsodium ' + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From 0311ff703242260ee3912d556888179dc1636724 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 14:32:56 +0200 Subject: [PATCH 0784/9987] adding easyconfigs: googletest-1.11.0-GCCcore-11.2.0.eb --- .../googletest-1.11.0-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.11.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.11.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.11.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..dee6a5104d1 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.11.0-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.11.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['b4870bf121ff7795ba20d20bcdd8627b8e088f2d1dab299a031c1034eddc93d5'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' From f29a5e12ec15482ca634f5236c7322a19b64ff22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 14:36:34 +0200 Subject: [PATCH 0785/9987] adding easyconfigs: scikit-build-0.11.1-GCCcore-11.2.0.eb --- .../scikit-build-0.11.1-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-GCCcore-11.2.0.eb new file mode 100755 index 00000000000..98a7716c214 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.11.1-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.11.1' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('distro', '1.6.0', { + 'checksums': ['83f5e5a09f9c5f68f60173de572930effbcc0287bb84fdc4426cb4168c088424'], + }), + (name, version, { + 'modulename': 'skbuild', + 'checksums': ['da40dfd69b2456fad1349a894b90180b43712152b8a85d2a00f4ae2ce8ac9a5c'], + }), +] + +moduleclass = 'lib' From e7c7ec316e0216b77af73bbce59edcd775f7a7be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 14:51:29 +0200 Subject: [PATCH 0786/9987] adding easyconfigs: pybind11-2.7.1-GCCcore-11.2.0.eb --- .../pybind11/pybind11-2.7.1-GCCcore-11.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b04d5c7b9b4 --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0.eb @@ -0,0 +1,23 @@ +name = 'pybind11' +version = '2.7.1' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['616d1c42e4cf14fa27b2a4ff759d7d7b33006fdc5ad8fd603bb2c22622f27020'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Eigen', '3.3.9'), +] +dependencies = [('Python', '3.9.6')] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +moduleclass = 'lib' From 006ef3275c8b2db745b32d4dbd42f23db3ce9371 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 14:55:17 +0200 Subject: [PATCH 0787/9987] adding easyconfigs: hypothesis-6.14.6-GCCcore-11.2.0.eb --- .../hypothesis-6.14.6-GCCcore-11.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-6.14.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.14.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.14.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c0818d95bc7 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.14.6-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '6.14.6' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2586eae07e48b35ab5a2d61d607d29ba76939ce140c427d66ccf5db4ddc788d2'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 70f410d25084e78b8e0675c85a8a919dca0f69d1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 16:24:19 +0200 Subject: [PATCH 0788/9987] adding easyconfigs: xarray-0.19.0-foss-2021a.eb --- .../x/xarray/xarray-0.19.0-foss-2021a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.19.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.19.0-foss-2021a.eb b/easybuild/easyconfigs/x/xarray/xarray-0.19.0-foss-2021a.eb new file mode 100644 index 00000000000..e31f5604cf3 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.19.0-foss-2021a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.19.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3a365ce09127fc841ba88baa63f37ca61376ffe389a6c5e66d52f2c88c23a62b'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From 076e7f4bd1a65d098e99d4438c33610ec2958d66 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 16:35:07 +0200 Subject: [PATCH 0789/9987] adding easyconfigs: plotly.py-5.1.0-GCCcore-10.3.0.eb --- .../plotly.py-5.1.0-GCCcore-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/plotly.py/plotly.py-5.1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..131ae94a737 --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '5.1.0' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [('Python', '3.9.5')] + +use_pip = True + +exts_list = [ + ('retrying', '1.3.3', { + 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], + }), + ('plotly', version, { + 'checksums': ['71f6744acdc524c22236c226d7cf1072d1a58ebacaf749c640998298472c8c44'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From b39c31912bc4ae0c9c32570652dd6ffd240ad64f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 16:56:52 +0200 Subject: [PATCH 0790/9987] Drop Werror on zeromq --- easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.2.0.eb index c649a3d7be3..64d3fe78fcb 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.2.0.eb @@ -28,7 +28,9 @@ dependencies = [ ('util-linux', '2.37'), ] -configopts = '--with-pic --with-pgm --with-libsodium ' +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = '--with-pic --with-pgm --with-libsodium --disable-Werror' sanity_check_paths = { 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], From a4b794a3281bffea7e9591f87a65f1c35be3495c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 10 Aug 2021 16:20:52 +0100 Subject: [PATCH 0791/9987] Build with EGL --- .../easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb | 2 +- .../easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb index 2bf072bd402..023da3d66a9 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('Mesa', '20.2.1'), ] -configopts = '-Degl=no --libdir %(installdir)s/lib ' +configopts = '-Degl=yes --libdir %(installdir)s/lib ' sanity_check_paths = { 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb index 012b599c942..7ceeb942e26 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('Mesa', '19.1.7'), ] -configopts = '-Degl=no --libdir %(installdir)s/lib ' +configopts = '-Degl=yes --libdir %(installdir)s/lib ' sanity_check_paths = { 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb index a99cf9d51f7..098cbf52a55 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('Mesa', '20.0.2'), ] -configopts = '-Degl=no --libdir %(installdir)s/lib ' +configopts = '-Degl=yes --libdir %(installdir)s/lib ' sanity_check_paths = { 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb index f5cd050faa3..3dff9284c3f 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('Mesa', '21.1.1'), ] -configopts = '-Degl=no --libdir %(installdir)s/lib ' +configopts = '-Degl=yes --libdir %(installdir)s/lib ' sanity_check_paths = { 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + From 23e95955bc042e52e64e5cc183f0166d3bd843ae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 18:33:08 +0200 Subject: [PATCH 0792/9987] adding easyconfigs: netcdf4-python-1.5.5.1-foss-2020b.eb, netcdf4-python-1.5.7-foss-2021a.eb --- .../netcdf4-python-1.5.5.1-foss-2020b.eb | 51 +++++++++++++++++++ .../netcdf4-python-1.5.7-foss-2021a.eb | 51 +++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb new file mode 100644 index 00000000000..58f903e1814 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.5.1-foss-2020b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.5.5.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('netCDF', '4.7.4'), + ('cURL', '7.72.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.4.1', { + 'checksums': ['7c55540bc164746c3c4f86a07c9c7b9ed4dfb0b0d988348ec63cec065c58766d'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'checksums': [ + 'd957e55a667d1fc651ddef22fea10ded0f142b7d9dbbf4d08c0012d32f445abd', # netCDF4-1.5.5.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-foss-2021a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-foss-2021a.eb new file mode 100644 index 00000000000..086e8da2d67 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-foss-2021a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.5.7' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('netCDF', '4.8.0'), + ('cURL', '7.76.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.5.0', { + 'checksums': ['b644bcb53346b6f4fe2fcc9f3b574740a2097637492dcca29632c817e0604f29'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'd145f9c12da29da3922d8b8aafea2a2a89501bcb28a219a46b7b828b57191594', # netCDF4-1.5.7.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' From 9beb091341f52fc62d24337f99027ea050d50bc6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 18:43:23 +0200 Subject: [PATCH 0793/9987] adding easyconfigs: openpyxl-3.0.7-GCCcore-10.3.0.eb, openpyxl-3.0.7-GCCcore-10.2.0.eb --- .../openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ .../openpyxl/openpyxl-3.0.7-GCCcore-10.3.0.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0ce06b699c7 --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.0.7' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('lxml', '4.6.2'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('et_xmlfile', '1.1.0', { + 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['6456a3b472e1ef0facb1129f3c6ef00713cebf62e736cd7a75bcc3247432f251'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d7a7f7f7663 --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.7-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.0.7' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('lxml', '4.6.3'), + ('Pillow', '8.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('et_xmlfile', '1.1.0', { + 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['6456a3b472e1ef0facb1129f3c6ef00713cebf62e736cd7a75bcc3247432f251'], + }), +] + +moduleclass = 'data' From 25466fd093df1ab21f799d5e32c088a5dfca0c25 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 18:47:55 +0200 Subject: [PATCH 0794/9987] adding easyconfigs: pandapower-2.7.0-foss-2020b.eb --- .../pandapower/pandapower-2.7.0-foss-2020b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb new file mode 100644 index 00000000000..8aefe245c9f --- /dev/null +++ b/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'pandapower' +version = '2.7.0' + +homepage = 'http://www.pandapower.org/' +description = """An easy to use open source tool for power system modeling, analysis and optimization with a high +degree of automation""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_ZIP] +checksums = ['abd64ade5bbaa107df2f5b69769ac7747c1190c7c8b7a03d83ef3a14da29f1cd'], + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), + ('XlsxWriter', '1.4.0'), + ('openpyxl', '3.0.7'), +] + +runtest = 'pytest' + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From b4f5238a1d17cd074379edd9ef01ffe2f1475297 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 19:52:01 +0200 Subject: [PATCH 0795/9987] adding easyconfigs: xarray-0.16.2-foss-2020b.eb --- .../x/xarray/xarray-0.16.2-foss-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb new file mode 100644 index 00000000000..e3caa965c46 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.16.2-foss-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.16.2' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['38e8439d6c91bcd5b7c0fca349daf8e0643ac68850c987262d53526e9d7d01e4'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'data' From a1f9599bb4843919f0211af26a746e4ddf9f69f2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 20:09:46 +0200 Subject: [PATCH 0796/9987] Drop extra comma --- .../easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb index 8aefe245c9f..b7d9b8c9208 100644 --- a/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pandapower/pandapower-2.7.0-foss-2020b.eb @@ -10,7 +10,7 @@ degree of automation""" toolchain = {'name': 'foss', 'version': '2020b'} sources = [SOURCE_ZIP] -checksums = ['abd64ade5bbaa107df2f5b69769ac7747c1190c7c8b7a03d83ef3a14da29f1cd'], +checksums = ['abd64ade5bbaa107df2f5b69769ac7747c1190c7c8b7a03d83ef3a14da29f1cd'] dependencies = [ ('Python', '3.8.6'), From 40a3c9973af4e3cfb2a3961e3754c905ab54e57c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 10 Aug 2021 19:13:02 +0100 Subject: [PATCH 0797/9987] Enhance sanity check --- .../libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb | 3 +- .../libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb | 36 ------------------- .../libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb | 3 +- .../libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb | 3 +- 4 files changed, 6 insertions(+), 39 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb index 023da3d66a9..a1bd6be54fb 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb @@ -28,7 +28,8 @@ dependencies = [ configopts = '-Degl=yes --libdir %(installdir)s/lib ' sanity_check_paths = { - 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + ['lib/libepoxy.%s' % SHLIB_EXT], 'dirs': ['lib'] } diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb deleted file mode 100644 index 7ceeb942e26..00000000000 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'libepoxy' -version = '1.5.4' - -homepage = 'https://github.com/anholt/libepoxy' -description = "Epoxy is a library for handling OpenGL function pointer management for you" - -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} - -github_account = 'anholt' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['c926fcc606901f3e03e371027056fd478da43e01ce2da7ffc48b5a0de0ca107c'] - -builddependencies = [ - ('binutils', '2.32'), - ('Meson', '0.51.2', '-Python-3.7.4'), - ('Ninja', '1.9.0'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('X11', '20190717'), - ('Mesa', '19.1.7'), -] - -configopts = '-Degl=yes --libdir %(installdir)s/lib ' - -sanity_check_paths = { - 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + - ['lib/libepoxy.%s' % SHLIB_EXT], - 'dirs': ['lib'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb index 098cbf52a55..988a8d4fc3f 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-9.3.0.eb @@ -28,7 +28,8 @@ dependencies = [ configopts = '-Degl=yes --libdir %(installdir)s/lib ' sanity_check_paths = { - 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + ['lib/libepoxy.%s' % SHLIB_EXT], 'dirs': ['lib'] } diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb index 3dff9284c3f..8e6f416421b 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-10.3.0.eb @@ -28,7 +28,8 @@ dependencies = [ configopts = '-Degl=yes --libdir %(installdir)s/lib ' sanity_check_paths = { - 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + ['lib/libepoxy.%s' % SHLIB_EXT], 'dirs': ['lib'] } From f2ce7b902eca354cb8b12f9c50f96185961f1585 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 23:28:04 +0200 Subject: [PATCH 0798/9987] adding easyconfigs: PYPOWER-5.1.15-foss-2020b.eb --- .../p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb b/easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb new file mode 100644 index 00000000000..966cf0a6e70 --- /dev/null +++ b/easybuild/easyconfigs/p/PYPOWER/PYPOWER-5.1.15-foss-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'PYPOWER' +version = '5.1.15' + +homepage = 'https://github.com/rwl/PYPOWER' +description = """PYPOWER is a power flow and Optimal Power Flow (OPF) solver. It is a port of MATPOWER to the Python +programming language.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d01e40f1850937e1a4e34ab3c7aa5c76006b23d4cc8a547818b26a808303c8a8'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From ce4d1c5d7ca914a871abb28f28760694627f4cff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 23:42:27 +0200 Subject: [PATCH 0799/9987] adding easyconfigs: Shapely-1.8a1-GCC-10.2.0.eb --- .../s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb new file mode 100644 index 00000000000..cac4a8093fe --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-GCC-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '1.8a1' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a748ab74c187060264e7ce838aaac30eead2a791bbea8cc3ab1dfc3cc0b4d067'] + +dependencies = [ + ('Python', '3.8.6'), + ('GEOS', '3.9.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From 1cfb0239d3069f6507b4fcdb1e8205952547fa1c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 10 Aug 2021 23:59:22 +0200 Subject: [PATCH 0800/9987] Fix new dep --- .../easyconfigs/p/plotly.py/plotly.py-5.1.0-GCCcore-10.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.1.0-GCCcore-10.3.0.eb index 131ae94a737..8c791642cf0 100644 --- a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.1.0-GCCcore-10.3.0.eb @@ -17,8 +17,8 @@ dependencies = [('Python', '3.9.5')] use_pip = True exts_list = [ - ('retrying', '1.3.3', { - 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], + ('tenacity', '8.0.1', { + 'checksums': ['43242a20e3e73291a28bcbcacfd6e000b02d3857a9a9fff56b297a27afdc932f'], }), ('plotly', version, { 'checksums': ['71f6744acdc524c22236c226d7cf1072d1a58ebacaf749c640998298472c8c44'], From d4c6d3fefd3547f0420b24b888b4aa451ad9bd6a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Aug 2021 01:06:42 +0200 Subject: [PATCH 0801/9987] adding easyconfigs: pyshp-2.1.3-GCCcore-10.2.0.eb --- .../p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..2abf70d7bd1 --- /dev/null +++ b/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'pyshp' +version = '2.1.3' + +homepage = 'https://github.com/GeospatialPython/pyshp' +description = """Pure Python read/write support for ESRI Shapefile format""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'GeospatialPython' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b9c5420a013ae04b81306d36435d42fb78d336a36dd18c31e1b365c18e319e05'] + +dependencies = [ + ('Python', '3.8.6'), + ('cURL', '7.72.0'), +] + +options = {'modulename': 'shapefile'} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From af947fdc2c1dad9cf92fa27118080b07e023a81e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Aug 2021 02:00:50 +0200 Subject: [PATCH 0802/9987] Fix binutils dep --- easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb index 2abf70d7bd1..96e075cd30d 100644 --- a/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pyshp/pyshp-2.1.3-GCCcore-10.2.0.eb @@ -13,6 +13,10 @@ source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] checksums = ['b9c5420a013ae04b81306d36435d42fb78d336a36dd18c31e1b365c18e319e05'] +builddependencies = [ + ('binutils', '2.35'), +] + dependencies = [ ('Python', '3.8.6'), ('cURL', '7.72.0'), From 22a0dbda4159f55716cf85637055604b799ce73f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Aug 2021 02:13:46 +0200 Subject: [PATCH 0803/9987] adding easyconfigs: Clp-1.17.6-foss-2020b.eb, Cgl-0.60.3-foss-2020b.eb, Cbc-2.10.5-foss-2020b.eb, CoinUtils-2.11.4-GCCcore-10.2.0.eb, Osi-0.108.6-GCCcore-10.2.0.eb --- .../c/Cbc/Cbc-2.10.5-foss-2020b.eb | 63 +++++++++++++++++++ .../c/Cgl/Cgl-0.60.3-foss-2020b.eb | 50 +++++++++++++++ .../c/Clp/Clp-1.17.6-foss-2020b.eb | 55 ++++++++++++++++ .../CoinUtils-2.11.4-GCCcore-10.2.0.eb | 38 +++++++++++ .../o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb | 50 +++++++++++++++ 5 files changed, 256 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb new file mode 100644 index 00000000000..427e25ee824 --- /dev/null +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2020b.eb @@ -0,0 +1,63 @@ +easyblock = "ConfigureMake" + +name = 'Cbc' +version = '2.10.5' + +homepage = "https://github.com/coin-or/Cbc" +description = """Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming +solver written in C++. It can be used as a callable library or using a +stand-alone executable.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['da1a945648679b21ba56b454b81e939451dc7951d9beb3c3e14f18f64dde6972'] + +builddependencies = [ + ('Autotools', '20200321'), + ('Doxygen', '1.8.20'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.3.5', '-metis'), + ('CoinUtils', '2.11.4'), + ('Osi', '0.108.6'), + ('Clp', '1.17.6'), + ('Cgl', '0.60.3'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# Use BLAS/LAPACK from OpenBLAS +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +# Use METIS AND MUMPS from EB +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +# Disable GLPK, dependencies have to be built with it as well +configopts += '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' +# Use Cgl from EB +configopts += '--with-cgl-lib="-lCgl" ' +configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb new file mode 100644 index 00000000000..e9e8533a7cc --- /dev/null +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2020b.eb @@ -0,0 +1,50 @@ +easyblock = "ConfigureMake" + +name = 'Cgl' +version = '0.60.3' + +homepage = "https://github.com/coin-or/Cgl" +description = """The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that +can be used with other COIN-OR packages that make use of cuts, such as, among +others, the linear solver Clp or the mixed integer linear programming solvers +Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or +communicate with a solver. It does not directly call a solver.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['cf11e3476d2182040cec412abb232d8bafa12ff5b619eca3b7b9ac1d220476c8'] + +builddependencies = [ + ('Autotools', '20200321'), + ('Doxygen', '1.8.20'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CoinUtils', '2.11.4'), + ('Osi', '0.108.6'), + ('Clp', '1.17.6'), +] + +# Use CoinUtils from EB +configopts = '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['lib/libCgl.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb new file mode 100644 index 00000000000..4a649579d28 --- /dev/null +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2020b.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'Clp' +version = '1.17.6' + +homepage = "https://github.com/coin-or/Clp" +description = """Clp (Coin-or linear programming) is an open-source linear programming solver. +It is primarily meant to be used as a callable library, but a basic, +stand-alone executable version is also available.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['f9cfcdd3db23bbc2d18b562012a7e25b99a40e8ce72dc296bd46dddb2970e12a'] + +builddependencies = [ + ('Autotools', '20200321'), + ('Doxygen', '1.8.20'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.3.5', '-metis'), + ('CoinUtils', '2.11.4'), + ('Osi', '0.108.6'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# Use BLAS/LAPACK from OpenBLAS +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +# Use METIS AND MUMPS from EB +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +# Disable GLPK because Clp requires headers from its sources +configopts += '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Osi from EB +configopts += '--with-osi-lib="-lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['Clp', 'ClpSolver', 'OsiClp']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..ebc08762adc --- /dev/null +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = "ConfigureMake" + +name = 'CoinUtils' +version = '2.11.4' + +homepage = "https://github.com/coin-or/CoinUtils" +description = """CoinUtils (Coin-OR Utilities) is an open-source collection of classes and +functions that are generally useful to more than one COIN-OR project.""" + + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['1b24f8f6057661b3225d24f4e671527f53bf13aff66e06cbbbd4f20cc7d31dce'] + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('Doxygen', '1.8.20'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/libCoinUtils.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6b7abcdbec6 --- /dev/null +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +easyblock = "ConfigureMake" + +name = 'Osi' +version = '0.108.6' + +homepage = "https://github.com/coin-or/Osi" +description = """Osi (Open Solver Interface) provides an abstract base class to a generic linear +programming (LP) solver, along with derived classes for specific solvers. Many +applications may be able to use the Osi to insulate themselves from a specific +LP solver. That is, programs written to the OSI standard may be linked to any +solver with an OSI interface and should produce correct results. The OSI has +been significantly extended compared to its first incarnation. Currently, the +OSI supports linear programming solvers and has rudimentary support for integer +programming.""" + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['57ef3f0c97995bac647504aee0ed34d31f79033ece04cd2cb86b4645f0a552d8'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('Doxygen', '1.8.20'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CoinUtils', '2.11.4'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# Disable GLPK because Osi requires GLPK<=4.48 +configopts = '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + +sanity_check_paths = { + 'files': ['lib/libOsi.%s' % SHLIB_EXT, 'lib/libOsiCommonTests.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" From 32ef85d16564d6477a43713dfe16eca1fd37333a Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Wed, 11 Aug 2021 16:22:30 +1000 Subject: [PATCH 0804/9987] Create shrinkwrap-1.1.0-GCCcore-10.2.0.eb New version, new compiler, new binutils, new dependencies etc. --- .../shrinkwrap-1.1.0-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a9387c69f64 --- /dev/null +++ b/easybuild/easyconfigs/s/shrinkwrap/shrinkwrap-1.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' + +name = 'shrinkwrap' +version = '1.1.0' + +homepage = "https://github.com/jonathonl/shrinkwrap" +description = """A std::streambuf wrapper for compression formats.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/jonathonl/shrinkwrap/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['833e85bdc41e7bf82a57f0fb52958795fb089f691981d2e3a2b68eee17128082'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('XZ', '5.2.5'), + ('zstd', '1.4.5'), +] + +sanity_check_paths = { + 'files': ['include/%%(name)s/%s.hpp' % i for i in ['gz', 'istream', 'xz', 'zstd']], + 'dirs': [], +} + +moduleclass = 'data' From e54a05967115d7bc141c45dc270d705dfde96f96 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 11 Aug 2021 09:37:21 +0100 Subject: [PATCH 0805/9987] Reinstate original libepoxy w/GCCcore-8.3.0 --- .../libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..012b599c942 --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.4' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['c926fcc606901f3e03e371027056fd478da43e01ce2da7ffc48b5a0de0ca107c'] + +builddependencies = [ + ('binutils', '2.32'), + ('Meson', '0.51.2', '-Python-3.7.4'), + ('Ninja', '1.9.0'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20190717'), + ('Mesa', '19.1.7'), +] + +configopts = '-Degl=no --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' From ae8acc7e61281e623fd8c93328a69dd79cfb73f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Aug 2021 11:02:31 +0200 Subject: [PATCH 0806/9987] adding easyconfigs: Dsuite-20210718-intel-compilers-2021.2.0.eb, Dsuite-20210718-GCC-10.3.0.eb --- .../d/Dsuite/Dsuite-20210718-GCC-10.3.0.eb | 29 +++++++++++++++++++ ...suite-20210718-intel-compilers-2021.2.0.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dsuite/Dsuite-20210718-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/d/Dsuite/Dsuite-20210718-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/d/Dsuite/Dsuite-20210718-GCC-10.3.0.eb b/easybuild/easyconfigs/d/Dsuite/Dsuite-20210718-GCC-10.3.0.eb new file mode 100644 index 00000000000..0fbc9622260 --- /dev/null +++ b/easybuild/easyconfigs/d/Dsuite/Dsuite-20210718-GCC-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'Dsuite' +version = '20210718' +local_commit = 'fd29369' + +homepage = 'https://github.com/millanek/Dsuite' +description = "Fast calculation of the ABBA-BABA statistics across many populations/species" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/millanek/Dsuite/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['4d56adf47119c0df6187a5372b9c2c2fed8da2b549af394c40e6edc0d76d7e8e'] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +files_to_copy = [(['Build/Dsuite'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Dsuite'], + 'dirs': [], +} + +sanity_check_commands = ["Dsuite --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/Dsuite/Dsuite-20210718-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/d/Dsuite/Dsuite-20210718-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..d5afc5d392d --- /dev/null +++ b/easybuild/easyconfigs/d/Dsuite/Dsuite-20210718-intel-compilers-2021.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'Dsuite' +version = '20210718' +local_commit = 'fd29369' + +homepage = 'https://github.com/millanek/Dsuite' +description = "Fast calculation of the ABBA-BABA statistics across many populations/species" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://github.com/millanek/Dsuite/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['4d56adf47119c0df6187a5372b9c2c2fed8da2b549af394c40e6edc0d76d7e8e'] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +files_to_copy = [(['Build/Dsuite'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Dsuite'], + 'dirs': [], +} + +sanity_check_commands = ["Dsuite --help"] + +moduleclass = 'bio' From 4fd729c2278fe3f0b82cb1dd172365c26d496e1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Aug 2021 11:20:12 +0200 Subject: [PATCH 0807/9987] adding easyconfigs: rgeos-0.5-5-foss-2021a-R-4.1.0.eb, rgdal-1.5-23-foss-2021a-R-4.1.0.eb, spatialreg-1.1-8-foss-2021a-R-4.1.0.eb --- .../rgdal/rgdal-1.5-23-foss-2021a-R-4.1.0.eb | 32 +++++++++++ .../r/rgeos/rgeos-0.5-5-foss-2021a-R-4.1.0.eb | 30 ++++++++++ .../spatialreg-1.1-8-foss-2021a-R-4.1.0.eb | 55 +++++++++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/r/rgdal/rgdal-1.5-23-foss-2021a-R-4.1.0.eb create mode 100644 easybuild/easyconfigs/r/rgeos/rgeos-0.5-5-foss-2021a-R-4.1.0.eb create mode 100644 easybuild/easyconfigs/s/spatialreg/spatialreg-1.1-8-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/r/rgdal/rgdal-1.5-23-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/rgdal/rgdal-1.5-23-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..5946db654fa --- /dev/null +++ b/easybuild/easyconfigs/r/rgdal/rgdal-1.5-23-foss-2021a-R-4.1.0.eb @@ -0,0 +1,32 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'RPackage' + +name = 'rgdal' +version = '1.5-23' +versionsuffix = '-R-%(rver)s' + +homepage = "https://rgdal.r-forge.r-project.org/" +description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and + access to projection/transformation operations from the 'PROJ.4' library.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['9ca5744b946e7a3c4ca26598612bf54e550d3a0c5811d56e22c30b73f83ccb6e'] + +dependencies = [ + ('R', '4.1.0'), + ('GDAL', '3.3.0'), +] + +sanity_check_paths = { + 'files': ['rgdal/R/rgdal'], + 'dirs': [], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rgeos/rgeos-0.5-5-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/rgeos/rgeos-0.5-5-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..0d64b41bc09 --- /dev/null +++ b/easybuild/easyconfigs/r/rgeos/rgeos-0.5-5-foss-2021a-R-4.1.0.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'rgeos' +version = '0.5-5' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rgeos/' +description = """R interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations + on geometries""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['4baa0dfe6ff76e87ddb67a030fc14fe963d28b518485a4d71058923b2606d420'] + +dependencies = [ + ('R', '4.1.0'), + ('GEOS', '3.9.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/spatialreg/spatialreg-1.1-8-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/s/spatialreg/spatialreg-1.1-8-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..913c5426184 --- /dev/null +++ b/easybuild/easyconfigs/s/spatialreg/spatialreg-1.1-8-foss-2021a-R-4.1.0.eb @@ -0,0 +1,55 @@ +# This easyconfig was created by James Carpenter of the BEAR Software team at the University of Birmingham. +easyblock = 'Bundle' + +name = 'spatialreg' +version = '1.1-8' +versionsuffix = '-R-%(rver)s' + +homepage = "https://cran.r-project.org/package=%(name)s" +description = """A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal + data using spatial weights matrices) contained up to now in 'spdep', 'sphet' and 'spse'.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('R', '4.1.0'), + ('GDAL', '3.3.0'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('wk', '0.5.0', { + 'checksums': ['71d500e0beaeed40501702adf214054d30278acb3171af6db4ae8dcdf5e7423a'], + }), + ('s2', '1.0.6', { + 'checksums': ['a6cc4ebf1e1c00abb632a324cd29e4ae061898b16bab46296e2081baee12a4f5'], + }), + ('sf', '1.0-2', { + 'checksums': ['ec850886ce61bbca5785a75ab4e99ac8b5aa0e2e776421fbcf5c3ee2f2240542'], + }), + ('spdep', version, { + 'checksums': ['f4403c2712d36518fb6c8ce4b73e47d43987079302f7cb1e77c0de894adf02cd'], + }), + (name, version, { + 'checksums': ['42f79661128758bcfa3a07a830d475c13b916b5a49af41648d5a9d15ffb1ae10'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': ['spatialreg/R/spatialreg'], + 'dirs': [], +} + +moduleclass = 'math' From b299961c9c8d61600a60dfc491c392ca43b595d8 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 11 Aug 2021 11:27:32 +0200 Subject: [PATCH 0808/9987] adding easyconfigs: imkl-2020.4.304-gompic-2020b.eb --- .../i/imkl/imkl-2020.4.304-gompic-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb new file mode 100644 index 00000000000..e07323d8ee3 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-gompic-2020b.eb @@ -0,0 +1,26 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.4.304' + +homepage = 'https://software.intel.com/mkl' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] + +dontcreateinstalldir = True + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +moduleclass = 'numlib' From 7d419d4d7c8e26c5484170a8f7db1b5e21357503 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 11 Aug 2021 11:28:34 +0200 Subject: [PATCH 0809/9987] adding easyconfigs: PyTorch-1.9.0-fosscuda-2020b-imkl.eb --- .../PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 129 ++++++++++++++++++ 1 file changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb new file mode 100644 index 00000000000..feaef854fa2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -0,0 +1,129 @@ +name = 'PyTorch' +version = '1.9.0' +versionsuffix = '-imkl' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_fix-arange-on-VSX.patch', + 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', + 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', + 'PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch', + 'PyTorch-1.9.0_fix-testnn-on-A100.patch', + 'PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', + 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', + 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', + 'PyTorch-1.9.0_skip-nccl-error-tests.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch + # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch + '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch + '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', + # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch + 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', + # PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch + 'edb180d6967c507c147400a64422ff4499bcd5519f9be8d332890c317359dbad', + '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch + # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch + '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', + '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + # PyTorch-1.9.0_increase-test-cuda-tolerance.patch + '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', + # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch + '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.9.0_skip-lstm-serialization-test.patch + '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', + '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.18.4'), + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('imkl', '2020.4.304'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + 'distributed/elastic/multiprocessing/api_test', + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From 812ad971bcc9926714fd7f7288e178acf10d67fd Mon Sep 17 00:00:00 2001 From: spottho1 Date: Wed, 11 Aug 2021 11:43:01 +0200 Subject: [PATCH 0810/9987] adding easyconfigs: sklearn-som-1.1.0-foss-2020b.eb --- .../sklearn-som-1.1.0-foss-2020b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb new file mode 100644 index 00000000000..45bf357d16b --- /dev/null +++ b/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'sklearn-som' +version = '1.1.0' + +homepage = 'https://github.com/rileypsmith/sklearn-som' +description = """A simple, planar self-organizing map with methods similar to clustering methods in Scikit Learn.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9b8107f42dfbd68db0d1aa75dd2007be4e0136bf0af96da51513e295f76646d9'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/sklearn_som/som.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sklearn_som'], +} + +sanity_check_commands = ['python -c "from sklearn_som.som import SOM"'] + +moduleclass = 'data' From db94eb520c6e4173bb4a8aa0ba5e704cf5f89139 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 11 Aug 2021 12:01:32 +0200 Subject: [PATCH 0811/9987] Increase test timeouts for PyTorch 1.8.1 and 1.9.0 --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 2 +- .../PyTorch-1.8.1_increase-distributed-test-timeout.patch | 4 ++-- easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb index 1d96d37ea37..b93b0e82420 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-foss-2020b.eb @@ -48,7 +48,7 @@ checksums = [ '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', 'a8fcb63cf963dc743e8b0a96b966f18d8edde6a4e76365d6de56aa2c71ce6d3f', # PyTorch-1.8.1_fix-vsx-vector-functions.patch # PyTorch-1.8.1_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index b7c08cd3003..95baaba3bc3 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -64,7 +64,7 @@ checksums = [ # PyTorch-1.8.1_honor_shared_cupti-setting.patch 'a6459fe544f9e2b61ab09ba54e8db5b294176ffdbf41c99e0d0b678e1e617b8f', # PyTorch-1.8.1_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.8.1_limit_world_size_for_zero_redundancy_opt_test.patch 'c3488fa24405eac6e2e36fbdf94e877bd39fd177e92fb3a0b6bbd5c8b7ddc7bc', # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_increase-distributed-test-timeout.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_increase-distributed-test-timeout.patch index c82f2fc6d30..e2231d01814 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_increase-distributed-test-timeout.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_increase-distributed-test-timeout.patch @@ -1,5 +1,5 @@ It seems the timeout for the distributed tests is set to low and spurious failures can be seen -Increase it by a factor of 3 similar to torch/testing/_internal/distributed/distributed_test.py +Increase it by a factor of 6 similar to torch/testing/_internal/distributed/distributed_test.py Author: Alexander Grund (TU Dresden) @@ -12,7 +12,7 @@ index 4f36b31a23..fbd2b9364a 100644 ) -TIMEOUT_DEFAULT = 100 -+TIMEOUT_DEFAULT = 300 ++TIMEOUT_DEFAULT = 600 TIMEOUT_OVERRIDE = {"test_ddp_uneven_inputs": 400} diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index d614502526d..34f2218ba3f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -43,7 +43,7 @@ checksums = [ # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', # PyTorch-1.8.1_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index ede9dfd996c..0fc9595a1b1 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -53,7 +53,7 @@ checksums = [ # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', # PyTorch-1.8.1_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch From 48297e12caed7f7809e5d0aa120a630338c61ae9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Aug 2021 12:12:44 +0200 Subject: [PATCH 0812/9987] add (bare) Python build dependency for poppler 21.06.1 --- easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.3.0.eb b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.3.0.eb index 2c00a04e7d0..bfbecae1c25 100644 --- a/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.3.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} builddependencies = [ ('CMake', '3.20.1'), ('pkg-config', '0.29.2'), + ('Python', '3.9.5', '-bare'), ] dependencies = [ From 14f386c323e5474908d7cf2d5212a6d471bfa94d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 11 Aug 2021 12:53:14 +0200 Subject: [PATCH 0813/9987] latest progress on jax installation --- .../jax-0.2.18-controlled_tf_tarball.patch | 12 +++ .../j/jax/jax-0.2.18-correct_libraries.patch | 78 +++++++++++++++++-- .../j/jax/jax-0.2.18-foss-2020b.eb | 69 ++++++++++++---- 3 files changed, 137 insertions(+), 22 deletions(-) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.18-controlled_tf_tarball.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-controlled_tf_tarball.patch b/easybuild/easyconfigs/j/jax/jax-0.2.18-controlled_tf_tarball.patch new file mode 100644 index 00000000000..4aa6bd90ffd --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-controlled_tf_tarball.patch @@ -0,0 +1,12 @@ +# using system environment variables +diff -ruN tensorflow-2.5.0_orig/third_party/mlir/tblgen.bzl tensorflow-2.5.0/third_party/mlir/tblgen.bzl +--- tensorflow-2.5.0_orig/third_party/mlir/tblgen.bzl 2021-05-12 15:26:41.000000000 +0200 ++++ tensorflow-2.5.0/third_party/mlir/tblgen.bzl 2021-08-11 12:23:34.301593036 +0200 +@@ -153,6 +153,7 @@ + inputs = trans_srcs, + executable = ctx.executable.tblgen, + arguments = [args], ++ use_default_shell_env = True, + ) + + return [DefaultInfo()] \ No newline at end of file diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch index 76b94b95f97..478bb70095f 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch @@ -1,20 +1,82 @@ -solving bug in jaxlib's tensorflow dependency by providing it with correct env variables +# using system environment variables + reparing build.py script + using EB downloaded TensorFlow tarball +diff -ruN jax_orig/build/build.py jax/build/build.py +--- jax_orig/build/build.py 2021-07-30 10:18:43.599233082 +0200 ++++ jax/build/build.py 2021-08-05 17:28:04.071995000 +0200 +@@ -208,15 +208,20 @@ + + + def check_bazel_version(bazel_path): +- try: +- version_output = shell([bazel_path, "--bazelrc=/dev/null", "version"]) +- except subprocess.CalledProcessError: +- return False +- match = re.search("Build label: *([0-9\\.]+)[^0-9\\.]", version_output) +- if match is None: +- return False +- actual_ints = [int(x) for x in match.group(1).split(".")] +- return actual_ints >= [2, 0, 0] ++ # try: ++ # version_output = shell([bazel_path, "--version"]) ++ # except subprocess.CalledProcessError: ++ # return False ++ # match = re.search("(Build label:|bazel) *([0-9\\.]+)", version_output) ++ try: ++ version_output = shell([bazel_path, "--bazelrc=/dev/null", "version"]) ++ except subprocess.CalledProcessError: ++ return False ++ match = re.search("Build label: *([0-9\\.]+)[^0-9\\.]", version_output) ++ if match is None: ++ return False ++ actual_ints = [int(x) for x in match.group(1).split(".")] ++ return actual_ints >= [2, 0, 0] + + + BAZELRC_TEMPLATE = """ +@@ -597,8 +602,7 @@ + f"--cpu={wheel_cpu}"]) + print(" ".join(command)) + shell(command) +- shell([bazel_path, "shutdown"]) +- ++ shell([bazel_path] + args.bazel_startup_options + ["shutdown"]) + + if __name__ == "__main__": + main() Binary files jax_orig/.git/index and jax/.git/index differ diff -ruN jax_orig/WORKSPACE jax/WORKSPACE --- jax_orig/WORKSPACE 2021-07-30 10:18:43.503078000 +0200 -+++ jax/WORKSPACE 2021-08-05 11:48:00.882688000 +0200 -@@ -12,13 +12,9 @@ - urls = [ - "https://github.com/tensorflow/tensorflow/archive/8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532.tar.gz", - ], -+ patch_cmds=['sed -i -e "s|arguments = \[args\],|arguments = \[args\],\\n\\tuse_default_shell_env = True,|" third_party/mlir/tblgen.bzl'] ++++ jax/WORKSPACE 2021-08-11 12:20:41.169549000 +0200 +@@ -5,20 +5,21 @@ + # b) get the sha256 hash of the commit by running: + # curl -L https://github.com/tensorflow/tensorflow/archive/.tar.gz | sha256sum + # and update the sha256 with the result. +-http_archive( ++# http_archive( ++# name = "org_tensorflow", ++# sha256 = "de22145c9dc51b3ed9399dbee2ab681f094f09e5213d6819451da500f163a14b", ++# strip_prefix = "tensorflow-8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532", ++# urls = [ ++# "https://github.com/tensorflow/tensorflow/archive/8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532.tar.gz", ++# ], ++# patch_cmds=['sed -i -e "s|arguments = \[args\],|arguments = \[args\],\\n\\tuse_default_shell_env = True,|" third_party/mlir/tblgen.bzl'] ++# ) ++ ++local_repository( + name = "org_tensorflow", +- sha256 = "de22145c9dc51b3ed9399dbee2ab681f094f09e5213d6819451da500f163a14b", +- strip_prefix = "tensorflow-8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532", +- urls = [ +- "https://github.com/tensorflow/tensorflow/archive/8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532.tar.gz", +- ], ++ path = "pathToSed", ) - +- -# For development, one can use a local TF repository instead. -# local_repository( -# name = "org_tensorflow", -# path = "tensorflow", -# ) ++# WIP load("//third_party/pocketfft:workspace.bzl", pocketfft = "repo") pocketfft() diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index b6cd028938c..38a16048f62 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -1,4 +1,6 @@ -easyblock = 'PythonPackage' +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' name = 'jax' version = '0.2.18' @@ -9,27 +11,66 @@ more""" toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = ['https://github.com/google/jax/archive/'] -sources = ['%(name)s-v%(version)s.tar.gz'] -patches = [ - 'jax-0.2.18-correct_libraries.patch', -] +# downloading TF tarball for better control of what Bazel will use during installation of Jax +local_tf_tarball_version = '2.5.0' -preinstallopts = 'python build/build.py ' -preinstallopts += '--bazel_startup_options="--output_user_root=%(builddir)s" ' -preinstallopts += '--bazel_options=--subcommands --bazel_options=--jobs=1 --bazel_options=--action_env=PYTHONPATH --bazel_options=--action_env=EBPYTHONPREFIXES && ' -preinstallopts += 'pip install --prefix %(installdir)s dist/*.whl && ' +builddependencies = [ + ('Bazel', '3.7.2'), +] dependencies = [ ('Python', '3.8.6'), - ('Bazel', '3.7.2'), ('SciPy-bundle', '2020.11'), ('Cython', '0.29.22'), + ('absl-py', '0.13.0'), + ('opt-einsum', '3.3.0'), + ('flatbuffers-python', '1.12'), ] -use_pip = True -download_dep_fail = True -sanity_pip_check = True +local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_tarball_version +local_jax_preinstallopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir +local_jax_preinstallopts += 'python build/build.py ' +local_jax_preinstallopts += '--bazel_startup_options="--output_user_root=%(builddir)s" ' +local_jax_preinstallopts += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' +local_jax_preinstallopts += '--bazel_options=--subcommands ' +local_jax_preinstallopts += '--bazel_options=--jobs=1 --bazel_options=--action_env=PYTHONPATH ' +local_jax_preinstallopts += '--bazel_options=--action_env=EBPYTHONPREFIXES && ' +local_jax_preinstallopts += 'pip install --prefix %(installdir)s dist/*.whl && ' + +exts_list = [ + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'modulename': 'opt_einsum', + }), + ('absl-py', '0.13.0', { + 'modulename': 'absl' + })] + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'sources': [ + '%(name)s-v%(version)s.zip', + { + 'download_filename': 'v%s.tar.gz' % local_tf_tarball_version, + 'filename': 'tensorflow_v%s.tar.gz' % local_tf_tarball_version, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('%s-%s-correct_libraries.patch' % (name, version), 1), + ('%s-%s-controlled_tf_tarball.patch' % (name, version), '../tensorflow-%s' % local_tf_tarball_version), + ], + 'start_dir': '%(name)s-%(name)s-v%(version)s', + 'preinstallopts': local_jax_preinstallopts, + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, + }), +] moduleclass = 'tools' From 59fbfd4a2e45368a6e1c41fe9460603dcba5d243 Mon Sep 17 00:00:00 2001 From: spottho1 Date: Wed, 11 Aug 2021 13:01:02 +0200 Subject: [PATCH 0814/9987] add download_dep_fail --- .../easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb index 45bf357d16b..75357f22791 100644 --- a/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/sklearn-som/sklearn-som-1.1.0-foss-2020b.eb @@ -18,6 +18,7 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True sanity_check_paths = { 'files': ['lib/python%(pyshortver)s/site-packages/sklearn_som/som.py'], From b82894e0db89980f4d422d15d1fdad6c4c479311 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Aug 2021 14:33:37 +0200 Subject: [PATCH 0815/9987] add sanity check command for OSPRay --- easybuild/easyconfigs/o/OSPRay/OSPRay-2.5.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OSPRay/OSPRay-2.5.0.eb b/easybuild/easyconfigs/o/OSPRay/OSPRay-2.5.0.eb index ea6780a19fe..e7c9f23e0aa 100644 --- a/easybuild/easyconfigs/o/OSPRay/OSPRay-2.5.0.eb +++ b/easybuild/easyconfigs/o/OSPRay/OSPRay-2.5.0.eb @@ -18,4 +18,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/ospray', 'lib64/cmake', 'doc'], } +sanity_check_commands = ["ospConvertRawToAMR --help 2>&1 | grep 'Usage: ospConvertRawToAMR'"] + moduleclass = 'vis' From 39a5740a459d0ff4088c243e27861d6604671461 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 11 Aug 2021 13:51:49 +0100 Subject: [PATCH 0816/9987] adding easyconfigs: SpaceRanger-1.3.0-GCC-10.3.0.eb, bcl2fastq2-2.20.0-GCC-10.3.0.eb --- .../bcl2fastq2-2.20.0-GCC-10.3.0.eb | 62 +++++++++++++++++++ .../SpaceRanger-1.3.0-GCC-10.3.0.eb | 33 ++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-1.3.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..987778c4625 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'bcl2fastq2' +version = '2.20.0' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html' +description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by + Illumina sequencing systems to standard FASTQ file formats for downstream analysis.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] +sources = [{ + 'filename': '%s-v%s-tar.zip' % (name, version.replace('.', '-')), + 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz +}] +patches = [ + 'bcl2fastq2-%(version)s-fix-cmake-target-libs.patch', + # bcl2fastq2 v2.20.0 is not compatible with recent Boost versions, use bundled Boost + 'bcl2fastq2-%(version)s-find-boost.patch', +] +checksums = [ + '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3', # bcl2fastq2-v2-20-0-tar.zip + '7908c268c213a6cfeafe05afcd5d3b34098241b6ab0a62c11ea47664cd0a63c5', # bcl2fastq2-2.20.0-fix-cmake-target-libs.patch + '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1', # bcl2fastq2-2.20.0-find-boost.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), +] + +start_dir = 'src' + +# check versions of libxml2 and libxslt from EB +local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' +local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} +preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} + +# remove hardcoded compilation flags +local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' +preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx + +configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' +configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' +configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' + +sanity_check_paths = { + 'files': ['bin/bcl2fastq'], + 'dirs': ['lib'], +} + +sanity_check_commands = ["bcl2fastq --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-1.3.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-1.3.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..8a7547c694a --- /dev/null +++ b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-1.3.0-GCC-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'SpaceRanger' +version = '1.3.0' + +homepage = 'https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger' +description = """ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output +and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, +perform clustering and gene expression analysis, and place spots in spatial context on the slide image. """ + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +# download sources from homepage, registration required +# https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c78d1617dcb449231c2f838d4f151257f880aefa1d597f94eb9e2334add38538'] + +dependencies = [ + ('bcl2fastq2', '2.20.0'), +] + +allow_prepend_abs_path = True +# prepend reference databases GRCh38 and mm10 to PATH +# modextrapaths = {'PATH': '/path/to/databases/%(namelower)s-%(version)s'} + +sanity_check_paths = { + 'files': ['bin/spaceranger'], + 'dirs': ['external', 'lib', 'mro'], +} + +sanity_check_commands = ['spaceranger -h'] + +moduleclass = 'bio' From 1064b650f482b8c33b33e1fb788628ffde2ec999 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 11 Aug 2021 15:18:45 +0200 Subject: [PATCH 0817/9987] Linting and reference reasons for excluding tests. --- .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index feaef854fa2..b880ebaefd5 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -112,10 +112,13 @@ excluded_tests = { '': [ # Bad tests: https://github.com/pytorch/pytorch/issues/60260 'distributed/elastic/utils/distributed_test', - 'distributed/test_distributed_fork', - 'distributed/test_distributed_spawn', 'distributed/elastic/multiprocessing/api_test', - 'test_optim', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', ] From 9888ab50a929f1d7ee21c6512e0cecbeff68553b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Aug 2021 15:23:30 +0200 Subject: [PATCH 0818/9987] fix name of patch for niworkflows extension in FMRIprep 1.4.1 easyconfig --- .../f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb index a1d620134f1..cab27a2cac9 100644 --- a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb @@ -29,8 +29,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('versioneer', '0.18', { 'checksums': ['ead1f78168150011189521b479d3a0dd2f55c94f5b07747b484fd693c3fbf335'], @@ -114,7 +112,7 @@ exts_list = [ 'checksums': ['14830702c293e870a69fdefca2928618179cdbb631ce84a99522aa859a1f4205'], }), ('niworkflows', '0.9.6', { - 'patches': ['niworkflows-%(version)s_fix-bus-error.patch'], + 'patches': ['niworkflows-0.9.6_fix-bus-error.patch'], 'checksums': [ '07275844f5e830562109acca7340f971b98e4a22e7938d8d5aceb2cb5891049c', # niworkflows-0.9.6.tar.gz 'd42ea11f54b4be75e68764a3bb74e6d202e60e4e6b174ded217fe18acb439133', # niworkflows-0.9.6_fix-bus-error.patch From 39376e7db24763c8868520fb3f4fe6a731278e73 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Aug 2021 15:48:20 +0200 Subject: [PATCH 0819/9987] Also build shared libs for MUMPS 5.3.5 --- .../m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb | 10 +++- .../m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb | 10 +++- .../m/MUMPS/MUMPS-5.3.5_shared-mumps.patch | 47 +++++++++++++++++ .../m/MUMPS/MUMPS-5.3.5_shared-pord.patch | 51 +++++++++++++++++++ 4 files changed, 116 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5_shared-mumps.patch create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5_shared-pord.patch diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb index ef32bdb8187..c3b9ed471b2 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb @@ -10,7 +10,15 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['http://mumps.enseeiht.fr/'] sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + 'e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4', # MUMPS_5.3.5.tar.gz + 'e39441eaf90191b5d967223e085b9fa9adbd4264c49f0dabdbf3c1a6685900fb', # MUMPS-5.3.5_shared-pord.patch + '3662a075d1eab1143409424278c63a1c198b6cd75572610b4bb17dd3d6f4d614', # MUMPS-5.3.5_shared-mumps.patch +] dependencies = [ ('SCOTCH', '6.1.0'), diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb index 162fb38b82c..3e9e86cfe09 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb @@ -10,7 +10,15 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['http://mumps.enseeiht.fr/'] sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + 'e5d665fdb7043043f0799ae3dbe3b37e5b200d1ab7a6f7b2a4e463fd89507fa4', # MUMPS_5.3.5.tar.gz + 'e39441eaf90191b5d967223e085b9fa9adbd4264c49f0dabdbf3c1a6685900fb', # MUMPS-5.3.5_shared-pord.patch + '3662a075d1eab1143409424278c63a1c198b6cd75572610b4bb17dd3d6f4d614', # MUMPS-5.3.5_shared-mumps.patch +] dependencies = [ ('SCOTCH', '6.1.0'), diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5_shared-mumps.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5_shared-mumps.patch new file mode 100644 index 00000000000..01c637b1586 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5_shared-mumps.patch @@ -0,0 +1,47 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared.patch +Author: micketeer@gmail.com + +diff -ru MUMPS_5.3.5.orig/src/Makefile MUMPS_5.3.5/src/Makefile +--- MUMPS_5.3.5.orig/src/Makefile 2021-08-11 11:43:32.097349091 +0200 ++++ MUMPS_5.3.5/src/Makefile 2021-08-11 12:02:10.305435406 +0200 +@@ -23,6 +23,8 @@ + include $(topdir)/Makefile.inc + + mumps_lib: $(incdir)/mumps_int_def.h \ ++ $(libdir)/libmumps_common$(PLAT).so \ ++ $(libdir)/lib$(ARITH)mumps$(PLAT).so \ + $(libdir)/libmumps_common$(PLAT)$(LIBEXT) \ + $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) + +@@ -196,6 +198,14 @@ + $(AR)$@ $? + $(RANLIB) $@ + ++$(libdir)/libmumps_common$(PLAT).so: $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) ++ $(FC) -shared $^ -Wl,-soname,libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) $(LORDERINGS) -lpthread $(MUMPS_LIBF77) $(MPIFLIB) $(MPICLIB) $(METISLIB) -o $(libdir)/libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libmumps_common$(PLAT)-$(SONAME_VERSION).so $@ ++ ++$(libdir)/lib$(ARITH)mumps$(PLAT).so: $(OBJS_MOD) $(OBJS_OTHER) ++ $(FC) -shared $^ -Wl,-soname,lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) -lmumps_common$(PLAT) -lpthread $(MUMPS_LIBF77) $(LORDERINGS) $(MPIFLIB) $(METISLIB) $(SCALAP) -o $(libdir)/lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $@ ++ + # Dependencies between modules: + # i) arithmetic-dependent modules: + $(ARITH)ana_aux.o: $(ARITH)mumps_struc_def.o \ +@@ -405,13 +415,13 @@ + + .SUFFIXES: .c .F .o + .F.o: +- $(FC) $(OPTF) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -c $*.F $(OUTF)$*.o ++ $(FC) $(OPTF) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -fPIC -c $*.F $(OUTF)$*.o + .c.o: +- $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -c $*.c $(OUTC)$*.o ++ $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -fPIC -c $*.c $(OUTC)$*.o + + $(ARITH)mumps_c.o: mumps_c.c + $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) -DMUMPS_ARITH=MUMPS_ARITH_$(ARITH) \ +- $(IORDERINGSC) $(ORDERINGSC) -c mumps_c.c $(OUTC)$@ ++ $(IORDERINGSC) $(ORDERINGSC) -fPIC -c mumps_c.c $(OUTC)$@ + + clean: + $(RM) *.o *.mod $(incdir)/mumps_int_def.h diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5_shared-pord.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5_shared-pord.patch new file mode 100644 index 00000000000..aa16a6608e9 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5_shared-pord.patch @@ -0,0 +1,51 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared-pord.patch +Author: micketeer@gmail.com + +diff -ru MUMPS_5.3.5.orig/Makefile MUMPS_5.3.5/Makefile +--- MUMPS_5.3.5.orig/Makefile 2021-08-11 11:43:32.368348352 +0200 ++++ MUMPS_5.3.5/Makefile 2021-08-11 12:06:13.277818857 +0200 +@@ -55,7 +55,7 @@ + multi_example: s d c z + (cd examples ; $(MAKE) multi) + +-requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) ++requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT).so + + # dummy MPI library (sequential version) + +@@ -72,6 +72,12 @@ + cp $(LPORDDIR)/libpord$(LIBEXT) $@; \ + fi; + ++$(libdir)/libpord$(PLAT).so: ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cd $(LPORDDIR); make CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" ARFUNCT= RANLIB="$(RANLIB)" libpord$(PLAT).so; fi; ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cp -a $(LPORDDIR)/libpord*.so lib/; fi; ++ + clean: + (cd src; $(MAKE) clean) + (cd examples; $(MAKE) clean) +diff -ru MUMPS_5.3.5.orig/PORD/lib/Makefile MUMPS_5.3.5/PORD/lib/Makefile +--- MUMPS_5.3.5.orig/PORD/lib/Makefile 2021-08-11 11:43:32.306348521 +0200 ++++ MUMPS_5.3.5/PORD/lib/Makefile 2021-08-11 12:04:40.183055088 +0200 +@@ -9,7 +9,7 @@ + + INCLUDES = -I../include + +-COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS) ++COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS) -fPIC + + OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \ + multisector.o gelim.o bucket.o tree.o \ +@@ -28,6 +28,10 @@ + $(AR)$@ $(OBJS) + $(RANLIB) $@ + ++libpord$(PLAT).so: $(OBJS) ++ $(CC) -shared $(OBJS) -Wl,-soname,libpord$(PLAT)-$(SONAME_VERSION).so -o libpord$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libpord$(PLAT)-$(SONAME_VERSION).so $@ ++ + clean: + rm -f *.o + From 00f1309dea2a4466ee113b2256820a77ed9806f6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 11 Aug 2021 16:48:23 +0100 Subject: [PATCH 0820/9987] adding easyconfigs: Cellpose-0.6.5-foss-2020b.eb, Cellpose-0.6.5-fosscuda-2020b.eb and patches: Cellpose-0.6.5_OpenCV.patch, Cellpose-0.6.5_PyQt5.patch --- .../c/Cellpose/Cellpose-0.6.5-foss-2020b.eb | 47 + .../Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb | 47 + .../c/Cellpose/Cellpose-0.6.5_OpenCV.patch | 14 + .../c/Cellpose/Cellpose-0.6.5_PyQt5.patch | 855 ++++++++++++++++++ 4 files changed, 963 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5_OpenCV.patch create mode 100644 easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5_PyQt5.patch diff --git a/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb new file mode 100644 index 00000000000..b86e1d18a3b --- /dev/null +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-foss-2020b.eb @@ -0,0 +1,47 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'Cellpose' +version = '0.6.5' + +homepage = "https://www.cellpose.org/" +description = """a generalist algorithm for cellular segmentation""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('numba', '0.53.1'), + ('OpenCV', '4.5.1', '-contrib'), + ('Python', '3.8.6'), + ('PyQt5', '5.15.1'), + ('PyQtGraph', '0.11.1'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('tifffile', '2021.8.8', { + 'checksums': ['8260f31c4700143e8374ff6cde5cef7fe54fc9b7313afe88329f407881901dc5'], + }), + (name, version, { + 'patches': [ + '%(name)s-%(version)s_OpenCV.patch', + '%(name)s-%(version)s_PyQt5.patch', + ], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'use_pip_extras': 'gui', + 'checksums': [ + '19aafedfe5723285f270ad55e7947fbd828abff943a13216a8205809e41fb870', # cellpose-0.6.5.tar.gz + 'b8fd5bece5b5ea66ce41a08f0468fe5785dd4b07cc281eac08a19dd38e3ef410', # Cellpose-0.6.5_OpenCV.patch + '97fc96189993127998fd1388228a4a1b52bbe15d7355162579259a795ebbd937', # Cellpose-0.6.5_PyQt5.patch + ], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb new file mode 100644 index 00000000000..47616f4265c --- /dev/null +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5-fosscuda-2020b.eb @@ -0,0 +1,47 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'Cellpose' +version = '0.6.5' + +homepage = "https://www.cellpose.org/" +description = """a generalist algorithm for cellular segmentation""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('numba', '0.53.1'), + ('OpenCV', '4.5.1', '-contrib'), + ('Python', '3.8.6'), + ('PyQt5', '5.15.1'), + ('PyQtGraph', '0.11.1'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('tifffile', '2021.8.8', { + 'checksums': ['8260f31c4700143e8374ff6cde5cef7fe54fc9b7313afe88329f407881901dc5'], + }), + (name, version, { + 'patches': [ + '%(name)s-%(version)s_OpenCV.patch', + '%(name)s-%(version)s_PyQt5.patch', + ], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'use_pip_extras': 'gui', + 'checksums': [ + '19aafedfe5723285f270ad55e7947fbd828abff943a13216a8205809e41fb870', # cellpose-0.6.5.tar.gz + 'b8fd5bece5b5ea66ce41a08f0468fe5785dd4b07cc281eac08a19dd38e3ef410', # Cellpose-0.6.5_OpenCV.patch + '97fc96189993127998fd1388228a4a1b52bbe15d7355162579259a795ebbd937', # Cellpose-0.6.5_PyQt5.patch + ], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5_OpenCV.patch b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5_OpenCV.patch new file mode 100644 index 00000000000..f04e4a54506 --- /dev/null +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5_OpenCV.patch @@ -0,0 +1,14 @@ +Remove opencv-python-headless as we'll use the EB OpenCV instead +Patch by Simon Branford (University of Birmingham) +--- setup.py.orig 2021-08-11 11:44:31.239366000 +0100 ++++ setup.py 2021-08-11 11:44:40.662227000 +0100 +@@ -3,8 +3,7 @@ + + install_deps = ['numpy', 'scipy', 'natsort', + 'tifffile', 'tqdm', 'numba', +- 'torch>=1.6', +- 'opencv-python-headless'] ++ 'torch>=1.6'] + + try: + import torch diff --git a/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5_PyQt5.patch b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5_PyQt5.patch new file mode 100644 index 00000000000..a4a33a8ae3e --- /dev/null +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-0.6.5_PyQt5.patch @@ -0,0 +1,855 @@ +From 9f030e804e729924344e1bb1c3676478b812fe8e Mon Sep 17 00:00:00 2001 +From: Carsen Stringer +Date: Mon, 9 Aug 2021 16:53:02 -0400 +Subject: [PATCH] fixing changes in pyqt5 imports (#298) + +--- + cellpose/gui/gui.py | 87 ++++++++++++++-------------- + cellpose/gui/guiparts.py | 121 ++++++++++++++++++--------------------- + cellpose/gui/io.py | 8 +-- + cellpose/gui/menus.py | 34 +++++------ + tests/test_train.py | 6 +- + 5 files changed, 123 insertions(+), 133 deletions(-) + +diff --git a/cellpose/gui/gui.py b/cellpose/gui/gui.py +index 5734bbb..28b2849 100644 +--- a/cellpose/gui/gui.py ++++ b/cellpose/gui/gui.py +@@ -4,6 +4,7 @@ + from tqdm import tqdm + + from PyQt5 import QtGui, QtCore, Qt, QtWidgets ++from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, QScrollBar, QSlider, QComboBox, QGridLayout, QPushButton, QFrame, QCheckBox, QLabel, QProgressBar, QLineEdit + import pyqtgraph as pg + from pyqtgraph import GraphicsScene + +@@ -32,11 +33,11 @@ + except: + SERVER_UPLOAD = False + +-class QHLine(QtGui.QFrame): ++class QHLine(QFrame): + def __init__(self): + super(QHLine, self).__init__() +- self.setFrameShape(QtGui.QFrame.HLine) +- self.setFrameShadow(QtGui.QFrame.Sunken) ++ self.setFrameShape(QFrame.HLine) ++ self.setFrameShadow(QFrame.Sunken) + + def avg3d(C): + """ smooth value of c across nearby points +@@ -115,7 +116,7 @@ def make_cmap(cm=0): + def run(image=None): + # Always start by initializing Qt (only once per application) + warnings.filterwarnings("ignore") +- app = QtGui.QApplication(sys.argv) ++ app = QApplication(sys.argv) + icon_path = pathlib.Path.home().joinpath('.cellpose', 'logo.png') + guip_path = pathlib.Path.home().joinpath('.cellpose', 'cellpose_gui.png') + if not icon_path.is_file(): +@@ -148,7 +149,7 @@ def get_unique_points(set): + set = list(np.unique(cps, axis=0)) + return set + +-class MainW(QtGui.QMainWindow): ++class MainW(QMainWindow): + def __init__(self, image=None): + super(MainW, self).__init__() + +@@ -187,8 +188,8 @@ def __init__(self, image=None): + self.loaded = False + + # ---- MAIN WIDGET LAYOUT ---- # +- self.cwidget = QtGui.QWidget(self) +- self.l0 = QtGui.QGridLayout() ++ self.cwidget = QWidget(self) ++ self.l0 = QGridLayout() + self.cwidget.setLayout(self.l0) + self.setCentralWidget(self.cwidget) + self.l0.setVerticalSpacing(6) +@@ -255,17 +256,17 @@ def make_buttons(self): + "selection-background-color: rgb(50,100,50);") + self.checkstyle = "color: rgb(190,190,190);" + +- label = QtGui.QLabel('Views:')#[\u2191 \u2193]') ++ label = QLabel('Views:')#[\u2191 \u2193]') + label.setStyleSheet(self.headings) + label.setFont(self.boldfont) + self.l0.addWidget(label, 0,0,1,1) + +- label = QtGui.QLabel('[up/down or W/S]') ++ label = QLabel('[up/down or W/S]') + label.setStyleSheet(label_style) + label.setFont(self.smallfont) + self.l0.addWidget(label, 1,0,1,1) + +- label = QtGui.QLabel('[pageup/down]') ++ label = QLabel('[pageup/down]') + label.setStyleSheet(label_style) + label.setFont(self.smallfont) + self.l0.addWidget(label, 1,1,1,1) +@@ -274,7 +275,7 @@ def make_buttons(self): + self.view = 0 # 0=image, 1=flowsXY, 2=flowsZ, 3=cellprob + self.color = 0 # 0=RGB, 1=gray, 2=R, 3=G, 4=B + self.RGBChoose = guiparts.RGBRadioButtons(self, b,1) +- self.RGBDropDown = QtGui.QComboBox() ++ self.RGBDropDown = QComboBox() + self.RGBDropDown.addItems(["RGB","gray","spectral","red","green","blue"]) + self.RGBDropDown.setFont(self.medfont) + self.RGBDropDown.currentIndexChanged.connect(self.color_choose) +@@ -292,21 +293,21 @@ def make_buttons(self): + line.setStyleSheet('color: white;') + self.l0.addWidget(line, b,0,1,2) + b+=1 +- label = QtGui.QLabel('Drawing:') ++ label = QLabel('Drawing:') + label.setStyleSheet(self.headings) + label.setFont(self.boldfont) + self.l0.addWidget(label, b,0,1,2) + + b+=1 + self.brush_size = 3 +- self.BrushChoose = QtGui.QComboBox() ++ self.BrushChoose = QComboBox() + self.BrushChoose.addItems(["1","3","5","7","9"]) + self.BrushChoose.currentIndexChanged.connect(self.brush_choose) + self.BrushChoose.setFixedWidth(60) + self.BrushChoose.setStyleSheet(self.dropdowns) + self.BrushChoose.setFont(self.medfont) + self.l0.addWidget(self.BrushChoose, b, 1,1,1) +- label = QtGui.QLabel('brush size: [, .]') ++ label = QLabel('brush size: [, .]') + label.setStyleSheet(label_style) + label.setFont(self.medfont) + self.l0.addWidget(label, b,0,1,1) +@@ -317,7 +318,7 @@ def make_buttons(self): + + b+=1 + # turn on draw mode +- self.SCheckBox = QtGui.QCheckBox('single stroke') ++ self.SCheckBox = QCheckBox('single stroke') + self.SCheckBox.setStyleSheet(self.checkstyle) + self.SCheckBox.setFont(self.medfont) + self.SCheckBox.toggled.connect(self.autosave_on) +@@ -325,7 +326,7 @@ def make_buttons(self): + + b+=1 + # turn on crosshairs +- self.CHCheckBox = QtGui.QCheckBox('cross-hairs') ++ self.CHCheckBox = QCheckBox('cross-hairs') + self.CHCheckBox.setStyleSheet(self.checkstyle) + self.CHCheckBox.setFont(self.medfont) + self.CHCheckBox.toggled.connect(self.cross_hairs) +@@ -335,7 +336,7 @@ def make_buttons(self): + # turn off masks + self.layer_off = False + self.masksOn = True +- self.MCheckBox = QtGui.QCheckBox('MASKS ON [X]') ++ self.MCheckBox = QCheckBox('MASKS ON [X]') + self.MCheckBox.setStyleSheet(self.checkstyle) + self.MCheckBox.setFont(self.medfont) + self.MCheckBox.setChecked(True) +@@ -345,7 +346,7 @@ def make_buttons(self): + b+=1 + # turn off outlines + self.outlinesOn = True +- self.OCheckBox = QtGui.QCheckBox('outlines on [Z]') ++ self.OCheckBox = QCheckBox('outlines on [Z]') + self.OCheckBox.setStyleSheet(self.checkstyle) + self.OCheckBox.setFont(self.medfont) + self.OCheckBox.setChecked(True) +@@ -354,7 +355,7 @@ def make_buttons(self): + + b+=1 + # send to server +- self.ServerButton = QtGui.QPushButton(' send manual seg. to server') ++ self.ServerButton = QPushButton(' send manual seg. to server') + self.ServerButton.clicked.connect(lambda: save_server(self)) + self.l0.addWidget(self.ServerButton, b,0,1,2) + self.ServerButton.setEnabled(False) +@@ -366,19 +367,19 @@ def make_buttons(self): + line.setStyleSheet('color: white;') + self.l0.addWidget(line, b,0,1,2) + b+=1 +- label = QtGui.QLabel('Segmentation:') ++ label = QLabel('Segmentation:') + label.setStyleSheet(self.headings) + label.setFont(self.boldfont) + self.l0.addWidget(label, b,0,1,2) + + b+=1 + self.diameter = 30 +- label = QtGui.QLabel('cell diameter (pixels) (click ENTER):') ++ label = QLabel('cell diameter (pixels) (click ENTER):') + label.setStyleSheet(label_style) + label.setFont(self.medfont) + label.setToolTip('you can manually enter the approximate diameter for your cells, \nor press “calibrate” to let the model estimate it. \nThe size is represented by a disk at the bottom of the view window \n(can turn this disk off by unchecking “scale disk on”)') + self.l0.addWidget(label, b, 0,1,2) +- self.Diameter = QtGui.QLineEdit() ++ self.Diameter = QLineEdit() + self.Diameter.setToolTip('you can manually enter the approximate diameter for your cells, \nor press “calibrate” to let the model estimate it. \nThe size is represented by a disk at the bottom of the view window \n(can turn this disk off by unchecking “scale disk on”)') + self.Diameter.setText(str(self.diameter)) + self.Diameter.setFont(self.medfont) +@@ -388,7 +389,7 @@ def make_buttons(self): + self.l0.addWidget(self.Diameter, b, 0,1,2) + + # recompute model +- self.SizeButton = QtGui.QPushButton(' calibrate') ++ self.SizeButton = QPushButton(' calibrate') + self.SizeButton.clicked.connect(self.calibrate_size) + self.l0.addWidget(self.SizeButton, b,1,1,1) + self.SizeButton.setEnabled(False) +@@ -398,7 +399,7 @@ def make_buttons(self): + # scale toggle + b+=1 + self.scale_on = True +- self.ScaleOn = QtGui.QCheckBox('scale disk on') ++ self.ScaleOn = QCheckBox('scale disk on') + self.ScaleOn.setFont(self.medfont) + self.ScaleOn.setStyleSheet('color: red;') + self.ScaleOn.setChecked(True) +@@ -408,7 +409,7 @@ def make_buttons(self): + + # use GPU + b+=1 +- self.useGPU = QtGui.QCheckBox('use GPU') ++ self.useGPU = QCheckBox('use GPU') + self.useGPU.setStyleSheet(self.checkstyle) + self.useGPU.setFont(self.medfont) + self.useGPU.setToolTip('if you have specially installed the cuda version of mxnet, then you can activate this, but it won’t give huge speedups when running single 2D images in the GUI.') +@@ -416,7 +417,7 @@ def make_buttons(self): + self.l0.addWidget(self.useGPU, b,0,1,1) + + # fast mode +- self.NetAvg = QtGui.QComboBox() ++ self.NetAvg = QComboBox() + self.NetAvg.addItems(['average 4 nets', '+ resample (slow)', 'run 1 net (fast)', ]) + self.NetAvg.setFont(self.medfont) + self.NetAvg.setToolTip('average 4 different fit networks (default) + resample for smooth masks (slow) or run 1 network (fast)') +@@ -424,7 +425,7 @@ def make_buttons(self): + + b+=1 + # choose models +- self.ModelChoose = QtGui.QComboBox() ++ self.ModelChoose = QComboBox() + self.model_dir = pathlib.Path.home().joinpath('.cellpose', 'models') + models = ['cyto', 'nuclei', 'cyto2'] + self.ModelChoose.addItems(models) +@@ -432,7 +433,7 @@ def make_buttons(self): + self.ModelChoose.setStyleSheet(self.dropdowns) + self.ModelChoose.setFont(self.medfont) + self.l0.addWidget(self.ModelChoose, b, 1,1,1) +- label = QtGui.QLabel('model: ') ++ label = QLabel('model: ') + label.setStyleSheet(label_style) + label.setFont(self.medfont) + label.setToolTip('there is a cyto model, a new cyto2 model from user submissions, and a nuclei model') +@@ -441,7 +442,7 @@ def make_buttons(self): + + b+=1 + # choose channel +- self.ChannelChoose = [QtGui.QComboBox(), QtGui.QComboBox()] ++ self.ChannelChoose = [QComboBox(), QComboBox()] + self.ChannelChoose[0].addItems(['gray','red','green','blue']) + self.ChannelChoose[1].addItems(['none','red','green','blue']) + cstr = ['chan to segment:', 'chan2 (optional): '] +@@ -449,7 +450,7 @@ def make_buttons(self): + self.ChannelChoose[i].setFixedWidth(70) + self.ChannelChoose[i].setStyleSheet(self.dropdowns) + self.ChannelChoose[i].setFont(self.medfont) +- label = QtGui.QLabel(cstr[i]) ++ label = QLabel(cstr[i]) + label.setStyleSheet(label_style) + label.setFont(self.medfont) + if i==0: +@@ -464,28 +465,28 @@ def make_buttons(self): + + # use inverted image for running cellpose + b+=1 +- self.invert = QtGui.QCheckBox('invert grayscale') ++ self.invert = QCheckBox('invert grayscale') + self.invert.setStyleSheet(self.checkstyle) + self.invert.setFont(self.medfont) + self.l0.addWidget(self.invert, b,0,1,2) + + b+=1 + # recompute model +- self.ModelButton = QtGui.QPushButton(' run segmentation') ++ self.ModelButton = QPushButton(' run segmentation') + self.ModelButton.clicked.connect(self.compute_model) + self.l0.addWidget(self.ModelButton, b,0,1,2) + self.ModelButton.setEnabled(False) + self.ModelButton.setStyleSheet(self.styleInactive) + self.ModelButton.setFont(self.boldfont) + b+=1 +- self.progress = QtGui.QProgressBar(self) ++ self.progress = QProgressBar(self) + self.progress.setStyleSheet('color: gray;') + self.l0.addWidget(self.progress, b,0,1,2) + + # post-hoc paramater tuning + + b+=1 +- label = QtGui.QLabel('model match threshold:') ++ label = QLabel('model match threshold:') + label.setToolTip('threshold on gradient match to accept a mask (set lower to get more cells)') + label.setStyleSheet(label_style) + label.setFont(self.medfont) +@@ -493,7 +494,7 @@ def make_buttons(self): + + b+=1 + self.threshold = 0.4 +- self.threshslider = QtGui.QSlider() ++ self.threshslider = QSlider() + self.threshslider.setOrientation(QtCore.Qt.Horizontal) + self.threshslider.setMinimum(1.0) + self.threshslider.setMaximum(30.0) +@@ -504,14 +505,14 @@ def make_buttons(self): + self.threshslider.setEnabled(False) + + b+=1 +- label = QtGui.QLabel('cell prob threshold:') ++ label = QLabel('cell prob threshold:') + label.setStyleSheet(label_style) + label.setFont(self.medfont) + self.l0.addWidget(label, b, 0,1,2) + label.setToolTip('cell probability threshold (set lower to get more cells)') + + b+=1 +- self.probslider = QtGui.QSlider() ++ self.probslider = QSlider() + self.probslider.setOrientation(QtCore.Qt.Horizontal) + self.probslider.setMinimum(-6.0) + self.probslider.setMaximum(6.0) +@@ -527,14 +528,14 @@ def make_buttons(self): + line.setStyleSheet('color: white;') + self.l0.addWidget(line, b,0,1,2) + +- self.autobtn = QtGui.QCheckBox('auto-adjust') ++ self.autobtn = QCheckBox('auto-adjust') + self.autobtn.setStyleSheet(self.checkstyle) + self.autobtn.setFont(self.medfont) + self.autobtn.setChecked(True) + self.l0.addWidget(self.autobtn, b+2,0,1,1) + + b+=1 +- label = QtGui.QLabel('Image saturation:') ++ label = QLabel('Image saturation:') + label.setStyleSheet(self.headings) + label.setFont(self.boldfont) + self.l0.addWidget(label, b,0,1,2) +@@ -545,18 +546,18 @@ def make_buttons(self): + self.slider.setMaximum(255) + self.slider.setLow(0) + self.slider.setHigh(255) +- self.slider.setTickPosition(QtGui.QSlider.TicksRight) ++ self.slider.setTickPosition(QSlider.TicksRight) + self.l0.addWidget(self.slider, b,1,1,1) + self.l0.setRowStretch(b, 1) + + b+=2 + # add z position underneath + self.currentZ = 0 +- label = QtGui.QLabel('Z:') ++ label = QLabel('Z:') + label.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter) + label.setStyleSheet(label_style) + self.l0.addWidget(label, b, 0,1,1) +- self.zpos = QtGui.QLineEdit() ++ self.zpos = QLineEdit() + self.zpos.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter) + self.zpos.setText(str(self.currentZ)) + self.zpos.returnPressed.connect(self.compute_scale) +@@ -564,7 +565,7 @@ def make_buttons(self): + self.l0.addWidget(self.zpos, b, 1,1,1) + + # add scrollbar underneath +- self.scroll = QtGui.QScrollBar(QtCore.Qt.Horizontal) ++ self.scroll = QScrollBar(QtCore.Qt.Horizontal) + self.scroll.setMaximum(10) + self.scroll.valueChanged.connect(self.move_in_Z) + self.l0.addWidget(self.scroll, b,3,1,20) +diff --git a/cellpose/gui/guiparts.py b/cellpose/gui/guiparts.py +index 6b9590b..841c514 100644 +--- a/cellpose/gui/guiparts.py ++++ b/cellpose/gui/guiparts.py +@@ -1,4 +1,6 @@ + from PyQt5 import QtGui, QtCore, QtWidgets ++from PyQt5.QtGui import QPainter, QPixmap ++from PyQt5.QtWidgets import QApplication, QRadioButton, QWidget, QDialog, QButtonGroup, QSlider, QStyle, QStyleOptionSlider, QGridLayout, QPushButton, QLabel + import pyqtgraph as pg + from pyqtgraph import functions as fn + from pyqtgraph import Point +@@ -7,7 +9,7 @@ + + def make_quadrants(parent): + """ make quadrant buttons """ +- parent.quadbtns = QtGui.QButtonGroup(parent) ++ parent.quadbtns = QButtonGroup(parent) + for b in range(9): + btn = QuadButton(b, ' '+str(b+1), parent) + parent.quadbtns.addButton(btn, b) +@@ -16,7 +18,7 @@ def make_quadrants(parent): + b += 1 + parent.quadbtns.setExclusive(True) + +-class QuadButton(QtGui.QPushButton): ++class QuadButton(QPushButton): + """ custom QPushButton class for quadrant plotting + requires buttons to put into a QButtonGroup (parent.quadbtns) + allows only 1 button to pressed at a time +@@ -104,29 +106,29 @@ def horizontal_slider_style(): + border-radius: 4px; + }""" + +-class ExampleGUI(QtGui.QDialog): ++class ExampleGUI(QDialog): + def __init__(self, parent=None): + super(ExampleGUI, self).__init__(parent) + self.setGeometry(100,100,1300,900) + self.setWindowTitle('GUI layout') +- self.win = QtGui.QWidget(self) +- layout = QtGui.QGridLayout() ++ self.win = QWidget(self) ++ layout = QGridLayout() + self.win.setLayout(layout) + guip_path = pathlib.Path.home().joinpath('.cellpose', 'cellpose_gui.png') + guip_path = str(guip_path.resolve()) +- pixmap = QtGui.QPixmap(guip_path) +- label = QtGui.QLabel(self) ++ pixmap = QPixmap(guip_path) ++ label = QLabel(self) + label.setPixmap(pixmap) + pixmap.scaled + layout.addWidget(label, 0, 0, 1, 1) + +-class HelpWindow(QtGui.QDialog): ++class HelpWindow(QDialog): + def __init__(self, parent=None): + super(HelpWindow, self).__init__(parent) + self.setGeometry(100,100,700,800) + self.setWindowTitle('cellpose help') +- self.win = QtGui.QWidget(self) +- layout = QtGui.QGridLayout() ++ self.win = QWidget(self) ++ layout = QGridLayout() + self.win.setLayout(layout) + + text = (''' +@@ -225,20 +227,20 @@ def __init__(self, parent=None): +

CHAN TO SEG: this is the channel in which the cytoplasm or nuclei exist

+

CHAN2 (OPT): if cytoplasm model is chosen, then choose the nuclear channel for this option

+ ''') +- label = QtGui.QLabel(text) ++ label = QLabel(text) + label.setFont(QtGui.QFont("Arial", 8)) + label.setWordWrap(True) + layout.addWidget(label, 0, 0, 1, 1) + self.show() + +-class TypeRadioButtons(QtGui.QButtonGroup): ++class TypeRadioButtons(QButtonGroup): + def __init__(self, parent=None, row=0, col=0): + super(TypeRadioButtons, self).__init__() + parent.color = 0 + self.parent = parent + self.bstr = self.parent.cell_types + for b in range(len(self.bstr)): +- button = QtGui.QRadioButton(self.bstr[b]) ++ button = QRadioButton(self.bstr[b]) + button.setStyleSheet('color: rgb(190,190,190);') + button.setFont(QtGui.QFont("Arial", 10)) + if b==0: +@@ -253,16 +255,16 @@ def btnpress(self, parent): + b = self.checkedId() + self.parent.cell_type = b + +-class RGBRadioButtons(QtGui.QButtonGroup): ++class RGBRadioButtons(QButtonGroup): + def __init__(self, parent=None, row=0, col=0): + super(RGBRadioButtons, self).__init__() + parent.color = 0 + self.parent = parent + self.bstr = ["image", "gradXY", "cellprob", "gradZ"] +- #self.buttons = QtGui.QButtonGroup() ++ #self.buttons = QButtonGroup() + self.dropdown = [] + for b in range(len(self.bstr)): +- button = QtGui.QRadioButton(self.bstr[b]) ++ button = QRadioButton(self.bstr[b]) + button.setStyleSheet('color: white;') + button.setFont(QtGui.QFont("Arial", 10)) + if b==0: +@@ -359,7 +361,7 @@ class ImageDraw(pg.ImageItem): + for controlling the levels and lookup table used to display the image. + """ + +- sigImageChanged = QtCore.Signal() ++ sigImageChanged = QtCore.pyqtSignal() + + def __init__(self, image=None, viewbox=None, parent=None, **kargs): + super(ImageDraw, self).__init__() +@@ -534,7 +536,7 @@ def setDrawKernel(self, kernel_size=3): + self.greenmask = np.concatenate((onmask,offmask,onmask,opamask), axis=-1) + + +-class RangeSlider(QtGui.QSlider): ++class RangeSlider(QSlider): + """ A slider for ranges. + + This class provides a dual-slider for ranges, where there is a defined +@@ -553,39 +555,35 @@ def __init__(self, parent=None, *args): + self._low = self.minimum() + self._high = self.maximum() + +- self.pressed_control = QtGui.QStyle.SC_None +- self.hover_control = QtGui.QStyle.SC_None ++ self.pressed_control = QStyle.SC_None ++ self.hover_control = QStyle.SC_None + self.click_offset = 0 + + self.setOrientation(QtCore.Qt.Vertical) +- self.setTickPosition(QtGui.QSlider.TicksRight) +- #self.setStyleSheet(\ +- # "QSlider::handle:vertical {\ +- # background-color: cyan;\ +- # border: 1px solid white;\ +- # border-radius: 2px;\ +- # border-color: white;\ +- # height: 16px;\ +- # width: 3px;\ +- # margin: 8px 2; \ +- # }") +- +- # set groove color +- +- self.opt = QtGui.QStyleOptionSlider() +- self.opt.orientation=QtCore.Qt.Vertical +- self.initStyleOption(self.opt) ++ self.setTickPosition(QSlider.TicksRight) ++ self.setStyleSheet(\ ++ "QSlider::handle:horizontal {\ ++ background-color: white;\ ++ border: 1px solid #5c5c5c;\ ++ border-radius: 0px;\ ++ border-color: black;\ ++ height: 8px;\ ++ width: 6px;\ ++ margin: -8px 2; \ ++ }") ++ ++ ++ #self.opt = QStyleOptionSlider() ++ #self.opt.orientation=QtCore.Qt.Vertical ++ #self.initStyleOption(self.opt) + # 0 for the low, 1 for the high, -1 for both + self.active_slider = 0 + self.parent = parent +- self.show() +- + + def level_change(self): + if self.parent is not None: + if self.parent.loaded: +- for z in range(self.parent.NZ): +- self.parent.saturation[z] = [self._low, self._high] ++ self.parent.ops_plot['saturation'] = [self._low, self._high] + self.parent.update_plot() + + def low(self): +@@ -604,47 +602,38 @@ def setHigh(self, high): + + def paintEvent(self, event): + # based on http://qt.gitorious.org/qt/qt/blobs/master/src/gui/widgets/qslider.cpp +- painter = QtGui.QPainter(self) +- style = QtGui.QApplication.style() ++ painter = QPainter(self) ++ style = QApplication.style() + + for i, value in enumerate([self._low, self._high]): +- opt = QtWidgets.QStyleOptionSlider() ++ opt = QStyleOptionSlider() + self.initStyleOption(opt) + + # Only draw the groove for the first slider so it doesn't get drawn + # on top of the existing ones every time + if i == 0: +- opt.subControls = QtWidgets.QStyle.SC_SliderGroove | QtWidgets.QStyle.SC_SliderHandle ++ opt.subControls = QStyle.SC_SliderHandle#QStyle.SC_SliderGroove | QStyle.SC_SliderHandle + else: +- opt.subControls = QtWidgets.QStyle.SC_SliderHandle ++ opt.subControls = QStyle.SC_SliderHandle + + if self.tickPosition() != self.NoTicks: +- opt.subControls |= QtWidgets.QStyle.SC_SliderTickmarks ++ opt.subControls |= QStyle.SC_SliderTickmarks + + if self.pressed_control: + opt.activeSubControls = self.pressed_control +- opt.state |= QtWidgets.QStyle.State_Sunken ++ opt.state |= QStyle.State_Sunken + else: + opt.activeSubControls = self.hover_control + + opt.sliderPosition = value + opt.sliderValue = value ++ style.drawComplexControl(QStyle.CC_Slider, opt, painter, self) ++ + +- if i==0: +- pen = QtGui.QPen() +- pen.setBrush(QtGui.QColor('#2e4f37')) +- pen.setCapStyle(QtCore.Qt.RoundCap) +- pen.setWidth(3) +- painter.setPen(pen) +- painter.setBrush(QtGui.QColor('#2e4f37')) +- x1,y1,x2,y2 = event.rect().getCoords() +- painter.drawRect(event.rect()) +- style.drawComplexControl(QtWidgets.QStyle.CC_Slider, opt, painter, self) +- + def mousePressEvent(self, event): + event.accept() + +- style = QtGui.QApplication.style() ++ style = QApplication.style() + button = event.button() + # In a normal slider control, when the user clicks on a point in the + # slider's total range, but not on the slider part of the control the +@@ -652,7 +641,7 @@ def mousePressEvent(self, event): + # For this control, clicks which are not direct hits will slide both + # slider parts + if button: +- opt = QtGui.QStyleOptionSlider() ++ opt = QStyleOptionSlider() + self.initStyleOption(opt) + + self.active_slider = -1 +@@ -671,7 +660,7 @@ def mousePressEvent(self, event): + break + + if self.active_slider < 0: +- self.pressed_control = QtGui.QStyle.SC_SliderHandle ++ self.pressed_control = QStyle.SC_SliderHandle + self.click_offset = self.__pixelPosToRangeValue(self.__pick(event.pos())) + self.triggerAction(self.SliderMove) + self.setRepeatAction(self.SliderNoAction) +@@ -679,13 +668,13 @@ def mousePressEvent(self, event): + event.ignore() + + def mouseMoveEvent(self, event): +- if self.pressed_control != QtGui.QStyle.SC_SliderHandle: ++ if self.pressed_control != QStyle.SC_SliderHandle: + event.ignore() + return + + event.accept() + new_pos = self.__pixelPosToRangeValue(self.__pick(event.pos())) +- opt = QtGui.QStyleOptionSlider() ++ opt = QStyleOptionSlider() + self.initStyleOption(opt) + + if self.active_slider < 0: +@@ -723,9 +712,9 @@ def __pick(self, pt): + + + def __pixelPosToRangeValue(self, pos): +- opt = QtGui.QStyleOptionSlider() ++ opt = QStyleOptionSlider() + self.initStyleOption(opt) +- style = QtGui.QApplication.style() ++ style = QApplication.style() + + gr = style.subControlRect(style.CC_Slider, opt, style.SC_SliderGroove, self) + sr = style.subControlRect(style.CC_Slider, opt, style.SC_SliderHandle, self) +diff --git a/cellpose/gui/io.py b/cellpose/gui/io.py +index 95711b9..cb6a6b5 100644 +--- a/cellpose/gui/io.py ++++ b/cellpose/gui/io.py +@@ -9,7 +9,7 @@ + from ..io import imread, imsave, outlines_to_text + + try: +- from PyQt5 import QtGui, QtCore, Qt, QtWidgets ++ from PyQt5.QtWidgets import QFileDialog + GUI = True + except: + GUI = False +@@ -23,7 +23,7 @@ + def _load_image(parent, filename=None): + """ load image with filename; if None, open QFileDialog """ + if filename is None: +- name = QtGui.QFileDialog.getOpenFileName( ++ name = QFileDialog.getOpenFileName( + parent, "Load image" + ) + filename = name[0] +@@ -131,7 +131,7 @@ def _initialize_images(parent, image, resize, X2): + def _load_seg(parent, filename=None, image=None, image_file=None): + """ load *_seg.npy with filename; if None, open QFileDialog """ + if filename is None: +- name = QtGui.QFileDialog.getOpenFileName( ++ name = QFileDialog.getOpenFileName( + parent, "Load labelled data", filter="*.npy" + ) + filename = name[0] +@@ -276,7 +276,7 @@ def _load_seg(parent, filename=None, image=None, image_file=None): + def _load_masks(parent, filename=None): + """ load zeros-based masks (0=no cell, 1=cell 1, ...) """ + if filename is None: +- name = QtGui.QFileDialog.getOpenFileName( ++ name = QFileDialog.getOpenFileName( + parent, "Load masks (PNG or TIFF)" + ) + filename = name[0] +diff --git a/cellpose/gui/menus.py b/cellpose/gui/menus.py +index b01f76a..2efbace 100644 +--- a/cellpose/gui/menus.py ++++ b/cellpose/gui/menus.py +@@ -1,4 +1,4 @@ +-from PyQt5 import QtGui, QtCore, Qt, QtWidgets ++from PyQt5.QtWidgets import QAction + from . import io + from .. import models + from ..io import save_server +@@ -7,51 +7,51 @@ def mainmenu(parent): + main_menu = parent.menuBar() + file_menu = main_menu.addMenu("&File") + # load processed data +- loadImg = QtGui.QAction("&Load image (*.tif, *.png, *.jpg)", parent) ++ loadImg = QAction("&Load image (*.tif, *.png, *.jpg)", parent) + loadImg.setShortcut("Ctrl+L") + loadImg.triggered.connect(lambda: io._load_image(parent)) + file_menu.addAction(loadImg) + +- parent.loadMasks = QtGui.QAction("Load &masks (*.tif, *.png, *.jpg)", parent) ++ parent.loadMasks = QAction("Load &masks (*.tif, *.png, *.jpg)", parent) + parent.loadMasks.setShortcut("Ctrl+M") + parent.loadMasks.triggered.connect(lambda: io._load_masks(parent)) + file_menu.addAction(parent.loadMasks) + parent.loadMasks.setEnabled(False) + +- loadManual = QtGui.QAction("Load &processed/labelled image (*_seg.npy)", parent) ++ loadManual = QAction("Load &processed/labelled image (*_seg.npy)", parent) + loadManual.setShortcut("Ctrl+P") + loadManual.triggered.connect(lambda: io._load_seg(parent)) + file_menu.addAction(loadManual) + +- #loadStack = QtGui.QAction("Load &numpy z-stack (*.npy nimgs x nchan x pixels x pixels)", parent) ++ #loadStack = QAction("Load &numpy z-stack (*.npy nimgs x nchan x pixels x pixels)", parent) + #loadStack.setShortcut("Ctrl+N") + #loadStack.triggered.connect(lambda: parent.load_zstack(None)) + #file_menu.addAction(loadStack) + +- parent.saveSet = QtGui.QAction("&Save masks and image (as *_seg.npy)", parent) ++ parent.saveSet = QAction("&Save masks and image (as *_seg.npy)", parent) + parent.saveSet.setShortcut("Ctrl+S") + parent.saveSet.triggered.connect(lambda: io._save_sets(parent)) + file_menu.addAction(parent.saveSet) + parent.saveSet.setEnabled(False) + +- parent.savePNG = QtGui.QAction("Save masks as P&NG", parent) ++ parent.savePNG = QAction("Save masks as P&NG", parent) + parent.savePNG.setShortcut("Ctrl+N") + parent.savePNG.triggered.connect(lambda: io._save_png(parent)) + file_menu.addAction(parent.savePNG) + parent.savePNG.setEnabled(False) + +- parent.saveOutlines = QtGui.QAction("Save &Outlines as text for imageJ", parent) ++ parent.saveOutlines = QAction("Save &Outlines as text for imageJ", parent) + parent.saveOutlines.setShortcut("Ctrl+O") + parent.saveOutlines.triggered.connect(lambda: io._save_outlines(parent)) + file_menu.addAction(parent.saveOutlines) + parent.saveOutlines.setEnabled(False) + +- parent.saveServer = QtGui.QAction("Send manually labelled data to server", parent) ++ parent.saveServer = QAction("Send manually labelled data to server", parent) + parent.saveServer.triggered.connect(lambda: save_server(parent)) + file_menu.addAction(parent.saveServer) + parent.saveServer.setEnabled(False) + +- parent.switchBackend = QtGui.QAction("Switch backend to MXNET if installed", parent) ++ parent.switchBackend = QAction("Switch backend to MXNET if installed", parent) + parent.switchBackend.triggered.connect(lambda: parent.check_gpu(False)) + file_menu.addAction(parent.switchBackend) + if models.MXNET_ENABLED: +@@ -62,25 +62,25 @@ def mainmenu(parent): + def editmenu(parent): + main_menu = parent.menuBar() + edit_menu = main_menu.addMenu("&Edit") +- parent.undo = QtGui.QAction('Undo previous mask/trace', parent) ++ parent.undo = QAction('Undo previous mask/trace', parent) + parent.undo.setShortcut("Ctrl+Z") + parent.undo.triggered.connect(parent.undo_action) + parent.undo.setEnabled(False) + edit_menu.addAction(parent.undo) + +- parent.redo = QtGui.QAction('Undo remove mask', parent) ++ parent.redo = QAction('Undo remove mask', parent) + parent.redo.setShortcut("Ctrl+Y") + parent.redo.triggered.connect(parent.undo_remove_action) + parent.redo.setEnabled(False) + edit_menu.addAction(parent.redo) + +- parent.ClearButton = QtGui.QAction('Clear all masks', parent) ++ parent.ClearButton = QAction('Clear all masks', parent) + parent.ClearButton.setShortcut("Ctrl+0") + parent.ClearButton.triggered.connect(parent.clear_all) + parent.ClearButton.setEnabled(False) + edit_menu.addAction(parent.ClearButton) + +- parent.remcell = QtGui.QAction('Remove selected cell (Ctrl+CLICK)', parent) ++ parent.remcell = QAction('Remove selected cell (Ctrl+CLICK)', parent) + parent.remcell.setShortcut("Ctrl+Click") + parent.remcell.triggered.connect(parent.remove_action) + parent.remcell.setEnabled(False) +@@ -90,16 +90,16 @@ def helpmenu(parent): + main_menu = parent.menuBar() + help_menu = main_menu.addMenu("&Help") + +- checkMKL = QtGui.QAction("Check CPU MKL -- see terminal", parent) ++ checkMKL = QAction("Check CPU MKL -- see terminal", parent) + checkMKL.triggered.connect(lambda: models.check_mkl(istorch=parent.torch)) + help_menu.addAction(checkMKL) + +- openHelp = QtGui.QAction("&Help window", parent) ++ openHelp = QAction("&Help window", parent) + openHelp.setShortcut("Ctrl+H") + openHelp.triggered.connect(parent.help_window) + help_menu.addAction(openHelp) + +- openGUI = QtGui.QAction("&GUI layout", parent) ++ openGUI = QAction("&GUI layout", parent) + openGUI.setShortcut("Ctrl+G") + openGUI.triggered.connect(parent.gui_window) + help_menu.addAction(openGUI) +diff --git a/tests/test_train.py b/tests/test_train.py +index 9d05545..bce599c 100644 +--- a/tests/test_train.py ++++ b/tests/test_train.py +@@ -6,7 +6,7 @@ + + os.environ["KMP_DUPLICATE_LIB_OK"]="TRUE" + +-def test_class_train(data_dir, image_names): ++def test_class_train(data_dir): + train_dir = str(data_dir.joinpath('2D').joinpath('train')) + model_dir = str(data_dir.joinpath('2D').joinpath('train').joinpath('models')) + shutil.rmtree(model_dir, ignore_errors=True) +@@ -18,7 +18,7 @@ def test_class_train(data_dir, image_names): + channels=[2,1], save_path=train_dir, n_epochs=10) + print('>>>> model trained and saved to %s'%cpmodel_path) + +-def test_cli_train(data_dir, image_names): ++def test_cli_train(data_dir): + train_dir = str(data_dir.joinpath('2D').joinpath('train')) + model_dir = str(data_dir.joinpath('2D').joinpath('train').joinpath('models')) + shutil.rmtree(model_dir, ignore_errors=True) +@@ -29,7 +29,7 @@ def test_cli_train(data_dir, image_names): + print(e) + raise ValueError(e) + +-def test_cli_train_pretrained(data_dir, image_names): ++def test_cli_train_pretrained(data_dir): + train_dir = str(data_dir.joinpath('2D').joinpath('train')) + model_dir = str(data_dir.joinpath('2D').joinpath('train').joinpath('models')) + shutil.rmtree(model_dir, ignore_errors=True) From 36e942f01eb0e23646897d2e1b0bde2a59e94882 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 11 Aug 2021 18:26:14 +0200 Subject: [PATCH 0821/9987] Add CMake to tbb 2020.03 --- easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb index 3b9ad904fe3..ee01f366853 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.2.0.eb @@ -12,7 +12,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['ebc4f6aa47972daed1f7bf71d100ae5bf6931c2e3144cf299c8cc7d041dca2f3'] builddependencies = [ - ('binutils', '2.35') + ('binutils', '2.35'), + ('CMake', '3.18.4'), ] moduleclass = 'lib' From cb1a33b923c4fa91742812f04eddf18631b3c48d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Aug 2021 22:35:36 +0200 Subject: [PATCH 0822/9987] Also build shared libs for MUMP 5.4.0 --- .../m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb | 10 ++- .../m/MUMPS/MUMPS-5.4.0_shared-mumps.patch | 62 +++++++++++++++++++ .../m/MUMPS/MUMPS-5.4.0_shared-pord.patch | 51 +++++++++++++++ 3 files changed, 122 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0_shared-mumps.patch create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0_shared-pord.patch diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb index a79a8570985..796b2daf523 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb @@ -13,7 +13,15 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['http://mumps.enseeiht.fr/'] sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['c613414683e462da7c152c131cebf34f937e79b30571424060dd673368bbf627'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + 'c613414683e462da7c152c131cebf34f937e79b30571424060dd673368bbf627', # MUMPS_5.4.0.tar.gz + '4c0558690998c12ca959c03856054a75e22f519583a65bd550393c1f81a0b170', # MUMPS-5.4.0_shared-pord.patch + 'd51c2df0de7d7b88d864ceba2d0eea46c755c24c7124003481aced106901109d', # MUMPS-5.4.0_shared-mumps.patch +] dependencies = [ ('SCOTCH', '6.1.0'), diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0_shared-mumps.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0_shared-mumps.patch new file mode 100644 index 00000000000..edadcc4dc15 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0_shared-mumps.patch @@ -0,0 +1,62 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared.patch +Author: micketeer@gmail.com + +diff -ru MUMPS_5.4.0.orig/src/Makefile MUMPS_5.4.0/src/Makefile +--- MUMPS_5.4.0.orig/src/Makefile 2021-08-11 16:22:27.340180216 +0200 ++++ MUMPS_5.4.0/src/Makefile 2021-08-11 16:40:23.930257697 +0200 +@@ -15,18 +15,23 @@ + + libcommon: $(incdir)/mumps_int_def.h + $(MAKE) $(libdir)/libmumps_common$(PLAT)$(LIBEXT) ++ $(MAKE) $(libdir)/libmumps_common$(PLAT).so + + s: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT).so + + d: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT).so + + c: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT).so + + z: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT).so + + include $(topdir)/Makefile.inc + +@@ -200,6 +205,14 @@ + $(AR)$@ $? + $(RANLIB) $@ + ++$(libdir)/libmumps_common$(PLAT).so: $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) ++ $(FC) -shared $^ -Wl,-soname,libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) $(LORDERINGS) -lpthread $(MUMPS_LIBF77) $(MPIFLIB) $(MPICLIB) $(METISLIB) -o $(libdir)/libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libmumps_common$(PLAT)-$(SONAME_VERSION).so $@ ++ ++$(libdir)/lib$(ARITH)mumps$(PLAT).so: $(OBJS_MOD) $(OBJS_OTHER) ++ $(FC) -shared $^ -Wl,-soname,lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) -lmumps_common$(PLAT) -lpthread $(MUMPS_LIBF77) $(LORDERINGS) $(MPIFLIB) $(METISLIB) $(SCALAP) -o $(libdir)/lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $@ ++ + # Dependencies between modules: + # i) arithmetic-dependent modules: + $(ARITH)ana_aux.o: $(ARITH)mumps_struc_def.o \ +@@ -411,13 +424,13 @@ + + .SUFFIXES: .c .F .o + .F.o: +- $(FC) $(OPTF) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -c $*.F $(OUTF)$*.o ++ $(FC) $(OPTF) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -fPIC -c $*.F $(OUTF)$*.o + .c.o: +- $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -c $*.c $(OUTC)$*.o ++ $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -fPIC -c $*.c $(OUTC)$*.o + + $(ARITH)mumps_c.o: mumps_c.c + $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) -DMUMPS_ARITH=MUMPS_ARITH_$(ARITH) \ +- $(IORDERINGSC) $(ORDERINGSC) -c mumps_c.c $(OUTC)$@ ++ $(IORDERINGSC) $(ORDERINGSC) -fPIC -c mumps_c.c $(OUTC)$@ + + clean: + $(RM) *.o *.mod $(incdir)/mumps_int_def.h build_mumps_int_def diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0_shared-pord.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0_shared-pord.patch new file mode 100644 index 00000000000..704a8f66e07 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0_shared-pord.patch @@ -0,0 +1,51 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared-pord.patch +Author: micketeer@gmail.com + +diff -ru MUMPS_5.4.0.orig/Makefile MUMPS_5.4.0/Makefile +--- MUMPS_5.4.0.orig/Makefile 2021-08-11 21:41:30.209055262 +0200 ++++ MUMPS_5.4.0/Makefile 2021-08-11 21:41:40.633028157 +0200 +@@ -42,7 +42,7 @@ + + include Makefile.inc + +-prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) ++prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT).so + + # dummy MPI library (sequential version) + +@@ -59,6 +59,12 @@ + cp $(LPORDDIR)/libpord$(LIBEXT) $@; \ + fi; + ++$(libdir)/libpord$(PLAT).so: ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cd $(LPORDDIR); make CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" ARFUNCT= RANLIB="$(RANLIB)" libpord$(PLAT).so; fi; ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cp -a $(LPORDDIR)/libpord*.so lib/; fi; ++ + clean: + (cd src; $(MAKE) clean) + (cd examples; $(MAKE) clean) +diff -ru MUMPS_5.4.0.orig/PORD/lib/Makefile MUMPS_5.4.0/PORD/lib/Makefile +--- MUMPS_5.4.0.orig/PORD/lib/Makefile 2021-08-11 16:22:27.481179848 +0200 ++++ MUMPS_5.4.0/PORD/lib/Makefile 2021-08-11 16:59:17.511334981 +0200 +@@ -9,7 +9,7 @@ + + INCLUDES = -I../include + +-COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS) ++COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS) -fPIC + + OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \ + multisector.o gelim.o bucket.o tree.o \ +@@ -28,6 +28,10 @@ + $(AR)$@ $(OBJS) + $(RANLIB) $@ + ++libpord$(PLAT).so: $(OBJS) ++ $(CC) -shared $(OBJS) -Wl,-soname,libpord$(PLAT)-$(SONAME_VERSION).so -o libpord$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libpord$(PLAT)-$(SONAME_VERSION).so $@ ++ + clean: + rm -f *.o + From 311468785a7eeb79b24694785a977dfb614103ed Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Thu, 12 Aug 2021 15:58:55 +1000 Subject: [PATCH 0823/9987] Create libsigsegv-2.13-GCCcore-10.2.0.eb New version, new compiler, new binutils --- .../libsigsegv-2.13-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.13-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.13-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..2f09752a341 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.13-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libsigsegv' +version = '2.13' + +homepage = 'https://www.gnu.org/software/libsigsegv/' + +description = "GNU libsigsegv is a library for handling page faults in user mode." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['be78ee4176b05f7c75ff03298d84874db90f4b6c9d5503f0da1226b3a3c48119'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['include/sigsegv.h', 'lib/libsigsegv.a', 'lib/libsigsegv.la'], + 'dirs': [], +} + +moduleclass = 'lib' From 885ebcbbe9041a6c58758d38ef26215af76fdc69 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 12 Aug 2021 10:52:43 +0200 Subject: [PATCH 0824/9987] removing absl-py from deps --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 38a16048f62..6b6b9bf621b 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -22,7 +22,6 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('Cython', '0.29.22'), - ('absl-py', '0.13.0'), ('opt-einsum', '3.3.0'), ('flatbuffers-python', '1.12'), ] From 544bda66009ead13ae9ce1fd932077be4517c4a2 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 12 Aug 2021 11:47:29 +0200 Subject: [PATCH 0825/9987] using buildcmd option --- .../j/jax/jax-0.2.18-correct_libraries.patch | 16 +++++----------- .../easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 17 ++++++++++------- 2 files changed, 15 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch index 478bb70095f..c99c95f9d53 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch @@ -1,8 +1,7 @@ -# using system environment variables + reparing build.py script + using EB downloaded TensorFlow tarball diff -ruN jax_orig/build/build.py jax/build/build.py --- jax_orig/build/build.py 2021-07-30 10:18:43.599233082 +0200 -+++ jax/build/build.py 2021-08-05 17:28:04.071995000 +0200 -@@ -208,15 +208,20 @@ ++++ jax/build/build.py 2021-08-12 11:27:08.067502000 +0200 +@@ -208,15 +208,15 @@ def check_bazel_version(bazel_path): @@ -15,16 +14,11 @@ diff -ruN jax_orig/build/build.py jax/build/build.py - return False - actual_ints = [int(x) for x in match.group(1).split(".")] - return actual_ints >= [2, 0, 0] -+ # try: -+ # version_output = shell([bazel_path, "--version"]) -+ # except subprocess.CalledProcessError: -+ # return False -+ # match = re.search("(Build label:|bazel) *([0-9\\.]+)", version_output) + try: -+ version_output = shell([bazel_path, "--bazelrc=/dev/null", "version"]) ++ version_output = shell([bazel_path, "--version"]) + except subprocess.CalledProcessError: + return False -+ match = re.search("Build label: *([0-9\\.]+)[^0-9\\.]", version_output) ++ match = re.search(r"bazel *([0-9\\.]+)", version_output) + if match is None: + return False + actual_ints = [int(x) for x in match.group(1).split(".")] @@ -32,7 +26,7 @@ diff -ruN jax_orig/build/build.py jax/build/build.py BAZELRC_TEMPLATE = """ -@@ -597,8 +602,7 @@ +@@ -597,8 +597,7 @@ f"--cpu={wheel_cpu}"]) print(" ".join(command)) shell(command) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 6b6b9bf621b..56654b8a7cb 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -29,13 +29,14 @@ dependencies = [ local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_tarball_version local_jax_preinstallopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir -local_jax_preinstallopts += 'python build/build.py ' -local_jax_preinstallopts += '--bazel_startup_options="--output_user_root=%(builddir)s" ' -local_jax_preinstallopts += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' -local_jax_preinstallopts += '--bazel_options=--subcommands ' -local_jax_preinstallopts += '--bazel_options=--jobs=1 --bazel_options=--action_env=PYTHONPATH ' -local_jax_preinstallopts += '--bazel_options=--action_env=EBPYTHONPREFIXES && ' -local_jax_preinstallopts += 'pip install --prefix %(installdir)s dist/*.whl && ' + +local_jax_build_cmd = 'python build/build.py ' +local_jax_build_cmd += '--bazel_startup_options="--output_user_root=%(builddir)s" ' +local_jax_build_cmd += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' +local_jax_build_cmd += '--bazel_options=--subcommands ' +local_jax_build_cmd += '--bazel_options=--jobs=1 --bazel_options=--action_env=PYTHONPATH ' +local_jax_build_cmd += '--bazel_options=--action_env=EBPYTHONPREFIXES && ' + exts_list = [ ('opt-einsum', '3.3.0', { @@ -69,6 +70,8 @@ components = [ 'use_pip': True, 'sanity_pip_check': True, 'download_dep_fail': True, + 'buildcmd': local_jax_build_cmd, + 'install_src': 'dist/*.whl', }), ] From bbde7152076f4bc36a29d0ecc9a2e4ea2aaa122e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 12:12:26 +0200 Subject: [PATCH 0826/9987] Revamp almost everything, add many more dependencies --- .../p/PyPSA/PyPSA-0.17.1-foss-2020b.eb | 49 +++++++++++++++++++ .../p/PyPSA/PyPSA-0.17.1-foss-2021a.eb | 33 ------------- .../p/Pyomo/Pyomo-6.0.1-foss-2020b.eb | 38 ++++++++++++++ 3 files changed, 87 insertions(+), 33 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb delete mode 100644 easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb new file mode 100644 index 00000000000..4a89af3e9d2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2020b.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'PyPSA' +version = '0.17.1' + +homepage = 'https://pypsa.readthedocs.io/' +description = """PyPSA is an open source toolbox for simulating and optimising modern power systems that include +features such as conventional generators with unit commitment, variable wind and solar generation, storage units, +coupling to other energy sectors, and mixed alternating and direct current networks. PyPSA is designed to scale +well with large networks and long time series.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pandapower', '2.7.0'), # Needed for some tests + ('PYPOWER', '5.1.15'), # Needed for some tests +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('networkx', '2.5'), + ('PyTables', '3.6.1'), + ('netcdf4-python', '1.5.5.1'), + ('xarray', '0.16.2'), + ('Pyomo', '6.0.1'), + ('Shapely', '1.8a1'), # for optional cartopy + ('PROJ', '7.2.1'), # for optional cartopy + ('pyshp', '2.1.3'), # for optional cartopy +] + +exts_list = [ + ('Cartopy', '0.19.0.post1', { + 'checksums': ['4b8b4773a98ed7009fe17d9b6ec87ac3ac62b7d14634d7768c190eadc647d576'], + }), + (name, version, { + # Single test fails, with no clear fix + 'runtest': "PYTHONPATH=.:$PYTHONPATH pytest --ignore=test/test_sclopf_scigrid.py ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['47811fc24b2daf663a2bb86749235e03e9988c7604a4d7fea48fbc8d9b4431c9'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2021a.eb deleted file mode 100644 index f66b994f932..00000000000 --- a/easybuild/easyconfigs/p/PyPSA/PyPSA-0.17.1-foss-2021a.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyPSA' -version = '0.17.1' - -homepage = 'https://pypsa.readthedocs.io/' -description = """PyPSA is an open source toolbox for simulating and optimising modern power systems that include -features such as conventional generators with unit commitment, variable wind and solar generation, storage units, -coupling to other energy sectors, and mixed alternating and direct current networks. PyPSA is designed to scale -well with large networks and long time series.""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -github_account = 'PyPSA' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['47811fc24b2daf663a2bb86749235e03e9988c7604a4d7fea48fbc8d9b4431c9'] - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('matplotlib', '3.4.2'), - ('networkx', '2.5.1'), - ('PyTables', '3.6.1'), - ('Pyomo', '6.0.1'), - ('netCDF', '4.8.0'), -] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb new file mode 100644 index 00000000000..d6de3792fcf --- /dev/null +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.0.1-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Pyomo' +version = '6.0.1' + +homepage = 'https://www.pyomo.org/' +description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization + capabilities for formulating and analyzing optimization models. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('GLPK', '4.65'), # Optional solver backend + ('Cbc', '2.10.5'), # Optional solver backend +] + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('PyUtilib', '6.0.0', { + 'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'], + }), + (name, version, { + 'checksums': ['4b27bc917b12a6011e7eb3442a54619f0f42f1087d4defa14b903dd985fdbe7c'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['pyomo -h'] + +moduleclass = 'math' From d02b5ae91cac91d68dae13424c7d8c92d8088d07 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Thu, 12 Aug 2021 12:29:08 +0200 Subject: [PATCH 0827/9987] Updating checksum for the revised timeout patch as per #13700. --- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index b880ebaefd5..a05a60e0fd0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -54,7 +54,7 @@ checksums = [ # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', # PyTorch-1.8.1_increase-distributed-test-timeout.patch - 'c94eda2289692d00873e2ae8cecaaf7a1e5e657dfa4cfcd94b56093f6f4766ad', + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch From 659d8f50eda09e0449f00a44909db2ed42a182dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 13:04:04 +0200 Subject: [PATCH 0828/9987] adding easyconfigs: UShER-0.4.1-gompi-2020b.eb and patches: UShER-0.4.1_external-tbb.patch --- .../u/UShER/UShER-0.4.1-gompi-2020b.eb | 40 +++++++++++++++++++ .../u/UShER/UShER-0.4.1_external-tbb.patch | 17 ++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/u/UShER/UShER-0.4.1_external-tbb.patch diff --git a/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb b/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb new file mode 100644 index 00000000000..2eabcf71638 --- /dev/null +++ b/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'UShER' +version = '0.4.1' + +homepage = 'https://github.com/yatisht/usher' +description = """UShER is now a package consisting of a family of programs for +rapid phylogenetic analyses, particularly suitable for the SARS-CoV-2 genomes.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'yatisht' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['UShER-%(version)s_external-tbb.patch'] +checksums = [ + '61acdeaec61f2b376704b4a519bba44b7cffdebf315f8126aba0a80ac3268b0e', # v0.4.1.tar.gz + 'a5b08fbf0ec65c3f548d794c2ad97b044ce536deab2f3362ad7f985a245bd677', # UShER-0.4.1_external-tbb.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] +dependencies = [ + ('tbb', '2020.3'), + ('protobuf', '3.14.0'), + ('MAFFT', '7.475', '-with-extensions'), + ('Boost', '1.74.0'), + ('Python', '3.8.6'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['usher', 'ripples', 'matOptimize', 'matUtils']], + 'dirs': [], +} + +sanity_check_commands = ['usher -h', 'ripples -h', 'matOptimize -h', 'matUtils -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/UShER/UShER-0.4.1_external-tbb.patch b/easybuild/easyconfigs/u/UShER/UShER-0.4.1_external-tbb.patch new file mode 100644 index 00000000000..eda2b2b3dd1 --- /dev/null +++ b/easybuild/easyconfigs/u/UShER/UShER-0.4.1_external-tbb.patch @@ -0,0 +1,17 @@ +Remove internal build of TBB. Use standard tbb instead of tbb_preview. +Author: micketeer@gmail.com + +diff -ru usher-0.4.1.orig/CMakeLists.txt usher-0.4.1/CMakeLists.txt +--- usher-0.4.1.orig/CMakeLists.txt 2021-08-12 12:23:07.248102942 +0200 ++++ usher-0.4.1/CMakeLists.txt 2021-08-12 12:23:26.353054422 +0200 +@@ -35,9 +35,7 @@ + + include_directories(${Protobuf_INCLUDE_DIRS}) + +-include(${TBB_DIR}/cmake/TBBBuild.cmake) +-tbb_build(TBB_ROOT ${TBB_DIR} CONFIG_DIR TBB_DIR MAKE_ARGS tbb_cpf=1) +-find_package(TBB REQUIRED tbbmalloc tbbmalloc_proxy tbb_preview) ++find_package(TBB REQUIRED tbbmalloc tbbmalloc_proxy tbb) + + FIND_PACKAGE(Boost COMPONENTS program_options iostreams filesystem date_time REQUIRED) + From 0f9f4ba9ee7cc63fc06c32db77bda664d5b6ae7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Aug 2021 13:53:20 +0200 Subject: [PATCH 0829/9987] adding easyconfigs: aria2-1.35.0-GCCcore-10.3.0.eb, CppUnit-1.15.1-GCCcore-10.3.0.eb, c-ares-1.17.2-GCCcore-10.3.0.eb --- .../a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb | 40 +++++++++++++++++++ .../CppUnit/CppUnit-1.15.1-GCCcore-10.3.0.eb | 28 +++++++++++++ .../c/c-ares/c-ares-1.17.2-GCCcore-10.3.0.eb | 23 +++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..341a8dd97ca --- /dev/null +++ b/easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'aria2' +version = '1.35.0' + +homepage = 'https://aria2.github.io' +description = "aria2 is a lightweight multi-protocol & multi-source command-line download utility." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/aria2/aria2/releases/download/release-%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['fd85589416f8246cefc4e6ba2fa52da54fdf11fd5602a2db4b6749f7c33b5b2d'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), + ('CppUnit', '1.15.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), + ('SQLite', '3.35.4'), + ('c-ares', '1.17.2'), + ('OpenSSL', '1.1', '', True), +] + +configopts = "--without-gnutls --with-openssl --enable-libaria2 --enable-static" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/aria2c'], + 'dirs': ['share'], +} + +sanity_check_commands = ["aria2c --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..853d8661541 --- /dev/null +++ b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'CppUnit' +version = '1.15.1' + +homepage = 'https://freedesktop.org/wiki/Software/cppunit/' + +description = """ + CppUnit is the C++ port of the famous JUnit framework for unit testing. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://dev-www.libreoffice.org/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['89c5c6665337f56fd2db36bc3805a5619709d51fb136e51937072f63fcc717a7'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +sanity_check_paths = { + 'files': ['lib/libcppunit.a', 'lib/libcppunit.%s' % SHLIB_EXT, + 'lib/pkgconfig/cppunit.pc'], + 'dirs': ['bin', 'include/cppunit', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8a1f5df0ed1 --- /dev/null +++ b/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'c-ares' +version = '1.17.2' + +homepage = 'https://c-ares.haxx.se' +description = "c-ares is a C library for asynchronous DNS requests (including name resolves)" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://c-ares.haxx.se/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4803c844ce20ce510ef0eb83f8ea41fa24ecaae9d280c468c582d2bb25b3913d'] + +builddependencies = [('binutils', '2.36.1')] + +sanity_check_paths = { + 'files': ['lib/libcares.a', 'lib/libcares.%s' % SHLIB_EXT, 'lib/pkgconfig/libcares.pc'], + 'dirs': ['include', 'share/man'], +} + +moduleclass = 'lib' From 516480fbbdae561940f9040478126d7f8d9346d3 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Thu, 12 Aug 2021 22:02:31 +1000 Subject: [PATCH 0830/9987] Create MATIO-1.5.21-GCCcore-10.2.0.eb New version, new compiler, new binutils --- .../m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..fcb5c5d7630 --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'MATIO' +version = '1.5.21' + +homepage = 'https://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] +checksums = ['bf1808a20412534a7c9e69c6eb0d2612'] + +preconfigopts = 'chmod +x configure && ' + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 8e3e034cdea72a48d7f0514910f80a8318bcf7f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Aug 2021 14:03:35 +0200 Subject: [PATCH 0831/9987] enable sanity_pip_check + add sanity check command for FMRIprep 1.4.1 --- .../f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb index cab27a2cac9..b12cefc9057 100644 --- a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb @@ -132,4 +132,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["fmriprep --help"] + +sanity_pip_check = True + moduleclass = 'bio' From 497398e16b5cbd04b1011437f9085a786ea4d91c Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 12 Aug 2021 16:29:37 +0200 Subject: [PATCH 0832/9987] latest progress on jax --- .../j/jax/jax-0.2.18-correct_libraries.patch | 66 ++++--------------- .../j/jax/jax-0.2.18-foss-2020b.eb | 25 ++++--- 2 files changed, 30 insertions(+), 61 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch index c99c95f9d53..b8a75f1374e 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch @@ -1,76 +1,36 @@ -diff -ruN jax_orig/build/build.py jax/build/build.py ---- jax_orig/build/build.py 2021-07-30 10:18:43.599233082 +0200 -+++ jax/build/build.py 2021-08-12 11:27:08.067502000 +0200 -@@ -208,15 +208,15 @@ - - - def check_bazel_version(bazel_path): -- try: -- version_output = shell([bazel_path, "--bazelrc=/dev/null", "version"]) -- except subprocess.CalledProcessError: -- return False -- match = re.search("Build label: *([0-9\\.]+)[^0-9\\.]", version_output) -- if match is None: -- return False -- actual_ints = [int(x) for x in match.group(1).split(".")] -- return actual_ints >= [2, 0, 0] -+ try: -+ version_output = shell([bazel_path, "--version"]) -+ except subprocess.CalledProcessError: -+ return False -+ match = re.search(r"bazel *([0-9\\.]+)", version_output) -+ if match is None: -+ return False -+ actual_ints = [int(x) for x in match.group(1).split(".")] -+ return actual_ints >= [2, 0, 0] - - - BAZELRC_TEMPLATE = """ -@@ -597,8 +597,7 @@ - f"--cpu={wheel_cpu}"]) - print(" ".join(command)) - shell(command) -- shell([bazel_path, "shutdown"]) -- -+ shell([bazel_path] + args.bazel_startup_options + ["shutdown"]) - - if __name__ == "__main__": - main() -Binary files jax_orig/.git/index and jax/.git/index differ -diff -ruN jax_orig/WORKSPACE jax/WORKSPACE ---- jax_orig/WORKSPACE 2021-07-30 10:18:43.503078000 +0200 -+++ jax/WORKSPACE 2021-08-11 12:20:41.169549000 +0200 -@@ -5,20 +5,21 @@ +diff -ruN jax-jaxlib-v0.1.70_orig/WORKSPACE jax-jaxlib-v0.1.70/WORKSPACE +--- jax-jaxlib-v0.1.70_orig/WORKSPACE 2021-08-12 13:12:54.025608000 +0200 ++++ jax-jaxlib-v0.1.70/WORKSPACE 2021-08-12 13:32:51.581961000 +0200 +@@ -5,21 +5,20 @@ # b) get the sha256 hash of the commit by running: # curl -L https://github.com/tensorflow/tensorflow/archive/.tar.gz | sha256sum # and update the sha256 with the result. -http_archive( +# http_archive( +# name = "org_tensorflow", -+# sha256 = "de22145c9dc51b3ed9399dbee2ab681f094f09e5213d6819451da500f163a14b", -+# strip_prefix = "tensorflow-8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532", ++# sha256 = "0f13410284b9186e436350e9617b3bed2d65f1dc1a220fd37ad9ef43c2035663", ++# strip_prefix = "tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d", +# urls = [ -+# "https://github.com/tensorflow/tensorflow/archive/8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532.tar.gz", ++# "https://github.com/tensorflow/tensorflow/archive/4039feeb743bc42cd0a3d8146ce63fc05d23eb8d.tar.gz", +# ], -+# patch_cmds=['sed -i -e "s|arguments = \[args\],|arguments = \[args\],\\n\\tuse_default_shell_env = True,|" third_party/mlir/tblgen.bzl'] +# ) + +local_repository( name = "org_tensorflow", -- sha256 = "de22145c9dc51b3ed9399dbee2ab681f094f09e5213d6819451da500f163a14b", -- strip_prefix = "tensorflow-8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532", +- sha256 = "0f13410284b9186e436350e9617b3bed2d65f1dc1a220fd37ad9ef43c2035663", +- strip_prefix = "tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d", - urls = [ -- "https://github.com/tensorflow/tensorflow/archive/8cc3ffa8d8e4dd659c1534849cf5984ef4ec3532.tar.gz", +- "https://github.com/tensorflow/tensorflow/archive/4039feeb743bc42cd0a3d8146ce63fc05d23eb8d.tar.gz", - ], + path = "pathToSed", ) -- + -# For development, one can use a local TF repository instead. -# local_repository( -# name = "org_tensorflow", -# path = "tensorflow", -# ) -+# WIP - +- load("//third_party/pocketfft:workspace.bzl", pocketfft = "repo") pocketfft() + diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 56654b8a7cb..9541cc592e7 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -4,7 +4,7 @@ easyblock = 'PythonBundle' name = 'jax' version = '0.2.18' - +local_jaxlib_ver = '0.1.70' homepage = 'https://pypi.python.org/pypi/jax' description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more""" @@ -30,12 +30,13 @@ local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_tarball_version local_jax_preinstallopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir -local_jax_build_cmd = 'python build/build.py ' +local_jax_build_cmd = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir +local_jax_build_cmd += 'python build/build.py ' local_jax_build_cmd += '--bazel_startup_options="--output_user_root=%(builddir)s" ' local_jax_build_cmd += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' local_jax_build_cmd += '--bazel_options=--subcommands ' local_jax_build_cmd += '--bazel_options=--jobs=1 --bazel_options=--action_env=PYTHONPATH ' -local_jax_build_cmd += '--bazel_options=--action_env=EBPYTHONPREFIXES && ' +local_jax_build_cmd += '--bazel_options=--action_env=EBPYTHONPREFIXES' exts_list = [ @@ -47,11 +48,16 @@ exts_list = [ 'modulename': 'absl' })] +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + components = [ - (name, version, { + ('jaxlib', local_jaxlib_ver, { 'easyblock': 'PythonPackage', 'sources': [ - '%(name)s-v%(version)s.zip', + 'jaxlib-v%s.zip' % local_jaxlib_ver, { 'download_filename': 'v%s.tar.gz' % local_tf_tarball_version, 'filename': 'tensorflow_v%s.tar.gz' % local_tf_tarball_version, @@ -62,10 +68,10 @@ components = [ 'https://github.com/tensorflow/tensorflow/archive/' ], 'patches': [ - ('%s-%s-correct_libraries.patch' % (name, version), 1), - ('%s-%s-controlled_tf_tarball.patch' % (name, version), '../tensorflow-%s' % local_tf_tarball_version), + ('jaxlib-%s-correct_libraries.patch' % local_jaxlib_ver, 1), + ('jaxlib-%s-controlled_tf_tarball.patch' % local_jaxlib_ver, '../tensorflow-%s' % local_tf_tarball_version), ], - 'start_dir': '%(name)s-%(name)s-v%(version)s', + 'start_dir': 'jax-jaxlib-v%s' % local_jaxlib_ver, 'preinstallopts': local_jax_preinstallopts, 'use_pip': True, 'sanity_pip_check': True, @@ -73,6 +79,9 @@ components = [ 'buildcmd': local_jax_build_cmd, 'install_src': 'dist/*.whl', }), + ('jax', '0.2.18', { + 'easyblock': 'PythonPackage', + }), ] moduleclass = 'tools' From dbbe6c110261f40aa81cadce1a50f28095cca6a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 16:32:55 +0200 Subject: [PATCH 0833/9987] Fix typo --- easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb b/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb index 2eabcf71638..3c336471f36 100644 --- a/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb +++ b/easybuild/easyconfigs/u/UShER/UShER-0.4.1-gompi-2020b.eb @@ -31,8 +31,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/' + x for x in ['usher', 'ripples', 'matOptimize', 'matUtils']], - 'dirs': [], + 'files': ['bin/' + x for x in ['usher', 'ripples', 'matOptimize', 'matUtils']], + 'dirs': [], } sanity_check_commands = ['usher -h', 'ripples -h', 'matOptimize -h', 'matUtils -h'] From f17c3d246a6fc5add6f6aadac2390d7b496a7a8e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 16:33:54 +0200 Subject: [PATCH 0834/9987] Update easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index a702b3a699e..7b66b43f294 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -6,7 +6,10 @@ description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +source_urls = [ + 'https://patch-diff.githubusercontent.com/raw/open-mpi/ompi/pull/', + 'https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads', +] sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', From f1dc0dbb3773a1e076974920b51d3576b4c65885 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 16:33:59 +0200 Subject: [PATCH 0835/9987] Update easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index 7b66b43f294..c8466635cb3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -14,6 +14,8 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' + '9212.patch', + '9213.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 From 3c4d39632612be7be3cf05063abb49682d40354d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 16:34:05 +0200 Subject: [PATCH 0836/9987] Update easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index c8466635cb3..5dd52256452 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -23,6 +23,8 @@ checksums = [ 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', + 'a85b09da354916c2a08c24922268e4f25352daf2787c7c90cd5d24ca4f8d892f', # 9212.patch + 'cd250609f2c7974774a4e8931873bc795c0769581f91530524df516490de4954', # 9213.patch ] builddependencies = [ From 7201b847f3a812e08a3e51526a2525a6a297b8fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 16:45:22 +0200 Subject: [PATCH 0837/9987] Update easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index 5dd52256452..9a76b9a2f8e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -13,7 +13,7 @@ source_urls = [ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', - 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' + 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', '9212.patch', '9213.patch', ] From 6101324bd2f706b4ba4ab3bbed854738bb796b50 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 12 Aug 2021 16:00:59 +0100 Subject: [PATCH 0838/9987] adding easyconfigs: igraph-0.9.4-foss-2021a.eb --- .../i/igraph/igraph-0.9.4-foss-2021a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.9.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.9.4-foss-2021a.eb b/easybuild/easyconfigs/i/igraph/igraph-0.9.4-foss-2021a.eb new file mode 100644 index 00000000000..60d6cf9f3e0 --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.9.4-foss-2021a.eb @@ -0,0 +1,51 @@ +# Author: Denis Krišťák (INUITS) +# Modified: Jasper Grimm (UoY) + +easyblock = 'CMakeMake' + +name = 'igraph' +version = '0.9.4' + +homepage = 'https://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['a3285cccf4f043c9ced2bc8d8d2609ff8398cb92ed49fdf86264ed91929137dd'] + +builddependencies = [ + ('Autotools', '20210128'), + ('pkg-config', '0.29.2'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('GLPK', '5.0'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('arpack-ng', '3.8.0'), +] + +# Build static and shared libraries +configopts = ["-DBUILD_SHARED_LIBS=OFF", "-DBUILD_SHARED_LIBS=ON"] + +# extra folder `igraph` is wrong, since all other software expects it to be in ./include folder directly +postinstallcmds = [ + 'mv %(installdir)s/include/igraph/* %(installdir)s/include/ && rmdir %(installdir)s/include/igraph ', +] + +_includes = ['include/igraph%s.h' % x for x in ['', '_blas', '_constants', '_lapack', '_types', '_version']] +_libs = ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]] + +sanity_check_paths = { + 'files': _includes + _libs, + 'dirs': [], +} + +moduleclass = 'lib' From 64d73834ed5af1c7318cd08b1eabdd770f6e75af Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 12 Aug 2021 16:02:30 +0100 Subject: [PATCH 0839/9987] adding easyconfigs: PyCairo-1.20.1-GCCcore-10.3.0.eb --- .../PyCairo/PyCairo-1.20.1-GCCcore-10.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8c06de67588 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-10.3.0.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'PyCairo' +version = '1.20.1' + +homepage = 'https://pycairo.readthedocs.io/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1ee72b035b21a475e1ed648e26541b04e5d7e753d75ca79de8c583b25785531b'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('cairo', '1.16.0'), +] + +# PyGTK needs PyCairo installed by pip +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# remove pyproject.toml, which causes trouble (header files and .pc file are not installed) +preinstallopts = "rm pyproject.toml && " + +# Don't build a wheel or the pkg-cfg file won't be installed +installopts = '--no-binary=%(namelower)s' + +sanity_check_paths = { + 'files': ['%s/py3cairo.%s' % (p, e) for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')]], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +options = {'modulename': 'cairo'} + +moduleclass = 'vis' From 1f179b3c9ef894b04418d5f7a02bb2ad0e1c3973 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 12 Aug 2021 16:43:15 +0100 Subject: [PATCH 0840/9987] adding easyconfigs: gompi-2021b.eb, OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb --- easybuild/easyconfigs/g/gompi/gompi-2021b.eb | 20 ++++++++++++++++ .../OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb | 24 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2021b.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2021b.eb b/easybuild/easyconfigs/g/gompi/gompi-2021b.eb new file mode 100644 index 00000000000..d5860d74ef0 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2021b.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2021b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '11.2.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.1.1', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb new file mode 100644 index 00000000000..d8ee2498fbe --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.7.1' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TGZ] +checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 3aef5d670e77d9e0ef32ec1f6f8fbbab2a101b0a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 12 Aug 2021 16:54:47 +0100 Subject: [PATCH 0841/9987] adding easyconfigs: Clang-12.0.1-GCCcore-10.3.0.eb --- .../c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c6ed800d787 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb @@ -0,0 +1,74 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '12.0.1' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'clang-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', + 'clang-tools-extra-%(version)s.src.tar.xz', + 'libunwind-%(version)s.src.tar.xz', +] +checksums = [ + '7d9a8405f557cefc5a21bf5672af73903b64749d9bc3a50322239f56f34ffddf', # llvm-12.0.1.src.tar.xz + '6e912133bcf56e9cfe6a346fa7e5c52c2cde3e4e48b7a6cc6fcc7c75047da45f', # clang-12.0.1.src.tar.xz + 'b4c8d5f2a802332987c1c0a95b5afb35b1a66a96fe44add4e4ed4792c4cba0a4', # compiler-rt-12.0.1.src.tar.xz + '2254e25312708a567b1ab00716362db379d265e47a97a94ed74211d57a4cd5f9', # polly-12.0.1.src.tar.xz + '60fe79440eaa9ebf583a6ea7f81501310388c02754dbe7dc210776014d06b091', # openmp-12.0.1.src.tar.xz + '690b3f6a76310e13a783a142f87500ade9cafe003e088b678364487ed873e361', # lld-12.0.1.src.tar.xz + 'a42089cd358f661823c490741f8be98701d983a7ee5152c8649075da681a9d15', # libcxx-12.0.1.src.tar.xz + '88efe8e391767a1e8f42b509879abe766c9f44b1781ad1900975ae6b516b91d0', # libcxxabi-12.0.1.src.tar.xz + '65659efdf97dbed70ae0caee989936b731f249dddc46f1cb4225b2f49b232ae5', # clang-tools-extra-12.0.1.src.tar.xz + '0bea6089518395ca65cf58b0a450716c5c99ce1f041079d3aa42d280ace15ca4', # libunwind-12.0.1.src.tar.xz +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.36.1'), + ('hwloc', '2.4.1'), + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), + ('GMP', '6.2.1'), + ('Z3', '4.8.11'), +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Python', '3.9.5'), + ('elfutils', '0.185'), +] + +assertions = True +usepolly = True +build_lld = True +libcxx = True +enable_rtti = True +build_extra_clang_tools = True + +skip_all_tests = True + +moduleclass = 'compiler' From 3fbf46c6e27d9c2b9f1decb2720c4fd6bd1d3304 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 12 Aug 2021 17:14:56 +0100 Subject: [PATCH 0842/9987] adding easyconfigs: python-igraph-0.9.6-foss-2021a.eb --- .../python-igraph-0.9.6-foss-2021a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.6-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.6-foss-2021a.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.6-foss-2021a.eb new file mode 100644 index 00000000000..a9d7cb4ed18 --- /dev/null +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.6-foss-2021a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'python-igraph' +version = '0.9.6' + +homepage = 'https://igraph.org/python' +description = """Python interface to the igraph high performance graph library, primarily aimed at complex network + research and analysis.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('igraph', '0.9.4'), + ('PyCairo', '1.20.1'), + ('Clang', '12.0.1'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), +] + +use_pip = True + +exts_list = [ + ('texttable', '1.6.4', { + 'checksums': ['42ee7b9e15f7b225747c3fa08f43c5d6c83bc899f80ff9bae9319334824076e9'], + }), + (name, version, { + 'installopts': '--install-option="--use-pkg-config"', + 'modulename': 'igraph', + 'patches': ['%(name)s-0.9.0_fix-igraph-libs.patch'], + 'checksums': [ + '1824ca0489068100534d717056395d580b2d19bf4fefb378465e6a37a20bf316', # python-igraph-0.9.6.tar.gz + # python-igraph-0.9.0_fix-igraph-libs.patch + '7af7a6e6a8b982ced7cdd939d82a98829512088744bebad34c714a3c4803f126', + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/igraph'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# cairo must be available for proper plotting support +sanity_check_commands = ["python -c 'from igraph.drawing.utils import find_cairo; cairo = find_cairo(); cairo.Context'"] + +sanity_pip_check = True + +moduleclass = 'lib' From 4d2de964a094cbb32513eb5b18104b755e380450 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 12 Aug 2021 18:55:00 +0200 Subject: [PATCH 0843/9987] adding easyconfigs: MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb --- ...onCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..85e8215a7f5 --- /dev/null +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ake Sandgren +# HPC2N +# Umea University + +name = 'MotionCor2' +version = '1.4.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://msg.ucsf.edu/' +description = """MotionCor2 correct anisotropic image motion at the +single pixel level across the whole frame, suitable for both single +particle and tomographic images. Iterative, patch-based motion detection +is combined with spatial and temporal constraints and dose weighting. + +Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, +Yifan Cheng and David A. Agard (2016) Anisotropic Correction of +Beam-induced Motion for Improved Single-particle Electron +Cryo-microscopy, Nature Methods, submitted. +BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +# No longer directly downloadable, available from https://msg.ucsf.edu/software +sources = [ + '%(name)s_%(version)s.zip', +] +checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] + +# CUDA is a build dependency to make sure it gets installed. +# It's actually a runtime dependency, but that's handled in the wrapper to +# make sure it doesn't conflict with whatever toolchain happens to be loaded. +# Change CUDA version to match the latest one used in this version +# of MotionCor2 +builddependencies = [ + ('binutils', '2.36.1'), + ('CUDAcore', '11.3.1', '', True), +] + +skip_rpath_check = True + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('XZ', '5.2.5'), + ('LibTIFF', '4.2.0'), + ('jbigkit', '2.1'), +] + +moduleclass = 'bio' From 43640d2b1cefad402b811ef303a462106f6a03a9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 18:56:42 +0200 Subject: [PATCH 0844/9987] adding easyconfigs: Mako-1.1.4-GCCcore-11.2.0.eb, LLVM-12.0.1-GCCcore-11.2.0.eb, libdrm-2.4.107-GCCcore-11.2.0.eb, libglvnd-1.3.3-GCCcore-11.2.0.eb, Mesa-21.2.0-GCCcore-11.2.0.eb --- .../l/LLVM/LLVM-12.0.1-GCCcore-11.2.0.eb | 40 +++++++++++ .../l/libdrm/libdrm-2.4.107-GCCcore-11.2.0.eb | 32 +++++++++ .../libglvnd/libglvnd-1.3.3-GCCcore-11.2.0.eb | 33 +++++++++ .../m/Mako/Mako-1.1.4-GCCcore-11.2.0.eb | 29 ++++++++ .../m/Mesa/Mesa-21.2.0-GCCcore-11.2.0.eb | 69 +++++++++++++++++++ 5 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.107-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.1.4-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-21.2.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..bc7a24dd95c --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-12.0.1-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +name = 'LLVM' +version = '12.0.1' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = ['llvm-%(version)s.src.tar.xz'] +checksums = ['7d9a8405f557cefc5a21bf5672af73903b64749d9bc3a50322239f56f34ffddf'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.107-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.107-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..842abee0870 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.107-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'libdrm' +version = '2.4.107' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c554cef03b033636a975543eab363cc19081cb464595d3da1ec129f87370f888'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), +] +dependencies = [('X11', '20210802')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '-Dman-pages=false' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b2bf5af2288 --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.3-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'libglvnd' +version = '1.3.3' + +homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] +sources = ['libglvnd-v%(version)s.tar.gz'] +checksums = ['e768f43a0b23d9a8c9f1bed425f7f15d8491a1780253945a4445ddc40e5f6f84'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), +] + +dependencies = [('X11', '20210802')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.1.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.1.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..df4dac07af5 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.1.4-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.1.4' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['17831f0b7087c313c0ffae2bcbbd3c1d5ba9eeac9c38f2eb7b50e8c99fe9d5ab'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ["mako-render --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-21.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-21.2.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1b5282e7583 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-21.2.0-GCCcore-11.2.0.eb @@ -0,0 +1,69 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers are enabled based on system architecture: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# Default renderer is llvmpipe. SWR can be enabled by setting the environment +# variable GALLIUM_DRIVER=swr + +name = 'Mesa' +version = '21.2.0' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0cb3c802f4b8e7699b1602c08c29d06a4d532ab5b8f7a64676c4ca6bb8f4d426'] + +builddependencies = [ + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('pkg-config', '0.29.2'), + ('Mako', '1.1.4'), + ('libxml2', '2.9.10'), + ('expat', '2.4.1'), + ('gettext', '0.21'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('zstd', '1.5.0'), + ('libdrm', '2.4.107'), + ('libglvnd', '1.3.3'), + ('libunwind', '1.5.0'), + ('LLVM', '12.0.1'), + ('X11', '20210802'), +] + +configopts = "-Dplatforms=x11 -Dosmesa=true -Ddri-drivers='' -Dvulkan-drivers='' " +configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast,swr -Dswr-arches=avx,avx2,skx,knl" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +# Tells libglvnd where to find EGL libraries +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} + +moduleclass = 'vis' From 6abf782532aadc38afdbe22e8c199ff00b0caa2f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 19:15:12 +0200 Subject: [PATCH 0845/9987] adding easyconfigs: APR-1.7.0-GCCcore-11.2.0.eb, APR-util-1.6.1-GCCcore-11.2.0.eb, utf8proc-2.6.1-GCCcore-11.2.0.eb, SCons-4.2.0-GCCcore-11.2.0.eb, Serf-1.3.9-GCCcore-11.2.0.eb, Subversion-1.14.1-GCCcore-11.2.0.eb --- .../APR-util/APR-util-1.6.1-GCCcore-11.2.0.eb | 32 ++++++++++++ .../a/APR/APR-1.7.0-GCCcore-11.2.0.eb | 22 +++++++++ .../s/SCons/SCons-4.2.0-GCCcore-11.2.0.eb | 33 +++++++++++++ .../s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb | 39 +++++++++++++++ .../Subversion-1.14.1-GCCcore-11.2.0.eb | 49 +++++++++++++++++++ .../utf8proc/utf8proc-2.6.1-GCCcore-11.2.0.eb | 30 ++++++++++++ 6 files changed, 205 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.2.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/Subversion/Subversion-1.14.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c55d9126fb7 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.1' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('APR', '1.7.0'), + ('SQLite', '3.36'), + ('expat', '2.4.1'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f8b0ca58f44 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.0' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.2.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2212975537f --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.2.0-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '4.2.0' + +homepage = 'https://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['691893b63f38ad14295f5104661d55cb738ec6514421c6261323351c25432b0a'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/sconsign'], + 'dirs': [], +} + +sanity_check_commands = ["scons --help"] + +sanity_pip_check = True + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c6fb0da1ec0 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'SCons' +name = 'Serf' +version = '1.3.9' + +homepage = 'https://serf.apache.org/' +description = """The serf library is a high performance C-based HTTP client library + built upon the Apache Portable Runtime (APR) library""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Serf-%(version)s_python3_scons.patch'] +checksums = [ + '549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc', # serf-1.3.9.tar.bz2 + 'db401893bfb464ddcf369b543cacb9a165a21f8ff9bf1a819e4b61550bb9d3d0', # Serf-1.3.9_python3_scons.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), + ('SCons', '4.2.0'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('OpenSSL', '1.1', '', True), +] + +buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" + +sanity_check_paths = { + 'files': ['include/serf-1/serf.h'] + + ['lib/libserf-1.%s' % x for x in ['a', 'so']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..10196a0d9c9 --- /dev/null +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.1-GCCcore-11.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'Subversion' +version = '1.14.1' + +homepage = 'https://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + 'https://apache.belnet.be/%(namelower)s', + 'http://www.eu.apache.org/dist/%(namelower)s', + 'http://www.us.apache.org/dist/%(namelower)s', + 'https://archive.apache.org/dist/%(namelower)s', +] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Subversion-1.12.0-no_swig.patch'] +checksums = [ + '2c5da93c255d2e5569fa91d92457fdb65396b0666fad4fd59b22e154d986e1a9', # subversion-1.14.1.tar.bz2 + '539ea2118f958d152d78438c81649eb727ff0b2e8491295702ee98e1f922041f', # Subversion-1.12.0-no_swig.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('SQLite', '3.36'), + ('zlib', '1.2.11'), + ('lz4', '1.9.3'), + ('utf8proc', '2.6.1'), + ('Serf', '1.3.9'), +] + +preconfigopts = './autogen.sh && ' + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-lz4=$EBROOTLZ4 --with-serf=$EBROOTSERF" + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b53f6ad6b27 --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.6.1' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4c06a9dc4017e8a2438ef80ee371d45868bda2237a98b26554de7a95406b283b'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 3b86b0c8c458c0fc0f030cca362f03414b5e60a9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 19:19:38 +0200 Subject: [PATCH 0846/9987] adding easyconfigs: SWIG-4.0.2-GCCcore-11.2.0.eb --- .../s/SWIG/SWIG-4.0.2-GCCcore-11.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..065ac6afc5f --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +name = 'SWIG' +version = '4.0.2' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d53be9730d8d58a16bf0cbd1f8ac0c0c3e1090573168bfa151b01eb47fa906fc'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('zlib', '1.2.11'), + ('PCRE', '8.45'), +] + +configopts = '--without-alllang --with-boost=no' + +moduleclass = 'devel' From 8ac307f7980ae587eb39ca86a4f556261b553671 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Aug 2021 19:20:27 +0200 Subject: [PATCH 0847/9987] remove unused buildcmd from libgpuarray easyconfigs --- .../libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb | 1 - .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb | 1 - .../libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb | 1 - .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb | 1 - 4 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb index 78364cb4e7e..227d24549a3 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb @@ -30,7 +30,6 @@ exts_default_options = { } exts_list = [ (name, version, { - 'buildcmd': 'build_ext', 'modulename': 'pygpu', 'source_tmpl': SOURCE_TAR_GZ, 'source_urls': ['https://github.com/Theano/%(name)s/releases/download/v%(version)s/'], diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb index c76c0d9b051..d65e2c7c358 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb @@ -31,7 +31,6 @@ exts_default_options = { } exts_list = [ (name, version, { - 'buildcmd': 'build_ext', 'modulename': 'pygpu', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb index 5b798cd4a45..3c578c8cc13 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb @@ -31,7 +31,6 @@ exts_default_options = { } exts_list = [ (name, version, { - 'buildcmd': 'build_ext', 'modulename': 'pygpu', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb index 21aa4a17f7d..d871b75c78a 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -33,7 +33,6 @@ exts_default_options = { } exts_list = [ (name, version, { - 'buildcmd': 'build_ext', 'modulename': 'pygpu', 'source_urls': ['https://github.com/Theano/libgpuarray/releases/download/v%(version)s/'], 'checksums': ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'], From 6efac2b83f37a5b81f8e58eb60fb1a48dd748aef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 19:27:53 +0200 Subject: [PATCH 0848/9987] adding easyconfigs: Tkinter-3.9.6-GCCcore-11.2.0.eb, Tk-8.6.11-GCCcore-11.2.0.eb --- .../t/Tk/Tk-8.6.11-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ .../t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb | 25 ++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.11-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.11-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.11-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..cccc8294a60 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.11-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.11' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] +checksums = [ + '5228a8187a7f70fa0791ef0f975270f068ba9557f57456f51eb02d9d4ea31282', # tk8.6.11-src.tar.gz + '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d', # Tk-8.6.4_different-prefix-with-tcl.patch +] + +builddependencies = [('binutils', '2.37')] +dependencies = [ + ('Tcl', version), + ('X11', '20210802'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6b58177d7d7 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb @@ -0,0 +1,25 @@ +name = 'Tkinter' +version = '3.9.6' + +homepage = 'https://python.org/' +description = "Tkinter module, built with the Python buildsystem" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['e0fbd5b6e1ee242524430dee3c91baf4cbbaba4a72dd1674b90fda87b713c7ab'] + +builddependencies = [ + ('binutils', '2.37'), + ('libffi', '3.4.2') +] + +dependencies = [ + ('Python', '3.9.6'), + ('Tk', '8.6.11'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' From 714a80e6214aea3782dc5bb9a8c10b6d59c5d9d9 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 12 Aug 2021 18:27:54 +0100 Subject: [PATCH 0849/9987] adding easyconfigs: MariaDB-10.6.4-GCC-10.3.0.eb, Kent_tools-418-GCC-10.3.0.eb --- .../k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb | 36 +++++++++++ .../m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb | 61 +++++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb new file mode 100644 index 00000000000..dbd3d358708 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'Kent_tools' +version = '418' + +homepage = 'https://genome.cse.ucsc.edu/' +description = """Kent utilities: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +source_urls = [ + 'https://hgdownload.cse.ucsc.edu/admin/exe/', + 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', +] +sources = ['userApps.v%(version)s.src.tgz'] +checksums = ['2ecb1a74f85129ebad71dbe4bf06ccc006fb24ef615ae5afa08ca2c008beabcf'] + +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + +dependencies = [ + ('MariaDB', '10.6.4'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('util-linux', '2.36'), +] + +buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..227928190fd --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb @@ -0,0 +1,61 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.6.4' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + '75bf9b147a95d38160d01a73b098d50a1960563b46d16a235971fff64d99643c', # mariadb-10.6.4.tar.gz + '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19', # MariaDB-10.1.13-link-rt-for-jemalloc.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('libaio', '0.3.112'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.3'), # optional + ('XZ', '5.2.5'), # optional + ('jemalloc', '5.2.1'), # optional + ('snappy', '1.1.8'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.9.10'), # needed by Connect XML + ('Boost', '1.76.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release " +configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=bundled " # using an external PCRE is broken, see https://bugs.exim.org/show_bug.cgi?id=2173 +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' From 06cbb55bc74c110a71d222c7fc686999dbd725fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 19:34:00 +0200 Subject: [PATCH 0850/9987] Checksum fix --- easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb index 6b58177d7d7..0c9ac99d4b0 100644 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb @@ -9,7 +9,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.python.org/ftp/python/%(version)s/'] sources = ['Python-%(version)s.tgz'] -checksums = ['e0fbd5b6e1ee242524430dee3c91baf4cbbaba4a72dd1674b90fda87b713c7ab'] +checksums = ['d0a35182e19e416fc8eae25a3dcd4d02d4997333e4ad1f2eee6010aadc3fe866'] builddependencies = [ ('binutils', '2.37'), From 03ec8957092d12d0508910c99077bc6c6ba03030 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 19:36:46 +0200 Subject: [PATCH 0851/9987] adding easyconfigs: FriBidi-1.0.10-GCCcore-11.2.0.eb, LAME-3.100-GCCcore-11.2.0.eb, FFmpeg-4.3.2-GCCcore-11.2.0.eb --- .../f/FFmpeg/FFmpeg-4.3.2-GCCcore-11.2.0.eb | 44 +++++++++++++++++++ .../FriBidi/FriBidi-1.0.10-GCCcore-11.2.0.eb | 32 ++++++++++++++ .../l/LAME/LAME-3.100-GCCcore-11.2.0.eb | 36 +++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ea81a575cad --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '4.3.2' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ffmpeg.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ab3a6d6a70358ba0a5f67f37f91f6656b7302b02e98e5b8c846c16763c99913a'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2') +] + +dependencies = [ + ('NASM', '2.15.05'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('x264', '20210613'), + ('LAME', '3.100'), + ('x265', '3.5'), + ('X11', '20210802'), + ('freetype', '2.11.0'), + ('fontconfig', '2.13.94'), + ('FriBidi', '1.0.10'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4a4084cbfb1 --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.10' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7f1c687c7831499bcacae5e8675945a39bacbad16ecaa945e9454a32df653c01'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +configopts = '--disable-docs' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1bb5846fed4 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +dependencies = [('ncurses', '6.2')] + +preconfigopts = "autoconf && " + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' From c0d5f3db6d23b99a84f420099a69c348be4550b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 19:47:35 +0200 Subject: [PATCH 0852/9987] adding easyconfigs: libogg-1.3.5-GCCcore-11.2.0.eb, libvorbis-1.3.7-GCCcore-11.2.0.eb, FLAC-1.3.3-GCCcore-11.2.0.eb, vorbis-tools-1.4.2-GCCcore-11.2.0.eb, libsndfile-1.0.31-GCCcore-11.2.0.eb --- .../f/FLAC/FLAC-1.3.3-GCCcore-11.2.0.eb | 30 +++++++++++++++++ .../l/libogg/libogg-1.3.5-GCCcore-11.2.0.eb | 25 ++++++++++++++ .../libsndfile-1.0.31-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ .../libvorbis-1.3.7-GCCcore-11.2.0.eb | 30 +++++++++++++++++ .../vorbis-tools-1.4.2-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ 5 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.31-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9e8c65680d0 --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.3-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.3.3' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['213e82bd716c9de6db2f98bcadbc4c24c7e2efe8c75939a1a84e28539c4e1748'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +sanity_check_commands = ["flac --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d70d332d245 --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.5' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705'] + +builddependencies = [('binutils', '2.37')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.31-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b7a16a424db --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.0.31-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsndfile' +version = '1.0.31' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/libsndfile/libsndfile/releases/download/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['a8cfb1c09ea6e90eff4ca87322d4168cdbe5035cb48717b40bf77e751cc02163'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('FLAC', '1.3.3'), + ('libvorbis', '1.3.7'), +] + +configopts = '--enable-octave=no' + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4ba927e476f --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..da06c6c4d4f --- /dev/null +++ b/easybuild/easyconfigs/v/vorbis-tools/vorbis-tools-1.4.2-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'vorbis-tools' +version = '1.4.2' + +homepage = 'https://xiph.org/vorbis/' +description = """Command-line tools for creating and playing Ogg Vorbis files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_GZ] +checksums = ['db7774ec2bf2c939b139452183669be84fda5774d6400fc57fde37f77624f0b0'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libvorbis', '1.3.7'), + ('FLAC', '1.3.3'), +] + +local_bins = ['oggdec', 'oggenc', 'ogginfo', 'vorbiscomment'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + ['bin/vcut'], + 'dirs': [], +} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'tools' From 45de65a1c4ac6b9fec2b359fee0fb93e2ce76dff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 20:41:37 +0200 Subject: [PATCH 0853/9987] adding easyconfigs: Pillow-8.3.1-GCCcore-11.2.0.eb, Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb --- .../Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb | 39 +++++++++++++++++++ .../p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb | 32 +++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9b2bde2adbc --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '8.3.1' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['bf77f392094e3bb24ca56ef8bbc4ea0d9752226ff348682d849c0aa8c1577980'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.11.0') +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..32bbaf622c5 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '8.3.1' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2cac53839bfc5cece8fdbe7f084d5e3ee61e1303cccc86511d351adcb9e2c792'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.11.0') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From f7fd93cee96b3a47381112cac39145e73a352cc4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 20:51:05 +0200 Subject: [PATCH 0854/9987] adding easyconfigs: mimalloc-1.7.2-GCCcore-11.2.0.eb, jemalloc-5.2.1-GCCcore-11.2.0.eb, gperftools-2.9.1-GCCcore-11.2.0.eb --- .../gperftools-2.9.1-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ .../jemalloc/jemalloc-5.2.1-GCCcore-11.2.0.eb | 37 ++++++++++++++++++ .../mimalloc/mimalloc-1.7.2-GCCcore-11.2.0.eb | 32 ++++++++++++++++ 3 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9cd22be218a --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.9.1-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.9.1' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'gperftools' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['484a88279d2fa5753d7e9dea5f86954b64975f20e796a6ffaf2f3426a674a06a'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), +] + +dependencies = [ + ('libunwind', '1.5.0'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8d8d04374eb --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.2.1' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ed51b0b37098af4ca6ed31c22324635263f8ad6471889e0592a9c0dba9136aea'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..75037315485 --- /dev/null +++ b/easybuild/easyconfigs/m/mimalloc/mimalloc-1.7.2-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'mimalloc' +version = '1.7.2' + +homepage = 'https://microsoft.github.io/mimalloc/' +description = """mimalloc is a general purpose allocator with excellent performance characteristics.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'microsoft' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b1912e354565a4b698410f7583c0f83934a6dbb3ade54ab7ddcb1569320936bd'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +sanity_check_paths = { + 'files': ['lib/mimalloc-%(version_major_minor)s/libmimalloc.a', 'lib/libmimalloc.%s' % SHLIB_EXT], + 'dirs': ['include/mimalloc-%(version_major_minor)s'], +} + +runtest = 'test' + +# mimalloc is a drop-in replacement for malloc and can be used in other programs without code changes, +# but we don't enable this by default, you need to opt-in by setting $LD_PRELOAD as follows +# modextrapaths = {'LD_PRELOAD': ['lib/libmimalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' From 02220d0d43d877aca9ccfa769435032308804b0d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 20:55:55 +0200 Subject: [PATCH 0855/9987] adding easyconfigs: elfutils-0.185-GCCcore-11.2.0.eb, patchelf-0.13-GCCcore-11.2.0.eb --- .../elfutils/elfutils-0.185-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ .../patchelf/patchelf-0.13-GCCcore-11.2.0.eb | 27 ++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.13-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e71a4d7646e --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.185-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.185' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['dc8d3e74ab209465e7f568e1b3bb9a5a142f8656e2b57d10049a73da2ae6b5a6'] + +builddependencies = [ + ('M4', '1.4.19'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('binutils', '2.37'), + ('bzip2', '1.0.8'), + ('libarchive', '3.5.1'), + ('XZ', '5.2.5'), + ('zstd', '1.5.0'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.13-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f553b4df4c1 --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.13-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.13' + +homepage = 'https://github.com/NixOS/patchelf' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['60c6aeadb673de9cc1838b630c81f61e31c501de324ef7f1e8094a2431197d09'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +moduleclass = 'tools' From 459fcf936d7b4d41a58926b0a32a205ea4f1a79a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 21:03:23 +0200 Subject: [PATCH 0856/9987] adding easyconfigs: JupyterLab-3.1.6-GCCcore-11.2.0.eb --- .../JupyterLab-3.1.6-GCCcore-11.2.0.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..64b0887fb60 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '3.1.6' + +homepage = "https://jupyter.org/" +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('IPython', '7.26.0'), +] + +use_pip = True +sanity_pip_check = True + + +exts_list = [ + ('anyio', '3.3.0', { + 'checksums': ['ae57a67583e5ff8b4af47666ff5651c3732d45fd26c929253748e796af860374'], + }), + ('json5', '0.9.6', { + 'checksums': ['9175ad1bc248e22bb8d95a8e8d765958bf0008fef2fe8abab5bc04e0f1ac8302'], + }), + ('jupyter_server', '1.10.2', { + 'checksums': ['d3a3b68ebc6d7bfee1097f1712cf7709ee39c92379da2cc08724515bb85e72bf'], + }), + ('requests-unixsocket', '0.2.0', { + 'checksums': ['9e5c1a20afc3cf786197ae59c79bcdb0e7565f218f27df5f891307ee8817c1ea'], + }), + ('sniffio', '1.2.0', { + 'checksums': ['c4666eecec1d3f50960c6bdf61ab7bc350648da6c126e3cf6898d8cd4ddcd3de'], + }), + ('websocket-client', '1.2.0', { + 'modulename': 'websocket', + 'checksums': ['7665ba6c645989b28b61670874ab753e6929179e9fc90565ace6ac090f59c559'], + }), + ('nbclassic', '0.3.1', { + 'checksums': ['f920f8d09849bea7950e1017ff3bd101763a8d68f565a51ce053572e65aa7947'], + }), + ('jupyterlab_server', '2.7.0', { + 'checksums': ['31457ef564febc42043bc539356c804f6f9144f602e2852150bf0820ed6d7e18'], + }), + (name, version, { + 'patches': ['%(name)s-1.2.5_set-app-path-for-easybuild.patch'], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': [ + '6d2ada6a333861f33a1b555d3cb7b07aa9d1ab80f07997b3d0c43878a98c1174', # jupyterlab-3.1.6.tar.gz + # JupyterLab-1.2.5_set-app-path-for-easybuild.patch + 'a219b1071f37f848f7e79c6800149c0b2386a2b748be43288bc32af8e7dab668', + ], + }), +] + +sanity_check_commands = ["jupyter lab --help"] + +modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} + +moduleclass = 'tools' From 4f773bec31ba42056280288794c722071f179523 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 21:14:58 +0200 Subject: [PATCH 0857/9987] adding easyconfigs: xprop-1.2.5-GCCcore-11.2.0.eb, FLTK-1.3.7-GCCcore-11.2.0.eb, libGLU-9.0.2-GCCcore-11.2.0.eb --- .../f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb | 42 +++++++++++++++++++ .../l/libGLU/libGLU-9.0.2-GCCcore-11.2.0.eb | 27 ++++++++++++ .../x/xprop/xprop-1.2.5-GCCcore-11.2.0.eb | 32 ++++++++++++++ 3 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..cdd2aa649c0 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.7' + +homepage = 'https://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-1.3.6_fix-LDFLAGS.patch'] +checksums = [ + '5d2ccb7ad94e595d3d97509c7a931554e059dd970b7b29e6fd84cb70fd5491c6', # fltk-1.3.7-source.tar.gz + 'f8af2414a1ee193a186b0d98d1e3567add0ee003f44ec64dce2ce2dfd6d95ebf', # FLTK-1.3.6_fix-LDFLAGS.patch +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +builddependencies = [ + ('binutils', '2.37') +] + +dependencies = [ + ('Mesa', '21.2.0'), + ('libGLU', '9.0.2'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('xprop', '1.2.5'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b2b2eb39bc3 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.2' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.gz'] +checksums = ['24effdfb952453cc00e275e1c82ca9787506aba0282145fff054498e60e19a65'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Mesa', '21.2.0'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6681455aa1d --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.5' + +homepage = "https://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftp.x.org/archive/individual/app/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b7bf6b6be6cf23e7966a153fc84d5901c14f01ee952fbd9d930aa48e2385d670'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210802'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' From b8797f2761905f2c0a6aa418d20406c91afe71f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Aug 2021 21:16:58 +0200 Subject: [PATCH 0858/9987] Fix style --- easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb index 0c9ac99d4b0..36acc188699 100644 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.9.6-GCCcore-11.2.0.eb @@ -13,7 +13,7 @@ checksums = ['d0a35182e19e416fc8eae25a3dcd4d02d4997333e4ad1f2eee6010aadc3fe866'] builddependencies = [ ('binutils', '2.37'), - ('libffi', '3.4.2') + ('libffi', '3.4.2'), ] dependencies = [ From 2a96df0890668185697d0345300d68519e041ea5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 13 Aug 2021 00:57:31 +0200 Subject: [PATCH 0859/9987] Add groff builddep --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb index cdd2aa649c0..de884dc7459 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb @@ -22,7 +22,8 @@ checksums = [ configopts = '--enable-shared --enable-threads --enable-xft' builddependencies = [ - ('binutils', '2.37') + ('binutils', '2.37'), + ('groff', '1.22.4'), ] dependencies = [ From 19a552a9d9dbf3dd883d5c95bfc218d66de09201 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 13 Aug 2021 09:13:24 +0200 Subject: [PATCH 0860/9987] added rpath correction --- .../MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb index 85e8215a7f5..8d0ed77770f 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -35,11 +35,14 @@ checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] # of MotionCor2 builddependencies = [ ('binutils', '2.36.1'), + ('patchelf', '0.12'), ('CUDAcore', '11.3.1', '', True), ] skip_rpath_check = True +postinstallcmds = ['patchelf --force-rpath --set-rpath $EBROOTCUDACORE/lib64:$EBROOTLIBTIFF/lib %(installdir)s/bin/MotionCor2_1.4.4_Cuda113'] + dependencies = [ ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.6'), From 98dbee5ff240d6123ff6e2221ed1d2aeb09f261d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 13 Aug 2021 10:48:12 +0200 Subject: [PATCH 0861/9987] latest progress on jax --- .../j/jax/jax-0.2.18-foss-2020b.eb | 23 +++++++++++-------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 9541cc592e7..ab9484568bc 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -28,10 +28,10 @@ dependencies = [ local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_tarball_version -local_jax_preinstallopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir +local_jax_prebuildopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir -local_jax_build_cmd = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir -local_jax_build_cmd += 'python build/build.py ' +# local_jax_build_cmd = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir +local_jax_build_cmd = 'python build/build.py ' local_jax_build_cmd += '--bazel_startup_options="--output_user_root=%(builddir)s" ' local_jax_build_cmd += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' local_jax_build_cmd += '--bazel_options=--subcommands ' @@ -44,16 +44,22 @@ exts_list = [ 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', 'modulename': 'opt_einsum', }), - ('absl-py', '0.13.0', { - 'modulename': 'absl' - })] + ('jax', '0.2.18', { + 'easyblock': 'PythonPackage', + }), +] default_component_specs = { 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], 'start_dir': '%(name)s-%(version)s', } components = [ + ('absl-py', '0.13.0', { + 'options': {'modulename': 'absl'}, + 'easyblock': 'PythonPackage', + }), ('jaxlib', local_jaxlib_ver, { 'easyblock': 'PythonPackage', 'sources': [ @@ -72,16 +78,13 @@ components = [ ('jaxlib-%s-controlled_tf_tarball.patch' % local_jaxlib_ver, '../tensorflow-%s' % local_tf_tarball_version), ], 'start_dir': 'jax-jaxlib-v%s' % local_jaxlib_ver, - 'preinstallopts': local_jax_preinstallopts, + 'preinstallopts': local_jax_prebuildopts, 'use_pip': True, 'sanity_pip_check': True, 'download_dep_fail': True, 'buildcmd': local_jax_build_cmd, 'install_src': 'dist/*.whl', }), - ('jax', '0.2.18', { - 'easyblock': 'PythonPackage', - }), ] moduleclass = 'tools' From a4988de58bce194e517d8032b857a1e7c023de4f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 13 Aug 2021 10:49:21 +0200 Subject: [PATCH 0862/9987] latest progress on jax --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index ab9484568bc..6c6f61d3781 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -78,7 +78,7 @@ components = [ ('jaxlib-%s-controlled_tf_tarball.patch' % local_jaxlib_ver, '../tensorflow-%s' % local_tf_tarball_version), ], 'start_dir': 'jax-jaxlib-v%s' % local_jaxlib_ver, - 'preinstallopts': local_jax_prebuildopts, + 'prebuildopts': local_jax_prebuildopts, 'use_pip': True, 'sanity_pip_check': True, 'download_dep_fail': True, From a7cb72ca2aea327c9e38e8a94257fe198aecaaab Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 13 Aug 2021 10:54:42 +0200 Subject: [PATCH 0863/9987] latest jax changes --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 6c6f61d3781..7a4eaa647c4 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -44,7 +44,7 @@ exts_list = [ 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', 'modulename': 'opt_einsum', }), - ('jax', '0.2.18', { + ('%(name)s', '%(version)s', { 'easyblock': 'PythonPackage', }), ] From a4c22ffab279b9035da7e2b074b2b2f7a189cf17 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 13 Aug 2021 10:31:22 +0100 Subject: [PATCH 0864/9987] Patch to fix building Qt5.10.1 against newer qlibc --- .../q/Qt5/Qt5-5.10.1-foss-2018b.eb | 6 ++++- .../q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb | 6 ++++- .../q/Qt5/Qt5-5.10.1-intel-2018b.eb | 6 ++++- .../q/Qt5/Qt5-5.10.1_glibc-fix.patch | 26 +++++++++++++++++++ 4 files changed, 41 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.10.1_glibc-fix.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-foss-2018b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-foss-2018b.eb index 9ecfb02053e..a2831b4034c 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-foss-2018b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-foss-2018b.eb @@ -14,7 +14,11 @@ source_urls = [ 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', ] sources = ['qt-everywhere-src-%(version)s.tar.xz'] -checksums = ['05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a'] +patches = [('%(name)s-%(version)s_glibc-fix.patch', 'qtbase')] +checksums = [ + '05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a', # qt-everywhere-src-5.10.1.tar.xz + 'd7939eaac79b145b031c18a0c17c09a4dd17301a9e21f7850a415183008b8d13', # Qt5-5.10.1_glibc-fix.patch +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb index f969e6b6e76..b97c1baf89c 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb @@ -14,7 +14,11 @@ source_urls = [ 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', ] sources = ['qt-everywhere-src-%(version)s.tar.xz'] -checksums = ['05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a'] +patches = ['%(name)s-%(version)s_glibc-fix.patch'] +checksums = [ + '05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a', # qt-everywhere-src-5.10.1.tar.xz + 'd7939eaac79b145b031c18a0c17c09a4dd17301a9e21f7850a415183008b8d13', # Qt5-5.10.1_glibc-fix.patch +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-intel-2018b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-intel-2018b.eb index 9f4a742d137..6313e872382 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-intel-2018b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-intel-2018b.eb @@ -14,7 +14,11 @@ source_urls = [ 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', ] sources = ['qt-everywhere-src-%(version)s.tar.xz'] -checksums = ['05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a'] +patches = ['%(name)s-%(version)s_glibc-fix.patch'] +checksums = [ + '05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a', # qt-everywhere-src-5.10.1.tar.xz + 'd7939eaac79b145b031c18a0c17c09a4dd17301a9e21f7850a415183008b8d13', # Qt5-5.10.1_glibc-fix.patch +] builddependencies = [('pkg-config', '0.29.2')] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1_glibc-fix.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1_glibc-fix.patch new file mode 100644 index 00000000000..766741eb027 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1_glibc-fix.patch @@ -0,0 +1,26 @@ +Fix Qt5.10.1 to build against newer qlibc. +This takes the relevant part of patch from https://code.qt.io/cgit/qt/qtbase.git/commit/?id=25feee4e061b99edab79503d81f5bd045c6c8e3d +Added to EasyBuild by Simon Branford (University of Birmingham) +index 3469ebe5e6..c5585ea32a 100644 +--- a/qtbase/src/corelib/global/qconfig-bootstrapped.h ++++ b/qtbase/src/corelib/global/qconfig-bootstrapped.h +@@ -98,9 +98,17 @@ + #define QT_NO_QOBJECT + #define QT_FEATURE_process -1 +-#define QT_FEATURE_renameat2 -1 ++#ifdef __GLIBC_PREREQ ++# define QT_FEATURE_renameat2 (__GLIBC_PREREQ(2, 28) ? 1 : -1) ++#else ++# define QT_FEATURE_renameat2 -1 ++#endif + #define QT_FEATURE_sharedmemory -1 + #define QT_FEATURE_slog2 -1 +-#define QT_FEATURE_statx -1 ++#ifdef __GLIBC_PREREQ ++# define QT_FEATURE_statx (__GLIBC_PREREQ(2, 28) ? 1 : -1) ++#else ++# define QT_FEATURE_statx -1 ++#endif + #define QT_FEATURE_syslog -1 + #define QT_NO_SYSTEMLOCALE + #define QT_FEATURE_systemsemaphore -1 From a413f6dc01829ac434320b6345b3725f1e70a782 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 13 Aug 2021 11:00:55 +0100 Subject: [PATCH 0865/9987] Add Python as a builddependency to recent fontconfig --- .../f/fontconfig/fontconfig-2.13.93-GCCcore-10.3.0.eb | 1 + .../f/fontconfig/fontconfig-2.13.94-GCCcore-11.2.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.93-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.93-GCCcore-10.3.0.eb index ce22e2d81eb..afc50b525be 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.93-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.93-GCCcore-10.3.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('binutils', '2.36.1'), ('gperf', '3.1'), ('pkg-config', '0.29.2'), + ('Python', '3.9.5', '-bare'), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.94-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.94-GCCcore-11.2.0.eb index 0a0da831671..6829e30b095 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.94-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.94-GCCcore-11.2.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('binutils', '2.37'), ('gperf', '3.1'), ('pkg-config', '0.29.2'), + ('Python', '3.9.6', '-bare'), ] dependencies = [ From 8a4ea93abb68bcfea31c8dae671e17b8280bfa33 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 13 Aug 2021 13:02:19 +0200 Subject: [PATCH 0866/9987] update source url --- easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb index 18a95c65a3f..2ee0a563be0 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb @@ -16,7 +16,7 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm toolchain = SYSTEM -source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast//executables/legacy/%(version)s/'] +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/%(version)s/'] sources = ['%(namelower)s-%(version)s-x64-linux.tar.gz'] sanity_check_paths = { From edc20607794439c69771fc9dc1ba8a1544936ce1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 13:27:39 +0200 Subject: [PATCH 0867/9987] remove opt-einsum dependency for jax, since it's installed as an extension + just use name/version rather than equivalent templates in exts_list --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 3 +-- ...tarball.patch => jaxlib-0.1.70-controlled_tf_tarball.patch} | 0 ...t_libraries.patch => jaxlib-0.1.70-correct_libraries.patch} | 0 3 files changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/j/jax/{jax-0.2.18-controlled_tf_tarball.patch => jaxlib-0.1.70-controlled_tf_tarball.patch} (100%) rename easybuild/easyconfigs/j/jax/{jax-0.2.18-correct_libraries.patch => jaxlib-0.1.70-correct_libraries.patch} (100%) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 7a4eaa647c4..677fc09291e 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -22,7 +22,6 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('Cython', '0.29.22'), - ('opt-einsum', '3.3.0'), ('flatbuffers-python', '1.12'), ] @@ -44,7 +43,7 @@ exts_list = [ 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', 'modulename': 'opt_einsum', }), - ('%(name)s', '%(version)s', { + (name, version, { 'easyblock': 'PythonPackage', }), ] diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-controlled_tf_tarball.patch b/easybuild/easyconfigs/j/jax/jaxlib-0.1.70-controlled_tf_tarball.patch similarity index 100% rename from easybuild/easyconfigs/j/jax/jax-0.2.18-controlled_tf_tarball.patch rename to easybuild/easyconfigs/j/jax/jaxlib-0.1.70-controlled_tf_tarball.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch b/easybuild/easyconfigs/j/jax/jaxlib-0.1.70-correct_libraries.patch similarity index 100% rename from easybuild/easyconfigs/j/jax/jax-0.2.18-correct_libraries.patch rename to easybuild/easyconfigs/j/jax/jaxlib-0.1.70-correct_libraries.patch From ea7145912b554b662df5643b2914bf344e565a2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 13:35:35 +0200 Subject: [PATCH 0868/9987] add checksums to jax easyconfig --- .../easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 677fc09291e..dc5da6e2584 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -37,14 +37,15 @@ local_jax_build_cmd += '--bazel_options=--subcommands ' local_jax_build_cmd += '--bazel_options=--jobs=1 --bazel_options=--action_env=PYTHONPATH ' local_jax_build_cmd += '--bazel_options=--action_env=EBPYTHONPREFIXES' - exts_list = [ ('opt-einsum', '3.3.0', { - 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', 'modulename': 'opt_einsum', + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], }), (name, version, { 'easyblock': 'PythonPackage', + 'checksums': ['b08d5137189a7384429541b39575a022d4bbf777cdb081e8c1bf6bc14eefcd41'], }), ] @@ -58,6 +59,7 @@ components = [ ('absl-py', '0.13.0', { 'options': {'modulename': 'absl'}, 'easyblock': 'PythonPackage', + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], }), ('jaxlib', local_jaxlib_ver, { 'easyblock': 'PythonPackage', @@ -76,6 +78,14 @@ components = [ ('jaxlib-%s-correct_libraries.patch' % local_jaxlib_ver, 1), ('jaxlib-%s-controlled_tf_tarball.patch' % local_jaxlib_ver, '../tensorflow-%s' % local_tf_tarball_version), ], + 'checksums': [ + '1205b180de70c98899d842f75bb589599c10a3c7a1c6099475c3a7d39b2e44ac', # jaxlib-v0.1.70.zip + '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # tensorflow_v2.5.0.tar.gz + # jaxlib-0.1.70-correct_libraries.patch + '4033a81a45b1b455ab6ef4fde697db1d08aa073851c2d86ddca881777ad95be8', + # jaxlib-0.1.70-controlled_tf_tarball.patch + 'b7120325113593bceb3e72b4145116024af8efc140a202967da9ca2e514155a7', + ], 'start_dir': 'jax-jaxlib-v%s' % local_jaxlib_ver, 'prebuildopts': local_jax_prebuildopts, 'use_pip': True, From b9ebe6fe9639d7dec5382785f8d191efff58d18e Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 13 Aug 2021 11:38:42 +0000 Subject: [PATCH 0869/9987] pangolin 3.1.10 created --- .../p/pangolin/pangolin-3.1.10-foss-2020b.eb | 75 +++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb new file mode 100644 index 00000000000..d4a0e70f0c1 --- /dev/null +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb @@ -0,0 +1,75 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on a EC provided by Paul Jähn +# uploaded by J. Sassmannshausen + +easyblock = 'PythonBundle' + +name = 'pangolin' +version = '3.1.10' + +homepage = 'https://cov-lineages.org/pangolin.html' +description = "Software package for assigning SARS-CoV-2 genome sequences to global lineages." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Biopython', '1.78'), + ('gofasta', '0.0.5', '', True), + ('minimap2', '2.20'), + ('Pysam', '0.16.0.1'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('snakemake', '6.1.0'), + ('UShER', '0.4.1'), + ('scikit-learn', '0.23.2'), +] + +use_pip = True +sanity_pip_check = True + +github_account = 'cov-lineages' +exts_list = [ + ('pangolin', '3.1.11', { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['ce64a3ef84de5b11d5c9f21f76341cae23c0fabbf46cc3c1b7b244701b36efbc'], + }), + ('pangoLEARN', '2021-08-09', { + 'modulename': 'pangoLEARN', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['ece55bc37b3e35dbdff2432fb8b9ea76fa53fe993394a425d1df67147484a81e'], + }), + ('scorpio', '0.3.12', { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['48390ed1c1a79bb5f801083042cdeddee060e2277f40c293fd30384882aced81'], + }), + ('constellations', '0.0.13', { + 'source_urls': ['https://github.com/%(github_account)s/%name)s/archive'], + 'sources': [{'download_filename': 'v%(version).tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['4aa3edae9491a59621ef6a3b5bbd21a13c68355986f6c097e46a1397d5b1d24b'], + }), + ('pango-designation', '1.2.59', { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['bd6c11b376c2f6955afa9e96938464184e5f6db22334589cbbbfefe1cbe35e86'], + }), +] + +_binaries = [ + 'constellations', 'extract_definitions.py', 'pango_designation', 'pangoLEARN', + 'pangolearn.smk', 'pangolin', 'scorpio', 'type_constellations.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + 'pangolin -pv && scorpio -v' +] + +moduleclass = 'bio' From 415ba09bb52e91cfc8b0d6902068b5a5ececae00 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 13 Aug 2021 14:45:33 +0200 Subject: [PATCH 0870/9987] latest jax changes --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 7a4eaa647c4..5643231ce7d 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -22,7 +22,6 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('Cython', '0.29.22'), - ('opt-einsum', '3.3.0'), ('flatbuffers-python', '1.12'), ] @@ -30,7 +29,6 @@ local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_tarball_version local_jax_prebuildopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir -# local_jax_build_cmd = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir local_jax_build_cmd = 'python build/build.py ' local_jax_build_cmd += '--bazel_startup_options="--output_user_root=%(builddir)s" ' local_jax_build_cmd += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' From 228604338b8e79c7732806a4b18ae872793eb0eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 15:43:36 +0200 Subject: [PATCH 0871/9987] remove commented out line from jax easyconfig --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index dc5da6e2584..069fe5d44bc 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -29,7 +29,6 @@ local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_tarball_version local_jax_prebuildopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir -# local_jax_build_cmd = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir local_jax_build_cmd = 'python build/build.py ' local_jax_build_cmd += '--bazel_startup_options="--output_user_root=%(builddir)s" ' local_jax_build_cmd += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' From d1cd880878e09419db64f596798c20628432503f Mon Sep 17 00:00:00 2001 From: "benjamin.czaja" Date: Fri, 13 Aug 2021 16:08:22 +0200 Subject: [PATCH 0872/9987] adding easyconfigs: biogeme-3.1.2-foss-2021a-Python-3.9.5.eb, biogeme-3.2.8-foss-2021a-Python-3.9.5.eb --- .../biogeme-3.1.2-foss-2021a-Python-3.9.5.eb | 36 +++++++++++++++++ .../biogeme-3.2.8-foss-2021a-Python-3.9.5.eb | 39 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a-Python-3.9.5.eb create mode 100644 easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..1c49b4a975c --- /dev/null +++ b/easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'biogeme' +version = '3.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/biogeme' +description = """Biogeme is a open source Python package designed for +the maximum likelihood estimation of parametric models in general, +with a special emphasis on discrete choice models.""" + +use_pip = True +sanity_pip_check = True + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05') +] + +exts_list = [ + ('Unidecode', '1.2.0', { + 'checksums': ['8d73a97d387a956922344f6b74243c2c6771594659778744b2dbdaad8f6b727d'], + }), + (name, version, { + 'checksums': ['28aecfa3701c293e3b3c6bcab68322d77d1721e10b18d987f592651333f1e438'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/biogeme'], +} + +moduleclass = 'math' \ No newline at end of file diff --git a/easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..bbdc72b9394 --- /dev/null +++ b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'biogeme' +version = '3.2.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/biogeme' +description = """Biogeme is a open source Python package designed for +the maximum likelihood estimation of parametric models in general, +with a special emphasis on discrete choice models.""" + +use_pip = True +sanity_pip_check = True + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05') +] + +exts_list = [ + ('Unidecode', '1.2.0', { + 'checksums': ['8d73a97d387a956922344f6b74243c2c6771594659778744b2dbdaad8f6b727d'], + }), + ('tqdm', '4.62.0', { + 'checksums': ['3642d483b558eec80d3c831e23953582c34d7e4540db86d9e5ed9dad238dabc6'], + }), + (name, version, { + 'checksums': ['eafb969bb086a014617fae92e652fb54dd98ac72516a360e40c837244935859c'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/biogeme'], +} + +moduleclass = 'math' \ No newline at end of file From 584a328d7563471f3486b8a559e96c7969c3402b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 13 Aug 2021 16:59:06 +0200 Subject: [PATCH 0873/9987] Drop Mesa 21.2.0 back to stable 21.1.7 --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.2.0.eb | 2 +- ...21.2.0-GCCcore-11.2.0.eb => Mesa-21.1.7-GCCcore-11.2.0.eb} | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/m/Mesa/{Mesa-21.2.0-GCCcore-11.2.0.eb => Mesa-21.1.7-GCCcore-11.2.0.eb} (96%) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb index de884dc7459..293f92a02b0 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.7-GCCcore-11.2.0.eb @@ -27,7 +27,7 @@ builddependencies = [ ] dependencies = [ - ('Mesa', '21.2.0'), + ('Mesa', '21.1.7'), ('libGLU', '9.0.2'), ('libpng', '1.6.37'), ('libjpeg-turbo', '2.0.6'), diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.2.0.eb index b2b2eb39bc3..669bc4bc96c 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.2.0.eb @@ -16,7 +16,7 @@ checksums = ['24effdfb952453cc00e275e1c82ca9787506aba0282145fff054498e60e19a65'] builddependencies = [('binutils', '2.37')] dependencies = [ - ('Mesa', '21.2.0'), + ('Mesa', '21.1.7'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-21.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-21.1.7-GCCcore-11.2.0.eb similarity index 96% rename from easybuild/easyconfigs/m/Mesa/Mesa-21.2.0-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/m/Mesa/Mesa-21.1.7-GCCcore-11.2.0.eb index 1b5282e7583..97e9bb87b40 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-21.2.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-21.1.7-GCCcore-11.2.0.eb @@ -10,7 +10,7 @@ # variable GALLIUM_DRIVER=swr name = 'Mesa' -version = '21.2.0' +version = '21.1.7' homepage = 'https://www.mesa3d.org/' description = """Mesa is an open-source implementation of the OpenGL specification - @@ -26,7 +26,7 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] -checksums = ['0cb3c802f4b8e7699b1602c08c29d06a4d532ab5b8f7a64676c4ca6bb8f4d426'] +checksums = ['e9e67c10654f2e4bf15b944bb048007a614292aa4792b1b7512eb700b7b3a7bb'] builddependencies = [ ('binutils', '2.37'), From 1210ab0d75511f444988e303bec6aeb81406797b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 17:17:33 +0200 Subject: [PATCH 0874/9987] stick to specific TensorFlow commit used by jaxlib 0.1.70, enable building jaxlib in parallel, use pip to install all Python packages, enable sanity_pip_check, fix and rename patch file for TensorFlow sources --- ...3d8146ce63fc05d23eb8d_mlir-build-env.patch | 12 +++++++ .../j/jax/jax-0.2.18-foss-2020b.eb | 35 +++++++++++-------- .../jaxlib-0.1.70-controlled_tf_tarball.patch | 12 ------- 3 files changed, 33 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/j/jax/TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d_mlir-build-env.patch delete mode 100644 easybuild/easyconfigs/j/jax/jaxlib-0.1.70-controlled_tf_tarball.patch diff --git a/easybuild/easyconfigs/j/jax/TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d_mlir-build-env.patch b/easybuild/easyconfigs/j/jax/TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d_mlir-build-env.patch new file mode 100644 index 00000000000..ad451807936 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d_mlir-build-env.patch @@ -0,0 +1,12 @@ +make TensorFlow pick up on build environment defined by EasyBuild +author: Denis Kristak, Pavel Grochal (INUITS) +--- tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d/third_party/mlir/tblgen.bzl.orig 2021-08-13 16:18:12.735593126 +0200 ++++ tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d/third_party/mlir/tblgen.bzl 2021-08-13 16:18:48.615675683 +0200 +@@ -173,6 +173,7 @@ + inputs = trans_srcs, + executable = ctx.executable.tblgen, + arguments = [args], ++ use_default_shell_env = True, + mnemonic = "TdGenerate", + ) + diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 069fe5d44bc..fe0e1e87e81 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -11,9 +11,6 @@ more""" toolchain = {'name': 'foss', 'version': '2020b'} -# downloading TF tarball for better control of what Bazel will use during installation of Jax -local_tf_tarball_version = '2.5.0' - builddependencies = [ ('Bazel', '3.7.2'), ] @@ -25,7 +22,11 @@ dependencies = [ ('flatbuffers-python', '1.12'), ] -local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_tarball_version +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = '4039feeb743bc42cd0a3d8146ce63fc05d23eb8d' + +local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_commit local_jax_prebuildopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir @@ -33,12 +34,13 @@ local_jax_build_cmd = 'python build/build.py ' local_jax_build_cmd += '--bazel_startup_options="--output_user_root=%(builddir)s" ' local_jax_build_cmd += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' local_jax_build_cmd += '--bazel_options=--subcommands ' -local_jax_build_cmd += '--bazel_options=--jobs=1 --bazel_options=--action_env=PYTHONPATH ' +local_jax_build_cmd += '--bazel_options=--jobs=%(parallel)s --bazel_options=--action_env=PYTHONPATH ' local_jax_build_cmd += '--bazel_options=--action_env=EBPYTHONPREFIXES' +use_pip = True + exts_list = [ ('opt-einsum', '3.3.0', { - 'modulename': 'opt_einsum', 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], }), @@ -59,14 +61,15 @@ components = [ 'options': {'modulename': 'absl'}, 'easyblock': 'PythonPackage', 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], + 'use_pip': True, }), ('jaxlib', local_jaxlib_ver, { 'easyblock': 'PythonPackage', 'sources': [ 'jaxlib-v%s.zip' % local_jaxlib_ver, { - 'download_filename': 'v%s.tar.gz' % local_tf_tarball_version, - 'filename': 'tensorflow_v%s.tar.gz' % local_tf_tarball_version, + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, } ], 'source_urls': [ @@ -75,15 +78,17 @@ components = [ ], 'patches': [ ('jaxlib-%s-correct_libraries.patch' % local_jaxlib_ver, 1), - ('jaxlib-%s-controlled_tf_tarball.patch' % local_jaxlib_ver, '../tensorflow-%s' % local_tf_tarball_version), + ('TensorFlow-%s_mlir-build-env.patch' % local_tf_commit, '../tensorflow-%s' % local_tf_commit), ], 'checksums': [ - '1205b180de70c98899d842f75bb589599c10a3c7a1c6099475c3a7d39b2e44ac', # jaxlib-v0.1.70.zip - '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # tensorflow_v2.5.0.tar.gz - # jaxlib-0.1.70-correct_libraries.patch + # jaxlib-v0.1.70.zip + '1205b180de70c98899d842f75bb589599c10a3c7a1c6099475c3a7d39b2e44ac', + # tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d.tar.gz + '0f13410284b9186e436350e9617b3bed2d65f1dc1a220fd37ad9ef43c2035663', + # jaxlib-0.1.70-correct_libraries.patch, '4033a81a45b1b455ab6ef4fde697db1d08aa073851c2d86ddca881777ad95be8', - # jaxlib-0.1.70-controlled_tf_tarball.patch - 'b7120325113593bceb3e72b4145116024af8efc140a202967da9ca2e514155a7', + # TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d-build-env.patch + 'd067836b1d18d66a8c69fb3db311855c8a56c0106d42a11299a1733c385e9c22', ], 'start_dir': 'jax-jaxlib-v%s' % local_jaxlib_ver, 'prebuildopts': local_jax_prebuildopts, @@ -95,4 +100,6 @@ components = [ }), ] +sanity_pip_check = True + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jaxlib-0.1.70-controlled_tf_tarball.patch b/easybuild/easyconfigs/j/jax/jaxlib-0.1.70-controlled_tf_tarball.patch deleted file mode 100644 index 4aa6bd90ffd..00000000000 --- a/easybuild/easyconfigs/j/jax/jaxlib-0.1.70-controlled_tf_tarball.patch +++ /dev/null @@ -1,12 +0,0 @@ -# using system environment variables -diff -ruN tensorflow-2.5.0_orig/third_party/mlir/tblgen.bzl tensorflow-2.5.0/third_party/mlir/tblgen.bzl ---- tensorflow-2.5.0_orig/third_party/mlir/tblgen.bzl 2021-05-12 15:26:41.000000000 +0200 -+++ tensorflow-2.5.0/third_party/mlir/tblgen.bzl 2021-08-11 12:23:34.301593036 +0200 -@@ -153,6 +153,7 @@ - inputs = trans_srcs, - executable = ctx.executable.tblgen, - arguments = [args], -+ use_default_shell_env = True, - ) - - return [DefaultInfo()] \ No newline at end of file From c1735cebe43dfb82e1d3eb3757b5964ca7e62f2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 17:35:10 +0200 Subject: [PATCH 0875/9987] enable building with native optimizations for build host (triggers use of -march=native) --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index fe0e1e87e81..b0bab654f7a 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -31,6 +31,7 @@ local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_commit local_jax_prebuildopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir local_jax_build_cmd = 'python build/build.py ' +local_jax_build_cmd += '--target_cpu_features=native ' local_jax_build_cmd += '--bazel_startup_options="--output_user_root=%(builddir)s" ' local_jax_build_cmd += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' local_jax_build_cmd += '--bazel_options=--subcommands ' From a994b6f0255c876e3f04b7bc43e4b45c328e89d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 18:29:06 +0200 Subject: [PATCH 0876/9987] adding easyconfigs: ReFrame-3.7.3.eb --- .../easyconfigs/r/ReFrame/ReFrame-3.7.3.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb new file mode 100644 index 00000000000..ed0c7106320 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.7.3' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.2.4', { + 'use_pip': False, + 'checksums': ['0eb8a1516c3d138ae8689c0c1a60fde7143310832f9dc77e11d8a4bc62de193b'], + }), + ('wheel', '0.37.0', { + 'checksums': ['e2ef7239991699e3355d54f8e968a21bb940a1dbf34a4d226741e64462516fad'], + }), + ('setuptools', '57.4.0', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], + }), + ('reframe', version, { + 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], + 'use_pip': True, + 'checksums': ['52427fbbaa558082b71f73b2b8aea37340584d14dc3b1aca1e9bdd8923fa4c65'], + }), +] + +postinstallcmds = [ + "cp -r tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -r share/completions %(installdir)s/share/completions", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['lib', 'tutorials', 'external'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions +modextrapaths = { + 'PATH': 'bin', + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 2115cf504ce489b6628c0072e38e44c6cc04aa02 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 13 Aug 2021 18:49:34 +0200 Subject: [PATCH 0877/9987] adding easyconfigs: GLib-2.69.1-GCCcore-11.2.0.eb, NSPR-4.32-GCCcore-11.2.0.eb, NSS-3.65-GCCcore-11.2.0.eb --- .../g/GLib/GLib-2.69.1-GCCcore-11.2.0.eb | 52 +++++++++++++++++++ .../n/NSPR/NSPR-4.32-GCCcore-11.2.0.eb | 30 +++++++++++ .../n/NSS/NSS-3.65-GCCcore-11.2.0.eb | 50 ++++++++++++++++++ 3 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.69.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.32-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.69.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.69.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..126241a9bf5 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.69.1-GCCcore-11.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.69.1' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['f92f34057a091fc8638d91f10cece842cb8618e9a1090b0ddb19cc15a21bf39c'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.9.6'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libffi', '3.4.2'), + ('gettext', '0.21'), + ('libxml2', '2.9.10'), + ('PCRE2', '10.37'), + ('util-linux', '2.37'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.32-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.32-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d97f4b7a45b --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.32-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.32' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb6bf4f534b9559cf123dcdc6f9cd8167de950314a90a88b2a329c16836e7f6c'] + +builddependencies = [('binutils', '2.37')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +sanity_check_commands = ["nspr-config --version"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..513c84318ac --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.65' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', +] +checksums = [ + '32170f6c188212a78bf9fdacffa2eeed0d564ef8faae63fd8ae971b208e8c637', # nss-3.65.tar.gz + '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch +] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('NSPR', '4.32'), + ('zlib', '1.2.11'), +] + +# building in parallel fails +parallel = 1 + +# fix for not being able to find header files +buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['lib/libnss.a'], + 'dirs': ['bin', 'include/dbm', 'include/nss'], +} + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' From 87a885b31bf7fc203e50ee6274ac9f393d081b51 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 13 Aug 2021 19:12:27 +0200 Subject: [PATCH 0878/9987] adding easyconfigs: re2c-2.2-GCCcore-11.2.0.eb --- .../r/re2c/re2c-2.2-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/r/re2c/re2c-2.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/r/re2c/re2c-2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/re2c/re2c-2.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..23695492f3d --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-2.2-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '2.2' + +homepage = 'https://re2c.org/' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['0fc45e4130a8a555d68e230d1795de0216dfe99096b61b28e67c86dfd7d86bda'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/re2c'], + 'dirs': [], +} + +sanity_check_commands = ["re2c --help"] + +moduleclass = 'tools' From 8324043b6b6e56b26243ffd3c78aad78edf13eee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 13 Aug 2021 19:58:57 +0200 Subject: [PATCH 0879/9987] adding easyconfigs: libepoxy-1.5.8-GCCcore-11.2.0.eb, Pango-1.48.8-GCCcore-11.2.0.eb, at-spi2-atk-2.38.0-GCCcore-11.2.0.eb, HarfBuzz-2.8.2-GCCcore-11.2.0.eb, at-spi2-core-2.40.3-GCCcore-11.2.0.eb, Gdk-Pixbuf-2.42.6-GCCcore-11.2.0.eb, ATK-2.36.0-GCCcore-11.2.0.eb, GObject-Introspection-1.68.0-GCCcore-11.2.0.eb, cairo-1.16.0-GCCcore-11.2.0.eb, ICU-69.1-GCCcore-11.2.0.eb --- .../a/ATK/ATK-2.36.0-GCCcore-11.2.0.eb | 39 ++++++++++++++++ .../at-spi2-atk-2.38.0-GCCcore-11.2.0.eb | 37 +++++++++++++++ .../at-spi2-core-2.40.3-GCCcore-11.2.0.eb | 39 ++++++++++++++++ .../c/cairo/cairo-1.16.0-GCCcore-11.2.0.eb | 46 +++++++++++++++++++ ...ect-Introspection-1.68.0-GCCcore-11.2.0.eb | 44 ++++++++++++++++++ .../Gdk-Pixbuf-2.42.6-GCCcore-11.2.0.eb | 46 +++++++++++++++++++ .../HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb | 38 +++++++++++++++ .../i/ICU/ICU-69.1-GCCcore-11.2.0.eb | 29 ++++++++++++ .../libepoxy/libepoxy-1.5.8-GCCcore-11.2.0.eb | 37 +++++++++++++++ .../p/Pango/Pango-1.48.8-GCCcore-11.2.0.eb | 41 +++++++++++++++++ 10 files changed, 396 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.68.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/i/ICU/ICU-69.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.48.8-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f387195260d --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.36.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['fb76247e369402be23f1f5c65d38a9639c1164d934e40f6a9cf3c9e96b652788'] + +builddependencies = [ + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.68.0'), +] + +dependencies = [ + ('GLib', '2.69.1'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c2424ec2c41 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.69.1'), + ('DBus', '1.13.18'), + ('at-spi2-core', '2.40.3'), + ('libxml2', '2.9.10'), + ('ATK', '2.36.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..bccb9a5ba84 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.40.3' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e49837c2ad30d71e1f29ca8e0968a54b95030272f7ff40b89b48968653f37a5c'] + +builddependencies = [ + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.69.1'), + ('DBus', '1.13.18'), + ('X11', '20210802'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e7f3d76f736 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-11.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.16.0' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5e7b29b3f113ef870d1e3ecf8adf21f923396401604bda16d44be45e66052331'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('freetype', '2.11.0'), + ('pixman', '0.40.0'), + ('expat', '2.4.1'), + ('GLib', '2.69.1'), + ('X11', '20210802'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.68.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.68.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4309184ce19 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.68.0-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.68.0' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['d229242481a201b84a0c66716de1752bca41db4133672cfcfb37c93eb6e54a27'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('cairo', '1.16.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('GLib', '2.69.1'), + ('libffi', '3.4.2'), + ('util-linux', '2.37'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..3e94b11e6ee --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.6-GCCcore-11.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.6' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4a6b75b7ed8f58ca48da830b9fa00ed96d668d3ab4b1f723dcf902f78bde77f'] + +builddependencies = [ + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.68.0'), +] + +dependencies = [ + ('GLib', '2.69.1'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('X11', '20210802'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..57ecf2bd16c --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '2.8.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['4164f68103e7b52757a732227cfa2a16cfa9984da513843bb4eb7669adc6f220'] + +builddependencies = [ + ('binutils', '2.37'), + ('GObject-Introspection', '1.68.0'), + ('pkg-config', '0.29.2'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('GLib', '2.69.1'), + ('ICU', '69.1'), + ('cairo', '1.16.0'), + ('freetype', '2.11.0'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ICU/ICU-69.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-69.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..df38950abb9 --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-69.1-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '69.1' + +homepage = 'https://icu-project.org/' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['4cba7b7acd1d3c42c44bb0c14be6637098c7faf2b330ce876bc5f3b915d09745'] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f8c76e4e55e --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.8-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.8' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['0cd80cb040b75cbe77fadd45c48282ebab82d845c597ce11ee5e8cb9c1efeabb'] + +builddependencies = [ + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210802'), + ('Mesa', '21.1.7'), +] + +configopts = '-Degl=yes --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.48.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.48.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b750dc8da67 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.48.8-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.48.8' + +homepage = 'https://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['009d9d830ecbe11911d6637e48eec1c51390d3d12eb286035ef7c641f3c87410'] + +builddependencies = [ + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('GObject-Introspection', '1.68.0'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210802'), + ('GLib', '2.69.1'), + ('cairo', '1.16.0'), + ('HarfBuzz', '2.8.2'), + ('FriBidi', '1.0.10'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 848bc084c2acbf8b2998275636fded42ffa57669 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 20:09:55 +0200 Subject: [PATCH 0880/9987] remove -DVTK_OPENGL_HAS_OSMESA=ON from ParaView 5.9.1 easyconfig --- .../p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb index a6ebb81f419..597a01985cc 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021a-mpi.eb @@ -45,17 +45,15 @@ configopts += '-DPARAVIEW_USE_PYTHON=ON ' configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' # OpenGL & Mesa -configopts += '-DVTK_USE_X:BOOL=OFF ' configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' -configopts += '-DVTK_OPENGL_HAS_OSMESA=ON ' sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'bin/pvpython'], - 'dirs': ['include/%(namelower)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], + 'files': ['bin/paraview', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ['python -c "import %(namelower)s"'] +sanity_check_commands = ['python -c "import paraview"'] modextrapaths = {'PYTHONPATH': ['lib64/python%(pyshortver)s/site-packages', 'lib/python%(pyshortver)s/site-packages']} From 71475e97daf2aae8c489ceef90291d19dea438c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 20:09:31 +0200 Subject: [PATCH 0881/9987] run jax test suite --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index b0bab654f7a..9da76ac7b7a 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -13,6 +13,8 @@ toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ ('Bazel', '3.7.2'), + ('pytest-xdist', '2.3.0'), + ('pytest-benchmark', '3.4.1'), ] dependencies = [ @@ -101,6 +103,13 @@ components = [ }), ] +# can't run tests in sanity check step, because build dependencies must be availabl +postinstallcmds = [ + "cd %%(builddir)s/jax-jaxlib-v%s && " + "PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:$PYTHONPATH " + "pytest -n auto tests" % local_jaxlib_ver, +] + sanity_pip_check = True moduleclass = 'tools' From 54fb8efadb4a451f85aea15f4f1d8c38f3051367 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 20:35:31 +0200 Subject: [PATCH 0882/9987] rename jax patch to prevent TensorFlow download during build --- easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb | 6 +++--- ...ies.patch => jaxlib-0.1.70_no-tensorflow-download.patch} | 2 ++ 2 files changed, 5 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/j/jax/{jaxlib-0.1.70-correct_libraries.patch => jaxlib-0.1.70_no-tensorflow-download.patch} (90%) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb index 9da76ac7b7a..0bfee3d492f 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb @@ -80,7 +80,7 @@ components = [ 'https://github.com/tensorflow/tensorflow/archive/' ], 'patches': [ - ('jaxlib-%s-correct_libraries.patch' % local_jaxlib_ver, 1), + ('jaxlib-%s_no-tensorflow-download.patch' % local_jaxlib_ver, 1), ('TensorFlow-%s_mlir-build-env.patch' % local_tf_commit, '../tensorflow-%s' % local_tf_commit), ], 'checksums': [ @@ -88,8 +88,8 @@ components = [ '1205b180de70c98899d842f75bb589599c10a3c7a1c6099475c3a7d39b2e44ac', # tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d.tar.gz '0f13410284b9186e436350e9617b3bed2d65f1dc1a220fd37ad9ef43c2035663', - # jaxlib-0.1.70-correct_libraries.patch, - '4033a81a45b1b455ab6ef4fde697db1d08aa073851c2d86ddca881777ad95be8', + # jaxlib-0.1.70_no-tensorflow-download.patch + '1496c6be9336fb563b997f8da83d690a9b3a0a6e29fdd87fac60409300a2fd95', # TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d-build-env.patch 'd067836b1d18d66a8c69fb3db311855c8a56c0106d42a11299a1733c385e9c22', ], diff --git a/easybuild/easyconfigs/j/jax/jaxlib-0.1.70-correct_libraries.patch b/easybuild/easyconfigs/j/jax/jaxlib-0.1.70_no-tensorflow-download.patch similarity index 90% rename from easybuild/easyconfigs/j/jax/jaxlib-0.1.70-correct_libraries.patch rename to easybuild/easyconfigs/j/jax/jaxlib-0.1.70_no-tensorflow-download.patch index b8a75f1374e..3c5bba917d5 100644 --- a/easybuild/easyconfigs/j/jax/jaxlib-0.1.70-correct_libraries.patch +++ b/easybuild/easyconfigs/j/jax/jaxlib-0.1.70_no-tensorflow-download.patch @@ -1,3 +1,5 @@ +avoid downloading TensorFlow during the build, add placeholder to inject location of pre-downloaded TensorFlow sources +author: Denis Kristak (INUITS) diff -ruN jax-jaxlib-v0.1.70_orig/WORKSPACE jax-jaxlib-v0.1.70/WORKSPACE --- jax-jaxlib-v0.1.70_orig/WORKSPACE 2021-08-12 13:12:54.025608000 +0200 +++ jax-jaxlib-v0.1.70/WORKSPACE 2021-08-12 13:32:51.581961000 +0200 From 94ccf126c94f81407d6f8e1188dc8969a427046a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 21:01:30 +0200 Subject: [PATCH 0883/9987] add easyconfigs for pytest-xdist and pytest-benchmark build dependencies of jax --- .../pytest-benchmark-3.4.1-GCCcore-10.2.0.eb | 41 ++++++++++++ .../pytest-xdist-2.3.0-GCCcore-10.2.0.eb | 62 +++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..fc22ef34689 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-benchmark/pytest-benchmark-3.4.1-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'pytest-benchmark' +version = '3.4.1' + +homepage = 'https://github.com/ionelmc/pytest-benchmark' +description = "A pytest fixture for benchmarking code." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True + +exts_list = [ + ('py-cpuinfo', '8.0.0', { + 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], + 'modulename': 'cpuinfo', + }), + (name, version, { + 'checksums': ['40e263f912de5a81d891619032983557d62a3d85843f9a9f30b98baea0cd7b47'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cpuinfo', 'bin/pytest-benchmark'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cpuinfo --help", + "pytest-benchmark --help", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..93631bf96c8 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'pytest-xdist' +version = '2.3.0' + +homepage = 'https://github.com/pytest-dev/pytest-xdist' +description = """xdist: pytest distributed testing plugin + +The pytest-xdist plugin extends pytest with some unique test execution modes: + + * test run parallelization: if you have multiple CPUs or hosts you + can use those for a combined test run. This allows to speed up + development or to use special resources of remote machines. + + * --looponfail: run your tests repeatedly in a subprocess. After + each run pytest waits until a file in your project changes and + then re-runs the previously failing tests. This is repeated + until all tests pass after which again a full run is + performed. + + * Multi-Platform coverage: you can specify different Python + interpreters or different platforms and run tests in parallel on + all of them. + +Before running tests remotely, pytest efficiently “rsyncs” your +program source code to the remote place. All test results are reported +back and displayed to your local terminal. You may specify different +Python versions and interpreters.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('apipkg', '1.5', { + 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], + }), + ('execnet', '1.9.0', { + 'checksums': ['8f694f3ba9cc92cab508b152dcfe322153975c29bda272e2fd7f3f00f36e47c5'], + }), + ('pytest-forked', '1.3.0', { + 'checksums': ['6aa9ac7e00ad1a539c41bec6d21011332de671e938c7637378ec9710204e37ca'], + }), + (name, version, { + 'modulename': 'xdist', + 'checksums': ['e8ecde2f85d88fbcadb7d28cb33da0fa29bca5cf7d5967fa89fc0e97e5299ea5'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From e0f7c0fc22a6efa25c54a46c67a60b898bb8db61 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Aug 2021 21:02:13 +0200 Subject: [PATCH 0884/9987] update to jax 0.2.19 --- ...foss-2020b.eb => jax-0.2.19-foss-2020b.eb} | 24 +++++++++---------- 1 file changed, 11 insertions(+), 13 deletions(-) rename easybuild/easyconfigs/j/jax/{jax-0.2.18-foss-2020b.eb => jax-0.2.19-foss-2020b.eb} (93%) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb similarity index 93% rename from easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb rename to easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index 0bfee3d492f..1efc76bfb92 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.18-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'jax' -version = '0.2.18' +version = '0.2.19' local_jaxlib_ver = '0.1.70' homepage = 'https://pypi.python.org/pypi/jax' description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and @@ -42,17 +42,6 @@ local_jax_build_cmd += '--bazel_options=--action_env=EBPYTHONPREFIXES' use_pip = True -exts_list = [ - ('opt-einsum', '3.3.0', { - 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', - 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], - }), - (name, version, { - 'easyblock': 'PythonPackage', - 'checksums': ['b08d5137189a7384429541b39575a022d4bbf777cdb081e8c1bf6bc14eefcd41'], - }), -] - default_component_specs = { 'sources': [SOURCE_TAR_GZ], 'source_urls': [PYPI_SOURCE], @@ -103,7 +92,16 @@ components = [ }), ] -# can't run tests in sanity check step, because build dependencies must be availabl +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'checksums': ['e55534680a05b6ced92dadde307bd3b2207efd1aaaec304e96197b00ad7560d3'], + }), +] + +# can't run tests in sanity check step, because build dependencies must be available postinstallcmds = [ "cd %%(builddir)s/jax-jaxlib-v%s && " "PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:$PYTHONPATH " From 29d6aab6d583a8a4fd9a8a3599c6da35c8721094 Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 13 Aug 2021 19:55:45 +0000 Subject: [PATCH 0885/9987] Typos corrected --- .../easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb index d4a0e70f0c1..c5aa8fcad17 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb @@ -47,8 +47,8 @@ exts_list = [ 'checksums': ['48390ed1c1a79bb5f801083042cdeddee060e2277f40c293fd30384882aced81'], }), ('constellations', '0.0.13', { - 'source_urls': ['https://github.com/%(github_account)s/%name)s/archive'], - 'sources': [{'download_filename': 'v%(version).tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['4aa3edae9491a59621ef6a3b5bbd21a13c68355986f6c097e46a1397d5b1d24b'], }), ('pango-designation', '1.2.59', { From 7222139d0c8f3449bb43c678d32dd350b98f2b76 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 13 Aug 2021 23:06:10 +0200 Subject: [PATCH 0886/9987] adding easyconfigs: LittleCMS-2.12-GCCcore-11.2.0.eb, Ghostscript-9.54.0-GCCcore-11.2.0.eb, ImageMagick-7.1.0-4-GCCcore-11.2.0.eb --- .../Ghostscript-9.54.0-GCCcore-11.2.0.eb | 58 +++++++++++++++++++ .../ImageMagick-7.1.0-4-GCCcore-11.2.0.eb | 40 +++++++++++++ .../LittleCMS-2.12-GCCcore-11.2.0.eb | 26 +++++++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.54.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.12-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.54.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..fa55b13e03a --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.54.0-GCCcore-11.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.54.0' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0646bb97f6f4d10a763f4919c54fa28b4fbdd3dff8e7de3410431c81762cade0'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('freetype', '2.11.0'), + ('libjpeg-turbo', '2.0.6'), + ('expat', '2.4.1'), + ('GLib', '2.69.1'), + ('cairo', '1.16.0'), + ('LibTIFF', '4.3.0'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +# Avoid race condition in build if too much parallelism is used +maxparallel = 4 + +postinstallcmds = [ + # build and install shared libs + "make so && make soinstall", + # install header files + "mkdir -p %(installdir)s/include/ghostscript", + "install -v -m644 base/*.h %(installdir)s/include/ghostscript", + "install -v -m644 psi/*.h %(installdir)s/include/ghostscript", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/ghostscript', 'include/ghostscript', 'share/man'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b1329a25dd6 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.1.0-4' + +homepage = 'https://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/ImageMagick/ImageMagick/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['3e840e01849a93cafa5f314087d2281422ff7ec1eb104b90787095c4c298e837'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20210802'), + ('Ghostscript', '9.54.0'), + ('JasPer', '2.0.33'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.3.0'), + ('LittleCMS', '2.12'), +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', + 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.12-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.12-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..fe03d4a2e3a --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.12-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.12' + +homepage = 'https://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%(version)s/'] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['18663985e864100455ac3e507625c438c3710354d85e5cbb7cd4043e11fe10f5'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('libjpeg-turbo', '2.0.6')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' From d435226d69bf6f820c5cdd30d0ea861ae449959a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 13 Aug 2021 23:24:44 +0200 Subject: [PATCH 0887/9987] Use PCRE1 instead as it doesn't seem to be PCRE2 compatible at all --- easybuild/easyconfigs/g/GLib/GLib-2.69.1-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.69.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.69.1-GCCcore-11.2.0.eb index 126241a9bf5..c9f6dab66c4 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.69.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.69.1-GCCcore-11.2.0.eb @@ -33,7 +33,7 @@ dependencies = [ ('libffi', '3.4.2'), ('gettext', '0.21'), ('libxml2', '2.9.10'), - ('PCRE2', '10.37'), + ('PCRE', '8.45'), ('util-linux', '2.37'), ] From d49dd74c1027be9d01cf9008d1a1443f75ed0efd Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 13 Aug 2021 14:52:38 -0700 Subject: [PATCH 0888/9987] {bio}[GCC/10.2.0] RAxML-NG 1.0.3 --- .../r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb new file mode 100644 index 00000000000..2eaf3ce90ce --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb @@ -0,0 +1,46 @@ +# EasyBuild easyconfig +# +# Contributed from Fred Hutchinson Cancer Research Center, Seattle WA, US +# John Dey jfdey@fredhutch.org +# +easyblock = 'CMakeMake' + +name = 'RAxML-NG' +version = '1.0.3' + +homepage = 'https://github.com/amkozlov/raxml-ng' +description = """RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) + optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree + Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/amkozlov', + 'repo_name': '%(namelower)s', + 'tag': '%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [ + '3bee0fd77b18d273349190ea47719211474dc4de2261579a06faa12d4cdb8219', +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' + From 27d21bf3cd3058ad83b84c18c8bbaf448c2e7bb8 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 13 Aug 2021 16:39:41 -0700 Subject: [PATCH 0889/9987] {math}[GCCcore 10.2.0] SpectrA 1.0.0 --- .../s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..49cc5f7278d --- /dev/null +++ b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# +# Fred Hutchinson Cancer Research Center - Seattle - Washington - US +# https://www.fredhutch.org +# John Dey +# +easyblock = 'CMakeMake' + +name = 'SpectrA' +version = '1.0.0' + +homepage = 'https://spectralib.org/' +description = """Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ + library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/yixuan/spectra/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['45228b7d77b916b5384245eb13aa24bc994f3b0375013a8ba6b85adfd2dafd67'] + +builddependencies = [('CMake', '3.18.4')] +dependencies = [('Eigen', '3.3.8')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +sanity_check_paths = { + 'files': ['include/Spectra/SymEigsSolver.h'], + 'dirs': [''], +} + +moduleclass = 'math' From 4ce31c1ffc83a44e7b06e4719a0bc8b6074aa64f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 06:38:57 +0200 Subject: [PATCH 0890/9987] adding easyconfigs: AlphaFold-2.0.0-foss-2020b.eb --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb new file mode 100644 index 00000000000..aa4d2744649 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.0.0' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '3.7.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('TensorFlow', '2.5.0'), + ('Biopython', '1.78'), + ('jax', '0.2.19'), # also provides absl-py +] + +use_pip = True + +exts_list = [ + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + # source tarball on PyPI is missing requirements.txt, + # see https://github.com/deepmind/dm-haiku/issues/44 + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + 'modulename': 'haiku', + }), + ('dm-tree', '0.1.6', { + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + 'modulename': 'tree', + }), + ('websocket-client', '1.2.1', { + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + 'modulename': 'websocket', + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + # see https://github.com/google/ml_collections/issues/7 + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + (name, version, { + 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From f09d31a220a60cc64597f6216480aecac27f13eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 06:47:07 +0200 Subject: [PATCH 0891/9987] enhance sanity check for SpectrA, remove easyconfig parameters that are set by default for CMakeMake --- .../easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb index 49cc5f7278d..8cb83e64445 100644 --- a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.0-GCC-10.2.0.eb @@ -20,15 +20,12 @@ sources = ['v%(version)s.tar.gz'] checksums = ['45228b7d77b916b5384245eb13aa24bc994f3b0375013a8ba6b85adfd2dafd67'] builddependencies = [('CMake', '3.18.4')] -dependencies = [('Eigen', '3.3.8')] - -separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release' +dependencies = [('Eigen', '3.3.8')] sanity_check_paths = { 'files': ['include/Spectra/SymEigsSolver.h'], - 'dirs': [''], + 'dirs': ['include/Spectra/LinAlg', 'share/spectra/cmake'], } moduleclass = 'math' From 7d72dd3485f65aab490092e786186970f06b5ca4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 07:20:21 +0200 Subject: [PATCH 0892/9987] restore error message on failing test suite, required by bot to determine end of output of test suite --- .github/workflows/unit_tests.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 252a6a166b0..22e9c3f9559 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -121,7 +121,8 @@ jobs: eb --show-system-info # run test suite - python -O -m test.easyconfigs.suite + # if tests failed, print error message that is picked up by boegelbot to determine end of test output + python -O -m test.easyconfigs.suite || echo "ERROR: Not all tests were successful" unset PYTHONPATH From e83e3dc8d34eb50e3be0c9bd2fd0cb812be02884 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 07:23:17 +0200 Subject: [PATCH 0893/9987] fix trivial style issues in RAxML-NG 1.0.3 easyconfig --- .../r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb index 2eaf3ce90ce..4d8a39740fe 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb @@ -18,11 +18,11 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} sources = [{ 'filename': '%(name)s-%(version)s.tar.gz', 'git_config': { - 'url': 'https://github.com/amkozlov', - 'repo_name': '%(namelower)s', - 'tag': '%(version)s', - 'recursive': True, - 'keep_git_dir': True, + 'url': 'https://github.com/amkozlov', + 'repo_name': '%(namelower)s', + 'tag': '%(version)s', + 'recursive': True, + 'keep_git_dir': True, } }] checksums = [ @@ -43,4 +43,3 @@ sanity_check_paths = { } moduleclass = 'bio' - From bad2cbac2b9f35661d568ecb530457a61769e407 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 07:27:05 +0200 Subject: [PATCH 0894/9987] don't use checksum in easyconfig for RAxML-NG 1.0.3, since git_config is used for sources --- easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb index 4d8a39740fe..a29ce5a9755 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.3-GCC-10.2.0.eb @@ -25,9 +25,7 @@ sources = [{ 'keep_git_dir': True, } }] -checksums = [ - '3bee0fd77b18d273349190ea47719211474dc4de2261579a06faa12d4cdb8219', -] +checksums = [None] builddependencies = [ ('CMake', '3.18.4'), From 34eb228fddf4cad61b03793d9ddf9bbe29516205 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 07:38:58 +0200 Subject: [PATCH 0895/9987] fix checksum for OpenFOAM v2106 source tarball --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb index 2f640516ac7..efb4319ace0 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb @@ -20,7 +20,7 @@ patches = [ 'OpenFOAM-v1906-wmake-ompi.patch', ] checksums = [ - 'e765881451d8d15ce33caa28850cdcc4534b8c4590e08ee6011bcafd11216940', # OpenFOAM-v2106.tgz + '11e41e5b9a253ef592a8f6b79f6aded623b28308192d02cec1327078523b5a37', # OpenFOAM-v2106.tgz 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch ] From 50948fdd59b2bb4bb59f3d91d3b6ac0b000f870c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 07:54:36 +0200 Subject: [PATCH 0896/9987] add Perl build dependency to recent Clang easyconfigs --- easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-8.3.0.eb | 1 + easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb | 1 + easybuild/easyconfigs/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb | 1 + easybuild/easyconfigs/c/Clang/Clang-11.0.0-GCCcore-9.3.0.eb | 1 + easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb | 1 + easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb | 1 + .../easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb | 1 + .../easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb | 1 + easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb | 1 + 10 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-8.3.0.eb index 6f8a7a931f0..a79db305136 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-8.3.0.eb @@ -61,6 +61,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.15.3'), ('Python', '2.7.16'), + ('Perl', '5.30.0'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb index 8fad61bc7f6..128ee20abef 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb @@ -61,6 +61,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.16.4'), ('Python', '2.7.18'), + ('Perl', '5.30.2'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb index 3cbe73d68a5..39259fafa23 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb @@ -61,6 +61,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.16.4'), ('Python', '2.7.18'), + ('Perl', '5.30.2'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.0-GCCcore-9.3.0.eb index 18ea431ce59..5886c77ae32 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-11.0.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.0-GCCcore-9.3.0.eb @@ -57,6 +57,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.16.4'), ('Python', '3.8.2'), + ('Perl', '5.30.2'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb index 6a528a4897c..a7ec71f94dd 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb @@ -57,6 +57,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.18.4'), ('Python', '3.8.6'), + ('Perl', '5.32.0'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb index 037c1ef7f84..34cb3620042 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb @@ -57,6 +57,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.18.4'), ('Python', '3.8.6'), + ('Perl', '5.32.0'), ('elfutils', '0.183'), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb index c6ed800d787..06e4bde84c9 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb @@ -59,6 +59,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.20.1'), ('Python', '3.9.5'), + ('Perl', '5.32.1'), ('elfutils', '0.185'), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb index c65903e6ddb..1cb298bfba1 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb @@ -60,6 +60,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.15.3'), ('Python', '2.7.16'), + ('Perl', '5.30.0'), ('libxml2', '2.9.9'), ('elfutils', '0.185'), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb index 6d9f2a9a9ac..ef88ee09de0 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb @@ -60,6 +60,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.15.3'), ('Python', '2.7.16'), + ('Perl', '5.30.0'), ('libxml2', '2.9.9'), ('elfutils', '0.185'), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb index 963df6df8c9..f9e2e51d164 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb @@ -56,6 +56,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.15.3'), ('Python', '2.7.16'), + ('Perl', '5.30.0'), ('libxml2', '2.9.9'), ] From 4d65a507ed330f7b71f19a63aa9daec5fb365117 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 14 Aug 2021 08:00:36 +0200 Subject: [PATCH 0897/9987] stick to TensorFlow 2.4.1 dependency for AlphaFold 2.0.0 with foss/2020b --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index aa4d2744649..9fe9c5a44e3 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('PyYAML', '5.3.1'), - ('TensorFlow', '2.5.0'), + ('TensorFlow', '2.4.1'), ('Biopython', '1.78'), ('jax', '0.2.19'), # also provides absl-py ] From 48fb70a6f6283ccbd5fdc8e0cd29f80032cef716 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Sat, 14 Aug 2021 20:02:27 +1000 Subject: [PATCH 0898/9987] Update MATIO-1.5.21-GCCcore-10.2.0.eb Fix checksum --- easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb index fcb5c5d7630..c8a95327a3c 100644 --- a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.21-GCCcore-10.2.0.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_ZIP] -checksums = ['bf1808a20412534a7c9e69c6eb0d2612'] +checksums = ['2ac1d5406e51f2bdfaa545a535d6dbf6347be89891a06323961d7a2acbf37be9'] preconfigopts = 'chmod +x configure && ' From 9b4f3c0d0686c25d93ba237b1ba787a446853fbf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 14 Aug 2021 17:23:09 +0200 Subject: [PATCH 0899/9987] adding easyconfigs: YACS-0.1.8-GCCcore-11.2.0.eb, Xerces-C++-3.2.3-GCCcore-11.2.0.eb, tmux-3.2a-GCCcore-11.2.0.eb, time-1.9-GCCcore-11.2.0.eb, PyYAML-5.4.1-GCCcore-11.2.0.eb, parallel-20210722-GCCcore-11.2.0.eb, Archive-Zip-1.68-GCCcore-11.2.0.eb, json-c-0.15-GCCcore-11.2.0.eb, JsonCpp-1.9.4-GCCcore-11.2.0.eb, lxml-4.6.3-GCCcore-11.2.0.eb, libxslt-1.1.34-GCCcore-11.2.0.eb --- .../Archive-Zip-1.68-GCCcore-11.2.0.eb | 32 +++++++++++++++ .../j/JsonCpp/JsonCpp-1.9.4-GCCcore-11.2.0.eb | 29 ++++++++++++++ .../j/json-c/json-c-0.15-GCCcore-11.2.0.eb | 30 ++++++++++++++ .../libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb | 31 +++++++++++++++ .../l/lxml/lxml-4.6.3-GCCcore-11.2.0.eb | 26 +++++++++++++ .../p/PyYAML/PyYAML-5.4.1-GCCcore-11.2.0.eb | 27 +++++++++++++ .../parallel-20210722-GCCcore-11.2.0.eb | 26 +++++++++++++ .../t/time/time-1.9-GCCcore-11.2.0.eb | 27 +++++++++++++ .../t/tmux/tmux-3.2a-GCCcore-11.2.0.eb | 36 +++++++++++++++++ .../Xerces-C++-3.2.3-GCCcore-11.2.0.eb | 39 +++++++++++++++++++ .../y/YACS/YACS-0.1.8-GCCcore-11.2.0.eb | 31 +++++++++++++++ 11 files changed, 334 insertions(+) create mode 100644 easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/lxml/lxml-4.6.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-5.4.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20210722-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/t/tmux/tmux-3.2a-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6a2f22d4535 --- /dev/null +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Archive-Zip' +version = '1.68' + +homepage = 'https://metacpan.org/pod/Archive::Zip' +description = "Provide an interface to ZIP archive files." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Perl', '5.34.0'), + ('UnZip', '6.0'), + ('Zip', '3.0'), +] + +options = {'modulename': 'Archive::Zip'} + +sanity_check_paths = { + 'files': ['bin/crc32'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e682bf7892c --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.4' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['e34a628a8142643b976c7233ef381457efad79468c67cb1ae0b83a33d7493999'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), + ('binutils', '2.37'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a0ddc75e305 --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.15' +local_suff = '-20200726' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['4ba9a090a42cf1e12b84c64e4464bb6fb893666841d5843cc5bef90774028882'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..22a0c0a33e9 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.34' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), +] + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.6.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.6.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..fe506e065cb --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-4.6.3-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '4.6.3' + +homepage = 'https://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['39b78571b3b30645ac77b95f7c69d1bffc4cf8c3b157c435a34da72e78c82468'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.4.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.4.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..85c970dbaf7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.4.1-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '5.4.1' + +homepage = "https://github.com/yaml/pyyaml" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['607774cbba28732bfa802b54baa7484215f530991055bb562efbed5b2f20a45e'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('libyaml', '0.2.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'yaml'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20210722-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20210722-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8b38cbfbf17 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20210722-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20210722' + +homepage = 'https://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['3239094bc043957be191e1e4376716ef0d1b369e545b5bf7d7824b7d46284a49'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Perl', '5.34.0')] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +sanity_check_commands = ["parallel --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..123bf9ab4ae --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'https://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] + +builddependencies = [('binutils', '2.37')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.2a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/tmux/tmux-3.2a-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f3c639199b8 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.2a-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.2a' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['551553a4f82beaa8dadc9256800bcc284d7c000081e47aa6ecbb6ff36eacd05f'] + +builddependencies = [ + ('binutils', '2.37'), + ('Bison', '3.7.6'), + ('make', '4.3'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.2'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..58d6a7a9a36 --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Xerces-C++' +version = '3.2.3' + +homepage = 'https://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['fb96fc49b1fb892d1e64e53a6ada8accf6f0e6d30ce0937956ec68d39bd72c7e'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +dependencies = [ + ('cURL', '7.78.0'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/XInclude', + 'include/xercesc/xinclude/XIncludeUtils.hpp', + 'lib/libxerces-c-3.2.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c38fe7797ee --- /dev/null +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'YACS' +version = '0.1.8' + +homepage = "https://github.com/rbgirshick/yacs" +description = """YACS was created as a lightweight library to define and +manage system configurations, such as those commonly found in software +designed for scientific experimentation. These "configurations" +typically cover concepts like hyperparameters used in training a machine +learning model or configurable model hyperparameters, such as the depth +of a convolutional neural network.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'lib' From fba59300df6a049d5932fcc878eff37cccd3d866 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 14 Aug 2021 21:01:30 +0200 Subject: [PATCH 0900/9987] Include patches --- easybuild/easyconfigs/o/OpenMPI/9212.patch | 64 +++++++++++++++ easybuild/easyconfigs/o/OpenMPI/9213.patch | 79 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 5 +- 3 files changed, 144 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/9212.patch create mode 100644 easybuild/easyconfigs/o/OpenMPI/9213.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/9212.patch b/easybuild/easyconfigs/o/OpenMPI/9212.patch new file mode 100644 index 00000000000..156d3d0a44b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/9212.patch @@ -0,0 +1,64 @@ +From 8b07775d1002cc9be887c41768aea9ac896c5ecd Mon Sep 17 00:00:00 2001 +From: Ralph Castain +Date: Tue, 10 Aug 2021 08:38:15 -0700 +Subject: [PATCH] Use an OPAL-prefixed abstraction for PMIX_PACKAGE_RANK + +If someone configures against PMIx v4.1 or above, the configure +logic will correctly detect the presence of PMIX_PACKAGE_RANK. +However, the internal code only includes the opal/mca/pmix headers +and thus only the OPAL-prefixed PMIx abstractions are available. +Add an OPAL_PMIX_PACKAGE_RANK abstraction and update the common/ofi +code to use it. + +Signed-off-by: Ralph Castain +--- + opal/mca/common/ofi/common_ofi.c | 6 ++---- + opal/mca/pmix/pmix_types.h | 2 ++ + 2 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/opal/mca/common/ofi/common_ofi.c b/opal/mca/common/ofi/common_ofi.c +index 12bed7eb6b8..769ecb75239 100644 +--- a/opal/mca/common/ofi/common_ofi.c ++++ b/opal/mca/common/ofi/common_ofi.c +@@ -312,19 +312,17 @@ static uint32_t get_package_rank(int32_t num_local_peers, uint16_t my_local_rank + char *local_peers = NULL; + char *locality_string = NULL; + char *mylocality = NULL; ++ uint16_t *package_rank_ptr; + + pname.jobid = OPAL_PROC_MY_NAME.jobid; + pname.vpid = OPAL_VPID_WILDCARD; + +-#if HAVE_DECL_PMIX_PACKAGE_RANK +- uint16_t *package_rank_ptr; + // Try to get the PACKAGE_RANK from PMIx +- OPAL_MODEX_RECV_VALUE_OPTIONAL(rc, PMIX_PACKAGE_RANK, ++ OPAL_MODEX_RECV_VALUE_OPTIONAL(rc, OPAL_PMIX_PACKAGE_RANK, + &pname, &package_rank_ptr, OPAL_UINT16); + if (OPAL_SUCCESS == rc) { + return (uint32_t)*package_rank_ptr; + } +-#endif + + // Get the local peers + OPAL_MODEX_RECV_VALUE(rc, OPAL_PMIX_LOCAL_PEERS, +diff --git a/opal/mca/pmix/pmix_types.h b/opal/mca/pmix/pmix_types.h +index d2643b2e549..816e386cbf1 100644 +--- a/opal/mca/pmix/pmix_types.h ++++ b/opal/mca/pmix/pmix_types.h +@@ -2,6 +2,7 @@ + * Copyright (c) 2014-2018 Intel, Inc. All rights reserved. + * Copyright (c) 2016 Research Organization for Information Science + * and Technology (RIST). All rights reserved. ++ * Copyright (c) 2021 Nanook Consulting. All rights reserved. + * $COPYRIGHT$ + * + * Additional copyrights may follow +@@ -130,6 +131,7 @@ BEGIN_C_DECLS + #define OPAL_PMIX_NPROC_OFFSET "pmix.offset" // (uint32_t) starting global rank of this job + #define OPAL_PMIX_LOCAL_RANK "pmix.lrank" // (uint16_t) rank on this node within this job + #define OPAL_PMIX_NODE_RANK "pmix.nrank" // (uint16_t) rank on this node spanning all jobs ++#define OPAL_PMIX_PACKAGE_RANK "pmix.pkgrank" // (uint16_t) rank within this job on the package where this proc resides + #define OPAL_PMIX_LOCALLDR "pmix.lldr" // (uint64_t) opal_identifier of lowest rank on this node within this job + #define OPAL_PMIX_APPLDR "pmix.aldr" // (uint32_t) lowest rank in this app within this job + #define OPAL_PMIX_PROC_PID "pmix.ppid" // (pid_t) pid of specified proc diff --git a/easybuild/easyconfigs/o/OpenMPI/9213.patch b/easybuild/easyconfigs/o/OpenMPI/9213.patch new file mode 100644 index 00000000000..f74907f563a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/9213.patch @@ -0,0 +1,79 @@ +From bd48a06e25c1058b7d3c3ba4414af388836c8219 Mon Sep 17 00:00:00 2001 +From: Ralph Castain +Date: Tue, 10 Aug 2021 13:01:11 -0700 +Subject: [PATCH] Protect the pmix3x component from a PMIx v4 attribute + +PMIx v4 introduced a new PMIX_TOPO2 attribute that takes a data type +unknown to PMIx 3. Unfortunately, that attribute can be provided by +the RM without our knowledge. We will update PMIx to try and detect +it and prevent it from slipping down to this level. Meantime, add +some simple protection here. + +Signed-off-by: Ralph Castain +--- + opal/mca/pmix/pmix3x/pmix3x.c | 29 +++++++++++++++++------------ + 1 file changed, 17 insertions(+), 12 deletions(-) + +diff --git a/opal/mca/pmix/pmix3x/pmix3x.c b/opal/mca/pmix/pmix3x/pmix3x.c +index 90670f6adb6..3b2a5353cc6 100644 +--- a/opal/mca/pmix/pmix3x/pmix3x.c ++++ b/opal/mca/pmix/pmix3x/pmix3x.c +@@ -8,6 +8,7 @@ + * Copyright (c) 2016 Cisco Systems, Inc. All rights reserved. + * Copyright (c) 2017 Los Alamos National Security, LLC. All rights + * reserved. ++ * Copyright (c) 2021 Nanook Consulting. All rights reserved. + * $COPYRIGHT$ + * + * Additional copyrights may follow +@@ -966,6 +967,7 @@ int pmix3x_value_unload(opal_value_t *kv, + opal_list_t *lt; + opal_value_t *ival; + size_t n; ++ pmix_info_t *iptr; + + switch(v->type) { + case PMIX_UNDEF: +@@ -1178,27 +1180,30 @@ int pmix3x_value_unload(opal_value_t *kv, + kv->data.pinfo.state = pmix3x_convert_state(v->data.pinfo->state); + break; + case PMIX_DATA_ARRAY: +- if (NULL == v->data.darray || NULL == v->data.darray->array) { ++ if (NULL == v->data.darray || NULL == v->data.darray->array || ++ PMIX_INFO != v->data.darray->type) { + kv->data.ptr = NULL; + break; + } + lt = OBJ_NEW(opal_list_t); + kv->type = OPAL_PTR; + kv->data.ptr = (void*)lt; ++ iptr = (pmix_info_t*)v->data.darray->array; + for (n=0; n < v->data.darray->size; n++) { ++ if (0 == strcmp("pmix.topo2", iptr[n].key)) { ++ /* we do not know (yet) how to convert the pmix.topo2 key from PMIx 4.0.0 ++ * but since we are not going to use it, simply ignore it and move on */ ++ continue; ++ } + ival = OBJ_NEW(opal_value_t); + opal_list_append(lt, &ival->super); +- /* handle the various types */ +- if (PMIX_INFO == v->data.darray->type) { +- pmix_info_t *iptr = (pmix_info_t*)v->data.darray->array; +- ival->key = strdup(iptr[n].key); +- rc = pmix3x_value_unload(ival, &iptr[n].value); +- if (OPAL_SUCCESS != rc) { +- OPAL_LIST_RELEASE(lt); +- kv->type = OPAL_UNDEF; +- kv->data.ptr = NULL; +- break; +- } ++ ival->key = strdup(iptr[n].key); ++ rc = pmix3x_value_unload(ival, &iptr[n].value); ++ if (OPAL_SUCCESS != rc) { ++ OPAL_LIST_RELEASE(lt); ++ kv->type = OPAL_UNDEF; ++ kv->data.ptr = NULL; ++ break; + } + } + break; diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index 9a76b9a2f8e..989f66906b9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -6,10 +6,7 @@ description = """The Open MPI Project is an open source MPI-3 implementation.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = [ - 'https://patch-diff.githubusercontent.com/raw/open-mpi/ompi/pull/', - 'https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads', -] +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', From caba291dc8c22fa1cce37e479f0a3fcfe33c2cac Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 15 Aug 2021 09:00:00 +0100 Subject: [PATCH 0901/9987] disable using system Valgrind in the json-c tests --- easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb | 2 ++ easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb index 3368d5ac787..150611776a2 100644 --- a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.2.0.eb @@ -20,6 +20,8 @@ builddependencies = [ ('CMake', '3.18.4'), ] +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' runtest = 'test' sanity_check_paths = { diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb index 195c011df45..6c6699becc4 100644 --- a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-10.3.0.eb @@ -20,6 +20,8 @@ builddependencies = [ ('CMake', '3.20.1'), ] +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' runtest = 'test' sanity_check_paths = { From ed3047d60351afb17aa5b9cdef76310b4bcea042 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 15 Aug 2021 12:47:07 +0200 Subject: [PATCH 0902/9987] Update easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-11.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-11.2.0.eb index a0ddc75e305..90622de3d49 100644 --- a/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/j/json-c/json-c-0.15-GCCcore-11.2.0.eb @@ -20,6 +20,8 @@ builddependencies = [ ('CMake', '3.21.1'), ] +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' runtest = 'test' sanity_check_paths = { From e14ba37f41f6f7e8f4a546e6aa9d3c375a1098d9 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Mon, 16 Aug 2021 10:21:40 +1000 Subject: [PATCH 0903/9987] Create MEGA-10.0.5.eb New version --- easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb | 27 +++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb diff --git a/easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb b/easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb new file mode 100644 index 00000000000..0bd04bcc95b --- /dev/null +++ b/easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'MEGA' +version = '10.0.5' + +homepage = 'http://www.megasoftware.net/' +description = """MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools + for statistics-based comparative analysis of molecular sequence data based on evolutionary principles.""" + +toolchain = SYSTEM + +# download requires agreeing with license & filling out a form, see http://www.megasoftware.net/ +sources = ['megacc-%(version)s.tar.gz'] + +checksums = ['c450a8339f8b48bc79433bb2f8c8af3ec58e23ad8f3f86b37f83f807e6bb5e9d'] + + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ['megacc'], + 'dirs': ['Examples'], +} + +moduleclass = 'bio' From 4c50f6065a58caa1eb7da59c3c3a88507a15dc2f Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 16 Aug 2021 08:10:20 +0200 Subject: [PATCH 0904/9987] add checksum --- easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb index 2ee0a563be0..df2b603098f 100644 --- a/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.2.26-Linux_x86_64.eb @@ -18,6 +18,7 @@ toolchain = SYSTEM source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/%(version)s/'] sources = ['%(namelower)s-%(version)s-x64-linux.tar.gz'] +checksums = ['8a2f986cf47f0f7cbdb3478c4fc7e25c7198941d2262264d0b6b86194b3d063d'] sanity_check_paths = { 'files': ["bin/blastall", "bin/impala", "bin/blastpgp"], From 75b034f4679c9c20eb352190abb0bd3754d3ee5d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 09:32:29 +0200 Subject: [PATCH 0905/9987] add patch for AlphaFold to fix setup.py, add OpenMM and PDBFixer dependencies, also install scripts and 'alphafold' command --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 25 +++++++++++++- .../AlphaFold-2.0.0_fix-packages.patch | 13 +++++++ .../p/PDBFixer/PDBFixer-1.7-foss-2020b.eb | 34 +++++++++++++++++++ 3 files changed, 71 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-packages.patch create mode 100644 easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 9fe9c5a44e3..6da221ba1a7 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -19,6 +19,8 @@ dependencies = [ ('PyYAML', '5.3.1'), ('TensorFlow', '2.4.1'), ('Biopython', '1.78'), + ('OpenMM', '7.5.1'), # for simtk + ('PDBFixer', '1.7'), ('jax', '0.2.19'), # also provides absl-py ] @@ -67,10 +69,31 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], 'sources': ['v%(version)s.tar.gz'], - 'checksums': ['78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2'], + 'patches': ['AlphaFold-%(version)s_fix-packages.patch'], + 'checksums': [ + '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + ], }), ] +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/AlphaFold/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/AlphaFold/alphafold-%(version)s/scripts %(installdir)s/", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/run_alphafold.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = ["alphafold --help"] + sanity_pip_check = True moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-packages.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-packages.patch new file mode 100644 index 00000000000..f42a59513e1 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-packages.patch @@ -0,0 +1,13 @@ +also include alphafold.data.tools and alphafold.model.tf, which are not picked up by find_packages() +author: Kenneth Hoste (HPC-UGent) +--- alphafold-2.0.0/setup.py.orig 2021-08-14 08:42:43.030919330 +0200 ++++ alphafold-2.0.0/setup.py 2021-08-14 08:43:59.183245602 +0200 +@@ -26,7 +26,7 @@ + author_email='alphafold@deepmind.com', + license='Apache License, Version 2.0', + url='https://github.com/deepmind/alphafold', +- packages=find_packages(), ++ packages=find_packages() + ['alphafold/data/tools', 'alphafold/model/tf'], + install_requires=[ + 'absl-py', + 'biopython', diff --git a/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb b/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb new file mode 100644 index 00000000000..89173238ef0 --- /dev/null +++ b/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'PDBFixer' +version = '1.7' + +homepage = 'https://github.com/openmm/pdbfixer' +description = """PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation +for simulating them.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/openmm/pdbfixer/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('OpenMM', '7.5.1'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/pdbfixer'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pdbfixer --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 34803f2eac7779117eb7007fef154d6cf60ff974 Mon Sep 17 00:00:00 2001 From: "benjamin.czaja" Date: Mon, 16 Aug 2021 10:06:30 +0200 Subject: [PATCH 0906/9987] Python version suffix removed from easyconfigs and eb filenames. Newline added to bottom of both eb configs --- .../b/biogeme/biogeme-3.1.2-foss-2021a.eb | 35 +++++++++++++++++ .../b/biogeme/biogeme-3.2.8-foss-2021a.eb | 38 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a.eb diff --git a/easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a.eb b/easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a.eb new file mode 100644 index 00000000000..dc22767d5d8 --- /dev/null +++ b/easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'biogeme' +version = '3.1.2' + +homepage = 'https://pypi.python.org/pypi/biogeme' +description = """Biogeme is a open source Python package designed for +the maximum likelihood estimation of parametric models in general, +with a special emphasis on discrete choice models.""" + +use_pip = True +sanity_pip_check = True + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05') +] + +exts_list = [ + ('Unidecode', '1.2.0', { + 'checksums': ['8d73a97d387a956922344f6b74243c2c6771594659778744b2dbdaad8f6b727d'], + }), + (name, version, { + 'checksums': ['28aecfa3701c293e3b3c6bcab68322d77d1721e10b18d987f592651333f1e438'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/biogeme'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a.eb b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a.eb new file mode 100644 index 00000000000..dca74cb3d2e --- /dev/null +++ b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'biogeme' +version = '3.2.8' + +homepage = 'https://pypi.python.org/pypi/biogeme' +description = """Biogeme is a open source Python package designed for +the maximum likelihood estimation of parametric models in general, +with a special emphasis on discrete choice models.""" + +use_pip = True +sanity_pip_check = True + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05') +] + +exts_list = [ + ('Unidecode', '1.2.0', { + 'checksums': ['8d73a97d387a956922344f6b74243c2c6771594659778744b2dbdaad8f6b727d'], + }), + ('tqdm', '4.62.0', { + 'checksums': ['3642d483b558eec80d3c831e23953582c34d7e4540db86d9e5ed9dad238dabc6'], + }), + (name, version, { + 'checksums': ['eafb969bb086a014617fae92e652fb54dd98ac72516a360e40c837244935859c'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/biogeme'], +} + +moduleclass = 'math' From 4b6b762d207a46c1e32604fe96a299c47cfc1af8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 10:36:19 +0200 Subject: [PATCH 0907/9987] enhance sanity check for HH-suite 3.3.0 + add path to scripts subdirectory to $PERL5LIB --- .../h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 27 +++++++++---------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index 6e6f5b7ed60..1c6f7bec0df 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -45,25 +45,24 @@ _binaries = [ 'hhmake', 'hhfilter', 'hhconsensus', ] -_scriptfiles = [ - 'a3m.py', 'check_a3m.py', 'cif2fasta.py', 'ffindex.py', 'get_a3m_size.py', - 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', -] - -_perlfiles = [ - 'addss.pl', 'create_profile_from_hmmer.pl', 'hhmakemodel.pl', - 'mergeali.pl', 'multithread.pl', 'pdb2fasta.pl', 'pdbfilter.pl', - 'reformat.pl', 'renumberpdb.pl', 'splitfasta.pl', -] - -fix_perl_shebang_for = ['scripts/%s' % z for z in _perlfiles] +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] sanity_check_paths = { 'files': ['bin/%s' % x for x in _binaries] + - ['scripts/%s' % y for y in _scriptfiles], + ['scripts/ffindex.py', 'scripts/hh_reader.py', 'scripts/hhmakemodel.pl', 'scripts/splitfasta.pl'], 'dirs': ['data', 'scripts'] } -modextrapaths = {'PATH': 'scripts'} +sanity_check_commands = [ + "hhsearch -h", + "ffindex.py --help", + "hhmakemodel.pl 2>&1 | grep 'hhmakemodel.pl from HHsuite'", +] + +modextrapaths = { + 'PATH': 'scripts', + 'PERL5LIB': 'scripts', +} moduleclass = 'bio' From c081a5873b9f39acf0381d22a07ed14f25bfae75 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 16 Aug 2021 09:26:31 +0000 Subject: [PATCH 0908/9987] Address suggested changes by Boegel --- .../h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index 6e6f5b7ed60..587b1efc8e4 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -46,17 +46,10 @@ _binaries = [ ] _scriptfiles = [ - 'a3m.py', 'check_a3m.py', 'cif2fasta.py', 'ffindex.py', 'get_a3m_size.py', 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', ] -_perlfiles = [ - 'addss.pl', 'create_profile_from_hmmer.pl', 'hhmakemodel.pl', - 'mergeali.pl', 'multithread.pl', 'pdb2fasta.pl', 'pdbfilter.pl', - 'reformat.pl', 'renumberpdb.pl', 'splitfasta.pl', -] - -fix_perl_shebang_for = ['scripts/%s' % z for z in _perlfiles] +fix_perl_shebang_for = ['scripts/*pl'] sanity_check_paths = { 'files': ['bin/%s' % x for x in _binaries] + @@ -64,6 +57,9 @@ sanity_check_paths = { 'dirs': ['data', 'scripts'] } -modextrapaths = {'PATH': 'scripts'} +modextrapaths = { + 'PATH': 'scripts', + 'PERL5LIB': 'scripts', +} moduleclass = 'bio' From 9fb09eeba11c0c47b9d5497cc2b22fb3d40b7690 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 11:34:21 +0200 Subject: [PATCH 0909/9987] add missing dependencies for AlphaFold + patch to pick up on them and take into account $ALPHAFOLD_DATA_DIR, fix sanity check command --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 11 ++- .../AlphaFold-2.0.0_data-dep-paths.patch | 96 +++++++++++++++++++ 2 files changed, 105 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 6da221ba1a7..af15e18801c 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -20,6 +20,9 @@ dependencies = [ ('TensorFlow', '2.4.1'), ('Biopython', '1.78'), ('OpenMM', '7.5.1'), # for simtk + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), ('PDBFixer', '1.7'), ('jax', '0.2.19'), # also provides absl-py ] @@ -69,10 +72,14 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], 'sources': ['v%(version)s.tar.gz'], - 'patches': ['AlphaFold-%(version)s_fix-packages.patch'], + 'patches': [ + 'AlphaFold-%(version)s_fix-packages.patch', + 'AlphaFold-%(version)s_data-dep-paths.patch', + ], 'checksums': [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '5a1b17002273cc05a06541297b8017b1928063fe54cffe0b133fa4b39b5435ad', # AlphaFold-2.0.0_data-dep-paths.patch ], }), ] @@ -92,7 +99,7 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } -sanity_check_commands = ["alphafold --help"] +sanity_check_commands = ["alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'"] sanity_pip_check = True diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch new file mode 100644 index 00000000000..96fea848153 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch @@ -0,0 +1,96 @@ +pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data +pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) +diff --git a/run_alphafold.py b/run_alphafold.py +index 61f7ef2..6d80d38 100644 +--- a/run_alphafold.py ++++ b/run_alphafold.py +@@ -36,6 +36,45 @@ from alphafold.model import model + from alphafold.relax import relax + # Internal import (7716). + ++ ++data_dir = os.getenv('ALPHAFOLD_DATA_DIR') ++if data_dir: ++ uniref90_database_path = os.path.join(data_dir, 'uniref90') ++ mgnify_database_path = os.path.join(data_dir, 'mgnify') ++ bfd_database_path = os.path.join(data_dir, 'bfd') ++ uniclust30_database_path = os.path.join(data_dir, 'uniclust30') ++ pdb70_database_path = os.path.join(data_dir, 'pdb70') ++ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif') ++ obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') ++else: ++ uniref90_database_path = None ++ mgnify_database_path = None ++ bfd_database_path = None ++ uniclust30_database_path = None ++ pdb70_database_path = None ++ template_mmcif_dir = None ++ obsolete_pdbs_path = None ++ ++hmmer_root = os.getenv('EBROOTHMMER') ++if hmmer_root: ++ jackhmmer_binary_path = os.path.join(hmmer_root, 'bin', 'jackhmmer') ++else: ++ jackhmmer_binary_path = '/usr/bin/jackhmmer' ++ ++hhsuite_root = os.getenv('EBROOTHHMINSUITE') ++if hhsuite_root: ++ hhblits_binary_path = os.path.join(hhsuite_root, 'bin', 'hhblits') ++ hhsearch_binary_path = os.path.join(hhsuite_root, 'bin', 'hhsearch') ++else: ++ hhblits_binary_path = '/usr/bin/hhblits' ++ hhsearch_binary_path = '/usr/bin/hhsearch' ++ ++kalign_root = os.getenv('EBROOTKALIGN') ++if kalign_root: ++ kalign_binary_path = os.path.join(kalign_root, 'bin', 'kalign') ++else: ++ kalign_binary_path = '/usr/bin/kalign' ++ + flags.DEFINE_list('fasta_paths', None, 'Paths to FASTA files, each containing ' + 'one sequence. Paths should be separated by commas. ' + 'All FASTA paths must have a unique basename as the ' +@@ -44,30 +83,30 @@ flags.DEFINE_list('fasta_paths', None, 'Paths to FASTA files, each containing ' + flags.DEFINE_string('output_dir', None, 'Path to a directory that will ' + 'store the results.') + flags.DEFINE_list('model_names', None, 'Names of models to use.') +-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') +-flags.DEFINE_string('jackhmmer_binary_path', '/usr/bin/jackhmmer', ++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') ++flags.DEFINE_string('jackhmmer_binary_path', jackhmmer_binary_path, + 'Path to the JackHMMER executable.') +-flags.DEFINE_string('hhblits_binary_path', '/usr/bin/hhblits', ++flags.DEFINE_string('hhblits_binary_path', hhblits_binary_path, + 'Path to the HHblits executable.') +-flags.DEFINE_string('hhsearch_binary_path', '/usr/bin/hhsearch', ++flags.DEFINE_string('hhsearch_binary_path', hhsearch_binary_path, + 'Path to the HHsearch executable.') +-flags.DEFINE_string('kalign_binary_path', '/usr/bin/kalign', ++flags.DEFINE_string('kalign_binary_path', kalign_binary_path, + 'Path to the Kalign executable.') +-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 ' ++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify ' ++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD ' ++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD ' + 'database for use by HHblits.') +-flags.DEFINE_string('uniclust30_database_path', None, 'Path to the Uniclust30 ' ++flags.DEFINE_string('uniclust30_database_path', uniclust30_database_path, 'Path to the Uniclust30 ' + 'database for use by HHblits.') +-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 ' ++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 ' + 'database for use by HHsearch.') +-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with ' ++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with ' + 'template mmCIF structures, each named .cif') + flags.DEFINE_string('max_template_date', None, 'Maximum template release date ' + 'to consider. Important if folding historical test sets.') +-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a ' ++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a ' + 'mapping from obsolete PDB IDs to the PDB IDs of their ' + 'replacements.') + flags.DEFINE_enum('preset', 'full_dbs', ['full_dbs', 'casp14'], From 7ecf851bb86ef903b28ca3c2afcf8ea7b822c903 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 11:49:08 +0200 Subject: [PATCH 0910/9987] avoid warnigns about non-default values for required options to run_alphafold.py script --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- .../AlphaFold-2.0.0_data-dep-paths.patch | 19 ++++++++++++++++++- 2 files changed, 19 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index af15e18801c..9038dac8d56 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -79,7 +79,7 @@ exts_list = [ 'checksums': [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '5a1b17002273cc05a06541297b8017b1928063fe54cffe0b133fa4b39b5435ad', # AlphaFold-2.0.0_data-dep-paths.patch + '7e19d944934b8004e4ee114c94f580d899ac503f3147fc7746c960cc5ca18c0d', # AlphaFold-2.0.0_data-dep-paths.patch ], }), ] diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch index 96fea848153..e7f052dcde7 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch @@ -2,7 +2,7 @@ pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild author: Kenneth Hoste (HPC-UGent) diff --git a/run_alphafold.py b/run_alphafold.py -index 61f7ef2..6d80d38 100644 +index 61f7ef2..96df783 100644 --- a/run_alphafold.py +++ b/run_alphafold.py @@ -36,6 +36,45 @@ from alphafold.model import model @@ -94,3 +94,20 @@ index 61f7ef2..6d80d38 100644 'mapping from obsolete PDB IDs to the PDB IDs of their ' 'replacements.') flags.DEFINE_enum('preset', 'full_dbs', ['full_dbs', 'casp14'], +@@ -268,16 +307,8 @@ if __name__ == '__main__': + 'fasta_paths', + 'output_dir', + 'model_names', +- 'data_dir', + 'preset', +- 'uniref90_database_path', +- 'mgnify_database_path', +- 'uniclust30_database_path', +- 'bfd_database_path', +- 'pdb70_database_path', +- 'template_mmcif_dir', + 'max_template_date', +- 'obsolete_pdbs_path', + ]) + + app.run(main) From b7b1ccdd5b84c4dc9baa3d678301cd5c21eb1f7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 11:52:30 +0200 Subject: [PATCH 0911/9987] fix default value for template_mmcif_dir based on \ALPHAFOLD_DATA_DIR --- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- .../a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 9038dac8d56..cab8b7153a4 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -79,7 +79,7 @@ exts_list = [ 'checksums': [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '7e19d944934b8004e4ee114c94f580d899ac503f3147fc7746c960cc5ca18c0d', # AlphaFold-2.0.0_data-dep-paths.patch + '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch ], }), ] diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch index e7f052dcde7..d23e7c15904 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch @@ -2,7 +2,7 @@ pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild author: Kenneth Hoste (HPC-UGent) diff --git a/run_alphafold.py b/run_alphafold.py -index 61f7ef2..96df783 100644 +index 61f7ef2..81c97a0 100644 --- a/run_alphafold.py +++ b/run_alphafold.py @@ -36,6 +36,45 @@ from alphafold.model import model @@ -17,7 +17,7 @@ index 61f7ef2..96df783 100644 + bfd_database_path = os.path.join(data_dir, 'bfd') + uniclust30_database_path = os.path.join(data_dir, 'uniclust30') + pdb70_database_path = os.path.join(data_dir, 'pdb70') -+ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif') ++ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') + obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') +else: + uniref90_database_path = None From c032e63216bc9cac93c566a85ad82f794f1d1ca6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 12:21:02 +0200 Subject: [PATCH 0912/9987] add patch for HHBlits and JackHmmer scripts to avoid hardcoded number of cores to use --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 + .../a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch | 48 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index cab8b7153a4..c3325e0a46a 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -75,11 +75,13 @@ exts_list = [ 'patches': [ 'AlphaFold-%(version)s_fix-packages.patch', 'AlphaFold-%(version)s_data-dep-paths.patch', + 'AlphaFold-%(version)s_n-cpu.patch', ], 'checksums': [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch + '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a', # AlphaFold-2.0.0_n-cpu.patch ], }), ] diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch new file mode 100644 index 00000000000..a61e8394395 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch @@ -0,0 +1,48 @@ +don't hardcode number of cores to use by HHBlits and Jackhmmer scripts +author: Kenneth Hoste (HPC-UGent) + +diff --git a/alphafold/data/tools/hhblits.py b/alphafold/data/tools/hhblits.py +index e0aa098..e624f3a 100644 +--- a/alphafold/data/tools/hhblits.py ++++ b/alphafold/data/tools/hhblits.py +@@ -27,6 +27,8 @@ from alphafold.data.tools import utils + _HHBLITS_DEFAULT_P = 20 + _HHBLITS_DEFAULT_Z = 500 + ++HHBLITS_N_CPU = os.getenv('ALPHAFOLD_HHBLITS_N_CPU', os.getenv('SLURM_CPUS_ON_NODE', 4)) ++ + + class HHBlits: + """Python wrapper of the HHblits binary.""" +@@ -35,7 +37,7 @@ class HHBlits: + *, + binary_path: str, + databases: Sequence[str], +- n_cpu: int = 4, ++ n_cpu: int = HHBLITS_N_CPU, + n_iter: int = 3, + e_value: float = 0.001, + maxseq: int = 1_000_000, +diff --git a/alphafold/data/tools/jackhmmer.py b/alphafold/data/tools/jackhmmer.py +index ae53df9..800bf99 100644 +--- a/alphafold/data/tools/jackhmmer.py ++++ b/alphafold/data/tools/jackhmmer.py +@@ -24,6 +24,9 @@ from alphafold.data.tools import utils + # Internal import (7716). + + ++JACKHMMER_N_CPU = os.getenv('ALPHAFOLD_JACKHMMER_N_CPU', os.getenv('SLURM_CPUS_ON_NODE', 4)) ++ ++ + class Jackhmmer: + """Python wrapper of the Jackhmmer binary.""" + +@@ -31,7 +34,7 @@ class Jackhmmer: + *, + binary_path: str, + database_path: str, +- n_cpu: int = 8, ++ n_cpu: int = JACKHMMER_N_CPU, + n_iter: int = 1, + e_value: float = 0.0001, + z_value: Optional[int] = None, From dfecbab04d03e950caf04af2011b607214f5f6cc Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 16 Aug 2021 11:25:50 +0000 Subject: [PATCH 0913/9987] Missing Python-3.8.6 added --- .../h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index 1c6f7bec0df..231c60d49b8 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -36,6 +36,7 @@ builddependencies = [ dependencies = [ ('Perl', '5.32.0'), + ('Python', '3.8.6'), ] _binaries = [ @@ -45,21 +46,18 @@ _binaries = [ 'hhmake', 'hhfilter', 'hhconsensus', ] -fix_perl_shebang_for = ['scripts/*.pl'] -fix_python_shebang_for = ['scripts/*.py'] +_scriptfiles = [ + 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', +] + +fix_perl_shebang_for = ['scripts/*pl'] sanity_check_paths = { 'files': ['bin/%s' % x for x in _binaries] + - ['scripts/ffindex.py', 'scripts/hh_reader.py', 'scripts/hhmakemodel.pl', 'scripts/splitfasta.pl'], + ['scripts/%s' % y for y in _scriptfiles], 'dirs': ['data', 'scripts'] } -sanity_check_commands = [ - "hhsearch -h", - "ffindex.py --help", - "hhmakemodel.pl 2>&1 | grep 'hhmakemodel.pl from HHsuite'", -] - modextrapaths = { 'PATH': 'scripts', 'PERL5LIB': 'scripts', From 08d29023d21179d62a433f3217926974c70d3fc8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 15:12:33 +0200 Subject: [PATCH 0914/9987] include stereo_chemical_props.txt in AlphaFold installaiton directory, switch to installing AlphaFold via 'components' because it now requires multiple source files --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 63 +++++++++++++------ .../AlphaFold-2.0.0_fix-scp-path.patch | 23 +++++++ 2 files changed, 68 insertions(+), 18 deletions(-) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-scp-path.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index c3325e0a46a..dafa3b16123 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -27,6 +27,44 @@ dependencies = [ ('jax', '0.2.19'), # also provides absl-py ] +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + 'v%(version)s.tar.gz', + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp -a %s .", + }, + ], + 'patches': [ + 'AlphaFold-%(version)s_fix-packages.patch', + 'AlphaFold-%(version)s_data-dep-paths.patch', + 'AlphaFold-%(version)s_n-cpu.patch', + 'AlphaFold-2.0.0_fix-scp-path.patch', + ], + 'checksums': [ + '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch + '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a', # AlphaFold-2.0.0_n-cpu.patch + '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + use_pip = True exts_list = [ @@ -69,31 +107,17 @@ exts_list = [ # see https://github.com/google/ml_collections/issues/7 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", }), - (name, version, { - 'source_urls': ['https://github.com/deepmind/alphafold/archive/refs/tags/'], - 'sources': ['v%(version)s.tar.gz'], - 'patches': [ - 'AlphaFold-%(version)s_fix-packages.patch', - 'AlphaFold-%(version)s_data-dep-paths.patch', - 'AlphaFold-%(version)s_n-cpu.patch', - ], - 'checksums': [ - '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz - '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch - '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a', # AlphaFold-2.0.0_n-cpu.patch - ], - }), ] postinstallcmds = [ "mkdir -p %(installdir)s/bin", # run_alphafold.py script is missing a shebang... "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", - "cat %(builddir)s/AlphaFold/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", "chmod a+x %(installdir)s/bin/run_alphafold.py", "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", - "cp -a %(builddir)s/AlphaFold/alphafold-%(version)s/scripts %(installdir)s/", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, ] sanity_check_paths = { @@ -101,7 +125,10 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } -sanity_check_commands = ["alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'"] +sanity_check_commands = [ + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] sanity_pip_check = True diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-scp-path.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-scp-path.patch new file mode 100644 index 00000000000..c44ee6be008 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_fix-scp-path.patch @@ -0,0 +1,23 @@ +fix path to stereo_chemical_props.txt when AlphaFold is installed with EasyBuild +author: Kenneth Hoste (HPC-UGent) +diff --git a/alphafold/common/residue_constants.py b/alphafold/common/residue_constants.py +index 318b44a..fd840e3 100644 +--- a/alphafold/common/residue_constants.py ++++ b/alphafold/common/residue_constants.py +@@ -19,6 +19,7 @@ import functools + from typing import Mapping, List, Tuple + + import numpy as np ++import os + import tree + + # Internal import (35fd). +@@ -403,7 +404,7 @@ def load_stereo_chemical_props() -> Tuple[Mapping[str, List[Bond]], + residue_bond_angles: dict that maps resname --> list of BondAngle tuples + """ + stereo_chemical_props_path = ( +- 'alphafold/common/stereo_chemical_props.txt') ++ os.path.join(os.getenv('EBROOTALPHAFOLD', 'alphafold/common'), 'stereo_chemical_props.txt')) + with open(stereo_chemical_props_path, 'rt') as f: + stereo_chemical_props = f.read() + lines_iter = iter(stereo_chemical_props.splitlines()) From e82389d431c23a0935d99621865191421fe23622 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 17:19:39 +0200 Subject: [PATCH 0915/9987] include patched OpenMM as component in AlphaFold installation --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 37 +++++++++++++-- .../a/AlphaFold/OpenMM-7.5.1_AlphaFold.patch | 45 +++++++++++++++++++ 2 files changed, 79 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/a/AlphaFold/OpenMM-7.5.1_AlphaFold.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index dafa3b16123..f91253267d6 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -9,8 +9,12 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ + # CMake/oxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), # required for installing dm-tree ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), ] dependencies = [ @@ -19,7 +23,6 @@ dependencies = [ ('PyYAML', '5.3.1'), ('TensorFlow', '2.4.1'), ('Biopython', '1.78'), - ('OpenMM', '7.5.1'), # for simtk ('HH-suite', '3.3.0'), ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), @@ -27,11 +30,29 @@ dependencies = [ ('jax', '0.2.19'), # also provides absl-py ] +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + # required to install OpenMM Python API + 'installopts': " && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s", + }), (name, version, { 'easyblock': 'PythonPackage', 'source_urls': [ @@ -39,7 +60,10 @@ components = [ 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, ], 'sources': [ - 'v%(version)s.tar.gz', + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, { 'download_filename': 'stereo_chemical_props.txt', 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, @@ -121,15 +145,22 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/run_alphafold.py'], + 'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } sanity_check_commands = [ + "python -m simtk.testInstallation", "python -c 'import alphafold'", "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + sanity_pip_check = True moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/OpenMM-7.5.1_AlphaFold.patch b/easybuild/easyconfigs/a/AlphaFold/OpenMM-7.5.1_AlphaFold.patch new file mode 100644 index 00000000000..878ffd11b03 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/OpenMM-7.5.1_AlphaFold.patch @@ -0,0 +1,45 @@ +custom patch for OpenMM to use in conjunction with AlphaFold +see https://github.com/deepmind/alphafold/blob/main/docker/openmm.patch + +Index: simtk/openmm/app/topology.py +=================================================================== +--- simtk.orig/openmm/app/topology.py ++++ simtk/openmm/app/topology.py +@@ -356,19 +356,35 @@ + def isCyx(res): + names = [atom.name for atom in res._atoms] + return 'SG' in names and 'HG' not in names ++ # This function is used to prevent multiple di-sulfide bonds from being ++ # assigned to a given atom. This is a DeepMind modification. ++ def isDisulfideBonded(atom): ++ for b in self._bonds: ++ if (atom in b and b[0].name == 'SG' and ++ b[1].name == 'SG'): ++ return True ++ ++ return False + + cyx = [res for res in self.residues() if res.name == 'CYS' and isCyx(res)] + atomNames = [[atom.name for atom in res._atoms] for res in cyx] + for i in range(len(cyx)): + sg1 = cyx[i]._atoms[atomNames[i].index('SG')] + pos1 = positions[sg1.index] ++ candidate_distance, candidate_atom = 0.3*nanometers, None + for j in range(i): + sg2 = cyx[j]._atoms[atomNames[j].index('SG')] + pos2 = positions[sg2.index] + delta = [x-y for (x,y) in zip(pos1, pos2)] + distance = sqrt(delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2]) +- if distance < 0.3*nanometers: +- self.addBond(sg1, sg2) ++ if distance < candidate_distance and not isDisulfideBonded(sg2): ++ candidate_distance = distance ++ candidate_atom = sg2 ++ # Assign bond to closest pair. ++ if candidate_atom: ++ self.addBond(sg1, candidate_atom) ++ ++ + + class Chain(object): + """A Chain object represents a chain within a Topology.""" From 6cf72d7645a5ba9fa064ce330bae693fb68c776f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 17:21:38 +0200 Subject: [PATCH 0916/9987] don't pick up on \SLURM_CPUS_ON_NODE, only add environment variable to avoid hardcoding core count for jackhmmer and hhblits --- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index f91253267d6..ecfaeb43f03 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -81,7 +81,7 @@ components = [ '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch - '90db20bf420c56ab787c1fdeddc190d47095f9717523e0058767d2c209e21a1a', # AlphaFold-2.0.0_n-cpu.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch ], 'start_dir': 'alphafold-%(version)s', diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch index a61e8394395..8849e17462c 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_n-cpu.patch @@ -1,4 +1,5 @@ -don't hardcode number of cores to use by HHBlits and Jackhmmer scripts +don't hardcode number of cores to use by HHBlits and Jackhmmer scripts; +see https://github.com/deepmind/alphafold/issues/110 author: Kenneth Hoste (HPC-UGent) diff --git a/alphafold/data/tools/hhblits.py b/alphafold/data/tools/hhblits.py @@ -9,7 +10,7 @@ index e0aa098..e624f3a 100644 _HHBLITS_DEFAULT_P = 20 _HHBLITS_DEFAULT_Z = 500 -+HHBLITS_N_CPU = os.getenv('ALPHAFOLD_HHBLITS_N_CPU', os.getenv('SLURM_CPUS_ON_NODE', 4)) ++HHBLITS_N_CPU = os.getenv('ALPHAFOLD_HHBLITS_N_CPU', 4) + class HHBlits: @@ -31,7 +32,7 @@ index ae53df9..800bf99 100644 # Internal import (7716). -+JACKHMMER_N_CPU = os.getenv('ALPHAFOLD_JACKHMMER_N_CPU', os.getenv('SLURM_CPUS_ON_NODE', 4)) ++JACKHMMER_N_CPU = os.getenv('ALPHAFOLD_JACKHMMER_N_CPU', 8) + + class Jackhmmer: From 0342cb8286b955c06325d27dbf74d51b38a815a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Aug 2021 17:37:07 +0200 Subject: [PATCH 0917/9987] fix default paths to downloaded AlphaFold data --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- .../a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch | 11 ++++++----- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index ecfaeb43f03..b0ff243dc72 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -80,7 +80,7 @@ components = [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '2ccf9a9c8dbae9d47ef1958ede78710cb7ebd4c5231bdb268f44664b45f4e950', # AlphaFold-2.0.0_data-dep-paths.patch + '1d426748bec4f0f3cc49448ebeb14c4350717f88287afd2aabf6738dea387d81', # AlphaFold-2.0.0_data-dep-paths.patch 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch ], diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch index d23e7c15904..0dcbedcdce8 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch @@ -1,4 +1,5 @@ pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data +(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py); pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild author: Kenneth Hoste (HPC-UGent) diff --git a/run_alphafold.py b/run_alphafold.py @@ -12,11 +13,11 @@ index 61f7ef2..81c97a0 100644 + +data_dir = os.getenv('ALPHAFOLD_DATA_DIR') +if data_dir: -+ uniref90_database_path = os.path.join(data_dir, 'uniref90') -+ mgnify_database_path = os.path.join(data_dir, 'mgnify') -+ bfd_database_path = os.path.join(data_dir, 'bfd') -+ uniclust30_database_path = os.path.join(data_dir, 'uniclust30') -+ pdb70_database_path = os.path.join(data_dir, 'pdb70') ++ uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') ++ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters.fa') ++ bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') ++ uniclust30_database_path = os.path.join(data_dir, 'uniclust30', 'uniclust30_2018_08', 'uniclust30_2018_08') ++ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') + template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') + obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') +else: From 1c9535d543333f31b4e4d5ed35b25e2846782f8a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 16 Aug 2021 18:25:39 +0200 Subject: [PATCH 0918/9987] fix sources of MEGA-10.0.5.eb --- easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb b/easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb index 0bd04bcc95b..cf1dd1d739b 100644 --- a/easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb +++ b/easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb @@ -10,11 +10,10 @@ description = """MEGA-CC (Molecular Evolutionary Genetics Analysis Computational toolchain = SYSTEM # download requires agreeing with license & filling out a form, see http://www.megasoftware.net/ -sources = ['megacc-%(version)s.tar.gz'] - +# the following sources correspond to "Other Linux" > "Command Line (CC)" > "MEGA X (64-bit)" +sources = ['megacc_%(version)s_amd64.tar.gz'] checksums = ['c450a8339f8b48bc79433bb2f8c8af3ec58e23ad8f3f86b37f83f807e6bb5e9d'] - modextrapaths = { 'PATH': '', } From f552f8333c1330eafc27b4097a4fd1aa14b9566f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 16 Aug 2021 18:26:16 +0200 Subject: [PATCH 0919/9987] fix homepage of MEGA-10.0.5.eb --- easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb b/easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb index cf1dd1d739b..c6c973b26e8 100644 --- a/easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb +++ b/easybuild/easyconfigs/m/MEGA/MEGA-10.0.5.eb @@ -3,7 +3,7 @@ easyblock = 'Tarball' name = 'MEGA' version = '10.0.5' -homepage = 'http://www.megasoftware.net/' +homepage = 'https://www.megasoftware.net/' description = """MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools for statistics-based comparative analysis of molecular sequence data based on evolutionary principles.""" From 7b4e88554608f548f0c0e32e7d3260ccea6d41ad Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 16 Aug 2021 18:14:03 +0100 Subject: [PATCH 0920/9987] adding easyconfigs: HMMER-3.3.2-gompic-2020b.eb, HH-suite-3.3.0-gompic-2020b.eb --- .../h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb | 66 ++++++++++++++++++ .../h/HMMER/HMMER-3.3.2-gompic-2020b.eb | 68 +++++++++++++++++++ 2 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb new file mode 100644 index 00000000000..e3d70a3e26a --- /dev/null +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb @@ -0,0 +1,66 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Updated to use gompi-2020b toolchain: +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'HH-suite' +version = '3.3.0' + +homepage = 'https://github.com/soedinglab/hh-suite' +description = """The HH-suite is an open-source software package +for sensitive protein sequence searching based on the pairwise +alignment of hidden Markov models (HMMs).""" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Perl', '5.32.0'), + ('Python', '3.8.6'), +] + +_binaries = [ + 'hhalign', 'hhalign_mpi', 'hhalign_omp', + 'hhblits', 'hhblits_mpi', 'hhblits_omp', + 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp', + 'hhmake', 'hhfilter', 'hhconsensus', +] + +_scriptfiles = [ + 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', +] + +fix_perl_shebang_for = ['scripts/*pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + ['scripts/%s' % y for y in _scriptfiles], + 'dirs': ['data', 'scripts'] +} + +modextrapaths = { + 'PATH': 'scripts', + 'PERL5LIB': 'scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb new file mode 100644 index 00000000000..bb136efe34d --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb @@ -0,0 +1,68 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompic', 'version': '2020b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] + +builddependencies = [('Python', '3.8.6')] + +configopts = '--enable-mpi' + +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From d0ebdf9dd16457dcfceffa3f56cca1ccfaeac99f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 16 Aug 2021 20:47:51 +0100 Subject: [PATCH 0921/9987] switch to SOURCELOWER_TAR_GZ --- easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb index bb136efe34d..f26e9cbaafc 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb @@ -34,7 +34,7 @@ source_urls = [ 'http://eddylab.org/software/hmmer/', 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] -sources = ['hmmer-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] builddependencies = [('Python', '3.8.6')] From 283563e0c5a0eecb01beaff2e4c2e85a2bdea6f8 Mon Sep 17 00:00:00 2001 From: jedokaplan Date: Tue, 17 Aug 2021 17:29:44 +0800 Subject: [PATCH 0922/9987] adding easyconfigs: Qwt-6.1.5-GCCcore-10.2.0.eb --- .../q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9ffe3f5f9dd --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.1.5' + +homepage = 'https://qwt.sourceforge.io/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Qwt-6.1.4_Fix_prefix_and_pkgconfig.patch'] +checksums = [ + '4076de63ec2b5e84379ddfebf27c7b29b8dc9074f3db7e2ca61d11a1d8adc041', # qwt-6.1.5.tar.bz2 + '82788aaa23e4bc764ab1f2769e9260d154976c7d7f043ba4e288330d6984b6a9', # Qwt-6.1.4_Fix_prefix_and_pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Qt5', '5.14.2'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export QWT_PREFIX=%(installdir)s && ' +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' From 7c9d3696057b716ff5189a983e5456f28613d4f3 Mon Sep 17 00:00:00 2001 From: jedokaplan Date: Tue, 17 Aug 2021 17:30:34 +0800 Subject: [PATCH 0923/9987] adding easyconfigs: QwtPolar-1.1.1-GCCcore-10.2.0.eb, QJson-0.9.0-GCCcore-10.2.0.eb --- .../q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb | 33 +++++++++++++++++ .../QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb | 36 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..fdf7452a362 --- /dev/null +++ b/easybuild/easyconfigs/q/QJson/QJson-0.9.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'QJson' +version = '0.9.0' + +homepage = 'http://qjson.sourceforge.net/' +description = "QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/flavio/qjson/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e812617477f3c2bb990561767a4cd8b1d3803a52018d4878da302529552610d4'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4') +] +dependencies = [ + ('Qt5', '5.14.2'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libqjson-qt5.%s' % SHLIB_EXT], + 'dirs': ['include/qjson-qt5', 'lib/cmake', 'lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0d2549e8115 --- /dev/null +++ b/easybuild/easyconfigs/q/QwtPolar/QwtPolar-1.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'QwtPolar' +version = '1.1.1' + +homepage = 'http://qwtpolar.sourceforge.net/' +description = "The QwtPolar library contains classes for displaying values on a polar coordinate system." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6168baa9dbc8d527ae1ebf2631313291a1d545da268a05f4caa52ceadbe8b295'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('Qwt', '6.1.5'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@INSTALL_PREFIX[ ]*=.*@INSTALL_PREFIX = %(installdir)s@g' qwtpolarconfig.pri && " +prebuildopts += "sed -i 's/QwtPolarExamples//g' qwtpolarconfig.pri && " +prebuildopts += "qmake qwtpolar.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwtpolar.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' From 178463798adc6db719de7efb506515d26515af3c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Aug 2021 11:38:17 +0200 Subject: [PATCH 0924/9987] make run_alphafold.py print a warning when $ALPHAFOLD_DATA_DIR is not defined --- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- .../a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index b0ff243dc72..91d5b657e7f 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -80,7 +80,7 @@ components = [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '1d426748bec4f0f3cc49448ebeb14c4350717f88287afd2aabf6738dea387d81', # AlphaFold-2.0.0_data-dep-paths.patch + '7223e297b23f90816219095696bc6453910c617add60b907a0d3e869da8733bb', # AlphaFold-2.0.0_data-dep-paths.patch 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch ], diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch index 0dcbedcdce8..674bcd2f935 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0_data-dep-paths.patch @@ -6,7 +6,7 @@ diff --git a/run_alphafold.py b/run_alphafold.py index 61f7ef2..81c97a0 100644 --- a/run_alphafold.py +++ b/run_alphafold.py -@@ -36,6 +36,45 @@ from alphafold.model import model +@@ -36,6 +36,46 @@ from alphafold.model import model from alphafold.relax import relax # Internal import (7716). @@ -21,6 +21,7 @@ index 61f7ef2..81c97a0 100644 + template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') + obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') +else: ++ sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!") + uniref90_database_path = None + mgnify_database_path = None + bfd_database_path = None From baca17d9942e0c0bdb2895a44245150f508000c0 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Tue, 17 Aug 2021 13:19:48 +0200 Subject: [PATCH 0925/9987] Update easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2021a.eb --- easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2021a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2021a.eb index 5276c7c689e..0bc6dfda7b5 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2021a.eb @@ -31,7 +31,7 @@ checksums = ['68f24a68eb6f94eaecf500e17448f566031946deab74f2cba072ee8368af0996'] dependencies = [ ('CubeLib', '4.6'), ('CubeWriter', '4.6'), - ('libunwind', '1.5.0'), + ('libunwind', '1.4.0'), ('OPARI2', '2.0.6'), ('OTF2', '2.3'), # Hardware counter support (optional): From b8bf8f412047adf5439f77483bb6a5856c764c15 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 17 Aug 2021 13:22:24 +0200 Subject: [PATCH 0926/9987] setting crisprdav easyblock explicitely --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index d6b5db719a7..10b66993053 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -1,3 +1,5 @@ +easyblock = 'EB_CRISPR_minus_DAV' + name = 'CRISPR-DAV' version = '2.3.4' From d2c98b14869b5ec2b4cb56e5c03336db2cc328f0 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 17 Aug 2021 13:29:42 +0200 Subject: [PATCH 0927/9987] Delete crispr-dav-2.3.4-foss-2020b.eb deleting old file (has old filename) --- .../crispr-dav/crispr-dav-2.3.4-foss-2020b.eb | 55 ------------------- 1 file changed, 55 deletions(-) delete mode 100644 easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb deleted file mode 100644 index 8adecc04755..00000000000 --- a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss-2020b.eb +++ /dev/null @@ -1,55 +0,0 @@ -easyblock = 'EB_crisprdav' - -name = 'crispr-dav' -version = '2.3.4' - -homepage = 'https://github.com/pinetree1/crispr-dav/' -description = """CRISPR-DAV is a pipeline to analyze -amplicon-based NGS data of CRISPR clones in a high throughput manner.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://github.com/pinetree1/crispr-dav/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch'] -checksums = [ - '49975cd48bdbf31fe5a9e2aaa3f5ed85d3cc6f65a422ee3aa8daed890159d2ae', # v2.3.4.tar.gz - # crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch - 'a06414a1cf00be359cea46a36133fc312f948f50c2e4bc9043d2e83f3a011e97', -] - -extract_sources = True - -dependencies = [ - ('R', '4.0.3'), - ('Perl', '5.32.0'), - ('NGS', '2.10.9'), - ('Pysam', '0.16.0.1'), - ('Excel-Writer-XLSX', '1.09'), - ('naturalsort', '0.1.3'), - ('pysamstats', '1.1.2'), - ('ABRA2', '2.23'), - ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), - ('SAMtools', '1.12'), - ('BEDTools', '2.30.0'), - ('FLASH', '2.2.00'), -] - -postinstallcmds = ' mkdir bin && ln -s crispr.pl bin/crispr.pl && chmod +x bin/crispr.pl ' - -modextrapaths = {'PATH': ['bin/']} - -sanity_check_paths = { - 'files': [], - 'dirs': ['Modules', 'Examples', 'Rscripts'], -} - -sanity_check_commands = [("""crispr.pl --conf $EBROOTCRISPRMINDAV/Examples/example1/conf.txt \ - --region $EBROOTCRISPRMINDAV/Examples/example1/amplicon.bed \ - --crispr $EBROOTCRISPRMINDAV/Examples/example1/site.bed \ - --sitemap $EBROOTCRISPRMINDAV/Examples/example1/sample.site \ - --fastqmap $EBROOTCRISPRMINDAV/Examples/example1/fastq.list \ - --genome genomex 2>&1 | grep 'Generated HTML report for GENEX_CR1'""", ''), - ("crispr.pl --help 2>&1 | grep 'Usage: '", '')] - -moduleclass = 'bio' From 03332317bb656a68c5498dd7c35db50944689087 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 17 Aug 2021 13:31:17 +0200 Subject: [PATCH 0928/9987] removing explicit crispr-dav easyblock --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index 10b66993053..d6b5db719a7 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_CRISPR_minus_DAV' - name = 'CRISPR-DAV' version = '2.3.4' From f33814d908ff539a984debe90a89bbe0e2b129a1 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 17 Aug 2021 13:30:29 +0100 Subject: [PATCH 0929/9987] Delete biogeme-3.2.8-foss-2021a-Python-3.9.5.eb Remove file with obsolete versionsuffix. --- .../biogeme-3.2.8-foss-2021a-Python-3.9.5.eb | 39 ------------------- 1 file changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a-Python-3.9.5.eb deleted file mode 100644 index bbdc72b9394..00000000000 --- a/easybuild/easyconfigs/b/biogeme/biogeme-3.2.8-foss-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'biogeme' -version = '3.2.8' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/biogeme' -description = """Biogeme is a open source Python package designed for -the maximum likelihood estimation of parametric models in general, -with a special emphasis on discrete choice models.""" - -use_pip = True -sanity_pip_check = True - -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05') -] - -exts_list = [ - ('Unidecode', '1.2.0', { - 'checksums': ['8d73a97d387a956922344f6b74243c2c6771594659778744b2dbdaad8f6b727d'], - }), - ('tqdm', '4.62.0', { - 'checksums': ['3642d483b558eec80d3c831e23953582c34d7e4540db86d9e5ed9dad238dabc6'], - }), - (name, version, { - 'checksums': ['eafb969bb086a014617fae92e652fb54dd98ac72516a360e40c837244935859c'], - }), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/biogeme'], -} - -moduleclass = 'math' \ No newline at end of file From 8f78c25135b7a98fe6b59a1dfdc9f15524aff565 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 17 Aug 2021 13:31:39 +0100 Subject: [PATCH 0930/9987] Delete biogeme-3.1.2-foss-2021a-Python-3.9.5.eb Delete second file with obsolete versionsuffix. --- .../biogeme-3.1.2-foss-2021a-Python-3.9.5.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a-Python-3.9.5.eb deleted file mode 100644 index 1c49b4a975c..00000000000 --- a/easybuild/easyconfigs/b/biogeme/biogeme-3.1.2-foss-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'biogeme' -version = '3.1.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pypi.python.org/pypi/biogeme' -description = """Biogeme is a open source Python package designed for -the maximum likelihood estimation of parametric models in general, -with a special emphasis on discrete choice models.""" - -use_pip = True -sanity_pip_check = True - -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05') -] - -exts_list = [ - ('Unidecode', '1.2.0', { - 'checksums': ['8d73a97d387a956922344f6b74243c2c6771594659778744b2dbdaad8f6b727d'], - }), - (name, version, { - 'checksums': ['28aecfa3701c293e3b3c6bcab68322d77d1721e10b18d987f592651333f1e438'], - }), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/biogeme'], -} - -moduleclass = 'math' \ No newline at end of file From fd5fbdc9d8a7d7f382a21996eb7d2cb1a8da6b73 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 17 Aug 2021 15:45:33 +0200 Subject: [PATCH 0931/9987] Update CRISPR-DAV-2.3.4-foss-2020b.eb adding archive-zip perl module --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index d6b5db719a7..176d5949c38 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -29,6 +29,7 @@ dependencies = [ ('SAMtools', '1.12'), ('BEDTools', '2.30.0'), ('FLASH', '2.2.00'), + ('Archive-Zip', '1.68'), ] moduleclass = 'bio' From b655d3aa62acc616889b755765742836e60083ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 17 Aug 2021 17:32:38 +0200 Subject: [PATCH 0932/9987] adding easyconfigs: Mish-Cuda-20210309-fosscuda-2020b.eb --- .../Mish-Cuda-20210309-fosscuda-2020b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b.eb b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b.eb new file mode 100644 index 00000000000..b4c899852b1 --- /dev/null +++ b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Mish-Cuda' +version = '20210309' +local_commit = '6f38976' + +homepage = 'https://github.com/JunnYu/mish-cuda' +description = """Mish-Cuda: Self Regularized Non-Monotonic Activation Function""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/JunnYu/mish-cuda/archive/'] +sources = [{'download_filename': local_commit + '.zip', 'filename': SOURCELOWER_ZIP}] +checksums = ['529a3afd00fa4b1bf73f65249a82d38659779d7d8bdb230fa32d37eb95f5622c'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', '1.9.0'), +] + +preinstallopts = 'export TORCH_CUDA_ARCH_LIST="%(cuda_cc_semicolon_sep)s" && ' + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From 65e1f96b73e9cdb7f0d544a68847d65da7bc9c06 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Aug 2021 19:35:08 +0200 Subject: [PATCH 0933/9987] Add jax/fosscuda and use EasyBlock for jaxlib --- .../jax/TensorFlow-2.1.0_fix-cuda-build.patch | 47 ++++++++ .../j/jax/jax-0.2.19-foss-2020b.eb | 64 +++++------ .../j/jax/jax-0.2.19-fosscuda-2020b.eb | 104 ++++++++++++++++++ ...ib-0.1.70_add-bazel-args-to-shutdown.patch | 18 +++ 4 files changed, 194 insertions(+), 39 deletions(-) create mode 100644 easybuild/easyconfigs/j/jax/TensorFlow-2.1.0_fix-cuda-build.patch create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/j/jax/jaxlib-0.1.70_add-bazel-args-to-shutdown.patch diff --git a/easybuild/easyconfigs/j/jax/TensorFlow-2.1.0_fix-cuda-build.patch b/easybuild/easyconfigs/j/jax/TensorFlow-2.1.0_fix-cuda-build.patch new file mode 100644 index 00000000000..5873bdc5ed0 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/TensorFlow-2.1.0_fix-cuda-build.patch @@ -0,0 +1,47 @@ +fix for "undeclared inclusion(s) in rule" errors when building TensorFlow 1.14.0 with CUDA support, +if the installation directory for GCC is hosted in a path that is a symlink to another path; +the symlinked path is resolved in several places (both by 'gcc' itself and by the TF build process), +which makes hard comparisons between paths fail +author: Alexander Grund based on original patch by Kenneth Hoste (HPC-UGent) +diff --git a/third_party/gpus/cuda_configure.bzl b/third_party/gpus/cuda_configure.bzl +index ba4bd8ad75..dab492ecda 100644 +--- a/third_party/gpus/cuda_configure.bzl ++++ b/third_party/gpus/cuda_configure.bzl +@@ -303,11 +303,36 @@ def _get_cxx_inc_directories_impl(repository_ctx, cc, lang_is_cpp): + else: + inc_dirs = result.stderr[index1 + 1:index2].strip() + +- return [ ++ compiler_includes = [ + _normalize_include_path(repository_ctx, _cxx_inc_convert(p)) + for p in inc_dirs.split("\n") + ] + ++ # fix include path by also including paths where resolved symlink is replaced by original path ++ # Try to find real path to CC installation to "see through" compiler wrappers ++ # GCC has the path to g++ ++ index1 = result.stderr.find("COLLECT_GCC=") ++ if index1 != -1: ++ index1 = result.stderr.find("=", index1) ++ index2 = result.stderr.find("\n", index1) ++ cc_topdir = repository_ctx.path(result.stderr[index1 + 1 : index2]).dirname.dirname ++ else: ++ # Clang has the directory ++ index1 = result.stderr.find("InstalledDir: ") ++ if index1 != -1: ++ index1 = result.stderr.find(" ", index1) ++ index2 = result.stderr.find("\n", index1) ++ cc_topdir = repository_ctx.path(result.stderr[index1 + 1 : index2]).dirname ++ else: ++ # Fallback to the CC path ++ cc_topdir = repository_ctx.path(cc).dirname.dirname ++ cc_topdir_resolved = str(cc_topdir.realpath).strip() ++ cc_topdir = str(cc_topdir).strip() ++ if cc_topdir_resolved != cc_topdir: ++ original_compiler_includes = [p.replace(cc_topdir_resolved, cc_topdir) for p in compiler_includes] ++ compiler_includes = compiler_includes + original_compiler_includes ++ return compiler_includes ++ + def get_cxx_inc_directories(repository_ctx, cc, tf_sysroot): + """Compute the list of default C and C++ include directories.""" + diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index 1efc76bfb92..98dfee38c88 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -4,61 +4,53 @@ easyblock = 'PythonBundle' name = 'jax' version = '0.2.19' -local_jaxlib_ver = '0.1.70' homepage = 'https://pypi.python.org/pypi/jax' -description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and -more""" +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ ('Bazel', '3.7.2'), + ('Cython', '0.29.22'), ('pytest-xdist', '2.3.0'), - ('pytest-benchmark', '3.4.1'), ] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('Cython', '0.29.22'), ('flatbuffers-python', '1.12'), ] # downloading TensorFlow tarball to avoid that Bazel downloads it during the build # note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE local_tf_commit = '4039feeb743bc42cd0a3d8146ce63fc05d23eb8d' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir -local_tf_builddir = "%%(builddir)s/tensorflow-%s" % local_tf_commit - -local_jax_prebuildopts = "sed -i -e 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir - -local_jax_build_cmd = 'python build/build.py ' -local_jax_build_cmd += '--target_cpu_features=native ' -local_jax_build_cmd += '--bazel_startup_options="--output_user_root=%(builddir)s" ' -local_jax_build_cmd += '--bazel_path="$EBROOTBAZEL/bin/bazel" ' -local_jax_build_cmd += '--bazel_options=--subcommands ' -local_jax_build_cmd += '--bazel_options=--jobs=%(parallel)s --bazel_options=--action_env=PYTHONPATH ' -local_jax_build_cmd += '--bazel_options=--action_env=EBPYTHONPREFIXES' +local_jax_prebuildopts = "sed -i 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir use_pip = True +default_easyblock = 'PythonPackage' default_component_specs = { 'sources': [SOURCE_TAR_GZ], 'source_urls': [PYPI_SOURCE], 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, } components = [ ('absl-py', '0.13.0', { 'options': {'modulename': 'absl'}, - 'easyblock': 'PythonPackage', 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], - 'use_pip': True, }), - ('jaxlib', local_jaxlib_ver, { - 'easyblock': 'PythonPackage', + ('jaxlib', '0.1.70', { + 'easyblock': 'EB_jaxlib', 'sources': [ - 'jaxlib-v%s.zip' % local_jaxlib_ver, + '%(name)s-v%(version)s.tar.gz', { 'download_filename': '%s.tar.gz' % local_tf_commit, 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, @@ -69,26 +61,24 @@ components = [ 'https://github.com/tensorflow/tensorflow/archive/' ], 'patches': [ - ('jaxlib-%s_no-tensorflow-download.patch' % local_jaxlib_ver, 1), - ('TensorFlow-%s_mlir-build-env.patch' % local_tf_commit, '../tensorflow-%s' % local_tf_commit), + '%(name)s-%(version)s_add-bazel-args-to-shutdown.patch', + '%(name)s-%(version)s_no-tensorflow-download.patch', + ('TensorFlow-%s_mlir-build-env.patch' % local_tf_commit, '../' + local_tf_dir), ], 'checksums': [ - # jaxlib-v0.1.70.zip - '1205b180de70c98899d842f75bb589599c10a3c7a1c6099475c3a7d39b2e44ac', + # jaxlib-v0.1.70.tar.gz + '5d136c4b72bb254a3700cbac276ebe77108841936ff6d728050775f24a8e36fe', # tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d.tar.gz '0f13410284b9186e436350e9617b3bed2d65f1dc1a220fd37ad9ef43c2035663', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', # jaxlib-0.1.70_no-tensorflow-download.patch '1496c6be9336fb563b997f8da83d690a9b3a0a6e29fdd87fac60409300a2fd95', # TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d-build-env.patch 'd067836b1d18d66a8c69fb3db311855c8a56c0106d42a11299a1733c385e9c22', ], - 'start_dir': 'jax-jaxlib-v%s' % local_jaxlib_ver, + 'start_dir': 'jax-jaxlib-v%(version)s', 'prebuildopts': local_jax_prebuildopts, - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, - 'buildcmd': local_jax_build_cmd, - 'install_src': 'dist/*.whl', }), ] @@ -97,17 +87,13 @@ exts_list = [ 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], }), (name, version, { - 'checksums': ['e55534680a05b6ced92dadde307bd3b2207efd1aaaec304e96197b00ad7560d3'], + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': ['fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c'], + 'runtest': 'pytest -n %(parallel)s tests', }), ] -# can't run tests in sanity check step, because build dependencies must be available -postinstallcmds = [ - "cd %%(builddir)s/jax-jaxlib-v%s && " - "PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:$PYTHONPATH " - "pytest -n auto tests" % local_jaxlib_ver, -] - sanity_pip_check = True moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb new file mode 100644 index 00000000000..0ef481960fb --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -0,0 +1,104 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.2.19' +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('Cython', '0.29.22'), + ('pytest-xdist', '2.3.0'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('flatbuffers-python', '1.12'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = '4039feeb743bc42cd0a3d8146ce63fc05d23eb8d' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +local_jax_prebuildopts = "sed -i 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '0.13.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], + }), + ('jaxlib', '0.1.70', { + 'easyblock': 'EB_jaxlib', + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + '%(name)s-%(version)s_add-bazel-args-to-shutdown.patch', + '%(name)s-%(version)s_no-tensorflow-download.patch', + ('TensorFlow-%s_mlir-build-env.patch' % local_tf_commit, '../' + local_tf_dir), + ('TensorFlow-2.1.0_fix-cuda-build.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.1.70.tar.gz + '5d136c4b72bb254a3700cbac276ebe77108841936ff6d728050775f24a8e36fe', + # tensorflow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d.tar.gz + '0f13410284b9186e436350e9617b3bed2d65f1dc1a220fd37ad9ef43c2035663', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', + # jaxlib-0.1.70_no-tensorflow-download.patch + '1496c6be9336fb563b997f8da83d690a9b3a0a6e29fdd87fac60409300a2fd95', + # TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d-build-env.patch + 'd067836b1d18d66a8c69fb3db311855c8a56c0106d42a11299a1733c385e9c22', + # TensorFlow-2.1.0_fix-cuda-build.patch + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': ['fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c'], + 'runtest': 'pytest -n %(parallel)s tests', + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jaxlib-0.1.70_add-bazel-args-to-shutdown.patch b/easybuild/easyconfigs/j/jax/jaxlib-0.1.70_add-bazel-args-to-shutdown.patch new file mode 100644 index 00000000000..674500ea870 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jaxlib-0.1.70_add-bazel-args-to-shutdown.patch @@ -0,0 +1,18 @@ +Pass bazel_startup_options also to the shutdown call to avoid it still using $HOME. +See https://github.com/google/jax/issues/7639 + +Author: Alexander Grund (TU Dresden) + +diff --git a/build/build.py b/build/build.py +index dc275042..44a68a71 100755 +--- a/build/build.py ++++ b/build/build.py +@@ -597,7 +597,7 @@ def main(): + f"--cpu={wheel_cpu}"]) + print(" ".join(command)) + shell(command) +- shell([bazel_path, "shutdown"]) ++ shell([bazel_path] + args.bazel_startup_options + ["shutdown"]) + + + if __name__ == "__main__": From 13c9ee79b65f43a6f00fb75c82dfa9775bb24e20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Aug 2021 09:16:23 +0200 Subject: [PATCH 0934/9987] stick to CGAL 4.x as dependency for OpenFOAM v2106 --- ...2.2-gompi-2021a.eb => CGAL-4.14.3-gompi-2021a.eb} | 12 ++++-------- .../o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb | 2 +- 2 files changed, 5 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/c/CGAL/{CGAL-5.2.2-gompi-2021a.eb => CGAL-4.14.3-gompi-2021a.eb} (72%) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.2.2-gompi-2021a.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021a.eb similarity index 72% rename from easybuild/easyconfigs/c/CGAL/CGAL-5.2.2-gompi-2021a.eb rename to easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021a.eb index a3c0f97b487..ca2489bf1e5 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-5.2.2-gompi-2021a.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021a.eb @@ -1,8 +1,5 @@ -## -# Author: Robert Mijakovic -## name = 'CGAL' -version = '5.2.2' +version = '4.14.3' homepage = 'https://www.cgal.org/' description = """The goal of the CGAL Open Source Project is to provide easy access to efficient @@ -11,9 +8,9 @@ description = """The goal of the CGAL Open Source Project is to provide easy acc toolchain = {'name': 'gompi', 'version': '2021a'} toolchainopts = {'strict': True} -source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/'] +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] sources = [SOURCE_TAR_XZ] -checksums = ['80b05049d20dc0e346f33037b6f87f69eb0b4407a3e27ffc10f7c71d45c05f7a'] +checksums = ['5bafe7abe8435beca17a1082062d363368ec1e3f0d6581bb0da8b010fb389fe4'] builddependencies = [ ('CMake', '3.20.1'), @@ -31,8 +28,7 @@ dependencies = [ ('Qt5', '5.15.2'), ] -configopts = "-DCGAL_HEADER_ONLY=OFF " -configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb index efb4319ace0..04918ceb50d 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2106-foss-2021a.eb @@ -31,7 +31,7 @@ dependencies = [ # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) ('METIS', '5.1.0'), ('SCOTCH', '6.1.0'), - ('CGAL', '5.2.2'), + ('CGAL', '4.14.3'), ('ParaView', '5.9.1', '-mpi'), ('gnuplot', '5.4.2'), ] From 19cf1da53361694aeb11c5d629366204d5533b1c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 18 Aug 2021 09:47:43 +0200 Subject: [PATCH 0935/9987] Remove easyblock line --- easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 1 - easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index 98dfee38c88..f47e5feef2e 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -48,7 +48,6 @@ components = [ 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], }), ('jaxlib', '0.1.70', { - 'easyblock': 'EB_jaxlib', 'sources': [ '%(name)s-v%(version)s.tar.gz', { diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index 0ef481960fb..ab1419f22c5 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -50,7 +50,6 @@ components = [ 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], }), ('jaxlib', '0.1.70', { - 'easyblock': 'EB_jaxlib', 'sources': [ '%(name)s-v%(version)s.tar.gz', { From 34fc599543049dec2a0925f981788fa75aea262d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Aug 2021 11:00:19 +0200 Subject: [PATCH 0936/9987] don't enable separate_build_dir in libcerf easyconfig (done by default) --- easybuild/easyconfigs/l/libcerf/libcerf-1.15-GCCcore-10.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.15-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.15-GCCcore-10.3.0.eb index f701c6f094e..f16f5171968 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-1.15-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.15-GCCcore-10.3.0.eb @@ -27,8 +27,6 @@ builddependencies = [ ('Perl', '5.32.1'), # required for pod2html ] -separate_build_dir = True - sanity_check_paths = { 'files': ['lib/libcerf.%s' % SHLIB_EXT], 'dirs': [] From 078b21eda442a40b924742b090a6d8743f03ab23 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 18 Aug 2021 10:01:38 +0100 Subject: [PATCH 0937/9987] Use Archive URL for spatstat.geom extension in Seurat --- .../easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb index 331b937181f..4e6edc0ad5b 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb @@ -31,6 +31,7 @@ exts_list = [ 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], }), ('spatstat.geom', '2.2-0', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'], 'checksums': ['70b063a7f317f531b2afb3afaedb047fce81b39ee481a4067962529d6069634c'], }), ('spatstat.sparse', '2.0-0', { From 95531b0f9fb73f4b29119efd9d926338655fc619 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Aug 2021 12:05:06 +0200 Subject: [PATCH 0938/9987] add naturalsort extension to recent R 4.x easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 3 +++ 7 files changed, 21 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 3f73cf6e804..94ed0c58004 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -2900,6 +2900,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 25bfe941168..f0423aca3a9 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -2910,6 +2910,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 600336ef2ae..52d2afb33e8 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2936,6 +2936,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 6410c41672c..1bb5fc2a92f 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2941,6 +2941,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 9d7859add85..172d381e034 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2945,6 +2945,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 044bfdd2951..22c4fba720b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2956,6 +2956,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index e6a51010b23..8df95932d40 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -2978,6 +2978,9 @@ exts_list = [ ('SBdecomp', '1.1', { 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), ('lwgeom', '0.2-7', { 'checksums': ['b34c155f3d7c4535ef3d02e3381b05a57990d19b3b1ec09a7458c101f8fafae1'], }), From fd34ce95a8fcbe84183ba5c0502a0912c9981c3c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 18 Aug 2021 12:53:42 +0100 Subject: [PATCH 0939/9987] Use Archive URL for spatstat.core extension --- .../easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb index 4e6edc0ad5b..d71472a2d5e 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb @@ -38,6 +38,7 @@ exts_list = [ 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], }), ('spatstat.core', '2.2-0', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'], 'checksums': ['0ecbc1ae688c8d4f41db3efa6253ac8db5c432ef714240d01a2b195950d65253'], }), ('Matrix', '1.3-4', { From c0c466175b7726f6c303ea21d06153f40671ac82 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 18 Aug 2021 14:34:28 +0200 Subject: [PATCH 0940/9987] Rename patches --- .../easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 8 ++++---- ...2.patch => OpenMPI-4.1.1_opal-pmix-package-rank.patch} | 0 .../{9213.patch => OpenMPI-4.1.1_pmix3x-protection.patch} | 0 3 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/o/OpenMPI/{9212.patch => OpenMPI-4.1.1_opal-pmix-package-rank.patch} (100%) rename easybuild/easyconfigs/o/OpenMPI/{9213.patch => OpenMPI-4.1.1_pmix3x-protection.patch} (100%) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index 989f66906b9..ab6724331f4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -11,8 +11,8 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', - '9212.patch', - '9213.patch', + 'OpenMPI-4.1.1_opal-pmix-package-rank.patch', + 'OpenMPI-4.1.1_pmix3x-protection.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -20,8 +20,8 @@ checksums = [ 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', - 'a85b09da354916c2a08c24922268e4f25352daf2787c7c90cd5d24ca4f8d892f', # 9212.patch - 'cd250609f2c7974774a4e8931873bc795c0769581f91530524df516490de4954', # 9213.patch + 'a85b09da354916c2a08c24922268e4f25352daf2787c7c90cd5d24ca4f8d892f', # OpenMPI-4.1.1_opal-pmix-package-rank.patch + 'cd250609f2c7974774a4e8931873bc795c0769581f91530524df516490de4954', # OpenMPI-4.1.1_pmix3x-protection.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/9212.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_opal-pmix-package-rank.patch similarity index 100% rename from easybuild/easyconfigs/o/OpenMPI/9212.patch rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_opal-pmix-package-rank.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/9213.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_pmix3x-protection.patch similarity index 100% rename from easybuild/easyconfigs/o/OpenMPI/9213.patch rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_pmix3x-protection.patch From f7bb1468fe71c70c3faeaa1dc03388e8fd3489ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Aug 2021 14:49:00 +0200 Subject: [PATCH 0941/9987] add reference to PRs in Open MPI GitHub repository in patches for OpenMPI 4.1.1 --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 4 ++-- .../o/OpenMPI/OpenMPI-4.1.1_opal-pmix-package-rank.patch | 2 ++ .../o/OpenMPI/OpenMPI-4.1.1_pmix3x-protection.patch | 2 ++ 3 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index ab6724331f4..ee8f19a6c14 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -20,8 +20,8 @@ checksums = [ 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', - 'a85b09da354916c2a08c24922268e4f25352daf2787c7c90cd5d24ca4f8d892f', # OpenMPI-4.1.1_opal-pmix-package-rank.patch - 'cd250609f2c7974774a4e8931873bc795c0769581f91530524df516490de4954', # OpenMPI-4.1.1_pmix3x-protection.patch + '04353672cf7be031e5306c94068d7012d99e6cd94b69d93230797ffcd7f31903', # OpenMPI-4.1.1_opal-pmix-package-rank.patch + '384ef9f1fa803b0d71dae2ec0748d0f20295992437532afedf21478bda164ff8', # OpenMPI-4.1.1_pmix3x-protection.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_opal-pmix-package-rank.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_opal-pmix-package-rank.patch index 156d3d0a44b..dbb0965eb44 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_opal-pmix-package-rank.patch +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_opal-pmix-package-rank.patch @@ -1,3 +1,5 @@ +see https://github.com/open-mpi/ompi/pull/9212 + From 8b07775d1002cc9be887c41768aea9ac896c5ecd Mon Sep 17 00:00:00 2001 From: Ralph Castain Date: Tue, 10 Aug 2021 08:38:15 -0700 diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_pmix3x-protection.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_pmix3x-protection.patch index f74907f563a..6dd3bfb4109 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_pmix3x-protection.patch +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_pmix3x-protection.patch @@ -1,3 +1,5 @@ +see https://github.com/open-mpi/ompi/pull/9213 + From bd48a06e25c1058b7d3c3ba4414af388836c8219 Mon Sep 17 00:00:00 2001 From: Ralph Castain Date: Tue, 10 Aug 2021 13:01:11 -0700 From a30b397cdf6f234d19da7e105cc1ea07cd2f1779 Mon Sep 17 00:00:00 2001 From: "benjamin.czaja" Date: Wed, 18 Aug 2021 16:20:46 +0200 Subject: [PATCH 0942/9987] adding easyconfigs: RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb, SOCI-4.0.2-GCC-10.3.0.eb, ant-1.10.11-Java-11.eb --- .../easyconfigs/a/ant/ant-1.10.11-Java-11.eb | 27 ++++++++ ...ver-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb | 66 +++++++++++++++++++ .../s/SOCI/SOCI-4.0.2-GCC-10.3.0.eb | 53 +++++++++++++++ 3 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.11-Java-11.eb create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb create mode 100644 easybuild/easyconfigs/s/SOCI/SOCI-4.0.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.11-Java-11.eb b/easybuild/easyconfigs/a/ant/ant-1.10.11-Java-11.eb new file mode 100644 index 00000000000..c41856971c3 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.11-Java-11.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'ant' +version = '1.10.11' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" + +toolchain = SYSTEM + +source_urls = ['https://archive.apache.org/dist/ant/binaries/'] +sources = ['apache-%(name)s-%(version)s-bin.tar.gz'] +checksums = ['0a3dc4624c863657daa609051763f12bfd286bc6da1d61ca48959ce3b94be0e7'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb new file mode 100644 index 00000000000..ed94dfd758d --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'RStudio-Server' +version = '1.4.1717' +versionsuffix = '-Java-%(javaver)s-R-%(rver)s' + +homepage = 'https://www.rstudio.com/' +description = """This is the RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3af234180fd7cef451aef40faac2c7b52860f14a322244c1c7aede029814d261'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('CMake', '3.20.1'), + ('ant', '1.10.11', '-Java-%(javaver)s', True), + ('SOCI', '4.0.2'), +] + +dependencies = [ + ('Boost', '1.76.0'), + ('R', '4.1.0'), + ('Java', '11', '', True), +] + +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] + +build_type = "Release" +local_dep_dir = "%(builddir)s/rstudio-%(version)s/dependencies/common" +preconfigopts = (("export RSTUDIO_TOOLS_ROOT={} && " + "cd {} && " + "./install-cef && " + "./install-dictionaries && " + "./install-mathjax && " + "./install-pandoc && " + "./install-packages && " + "./install-yaml-cpp && " + "./install-npm-dependencies && " + "cd ../../ && " + "mkdir build && cd build && ").format("%(builddir)s", local_dep_dir)) + +configopts = "-DRSTUDIO_TARGET=Server -DRSTUDIO_BOOST_SIGNALS_VERSION=2 " +configopts += "-DSOCI_CORE_LIB=$EBROOTSOCI/lib/libsoci_core.a " +configopts += "-DSOCI_POSTGRESQL_LIB=$EBROOTSOCI/lib/libsoci_postgresql.a " +configopts += "-DSOCI_SQLITE_LIB=$EBROOTSOCI/lib/libsoci_sqlite3.a " + +prebuildopts = (("cd {} && cd build && ")).format("%(builddir)s/rstudio-%(version)s") +preinstallopts = (("cd {} && cd build && ")).format("%(builddir)s/rstudio-%(version)s") + + +sanity_check_paths = { + 'files': ["bin/rstudio-server"], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.2-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..b583aed0151 --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.2-GCC-10.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.2' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f293192a412ed82693d17dfe46e2734b140bff835bc3259e3cbd7c315e5e2d74'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Boost', '1.76.0'), + ('SQLite', '3.35.4'), + ('PostgreSQL', '13.3'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' From 5cd9291cc85c97ee7aa86d0df0ee0339e0ee0e11 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 18 Aug 2021 16:55:10 +0200 Subject: [PATCH 0943/9987] add dependency on pkg-config to OpenSSL wrappers --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb | 5 ++++- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb index ae64518e2d7..ad98a749349 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb @@ -11,7 +11,10 @@ description = """The OpenSSL Project is a collaborative effort to develop a robu toolchain = SYSTEM toolchainopts = {'pic': True} -osdependencies = ['perl'] +osdependencies = [ + ('pkg-config', 'pkgconfig'), + 'perl', +] # This easyconfig will wrap the OpenSSL installation in the host system. # If the system provides the required binary, header files, and libraries for this diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb index a49a797ca06..a43112f5590 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb @@ -12,7 +12,10 @@ description = """The OpenSSL Project is a collaborative effort to develop a robu toolchain = SYSTEM toolchainopts = {'pic': True} -osdependencies = ['perl'] +osdependencies = [ + ('pkg-config', 'pkgconfig'), + 'perl', +] # This easyconfig will wrap the OpenSSL installation in the host system. # If the system provides the required binary, header files, and libraries for From 994c1a4d5c7252c3403623a0428fb90b2a45ffe8 Mon Sep 17 00:00:00 2001 From: software Date: Wed, 18 Aug 2021 16:09:25 +0000 Subject: [PATCH 0944/9987] Add finalfit and gtsummary to R-4.0.4 --- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 52d2afb33e8..1116a5461ae 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2939,6 +2939,21 @@ exts_list = [ ('naturalsort', '0.1.3', { 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], }), + ('finalfit', '1.0.3', { + 'checksums': ['bbfa841a2b1a7b1f8c153d773ff076a2e465e451815f8166ff0ce8c4018ff61e'], + }), + ('broom.helpers', '1.3.0', { + 'checksums': ['e02531f37a3cd56513ec3a9a083070b5f0ec9b438b2cc7d8e036f7bcedfeb7b0'], + }), + ('sass', '0.4.0', { + 'checksums': ['7d06ca15239142a49e88bb3be494515abdd8c75f00f3f1b0ee7bccb55019bc2b'], + }), + ('gt', '0.3.1', { + 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], + }), + ('gtsummary', '1.4.2', { + 'checksums': ['3fe958077df9e604bf536eeda73eb825ee6ae7fcac716b7a42d5a9d867bd4122'], + }), ] moduleclass = 'lang' From 4811b1a45fb925e834cb87d03c1990433417c20a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Aug 2021 18:13:07 +0200 Subject: [PATCH 0945/9987] adding easyconfigs: OpenFOAM-9-foss-2021a.eb --- .../o/OpenFOAM/OpenFOAM-9-foss-2021a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-foss-2021a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-foss-2021a.eb new file mode 100644 index 00000000000..7aadfac08d9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-foss-2021a.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '9' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +# toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-%(version)s-cleanup.patch'] +checksums = [ + '0c48fb56e2fbb4dd534112811364d3b2dc12106e670a6486b361e4f864b435ee', # version-9.tar.gz + '4b638891f32badde1a5b1b364bc3bd5e0eda180b9d9a8afdf797d5818b8b494e', # OpenFOAM-9-cleanup.patch +] + +builddependencies = [ + ('Bison', '3.7.6'), + ('CMake', '3.20.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.1'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('CGAL', '4.14.3'), + ('ParaView', '5.9.1', '-mpi'), + ('gnuplot', '5.4.2'), +] + +moduleclass = 'cae' From 0d8c3c11f705d6188a6eb0a63728bb94e5b463a9 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 18 Aug 2021 18:30:19 +0200 Subject: [PATCH 0946/9987] added andi-0.13-foss-2018b.eb --- .../a/andi/andi-0.13-foss-2018b.eb | 40 +++++++++++++++++++ .../libdivsufsort-2.0.1-foss-2018b.eb | 33 +++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/a/andi/andi-0.13-foss-2018b.eb create mode 100644 easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb diff --git a/easybuild/easyconfigs/a/andi/andi-0.13-foss-2018b.eb b/easybuild/easyconfigs/a/andi/andi-0.13-foss-2018b.eb new file mode 100644 index 00000000000..9da66d8d4e6 --- /dev/null +++ b/easybuild/easyconfigs/a/andi/andi-0.13-foss-2018b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'andi' +version = '0.13' + +homepage = 'https://github.com/evolbioinf/andi/' +description = """This is the andi program for estimating the evolutionary distance between closely related genomes. +These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full +alignments, it is so efficient that it scales even up to thousands of bacterial genomes.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/EvolBioInf/andi/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['03e493ee22b6773a600b47cbfb121f4c2affd6e646ea16dad0d322e9276b3943'] + +builddependencies = [ + ('Autoconf', '2.69') +] + +dependencies = [ + ('GSL', '2.5'), + ('libdivsufsort', '2.0.1') +] + +parallel = 1 + +preconfigopts = "autoreconf -fi -Im4 && " + +sanity_check_paths = { + 'files': ['bin/andi'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb b/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb new file mode 100644 index 00000000000..48a9914d557 --- /dev/null +++ b/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb @@ -0,0 +1,33 @@ +# Author: Iñaki Mtz de Ilarduya +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'libdivsufsort' +version = '2.0.1' + +homepage = 'https://github.com/y-256/libdivsufsort' +description = """libdivsufsort is a software library that implements a lightweight suffix + array construction algorithm.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/y-256/libdivsufsort/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9164cb6044dcb6e430555721e3318d5a8f38871c2da9fd9256665746a69351e0'] + +unpack_options = '--strip-components=1' + +separate_build_dir = True + +builddependencies = [ + ('CMake', '3.12.1'), +] + +sanity_check_paths = { + 'files': ['lib/libdivsufsort.so'], + 'dirs': [], +} + +moduleclass = 'lib' From c39d3e0e3f8d2095405b82429538ecab9d012e44 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Wed, 18 Aug 2021 18:50:55 +0200 Subject: [PATCH 0947/9987] added Co-phylog-20201012-GCC-7.3.0-2.30.eb --- .../Co-phylog-20201012-GCC-7.3.0-2.30.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/Co-phylog/Co-phylog-20201012-GCC-7.3.0-2.30.eb diff --git a/easybuild/easyconfigs/c/Co-phylog/Co-phylog-20201012-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/c/Co-phylog/Co-phylog-20201012-GCC-7.3.0-2.30.eb new file mode 100644 index 00000000000..c0ca6b19958 --- /dev/null +++ b/easybuild/easyconfigs/c/Co-phylog/Co-phylog-20201012-GCC-7.3.0-2.30.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CmdCp' + +name = 'Co-phylog' +version = '20201012' + +homepage = 'https://github.com/yhg926/co-phylog' +description = """Co-phylog: an assembly-free phylogenomic approach for closely +related organisms H Yi, L Jin Nucleic acids research 41 (7), e75-e75""" + +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} + +source_urls = ['https://github.com/yhg926/co-phylog/archive/'] +local_git_commit = '6f29045' +sources = ['%s.tar.gz' % (local_git_commit)] +checksums = ['2cafdda678f9fea32d79460be9867e98846c68f9e6affd56920e7449306345a7'] + +cmds_map = [ + ('.*', "$CC fasta2co_v18.3.c -O6 -Wall -o fasta2co"), + ('.*', "$CC fastq2co.c -O6 -Wall -o fastq2co"), + ('.*', "$CC co2dist2.c -O6 -Wall -o co2dist"), + ('.*', "$CC readco.c -Wall -o readco") +] + +files_to_copy = [(['fasta2co', 'fastq2co', 'co2dist', 'readco'], 'bin')] + +postinstallcmds = ["chmod 755 %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['bin/fasta2co', 'bin/fastq2co', 'bin/co2dist', 'bin/readco'], + 'dirs': [], +} + +moduleclass = 'bio' From e47dc6d7432d00c6f75b82e405bffdc58a9852dd Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 18 Aug 2021 18:00:45 +0100 Subject: [PATCH 0948/9987] Remove sass duplicate --- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 1116a5461ae..af85bdbea5a 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -2945,9 +2945,6 @@ exts_list = [ ('broom.helpers', '1.3.0', { 'checksums': ['e02531f37a3cd56513ec3a9a083070b5f0ec9b438b2cc7d8e036f7bcedfeb7b0'], }), - ('sass', '0.4.0', { - 'checksums': ['7d06ca15239142a49e88bb3be494515abdd8c75f00f3f1b0ee7bccb55019bc2b'], - }), ('gt', '0.3.1', { 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], }), From 7e5942868a3cafe77b0d9545fae6c6666da9d0c6 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:13:24 +0200 Subject: [PATCH 0949/9987] Delete crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch removing old patch (moved to another folder) --- ...av-2.3.4-foss2020b_remove_hardcoding.patch | 128 ------------------ 1 file changed, 128 deletions(-) delete mode 100644 easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch diff --git a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch b/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch deleted file mode 100644 index 5fd3b89e92c..00000000000 --- a/easybuild/easyconfigs/c/crispr-dav/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch +++ /dev/null @@ -1,128 +0,0 @@ -# changing example command to contain absolute paths + tabs escaping + changing plotting type to cairo -diff -ruN crispr-dav-2.3.4_orig/Examples/example1/run.sh crispr-dav-2.3.4/Examples/example1/run.sh ---- crispr-dav-2.3.4_orig/Examples/example1/run.sh 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Examples/example1/run.sh 2021-06-22 12:57:41.700453098 +0200 -@@ -4,6 +4,7 @@ - - ## If there is problem loading Perl modules., set PERL5LIB accordingly. - #export PERL5LIB=$HOME/perlmod/lib/perl5:$PERL5LIB --../../crispr.pl --conf conf.txt --region amplicon.bed --crispr site.bed \ -- --sitemap sample.site --fastqmap fastq.list --genome genomex -+ -+$EBROOTCRISPRMINDAV/crispr.pl --conf $EBROOTCRISPRMINDAV/Examples/example1/conf.txt --region $EBROOTCRISPRMINDAV/Examples/example1/amplicon.bed --crispr $EBROOTCRISPRMINDAV/Examples/example1/site.bed \ -+ --sitemap $EBROOTCRISPRMINDAV/Examples/example1/sample.site --fastqmap $EBROOTCRISPRMINDAV/Examples/example1/fastq.list --genome genomex --verbose 1 - -diff -ruN crispr-dav-2.3.4_orig/Modules/NGS.pm crispr-dav-2.3.4/Modules/NGS.pm ---- crispr-dav-2.3.4_orig/Modules/NGS.pm 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Modules/NGS.pm 2021-06-21 17:37:39.381993860 +0200 -@@ -296,7 +296,7 @@ - my $cmd = "$self->{bwa} mem"; - $cmd .= " $h{param}" if $h{param}; - if ( $h{id} && $h{sm} ) { -- $cmd .= " -R \'\@RG\tID:$h{id}\tSM:$h{sm}\tPL:$h{pl}\'"; -+ $cmd .= " -R \'\@RG\\tID:$h{id}\\tSM:$h{sm}\\tPL:$h{pl}\'"; - } - $cmd .= " $h{idxbase} $h{read1_inf}"; - $cmd .= " $h{read2_inf}" if -f $h{read2_inf}; -@@ -558,7 +558,7 @@ - # file is already indexed. - my $cmd = "rm -rf $workdir && mkdir -p $workdir" . - " && $self->{java} -Djava.io.tmpdir=$tmpdir -jar $h{abra} --threads 2" . -- " --ref $h{ref_fasta} --targets $h{target_bed} --working $workdir" . -+ " --ref $h{ref_fasta} --targets $h{target_bed} --tmpdir $workdir" . - " --in $h{bam_inf} --out $h{bam_outf}"; - - if ($h{single}) { -diff -ruN crispr-dav-2.3.4_orig/Rscripts/allele.R crispr-dav-2.3.4/Rscripts/allele.R ---- crispr-dav-2.3.4_orig/Rscripts/allele.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/allele.R 2021-06-22 13:13:45.868418215 +0200 -@@ -114,7 +114,7 @@ - } else { - h<-400 - w<- ifelse(n>40, 13*n, h*1.25) -- png(filename=outfile, height=h, width=w) -+ png(filename=outfile, type='cairo', height=h, width=w) - } - - on.exit(dev.off()) -diff -ruN crispr-dav-2.3.4_orig/Rscripts/amplicon.R crispr-dav-2.3.4/Rscripts/amplicon.R ---- crispr-dav-2.3.4_orig/Rscripts/amplicon.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/amplicon.R 2021-06-22 13:13:45.868418215 +0200 -@@ -111,7 +111,7 @@ - if ( high_res ) { - tiff(filename=outfile, width=5, height=4, units='in', res=1200) - } else { -- png(filename=outfile, width=500, height=400) -+ png(filename=outfile, type='cairo', width=500, height=400) - } - on.exit(dev.off()) - print(p) -diff -ruN crispr-dav-2.3.4_orig/Rscripts/hdr.R crispr-dav-2.3.4/Rscripts/hdr.R ---- crispr-dav-2.3.4_orig/Rscripts/hdr.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/hdr.R 2021-06-22 13:13:45.868418215 +0200 -@@ -102,7 +102,7 @@ - h<-400 - barspace=60 - w<- ifelse( n*barspace10, 50*n, h) -- png(filename=imgfile, height=h, width=w) -+ png(filename=imgfile, type='cairo', height=h, width=w) - } - - on.exit(dev.off()) -diff -ruN crispr-dav-2.3.4_orig/Rscripts/read_chr.R crispr-dav-2.3.4/Rscripts/read_chr.R ---- crispr-dav-2.3.4_orig/Rscripts/read_chr.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/read_chr.R 2021-06-22 13:13:45.868418215 +0200 -@@ -72,7 +72,7 @@ - w<-ifelse(n>5, 100*n, 550) - max_w=1000 - w <- ifelse(w>max_w, max_w, w) -- png(filename=outfile, height=h, width=w) -+ png(filename=outfile, type='cairo', height=h, width=w) - } - - print(p) -diff -ruN crispr-dav-2.3.4_orig/Rscripts/read_stats.R crispr-dav-2.3.4/Rscripts/read_stats.R ---- crispr-dav-2.3.4_orig/Rscripts/read_stats.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/read_stats.R 2021-06-22 13:13:45.868418215 +0200 -@@ -69,7 +69,7 @@ - } else { - h<-400 - w<- ifelse(n>10, 50*n, h) -- png(filename=outfile, height=h, width=w) -+ png(filename=outfile, type='cairo', height=h, width=w) - } - - p <- ggplot(dat.m, aes(x=Sample, y=value, fill=variable)) + -diff -ruN crispr-dav-2.3.4_orig/Rscripts/snp.R crispr-dav-2.3.4/Rscripts/snp.R ---- crispr-dav-2.3.4_orig/Rscripts/snp.R 2019-07-26 21:15:08.000000000 +0200 -+++ crispr-dav-2.3.4/Rscripts/snp.R 2021-06-22 13:13:45.868418215 +0200 -@@ -76,7 +76,7 @@ - if ( high_res ) { - tiff(filename=outfile, width=5, height=4, units='in', res=1200) - } else { -- png(filename=outfile, width=500, height=400) -+ png(filename=outfile, type='cairo', width=500, height=400) - } - print(p) - invisible(dev.off()) -@@ -182,7 +182,7 @@ - wt <- 600 - } - ht <- 400 -- png(filename=outfile, width=wt, height=ht) -+ png(filename=outfile, type='cairo', width=wt, height=ht) - } - - print(p) From 59b8101d5b4a5c62067f47fe5d927bfc05cbc5c1 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:14:11 +0200 Subject: [PATCH 0950/9987] Rename crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch to crispr-dav-2.3.4_remove_hardcoding.patch renaming patchfile --- ..._hardcoding.patch => crispr-dav-2.3.4_remove_hardcoding.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/CRISPR-DAV/{crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch => crispr-dav-2.3.4_remove_hardcoding.patch} (100%) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch b/easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4_remove_hardcoding.patch similarity index 100% rename from easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch rename to easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4_remove_hardcoding.patch From 37abf2dc9bf55b556462a419cd515d68a8e5775a Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:14:57 +0200 Subject: [PATCH 0951/9987] Update CRISPR-DAV-2.3.4-foss-2020b.eb renaming patchfile --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index 176d5949c38..e7460b08d0a 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/pinetree1/crispr-dav/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch'] +patches = ['crispr-dav-2.3.4_remove_hardcoding.patch'] checksums = [ '49975cd48bdbf31fe5a9e2aaa3f5ed85d3cc6f65a422ee3aa8daed890159d2ae', # v2.3.4.tar.gz # crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch From 3b79f49af2fc1e3d56b926e50048e826dd7e696d Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:15:05 +0200 Subject: [PATCH 0952/9987] Create CRISPR-DAV-2.3.4-foss-2020b.eb renaming patchfile From 610d63dd28375236dd4642be38a6acf26acc619e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Aug 2021 19:15:08 +0200 Subject: [PATCH 0953/9987] add patch for OpenFOAM 9 --- .../o/OpenFOAM/OpenFOAM-9-cleanup.patch | 301 ++++++++++++++++++ 1 file changed, 301 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-cleanup.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-cleanup.patch new file mode 100644 index 00000000000..b55c71bab04 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-cleanup.patch @@ -0,0 +1,301 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Lastly, we also fix a small compile issue in 'ptscotchDecomp.C' +# by Jiri Furst , based on patch for OpenFOAM 5.0 and 4.1 by +# Kenneth Hoste (HPC-UGent) and Ward Poelmans +diff -ru OpenFOAM-9.orig/applications/utilities/mesh/manipulation/setSet/Allwmake OpenFOAM-9/applications/utilities/mesh/manipulation/setSet/Allwmake +--- OpenFOAM-9.orig/applications/utilities/mesh/manipulation/setSet/Allwmake 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/applications/utilities/mesh/manipulation/setSet/Allwmake 2021-08-17 15:25:23.776492000 +0200 +@@ -7,19 +7,12 @@ + unset COMP_FLAGS LINK_FLAGS + + # Use readline if available +-if [ -f /usr/include/readline/readline.h ] ++if [ -f $EBROOTLIBREADLINE/include/readline/readline.h ] + then + echo " found -- enabling readline support." + export COMP_FLAGS="-DHAS_READLINE" + +- # readline may require ncurses +- if [ -f /usr/include/ncurses/ncurses.h ] +- then +- echo " found -- maybe required by readline." +- export LINK_FLAGS="-lreadline -lncurses" +- else +- export LINK_FLAGS="-lreadline" +- fi ++ export LINK_FLAGS="-L$EBROOTLIBREADLINE/lib -lreadline -L$EBROOTNCURSES -lncurses" + fi + + wmake $targetType +diff -ru OpenFOAM-9.orig/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-9/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-9.orig/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2021-08-17 15:25:23.778422000 +0200 +@@ -17,8 +17,8 @@ + fi + + # Ensure CMake gets the correct C/C++ compilers +-[ -n "$WM_CC" ] && export CC="$WM_CC" +-[ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++#[ -n "$WM_CC" ] && export CC="$WM_CC" ++#[ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVblockMesh + wmake $targetType vtkPVFoam +diff -ru OpenFOAM-9.orig/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt OpenFOAM-9/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +--- OpenFOAM-9.orig/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt 2021-08-17 15:25:23.779287000 +0200 +@@ -2,6 +2,8 @@ + + PROJECT(PVReaders) + ++FIND_PACKAGE(MPI REQUIRED) ++ + FIND_PACKAGE(ParaView REQUIRED) + + INCLUDE(GNUInstallDirs) +diff -ru OpenFOAM-9.orig/etc/bashrc OpenFOAM-9/etc/bashrc +--- OpenFOAM-9.orig/etc/bashrc 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/etc/bashrc 2021-08-17 15:25:23.781332000 +0200 +@@ -43,8 +43,9 @@ + # Please set to the appropriate path if the default is not correct. + # + [ "$BASH" -o "$ZSH_NAME" ] && \ +-export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++#export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \ ++#export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ru OpenFOAM-9.orig/etc/config.sh/CGAL OpenFOAM-9/etc/config.sh/CGAL +--- OpenFOAM-9.orig/etc/config.sh/CGAL 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/etc/config.sh/CGAL 2021-08-17 15:25:23.783035000 +0200 +@@ -39,22 +39,7 @@ + # + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-#boost_version=boost-1.55.0 +-#boost_version=boost-1.72.0 +- +-cgal_version=cgal-system +-#cgal_version=CGAL-4.10 +-#cgal_version=CGAL-5.0.2 +- +-if [ "$boost_version" != "boost-system" ] +-then +- export BOOST_ARCH_PATH=$WM_THIRD_PARTY_DIR/$boost_version +-fi +- +-if [ "$cgal_version" != "cgal-system" ] +-then +- export CGAL_ARCH_PATH=$WM_THIRD_PARTY_DIR/$cgal_version +-fi ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-9.orig/etc/config.sh/gperftools OpenFOAM-9/etc/config.sh/gperftools +--- OpenFOAM-9.orig/etc/config.sh/gperftools 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/etc/config.sh/gperftools 2021-08-17 15:25:23.783947000 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-9.orig/etc/config.sh/metis OpenFOAM-9/etc/config.sh/metis +--- OpenFOAM-9.orig/etc/config.sh/metis 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/etc/config.sh/metis 2021-08-17 15:25:23.784897000 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-9.orig/etc/config.sh/mpi OpenFOAM-9/etc/config.sh/mpi +--- OpenFOAM-9.orig/etc/config.sh/mpi 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/etc/config.sh/mpi 2021-08-17 15:25:23.786292744 +0200 +@@ -254,6 +254,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib/release + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-9.orig/etc/config.sh/paraview OpenFOAM-9/etc/config.sh/paraview +--- OpenFOAM-9.orig/etc/config.sh/paraview 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/etc/config.sh/paraview 2021-08-17 15:28:54.926163000 +0200 +@@ -41,25 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used. Take the most recent. +-unset CMAKE_HOME CMAKE_ROOT +-for cmake in $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/cmake-* +-do +- if [ -d $cmake ] +- then +- if [ -z $CMAKE_HOME ] || \ +- $WM_PROJECT_DIR/bin/tools/foamVersionCompare $CMAKE_HOME lt $cmake +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- fi +- fi +-done +-if [ -n $CMAKE_HOME ] +-then +- export PATH=$cmake/bin:$PATH +-fi +- + #- ParaView version, automatically determine major version + #export ParaView_VERSION=4.0.1 + #export ParaView_VERSION=4.1.0 +@@ -69,7 +50,8 @@ + #export ParaView_VERSION=5.0.1 + #export ParaView_VERSION=5.4.0 + #export ParaView_VERSION=5.5.0 +-export ParaView_VERSION=5.6.3 ++#export ParaView_VERSION=5.6.3 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + #export ParaView_GL=system +@@ -109,7 +91,8 @@ + export ParaView_VERSION ParaView_MAJOR + + # Set the binary and source directories +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION ++# export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION ++export ParaView_DIR=$EBROOTPARAVIEW + paraviewSrcDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + + # Set paths if binaries or source are present +@@ -129,8 +112,6 @@ + fi + export ParaView_LIB_DIR=$ParaView_DIR/lib$paraviewArch$paraviewLibSubDir + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -142,18 +123,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi +- + # Alias paraview to launch with mesa if necessary + if [ "$ParaView_GL" = mesa ] + then +diff -ru OpenFOAM-9.orig/etc/config.sh/scotch OpenFOAM-9/etc/config.sh/scotch +--- OpenFOAM-9.orig/etc/config.sh/scotch 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/etc/config.sh/scotch 2021-08-17 15:25:23.789570000 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.9 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-9.orig/etc/config.sh/settings OpenFOAM-9/etc/config.sh/settings +--- OpenFOAM-9.orig/etc/config.sh/settings 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/etc/config.sh/settings 2021-08-17 15:25:23.790563432 +0200 +@@ -61,11 +61,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ru OpenFOAM-9.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-9/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-9.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/src/parallel/decompose/ptscotchDecomp/Make/options 2021-08-17 15:25:23.793413000 +0200 +@@ -4,14 +4,7 @@ + $(PFLAGS) $(PINC) \ + -I$(FOAM_SRC)/Pstream/mpi/lnInclude \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ARCH_PATH)/lib \ +- -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \ +- -lptscotch \ +- -lptscotcherrexit \ +- -lscotch \ +- -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-9.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-9/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-9.orig/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2021-08-17 15:25:23.794849806 +0200 +@@ -31,10 +31,11 @@ + #include "SubField.H" + #include "PstreamGlobals.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-9.orig/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-9/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-9.orig/src/parallel/decompose/scotchDecomp/Make/options 2021-07-15 16:07:54.000000000 +0200 ++++ OpenFOAM-9/src/parallel/decompose/scotchDecomp/Make/options 2021-08-17 15:25:23.796687000 +0200 +@@ -6,7 +6,6 @@ + EXE_INC = \ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ From daf8db7eb944aa2a440bba34506331d55423ad6e Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:17:30 +0200 Subject: [PATCH 0954/9987] Update Excel-Writer-XLSX-1.09-foss-2020b.eb better sanity check --- .../e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb index c5eb8676cc9..103890e6bd6 100644 --- a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb +++ b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb @@ -23,7 +23,7 @@ options = {'modulename': 'Excel::Writer::XLSX'} sanity_check_paths = { 'files': ['bin/extract_vba'], - 'dirs': ['lib', 'bin'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Excel/Writer/XLSX'], } sanity_check_commands = ['extract_vba --help 2>&1 | grep "This utility is used to extract the VBA project binary from an Excel"'] From 852ce7a320c4fca6bf245051bbd37e6dfdc6bd8a Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:18:20 +0200 Subject: [PATCH 0955/9987] Update FLASH-2.2.00-foss-2020b.eb better postinstallcmds --- easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb index 858caac9c7b..30f9a870528 100644 --- a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb @@ -20,7 +20,7 @@ checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] files_to_copy = [(['flash2'], 'bin')] -postinstallcmds = ['ln -s %(installdir)s/bin/flash2 %(installdir)s/bin/flash'] +postinstallcmds = ["cd %(installdir)s/bin && ln -s flash2 flash"] sanity_check_paths = { 'files': ['bin/flash2', 'bin/flash'], 'dirs': [], From 37cc7495a314298a2642741389666dae9bf5767d Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:20:19 +0200 Subject: [PATCH 0956/9987] Update FLASH-2.2.00-foss-2020b.eb adding sanity_check_commands --- easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb index 30f9a870528..68775a2c869 100644 --- a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2020b.eb @@ -21,9 +21,14 @@ checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] files_to_copy = [(['flash2'], 'bin')] postinstallcmds = ["cd %(installdir)s/bin && ln -s flash2 flash"] + sanity_check_paths = { 'files': ['bin/flash2', 'bin/flash'], 'dirs': [], } +sanity_check_commands = [ + "flash --help", +] + moduleclass = 'bio' From 0464e66350ecb85e04c1af5fd8d30157fd1b43ad Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:39:43 +0200 Subject: [PATCH 0957/9987] Delete naturalsort-0.1.3-foss-2020b.eb removing, is an R extension --- .../naturalsort-0.1.3-foss-2020b.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb b/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb deleted file mode 100644 index b5b5ae7f56b..00000000000 --- a/easybuild/easyconfigs/n/naturalsort/naturalsort-0.1.3-foss-2020b.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'RPackage' - -name = 'naturalsort' -version = '0.1.3' - -homepage = 'https://github.com/kos59125/naturalsort/' -description = """The package provides functions related to human natural ordering.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://cran.r-project.org/src/contrib/'] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'] - -dependencies = [ - ('R', '4.0.3'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['naturalsort'], -} - -moduleclass = 'tools' From 1b1c3c684fa68c19a4ea5e855b3c45657ace6daf Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:40:59 +0200 Subject: [PATCH 0958/9987] Update pysamstats-1.1.2-foss-2020b.eb adding sanity_check_commands --- .../easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb index b0cebf283a5..ee98447beae 100644 --- a/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pysamstats/pysamstats-1.1.2-foss-2020b.eb @@ -25,6 +25,10 @@ dependencies = [ ('PyTables', '3.6.1'), ] +sanity_check_commands = [ + "pysamstats --help", +] + sanity_pip_check = True moduleclass = 'bio' From 8e7282e54e2febd7a82c42bc29924ba044ad1e6a Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 18 Aug 2021 18:43:44 +0100 Subject: [PATCH 0959/9987] revert #13745 --- .github/workflows/unit_tests.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 22e9c3f9559..252a6a166b0 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -121,8 +121,7 @@ jobs: eb --show-system-info # run test suite - # if tests failed, print error message that is picked up by boegelbot to determine end of test output - python -O -m test.easyconfigs.suite || echo "ERROR: Not all tests were successful" + python -O -m test.easyconfigs.suite unset PYTHONPATH From e554aff4dcfbbf51e0ac365b662ee91aa8fb8635 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 18 Aug 2021 19:42:24 +0100 Subject: [PATCH 0960/9987] desired behaviour --- .github/workflows/unit_tests.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 252a6a166b0..ea157514055 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -121,7 +121,8 @@ jobs: eb --show-system-info # run test suite - python -O -m test.easyconfigs.suite + # if tests failed, print error message that is picked up by boegelbot to determine end of test output + python -O -m test.easyconfigs.suite || (echo "ERROR: Not all tests were successful" && exit 1) unset PYTHONPATH From f231d8367b9c950be6e8d36f44948aa656ec81ef Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 19 Aug 2021 11:46:58 +0200 Subject: [PATCH 0961/9987] Update CRISPR-DAV-2.3.4-foss-2020b.eb removed naturalsort, added comment about it --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index e7460b08d0a..fdf461c95d4 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -16,13 +16,14 @@ checksums = [ '41475a09754d65cc2c88d4161be6eacdfc98242bccbe49778c4f1f74210a6cb2', ] +# also needs `naturalsort`, which is now an R extension - see https://github.com/easybuilders/easybuild-easyconfigs/pull/13762 +# if missing, try reinstalling R (https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip) dependencies = [ ('R', '4.0.3'), ('Perl', '5.32.0'), ('NGS', '2.10.9'), ('Pysam', '0.16.0.1'), ('Excel-Writer-XLSX', '1.09'), - ('naturalsort', '0.1.3'), ('pysamstats', '1.1.2'), ('ABRA2', '2.23'), ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), From d6f90fcdb0cc6ba7bd70d3b975868701cfb0909e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 19 Aug 2021 12:00:49 +0100 Subject: [PATCH 0962/9987] switch to 2021.07 while testing --- ...mpi-2021b.eb => OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/o/OSU-Micro-Benchmarks/{OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb => OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb} (92%) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb similarity index 92% rename from easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb rename to easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb index d8ee2498fbe..fbe580b2712 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb @@ -6,7 +6,7 @@ version = '5.7.1' homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" -toolchain = {'name': 'gompi', 'version': '2021b'} +toolchain = {'name': 'gompi', 'version': '2021.07'} toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] From 3485534fdbc4fb80a482656ba201a6c11aeaa433 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 19 Aug 2021 12:02:41 +0100 Subject: [PATCH 0963/9987] fix a copy and paste fail on the last commit --- .../easyconfigs/g/gompi/{gompi-2021b.eb => gompi-2021.07.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/g/gompi/{gompi-2021b.eb => gompi-2021.07.eb} (95%) diff --git a/easybuild/easyconfigs/g/gompi/gompi-2021b.eb b/easybuild/easyconfigs/g/gompi/gompi-2021.07.eb similarity index 95% rename from easybuild/easyconfigs/g/gompi/gompi-2021b.eb rename to easybuild/easyconfigs/g/gompi/gompi-2021.07.eb index d5860d74ef0..ae0258dc1a6 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2021b.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2021.07.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'gompi' -version = '2021b' +version = '2021.07' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, From 39405f9b5146a157608c9c3ff7486d23acbc8698 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Aug 2021 15:23:40 +0200 Subject: [PATCH 0964/9987] also add patches to fix TensorFlow 1.13.1 installation to other TensorFlow 1.13.1 easyconfigs --- .../TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb | 9 +++++++++ .../TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb | 6 ++++++ 2 files changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb index 576544b8554..3ed250e37db 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb @@ -82,6 +82,9 @@ exts_list = [ 'TensorFlow-1.11.0_swig-env.patch', 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.13.1_lrt-flag.patch', + 'TensorFlow-1.13.1_fix_protobuf_problem.patch', + 'TensorFlow-1.13.1_icu_sha_changed.patch', + 'TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch', ], 'checksums': [ '7cd19978e6bc7edc2c847bce19f95515a742b34ea5e28e4389dade35348f58ed', # v1.13.1.tar.gz @@ -89,6 +92,12 @@ exts_list = [ # TensorFlow-1.11.0_remove-msse-hardcoding.patch 'a0f00ee4d03bb4fd3a645ee06045cedaf97d0b85675ec35187e9dd7e479d7bb6', 'b388be35f2581786bcd533b1bfa375165d7f35e38a3aab74570019312816bf1b', # TensorFlow-1.13.1_lrt-flag.patch + # TensorFlow-1.13.1_fix_protobuf_problem.patch + 'd2fab1497078a2980a68adeea4d0f8719be5bef03741ea4775163745a1e52d40', + # TensorFlow-1.13.1_icu_sha_changed.patch + '936611ef1baf213a430d2706459dd0274a088472c3b2657173f450e2d4d72e0f', + # TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch + '4fb1234cd548f91ee131ac72017007ec5ebf962362d5eae8511721400e76a057', ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb index 040263d7fa2..5dcc31eee1b 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2019a-Python-3.7.2.eb @@ -90,6 +90,8 @@ exts_list = [ 'TensorFlow-1.11.0_remove-msse-hardcoding.patch', 'TensorFlow-1.13.1_lrt-flag.patch', 'TensorFlow-1.13.1_fix_protobuf_problem.patch', + 'TensorFlow-1.13.1_icu_sha_changed.patch', + 'TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch', ], 'checksums': [ '7cd19978e6bc7edc2c847bce19f95515a742b34ea5e28e4389dade35348f58ed', # v1.13.1.tar.gz @@ -99,6 +101,10 @@ exts_list = [ 'b388be35f2581786bcd533b1bfa375165d7f35e38a3aab74570019312816bf1b', # TensorFlow-1.13.1_lrt-flag.patch # TensorFlow-1.13.1_fix_protobuf_problem.patch 'd2fab1497078a2980a68adeea4d0f8719be5bef03741ea4775163745a1e52d40', + # TensorFlow-1.13.1_icu_sha_changed.patch + '936611ef1baf213a430d2706459dd0274a088472c3b2657173f450e2d4d72e0f', + # TensorFlow-1.13.1_cloud_impotred_w_nogcp.patch + '4fb1234cd548f91ee131ac72017007ec5ebf962362d5eae8511721400e76a057', ], }), ] From 04236aa565e0eb1dc5d4ef498b7616ecde84353b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Aug 2021 16:10:31 +0200 Subject: [PATCH 0965/9987] enable sanity_pip_check + add missing checksum for TensorFlow 1.13.1 easyconfig using foss/2018b toolchain --- .../t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb index 3ed250e37db..cacd64277ec 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.13.1-foss-2018b-Python-3.6.6.eb @@ -23,6 +23,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_list = [ ('protobuf-python', '3.6.1', { @@ -73,6 +74,7 @@ exts_list = [ }), ('tensorflow-estimator', '1.13.0', { 'source_tmpl': 'tensorflow_estimator-1.13.0-py2.py3-none-any.whl', + 'checksums': ['7cfdaa3e83e3532f31713713feb98be7ea9f3065722be4267e49b6c301271419'], 'unpack_sources': False, }), (name, version, { From 8223f258e8defac65d048a65c0e0e54b6dc693d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Aug 2021 16:57:50 +0200 Subject: [PATCH 0966/9987] remove commented out toolchainopts from OpenFOAM 9 easyconfig --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-foss-2021a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-foss-2021a.eb index 7aadfac08d9..3eef426331e 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-foss-2021a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-foss-2021a.eb @@ -8,7 +8,6 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2021a'} -# toolchainopts = {'cstd': 'c++11'} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] From 47df65669f6fa2d26648e988c734d19abb5304a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Aug 2021 16:48:34 +0200 Subject: [PATCH 0967/9987] fix suggestions for ABRA2, CRISPR-DAV, PRINSEQ easyconfigs --- .../a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb | 5 ++--- .../CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 6 ++---- ...> CRISPR-DAV-2.3.4_remove_hardcoding.patch} | 0 .../PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb | 18 ++++++++---------- 4 files changed, 12 insertions(+), 17 deletions(-) rename easybuild/easyconfigs/c/CRISPR-DAV/{crispr-dav-2.3.4_remove_hardcoding.patch => CRISPR-DAV-2.3.4_remove_hardcoding.patch} (100%) diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb index 734e544fc9f..f62a0b1e28b 100644 --- a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb @@ -41,8 +41,7 @@ sanity_check_paths = { 'dirs': [], } -modextravars = { - "LC_ALL": "en_US.UTF-8", -} +# required to work around localization bug, see https://github.com/mozack/abra2/issues/25 +modextravars = {'LC_ALL': 'en_US.UTF-8'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index fdf461c95d4..e4693c5f0e3 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -9,17 +9,15 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/pinetree1/crispr-dav/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['crispr-dav-2.3.4_remove_hardcoding.patch'] +patches = ['CRISPR-DAV-%(version)s_remove_hardcoding.patch'] checksums = [ '49975cd48bdbf31fe5a9e2aaa3f5ed85d3cc6f65a422ee3aa8daed890159d2ae', # v2.3.4.tar.gz # crispr-dav-2.3.4-foss2020b_remove_hardcoding.patch '41475a09754d65cc2c88d4161be6eacdfc98242bccbe49778c4f1f74210a6cb2', ] -# also needs `naturalsort`, which is now an R extension - see https://github.com/easybuilders/easybuild-easyconfigs/pull/13762 -# if missing, try reinstalling R (https://docs.easybuild.io/en/latest/Partial_installations.html#installing-additional-extensions-using-k-skip) dependencies = [ - ('R', '4.0.3'), + ('R', '4.0.3'), # provides naturalsort R package ('Perl', '5.32.0'), ('NGS', '2.10.9'), ('Pysam', '0.16.0.1'), diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4_remove_hardcoding.patch b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4_remove_hardcoding.patch similarity index 100% rename from easybuild/easyconfigs/c/CRISPR-DAV/crispr-dav-2.3.4_remove_hardcoding.patch rename to easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4_remove_hardcoding.patch diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb index c7576441aed..c2fccb2c6a2 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb @@ -77,23 +77,21 @@ exts_list = [ }), ] -# this is the script which relies in many extra Perl libraries so we verify it's working fine -sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl'] +fix_perl_shebang_for = ["*.pl"] -modextrapaths = { - 'PATH': '', - 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', -} +postinstallcmds = ["chmod +x %(installdir)s/*.pl"] -postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", - "chmod +x %(installdir)s/*.pl", -] +# this is the script which relies in many extra Perl libraries so we verify it's working fine +sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl'] sanity_check_paths = { 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], 'dirs': [] } +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} moduleclass = 'bio' From 26d5a95ef67b0fb0f95b51e7db2e46b4baa3dd2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Aug 2021 17:09:14 +0200 Subject: [PATCH 0968/9987] adding easyconfigs: GROMACS-2021.3-foss-2021a.eb --- .../g/GROMACS/GROMACS-2021.3-foss-2021a.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a.eb new file mode 100644 index 00000000000..9e518ea3825 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a.eb @@ -0,0 +1,88 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021.3' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI builds +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', +] +checksums = [ + 'e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6', # gromacs-2021.3.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch + '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('networkx', '2.5.1'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From db6b328407bc30516ccba6a2053fc9486ea24218 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Aug 2021 17:27:08 +0200 Subject: [PATCH 0969/9987] fix long line in Excel-Writer-XLSX easyconfig --- .../e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb index 103890e6bd6..cffa913c11c 100644 --- a/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb +++ b/easybuild/easyconfigs/e/Excel-Writer-XLSX/Excel-Writer-XLSX-1.09-foss-2020b.eb @@ -26,7 +26,8 @@ sanity_check_paths = { 'dirs': ['lib/perl5/site_perl/%(perlver)s/Excel/Writer/XLSX'], } -sanity_check_commands = ['extract_vba --help 2>&1 | grep "This utility is used to extract the VBA project binary from an Excel"'] - +sanity_check_commands = [ + 'extract_vba --help 2>&1 | grep "This utility is used to extract the VBA project binary from an Excel"', +] moduleclass = 'tools' From c062a0efa30be97c7472ea4953ba06222dfb221b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Aug 2021 19:03:52 +0200 Subject: [PATCH 0970/9987] stick to SAMtools 1.11 as dependency for CRISPR-DAV --- .../easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb index e4693c5f0e3..52537f135f4 100644 --- a/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPR-DAV/CRISPR-DAV-2.3.4-foss-2020b.eb @@ -25,7 +25,7 @@ dependencies = [ ('pysamstats', '1.1.2'), ('ABRA2', '2.23'), ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), - ('SAMtools', '1.12'), + ('SAMtools', '1.11'), ('BEDTools', '2.30.0'), ('FLASH', '2.2.00'), ('Archive-Zip', '1.68'), From 1fc497c580434e9c8d6c7ecefc669692ee90ae6e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Aug 2021 20:29:25 +0200 Subject: [PATCH 0971/9987] add pkgconfig dirs in system to default search paths of pkg-config-0.29.2.eb --- easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb index 46d7ee378a4..18c253b8f94 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb @@ -22,7 +22,11 @@ checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] # don't use PAX, it might break. tar_config_opts = True -configopts = " --with-internal-glib" +# add pkgconfig directories in the system to list of default search paths +preconfigopts = 'EB_SYS_PC_PATH=":$(find /usr -type d -name "pkgconfig" -printf %p: 2>/dev/null)";' +configopts = '--with-pc-path="%(installdir)s/lib/pkgconfig:%(installdir)s/share/pkgconfig${EB_SYS_PC_PATH%:}"' + +configopts += " --with-internal-glib" sanity_check_paths = { 'files': ['bin/pkg-config'], From 22cdff17d3594e20873efb8c344426e1c78ef5eb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Aug 2021 20:31:25 +0200 Subject: [PATCH 0972/9987] switch dependency on pkg-config to build dep --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb | 7 +++---- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb | 7 +++---- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb index ad98a749349..89b0fa362da 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb @@ -11,10 +11,9 @@ description = """The OpenSSL Project is a collaborative effort to develop a robu toolchain = SYSTEM toolchainopts = {'pic': True} -osdependencies = [ - ('pkg-config', 'pkgconfig'), - 'perl', -] +osdependencies = ['perl'] + +builddependencies = [('pkg-config', '0.29.2')] # This easyconfig will wrap the OpenSSL installation in the host system. # If the system provides the required binary, header files, and libraries for this diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb index a43112f5590..336394a94e0 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb @@ -12,10 +12,9 @@ description = """The OpenSSL Project is a collaborative effort to develop a robu toolchain = SYSTEM toolchainopts = {'pic': True} -osdependencies = [ - ('pkg-config', 'pkgconfig'), - 'perl', -] +osdependencies = ['perl'] + +builddependencies = [('pkg-config', '0.29.2')] # This easyconfig will wrap the OpenSSL installation in the host system. # If the system provides the required binary, header files, and libraries for From 47a82a41bd3c68a8a6b07669c78cb9422396a9a8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 20 Aug 2021 09:26:54 +0200 Subject: [PATCH 0973/9987] adding easyconfigs: Siesta-4.1.5-foss-2020a.eb --- .../s/Siesta/Siesta-4.1.5-foss-2020a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2020a.eb diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2020a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2020a.eb new file mode 100644 index 00000000000..1071a122684 --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2020a.eb @@ -0,0 +1,25 @@ +name = 'Siesta' +version = '4.1.5' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True, 'precise': True} + +source_urls = ['https://gitlab.com/siesta-project/siesta/-/releases/v%(version)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('netCDF-Fortran', '4.5.2'), + ('METIS', '5.1.0'), + ('ELPA', '2019.11.001'), +] + +# transiesta is now siesta --electrode +with_transiesta = False + +runtest = 'check' + +moduleclass = 'phys' From 7da16ef2547382834f80068cf4cd1806bddccf8d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 10:02:47 +0200 Subject: [PATCH 0974/9987] add sanity check command for andi, use SHLIB_EXT in libdivsufsort easyconfig --- easybuild/easyconfigs/a/andi/andi-0.13-foss-2018b.eb | 6 ++++-- .../l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb | 10 ++++------ 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/andi/andi-0.13-foss-2018b.eb b/easybuild/easyconfigs/a/andi/andi-0.13-foss-2018b.eb index 9da66d8d4e6..8cedd481301 100644 --- a/easybuild/easyconfigs/a/andi/andi-0.13-foss-2018b.eb +++ b/easybuild/easyconfigs/a/andi/andi-0.13-foss-2018b.eb @@ -28,13 +28,15 @@ dependencies = [ ('libdivsufsort', '2.0.1') ] -parallel = 1 - preconfigopts = "autoreconf -fi -Im4 && " +parallel = 1 + sanity_check_paths = { 'files': ['bin/andi'], 'dirs': [] } +sanity_check_commands = ["andi --help"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb b/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb index 48a9914d557..114f4c62251 100644 --- a/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb +++ b/easybuild/easyconfigs/l/libdivsufsort/libdivsufsort-2.0.1-foss-2018b.eb @@ -2,7 +2,7 @@ # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics -easyblock = "CMakeMake" +easyblock = 'CMakeMake' name = 'libdivsufsort' version = '2.0.1' @@ -17,16 +17,14 @@ source_urls = ['https://github.com/y-256/libdivsufsort/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] checksums = ['9164cb6044dcb6e430555721e3318d5a8f38871c2da9fd9256665746a69351e0'] -unpack_options = '--strip-components=1' - -separate_build_dir = True - builddependencies = [ ('CMake', '3.12.1'), ] +unpack_options = '--strip-components=1' + sanity_check_paths = { - 'files': ['lib/libdivsufsort.so'], + 'files': ['lib/libdivsufsort.%s' % SHLIB_EXT], 'dirs': [], } From 2307e30f90c46b59d06e854a2d556ae17cb072fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 11:00:44 +0200 Subject: [PATCH 0975/9987] fix rebuild of binaries in Co-phylog easyconfig + use $CFLAGS rather than -O6 --- .../c/Co-phylog/Co-phylog-20201012-GCC-7.3.0-2.30.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Co-phylog/Co-phylog-20201012-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/c/Co-phylog/Co-phylog-20201012-GCC-7.3.0-2.30.eb index c0ca6b19958..69b8c501ef1 100644 --- a/easybuild/easyconfigs/c/Co-phylog/Co-phylog-20201012-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/c/Co-phylog/Co-phylog-20201012-GCC-7.3.0-2.30.eb @@ -20,10 +20,12 @@ sources = ['%s.tar.gz' % (local_git_commit)] checksums = ['2cafdda678f9fea32d79460be9867e98846c68f9e6affd56920e7449306345a7'] cmds_map = [ - ('.*', "$CC fasta2co_v18.3.c -O6 -Wall -o fasta2co"), - ('.*', "$CC fastq2co.c -O6 -Wall -o fastq2co"), - ('.*', "$CC co2dist2.c -O6 -Wall -o co2dist"), - ('.*', "$CC readco.c -Wall -o readco") + ('.*', ' && '.join([ + "$CC fasta2co_v18.3.c $CFLAGS -Wall -o fasta2co", + "$CC fastq2co.c $CFLAGS -Wall -o fastq2co", + "$CC co2dist2.c $CFLAGS -Wall -o co2dist", + "$CC readco.c $CFLAGS -Wall -o readco", + ])), ] files_to_copy = [(['fasta2co', 'fastq2co', 'co2dist', 'readco'], 'bin')] From 2978b4f3c19e9456813867c2c4dc832a6a911179 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 11:14:14 +0200 Subject: [PATCH 0976/9987] remove unused patch for CRISPResso2 --- ...-2.1.2-foss-2020b_remove_strict_deps.patch | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch deleted file mode 100644 index d6733f0f0ce..00000000000 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b_remove_strict_deps.patch +++ /dev/null @@ -1,22 +0,0 @@ -# unimportantly strict dependency version requirements -# Author: Denis Kristak -diff -ruN "CRISPResso2-2.1.2 copy/setup.py" CRISPResso2-2.1.2/setup.py ---- "CRISPResso2-2.1.2 copy/setup.py" 2021-06-28 15:30:43.197061000 +0200 -+++ CRISPResso2-2.1.2/setup.py 2021-06-28 15:36:03.124070000 +0200 -@@ -89,12 +89,12 @@ - 'Programming Language :: Cython', - ], - install_requires=[ -- 'pandas>=0.15,<=0.24', -- 'matplotlib>=1.3.1,<=2.2.3', -+ 'pandas>=0.15', -+ 'matplotlib>=1.3.1', - 'argparse>=1.3,<=1.4', - 'seaborn>0.7.1,<0.10', -- 'jinja2==2.10', -- 'scipy==1.1.0', -+ 'jinja2>=2.10', -+ 'scipy>=1.1.0', - 'numpy>=1.9,<=1.16.6', - 'kiwisolver<1.2', - 'pyparsing<3', From 37a8867fb8179dd71bb70beea006afac2c94e136 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 11:21:48 +0200 Subject: [PATCH 0977/9987] fix import check for CRISPResso2 --- .../CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb index 571c2db3c06..9cf48eb4e3e 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -34,10 +34,9 @@ dependencies = [ ('Bowtie2', '2.4.2'), ('Seaborn', '0.9.1', '-Python-%(pyver)s'), ] + download_dep_fail = True use_pip = True -options = {'modulename': False} -sanity_pip_check = True # strip out too strict version requirements for dependencies preinstallopts = "sed -i 's/,<=[0-9]*//g' setup.py && sed -i 's/==/>=/g' setup.py && " @@ -56,6 +55,10 @@ sanity_check_commands = [ local_test_cmd, ] +sanity_pip_check = True + +options = {'modulename': name} + modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} moduleclass = 'bio' From c381dd750ac5a6e5d204887ee1b3ef1b868c7920 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 11:22:44 +0200 Subject: [PATCH 0978/9987] stick to SAMtools 1.11 for CRISPResso2 with foss/2020b --- .../c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb index 9cf48eb4e3e..4024c882cdb 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -30,7 +30,7 @@ dependencies = [ ('matplotlib', '2.2.5', '-Python-%(pyver)s'), ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), ('FLASH', '2.2.00'), - ('SAMtools', '1.12'), + ('SAMtools', '1.11'), ('Bowtie2', '2.4.2'), ('Seaborn', '0.9.1', '-Python-%(pyver)s'), ] From 613ecbee69d9c0f95df464e44728bb9e008ec3a0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 20 Aug 2021 11:37:50 +0200 Subject: [PATCH 0979/9987] Add missing checksums. --- easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2020a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2020a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2020a.eb index 1071a122684..5eff815b77c 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2020a.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2020a.eb @@ -10,6 +10,7 @@ toolchainopts = {'usempi': True, 'precise': True} source_urls = ['https://gitlab.com/siesta-project/siesta/-/releases/v%(version)s/downloads'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['518df31aa6213af5e24cc73abb537b2c89a925b487171f5339d743d0c7140b3f'] dependencies = [ ('netCDF-Fortran', '4.5.2'), From 7dae0eb3cbf3f739f41b8c3dd80aa0eddbb59302 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 13:32:18 +0200 Subject: [PATCH 0980/9987] adding easyconfigs: CRISPResso2-2.2.1-foss-2020b.eb --- .../CRISPResso2-2.2.1-foss-2020b.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb new file mode 100644 index 00000000000..10d20ead474 --- /dev/null +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb @@ -0,0 +1,63 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'CRISPResso2' +version = '2.2.1' + +homepage = 'https://github.com/pinellolab/CRISPResso2/' +description = """CRISPResso2 is a software pipeline designed to enable rapid and +intuitive interpretation of genome editing experiments.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [ + {'source_urls': ['https://github.com/pinellolab/CRISPResso2/archive/'], + 'filename': 'v%(version)s.tar.gz'}, + {'source_urls': ['https://crispresso.pinellolab.partners.org/static/demo/'], + 'filename': 'base_editor_v%(version)s.fastq.gz', 'download_filename': 'base_editor.fastq.gz', + 'extract_cmd': 'cp %s %(builddir)s'}] +checksums = [ + '8bc46661759dbe300e927f353d5859ec0abd1ee4ddcaf4e18dacc6859be2fcb7', # v2.2.1.tar.gz + '371aad07a164721188deaa80ca7589f5cd4b871119d90d55a984c6d9c8d31c7a', # base_editor_v2.2.1.fastq.gz +] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('FLASH', '2.2.00'), + ('SAMtools', '1.11'), + ('Bowtie2', '2.4.2'), + ('Seaborn', '0.11.1'), +] + +download_dep_fail = True +use_pip = True + +# strip out too strict version requirements for dependencies +preinstallopts = "sed -i 's/,<=[0-9]*//g' setup.py && sed -i 's/==/>=/g' setup.py && " + +# this is an example command from: +# https://github.com/pinellolab/CRISPResso2#example-run-base-editing-experiment +local_seq_str = 'GGCCCCAGTGGCTGCTCTGGGGGCCTCCTGAGTTTCTCATCTGTGCCCCTCCCTCCCTGGCCCAGGTGAAGGTGTGGTTCCAGAACCGGAGGACAAAGTAC' +local_seq_str += 'AAACGGCAGAAGCTGGAGGAGGAAGGGCCTGAGTCCGAGCAGAAGAAGAAGGGCTCCCATCACATCAACCGGTGGCGCATTGCCACGAAGCAGGCCAATG' +local_seq_str += 'GGGAGGACATCGATGTCACCTCCAATGACTAGGGTGG' +local_test_cmd = "CRISPResso --fastq_r1 %(builddir)s/base_editor_v%(version)s.fastq.gz " +local_test_cmd += "--amplicon_seq %s " % local_seq_str +local_test_cmd += "--guide_seq GAGTCCGAGCAGAAGAAGAA --quantification_window_size 10 " +local_test_cmd += "--quantification_window_center -10 --base_editor_output" +sanity_check_commands = [ + "CRISPResso -h", + local_test_cmd, +] + +sanity_pip_check = True + +options = {'modulename': name} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/CRISPResso2']} + +moduleclass = 'bio' From f37ca098672f820dda3d2e4562a10a69dd3d0e0f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Aug 2021 14:10:17 +0200 Subject: [PATCH 0981/9987] adding easyconfigs: nlohmann_json-3.10.0-GCCcore-10.3.0.eb --- .../nlohmann_json-3.10.0-GCCcore-10.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..135915c62a4 --- /dev/null +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.0-GCCcore-10.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'nlohmann_json' +version = '3.10.0' + +homepage = 'https://github.com/nlohmann/json' +description = """UShER is now a package consisting of a family of programs for +rapid phylogenetic analyses, particularly suitable for the SARS-CoV-2 genomes.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['eb8b07806efa5f95b349766ccc7a8ec2348f3b2ee9975ad879259a371aea8084'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['include/nlohmann/json.hpp'], + 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 4df80d8270afbfaaf8e2a3bb98fd000cf341d0bd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Aug 2021 14:27:35 +0200 Subject: [PATCH 0982/9987] adding easyconfigs: spdlog-1.9.2-GCCcore-10.3.0.eb --- .../s/spdlog/spdlog-1.9.2-GCCcore-10.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/spdlog/spdlog-1.9.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/s/spdlog/spdlog-1.9.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/spdlog/spdlog-1.9.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..a60e3ad12cb --- /dev/null +++ b/easybuild/easyconfigs/s/spdlog/spdlog-1.9.2-GCCcore-10.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'spdlog' +version = '1.9.2' + +homepage = 'https://github.com/gabime/spdlog' +description = 'Very fast, header-only/compiled, C++ logging library.' +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/gabime/spdlog/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6fff9215f5cb81760be4cc16d033526d1080427d236e86d70bb02994f85e3d38'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['include/spdlog/spdlog.hpp'], + 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 905cf49123b6ee4b071e3b06a1a31c45ea19cdbe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Aug 2021 14:31:40 +0200 Subject: [PATCH 0983/9987] fix sanity check --- easybuild/easyconfigs/s/spdlog/spdlog-1.9.2-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spdlog/spdlog-1.9.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/spdlog/spdlog-1.9.2-GCCcore-10.3.0.eb index a60e3ad12cb..cd1597fa84b 100644 --- a/easybuild/easyconfigs/s/spdlog/spdlog-1.9.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/s/spdlog/spdlog-1.9.2-GCCcore-10.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['include/spdlog/spdlog.hpp'], + 'files': ['include/spdlog/spdlog.h'], 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], } From 55aee3dc2c7c40a40fc6763529dc113a07125d35 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Aug 2021 14:53:57 +0200 Subject: [PATCH 0984/9987] adding easyconfigs: muparserx-4.0.8-GCCcore-10.3.0.eb --- .../muparserx-4.0.8-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e7434165123 --- /dev/null +++ b/easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'muparserx' +version = '4.0.8' + +homepage = 'https://beltoforion.de/en/muparserx/' +description = 'Very fast, header-only/compiled, C++ logging library.' +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'beltoforion' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5913e0a4ca29a097baad1b78a4674963bc7a06e39ff63df3c73fbad6fadb34e1'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['lib64/libmuparserx.a', 'lib64/libmuparserx.%s' % SHLIB_EXT], + 'dirs': ['include/muparserx'], +} + +moduleclass = 'lib' From 8ff887089a8b5d6005faeca16dfc40331a52ce0b Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Fri, 20 Aug 2021 16:22:21 +0100 Subject: [PATCH 0985/9987] adding easyconfigs: Siesta-4.1.5-intel-2020a.eb --- .../s/Siesta/Siesta-4.1.5-intel-2020a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2020a.eb diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2020a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2020a.eb new file mode 100644 index 00000000000..50527cd229e --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2020a.eb @@ -0,0 +1,26 @@ +name = 'Siesta' +version = '4.1.5' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True, 'precise': True} + +source_urls = ['https://gitlab.com/siesta-project/siesta/-/releases/v%(version)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['518df31aa6213af5e24cc73abb537b2c89a925b487171f5339d743d0c7140b3f'] + +dependencies = [ + ('netCDF-Fortran', '4.5.2'), + ('METIS', '5.1.0'), + ('ELPA', '2019.11.001'), +] + +# transiesta is now siesta --electrode +with_transiesta = False + +runtest = 'check' + +moduleclass = 'phys' From 656d723a2070c71707ab2135be4fc8ac90124001 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 20 Aug 2021 17:35:34 +0200 Subject: [PATCH 0986/9987] adding easyconfigs: Cartopy-0.19.0.post1-foss-2020b.eb, Fiona-1.8.20-foss-2020b.eb, Cartopy-0.19.0.post1-intel-2020b.eb, Fiona-1.8.20-intel-2020b.eb, Shapely-1.8a1-iccifort-2020.4.304.eb --- .../Cartopy-0.19.0.post1-foss-2020b.eb | 51 +++++++++++++++++++ .../Cartopy-0.19.0.post1-intel-2020b.eb | 51 +++++++++++++++++++ .../f/Fiona/Fiona-1.8.20-foss-2020b.eb | 49 ++++++++++++++++++ .../f/Fiona/Fiona-1.8.20-intel-2020b.eb | 49 ++++++++++++++++++ .../Shapely-1.8a1-iccifort-2020.4.304.eb | 26 ++++++++++ 5 files changed, 226 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb new file mode 100644 index 00000000000..804988f11bc --- /dev/null +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Cartopy' +version = '0.19.0.post1' + +homepage = 'https://scitools.org.uk/cartopy/docs/latest/' +description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Fiona', '1.8.20'), + ('GDAL', '3.2.1'), + ('GEOS', '3.9.1'), + ('matplotlib', '3.3.3'), + ('pyproj', '3.0.1'), + ('SciPy-bundle', '2020.11'), + ('Shapely', '1.8a1'), + ('lxml', '4.6.2'), + ('Pillow', '8.0.1'), + ('PROJ', '7.2.1'), + ('PyYAML', '5.3.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +exts_list = [ + ('OWSLib', '0.24.1', { + 'checksums': ['4973c2ba65ec850a3fcc1fb94cefe5ed2fed83aaf2a5e2135c78810ad2a8f0e1'], + }), + ('pyepsg', '0.4.0', { + 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], + }), + ('pykdtree', '1.3.4', { + 'checksums': ['bebe5c608129f2997e88510c00010b9a78581b394924c0e3ecd131d52415165d'], + }), + ('pyshp', '2.1.3', { + 'modulename': 'shapefile', + 'checksums': ['e32b4a6832a3b97986df442df63b4c4a7dcc846b326c903189530a5cc6df0260'], + }), + (name, version, { + 'checksums': ['4b8b4773a98ed7009fe17d9b6ec87ac3ac62b7d14634d7768c190eadc647d576'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb new file mode 100644 index 00000000000..8928cbebb25 --- /dev/null +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Cartopy' +version = '0.19.0.post1' + +homepage = 'https://scitools.org.uk/cartopy/docs/latest/' +description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Fiona', '1.8.20'), + ('GDAL', '3.2.1'), + ('GEOS', '3.9.1'), + ('matplotlib', '3.3.3'), + ('pyproj', '3.0.1'), + ('SciPy-bundle', '2020.11'), + ('Shapely', '1.8a1'), + ('lxml', '4.6.2'), + ('Pillow', '8.0.1'), + ('PROJ', '7.2.1'), + ('PyYAML', '5.3.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +exts_list = [ + ('OWSLib', '0.24.1', { + 'checksums': ['4973c2ba65ec850a3fcc1fb94cefe5ed2fed83aaf2a5e2135c78810ad2a8f0e1'], + }), + ('pyepsg', '0.4.0', { + 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], + }), + ('pykdtree', '1.3.4', { + 'checksums': ['bebe5c608129f2997e88510c00010b9a78581b394924c0e3ecd131d52415165d'], + }), + ('pyshp', '2.1.3', { + 'modulename': 'shapefile', + 'checksums': ['e32b4a6832a3b97986df442df63b4c4a7dcc846b326c903189530a5cc6df0260'], + }), + (name, version, { + 'checksums': ['4b8b4773a98ed7009fe17d9b6ec87ac3ac62b7d14634d7768c190eadc647d576'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb new file mode 100644 index 00000000000..370e0e41f5d --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.8.20' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('GDAL', '3.2.1'), + ('Shapely', '1.8a1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'checksums': ['a70502d2857b82f749c09cb0dea3726787747933a2a1599b5ab787d74e3c143b'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb new file mode 100644 index 00000000000..7457c0fdab8 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.8.20' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('GDAL', '3.2.1'), + ('Shapely', '1.8a1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'checksums': ['a70502d2857b82f749c09cb0dea3726787747933a2a1599b5ab787d74e3c143b'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..a87575e17a5 --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8a1-iccifort-2020.4.304.eb @@ -0,0 +1,26 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '1.8a1' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a748ab74c187060264e7ce838aaac30eead2a791bbea8cc3ab1dfc3cc0b4d067'] + +dependencies = [ + ('Python', '3.8.6'), + ('GEOS', '3.9.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From d8bab987863657d3e4eb703c39d91eb6320b3da8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 17:43:43 +0200 Subject: [PATCH 0987/9987] also add pkg-config build dependency to Rust 1.54.0 easyconfig --- easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb index a03a5a29908..efafcecfca8 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb @@ -17,6 +17,7 @@ builddependencies = [ ('binutils', '2.37'), ('CMake', '3.21.1'), ('Python', '3.9.6', '-bare'), + ('pkg-config', '0.29.2'), ] dependencies = [ From dee1fcb007fbc72ed6575253d899e547f539674c Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 20 Aug 2021 17:48:08 +0200 Subject: [PATCH 0988/9987] removing download_dep_fail, since its a bundle --- .../easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb | 1 - .../easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb | 1 - easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb | 1 - easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb | 1 - 4 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb index 804988f11bc..4ce73ac7ec1 100644 --- a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-foss-2020b.eb @@ -27,7 +27,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('OWSLib', '0.24.1', { diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb index 8928cbebb25..2301189a3a7 100644 --- a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.19.0.post1-intel-2020b.eb @@ -27,7 +27,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('OWSLib', '0.24.1', { diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb index 370e0e41f5d..70c9cf78c38 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb @@ -21,7 +21,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb index 7457c0fdab8..47f6971d118 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb @@ -21,7 +21,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From 392ec0140ddae71c13486408b06cc00416aa0692 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 20 Aug 2021 17:53:12 +0200 Subject: [PATCH 0989/9987] Update Fiona-1.8.20-foss-2020b.eb removing extra line --- easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb index 70c9cf78c38..d218269306e 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb @@ -38,8 +38,6 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/fio'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From c8d83b7a84031ec5a61fdf5addc2d837445c9e9d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Aug 2021 18:29:33 +0200 Subject: [PATCH 0990/9987] remove duplicate sanity_pip_check in Fiona easyconfig + add custom sanity check command --- easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb | 5 ++++- easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb | 7 ++++--- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb index d218269306e..fd9e2798fc3 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2020b.eb @@ -21,7 +21,6 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True exts_list = [ ('cligj', '0.7.2', { @@ -43,4 +42,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["fio --help"] + +sanity_pip_check = True + moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb index 47f6971d118..4deaf150393 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-intel-2020b.eb @@ -21,7 +21,6 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True exts_list = [ ('cligj', '0.7.2', { @@ -38,11 +37,13 @@ exts_list = [ }), ] -sanity_pip_check = True - sanity_check_paths = { 'files': ['bin/fio'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["fio --help"] + +sanity_pip_check = True + moduleclass = 'data' From 8bc30437ebbcc07507e23618b6e675e4fb570a13 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Aug 2021 19:02:59 +0200 Subject: [PATCH 0991/9987] adding easyconfigs: Qiskit-0.29.0-foss-2021a.eb --- .../q/Qiskit/Qiskit-0.29.0-foss-2021a.eb | 161 ++++++++++++++++++ 1 file changed, 161 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb new file mode 100644 index 00000000000..18cd65a6b66 --- /dev/null +++ b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb @@ -0,0 +1,161 @@ +easyblock = 'PythonBundle' + +name = 'Qiskit' +version = '0.29.0' +local_aerver = '0.8.2' # version of qiskit-aer + +homepage = 'https://qiskit.org' +description = """Qiskit is an open-source framework for working with noisy quantum computers + at the level of pulses, circuits, and algorithms.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + # required for building/installing qiskit-aer + ('CMake', '3.20.1'), + ('Ninja', '1.10.2'), + ('scikit-build', '0.11.1'), + ('pybind11', '2.6.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('sympy', '1.8'), + ('numba', '0.53.1'), + ('dill', '0.3.4'), + ('h5py', '3.2.1'), + ('retworkx', '0.9.0'), + ('networkx', '2.5.1'), + ('scikit-learn', '0.24.2'), + ('CVXOPT', '1.2.6'), + ('Quandl', '3.6.1'), + ('PySCF', '1.7.6'), + ('SymEngine-python', '0.7.2'), + ('lxml', '4.6.3'), + ('nlohmann_json', '3.10.0'), + ('spdlog', '1.9.2'), + ('muparserx', '4.0.8'), +] + +use_pip = True +sanity_pip_check = True +# Aer +preconfigopts = 'export DISABLE_CONAN=ON &&' +prebuildopts = 'export DISABLE_CONAN=ON &&' +preinstallopts = 'export DISABLE_CONAN=ON &&' + +exts_list = [ + ('marshmallow', '3.13.0', { + 'checksums': ['c67929438fd73a2be92128caa0325b1b5ed8b626d91a094d2f7f2771bf1f1c0e'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('marshmallow-polyfield', '5.10', { + 'checksums': ['75d0e31b725650e91428f975a66ed30f703cc6f9fcfe45b8436ee6d676921691'], + }), + ('pylatexenc', '2.10', { + 'checksums': ['3dd8fd84eb46dc30bee1e23eaab8d8fb5a7f507347b23e5f38ad9675c84f40d3'], + }), + ('fastdtw', '0.3.4', { + 'checksums': ['2350fa6ec36bcad186eaf81f46eff35181baf04e324f522de8aeb43d0243f64f'], + }), + ('dlx', '1.0.4', { + 'checksums': ['ef75bc9d590216ebde7d4811f9ae6b2d6c6dc2a54772d94ae13384dc517a5aae'], + }), + ('docloud', '1.0.375', { + 'checksums': ['996d55407498fd01e6c6c480f367048f92255e9ca9db0e9ea19aaef91328a441'], + }), + ('docplex', '2.21.207', { + 'checksums': ['4f1781592be2b093db939772db8c6575a0f017041fb0cfd784bedf4222ac5e58'], + }), + ('websockets', '9.1', { + 'checksums': ['276d2339ebf0df4f45df453923ebd2270b87900eda5dfd4a6b0cfa15f82111c3'], + }), + ('ntlm-auth', '1.5.0', { + 'checksums': ['c9667d361dc09f6b3750283d503c689070ff7d89f2f6ff0d38088d5436ff8543'], + }), + ('requests_ntlm', '1.1.0', { + 'checksums': ['9189c92e8c61ae91402a64b972c4802b2457ce6a799d658256ebf084d5c7eb71'], + }), + ('nest-asyncio', '1.5.1', { + 'source_tmpl': 'nest_asyncio-%(version)s.tar.gz', + 'checksums': ['afc5a1c515210a23c461932765691ad39e8eba6551c055ac8d5546e69250d0aa'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('python-constraint', '1.4.0', { + 'modulename': 'constraint', + 'source_tmpl': '%(name)s-%(version)s.tar.bz2', + 'checksums': ['501d6f17afe0032dfc6ea6c0f8acc12e44f992733f00e8538961031ef27ccb8e'], + }), + ('sparse', '0.12.0', { + 'checksums': ['2c95c3b8ee00211a5aa4ef5e46006d25bf35009a66e406b7ea9b25b327fb9516'], + }), + ('fastjsonschema', '2.15.1', { + 'checksums': ['671f36d225b3493629b5e789428660109528f373cf4b8a22bac6fa2f8191c2d2'], + }), + ('tweedledum', '1.1.0', { + 'checksums': ['5779e3127c87414a5e2cc64511517881a657ff2336d00b3d8c0da0c8098066c5'], + }), + ('websocket-client', '1.1.1', { + 'modulename': 'constraint', + }), + ('multitasking', '0.0.9', { + }), + ('yfinance', '0.1.62', { + }), + ('qiskit-terra', '0.18.1', { + 'modulename': 'qiskit.qobj', + 'patches': ['qiskit-terra-%(version)s_fix-qiskit-version-env.patch'], + 'checksums': [ + '7673fa59cecdd7f7f3f22aafc8d45c76cd0b5518c72de7ae464b3823c0e2b10c', # qiskit-terra-0.18.1.tar.gz + # qiskit-terra-0.18.1_fix-qiskit-version-env.patch + '1296cc650a7d4d2d908a6a5de6b4ce52106748464a54d47744a4648494f4c24e', + ], + }), + ('qiskit-ignis', '0.6.0', { + 'modulename': 'qiskit.ignis', + 'checksums': ['b41bbbc90a042f89d1a5bb01100d59d72facdfe18cb9fc336af74f0e94aae7fc'], + }), + ('qiskit-ibmq-provider', '0.16.0', { + 'modulename': 'qiskit.providers.ibmq', + 'checksums': ['d3fbe8ad73b89cf8b0034a149c61b12a39d5e567ff5ccad9865ce3bb36acef3d'], + }), + ('qiskit-optimization', '0.2.1', { + 'modulename': 'qiskit_optimization', + 'checksums': ['718ae02f981e4dd9c4093a6ecafea7dfa97987c9fcc167afaa381bd98d514de5'], + }), + ('qiskit-finance', '0.2.0', { + 'modulename': 'qiskit_finance', + 'checksums': ['2b1ba19d09ec8fc06dd8f60d123b8ee78c7e856449d172f21da5a45d18649b58'], + }), + ('qiskit-nature', '0.1.5', { + 'modulename': 'qiskit_nature', + 'checksums': ['b5b761d9a19ce5012892c13ef5a52c2ea1576ef608c703aeed6a8062039332a6'], + }), + ('qiskit-machine-learning', '0.2.0', { + 'modulename': 'qiskit_machine_learning', + 'checksums': ['de83b3dc0a4ab01a27abfcb01a6a592d6b4d9cdfb7adb003ed37fa3eb7f48b3f'], + }), + ('qiskit-aqua', '0.9.4', { + 'modulename': 'qiskit.aqua', + 'checksums': ['fd0932b84ed86c3fb7c10e4931c6e99bb7c02883220f7e919851753a1c92598b'], + }), + ('qiskit-aer', local_aerver, { + 'modulename': 'qiskit.providers.aer', + 'checksums': ['33eed3ae158e458bf5c68b0384e5d49ee1d534bfeb2bbdc79c438e744dd54ed2'], + }), + ('qiskit', version, { + 'checksums': ['9c89419ed20cab2f18baf542805684c7a9758a87fa9a1377a5de81fcd469c077'], + }), +] + +postinstallcmds = [ + # qiskit/providers/aer/VERSION.txt does not get installed, but is required by qiskit/providers/aer/version.py + "echo %s > %%(installdir)s/lib/python%%(pyshortver)s/site-packages/qiskit/providers/aer/VERSION.txt" % local_aerver, +] + +moduleclass = 'quantum' From 8a238a44902e865d342dd706c4c1e92bc2b4be47 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Aug 2021 19:06:08 +0200 Subject: [PATCH 0992/9987] Cleanup --- easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb index 18cd65a6b66..2079731703f 100644 --- a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb +++ b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb @@ -40,9 +40,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -# Aer -preconfigopts = 'export DISABLE_CONAN=ON &&' -prebuildopts = 'export DISABLE_CONAN=ON &&' preinstallopts = 'export DISABLE_CONAN=ON &&' exts_list = [ From aa997a7e6cd96b09a50f3816e179eeffb8306ee8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Aug 2021 19:52:58 +0200 Subject: [PATCH 0993/9987] Update easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-10.3.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-10.3.0.eb index e7434165123..510fe1de689 100644 --- a/easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-10.3.0.eb @@ -4,7 +4,7 @@ name = 'muparserx' version = '4.0.8' homepage = 'https://beltoforion.de/en/muparserx/' -description = 'Very fast, header-only/compiled, C++ logging library.' +description = 'A C++ Library for Parsing Expressions with Strings, Complex Numbers, Vectors, Matrices and more.' toolchain = {'name': 'GCCcore', 'version': '10.3.0'} github_account = 'beltoforion' From 2893b956d2ea5be2e5ae7cd1faea89cd12980aea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Aug 2021 19:53:17 +0200 Subject: [PATCH 0994/9987] Update easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.0-GCCcore-10.3.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../n/nlohmann_json/nlohmann_json-3.10.0-GCCcore-10.3.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.0-GCCcore-10.3.0.eb index 135915c62a4..768df37e3ef 100644 --- a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.0-GCCcore-10.3.0.eb @@ -4,8 +4,7 @@ name = 'nlohmann_json' version = '3.10.0' homepage = 'https://github.com/nlohmann/json' -description = """UShER is now a package consisting of a family of programs for -rapid phylogenetic analyses, particularly suitable for the SARS-CoV-2 genomes.""" +description = """JSON for Modern C++""" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} From a963a39cf73512c5e12f4b05168e2915583bd619 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Aug 2021 20:00:48 +0200 Subject: [PATCH 0995/9987] Add qiskit-terra patch, checksums --- .../q/Qiskit/Qiskit-0.29.0-foss-2021a.eb | 3 +++ ...qiskit-terra-0.18.1_fix-qiskit-version-env.patch | 13 +++++++++++++ 2 files changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qiskit/qiskit-terra-0.18.1_fix-qiskit-version-env.patch diff --git a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb index 2079731703f..4d63ce49e73 100644 --- a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb +++ b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb @@ -99,10 +99,13 @@ exts_list = [ }), ('websocket-client', '1.1.1', { 'modulename': 'constraint', + 'checksums': ['4cf754af7e3b3ba76589d49f9e09fd9a6c0aae9b799a89124d656009c01a261d'], }), ('multitasking', '0.0.9', { + 'checksums': ['b59d99f709d2e17d60ccaa2be09771b6e9ed9391c63f083c0701e724f624d2e0'], }), ('yfinance', '0.1.62', { + 'checksums': ['0356eaeef89ed225d272b16a0bb8393870cc68506f9aff545f9f030436044111'], }), ('qiskit-terra', '0.18.1', { 'modulename': 'qiskit.qobj', diff --git a/easybuild/easyconfigs/q/Qiskit/qiskit-terra-0.18.1_fix-qiskit-version-env.patch b/easybuild/easyconfigs/q/Qiskit/qiskit-terra-0.18.1_fix-qiskit-version-env.patch new file mode 100644 index 00000000000..cb8ad5c1f95 --- /dev/null +++ b/easybuild/easyconfigs/q/Qiskit/qiskit-terra-0.18.1_fix-qiskit-version-env.patch @@ -0,0 +1,13 @@ +also include $LD_LIBRARY_PATH in environment where "python -m pip freeze" is run on 'import qiskit' +author: Kenneth Hoste (HPC-UGent) +--- qiskit/version.py.orig 2021-08-04 16:34:17.261482728 +0200 ++++ qiskit/version.py 2021-08-04 16:34:26.087460624 +0200 +@@ -25,7 +25,7 @@ + def _minimal_ext_cmd(cmd): + # construct minimal environment + env = {} +- for k in ["SYSTEMROOT", "PATH"]: ++ for k in ["SYSTEMROOT", "PATH", "LD_LIBRARY_PATH"]: + v = os.environ.get(k) + if v is not None: + env[k] = v From 8e752b97a729d73853505186f4fe8b0f029f552a Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Sat, 21 Aug 2021 14:50:25 +1000 Subject: [PATCH 0996/9987] Create TetGen-1.6.0-GCCcore-10.2.0.eb New version, new compiler --- .../t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..34b80d080b5 --- /dev/null +++ b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'TetGen' +version = '1.6.0' + +homepage = 'http://wias-berlin.de/software/index.jsp?id=TetGen' +description = """ A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# Fill in a form and download from above URL +sources = ['tetgen1.6.0.tar.gz'] +checksums = ['87b5e61ebd3a471fc4f2cdd7124c2b11dd6639f4feb1f941a5d2f5110d05ce39'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +separate_build_dir = True + +skipsteps = ['install'] + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin/ && cp tetgen %(installdir)s/bin/', + 'mkdir -p %(installdir)s/lib/ && cp libtet.a %(installdir)s/lib/', +] + +sanity_check_paths = { + 'files': ['bin/tetgen', 'lib/libtet.a'], + 'dirs': [], +} + +moduleclass = 'numlib' From 29361d63fc9b410a7a298094793e153f3e272c4d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 21 Aug 2021 09:35:58 +0100 Subject: [PATCH 0997/9987] add PyTorch versionsuffix to Mish-Cuda --- ...h-Cuda-20210309-fosscuda-2020b-PyTorch-%(local_ptver)s.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/m/Mish-Cuda/{Mish-Cuda-20210309-fosscuda-2020b.eb => Mish-Cuda-20210309-fosscuda-2020b-PyTorch-%(local_ptver)s.eb} (88%) diff --git a/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b.eb b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-%(local_ptver)s.eb similarity index 88% rename from easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b.eb rename to easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-%(local_ptver)s.eb index b4c899852b1..f6675c6e95c 100644 --- a/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-%(local_ptver)s.eb @@ -3,6 +3,8 @@ easyblock = 'PythonPackage' name = 'Mish-Cuda' version = '20210309' local_commit = '6f38976' +local_ptver = '1.9.0' +versionsuffix = '-PyTorch-%(local_ptver)s' homepage = 'https://github.com/JunnYu/mish-cuda' description = """Mish-Cuda: Self Regularized Non-Monotonic Activation Function""" @@ -17,7 +19,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '3.8.6'), - ('PyTorch', '1.9.0'), + ('PyTorch', local_ptver), ] preinstallopts = 'export TORCH_CUDA_ARCH_LIST="%(cuda_cc_semicolon_sep)s" && ' From f02a11aedc379c60e76c055549a60a5dea29b3ca Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 21 Aug 2021 09:38:14 +0100 Subject: [PATCH 0998/9987] sort out bug introduced by --new-pr --- ...er)s.eb => Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/Mish-Cuda/{Mish-Cuda-20210309-fosscuda-2020b-PyTorch-%(local_ptver)s.eb => Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb} (100%) diff --git a/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-%(local_ptver)s.eb b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb similarity index 100% rename from easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-%(local_ptver)s.eb rename to easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb From 423ed3902cce686078d1a321581d36205355c251 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 21 Aug 2021 09:50:24 +0100 Subject: [PATCH 0999/9987] correct syntax --- .../Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb index f6675c6e95c..fa7173c5142 100644 --- a/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/m/Mish-Cuda/Mish-Cuda-20210309-fosscuda-2020b-PyTorch-1.9.0.eb @@ -4,7 +4,7 @@ name = 'Mish-Cuda' version = '20210309' local_commit = '6f38976' local_ptver = '1.9.0' -versionsuffix = '-PyTorch-%(local_ptver)s' +versionsuffix = '-PyTorch-%s' % local_ptver homepage = 'https://github.com/JunnYu/mish-cuda' description = """Mish-Cuda: Self Regularized Non-Monotonic Activation Function""" From e7badbb437f8057c1d0e1bad2dbca95be2f794c5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 21 Aug 2021 10:42:42 +0100 Subject: [PATCH 1000/9987] glibc is the correct spelling --- easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-foss-2018b.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-intel-2018b.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.10.1_glibc-fix.patch | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-foss-2018b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-foss-2018b.eb index a2831b4034c..918a6ab56a7 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-foss-2018b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-foss-2018b.eb @@ -17,7 +17,7 @@ sources = ['qt-everywhere-src-%(version)s.tar.xz'] patches = [('%(name)s-%(version)s_glibc-fix.patch', 'qtbase')] checksums = [ '05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a', # qt-everywhere-src-5.10.1.tar.xz - 'd7939eaac79b145b031c18a0c17c09a4dd17301a9e21f7850a415183008b8d13', # Qt5-5.10.1_glibc-fix.patch + '47fb63019aa48c18896350a56d9bdf788a2af6dc838ccb8fd098b26a441fab94', # Qt5-5.10.1_glibc-fix.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb index b97c1baf89c..41d3a31e594 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-fosscuda-2018b.eb @@ -17,7 +17,7 @@ sources = ['qt-everywhere-src-%(version)s.tar.xz'] patches = ['%(name)s-%(version)s_glibc-fix.patch'] checksums = [ '05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a', # qt-everywhere-src-5.10.1.tar.xz - 'd7939eaac79b145b031c18a0c17c09a4dd17301a9e21f7850a415183008b8d13', # Qt5-5.10.1_glibc-fix.patch + '47fb63019aa48c18896350a56d9bdf788a2af6dc838ccb8fd098b26a441fab94', # Qt5-5.10.1_glibc-fix.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-intel-2018b.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-intel-2018b.eb index 6313e872382..8315688266b 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-intel-2018b.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1-intel-2018b.eb @@ -17,7 +17,7 @@ sources = ['qt-everywhere-src-%(version)s.tar.xz'] patches = ['%(name)s-%(version)s_glibc-fix.patch'] checksums = [ '05ffba7b811b854ed558abf2be2ddbd3bb6ddd0b60ea4b5da75d277ac15e740a', # qt-everywhere-src-5.10.1.tar.xz - 'd7939eaac79b145b031c18a0c17c09a4dd17301a9e21f7850a415183008b8d13', # Qt5-5.10.1_glibc-fix.patch + '47fb63019aa48c18896350a56d9bdf788a2af6dc838ccb8fd098b26a441fab94', # Qt5-5.10.1_glibc-fix.patch ] builddependencies = [('pkg-config', '0.29.2')] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1_glibc-fix.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1_glibc-fix.patch index 766741eb027..48e9b6e243b 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1_glibc-fix.patch +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.10.1_glibc-fix.patch @@ -1,4 +1,4 @@ -Fix Qt5.10.1 to build against newer qlibc. +Fix Qt5.10.1 to build against newer glibc. This takes the relevant part of patch from https://code.qt.io/cgit/qt/qtbase.git/commit/?id=25feee4e061b99edab79503d81f5bd045c6c8e3d Added to EasyBuild by Simon Branford (University of Birmingham) index 3469ebe5e6..c5585ea32a 100644 From 7de39f7fce2d845ece1d0538ead6e863fe9da64b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 21 Aug 2021 10:50:12 +0100 Subject: [PATCH 1001/9987] add ld.gold relocts patch to binutils 2.30 --- .../easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb | 7 ++++++- .../easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb | 7 ++++++- easybuild/easyconfigs/b/binutils/binutils-2.30.eb | 3 +++ 3 files changed, 15 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb index ed6a58e814e..562cf4dc332 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb @@ -8,10 +8,15 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['binutils-%(version)s_fix-assertion-fail-elf.patch'] +patches = [ + 'binutils-%(version)s_fix-assertion-fail-elf.patch', + 'binutils-2.31.1-gold-ignore-discarded-note-relocts.patch', +] checksums = [ '8c3850195d1c093d290a716e20ebcaa72eda32abf5e3d8611154b39cff79e9ea', # binutils-2.30.tar.gz '7a661190c973287642296dd9fb30ff45dc26ae2138f7761cd8362f7e412ff5ab', # binutils-2.30_fix-assertion-fail-elf.patch + # binutils-2.31.1-gold-ignore-discarded-note-relocts.patch + '17f22cc9136d0e81cfe8cbe310328c794a78a864e7fe7ca5827ee6678f65af32', ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb index f9766dc94cc..51db6bef353 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb @@ -8,10 +8,15 @@ toolchain = {'name': 'GCCcore', 'version': '8.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['binutils-%(version)s_fix-assertion-fail-elf.patch'] +patches = [ + 'binutils-%(version)s_fix-assertion-fail-elf.patch', + 'binutils-2.31.1-gold-ignore-discarded-note-relocts.patch', +] checksums = [ '8c3850195d1c093d290a716e20ebcaa72eda32abf5e3d8611154b39cff79e9ea', # binutils-2.30.tar.gz '7a661190c973287642296dd9fb30ff45dc26ae2138f7761cd8362f7e412ff5ab', # binutils-2.30_fix-assertion-fail-elf.patch + # binutils-2.31.1-gold-ignore-discarded-note-relocts.patch + '17f22cc9136d0e81cfe8cbe310328c794a78a864e7fe7ca5827ee6678f65af32', ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb index bb473df1b22..7b7de292ee6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30.eb @@ -12,11 +12,14 @@ sources = [SOURCE_TAR_GZ] patches = [ 'binutils-%(version)s_fix-assertion-fail-elf.patch', 'binutils-2.32_gold-include-cpp-headers.patch', + 'binutils-2.31.1-gold-ignore-discarded-note-relocts.patch', ] checksums = [ '8c3850195d1c093d290a716e20ebcaa72eda32abf5e3d8611154b39cff79e9ea', # binutils-2.30.tar.gz '7a661190c973287642296dd9fb30ff45dc26ae2138f7761cd8362f7e412ff5ab', # binutils-2.30_fix-assertion-fail-elf.patch 'cbb53f29693b06a501e8395eedc7bfdd8fec7d8a74af7482921fa51784dd1c2f', # binutils-2.32_gold-include-cpp-headers.patch + # binutils-2.31.1-gold-ignore-discarded-note-relocts.patch + '17f22cc9136d0e81cfe8cbe310328c794a78a864e7fe7ca5827ee6678f65af32', ] builddependencies = [ From 235f6a618ae2ec2b45bcfefc8b940bc48d95a3de Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Sat, 21 Aug 2021 20:35:06 +1000 Subject: [PATCH 1002/9987] Update easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb index 34b80d080b5..9b22fcf1e0f 100644 --- a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["%(namelower)s -h"] + moduleclass = 'numlib' From 789c364bc2e1f4f5e3595f44e0285aa9eb193c37 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Sat, 21 Aug 2021 20:35:16 +1000 Subject: [PATCH 1003/9987] Update easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb index 9b22fcf1e0f..08661910bc5 100644 --- a/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/TetGen/TetGen-1.6.0-GCCcore-10.2.0.eb @@ -17,8 +17,6 @@ builddependencies = [ ('binutils', '2.35'), ] -separate_build_dir = True - skipsteps = ['install'] postinstallcmds = [ From 2b4a5edbe1c97f59ceb4d07f12d0386e2db2eb09 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Aug 2021 12:42:00 +0200 Subject: [PATCH 1004/9987] add missing Python + Zip build dependencies for old Bazel versions used as build dep for TensorFlow 1.12.0 + 1.13.1 --- .../b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb | 10 ++++- .../b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb | 10 ++++- .../b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb | 1 + .../z/Zip/Zip-3.0-GCCcore-7.3.0.eb | 40 +++++++++++++++++++ 4 files changed, 57 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-7.3.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb index 5ab551a7b04..088dbc8deb5 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb @@ -15,7 +15,13 @@ checksums = [ '55fd52c512a578dc8242fbf204cf42f28aa93611910a5a791e0dda4c3a1c7d60', # Bazel-0.18.0_remove_define_DATE.patch ] -builddependencies = [('binutils', '2.30')] -dependencies = [('Java', '1.8', '', True)] +builddependencies = [ + ('binutils', '2.30'), + ('Python', '2.7.15', '-bare'), + ('Zip', '3.0'), +] +dependencies = [ + ('Java', '1.8', '', True), +] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb index ed2f9ae9dbd..c98144ae9a1 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb @@ -15,7 +15,13 @@ checksums = [ '55fd52c512a578dc8242fbf204cf42f28aa93611910a5a791e0dda4c3a1c7d60', # Bazel-0.18.0_remove_define_DATE.patch ] -builddependencies = [('binutils', '2.30')] -dependencies = [('Java', '1.8', '', True)] +builddependencies = [ + ('binutils', '2.30'), + ('Python', '2.7.15', '-bare'), + ('Zip', '3.0'), +] +dependencies = [ + ('Java', '1.8', '', True), +] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb index 44d39d8c643..72f11b4ee5b 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb @@ -17,6 +17,7 @@ checksums = [ builddependencies = [ ('binutils', '2.31.1'), + ('Python', '3.7.2'), ('Zip', '3.0'), ] dependencies = [('Java', '1.8', '', True)] diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..2de4b21bdfd --- /dev/null +++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-7.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Zip' +version = '3.0' + +homepage = 'http://www.info-zip.org/Zip.html' +description = """Zip is a compression and file packaging/archive utility. +Although highly compatible both with PKWARE's PKZIP and PKUNZIP +utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives +have been portability and other-than-MSDOS functionality""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] + +builddependencies = [ + ('binutils', '2.30'), +] +dependencies = [ + ('bzip2', '1.0.6'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' +buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' +buildopts += 'generic_gcc' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["zip --version"] + +moduleclass = 'tools' From cdd6b8c02ed4f02c603e982af4294aabefdbc082 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Sat, 21 Aug 2021 20:50:22 +1000 Subject: [PATCH 1005/9987] Create unrar-6.0.2-GCCcore-10.2.0.eb New version, new compiler --- .../u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9081313486a --- /dev/null +++ b/easybuild/easyconfigs/u/unrar/unrar-6.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'unrar' +version = '6.0.2' + +homepage = 'https://www.rarlab.com/' +description = "RAR is a powerful archive manager." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://www.rarlab.com/rar/'] +sources = ['unrarsrc-%(version)s.tar.gz'] +checksums = ['81bf188333f89c976780a477af27f651f54aa7da9312303d8d1a804696d3edd3'] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' +installopts = 'DESTDIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/unrar'], + 'dirs': [], +} + +moduleclass = 'tools' From ab0d38e843c49ef360def4e17853f105cfd85238 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 21 Aug 2021 15:11:01 +0200 Subject: [PATCH 1006/9987] Bump NSS version --- ...{NSS-3.65-GCCcore-11.2.0.eb => NSS-3.69-GCCcore-11.2.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/n/NSS/{NSS-3.65-GCCcore-11.2.0.eb => NSS-3.69-GCCcore-11.2.0.eb} (93%) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb similarity index 93% rename from easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb index 513c84318ac..ba74b4447ab 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'MakeCp' name = 'NSS' -version = '3.65' +version = '3.69' homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development @@ -15,7 +15,7 @@ patches = [ 'NSS-3.39_pkgconfig.patch', ] checksums = [ - '32170f6c188212a78bf9fdacffa2eeed0d564ef8faae63fd8ae971b208e8c637', # nss-3.65.tar.gz + 'c880205a365e0dd488ff29fdea82716ff9fcde9da6f3b703d636f8fc08008799', # nss-3.69.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch ] From 64881659bf739a1151268a14ba8fca71526c6763 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 21 Aug 2021 16:18:41 +0100 Subject: [PATCH 1007/9987] adding easyconfigs: FFTW-3.3.9-gompi-2021.07.eb, FlexiBLAS-3.0.4-GCC-11.2.0.eb, ScaLAPACK-2.1.0-gompi-2021.07-fb.eb, foss-2021.07.eb --- .../f/FFTW/FFTW-3.3.9-gompi-2021.07.eb | 17 ++++++++ .../f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 27 ++++++++++++ easybuild/easyconfigs/f/foss/foss-2021.07.eb | 27 ++++++++++++ .../ScaLAPACK-2.1.0-gompi-2021.07-fb.eb | 43 +++++++++++++++++++ 4 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.9-gompi-2021.07.eb create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2021.07.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021.07-fb.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.9-gompi-2021.07.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.9-gompi-2021.07.eb new file mode 100644 index 00000000000..97447296805 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.9-gompi-2021.07.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.9' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2021.07'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bf2c7ce40b04ae811af714deb512510cc2c17b9ab9d6ddcf49fe4487eea7af3d'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb new file mode 100644 index 00000000000..c0a4b42ebf0 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -0,0 +1,27 @@ +name = 'FlexiBLAS' +version = '3.0.4' + +homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' +description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation +used by a program without recompiling or relinking it.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" +toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} + +source_urls = ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Python', '3.9.6'), # required for running the tests +] + +# note: first listed library will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +dependencies = [ + ('OpenBLAS', '0.3.17'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/foss/foss-2021.07.eb b/easybuild/easyconfigs/f/foss/foss-2021.07.eb new file mode 100644 index 00000000000..50ec77cbbc3 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2021.07.eb @@ -0,0 +1,27 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2021.07' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '11.2.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.1.1', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.0.4', '', ('GCC', local_gccver)), + ('FFTW', '3.3.9', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.1.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021.07-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021.07-fb.eb new file mode 100644 index 00000000000..ee29d7ef99c --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021.07-fb.eb @@ -0,0 +1,43 @@ +name = 'ScaLAPACK' +version = '2.1.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2021.07'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6', # scalapack-2.1.0.tgz + 'bbb713c9fcabac802811c7f2c3a957c2d5d19dfd118ed1f6578c1436b82c7c43', # ScaLAPACK-2.1.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('FlexiBLAS', '3.0.4'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From 15e53fb5afa7dc7299db9c8d44d50168fef2a166 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 21 Aug 2021 16:19:43 +0100 Subject: [PATCH 1008/9987] adding easyconfigs: SciPy-bundle-2021.07-foss-2021.07.eb --- .../SciPy-bundle-2021.07-foss-2021.07.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb new file mode 100644 index 00000000000..e563ec41fc4 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2021.07' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'foss', 'version': '2021.07'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [('hypothesis', '6.14.6')] + +dependencies = [ + ('Python', '3.9.6'), + ('pybind11', '2.7.1'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.21.2', { + 'sources': ['%(name)s-%(version)s.zip'], + 'patches': ['numpy-1.20.3_skip-ppc-long-complex-test.patch'], + 'checksums': [ + '423216d8afc5923b15df86037c6053bf030d15cc9e3224206ef868c2d63dd6dc', # numpy-1.21.2.zip + # numpy-1.20.3_skip-ppc-long-complex-test.patch + '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4', + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.2', { + 'checksums': ['f81fcefa8b982624a31c9e4ec7761325a88a0eba60d36d1da90e47f8fe3c67f7'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.9.12.post1', { + 'checksums': ['e7589cf83b0befa9a1b55e98223caf89aff887d9e3f14be912cf8703a717f185'], + }), + ('scipy', '1.7.1', { + 'checksums': ['6b47d5fa7ea651054362561a28b1ccc8da9368a39514c1bbf6c0977a1c376764'], + }), + ('mpi4py', '3.1.1', { + 'checksums': ['e11f8587a3b93bb24c8526addec664b586b965d83c0882b884c14dc3fd6b9f5c'], + }), + ('numexpr', '2.7.3', { + 'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '1.3.2', { + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'checksums': ['cbcb84d63867af3411fa063af3de64902665bb5b3d40b25b2059e40603594e87'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From c6ea69f10e23a81fec27dce85cc53406a91c3cb7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Aug 2021 19:55:50 +0200 Subject: [PATCH 1009/9987] add patches for jaxlib and jax to fix/skip failing tests + use 'CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true' for running jax tests --- .../j/jax/jax-0.2.19-fosscuda-2020b.eb | 18 +++- .../jax-0.2.19_skip-heap-profiler-test.patch | 14 +++ ...xlib-0.1.70_fix-gpu-translation-rule.patch | 100 ++++++++++++++++++ 3 files changed, 130 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.19_skip-heap-profiler-test.patch create mode 100644 easybuild/easyconfigs/j/jax/jaxlib-0.1.70_fix-gpu-translation-rule.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index ab1419f22c5..b0b732b7292 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -64,6 +64,7 @@ components = [ 'patches': [ '%(name)s-%(version)s_add-bazel-args-to-shutdown.patch', '%(name)s-%(version)s_no-tensorflow-download.patch', + '%(name)s-%(version)s_fix-gpu-translation-rule.patch', ('TensorFlow-%s_mlir-build-env.patch' % local_tf_commit, '../' + local_tf_dir), ('TensorFlow-2.1.0_fix-cuda-build.patch', '../' + local_tf_dir), ], @@ -76,6 +77,8 @@ components = [ 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', # jaxlib-0.1.70_no-tensorflow-download.patch '1496c6be9336fb563b997f8da83d690a9b3a0a6e29fdd87fac60409300a2fd95', + # jaxlib-0.1.70_fix-gpu-translation-rule.patch + 'ce3cf8ee3b393f6580fb88bc39cc2660be46f2a48a315a3779403725ad49f946', # TensorFlow-4039feeb743bc42cd0a3d8146ce63fc05d23eb8d-build-env.patch 'd067836b1d18d66a8c69fb3db311855c8a56c0106d42a11299a1733c385e9c22', # TensorFlow-2.1.0_fix-cuda-build.patch @@ -93,8 +96,19 @@ exts_list = [ (name, version, { 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], - 'checksums': ['fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c'], - 'runtest': 'pytest -n %(parallel)s tests', + 'patches': ['jax-%(version)s_skip-heap-profiler-test.patch'], + 'checksums': [ + 'fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c', # jax-v0.2.19.tar.gz + # jax-0.2.19_skip-heap-profiler-test.patch + 'a431ce1b6588b5098872f36575dc2c5023b1010760bf6aaa889125c9a09227b0', + ], + # deliberately not testing in parallel, as that results in (additional) failing tests; + # use XLA_PYTHON_CLIENT_ALLOCATOR=platform when running GPU tests in parallel, + # to avoid each test fully allocating the GPU memory..., + # see https://github.com/google/jax/issues/7323 and + # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; + # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; + 'runtest': 'CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests', }), ] diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19_skip-heap-profiler-test.patch b/easybuild/easyconfigs/j/jax/jax-0.2.19_skip-heap-profiler-test.patch new file mode 100644 index 00000000000..7284c016b9c --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19_skip-heap-profiler-test.patch @@ -0,0 +1,14 @@ +skip this test with jax 0.2.19 + jaxlib 0.1.70, since it's broken: +RuntimeError: Invalid argument: GetOnDeviceSizeInBytes called on deleted or donated buffer +author: Kenneth Hoste (HPC-UGent) +--- jax-jax-v0.2.19/tests/heap_profiler_test.py.orig 2021-08-21 14:50:01.396950980 +0200 ++++ jax-jax-v0.2.19/tests/heap_profiler_test.py 2021-08-21 14:50:17.368215928 +0200 +@@ -27,7 +27,7 @@ + # These tests simply test that the heap profiler API does not crash; they do + # not check functional correctness. + +- def testBasics(self): ++ def disabled_testBasics(self): + client = jax.lib.xla_bridge.get_backend() + _ = client.heap_profile() + diff --git a/easybuild/easyconfigs/j/jax/jaxlib-0.1.70_fix-gpu-translation-rule.patch b/easybuild/easyconfigs/j/jax/jaxlib-0.1.70_fix-gpu-translation-rule.patch new file mode 100644 index 00000000000..10f841afd9c --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jaxlib-0.1.70_fix-gpu-translation-rule.patch @@ -0,0 +1,100 @@ +see https://github.com/google/jax/pull/7560 + +From f8081a9a529e82e6390275491b2c6d6becbb3283 Mon Sep 17 00:00:00 2001 +From: Jake VanderPlas +Date: Tue, 10 Aug 2021 10:13:29 -0700 +Subject: [PATCH] [sparse] fix GPU translation rule for coo/csr matmat + +--- + jaxlib/cusparse.py | 12 ++++++------ + tests/sparse_test.py | 18 +++++++++++++++++- + 2 files changed, 23 insertions(+), 7 deletions(-) + +diff --git a/jaxlib/cusparse.py b/jaxlib/cusparse.py +index 6264c7ba48..7e0adf21a1 100644 +--- a/jaxlib/cusparse.py ++++ b/jaxlib/cusparse.py +@@ -137,8 +137,9 @@ def csr_matmat(c, data, indices, indptr, B, *, shape, transpose=False, compute_d + dtype = np.dtype(c.get_shape(data).element_type()) + index_dtype = np.dtype(c.get_shape(indices).element_type()) + B_dtype = np.dtype(c.get_shape(B).element_type()) ++ B_shape = c.get_shape(B).dimensions() + rows, cols = shape +- _, Ccols = c.get_shape(B).dimensions() ++ _, Ccols = B_shape + nnz, = c.get_shape(data).dimensions() + + if compute_dtype is None: +@@ -154,11 +155,10 @@ def csr_matmat(c, data, indices, indptr, B, *, shape, transpose=False, compute_d + b"cusparse_csr_matmat", + operands=(data, indices, indptr, B), + operand_shapes_with_layout=( +- # All are 1D, so no layout necessary + c.get_shape(data), + c.get_shape(indices), + c.get_shape(indptr), +- c.get_shape(B), ++ _Shape.array_shape(B_dtype, B_shape, (1, 0)), + ), + shape_with_layout=_Shape.tuple_shape(( + _Shape.array_shape(compute_dtype, (out_size, Ccols), (1, 0)), +@@ -272,8 +272,9 @@ def coo_matmat(c, data, row, col, B, *, shape, transpose=False, compute_dtype=No + dtype = np.dtype(c.get_shape(data).element_type()) + index_dtype = np.dtype(c.get_shape(row).element_type()) + B_dtype = np.dtype(c.get_shape(B).element_type()) ++ B_shape = c.get_shape(B).dimensions() + rows, cols = shape +- _, Ccols = c.get_shape(B).dimensions() ++ _, Ccols = B_shape + nnz, = c.get_shape(data).dimensions() + + if compute_dtype is None: +@@ -289,11 +290,10 @@ def coo_matmat(c, data, row, col, B, *, shape, transpose=False, compute_dtype=No + b"cusparse_coo_matmat", + operands=(data, row, col, B), + operand_shapes_with_layout=( +- # All are 1D, so no layout necessary + c.get_shape(data), + c.get_shape(row), + c.get_shape(col), +- c.get_shape(B), ++ _Shape.array_shape(B_dtype, B_shape, (1, 0)), + ), + shape_with_layout=_Shape.tuple_shape(( + _Shape.array_shape(compute_dtype, (out_size, Ccols), (1, 0)), +diff --git a/tests/sparse_test.py b/tests/sparse_test.py +index 993d995afd..af30e27aec 100644 +--- a/tests/sparse_test.py ++++ b/tests/sparse_test.py +@@ -202,7 +202,6 @@ def test_coo_matvec(self, shape, dtype, transpose): + self.assertAllClose(op(M) @ v, matvec(*args), rtol=MATMUL_TOL) + self.assertAllClose(op(M) @ v, jit(matvec)(*args), rtol=MATMUL_TOL) + +- @unittest.skipIf(jtu.device_under_test() != "gpu", "test requires GPU") + @parameterized.named_parameters(jtu.cases_from_list( + {"testcase_name": "_{}_T={}".format(jtu.format_shape_dtype_string(shape, dtype), transpose), + "shape": shape, "dtype": dtype, "transpose": transpose} +@@ -229,6 +228,23 @@ def test_coo_matmat(self, shape, dtype, transpose): + y, dy = jvp(lambda x: sparse.coo_matmat(x, M.row, M.col, B, shape=shape, transpose=transpose).sum(), (M.data, ), (jnp.ones_like(M.data), )) + self.assertAllClose((op(M) @ B).sum(), y, rtol=MATMUL_TOL) + ++ def test_coo_matmat_layout(self): ++ # Regression test for https://github.com/google/jax/issues/7533 ++ d = jnp.array([1.0, 2.0, 3.0, 4.0]) ++ i = jnp.array([0, 0, 1, 2]) ++ j = jnp.array([0, 2, 0, 0]) ++ shape = (3, 3) ++ ++ x = jnp.arange(9).reshape(3, 3).astype(d.dtype) ++ ++ def f(x): ++ return sparse.coo_matmat(d, i, j, x.T, shape=shape) ++ ++ result = f(x) ++ result_jit = jit(f)(x) ++ ++ self.assertAllClose(result, result_jit) ++ + @unittest.skipIf(jtu.device_under_test() != "gpu", "test requires GPU") + def test_gpu_translation_rule(self): + version = xla_bridge.get_backend().platform_version From 4884fc01e288a8b7d45aa34ce8f5a374061247a7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 22 Aug 2021 10:15:16 +0100 Subject: [PATCH 1010/9987] Add alternative checksum for AFNI 18.3.00 --- .../a/AFNI/AFNI-18.3.00-foss-2018b-Python-3.6.6.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-18.3.00-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/AFNI/AFNI-18.3.00-foss-2018b-Python-3.6.6.eb index b2ba202d6c2..83e27995d39 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-18.3.00-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-18.3.00-foss-2018b-Python-3.6.6.eb @@ -15,7 +15,9 @@ source_urls = ['https://github.com/afni/afni/archive/'] sources = ['AFNI_%(version)s.tar.gz'] patches = ['AFNI-18.1.09_omp-pragma-statement-fix.patch'] checksums = [ - '01ecba09b1dfe270937f8cde204c18f38f9c4d543b1af3a7ccb17b04688f632d', # AFNI_18.3.00.tar.gz + # AFNI_18.3.00.tar.gz + ('01ecba09b1dfe270937f8cde204c18f38f9c4d543b1af3a7ccb17b04688f632d', + '4a22f277f271f8d2ab9680902e5e2b9e9622fdbc23c536b531f5ef9eb1882eed'), '8b739ddc09d6e398ac7fa86d89f6a02f26f2b58b17caea627d5c07de5282aab2', # AFNI-18.1.09_omp-pragma-statement-fix.patch ] From ae20e5db355b60f462387df2ba28e5a594cc7a85 Mon Sep 17 00:00:00 2001 From: Sassy Date: Sun, 22 Aug 2021 22:31:37 +0000 Subject: [PATCH 1011/9987] Some tidy up in the extension-list: replaced URLs with GITHUB_SOURCE --- .../p/pangolin/pangolin-3.1.10-foss-2020b.eb | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb index c5aa8fcad17..d96cfbd5189 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb @@ -31,45 +31,46 @@ sanity_pip_check = True github_account = 'cov-lineages' exts_list = [ ('pangolin', '3.1.11', { - 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'source_urls': [GITHUB_SOURCE], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['ce64a3ef84de5b11d5c9f21f76341cae23c0fabbf46cc3c1b7b244701b36efbc'], }), ('pangoLEARN', '2021-08-09', { 'modulename': 'pangoLEARN', - 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'source_urls': [GITHUB_SOURCE], 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['ece55bc37b3e35dbdff2432fb8b9ea76fa53fe993394a425d1df67147484a81e'], }), ('scorpio', '0.3.12', { - 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'source_urls': [GITHUB_SOURCE], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['48390ed1c1a79bb5f801083042cdeddee060e2277f40c293fd30384882aced81'], }), ('constellations', '0.0.13', { - 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'source_urls': [GITHUB_SOURCE], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['4aa3edae9491a59621ef6a3b5bbd21a13c68355986f6c097e46a1397d5b1d24b'], }), ('pango-designation', '1.2.59', { - 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'source_urls': [GITHUB_SOURCE], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['bd6c11b376c2f6955afa9e96938464184e5f6db22334589cbbbfefe1cbe35e86'], }), ] -_binaries = [ +local_binaries = [ 'constellations', 'extract_definitions.py', 'pango_designation', 'pangoLEARN', 'pangolearn.smk', 'pangolin', 'scorpio', 'type_constellations.py' ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in _binaries], + 'files': ['bin/%s' % x for x in local_binaries], 'dirs': ['lib'], } sanity_check_commands = [ - 'pangolin -pv && scorpio -v' + 'pangolin -pv', + 'scorpio -v' ] moduleclass = 'bio' From 4be772446193d60a4ab0c6cc21a296c4ce6e6c50 Mon Sep 17 00:00:00 2001 From: Sassy Date: Sun, 22 Aug 2021 22:37:43 +0000 Subject: [PATCH 1012/9987] Kent_tools added as removed from UShER PR 13694 --- easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb index d96cfbd5189..88410f8df90 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb @@ -23,6 +23,7 @@ dependencies = [ ('snakemake', '6.1.0'), ('UShER', '0.4.1'), ('scikit-learn', '0.23.2'), + ('Kent_tools', '411'), ] use_pip = True From b178406e2aa6820a850f2e8004b79aec81e23fdf Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 23 Aug 2021 09:30:36 +0200 Subject: [PATCH 1013/9987] adding easyconfigs: PyTorch-Geometric-1.6.3-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb, PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb, torchvision-0.9.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb, pybind11-2.6.0-GCCcore-8.3.0-Python-3.7.4.eb --- ...sscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb | 59 ++++++++ ...Torch-1.8.1-fosscuda-2019b-Python-3.7.4.eb | 128 ++++++++++++++++++ ...bind11-2.6.0-GCCcore-8.3.0-Python-3.7.4.eb | 24 ++++ ...sscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb | 26 ++++ 4 files changed, 237 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-8.3.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.9.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb new file mode 100644 index 00000000000..b53fec4e9c1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-1.6.3-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '1.6.3' +local_pytorch_ver = '1.8.1' +versionsuffix = '-Python-%%(pyver)s-PyTorch-%s' % local_pytorch_ver + +homepage = 'https://github.com/rusty1s/pytorch_geometric' +description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch." + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +local_pysuff = '-Python-%(pyver)s' +dependencies = [ + ('Python', '3.7.4'), + ('PyTorch', local_pytorch_ver, local_pysuff), + ('scikit-learn', '0.21.3', local_pysuff), + ('scikit-image', '0.16.2', local_pysuff), + ('numba', '0.47.0', local_pysuff), + ('h5py', '2.10.0', local_pysuff), + ('RDFlib', '4.2.2'), + ('tqdm', '4.41.1'), + ('ASE', '3.19.0', local_pysuff), +] + +use_pip = True + +exts_list = [ + ('googledrivedownloader', '0.4', { + 'modulename': 'google_drive_downloader', + 'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'], + }), + ('plyfile', '0.7.3', { + 'checksums': ['5ac55b685cfcb3e8f70f3c5c2660bd1f6431a892a5319a612792b1ec09aec0f0'], + }), + ('torch_scatter', '2.0.8', { + 'checksums': ['d71aab489b5288a6c96e9f9a7c9e13c54774dcb55a99a40e6cd1aca8be9ef3e6'], + }), + ('torch_sparse', '0.6.11', { + 'checksums': ['1d57bc0fc9d9b6cfdc9dcc12017dc371c89c901e5d7a73e6149c8b866eca1267'], + }), + ('torch_cluster', '1.5.9', { + 'checksums': ['96209e9f3f073c8e7fe91fbf7dd2cdd8655622d14dfc95a7618b4893a658dca5'], + }), + ('torch_spline_conv', '1.2.1', { + 'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'], + }), + ('python-louvain', '0.15', { + 'checksums': ['2a856edfbe29952a60a5538a84bb78cca18f6884a88b9325e85a11c8dd4917eb'], + 'modulename': 'community.community_louvain', + }), + ('torch_geometric', version, { + 'checksums': ['347f693bebcc8a621eda4867dafab91c04db5f596d7ed7ecb89b242f8ab5c6a1'], + }), +] + +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..1b35df7a84f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,128 @@ +name = 'PyTorch' +version = '1.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch', + 'PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.8.0_correct-skip-tests-decorators.patch', + 'PyTorch-1.8.0_fix-noMKL-linear-algebra.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_fix-arange-on-VSX.patch', + 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.8.1_fix-testnn-on-A100.patch', + 'PyTorch-1.8.1_fix-vsx-vector-functions.patch', + 'PyTorch-1.8.1_honor_shared_cupti-setting.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.8.1_limit_world_size_for_zero_redundancy_opt_test.patch', + 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', + 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', + 'PyTorch-1.8.1_skip-nccl-error-tests.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + # PyTorch-1.7.1_disable-tf32-in-distributed-tests.patch + '18ecad081a8c940add64040ad9698d3273366acf738a8a44eab1c793d3f49950', + # PyTorch-1.7.1_fix-alias-violation-in-bitwise-ops.patch + 'e92f054f1297df83ace901e7af38222787b709ee29580f5f2b89a300ca03666b', + # PyTorch-1.7.1_fix-use-after-destruct-in-cudaipctypes.patch + '250345aad08fb72deaaee9b249d9661d4ce93d08661b32d7856ed57e4aa8142e', + # PyTorch-1.8.0_correct-skip-tests-decorators.patch + 'eb0ca83e88196cc5cf9bc8a50f6ee4c7fd4ae045ab0d549896b82b0526ee50f9', + 'a1ca9382b0eb333090536633092bab6fa281d26b491bf7b1849117f68ab0730c', # PyTorch-1.8.0_fix-noMKL-linear-algebra.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + 'eca718ce0ecc61b57659808179cc660919b3c25b5dce326f51c1cc5a5bfb9829', # PyTorch-1.8.1_fix-arange-on-VSX.patch + # PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch + '1601eacd336e01176bdbdbc5a2207743dc2999b535a738a8e36b3da3e8a2f3b6', + '241561a0497dd27adffd71b8b0815be1fe924800f4ee336d95e0cc3881fac98b', # PyTorch-1.8.1_fix-testnn-on-A100.patch + 'a8fcb63cf963dc743e8b0a96b966f18d8edde6a4e76365d6de56aa2c71ce6d3f', # PyTorch-1.8.1_fix-vsx-vector-functions.patch + # PyTorch-1.8.1_honor_shared_cupti-setting.patch + 'a6459fe544f9e2b61ab09ba54e8db5b294176ffdbf41c99e0d0b678e1e617b8f', + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', + # PyTorch-1.8.1_limit_world_size_for_zero_redundancy_opt_test.patch + 'c3488fa24405eac6e2e36fbdf94e877bd39fd177e92fb3a0b6bbd5c8b7ddc7bc', + # PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch + 'b0000aa9e028ad24ac4bb62d42db9e56ab78818e812aa4a4943a4456505927c7', + # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch + '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', + '33704164ad2da7426a6c21482389826345b92690d37cbf938896eef421a62575', # PyTorch-1.8.1_skip-nccl-error-tests.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.15.3'), + ('hypothesis', '4.44.2', versionsuffix), +] + +dependencies = [ + ('Ninja', '1.9.0'), # Required for JIT compilation of C++ extensions + ('Python', '3.7.4'), + ('protobuf', '3.10.0'), + ('protobuf-python', '3.10.0', versionsuffix), + ('pybind11', '2.6.0', versionsuffix), + ('SciPy-bundle', '2019.10', versionsuffix), + ('typing-extensions', '3.7.4.3', versionsuffix), + ('PyYAML', '5.1.2'), + ('MPFR', '4.0.2'), + ('GMP', '6.1.2'), + ('numactl', '2.0.12'), + ('FFmpeg', '4.2.1'), + ('Pillow', '6.2.1'), + ('cuDNN', '7.6.2.24', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.4.8'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + 'POWER': [ + # https://github.com/pytorch/pytorch/issues/57617 + 'test_autograd', + ], + '': [ + # Test from this suite timeout often. The process group backend is deprecated anyway + 'distributed/rpc/test_process_group_agent', + # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! + # https://github.com/pytorch/pytorch/issues/43209 + 'test_quantization', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..fbde075fe2e --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,24 @@ +name = 'pybind11' +version = '2.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571'] + +builddependencies = [ + ('binutils', '2.32'), + ('CMake', '3.15.3'), + ('Eigen', '3.3.7', '', True), +] +dependencies = [('Python', '3.7.4')] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.9.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.9.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb new file mode 100644 index 00000000000..875fe8a1d47 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.9.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb @@ -0,0 +1,26 @@ +name = 'torchvision' +version = '0.9.1' +local_pytorch_version = '1.8.1' +versionsuffix = '-Python-%%(pyver)s-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['79964773729880e0eee0e6af13f336041121d4cc8491a3e2c0e5f184cac8a718'] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('Python', '3.7.4'), + ('Pillow-SIMD', '6.0.x.post0'), + ('PyTorch', local_pytorch_version, '-Python-%(pyver)s'), +] + +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] + +moduleclass = 'vis' From b6cea6da6461fe25367da85aae589f98a8ff94b8 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 23 Aug 2021 09:37:47 +0200 Subject: [PATCH 1014/9987] adding easyconfigs: dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb, PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb, lie_learn-0.0.1.post1-fosscuda-2019b-Python-3.7.4.eb and patches: lie_learn-0.0.1.post1_no_cython.patch --- ...sscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb | 32 +++++++++++++++++ ...0.0.1.post1-fosscuda-2019b-Python-3.7.4.eb | 34 ++++++++++++++++++ .../lie_learn-0.0.1.post1_no_cython.patch | 35 +++++++++++++++++++ ....release-292-GCCcore-8.3.0-Python-3.7.4.eb | 29 +++++++++++++++ 4 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/d/dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb create mode 100644 easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1_no_cython.patch create mode 100644 easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/d/dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb b/easybuild/easyconfigs/d/dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb new file mode 100644 index 00000000000..314c8888859 --- /dev/null +++ b/easybuild/easyconfigs/d/dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'dgl' +version = '0.6.1' +local_pytorch_version = '1.8.1' +local_pysuff = '-Python-%(pyver)s' +versionsuffix = local_pysuff + '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://dgl.ai' +description = """DGL is an easy-to-use, high performance and scalable Python package for deep learning on graphs. +DGL is framework agnostic, meaning if a deep graph model is a component of an end-to-end application, the rest +of the logics can be implemented in any major frameworks, such as PyTorch, Apache MXNet or TensorFlow.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s_cu101'] +sources = ['%(name)s_cu101-%(version)s-cp37-cp37m-manylinux1_%(arch)s.whl'] + +checksums = ['6dbc7830fec82f29d4f884790290fef41c2cea45b0052748af2ec30679cf9cb2'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', local_pysuff), + ('networkx', '2.4', local_pysuff), + ('PyTorch', local_pytorch_version, local_pysuff), +] + +use_pip = True + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..6ffd3ccf718 --- /dev/null +++ b/easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'lie_learn' +version = '0.0.1.post1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/AMLab-Amsterdam/lie_learn' +description = """lie_learn is a python package that knows how to do various tricky computations +related to Lie groups and manifolds (mainly the sphere S2 and rotation group SO3).""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +github_account = 'AMLab-Amsterdam' + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +patches = [ + 'lie_learn-0.0.1.post1_no_cython.patch', +] + +checksums = [ + 'de8f5dcb387bf39ba7470830b86b9085ceaaedf07392629ff512c76571dc6020', # lie_learn-0.0.1.post1.tar.gz + '82931c5db79160d3b4943bb5e081abd53bc91d6a950e9cee9a3d85e9eb329e05', # lie_learn-0.0.1.post1_no_cython.patch +] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1_no_cython.patch b/easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1_no_cython.patch new file mode 100644 index 00000000000..74cc2cd8b75 --- /dev/null +++ b/easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1_no_cython.patch @@ -0,0 +1,35 @@ +Using cython for extensions breaks builds +author: Christoph Siegert (Leipzig University) + +diff -ruN lie_learn-0.0.1.post1.orig/setup.py lie_learn-0.0.1.post1/setup.py +--- lie_learn-0.0.1.post1.orig/setup.py 2021-08-18 18:01:14.428449724 +0200 ++++ lie_learn-0.0.1.post1/setup.py 2021-08-18 18:13:33.294356898 +0200 +@@ -4,13 +4,6 @@ + + from setuptools import dist, find_packages, setup, Extension + +-try: +- from Cython.Build import cythonize +- +- use_cython = True +-except ImportError: +- use_cython = False +- + if sys.version_info[0] < 3: + setup_requires_list = ['numpy<1.17'] + else: +@@ -20,13 +13,9 @@ + + import numpy as np + +-ext = '.pyx' if use_cython else '.c' ++ext = '.c' + files = glob.glob('lie_learn/**/*' + ext, recursive=True) + extensions = [Extension(file.split('.')[0].replace('/', '.'), [file]) for file in files] +-if use_cython: +- from Cython.Build import cythonize +- +- extensions = cythonize(extensions) + + setup( + name='lie_learn', diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..2b44b28bb96 --- /dev/null +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyRosetta' +version = '4.release-292' +versionsuffix = '-Python-%(pyver)s' +description = """PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. +It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods +and energy functions.""" +homepage = 'https://www.pyrosetta.org/' + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +sources = ['%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2'] + +checksums = [ + # PyRosetta4.Release.python37.linux.release-290.tar.bz2 + 'bffe04acb515628200129ded6f0a2ceeeef70f71d59c041f4390764954acac02' +] + +dependencies = [ + ('Python', '3.7.4'), +] + +start_dir = "setup" + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' From 4aa36254e393de1b74f4651484a94a20a4ee8b02 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 23 Aug 2021 09:50:28 +0200 Subject: [PATCH 1015/9987] set download_dep_fail --- .../dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb | 2 +- .../lie_learn-0.0.1.post1-fosscuda-2019b-Python-3.7.4.eb | 3 ++- .../PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb | 1 + 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb b/easybuild/easyconfigs/d/dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb index 314c8888859..fb3fd04fd0f 100644 --- a/easybuild/easyconfigs/d/dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/d/dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb @@ -25,8 +25,8 @@ dependencies = [ ('PyTorch', local_pytorch_version, local_pysuff), ] +download_dep_fail = True use_pip = True - sanity_pip_check = True moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1-fosscuda-2019b-Python-3.7.4.eb index 6ffd3ccf718..c1adcc652a5 100644 --- a/easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/l/lie_learn/lie_learn-0.0.1.post1-fosscuda-2019b-Python-3.7.4.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'fosscuda', 'version': '2019b'} github_account = 'AMLab-Amsterdam' sources = [SOURCE_TAR_GZ] -source_urls = [PYPI_SOURCE] patches = [ 'lie_learn-0.0.1.post1_no_cython.patch', @@ -28,6 +27,8 @@ dependencies = [ ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), ] + +download_dep_fail = True use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb index 2b44b28bb96..340dd1c8232 100644 --- a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb @@ -23,6 +23,7 @@ dependencies = [ start_dir = "setup" +download_dep_fail = True use_pip = True sanity_pip_check = True From 67243cc7b0d06237f6f866b31efeeab031244a97 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 23 Aug 2021 10:10:28 +0200 Subject: [PATCH 1016/9987] add binutils as build dependency --- .../PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb index 340dd1c8232..f7cb8335e05 100644 --- a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb @@ -13,10 +13,11 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} sources = ['%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2'] checksums = [ - # PyRosetta4.Release.python37.linux.release-290.tar.bz2 'bffe04acb515628200129ded6f0a2ceeeef70f71d59c041f4390764954acac02' ] +builddependencies = [('binutils', '2.3.2')] + dependencies = [ ('Python', '3.7.4'), ] From c2a3875a83e33acc252c61fb44eeacbf96fafadd Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 23 Aug 2021 10:43:55 +0200 Subject: [PATCH 1017/9987] fix binutils version --- .../PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb index f7cb8335e05..7ce568784c4 100644 --- a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb @@ -16,7 +16,7 @@ checksums = [ 'bffe04acb515628200129ded6f0a2ceeeef70f71d59c041f4390764954acac02' ] -builddependencies = [('binutils', '2.3.2')] +builddependencies = [('binutils', '2.32')] dependencies = [ ('Python', '3.7.4'), From ccd952865f9fee07c23e516fe58df2c23beb7c6d Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 23 Aug 2021 11:02:49 +0200 Subject: [PATCH 1018/9987] adding easyconfigs: lddt-1.2.eb, psipred-4.02-GCC-8.3.0.eb, csblast-2.2.3-GCCcore-8.3.0.eb and patches: psipred-4.02_fix_segfault.patch --- .../c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb | 33 +++++++++++++++ easybuild/easyconfigs/l/lddt/lddt-1.2.eb | 23 ++++++++++ .../p/psipred/psipred-4.02-GCC-8.3.0.eb | 32 ++++++++++++++ .../p/psipred/psipred-4.02_fix_segfault.patch | 42 +++++++++++++++++++ 4 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/l/lddt/lddt-1.2.eb create mode 100644 easybuild/easyconfigs/p/psipred/psipred-4.02-GCC-8.3.0.eb create mode 100644 easybuild/easyconfigs/p/psipred/psipred-4.02_fix_segfault.patch diff --git a/easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..46fdc61a823 --- /dev/null +++ b/easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'csblast' +version = '2.2.3' + +homepage = 'https://github.com/soedinglab/csblast/' +description = """Context-specific extension of BLAST that significantly improves sensitivity and alignment quality.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +github_account = 'soedinglab' +sources = ['v%(version)s.tar.gz'] +source_urls = [GITHUB_SOURCE] +checksums = ['3cf8dc251e85af6942552eae3d33e45a5a1c6d73c5e7f1a00ce26d6974c0d434'] # csblast-2.2.3.tar.gz + +dependencies = [ + ('sparsehash', '2.0.3'), +] + +start_dir = 'src' + +build_cmd_targets = 'csblast csbuild' + +buildopts = 'FLAGS=-fpermissive' + +files_to_copy = ['bin', 'data', 'LICENSE', 'README_CSBLAST'] + +sanity_check_paths = { + 'files': ['bin/csblast', 'bin/csbuild', 'data/K4000.crf', 'data/K4000.lib'], + 'dirs': ['bin', 'data'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lddt/lddt-1.2.eb b/easybuild/easyconfigs/l/lddt/lddt-1.2.eb new file mode 100644 index 00000000000..ed4ea8a1ca5 --- /dev/null +++ b/easybuild/easyconfigs/l/lddt/lddt-1.2.eb @@ -0,0 +1,23 @@ +easyblock = 'Tarball' + +name = 'lddt' +version = '1.2' + +homepage = 'https://openstructure.org' +description = """The local Distance Difference Test (lDDT) is a superposition-free score which evaluates local distance +differences in a model compared to a reference structure.""" + +toolchain = SYSTEM + +source_urls = ['https://openstructure.org/static/'] +sources = ['%(name)s-linux.zip'] +checksums = ['3f4f72dc790f64431d29f7ff04353d3bbade8c8c12a487a1a99240a82fc4fcec'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['lddt', 'stereo_chemical_props.txt'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/psipred/psipred-4.02-GCC-8.3.0.eb b/easybuild/easyconfigs/p/psipred/psipred-4.02-GCC-8.3.0.eb new file mode 100644 index 00000000000..e1202b90bd9 --- /dev/null +++ b/easybuild/easyconfigs/p/psipred/psipred-4.02-GCC-8.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'psipred' +version = '4.02' + +homepage = 'http://bioinf.cs.ucl.ac.uk' +description = 'Accurate protein secondary structure prediction' + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +sources = ['%(name)s.%(version)s.tar.gz'] +source_urls = ['http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/'] + +patches = ['psipred-4.02_fix_segfault.patch'] + +checksums = [ + 'b4009b6a5f8b76c6d60ac91c4a743512d844864cf015c492fb6d1dc0d092c467', # psipred.4.02.tar.gz + 'd9e52ecf43b04640ebd0693df37871659d598abaec7a2c66264e9a79ee1baa82', # psipred-4.02_fix_segfault.patch +] + +parallel = 1 +start_dir = 'src' +build_cmd_targets = 'all install' # install copies binaries to ../bin + +files_to_copy = ['bin', 'data', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/chkparse', 'bin/psipass2', 'bin/psipred', 'bin/seq2mtx'], + 'dirs': ['bin', 'data'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/psipred/psipred-4.02_fix_segfault.patch b/easybuild/easyconfigs/p/psipred/psipred-4.02_fix_segfault.patch new file mode 100644 index 00000000000..0826c775f5d --- /dev/null +++ b/easybuild/easyconfigs/p/psipred/psipred-4.02_fix_segfault.patch @@ -0,0 +1,42 @@ +Fixes a segmentation fault for inputs with lines longer than 254 characters +author: Christoph Siegert (Leipzig University) + +diff --git a/src/sspred_avpred.c b/src/sspred_avpred.c +index a6af260..a68b653 100644 +--- a/src/sspred_avpred.c ++++ b/src/sspred_avpred.c +@@ -44,6 +44,8 @@ int seqlen; + + char seq[MAXSEQLEN]; + ++char buf[4096]; ++ + enum aacodes + { + ALA, ARG, ASN, ASP, CYS, +@@ -238,7 +240,6 @@ predict(int argc, char **argv) + int getmtx(FILE *lfil) + { + int aa, i, j, naa; +- char buf[256], *p; + + if (fscanf(lfil, "%d", &naa) != 1) + fail("Bad mtx file - no sequence length!"); +@@ -251,7 +252,7 @@ int getmtx(FILE *lfil) + + while (!feof(lfil)) + { +- if (!fgets(buf, 65536, lfil)) ++ if (!fgets(buf, sizeof(buf), lfil)) + fail("Bad mtx file!"); + if (!strncmp(buf, "-32768 ", 7)) + { +@@ -262,7 +263,7 @@ int getmtx(FILE *lfil) + aa = aanum(seq[j]); + if (aa < 20) + profile[j][aa] += 0000; +- if (!fgets(buf, 65536, lfil)) ++ if (!fgets(buf, sizeof(buf), lfil)) + break; + } + } From ec9b639b3a46a7a8663e713d93c6e1cccd49b7a5 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 23 Aug 2021 11:20:40 +0200 Subject: [PATCH 1019/9987] add binutils build dependency --- .../easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb index 46fdc61a823..8159f8bbf4c 100644 --- a/easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb @@ -13,6 +13,10 @@ sources = ['v%(version)s.tar.gz'] source_urls = [GITHUB_SOURCE] checksums = ['3cf8dc251e85af6942552eae3d33e45a5a1c6d73c5e7f1a00ce26d6974c0d434'] # csblast-2.2.3.tar.gz +builddependencies = [ + ('binutils', '2.32'), +] + dependencies = [ ('sparsehash', '2.0.3'), ] From f163e7baa58b5839ee83102dd41add0c4dab7af5 Mon Sep 17 00:00:00 2001 From: software Date: Mon, 23 Aug 2021 10:07:53 +0000 Subject: [PATCH 1020/9987] Port update to other recent R easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 12 ++++++++++++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 12 ++++++++++++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 12 ++++++++++++ easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 12 ++++++++++++ 4 files changed, 48 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 1bb5fc2a92f..2fa4574e87b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -2944,6 +2944,18 @@ exts_list = [ ('naturalsort', '0.1.3', { 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], }), + ('finalfit', '1.0.3', { + 'checksums': ['bbfa841a2b1a7b1f8c153d773ff076a2e465e451815f8166ff0ce8c4018ff61e'], + }), + ('broom.helpers', '1.3.0', { + 'checksums': ['e02531f37a3cd56513ec3a9a083070b5f0ec9b438b2cc7d8e036f7bcedfeb7b0'], + }), + ('gt', '0.3.1', { + 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], + }), + ('gtsummary', '1.4.2', { + 'checksums': ['3fe958077df9e604bf536eeda73eb825ee6ae7fcac716b7a42d5a9d867bd4122'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 172d381e034..10ac6803faa 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -2948,6 +2948,18 @@ exts_list = [ ('naturalsort', '0.1.3', { 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], }), + ('finalfit', '1.0.3', { + 'checksums': ['bbfa841a2b1a7b1f8c153d773ff076a2e465e451815f8166ff0ce8c4018ff61e'], + }), + ('broom.helpers', '1.3.0', { + 'checksums': ['e02531f37a3cd56513ec3a9a083070b5f0ec9b438b2cc7d8e036f7bcedfeb7b0'], + }), + ('gt', '0.3.1', { + 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], + }), + ('gtsummary', '1.4.2', { + 'checksums': ['3fe958077df9e604bf536eeda73eb825ee6ae7fcac716b7a42d5a9d867bd4122'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 22c4fba720b..a4b74635831 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -2959,6 +2959,18 @@ exts_list = [ ('naturalsort', '0.1.3', { 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], }), + ('finalfit', '1.0.3', { + 'checksums': ['bbfa841a2b1a7b1f8c153d773ff076a2e465e451815f8166ff0ce8c4018ff61e'], + }), + ('broom.helpers', '1.3.0', { + 'checksums': ['e02531f37a3cd56513ec3a9a083070b5f0ec9b438b2cc7d8e036f7bcedfeb7b0'], + }), + ('gt', '0.3.1', { + 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], + }), + ('gtsummary', '1.4.2', { + 'checksums': ['3fe958077df9e604bf536eeda73eb825ee6ae7fcac716b7a42d5a9d867bd4122'], + }), # Specific packages for GPUs ('OpenCL', '0.2-1', { 'checksums': ['5cc80395bf3c28a27ff124e3d602e8037487f8f6d1800ccb6c145eb432c716ae'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index 8df95932d40..99150e5d53e 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -2984,6 +2984,18 @@ exts_list = [ ('lwgeom', '0.2-7', { 'checksums': ['b34c155f3d7c4535ef3d02e3381b05a57990d19b3b1ec09a7458c101f8fafae1'], }), + ('finalfit', '1.0.3', { + 'checksums': ['bbfa841a2b1a7b1f8c153d773ff076a2e465e451815f8166ff0ce8c4018ff61e'], + }), + ('broom.helpers', '1.3.0', { + 'checksums': ['e02531f37a3cd56513ec3a9a083070b5f0ec9b438b2cc7d8e036f7bcedfeb7b0'], + }), + ('gt', '0.3.1', { + 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], + }), + ('gtsummary', '1.4.2', { + 'checksums': ['3fe958077df9e604bf536eeda73eb825ee6ae7fcac716b7a42d5a9d867bd4122'], + }), ] moduleclass = 'lang' From 1358f85551331059584e1c8f186a1f48bf6b3095 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 23 Aug 2021 12:30:35 +0200 Subject: [PATCH 1021/9987] adding easyconfigs: neptune-client-0.10.5-foss-2020b.eb --- .../neptune-client-0.10.5-foss-2020b.eb | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb new file mode 100644 index 00000000000..f0f48378f5f --- /dev/null +++ b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb @@ -0,0 +1,80 @@ +easyblock = 'PythonBundle' + +name = 'neptune-client' +version = '0.10.5' + +homepage = 'https://docs.neptune.ai' +description = """ +Neptune is an experiment tracking hub that brings organization and collaboration to your data science team. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('GitPython', '3.1.14'), + ('Pillow-SIMD', '7.1.2'), + ('PyYAML', '5.3.1'), +] + +use_pip = True + +exts_list = [ + ('monotonic', '1.6', { + 'checksums': ['3a55207bcfed53ddd5c5bae174524062935efed17792e9de2ad0205ce9ad63f7'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('pyrsistent', '0.18.0', { + 'checksums': ['773c781216f8c2900b42a7b638d5b517bb134ae1acbebe4d1e8f1f41ea60eb4b'], + }), + ('swagger-spec-validator', '2.7.3', { + 'checksums': ['f4f23ee4dbd52bfcde90b1144dde22304add6260e9f29252e9fd7814c9b8fd16'], + }), + ('jsonref', '0.2', { + 'checksums': ['f3c45b121cf6257eafabdc3a8008763aed1cd7da06dbabc59a9e4d2a5e4e6697'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('simplejson', '3.17.4', { + 'checksums': ['2af85e028714c4b6cb2eb6fc03aa91f39ffd654f2eb2f6f8f860e14aeefa6be1'], + }), + ('typing-extensions', '3.10.0.0', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342'], + }), + ('bravado-core', '5.17.0', { + 'checksums': ['b3b06ae86d3c80de5694340e55df7c9097857ff965b76642979e2a961f332abf'], + }), + ('bravado', '11.0.3', { + 'checksums': ['1bb6ef75d84140c851fffe6420baaee5037d840070cfe11d60913be6ab8e0530'], + }), + ('PyJWT', '2.1.0', { + 'modulename': 'jwt', + 'checksums': ['fba44e7898bbca160a2b2b501f492824fc8382485d3a6f11ba5d0c1937ce6130'], + }), + ('blinker', '1.4', { + 'checksums': ['471aee25f3992bd325afa3772f1063dbdbbca947a041b8b89466dc00d606f8b6'], + }), + ('oauthlib', '3.1.1', { + 'checksums': ['8f0215fcc533dd8dd1bee6f4c412d4f0cd7297307d43ac61666389e3bc3198a3'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('websocket-client', '0.59.0', { + 'modulename': 'websocket', + 'checksums': ['d376bd60eace9d437ab6d7ee16f4ab4e821c9dae591e1b783c58ebd8aaf80c5c'], + }), + (name, version, { + 'modulename': 'neptune', + 'checksums': ['cb534c0db8e9fc6c6f1f578943ce76fd46d16fb42c6fbc2e2fa2e92b5125ef5e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 1b441e682bc6d883274c81b5cec4aa51e8773c86 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 23 Aug 2021 12:55:17 +0200 Subject: [PATCH 1022/9987] Using existing pybind11 as it seems to work for PyTorch 1.8.1 --- ...Torch-1.8.1-fosscuda-2019b-Python-3.7.4.eb | 2 +- ...bind11-2.6.0-GCCcore-8.3.0-Python-3.7.4.eb | 24 ------------------- 2 files changed, 1 insertion(+), 25 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb index 1b35df7a84f..30da3e979e0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb @@ -87,7 +87,7 @@ dependencies = [ ('Python', '3.7.4'), ('protobuf', '3.10.0'), ('protobuf-python', '3.10.0', versionsuffix), - ('pybind11', '2.6.0', versionsuffix), + ('pybind11', '2.4.3', versionsuffix), ('SciPy-bundle', '2019.10', versionsuffix), ('typing-extensions', '3.7.4.3', versionsuffix), ('PyYAML', '5.1.2'), diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-8.3.0-Python-3.7.4.eb deleted file mode 100644 index fbde075fe2e..00000000000 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-8.3.0-Python-3.7.4.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'pybind11' -version = '2.6.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://pybind11.readthedocs.io' -description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, - mainly to create Python bindings of existing C++ code.""" - -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} - -source_urls = ['https://github.com/pybind/pybind11/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571'] - -builddependencies = [ - ('binutils', '2.32'), - ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), -] -dependencies = [('Python', '3.7.4')] - -configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" - -moduleclass = 'lib' From 926f9e6bd460db07cc2bcbe702c5e754326f9ee0 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 23 Aug 2021 12:59:16 +0200 Subject: [PATCH 1023/9987] adding easyconfigs: HH-suite-3.2.0-fosscuda-2019b.eb --- .../HH-suite/HH-suite-3.2.0-fosscuda-2019b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/HH-suite/HH-suite-3.2.0-fosscuda-2019b.eb diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.2.0-fosscuda-2019b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.2.0-fosscuda-2019b.eb new file mode 100644 index 00000000000..65e1c4e22b6 --- /dev/null +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.2.0-fosscuda-2019b.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'CMakeMake' + +name = "HH-suite" +version = "3.2.0" + +homepage = 'https://github.com/soedinglab/hh-suite' +description = """HH-suite is an open-source software package for sensitive protein sequence searching. + It contains programs that can search for similar protein sequences in protein sequence databases.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'openmp': True} + +source_urls = ["https://github.com/soedinglab/hh-suite/archive"] +sources = ["v%(version)s.tar.gz"] +checksums = ['6b870dcfbc1ffb9dd664a45415fcd13cf5970f49d1c7b824160c260fa138e6d6'] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +dependencies = [ + ('libpng', '1.6.37'), +] + +sanity_check_paths = { + 'files': ["bin/hhalign", "bin/hhblits", "bin/hhconsensus", "bin/hhfilter", "bin/hhmake", "bin/hhsearch"], + 'dirs': [] +} + +moduleclass = 'bio' From 58a958c745bcc4e7860bb4a297b6a0bed5f56ddf Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 23 Aug 2021 13:17:17 +0200 Subject: [PATCH 1024/9987] adding easyconfigs: Bazel-3.7.2-GCCcore-10.3.0.eb --- .../b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3a938da6095 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +name = 'Bazel' +version = '3.7.2' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = [ + '%(name)s-3.4.1-fix-grpc-protoc.patch', + '%(name)s-%(version_major_minor)s.1_fix-protobuf-env.patch', +] +checksums = [ + 'de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1', # %(namelower)s-%(version)s-dist.zip + 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', # %(name)s-3.4.1-fix-grpc-protoc.patch + '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', # %(name)s-%(version_major_minor)s.1_fix-protobuf-env.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), + ('Zip', '3.0'), +] +dependencies = [ + ('Java', '11', '', True), +] + +runtest = True +testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." + +moduleclass = 'devel' From 12b82a13b43f756cbc41ae1b84d97d7135f31976 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 23 Aug 2021 13:18:14 +0200 Subject: [PATCH 1025/9987] added exception for llvm dependency as PyTorch-Geometric requires numba --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 6424e7a3806..297b7b9488b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -443,7 +443,7 @@ def check_dep_vars(self, gen, dep, dep_vars): 'LLVM': [ # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) (r'8\.', [r'numba-0\.47\.0-', r'librosa-0\.7\.2-', r'BirdNET-20201214-', - r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[34]\.2']), + r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[346]\.[23]']), (r'10\.0\.1', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), From c1c8e081a2b23a8e86c8318375d7ce1a726491fd Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 23 Aug 2021 13:39:33 +0200 Subject: [PATCH 1026/9987] Use cuDNN from toolchain instead of SYSTEM --- .../p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb index 30da3e979e0..1dbf4cc53fb 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb @@ -96,7 +96,7 @@ dependencies = [ ('numactl', '2.0.12'), ('FFmpeg', '4.2.1'), ('Pillow', '6.2.1'), - ('cuDNN', '7.6.2.24', '-CUDA-%(cudaver)s', True), + ('cuDNN', '7.6.4.38'), ('magma', '2.5.4'), ('NCCL', '2.4.8'), ] From 8166fea7f06de89055bcaa08b0f9657379f57e08 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 23 Aug 2021 14:34:22 +0200 Subject: [PATCH 1027/9987] remove extensions in base Python from neptune-client-0.10.5-foss-2020b.eb --- .../neptune-client-0.10.5-foss-2020b.eb | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb index f0f48378f5f..e48419cb64a 100644 --- a/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb +++ b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.10.5-foss-2020b.eb @@ -24,24 +24,12 @@ exts_list = [ ('monotonic', '1.6', { 'checksums': ['3a55207bcfed53ddd5c5bae174524062935efed17792e9de2ad0205ce9ad63f7'], }), - ('msgpack', '1.0.2', { - 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], - }), - ('pyrsistent', '0.18.0', { - 'checksums': ['773c781216f8c2900b42a7b638d5b517bb134ae1acbebe4d1e8f1f41ea60eb4b'], - }), ('swagger-spec-validator', '2.7.3', { 'checksums': ['f4f23ee4dbd52bfcde90b1144dde22304add6260e9f29252e9fd7814c9b8fd16'], }), ('jsonref', '0.2', { 'checksums': ['f3c45b121cf6257eafabdc3a8008763aed1cd7da06dbabc59a9e4d2a5e4e6697'], }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), - ('simplejson', '3.17.4', { - 'checksums': ['2af85e028714c4b6cb2eb6fc03aa91f39ffd654f2eb2f6f8f860e14aeefa6be1'], - }), ('typing-extensions', '3.10.0.0', { 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', 'checksums': ['50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342'], From 5ec098591716eb123ffc47b40c526044a816872a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 23 Aug 2021 13:42:14 +0100 Subject: [PATCH 1028/9987] adding easyconfigs: SyRI-1.4-foss-2021a.eb, longestrunsubsequence-1.0.1-GCCcore-10.3.0.eb and patches: SyRI-1.4_install-scripts.patch --- ...gestrunsubsequence-1.0.1-GCCcore-10.3.0.eb | 37 +++++++++++++++++ .../easyconfigs/s/SyRI/SyRI-1.4-foss-2021a.eb | 40 +++++++++++++++++++ .../s/SyRI/SyRI-1.4_install-scripts.patch | 11 +++++ 3 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/l/longestrunsubsequence/longestrunsubsequence-1.0.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/SyRI/SyRI-1.4-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/SyRI/SyRI-1.4_install-scripts.patch diff --git a/easybuild/easyconfigs/l/longestrunsubsequence/longestrunsubsequence-1.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/longestrunsubsequence/longestrunsubsequence-1.0.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e6ae8843126 --- /dev/null +++ b/easybuild/easyconfigs/l/longestrunsubsequence/longestrunsubsequence-1.0.1-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +# Author: Jasper Grimm + +easyblock = 'PythonBundle' + +name = 'longestrunsubsequence' +version = '1.0.1' + +homepage = 'https://pypi.org/project/longestrunsubsequence/' +description = """Implementation of a solver for the Longest Run Subsequence Problem. Given a + sequence as input, compute a longest subsequence such that there is at most one run for every + character. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +dependencies = [ + ('Python', '3.9.5'), + # PuLP supports various solvers: Cbc, CPLEX, GLPK, Gurobi, Mosek + ('GLPK', '5.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('PuLP', '2.5.0', { + # all tests are skipped if no solvers available + 'runtest': 'python -c "import pulp; pulp.pulpTestAll()"', + 'checksums': ['5dc7d76bfb1da06ac048066ced75603340d0d7ba8a7dbfce4040d6f126eda0d5'], + }), + (name, version, { + 'use_pip_extras': 'ILP-acceleration', + 'checksums': ['c49134880da428425de2150569b6e6f7049509b6693cef920c32fca7ddf5e03f'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SyRI/SyRI-1.4-foss-2021a.eb b/easybuild/easyconfigs/s/SyRI/SyRI-1.4-foss-2021a.eb new file mode 100644 index 00000000000..beb22407955 --- /dev/null +++ b/easybuild/easyconfigs/s/SyRI/SyRI-1.4-foss-2021a.eb @@ -0,0 +1,40 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'SyRI' +version = '1.4' + +homepage = 'https://schneebergerlab.github.io/syri/' +description = "Synteny and Rearrangement Identifier (SyRI)." + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'schneebergerlab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.4_install-scripts.patch'] +checksums = [ + '951bdf1fc978f8ae924422c570c0e75f1de4747fece61867ee2eecb9a43de6e1', # v1.4.tar.gz + '8e2990e97a44ae98882b69874494edc2a0c1dfbc725215013f6f35bc5a54da44', # SyRI-1.4_install-scripts.patch +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('Biopython', '1.79'), + ('python-igraph', '0.9.6'), + ('Pysam', '0.16.0.1'), + # Optional, only required to use `chroder`: + ('longestrunsubsequence', '1.0.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bins = ['chroder', 'plotsr', 'regAnno', 'syri'] +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SyRI/SyRI-1.4_install-scripts.patch b/easybuild/easyconfigs/s/SyRI/SyRI-1.4_install-scripts.patch new file mode 100644 index 00000000000..d6dc696ea6c --- /dev/null +++ b/easybuild/easyconfigs/s/SyRI/SyRI-1.4_install-scripts.patch @@ -0,0 +1,11 @@ +Author: Jasper Grimm +Add `scripts` parameter to setup.py to ensure these are installed to the correct directory +diff -Nru syri-1.4.orig/setup.py syri-1.4/setup.py +--- syri-1.4.orig/setup.py 2021-08-23 11:37:57.000000000 +0100 ++++ syri-1.4/setup.py 2021-08-23 11:39:36.000000000 +0100 +@@ -19,4 +19,5 @@ + Extension('syri.findsv',['syri/pyxFiles/findsv.pyx']), + Extension('syri.writeout',['syri/pyxFiles/writeout.pyx'])]), + packages=["syri","syri.bin", "syri.bin.func"], ++ scripts=['syri/bin/%s' % x for x in ['chroder', 'chrrev.py', 'plotsr', 'regAnno', 'syri']], + include_dirs=[numpy.get_include()]) From cbd95782ff872cedde8e69a02cc9dcbddaf39843 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 23 Aug 2021 14:17:51 +0100 Subject: [PATCH 1029/9987] Add binutils builddep --- .../longestrunsubsequence-1.0.1-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/longestrunsubsequence/longestrunsubsequence-1.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/longestrunsubsequence/longestrunsubsequence-1.0.1-GCCcore-10.3.0.eb index e6ae8843126..54ea130b233 100644 --- a/easybuild/easyconfigs/l/longestrunsubsequence/longestrunsubsequence-1.0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/longestrunsubsequence/longestrunsubsequence-1.0.1-GCCcore-10.3.0.eb @@ -13,6 +13,8 @@ description = """Implementation of a solver for the Longest Run Subsequence Prob toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +builddependencies = [('binutils', '2.36.1')] + dependencies = [ ('Python', '3.9.5'), # PuLP supports various solvers: Cbc, CPLEX, GLPK, Gurobi, Mosek From d329d6a233c2b3819459adb17c66a6b398ad69ca Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 23 Aug 2021 16:45:13 +0100 Subject: [PATCH 1030/9987] adding easyconfigs: MINPACK-19961126-GCC-10.3.0.eb --- .../m/MINPACK/MINPACK-19961126-GCC-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/MINPACK/MINPACK-19961126-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MINPACK/MINPACK-19961126-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MINPACK/MINPACK-19961126-GCC-10.3.0.eb new file mode 100644 index 00000000000..b72a883fe66 --- /dev/null +++ b/easybuild/easyconfigs/m/MINPACK/MINPACK-19961126-GCC-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'MINPACK' +version = '19961126' + +homepage = 'https://www.netlib.org/minpack/' +description = """Minpack includes software for solving nonlinear equations and + nonlinear least squares problems. Five algorithmic paths each include + a core subroutine and an easy-to-use driver. The algorithms proceed + either from an analytic specification of the Jacobian matrix or + directly from the problem functions. The paths include facilities for + systems of equations with a banded Jacobian matrix, for least squares + problems with a large amount of data, and for checking the consistency + of the Jacobian matrix with the functions. +""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://ftp.debian.org/debian/pool/main/m/minpack'] +sources = ['%(namelower)s_%(version)s+dfsg1.orig.tar.gz'] +checksums = ['7d10509cc0faefcbe38a06453cb13a40aaecd2bebc1594fb7ee0943429d8f6d1'] + +builddependencies = [ + ('Autotools', '20210128'), + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = 'autoreconf -if &&' + +_libs = ['lib/lib%%(namelower)s.%s' % x for x in ['a', 'la', SHLIB_EXT]] +sanity_check_paths = { + 'files': ['include/%(namelower)s.h'] + _libs, + 'dirs': [], +} + +moduleclass = 'numlib' From e20c593a52395f201daa2df96780166c0d110d36 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 23 Aug 2021 18:36:35 +0200 Subject: [PATCH 1031/9987] Clean-up FORD v6.1.1 EB file for GCCcore/10.2.0 --- easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb index f51c81c9289..25617e478e8 100644 --- a/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FORD/FORD-6.1.1-GCCcore-10.2.0.eb @@ -8,15 +8,12 @@ description = 'FORD is an automatic documentation generator for modern Fortran p toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -dependencies = [ - ('Python', '3.8.6'), -] - builddependencies = [ ('binutils', '2.35'), ] dependencies = [ + ('Python', '3.8.6'), ('Graphviz', '2.47.0', '-Java-11'), ('BeautifulSoup', '4.9.3'), ] From 1574fa8476e73f74f3087e38068b3f2d8c749ed2 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Tue, 24 Aug 2021 09:40:20 +0200 Subject: [PATCH 1032/9987] use proper capitalization for names --- .../CSBLAST-2.2.3-GCCcore-8.3.0.eb} | 2 +- .../easyconfigs/l/{lddt/lddt-1.2.eb => lDDT/lDDT-1.2.eb} | 4 ++-- .../PSIPRED-4.02-GCC-8.3.0.eb} | 8 ++++---- .../PSIPRED-4.02_fix_segfault.patch} | 0 4 files changed, 7 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/c/{csblast/csblast-2.2.3-GCCcore-8.3.0.eb => CSBLAST/CSBLAST-2.2.3-GCCcore-8.3.0.eb} (98%) rename easybuild/easyconfigs/l/{lddt/lddt-1.2.eb => lDDT/lDDT-1.2.eb} (91%) rename easybuild/easyconfigs/p/{psipred/psipred-4.02-GCC-8.3.0.eb => PSIPRED/PSIPRED-4.02-GCC-8.3.0.eb} (82%) rename easybuild/easyconfigs/p/{psipred/psipred-4.02_fix_segfault.patch => PSIPRED/PSIPRED-4.02_fix_segfault.patch} (100%) diff --git a/easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.3-GCCcore-8.3.0.eb similarity index 98% rename from easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb rename to easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.3-GCCcore-8.3.0.eb index 8159f8bbf4c..c29516caf75 100644 --- a/easybuild/easyconfigs/c/csblast/csblast-2.2.3-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.3-GCCcore-8.3.0.eb @@ -1,6 +1,6 @@ easyblock = 'MakeCp' -name = 'csblast' +name = 'CSBLAST' version = '2.2.3' homepage = 'https://github.com/soedinglab/csblast/' diff --git a/easybuild/easyconfigs/l/lddt/lddt-1.2.eb b/easybuild/easyconfigs/l/lDDT/lDDT-1.2.eb similarity index 91% rename from easybuild/easyconfigs/l/lddt/lddt-1.2.eb rename to easybuild/easyconfigs/l/lDDT/lDDT-1.2.eb index ed4ea8a1ca5..11de30685c2 100644 --- a/easybuild/easyconfigs/l/lddt/lddt-1.2.eb +++ b/easybuild/easyconfigs/l/lDDT/lDDT-1.2.eb @@ -1,6 +1,6 @@ easyblock = 'Tarball' -name = 'lddt' +name = 'lDDT' version = '1.2' homepage = 'https://openstructure.org' @@ -10,7 +10,7 @@ differences in a model compared to a reference structure.""" toolchain = SYSTEM source_urls = ['https://openstructure.org/static/'] -sources = ['%(name)s-linux.zip'] +sources = ['%(namelower)s-linux.zip'] checksums = ['3f4f72dc790f64431d29f7ff04353d3bbade8c8c12a487a1a99240a82fc4fcec'] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/p/psipred/psipred-4.02-GCC-8.3.0.eb b/easybuild/easyconfigs/p/PSIPRED/PSIPRED-4.02-GCC-8.3.0.eb similarity index 82% rename from easybuild/easyconfigs/p/psipred/psipred-4.02-GCC-8.3.0.eb rename to easybuild/easyconfigs/p/PSIPRED/PSIPRED-4.02-GCC-8.3.0.eb index e1202b90bd9..5a90644027a 100644 --- a/easybuild/easyconfigs/p/psipred/psipred-4.02-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/p/PSIPRED/PSIPRED-4.02-GCC-8.3.0.eb @@ -1,6 +1,6 @@ easyblock = 'MakeCp' -name = 'psipred' +name = 'PSIPRED' version = '4.02' homepage = 'http://bioinf.cs.ucl.ac.uk' @@ -8,14 +8,14 @@ description = 'Accurate protein secondary structure prediction' toolchain = {'name': 'GCC', 'version': '8.3.0'} -sources = ['%(name)s.%(version)s.tar.gz'] +sources = ['%(namelower)s.%(version)s.tar.gz'] source_urls = ['http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/'] -patches = ['psipred-4.02_fix_segfault.patch'] +patches = ['PSIPRED-4.02_fix_segfault.patch'] checksums = [ 'b4009b6a5f8b76c6d60ac91c4a743512d844864cf015c492fb6d1dc0d092c467', # psipred.4.02.tar.gz - 'd9e52ecf43b04640ebd0693df37871659d598abaec7a2c66264e9a79ee1baa82', # psipred-4.02_fix_segfault.patch + 'd9e52ecf43b04640ebd0693df37871659d598abaec7a2c66264e9a79ee1baa82', # PSIPRED-4.02_fix_segfault.patch ] parallel = 1 diff --git a/easybuild/easyconfigs/p/psipred/psipred-4.02_fix_segfault.patch b/easybuild/easyconfigs/p/PSIPRED/PSIPRED-4.02_fix_segfault.patch similarity index 100% rename from easybuild/easyconfigs/p/psipred/psipred-4.02_fix_segfault.patch rename to easybuild/easyconfigs/p/PSIPRED/PSIPRED-4.02_fix_segfault.patch From 07ebb62d310aa34c1f95f9f32861b463ff1e03cd Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Tue, 24 Aug 2021 09:42:53 +0200 Subject: [PATCH 1033/9987] add sanity check command --- easybuild/easyconfigs/l/lDDT/lDDT-1.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/lDDT/lDDT-1.2.eb b/easybuild/easyconfigs/l/lDDT/lDDT-1.2.eb index 11de30685c2..2ef169d82e5 100644 --- a/easybuild/easyconfigs/l/lDDT/lDDT-1.2.eb +++ b/easybuild/easyconfigs/l/lDDT/lDDT-1.2.eb @@ -20,4 +20,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['lddt -e'] + moduleclass = 'bio' From 60a7a6057c44be934014b4b9a0ece2684619fc59 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 24 Aug 2021 10:56:46 +0200 Subject: [PATCH 1034/9987] adding easyconfigs: sympy-1.7.1-intel-2020b.eb, gmpy2-2.1.0b5-iccifort-2020.4.304.eb --- .../gmpy2-2.1.0b5-iccifort-2020.4.304.eb | 25 +++++++++++++ .../s/sympy/sympy-1.7.1-intel-2020b.eb | 35 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..3d95fae8add --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0b5-iccifort-2020.4.304.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.0b5' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8951bcfc61c0f40102b92a4777daf9eb85445b537c4d09086deb0e097190bef0'] + +dependencies = [ + ('Python', '3.8.6'), + ('GMP', '6.2.0'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb new file mode 100644 index 00000000000..8e61d9b6f41 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.7.1-intel-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.7.1' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a3de9261e97535b83bb8607b0da2c7d03126650fafea2b2789657b229c246b2e'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('gmpy2', '2.1.0b5'), +] + +download_dep_fail = True +use_pip = True + +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +moduleclass = 'math' From e13dc26ddc9d63336078cc5bb458f745f153aa65 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 24 Aug 2021 11:59:28 +0200 Subject: [PATCH 1035/9987] adding easyconfigs: HPL-2.3-foss-2021.07.eb, HPCG-3.1-foss-2021.07.eb --- .../h/HPCG/HPCG-3.1-foss-2021.07.eb | 24 +++++++++++++++++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2021.07.eb | 21 ++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021.07.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2021.07.eb diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021.07.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021.07.eb new file mode 100644 index 00000000000..3a04b8e54f5 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021.07.eb @@ -0,0 +1,24 @@ +name = 'HPCG' +version = '3.1' + +homepage = 'https://software.sandia.gov/hpcg' +description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than + the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" + +toolchain = {'name': 'foss', 'version': '2021.07'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://www.hpcg-benchmark.org/downloads'] +sources = [SOURCELOWER_TAR_GZ] +# Newer compilers require loop's upper-bound variable to be +# explicitly designated as private/shared/firstprivate/lastprivate +patches = ['HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch'] +checksums = [ + '33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4', # hpcg-3.1.tar.gz + # HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch + '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482', +] + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2021.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2021.07.eb new file mode 100644 index 00000000000..07b786dec63 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2021.07.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2021.07'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' From 33755ac2422c55d1b9d929eac978790289fd15c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 24 Aug 2021 13:50:59 +0200 Subject: [PATCH 1036/9987] Use fixed version string in extension patch --- easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb index 4d63ce49e73..fe120508f1d 100644 --- a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb +++ b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb @@ -109,7 +109,7 @@ exts_list = [ }), ('qiskit-terra', '0.18.1', { 'modulename': 'qiskit.qobj', - 'patches': ['qiskit-terra-%(version)s_fix-qiskit-version-env.patch'], + 'patches': ['qiskit-terra-0.18.1_fix-qiskit-version-env.patch'], 'checksums': [ '7673fa59cecdd7f7f3f22aafc8d45c76cd0b5518c72de7ae464b3823c0e2b10c', # qiskit-terra-0.18.1.tar.gz # qiskit-terra-0.18.1_fix-qiskit-version-env.patch From 48644f658232f3ecd39223d28ee3f9f6efd1fe73 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 24 Aug 2021 13:34:43 +0100 Subject: [PATCH 1037/9987] add gzip dependency Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb index fd94307bacb..d9d4acfd718 100644 --- a/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb @@ -30,6 +30,7 @@ dependencies = [ ('BCFtools', '1.10.2'), ('BEDTools', '2.29.2'), ('freebayes', '1.3.5', local_pyversuffix), + ('gzip', '1.10'), ('minimap2', '2.17'), ('parallel', '20200522'), ('samclip', '0.4.0'), From db811afe4c585f2f78b5ee31b5105acc8db80533 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 24 Aug 2021 13:44:51 +0100 Subject: [PATCH 1038/9987] actually run tests Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb index d9d4acfd718..badfe711eed 100644 --- a/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb @@ -46,7 +46,7 @@ dependencies = [ skipsteps = ['configure', 'build'] pretestopts = "cd test && " -runtest = '' +runtest = ' ' files_to_copy = ['bin', 'etc', 'perl5', 'LICENSE', 'README.md'] From 60c60a94218832bc1df9f6d154634f690f85205b Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 24 Aug 2021 14:07:40 +0100 Subject: [PATCH 1039/9987] Add pkg-config to builddependencies --- ...meTools-1.5.10-foss-2018b-Python-2.7.15.eb | 1 + .../GenomeTools-1.5.10-foss-2018b.eb | 1 + .../GenomeTools-1.6.1-GCC-10.2.0.eb | 1 + ...nomeTools-1.6.1-GCC-8.3.0-Python-2.7.16.eb | 1 + .../GenomeTools-1.6.1-GCC-8.3.0.eb | 1 + .../GenomeTools-1.6.1-GCC-9.3.0.eb | 36 +++++++++++++++++++ 6 files changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.5.10-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.5.10-foss-2018b-Python-2.7.15.eb index 83da6f1465b..ddd7ce465e2 100644 --- a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.5.10-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.5.10-foss-2018b-Python-2.7.15.eb @@ -17,6 +17,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} # Bundled libraries can be globally disabled with the option useshared=yes # However, it is preferable to use the bundled libraries due to the very old versions of some of them +builddependencies = [('pkg-config', '0.29.2')] dependencies = [ ('Python', '2.7.15'), ('Pango', '1.42.4'), diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.5.10-foss-2018b.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.5.10-foss-2018b.eb index f15f088c3d1..ee56c245a32 100644 --- a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.5.10-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.5.10-foss-2018b.eb @@ -20,6 +20,7 @@ checksums = ['a6aa7f158a3cef90fea8d0fe24bfad0c3ee96b17b3ba0c1f6462582593af679e'] # Bundled libraries can be globally disabled with the option useshared=yes # However, it is preferable to use the bundled libraries due to the very old versions of some of them +builddependencies = [('pkg-config', '0.29.2')] dependencies = [('Pango', '1.42.4')] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb index 26842544fe9..7b91aa07cbe 100644 --- a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-10.2.0.eb @@ -24,6 +24,7 @@ checksums = [ # Bundled libraries can be globally disabled with the option useshared=yes # However, it is preferable to use the bundled libraries due to the very old versions of some of them +builddependencies = [('pkg-config', '0.29.2')] dependencies = [('Pango', '1.47.0')] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-8.3.0-Python-2.7.16.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-8.3.0-Python-2.7.16.eb index af5b1a01f65..0b7164cb4e3 100644 --- a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-8.3.0-Python-2.7.16.eb +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-8.3.0-Python-2.7.16.eb @@ -17,6 +17,7 @@ toolchain = {'name': 'GCC', 'version': '8.3.0'} # Bundled libraries can be globally disabled with the option useshared=yes # However, it is preferable to use the bundled libraries due to the very old versions of some of them +builddependencies = [('pkg-config', '0.29.2')] dependencies = [ ('Python', '2.7.16'), ('Pango', '1.44.7'), diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-8.3.0.eb index 4acb5dc3a59..eb8943ccadd 100644 --- a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-8.3.0.eb @@ -20,6 +20,7 @@ checksums = ['528ca143a7f1d42af8614d60ea1e5518012913a23526d82e434f0dad2e2d863f'] # Bundled libraries can be globally disabled with the option useshared=yes # However, it is preferable to use the bundled libraries due to the very old versions of some of them +builddependencies = [('pkg-config', '0.29.2')] dependencies = [('Pango', '1.44.7')] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-9.3.0.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-9.3.0.eb new file mode 100644 index 00000000000..61723dec866 --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.1-GCC-9.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'GenomeTools' +version = '1.6.1' + +homepage = 'http://genometools.org' +description = "A comprehensive software library for efficient processing of structured genome annotations." + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +github_account = 'genometools' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['528ca143a7f1d42af8614d60ea1e5518012913a23526d82e434f0dad2e2d863f'] + +# GenomeTools-1.6.1 has the following libraries bundled with it: +# bzip2-1.0.6, cgilua-5.1.3, expat-2.0.1, lpeg-0.10.2, lua-5.1.5, luafilesystem-1.5.0, md5-1.2, +# samtools-0.1.18, sqlite-3.8.7.1, tre-0.8.0, zlib-1.2.8 +# +# Bundled libraries can be globally disabled with the option useshared=yes +# However, it is preferable to use the bundled libraries due to the very old versions of some of them + +builddependencies = [('pkg-config', '0.29.2')] +dependencies = [('Pango', '1.44.7')] + +skipsteps = ['configure'] + +buildopts = 'useshared=no errorcheck=no cairo=yes' +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/gt', 'bin/genometools-config', 'lib/libgenometools.a', 'lib/libgenometools.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'bio' From c9f52eb6d1455ce6b0780b8d8744f337c3f4ea63 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 24 Aug 2021 14:13:22 +0100 Subject: [PATCH 1040/9987] adding easyconfigs: GenomeTools-1.6.2-GCC-10.3.0.eb --- .../GenomeTools-1.6.2-GCC-10.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..00b9948dcb4 --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'GenomeTools' +version = '1.6.2' + +homepage = 'http://genometools.org' +description = "A comprehensive software library for efficient processing of structured genome annotations." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'genometools' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['974825ddc42602bdce3d5fbe2b6e2726e7a35e81b532a0dc236f6e375d18adac'] + +# GenomeTools-1.6.2 has the following libraries bundled with it: +# bzip2-1.0.6, cgilua-5.1.3, expat-2.0.1, lpeg-0.10.2, lua-5.1.5, luafilesystem-1.5.0, md5-1.2, +# samtools-0.1.18, sqlite-3.33.0, tre-0.8.0, zlib-1.2.8 +# +# Bundled libraries can be globally disabled with the option useshared=yes +# However, it is preferable to use the bundled libraries due to the very old versions of some of them + +builddependencies = [('pkg-config', '0.29.2')] +dependencies = [('Pango', '1.48.5')] + +skipsteps = ['configure'] + +buildopts = 'useshared=no errorcheck=no cairo=yes threads=yes' +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/gt', 'bin/genometools-config', 'lib/libgenometools.a', 'lib/libgenometools.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'bio' From bec76a1369904fd7ff9bd35b150ae600791a72ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Aug 2021 15:28:08 +0200 Subject: [PATCH 1041/9987] {bio}[GCC/10.3.0,intel-compilers/2021.2.0] Clustal-Omega v1.2.4, argtable v2.13 --- .../argtable/argtable-2.13-GCCcore-10.3.0.eb | 30 ++++++++++++++++ .../Clustal-Omega-1.2.4-GCC-10.3.0.eb | 35 +++++++++++++++++++ ...al-Omega-1.2.4-intel-compilers-2021.2.0.eb | 35 +++++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3192e22d110 --- /dev/null +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'argtable' +version = '2.13' + +homepage = 'http://argtable.sourceforge.net/' +description = """ Argtable is an ANSI C library for parsing GNU style + command line options with a minimum of fuss. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))] +checksums = ['8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf'] + +builddependencies = [('binutils', '2.36.1')] + +sanity_check_paths = { + 'files': ['include/argtable2.h', 'lib/libargtable2.%s' % SHLIB_EXT, 'lib/libargtable2.a'], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.3.0.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..650cb3c75ba --- /dev/null +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.3.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by Adam Huffman +# Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Clustal-Omega' +version = '1.2.4' + +homepage = 'http://www.clustal.org/omega/' +description = """ Clustal Omega is a multiple sequence alignment + program for proteins. It produces biologically meaningful multiple + sequence alignments of divergent sequences. Evolutionary relationships + can be seen via viewing Cladograms or Phylograms """ + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'openmp': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee'] + +dependencies = [('argtable', '2.13')] + +sanity_check_paths = { + 'files': ['bin/clustalo'], + 'dirs': [], +} + +sanity_check_commands = ["clustalo --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..4bd5b52b6a1 --- /dev/null +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-intel-compilers-2021.2.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by Adam Huffman +# Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Clustal-Omega' +version = '1.2.4' + +homepage = 'http://www.clustal.org/omega/' +description = """ Clustal Omega is a multiple sequence alignment + program for proteins. It produces biologically meaningful multiple + sequence alignments of divergent sequences. Evolutionary relationships + can be seen via viewing Cladograms or Phylograms """ + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} +toolchainopts = {'openmp': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee'] + +dependencies = [('argtable', '2.13')] + +sanity_check_paths = { + 'files': ['bin/clustalo'], + 'dirs': [], +} + +sanity_check_commands = ["clustalo --help"] + +moduleclass = 'bio' From 8af3a177ea5ccec00049e66a25e991af86009e68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Aug 2021 16:24:31 +0200 Subject: [PATCH 1042/9987] consistently add pkg-config as build dependency for GDAL 3.2.1 --- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb | 4 ++++ easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb index efb8bd1d9a8..bcba374a615 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb @@ -20,6 +20,10 @@ checksums = [ '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch ] +builddependencies = [ + ('pkg-config', '0.29.2'), +] + dependencies = [ ('Python', '3.8.6'), ('netCDF', '4.7.4'), diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb index f41af638de0..74166337429 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb @@ -24,6 +24,10 @@ checksums = [ 'fdf6a84d16141ccc9bc4ce98a762357ba374dea87d1f2a41a1a23be80b7ca69d', # GDAL-3.2.1_cpp-conformance.patch ] +builddependencies = [ + ('pkg-config', '0.29.2'), +] + dependencies = [ ('Python', '3.8.6'), ('netCDF', '4.7.4'), From a0b71cdbe8a36aa6adb151be968d5aba3eba5e4d Mon Sep 17 00:00:00 2001 From: spottho1 Date: Tue, 24 Aug 2021 16:39:49 +0200 Subject: [PATCH 1043/9987] add '--release' flag when calling setup.py --- .../tensorflow-probability-0.12.1-foss-2020b.eb | 1 + .../tensorflow-probability-0.12.1-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb index a33fbf38cd5..8996e231286 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-foss-2020b.eb @@ -31,6 +31,7 @@ exts_list = [ 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], }), (name, version, { + 'installopts': '--install-option="--release"', 'modulename': 'tensorflow_probability', 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/probability/archive/'], diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb index 28b222eb331..c31071c495f 100644 --- a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.12.1-fosscuda-2020b.eb @@ -31,6 +31,7 @@ exts_list = [ 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], }), (name, version, { + 'installopts': '--install-option="--release"', 'modulename': 'tensorflow_probability', 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/probability/archive/'], From 108b15831d49bd649786d23e64d0000f30d4eebf Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 24 Aug 2021 19:04:33 +0200 Subject: [PATCH 1044/9987] adding easyconfigs: PyGEOS-0.10.2-intel-2020b.eb --- .../p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb diff --git a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb new file mode 100644 index 00000000000..34cef2e0710 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.10.2-intel-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'PyGEOS' +version = '0.10.2' + +homepage = "https://pygeos.readthedocs.io" +description = """PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in + the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance + improvement when operating on arrays of geometries.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['08cd7fe047a7d7f9f94eaa9a65e0b4fd4057ffebc15e6179a0290a9576a0bbbc'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('GEOS', '3.9.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'geo' From e4da69746c13c997c4226bcc112978586ed36a52 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Aug 2021 19:56:37 +0200 Subject: [PATCH 1045/9987] fix source URL for DB 18.1.32 --- easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb | 6 ++---- easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.3.0.eb | 6 ++---- easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb | 6 ++---- 3 files changed, 6 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb index 0993a0905ba..dd87d00a8cf 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb @@ -10,10 +10,8 @@ description = """Berkeley DB enables the development of custom data management toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -# use Homebrew source mirror to allow auto-downloading source tarball -# (Oracle website requires reigstration) -source_urls = ['https://bintray.com/homebrew/mirror/download_file?file_path='] -sources = [{'download_filename': 'berkeley-db-%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +source_urls = ['https://gentoo.osuosl.org/distfiles/'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['fa1fe7de9ba91ad472c25d026f931802597c29f28ae951960685cde487c8d654'] builddependencies = [('binutils', '2.31.1')] diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.3.0.eb index 3b297f7f57b..d0803aa74f9 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.3.0.eb @@ -10,10 +10,8 @@ description = """Berkeley DB enables the development of custom data management toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -# use Homebrew source mirror to allow auto-downloading source tarball -# (Oracle website requires reigstration) -source_urls = ['https://bintray.com/homebrew/mirror/download_file?file_path='] -sources = [{'download_filename': 'berkeley-db-%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +source_urls = ['https://gentoo.osuosl.org/distfiles/'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['fa1fe7de9ba91ad472c25d026f931802597c29f28ae951960685cde487c8d654'] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb index 2c9691d0d9a..5997790bf6f 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb @@ -10,10 +10,8 @@ description = """Berkeley DB enables the development of custom data management toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -# use Homebrew source mirror to allow auto-downloading source tarball -# (Oracle website requires reigstration) -source_urls = ['https://bintray.com/homebrew/mirror/download_file?file_path='] -sources = [{'download_filename': 'berkeley-db-%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +source_urls = ['https://gentoo.osuosl.org/distfiles/'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['fa1fe7de9ba91ad472c25d026f931802597c29f28ae951960685cde487c8d654'] builddependencies = [('binutils', '2.34')] From b3ac90a31a95025ad419ced9dfc11c43bebe78de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Aug 2021 00:35:03 +0200 Subject: [PATCH 1046/9987] Update easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb --- easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb index 73df2b8f6b0..f157cad034a 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020b.eb @@ -41,4 +41,6 @@ sanity_check_commands = [ "pyretisrun --help", ] +sanity_pip_check = True + moduleclass = 'chem' From dd74183f7e8443b9f25bed1c25f5281094893860 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Aug 2021 00:35:09 +0200 Subject: [PATCH 1047/9987] Update easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb --- easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb index 223cac29600..bd934ce0e10 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020b.eb @@ -41,4 +41,6 @@ sanity_check_commands = [ "pyretisrun --help", ] +sanity_pip_check = True + moduleclass = 'chem' From d9876c77b8153b4346f77eedc6ae3c0af9e52ffe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Aug 2021 00:58:03 +0200 Subject: [PATCH 1048/9987] adding easyconfigs: matplotlib-3.1.1-intelcuda-2019b-Python-3.7.4.eb, networkx-2.4-intelcuda-2019b-Python-3.7.4.eb --- ...tlib-3.1.1-intelcuda-2019b-Python-3.7.4.eb | 55 +++++++++++++++++++ ...tworkx-2.4-intelcuda-2019b-Python-3.7.4.eb | 25 +++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-intelcuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.4-intelcuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-intelcuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-intelcuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..aa1e4af72fd --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.1.1-intelcuda-2019b-Python-3.7.4.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intelcuda', 'version': '2019b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('libpng', '1.6.37'), + ('freetype', '2.10.1'), + ('Tkinter', '%(pyver)s'), +] + +use_pip = True +check_ldshared = True +sanity_pip_check = True + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.1.0', { + 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'checksums': ['1febd22afe1489b13c6749ea059d392c03261b2950d1d45c17e3aed812080c93'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.4-intelcuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/networkx/networkx-2.4-intelcuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..f8550c60a9a --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.4-intelcuda-2019b-Python-3.7.4.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intelcuda', 'version': '2019b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 7d652bc3ebd33a9afd799e5973bbcca72efdf508 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Aug 2021 02:07:40 +0200 Subject: [PATCH 1049/9987] adding easyconfigs: spglib-python-1.16.0-fosscuda-2019b-Python-3.7.4.eb, spglib-python-1.16.0-intelcuda-2019b-Python-3.7.4.eb --- ...thon-1.16.0-fosscuda-2019b-Python-3.7.4.eb | 36 +++++++++++++++++++ ...hon-1.16.0-intelcuda-2019b-Python-3.7.4.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intelcuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..805804eaa14 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['94d056e48e7e6fe2e6fe4161471e774ac03221a6225fd83d551d3184220c1edf'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intelcuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intelcuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..76f8fc62c41 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intelcuda-2019b-Python-3.7.4.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" + +toolchain = {'name': 'intelcuda', 'version': '2019b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['94d056e48e7e6fe2e6fe4161471e774ac03221a6225fd83d551d3184220c1edf'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_pip_check = True + +moduleclass = 'chem' From c6c7c33cb99056e7ac8b4b4ad863f6cc594e3bf3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Aug 2021 03:52:16 +0200 Subject: [PATCH 1050/9987] Include NSS patch from debian --- ...55_fix-ftbfs-glibc-invalid-oob-error.patch | 32 +++++++++++++++++++ .../n/NSS/NSS-3.69-GCCcore-11.2.0.eb | 3 ++ 2 files changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch b/easybuild/easyconfigs/n/NSS/NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch new file mode 100644 index 00000000000..5092b5be08d --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch @@ -0,0 +1,32 @@ +Description: Fix FTBFS due to erroneous nonnull annotation in glibc getcwd() +Author: Alex Murray + +This is still unresolved upstream but workaround it for now with this patch +to just disable the nonnull warnings via gcc pragmas around these call +sites + +Upstream bug: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=96832 +--- a/nss/coreconf/nsinstall/nsinstall.c ++++ b/nss/coreconf/nsinstall/nsinstall.c +@@ -236,14 +236,20 @@ main(int argc, char **argv) + return 0; + + if (!cwd) { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wnonnull" + cwd = GETCWD(0, PATH_MAX); ++#pragma GCC diagnostic pop + if (!cwd) + fail("could not get CWD"); + } + + /* make sure we can get into todir. */ + xchdir(todir); ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Wnonnull" + todir = GETCWD(0, PATH_MAX); ++#pragma GCC diagnostic pop + if (!todir) + fail("could not get CWD in todir"); + tdlen = strlen(todir); + diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb index ba74b4447ab..b03a54c6f96 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb @@ -13,10 +13,13 @@ source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_ sources = [SOURCELOWER_TAR_GZ] patches = [ 'NSS-3.39_pkgconfig.patch', + 'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', ] checksums = [ 'c880205a365e0dd488ff29fdea82716ff9fcde9da6f3b703d636f8fc08008799', # nss-3.69.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + # NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch + '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b', ] builddependencies = [('binutils', '2.37')] From 9505f282f51bdd6f9bbd6e89c1f930d645dcc3f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Aug 2021 04:21:09 +0200 Subject: [PATCH 1051/9987] adding easyconfigs: Qhull-2020.2-GCCcore-11.2.0.eb --- .../q/Qhull/Qhull-2020.2-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..14e2a0d4bec --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' From fafbab5b15c1c9abf9692c362dd213c361ddafd0 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 25 Aug 2021 03:09:04 +0000 Subject: [PATCH 1052/9987] adding easyconfigs: Coin-4.0.0-GCC-10.3.0.eb --- .../c/Coin/Coin-4.0.0-GCC-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb b/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..3d1a0864e8a --- /dev/null +++ b/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'Coin' +version = '4.0.0' + +homepage = 'https://sourceforge.net/projects/sox' +description = """Coin is an OpenGL-based, 3D graphics library that has its roots in the +Open Inventor 2.1 API, which Coin still is compatible with.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ["https://github.com/coin3d/%(namelower)s/releases/download/%(name)s-%(version)s"] +sources = ["%(namelower)s-%(version)s-src.tar.gz"] +checksums = ['e4f4bd57804b8ed0e017424ad2e45c112912a928b83f86c89963df9015251476'] + +# Boost is a header-only dependency +builddependencies = [ + ('Boost', '1.76.0'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('X11', '20210518'), + ('Mesa', '21.1.1'), + ('libGLU', '9.0.1'), +] + +configopts = "-DCOIN_BUILD_TESTS=OFF" + +moduleclass = 'vis' From a46358658e2eb2735590b1a08a9ccb847fbc8847 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 25 Aug 2021 03:13:34 +0000 Subject: [PATCH 1053/9987] fix homepage --- easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb b/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb index 3d1a0864e8a..0db00137b74 100644 --- a/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'Coin' version = '4.0.0' -homepage = 'https://sourceforge.net/projects/sox' +homepage = 'https://coin3d.github.io' description = """Coin is an OpenGL-based, 3D graphics library that has its roots in the Open Inventor 2.1 API, which Coin still is compatible with.""" From 3ef4e3552f65a07455618b8ad3612198aa5fd7bd Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 25 Aug 2021 03:25:58 +0000 Subject: [PATCH 1054/9987] Add sanity_check_paths --- easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb b/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb index 0db00137b74..964f5e79f45 100644 --- a/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb @@ -27,4 +27,9 @@ dependencies = [ configopts = "-DCOIN_BUILD_TESTS=OFF" +sanity_check_paths = { + 'files': ['lib/libCoin.so.80', 'lib/libCoin.so.%(version)s'], + 'dirs': ['lib/pkgconfig'] +} + moduleclass = 'vis' From d0f137d9783de823bed2e4c0a1282e9354cce4f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Wed, 25 Aug 2021 08:58:14 +0200 Subject: [PATCH 1055/9987] adding easyconfigs: hipSYCL-0.9.1-gcccuda-2020b.eb --- .../h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb diff --git a/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb b/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb new file mode 100644 index 00000000000..91fe900751e --- /dev/null +++ b/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-gcccuda-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'hipSYCL' +version = '0.9.1' + +homepage = 'https://github.com/illuhad/hipSYCL' +description = """hipSYCL is a modern SYCL implementation targeting CPUs and +GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP""" + +toolchain = {'name': 'gcccuda', 'version': '2020b'} + +source_urls = ["https://github.com/illuhad/hipSYCL/archive/refs/tags/"] +sources = ["v%(version)s.tar.gz"] +checksums = ['0a1ae3a79c743fd826dd9d666e0b9cec8b66940756d4ab6e4961e93604dff559'] + +dependencies = [ + ('Boost', '1.74.0'), + ('Clang', '11.0.1'), + ('Python', '3.8.6'), +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +configopts = '-DCMAKE_C_COMPILER="$EBROOTCLANG/bin/clang" ' +configopts += '-DCMAKE_CXX_COMPILER="$EBROOTCLANG/bin/clang++" ' +configopts += '-DLLVM_DIR=$EBROOTCLANG ' +configopts += '-DCLANG_EXECUTABLE_PATH=$EBROOTCLANG/bin/clang++ ' +configopts += '-DWITH_CPU_BACKEND=ON ' +configopts += '-DWITH_CUDA_BACKEND=ON ' + +sanity_check_paths = { + 'files': ['bin/syclcc-clang', 'include/sycl/sycl.hpp', + 'lib/hipSYCL/librt-backend-cuda.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'include/hipSYCL', 'include/SYCL', 'lib'], +} +sanity_check_commands = ['syclcc --help'] + +moduleclass = 'compiler' From 945430a3fb6b24a78d7ea10113719b4af37a86d8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 25 Aug 2021 09:00:25 +0100 Subject: [PATCH 1056/9987] Update easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2019b-Python-3.7.4.eb --- .../spglib-python-1.16.0-fosscuda-2019b-Python-3.7.4.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2019b-Python-3.7.4.eb index 805804eaa14..4aab4c18674 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-fosscuda-2019b-Python-3.7.4.eb @@ -18,9 +18,6 @@ dependencies = [ ('SciPy-bundle', '2019.10', versionsuffix), ] -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True - download_dep_fail = True use_pip = True From 985cfa8d71a95b9736c12d026b6afb954d0aa3d0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 25 Aug 2021 09:21:49 +0100 Subject: [PATCH 1057/9987] adding easyconfigs: JAGS-4.3.0-foss-2021a.eb, rjags-4-10-foss-2020b-R-4.0.3.eb, rjags-4-10-foss-2020b-R-4.0.4.eb, rjags-4-10-foss-2020b-R-4.0.5.eb, rjags-4-10-fosscuda-2020b-R-4.0.3.eb, rjags-4-10-fosscuda-2020b-R-4.0.4.eb, rjags-4-10-fosscuda-2020b-R-4.0.5.eb, rjags-4-10-foss-2021a-R-4.1.0.eb --- .../j/JAGS/JAGS-4.3.0-foss-2021a.eb | 36 +++++++++++++++++++ .../r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb | 29 +++++++++++++++ .../r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb | 29 +++++++++++++++ .../r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb | 29 +++++++++++++++ .../r/rjags/rjags-4-10-foss-2021a-R-4.1.0.eb | 29 +++++++++++++++ .../rjags-4-10-fosscuda-2020b-R-4.0.3.eb | 29 +++++++++++++++ .../rjags-4-10-fosscuda-2020b-R-4.0.4.eb | 29 +++++++++++++++ .../rjags-4-10-fosscuda-2020b-R-4.0.5.eb | 29 +++++++++++++++ 8 files changed, 239 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2021a-R-4.1.0.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.3.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.4.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.5.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2021a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2021a.eb new file mode 100644 index 00000000000..f8c13975668 --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2021a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.3.0' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download') +] +sources = [SOURCE_TAR_GZ] +checksums = ['8ac5dd57982bfd7d5f0ee384499d62f3e0bb35b5f1660feb368545f1186371fc'] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/%(name)s', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb new file mode 100644 index 00000000000..415dee78ed6 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.3'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb new file mode 100644 index 00000000000..7694a11ea49 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.4.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.4'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb new file mode 100644 index 00000000000..9de5eae8959 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2020b-R-4.0.5.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.5'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..b05c237aa37 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-foss-2021a-R-4.1.0.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.1.0'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.3.eb new file mode 100644 index 00000000000..42d5cdf10fe --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.3'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.4.eb new file mode 100644 index 00000000000..eafcc9b44f6 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.4.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.4'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.5.eb b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.5.eb new file mode 100644 index 00000000000..bb7c0dda508 --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-10-fosscuda-2020b-R-4.0.5.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['bd3e0bdf50b23b63061a0caa2428be585ccbf0b3f5d28eaa690e714e508d0ada'] + +dependencies = [ + ('R', '4.0.5'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' From 53c29a4e4b7dbb629bd57d4ff3efb4eee7addfb5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 25 Aug 2021 09:39:08 +0100 Subject: [PATCH 1058/9987] Add missing JAGS for fosscuda/2020b --- .../j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..78f0374a76a --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-fosscuda-2020b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.3.0' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [ + ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download') +] +sources = [SOURCE_TAR_GZ] +checksums = ['8ac5dd57982bfd7d5f0ee384499d62f3e0bb35b5f1660feb368545f1186371fc'] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/%(name)s', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' From 86dbec1b4e9708ea97464a0710d9ad9cb8ba2525 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Aug 2021 11:22:37 +0200 Subject: [PATCH 1059/9987] adding easyconfigs: cuDNN-8.2.2.26-CUDA-11.4.1.eb --- .../c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.1.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.1.eb new file mode 100644 index 00000000000..8db5880e0bc --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.1.eb @@ -0,0 +1,37 @@ +name = 'cuDNN' +version = '8.2.2.26' +local_cuda_version = '11.4.1' +local_cuda_version_majmin = '.'.join(local_cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] +local_tarball_tmpl = '-'.join(['%%(namelower)s', local_cuda_version_majmin, 'linux', '%s', 'v%%(version)s.tgz']) +sources = [local_tarball_tmpl % '%(cudnnarch)s'] +checksums = [ + { + local_tarball_tmpl % 'x64': + 'fbc631ce19688e87d7d2420403b20db97885b17f718f0f51d7e9fc0905d86e07', + local_tarball_tmpl % 'ppc64le': + 'b11b9e515a86978dc21ab50a7d2320bfb505cbce9dffa25480225c597c682b43', + local_tarball_tmpl % 'aarch64sbsa': + 'e240d45d79eecb2257fcb8a219324f19d8e2d6e145fbd035a38d267580d65e9a', + } +] + +dependencies = [('CUDAcore', local_cuda_version)] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From 2e25bf3a38db613e754297b5840df6351b652eb2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 25 Aug 2021 12:07:31 +0200 Subject: [PATCH 1060/9987] Add git to build deps Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 2 ++ easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index f47e5feef2e..ddce20e23f4 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -14,6 +14,8 @@ builddependencies = [ ('Bazel', '3.7.2'), ('Cython', '0.29.22'), ('pytest-xdist', '2.3.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.28.0', '-nodocs'), ] dependencies = [ diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index b0b732b7292..41f5cbd5db0 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -14,6 +14,8 @@ builddependencies = [ ('Bazel', '3.7.2'), ('Cython', '0.29.22'), ('pytest-xdist', '2.3.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.28.0', '-nodocs'), ] dependencies = [ From 9d4333b23eea65a12283ab7e41bfedfe68061ff9 Mon Sep 17 00:00:00 2001 From: Laurence Alexander Hurst Date: Wed, 25 Aug 2021 10:19:08 +0000 Subject: [PATCH 1061/9987] Added missing depency for matplotlib. pip will ordinarially fetch this automatically during install but not all build systems have internet access. --- .../c/cppy/cppy-1.1.0-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ .../matplotlib/matplotlib-3.4.2-foss-2021a.eb | 3 ++- 2 files changed, 29 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f77ee27d31a --- /dev/null +++ b/easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'cppy' +version = '1.1.0' + +homepage = "https://github.com/nucleic/cppy" +description = """A small C++ header library which makes it easier to write +Python extension modules. The primary feature is a PyObject smart pointer +which automatically handles reference counting and provides convenience +methods for performing common object operations.""" + + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +dependencies = [ + ('Python', '3.9.5'), +] + +source_urls = ['https://github.com/nucleic/cppy/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['40a9672df1ec2d7f0b54f70e574101f42131c0f5e47980769f68085e728a4934'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb index 85becc1cab4..dfd08699e69 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb @@ -21,7 +21,8 @@ dependencies = [ ('freetype', '2.10.4'), ('Tkinter', '%(pyver)s'), ('Pillow', '8.2.0'), - ('Qhull', '2020.2') + ('Qhull', '2020.2'), + ('cppy', '1.1.0') ] use_pip = True From 6e6fe54c9faf87aa39a2b20e31cd5e652db2a2c9 Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 25 Aug 2021 11:50:24 +0100 Subject: [PATCH 1062/9987] Adding builddependency on binutils Satisfying 'binutils or GCC is a build dep' in EasyBuild test suite --- easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-10.3.0.eb index f77ee27d31a..b8528af84e4 100644 --- a/easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-10.3.0.eb @@ -12,6 +12,8 @@ methods for performing common object operations.""" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +builddependencies = [('binutils', '2.36.1')] + dependencies = [ ('Python', '3.9.5'), ] From 1c65c097bd413e0f57c0f816fa0f647c8870956e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 25 Aug 2021 13:46:40 +0200 Subject: [PATCH 1063/9987] adding easyconfigs: MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb --- ...OOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..16f3bf08a8c --- /dev/null +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,66 @@ +easyblock = 'Binary' + +name = 'MOOSE' +# corresponds to commit f5fa9f0 +version = '2021-05-18' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://mooseframework.inl.gov' +description = """The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics +framework primarily developed by Idaho National Laboratory""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.7.4'), + ('libpng', '1.6.37'), + ('PETSc', '3.12.4', versionsuffix), + ('SLEPc', '3.12.2', versionsuffix), + ('VTK', '8.2.0', versionsuffix), + ('sympy', '1.5.1', versionsuffix), + ('ParMETIS', '4.0.3'), +] + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/idaholab', + 'repo_name': 'moose', + 'tag': version, + 'recursive': True, + 'keep_git_dir': True, + }, +}] +checksums = [None] + +extract_sources = True + +buildininstalldir = True + +# see https://mooseframework.inl.gov/getting_started/installation/hpc_install_moose.html +# enable building libmesh with -march=native +local_libmesg_configopts = "--disable-warnings --enable-march --with-mpi=$EBROOTMPI" +install_cmd = "sed 's/--disable-warnings/%s/g' scripts/update_and_rebuild_libmesh.sh && " % local_libmesg_configopts +# build vendored copy of libmesh +install_cmd += 'export CXXFLAGS="$CXXFLAGS -fpermissive" && export MOOSE_JOBS="%(parallel)s V=1" && ' +install_cmd += "./scripts/update_and_rebuild_libmesh.sh --skip-submodule-update && " +# build MOOSE itself +install_cmd += "cd test && pwd && make -j %(parallel)s && make -j %(parallel)s hit && " +# run tests +install_cmd += "echo 'running tests' && export PYTHONPATH=%(installdir)s/moose/moosetools/contrib/hit:$PYTHONPATH && " +# run tests, but tolerate failures +install_cmd += "(python run_tests -j %(parallel)s || echo 'Some tests are failing!' >&2 ) " + +sanity_check_paths = { + 'files': ['moose/framework/libmoose-opt.%s' % SHLIB_EXT, + 'moose/moosetools/contrib/hit/hit.%s' % SHLIB_EXT, + 'moose/moosetools/contrib/hit/libhit-opt.%s' % SHLIB_EXT], + 'dirs': ['moose/libmesh', 'moose/python', 'moose/scripts'], +} + +modextrapaths = {'PYTHONPATH': ['moose/python', 'moose/moosetools/contrib/hit']} + +modextravars = {'MOOSE_DIR': '%(installdir)s/moose'} + +moduleclass = 'phys' From 06537311f538d3952119d1a51bffbb8dfcd7ab27 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 25 Aug 2021 12:03:27 +0000 Subject: [PATCH 1064/9987] adding easyconfigs: SoQt-1.6.0-GCC-10.3.0.eb --- .../s/SoQt/SoQt-1.6.0-GCC-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..e4f6f6531b5 --- /dev/null +++ b/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'SoQt' +version = '1.6.0' + +homepage = 'https://coin3d.github.io/SoQt/html' +description = """SoQt is a Qt GUI component toolkit library for Coin. It is also compatible +with SGI and TGS Open Inventor, and the API is based on the API of the +InventorXt GUI component toolkit.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ["https://github.com/coin3d/%(namelower)s/releases/download/%(name)s-%(version)s"] +sources = ["%(namelower)s-%(version)s-src.tar.gz"] +checksums = ['9f535af59f07c907022815679681bd345c9dec2f408c74833f6b1b24bca40e1f'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Coin', '4.0.0'), + ('Qt5', '5.15.2'), +] + +sanity_check_paths = { + 'files': ['lib/libSoQt.so.20', 'lib/libSoQt.so.%(version)s'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'vis' From 30fb5d18c95bf63411e99415c20e3ca4dfab7942 Mon Sep 17 00:00:00 2001 From: h_zimm01 Date: Wed, 25 Aug 2021 16:39:23 +0200 Subject: [PATCH 1065/9987] adding easyconfigs: likwid-5.2.0-GCCcore-10.2.0.eb --- .../l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..eaef19cf7ae --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ + Likwid stands for Like I knew what I am doing. This project contributes easy + to use command line tools for Linux to support programmers in developing high + performance multi threaded programs. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' + +maxparallel = 1 + +installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ=""' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' From 8ba00186d7975e42106452178c7c7bf7346f9136 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 25 Aug 2021 16:46:38 +0200 Subject: [PATCH 1066/9987] Skip test_collect_shards if not multi gpu --- ...Torch-1.8.1-fosscuda-2019b-Python-3.7.4.eb | 2 ++ ...yTorch-1.8.1_fix_test_collect_shards.patch | 24 +++++++++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix_test_collect_shards.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb index 1dbf4cc53fb..ada49ac9f07 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb @@ -38,6 +38,7 @@ patches = [ 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', 'PyTorch-1.8.1_skip-nccl-error-tests.patch', + 'PyTorch-1.8.1_fix_test_collect_shards.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -73,6 +74,7 @@ checksums = [ # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', '33704164ad2da7426a6c21482389826345b92690d37cbf938896eef421a62575', # PyTorch-1.8.1_skip-nccl-error-tests.patch + '8d0f60bb4025ca90bbf21d945867a934738560323d232e3b69ae478c364156d3', # PyTorch-1.8.1_fix_test_collect_shards.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix_test_collect_shards.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix_test_collect_shards.patch new file mode 100644 index 00000000000..cae99d01ecc --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix_test_collect_shards.patch @@ -0,0 +1,24 @@ +Resolves test failure on single gpu systems +adapted from https://github.com/pytorch/pytorch/pull/53564 + +diff --git a/test/distributed/optim/test_zero_redundancy_optimizer.py b/test/distributed/optim/test_zero_redundancy_optimizer.py +index 06f1b4f484..0ae12d41e7 100644 +--- a/test/distributed/optim/test_zero_redundancy_optimizer.py ++++ b/test/distributed/optim/test_zero_redundancy_optimizer.py +@@ -16,7 +16,7 @@ from torch.distributed.optim import ZeroRedundancyOptimizer + from torch.optim import SGD + from torch.testing._internal.common_distributed import skip_if_no_gpu, MultiProcessTestCase + from torch.distributed.optim.zero_redundancy_optimizer import _broadcast_object +-from torch.testing._internal.common_distributed import skip_if_rocm ++from torch.testing._internal.common_distributed import skip_if_rocm, skip_if_not_multigpu + + import copy + from torch.nn.parallel import DistributedDataParallel as DDP +@@ -367,6 +367,7 @@ class TestZeroRedundancyOptimizerDistributed(TestZeroRedundancyOptimizer): + all_trainable() + some_trainable() + ++ @skip_if_not_multigpu + def test_collect_shards(self): + """ Check the state consolidation mechanism, and the state dict exposed by ZeroRedundancyOptimizer""" + self.dist_init(self.rank) From 79bdb12b9234af592924a463cfbb9eb95a3c127b Mon Sep 17 00:00:00 2001 From: LHurst-JM <78206052+LHurst-JM@users.noreply.github.com> Date: Wed, 25 Aug 2021 16:06:48 +0100 Subject: [PATCH 1067/9987] Moved cppy to builddependencies --- .../easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb index dfd08699e69..0687beb7aad 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-foss-2021a.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ ('pkg-config', '0.29.2'), + ('cppy', '1.1.0') ] dependencies = [ @@ -21,8 +22,7 @@ dependencies = [ ('freetype', '2.10.4'), ('Tkinter', '%(pyver)s'), ('Pillow', '8.2.0'), - ('Qhull', '2020.2'), - ('cppy', '1.1.0') + ('Qhull', '2020.2') ] use_pip = True From 88ae93d3dfe918ed38a28898f79d507d96eaffd8 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 25 Aug 2021 15:16:51 +0000 Subject: [PATCH 1068/9987] Use SHLIB_EXT --- easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb | 2 +- easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-10.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb b/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb index 964f5e79f45..a5b010a2a9c 100644 --- a/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-10.3.0.eb @@ -28,7 +28,7 @@ dependencies = [ configopts = "-DCOIN_BUILD_TESTS=OFF" sanity_check_paths = { - 'files': ['lib/libCoin.so.80', 'lib/libCoin.so.%(version)s'], + 'files': ['lib/libCoin.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'] } diff --git a/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-10.3.0.eb index e4f6f6531b5..96f280bd3cf 100644 --- a/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-10.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libSoQt.so.20', 'lib/libSoQt.so.%(version)s'], + 'files': ['lib/libSoQt.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'] } From 640eebc9b8866987a51ebacb08acac1f9428d1e7 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Wed, 25 Aug 2021 19:35:26 +0200 Subject: [PATCH 1069/9987] Added NCL and dependencies for 2021a --- .../g/g2clib/g2clib-1.6.3-GCCcore-10.3.0.eb | 26 ++++++++++ .../g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb | 32 ++++++++++++ .../g/g2lib/g2lib-3.2.0_makefile.patch | 40 ++++++++++++++ .../makedepend-1.0.6-GCCcore-10.3.0.eb | 26 ++++++++++ .../easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb | 52 +++++++++++++++++++ .../NCL/NCL-6.6.2_integer4_boz_operands.patch | 27 ++++++++++ .../NCL/NCL-6.6.2_multiple_definitions.patch | 30 +++++++++++ 7 files changed, 233 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_makefile.patch create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.6.2_integer4_boz_operands.patch create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.6.2_multiple_definitions.patch diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ab1dd89b2dd --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.3.0.eb @@ -0,0 +1,26 @@ +name = 'g2clib' +version = '1.6.3' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +checksums = [ + '83e4f2061b3d4a8bd431ba860dda8c5cf103b25f42d265b7b724b9acafad177c', # g2clib-1.6.0.tar +] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('JasPer', '2.0.28'), + ('libpng', '1.6.37'), +] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b2210185d88 --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +name = 'g2lib' +version = '3.2.0' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = [ + '%(name)s-%(version)s_makefile.patch', +] +checksums = [ + '9d3866de32e13e80798bfb08dbbea9223f32cec3fce3c57b6838e76f27d5a1d3', # g2lib-3.2.0.tar + 'e434394a6ec8bd68dbd57e3fdb44c47372b07380e362ed955bb038b78dd81812', # g2lib-3.2.0_makefile.patch +] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('JasPer', '2.0.28'), + ('libpng', '1.6.37'), +] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FFLAGS="$FFLAGS -fno-range-check \ +-fallow-invalid-boz -fallow-argument-mismatch -I." FC=$FC CC=$CC' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_makefile.patch b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_makefile.patch new file mode 100644 index 00000000000..1841fa47e0f --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_makefile.patch @@ -0,0 +1,40 @@ +# Author: maxim-masterov (SURF) +# Based on: g2lib-3.1.0_makefile.patch by Samuel Moors (VUB) +# Fixes order of compilation and indentation in the makefile +diff -Nru g2lib-3.2.0.orig/makefile g2lib-3.2.0/makefile +--- g2lib-3.2.0.orig/makefile 2021-08-20 11:12:18.401270276 +0200 ++++ g2lib-3.2.0/makefile 2021-08-20 11:16:07.212439526 +0200 +@@ -171,6 +171,7 @@ + .SUFFIXES: .a .f .F .c + + $(LIB): $(LIB)(gridtemplates.o) \ ++ $(LIB)(intmath.o) \ + $(LIB)(pdstemplates.o) \ + $(LIB)(drstemplates.o) \ + $(LIB)(gribmod.o) \ +@@ -182,7 +183,6 @@ + $(LIB)(gb_info.o) \ + $(LIB)(gf_getfld.o) \ + $(LIB)(gf_free.o) \ +- $(LIB)(intmath.o) \ + $(LIB)(gf_unpack1.o) \ + $(LIB)(gf_unpack2.o) \ + $(LIB)(gf_unpack3.o) \ +@@ -217,7 +217,7 @@ + $(LIB)(pngunpack.o) \ + $(LIB)(enc_png.o) \ + $(LIB)(dec_png.o) \ +- $(LIB)(mova2i.o) \ ++ $(LIB)(mova2i.o) \ + $(LIB)(g2_gbytesc.o) \ + $(LIB)(skgb.o) \ + $(LIB)(ixgb2.o) \ +@@ -232,7 +232,7 @@ + $(LIB)(putgb2.o) \ + $(LIB)(g2grids.o) \ + $(LIB)(params.o) \ +- $(LIB)(params_ecmwf.o) \ ++ $(LIB)(params_ecmwf.o) \ + $(LIB)(getidx.o) \ + $(LIB)(gdt2gds.o) + diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c4a684c45da --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.6' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['845f6708fc850bf53f5b1d0fb4352c4feab3949f140b26f71b22faba354c3365'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.3'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb new file mode 100644 index 00000000000..d60b3431ba3 --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb @@ -0,0 +1,52 @@ +name = 'NCL' +version = '6.6.2' + +homepage = 'https://www.ncl.ucar.edu' +description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'cstd': 'c99', 'openmp': True, 'pic': True, 'extra_fflags': '-fno-range-check -fallow-invalid-boz -fallow-argument-mismatch'} + +source_urls = ['https://github.com/NCAR/ncl/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'NCL-6.4.0_fix-types.patch', + 'NCL-6.6.2_integer4_boz_operands.patch', + 'NCL-6.6.2_multiple_definitions.patch', +] +checksums = [ + 'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e', # 6.6.2.tar.gz + 'f6dfaf95e5de9045745e122cb44f9c035f81fab92f5892991ddfe93945891c8f', # NCL-6.4.0_fix-types.patch + '64abcb63ab389cd97a3d13f469ed008f80c9d1d205aa78708383d2f5e9823aa0', # NCL-6.6.2_integer4_boz_operands.patch + 'e21503dc46fe6fd360ba7ca4897aa93bf9ec2961bc48634ca46de582710448f7', # NCL-6.6.2_multiple_definitions.patch +] + +builddependencies = [ + ('makedepend', '1.0.6'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] +dependencies = [ + ('cURL', '7.76.0'), + ('JasPer', '2.0.28'), + ('g2lib', '3.2.0'), + ('g2clib', '1.6.3'), + ('HDF', '4.2.15'), + ('HDF5', '1.10.7'), + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), + ('Szip', '2.1.1'), + ('freetype', '2.10.4'), + ('zlib', '1.2.11'), + ('GDAL', '3.3.0'), + ('UDUNITS', '2.2.28'), + ('ESMF', '8.1.1'), + ('bzip2', '1.0.8'), + ('cairo', '1.16.0'), + ('libiconv', '1.16'), + ('GSL', '2.7'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2_integer4_boz_operands.patch b/easybuild/easyconfigs/n/NCL/NCL-6.6.2_integer4_boz_operands.patch new file mode 100644 index 00000000000..912957c7df7 --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2_integer4_boz_operands.patch @@ -0,0 +1,27 @@ +# Author: @maxim-masterov (SURF) +# This patch fixes the error with the operands of a binary numeric operator "/". +diff -Nru ncl-6.6.2.orig/ncarg2d/src/libncarg/areasC/c_argeti.c ncl-6.6.2/ncarg2d/src/libncarg/areasC/c_argeti.c +--- ncl-6.6.2.orig/ncarg2d/src/libncarg/areasC/c_argeti.c 2021-08-23 11:15:57.122195429 +0200 ++++ ncl-6.6.2/ncarg2d/src/libncarg/areasC/c_argeti.c 2021-08-23 11:18:42.945882692 +0200 +@@ -12,6 +12,7 @@ + ************************************************************************/ + + #include ++#include + + extern void NGCALLF(argeti,ARGETI)(NGstring,int*,int); + +diff -Nru ncl-6.6.2.orig/ncarg2d/src/libncarg_gks/bwi/argb2ci.f ncl-6.6.2/ncarg2d/src/libncarg_gks/bwi/argb2ci.f +--- ncl-6.6.2.orig/ncarg2d/src/libncarg_gks/bwi/argb2ci.f 2021-08-23 11:16:04.115140069 +0200 ++++ ncl-6.6.2/ncarg2d/src/libncarg_gks/bwi/argb2ci.f 2021-08-25 16:58:47.574322219 +0200 +@@ -31,8 +31,8 @@ + mindist = 2e31 + nearest = 0 + do i=1,mol +- r = (iand(index, RMASK) / Z'0000FFFF') / 255. +- g = (iand(index, GMASK) / Z'000000FF') / 255. ++ r = (iand(index, RMASK) / int(Z'0000FFFF', 4)) / 255. ++ g = (iand(index, GMASK) / int(Z'000000FF', 4)) / 255. + b = (iand(index, BMASK)) / 255. + + C we don't need absolute distance, so forego the sqrt operation... diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2_multiple_definitions.patch b/easybuild/easyconfigs/n/NCL/NCL-6.6.2_multiple_definitions.patch new file mode 100644 index 00000000000..04806be95d9 --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2_multiple_definitions.patch @@ -0,0 +1,30 @@ +# Author: @maxim-masterov (SURF) +# This patch fixes the error with the multiple definitions of global variables. +diff -Nru ncl-6.6.2.orig/ni/src/ncl/NclApi.c ncl-6.6.2/ni/src/ncl/NclApi.c +--- ncl-6.6.2.orig/ni/src/ncl/NclApi.c 2021-08-23 11:16:17.620033156 +0200 ++++ ncl-6.6.2/ni/src/ncl/NclApi.c 2021-08-25 18:15:32.792728681 +0200 +@@ -140,9 +140,9 @@ + extern char *the_input_buffer_ptr; + extern int the_input_buffer_size; + +-FILE *thefptr; +-FILE *theoptr; +-int cmd_line; ++extern FILE *thefptr; ++extern FILE *theoptr; ++extern int cmd_line; + extern int cur_line_number; + extern char *cur_line_text; + extern int cur_line_maxsize; +diff -Nru ncl-6.6.2.orig/ni/src/ncl/NclNewHDF5.c ncl-6.6.2/ni/src/ncl/NclNewHDF5.c +--- ncl-6.6.2.orig/ni/src/ncl/NclNewHDF5.c 2021-08-23 11:16:18.450026586 +0200 ++++ ncl-6.6.2/ni/src/ncl/NclNewHDF5.c 2021-08-25 18:12:58.378953245 +0200 +@@ -82,7 +82,7 @@ + + #define NUMPOSDIMNAMES 6 + +-NclQuark possibleDimNames[NUMPOSDIMNAMES]; ++extern NclQuark possibleDimNames[NUMPOSDIMNAMES]; + + #ifndef FALSE + #define FALSE 0 From 15167956447c024c8d690a8340d6fc1f00f56f49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 25 Aug 2021 20:07:25 +0200 Subject: [PATCH 1070/9987] update to libjxl 0.5 + disable building of man pages (fixes #13827) --- ...e-10.3.0.eb => libjxl-0.5-GCCcore-10.3.0.eb} | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/l/libjxl/{libjxl-0.3.7-GCCcore-10.3.0.eb => libjxl-0.5-GCCcore-10.3.0.eb} (77%) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.3.0.eb similarity index 77% rename from easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.3.0.eb index b0a69f2ad40..710103c7ef0 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.3.0.eb @@ -1,12 +1,11 @@ easyblock = 'CMakeMake' name = 'libjxl' -version = '0.3.7' +version = '0.5' local_lodepng_version = "48e5364" homepage = 'https://github.com/libjxl/libjxl' - -description = """JPEG XL image format reference implementation""" +description = "JPEG XL image format reference implementation" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'optarch': False} # optarch causes some test failures @@ -20,14 +19,10 @@ sources = [ 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, ] -patches = [ - 'libjxl-%(version)s_openexr-3.0_compat.patch', - 'libjxl-%(version)s_external_lcms2.patch', -] +patches = ['libjxl-0.3.7_external_lcms2.patch'] checksums = [ - '8318a5d1ce82e5683a52512b6f242d2b33a1191e89fc76f7c0ead0a1d60f6c60', # v0.3.7.tar.gz + '911cb4b50eb621131ca22382166f40d4914a4ff4453dd299ade1e3292f311f89', # v0.5.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz - 'b5bf92b8eb8f41e7cedce1b43ea3fe7a9407d3cc0e29bb2afec652cabe084cee', # libjxl-0.3.7_openexr-3.0_compat.patch '9e6decaf6be74eeccfd5728df175930b4be33de6cbdf9e1816f68cb4b718fa1b', # libjxl-0.3.7_external_lcms2.patch ] @@ -51,7 +46,9 @@ dependencies = [ ('gperftools', '2.9.1'), ] -configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF' +configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' +# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) +configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF' runtest = "test" From 478e4aa84db1af73485ea2f2f4c90212d8095833 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Wed, 25 Aug 2021 20:10:00 +0200 Subject: [PATCH 1071/9987] Added missing dependency --- .../e/ESMF/ESMF-8.1.1-foss-2021a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.1.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.1.1-foss-2021a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.1.1-foss-2021a.eb new file mode 100644 index 00000000000..b6bf9ddfb37 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.1.1-foss-2021a.eb @@ -0,0 +1,34 @@ +name = 'ESMF' +version = '8.1.1' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['%%(name)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + '58c2e739356f21a1b32673aa17a713d3c4af9d45d572f4ba9168c357d586dc75', # ESMF_8_1_1.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +dependencies = [ + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), + ('netCDF-C++4', '4.3.1'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' From 67fe6784a2062047283d81df77d12f1c3e996828 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Wed, 25 Aug 2021 20:10:23 +0200 Subject: [PATCH 1072/9987] Fixed style --- easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb index d60b3431ba3..33869d74c4a 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb @@ -5,7 +5,10 @@ homepage = 'https://www.ncl.ucar.edu' description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'cstd': 'c99', 'openmp': True, 'pic': True, 'extra_fflags': '-fno-range-check -fallow-invalid-boz -fallow-argument-mismatch'} +toolchainopts = { + 'cstd': 'c99', 'openmp': True, 'pic': True, + 'extra_fflags': '-fallow-invalid-boz -fallow-argument-mismatch', +} source_urls = ['https://github.com/NCAR/ncl/archive/'] sources = ['%(version)s.tar.gz'] From 5b4c76fe584eb75f099724091974e2c96bdbb7ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 25 Aug 2021 20:51:27 +0200 Subject: [PATCH 1073/9987] remove now unused patch for libjxl 0.3.7 --- .../libjxl-0.3.7_openexr-3.0_compat.patch | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_openexr-3.0_compat.patch diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_openexr-3.0_compat.patch b/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_openexr-3.0_compat.patch deleted file mode 100644 index 0b29f2041c3..00000000000 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.3.7_openexr-3.0_compat.patch +++ /dev/null @@ -1,28 +0,0 @@ -# Compatibility with OpenEXR 3.0 series. -# Taken from https://gitlab.com/wg1/jpeg-xl/-/issues/238 - -diff -urN a/lib/extras/codec_exr.cc b/lib/extras/codec_exr.cc ---- a/lib/extras/codec_exr.cc 2021-03-29 20:31:10.000000000 +0900 -+++ b/lib/extras/codec_exr.cc 2021-05-02 16:14:52.532445954 +0900 -@@ -90,8 +90,8 @@ - return pos_ < bytes_.size(); - } - -- OpenEXR::Int64 tellg() override { return pos_; } -- void seekg(const OpenEXR::Int64 pos) override { -+ uint64_t tellg() override { return pos_; } -+ void seekg(const uint64_t pos) override { - JXL_ASSERT(pos + 1 <= bytes_.size()); - pos_ = pos; - } -@@ -115,8 +115,8 @@ - pos_ += n; - } - -- OpenEXR::Int64 tellp() override { return pos_; } -- void seekp(const OpenEXR::Int64 pos) override { -+ uint64_t tellp() override { return pos_; } -+ void seekp(const uint64_t pos) override { - if (bytes_.size() + 1 < pos) { - bytes_.resize(pos - 1); - } From 1abf2a35c901af00ef88d8b7a74694c7b24de8c5 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 25 Aug 2021 23:38:38 +0000 Subject: [PATCH 1074/9987] adding easyconfigs: AUTO-07p-0.9.3-foss-2021a.eb --- .../a/AUTO-07p/AUTO-07p-0.9.3-foss-2021a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUTO-07p/AUTO-07p-0.9.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/AUTO-07p/AUTO-07p-0.9.3-foss-2021a.eb b/easybuild/easyconfigs/a/AUTO-07p/AUTO-07p-0.9.3-foss-2021a.eb new file mode 100644 index 00000000000..821240dd581 --- /dev/null +++ b/easybuild/easyconfigs/a/AUTO-07p/AUTO-07p-0.9.3-foss-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'AUTO-07p' +version = '0.9.3' + +homepage = 'https://github.com/auto-07p' +description = """AUTO is a publicly available software for continuation and bifurcation problems +in ordinary differential equations originally written in 1980 and widely used in the dynamical +systems community.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = ['auto-%(version)s.tar.gz'] +checksums = ['c9cb3365be5736f6b8ca4040cf206e204eb6dd327f886ad0effd21db27dd8f7b'] + +dependencies = [ + ('Python', '3.9.5'), + ('Tkinter', '%(pyver)s'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('Coin', '4.0.0'), + ('SoQt', '1.6.0'), +] + +configopts = '--with-mpi' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/auto'], + 'dirs': ['lib/auto-07p'], +} + +modextravars = {'AUTO_DIR': '%(installdir)s/lib/%(namelower)s'} +modextrapaths = {'PATH': 'lib/%(namelower)s/cmds'} + +moduleclass = 'math' From f4919d30adf163e38819c57aacf0634faac88d0c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 26 Aug 2021 09:46:39 +0200 Subject: [PATCH 1075/9987] adding easyconfigs: netCDF-C++4-4.3.1-iimpi-2021a.eb --- .../netCDF-C++4-4.3.1-iimpi-2021a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2021a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2021a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2021a.eb new file mode 100644 index 00000000000..73c1e9448c3 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2021a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.8.0')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' From 27a190c8369ba0ded3f1b902efc94cc9dfc0c264 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 26 Aug 2021 09:47:10 +0200 Subject: [PATCH 1076/9987] adding easyconfigs: ESMF-8.1.1-intel-2021a.eb --- .../e/ESMF/ESMF-8.1.1-intel-2021a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.1.1-intel-2021a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.1.1-intel-2021a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.1.1-intel-2021a.eb new file mode 100644 index 00000000000..6f09d884524 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.1.1-intel-2021a.eb @@ -0,0 +1,31 @@ +name = 'ESMF' +version = '8.1.1' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['%%(name)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + '58c2e739356f21a1b32673aa17a713d3c4af9d45d572f4ba9168c357d586dc75', # ESMF_8_1_1.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +dependencies = [ + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), + ('netCDF-C++4', '4.3.1'), +] + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' From 1a4ab93274f5b6fbf8449512c1dad3c6eaa8198e Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Thu, 26 Aug 2021 10:28:17 +0200 Subject: [PATCH 1077/9987] Fixed comment --- easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb | 4 ++-- ...boz_operands.patch => NCL-6.6.2_header_and_operands.patch} | 4 +++- 2 files changed, 5 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/n/NCL/{NCL-6.6.2_integer4_boz_operands.patch => NCL-6.6.2_header_and_operands.patch} (91%) diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb index 33869d74c4a..3a8fd377df9 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2021a.eb @@ -14,13 +14,13 @@ source_urls = ['https://github.com/NCAR/ncl/archive/'] sources = ['%(version)s.tar.gz'] patches = [ 'NCL-6.4.0_fix-types.patch', - 'NCL-6.6.2_integer4_boz_operands.patch', + 'NCL-6.6.2_header_and_operands.patch', 'NCL-6.6.2_multiple_definitions.patch', ] checksums = [ 'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e', # 6.6.2.tar.gz 'f6dfaf95e5de9045745e122cb44f9c035f81fab92f5892991ddfe93945891c8f', # NCL-6.4.0_fix-types.patch - '64abcb63ab389cd97a3d13f469ed008f80c9d1d205aa78708383d2f5e9823aa0', # NCL-6.6.2_integer4_boz_operands.patch + '5cb62d9a37de8af485b94487692f7e739ca5eb103a6b447e0290a68a6c094808', # NCL-6.6.2_header_and_operands.patch 'e21503dc46fe6fd360ba7ca4897aa93bf9ec2961bc48634ca46de582710448f7', # NCL-6.6.2_multiple_definitions.patch ] diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2_integer4_boz_operands.patch b/easybuild/easyconfigs/n/NCL/NCL-6.6.2_header_and_operands.patch similarity index 91% rename from easybuild/easyconfigs/n/NCL/NCL-6.6.2_integer4_boz_operands.patch rename to easybuild/easyconfigs/n/NCL/NCL-6.6.2_header_and_operands.patch index 912957c7df7..e22a388ac6c 100644 --- a/easybuild/easyconfigs/n/NCL/NCL-6.6.2_integer4_boz_operands.patch +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2_header_and_operands.patch @@ -1,5 +1,7 @@ # Author: @maxim-masterov (SURF) -# This patch fixes the error with the operands of a binary numeric operator "/". +# This patch fixes: +# - the error with the missing header +# - the error with the operands of a binary numeric operator "/". diff -Nru ncl-6.6.2.orig/ncarg2d/src/libncarg/areasC/c_argeti.c ncl-6.6.2/ncarg2d/src/libncarg/areasC/c_argeti.c --- ncl-6.6.2.orig/ncarg2d/src/libncarg/areasC/c_argeti.c 2021-08-23 11:15:57.122195429 +0200 +++ ncl-6.6.2/ncarg2d/src/libncarg/areasC/c_argeti.c 2021-08-23 11:18:42.945882692 +0200 From 4ec79d59868d0ea076d0a3e9f827e178e8a1f1e5 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 26 Aug 2021 10:28:30 +0200 Subject: [PATCH 1078/9987] x264 needs pkg-config as builddep --- easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/x/x264/x264-20210414-GCCcore-10.3.0.eb | 1 + easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb index ab66b16bf18..002c6362201 100644 --- a/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb @@ -20,6 +20,7 @@ checksums = ['4dba5ab9e744f85d8a37ccdcc9467d27c5409c7e4f7e397580b5921be09b4d1e'] builddependencies = [ ('binutils', '2.35'), + ('pkg-config', '0.29.2'), ('NASM', '2.15.05'), ] diff --git a/easybuild/easyconfigs/x/x264/x264-20210414-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/x264/x264-20210414-GCCcore-10.3.0.eb index dded9d497db..4660cea330c 100644 --- a/easybuild/easyconfigs/x/x264/x264-20210414-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/x264/x264-20210414-GCCcore-10.3.0.eb @@ -20,6 +20,7 @@ checksums = ['88b8f738e420bcb1dcc6ef27e13d10261dbcddd047712a31867a946a265eec4d'] builddependencies = [ ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), ('NASM', '2.15.05'), ] diff --git a/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb index c51d6bdacf0..93be9bbf894 100644 --- a/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb @@ -20,6 +20,7 @@ checksums = ['9b5543a5f114f4c6905a2319ea4c2063d6ebd2db209b41642086df3c1f7b6f50'] builddependencies = [ ('binutils', '2.37'), + ('pkg-config', '0.29.2'), ('NASM', '2.15.05'), ] From 39348fefe7714832ce3c7feec704de6cf6b142c9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 26 Aug 2021 11:04:44 +0200 Subject: [PATCH 1079/9987] x264: Explicitly turn off bashcompletion. --- easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/x/x264/x264-20210414-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb index 002c6362201..c7bbcc82b27 100644 --- a/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/x264/x264-20201026-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('NASM', '2.15.05'), ] -configopts = " --enable-shared --enable-static" +configopts = " --enable-shared --enable-static --disable-bashcompletion" sanity_check_paths = { 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', diff --git a/easybuild/easyconfigs/x/x264/x264-20210414-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/x264/x264-20210414-GCCcore-10.3.0.eb index 4660cea330c..f8f6e33e213 100644 --- a/easybuild/easyconfigs/x/x264/x264-20210414-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/x264/x264-20210414-GCCcore-10.3.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('NASM', '2.15.05'), ] -configopts = " --enable-shared --enable-static" +configopts = " --enable-shared --enable-static --disable-bashcompletion" sanity_check_paths = { 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', diff --git a/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb index 93be9bbf894..410e3fbee86 100644 --- a/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x264/x264-20210613-GCCcore-11.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('NASM', '2.15.05'), ] -configopts = " --enable-shared --enable-static" +configopts = " --enable-shared --enable-static --disable-bashcompletion" sanity_check_paths = { 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', From f43ad848b19c54ba9475063cc80580f608ab3446 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 26 Aug 2021 11:34:55 +0200 Subject: [PATCH 1080/9987] ELPA requires Perl as builddep --- .../e/ELPA/ELPA-2021.05.001-foss-2021a.eb | 8 ++- .../e/ELPA/ELPA-2021.05.001-intel-2021a.eb | 17 ++++++- ...-2021.05.001_fix_hardcoded_perl_path.patch | 49 +++++++++++++++++++ 3 files changed, 72 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001_fix_hardcoded_perl_path.patch diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb index 7d5757ab807..063922e54e7 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb @@ -17,12 +17,18 @@ toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] sources = ['elpa-new_release_%(version)s.tar.gz'] -checksums = ['aea66a18e87574c7c292e852e45943e16f8bc3839f456635d1d610957840d146'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + 'aea66a18e87574c7c292e852e45943e16f8bc3839f456635d1d610957840d146', # elpa-new_release_2021.05.001.tar.gz + # ELPA-2021.05.001_fix_hardcoded_perl_path.patch + 'af3f8cd063100d403cb2fe53cfc85eb2d5a2ef3348a3e6d5cf2d3680ebb4ec02', +] builddependencies = [ ('Autotools', '20210128'), # remove_xcompiler script requires 'python' command, ('Python', '3.9.5'), + ('Perl', '5.32.1'), ] preconfigopts = './autogen.sh && ' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb index fcca817c0ea..3bf4eea1cd4 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb @@ -17,14 +17,29 @@ toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] sources = ['elpa-new_release_%(version)s.tar.gz'] -checksums = ['aea66a18e87574c7c292e852e45943e16f8bc3839f456635d1d610957840d146'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + 'aea66a18e87574c7c292e852e45943e16f8bc3839f456635d1d610957840d146', # elpa-new_release_2021.05.001.tar.gz + # ELPA-2021.05.001_fix_hardcoded_perl_path.patch + 'af3f8cd063100d403cb2fe53cfc85eb2d5a2ef3348a3e6d5cf2d3680ebb4ec02', +] builddependencies = [ ('Autotools', '20210128'), # remove_xcompiler script requires 'python' command, ('Python', '3.9.5'), + ('Perl', '5.32.1'), ] preconfigopts = './autogen.sh && ' +# If the build is running in a batch job, make sure Intel libmpi does +# not try to use Slurm to run the MPI_THREAD test code that ELPA's +# configure is running without "mpirun". +preconfigopts += 'unset SLURM_JOBID && unset SLURM_NODELIST && unset I_MPI_PMI_LIBRARY && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001_fix_hardcoded_perl_path.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001_fix_hardcoded_perl_path.patch new file mode 100644 index 00000000000..bab15ed19e8 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001_fix_hardcoded_perl_path.patch @@ -0,0 +1,49 @@ +Fix hardcoded paths to perl. +We depend on EasyBuild Perl. + +Åke Sandgren, 20210824 +diff -ru elpa-new_release_2021.05.001.orig/fdep/fortran_dependencies.pl elpa-new_release_2021.05.001/fdep/fortran_dependencies.pl +--- elpa-new_release_2021.05.001.orig/fdep/fortran_dependencies.pl 2021-06-07 11:35:08.000000000 +0200 ++++ elpa-new_release_2021.05.001/fdep/fortran_dependencies.pl 2021-08-24 18:15:00.133701035 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Copyright 2015 Lorenz Hüdepohl + # +diff -ru elpa-new_release_2021.05.001.orig/test_project_1stage/fdep/fortran_dependencies.pl elpa-new_release_2021.05.001/test_project_1stage/fdep/fortran_dependencies.pl +--- elpa-new_release_2021.05.001.orig/test_project_1stage/fdep/fortran_dependencies.pl 2021-06-07 11:35:08.000000000 +0200 ++++ elpa-new_release_2021.05.001/test_project_1stage/fdep/fortran_dependencies.pl 2021-08-24 18:15:33.421492236 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +diff -ru elpa-new_release_2021.05.001.orig/test_project_2stage/fdep/fortran_dependencies.pl elpa-new_release_2021.05.001/test_project_2stage/fdep/fortran_dependencies.pl +--- elpa-new_release_2021.05.001.orig/test_project_2stage/fdep/fortran_dependencies.pl 2021-06-07 11:35:08.000000000 +0200 ++++ elpa-new_release_2021.05.001/test_project_2stage/fdep/fortran_dependencies.pl 2021-08-24 18:15:36.101475423 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +diff -ru elpa-new_release_2021.05.001.orig/test_project_C/fdep/fortran_dependencies.pl elpa-new_release_2021.05.001/test_project_C/fdep/fortran_dependencies.pl +--- elpa-new_release_2021.05.001.orig/test_project_C/fdep/fortran_dependencies.pl 2021-06-07 11:35:08.000000000 +0200 ++++ elpa-new_release_2021.05.001/test_project_C/fdep/fortran_dependencies.pl 2021-08-24 18:15:38.653459416 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +diff -ru elpa-new_release_2021.05.001.orig/test_project_C_2stage/fdep/fortran_dependencies.pl elpa-new_release_2021.05.001/test_project_C_2stage/fdep/fortran_dependencies.pl +--- elpa-new_release_2021.05.001.orig/test_project_C_2stage/fdep/fortran_dependencies.pl 2021-06-07 11:35:08.000000000 +0200 ++++ elpa-new_release_2021.05.001/test_project_C_2stage/fdep/fortran_dependencies.pl 2021-08-24 18:15:41.533441354 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + From 15490df9cde268a558fd4f1511327252924216b8 Mon Sep 17 00:00:00 2001 From: Stig Rune Jensen Date: Thu, 26 Aug 2021 12:49:19 +0200 Subject: [PATCH 1081/9987] adding easyconfigs: hipSYCL-0.9.1-GCC-10.2.0.eb --- .../h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb b/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb new file mode 100644 index 00000000000..98698a165f1 --- /dev/null +++ b/easybuild/easyconfigs/h/hipSYCL/hipSYCL-0.9.1-GCC-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'hipSYCL' +version = '0.9.1' + +homepage = 'https://github.com/illuhad/hipSYCL' +description = """hipSYCL is a modern SYCL implementation targeting CPUs and +GPUs, with a focus on leveraging existing toolchains such as CUDA or HIP""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ["https://github.com/illuhad/hipSYCL/archive/refs/tags/"] +sources = ["v%(version)s.tar.gz"] +checksums = ['0a1ae3a79c743fd826dd9d666e0b9cec8b66940756d4ab6e4961e93604dff559'] + +dependencies = [ + ('Boost', '1.74.0'), + ('Clang', '11.0.1'), + ('Python', '3.8.6'), +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +configopts = '-DCMAKE_C_COMPILER="$EBROOTCLANG/bin/clang" ' +configopts += '-DCMAKE_CXX_COMPILER="$EBROOTCLANG/bin/clang++" ' +configopts += '-DLLVM_DIR=$EBROOTCLANG ' +configopts += '-DCLANG_EXECUTABLE_PATH=$EBROOTCLANG/bin/clang++ ' +configopts += '-DWITH_CPU_BACKEND=ON ' +configopts += '-DWITH_CUDA_BACKEND=OFF ' +configopts += '-DWITH_ROCM_BACKEND=OFF ' + +sanity_check_paths = { + 'files': ['bin/syclcc-clang', 'include/sycl/sycl.hpp', + 'lib/hipSYCL/librt-backend-omp.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'include/hipSYCL', 'include/SYCL', 'lib'], +} +sanity_check_commands = ['syclcc --help'] + +moduleclass = 'compiler' From e2b4885425e4acca10b15b3f977a8078dc010539 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Thu, 26 Aug 2021 12:58:18 +0200 Subject: [PATCH 1082/9987] Added NCO --- .../ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb | 33 +++++++++++++++ .../l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb | 37 +++++++++++++++++ .../easyconfigs/n/NCO/NCO-5.0.1-foss-2021a.eb | 41 +++++++++++++++++++ ...NCO-5.0.1_fix_build_of_cxx_interface.patch | 14 +++++++ 4 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb create mode 100644 easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.0.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.0.1_fix_build_of_cxx_interface.patch diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb new file mode 100644 index 00000000000..e1357bf2785 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +builddependencies = [('binutils', '2.36.1')] +dependencies = [('Java', '11', '', True)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e2bb8f718ab --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.7-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.20.7' + +homepage = 'https://www.opendap.org/software/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 and + DAP4.0. This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6856813d0b29e70a36e8a53e9cf20ad680d21d615952263e9c6586704539e78c'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '7.76.0'), + ('libxml2', '2.9.10'), + ('libtirpc', '1.3.2'), + ('PCRE', '8.44'), + ('util-linux', '2.36'), +] + +configopts = 'TIRPC_LIBS="-ltirpc"' + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.0.1-foss-2021a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.0.1-foss-2021a.eb new file mode 100644 index 00000000000..f8ae05c77a4 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.0.1-foss-2021a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' +name = 'NCO' +version = '5.0.1' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['NCO-%(version)s_fix_build_of_cxx_interface.patch'] +checksums = [ + '37d11ffe582aa0ee89f77a7b9a176b41e41900e9ab709e780ec0caf52ad60c4b', # 5.0.1.tar.gz + 'ea1bdaafd7b8bf8b84569634373868f2d8463d65bd9ec6f56143f4f7362f5c99', # NCO-5.0.1_fix_build_of_cxx_interface.patch +] + +builddependencies = [ + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.2.9'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.7'), + ('GSL', '2.7'), + ('netCDF', '4.8.0'), + ('ESMF', '8.1.1'), # ncremap needs ESMF_RegridWeightGen +] + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.0.1_fix_build_of_cxx_interface.patch b/easybuild/easyconfigs/n/NCO/NCO-5.0.1_fix_build_of_cxx_interface.patch new file mode 100644 index 00000000000..8b52061cc38 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.0.1_fix_build_of_cxx_interface.patch @@ -0,0 +1,14 @@ +# Author: @maxim-masterov (SURF) +# Fixes build of the NCO C++ interface library +diff -Nru nco-5.0.1.orig/configure nco-5.0.1/configure +--- nco-5.0.1.orig/configure 2021-08-23 16:37:36.355221743 +0200 ++++ nco-5.0.1/configure 2021-08-26 12:44:59.298990140 +0200 +@@ -21531,7 +21531,7 @@ + # Treat essential and man files now, defer doc files (that rely on makeinfo) to below + ac_config_files="$ac_config_files Makefile data/Makefile src/Makefile src/nco/Makefile man/Makefile" + +-if test "${ac_cv_cxx_have_valarray}" = 'yes' && test "${enable_nco_cxx}" = 'yes' ; then ++if test "${enable_nco_cxx}" = 'yes' ; then + ac_config_files="$ac_config_files src/nco_c++/Makefile" + + NCO_CXX="nco_c++" From ea409952001a12d6962965ff9967f79f193e510e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 26 Aug 2021 13:30:03 +0200 Subject: [PATCH 1083/9987] adding easyconfigs: WIEN2k-21.1-intel-2021a.eb --- .../w/WIEN2k/WIEN2k-21.1-intel-2021a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb new file mode 100644 index 00000000000..587ee1793d3 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb @@ -0,0 +1,57 @@ +name = 'WIEN2k' +version = '21.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +sources = ['%(name)s_%(version)s.tar'] + +dependencies = [ + ('Perl', '5.32.1'), + ('DFT-D3', '3.2.0'), + ('ELPA', '2021.05.001'), + ('FFTW', '3.3.9'), + ('libxc', '5.1.5'), +] + +osdependencies = [('glibc-devel', 'libc6-dev')] # required for libpthread.a + +#remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ _EXEC_' +use_remote = False +mpi_remote = False +wien_granularity = True +taskset = 'no' + +# Change as needed, these are the defaults +# nmatmax = 19000 +# nume = 6000 + +fix_perl_shebang_for = [ + 'iniel_pressure_in2reader.pl_lapw', + 'iniel_pressure_reader.pl_lapw', + 'setrmt_lapw', + 'elast_setup_input.pl_lapw', + 'bashtime2csh.pl_lapw', +] + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1', r'^:ENE.*-1248.14']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*15.*total forces', + ]), +] + +moduleclass = 'chem' From 99d3c2a628d19b30af100ea2c87f6ee8caf3b55a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 26 Aug 2021 13:30:58 +0200 Subject: [PATCH 1084/9987] adding easyconfigs: PnetCDF-1.12.2-iimpi-2021a.eb --- .../p/PnetCDF/PnetCDF-1.12.2-iimpi-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-iimpi-2021a.eb diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-iimpi-2021a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-iimpi-2021a.eb new file mode 100644 index 00000000000..ff8f8e56b30 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.2-iimpi-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = "1.12.2" + +homepage = 'https://trac.mcs.anl.gov/projects/parallel-netcdf' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'iimpi', 'version': '2021a'} + +source_urls = ['https://parallel-netcdf.github.io/Release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3ef1411875b07955f519a5b03278c31e566976357ddfc74c2493a1076e7d7c74'] + +builddependencies = [ + ('Autotools', '20210128'), + ('Perl', '5.32.1'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' From 0127299626bb338e8ac172b6aaee406577ec0eda Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 26 Aug 2021 13:34:20 +0200 Subject: [PATCH 1085/9987] Add missing checksum --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb index 587ee1793d3..d1e37543855 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb @@ -10,6 +10,7 @@ WIEN2k is an all-electron scheme including relativistic effects and has many fea toolchain = {'name': 'intel', 'version': '2021a'} sources = ['%(name)s_%(version)s.tar'] +checksums = ['32590778440a9280322bf2dc0d63f4f42a9fc48814fa6b8b7ee2d199c94bed11'] dependencies = [ ('Perl', '5.32.1'), From 943b9e1602f1d1f3d86808408bbe896e258a7af0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 26 Aug 2021 13:43:38 +0200 Subject: [PATCH 1086/9987] WIEN2k: Add missing config for the DFT-D3/3.2.0 dependency --- .../d/DFT-D3/DFT-D3-3.2.0-intel-2021a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2021a.eb diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2021a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2021a.eb new file mode 100644 index 00000000000..9e90b78487d --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2021a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'DFT-D3' +version = '3.2.0' + +homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical + quantum chemical methods.""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +source_urls = ['https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3'] +# Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version +# numbering. Also, the authors are prone (alas) to stealth upgrades, so that two +# tarballs with the same version number can have different checksums. For this +# reason, it is suggested to manually download and rename the tarball. The +# checksum may also need updating from time to time. +# Checksum last updated: 20 September 2018 +# Date tarball was reported to have been modified: 14 June 2016 +sources = [{'download_filename': 'dftd3.tgz', 'filename': SOURCELOWER_TGZ}] +checksums = ['d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59'] + +prebuildopts = "sed -i 's/OSTYPE=LINUXL/OSTYPE=LINUXI/' Makefile && " + +files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/dftd3'], + 'dirs': [], +} + +moduleclass = 'chem' From 6e99a20bd89c958cce48569f07ec95a903996bb6 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Thu, 26 Aug 2021 14:39:49 +0200 Subject: [PATCH 1087/9987] Put checksum comments on separate lines to please allmighty boegelbot --- .../easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb index 3a938da6095..32ed844cbb5 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb @@ -14,9 +14,12 @@ patches = [ '%(name)s-%(version_major_minor)s.1_fix-protobuf-env.patch', ] checksums = [ - 'de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1', # %(namelower)s-%(version)s-dist.zip - 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', # %(name)s-3.4.1-fix-grpc-protoc.patch - '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', # %(name)s-%(version_major_minor)s.1_fix-protobuf-env.patch + # bazel-3.7.2-dist.zip + 'de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1', + # Bazel-3.4.1-fix-grpc-protoc.patch + 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', + # Bazel-3.7.1_fix-protobuf-env.patch + '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', ] builddependencies = [ From 58d03c495241730d8c0ef295b9b797d8f24c6b32 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 26 Aug 2021 15:35:15 +0200 Subject: [PATCH 1088/9987] Fix comment style typo. --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb index d1e37543855..082ec3712d0 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb @@ -22,7 +22,7 @@ dependencies = [ osdependencies = [('glibc-devel', 'libc6-dev')] # required for libpthread.a -#remote = 'pbsssh' +# remote = 'pbsssh' wien_mpirun = 'mpirun -np _NP_ _EXEC_' use_remote = False mpi_remote = False From 90e35bf8a8a706240735e1e65b9254560cdb2e70 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Thu, 26 Aug 2021 15:53:54 +0200 Subject: [PATCH 1089/9987] Skip test_kineto on CUDA 10.1 --- ...Torch-1.8.1-fosscuda-2019b-Python-3.7.4.eb | 2 ++ ...PyTorch-1.8.1_skip_test_kineto_cu101.patch | 24 +++++++++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip_test_kineto_cu101.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb index ada49ac9f07..0adebd46525 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2019b-Python-3.7.4.eb @@ -39,6 +39,7 @@ patches = [ 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', 'PyTorch-1.8.1_skip-nccl-error-tests.patch', 'PyTorch-1.8.1_fix_test_collect_shards.patch', + 'PyTorch-1.8.1_skip_test_kineto_cu101.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -75,6 +76,7 @@ checksums = [ '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', '33704164ad2da7426a6c21482389826345b92690d37cbf938896eef421a62575', # PyTorch-1.8.1_skip-nccl-error-tests.patch '8d0f60bb4025ca90bbf21d945867a934738560323d232e3b69ae478c364156d3', # PyTorch-1.8.1_fix_test_collect_shards.patch + 'cc493437740479e23f6e48f886c979245d038705cba4b781d910d69a00229390', # PyTorch-1.8.1_skip_test_kineto_cu101.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip_test_kineto_cu101.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip_test_kineto_cu101.patch new file mode 100644 index 00000000000..4bc085652c7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_skip_test_kineto_cu101.patch @@ -0,0 +1,24 @@ +Skip test_kineto on CUDA 10.1 because it uses CUPTI which requires root due to a vulnerability +on that CUDA version. +author: Christoph Siegert (Leipzig University) + +diff --git a/test/test_profiler.py b/test/test_profiler.py +index 585f569aa7..35f3ff6015 100644 +--- a/test/test_profiler.py ++++ b/test/test_profiler.py +@@ -113,6 +113,7 @@ class TestProfiler(TestCase): + + @unittest.skipIf(not kineto_available(), "Kineto is required") + @unittest.skipIf(not torch.cuda.is_available(), "CUDA is required") ++ @unittest.skipIf(torch.version.cuda == "10.1", "CUPTI requires root on CUDA 10.1") + def test_kineto(self): + with _profile(use_cuda=True, use_kineto=True): + self.payload() +@@ -136,6 +137,7 @@ class TestProfiler(TestCase): + + @unittest.skipIf(not kineto_available(), "Kineto is required") + @unittest.skipIf(not TEST_MULTIGPU, "Multiple GPUs needed") ++ @unittest.skipIf(torch.version.cuda == "10.1", "CUPTI requires root on CUDA 10.1") + def test_kineto_multigpu(self): + with profile( + activities=[ From 16826715268d7ee41d8e33e865466ed2da9f641e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 26 Aug 2021 15:46:51 +0200 Subject: [PATCH 1090/9987] add archive source URL to Spark 3.x easyconfigs to fix broken download --- .../s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb | 5 ++--- .../s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb | 5 ++--- .../s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb | 1 + easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 1 + 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb index acff4d94720..adae6b1c2c7 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb @@ -10,9 +10,8 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'foss', 'version': '2018b'} source_urls = [ - 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', - 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', - 'https://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', + 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' ] sources = ['spark-%(version)s-bin-hadoop2.7.tgz'] checksums = ['98f6b92e5c476d7abb93cc179c2616aa5dc897da25753bd197e20ef54a28d945'] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb index b090aaef033..8e54f654021 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb @@ -10,9 +10,8 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'intel', 'version': '2018b'} source_urls = [ - 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', - 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', - 'https://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', + 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' ] sources = ['spark-%(version)s-bin-hadoop2.7.tgz'] checksums = ['98f6b92e5c476d7abb93cc179c2616aa5dc897da25753bd197e20ef54a28d945'] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb index a6e616bd811..cecf3035382 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb @@ -12,6 +12,7 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'foss', 'version': '2020a'} source_urls = [ + 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' ] sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index 71ff15224de..b4585778e53 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -11,6 +11,7 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = [ + 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' ] sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] From 31d3137af519a6f9bd7115f8ea874dcd297e4a46 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Thu, 26 Aug 2021 17:05:10 +0200 Subject: [PATCH 1091/9987] skip test_collect_shards on single gpu systems --- .../p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 2 ++ ...yTorch-1.8.1_fix_test_collect_shards.patch | 24 +++++++++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix_test_collect_shards.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index 95baaba3bc3..a32c54ea29e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -37,6 +37,7 @@ patches = [ 'PyTorch-1.8.1_skip-complex-grad-check-on-ppc.patch', 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', 'PyTorch-1.8.1_skip-nccl-error-tests.patch', + 'PyTorch-1.8.1_fix_test_collect_shards.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -72,6 +73,7 @@ checksums = [ # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', '33704164ad2da7426a6c21482389826345b92690d37cbf938896eef421a62575', # PyTorch-1.8.1_skip-nccl-error-tests.patch + '8d0f60bb4025ca90bbf21d945867a934738560323d232e3b69ae478c364156d3', # PyTorch-1.8.1_fix_test_collect_shards.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix_test_collect_shards.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix_test_collect_shards.patch new file mode 100644 index 00000000000..cae99d01ecc --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1_fix_test_collect_shards.patch @@ -0,0 +1,24 @@ +Resolves test failure on single gpu systems +adapted from https://github.com/pytorch/pytorch/pull/53564 + +diff --git a/test/distributed/optim/test_zero_redundancy_optimizer.py b/test/distributed/optim/test_zero_redundancy_optimizer.py +index 06f1b4f484..0ae12d41e7 100644 +--- a/test/distributed/optim/test_zero_redundancy_optimizer.py ++++ b/test/distributed/optim/test_zero_redundancy_optimizer.py +@@ -16,7 +16,7 @@ from torch.distributed.optim import ZeroRedundancyOptimizer + from torch.optim import SGD + from torch.testing._internal.common_distributed import skip_if_no_gpu, MultiProcessTestCase + from torch.distributed.optim.zero_redundancy_optimizer import _broadcast_object +-from torch.testing._internal.common_distributed import skip_if_rocm ++from torch.testing._internal.common_distributed import skip_if_rocm, skip_if_not_multigpu + + import copy + from torch.nn.parallel import DistributedDataParallel as DDP +@@ -367,6 +367,7 @@ class TestZeroRedundancyOptimizerDistributed(TestZeroRedundancyOptimizer): + all_trainable() + some_trainable() + ++ @skip_if_not_multigpu + def test_collect_shards(self): + """ Check the state consolidation mechanism, and the state dict exposed by ZeroRedundancyOptimizer""" + self.dist_init(self.rank) From 1aa73a7631a1f6c0090545dcdb16a4d9de6d0e51 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Aug 2021 09:52:27 +0200 Subject: [PATCH 1092/9987] add missing source URL for py4j extension in Spark 3.0.0 easyconfig using intel/2018b --- .../easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb index 8e54f654021..df8e7e468b1 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb @@ -25,6 +25,7 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } From 7c9ad3944c8b782df8206ae46c127142640fd9f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Aug 2021 10:51:14 +0200 Subject: [PATCH 1093/9987] limit parallelism to 10 for jax with foss/2020b, to avoid failing tests because not enough threads can be started --- easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index ddce20e23f4..d7edc77e8a7 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -34,6 +34,10 @@ local_jax_prebuildopts = "sed -i 's$pathToSed$%s$g' WORKSPACE && " % local_tf_bu use_pip = True +# running the tests with lots of cores results in test failures because not enough threads can be started, +# so limit to a reasonable number of cores to use at maximum +maxparallel = 10 + default_easyblock = 'PythonPackage' default_component_specs = { 'sources': [SOURCE_TAR_GZ], From e2d219add02448fb1af159c4157089d702e37447 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 27 Aug 2021 11:11:37 +0200 Subject: [PATCH 1094/9987] use proper capitalization for DGL --- .../DGL-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/d/{dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb => DGL/DGL-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb} (89%) diff --git a/easybuild/easyconfigs/d/dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb b/easybuild/easyconfigs/d/DGL/DGL-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb similarity index 89% rename from easybuild/easyconfigs/d/dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb rename to easybuild/easyconfigs/d/DGL/DGL-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb index fb3fd04fd0f..2a90696e436 100644 --- a/easybuild/easyconfigs/d/dgl/dgl-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/d/DGL/DGL-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'dgl' +name = 'DGL' version = '0.6.1' local_pytorch_version = '1.8.1' local_pysuff = '-Python-%(pyver)s' @@ -13,8 +13,8 @@ of the logics can be implemented in any major frameworks, such as PyTorch, Apach toolchain = {'name': 'fosscuda', 'version': '2019b'} -source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s_cu101'] -sources = ['%(name)s_cu101-%(version)s-cp37-cp37m-manylinux1_%(arch)s.whl'] +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/%(namelower)s_cu101'] +sources = ['%(namelower)s_cu101-%(version)s-cp37-cp37m-manylinux1_%(arch)s.whl'] checksums = ['6dbc7830fec82f29d4f884790290fef41c2cea45b0052748af2ec30679cf9cb2'] From 97f69ff0fc396eb9ddfb23ca711fe02b92364e5f Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 27 Aug 2021 11:12:42 +0200 Subject: [PATCH 1095/9987] fix homepage url --- .../DGL/DGL-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DGL/DGL-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb b/easybuild/easyconfigs/d/DGL/DGL-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb index 2a90696e436..174ca4ba226 100644 --- a/easybuild/easyconfigs/d/DGL/DGL-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/d/DGL/DGL-0.6.1-fosscuda-2019b-Python-3.7.4-PyTorch-1.8.1.eb @@ -6,7 +6,7 @@ local_pytorch_version = '1.8.1' local_pysuff = '-Python-%(pyver)s' versionsuffix = local_pysuff + '-PyTorch-%s' % local_pytorch_version -homepage = 'https://dgl.ai' +homepage = 'https://www.dgl.ai' description = """DGL is an easy-to-use, high performance and scalable Python package for deep learning on graphs. DGL is framework agnostic, meaning if a deep graph model is a component of an end-to-end application, the rest of the logics can be implemented in any major frameworks, such as PyTorch, Apache MXNet or TensorFlow.""" From ceb88c22652945b91e52aeb12fe6506c72793b72 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 27 Aug 2021 11:21:38 +0200 Subject: [PATCH 1096/9987] add download link and explanation --- .../PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb index 7ce568784c4..37b027f656d 100644 --- a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-292-GCCcore-8.3.0-Python-3.7.4.eb @@ -10,6 +10,9 @@ homepage = 'https://www.pyrosetta.org/' toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +# After aquiring a license here https://els2.comotion.uw.edu/product/pyrosetta, +# PyRosetta4.Release.python37.linux.release-292.tar.bz2 can be downloaded from +# https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python37.linux/ sources = ['%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2'] checksums = [ From b2110071adbacc0f93f69112243d090e0b0f216f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 27 Aug 2021 12:37:43 +0100 Subject: [PATCH 1097/9987] adding easyconfigs: inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb, inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb --- .../inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb | 34 +++++++++++++++++++ .../inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb create mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..7262a984813 --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'inferCNV' +version = '1.3.3' +versionsuffix = '-Python-%(pyver)s' +local_biocver = '3.12' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +source_urls = [GITHUB_SOURCE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['693f7399a232a6cdd7f84bb4038420bdc5ca681545f9b124edb256c390fba541'] + +github_account = 'broadinstitute' +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('R', '4.0.3'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-10', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +options = {'modulename': 'infercnv'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..246b84b605d --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'inferCNV' +version = '1.3.3' +versionsuffix = '-Python-%(pyver)s' +local_biocver = '3.13' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +source_urls = [GITHUB_SOURCE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['693f7399a232a6cdd7f84bb4038420bdc5ca681545f9b124edb256c390fba541'] + +github_account = 'broadinstitute' +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('R', '4.1.0'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-10', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +options = {'modulename': 'infercnv'} + +moduleclass = 'bio' From 44488128d34fec7da0dda5a9f9d0775dadf49165 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 27 Aug 2021 12:49:33 +0100 Subject: [PATCH 1098/9987] Remove versionsuffix for newer toolchains --- .../i/inferCNV/inferCNV-1.3.3-foss-2020b.eb | 33 +++++++++++++++++++ .../i/inferCNV/inferCNV-1.3.3-foss-2021a.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b.eb new file mode 100644 index 00000000000..7236c47e7ff --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'RPackage' + +name = 'inferCNV' +version = '1.3.3' +local_biocver = '3.12' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +source_urls = [GITHUB_SOURCE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['693f7399a232a6cdd7f84bb4038420bdc5ca681545f9b124edb256c390fba541'] + +github_account = 'broadinstitute' +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('R', '4.0.3'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-10', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +options = {'modulename': 'infercnv'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a.eb new file mode 100644 index 00000000000..153e7e14922 --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a.eb @@ -0,0 +1,33 @@ +easyblock = 'RPackage' + +name = 'inferCNV' +version = '1.3.3' +local_biocver = '3.13' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +source_urls = [GITHUB_SOURCE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['693f7399a232a6cdd7f84bb4038420bdc5ca681545f9b124edb256c390fba541'] + +github_account = 'broadinstitute' +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('R', '4.1.0'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-10', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +options = {'modulename': 'infercnv'} + +moduleclass = 'bio' From c9089f5a78a2c91e5540defb4e362d61ba0e0e9e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 27 Aug 2021 12:50:03 +0100 Subject: [PATCH 1099/9987] Delete inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb Remove versionsuffix version --- .../inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb deleted file mode 100644 index 7262a984813..00000000000 --- a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2020b-Python-3.8.6.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'RPackage' - -name = 'inferCNV' -version = '1.3.3' -versionsuffix = '-Python-%(pyver)s' -local_biocver = '3.12' - -homepage = 'https://github.com/broadinstitute/inferCNV/wiki' -description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence - for somatic large-scale chromosomal copy number alterations, such as gains or - deletions of entire chromosomes or large segments of chromosomes.""" - -source_urls = [GITHUB_SOURCE] -sources = ['%(namelower)s-v%(version)s.tar.gz'] -checksums = ['693f7399a232a6cdd7f84bb4038420bdc5ca681545f9b124edb256c390fba541'] - -github_account = 'broadinstitute' -toolchain = {'name': 'foss', 'version': '2020b'} - -dependencies = [ - ('Python', '3.8.6'), - ('R', '4.0.3'), - ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), - ('rjags', '4-10', '-R-%(rver)s'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['infercnv'], -} - -options = {'modulename': 'infercnv'} - -moduleclass = 'bio' From dab95e6c186ee2d813f5715429fa92cf4a8cda9c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 27 Aug 2021 12:50:19 +0100 Subject: [PATCH 1100/9987] Delete inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb Remove versionsuffix version --- .../inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb deleted file mode 100644 index 246b84b605d..00000000000 --- a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.3.3-foss-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'RPackage' - -name = 'inferCNV' -version = '1.3.3' -versionsuffix = '-Python-%(pyver)s' -local_biocver = '3.13' - -homepage = 'https://github.com/broadinstitute/inferCNV/wiki' -description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence - for somatic large-scale chromosomal copy number alterations, such as gains or - deletions of entire chromosomes or large segments of chromosomes.""" - -source_urls = [GITHUB_SOURCE] -sources = ['%(namelower)s-v%(version)s.tar.gz'] -checksums = ['693f7399a232a6cdd7f84bb4038420bdc5ca681545f9b124edb256c390fba541'] - -github_account = 'broadinstitute' -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', '3.9.5'), - ('R', '4.1.0'), - ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), - ('rjags', '4-10', '-R-%(rver)s'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['infercnv'], -} - -options = {'modulename': 'infercnv'} - -moduleclass = 'bio' From dba95a0f91a631c950e766a987f13f73b31036f0 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 27 Aug 2021 16:10:38 +0200 Subject: [PATCH 1101/9987] adding easyconfigs: sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb --- .../sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..03810b3b73c --- /dev/null +++ b/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'sinto' + +version = '0.7.3.1' + +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://timoast.github.io/sinto/index.html' + +description = """Sinto is a toolkit for processing aligned single-cell data. Sinto includes functions to: + + Subset reads from a BAM file by cell barcode + + Create a scATAC-seq fragments file from a BAM file + + Add read tags to a BAM file according to cell barcode information +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c4f3c1413a5c5e2d3587654f7bf53669df883e4d77bb64a846bcbc3c74757c53'] + +dependencies = [ + ('Python', '3.8.6'), + ('Pysam', '0.16.0.1'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'bio' From 633e67b11c21124522047a57839ad7675e29c826 Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 27 Aug 2021 17:43:52 +0000 Subject: [PATCH 1102/9987] Explicitly stated in module description that faToVcf is included in this module --- easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb index 88410f8df90..27fb032225b 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb @@ -9,7 +9,8 @@ name = 'pangolin' version = '3.1.10' homepage = 'https://cov-lineages.org/pangolin.html' -description = "Software package for assigning SARS-CoV-2 genome sequences to global lineages." +description = """Software package for assigning SARS-CoV-2 genome sequences to global lineages. +This module also contains the faToVcf tool""" toolchain = {'name': 'foss', 'version': '2020b'} From 87e7639bb6e1265e78fa4cb9e56054bb64fed18a Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 27 Aug 2021 18:35:29 +0000 Subject: [PATCH 1103/9987] minimap2 downgraded to 2.18 to honor the one version rule --- easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb index 27fb032225b..dcde3cd6fc9 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Biopython', '1.78'), ('gofasta', '0.0.5', '', True), - ('minimap2', '2.20'), + ('minimap2', '2.18'), ('Pysam', '0.16.0.1'), ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), From e271070f6b00b98e58f5d96673aa4fd210982dda Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 28 Aug 2021 10:41:31 +0200 Subject: [PATCH 1104/9987] clean up pangolin easyconfig by leveraging exts_default_options --- .../p/pangolin/pangolin-3.1.10-foss-2020b.eb | 26 ++++++++++--------- 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb index dcde3cd6fc9..fa6a5add039 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb @@ -31,31 +31,33 @@ use_pip = True sanity_pip_check = True github_account = 'cov-lineages' +exts_default_options = { + 'source_urls': [GITHUB_SOURCE], + 'sources': [{ + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], +} + exts_list = [ ('pangolin', '3.1.11', { - 'source_urls': [GITHUB_SOURCE], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['ce64a3ef84de5b11d5c9f21f76341cae23c0fabbf46cc3c1b7b244701b36efbc'], }), ('pangoLEARN', '2021-08-09', { 'modulename': 'pangoLEARN', - 'source_urls': [GITHUB_SOURCE], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{ + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], 'checksums': ['ece55bc37b3e35dbdff2432fb8b9ea76fa53fe993394a425d1df67147484a81e'], }), ('scorpio', '0.3.12', { - 'source_urls': [GITHUB_SOURCE], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['48390ed1c1a79bb5f801083042cdeddee060e2277f40c293fd30384882aced81'], }), ('constellations', '0.0.13', { - 'source_urls': [GITHUB_SOURCE], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['4aa3edae9491a59621ef6a3b5bbd21a13c68355986f6c097e46a1397d5b1d24b'], }), ('pango-designation', '1.2.59', { - 'source_urls': [GITHUB_SOURCE], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['bd6c11b376c2f6955afa9e96938464184e5f6db22334589cbbbfefe1cbe35e86'], }), ] @@ -67,12 +69,12 @@ local_binaries = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in local_binaries], - 'dirs': ['lib'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ 'pangolin -pv', - 'scorpio -v' + 'scorpio -v', ] moduleclass = 'bio' From e287b73e69cc1a4bebaa2f993262fe24161e8fa4 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 28 Aug 2021 10:10:49 +0100 Subject: [PATCH 1105/9987] minor layout improvements --- easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.3.0.eb | 4 +--- easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb | 4 ++-- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.3.0.eb index ab1dd89b2dd..f71f64347e5 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.3.0.eb @@ -9,9 +9,7 @@ toolchainopts = {'pic': True} source_urls = [homepage] sources = ['%(name)s-%(version)s.tar'] -checksums = [ - '83e4f2061b3d4a8bd431ba860dda8c5cf103b25f42d265b7b724b9acafad177c', # g2clib-1.6.0.tar -] +checksums = ['83e4f2061b3d4a8bd431ba860dda8c5cf103b25f42d265b7b724b9acafad177c'] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb index b2210185d88..5d3b36cf9d7 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb @@ -23,8 +23,8 @@ dependencies = [ ('libpng', '1.6.37'), ] -buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FFLAGS="$FFLAGS -fno-range-check \ --fallow-invalid-boz -fallow-argument-mismatch -I." FC=$FC CC=$CC' +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FC=$FC CC=$CC ' +buildopts += 'FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -fallow-argument-mismatch -I."' # parallel build tends to fail parallel = 1 From 945b0f382ee8ad4e2360b0dbc08825bdc1e2579b Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 28 Aug 2021 10:25:59 +0100 Subject: [PATCH 1106/9987] Update easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb --- easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb index 5d3b36cf9d7..3933cb8116e 100644 --- a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.3.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('libpng', '1.6.37'), ] -buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FC=$FC CC=$CC ' +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FC=$FC CC=$CC ' buildopts += 'FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -fallow-argument-mismatch -I."' # parallel build tends to fail From 376df95ea4dd7ab2c58961886ec1c2956a61b3c6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 28 Aug 2021 10:39:23 +0100 Subject: [PATCH 1107/9987] adding easyconfigs: pangolin-3.1.11-foss-2020b.eb --- .../p/pangolin/pangolin-3.1.11-foss-2020b.eb | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb new file mode 100644 index 00000000000..a782c5e9a6a --- /dev/null +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb @@ -0,0 +1,81 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on a EC provided by Paul Jähne +# uploaded by J. Sassmannshausen + +easyblock = 'PythonBundle' + +name = 'pangolin' +version = '3.1.11' + +homepage = 'https://cov-lineages.org/pangolin.html' +description = """Software package for assigning SARS-CoV-2 genome sequences to global lineages. +This module also contains the faToVcf tool""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Biopython', '1.78'), + ('gofasta', '0.0.5', '', True), + ('minimap2', '2.18'), + ('Pysam', '0.16.0.1'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('snakemake', '6.1.0'), + ('UShER', '0.4.1'), + ('scikit-learn', '0.23.2'), + ('Kent_tools', '411'), +] + +use_pip = True +sanity_pip_check = True + +github_account = 'cov-lineages' +exts_default_options = { + 'source_urls': [GITHUB_SOURCE], + 'sources': [{ + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], +} + +exts_list = [ + (name, version, { + 'checksums': ['ce64a3ef84de5b11d5c9f21f76341cae23c0fabbf46cc3c1b7b244701b36efbc'], + }), + ('pangoLEARN', '2021-08-09', { + 'modulename': 'pangoLEARN', + 'sources': [{ + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], + 'checksums': ['ece55bc37b3e35dbdff2432fb8b9ea76fa53fe993394a425d1df67147484a81e'], + }), + ('scorpio', '0.3.12', { + 'checksums': ['48390ed1c1a79bb5f801083042cdeddee060e2277f40c293fd30384882aced81'], + }), + ('constellations', '0.0.13', { + 'checksums': ['4aa3edae9491a59621ef6a3b5bbd21a13c68355986f6c097e46a1397d5b1d24b'], + }), + ('pango-designation', '1.2.59', { + 'checksums': ['bd6c11b376c2f6955afa9e96938464184e5f6db22334589cbbbfefe1cbe35e86'], + }), +] + +local_binaries = [ + 'constellations', 'extract_definitions.py', 'pango_designation', 'pangoLEARN', + 'pangolearn.smk', 'pangolin', 'scorpio', 'type_constellations.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'pangolin -v', + 'pangolin -pv', + 'scorpio -v', +] + +moduleclass = 'bio' From 0a3fe4562f9f1f55fcebe3e8705a291c4cdecccc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 28 Aug 2021 10:40:11 +0100 Subject: [PATCH 1108/9987] delete existing pangolin ec --- .../p/pangolin/pangolin-3.1.10-foss-2020b.eb | 80 ------------------- 1 file changed, 80 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb deleted file mode 100644 index fa6a5add039..00000000000 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.10-foss-2020b.eb +++ /dev/null @@ -1,80 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# Based on a EC provided by Paul Jähn -# uploaded by J. Sassmannshausen - -easyblock = 'PythonBundle' - -name = 'pangolin' -version = '3.1.10' - -homepage = 'https://cov-lineages.org/pangolin.html' -description = """Software package for assigning SARS-CoV-2 genome sequences to global lineages. -This module also contains the faToVcf tool""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -dependencies = [ - ('Biopython', '1.78'), - ('gofasta', '0.0.5', '', True), - ('minimap2', '2.18'), - ('Pysam', '0.16.0.1'), - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('snakemake', '6.1.0'), - ('UShER', '0.4.1'), - ('scikit-learn', '0.23.2'), - ('Kent_tools', '411'), -] - -use_pip = True -sanity_pip_check = True - -github_account = 'cov-lineages' -exts_default_options = { - 'source_urls': [GITHUB_SOURCE], - 'sources': [{ - 'download_filename': 'v%(version)s.tar.gz', - 'filename': SOURCE_TAR_GZ, - }], -} - -exts_list = [ - ('pangolin', '3.1.11', { - 'checksums': ['ce64a3ef84de5b11d5c9f21f76341cae23c0fabbf46cc3c1b7b244701b36efbc'], - }), - ('pangoLEARN', '2021-08-09', { - 'modulename': 'pangoLEARN', - 'sources': [{ - 'download_filename': '%(version)s.tar.gz', - 'filename': SOURCE_TAR_GZ, - }], - 'checksums': ['ece55bc37b3e35dbdff2432fb8b9ea76fa53fe993394a425d1df67147484a81e'], - }), - ('scorpio', '0.3.12', { - 'checksums': ['48390ed1c1a79bb5f801083042cdeddee060e2277f40c293fd30384882aced81'], - }), - ('constellations', '0.0.13', { - 'checksums': ['4aa3edae9491a59621ef6a3b5bbd21a13c68355986f6c097e46a1397d5b1d24b'], - }), - ('pango-designation', '1.2.59', { - 'checksums': ['bd6c11b376c2f6955afa9e96938464184e5f6db22334589cbbbfefe1cbe35e86'], - }), -] - -local_binaries = [ - 'constellations', 'extract_definitions.py', 'pango_designation', 'pangoLEARN', - 'pangolearn.smk', 'pangolin', 'scorpio', 'type_constellations.py' -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_binaries], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - 'pangolin -pv', - 'scorpio -v', -] - -moduleclass = 'bio' From ff3497d119ba937e9425b98996add8713d7f7367 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 28 Aug 2021 15:04:32 +0100 Subject: [PATCH 1109/9987] remove unneeded source_urls --- easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb index a67dbeea4c2..6297f03ff60 100644 --- a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb @@ -9,7 +9,6 @@ description = """Imageio is a Python library that provides an easy interface to toolchain = {'name': 'fosscuda', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] From 0dd5ba041d50c44ca79a48ba19e80c838ca869ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Aug 2021 12:12:06 +0200 Subject: [PATCH 1110/9987] avoid that existing OpenMM Python bindings get wiped + run tests for run_alphafold.py script --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 91d5b657e7f..084f05c3353 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -33,6 +33,11 @@ dependencies = [ local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' @@ -50,8 +55,7 @@ components = [ ], 'start_dir': 'openmm-%(version)s', 'preinstallopts': local_openmm_preinstallopts, - # required to install OpenMM Python API - 'installopts': " && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s", + 'installopts': local_openmm_installopts, }), (name, version, { 'easyblock': 'PythonPackage', @@ -142,12 +146,16 @@ postinstallcmds = [ "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", ] sanity_check_paths = { 'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts', 'stereo_chemical_props.txt'], } sanity_check_commands = [ @@ -156,11 +164,11 @@ sanity_check_commands = [ "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] +sanity_pip_check = True + modextrapaths = { 'OPENMM_INCLUDE_PATH': 'include', 'OPENMM_LIB_PATH': 'lib', } -sanity_pip_check = True - moduleclass = 'bio' From a53f6c809eb2401b3d417c6369db7d0e3c52f330 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Aug 2021 13:47:17 +0200 Subject: [PATCH 1111/9987] fix AlphaFold sanity check (stereo_chemical_props.txt is a file, not a directory) --- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 084f05c3353..68e9ef8b855 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -154,8 +154,8 @@ postinstallcmds = [ sanity_check_paths = { 'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts', 'stereo_chemical_props.txt'], + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } sanity_check_commands = [ From 9c92440813faa5898364c42f9ccf550edb3a945f Mon Sep 17 00:00:00 2001 From: Guillaume Moutier Date: Mon, 30 Aug 2021 08:28:31 -0400 Subject: [PATCH 1112/9987] fix sanity check error --- .../o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb | 17 ++++++++++++++++- .../OpenCV-4.5.1-fosscuda-2020b-contrib.eb | 17 ++++++++++++++++- 2 files changed, 32 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb index 82699bcc1ef..cf24b5ca039 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb @@ -37,6 +37,8 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # for numpy ('zlib', '1.2.11'), ('FFmpeg', '4.3.1'), + ('freetype', '2.10.3'), + ('HarfBuzz', '2.6.7'), ('libjpeg-turbo', '2.0.5'), ('libpng', '1.6.37'), ('LibTIFF', '4.1.0'), @@ -50,7 +52,20 @@ dependencies = [ ('HDF5', '1.10.7'), # needed by hdf from contrib ] -configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules' +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules ' +configopts += '-DFREETYPE_FOUND=ON ' +configopts += '-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/ ' +configopts += '-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DHARFBUZZ_FOUND=ON ' +configopts += '-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz ' +configopts += '-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DBUILD_opencv_python2=OFF ' enhance_sanity_check = True diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb index dd102dc3aed..5fe200231f7 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb @@ -37,6 +37,8 @@ dependencies = [ ('SciPy-bundle', '2020.11'), # for numpy ('zlib', '1.2.11'), ('FFmpeg', '4.3.1'), + ('freetype', '2.10.3'), + ('HarfBuzz', '2.6.7'), ('libjpeg-turbo', '2.0.5'), ('libpng', '1.6.37'), ('LibTIFF', '4.1.0'), @@ -50,7 +52,20 @@ dependencies = [ ('HDF5', '1.10.7'), # needed by hdf from contrib ] -configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules' +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules ' +configopts += '-DFREETYPE_FOUND=ON ' +configopts += '-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/ ' +configopts += '-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DHARFBUZZ_FOUND=ON ' +configopts += '-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz ' +configopts += '-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DBUILD_opencv_python2=OFF ' enhance_sanity_check = True From bf7ab99cb86b28677dcff6e9e27f0df8dd74bb04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Aug 2021 15:13:06 +0200 Subject: [PATCH 1113/9987] collapse PDBFixer easyconfig as extension into AlphaFold easyconfig, to avoid depending on two variants of OpenMM --- .../a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 9 +++-- .../p/PDBFixer/PDBFixer-1.7-foss-2020b.eb | 34 ------------------- 2 files changed, 7 insertions(+), 36 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 68e9ef8b855..624edcc5ab5 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -26,7 +26,6 @@ dependencies = [ ('HH-suite', '3.3.0'), ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), - ('PDBFixer', '1.7'), ('jax', '0.2.19'), # also provides absl-py ] @@ -96,6 +95,11 @@ components = [ use_pip = True exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), ('toolz', '0.11.1', { 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], }), @@ -153,12 +157,13 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } sanity_check_commands = [ + "pdbfixer --help", "python -m simtk.testInstallation", "python -c 'import alphafold'", "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", diff --git a/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb b/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb deleted file mode 100644 index 89173238ef0..00000000000 --- a/easybuild/easyconfigs/p/PDBFixer/PDBFixer-1.7-foss-2020b.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PDBFixer' -version = '1.7' - -homepage = 'https://github.com/openmm/pdbfixer' -description = """PDBFixer is an easy to use application for fixing problems in Protein Data Bank files in preparation -for simulating them.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://github.com/openmm/pdbfixer/archive/refs/tags/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'] - -dependencies = [ - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('OpenMM', '7.5.1'), -] - -download_dep_fail = True -use_pip = True - -sanity_check_paths = { - 'files': ['bin/pdbfixer'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["pdbfixer --help"] - -sanity_pip_check = True - -moduleclass = 'bio' From f9c5efa34b522e5f3c2d5f8ba6da4fcdd9f77591 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 30 Aug 2021 15:19:29 +0200 Subject: [PATCH 1114/9987] consistently use %(version)s template in list of patches for AlphaFold --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index 624edcc5ab5..bcfc97f3b65 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -77,7 +77,7 @@ components = [ 'AlphaFold-%(version)s_fix-packages.patch', 'AlphaFold-%(version)s_data-dep-paths.patch', 'AlphaFold-%(version)s_n-cpu.patch', - 'AlphaFold-2.0.0_fix-scp-path.patch', + 'AlphaFold-%(version)s_fix-scp-path.patch', ], 'checksums': [ '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz From e8b87aaa6713c8b8bb1b3174b17e5ce374efb77e Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 30 Aug 2021 13:42:30 +0000 Subject: [PATCH 1115/9987] artic updated to latest version and foss-2020b, WIP --- .../artic-ncov2019-2021.06.21-foss-2020b.eb | 143 ++++++++++++++++++ 1 file changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.21-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.21-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.21-foss-2020b.eb new file mode 100644 index 00000000000..3e5ba7f8c42 --- /dev/null +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.21-foss-2020b.eb @@ -0,0 +1,143 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to latest version 24. Jun 2021 and bumped to foss-2020b +# to use it with pangolin +# J. Sassmannshausen (GSTT/NHS UK) + +easyblock = 'PythonBundle' + +name = 'artic-ncov2019' +local_commit = 'b3f2dda5e6d95bc1c5d95a04d4ef37d304479477' +version = '2021.06.21' + +homepage = "https://github.com/artic-network/artic-ncov2019" +description = """Initial implementation of an ARTIC bioinformatics platform +for nanopore sequencing of nCoV2019 novel coronavirus.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), # pandas, + ('Biopython', '1.78'), + ('Pysam', '0.16.0.1'), + ('BWA', '0.7.17'), + ('Eigen', '3.3.4', '', True), + ('minimap2', '2.20'), + ('SAMtools', '1.12'), + ('MUSCLE', '3.8.31'), + ('ETE', '3.1.2'), + ('MAFFT', '7.475', '-with-extensions'), + ('IQ-TREE', '2.1.2'), + ('snakemake', '6.1.0'), + ('Longshot', '0.4.3'), + ('medaka', '0.11.4'), + ('python-parasail', '1.2.4'), + ('PhyML', '3.3.20190321'), + ('nodejs', '12.19.0'), + ('goalign', '0.3.2', '', True), + ('gotree', '0.4.0', '', True), + ('rampart', '1.2.0rc3'), + ('libdeflate', '1.5'), + ('nanopolish', '0.13.3'), + ('seqtk', '1.3'), + ('BCFtools', '1.9'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('zipp', '1.0.0', { + 'checksums': ['d38fbe01bbf7a3593a32bc35a9c4453c32bc42b98c377f9bff7e9f8da157786c'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('py', '1.8.1', { + 'checksums': ['5e27081401262157467ad6e7f851b7aa402c5852dbcb3dae06768434de5752aa'], + }), + ('wcwidth', '0.1.9', { + 'checksums': ['ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1'], + }), + ('attrs', '19.3.0', { + 'modulename': 'attr', + 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], + }), + ('importlib-metadata', '1.6.0', { + 'modulename': 'importlib_metadata', + 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', + 'checksums': ['34513a8a0c4962bc66d35b359558fd8a5e10cd472d37aec5f66858addef32c1e'], + }), + ('more-itertools', '8.2.0', { + 'modulename': 'more_itertools', + 'checksums': ['b1ddb932186d8a6ac451e1d95844b382f55e12686d51ca0c68b6f61f2ab7a507'], + }), + ('packaging', '14.5', { + 'checksums': ['363f9193daa14085b8dfeeb2bf64227bcf1dc85c02ae2a5c6018b01f77e46491'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('pytest', '5.4.1', { + 'checksums': ['84dde37075b8805f3d1f392cc47e38a0e59518fb46a431cfdaf7cf1ce805f970'], + }), + ('tqdm', '4.45.0', { + 'checksums': ['00339634a22c10a7a22476ee946bbde2dbe48d042ded784e4d88e0236eca5d81'], + }), + ('fieldbioinformatics', '1.1.0-rc2', { + 'modulename': False, + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/fieldbioinformatics/archive'], + 'checksums': [('7083f67b1188e8f9b55f8bd4f7a46853e9c74ae7dde324b1fc8e792a85e58073', + '778ed3cf2f1b0457c696acbed8b99951b2ec042a2035f08bddd95da3884b146b')], + }), + # This is not upstream version, but artic tweaked one, which is exactly required. + ('Porechop', '0.3.2pre', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/Porechop/archive'], + 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], + }), + ('binlorry', '1.3.1', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/rambaut/binlorry/archive'], + 'checksums': ['001b74cad497b7253b821ceaac8c0b829b2787396a896fc2d3940a704a149b48'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('PyVCF', '0.6.8', { + 'modulename': 'vcf', + 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], + }), + ('ont-fast5-api', '3.1.1', { + 'modulename': 'ont_fast5_api', + 'checksums': ['ce5a955c5e90a393f040fb36fc461382339fc0b9cd63e3969b9763127dc2b0d3'], + }), +] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': ['https://github.com/artic-network/artic-ncov2019/archive/'], + 'sources': [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, + }], + 'checksums': ['26bc96742e291795d4a7c1154336715d98168d8ce3524ad7adfea0b5562eb34d'], + }), +] +local_artic_bins = [ + 'artic', 'artic_fasta_header', 'artic_make_depth_mask', 'artic_mask', 'artic_vcf_filter', 'artic_vcf_merge' +] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_artic_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'artic -v', +] + +moduleclass = 'bio' From cefa79984c1e4f8e0d6d10c361d9ec41d58abe38 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 30 Aug 2021 13:44:22 +0000 Subject: [PATCH 1116/9987] medaka updated to latest version and foss-2020b, required by artic (PR# 13852), WIP --- .../m/medaka/medaka-1.4.3-foss-2020b.eb | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb new file mode 100644 index 00000000000..b82b55027f4 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -0,0 +1,83 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.4.3' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [('Autotools', '20200321')] + +dependencies = [ + ('Python', '3.8.6'), # includes cffi + # TensorFlow 2.2.2 required by medaka 1.4.3, see requirements.txt + ('TensorFlow', '2.2.2'), + ('Biopython', '1.78'), + ('h5py', '3.1.0'), + # Pysam 0.16.0.1 is strictly required, see requirements.txt + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.12'), + # minimap2 is version 2.18 in pangolin, so we need the same version here + ('minimap2', '2.18'), + ('HTSlib', '1.11'), # for tabix, bgzip + ('Racon', '1.4.21'), + ('spoa', '4.0.7'), + ('networkx', '2.6.2'), + ('edlib', '1.3.9'), + ('pyspoa', '0.0.8'), + ('ont-fast5-api', '3.3.0'), + ('pyfaidx', '0.5.9.5'), +] + +use_pip = True + +exts_list = [ + ('mappy', '2.20', { + 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], + }), + ('parasail', '1.2.4', { + 'checksums': ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'], + }), + ('isal', '0.10.0', { + 'checksums': ['3f89471065c2837d1235877dbdcdbd8b7649068723026b0582010fa106a71ff3'], + }), + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + ('whatshap', '1.1', { + 'checksums': ['4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + (name, version, { + 'patches': ['medaka-1.4.3_use-SAMtools-dep.patch'], + 'checksums': [ + '59997b5fdaff6f2040f2df2d3d3eb2d6d1805916a720e8275309caf4d2d4b8a5', # medaka-1.4.3.tar.gz + '06b1d8344035ebcfaf1893e62f37db9b4cab0053ad7a073113630872d44be33e', # medaka-1.4.3_use-SAMtools-dep.patch + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["medaka --help"] + +moduleclass = 'bio' From 0f1979182c43275754ce9178199fa27300411243 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 30 Aug 2021 13:46:02 +0000 Subject: [PATCH 1117/9987] TF bumped to foss-2020b for the fixed requirement for medaka (PR# 13853), WIP --- .../TensorFlow/TensorFlow-2.2.2-foss-2020b.eb | 162 ++++++++++++++++++ 1 file changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.2-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.2-foss-2020b.eb new file mode 100644 index 00000000000..704b782b864 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.2-foss-2020b.eb @@ -0,0 +1,162 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.2.2' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '2.0.0'), + ('protobuf', '3.14.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.28.0', '-nodocs'), + ('pybind11', '2.6.0'), + ('pkgconfig', '1.5.1', '-python'), # For h5py +] +dependencies = [ + ('Python', '3.8.6'), + # Next 2 are for h5py + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), + ('cURL', '7.72.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.2.0'), + ('ICU', '67.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.5'), + ('LMDB', '0.9.24'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.33.0'), + ('PCRE', '8.44'), + ('protobuf-python', '3.14.0'), + ('flatbuffers-python', '1.12'), + ('typing-extensions', '3.7.4.3'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), + # TF 2.2 requires SciPy 1.4.1 due to potential crashes with other versions + # See https://github.com/tensorflow/tensorflow/commit/54daf3c5700897a6062313983933ca28e92c410d + # Add at bottom so it will be loaded after any dependency loading the SciPy-Bundle +# ('scipy', '1.4.1'), +] + +sanity_pip_check = True +use_pip = True + +# We copy this section from TensorFlow-2.2.2-foss-2019b-Python-3.7.4.eb +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.1', { + 'checksums': ['f469e29e7aa4cff64d8de4aad95ce76de8ea1125a16c68e0d93f65c3c3dc92e9'], + }), + ('google-auth', '1.28.0', { + 'modulename': 'google.auth', + 'checksums': ['9bd436d19ab047001a1340720d2b629eb96dd503258c524921ec2af3ee88a80e'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.4', { + 'checksums': ['09832c6e75032f93818edf1affe4746121d640c625a5bef9b5c96af676e98eee'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('absl-py', '0.12.0', { + 'modulename': 'absl', + 'checksums': ['b44f68984a5ceb2607d135a615999b93924c771238a63920d17d3387b0d229d5'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.36.1', { + 'modulename': 'grpc', + 'checksums': ['a66ea59b20f3669df0f0c6a3bd57b985e5b2d1dcf3e4c29819bb8dc232d0fd38'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard', version, { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['a3feb73e1221c0a512398ad2cd08570fb082d8a2ba364aa0562543ecbd3659ef'], + }), + ('tensorboard-plugin-wit', '1.8.0', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard-plugin-profile', '2.2.0', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['fcd2f4a17c53fb080390044459ee03fb8d9e8d109ae5838516fdcbda69ce99f9'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', '2.2.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['d09dacdd127f2579cea8d5af21f4a918036b8ae246adc82f26b61f91cc247dc2'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-system-jsoncpp.patch', + 'TensorFlow-2.1.0_fix-system-nasm.patch', + 'TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'checksums': [ + 'fb4b5d26c5b983350f7ce8297b71176a86a69e91faf66e6ebb1e58538ad3bb51', # v2.2.2.tar.gz + # TensorFlow-2.1.0_fix-system-jsoncpp.patch + 'd0c8ca54a9e2c232908016e08b982dbb63765de3472253cba5ae38d823d5f156', + # TensorFlow-2.1.0_fix-system-nasm.patch + '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', + # TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch + '093f4dd3ec372a82d50dffe32eea6821025cd1c406911a746c4367a40bc38486', + ], + }), +] + +moduleclass = 'lib' From 9d388951612e3ed840ccefb9e26a71e401a0ab1c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 30 Aug 2021 17:27:38 +0200 Subject: [PATCH 1118/9987] adding easyconfigs: Bazel-2.0.0-GCCcore-10.2.0.eb --- .../b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..bac3fa512ec --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +name = 'Bazel' +version = '2.0.0' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = ['Bazel-0.29.1_fix-gold-flag.patch'] +checksums = [ + '724da3c656f68e787a86ebb9844773aa1c2e3a873cc39462a8f1b336153d6cbb', # bazel-2.0.0-dist.zip + '99928d0902beeaf962a8ad14db8432f8e5114645e3caf64c7ee2fa136c31609f', # Bazel-0.29.1_fix-gold-flag.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), + ('Zip', '3.0'), +] +dependencies = [('Java', '1.8', '', True)] + +runtest = True +testopts = ' '.join([ + '--', + '//examples/cpp:hello-success_test', + '//examples/py/...', + '//examples/py_native:test', + '//examples/shell/...', +]) + +moduleclass = 'devel' From b082b43b5230f0d66f09ea7fa706747ea2d0501d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 30 Aug 2021 18:09:15 +0200 Subject: [PATCH 1119/9987] Use Java 11 --- easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb index bac3fa512ec..64cebdfa53f 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Python', '3.8.6'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '11', '', True)] runtest = True testopts = ' '.join([ From 807e0a2068b1ba1c3d9b087619c909c9f8050839 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Aug 2021 19:41:47 +0100 Subject: [PATCH 1120/9987] adding easyconfigs: Xvfb-1.20.13-GCCcore-11.2.0.eb --- .../x/Xvfb/Xvfb-1.20.13-GCCcore-11.2.0.eb | 110 ++++++++++++++++++ 1 file changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.13-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.13-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8260693dbd9 --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.13-GCCcore-11.2.0.eb @@ -0,0 +1,110 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '1.20.13' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('Python', '3.9.6', '-bare'), +] + +dependencies = [ + ('X11', '20210802'), + ('pixman', '0.40.0'), + ('libdrm', '2.4.107'), + ('Mesa', '21.1.7'), + ('nettle', '3.7.3'), + ('libunwind', '1.5.0'), + ('XZ', '5.2.5'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['e5b687029e44d0bd3ccd254a4da6a5cbfc40350aa8b43fcca16ef6e9b9bb9f22'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.3.2', { + 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], + }), + ('font-misc-misc', '1.1.2', { + 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], + 'preconfigopts': local_font_misc_preconfigopts, + }), + ('xkbcomp', '1.4.5', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['e88a4d86b9925ea1e8685dd5ea29c815abafb8ddf19bf5f1a1e0650839252c23'], + }), + ('xkeyboard-config', '2.33', { + 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], + 'checksums': ['112df68e1150e8da421bc0abe79eebeacca16a91e54e1877cb39fc878d17b365'], + 'configopts': '--with-xkb-rules-symlink=xorg', + }), + ('xauth', '1.1', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['e9fce796c8c5c9368594b9e8bbba237fb54b6615f5fd60e8d0a5b3c52a92c5ef'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual/xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + '26f801f4d92216995f389873cf3b4e90069cf63e94bc5dd09ebbf7fd7e1ddcc2', # xorg-server-1.20.13.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' From 3319afa7bb15380d6115fce440082bde410a46b6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Aug 2021 19:42:46 +0100 Subject: [PATCH 1121/9987] adding easyconfigs: UDUNITS-2.2.28-GCCcore-11.2.0.eb --- .../UDUNITS/UDUNITS-2.2.28-GCCcore-11.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..67c01b52a1d --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.28' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/', + 'https://sources.easybuild.io/u/UDUNITS/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['590baec83161a3fd62c00efa66f6113cec8a7c461e3f61a5182167e0cc5d579e'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('expat', '2.4.1')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From 5390ecfc2568ef9973cb7f69d56f7413f6fff9d1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Aug 2021 19:43:14 +0100 Subject: [PATCH 1122/9987] adding easyconfigs: GSL-2.7-GCC-11.2.0.eb --- .../easyconfigs/g/GSL/GSL-2.7-GCC-11.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-11.2.0.eb new file mode 100644 index 00000000000..7c9005c5f82 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.7' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' From 241f69b07aa4e359fd077e8b2b18f5351fd49b8d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Aug 2021 20:05:24 +0100 Subject: [PATCH 1123/9987] adding easyconfigs: HDF-4.2.15-GCCcore-11.2.0.eb, libtirpc-1.3.2-GCCcore-11.2.0.eb --- .../h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb | 62 +++++++++++++++++++ .../libtirpc/libtirpc-1.3.2-GCCcore-11.2.0.eb | 28 +++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..fc36bb04673 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.15' + +homepage = 'https://www.hdfgroup.org/products/hdf4/' + +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['HDF-4.2.15_fix-aarch64.patch'] +checksums = [ + 'dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459', # hdf-4.2.15.tar.gz + '1b4341e309cccefc6ea4310c8f8b08cc3dfe1fa9609b7fa7aee80e4dac598473', # HDF-4.2.15_fix-aarch64.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '2.0.6'), + ('Szip', '2.1.1'), + ('zlib', '1.2.11'), + ('libtirpc', '1.3.2'), +] + +preconfigopts = "LIBS='-ltirpc' " +local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' +local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' +configopts = [ + # -fallow-argument-mismatch is required to compile with GCC 10.x + local_common_configopts + 'FFLAGS="$FFLAGS -fallow-argument-mismatch"', + # Cannot build shared libraries and Fortran... + # https://trac.osgeo.org/gdal/wiki/HDF#IncompatibilitywithNetCDFLibraries + # netcdf must be disabled to allow HDF to be used by GDAL + local_common_configopts + "--enable-shared --disable-fortran --disable-netcdf", +] + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', + 'lib/libmfhdf.%s' % SHLIB_EXT], + 'dirs': ['include/hdf'], +} + +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1721b5f770d --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.2' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['e24eb88b8ce7db3b7ca6eb80115dd1284abc5ec32a8deccfed2224fc2532b9fd'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.37') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' From 07b9d0358c514e71509ccdf19786021db006ca3e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Aug 2021 20:06:00 +0100 Subject: [PATCH 1124/9987] adding easyconfigs: GEOS-3.9.1-GCC-11.2.0.eb, libgeotiff-1.7.0-GCCcore-11.2.0.eb, PROJ-8.1.0-GCCcore-11.2.0.eb --- .../g/GEOS/GEOS-3.9.1-GCC-11.2.0.eb | 20 +++++++++ .../libgeotiff-1.7.0-GCCcore-11.2.0.eb | 36 ++++++++++++++++ .../p/PROJ/PROJ-8.1.0-GCCcore-11.2.0.eb | 42 +++++++++++++++++++ 3 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-8.1.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..f929067beb6 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-GCC-11.2.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.9.1' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7e630507dcac9dc07565d249a26f06a15c9f5b0c52dd29129a0e3d381d7e382a'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a15eb4dbf2a --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.0-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.7.0' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['fc304d8839ca5947cfbeb63adb9d1aa47acef38fc6d6689e622926e672a99a7e'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('PROJ', '8.1.0'), + ('libjpeg-turbo', '2.0.6'), + ('zlib', '1.2.11'), + ('SQLite', '3.36'), + ('LibTIFF', '4.3.0'), + ('cURL', '7.78.0'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-8.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-8.1.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d50f286db7c --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-8.1.0-GCCcore-11.2.0.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '8.1.0' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['22c5cdc5aa0832077b16c95ebeec748a0942811c1c3438c33d43c8d2ead59f48'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.37'), +] + +dependencies = [ + ('SQLite', '3.36'), + ('LibTIFF', '4.3.0'), + ('cURL', '7.78.0'), +] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 7ddae463f4588ed2cd20102ca6525fddd7ea4183 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 30 Aug 2021 20:45:30 +0100 Subject: [PATCH 1125/9987] switch to PCRE in GDAL 3.2.1 and 3.3.0 --- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb | 4 ++-- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb | 4 ++-- easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb | 4 ++-- easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb index a164b3b0354..71748cbee23 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb @@ -37,7 +37,7 @@ dependencies = [ ('LibTIFF', '4.1.0'), ('zlib', '1.2.11'), ('cURL', '7.72.0'), - ('PCRE2', '10.35'), + ('PCRE', '8.44'), ('PROJ', '7.2.1'), ('libgeotiff', '1.6.0'), ('SciPy-bundle', '2020.11'), @@ -50,7 +50,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' -configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb index bcba374a615..606bd64d0d3 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb @@ -37,7 +37,7 @@ dependencies = [ ('LibTIFF', '4.1.0'), ('zlib', '1.2.11'), ('cURL', '7.72.0'), - ('PCRE2', '10.35'), + ('PCRE', '8.44'), ('PROJ', '7.2.1'), ('libgeotiff', '1.6.0'), ('SciPy-bundle', '2020.11'), @@ -50,7 +50,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' -configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb index 74166337429..09c2c1bb820 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb @@ -41,7 +41,7 @@ dependencies = [ ('LibTIFF', '4.1.0'), ('zlib', '1.2.11'), ('cURL', '7.72.0'), - ('PCRE2', '10.35'), + ('PCRE', '8.44'), ('PROJ', '7.2.1'), ('libgeotiff', '1.6.0'), ('SciPy-bundle', '2020.11'), @@ -54,7 +54,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' -configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' prebuildopts = "env LDSHARED='icc -shared' " diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb index dd20522630b..22efb63f6f7 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb @@ -37,7 +37,7 @@ dependencies = [ ('LibTIFF', '4.2.0'), ('zlib', '1.2.11'), ('cURL', '7.76.0'), - ('PCRE2', '10.36'), + ('PCRE', '8.44'), ('PROJ', '8.0.1'), ('libgeotiff', '1.6.0'), ('SciPy-bundle', '2021.05'), @@ -50,7 +50,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' -configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE2 --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 2b1c9d87629e974f1521dd7d6b2bfaa5ddda2cff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 31 Aug 2021 11:32:38 +0200 Subject: [PATCH 1126/9987] adding easyconfigs: QD-0.8.9-foss-2021a.eb --- .../easyconfigs/q/QD/QD-0.8.9-foss-2021a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/q/QD/QD-0.8.9-foss-2021a.eb diff --git a/easybuild/easyconfigs/q/QD/QD-0.8.9-foss-2021a.eb b/easybuild/easyconfigs/q/QD/QD-0.8.9-foss-2021a.eb new file mode 100644 index 00000000000..21c99df9cf6 --- /dev/null +++ b/easybuild/easyconfigs/q/QD/QD-0.8.9-foss-2021a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'QD' +version = '0.8.9' + +# Actual homepage is down. +homepage = 'https://pypi.org/project/qd/' +description = "QD-Engineering Python Library for CAE" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [('binutils', '2.36.1')] +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('diversipy', '0.8', { + 'checksums': ['6abc959e64821c7122137c4352a7c9d45217a26feb2b4d4830d627b0c82b04d4'], + }), + (name, version, { + 'patches': ['QD-%(version)s_remove_pybind_requirement.patch'], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': [ + '711fcc0772011dccddbd971407d79b9bea06f11745162066c6dbbca0f6ff5211', # qd-0.8.9.tar.gz + # QD-0.8.9_remove_pybind_requirement.patch + 'e71750960460221a601deaf1af18aec303998a2a98f0883f9e5da292728147e8', + ], + }), +] + +moduleclass = 'lib' From 9a68bf9ff979887292be0a9df1948eeee91976e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 31 Aug 2021 12:08:54 +0200 Subject: [PATCH 1127/9987] Add patch --- .../q/QD/QD-0.8.9_remove_pybind_requirement.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/q/QD/QD-0.8.9_remove_pybind_requirement.patch diff --git a/easybuild/easyconfigs/q/QD/QD-0.8.9_remove_pybind_requirement.patch b/easybuild/easyconfigs/q/QD/QD-0.8.9_remove_pybind_requirement.patch new file mode 100644 index 00000000000..c36925961b5 --- /dev/null +++ b/easybuild/easyconfigs/q/QD/QD-0.8.9_remove_pybind_requirement.patch @@ -0,0 +1,13 @@ +Requirement on pybind11 is unncessarily strict. +Author: micketeer@gmail.com +--- setup.py.orig 2021-08-31 11:25:48.110514794 +0200 ++++ setup.py 2021-08-31 11:25:53.937501309 +0200 +@@ -325,7 +325,7 @@ + ext_package='qd.cae', # where to place c extensions + ext_modules=[dyna_extension], + install_requires=['numpy>=1.8', +- 'diversipy', 'pybind11==2.1.1', 'h5py'], ++ 'diversipy', 'pybind11', 'h5py'], + keywords=['cae', + 'simulation', + 'engineering', From fafc30b526dc03eb54872f38abc39053c8592303 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 31 Aug 2021 13:47:37 +0200 Subject: [PATCH 1128/9987] adding easyconfigs: GMT-6.2.0-foss-2019b.eb, GMT-6.2.0-foss-2020b.eb --- .../easyconfigs/g/GMT/GMT-6.2.0-foss-2019b.eb | 62 +++++++++++++++++++ .../easyconfigs/g/GMT/GMT-6.2.0-foss-2020b.eb | 62 +++++++++++++++++++ 2 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2019b.eb create mode 100644 easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2019b.eb b/easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2019b.eb new file mode 100644 index 00000000000..98a54697a3e --- /dev/null +++ b/easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2019b.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'GMT' +version = '6.2.0' +local_gshhg_ver = '2.3.7' +local_dcw_ver = '2.0.0' + +homepage = 'https://www.generic-mapping-tools.org/' +description = """GMT is an open source collection of about 80 command-line tools for manipulating + geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, + etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps + to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another + 40 more specialized and discipline-specific tools. """ + +toolchain = {'name': 'foss', 'version': '2019b'} + +# 'https://gmt.soest.hawaii.edu/files/download?name=' needs browser with javascript magic +source_urls = [ + 'ftp://ftp.soest.hawaii.edu/gmt', + 'ftp://ftp.soest.hawaii.edu/gshhg', + 'ftp://ftp.soest.hawaii.edu/dcw', +] +sources = [ + '%(namelower)s-%(version)s-src.tar.gz', + # coastlines, rivers, and political boundaries + 'gshhg-gmt-%s.tar.gz' % local_gshhg_ver, + # country polygons + 'dcw-gmt-%s.tar.gz' % local_dcw_ver, +] +patches = ['GMT-5.1.2_netCDF.patch'] +checksums = [ + 'ab7062912aeead1021770fad4756e0a99860fde8ea9b428fb00c22fa15a3bbfc', # gmt-6.2.0-src.tar.gz + '9bb1a956fca0718c083bef842e625797535a00ce81f175df08b042c2a92cfe7f', # gshhg-gmt-2.3.7.tar.gz + 'd71d209c837a805fed0773c03fadbb26e8c90eb6b68e496ac4a1298c3246cc7a', # dcw-gmt-2.0.0.tar.gz + '2ebe26d55521fba8d0eae48f662611491f7cc0e489833bded11628e9a71f252f', # GMT-5.1.2_netCDF.patch +] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('PCRE', '8.43'), + ('GDAL', '3.0.2', '-Python-3.7.4'), + ('netCDF', '4.7.1'), + ('Ghostscript', '9.50'), + ('cURL', '7.66.0'), + ('zlib', '1.2.11'), +] + +separate_build_dir = True + +configopts = '-DCOPY_GSHHG=TRUE -DGSHHG_ROOT=%%(builddir)s/gshhg-gmt-%s ' % local_gshhg_ver +configopts += '-DCOPY_DCW=TRUE -DDCW_ROOT=%%(builddir)s/dcw-gmt-%s ' % local_dcw_ver + +sanity_check_paths = { + 'files': ['bin/%s' % b for b in ['gmt', 'isogmt', 'gmtswitch', 'gmt_shell_functions.sh']] + + ['lib64/libgmt.%s.%s' % (SHLIB_EXT, version)], + 'dirs': ['include/%(namelower)s', 'share'] +} + +modextrapaths = {'GMTHOME': ''} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2020b.eb new file mode 100644 index 00000000000..51623405d17 --- /dev/null +++ b/easybuild/easyconfigs/g/GMT/GMT-6.2.0-foss-2020b.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'GMT' +version = '6.2.0' +local_gshhg_ver = '2.3.7' +local_dcw_ver = '2.0.0' + +homepage = 'https://www.generic-mapping-tools.org/' +description = """GMT is an open source collection of about 80 command-line tools for manipulating + geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, + etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps + to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another + 40 more specialized and discipline-specific tools. """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +# 'https://gmt.soest.hawaii.edu/files/download?name=' needs browser with javascript magic +source_urls = [ + 'ftp://ftp.soest.hawaii.edu/gmt', + 'ftp://ftp.soest.hawaii.edu/gshhg', + 'ftp://ftp.soest.hawaii.edu/dcw', +] +sources = [ + '%(namelower)s-%(version)s-src.tar.gz', + # coastlines, rivers, and political boundaries + 'gshhg-gmt-%s.tar.gz' % local_gshhg_ver, + # country polygons + 'dcw-gmt-%s.tar.gz' % local_dcw_ver, +] +patches = ['GMT-5.1.2_netCDF.patch'] +checksums = [ + 'ab7062912aeead1021770fad4756e0a99860fde8ea9b428fb00c22fa15a3bbfc', # gmt-6.2.0-src.tar.gz + '9bb1a956fca0718c083bef842e625797535a00ce81f175df08b042c2a92cfe7f', # gshhg-gmt-2.3.7.tar.gz + 'd71d209c837a805fed0773c03fadbb26e8c90eb6b68e496ac4a1298c3246cc7a', # dcw-gmt-2.0.0.tar.gz + '2ebe26d55521fba8d0eae48f662611491f7cc0e489833bded11628e9a71f252f', # GMT-5.1.2_netCDF.patch +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('PCRE', '8.44'), + ('GDAL', '3.2.1'), + ('netCDF', '4.7.4'), + ('Ghostscript', '9.53.3'), + ('cURL', '7.72.0'), + ('zlib', '1.2.11'), +] + +separate_build_dir = True + +configopts = '-DCOPY_GSHHG=TRUE -DGSHHG_ROOT=%%(builddir)s/gshhg-gmt-%s ' % local_gshhg_ver +configopts += '-DCOPY_DCW=TRUE -DDCW_ROOT=%%(builddir)s/dcw-gmt-%s ' % local_dcw_ver + +sanity_check_paths = { + 'files': ['bin/%s' % b for b in ['gmt', 'isogmt', 'gmtswitch', 'gmt_shell_functions.sh']] + + ['lib64/libgmt.%s.%s' % (SHLIB_EXT, version)], + 'dirs': ['include/%(namelower)s', 'share'] +} + +modextrapaths = {'GMTHOME': ''} + +moduleclass = 'geo' From b9ab749cc218457a726628fa116522873ae28ca3 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 31 Aug 2021 14:18:28 +0200 Subject: [PATCH 1129/9987] adding easyconfigs: ANTs-2.3.5-foss-2021a.eb --- .../a/ANTs/ANTs-2.3.5-foss-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTs/ANTs-2.3.5-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.5-foss-2021a.eb b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.5-foss-2021a.eb new file mode 100644 index 00000000000..fe0bc0c4e22 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.5-foss-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'ANTs' +version = '2.3.5' + +homepage = 'https://stnava.github.io/ANTs/' +description = """ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, + interpreting and visualizing multidimensional data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ANTsX/ANTs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2fddfd5f274a47f1c383e734a7e763b627c4a8383d2d3b9971561f335016bb0a'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('VTK', '9.0.1'), +] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release ' +configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON ' +configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF' + +preinstallopts = "cd ANTS-build && " + +sanity_check_paths = { + 'files': ['bin/ANTS', 'bin/antsBrainExtraction.sh'], + 'dirs': ['lib'], +} + +modextravars = {'ANTSPATH': '%(installdir)s/bin'} + +moduleclass = 'data' From 2b90a0cade6538603ff0620fae98157b8a9535d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Tue, 31 Aug 2021 14:24:50 +0200 Subject: [PATCH 1130/9987] adding easyconfigs: Centrifuge-1.0.4-gompi-2020b.eb --- .../Centrifuge-1.0.4-gompi-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2020b.eb diff --git a/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2020b.eb b/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2020b.eb new file mode 100644 index 00000000000..10d20754e0d --- /dev/null +++ b/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Centrifuge' +version = '1.0.4' + +homepage = 'https://ccb.jhu.edu/software/centrifuge' +description = 'Classifier for metagenomic sequences' + +toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/DaehwanKimLab/centrifuge/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '929daed0f84739f7636cc1ea2757527e83373f107107ffeb5937a403ba5201bc', # v1.0.4.tar.gz +] + +dependencies = [ + ('NGS', '2.10.9'), + ('ncbi-vdb', '2.10.9'), +] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CXXFLAGS" ' +buildopts += 'USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB' + +installopts = "prefix=%(installdir)s" + +fix_perl_shebang_for = ['bin/centrifuge*.pl'] + +sanity_check_paths = { + 'files': ['bin/centrifuge%s' % x for x in ['', '-build', '-build-bin', '-class', '-download', + '-inspect', '-inspect-bin']], + 'dirs': [], +} + +sanity_check_commands = ["centrifuge --help"] + +moduleclass = 'bio' From f0ba466ff6f4efa47460b319fc088fd2c95ab3b9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 31 Aug 2021 16:45:17 +0200 Subject: [PATCH 1131/9987] Update and rename TensorFlow-2.2.2-foss-2020b.eb to TensorFlow-2.2.3-foss-2020b.eb Add tests and fix deps --- ...020b.eb => TensorFlow-2.2.3-foss-2020b.eb} | 82 +++++++++++++------ 1 file changed, 57 insertions(+), 25 deletions(-) rename easybuild/easyconfigs/t/TensorFlow/{TensorFlow-2.2.2-foss-2020b.eb => TensorFlow-2.2.3-foss-2020b.eb} (63%) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.2-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb similarity index 63% rename from easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.2-foss-2020b.eb rename to easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb index 704b782b864..d1d6fc11dc3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.2-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'TensorFlow' -version = '2.2.2' +version = '2.2.3' homepage = 'https://www.tensorflow.org/' description = "An open-source software library for Machine Intelligence" @@ -19,9 +19,8 @@ builddependencies = [ ] dependencies = [ ('Python', '3.8.6'), - # Next 2 are for h5py ('SciPy-bundle', '2020.11'), - ('HDF5', '1.10.7'), + ('HDF5', '1.10.7'), # For h5py ('cURL', '7.72.0'), ('double-conversion', '3.1.5'), ('flatbuffers', '1.12.0'), @@ -40,18 +39,24 @@ dependencies = [ ('typing-extensions', '3.7.4.3'), ('libpng', '1.6.37'), ('snappy', '1.1.8'), + ('SWIG', '4.0.2'), ('zlib', '1.2.11'), - # TF 2.2 requires SciPy 1.4.1 due to potential crashes with other versions - # See https://github.com/tensorflow/tensorflow/commit/54daf3c5700897a6062313983933ca28e92c410d - # Add at bottom so it will be loaded after any dependency loading the SciPy-Bundle -# ('scipy', '1.4.1'), ] sanity_pip_check = True use_pip = True -# We copy this section from TensorFlow-2.2.2-foss-2019b-Python-3.7.4.eb exts_list = [ + # TF <= 2.4 needs h5py 2.10, later versions allow 3.x + ('h5py', '2.10.0', { + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], + 'checksums': [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + # h5py-2.10.0_avoid-mpi-init.patch + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', + ], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + }), ('Markdown', '3.3.4', { 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], }), @@ -61,24 +66,24 @@ exts_list = [ ('rsa', '4.7.2', { 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], }), - ('cachetools', '4.2.1', { - 'checksums': ['f469e29e7aa4cff64d8de4aad95ce76de8ea1125a16c68e0d93f65c3c3dc92e9'], + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], }), - ('google-auth', '1.28.0', { + ('google-auth', '1.35.0', { 'modulename': 'google.auth', - 'checksums': ['9bd436d19ab047001a1340720d2b629eb96dd503258c524921ec2af3ee88a80e'], + 'checksums': ['b7033be9028c188ee30200b204ea00ed82ea1162e8ac1df4aa6ded19a191d88e'], }), - ('oauthlib', '3.1.0', { - 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + ('oauthlib', '3.1.1', { + 'checksums': ['8f0215fcc533dd8dd1bee6f4c412d4f0cd7297307d43ac61666389e3bc3198a3'], }), ('requests-oauthlib', '1.3.0', { 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], }), - ('google-auth-oauthlib', '0.4.4', { - 'checksums': ['09832c6e75032f93818edf1affe4746121d640c625a5bef9b5c96af676e98eee'], + ('google-auth-oauthlib', '0.4.5', { + 'checksums': ['4ab58e6c3dc6ccf112f921fcced40e5426fba266768986ea502228488276eaba'], }), - ('Werkzeug', '1.0.1', { - 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + ('Werkzeug', '2.0.1', { + 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], }), ('absl-py', '0.12.0', { 'modulename': 'absl', @@ -87,15 +92,15 @@ exts_list = [ ('astunparse', '1.6.3', { 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], }), - ('grpcio', '1.36.1', { + ('grpcio', '1.39.0', { 'modulename': 'grpc', - 'checksums': ['a66ea59b20f3669df0f0c6a3bd57b985e5b2d1dcf3e4c29819bb8dc232d0fd38'], + 'checksums': ['57974361a459d6fe04c9ae0af1845974606612249f467bbd2062d963cb90f407'], }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], }), - ('tensorboard', version, { + ('tensorboard', '2.2.2', { 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'unpack_sources': False, 'checksums': ['a3feb73e1221c0a512398ad2cd08570fb082d8a2ba364aa0562543ecbd3659ef'], @@ -138,24 +143,51 @@ exts_list = [ 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], }), + # For tests + ('portpicker', '1.4.0', { + 'checksums': ['c2831ff4328a21e928ffc9e52124bcafacaf5816d38a1a72dc329680dc1bb7ba'], + }), (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'patches': [ 'TensorFlow-2.1.0_fix-system-jsoncpp.patch', 'TensorFlow-2.1.0_fix-system-nasm.patch', 'TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch', + 'TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch', + 'TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch', + 'TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch', + 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], - 'test_script': 'TensorFlow-2.x_mnist-test.py', 'checksums': [ - 'fb4b5d26c5b983350f7ce8297b71176a86a69e91faf66e6ebb1e58538ad3bb51', # v2.2.2.tar.gz + '5e6c779ca8392864d436d88893461dcce783c3a8d46dcb2b2f2ee8ece3cc4538', # v2.2.3.tar.gz # TensorFlow-2.1.0_fix-system-jsoncpp.patch 'd0c8ca54a9e2c232908016e08b982dbb63765de3472253cba5ae38d823d5f156', # TensorFlow-2.1.0_fix-system-nasm.patch '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', # TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch '093f4dd3ec372a82d50dffe32eea6821025cd1c406911a746c4367a40bc38486', + # TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch + '85c3023892e21692e14750e43a7d1db3c83c6e86a75ac1559c9dba39e0a160ae', + # TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch + 'd80e0103aeefb5244b57dd0e01bb7a0c1e6a750fba41833706547be87d3829e4', + # TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch + '9588f324b4ac5b90e77f8c1d64bd65f3ef64677f82603c0742e4f3a9e99ac171', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'with_xla': True, }), ] From d5766e7c3cf96d72764f9e9d29835146a68510c4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 31 Aug 2021 16:48:20 +0200 Subject: [PATCH 1132/9987] Add patches --- ...sorflow_core_graph_mkl_related_tests.patch | 207 ++++++++++++++++++ ...low-2.2.3_fix-numpy-UFunc-sig-change.patch | 108 +++++++++ ....3_fix-source_utils_test-in-python38.patch | 93 ++++++++ 3 files changed, 408 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch new file mode 100644 index 00000000000..37586b4798b --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch @@ -0,0 +1,207 @@ +From 67fcf3d1efef47c16602ca6ced118a34302d6b78 Mon Sep 17 00:00:00 2001 +From: Mahmoud Abuzaina +Date: Thu, 5 Mar 2020 13:24:22 -0800 +Subject: [PATCH] Fixing __tensorflow_core_graph_mkl_related_tests + +--- + .../core/graph/mkl_tfconversion_pass_test.cc | 84 ++++++++++--------- + 1 file changed, 44 insertions(+), 40 deletions(-) + +diff --git a/tensorflow/core/graph/mkl_tfconversion_pass_test.cc b/tensorflow/core/graph/mkl_tfconversion_pass_test.cc +index 68b6750961f4b..b8235e5140eba 100644 +--- a/tensorflow/core/graph/mkl_tfconversion_pass_test.cc ++++ b/tensorflow/core/graph/mkl_tfconversion_pass_test.cc +@@ -107,20 +107,19 @@ class MklToTfConversionPass : public ::testing::Test { + string original_; + }; + +-REGISTER_OP("Input").Output("o: float").SetIsStateful(); +-REGISTER_OP("HalfInput").Output("o: half").SetIsStateful(); +-REGISTER_OP("_MklInput").Output("o: uint8").SetIsStateful(); ++REGISTER_OP("Float_Input").Output("o: float").SetIsStateful(); ++REGISTER_OP("_Mkl_Input").Output("o: uint8").SetIsStateful(); + + TEST_F(MklToTfConversionPass, Basic) { + InitGraph( +- "node { name: 'A' op: 'Input'}" +- "node { name: 'B' op: 'Input'}" ++ "node { name: 'A' op: 'Float_Input'}" ++ "node { name: 'B' op: 'Float_Input'}" + "node { name: 'C' op: 'Mul' attr { key: 'T' value { type: DT_FLOAT } }" + " input: ['A', 'B'] }" + "node { name: 'D' op: 'Mul' attr { key: 'T' value { type: DT_FLOAT } }" + " input: ['A', 'B'] }"); + EXPECT_EQ(DoRunMklToTfConversionPass(), +- "A(Input);B(Input);C(Mul);D(Mul)|" ++ "A(Float_Input);B(Float_Input);C(Mul);D(Mul)|" + "A->C;A->D;B->C:1;B->D:1"); + } + +@@ -130,10 +129,10 @@ TEST_F(MklToTfConversionPass, Basic) { + TEST_F(MklToTfConversionPass, Positive) { + if (kTensorOrdering == MklTfTensorOrdering::TENSORS_INTERLEAVED) { + InitGraph( +- "node { name: 'A' op: 'Input'}" +- "node { name: 'M' op: '_MklInput'}" +- "node { name: 'B' op: 'Input'}" +- "node { name: 'N' op: '_MklInput'}" ++ "node { name: 'A' op: 'Float_Input'}" ++ "node { name: 'M' op: '_Mkl_Input'}" ++ "node { name: 'B' op: 'Float_Input'}" ++ "node { name: 'N' op: '_Mkl_Input'}" + "node { name: 'C' op: '_MklConv2D'" + " attr { key: 'T' value { type: DT_FLOAT } }" + " attr { key: 'data_format' value { s: 'NCHW' } }" +@@ -142,21 +141,22 @@ TEST_F(MklToTfConversionPass, Positive) { + "}" + " attr { key: 'padding' value { s: 'SAME' } }" + " input: ['A', 'M', 'B', 'N']}" +- "node { name: 'D' op: 'Input'}" ++ "node { name: 'D' op: 'Float_Input'}" + "node { name: 'E' op: 'Sub'" + " attr {key: 'T' value { type: DT_FLOAT } }" + " input: ['C', 'D']}"); + EXPECT_EQ(DoRunMklToTfConversionPass(), +- "A(Input);B(Input);C(_MklConv2D);D(Input);E(Sub);M(_MklInput);" +- "Mkl2Tf/_0(_MklToTf);N(_MklInput)|A->C;B->C:2;C->Mkl2Tf/_0;" ++ "A(Float_Input);B(Float_Input);C(_MklConv2D);D(Float_Input);E(" ++ "Sub);M(_Mkl_Input);" ++ "Mkl2Tf/_0(_MklToTf);N(_Mkl_Input)|A->C;B->C:2;C->Mkl2Tf/_0;" + "C:1->Mkl2Tf/_0:1;D->E:1;M->C:1;Mkl2Tf/_0->E;N->C:3"); + } else { + CHECK_EQ(kTensorOrdering, MklTfTensorOrdering::TENSORS_CONTIGUOUS); + InitGraph( +- "node { name: 'A' op: 'Input'}" +- "node { name: 'B' op: 'Input'}" +- "node { name: 'M' op: '_MklInput'}" +- "node { name: 'N' op: '_MklInput'}" ++ "node { name: 'A' op: 'Float_Input'}" ++ "node { name: 'B' op: 'Float_Input'}" ++ "node { name: 'M' op: '_Mkl_Input'}" ++ "node { name: 'N' op: '_Mkl_Input'}" + "node { name: 'C' op: '_MklConv2D'" + " attr { key: 'T' value { type: DT_FLOAT } }" + " attr { key: 'data_format' value { s: 'NCHW' } }" +@@ -165,13 +165,14 @@ TEST_F(MklToTfConversionPass, Positive) { + "}" + " attr { key: 'padding' value { s: 'SAME' } }" + " input: ['A', 'B', 'M', 'N']}" +- "node { name: 'D' op: 'Input'}" ++ "node { name: 'D' op: 'Float_Input'}" + "node { name: 'E' op: 'Sub'" + " attr {key: 'T' value { type: DT_FLOAT } }" + " input: ['C', 'D']}"); + EXPECT_EQ(DoRunMklToTfConversionPass(), +- "A(Input);B(Input);C(_MklConv2D);D(Input);E(Sub);M(_MklInput);" +- "Mkl2Tf/_0(_MklToTf);N(_MklInput)|A->C;B->C:1;C->Mkl2Tf/_0;" ++ "A(Float_Input);B(Float_Input);C(_MklConv2D);D(Float_Input);E(" ++ "Sub);M(_Mkl_Input);" ++ "Mkl2Tf/_0(_MklToTf);N(_Mkl_Input)|A->C;B->C:1;C->Mkl2Tf/_0;" + "C:2->Mkl2Tf/_0:1;D->E:1;M->C:2;Mkl2Tf/_0->E;N->C:3"); + } + } +@@ -183,10 +184,10 @@ TEST_F(MklToTfConversionPass, Positive) { + TEST_F(MklToTfConversionPass, Negative_DoubleInsert) { + if (kTensorOrdering == MklTfTensorOrdering::TENSORS_INTERLEAVED) { + InitGraph( +- "node { name: 'A' op: 'Input'}" +- "node { name: 'M' op: '_MklInput'}" +- "node { name: 'B' op: 'Input'}" +- "node { name: 'N' op: '_MklInput'}" ++ "node { name: 'A' op: 'Float_Input'}" ++ "node { name: 'M' op: '_Mkl_Input'}" ++ "node { name: 'B' op: 'Float_Input'}" ++ "node { name: 'N' op: '_Mkl_Input'}" + "node { name: 'C' op: '_MklConv2D'" + " attr { key: 'T' value { type: DT_FLOAT } }" + " attr { key: 'data_format' value { s: 'NCHW' } }" +@@ -199,21 +200,22 @@ TEST_F(MklToTfConversionPass, Negative_DoubleInsert) { + " attr { key: 'T' value { type: DT_FLOAT } }" + " attr { key: 'data_format' value { s: 'NCHW' } }" + " input: ['C:0', 'C:1']}" +- "node { name: 'E' op: 'Input'}" ++ "node { name: 'E' op: 'Float_Input'}" + "node { name: 'F' op: 'Sub'" + " attr {key: 'T' value { type: DT_FLOAT } }" + " input: ['D', 'E']}"); + EXPECT_EQ(DoRunMklToTfConversionPass(), +- "A(Input);B(Input);C(_MklConv2D);D(_MklToTf);E(Input);" +- "F(Sub);M(_MklInput);N(_MklInput)|" ++ "A(Float_Input);B(Float_Input);C(_MklConv2D);D(_MklToTf);E(Float_" ++ "Input);" ++ "F(Sub);M(_Mkl_Input);N(_Mkl_Input)|" + "A->C;B->C:2;C->D;C:1->D:1;D->F;E->F:1;M->C:1;N->C:3"); + } else { + CHECK_EQ(kTensorOrdering, MklTfTensorOrdering::TENSORS_CONTIGUOUS); + InitGraph( +- "node { name: 'A' op: 'Input'}" +- "node { name: 'B' op: 'Input'}" +- "node { name: 'M' op: '_MklInput'}" +- "node { name: 'N' op: '_MklInput'}" ++ "node { name: 'A' op: 'Float_Input'}" ++ "node { name: 'B' op: 'Float_Input'}" ++ "node { name: 'M' op: '_Mkl_Input'}" ++ "node { name: 'N' op: '_Mkl_Input'}" + "node { name: 'C' op: '_MklConv2D'" + " attr { key: 'T' value { type: DT_FLOAT } }" + " attr { key: 'data_format' value { s: 'NCHW' } }" +@@ -226,13 +228,14 @@ TEST_F(MklToTfConversionPass, Negative_DoubleInsert) { + " attr { key: 'T' value { type: DT_FLOAT } }" + " attr { key: 'data_format' value { s: 'NCHW' } }" + " input: ['C:0', 'C:2']}" +- "node { name: 'E' op: 'Input'}" ++ "node { name: 'E' op: 'Float_Input'}" + "node { name: 'F' op: 'Sub'" + " attr {key: 'T' value { type: DT_FLOAT } }" + " input: ['D', 'E']}"); + EXPECT_EQ(DoRunMklToTfConversionPass(), +- "A(Input);B(Input);C(_MklConv2D);D(_MklToTf);E(Input);" +- "F(Sub);M(_MklInput);N(_MklInput)|" ++ "A(Float_Input);B(Float_Input);C(_MklConv2D);D(_MklToTf);E(Float_" ++ "Input);" ++ "F(Sub);M(_Mkl_Input);N(_Mkl_Input)|" + "A->C;B->C:1;C->D;C:2->D:1;D->F;E->F:1;M->C:2;N->C:3"); + } + } +@@ -241,8 +244,8 @@ TEST_F(MklToTfConversionPass, Negative_DoubleInsert) { + // There is no Mkl layer so no conversion op should be inserted. + TEST_F(MklToTfConversionPass, Negative_NoMklLayer) { + InitGraph( +- "node { name: 'A' op: 'Input'}" +- "node { name: 'B' op: 'Input'}" ++ "node { name: 'A' op: 'Float_Input'}" ++ "node { name: 'B' op: 'Float_Input'}" + "node { name: 'C' op: 'Conv2D'" + " attr { key: 'T' value { type: DT_FLOAT } }" + " attr { key: 'data_format' value { s: 'NCHW' } }" +@@ -250,17 +253,18 @@ TEST_F(MklToTfConversionPass, Negative_NoMklLayer) { + " attr { key: 'strides' value { list: {i: 1, i:1, i:1, i:1} } }" + " attr { key: 'padding' value { s: 'SAME' } }" + " input: ['A', 'B']}" +- "node { name: 'D' op: 'Input'}" ++ "node { name: 'D' op: 'Float_Input'}" + "node { name: 'E' op: 'BiasAdd'" + " attr { key: 'T' value { type: DT_FLOAT } }" + " attr { key: 'data_format' value { s: 'NCHW' } }" + " input: ['C', 'D'] }" +- "node { name: 'Y' op: 'Input'}" ++ "node { name: 'Y' op: 'Float_Input'}" + "node { name: 'Z' op: 'Sub'" + " attr {key: 'T' value { type: DT_FLOAT } }" + " input: ['E', 'Y']}"); + EXPECT_EQ(DoRunMklToTfConversionPass(), +- "A(Input);B(Input);C(Conv2D);D(Input);E(BiasAdd);Y(Input);Z(Sub)|" ++ "A(Float_Input);B(Float_Input);C(Conv2D);D(Float_Input);E(BiasAdd);" ++ "Y(Float_Input);Z(Sub)|" + "A->C;B->C:1;C->E;D->E:1;E->Z;Y->Z:1"); + } + +@@ -268,7 +272,7 @@ static void BM_RunMklToTfConversionPass(int iters, int op_nodes) { + testing::StopTiming(); + string s; + for (int in = 0; in < 10; in++) { +- s += strings::Printf("node { name: 'in%04d' op: 'Input'}", in); ++ s += strings::Printf("node { name: 'in%04d' op: 'Float_Input'}", in); + } + random::PhiloxRandom philox(301, 17); + random::SimplePhilox rnd(&philox); diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch new file mode 100644 index 00000000000..2e21e40fe09 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch @@ -0,0 +1,108 @@ +From 84cc21ab082a1bb4b3dfd2ee5d32e18598f60282 Mon Sep 17 00:00:00 2001 +From: Emil Dudev +Date: Tue, 23 Jun 2020 22:13:04 +0200 +Subject: [PATCH] Const-qulify PyUFuncGenericFunction's arguments + +Remove the limit of numpy's version +--- + tensorflow/compiler/xla/python/bfloat16.cc | 20 ++++++++++---------- + tensorflow/python/lib/core/bfloat16.cc | 6 +++--- + tensorflow/tools/pip_package/setup.py | 4 +--- + 3 files changed, 14 insertions(+), 16 deletions(-) + +diff --git a/tensorflow/compiler/xla/python/bfloat16.cc b/tensorflow/compiler/xla/python/bfloat16.cc +index 0b98d0c5f9bd0..1490ce59a2f50 100644 +--- a/tensorflow/compiler/xla/python/bfloat16.cc ++++ b/tensorflow/compiler/xla/python/bfloat16.cc +@@ -708,8 +708,8 @@ struct UnaryUFunc { + static std::vector Types() { + return {TypeDescriptor::Dtype(), TypeDescriptor::Dtype()}; + } +- static void Call(char** args, npy_intp* dimensions, npy_intp* steps, +- void* data) { ++ static void Call(char** args, const npy_intp* dimensions, ++ const npy_intp* steps, void* data) { + const char* i0 = args[0]; + char* o = args[1]; + for (npy_intp k = 0; k < *dimensions; k++) { +@@ -728,8 +728,8 @@ struct UnaryUFunc2 { + return {TypeDescriptor::Dtype(), TypeDescriptor::Dtype(), + TypeDescriptor::Dtype()}; + } +- static void Call(char** args, npy_intp* dimensions, npy_intp* steps, +- void* data) { ++ static void Call(char** args, const npy_intp* dimensions, ++ const npy_intp* steps, void* data) { + const char* i0 = args[0]; + char* o0 = args[1]; + char* o1 = args[2]; +@@ -751,8 +751,8 @@ struct BinaryUFunc { + return {TypeDescriptor::Dtype(), TypeDescriptor::Dtype(), + TypeDescriptor::Dtype()}; + } +- static void Call(char** args, npy_intp* dimensions, npy_intp* steps, +- void* data) { ++ static void Call(char** args, const npy_intp* dimensions, ++ const npy_intp* steps, void* data) { + const char* i0 = args[0]; + const char* i1 = args[1]; + char* o = args[2]; +@@ -774,8 +774,8 @@ struct BinaryUFunc2 { + return {TypeDescriptor::Dtype(), TypeDescriptor::Dtype(), + TypeDescriptor::Dtype()}; + } +- static void Call(char** args, npy_intp* dimensions, npy_intp* steps, +- void* data) { ++ static void Call(char** args, const npy_intp* dimensions, ++ const npy_intp* steps, void* data) { + const char* i0 = args[0]; + const char* i1 = args[1]; + char* o = args[2]; +@@ -873,8 +873,8 @@ struct DivmodUFunc { + static std::vector Types() { + return {npy_bfloat16, npy_bfloat16, npy_bfloat16, npy_bfloat16}; + } +- static void Call(char** args, npy_intp* dimensions, npy_intp* steps, +- void* data) { ++ static void Call(char** args, const npy_intp* dimensions, ++ const npy_intp* steps, void* data) { + const char* i0 = args[0]; + const char* i1 = args[1]; + char* o0 = args[2]; +diff --git a/tensorflow/python/lib/core/bfloat16.cc b/tensorflow/python/lib/core/bfloat16.cc +index feb01f11a1af2..ceb49a97c0a9c 100644 +--- a/tensorflow/python/lib/core/bfloat16.cc ++++ b/tensorflow/python/lib/core/bfloat16.cc +@@ -517,7 +517,7 @@ bool RegisterBfloat16Cast(int numpy_type, bool cast_is_safe) { + } + + template +-void BinaryUFunc(char** args, npy_intp* dimensions, npy_intp* steps, ++void BinaryUFunc(char** args, const npy_intp* dimensions, const npy_intp* steps, + void* data) { + const char* i0 = args[0]; + const char* i1 = args[1]; +@@ -533,8 +533,8 @@ void BinaryUFunc(char** args, npy_intp* dimensions, npy_intp* steps, + } + + template +-void CompareUFunc(char** args, npy_intp* dimensions, npy_intp* steps, +- void* data) { ++void CompareUFunc(char** args, const npy_intp* dimensions, ++ const npy_intp* steps, void* data) { + BinaryUFunc(args, dimensions, steps, data); + } + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index 42233f80c1c9f..92061b396ce3e 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -58,7 +58,7 @@ + 'google_pasta >= 0.1.8', + 'h5py >= 2.10.0, < 2.11.0', + 'keras_preprocessing >= 1.1.0', +- 'numpy >= 1.16.0, < 1.19.0', ++ 'numpy >= 1.16.0, < 2.0', + 'opt_einsum >= 2.3.2', + 'protobuf >= 3.8.0', + 'tensorboard >= 2.2.0, < 2.3.0', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch new file mode 100644 index 00000000000..0d56611f791 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch @@ -0,0 +1,93 @@ +From fb416f16e2b01252326816bb311c3e6165d13bcf Mon Sep 17 00:00:00 2001 +From: Shanqing Cai +Date: Mon, 18 May 2020 06:28:20 -0700 +Subject: [PATCH] [tfdbg] Fix source_utils_test in Python 3.8+ + +This is related to https://bugs.python.org/issue12458 + +In python 3.8, traceback reports the first instead of last line in +a multi-line continuation block. + +Certain parts of source_utils_test.py assume that traceback always +returns the last line, which is true all the way up to 3.7. + +In order to fix this, we use the `ast` module to extract the lineno +of the first line in a multi-line continuation block. + +PiperOrigin-RevId: 312067389 +Change-Id: I8a3ac129b3d75230a3eedd64c3605779dcab5336 +--- + tensorflow/python/debug/BUILD | 1 - + .../python/debug/lib/source_utils_test.py | 38 ++++++++++++++++++- + 2 files changed, 37 insertions(+), 2 deletions(-) + +diff --git a/tensorflow/python/debug/BUILD b/tensorflow/python/debug/BUILD +index 956e90999c7fa..1ef0504ecb836 100644 +--- a/tensorflow/python/debug/BUILD ++++ b/tensorflow/python/debug/BUILD +@@ -840,8 +840,7 @@ py_test( + python_version = "PY3", + srcs_version = "PY2AND3", + tags = [ + "no_mac", +- "no_oss_py38", #TODO(b/151449908) + "no_windows", + ], + deps = [ +diff --git a/tensorflow/python/debug/lib/source_utils_test.py b/tensorflow/python/debug/lib/source_utils_test.py +index faf2365fc9cb3..89964a21ba769 100644 +--- a/tensorflow/python/debug/lib/source_utils_test.py ++++ b/tensorflow/python/debug/lib/source_utils_test.py +@@ -18,7 +18,9 @@ + from __future__ import division + from __future__ import print_function + ++import ast + import os ++import sys + import tempfile + import zipfile + +@@ -43,7 +45,41 @@ + + + def line_number_above(): +- return tf_inspect.stack()[1][2] - 1 ++ """Get lineno of the AST node immediately above this function's call site. ++ ++ It is assumed that there is no empty line(s) between the call site and the ++ preceding AST node. ++ ++ Returns: ++ The lineno of the preceding AST node, at the same level of the AST. ++ If the preceding AST spans multiple lines: ++ - In Python 3.8+, the lineno of the first line is returned. ++ - In older Python versions, the lineno of the last line is returned. ++ """ ++ # https://bugs.python.org/issue12458: In Python 3.8, traceback started ++ # to return the lineno of the first line of a multi-line continuation block, ++ # instead of that of the last line. Therefore, in Python 3.8+, we use `ast` to ++ # get the lineno of the first line. ++ call_site_lineno = tf_inspect.stack()[1][2] ++ if sys.version_info < (3, 8): ++ return call_site_lineno - 1 ++ else: ++ with open(__file__, "rb") as f: ++ source_text = f.read().decode("utf-8") ++ source_tree = ast.parse(source_text) ++ prev_node = _find_preceding_ast_node(source_tree, call_site_lineno) ++ return prev_node.lineno ++ ++ ++def _find_preceding_ast_node(node, lineno): ++ """Find the ast node immediately before and not including lineno.""" ++ for i, child_node in enumerate(node.body): ++ if child_node.lineno == lineno: ++ return node.body[i - 1] ++ if hasattr(child_node, "body"): ++ found_node = _find_preceding_ast_node(child_node, lineno) ++ if found_node: ++ return found_node + + + class GuessIsTensorFlowLibraryTest(test_util.TensorFlowTestCase): From 05e31bd2d23502435ac8b9d36a6fd540cf22ec3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Aug 2021 16:59:43 +0200 Subject: [PATCH 1133/9987] adding easyconfigs: AlphaFold-2.0.0-fosscuda-2020b.eb --- .../AlphaFold-2.0.0-fosscuda-2020b.eb | 186 ++++++++++++++++++ 1 file changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..fe2744c806c --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb @@ -0,0 +1,186 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.0.0' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + # CMake/oxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('TensorFlow', '2.4.1'), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.19'), # also provides absl-py +] + +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp -a %s .", + }, + ], + 'patches': [ + 'AlphaFold-%(version)s_fix-packages.patch', + 'AlphaFold-%(version)s_data-dep-paths.patch', + 'AlphaFold-%(version)s_n-cpu.patch', + 'AlphaFold-%(version)s_fix-scp-path.patch', + ], + 'checksums': [ + '78cf443a2d9250917b05f5d40ede140ed8e8341b42fdfa54340336aca52f53f2', # v2.0.0.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '7223e297b23f90816219095696bc6453910c617add60b907a0d3e869da8733bb', # AlphaFold-2.0.0_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + # source tarball on PyPI is missing requirements.txt, + # see https://github.com/deepmind/dm-haiku/issues/44 + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + 'modulename': 'haiku', + }), + ('dm-tree', '0.1.6', { + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + 'modulename': 'tree', + }), + ('websocket-client', '1.2.1', { + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + 'modulename': 'websocket', + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + # see https://github.com/google/ml_collections/issues/7 + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', +} + +moduleclass = 'bio' From f9cb7a7e6bdbc2381ce7ff79ce81164062419c5d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 31 Aug 2021 17:49:24 +0200 Subject: [PATCH 1134/9987] adding easyconfigs: NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb --- .../NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb new file mode 100644 index 00000000000..f1f7c22b31e --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -0,0 +1,23 @@ +name = 'NCCL' +version = '2.10.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('CUDAcore', '11.4.1', '', True), + ('UCX-CUDA', '1.11.0', versionsuffix), +] + +moduleclass = 'lib' From 3c4b638b6e6fa3893e90f35924ec0d8d86c81a86 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 31 Aug 2021 17:00:54 +0100 Subject: [PATCH 1135/9987] adding easyconfigs: nodejs-14.17.6-GCCcore-11.2.0.eb --- .../n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..569932aa452 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '14.17.6' # LTS on 2020-08-31 +local_libversion = '83' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['f64559c87faa2f1ce93c3d2cd09723af254ec320a53cbfd1a2ba8fba28e488d0'] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6', '-bare'), +] + +configopts = [ + '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library + '--shared --with-intl=none', # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +postinstallcmds = [ + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'dirs': ['lib/node_modules', 'include/node'] +} + +moduleclass = 'lang' From eae50e140616da8d7b5778edb83aa7eca70696c2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 31 Aug 2021 18:16:22 +0200 Subject: [PATCH 1136/9987] Fix usage of /usr/bin/perl in HMMER. --- .../h/HMMER/HMMER-3.3.2-gompi-2020b.eb | 14 +- .../h/HMMER/HMMER-3.3.2-gompic-2020b.eb | 14 +- .../h/HMMER/HMMER-3.3.2-iimpi-2020b.eb | 14 +- .../h/HMMER/HMMER-3.3.2_fix_perl.patch | 796 ++++++++++++++++++ 4 files changed, 832 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2_fix_perl.patch diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb index a39fc442b6c..6d95f779faf 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb @@ -35,12 +35,22 @@ source_urls = [ 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] sources = ['hmmer-%(version)s.tar.gz'] -checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] -builddependencies = [('Python', '3.8.6')] +builddependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0', '-minimal'), +] configopts = '--enable-mpi' +buildopts = ' V=1 ' + +testopts = buildopts runtest = 'check' installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb index f26e9cbaafc..bb4ec04a67b 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompic-2020b.eb @@ -35,12 +35,22 @@ source_urls = [ 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] sources = [SOURCELOWER_TAR_GZ] -checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] -builddependencies = [('Python', '3.8.6')] +builddependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0', '-minimal'), +] configopts = '--enable-mpi' +buildopts = ' V=1 ' + +testopts = buildopts runtest = 'check' installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb index ea00c7b7ecb..0f903bc0639 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb @@ -35,12 +35,22 @@ source_urls = [ 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] sources = ['hmmer-%(version)s.tar.gz'] -checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] -builddependencies = [('Python', '3.8.6')] +builddependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0', '-minimal'), +] configopts = '--enable-mpi' +buildopts = ' V=1 ' + +testopts = buildopts runtest = 'check' installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2_fix_perl.patch b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2_fix_perl.patch new file mode 100644 index 00000000000..d9db1ff3190 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2_fix_perl.patch @@ -0,0 +1,796 @@ +HMMER uses /usr/bin/perl in lots of places. +Use EB built perl instead. + +Åke Sandgren, 20210831 +diff -ru hmmer-3.3.2.orig/easel/demotic/blast2profmark hmmer-3.3.2/easel/demotic/blast2profmark +--- hmmer-3.3.2.orig/easel/demotic/blast2profmark 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/demotic/blast2profmark 2021-08-31 18:04:58.046079800 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use demotic_blast; + +diff -ru hmmer-3.3.2.orig/easel/demotic/blast2tbl hmmer-3.3.2/easel/demotic/blast2tbl +--- hmmer-3.3.2.orig/easel/demotic/blast2tbl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/demotic/blast2tbl 2021-08-31 18:04:58.038079850 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use demotic_blast; + +diff -ru hmmer-3.3.2.orig/easel/demotic/fasta2profmark hmmer-3.3.2/easel/demotic/fasta2profmark +--- hmmer-3.3.2.orig/easel/demotic/fasta2profmark 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/demotic/fasta2profmark 2021-08-31 18:04:58.038079850 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use demotic_fasta; + +diff -ru hmmer-3.3.2.orig/easel/demotic/fasta2tbl hmmer-3.3.2/easel/demotic/fasta2tbl +--- hmmer-3.3.2.orig/easel/demotic/fasta2tbl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/demotic/fasta2tbl 2021-08-31 18:04:58.054079751 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use demotic_fasta; + +diff -ru hmmer-3.3.2.orig/easel/demotic/h22profmark hmmer-3.3.2/easel/demotic/h22profmark +--- hmmer-3.3.2.orig/easel/demotic/h22profmark 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/demotic/h22profmark 2021-08-31 18:04:58.054079751 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use demotic_h2; + +diff -ru hmmer-3.3.2.orig/easel/demotic/h22tbl hmmer-3.3.2/easel/demotic/h22tbl +--- hmmer-3.3.2.orig/easel/demotic/h22tbl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/demotic/h22tbl 2021-08-31 18:04:58.050079776 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use demotic_h2; + +diff -ru hmmer-3.3.2.orig/easel/demotic/hmmer2profmark hmmer-3.3.2/easel/demotic/hmmer2profmark +--- hmmer-3.3.2.orig/easel/demotic/hmmer2profmark 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/demotic/hmmer2profmark 2021-08-31 18:04:58.042079825 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use demotic_hmmer; + +diff -ru hmmer-3.3.2.orig/easel/demotic/hmmer2tbl hmmer-3.3.2/easel/demotic/hmmer2tbl +--- hmmer-3.3.2.orig/easel/demotic/hmmer2tbl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/demotic/hmmer2tbl 2021-08-31 18:04:58.058079726 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use demotic_hmmer; + +diff -ru hmmer-3.3.2.orig/easel/demotic/infernal_tab2gff.pl hmmer-3.3.2/easel/demotic/infernal_tab2gff.pl +--- hmmer-3.3.2.orig/easel/demotic/infernal_tab2gff.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/demotic/infernal_tab2gff.pl 2021-08-31 18:04:58.046079800 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w -I/groups/eddy/home/jonest/Demotic ++#!/usr/bin/env perl + + # TAJ 6/23/08 last mod 7/10/08 + # Purpose: flexibly convert "cmsearch --tabfile TAB.out" output to GFF format +diff -ru hmmer-3.3.2.orig/easel/demotic/test.pl hmmer-3.3.2/easel/demotic/test.pl +--- hmmer-3.3.2.orig/easel/demotic/test.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/demotic/test.pl 2021-08-31 18:04:58.042079825 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + use demotic_blast; + +diff -ru hmmer-3.3.2.orig/easel/devkit/autodoc hmmer-3.3.2/easel/devkit/autodoc +--- hmmer-3.3.2.orig/easel/devkit/autodoc 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/devkit/autodoc 2021-08-31 18:04:58.074079627 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Usage: + # ./autodoc +diff -ru hmmer-3.3.2.orig/easel/devkit/c2optlist hmmer-3.3.2/easel/devkit/c2optlist +--- hmmer-3.3.2.orig/easel/devkit/c2optlist 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/devkit/c2optlist 2021-08-31 18:04:58.086079553 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + + # c2optlist
+diff -ru hmmer-3.3.2.orig/easel/devkit/cexcerpt hmmer-3.3.2/easel/devkit/cexcerpt +--- hmmer-3.3.2.orig/easel/devkit/cexcerpt 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/devkit/cexcerpt 2021-08-31 18:04:58.082079577 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # cexcerpt + # +diff -ru hmmer-3.3.2.orig/easel/devkit/ctags-fix hmmer-3.3.2/easel/devkit/ctags-fix +--- hmmer-3.3.2.orig/easel/devkit/ctags-fix 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/devkit/ctags-fix 2021-08-31 18:04:58.070079651 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # To be used in an idiomatic pipe for listing all keywords in a codebase: + # +diff -ru hmmer-3.3.2.orig/easel/devkit/man2optlist hmmer-3.3.2/easel/devkit/man2optlist +--- hmmer-3.3.2.orig/easel/devkit/man2optlist 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/devkit/man2optlist 2021-08-31 18:04:58.074079627 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + + # man2optlist <.man file> +diff -ru hmmer-3.3.2.orig/easel/devkit/rmanprocess.pl hmmer-3.3.2/easel/devkit/rmanprocess.pl +--- hmmer-3.3.2.orig/easel/devkit/rmanprocess.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/devkit/rmanprocess.pl 2021-08-31 18:04:58.078079602 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # rmanprocess.pl + # +diff -ru hmmer-3.3.2.orig/easel/devkit/sedition hmmer-3.3.2/easel/devkit/sedition +--- hmmer-3.3.2.orig/easel/devkit/sedition 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/devkit/sedition 2021-08-31 18:04:58.090079528 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # sedition [ ]... + # +diff -ru hmmer-3.3.2.orig/easel/devkit/sedition-pp hmmer-3.3.2/easel/devkit/sedition-pp +--- hmmer-3.3.2.orig/easel/devkit/sedition-pp 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/devkit/sedition-pp 2021-08-31 18:04:58.078079602 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # sedition-pp + # +diff -ru hmmer-3.3.2.orig/easel/devkit/sqc hmmer-3.3.2/easel/devkit/sqc +--- hmmer-3.3.2.orig/easel/devkit/sqc 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/devkit/sqc 2021-08-31 18:04:58.086079553 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # sqc :: + # quality control script for exercising code, regression testing, +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-afetch.itest.pl hmmer-3.3.2/easel/miniapps/esl-afetch.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-afetch.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-afetch.itest.pl 2021-08-31 18:04:58.034079874 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Testing the esl-afetch miniapp + # +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-alimanip.itest.pl hmmer-3.3.2/easel/miniapps/esl-alimanip.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-alimanip.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-alimanip.itest.pl 2021-08-31 18:04:58.010080022 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-alimanip miniapp. + # +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-alimap.itest.pl hmmer-3.3.2/easel/miniapps/esl-alimap.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-alimap.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-alimap.itest.pl 2021-08-31 18:04:58.014079998 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-alimap miniapp. + # +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-alimask.itest.pl hmmer-3.3.2/easel/miniapps/esl-alimask.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-alimask.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-alimask.itest.pl 2021-08-31 18:04:58.010080022 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of esl-alimask miniapp. + # +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-alimerge.itest.pl hmmer-3.3.2/easel/miniapps/esl-alimerge.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-alimerge.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-alimerge.itest.pl 2021-08-31 18:04:58.022079948 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of esl-alimerge miniapp. + # +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-alistat.itest.pl hmmer-3.3.2/easel/miniapps/esl-alistat.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-alistat.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-alistat.itest.pl 2021-08-31 18:04:58.018079973 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-alistat miniapp. + # +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-compalign.itest.pl hmmer-3.3.2/easel/miniapps/esl-compalign.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-compalign.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-compalign.itest.pl 2021-08-31 18:04:58.014079998 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-compalign miniapp. + # +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-construct.itest.pl hmmer-3.3.2/easel/miniapps/esl-construct.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-construct.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-construct.itest.pl 2021-08-31 18:04:58.030079899 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-construct miniapp. + # +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-mask.itest.pl hmmer-3.3.2/easel/miniapps/esl-mask.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-mask.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-mask.itest.pl 2021-08-31 18:04:58.018079973 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of esl-mask miniapp. + # +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-seqrange.itest.pl hmmer-3.3.2/easel/miniapps/esl-seqrange.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-seqrange.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-seqrange.itest.pl 2021-08-31 18:04:58.030079899 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-seqrange miniapp. + # +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-ssdraw.itest.pl hmmer-3.3.2/easel/miniapps/esl-ssdraw.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-ssdraw.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-ssdraw.itest.pl 2021-08-31 18:04:58.026079924 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of the esl-ssdraw miniapp. + # +diff -ru hmmer-3.3.2.orig/easel/miniapps/esl-translate.itest.pl hmmer-3.3.2/easel/miniapps/esl-translate.itest.pl +--- hmmer-3.3.2.orig/easel/miniapps/esl-translate.itest.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/miniapps/esl-translate.itest.pl 2021-08-31 18:04:58.026079924 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + BEGIN { + $builddir = shift; +diff -ru hmmer-3.3.2.orig/easel/testsuite/coverage_report.pl hmmer-3.3.2/easel/testsuite/coverage_report.pl +--- hmmer-3.3.2.orig/easel/testsuite/coverage_report.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/testsuite/coverage_report.pl 2021-08-31 18:04:58.070079651 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Measures testsuite coverage (as percentage of source lines), + # using gcov. +diff -ru hmmer-3.3.2.orig/easel/testsuite/i1-degen-residues.pl hmmer-3.3.2/easel/testsuite/i1-degen-residues.pl +--- hmmer-3.3.2.orig/easel/testsuite/i1-degen-residues.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/testsuite/i1-degen-residues.pl 2021-08-31 18:04:58.062079701 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integration tests of reading all valid protein sequence residue characters. + # +diff -ru hmmer-3.3.2.orig/easel/testsuite/i2-ncbi-indices.pl hmmer-3.3.2/easel/testsuite/i2-ncbi-indices.pl +--- hmmer-3.3.2.orig/easel/testsuite/i2-ncbi-indices.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/testsuite/i2-ncbi-indices.pl 2021-08-31 18:04:58.058079726 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Testing that we can read FASTA files, even if they have NCBI + # formatted BLAST databases in the same directory. +diff -ru hmmer-3.3.2.orig/easel/testsuite/i3-blank-gf.pl hmmer-3.3.2/easel/testsuite/i3-blank-gf.pl +--- hmmer-3.3.2.orig/easel/testsuite/i3-blank-gf.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/testsuite/i3-blank-gf.pl 2021-08-31 18:04:58.062079701 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Bug #e5: blank text line following #=GF handled improperly. + # +diff -ru hmmer-3.3.2.orig/easel/testsuite/valgrind_report.pl hmmer-3.3.2/easel/testsuite/valgrind_report.pl +--- hmmer-3.3.2.orig/easel/testsuite/valgrind_report.pl 2020-11-26 22:17:20.000000000 +0100 ++++ hmmer-3.3.2/easel/testsuite/valgrind_report.pl 2021-08-31 18:04:58.066079676 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Run the testsuite under Valgrind, to check for memory leakage. + # +diff -ru hmmer-3.3.2.orig/profmark/pmark-master.pl hmmer-3.3.2/profmark/pmark-master.pl +--- hmmer-3.3.2.orig/profmark/pmark-master.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/pmark-master.pl 2021-08-31 18:04:57.970080270 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # The top level script that runs a pmark benchmark. + # +diff -ru hmmer-3.3.2.orig/profmark/rocplot.pl hmmer-3.3.2/profmark/rocplot.pl +--- hmmer-3.3.2.orig/profmark/rocplot.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/rocplot.pl 2021-08-31 18:04:57.982080196 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + $nsearches = 2809; + +diff -ru hmmer-3.3.2.orig/profmark/x-fps-fasta hmmer-3.3.2/profmark/x-fps-fasta +--- hmmer-3.3.2.orig/profmark/x-fps-fasta 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-fps-fasta 2021-08-31 18:04:57.974080245 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for FASTA searches by FPS + # (family-pairwise-search; best E-value of all individual queries). +diff -ru hmmer-3.3.2.orig/profmark/x-fps-ncbiblast hmmer-3.3.2/profmark/x-fps-ncbiblast +--- hmmer-3.3.2.orig/profmark/x-fps-ncbiblast 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-fps-ncbiblast 2021-08-31 18:04:57.998080097 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for NCBI BLASTP searches by FPS + # (family-pairwise-search; best E-value of all individual queries). +diff -ru hmmer-3.3.2.orig/profmark/x-fps-ncbiblast+ hmmer-3.3.2/profmark/x-fps-ncbiblast+ +--- hmmer-3.3.2.orig/profmark/x-fps-ncbiblast+ 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-fps-ncbiblast+ 2021-08-31 18:04:57.986080171 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for NCBI BLASTP+ searches by FPS + # (family-pairwise-search; best E-value of all individual queries). +diff -ru hmmer-3.3.2.orig/profmark/x-fps-phmmer hmmer-3.3.2/profmark/x-fps-phmmer +--- hmmer-3.3.2.orig/profmark/x-fps-phmmer 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-fps-phmmer 2021-08-31 18:04:58.002080072 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for phmmer searches by FPS + # (family-pairwise-search; best E-value of all individual queries). +diff -ru hmmer-3.3.2.orig/profmark/x-fps-ssearch hmmer-3.3.2/profmark/x-fps-ssearch +--- hmmer-3.3.2.orig/profmark/x-fps-ssearch 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-fps-ssearch 2021-08-31 18:04:57.974080245 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for SSEARCH searches by FPS + # (family-pairwise-search; best E-value of all individual queries). +diff -ru hmmer-3.3.2.orig/profmark/x-fps-wublast hmmer-3.3.2/profmark/x-fps-wublast +--- hmmer-3.3.2.orig/profmark/x-fps-wublast 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-fps-wublast 2021-08-31 18:04:57.994080122 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for WU-BLAST searches by FPS + # (family-pairwise-search; best E-value of all individual queries). +diff -ru hmmer-3.3.2.orig/profmark/x-h2-fs hmmer-3.3.2/profmark/x-h2-fs +--- hmmer-3.3.2.orig/profmark/x-h2-fs 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-h2-fs 2021-08-31 18:04:57.966080295 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for H2's hmmsearch. + # +diff -ru hmmer-3.3.2.orig/profmark/x-h2-ls hmmer-3.3.2/profmark/x-h2-ls +--- hmmer-3.3.2.orig/profmark/x-h2-ls 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-h2-ls 2021-08-31 18:04:57.958080344 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for H2's hmmsearch (ls mode). + # +diff -ru hmmer-3.3.2.orig/profmark/x-hmmsearch hmmer-3.3.2/profmark/x-hmmsearch +--- hmmer-3.3.2.orig/profmark/x-hmmsearch 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-hmmsearch 2021-08-31 18:04:57.986080171 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for hmmsearch. + # +diff -ru hmmer-3.3.2.orig/profmark/x-hmmsearch-max hmmer-3.3.2/profmark/x-hmmsearch-max +--- hmmer-3.3.2.orig/profmark/x-hmmsearch-max 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-hmmsearch-max 2021-08-31 18:04:57.998080097 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for hmmsearch --max. + # +diff -ru hmmer-3.3.2.orig/profmark/x-iterate-jackhmmer hmmer-3.3.2/profmark/x-iterate-jackhmmer +--- hmmer-3.3.2.orig/profmark/x-iterate-jackhmmer 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-iterate-jackhmmer 2021-08-31 18:04:57.994080122 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + $n_iterations = 1; + # $n_iterations = 2; # uncomment as needed for -n2, -n3 tests... +diff -ru hmmer-3.3.2.orig/profmark/x-iterate-psiblast hmmer-3.3.2/profmark/x-iterate-psiblast +--- hmmer-3.3.2.orig/profmark/x-iterate-psiblast 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-iterate-psiblast 2021-08-31 18:04:57.970080270 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + BEGIN { + $top_builddir = shift; +diff -ru hmmer-3.3.2.orig/profmark/x-phmmer-consensus hmmer-3.3.2/profmark/x-phmmer-consensus +--- hmmer-3.3.2.orig/profmark/x-phmmer-consensus 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-phmmer-consensus 2021-08-31 18:04:57.978080221 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for phmmer searches using a + # consensus sequence query. +diff -ru hmmer-3.3.2.orig/profmark/x-psiblast hmmer-3.3.2/profmark/x-psiblast +--- hmmer-3.3.2.orig/profmark/x-psiblast 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-psiblast 2021-08-31 18:04:58.006080047 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for PSI-BLAST + # +diff -ru hmmer-3.3.2.orig/profmark/x-psiblast+ hmmer-3.3.2/profmark/x-psiblast+ +--- hmmer-3.3.2.orig/profmark/x-psiblast+ 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-psiblast+ 2021-08-31 18:04:57.962080319 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for PSI-BLAST+ + # +diff -ru hmmer-3.3.2.orig/profmark/x-sam hmmer-3.3.2/profmark/x-sam +--- hmmer-3.3.2.orig/profmark/x-sam 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-sam 2021-08-31 18:04:57.990080147 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + # Do a piece of a profmark benchmark, for SAM. + # +diff -ru hmmer-3.3.2.orig/profmark/x-single-ncbiblast hmmer-3.3.2/profmark/x-single-ncbiblast +--- hmmer-3.3.2.orig/profmark/x-single-ncbiblast 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-single-ncbiblast 2021-08-31 18:04:58.002080072 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + BEGIN { + $top_builddir = shift; +diff -ru hmmer-3.3.2.orig/profmark/x-single-phmmer hmmer-3.3.2/profmark/x-single-phmmer +--- hmmer-3.3.2.orig/profmark/x-single-phmmer 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-single-phmmer 2021-08-31 18:04:57.982080196 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + $top_builddir = shift; + $top_srcdir = shift; +diff -ru hmmer-3.3.2.orig/profmark/x-single-ssearch hmmer-3.3.2/profmark/x-single-ssearch +--- hmmer-3.3.2.orig/profmark/x-single-ssearch 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/profmark/x-single-ssearch 2021-08-31 18:04:57.966080295 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl -w ++#!/usr/bin/env perl + + BEGIN { + $top_builddir = shift; +diff -ru hmmer-3.3.2.orig/src/hmmpress.itest.pl hmmer-3.3.2/src/hmmpress.itest.pl +--- hmmer-3.3.2.orig/src/hmmpress.itest.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/src/hmmpress.itest.pl 2021-08-31 18:04:58.090079528 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Integrated test of hmmpress + # +diff -ru hmmer-3.3.2.orig/test-speed/component-benchmark.pl hmmer-3.3.2/test-speed/component-benchmark.pl +--- hmmer-3.3.2.orig/test-speed/component-benchmark.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/component-benchmark.pl 2021-08-31 18:04:57.910080641 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Component speed benchmarks + # +diff -ru hmmer-3.3.2.orig/test-speed/speedA-list.pl hmmer-3.3.2/test-speed/speedA-list.pl +--- hmmer-3.3.2.orig/test-speed/speedA-list.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/speedA-list.pl 2021-08-31 18:04:57.902080691 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Usage: ./speedA-list.pl + # Example: hmmstat Pfam-A.hmm | ./speedA-list.pl +diff -ru hmmer-3.3.2.orig/test-speed/speed-master.pl hmmer-3.3.2/test-speed/speed-master.pl +--- hmmer-3.3.2.orig/test-speed/speed-master.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/speed-master.pl 2021-08-31 18:04:57.898080716 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # The top level script that runs speed benchmarks + # +diff -ru hmmer-3.3.2.orig/test-speed/x-fasta hmmer-3.3.2/test-speed/x-fasta +--- hmmer-3.3.2.orig/test-speed/x-fasta 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/x-fasta 2021-08-31 18:04:57.914080616 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # We assume that a FASTA install tree is in $top_builddir + # $top_srcdir is unused: pass "." or $top_builddir +diff -ru hmmer-3.3.2.orig/test-speed/x-hmmer2 hmmer-3.3.2/test-speed/x-hmmer2 +--- hmmer-3.3.2.orig/test-speed/x-hmmer2 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/x-hmmer2 2021-08-31 18:04:57.894080740 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # We assume that a HMMER2 build tree is in $top_builddir + # $top_srcdir is unused: pass "." or $top_builddir +diff -ru hmmer-3.3.2.orig/test-speed/x-hmmsearch hmmer-3.3.2/test-speed/x-hmmsearch +--- hmmer-3.3.2.orig/test-speed/x-hmmsearch 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/x-hmmsearch 2021-08-31 18:04:57.906080666 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # We assume that a HMMER3 build tree is in $top_builddir, with binaries in src/ subdir of it + # $top_srcdir is unused: pass "." or $top_builddir +diff -ru hmmer-3.3.2.orig/test-speed/x-ncbiblast hmmer-3.3.2/test-speed/x-ncbiblast +--- hmmer-3.3.2.orig/test-speed/x-ncbiblast 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/x-ncbiblast 2021-08-31 18:04:57.910080641 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # We assume that an NCBI BLAST install tree is in $top_builddir + # $top_srcdir is unused: pass "." or $top_builddir +diff -ru hmmer-3.3.2.orig/test-speed/x-ncbiblast+ hmmer-3.3.2/test-speed/x-ncbiblast+ +--- hmmer-3.3.2.orig/test-speed/x-ncbiblast+ 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/x-ncbiblast+ 2021-08-31 18:04:57.898080716 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # We assume that an NCBI BLAST+ install tree is in $top_builddir + # $top_srcdir is unused: pass "." or $top_builddir +diff -ru hmmer-3.3.2.orig/test-speed/x-psiblast hmmer-3.3.2/test-speed/x-psiblast +--- hmmer-3.3.2.orig/test-speed/x-psiblast 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/x-psiblast 2021-08-31 18:04:57.918080592 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # We assume that an NCBI BLAST install tree is in $top_builddir + # $top_srcdir is unused: pass "." or $top_builddir +diff -ru hmmer-3.3.2.orig/test-speed/x-psiblast+ hmmer-3.3.2/test-speed/x-psiblast+ +--- hmmer-3.3.2.orig/test-speed/x-psiblast+ 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/x-psiblast+ 2021-08-31 18:04:57.890080765 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # We assume that an NCBI BLAST+ install tree is in $top_builddir + # $top_srcdir is unused: pass "." or $top_builddir +diff -ru hmmer-3.3.2.orig/test-speed/x-sam hmmer-3.3.2/test-speed/x-sam +--- hmmer-3.3.2.orig/test-speed/x-sam 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/x-sam 2021-08-31 18:04:57.906080666 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # We assume that a SAM binary install is in $top_builddir + # $top_srcdir is unused: pass "." or $top_builddir +diff -ru hmmer-3.3.2.orig/test-speed/x-ssearch hmmer-3.3.2/test-speed/x-ssearch +--- hmmer-3.3.2.orig/test-speed/x-ssearch 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/x-ssearch 2021-08-31 18:04:57.894080740 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # We assume that a FASTA install tree is in $top_builddir + # $top_srcdir is unused: pass "." or $top_builddir +diff -ru hmmer-3.3.2.orig/test-speed/x-wublast hmmer-3.3.2/test-speed/x-wublast +--- hmmer-3.3.2.orig/test-speed/x-wublast 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/test-speed/x-wublast 2021-08-31 18:04:57.914080616 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # We assume that a WU BLAST install tree is in $top_builddir + # $top_srcdir is unused: pass "." or $top_builddir +diff -ru hmmer-3.3.2.orig/testsuite/h3.pm hmmer-3.3.2/testsuite/h3.pm +--- hmmer-3.3.2.orig/testsuite/h3.pm 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/h3.pm 2021-08-31 18:04:57.922080567 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + package h3; + +diff -ru hmmer-3.3.2.orig/testsuite/i10-duplicate-names.pl hmmer-3.3.2/testsuite/i10-duplicate-names.pl +--- hmmer-3.3.2.orig/testsuite/i10-duplicate-names.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i10-duplicate-names.pl 2021-08-31 18:04:57.946080419 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Check how we handle duplicate names, for both queries and targets. + # Indexing HMM or sequence files does require unique names/accessions. +diff -ru hmmer-3.3.2.orig/testsuite/i11-hmmalign-mapali.pl hmmer-3.3.2/testsuite/i11-hmmalign-mapali.pl +--- hmmer-3.3.2.orig/testsuite/i11-hmmalign-mapali.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i11-hmmalign-mapali.pl 2021-08-31 18:04:57.930080517 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Another test of the hmmalign --mapali option, after Elena reports + # bug #h73 in bad interaction of checksum calculation and marking +diff -ru hmmer-3.3.2.orig/testsuite/i12-delete-corruption.pl hmmer-3.3.2/testsuite/i12-delete-corruption.pl +--- hmmer-3.3.2.orig/testsuite/i12-delete-corruption.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i12-delete-corruption.pl 2021-08-31 18:04:57.934080493 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Bug #h77: hmmalign corrupts column preceding an all-delete column + # +diff -ru hmmer-3.3.2.orig/testsuite/i13-msa-integrity.pl hmmer-3.3.2/testsuite/i13-msa-integrity.pl +--- hmmer-3.3.2.orig/testsuite/i13-msa-integrity.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i13-msa-integrity.pl 2021-08-31 18:04:57.958080344 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Look for any problems in hmmalign that corrupt the input sequences. + # +diff -ru hmmer-3.3.2.orig/testsuite/i14-hmmemit-consensus.pl hmmer-3.3.2/testsuite/i14-hmmemit-consensus.pl +--- hmmer-3.3.2.orig/testsuite/i14-hmmemit-consensus.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i14-hmmemit-consensus.pl 2021-08-31 18:04:57.938080468 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Tests hmmemit -c and hmmemit -C consensus-generating options. + # +diff -ru hmmer-3.3.2.orig/testsuite/i15-hmmconvert.pl hmmer-3.3.2/testsuite/i15-hmmconvert.pl +--- hmmer-3.3.2.orig/testsuite/i15-hmmconvert.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i15-hmmconvert.pl 2021-08-31 18:04:57.922080567 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Bug #h80: hmmconvert can't read H2 Nucleic files + # +diff -ru hmmer-3.3.2.orig/testsuite/i16-build-allins.pl hmmer-3.3.2/testsuite/i16-build-allins.pl +--- hmmer-3.3.2.orig/testsuite/i16-build-allins.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i16-build-allins.pl 2021-08-31 18:04:57.954080369 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Bug #h82: hmmbuild corrupts resave alignment on all-insert seq + # +diff -ru hmmer-3.3.2.orig/testsuite/i17-stdin.pl hmmer-3.3.2/testsuite/i17-stdin.pl +--- hmmer-3.3.2.orig/testsuite/i17-stdin.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i17-stdin.pl 2021-08-31 18:04:57.942080443 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test that programs accept and reject argument of '-' (for reading + # data from stdin, rather than from files) as they're supposed to. +diff -ru hmmer-3.3.2.orig/testsuite/i18-nhmmer-generic.pl hmmer-3.3.2/testsuite/i18-nhmmer-generic.pl +--- hmmer-3.3.2.orig/testsuite/i18-nhmmer-generic.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i18-nhmmer-generic.pl 2021-08-31 18:04:57.938080468 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test of hmmbuild/nhmmer as used to build a DNA model, then query a + # a database of long (1MB). +diff -ru hmmer-3.3.2.orig/testsuite/i20-fmindex-core.pl hmmer-3.3.2/testsuite/i20-fmindex-core.pl +--- hmmer-3.3.2.orig/testsuite/i20-fmindex-core.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i20-fmindex-core.pl 2021-08-31 18:04:57.950080394 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test of makenhmmerdb and the core fm-index search functionality, using extactmatch + # +diff -ru hmmer-3.3.2.orig/testsuite/i21-rewind.pl hmmer-3.3.2/testsuite/i21-rewind.pl +--- hmmer-3.3.2.orig/testsuite/i21-rewind.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i21-rewind.pl 2021-08-31 18:04:57.930080517 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test that the search tools (hmmsearch, phmmer, nhmmer) + # produce the correct set of hits when the target sequence +diff -ru hmmer-3.3.2.orig/testsuite/i5-hmmbuild-naming.pl hmmer-3.3.2/testsuite/i5-hmmbuild-naming.pl +--- hmmer-3.3.2.orig/testsuite/i5-hmmbuild-naming.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i5-hmmbuild-naming.pl 2021-08-31 18:04:57.942080443 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test that HMM naming in hmmbuild works as advertised. + # Written to test for #h50. +diff -ru hmmer-3.3.2.orig/testsuite/i6-hmmalign-mapali.pl hmmer-3.3.2/testsuite/i6-hmmalign-mapali.pl +--- hmmer-3.3.2.orig/testsuite/i6-hmmalign-mapali.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i6-hmmalign-mapali.pl 2021-08-31 18:04:57.950080394 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test the hmmalign --mapali option. + # +diff -ru hmmer-3.3.2.orig/testsuite/i7-hmmbuild-fragments.pl hmmer-3.3.2/testsuite/i7-hmmbuild-fragments.pl +--- hmmer-3.3.2.orig/testsuite/i7-hmmbuild-fragments.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i7-hmmbuild-fragments.pl 2021-08-31 18:04:57.926080542 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Test the ability of hmmbuild to deal with crappy alignments + # of lots of sequence fragments. +diff -ru hmmer-3.3.2.orig/testsuite/i8-nonresidues.pl hmmer-3.3.2/testsuite/i8-nonresidues.pl +--- hmmer-3.3.2.orig/testsuite/i8-nonresidues.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i8-nonresidues.pl 2021-08-31 18:04:57.926080542 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Regression test of handling a nonresidue '*' character. By design, + # '*' residues score 0 in insert states and N,C,J; and -inf in match +diff -ru hmmer-3.3.2.orig/testsuite/i9-optional-annotation.pl hmmer-3.3.2/testsuite/i9-optional-annotation.pl +--- hmmer-3.3.2.orig/testsuite/i9-optional-annotation.pl 2020-11-26 22:16:58.000000000 +0100 ++++ hmmer-3.3.2/testsuite/i9-optional-annotation.pl 2021-08-31 18:04:57.954080369 +0200 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#!/usr/bin/env perl + + # Check that we can deal with HMMs with no optional annotation, in either + # hmmscan or hmmsearch mode. From 76e7746bc9a4e98f188b9944bd0cff8c1d653d91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Sep 2021 08:50:52 +0200 Subject: [PATCH 1137/9987] fix typo in comment in AlphaFold easyconfigs (oxygen -> Doxygen) --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 2 +- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index bcfc97f3b65..c36bafa8196 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -9,7 +9,7 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ - # CMake/oxygen/SWIG are required for building OpenMM + # CMake/Doxygen/SWIG are required for building OpenMM ('CMake', '3.18.4'), ('Doxygen', '1.8.20'), # required for installing dm-tree diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb index fe2744c806c..08ad07e9501 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb @@ -9,7 +9,7 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ - # CMake/oxygen/SWIG are required for building OpenMM + # CMake/Doxygen/SWIG are required for building OpenMM ('CMake', '3.18.4'), ('Doxygen', '1.8.20'), # required for installing dm-tree From 09ea3ce3ebb30d00cfc741b284c8659d8da3ca8f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 1 Sep 2021 16:37:07 +0200 Subject: [PATCH 1138/9987] Rename CUDAcore -> CUDA after merging foss/fosscuda since we no longer need the name. Much cleaner code, but most importantly, fixes the issue of nonexistent get_software_root('CUDA') --- .../c/{CUDAcore/CUDAcore-11.3.1.eb => CUDA/CUDA-11.3.1.eb} | 4 +--- .../c/{CUDAcore/CUDAcore-11.4.1.eb => CUDA/CUDA-11.4.1.eb} | 4 +--- .../c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.1.32-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.1.eb | 2 +- .../easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb | 2 +- .../n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb | 2 +- easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-CUDA-11.3.1.eb | 2 +- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb | 2 +- .../u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb | 2 +- .../u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb | 2 +- 12 files changed, 12 insertions(+), 16 deletions(-) rename easybuild/easyconfigs/c/{CUDAcore/CUDAcore-11.3.1.eb => CUDA/CUDA-11.3.1.eb} (96%) rename easybuild/easyconfigs/c/{CUDAcore/CUDAcore-11.4.1.eb => CUDA/CUDA-11.4.1.eb} (96%) diff --git a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.3.1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.3.1.eb similarity index 96% rename from easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.3.1.eb rename to easybuild/easyconfigs/c/CUDA/CUDA-11.3.1.eb index 87255c2b4e4..3f9321a0369 100644 --- a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.3.1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.3.1.eb @@ -1,6 +1,4 @@ -easyblock = 'EB_CUDA' - -name = 'CUDAcore' +name = 'CUDA' version = '11.3.1' local_nv_version = '465.19.01' diff --git a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.1.eb similarity index 96% rename from easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.1.eb rename to easybuild/easyconfigs/c/CUDA/CUDA-11.4.1.eb index d615b89734c..29d43ce1d79 100644 --- a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.4.1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.1.eb @@ -1,6 +1,4 @@ -easyblock = 'EB_CUDA' - -name = 'CUDAcore' +name = 'CUDA' version = '11.4.1' local_nv_version = '470.57.02' diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb index 8a560eca003..8a1c4c6c03a 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb @@ -35,7 +35,7 @@ dependencies = [ ('LibTIFF', '4.2.0'), ('GSL', '2.7'), ('wxWidgets', '3.1.5'), - ('CUDAcore', '11.3.1', '', True), + ('CUDA', '11.3.1', '', True), ] configopts = '--enable-openmp ' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.1.32-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.1.32-CUDA-11.3.1.eb index bad4ffe62ab..1c264d4ece5 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.1.32-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.1.32-CUDA-11.3.1.eb @@ -27,7 +27,7 @@ checksums = [ } ] -dependencies = [('CUDAcore', local_cuda_version)] +dependencies = [('CUDA', local_cuda_version)] sanity_check_paths = { 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.1.eb index 8db5880e0bc..cb08c8800bc 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.2.2.26-CUDA-11.4.1.eb @@ -27,7 +27,7 @@ checksums = [ } ] -dependencies = [('CUDAcore', local_cuda_version)] +dependencies = [('CUDA', local_cuda_version)] sanity_check_paths = { 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb index be9537ac8bb..8b6cf89878b 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb @@ -24,7 +24,7 @@ builddependencies = [ ] dependencies = [ - ('CUDAcore', '11.3.1', '', True), + ('CUDA', '11.3.1', '', True), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb index d24e1b214b6..ce83714e0e1 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -16,7 +16,7 @@ checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] builddependencies = [('binutils', '2.36.1')] dependencies = [ - ('CUDAcore', '11.3.1', '', True), + ('CUDA', '11.3.1', '', True), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb index f1f7c22b31e..1bfa2329ebc 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -16,7 +16,7 @@ checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] builddependencies = [('binutils', '2.37')] dependencies = [ - ('CUDAcore', '11.4.1', '', True), + ('CUDA', '11.4.1', '', True), ('UCX-CUDA', '1.11.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-CUDA-11.3.1.eb index 1bc204ed7ce..21c52b820b1 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.9.9-CUDA-11.3.1.eb @@ -29,7 +29,7 @@ checksums = [ } ] -dependencies = [('CUDAcore', local_cuda_version)] +dependencies = [('CUDA', local_cuda_version)] skipsteps = ['build'] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb index fa684c6a3e8..18229cdc3e2 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] dependencies = [ - ('CUDAcore', '11.3.1', '', True), + ('CUDA', '11.3.1', '', True), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb index e34d13f9868..67d9cdb0044 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -35,7 +35,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('UCX', version), - ('CUDAcore', '11.3.1', '', True), + ('CUDA', '11.3.1', '', True), ('GDRCopy', '2.2'), ] diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb index cd0cd5581fa..1dad569119f 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -35,7 +35,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('UCX', version), - ('CUDAcore', '11.4.1', '', True), + ('CUDA', '11.4.1', '', True), ('GDRCopy', '2.3'), ] From a2a7e7446458fa42e79d285cd179c1398977c4a9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 1 Sep 2021 17:41:26 +0200 Subject: [PATCH 1139/9987] Use CUDA instead of CUDAcore in recent NVHPC comments --- easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb | 4 ++-- easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb index 236a16334b5..7b6a40124e2 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.5.eb @@ -52,8 +52,8 @@ default_cuda_version = '11.3' # in this easyconfig file; alternatively, it can be specified through the command line during installation with # --try-amend=default_cuda_version="10.2" # 2) CUDA provided via EasyBuild -# Use CUDAcore as a dependency, for example -# dependencies = [('CUDAcore', '11.3.1')] +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.3.1')] # The parameter default_cuda_version still can be set as above. # If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) # diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb index 4b6b2fbe1a2..57a446c79db 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.7.eb @@ -52,8 +52,8 @@ default_cuda_version = '11.4' # in this easyconfig file; alternatively, it can be specified through the command line during installation with # --try-amend=default_cuda_version="10.2" # 2) CUDA provided via EasyBuild -# Use CUDAcore as a dependency, for example -# dependencies = [('CUDAcore', '11.4.0')] +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.4.1')] # The parameter default_cuda_version still can be set as above. # If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) # From 4f59fc59e2beb5d622bfab27b59745f7aa9815d5 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Wed, 1 Sep 2021 18:30:28 +0200 Subject: [PATCH 1140/9987] Added NWChem for 2021a --- .../n/NWChem/NWChem-7.0.2-intel-2021a.eb | 38 +++++++++++++++++++ .../NWChem/NWChem-7.0.2_fix_gnumakefile.patch | 25 ++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_gnumakefile.patch diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb new file mode 100644 index 00000000000..bf7f84cca15 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb @@ -0,0 +1,38 @@ +name = 'NWChem' +version = '7.0.2' +versionsuffix = '-Python-%(pyver)s' +local_verdate = '2020-10-12' +local_revision = 'b9985dfa' + +homepage = 'https://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'i8': True} + +source_urls = ['https://github.com/nwchemgit/nwchem/releases/download/v%(version)s-release/'] +sources = ['nwchem-%%(version)s-release.revision-%s-src.%s.tar.bz2' % (local_revision, local_verdate)] +patches = [ + 'NWChem-7.0.2_fix_gnumakefile.patch', +] +checksums = [ + # nwchem-7.0.2-release.revision-b9985dfa-src.2020-10-12.tar.bz2 + 'd9d19d87e70abf43d61b2d34e60c293371af60d14df4a6333bf40ea63f6dc8ce', + '89c634a652d4c8c358f8388ac01ee441659e3c0256c39b6494e2885c91f9aca4', # NWChem-7.0.2_fix_gnumakefile.patch +] + +dependencies = [ + ('GlobalArrays', '5.8'), + ('Python', '3.9.5'), +] + +preconfigopts = 'export EXTRA_LIBS=-lutil && ' + +modules = 'all python' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_gnumakefile.patch b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_gnumakefile.patch new file mode 100644 index 00000000000..edc5988f042 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_gnumakefile.patch @@ -0,0 +1,25 @@ +# Author: @maxim-masterov (SURF) +# Fixes quotes in the makefile to ensure correct variable substitution in the source code. +diff -Nru nwchem-7.0.2.orig/src/GNUmakefile nwchem-7.0.2/src/GNUmakefile +--- nwchem-7.0.2.orig/src/GNUmakefile 2021-08-30 13:39:57.168736415 +0200 ++++ nwchem-7.0.2/src/GNUmakefile 2021-09-01 12:41:02.105915193 +0200 +@@ -5,13 +5,13 @@ + + SUBDIRS = $(NWSUBDIRS) + +- LIB_DEFINES = -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" \ +- -DCOMPILATION_DIR="'$(TOPDIR)'" \ +- -DNWCHEM_BRANCH="'$(CODE_BRANCH)'" ++ LIB_DEFINES = -DCOMPILATION_DATE=\"`date +%a_%b_%d_%H:%M:%S_%Y`\" \ ++ -DCOMPILATION_DIR=\"$(TOPDIR)\" \ ++ -DNWCHEM_BRANCH=\"$(CODE_BRANCH)\" + ifeq ($(XLFMAC),y) +- FOPTIONS += -WF,-DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" \ +- -WF,-DCOMPILATION_DIR="'$(TOPDIR)'" \ +- -WF,-DNWCHEM_BRANCH="'$(CODE_BRANCH)'" ++ FOPTIONS += -WF,-DCOMPILATION_DATE=\"`date +%a_%b_%d_%H:%M:%S_%Y`\" \ ++ -WF,-DCOMPILATION_DIR=\"$(TOPDIR)\" \ ++ -WF,-DNWCHEM_BRANCH=\"$(CODE_BRANCH)\" + LIB_DEFINES= + DEFINES= + endif From 7908075ef11d82be62dad9092436bcc9826fbc3f Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Wed, 1 Sep 2021 18:57:53 +0200 Subject: [PATCH 1141/9987] Removed Python suffix --- easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb index bf7f84cca15..b613590b4a3 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb @@ -1,6 +1,5 @@ name = 'NWChem' version = '7.0.2' -versionsuffix = '-Python-%(pyver)s' local_verdate = '2020-10-12' local_revision = 'b9985dfa' From 097ad581dcbe7c0ab1cccd2731716b35b0dc113c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Sep 2021 09:36:03 +0200 Subject: [PATCH 1142/9987] consistently use patch for HMMER 3.3.2 to use Perl provided through EasyBuild --- .../h/HMMER/HMMER-3.3.2-gompi-2019b.eb | 16 +++++++++++++--- .../h/HMMER/HMMER-3.3.2-gompi-2020a.eb | 16 +++++++++++++--- .../h/HMMER/HMMER-3.3.2-gompi-2020b.eb | 2 +- .../h/HMMER/HMMER-3.3.2-gompi-2021a.eb | 18 ++++++++++++++---- .../h/HMMER/HMMER-3.3.2-iimpi-2020b.eb | 2 +- 5 files changed, 42 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2019b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2019b.eb index 60c018b7653..16d64bf06ba 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2019b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2019b.eb @@ -34,13 +34,23 @@ source_urls = [ 'http://eddylab.org/software/hmmer/', 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] -sources = ['hmmer-%(version)s.tar.gz'] -checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] -builddependencies = [('Python', '3.7.4')] +builddependencies = [ + ('Python', '3.7.4'), + ('Perl', '5.30.0'), +] configopts = '--enable-mpi' +buildopts = ' V=1 ' + +testopts = buildopts runtest = 'check' installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020a.eb index da4b727da5e..587aa80b012 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020a.eb @@ -34,13 +34,23 @@ source_urls = [ 'http://eddylab.org/software/hmmer/', 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] -sources = ['hmmer-%(version)s.tar.gz'] -checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] -builddependencies = [('Python', '3.8.2')] +builddependencies = [ + ('Python', '3.8.2'), + ('Perl', '5.30.2', '-minimal'), +] configopts = '--enable-mpi' +buildopts = ' V=1 ' + +testopts = buildopts runtest = 'check' installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb index 6d95f779faf..55a9044d7fb 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2020b.eb @@ -34,7 +34,7 @@ source_urls = [ 'http://eddylab.org/software/hmmer/', 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] -sources = ['hmmer-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_fix_perl.patch'] checksums = [ '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021a.eb index 7d4fadc98a4..c7d127f9f00 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021a.eb @@ -31,16 +31,26 @@ description = """HMMER is used for searching sequence databases for homologs toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = [ - 'http://eddylab.org/software/%(namelower)s/', - 'http://eddylab.org/software/%(namelower)s%(version_major)s/%(version)s/', + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] sources = [SOURCELOWER_TAR_GZ] -checksums = ['92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] -builddependencies = [('Python', '3.9.5')] +builddependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1', '-minimal'), +] configopts = '--enable-mpi' +buildopts = ' V=1 ' + +testopts = buildopts runtest = 'check' installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb index 0f903bc0639..3c33d7fa1ec 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2020b.eb @@ -34,7 +34,7 @@ source_urls = [ 'http://eddylab.org/software/hmmer/', 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', ] -sources = ['hmmer-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_fix_perl.patch'] checksums = [ '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz From b331a6f6064607fc7b745d7f823d97a3075268f5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Sep 2021 14:12:14 +0200 Subject: [PATCH 1143/9987] adding easyconfigs: TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb and patches: TensorFlow-2.6.0_add-default-shell-env.patch, TensorFlow-2.6.0_downgrade-required-versions.patch, TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch, TensorFlow-2.5.0_fix_protobuf_error_message.patch --- ...w-2.5.0_fix_numpy_1.20_compatibility.patch | 55 +++++ ...low-2.5.0_fix_protobuf_error_message.patch | 30 +++ ...TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 232 ++++++++++++++++++ ...nsorFlow-2.6.0_add-default-shell-env.patch | 98 ++++++++ ...ow-2.6.0_downgrade-required-versions.patch | 36 +++ 5 files changed, 451 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix_protobuf_error_message.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0_add-default-shell-env.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0_downgrade-required-versions.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch new file mode 100644 index 00000000000..d05986a8eb2 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch @@ -0,0 +1,55 @@ +TF-2.5.0 and 2.6.0 are not compatible with numpy > 1.20 +During the testing phase, TensorFlow throws errors like this +"Cannot convert a symbolic Tensor (lstm/strided_slice:0) to a numpy array. +This error may indicate that you're trying to pass a Tensor to a NumPy call, which is not supported" +See https://github.com/tensorflow/tensorflow/pull/48935 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/python/framework/ops.py b/tensorflow/python/framework/ops.py +index 4e12a8a1d17..73afdd4ed8a 100644 +--- a/tensorflow/python/framework/ops.py ++++ b/tensorflow/python/framework/ops.py +@@ -864,7 +864,7 @@ class Tensor(internal.NativeObject, core_tf_types.Tensor): + __array_priority__ = 100 + + def __array__(self): +- raise NotImplementedError( ++ raise TypeError( + "Cannot convert a symbolic Tensor ({}) to a numpy array." + " This error may indicate that you're trying to pass a Tensor to" + " a NumPy call, which is not supported".format(self.name)) +diff --git a/tensorflow/python/framework/ops_test.py b/tensorflow/python/framework/ops_test.py +index c72b18e8df5..f69ec4a9ae2 100644 +--- a/tensorflow/python/framework/ops_test.py ++++ b/tensorflow/python/framework/ops_test.py +@@ -188,7 +188,7 @@ class TensorAndShapeTest(test_util.TensorFlowTestCase): + with ops.Graph().as_default(): + x = array_ops.ones((3, 4), name="test_ones") + +- with self.assertRaisesRegex(NotImplementedError, ++ with self.assertRaisesRegex(TypeError, + r"Cannot convert a symbolic.+test_ones"): + np.array(x) + +diff --git a/tensorflow/python/ops/array_ops.py b/tensorflow/python/ops/array_ops.py +index 77cebdad660..3c650d7808f 100644 +--- a/tensorflow/python/ops/array_ops.py ++++ b/tensorflow/python/ops/array_ops.py +@@ -36,6 +36,7 @@ from tensorflow.python.framework import tensor_util + from tensorflow.python.framework.constant_op import constant + from tensorflow.python.ops import gen_array_ops + from tensorflow.python.ops import gen_math_ops ++from tensorflow.python.ops import math_ops + # go/tf-wildcard-import + # pylint: disable=wildcard-import + from tensorflow.python.ops.gen_array_ops import * +@@ -2897,7 +2898,7 @@ def matrix_set_diag( + + def _constant_if_small(value, shape, dtype, name): + try: +- if np.prod(shape) < 1000: ++ if math_ops.reduce_prod(shape) < 1000: + return constant(value, shape=shape, dtype=dtype, name=name) + except (NotImplementedError, TypeError): + # Happens when shape is a Tensor, list with Tensor elements, etc. diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix_protobuf_error_message.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix_protobuf_error_message.patch new file mode 100644 index 00000000000..addc55bd710 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix_protobuf_error_message.patch @@ -0,0 +1,30 @@ +Fix an issue where TensorFlow 2.5/2.6 won't build with a protobuf newer than 3.14 +Additionally, a TypeError ("expected tensorflow.TensorShapeProto got tensorflow.TensorShapeProto") +is fixed by inverting the import statements. +Solution/patch obtained from https://bugs.gentoo.org/800824 + +diff -Nrup tensorflow-2.5.0_old/tensorflow/core/kernels/example_parsing_ops.cc tensorflow-2.5.0/tensorflow/core/kernels/example_parsing_ops.cc +--- tensorflow-2.5.0_old/tensorflow/core/kernels/example_parsing_ops.cc 2021-05-12 15:26:41.000000000 +0200 ++++ tensorflow-2.5.0/tensorflow/core/kernels/example_parsing_ops.cc 2021-07-14 08:09:39.927536430 +0200 +@@ -1218,7 +1218,7 @@ class DecodeJSONExampleOp : public OpKer + resolver_.get(), "type.googleapis.com/tensorflow.Example", &in, &out); + OP_REQUIRES(ctx, status.ok(), + errors::InvalidArgument("Error while parsing JSON: ", +- string(status.error_message()))); ++ string(status.message()))); + } + } + +diff -Nrup tensorflow-2.5.0_old/tensorflow/python/__init__.py tensorflow-2.5.0/tensorflow/python/__init__.py +--- tensorflow-2.5.0_old/tensorflow/python/__init__.py 2021-05-12 15:26:41.000000000 +0200 ++++ tensorflow-2.5.0/tensorflow/python/__init__.py 2021-07-14 08:09:55.696294764 +0200 +@@ -37,8 +37,8 @@ import traceback + # go/tf-wildcard-import + # pylint: disable=wildcard-import,g-bad-import-order,g-import-not-at-top + +-from tensorflow.python.eager import context + from tensorflow.python import pywrap_tensorflow as _pywrap_tensorflow ++from tensorflow.python.eager import context + + # pylint: enable=wildcard-import + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..8c5bc0eff47 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,232 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.6.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.17.3'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.32.0', '-nodocs'), + ('pybind11', '2.6.2'), +] +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('UCX-CUDA', '1.10.0', versionsuffix), + ('cuDNN', '8.2.1.32', versionsuffix, True), + ('NCCL', '2.10.3', versionsuffix), + ('Python', '3.9.5'), + ('h5py', '3.2.1'), + ('cURL', '7.76.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.4.1'), + ('ICU', '69.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.28'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.35.4'), + ('protobuf-python', '3.17.3'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.0'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('google-auth', '1.35.0', { + 'modulename': 'google.auth', + 'checksums': ['b7033be9028c188ee30200b204ea00ed82ea1162e8ac1df4aa6ded19a191d88e'], + }), + ('oauthlib', '3.1.1', { + 'checksums': ['8f0215fcc533dd8dd1bee6f4c412d4f0cd7297307d43ac61666389e3bc3198a3'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.5', { + 'checksums': ['4ab58e6c3dc6ccf112f921fcced40e5426fba266768986ea502228488276eaba'], + }), + ('Werkzeug', '2.0.1', { + 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], + }), + ('absl-py', '0.13.0', { + 'modulename': 'absl', + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.39.0', { + 'modulename': 'grpc', + 'checksums': ['57974361a459d6fe04c9ae0af1845974606612249f467bbd2062d963cb90f407'], + }), + # Required for tensorboard_plugin_profile + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': SOURCE_PY3_WHL, # Requires Rust to build, take the dummy for now + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['f7dac4cdfb52d14c9e3f74585ce2aaf8e6203620a864e51faf84988b09f7bbdb'], + }), + ('tensorboard_plugin_wit', '1.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard_plugin_profile', '2.5.0', { + 'checksums': ['f832698d87a773b9a017fc4dd5cf598a1ff942ccfbf3392c83fe12c949ab9f52'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow_estimator', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['cf78528998efdb637ac0abaf525c929bf192767544eb24ae20d9266effcf5afd'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('clang', '5.0', { + 'checksums': ['ceccae97eda0225a5b44d42ffd61102e248325c2865ca53e4407746464a5333a'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.4.0', { + 'checksums': ['c2831ff4328a21e928ffc9e52124bcafacaf5816d38a1a72dc329680dc1bb7ba'], + }), + ('keras', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['504af5656a9829fe803ce48a8580ef16916e89906aceddad9e098614269437e7'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch', + 'TensorFlow-2.5.0_fix_protobuf_error_message.patch', + 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.6.0_add-default-shell-env.patch', + 'TensorFlow-2.6.0_downgrade-required-versions.patch', + ], + 'checksums': [ + '41b32eeaddcbc02b0583660bcf508469550e4cd0f86b22d2abe72dfebeacde0f', # v2.5.0.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', + # TensorFlow-2.5.0_disable-avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_fix-crash-on-shutdown.patch + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', + # TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch + '4c32aba417e6ecb2642d5828b4ac618f1e4395f6c217cd621fa08a74433faa55', + # TensorFlow-2.5.0_fix_protobuf_error_message.patch + '4ca80aac8f7394f4c83af5e8b237f6264dde3d55d10bf0dcb93e49ee5e1c5697', + # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch + 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', + # TensorFlow-2.6.0_add-default-shell-env.patch + '8cc54ff4bc8e5fc8edd3a5e41ad338532e16db5c64a941cc45e1011d4b40dba7', + # TensorFlow-2.6.0_downgrade-required-versions.patch + 'e941df7025d39a6b57f508779775cf896691c34abe61d5f2eba9b891ef20d51a', + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' + '-benchmark-test,-v1only'), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0_add-default-shell-env.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0_add-default-shell-env.patch new file mode 100644 index 00000000000..b80d92f0210 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0_add-default-shell-env.patch @@ -0,0 +1,98 @@ +Make TensorFlow use the environment as set by EasyBuild + +From https://github.com/tensorflow/tensorflow/pull/44549 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/core/kernels/mlir_generated/build_defs.bzl b/tensorflow/core/kernels/mlir_generated/build_defs.bzl +index a6a136b8e38..e614b20bb02 100644 +--- a/tensorflow/core/kernels/mlir_generated/build_defs.bzl ++++ b/tensorflow/core/kernels/mlir_generated/build_defs.bzl +@@ -68,6 +68,7 @@ def _gen_mlir_op_impl(ctx): + ctx.outputs.out.path, + ) + ), ++ use_default_shell_env = True, + ) + + _gen_mlir_op_rule = rule( +@@ -157,6 +158,7 @@ def _gen_kernel_bin_impl(ctx): + "--enable_ftz=%s" % (ctx.attr.data_type == "f32"), + "--cpu_codegen=%s" % ctx.attr.cpu_codegen, + ], ++ use_default_shell_env = True, + mnemonic = "compile", + ) + compilation_outputs = cc_common.create_compilation_outputs( +diff --git a/third_party/flatbuffers/build_defs.bzl b/third_party/flatbuffers/build_defs.bzl +index d409f836cb0..754db3f5d86 100644 +--- a/third_party/flatbuffers/build_defs.bzl ++++ b/third_party/flatbuffers/build_defs.bzl +@@ -394,6 +394,7 @@ def _concat_flatbuffer_py_srcs_impl(ctx): + ctx.attr.deps[0].files.to_list()[0].path, + ctx.outputs.out.path, + ), ++ use_default_shell_env = True, + ) + + _concat_flatbuffer_py_srcs = rule( +diff --git a/third_party/mlir/tblgen.bzl b/third_party/mlir/tblgen.bzl +index 37577ed31ef..448284daefe 100644 +--- a/third_party/mlir/tblgen.bzl ++++ b/third_party/mlir/tblgen.bzl +@@ -154,6 +154,7 @@ def _gentbl_rule_impl(ctx): + executable = ctx.executable.tblgen, + arguments = [args], + mnemonic = "TdGenerate", # Kythe extractor hook. ++ use_default_shell_env = True, + ) + + return [DefaultInfo()] +diff --git a/third_party/nccl/build_defs.bzl.tpl b/third_party/nccl/build_defs.bzl.tpl +index c8757174038..fe163741f87 100644 +--- a/third_party/nccl/build_defs.bzl.tpl ++++ b/third_party/nccl/build_defs.bzl.tpl +@@ -100,6 +100,7 @@ def _device_link_impl(ctx): + "--output-file=%s" % cubin.path, + ] + [file.path for file in inputs], + mnemonic = "nvlink", ++ use_default_shell_env = True, + ) + cubins.append(cubin) + images.append("--image=profile=%s,file=%s" % (arch, cubin.path)) +@@ -125,6 +126,7 @@ def _device_link_impl(ctx): + arguments = arguments_list + images, + tools = [bin2c], + mnemonic = "fatbinary", ++ use_default_shell_env = True, + ) + + # Generate the source file #including the headers generated above. +@@ -203,6 +205,7 @@ def _prune_relocatable_code_impl(ctx): + executable = ctx.file._nvprune, + arguments = arguments, + mnemonic = "nvprune", ++ use_default_shell_env = True, + ) + outputs.append(output) + +@@ -236,6 +239,7 @@ def _merge_archive_impl(ctx): + inputs = ctx.files.srcs, # + ctx.files._crosstool, + outputs = [ctx.outputs.out], + command = "echo -e \"%s\" | %s -M" % (mri_script, cc_toolchain.ar_executable), ++ use_default_shell_env = True, + ) + + _merge_archive = rule( +diff --git a/third_party/systemlibs/grpc.bazel.generate_cc.bzl b/third_party/systemlibs/grpc.bazel.generate_cc.bzl +index 1534e526fd1..cd7304a9515 100644 +--- a/third_party/systemlibs/grpc.bazel.generate_cc.bzl ++++ b/third_party/systemlibs/grpc.bazel.generate_cc.bzl +@@ -140,6 +140,7 @@ def generate_cc_impl(ctx): + outputs = out_files, + executable = ctx.executable._protoc, + arguments = arguments, ++ use_default_shell_env = True, + ) + + return struct(files = depset(out_files)) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0_downgrade-required-versions.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0_downgrade-required-versions.patch new file mode 100644 index 00000000000..15ec3859882 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0_downgrade-required-versions.patch @@ -0,0 +1,36 @@ +TF introduced a change pinning versions to fixed major.minor or even patch versions +Loosen those a bit so we can build it with our versions. +See https://github.com/tensorflow/tensorflow/issues/44654 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index 3d4a64de2b4..b89d077a150 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -78,20 +78,20 @@ REQUIRED_PACKAGES = [ + # NOTE: As numpy has releases that break semver guarantees and several other + # deps depend on numpy without an upper bound, we must install numpy before + # everything else. +- 'numpy ~= 1.19.2', ++ 'numpy >= 1.19.2', + # Install other dependencies + 'absl-py ~= 0.10', + 'astunparse ~= 1.6.3', + 'clang ~= 5.0', +- 'flatbuffers ~= 1.12.0', ++ 'flatbuffers >= 1.12.0', + 'google_pasta ~= 0.2', +- 'h5py ~= 3.1.0', ++ 'h5py ~= 3.1', + 'keras_preprocessing ~= 1.1.2', + 'opt_einsum ~= 3.3.0', + 'protobuf >= 3.9.2', +- 'six ~= 1.15.0', ++ 'six >= 1.15.0', + 'termcolor ~= 1.1.0', +- 'typing_extensions ~= 3.7.4', ++ 'typing_extensions >= 3.7.4', + 'wheel ~= 0.35', + 'wrapt ~= 1.12.1', + # These packages need to be pinned exactly as newer versions are From 12b08048075deec42a7debdcaf44e1e3650ea558 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Sep 2021 14:37:59 +0200 Subject: [PATCH 1144/9987] Drop DFT-D3 to intel-compilers level --- ...-intel-2021a.eb => DFT-D3-3.2.0-intel-compilers-2021.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/d/DFT-D3/{DFT-D3-3.2.0-intel-2021a.eb => DFT-D3-3.2.0-intel-compilers-2021.2.0.eb} (95%) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2021a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.2.0.eb similarity index 95% rename from easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2021a.eb rename to easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.2.0.eb index 9e90b78487d..88dfa0f4cac 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2021a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.2.0.eb @@ -7,7 +7,7 @@ homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsectio description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" -toolchain = {'name': 'intel', 'version': '2021a'} +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} source_urls = ['https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3'] # Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version From 3c4b87a6c19a2d229a4708d347027e27fbf09c8f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Sep 2021 15:05:18 +0200 Subject: [PATCH 1145/9987] adding easyconfigs: protobuf-3.17.3-GCCcore-11.2.0.eb, protobuf-python-3.17.3-GCCcore-11.2.0.eb, nsync-1.24.0-GCCcore-11.2.0.eb --- .../n/nsync/nsync-1.24.0-GCCcore-11.2.0.eb | 26 ++++++++++++++ .../protobuf-python-3.17.3-GCCcore-11.2.0.eb | 35 +++++++++++++++++++ .../protobuf-3.17.3-GCCcore-11.2.0.eb | 29 +++++++++++++++ 3 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.17.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.17.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0cdb6dc3887 --- /dev/null +++ b/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeNinja' + +name = 'nsync' +version = '1.24.0' + +homepage = 'https://github.com/google/nsync' +description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/google/nsync/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['47a6eb2a295be5121a1904a6a775722338a20dc02ee3eec4169ed2c3f203617a'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Ninja', '1.10.2'), +] + +sanity_check_paths = { + 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.17.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.17.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a37091edc78 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.17.3-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.17.3' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = [{'download_filename': 'protobuf-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['72804ea5eaa9c22a090d2803813e280fb273b62d5ae497aaf3553d141c4fdd7b'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('protobuf', version) +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.17.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.17.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..826ee80c352 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.17.3-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '3.17.3' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c6003e1d2e7fefa78a3039f19f383b4f3a61e81be8c19356f85b6461998ad3db'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +srcdir = 'cmake' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From 55b50c1f465ed66dfaf311ca6c384b47577dcde3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Sep 2021 16:59:48 +0200 Subject: [PATCH 1146/9987] adding easyconfigs: Horovod-0.21.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb --- ...foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb new file mode 100644 index 00000000000..2e025f50b68 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.21.1' +local_tf_version = '2.6.0' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-TensorFlow-%s' % local_tf_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('CMake', '3.20.1'), + ('flatbuffers', '2.0.0'), +] +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('UCX-CUDA', '1.10.0', local_cuda_suffix), + ('NCCL', '2.10.3', local_cuda_suffix), + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('TensorFlow', local_tf_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + 'maxparallel': 1, + 'checksums': ['874dd3ac469944464bb77e1a42296500d0028177183ad5ab5af8ec61a34a1ed7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From b4115f45b3a5cd508494811ebab545c925e5750a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Sep 2021 17:16:24 +0200 Subject: [PATCH 1147/9987] Fix Horovod version --- ...Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/h/Horovod/{Horovod-0.21.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb => Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb} (92%) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb similarity index 92% rename from easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb rename to easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb index 2e025f50b68..d59045a9559 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'Horovod' -version = '0.21.1' +version = '0.22.1' local_tf_version = '2.6.0' local_cuda_suffix = '-CUDA-%(cudaver)s' versionsuffix = local_cuda_suffix + '-TensorFlow-%s' % local_tf_version @@ -37,7 +37,7 @@ exts_list = [ ('horovod', version, { # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend 'maxparallel': 1, - 'checksums': ['874dd3ac469944464bb77e1a42296500d0028177183ad5ab5af8ec61a34a1ed7'], + 'checksums': ['c45bfcb9bd96852d79c62976eda12e9320b58b64f55bee3772877b3fc6243f2a'], }), ] From 2f4a84ab42217064a37593b18f9c74329d29e67a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Sep 2021 17:31:46 +0200 Subject: [PATCH 1148/9987] Move maxparallel --- ...Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb index d59045a9559..4ad47ea0521 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb @@ -30,13 +30,14 @@ sanity_pip_check = True preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' +# Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend +maxparallel = 1 + exts_list = [ ('cloudpickle', '1.6.0', { 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], }), ('horovod', version, { - # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend - 'maxparallel': 1, 'checksums': ['c45bfcb9bd96852d79c62976eda12e9320b58b64f55bee3772877b3fc6243f2a'], }), ] From e190614397a0c6494918eda632b8ac25d3711c47 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Sep 2021 17:49:06 +0200 Subject: [PATCH 1149/9987] Remove UCX-CUDA from TensorFlow 2.6 --- .../t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index 8c5bc0eff47..fb1e4cc8989 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -19,7 +19,6 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.3.1', '', True), - ('UCX-CUDA', '1.10.0', versionsuffix), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), From a3149eb7cf7c97ed00c06a19cc53adcb9aebaf9e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Sep 2021 17:52:45 +0200 Subject: [PATCH 1150/9987] adding easyconfigs: TensorFlow-2.6.0-foss-2021a.eb --- .../TensorFlow/TensorFlow-2.6.0-foss-2021a.eb | 212 ++++++++++++++++++ 1 file changed, 212 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb new file mode 100644 index 00000000000..f80b5a9899e --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb @@ -0,0 +1,212 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.6.0' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.17.3'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.32.0', '-nodocs'), + ('pybind11', '2.6.2'), +] +dependencies = [ + ('Python', '3.9.5'), + ('h5py', '3.2.1'), + ('cURL', '7.76.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.4.1'), + ('ICU', '69.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.28'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.35.4'), + ('protobuf-python', '3.17.3'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.0'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('google-auth', '1.35.0', { + 'modulename': 'google.auth', + 'checksums': ['b7033be9028c188ee30200b204ea00ed82ea1162e8ac1df4aa6ded19a191d88e'], + }), + ('oauthlib', '3.1.1', { + 'checksums': ['8f0215fcc533dd8dd1bee6f4c412d4f0cd7297307d43ac61666389e3bc3198a3'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.5', { + 'checksums': ['4ab58e6c3dc6ccf112f921fcced40e5426fba266768986ea502228488276eaba'], + }), + ('Werkzeug', '2.0.1', { + 'checksums': ['1de1db30d010ff1af14a009224ec49ab2329ad2cde454c8a708130642d579c42'], + }), + ('absl-py', '0.13.0', { + 'modulename': 'absl', + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.39.0', { + 'modulename': 'grpc', + 'checksums': ['57974361a459d6fe04c9ae0af1845974606612249f467bbd2062d963cb90f407'], + }), + # Required for tensorboard_plugin_profile + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': SOURCE_PY3_WHL, # Requires Rust to build, take the dummy for now + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['f7dac4cdfb52d14c9e3f74585ce2aaf8e6203620a864e51faf84988b09f7bbdb'], + }), + ('tensorboard_plugin_wit', '1.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard_plugin_profile', '2.5.0', { + 'checksums': ['f832698d87a773b9a017fc4dd5cf598a1ff942ccfbf3392c83fe12c949ab9f52'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow_estimator', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['cf78528998efdb637ac0abaf525c929bf192767544eb24ae20d9266effcf5afd'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('clang', '5.0', { + 'checksums': ['ceccae97eda0225a5b44d42ffd61102e248325c2865ca53e4407746464a5333a'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.4.0', { + 'checksums': ['c2831ff4328a21e928ffc9e52124bcafacaf5816d38a1a72dc329680dc1bb7ba'], + }), + ('keras', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['504af5656a9829fe803ce48a8580ef16916e89906aceddad9e098614269437e7'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch', + 'TensorFlow-2.5.0_fix_protobuf_error_message.patch', + 'TensorFlow-2.6.0_add-default-shell-env.patch', + 'TensorFlow-2.6.0_downgrade-required-versions.patch', + ], + 'checksums': [ + '41b32eeaddcbc02b0583660bcf508469550e4cd0f86b22d2abe72dfebeacde0f', # v2.5.0.tar.gz + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', + # TensorFlow-2.5.0_disable-avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_fix-crash-on-shutdown.patch + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', + # TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch + '4c32aba417e6ecb2642d5828b4ac618f1e4395f6c217cd621fa08a74433faa55', + # TensorFlow-2.5.0_fix_protobuf_error_message.patch + '4ca80aac8f7394f4c83af5e8b237f6264dde3d55d10bf0dcb93e49ee5e1c5697', + # TensorFlow-2.6.0_add-default-shell-env.patch + '8cc54ff4bc8e5fc8edd3a5e41ad338532e16db5c64a941cc45e1011d4b40dba7', + # TensorFlow-2.6.0_downgrade-required-versions.patch + 'e941df7025d39a6b57f508779775cf896691c34abe61d5f2eba9b891ef20d51a', + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_distributed_test', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'with_xla': True, + }), +] + +moduleclass = 'lib' From 1eee1251f042fddc1667eddd8a343a79a3c48223 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Sep 2021 19:39:42 +0200 Subject: [PATCH 1151/9987] add missing flex build dependency for leidenalg --- .../l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb | 3 +++ .../easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb | 1 + .../easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb | 1 + 3 files changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb index 159d9f4e461..e742d1f8b77 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb @@ -13,6 +13,9 @@ toolchain = {'name': 'foss', 'version': '2020a'} builddependencies = [ ('pkg-config', '0.29.2'), ('PyYAML', '5.3'), + ('Bison', '3.5.3'), + ('libtool', '2.4.6'), + ('flex', '2.6.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb index b5307684eb1..6df451ff574 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-foss-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('PyYAML', '5.3.1'), ('Bison', '3.7.1'), ('libtool', '2.4.6'), + ('flex', '2.6.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb index 66efa3a2fc8..8aad4bf9f15 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.3-fosscuda-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('PyYAML', '5.3.1'), ('Bison', '3.7.1'), ('libtool', '2.4.6'), + ('flex', '2.6.4'), ] dependencies = [ From f91fe9abb6219c00738db8086541da0a2c249931 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Sep 2021 21:14:10 +0200 Subject: [PATCH 1152/9987] adding easyconfigs: ReFrame-3.8.0.eb --- .../easyconfigs/r/ReFrame/ReFrame-3.8.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb new file mode 100644 index 00000000000..d8240a82ea3 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.8.0' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.2.4', { + 'use_pip': False, + 'checksums': ['0eb8a1516c3d138ae8689c0c1a60fde7143310832f9dc77e11d8a4bc62de193b'], + }), + ('wheel', '0.37.0', { + 'checksums': ['e2ef7239991699e3355d54f8e968a21bb940a1dbf34a4d226741e64462516fad'], + }), + ('setuptools', '57.4.0', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], + }), + ('reframe', version, { + 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], + 'checksums': ['b8a0486fd78786606586364968d1e2a4e7fc424d523b12b2c0ea8a227b485e30'], + }), +] + +postinstallcmds = [ + "cp -r tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -r share/completions %(installdir)s/share/completions", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['lib', 'tutorials', 'external'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions +modextrapaths = { + 'PATH': 'bin', + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 94813c5e22fde986a6c53b967f665a87c15ff32e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Sep 2021 21:30:51 +0200 Subject: [PATCH 1153/9987] fix long line in ReFrame 3.8.0 easyconfig --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb index d8240a82ea3..0b0383bc951 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb @@ -28,7 +28,8 @@ exts_list = [ 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], }), ('reframe', version, { - 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], 'checksums': ['b8a0486fd78786606586364968d1e2a4e7fc424d523b12b2c0ea8a227b485e30'], From babaa521ee703c02e91aa624a0a18b468af76fbb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 09:17:48 +0200 Subject: [PATCH 1154/9987] adding easyconfigs: ABAQUS-2021-hotfix-2132.eb --- .../a/ABAQUS/ABAQUS-2021-hotfix-2132.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABAQUS/ABAQUS-2021-hotfix-2132.eb diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2021-hotfix-2132.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2021-hotfix-2132.eb new file mode 100644 index 00000000000..c3b4601ac6f --- /dev/null +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2021-hotfix-2132.eb @@ -0,0 +1,37 @@ +name = 'ABAQUS' +version = '2021' +local_hotfix = '2132' +versionsuffix = '-hotfix-%s' % local_hotfix + +homepage = 'http://www.simulia.com/products/abaqus_fea.html' +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" + +toolchain = SYSTEM + +sources = [ + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-5.tar', + # hotfixes + '%%(version)s.FP.CFA.%s.Part_SIMULIA_Documentation.AllOS.tar' % local_hotfix, + '%%(version)s.FP.CFA.%s.Part_SIMULIA_EstPrd.Linux64.tar' % local_hotfix, + '%%(version)s.FP.CFA.%s.Part_SIMULIA_Isight.Linux64.tar' % local_hotfix, +] +checksums = [ + 'fbc93662c2c0ea9294df79ed9c9678246582d1f63598ad999bbb17fee0dbf54a', # 2021.AM_SIM_Abaqus_Extend.AllOS.1-5.tar + '4433dee911274f559a9372291c007f359108e8e1ab2db6abe570727e1b13741a', # 2021.AM_SIM_Abaqus_Extend.AllOS.2-5.tar + 'ddd79bfa40c238b12cc36c2d37ee3a351c21684fd5d6aba402a87051ee27096d', # 2021.AM_SIM_Abaqus_Extend.AllOS.3-5.tar + 'c7b5b04388c1a29f4c5ad46da35e2f5e6d2d493832611fc90860644ff837ded0', # 2021.AM_SIM_Abaqus_Extend.AllOS.4-5.tar + 'fafb50a0ee12128cd604563eb9b5b845cbeb4383c24df837220cbce847bd5c58', # 2021.AM_SIM_Abaqus_Extend.AllOS.5-5.tar + # 2021.FP.CFA.2132.Part_SIMULIA_Documentation.AllOS.tar + 'ac62bdeda3939c83dfc7683eced82816e1dbfdf6e93b7ac5b87967a239438bd4', + # 2021.FP.CFA.2132.Part_SIMULIA_EstPrd.Linux64.tar + 'b3e98f05db92c0a15520feef3494fb80d260d3ecdb67610059c3fd229426d78b', + # 2021.FP.CFA.2132.Part_SIMULIA_Isight.Linux64.tar + 'b27a90484f89989c3f27133239a85483ee24092af5d8a2159681b2cc1fada46c', +] + +moduleclass = 'cae' From 6ca60b8e9789a47ba2d8552a54c29ed3c4553cc0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 09:22:59 +0200 Subject: [PATCH 1155/9987] update CMake build dependency for Eigen 3.3.4 + 3.3.5 --- easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb | 6 +++--- easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb index 6147a422071..b118fa6bee6 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.4.eb @@ -16,9 +16,9 @@ checksums = ['b170583f59d6778be4bfeae88583c77ed610df5b803ce5cb4aa850d0e8017c2f'] # building CMake at core level is often difficult. # Change the GCCcore version if you want to reuse a different CMake you already have installed. builddependencies = [ - ('GCCcore', '6.4.0'), # Needed to access CMake when using HMNS - ('binutils', '2.28'), # Needed to pass CMakes compiler health check on old systems - ('CMake', '3.11.1', '-GCCcore-6.4.0'), + ('GCCcore', '7.3.0'), # Needed to access CMake when using HMNS + ('binutils', '2.30'), # Needed to pass CMakes compiler health check on old systems + ('CMake', '3.12.1', '-GCCcore-7.3.0'), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb index 18ba0bdce86..e2bc644be1a 100644 --- a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.5.eb @@ -16,9 +16,9 @@ checksums = ['0208f8d3d5f3b9fd1a022c5f47d6ebbd6f11c4ed6e756764871bf4ffb1e117a1'] # building CMake at core level is often difficult. # Change the GCCcore version if you want to reuse a different CMake you already have installed. builddependencies = [ - ('GCCcore', '6.4.0'), # Needed to access CMake when using HMNS - ('binutils', '2.28'), # Needed to pass CMakes compiler health check on old systems - ('CMake', '3.11.1', '-GCCcore-6.4.0'), + ('GCCcore', '7.3.0'), # Needed to access CMake when using HMNS + ('binutils', '2.30'), # Needed to pass CMakes compiler health check on old systems + ('CMake', '3.12.1', '-GCCcore-7.3.0'), ] moduleclass = 'math' From a80bd28d82d7d27baa1a2b96eca564fea4407272 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 11:00:23 +0200 Subject: [PATCH 1156/9987] adding easyconfigs: scanpy-1.8.1-foss-2020b.eb --- .../s/scanpy/scanpy-1.8.1-foss-2020b.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb new file mode 100644 index 00000000000..76668a416ae --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.8.1' + +homepage = 'https://scanpy.readthedocs.io/en/stable/' +description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('networkx', '2.5'), + ('numba', '0.52.0'), + ('PyTables', '3.6.1'), + ('statsmodels', '0.12.1'), + ('scikit-learn', '0.23.2'), + ('Seaborn', '0.11.1'), + ('tqdm', '4.56.2'), + ('leidenalg', '0.8.3'), +] + +use_pip = True + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('anndata', '0.7.6', { + 'checksums': ['a3cc67bba9a4cd4b5984aec64c4f577c2d5a4695f4064027f8e6a9dac1f508b2'], + }), + ('pynndescent', '0.5.4', { + 'checksums': ['221124cbad8e3cf3ed421a4089d80ac5a29d3215e76cb49effc1df887533d2a8'], + }), + ('umap-learn', '0.5.1', { + 'modulename': 'umap', + 'checksums': ['3e3e5e526109866012a9da79f423c922edc379c6cac9bf65ea08fbb9dd93ff3a'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.4', { + 'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'], + }), + (name, version, { + 'checksums': ['1b8603a868d783bd6c18c8db763a450153feefc8daed862c440749790d47c654'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "natsort --help", + "scanpy --help", +] + +moduleclass = 'bio' From 3e032c6c9c800792a14bed1e4ae46934a653db02 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 11:44:32 +0200 Subject: [PATCH 1157/9987] use numba 0.53.1 as dependency for scanpy 1.8.1 --- easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb index 76668a416ae..bc44c5abc43 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2020b.eb @@ -18,7 +18,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('h5py', '3.1.0'), ('networkx', '2.5'), - ('numba', '0.52.0'), + ('numba', '0.53.1'), ('PyTables', '3.6.1'), ('statsmodels', '0.12.1'), ('scikit-learn', '0.23.2'), From c4525540e55a8f0ed04e3f6ac6867c9f6308f4f0 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 3 Sep 2021 11:36:09 +0100 Subject: [PATCH 1158/9987] adding easyconfigs: Gradle-6.9.1.eb --- .../easyconfigs/g/Gradle/Gradle-6.9.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gradle/Gradle-6.9.1.eb diff --git a/easybuild/easyconfigs/g/Gradle/Gradle-6.9.1.eb b/easybuild/easyconfigs/g/Gradle/Gradle-6.9.1.eb new file mode 100644 index 00000000000..ed371c4b234 --- /dev/null +++ b/easybuild/easyconfigs/g/Gradle/Gradle-6.9.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PackedBinary' + +name = 'Gradle' +version = '6.9.1' + +homepage = 'https://gradle.org' +description = """Complete Gradle install. +From mobile apps to microservices, from small startups to big enterprises, +Gradle helps teams build, automate and deliver better software, faster. +""" + +toolchain = SYSTEM + +source_urls = ['https://services.gradle.org/distributions'] +sources = ['gradle-%(version)s-all.zip'] +checksums = ['b13f5d97f08000996bf12d9dd70af3f2c6b694c2c663ab1b545e9695562ad1ee'] + +sanity_check_paths = { + 'files': ['bin/gradle'], + 'dirs': [], +} + +moduleclass = 'devel' From 641ba09d584e90bab51f496834ff8ea4302a600d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 3 Sep 2021 11:37:10 +0100 Subject: [PATCH 1159/9987] adding easyconfigs: ant-1.10.11-Java-13.eb --- .../easyconfigs/a/ant/ant-1.10.11-Java-13.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.11-Java-13.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.11-Java-13.eb b/easybuild/easyconfigs/a/ant/ant-1.10.11-Java-13.eb new file mode 100644 index 00000000000..31eec4f38ec --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.11-Java-13.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'ant' +version = '1.10.11' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" + +toolchain = SYSTEM + +source_urls = ['https://archive.apache.org/dist/ant/binaries/'] +sources = ['apache-%(name)s-%(version)s-bin.tar.gz'] +checksums = ['0a3dc4624c863657daa609051763f12bfd286bc6da1d61ca48959ce3b94be0e7'] + +dependencies = [('Java', '13')] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' From acba4c74b3a01a6e1a404e26e1021d64847ccdbc Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 3 Sep 2021 11:38:03 +0100 Subject: [PATCH 1160/9987] adding easyconfigs: GTK2-2.24.33-GCCcore-10.3.0.eb, GTK3-3.24.29-GCCcore-10.3.0.eb --- .../g/GTK2/GTK2-2.24.33-GCCcore-10.3.0.eb | 35 +++++++++ .../g/GTK3/GTK3-3.24.29-GCCcore-10.3.0.eb | 76 +++++++++++++++++++ 2 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.29-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..7fbe95339ed --- /dev/null +++ b/easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GTK2' +version = '2.24.33' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/gtk+/%(version_major_minor)s'] +sources = ['gtk+-%(version)s.tar.xz'] +checksums = ['ac2ac757f5942d318a311a54b0c80b5ef295f299c2a73c632f6bfb1ff49cc6da'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.68.0'), +] +dependencies = [ + ('ATK', '2.36.0'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.5'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.29-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.29-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..646bff77c6a --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.29-GCCcore-10.3.0.eb @@ -0,0 +1,76 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.29' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('cairo', '1.16.0'), + ('Perl', '5.32.1'), +] + +dependencies = [ + ('ATK', '2.36.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.5'), + ('libepoxy', '1.5.8'), + ('X11', '20210518'), + ('FriBidi', '1.0.10'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['f57ec4ade8f15cab0c23a80dcaee85b876e70a8823d9105f067ce335a8268caa'], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '3.38.0', { + 'preconfigopts': 'autoreconf -f -i && ', + 'source_urls': [FTPGNOME_SOURCE], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' From db7415e6e7d9fd2a42e2c2139c14d6bb559e0326 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 3 Sep 2021 12:21:17 +0100 Subject: [PATCH 1161/9987] Add adwaita patch --- ...con-theme-3.34.3_disable-svg-conversion.patch | 16 ++++++++++++++++ ...con-theme-3.34.3_disable-svg-conversion.patch | 16 ++++++++++++++++ 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK2/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch create mode 100644 easybuild/easyconfigs/g/GTK3/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch diff --git a/easybuild/easyconfigs/g/GTK2/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch b/easybuild/easyconfigs/g/GTK2/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch new file mode 100644 index 00000000000..bf0b97f9489 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK2/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch @@ -0,0 +1,16 @@ +As we don't have SVG support we disable the search for the converter. + +Author: Alexander Grund (TU Dresden) + +diff -aur a/configure.ac b/configure.ac +--- a/configure.ac 2021-07-16 15:16:15.774630738 +0200 ++++ b/configure.ac 2021-07-16 15:15:10.138814059 +0200 +@@ -49,7 +49,7 @@ + AM_CONDITIONAL(ALLOW_RENDERING, test "x$allow_rendering" = "xyes") + + symbolic_encode_sizes="16x16 24x24 32x32 48x48 64x64 96x96" +-AC_PATH_PROG([GTK_ENCODE_SYMBOLIC_SVG], [gtk-encode-symbolic-svg], [false]) ++GTK_ENCODE_SYMBOLIC_SVG="false" + if test "x$GTK_ENCODE_SYMBOLIC_SVG" = "xfalse"; then + symbolic_encode_sizes="" + fi diff --git a/easybuild/easyconfigs/g/GTK3/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch b/easybuild/easyconfigs/g/GTK3/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch new file mode 100644 index 00000000000..bf0b97f9489 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch @@ -0,0 +1,16 @@ +As we don't have SVG support we disable the search for the converter. + +Author: Alexander Grund (TU Dresden) + +diff -aur a/configure.ac b/configure.ac +--- a/configure.ac 2021-07-16 15:16:15.774630738 +0200 ++++ b/configure.ac 2021-07-16 15:15:10.138814059 +0200 +@@ -49,7 +49,7 @@ + AM_CONDITIONAL(ALLOW_RENDERING, test "x$allow_rendering" = "xyes") + + symbolic_encode_sizes="16x16 24x24 32x32 48x48 64x64 96x96" +-AC_PATH_PROG([GTK_ENCODE_SYMBOLIC_SVG], [gtk-encode-symbolic-svg], [false]) ++GTK_ENCODE_SYMBOLIC_SVG="false" + if test "x$GTK_ENCODE_SYMBOLIC_SVG" = "xfalse"; then + symbolic_encode_sizes="" + fi From 3322a3f105d70237e607be85e23839b8373cd808 Mon Sep 17 00:00:00 2001 From: Loris Bennett Date: Fri, 3 Sep 2021 14:11:16 +0200 Subject: [PATCH 1162/9987] {vis}[GCCcore-10.2.0] GtkSourceView v3.24.11 --- .../GtkSourceView-3.24.11-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0319076daf4 --- /dev/null +++ b/easybuild/easyconfigs/g/GtkSourceView/GtkSourceView-3.24.11-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GtkSourceView' +version = '3.24.11' + +homepage = 'https://wiki.gnome.org/Projects/GtkSourceView' +description = """ + GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ + widget for multiline text editing. GtkSourceView adds support for syntax + highlighting, undo/redo, file loading and saving, search and replace, a + completion system, printing, displaying line numbers, and other features + typical of a source code editor. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['691b074a37b2a307f7f48edc5b8c7afa7301709be56378ccf9cc9735909077fd'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.66.1'), +] + +dependencies = [ + ('GLib', '2.66.1'), + ('GTK+', '3.24.23'), + ('libxml2', '2.9.10'), +] + +configopts = "--disable-silent-rules --enable-introspection=yes " + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['include/%(namelower)s-%(version_major)s.0', 'share'], +} + +moduleclass = 'vis' From 2bdc203bc01c776d9bde8e62d9b10492b1b78ff5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 14:26:24 +0200 Subject: [PATCH 1163/9987] strip out custom sanity check paths from VTune 2021.6.0 easyconfig --- easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb index fa93be8f89a..9b6582a6610 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2021.6.0.eb @@ -17,11 +17,4 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/1801 sources = ['l_oneapi_vtune_p_%(version)s.411_offline.sh'] checksums = ['6b1df7da713337aa665bcc6ff23e4a006695b5bfaf71dffd305cbadca2e5560c'] -sanity_check_paths = { - 'files': ['%(namelower)s/%(version)s/bin64/amplxe-perf'], - 'dirs': ['%(namelower)s/%(version)s/bin64', - '%(namelower)s/%(version)s/lib64', - '%(namelower)s/%(version)s/include/intel64'] -} - moduleclass = 'tools' From 3d1059509ae1605b309f5320d14d36b7401c1a18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 14:38:42 +0200 Subject: [PATCH 1164/9987] remove SHA256 checksum for IMOD 4.11.5 source tarball + fix installation on top of Python 3 --- .../i/IMOD/IMOD-4.11.5-foss-2020b.eb | 19 +++++++++++----- .../i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 18 ++++++++++----- .../IMOD/IMOD-4.11.5_fix-csvtohtml-py3.patch | 22 +++++++++++++++++++ 3 files changed, 48 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/i/IMOD/IMOD-4.11.5_fix-csvtohtml-py3.patch diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index 1758cf4d8a7..0a9e8fa0357 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -16,17 +16,20 @@ Kremer, Quanren Xiong, and John Heumann at the University of Colorado.""" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'openmp': True} -sources = [SOURCE_TAR_GZ] -checksums = ['5c50f1457134fe5113b95e0939d3181b948d211f25d9a05ad2b4ec0f23251c79'] - -# mercurial repository +# download manually from mercurial repository and create source tarball: # hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD # get lunch # cd IMOD # hg update -r IMOD_4-11-5 # cd .. # tar czf IMOD-4.11.5.tar.gz IMOD - +sources = [SOURCE_TAR_GZ] +patches = ['IMOD-%(version)s_fix-csvtohtml-py3.patch'] +checksums = [ + # can't include a valid checksum for source tarball, since it has to be created manually + None, # IMOD-4.11.5.tar.gz + '8ba0c3cbe30d755ab3fb918688982e818795b9f7f41218bd6bf231c85bea4971', # IMOD-4.11.5_fix-csvtohtml-py3.patch +] dependencies = [ ('LibTIFF', '4.1.0'), @@ -61,7 +64,11 @@ configure_cmd += ' #' # avoid passing unknown arg --prefix prebuildopts = local_exports # create some missing directories required for installation process: -preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&' +preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p && ' + +# patch hardcoded /usr/bin/python to use Python included as dependency +preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && " +preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && " modextravars = { 'IMOD_DIR': "%(installdir)s", diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index 803e0308fe5..733bdf9aa9f 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -18,17 +18,21 @@ toolchainopts = {'pic': True, 'openmp': True} # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] -sources = [SOURCE_TAR_GZ] -checksums = ['5c50f1457134fe5113b95e0939d3181b948d211f25d9a05ad2b4ec0f23251c79'] - -# mercurial repository +# download manually from mercurial repository and create source tarball: # hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD # get lunch # cd IMOD # hg update -r IMOD_4-11-5 # cd .. # tar czf IMOD-4.11.5.tar.gz IMOD - +sources = [SOURCE_TAR_GZ] +# can't include a valid checksum, since tarball has to be created manually +patches = ['IMOD-%(version)s_fix-csvtohtml-py3.patch'] +checksums = [ + # can't include a valid checksum for source tarball, since it has to be created manually + None, # IMOD-4.11.5.tar.gz + '8ba0c3cbe30d755ab3fb918688982e818795b9f7f41218bd6bf231c85bea4971', # IMOD-4.11.5_fix-csvtohtml-py3.patch +] dependencies = [ ('LibTIFF', '4.1.0'), @@ -75,6 +79,10 @@ prebuildopts = local_exports # create some missing directories required for installation process: preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&' +# patch hardcoded /usr/bin/python to use Python included as dependency +preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && " +preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && " + modextravars = { 'IMOD_DIR': "%(installdir)s", 'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug', diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5_fix-csvtohtml-py3.patch b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5_fix-csvtohtml-py3.patch new file mode 100644 index 00000000000..868084826ef --- /dev/null +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5_fix-csvtohtml-py3.patch @@ -0,0 +1,22 @@ +fix csvtohtml for use with Python 3 +author: Kenneth Hoste (HPC-UGent) +--- IMOD/manpages/csvtohtml.orig 2021-09-03 13:27:28.865210827 +0200 ++++ IMOD/manpages/csvtohtml 2021-09-03 13:27:34.320159119 +0200 +@@ -15,7 +15,7 @@ + return last + + import csv, sys +-sys.path.append('../pysrc') ++sys.path.insert(0, '../pysrc') + from imodpy import * + + insertTag = 'INSERT CSV FILE' +@@ -80,7 +80,7 @@ + inrows.append(row) + maxlen = min(maxUse, max(maxlen, len(row))) + +-print maxlen ++print(maxlen) + + for row in inrows: + lastNonEmpty = lastNonEmptyIndex(row) From 3397a25bdc80312271353e490171f59827f3b7ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 15:23:43 +0200 Subject: [PATCH 1165/9987] consistently apply fix-docs patch for LAMMPS 3Mar2020 --- .../LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb | 2 ++ .../LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb | 6 +++++- .../LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb | 6 +++++- 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb index b0941e89897..5649a33478f 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb @@ -25,9 +25,11 @@ sources = [ 'stable_%(version)s.tar.gz', {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] +patches = ['LAMMPS-3Mar2020_fix-docs-build.patch'] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py + '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch ] local_source_dir_name = '%(namelower)s-%(version)s' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb index 9cc825d8371..64fb76ca4d1 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb @@ -26,10 +26,14 @@ sources = [ {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] # see https://github.com/lammps/lammps/pull/1483 for why this is needed -patches = ['lammps-stable_3Mar2020_hack_openmp_gcc9.patch'] +patches = [ + 'LAMMPS-3Mar2020_fix-docs-build.patch', + 'lammps-stable_3Mar2020_hack_openmp_gcc9.patch', +] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py + '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch '41a0bcb828be22d38bb489bbd4b1fd7803d7771a2308371f01e961c52b8c869f', # lammps-stable_3Mar2020_hack_openmp_gcc9.patch ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index 41af48624a3..722f37b89e8 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -25,10 +25,14 @@ sources = [ 'stable_%(version)s.tar.gz', {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] -patches = ['lammps-stable_3Mar2020_intel_ebflag.patch'] +patches = [ + 'LAMMPS-3Mar2020_fix-docs-build.patch', + 'lammps-stable_3Mar2020_intel_ebflag.patch', +] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py + '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch '3b04681bf8d5c60818a197905f68c83e477ef41824278ebc05d437ecac6d5c0a', # lammps-stable_3Mar2020_intel_ebflag.patch ] From d677f5e14d7b741321a82633ebe49e83ae2993eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 15:27:20 +0200 Subject: [PATCH 1166/9987] set parallel = 1 for IMOD 4.11.5 to avoid failing parallel build --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb | 3 +++ easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index 0a9e8fa0357..650693addb9 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -39,6 +39,9 @@ dependencies = [ ('Python', '3.8.6'), ] +# parallel build sometimes fails +parallel = 1 + # modify all qmake pro files in order to pass CFLAGS local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&" diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index 733bdf9aa9f..33a8617ba3e 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -42,6 +42,9 @@ dependencies = [ ('Python', '3.8.6'), ] +# parallel build sometimes fails +parallel = 1 + # replace hardcoded CUDA compute capabilitites in machines/rhlinux. local_cuda_replace = 'echo %(cuda_cc_space_sep)s|sed "s/\\.//g"|' local_cuda_replace += ' awk \'{' From ee4bec2a3b89ea9cc585f4ccda3402dafde7b310 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 3 Sep 2021 14:41:58 +0100 Subject: [PATCH 1167/9987] Split GTK+ into GTK2 and GTK3 for GCC 10.3.0 toolchain --- .../g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb | 2 +- .../GST-plugins-base-1.18.4-GCC-10.3.0.eb | 2 +- .../GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb | 2 +- .../g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb | 35 --------- .../g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb | 76 ------------------- .../w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb | 4 +- 6 files changed, 5 insertions(+), 116 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb delete mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb index 6948840be8f..4cbc9293217 100644 --- a/easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/GIMP/GIMP-2.10.24-GCC-10.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ] dependencies = [ - ('GTK+', '2.24.33'), + ('GTK2', '2.24.33'), ('Gdk-Pixbuf', '2.42.6'), ('babl', '0.1.86'), ('GEGL', '0.4.30'), diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb index e6f5b7d514d..04579014adc 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.4-GCC-10.3.0.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('GLib', '2.68.2'), - ('GTK+', '3.24.29'), + ('GTK3', '3.24.29'), ('GStreamer', '1.18.4'), ('Gdk-Pixbuf', '2.42.6'), ('X11', '20210518'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb index f782b1ed825..2c38b4b9151 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('GMP', '6.2.1'), ('GSL', '2.7'), ('GLib', '2.68.2'), - ('GTK+', '3.24.29'), + ('GTK3', '3.24.29'), ('libunwind', '1.4.0'), ] diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb deleted file mode 100644 index acb18837be2..00000000000 --- a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GTK+' -version = '2.24.33' - -homepage = 'https://developer.gnome.org/gtk+/stable/' -description = """ - The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. -""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['ac2ac757f5942d318a311a54b0c80b5ef295f299c2a73c632f6bfb1ff49cc6da'] - -builddependencies = [ - ('binutils', '2.36.1'), - ('pkg-config', '0.29.2'), - ('GObject-Introspection', '1.68.0'), -] -dependencies = [ - ('ATK', '2.36.0'), - ('Gdk-Pixbuf', '2.42.6'), - ('Pango', '1.48.5'), -] - -configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " - -sanity_check_paths = { - 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], - 'dirs': ['include/gtk-2.0'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb deleted file mode 100644 index bf8d243b92b..00000000000 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.29-GCCcore-10.3.0.eb +++ /dev/null @@ -1,76 +0,0 @@ -easyblock = 'Bundle' - -name = 'GTK+' -version = '3.24.29' - -homepage = 'https://developer.gnome.org/gtk3/stable/' -description = """GTK+ is the primary library used to construct user interfaces in GNOME. It - provides all the user interface controls, or widgets, used in a common - graphical application. Its object-oriented API allows you to construct - user interfaces without dealing with the low-level details of drawing and - device interaction. -""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -builddependencies = [ - ('binutils', '2.36.1'), - ('Autotools', '20210128'), - ('GObject-Introspection', '1.68.0'), - ('gettext', '0.21'), - ('pkg-config', '0.29.2'), - ('cairo', '1.16.0'), - ('Perl', '5.32.1'), -] - -dependencies = [ - ('ATK', '2.36.0'), - ('at-spi2-atk', '2.38.0'), - ('Gdk-Pixbuf', '2.42.6'), - ('Pango', '1.48.5'), - ('libepoxy', '1.5.8'), - ('X11', '20210518'), - ('FriBidi', '1.0.10'), -] - -default_easyblock = 'ConfigureMake' - -default_component_specs = { - 'sources': [SOURCELOWER_TAR_XZ], - 'start_dir': '%(namelower)s-%(version)s', -} - -components = [ - (name, version, { - 'source_urls': [FTPGNOME_SOURCE], - 'checksums': ['f57ec4ade8f15cab0c23a80dcaee85b876e70a8823d9105f067ce335a8268caa'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", - }), - ('hicolor-icon-theme', '0.17', { - 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], - 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], - }), - ('adwaita-icon-theme', '3.38.0', { - 'preconfigopts': 'autoreconf -f -i && ', - 'source_urls': [FTPGNOME_SOURCE], - 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], - 'checksums': [ - '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', - # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch - 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', - ], - }), -] - -postinstallcmds = ['gtk-update-icon-cache'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', - 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', - 'gtk-update-icon-cache']] + - ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], - 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + - ['share/icons/hicolor', 'share/icons/Adwaita'], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb index 4867d22fcd0..59a4e8adb94 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-10.3.0.eb @@ -32,7 +32,7 @@ dependencies = [ ('jbigkit', '2.1'), ('LibTIFF', '4.2.0'), ('expat', '2.2.9'), - ('GTK+', '3.24.29'), + ('GTK3', '3.24.29'), ('X11', '20210518'), ('Mesa', '21.1.1'), ('libGLU', '9.0.1'), @@ -49,7 +49,7 @@ preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext configopts = '--enable-intl --enable-ipv6 ' # Options required by wxPython configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' -# Note: the configure step might claim to find OpenGL headers in +# Note: the configure step might claim to find OpenGL headers in # /usr/include, but it will still use the ones from the Mesa dependency above configopts += '--with-opengl ' configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' From 2de49c49be01734dc42d30d0f06bea9fc832b2ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 15:58:36 +0200 Subject: [PATCH 1168/9987] also patch IMOD's makeqhp script to not use /usr/bin/python --- easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb | 1 + easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index 650693addb9..fa2d35b964b 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -72,6 +72,7 @@ preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/ # patch hardcoded /usr/bin/python to use Python included as dependency preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && " preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && " +preinstallopts += "xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' html/makeqhp && " modextravars = { 'IMOD_DIR': "%(installdir)s", diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index 33a8617ba3e..d2bc021cbb9 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -85,6 +85,7 @@ preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/ # patch hardcoded /usr/bin/python to use Python included as dependency preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && " preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && " +preinstallopts += "xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' html/makeqhp && " modextravars = { 'IMOD_DIR': "%(installdir)s", From d05c7ce450699d2ad2c7d44dbd55f5e5de56a9bc Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 3 Sep 2021 14:59:06 +0100 Subject: [PATCH 1169/9987] Restore GTK+-2.24.33-GCCcore-10.3.0.eb --- .../g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..acb18837be2 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-2.24.33-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GTK+' +version = '2.24.33' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac2ac757f5942d318a311a54b0c80b5ef295f299c2a73c632f6bfb1ff49cc6da'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.68.0'), +] +dependencies = [ + ('ATK', '2.36.0'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.5'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + +moduleclass = 'vis' From 2d43ccc2dd965e40d9e62791d53b85685631aa15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 16:57:33 +0200 Subject: [PATCH 1170/9987] fix source URL for Yasm 1.3.0 (+ add missing checksum) --- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb | 3 ++- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb | 3 ++- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb | 3 ++- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb | 3 ++- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb | 3 ++- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb | 3 ++- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb | 3 ++- easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb | 3 ++- 16 files changed, 24 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb index 30cc501ddab..4614e5786e6 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.2.0.eb @@ -21,7 +21,7 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = ['https://www.tortall.net/projects/yasm/releases/'] +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.3.0.eb index 0d99744bb65..c85937534cf 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-10.3.0.eb @@ -9,7 +9,7 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -source_urls = ['https://www.tortall.net/projects/yasm/releases/'] +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.2.0.eb index 4d56392bf0c..93a7e18fb8d 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.2.0.eb @@ -9,7 +9,7 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['https://www.tortall.net/projects/yasm/releases/'] +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb index 691d1170d58..c1e90953f6b 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-6.4.0.eb @@ -21,7 +21,7 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-7.3.0.eb index 99575db90a7..22884a4a48a 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-7.3.0.eb @@ -21,7 +21,7 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.2.0.eb index 55cf6f77509..81219e09cc8 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.2.0.eb @@ -21,7 +21,7 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.3.0.eb index e938b0a2513..9bbad659ca5 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-8.3.0.eb @@ -21,7 +21,7 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['https://www.tortall.net/projects/yasm/releases/'] +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb index c493ee1fb51..f0ce46c5d3f 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-9.3.0.eb @@ -21,7 +21,7 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -source_urls = ['https://www.tortall.net/projects/yasm/releases/'] +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb index 5d91905b00e..e0a28c20b97 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016a.eb @@ -20,8 +20,9 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'foss', 'version': '2016a'} +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] sanity_check_paths = { 'files': ['bin/yasm'], diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb index 2b3b53fc138..4816f7cd366 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2016b.eb @@ -20,8 +20,9 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'foss', 'version': '2016b'} +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] sanity_check_paths = { 'files': ['bin/yasm'], diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb index 884d55d98dc..0d093060e1e 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-foss-2017a.eb @@ -20,8 +20,9 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'foss', 'version': '2017a'} +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] sanity_check_paths = { 'files': ['bin/yasm'], diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb index 54da1bfc1c5..eda5dbeabe6 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2.11.5.eb @@ -20,8 +20,9 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'gimkl', 'version': '2.11.5'} +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] sanity_check_paths = { 'files': ['bin/yasm'], diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb index 190f07dd2b4..7affe0bbed3 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-gimkl-2017a.eb @@ -20,8 +20,9 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'gimkl', 'version': '2017a'} +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] sanity_check_paths = { 'files': ['bin/yasm'], diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb index 31172f8c406..661d942ffa1 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016a.eb @@ -20,8 +20,9 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'intel', 'version': '2016a'} +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] sanity_check_paths = { 'files': ['bin/yasm'], diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb index a838254d152..111e8ed6217 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb @@ -20,8 +20,9 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'intel', 'version': '2016b'} +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] sanity_check_paths = { 'files': ['bin/yasm'], diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb index 89a5a1ab38a..09623a27b7e 100644 --- a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2017a.eb @@ -20,8 +20,9 @@ description = """Yasm: Complete rewrite of the NASM assembler with BSD license"" toolchain = {'name': 'intel', 'version': '2017a'} +source_urls = ['https://github.com/yasm/yasm/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.tortall.net/projects/yasm/releases/'] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] sanity_check_paths = { 'files': ['bin/yasm'], From b47903b59251448c65a63d37641dd8afc89583b1 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 3 Sep 2021 17:42:43 +0200 Subject: [PATCH 1171/9987] adding easyconfigs: InChI-1.06-GCC-10.3.0.eb and patches: InChI-1.06.patch --- .../i/InChI/InChI-1.06-GCC-10.3.0.eb | 72 +++++++++++++++++++ .../easyconfigs/i/InChI/InChI-1.06.patch | 54 ++++++++++++++ 2 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/i/InChI/InChI-1.06.patch diff --git a/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb new file mode 100644 index 00000000000..347d03ced23 --- /dev/null +++ b/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb @@ -0,0 +1,72 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Notes:: based on Fedora RPM spec file https://src.fedoraproject.org/rpms/inchi/blob/rawhide/f/inchi.spec +## +easyblock = 'MakeCp' + +name = 'InChI' +version = '1.06' + +# NOTE not in the license list of EB +# software_license = 'IUPAC/InChI-Trust Licence' +software_license_urls = ['https://www.inchi-trust.org/download/%s/LICENCE.pdf' % version.replace('.', '')] +docurls = [ + 'https://www.inchi-trust.org/download/%s/INCHI-1-DOC.zip' % version.replace('.', ''), + 'https://www.inchi-trust.org/download/%s/readme.txt' % version.replace('.', ''), +] + +homepage = 'https://www.inchi-trust.org/' +description = """The IUPAC International Chemical Identifier (InChI TM) is a non-proprietary +identifier for chemical substances that can be used in printed and electronic +data sources thus enabling easier linking of diverse data compilations.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://www.inchi-trust.org/download/%s/' % version.replace('.', '')] +sources = ['INCHI-1-SRC.zip', 'INCHI-1-TEST.zip'] +patches = ['InChI-%(version)s.patch'] +checksums = [ + '4874e310c0f2f81b881e90dd0c534752e1b9421d7d92ccfb037710022c7e7efd', # INCHI-1-SRC.zip + '3c870ef97c8ebc86f64946db395582b87d79732000fa73d173f46c05ca19c1ff', # INCHI-1-TEST.zip + 'a614c5310188d1f0397c6a3469795f60c3162b1bac531ad1a485ec195ad28f5a', # InChI-1.06.patch +] + + +# dos2unix may be useful to "clean" some files +builddependencies = [ + ('make', '4.3'), +] + +build_cmd = 'cd INCHI_API/demos/inchi_main/gcc && ' +build_cmd += 'make -Wno-comment -Wno-parentheses -Wno-unused -Wno-unused-but-set-variable -j %(parallel)s && ' +build_cmd += 'cd - && cd INCHI_EXE/inchi-1/gcc && ' +build_cmd += 'make -Wno-comment -Wno-parentheses -Wno-unused -Wno-unused-but-set-variable' + + +files_to_copy = [ + (['INCHI_EXE/bin/Linux/inchi-1'], 'bin'), + (['INCHI_API/bin/Linux/libinchi.so*'], 'lib'), + (['INCHI_BASE/src/ichisize.h', 'INCHI_BASE/src/inchi_api.h', 'INCHI_BASE/src/ixa.h'], 'include'), + 'LICENCE.pdf', + 'readme.txt', +] + +# NOTE libinchi.so are not symlinks in the final build, but redundant copies! +# NOTE `keepsymlinks = True` does not look to do it, so use this trick +postinstallcmds = ["cd %(installdir)s/lib/ && rm -f libinchi.so.1 && " + "ln -s libinchi.so.1.* libinchi.so.1 && ln -s libinchi.so.1 libinchi.so"] + + +sanity_check_paths = { + 'files': ["bin/inchi-1", "LICENCE.pdf", "readme.txt"], + 'dirs': ['lib', 'include'] +} + +sanity_check_commands = ["inchi-1"] +# NOTE currently no real tests because they are complicated to run (not in a good format, zipped, ...) + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/i/InChI/InChI-1.06.patch b/easybuild/easyconfigs/i/InChI/InChI-1.06.patch new file mode 100644 index 00000000000..cbc0e67159a --- /dev/null +++ b/easybuild/easyconfigs/i/InChI/InChI-1.06.patch @@ -0,0 +1,54 @@ +diff -up INCHI-1-SRC/INCHI_API/demos/inchi_main/gcc/makefile.r INCHI-1-SRC/INCHI_API/demos/inchi_main/gcc/makefile +--- INCHI-1-SRC/INCHI_API/demos/inchi_main/gcc/makefile.r 2019-06-22 20:25:28.000000000 +0200 ++++ INCHI-1-SRC/INCHI_API/demos/inchi_main/gcc/makefile 2020-10-13 14:18:22.809829859 +0200 +@@ -30,7 +30,7 @@ INCHI_LIB_PATHNAME = $(LIB_DIR)/$(INCHI_ + # === Main program name ==== + ifndef API_CALLER_NAME + ifndef CALLER_IS_MOL2INCHI +- API_CALLER_NAME = inchi_main$ ++ API_CALLER_NAME = inchi_main + else + API_CALLER_NAME = mol2inchi$ + endif +@@ -43,9 +43,9 @@ endif + # === Linker to create Main program ===== + ifndef LINKER + ifdef ISLINUX +- LINKER_CWD_PATH = -Wl,-R,"" ++ LINKER_CWD_PATH = + endif +- LINKER = gcc -s $(LINKER_CWD_PATH) ++ LINKER = gcc $(LINKER_CWD_PATH) + endif + ifndef P_LIBR + P_LIBR = ../../../libinchi/src/ +@@ -70,7 +70,7 @@ endif + # === C Compiler Options ======= + ifndef C_OPTIONS + ifndef CALLER_IS_MOL2INCHI +- C_OPTIONS = -ansi -O3 -c ++ C_OPTIONS = -ansi $(OPTFLAGS) -c + else + C_OPTIONS = -O3 -c + endif +diff -up INCHI-1-SRC/INCHI_EXE/inchi-1/gcc/makefile.r INCHI-1-SRC/INCHI_EXE/inchi-1/gcc/makefile +--- INCHI-1-SRC/INCHI_EXE/inchi-1/gcc/makefile.r 2016-09-08 19:08:16.000000000 +0200 ++++ INCHI-1-SRC/INCHI_EXE/inchi-1/gcc/makefile 2020-10-13 14:18:22.809829859 +0200 +@@ -13,7 +13,7 @@ ifndef CPP_COMPILER + CPP_COMPILER = g++ + endif + ifndef LINKER +- LINKER = g++ -s ++ LINKER = gcc + endif + ifndef INCHI_EXECUTABLE_NAME + ifdef windir +@@ -36,7 +36,7 @@ ifndef P_BASE + endif + #P_INCL = -I$(P_MAIN) -I$(P_BASE) + P_INCL = -I$(P_MAIN) -I$(P_BASE) +-C_COMPILER_OPTIONS = $(P_INCL) -ansi -DCOMPILE_ANSI_ONLY -DTARGET_EXE_STANDALONE -O3 -c ++C_COMPILER_OPTIONS = $(P_INCL) -ansi -DCOMPILE_ANSI_ONLY -DTARGET_EXE_STANDALONE $(OPTFLAGS) -c + #C_COMPILER_OPTIONS = -c $(P_INCL) -ansi -O3 -fsigned-char -ffunction-sections -fexpensive-optimizations -fstack-check -fexceptions -Wall -pedantic -Wbad-function-cast -Wreturn-type -Wformat -Wuninitialized -Wcast-align -Wshadow -Wunused -Wunused-value -Wunused-variable -Wunused-function -Wunused-parameter -Wunused-label -Wcomment -Wcast-qual -Wconversion -Wimplicit-int -Wmissing-braces -Wmissing-declarations -Wmissing-prototypes -Wredundant-decls -Wsign-compare -Wfloat-equal -Wstrict-prototypes -Wwrite-strings -Wundef -Waggregate-return -Wchar-subscripts -Wformat-nonliteral -Wnested-externs -Wsequence-point -Wpointer-arith -mfancy-math-387 -mieee-fp -mno-soft-float + ifdef windir + # no -ansi option due to reported MinGw bug From 366057c66860bce95ad5ebf65f2943c1b65d212c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 17:48:18 +0200 Subject: [PATCH 1172/9987] add patch to remove broken test for libjxl 0.5 --- .../l/libjxl/libjxl-0.5-GCCcore-10.3.0.eb | 6 +- .../libjxl-0.5_remove-broken-test.patch | 64 +++++++++++++++++++ 2 files changed, 69 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.5_remove-broken-test.patch diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.3.0.eb index 710103c7ef0..2cd9083e979 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.3.0.eb @@ -19,11 +19,15 @@ sources = [ 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, ] -patches = ['libjxl-0.3.7_external_lcms2.patch'] +patches = [ + 'libjxl-0.3.7_external_lcms2.patch', + 'libjxl-%(version)s_remove-broken-test.patch', +] checksums = [ '911cb4b50eb621131ca22382166f40d4914a4ff4453dd299ade1e3292f311f89', # v0.5.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz '9e6decaf6be74eeccfd5728df175930b4be33de6cbdf9e1816f68cb4b718fa1b', # libjxl-0.3.7_external_lcms2.patch + '5b62751da5b3b3c4aad58a841d49cc506bc330425bbd0df7f19f99aa98c52c26', # libjxl-0.5_remove-broken-test.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.5_remove-broken-test.patch b/easybuild/easyconfigs/l/libjxl/libjxl-0.5_remove-broken-test.patch new file mode 100644 index 00000000000..7b751532edc --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.5_remove-broken-test.patch @@ -0,0 +1,64 @@ +remove broken test, see also https://github.com/libjxl/libjxl/issues/500 +author: Kenneth Hoste (HPC-UGent) +--- libjxl-0.5/lib/jxl/decode_test.cc.orig 2021-09-03 17:43:40.833113581 +0200 ++++ libjxl-0.5/lib/jxl/decode_test.cc 2021-09-03 17:43:51.029009242 +0200 +@@ -1701,59 +1701,6 @@ + JxlDecoderDestroy(dec); + } + +-TEST(DecodeTest, PixelTestWithICCProfileLossy) { +- JxlDecoder* dec = JxlDecoderCreate(NULL); +- +- size_t xsize = 123, ysize = 77; +- size_t num_pixels = xsize * ysize; +- std::vector pixels = jxl::test::GetSomeTestImage(xsize, ysize, 3, 0); +- JxlPixelFormat format_orig = {3, JXL_TYPE_UINT16, JXL_BIG_ENDIAN, 0}; +- jxl::CompressParams cparams; +- jxl::PaddedBytes compressed = jxl::CreateTestJXLCodestream( +- jxl::Span(pixels.data(), pixels.size()), xsize, ysize, 3, +- cparams, kCSBF_None, JXL_ORIENT_IDENTITY, /*add_preview=*/false, +- /*add_icc_profile=*/true); +- uint32_t channels = 3; +- +- JxlPixelFormat format = {channels, JXL_TYPE_FLOAT, JXL_LITTLE_ENDIAN, 0}; +- +- std::vector pixels2 = jxl::DecodeWithAPI( +- dec, jxl::Span(compressed.data(), compressed.size()), +- format, /*use_callback=*/false, /*set_buffer_early=*/true, +- /*use_resizable_runner=*/false); +- JxlDecoderReset(dec); +- EXPECT_EQ(num_pixels * channels * 4, pixels2.size()); +- +- // The input pixels use the profile matching GetIccTestProfile, since we set +- // add_icc_profile for CreateTestJXLCodestream to true. +- jxl::ColorEncoding color_encoding0; +- EXPECT_TRUE(color_encoding0.SetICC(GetIccTestProfile())); +- jxl::Span span0(pixels.data(), pixels.size()); +- jxl::CodecInOut io0; +- io0.SetSize(xsize, ysize); +- EXPECT_TRUE(ConvertFromExternal( +- span0, xsize, ysize, color_encoding0, +- /*has_alpha=*/false, false, 16, format_orig.endianness, +- /*flipped_y=*/false, /*pool=*/nullptr, &io0.Main())); +- +- // The output pixels are expected to be in the same colorspace as the input +- // profile, as the profile can be represented by enum values. +- jxl::ColorEncoding color_encoding1 = color_encoding0; +- jxl::Span span1(pixels2.data(), pixels2.size()); +- jxl::CodecInOut io1; +- io1.SetSize(xsize, ysize); +- EXPECT_TRUE( +- ConvertFromExternal(span1, xsize, ysize, color_encoding1, +- /*has_alpha=*/false, false, 32, format.endianness, +- /*flipped_y=*/false, /*pool=*/nullptr, &io1.Main())); +- +- jxl::ButteraugliParams ba; +- EXPECT_LE(ButteraugliDistance(io0, io1, ba, /*distmap=*/nullptr, nullptr), +- 2.4f); +- +- JxlDecoderDestroy(dec); +-} +- + // Tests the case of lossy sRGB image without alpha channel, decoded to RGB8 + // and to RGBA8 + TEST(DecodeTest, PixelTestOpaqueSrgbLossy) { From e266cb81540d4c8fd56058d84e52ee57252c6e68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 19:57:36 +0200 Subject: [PATCH 1173/9987] adding easyconfigs: AutoGeneS-1.0.4-foss-2020b.eb --- .../a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb new file mode 100644 index 00000000000..d37a02530cf --- /dev/null +++ b/easybuild/easyconfigs/a/AutoGeneS/AutoGeneS-1.0.4-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'AutoGeneS' +version = '1.0.4' + +homepage = 'https://github.com/theislab/AutoGeneS' +description = """AutoGeneS automatically extracts informative genes and reveals the cellular heterogeneity +of bulk RNA samples.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('dill', '0.3.3'), + ('scikit-learn', '0.23.2'), + ('h5py', '3.1.0'), +] + +use_pip = True + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('anndata', '0.7.6', { + 'checksums': ['a3cc67bba9a4cd4b5984aec64c4f577c2d5a4695f4064027f8e6a9dac1f508b2'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('autogenes', version, { + 'checksums': ['8daa6e9aa97c7ddf45ab0906307a4875a25bd99301be0838bb17e313d837446a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From bbad3a71e783a9461bc00ddc6d5f20676115d680 Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Fri, 3 Sep 2021 22:55:07 +0200 Subject: [PATCH 1174/9987] adding easyconfigs: SLEPc-3.14.2-foss-2020b.eb --- .../s/SLEPc/SLEPc-3.14.2-foss-2020b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SLEPc/SLEPc-3.14.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.14.2-foss-2020b.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.14.2-foss-2020b.eb new file mode 100644 index 00000000000..87ff7d8c441 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.14.2-foss-2020b.eb @@ -0,0 +1,21 @@ +name = 'SLEPc' +version = '3.14.2' + +homepage = 'https://slepc.upv.es/' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://slepc.upv.es/download/distrib'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3e54578dda1f4c54d35ac27d02f70a43f6837906cb7604dbcec0e033cfb264c8'] + +dependencies = [('PETSc', '3.14.4')] + +petsc_arch = 'installed-arch-linux2-c-opt' + +moduleclass = 'numlib' From 7d0111504e7bc3377c00066c82b37852acc17906 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Sep 2021 14:36:08 +0100 Subject: [PATCH 1175/9987] adding easyconfigs: Yices-2.6.2-GCCcore-10.2.0.eb --- .../y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d6c493931c8 --- /dev/null +++ b/easybuild/easyconfigs/y/Yices/Yices-2.6.2-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Yices' +version = '2.6.2' + +homepage = "https://yices.csl.sri.com/index.html" +description = """Yices 2 is an SMT solver that decides the satisfiability of formulas containing uninterpreted + function symbols with equality, real and integer arithmetic, bitvectors, scalar types, and tuples. Yices 2 supports + both linear and nonlinear arithmetic.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://yices.csl.sri.com/releases/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +checksums = ['1f205c056dd430f830c688fba6c87d8bd07bd8fa05f65936e12c27e71fa3576a'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('GMP', '6.2.0'), + ('gperf', '3.1'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libyices.a', 'lib/libyices.%s' % SHLIB_EXT, 'include/yices.h'], + 'dirs': [], +} + +sanity_check_commands = ['%s --help' % x for x in ['yices', 'yices-sat', 'yices-smt', 'yices-smt2']] + +moduleclass = 'tools' From 9aa3509b8809f843414ea9a774f65cc61e0ff175 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Sep 2021 14:36:43 +0100 Subject: [PATCH 1176/9987] adding easyconfigs: BuDDy-2.4-GCCcore-10.2.0.eb --- .../b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..719cac72c8e --- /dev/null +++ b/easybuild/easyconfigs/b/BuDDy/BuDDy-2.4-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'BuDDy' +version = '2.4' + +homepage = "http://buddy.sourceforge.net/" +description = """A Binary Decision Diagram library, with many highly efficient vectorized BDD operations, dynamic + variable reordering, automated garbage collection, a C++ interface with automatic reference counting, and much + more.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d3df80a6a669d9ae408cb46012ff17bd33d855529d20f3a7e563d0d913358836'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), + ('libtool', '2.4.6'), +] + +sanity_check_paths = { + 'files': ['lib/libbdd.a', 'lib/libbdd.%s' % SHLIB_EXT, 'include/bdd.h'], + 'dirs': [], +} + +moduleclass = 'tools' From 97951da51b5eeb29d19a432f5237f50e2ecceaa6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Sep 2021 14:37:24 +0100 Subject: [PATCH 1177/9987] adding easyconfigs: libtecla-1.6.3-GCCcore-10.2.0.eb --- .../libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..383ab0e1814 --- /dev/null +++ b/easybuild/easyconfigs/l/libtecla/libtecla-1.6.3-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libtecla' +version = '1.6.3' + +homepage = "https://sites.astro.caltech.edu/~mcs/tecla/" +description = """The tecla library provides UNIX and LINUX programs with interactive command line editing facilities, + similar to those of the UNIX tcsh shell. In addition to simple command-line editing, it supports recall of previously + entered command lines, TAB completion of file names or other tokens, and in-line wild-card expansion of filenames. + The internal functions which perform file-name completion and wild-card expansion are also available externally for + optional use by programs. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://sites.astro.caltech.edu/~mcs/tecla/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2757cc55040859fcf8f59a0b7b26e0184a22bece44ed9568a4534a478c1ee1a'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('ncurses', '6.2'), +] + +configopts = '--with-man-pages=no' + +sanity_check_paths = { + 'files': ['bin/enhance', 'lib/libtecla.a', 'lib/libtecla.%s' % SHLIB_EXT, 'include/libtecla.h'], + 'dirs': [], +} + +moduleclass = 'tools' From 551e60b622a36b58588e2babb49ce103f55bfd4b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Sep 2021 14:45:40 +0100 Subject: [PATCH 1178/9987] adding easyconfigs: Maude-3.1-GCCcore-10.2.0.eb --- .../m/Maude/Maude-3.1-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..038cb68a583 --- /dev/null +++ b/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Maude' +version = '3.1' + +homepage = "https://maude.cs.illinois.edu/w/index.php/The_Maude_System" +description = """Maude is a high-performance reflective language and system supporting both equational and rewriting + logic specification and programming for a wide range of applications. Maude has been influenced in important ways by + the OBJ3 language, which can be regarded as an equational logic sublanguage. Besides supporting equational + specification and programming, Maude also supports rewriting logic computation. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://maude.cs.illinois.edu/w/images/d/d3/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b112d7843f65217e3b5a9d40461698ef8dab7cbbe830af21216dfb924dc88a2f'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('BuDDy', '2.4'), + ('GMP', '6.2.0'), + ('libsigsegv', '2.13'), + ('libtecla', '1.6.3'), + ('Yices', '2.6.2'), +] + +# Building in parallel sometimes errors +maxparallel = 1 + +runtest = 'check' + +modextravars = {'MAUDE_LIB': '%(installdir)s/share'} + +sanity_check_paths = { + 'files': ['share/%s.maude' % x for x in ['file', 'linear', 'prelude', 'smt']], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'tools' From e6edf2ee4af0cb270200e1dfc349b9baf73108ca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Sep 2021 16:04:55 +0200 Subject: [PATCH 1179/9987] update to Meson 0.59.1 build dependency for easyconfigs to fix failing RPATH sanity check (fixes #13880) --- .../a/ATK/ATK-2.34.1-GCCcore-8.3.0.eb | 2 +- .../at-spi2-atk-2.34.1-GCCcore-8.3.0.eb | 2 +- .../at-spi2-core-2.34.0-GCCcore-8.3.0.eb | 2 +- .../g/GLib/GLib-2.62.0-GCCcore-8.3.0.eb | 2 +- ...ction-1.63.1-GCCcore-8.3.0-Python-3.7.4.eb | 2 +- .../GST-plugins-base-1.16.2-GCC-8.3.0.eb | 2 +- .../Gdk-Pixbuf-2.38.2-GCCcore-8.3.0.eb | 2 +- .../l/LibSoup/LibSoup-2.70.0-GCCcore-8.3.0.eb | 2 +- .../libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb | 2 +- .../m/Mesa/Mesa-19.1.7-GCCcore-8.3.0.eb | 3 +- .../m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb | 2 +- ...Meson-0.59.1-GCCcore-8.3.0-Python-3.7.4.eb | 37 +++++++++++++++++++ .../p/Pango/Pango-1.44.7-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/x/xtb/xtb-6.2.3-foss-2019b.eb | 2 +- 14 files changed, 51 insertions(+), 13 deletions(-) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.59.1-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.34.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.34.1-GCCcore-8.3.0.eb index 4801dcf23aa..2f0967f68b4 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.34.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.34.1-GCCcore-8.3.0.eb @@ -18,7 +18,7 @@ checksums = ['d4f0e3b3d21265fcf2bc371e117da51c42ede1a71f6db1c834e6976bb20997cb'] builddependencies = [ ('binutils', '2.32'), - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('pkg-config', '0.29.2'), ('GObject-Introspection', '1.63.1', '-Python-3.7.4'), diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.34.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.34.1-GCCcore-8.3.0.eb index a31842d7f5d..af03cbf2fe6 100644 --- a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.34.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.34.1-GCCcore-8.3.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('binutils', '2.32'), - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.34.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.34.0-GCCcore-8.3.0.eb index 6e6e47d96df..a52b0aa0eda 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.34.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.34.0-GCCcore-8.3.0.eb @@ -16,7 +16,7 @@ checksums = ['d629cdbd674e539f8912028512af583990938c7b49e25184c126b00121ef11c6'] builddependencies = [ ('binutils', '2.32'), - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('GObject-Introspection', '1.63.1', '-Python-3.7.4'), ('gettext', '0.20.1'), diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.62.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.62.0-GCCcore-8.3.0.eb index bce91181c63..d75c72c3c0d 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.62.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.62.0-GCCcore-8.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ # (build)dependency on Python or it will use the system version # EasyBuild itself uses. ('Python', '3.7.4'), - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('binutils', '2.32'), ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.63.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.63.1-GCCcore-8.3.0-Python-3.7.4.eb index 7935cf54c15..afc3ea274bb 100644 --- a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.63.1-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.63.1-GCCcore-8.3.0-Python-3.7.4.eb @@ -20,7 +20,7 @@ checksums = ['476379bde8d080d92dd1bb1684f6aa8d79d90ddb81fc85dfa3576e36f9777ab6'] builddependencies = [ ('binutils', '2.32'), ('pkg-config', '0.29.2'), - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('flex', '2.6.4'), ('Bison', '3.3.2'), diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb index 3954ca17648..504355c6118 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.16.2-GCC-8.3.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['b13e73e2fe74a4166552f9577c3dcb24bed077021b9c7fa600d910ec6987816a'] builddependencies = [ - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('GObject-Introspection', '1.63.1', '-Python-3.7.4'), ('gettext', '0.20.1'), diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.2-GCCcore-8.3.0.eb index de84656767c..c5c7b931108 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.38.2-GCCcore-8.3.0.eb @@ -22,7 +22,7 @@ checksums = [ ] builddependencies = [ - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('binutils', '2.32'), ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-2.70.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.70.0-GCCcore-8.3.0.eb index 3f85cfec974..00e1326a7f7 100644 --- a/easybuild/easyconfigs/l/LibSoup/LibSoup-2.70.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.70.0-GCCcore-8.3.0.eb @@ -18,7 +18,7 @@ checksums = ['54b020f74aefa438918d8e53cff62e2b1e59efe2de53e06b19a4b07b1f4d5342'] builddependencies = [ ('binutils', '2.32'), - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('pkg-config', '0.29.2'), ('GObject-Introspection', '1.63.1', '-Python-3.7.4'), diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb index 012b599c942..b886697deca 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-8.3.0.eb @@ -15,7 +15,7 @@ checksums = ['c926fcc606901f3e03e371027056fd478da43e01ce2da7ffc48b5a0de0ca107c'] builddependencies = [ ('binutils', '2.32'), - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.1.7-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.1.7-GCCcore-8.3.0.eb index 696489871d8..1b116a43622 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.1.7-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.1.7-GCCcore-8.3.0.eb @@ -31,7 +31,7 @@ checksums = ['e287920fdb38712a9fed448dc90b3ca95048c7face5db52e58361f8b6e0f3cd5'] builddependencies = [ ('binutils', '2.32'), - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('flex', '2.6.4'), ('Bison', '3.3.2'), @@ -49,6 +49,7 @@ dependencies = [ ('LLVM', '9.0.0'), ('X11', '20190717'), ('libunwind', '1.3.1'), + ('ncurses', '6.1'), ] configopts = " -Dplatforms=x11 -Dosmesa=gallium -Ddri3=false -Ddri-drivers='' -Dvulkan-drivers=''" diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb index 5679d2d2e9a..4038caecb18 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb @@ -37,7 +37,7 @@ checksums = [ builddependencies = [ ('binutils', '2.32'), - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('flex', '2.6.4'), ('Bison', '3.3.2'), diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.59.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/m/Meson/Meson-0.59.1-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..7d04de0f798 --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.59.1-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.59.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['db586a451650d46bbe10984a87b79d9bcdc1caebf38d8e189f8848f8d502356d'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('Python', '3.7.4'), + ('Ninja', '1.9.0'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["meson --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.44.7-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.44.7-GCCcore-8.3.0.eb index b95a6c58317..9577b502030 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.44.7-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.44.7-GCCcore-8.3.0.eb @@ -16,7 +16,7 @@ checksums = ['66a5b6cc13db73efed67b8e933584509f8ddb7b10a8a40c3850ca4a985ea1b1f'] builddependencies = [ ('binutils', '2.32'), - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ('GObject-Introspection', '1.63.1', '-Python-3.7.4'), ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.2.3-foss-2019b.eb b/easybuild/easyconfigs/x/xtb/xtb-6.2.3-foss-2019b.eb index 01d4d8a2773..978dc4fd344 100644 --- a/easybuild/easyconfigs/x/xtb/xtb-6.2.3-foss-2019b.eb +++ b/easybuild/easyconfigs/x/xtb/xtb-6.2.3-foss-2019b.eb @@ -14,7 +14,7 @@ checksums = ['620dfb93aa07fd5144d25134613a5d7f4c1fa4fb5070c30768a6335c8c0b4187'] github_account = 'grimme-lab' builddependencies = [ - ('Meson', '0.51.2', '-Python-3.7.4'), + ('Meson', '0.59.1', '-Python-3.7.4'), ('Ninja', '1.9.0'), ] From 59c6e1f4f7b2784ef16e8c23614133cb9c8b5de3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Sep 2021 16:33:33 +0200 Subject: [PATCH 1180/9987] enable sanity_pip_check in easyconfig for Meson 0.59.1 --- .../m/Meson/Meson-0.59.1-GCCcore-8.3.0-Python-3.7.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.59.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/m/Meson/Meson-0.59.1-GCCcore-8.3.0-Python-3.7.4.eb index 7d04de0f798..2f076795e67 100644 --- a/easybuild/easyconfigs/m/Meson/Meson-0.59.1-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/Meson/Meson-0.59.1-GCCcore-8.3.0-Python-3.7.4.eb @@ -34,4 +34,6 @@ sanity_check_paths = { sanity_check_commands = ["meson --help"] +sanity_pip_check = True + moduleclass = 'tools' From a90bdd4a1c0a12a835a191bf75f87adb31dc88f4 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 4 Sep 2021 15:53:11 +0100 Subject: [PATCH 1181/9987] Update easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb index 038cb68a583..f9de690f36e 100644 --- a/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Maude/Maude-3.1-GCCcore-10.2.0.eb @@ -37,7 +37,7 @@ runtest = 'check' modextravars = {'MAUDE_LIB': '%(installdir)s/share'} sanity_check_paths = { - 'files': ['share/%s.maude' % x for x in ['file', 'linear', 'prelude', 'smt']], + 'files': ['bin/maude'] + ['share/%s.maude' % x for x in ['file', 'linear', 'prelude', 'smt']], 'dirs': [], } From f1c5f8bd0239d5dc713040252b4ed35fa3a3a178 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 Sep 2021 10:08:36 +0200 Subject: [PATCH 1182/9987] fix shebang for RepeatMasker 4.1.2-p1 Perl script --- .../r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb index 726cafbe039..9d3c0d87244 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb @@ -39,7 +39,8 @@ local_default_search_engine = 'RMBlast' preinstall_cmd = './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' preinstall_cmd += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' preinstall_cmd += '-default_search_engine %s' % local_default_search_engine.lower() -# preinstall_cmd += '-libdir="RepeatMasker/Libraries" + +fix_perl_shebang_for = ['RepeatMasker'] sanity_check_paths = { 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], From dcf3bc63394d1311ecef7afcd0c331058ea9bd6f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 6 Sep 2021 12:15:57 +0800 Subject: [PATCH 1183/9987] prepare release notes for EasyBuild v4.4.2 + bump version to 4.4.2 --- RELEASE_NOTES | 109 ++++++++++++++++++++++++++++++++++++++++++++++++++ setup.py | 2 +- 2 files changed, 110 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 7dfcc97840b..4593ba5d1f4 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -7,6 +7,115 @@ The latest version of easybuild-easyconfig provides 12,607 easyconfig files, for incl. 36 different (compiler) toolchains. +v4.4.2 (September 7th 2021) +--------------------------- + +update/bugfix release + +- added example easyconfig files for 82 new software packages: + - AlphaFold (#13867), andi (#13768), aria2 (#13709), AUTO-07p (#13831), babl (#13216), BAli-Phy (#13484), biogeme (#13735), Bio-SearchIO-hmmer (#13419), BuDDy (#13907), c-ares (#13709), CellRank (#13408), Coin (#13818), Co-phylog (#13769), cppy (#13823), CREST (#13648), CRISPR-DAV (#13139), CSBLAST (#13794), DGL (#13793), DistributedStream (#13659), Excel-Writer-XLSX (#13139), FBPIC (#13500), freebayes (#12859), freud-analysis (#13354), fumi_tools (#13517), GEGL (#13216), GIMP (#13216), glib-networking (#13216), GOATOOLS (#13629), gofasta (#13651), GTK2 (#13900), GTK3 (#13900), Highway (#13453), hipSYCL (#13837), ISA-L (#13663), jax (#13760), JSON-GLib (#13216), Kalign (#13463), LADR (#13351), lDDT (#13794), libdivsufsort (#13768), libjxl (#13829), libmypaint (#13216), libtecla (#13908), lie_learn (#13793), longestrunsubsequence (#13800), Maude (#13909), mimalloc (#13726), MINPACK (#13802), Mish-Cuda (#13784), muparserx (#13779), nlohmann_json (#13777), OpenStackClient (#13644), OSPRay (#12852), pandapower (#13687), pangolin (#13848), PSIPRED (#13794), PYPOWER (#13689), PyPSA (#13673), PyRosetta (#13793), pysamstats (#13139), pytest-benchmark (#13622), python-isal (#13663), QCxMS (#13650), RepeatModeler (#13126), Schrodinger (#11698), sklearn-som (#13699), Snippy (#12893), SoQt (#13818), spdlog (#13778), SpectrA (#13743), SymEngine-python (#13652), SyRI (#13800), torchinfo (#13662), TRAVIS-Analyzer (#13503), TWL-NINJA (#13529), UShER (#13708), Vampire (#13352), VBZ-Compression (#13536), VisPy (#13468), wgsim (#13475), xTB (#13649), Yices (#13906) +- added additional easyconfigs for various supported software packages, including: + - ABAQUS 2020.eb, ABINIT 9.4.2, ABRA2 2.23, ack 3.5.0, AdapterRemoval 2.3.2, Advisor 2021.2.0.eb, almosthere 2.0.2, AlphaFold 2.0.0, AlphaFold 2.0.0, Anaconda3 2021.05.eb, andi 0.13, ant 1.10.11, ant 1.10.11, ANTLR 2.7.7, ANTs 2.3.5, any2fasta 0.4.2, AOCC 3.1.0, AOCC 3.1.0, APR 1.7.0, APR util, Arb 2.19.0, Archive Zip, Archive Zip, archspec 0.1.2, archspec 0.1.2, argtable 2.13, aria2 1.35.0, Armadillo 10.5.3, arpack ng, Arriba 2.1.0, ASE 3.22.0, ATK 2.36.0, at spi2, at spi2, at spi2, at spi2, AUTO 07p, Autoconf 2.71, Automake 1.16.4, Autotools 20210726, babl 0.1.86, BAli Phy, BamTools 2.5.2, barrnap 0.9, Bazel 0.29.1, Bazel 2.0.0, Bazel 3.7.2, BCFtools 1.12, bcl2fastq2 2.20.0, BEDTools 2.30.0, bgen 4.1.3, binutils 2.37, binutils 2.37.eb, bioawk 1.0, biogeme 3.1.2, biogeme 3.2.8, Biopython 1.79, Bio SearchIO, Bison 3.7.6, bitarray 1.5.3, BLIS 3.0.1, BLIS 3.0.1, Blosc 1.21.0, Boost 1.76.0, Boost 1.76.0, Bowtie2 2.4.4, bpytop 1.0.67, Brotli 1.0.9, BuDDy 2.4, bx python, bzip2 1.0.8, cairo 1.16.0, c ares, Cartopy 0.19.0.post1, Cartopy 0.19.0.post1, Cbc 2.10.5, CDO 1.9.10, CellRank 1.4.0, Centrifuge 1.0.4, CGAL 4.14.3, Cgl 0.60.3, CharLS 2.2.0, Clang 12.0.1, Clp 1.17.6, Clustal Omega, Clustal Omega, ClustalW2 2.1, CMake 3.21.1, Coin 4.0.0, CoinUtils 2.11.4, configurable http, Control FREEC, Co phylog, coverage 5.5, CP2K 5.1, CP2K 7.1, CppUnit 1.15.1, cppy 1.1.0, CREST 2.11, CRISPR DAV, CRISPResso2 2.1.2, CRISPResso2 2.2.1, CSBLAST 2.2.3, ctffind 4.1.14, CubeGUI 4.6, CubeLib 4.6, CubeWriter 4.6, CUDA 11.3.1.eb, CUDA 11.4.1.eb, cuDNN 8.2.2.26, cURL 7.78.0, cutadapt 3.4, CVXOPT 1.2.6, DB 18.1.40, DBus 1.13.18, DFT D3, DFT D3, DGL 0.6.1, DIAMOND 2.0.11, DistributedStream 1.0, double conversion, Doxygen 1.9.1, DROP 1.1.0, Dsuite 20210718, Dsuite 20210718, dtcmp 1.1.2, EasyBuild 4.4.1.eb, ecCodes 2.22.1, Eigen 3.3.9, elfutils 0.185, Elk 7.2.42, ESMF 8.1.1, ESMF 8.1.1, Excel Writer, expat 2.4.1, fastahack 1.0.0, fastq tools, FASTX Toolkit, FBPIC 0.20.3, fermi lite, FFmpeg 4.3.2, FFTW 3.3.9, file 5.40, filevercmp 20191210, Fiona 1.8.20, Fiona 1.8.20, FLAC 1.3.3, FLASH 2.2.00, Flask 1.1.4, flex 2.6.4, FlexiBLAS 3.0.4, FLINT 2.7.1, FLTK 1.3.7, fontconfig 2.13.94, foss 2021.07.eb, freebayes 1.3.5, freebayes 1.3.5, FreeImage 3.18.0, freetype 2.11.0, freud analysis, FriBidi 1.0.10, fsom 20141119, fumi_tools 0.18.2, fumi_tools 0.18.2, g2clib 1.6.3, g2lib 3.2.0, GCC 11.2.0.eb, GCCcore 11.2.0.eb, GDCM 3.0.8, GDCM 3.0.8, Gdk Pixbuf, GDRCopy 2.3, GEGL 0.4.30, GenomeTools 1.6.1, GenomeTools 1.6.2, GEOS 3.9.1, gettext 0.21, GffCompare 0.12.2, gffread 0.12.7, gflags 2.2.2, Ghostscript 9.54.0, giflib 5.2.1, GIMP 2.10.24, GLib 2.69.1, glib networking, GlobalArrays 5.8, glog 0.5.0, GLPK 5.0, GMP 6.2.1, gmpy2 2.1.0b5, GMT 6.2.0, GMT 6.2.0, Go 1.16.6.eb, GOATOOLS 1.1.6, GObject Introspection, gofasta 0.0.5.eb, gompi 2021.07.eb, googletest 1.11.0, GPAW 21.6.0, gperf 3.1, gperftools 2.9.1, gpustat 0.6.0, Gradle 6.9.1.eb, groff 1.22.4, GROMACS 2021.3, GSL 2.7, GST plugins, GStreamer 1.18.4, GTK2 2.24.33, GTK3 3.24.29, GtkSourceView 3.24.11, gzip 1.10, h4toh5 2.2.3, h5py 2.10.0, h5py 2.10.0, HarfBuzz 2.8.2, HDF 4.2.15, HDF5 1.12.1, HDF EOS, HDF EOS5, help2man 1.48.3, HH suite, HH suite, HH suite, Highway 0.12.2, hipSYCL 0.9.1, hipSYCL 0.9.1, HMMER 3.3.2, HMMER 3.3.2, Horovod 0.22.1, horton 2.1.1, HPCG 3.1, HPCG 3.1, HPCG 3.1, HPL 2.3, HPL 2.3, HTSlib 1.12, hwloc 2.5.0, hypothesis 6.14.6, Hypre 2.20.0, Hypre 2.21.0, ICU 69.1, igraph 0.9.4, ImageMagick 7.1.0, imake 1.0.8, imkl 2020.4.304, imkl 2021.2.0, IMOD 4.11.5, IMOD 4.11.5, inferCNV 1.3.3, inferCNV 1.3.3, intel compilers, intervaltree 0.1, intltool 0.51.0, iomkl 2021a.eb, iompi 2021a.eb, IPython 7.26.0, IRkernel 1.2, ISA L, ISL 0.24, JAGS 4.3.0, JAGS 4.3.0, JasPer 2.0.33, Java 16.0.1.eb, Java 16.eb, jax 0.2.19, jax 0.2.19, jbigkit 2.1, Jellyfish 2.3.0, jemalloc 5.2.1, jemalloc 5.2.1, json c, json c, JsonCpp 1.9.4, JSON GLib, Julia 1.6.2, JupyterHub 1.4.1, JupyterLab 3.1.6, Kalign 2.0.4, Kalign 3.3.1, Kent_tools 418, kim api, KronaTools 2.8, LADR 2009, LAME 3.100, lavaan 0.6, lDDT 1.2.eb, libarchive 3.5.1, libcerf 1.15, libcircle 0.3, libdap 3.20.7, libdeflate 1.7, libdivsufsort 2.0.1, libdrm 2.4.107, libepoxy 1.5.8, libevent 2.1.12, libfabric 1.13.0, libffcall 2.4, libffi 3.4.2, libgcrypt 1.9.3, libgeotiff 1.7.0, libgit2 1.1.1, libGLU 9.0.2, libglvnd 1.3.3, libgpg error, libiconv 1.16, libidn 1.38, libidn2 2.3.2, Libint 1.1.6, libjpeg turbo, libjxl 0.5, libmypaint 1.6.1, libogg 1.3.5, libpci 3.7.0, libpciaccess 0.16, libpng 1.6.37, libpsl 0.21.1, libreadline 8.1, libRmath 4.1.0, librsvg 2.51.2, libsigsegv 2.13, libsndfile 1.0.31, libsodium 1.0.18, LIBSVM 3.25, libtecla 1.6.3, LibTIFF 4.3.0, libtirpc 1.3.2, libtool 2.4.6, libunwind 1.5.0, libvdwxc 0.4.0, libvorbis 1.3.7, libwebp 1.2.0, libxc 3.0.1, libxml2 2.9.10, libxslt 1.1.34, libxslt 1.1.34, libyaml 0.2.5, libzip 1.7.3, lie_learn 0.0.1.post1, likwid 5.2.0, LittleCMS 2.12, LLVM 12.0.1, LLVM 12.0.1, LMDB 0.9.29, longestrunsubsequence 1.0.1, lwgrp 1.0.3, lxml 4.6.3, lxml 4.6.3, lz4 1.9.3, LZO 2.10, M4 1.4.19, magma 2.6.1, make 4.3, makedepend 1.0.6, Mako 1.1.4, MariaDB 10.6.4, MariaDB connector, MATIO 1.5.21, matplotlib 3.1.1, matplotlib 3.4.2, Maude 3.1, MEGA 10.0.5.eb, Mesa 21.1.7, Meson 0.58.2, Meson 0.59.1, Metal 2020, mhcnuggets 2.3, mhcnuggets 2.3, mimalloc 1.7.2, mimalloc 1.7.2, minimap2 2.20, Mini XML, MINPACK 19961126, Mish Cuda, MiXCR 3.0.13, molmod 1.4.8, MPC 1.2.1, MPFR 4.1.0, MPICH 3.4.2, multichoose 1.0.3, MUMPS 5.3.5, muparserx 4.0.8, nanopolish 0.13.3, NASM 2.15.05, NCCL 2.10.3, NCCL 2.10.3, ncdf4 1.17, ncdu 1.16, NCL 6.6.2, NCO 5.0.1, ncurses 6.2, neptune client, netcdf4 python, netcdf4 python, netCDF C++4, netCDF C++4, nettle 3.7.3, networkx 2.4, networkx 2.5.1, Ninja 1.10.2, nlohmann_json 3.10.0, NLopt 2.7.0, nodejs 14.17.2, nodejs 14.17.6, NSPR 4.32, NSS 3.69, nsync 1.24.0, numactl 2.0.14, numba 0.53.1, NVHPC 21.7.eb, OPARI2 2.0.6, OpenBLAS 0.3.17, OpenBLAS 0.3.17, OpenEXR 3.1.1, OpenFOAM 9, OpenFOAM v2006, OpenFOAM v2106, OpenJPEG 2.4.0, OpenMM 7.5.1, OpenMM 7.5.1, OpenMolcas 21.06, OpenMPI 4.1.1, OpenMPI 4.1.1, OpenPGM 5.2.122, openpyxl 3.0.7, openpyxl 3.0.7, OpenStackClient 5.5.0, ORCA 5.0.0, ORCA 5.0.0, ORCA 5.0.1, ORCA 5.0.1, Osi 0.108.6, OSPRay 2.5.0.eb, OSU Micro, OSU Micro, OSU Micro, OTF2 2.3, p7zip 17.04, pandapower 2.7.0, Pango 1.48.8, pangolin 3.1.11, parallel 20210722, Paraver 4.9.2, ParaView 5.9.1, patchelf 0.12, patchelf 0.13, PCRE2 10.37, PCRE 8.45, PDT 3.25.1, PEAR 0.9.11, Perl 5.34.0, PETSc 3.14.4, PETSc 3.15.1, petsc4py 3.15.0, pigz 2.6, Pillow 8.3.1, Pillow SIMD, Pillow SIMD, pixman 0.40.0, pkg config, plotly.py 5.1.0, PLUMED 2.7.2, PMIx 4.1.0, PnetCDF 1.12.2, PnetCDF 1.12.2, poppler 21.06.1, PostgreSQL 13.3, preseq 3.1.2, PRINSEQ 0.20.4, PROJ 8.1.0, protobuf 3.17.3, protobuf python, PRSice 2.3.3, PSIPRED 4.02, pyBigWig 0.3.18, pybind11 2.7.1, PyCairo 1.20.1, pyFFTW 0.12.0, PyGEOS 0.10.2, Pyomo 6.0.1, Pyomo 6.0.1, PYPOWER 5.1.15, PyPSA 0.17.1, PyQt5 5.15.4, PyRETIS 2.5.0, PyRETIS 2.5.0, PyRosetta 4.release, Pysam 0.16.0.1, pysamstats 1.1.2, pyshp 2.1.3, PyTables 3.6.1, pytest benchmark, pytest xdist, Python 3.9.6, Python 3.9.6, python igraph, python isal, PyTorch 1.8.1, PyTorch 1.9.0, PyTorch Geometric, PyYAML 5.4.1, QCxMS 5.0.3.eb, Qhull 2020.2, Qhull 2020.2, QJson 0.9.0, Qt5Webkit 5.212.0, QTLtools 1.3.1, Qualimap 2.2.1, Quandl 3.6.1, Qwt 6.1.5, QwtPolar 1.1.1, RAxML 8.2.12, RAxML NG, R bundle, re2c 2.2, ReFrame 3.6.3.eb, ReFrame 3.7.3.eb, ReFrame 3.8.0.eb, RepeatModeler 2.0.2a, rgdal 1.5, rgeos 0.5, rjags 4, rjags 4, rjags 4, rjags 4, rjags 4, rjags 4, rjags 4, RSeQC 4.0.0, RStudio Server, Rust 1.54.0, samclip 0.4.0, SAMtools 1.12, ScaFaCoS 1.0.1, ScaFaCoS 1.0.1, ScaLAPACK 2.1.0, Scalasca 2.6, Schrodinger 2020, scikit build, SCons 4.2.0, Score P, scVelo 0.2.3, SDL2 2.0.14, segemehl 0.3.4, SeqLib 1.2.0, Serf 1.3.9, Shapely 1.8a1, Shapely 1.8a1, Shapely 1.8a1, shrinkwrap 1.1.0, SIONlib 1.7.6, sklearn som, SLEPc 3.14.2, SLEPc 3.15.1, slepc4py 3.15.1, smithwaterman 20160702, snakemake 6.6.1, snappy 1.1.9, snippy 4.6.0, Snippy 4.6.0, snpEff 5.0e, snp sites, SOCI 4.0.2, SoQt 1.6.0, SpaceRanger 1.3.0, Spack 0.16.2.eb, spatialreg 1.1, spdlog 1.9.2, SpectrA 1.0.0, spglib python, spglib python, spglib python, SQLite 3.36, SSW 1.1, STAR 2.7.9a, statsmodels 0.12.2, StringTie 2.1.7, Subread 2.0.3, Subversion 1.14.1, SuiteSparse 5.8.1, SWIG 4.0.2, SymEngine 0.7.0, SymEngine python, sympy 1.7.1, SyRI 1.4, Szip 2.1.1, tabix 0.2.6, tabix 0.2.6, Tcl 8.6.11, TCLAP 1.2.4, tcsh 6.22.04, TensorFlow 2.6.0, TensorFlow 2.6.0, TetGen 1.6.0, time 1.9, time 1.9, Tk 8.6.11, Tkinter 3.9.5, Tkinter 3.9.6, tmux 3.2a, torchinfo 1.5.2, torchinfo 1.5.2, torchtext 0.9.1, torchvision 0.9.1, tqdm 4.61.1, tqdm 4.61.2, TRAVIS Analyzer, TWL NINJA, UCX 1.11.0, UCX CUDA, UDUNITS 2.2.28, unrar 6.0.2, UnZip 6.0, UShER 0.4.1, utf8proc 2.6.1, util linux, Vampire 4.5.1, VBZ Compression, vcflib 1.0.2, VCFtools 0.1.16, velocyto 0.17.17, VisPy 0.6.6, VisPy 0.6.6, vorbis tools, Voro++ 0.4.6, Voro++ 0.4.6, vt 0.57721, VTune 2021.6.0.eb, wgsim 20111017, WIEN2k 19.2, WIEN2k 21.1, WPS 4.2, WRF 4.2.2, WRF 4.3, wxWidgets 3.1.5, X11 20210802, x264 20210613, x265 3.5, xarray 0.16.2, xarray 0.19.0, Xerces C++, Xerces C++, XlsxWriter 1.4.4, XML Parser, xorg macros, xprop 1.2.5, xproto 7.0.31, xTB 6.4.1, Xvfb 1.20.13, XZ 5.2.5, YACS 0.1.8, YACS 0.1.8, Yasm 1.3.0, YAXT 0.9.1, Yices 2.6.2, ZeroMQ 4.3.4, Zip 3.0, Zip 3.0, zlib 1.2.11, zstd 1.5.0 +- minor enhancements, including: + - add PCAmatchR extension to recent R easyconfigs (#13448) + - add hal9001 extension to recent R v4.x easyconfigs (#13451) + - add VBZ compress capability to nanopolish 0.13.3 (for fast5 files) (#13536) + - add cobalt extension for recent R 4.0.x and 4.1.0 easyconfigs (#13544) + - add CBPS extension for recent R 4.0.x and 4.1.0 easyconfigs (#13549) + - add SBdecomp extension for recent R 4.0.x and 4.1.0 easyconfigs (#13565) + - add patch for OpenBLAS v0.3.17 to workaround problem in C/ZBLAS3 tests with GCC 11.x and -ftree-vectorize (#13625) + - improve configuration of SymEngine 0.7.0 + add FLINT as dependency (#13647) + - add lwgeom extension to R 4.1.0 easyconfig (#13674) + - add CMake build dependency to easyconfig for tbb 2020.03 (#13704) + - also build shared libs for MUMPS 5.3.5 (#13702) and 5.4.0 (#13705) + - add naturalsort extension to recent R 4.x easyconfigs (#13762) + - add dependency on pkg-config to OpenSSL wrappers (#13765) + - Add finalfit and gtsummary to R >= 4.0.4 (#13766) +- various bug fixes, including: + - fix LAMMPS 3Mar2020 easyconfigs using intel toolchain on AMD CPUs by patching out hardcoded -xHost (#11577) + - fix sanity check error for OpenCV v4.5.1 by adding (and using) freetype and HarfBuzz dependencies (#12517) + - add patches for TensorFlow 1.13.1 to fix installation (#13326) + - remove Python 2.6 from list of supported Python versions in setup.py (#13349) + - switch back to Bundle easyblock for PyQt5 5.15.1 + add back source URLs for components (#13371) + - add pkg-config build dependency for GDAL 3.2.1 (to pick up libxml2) (#13383) + - add missing Python 3 build dependency for Rust v1.52.1 (#13399) + - fix order of cffi extension in old Python easyconfigs (#13400) + - patch out __asm__ use in ctffind to avoid build failure on ppc64le (#13409) + - disable building man pages in Gdk-Pixbuf (#13410) + - prokka needs Bio-Search-hmmer, but it is not part of BioPerl>1.7.3 (#13419) + - avoid downloading old numpy version during install for h5py (#13428) + - add patch for Qt5 5.8.0 to fix compilation failure in webkit (#13434) + - avoid downloading and building freetype and qhull for matplotlib 3.4.2 (#13437) + - fix order of components in recent GTK+ easyconfigs to avoid dependency on system GTK+ in GTK+ themes (#13449) + - fix Python 2.7.13 easyconfigs by adding missing extensions (#13456) + - add TensorFlow patch to fix crash on shutdown (#13462) + - allow for non-x86_64 in postinstallcmds for CuPy (#13501) + - disable default EULA acceptance in easyconfig for NVHPC v21.5 (#13516) + - rename NINJA to TWL-NINJA to avoid nameclash (#13529) + - add pkg-config build dependency to recent Rust easyconfigs (#13538) + - fix error with p7zip's 7z command not finding 7z.dll (#13542) + - patch so that MaxBin2 uses the EB provided Perl dependency (#13551) + - add missing zlib dependency to libarchive (#13579) + - fix pkgconfig version in patch for bzip 1.0.8 (+ add easyconfig with GCCcore/11.2.0 toolchain) (#13581) + - fix build of DIRAC 19.0 easyconfig with high compiler optimizations (#13613) + - fix source URLs and add alternative checksum for Hypre 2.15.1 (since it moved to a different GitHub repo) (#13616) + - avoid MPICXX dependency in SimpleElastics ITK (#13623) + - add upstream patch for GCC 9.x, 10.x, 11.x to avoid spurious FPE on avx512 (affects UCX) (#13628) + - don't include unversioned go-basic.odo and goslin_generic.odo files in GOATOOLS installation (renamed from goatools) (#13629) + - add patch for ctffind 4.1.14 to declare functions without return as void (fixes segfault) (#13665) + - enable EGL in recent libepoxy ECs (#13684) + - remove unused buildcmd from libgpuarray easyconfigs (#13720) + - add patch to fix building Qt5.10.1 against newer glibc (#13730) + - add Python 3 as a builddependency to recent fontconfig easyconfigs (#13731) + - update source_url in BLAST-2.2.26-Linux_x86_64 easyconfig (#13732) + - restore error message on failing test suite, required by bot to determine end of output of test suite (#13745) + - add Perl build dependency to recent Clang easyconfigs (#13746) + - disable using system Valgrind in the json-c tests (#13750) + - use Archive source URL for spatstat.geom extension in Seurat (#13761) + - make the testsuite print error and still return a non-zero exitcode (#13770) + - add PyTorch versionsuffix to Mish-Cuda (#13784) + - add ld.gold relocts patch to binutils 2.30 (#13785) + - add missing Python + Zip build dependencies for old Bazel versions used as build dep for TensorFlow 1.12.0 + 1.13.1 (#13786) + - add alternative checksum for AFNI 18.3.00 (#13790) + - add build dependency on pkg-config to GenomeTools easyconfig to fix finding of cairo (#13805) + - consistently add pkg-config as build dependency for GDAL 3.2.1 (#13808) + - update tensorflow-probability easyconfigs to include '--release' flag in installopts (#13810) + - fix source URL for DB 18.1.32 (#13813) + - add missing cppy build dependency for matplotlib 3.4.2 (#13823) + - update to libjxl 0.5 + disable building of man pages (#13829) + - add pkg-config build dependency + disable bash completion in recent x264 easyconfigs (#13834) + - add Perl as build dependency for ELPA 2021.05.001 + patch to fix hardcoded /usr/bin/perl (#13835) + - add archive source URL to Spark 3.x easyconfigs to fix broken download (#13842) + - correct the version, fix spelling of a name, and add an extra sanity check command in pangolin (#13848) + - fix PCRE dependency for GDAL 3.2.1 and 3.3.0, don't use PCRE2 (#13861) + - add Perl build dependency for HMMER 3.3.2 + patch to ensure it is used (#13870) + - stick to intel-compilers toolchain for DFT-D3 v3.2.0 (#13878) + - remove UCX-CUDA dependency from TensorFlow 2.6 easyconfig (not needed as direct dependency) (#13882) + - add missing flex build dependency for leidenalg (#13884) + - update CMake build dependency for Eigen 3.3.4 + 3.3.5 (#13889) + - remove SHA256 checksum for IMOD 4.11.5 source tarball + fix installation on top of Python 3 (#13899) + - fix source URL for Yasm 1.3.0 (+ add missing checksum) (#13901) + - update to more recent Meson build dependency for easyconfigs to fix failing RPATH sanity check (#13910) + - fix shebang for RepeatMasker 4.1.2-p1 Perl script (#13911) +- other changes: + - use orca easyblock in easyconfigs of ORCA v4.x (#13348) + - move archive files to correct folder (#13422) + - remove superflous configopts and add sanity checks/checksums in CLHEP easyconfigs (#13614) + - remove superflous -DCMAKE_BUILD_TYPE configuration option in Arrow easyconfigs (#13615) + - add new source URL for Mesa easyconfigs using 2017b toolchain (#13617) + - switch ITK easyconfigs to CMakePythonPackage easyblock, also enable -DITK_USE_SYSTEM_HDF5 configuration option, fix download URLs (#13619) + - use build_type instead of -DCMAKE_BUILD_TYPE=RELEASE in configopts in MMseqs2 easyconfigs (#13620) + - avoid using system GTK+3 and remove -DCMAKE_BUILD_TYPE=RELEASE configure option in OpenCV easyconfigs (#13621) + - remove -DCMAKE_BUILD_TYPE=RELEASE configure option and add checksums in LLVM easyconfigs (#13624) + - create libtinfo symlinks in easyconfigs for ncurses with system toolchain (#13658), 6.1 (#13661) and 6.2 (#13660) + - increase test timeouts for PyTorch 1.8.1 and 1.9.0 (#13700) + - drop Mesa 21.2.0 back to stable 21.1.7 (#13736) + - rename CUDAcore to CUDA for v11.3.1 and v11.4.1 after merging foss/fosscuda, to ensure that get_software_root('CUDA') used in easyblocks works (#13874) + - use CUDA instead of CUDAcore in recent NVHPC comments (#13875) + - strip out custom sanity check paths from VTune 2021.6.0 easyconfig (#13898) + - use GTK2 and GTK3 as dependencies rather than GTK+ for easyconfigs using GCC/10.3.0 toolchain (#13900) + + v4.4.1 (July 6th 2021) ---------------------- diff --git a/setup.py b/setup.py index e382efdb250..5db57acf947 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.4.2.dev0' +VERSION = '4.4.2' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 508d096474e79c00dd2f9e6d616df3b457319de3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Sep 2021 16:37:07 +0200 Subject: [PATCH 1184/9987] fix software name for Snippy to snippy --- .../snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/{Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb => snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb} (96%) diff --git a/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb similarity index 96% rename from easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb rename to easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb index badfe711eed..3d829256a63 100644 --- a/easybuild/easyconfigs/s/Snippy/Snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb @@ -2,7 +2,7 @@ easyblock = 'CmdCp' -name = 'Snippy' +name = 'snippy' version = '4.6.0' local_pyversuffix = '-Python-%(pyver)s' local_javaversuffix = '-Java-%(javaver)s' @@ -16,7 +16,7 @@ description = """Snippy finds SNPs between a haploid reference genome and your N toolchain = {'name': 'GCC', 'version': '9.3.0'} github_account = 'tseemann' -source_urls = [GITHUB_LOWER_SOURCE] +source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['7264e3819e249387effd3eba170ff49404b1cf7347dfa25944866f5aeb6b11c3'] From e61b93077b3002417704fa96a0b56a150c53f3f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Sep 2021 16:59:59 +0200 Subject: [PATCH 1185/9987] fix software name for xTB to xtb --- .../xTB-6.4.1-intel-2021a.eb => xtb/xtb-6.4.1-intel-2021a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/x/{xTB/xTB-6.4.1-intel-2021a.eb => xtb/xtb-6.4.1-intel-2021a.eb} (98%) diff --git a/easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb b/easybuild/easyconfigs/x/xtb/xtb-6.4.1-intel-2021a.eb similarity index 98% rename from easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb rename to easybuild/easyconfigs/x/xtb/xtb-6.4.1-intel-2021a.eb index cf9d7725cde..f9f9e4a8212 100644 --- a/easybuild/easyconfigs/x/xTB/xTB-6.4.1-intel-2021a.eb +++ b/easybuild/easyconfigs/x/xtb/xtb-6.4.1-intel-2021a.eb @@ -2,7 +2,7 @@ easyblock = 'MesonNinja' -name = 'xTB' +name = 'xtb' version = '6.4.1' homepage = 'https://xtb-docs.readthedocs.io' From 91140e0b126d3a1f5bb14297e94c7cd6b9991d7f Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 6 Sep 2021 17:28:14 +0200 Subject: [PATCH 1186/9987] add missing brotli dependency to freetype --- .../b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb | 36 +++++++++++++++++++ .../freetype-2.10.3-GCCcore-10.2.0.eb | 1 + .../freetype-2.10.4-GCCcore-10.3.0.eb | 1 + 3 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..72c9f12ad60 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' +name = 'Brotli' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brotli-%(version)s_pc_link_flags.patch'] +checksums = [ + 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz + '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch +] + +separate_build_dir = True + +dependencies = [('binutils', '2.35')] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb index c9318c29a87..841fd645934 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb @@ -27,6 +27,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('libpng', '1.6.37'), ('zlib', '1.2.11'), + ('Brotli', '1.0.9'), ] configopts = '--enable-freetype-config --with-harfbuzz=no' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.10.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.10.4-GCCcore-10.3.0.eb index 57a183eaabc..35b5de5ccc5 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.10.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.10.4-GCCcore-10.3.0.eb @@ -27,6 +27,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('libpng', '1.6.37'), ('zlib', '1.2.11'), + ('Brotli', '1.0.9'), ] configopts = '--enable-freetype-config --with-harfbuzz=no' From 96316cdd7258a705073e7cfc3a8b4e7ef2654680 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Sep 2021 17:29:44 +0200 Subject: [PATCH 1187/9987] minor tweaks to v4.4.2 release notes --- RELEASE_NOTES | 94 ++++++++++++++++++++++++++++++--------------------- 1 file changed, 56 insertions(+), 38 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 4593ba5d1f4..5f726e1b4a8 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 12,607 easyconfig files, for 2,388 different software packages, +The latest version of easybuild-easyconfig provides 13,265 easyconfig files, for 2,467 different software packages, incl. 36 different (compiler) toolchains. @@ -12,37 +12,68 @@ v4.4.2 (September 7th 2021) update/bugfix release -- added example easyconfig files for 82 new software packages: - - AlphaFold (#13867), andi (#13768), aria2 (#13709), AUTO-07p (#13831), babl (#13216), BAli-Phy (#13484), biogeme (#13735), Bio-SearchIO-hmmer (#13419), BuDDy (#13907), c-ares (#13709), CellRank (#13408), Coin (#13818), Co-phylog (#13769), cppy (#13823), CREST (#13648), CRISPR-DAV (#13139), CSBLAST (#13794), DGL (#13793), DistributedStream (#13659), Excel-Writer-XLSX (#13139), FBPIC (#13500), freebayes (#12859), freud-analysis (#13354), fumi_tools (#13517), GEGL (#13216), GIMP (#13216), glib-networking (#13216), GOATOOLS (#13629), gofasta (#13651), GTK2 (#13900), GTK3 (#13900), Highway (#13453), hipSYCL (#13837), ISA-L (#13663), jax (#13760), JSON-GLib (#13216), Kalign (#13463), LADR (#13351), lDDT (#13794), libdivsufsort (#13768), libjxl (#13829), libmypaint (#13216), libtecla (#13908), lie_learn (#13793), longestrunsubsequence (#13800), Maude (#13909), mimalloc (#13726), MINPACK (#13802), Mish-Cuda (#13784), muparserx (#13779), nlohmann_json (#13777), OpenStackClient (#13644), OSPRay (#12852), pandapower (#13687), pangolin (#13848), PSIPRED (#13794), PYPOWER (#13689), PyPSA (#13673), PyRosetta (#13793), pysamstats (#13139), pytest-benchmark (#13622), python-isal (#13663), QCxMS (#13650), RepeatModeler (#13126), Schrodinger (#11698), sklearn-som (#13699), Snippy (#12893), SoQt (#13818), spdlog (#13778), SpectrA (#13743), SymEngine-python (#13652), SyRI (#13800), torchinfo (#13662), TRAVIS-Analyzer (#13503), TWL-NINJA (#13529), UShER (#13708), Vampire (#13352), VBZ-Compression (#13536), VisPy (#13468), wgsim (#13475), xTB (#13649), Yices (#13906) +- added easyconfig for foss/2021.07 (candidate for foss/2021b) (#13788) and iomkl/2021a (#13521) toolchains +- added example easyconfig files for 79 new software packages: + - AlphaFold (#13867), andi (#13768), aria2 (#13709), AUTO-07p (#13831), babl (#13216), BAli-Phy (#13484), + biogeme (#13735), Bio-SearchIO-hmmer (#13419), BuDDy (#13907), c-ares (#13709), CellRank (#13408), Coin (#13818), + Co-phylog (#13769), cppy (#13823), CREST (#13648), CRISPR-DAV (#13139), CSBLAST (#13794), DGL (#13793), + DistributedStream (#13659), Excel-Writer-XLSX (#13139), FBPIC (#13500), freebayes (#12859), freud-analysis (#13354), + fumi_tools (#13517), GEGL (#13216), GIMP (#13216), glib-networking (#13216), GOATOOLS (#13364, #13629), + gofasta (#13651), GTK2 (#13900), GTK3 (#13900), Highway (#13453), hipSYCL (#13837), ISA-L (#13663), jax (#13760), + JSON-GLib (#13216), Kalign (#13463), LADR (#13351), lDDT (#13794), libdivsufsort (#13768), libjxl (#13453, #13829), + libmypaint (#13216), libtecla (#13908), lie_learn (#13793), longestrunsubsequence (#13800), Maude (#13909), + mimalloc (#13726), MINPACK (#13802), Mish-Cuda (#13759, #13784), muparserx (#13779), nlohmann_json (#13777), + OpenStackClient (#13644), OSPRay (#12852), pandapower (#13687), pangolin (#13733, #13848), PSIPRED (#13794), + PYPOWER (#13689), PyPSA (#13673), PyRosetta (#13793), pysamstats (#13139), pytest-benchmark (#13622), + python-isal (#13663), QCxMS (#13650), RepeatModeler (#13126), Schrodinger (#11698), sklearn-som (#13699), + SoQt (#13818), spdlog (#13778), SpectrA (#13743), SymEngine-python (#13652), SyRI (#13800), torchinfo (#13662), + TRAVIS-Analyzer (#13503), UShER (#13708), Vampire (#13352), VBZ-Compression (#13536), VisPy (#13468), + wgsim (#13475), Yices (#13906) - added additional easyconfigs for various supported software packages, including: - - ABAQUS 2020.eb, ABINIT 9.4.2, ABRA2 2.23, ack 3.5.0, AdapterRemoval 2.3.2, Advisor 2021.2.0.eb, almosthere 2.0.2, AlphaFold 2.0.0, AlphaFold 2.0.0, Anaconda3 2021.05.eb, andi 0.13, ant 1.10.11, ant 1.10.11, ANTLR 2.7.7, ANTs 2.3.5, any2fasta 0.4.2, AOCC 3.1.0, AOCC 3.1.0, APR 1.7.0, APR util, Arb 2.19.0, Archive Zip, Archive Zip, archspec 0.1.2, archspec 0.1.2, argtable 2.13, aria2 1.35.0, Armadillo 10.5.3, arpack ng, Arriba 2.1.0, ASE 3.22.0, ATK 2.36.0, at spi2, at spi2, at spi2, at spi2, AUTO 07p, Autoconf 2.71, Automake 1.16.4, Autotools 20210726, babl 0.1.86, BAli Phy, BamTools 2.5.2, barrnap 0.9, Bazel 0.29.1, Bazel 2.0.0, Bazel 3.7.2, BCFtools 1.12, bcl2fastq2 2.20.0, BEDTools 2.30.0, bgen 4.1.3, binutils 2.37, binutils 2.37.eb, bioawk 1.0, biogeme 3.1.2, biogeme 3.2.8, Biopython 1.79, Bio SearchIO, Bison 3.7.6, bitarray 1.5.3, BLIS 3.0.1, BLIS 3.0.1, Blosc 1.21.0, Boost 1.76.0, Boost 1.76.0, Bowtie2 2.4.4, bpytop 1.0.67, Brotli 1.0.9, BuDDy 2.4, bx python, bzip2 1.0.8, cairo 1.16.0, c ares, Cartopy 0.19.0.post1, Cartopy 0.19.0.post1, Cbc 2.10.5, CDO 1.9.10, CellRank 1.4.0, Centrifuge 1.0.4, CGAL 4.14.3, Cgl 0.60.3, CharLS 2.2.0, Clang 12.0.1, Clp 1.17.6, Clustal Omega, Clustal Omega, ClustalW2 2.1, CMake 3.21.1, Coin 4.0.0, CoinUtils 2.11.4, configurable http, Control FREEC, Co phylog, coverage 5.5, CP2K 5.1, CP2K 7.1, CppUnit 1.15.1, cppy 1.1.0, CREST 2.11, CRISPR DAV, CRISPResso2 2.1.2, CRISPResso2 2.2.1, CSBLAST 2.2.3, ctffind 4.1.14, CubeGUI 4.6, CubeLib 4.6, CubeWriter 4.6, CUDA 11.3.1.eb, CUDA 11.4.1.eb, cuDNN 8.2.2.26, cURL 7.78.0, cutadapt 3.4, CVXOPT 1.2.6, DB 18.1.40, DBus 1.13.18, DFT D3, DFT D3, DGL 0.6.1, DIAMOND 2.0.11, DistributedStream 1.0, double conversion, Doxygen 1.9.1, DROP 1.1.0, Dsuite 20210718, Dsuite 20210718, dtcmp 1.1.2, EasyBuild 4.4.1.eb, ecCodes 2.22.1, Eigen 3.3.9, elfutils 0.185, Elk 7.2.42, ESMF 8.1.1, ESMF 8.1.1, Excel Writer, expat 2.4.1, fastahack 1.0.0, fastq tools, FASTX Toolkit, FBPIC 0.20.3, fermi lite, FFmpeg 4.3.2, FFTW 3.3.9, file 5.40, filevercmp 20191210, Fiona 1.8.20, Fiona 1.8.20, FLAC 1.3.3, FLASH 2.2.00, Flask 1.1.4, flex 2.6.4, FlexiBLAS 3.0.4, FLINT 2.7.1, FLTK 1.3.7, fontconfig 2.13.94, foss 2021.07.eb, freebayes 1.3.5, freebayes 1.3.5, FreeImage 3.18.0, freetype 2.11.0, freud analysis, FriBidi 1.0.10, fsom 20141119, fumi_tools 0.18.2, fumi_tools 0.18.2, g2clib 1.6.3, g2lib 3.2.0, GCC 11.2.0.eb, GCCcore 11.2.0.eb, GDCM 3.0.8, GDCM 3.0.8, Gdk Pixbuf, GDRCopy 2.3, GEGL 0.4.30, GenomeTools 1.6.1, GenomeTools 1.6.2, GEOS 3.9.1, gettext 0.21, GffCompare 0.12.2, gffread 0.12.7, gflags 2.2.2, Ghostscript 9.54.0, giflib 5.2.1, GIMP 2.10.24, GLib 2.69.1, glib networking, GlobalArrays 5.8, glog 0.5.0, GLPK 5.0, GMP 6.2.1, gmpy2 2.1.0b5, GMT 6.2.0, GMT 6.2.0, Go 1.16.6.eb, GOATOOLS 1.1.6, GObject Introspection, gofasta 0.0.5.eb, gompi 2021.07.eb, googletest 1.11.0, GPAW 21.6.0, gperf 3.1, gperftools 2.9.1, gpustat 0.6.0, Gradle 6.9.1.eb, groff 1.22.4, GROMACS 2021.3, GSL 2.7, GST plugins, GStreamer 1.18.4, GTK2 2.24.33, GTK3 3.24.29, GtkSourceView 3.24.11, gzip 1.10, h4toh5 2.2.3, h5py 2.10.0, h5py 2.10.0, HarfBuzz 2.8.2, HDF 4.2.15, HDF5 1.12.1, HDF EOS, HDF EOS5, help2man 1.48.3, HH suite, HH suite, HH suite, Highway 0.12.2, hipSYCL 0.9.1, hipSYCL 0.9.1, HMMER 3.3.2, HMMER 3.3.2, Horovod 0.22.1, horton 2.1.1, HPCG 3.1, HPCG 3.1, HPCG 3.1, HPL 2.3, HPL 2.3, HTSlib 1.12, hwloc 2.5.0, hypothesis 6.14.6, Hypre 2.20.0, Hypre 2.21.0, ICU 69.1, igraph 0.9.4, ImageMagick 7.1.0, imake 1.0.8, imkl 2020.4.304, imkl 2021.2.0, IMOD 4.11.5, IMOD 4.11.5, inferCNV 1.3.3, inferCNV 1.3.3, intel compilers, intervaltree 0.1, intltool 0.51.0, iomkl 2021a.eb, iompi 2021a.eb, IPython 7.26.0, IRkernel 1.2, ISA L, ISL 0.24, JAGS 4.3.0, JAGS 4.3.0, JasPer 2.0.33, Java 16.0.1.eb, Java 16.eb, jax 0.2.19, jax 0.2.19, jbigkit 2.1, Jellyfish 2.3.0, jemalloc 5.2.1, jemalloc 5.2.1, json c, json c, JsonCpp 1.9.4, JSON GLib, Julia 1.6.2, JupyterHub 1.4.1, JupyterLab 3.1.6, Kalign 2.0.4, Kalign 3.3.1, Kent_tools 418, kim api, KronaTools 2.8, LADR 2009, LAME 3.100, lavaan 0.6, lDDT 1.2.eb, libarchive 3.5.1, libcerf 1.15, libcircle 0.3, libdap 3.20.7, libdeflate 1.7, libdivsufsort 2.0.1, libdrm 2.4.107, libepoxy 1.5.8, libevent 2.1.12, libfabric 1.13.0, libffcall 2.4, libffi 3.4.2, libgcrypt 1.9.3, libgeotiff 1.7.0, libgit2 1.1.1, libGLU 9.0.2, libglvnd 1.3.3, libgpg error, libiconv 1.16, libidn 1.38, libidn2 2.3.2, Libint 1.1.6, libjpeg turbo, libjxl 0.5, libmypaint 1.6.1, libogg 1.3.5, libpci 3.7.0, libpciaccess 0.16, libpng 1.6.37, libpsl 0.21.1, libreadline 8.1, libRmath 4.1.0, librsvg 2.51.2, libsigsegv 2.13, libsndfile 1.0.31, libsodium 1.0.18, LIBSVM 3.25, libtecla 1.6.3, LibTIFF 4.3.0, libtirpc 1.3.2, libtool 2.4.6, libunwind 1.5.0, libvdwxc 0.4.0, libvorbis 1.3.7, libwebp 1.2.0, libxc 3.0.1, libxml2 2.9.10, libxslt 1.1.34, libxslt 1.1.34, libyaml 0.2.5, libzip 1.7.3, lie_learn 0.0.1.post1, likwid 5.2.0, LittleCMS 2.12, LLVM 12.0.1, LLVM 12.0.1, LMDB 0.9.29, longestrunsubsequence 1.0.1, lwgrp 1.0.3, lxml 4.6.3, lxml 4.6.3, lz4 1.9.3, LZO 2.10, M4 1.4.19, magma 2.6.1, make 4.3, makedepend 1.0.6, Mako 1.1.4, MariaDB 10.6.4, MariaDB connector, MATIO 1.5.21, matplotlib 3.1.1, matplotlib 3.4.2, Maude 3.1, MEGA 10.0.5.eb, Mesa 21.1.7, Meson 0.58.2, Meson 0.59.1, Metal 2020, mhcnuggets 2.3, mhcnuggets 2.3, mimalloc 1.7.2, mimalloc 1.7.2, minimap2 2.20, Mini XML, MINPACK 19961126, Mish Cuda, MiXCR 3.0.13, molmod 1.4.8, MPC 1.2.1, MPFR 4.1.0, MPICH 3.4.2, multichoose 1.0.3, MUMPS 5.3.5, muparserx 4.0.8, nanopolish 0.13.3, NASM 2.15.05, NCCL 2.10.3, NCCL 2.10.3, ncdf4 1.17, ncdu 1.16, NCL 6.6.2, NCO 5.0.1, ncurses 6.2, neptune client, netcdf4 python, netcdf4 python, netCDF C++4, netCDF C++4, nettle 3.7.3, networkx 2.4, networkx 2.5.1, Ninja 1.10.2, nlohmann_json 3.10.0, NLopt 2.7.0, nodejs 14.17.2, nodejs 14.17.6, NSPR 4.32, NSS 3.69, nsync 1.24.0, numactl 2.0.14, numba 0.53.1, NVHPC 21.7.eb, OPARI2 2.0.6, OpenBLAS 0.3.17, OpenBLAS 0.3.17, OpenEXR 3.1.1, OpenFOAM 9, OpenFOAM v2006, OpenFOAM v2106, OpenJPEG 2.4.0, OpenMM 7.5.1, OpenMM 7.5.1, OpenMolcas 21.06, OpenMPI 4.1.1, OpenMPI 4.1.1, OpenPGM 5.2.122, openpyxl 3.0.7, openpyxl 3.0.7, OpenStackClient 5.5.0, ORCA 5.0.0, ORCA 5.0.0, ORCA 5.0.1, ORCA 5.0.1, Osi 0.108.6, OSPRay 2.5.0.eb, OSU Micro, OSU Micro, OSU Micro, OTF2 2.3, p7zip 17.04, pandapower 2.7.0, Pango 1.48.8, pangolin 3.1.11, parallel 20210722, Paraver 4.9.2, ParaView 5.9.1, patchelf 0.12, patchelf 0.13, PCRE2 10.37, PCRE 8.45, PDT 3.25.1, PEAR 0.9.11, Perl 5.34.0, PETSc 3.14.4, PETSc 3.15.1, petsc4py 3.15.0, pigz 2.6, Pillow 8.3.1, Pillow SIMD, Pillow SIMD, pixman 0.40.0, pkg config, plotly.py 5.1.0, PLUMED 2.7.2, PMIx 4.1.0, PnetCDF 1.12.2, PnetCDF 1.12.2, poppler 21.06.1, PostgreSQL 13.3, preseq 3.1.2, PRINSEQ 0.20.4, PROJ 8.1.0, protobuf 3.17.3, protobuf python, PRSice 2.3.3, PSIPRED 4.02, pyBigWig 0.3.18, pybind11 2.7.1, PyCairo 1.20.1, pyFFTW 0.12.0, PyGEOS 0.10.2, Pyomo 6.0.1, Pyomo 6.0.1, PYPOWER 5.1.15, PyPSA 0.17.1, PyQt5 5.15.4, PyRETIS 2.5.0, PyRETIS 2.5.0, PyRosetta 4.release, Pysam 0.16.0.1, pysamstats 1.1.2, pyshp 2.1.3, PyTables 3.6.1, pytest benchmark, pytest xdist, Python 3.9.6, Python 3.9.6, python igraph, python isal, PyTorch 1.8.1, PyTorch 1.9.0, PyTorch Geometric, PyYAML 5.4.1, QCxMS 5.0.3.eb, Qhull 2020.2, Qhull 2020.2, QJson 0.9.0, Qt5Webkit 5.212.0, QTLtools 1.3.1, Qualimap 2.2.1, Quandl 3.6.1, Qwt 6.1.5, QwtPolar 1.1.1, RAxML 8.2.12, RAxML NG, R bundle, re2c 2.2, ReFrame 3.6.3.eb, ReFrame 3.7.3.eb, ReFrame 3.8.0.eb, RepeatModeler 2.0.2a, rgdal 1.5, rgeos 0.5, rjags 4, rjags 4, rjags 4, rjags 4, rjags 4, rjags 4, rjags 4, RSeQC 4.0.0, RStudio Server, Rust 1.54.0, samclip 0.4.0, SAMtools 1.12, ScaFaCoS 1.0.1, ScaFaCoS 1.0.1, ScaLAPACK 2.1.0, Scalasca 2.6, Schrodinger 2020, scikit build, SCons 4.2.0, Score P, scVelo 0.2.3, SDL2 2.0.14, segemehl 0.3.4, SeqLib 1.2.0, Serf 1.3.9, Shapely 1.8a1, Shapely 1.8a1, Shapely 1.8a1, shrinkwrap 1.1.0, SIONlib 1.7.6, sklearn som, SLEPc 3.14.2, SLEPc 3.15.1, slepc4py 3.15.1, smithwaterman 20160702, snakemake 6.6.1, snappy 1.1.9, snippy 4.6.0, Snippy 4.6.0, snpEff 5.0e, snp sites, SOCI 4.0.2, SoQt 1.6.0, SpaceRanger 1.3.0, Spack 0.16.2.eb, spatialreg 1.1, spdlog 1.9.2, SpectrA 1.0.0, spglib python, spglib python, spglib python, SQLite 3.36, SSW 1.1, STAR 2.7.9a, statsmodels 0.12.2, StringTie 2.1.7, Subread 2.0.3, Subversion 1.14.1, SuiteSparse 5.8.1, SWIG 4.0.2, SymEngine 0.7.0, SymEngine python, sympy 1.7.1, SyRI 1.4, Szip 2.1.1, tabix 0.2.6, tabix 0.2.6, Tcl 8.6.11, TCLAP 1.2.4, tcsh 6.22.04, TensorFlow 2.6.0, TensorFlow 2.6.0, TetGen 1.6.0, time 1.9, time 1.9, Tk 8.6.11, Tkinter 3.9.5, Tkinter 3.9.6, tmux 3.2a, torchinfo 1.5.2, torchinfo 1.5.2, torchtext 0.9.1, torchvision 0.9.1, tqdm 4.61.1, tqdm 4.61.2, TRAVIS Analyzer, TWL NINJA, UCX 1.11.0, UCX CUDA, UDUNITS 2.2.28, unrar 6.0.2, UnZip 6.0, UShER 0.4.1, utf8proc 2.6.1, util linux, Vampire 4.5.1, VBZ Compression, vcflib 1.0.2, VCFtools 0.1.16, velocyto 0.17.17, VisPy 0.6.6, VisPy 0.6.6, vorbis tools, Voro++ 0.4.6, Voro++ 0.4.6, vt 0.57721, VTune 2021.6.0.eb, wgsim 20111017, WIEN2k 19.2, WIEN2k 21.1, WPS 4.2, WRF 4.2.2, WRF 4.3, wxWidgets 3.1.5, X11 20210802, x264 20210613, x265 3.5, xarray 0.16.2, xarray 0.19.0, Xerces C++, Xerces C++, XlsxWriter 1.4.4, XML Parser, xorg macros, xprop 1.2.5, xproto 7.0.31, xTB 6.4.1, Xvfb 1.20.13, XZ 5.2.5, YACS 0.1.8, YACS 0.1.8, Yasm 1.3.0, YAXT 0.9.1, Yices 2.6.2, ZeroMQ 4.3.4, Zip 3.0, Zip 3.0, zlib 1.2.11, zstd 1.5.0 + - ABAQUS 2020.eb, ANTs 2.3.5, AOCC 3.1.0, Arb 2.19.0, archspec 0.1.2, Armadillo 10.5.3, ASE 3.22.0, + Autotools 20210726, BamTools 2.5.2, bgen 4.1.3, Biopython 1.79, bitarray 1.5.3, Boost 1.76.0, Bowtie2 2.4.4, + bpytop 1.0.67, Cartopy 0.19.0.post1, Centrifuge 1.0.4, Clang 12.0.1, CMake 3.21.1, CRISPResso2 2.2.1, CUDA 11.4.1, + cuDNN 8.2.2.26, cURL 7.78.0, cutadapt 3.4, DIAMOND 2.0.11, DROP 1.1.0, Dsuite 20210718, dtcmp 1.1.2, ecCodes 2.22.1, + Elk 7.2.42, ESMF 8.1.1, expat 2.4.1, fastq-tools 0.8.3, Fiona 1.8.20, FLINT 2.7.1, g2clib 1.6.3, g2lib 3.2.0, + GCC(core) 11.2.0, GDCM 3.0.8, GDRCopy 2.3, GenomeTools 1.6.2, GffCompare 0.12.2, gffread 0.12.7, GLib 2.69.1, + GMT 6.2.0, Go 1.16.6, GPAW 21.6.0, Gradle 6.9.1.eb, GROMACS 2021.3, HarfBuzz 2.8.2, HDF5 1.12.1, Horovod 0.22.1, + hwloc 2.5.0, hypothesis 6.14.6, igraph 0.9.4, ImageMagick 7.1.0, IMOD 4.11.5, IPython 7.26.0, Java 16, + Julia 1.6.2, JupyterHub 1.4.1, JupyterLab 3.1.6, Kent_tools 418, lavaan 0.6-9, libfabric 1.13.0, libffcall 2.4, + libffi 3.4.2, libgeotiff 1.7.0, libRmath 4.1.0, LIBSVM 3.25, LibTIFF 4.3.0, likwid 5.2.0, LLVM 12.0.1, LMDB 0.9.29, + magma 2.6.1, MariaDB 10.6.4, MATIO 1.5.21, matplotlib 3.4.2, MEGA 10.0.5, Mesa 21.1.7, Meson 0.59.1, + Metal 2020-05-05, Mini-XML 3.2, molmod 1.4.8, MPICH 3.4.2, nanopolish 0.13.3, NCCL 2.10.3, ncdu 1.16, NCO 5.0.1, + neptune-client 0.10.5, netcdf4-python 1.5.7, networkx 2.5.1, nodejs 14.17.6, NSPR 4.32, NSS 3.69, NVHPC 21.7, + OpenBLAS 0.3.17, OpenEXR 3.1.1, OpenFOAM 9, OpenFOAM v2106, OpenMM 7.5.1, OpenMolcas 21.06, openpyxl 3.0.7, + Pango 1.48.8, parallel 20210722, Paraver 4.9.2, ParaView 5.9.1, patchelf 0.13, PCRE2 10.37, PCRE 8.45, Perl 5.34.0, + PETSc 3.15.1, petsc4py 3.15.0, Pillow 8.3.1, Pillow-SIMD 8.3.1, plotly.py 5.1.0, PLUMED 2.7.2, PMIx 4.1.0, + poppler 21.06.1, PostgreSQL 13.3, preseq 3.1.2, pybind11 2.7.1, pyFFTW 0.12.0, PyGEOS 0.10.2, Pyomo 6.0.1, + PyQt5 5.15.4, pyshp 2.1.3, Python 3.9.6, python-igraph 0.9.6, QTLtools 1.3.1, RAxML-NG 1.0.3, + R-bundle-Bioconductor 3.13, re2c 2.2, ReFrame 3.8.0., RStudio-Server 1.4.1717, Rust 1.54.0, Scalasca 2.6, + scVelo 0.2.3, Shapely 1.8a1, shrinkwrap 1.1.0, SLEPc 3.15.1, slepc4py 3.15.1, snakemake 6.6.1, snappy 1.1.9, + snippy 4.6.0, snpEff 5.0e, SOCI 4.0.2, SpaceRanger 1.3.0, Spack 0.16.2, spatialreg 1.1-8, + spglib-python 1.16.1, SQLite 3.36, STAR 2.7.9a, statsmodels 0.12.2, StringTie 2.1.7, Subread 2.0.3, SymEngine 0.7.0, + TensorFlow 2.6.0, TetGen 1.6.0, Tkinter 3.9.6, torchtext 0.9.1, tqdm 4.61.2, UCX 1.11.0, UCX-CUDA 1.11.0, + unrar 6.0.2, util-linux 2.37, VTune 2021.6.0, WIEN2k 21.1, WPS 4.2, WRF 4.3, X11 20210802, + x264 20210613, xarray 0.19.0, XlsxWriter 1.4.4, XML-Parser 2.46, zstd 1.5.0 - minor enhancements, including: - - add PCAmatchR extension to recent R easyconfigs (#13448) - - add hal9001 extension to recent R v4.x easyconfigs (#13451) + - add extensions to recent R v4.x easyconfigs: PCAmatchR (#13448), hal9001 (#13451), cobalt (#13544), CBPS (#13549), + SBdecomp (#13565), lwgeom (#13674), naturalsort (#13762), finalfit + gtsummary (#13766) - add VBZ compress capability to nanopolish 0.13.3 (for fast5 files) (#13536) - - add cobalt extension for recent R 4.0.x and 4.1.0 easyconfigs (#13544) - - add CBPS extension for recent R 4.0.x and 4.1.0 easyconfigs (#13549) - - add SBdecomp extension for recent R 4.0.x and 4.1.0 easyconfigs (#13565) - - add patch for OpenBLAS v0.3.17 to workaround problem in C/ZBLAS3 tests with GCC 11.x and -ftree-vectorize (#13625) - - improve configuration of SymEngine 0.7.0 + add FLINT as dependency (#13647) - - add lwgeom extension to R 4.1.0 easyconfig (#13674) - add CMake build dependency to easyconfig for tbb 2020.03 (#13704) - also build shared libs for MUMPS 5.3.5 (#13702) and 5.4.0 (#13705) - - add naturalsort extension to recent R 4.x easyconfigs (#13762) - add dependency on pkg-config to OpenSSL wrappers (#13765) - - Add finalfit and gtsummary to R >= 4.0.4 (#13766) - various bug fixes, including: - fix LAMMPS 3Mar2020 easyconfigs using intel toolchain on AMD CPUs by patching out hardcoded -xHost (#11577) - fix sanity check error for OpenCV v4.5.1 by adding (and using) freetype and HarfBuzz dependencies (#12517) - add patches for TensorFlow 1.13.1 to fix installation (#13326) - remove Python 2.6 from list of supported Python versions in setup.py (#13349) - switch back to Bundle easyblock for PyQt5 5.15.1 + add back source URLs for components (#13371) - - add pkg-config build dependency for GDAL 3.2.1 (to pick up libxml2) (#13383) + - add pkg-config build dependency for GDAL 3.2.1 (#13383, #13808), Rust (#13538), GenomeTools (#13805), x264 (#13834) - add missing Python 3 build dependency for Rust v1.52.1 (#13399) - fix order of cffi extension in old Python easyconfigs (#13400) - patch out __asm__ use in ctffind to avoid build failure on ppc64le (#13409) - disable building man pages in Gdk-Pixbuf (#13410) - - prokka needs Bio-Search-hmmer, but it is not part of BioPerl>1.7.3 (#13419) + - add missing Bio-Search-hmmer dependency for prokka (#13419) - avoid downloading old numpy version during install for h5py (#13428) - add patch for Qt5 5.8.0 to fix compilation failure in webkit (#13434) - avoid downloading and building freetype and qhull for matplotlib 3.4.2 (#13437) @@ -51,69 +82,56 @@ update/bugfix release - add TensorFlow patch to fix crash on shutdown (#13462) - allow for non-x86_64 in postinstallcmds for CuPy (#13501) - disable default EULA acceptance in easyconfig for NVHPC v21.5 (#13516) - - rename NINJA to TWL-NINJA to avoid nameclash (#13529) - - add pkg-config build dependency to recent Rust easyconfigs (#13538) - fix error with p7zip's 7z command not finding 7z.dll (#13542) - - patch so that MaxBin2 uses the EB provided Perl dependency (#13551) + - patch MaxBin2 Perl script to use provided Perl dependency (#13551) - add missing zlib dependency to libarchive (#13579) - fix pkgconfig version in patch for bzip 1.0.8 (+ add easyconfig with GCCcore/11.2.0 toolchain) (#13581) - fix build of DIRAC 19.0 easyconfig with high compiler optimizations (#13613) - fix source URLs and add alternative checksum for Hypre 2.15.1 (since it moved to a different GitHub repo) (#13616) + - add new source URL for Mesa easyconfigs using 2017b toolchain (#13617) - avoid MPICXX dependency in SimpleElastics ITK (#13623) - add upstream patch for GCC 9.x, 10.x, 11.x to avoid spurious FPE on avx512 (affects UCX) (#13628) - - don't include unversioned go-basic.odo and goslin_generic.odo files in GOATOOLS installation (renamed from goatools) (#13629) - add patch for ctffind 4.1.14 to declare functions without return as void (fixes segfault) (#13665) - enable EGL in recent libepoxy ECs (#13684) - remove unused buildcmd from libgpuarray easyconfigs (#13720) - add patch to fix building Qt5.10.1 against newer glibc (#13730) - add Python 3 as a builddependency to recent fontconfig easyconfigs (#13731) - - update source_url in BLAST-2.2.26-Linux_x86_64 easyconfig (#13732) - - restore error message on failing test suite, required by bot to determine end of output of test suite (#13745) + - update source_URL in BLAST 2.2.26 easyconfig (#13732) + - restore error message on failing easyconfigs test suite, required by bot to determine end of output of test suite (#13745, #13770) - add Perl build dependency to recent Clang easyconfigs (#13746) - disable using system Valgrind in the json-c tests (#13750) - use Archive source URL for spatstat.geom extension in Seurat (#13761) - - make the testsuite print error and still return a non-zero exitcode (#13770) - - add PyTorch versionsuffix to Mish-Cuda (#13784) - add ld.gold relocts patch to binutils 2.30 (#13785) - add missing Python + Zip build dependencies for old Bazel versions used as build dep for TensorFlow 1.12.0 + 1.13.1 (#13786) - add alternative checksum for AFNI 18.3.00 (#13790) - - add build dependency on pkg-config to GenomeTools easyconfig to fix finding of cairo (#13805) - - consistently add pkg-config as build dependency for GDAL 3.2.1 (#13808) - update tensorflow-probability easyconfigs to include '--release' flag in installopts (#13810) - fix source URL for DB 18.1.32 (#13813) - add missing cppy build dependency for matplotlib 3.4.2 (#13823) - - update to libjxl 0.5 + disable building of man pages (#13829) - - add pkg-config build dependency + disable bash completion in recent x264 easyconfigs (#13834) + - disable bash completion in recent x264 easyconfigs (#13834) - add Perl as build dependency for ELPA 2021.05.001 + patch to fix hardcoded /usr/bin/perl (#13835) - add archive source URL to Spark 3.x easyconfigs to fix broken download (#13842) - - correct the version, fix spelling of a name, and add an extra sanity check command in pangolin (#13848) - fix PCRE dependency for GDAL 3.2.1 and 3.3.0, don't use PCRE2 (#13861) - add Perl build dependency for HMMER 3.3.2 + patch to ensure it is used (#13870) - stick to intel-compilers toolchain for DFT-D3 v3.2.0 (#13878) - - remove UCX-CUDA dependency from TensorFlow 2.6 easyconfig (not needed as direct dependency) (#13882) - add missing flex build dependency for leidenalg (#13884) - update CMake build dependency for Eigen 3.3.4 + 3.3.5 (#13889) - - remove SHA256 checksum for IMOD 4.11.5 source tarball + fix installation on top of Python 3 (#13899) - fix source URL for Yasm 1.3.0 (+ add missing checksum) (#13901) - - update to more recent Meson build dependency for easyconfigs to fix failing RPATH sanity check (#13910) + - update to more recent Meson build dependency for GCCcore/8.3.0 easyconfigs to fix failing RPATH sanity check (#13910) - fix shebang for RepeatMasker 4.1.2-p1 Perl script (#13911) - other changes: - - use orca easyblock in easyconfigs of ORCA v4.x (#13348) - - move archive files to correct folder (#13422) + - use custom ORCA easyblock in easyconfigs for ORCA v4.x (#13348) + - move archived easyconfig files to correct __archive__ folder (#13422) + - rename NINJA to TWL-NINJA to avoid nameclash (#13529) - remove superflous configopts and add sanity checks/checksums in CLHEP easyconfigs (#13614) - remove superflous -DCMAKE_BUILD_TYPE configuration option in Arrow easyconfigs (#13615) - - add new source URL for Mesa easyconfigs using 2017b toolchain (#13617) - switch ITK easyconfigs to CMakePythonPackage easyblock, also enable -DITK_USE_SYSTEM_HDF5 configuration option, fix download URLs (#13619) - use build_type instead of -DCMAKE_BUILD_TYPE=RELEASE in configopts in MMseqs2 easyconfigs (#13620) - avoid using system GTK+3 and remove -DCMAKE_BUILD_TYPE=RELEASE configure option in OpenCV easyconfigs (#13621) - remove -DCMAKE_BUILD_TYPE=RELEASE configure option and add checksums in LLVM easyconfigs (#13624) - create libtinfo symlinks in easyconfigs for ncurses with system toolchain (#13658), 6.1 (#13661) and 6.2 (#13660) - increase test timeouts for PyTorch 1.8.1 and 1.9.0 (#13700) - - drop Mesa 21.2.0 back to stable 21.1.7 (#13736) - rename CUDAcore to CUDA for v11.3.1 and v11.4.1 after merging foss/fosscuda, to ensure that get_software_root('CUDA') used in easyblocks works (#13874) - use CUDA instead of CUDAcore in recent NVHPC comments (#13875) - - strip out custom sanity check paths from VTune 2021.6.0 easyconfig (#13898) - - use GTK2 and GTK3 as dependencies rather than GTK+ for easyconfigs using GCC/10.3.0 toolchain (#13900) v4.4.1 (July 6th 2021) From e933b5fe918ec86fc4220484fd35ab379f869ec8 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 7 Sep 2021 14:12:17 +0800 Subject: [PATCH 1188/9987] adding easyconfigs: EasyBuild-4.4.2.eb --- .../e/EasyBuild/EasyBuild-4.4.2.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.2.eb new file mode 100644 index 00000000000..442f64876f1 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.2.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.4.2' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/4d/19/af2ba0d1dd90a54520bc9f41f2fcb6f01ea31dfb0c7244b54a32cfef1732/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/36/57/be2bbdf3003ed0bdc426181a179f477b12792a450b8dbab1b7a14209e8f7/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/33/2c/946a7f95b81bc0031706d6754ce9f976a8c385bdb400ba439ef431393d00/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '1e6580f210bc742ee1518d0a85389b32199b692de80548c80e93fa2a1a32dd01', # easybuild-framework-4.4.2.tar.gz + '4918f13ffcd97c8b9eb0a10517bdc5b28f67c3602882d4be0bee3afc401fd78c', # easybuild-easyblocks-4.4.2.tar.gz + '6ec2fa4d9116d45298318f31292726b6f6d1257580cff82138904c69ab38bc46', # easybuild-easyconfigs-4.4.2.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 05a60c52cd8dd4c3ac41edc329b2fbd588303843 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Sep 2021 09:03:24 +0200 Subject: [PATCH 1189/9987] bump version to 4.4.3dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 5db57acf947..d3bc5581812 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.4.2' +VERSION = '4.4.3.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 90780ce7cfbad2bcd9b485e0f179e7e6f4eeb6b5 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 7 Sep 2021 14:21:36 +0200 Subject: [PATCH 1190/9987] Drop help2man from flex at SYSTEM level. help2man depends on Perl and we do not want Perl at SYSTEM level. --- easybuild/easyconfigs/f/flex/flex-2.6.3.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb index ab3d8511d39..fdf45e1d1ac 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb @@ -17,9 +17,9 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] +# Do not add help2man, it depends on Perl and we do not want Perl at SYSTEM level. builddependencies = [ ('Bison', '3.0.4'), - ('help2man', '1.47.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb index e15e819b098..1bd3cec86e9 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb @@ -16,9 +16,9 @@ source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] +# Do not add help2man, it depends on Perl and we do not want Perl at SYSTEM level. builddependencies = [ ('Bison', '3.5.3'), - ('help2man', '1.47.4'), ] dependencies = [ From 59a5d90c985d01082989d32e2c534e38aa29ee69 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 7 Sep 2021 14:29:55 +0200 Subject: [PATCH 1191/9987] Enhance comment about not using help2man. --- easybuild/easyconfigs/f/flex/flex-2.6.3.eb | 1 + easybuild/easyconfigs/f/flex/flex-2.6.4.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb index fdf45e1d1ac..a65a93c17f2 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb @@ -18,6 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] # Do not add help2man, it depends on Perl and we do not want Perl at SYSTEM level. +# This results in not building man pages for the flex at SYSTEM level. builddependencies = [ ('Bison', '3.0.4'), ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb index 1bd3cec86e9..1beedb7a51c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb @@ -17,6 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] # Do not add help2man, it depends on Perl and we do not want Perl at SYSTEM level. +# This results in not building man pages for the flex at SYSTEM level. builddependencies = [ ('Bison', '3.5.3'), ] From 4b6a7b9fb9b833de8d141d9a29bb5dfb68c00d3f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Sep 2021 14:34:52 +0200 Subject: [PATCH 1192/9987] add patch for OpenBLAS 0.3.15 to fix failing numpy tests on aarch64 (fixes #11959) --- .../o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb | 4 ++- .../OpenBLAS-0.3.15_fix-aarch64.patch | 27 +++++++++++++++++++ 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_fix-aarch64.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb index fa72e0dfc56..ef8207f8887 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb @@ -15,13 +15,15 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), - '%(name)s-%(version)s_icelake-detection.patch', + 'OpenBLAS-%(version)s_icelake-detection.patch', + 'OpenBLAS-%(version)s_fix-aarch64.patch', ] checksums = [ '30a99dec977594b387a17f49904523e6bc8dd88bd247266e83485803759e4bbe', # v0.3.15.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', # OpenBLAS-0.3.15_icelake-detection.patch + 'ba7bd45af9fe0516f8c9b1cf047eec7b833996e481bc925d4fb2563865d3db38', # OpenBLAS-0.3.15_fix-aarch64.patch ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_fix-aarch64.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_fix-aarch64.patch new file mode 100644 index 00000000000..d5b4cf40cb8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_fix-aarch64.patch @@ -0,0 +1,27 @@ +see https://github.com/xianyi/OpenBLAS/pull/3270 + +From 9d292d37b2cea829763f8f6bf8e5f4053bbf2a00 Mon Sep 17 00:00:00 2001 +From: Gilles Gouaillardet +Date: Mon, 14 Jun 2021 17:01:28 +0900 +Subject: [PATCH] arm64: add the missing d9 register to the clobber list + +Refs. numpy/numpy#18422 + +Signed-off-by: Gilles Gouaillardet +--- + kernel/arm64/dznrm2_thunderx2t99.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/kernel/arm64/dznrm2_thunderx2t99.c b/kernel/arm64/dznrm2_thunderx2t99.c +index b021a28321..fba2fe8ce7 100644 +--- a/kernel/arm64/dznrm2_thunderx2t99.c ++++ b/kernel/arm64/dznrm2_thunderx2t99.c +@@ -321,7 +321,7 @@ static void nrm2_compute(BLASLONG n, FLOAT *x, BLASLONG inc_x, + : "cc", + "memory", + "x0", "x1", "x2", "x3", "x4", "x5", "x6", +- "d0", "d1", "d2", "d3", "d4", "d5", "d6", "d7", "d8" ++ "d0", "d1", "d2", "d3", "d4", "d5", "d6", "d7", "d8", REGINF + ); + + } From 87c6f4c4c3863d2ad81a5e7204d3353db49d6565 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 7 Sep 2021 15:00:10 +0200 Subject: [PATCH 1193/9987] Update checksum to sha256 version. --- easybuild/easyconfigs/f/flex/flex-2.6.3.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb index a65a93c17f2..21e844915f7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3.eb @@ -14,8 +14,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] - -checksums = ['a5f65570cd9107ec8a8ec88f17b31bb1'] +checksums = ['68b2742233e747c462f781462a2a1e299dc6207401dac8f0bbb316f48565c2aa'] # Do not add help2man, it depends on Perl and we do not want Perl at SYSTEM level. # This results in not building man pages for the flex at SYSTEM level. From cf8911497a0953b3ef193d98f696d06a76e32082 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 7 Sep 2021 15:03:05 +0200 Subject: [PATCH 1194/9987] adding easyconfigs: HMMER2-2.3.2-GCC-10.3.0.eb --- .../h/HMMER2/HMMER2-2.3.2-GCC-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.3.0.eb b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..e143715f7b6 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'HMMER2' +version = '2.3.2' + +homepage = 'http://hmmer.org' +description = """HMMER is used for searching sequence databases for sequence homologs, + and for making sequence alignments.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['http://eddylab.org/software/hmmer'] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4'] + +postinstallcmds = ["cd %(installdir)s/bin && for cmd in $(ls); do mv ${cmd} ${cmd}2; done"] + +local_cmd_suffixes = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'index', 'pfam', 'search'] + +sanity_check_paths = { + 'files': ['bin/hmm%s2' % x for x in local_cmd_suffixes], + 'dirs': ['man'], +} + +sanity_check_commands = ["hmm%s2 -h" % x for x in local_cmd_suffixes] + +moduleclass = 'bio' From eb460df73d49f267f69e8bf6fda191c16184ed9e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 7 Sep 2021 15:16:09 +0200 Subject: [PATCH 1195/9987] adding easyconfigs: BLAST+-2.11.0-gompi-2021a.eb --- .../b/BLAST+/BLAST+-2.11.0-gompi-2021a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021a.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021a.eb new file mode 100644 index 00000000000..726f9d101b6 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021a.eb @@ -0,0 +1,57 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.11.0' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('PCRE', '8.44'), + ('Boost', '1.74.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.28'), +] + + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' From 82ad9696b0d14df50b568674b441197e64f46513 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 7 Sep 2021 16:40:35 +0200 Subject: [PATCH 1196/9987] Update boost dependency version to 1.76.0 --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021a.eb index 726f9d101b6..edd524d4568 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021a.eb @@ -31,7 +31,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.8'), ('PCRE', '8.44'), - ('Boost', '1.74.0'), + ('Boost', '1.76.0'), ('GMP', '6.2.1'), ('libpng', '1.6.37'), ('libjpeg-turbo', '2.0.6'), From 92a3c9aaae3e6160cfc06cc851366f9cad18c5fb Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 7 Sep 2021 18:42:34 +0200 Subject: [PATCH 1197/9987] adding easyconfigs: TOML-Fortran-0.2.2-GCC-10.2.0.eb, TOML-Fortran-0.2.2-iccifort-2020.4.304.eb --- .../TOML-Fortran-0.2.2-GCC-10.2.0.eb | 26 +++++++++++++++++++ .../TOML-Fortran-0.2.2-iccifort-2020.4.304.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb new file mode 100644 index 00000000000..f10a440e00a --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.2.2' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c3e5e1f57de00977b5e41d3a857ddb7e6b41f0b9116ed608cf89f295d9ef24c6'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['include/toml-f/GNU-10.2.0/tomlf.mod', 'lib/libtoml-f.a'], + 'dirs': ['include/toml-f/GNU-10.2.0', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..5b63c171848 --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.2.2' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c3e5e1f57de00977b5e41d3a857ddb7e6b41f0b9116ed608cf89f295d9ef24c6'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['include/toml-f/Intel-19.1.3.20200925/tomlf.mod', 'lib/libtoml-f.a'], + 'dirs': ['include/toml-f/Intel-19.1.3.20200925', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' From 5f6e21ea2062d2c9abf5066745061322a387b83c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 7 Sep 2021 19:11:30 +0200 Subject: [PATCH 1198/9987] adding easyconfigs: python-docx-0.8.11-GCCcore-10.2.0.eb --- .../python-docx-0.8.11-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..f5f38e76007 --- /dev/null +++ b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'python-docx' +version = '0.8.11' + +homepage = 'https://python-docx.readthedocs.io/en/latest/' +description = 'python-docx is a Python library for creating and updating Microsoft Word (.docx) files' + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1105d233a0956dd8dd1e710d20b159e2d72ac3c301041b95f4d4ceb3e0ebebc4'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('lxml', '4.6.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'docx'} + +moduleclass = 'tools' From 28660f9282d1afcedf92d3719cb247d850123907 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Sep 2021 20:41:09 +0200 Subject: [PATCH 1199/9987] improve sanity check for libctl Co-authored-by: Alex Domingo --- easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb b/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb index 847a07cf640..26199f5ebfa 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb @@ -19,8 +19,8 @@ dependencies = [('Guile', '2.2.4')] configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib'] + 'files': ['bin/gen-ctl-io', 'lib/libctl.a', 'lib/libctlgeom.a'], + 'dirs': ['include', 'share/libctl'] } moduleclass = 'chem' From 731734979b5e2482182d3a7ad3b7368c947cb024 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Sep 2021 20:41:40 +0200 Subject: [PATCH 1200/9987] use lib moduleclass for libctl Co-authored-by: Alex Domingo --- easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb b/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb index 26199f5ebfa..b2892d83883 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb @@ -23,4 +23,4 @@ sanity_check_paths = { 'dirs': ['include', 'share/libctl'] } -moduleclass = 'chem' +moduleclass = 'lib' From 22ce3e25b00f046ab878c3ddf79ea2e3866e0c68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Sep 2021 20:44:05 +0200 Subject: [PATCH 1201/9987] don't enable optarch toolchain option, already done by default --- easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb b/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb index b2892d83883..e20c9f0d5dd 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-4.0.0-intel-2020a.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/stevengj/libctl' description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations.""" toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = ['https://github.com/stevengj/libctl/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] From d0363ab99e8c0a58a14862c4932c88cc34c1e854 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Sep 2021 22:48:07 +0200 Subject: [PATCH 1202/9987] don't enable optarch toolchain option, already done by default --- easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb index 6ba80a1738f..d3bd657573b 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb @@ -8,7 +8,7 @@ description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) s developed at MIT to model electromagnetic systems.""" toolchain = {'name': 'intel', 'version': '2020a'} -toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': True, 'pic': True} +toolchainopts = {'usempi': True, 'opt': True, 'unroll': True, 'pic': True} source_urls = ['https://github.com/stevengj/meep/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] From 10fef757099f800bedeef55e2e1400f969416a4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Sep 2021 22:59:57 +0200 Subject: [PATCH 1203/9987] use more specific sanity_check_paths for Meep 1.4.3 --- easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb index d3bd657573b..db639ea5fe1 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.4.3-intel-2020a.eb @@ -34,8 +34,8 @@ configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib'] + 'files': ['bin/meep', 'include/meep.hpp', 'lib/libmeep.a', 'lib/libmeep.%s' % SHLIB_EXT, 'lib/pkgconfig/meep.pc'], + 'dirs': ['include/meep', 'share/meep'], } moduleclass = 'phys' From 8ed45ac0909b1c3acbb1bb668397d41032c6b0c2 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Wed, 8 Sep 2021 03:49:37 +0000 Subject: [PATCH 1204/9987] adding easyconfigs: DB-18.1.40-GCCcore-8.3.0.eb --- .../d/DB/DB-18.1.40-GCCcore-8.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..0c21b4fc363 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.32')] + +dependencies = [('OpenSSL', '1.1', '', True)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From e605cd5ae9f23b106998deb447d074ea4cef96f6 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Wed, 8 Sep 2021 03:50:55 +0000 Subject: [PATCH 1205/9987] adding easyconfigs: DB-18.1.40-GCCcore-8.2.0.eb --- .../d/DB/DB-18.1.40-GCCcore-8.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb new file mode 100644 index 00000000000..c78178d6997 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.31.1')] + +dependencies = [('OpenSSL', '1.1', '', True)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From 2201320e031466bb33aeda778fb5543214759196 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Wed, 8 Sep 2021 03:53:52 +0000 Subject: [PATCH 1206/9987] URL no longer accessible, moved to github --- .../easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb index 6485dfbc593..77a4b348b2d 100644 --- a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb +++ b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb @@ -3,20 +3,23 @@ easyblock = 'PackedBinary' name = 'ADMIXTURE' version = '1.3.0' -homepage = 'http://software.genetics.ucla.edu/admixture' +homepage = 'https://dalexander.github.io/admixture/' description = """ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.""" toolchain = SYSTEM -source_urls = ['http://software.genetics.ucla.edu/%(namelower)s/binaries/'] +source_urls = ['https://dalexander.github.io/admixture/binaries/'] sources = ['%(namelower)s_linux-%(version)s.tar.gz'] -checksums = ['41f209817a17981a717c9a4aa3d799da718ed080f3386e703927628c74ca6ca6'] +checksums = ['353e8b170c81f8d95946bf18bc78afda5d6bd32645b2a68658bd6781ff35703c'] + + +modextrapaths = {'PATH': 'admixture_linux-1.3.0'} sanity_check_paths = { - 'files': ['admixture', 'admixture32'], - 'dirs': [] + 'files': ['admixture_linux-1.3.0/admixture', 'admixture_linux-1.3.0/admixture32'], + 'dirs': ['admixture_linux-1.3.0'] } moduleclass = 'bio' From 091f506ee12f29260a72c19fbb52692c1ec69294 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Wed, 8 Sep 2021 03:59:11 +0000 Subject: [PATCH 1207/9987] adding easyconfigs: AdapterRemoval-2.3.2-foss-2020b.eb --- .../AdapterRemoval-2.3.2-foss-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-foss-2020b.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-foss-2020b.eb new file mode 100644 index 00000000000..17c26d5f01d --- /dev/null +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-foss-2020b.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'AdapterRemoval' +version = '2.3.2' + +github_account = 'MikkelSchubert' +homepage = 'https://github.com/%/(github_account)s/%(namelower)s' +description = """AdapterRemoval searches for and removes remnant adapter sequences + from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases + from the 3' end of reads following adapter removal.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ded7e08fb64e1b19f5c3de623de276d9cbb657a52b23a844ff74576d1b4f8d4'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] +} + +sanity_check_commands = [('%(name)s', '--version')] + +moduleclass = 'bio' From ff64fe0245af05528f780824f9230e1faefd6044 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Wed, 8 Sep 2021 03:59:39 +0000 Subject: [PATCH 1208/9987] adding easyconfigs: rclone-1.56.0.eb --- .../easyconfigs/r/rclone/rclone-1.56.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.56.0.eb diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.56.0.eb b/easybuild/easyconfigs/r/rclone/rclone-1.56.0.eb new file mode 100644 index 00000000000..5a754b38f99 --- /dev/null +++ b/easybuild/easyconfigs/r/rclone/rclone-1.56.0.eb @@ -0,0 +1,37 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'MakeCp' + +name = 'rclone' +version = '1.56.0' +#versionsuffix = '-amd64' + +homepage = 'https://rclone.org/' + +description = """ + Rclone is a command line program to sync files and directories to and from + a variety of online storage services +""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.%(name)s.org/v%(version)s/'] +sources = ['%(name)s-v%(version)s-linux-amd64.zip'] +#checksums = ['c52cbf3646a2d15765b87cf05fc3b2bca3b1d2782d4922046c597bd979e42720'] + +skipsteps = ['build'] + +files_to_copy = [ + (['rclone'], 'bin'), + (['rclone.1'], 'share/man/man1'), + (['README.*'], 'share/doc'), +] + +sanity_check_paths = { + 'files': ['bin/rclone', 'share/doc/README.txt', 'share/man/man1/rclone.1'], + 'dirs': [] +} + +sanity_check_commands = ['rclone --version'] + +moduleclass = 'tools' From 0d2c90eba4c4e21a87e454cda5ca636357972518 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 8 Sep 2021 14:53:20 +0200 Subject: [PATCH 1209/9987] Fix compilation option usage + Update style + Add patch doc --- .../i/InChI/InChI-1.06-GCC-10.3.0.eb | 29 ++++++++++++------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb index 347d03ced23..e7ce6ad45b0 100644 --- a/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb @@ -4,7 +4,9 @@ # # Authors:: Sebastien Moretti # -# Notes:: based on Fedora RPM spec file https://src.fedoraproject.org/rpms/inchi/blob/rawhide/f/inchi.spec +# Notes:: Based on Fedora RPM spec file https://src.fedoraproject.org/rpms/inchi/blob/rawhide/f/inchi.spec +# Patch made by Fedora to fix program name, linker and compilation options +# https://src.fedoraproject.org/rpms/inchi/blob/rawhide/f/inchi-rpm.patch ## easyblock = 'MakeCp' @@ -13,10 +15,10 @@ version = '1.06' # NOTE not in the license list of EB # software_license = 'IUPAC/InChI-Trust Licence' -software_license_urls = ['https://www.inchi-trust.org/download/%s/LICENCE.pdf' % version.replace('.', '')] +software_license_urls = ['https://www.inchi-trust.org/download/%(version_major)s%(version_minor)s/LICENCE.pdf'] docurls = [ - 'https://www.inchi-trust.org/download/%s/INCHI-1-DOC.zip' % version.replace('.', ''), - 'https://www.inchi-trust.org/download/%s/readme.txt' % version.replace('.', ''), + 'https://www.inchi-trust.org/download/%(version_major)s%(version_minor)s/INCHI-1-DOC.zip', + 'https://www.inchi-trust.org/download/%(version_major)s%(version_minor)s/readme.txt', ] homepage = 'https://www.inchi-trust.org/' @@ -26,8 +28,11 @@ data sources thus enabling easier linking of diverse data compilations.""" toolchain = {'name': 'GCC', 'version': '10.3.0'} -source_urls = ['https://www.inchi-trust.org/download/%s/' % version.replace('.', '')] -sources = ['INCHI-1-SRC.zip', 'INCHI-1-TEST.zip'] +source_urls = ['https://www.inchi-trust.org/download/%(version_major)s%(version_minor)s/'] +sources = [ + {'download_filename': 'INCHI-1-SRC.zip', 'filename': 'INCHI-%(version)s-SRC.zip'}, + {'download_filename': 'INCHI-1-TEST.zip', 'filename': 'INCHI-%(version)s-TEST.zip'}, +] patches = ['InChI-%(version)s.patch'] checksums = [ '4874e310c0f2f81b881e90dd0c534752e1b9421d7d92ccfb037710022c7e7efd', # INCHI-1-SRC.zip @@ -36,15 +41,19 @@ checksums = [ ] -# dos2unix may be useful to "clean" some files +# dos2unix may be another builddependency useful to "clean" some files builddependencies = [ ('make', '4.3'), ] build_cmd = 'cd INCHI_API/demos/inchi_main/gcc && ' -build_cmd += 'make -Wno-comment -Wno-parentheses -Wno-unused -Wno-unused-but-set-variable -j %(parallel)s && ' +build_cmd += 'SHARED_LINK_PARM="$OPTFLAGS" ' +build_cmd += 'OPTFLAGS="$OPTFLAGS -Wno-comment -Wno-parentheses -Wno-unused -Wno-unused-but-set-variable" ' +build_cmd += 'make -j %(parallel)s && ' build_cmd += 'cd - && cd INCHI_EXE/inchi-1/gcc && ' -build_cmd += 'make -Wno-comment -Wno-parentheses -Wno-unused -Wno-unused-but-set-variable' +build_cmd += 'LINKER_OPTIONS="$OPTFLAGS" ' +build_cmd += 'OPTFLAGS="$OPTFLAGS -Wno-comment -Wno-parentheses -Wno-unused -Wno-unused-but-set-variable" ' +build_cmd += 'make' files_to_copy = [ @@ -62,7 +71,7 @@ postinstallcmds = ["cd %(installdir)s/lib/ && rm -f libinchi.so.1 && " sanity_check_paths = { - 'files': ["bin/inchi-1", "LICENCE.pdf", "readme.txt"], + 'files': ["bin/inchi-1", "lib/libinchi.so", "LICENCE.pdf", "readme.txt"], 'dirs': ['lib', 'include'] } From a38c404e1c6e9d477e2f309b1888a9b5fd58b4c2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 8 Sep 2021 14:55:44 +0200 Subject: [PATCH 1210/9987] Do not use cp -a when not needed. --- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb | 4 ++-- .../easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb index c36bafa8196..fa55dd0f5a0 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-foss-2020b.eb @@ -70,7 +70,7 @@ components = [ { 'download_filename': 'stereo_chemical_props.txt', 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, - 'extract_cmd': "cp -a %s .", + 'extract_cmd': "cp %s .", }, ], 'patches': [ @@ -149,7 +149,7 @@ postinstallcmds = [ "chmod a+x %(installdir)s/bin/run_alphafold.py", "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", - "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, # run tests for run_alphafold.py script; # shouldn't do this in sanity check to avoid breaking use of --module-only "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb index 08ad07e9501..4d23d09d295 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.0-fosscuda-2020b.eb @@ -70,7 +70,7 @@ components = [ { 'download_filename': 'stereo_chemical_props.txt', 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, - 'extract_cmd': "cp -a %s .", + 'extract_cmd': "cp %s .", }, ], 'patches': [ @@ -149,7 +149,7 @@ postinstallcmds = [ "chmod a+x %(installdir)s/bin/run_alphafold.py", "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", - "cp -a %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, # run tests for run_alphafold.py script; # shouldn't do this in sanity check to avoid breaking use of --module-only "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " From 159b4840e2d4cddd2689470219a74ba6357c257e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 8 Sep 2021 15:02:23 +0200 Subject: [PATCH 1211/9987] adding easyconfigs: libharu-2.3.0-foss-2021a.eb --- .../l/libharu/libharu-2.3.0-foss-2021a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb new file mode 100644 index 00000000000..a4491d850a8 --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Modified for foss-2016b by: +# Adam Huffman +# The Francis Crick Institute +# foss-2020b modified by: +# Sebastien Moretti +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'http://libharu.org/' +description = """libHaru is a free, cross platform, open source library for generating PDF files.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/libharu/libharu/archive/'] +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [('libpng', '1.6.37', '', ('GCCcore', '10.3.0'))] + +builddependencies = [('CMake', '3.20.1', '', ('GCCcore', '10.3.0'))] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': ['if', 'include', 'lib'] +} + +moduleclass = 'lib' From 978f2a4d28300bd44f194a71a1e2f40f97240944 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 8 Sep 2021 15:09:47 +0200 Subject: [PATCH 1212/9987] adding easyconfigs: DB_File-1.856-GCCcore-10.3.0.eb --- .../d/DB_File/DB_File-1.856-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..880fe133479 --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.856' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['cdf9ba922fe39159d36b73f9fb815f5eaa375f3a3e4dc4de78e053b444cd66a9'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Perl', '5.32.1'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' From ee9eddeb1af1f68a308510e419a853712d5af13a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Sep 2021 18:20:19 +0200 Subject: [PATCH 1213/9987] drop enabling of separate_build_dir, already done by default by CMakeMake --- .../easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb | 2 -- .../t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb index f10a440e00a..53a8eb3a500 100644 --- a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-GCC-10.2.0.eb @@ -16,8 +16,6 @@ builddependencies = [ ('CMake', '3.18.4'), ] -separate_build_dir = True - sanity_check_paths = { 'files': ['include/toml-f/GNU-10.2.0/tomlf.mod', 'lib/libtoml-f.a'], 'dirs': ['include/toml-f/GNU-10.2.0', 'lib/pkgconfig', 'share'], diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb index 5b63c171848..2a70b5b6769 100644 --- a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.2.2-iccifort-2020.4.304.eb @@ -16,8 +16,6 @@ builddependencies = [ ('CMake', '3.18.4'), ] -separate_build_dir = True - sanity_check_paths = { 'files': ['include/toml-f/Intel-19.1.3.20200925/tomlf.mod', 'lib/libtoml-f.a'], 'dirs': ['include/toml-f/Intel-19.1.3.20200925', 'lib/pkgconfig', 'share'], From 9f2143171afb897340f4fbbc36834c828f09e610 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Wed, 8 Sep 2021 18:00:13 +0000 Subject: [PATCH 1214/9987] added checksum and version suffix --- .../r/rclone/rclone-1.56.0-amd64.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.56.0-amd64.eb diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.56.0-amd64.eb b/easybuild/easyconfigs/r/rclone/rclone-1.56.0-amd64.eb new file mode 100644 index 00000000000..3e117054360 --- /dev/null +++ b/easybuild/easyconfigs/r/rclone/rclone-1.56.0-amd64.eb @@ -0,0 +1,37 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'MakeCp' + +name = 'rclone' +version = '1.56.0' +versionsuffix = '-amd64' + +homepage = 'https://rclone.org/' + +description = """ + Rclone is a command line program to sync files and directories to and from + a variety of online storage services +""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.%(name)s.org/v%(version)s/'] +sources = ['%(name)s-v%(version)s-linux-%(versionsuffix)s.zip'] +checksums = ['d23d0c1f295a7399114b9a07fa987e7dc216dbe989b5d88530eb01d3c87c9c1f'] + +skipsteps = ['build'] + +files_to_copy = [ + (['rclone'], 'bin'), + (['rclone.1'], 'share/man/man1'), + (['README.*'], 'share/doc'), +] + +sanity_check_paths = { + 'files': ['bin/rclone', 'share/doc/README.txt', 'share/man/man1/rclone.1'], + 'dirs': [] +} + +sanity_check_commands = ['rclone --version'] + +moduleclass = 'tools' From 054e69b7ab916c77d06d005f8cba135f9613ba8a Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Wed, 8 Sep 2021 18:12:31 +0000 Subject: [PATCH 1215/9987] url without vars and switch to toolchain GCCcore --- .../AdapterRemoval-2.3.2-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b8134ccc3ef --- /dev/null +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ + +easyblock = 'ConfigureMake' + +name = 'AdapterRemoval' +version = '2.3.2' + +github_account = 'MikkelSchubert' +homepage = 'https://github.com/MikkelSchubert/adapterremoval' +description = """AdapterRemoval searches for and removes remnant adapter sequences + from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases + from the 3' end of reads following adapter removal.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ded7e08fb64e1b19f5c3de623de276d9cbb657a52b23a844ff74576d1b4f8d4'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] +} + +sanity_check_commands = [('%(name)s', '--version')] + +moduleclass = 'bio' From e389d3fa5ef7d1b3d043d87f3d288f878d2ffc49 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 9 Sep 2021 08:54:10 +0200 Subject: [PATCH 1216/9987] Clean dependencies toolchain --- easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb index a4491d850a8..c739f8feef7 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb @@ -28,9 +28,9 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/libharu/libharu/archive/'] sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] -dependencies = [('libpng', '1.6.37', '', ('GCCcore', '10.3.0'))] +dependencies = [('libpng', '1.6.37')] -builddependencies = [('CMake', '3.20.1', '', ('GCCcore', '10.3.0'))] +builddependencies = [('CMake', '3.20.1')] parallel = 1 From 4b5b2b51456f41c9d165e202751750c6cb3bb71e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 9 Sep 2021 15:38:20 +0800 Subject: [PATCH 1217/9987] adding easyconfigs: bashplotlib-0.6.5-GCCcore-10.3.0.eb --- .../bashplotlib-0.6.5-GCCcore-10.3.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/bashplotlib/bashplotlib-0.6.5-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/bashplotlib/bashplotlib-0.6.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bashplotlib/bashplotlib-0.6.5-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d495385be12 --- /dev/null +++ b/easybuild/easyconfigs/b/bashplotlib/bashplotlib-0.6.5-GCCcore-10.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'bashplotlib' +version = '0.6.5' + +homepage = "https://github.com/glamp/bashplotlib" +description = """bashplotlib is a python package and command line tool for making basic plots in the terminal. + It's a quick way to visualize data when you don't have a GUI.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b1b59be49d6254a5bd808919e0a23a75a703a02e7e84478edda765714e0bfaee'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From ccbe26d798451eaf2394f6981eb72f00696419b6 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 9 Sep 2021 09:59:10 +0200 Subject: [PATCH 1218/9987] Add checksum --- easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb index c739f8feef7..22528027934 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021a.eb @@ -11,7 +11,8 @@ # Modified for foss-2016b by: # Adam Huffman # The Francis Crick Institute -# foss-2020b modified by: +# +# Modified for foss-2020b by: # Sebastien Moretti # SIB Swiss Institute of Bioinformatics @@ -27,6 +28,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/libharu/libharu/archive/'] sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] dependencies = [('libpng', '1.6.37')] From ff8b0837a70a5509e067c037422acad11f205251 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 9 Sep 2021 11:57:40 +0200 Subject: [PATCH 1219/9987] adding easyconfigs: EMBOSS-6.6.0-foss-2021a.eb --- .../e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb new file mode 100644 index 00000000000..3eb8c921e8d --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb @@ -0,0 +1,58 @@ +# authors: Kenneth Hoste (Ghent University) +# George Tsouloupas +# Fotis Georgatos +# +# This work implements a part of the HPCBIOS project and is a component +# of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute +# foss-2021a modified by: +# Sebastien Moretti +# SIB Swiss Institute of Bioinformatics +easyblock = 'ConfigureMake' + +name = 'EMBOSS' +version = '6.6.0' + +homepage = 'http://emboss.sourceforge.net/' +description = """EMBOSS is 'The European Molecular Biology Open Software Suite' +. EMBOSS is a free Open Source software analysis package specially developed + for the needs of the molecular biology (e.g. EMBnet) user community.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'ftp://emboss.open-bio.org/pub/EMBOSS/', + 'ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0', +] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_disable-embossupdate.patch'] +checksums = [ + '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', # EMBOSS-6.6.0.tar.gz + '7e0a7deffd76f60093be9c5253605f2d6d2e3b0c2d3c9365035cc6bda43eb46c', # EMBOSS-6.6.0_disable-embossupdate.patch +] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('X11', '20210518'), + ('libharu', '2.3.0'), + ('Java', '11.0.2', '', True), +] + +configopts = " --with-hpdf=$EBROOTLIBHARU " + +# jemboss.jar does not build in a parallel build +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', + 'epcre', 'eplplot', 'ezlib', 'nucleus']] + + ['share/EMBOSS/jemboss/lib/jemboss.jar'], + 'dirs': [], +} + +moduleclass = 'bio' From 6ae5a69b56e60a31965900fbc91a422e576f2bd7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 9 Sep 2021 13:42:51 +0200 Subject: [PATCH 1220/9987] adding easyconfigs: LibUUID-1.0.3-GCCcore-8.3.0.eb --- .../l/LibUUID/LibUUID-1.0.3-GCCcore-8.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..75b312a23e8 --- /dev/null +++ b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-GCCcore-8.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'LibUUID' +version = '1.0.3' + +homepage = 'http://sourceforge.net/projects/libuuid/' + +description = """Portable uuid C library""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://raw.githubusercontent.com/karelzak/util-linux/stable/v2.32/libuuid/src', +] +sources = [ + SOURCELOWER_TAR_GZ, + {'filename': 'libuuid.sym', 'extract_cmd': 'cp %s %(builddir)s'}, +] +checksums = [ + '46af3275291091009ad7f1b899de3d0cea0252737550e7919d17237997db5644', # libuuid-1.0.3.tar.gz + '5932866797560bf5822c3340b64dff514afb6cef23a824f96991f8e9e9d29028', # libuuid.sym +] + +builddependencies = [ + ('binutils', '2.32'), +] + +preconfigopts = 'LDFLAGS="$LDFLAGS -Wl,--version-script=%(builddir)s/libuuid.sym"' + +sanity_check_paths = { + 'files': [ + 'include/uuid/uuid.h', + 'lib/libuuid.a', + 'lib/libuuid.%s' % SHLIB_EXT + ], + 'dirs': [], +} + +moduleclass = 'lib' From 2928704ece99f00632bb6549523354293f04d44f Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 9 Sep 2021 14:52:48 +0200 Subject: [PATCH 1221/9987] adding easyconfigs: CoinUtils-2.11.4-GCC-10.3.0.eb, Cbc-2.10.5-foss-2021a.eb, Cgl-0.60.3-foss-2021a.eb, Clp-1.17.6-foss-2021a.eb, Osi-0.108.6-GCC-10.3.0.eb --- .../c/Cbc/Cbc-2.10.5-foss-2021a.eb | 63 +++++++++++++++++++ .../c/Cgl/Cgl-0.60.3-foss-2021a.eb | 50 +++++++++++++++ .../c/Clp/Clp-1.17.6-foss-2021a.eb | 56 +++++++++++++++++ .../CoinUtils/CoinUtils-2.11.4-GCC-10.3.0.eb | 36 +++++++++++ .../o/Osi/Osi-0.108.6-GCC-10.3.0.eb | 49 +++++++++++++++ 5 files changed, 254 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb create mode 100644 easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb create mode 100644 easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb new file mode 100644 index 00000000000..5e534745fd7 --- /dev/null +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb @@ -0,0 +1,63 @@ +easyblock = "ConfigureMake" + +name = 'Cbc' +version = '2.10.5' + +homepage = "https://github.com/coin-or/Cbc" +description = """Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming +solver written in C++. It can be used as a callable library or using a +stand-alone executable.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['da1a945648679b21ba56b454b81e939451dc7951d9beb3c3e14f18f64dde6972'] + +builddependencies = [ + ('Autotools', '20210128'), + ('Doxygen', '1.9.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.4.0', '-metis'), + ('CoinUtils', '2.11.4'), + ('Osi', '0.108.6'), + ('Clp', '1.17.6'), + ('Cgl', '0.60.3'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# Use BLAS/LAPACK from OpenBLAS +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +# Use METIS AND MUMPS from EB +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +# Disable GLPK, dependencies have to be built with it as well +configopts += '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' +# Use Cgl from EB +configopts += '--with-cgl-lib="-lCgl" ' +configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2021a.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2021a.eb new file mode 100644 index 00000000000..43439554451 --- /dev/null +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.3-foss-2021a.eb @@ -0,0 +1,50 @@ +easyblock = "ConfigureMake" + +name = 'Cgl' +version = '0.60.3' + +homepage = "https://github.com/coin-or/Cgl" +description = """The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that +can be used with other COIN-OR packages that make use of cuts, such as, among +others, the linear solver Clp or the mixed integer linear programming solvers +Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or +communicate with a solver. It does not directly call a solver.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['cf11e3476d2182040cec412abb232d8bafa12ff5b619eca3b7b9ac1d220476c8'] + +builddependencies = [ + ('Autotools', '20210128'), + ('Doxygen', '1.9.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CoinUtils', '2.11.4'), + ('Osi', '0.108.6'), + ('Clp', '1.17.6'), +] + +# Use CoinUtils from EB +configopts = '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['lib/libCgl.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb new file mode 100644 index 00000000000..ba731d6f183 --- /dev/null +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'Clp' +version = '1.17.6' + +homepage = "https://github.com/coin-or/Clp" +description = """Clp (Coin-or linear programming) is an open-source linear programming solver. +It is primarily meant to be used as a callable library, but a basic, +stand-alone executable version is also available.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['f9cfcdd3db23bbc2d18b562012a7e25b99a40e8ce72dc296bd46dddb2970e12a'] + +builddependencies = [ + ('Autotools', '20210128'), + ('Doxygen', '1.9.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.4.0', '-metis'), + ('CoinUtils', '2.11.4'), + ('Osi', '0.108.6'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# Use BLAS/LAPACK from OpenBLAS +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +# Use METIS AND MUMPS from EB +configopts += '--with-metis-lib="-lmetis" ' # --with-metis-lib is ignored +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr -lscalapack" ' +# Disable GLPK because Clp requires headers from its sources +configopts += '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + +# Use Osi from EB +configopts += '--with-osi-lib="-lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['Clp', 'ClpSolver', 'OsiClp']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..ade743d252a --- /dev/null +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.4-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = "ConfigureMake" + +name = 'CoinUtils' +version = '2.11.4' + +homepage = "https://github.com/coin-or/CoinUtils" +description = """CoinUtils (Coin-OR Utilities) is an open-source collection of classes and +functions that are generally useful to more than one COIN-OR project.""" + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['1b24f8f6057661b3225d24f4e671527f53bf13aff66e06cbbbd4f20cc7d31dce'] + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +builddependencies = [ + ('Autotools', '20210128'), + ('Doxygen', '1.9.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/libCoinUtils.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCC-10.3.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCC-10.3.0.eb new file mode 100644 index 00000000000..44f3773ced0 --- /dev/null +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.6-GCC-10.3.0.eb @@ -0,0 +1,49 @@ +easyblock = "ConfigureMake" + +name = 'Osi' +version = '0.108.6' + +homepage = "https://github.com/coin-or/Osi" +description = """Osi (Open Solver Interface) provides an abstract base class to a generic linear +programming (LP) solver, along with derived classes for specific solvers. Many +applications may be able to use the Osi to insulate themselves from a specific +LP solver. That is, programs written to the OSI standard may be linked to any +solver with an OSI interface and should produce correct results. The OSI has +been significantly extended compared to its first incarnation. Currently, the +OSI supports linear programming solvers and has rudimentary support for integer +programming.""" + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['57ef3f0c97995bac647504aee0ed34d31f79033ece04cd2cb86b4645f0a552d8'] + +builddependencies = [ + ('Autotools', '20210128'), + ('Doxygen', '1.9.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CoinUtils', '2.11.4'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# Disable GLPK because Osi requires GLPK<=4.48 +configopts = '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + +sanity_check_paths = { + 'files': ['lib/libOsi.%s' % SHLIB_EXT, 'lib/libOsiCommonTests.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" From 85393636988af2e672b962b3b30359ba5ba8b6d0 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 9 Sep 2021 16:41:53 +0200 Subject: [PATCH 1222/9987] adding easyconfigs: RapidJSON-1.1.0-GCCcore-10.3.0.eb --- .../RapidJSON-1.1.0-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..a063946f946 --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +version = '1.1.0' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-compiler-errors.patch'] +checksums = [ + 'bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e', # v1.1.0.tar.gz + # %(name)s-%(version_major_minor)s.0_fix-compiler-errors.patch + '2e40ef6c46bf355feac16cd84faad5b7aca0ad54273117b85534b1b781f411c7', +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' From 23072321acd0728efaf36f7f4d5544e9d6a76012 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Sep 2021 22:10:09 +0200 Subject: [PATCH 1223/9987] strip out duplicate empty line from RapidJSON easyconfig --- .../easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb index a063946f946..39a23ca4bec 100644 --- a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb @@ -22,7 +22,6 @@ builddependencies = [ ('CMake', '3.20.1'), ] - sanity_check_paths = { 'files': ['lib/pkgconfig/%(name)s.pc'], 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], From 4b0987bf0c41a7021e82c82d18e99862e6d14689 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Thu, 9 Sep 2021 19:39:50 -0400 Subject: [PATCH 1224/9987] Delete rclone-1.56.0.eb removed previous eb file --- .../easyconfigs/r/rclone/rclone-1.56.0.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.56.0.eb diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.56.0.eb b/easybuild/easyconfigs/r/rclone/rclone-1.56.0.eb deleted file mode 100644 index 5a754b38f99..00000000000 --- a/easybuild/easyconfigs/r/rclone/rclone-1.56.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu - -easyblock = 'MakeCp' - -name = 'rclone' -version = '1.56.0' -#versionsuffix = '-amd64' - -homepage = 'https://rclone.org/' - -description = """ - Rclone is a command line program to sync files and directories to and from - a variety of online storage services -""" - -toolchain = SYSTEM - -source_urls = ['https://downloads.%(name)s.org/v%(version)s/'] -sources = ['%(name)s-v%(version)s-linux-amd64.zip'] -#checksums = ['c52cbf3646a2d15765b87cf05fc3b2bca3b1d2782d4922046c597bd979e42720'] - -skipsteps = ['build'] - -files_to_copy = [ - (['rclone'], 'bin'), - (['rclone.1'], 'share/man/man1'), - (['README.*'], 'share/doc'), -] - -sanity_check_paths = { - 'files': ['bin/rclone', 'share/doc/README.txt', 'share/man/man1/rclone.1'], - 'dirs': [] -} - -sanity_check_commands = ['rclone --version'] - -moduleclass = 'tools' From 24f4da5a2ad130d26e5d2eefa9c41c8ccf981c45 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Thu, 9 Sep 2021 19:42:01 -0400 Subject: [PATCH 1225/9987] Delete AdapterRemoval-2.3.2-foss-2020b.eb removed previous eb file --- .../AdapterRemoval-2.3.2-foss-2020b.eb | 39 ------------------- 1 file changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-foss-2020b.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-foss-2020b.eb deleted file mode 100644 index 17c26d5f01d..00000000000 --- a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-foss-2020b.eb +++ /dev/null @@ -1,39 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'ConfigureMake' - -name = 'AdapterRemoval' -version = '2.3.2' - -github_account = 'MikkelSchubert' -homepage = 'https://github.com/%/(github_account)s/%(namelower)s' -description = """AdapterRemoval searches for and removes remnant adapter sequences - from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases - from the 3' end of reads following adapter removal.""" - -toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'pic': True} - -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['3ded7e08fb64e1b19f5c3de623de276d9cbb657a52b23a844ff74576d1b4f8d4'] - -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), -] - -skipsteps = ['configure'] - -installopts = "PREFIX=%(installdir)s" - -runtest = 'test' - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': ['share'] -} - -sanity_check_commands = [('%(name)s', '--version')] - -moduleclass = 'bio' From 906e98981a0d4cc79086307088df896472457a4b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 10 Sep 2021 08:52:28 +0800 Subject: [PATCH 1226/9987] customize sanity check --- .../b/bashplotlib/bashplotlib-0.6.5-GCCcore-10.3.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/b/bashplotlib/bashplotlib-0.6.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bashplotlib/bashplotlib-0.6.5-GCCcore-10.3.0.eb index d495385be12..8d3edb2ea9e 100644 --- a/easybuild/easyconfigs/b/bashplotlib/bashplotlib-0.6.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/bashplotlib/bashplotlib-0.6.5-GCCcore-10.3.0.eb @@ -20,4 +20,11 @@ use_pip = True download_dep_fail = True sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/hist', 'bin/scatter'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["hist --help", "scatter --help"] + moduleclass = 'vis' From 5369436d1584534d1c1e1f370985a5d67b24cc59 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Fri, 10 Sep 2021 02:41:51 +0000 Subject: [PATCH 1227/9987] adding easyconfigs: FreeTDS-1.3.3-GCCcore-10.3.0.eb --- .../f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b95209b5e0e --- /dev/null +++ b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb @@ -0,0 +1,45 @@ +# easybuild easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +# +easyblock = 'ConfigureMake' + +name = 'FreeTDS' +version = '1.3.3' + +homepage = "https://www.freetds.org/" +description = """FreeTDS is a set of libraries for Unix and Linux that allows your programs to + natively talk to Microsoft SQL Server and Sybase databases.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.freetds.org/files/stable'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('libreadline', '8.1'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bsqldb', 'datacopy', 'defncopy', 'fisql', 'freebcp', + 'osql', 'tdspool', 'tsql']] + + ['etc/%s' % x for x in ['freetds.conf', 'locales.conf', 'pool.conf']] + + ['include/%s' % x for x in ['bkpublic.h', 'cstypes.h', 'odbcss.h', 'sqlfront.h', + 'syberror.h', 'tds_sysdep_public.h', 'cspublic.h', + 'ctpublic.h', 'sqldb.h', 'sybdb.h', 'sybfront.h']] + + ['lib/libct.%s' % x for x in ['a', 'la', 'so', 'so.4', 'so.4.0.0']] + + ['lib/libsybdb.%s' % x for x in ['a', 'la', 'so', 'so.5', 'so.5.1.0']], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share/doc', 'share/man', 'share/man/man5'], +} + +moduleclass = 'data' From 0de68477153a05d7775c4af453be83592614b124 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 10 Sep 2021 09:32:57 +0200 Subject: [PATCH 1228/9987] fixed style issues --- easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb | 2 +- easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb | 11 ++++++++--- 2 files changed, 9 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb index 5e534745fd7..e607dfe7c99 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb @@ -53,7 +53,7 @@ configopts += '--with-cgl-lib="-lCgl" ' configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' sanity_check_paths = { - 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in ['Cbc', 'CbcSolver', 'OsiCbc']], 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb index ba731d6f183..effc2008eaa 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb @@ -32,11 +32,16 @@ dependencies = [ # Use BLAS/LAPACK from OpenBLAS configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' + # Use METIS AND MUMPS from EB -configopts += '--with-metis-lib="-lmetis" ' # --with-metis-lib is ignored -configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh -lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr -lscalapack" ' +# --with-metis-lib is ignored +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh ' +configopts += '-lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr -lscalapack" ' + # Disable GLPK because Clp requires headers from its sources configopts += '--without-glpk ' + # Use CoinUtils from EB configopts += '--with-coinutils-lib="-lCoinUtils" ' configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' @@ -46,7 +51,7 @@ configopts += '--with-osi-lib="-lOsi" ' configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' sanity_check_paths = { - 'files': ['bin/clp'] + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['Clp', 'ClpSolver', 'OsiClp']], + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in ['Clp', 'ClpSolver', 'OsiClp']], 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } From 895ec44e1bc87e75fd5a0ae7b4299f251dd63216 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Sep 2021 09:39:20 +0200 Subject: [PATCH 1229/9987] Use Java/11 wrapper, rather than a specific version --- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb index 3eb8c921e8d..2b478b1b9ea 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb @@ -39,7 +39,7 @@ builddependencies = [('CMake', '3.20.1')] dependencies = [ ('X11', '20210518'), ('libharu', '2.3.0'), - ('Java', '11.0.2', '', True), + ('Java', '11', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " From bf2486e7b750dfd8b20fece4966125bd9781df53 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Sep 2021 09:50:19 +0200 Subject: [PATCH 1230/9987] adding easyconfigs: Chemaxon_Marvin-21.14.eb --- .../Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb new file mode 100644 index 00000000000..b54cae19c1b --- /dev/null +++ b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb @@ -0,0 +1,69 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +# rpm file extension does not look to be known yet: Unknown file type for file *.rpm (at easybuild/tools/filetools.py) +# easyblock = 'Rpm' +easyblock = 'Binary' + +name = 'Chemaxon_Marvin' +version = '21.14' + +homepage = 'https://chemaxon.com/products/marvin' +description = """Marvin suite is a chemically intelligent desktop toolkit built +to help you draw, edit, publish, render, import and export your chemical structures +and as well as allowing you to convert between various chemical and graphical file +formats. It is free for individual, academic and non-commercial use.""" + +# NOTE not in the license list of EB +# software_license = 'Proprietary: Personal, Commercial or Academic' +software_license_urls = ['https://www.chemaxon.com/marvin/license.html'] +docurls = [ + 'https://docs.chemaxon.com/display/docs/marvinsketch-user-s-guide.md', + 'https://docs.chemaxon.com/display/docs/marvinview-user-s-guide.md', + 'https://docs.chemaxon.com/display/docs/file-formats.md', +] + +toolchain = SYSTEM + +sources = ['marvin_linux_%(version)s.rpm'] +checksums = ['3102f30479a365758fd14ca5efcdacfe0624db80a35b146ba9a5d07e948bd8dc'] + + +osdependencies = [('rpm', 'cpio')] # for extracting rpm-files + +dependencies = [ + ('Java', '11'), +] + +extract_sources = False + +install_cmd = 'rpm2cpio ' + sources[0] + ' | cpio -idmv && ' +install_cmd += 'cd opt/chemaxon/marvinsuite/ && ' +install_cmd += 'chmod -x bin/*.bat && ' +install_cmd += 'cp -ar . %(installdir)s/' + +# plugins directory is empty +sanity_check_paths = { + 'files': ["bin/cxcalc", "bin/cxtrain", "bin/evaluate", "bin/molconvert", + "bin/msketch", "bin/mview", "EULA.html", "README"], + 'dirs': ['lib'] +} + +sanity_check_commands = ["molconvert"] + +# You need a key/license file to fully activate Chemaxon Marvin +# +# COMMERCIAL +# For commercial use please contact sales@chemaxon.com +# NON-COMMERCIAL +# For personal use get a key to be renewed every 2 months at https://chemaxon.com/products/marvin/download +# For academic use get a key for research or educational purposes at https://chemaxon.com/academic-license +# +# The license file "license.cxl" has to be placed in $HOME/.chemaxon/ + +moduleclass = 'chem' From 56e4fa174addaa47b842c6ed890869228b4cea44 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 10 Sep 2021 10:25:25 +0200 Subject: [PATCH 1231/9987] fix typo in sources filename --- easybuild/easyconfigs/r/rclone/rclone-1.56.0-amd64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.56.0-amd64.eb b/easybuild/easyconfigs/r/rclone/rclone-1.56.0-amd64.eb index 3e117054360..399444446e3 100644 --- a/easybuild/easyconfigs/r/rclone/rclone-1.56.0-amd64.eb +++ b/easybuild/easyconfigs/r/rclone/rclone-1.56.0-amd64.eb @@ -16,7 +16,7 @@ description = """ toolchain = SYSTEM source_urls = ['https://downloads.%(name)s.org/v%(version)s/'] -sources = ['%(name)s-v%(version)s-linux-%(versionsuffix)s.zip'] +sources = ['%(name)s-v%(version)s-linux%(versionsuffix)s.zip'] checksums = ['d23d0c1f295a7399114b9a07fa987e7dc216dbe989b5d88530eb01d3c87c9c1f'] skipsteps = ['build'] From ac27548b618a51774b58a5b7df75382305ead627 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 10 Sep 2021 10:35:34 +0200 Subject: [PATCH 1232/9987] switch AdapterRemoval from GCCcore 10.2.0 to GCC 10.2.0 --- ...2-GCCcore-10.2.0.eb => AdapterRemoval-2.3.2-GCC-10.2.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/a/AdapterRemoval/{AdapterRemoval-2.3.2-GCCcore-10.2.0.eb => AdapterRemoval-2.3.2-GCC-10.2.0.eb} (94%) diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.2.0.eb similarity index 94% rename from easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCCcore-10.2.0.eb rename to easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.2.0.eb index b8134ccc3ef..310e4f767de 100644 --- a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-10.2.0.eb @@ -4,15 +4,15 @@ easyblock = 'ConfigureMake' name = 'AdapterRemoval' version = '2.3.2' -github_account = 'MikkelSchubert' homepage = 'https://github.com/MikkelSchubert/adapterremoval' description = """AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal.""" -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'pic': True} +github_account = 'MikkelSchubert' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['3ded7e08fb64e1b19f5c3de623de276d9cbb657a52b23a844ff74576d1b4f8d4'] From 323c0b438e12959c6f965d294a75269d2772b64e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Sep 2021 10:37:55 +0200 Subject: [PATCH 1233/9987] Clarify where to get download files and license + Clarify why *easyblock = "Rpm"* cannot be used --- .../easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb index b54cae19c1b..d7523baf6be 100644 --- a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb +++ b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb @@ -6,8 +6,8 @@ # ## -# rpm file extension does not look to be known yet: Unknown file type for file *.rpm (at easybuild/tools/filetools.py) -# easyblock = 'Rpm' +# Cannot use *easyblock = 'Rpm'* because the RPM misses some fields: +# Summary and License fields must be present in package: (main package) easyblock = 'Binary' name = 'Chemaxon_Marvin' @@ -30,10 +30,10 @@ docurls = [ toolchain = SYSTEM +# Download and license at https://chemaxon.com/products/marvin sources = ['marvin_linux_%(version)s.rpm'] checksums = ['3102f30479a365758fd14ca5efcdacfe0624db80a35b146ba9a5d07e948bd8dc'] - osdependencies = [('rpm', 'cpio')] # for extracting rpm-files dependencies = [ From e2b852d71182db58aa75ac45ce48738a5ebe4b02 Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Fri, 10 Sep 2021 11:29:06 +0200 Subject: [PATCH 1234/9987] Update easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb index effc2008eaa..70641c88028 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.6-foss-2021a.eb @@ -51,7 +51,7 @@ configopts += '--with-osi-lib="-lOsi" ' configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' sanity_check_paths = { - 'files': ['bin/clp'] + ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in ['Clp', 'ClpSolver', 'OsiClp']], + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Clp', 'ClpSolver', 'OsiClp']], 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } From 4141aee5b92030efadc4a084715aca48f5ef7a95 Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Fri, 10 Sep 2021 11:29:13 +0200 Subject: [PATCH 1235/9987] Update easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb index e607dfe7c99..99baf18d76b 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2021a.eb @@ -53,7 +53,7 @@ configopts += '--with-cgl-lib="-lCgl" ' configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' sanity_check_paths = { - 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Cbc', 'CbcSolver', 'OsiCbc']], 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] } From c219ec105e0beb6a181a2b0844679d85883c661f Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 10 Sep 2021 11:31:10 +0200 Subject: [PATCH 1236/9987] adding easyconfigs: WildMagic-5.17-GCCcore-10.3.0.eb --- .../WildMagic-5.17-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..669dcdf5ca3 --- /dev/null +++ b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = "MakeCp" + +name = 'WildMagic' +version = '5.17' + +homepage = "https://www.geometrictools.com/index.html" +description = """Wild Magic 5.17""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.geometrictools.com/Downloads/'] +sources = ['WildMagic5p17.zip'] +checksums = ['b2caf7aa0c5309eb40965ed26439388dc1c93eb632312b40573f83e4746a9ecf'] + +dependencies = [ + ('freeglut', '3.2.1'), +] + +buildopts = "CFG=ReleaseDynamic -f makefile.wm5" + +files_to_copy = [ + (['SDK/Library/ReleaseDynamic/*'], 'lib'), + (['SDK/Include/*'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/libWm5%s.%s' % (x, SHLIB_EXT) for x in [ + 'Core', 'Applications', 'Graphics', 'Imagics', 'Mathematics', 'Physics' + ]], + 'dirs': ['include', 'lib'], +} + +moduleclass = "math" From 4894170a9105e6cb889a96fecd545a46620149b3 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Sep 2021 12:20:33 +0200 Subject: [PATCH 1237/9987] adding easyconfigs: Boost.Python-1.76.0-GCC-10.3.0.eb --- .../Boost.Python-1.76.0-GCC-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.76.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.76.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.76.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..d16abdfa5c0 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.76.0-GCC-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.76.0' + +homepage = 'https://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-1.71.0_fix-Python3.patch'] +checksums = [ + '7bd7ddceec1a1dfdcbdb3e609b60d01739c38390a5f956385a12f3122049f0ca', # boost_1_76_0.tar.gz + '60e3aede2f444a3855f4efed94d1de5c2887983876e0fae21f6ca5cfdc53ea96', # Boost-1.71.0_fix-Python3.patch +] + +multi_deps = {'Python': ['3.9.5']} + +dependencies = [('Boost', version)] + +only_python_bindings = True + +moduleclass = 'lib' From 2d5917a03663003463be12d0714d050aa8db5990 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Sep 2021 13:14:05 +0200 Subject: [PATCH 1238/9987] TensorFlow 2.4.1: add UnZip builddependency --- .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 1 + .../t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index b3b7e485294..ed118dbbdd0 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py + ('UnZip', '6.0.0'), ] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb index 55b550b6e69..73707cb8436 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb @@ -16,6 +16,7 @@ builddependencies = [ # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.23.0', '-nodocs'), ('pybind11', '2.4.3', versionsuffix), + ('UnZip', '6.0.0'), ] dependencies = [ ('cuDNN', '7.6.4.38'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 7693cdd06a7..a9a6494a69e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py + ('UnZip', '6.0.0'), ] dependencies = [ ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), From 4766784f9d5ecc479a12a7b0fa553068811963d8 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Sep 2021 13:14:30 +0200 Subject: [PATCH 1239/9987] TensorFlow 2.5.0: add UnZip builddependency --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 015fdb2f972..edb84d52b2c 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py + ('UnZip', '6.0.0'), ] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index bafbef6444f..230444abd3e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -16,6 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py + ('UnZip', '6.0.0'), ] dependencies = [ ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), From 99412a7e97aaad133b6276c410428e4819dab34a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Sep 2021 13:14:43 +0200 Subject: [PATCH 1240/9987] TensorFlow 2.6.0: add UnZip builddependency --- .../t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index fb1e4cc8989..27e25289f1e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -16,6 +16,7 @@ builddependencies = [ # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.32.0', '-nodocs'), ('pybind11', '2.6.2'), + ('UnZip', '6.0.0'), ] dependencies = [ ('CUDA', '11.3.1', '', True), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb index f80b5a9899e..99e6d8c5fc0 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb @@ -15,6 +15,7 @@ builddependencies = [ # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.32.0', '-nodocs'), ('pybind11', '2.6.2'), + ('UnZip', '6.0.0'), ] dependencies = [ ('Python', '3.9.5'), From b8f45df8e87846430e9c3f75431abcbf7cdcf260 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Sep 2021 13:20:35 +0200 Subject: [PATCH 1241/9987] TensorFlow 2.6.0: add UnZip builddependency --- .../t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index 27e25289f1e..98a76cbbd0d 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -16,7 +16,7 @@ builddependencies = [ # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.32.0', '-nodocs'), ('pybind11', '2.6.2'), - ('UnZip', '6.0.0'), + ('UnZip', '6.0'), ] dependencies = [ ('CUDA', '11.3.1', '', True), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb index 99e6d8c5fc0..6d0178ed29e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb @@ -15,7 +15,7 @@ builddependencies = [ # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.32.0', '-nodocs'), ('pybind11', '2.6.2'), - ('UnZip', '6.0.0'), + ('UnZip', '6.0'), ] dependencies = [ ('Python', '3.9.5'), From a0fb13d81f9af169d310dba259664a896a51bc8f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Sep 2021 13:21:23 +0200 Subject: [PATCH 1242/9987] TensorFlow 2.5.0: add UnZip builddependency --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 2 +- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index edb84d52b2c..b8e0b20e478 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py - ('UnZip', '6.0.0'), + ('UnZip', '6.0'), ] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 230444abd3e..7c571141ead 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py - ('UnZip', '6.0.0'), + ('UnZip', '6.0'), ] dependencies = [ ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), From 4a652848ef774c650ad61142984cd53dc521c3d2 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Sep 2021 13:21:50 +0200 Subject: [PATCH 1243/9987] TensorFlow 2.4.1: add UnZip builddependency --- .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 2 +- .../TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index ed118dbbdd0..2c463ccdf36 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py - ('UnZip', '6.0.0'), + ('UnZip', '6.0'), ] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb index 73707cb8436..e6fb64444a9 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb @@ -16,7 +16,7 @@ builddependencies = [ # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.23.0', '-nodocs'), ('pybind11', '2.4.3', versionsuffix), - ('UnZip', '6.0.0'), + ('UnZip', '6.0'), ] dependencies = [ ('cuDNN', '7.6.4.38'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index a9a6494a69e..34a3a4c37f9 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -16,7 +16,7 @@ builddependencies = [ ('git', '2.28.0', '-nodocs'), ('pybind11', '2.6.0'), ('pkgconfig', '1.5.1', '-python'), # For h5py - ('UnZip', '6.0.0'), + ('UnZip', '6.0'), ] dependencies = [ ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), From e69011fc3a1429b917e716cf08fd1dbfe1f86a20 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 Sep 2021 13:31:45 +0200 Subject: [PATCH 1244/9987] Newer WIEN2k versions depend on Python --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb index 082ec3712d0..dfa95226051 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb @@ -13,6 +13,7 @@ sources = ['%(name)s_%(version)s.tar'] checksums = ['32590778440a9280322bf2dc0d63f4f42a9fc48814fa6b8b7ee2d199c94bed11'] dependencies = [ + ('Python', '3.9.5'), ('Perl', '5.32.1'), ('DFT-D3', '3.2.0'), ('ELPA', '2021.05.001'), From 7c1aea35d9bb78245731bf1196f970c713fbf984 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 10 Sep 2021 13:29:55 +0100 Subject: [PATCH 1245/9987] add JASPAR2020 to R-bundle-Bioconductor 3.13 --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index 05c3d062d71..b13d518ab71 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -1047,6 +1047,9 @@ exts_list = [ ('GenABEL', '1.8-0', { 'checksums': ['434fc806b918738ec67171a37a47099d1706332819317e368fe0ccb8f149a469'], }), + ('JASPAR2020', '0.99.10', { + 'checksums': ['b9b92d141a317ebb32a14708229f6b82522ceeb5f1b88360d93b0a7cfe30375b'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 9d61067d11ad129dce6221cfe023b8bfde4d5f1a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Sep 2021 14:49:45 +0200 Subject: [PATCH 1246/9987] adding easyconfigs: scGeneFit-1.0.2-foss-2021a.eb --- .../s/scGeneFit/scGeneFit-1.0.2-foss-2021a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/scGeneFit/scGeneFit-1.0.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/scGeneFit/scGeneFit-1.0.2-foss-2021a.eb b/easybuild/easyconfigs/s/scGeneFit/scGeneFit-1.0.2-foss-2021a.eb new file mode 100644 index 00000000000..8348cb955c0 --- /dev/null +++ b/easybuild/easyconfigs/s/scGeneFit/scGeneFit-1.0.2-foss-2021a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'scGeneFit' +version = '1.0.2' + +homepage = 'https://github.com/solevillar/scGeneFit-python' +description = "Python code for genetic marker selection using linear programming." + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['0912def5dfef0a5dbc8fce054acb7c7331c303f0b02f36007ff7b8b8da847132'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('scikit-learn', '0.24.2'), +] + +download_dep_fail = True +use_pip = True + +# correct name is scikit-learn, see also https://pypi.org/project/sklearn +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' From b6171eeda8f0c29af41421123744768ba8b84ffd Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Sep 2021 15:22:52 +0200 Subject: [PATCH 1247/9987] adding easyconfigs: GD-2.73-GCCcore-10.3.0.eb --- .../g/GD/GD-2.73-GCCcore-10.3.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..5cb5845e82f --- /dev/null +++ b/easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb @@ -0,0 +1,56 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester (The Francis Crick Insitute, London, UK) +# Update to v2.71: Alex Domingo (Vrije Universiteit Brussel) +# Update to v2.73: Sebastien Moretti (SIB Swiss Institute of Bioinformatics) +# + +easyblock = 'Bundle' + +name = 'GD' +version = '2.73' + +homepage = 'https://github.com/lstein/Perl-GD' +description = """GD.pm - Interface to Gd Graphics Library""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Perl', '5.32.1'), + ('libgd', '2.3.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::PkgConfig', '1.16', { + 'source_tmpl': 'ExtUtils-PkgConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e'], + }), + (name, version, { + 'source_tmpl': 'release_%(version_major)s_%(version_minor)s.tar.gz', + 'source_urls': ['https://github.com/lstein/Perl-GD/archive/'], + 'checksums': ['55a666ef35588eeb89bea6936a335b711f9356c9c1b737bea164fb8d1b15061f'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bdf2gdfont.pl', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s'], +} + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +moduleclass = 'bio' From ca592c8dc51035e17aebc54c5c83057b323e21cd Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 10 Sep 2021 15:38:15 +0200 Subject: [PATCH 1248/9987] Add patch to SRC_lapw0 Makefile.orig to make it build lapw0_mpi correctly with libxc. --- .../w/WIEN2k/WIEN2k-21.1-intel-2021a.eb | 6 +++- .../WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch | 30 +++++++++++++++++++ 2 files changed, 35 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb index dfa95226051..19190815ace 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb @@ -10,7 +10,11 @@ WIEN2k is an all-electron scheme including relativistic effects and has many fea toolchain = {'name': 'intel', 'version': '2021a'} sources = ['%(name)s_%(version)s.tar'] -checksums = ['32590778440a9280322bf2dc0d63f4f42a9fc48814fa6b8b7ee2d199c94bed11'] +patches = ['%(name)s-%(version)s_fix_libxc_for_lapw0_mpi.patch'] +checksums = [ + '32590778440a9280322bf2dc0d63f4f42a9fc48814fa6b8b7ee2d199c94bed11', # WIEN2k_21.1.tar + '1cc480a4824d9185ad5918dfc68c47bcb7826114626c8133d573be901bbdca84', # WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch +] dependencies = [ ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch new file mode 100644 index 00000000000..473da9ef378 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch @@ -0,0 +1,30 @@ +The Makefile.orig lapw0 is not updated according to how the Makefile works. +That causes a build failure for lapw0_mpi with libxc + +Åke Sandgren, 20210910 +diff -ru wien2k.orig/SRC_lapw0/Makefile.orig wien2k/SRC_lapw0/Makefile.orig +--- wien2k.orig/SRC_lapw0/Makefile.orig 2021-03-13 09:40:10.023772496 +0100 ++++ wien2k/SRC_lapw0/Makefile.orig 2021-09-10 14:53:07.875144996 +0200 +@@ -55,7 +55,9 @@ + #-------------- loader options ------------- + LDFLAGS = _LDFLAGS_ + R_LIBS = $(FFTW_LIBS) _R_LIBS_ $(LIBXC_LIBS) ++RR_LIBS = $(FFTW_LIBS) $(R_LIBS) $(LIBXC_LIBS) + RP_LIBS = $(FFTW_PLIBS) _RP_LIBS_ ++RPP_LIBS = $(FFTW_PLIBS) $(FFTW_LIBS) $(RP_LIBS) $(LIBXC_LIBS) + + ############################################################################### + # End of user defined variables # +@@ -128,10 +130,10 @@ + #.............................................................................. + + $(S_EXEC): $(OBJS) +- $(FORT) -o $(S_EXEC) $(OBJS) $(LDFLAGS) $(R_LIBS) ++ $(FORT) -o $(S_EXEC) $(OBJS) $(LDFLAGS) $(RR_LIBS) + + $(P_EXEC): $(OBJS) +- $(FORT) -o $(P_EXEC) $(OBJS) $(LDFLAGS) $(RP_LIBS) ++ $(FORT) -o $(P_EXEC) $(OBJS) $(LDFLAGS) $(RPP_LIBS) + + # sequential + keep_s_files: From e01001c2267a9a96bd69600c844d7fd175c8b16e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Sep 2021 17:23:25 +0200 Subject: [PATCH 1249/9987] adding easyconfigs: XML-LibXML-2.0207-GCCcore-10.3.0.eb --- .../XML-LibXML-2.0207-GCCcore-10.3.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1ce2f4c107a --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0207' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Perl', '5.32.1'), + ('libxml2', '2.9.10'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1010', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['efc121f40bd7a0f62f8ec9b8bc70f7f5409d81cd705e37008596c8efc4452b01'], + }), + ('Alien::Base', '2.41', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['aaa738117131b016f17f103b167deae2588f03bb72aa3fe15cbb1bad344cf2a4'], + }), + ('Alien::Libxml2', '0.17', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['73b45244f0b5c36e5332c33569b82a1ab2c33e263f1d00785d2003bcaec68db3'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['903436c9859875bef5593243aae85ced329ad0fb4b57bbf45975e32547c50c15'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' From 6e98ab419dcfbeb11b0d0344e9c89f368e71c71e Mon Sep 17 00:00:00 2001 From: Guillaume Moutier Date: Fri, 10 Sep 2021 11:31:43 -0400 Subject: [PATCH 1250/9987] fix checksum for lhs R extension --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 94ed0c58004..911665c64da 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -1493,7 +1493,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.1', { 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index f0423aca3a9..2f3e45e81f2 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -1502,7 +1502,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.1', { 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index af85bdbea5a..2629887653a 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -1521,7 +1521,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 2fa4574e87b..2bd26acea1b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -1525,7 +1525,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index 10ac6803faa..aa820215281 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -1533,7 +1533,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index a4b74635831..caaf8729952 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -1543,7 +1543,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index 99150e5d53e..58787d6eeb2 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -1549,7 +1549,7 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc'], + 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], From 1906a9b681ebed4fb93e0f2d0811453fc67d5c5d Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Fri, 10 Sep 2021 18:12:59 +0000 Subject: [PATCH 1251/9987] injected checksums and removed OS dependency --- .../easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb index b95209b5e0e..5196f6ce4a7 100644 --- a/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb @@ -1,9 +1,5 @@ # easybuild easyconfig # -# John Dey -# -# Fred Hutchinson Cancer Research Center - Seattle Washington - US -# easyblock = 'ConfigureMake' name = 'FreeTDS' @@ -17,7 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://www.freetds.org/files/stable'] sources = [SOURCELOWER_TAR_GZ] -checksums = [] +checksums = ['a21a0aa351185049e11e237a795a61e3ca68d2e798259b3b5ea4a9797d5a5535'] builddependencies = [ ('binutils', '2.36.1'), @@ -28,7 +24,7 @@ dependencies = [ ('libreadline', '8.1'), ] -osdependencies = [OS_PKG_OPENSSL_DEV] +# osdependencies = [OS_PKG_OPENSSL_DEV] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bsqldb', 'datacopy', 'defncopy', 'fisql', 'freebcp', From c9e59109519f824c9b6be7075f45ea4411112610 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Sep 2021 20:20:39 +0200 Subject: [PATCH 1252/9987] adding easyconfigs: scanpy-1.8.1-foss-2021a.eb, Seaborn-0.11.2-foss-2021a.eb, leidenalg-0.8.7-foss-2021a.eb --- .../l/leidenalg/leidenalg-0.8.7-foss-2021a.eb | 51 +++++++++++++ .../s/Seaborn/Seaborn-0.11.2-foss-2021a.eb | 28 +++++++ .../s/scanpy/scanpy-1.8.1-foss-2021a.eb | 73 +++++++++++++++++++ 3 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.7-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.7-foss-2021a.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.7-foss-2021a.eb new file mode 100644 index 00000000000..f5ea670b55d --- /dev/null +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.7-foss-2021a.eb @@ -0,0 +1,51 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'leidenalg' +version = '0.8.7' + +homepage = 'https://github.com/vtraag/leidenalg' +description = """Implementation of the Leiden algorithm for various quality +functions to be used with igraph in Python.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('PyYAML', '5.4.1'), + ('Bison', '3.7.6'), + ('libtool', '2.4.6'), + ('flex', '2.6.4'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('igraph', '0.9.4'), + ('python-igraph', '0.9.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ddt', '1.4.2', { + 'checksums': ['64a67366a2715e636b88694cc6075cc02db292f01098b8e385397c894d395378'], + }), + (name, version, { + 'checksums': ['4cde1c51bc110e567b63a5f17f4321ff4073d79c67e8c3c7d956f07dc90ff7be'], + 'preinstallopts': "python setup.py build --use-pkg-config && ", + }), +] + +sanity_check_commands = [ + # tests require that 'leidenalg' Python module is available, + # so needs to be run after installation + "cd %(builddir)s/leidenalg/leidenalg-%(version)s && python setup.py test --use-pkg-config", + "python -c 'import leidenalg; import igraph as ig; " + "leidenalg.find_partition(ig.Graph.Erdos_Renyi(100, 0.1), " + "leidenalg.ModularityVertexPartition)'", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.2-foss-2021a.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.2-foss-2021a.eb new file mode 100644 index 00000000000..9166744daa0 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.2-foss-2021a.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.11.2' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cf45e9286d40826864be0e3c066f98536982baf701a7caa386511792d61ff4f6'] + +dependencies = [ + ('Python', '3.9.5'), + ('matplotlib', '3.4.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2021a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2021a.eb new file mode 100644 index 00000000000..d6c2584f92e --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.1-foss-2021a.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.8.1' + +homepage = 'https://scanpy.readthedocs.io/en/stable/' +description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), + ('networkx', '2.5.1'), + ('numba', '0.53.1'), + ('PyTables', '3.6.1'), + ('statsmodels', '0.12.2'), + ('scikit-learn', '0.24.2'), + ('Seaborn', '0.11.2'), + ('tqdm', '4.61.2'), + ('leidenalg', '0.8.7'), +] + +use_pip = True + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + # anndata 0.7.6 needs xlrd<2.0 + ('xlrd', '1.2.0', { + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('anndata', '0.7.6', { + 'checksums': ['a3cc67bba9a4cd4b5984aec64c4f577c2d5a4695f4064027f8e6a9dac1f508b2'], + }), + ('pynndescent', '0.5.4', { + 'checksums': ['221124cbad8e3cf3ed421a4089d80ac5a29d3215e76cb49effc1df887533d2a8'], + }), + ('umap-learn', '0.5.1', { + 'modulename': 'umap', + 'checksums': ['3e3e5e526109866012a9da79f423c922edc379c6cac9bf65ea08fbb9dd93ff3a'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.4', { + 'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'], + }), + (name, version, { + 'checksums': ['1b8603a868d783bd6c18c8db763a450153feefc8daed862c440749790d47c654'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "natsort --help", + "scanpy --help", +] + +moduleclass = 'bio' From 64677cab42569e1996b4c4ec3826e002258f165d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Sep 2021 21:57:25 +0200 Subject: [PATCH 1253/9987] accept both valid SHA256 checksums for lhs 1.1.1 extension in recent R easyconfigs --- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 3 ++- 7 files changed, 14 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 911665c64da..d8bbd8572a8 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -1493,7 +1493,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.1', { 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 2f3e45e81f2..9e5053e29bb 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -1502,7 +1502,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.1', { 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 2629887653a..e3dbbcb551d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -1521,7 +1521,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 2bd26acea1b..9d9ad1166d3 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -1525,7 +1525,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index aa820215281..d1f3feab30c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -1533,7 +1533,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index caaf8729952..2f1b150a616 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -1543,7 +1543,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index 58787d6eeb2..6a6012353a2 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -1549,7 +1549,8 @@ exts_list = [ 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], }), ('lhs', '1.1.1', { - 'checksums': ['00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2'], + 'checksums': [('903e9f2adde87f6f9ad41dd52ff83d28a645dba69934c7535142cb48f10090dc', + '00278a65b18c86799301d27c55e3d32c6c307aed745ea69c9b96bbb1d0a352c2')], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], From 8cf41c8dd3968835ce0d002b00fd51f092ba73e2 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 11 Sep 2021 14:15:52 +0100 Subject: [PATCH 1254/9987] Update easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb Co-authored-by: SebastianAchilles --- .../s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb index e563ec41fc4..7c95541301b 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb @@ -9,7 +9,10 @@ description = "Bundle of Python packages for scientific software" toolchain = {'name': 'foss', 'version': '2021.07'} toolchainopts = {'pic': True, 'lowopt': True} -builddependencies = [('hypothesis', '6.14.6')] +builddependencies = [ + ('hypothesis', '6.14.6'), + ('UnZip', '6.0'), +] dependencies = [ ('Python', '3.9.6'), From 414998f484aad3e51b632751c06ac0d8a99b8ec3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 11 Sep 2021 16:13:38 +0200 Subject: [PATCH 1255/9987] Fix Fortran system call stderr redirection to use bourneshell syntax. No one uses (t)csh any longer. --- .../w/WIEN2k/WIEN2k-21.1-intel-2021a.eb | 9 +++-- ...k-21.1_fix_system_stderr_redirection.patch | 34 +++++++++++++++++++ 2 files changed, 41 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_system_stderr_redirection.patch diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb index 19190815ace..c1dda1b9ec7 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb @@ -10,10 +10,15 @@ WIEN2k is an all-electron scheme including relativistic effects and has many fea toolchain = {'name': 'intel', 'version': '2021a'} sources = ['%(name)s_%(version)s.tar'] -patches = ['%(name)s-%(version)s_fix_libxc_for_lapw0_mpi.patch'] +patches = [ + '%(name)s-%(version)s_fix_libxc_for_lapw0_mpi.patch', + '%(name)s-%(version)s_fix_system_stderr_redirection.patch', +] checksums = [ '32590778440a9280322bf2dc0d63f4f42a9fc48814fa6b8b7ee2d199c94bed11', # WIEN2k_21.1.tar '1cc480a4824d9185ad5918dfc68c47bcb7826114626c8133d573be901bbdca84', # WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch + # WIEN2k-21.1_fix_system_stderr_redirection.patch + 'd42d0f3ac13ce3ea81817b81b412f0e944d135b94f8d371fd42620735e81fee5', ] dependencies = [ @@ -28,7 +33,7 @@ dependencies = [ osdependencies = [('glibc-devel', 'libc6-dev')] # required for libpthread.a # remote = 'pbsssh' -wien_mpirun = 'mpirun -np _NP_ _EXEC_' +wien_mpirun = 'srun -n_NP_ _EXEC_' use_remote = False mpi_remote = False wien_granularity = True diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_system_stderr_redirection.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_system_stderr_redirection.patch new file mode 100644 index 00000000000..ea32e0b3087 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_system_stderr_redirection.patch @@ -0,0 +1,34 @@ +WIEN2k assumes that user shell is (t)csh, that's almost never true any longer. +Make sure Fortran system call uses /bin/sh style stderr redirection. + +Åke Sandgren, 20210911 +diff -ru wien2k.orig/SRC_Globals/W2kinit.F wien2k/SRC_Globals/W2kinit.F +--- wien2k.orig/SRC_Globals/W2kinit.F 2021-03-17 16:56:42.301680962 +0100 ++++ wien2k/SRC_Globals/W2kinit.F 2021-09-11 16:05:18.300479374 +0200 +@@ -398,7 +398,7 @@ + logical AVX512, AVX2, AVX, SSE + integer istat, system + AVX512=.false.; AVX2=.false.; AVX=.false.; SSE=.false. +- istat=system('ls /proc/cpuinfo >& /dev/null') ++ istat=system('ls /proc/cpuinfo 2> /dev/null') + if(istat.ne.0.and.myid.eq.0) then + print*, "Could not read your /proc/cpuinfo. The default kernel of your ELPA installation" + print*, "will be used." +@@ -408,13 +408,13 @@ + !_REAL print*, " ELPA_DEFAULT_real_kernel" + !_COMPLEX print*, " ELPA_DEFAULT_complex_kernel" + else +- istat=system('grep -i avx512 /proc/cpuinfo >& /dev/null') ++ istat=system('grep -i avx512 /proc/cpuinfo 2> /dev/null') + if(istat.eq.0) AVX512=.true. +- istat=system('grep -i avx2 /proc/cpuinfo >& /dev/null') ++ istat=system('grep -i avx2 /proc/cpuinfo 2> /dev/null') + if(istat.eq.0) AVX2=.true. +- istat=system('grep -i avx /proc/cpuinfo >& /dev/null') ++ istat=system('grep -i avx /proc/cpuinfo 2> /dev/null') + if(istat.eq.0) AVX=.true. +- istat=system('grep -i sse /proc/cpuinfo >& /dev/null') ++ istat=system('grep -i sse /proc/cpuinfo 2> /dev/null') + if(istat.eq.0) SSE=.true. + endif + return From 955e8fc6be6dc75cff71fb4b14afd2c7078c8fd1 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 11 Sep 2021 16:59:57 +0200 Subject: [PATCH 1256/9987] adding easyconfigs: abtem-1.0.0b24-fosscuda-2020b.eb, ASE-3.22.0-fosscuda-2020b.eb, imageio-2.9.0-fosscuda-2020b.eb --- .../a/ASE/ASE-3.22.0-fosscuda-2020b.eb | 47 +++++++++++++++++++ .../a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb | 39 +++++++++++++++ .../i/imageio/imageio-2.9.0-fosscuda-2020b.eb | 25 ++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..1754c068f50 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-fosscuda-2020b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Flask', '1.1.2'), + ('matplotlib', '3.3.3'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['e60259c7b50867b1cb817caf938fcc1ed383702413df6d2e1afe7ea07f65acee'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb b/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb new file mode 100644 index 00000000000..7cc095d8bf2 --- /dev/null +++ b/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'abtem' +version = '1.0.0b24' + +homepage = 'https://imageio.github.io' +description = """abTEM provides a Python API for running simulations +of Transmission Electron Microscopy images. It is written entirely in +Python, which enables easy integration with first-principles codes and +analysis tools accessible from Python, and allows for a simple and +intuitive user interface. The computationally demanding parts are +implemented using jit-compiled Numba code and high-performance +libraries, maintaining speed while ensuring portability. + +abTEM works with the Atomic Simulation Environment and the density +functional theory code GPAW to provide an seamless environment for +simulating images from first principles.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['503e7775f9764cf8298cbd2d06c4a36a9c83efbd84d58721eee638adfd1e626e'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', '3.22.0'), + ('h5py', '3.1.0'), + ('numba', '0.53.1'), + ('pyFFTW', '0.12.0'), + ('tqdm', '4.60.0'), + ('imageio', '2.9.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..2213be16264 --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-fosscuda-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.9.0' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow', '8.0.1'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 6506c659a34c62fe457cd56a1e0d5d5aa50b7aba Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 11 Sep 2021 17:14:12 +0200 Subject: [PATCH 1257/9987] Downgrade tqdm for toolchain consistency. --- easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb b/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb index 7cc095d8bf2..e0980a7e1c5 100644 --- a/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb @@ -28,7 +28,7 @@ dependencies = [ ('h5py', '3.1.0'), ('numba', '0.53.1'), ('pyFFTW', '0.12.0'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ('imageio', '2.9.0'), ] From 600a8459835b887eec357fe4de5615149464c5f4 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 11 Sep 2021 17:28:10 +0200 Subject: [PATCH 1258/9987] Removing check_ldshared as suggested by @boegel --- easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb | 4 ---- .../easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb | 3 --- 2 files changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb index a31426b7e1f..e1212c23810 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2020b.eb @@ -24,10 +24,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -# required because we're building Python packages (MarkupSafe, -# ase-ext) using Intel compilers on top of Python built with GCC. -check_ldshared = True - exts_list = [ ('pytest-mock', '3.6.1', { 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb index 362e25c7825..bedc11e9043 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -40,9 +40,6 @@ download_dep_fail = True use_pip = True sanity_pip_check = True -# required because we're building a Python package using Intel compilers on top of Python built with GCC. -check_ldshared = True - sanity_check_paths = { 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', '-runscript', '-setup', '-upfplot']], From a956ce67865aeee4e7278b0bd97f4cc54dffe658 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 11 Sep 2021 17:39:43 +0200 Subject: [PATCH 1259/9987] Add versionsuffix for ASE. --- ...a-2020b.eb => abtem-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/a/abtem/{abtem-1.0.0b24-fosscuda-2020b.eb => abtem-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb} (93%) diff --git a/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb b/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb similarity index 93% rename from easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb rename to easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb index e0980a7e1c5..96147f5d3c1 100644 --- a/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb @@ -2,6 +2,8 @@ easyblock = 'PythonPackage' name = 'abtem' version = '1.0.0b24' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion homepage = 'https://imageio.github.io' description = """abTEM provides a Python API for running simulations @@ -24,7 +26,7 @@ checksums = ['503e7775f9764cf8298cbd2d06c4a36a9c83efbd84d58721eee638adfd1e626e'] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('ASE', '3.22.0'), + ('ASE', _aseversion), ('h5py', '3.1.0'), ('numba', '0.53.1'), ('pyFFTW', '0.12.0'), From cdc72057d854b5c4f7a246714c74ec85c044729b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 11 Sep 2021 18:42:16 +0200 Subject: [PATCH 1260/9987] Revert back to standard mpirun for wien_mpirun --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb index c1dda1b9ec7..61a3f8ece22 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb @@ -33,7 +33,9 @@ dependencies = [ osdependencies = [('glibc-devel', 'libc6-dev')] # required for libpthread.a # remote = 'pbsssh' -wien_mpirun = 'srun -n_NP_ _EXEC_' +# If using a Slurm batch system it is highly recommended to use +# 'srun -n_NP_ _EXEC_' for wien_mpirun +wien_mpirun = 'mpirun -np _NP_ _EXEC_' use_remote = False mpi_remote = False wien_granularity = True From 34cf50b8a4e1276ef2748f7258f01e429ad97a6d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 11 Sep 2021 19:09:05 +0200 Subject: [PATCH 1261/9987] Use commands that do not produce output at all instead of relying on redirection. --- .../w/WIEN2k/WIEN2k-21.1-intel-2021a.eb | 2 +- ...WIEN2k-21.1_fix_system_stderr_redirection.patch | 14 +++++++------- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb index 61a3f8ece22..1d4834be63a 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021a.eb @@ -18,7 +18,7 @@ checksums = [ '32590778440a9280322bf2dc0d63f4f42a9fc48814fa6b8b7ee2d199c94bed11', # WIEN2k_21.1.tar '1cc480a4824d9185ad5918dfc68c47bcb7826114626c8133d573be901bbdca84', # WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch # WIEN2k-21.1_fix_system_stderr_redirection.patch - 'd42d0f3ac13ce3ea81817b81b412f0e944d135b94f8d371fd42620735e81fee5', + 'cdba467b0b6f2b310c2e1e2a3e6cabe75f8fd15ee0f7c14f8ef80c7e48073bdd', ] dependencies = [ diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_system_stderr_redirection.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_system_stderr_redirection.patch index ea32e0b3087..9e1ad379a28 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_system_stderr_redirection.patch +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1_fix_system_stderr_redirection.patch @@ -1,16 +1,16 @@ WIEN2k assumes that user shell is (t)csh, that's almost never true any longer. -Make sure Fortran system call uses /bin/sh style stderr redirection. +Use commands that don't produce output at all instead of relying on redirection Åke Sandgren, 20210911 diff -ru wien2k.orig/SRC_Globals/W2kinit.F wien2k/SRC_Globals/W2kinit.F --- wien2k.orig/SRC_Globals/W2kinit.F 2021-03-17 16:56:42.301680962 +0100 -+++ wien2k/SRC_Globals/W2kinit.F 2021-09-11 16:05:18.300479374 +0200 ++++ wien2k/SRC_Globals/W2kinit.F 2021-09-11 19:02:28.742392699 +0200 @@ -398,7 +398,7 @@ logical AVX512, AVX2, AVX, SSE integer istat, system AVX512=.false.; AVX2=.false.; AVX=.false.; SSE=.false. - istat=system('ls /proc/cpuinfo >& /dev/null') -+ istat=system('ls /proc/cpuinfo 2> /dev/null') ++ istat=system('test -f /proc/cpuinfo') if(istat.ne.0.and.myid.eq.0) then print*, "Could not read your /proc/cpuinfo. The default kernel of your ELPA installation" print*, "will be used." @@ -19,16 +19,16 @@ diff -ru wien2k.orig/SRC_Globals/W2kinit.F wien2k/SRC_Globals/W2kinit.F !_COMPLEX print*, " ELPA_DEFAULT_complex_kernel" else - istat=system('grep -i avx512 /proc/cpuinfo >& /dev/null') -+ istat=system('grep -i avx512 /proc/cpuinfo 2> /dev/null') ++ istat=system('grep -qi avx512 /proc/cpuinfo') if(istat.eq.0) AVX512=.true. - istat=system('grep -i avx2 /proc/cpuinfo >& /dev/null') -+ istat=system('grep -i avx2 /proc/cpuinfo 2> /dev/null') ++ istat=system('grep -qi avx2 /proc/cpuinfo') if(istat.eq.0) AVX2=.true. - istat=system('grep -i avx /proc/cpuinfo >& /dev/null') -+ istat=system('grep -i avx /proc/cpuinfo 2> /dev/null') ++ istat=system('grep -qi avx /proc/cpuinfo') if(istat.eq.0) AVX=.true. - istat=system('grep -i sse /proc/cpuinfo >& /dev/null') -+ istat=system('grep -i sse /proc/cpuinfo 2> /dev/null') ++ istat=system('grep -qi sse /proc/cpuinfo') if(istat.eq.0) SSE=.true. endif return From fdb18b94684a3106cdcfbc921e534f8d6c672db1 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Sat, 11 Sep 2021 23:13:40 -0400 Subject: [PATCH 1262/9987] Update easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb index 77a4b348b2d..5cfca4bad48 100644 --- a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb +++ b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb @@ -12,7 +12,8 @@ toolchain = SYSTEM source_urls = ['https://dalexander.github.io/admixture/binaries/'] sources = ['%(namelower)s_linux-%(version)s.tar.gz'] -checksums = ['353e8b170c81f8d95946bf18bc78afda5d6bd32645b2a68658bd6781ff35703c'] +checksums = [('41f209817a17981a717c9a4aa3d799da718ed080f3386e703927628c74ca6ca6', + '353e8b170c81f8d95946bf18bc78afda5d6bd32645b2a68658bd6781ff35703c')] modextrapaths = {'PATH': 'admixture_linux-1.3.0'} From 1e2a70d195c842e7a9c169c0ae72115bc46a157b Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Sat, 11 Sep 2021 23:13:47 -0400 Subject: [PATCH 1263/9987] Update easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb index 5cfca4bad48..a4b219b4a45 100644 --- a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb +++ b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb @@ -16,7 +16,7 @@ checksums = [('41f209817a17981a717c9a4aa3d799da718ed080f3386e703927628c74ca6ca6' '353e8b170c81f8d95946bf18bc78afda5d6bd32645b2a68658bd6781ff35703c')] -modextrapaths = {'PATH': 'admixture_linux-1.3.0'} +postinstallcmds = ["mkdir %(installdir)s/bin && mv %(installdir)s/admixture{,32} %(installdir)s/bin/"] sanity_check_paths = { 'files': ['admixture_linux-1.3.0/admixture', 'admixture_linux-1.3.0/admixture32'], From 15103f6873dcbe90827848202c3ba551bdd2bd88 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Sat, 11 Sep 2021 23:13:55 -0400 Subject: [PATCH 1264/9987] Update easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb index a4b219b4a45..25177d59d3a 100644 --- a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb +++ b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb @@ -19,8 +19,11 @@ checksums = [('41f209817a17981a717c9a4aa3d799da718ed080f3386e703927628c74ca6ca6' postinstallcmds = ["mkdir %(installdir)s/bin && mv %(installdir)s/admixture{,32} %(installdir)s/bin/"] sanity_check_paths = { - 'files': ['admixture_linux-1.3.0/admixture', 'admixture_linux-1.3.0/admixture32'], - 'dirs': ['admixture_linux-1.3.0'] +sanity_check_paths = { + 'files': ['bin/admixture', 'bin/admixture32'], + 'dirs': [] } +sanity_check_commands = ["admixture --help"] + moduleclass = 'bio' From 45ca7666c9d43607b5d70469d0d3c80e44b641c4 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Sat, 11 Sep 2021 23:16:44 -0400 Subject: [PATCH 1265/9987] Update ADMIXTURE-1.3.0.eb --- easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb index 25177d59d3a..52bc092b0b0 100644 --- a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb +++ b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb @@ -18,7 +18,6 @@ checksums = [('41f209817a17981a717c9a4aa3d799da718ed080f3386e703927628c74ca6ca6' postinstallcmds = ["mkdir %(installdir)s/bin && mv %(installdir)s/admixture{,32} %(installdir)s/bin/"] -sanity_check_paths = { sanity_check_paths = { 'files': ['bin/admixture', 'bin/admixture32'], 'dirs': [] From 8215a0d1c2cd61789657bd383d825880decbc264 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Sun, 12 Sep 2021 03:27:45 +0000 Subject: [PATCH 1266/9987] fixing path issue --- easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb index 52bc092b0b0..5f81062802a 100644 --- a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb +++ b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb @@ -1,3 +1,4 @@ + easyblock = 'PackedBinary' name = 'ADMIXTURE' @@ -16,7 +17,7 @@ checksums = [('41f209817a17981a717c9a4aa3d799da718ed080f3386e703927628c74ca6ca6' '353e8b170c81f8d95946bf18bc78afda5d6bd32645b2a68658bd6781ff35703c')] -postinstallcmds = ["mkdir %(installdir)s/bin && mv %(installdir)s/admixture{,32} %(installdir)s/bin/"] +postinstallcmds = ["mkdir -p %(installdir)s/bin && mv %(installdir)s/admixture_linux-1.3.0/admixture{,32} %(installdir)s/bin/"] sanity_check_paths = { 'files': ['bin/admixture', 'bin/admixture32'], @@ -26,3 +27,4 @@ sanity_check_paths = { sanity_check_commands = ["admixture --help"] moduleclass = 'bio' + From a80123b63402f02c4b0550c67556071e2bf39712 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 12 Sep 2021 09:25:51 +0100 Subject: [PATCH 1267/9987] adding easyconfigs: GDAL-3.3.2-foss-2021.07.eb, netCDF-4.8.1-gompi-2021.07.eb, HDF5-1.12.1-gompi-2021.07.eb --- .../g/GDAL/GDAL-3.3.2-foss-2021.07.eb | 65 +++++++++++++++++++ .../h/HDF5/HDF5-1.12.1-gompi-2021.07.eb | 21 ++++++ .../n/netCDF/netCDF-4.8.1-gompi-2021.07.eb | 37 +++++++++++ 3 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021.07.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2021.07.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb new file mode 100644 index 00000000000..0e7b0e81b4c --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.3.2' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2021.07'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] +checksums = [ + '630e34141cf398c3078d7d8f08bb44e804c65bbf09807b3610dcbfbc37115cc3', # gdal-3.3.2.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('netCDF', '4.8.1'), + ('expat', '2.4.1'), + ('GEOS', '3.9.1'), + ('SQLite', '3.36'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('JasPer', '2.0.33'), + ('LibTIFF', '4.3.0'), + ('zlib', '1.2.11'), + ('cURL', '7.78.0'), + ('PCRE', '8.45'), + ('PROJ', '8.1.0'), + ('libgeotiff', '1.7.0'), + ('SciPy-bundle', '2021.07'), + ('HDF5', '1.12.1'), + ('HDF', '4.2.15'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import osgeo.gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021.07.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021.07.eb new file mode 100644 index 00000000000..abc302b0c14 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021.07.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.12.1' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2021.07'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['79c66ff67e666665369396e9c90b32e238e501f345afd2234186bfb8331081ca'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2021.07.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2021.07.eb new file mode 100644 index 00000000000..e98ecfdb739 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2021.07.eb @@ -0,0 +1,37 @@ +name = 'netCDF' +version = '4.8.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2021.07'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bc018cc30d5da402622bf76462480664c6668b55eb16ba205a0dfb8647161dd0'] + +builddependencies = [ + ('Autotools', '20210726'), + ('CMake', '3.21.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('HDF5', '1.12.1'), + ('cURL', '7.78.0'), + ('Szip', '2.1.1'), +] + +# HDF5 version detection is missed in netCDF 4.8.1 when HDF5_C_LIBRARY, HDF5_INCLUDE_DIR, and HDF5_HL_LIBRARY are set +local_hdf5_version_fix = '-DHDF5_VERSION=$EBVERSIONHDF5' + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF %s " % local_hdf5_version_fix, + "-DBUILD_SHARED_LIBS=ON %s " % local_hdf5_version_fix, +] + +moduleclass = 'data' From 2a89bcd4421f5be79afc9fe4540f66f7c6cf6953 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 13 Sep 2021 11:03:17 +0200 Subject: [PATCH 1268/9987] adding easyconfigs: OrthoFinder-2.5.4-foss-2020b.eb --- .../OrthoFinder-2.5.4-foss-2020b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb new file mode 100644 index 00000000000..3c6475ccad6 --- /dev/null +++ b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.4-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'OrthoFinder' +version = '2.5.4' + +homepage = 'https://github.com/davidemms/OrthoFinder' +description = "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'davidemms' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9d8bd52426ebab4a5f377f8699cc9ee16559152830c9a67229c2ba81326d3f51'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('BLAST+', '2.11.0'), + ('DIAMOND', '2.0.7'), + ('FastME', '2.1.6.1'), + ('MCL', '14.137'), + ('MMseqs2', '13-45111'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'scripts_of'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['convert_orthofinder_tree_ids', 'make_ultrametric', 'orthofinder', + 'primary_transcript']], + 'dirs': ['ExampleData', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["orthofinder --help"] + +moduleclass = 'bio' From 5218f78c13f17f824d2b0cbc980eef71ec4eb0d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Sep 2021 11:29:16 +0200 Subject: [PATCH 1269/9987] remove binutils build dependency, since GCC toolchain is used MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb index 7b8029d3783..d835df6e321 100644 --- a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.1-GCC-10.2.0.eb @@ -13,7 +13,6 @@ sources = ['FastME-v%(version)s.tar.gz'] checksums = ['fae0609576873cb137ad4f63529b3ccba8f747b857c23c7870236aba440076ca'] builddependencies = [ - ('binutils', '2.35'), ('Autotools', '20200321'), ] From 5d3d78eb4e27b332a3bf3c9ebde6edc570855ed8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 13 Sep 2021 11:32:48 +0200 Subject: [PATCH 1270/9987] No more Python multi-dependencies --- .../b/Boost.Python/Boost.Python-1.76.0-GCC-10.3.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.76.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.76.0-GCC-10.3.0.eb index d16abdfa5c0..2112fdf8187 100644 --- a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.76.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.76.0-GCC-10.3.0.eb @@ -18,9 +18,10 @@ checksums = [ '60e3aede2f444a3855f4efed94d1de5c2887983876e0fae21f6ca5cfdc53ea96', # Boost-1.71.0_fix-Python3.patch ] -multi_deps = {'Python': ['3.9.5']} - -dependencies = [('Boost', version)] +dependencies = [ + ('Boost', version), + ('Python', '3.9.5'), +] only_python_bindings = True From b75326db5a75727d8da832ca65c58abf28edd7e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Sep 2021 11:42:39 +0200 Subject: [PATCH 1271/9987] reuse existing easyconfigs for DIAMOND 2.0.7 and MMseqs2 13-45111 as dependencies for OrthoFinder 2.5.2 --- .../d/DIAMOND/DIAMOND-2.0.6-GCC-10.2.0.eb | 26 -------------- .../m/MMseqs2/MMseqs2-12-113e3-gompi-2020b.eb | 36 ------------------- .../OrthoFinder-2.5.2-foss-2020b.eb | 4 +-- 3 files changed, 2 insertions(+), 64 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.6-GCC-10.2.0.eb delete mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-12-113e3-gompi-2020b.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.6-GCC-10.2.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.6-GCC-10.2.0.eb deleted file mode 100644 index de62849aa4b..00000000000 --- a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.6-GCC-10.2.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'DIAMOND' -version = '2.0.6' - -homepage = 'https://github.com/bbuchfink/diamond' -description = "Accelerated BLAST compatible local sequence aligner" - -toolchain = {'name': 'GCC', 'version': '10.2.0'} - -source_urls = ['https://github.com/bbuchfink/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['4231f6ed75191fc9757f22b60f9068f4b4412918bf2e8c37367880d189667f80'] - -builddependencies = [ - ('CMake', '3.18.4') -] -dependencies = [('zlib', '1.2.11')] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [], -} -sanity_check_commands = ["diamond help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-12-113e3-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-12-113e3-gompi-2020b.eb deleted file mode 100644 index 5137ffe33fa..00000000000 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-12-113e3-gompi-2020b.eb +++ /dev/null @@ -1,36 +0,0 @@ -# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'CMakeMake' - -name = 'MMseqs2' -version = '12-113e3' - -homepage = 'https://mmseqs.com' -description = "MMseqs2: ultra fast and sensitive search and clustering suite" - -toolchain = {'name': 'gompi', 'version': '2020b'} - -github_account = 'soedinglab' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['81fa0d77eab9d74b429567da00aa7ec2d46049537ce469595d7356b6d8b5458a'] - -builddependencies = [('CMake', '3.18.4')] - -dependencies = [('bzip2', '1.0.8')] - -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=RELEASE' - -sanity_check_paths = { - 'files': ['bin/mmseqs'], - 'dirs': [], -} - -sanity_check_commands = ["mmseqs --help"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb index ff9a4ad647a..abe97dde5d2 100644 --- a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.2-foss-2020b.eb @@ -17,10 +17,10 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('BLAST+', '2.11.0'), - ('DIAMOND', '2.0.6'), + ('DIAMOND', '2.0.7'), ('FastME', '2.1.6.1'), ('MCL', '14.137'), - ('MMseqs2', '12-113e3'), + ('MMseqs2', '13-45111'), ] download_dep_fail = True From 951c9cfdc206a04cdc50f714bd3aae7321cd7d2e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Sep 2021 11:46:58 +0200 Subject: [PATCH 1272/9987] switch ADMIXTURE v1.3.0 from PackedBinary to Tarball --- easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb index 5f81062802a..14699cfc6e4 100644 --- a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb +++ b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb @@ -1,5 +1,4 @@ - -easyblock = 'PackedBinary' +easyblock = 'Tarball' name = 'ADMIXTURE' version = '1.3.0' @@ -16,8 +15,7 @@ sources = ['%(namelower)s_linux-%(version)s.tar.gz'] checksums = [('41f209817a17981a717c9a4aa3d799da718ed080f3386e703927628c74ca6ca6', '353e8b170c81f8d95946bf18bc78afda5d6bd32645b2a68658bd6781ff35703c')] - -postinstallcmds = ["mkdir -p %(installdir)s/bin && mv %(installdir)s/admixture_linux-1.3.0/admixture{,32} %(installdir)s/bin/"] +postinstallcmds = ["mkdir %(installdir)s/bin && mv %(installdir)s/admixture{,32} %(installdir)s/bin/"] sanity_check_paths = { 'files': ['bin/admixture', 'bin/admixture32'], From ace1fcfbe6835eef16959848583c54995e212510 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Sep 2021 11:50:48 +0200 Subject: [PATCH 1273/9987] remove blank lines in ADMIXTURE v1.3.0 --- easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb index 14699cfc6e4..709a656ede2 100644 --- a/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb +++ b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb @@ -25,4 +25,3 @@ sanity_check_paths = { sanity_check_commands = ["admixture --help"] moduleclass = 'bio' - From e869aee22e456a1f4a1759b48a0e09397d25857f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Sep 2021 12:21:41 +0200 Subject: [PATCH 1274/9987] switch to Meson 0.59.1 as build dependency for DFT-D4 --- .../DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb | 2 +- ...Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb | 36 ------------------- 2 files changed, 1 insertion(+), 37 deletions(-) delete mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb index 5dbd6861084..857b136cb32 100644 --- a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.2.0-intel-2019b-Python-3.7.4.eb @@ -19,7 +19,7 @@ checksums = [ builddependencies = [ ('Ninja', '1.9.0'), - ('Meson', '0.58.0', versionsuffix), + ('Meson', '0.59.1', versionsuffix), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb deleted file mode 100644 index 6ba9f6a7b73..00000000000 --- a/easybuild/easyconfigs/m/Meson/Meson-0.58.0-GCCcore-8.3.0-Python-3.7.4.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Meson' -version = '0.58.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://mesonbuild.com' -description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." - -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['f4820df0bc969c99019fd4af8ca5f136ee94c63d8a5ad67e7eb73bdbc9182fdd'] - -builddependencies = [ - ('binutils', '2.32'), -] - -dependencies = [ - ('Python', '3.7.4'), - ('Ninja', '1.9.0'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -options = {'modulename': 'mesonbuild'} - -sanity_check_paths = { - 'files': ['bin/meson'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' From f236bae217e799a452ffcc006544f695e36e4763 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Mon, 13 Sep 2021 16:38:25 +0200 Subject: [PATCH 1275/9987] adding easyconfigs: isoCirc-1.0.4-foss-2020b.eb --- .../i/isoCirc/isoCirc-1.0.4-foss-2020b.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb new file mode 100644 index 00000000000..7f0bf29567b --- /dev/null +++ b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'isoCirc' +version = '1.0.4' + +homepage = 'https://github.com/Xinglab/isoCirc' +description = """isoCirc: computational pipeline to identify high-confidence +BSJs and full-length circRNA isoforms from isoCirc long-read data +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Biopython', '1.78'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Pysam', '0.16.0.1'), + ('pybedtools', '0.8.2'), + ('minimap2', '2.18'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('argcomplete', '1.12.3', { + 'checksums': ['2c7dbffd8c045ea534921e63b0be6fe65e88599990d8dc408ac8c542b72a5445'], + }), + ('argh', '0.26.2', { + 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], + }), + ('crlibm', '1.0.3', { + 'checksums': ['48e17981f90d69c6bb0013f68bacbe7a157de864a533d15dd196ca7e98348a35'], + }), + ('gffutils', '0.10.1', { + 'checksums': ['a8fc39006d7aa353147238160640e2210b168f7849cb99896be3fc9441e351cb'], + }), + ('mappy', '2.20', { + 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], + }), + ('pyfaidx', '0.6.2', { + 'checksums': ['d1258f8d053cba0c90fe329254e8ec59eb28b535b48d9d06e8c7f1d74b8e4531'], + }), + ('pyinterval', '1.2.0', { + 'modulename': 'interval', + 'checksums': ['8c46224a05815affa803ed5620432236bba620a246701b860d98ae7358a41d21'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/Xinglab/isoCirc/archive'], + 'start_dir': 'isoCirc_pipeline', + 'checksums': ['c5879820d7e61b4fc25a4357df8967d65f6d6c05aff705d5338a16707ffa849d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['isocirc', 'isocircPlot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "isocirc --help", + ( + "cd %(builddir)s/%(name)s/%(name)s-%(version)s/test_data && " + "isocirc -t 1 read_toy.fa chr16_toy.fa chr16_toy.gtf chr16_circRNA_toy.bed output" + ), +] + +moduleclass = 'bio' From 387c723d3631ea8a288f2cc8f8bec54940f70ad8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Sep 2021 09:43:54 +0200 Subject: [PATCH 1276/9987] adding easyconfigs: FLUENT-2021R2.eb --- easybuild/easyconfigs/f/FLUENT/FLUENT-2021R2.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLUENT/FLUENT-2021R2.eb diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-2021R2.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-2021R2.eb new file mode 100644 index 00000000000..234dcfa4bfc --- /dev/null +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-2021R2.eb @@ -0,0 +1,17 @@ +name = 'FLUENT' +version = '2021R2' + +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' +description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed +to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from +air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, +from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" + +toolchain = SYSTEM + +sources = ['FLUIDS_%(version)s_LINX64.tgz'] +checksums = ['6d6a10e8db5fc807bea6b046521bd489fd452f93d1c9040fc44426e72e417b12'] + +subdir_version = '212' + +moduleclass = 'cae' From dbf80557ed0026e3c8312154d05836c7ee98644e Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 14 Sep 2021 09:44:40 +0200 Subject: [PATCH 1277/9987] adding easyconfigs: CIRI-long-1.0.2-foss-2020b.eb --- .../c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb new file mode 100644 index 00000000000..1a6d54aa7e2 --- /dev/null +++ b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'CIRI-long' +version = '1.0.2' + +homepage = 'https://github.com/bioinfo-biols/CIRI-long/' +description = "Circular RNA Identification for Long-Reads Nanopore Sequencing Data" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('Pysam', '0.16.0.1'), + ('minimap2', '2.18'), + ('Cython', '0.29.22'), + ('SAMtools', '1.12'), + ('Biopython', '1.78'), + ('pyspoa', '0.0.8'), +] + +use_pip = True + +exts_list = [ + ('mappy', '2.17', { + 'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'], + }), + ('python-Levenshtein', '0.12.1', { + 'modulename': 'Levenshtein', + 'checksums': ['554e273a88060d177e7b3c1e6ea9158dde11563bfae8f7f661f73f47e5ff0911'], + }), + ('bwapy', '0.1.4', { + 'checksums': ['fcdad0c7311753d550b3a3aefbc2619380e7e35e7aeaa386fd491cba47e71824'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + (name, version, { + 'modulename': 'CIRI_long', + 'preinstallopts': "make lib && sed -i '/install_requires/,+4d' setup.py && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/bioinfo-biols/CIRI-long/archive'], + 'checksums': ['4c83d18fb147cc37be99b79f94acbbc24caa9954286afc8ff24058a9db7e9e48'], + }), +] + +sanity_check_paths = { + 'files': ['bin/CIRI-long'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'cd %(builddir)s/CIRIlong/%(name)s-%(version)s && make test', + 'CIRI-long --help', +] +sanity_pip_check = True + +moduleclass = 'bio' From f2a04ddd627f8d9c02ab560e7a7afa6413af7444 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 14 Sep 2021 09:52:43 +0200 Subject: [PATCH 1278/9987] isoCirc: don't use download_dep_fail --- easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb index 7f0bf29567b..be32d45ae99 100644 --- a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb @@ -21,8 +21,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True -sanity_pip_check = True exts_list = [ ('argcomplete', '1.12.3', { @@ -59,7 +57,6 @@ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['isocirc', 'isocircPlot']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } - sanity_check_commands = [ "isocirc --help", ( @@ -67,5 +64,6 @@ sanity_check_commands = [ "isocirc -t 1 read_toy.fa chr16_toy.fa chr16_toy.gtf chr16_circRNA_toy.bed output" ), ] +sanity_pip_check = True moduleclass = 'bio' From dbe176a2c43d3ad6f30ff93cac1841b1fed01047 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 14 Sep 2021 10:09:04 +0200 Subject: [PATCH 1279/9987] CIRI-long: avoid multivariant deps --- easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb index 1a6d54aa7e2..136959b5a01 100644 --- a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb @@ -15,7 +15,7 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('minimap2', '2.18'), ('Cython', '0.29.22'), - ('SAMtools', '1.12'), + ('SAMtools', '1.11'), ('Biopython', '1.78'), ('pyspoa', '0.0.8'), ] From a5033c70c71113d39bed5a819518a52f7a3675c9 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 14 Sep 2021 10:51:49 +0200 Subject: [PATCH 1280/9987] Add X11 dependency for Xpm requirement --- easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb index 5cb5845e82f..bf13eba9f37 100644 --- a/easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb @@ -23,6 +23,7 @@ builddependencies = [ dependencies = [ ('Perl', '5.32.1'), + ('X11', '20210518'), ('libgd', '2.3.1'), ('libpng', '1.6.37'), ('libjpeg-turbo', '2.0.6'), From b65bbfc116083c445e6429691b3be8023c829747 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 14 Sep 2021 11:33:59 +0200 Subject: [PATCH 1281/9987] Fix name, homepage, description. Patch issue 53. Patch multithreading --- .../abTEM-1.0.0b24-MTF-bug-fix-issue-53.patch | 34 +++++++++++++++ ...24-Make-FFTW-multithreading-optional.patch | 18 ++++++++ ...bTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb | 41 +++++++++++++++++++ ...btem-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb | 41 ------------------- 4 files changed, 93 insertions(+), 41 deletions(-) create mode 100644 easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-MTF-bug-fix-issue-53.patch create mode 100644 easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch create mode 100644 easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb delete mode 100644 easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-MTF-bug-fix-issue-53.patch b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-MTF-bug-fix-issue-53.patch new file mode 100644 index 00000000000..e9ae5e6ffa7 --- /dev/null +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-MTF-bug-fix-issue-53.patch @@ -0,0 +1,34 @@ +From c2793bb69c4c49df6e5427ba62e7414fee571a84 Mon Sep 17 00:00:00 2001 +From: Matthew Helmi Leth Larsen +Date: Sun, 12 Sep 2021 17:54:41 +0200 +Subject: [PATCH 2/2] Bug related to spacial frequencies being 1D arrays fixed. + +--- + abtem/mtf.py | 9 ++++++--- + 1 file changed, 6 insertions(+), 3 deletions(-) + +diff --git a/abtem/mtf.py b/abtem/mtf.py +index b8d7842..6e82946 100644 +--- a/abtem/mtf.py ++++ b/abtem/mtf.py +@@ -80,13 +80,16 @@ class MTF: + + # Get spatial frequencies + kx, ky = spatial_frequencies(gpts, sampling) +- k = np.sqrt(kx ** 2 + ky ** 2) ++ ++ # Create 2D grid ++ Ky, Kx = np.meshgrid(ky,kx) ++ K = np.sqrt(Kx ** 2 + Ky ** 2) + + # Compute MTF +- mtf = self.f(k, **self.params) ++ mtf = self.f(K, **self.params) + + # Apply MTF +- img = np.fft.ifft2(np.fft.fft2(img) * np.sqrt(mtf)) ++ img = np.fft.ifft2(np.fft.fft2(img) * mtf) + measurement.array[:] = img.real + + return measurement + diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch new file mode 100644 index 00000000000..be06bff30a3 --- /dev/null +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch @@ -0,0 +1,18 @@ +--- abtem/device.py.orig 2021-09-13 20:15:59.190194233 +0200 ++++ abtem/device.py 2021-09-13 20:17:43.763802138 +0200 +@@ -3,13 +3,14 @@ + import numpy as np + import psutil + import pyfftw ++import os + from numpy.core.numeric import normalize_axis_tuple + + from abtem.cpu_kernels import abs2, complex_exponential, interpolate_radial_functions, sum_run_length_encoded + from abtem.interpolate import interpolate_bilinear_cpu + + FFTW_EFFORT = 'FFTW_MEASURE' +-FFTW_THREADS = 12 ++FFTW_THREADS = int(os.getenv('ABTEM_FFTW_THREADS', '1')) + FFTW_TIMELIMIT = 600 + + try: # This should be the only place import cupy, to make it a non-essential dependency diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb new file mode 100644 index 00000000000..bbc631dca58 --- /dev/null +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'abTEM' +version = '1.0.0b24' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/abTEM' +description = """abTEM provides a Python API for running simulations +of Transmission Electron Microscopy images.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch', + 'abTEM-1.0.0b24-MTF-bug-fix-issue-53.patch', +] +checksums = [ + '503e7775f9764cf8298cbd2d06c4a36a9c83efbd84d58721eee638adfd1e626e', # abtem-1.0.0b24.tar.gz + # abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch + '49eee97f444ff16b45745adcd70dbbf63d5ddb842d7d6539ec303f388b4293da', + '0d4a0500e4947e4967858e6644969796d5bd76bc556a9c09fdc80461dcbcaed6', # abTEM-1.0.0b24-MTF-bug-fix-issue-53.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('h5py', '3.1.0'), + ('numba', '0.53.1'), + ('pyFFTW', '0.12.0'), + ('tqdm', '4.56.2'), + ('imageio', '2.9.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb deleted file mode 100644 index 96147f5d3c1..00000000000 --- a/easybuild/easyconfigs/a/abtem/abtem-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'abtem' -version = '1.0.0b24' -_aseversion = '3.22.0' -versionsuffix = '-ASE-' + _aseversion - -homepage = 'https://imageio.github.io' -description = """abTEM provides a Python API for running simulations -of Transmission Electron Microscopy images. It is written entirely in -Python, which enables easy integration with first-principles codes and -analysis tools accessible from Python, and allows for a simple and -intuitive user interface. The computationally demanding parts are -implemented using jit-compiled Numba code and high-performance -libraries, maintaining speed while ensuring portability. - -abTEM works with the Atomic Simulation Environment and the density -functional theory code GPAW to provide an seamless environment for -simulating images from first principles.""" - -toolchain = {'name': 'fosscuda', 'version': '2020b'} - -sources = [SOURCE_TAR_GZ] -checksums = ['503e7775f9764cf8298cbd2d06c4a36a9c83efbd84d58721eee638adfd1e626e'] - -dependencies = [ - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('ASE', _aseversion), - ('h5py', '3.1.0'), - ('numba', '0.53.1'), - ('pyFFTW', '0.12.0'), - ('tqdm', '4.56.2'), - ('imageio', '2.9.0'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -moduleclass = 'vis' From 7bbb558141f6109ae92ccf8db427ff5d88344cb5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Sep 2021 12:04:22 +0200 Subject: [PATCH 1282/9987] use proper dependency for python-Levenshtein in CIRI-long easyconfig --- .../c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb | 8 +----- .../python-Levenshtein-0.12.1-foss-2020b.eb | 25 +++++++++++++++++++ 2 files changed, 26 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb index 136959b5a01..a52d5879330 100644 --- a/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CIRI-long/CIRI-long-1.0.2-foss-2020b.eb @@ -18,6 +18,7 @@ dependencies = [ ('SAMtools', '1.11'), ('Biopython', '1.78'), ('pyspoa', '0.0.8'), + ('python-Levenshtein', '0.12.1'), ] use_pip = True @@ -26,16 +27,9 @@ exts_list = [ ('mappy', '2.17', { 'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'], }), - ('python-Levenshtein', '0.12.1', { - 'modulename': 'Levenshtein', - 'checksums': ['554e273a88060d177e7b3c1e6ea9158dde11563bfae8f7f661f73f47e5ff0911'], - }), ('bwapy', '0.1.4', { 'checksums': ['fcdad0c7311753d550b3a3aefbc2619380e7e35e7aeaa386fd491cba47e71824'], }), - ('nose', '1.3.7', { - 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], - }), (name, version, { 'modulename': 'CIRI_long', 'preinstallopts': "make lib && sed -i '/install_requires/,+4d' setup.py && ", diff --git a/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb new file mode 100644 index 00000000000..9934a63e080 --- /dev/null +++ b/easybuild/easyconfigs/p/python-Levenshtein/python-Levenshtein-0.12.1-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'python-Levenshtein' +version = '0.12.1' + +homepage = 'https://pypi.org/project/python-Levenshtein/' +description = 'Python extension for computing string edit distances and similarities.' + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['554e273a88060d177e7b3c1e6ea9158dde11563bfae8f7f661f73f47e5ff0911'] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'Levenshtein'} + +sanity_pip_check = True + +moduleclass = 'data' From 99cc4d8ab6cef6e35a1b06d7e997ef7d791e353e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Sep 2021 12:23:14 +0200 Subject: [PATCH 1283/9987] add -DLIBMESH_HAVE_XDR to $CXXFLAGS for LibMesh in MOOSE easyconfig Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb index 16f3bf08a8c..99576611ef9 100644 --- a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -43,7 +43,7 @@ buildininstalldir = True local_libmesg_configopts = "--disable-warnings --enable-march --with-mpi=$EBROOTMPI" install_cmd = "sed 's/--disable-warnings/%s/g' scripts/update_and_rebuild_libmesh.sh && " % local_libmesg_configopts # build vendored copy of libmesh -install_cmd += 'export CXXFLAGS="$CXXFLAGS -fpermissive" && export MOOSE_JOBS="%(parallel)s V=1" && ' +install_cmd += 'export CXXFLAGS="$CXXFLAGS -fpermissive -DLIBMESH_HAVE_XDR" && export MOOSE_JOBS="%(parallel)s V=1" && ' install_cmd += "./scripts/update_and_rebuild_libmesh.sh --skip-submodule-update && " # build MOOSE itself install_cmd += "cd test && pwd && make -j %(parallel)s && make -j %(parallel)s hit && " From 89690026f8d3b213f331f4aaebe26b25cf02854e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Sep 2021 12:23:32 +0200 Subject: [PATCH 1284/9987] add libtirpc dependency in MOOSE easyconfig Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb index 99576611ef9..29000d825e4 100644 --- a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -15,6 +15,7 @@ toolchainopts = {'usempi': True} dependencies = [ ('Python', '3.7.4'), ('libpng', '1.6.37'), + ('libtirpc', '1.2.6'), ('PETSc', '3.12.4', versionsuffix), ('SLEPc', '3.12.2', versionsuffix), ('VTK', '8.2.0', versionsuffix), From 5f9258cadd5c0c99632c6e1ff24b29a011a85277 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 14 Sep 2021 12:59:21 +0200 Subject: [PATCH 1285/9987] isoCirc: use packaged pyfaidx --- easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb index be32d45ae99..1e5a19bc40a 100644 --- a/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/i/isoCirc/isoCirc-1.0.4-foss-2020b.eb @@ -18,6 +18,7 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('pybedtools', '0.8.2'), ('minimap2', '2.18'), + ('pyfaidx', '0.5.9.5'), ] use_pip = True @@ -38,9 +39,6 @@ exts_list = [ ('mappy', '2.20', { 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], }), - ('pyfaidx', '0.6.2', { - 'checksums': ['d1258f8d053cba0c90fe329254e8ec59eb28b535b48d9d06e8c7f1d74b8e4531'], - }), ('pyinterval', '1.2.0', { 'modulename': 'interval', 'checksums': ['8c46224a05815affa803ed5620432236bba620a246701b860d98ae7358a41d21'], From 22f1dfbad9e1338af46a0a44dd2acc73372dcfbf Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 14 Sep 2021 18:15:10 +0200 Subject: [PATCH 1286/9987] added binutils --- .../easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb index 669dcdf5ca3..a2b8f7af57a 100644 --- a/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb @@ -13,6 +13,7 @@ sources = ['WildMagic5p17.zip'] checksums = ['b2caf7aa0c5309eb40965ed26439388dc1c93eb632312b40573f83e4746a9ecf'] dependencies = [ + ('binutils', '2.36.1'), ('freeglut', '3.2.1'), ] From 61acc42159f74c91d01f554256ded80f4345ece1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Sep 2021 21:09:39 +0200 Subject: [PATCH 1287/9987] run MOOSE tests with --max-fails 10000 Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb index 29000d825e4..a75bf142bb7 100644 --- a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -51,7 +51,7 @@ install_cmd += "cd test && pwd && make -j %(parallel)s && make -j %(parallel)s h # run tests install_cmd += "echo 'running tests' && export PYTHONPATH=%(installdir)s/moose/moosetools/contrib/hit:$PYTHONPATH && " # run tests, but tolerate failures -install_cmd += "(python run_tests -j %(parallel)s || echo 'Some tests are failing!' >&2 ) " +install_cmd += "(python run_tests -j %(parallel)s --max-fails 10000 || echo 'Some tests are failing!' >&2 ) " sanity_check_paths = { 'files': ['moose/framework/libmoose-opt.%s' % SHLIB_EXT, From d9f70fd364324c12d84691bc317d5fb14c182d98 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Wed, 15 Sep 2021 10:56:06 +0200 Subject: [PATCH 1288/9987] adding easyconfigs: longread_umi-0.3.2-foss-2020b.eb, VSEARCH-2.18.0-GCC-10.2.0.eb, Racon-1.4.13-GCCcore-10.2.0.eb, medaka-1.4.3-foss-2020b.eb, cutadapt-3.4-GCCcore-10.2.0.eb, edlib-1.3.9-GCC-10.2.0.eb, python-isal-0.11.0-GCCcore-10.2.0.eb, ISA-L-2.30.0-GCCcore-10.2.0.eb and patches: Racon-1.4.13-std_invalid_argument.patch --- .../c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb | 52 ++++++++++++ .../e/edlib/edlib-1.3.9-GCC-10.2.0.eb | 22 ++++++ .../i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb | 46 +++++++++++ .../longread_umi-0.3.2-foss-2020b.eb | 79 +++++++++++++++++++ .../m/medaka/medaka-1.4.3-foss-2020b.eb | 77 ++++++++++++++++++ .../python-isal-0.11.0-GCCcore-10.2.0.eb | 37 +++++++++ .../r/Racon/Racon-1.4.13-GCCcore-10.2.0.eb | 31 ++++++++ .../Racon-1.4.13-std_invalid_argument.patch | 46 +++++++++++ .../v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb | 40 ++++++++++ 9 files changed, 430 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.4.13-std_invalid_argument.patch create mode 100644 easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..64cfa8b2538 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb @@ -0,0 +1,52 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '3.4' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('python-isal', '0.11.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + ('dnaio', '0.5.1', { + 'checksums': ['c68ecffbf653dfe122f1c10fb8d7c5957ad68acc5c9035c66f81eba1a591d31c'], + }), + (name, version, { + 'checksums': ['eb8d52d45a7d38bd3ddc901eb397599bca8716a20d39e2b1feeb20242352dab2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cutadapt --help", "cutadapt --version"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb new file mode 100644 index 00000000000..e79e34bf1e4 --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'edlib' +version = '1.3.9' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766'] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..df76b6b84fa --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.30.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['bcf592c04fdfa19e723d2adf53d3e0f4efd5b956bb618fed54a1108d76a6eb56'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [('NASM', '2.15.05')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +_bins = ['bin/igzip'] +_includes = ['include/%(namelower)s.h'] +_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test', 'types']] +_libs = ['lib/libisal.%s' % l for l in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': _bins + _includes + _libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb new file mode 100644 index 00000000000..dc667caa8cf --- /dev/null +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -0,0 +1,79 @@ +easyblock = 'Bundle' + +name = 'longread_umi' +version = '0.3.2' + +homepage = 'https://github.com/SorenKarst/longread_umi' +description = "A collection of scripts for processing longread UMI data." +github_account = 'SorenKarst' + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('cutadapt', '3.4'), + ('BCFtools', '1.11'), + ('BWA', '0.7.17'), + ('Filtlong', '0.2.0'), + ('gawk', '5.1.0'), + ('medaka', '1.4.3'), + ('minimap2', '2.18'), + ('parallel', '20210322'), + ('Pysam', '0.16.0.1'), + ('Racon', '1.4.13'), + ('SAMtools', '1.11'), + ('seqtk', '1.3'), + ('VSEARCH', '2.18.0'), +] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['62b8e156c00c0ec10fa8eae1cde5430922462f167fc537417ce0b47cd50a20cb'], + 'start_dir': '%(name)s-%(version)s', + }), + ('Porechop', '0.2.4', { + 'easyblock': 'PythonPackage', + 'source_urls': ['https://github.com/rrwick/Porechop/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +# Adapt the build-in tool check, but make it fail on error +local_deps_patch = ( + "sed -i" + "-e '2s;^;set -e ;' " + "-e 's/USEARCH=usearch/USEARCH=vsearch/'" + "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;'" + "%(installdir)s/scripts/dependencies.sh" +) + +postinstallcmds = [ + 'find %(installdir)s -name "*.sh" -exec chmod +x {} \;', + 'ln -s %(installdir)s/longread_umi.sh %(installdir)s/bin/longread_umi', + 'cp %(installdir)s/scripts/adapters.py %(installdir)s/lib/python%(pyshortver)s/site-packages/porechop/', + local_deps_patch, +] + +sanity_check_paths = { + 'files': ['bin/longread_umi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'longread_umi -h | grep qc_pipeline', + 'longread_umi nanopore_pipeline -h | grep rrna_operon', + 'source %(installdir)s/scripts/dependencies.sh && longread_umi_version_dump', +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb new file mode 100644 index 00000000000..e789ea6b684 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -0,0 +1,77 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.4.3' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [('Autotools', '20200321')] + +dependencies = [ + ('Python', '3.8.6'), + ('TensorFlow', '2.5.0'), + ('Biopython', '1.78'), + ('h5py', '3.1.0'), + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.11'), + ('minimap2', '2.18'), + ('HTSlib', '1.11'), + ('Racon', '1.4.13'), + ('spoa', '4.0.7'), + ('networkx', '2.5'), + ('edlib', '1.3.9'), + ('pyspoa', '0.0.8'), + ('ont-fast5-api', '3.3.0'), + ('pyfaidx', '0.5.9.5'), + ('python-isal', '0.11.0'), +] + +use_pip = True + +exts_list = [ + ('mappy', '2.20', { + 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], + }), + ('parasail', '1.2.4', { + 'checksums': ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'], + }), + ('xopen', '1.1.0', { + 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], + }), + ('whatshap', '1.1', { + 'checksums': ['4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + (name, version, { + 'patches': ['medaka-1.4.3_use-SAMtools-dep.patch'], + 'preinstallopts': 'sed -i -e "s/h5py<3.0.0/h5py/" -e "s/tensorflow==2.2.2/tensorflow/" requirements.txt &&', + 'checksums': [ + '59997b5fdaff6f2040f2df2d3d3eb2d6d1805916a720e8275309caf4d2d4b8a5', # medaka-1.4.3.tar.gz + '06b1d8344035ebcfaf1893e62f37db9b4cab0053ad7a073113630872d44be33e', # medaka-1.4.3_use-SAMtools-dep.patch + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["medaka --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..fd2df03c9ca --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '0.11.0' +_modname = 'isal' + +homepage = 'https://github.com/pycompression/python-isal' +description = """Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'pycompression' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3959ce30f1043ae591bc9d6ee9edb5781c09cc15c69dd5361517d29b56327260'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('ISA-L', '2.30.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' +installopts = '--no-binary isal' + +options = {'modulename': _modname} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..8b398e16c58 --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.4.13' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/lbcb-sci/racon/releases/download/%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +patches = ['Racon-1.4.13-std_invalid_argument.patch'] +checksums = [ + '4220e98bf84768483bd94eef62a0821cffc74f4e7139c74685c08161909263b0', # racon-v1.4.13.tar.gz + '7bdfff1b431f2fc105b08ad8336c90472d5a17a03caf109c97d0c6ab716c8092', # Racon-1.4.13-std_invalid_argument.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.4.13-std_invalid_argument.patch b/easybuild/easyconfigs/r/Racon/Racon-1.4.13-std_invalid_argument.patch new file mode 100644 index 00000000000..2cedd7e2f16 --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.4.13-std_invalid_argument.patch @@ -0,0 +1,46 @@ +Binary files racon-v1.4.13-old/.git/modules/vendor/spoa/index and racon-v1.4.13/.git/modules/vendor/spoa/index differ +diff -ruN racon-v1.4.13-old/vendor/spoa/src/alignment_engine.cpp racon-v1.4.13/vendor/spoa/src/alignment_engine.cpp +--- racon-v1.4.13-old/vendor/spoa/src/alignment_engine.cpp 2021-09-14 14:24:53.358413371 +0200 ++++ racon-v1.4.13/vendor/spoa/src/alignment_engine.cpp 2021-09-14 14:26:58.046107581 +0200 +@@ -7,6 +7,7 @@ + #include + #include + #include ++#include + + #include "sisd_alignment_engine.hpp" + #include "simd_alignment_engine.hpp" +diff -ruN racon-v1.4.13-old/vendor/spoa/src/graph.cpp racon-v1.4.13/vendor/spoa/src/graph.cpp +--- racon-v1.4.13-old/vendor/spoa/src/graph.cpp 2021-09-14 14:24:53.358413371 +0200 ++++ racon-v1.4.13/vendor/spoa/src/graph.cpp 2021-09-14 14:26:52.550165125 +0200 +@@ -8,6 +8,7 @@ + #include + #include + #include ++#include + + #include "spoa/graph.hpp" + +diff -ruN racon-v1.4.13-old/vendor/spoa/src/main.cpp racon-v1.4.13/vendor/spoa/src/main.cpp +--- racon-v1.4.13-old/vendor/spoa/src/main.cpp 2021-09-14 14:24:53.358413371 +0200 ++++ racon-v1.4.13/vendor/spoa/src/main.cpp 2021-09-14 14:26:43.670258101 +0200 +@@ -3,6 +3,7 @@ + #include + #include + #include ++#include + #include + + #include "sequence.hpp" +diff -ruN racon-v1.4.13-old/vendor/spoa/test/spoa_test.cpp racon-v1.4.13/vendor/spoa/test/spoa_test.cpp +--- racon-v1.4.13-old/vendor/spoa/test/spoa_test.cpp 2021-09-14 14:24:53.357413382 +0200 ++++ racon-v1.4.13/vendor/spoa/test/spoa_test.cpp 2021-09-14 14:27:13.949941070 +0200 +@@ -4,6 +4,8 @@ + * @brief Spoa unit test source file + */ + ++#include ++ + #include "spoa_test_config.h" + + #include "sequence.hpp" diff --git a/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..0e0ca81463a --- /dev/null +++ b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.18.0-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'VSEARCH' +version = '2.18.0' + +homepage = 'https://github.com/torognes/vsearch' +description = """VSEARCH supports de novo and reference based chimera detection, + clustering, full-length and prefix dereplication, rereplication, + reverse complementation, masking, all-vs-all pairwise global alignment, + exact and global alignment searching, shuffling, subsampling and sorting. + It also supports FASTQ file analysis, filtering, + conversion and merging of paired-end reads.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/torognes/vsearch/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['faa585ec2767e15a8ad3c2b78921b789a3b174fe3b0eecb3397b1c795808e982'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +preconfigopts = './autogen.sh &&' + +configopts = '--disable-pdfman ' + +sanity_check_paths = { + 'files': ['bin/vsearch'], + 'dirs': [], +} + +sanity_check_commands = ['vsearch --help'] + +moduleclass = 'bio' From 7708438eab251fd4e309763b244f8d880393ae36 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 15 Sep 2021 11:27:33 +0100 Subject: [PATCH 1289/9987] Add OpenSSL to fix a link error --- easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb index dbd3d358708..aba92e6debb 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb @@ -21,6 +21,7 @@ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), ('util-linux', '2.36'), + ('OpenSSL', '1.1.1k'), ] buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' From e475cd9cb291feee51c1cc4663267750c8bbc8fb Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 12:26:50 +0000 Subject: [PATCH 1290/9987] ETE bumped to 3.1.2, required for artic --- .../easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb new file mode 100644 index 00000000000..f4d0c02af99 --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.2' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +checksums = ['4fc987b8c529889d6608fab1101f1455cb5cbd42722788de6aea9c7d0a8e59e9'] + +dependencies = [ + ('lxml', '4.6.2'), + ('Python', '3.8.6'), + ('PyQt5', '5.15.1'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From e1142f473b3fc2b38053ff0a87df400ad00d4c57 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 12:31:28 +0000 Subject: [PATCH 1291/9987] {bio}[foss/2020b] IQ-TREE bumped to 2.1.2, required for artic --- .../i/IQ-TREE/IQ-TREE-2.1.2-foss-2020b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-foss-2020b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-foss-2020b.eb new file mode 100644 index 00000000000..6cffe4a16df --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-foss-2020b.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.1.2' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'foss', 'version': '2020b'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_use_EB_LSD2.patch'] +checksums = [ + '3aaf5ac7f60d852ac8b733fb82832c049ca48b7203a6a865e99c5af359fcca5a', # v2.1.2.tar.gz + 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816', # IQ-TREE-2.1.2_use_EB_LSD2.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Eigen', '3.3.9'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.74.0'), + ('LSD2', '2.2'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +moduleclass = 'bio' From 33ec7cf1cae8cfc6ab8ec7972d33ffa666000d15 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 12:36:31 +0000 Subject: [PATCH 1292/9987] {bio}[GCCcore/10.2.0] LSD2 bumped to 2.2, required for artic #13852 --- .../l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..82407cd707a --- /dev/null +++ b/easybuild/easyconfigs/l/LSD2/LSD2-2.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'LSD2' +version = '2.2' + +homepage = 'https://github.com/tothuhien/lsd2' +description = "Least-squares methods to estimate rates and dates from phylogenies" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'tothuhien' + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v.%(version)s.tar.gz'] +patches = ['%(name)s-1.9.7_fix_cmake_to_build_lib_and_binary.patch'] +checksums = [ + '6573398d0e77bc5fe76587d8676428b77fe15fe6e45fb8526f448d1c739d3cd9', # v.2.2.tar.gz + # LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch + '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6', +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From 67a76ebbb7b10573741f40e8152b03b8c9436295 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 15 Sep 2021 14:56:54 +0200 Subject: [PATCH 1293/9987] adding easyconfigs: BioPerl-1.7.8-GCCcore-10.3.0.eb --- .../b/BioPerl/BioPerl-1.7.8-GCCcore-10.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e9f1133c432 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-10.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'Bundle' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Perl', '5.32.1'), + ('XML-LibXML', '2.0207'), + ('DB_File', '1.856'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + ('XML::DOM::XPath', '0.14', { + 'source_tmpl': 'XML-DOM-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': ['0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), + ('BioPerl', version, { + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' From cd1782e3119b587619323c6dfb0897d939905cb4 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 15 Sep 2021 14:59:01 +0200 Subject: [PATCH 1294/9987] adding easyconfigs: ClustalW2-2.1-foss-2021a.eb --- .../c/ClustalW2/ClustalW2-2.1-foss-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2021a.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2021a.eb new file mode 100644 index 00000000000..194049ef2c4 --- /dev/null +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-foss-2021a.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute +# foss-2021a modified by: +# Sebastien Moretti +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'ClustalW2' +version = '2.1' + +# license = LGPL3.0 +homepage = 'http://www.clustal.org/clustal2/' +description = """ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.clustal.org/download/%(version)s'] +sources = ['clustalw-%(version)s.tar.gz'] +checksums = ['e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' From 30e0a63438ea852e6d9b9a7bf1ce4ea6ea19fc4b Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 13:36:43 +0000 Subject: [PATCH 1295/9987] {bio}[GCCcore/10.2.0] Longshot bumped to 0.4.3, required for artic #13852 --- .../Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..07d70a35c94 --- /dev/null +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +# Updated to 0.4.3 and GCCcore-10.2.0 +# J. Sassmannshausen (GSTT/NHS UK) +# +easyblock = 'Binary' + +name = 'Longshot' +version = '0.4.3' + +homepage = 'https://github.com/pjedge/longshot' +description = """Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific + Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs + a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can + be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/pjedge/longshot/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb2a27a165567ed10b43eb915b195d72193005008d6a91e0d9393282f22f3192'] + +builddependencies = [ + ('binutils', '2.35'), + ('Rust', '1.52.1'), + ('Clang', '11.0.1'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +extract_sources = True + +install_cmd = "cargo install --root %(installdir)s --path ." + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' From 45c1a00d49d9b11b01fc50de6d55d44ad7b171b6 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 13:40:18 +0000 Subject: [PATCH 1296/9987] {bio}[GCCcore/10.2.0] Muscle bumped to 3.8.31, required for artic #13852 --- .../m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6487d58f18e --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' From d113969c644eec049f2984c4b1640e9429b38e47 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 13:43:12 +0000 Subject: [PATCH 1297/9987] {bio}[GCCcore/10.2.0] Racon bumped to 1.4.21, required for artic #13852 --- .../r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..dfa9bddceeb --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.4.21' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/lbcb-sci/racon/releases/download/%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['df99208ebef6a12e1da11a31dade2eafe13a4cd80b4917cce44d44d879b5aee4'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' From b3086786d7ca5262b726c6897c90559fee917d1b Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 13:55:03 +0000 Subject: [PATCH 1298/9987] {lang}[GCCcore/10.2.0] Rust bumped to 1.52.1, required for artic #13852 --- .../r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c8843bcda9f --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.52.1' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +checksums = ['3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' From ec3af0860cf8ef8acc7b830ec928af09739c4cce Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 13:57:14 +0000 Subject: [PATCH 1299/9987] {bio}[GCCcore/10.2.0] edlib bumped to 1.3.9, required for artic #13852 --- .../e/edlib/edlib-1.3.9-GCC-10.2.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb new file mode 100644 index 00000000000..e79e34bf1e4 --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'edlib' +version = '1.3.9' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766'] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' From 2679197f38931887eb053d2d15dcc019589e8d02 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 14:00:06 +0000 Subject: [PATCH 1300/9987] {tools}[foss/2020b] networkx bumped to 2.6.2, required for artic #13852 --- .../n/networkx/networkx-2.6.2-foss-2020b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb new file mode 100644 index 00000000000..8a5bed3a719 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.6.2-foss-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.6.2' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2306f1950ce772c5a59a57f5486d59bb9cab98497c45fc49cbc45ac0dec119bb'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 9f88e2988dd2eacb8ea59ed93517e8d4c648bfa0 Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 15 Sep 2021 16:04:22 +0200 Subject: [PATCH 1301/9987] adding easyconfigs: QIIME2-2021.8.eb --- .../easyconfigs/q/QIIME2/QIIME2-2021.8.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/q/QIIME2/QIIME2-2021.8.eb diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2021.8.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2021.8.eb new file mode 100644 index 00000000000..27c300f63a1 --- /dev/null +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2021.8.eb @@ -0,0 +1,31 @@ +# EasyBuild recipy for QIIME2 +# Author: Caspar van Leeuwen +# SURFsara - The Netherlands + +easyblock = 'Conda' + +name = 'QIIME2' +version = '2021.8' + +homepage = 'http://qiime2.org/' +description = """QIIME is an open-source bioinformatics pipeline for performing microbiome analysis + from raw DNA sequencing data.""" + +source_urls = ['https://data.qiime2.org/distro/core/'] +sources = ['qiime2-%(version)s-py38-linux-conda.yml'] +checksums = ['af381370dd034b71fe72925b1890cc7bc7566e5d4409eaef91825ffb446455a0'] + +toolchain = SYSTEM + +builddependencies = [('Miniconda3', '4.9.2')] + +environment_file = 'qiime2-%(version)s-py38-linux-conda.yml' + +sanity_check_commands = ['qiime info'] + +sanity_check_paths = { + 'files': ["bin/qiime"], + 'dirs': ["lib", "include"], +} + +moduleclass = 'bio' From 86574dcee19ee2bf7b1f799eef6d78c5a38149a8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 15 Sep 2021 15:37:46 +0100 Subject: [PATCH 1302/9987] Use OpenSSL link wrapper --- easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb index aba92e6debb..b8b507b2aa4 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), ('util-linux', '2.36'), - ('OpenSSL', '1.1.1k'), + ('OpenSSL', '1.1.', '', True), ] buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' From 563b19876d3ab0705bf2bb79f740fa0deb9092cf Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 15 Sep 2021 15:40:49 +0100 Subject: [PATCH 1303/9987] Fix link wrapper typo --- easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb index b8b507b2aa4..e5ec4e0190e 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), ('util-linux', '2.36'), - ('OpenSSL', '1.1.', '', True), + ('OpenSSL', '1.1', '', True), ] buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' From ebb4342352c22be7d021f6e874ca80e4febf0983 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Sep 2021 16:43:08 +0200 Subject: [PATCH 1304/9987] add missing Brotli dependency for freetype 2.11.0 + add sanity check command --- .../b/Brotli/Brotli-1.0.9-GCCcore-11.2.0.eb | 36 +++++++++++++++++++ .../freetype-2.11.0-GCCcore-11.2.0.eb | 3 ++ 2 files changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..620677d96b1 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Brotli' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brotli-%(version)s_pc_link_flags.patch'] +checksums = [ + 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz + '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'dirs': [], +} + +sanity_check_commands = ["brotli --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.11.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.11.0-GCCcore-11.2.0.eb index 3f312567b39..5531188111c 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.11.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.11.0-GCCcore-11.2.0.eb @@ -27,6 +27,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('libpng', '1.6.37'), ('zlib', '1.2.11'), + ('Brotli', '1.0.9'), ] configopts = '--enable-freetype-config --with-harfbuzz=no' @@ -37,4 +38,6 @@ sanity_check_paths = { 'dirs': ['include/freetype2'], } +sanity_check_commands = ["freetype-config --help"] + moduleclass = 'vis' From 7d4fcf01417cb77d6fad2e6bce03f44246dc7af1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Sep 2021 16:48:50 +0200 Subject: [PATCH 1305/9987] adding easyconfigs: jax-0.2.20-foss-2021a.eb and patches: jaxlib-0.1.71_no-tensorflow-download.patch --- .../j/jax/jax-0.2.20-foss-2021a.eb | 100 ++++++++++++++++++ ...jaxlib-0.1.71_no-tensorflow-download.patch | 30 ++++++ 2 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb create mode 100644 easybuild/easyconfigs/j/jax/jaxlib-0.1.71_no-tensorflow-download.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb new file mode 100644 index 00000000000..16a67803d1a --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb @@ -0,0 +1,100 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.2.20' +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('pytest-xdist', '2.3.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.32.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = 'b5b1ff47ad250c3e38dcadef5f6bc414b0a533ee' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +local_jax_prebuildopts = "sed -i 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir + +use_pip = True + +# running the tests with lots of cores results in test failures because not enough threads can be started, +# so limit to a reasonable number of cores to use at maximum +maxparallel = 10 + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '0.13.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], + }), + ('jaxlib', '0.1.71', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + 'jaxlib-0.1.70_add-bazel-args-to-shutdown.patch', + 'jaxlib-%(version)s_no-tensorflow-download.patch', + ], + 'checksums': [ + # jaxlib-v0.1.71.tar.gz + '07a602e4e2e37fe46c17eeb6c25e80932f6abc5d1dde59e7868e7e3bb08f46c6', + # tensorflow-b5b1ff47ad250c3e38dcadef5f6bc414b0a533ee.tar.gz + '6b14b66a74728736359afcb491820fa3e713ea4a74bff0defe920f3453a3a0f0', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', + # jaxlib-0.1.71_no-tensorflow-download.patch + '693cff114553fa5591aa4cb3d777c9b7dea1ded1effef76d7d45d11cd2fc3819', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'runtest': "pytest -n %(parallel)s tests", + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': ['2e40bd8e2493a3609177b122c583636c0c88c5e695f8041190eefdfd42a6fc5b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jaxlib-0.1.71_no-tensorflow-download.patch b/easybuild/easyconfigs/j/jax/jaxlib-0.1.71_no-tensorflow-download.patch new file mode 100644 index 00000000000..972056bfd46 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jaxlib-0.1.71_no-tensorflow-download.patch @@ -0,0 +1,30 @@ +avoid downloading TensorFlow during the build, add placeholder to inject location of pre-downloaded TensorFlow sources +author: Denis Kristak (INUITS), updated for jaxlib 0.1.71 by Kenneth Hoste (HPC-UGent) +--- jax-jaxlib-v0.1.71/WORKSPACE.orig 2021-09-07 17:47:01.537446458 +0200 ++++ jax-jaxlib-v0.1.71/WORKSPACE 2021-09-07 18:58:49.934107116 +0200 +@@ -5,13 +5,18 @@ + # b) get the sha256 hash of the commit by running: + # curl -L https://github.com/tensorflow/tensorflow/archive/.tar.gz | sha256sum + # and update the sha256 with the result. +-http_archive( +- name = "org_tensorflow", +- sha256 = "6b14b66a74728736359afcb491820fa3e713ea4a74bff0defe920f3453a3a0f0", +- strip_prefix = "tensorflow-b5b1ff47ad250c3e38dcadef5f6bc414b0a533ee", +- urls = [ +- "https://github.com/tensorflow/tensorflow/archive/b5b1ff47ad250c3e38dcadef5f6bc414b0a533ee.tar.gz", +- ], ++#http_archive( ++# name = "org_tensorflow", ++# sha256 = "6b14b66a74728736359afcb491820fa3e713ea4a74bff0defe920f3453a3a0f0", ++# strip_prefix = "tensorflow-b5b1ff47ad250c3e38dcadef5f6bc414b0a533ee", ++# urls = [ ++# "https://github.com/tensorflow/tensorflow/archive/b5b1ff47ad250c3e38dcadef5f6bc414b0a533ee.tar.gz", ++# ], ++#) ++ ++local_repository( ++ name = "org_tensorflow", ++ path = "pathToSed", + ) + + # For development, one can use a local TF repository instead. From 8ccc74d4cce8e8ce2181f93a5d1001785c05cb0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Sep 2021 16:59:28 +0200 Subject: [PATCH 1306/9987] make binutils a build-only dependency for Brotli + add sanity check command --- .../b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb | 8 ++++---- .../b/Brotli/Brotli-1.0.9-GCCcore-10.3.0.eb | 8 ++++---- .../b/Brotli/Brotli-1.0.9-GCCcore-8.3.0.eb | 11 ++++++----- 3 files changed, 14 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb index 72c9f12ad60..8626bb27334 100644 --- a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.2.0.eb @@ -1,4 +1,5 @@ easyblock = 'CMakeMake' + name = 'Brotli' version = '1.0.9' @@ -19,11 +20,8 @@ checksums = [ '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch ] -separate_build_dir = True - -dependencies = [('binutils', '2.35')] - builddependencies = [ + ('binutils', '2.35'), ('CMake', '3.18.4'), ] @@ -33,4 +31,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["brotli --help"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.3.0.eb index b5eb9cab797..7483df479f4 100644 --- a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-10.3.0.eb @@ -1,4 +1,5 @@ easyblock = 'CMakeMake' + name = 'Brotli' version = '1.0.9' @@ -19,11 +20,8 @@ checksums = [ '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch ] -separate_build_dir = True - -dependencies = [('binutils', '2.36.1')] - builddependencies = [ + ('binutils', '2.36.1'), ('CMake', '3.20.1'), ] @@ -33,4 +31,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["brotli --help"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-8.3.0.eb index 23cf970b408..02b2b379aaf 100644 --- a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-8.3.0.eb @@ -5,6 +5,7 @@ # Fred Hutchinson Cancer Research Center - Seattle Washington - US # easyblock = 'CMakeMake' + name = 'Brotli' version = '1.0.9' @@ -21,17 +22,17 @@ source_urls = ['https://github.com/google/brotli/archive'] sources = ['v%(version)s.tar.gz'] checksums = ['f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46'] -separate_build_dir = True - -dependencies = [('binutils', '2.32')] - builddependencies = [ + ('binutils', '2.32'), ('CMake', '3.15.3'), ] sanity_check_paths = { - 'files': ['bin/brotli'], + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], 'dirs': [], } +sanity_check_commands = ["brotli --help"] + moduleclass = 'lib' From d6ff096b1be3bd7169a66ff409f21268996ff269 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 16:22:47 +0000 Subject: [PATCH 1307/9987] Included TF-2.2.3, patched to remove the hard-coded TF version --- .../m/medaka/h5py-2.10.0_avoid-mpi-init.patch | 85 +++++++++++++++++++ .../medaka/medaka-1.4.3-TF-version-fix.patch | 15 ++++ .../m/medaka/medaka-1.4.3-foss-2020b.eb | 33 +++++-- 3 files changed, 128 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/m/medaka/h5py-2.10.0_avoid-mpi-init.patch create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.4.3-TF-version-fix.patch diff --git a/easybuild/easyconfigs/m/medaka/h5py-2.10.0_avoid-mpi-init.patch b/easybuild/easyconfigs/m/medaka/h5py-2.10.0_avoid-mpi-init.patch new file mode 100644 index 00000000000..98034776400 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/h5py-2.10.0_avoid-mpi-init.patch @@ -0,0 +1,85 @@ +avoid that 'import h5py' triggers MPI_Init via mpi4py + +backported to h5py 2.10.0 from https://github.com/h5py/h5py/pull/1552 by Kenneth Hoste (HPC-UGent) + +diff -ru h5py-2.10.0.orig/h5py/api_types_ext.pxd h5py-2.10.0/h5py/api_types_ext.pxd +--- h5py-2.10.0.orig/h5py/api_types_ext.pxd 2019-09-06 23:29:33.000000000 +0200 ++++ h5py-2.10.0/h5py/api_types_ext.pxd 2020-05-25 19:30:30.000000000 +0200 +@@ -12,7 +12,7 @@ + include 'config.pxi' + + IF MPI: +- from mpi4py.MPI cimport MPI_Comm, MPI_Info, Comm, Info ++ from mpi4py.libmpi cimport MPI_Comm, MPI_Info + + cdef extern from "stdlib.h": + ctypedef long size_t +@@ -52,6 +52,7 @@ + cdef extern from "Python.h": + ctypedef void PyObject + ctypedef ssize_t Py_ssize_t ++ ctypedef size_t Py_uintptr_t + + PyObject* PyErr_Occurred() + void PyErr_SetString(object type, char *message) +diff -ru h5py-2.10.0.orig/h5py/h5p.pyx h5py-2.10.0/h5py/h5p.pyx +--- h5py-2.10.0.orig/h5py/h5p.pyx 2019-09-06 23:29:33.000000000 +0200 ++++ h5py-2.10.0/h5py/h5p.pyx 2020-05-25 19:33:24.000000000 +0200 +@@ -17,6 +17,7 @@ + from cpython.buffer cimport PyObject_CheckBuffer, \ + PyObject_GetBuffer, PyBuffer_Release, \ + PyBUF_SIMPLE ++from cpython.long cimport PyLong_AsVoidPtr + + from utils cimport require_tuple, convert_dims, convert_tuple, \ + emalloc, efree, \ +@@ -1161,7 +1162,7 @@ + + IF MPI: + @with_phil +- def set_fapl_mpio(self, Comm comm not None, Info info not None): ++ def set_fapl_mpio(self, comm, info): + """ (Comm comm, Info info) + + Set MPI-I/O Parallel HDF5 driver. +@@ -1169,7 +1170,12 @@ + Comm: An mpi4py.MPI.Comm instance + Info: An mpi4py.MPI.Info instance + """ +- H5Pset_fapl_mpio(self.id, comm.ob_mpi, info.ob_mpi) ++ from mpi4py.MPI import Comm, Info, _handleof ++ assert isinstance(comm, Comm) ++ assert isinstance(info, Info) ++ cdef Py_uintptr_t _comm = _handleof(comm) ++ cdef Py_uintptr_t _info = _handleof(info) ++ H5Pset_fapl_mpio(self.id, _comm, _info) + + + @with_phil +@@ -1183,20 +1189,22 @@ + """ + cdef MPI_Comm comm + cdef MPI_Info info ++ from mpi4py.MPI import Comm, Info, _addressof + + H5Pget_fapl_mpio(self.id, &comm, &info) + pycomm = Comm() +- pyinfo = Info() +- MPI_Comm_dup(comm, &pycomm.ob_mpi) +- MPI_Info_dup(info, &pyinfo.ob_mpi) ++ MPI_Comm_dup(comm, PyLong_AsVoidPtr(_addressof(pycomm))) + MPI_Comm_free(&comm) ++ ++ pyinfo = Info() ++ MPI_Info_dup(info, PyLong_AsVoidPtr(_addressof(pyinfo))) + MPI_Info_free(&info) + + return (pycomm, pyinfo) + + + @with_phil +- def set_fapl_mpiposix(self, Comm comm not None, bint use_gpfs_hints=0): ++ def set_fapl_mpiposix(self, comm, bint use_gpfs_hints=0): + """ Obsolete. + """ + raise RuntimeError("MPI-POSIX driver is broken; removed in h5py 2.3.1") diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-TF-version-fix.patch b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-TF-version-fix.patch new file mode 100644 index 00000000000..a79ce93b09c --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-TF-version-fix.patch @@ -0,0 +1,15 @@ +Removing hard-coded version for TensorFlow +author: J. Sassmannshausen (NHS/GSTT) +diff --git a/medaka-1.4.3.orig/requirements.txt b/medaka-1.4.3/requirements.txt +index 58f6187..3eaf4c3 100644 +--- a/medaka-1.4.3.orig/requirements.txt ++++ b/medaka-1.4.3/requirements.txt +@@ -6,7 +6,7 @@ edlib + grpcio + h5py<3.0.0 # tf has a pin for this, but pip gets confused + intervaltree +-tensorflow==2.2.2 ++tensorflow~=2.2.2 + numpy + mappy + ont_fast5_api diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index b82b55027f4..8c4f387a624 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -19,10 +19,10 @@ builddependencies = [('Autotools', '20200321')] dependencies = [ ('Python', '3.8.6'), # includes cffi - # TensorFlow 2.2.2 required by medaka 1.4.3, see requirements.txt - ('TensorFlow', '2.2.2'), + # TensorFlow 2.2.3 required by medaka 1.4.3, see requirements.txt + # We need to patch medaka to use that version, see below. + ('TensorFlow', '2.2.3'), ('Biopython', '1.78'), - ('h5py', '3.1.0'), # Pysam 0.16.0.1 is strictly required, see requirements.txt ('Pysam', '0.16.0.1'), ('SAMtools', '1.12'), @@ -34,13 +34,32 @@ dependencies = [ ('networkx', '2.6.2'), ('edlib', '1.3.9'), ('pyspoa', '0.0.8'), - ('ont-fast5-api', '3.3.0'), ('pyfaidx', '0.5.9.5'), ] use_pip = True +sanity_pip_check = True exts_list = [ + # TF <= 2.4 needs h5py 2.10, later versions allow 3.x + ('h5py', '2.10.0', { + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], + 'checksums': [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + # h5py-2.10.0_avoid-mpi-init.patch + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', + ], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + }), + # This is a requirement for ont-fast5-api below + ('progressbar33', '2.4', { + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + 'modulename': 'progressbar', + }), + # ont-fast-5-api in EB uses h5py-3.x, but see above. So we put it here + ('ont-fast5-api', '3.3.0', { + 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], + }), ('mappy', '2.20', { 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], }), @@ -63,10 +82,14 @@ exts_list = [ 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], }), (name, version, { - 'patches': ['medaka-1.4.3_use-SAMtools-dep.patch'], + 'patches': [ + 'medaka-1.4.3_use-SAMtools-dep.patch', + 'medaka-1.4.3-TF-version-fix.patch', + ], 'checksums': [ '59997b5fdaff6f2040f2df2d3d3eb2d6d1805916a720e8275309caf4d2d4b8a5', # medaka-1.4.3.tar.gz '06b1d8344035ebcfaf1893e62f37db9b4cab0053ad7a073113630872d44be33e', # medaka-1.4.3_use-SAMtools-dep.patch + 'cdafcd05150a8193747d8d240d9b2d3499ae901483917e9252bb91b02fa56b03', # medaka-1.4.3-TF-version-fix.patch ], }), ] From 8e6ef1753988eac6ff1fdb5c43d49d70b24d6dfc Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Sep 2021 16:51:40 +0000 Subject: [PATCH 1308/9987] Added missing binutils --- .../easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb index 6487d58f18e..2230dff6fce 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.2.0.eb @@ -20,6 +20,10 @@ checksums = [ '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch ] +builddependencies = [ + ('binutils', '2.35'), +] + files_to_copy = [ (["muscle"], 'bin')] From e15082589c4585c15a70822b03cb8a361a53d77f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Sep 2021 11:05:42 +0200 Subject: [PATCH 1309/9987] don't install h5py 2.10.0 as extension in medaka easyconfig, already included with TensorFlow 2.2.3 --- .../m/medaka/h5py-2.10.0_avoid-mpi-init.patch | 85 ------------------- .../m/medaka/medaka-1.4.3-foss-2020b.eb | 15 +--- 2 files changed, 3 insertions(+), 97 deletions(-) delete mode 100644 easybuild/easyconfigs/m/medaka/h5py-2.10.0_avoid-mpi-init.patch diff --git a/easybuild/easyconfigs/m/medaka/h5py-2.10.0_avoid-mpi-init.patch b/easybuild/easyconfigs/m/medaka/h5py-2.10.0_avoid-mpi-init.patch deleted file mode 100644 index 98034776400..00000000000 --- a/easybuild/easyconfigs/m/medaka/h5py-2.10.0_avoid-mpi-init.patch +++ /dev/null @@ -1,85 +0,0 @@ -avoid that 'import h5py' triggers MPI_Init via mpi4py - -backported to h5py 2.10.0 from https://github.com/h5py/h5py/pull/1552 by Kenneth Hoste (HPC-UGent) - -diff -ru h5py-2.10.0.orig/h5py/api_types_ext.pxd h5py-2.10.0/h5py/api_types_ext.pxd ---- h5py-2.10.0.orig/h5py/api_types_ext.pxd 2019-09-06 23:29:33.000000000 +0200 -+++ h5py-2.10.0/h5py/api_types_ext.pxd 2020-05-25 19:30:30.000000000 +0200 -@@ -12,7 +12,7 @@ - include 'config.pxi' - - IF MPI: -- from mpi4py.MPI cimport MPI_Comm, MPI_Info, Comm, Info -+ from mpi4py.libmpi cimport MPI_Comm, MPI_Info - - cdef extern from "stdlib.h": - ctypedef long size_t -@@ -52,6 +52,7 @@ - cdef extern from "Python.h": - ctypedef void PyObject - ctypedef ssize_t Py_ssize_t -+ ctypedef size_t Py_uintptr_t - - PyObject* PyErr_Occurred() - void PyErr_SetString(object type, char *message) -diff -ru h5py-2.10.0.orig/h5py/h5p.pyx h5py-2.10.0/h5py/h5p.pyx ---- h5py-2.10.0.orig/h5py/h5p.pyx 2019-09-06 23:29:33.000000000 +0200 -+++ h5py-2.10.0/h5py/h5p.pyx 2020-05-25 19:33:24.000000000 +0200 -@@ -17,6 +17,7 @@ - from cpython.buffer cimport PyObject_CheckBuffer, \ - PyObject_GetBuffer, PyBuffer_Release, \ - PyBUF_SIMPLE -+from cpython.long cimport PyLong_AsVoidPtr - - from utils cimport require_tuple, convert_dims, convert_tuple, \ - emalloc, efree, \ -@@ -1161,7 +1162,7 @@ - - IF MPI: - @with_phil -- def set_fapl_mpio(self, Comm comm not None, Info info not None): -+ def set_fapl_mpio(self, comm, info): - """ (Comm comm, Info info) - - Set MPI-I/O Parallel HDF5 driver. -@@ -1169,7 +1170,12 @@ - Comm: An mpi4py.MPI.Comm instance - Info: An mpi4py.MPI.Info instance - """ -- H5Pset_fapl_mpio(self.id, comm.ob_mpi, info.ob_mpi) -+ from mpi4py.MPI import Comm, Info, _handleof -+ assert isinstance(comm, Comm) -+ assert isinstance(info, Info) -+ cdef Py_uintptr_t _comm = _handleof(comm) -+ cdef Py_uintptr_t _info = _handleof(info) -+ H5Pset_fapl_mpio(self.id, _comm, _info) - - - @with_phil -@@ -1183,20 +1189,22 @@ - """ - cdef MPI_Comm comm - cdef MPI_Info info -+ from mpi4py.MPI import Comm, Info, _addressof - - H5Pget_fapl_mpio(self.id, &comm, &info) - pycomm = Comm() -- pyinfo = Info() -- MPI_Comm_dup(comm, &pycomm.ob_mpi) -- MPI_Info_dup(info, &pyinfo.ob_mpi) -+ MPI_Comm_dup(comm, PyLong_AsVoidPtr(_addressof(pycomm))) - MPI_Comm_free(&comm) -+ -+ pyinfo = Info() -+ MPI_Info_dup(info, PyLong_AsVoidPtr(_addressof(pyinfo))) - MPI_Info_free(&info) - - return (pycomm, pyinfo) - - - @with_phil -- def set_fapl_mpiposix(self, Comm comm not None, bint use_gpfs_hints=0): -+ def set_fapl_mpiposix(self, comm, bint use_gpfs_hints=0): - """ Obsolete. - """ - raise RuntimeError("MPI-POSIX driver is broken; removed in h5py 2.3.1") diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 8c4f387a624..17bab30f8aa 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -41,22 +41,13 @@ use_pip = True sanity_pip_check = True exts_list = [ - # TF <= 2.4 needs h5py 2.10, later versions allow 3.x - ('h5py', '2.10.0', { - 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], - 'checksums': [ - '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz - # h5py-2.10.0_avoid-mpi-init.patch - '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', - ], - 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', - }), - # This is a requirement for ont-fast5-api below + # required for ont-fast5-api ('progressbar33', '2.4', { 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], 'modulename': 'progressbar', }), - # ont-fast-5-api in EB uses h5py-3.x, but see above. So we put it here + # ont-fast-5-api easyconfig depends on h5py but we need to stick to h5py 2.x for TensorFlow 2.2.3, + # so we install it as an extension here ('ont-fast5-api', '3.3.0', { 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], }), From 33c3c30380430ff349d27c6be09c8194f1b2f4cf Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 09:15:12 +0000 Subject: [PATCH 1310/9987] adding easyconfigs: rampart-1.2.0-foss-2020b.eb --- .../r/rampart/rampart-1.2.0-foss-2020b.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb b/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb new file mode 100644 index 00000000000..e4b3d5e9c7a --- /dev/null +++ b/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb @@ -0,0 +1,67 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# updated to version 1.0.6 +# J. Sassmannshausen (GSTT(NHS) +# +easyblock = 'PythonBundle' + +name = 'rampart' +version = '1.2.0' + +homepage = "https://github.com/artic-network/rampart/" +description = "Read Assignment, Mapping, and Phylogenetic Analysis in Real Time." +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('nodejs', '12.19.0'), + ('Python', '3.8.6'), + ('Biopython', '1.78'), + ('snakemake', '6.1.0'), + ('minimap2', '2.20'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + # This is not upstream version, but artic tweaked one, which is exactly required. + ('Porechop', '0.3.2pre', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/Porechop/archive'], + 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], + }), + ('binlorry', '1.3.1', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/rambaut/binlorry/archive'], + 'checksums': ['001b74cad497b7253b821ceaac8c0b829b2787396a896fc2d3940a704a149b48'], + }), +] + +# Don't ever try to install unpacked source of nodejs globally! +# Always use 'npm install -g downloaded_file.tar.gz` or you will end up having broken links and installation will fail. +# -d (debug) and --timing can show errors while downloading dependencies +local_install_cmd = "npm install -d --timing --prefix %(installdir)s -g v%(version)s.tar.gz" + +components = [ + (name, version, { + 'easyblock': 'Binary', + 'source_urls': ['https://github.com/artic-network/rampart/archive/'], + 'sources': [{ + 'filename': 'v%(version)s.tar.gz', + # Don't extract downloaded .tar.gz, just copy that to builddir + 'extract_cmd': "cp %s .", + }], + 'checksums': ['96dc10a429e39c1ab241a76c4706a50754908f79f821b5d047be7f420aaf15be'], + 'install_cmd': local_install_cmd, + }), +] + +sanity_check_paths = { + 'files': ['bin/binlorry', 'bin/porechop', 'bin/rampart'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'rampart --help' +] + +moduleclass = 'bio' From 22cd07c69ffa35abfb7139228e13a718f08e8aa0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Sep 2021 11:19:24 +0200 Subject: [PATCH 1311/9987] replace patch by sed command in preinstallopts to loosen up TensorFlow version requirement for medaka --- .../m/medaka/medaka-1.4.3-TF-version-fix.patch | 15 --------------- .../m/medaka/medaka-1.4.3-foss-2020b.eb | 9 +++------ 2 files changed, 3 insertions(+), 21 deletions(-) delete mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.4.3-TF-version-fix.patch diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-TF-version-fix.patch b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-TF-version-fix.patch deleted file mode 100644 index a79ce93b09c..00000000000 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-TF-version-fix.patch +++ /dev/null @@ -1,15 +0,0 @@ -Removing hard-coded version for TensorFlow -author: J. Sassmannshausen (NHS/GSTT) -diff --git a/medaka-1.4.3.orig/requirements.txt b/medaka-1.4.3/requirements.txt -index 58f6187..3eaf4c3 100644 ---- a/medaka-1.4.3.orig/requirements.txt -+++ b/medaka-1.4.3/requirements.txt -@@ -6,7 +6,7 @@ edlib - grpcio - h5py<3.0.0 # tf has a pin for this, but pip gets confused - intervaltree --tensorflow==2.2.2 -+tensorflow~=2.2.2 - numpy - mappy - ont_fast5_api diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 17bab30f8aa..c6ebdb16942 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -38,7 +38,6 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True exts_list = [ # required for ont-fast5-api @@ -73,15 +72,13 @@ exts_list = [ 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], }), (name, version, { - 'patches': [ - 'medaka-1.4.3_use-SAMtools-dep.patch', - 'medaka-1.4.3-TF-version-fix.patch', - ], + 'patches': ['medaka-1.4.3_use-SAMtools-dep.patch'], 'checksums': [ '59997b5fdaff6f2040f2df2d3d3eb2d6d1805916a720e8275309caf4d2d4b8a5', # medaka-1.4.3.tar.gz '06b1d8344035ebcfaf1893e62f37db9b4cab0053ad7a073113630872d44be33e', # medaka-1.4.3_use-SAMtools-dep.patch - 'cdafcd05150a8193747d8d240d9b2d3499ae901483917e9252bb91b02fa56b03', # medaka-1.4.3-TF-version-fix.patch ], + # loosen up TensorFlow version requirements, see also https://github.com/nanoporetech/medaka/issues/323 + 'preinstallopts': "sed -i 's/tensorflow==/tensorflow~=/g' requirements.txt && ", }), ] From 774e8529d0a5c7792385dbb87259e3e492e8c010 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Sep 2021 11:29:11 +0200 Subject: [PATCH 1312/9987] add Python + pkg-config as build dependencies for Rust 1.52.1 with GCCcore/10.2.0 --- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index c8843bcda9f..2e64f844463 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -16,6 +16,8 @@ checksums = ['3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98'] builddependencies = [ ('binutils', '2.35'), ('CMake', '3.18.4'), + ('Python', '3.8.6'), + ('pkg-config', '0.29.2'), ] dependencies = [ From 97242aadde855990be2a0b039dc33dd25b6927de Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 09:42:30 +0000 Subject: [PATCH 1313/9987] minimap downgraded to 2.18 for consistency --- easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb b/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb index e4b3d5e9c7a..841aded3144 100644 --- a/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/r/rampart/rampart-1.2.0-foss-2020b.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.8.6'), ('Biopython', '1.78'), ('snakemake', '6.1.0'), - ('minimap2', '2.20'), + ('minimap2', '2.18'), ] use_pip = True From fbff1288c7038baa386f6d03ee847309fd807289 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 09:48:05 +0000 Subject: [PATCH 1314/9987] adding easyconfigs: Eigen-3.3.9-GCCcore-10.2.0.eb --- .../e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..749a4d82e86 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.3.9-GCCcore-10.2.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.3.9' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['0fa5cafe78f66d2b501b43016858070d52ba47bd9b1016b0165a7b8e04675677'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.35'), # to make CMake compiler health check pass on old systems + ('CMake', '3.18.4'), +] + +moduleclass = 'math' From fc3c3028858c0b886dde3d158fe69601e2fa240b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 16 Sep 2021 11:52:58 +0200 Subject: [PATCH 1315/9987] Fix Racon-1.4.7-gcccuda-2019b.eb --- .../r/Racon/Racon-1.4.7-gcccuda-2019b.eb | 50 +++++++------------ 1 file changed, 18 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.4.7-gcccuda-2019b.eb b/easybuild/easyconfigs/r/Racon/Racon-1.4.7-gcccuda-2019b.eb index 34a23165aa8..127f585c034 100644 --- a/easybuild/easyconfigs/r/Racon/Racon-1.4.7-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/r/Racon/Racon-1.4.7-gcccuda-2019b.eb @@ -11,7 +11,8 @@ description = "Ultrafast consensus module for raw de novo genome assembly of lon toolchain = {'name': 'gcccuda', 'version': '2019b'} -local_bioparser_commit = '0d66534d75b319f43ce5c59fe6548eee48f8f651' +local_vendor_dir = '%(builddir)s/racon-gpu-%(version)s/vendor' +local_extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' sources = [ { @@ -22,59 +23,72 @@ sources = [ 'source_urls': ['https://github.com/clara-genomics/ClaraGenomicsAnalysis/archive'], 'filename': 'ClaraGenomicsAnalysis-20190814.tar.gz', 'download_filename': '416af9f1817a4a70745b3f7cdb7418125159f75c.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_vendor_dir, 'ClaraGenomicsAnalysis'), }, { 'source_urls': ['https://github.com/rvaser/bioparser/archive'], 'filename': 'bioparser-20190817.tar.gz', - 'download_filename': '%s.tar.gz' % local_bioparser_commit, + 'download_filename': '0d66534d75b319f43ce5c59fe6548eee48f8f651.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_vendor_dir, 'bioparser'), }, { 'source_urls': ['https://github.com/martinsos/edlib/archive'], 'filename': 'edlib-20171127.tar.gz', 'download_filename': 'ee36875e944b63abf6f9b9e14c010b445529427d.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_vendor_dir, 'edlib'), }, { 'source_urls': ['https://github.com/google/googletest/archive'], 'filename': 'googletest-20180131.tar.gz', 'download_filename': 'ea31cb15f0c2ab9f5f5b18e82311eb522989d747.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_vendor_dir, 'googletest'), }, { 'source_urls': ['https://github.com/rvaser/logger/archive'], 'filename': 'logger-20190728.tar.gz', 'download_filename': 'b88c8ee8ba59fd07b40c022957b7bdce1a5f8502.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_vendor_dir, 'logger'), }, { 'source_urls': ['https://github.com/rvaser/rampler/archive'], 'filename': 'rampler-20190905.tar.gz', 'download_filename': 'a6dec0140878ba81da90387c77740756fefa4920.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_vendor_dir, 'rampler'), }, { 'source_urls': ['https://github.com/rvaser/spoa/archive'], 'filename': 'spoa-20180523.tar.gz', 'download_filename': '11219575bdcb356c57fb32f54cf23b8da2abc4f0.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_vendor_dir, 'spoa'), }, { 'source_urls': ['https://github.com/rvaser/thread_pool/archive'], 'filename': 'thread_pool-20190530.tar.gz', 'download_filename': '048da9485390ee8b8a7ecedccc598a06ca4429e2.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_vendor_dir, 'thread_pool'), }, { 'source_urls': ['https://github.com/google/benchmark/archive'], 'filename': 'benchmark-20190513.tar.gz', 'download_filename': '090faecb454fbd6e6e17a75ef8146acb037118d4.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_vendor_dir, 'ClaraGenomicsAnalysis/3rdparty/benchmark'), }, { 'source_urls': ['https://github.com/gabime/spdlog/archive'], 'filename': 'spdlog-20190417.tar.gz', 'download_filename': '366935142780e3754b358542f0fd5ed83793b263.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_vendor_dir, 'ClaraGenomicsAnalysis/3rdparty/spdlog'), }, ] patches = [ - ('%(name)s-%(version)s_patch_bioparsers_zlib.patch', '../bioparser-%s' % local_bioparser_commit) + ('%(name)s-%(version)s_patch_bioparsers_zlib.patch', '%s/bioparser' % local_vendor_dir) ] checksums = [ '7d59c310eb8e7472f6b7bb523206cb0642fe7db32335011cd6b9e7b31cd549ee', # 1.4.7.tar.gz - '807b337c6016f92a03238a29ca646679cdd7cb9f48ea0f77ccb8ebcbe2596dba', # ClaraGenomicsAnalysis-20190814.tar.gz + # ClaraGenomicsAnalysis-20190814.tar.gz + ('807b337c6016f92a03238a29ca646679cdd7cb9f48ea0f77ccb8ebcbe2596dba', + 'e98fa393a5dd31401300cf00719cde3fd0625bcc751523b41355bfd75652b135', # Repo renamed + ), '67a327e3686e76e7502b7462b5fcd2d04c3dc6c23496b11699aa1a992de091d5', # bioparser-20190817.tar.gz '60c79ef9476d6c874beee79ea63597000b39b6ced8c6c406e8037e8f4b25093f', # edlib-20171127.tar.gz '41a782bacfed269409e533599f2272910e6c7ccd0c3d03f9694c693916070180', # googletest-20180131.tar.gz @@ -92,35 +106,7 @@ builddependencies = [ ('zlib', '1.2.11'), ] -local_vendor_dir = '%(builddir)s/racon-gpu-%(version)s/vendor/' - -# Move downloaded source to submodule dirs -# ClaraGenomicsAnalysis -preconfigopts = "mv %%(builddir)s/ClaraGenomicsAnalysis-*/* %s/ClaraGenomicsAnalysis/ && " % local_vendor_dir -# bioparser -preconfigopts += "mv %%(builddir)s/bioparser-*/* %s/bioparser/ && " % local_vendor_dir -# edlib -preconfigopts += "mv %%(builddir)s/edlib-*/* %s/edlib/ && " % local_vendor_dir -# googletest -preconfigopts += "mv %%(builddir)s/googletest-*/* %s/googletest/ && " % local_vendor_dir -# logger -preconfigopts += "mv %%(builddir)s/logger-*/* %s/logger/ && " % local_vendor_dir -# rampler -preconfigopts += "mv %%(builddir)s/rampler-*/* %s/rampler/ && " % local_vendor_dir -# spoa -preconfigopts += "mv %%(builddir)s/spoa-*/* %s/spoa/ && " % local_vendor_dir -# thread_pool -preconfigopts += "mv %%(builddir)s/thread_pool-*/* %s/thread_pool/ && " % local_vendor_dir - -# Submodules of submodules -# benchmark -preconfigopts += "mv %%(builddir)s/benchmark-*/* %s/ClaraGenomicsAnalysis/3rdparty/benchmark/ && " % local_vendor_dir -# spdlog -preconfigopts += "mv %%(builddir)s/spdlog-*/* %s/ClaraGenomicsAnalysis/3rdparty/spdlog/ && " % local_vendor_dir - configopts = '-Dracon_enable_cuda=ON' -separate_build_dir = True -build_type = 'Release' sanity_check_paths = { 'files': ['bin/racon'], From 2147764ffa24e20a741bacb397d0c1de3de93626 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Thu, 16 Sep 2021 11:27:54 +0100 Subject: [PATCH 1316/9987] Update medaka-1.4.3-foss-2020b.eb networkx version changed to 2.5 for consistency --- easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index c6ebdb16942..4cdca5b141a 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -31,7 +31,7 @@ dependencies = [ ('HTSlib', '1.11'), # for tabix, bgzip ('Racon', '1.4.21'), ('spoa', '4.0.7'), - ('networkx', '2.6.2'), + ('networkx', '2.5'), ('edlib', '1.3.9'), ('pyspoa', '0.0.8'), ('pyfaidx', '0.5.9.5'), From e9d6f7a596bccab420556aa164dd5fbe2bae492c Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Thu, 16 Sep 2021 12:53:22 +0200 Subject: [PATCH 1317/9987] adding easyconfigs: pyqstem-1.0.3-foss-2020b.eb, pyqstem-1.0.3-fosscuda-2020b.eb --- .../p/pyqstem/pyqstem-1.0.3-foss-2020b.eb | 41 +++++++++++++++++++ .../p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb | 41 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb new file mode 100644 index 00000000000..37f0e99e6cf --- /dev/null +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = "PythonPackage" + +name = 'pyqstem' +version = '1.0.3' + +homepage = 'https://github.com/jacobjma/PyQSTEM' +description = """QSTEM is a program for quantitative image simulation in electron +microscopy, including TEM, STEM and CBED image simulation. + +This project interfaces the QSTEM code with Python and the Atomic +Simulation Environment (ASE) to provide a single environment for +building models, simulating and analysing images.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), +] +checksums = [ + '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz + # pyqstem-1.0.3-Remove-unused-scipy-import.patch + 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', +] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-image', '0.18.1'), + ('ASE', '3.22.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb new file mode 100644 index 00000000000..bfd19a0d087 --- /dev/null +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb @@ -0,0 +1,41 @@ +easyblock = "PythonPackage" + +name = 'pyqstem' +version = '1.0.3' + +homepage = 'https://github.com/jacobjma/PyQSTEM' +description = """QSTEM is a program for quantitative image simulation in electron +microscopy, including TEM, STEM and CBED image simulation. + +This project interfaces the QSTEM code with Python and the Atomic +Simulation Environment (ASE) to provide a single environment for +building models, simulating and analysing images.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), +] +checksums = [ + '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz + # pyqstem-1.0.3-Remove-unused-scipy-import.patch + 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', +] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-image', '0.18.1'), + ('ASE', '3.22.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' From 8f3d882664caea0ea5dc0869d93c41b00a3754ec Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 16 Sep 2021 12:29:08 +0100 Subject: [PATCH 1318/9987] adding easyconfigs: pycoQC-2.5.2-foss-2021a.eb --- .../p/pycoQC/pycoQC-2.5.2-foss-2021a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/pycoQC/pycoQC-2.5.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pycoQC/pycoQC-2.5.2-foss-2021a.eb b/easybuild/easyconfigs/p/pycoQC/pycoQC-2.5.2-foss-2021a.eb new file mode 100644 index 00000000000..d1f92dcc068 --- /dev/null +++ b/easybuild/easyconfigs/p/pycoQC/pycoQC-2.5.2-foss-2021a.eb @@ -0,0 +1,42 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'pycoQC' +version = '2.5.2' + +homepage = 'https://tleonardi.github.io/pycoQC' +description = """PycoQC computes metrics and generates interactive QC plots for + Oxford Nanopore technologies sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8ceba86bb9a08bdf7c329a165d0218ad8b026f6772efa661fcc98750acc2c8ce'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), + ('plotly.py', '5.1.0'), + ('tqdm', '4.61.2'), + ('Pysam', '0.16.0.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': name} + +# Loosen unneccessarily strict version dependency for plotly +preinstallopts = "sed -i 's|plotly==|plotly>=|g' setup.py &&" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [name, 'Barcode_split', 'Fast5_to_seq_summary']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ["%(name)s --help", "%(name)s --version"] + +moduleclass = 'bio' From 6aad957ab4c9ece1538e1fc3562d4cfa97d1f4fe Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 16 Sep 2021 12:30:38 +0100 Subject: [PATCH 1319/9987] Fix typo in comment --- easybuild/easyconfigs/p/pycoQC/pycoQC-2.5.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pycoQC/pycoQC-2.5.2-foss-2021a.eb b/easybuild/easyconfigs/p/pycoQC/pycoQC-2.5.2-foss-2021a.eb index d1f92dcc068..8d84121978f 100644 --- a/easybuild/easyconfigs/p/pycoQC/pycoQC-2.5.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pycoQC/pycoQC-2.5.2-foss-2021a.eb @@ -29,7 +29,7 @@ sanity_pip_check = True options = {'modulename': name} -# Loosen unneccessarily strict version dependency for plotly +# Loosen unnecessarily strict version dependency for plotly preinstallopts = "sed -i 's|plotly==|plotly>=|g' setup.py &&" sanity_check_paths = { From e3f8c8b57fa7e8ac67db8f57bb6df8d7fb7748ce Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 16 Sep 2021 14:46:59 +0200 Subject: [PATCH 1320/9987] Update KEGG.db link because deprecated lib now --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index b13d518ab71..99b419b20e0 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -136,7 +136,10 @@ exts_list = [ ('AnnotationForge', '1.34.0', { 'checksums': ['5dc133355a2707197d453462f85bb0ef9c20c9ad277176d24c00110f7c6cc3af'], }), + # Is *deprecated* so not available anymore in release 3.13 and afterwards ('KEGG.db', '3.2.4', { + 'source_tmpl': '%(name)s_%(version)s.tar.gz', + 'source_urls': ['http://bioconductor.org/packages/3.12/data/annotation/src/contrib/'], 'checksums': ['2e60d1b664cbd1491cc00ed13a22904706c5a4651150f70daca04bf3ba9ead88'], }), ('annaffy', '1.63.1', { @@ -1047,9 +1050,6 @@ exts_list = [ ('GenABEL', '1.8-0', { 'checksums': ['434fc806b918738ec67171a37a47099d1706332819317e368fe0ccb8f149a469'], }), - ('JASPAR2020', '0.99.10', { - 'checksums': ['b9b92d141a317ebb32a14708229f6b82522ceeb5f1b88360d93b0a7cfe30375b'], - }), ] modextrapaths = {'R_LIBS_SITE': ''} From 735568d430850450fc630d3ef50cd9c3a46522d4 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 14:06:43 +0000 Subject: [PATCH 1321/9987] adding easyconfigs: python-parasail-1.2.4-foss-2020b.eb --- .../python-parasail-1.2.4-foss-2020b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb new file mode 100644 index 00000000000..cd8f3bb5c6d --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.2.4' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'] + +builddependencies = [ + ('parasail', '2.4.3'), +] +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' From 2eda0710bf0a47749d65137c484827d9314fadaa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Sep 2021 16:28:36 +0200 Subject: [PATCH 1322/9987] add exception to easyconfigs test suite for TensorFlow 2.2.3 dependency for medaka 1.4.3 with foss/2020b --- test/easyconfigs/easyconfigs.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 297b7b9488b..1008461fa69 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -472,8 +472,10 @@ def check_dep_vars(self, gen, dep, dep_vars): # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 ('2.2.0;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'Horovod-0.19.5-', 'decona-0.1.2-', 'NGSpeciesID-0.1.1.1-']), - # medaka 1.4.3 depends on TensorFlow 2.2.2 + # medaka 1.4.3 (foss/2019b) depends on TensorFlow 2.2.2 ('2.2.2;', ['medaka-1.4.3-']), + # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3 + ('2.2.3;', ['medaka-1.4.3-']), ], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; From 3705c81983cfe515108394e43180b0aaab21180a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Sep 2021 17:30:38 +0200 Subject: [PATCH 1323/9987] stick to SAMtools 1.11 as dependency for medaka with foss/2020b --- easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 4cdca5b141a..38b5e7d0ffd 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -25,7 +25,7 @@ dependencies = [ ('Biopython', '1.78'), # Pysam 0.16.0.1 is strictly required, see requirements.txt ('Pysam', '0.16.0.1'), - ('SAMtools', '1.12'), + ('SAMtools', '1.11'), # minimap2 is version 2.18 in pangolin, so we need the same version here ('minimap2', '2.18'), ('HTSlib', '1.11'), # for tabix, bgzip From 9b914d5b80bb8752d44bdb2a05bce69dbd2be161 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 15:43:26 +0000 Subject: [PATCH 1324/9987] adding easyconfigs: PhyML-3.3.20200621-foss-2020b.eb --- .../p/PhyML/PhyML-3.3.20200621-foss-2020b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb new file mode 100644 index 00000000000..bb741493221 --- /dev/null +++ b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated to version 3.3.20200621 +# J. Sassmannshausen (GSTT/NHS) + +easyblock = 'ConfigureMake' + +name = 'PhyML' +version = '3.3.20200621' + +homepage = 'https://github.com/stephaneguindon/phyml' +description = "Phylogenetic estimation using (Maximum) Likelihood" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/stephaneguindon/phyml/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a8243923ee08c74cab609a4b086ade66c6156fc2b24450e2a500108dc644c867'] + +builddependencies = [ + ('Autoconf', '2.69'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = 'sh autogen.sh && ' + +configopts = ['--enable-phyml', '--enable-phytime', '--enable-phyrex', '--enable-mpi --enable-phyml'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/phyml', 'bin/phyml-mpi', 'bin/phyrex', 'bin/phytime'], + 'dirs': [] +} + +moduleclass = 'bio' From 1c860f2795810b9e19f342c8bda37025800d2e2b Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 16:30:42 +0000 Subject: [PATCH 1325/9987] Corrected the --enable-mpi build --- easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb index bb741493221..92820f73d60 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb @@ -26,7 +26,7 @@ builddependencies = [ preconfigopts = 'sh autogen.sh && ' -configopts = ['--enable-phyml', '--enable-phytime', '--enable-phyrex', '--enable-mpi --enable-phyml'] +configopts = ['--enable-phyml', '--enable-phytime', '--enable-phyrex', '--enable-mpi '] parallel = 1 From 2648ceefb4e68f1947143f0f562821c6cf274258 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 16 Sep 2021 18:44:53 +0200 Subject: [PATCH 1326/9987] adding easyconfigs: glew-2.2.0-GCCcore-11.2.0-egl.eb, glew-2.2.0-GCCcore-11.2.0-glx.eb, glew-2.2.0-GCCcore-11.2.0-osmesa.eb --- .../g/glew/glew-2.2.0-GCCcore-11.2.0-egl.eb | 43 +++++++++++++++++++ .../g/glew/glew-2.2.0-GCCcore-11.2.0-glx.eb | 43 +++++++++++++++++++ .../glew/glew-2.2.0-GCCcore-11.2.0-osmesa.eb | 43 +++++++++++++++++++ 3 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-egl.eb create mode 100644 easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-glx.eb create mode 100644 easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-osmesa.eb diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-egl.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-egl.eb new file mode 100644 index 00000000000..0f0590e91a8 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-egl.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' +versionsuffix = '-egl' +# available: -glx, -osmesa, -egl +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# offscreen), and OSMESA (offscreen software only). + +name = 'glew' +version = '2.2.0' + +homepage = 'https://github.com/nigels-com/glew' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Mesa', '21.1.7'), + ('X11', '20210802'), +] + +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all ' + local_system + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-glx.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-glx.eb new file mode 100644 index 00000000000..ee2333cef8f --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-glx.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' +versionsuffix = '-glx' +# available: -glx, -osmesa, -egl +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# offscreen), and OSMESA (offscreen software only). + +name = 'glew' +version = '2.2.0' + +homepage = 'https://github.com/nigels-com/glew' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Mesa', '21.1.7'), + ('X11', '20210802'), +] + +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all ' + local_system + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-osmesa.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-osmesa.eb new file mode 100644 index 00000000000..7380689e647 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.2.0-osmesa.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' +versionsuffix = '-osmesa' +# available: -glx, -osmesa, -egl +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# offscreen), and OSMESA (offscreen software only). + +name = 'glew' +version = '2.2.0' + +homepage = 'https://github.com/nigels-com/glew' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Mesa', '21.1.7'), + ('X11', '20210802'), +] + +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all ' + local_system + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': [] +} + +moduleclass = 'devel' From 9eed9be9b112b27b7df683412662f46a403b62fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 16 Sep 2021 19:40:11 +0200 Subject: [PATCH 1327/9987] adding easyconfigs: Qt5-5.15.2-GCCcore-11.2.0.eb --- .../q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0ae4b2b7fe1 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -0,0 +1,69 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.15.2' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +patches = [ + 'Qt5-5.13.1_fix-avx2.patch', + 'Qt5-5.13.1_fix-qmake-libdir.patch', + 'Qt5-5.14.1_fix-OF-Gentoo.patch', +] +checksums = [ + '3a530d1b243b5dec00bc54937455471aaa3e56849d2593edb8ded07228202240', # qt-everywhere-src-5.15.2.tar.xz + '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch + '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch + '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + # deps for QtWebEngine + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.10.2'), + ('Python', '3.9.6', '-bare'), + ('re2c', '2.2'), +] + +dependencies = [ + ('double-conversion', '3.1.5'), + ('GLib', '2.69.1'), + ('PCRE2', '10.37'), + ('libpng', '1.6.37'), + # deps for QtWebEngine + ('X11', '20210802'), + ('fontconfig', '2.13.94'), + ('DBus', '1.13.18'), + ('libevent', '2.1.12'), + ('libGLU', '9.0.2'), + ('libjpeg-turbo', '2.0.6'), + ('NSS', '3.69'), + ('snappy', '1.1.9'), + ('JasPer', '2.0.33'), + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', True), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +# qtwayland fails to build on (some) Centos 7 systems +configopts = '-skip qtgamepad -skip qtwayland' + +# make sure QtWebEngine component is being built & installed +check_qtwebengine = True + +moduleclass = 'devel' From d6dc9580a23f74ddfbc0ee44b2e048fe867e07df Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 16 Sep 2021 19:53:26 +0200 Subject: [PATCH 1328/9987] Add BLIS PR#544 on top of 0.8.1 to fix problem with dgemm causing FPE signalling on Broadwell. --- .../b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb | 9 +- ...ix_dgemm-fpe-signalling-on-broadwell.patch | 2219 +++++++++++++++++ 2 files changed, 2227 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb index edd74346c91..9de3cfacf85 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb @@ -11,7 +11,14 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/flame/blis/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['729694128719801e82fae7b5f2489ab73e4a467f46271beff09588c9265a697b'] +patches = [ + '%(name)s-%(version)s_fix_dgemm-fpe-signalling-on-broadwell.patch', +] +checksums = [ + '729694128719801e82fae7b5f2489ab73e4a467f46271beff09588c9265a697b', # 0.8.1.tar.gz + # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch + 'ec3f4f7bddf43fad2d362fcd930684d027d7e572fc6104cdd5a7e605b7ac3ccb', +] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch new file mode 100644 index 00000000000..3c6a7167ee7 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch @@ -0,0 +1,2219 @@ +Taken from https://github.com/flame/blis/pull/544 +Fixes a problem with DGEMM causing FPR signalling on Broadwell +See https://github.com/flame/blis/pull/544 + +Åke Sandgren, 20210916 + +commit 5191c43faccf45975f577c60b9089abee25722c9 +Author: Devin Matthews +Date: Thu Sep 16 10:16:17 2021 -0500 + + Fix more copy-paste errors in the haswell gemmsup code. + + Fixes #486. + +diff --git a/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx4.c b/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx4.c +index 4c6094b1..21dd3b89 100644 +--- a/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx4.c ++++ b/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx4.c +@@ -101,7 +101,7 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + begin_asm() + + //vzeroall() // zero all xmm/ymm registers. +- ++ + mov(var(a), r14) // load address of a. + mov(var(rs_a), r8) // load rs_a + //mov(var(cs_a), r9) // load cs_a +@@ -119,7 +119,7 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + + lea(mem(r11, r11, 2), r13) // r13 = 3*cs_b + lea(mem(r8, r8, 2), r10) // r10 = 3*rs_a +- ++ + + mov(var(c), r12) // load address of c + mov(var(rs_c), rdi) // load rs_c +@@ -172,19 +172,19 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + prefetch(0, mem(rcx, rdi, 2, 3*8)) // prefetch c + 2*rs_c + #endif + lea(mem(r8, r8, 4), rbp) // rbp = 5*rs_a +- + +- +- ++ ++ ++ + mov(var(k_iter16), rsi) // i = k_iter16; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKITER4) // if i == 0, jump to code that + // contains the k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER16) // MAIN LOOP +- +- ++ ++ + // ---------------------------------- iteration 0 + + #if 0 +@@ -219,7 +219,7 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + vfmadd231pd(ymm1, ymm3, ymm14) + vfmadd231pd(ymm2, ymm3, ymm15) + +- ++ + // ---------------------------------- iteration 1 + + vmovupd(mem(rax ), ymm0) +@@ -250,7 +250,7 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + + + // ---------------------------------- iteration 2 +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -312,27 +312,27 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + vfmadd231pd(ymm1, ymm3, ymm14) + vfmadd231pd(ymm2, ymm3, ymm15) + +- ++ + + dec(rsi) // i -= 1; + jne(.DLOOPKITER16) // iterate again if i != 0. +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + label(.DCONSIDKITER4) +- ++ + mov(var(k_iter4), rsi) // i = k_iter4; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKLEFT1) // if i == 0, jump to code that + // considers k_left1 loop. + // else, we prepare to enter k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER4) // EDGE LOOP (ymm) +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -343,7 +343,7 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + vmovupd(mem(rax, r8, 1), ymm1) + vmovupd(mem(rax, r8, 2), ymm2) + add(imm(4*8), rax) // a += 4*cs_b = 4*8; +- ++ + vmovupd(mem(rbx ), ymm3) + vfmadd231pd(ymm0, ymm3, ymm4) + vfmadd231pd(ymm1, ymm3, ymm5) +@@ -365,21 +365,21 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + vfmadd231pd(ymm1, ymm3, ymm14) + vfmadd231pd(ymm2, ymm3, ymm15) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKITER4) // iterate again if i != 0. +- +- +- ++ ++ ++ + + label(.DCONSIDKLEFT1) +- ++ + mov(var(k_left1), rsi) // i = k_left1; + test(rsi, rsi) // check i via logical AND. + je(.DPOSTACCUM) // if i == 0, we're done; jump to end. + // else, we prepare to enter k_left1 loop. +- +- ++ ++ + + + label(.DLOOPKLEFT1) // EDGE LOOP (scalar) +@@ -387,12 +387,12 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + // using the xmm registers would zero out the + // high bits of the destination registers, + // which would destory intermediate results. +- ++ + vmovsd(mem(rax ), xmm0) + vmovsd(mem(rax, r8, 1), xmm1) + vmovsd(mem(rax, r8, 2), xmm2) + add(imm(1*8), rax) // a += 1*cs_a = 1*8; +- ++ + vmovsd(mem(rbx ), xmm3) + vfmadd231pd(ymm0, ymm3, ymm4) + vfmadd231pd(ymm1, ymm3, ymm5) +@@ -414,12 +414,12 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + vfmadd231pd(ymm1, ymm3, ymm14) + vfmadd231pd(ymm2, ymm3, ymm15) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKLEFT1) // iterate again if i != 0. +- +- +- ++ ++ ++ + + + +@@ -427,11 +427,11 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + label(.DPOSTACCUM) + + +- +- // ymm4 ymm7 ymm10 ymm13 ++ ++ // ymm4 ymm7 ymm10 ymm13 + // ymm5 ymm8 ymm11 ymm14 + // ymm6 ymm9 ymm12 ymm15 +- ++ + vhaddpd( ymm7, ymm4, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm0 ) +@@ -469,7 +469,7 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + // xmm6[0:3] = sum(ymm6) sum(ymm9) sum(ymm12) sum(ymm15) + + +- ++ + //mov(var(rs_c), rdi) // load rs_c + //lea(mem(, rdi, 8), rdi) // rs_c *= sizeof(double) + +@@ -477,73 +477,73 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + mov(var(beta), rbx) // load address of beta + vbroadcastsd(mem(rax), ymm0) // load alpha and duplicate + vbroadcastsd(mem(rbx), ymm3) // load beta and duplicate +- ++ + vmulpd(ymm0, ymm4, ymm4) // scale by alpha + vmulpd(ymm0, ymm5, ymm5) + vmulpd(ymm0, ymm6, ymm6) +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + //mov(var(cs_c), rsi) // load cs_c + //lea(mem(, rsi, 8), rsi) // rsi = cs_c * sizeof(double) +- +- +- ++ ++ ++ + // now avoid loading C if beta == 0 +- ++ + vxorpd(ymm0, ymm0, ymm0) // set ymm0 to zero. + vucomisd(xmm0, xmm3) // set ZF if beta == 0. + je(.DBETAZERO) // if ZF = 1, jump to beta == 0 case +- + +- ++ ++ + label(.DROWSTORED) +- +- ++ ++ + vfmadd231pd(mem(rcx), ymm3, ymm4) + vmovupd(ymm4, mem(rcx)) + add(rdi, rcx) +- ++ + vfmadd231pd(mem(rcx), ymm3, ymm5) + vmovupd(ymm5, mem(rcx)) + add(rdi, rcx) +- ++ + vfmadd231pd(mem(rcx), ymm3, ymm6) + vmovupd(ymm6, mem(rcx)) + //add(rdi, rcx) +- +- +- ++ ++ ++ + jmp(.DDONE) // jump to end. +- +- +- +- ++ ++ ++ ++ + label(.DBETAZERO) +- + +- ++ ++ + label(.DROWSTORBZ) +- +- ++ ++ + vmovupd(ymm4, mem(rcx)) + add(rdi, rcx) +- ++ + vmovupd(ymm5, mem(rcx)) + add(rdi, rcx) +- ++ + vmovupd(ymm6, mem(rcx)) + //add(rdi, rcx) +- +- +- +- ++ ++ ++ ++ + label(.DDONE) +- +- ++ ++ + + + lea(mem(r12, rdi, 2), r12) // +@@ -560,7 +560,7 @@ void bli_dgemmsup_rd_haswell_asm_6x4 + + label(.DRETURN) + +- ++ + + end_asm( + : // output operands (none) +@@ -629,7 +629,7 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + // ------------------------------------------------------------------------- + + begin_asm() +- ++ + //vzeroall() // zero all xmm/ymm registers. + + mov(var(a), rax) // load address of a. +@@ -649,7 +649,7 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + + lea(mem(r11, r11, 2), r13) // r13 = 3*cs_b + //lea(mem(r8, r8, 2), r10) // r10 = 3*rs_a +- ++ + + mov(var(c), rcx) // load address of c + mov(var(rs_c), rdi) // load rs_c +@@ -682,7 +682,7 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + //lea(mem(r14), rax) // rax = a; + //lea(mem(rdx), rbx) // rbx = b; + +- ++ + #if 1 + //mov(var(rs_c), rdi) // load rs_c + //lea(mem(, rdi, 8), rdi) // rs_c *= sizeof(double) +@@ -690,18 +690,18 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + prefetch(0, mem(rcx, rdi, 1, 3*8)) // prefetch c + 1*rs_c + #endif + +- +- +- ++ ++ ++ + mov(var(k_iter16), rsi) // i = k_iter16; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKITER4) // if i == 0, jump to code that + // contains the k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER16) // MAIN LOOP +- +- ++ ++ + // ---------------------------------- iteration 0 + + #if 0 +@@ -730,7 +730,7 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + vfmadd231pd(ymm0, ymm3, ymm13) + vfmadd231pd(ymm1, ymm3, ymm14) + +- ++ + // ---------------------------------- iteration 1 + + vmovupd(mem(rax ), ymm0) +@@ -756,7 +756,7 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + + + // ---------------------------------- iteration 2 +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -807,27 +807,27 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + vfmadd231pd(ymm0, ymm3, ymm13) + vfmadd231pd(ymm1, ymm3, ymm14) + +- ++ + + dec(rsi) // i -= 1; + jne(.DLOOPKITER16) // iterate again if i != 0. +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + label(.DCONSIDKITER4) +- ++ + mov(var(k_iter4), rsi) // i = k_iter4; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKLEFT1) // if i == 0, jump to code that + // considers k_left1 loop. + // else, we prepare to enter k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER4) // EDGE LOOP (ymm) +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -836,7 +836,7 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + vmovupd(mem(rax ), ymm0) + vmovupd(mem(rax, r8, 1), ymm1) + add(imm(4*8), rax) // a += 4*cs_b = 4*8; +- ++ + vmovupd(mem(rbx ), ymm3) + vfmadd231pd(ymm0, ymm3, ymm4) + vfmadd231pd(ymm1, ymm3, ymm5) +@@ -854,21 +854,21 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + vfmadd231pd(ymm0, ymm3, ymm13) + vfmadd231pd(ymm1, ymm3, ymm14) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKITER4) // iterate again if i != 0. +- +- +- ++ ++ ++ + + label(.DCONSIDKLEFT1) +- ++ + mov(var(k_left1), rsi) // i = k_left1; + test(rsi, rsi) // check i via logical AND. + je(.DPOSTACCUM) // if i == 0, we're done; jump to end. + // else, we prepare to enter k_left1 loop. +- +- ++ ++ + + + label(.DLOOPKLEFT1) // EDGE LOOP (scalar) +@@ -876,11 +876,11 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + // using the xmm registers would zero out the + // high bits of the destination registers, + // which would destory intermediate results. +- ++ + vmovsd(mem(rax ), xmm0) + vmovsd(mem(rax, r8, 1), xmm1) + add(imm(1*8), rax) // a += 1*cs_a = 1*8; +- ++ + vmovsd(mem(rbx ), xmm3) + vfmadd231pd(ymm0, ymm3, ymm4) + vfmadd231pd(ymm1, ymm3, ymm5) +@@ -898,12 +898,12 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + vfmadd231pd(ymm0, ymm3, ymm13) + vfmadd231pd(ymm1, ymm3, ymm14) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKLEFT1) // iterate again if i != 0. +- +- +- ++ ++ ++ + + + +@@ -911,10 +911,10 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + label(.DPOSTACCUM) + + +- +- // ymm4 ymm7 ymm10 ymm13 ++ ++ // ymm4 ymm7 ymm10 ymm13 + // ymm5 ymm8 ymm11 ymm14 +- ++ + vhaddpd( ymm7, ymm4, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm0 ) +@@ -943,75 +943,75 @@ void bli_dgemmsup_rd_haswell_asm_2x4 + + //mov(var(rs_c), rdi) // load rs_c + //lea(mem(, rdi, 4), rdi) // rs_c *= sizeof(float) +- ++ + mov(var(alpha), rax) // load address of alpha + mov(var(beta), rbx) // load address of beta + vbroadcastsd(mem(rax), ymm0) // load alpha and duplicate + vbroadcastsd(mem(rbx), ymm3) // load beta and duplicate +- ++ + vmulpd(ymm0, ymm4, ymm4) // scale by alpha + vmulpd(ymm0, ymm5, ymm5) +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + //mov(var(cs_c), rsi) // load cs_c + //lea(mem(, rsi, 8), rsi) // rsi = cs_c * sizeof(double) +- +- +- ++ ++ ++ + // now avoid loading C if beta == 0 +- ++ + vxorpd(ymm0, ymm0, ymm0) // set ymm0 to zero. + vucomisd(xmm0, xmm3) // set ZF if beta == 0. + je(.DBETAZERO) // if ZF = 1, jump to beta == 0 case +- + +- ++ ++ + label(.DROWSTORED) +- +- ++ ++ + vfmadd231pd(mem(rcx), ymm3, ymm4) + vmovupd(ymm4, mem(rcx)) + add(rdi, rcx) +- ++ + vfmadd231pd(mem(rcx), ymm3, ymm5) + vmovupd(ymm5, mem(rcx)) + //add(rdi, rcx) +- +- +- ++ ++ ++ + jmp(.DDONE) // jump to end. +- +- +- +- ++ ++ ++ ++ + label(.DBETAZERO) +- + +- ++ ++ + label(.DROWSTORBZ) +- +- ++ ++ + vmovupd(ymm4, mem(rcx)) + add(rdi, rcx) +- ++ + vmovupd(ymm5, mem(rcx)) + //add(rdi, rcx) +- +- +- +- ++ ++ ++ ++ + label(.DDONE) + + + + + label(.DRETURN) +- +- ++ ++ + + end_asm( + : // output operands (none) +@@ -1079,7 +1079,7 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + // ------------------------------------------------------------------------- + + begin_asm() +- ++ + //vzeroall() // zero all xmm/ymm registers. + + mov(var(a), rax) // load address of a. +@@ -1099,7 +1099,7 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + + lea(mem(r11, r11, 2), r13) // r13 = 3*cs_b + //lea(mem(r8, r8, 2), r10) // r10 = 3*rs_a +- ++ + + mov(var(c), rcx) // load address of c + mov(var(rs_c), rdi) // load rs_c +@@ -1128,26 +1128,26 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + //lea(mem(r14), rax) // rax = a; + //lea(mem(rdx), rbx) // rbx = b; + +- ++ + #if 1 + //mov(var(rs_c), rdi) // load rs_c + //lea(mem(, rdi, 8), rdi) // rs_c *= sizeof(double) + prefetch(0, mem(rcx, 3*8)) // prefetch c + 0*rs_c +- prefetch(0, mem(rcx, rdi, 1, 3*8)) // prefetch c + 1*rs_c ++ //prefetch(0, mem(rcx, rdi, 1, 3*8)) // prefetch c + 1*rs_c + #endif + +- +- +- ++ ++ ++ + mov(var(k_iter16), rsi) // i = k_iter16; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKITER4) // if i == 0, jump to code that + // contains the k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER16) // MAIN LOOP +- +- ++ ++ + // ---------------------------------- iteration 0 + + #if 0 +@@ -1170,7 +1170,7 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + add(imm(4*8), rbx) // b += 4*rs_b = 4*8; + vfmadd231pd(ymm0, ymm3, ymm13) + +- ++ + // ---------------------------------- iteration 1 + + vmovupd(mem(rax ), ymm0) +@@ -1191,7 +1191,7 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + + + // ---------------------------------- iteration 2 +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + #endif +@@ -1231,27 +1231,27 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + add(imm(4*8), rbx) // b += 4*rs_b = 4*8; + vfmadd231pd(ymm0, ymm3, ymm13) + +- ++ + + dec(rsi) // i -= 1; + jne(.DLOOPKITER16) // iterate again if i != 0. +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + label(.DCONSIDKITER4) +- ++ + mov(var(k_iter4), rsi) // i = k_iter4; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKLEFT1) // if i == 0, jump to code that + // considers k_left1 loop. + // else, we prepare to enter k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER4) // EDGE LOOP (ymm) +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -1259,7 +1259,7 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + + vmovupd(mem(rax ), ymm0) + add(imm(4*8), rax) // a += 4*cs_b = 4*8; +- ++ + vmovupd(mem(rbx ), ymm3) + vfmadd231pd(ymm0, ymm3, ymm4) + +@@ -1273,21 +1273,21 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + add(imm(4*8), rbx) // b += 4*rs_b = 4*8; + vfmadd231pd(ymm0, ymm3, ymm13) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKITER4) // iterate again if i != 0. +- +- +- ++ ++ ++ + + label(.DCONSIDKLEFT1) +- ++ + mov(var(k_left1), rsi) // i = k_left1; + test(rsi, rsi) // check i via logical AND. + je(.DPOSTACCUM) // if i == 0, we're done; jump to end. + // else, we prepare to enter k_left1 loop. +- +- ++ ++ + + + label(.DLOOPKLEFT1) // EDGE LOOP (scalar) +@@ -1295,10 +1295,10 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + // using the xmm registers would zero out the + // high bits of the destination registers, + // which would destory intermediate results. +- ++ + vmovsd(mem(rax ), xmm0) + add(imm(1*8), rax) // a += 1*cs_a = 1*8; +- ++ + vmovsd(mem(rbx ), xmm3) + vfmadd231pd(ymm0, ymm3, ymm4) + +@@ -1312,12 +1312,12 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + add(imm(1*8), rbx) // b += 1*rs_b = 1*8; + vfmadd231pd(ymm0, ymm3, ymm13) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKLEFT1) // iterate again if i != 0. +- +- +- ++ ++ ++ + + + +@@ -1325,9 +1325,9 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + label(.DPOSTACCUM) + + +- +- // ymm4 ymm7 ymm10 ymm13 +- ++ ++ // ymm4 ymm7 ymm10 ymm13 ++ + vhaddpd( ymm7, ymm4, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm0 ) +@@ -1339,15 +1339,15 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + vperm2f128(imm(0x20), ymm2, ymm0, ymm4 ) + + +- vhaddpd( ymm8, ymm5, ymm0 ) +- vextractf128(imm(1), ymm0, xmm1 ) +- vaddpd( xmm0, xmm1, xmm0 ) ++ //vhaddpd( ymm8, ymm5, ymm0 ) ++ //vextractf128(imm(1), ymm0, xmm1 ) ++ //vaddpd( xmm0, xmm1, xmm0 ) + +- vhaddpd( ymm14, ymm11, ymm2 ) +- vextractf128(imm(1), ymm2, xmm1 ) +- vaddpd( xmm2, xmm1, xmm2 ) ++ //vhaddpd( ymm14, ymm11, ymm2 ) ++ //vextractf128(imm(1), ymm2, xmm1 ) ++ //vaddpd( xmm2, xmm1, xmm2 ) + +- vperm2f128(imm(0x20), ymm2, ymm0, ymm5 ) ++ //vperm2f128(imm(0x20), ymm2, ymm0, ymm5 ) + + // xmm4[0:3] = sum(ymm4) sum(ymm7) sum(ymm10) sum(ymm13) + +@@ -1355,67 +1355,67 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + + //mov(var(rs_c), rdi) // load rs_c + //lea(mem(, rdi, 4), rdi) // rs_c *= sizeof(float) +- ++ + mov(var(alpha), rax) // load address of alpha + mov(var(beta), rbx) // load address of beta + vbroadcastsd(mem(rax), ymm0) // load alpha and duplicate + vbroadcastsd(mem(rbx), ymm3) // load beta and duplicate +- ++ + vmulpd(ymm0, ymm4, ymm4) // scale by alpha +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + //mov(var(cs_c), rsi) // load cs_c + //lea(mem(, rsi, 8), rsi) // rsi = cs_c * sizeof(double) +- +- +- ++ ++ ++ + // now avoid loading C if beta == 0 +- ++ + vxorpd(ymm0, ymm0, ymm0) // set ymm0 to zero. + vucomisd(xmm0, xmm3) // set ZF if beta == 0. + je(.DBETAZERO) // if ZF = 1, jump to beta == 0 case +- + +- ++ ++ + label(.DROWSTORED) +- +- ++ ++ + vfmadd231pd(mem(rcx), ymm3, ymm4) + vmovupd(ymm4, mem(rcx)) + //add(rdi, rcx) +- +- +- ++ ++ ++ + jmp(.DDONE) // jump to end. +- +- +- +- ++ ++ ++ ++ + label(.DBETAZERO) +- + +- ++ ++ + label(.DROWSTORBZ) +- +- ++ ++ + vmovupd(ymm4, mem(rcx)) + //add(rdi, rcx) +- +- +- +- ++ ++ ++ ++ + label(.DDONE) + + + + + label(.DRETURN) +- +- ++ ++ + + end_asm( + : // output operands (none) +commit e3dc1954ffb5eee2a8b41fce85ba589f75770eea +Author: Devin Matthews +Date: Thu Sep 16 10:59:37 2021 -0500 + + Fix problem where uninitialized registers are included in vhaddpd in the Mx1 gemmsup kernels for haswell. + + The fix is to use the same (valid) source register twice in the horizontal addition. + +diff --git a/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx1.c b/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx1.c +index 6e3c1a0e..457ef9f2 100644 +--- a/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx1.c ++++ b/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx1.c +@@ -99,9 +99,9 @@ void bli_dgemmsup_rd_haswell_asm_6x1 + // ------------------------------------------------------------------------- + + begin_asm() +- ++ + //vzeroall() // zero all xmm/ymm registers. +- ++ + mov(var(a), rax) // load address of a. + mov(var(rs_a), r8) // load rs_a + //mov(var(cs_a), r9) // load cs_a +@@ -119,7 +119,7 @@ void bli_dgemmsup_rd_haswell_asm_6x1 + + //lea(mem(r11, r11, 2), r13) // r13 = 3*cs_b + //lea(mem(r8, r8, 2), r10) // r10 = 3*rs_a +- ++ + + mov(var(c), rcx) // load address of c + mov(var(rs_c), rdi) // load rs_c +@@ -163,19 +163,19 @@ void bli_dgemmsup_rd_haswell_asm_6x1 + prefetch(0, mem(r10, rdi, 1, 1*8)) // prefetch c + 4*rs_c + prefetch(0, mem(r10, rdi, 2, 1*8)) // prefetch c + 5*rs_c + #endif +- + +- +- ++ ++ ++ + mov(var(k_iter16), rsi) // i = k_iter16; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKITER4) // if i == 0, jump to code that + // contains the k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER16) // MAIN LOOP +- +- ++ ++ + // ---------------------------------- iteration 0 + + #if 0 +@@ -206,7 +206,7 @@ void bli_dgemmsup_rd_haswell_asm_6x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm14) + +- ++ + // ---------------------------------- iteration 1 + + vmovupd(mem(rbx ), ymm0) +@@ -233,7 +233,7 @@ void bli_dgemmsup_rd_haswell_asm_6x1 + + + // ---------------------------------- iteration 2 +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -287,27 +287,27 @@ void bli_dgemmsup_rd_haswell_asm_6x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm14) + +- ++ + + dec(rsi) // i -= 1; + jne(.DLOOPKITER16) // iterate again if i != 0. +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + label(.DCONSIDKITER4) +- ++ + mov(var(k_iter4), rsi) // i = k_iter4; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKLEFT1) // if i == 0, jump to code that + // considers k_left1 loop. + // else, we prepare to enter k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER4) // EDGE LOOP (ymm) +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -336,21 +336,21 @@ void bli_dgemmsup_rd_haswell_asm_6x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm14) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKITER4) // iterate again if i != 0. +- +- +- ++ ++ ++ + + label(.DCONSIDKLEFT1) +- ++ + mov(var(k_left1), rsi) // i = k_left1; + test(rsi, rsi) // check i via logical AND. + je(.DPOSTACCUM) // if i == 0, we're done; jump to end. + // else, we prepare to enter k_left1 loop. +- +- ++ ++ + + + label(.DLOOPKLEFT1) // EDGE LOOP (scalar) +@@ -358,7 +358,7 @@ void bli_dgemmsup_rd_haswell_asm_6x1 + // using the xmm registers would zero out the + // high bits of the destination registers, + // which would destory intermediate results. +- ++ + vmovsd(mem(rbx ), xmm0) + add(imm(1*8), rbx) // b += 1*rs_b = 1*8; + +@@ -381,12 +381,12 @@ void bli_dgemmsup_rd_haswell_asm_6x1 + add(imm(1*8), rax) // a += 1*cs_a = 1*8; + vfmadd231pd(ymm0, ymm3, ymm14) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKLEFT1) // iterate again if i != 0. +- +- +- ++ ++ ++ + + + +@@ -399,28 +399,28 @@ void bli_dgemmsup_rd_haswell_asm_6x1 + // ymm10 + // ymm12 + // ymm14 +- +- vhaddpd( ymm5, ymm4, ymm0 ) ++ ++ vhaddpd( ymm4, ymm4, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm4 ) + +- vhaddpd( ymm7, ymm6, ymm0 ) ++ vhaddpd( ymm6, ymm6, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm6 ) + +- vhaddpd( ymm9, ymm8, ymm0 ) ++ vhaddpd( ymm8, ymm8, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm8 ) + +- vhaddpd( ymm11, ymm10, ymm0 ) ++ vhaddpd( ymm10, ymm10, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm10 ) + +- vhaddpd( ymm13, ymm12, ymm0 ) ++ vhaddpd( ymm12, ymm12, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm12 ) + +- vhaddpd( ymm15, ymm14, ymm0 ) ++ vhaddpd( ymm14, ymm14, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm14 ) + +@@ -435,114 +435,114 @@ void bli_dgemmsup_rd_haswell_asm_6x1 + + //mov(var(rs_c), rdi) // load rs_c + //lea(mem(, rdi, 4), rdi) // rs_c *= sizeof(double) +- ++ + mov(var(alpha), rax) // load address of alpha + mov(var(beta), rbx) // load address of beta + vbroadcastsd(mem(rax), ymm0) // load alpha and duplicate + vbroadcastsd(mem(rbx), ymm3) // load beta and duplicate +- ++ + vmulpd(xmm0, xmm4, xmm4) // scale by alpha + vmulpd(xmm0, xmm6, xmm6) + vmulpd(xmm0, xmm8, xmm8) + vmulpd(xmm0, xmm10, xmm10) + vmulpd(xmm0, xmm12, xmm12) + vmulpd(xmm0, xmm14, xmm14) +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + //mov(var(cs_c), rsi) // load cs_c + //lea(mem(, rsi, 8), rsi) // rsi = cs_c * sizeof(double) +- +- +- ++ ++ ++ + // now avoid loading C if beta == 0 +- ++ + vxorpd(ymm0, ymm0, ymm0) // set ymm0 to zero. + vucomisd(xmm0, xmm3) // set ZF if beta == 0. + je(.DBETAZERO) // if ZF = 1, jump to beta == 0 case +- + +- ++ ++ + label(.DROWSTORED) +- + +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm4) + vmovsd(xmm4, mem(rcx)) + add(rdi, rcx) +- +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm6) + vmovsd(xmm6, mem(rcx)) + add(rdi, rcx) +- +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm8) + vmovsd(xmm8, mem(rcx)) + add(rdi, rcx) +- +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm10) + vmovsd(xmm10, mem(rcx)) + add(rdi, rcx) +- +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm12) + vmovsd(xmm12, mem(rcx)) + add(rdi, rcx) +- +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm14) + vmovsd(xmm14, mem(rcx)) + //add(rdi, rcx) +- +- +- ++ ++ ++ + jmp(.DDONE) // jump to end. +- +- +- +- ++ ++ ++ ++ + label(.DBETAZERO) +- + +- ++ ++ + label(.DROWSTORBZ) +- +- ++ ++ + vmovsd(xmm4, mem(rcx)) + add(rdi, rcx) +- ++ + vmovsd(xmm6, mem(rcx)) + add(rdi, rcx) +- ++ + vmovsd(xmm8, mem(rcx)) + add(rdi, rcx) +- ++ + vmovsd(xmm10, mem(rcx)) + add(rdi, rcx) +- ++ + vmovsd(xmm12, mem(rcx)) + add(rdi, rcx) +- ++ + vmovsd(xmm14, mem(rcx)) + //add(rdi, rcx) +- + +- +- +- ++ ++ ++ ++ + label(.DDONE) +- ++ + + + + label(.DRETURN) + +- ++ + + end_asm( + : // output operands (none) +@@ -613,9 +613,9 @@ void bli_dgemmsup_rd_haswell_asm_3x1 + // ------------------------------------------------------------------------- + + begin_asm() +- ++ + //vzeroall() // zero all xmm/ymm registers. +- ++ + mov(var(a), rax) // load address of a. + mov(var(rs_a), r8) // load rs_a + //mov(var(cs_a), r9) // load cs_a +@@ -633,7 +633,7 @@ void bli_dgemmsup_rd_haswell_asm_3x1 + + //lea(mem(r11, r11, 2), r13) // r13 = 3*cs_b + //lea(mem(r8, r8, 2), r10) // r10 = 3*rs_a +- ++ + + mov(var(c), rcx) // load address of c + mov(var(rs_c), rdi) // load rs_c +@@ -671,19 +671,19 @@ void bli_dgemmsup_rd_haswell_asm_3x1 + prefetch(0, mem(rcx, rdi, 1, 1*8)) // prefetch c + 1*rs_c + prefetch(0, mem(rcx, rdi, 2, 1*8)) // prefetch c + 2*rs_c + #endif +- + +- +- ++ ++ ++ + mov(var(k_iter16), rsi) // i = k_iter16; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKITER4) // if i == 0, jump to code that + // contains the k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER16) // MAIN LOOP +- +- ++ ++ + // ---------------------------------- iteration 0 + + #if 0 +@@ -705,7 +705,7 @@ void bli_dgemmsup_rd_haswell_asm_3x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm8) + +- ++ + // ---------------------------------- iteration 1 + + vmovupd(mem(rbx ), ymm0) +@@ -723,7 +723,7 @@ void bli_dgemmsup_rd_haswell_asm_3x1 + + + // ---------------------------------- iteration 2 +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -759,27 +759,27 @@ void bli_dgemmsup_rd_haswell_asm_3x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm8) + +- ++ + + dec(rsi) // i -= 1; + jne(.DLOOPKITER16) // iterate again if i != 0. +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + label(.DCONSIDKITER4) +- ++ + mov(var(k_iter4), rsi) // i = k_iter4; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKLEFT1) // if i == 0, jump to code that + // considers k_left1 loop. + // else, we prepare to enter k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER4) // EDGE LOOP (ymm) +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -799,21 +799,21 @@ void bli_dgemmsup_rd_haswell_asm_3x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm8) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKITER4) // iterate again if i != 0. +- +- +- ++ ++ ++ + + label(.DCONSIDKLEFT1) +- ++ + mov(var(k_left1), rsi) // i = k_left1; + test(rsi, rsi) // check i via logical AND. + je(.DPOSTACCUM) // if i == 0, we're done; jump to end. + // else, we prepare to enter k_left1 loop. +- +- ++ ++ + + + label(.DLOOPKLEFT1) // EDGE LOOP (scalar) +@@ -821,7 +821,7 @@ void bli_dgemmsup_rd_haswell_asm_3x1 + // using the xmm registers would zero out the + // high bits of the destination registers, + // which would destory intermediate results. +- ++ + vmovsd(mem(rbx ), xmm0) + add(imm(1*8), rbx) // b += 1*rs_b = 1*8; + +@@ -835,12 +835,12 @@ void bli_dgemmsup_rd_haswell_asm_3x1 + add(imm(1*8), rax) // a += 1*cs_a = 1*8; + vfmadd231pd(ymm0, ymm3, ymm8) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKLEFT1) // iterate again if i != 0. +- +- +- ++ ++ ++ + + + +@@ -850,16 +850,16 @@ void bli_dgemmsup_rd_haswell_asm_3x1 + // ymm4 + // ymm6 + // ymm8 +- +- vhaddpd( ymm5, ymm4, ymm0 ) ++ ++ vhaddpd( ymm4, ymm4, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm4 ) + +- vhaddpd( ymm7, ymm6, ymm0 ) ++ vhaddpd( ymm6, ymm6, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm6 ) + +- vhaddpd( ymm9, ymm8, ymm0 ) ++ vhaddpd( ymm8, ymm8, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm8 ) + +@@ -871,87 +871,87 @@ void bli_dgemmsup_rd_haswell_asm_3x1 + + //mov(var(rs_c), rdi) // load rs_c + //lea(mem(, rdi, 4), rdi) // rs_c *= sizeof(double) +- ++ + mov(var(alpha), rax) // load address of alpha + mov(var(beta), rbx) // load address of beta + vbroadcastsd(mem(rax), ymm0) // load alpha and duplicate + vbroadcastsd(mem(rbx), ymm3) // load beta and duplicate +- ++ + vmulpd(xmm0, xmm4, xmm4) // scale by alpha + vmulpd(xmm0, xmm6, xmm6) + vmulpd(xmm0, xmm8, xmm8) +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + //mov(var(cs_c), rsi) // load cs_c + //lea(mem(, rsi, 8), rsi) // rsi = cs_c * sizeof(double) +- +- +- ++ ++ ++ + // now avoid loading C if beta == 0 +- ++ + vxorpd(ymm0, ymm0, ymm0) // set ymm0 to zero. + vucomisd(xmm0, xmm3) // set ZF if beta == 0. + je(.DBETAZERO) // if ZF = 1, jump to beta == 0 case +- + +- ++ ++ + label(.DROWSTORED) +- + +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm4) + vmovsd(xmm4, mem(rcx)) + add(rdi, rcx) +- +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm6) + vmovsd(xmm6, mem(rcx)) + add(rdi, rcx) +- +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm8) + vmovsd(xmm8, mem(rcx)) + //add(rdi, rcx) +- +- +- ++ ++ ++ + jmp(.DDONE) // jump to end. +- +- +- +- ++ ++ ++ ++ + label(.DBETAZERO) +- + +- ++ ++ + label(.DROWSTORBZ) +- +- ++ ++ + vmovsd(xmm4, mem(rcx)) + add(rdi, rcx) +- ++ + vmovsd(xmm6, mem(rcx)) + add(rdi, rcx) +- ++ + vmovsd(xmm8, mem(rcx)) + //add(rdi, rcx) +- + +- +- +- ++ ++ ++ ++ + label(.DDONE) +- ++ + + + + label(.DRETURN) + +- ++ + + end_asm( + : // output operands (none) +@@ -1022,9 +1022,9 @@ void bli_dgemmsup_rd_haswell_asm_2x1 + // ------------------------------------------------------------------------- + + begin_asm() +- ++ + //vzeroall() // zero all xmm/ymm registers. +- ++ + mov(var(a), rax) // load address of a. + mov(var(rs_a), r8) // load rs_a + //mov(var(cs_a), r9) // load cs_a +@@ -1042,7 +1042,7 @@ void bli_dgemmsup_rd_haswell_asm_2x1 + + //lea(mem(r11, r11, 2), r13) // r13 = 3*cs_b + //lea(mem(r8, r8, 2), r10) // r10 = 3*rs_a +- ++ + + mov(var(c), rcx) // load address of c + mov(var(rs_c), rdi) // load rs_c +@@ -1078,19 +1078,19 @@ void bli_dgemmsup_rd_haswell_asm_2x1 + prefetch(0, mem(rcx, 1*8)) // prefetch c + 0*rs_c + prefetch(0, mem(rcx, rdi, 1, 1*8)) // prefetch c + 1*rs_c + #endif +- + +- +- ++ ++ ++ + mov(var(k_iter16), rsi) // i = k_iter16; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKITER4) // if i == 0, jump to code that + // contains the k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER16) // MAIN LOOP +- +- ++ ++ + // ---------------------------------- iteration 0 + + #if 0 +@@ -1109,7 +1109,7 @@ void bli_dgemmsup_rd_haswell_asm_2x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm6) + +- ++ + // ---------------------------------- iteration 1 + + vmovupd(mem(rbx ), ymm0) +@@ -1124,7 +1124,7 @@ void bli_dgemmsup_rd_haswell_asm_2x1 + + + // ---------------------------------- iteration 2 +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -1154,27 +1154,27 @@ void bli_dgemmsup_rd_haswell_asm_2x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm6) + +- ++ + + dec(rsi) // i -= 1; + jne(.DLOOPKITER16) // iterate again if i != 0. +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + label(.DCONSIDKITER4) +- ++ + mov(var(k_iter4), rsi) // i = k_iter4; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKLEFT1) // if i == 0, jump to code that + // considers k_left1 loop. + // else, we prepare to enter k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER4) // EDGE LOOP (ymm) +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -1191,21 +1191,21 @@ void bli_dgemmsup_rd_haswell_asm_2x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm6) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKITER4) // iterate again if i != 0. +- +- +- ++ ++ ++ + + label(.DCONSIDKLEFT1) +- ++ + mov(var(k_left1), rsi) // i = k_left1; + test(rsi, rsi) // check i via logical AND. + je(.DPOSTACCUM) // if i == 0, we're done; jump to end. + // else, we prepare to enter k_left1 loop. +- +- ++ ++ + + + label(.DLOOPKLEFT1) // EDGE LOOP (scalar) +@@ -1213,7 +1213,7 @@ void bli_dgemmsup_rd_haswell_asm_2x1 + // using the xmm registers would zero out the + // high bits of the destination registers, + // which would destory intermediate results. +- ++ + vmovsd(mem(rbx ), xmm0) + add(imm(1*8), rbx) // b += 1*rs_b = 1*8; + +@@ -1224,12 +1224,12 @@ void bli_dgemmsup_rd_haswell_asm_2x1 + add(imm(1*8), rax) // a += 1*cs_a = 1*8; + vfmadd231pd(ymm0, ymm3, ymm6) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKLEFT1) // iterate again if i != 0. +- +- +- ++ ++ ++ + + + +@@ -1238,12 +1238,12 @@ void bli_dgemmsup_rd_haswell_asm_2x1 + + // ymm4 + // ymm6 +- +- vhaddpd( ymm5, ymm4, ymm0 ) ++ ++ vhaddpd( ymm4, ymm4, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm4 ) + +- vhaddpd( ymm7, ymm6, ymm0 ) ++ vhaddpd( ymm6, ymm6, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm6 ) + +@@ -1254,78 +1254,78 @@ void bli_dgemmsup_rd_haswell_asm_2x1 + + //mov(var(rs_c), rdi) // load rs_c + //lea(mem(, rdi, 4), rdi) // rs_c *= sizeof(double) +- ++ + mov(var(alpha), rax) // load address of alpha + mov(var(beta), rbx) // load address of beta + vbroadcastsd(mem(rax), ymm0) // load alpha and duplicate + vbroadcastsd(mem(rbx), ymm3) // load beta and duplicate +- ++ + vmulpd(xmm0, xmm4, xmm4) // scale by alpha + vmulpd(xmm0, xmm6, xmm6) +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + //mov(var(cs_c), rsi) // load cs_c + //lea(mem(, rsi, 8), rsi) // rsi = cs_c * sizeof(double) +- +- +- ++ ++ ++ + // now avoid loading C if beta == 0 +- ++ + vxorpd(ymm0, ymm0, ymm0) // set ymm0 to zero. + vucomisd(xmm0, xmm3) // set ZF if beta == 0. + je(.DBETAZERO) // if ZF = 1, jump to beta == 0 case +- + +- ++ ++ + label(.DROWSTORED) +- + +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm4) + vmovsd(xmm4, mem(rcx)) + add(rdi, rcx) +- +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm6) + vmovsd(xmm6, mem(rcx)) + //add(rdi, rcx) +- +- +- ++ ++ ++ + jmp(.DDONE) // jump to end. +- +- +- +- ++ ++ ++ ++ + label(.DBETAZERO) +- + +- ++ ++ + label(.DROWSTORBZ) +- +- ++ ++ + vmovsd(xmm4, mem(rcx)) + add(rdi, rcx) +- ++ + vmovsd(xmm6, mem(rcx)) + //add(rdi, rcx) +- + +- +- +- ++ ++ ++ ++ + label(.DDONE) +- ++ + + + + label(.DRETURN) + +- ++ + + end_asm( + : // output operands (none) +@@ -1396,9 +1396,9 @@ void bli_dgemmsup_rd_haswell_asm_1x1 + // ------------------------------------------------------------------------- + + begin_asm() +- ++ + //vzeroall() // zero all xmm/ymm registers. +- ++ + mov(var(a), rax) // load address of a. + mov(var(rs_a), r8) // load rs_a + //mov(var(cs_a), r9) // load cs_a +@@ -1416,7 +1416,7 @@ void bli_dgemmsup_rd_haswell_asm_1x1 + + //lea(mem(r11, r11, 2), r13) // r13 = 3*cs_b + //lea(mem(r8, r8, 2), r10) // r10 = 3*rs_a +- ++ + + mov(var(c), rcx) // load address of c + mov(var(rs_c), rdi) // load rs_c +@@ -1450,19 +1450,19 @@ void bli_dgemmsup_rd_haswell_asm_1x1 + //lea(mem(r10, rdi, 1), r10) // rdx = c + 3*rs_c; + prefetch(0, mem(rcx, 1*8)) // prefetch c + 0*rs_c + #endif +- + +- +- ++ ++ ++ + mov(var(k_iter16), rsi) // i = k_iter16; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKITER4) // if i == 0, jump to code that + // contains the k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER16) // MAIN LOOP +- +- ++ ++ + // ---------------------------------- iteration 0 + + #if 0 +@@ -1478,7 +1478,7 @@ void bli_dgemmsup_rd_haswell_asm_1x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm4) + +- ++ + // ---------------------------------- iteration 1 + + vmovupd(mem(rbx ), ymm0) +@@ -1490,7 +1490,7 @@ void bli_dgemmsup_rd_haswell_asm_1x1 + + + // ---------------------------------- iteration 2 +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -1514,27 +1514,27 @@ void bli_dgemmsup_rd_haswell_asm_1x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm4) + +- ++ + + dec(rsi) // i -= 1; + jne(.DLOOPKITER16) // iterate again if i != 0. +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + label(.DCONSIDKITER4) +- ++ + mov(var(k_iter4), rsi) // i = k_iter4; + test(rsi, rsi) // check i via logical AND. + je(.DCONSIDKLEFT1) // if i == 0, jump to code that + // considers k_left1 loop. + // else, we prepare to enter k_iter4 loop. +- +- ++ ++ + label(.DLOOPKITER4) // EDGE LOOP (ymm) +- ++ + #if 0 + prefetch(0, mem(rax, r10, 1, 0*8)) // prefetch rax + 3*cs_a + prefetch(0, mem(rax, r8, 4, 0*8)) // prefetch rax + 4*cs_a +@@ -1548,21 +1548,21 @@ void bli_dgemmsup_rd_haswell_asm_1x1 + add(imm(4*8), rax) // a += 4*cs_a = 4*8; + vfmadd231pd(ymm0, ymm3, ymm4) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKITER4) // iterate again if i != 0. +- +- +- ++ ++ ++ + + label(.DCONSIDKLEFT1) +- ++ + mov(var(k_left1), rsi) // i = k_left1; + test(rsi, rsi) // check i via logical AND. + je(.DPOSTACCUM) // if i == 0, we're done; jump to end. + // else, we prepare to enter k_left1 loop. +- +- ++ ++ + + + label(.DLOOPKLEFT1) // EDGE LOOP (scalar) +@@ -1570,7 +1570,7 @@ void bli_dgemmsup_rd_haswell_asm_1x1 + // using the xmm registers would zero out the + // high bits of the destination registers, + // which would destory intermediate results. +- ++ + vmovsd(mem(rbx ), xmm0) + add(imm(1*8), rbx) // b += 1*rs_b = 1*8; + +@@ -1578,12 +1578,12 @@ void bli_dgemmsup_rd_haswell_asm_1x1 + add(imm(1*8), rax) // a += 1*cs_a = 1*8; + vfmadd231pd(ymm0, ymm3, ymm4) + +- ++ + dec(rsi) // i -= 1; + jne(.DLOOPKLEFT1) // iterate again if i != 0. +- +- +- ++ ++ ++ + + + +@@ -1591,8 +1591,8 @@ void bli_dgemmsup_rd_haswell_asm_1x1 + label(.DPOSTACCUM) + + // ymm4 +- +- vhaddpd( ymm5, ymm4, ymm0 ) ++ ++ vhaddpd( ymm4, ymm4, ymm0 ) + vextractf128(imm(1), ymm0, xmm1 ) + vaddpd( xmm0, xmm1, xmm4 ) + +@@ -1602,69 +1602,69 @@ void bli_dgemmsup_rd_haswell_asm_1x1 + + //mov(var(rs_c), rdi) // load rs_c + //lea(mem(, rdi, 4), rdi) // rs_c *= sizeof(double) +- ++ + mov(var(alpha), rax) // load address of alpha + mov(var(beta), rbx) // load address of beta + vbroadcastsd(mem(rax), ymm0) // load alpha and duplicate + vbroadcastsd(mem(rbx), ymm3) // load beta and duplicate +- ++ + vmulpd(xmm0, xmm4, xmm4) // scale by alpha +- +- +- +- +- +- ++ ++ ++ ++ ++ ++ + //mov(var(cs_c), rsi) // load cs_c + //lea(mem(, rsi, 8), rsi) // rsi = cs_c * sizeof(double) +- +- +- ++ ++ ++ + // now avoid loading C if beta == 0 +- ++ + vxorpd(ymm0, ymm0, ymm0) // set ymm0 to zero. + vucomisd(xmm0, xmm3) // set ZF if beta == 0. + je(.DBETAZERO) // if ZF = 1, jump to beta == 0 case +- + +- ++ ++ + label(.DROWSTORED) +- + +- vmovsd(mem(rcx), xmm0) ++ ++ vmovsd(mem(rcx), xmm0) + vfmadd231pd(xmm0, xmm3, xmm4) + vmovsd(xmm4, mem(rcx)) + //add(rdi, rcx) +- +- +- ++ ++ ++ + jmp(.DDONE) // jump to end. +- +- +- +- ++ ++ ++ ++ + label(.DBETAZERO) +- + +- ++ ++ + label(.DROWSTORBZ) +- +- ++ ++ + vmovsd(xmm4, mem(rcx)) + //add(rdi, rcx) +- + +- +- +- ++ ++ ++ ++ + label(.DDONE) +- ++ + + + + label(.DRETURN) + +- ++ + + end_asm( + : // output operands (none) +diff --git a/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx4.c b/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx4.c +index 21dd3b89..516bfced 100644 +--- a/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx4.c ++++ b/kernels/haswell/3/sup/d6x8/bli_gemmsup_rd_haswell_asm_dMx4.c +@@ -1338,17 +1338,6 @@ void bli_dgemmsup_rd_haswell_asm_1x4 + + vperm2f128(imm(0x20), ymm2, ymm0, ymm4 ) + +- +- //vhaddpd( ymm8, ymm5, ymm0 ) +- //vextractf128(imm(1), ymm0, xmm1 ) +- //vaddpd( xmm0, xmm1, xmm0 ) +- +- //vhaddpd( ymm14, ymm11, ymm2 ) +- //vextractf128(imm(1), ymm2, xmm1 ) +- //vaddpd( xmm2, xmm1, xmm2 ) +- +- //vperm2f128(imm(0x20), ymm2, ymm0, ymm5 ) +- + // xmm4[0:3] = sum(ymm4) sum(ymm7) sum(ymm10) sum(ymm13) + + From fd4a584f28949004c8f104a396c016feabd46091 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 17:58:56 +0000 Subject: [PATCH 1329/9987] Updated file to final version, corrected version or artic to 24.6.2020 --- ...> artic-ncov2019-2021.06.24-foss-2020b.eb} | 73 ++++++++----------- 1 file changed, 29 insertions(+), 44 deletions(-) rename easybuild/easyconfigs/a/artic-ncov2019/{artic-ncov2019-2021.06.21-foss-2020b.eb => artic-ncov2019-2021.06.24-foss-2020b.eb} (55%) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.21-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb similarity index 55% rename from easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.21-foss-2020b.eb rename to easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 3e5ba7f8c42..f9836bd9182 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.21-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -8,7 +8,7 @@ easyblock = 'PythonBundle' name = 'artic-ncov2019' local_commit = 'b3f2dda5e6d95bc1c5d95a04d4ef37d304479477' -version = '2021.06.21' +version = '2021.06.24' homepage = "https://github.com/artic-network/artic-ncov2019" description = """Initial implementation of an ARTIC bioinformatics platform @@ -17,11 +17,11 @@ for nanopore sequencing of nCoV2019 novel coronavirus.""" toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ - ('Python', '3.8.6'), # pandas, + ('Python', '3.8.6'), ('Biopython', '1.78'), ('Pysam', '0.16.0.1'), ('BWA', '0.7.17'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.9'), ('minimap2', '2.20'), ('SAMtools', '1.12'), ('MUSCLE', '3.8.31'), @@ -30,77 +30,62 @@ dependencies = [ ('IQ-TREE', '2.1.2'), ('snakemake', '6.1.0'), ('Longshot', '0.4.3'), - ('medaka', '0.11.4'), + ('medaka', '1.4.3'), ('python-parasail', '1.2.4'), - ('PhyML', '3.3.20190321'), + ('PhyML', '3.3.20200621'), ('nodejs', '12.19.0'), ('goalign', '0.3.2', '', True), ('gotree', '0.4.0', '', True), - ('rampart', '1.2.0rc3'), - ('libdeflate', '1.5'), + ('rampart', '1.2.0'), + ('libdeflate', '1.7'), ('nanopolish', '0.13.3'), ('seqtk', '1.3'), - ('BCFtools', '1.9'), + ('BCFtools', '1.12'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('zipp', '1.0.0', { - 'checksums': ['d38fbe01bbf7a3593a32bc35a9c4453c32bc42b98c377f9bff7e9f8da157786c'], + ('zipp', '3.5.0', { + 'checksums': ['f5812b1e007e48cff63449a5e9f4e7ebea716b4111f9c4f9a645f91d579bf0c4'], }), - ('pluggy', '0.13.1', { - 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + ('pluggy', '1.0.0', { + 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], }), - ('py', '1.8.1', { - 'checksums': ['5e27081401262157467ad6e7f851b7aa402c5852dbcb3dae06768434de5752aa'], + ('py', '1.10.0', { + 'checksums': ['21b81bda15b66ef5e1a777a21c4dcd9c20ad3efd0b3f817e7a809035269e1bd3'], }), - ('wcwidth', '0.1.9', { - 'checksums': ['ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1'], + ('wcwidth', '0.2.5', { + 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], }), - ('attrs', '19.3.0', { + ('attrs', '21.2.0', { 'modulename': 'attr', - 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], + 'checksums': ['ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb'], }), - ('importlib-metadata', '1.6.0', { + ('importlib-metadata', '4.8.1', { 'modulename': 'importlib_metadata', 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', - 'checksums': ['34513a8a0c4962bc66d35b359558fd8a5e10cd472d37aec5f66858addef32c1e'], + 'checksums': ['f284b3e11256ad1e5d03ab86bb2ccd6f5339688ff17a4d797a0fe7df326f23b1'], }), - ('more-itertools', '8.2.0', { + ('more-itertools', '8.9.0', { 'modulename': 'more_itertools', - 'checksums': ['b1ddb932186d8a6ac451e1d95844b382f55e12686d51ca0c68b6f61f2ab7a507'], - }), - ('packaging', '14.5', { - 'checksums': ['363f9193daa14085b8dfeeb2bf64227bcf1dc85c02ae2a5c6018b01f77e46491'], + 'checksums': ['8c746e0d09871661520da4f1241ba6b908dc903839733c8203b552cffaf173bd'], }), ('args', '0.1.0', { 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], }), - ('pytest', '5.4.1', { - 'checksums': ['84dde37075b8805f3d1f392cc47e38a0e59518fb46a431cfdaf7cf1ce805f970'], + ('pytest', '6.2.5', { + 'checksums': ['131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89'], }), - ('tqdm', '4.45.0', { - 'checksums': ['00339634a22c10a7a22476ee946bbde2dbe48d042ded784e4d88e0236eca5d81'], + ('tqdm', '4.62.2', { + 'checksums': ['a4d6d112e507ef98513ac119ead1159d286deab17dffedd96921412c2d236ff5'], }), - ('fieldbioinformatics', '1.1.0-rc2', { + ('fieldbioinformatics', '1.2.1', { 'modulename': False, 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/artic-network/fieldbioinformatics/archive'], - 'checksums': [('7083f67b1188e8f9b55f8bd4f7a46853e9c74ae7dde324b1fc8e792a85e58073', - '778ed3cf2f1b0457c696acbed8b99951b2ec042a2035f08bddd95da3884b146b')], - }), - # This is not upstream version, but artic tweaked one, which is exactly required. - ('Porechop', '0.3.2pre', { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/artic-network/Porechop/archive'], - 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], - }), - ('binlorry', '1.3.1', { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/rambaut/binlorry/archive'], - 'checksums': ['001b74cad497b7253b821ceaac8c0b829b2787396a896fc2d3940a704a149b48'], + 'checksums': ['74b5fdb18dca57e73fbe872c5c4e25c110e7826fac7a062f0eb0a5453e4e7b20'], }), ('clint', '0.5.1', { 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], @@ -126,7 +111,7 @@ components = [ 'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ, }], - 'checksums': ['26bc96742e291795d4a7c1154336715d98168d8ce3524ad7adfea0b5562eb34d'], + 'checksums': ['ac0dbf7d29038ace8e24dc172ae4dbba9a76d6803809c8f28a9fa228f98aecb6'], }), ] local_artic_bins = [ From c40440e604705f7da270aab08773e3635d040eaf Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Sep 2021 18:36:51 +0000 Subject: [PATCH 1330/9987] Added missing artic_get_stats script --- .../a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index f9836bd9182..87e4bb0201e 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -115,7 +115,8 @@ components = [ }), ] local_artic_bins = [ - 'artic', 'artic_fasta_header', 'artic_make_depth_mask', 'artic_mask', 'artic_vcf_filter', 'artic_vcf_merge' + 'artic', 'artic_fasta_header', 'artic_get_stats', 'artic_make_depth_mask', + 'artic_mask', 'artic_vcf_filter', 'artic_vcf_merge' ] sanity_check_paths = { 'files': ['bin/%s' % f for f in local_artic_bins], From 99adcb135a1f9de95c8fa05ffe78a170afb1cdae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Sep 2021 20:57:22 +0200 Subject: [PATCH 1331/9987] update mappy + isal extensions in medaka 1.4.3 easyconfig using foss/2020b --- easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 38b5e7d0ffd..2de5d46e27f 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -50,14 +50,14 @@ exts_list = [ ('ont-fast5-api', '3.3.0', { 'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'], }), - ('mappy', '2.20', { - 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], + ('mappy', '2.22', { + 'checksums': ['219c93ab7f8d5d7c26face512a9e738a7306f3376ebfa3017eac70676ba97840'], }), ('parasail', '1.2.4', { 'checksums': ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'], }), - ('isal', '0.10.0', { - 'checksums': ['3f89471065c2837d1235877dbdcdbd8b7649068723026b0582010fa106a71ff3'], + ('isal', '0.11.1', { + 'checksums': ['8d07a07caacc3be4f478ceff8353941f360f922e8854ff1cbee4a44b443eb2af'], }), ('xopen', '1.1.0', { 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], From 9d83571c507737a30aa5f548d5bfdfb0e00ee0e7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 17 Sep 2021 08:08:17 +0200 Subject: [PATCH 1332/9987] Fix typo in BLIS patch comment. --- .../BLIS/BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch index 3c6a7167ee7..ad6dee6c3de 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch @@ -1,6 +1,6 @@ Taken from https://github.com/flame/blis/pull/544 Fixes a problem with DGEMM causing FPR signalling on Broadwell -See https://github.com/flame/blis/pull/544 +See https://github.com/flame/blis/issues/486 Åke Sandgren, 20210916 From 3e8f31995517a2ab313e6122771d6513c8c7af12 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 17 Sep 2021 08:18:26 +0200 Subject: [PATCH 1333/9987] adding easyconfigs: gobff-2021a.eb --- easybuild/easyconfigs/g/gobff/gobff-2021a.eb | 31 +++++++++++ .../libFLAME/libFLAME-5.2.0-GCCcore-10.3.0.eb | 53 +++++++++++++++++++ .../ScaLAPACK-2.1.0-gompi-2021a-bf.eb | 44 +++++++++++++++ 3 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/g/gobff/gobff-2021a.eb create mode 100644 easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb diff --git a/easybuild/easyconfigs/g/gobff/gobff-2021a.eb b/easybuild/easyconfigs/g/gobff/gobff-2021a.eb new file mode 100644 index 00000000000..847ca2b5a29 --- /dev/null +++ b/easybuild/easyconfigs/g/gobff/gobff-2021a.eb @@ -0,0 +1,31 @@ +easyblock = "Toolchain" + +name = 'gobff' +version = '2021a' + +homepage = '(none)' +description = 'GCC and GFortran based compiler toolchain with OpenMPI, BLIS, libFLAME, ScaLAPACK and FFTW.' + +toolchain = SYSTEM + +local_comp_name = 'GCC' +local_comp_version = '10.3.0' +local_comp = (local_comp_name, local_comp_version) + +local_gcccore = ('GCCcore', local_comp_version) + +# toolchain used to build dependencies +local_comp_mpi_tc_name = 'gompi' +local_comp_mpi_tc = (local_comp_mpi_tc_name, version) + +# compiler toolchain dependencies +dependencies = [ + local_comp, + ('OpenMPI', '4.1.1', '', local_comp), # part of gompi toolchain + ('BLIS', '0.8.1', '', local_gcccore), + ('libFLAME', '5.2.0', '', local_gcccore), + ('ScaLAPACK', '2.1.0', '-bf', local_comp_mpi_tc), + ('FFTW', '3.3.9', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..0ee04fd3c5c --- /dev/null +++ b/easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'libFLAME' +version = '5.2.0' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame' +description = """libFLAME is a portable library for dense matrix computations, +providing much of the functionality present in LAPACK.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/flame/libflame/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['997c860f351a5c7aaed8deec00f502167599288fd0559c92d5bfd77d0b4d475c'] + +# '--enable-max-arg-list-hack --enable-dynamic-build' requires 'file' function from GNU Make 4.x +builddependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), + ('make', '4.3'), # needed on Cent OS 7 where make 3 is installed +] + +dependencies = [('BLIS', '0.8.1')] + +# Use unset FLIBS to let configure pick up LDFLAGS +preconfigopts = 'unset FLIBS && ' +preconfigopts += 'LIBS="-lblis $LIBS" ' +preconfigopts += 'LDFLAGS="$LDFLAGS -L$EBROOTBLIS/lib -fopenmp -lm -lpthread" ' +preconfigopts += 'CFLAGS="$CFLAGS -I$EBROOTBLIS/include/blis" ' + +configopts = '--enable-max-arg-list-hack ' +configopts += '--enable-lapack2flame ' +configopts += '--enable-external-lapack-interfaces ' +configopts += '--enable-cblas-interfaces ' +configopts += '--enable-dynamic-build ' +configopts += '--enable-multithreading=openmp ' + +# libFLAME C++ Template API tests +# runtest = 'checkcpp LIBBLAS=$EBROOTBLIS/lib/libblis.a' + +# sanity_check_commands = [ +# 'cd %(builddir)s/%(namelower)s-%(version)s/test ' +# '&& make LIBBLAS=$EBROOTBLIS/lib/libblis-mt.so LDFLAGS="-fopenmp -lm -lpthread" ' +# '&& ./test_libfame.x' +# ] + +sanity_check_paths = { + 'files': ['include/FLAME.h', 'lib/libflame.a', 'lib/libflame.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb new file mode 100644 index 00000000000..968586fe952 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb @@ -0,0 +1,44 @@ +name = 'ScaLAPACK' +version = '2.1.0' +versionsuffix = '-bf' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6', # scalapack-2.1.0.tgz + 'bbb713c9fcabac802811c7f2c3a957c2d5d19dfd118ed1f6578c1436b82c7c43', # ScaLAPACK-2.1.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('BLIS', '0.8.1'), + ('libFLAME', '5.2.0'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' +configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From 58a43c1cb9f692ddc8d5a3a950c621dc6c15e32f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 17 Sep 2021 08:21:08 +0200 Subject: [PATCH 1334/9987] Add HPL/2.3 to gobff/2021a for testing. --- .../easyconfigs/h/HPL/HPL-2.3-gobff-2021a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-gobff-2021a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-gobff-2021a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-gobff-2021a.eb new file mode 100644 index 00000000000..f7aeff9dc56 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-gobff-2021a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gobff', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' From a39d9276cce99454c9c81355c5cc5c31b2a09de0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 17 Sep 2021 08:30:26 +0200 Subject: [PATCH 1335/9987] Forgot to update checksum after changing comment in patch. --- easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb index 9de3cfacf85..754d814d8a5 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb @@ -17,7 +17,7 @@ patches = [ checksums = [ '729694128719801e82fae7b5f2489ab73e4a467f46271beff09588c9265a697b', # 0.8.1.tar.gz # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch - 'ec3f4f7bddf43fad2d362fcd930684d027d7e572fc6104cdd5a7e605b7ac3ccb', + '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', ] builddependencies = [ From 73be498bdb7c0dfc63a113f35cf1943e5645eee9 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 17 Sep 2021 08:30:31 +0200 Subject: [PATCH 1336/9987] Modifications based on last file version in develop --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index 99b419b20e0..c0a68c827e5 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -1050,6 +1050,9 @@ exts_list = [ ('GenABEL', '1.8-0', { 'checksums': ['434fc806b918738ec67171a37a47099d1706332819317e368fe0ccb8f149a469'], }), + ('JASPAR2020', '0.99.10', { + 'checksums': ['b9b92d141a317ebb32a14708229f6b82522ceeb5f1b88360d93b0a7cfe30375b'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From f64e03af3c6a3692f9ae527566c4f72aff271b12 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 17 Sep 2021 12:04:01 +0200 Subject: [PATCH 1337/9987] adding easyconfigs: Gurobi-9.1.2-GCCcore-10.3.0.eb --- .../g/Gurobi/Gurobi-9.1.2-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d72ce99ad8b --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +name = 'Gurobi' +version = '9.1.2' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +patches = ['%(name)s-9.0.1_use-eb-python-gurobi-shell.patch'] +checksums = [ + '7f60bd675f79476bb2b32cd632aa1d470f8246f2b033b7652d8de86f6e7e429b', # gurobi9.1.2_linux64.tar.gz + 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01', # Gurobi-9.0.1_use-eb-python-gurobi-shell.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +license_file = HOME + '/licenses/%(name)s.lic' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' From 224fcf66346a874c99aacf6879433e6126555834 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 17 Sep 2021 14:17:21 +0200 Subject: [PATCH 1338/9987] Add patch to build jax --- easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb index 16a67803d1a..2ec70c03163 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb @@ -32,6 +32,7 @@ local_tf_builddir = '%(builddir)s/' + local_tf_dir local_jax_prebuildopts = "sed -i 's$pathToSed$%s$g' WORKSPACE && " % local_tf_builddir use_pip = True +sanity_pip_check = True # running the tests with lots of cores results in test failures because not enough threads can be started, # so limit to a reasonable number of cores to use at maximum @@ -67,6 +68,7 @@ components = [ 'patches': [ 'jaxlib-0.1.70_add-bazel-args-to-shutdown.patch', 'jaxlib-%(version)s_no-tensorflow-download.patch', + ('jaxlib-%(version)s_fix-llvm-env.patch', '../' + local_tf_dir), ], 'checksums': [ # jaxlib-v0.1.71.tar.gz From ede38b1fae2c0aa9ccd661aec0cf02b08c7fba32 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 17 Sep 2021 14:18:10 +0200 Subject: [PATCH 1339/9987] Remove duplicate pip check --- easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb index 2ec70c03163..112898c2162 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb @@ -97,6 +97,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' From b779666dd768895711d436c30abcad3478445ca9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 17 Sep 2021 14:18:49 +0200 Subject: [PATCH 1340/9987] Add patch --- .../j/jax/jaxlib-0.1.71_fix-llvm-env.patch | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jaxlib-0.1.71_fix-llvm-env.patch diff --git a/easybuild/easyconfigs/j/jax/jaxlib-0.1.71_fix-llvm-env.patch b/easybuild/easyconfigs/j/jax/jaxlib-0.1.71_fix-llvm-env.patch new file mode 100644 index 00000000000..ad81aa52065 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jaxlib-0.1.71_fix-llvm-env.patch @@ -0,0 +1,28 @@ +diff --git a/third_party/llvm/workspace.bzl b/third_party/llvm/workspace.bzl +index c0c7ef3db29..63ccda6dc65 100644 +--- a/third_party/llvm/workspace.bzl ++++ b/third_party/llvm/workspace.bzl +@@ -16,4 +16,5 @@ def repo(name): + "https://github.com/llvm/llvm-project/archive/{commit}.tar.gz".format(commit = LLVM_COMMIT), + ], + build_file = "//third_party/llvm:BUILD.bazel", ++ patch_file = "//third_party/llvm:fix-ctx.run.patch", + ) +diff --git a/third_party/llvm/fix-ctx.run.patch b/third_party/llvm/fix-ctx.run.patch +new file mode 100644 +index 00000000000..65aff1fcd3f +--- /dev/null ++++ b/third_party/llvm/fix-ctx.run.patch +@@ -0,0 +1,12 @@ ++diff --git a/utils/bazel/llvm-project-overlay/mlir/tblgen.bzl b/utils/bazel/llvm-project-overlay/mlir/tblgen.bzl ++index 64685aa1cbc10..177789797a3e0 100644 ++--- a/utils/bazel/llvm-project-overlay/mlir/tblgen.bzl +++++ b/utils/bazel/llvm-project-overlay/mlir/tblgen.bzl ++@@ -169,6 +169,7 @@ def _gentbl_rule_impl(ctx): ++ inputs = trans_srcs, ++ executable = ctx.executable.tblgen, ++ arguments = [args], +++ use_default_shell_env = True, ++ mnemonic = "TdGenerate", ++ ) ++ From e5dffcd8ad620ff1156246f170484bb26816e49c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 17 Sep 2021 14:54:49 +0200 Subject: [PATCH 1341/9987] Update jaxlib-0.1.71_fix-llvm-env.patch --- easybuild/easyconfigs/j/jax/jaxlib-0.1.71_fix-llvm-env.patch | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/j/jax/jaxlib-0.1.71_fix-llvm-env.patch b/easybuild/easyconfigs/j/jax/jaxlib-0.1.71_fix-llvm-env.patch index ad81aa52065..60660b0d2a9 100644 --- a/easybuild/easyconfigs/j/jax/jaxlib-0.1.71_fix-llvm-env.patch +++ b/easybuild/easyconfigs/j/jax/jaxlib-0.1.71_fix-llvm-env.patch @@ -1,3 +1,8 @@ +Enable use_default_shell_env for the MLIR table generator so that the environment (action_env etc.) is correctly passed to the tool +See https://github.com/google/jax/issues/7842 + +Author: Alexander Grund (TU Dresden) + diff --git a/third_party/llvm/workspace.bzl b/third_party/llvm/workspace.bzl index c0c7ef3db29..63ccda6dc65 100644 --- a/third_party/llvm/workspace.bzl From 4efae93674fe1a36f947aeda495e341ee7028bc2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 17 Sep 2021 15:26:11 +0200 Subject: [PATCH 1342/9987] Fix TensorFlow 2.2.3 on PPC --- .../TensorFlow/TensorFlow-2.2.3-foss-2020b.eb | 3 + ...w-2.2.3_fix-bfloat16-alias-violation.patch | 192 ++++++++++++++++++ 2 files changed, 195 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb index d1d6fc11dc3..c6b0c25ff66 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -155,6 +155,7 @@ exts_list = [ 'TensorFlow-2.1.0_fix-system-nasm.patch', 'TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch', 'TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch', + 'TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch', 'TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch', 'TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', @@ -169,6 +170,8 @@ exts_list = [ '093f4dd3ec372a82d50dffe32eea6821025cd1c406911a746c4367a40bc38486', # TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch '85c3023892e21692e14750e43a7d1db3c83c6e86a75ac1559c9dba39e0a160ae', + # TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch + '23223e2f27677c9485ccb9ee8cae7818109ad600a83cc5514fbf7a9a4a0d719f', # TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch 'd80e0103aeefb5244b57dd0e01bb7a0c1e6a750fba41833706547be87d3829e4', # TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch new file mode 100644 index 00000000000..86a2437cb14 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch @@ -0,0 +1,192 @@ +TF uses invalid reinterpret_cast causing miscompilation at least on POWER +Fix by proper code + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/core/framework/BUILD b/tensorflow/core/framework/BUILD +index d47c74a629d..8ae68b53f3b 100644 +--- a/tensorflow/core/framework/BUILD ++++ b/tensorflow/core/framework/BUILD +@@ -597,6 +597,7 @@ cc_library( + ":numeric_types", + "//tensorflow/core/platform:byte_order", + "//tensorflow/core/platform:types", ++ "//third_party/eigen3", + ], + alwayslink = 1, + ) +diff --git a/tensorflow/core/framework/bfloat16.cc b/tensorflow/core/framework/bfloat16.cc +index 6025be51704..c7fdda163b7 100644 +--- a/tensorflow/core/framework/bfloat16.cc ++++ b/tensorflow/core/framework/bfloat16.cc +@@ -15,36 +15,28 @@ limitations under the License. + + #include "tensorflow/core/framework/bfloat16.h" + ++#include "third_party/eigen3/Eigen/Core" ++ + namespace tensorflow { + + void FloatToBFloat16(const float* src, bfloat16* dst, int64 size) { +- const uint16_t* p = reinterpret_cast(src); +- uint16_t* q = reinterpret_cast(dst); ++ for (; size != 0; src++, dst++, size--) { + #if __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__ +- for (; size != 0; p += 2, q++, size--) { +- *q = p[0]; +- } ++ memcpy(dst, src, sizeof(bfloat16)); + #else +- for (; size != 0; p += 2, q++, size--) { +- *q = p[1]; +- } ++ memcpy( ++ dst, ++ reinterpret_cast(src) + sizeof(float) - sizeof(bfloat16), ++ sizeof(bfloat16)); + #endif ++ } + } + + void BFloat16ToFloat(const bfloat16* src, float* dst, int64 size) { +- const uint16_t* p = reinterpret_cast(src); +- uint16_t* q = reinterpret_cast(dst); +-#if __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__ +- for (; size != 0; p++, q += 2, size--) { +- q[0] = *p; +- q[1] = 0; +- } +-#else +- for (; size != 0; p++, q += 2, size--) { +- q[0] = 0; +- q[1] = *p; +- } +-#endif ++ Eigen::Map> src_eigen(src, ++ size); ++ Eigen::Map dst_eigen(dst, size); ++ dst_eigen = src_eigen.cast(); + } + + } // end namespace tensorflow +diff --git a/tensorflow/core/framework/numeric_types.h b/tensorflow/core/framework/numeric_types.h +index 6d80a1c519c..916c2d302d1 100644 +--- a/tensorflow/core/framework/numeric_types.h ++++ b/tensorflow/core/framework/numeric_types.h +@@ -47,13 +47,9 @@ typedef Eigen::QUInt16 quint16; + + + static inline tensorflow::bfloat16 FloatToBFloat16(float float_val) { +-#if __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__ +- return *reinterpret_cast( +- reinterpret_cast(&float_val)); +-#else +- return *reinterpret_cast( +- &(reinterpret_cast(&float_val)[1])); +-#endif ++ tensorflow::bfloat16 result; ++ result.value = absl::bit_cast(float_val) >> 16; ++ return result; + } + + namespace Eigen { +diff --git a/tensorflow/core/kernels/cast_op.h b/tensorflow/core/kernels/cast_op.h +index 84c44f6b5e7..19c73fa4975 100644 +--- a/tensorflow/core/kernels/cast_op.h ++++ b/tensorflow/core/kernels/cast_op.h +@@ -285,18 +285,7 @@ struct scalar_cast_op<::tensorflow::bfloat16, float> { + typedef float result_type; + EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE float operator()( + const ::tensorflow::bfloat16& a) const { +- float ret; +- uint16_t* p = reinterpret_cast(&ret); +-#if __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__ +- p[0] = a.value; +- p[1] = 0; +-#else +- static_assert(::tensorflow::port::kLittleEndian, +- "Not a little endian system!"); +- p[0] = 0; +- p[1] = a.value; +-#endif +- return ret; ++ return static_cast(a); + } + }; + +diff --git a/tensorflow/core/kernels/sparse_matmul_op.cc b/tensorflow/core/kernels/sparse_matmul_op.cc +index eb460147d71..71897681d0b 100644 +--- a/tensorflow/core/kernels/sparse_matmul_op.cc ++++ b/tensorflow/core/kernels/sparse_matmul_op.cc +@@ -282,14 +282,7 @@ const int kNumOperands = (sizeof(Packet) / sizeof(float)); + #define FMA(a, b, c, d) d = Eigen::internal::pmadd(a, b, c); + + ALWAYS_INLINE float ConvertBfloat16ToFloat(const bfloat16* src) { +- float out = 0; +- auto tmp = reinterpret_cast(&out); +-#if __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__ +- tmp[0] = *src; +-#else +- tmp[1] = *src; +-#endif +- return out; ++ return static_cast(*src); + } + + ALWAYS_INLINE Packet ConvertFourBfloat16ToFloat(const bfloat16* src) { +diff --git a/tensorflow/core/lib/bfloat16/BUILD b/tensorflow/core/lib/bfloat16/BUILD +index 53c2059f06d..2564ac6ab37 100644 +--- a/tensorflow/core/lib/bfloat16/BUILD ++++ b/tensorflow/core/lib/bfloat16/BUILD +@@ -17,6 +17,7 @@ cc_library( + deps = [ + "//tensorflow/core/platform:byte_order", + "//third_party/eigen3", ++ "@com_google_absl//absl/base", + ], + ) + +diff --git a/tensorflow/core/lib/bfloat16/bfloat16.h b/tensorflow/core/lib/bfloat16/bfloat16.h +index 54d78480066..72ea6aa911e 100644 +--- a/tensorflow/core/lib/bfloat16/bfloat16.h ++++ b/tensorflow/core/lib/bfloat16/bfloat16.h +@@ -21,6 +21,7 @@ limitations under the License. + #include + #include + ++#include "absl/base/casts.h" + #include "tensorflow/core/platform/byte_order.h" + + #if defined(__CUDACC__) || (defined(__HIPCC__) && defined(__HIP__)) +@@ -59,12 +60,7 @@ struct bfloat16 { + output.value = std::signbit(v) ? 0x8000 : 0; + return output; + } +- const uint16_t* p = reinterpret_cast(&v); +-#if __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__ +- output.value = p[0]; +-#else +- output.value = p[1]; +-#endif ++ output.value = absl::bit_cast(v) >> 16; + return output; + } + +@@ -102,16 +98,7 @@ struct bfloat16 { + : bfloat16(static_cast(val)) {} + + B16_DEVICE_FUNC explicit operator float() const { +- float result = 0; +- +- uint16_t* q = reinterpret_cast(&result); +- +-#if __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__ +- q[0] = value; +-#else +- q[1] = value; +-#endif +- return result; ++ return absl::bit_cast(static_cast(value) << 16); + } + + B16_DEVICE_FUNC explicit operator bool() const { From ec24d211f966e6775a468a7dcccdf81f374aed86 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 17 Sep 2021 15:33:09 +0200 Subject: [PATCH 1343/9987] Fix checksum --- .../easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb index c6b0c25ff66..9678677ff31 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -171,7 +171,7 @@ exts_list = [ # TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch '85c3023892e21692e14750e43a7d1db3c83c6e86a75ac1559c9dba39e0a160ae', # TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch - '23223e2f27677c9485ccb9ee8cae7818109ad600a83cc5514fbf7a9a4a0d719f', + '6e845c44c27477740d16e9c525cdd4c2a96ac3deb2709ac62e21c3de79c4583b', # TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch 'd80e0103aeefb5244b57dd0e01bb7a0c1e6a750fba41833706547be87d3829e4', # TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch From 8a11607c023e0e4f1f3a5b090ac9da31c6daf962 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 17 Sep 2021 16:21:24 +0200 Subject: [PATCH 1344/9987] Add checksum --- easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb index 112898c2162..76ea09ba96a 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb @@ -79,6 +79,8 @@ components = [ 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', # jaxlib-0.1.71_no-tensorflow-download.patch '693cff114553fa5591aa4cb3d777c9b7dea1ded1effef76d7d45d11cd2fc3819', + # jaxlib-0.1.71_fix-llvm-env.patch + '9f1ee59ff7cfcfb272c4baebbc1c5b3b26fd9b9ddf05c1ffa77c8ebd2ba70b7e', ], 'start_dir': 'jax-jaxlib-v%(version)s', 'prebuildopts': local_jax_prebuildopts, From 07f9378f85be51d67fda3fa75b3eecd2eb6df96b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 17 Sep 2021 16:34:11 +0200 Subject: [PATCH 1345/9987] adding easyconfigs: CD-HIT-4.8.1-GCC-10.3.0.eb --- .../c/CD-HIT/CD-HIT-4.8.1-GCC-10.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..dd2043cf707 --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-10.3.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.32.1'), + ('zlib', '1.2.11'), +] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + +moduleclass = 'bio' From 8cdbd769ea68d791386424ef93b633445c179723 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 17 Sep 2021 16:47:44 +0200 Subject: [PATCH 1346/9987] adding easyconfigs: MAFFT-7.487-gompi-2021a-with-extensions.eb --- ...MAFFT-7.487-gompi-2021a-with-extensions.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.487-gompi-2021a-with-extensions.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.487-gompi-2021a-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.487-gompi-2021a-with-extensions.eb new file mode 100644 index 00000000000..a955aa928a7 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.487-gompi-2021a-with-extensions.eb @@ -0,0 +1,52 @@ +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.487' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], + 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'checksums': ['ea05f55e51d980925ce00b2289948ccd2a3ddd0397ebd60feaddc41ddd5d8ef1'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + }), + ('%s MPI' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/MPI', + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft'] + ['libexec/mafft/%s' % x for x in [ + 'mxscarnamod', # installed by MAFFT Extensions + 'mpiscript', 'nodepair_mpi', # installed by MAFFT MPI + ]], + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +modextravars = {'MAFFT_N_THREADS_PER_PROCESS': '1'} +# MAFFT MPI requires other environment variables that depend on job resources +# More information at at https://mafft.cbrc.jp/alignment/software/mpi.html + +moduleclass = 'bio' From 831fd07d35a685285513afc5a8338840593b7fef Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 17 Sep 2021 17:23:32 +0200 Subject: [PATCH 1347/9987] Upload test report --- easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.3.0.eb index d72ce99ad8b..b4f9b36ccdf 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.1.2-GCCcore-10.3.0.eb @@ -28,6 +28,7 @@ dependencies = [ # remove bundled Python interpreter in favour of the dependency in EB postinstallcmds = ['rm %(installdir)s/bin/python*'] +# license is not mandatory for installation license_file = HOME + '/licenses/%(name)s.lic' modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` From 12491804967615a8ad17d9cfa355ef9c3160e61f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 17:33:44 +0200 Subject: [PATCH 1348/9987] stick to gompi/2020b toolchain for IQ-TREE 2.1.2 --- ...-TREE-2.1.2-foss-2020b.eb => IQ-TREE-2.1.2-gompi-2020b.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/i/IQ-TREE/{IQ-TREE-2.1.2-foss-2020b.eb => IQ-TREE-2.1.2-gompi-2020b.eb} (91%) diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-foss-2020b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-gompi-2020b.eb similarity index 91% rename from easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-foss-2020b.eb rename to easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-gompi-2020b.eb index 6cffe4a16df..9f3d8686a6b 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.2-gompi-2020b.eb @@ -7,7 +7,7 @@ version = '2.1.2' homepage = 'http://www.iqtree.org/' description = """Efficient phylogenomic software by maximum likelihood""" -toolchain = {'name': 'foss', 'version': '2020b'} +toolchain = {'name': 'gompi', 'version': '2020b'} # Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary source_urls = ['https://github.com/iqtree/iqtree2/archive/'] @@ -39,4 +39,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["iqtree2 --help"] + moduleclass = 'bio' From ee3c1f56c1caa7e9ee5c44be0db0b54dcb2f6ce2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 17:48:29 +0200 Subject: [PATCH 1349/9987] bump python-isal to 0.11.1 (latest) and use in medaka 1.4.3 with foss/2020b --- easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb | 4 +--- ...CCcore-10.2.0.eb => python-isal-0.11.1-GCCcore-10.2.0.eb} | 5 ++--- 2 files changed, 3 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/p/python-isal/{python-isal-0.11.0-GCCcore-10.2.0.eb => python-isal-0.11.1-GCCcore-10.2.0.eb} (91%) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 2de5d46e27f..6619e4a1e9b 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -35,6 +35,7 @@ dependencies = [ ('edlib', '1.3.9'), ('pyspoa', '0.0.8'), ('pyfaidx', '0.5.9.5'), + ('python-isal', '0.11.1'), ] use_pip = True @@ -56,9 +57,6 @@ exts_list = [ ('parasail', '1.2.4', { 'checksums': ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'], }), - ('isal', '0.11.1', { - 'checksums': ['8d07a07caacc3be4f478ceff8353941f360f922e8854ff1cbee4a44b443eb2af'], - }), ('xopen', '1.1.0', { 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], }), diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb similarity index 91% rename from easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.2.0.eb rename to easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb index fd2df03c9ca..8a7daf5569c 100644 --- a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb @@ -3,8 +3,7 @@ easyblock = 'PythonPackage' name = 'python-isal' -version = '0.11.0' -_modname = 'isal' +version = '0.11.1' homepage = 'https://github.com/pycompression/python-isal' description = """Faster zlib and gzip compatible compression and decompression @@ -32,6 +31,6 @@ sanity_pip_check = True preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' installopts = '--no-binary isal' -options = {'modulename': _modname} +options = {'modulename': 'isal'} moduleclass = 'lib' From f1fea2f76c31f0ed65d4af0716320e762ae009db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 17:49:25 +0200 Subject: [PATCH 1350/9987] one sanity check command per line in cutadapt 3.4 easyconfigs --- .../easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb | 5 ++++- .../easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb index 64cfa8b2538..558e3819c5d 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb @@ -47,6 +47,9 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["cutadapt --help", "cutadapt --version"] +sanity_check_commands = [ + "cutadapt --help", + "cutadapt --version", +] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb index 4a74f24cfe2..4477ce27073 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb @@ -47,6 +47,9 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["cutadapt --help", "cutadapt --version"] +sanity_check_commands = [ + "cutadapt --help", + "cutadapt --version", +] moduleclass = 'bio' From 4b08525a3d5f8c6b285f695f7cb54061c72d674a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 20:23:31 +0200 Subject: [PATCH 1351/9987] bump dependency for python-isal to v0.11.1 + use dnaio 0.5.2 extension for cutadapt 3.4 --- .../c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb | 6 +-- .../r/Racon/Racon-1.4.13-GCCcore-10.2.0.eb | 31 ------------- .../Racon-1.4.13-std_invalid_argument.patch | 46 ------------------- 3 files changed, 3 insertions(+), 80 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.4.13-std_invalid_argument.patch diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb index 558e3819c5d..f3ffcc20e05 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '3.8.6'), - ('python-isal', '0.11.0'), + ('python-isal', '0.11.1'), ] use_pip = True @@ -34,8 +34,8 @@ exts_list = [ ('xopen', '1.1.0', { 'checksums': ['38277eb96313b2e8822e19e793791801a1f41bf13ee5b48616a97afc65e9adb3'], }), - ('dnaio', '0.5.1', { - 'checksums': ['c68ecffbf653dfe122f1c10fb8d7c5957ad68acc5c9035c66f81eba1a591d31c'], + ('dnaio', '0.5.2', { + 'checksums': ['549e1c6afa192a4bf79c112b57cc5e927b286ab9a3c2803d6577613a7e3ff180'], }), (name, version, { 'checksums': ['eb8d52d45a7d38bd3ddc901eb397599bca8716a20d39e2b1feeb20242352dab2'], diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-10.2.0.eb deleted file mode 100644 index 8b398e16c58..00000000000 --- a/easybuild/easyconfigs/r/Racon/Racon-1.4.13-GCCcore-10.2.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Racon' -version = '1.4.13' - -homepage = 'https://github.com/lbcb-sci/racon' -description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = ['https://github.com/lbcb-sci/racon/releases/download/%(version)s/'] -sources = ['%(namelower)s-v%(version)s.tar.gz'] -patches = ['Racon-1.4.13-std_invalid_argument.patch'] -checksums = [ - '4220e98bf84768483bd94eef62a0821cffc74f4e7139c74685c08161909263b0', # racon-v1.4.13.tar.gz - '7bdfff1b431f2fc105b08ad8336c90472d5a17a03caf109c97d0c6ab716c8092', # Racon-1.4.13-std_invalid_argument.patch -] - -builddependencies = [ - ('CMake', '3.18.4'), - ('binutils', '2.35'), -] - -sanity_check_paths = { - 'files': ['bin/racon'], - 'dirs': [], -} - -sanity_check_commands = ['racon --help'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.4.13-std_invalid_argument.patch b/easybuild/easyconfigs/r/Racon/Racon-1.4.13-std_invalid_argument.patch deleted file mode 100644 index 2cedd7e2f16..00000000000 --- a/easybuild/easyconfigs/r/Racon/Racon-1.4.13-std_invalid_argument.patch +++ /dev/null @@ -1,46 +0,0 @@ -Binary files racon-v1.4.13-old/.git/modules/vendor/spoa/index and racon-v1.4.13/.git/modules/vendor/spoa/index differ -diff -ruN racon-v1.4.13-old/vendor/spoa/src/alignment_engine.cpp racon-v1.4.13/vendor/spoa/src/alignment_engine.cpp ---- racon-v1.4.13-old/vendor/spoa/src/alignment_engine.cpp 2021-09-14 14:24:53.358413371 +0200 -+++ racon-v1.4.13/vendor/spoa/src/alignment_engine.cpp 2021-09-14 14:26:58.046107581 +0200 -@@ -7,6 +7,7 @@ - #include - #include - #include -+#include - - #include "sisd_alignment_engine.hpp" - #include "simd_alignment_engine.hpp" -diff -ruN racon-v1.4.13-old/vendor/spoa/src/graph.cpp racon-v1.4.13/vendor/spoa/src/graph.cpp ---- racon-v1.4.13-old/vendor/spoa/src/graph.cpp 2021-09-14 14:24:53.358413371 +0200 -+++ racon-v1.4.13/vendor/spoa/src/graph.cpp 2021-09-14 14:26:52.550165125 +0200 -@@ -8,6 +8,7 @@ - #include - #include - #include -+#include - - #include "spoa/graph.hpp" - -diff -ruN racon-v1.4.13-old/vendor/spoa/src/main.cpp racon-v1.4.13/vendor/spoa/src/main.cpp ---- racon-v1.4.13-old/vendor/spoa/src/main.cpp 2021-09-14 14:24:53.358413371 +0200 -+++ racon-v1.4.13/vendor/spoa/src/main.cpp 2021-09-14 14:26:43.670258101 +0200 -@@ -3,6 +3,7 @@ - #include - #include - #include -+#include - #include - - #include "sequence.hpp" -diff -ruN racon-v1.4.13-old/vendor/spoa/test/spoa_test.cpp racon-v1.4.13/vendor/spoa/test/spoa_test.cpp ---- racon-v1.4.13-old/vendor/spoa/test/spoa_test.cpp 2021-09-14 14:24:53.357413382 +0200 -+++ racon-v1.4.13/vendor/spoa/test/spoa_test.cpp 2021-09-14 14:27:13.949941070 +0200 -@@ -4,6 +4,8 @@ - * @brief Spoa unit test source file - */ - -+#include -+ - #include "spoa_test_config.h" - - #include "sequence.hpp" From 708d8e94ccbb5fc51f1f9f47659b8effda776696 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 20:24:20 +0200 Subject: [PATCH 1352/9987] bump Racon dependency to 1.4.21 in longread_umi 0.3.2 easyconfig --- .../easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index dc667caa8cf..2ed9f132fb8 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -20,7 +20,7 @@ dependencies = [ ('minimap2', '2.18'), ('parallel', '20210322'), ('Pysam', '0.16.0.1'), - ('Racon', '1.4.13'), + ('Racon', '1.4.21'), ('SAMtools', '1.11'), ('seqtk', '1.3'), ('VSEARCH', '2.18.0'), From d817fc7db5abd62f06cd33f6536e3750a9b49a7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 20:26:30 +0200 Subject: [PATCH 1353/9987] add exception for longread_umi's transitive dependency on TensorFlow 2.2.3 --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 1008461fa69..f23cb77bd5f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -474,8 +474,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'NGSpeciesID-0.1.1.1-']), # medaka 1.4.3 (foss/2019b) depends on TensorFlow 2.2.2 ('2.2.2;', ['medaka-1.4.3-']), - # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3 - ('2.2.3;', ['medaka-1.4.3-']), + # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi depends on medaka + ('2.2.3;', ['medaka-1.4.3-', 'longread_umi-0.3.2-']), ], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; From 339f035fa66973e069434aa4b993721f99a46a0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 20:28:57 +0200 Subject: [PATCH 1354/9987] fix AmberTools v20 easyconfig (WIP) --- .../AmberTools-20-intel-2020a-Python-3.8.2.eb | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb index 4eb64536037..9522267acdf 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb @@ -19,26 +19,37 @@ sources = [{ 'download_filename': local_download_credentials, 'filename': SOURCE_TAR_BZ2, }] -patches = ['Amber-20_fix-hardcoding.patch'] +patches = [ + 'Amber-20_fix-hardcoding.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_cmake-locate-netcdf.patch', +] checksums = [ 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools-20.tar.bz2 'a71f1bd70bac8d5e25386d6db90e95874ad300b956ed5b5afbc8848b7c1e00dc', # Amber-20_fix-hardcoding.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch' + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch ] builddependencies = [ ('Bison', '3.5.3'), ('pkg-config', '0.29.2'), + ('CMake', '3.16.4'), ] dependencies = [ ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('matplotlib', '3.2.1', versionsuffix), ('netCDF', '4.7.4'), ('netCDF-Fortran', '4.5.2'), + ('FFTW', '3.3.8'), ] # fix linking to netCDF library: also requires linking to HDF5 & cURL libs, which in turns require others, # all of which are indirect dependencies via netCDF local_netcdf_libs = "-lnetcdf -lhdf5 -lsz -ldl -liomp5 -lcurl -lssl -lcrypto -lz -lm -lpthread" -preconfigopts = "sed -i'' 's/-lnetcdf/%s/g' AmberTools/src/cpptraj/configure && " % local_netcdf_libs +preconfigopts = "sed -i'' 's/-lnetcdf/%s/g' %%(builddir)s/AmberTools/src/cpptraj/configure && " % local_netcdf_libs configopts = "-nosanderapi" moduleclass = 'chem' From efc0d03ee18d882146eaa8fd0b3bfc49280b6772 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 20:39:49 +0200 Subject: [PATCH 1355/9987] fix checksum for jaxlib-0.1.71_fix-llvm-env.patch --- easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb index 76ea09ba96a..ee86eebb067 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb @@ -80,7 +80,7 @@ components = [ # jaxlib-0.1.71_no-tensorflow-download.patch '693cff114553fa5591aa4cb3d777c9b7dea1ded1effef76d7d45d11cd2fc3819', # jaxlib-0.1.71_fix-llvm-env.patch - '9f1ee59ff7cfcfb272c4baebbc1c5b3b26fd9b9ddf05c1ffa77c8ebd2ba70b7e', + '73f5a83dd13c71cc1ed2c3db084a67861d418a8dd56d862cb2310a522de1a4ee', ], 'start_dir': 'jax-jaxlib-v%(version)s', 'prebuildopts': local_jax_prebuildopts, From 48ff8e33b586762bd3ac3fc1c3ac5ca0404316ca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Sep 2021 20:45:08 +0200 Subject: [PATCH 1356/9987] fix checksum in python-isal 0.11.1 easyconfig --- .../p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb index 8a7daf5569c..a8d2cb81ce6 100644 --- a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-10.2.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} github_account = 'pycompression' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['3959ce30f1043ae591bc9d6ee9edb5781c09cc15c69dd5361517d29b56327260'] +checksums = ['43d885814f1ee19f5c3a7e9ada3d696fe75f19c0853728fe0ade564bc021a78f'] builddependencies = [('binutils', '2.35')] From 73b0ffbd844e5fd700afa6b64fa51702577ee1e5 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 18 Sep 2021 18:43:15 +0200 Subject: [PATCH 1357/9987] adding easyconfigs: BLIS-3.0.1-GCCcore-11.2.0-amd.eb --- .../b/BLIS/BLIS-3.0.1-GCCcore-11.2.0-amd.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-11.2.0-amd.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-11.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-11.2.0-amd.eb new file mode 100644 index 00000000000..125993747b0 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-11.2.0-amd.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '3.0.1' +versionsuffix = '-amd' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' +description = """AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/amd/blis/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e'] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), + ('Perl', '5.34.0'), +] + +# Build Serial and multithreaded library +configopts = ['--enable-cblas --enable-shared CC="$CC" auto', + '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto'] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT, + 'lib/libblis-mt.a', 'lib/libblis-mt.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' From d9ab7f05410e76ffb6fd84296cecb014ed4f9722 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 18 Sep 2021 22:27:00 +0200 Subject: [PATCH 1358/9987] adding easyconfigs: ELPA-2021.05.001-foss-2021.07.eb --- .../e/ELPA/ELPA-2021.05.001-foss-2021.07.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021.07.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021.07.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021.07.eb new file mode 100644 index 00000000000..e3d0f13dc3c --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021.07.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2021.05.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'foss', 'version': '2021.07'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + 'aea66a18e87574c7c292e852e45943e16f8bc3839f456635d1d610957840d146', # elpa-new_release_2021.05.002.tar.gz + # ELPA-2021.05.001_fix_hardcoded_perl_path.patch + 'af3f8cd063100d403cb2fe53cfc85eb2d5a2ef3348a3e6d5cf2d3680ebb4ec02', +] + +builddependencies = [ + ('Autotools', '20210726'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.9.6'), + ('Perl', '5.34.0'), +] + +preconfigopts = './autogen.sh && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' From 645408c8c4cd4f33028b1ffe3757def1a832b60a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 18 Sep 2021 22:28:02 +0200 Subject: [PATCH 1359/9987] adding easyconfigs: libxc-5.1.6-GCC-11.2.0.eb --- .../l/libxc/libxc-5.1.6-GCC-11.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb new file mode 100644 index 00000000000..f36ec4c4923 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '5.1.6' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['0d0496513114ed84987c32649912f9a65d234696dab13a4b00ce8c420bfc0a1d'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Perl', '5.34.0'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' From 39f921555e6ac6eb1601243f7e2b95d2e76c85f3 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 18 Sep 2021 22:45:51 +0200 Subject: [PATCH 1360/9987] adding easyconfigs: QuantumESPRESSO-6.8-foss-2021a.eb, QuantumESPRESSO-6.8-intel-2021a.eb --- .../QuantumESPRESSO-6.8-foss-2021a.eb | 44 +++++++++++++++++++ .../QuantumESPRESSO-6.8-intel-2021a.eb | 44 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb new file mode 100644 index 00000000000..36c8fdf64b0 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021a.eb @@ -0,0 +1,44 @@ +name = 'QuantumESPRESSO' +version = '6.8' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s/', + 'https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + 'qe-gipaw-%(version)s.tar.gz', + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + 'fc9b8141705d31db30f6cfe61d4e49867c7c3b04a59533eb7f90301fa8bd50ce', # qe-%(version)s-ReleasePack.tgz + 'ec6212b1f1084818a91b9980c6c24e4f9f7da2212e534732e0af6072addfb4dd', # qe-gipaw-%(version)s.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('ELPA', '2021.05.001'), + ('libxc', '5.1.5'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb new file mode 100644 index 00000000000..4b187cd70ee --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-intel-2021a.eb @@ -0,0 +1,44 @@ +name = 'QuantumESPRESSO' +version = '6.8' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s/', + 'https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + 'qe-gipaw-%(version)s.tar.gz', + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + 'fc9b8141705d31db30f6cfe61d4e49867c7c3b04a59533eb7f90301fa8bd50ce', # qe-%(version)s-ReleasePack.tgz + 'ec6212b1f1084818a91b9980c6c24e4f9f7da2212e534732e0af6072addfb4dd', # qe-gipaw-%(version)s.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('ELPA', '2021.05.001'), + ('libxc', '5.1.5'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' From c050cb3e48ddb7bbb01243b7d47ef2c98a0d52c3 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Sat, 18 Sep 2021 23:30:47 +0000 Subject: [PATCH 1361/9987] fixed openssl issue --- .../easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb index 5196f6ce4a7..187877371cc 100644 --- a/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb @@ -22,9 +22,10 @@ builddependencies = [ dependencies = [ ('libreadline', '8.1'), + ('OpenSSL', '1.1', '', True), ] -# osdependencies = [OS_PKG_OPENSSL_DEV] +configopts = '--with-openssl' sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bsqldb', 'datacopy', 'defncopy', 'fisql', 'freebcp', From e76b4345520fdbf251533047a373f945581f5221 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Sun, 19 Sep 2021 07:01:30 +0000 Subject: [PATCH 1362/9987] adding easyconfigs: TRUST4-1.0.5.1.eb --- .../easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb diff --git a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb new file mode 100644 index 00000000000..d4d9ee94187 --- /dev/null +++ b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb @@ -0,0 +1,24 @@ + +easyblock = 'Conda' + +name = "TRUST4" +version = "1.0.5.1" + +homepage = 'https://github.com/liulab-dfci/TRUST4' +description = """Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. +""" + +toolchain = SYSTEM + +requirements = "%(namelower)s=%(version)s" +channels = ['bioconda'] + +builddependencies = [('Miniconda3', '4.9.2')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['trust4', 'run-trust4', 'bam-extractor', + 'fastq-extractor']], + 'dirs': ['bin', 'conda-meta', 'lib'] +} + +moduleclass = 'bio' From 1d9af29eb869fa7b59c82ed3f18004d06972ac12 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Sun, 19 Sep 2021 12:46:32 -0400 Subject: [PATCH 1363/9987] Update easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb index d4d9ee94187..b62aae131e2 100644 --- a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb +++ b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb @@ -1,4 +1,3 @@ - easyblock = 'Conda' name = "TRUST4" From 5418566581b47cfb7c174233bd60febedac2321a Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Sun, 19 Sep 2021 12:46:41 -0400 Subject: [PATCH 1364/9987] Update easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb index b62aae131e2..66c9c94e482 100644 --- a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb +++ b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb @@ -4,8 +4,11 @@ name = "TRUST4" version = "1.0.5.1" homepage = 'https://github.com/liulab-dfci/TRUST4' -description = """Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. -""" +description = """Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to +analyze TCR and BCR sequences using unselected RNA sequencing data, profiled +from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, +C genes including the hypervariable complementarity-determining region 3 (CDR3) +and reports consensus of BCR/TCR sequences.""" toolchain = SYSTEM From 51588212db9c441a0d797b56aa7e69a2697f0ba7 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Sun, 19 Sep 2021 12:46:59 -0400 Subject: [PATCH 1365/9987] Update easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb index 66c9c94e482..23e4ab181ac 100644 --- a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb +++ b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.5.1.eb @@ -18,7 +18,7 @@ channels = ['bioconda'] builddependencies = [('Miniconda3', '4.9.2')] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['trust4', 'run-trust4', 'bam-extractor', + 'files': ['bin/%s' % x for x in ['trust4', 'run-trust4', 'bam-extractor', 'fastq-extractor']], 'dirs': ['bin', 'conda-meta', 'lib'] } From 6e503c24e37cfb7b496c9e3f7d6fb4c567ef32d6 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Mon, 20 Sep 2021 01:19:54 +0000 Subject: [PATCH 1366/9987] fixing: USEARCH-11.0.667-i86linux32.eb . previous version was not downloading from web and had a non-functioning chmod command --- .../u/USEARCH/USEARCH-11.0.667-i86linux32.eb | 22 ++++++++++--------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/u/USEARCH/USEARCH-11.0.667-i86linux32.eb b/easybuild/easyconfigs/u/USEARCH/USEARCH-11.0.667-i86linux32.eb index 08e4ea64664..a2640054429 100644 --- a/easybuild/easyconfigs/u/USEARCH/USEARCH-11.0.667-i86linux32.eb +++ b/easybuild/easyconfigs/u/USEARCH/USEARCH-11.0.667-i86linux32.eb @@ -1,4 +1,6 @@ -easyblock = 'Binary' +# the 64-bit version is commercial + +easyblock = 'PackedBinary' name = 'USEARCH' version = '11.0.667' @@ -10,16 +12,16 @@ description = """USEARCH is a unique sequence analysis tool which offers search toolchain = SYSTEM -# download via https://www.drive5.com/usearch/download.html +source_urls = ['http://www.drive5.com/downloads'] +sources = ['usearch%s_%s.gz' % (version, versionsuffix[1:])] +checksums = ['1be0faa1380100296029064e4cf9665d723d43f03c794da444c5b1a6b6799ac2'] + local_usearch_bin = 'usearch%s_%s' % (version, versionsuffix[1:]) -sources = [local_usearch_bin] -checksums = [ - # Download of the binary creates unique checksum due to licensing being injected into application - None -] -install_cmd = "mkdir -p %%(installdir)s/bin && mv %s %%(installdir)s/bin/%%(namelower)s && " % local_usearch_bin -install_cmd += "chmod a=x %(installdir)s/bin/%(namelower)s" +postinstallcmds = [ + "chmod +rx %%(installdir)s/%s" % local_usearch_bin, + "ln -s %%(installdir)s/%s %%(installdir)s/%%(namelower)s" % local_usearch_bin +] modloadmsg = """USEARCH (32-bit) is licensed software but can be used for free by individuals when registered. A 64-bit version is @@ -27,7 +29,7 @@ modloadmsg = """USEARCH (32-bit) is licensed software but """ sanity_check_paths = { - 'files': ['bin/%(namelower)s'], + 'files': ['%(namelower)s'], 'dirs': [], } From 1d8167a0fd631d0c43d8e1664d341e3b3ea78d15 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Mon, 20 Sep 2021 10:44:27 +0200 Subject: [PATCH 1367/9987] Apply suggestions from code review --- .../easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb | 10 ++++++---- .../easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb | 10 ++++++---- 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb index 8b083ceb2b2..38ed401f349 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb @@ -19,7 +19,9 @@ checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0'] dependencies = [ ('libxc', '4.3.4'), + ('netCDF', '4.7.1'), ('netCDF-Fortran', '4.5.2'), + ('HDF5', '1.10.5'), ] # Ensure MPI. @@ -34,10 +36,10 @@ configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lff # libxc support configopts += '--with-libxc=${EBROOTLIBXC} ' -# hdf5/netcdf4. -configopts += 'with_netcdf="${EBROOTNETCDF}" ' -configopts += 'with_netcdf_fortran="${EBROOTNETCDFMINFORTRAN}" ' -configopts += 'with_hdf5="${EBROOTHDF5}" ' +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' # make sure --free-line-length-none is added to FCFLAGS configopts += 'FCFLAGS="${FCFLAGS} --free-line-length-none" ' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb index edcf0b65eee..4a255ae464f 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb @@ -20,7 +20,9 @@ checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0'] dependencies = [ ("imkl", "2019.5.281"), ('libxc', '4.3.4'), + ('netCDF', '4.7.1'), ('netCDF-Fortran', '4.5.2'), + ('HDF5', '1.10.5'), ] # Ensure MPI with intel wrappers. @@ -36,10 +38,10 @@ configopts += '--with-fft-flavor=dfti ' # libxc support configopts += '--with-libxc=${EBROOTLIBXC} ' -# hdf5/netcdf4. -configopts += 'with_netcdf="${EBROOTNETCDF}" ' -configopts += 'with_netcdf_fortran="${EBROOTNETCDFMINFORTRAN}" ' -configopts += 'with_hdf5="${EBROOTHDF5}" ' +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' # `make check` is just executing some basic unit tests. # In principle, one should run `make tests_v1`` to have some basic validation From 3ecd2fda30ee8957dc1159bb3081f00a2a1831e1 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 20 Sep 2021 12:16:31 +0000 Subject: [PATCH 1368/9987] Surplus ont-fast5-api module removed --- .../a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 87e4bb0201e..706aca4a419 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -97,10 +97,6 @@ exts_list = [ 'modulename': 'vcf', 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], }), - ('ont-fast5-api', '3.1.1', { - 'modulename': 'ont_fast5_api', - 'checksums': ['ce5a955c5e90a393f040fb36fc461382339fc0b9cd63e3969b9763127dc2b0d3'], - }), ] components = [ From dd0302095811556e9f577b47c7a1458c84d57024 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 20 Sep 2021 13:36:30 +0000 Subject: [PATCH 1369/9987] Downgraded SAMtools and BCFtools to 1.11, minimap2 to 2.18. Version for Eigen and TF need to stay as they are though (medaka)! --- .../artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 706aca4a419..085ca59dfe1 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -22,8 +22,8 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('BWA', '0.7.17'), ('Eigen', '3.3.9'), - ('minimap2', '2.20'), - ('SAMtools', '1.12'), + ('minimap2', '2.18'), + ('SAMtools', '1.11'), ('MUSCLE', '3.8.31'), ('ETE', '3.1.2'), ('MAFFT', '7.475', '-with-extensions'), @@ -40,7 +40,7 @@ dependencies = [ ('libdeflate', '1.7'), ('nanopolish', '0.13.3'), ('seqtk', '1.3'), - ('BCFtools', '1.12'), + ('BCFtools', '1.11'), ] use_pip = True From d61d8cde44c4618cc29da5aa53e0057ab59f923f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Mon, 20 Sep 2021 15:03:20 +0100 Subject: [PATCH 1370/9987] Update to include artic-ncov2019-2021.06.24 Added artic-ncov2019-2021.06.24 for TF version 2.2.3 as artic-ncov2019-2021.06.24 required medaka which itself required TF-2.2.3. --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 1008461fa69..b25f0e06925 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -474,8 +474,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'NGSpeciesID-0.1.1.1-']), # medaka 1.4.3 (foss/2019b) depends on TensorFlow 2.2.2 ('2.2.2;', ['medaka-1.4.3-']), - # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3 - ('2.2.3;', ['medaka-1.4.3-']), + # medaka 1.4.3 (foss/2020b) and thus artic-ncov2019-2021.06.24 depend on TensorFlow 2.2.3 + ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24artic-ncov2019-2021.06.24']), ], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; From 2bf0ecdcdb1a241a324aa507a3f7ca76b2d54ee2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Mon, 20 Sep 2021 15:15:33 +0100 Subject: [PATCH 1371/9987] Update test/easyconfigs/easyconfigs.py Co-authored-by: SebastianAchilles --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index b25f0e06925..4474961cf42 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -475,7 +475,7 @@ def check_dep_vars(self, gen, dep, dep_vars): # medaka 1.4.3 (foss/2019b) depends on TensorFlow 2.2.2 ('2.2.2;', ['medaka-1.4.3-']), # medaka 1.4.3 (foss/2020b) and thus artic-ncov2019-2021.06.24 depend on TensorFlow 2.2.3 - ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24artic-ncov2019-2021.06.24']), + ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-']), ], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; From 7a89b56ad713d388425f1c55bcd93213f8fb3a3b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 20 Sep 2021 16:36:10 +0200 Subject: [PATCH 1372/9987] Move BLIS/libFLAME to GCC level in gobff/2021a --- .../b/BLIS/BLIS-0.8.1-GCC-10.3.0.eb | 40 ++++++++++++++ easybuild/easyconfigs/g/gobff/gobff-2021a.eb | 6 +-- .../l/libFLAME/libFLAME-5.2.0-GCC-10.3.0.eb | 52 +++++++++++++++++++ 3 files changed, 94 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-10.3.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..d5672a2ca4b --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.8.1' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fix_dgemm-fpe-signalling-on-broadwell.patch', +] +checksums = [ + '729694128719801e82fae7b5f2489ab73e4a467f46271beff09588c9265a697b', # 0.8.1.tar.gz + # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch + '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', +] + +builddependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), +] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gobff/gobff-2021a.eb b/easybuild/easyconfigs/g/gobff/gobff-2021a.eb index 847ca2b5a29..11ed05a0dee 100644 --- a/easybuild/easyconfigs/g/gobff/gobff-2021a.eb +++ b/easybuild/easyconfigs/g/gobff/gobff-2021a.eb @@ -12,8 +12,6 @@ local_comp_name = 'GCC' local_comp_version = '10.3.0' local_comp = (local_comp_name, local_comp_version) -local_gcccore = ('GCCcore', local_comp_version) - # toolchain used to build dependencies local_comp_mpi_tc_name = 'gompi' local_comp_mpi_tc = (local_comp_mpi_tc_name, version) @@ -22,8 +20,8 @@ local_comp_mpi_tc = (local_comp_mpi_tc_name, version) dependencies = [ local_comp, ('OpenMPI', '4.1.1', '', local_comp), # part of gompi toolchain - ('BLIS', '0.8.1', '', local_gcccore), - ('libFLAME', '5.2.0', '', local_gcccore), + ('BLIS', '0.8.1', '', local_comp), + ('libFLAME', '5.2.0', '', local_comp), ('ScaLAPACK', '2.1.0', '-bf', local_comp_mpi_tc), ('FFTW', '3.3.9', '', local_comp_mpi_tc), ] diff --git a/easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..3906b94a407 --- /dev/null +++ b/easybuild/easyconfigs/l/libFLAME/libFLAME-5.2.0-GCC-10.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'libFLAME' +version = '5.2.0' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame' +description = """libFLAME is a portable library for dense matrix computations, +providing much of the functionality present in LAPACK.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/flame/libflame/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['997c860f351a5c7aaed8deec00f502167599288fd0559c92d5bfd77d0b4d475c'] + +# '--enable-max-arg-list-hack --enable-dynamic-build' requires 'file' function from GNU Make 4.x +builddependencies = [ + ('Python', '3.9.5'), + ('make', '4.3'), # needed on Cent OS 7 where make 3 is installed +] + +dependencies = [('BLIS', '0.8.1')] + +# Use unset FLIBS to let configure pick up LDFLAGS +preconfigopts = 'unset FLIBS && ' +preconfigopts += 'LIBS="-lblis $LIBS" ' +preconfigopts += 'LDFLAGS="$LDFLAGS -L$EBROOTBLIS/lib -fopenmp -lm -lpthread" ' +preconfigopts += 'CFLAGS="$CFLAGS -I$EBROOTBLIS/include/blis" ' + +configopts = '--enable-max-arg-list-hack ' +configopts += '--enable-lapack2flame ' +configopts += '--enable-external-lapack-interfaces ' +configopts += '--enable-cblas-interfaces ' +configopts += '--enable-dynamic-build ' +configopts += '--enable-multithreading=openmp ' + +# libFLAME C++ Template API tests +# runtest = 'checkcpp LIBBLAS=$EBROOTBLIS/lib/libblis.a' + +# sanity_check_commands = [ +# 'cd %(builddir)s/%(namelower)s-%(version)s/test ' +# '&& make LIBBLAS=$EBROOTBLIS/lib/libblis-mt.so LDFLAGS="-fopenmp -lm -lpthread" ' +# '&& ./test_libfame.x' +# ] + +sanity_check_paths = { + 'files': ['include/FLAME.h', 'lib/libflame.a', 'lib/libflame.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'numlib' From 97d1377fb202b60d71afe757c458732488d91635 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 20 Sep 2021 14:42:21 +0000 Subject: [PATCH 1373/9987] Removed Eigen as dependency --- .../a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 085ca59dfe1..6575f6de6ef 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -21,7 +21,6 @@ dependencies = [ ('Biopython', '1.78'), ('Pysam', '0.16.0.1'), ('BWA', '0.7.17'), - ('Eigen', '3.3.9'), ('minimap2', '2.18'), ('SAMtools', '1.11'), ('MUSCLE', '3.8.31'), From 9cb314d6dbb84a4a277943c54fee98a1519cd6be Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Mon, 20 Sep 2021 23:10:42 +0000 Subject: [PATCH 1374/9987] adding easyconfigs: vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb --- ...vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..3de8d93cef7 --- /dev/null +++ b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb @@ -0,0 +1,34 @@ + +easyblock = 'PackedBinary' + +name = 'vawk' +version = '0.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/cc2qe/vawk' +description = """An awk-like VCF parser +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '2.7.18'), +] + +source_urls = ['https://github.com/cc2qe/vawk/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['90cf5a57428ccaf3490ac98fc5c9f5f2c11ea2d1824188d9310bd34a8ef18d6f'] + +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i '1 i#!/usr/bin/env python' %(installdir)s/%(namelower)s", +] + +sanity_check_paths = { + 'files': ['vawk'], + 'dirs': [], +} + +sanity_check_commands = ["vawk -h"] + +moduleclass = 'bio' From 299424403cac892b4b100d3643ebd69bc63179f8 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt Date: Mon, 20 Sep 2021 23:45:30 +0000 Subject: [PATCH 1375/9987] adding easyconfigs: MixMHC2pred-1.2.eb --- .../m/MixMHC2pred/MixMHC2pred-1.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb diff --git a/easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb b/easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb new file mode 100644 index 00000000000..3beeb99c0c8 --- /dev/null +++ b/easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb @@ -0,0 +1,29 @@ + +easyblock = 'PackedBinary' + +name = 'MixMHC2pred' +version = '1.2' + +homepage = 'https://github.com/GfellerLab/MixMHC2pred' +description = """MixMHC2pred is a predictor of HLA class II ligands and epitopes. +It is described in publication Racle, J., et al. Robust prediction of HLA class II +epitopes by deep motif deconvolution of immunopeptidomes""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/GfellerLab/MixMHC2pred/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['839ebf71db3eb399b22e7522b71dc0e071ef9419ee0ab60dc4627d65264d9698'] + +postinstallcmds = [ + "chmod +rx %(installdir)s/%(name)s_unix", + "mv %(installdir)s/%(name)s %(installdir)s/%(name)s_mac", + "ln -s %(installdir)s/%(name)s_unix %(installdir)s/%(name)s" +] + +sanity_check_paths = { + 'files': ['%(name)s_unix'], + 'dirs': [], +} + +moduleclass = 'bio' From aacaf62b35f161b7dd0418664b32fabd31772e72 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Tue, 21 Sep 2021 12:07:43 +0200 Subject: [PATCH 1376/9987] Added Cartopy-0.20.0 and dependencies --- .../c/Cartopy/Cartopy-0.20.0-foss-2021a.eb | 50 +++++++++++++++++++ .../f/Fiona/Fiona-1.8.20-foss-2021a.eb | 45 +++++++++++++++++ .../p/pyproj/pyproj-3.1.0-GCCcore-10.3.0.eb | 37 ++++++++++++++ 3 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.0-foss-2021a.eb new file mode 100644 index 00000000000..7cf98863f44 --- /dev/null +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.0-foss-2021a.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Cartopy' +version = '0.20.0' + +homepage = 'https://scitools.org.uk/cartopy/docs/latest/' +description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Fiona', '1.8.20'), + ('GDAL', '3.3.0'), + ('GEOS', '3.9.1'), + ('matplotlib', '3.4.2'), + ('pyproj', '3.1.0'), + ('SciPy-bundle', '2021.05'), + ('Shapely', '1.8a1'), + ('lxml', '4.6.3'), + ('Pillow', '8.2.0'), + ('PROJ', '8.0.1'), + ('PyYAML', '5.4.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('OWSLib', '0.25.0', { + 'checksums': ['20d79bce0be10277caa36f3134826bd0065325df0301a55b2c8b1c338d8d8f0a'], + }), + ('pyepsg', '0.4.0', { + 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], + }), + ('pykdtree', '1.3.4', { + 'checksums': ['bebe5c608129f2997e88510c00010b9a78581b394924c0e3ecd131d52415165d'], + }), + ('pyshp', '2.1.3', { + 'modulename': 'shapefile', + 'checksums': ['e32b4a6832a3b97986df442df63b4c4a7dcc846b326c903189530a5cc6df0260'], + }), + (name, version, { + 'checksums': ['eae58aff26806e63cf115b2bce9477cedc4aa9f578c5e477b2c25cfa404f2b7a'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2021a.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2021a.eb new file mode 100644 index 00000000000..a8d625ae931 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.8.20' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('GDAL', '3.3.0'), + ('Shapely', '1.8a1'), # optional +] + +use_pip = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'checksums': ['a70502d2857b82f749c09cb0dea3726787747933a2a1599b5ab787d74e3c143b'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8e5edebbcc3 --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.1.0' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['67b94f4e694ae33fc90dfb7da0e6b5ed5f671dd0acc2f6cf46e9c39d56e16e1a'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('PROJ', '8.0.1'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' From 05d0631cc40f12e2ea5035e819fb62d5a9f987eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Tue, 21 Sep 2021 12:12:59 +0200 Subject: [PATCH 1377/9987] longread_umi: incorporate feedback --- .../l/longread_umi/longread_umi-0.3.2-foss-2020b.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index 2ed9f132fb8..15db976ec6c 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -46,9 +46,9 @@ components = [ }), ] -# Adapt the build-in tool check, but make it fail on error +# Adapt the built-in tool check but make it fail on error, replace usearch with vsearch and use our version local_deps_patch = ( - "sed -i" + "sed -i " "-e '2s;^;set -e ;' " "-e 's/USEARCH=usearch/USEARCH=vsearch/'" "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;'" @@ -58,6 +58,7 @@ local_deps_patch = ( postinstallcmds = [ 'find %(installdir)s -name "*.sh" -exec chmod +x {} \;', 'ln -s %(installdir)s/longread_umi.sh %(installdir)s/bin/longread_umi', + # Part of the installation process; longread uses porechop with custom adapters 'cp %(installdir)s/scripts/adapters.py %(installdir)s/lib/python%(pyshortver)s/site-packages/porechop/', local_deps_patch, ] From f67572bc7aa9924b3834951f4ed7e7c791cb422e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Tue, 21 Sep 2021 12:39:05 +0200 Subject: [PATCH 1378/9987] flake8 lint --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index ac804187af0..b728edb2c2a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -474,7 +474,7 @@ def check_dep_vars(self, gen, dep, dep_vars): 'NGSpeciesID-0.1.1.1-']), # medaka 1.4.3 (foss/2019b) depends on TensorFlow 2.2.2 ('2.2.2;', ['medaka-1.4.3-']), - # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic-ncov2019 depend on medaka + # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), ], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, From c48583b092f748219a15e3361554a37c5d71f8b1 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 21 Sep 2021 10:46:59 +0000 Subject: [PATCH 1379/9987] Removed apparently surplus Python modules as suggested, changed module name from False to artic --- .../artic-ncov2019-2021.06.24-foss-2020b.eb | 43 +++---------------- 1 file changed, 6 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 6575f6de6ef..9aedc07f208 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -46,56 +46,25 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('zipp', '3.5.0', { - 'checksums': ['f5812b1e007e48cff63449a5e9f4e7ebea716b4111f9c4f9a645f91d579bf0c4'], - }), - ('pluggy', '1.0.0', { - 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], - }), - ('py', '1.10.0', { - 'checksums': ['21b81bda15b66ef5e1a777a21c4dcd9c20ad3efd0b3f817e7a809035269e1bd3'], - }), - ('wcwidth', '0.2.5', { - 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], - }), - ('attrs', '21.2.0', { - 'modulename': 'attr', - 'checksums': ['ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb'], - }), - ('importlib-metadata', '4.8.1', { - 'modulename': 'importlib_metadata', - 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', - 'checksums': ['f284b3e11256ad1e5d03ab86bb2ccd6f5339688ff17a4d797a0fe7df326f23b1'], - }), - ('more-itertools', '8.9.0', { - 'modulename': 'more_itertools', - 'checksums': ['8c746e0d09871661520da4f1241ba6b908dc903839733c8203b552cffaf173bd'], + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], }), ('args', '0.1.0', { 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], }), - ('pytest', '6.2.5', { - 'checksums': ['131b36680866a76e6781d13f101efb86cf674ebb9762eb70d3082b6f29889e89'], + ('PyVCF', '0.6.8', { + 'modulename': 'vcf', + 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], }), ('tqdm', '4.62.2', { 'checksums': ['a4d6d112e507ef98513ac119ead1159d286deab17dffedd96921412c2d236ff5'], }), ('fieldbioinformatics', '1.2.1', { - 'modulename': False, + 'modulename': 'artic', 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/artic-network/fieldbioinformatics/archive'], 'checksums': ['74b5fdb18dca57e73fbe872c5c4e25c110e7826fac7a062f0eb0a5453e4e7b20'], }), - ('clint', '0.5.1', { - 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], - }), - ('datrie', '0.8.2', { - 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], - }), - ('PyVCF', '0.6.8', { - 'modulename': 'vcf', - 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], - }), ] components = [ From e94daab173df8ac394b7084804064160884e0a84 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Tue, 21 Sep 2021 13:16:34 +0200 Subject: [PATCH 1380/9987] longread_umi: resolve conflicts --- .../easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb index 3cbbee3f5c9..9678677ff31 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -170,11 +170,8 @@ exts_list = [ '093f4dd3ec372a82d50dffe32eea6821025cd1c406911a746c4367a40bc38486', # TensorFlow-2.2.3_fix-__tensorflow_core_graph_mkl_related_tests.patch '85c3023892e21692e14750e43a7d1db3c83c6e86a75ac1559c9dba39e0a160ae', -<<<<<<< HEAD -======= # TensorFlow-2.2.3_fix-bfloat16-alias-violation.patch '6e845c44c27477740d16e9c525cdd4c2a96ac3deb2709ac62e21c3de79c4583b', ->>>>>>> upstream/develop # TensorFlow-2.2.3_fix-numpy-UFunc-sig-change.patch 'd80e0103aeefb5244b57dd0e01bb7a0c1e6a750fba41833706547be87d3829e4', # TensorFlow-2.2.3_fix-source_utils_test-in-python38.patch From 3f3b1aff5f44ecf9275025daf6f4ce6ca50b31c0 Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 21 Sep 2021 13:20:08 +0200 Subject: [PATCH 1381/9987] adding easyconfigs: Scalasca-2.6-gompi-2021a.eb --- .../s/Scalasca/Scalasca-2.6-gompi-2021a.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompi-2021a.eb diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompi-2021a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompi-2021a.eb new file mode 100644 index 00000000000..9621861f23f --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6-gompi-2021a.eb @@ -0,0 +1,52 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Scalasca' +version = '2.6' + +homepage = 'https://www.scalasca.org/' +description = """ + Scalasca is a software tool that supports the performance optimization of + parallel programs by measuring and analyzing their runtime behavior. The + analysis identifies potential performance bottlenecks -- in particular + those concerning communication and synchronization -- and offers guidance + in exploring their causes. +""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b3f9cb1d58f3e25090a39da777bae8ca2769fd10cbd6dfb9a4887d873ee2441e'] + +builddependencies = [ + ('CubeWriter', '4.6'), +] + +dependencies = [ + ('CubeGUI', '4.6'), + ('CubeLib', '4.6'), + ('OTF2', '2.3'), + ('Score-P', '7.0'), +] + +sanity_check_paths = { + 'files': ['bin/scalasca', 'lib/libpearl.replay.a'], + 'dirs': [], +} + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scalasca/patterns'} + +moduleclass = 'perf' From 77b79e8a92231acdef7b818c9967c1d53b3294a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Sep 2021 14:44:31 +0200 Subject: [PATCH 1382/9987] add patch files for AmberTools 20 --- .../AmberTools-20_cmake-locate-netcdf.patch | 13 ++++++++++++ ...ols-20_fix_missing_MPI_LIBRARY_error.patch | 21 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-20_cmake-locate-netcdf.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-20_cmake-locate-netcdf.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-20_cmake-locate-netcdf.patch new file mode 100644 index 00000000000..3ece09e84c1 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-20_cmake-locate-netcdf.patch @@ -0,0 +1,13 @@ +Ensure that CMake recurses available paths if the Fortran libs aren't available in the netCDF module + +James Carpenter 2021-01-23 +--- amber20_src/cmake/jedbrown/FindNetCDF.cmake.orig 2020-04-28 02:19:51.000000000 +0100 ++++ amber20_src/cmake/jedbrown/FindNetCDF.cmake 2021-01-25 11:41:47.005657000 +0000 +@@ -52,6 +52,7 @@ + + macro (NetCDF_check_interface lang header libs) + find_path (NetCDF_INCLUDES_${lang} NAMES ${header} HINTS "${NetCDF_INCLUDES}" NO_DEFAULT_PATH) ++ find_path (NetCDF_INCLUDES_${lang} NAMES ${header} HINTS "${NetCDF_INCLUDES}") + + find_library (NetCDF_LIBRARIES_${lang} NAMES ${libs} HINTS "${NetCDF_lib_dirs}") + diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch new file mode 100644 index 00000000000..21263acfebd --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch @@ -0,0 +1,21 @@ +When using "usempi" there will be no MPI_xxx_LIBRARIES set and that causes +import_libraries to error out. We know it is correct so comment out that +FATAL_ERROR. + +Åke Sandgren, 2021-06-16 +diff -ru AmberTools.orig/cmake/LibraryTracking.cmake AmberTools/cmake/LibraryTracking.cmake +--- AmberTools.orig/cmake/LibraryTracking.cmake 2021-04-25 02:51:44.000000000 +0200 ++++ AmberTools/cmake/LibraryTracking.cmake 2021-06-16 13:30:26.568317368 +0200 +@@ -170,9 +170,9 @@ + + cmake_parse_arguments(IMP_LIBS "" "" "LIBRARIES;INCLUDES" ${ARGN}) + +- if("${IMP_LIBS_LIBRARIES}" STREQUAL "") +- message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") +- endif() ++ #if("${IMP_LIBS_LIBRARIES}" STREQUAL "") ++ # message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") ++ #endif() + + if(NOT "${IMP_LIBS_UNPARSED_ARGUMENTS}" STREQUAL "") + message(FATAL_ERROR "Incorrect usage. Extra arguments provided.") From 2d0ae469ab909fd9f32a987a26e20d0a9a740936 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 21 Sep 2021 14:56:20 +0200 Subject: [PATCH 1383/9987] adding easyconfigs: MEME-5.4.1-GCC-10.3.0.eb --- .../m/MEME/MEME-5.4.1-GCC-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..4858375aeaf --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-10.3.0.eb @@ -0,0 +1,39 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.4.1' + +homepage = 'https://meme-suite.org/meme/index.html' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://%(namelower)s-suite.org/%(namelower)s/%(namelower)s-software/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c07fb8afafa60fc5e84ca24493c82fa6f4bd1df1a2622102edbf86a1c30fd11f'] + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), + ('Perl', '5.32.1'), + ('Python', '3.9.5') +] + +configopts = '--enable-build-libxml2 --enable-build-libxslt ' +configopts += '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' + +sanity_check_paths = { + 'files': ["bin/%(namelower)s", "bin/dreme", "bin/%(namelower)s-chip"], + 'dirs': ["lib"], +} + +moduleclass = 'bio' From 77b79f5748ca93f9ca9bbee55c1dd64e6ab72f65 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Tue, 21 Sep 2021 15:18:30 +0200 Subject: [PATCH 1384/9987] Added sanity check command --- easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2021a.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2021a.eb index a8d625ae931..0e2c959b361 100644 --- a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2021a.eb +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.20-foss-2021a.eb @@ -42,4 +42,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["fio --help"] + moduleclass = 'data' From ebd4ea823157749b8a908d4e88433b40a932e1df Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 21 Sep 2021 15:27:55 +0200 Subject: [PATCH 1385/9987] added old ITK to exceptions for one-version-per-toolchain-gen tests --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4474961cf42..bf32ed93ff7 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -427,6 +427,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # EMAN2 2.3 requires Boost(.Python) 1.64.0 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], + # VMTK 1.4.x requires ITK 4.13.x + 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) 'Jellyfish': [(r'1\.', [r'Kraken-1\.', r'Roary-3\.12\.0', r'metaWRAP-1\.2'])], # Libint 1.1.6 is required by older CP2K versions From bde6ea5432e581b25b7db2d68603234fd054b01d Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Tue, 21 Sep 2021 12:37:44 -0400 Subject: [PATCH 1386/9987] Update easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb b/easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb index 3beeb99c0c8..b7f615d0743 100644 --- a/easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb +++ b/easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb @@ -17,7 +17,7 @@ checksums = ['839ebf71db3eb399b22e7522b71dc0e071ef9419ee0ab60dc4627d65264d9698'] postinstallcmds = [ "chmod +rx %(installdir)s/%(name)s_unix", - "mv %(installdir)s/%(name)s %(installdir)s/%(name)s_mac", + "mv %(installdir)s/%(name)s %(installdir)s/%(name)s_mac", "ln -s %(installdir)s/%(name)s_unix %(installdir)s/%(name)s" ] From 1cebb383004e4381df53d7f9b0032286f8142f76 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Tue, 21 Sep 2021 12:39:00 -0400 Subject: [PATCH 1387/9987] Update easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb Co-authored-by: SebastianAchilles --- .../v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb index 3de8d93cef7..d526c59388f 100644 --- a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb @@ -9,7 +9,7 @@ homepage = 'https://github.com/cc2qe/vawk' description = """An awk-like VCF parser """ -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [ ('Python', '2.7.18'), From 73e62292f1967ab3bbfe061877c51c53f9630979 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Tue, 21 Sep 2021 20:12:30 +0200 Subject: [PATCH 1388/9987] Initial commit of ucx-py for foss 2020b --- .../u/ucx-py/ucx-py-0.21.0-foss-2020b.eb | 39 +++++++++++++++++++ .../ucx-py/ucx-py-setup-get_ucx_incpath.patch | 34 ++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/u/ucx-py/ucx-py-setup-get_ucx_incpath.patch diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb new file mode 100644 index 00000000000..afa7ab8a549 --- /dev/null +++ b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'ucx-py' +version = '0.21.0' + +github_account = 'rapidsai' + +homepage = "https://ucx-py.readthedocs.io" +description = """UCX-Py is the Python interface for UCX, a low-level high-performance networking library. +UCX and UCX-Py supports several transport methods including InfiniBand and NVLink +while still using traditional networking protocols like TCP.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pynvml', '11.0.0', { + 'checksums': ['d5fc4a22d355b40c341d6ba0aa888a2d4d2253177d243900f8401b7e6cacb1bb'], + }), + (name, version, { + 'modulename': 'ucp', + 'patches': ['ucx-py-setup-get_ucx_incpath.patch'], + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': [ + '751da668ba43ad15b53cdb0bfd4084bd4b07200db57b604a9a09aa99d8a3bc1b', # v0.21.0.tar.gz + '123c9aee92ae6e8567e381bef0a4a590f1f7898708b3df1911e41d5ac498cdb3', # ucx-py-setup-get_ucx_incpath.patch + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-setup-get_ucx_incpath.patch b/easybuild/easyconfigs/u/ucx-py/ucx-py-setup-get_ucx_incpath.patch new file mode 100644 index 00000000000..77233ef773e --- /dev/null +++ b/easybuild/easyconfigs/u/ucx-py/ucx-py-setup-get_ucx_incpath.patch @@ -0,0 +1,34 @@ +--- setup.py ++++ setup.py +@@ -24,9 +24,30 @@ library_dirs = [get_config_var("LIBDIR")] + libraries = ["ucp", "uct", "ucm", "ucs", "hwloc"] + extra_compile_args = ["-std=c99", "-Werror"] + ++def get_ucx_incpath(): ++ import os, subprocess ++ res = include_dirs[0] ++ # get output of ucx_info configuration ++ p = subprocess.Popen("ucx_info -c", stdout=subprocess.PIPE, shell=True) ++ (output, err) = p.communicate() ++ p.wait() ++ # get value of UCX_MODULE_DIR key and return path relative to it ++ lines = output.decode("utf-8").split('\n') ++ ucx_config = {} ++ for line in lines: ++ if line: ++ key, val = line.split('=') ++ ucx_config[key] = val ++ if 'UCX_MODULE_DIR' in ucx_config.keys(): ++ res = ucx_config['UCX_MODULE_DIR'] ++ # remove lib/ucx ++ res = os.path.dirname(os.path.dirname(res)) ++ # add include ++ res = os.path.join(res,'include') ++ return res + + def get_ucp_version(): +- with open(include_dirs[0] + "/ucp/api/ucp_version.h") as f: ++ with open(get_ucx_incpath() + "/ucp/api/ucp_version.h") as f: + ftext = f.read() + major = re.findall("^#define.*UCP_API_MAJOR.*", ftext, re.MULTILINE) + minor = re.findall("^#define.*UCP_API_MINOR.*", ftext, re.MULTILINE) From db58a52d6be0d5388618869bc15013befd830add Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Wed, 22 Sep 2021 09:58:37 +0200 Subject: [PATCH 1389/9987] longread_umi: named sources --- .../l/longread_umi/longread_umi-0.3.2-foss-2020b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index 15db976ec6c..64b0518d0ec 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -30,14 +30,14 @@ components = [ (name, version, { 'easyblock': 'Tarball', 'source_urls': [GITHUB_LOWER_SOURCE], - 'sources': ['v%(version)s.tar.gz'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], 'checksums': ['62b8e156c00c0ec10fa8eae1cde5430922462f167fc537417ce0b47cd50a20cb'], 'start_dir': '%(name)s-%(version)s', }), ('Porechop', '0.2.4', { 'easyblock': 'PythonPackage', 'source_urls': ['https://github.com/rrwick/Porechop/archive'], - 'sources': ['v%(version)s.tar.gz'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], 'checksums': ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'], 'start_dir': '%(name)s-%(version)s', 'use_pip': True, @@ -50,8 +50,8 @@ components = [ local_deps_patch = ( "sed -i " "-e '2s;^;set -e ;' " - "-e 's/USEARCH=usearch/USEARCH=vsearch/'" - "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;'" + "-e 's/USEARCH=usearch/USEARCH=vsearch/' " + "-e 's;$(git --git-dir ${LONGREAD_UMI_PATH}/.git describe --tag);%(version)s;' " "%(installdir)s/scripts/dependencies.sh" ) From 676b135bba322aa4f21154df96bff2811021bdc7 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 22 Sep 2021 11:37:01 +0200 Subject: [PATCH 1390/9987] adding easyconfigs: PostgreSQL-13.4-GCCcore-11.2.0.eb --- .../PostgreSQL-13.4-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8c788d103e7 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '13.4' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['59d7bc523e78570c549876fed297ec3e46dd307e90f5b1d22f49181191cf203e'] + +builddependencies = [ + ('binutils', '2.37'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('Perl', '5.34.0'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('libreadline', '8.1'), + ('zlib', '1.2.11'), + ('OpenSSL', '1.1', '', True), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' From 0ebcbf1f19f81dbe213dbc3e415e831e0001f74b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 22 Sep 2021 11:47:35 +0200 Subject: [PATCH 1391/9987] adding easyconfigs: gflags-2.2.2-GCCcore-10.3.0.eb, gflags-2.2.2-GCCcore-11.2.0.eb --- .../g/gflags/gflags-2.2.2-GCCcore-10.3.0.eb | 35 +++++++++++++++++++ .../g/gflags/gflags-2.2.2-GCCcore-11.2.0.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..810cfe2af93 --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c5cf77e7e41 --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' From 4d75e1627ac06999e5caab271d3cf6da062957f8 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 22 Sep 2021 12:47:39 +0200 Subject: [PATCH 1392/9987] messed up git, pushing my ECs again --- .../ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb | 63 +++++++++++++ .../VMTK-1.4.0-foss-2019b-Python-3.7.4.eb | 90 +++++++++++++++++++ 2 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/v/VMTK/VMTK-1.4.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..4bbc63d71e0 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,63 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak (INUITS) +easyblock = 'CMakePythonPackage' + +name = 'ITK' +version = '4.13.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'pic': True} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b352060d8b7289916a3cb033dfdbcf423423ba474643b79706966e679268e3d7'] + +builddependencies = [ + ('CMake', '3.15.3'), + ('Bison', '3.3.2'), + ('Eigen', '3.3.7', '', True), +] + +dependencies = [ + ('Python', '3.7.4'), + ('double-conversion', '3.1.4'), + ('expat', '2.2.7'), + ('HDF5', '1.10.5'), + ('libjpeg-turbo', '2.0.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.0.10'), + ('VTK', '8.2.0', versionsuffix), + ('zlib', '1.2.11'), + ('SWIG', '4.0.1'), + ('PCRE', '8.43'), +] + +configopts = '-DCMAKE_BUILD_TYPE=Release -DITK_WRAP_PYTHON=ON ' +configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON -DITK_USE_SYSTEM_HDF5=ON' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' + +# preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +separate_build_dir = True + +# modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/itkTestDriver', + 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkhdf5.a', + 'lib/libitkjpeg-%(version_major_minor)s.a', 'lib/libitkpng-%(version_major_minor)s.a'], + 'dirs': ['include/ITK-%(version_major_minor)s', + 'lib/python%(pyshortver)s/site-packages', + 'share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/v/VMTK/VMTK-1.4.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/v/VMTK/VMTK-1.4.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..23072c44c57 --- /dev/null +++ b/easybuild/easyconfigs/v/VMTK/VMTK-1.4.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,90 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak (INUITS) + +easyblock = "CMakeMake" + +name = 'VMTK' +version = '1.4.0' + +homepage = 'https://vmtk.org' +description = """vmtk is a collection of libraries and tools +for 3D reconstruction, geometric analysis, mesh generation and +surface data analysis for image-based modeling of blood vessels. """ + +toolchain = {'name': 'foss', 'version': '2019b'} +versionsuffix = '-Python-%(pyver)s' +local_vtk_shortver = '8.2' +local_itk_shortver = '4.13' + +# fetching specific commit of VMTK bcs of some bugfixes +local_commit = '63a3b99' + +local_vmtk_test_commit = "cbf09e4da03aa332c584b2709c4254017db9d4ef" +source_urls = [ + 'https://github.com/vmtk/vmtk/archive/', + "https://raw.githubusercontent.com/vmtk/vmtk-test-data/%s/input/" % local_vmtk_test_commit, +] +sources = [ + { + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ}, + { + 'download_filename': 'vase.vti', + 'filename': 'vase-20180313.vti', + 'extract_cmd': 'cp %s %(builddir)s/vase.vti', + }, +] +checksums = [ + '39aeb1de6bba8511dff45f0a69c9d6dc8d61f323739312ddceb22f8773e21459', # VMTK-1.4.0.tar.gz + 'b5f761d7a923ee19cd9cc8df7fbc794ffaa16aca101455fcdf9ceaa610ca3f57', # vase-20180313.vti +] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('Python', '3.7.4'), + ('VTK', '8.2.0', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + ('SciPy-bundle', '2019.10', versionsuffix), + # vmtk now works well with ITK 4.x only. see https://github.com/vmtk/vmtk/issues/381 + ('ITK', local_itk_shortver + '.1', versionsuffix), + ('X11', '20190717'), + ('libGLU', '9.0.1'), + ('zlib', '1.2.11'), + ('Mesa', '19.1.7'), + ('Tkinter', '3.7.4'), +] + +preconfigopts = "export CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH:$EBROOTITK/lib/cmake/ITK-%s/ && " % local_itk_shortver + +configopts = '-DITK_USE_SYSTEM_DOUBLECONVERSION=ON -DITK_USE_SYSTEM_EIGEN=ON -DITK_USE_SYSTEM_EXPAT=ON ' +configopts += '-DITK_USE_SYSTEM_JPEG=ON -DITK_USE_SYSTEM_PNG=ON -DITK_USE_SYSTEM_TIFF=ON ' +configopts += '-DITK_USE_SYSTEM_ZLIB=ON ' +configopts += ' -DUSE_SYSTEM_VTK=ON ' +configopts += ' -DVTK_DIR=$EBROOTVTK ' +configopts += ' -DUSE_SYSTEM_ITK=ON ' +configopts += ' -DCMAKE_MODULE_PATH=$EBROOTVTK/lib/cmake/vtk-%s/Modules ' % local_vtk_shortver +configopts += ' -DSUPERBUILD_INSTALL_PREFIX=%(installdir)s ' +configopts += ' -DVMTK_BUILD_TESTING=ON ' + +preinstallopts = 'cd VMTK-Build && ' + +# postinstallcmds = [ +# "cp %(builddir)s/vase.vti %(installdir)s/" +# ] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': ['bin/vmtk', 'bin/vmtkactivetubes'], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages', 'include'], +} + +sanity_check_commands = [ + "cd %(builddir)s && vmtkimagereader -ifile vase.vti", + "vmtk --help", +] + +moduleclass = 'bio' From 21fdfd1e10fff3072d1dc73c5595faf4c18d548b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Wed, 22 Sep 2021 13:49:13 +0200 Subject: [PATCH 1393/9987] longread_umi: add comment --- .../easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index 64b0518d0ec..8b9541720e2 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -34,6 +34,8 @@ components = [ 'checksums': ['62b8e156c00c0ec10fa8eae1cde5430922462f167fc537417ce0b47cd50a20cb'], 'start_dir': '%(name)s-%(version)s', }), + # PythonPackage executes Bundle-level postinstallcmds for some reason, + # which rely on both components being installed, so Porechop is installed second ('Porechop', '0.2.4', { 'easyblock': 'PythonPackage', 'source_urls': ['https://github.com/rrwick/Porechop/archive'], From fa7cd53bd0a2f8665afc011480eda9537c7f0377 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 22 Sep 2021 13:55:53 +0200 Subject: [PATCH 1394/9987] adding easyconfigs: RInChI-1.00-x86_64.eb --- .../r/RInChI/RInChI-1.00-x86_64.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/r/RInChI/RInChI-1.00-x86_64.eb diff --git a/easybuild/easyconfigs/r/RInChI/RInChI-1.00-x86_64.eb b/easybuild/easyconfigs/r/RInChI/RInChI-1.00-x86_64.eb new file mode 100644 index 00000000000..f70086e99cc --- /dev/null +++ b/easybuild/easyconfigs/r/RInChI/RInChI-1.00-x86_64.eb @@ -0,0 +1,63 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# A makefile is provided to build the librinchi.so.1.0.0 library BUT +# no information about how to build the command line tool rinchi_cmdline. +# +# Also tests look broken, or incomplete. +# +# SO use the pre-compiled binaries! +## + +easyblock = 'Binary' + +name = 'RInChI' +version = '1.00' +versionsuffix = '-x86_64' + +# NOTE not in the license list of EB +# software_license = 'IUPAC/InChI-Trust Licence' +software_license_urls = ['https://www.inchi-trust.org/download/RInChI/LICENCES.zip'] +docurls = [ + 'https://www.inchi-trust.org/download/RInChI/RInChI%20V1-00-0.pdf', +] + +homepage = 'https://www.inchi-trust.org/' +description = """The reaction IUPAC International Chemical Identifier (RInChI TM) is a non-proprietary +identifier for chemical reactions that can be used in printed and electronic +data sources thus enabling easier linking of diverse data compilations.""" + +toolchain = SYSTEM + +source_urls = ['https://www.inchi-trust.org/download/RInChI/'] +sources = ['RInChI-V%(version_major)s-%(version_minor)s.zip'] +checksums = ['e115b941185ee64e444bfbd57f1b9e80d7fd14e39bc803975843dfface2a163c'] + + +extract_sources = True + +install_cmd = 'mkdir -p %(installdir)s/bin/ && ' +install_cmd += 'install bin/rinchi_cmdline/linux/x86_64/* %(installdir)s/bin/ && ' +install_cmd += 'cp docs/* rinchi/LICENCES/* %(installdir)s/ && ' +install_cmd += 'mkdir -p %(installdir)s/lib64/ && ' +install_cmd += 'install bin/rinchi_lib/linux/x86_64/* %(installdir)s/lib64/' + +# NOTE librinchi.so are not symlinks in the final build, but redundant copies! +# NOTE `keepsymlinks = True` does not look to do it, so use this trick +postinstallcmds = ["cd %(installdir)s/lib64/ && " + "ln -s librinchi.so.1.* librinchi.so.1.0 && " + "ln -s librinchi.so.1.0 librinchi.so.1 && " + "ln -s librinchi.so.1 librinchi.so"] + + +sanity_check_paths = { + 'files': ["bin/rinchi_cmdline", "lib64/librinchi.so", "RINCHI_LICENCE.TXT"], + 'dirs': ['lib64'] +} + +sanity_check_commands = ["rinchi_cmdline || true"] + +moduleclass = 'chem' From c3b81f6e7262ee445e0264c85e7f14f9cf2c9aee Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 22 Sep 2021 13:57:33 +0200 Subject: [PATCH 1395/9987] adding easyconfigs: libSBML-5.19.0-GCC-10.3.0.eb and patches: libsbml-fix_install_libpaths.patch, libsbml-fix_perl_auto_case.patch --- .../l/libSBML/libSBML-5.19.0-GCC-10.3.0.eb | 81 +++++++++++++++++++ .../libsbml-fix_install_libpaths.patch | 46 +++++++++++ .../libSBML/libsbml-fix_perl_auto_case.patch | 11 +++ 3 files changed, 138 insertions(+) create mode 100644 easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libSBML/libsbml-fix_install_libpaths.patch create mode 100644 easybuild/easyconfigs/l/libSBML/libsbml-fix_perl_auto_case.patch diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..858ea5e7787 --- /dev/null +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.3.0.eb @@ -0,0 +1,81 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Notes:: Patch libsbml-fix_install_libpaths.patch comes from Fedora +# https://src.fedoraproject.org/rpms/libsbml/blob/rawhide/f/libsbml-fix_install_libpaths.patch +## +easyblock = 'CMakeMake' + +name = 'libSBML' +version = '5.19.0' + +# NOTE not in the license list of EB +# software_license = 'LGPLv2+' +software_license_urls = ['http://sbml.org/Software/libSBML/LibSBML_License'] +docurls = [ + 'https://github.com/sbmlteam/libsbml/releases/tag/v%(version)s', + 'http://sbml.org/Software/libSBML', +] + +homepage = 'http://sbml.org/Software/libSBML' +description = """libSBML (Systems Biology Markup Language library) is a free, open-source +programming library to help you read, write, manipulate, translate, and +validate SBML files and data streams. It's not an application itself (though +it does come with example programs), but rather a library you embed in your +own applications.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://downloads.sourceforge.net/project/sbml/libsbml/%(version)s/stable/'] +sources = ['libSBML-%(version)s-core-plus-packages-src.tar.gz'] +patches = [ + 'libsbml-fix_install_libpaths.patch', # Fix some installation library paths (from Fedora) + 'libsbml-fix_perl_auto_case.patch', # Fix the misname for Perl .so binding folder + # (https://sourceforge.net/p/sbml/libsbml/476/) +] +checksums = [ + 'a7f0e18be78ff0e064e4cdb1cd86634d08bc33be5250db4a1878bd81eeb8b547', # libSBML-5.19.0-core-plus-packages-src.tar.gz + '1975b9372be00c5056e1f3408b8829e749adb1edb3345fd109d5c802b5219e45', # libsbml-fix_install_libpaths.patch + '52b3274ce1fdfb329bc53feb67b9862833a1240539eca2f137fcdca00800e34e', # libsbml-fix_perl_auto_case.patch +] + + +builddependencies = [ + ('CMake', '3.20.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Perl', '5.32.1'), +] + +# Java jar, Ruby or Octave can also be build here. +# Python libSBML binding better done from https://pypi.org/project/python-libsbml/ +configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX=%(installdir)s -DWITH_JAVA=OFF ' +configure_cmd += '-DWITH_CHECK=ON -DWITH_SWIG=ON -DWITH_PERL=ON -DWITH_PYTHON=OFF ' +configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF ' +configure_cmd += '-DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER,GROUPS,MULTI,DISTRIB}=ON ' +configure_cmd += '../libSBML-%(version)s-Source/' + + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib64/libsbml.so', 'lib64/perl5/vendor_perl/LibSBML.pm'], + 'dirs': ['lib64', 'include', 'share'] +} + +modextrapaths = { + 'PERL5LIB': 'lib64/perl5/vendor_perl/', +} + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libSBML/libsbml-fix_install_libpaths.patch b/easybuild/easyconfigs/l/libSBML/libsbml-fix_install_libpaths.patch new file mode 100644 index 00000000000..42acbc65623 --- /dev/null +++ b/easybuild/easyconfigs/l/libSBML/libsbml-fix_install_libpaths.patch @@ -0,0 +1,46 @@ +##This patch sets libraries' installation paths according to the Fedora packaging guidelines +--- a/src/bindings/ruby/CMakeLists.orig.txt 2014-11-26 13:31:14.000000000 +0100 ++++ b/src/bindings/ruby/CMakeLists.txt 2014-12-28 23:25:47.035666311 +0100 +@@ -177,7 +177,7 @@ + if (UNIX OR CYGWIN) + execute_process(COMMAND "${RUBY_EXECUTABLE}" -e "print RUBY_PLATFORM" + OUTPUT_VARIABLE RUBY_PLATFORM) +- set(RUBY_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/ruby/site_ruby/${RUBY_VERSION_MAJOR}.${RUBY_VERSION_MINOR}/${RUBY_PLATFORM}) ++ set(RUBY_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/ruby/vendor_ruby) + else() + set(RUBY_PACKAGE_INSTALL_DIR ${MISC_PREFIX}bindings/ruby) + endif() +--- a/src/bindings/csharp/CMakeLists.orig.txt 2014-11-26 13:31:17.000000000 +0100 ++++ b/src/bindings/csharp/CMakeLists.txt 2014-12-29 11:37:43.839593422 +0100 +@@ -213,7 +213,7 @@ + # + set(CSHAPR_PACKAGE_INSTALL_DIR) + if (UNIX OR CYGWIN) +- set(CSHAPR_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/mono/libsbmlcsP) ++ set(CSHAPR_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib/mono/libsbmlcsP) + else() + set(CSHAPR_PACKAGE_INSTALL_DIR ${MISC_PREFIX}bindings/csharp) + endif() +--- a/src/bindings/octave/CMakeLists.orig.txt 2014-11-26 13:31:10.000000000 +0100 ++++ b/src/bindings/octave/CMakeLists.txt 2014-12-29 11:44:51.031069073 +0100 +@@ -67,7 +67,7 @@ + if (UNIX OR CYGWIN) + execute_process(COMMAND "${OCTAVE_CONFIG_EXECUTABLE}" -p CANONICAL_HOST_TYPE + OUTPUT_VARIABLE OCTAVE_PLATFORM OUTPUT_STRIP_TRAILING_WHITESPACE) +- set(OCTAVE_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/octave/site/oct/${OCTAVE_PLATFORM}) ++ set(OCTAVE_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/octave/packages/SBML-${PACKAGE_VERSION}) + else() + set(OCTAVE_PACKAGE_INSTALL_DIR ${MISC_PREFIX}bindings/octave) + endif() +--- a/src/bindings/perl/CMakeLists.orig.txt 2014-11-26 13:31:13.000000000 +0100 ++++ b/src/bindings/perl/CMakeLists.txt 2014-12-29 11:48:53.705649453 +0100 +@@ -232,7 +232,7 @@ + string(REPLACE "'" "" PERL_PLATFORM ${PERL_PLATFORM}) + string(REPLACE ";" "" PERL_PLATFORM ${PERL_PLATFORM}) + string(REPLACE "archname=" "" PERL_PLATFORM ${PERL_PLATFORM}) +- set(PERL_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/perl5/site_perl/${PERL_VERSION}/${PERL_PLATFORM}) ++ set(PERL_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/perl5/vendor_perl) + set(PERL_PACKAGE_INSTALL_BIN_DIR ${PERL_PACKAGE_INSTALL_DIR}/auto/libSBML) + else() + set(PERL_PACKAGE_INSTALL_DIR ${MISC_PREFIX}bindings/perl) + diff --git a/easybuild/easyconfigs/l/libSBML/libsbml-fix_perl_auto_case.patch b/easybuild/easyconfigs/l/libSBML/libsbml-fix_perl_auto_case.patch new file mode 100644 index 00000000000..d9408e93218 --- /dev/null +++ b/easybuild/easyconfigs/l/libSBML/libsbml-fix_perl_auto_case.patch @@ -0,0 +1,11 @@ +--- src/bindings/perl/CMakeLists.orig.txt 2021-08-05 09:58:34.411549348 +0200 ++++ src/bindings/perl/CMakeLists.txt 2021-08-05 09:59:17.520293364 +0200 +@@ -233,7 +233,7 @@ + string(REPLACE ";" "" PERL_PLATFORM ${PERL_PLATFORM}) + string(REPLACE "archname=" "" PERL_PLATFORM ${PERL_PLATFORM}) + set(PERL_PACKAGE_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR}/perl5/vendor_perl) +- set(PERL_PACKAGE_INSTALL_BIN_DIR ${PERL_PACKAGE_INSTALL_DIR}/auto/libSBML) ++ set(PERL_PACKAGE_INSTALL_BIN_DIR ${PERL_PACKAGE_INSTALL_DIR}/auto/LibSBML) + else() + set(PERL_PACKAGE_INSTALL_DIR ${MISC_PREFIX}bindings/perl) + set(PERL_PACKAGE_INSTALL_BIN_DIR ${PERL_PACKAGE_INSTALL_DIR}) From 868b4c35eaa4e448f38f9764a17f206e4ce27183 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 22 Sep 2021 14:19:24 +0200 Subject: [PATCH 1396/9987] updates bcs of review --- .../easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb | 6 +----- .../v/VMTK/VMTK-1.4.0-foss-2019b-Python-3.7.4.eb | 4 ---- 2 files changed, 1 insertion(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb index 4bbc63d71e0..27fd470afe2 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb @@ -42,15 +42,11 @@ dependencies = [ ] configopts = '-DCMAKE_BUILD_TYPE=Release -DITK_WRAP_PYTHON=ON ' -configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON -DITK_USE_SYSTEM_HDF5=ON' +configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON ' # -DITK_USE_SYSTEM_HDF5=ON' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' -# preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - separate_build_dir = True -# modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/itkTestDriver', 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkhdf5.a', diff --git a/easybuild/easyconfigs/v/VMTK/VMTK-1.4.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/v/VMTK/VMTK-1.4.0-foss-2019b-Python-3.7.4.eb index 23072c44c57..47f24e87b29 100644 --- a/easybuild/easyconfigs/v/VMTK/VMTK-1.4.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/v/VMTK/VMTK-1.4.0-foss-2019b-Python-3.7.4.eb @@ -69,10 +69,6 @@ configopts += ' -DVMTK_BUILD_TESTING=ON ' preinstallopts = 'cd VMTK-Build && ' -# postinstallcmds = [ -# "cp %(builddir)s/vase.vti %(installdir)s/" -# ] - modextrapaths = { 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], } From c819997d0d43e428784869c636894ad2f3d4d748 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 22 Sep 2021 15:14:09 +0200 Subject: [PATCH 1397/9987] Dropping the h5py dep so Keras just uses h5py through the TensorFlow (req. h5py~=2.1.0) dep --- easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb index 48fc18c305e..06a6be6a596 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b.eb @@ -14,8 +14,7 @@ dependencies = [ ('Python', '3.8.6'), ('Theano', '1.1.2', '-PyMC'), ('PyYAML', '5.3.1'), - ('h5py', '3.1.0'), - ('TensorFlow', '2.4.1'), + ('TensorFlow', '2.4.1'), # provides h5py 2.1.0 ] use_pip = True From df887a0e60a2571fcd58538f30e631dfba50df9c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 22 Sep 2021 15:20:28 +0200 Subject: [PATCH 1398/9987] Dropping the h5py dep so Keras just uses h5py through the TensorFlow (req. h5py~=2.1.0) dep --- easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb index 32ae992ae3b..2f81c7cf31e 100644 --- a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-foss-2020b.eb @@ -14,8 +14,7 @@ dependencies = [ ('Python', '3.8.6'), ('Theano', '1.1.2', '-PyMC'), ('PyYAML', '5.3.1'), - ('h5py', '3.1.0'), - ('TensorFlow', '2.4.1'), + ('TensorFlow', '2.4.1'), # provides h5py 2.1.0 ] use_pip = True From 795ac7f0653bf1d5e77e835060249141c17d6927 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Sep 2021 18:40:08 +0200 Subject: [PATCH 1399/9987] sync easyconfig for ITK 4.13.1 with foss/2019b with existing easyconfigs for ITK 4.13.1 --- .../i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb index 27fd470afe2..8108fd7121c 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb @@ -41,15 +41,22 @@ dependencies = [ ('PCRE', '8.43'), ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DITK_WRAP_PYTHON=ON ' -configopts += '-DBUILD_TESTING=OFF -DITK_USE_SYSTEM_SWIG=ON ' # -DITK_USE_SYSTEM_HDF5=ON' +local_sys_deps = ['HDF5', 'SWIG'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DITK_WRAP_PYTHON=ON ' +configopts += '-DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON ' +configopts += ' '.join(local_sys_cmake) +# Don't depend on MPICXX (which makes linking to ITK painful) +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -DOMPI_SKIP_MPICXX"' -separate_build_dir = True +# See https://insightsoftwareconsortium.atlassian.net/browse/ITK-3538 +prebuildopts = "LC_ALL=C " sanity_check_paths = { 'files': ['bin/itkTestDriver', - 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkhdf5.a', + 'lib/libITKVtkGlue-%(version_major_minor)s.a', 'lib/libitkjpeg-%(version_major_minor)s.a', 'lib/libitkpng-%(version_major_minor)s.a'], 'dirs': ['include/ITK-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages', From b8b5349d2ac0ac45a6345ff2924a01202e50df5a Mon Sep 17 00:00:00 2001 From: RC Build Date: Wed, 22 Sep 2021 15:25:10 -0500 Subject: [PATCH 1400/9987] Adding Nextflow v21.08.0 easyconfig, with Java/13 --- .../n/Nextflow/Nextflow-21.08.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb new file mode 100644 index 00000000000..7e99ffb9bd6 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CmdCp' + +name = 'Nextflow' +version = '21.08.0' + +homepage = 'https://www.nextflow.io' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/archive'] +sources = ['v%(version)s-edge.tar.gz'] +checksums = ['ab47af92e6f5c5c08a43b70e60cc3d8720e267a507f21af62ac24805b02a2e8b'] + +# specify dependency on Java/13 "wrapper", rather than a specific Java version +dependencies = [('Java', '13', '', True)] + +skipsteps = ['configure', 'build'] + +_exe_files = ['nextflow', 'gradlew'] + +files_to_copy = [ + (_exe_files, '%(installdir)s/bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' From d1a14a2f7d48a15653330ced89f1b5af7d7dc6b4 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 23 Sep 2021 09:54:44 +0200 Subject: [PATCH 1401/9987] Useful sanity check now --- easybuild/easyconfigs/r/RInChI/RInChI-1.00-x86_64.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RInChI/RInChI-1.00-x86_64.eb b/easybuild/easyconfigs/r/RInChI/RInChI-1.00-x86_64.eb index f70086e99cc..98356fae35c 100644 --- a/easybuild/easyconfigs/r/RInChI/RInChI-1.00-x86_64.eb +++ b/easybuild/easyconfigs/r/RInChI/RInChI-1.00-x86_64.eb @@ -58,6 +58,7 @@ sanity_check_paths = { 'dirs': ['lib64'] } -sanity_check_commands = ["rinchi_cmdline || true"] +# NOTE help message returns a non-zero exit code. So use this trick +sanity_check_commands = ["rinchi_cmdline 2>&1 | grep 'Usage: rinchi_cmdline'"] moduleclass = 'chem' From 825be77da33d82c2d2d4fe8052605bdcd0b684f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Sep 2021 11:58:15 +0200 Subject: [PATCH 1402/9987] adding easyconfigs: Kalign-3.3.1-GCCcore-10.3.0.eb --- .../k/Kalign/Kalign-3.3.1-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..dcdd0424498 --- /dev/null +++ b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.1-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'Kalign' +version = '3.3.1' + +homepage = 'https://github.com/TimoLassmann/kalign' +description = "Kalign is a fast multiple sequence alignment program for biological sequences." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7f10acf9a3fa15deabbc0304e7c14efa25cea39108318c9f02b47257de2d7390'] # 3.3.1.tar.gz + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), +] + +configure_cmd_prefix = "autoreconf -vfi && " + +sanity_check_paths = { + 'files': ['bin/kchaos', 'bin/kalign'], + 'dirs': [], +} + +sanity_check_commands = ["kalign --help"] + +moduleclass = 'bio' From 5c6b28233bf8c57c9744b72d94859327ecf486e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Sep 2021 11:58:38 +0200 Subject: [PATCH 1403/9987] adding easyconfigs: HH-suite-3.3.0-gompi-2021a.eb --- .../h/HH-suite/HH-suite-3.3.0-gompi-2021a.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021a.eb diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021a.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021a.eb new file mode 100644 index 00000000000..c9dcd2ac6eb --- /dev/null +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021a.eb @@ -0,0 +1,66 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Updated to use gompi-2020b toolchain: +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'HH-suite' +version = '3.3.0' + +homepage = 'https://github.com/soedinglab/hh-suite' +description = """The HH-suite is an open-source software package +for sensitive protein sequence searching based on the pairwise +alignment of hidden Markov models (HMMs).""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Perl', '5.32.1'), + ('Python', '3.9.5'), +] + +_binaries = [ + 'hhalign', 'hhalign_mpi', 'hhalign_omp', + 'hhblits', 'hhblits_mpi', 'hhblits_omp', + 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp', + 'hhmake', 'hhfilter', 'hhconsensus', +] + +_scriptfiles = [ + 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', +] + +fix_perl_shebang_for = ['scripts/*pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + ['scripts/%s' % y for y in _scriptfiles], + 'dirs': ['data', 'scripts'] +} + +modextrapaths = { + 'PATH': 'scripts', + 'PERL5LIB': 'scripts', +} + +moduleclass = 'bio' From d645acb8308162572374e462a8f5686183f9b7c7 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 23 Sep 2021 14:23:19 +0200 Subject: [PATCH 1404/9987] adding easyconfigs: pftoolsV3-3.2.8-foss-2021a.eb --- .../p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb new file mode 100644 index 00000000000..b0fd75c4081 --- /dev/null +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb @@ -0,0 +1,53 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## +easyblock = 'CMakeMake' + +name = 'pftoolsV3' +version = '3.2.8' + +homepage = 'https://github.com/sib-swiss/pftools3' +description = """A suite of tools to build and search generalized profiles (protein and DNA).""" +software_license = 'LicenseGPLv2' + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/'] +checksums = ['aefc1ef07fb70b49d4e6ee0841796342c32245ce699287b12ff03e5613f771bf'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('make', '4.3'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Perl', '5.32.1'), + ('PCRE', '8.44'), + ('libharu', '2.3.0'), + ('zlib', '1.2.11'), + ('libgd', '2.3.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), +] + +configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX:PATH=%(installdir)s -DCMAKE_BUILD_TYPE=Release ' +configure_cmd += '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON ' +configure_cmd += '../pftools3-%(version)s' + +runtest = 'test' + +sanity_check_paths = { + 'files': [ + 'bin/ptof', 'bin/htop', 'bin/6ft', 'bin/2ft', 'bin/pfdump', 'bin/pfscan', 'bin/pfsearch', + 'bin/pfscanV3', 'bin/pfsearchV3', + ], + 'dirs': ['share/doc', 'share/man'], +} + +moduleclass = 'bio' From 17293e94eaea5044c788e50d18b09442fb30e96c Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 23 Sep 2021 16:42:37 +0000 Subject: [PATCH 1405/9987] Upgraded Eigen to 3.3.9 as 3.3.7 version requires older GCC version --- .../easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb index d7aeb4c75de..9d020bb9a5c 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.3-foss-2020b.eb @@ -21,7 +21,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.7', '', True)] +builddependencies = [('Eigen', '3.3.9')] dependencies = [ ('zlib', '1.2.11'), From ed07a11da18cb7e505c17f3ed9097b1ddd0b4aea Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 24 Sep 2021 08:37:29 +0200 Subject: [PATCH 1406/9987] adding easyconfigs: libxsmm-1.16.2-GCC-10.3.0.eb, libxsmm-1.16.2-intel-compilers-2021.2.0.eb --- .../l/libxsmm/libxsmm-1.16.2-GCC-10.3.0.eb | 27 +++++++++++++++++++ ...libxsmm-1.16.2-intel-compilers-2021.2.0.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..41104ec8354 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-GCC-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.16.2' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['bdc7554b56b9e0a380fc9c7b4f4394b41be863344858bc633bc9c25835c4c64e'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..86f5f13c7e4 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.2-intel-compilers-2021.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.16.2' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['bdc7554b56b9e0a380fc9c7b4f4394b41be863344858bc633bc9c25835c4c64e'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' From 3193a71cefe4d825fd957e0c099875a29d47e10e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 24 Sep 2021 10:54:52 +0100 Subject: [PATCH 1407/9987] adding easyconfigs: HDBSCAN-0.8.27-foss-2021a.eb --- .../h/HDBSCAN/HDBSCAN-0.8.27-foss-2021a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.27-foss-2021a.eb diff --git a/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.27-foss-2021a.eb b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.27-foss-2021a.eb new file mode 100644 index 00000000000..31a036d1a47 --- /dev/null +++ b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.27-foss-2021a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'HDBSCAN' +version = '0.8.27' + +homepage = 'http://hdbscan.readthedocs.io/en/latest/' +description = """The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense + regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library + provides a high performance implementation of this algorithm, along with tools for analysing the resulting + clustering.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e3a418d0d36874f7b6a1bf0b7461f3857fc13a525fd48ba34caed2fe8973aa26'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-learn', '0.24.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From 0bb5f96f8d7225955547661aa2d17923de533a02 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 24 Sep 2021 14:08:22 +0200 Subject: [PATCH 1408/9987] Fix environment variable that should have been renamed CUDACORE -> CUDA when we renamed the easyconfigs --- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb index 18229cdc3e2..fed7bf6bdb8 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb @@ -19,7 +19,7 @@ dependencies = [ ] configopts = 'CC="$MPICC" CXX="$MPICC"' -configopts += ' --enable-cuda --with-cuda=$EBROOTCUDACORE' +configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] modextrapaths = {'PATH': local_benchmark_dirs} From b1d7be3e517e61cb3f95e29f505e87936d7fec09 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 24 Sep 2021 16:55:50 +0200 Subject: [PATCH 1409/9987] adding easyconfigs: Bazel-3.7.2-GCCcore-8.3.0.eb, Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb, TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb and patches: TensorFlow-2.5.0_downgrade-required-versions.patch, TensorFlow-2.5.0_fix-CUDA10-build.patch, TensorFlow-2.5.0_fix-cub-cuda-dep.patch --- .../b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb | 38 +++ ...uda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb | 45 ++++ ...rFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb | 229 ++++++++++++++++++ ...ow-2.5.0_downgrade-required-versions.patch | 45 ++++ .../TensorFlow-2.5.0_fix-CUDA10-build.patch | 21 ++ .../TensorFlow-2.5.0_fix-cub-cuda-dep.patch | 20 ++ 6 files changed, 398 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_downgrade-required-versions.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-CUDA10-build.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-cub-cuda-dep.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..76be3bcb656 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb @@ -0,0 +1,38 @@ +name = 'Bazel' +version = '3.7.2' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = [ + '%(name)s-3.4.1-fix-grpc-protoc.patch', + 'Bazel-3.7.1_fix-protobuf-env.patch', +] +checksums = [ + 'de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1', # bazel-3.7.2-dist.zip + 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', # Bazel-3.4.1-fix-grpc-protoc.patch + '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', # Bazel-3.7.1_fix-protobuf-env.patch +] + +builddependencies = [ + ('binutils', '2.32'), + ('Python', '3.7.4'), + ('Zip', '3.0'), +] +dependencies = [('Java', '1.8', '', True)] + +runtest = True +testopts = ' '.join([ + '--', + '//examples/cpp:hello-success_test', + '//examples/py/...', + '//examples/py_native:test', + '//examples/shell/...', +]) + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb new file mode 100644 index 00000000000..56afd882edc --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.22.1' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-%s-Python-%%(pyver)s' % local_tf_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +builddependencies = [ + ('CMake', '3.15.3'), + ('flatbuffers', '1.12.0'), +] +dependencies = [ + ('Python', '3.7.4'), + ('PyYAML', '5.1.2'), + ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '1.5.0', { + 'checksums': ['820c9245cebdec7257211cbe88745101d5d6a042bca11336d78ebd4897ddbc82'], + }), + ('horovod', version, { + 'checksums': ['c45bfcb9bd96852d79c62976eda12e9320b58b64f55bee3772877b3fc6243f2a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..d3236a6a8a0 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,229 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.10.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.23.0', '-nodocs'), + ('pybind11', '2.4.3', versionsuffix), +] +dependencies = [ + ('cuDNN', '7.6.4.38'), + ('NCCL', '2.4.8'), + ('Python', '3.7.4'), + ('h5py', '2.10.0', versionsuffix), + ('cURL', '7.66.0'), + ('double-conversion', '3.1.4'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '1.11.12'), + ('ICU', '64.2'), + ('JsonCpp', '1.9.3'), + ('libjpeg-turbo', '2.0.3'), + ('LMDB', '0.9.24'), + ('NASM', '2.14.02'), + ('nsync', '1.24.0'), + ('SQLite', '3.29.0'), + ('PCRE', '8.43'), + ('protobuf-python', '3.10.0', versionsuffix), + ('flatbuffers-python', '1.12', versionsuffix), + ('typing-extensions', '3.7.4.3', versionsuffix), + ('libpng', '1.6.37'), + ('snappy', '1.1.7'), + ('zlib', '1.2.11'), +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.2', { + 'checksums': ['61b5ed1e22a0924aed1d23b478f37e8d52549ff8a961de2909c69bf950020cff'], + }), + ('google-auth', '1.30.0', { + 'modulename': 'google.auth', + 'checksums': ['9ad25fba07f46a628ad4d0ca09f38dcb262830df2ac95b217f9b0129c9e42206'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.4', { + 'checksums': ['09832c6e75032f93818edf1affe4746121d640c625a5bef9b5c96af676e98eee'], + }), + ('Werkzeug', '2.0.0', { + 'checksums': ['3389bbfe6d40c6dd25e6d3f974155163c8b3de5bbda6a89342d4ab93fae80ba0'], + }), + ('absl-py', '0.12.0', { + 'modulename': 'absl', + 'checksums': ['b44f68984a5ceb2607d135a615999b93924c771238a63920d17d3387b0d229d5'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.34.1', { + 'modulename': 'grpc', + 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + }), + ('gviz-api', '1.9.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['43d13ccc21834d0501b33a291ef3265e933dbb4bbdca3d34b1ed0a048c0ef640'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': SOURCE_PY3_WHL, # Requires Rust to build, take the dummy for now + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e167460085b6528956b33bab1c970c989cdce47a6616273880733f5e7bde452e'], + }), + ('tensorboard_plugin_wit', '1.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2a80d1c551d741e99b2f197bb915d8a133e24adb8da1732b840041860f91183a'], + }), + ('tensorboard_plugin_profile', '2.4.0', { + 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow_estimator', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['efb7f6cb65dba7087c1e111bb5390291ba3616741f96840bfc75792a1a9b5ded'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.3.1', { + 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_fix-min-priority-test.patch', + 'TensorFlow-2.5.0_add-default-shell-env.patch', + 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0_downgrade-required-versions.patch', + 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-CUDA10-build.patch', + 'TensorFlow-2.5.0_fix-cub-cuda-dep.patch', + 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + ], + 'checksums': [ + '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_fix-min-priority-test.patch + '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', + # TensorFlow-2.5.0_add-default-shell-env.patch + '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', + # TensorFlow-2.5.0_add-protobuf-deps.patch + '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', + # TensorFlow-2.5.0_disable-avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0_downgrade-required-versions.patch + '019f7bbf6604f581a8028a7c9caa9ce05dcc336523822177c4c5e76b9a99a95a', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_fix-CUDA10-build.patch + 'f6b44c82855bd2892ca67b528076acdaa75d8b9158aa25d84c808d1ce4d89256', + # TensorFlow-2.5.0_fix-cub-cuda-dep.patch + '072887146b66af61aeab22cbd1561d69fba691d996d11b58529ba935a2f61593', + # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch + 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' + '-benchmark-test,-v1only'), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_downgrade-required-versions.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_downgrade-required-versions.patch new file mode 100644 index 00000000000..24bad756b03 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_downgrade-required-versions.patch @@ -0,0 +1,45 @@ +TF introduced a change pinning versions to fixed major.minor or even patch versions +Loosen those a bit so we can build it with our versions. +See https://github.com/tensorflow/tensorflow/issues/44654 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index 354657a7bfc..d4c880402f7 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -78,20 +78,20 @@ REQUIRED_PACKAGES = [ + # NOTE: As numpy has releases that break semver guarantees and several other + # deps depend on numpy without an upper bound, we must install numpy before + # everything else. +- 'numpy ~= 1.19.2', ++ 'numpy >= 1.17.3', + # Install other dependencies + 'absl-py ~= 0.10', + 'astunparse ~= 1.6.3', + 'flatbuffers ~= 1.12.0', + 'google_pasta ~= 0.2', +- 'h5py ~= 3.1.0', ++ 'h5py >= 2.10.0', + 'keras_preprocessing ~= 1.1.2', + 'opt_einsum ~= 3.3.0', + 'protobuf >= 3.9.2', +- 'six ~= 1.15.0', ++ 'six >= 1.12.0', + 'termcolor ~= 1.1.0', + 'typing_extensions ~= 3.7.4', +- 'wheel ~= 0.35', ++ 'wheel >= 0.33', + 'wrapt ~= 1.12.1', + # These packages need to be pinned exactly as newer versions are + # incompatible with the rest of the ecosystem +@@ -102,9 +102,6 @@ REQUIRED_PACKAGES = [ + # When updating these, please also update the nightly versions below + 'tensorboard ~= 2.5', + 'tensorflow-estimator >= 2.5.0rc0 , < 2.6.0', +- # TODO(scottzhu): OSS keras hasn't been formally released yet. +- # Use keras-nightly at the moment. +- 'keras-nightly ~= 2.5.0.dev', + ] + + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-CUDA10-build.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-CUDA10-build.patch new file mode 100644 index 00000000000..b82cabaffbc --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-CUDA10-build.patch @@ -0,0 +1,21 @@ +Disable TF_CORD_SUPPORT for CUDA due to CUDA 10 compiler issues + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/core/platform/default/cord.h b/tensorflow/core/platform/default/cord.h +index 0dbdc051f4865..cdfab1e5da905 100644 +--- a/tensorflow/core/platform/default/cord.h ++++ b/tensorflow/core/platform/default/cord.h +@@ -16,7 +16,12 @@ limitations under the License. + #ifndef TENSORFLOW_CORE_PLATFORM_DEFAULT_CORD_H_ + #define TENSORFLOW_CORE_PLATFORM_DEFAULT_CORD_H_ + ++#if !defined(__CUDACC__) ++ ++// TODO(frankchn): Resolve compilation errors when building absl::Cord with CUDA + #include "absl/strings/cord.h" + #define TF_CORD_SUPPORT 1 + ++#endif // __CUDACC__ ++ + #endif // TENSORFLOW_CORE_PLATFORM_DEFAULT_CORD_H_ diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-cub-cuda-dep.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-cub-cuda-dep.patch new file mode 100644 index 00000000000..290b1f108d9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-cub-cuda-dep.patch @@ -0,0 +1,20 @@ +From ef1f781ae856fbdc7fc42da0284d61e7e5ed7713 Mon Sep 17 00:00:00 2001 +From: Nishidha Panpaliya +Date: Thu, 8 Apr 2021 01:22:21 -0500 +Subject: [PATCH] Fix cub BUILD file for local_config_cuda reference + +--- + third_party/cub.BUILD | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/third_party/cub.BUILD b/third_party/cub.BUILD +index 581d8dd9421ac..c446f0517d3da 100644 +--- a/third_party/cub.BUILD ++++ b/third_party/cub.BUILD +@@ -11,5 +11,5 @@ exports_files(["LICENSE.TXT"]) + cc_library( + name = "cub", + hdrs = glob(["cub/**"]), +- deps = ["@local_cuda//:cuda_headers"], ++ deps = ["@local_config_cuda//cuda:cuda_headers"], + ) From e0f285f6ce2f8942399951a2f9c75342ed56d6ca Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 24 Sep 2021 17:00:56 +0200 Subject: [PATCH 1410/9987] adding easyconfigs: Horovod-0.22.0-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb --- ...uda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb new file mode 100644 index 00000000000..3842dcfa438 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.22.0' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-{}-Python-%(pyver)s'.format(local_tf_version) + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), + ('flatbuffers', '1.12.0'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + 'checksums': ['ed7526eeb5a9aca8a8a49a04a41a4648cb7b0a265857875fc5d6a04a739fdb37'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 5a30f16347daed875b4e53b0e91aa4467f7d6dc6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 24 Sep 2021 17:06:21 +0200 Subject: [PATCH 1411/9987] Move BLIS to GCC level --- ...3.0.1-GCCcore-11.2.0-amd.eb => BLIS-3.0.1-GCC-11.2.0-amd.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/b/BLIS/{BLIS-3.0.1-GCCcore-11.2.0-amd.eb => BLIS-3.0.1-GCC-11.2.0-amd.eb} (95%) diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-11.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb similarity index 95% rename from easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-11.2.0-amd.eb rename to easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb index 125993747b0..5785b675f7c 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-11.2.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb @@ -8,7 +8,7 @@ homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' description = """AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.""" -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ['https://github.com/amd/blis/archive/'] sources = ['%(version)s.tar.gz'] From ddd2ea9d6bdda4b79840a2b513f5abec3aa714dd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 24 Sep 2021 17:06:36 +0200 Subject: [PATCH 1412/9987] Update version --- ...od-0.22.1-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/h/Horovod/{Horovod-0.22.0-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb => Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb} (91%) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb similarity index 91% rename from easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb rename to easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb index 3842dcfa438..9554414f582 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'Horovod' -version = '0.22.0' +version = '0.22.1' local_tf_version = '2.5.0' versionsuffix = '-TensorFlow-{}-Python-%(pyver)s'.format(local_tf_version) @@ -34,7 +34,7 @@ exts_list = [ 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], }), ('horovod', version, { - 'checksums': ['ed7526eeb5a9aca8a8a49a04a41a4648cb7b0a265857875fc5d6a04a739fdb37'], + 'checksums': ['c45bfcb9bd96852d79c62976eda12e9320b58b64f55bee3772877b3fc6243f2a'], }), ] From 1eaf6bc9d2a54b3e8c356eac611f3928c47ff0d6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 24 Sep 2021 17:15:48 +0200 Subject: [PATCH 1413/9987] Update version --- ...8.6.eb => Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/h/Horovod/{Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb => Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb} (94%) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb similarity index 94% rename from easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb rename to easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb index 9554414f582..9a44e9d7422 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0-Python-3.8.6.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'Horovod' version = '0.22.1' local_tf_version = '2.5.0' -versionsuffix = '-TensorFlow-{}-Python-%(pyver)s'.format(local_tf_version) +versionsuffix = '-TensorFlow-{}'.format(local_tf_version) homepage = 'https://github.com/uber/horovod' description = "Horovod is a distributed training framework for TensorFlow." From 7d0d2b2013e712e5d90a712c5e197269bfe2a2ca Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 24 Sep 2021 17:21:26 +0200 Subject: [PATCH 1414/9987] add Broadwell patch --- .../easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb index 5785b675f7c..19964643cff 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb @@ -12,7 +12,14 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ['https://github.com/amd/blis/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e'] +patches = [ + '%(name)s-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch', +] +checksums = [ + 'dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e' # 3.0.1.tar.gz + # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch + '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', +] builddependencies = [ ('binutils', '2.37'), From 01b615b08bbc86074934122f60f6a483620a35a1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 24 Sep 2021 17:27:02 +0200 Subject: [PATCH 1415/9987] add Broadwell patch --- easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb index 19964643cff..8b98f370a16 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb @@ -16,7 +16,7 @@ patches = [ '%(name)s-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch', ] checksums = [ - 'dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e' # 3.0.1.tar.gz + 'dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e', # 3.0.1.tar.gz # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', ] From ed9c40cc553842dae8d835196d354fdb24b5ff49 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 24 Sep 2021 17:28:09 +0200 Subject: [PATCH 1416/9987] Update version --- .../h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb index 9a44e9d7422..1382aa8245d 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.8.6'), ('PyYAML', '5.3.1'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), - ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), + ('TensorFlow', local_tf_version), ] use_pip = True From fea0201c3ba2fd128ddb94173bb4d9ef9557e3fa Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Fri, 24 Sep 2021 17:31:58 +0200 Subject: [PATCH 1417/9987] Update easybuild/easyconfigs/c/CP2K/CP2K-8.2-foss-2021a.eb --- easybuild/easyconfigs/c/CP2K/CP2K-8.2-foss-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-8.2-foss-2021a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-8.2-foss-2021a.eb index ba96f807c90..4e085b00cc9 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-8.2-foss-2021a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-8.2-foss-2021a.eb @@ -20,9 +20,9 @@ checksums = ['2e24768720efed1a5a4a58e83e2aca502cd8b95544c21695eb0de71ed652f20a'] dependencies = [ ('Libint', '2.6.0', '-lmax-6-cp2k'), ('libxc', '5.1.5'), - ('libxsmm', '1.16.1'), + ('libxsmm', '1.16.2'), ('FFTW', '3.3.9'), - ('PLUMED', '2.6.3'), + ('PLUMED', '2.7.2'), ] builddependencies = [ From 66799a46ab9943d56c2a0729ebe87a7818ca4f60 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 24 Sep 2021 18:13:08 +0200 Subject: [PATCH 1418/9987] Fix jax test failures on recent kernels --- .../easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 9 ++++++++- .../j/jax/jax-0.2.19-fosscuda-2020b.eb | 7 ++++++- ....2.19_fix-update-of-cache-access-time.patch | 18 ++++++++++++++++++ 3 files changed, 32 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.19_fix-update-of-cache-access-time.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index d7edc77e8a7..62e34b24ad7 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -94,7 +94,14 @@ exts_list = [ (name, version, { 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], - 'checksums': ['fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c'], + 'patches': [ + 'jax-%(version)s_fix-update-of-cache-access-time.patch', + ], + 'checksums': [ + 'fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c', # jax-v0.2.19.tar.gz + # jax-0.2.19_fix-update-of-cache-access-time.patch + 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + ], 'runtest': 'pytest -n %(parallel)s tests', }), ] diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index 41f5cbd5db0..1da5dfa47ae 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -98,9 +98,14 @@ exts_list = [ (name, version, { 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], - 'patches': ['jax-%(version)s_skip-heap-profiler-test.patch'], + 'patches': [ + 'jax-%(version)s_fix-update-of-cache-access-time.patch', + 'jax-%(version)s_skip-heap-profiler-test.patch' + ], 'checksums': [ 'fb6f665b1461ac67954c1004da00d12e1c41b65b744a5fa0311d26d1a784a96c', # jax-v0.2.19.tar.gz + # jax-0.2.19_increase-cache-test-sleep-time.patch + 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', # jax-0.2.19_skip-heap-profiler-test.patch 'a431ce1b6588b5098872f36575dc2c5023b1010760bf6aaa889125c9a09227b0', ], diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19_fix-update-of-cache-access-time.patch b/easybuild/easyconfigs/j/jax/jax-0.2.19_fix-update-of-cache-access-time.patch new file mode 100644 index 00000000000..adf64ed5098 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19_fix-update-of-cache-access-time.patch @@ -0,0 +1,18 @@ +Recent kernels do not update the access time on read. +So do that manually. +See https://github.com/google/jax/issues/7944 + +Author: Alexander Grund (TU Dresden) + +diff --git a/jax/experimental/compilation_cache/file_system_cache.py b/jax/experimental/compilation_cache/file_system_cache.py +index b85969de..4c22d8e3 100644 +--- a/jax/experimental/compilation_cache/file_system_cache.py ++++ b/jax/experimental/compilation_cache/file_system_cache.py +@@ -33,6 +33,7 @@ class FileSystemCache(CacheInterface): + path_to_key = os.path.join(self._path, key) + if os.path.exists(path_to_key): + with open(path_to_key, "rb") as file: ++ os.utime(file.fileno()) + return file.read() + else: + return None From 7a35efee6f33de1c5d7d98cd326b0fbad4a2a00f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 24 Sep 2021 21:59:29 +0200 Subject: [PATCH 1419/9987] adding easyconfigs: Clang-12.0.1-GCCcore-11.2.0.eb, Z3-4.8.12-GCCcore-11.2.0.eb --- .../c/Clang/Clang-12.0.1-GCCcore-11.2.0.eb | 75 +++++++++++++++++++ .../z/Z3/Z3-4.8.12-GCCcore-11.2.0.eb | 33 ++++++++ 2 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.8.12-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e95723acdc8 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-11.2.0.eb @@ -0,0 +1,75 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '12.0.1' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'clang-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', + 'clang-tools-extra-%(version)s.src.tar.xz', + 'libunwind-%(version)s.src.tar.xz', +] +checksums = [ + '7d9a8405f557cefc5a21bf5672af73903b64749d9bc3a50322239f56f34ffddf', # llvm-12.0.1.src.tar.xz + '6e912133bcf56e9cfe6a346fa7e5c52c2cde3e4e48b7a6cc6fcc7c75047da45f', # clang-12.0.1.src.tar.xz + 'b4c8d5f2a802332987c1c0a95b5afb35b1a66a96fe44add4e4ed4792c4cba0a4', # compiler-rt-12.0.1.src.tar.xz + '2254e25312708a567b1ab00716362db379d265e47a97a94ed74211d57a4cd5f9', # polly-12.0.1.src.tar.xz + '60fe79440eaa9ebf583a6ea7f81501310388c02754dbe7dc210776014d06b091', # openmp-12.0.1.src.tar.xz + '690b3f6a76310e13a783a142f87500ade9cafe003e088b678364487ed873e361', # lld-12.0.1.src.tar.xz + 'a42089cd358f661823c490741f8be98701d983a7ee5152c8649075da681a9d15', # libcxx-12.0.1.src.tar.xz + '88efe8e391767a1e8f42b509879abe766c9f44b1781ad1900975ae6b516b91d0', # libcxxabi-12.0.1.src.tar.xz + '65659efdf97dbed70ae0caee989936b731f249dddc46f1cb4225b2f49b232ae5', # clang-tools-extra-12.0.1.src.tar.xz + '0bea6089518395ca65cf58b0a450716c5c99ce1f041079d3aa42d280ace15ca4', # libunwind-12.0.1.src.tar.xz +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.37'), + ('hwloc', '2.5.0'), + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), + ('GMP', '6.2.1'), + ('Z3', '4.8.12'), +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('elfutils', '0.185'), +] + +assertions = True +usepolly = True +build_lld = True +libcxx = True +enable_rtti = True +build_extra_clang_tools = True + +skip_all_tests = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.12-GCCcore-11.2.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.12-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e5532af3956 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.8.12-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Z3' +version = '4.8.12' + +homepage = 'https://github.com/Z3Prover/z3' +description = """ + Z3 is a theorem prover from Microsoft Research. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/Z3Prover/z3/archive/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e3aaefde68b839299cbc988178529535e66048398f7d083b40c69fe0da55f8b7'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('binutils', '2.37'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = '-DZ3_USE_LIB_GMP=ON -DZ3_LINK_TIME_OPTIMIZATION=ON ' + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From 2d9c56c4985197873c038e2d3d1a4e8bcfa32ef8 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Fri, 24 Sep 2021 20:13:05 -0400 Subject: [PATCH 1420/9987] Update easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb b/easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb index b7f615d0743..2c4cafc13de 100644 --- a/easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb +++ b/easybuild/easyconfigs/m/MixMHC2pred/MixMHC2pred-1.2.eb @@ -1,4 +1,3 @@ - easyblock = 'PackedBinary' name = 'MixMHC2pred' From ac7d40421eb8b0eb9d9349e5f36ff9d4ffc7f4b5 Mon Sep 17 00:00:00 2001 From: scicomp-moffitt <90271624+scicomp-moffitt@users.noreply.github.com> Date: Fri, 24 Sep 2021 20:19:15 -0400 Subject: [PATCH 1421/9987] Update easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb Co-authored-by: SebastianAchilles --- .../v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb index d526c59388f..dca621dd7c2 100644 --- a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb @@ -9,7 +9,7 @@ homepage = 'https://github.com/cc2qe/vawk' description = """An awk-like VCF parser """ -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchain = {'name': 'GCC', 'version': '10.2.0'} dependencies = [ ('Python', '2.7.18'), From 464b2a182f54b97940c5e8393e7d247f78b51edf Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 25 Sep 2021 09:11:11 +0100 Subject: [PATCH 1422/9987] adding easyconfigs: HPDBSCAN-20210826-foss-2020b.eb --- .../HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb new file mode 100644 index 00000000000..f106d8a2279 --- /dev/null +++ b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb @@ -0,0 +1,54 @@ +easyblock = 'CMakeMakeCp' + +name = 'HPDBSCAN' +version = '20210826' +local_commit = 'ae0c74c' + +homepage = 'https://github.com/Markus-Goetz/hpdbscan' +description = "Highly parallel density based spatial clustering for application with noise" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Markus-Goetz/hpdbscan/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['52ff343f77aeea5a425a911d88a57314c6bc877c18209eb53819d114421a868d'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('SciPy-bundle', '2020.11'), # for mpi4py + ('SWIG', '4.0.2'), +] + +# There is not an install method, so build in the source directory to simplify files_to_copy +separate_build_dir = False + +files_to_copy = [ + (['hpdbscan'], 'bin'), + (['libhpdbscan.%s' % SHLIB_EXT], 'lib'), + (['hpdbscan.py', '_hpdbscan.%s' % SHLIB_EXT], 'lib/python%(pyshortver)s/site-packages'), + 'include', 'LICENSE.txt', +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/hpdbscan', 'lib/libhpdbscan.%s' % SHLIB_EXT, 'include/hpdbscan.h'], + 'dirs': [], +} + +# Check the Python bindings +_hpdbscan_python_check = 'python -c "import hpdbscan; import numpy; ' +_hpdbscan_python_check += 'clusterer = hpdbscan.HPDBSCAN(epsilon=0.3, min_points=4); ' +_hpdbscan_python_check += 'clusterer.cluster(numpy.random.rand(100, 3))"' + +sanity_check_commands = [ + "hpdbscan --help", + _hpdbscan_python_check, +] + +moduleclass = 'tools' From 7a07a0bded14625c58b224e70384892e0c0e813e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Sat, 25 Sep 2021 11:26:57 +0200 Subject: [PATCH 1423/9987] Limit parallelism a bit more --- easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb index 62e34b24ad7..e583b752f42 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-foss-2020b.eb @@ -36,7 +36,7 @@ use_pip = True # running the tests with lots of cores results in test failures because not enough threads can be started, # so limit to a reasonable number of cores to use at maximum -maxparallel = 10 +maxparallel = 5 default_easyblock = 'PythonPackage' default_component_specs = { From a13ded44d4e1a9b219641fa963c460b3d628798e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Sep 2021 17:13:30 +0200 Subject: [PATCH 1424/9987] add patch to fix failing file system cache test for jax 0.2.20 on recent Linux kernels --- .../easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb index ee86eebb067..a0492416164 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.20-foss-2021a.eb @@ -4,6 +4,7 @@ easyblock = 'PythonBundle' name = 'jax' version = '0.2.20' + homepage = 'https://pypi.python.org/pypi/jax' description = """Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more""" @@ -36,7 +37,7 @@ sanity_pip_check = True # running the tests with lots of cores results in test failures because not enough threads can be started, # so limit to a reasonable number of cores to use at maximum -maxparallel = 10 +maxparallel = 5 default_easyblock = 'PythonPackage' default_component_specs = { @@ -92,10 +93,17 @@ exts_list = [ 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], }), (name, version, { - 'runtest': "pytest -n %(parallel)s tests", 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], - 'checksums': ['2e40bd8e2493a3609177b122c583636c0c88c5e695f8041190eefdfd42a6fc5b'], + 'patches': [ + 'jax-0.2.19_fix-update-of-cache-access-time.patch', + ], + 'checksums': [ + '2e40bd8e2493a3609177b122c583636c0c88c5e695f8041190eefdfd42a6fc5b', # jax-v0.2.20.tar.gz + # jax-0.2.19_fix-update-of-cache-access-time.patch + 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + ], + 'runtest': "pytest -n %(parallel)s tests", }), ] From 2ace8f1da303fd47e61ad20361fa1f49acea1e7c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 27 Sep 2021 16:29:37 +0200 Subject: [PATCH 1425/9987] Add newer NCCL and Unzip --- .../b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb | 1 + ...NCCL-2.11.4-GCCcore-8.3.0-CUDA-10.1.243.eb | 20 +++++++++++++++++++ ...rFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb | 3 ++- 3 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-GCCcore-8.3.0-CUDA-10.1.243.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb index 76be3bcb656..c72ee0d0455 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb @@ -23,6 +23,7 @@ builddependencies = [ ('binutils', '2.32'), ('Python', '3.7.4'), ('Zip', '3.0'), + ('UnZip', '6.0'), ] dependencies = [('Java', '1.8', '', True)] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-GCCcore-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-GCCcore-8.3.0-CUDA-10.1.243.eb new file mode 100644 index 00000000000..38c1b6108f0 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-GCCcore-8.3.0-CUDA-10.1.243.eb @@ -0,0 +1,20 @@ +name = 'NCCL' +version = '2.11.4' +local_gcc_ver = '8.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [('GCC', '%(toolchain_version)s', '', True)] +dependencies = [('CUDA', '10.1.243', '', True)] + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['db4e9a0277a64f9a31ea9b5eea22e63f10faaed36dded4587bbc8a0d8eceed10'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb index d3236a6a8a0..09d6e204a68 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb @@ -16,10 +16,11 @@ builddependencies = [ # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.23.0', '-nodocs'), ('pybind11', '2.4.3', versionsuffix), + ('UnZip', '6.0'), ] dependencies = [ ('cuDNN', '7.6.4.38'), - ('NCCL', '2.4.8'), + ('NCCL', '2.11.4', '-CUDA-%(cudaver)s'), ('Python', '3.7.4'), ('h5py', '2.10.0', versionsuffix), ('cURL', '7.66.0'), From 46a9621511f450e016d53fab88a46381498b6d81 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 28 Sep 2021 09:18:46 +0200 Subject: [PATCH 1426/9987] adding easyconfigs: UnZip-6.0.eb, bzip2-1.0.8.eb --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb | 28 +++++++++++ easybuild/easyconfigs/u/UnZip/UnZip-6.0.eb | 52 ++++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb new file mode 100644 index 00000000000..8e6258a749f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb @@ -0,0 +1,28 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.37'), +] + + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0.eb new file mode 100644 index 00000000000..130e8bc2afd --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = SYSTEM + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' +buildopts += 'LF2="$LDFLAGS" ' +# Note: CF is multiple lines +buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' +buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' +buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From a02e8df8fafa8ea44ddb93b46bb878050062205f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 28 Sep 2021 09:20:50 +0200 Subject: [PATCH 1427/9987] bzip2: add buildopts --- easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb index 8e6258a749f..5411fd08371 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb @@ -24,5 +24,9 @@ builddependencies = [ ('binutils', '2.37'), ] +buildopts = "CC=gcc CFLAGS='-Wall -Winline -O3 -fPIC -g $(BIGFILES)'" + +# building of shared libraries doesn't work on OS X (where 'gcc' is actually Clang...) +with_shared_libs = OS_TYPE == 'Linux' moduleclass = 'tools' From 53c6f0222769bfcdc505b6b145aa061d2bc79365 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Sep 2021 09:34:16 +0200 Subject: [PATCH 1428/9987] use SHLIB_EXT; add sanity_check_commands --- .../easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb index 187877371cc..e56c85b532c 100644 --- a/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb @@ -34,9 +34,12 @@ sanity_check_paths = { ['include/%s' % x for x in ['bkpublic.h', 'cstypes.h', 'odbcss.h', 'sqlfront.h', 'syberror.h', 'tds_sysdep_public.h', 'cspublic.h', 'ctpublic.h', 'sqldb.h', 'sybdb.h', 'sybfront.h']] + - ['lib/libct.%s' % x for x in ['a', 'la', 'so', 'so.4', 'so.4.0.0']] + - ['lib/libsybdb.%s' % x for x in ['a', 'la', 'so', 'so.5', 'so.5.1.0']], + ['lib/libct.%s' % x for x in ['a', 'la', SHLIB_EXT]] + + ['lib/libsybdb.%s' % x for x in ['a', 'la', SHLIB_EXT]], 'dirs': ['bin', 'etc', 'include', 'lib', 'share/doc', 'share/man', 'share/man/man5'], } +_bins = ['bsqldb', 'datacopy', 'defncopy', 'fisql', 'freebcp', 'tdspool', 'tsql'] +sanity_check_commands = ['%s -h 2>&1 |grep -i "^usage:"' % x for x in _bins] + moduleclass = 'data' From 79eee0c3c30dfb2a8f8a9f9af6cb5c7b13bfb26f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Sep 2021 09:45:19 +0200 Subject: [PATCH 1429/9987] use GCCcore toolchain and ad binutils as builddep --- .../v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb index dca621dd7c2..aef3494ecb2 100644 --- a/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/v/vawk/vawk-0.0.1-GCCcore-10.2.0-Python-2.7.18.eb @@ -9,8 +9,9 @@ homepage = 'https://github.com/cc2qe/vawk' description = """An awk-like VCF parser """ -toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '2.7.18'), ] From 3cebc6e57090e6530d972226add20232d1ee9e9a Mon Sep 17 00:00:00 2001 From: Zdenek Date: Tue, 28 Sep 2021 09:47:34 +0200 Subject: [PATCH 1430/9987] Adding author + short description to the top of the patch --- .../easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb | 2 +- .../u/ucx-py/ucx-py-setup-get_ucx_incpath.patch | 8 ++++++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb index afa7ab8a549..3c5750df678 100644 --- a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb +++ b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb @@ -31,7 +31,7 @@ exts_list = [ 'sources': ['v%(version)s.tar.gz'], 'checksums': [ '751da668ba43ad15b53cdb0bfd4084bd4b07200db57b604a9a09aa99d8a3bc1b', # v0.21.0.tar.gz - '123c9aee92ae6e8567e381bef0a4a590f1f7898708b3df1911e41d5ac498cdb3', # ucx-py-setup-get_ucx_incpath.patch + 'faeb61c302ffb37e72221d18c83fc929e47a6c5cd84c4208b01c5a21f570f561', # ucx-py-setup-get_ucx_incpath.patch ], }), ] diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-setup-get_ucx_incpath.patch b/easybuild/easyconfigs/u/ucx-py/ucx-py-setup-get_ucx_incpath.patch index 77233ef773e..6cd374fea10 100644 --- a/easybuild/easyconfigs/u/ucx-py/ucx-py-setup-get_ucx_incpath.patch +++ b/easybuild/easyconfigs/u/ucx-py/ucx-py-setup-get_ucx_incpath.patch @@ -1,3 +1,7 @@ +description: setup.py extension to locate ucp headers from UCX_MODULE_DIR + configuraton key provided by ucx_info. +issue: https://github.com/rapidsai/ucx-py/issues/783 +author: Zdenek Matej, MAX IV Laboratory, Lund University --- setup.py +++ setup.py @@ -24,9 +24,30 @@ library_dirs = [get_config_var("LIBDIR")] @@ -5,7 +9,7 @@ extra_compile_args = ["-std=c99", "-Werror"] +def get_ucx_incpath(): -+ import os, subprocess ++ import subprocess + res = include_dirs[0] + # get output of ucx_info configuration + p = subprocess.Popen("ucx_info -c", stdout=subprocess.PIPE, shell=True) @@ -28,7 +32,7 @@ def get_ucp_version(): - with open(include_dirs[0] + "/ucp/api/ucp_version.h") as f: -+ with open(get_ucx_incpath() + "/ucp/api/ucp_version.h") as f: ++ with open(os.path.join(get_ucx_incpath(),"ucp/api/ucp_version.h")) as f: ftext = f.read() major = re.findall("^#define.*UCP_API_MAJOR.*", ftext, re.MULTILINE) minor = re.findall("^#define.*UCP_API_MINOR.*", ftext, re.MULTILINE) From fb0f60b5ea42bdeb7df0e336676529020994d398 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Sep 2021 10:42:26 +0200 Subject: [PATCH 1431/9987] add version to patch name --- easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb | 2 +- ..._incpath.patch => ucx-py-0.21.0_setup-get-ucx-incpath.patch} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/u/ucx-py/{ucx-py-setup-get_ucx_incpath.patch => ucx-py-0.21.0_setup-get-ucx-incpath.patch} (100%) diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb index 3c5750df678..514e47c1fa4 100644 --- a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb +++ b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb @@ -26,7 +26,7 @@ exts_list = [ }), (name, version, { 'modulename': 'ucp', - 'patches': ['ucx-py-setup-get_ucx_incpath.patch'], + 'patches': ['ucx-py-%(version)s_setup-get-ucx-incpath.patch'], 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], 'sources': ['v%(version)s.tar.gz'], 'checksums': [ diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-setup-get_ucx_incpath.patch b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0_setup-get-ucx-incpath.patch similarity index 100% rename from easybuild/easyconfigs/u/ucx-py/ucx-py-setup-get_ucx_incpath.patch rename to easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0_setup-get-ucx-incpath.patch From 9a3b0196377d3312fbd670f0afcd969da720f8c6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 28 Sep 2021 10:42:59 +0200 Subject: [PATCH 1432/9987] Fix compilation of BWA on PPC --- easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb index 48f02d30376..b6825ba6a83 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.2.0.eb @@ -34,6 +34,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' moduleclass = 'bio' From 16043542a5aa0cd1b4aadce4650a2f1a316cd6c8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 28 Sep 2021 10:52:08 +0200 Subject: [PATCH 1433/9987] Add NCCL to Horovod --- ...orovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb index 56afd882edc..8ec494b3d6f 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb @@ -17,6 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.7.4'), ('PyYAML', '5.1.2'), + ('NCCL', '2.11.4', '-CUDA-%(cudaver)s'), ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), ] From 616e6023368aa3fa8a11443e40ae9fa4fc42c5ec Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Sep 2021 10:57:42 +0200 Subject: [PATCH 1434/9987] update patch comment --- easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb index 514e47c1fa4..ab94cdba534 100644 --- a/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb +++ b/easybuild/easyconfigs/u/ucx-py/ucx-py-0.21.0-foss-2020b.eb @@ -31,7 +31,8 @@ exts_list = [ 'sources': ['v%(version)s.tar.gz'], 'checksums': [ '751da668ba43ad15b53cdb0bfd4084bd4b07200db57b604a9a09aa99d8a3bc1b', # v0.21.0.tar.gz - 'faeb61c302ffb37e72221d18c83fc929e47a6c5cd84c4208b01c5a21f570f561', # ucx-py-setup-get_ucx_incpath.patch + # ucx-py-0.21.0_setup-get-ucx-incpath.patch + 'faeb61c302ffb37e72221d18c83fc929e47a6c5cd84c4208b01c5a21f570f561', ], }), ] From 7335e09795a7e345b0ad5a438bedb4ba772b7043 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 28 Sep 2021 11:25:28 +0200 Subject: [PATCH 1435/9987] adding easyconfigs: MotionCor2-1.4.4-GCCcore-10.2.0.eb --- .../MotionCor2-1.4.4-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..e040a5698e6 --- /dev/null +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ake Sandgren +# HPC2N +# Umea University + +name = 'MotionCor2' +version = '1.4.4' + +homepage = 'https://msg.ucsf.edu/' +description = """MotionCor2 correct anisotropic image motion at the +single pixel level across the whole frame, suitable for both single +particle and tomographic images. Iterative, patch-based motion detection +is combined with spatial and temporal constraints and dose weighting. + +Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, +Yifan Cheng and David A. Agard (2016) Anisotropic Correction of +Beam-induced Motion for Improved Single-particle Electron +Cryo-microscopy, Nature Methods, submitted. +BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [{ + 'filename': '%(name)s_%(version)s.zip', + 'extract_cmd': 'unzip -j %s' +}] +checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] + +# No longer directly downloadable, available from https://msg.ucsf.edu/software +# CUDA is a build dependency to make sure it gets installed. +# It's actually a runtime dependency, but that's handled in the wrapper to +# make sure it doesn't conflict with whatever toolchain happens to be loaded. +# Change CUDA version to match the latest one used in this version +# of MotionCor2 +builddependencies = [ + ('binutils', '2.35'), + ('CUDAcore', '11.1.1', '', True), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.5'), + ('LibTIFF', '4.1.0'), +] +moduleclass = 'bio' From cf04a56a341c9c7bd4153c8db1b6b621e790b2e5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 28 Sep 2021 12:50:41 +0200 Subject: [PATCH 1436/9987] Lift NCCL EC to gcccuda --- ...-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb | 2 +- ...8.3.0-CUDA-10.1.243.eb => NCCL-2.11.4-gcccuda-2019b.eb} | 7 +------ .../TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb | 2 +- 3 files changed, 3 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/n/NCCL/{NCCL-2.11.4-GCCcore-8.3.0-CUDA-10.1.243.eb => NCCL-2.11.4-gcccuda-2019b.eb} (67%) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb index 8ec494b3d6f..26d34bc73f7 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-fosscuda-2019b-TensorFlow-2.5.0-Python-3.7.4.eb @@ -17,7 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.7.4'), ('PyYAML', '5.1.2'), - ('NCCL', '2.11.4', '-CUDA-%(cudaver)s'), + ('NCCL', '2.11.4'), ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-GCCcore-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb similarity index 67% rename from easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-GCCcore-8.3.0-CUDA-10.1.243.eb rename to easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb index 38c1b6108f0..a80da45c38a 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-GCCcore-8.3.0-CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb @@ -1,16 +1,11 @@ name = 'NCCL' version = '2.11.4' -local_gcc_ver = '8.3.0' -versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://developer.nvidia.com/nccl' description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.""" -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} - -builddependencies = [('GCC', '%(toolchain_version)s', '', True)] -dependencies = [('CUDA', '10.1.243', '', True)] +toolchain = {'name': 'gcccuda', 'version': '2019b'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb index 09d6e204a68..bf58ba20594 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ ('cuDNN', '7.6.4.38'), - ('NCCL', '2.11.4', '-CUDA-%(cudaver)s'), + ('NCCL', '2.11.4'), ('Python', '3.7.4'), ('h5py', '2.10.0', versionsuffix), ('cURL', '7.66.0'), From 9da96f6ea0d562d0fb716def077769743bfe9e88 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 28 Sep 2021 14:31:04 +0200 Subject: [PATCH 1437/9987] Add exclusion rule for NCCL --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 7d0730fd15a..1b89add6850 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -450,6 +450,8 @@ def check_dep_vars(self, gen, dep, dep_vars): r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), ], + # TF (and by extension Horovod) 2.5+ requires a more recent NCCL + 'NCCL': [(r'2\.11\.4', [r'TensorFlow-2\.[5-9]\.', r'Horovod-0\.2[2-9]'])], # rampart requires nodejs > 10, artic-ncov2019 requires rampart 'nodejs': [('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13'])], # some software depends on an older numba; From 3c1037760e5d7b17f6e49d29b4eadd140b99f814 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 28 Sep 2021 16:21:41 +0200 Subject: [PATCH 1438/9987] adding easyconfigs: IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb --- ...-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb new file mode 100644 index 00000000000..1a94253258b --- /dev/null +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -0,0 +1,65 @@ +# Thomas Hofffmann, EMBL Heidelberg, structures-it@embl.de, 2021/09 +easyblock = 'Tarball' # there is no setup.py -> unpack tarball and move to site-packages in postinstall. + +name = 'IsoNet' +# There is no version tag available in github. Using commit and date instead. +local_commit = '674f67f1afb8aa1353c0d67ccb55263c1f20576f' +local_version = '0.1' +local_commit_date = '20210822' +local_commit_count = '04' +version = '%s_%s_%s_%s' % (local_version, local_commit_date, local_commit_count, local_commit[:7]) + +homepage = 'https://github.com/Heng-Z/IsoNet' +description = """IsoNet stands for for ISOtropic reconstructioN of Electron Tomography. It trains +deep convolutional neural networks to reconstruct meaningful contents in the mis +sing wedge for electron tomography, and to increase signal-to-noise ratio, +using the information learned from the original tomogram. The software requires +tomograms as input. Observing at about 30A resolution, the IsoNet generated +tomograms are largely isotropic.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/Heng-Z/IsoNet/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['dac1583bbab0d6b09496657b5d237b9c35c9a70ee9c0089a174e571b78892d49'] + +install_type = 'subdir' +postinstallcmds = [ + 'find %(installdir)s/isonet -name \'*.pyc\' -exec rm {} \\;' + '&& mv %(installdir)s/isonet %(installdir)s/lib/python%(pyshortver)s/site-packages/IsoNet' +] + +dependencies = [ + ('Python', '3.8.6'), + ('TensorFlow', '2.4.1'), + ('PyQt5', '5.15.1'), + ('SciPy-bundle', '2020.11'), + ('mrcfile', '1.3.0'), + ('tqdm', '4.60.0'), + ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! +] +sanity_pip_check = True +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('fire', '0.4.0', { + 'modulename': 'fire', + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], + 'use_pip': True, + 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], + }), +] + +modextrapaths = { + 'PATH': 'lib/python%(pyshortver)s/site-packages/IsoNet/bin', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/' +} +sanity_check_commands = [ + 'isonet.py check', + 'isonet.py --help', +] +sanity_check_paths = { + 'files': [], + 'dirs': ["lib/python%(pyshortver)s/site-packages/IsoNet"] +} + +moduleclass = 'bio' From 921bc1f6781802a307117534796fd67d666ada83 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 28 Sep 2021 16:35:39 +0200 Subject: [PATCH 1439/9987] Update IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb --- .../i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index 1a94253258b..6efea4b1dbe 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -38,7 +38,6 @@ dependencies = [ ('tqdm', '4.60.0'), ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! ] -sanity_pip_check = True exts_defaultclass = 'PythonPackage' exts_list = [ ('fire', '0.4.0', { From 84f1d6f60403d38f2e27c7ed27f09749f4e05f71 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 28 Sep 2021 17:17:28 +0200 Subject: [PATCH 1440/9987] downgrade tqdm dep --- .../i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index 6efea4b1dbe..05c2b7e4727 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -35,7 +35,7 @@ dependencies = [ ('PyQt5', '5.15.1'), ('SciPy-bundle', '2020.11'), ('mrcfile', '1.3.0'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! ] exts_defaultclass = 'PythonPackage' From 6fc65348415f87112ae451f1a6429f756f2d83c0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 28 Sep 2021 17:42:55 +0200 Subject: [PATCH 1441/9987] exts_default_options --- .../IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb index 05c2b7e4727..48e8d55811f 100644 --- a/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IsoNet/IsoNet-0.1_20210822_04_674f67f-fosscuda-2020b.eb @@ -38,12 +38,15 @@ dependencies = [ ('tqdm', '4.56.2'), ('scikit-image', '0.18.1') # acc. to requirements.txt: ==0.17.2 ! ] +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} exts_defaultclass = 'PythonPackage' exts_list = [ ('fire', '0.4.0', { 'modulename': 'fire', 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], - 'use_pip': True, 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], }), ] From ee4a49fcdc3638b5bcd7392132499f071db736ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 29 Sep 2021 01:57:26 +0200 Subject: [PATCH 1442/9987] adding easyconfigs: networkx-2.6.3-foss-2021a.eb --- .../n/networkx/networkx-2.6.3-foss-2021a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.6.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.6.3-foss-2021a.eb b/easybuild/easyconfigs/n/networkx/networkx-2.6.3-foss-2021a.eb new file mode 100644 index 00000000000..55837fad044 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.6.3-foss-2021a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.6.3' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c0946ed31d71f1b732b5aaa6da5a0388a345019af232ce2f49c766e2d6795c51'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 59fdfc7f5a0cc7042eca9f15f295c1639ab2a4bc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 29 Sep 2021 14:11:41 +0100 Subject: [PATCH 1443/9987] adding easyconfigs: PEPT-0.4.1-foss-2021a.eb --- .../p/PEPT/PEPT-0.4.1-foss-2021a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEPT/PEPT-0.4.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PEPT/PEPT-0.4.1-foss-2021a.eb b/easybuild/easyconfigs/p/PEPT/PEPT-0.4.1-foss-2021a.eb new file mode 100644 index 00000000000..09a0ee28c7d --- /dev/null +++ b/easybuild/easyconfigs/p/PEPT/PEPT-0.4.1-foss-2021a.eb @@ -0,0 +1,45 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'PEPT' +version = '0.4.1' + +homepage = "https://pept.readthedocs.io/en/latest/" +description = """A Python library that integrates all the tools necessary to perform research using Positron Emission + Particle Tracking (PEPT). The library includes algorithms for the location, identification and tracking of particles, + in addition to tools for visualisation and analysis, and utilities allowing the realistic simulation of PEPT data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('scikit-learn', '0.24.2'), + ('tqdm', '4.61.2'), + ('plotly.py', '5.1.0'), + ('numba', '0.53.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('beartype', '0.8.1', { + 'checksums': ['c2a2bac961cae7f022d88b892c0d23e91314915aea3e01f316880b4fb00d7d2c'], + }), + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('hdbscan', '0.8.27', { + 'checksums': ['e3a418d0d36874f7b6a1bf0b7461f3857fc13a525fd48ba34caed2fe8973aa26'], + }), + ('cma', '3.1.0', { + 'checksums': ['3b83077fe3a52be1d8c82d61a22f600401c772b1add6ed5dd8152e1a2d15e3c6'], + }), + ('pept', version, { + 'checksums': ['1f4f5a64715bfe9552aba4e13ee5f96534e402293162a6c3396d19b77e1fb5d2'], + }), +] + +moduleclass = 'bio' From b390535abf5cfa942d296152633255b9f950f405 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 29 Sep 2021 15:28:55 +0200 Subject: [PATCH 1444/9987] Disable CPU affinity for tests --- easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb index b0fd75c4081..13144d3f39f 100644 --- a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/'] -checksums = ['aefc1ef07fb70b49d4e6ee0841796342c32245ce699287b12ff03e5613f771bf'] +checksums = ['a87363e27102da28b828c5596ac7700a3972acc65ca52c0df13440824039639e'] builddependencies = [ ('CMake', '3.20.1'), From 07247a5840ff2518bf1a0871eb6dcb5b231966cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 30 Sep 2021 09:20:42 +0200 Subject: [PATCH 1445/9987] clarify comment on diverging NCCL version for TensorFlow 2.5.0 with fosscuda/2019b --- test/easyconfigs/easyconfigs.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 1b89add6850..d304b94d594 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -450,7 +450,8 @@ def check_dep_vars(self, gen, dep, dep_vars): r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), ], - # TF (and by extension Horovod) 2.5+ requires a more recent NCCL + # TensorFlow 2.5+ requires a more recent NCCL than version 2.4.8 used in 2019b generation; + # Horovod depends on TensorFlow, so same exception required there 'NCCL': [(r'2\.11\.4', [r'TensorFlow-2\.[5-9]\.', r'Horovod-0\.2[2-9]'])], # rampart requires nodejs > 10, artic-ncov2019 requires rampart 'nodejs': [('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13'])], From 326c34198034adab82f55b9a866b2ca0c41ce144 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 30 Sep 2021 10:18:00 +0200 Subject: [PATCH 1446/9987] Disable CPU affinity for tests --- .../p/pftoolsV3/pftoolsV3-3.2.9-foss-2021a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.9-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.9-foss-2021a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.9-foss-2021a.eb new file mode 100644 index 00000000000..55883fbb0da --- /dev/null +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.9-foss-2021a.eb @@ -0,0 +1,53 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## +easyblock = 'CMakeMake' + +name = 'pftoolsV3' +version = '3.2.9' + +homepage = 'https://github.com/sib-swiss/pftools3' +description = """A suite of tools to build and search generalized profiles (protein and DNA).""" +software_license = 'LicenseGPLv2' + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/'] +checksums = ['f074a34b182110a851aae74c3a0406b0561d9020c027933690f1dc701b751f9c'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('make', '4.3'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Perl', '5.32.1'), + ('PCRE', '8.44'), + ('libharu', '2.3.0'), + ('zlib', '1.2.11'), + ('libgd', '2.3.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), +] + +configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX:PATH=%(installdir)s -DCMAKE_BUILD_TYPE=Release ' +configure_cmd += '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON ' +configure_cmd += '../pftools3-%(version)s' + +runtest = 'test' + +sanity_check_paths = { + 'files': [ + 'bin/ptof', 'bin/htop', 'bin/6ft', 'bin/2ft', 'bin/pfdump', 'bin/pfscan', 'bin/pfsearch', + 'bin/pfscanV3', 'bin/pfsearchV3', + ], + 'dirs': ['share/doc', 'share/man'], +} + +moduleclass = 'bio' From cf84993edf2ce9481fad5d217c6c9e0777ad1efc Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 30 Sep 2021 10:29:39 +0200 Subject: [PATCH 1447/9987] Delete pftoolsV3-3.2.8-foss-2021a.eb replaced with new version --- .../p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb | 53 ------------------- 1 file changed, 53 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb deleted file mode 100644 index 13144d3f39f..00000000000 --- a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.8-foss-2021a.eb +++ /dev/null @@ -1,53 +0,0 @@ -## -# This is a contribution from SIB Swiss Institute of Bioinformatics -# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it -# -# Authors:: Sebastien Moretti -# -## -easyblock = 'CMakeMake' - -name = 'pftoolsV3' -version = '3.2.8' - -homepage = 'https://github.com/sib-swiss/pftools3' -description = """A suite of tools to build and search generalized profiles (protein and DNA).""" -software_license = 'LicenseGPLv2' - -toolchain = {'name': 'foss', 'version': '2021a'} - -sources = ['v%(version)s.tar.gz'] -source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/'] -checksums = ['a87363e27102da28b828c5596ac7700a3972acc65ca52c0df13440824039639e'] - -builddependencies = [ - ('CMake', '3.20.1'), - ('make', '4.3'), - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Perl', '5.32.1'), - ('PCRE', '8.44'), - ('libharu', '2.3.0'), - ('zlib', '1.2.11'), - ('libgd', '2.3.1'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.6'), -] - -configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX:PATH=%(installdir)s -DCMAKE_BUILD_TYPE=Release ' -configure_cmd += '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON ' -configure_cmd += '../pftools3-%(version)s' - -runtest = 'test' - -sanity_check_paths = { - 'files': [ - 'bin/ptof', 'bin/htop', 'bin/6ft', 'bin/2ft', 'bin/pfdump', 'bin/pfscan', 'bin/pfsearch', - 'bin/pfscanV3', 'bin/pfsearchV3', - ], - 'dirs': ['share/doc', 'share/man'], -} - -moduleclass = 'bio' From f7fd274a2be934e074c5cee6572bac1240b1f950 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 30 Sep 2021 11:20:17 +0100 Subject: [PATCH 1448/9987] adding easyconfigs: lifelines-0.26.3-fosscuda-2020b.eb --- .../lifelines-0.26.3-fosscuda-2020b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb new file mode 100644 index 00000000000..3c8696a9d2b --- /dev/null +++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb @@ -0,0 +1,45 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'lifelines' +version = '0.26.3' + +homepage = "https://lifelines.readthedocs.io/en/latest/" +description = """lifelines is a complete survival analysis library, written in pure Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('interface_meta', '1.2.4', { + 'checksums': ['4c7725dd4b80f97b7eecfb26023e1a8a7cdbb6d6a7207a8e93f9d4bfef9ee566'], + }), + ('autograd', '1.3', { + 'checksums': ['a15d147577e10de037de3740ca93bfa3b5a7cdfbc34cfb9105429c3580a33ec4'], + }), + ('autograd-gamma', '0.5.0', { + 'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'], + }), + ('formulaic', '0.2.4', { + 'checksums': ['15b71ea8972fb451f80684203cddd49620fc9ed5c2e35f31e0874e9c41910d1a'], + }), + (name, version, { + 'checksums': ['f3dc77601927b9dbebb77d1b4d6f5bd4e5e3e169f6e8d7c2beb31a9a36fcbe1b'], + }), +] + +moduleclass = 'data' From 8a820ee295b09137289a753cf081c010913f8447 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 30 Sep 2021 11:53:06 +0100 Subject: [PATCH 1449/9987] keep bio as the moduleclass --- .../easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb index 3c8696a9d2b..2458724db72 100644 --- a/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.26.3-fosscuda-2020b.eb @@ -42,4 +42,4 @@ exts_list = [ }), ] -moduleclass = 'data' +moduleclass = 'bio' From c8c407d2407fabfff025f4147b264c93ad195333 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 30 Sep 2021 13:39:07 +0200 Subject: [PATCH 1450/9987] Disable CPU affinity at compile time --- ...3-3.2.9-foss-2021a.eb => pftoolsV3-3.2.10-foss-2021a.eb} | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/pftoolsV3/{pftoolsV3-3.2.9-foss-2021a.eb => pftoolsV3-3.2.10-foss-2021a.eb} (88%) diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.9-foss-2021a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.10-foss-2021a.eb similarity index 88% rename from easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.9-foss-2021a.eb rename to easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.10-foss-2021a.eb index 55883fbb0da..0f27a4e56f9 100644 --- a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.9-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.10-foss-2021a.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'pftoolsV3' -version = '3.2.9' +version = '3.2.10' homepage = 'https://github.com/sib-swiss/pftools3' description = """A suite of tools to build and search generalized profiles (protein and DNA).""" @@ -18,7 +18,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/'] -checksums = ['f074a34b182110a851aae74c3a0406b0561d9020c027933690f1dc701b751f9c'] +checksums = ['a0376f67531655985d7f52468d4f2a491c122c799ac8bfed486990cb0c1f6171'] builddependencies = [ ('CMake', '3.20.1'), @@ -38,6 +38,8 @@ dependencies = [ configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX:PATH=%(installdir)s -DCMAKE_BUILD_TYPE=Release ' configure_cmd += '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON ' +# Disable affinity at compile time for old processors +configure_cmd += '-DUSE_AFFINITY=OFF ' configure_cmd += '../pftools3-%(version)s' runtest = 'test' From 106c9de090d87fbab0653e4f0dc51b694e76cf8b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 30 Sep 2021 15:17:20 +0200 Subject: [PATCH 1451/9987] add missing XZ dependency for recent LibTIFF versions --- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 5 +++-- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb | 5 +++-- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb | 5 +++-- .../easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb | 3 ++- .../easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb | 3 ++- 5 files changed, 13 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb index 43be2ea49e0..13c0efa7735 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -7,7 +7,7 @@ # $Id$ # # This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ +# https://hpcbios.readthedocs.org/en/latest/ ## easyblock = 'ConfigureMake' @@ -30,7 +30,8 @@ builddependencies = [('binutils', '2.35')] dependencies = [ ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.5') + ('libjpeg-turbo', '2.0.5'), + ('XZ', '5.2.5'), ] configopts = " --enable-ld-version-script " diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb index afb2bc14767..08840af0126 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb @@ -7,7 +7,7 @@ # $Id$ # # This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ +# https://hpcbios.readthedocs.org/en/latest/ ## easyblock = 'ConfigureMake' @@ -30,7 +30,8 @@ builddependencies = [('binutils', '2.32')] dependencies = [ ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.3') + ('libjpeg-turbo', '2.0.3'), + ('XZ', '5.2.4'), ] configopts = " --enable-ld-version-script " diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb index ee0d9664265..bd383fd4d95 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb @@ -7,7 +7,7 @@ # $Id$ # # This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/ +# https://hpcbios.readthedocs.org/en/latest/ ## easyblock = 'ConfigureMake' @@ -30,7 +30,8 @@ builddependencies = [('binutils', '2.34')] dependencies = [ ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.4') + ('libjpeg-turbo', '2.0.4'), + ('XZ', '5.2.5'), ] configopts = " --enable-ld-version-script " diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb index ea453d26399..1635714a985 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb @@ -19,7 +19,8 @@ builddependencies = [('binutils', '2.36.1')] dependencies = [ ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.6') + ('libjpeg-turbo', '2.0.6'), + ('XZ', '5.2.5'), ] configopts = " --enable-ld-version-script " diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb index d6c6f6e6216..434419116fc 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb @@ -19,7 +19,8 @@ builddependencies = [('binutils', '2.37')] dependencies = [ ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.6') + ('libjpeg-turbo', '2.0.6'), + ('XZ', '5.2.5'), ] configopts = " --enable-ld-version-script " From 17d125b78d5ae754fadd177b7e87147437c01cb4 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 30 Sep 2021 15:49:21 +0200 Subject: [PATCH 1452/9987] changed CUDAcore -> CUDA --- .../m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb index 8d0ed77770f..167c912f097 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -36,7 +36,7 @@ checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] builddependencies = [ ('binutils', '2.36.1'), ('patchelf', '0.12'), - ('CUDAcore', '11.3.1', '', True), + ('CUDA', '11.3.1', '', True), ] skip_rpath_check = True From e024b728695e89487acc2cc64bdceae8f0f30b37 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 30 Sep 2021 18:15:54 +0200 Subject: [PATCH 1453/9987] adding easyconfigs: buildenv-default-intel-2021a.eb, buildenv-default-foss-2021a.eb, buildenv-default-foss-2021a-CUDA-11.3.1.eb --- ...buildenv-default-foss-2021a-CUDA-11.3.1.eb | 19 +++++++++++++++++++ .../b/buildenv/buildenv-default-foss-2021a.eb | 13 +++++++++++++ .../buildenv/buildenv-default-intel-2021a.eb | 13 +++++++++++++ 3 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2021a.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..1cba3eeb025 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,19 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('UCX-CUDA', '1.10.0', versionsuffix), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a.eb new file mode 100644 index 00000000000..f45715e4ed9 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2021a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2021a.eb new file mode 100644 index 00000000000..c7230112191 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2021a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2021a'} + +moduleclass = 'devel' From 5c263892bec946edc0a2836cbb15d111f4b87d1b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 30 Sep 2021 21:54:21 +0200 Subject: [PATCH 1454/9987] also add jbigkit and zstd --- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 5 ++++- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb | 5 ++++- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb | 5 ++++- .../easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb | 5 ++++- .../easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb | 5 ++++- 5 files changed, 20 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb index 13c0efa7735..c2e41230be6 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -32,9 +32,12 @@ dependencies = [ ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.5'), ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('zstd', '1.4.5'), ] -configopts = " --enable-ld-version-script " +configopts = "--enable-ld-version-script " +configopts += '--disable-webp --disable-libdeflate ' sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb index 08840af0126..43672697339 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb @@ -32,9 +32,12 @@ dependencies = [ ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.3'), ('XZ', '5.2.4'), + ('jbigkit', '2.1'), + ('zstd', '1.4.4'), ] -configopts = " --enable-ld-version-script " +configopts = "--enable-ld-version-script " +configopts += '--disable-webp --disable-libdeflate ' sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb index bd383fd4d95..69ec3684019 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb @@ -32,9 +32,12 @@ dependencies = [ ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.4'), ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('zstd', '1.4.4'), ] -configopts = " --enable-ld-version-script " +configopts = "--enable-ld-version-script " +configopts += '--disable-webp --disable-libdeflate ' sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb index 1635714a985..bf4e3e54c68 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb @@ -21,9 +21,12 @@ dependencies = [ ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.6'), ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('zstd', '1.4.9'), ] -configopts = " --enable-ld-version-script " +configopts = "--enable-ld-version-script " +configopts += '--disable-webp --disable-libdeflate ' sanity_check_paths = { 'files': ['bin/tiffinfo'], diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb index 434419116fc..7d9585aa7b5 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb @@ -21,9 +21,12 @@ dependencies = [ ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.6'), ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('zstd', '1.5.0'), ] -configopts = " --enable-ld-version-script " +configopts = "--enable-ld-version-script " +configopts += '--disable-webp --disable-libdeflate ' sanity_check_paths = { 'files': ['bin/tiffinfo'], From 1acb4b1cebabc57fa7d5a87d3d72e639168c8bec Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 30 Sep 2021 22:23:31 +0200 Subject: [PATCH 1455/9987] adding easyconfigs: jbigkit-2.1-GCCcore-11.2.0.eb --- .../j/jbigkit/jbigkit-2.1-GCCcore-11.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..038787a2fc9 --- /dev/null +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'jbigkit' +version = '2.1' + +homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' + +description = """JBIG-KIT is a software implementation of the JBIG1 data + compression standard (ITU-T T.82), which was designed for bi-level image + data, such as scanned documents.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_libpath.patch', + '%(name)s-%(version)s_shlib.patch', +] +checksums = [ + 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932', # jbigkit-2.1.tar.gz + '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce', # jbigkit-2.1_libpath.patch + '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696', # jbigkit-2.1_shlib.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +files_to_copy = [ + (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), + (['libjbig/jbig85.h', 'libjbig/jbig.h'], 'include'), + (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libjbig85.a', 'lib/libjbig.a', + 'bin/pbmtojbg', 'bin/jbgtopbm', + 'include/jbig.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' From 61abae10d71fbf1dc68edd46d42edea4eaf14ccc Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 1 Oct 2021 13:54:23 +0200 Subject: [PATCH 1456/9987] adding easyconfigs: intel-2021.09.eb, HPL-2.3-intel-2021.09.eb, HPCG-3.1-intel-2021.09.eb, intel-compilers-2021.4.0.eb, UCX-1.11.2-GCCcore-11.2.0.eb, impi-2021.4.0-intel-compilers-2021.4.0.eb, iimpi-2021.09.eb, imkl-2021.4.0-iimpi-2021.09.eb --- .../h/HPCG/HPCG-3.1-intel-2021.09.eb | 17 +++++++ .../h/HPL/HPL-2.3-intel-2021.09.eb | 21 ++++++++ .../easyconfigs/i/iimpi/iimpi-2021.09.eb | 18 +++++++ .../i/imkl/imkl-2021.4.0-iimpi-2021.09.eb | 14 ++++++ .../impi-2021.4.0-intel-compilers-2021.4.0.eb | 16 ++++++ .../intel-compilers-2021.4.0.eb | 32 ++++++++++++ .../easyconfigs/i/intel/intel-2021.09.eb | 21 ++++++++ .../u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb | 50 +++++++++++++++++++ 8 files changed, 189 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021.09.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2021.09.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2021.09.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iimpi-2021.09.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2021.09.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021.09.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021.09.eb new file mode 100644 index 00000000000..b1e53b4652b --- /dev/null +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021.09.eb @@ -0,0 +1,17 @@ +name = 'HPCG' +version = '3.1' + +homepage = 'https://software.sandia.gov/hpcg' +description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than + the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" + +toolchain = {'name': 'intel', 'version': '2021.09'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://www.hpcg-benchmark.org/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4'] + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2021.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2021.09.eb new file mode 100644 index 00000000000..838465dd999 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2021.09.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2021.09'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2021.09.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2021.09.eb new file mode 100644 index 00000000000..5bc754033a7 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2021.09.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2021.09' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2021.4.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', local_comp_ver, '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iimpi-2021.09.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iimpi-2021.09.eb new file mode 100644 index 00000000000..2e474b7e657 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iimpi-2021.09.eb @@ -0,0 +1,14 @@ +name = 'imkl' +version = '2021.4.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2021.09'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] +sources = ['l_onemkl_p_%(version)s.640_offline.sh'] +checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..a0c8a98edd8 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.4.0-intel-compilers-2021.4.0.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.4.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18186/'] +sources = ['l_mpi_oneapi_p_%(version)s.441_offline.sh'] +checksums = ['cc4b7072c61d0bd02b1c431b22d2ea3b84b967b59d2e587e77a9e7b2c24f2a29'] + +dependencies = [('UCX', '1.11.2')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..b12d0b8bb3c --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2021.4.0.eb @@ -0,0 +1,32 @@ +name = 'intel-compilers' +version = '2021.4.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18209/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.3201_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18210/'], + 'filename': 'l_fortran-compiler_p_%(version)s.3224_offline.sh', + }, +] +checksums = [ + # l_dpcpp-cpp-compiler_p_2021.4.0.3201_offline.sh + '9206bff1c2fdeb1ca0d5f79def90dcf3e6c7d5711b9b5adecd96a2ba06503828', + 'de2fcf40e296c2e882e1ddf2c45bb8d25aecfbeff2f75fcd7494068d621eb7e0', # l_fortran-compiler_p_2021.4.0.3224_offline.sh +] + +local_gccver = '11.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.37', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2021.09.eb b/easybuild/easyconfigs/i/intel/intel-2021.09.eb new file mode 100644 index 00000000000..34c8a44dfe7 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2021.09.eb @@ -0,0 +1,21 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2021.09' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2021.4.0' +local_gccver = '11.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.37', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', local_comp_ver, '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5fcb4154143 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.11.2' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = ['UCX-1.10.0-dynamic_modules.patch'] +checksums = [ + 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df', # ucx-1.11.2.tar.gz + '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.11'), + ('numactl', '2.0.14'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From 6d003a8137de86dbd070116521e7d64bac794e33 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 1 Oct 2021 15:17:39 +0100 Subject: [PATCH 1457/9987] adding easyconfigs: OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb --- .../OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb new file mode 100644 index 00000000000..409a191aeb9 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.8' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpi', 'version': '2021.09'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TGZ] +checksums = ['0e24c39bf68194f27a3b630aa99c17a11cd0c86020a2a8fb5cf1465dc1e344a5'] + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From e7a5e6c62c25ef7fbcb716995977333482241e29 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 1 Oct 2021 16:29:47 +0200 Subject: [PATCH 1458/9987] Update to UCX 1.11.2 and remove 1.11.0 --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 2 +- ...-1.11.0-GCCcore-11.2.0.eb => UCX-1.11.2-GCCcore-11.2.0.eb} | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/u/UCX/{UCX-1.11.0-GCCcore-11.2.0.eb => UCX-1.11.2-GCCcore-11.2.0.eb} (91%) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index ee8f19a6c14..32613c0931f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -32,7 +32,7 @@ dependencies = [ ('zlib', '1.2.11'), ('hwloc', '2.5.0'), ('libevent', '2.1.12'), - ('UCX', '1.11.0'), + ('UCX', '1.11.2'), ('libfabric', '1.13.0'), ('PMIx', '4.1.0'), ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb similarity index 91% rename from easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb index 847d1c18e3b..5fcb4154143 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'UCX' -version = '1.11.0' +version = '1.11.2' homepage = 'https://www.openucx.org/' description = """Unified Communication X @@ -16,7 +16,7 @@ source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.gz'] patches = ['UCX-1.10.0-dynamic_modules.patch'] checksums = [ - 'b7189b69fe0e16e3c03784ef674e45687a9c520750bd74a45125c460ede37647', # ucx-1.11.0.tar.gz + 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df', # ucx-1.11.2.tar.gz '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch ] From d2a86a4df1224e7d83ac2af15a4922c9cc2e5ea0 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Fri, 1 Oct 2021 15:48:23 +0100 Subject: [PATCH 1459/9987] Updated source_urls since the old one stopped working. --- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-foss-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-foss-2019b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-foss-2019b.eb index d41c0493821..7c93955f97a 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-foss-2019b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-foss-2019b.eb @@ -10,7 +10,7 @@ description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} -source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['fb22d14fad42203809dc46d046b001149ec4e901b23882bd4a80619157fd9b21'] From 11f755b46666cd6e016f1bac2816e5b92a214374 Mon Sep 17 00:00:00 2001 From: "benjamin.czaja" Date: Fri, 1 Oct 2021 17:37:31 +0200 Subject: [PATCH 1460/9987] adding easyconfigs: ABINIT-9.4.2-foss-2021a.eb --- .../a/ABINIT/ABINIT-9.4.2-foss-2021a.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-foss-2021a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-foss-2021a.eb new file mode 100644 index 00000000000..5308b74a7de --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-foss-2021a.eb @@ -0,0 +1,67 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.4.2' + +homepage = 'https://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d40886f5c8b138bb4aa1ca05da23388eb70a682790cfe5020ecce4db1b1a76bc'] + +builddependencies = [ + ('Python', '3.9.5'), +] +dependencies = [ + ('libxc', '5.1.5'), + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), + ('HDF5', '1.10.7'), + ('Wannier90', '3.1.0'), +] + + + +# Needed due to changes in GCC10. +configopts = 'FCFLAGS="-fallow-argument-mismatch -ffree-line-length-none $FCFLAGS" ' +configopts += 'FFLAGS="-fallow-argument-mismatch $FFLAGS" ' + +# Ensure MPI +configopts += '--with-mpi="yes" --enable-openmp="no" ' +# configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# BLAS/Lapack from OpenBLAS +configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="${LIBLAPACK_MT}" ' + +# FFTW +configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' From 9ebb43e0fc3abef68ecd7eb5c07da7ff8e9a3a5c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Oct 2021 02:03:29 +0200 Subject: [PATCH 1461/9987] adding easyconfigs: PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb --- ...tric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 00000000000..b9d2000662f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '2.0.1' +local_pytorchver = '1.9.0' +versionsuffix = '-PyTorch-%s' % local_pytorchver + +homepage = 'https://github.com/rusty1s/pytorch_geometric' +description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', local_pytorchver), + ('scikit-learn', '0.23.2'), + ('scikit-image', '0.18.1'), + ('numba', '0.52.0'), + ('h5py', '3.1.0'), + ('tqdm', '4.56.2'), + ('RDFlib', '5.0.0'), + ('ASE', '3.20.1'), +] + +use_pip = True + +exts_list = [ + ('googledrivedownloader', '0.4', { + 'modulename': 'google_drive_downloader', + 'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'], + }), + ('plyfile', '0.7.4', { + 'checksums': ['9e9a18d22a3158fcd74df38761d43a7facc6df75126f2ab9f4e9a5d4d2188652'], + }), + ('torch_scatter', '2.0.8', { + 'checksums': ['d71aab489b5288a6c96e9f9a7c9e13c54774dcb55a99a40e6cd1aca8be9ef3e6'], + }), + ('torch_sparse', '0.6.12', { + 'checksums': ['85db85bd45855cde4be093c7e2413b962b21b31151ad7eacd19ca4e2808bced2'], + }), + ('torch_cluster', '1.5.9', { + 'checksums': ['96209e9f3f073c8e7fe91fbf7dd2cdd8655622d14dfc95a7618b4893a658dca5'], + }), + ('torch_spline_conv', '1.2.1', { + 'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'], + }), + ('python-louvain', '0.15', { + 'modulename': 'community.community_louvain', + 'checksums': ['2a856edfbe29952a60a5538a84bb78cca18f6884a88b9325e85a11c8dd4917eb'], + }), + ('torch_geometric', version, { + 'checksums': ['6ec91a407ca95959c1ca2009f6702983540ccafabc7f2553d56755ff8b393f4f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From f30a7ec653e132c5877b55537d7cc8e5f69fdde9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Oct 2021 02:42:19 +0200 Subject: [PATCH 1462/9987] Update to newer numba --- .../PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb index b9d2000662f..eabae5e96c2 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -15,7 +15,7 @@ dependencies = [ ('PyTorch', local_pytorchver), ('scikit-learn', '0.23.2'), ('scikit-image', '0.18.1'), - ('numba', '0.52.0'), + ('numba', '0.53.1'), ('h5py', '3.1.0'), ('tqdm', '4.56.2'), ('RDFlib', '5.0.0'), From 262792b4f8b1341b532f44af8abe9e9fbe93afbb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 3 Oct 2021 16:21:10 +0200 Subject: [PATCH 1463/9987] Update easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb Co-authored-by: SebastianAchilles --- .../PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb index eabae5e96c2..c3de9720e69 100644 --- a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.0.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -20,6 +20,7 @@ dependencies = [ ('tqdm', '4.56.2'), ('RDFlib', '5.0.0'), ('ASE', '3.20.1'), + ('YACS', '0.1.8'), ] use_pip = True From 66a3d71d0877fc693dbc1b8b4c23511770b22d40 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 3 Oct 2021 20:09:07 +0200 Subject: [PATCH 1464/9987] add missing header file --- .../easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb | 4 ++-- .../easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.3.0.eb | 4 ++-- .../easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.2.0.eb | 4 ++-- .../easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-8.3.0.eb | 7 ++++--- .../easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-9.3.0.eb | 4 ++-- 5 files changed, 12 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb index 5d3338697be..cc565979b70 100644 --- a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.2.0.eb @@ -32,14 +32,14 @@ builddependencies = [ files_to_copy = [ (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), - (['libjbig/jbig85.h', 'libjbig/jbig.h'], 'include'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), ] sanity_check_paths = { 'files': ['lib/libjbig85.a', 'lib/libjbig.a', 'bin/pbmtojbg', 'bin/jbgtopbm', - 'include/jbig.h', + 'include/jbig.h', 'include/jbig_ar.h', ], 'dirs': ['bin', 'include', 'lib'] } diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.3.0.eb index cad518c7e6f..c457de1248e 100644 --- a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-10.3.0.eb @@ -31,14 +31,14 @@ builddependencies = [ files_to_copy = [ (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), - (['libjbig/jbig85.h', 'libjbig/jbig.h'], 'include'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), ] sanity_check_paths = { 'files': ['lib/libjbig85.a', 'lib/libjbig.a', 'bin/pbmtojbg', 'bin/jbgtopbm', - 'include/jbig.h', + 'include/jbig.h', 'include/jbig_ar.h', ], 'dirs': ['bin', 'include', 'lib'] } diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.2.0.eb index 038787a2fc9..c6915b68bf7 100644 --- a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.2.0.eb @@ -31,14 +31,14 @@ builddependencies = [ files_to_copy = [ (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), - (['libjbig/jbig85.h', 'libjbig/jbig.h'], 'include'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), ] sanity_check_paths = { 'files': ['lib/libjbig85.a', 'lib/libjbig.a', 'bin/pbmtojbg', 'bin/jbgtopbm', - 'include/jbig.h', + 'include/jbig.h', 'include/jbig_ar.h', ], 'dirs': ['bin', 'include', 'lib'] } diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-8.3.0.eb index 56ad0a98b56..127ae1d7b62 100644 --- a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-8.3.0.eb @@ -4,7 +4,8 @@ easyblock = 'MakeCp' name = 'jbigkit' version = '2.1' -homepage = '' +homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' + description = """JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents.""" @@ -31,14 +32,14 @@ builddependencies = [ files_to_copy = [ (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), - (['libjbig/jbig85.h', 'libjbig/jbig.h'], 'include'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), ] sanity_check_paths = { 'files': ['lib/libjbig85.a', 'lib/libjbig.a', 'bin/pbmtojbg', 'bin/jbgtopbm', - 'include/jbig.h', + 'include/jbig.h', 'include/jbig_ar.h', ], 'dirs': ['bin', 'include', 'lib'] } diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-9.3.0.eb index 5a349c2cea2..17e3d06b740 100644 --- a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-9.3.0.eb @@ -32,14 +32,14 @@ builddependencies = [ files_to_copy = [ (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), - (['libjbig/jbig85.h', 'libjbig/jbig.h'], 'include'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), ] sanity_check_paths = { 'files': ['lib/libjbig85.a', 'lib/libjbig.a', 'bin/pbmtojbg', 'bin/jbgtopbm', - 'include/jbig.h', + 'include/jbig.h', 'include/jbig_ar.h', ], 'dirs': ['bin', 'include', 'lib'] } From 4a591bb3ed435971a4170e805243380c7a6a5078 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Oct 2021 09:39:56 +0200 Subject: [PATCH 1465/9987] fix source URL for SUNDIALS 5.x --- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb | 2 +- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb | 4 ++-- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb | 2 +- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb index 5418498d31f..e1d296dc51e 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb @@ -10,7 +10,7 @@ description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} -source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['fb22d14fad42203809dc46d046b001149ec4e901b23882bd4a80619157fd9b21'] diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb index cf95385b969..f7e64184772 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb @@ -10,9 +10,9 @@ description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} -source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] +checksums = ['48da7baa8152ddb22aed1b02d82d1dbb4fbfea22acf67634011aa0303a100a43'] builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb index 33df49c169e..8bc61e3d1eb 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb @@ -10,7 +10,7 @@ description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation toolchain = {'name': 'fosscuda', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} -source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb index 218050a7703..2568c787c13 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb @@ -10,7 +10,7 @@ description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} -source_urls = ['https://computation.llnl.gov/projects/sundials/download/'] +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] From 4d97691d4ba52a936a018c38e49f779f857c8570 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 4 Oct 2021 08:51:44 +0100 Subject: [PATCH 1466/9987] Add Perl and Python runtime dependencies to Bowtie2 --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb | 4 ++++ easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb | 4 ++++ easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb | 4 ++++ easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb | 4 ++++ 4 files changed, 16 insertions(+) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb index 279170f1b0e..d2fc1902e1e 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb @@ -28,9 +28,13 @@ checksums = ['566d6fb01a361883747103d797308ee4bdb70f6db7d27bfc72a520587815df22'] dependencies = [ ('tbb', '2020.1'), ('zlib', '1.2.11'), + ('Perl', '5.30.2'), + ('Python', '3.8.2'), ] # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} +sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb index 2a3ee99cd47..90ac886ce21 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb @@ -28,9 +28,13 @@ checksums = ['4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e'] dependencies = [ ('tbb', '2020.3'), ('zlib', '1.2.11'), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), ] # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} +sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb index c7e85fbbdc5..ee714aaff14 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb @@ -28,9 +28,13 @@ checksums = ['4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e'] dependencies = [ ('tbb', '2020.1'), ('zlib', '1.2.11'), + ('Perl', '5.30.2'), + ('Python', '3.8.2'), ] # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} +sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb index ce1402a0d0f..85afb32d7a8 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb @@ -27,9 +27,13 @@ checksums = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] dependencies = [ ('zlib', '1.2.11'), + ('Perl', '5.32.1'), + ('Python', '3.9.5'), ] # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} +sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] + moduleclass = 'bio' From 2566ceda5b4bf153d84fd05b9db7925ca7bfe3c4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 4 Oct 2021 09:08:25 +0100 Subject: [PATCH 1467/9987] revert changes to GCC 9.3.0 and 10.2.0 versions due to pipeline failures --- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb | 4 ---- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb | 4 ---- easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb | 4 ---- 3 files changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb index d2fc1902e1e..279170f1b0e 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.1-GCC-9.3.0.eb @@ -28,13 +28,9 @@ checksums = ['566d6fb01a361883747103d797308ee4bdb70f6db7d27bfc72a520587815df22'] dependencies = [ ('tbb', '2020.1'), ('zlib', '1.2.11'), - ('Perl', '5.30.2'), - ('Python', '3.8.2'), ] # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} -sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb index 90ac886ce21..2a3ee99cd47 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-10.2.0.eb @@ -28,13 +28,9 @@ checksums = ['4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e'] dependencies = [ ('tbb', '2020.3'), ('zlib', '1.2.11'), - ('Perl', '5.32.0'), - ('Python', '3.8.6'), ] # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} -sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb index ee714aaff14..c7e85fbbdc5 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.2-GCC-9.3.0.eb @@ -28,13 +28,9 @@ checksums = ['4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e'] dependencies = [ ('tbb', '2020.1'), ('zlib', '1.2.11'), - ('Perl', '5.30.2'), - ('Python', '3.8.2'), ] # to add script folder to path just uncomment this line # modextrapaths = {'PATH': 'scripts'} -sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] - moduleclass = 'bio' From 5ee46cd155aacefeca947673cd15b659a799bd36 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 4 Oct 2021 10:17:22 +0200 Subject: [PATCH 1468/9987] simple source specification with new easyblock. use CUDA/11.3.1 --- .../m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb index e040a5698e6..ed127443bf8 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb @@ -21,10 +21,7 @@ BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -sources = [{ - 'filename': '%(name)s_%(version)s.zip', - 'extract_cmd': 'unzip -j %s' -}] +sources = ['%(name)s_%(version)s.zip'] checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] # No longer directly downloadable, available from https://msg.ucsf.edu/software @@ -35,7 +32,7 @@ checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] # of MotionCor2 builddependencies = [ ('binutils', '2.35'), - ('CUDAcore', '11.1.1', '', True), + ('CUDA', '11.3.1', '', True), ] dependencies = [ From 538c3867a185a4a38b8f0e6e2b075d087611dd76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Oct 2021 10:26:47 +0200 Subject: [PATCH 1469/9987] add alternate valid checksum for SUNDIALS 5.7.0 source tarball (only PDF files in doc/ differ) --- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb | 5 ++++- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb | 5 ++++- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb index f7e64184772..51543acdb79 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb @@ -12,7 +12,10 @@ toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['48da7baa8152ddb22aed1b02d82d1dbb4fbfea22acf67634011aa0303a100a43'] +# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, +# other for new source tarball downloaded from GitHub +checksums = [('8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3', + '48da7baa8152ddb22aed1b02d82d1dbb4fbfea22acf67634011aa0303a100a43')] builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb index 8bc61e3d1eb..ccf4e479638 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb @@ -12,7 +12,10 @@ toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] +# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, +# other for new source tarball downloaded from GitHub +checksums = [('8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3', + '48da7baa8152ddb22aed1b02d82d1dbb4fbfea22acf67634011aa0303a100a43')] builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb index 2568c787c13..5c283e4de39 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb @@ -12,7 +12,10 @@ toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3'] +# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, +# other for new source tarball downloaded from GitHub +checksums = [('8d6dd094feccbb8d6ecc41340ec16a65fabac82ed4415023f6d7c1c2390ea2f3', + '48da7baa8152ddb22aed1b02d82d1dbb4fbfea22acf67634011aa0303a100a43')] builddependencies = [('CMake', '3.18.4')] From df5651b5369bb31ff21cd111447b239e498a64be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 4 Oct 2021 17:54:05 +0200 Subject: [PATCH 1470/9987] New download urls for SCOTCH 6.1.0 --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb | 6 +++--- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb | 6 +++--- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb index 4963e9ab5b4..08a103b4d30 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb @@ -8,9 +8,9 @@ static mapping, and sparse matrix block ordering, and sequential mesh and hyperg toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'pic': True} -source_urls = ['https://gforge.inria.fr/frs/download.php/file/38352/'] -sources = ['%(namelower)s_%(version)s.tar.gz'] -checksums = ['a3bc3fa3b243fcb52f8d68de4272562a0328afb18a96f535724d284e36730485'] +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb index 1b0ac4abc44..19d7a5bdb04 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb @@ -11,9 +11,9 @@ static mapping, and sparse matrix block ordering, and sequential mesh and hyperg toolchain = {'name': 'gompi', 'version': '2021a'} toolchainopts = {'pic': True} -source_urls = ['https://gforge.inria.fr/frs/download.php/file/38352/'] -sources = ['%(namelower)s_%(version)s.tar.gz'] -checksums = ['a3bc3fa3b243fcb52f8d68de4272562a0328afb18a96f535724d284e36730485'] +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb index 2bded2513ca..6e94531d821 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb @@ -8,9 +8,9 @@ static mapping, and sparse matrix block ordering, and sequential mesh and hyperg toolchain = {'name': 'iimpi', 'version': '2020b'} toolchainopts = {'pic': True} -source_urls = ['https://gforge.inria.fr/frs/download.php/file/38352/'] -sources = ['%(namelower)s_%(version)s.tar.gz'] -checksums = ['a3bc3fa3b243fcb52f8d68de4272562a0328afb18a96f535724d284e36730485'] +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] dependencies = [ ('zlib', '1.2.11'), From 73a0f392ec66ec48bb97294399292918300ed5bb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 5 Oct 2021 14:23:45 +0200 Subject: [PATCH 1471/9987] adding easyconfigs: Dalton-2020.0-intel-2021a-i8.eb and patches: Dalton-2020.0_fix-uninits.patch, Dalton-2020.0_use-EB-install-for-dalton-script.patch --- .../d/Dalton/Dalton-2020.0-intel-2021a-i8.eb | 58 +++++++++++++++++ .../d/Dalton/Dalton-2020.0_fix-uninits.patch | 65 +++++++++++++++++++ ...0.0_use-EB-install-for-dalton-script.patch | 35 ++++++++++ 3 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2020.0_fix-uninits.patch create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use-EB-install-for-dalton-script.patch diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb new file mode 100644 index 00000000000..26faa7184bb --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'Dalton' +version = '2020.0' +versionsuffix = '-i8' + +homepage = 'https://daltonprogram.org/' +description = """The Dalton code is a powerful tool for a wide range of molecular properties + at different levels of theory. + Any published work arising from use of one of the Dalton2016 programs + must acknowledge that by a proper reference, + https://www.daltonprogram.org/www/citation.html.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'i8': True, 'usempi': True, 'openmp': True} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://gitlab.com/dalton', + 'repo_name': 'dalton', + 'tag': '2020.0', + 'recursive': True, + }, +}] +patches = [ + '%(name)s-2016-fix-cmake-install.patch', + '%(name)s-%(version)s_use-EB-install-for-dalton-script.patch', + '%(name)s-%(version)s_fix-uninits.patch', + '%(name)s-2016-fix-bad-includepath-add.patch', +] +checksums = [ + None, # no checksum for Dalton-2020.0.tar.gz source tarball which is created via 'git clone' + '3159b03a488d6f5ee23d468be02ea62eacd08cbdf68cd64ef4e5a0d469a6718b', # Dalton-2016-fix-cmake-install.patch + # Dalton-2020.0_use-EB-install-for-dalton-script.patch + '507f17638f687c4482263c2f1ccc938278772868eb78694db0be3cd58c3162d1', + 'bc446cd1a9fb63836d1d621eb92be65fcd3a46095a0ba4ecb5b7f292dccbb609', # Dalton-2020.0_fix-uninits.patch + '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Python', '3.9.5'), +] + +configopts = '-DENABLE_MPI=ON ' +configopts += '-DENABLE_OMP=ON ' +# Only enable for BLAS/LAPACK having 8 byte integers (basically MKL) adjust the configopts 'i8' option accordingly +configopts += '-DENABLE_64BIT_INTEGERS=ON ' +configopts += '-DENABLE_SCALAPACK=ON ' +configopts += '-DBLACS_IMPLEMENTATION=intelmpi ' + +sanity_check_paths = { + 'files': ['bin/dalton', 'bin/dalton.x'], + 'dirs': ['basis'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_fix-uninits.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_fix-uninits.patch new file mode 100644 index 00000000000..e1725c45f54 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_fix-uninits.patch @@ -0,0 +1,65 @@ +# Fix a bunch of uninitialized variables. +# +# Åke Sandgren +diff -ru dalton.orig/DALTON/abacus/herpar.F dalton/DALTON/abacus/herpar.F +--- dalton.orig/DALTON/abacus/herpar.F 2021-10-05 13:33:24.000000000 +0200 ++++ dalton/DALTON/abacus/herpar.F 2021-10-05 13:48:35.109344495 +0200 +@@ -1351,6 +1351,15 @@ + kfree = kwork + lfree = lwork + ++#ifdef VAR_MPI ++ ! Make dummy allocation so we don't trip on uninitialized ++ ! variables in call to HER_RVINIT ++ nelement_d = 1 ++ nelement_f = 1 ++ call memallocmpi(nelement_d*8,dmat_p) ++ call memallocmpi(nelement_f*8,fmat_p) ++#endif ++ + ! Receive initialization from master - 1 - common block information + ! ================================================================= + ! +@@ -1375,6 +1384,9 @@ + nelement_f = n2basx*rma_win_info%nmat_max_wo_win + end if + #ifdef VAR_MPI ++ ! Free the dummy allocations before doing the real allocations ++ call memfreempi(dmat_buff) ++ call memfreempi(fmat_buff) + call memallocmpi(nelement_d*8,dmat_p) + call memallocmpi(nelement_f*8,fmat_p) + #endif +diff -ru dalton.orig/DALTON/cc/ccsd_input.F dalton/DALTON/cc/ccsd_input.F +--- dalton.orig/DALTON/cc/ccsd_input.F 2021-10-05 13:33:24.000000000 +0200 ++++ dalton/DALTON/cc/ccsd_input.F 2021-10-05 13:50:01.384748651 +0200 +@@ -101,6 +101,7 @@ + LOGICAL SET, NEWDEF, SIRFF + CHARACTER PROMPT*1, WORD*7, TABLE(NTABLE)*7, WORD1*7 + CHARACTER*(80) LINE ++ INTEGER ITEST + C + SAVE SET + CSONIA/FRAN/TBPEDERSEN +@@ -138,6 +139,9 @@ + C + IF (SET) RETURN + SET = .TRUE. ++ ++ ITEST = 0 ++ + C + CSPAS:8/11-13: Initialization of CCSDINP, CCLR, CCSDSYM + C and other common blocks is moved to a new routine +diff -ru dalton.orig/DALTON/sirius/sirqmmm.F dalton/DALTON/sirius/sirqmmm.F +--- dalton.orig/DALTON/sirius/sirqmmm.F 2021-10-05 13:33:24.000000000 +0200 ++++ dalton/DALTON/sirius/sirqmmm.F 2021-10-05 13:50:43.212473540 +0200 +@@ -4333,6 +4333,8 @@ + CALL MPIXBCAST(CONMAT,1,'LOGICAL',MASTER) + + KELF = 1 ++ KELFEL = 1 ++ KELFNU = 1 + IF (SPLDIP) THEN + KELFEL = KELF + 3*POLDIM + KELFNU = KELFEL + 3*POLDIM diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use-EB-install-for-dalton-script.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use-EB-install-for-dalton-script.patch new file mode 100644 index 00000000000..63059233bd0 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use-EB-install-for-dalton-script.patch @@ -0,0 +1,35 @@ +# Use EasyBuild installation dir for dalton wrapper. +# No need to try to find it in a complicated way. +# +# Åke Sandgren +diff -ru dalton.orig/dalton.in dalton/dalton.in +--- dalton.orig/dalton.in 2021-10-05 13:33:25.000000000 +0200 ++++ dalton/dalton.in 2021-10-05 13:41:38.244136976 +0200 +@@ -16,17 +16,7 @@ + dalton="dalton" + DALTON="DALTON" + +-# radovan: this is to figure out the location of this script +-# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in +-SOURCE="${BASH_SOURCE[0]}" +-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink +- SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" +- SOURCE="$(readlink "$SOURCE")" +- # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +- [[ $SOURCE != /* ]] && SOURCE="$SCRIPT_DIR/$SOURCE" +-done +-SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" +- ++SCRIPT_DIR="$EBROOTDALTON" + + ## If your computer ressource uses modules, then you can make sure the right modules are loaded + ## by uncommenting and adapting the two lines starting with #module following this comment. +@@ -38,7 +28,7 @@ + #module purge + #module load python intel openmpi-i8 + +-DALTON_EXECUTABLE=$SCRIPT_DIR/$dalton.x ++DALTON_EXECUTABLE=$SCRIPT_DIR/bin/$dalton.x + + which mpirun > /dev/null # check if mpirun exists, if not, then assume mpiexec + if [ $? -eq 0 ]; then From 36a1010780211c210beb5faf617f32dacff5327a Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 5 Oct 2021 15:53:12 +0200 Subject: [PATCH 1472/9987] first installation of nanomax-analysis-utils into 2020b --- .../f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb | 26 ++++++++++++ ...nanomax-analysis-utils-0.4.3-foss-2020b.eb | 27 ++++++++++++ ...max-analysis-utils-0.4.3-fosscuda-2020b.eb | 27 ++++++++++++ .../PyOpenCL-2021.1.2-fosscuda-2020b.eb | 33 +++++++++++++++ .../s/silx/silx-0.14.0-fosscuda-2020b.eb | 41 +++++++++++++++++++ 5 files changed, 154 insertions(+) create mode 100644 easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..7126f817a8a --- /dev/null +++ b/easybuild/easyconfigs/f/FabIO/FabIO-0.11.0-fosscuda-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'FabIO' +version = '0.11.0' + +homepage = 'http://www.silx.org' +description = """FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. +FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), +for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers +(as a python dictionary) and datasets (as a numpy ndarray of integers or floats).""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1d2fcf58006c82548a16004e607d4518613d49e4a2f02a3797703eee2b39c6d8'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb new file mode 100644 index 00000000000..4affa742800 --- /dev/null +++ b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'nanomax-analysis-utils' +version = '0.4.3' + +github_account = 'maxiv-science' +homepage = "https://github.com/%(github_account)s/nanomax-analysis-utils" +description = """A set of tools for handling and analysing data at the NanoMAX beamline.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('silx', '0.14.0'), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['887874f9ab8ba42b31e47a51503aa85be7b215073151415d38b231f748072a42'] + +options = {'modulename': 'nmutils'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb new file mode 100644 index 00000000000..738e464088f --- /dev/null +++ b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.3-fosscuda-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'nanomax-analysis-utils' +version = '0.4.3' + +github_account = 'maxiv-science' +homepage = "https://github.com/%(github_account)s/nanomax-analysis-utils" +description = """A set of tools for handling and analysing data at the NanoMAX beamline.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('silx', '0.14.0'), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['887874f9ab8ba42b31e47a51503aa85be7b215073151415d38b231f748072a42'] + +options = {'modulename': 'nmutils'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb new file mode 100644 index 00000000000..cec1342f8e7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2021.1.2' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('pocl', '1.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2021.1', { + 'checksums': ['073ae22a0ae946e2db97164f2eb24a599cd3a51430384aa40859dffd73056c40'], + }), + ('pyopencl', version, { + 'checksums': ['18871bc80c5a94869521189cf2c04d72c88367a441a9a033f72f66792ac33d29'], + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..fc63b3528ed --- /dev/null +++ b/easybuild/easyconfigs/s/silx/silx-0.14.0-fosscuda-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'silx' +version = '0.14.0' + +homepage = "http://www.silx.org/" +description = """The silx project provides a collection of Python packages to support the +development of data assessment, reduction and analysis applications at synchrotron radiation facilities.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('PyOpenGL', '3.1.5'), + ('matplotlib', '3.3.3'), + ('Mako', '1.1.3'), + ('Pillow', '8.0.1'), + ('FabIO', '0.11.0'), + ('Qtconsole', '5.0.2'), + ('PyOpenCL', '2021.1.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('hdf5plugin', '2.3.1', { + 'checksums': ['2f6d886012c37bf7e8e002173dd6b16e6879b8e0e9f7d2f2ef9f79db97ed28d2'], + }), + (name, version, { + 'checksums': ['17c595fe18c9eb3403a9d1f0ee6ea7b523607043c46c944573ecf406f6997866'], + }), +] + +modextrapaths = { + 'HDF5_PLUGIN_PATH': 'lib/python%(pyshortver)s/site-packages/hdf5plugin/plugins', +} + +moduleclass = 'vis' From 4d138547d54797c8985603ac7b25fe84f069e3ba Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 5 Oct 2021 16:44:30 +0100 Subject: [PATCH 1473/9987] adding easyconfigs: NAMD-2.14-foss-2020b-mpi.eb, NAMD-2.14-fosscuda-2020b.eb --- .../n/NAMD/NAMD-2.14-foss-2020b-mpi.eb | 31 +++++++++++++++++ .../n/NAMD/NAMD-2.14-fosscuda-2020b.eb | 34 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb new file mode 100644 index 00000000000..7fd2267fc96 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb @@ -0,0 +1,31 @@ +name = 'NAMD' +version = '2.14' +versionsuffix = '-mpi' + +homepage = 'https://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': False, 'pic': True} + +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] +sources = ['%(name)s_%(version)s_Source.tar.gz'] +patches = ['%(name)s-%(version)s-use_system_mremap_decl.patch'] +checksums = [ + '34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235', # NAMD_2.14_Source.tar.gz + 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch +] + +dependencies = [ + ('Tcl', '8.6.10'), +] + +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + +# Hard to make charm build the mpi version with gcc on POWER, so we don't currently try. +charm_arch = 'mpi-linux-x86_64' +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb new file mode 100644 index 00000000000..98aeeb12b8e --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb @@ -0,0 +1,34 @@ +name = 'NAMD' +version = '2.14' + +homepage = 'https://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': False, 'openmp': False, 'pic': True} + +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] +sources = [{'filename': 'NAMD_%(version)s_Source.tar.gz'}] +patches = [ + "%(name)s-%(version)s_Linux-POWER-cuda.patch", + "%(name)s-%(version)s-use_system_mremap_decl.patch" +] +checksums = [ + '34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235', # NAMD_2.14_Source.tar.gz + 'db4aeb482dfa805c859ea18940026395763169e0257401ee5341ca550029031c', # NAMD-2.14_Linux-POWER-cuda.patch + 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch +] + +# support for GCC 8+ on POWER +dependencies = [ + ('Tcl', '8.6.10'), +] + +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + +charm_arch = "multicore-linux-%(arch)s" +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' From 8f30314fc62b7eaaea77dddeb8f5cdf7d55496f3 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 6 Oct 2021 11:42:38 +0200 Subject: [PATCH 1474/9987] Added pyFAI in foss and fosscuda --- .../p/pyFAI/pyFAI-0.20.0-foss-2020b.eb | 32 +++++++++++++++++++ .../p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb new file mode 100644 index 00000000000..0bff738d5dd --- /dev/null +++ b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pyFAI' +version = '0.20.0' +versionsuffix = '-Python-%(pyver)s' + +github_account = 'silx-kit' +homepage = "https://github.com/%(github_account)s/pyFAI" +description = """Python implementation of fast azimuthal integration.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('silx', '0.14.0'), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f39f56ff58868ab7f12d6fa5c7bf6b7d111b7fa687f3816c5d8d11cb75fa82f0'] + +options = {'modulename': 'pyFAI'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +modextravars = { + 'PYFAI_OPENCL': '0', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..a034f6b4804 --- /dev/null +++ b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pyFAI' +version = '0.20.0' +versionsuffix = '-Python-%(pyver)s' + +github_account = 'silx-kit' +homepage = "https://github.com/%(github_account)s/pyFAI" +description = """Python implementation of fast azimuthal integration.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('silx', '0.14.0'), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f39f56ff58868ab7f12d6fa5c7bf6b7d111b7fa687f3816c5d8d11cb75fa82f0'] + +options = {'modulename': 'pyFAI'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +modextravars = { + 'PYFAI_OPENCL': '0', +} + +moduleclass = 'data' From 6abe1d0cf295c590c4cd057fe3f67084b48b0aed Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 6 Oct 2021 14:23:12 +0200 Subject: [PATCH 1475/9987] adding easyconfigs: Virtuoso-opensource-7.2.6.1-foss-2021a.eb --- .../Virtuoso-opensource-7.2.6.1-foss-2021a.eb | 75 +++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-foss-2021a.eb b/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-foss-2021a.eb new file mode 100644 index 00000000000..d5337dc0432 --- /dev/null +++ b/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-foss-2021a.eb @@ -0,0 +1,75 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## +easyblock = 'ConfigureMake' + +name = 'Virtuoso-opensource' +version = '7.2.6.1' + +homepage = 'https://github.com/openlink/virtuoso-opensource' +description = """Virtuoso is a high-performance and scalable Multi-Model RDBMS, Data +Integration Middleware, Linked Data Deployment, and HTTP Application Server Platform.""" +software_license = 'LicenseGPLv2' + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/openlink/virtuoso-opensource/archive/refs/tags/'] +checksums = ['73dc3d0073d3d5694da075063b75a404649c027a1f5c635a25ede52713ff7942'] + +builddependencies = [ + ('Autoconf', '2.71'), + ('Automake', '1.16.3'), + ('libtool', '2.4.6'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('gperf', '3.1'), + ('M4', '1.4.18'), + ('make', '4.3'), +] + +osdependencies = ['gawk'] +dependencies = [ + ('OpenSSL', '1.1', '', True), + ('libreadline', '8.1'), +] + +configure_cmd = 'export CFLAGS="-O3 -m64" && ' +configure_cmd += './autogen.sh && ' +configure_cmd += './configure ' +configure_cmd += ' --enable-shared --disable-static' +configure_cmd += ' --disable-imagemagick' +configure_cmd += ' --enable-aio' +configure_cmd += ' --enable-bpel-vad' +configure_cmd += ' --enable-conductor-vad' +configure_cmd += ' --disable-dbpedia-vad' +configure_cmd += ' --enable-demo-vad' +configure_cmd += ' --enable-fct-vad' +configure_cmd += ' --enable-isparql-vad' +configure_cmd += ' --enable-ods-vad' +configure_cmd += ' --enable-rdfmappers-vad' +configure_cmd += ' --enable-rdb2rdf-vad' +configure_cmd += ' --enable-sparqldemo-vad' +configure_cmd += ' --enable-syncml-vad' +configure_cmd += ' --enable-tutorial-vad' +configure_cmd += ' --with-iodbc' +configure_cmd += ' --with-readline' +configure_cmd += ' --with-pthreads' +configure_cmd += ' --with-port=11111' + +# NOTE Rename the "isql" executable (the virtuoso client), because there may be another package +# unixODBC that provides an executable with the same name. +postinstallcmds = ["cd %(installdir)s/bin/ && mv isql isqlv"] + +sanity_check_paths = { + 'files': ['bin/virtuoso-t', 'bin/isqlv'], + 'dirs': ['lib', 'var'], +} + +sanity_check_commands = ["isqlv --help"] + +moduleclass = 'data' From 03b1758b36bea4b1b740fa519417d96380a84c52 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 6 Oct 2021 14:47:17 +0200 Subject: [PATCH 1476/9987] added pyFAI (foss and fosscuda 2020b) as well as pmca for fosscuda 2020b --- .../p/pyFAI/pyFAI-0.20.0-foss-2020b.eb | 1 - .../p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb | 1 - .../p/pymca/pymca-5.6.3-fosscuda-2020b.eb | 35 +++++++++++++++++++ 3 files changed, 35 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb index 0bff738d5dd..1a72ee67c64 100644 --- a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-foss-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonPackage' name = 'pyFAI' version = '0.20.0' -versionsuffix = '-Python-%(pyver)s' github_account = 'silx-kit' homepage = "https://github.com/%(github_account)s/pyFAI" diff --git a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb index a034f6b4804..c5766420e2b 100644 --- a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.20.0-fosscuda-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonPackage' name = 'pyFAI' version = '0.20.0' -versionsuffix = '-Python-%(pyver)s' github_account = 'silx-kit' homepage = "https://github.com/%(github_account)s/pyFAI" diff --git a/easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb new file mode 100644 index 00000000000..473c95d50eb --- /dev/null +++ b/easybuild/easyconfigs/p/pymca/pymca-5.6.3-fosscuda-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'pymca' +version = '5.6.3' + +github_account = 'vasole' +homepage = "https://github.com/%(github_account)s/pymca" +description = """The PyMca X-Ray Fluorescence Toolkit, including PyMca5 and fisx.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('silx', '0.14.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = { + 'source_urls': [GITHUB_SOURCE], + 'sources': ['v%(version)s.tar.gz'], +} + +exts_list = [ + ('fisx', '1.2.0', { + 'checksums': ['868642045725552126d43331cdec7d7a6a85251d54011b4a0360fc90b02041e4'], + }), + (name, version, { + 'checksums': ['36b37f51a550b1262346e853ec8d3f1e8dd45adfc1a80e3626dc35e197eadb8c'], + 'modulename': 'PyMca5', + }), +] + +moduleclass = 'data' From 14e90605951d0bc8a57bb8bd47332a8eaf80db6e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 6 Oct 2021 17:43:20 +0100 Subject: [PATCH 1477/9987] adding easyconfigs: SHAPEIT4-4.2.2-foss-2020b.eb, SHAPEIT4-4.2.2-foss-2021a.eb and patches: SHAPEIT4_4.2.2_use_EB_settings.patch --- .../s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb | 45 +++++++++++++++++++ .../s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2021a.eb | 45 +++++++++++++++++++ .../SHAPEIT4_4.2.2_use_EB_settings.patch | 38 ++++++++++++++++ 3 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4_4.2.2_use_EB_settings.patch diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb new file mode 100644 index 00000000000..e19de04e820 --- /dev/null +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb @@ -0,0 +1,45 @@ +easyblock = "MakeCp" + +name = 'SHAPEIT4' +version = '4.2.2' + +homepage = 'https://odelaneau.github.io/shapeit4/' +description = """ +SHAPEIT4 is a fast and accurate method for estimation of haplotypes +(aka phasing) for SNP array and high coverage sequencing data. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True, 'cstd': 'c++11'} + +github_account = 'odelaneau' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch'] +checksums = [ + '9f109e307b5cc22ab68e7bf77de2429a9bbb2212d66303386e6a3dd81a5bc556', # v4.2.2.tar.gz + '92ed45545bfcde7b1fbe079e6321ccae00865c8f0f66a924e872967d762df885', # SHAPEIT4_4.2.2_use_EB_settings.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('Boost', '1.74.0'), + ('HTSlib', '1.12'), +] + +buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts ' +buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options ' +buildopts += 'CXX="$CXX" CXXFLAG="$CXXFLAGS" LDFLAG="$CXXFLAGS" ' + +files_to_copy = [(['bin/shapeit4.2'], 'bin'), 'maps'] + +sanity_check_paths = { + 'files': ["bin/shapeit4.2"], + 'dirs': ['maps'] +} + +sanity_check_commands = ['shapeit4.2 --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2021a.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2021a.eb new file mode 100644 index 00000000000..0b8cc7f9c21 --- /dev/null +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = "MakeCp" + +name = 'SHAPEIT4' +version = '4.2.2' + +homepage = 'https://odelaneau.github.io/shapeit4/' +description = """ +SHAPEIT4 is a fast and accurate method for estimation of haplotypes +(aka phasing) for SNP array and high coverage sequencing data. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True, 'cstd': 'c++11'} + +github_account = 'odelaneau' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch'] +checksums = [ + '9f109e307b5cc22ab68e7bf77de2429a9bbb2212d66303386e6a3dd81a5bc556', # v4.2.2.tar.gz + '92ed45545bfcde7b1fbe079e6321ccae00865c8f0f66a924e872967d762df885', # SHAPEIT4_4.2.2_use_EB_settings.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('Boost', '1.76.0'), + ('HTSlib', '1.12'), +] + +buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts ' +buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options ' +buildopts += 'CXX="$CXX" CXXFLAG="$CXXFLAGS" LDFLAG="$CXXFLAGS" ' + +files_to_copy = [(['bin/shapeit4.2'], 'bin'), 'maps'] + +sanity_check_paths = { + 'files': ["bin/shapeit4.2"], + 'dirs': ['maps'] +} + +sanity_check_commands = ['shapeit4.2 --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4_4.2.2_use_EB_settings.patch b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4_4.2.2_use_EB_settings.patch new file mode 100644 index 00000000000..37300b3dfea --- /dev/null +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4_4.2.2_use_EB_settings.patch @@ -0,0 +1,38 @@ +--- shapeit4-4.2.2/makefile 2021-09-07 13:08:23.000000000 +0100 ++++ shapeit4-4.2.2.new/makefile 2021-10-06 17:34:49.006112748 +0100 +@@ -1,14 +1,14 @@ + #COMPILER MODE C++11 +-CXX=g++ -std=c++11 ++#CXX=g++ -std=c++11 + + #HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS] +-HTSLIB_INC=$(HOME)/Tools/htslib-1.11 +-HTSLIB_LIB=$(HOME)/Tools/htslib-1.11/libhts.a ++#HTSLIB_INC=$(HOME)/Tools/htslib-1.11 ++#HTSLIB_LIB=$(HOME)/Tools/htslib-1.11/libhts.a + + #BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS] +-BOOST_INC=/usr/include +-BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a +-BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a ++#BOOST_INC=/usr/include ++#BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a ++#BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a + + #HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS] + #HTSLIB_INC=/software/UHTS/Analysis/samtools/1.4/include +@@ -25,12 +25,12 @@ + #CXXFLAG=-O3 -march=native + + #Good performance and portable on most CPUs +-CXXFLAG=-O3 -mavx2 -mfma ++#CXXFLAG=-O3 -mavx2 -mfma + + #Portable version without avx2 (much slower) + #CXXFLAG=-O3 + +-LDFLAG=-O3 ++#LDFLAG=-O3 + + + #DYNAMIC LIBRARIES From a81e0a4efe865e2d4b686da37751b0f32a34ce5c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 6 Oct 2021 17:53:58 +0100 Subject: [PATCH 1478/9987] Use HTSlib 1.11 for 2020/b for consistency --- easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb index e19de04e820..c3694317b3e 100644 --- a/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2020b.eb @@ -26,7 +26,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('XZ', '5.2.5'), ('Boost', '1.74.0'), - ('HTSlib', '1.12'), + ('HTSlib', '1.11'), ] buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts ' From 89b5e957079d5714b77d284a22d7168facccf37a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Oct 2021 20:34:49 +0200 Subject: [PATCH 1479/9987] adding easyconfigs: OpenBLAS-0.3.18-GCC-11.2.0.eb --- .../o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb new file mode 100644 index 00000000000..04bb5898705 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +name = 'OpenBLAS' +version = '0.3.18' + +homepage = 'http://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), +] +checksums = [ + '1632c1e8cca62d8bed064b37747e331a1796fc46f688626337362bf0d16aeadb', # v0.3.18.tar.gz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From 395e39b810c15e9573a3196e03188af33fa8dc1b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 6 Oct 2021 20:57:52 +0100 Subject: [PATCH 1480/9987] adding easyconfigs: expecttest-0.1.3-GCCcore-10.3.0.eb --- .../expecttest-0.1.3-GCCcore-10.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1b233bad335 --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.1.3' + +homepage = "https://github.com/ezyang/expecttest" +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['83057695811d94128aed13ed094a070db90e0a92ea40071f8ee073cbab57149a'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 91b7cac1d7fbc255c05bed6a48e8f5228f392a7d Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Thu, 7 Oct 2021 17:36:32 +0200 Subject: [PATCH 1481/9987] Adds Autotools as build dependency, since an autoreconf is done --- easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb index 76c9562ade8..96ae02657f9 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.6-GCCcore-10.3.0.eb @@ -41,6 +41,7 @@ preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' builddependencies = [ # use same binutils version that was used when building GCCcore ('binutils', '2.36.1'), + ('Autotools', '20210128'), ('CubeLib', '4.6'), ] From 046af184b0775b9adfbf9ca3914bb7c0c42aeb5e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 7 Oct 2021 17:45:11 +0200 Subject: [PATCH 1482/9987] adding easyconfigs: libspatialindex-1.9.3-GCCcore-11.2.0.eb --- .../libspatialindex-1.9.3-GCCcore-11.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e23f052cdc4 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'libspatialindex' +version = '1.9.3' + +homepage = 'https://libspatialindex.org' +description = """C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/libspatialindex/libspatialindex/releases/download/%(version)s/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['47d8779e32477b330e46b62fb7e62cb812caee5d8e684c35cb635a42a749f3fc'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +sanity_check_paths = { + 'files': ['lib/libspatialindex.so', 'lib/libspatialindex.%s' % SHLIB_EXT], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' From b91bc11abaa3cf1d3e2d16938c1cc0708e54d648 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 7 Oct 2021 18:02:45 +0200 Subject: [PATCH 1483/9987] adding easyconfigs: AlphaFold-2.0.1-foss-2020b.eb, AlphaFold-2.0.1-fosscuda-2020b.eb and patches: AlphaFold-2.0.1_data-dep-paths.patch, AlphaFold-2.0.1_setup_rm_tfcpu.patch --- .../a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb | 181 +++++++++++++++++ .../AlphaFold-2.0.1-fosscuda-2020b.eb | 185 ++++++++++++++++++ .../AlphaFold-2.0.1_data-dep-paths.patch | 147 ++++++++++++++ .../AlphaFold-2.0.1_setup_rm_tfcpu.patch | 15 ++ 4 files changed, 528 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_data-dep-paths.patch create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_setup_rm_tfcpu.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb new file mode 100644 index 00000000000..8806522d263 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-foss-2020b.eb @@ -0,0 +1,181 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.0.1' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('TensorFlow', '2.4.1'), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.19'), # also provides absl-py +] + +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.0.1_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.0.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + 'b3dfdd3877343516f98bc49f8adbbb5101e8900524470816d4495a22ed986857', # v2.0.1.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '60c60abc254e713787843a1a53fcccefc56d242fa1cfa826701a5ff39227bd52', # AlphaFold-2.0.1_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + # source tarball on PyPI is missing requirements.txt, + # see https://github.com/deepmind/dm-haiku/issues/44 + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + 'modulename': 'haiku', + }), + ('dm-tree', '0.1.6', { + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + 'modulename': 'tree', + }), + ('websocket-client', '1.2.1', { + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + 'modulename': 'websocket', + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + # see https://github.com/google/ml_collections/issues/7 + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb new file mode 100644 index 00000000000..5c6a924e870 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1-fosscuda-2020b.eb @@ -0,0 +1,185 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.0.1' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('TensorFlow', '2.4.1'), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.19'), # also provides absl-py +] +configopts = "-DCUDA_CUDA_LIBRARY=${EBROOTCUDA}/lib64/stubs/libcuda.so " +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.0.1_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.0.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + 'b3dfdd3877343516f98bc49f8adbbb5101e8900524470816d4495a22ed986857', # v2.0.1.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '60c60abc254e713787843a1a53fcccefc56d242fa1cfa826701a5ff39227bd52', # AlphaFold-2.0.1_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '83dc82a8b1c647eb7e217aef683153e98a4fc7f871a85280976c92a1bfe28f27', # AlphaFold-2.0.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_data-dep-paths.patch new file mode 100644 index 00000000000..d5ab8482924 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_data-dep-paths.patch @@ -0,0 +1,147 @@ +pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data +(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py); +pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) +update 2.0.0 -> 2.0.1: Thomas Hoffmann (EMBL); allow feature --preset=reduced_dbs +diff -ru alphafold-2.0.1/run_alphafold.py alphafold-2.0.1_data-dep-paths/run_alphafold.py +--- alphafold-2.0.1/run_alphafold.py 2021-09-10 14:34:22.000000000 +0200 ++++ alphafold-2.0.1_data-dep-paths/run_alphafold.py 2021-10-07 12:22:23.393621081 +0200 +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python + # Copyright 2021 DeepMind Technologies Limited + # + # Licensed under the Apache License, Version 2.0 (the "License"); +@@ -36,6 +37,54 @@ + import numpy as np + # Internal import (7716). + ++use_reduced_dbs = any("--preset=reduced_dbs" in s for s in sys.argv[1:]) ++ ++data_dir = os.getenv('ALPHAFOLD_DATA_DIR') ++if data_dir: ++ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters.fa') ++ uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') ++ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') ++ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') ++ obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') ++ if use_reduced_dbs: ++ small_bfd_database_path = os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta') ++ uniclust30_database_path = None ++ bfd_database_path = None ++ else: ++ small_bfd_database_path = None ++ bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') ++ uniclust30_database_path = os.path.join(data_dir, 'uniclust30', 'uniclust30_2018_08', 'uniclust30_2018_08') ++else: ++ sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!") ++ uniref90_database_path = None ++ mgnify_database_path = None ++ bfd_database_path = None ++ uniclust30_database_path = None ++ pdb70_database_path = None ++ template_mmcif_dir = None ++ obsolete_pdbs_path = None ++ small_bfd_database_path = None ++ ++hmmer_root = os.getenv('EBROOTHMMER') ++if hmmer_root: ++ jackhmmer_binary_path = os.path.join(hmmer_root, 'bin', 'jackhmmer') ++else: ++ jackhmmer_binary_path = '/usr/bin/jackhmmer' ++ ++hhsuite_root = os.getenv('EBROOTHHMINSUITE') ++if hhsuite_root: ++ hhblits_binary_path = os.path.join(hhsuite_root, 'bin', 'hhblits') ++ hhsearch_binary_path = os.path.join(hhsuite_root, 'bin', 'hhsearch') ++else: ++ hhblits_binary_path = '/usr/bin/hhblits' ++ hhsearch_binary_path = '/usr/bin/hhsearch' ++ ++kalign_root = os.getenv('EBROOTKALIGN') ++if kalign_root: ++ kalign_binary_path = os.path.join(kalign_root, 'bin', 'kalign') ++else: ++ kalign_binary_path = '/usr/bin/kalign' ++ + flags.DEFINE_list('fasta_paths', None, 'Paths to FASTA files, each containing ' + 'one sequence. Paths should be separated by commas. ' + 'All FASTA paths must have a unique basename as the ' +@@ -44,32 +93,32 @@ + flags.DEFINE_string('output_dir', None, 'Path to a directory that will ' + 'store the results.') + flags.DEFINE_list('model_names', None, 'Names of models to use.') +-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') +-flags.DEFINE_string('jackhmmer_binary_path', '/usr/bin/jackhmmer', ++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') ++flags.DEFINE_string('jackhmmer_binary_path', jackhmmer_binary_path, + 'Path to the JackHMMER executable.') +-flags.DEFINE_string('hhblits_binary_path', '/usr/bin/hhblits', ++flags.DEFINE_string('hhblits_binary_path', hhblits_binary_path, + 'Path to the HHblits executable.') +-flags.DEFINE_string('hhsearch_binary_path', '/usr/bin/hhsearch', ++flags.DEFINE_string('hhsearch_binary_path', hhsearch_binary_path, + 'Path to the HHsearch executable.') +-flags.DEFINE_string('kalign_binary_path', '/usr/bin/kalign', ++flags.DEFINE_string('kalign_binary_path', kalign_binary_path, + 'Path to the Kalign executable.') +-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 ' ++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify ' ++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD ' ++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD ' + 'database for use by HHblits.') +-flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small ' ++flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small ' + 'version of BFD used with the "reduced_dbs" preset.') +-flags.DEFINE_string('uniclust30_database_path', None, 'Path to the Uniclust30 ' ++flags.DEFINE_string('uniclust30_database_path', uniclust30_database_path, 'Path to the Uniclust30 ' + 'database for use by HHblits.') +-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 ' ++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 ' + 'database for use by HHsearch.') +-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with ' ++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with ' + 'template mmCIF structures, each named .cif') + flags.DEFINE_string('max_template_date', None, 'Maximum template release date ' + 'to consider. Important if folding historical test sets.') +-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a ' ++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a ' + 'mapping from obsolete PDB IDs to the PDB IDs of their ' + 'replacements.') + flags.DEFINE_enum('preset', 'full_dbs', +@@ -89,7 +138,6 @@ + 'deterministic, because processes like GPU inference are ' + 'nondeterministic.') + FLAGS = flags.FLAGS +- + MAX_TEMPLATE_HITS = 20 + RELAX_MAX_ITERATIONS = 0 + RELAX_ENERGY_TOLERANCE = 2.39 +@@ -217,6 +265,9 @@ + raise app.UsageError('Too many command-line arguments.') + + use_small_bfd = FLAGS.preset == 'reduced_dbs' ++ if use_small_bfd and data_dir: ++ bfd_database_path = None ++ uniclust30_database_path = None + _check_flag('small_bfd_database_path', FLAGS.preset, + should_be_set=use_small_bfd) + _check_flag('bfd_database_path', FLAGS.preset, +@@ -297,14 +348,8 @@ + 'fasta_paths', + 'output_dir', + 'model_names', +- 'data_dir', + 'preset', +- 'uniref90_database_path', +- 'mgnify_database_path', +- 'pdb70_database_path', +- 'template_mmcif_dir', + 'max_template_date', +- 'obsolete_pdbs_path', + ]) + + app.run(main) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_setup_rm_tfcpu.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_setup_rm_tfcpu.patch new file mode 100644 index 00000000000..04c18169b24 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_setup_rm_tfcpu.patch @@ -0,0 +1,15 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/09 +# change requirements in setup.py from tensorflow-cpu to tensorflow. +diff -ru alphafold-1d43aaff941c84dc56311076b58795797e49107b/setup.py alphafold-1d43aaff941c84dc56311076b58795797e49107b_setup_py_remove_tfcpu/setup.py +--- alphafold-1d43aaff941c84dc56311076b58795797e49107b/setup.py 2021-09-10 14:34:22.000000000 +0200 ++++ alphafold-1d43aaff941c84dc56311076b58795797e49107b_setup_py_remove_tfcpu/setup.py 2021-09-20 11:13:44.817481819 +0200 +@@ -39,7 +39,7 @@ + 'ml-collections', + 'numpy', + 'scipy', +- 'tensorflow-cpu', ++ 'tensorflow', + ], + tests_require=['mock'], + classifiers=[ +Only in alphafold-1d43aaff941c84dc56311076b58795797e49107b_setup_py_remove_tfcpu: .setup.py.swo From 0d0e327e77a1d0f9cfc7aa4ca86fe5d665fed7cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Oct 2021 20:31:59 +0200 Subject: [PATCH 1484/9987] adding easyconfigs: MMseqs2-13-45111-20211006-gompi-2020b.eb --- .../MMseqs2-13-45111-20211006-gompi-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211006-gompi-2020b.eb diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211006-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211006-gompi-2020b.eb new file mode 100644 index 00000000000..59646fc55e3 --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211006-gompi-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +local_commit = '49c2b70' +version = '13-45111-20211006' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['bb70cd38e6e27f136263250c0c6a9f045d1e4a883d2a93a54e708fb8e2ec4098'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [('bzip2', '1.0.8')] + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' From b28f9670bb731751e2872bcf7656a2d0c14e24a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Oct 2021 20:44:25 +0200 Subject: [PATCH 1485/9987] adding easyconfigs: canu-2.2-GCCcore-10.3.0.eb --- .../c/canu/canu-2.2-GCCcore-10.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..688753bfca0 --- /dev/null +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'canu' +version = '2.2' + +homepage = 'https://canu.readthedocs.io' +description = "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/marbl/canu/releases/download/v%(version)s/'] +sources = ['canu-%(version)s.tar.xz'] +checksums = ['e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404'] + +builddependencies = [ + ('binutils', '2.36.1'), + # Makefile checks git version, before making (futile) attempt to update git submodules + ('git', '2.32.0', '-nodocs'), +] + +dependencies = [ + ('Java', '11', '', True), + ('Perl', '5.32.1'), + ('gnuplot', '5.4.2'), +] + +start_dir = 'src' + +files_to_copy = ['build/bin', 'build/lib', 'build/share', 'README*'] + +sanity_check_paths = { + 'files': ['bin/bogart', 'bin/canu', 'bin/meryl', 'bin/overlapPair', 'lib/libcanu.a'], + 'dirs': ['lib/site_perl', 'share'], +} +sanity_check_commands = [ + "canu -version", + "canu -options", +] + +moduleclass = 'bio' From 12924ddac75c0c31a8fd61e4194a50ae7c544db2 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 8 Oct 2021 09:08:56 +0200 Subject: [PATCH 1486/9987] adding easyconfigs: swifter-1.0.9-foss-2020b.eb, swifter-1.0.9-fosscuda-2020b.eb --- .../s/swifter/swifter-1.0.9-foss-2020b.eb | 33 +++++++++++++++++++ .../s/swifter/swifter-1.0.9-fosscuda-2020b.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb new file mode 100644 index 00000000000..c379d2ef490 --- /dev/null +++ b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-foss-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'swifter' +version = '1.0.9' + +homepage = 'https://github.com/jmcarpenter2/swifter' +description = """ +A package which efficiently applies any function to a pandas dataframe or +series in the fastest available manner.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('dask', '2021.2.0'), + ('tqdm', '4.56.2'), + ('IPython', '7.18.1'), +] + +exts_list = [ + ('modin', '0.8.2', { + 'checksums': ['0e224911e21e6a7134baa2a3162c91af2594bf75b9c2d7e39a3f0d10e38793a5'], + }), + (name, version, { + 'checksums': ['14cec10ff1ecdfbcfdd68985366b07add5f9b7bb77116720f47c88f29f048c3e'], + }), +] + +sanity_pip_check = True +use_pip = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb new file mode 100644 index 00000000000..083b6cf0603 --- /dev/null +++ b/easybuild/easyconfigs/s/swifter/swifter-1.0.9-fosscuda-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'swifter' +version = '1.0.9' + +homepage = 'https://github.com/jmcarpenter2/swifter' +description = """ +A package which efficiently applies any function to a pandas dataframe or +series in the fastest available manner.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('dask', '2021.2.0'), + ('tqdm', '4.56.2'), + ('IPython', '7.18.1'), +] + +exts_list = [ + ('modin', '0.8.2', { + 'checksums': ['0e224911e21e6a7134baa2a3162c91af2594bf75b9c2d7e39a3f0d10e38793a5'], + }), + (name, version, { + 'checksums': ['14cec10ff1ecdfbcfdd68985366b07add5f9b7bb77116720f47c88f29f048c3e'], + }), +] + +sanity_pip_check = True +use_pip = True + +moduleclass = 'data' From c0150fc5378680f8fac6dde885588b6876a9bbb7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Oct 2021 09:42:53 +0100 Subject: [PATCH 1487/9987] adding easyconfigs: OpenCV-4.5.3-foss-2021a-contrib.eb, OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb --- ...CV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb | 85 +++++++++++++++++++ .../OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb | 84 ++++++++++++++++++ 2 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb new file mode 100644 index 00000000000..89445e4b399 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb @@ -0,0 +1,85 @@ +name = 'OpenCV' +version = '4.5.3' +versionsuffix = '-CUDA-%(cudaver)s-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [ + {'source_urls': ['https://github.com/opencv/opencv/archive/'], + 'download_filename': '%(version)s.zip', 'filename': SOURCELOWER_ZIP}, + {'source_urls': ['https://github.com/opencv/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', 'filename': '%(namelower)s_contrib-%(version)s.zip'}, + {'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + 'a61e7a4618d353140c857f25843f39b2abe5f451b018aab1604ef0bc34cd23d5', # opencv-4.5.3.zip + 'dc3317950cf0d6cab6d24ec8df864d5e7c4efe39627dbd1c7c177dc12a8bcd78', # opencv_contrib-4.5.3.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.2'), + ('freetype', '2.10.4'), + ('HarfBuzz', '2.8.1'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.2.0'), + ('libwebp', '1.2.0'), + ('OpenEXR', '3.0.1'), + ('JasPer', '2.0.28'), + ('Java', '11', '', True), + ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('GLib', '2.68.2'), + ('GTK3', '3.24.29'), + ('HDF5', '1.10.7'), # needed by hdf from contrib + ('CUDA', '11.3.1', '', True), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules ' +configopts += '-DFREETYPE_FOUND=ON ' +configopts += '-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/ ' +configopts += '-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DHARFBUZZ_FOUND=ON ' +configopts += '-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz ' +configopts += '-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DBUILD_opencv_python2=OFF ' + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (l, SHLIB_EXT) for l in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb new file mode 100644 index 00000000000..9dd6c211740 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb @@ -0,0 +1,84 @@ +name = 'OpenCV' +version = '4.5.3' +versionsuffix = '-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [ + {'source_urls': ['https://github.com/opencv/opencv/archive/'], + 'download_filename': '%(version)s.zip', 'filename': SOURCELOWER_ZIP}, + {'source_urls': ['https://github.com/opencv/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', 'filename': '%(namelower)s_contrib-%(version)s.zip'}, + {'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + 'a61e7a4618d353140c857f25843f39b2abe5f451b018aab1604ef0bc34cd23d5', # opencv-4.5.3.zip + 'dc3317950cf0d6cab6d24ec8df864d5e7c4efe39627dbd1c7c177dc12a8bcd78', # opencv_contrib-4.5.3.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.2'), + ('freetype', '2.10.4'), + ('HarfBuzz', '2.8.1'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.2.0'), + ('libwebp', '1.2.0'), + ('OpenEXR', '3.0.1'), + ('JasPer', '2.0.28'), + ('Java', '11', '', True), + ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('GLib', '2.68.2'), + ('GTK3', '3.24.29'), + ('HDF5', '1.10.7'), # needed by hdf from contrib +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules ' +configopts += '-DFREETYPE_FOUND=ON ' +configopts += '-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/ ' +configopts += '-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DHARFBUZZ_FOUND=ON ' +configopts += '-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz ' +configopts += '-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DBUILD_opencv_python2=OFF ' + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (l, SHLIB_EXT) for l in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' From 615414fee8e64db164efb2ad7ac4fc558f60b649 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Oct 2021 09:52:43 +0100 Subject: [PATCH 1488/9987] add cuDNN --- .../o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb index 89445e4b399..f9b43027447 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb @@ -51,6 +51,7 @@ dependencies = [ ('GTK3', '3.24.29'), ('HDF5', '1.10.7'), # needed by hdf from contrib ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), ] # XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz From 159730456dc51ac87f8d97f89d65a43ad7322a70 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 11 Oct 2021 11:50:30 +0200 Subject: [PATCH 1489/9987] {bio}[foss/2020b] QUAST 5.0.2 /w foss-2020b and Python 3 --- .../q/QUAST/QUAST-5.0.2-foss-2020b.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb new file mode 100644 index 00000000000..c9d652ca8b8 --- /dev/null +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'QUAST' +version = '5.0.2' + +homepage = 'https://github.com/ablab/%(namelower)s' +description = """QUAST evaluates genome assemblies by computing various metrics. +It works both with and without reference genomes. The tool accepts multiple +assemblies, thus is suitable for comparison.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + + +dependencies = [ + ('Python', '3.8.6'), + ('Perl', '5.32.0'), + ('matplotlib', '3.3.3'), + ('Java', '11', '', True), + ('Boost', '1.74.0'), +] + +use_pip = True + +exts_list = [ + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + (name, version, { + 'install_target': 'install_full', + 'modulename': 'quast_libs', + 'patches': ['QUAST-%(version)s_fix-Python-3.8.patch'], + 'source_tmpl': 'quast_%(version)s.tar.gz', + 'source_urls': ['https://github.com/ablab/quast/archive/'], + 'checksums': [ + '9f30c03e0bfd261492fe6b72fb07645bdee5b29d741f75fc75857b6fa095d91d', # quast_5.0.2.tar.gz + '8ae7ebf45e5368ebc058fc208822a23d32ce1052bd53fd8c3aaa4ad14d3c95aa', # QUAST-5.0.2_fix-Python-3.8.patch + ], + }), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s quast.py quast"] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "wget quast.sf.net/test_data.tar.gz && " + "tar xzf test_data.tar.gz && " + "%(namelower)s.py --test && " + "rm ./test_data.tar.gz ./test_data -rf", + "%(namelower)s -h", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 2add5bbe07483098f3b33ae131941cbacb67e55d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 11 Oct 2021 12:17:32 +0200 Subject: [PATCH 1490/9987] rm switches should be before arguments --- easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb index c9d652ca8b8..53e95a0065d 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb @@ -50,7 +50,7 @@ sanity_check_commands = [ "wget quast.sf.net/test_data.tar.gz && " "tar xzf test_data.tar.gz && " "%(namelower)s.py --test && " - "rm ./test_data.tar.gz ./test_data -rf", + "rm -rf ./test_data.tar.gz ./test_data", "%(namelower)s -h", ] From c9e32e302baf1b048a4c756c4242c8dd6bab0697 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 11 Oct 2021 14:38:15 +0200 Subject: [PATCH 1491/9987] Drop tcmalloc from SymEngine as it causes crashes with scipy --- .../easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb index 714a0b11fbf..fc0fedead98 100644 --- a/easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/SymEngine/SymEngine-0.7.0-GCC-10.3.0.eb @@ -23,11 +23,10 @@ dependencies = [ ('MPC', '1.2.1'), ('LLVM', '11.1.0'), ('FLINT', '2.7.1'), - ('gperftools', '2.9.1'), ] local_opts = '-DWITH_OPENMP=ON -DWITH_SYMENGINE_RCP=ON -DWITH_COTIRE=OFF ' -local_opts += '-DWITH_MPFR=ON -DWITH_MPC=ON -DWITH_LLVM=ON -DWITH_BFD=ON -DWITH_TCMALLOC=ON -DWITH_FLINT=ON ' +local_opts += '-DWITH_MPFR=ON -DWITH_MPC=ON -DWITH_LLVM=ON -DWITH_BFD=ON -DWITH_FLINT=ON ' configopts = [local_opts + '-DBUILD_SHARED_LIBS=OFF', local_opts + '-DBUILD_SHARED_LIBS=ON'] runtest = 'test' From 959e31694f38dd5c7c28a97486550c1a4407e9b7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 12 Oct 2021 12:50:31 +0200 Subject: [PATCH 1492/9987] Dependencies of a commercial software (almost a bee) --- .../GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb | 58 +++++++++++++++++++ .../i/imkl/imkl-2020.4.304-NVHPC-21.2.eb | 39 +++++++++++++ .../OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 34 +++++++++++ .../q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb | 21 +++++++ .../UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb | 52 +++++++++++++++++ 5 files changed, 204 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb create mode 100644 easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb new file mode 100644 index 00000000000..4e78c65fb6b --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.1' +local_cudaversion = '11.2.1' +versionsuffix = '-CUDA-%s' % local_cudaversion + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cecc7dcc071107f77396f5553c9109790b6d2298ae29eb2dbbdd52b2a213e4ea'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CUDAcore', local_cudaversion, '', True), # needed by GDRCopy binaries, which are tools for testing + ('Check', '0.15.2'), +] + +# This easyconfig only installs the library and binaries of GDRCopy. Please +# keep in mind that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] + +local_envopts = "PREFIX=%(installdir)s CUDA=$EBROOTCUDACORE" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib exes %s" % local_envopts +installopts = local_envopts + +sanity_check_paths = { + 'files': ['bin/copybw', 'bin/copylat', 'bin/sanity', 'lib/libgdrapi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb new file mode 100644 index 00000000000..bf4b096ac1f --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.4.304' + +homepage = 'https://software.intel.com/mkl' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'NVHPC', 'version': '21.2'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16917/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['2314d46536974dbd08f2a4e4f9e9a155dc7e79e2798c74e7ddfaad00a5917ea5'] + +dontcreateinstalldir = True + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb new file mode 100644 index 00000000000..8ef2dc343ed --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -0,0 +1,34 @@ +name = 'OpenMPI' +version = '4.0.5' +versionsuffix = '-CUDA-11.2.1' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'NVHPC', 'version': '21.2'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), + ('libevent', '2.1.12'), + ('UCX', '1.9.0', versionsuffix), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), +] + +# disable MPI1 compatibility for now, see what breaks... +configopts = '--with-cuda=$EBROOTCUDACORE ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb b/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb new file mode 100644 index 00000000000..6fc8e3fd56e --- /dev/null +++ b/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'QD' +version = '2.3.17' +versionsuffix = '-20160110' +local_gitcommit = 'a5dbb61' + +homepage = 'https://github.com/scibuilder/QD' +description = "Quad Double computation package" + +toolchain = {'name': 'NVHPC', 'version': '21.2'} + +source_urls = ['https://github.com/scibuilder/QD/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_gitcommit, 'filename': SOURCE_TAR_GZ}] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['qdmod', 'qd']], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb new file mode 100644 index 00000000000..fd3d6e7b5dc --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -0,0 +1,52 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.9.0' +local_cudaversion = '11.2.1' +versionsuffix = '-CUDA-%s' % local_cudaversion + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['a7a2c8841dc0d5444088a4373dc9b9cc68dbffcd917c1eba92ca8ed8e5e635fb'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('numactl', '2.0.13'), + ('CUDAcore', local_cudaversion, '', True), + ('GDRCopy', '2.1', versionsuffix), +] + +configure_cmd = "contrib/configure-release" +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' +configopts += '--with-cuda=$EBROOTCUDACORE --with-gdrcopy=$EBROOTGDRCOPY ' + +prebuildopts = 'unset CUDA_CFLAGS && unset LIBS && ' +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From 1109711e9e1cf283ec5b453c83b58777a7a89db2 Mon Sep 17 00:00:00 2001 From: paulm Date: Tue, 12 Oct 2021 13:54:45 +0200 Subject: [PATCH 1493/9987] adding easyconfigs: Mesa-demos-8.4.0-GCCcore-10.3.0.eb --- .../Mesa-demos-8.4.0-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c23446f9094 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +# Mesa demos and utilities, such as glxinfo, eglinfo and lots more + +name = 'Mesa-demos' +version = '8.4.0' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/demos/' +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['01e99c94a0184e63e796728af89bfac559795fb2a0d6f506fa900455ca5fff7d'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('freetype', '2.10.4'), +] + +dependencies = [ + ('Mesa', '21.1.1'), + ('glew', '2.1.0'), + ('libGLU', '9.0.1'), + ('freeglut', '3.2.1'), +] + +#configopts = '' + +sanity_check_paths = { + 'files': ['bin/eglinfo', 'bin/glxinfo'], + 'dirs': [] +} + +moduleclass = 'vis' From a1d9dcee549d351d3ceb3ba4c418302ffc380cc2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Tue, 12 Oct 2021 14:15:57 +0200 Subject: [PATCH 1494/9987] adding easyconfigs: radeontop-1.3-GCC-10.3.0.eb --- .../r/radeontop/radeontop-1.3-GCC-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCC-10.3.0.eb b/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..5dd45aebe3f --- /dev/null +++ b/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCC-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'radeontop' +version = '1.3' + +homepage = 'https://github.com/clbr/radeontop' +description = """View your GPU utilization, both for the total activity percent and individual blocks.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +source_urls = ['https://github.com/clbr/radeontop/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0e6abacafa3c795ee783be18b736f6dfc7ff93c6e3c3237cc7c1684863e08100'] + +dependencies = [ + ('libdrm', '2.4.106'), + ('libpciaccess', '0.16'), + ('ncurses', '6.2'), + ('X11', '20210518'), +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +buildopts = "amdgpu=1 nls=0" + +files_to_copy = [(['radeontop'], 'bin'), (['radeontop.1'], 'share/man/man1')] + +sanity_check_paths = { + 'files': ['bin/radeontop', 'share/man/man1/radeontop.1'], + 'dirs': [], +} +# We should run the below to ensure it is working, but for some reason the +# 'radeontop' tool outputs 1 for '--help' and '--version' +# sanity_check_commands = ['radeontop --help'] + +moduleclass = 'tools' From aa86ee6bfbd1dabae09011b7f018187707e25c16 Mon Sep 17 00:00:00 2001 From: paulm Date: Tue, 12 Oct 2021 14:18:45 +0200 Subject: [PATCH 1495/9987] Fix comment issue --- .../easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb index c23446f9094..1581f494543 100644 --- a/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb @@ -29,8 +29,6 @@ dependencies = [ ('freeglut', '3.2.1'), ] -#configopts = '' - sanity_check_paths = { 'files': ['bin/eglinfo', 'bin/glxinfo'], 'dirs': [] From 9a367f15847fcd8b66a186bb6c7de8c118f2c9bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Oct 2021 14:32:56 +0200 Subject: [PATCH 1496/9987] fix homepage + description in SimpleITK easyconfigs --- .../s/SimpleITK/SimpleITK-1.1.0-foss-2018a-Python-3.6.4.eb | 7 ++++--- .../s/SimpleITK/SimpleITK-1.1.0-foss-2018b-Python-3.6.6.eb | 7 ++++--- .../s/SimpleITK/SimpleITK-1.2.4-foss-2019b-Python-3.7.4.eb | 7 ++++--- 3 files changed, 12 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.1.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.1.0-foss-2018a-Python-3.6.4.eb index ccc450ac5bc..3287f55dc25 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.1.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.1.0-foss-2018a-Python-3.6.4.eb @@ -4,9 +4,10 @@ name = 'SimpleITK' version = '1.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' -description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in - datasets showing strong between-class imbalance.""" +homepage = 'http://www.simpleitk.org' +description = """ITK is an open-source, cross-platform system that provides developers with an extensive suite of + software tools for image analysis. Among them, SimpleITK is a simplified layer built on top of ITK, intended to + facilitate its use in rapid prototyping, education, interpreted languages.""" toolchain = {'name': 'foss', 'version': '2018a'} diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.1.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.1.0-foss-2018b-Python-3.6.6.eb index 251caa1d459..b354378cad9 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.1.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.1.0-foss-2018b-Python-3.6.6.eb @@ -4,9 +4,10 @@ name = 'SimpleITK' version = '1.1.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' -description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in - datasets showing strong between-class imbalance.""" +homepage = 'http://www.simpleitk.org' +description = """ITK is an open-source, cross-platform system that provides developers with an extensive suite of + software tools for image analysis. Among them, SimpleITK is a simplified layer built on top of ITK, intended to + facilitate its use in rapid prototyping, education, interpreted languages.""" toolchain = {'name': 'foss', 'version': '2018b'} diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.2.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.2.4-foss-2019b-Python-3.7.4.eb index b68bf5bcba6..9bb81967762 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.2.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-1.2.4-foss-2019b-Python-3.7.4.eb @@ -4,9 +4,10 @@ name = 'SimpleITK' version = '1.2.4' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' -description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in - datasets showing strong between-class imbalance.""" +homepage = 'http://www.simpleitk.org' +description = """ITK is an open-source, cross-platform system that provides developers with an extensive suite of + software tools for image analysis. Among them, SimpleITK is a simplified layer built on top of ITK, intended to + facilitate its use in rapid prototyping, education, interpreted languages.""" toolchain = {'name': 'foss', 'version': '2019b'} From f9948de66e8332c9318b5cb9ccbac23c2ce7742c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 12 Oct 2021 16:43:54 +0200 Subject: [PATCH 1497/9987] swicth radeontop v1.3 to GCCcore --- ...ntop-1.3-GCC-10.3.0.eb => radeontop-1.3-GCCcore-10.3.0.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/r/radeontop/{radeontop-1.3-GCC-10.3.0.eb => radeontop-1.3-GCCcore-10.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCC-10.3.0.eb b/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb similarity index 92% rename from easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCC-10.3.0.eb rename to easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb index 5dd45aebe3f..82bd7e95a15 100644 --- a/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb @@ -6,7 +6,7 @@ version = '1.3' homepage = 'https://github.com/clbr/radeontop' description = """View your GPU utilization, both for the total activity percent and individual blocks.""" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/clbr/radeontop/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] checksums = ['0e6abacafa3c795ee783be18b736f6dfc7ff93c6e3c3237cc7c1684863e08100'] @@ -20,6 +20,7 @@ dependencies = [ builddependencies = [ ('pkg-config', '0.29.2'), + ('binutils', '2.36.1'), ] buildopts = "amdgpu=1 nls=0" @@ -30,6 +31,7 @@ sanity_check_paths = { 'files': ['bin/radeontop', 'share/man/man1/radeontop.1'], 'dirs': [], } + # We should run the below to ensure it is working, but for some reason the # 'radeontop' tool outputs 1 for '--help' and '--version' # sanity_check_commands = ['radeontop --help'] From 0012656fa8833a3db9931a2943e7fe13b7ee3919 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 12 Oct 2021 16:48:10 +0200 Subject: [PATCH 1498/9987] clarify comment about lack of sanity checks in radeontop --- .../easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb index 82bd7e95a15..73d2e7e1804 100644 --- a/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb @@ -7,6 +7,7 @@ homepage = 'https://github.com/clbr/radeontop' description = """View your GPU utilization, both for the total activity percent and individual blocks.""" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + source_urls = ['https://github.com/clbr/radeontop/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] checksums = ['0e6abacafa3c795ee783be18b736f6dfc7ff93c6e3c3237cc7c1684863e08100'] @@ -32,8 +33,8 @@ sanity_check_paths = { 'dirs': [], } -# We should run the below to ensure it is working, but for some reason the -# 'radeontop' tool outputs 1 for '--help' and '--version' +# radeontop requires special permissions to access the GPU hardware and basic +# options such as '--help' and '--version' output a non-zero exit code # sanity_check_commands = ['radeontop --help'] moduleclass = 'tools' From d26ff73b844c1bb4ee311eb8ae03cab0d412d3d1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 12 Oct 2021 16:49:10 +0200 Subject: [PATCH 1499/9987] use github_account in radeontop v1.3 --- .../easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb index 73d2e7e1804..7df599480a5 100644 --- a/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/radeontop/radeontop-1.3-GCCcore-10.3.0.eb @@ -8,7 +8,8 @@ description = """View your GPU utilization, both for the total activity percent toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -source_urls = ['https://github.com/clbr/radeontop/archive/refs/tags'] +github_account = 'clbr' +source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['0e6abacafa3c795ee783be18b736f6dfc7ff93c6e3c3237cc7c1684863e08100'] From a55f886f39cb1a66269f8a7663d9418fb328be4e Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 12 Oct 2021 17:24:58 +0200 Subject: [PATCH 1500/9987] Dir with OSU MPI startup tests was missing from the PATH --- .../OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb | 2 +- .../OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb | 2 +- .../OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb | 2 +- .../OSU-Micro-Benchmarks-5.7-gompi-2020b.eb | 2 +- .../OSU-Micro-Benchmarks-5.7-gompic-2020b.eb | 2 +- .../OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb | 2 +- .../OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb | 2 +- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb | 2 +- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb | 4 ++-- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb | 2 +- .../OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb | 2 +- .../OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb | 2 +- 23 files changed, 24 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb index 3d16b6a49f6..00babb7200d 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb index ed6d2b89b2e..413b503adf5 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb index 815081e2872..dd9c785dbc2 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb @@ -14,7 +14,7 @@ checksums = ['2ecb90abd85398786823c0716d92448d7094657d3f017c65d270ffe39afc7b95'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb index f47bdd4fe14..dde5932f128 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb @@ -14,7 +14,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb index 05e16cd6d3f..d60866bd7fe 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb @@ -14,7 +14,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb index b13a760b9da..f66e7e0c428 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb @@ -14,7 +14,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb index 42213c26c50..155cfb265f7 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb @@ -15,7 +15,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb index 18cc95538cc..ab3d5b104ef 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb @@ -15,7 +15,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb index ac8bdfeb940..b8728c97823 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb @@ -14,7 +14,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb index 1593594953d..814919e542c 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb @@ -14,7 +14,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb index 5afa283a9b8..e590b4a270f 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb @@ -14,7 +14,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb index 169f9124866..a36a6b2ea09 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb @@ -14,7 +14,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb index 71f0f3c132c..bab6b020875 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb @@ -15,7 +15,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb index eaa6dc791d6..590fad49284 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb @@ -15,7 +15,7 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb index f569964b497..36fcdf48c81 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb @@ -17,7 +17,7 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb index a3c2312f7d8..45a7c6a32a8 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb @@ -18,7 +18,7 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb index 0762e17f6cc..8a01b3f40ba 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb @@ -17,7 +17,7 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb index af9ecac7a08..50891ead8ef 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb @@ -13,7 +13,7 @@ source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb index fbe580b2712..4354202c6c0 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb @@ -13,7 +13,7 @@ source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb index fed7bf6bdb8..0007e54d651 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb @@ -19,9 +19,9 @@ dependencies = [ ] configopts = 'CC="$MPICC" CXX="$MPICC"' -configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' +configopts += ' --enable-cuda --with-cuda=$EBROOTCUDACORE' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb index 561f053d707..b5372ed93ec 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb @@ -13,7 +13,7 @@ source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb index 672d136bce4..023b5515df6 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb @@ -16,7 +16,7 @@ source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb index b6b6cf0d108..9c73e01b77a 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb @@ -13,7 +13,7 @@ source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { From f903b55c9d55da3787f9c581056667283fe96a52 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 12 Oct 2021 16:40:04 +0100 Subject: [PATCH 1501/9987] also add the 'startup' directory to the path --- .../OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb index 409a191aeb9..04466537e18 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb @@ -13,7 +13,7 @@ source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['0e24c39bf68194f27a3b630aa99c17a11cd0c86020a2a8fb5cf1465dc1e344a5'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { From 30b94eb1514e195828d6f03ce865c926053d5358 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 12 Oct 2021 18:13:40 +0200 Subject: [PATCH 1502/9987] Added checksums to two eb files, fixed line that became too long --- .../OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb | 5 ++++- .../OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb | 5 ++++- .../OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7-gompi-2020b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7-gompic-2020b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb | 4 +++- .../OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb | 4 +++- 23 files changed, 71 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb index 00babb7200d..a6f8200b579 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2016a.eb @@ -10,10 +10,13 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['b0ac3fb2281453046ccad464f257681d07d7f15029c63e0cc10c9dc673497340'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb index 413b503adf5..4bcbf5e356d 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.3.2-foss-2017a.eb @@ -10,10 +10,13 @@ toolchain = {'name': 'foss', 'version': '2017a'} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['b0ac3fb2281453046ccad464f257681d07d7f15029c63e0cc10c9dc673497340'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb index dd9c785dbc2..ea96854672c 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb @@ -14,7 +14,9 @@ checksums = ['2ecb90abd85398786823c0716d92448d7094657d3f017c65d270ffe39afc7b95'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb index dde5932f128..46eea2ef0b0 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb @@ -14,7 +14,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb index d60866bd7fe..4ad894f72b0 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb @@ -14,7 +14,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb index f66e7e0c428..739dde4021e 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb @@ -14,7 +14,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb index 155cfb265f7..b3a19557826 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb @@ -15,7 +15,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb index ab3d5b104ef..119a307b011 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb @@ -15,7 +15,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb index b8728c97823..d4c91ad814c 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb @@ -14,7 +14,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb index 814919e542c..a35cd292de5 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb @@ -14,7 +14,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb index e590b4a270f..347f1df9943 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb @@ -14,7 +14,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb index a36a6b2ea09..94f086b13d2 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb @@ -14,7 +14,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb index bab6b020875..6d403d0fb27 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb @@ -15,7 +15,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb index 590fad49284..6145c20ceb8 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb @@ -15,7 +15,9 @@ checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb index 36fcdf48c81..7df7a5b835e 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb @@ -17,7 +17,9 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb index 45a7c6a32a8..1dd7a5a6e62 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb @@ -18,7 +18,9 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb index 8a01b3f40ba..a1e5881a089 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb @@ -17,7 +17,9 @@ checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] configopts = 'CC="$MPICC" CXX="$MPICC"' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb index 50891ead8ef..d5dc6602bbc 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-ffmpi-4.5.0.eb @@ -13,7 +13,9 @@ source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb index 4354202c6c0..b803b03edb8 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb @@ -13,7 +13,9 @@ source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb index 0007e54d651..93d9f7bf2e3 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb @@ -21,7 +21,9 @@ dependencies = [ configopts = 'CC="$MPICC" CXX="$MPICC"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDACORE' -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb index b5372ed93ec..d534a221cb2 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb @@ -13,7 +13,9 @@ source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb index 023b5515df6..372930aab76 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iimpi-2021a.eb @@ -16,7 +16,9 @@ source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb index 9c73e01b77a..5fa850b07fc 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-iompi-2021a.eb @@ -13,7 +13,9 @@ source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { From c38c4310aec420c8437f67438d99d1797ff7e85e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Oct 2021 20:13:05 +0200 Subject: [PATCH 1503/9987] use correct CUDA install prefix in OSU-Micro-Benchmarks easyconfig with gompi/2021a --- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb index 93d9f7bf2e3..457f9974cbc 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb @@ -19,7 +19,7 @@ dependencies = [ ] configopts = 'CC="$MPICC" CXX="$MPICC"' -configopts += ' --enable-cuda --with-cuda=$EBROOTCUDACORE' +configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] From ed4742ef12c48df3fbf9e57adbd420435e5b55f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Oct 2021 08:33:55 +0200 Subject: [PATCH 1504/9987] adding easyconfigs: Subread-2.0.3-GCC-9.3.0.eb --- .../s/Subread/Subread-2.0.3-GCC-9.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-9.3.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-9.3.0.eb new file mode 100644 index 00000000000..daf32f69a05 --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-9.3.0.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'MakeCp' + +name = 'Subread' +version = '2.0.3' + +# HTTPS is not valid +homepage = 'http://%(namelower)s.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] + +checksums = ['56cef3a2f914d432713069d5c282f48831c3a1ecc89432ad5580caa322a5f56b'] + +start_dir = 'src' + +prebuildopts = "sed -i 's/-mtune=core2//g' Makefile.Linux && " +prebuildopts += "sed -i 's/-mtune=core2//g' longread-one/Makefile && " + +buildopts = " -f Makefile.Linux" + +files_to_copy = ['bin'] + +local_binaries_list = [ + 'exactSNP', 'featureCounts', 'subindel', 'subjunc', 'sublong', 'subread-align', 'subread-buildindex', +] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_binaries_list], + 'dirs': ['bin/utilities'], +} + +sanity_check_commands = [ + 'cd %(builddir)s/%(namelower)s-%(version)s-source/test && bash test_all.sh' +] + +moduleclass = 'bio' From 6db2e968ad86ec57bc0852f78cfa7085883e9b8e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 13 Oct 2021 10:59:14 +0200 Subject: [PATCH 1505/9987] adjusted config according to 14074 --- ...otionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb | 16 ++-------------- 1 file changed, 2 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb index 167c912f097..642b53c9aeb 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -5,7 +5,6 @@ name = 'MotionCor2' version = '1.4.4' -versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://msg.ucsf.edu/' description = """MotionCor2 correct anisotropic image motion at the @@ -22,12 +21,10 @@ BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -# No longer directly downloadable, available from https://msg.ucsf.edu/software -sources = [ - '%(name)s_%(version)s.zip', -] +sources = ['%(name)s_%(version)s.zip'] checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] +# No longer directly downloadable, available from https://msg.ucsf.edu/software # CUDA is a build dependency to make sure it gets installed. # It's actually a runtime dependency, but that's handled in the wrapper to # make sure it doesn't conflict with whatever toolchain happens to be loaded. @@ -35,20 +32,11 @@ checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] # of MotionCor2 builddependencies = [ ('binutils', '2.36.1'), - ('patchelf', '0.12'), ('CUDA', '11.3.1', '', True), ] -skip_rpath_check = True - -postinstallcmds = ['patchelf --force-rpath --set-rpath $EBROOTCUDACORE/lib64:$EBROOTLIBTIFF/lib %(installdir)s/bin/MotionCor2_1.4.4_Cuda113'] - dependencies = [ - ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.6'), - ('XZ', '5.2.5'), ('LibTIFF', '4.2.0'), - ('jbigkit', '2.1'), ] moduleclass = 'bio' From 48f57355eb4e2897b56f6cf4771b87230a4a696b Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 13 Oct 2021 11:00:20 +0200 Subject: [PATCH 1506/9987] removed CUDA suffix --- ...e-10.3.0-CUDA-11.3.1.eb => MotionCor2-1.4.4-GCCcore-10.3.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MotionCor2/{MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb => MotionCor2-1.4.4-GCCcore-10.3.0.eb} (100%) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb similarity index 100% rename from easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0-CUDA-11.3.1.eb rename to easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb From b21a3e1195d7df2fad259ff9e7a41552eaaafb97 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 13 Oct 2021 11:22:29 +0200 Subject: [PATCH 1507/9987] added zlib and jpeg deps --- .../easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb index 642b53c9aeb..c5b0cd9612e 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb @@ -36,6 +36,8 @@ builddependencies = [ ] dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), ('LibTIFF', '4.2.0'), ] From 1091f7bf96fa73bc643d22433b7e6781e8af44f8 Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Wed, 13 Oct 2021 11:35:32 +0200 Subject: [PATCH 1508/9987] libjpeg and zlib are loaded through libtiff --- .../easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb index c5b0cd9612e..642b53c9aeb 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb @@ -36,8 +36,6 @@ builddependencies = [ ] dependencies = [ - ('zlib', '1.2.11'), - ('libjpeg-turbo', '2.0.6'), ('LibTIFF', '4.2.0'), ] From 5d48f55ce19a018778c0718a9dc5a2a8cd1e7e2f Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 13 Oct 2021 11:57:19 +0200 Subject: [PATCH 1509/9987] Update libGridXC-0.9.6-gompi-2020b.eb --- .../easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb index a46d4f4f179..4cfcff47e52 100644 --- a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2020b.eb @@ -28,7 +28,7 @@ sanity_check_paths = { ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], - 'dirs': ['include'], + 'dirs': [], } moduleclass = 'phys' From f530f0cee1c61929a37217debcd9e46ee1f318c7 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 13 Oct 2021 11:57:32 +0200 Subject: [PATCH 1510/9987] Update libGridXC-0.9.6-iimpi-2020b.eb --- .../easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb index 3c9d3dbdceb..e8ca5b58839 100644 --- a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2020b.eb @@ -28,7 +28,7 @@ sanity_check_paths = { ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], - 'dirs': ['include'], + 'dirs': [], } moduleclass = 'phys' From 05827eaccaa80a4dbbfe78dd411f39e3533f6c3b Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 29 Jan 2021 16:13:28 +0100 Subject: [PATCH 1511/9987] Add xmlf90-1.5.4-GCC-10.2.0. --- .../x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb new file mode 100644 index 00000000000..100e2c26968 --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.2.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'xmlf90' +version = '1.5.4' + +homepage = 'https://launchpad.net/xmlf90' +description = """xmlf90 is a basic XML parsing library written in Fortran.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a0b1324ff224d5b5ad1127a6ad4f90979f6b127f1a517f98253eea377237bbe4'] + +sanity_check_paths = { + 'files': ['include/xmlf90_%s.mod' % x for x in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], + 'dirs': ['share/org.siesta-project'], +} + +moduleclass = 'data' From 61e725777037de2135f1c2cad5ce10f10cc7c2a6 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 12 Mar 2021 13:50:10 +0000 Subject: [PATCH 1512/9987] update libpsml to 1.1.0 and GCC-10.2.0 --- .../l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb new file mode 100644 index 00000000000..e6dce0ffa00 --- /dev/null +++ b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libpsml' +version = '1.1.10' + +homepage = 'https://launchpad.net/libpsml' +description = """LibPSML provides a Fortran API to parse files in the + PSeudopotential Markup Language (PSML) format.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libpsml/uploads/95c4d83d750d1ca87659b6395c8f7ea7/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['67c38b5bc26acbb77fd13794d1d92f41197a44311314f5453c82506205e0717b'] + +dependencies = [ + ('xmlf90', '1.5.4'), +] + +sanity_check_paths = { + 'files': ['include/m_psml.mod', 'lib/libpsml.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' From d8a6337f49c398488d69ef00dd71d0e39e0bb2bf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Oct 2021 12:12:17 +0200 Subject: [PATCH 1513/9987] update description of Mesa-demos --- .../m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb index 1581f494543..16c730bb5af 100644 --- a/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb @@ -1,19 +1,14 @@ easyblock = 'ConfigureMake' -# Mesa demos and utilities, such as glxinfo, eglinfo and lots more - name = 'Mesa-demos' version = '8.4.0' homepage = 'https://www.mesa3d.org/' -description = """Mesa is an open-source implementation of the OpenGL specification - - a system for rendering interactive 3D graphics.""" +description = "Mesa utility and demo programs, including glxinfo and eglinfo." toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -source_urls = [ - 'https://mesa.freedesktop.org/archive/demos/' -] +source_urls = ['https://mesa.freedesktop.org/archive/demos/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['01e99c94a0184e63e796728af89bfac559795fb2a0d6f506fa900455ca5fff7d'] From 5bf1b056022be07175e7f02ff1363b796e29fddf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Oct 2021 12:19:14 +0200 Subject: [PATCH 1514/9987] add build dependency on pkg-config to Mesa-demos --- .../easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb index 16c730bb5af..3cac0a108cb 100644 --- a/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa-demos/Mesa-demos-8.4.0-GCCcore-10.3.0.eb @@ -15,6 +15,7 @@ checksums = ['01e99c94a0184e63e796728af89bfac559795fb2a0d6f506fa900455ca5fff7d'] builddependencies = [ ('binutils', '2.36.1'), ('freetype', '2.10.4'), + ('pkg-config', '0.29.2'), ] dependencies = [ From 5e552aa292f9051fff404a26f6144151b6633bb6 Mon Sep 17 00:00:00 2001 From: alin m elena Date: Wed, 13 Oct 2021 11:35:25 +0100 Subject: [PATCH 1515/9987] change version to indicate is serial --- ...-0.2.2-foss-2020b.eb => libfdf-0.2.2-foss-2020b-serial.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/l/libfdf/{libfdf-0.2.2-foss-2020b.eb => libfdf-0.2.2-foss-2020b-serial.eb} (94%) diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b-serial.eb similarity index 94% rename from easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b.eb rename to easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b-serial.eb index b3aa3054822..2221f6d2dfb 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b-serial.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'libfdf' version = '0.2.2' - +version_suffix = 'serial' homepage = 'https://launchpad.net/libfdf' description = """LibFDF provides a Fortran API to parse files in the Flexible Data Format (FDF).""" @@ -19,7 +19,7 @@ configopts = ' --without-mpi ' sanity_check_paths = { 'files': ['include/fdf.mod', ('lib/libfdf.a', 'lib64/libfdf.a')], - 'dirs': ['include'], + 'dirs': [''], } moduleclass = 'data' From 9f6532bff08e6d2a670f4a078a87f43b1a6321f7 Mon Sep 17 00:00:00 2001 From: alin m elena Date: Wed, 13 Oct 2021 11:38:04 +0100 Subject: [PATCH 1516/9987] change version to indicate is serial --- ...2-foss-2020b-serial.eb => libfdf-0.2.2-GCC-10.2.0-serial.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/libfdf/{libfdf-0.2.2-foss-2020b-serial.eb => libfdf-0.2.2-GCC-10.2.0-serial.eb} (93%) diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb similarity index 93% rename from easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b-serial.eb rename to easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb index 2221f6d2dfb..80974c51552 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-foss-2020b-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb @@ -7,7 +7,7 @@ homepage = 'https://launchpad.net/libfdf' description = """LibFDF provides a Fortran API to parse files in the Flexible Data Format (FDF).""" -toolchain = {'name': 'foss', 'version': '2020b'} +toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'usempi': False} source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] From 332e44519eccc7bbc69549e091af9f3cc78c36f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Oct 2021 13:16:09 +0200 Subject: [PATCH 1517/9987] adding easyconfigs: GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb --- .../GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb | 89 +++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..738d6c86b6b --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,89 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI builds. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', +] +checksums = [ + 'e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6', # gromacs-2021.3.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch + '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('networkx', '2.5.1'), + ('CUDA', '11.3.1', '', True), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From a2159f01508c1cf1f117831850ab6a5d79efefbb Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 13 Oct 2021 14:00:53 +0200 Subject: [PATCH 1518/9987] Add missing scripts from utils and analysis_scripts to bin --- .../cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb index 5d9c5f8d478..a8269f3c486 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -47,9 +47,26 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/zhonge/cryodrgn/archive'], 'checksums': ['1efecc2a0add2392411076082c122039a490f5ddf3e01f1da38aea1a81592077'], + 'postinstallcmds': [ + "sed -i '1s|^|#!/usr/bin/env python\\n|' utils/* analysis_scripts/*", + 'cp utils/* analysis_scripts/* %(installdir)s/bin', + 'chmod +x %(installdir)s/bin/*.py' + ] }), ] -sanity_check_commands = ["%(namelower)s --help"] +local_scripts = [ + 'add_psize', 'filter_mrcs', 'filter_pkl', 'filter_star', 'flip_hand', 'fsc', 'invert_contrast', 'kmeans', + 'phase_flip', 'plotfsc', 'plot_loss', 'plot_z1', 'plot_z2', 'plot_z_pca', 'run_umap', 'translate_stack', 'tsne', + 'view_header', 'view_stack', 'write_starfile' +] + +sanity_check_paths = { + 'files': ['bin/%s.py' % x for x in local_scripts], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s --help'] +sanity_check_commands += ['%s.py -h' % x for x in local_scripts] moduleclass = 'chem' From 969f6122564c2895b7e3b9a5e056a2465278f6e2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 13 Oct 2021 14:46:23 +0200 Subject: [PATCH 1519/9987] adding easyconfigs: crb-blast-0.6.9-gompi-2021a-Ruby-3.0.1.eb --- .../crb-blast-0.6.9-gompi-2021a-Ruby-3.0.1.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a-Ruby-3.0.1.eb diff --git a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a-Ruby-3.0.1.eb b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a-Ruby-3.0.1.eb new file mode 100644 index 00000000000..921d6024116 --- /dev/null +++ b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a-Ruby-3.0.1.eb @@ -0,0 +1,63 @@ +easyblock = 'Bundle' + +name = 'crb-blast' +version = '0.6.9' +local_rubyver = '3.0.1' +versionsuffix = '-Ruby-%s' % local_rubyver + +homepage = 'https://github.com/cboursnell/crb-blast' +description = """Conditional Reciprocal Best BLAST - high confidence ortholog assignment. + CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. + This is particularly useful in genome and transcriptome annotation.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +dependencies = [ + ('Ruby', local_rubyver), + ('BLAST+', '2.11.0'), +] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# this is a bundle of Ruby gems +exts_defaultclass = 'RubyGem' + +exts_list = [ + ('facade', '1.2.1', { + 'checksums': ['0764de5519088227675a2a67da23322500c3c507b89486d91296e031d87d036e'], + }), + ('pathname2', '1.8.4', { + 'checksums': ['1711264f3f7c1b380f96e1f0383b135d9703488f7b1acf66346a176efc257b7a'], + }), + ('fixwhich', '1.0.2', { + 'checksums': ['c6a8f796a7eb60ffbc29f0d2af85461761a36c2864d25e445ff18bfbd1657078'], + }), + ('bindeps', '1.2.1', { + 'checksums': ['3c11d75aa722bed67246852bb430a182361a128910d384b664b91f3e65bc34b5'], + }), + ('threach', '0.2.0', { + 'checksums': ['432cbf3569bf9b09e26f93d0959fd6fb911c71e790e8a4cc4d1110e139a2ffca'], + }), + ('bio', '1.5.2', { + 'checksums': ['68a453cdb87e5c8d7ad4b2ad5e76e81822193be0623f53cf53356ca95b55a6b4'], + }), + ('trollop', '2.9.10', { + 'checksums': ['ceca2d91f349163d6ee3e792d356d4ded7472e6da31ac6dcc5956d1b03607bf7'], + }), + (name, version, { + 'checksums': ['69c346e7d83efe9b9a383a39b57e7cce186a82b7074f275b14906f8f05678e3e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bioruby', 'bin/br_biofetch.rb', 'bin/br_bioflat.rb', 'bin/br_biogetseq.rb', + 'bin/br_pmfetch.rb', 'bin/%(name)s'], + 'dirs': ['gems'], +} + +modextrapaths = {'GEM_PATH': ['']} + +moduleclass = 'bio' From bcc8c9d8fbc5ea631753c0661a5c3959b7051c70 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 13 Oct 2021 15:04:03 +0200 Subject: [PATCH 1520/9987] adding easyconfigs: Kraken2-2.1.2-gompi-2021a.eb --- .../k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb new file mode 100644 index 00000000000..a38fa3a3bf5 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb @@ -0,0 +1,49 @@ +easyblock = 'PackedBinary' + +name = 'Kraken2' +version = '2.1.2' + +homepage = 'https://github.com/DerrickWood/kraken2/wiki' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# part is compiled with $CXX, the rest is in Perl +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['Kraken2-2.1.1_fix_installation_for_easybuild.patch'] +checksums = [ + 'e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3', # v2.1.2.tar.gz + # Kraken2-2.1.1_fix_installation_for_easybuild.patch + '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11', +] + +dependencies = [ + ('Perl', '5.32.1'), + ('BLAST+', '2.11.0'), + ('wget', '1.21.1'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken2.sh %(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + '16S_gg_installation.sh', '16S_rdp_installation.sh', '16S_silva_installation.sh', 'add_to_library.sh', + 'build_db', 'build_gg_taxonomy.pl', 'build_kraken2_db.sh', 'build_rdp_taxonomy.pl', 'build_silva_taxonomy.pl', + 'classify', 'clean_db.sh', 'cp_into_tempfile.pl', 'download_genomic_library.sh', 'download_taxonomy.sh', + 'dump_table', 'estimate_capacity', 'kraken2', 'kraken2-build', 'kraken2-inspect', 'kraken2lib.pm', + 'lookup_accession_numbers.pl', 'make_seqid2taxid_map.pl', 'mask_low_complexity.sh', 'rsync_from_ncbi.pl', + 'scan_fasta_file.pl']], + 'dirs': [], +} + +moduleclass = 'bio' From 2fb547244a389b2769a338ef9c823c095597315e Mon Sep 17 00:00:00 2001 From: alin m elena Date: Wed, 13 Oct 2021 14:06:43 +0100 Subject: [PATCH 1521/9987] inject checksum --- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb | 2 +- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb | 2 +- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb | 2 +- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb index 149f34fc779..107a6971042 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] +checksums = ['0f9ee2c69dfc2fd085127aae4b3b794fad20ef5c2dad6c89728ce5fbf300eb75'] builddependencies = [ ('CMake', '3.18.4') diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb index 5ca94201575..61e9aea6c26 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] +checksums = ['0f9ee2c69dfc2fd085127aae4b3b794fad20ef5c2dad6c89728ce5fbf300eb75'] builddependencies = [ ('CMake', '3.20.1') diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb index 32d0079345c..56558c52778 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'intel', 'version': '2020b'} source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] +checksums = ['0f9ee2c69dfc2fd085127aae4b3b794fad20ef5c2dad6c89728ce5fbf300eb75'] builddependencies = [ ('CMake', '3.18.4') diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb index 2528a42bc11..4dba5307eaf 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'intel', 'version': '2021a'} source_urls = ['https://github.com/libmbd/libmbd/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -# checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] +checksums = ['0f9ee2c69dfc2fd085127aae4b3b794fad20ef5c2dad6c89728ce5fbf300eb75'] builddependencies = [ ('CMake', '3.20.1') From 03782337d446553e261585339fcd6da4887b8574 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Oct 2021 15:18:46 +0200 Subject: [PATCH 1522/9987] adding easyconfigs: CUDA-11.4.2.eb --- easybuild/easyconfigs/c/CUDA/CUDA-11.4.2.eb | 26 +++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.4.2.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.4.2.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.2.eb new file mode 100644 index 00000000000..ba572b6a631 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.2.eb @@ -0,0 +1,26 @@ +name = 'CUDA' +version = '11.4.2' +local_nv_version = '470.57.02' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + 'bbd87ca0e913f837454a796367473513cddef555082e4d86ed9a38659cc81f0a', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'a917c2e53dc13fdda7def71fd40920bf3809d5a2caa3e9acfe377fb9fb22f12d', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'f2c4a52e06329606c8dfb7c5ea3f4cb4c0b28f9d3fdffeeb734fcc98daf580d8', + } +] + +moduleclass = 'system' From 5610e1111457579888f9a3ab36dd10ff429bdb32 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 13 Oct 2021 15:31:28 +0200 Subject: [PATCH 1523/9987] Keep easyconfig for UCX v1.11.0 --- .../u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..847d1c18e3b --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.11.0' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = ['UCX-1.10.0-dynamic_modules.patch'] +checksums = [ + 'b7189b69fe0e16e3c03784ef674e45687a9c520750bd74a45125c460ede37647', # ucx-1.11.0.tar.gz + '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.11'), + ('numactl', '2.0.14'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From c37837747915aef3a043585446f342fd860414d1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 13 Oct 2021 15:34:20 +0200 Subject: [PATCH 1524/9987] adding easyconfigs: UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb and update dependency in NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb --- .../NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb | 2 +- ...-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb | 42 +++++++++++++++++++ 2 files changed, 43 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb index 1bfa2329ebc..6375266362f 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -17,7 +17,7 @@ builddependencies = [('binutils', '2.37')] dependencies = [ ('CUDA', '11.4.1', '', True), - ('UCX-CUDA', '1.11.0', versionsuffix), + ('UCX-CUDA', '1.11.2', versionsuffix), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb new file mode 100644 index 00000000000..b676452b9af --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -0,0 +1,42 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.11.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['ucx-%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_link_against_existing_UCX_libs.patch', +] +checksums = [ + 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df', # ucx-1.11.2.tar.gz + # UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch + 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3', +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('UCX', version), + ('CUDA', '11.4.1', '', True), + ('GDRCopy', '2.3'), +] + +moduleclass = 'lib' From 979e2e441a29d50bf86f9a2ea921105bc7f91930 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 13 Oct 2021 14:57:53 +0100 Subject: [PATCH 1525/9987] adding easyconfigs: spglib-1.16.2-GCCcore-10.3.0.eb --- .../s/spglib/spglib-1.16.2-GCCcore-10.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/spglib/spglib-1.16.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.16.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/spglib/spglib-1.16.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8b829cf3f69 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.16.2-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spglib' +version = '1.16.2' + +homepage = 'https://spglib.github.io/spglib/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/spglib/spglib/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5723789bee7371ebba91d78c729d2a608f198fad5e1c95eebe18fda9f2914ec8'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +sanity_check_paths = { + 'files': [ + 'include/spglib.h', + 'lib/libsymspg.a', + 'lib/libsymspg.%s' % SHLIB_EXT + ], + 'dirs': [], +} + +moduleclass = 'chem' From 2789c5637cb643558bb1968c970c2565073cca0b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 13 Oct 2021 16:12:23 +0200 Subject: [PATCH 1526/9987] update easyconfigs: UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb --- .../u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb index b676452b9af..bc3201ec688 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -18,7 +18,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['ucx-%(version)s.tar.gz'] patches = [ - '%(name)s-%(version)s_link_against_existing_UCX_libs.patch', + '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', ] checksums = [ 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df', # ucx-1.11.2.tar.gz From ecc86ed51496d522cf9cf1a14d63aeab4c45b3c0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 13 Oct 2021 16:19:23 +0200 Subject: [PATCH 1527/9987] update libspatialindex-1.9.3-GCCcore-11.2.0.eb: fix sanity files check --- .../l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.2.0.eb index e23f052cdc4..c0692dca07a 100644 --- a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.2.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['lib/libspatialindex.so', 'lib/libspatialindex.%s' % SHLIB_EXT], + 'files': ['lib/libspatialindex.%s' % SHLIB_EXT], 'dirs': ['include/spatialindex'], } From a905bcb9e3befde71b861d2c1cb4b0b37b405d39 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Maxime=20Mog=C3=A9?= Date: Wed, 13 Oct 2021 18:09:38 +0200 Subject: [PATCH 1528/9987] adding easyconfigs: Stata-17-GCCcore-10.3.0.eb --- .../s/Stata/Stata-17-GCCcore-10.3.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..66676cb2c6a --- /dev/null +++ b/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb @@ -0,0 +1,21 @@ +name = 'Stata' +version = '17' + +homepage = 'https://www.stata.com/' +description = """Stata is a complete, integrated statistical software package that provides everything you need + for data analysis, data management, and graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +# requires license to access source files +sources = ['%(name)s%(version)sLinux64.tar.gz'] +checksums = ['744314cdac7ba7316c82dccebe7c7de8f7fab68841d8fa7de13f8eb4472e6015'] + +dependencies = [ + ('libpng', '1.6.37'), + ('ncurses', '6.2'), +] + +sanity_check_commands = ['stata -h'] + +moduleclass = 'data' From de8f0fa48f28e3599a261fa8f413c1b0d7387e6b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 13 Oct 2021 22:45:55 +0200 Subject: [PATCH 1529/9987] add exception to keep UCX and UCX-CUDA v1.11.0 and v1.11.2 --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d304b94d594..47b1013e813 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -482,6 +482,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), ], + # For 2021b we want to keep UCX-CUDA v1.11.2 and v1.11.0 which depends on UCX v1.11.0 + 'UCX-CUDA': [('1.11.0;', ['UCX-1.11.0']),], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 From ef8b6bbf0c34bbe051a5c360d7f0940248132e01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Oct 2021 23:02:37 +0200 Subject: [PATCH 1530/9987] fix exceptions for UCX 1.11.0 dependency (used in UCX-CUDA 1.11.0 easyconfig) --- test/easyconfigs/easyconfigs.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 47b1013e813..b4753cd52f9 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -482,8 +482,9 @@ def check_dep_vars(self, gen, dep, dep_vars): # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), ], - # For 2021b we want to keep UCX-CUDA v1.11.2 and v1.11.0 which depends on UCX v1.11.0 - 'UCX-CUDA': [('1.11.0;', ['UCX-1.11.0']),], + # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 + # (for 2021b, UCX was updated to v1.11.2) + 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-']),], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 From cb3ffc22e2694a1d84eef057976d25dcf50a6b8b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Oct 2021 23:17:42 +0200 Subject: [PATCH 1531/9987] trivial style fix: drop trailing comma --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index b4753cd52f9..c71abed2a75 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -484,7 +484,7 @@ def check_dep_vars(self, gen, dep, dep_vars): ], # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 # (for 2021b, UCX was updated to v1.11.2) - 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-']),], + 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 From ca068c6d05d7b28d788cb53b51ebad113ddce90d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Oct 2021 00:59:59 +0200 Subject: [PATCH 1532/9987] remove format mapping from homepage of Subread easyconfigs --- easybuild/easyconfigs/s/Subread/Subread-1.6.3-foss-2018b.eb | 2 +- easybuild/easyconfigs/s/Subread/Subread-1.6.4-foss-2018b.eb | 2 +- .../easyconfigs/s/Subread/Subread-2.0.0-GCC-7.3.0-2.30.eb | 3 ++- easybuild/easyconfigs/s/Subread/Subread-2.0.0-GCC-8.3.0.eb | 2 +- easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-10.3.0.eb | 2 +- easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-9.3.0.eb | 2 +- 7 files changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.6.3-foss-2018b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.6.3-foss-2018b.eb index 96b1f09f0f9..05faabc5799 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.6.3-foss-2018b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.6.3-foss-2018b.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'Subread' version = '1.6.3' -homepage = 'http://%(namelower)s.sourceforge.net/' +homepage = 'http://subread.sourceforge.net/' description = """High performance read alignment, quantification and mutation discovery""" toolchain = {'name': 'foss', 'version': '2018b'} diff --git a/easybuild/easyconfigs/s/Subread/Subread-1.6.4-foss-2018b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.6.4-foss-2018b.eb index 4165d53a635..da971c3f6af 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-1.6.4-foss-2018b.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-1.6.4-foss-2018b.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'Subread' version = '1.6.4' -homepage = 'http://%(namelower)s.sourceforge.net/' +homepage = 'http://subread.sourceforge.net/' description = """High performance read alignment, quantification and mutation discovery""" toolchain = {'name': 'foss', 'version': '2018b'} diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.0-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.0-GCC-7.3.0-2.30.eb index e3b70759204..fcfcd61caf9 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-2.0.0-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.0-GCC-7.3.0-2.30.eb @@ -6,7 +6,8 @@ easyblock = 'MakeCp' name = 'Subread' version = '2.0.0' -homepage = 'http://%(namelower)s.sourceforge.net/' +# HTTPS is not valid +homepage = 'http://subread.sourceforge.net/' description = """High performance read alignment, quantification and mutation discovery""" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.0-GCC-8.3.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.0-GCC-8.3.0.eb index 6e77ef33fdd..8d2db967a4d 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-2.0.0-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.0-GCC-8.3.0.eb @@ -7,7 +7,7 @@ name = 'Subread' version = '2.0.0' # HTTPS is not valid -homepage = 'http://%(namelower)s.sourceforge.net/' +homepage = 'http://subread.sourceforge.net/' description = """High performance read alignment, quantification and mutation discovery""" toolchain = {'name': 'GCC', 'version': '8.3.0'} diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb index 17cdbfec0d0..cb9042bbb72 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.2-GCC-10.2.0.eb @@ -7,7 +7,7 @@ name = 'Subread' version = '2.0.2' # HTTPS is not valid -homepage = 'http://%(namelower)s.sourceforge.net/' +homepage = 'http://subread.sourceforge.net/' description = """High performance read alignment, quantification and mutation discovery""" toolchain = {'name': 'GCC', 'version': '10.2.0'} diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-10.3.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-10.3.0.eb index fc8c40d5c2b..80fb163f188 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-10.3.0.eb @@ -7,7 +7,7 @@ name = 'Subread' version = '2.0.3' # HTTPS is not valid -homepage = 'http://%(namelower)s.sourceforge.net/' +homepage = 'http://subread.sourceforge.net/' description = """High performance read alignment, quantification and mutation discovery""" toolchain = {'name': 'GCC', 'version': '10.3.0'} diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-9.3.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-9.3.0.eb index daf32f69a05..a9ad4aecc98 100644 --- a/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-9.3.0.eb @@ -7,7 +7,7 @@ name = 'Subread' version = '2.0.3' # HTTPS is not valid -homepage = 'http://%(namelower)s.sourceforge.net/' +homepage = 'http://subread.sourceforge.net/' description = """High performance read alignment, quantification and mutation discovery""" toolchain = {'name': 'GCC', 'version': '9.3.0'} From 9dfc1d2deaf62f66f22dddbd1b76b73e99c4bee5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Oct 2021 01:27:59 +0200 Subject: [PATCH 1533/9987] remove versionsuffix from crb-blast-0.6.9-gompi-2021a-Ruby-3.0.1.eb --- ...mpi-2021a-Ruby-3.0.1.eb => crb-blast-0.6.9-gompi-2021a.eb} | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) rename easybuild/easyconfigs/c/crb-blast/{crb-blast-0.6.9-gompi-2021a-Ruby-3.0.1.eb => crb-blast-0.6.9-gompi-2021a.eb} (95%) diff --git a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a-Ruby-3.0.1.eb b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a.eb similarity index 95% rename from easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a-Ruby-3.0.1.eb rename to easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a.eb index 921d6024116..6e2239cbb18 100644 --- a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a-Ruby-3.0.1.eb +++ b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a.eb @@ -2,8 +2,6 @@ easyblock = 'Bundle' name = 'crb-blast' version = '0.6.9' -local_rubyver = '3.0.1' -versionsuffix = '-Ruby-%s' % local_rubyver homepage = 'https://github.com/cboursnell/crb-blast' description = """Conditional Reciprocal Best BLAST - high confidence ortholog assignment. @@ -13,7 +11,7 @@ description = """Conditional Reciprocal Best BLAST - high confidence ortholog as toolchain = {'name': 'gompi', 'version': '2021a'} dependencies = [ - ('Ruby', local_rubyver), + ('Ruby', '3.0.1'), ('BLAST+', '2.11.0'), ] From 48c715e9574604775066cde0365f843c03f2aeb3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Oct 2021 01:28:32 +0200 Subject: [PATCH 1534/9987] add sanity check command to crb-blast-0.6.9-gompi-2021a.eb --- .../easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a.eb b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a.eb index 6e2239cbb18..e52b70cf4a8 100644 --- a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a.eb +++ b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021a.eb @@ -56,6 +56,8 @@ sanity_check_paths = { 'dirs': ['gems'], } +sanity_check_commands = ["crb-blast --help"] + modextrapaths = {'GEM_PATH': ['']} moduleclass = 'bio' From dbdb285033dd99f0fcf2e147005c6fb25bd572c6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Oct 2021 01:38:50 +0200 Subject: [PATCH 1535/9987] replace sed with fix_python_shebang_for in cryoDRGN v0.3.2 --- .../c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb index a8269f3c486..2a47fefb4a8 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.2-fosscuda-2020b.eb @@ -48,13 +48,14 @@ exts_list = [ 'source_urls': ['https://github.com/zhonge/cryodrgn/archive'], 'checksums': ['1efecc2a0add2392411076082c122039a490f5ddf3e01f1da38aea1a81592077'], 'postinstallcmds': [ - "sed -i '1s|^|#!/usr/bin/env python\\n|' utils/* analysis_scripts/*", - 'cp utils/* analysis_scripts/* %(installdir)s/bin', - 'chmod +x %(installdir)s/bin/*.py' - ] + 'cp utils/* analysis_scripts/* %(installdir)s/bin', + 'chmod +x %(installdir)s/bin/*.py', + ], }), ] +fix_python_shebang_for = ['bin/*.py'] + local_scripts = [ 'add_psize', 'filter_mrcs', 'filter_pkl', 'filter_star', 'flip_hand', 'fsc', 'invert_contrast', 'kmeans', 'phase_flip', 'plotfsc', 'plot_loss', 'plot_z1', 'plot_z2', 'plot_z_pca', 'run_umap', 'translate_stack', 'tsne', From fc613ab1e7905851783b49e460a5e50b59ff96eb Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 14 Oct 2021 02:08:56 +0000 Subject: [PATCH 1536/9987] adding easyconfigs: imkl-2021.4.0.eb, imkl-FFTW-2021.4.0-gompi-2021.07.eb --- .../imkl-FFTW-2021.4.0-gompi-2021.07.eb | 11 +++++++++++ easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb | 16 ++++++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb new file mode 100644 index 00000000000..58097bb6206 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2021.4.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'gompi', 'version': '2021.07'} + +dependencies = [('imkl', version)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb new file mode 100644 index 00000000000..f3e3040b1ee --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0.eb @@ -0,0 +1,16 @@ +name = 'imkl' +version = '2021.4.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] +sources = ['l_onemkl_p_%(version)s.640_offline.sh'] +checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] + +interfaces = False + +moduleclass = 'numlib' From 4230097843802f9f984c452c37a9d31ac1b83702 Mon Sep 17 00:00:00 2001 From: alin m elena Date: Thu, 14 Oct 2021 08:12:55 +0100 Subject: [PATCH 1537/9987] address the comments --- .../easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb index 80974c51552..a7fbdaa174d 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb @@ -2,23 +2,21 @@ easyblock = 'ConfigureMake' name = 'libfdf' version = '0.2.2' -version_suffix = 'serial' +versionsuffix = 'serial' homepage = 'https://launchpad.net/libfdf' description = """LibFDF provides a Fortran API to parse files in the Flexible Data Format (FDF).""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -toolchainopts = {'usempi': False} source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] sources = ['libfdf-%(version)s.tar.gz'] checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] -preconfigopts = 'unset MPIFC && unset MPICC && ' configopts = ' --without-mpi ' sanity_check_paths = { - 'files': ['include/fdf.mod', ('lib/libfdf.a', 'lib64/libfdf.a')], + 'files': ['include/fdf.mod', 'lib/libfdf.a'], 'dirs': [''], } From 8de6f1f20ae636e43266a119dd6ab5f78ec06de3 Mon Sep 17 00:00:00 2001 From: alin m elena Date: Thu, 14 Oct 2021 08:16:21 +0100 Subject: [PATCH 1538/9987] address the comments --- .../easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb index 93bb74df602..87e76b10a62 100644 --- a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.2.0.eb @@ -8,16 +8,16 @@ description = """libpspio is a library to read and write pseudopotentials in mul toolchain = {'name': 'GCC', 'version': '10.2.0'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://gitlab.e-cam2020.eu/esl/pspio/uploads/7efa924be97bd46354237ca3fb89495e/'] -checksums = ['740861617e1feb50a9e00609769b12d8'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cb3d51ffa6b822305bb943edc7ddfaf1cfc1b928f0594330d732330bfc081850'] configopts = ' --enable-gsl --enable-fortran ' dependencies = [('GSL', '2.6')] sanity_check_paths = { - 'files': ['include/pspiof_m.mod', 'include/pspio.h'] + [('lib/libpspiof.a', 'lib64/libpspiof.a')], + 'files': ['include/pspiof_m.mod', 'include/pspio.h', 'lib/libpspiof.a'], 'dirs': [], } From 72d7aa8cf86441774ac867972228bfc44f89b27d Mon Sep 17 00:00:00 2001 From: alin m elena Date: Thu, 14 Oct 2021 08:34:58 +0100 Subject: [PATCH 1539/9987] keep style happy --- .../easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb index a7fbdaa174d..71cbe3216a6 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'libfdf' version = '0.2.2' -versionsuffix = 'serial' +versionsuffix = '-serial' homepage = 'https://launchpad.net/libfdf' description = """LibFDF provides a Fortran API to parse files in the Flexible Data Format (FDF).""" From b698108e45ac8cd51c73238409dd3bfcc082f51f Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 10:23:31 +0200 Subject: [PATCH 1540/9987] Update libmbd-0.10.4-foss-2020b.eb --- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb index 107a6971042..94410426c23 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -35,16 +35,15 @@ local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" parallel = 1 -# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# make sure that built libraries (libmbd.so) in build directory are picked when running tests # this is required when RPATH linking is used pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " runtest = 'test' sanity_check_paths = { - 'files': ['lib/libmbd.so'] + - ['lib64/libmbd.so'], + 'files': ['lib/libmbd.%s' % SHLIB_EXT], 'dirs': ['include', 'lib/cmake/mbd'], } -moduleclass = 'chem' +moduleclass = 'phys' From 461400e83b45f1405c0d8f5d8293711f60070b2b Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 10:25:30 +0200 Subject: [PATCH 1541/9987] Update libmbd-0.10.4-foss-2020b.eb --- easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb index 94410426c23..f9a79031afc 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2020b.eb @@ -42,8 +42,8 @@ pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PAT runtest = 'test' sanity_check_paths = { - 'files': ['lib/libmbd.%s' % SHLIB_EXT], - 'dirs': ['include', 'lib/cmake/mbd'], + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd.h', 'include/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], } moduleclass = 'phys' From cfbe909aa9e7b7ae60d777ecc812a659aada1202 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 10:26:30 +0200 Subject: [PATCH 1542/9987] Update libmbd-0.10.4-foss-2021a.eb --- .../easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb index 61e9aea6c26..c6830cec26c 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-foss-2021a.eb @@ -35,16 +35,15 @@ local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" parallel = 1 -# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# make sure that built libraries (libmbd.so) in build directory are picked when running tests # this is required when RPATH linking is used pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " runtest = 'test' sanity_check_paths = { - 'files': ['lib/libmbd.so'] + - ['lib64/libmbd.so'], - 'dirs': ['include', 'lib/cmake/mbd'], + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd.h', 'include/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], } -moduleclass = 'chem' +moduleclass = 'phys' From b22fd4e39dbb0338bc66cfdc1abde10dbafafbce Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 10:27:03 +0200 Subject: [PATCH 1543/9987] Update libmbd-0.10.4-intel-2020b.eb --- .../easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb index 56558c52778..f33ad17becd 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2020b.eb @@ -35,16 +35,15 @@ local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" parallel = 1 -# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# make sure that built libraries (libmbd.so) in build directory are picked when running tests # this is required when RPATH linking is used pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " runtest = 'test' sanity_check_paths = { - 'files': ['lib/libmbd.so'] + - ['lib64/libmbd.so'], - 'dirs': ['include', 'lib/cmake/mbd'], + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd.h', 'include/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], } -moduleclass = 'chem' +moduleclass = 'phys' From f4220fc09c9cfe8461ea064ea11085c7c3b6a769 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 10:27:27 +0200 Subject: [PATCH 1544/9987] Update libmbd-0.10.4-intel-2021a.eb --- .../easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb index 4dba5307eaf..0099552e4a2 100644 --- a/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb +++ b/easybuild/easyconfigs/l/libmbd/libmbd-0.10.4-intel-2021a.eb @@ -35,16 +35,15 @@ local_common_configopts = "-DENABLE_SCALAPACK_MPI=ON" parallel = 1 -# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# make sure that built libraries (libmbd.so) in build directory are picked when running tests # this is required when RPATH linking is used pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " runtest = 'test' sanity_check_paths = { - 'files': ['lib/libmbd.so'] + - ['lib64/libmbd.so'], - 'dirs': ['include', 'lib/cmake/mbd'], + 'files': ['lib/libmbd.%s' % SHLIB_EXT, 'include/mbd.h', 'include/mbd.mod'], + 'dirs': ['lib/cmake/mbd'], } -moduleclass = 'chem' +moduleclass = 'phys' From 2a85967413cd31736ccc46d53fb908440d135c98 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 10:38:39 +0200 Subject: [PATCH 1545/9987] Explicitly set compiler and compilation flags --- easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb index d4ec2b5be50..7551ae8627f 100644 --- a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb @@ -14,6 +14,9 @@ source_urls = ['https://github.com/zerothi/fdict/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] +# Create file that sets the compiler (and compilation flags) to use +prebuildopts = 'echo FC=$FC > setup.make && echo FFLAGS=$FFLAGS >> setup.make &&' + files_to_copy = [(['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), (['settings.bash'], 'bin')] sanity_check_paths = { From b40f4f4d3bd84a90a7fb3cefa58775698382cc36 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 13 Oct 2021 16:14:26 +0200 Subject: [PATCH 1546/9987] Add ELSI-RCI v0.1.0 for foss/2020b and intel/2020b. --- .../e/ELSI-RCI/ELSI-RCI-0.1.0-cmake.patch | 15 +++++++ .../e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb | 41 +++++++++++++++++++ .../e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb | 40 ++++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-cmake.patch create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-cmake.patch b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-cmake.patch new file mode 100644 index 00000000000..7c836666dfa --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-cmake.patch @@ -0,0 +1,15 @@ +Patch to install the Fortran modules and the pkgconfig file. +author: Alin M. Elena (STFC UKRI) +--- CMakeLists.txt.orig 2020-02-24 16:34:41.401661825 +0000 ++++ CMakeLists.txt 2020-02-24 18:55:41.086406296 +0000 +@@ -52,3 +52,10 @@ ENDIF() + CONFIGURE_FILE(${PROJECT_SOURCE_DIR}/.elsi_rci.pc.in + ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}/pkgconfig/elsi_rci.pc + @ONLY) ++install( ++ FILES ${PROJECT_BINARY_DIR}/lib/pkgconfig/elsi_rci.pc ++ DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig ++ COMPONENT pkgconfig) ++ ++install(DIRECTORY ${CMAKE_Fortran_MODULE_DIRECTORY}/ DESTINATION include/ ++ FILES_MATCHING PATTERN "*.mod") diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb new file mode 100644 index 00000000000..1416d145598 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + + +# Compilation of tests seem to be broken, so are disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb new file mode 100644 index 00000000000..1c578e61e18 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +# Compilation of tests seem to be broken, so are disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' From 118c9dc064561a9570baa1fbfde0647f90cd7888 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Oct 2021 11:33:14 +0200 Subject: [PATCH 1547/9987] patch rsync_from_ncbi.pl in Kraken2 v2.1.2 --- .../k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb | 15 ++++++++++++++- .../Kraken2-2.1.2_fix_ncbi_https_server.patch | 13 +++++++++++++ 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2_fix_ncbi_https_server.patch diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb index a38fa3a3bf5..e8688321acd 100644 --- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb @@ -19,11 +19,15 @@ toolchainopts = {'openmp': True, 'cstd': 'c++11'} github_account = 'DerrickWood' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['Kraken2-2.1.1_fix_installation_for_easybuild.patch'] +patches = [ + 'Kraken2-2.1.1_fix_installation_for_easybuild.patch', + 'Kraken2-2.1.2_fix_ncbi_https_server.patch', +] checksums = [ 'e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3', # v2.1.2.tar.gz # Kraken2-2.1.1_fix_installation_for_easybuild.patch '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11', + '1b2f6071bb272b36fb282312681c7f3dcc202aea5007b4cdad60fcbf49d830d0', # Kraken2-2.1.2_fix_ncbi_https_server.patch ] dependencies = [ @@ -35,6 +39,15 @@ dependencies = [ install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' install_cmd += './install_kraken2.sh %(installdir)s/bin' +# Kraken2 databases can be downloaded from https://benlangmead.github.io/aws-indexes/k2 +# or built as described in https://github.com/DerrickWood/kraken2/wiki/Manual#kraken-2-databases +# The following commands will build and install the standard databases (100GB) in local_db_path +# local_db_path = '%(installdir)s/db' +# postinstallcmds = [ +# 'mkdir %s' % local_db_path, +# 'cd %%(installdir)s/bin && ./kraken2-build --standard --threads %%(parallel)s --db %s' % local_db_path, +# ] + sanity_check_paths = { 'files': ['bin/%s' % x for x in [ '16S_gg_installation.sh', '16S_rdp_installation.sh', '16S_silva_installation.sh', 'add_to_library.sh', diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2_fix_ncbi_https_server.patch b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2_fix_ncbi_https_server.patch new file mode 100644 index 00000000000..16431534bb4 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2_fix_ncbi_https_server.patch @@ -0,0 +1,13 @@ +Allow syncing from NCBI servers using HTTPS +author: Alex Domingo (Vrije Universiteit Brussel) +--- a/scripts/rsync_from_ncbi.pl 2021-10-14 01:16:34.847950000 +0200 ++++ b/scripts/rsync_from_ncbi.pl 2021-10-14 01:16:55.110006000 +0200 +@@ -43,7 +43,7 @@ + my $full_path = $ftp_path . "/" . basename($ftp_path) . $suffix; + # strip off server/leading dir name to allow --files-from= to work w/ rsync + # also allows filenames to just start with "all/", which is nice +- if (! ($full_path =~ s#^ftp://${qm_server}${qm_server_path}/##)) { ++ if (! ($full_path =~ s#^(ftp|https)://${qm_server}${qm_server_path}/##)) { + die "$PROG: unexpected FTP path (new server?) for $ftp_path\n"; + } + $manifest{$full_path} = $taxid; From 8cfa45c2816191c17547d8f45513693d3da730be Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Oct 2021 11:38:31 +0200 Subject: [PATCH 1548/9987] add link to issue in Kraken2-2.1.2_fix_ncbi_https_server.patch --- easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb | 2 +- .../k/Kraken2/Kraken2-2.1.2_fix_ncbi_https_server.patch | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb index e8688321acd..9c1671e01bd 100644 --- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021a.eb @@ -27,7 +27,7 @@ checksums = [ 'e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3', # v2.1.2.tar.gz # Kraken2-2.1.1_fix_installation_for_easybuild.patch '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11', - '1b2f6071bb272b36fb282312681c7f3dcc202aea5007b4cdad60fcbf49d830d0', # Kraken2-2.1.2_fix_ncbi_https_server.patch + '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116', # Kraken2-2.1.2_fix_ncbi_https_server.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2_fix_ncbi_https_server.patch b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2_fix_ncbi_https_server.patch index 16431534bb4..039833e73ff 100644 --- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2_fix_ncbi_https_server.patch +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2_fix_ncbi_https_server.patch @@ -1,4 +1,5 @@ Allow syncing from NCBI servers using HTTPS +Fixes issue https://github.com/DerrickWood/kraken2/issues/508 author: Alex Domingo (Vrije Universiteit Brussel) --- a/scripts/rsync_from_ncbi.pl 2021-10-14 01:16:34.847950000 +0200 +++ b/scripts/rsync_from_ncbi.pl 2021-10-14 01:16:55.110006000 +0200 From 91a75563598e6f59c118d9929dcf80cc5495cd90 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 14 Oct 2021 12:06:03 +0200 Subject: [PATCH 1549/9987] Bump versions because why not --- .../q/Qiskit/Qiskit-0.31.0-foss-2021a.eb | 156 ++++++++++++++++++ ...terra-0.18.3_fix-qiskit-version-env.patch} | 0 2 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qiskit/Qiskit-0.31.0-foss-2021a.eb rename easybuild/easyconfigs/q/Qiskit/{qiskit-terra-0.18.1_fix-qiskit-version-env.patch => qiskit-terra-0.18.3_fix-qiskit-version-env.patch} (100%) diff --git a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.31.0-foss-2021a.eb b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.31.0-foss-2021a.eb new file mode 100644 index 00000000000..ee6da687228 --- /dev/null +++ b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.31.0-foss-2021a.eb @@ -0,0 +1,156 @@ +easyblock = 'PythonBundle' + +name = 'Qiskit' +version = '0.31.0' + +homepage = 'https://qiskit.org' +description = """Qiskit is an open-source framework for working with noisy quantum computers + at the level of pulses, circuits, and algorithms.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'lowopt': True, 'vectorize': False, 'debug': True} + +builddependencies = [ + # required for building/installing qiskit-aer + ('CMake', '3.20.1'), + ('Ninja', '1.10.2'), + ('scikit-build', '0.11.1'), + ('pybind11', '2.6.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('sympy', '1.8'), + ('numba', '0.53.1'), + ('dill', '0.3.4'), + ('h5py', '3.2.1'), + ('retworkx', '0.9.0'), + ('networkx', '2.5.1'), + ('scikit-learn', '0.24.2'), + ('CVXOPT', '1.2.6'), + ('Quandl', '3.6.1'), + ('PySCF', '1.7.6'), + ('SymEngine-python', '0.7.2'), + ('lxml', '4.6.3'), + ('nlohmann_json', '3.10.0'), + ('spdlog', '1.9.2'), + ('muparserx', '4.0.8'), +] + +use_pip = True +sanity_pip_check = True +preinstallopts = 'export DISABLE_CONAN=ON &&' + +exts_list = [ + ('marshmallow', '3.13.0', { + 'checksums': ['c67929438fd73a2be92128caa0325b1b5ed8b626d91a094d2f7f2771bf1f1c0e'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('marshmallow-polyfield', '5.10', { + 'checksums': ['75d0e31b725650e91428f975a66ed30f703cc6f9fcfe45b8436ee6d676921691'], + }), + ('pylatexenc', '2.10', { + 'checksums': ['3dd8fd84eb46dc30bee1e23eaab8d8fb5a7f507347b23e5f38ad9675c84f40d3'], + }), + ('fastdtw', '0.3.4', { + 'checksums': ['2350fa6ec36bcad186eaf81f46eff35181baf04e324f522de8aeb43d0243f64f'], + }), + ('dlx', '1.0.4', { + 'checksums': ['ef75bc9d590216ebde7d4811f9ae6b2d6c6dc2a54772d94ae13384dc517a5aae'], + }), + ('docloud', '1.0.375', { + 'checksums': ['996d55407498fd01e6c6c480f367048f92255e9ca9db0e9ea19aaef91328a441'], + }), + ('docplex', '2.22.213', { + 'checksums': ['8a86bba42b5b65f2e0f88ed350115efeb783b444661e2cfcf3a67d5c59bcb0bd'], + }), + ('websockets', '10.0', { + 'checksums': ['c4fc9a1d242317892590abe5b61a9127f1a61740477bfb121743f290b8054002'], + }), + ('ntlm-auth', '1.5.0', { + 'checksums': ['c9667d361dc09f6b3750283d503c689070ff7d89f2f6ff0d38088d5436ff8543'], + }), + ('requests_ntlm', '1.1.0', { + 'checksums': ['9189c92e8c61ae91402a64b972c4802b2457ce6a799d658256ebf084d5c7eb71'], + }), + ('nest-asyncio', '1.5.1', { + 'source_tmpl': 'nest_asyncio-%(version)s.tar.gz', + 'checksums': ['afc5a1c515210a23c461932765691ad39e8eba6551c055ac8d5546e69250d0aa'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('python-constraint', '1.4.0', { + 'modulename': 'constraint', + 'source_tmpl': '%(name)s-%(version)s.tar.bz2', + 'checksums': ['501d6f17afe0032dfc6ea6c0f8acc12e44f992733f00e8538961031ef27ccb8e'], + }), + ('sparse', '0.13.0', { + 'checksums': ['685dc994aa770ee1b23f2d5392819c8429f27958771f8dceb2c4fb80210d5915'], + }), + ('fastjsonschema', '2.15.1', { + 'checksums': ['671f36d225b3493629b5e789428660109528f373cf4b8a22bac6fa2f8191c2d2'], + }), + ('tweedledum', '1.1.1', { + 'checksums': ['58d6f7a988b10c31be3faa1faf3e58288ef7e8159584bfa6ded45742f390309f'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('multitasking', '0.0.9', { + 'checksums': ['b59d99f709d2e17d60ccaa2be09771b6e9ed9391c63f083c0701e724f624d2e0'], + }), + ('yfinance', '0.1.63', { + 'checksums': ['11364fe94f1cf7811c45fc620acb61c8c45fcb88de317c7718bbdbc9c1573a4c'], + }), + ('qiskit-terra', '0.18.3', { + 'modulename': 'qiskit.qobj', + 'patches': ['qiskit-terra-0.18.3_fix-qiskit-version-env.patch'], + 'checksums': [ + '8737c8f1f4c6f29ec2fb02d73023f4854a396c33f78f4629a861a3e48fc789cc', # qiskit-terra-0.18.3.tar.gz + # qiskit-terra-0.18.3_fix-qiskit-version-env.patch + '1296cc650a7d4d2d908a6a5de6b4ce52106748464a54d47744a4648494f4c24e', + ], + }), + ('qiskit-ignis', '0.6.0', { + 'modulename': 'qiskit.ignis', + 'checksums': ['b41bbbc90a042f89d1a5bb01100d59d72facdfe18cb9fc336af74f0e94aae7fc'], + }), + ('qiskit-ibmq-provider', '0.17.0', { + 'modulename': 'qiskit.providers.ibmq', + 'checksums': ['3ffe3e43a229191f9b9dba6c05254cd0d5687f99728ba4dee8d143c59b5f0db5'], + }), + ('qiskit-optimization', '0.2.3', { + 'modulename': 'qiskit_optimization', + 'checksums': ['939c994adbb599b5039abccda70afca4da7becc21ef5ebbe3cd5d5ef71ddefce'], + }), + ('qiskit-finance', '0.2.1', { + 'modulename': 'qiskit_finance', + 'checksums': ['063f3c267efb21002f3fb8bf6766f6a4e6299fafa849a9560f2962745c83bc95'], + }), + ('qiskit-nature', '0.2.2', { + 'modulename': 'qiskit_nature', + 'checksums': ['ce3558d4acf2511111cc398361146af36391d67e5a9fe9c4bd0f727cb56022bf'], + }), + ('qiskit-machine-learning', '0.2.1', { + 'modulename': 'qiskit_machine_learning', + 'checksums': ['4afb429b36da48d9b45167758454ca53b12018320863dc2f0748b877b3ab1c29'], + }), + ('qiskit-aqua', '0.9.5', { + 'modulename': 'qiskit.aqua', + 'checksums': ['3ae50cfb008726e9862a17ba49d23bf987bc918239149db36f51c0f94e9cd36d'], + }), + ('qiskit-aer', '0.9.1', { + 'modulename': 'qiskit.providers.aer', + 'checksums': ['3bf5f615aaae7cc5f816c39a4e9108aabaed0cc894fb6f841e48ffd56574e7eb'], + }), + ('qiskit', version, { + 'checksums': ['9f5c185332ae6aa1fe02b2ec66a9b6b2442e72cc94d078c3e6c534f4db63d455'], + }), +] + +moduleclass = 'quantum' diff --git a/easybuild/easyconfigs/q/Qiskit/qiskit-terra-0.18.1_fix-qiskit-version-env.patch b/easybuild/easyconfigs/q/Qiskit/qiskit-terra-0.18.3_fix-qiskit-version-env.patch similarity index 100% rename from easybuild/easyconfigs/q/Qiskit/qiskit-terra-0.18.1_fix-qiskit-version-env.patch rename to easybuild/easyconfigs/q/Qiskit/qiskit-terra-0.18.3_fix-qiskit-version-env.patch From 6b342a744bb15f05575c76c994dfc6832154951a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 14 Oct 2021 12:08:27 +0200 Subject: [PATCH 1550/9987] Remove old version --- .../q/Qiskit/Qiskit-0.29.0-foss-2021a.eb | 161 ------------------ 1 file changed, 161 deletions(-) delete mode 100644 easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb b/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb deleted file mode 100644 index fe120508f1d..00000000000 --- a/easybuild/easyconfigs/q/Qiskit/Qiskit-0.29.0-foss-2021a.eb +++ /dev/null @@ -1,161 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Qiskit' -version = '0.29.0' -local_aerver = '0.8.2' # version of qiskit-aer - -homepage = 'https://qiskit.org' -description = """Qiskit is an open-source framework for working with noisy quantum computers - at the level of pulses, circuits, and algorithms.""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -builddependencies = [ - # required for building/installing qiskit-aer - ('CMake', '3.20.1'), - ('Ninja', '1.10.2'), - ('scikit-build', '0.11.1'), - ('pybind11', '2.6.2'), -] - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('sympy', '1.8'), - ('numba', '0.53.1'), - ('dill', '0.3.4'), - ('h5py', '3.2.1'), - ('retworkx', '0.9.0'), - ('networkx', '2.5.1'), - ('scikit-learn', '0.24.2'), - ('CVXOPT', '1.2.6'), - ('Quandl', '3.6.1'), - ('PySCF', '1.7.6'), - ('SymEngine-python', '0.7.2'), - ('lxml', '4.6.3'), - ('nlohmann_json', '3.10.0'), - ('spdlog', '1.9.2'), - ('muparserx', '4.0.8'), -] - -use_pip = True -sanity_pip_check = True -preinstallopts = 'export DISABLE_CONAN=ON &&' - -exts_list = [ - ('marshmallow', '3.13.0', { - 'checksums': ['c67929438fd73a2be92128caa0325b1b5ed8b626d91a094d2f7f2771bf1f1c0e'], - }), - ('ply', '3.11', { - 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], - }), - ('marshmallow-polyfield', '5.10', { - 'checksums': ['75d0e31b725650e91428f975a66ed30f703cc6f9fcfe45b8436ee6d676921691'], - }), - ('pylatexenc', '2.10', { - 'checksums': ['3dd8fd84eb46dc30bee1e23eaab8d8fb5a7f507347b23e5f38ad9675c84f40d3'], - }), - ('fastdtw', '0.3.4', { - 'checksums': ['2350fa6ec36bcad186eaf81f46eff35181baf04e324f522de8aeb43d0243f64f'], - }), - ('dlx', '1.0.4', { - 'checksums': ['ef75bc9d590216ebde7d4811f9ae6b2d6c6dc2a54772d94ae13384dc517a5aae'], - }), - ('docloud', '1.0.375', { - 'checksums': ['996d55407498fd01e6c6c480f367048f92255e9ca9db0e9ea19aaef91328a441'], - }), - ('docplex', '2.21.207', { - 'checksums': ['4f1781592be2b093db939772db8c6575a0f017041fb0cfd784bedf4222ac5e58'], - }), - ('websockets', '9.1', { - 'checksums': ['276d2339ebf0df4f45df453923ebd2270b87900eda5dfd4a6b0cfa15f82111c3'], - }), - ('ntlm-auth', '1.5.0', { - 'checksums': ['c9667d361dc09f6b3750283d503c689070ff7d89f2f6ff0d38088d5436ff8543'], - }), - ('requests_ntlm', '1.1.0', { - 'checksums': ['9189c92e8c61ae91402a64b972c4802b2457ce6a799d658256ebf084d5c7eb71'], - }), - ('nest-asyncio', '1.5.1', { - 'source_tmpl': 'nest_asyncio-%(version)s.tar.gz', - 'checksums': ['afc5a1c515210a23c461932765691ad39e8eba6551c055ac8d5546e69250d0aa'], - }), - ('ply', '3.11', { - 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], - }), - ('python-constraint', '1.4.0', { - 'modulename': 'constraint', - 'source_tmpl': '%(name)s-%(version)s.tar.bz2', - 'checksums': ['501d6f17afe0032dfc6ea6c0f8acc12e44f992733f00e8538961031ef27ccb8e'], - }), - ('sparse', '0.12.0', { - 'checksums': ['2c95c3b8ee00211a5aa4ef5e46006d25bf35009a66e406b7ea9b25b327fb9516'], - }), - ('fastjsonschema', '2.15.1', { - 'checksums': ['671f36d225b3493629b5e789428660109528f373cf4b8a22bac6fa2f8191c2d2'], - }), - ('tweedledum', '1.1.0', { - 'checksums': ['5779e3127c87414a5e2cc64511517881a657ff2336d00b3d8c0da0c8098066c5'], - }), - ('websocket-client', '1.1.1', { - 'modulename': 'constraint', - 'checksums': ['4cf754af7e3b3ba76589d49f9e09fd9a6c0aae9b799a89124d656009c01a261d'], - }), - ('multitasking', '0.0.9', { - 'checksums': ['b59d99f709d2e17d60ccaa2be09771b6e9ed9391c63f083c0701e724f624d2e0'], - }), - ('yfinance', '0.1.62', { - 'checksums': ['0356eaeef89ed225d272b16a0bb8393870cc68506f9aff545f9f030436044111'], - }), - ('qiskit-terra', '0.18.1', { - 'modulename': 'qiskit.qobj', - 'patches': ['qiskit-terra-0.18.1_fix-qiskit-version-env.patch'], - 'checksums': [ - '7673fa59cecdd7f7f3f22aafc8d45c76cd0b5518c72de7ae464b3823c0e2b10c', # qiskit-terra-0.18.1.tar.gz - # qiskit-terra-0.18.1_fix-qiskit-version-env.patch - '1296cc650a7d4d2d908a6a5de6b4ce52106748464a54d47744a4648494f4c24e', - ], - }), - ('qiskit-ignis', '0.6.0', { - 'modulename': 'qiskit.ignis', - 'checksums': ['b41bbbc90a042f89d1a5bb01100d59d72facdfe18cb9fc336af74f0e94aae7fc'], - }), - ('qiskit-ibmq-provider', '0.16.0', { - 'modulename': 'qiskit.providers.ibmq', - 'checksums': ['d3fbe8ad73b89cf8b0034a149c61b12a39d5e567ff5ccad9865ce3bb36acef3d'], - }), - ('qiskit-optimization', '0.2.1', { - 'modulename': 'qiskit_optimization', - 'checksums': ['718ae02f981e4dd9c4093a6ecafea7dfa97987c9fcc167afaa381bd98d514de5'], - }), - ('qiskit-finance', '0.2.0', { - 'modulename': 'qiskit_finance', - 'checksums': ['2b1ba19d09ec8fc06dd8f60d123b8ee78c7e856449d172f21da5a45d18649b58'], - }), - ('qiskit-nature', '0.1.5', { - 'modulename': 'qiskit_nature', - 'checksums': ['b5b761d9a19ce5012892c13ef5a52c2ea1576ef608c703aeed6a8062039332a6'], - }), - ('qiskit-machine-learning', '0.2.0', { - 'modulename': 'qiskit_machine_learning', - 'checksums': ['de83b3dc0a4ab01a27abfcb01a6a592d6b4d9cdfb7adb003ed37fa3eb7f48b3f'], - }), - ('qiskit-aqua', '0.9.4', { - 'modulename': 'qiskit.aqua', - 'checksums': ['fd0932b84ed86c3fb7c10e4931c6e99bb7c02883220f7e919851753a1c92598b'], - }), - ('qiskit-aer', local_aerver, { - 'modulename': 'qiskit.providers.aer', - 'checksums': ['33eed3ae158e458bf5c68b0384e5d49ee1d534bfeb2bbdc79c438e744dd54ed2'], - }), - ('qiskit', version, { - 'checksums': ['9c89419ed20cab2f18baf542805684c7a9758a87fa9a1377a5de81fcd469c077'], - }), -] - -postinstallcmds = [ - # qiskit/providers/aer/VERSION.txt does not get installed, but is required by qiskit/providers/aer/version.py - "echo %s > %%(installdir)s/lib/python%%(pyshortver)s/site-packages/qiskit/providers/aer/VERSION.txt" % local_aerver, -] - -moduleclass = 'quantum' From 5a2ce661e8400bba7f3256fa8c05a56e3a5544c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 14:25:16 +0200 Subject: [PATCH 1551/9987] filter out CUDAcore dependency variants if -CUDA-* is used in versionsuffix --- test/easyconfigs/easyconfigs.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d304b94d594..82a76669cd5 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -393,7 +393,14 @@ def check_dep_vars(self, gen, dep, dep_vars): # for some dependencies, we allow exceptions for software that depends on a particular version, # as long as that's indicated by the versionsuffix - if dep in ['ASE', 'Boost', 'Java', 'Lua', 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] and len(dep_vars) > 1: + versionsuffix_deps = ['ASE', 'Boost', 'CUDAcore', 'CUDA', 'Java', 'Lua', + 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] + if dep in versionsuffix_deps and len(dep_vars) > 1: + + # check for '-CUDA-*' versionsuffix for CUDAcore dependency + if dep == 'CUDAcore': + dep = 'CUDA' + for key in list(dep_vars): dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') # use version of Java wrapper rather than full Java version From 6c4f5be8ea77062d30db8f81c6f2c1388a70c2f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 14:26:52 +0200 Subject: [PATCH 1552/9987] add SHA256 checksum for QD 2.3.17 --- easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb b/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb index 6fc8e3fd56e..5d803a7d745 100644 --- a/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb +++ b/easybuild/easyconfigs/q/QD/QD-2.3.17-NVHPC-21.2-20160110.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'NVHPC', 'version': '21.2'} source_urls = ['https://github.com/scibuilder/QD/archive/'] sources = [{'download_filename': '%s.tar.gz' % local_gitcommit, 'filename': SOURCE_TAR_GZ}] +checksums = ['1e5949b7d20434193d496c28070d8f2fb6406a7688a86080dfdac57fbe730624'] sanity_check_paths = { 'files': ['lib/lib%s.a' % x for x in ['qdmod', 'qd']], From ad465f9322ff6e8de7c289643992b358851cb379 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 14:30:59 +0200 Subject: [PATCH 1553/9987] skip mkl_fused_batch_norm_op_test test for TensorFlow 2.5.0 (broken on AMD EPYC systems) --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 2 ++ .../TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb | 2 ++ .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index b8e0b20e478..a3949214369 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -203,6 +203,8 @@ exts_list = [ # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 '-//tensorflow/core/common_runtime:mkl_layout_pass_test', '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", 'with_xla': True, diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb index bf58ba20594..c49c3eddf10 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb @@ -219,6 +219,8 @@ exts_list = [ # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 '-//tensorflow/core/common_runtime:mkl_layout_pass_test', '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 7c571141ead..9794ccd9035 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -218,6 +218,8 @@ exts_list = [ # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 '-//tensorflow/core/common_runtime:mkl_layout_pass_test', '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + From e093ae06c8009f66f359afa20cdb2cea2f9ebfc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 14:38:22 +0200 Subject: [PATCH 1554/9987] always filter dependency variants with -CUDA-* in versionsuffix, until there's only one left --- test/easyconfigs/easyconfigs.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 82a76669cd5..55a14e2049f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -424,10 +424,12 @@ def check_dep_vars(self, gen, dep, dep_vars): # filter out variants that are specific to a particular version of CUDA cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] - if len(dep_vars) > len(cuda_dep_vars): + if len(dep_vars) >= len(cuda_dep_vars): for key in list(dep_vars): if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key): dep_vars.pop(key) + if len(dep_vars) == 1: + break # some software packages require a specific (older/newer) version of a particular dependency old_dep_versions = { From 29fa0f4a9efded60aa86e4061152e40f4abcc6b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 14:47:58 +0200 Subject: [PATCH 1555/9987] bump datestamp for morphology.zip source for ImageJ 1.52q + fix checksum --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb index 1518619044e..6e9033c0fd9 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb @@ -16,11 +16,11 @@ source_urls = [ sources = [ 'ij%(version_major)s%(version_minor)s-src.zip', # datestamp is determined by most recent file in zipball - {'download_filename': 'morphology.zip', 'filename': 'morphology-20190912.zip'}, + {'download_filename': 'morphology.zip', 'filename': 'morphology-20210426.zip'}, ] checksums = [ '2181455c75b630b9fbc11f838fe76ab490ac6d41e4aa39fcc467155847deae0e', # ij152q-src.zip - '5701de853d2b5f606f2cf0f1d3db72767b6a432bf2123a656cff06e979852079', # morphology-20190912.zip + '157f4b55759bf58458acfe073eff9af2e6bb305add2c8658f03f0ce579b3d578', # morphology-20210426.zip ] dependencies = [ From e9516ff972d193219d8ef0bc9f58d206f62473d5 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 14:49:01 +0200 Subject: [PATCH 1556/9987] Update libpsml-1.1.10-GCC-10.2.0.eb --- easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb index e6dce0ffa00..ef3d2cdb6b6 100644 --- a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ sanity_check_paths = { 'files': ['include/m_psml.mod', 'lib/libpsml.a'], - 'dirs': ['include', 'lib'], + 'dirs': [], } moduleclass = 'data' From 492fc492f134d9089d295fd8d3d7b046caa52871 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 14:56:11 +0200 Subject: [PATCH 1557/9987] fix download URL for morphology.zip in ImageJ 1.52q easyconfig --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb index 6e9033c0fd9..d0d8066f7cc 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM source_urls = [ 'https://imagej.nih.gov/ij/download/src/', - 'https://beardatashare.bham.ac.uk/dl/fiLUS55SmtWwJKijDRbwqv9p/', + 'https://github.com/landinig/IJ-Morphology/raw/main/', ] sources = [ 'ij%(version_major)s%(version_minor)s-src.zip', From 51302c5229d052dd3eb3497e74fe9d08ee7db5a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 15:03:25 +0200 Subject: [PATCH 1558/9987] fix incorrect module load message for ImageJ 1.51k --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb index 2beb2a43b9f..c9577b66ec8 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb @@ -36,6 +36,6 @@ sanity_check_paths = { 'dirs': ['plugins'], } -modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -Dij1.plugins.dir=$EBROOTIMAGEJ/plugins'\n" +modloadmsg = "To use ImageJ, run 'java -jar $EBROOTIMAGEJ/ij.jar -ijpath $EBROOTIMAGEJ'\n" moduleclass = 'tools' From 3fcb19a3263101d1300c946819349a008d18972a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 15:04:48 +0200 Subject: [PATCH 1559/9987] skip mkl_fused_batch_norm_op_test test for TensorFlow 2.6.0 (broken on AMD EPYC systems) --- .../t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 2 ++ .../easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index 98a76cbbd0d..a364baf0775 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -221,6 +221,8 @@ exts_list = [ # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 '-//tensorflow/core/common_runtime:mkl_layout_pass_test', '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb index 6d0178ed29e..60b3de282bc 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb @@ -204,6 +204,8 @@ exts_list = [ # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 '-//tensorflow/core/common_runtime:mkl_layout_pass_test', '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", 'with_xla': True, From 3af257283ec681bbc2ae4d7c2611b6397d7ead02 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 15:18:38 +0200 Subject: [PATCH 1560/9987] avoid hardcoding 2.2 version in source URL for ARTS 2.2.64 --- easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb b/easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb index 7d197a651e6..ce1e01a492b 100644 --- a/easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb +++ b/easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb @@ -16,7 +16,7 @@ description = """ toolchain = {'name': 'gompi', 'version': '2019a'} toolchainopts = {'opt': True, 'cstd': 'gnu++98', 'openmp': True} -source_urls = ['http://www.radiativetransfer.org/misc/download/stable/2.2/'] +source_urls = ['http://www.radiativetransfer.org/misc/download/stable/%(version_major_minor)s/'] sources = [ SOURCELOWER_TAR_GZ, '%(namelower)s-xml-data-2.2.5.tar.gz', From 3044833ccccb5c2e9df84cb4719d6312cae65945 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 15:32:57 +0200 Subject: [PATCH 1561/9987] style fixes for ARTS easyconfig + add sanity check command --- .../a/ARTS/ARTS-2.2.64-gompi-2019a.eb | 24 ++++++++----------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb b/easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb index ce1e01a492b..e34b81eb44a 100644 --- a/easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb +++ b/easybuild/easyconfigs/a/ARTS/ARTS-2.2.64-gompi-2019a.eb @@ -6,17 +6,14 @@ name = 'ARTS' version = '2.2.64' homepage = 'http://www.radiativetransfer.org/' - -description = """ - ARTS is a radiative transfer model for the millimeter and sub-millimeter +description = """ARTS is a radiative transfer model for the millimeter and sub-millimeter spectral range. There are a number of models mostly developed explicitly - for the different sensors. -""" + for the different sensors.""" toolchain = {'name': 'gompi', 'version': '2019a'} toolchainopts = {'opt': True, 'cstd': 'gnu++98', 'openmp': True} -source_urls = ['http://www.radiativetransfer.org/misc/download/stable/%(version_major_minor)s/'] +source_urls = ['http://www.radiativetransfer.org/misc/download/stable/2.2/'] sources = [ SOURCELOWER_TAR_GZ, '%(namelower)s-xml-data-2.2.5.tar.gz', @@ -38,17 +35,16 @@ dependencies = [ separate_build_dir = True -configopts = """\ - -DENABLE_FORTRAN=1\ - -DARTS_XML_DATA_PATH=../arts-xml-data-2.2.5\ - -DNETCDF_INCLUDE_DIR=$EBROOTNETCDF/include\ - -DNETCDF_LIBRARY=$EBROOTNETCDF/lib64/libnetcdf.so\ - -DNETCDFXX_LIBRARY=$EBROOTNETCDFMINCPLUSPLUS4/lib/libnetcdf_c++4.so\ -""" +configopts = "-DENABLE_FORTRAN=1 -DARTS_XML_DATA_PATH=../arts-xml-data-2.2.5 " +configopts += "-DNETCDF_INCLUDE_DIR=$EBROOTNETCDF/include " +configopts += "-DNETCDF_LIBRARY=$EBROOTNETCDF/lib64/libnetcdf.%s " % SHLIB_EXT +configopts += "-DNETCDFXX_LIBRARY=$EBROOTNETCDFMINCPLUSPLUS4/lib/libnetcdf_c++4.%s" % SHLIB_EXT sanity_check_paths = { - 'dirs': ['bin', 'share/arts/controlfiles/artscomponents'], 'files': ['bin/arts'], + 'dirs': ['bin', 'share/arts/controlfiles/artscomponents'], } +sanity_check_commands = ["arts --help"] + moduleclass = 'phys' From ef9e2f2158a4cc4a5272fc9c95a6dc90c0fabee2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 17:13:31 +0200 Subject: [PATCH 1562/9987] style fixes + add sanity check command for bbFTP 3.2.1 --- .../b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb | 16 ++++++++++------ easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb | 14 ++++++++------ 2 files changed, 18 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb index f9fbe576f84..9eb0166e5fc 100644 --- a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1-GCCcore-9.3.0.eb @@ -24,23 +24,27 @@ description = """bbFTP is a file transfer software. It implements its own transf toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -source_urls = [homepage + 'dist'] -sources = ['%s-client-%s.tar.gz' % (name.lower(), version)] +source_urls = ['https://software.in2p3.fr/bbftp/dist'] +sources = ['%(namelower)s-client-%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_fix-openssl-1.1.patch'] checksums = [ '4000009804d90926ad3c0e770099874084fb49013e8b0770b82678462304456d', # bbftp-client-3.2.1.tar.gz 'de8f23637a5d7b6874372c1e989fb3d7aaca6457312272021799354ee50eeb06', # bbFTP-3.2.1_fix-openssl-1.1.patch ] -start_dir = 'bbftpc' - builddependencies = [('binutils', '2.34')] + dependencies = [('zlib', '1.2.11')] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +start_dir = 'bbftpc' sanity_check_paths = { 'files': ['bin/bbftp'], - 'dirs': [] + 'dirs': [], } +sanity_check_commands = ["bbftp -v"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb index b3cd1205071..b63e78839f4 100644 --- a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb +++ b/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.1.eb @@ -24,24 +24,26 @@ description = """bbFTP is a file transfer software. It implements its own transf toolchain = SYSTEM -source_urls = [homepage + 'dist'] -sources = ['%s-client-%s.tar.gz' % (name.lower(), version)] +source_urls = ['https://software.in2p3.fr/bbftp/dist'] +sources = ['%(namelower)s-client-%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_fix-openssl-1.1.patch'] checksums = [ '4000009804d90926ad3c0e770099874084fb49013e8b0770b82678462304456d', # bbftp-client-3.2.1.tar.gz 'de8f23637a5d7b6874372c1e989fb3d7aaca6457312272021799354ee50eeb06', # bbFTP-3.2.1_fix-openssl-1.1.patch ] -start_dir = 'bbftpc' - osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), + OS_PKG_OPENSSL_DEV, ('zlib-devel', 'zlib1g-dev'), ] +start_dir = 'bbftpc' + sanity_check_paths = { 'files': ['bin/bbftp'], - 'dirs': [] + 'dirs': [], } +sanity_check_commands = ["bbftp -v"] + moduleclass = 'tools' From c0ab6aa2f149d2a76e0bf51b00c33270585caa15 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 14 Oct 2021 17:26:59 +0200 Subject: [PATCH 1563/9987] adding easyconfigs: Dalton-2020.0-foss-2021a.eb and patches: Dalton-2020.0_use_flexiblas.patch --- .../d/Dalton/Dalton-2020.0-foss-2021a.eb | 58 +++++++++++++++++++ .../Dalton/Dalton-2020.0_use_flexiblas.patch | 32 ++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use_flexiblas.patch diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb new file mode 100644 index 00000000000..02716d869c4 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'Dalton' +version = '2020.0' +#versionsuffix = '-i8' + +homepage = 'https://daltonprogram.org/' +description = """The Dalton code is a powerful tool for a wide range of molecular properties + at different levels of theory. + Any published work arising from use of one of the Dalton2016 programs + must acknowledge that by a proper reference, + https://www.daltonprogram.org/www/citation.html.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://gitlab.com/dalton', + 'repo_name': 'dalton', + 'tag': '2020.0', + 'recursive': True, + }, +}] +patches = [ + '%(name)s-2016-fix-cmake-install.patch', + '%(name)s-%(version)s_use-EB-install-for-dalton-script.patch', + '%(name)s-%(version)s_fix-uninits.patch', + '%(name)s-2016-fix-bad-includepath-add.patch', + '%(name)s-%(version)s_use_flexiblas.patch', +] +checksums = [ + None, # Dalton-2020.0.tar.gz + '3159b03a488d6f5ee23d468be02ea62eacd08cbdf68cd64ef4e5a0d469a6718b', # Dalton-2016-fix-cmake-install.patch + # Dalton-2020.0_use-EB-install-for-dalton-script.patch + '507f17638f687c4482263c2f1ccc938278772868eb78694db0be3cd58c3162d1', + 'bc446cd1a9fb63836d1d621eb92be65fcd3a46095a0ba4ecb5b7f292dccbb609', # Dalton-2020.0_fix-uninits.patch + '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch + 'c1ac29f4ebfcf42b2b3858008cbd25ffbe7035675b9d954b63a5851183f72abb', # Dalton-2020.0_use_flexiblas.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Python', '3.9.5'), +] + +configopts = '-DENABLE_MPI=ON ' +configopts += '-DENABLE_OMP=ON ' +# Only enable for BLAS/LAPACK having 8 byte integers (basically MKL) adjust the toolchainopts 'i8' option accordingly +#configopts += '-DENABLE_64BIT_INTEGERS=ON ' + +sanity_check_paths = { + 'files': ['bin/dalton', 'bin/dalton.x'], + 'dirs': ['basis'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use_flexiblas.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use_flexiblas.patch new file mode 100644 index 00000000000..daa7d942ab8 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use_flexiblas.patch @@ -0,0 +1,32 @@ +Use Flexiblas for foss/2021a toolchain + +Åke Sandgren, 20211007 +diff -ru dalton.orig/cmake/math/MathLibs.cmake dalton/cmake/math/MathLibs.cmake +--- dalton.orig/cmake/math/MathLibs.cmake 2021-10-05 14:33:14.000000000 +0200 ++++ dalton/cmake/math/MathLibs.cmake 2021-10-07 19:19:10.571066231 +0200 +@@ -74,19 +74,18 @@ + + #------------------------------------------------------------------------------- + # OPENBLAS +-# no lapack in OPENBLAS, set OPENBLAS_LAPACK_* to ATLAS and SYSTEM-NATIVE values + + set(OPENBLAS_BLAS_INCLUDE_PATH_SUFFIXES) +-set(OPENBLAS_LAPACK_INCLUDE_PATH_SUFFIXES atlas) ++set(OPENBLAS_LAPACK_INCLUDE_PATH_SUFFIXES) + +-set(OPENBLAS_BLAS_HEADERS cblas_openblas.h) +-set(OPENBLAS_LAPACK_HEADERS clapack.h) ++set(OPENBLAS_BLAS_HEADERS cblas.h) ++set(OPENBLAS_LAPACK_HEADERS lapack.h) + + set(OPENBLAS_BLAS_LIBRARY_PATH_SUFFIXES) +-set(OPENBLAS_LAPACK_LIBRARY_PATH_SUFFIXES atlas atlas-base atlas-base/atlas atlas-sse3) ++set(OPENBLAS_LAPACK_LIBRARY_PATH_SUFFIXES) + +-set(OPENBLAS_BLAS_LIBS openblas) +-set(OPENBLAS_LAPACK_LIBS atlas lapack) ++set(OPENBLAS_BLAS_LIBS flexiblas) ++set(OPENBLAS_LAPACK_LIBS flexiblas) + + #------------------------------------------------------------------------------- + # MKL From 6042d453a0c781a0ff890f8ee7ce1864eb1d88a9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 14 Oct 2021 17:48:56 +0200 Subject: [PATCH 1564/9987] Drop useless comments --- easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb index 02716d869c4..fd21030fa02 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb @@ -2,7 +2,6 @@ easyblock = 'CMakeMake' name = 'Dalton' version = '2020.0' -#versionsuffix = '-i8' homepage = 'https://daltonprogram.org/' description = """The Dalton code is a powerful tool for a wide range of molecular properties @@ -47,8 +46,6 @@ builddependencies = [ configopts = '-DENABLE_MPI=ON ' configopts += '-DENABLE_OMP=ON ' -# Only enable for BLAS/LAPACK having 8 byte integers (basically MKL) adjust the toolchainopts 'i8' option accordingly -#configopts += '-DENABLE_64BIT_INTEGERS=ON ' sanity_check_paths = { 'files': ['bin/dalton', 'bin/dalton.x'], From 1226c487212f405b74421872d04909e73b66739c Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 14 Oct 2021 17:57:30 +0200 Subject: [PATCH 1565/9987] Make sure to set up the makefile and use Lua as a dep --- .../f/flook/flook-0.8.1-GCC-10.2.0.eb | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb index 6b9f747a77f..8ddf6098dd0 100644 --- a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb @@ -14,7 +14,21 @@ source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] sources = ['v%(version)s/flook-%(version)s.tar.gz'] checksums = ['beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'] -dependencies = [('libreadline', '8.0')] +dependencies = [('Lua', '5.4.2')] + +# Construct the 'setup.make' file +prebuildopts = 'echo CC = $CC > setup.make &&' +prebuildopts += 'echo FC = "$FC" >> setup.make &&' +prebuildopts += 'echo CFLAGS = "$CFLAGS" >> setup.make &&' +prebuildopts += 'echo FFLAGS = "$FFLAGS" >> setup.make &&' +prebuildopts += 'echo ".f90.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo ".F90.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo ".c.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(CC) -c \$(CFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo "LUA_DIR = $EBROOTLUA" >> setup.make &&' +prebuildopts += 'echo "INC += -I\$(LUA_DIR)/include" >> setup.make &&' buildopts = ' liball ' parallel = 1 From e48ac2a9622f8b5bd19c25f5ef3f6ccea078cad2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 19:33:57 +0200 Subject: [PATCH 1566/9987] ensure that at least one dep variant is retained --- test/easyconfigs/easyconfigs.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 55a14e2049f..5ff653023d4 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -393,7 +393,7 @@ def check_dep_vars(self, gen, dep, dep_vars): # for some dependencies, we allow exceptions for software that depends on a particular version, # as long as that's indicated by the versionsuffix - versionsuffix_deps = ['ASE', 'Boost', 'CUDAcore', 'CUDA', 'Java', 'Lua', + versionsuffix_deps = ['ASE', 'Boost', 'CUDAcore', 'Java', 'Lua', 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] if dep in versionsuffix_deps and len(dep_vars) > 1: @@ -424,10 +424,11 @@ def check_dep_vars(self, gen, dep, dep_vars): # filter out variants that are specific to a particular version of CUDA cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] - if len(dep_vars) >= len(cuda_dep_vars): + if len(dep_vars) >= len(cuda_dep_vars) and len(dep_vars) > 1: for key in list(dep_vars): if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key): dep_vars.pop(key) + # always retain at least one dep variant if len(dep_vars) == 1: break From 33f18b4c6a633300c3875f8e4ef4a8a36dc39d0f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 14 Oct 2021 19:17:53 +0100 Subject: [PATCH 1567/9987] Fix AmberTools build with intel compiler --- .../AmberTools-20-intel-2020a-Python-3.8.2.eb | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb index 9522267acdf..5269f85d1b1 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb @@ -20,13 +20,11 @@ sources = [{ 'filename': SOURCE_TAR_BZ2, }] patches = [ - 'Amber-20_fix-hardcoding.patch', 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_cmake-locate-netcdf.patch', ] checksums = [ 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools-20.tar.bz2 - 'a71f1bd70bac8d5e25386d6db90e95874ad300b956ed5b5afbc8848b7c1e00dc', # Amber-20_fix-hardcoding.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch' '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch @@ -46,10 +44,11 @@ dependencies = [ ('FFTW', '3.3.8'), ] -# fix linking to netCDF library: also requires linking to HDF5 & cURL libs, which in turns require others, -# all of which are indirect dependencies via netCDF -local_netcdf_libs = "-lnetcdf -lhdf5 -lsz -ldl -liomp5 -lcurl -lssl -lcrypto -lz -lm -lpthread" -preconfigopts = "sed -i'' 's/-lnetcdf/%s/g' %%(builddir)s/AmberTools/src/cpptraj/configure && " % local_netcdf_libs -configopts = "-nosanderapi" +# pysander should link with icc and not gcc +prebuildopts = """sed -i 's/import sys/import sys; os.environ["LDSHARED"] = "icc -shared "/g' """ +prebuildopt + = "%(builddir)s/AmberTools/src/pysander/setup.py && " + +# Tests use pmemd which is not part of AmberTools +runtest = False moduleclass = 'chem' From 7dc647a8f665d1f8b92d2e37ad42a04e8a632b6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 20:33:25 +0200 Subject: [PATCH 1568/9987] strip out extracting of examples in imkl easyconfig, now done by imkl easyblock --- .../i/imkl/imkl-2020.4.304-NVHPC-21.2.eb | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb index bf4b096ac1f..75ac380269e 100644 --- a/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.4.304-NVHPC-21.2.eb @@ -23,17 +23,4 @@ license_file = HOME + '/licenses/intel/license.lic' interfaces = True -postinstallcmds = [ - # extract the examples - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', - 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', -] - -modextravars = { - 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', -} - moduleclass = 'numlib' From 035d68917deb1a048771ec30f4f66a5d49d6b09b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 20:48:19 +0200 Subject: [PATCH 1569/9987] add missing patch for OpenMPI 4.0.5, add back commented out configure option to re-enable MPI-1 --- .../o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb index 8ef2dc343ed..949050f89e9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -10,7 +10,12 @@ toolchainopts = {'pic': True} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] +patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +checksums = [ + '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz + # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', +] builddependencies = [ ('pkg-config', '0.29.2'), @@ -25,9 +30,11 @@ dependencies = [ ('PMIx', '3.1.5'), ] -# disable MPI1 compatibility for now, see what breaks... configopts = '--with-cuda=$EBROOTCUDACORE ' +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + # to enable SLURM integration (site-specific) # configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' From 76e4db6be334afbfcc212c4186aa5abc5d370ada Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Oct 2021 20:50:51 +0200 Subject: [PATCH 1570/9987] fix typo in prebuildopts in AmberTools 20 easyconfig --- .../a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb index 5269f85d1b1..5f2a5ab4633 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb @@ -46,7 +46,7 @@ dependencies = [ # pysander should link with icc and not gcc prebuildopts = """sed -i 's/import sys/import sys; os.environ["LDSHARED"] = "icc -shared "/g' """ -prebuildopt + = "%(builddir)s/AmberTools/src/pysander/setup.py && " +prebuildopts += "%(builddir)s/AmberTools/src/pysander/setup.py && " # Tests use pmemd which is not part of AmberTools runtest = False From 05b5886b802768775d7528540f6d27575c574a90 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 15 Oct 2021 09:09:07 +0200 Subject: [PATCH 1571/9987] Update ELSI-RCI-0.1.0-foss-2020b.eb --- easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb index 1416d145598..24ee50dfb95 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2020b.eb @@ -25,7 +25,7 @@ builddependencies = [ ] -# Compilation of tests seem to be broken, so are disable it +# Compilation of tests seem to be broken, so disable it configopts = [ "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" From b2e09d357de3c03fb4b632f2f8f51063ee1c3982 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 15 Oct 2021 09:09:30 +0200 Subject: [PATCH 1572/9987] Update ELSI-RCI-0.1.0-intel-2020b.eb --- easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb index 1c578e61e18..8e5e7166b30 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2020b.eb @@ -24,7 +24,7 @@ builddependencies = [ ('CMake', '3.18.4'), ] -# Compilation of tests seem to be broken, so are disable it +# Compilation of tests seem to be broken, so disable it configopts = [ "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" From 7263fe5c4e6e4f510be3f4ca95c066a6903327a1 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 15 Oct 2021 09:17:09 +0200 Subject: [PATCH 1573/9987] Affinity must be enabled to compile on Rocky Linux 8 (and other recent OS) --- .../easyconfigs/p/pftoolsV3/pftoolsV3-3.2.10-foss-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.10-foss-2021a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.10-foss-2021a.eb index 0f27a4e56f9..bd87527dfce 100644 --- a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.10-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.10-foss-2021a.eb @@ -38,8 +38,6 @@ dependencies = [ configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX:PATH=%(installdir)s -DCMAKE_BUILD_TYPE=Release ' configure_cmd += '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON ' -# Disable affinity at compile time for old processors -configure_cmd += '-DUSE_AFFINITY=OFF ' configure_cmd += '../pftools3-%(version)s' runtest = 'test' From be67f00d876e9faf142d5dc898ebb4bdce5d62c2 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 29 Jan 2021 16:34:26 +0100 Subject: [PATCH 1574/9987] Add NTPoly-2.5.1-foss-2020b.eb. --- .../n/NTPoly/NTPoly-2.5.1-foss-2020b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb new file mode 100644 index 00000000000..148464f5a74 --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.5.1' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5d1abd3dc3286167caf0c326ef14838ac8360aa1e912bd7bd6d212259fbff1ac'] + +configopts = ['-DBUILD_SHARED_LIBS=on'] + +builddependencies = [('CMake', '3.18.4')] + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From 586e441da780b2888ebc2088ad58cfa5fbfb0b69 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 9 Jun 2021 15:23:59 +0200 Subject: [PATCH 1575/9987] Add Bison-3.5.3-GCCcore-10.2.0.eb. This is required to compile ELSI-2.6.4, as it does not seem to work with newer versions of Bison. --- .../b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c20e3f3948d --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.5.3' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['34e201d963156618a0ea5bc87220f660a1e08403dd3c7c7903d4f38db3f40039'] + +builddependencies = [ + ('M4', '1.4.18'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.35', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' From f07fed7cebacad61960a6d046a86c246dd2d940f Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 9 Jun 2021 15:50:42 +0200 Subject: [PATCH 1576/9987] Add ELSI-2.6.4-foss-2020b with external NTPoly. --- .../e/ELSI/ELSI-2.6.4-foss-2020b.eb | 39 +++++ .../e/ELSI/pexsi-1.2.0-mpi30.patch | 165 ++++++++++++++++++ 2 files changed, 204 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b.eb create mode 100644 easybuild/easyconfigs/e/ELSI/pexsi-1.2.0-mpi30.patch diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b.eb new file mode 100644 index 00000000000..b80892bb43d --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b.eb @@ -0,0 +1,39 @@ +name = 'ELSI' +version = '2.6.4' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['pexsi-1.2.0-mpi30.patch'] +checksums = [ + 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz + 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.5.3'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('ELPA', '2020.11.001'), + ('NTPoly', '2.5.1'), +] + +build_internal_pexsi = True + +configopts = "-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS='-fallow-argument-mismatch' -DCMAKE_CXX_FLAGS='-std=c++11'" + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/pexsi-1.2.0-mpi30.patch b/easybuild/easyconfigs/e/ELSI/pexsi-1.2.0-mpi30.patch new file mode 100644 index 00000000000..d1378648fe3 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/pexsi-1.2.0-mpi30.patch @@ -0,0 +1,165 @@ +Patch to fix compilation with MPI 4. +author: Alin M. Elena (STFC UKRI) +--- external/PEXSI/include/pexsi/utility_impl.hpp.orig 2020-12-04 16:27:25.652001387 +0000 ++++ external/PEXSI/include/pexsi/utility_impl.hpp 2020-12-04 16:40:14.523500099 +0000 +@@ -367,12 +367,12 @@ inline void ParaWriteDistSparseMatrix ( + + /* create memory type */ + Int np1 = pspmat.size+1; +- MPI_Address( (void *)&np1, &disps[0]); +- MPI_Address(colptrChunk.Data(), &disps[1]); +- MPI_Address( (void *)&pspmat.nnz, &disps[2]); +- MPI_Address((void *)pspmat.rowindLocal.Data(), &disps[3]); +- MPI_Address( (void *)&pspmat.nnz, &disps[4]); +- MPI_Address((void *)pspmat.nzvalLocal.Data(), &disps[5]); ++ MPI_Get_address( (void *)&np1, &disps[0]); ++ MPI_Get_address(colptrChunk.Data(), &disps[1]); ++ MPI_Get_address( (void *)&pspmat.nnz, &disps[2]); ++ MPI_Get_address((void *)pspmat.rowindLocal.Data(), &disps[3]); ++ MPI_Get_address( (void *)&pspmat.nnz, &disps[4]); ++ MPI_Get_address((void *)pspmat.nzvalLocal.Data(), &disps[5]); + + MPI_Type_create_struct(6, blklens, disps, types, &memtype); + MPI_Type_commit(&memtype); +@@ -440,11 +440,11 @@ inline void ParaReadDistSparseMatrix ( c + /* define a struct that describes all our data */ + lens[0] = 1; + lens[1] = 1; +- MPI_Address(&pspmat.size, &disps[0]); +- MPI_Address(&pspmat.nnz, &disps[1]); ++ MPI_Get_address(&pspmat.size, &disps[0]); ++ MPI_Get_address(&pspmat.nnz, &disps[1]); + types[0] = MPI_INT; + types[1] = MPI_INT; +- MPI_Type_struct(2, lens, disps, types, &type); ++ MPI_Type_create_struct(2, lens, disps, types, &type); + MPI_Type_commit(&type); + + +@@ -470,10 +470,10 @@ inline void ParaReadDistSparseMatrix ( c + lens[0] = (mpirank==0)?1:0; + lens[1] = numColLocal + 1; + +- MPI_Address(&np1, &disps[0]); +- MPI_Address(pspmat.colptrLocal.Data(), &disps[1]); ++ MPI_Get_address(&np1, &disps[0]); ++ MPI_Get_address(pspmat.colptrLocal.Data(), &disps[1]); + +- MPI_Type_hindexed(2, lens, disps, MPI_INT, &type); ++ MPI_Type_create_hindexed(2, lens, disps, MPI_INT, &type); + MPI_Type_commit(&type); + + err= MPI_File_read_at_all(fin, myColPtrOffset, MPI_BOTTOM, 1, type, &status); +@@ -496,10 +496,10 @@ inline void ParaReadDistSparseMatrix ( c + lens[0] = (mpirank==0)?1:0; + lens[1] = pspmat.nnzLocal; + +- MPI_Address(&np1, &disps[0]); +- MPI_Address(pspmat.rowindLocal.Data(), &disps[1]); ++ MPI_Get_address(&np1, &disps[0]); ++ MPI_Get_address(pspmat.rowindLocal.Data(), &disps[1]); + +- MPI_Type_hindexed(2, lens, disps, MPI_INT, &type); ++ MPI_Type_create_hindexed(2, lens, disps, MPI_INT, &type); + MPI_Type_commit(&type); + + err= MPI_File_read_at_all(fin, myRowIdxOffset, MPI_BOTTOM, 1, type,&status); +@@ -516,8 +516,8 @@ inline void ParaReadDistSparseMatrix ( c + // lens[0] = (mpirank==0)?1:0; + // lens[1] = pspmat.nnzLocal; + // +-// MPI_Address(&np1, &disps[0]); +-// MPI_Address(pspmat.nzvalLocal.Data(), &disps[1]); ++// MPI_Get_address(&np1, &disps[0]); ++// MPI_Get_address(pspmat.nzvalLocal.Data(), &disps[1]); + // + // types[0] = MPI_INT; + // types[1] = MPI_DOUBLE; +@@ -748,11 +748,11 @@ inline void ParaReadDistSparseMatrix ( c + /* define a struct that describes all our data */ + lens[0] = 1; + lens[1] = 1; +- MPI_Address(&pspmat.size, &disps[0]); +- MPI_Address(&pspmat.nnz, &disps[1]); ++ MPI_Get_address(&pspmat.size, &disps[0]); ++ MPI_Get_address(&pspmat.nnz, &disps[1]); + types[0] = MPI_INT; + types[1] = MPI_INT; +- MPI_Type_struct(2, lens, disps, types, &type); ++ MPI_Type_create_struct(2, lens, disps, types, &type); + MPI_Type_commit(&type); + + +@@ -778,10 +778,10 @@ inline void ParaReadDistSparseMatrix ( c + lens[0] = (mpirank==0)?1:0; + lens[1] = numColLocal + 1; + +- MPI_Address(&np1, &disps[0]); +- MPI_Address(pspmat.colptrLocal.Data(), &disps[1]); ++ MPI_Get_address(&np1, &disps[0]); ++ MPI_Get_address(pspmat.colptrLocal.Data(), &disps[1]); + +- MPI_Type_hindexed(2, lens, disps, MPI_INT, &type); ++ MPI_Type_create_hindexed(2, lens, disps, MPI_INT, &type); + MPI_Type_commit(&type); + + err= MPI_File_read_at_all(fin, myColPtrOffset, MPI_BOTTOM, 1, type, &status); +@@ -804,11 +804,11 @@ inline void ParaReadDistSparseMatrix ( c + lens[0] = (mpirank==0)?1:0; + lens[1] = pspmat.nnzLocal; + +- MPI_Address(&np1, &disps[0]); +- MPI_Address(pspmat.rowindLocal.Data(), &disps[1]); ++ MPI_Get_address(&np1, &disps[0]); ++ MPI_Get_address(pspmat.rowindLocal.Data(), &disps[1]); + +-// MPI_Type_hindexed(2, lens, disps, MPI_INT, &type); +- MPI_Type_hindexed(2, lens, disps, MPI_INT, &type); ++// MPI_Type_create_hindexed(2, lens, disps, MPI_INT, &type); ++ MPI_Type_create_hindexed(2, lens, disps, MPI_INT, &type); + MPI_Type_commit(&type); + + err= MPI_File_read_at_all(fin, myRowIdxOffset, MPI_BOTTOM, 1, type,&status); +@@ -825,8 +825,8 @@ inline void ParaReadDistSparseMatrix ( c + // lens[0] = ((mpirank==0)?1:0)*sizeof(Int); + // lens[1] = pspmat.nnzLocal*sizeof(Complex); + // +-// MPI_Address(&np1, &disps[0]); +-// MPI_Address(pspmat.nzvalLocal.Data(), &disps[1]); ++// MPI_Get_address(&np1, &disps[0]); ++// MPI_Get_address(pspmat.nzvalLocal.Data(), &disps[1]); + // + // types[0] = MPI_INT; + // types[1] = MPI_DOUBLE_COMPLEX; +@@ -963,12 +963,12 @@ inline void ParaWriteDistSparseMatrix ( + + /* create memory type */ + Int np1 = pspmat.size+1; +- MPI_Address( (void *)&np1, &disps[0]); +- MPI_Address(colptrChunk.Data(), &disps[1]); +- MPI_Address( (void *)&pspmat.nnz, &disps[2]); +- MPI_Address((void *)pspmat.rowindLocal.Data(), &disps[3]); +- MPI_Address( (void *)&pspmat.nnz, &disps[4]); +- MPI_Address((void *)pspmat.nzvalLocal.Data(), &disps[5]); ++ MPI_Get_address( (void *)&np1, &disps[0]); ++ MPI_Get_address(colptrChunk.Data(), &disps[1]); ++ MPI_Get_address( (void *)&pspmat.nnz, &disps[2]); ++ MPI_Get_address((void *)pspmat.rowindLocal.Data(), &disps[3]); ++ MPI_Get_address( (void *)&pspmat.nnz, &disps[4]); ++ MPI_Get_address((void *)pspmat.nzvalLocal.Data(), &disps[5]); + + MPI_Type_create_struct(6, blklens, disps, types, &memtype); + MPI_Type_commit(&memtype); +--- external/PEXSI/include/pexsi/TreeBcast_v2_impl.hpp.orig 2020-12-18 18:03:17.282895534 +0000 ++++ external/PEXSI/include/pexsi/TreeBcast_v2_impl.hpp 2020-12-18 18:04:57.686747053 +0000 +@@ -64,8 +64,8 @@ namespace PEXSI{ + sendPostedCount_ = 0; + mainRoot_=ranks[0]; + #ifdef CHECK_MPI_ERROR +- MPI_Errhandler_set(this->comm_, MPI_ERRORS_RETURN); +- MPI_Errhandler_set(MPI_COMM_WORLD, MPI_ERRORS_RETURN); ++ MPI_Comm_set_errhandler(this->comm_, MPI_ERRORS_RETURN); ++ MPI_Comm_set_errhandler(MPI_COMM_WORLD, MPI_ERRORS_RETURN); + #endif + } + From 8f9579edcf6417547fdb1c6d6c1fa4b57a4e4f8e Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 9 Jun 2021 17:40:24 +0200 Subject: [PATCH 1577/9987] Add ELSI-2.6.4-intel-2020b and NTPoly-2.5.1-intel-2020b. --- .../e/ELSI/ELSI-2.6.4-intel-2020b.eb | 37 +++++++++++++++++++ .../n/NTPoly/NTPoly-2.5.1-intel-2020b.eb | 27 ++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b.eb create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b.eb new file mode 100644 index 00000000000..e4a90c9f5af --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b.eb @@ -0,0 +1,37 @@ +name = 'ELSI' +version = '2.6.4' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.5.3'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('ELPA', '2020.11.001'), + ('NTPoly', '2.5.1'), +] + +build_internal_pexsi = True + +configopts = "-DENABLEBSEPACK=ON" + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb new file mode 100644 index 00000000000..38ed055e46a --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.5.1' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5d1abd3dc3286167caf0c326ef14838ac8360aa1e912bd7bd6d212259fbff1ac'] + +configopts = ['-DBUILD_SHARED_LIBS=on'] + +builddependencies = [('CMake', '3.18.4')] + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From 8e984750e81391e3ca26e74a0f63176c22075f57 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 15 Oct 2021 10:59:12 +0200 Subject: [PATCH 1578/9987] adding easyconfigs: GLUI-2.37-intel-2020b.eb, lpeg-1.0.2-intel-2020b.eb, SMV-6.7.17-intel-2020b.eb and patches: SMV-6.7.17_missing-includes.patch --- .../g/GLUI/GLUI-2.37-intel-2020b.eb | 48 +++ .../l/lpeg/lpeg-1.0.2-intel-2020b.eb | 39 +++ .../s/SMV/SMV-6.7.17-intel-2020b.eb | 59 ++++ .../s/SMV/SMV-6.7.17_missing-includes.patch | 313 ++++++++++++++++++ 4 files changed, 459 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb create mode 100644 easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb create mode 100644 easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb create mode 100644 easybuild/easyconfigs/s/SMV/SMV-6.7.17_missing-includes.patch diff --git a/easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb b/easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb new file mode 100644 index 00000000000..78db8320618 --- /dev/null +++ b/easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +## + +easyblock = 'CMakeMake' + +name = 'GLUI' +version = '2.37' + +homepage = 'https://github.com/libglui/glui' +description = """This distribution contains the latest community-maintained fork of +the GLUI Library, now under the ZLIB license.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://github.com//libglui/glui/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('freeglut', '3.2.1'), + ('Mesa', '20.2.1'), +] + +configopts = ' -DCMAKE_CXX_FLAGS="$CXXFLAGS" ' + +skipsteps = ['install'] + +postinstallcmds = [ + 'mv %(installdir)s/include %(installdir)s/glui.h', + 'mkdir %(installdir)s/include ', + 'mv %(installdir)s/glui.h %(installdir)s/include ', + 'cp %(builddir)s/easybuild_obj/libglui.so %(installdir)s/lib ', + 'cp %(builddir)s/easybuild_obj/libglui_static.a %(installdir)s/lib ', + 'cp %(builddir)s/glui-%(version)s/*.h %(installdir)s/include/ ', +] + +sanity_check_paths = { + 'files': ['lib/libglui.so', 'lib/libglui_static.a'], + 'dirs': ['lib'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb b/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb new file mode 100644 index 00000000000..17dca8b71da --- /dev/null +++ b/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +## + +easyblock = 'MakeCp' + +name = 'lpeg' +version = '1.0.2' + +homepage = 'http://www.inf.puc-rio.br/~roberto/lpeg/' +description = """LPeg is a new pattern-matching library for Lua, based on Parsing Expression Grammars (PEGs).""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['http://www.inf.puc-rio.br/~roberto/lpeg/'] +sources = ['%(name)s-%(version)s.tar.gz'] + +dependencies = [ + ('Lua', '5.4.2'), +] + +# list of all the libraries we need before installation: +# /user/gent/438/vsc43810/eb_inuits/210_smokeview/smv-SMV6.7.17/Build/LIBS/intel_linux_64/make_LIBS.make +# make sure to include those libraries in make commands when building SMV + +# shell script which runs makefile. actual smokeview: +# /user/gent/438/vsc43810/eb_inuits/210_smokeview/smv-SMV6.7.17/Build/smokeview/intel_linux_64/make_smokeview_db.sh + +# universal makefile for all OS - /user/gent/438/vsc43810/eb_inuits/210_smokeview/smv-SMV6.7.17/Build/smokeview/Makefile + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ["lpcode.o", "lpprint.o", "lptree.o", "lpvm.o"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb new file mode 100644 index 00000000000..2bf1ff1284a --- /dev/null +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb @@ -0,0 +1,59 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +## + +easyblock = 'MakeCp' + +name = 'SMV' # SmokeView +version = '6.7.17' + +homepage = 'https://github.com/firemodels/smv' +description = """Smokeview is a visualization program that displays output of FDS and CFAST simulations.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://github.com/firemodels/%(name)s/archive/refs/tags/'] +sources = ['%(name)s%(version)s.tar.gz'] +patches = ['SMV-%(version)s_missing-includes.patch'] +checksums = ['2e718af991e48228bf374fdefcce00d2e8b5827cc29ae2138ae267fda896f127'] + +dependencies = [ + ('libgd', '2.3.0'), + ('freeglut', '3.2.1'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('Lua', '5.4.2'), + ('lpeg', '1.0.2'), + ('libGLU', '9.0.1'), + ('glew', '2.1.0'), +] + +local_compiler_lib_append = '/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64_lin/' + +local_buildopts = ' -lglui -lglut -lfreeglut -lGLU -lGL LDFLAGS=" -L%(installdir)s -L$EBROOTFREEGLUT/lib " ' +local_buildopts += ' IFLAGS=" -I$EBROOTFREEGLUT/include/GL -I%(builddir)s/smv-SMV%(version)s/Source/glui_v2_1_beta/ ' +local_buildopts += ' -I%(builddir)s/smv-SMV%(version)s/Source/glui_gl/GL/glut.h "' +local_buildopts += ' EB_L_PATH=%(installdir)s ' +local_buildopts += ' CFLAGS="-Dpp_LINUX" ' + +prebuildopts = "cd %(builddir)s/smv-SMV%(version)s/Build/LIBS/intel_linux_64/ && " +prebuildopts += " make all -f make_LIBS.make " +prebuildopts += "SRCDIR=%(builddir)s/smv-SMV%(version)s/Source/ LIBDIR=%(installdir)s && " +prebuildopts += "cd %(builddir)s/smv-SMV%(version)s/Build/smokeview/ && " +prebuildopts += "export IFORT_COMPILER_LIB=$EBROOTICCIFORT%s && " % local_compiler_lib_append + +buildopts = ' intel_linux_64 ' + local_buildopts +buildopts += ' && make -j 36 intel_linux_64_db ' + local_buildopts + +files_to_copy = [ + (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64", "./Build/smokeview/smokeview_linux_64_db"], 'bin') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["bin"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17_missing-includes.patch b/easybuild/easyconfigs/s/SMV/SMV-6.7.17_missing-includes.patch new file mode 100644 index 00000000000..5d6702a0958 --- /dev/null +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17_missing-includes.patch @@ -0,0 +1,313 @@ +diff -ruN smv-SMV6.7.17_orig/Build/LIBS/intel_linux_64/make_LIBS.make smv-SMV6.7.17/Build/LIBS/intel_linux_64/make_LIBS.make +--- smv-SMV6.7.17_orig/Build/LIBS/intel_linux_64/make_LIBS.make 2021-10-11 15:54:47.661332000 +0200 ++++ smv-SMV6.7.17/Build/LIBS/intel_linux_64/make_LIBS.make 2021-10-14 13:59:41.548566000 +0200 +@@ -1,18 +1,12 @@ + OPTS="-I $*" +-LIBDIR=$(shell pwd) +-SRCDIR=$(LIBDIR)/../../../Source ++LIBDIR?=$(shell pwd) ++SRCDIR?=$(LIBDIR)/../../../Source + +-all: libgd.a libglui.a libglut.a libjpeg.a libpng.a libz.a +- +-# GD +-libgd.a: +- @echo $(LIBDIR) +- cd $(SRCDIR)/gd-2.0.15; \ +- ./makelib.sh $(OPTS); \ +- cp libgd.a $(LIBDIR)/. ++all: libglui.a libglut.a + + # GLUI + libglui.a: ++ @echo $(LIBDIR); + cd $(SRCDIR)/glui_v2_1_beta; \ + ./makelib.sh $(OPTS); \ + cp libglui.a $(LIBDIR)/. +@@ -24,38 +18,4 @@ + ./makelib.sh $(OPTS); \ + cp libglut.a $(LIBDIR)/. + +-# JPEG +-libjpeg.a: +- cd $(SRCDIR)/jpeg-9b; \ +- ./makelib.sh $(OPTS); \ +- cp libjpeg.a $(LIBDIR)/. +- +-# PNG +-libpng.a: +- cd $(SRCDIR)/png-1.6.21; \ +- ./makelib.sh $(OPTS); \ +- cp libpng.a $(LIBDIR)/. +- +-# ZLIB +-libz.a: +- cd $(SRCDIR)/zlib128; \ +- ./makelib.sh $(OPTS); \ +- cp libz.a $(LIBDIR)/. +- +-# Lua # Lua interpreter +-liblua.a: +- cd $(SRCDIR)/lua-5.3.1; \ +- export TARGET=linux; \ +- ./makelib.sh $(OPTS); \ +- cp src/liblua.a $(LIBDIR)/. +- +-# LPEG # Lua parsing libarary to parse SSF files +-# This depends on lua being built first +-lpeg.so: liblua.a +- cd $(SRCDIR)/lpeg-1.0.0; \ +- pwd; \ +- export TARGET=linux; \ +- ./makelib.sh $(OPTS); \ +- cp lpeg.so $(LIBDIR)/. +- + .PHONY: all +diff -ruN smv-SMV6.7.17_orig/Build/smokeview/Makefile smv-SMV6.7.17/Build/smokeview/Makefile +--- smv-SMV6.7.17_orig/Build/smokeview/Makefile 2021-10-11 15:54:45.856668000 +0200 ++++ smv-SMV6.7.17/Build/smokeview/Makefile 2021-10-11 14:19:20.498029000 +0200 +@@ -3,8 +3,8 @@ + + #To use this Makefile cd to a sub-directory and type make_smv.sh or make_smv.bat + +-SOURCE_DIR = ../../../Source/ +-BUILD_DIR = ../../../Build ++SOURCE_DIR = ../../Source/ ++BUILD_DIR = ../../Build + LIB_DIR = $(BUILD_DIR)/LIBS + + # Set the C standard we are using. Currently this is just the appropriate flag +@@ -18,27 +18,16 @@ + SMV_PROFILESTRING = + COMP_VERSION = + LUA_SCRIPTING = +-ifeq ($(shell echo "check_quotes"),"check_quotes") +- GIT_HASH := $(shell ..\..\..\Utilities\Scripts\githash) +- GIT_DATE := $(shell ..\..\..\Utilities\Scripts\gitlog) +- GIT_BRANCH := $(shell ..\..\..\Utilities\Scripts\gitbranch) +-else +- GLIBVERS := $(shell echo $(GLIBVERS)) +- GIT_HASH := $(shell git describe --long --dirty) +- GIT_DATE := $(shell git log -1 --format=%cd) +- GIT_BRANCH := $(shell git rev-parse --abbrev-ref HEAD) +-endif +-GITINFO=-Dpp_GITHASH=\"$(GIT_HASH)-$(GIT_BRANCH)\" -Dpp_GITDATE=\""$(GIT_DATE)\"" + + ifeq ($(shell echo "check_quotes"),"check_quotes") +- INTEL_COMPVERSION := $(shell ..\..\..\Utilities\Scripts\intel_compversion) +- GNU_COMPVERSION := $(shell ..\..\..\Utilities\Scripts\gnu_compversion) ++ INTEL_COMPVERSION := $(shell ..\..\Utilities\Scripts\intel_compversion) ++ GNU_COMPVERSION := $(shell ..\..\Utilities\Scripts\gnu_compversion) + else +- INTEL_COMPVERSION := $(shell ../../../Utilities/Scripts/intel_compversion.sh) +- GNU_COMPVERSION := $(shell ../../../Utilities/Scripts/gnu_compversion.sh) ++ INTEL_COMPVERSION := $(shell ../../Utilities/Scripts/intel_compversion.sh) ++ GNU_COMPVERSION := $(shell ../../Utilities/Scripts/gnu_compversion.sh) + endif +-INTEL_COMPINFO=-Dpp_COMPVER=\"$(INTEL_COMPVERSION)\" +-GNU_COMPINFO=-Dpp_COMPVER=\"$(GNU_COMPVERSION)\" ++ INTEL_COMPINFO=-Dpp_COMPVER=\"$(INTEL_COMPVERSION)\" ++ GNU_COMPINFO=-Dpp_COMPVER=\"$(GNU_COMPVERSION)\" + + .rc.obj: + windres $< -o $@ +@@ -84,7 +73,7 @@ + + objwin = $(obj:.o=.obj) + +-INC += -I $(SOURCE_DIR)/glui_v2_1_beta -I $(SOURCE_DIR)/gd-2.0.15 -I $(SOURCE_DIR)/shared -I $(SOURCE_DIR)/smokeview -I $(SOURCE_DIR)/glew -I $(SOURCE_DIR)/zlib128 ++INC += -I $(SOURCE_DIR)/glui_v2_1_beta -I$(EBROOTLIBGD)/include -I $(SOURCE_DIR)/shared -I $(SOURCE_DIR)/smokeview -I $(EBROOTGLEW)/include/GL -I $(EBROOTZLIB)/include + + # windows include directories + +@@ -175,7 +164,7 @@ + + intel_win_64_db : INC += $(WININC) -I $(SOURCE_DIR)/shared -I $(SOURCE_DIR)/smokeview + intel_win_64_db : FFLAGS = /Od /iface:stdref /fpp -D WIN32 /Zi /nologo /fpscomp:general /debug:full /extend_source:132 /warn:unused /warn:nointerfaces /Qtrapuv /fp:strict /fp:except /traceback /check:all /stand:f18 +-intel_win_64_db : CFLAGS = /Od /W4 /debug:full /Zi -D _DEBUG -D WIN32 -D _CONSOLE -D X64 -D GLEW_STATIC -D PTW32_STATIC_LIB $(SMV_TESTFLAG) $(GITINFO) $(INTEL_COMPINFO) ++intel_win_64_db : CFLAGS = /Od /W4 /debug:full /Zi -D _DEBUG -D WIN32 -D _CONSOLE -D X64 -D GLEW_STATIC -D PTW32_STATIC_LIB $(SMV_TESTFLAG) $(INTEL_COMPINFO) + ifeq ($(GLUT),freeglut) + intel_win_64_db : CFLAGS += -D FREEGLUT_STATIC + endif +@@ -195,7 +184,7 @@ + intel_win_64 : INC += -I $(SOURCE_DIR)/lua-5.3.1/src + endif + intel_win_64 : FFLAGS = -O2 /iface:stdref /fpp -D WIN32 /fpscomp:general /stand:f18 +-intel_win_64 : CFLAGS = -O1 -D WIN32 -D _CONSOLE -D X64 -D GLEW_STATIC -D PTW32_STATIC_LIB $(SMV_TESTFLAG) $(GITINFO) $(INTEL_COMPINFO) ++intel_win_64 : CFLAGS = -O1 -D WIN32 -D _CONSOLE -D X64 -D GLEW_STATIC -D PTW32_STATIC_LIB $(SMV_TESTFLAG) $(INTEL_COMPINFO) + ifeq ($(GLUT),freeglut) + intel_win_64 : CFLAGS += -D FREEGLUT_STATIC + endif +@@ -219,7 +208,7 @@ + + gnu_win_64 : INC += -I $(SOURCE_DIR)/glui_gl -I $(SOURCE_DIR)/shared -I $(SOURCE_DIR)/smokeview + gnu_win_64 : FFLAGS = -O0 -m64 -x f95-cpp-input -D pp_GCC -ffree-form -frecord-marker=4 $(SMV_PROFILEFLAG) +-gnu_win_64 : CFLAGS = -O0 -m64 $(D_FREEGLUT) -D GLEW_STATIC -D WIN32 -D pp_GCC -D __MINGW32__ -fno-builtin -Wno-write-strings $(GITINFO) $(GNU_COMPINFO) $(SMV_PROFILEFLAG) ++gnu_win_64 : CFLAGS = -O0 -m64 $(D_FREEGLUT) -D GLEW_STATIC -D WIN32 -D pp_GCC -D __MINGW32__ -fno-builtin -Wno-write-strings $(GNU_COMPINFO) $(SMV_PROFILEFLAG) + gnu_win_64 : LFLAGS = -m64 $(SMV_LIBS_GNU) -lgfortran -lm -lopengl32 -lglu32 -lgdi32 -lwinmm -lcomdlg32 -lhid -lquadmath $(SMV_PROFILEFLAG) + gnu_win_64 : CC = gcc + gnu_win_64 : CPP = g++ +@@ -241,7 +230,7 @@ + + gnu_win_64_db : INC += -I $(SOURCE_DIR)/glui_gl -I $(SOURCE_DIR)/shared -I $(SOURCE_DIR)/smokeview + gnu_win_64_db : FFLAGS = -O0 -m64 -x f95-cpp-input -D _DEBUG -D pp_GCC -ffree-form -frecord-marker=4 $(SMV_PROFILEFLAG) +-gnu_win_64_db : CFLAGS = -O0 -m64 -g -Wunused-label -Wunused-value -Wunused-variable $(D_FREEGLUT) $(SMV_PROFILEFLAG) -D GLEW_STATIC -D WIN32 -D pp_GCC -D __MINGW32__ -fno-builtin -Wno-write-strings $(GITINFO) $(GNU_COMPINFO) ++gnu_win_64_db : CFLAGS = -O0 -m64 -g -Wunused-label -Wunused-value -Wunused-variable $(D_FREEGLUT) $(SMV_PROFILEFLAG) -D GLEW_STATIC -D WIN32 -D pp_GCC -D __MINGW32__ -fno-builtin -Wno-write-strings $(GNU_COMPINFO) + gnu_win_64_db : LFLAGS = -m64 $(SMV_LIBS_GNU) -lgfortran -lm -lopengl32 -lglu32 -lgdi32 -lwinmm -lcomdlg32 -lhid -lquadmath $(SMV_PROFILEFLAG) + gnu_win_64_db : CC = gcc + gnu_win_64_db : CPP = g++ +@@ -269,7 +258,7 @@ + + intel_linux_64 : LIB_DIR_PLAT = $(LIB_DIR)/intel_linux_64 + intel_linux_64 : FFLAGS = -O0 -traceback -m64 -static-intel -fpp -stand:f18 $(SMV_PROFILEFLAG) +-intel_linux_64 : CFLAGS = -O0 -traceback -m64 -static-intel -D pp_LINUX $(SMV_TESTFLAG) $(SMV_PROFILEFLAG) $(GITINFO) $(INTEL_COMPINFO) ++intel_linux_64 : CFLAGS = -O0 -traceback -m64 -static-intel -D pp_LINUX $(SMV_TESTFLAG) $(SMV_PROFILEFLAG) $(INTEL_COMPINFO) + intel_linux_64 : LIBLUA = + ifeq ($(LUA_SCRIPTING),true) + intel_linux_64 : CFLAGS += -D pp_LUA +@@ -283,12 +272,12 @@ + intel_linux_64 : exe = smokeview_linux_$(SMV_TESTSTRING)64$(SMV_PROFILESTRING) + + intel_linux_64 : $(obj) $(if $(LUA_SCRIPTING),smvluacore) +- $(CPP) -o $(bin)/$(exe) $(obj) $(LFLAGS) -L$(LIB_DIR_PLAT) $(SMV_LIBS_LINUX) $(INTEL_LIBS_LINUX) $(SYSTEM_LIBS_LINUX) $(LIBLUA) ++ $(CPP) -o $(bin)/$(exe) $(obj) $(LFLAGS) -L$(LIB_DIR_PLAT) -L$(EB_L_PATH) $(SMV_LIBS_LINUX) $(INTEL_LIBS_LINUX) $(SYSTEM_LIBS_LINUX) $(LIBLUA) + + # ------------- intel_linux_64_db ---------------- + + intel_linux_64_db : FFLAGS = -O0 -m64 -static-intel -traceback -g -fpe0 -fltconsistency -WB -fpp -stand:f18 $(SMV_PROFILEFLAG) +-intel_linux_64_db : CFLAGS = -O0 -g -m64 -static-intel $(SMV_TESTFLAG) -D _DEBUG -D pp_LINUX $(SMV_PROFILEFLAG) -traceback -Wall -Wextra -check=stack,uninit -fp-stack-check -fp-trap-all=divzero,invalid,overflow -ftrapuv -Wuninitialized -Wunused-function -Wunused-variable $(GITINFO) $(INTEL_COMPINFO) ++intel_linux_64_db : CFLAGS = -O0 -g -m64 -static-intel $(SMV_TESTFLAG) -D _DEBUG -D pp_LINUX $(SMV_PROFILEFLAG) -traceback -Wall -Wextra -check=stack,uninit -fp-stack-check -fp-trap-all=divzero,invalid,overflow -ftrapuv -Wuninitialized -Wunused-function -Wunused-variable $(INTEL_COMPINFO) + intel_linux_64_db : LFLAGS = -m64 -static-intel -no-cilk $(INTEL_LIBS_LINUX) -traceback $(SMV_PROFILEFLAG) + intel_linux_64_db : CC = icc + intel_linux_64_db : CPP = icpc +@@ -296,13 +285,13 @@ + intel_linux_64_db : exe = smokeview_linux_$(SMV_TESTSTRING)64_db$(SMV_PROFILESTRING) + + intel_linux_64_db : $(obj) +- $(CPP) -o $(bin)/$(exe) $(obj) $(LFLAGS) -L$(LIB_DIR)/intel_linux_64 $(SMV_LIBS_LINUX) $(INTEL_LIBS_LINUX) $(SYSTEM_LIBS_LINUX) ++ $(CPP) -o $(bin)/$(exe) $(obj) $(LFLAGS) -L$(LIB_DIR)/intel_linux_64 $(SMV_LIBS_LINUX) $(INTEL_LIBS_LINUX) $(SYSTEM_LIBS_LINUX) -L$(EB_L_PATH) + + # ------------- gnu_linux_64_db ---------------- + + gnu_linux_64_db : LIB_DIR_PLAT = $(LIB_DIR)/gnu_linux_64 + gnu_linux_64_db : FFLAGS = -O0 -m64 -ggdb -Wall -x f95-cpp-input -D pp_GCC -ffree-form -frecord-marker=4 -fcheck=all -fbacktrace $(SMV_PROFILEFLAG) +-gnu_linux_64_db : CFLAGS = -O0 -m64 -ggdb -Wall -Wno-parentheses -Wno-unknown-pragmas -Wno-comment -Wno-write-strings -D _DEBUG -D pp_LINUX -D pp_GCC $(SMV_TESTFLAG) $(GNU_COMPINFO) $(GITINFO) $(SMV_PROFILEFLAG) ++gnu_linux_64_db : CFLAGS = -O0 -m64 -ggdb -Wall -Wno-parentheses -Wno-unknown-pragmas -Wno-comment -Wno-write-strings -D _DEBUG -D pp_LINUX -D pp_GCC $(SMV_TESTFLAG) $(GNU_COMPINFO) $(SMV_PROFILEFLAG) + ifeq ($(LUA_SCRIPTING),true) + gnu_linux_64_db : CFLAGS += -D pp_LUA + gnu_linux_64_db : SMVLUACORE_FILES += $(LIB_DIR_PLAT)/lpeg.so +@@ -315,14 +304,14 @@ + + gnu_linux_64_db : $(obj) + $(CPP) -o $(bin)/$(exe) $(obj) $(LFLAGS) -L $(LIB_DIR_PLAT) \ +- $(SMV_LIBS_LINUX) -lgfortran $(SYSTEM_LIBS_LINUX) \ ++ $(SMV_LIBS_LINUX) -lgfortran $(SYSTEM_LIBS_LINUX) -L$(EB_L_PATH) \ + $(if $(LUA_SCRIPTING),$(LIB_DIR_PLAT)/liblua.a -ldl) + + # ------------- gnu_linux_64 ---------------- + + gnu_linux_64 : LIB_DIR_PLAT = $(LIB_DIR)/gnu_linux_64 + gnu_linux_64 : FFLAGS = -O0 -m64 -ggdb -Wall -x f95-cpp-input -D pp_GCC -ffree-form -frecord-marker=4 -fcheck=all -fbacktrace $(SMV_PROFILEFLAG) +-gnu_linux_64 : CFLAGS = -O0 -m64 -ggdb -Wall -Wno-parentheses -Wno-unknown-pragmas -Wno-comment -Wno-write-strings -D pp_LINUX -D pp_GCC $(SMV_TESTFLAG) $(GNU_COMPINFO) $(GITINFO) $(SMV_PROFILEFLAG) ++gnu_linux_64 : CFLAGS = -O0 -m64 -ggdb -Wall -Wno-parentheses -Wno-unknown-pragmas -Wno-comment -Wno-write-strings -D pp_LINUX -D pp_GCC $(SMV_TESTFLAG) $(GNU_COMPINFO) $(SMV_PROFILEFLAG) + ifeq ($(LUA_SCRIPTING),true) + gnu_linux_64 : CFLAGS += -D pp_LUA + gnu_linux_64 : SMVLUACORE_FILES += $(LIB_DIR_PLAT)/lpeg.so +@@ -335,7 +324,7 @@ + + gnu_linux_64 : $(obj) $(if $(LUA_SCRIPTING),smvluacore) + $(CPP) -o $(bin)/$(exe) $(obj) $(LFLAGS) -L $(LIB_DIR_PLAT) \ +- $(SMV_LIBS_LINUX) -lgfortran $(SYSTEM_LIBS_LINUX) \ ++ $(SMV_LIBS_LINUX) -lgfortran $(SYSTEM_LIBS_LINUX) -L$(EB_L_PATH) \ + $(if $(LUA_SCRIPTING),$(LIB_DIR_PLAT)/liblua.a -ldl) + + # ------------- mingw_win_64 ---------------- +@@ -385,7 +374,7 @@ + # ------------- intel_osx_64 ---------------- + + intel_osx_64 : FFLAGS = -O0 -m64 -traceback -static-intel -fpp -D pp_OSX -mmacosx-version-min=10.9 -stand:f18 +-intel_osx_64 : CFLAGS = -O0 -m64 -I $(SOURCE_DIR)/glui_gl -traceback -static-intel -D pp_OSX $(SMV_TESTFLAG) $(GITINFO) $(INTEL_COMPINFO) -mmacosx-version-min=10.9 ++intel_osx_64 : CFLAGS = -O0 -m64 -I $(SOURCE_DIR)/glui_gl -traceback -static-intel -D pp_OSX $(SMV_TESTFLAG) $(INTEL_COMPINFO) -mmacosx-version-min=10.9 + intel_osx_64 : LIBLUA = + ifeq ($(LUA_SCRIPTING),true) + intel_osx_64 : CFLAGS += -D pp_LUA +@@ -415,7 +404,7 @@ + # ------------- intel_osx_64_db ---------------- + + intel_osx_64_db : FFLAGS = -O0 -g -m64 -traceback -static-intel -fpp -D pp_OSX -mmacosx-version-min=10.9 -stand:f18 +-intel_osx_64_db : CFLAGS = -O0 -g -m64 -I $(SOURCE_DIR)/glui_gl -traceback -static-intel -D _DEBUG -D pp_OSX $(SMV_TESTFLAG) $(GITINFO) $(INTEL_COMPINFO) -mmacosx-version-min=10.9 ++intel_osx_64_db : CFLAGS = -O0 -g -m64 -I $(SOURCE_DIR)/glui_gl -traceback -static-intel -D _DEBUG -D pp_OSX $(SMV_TESTFLAG) $(INTEL_COMPINFO) -mmacosx-version-min=10.9 + intel_osx_64_db : LIBLUA = + ifeq ($(LUA_SCRIPTING),true) + intel_osx_64_db : CFLAGS += -D pp_LUA +@@ -444,7 +433,7 @@ + # ------------- gnu_osx_64_db ---------------- + + gnu_osx_64_db : FFLAGS = -O0 -m64 -x f95-cpp-input -D pp_GCC -ffree-form $(SMV_PROFILEFLAG) +-gnu_osx_64_db : CFLAGS = -O0 -ggdb -m64 -D _DEBUG -D pp_OSX -D pp_GCC $(SMV_TESTFLAG) -Wall -Wno-comment -Wno-deprecated-declarations -Wno-write-strings $(GNU_COMPINFO) $(GITINFO) $(SMV_PROFILEFLAG) ++gnu_osx_64_db : CFLAGS = -O0 -ggdb -m64 -D _DEBUG -D pp_OSX -D pp_GCC $(SMV_TESTFLAG) -Wall -Wno-comment -Wno-deprecated-declarations -Wno-write-strings $(GNU_COMPINFO) $(SMV_PROFILEFLAG) + gnu_osx_64_db : LFLAGS = -m64 -L$(LIB_DIR)/gnu_osx_64 $(SMV_LIBS_OSX) $(GLIBDIROPT) -lgfortran $(SMV_PROFILEFLAG) + ifeq ($(GLUT),freeglut) + gnu_osx_64_db : LFLAGS += -L /opt/X11/lib -lX11 -lXmu -lGLU -lGL +@@ -467,7 +456,7 @@ + # ------------- gnu_osx_64 ---------------- + + gnu_osx_64 : FFLAGS = -O0 -m64 -x f95-cpp-input -D pp_GCC -ffree-form $(SMV_PROFILEFLAG) +-gnu_osx_64 : CFLAGS = -O0 -m64 -D pp_OSX -D pp_GCC $(SMV_TESTFLAG) -Wall -Wno-comment -Wno-deprecated-declarations -Wno-write-strings $(GNU_COMPINFO) $(GITINFO) $(SMV_PROFILEFLAG) ++gnu_osx_64 : CFLAGS = -O0 -m64 -D pp_OSX -D pp_GCC $(SMV_TESTFLAG) -Wall -Wno-comment -Wno-deprecated-declarations -Wno-write-strings $(GNU_COMPINFO) $(SMV_PROFILEFLAG) + gnu_osx_64 : LFLAGS = -m64 -L$(LIB_DIR)/gnu_osx_64 $(SMV_LIBS_OSX) $(GLIBDIROPT) -lgfortran $(SMV_PROFILEFLAG) + ifeq ($(GLUT),freeglut) + gnu_osx_64 : LFLAGS += -L /opt/X11/lib -lX11 -lXmu -lGLU -lGL +diff -ruN smv-SMV6.7.17_orig/Source/shared/file_util.c smv-SMV6.7.17/Source/shared/file_util.c +--- smv-SMV6.7.17_orig/Source/shared/file_util.c 2021-10-11 15:54:46.718505000 +0200 ++++ smv-SMV6.7.17/Source/shared/file_util.c 2021-10-11 15:19:55.038992000 +0200 +@@ -25,6 +25,7 @@ + #include + #endif + #include "MALLOCC.h" ++#include + + FILE *alt_stdout=NULL; + +diff -ruN smv-SMV6.7.17_orig/Source/shared/file_util.h smv-SMV6.7.17/Source/shared/file_util.h +--- smv-SMV6.7.17_orig/Source/shared/file_util.h 2021-10-11 15:54:46.718987000 +0200 ++++ smv-SMV6.7.17/Source/shared/file_util.h 2021-10-11 15:20:05.595248000 +0200 +@@ -11,12 +11,12 @@ + #ifdef pp_GCC + #include + #endif +-#ifdef pp_LINUX + #include +-#endif + #ifndef WIN32 + #include + #endif ++#include ++#include + + // vvvvvvvvvvvvvvvvvvvvvvvv structures vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv + +diff -ruN smv-SMV6.7.17_orig/Source/smokeview/glui_colorbar.cpp smv-SMV6.7.17/Source/smokeview/glui_colorbar.cpp +--- smv-SMV6.7.17_orig/Source/smokeview/glui_colorbar.cpp 2021-10-11 15:54:46.778813000 +0200 ++++ smv-SMV6.7.17/Source/smokeview/glui_colorbar.cpp 2021-10-07 15:35:13.135085000 +0200 +@@ -168,7 +168,7 @@ + char *clabel; + + cbi = colorbarinfo + colorbartype; +- clabel = EDITTEXT_colorbar_label->get_text(); ++ strcpy(clabel, EDITTEXT_colorbar_label->get_text()); + strcpy(cbi->label, clabel); + LISTBOX_colorbar->delete_item(colorbartype); + LISTBOX_colorbar->add_item(colorbartype, colorbar_label); +diff -ruN smv-SMV6.7.17_orig/Source/smokeview/main.c smv-SMV6.7.17/Source/smokeview/main.c +--- smv-SMV6.7.17_orig/Source/smokeview/main.c 2021-10-11 15:54:46.838073000 +0200 ++++ smv-SMV6.7.17/Source/smokeview/main.c 2021-10-11 15:20:33.131615000 +0200 +@@ -5,6 +5,8 @@ + #include + #include + #include ++#include ++ + #include GLUT_H + + #include "string_util.h" From e9179302603609e5fe5042d3ebe95ca0f84a355b Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 15 Oct 2021 11:16:44 +0200 Subject: [PATCH 1579/9987] checksums --- easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb | 1 + easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb | 1 + easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb | 5 ++++- 3 files changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb b/easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb index 78db8320618..b35a147312a 100644 --- a/easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'intel', 'version': '2020b'} source_urls = ['https://github.com//libglui/glui/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] +checksums = ['f7f6983f7410fe8dfaa032b2b7b1aac2232ec6a400a142b73f680683dad795f8'] builddependencies = [ ('CMake', '3.18.4'), diff --git a/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb b/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb index 17dca8b71da..ecf73a8bb5e 100644 --- a/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb +++ b/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'intel', 'version': '2020b'} source_urls = ['http://www.inf.puc-rio.br/~roberto/lpeg/'] sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['48d66576051b6c78388faad09b70493093264588fcd0f258ddaab1cdd4a15ffe'] dependencies = [ ('Lua', '5.4.2'), diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb index 2bf1ff1284a..1afe4586b30 100644 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb @@ -16,7 +16,10 @@ toolchain = {'name': 'intel', 'version': '2020b'} source_urls = ['https://github.com/firemodels/%(name)s/archive/refs/tags/'] sources = ['%(name)s%(version)s.tar.gz'] patches = ['SMV-%(version)s_missing-includes.patch'] -checksums = ['2e718af991e48228bf374fdefcce00d2e8b5827cc29ae2138ae267fda896f127'] +checksums = [ + '2e718af991e48228bf374fdefcce00d2e8b5827cc29ae2138ae267fda896f127', # SMV6.7.17.tar.gz + '5f69669b45ad7be0510785fe2d956b000c81cbe622fc31c256fd4eb2c8d470a4', # SMV-6.7.17_missing-includes.patch +] dependencies = [ ('libgd', '2.3.0'), From cfae3a53cfa7e473cd0befa83849bc48850e5fe9 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 15 Oct 2021 11:35:29 +0200 Subject: [PATCH 1580/9987] code style --- easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb index 1afe4586b30..a2644d9f319 100644 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb @@ -51,7 +51,7 @@ buildopts = ' intel_linux_64 ' + local_buildopts buildopts += ' && make -j 36 intel_linux_64_db ' + local_buildopts files_to_copy = [ - (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64", "./Build/smokeview/smokeview_linux_64_db"], 'bin') + (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64*"], 'bin') ] sanity_check_paths = { From c6b62d9cfa1f8b476083670cdab4fe866aad3212 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 15 Oct 2021 11:56:55 +0200 Subject: [PATCH 1581/9987] Added a version suffix to ELSI-2.6.4-intel-2020b and ELSI-2.6.4-foss-2020b to make it consistent with older easyconfigs. --- .../{ELSI-2.6.4-foss-2020b.eb => ELSI-2.6.4-foss-2020b-PEXSI.eb} | 1 + ...ELSI-2.6.4-intel-2020b.eb => ELSI-2.6.4-intel-2020b-PEXSI.eb} | 1 + 2 files changed, 2 insertions(+) rename easybuild/easyconfigs/e/ELSI/{ELSI-2.6.4-foss-2020b.eb => ELSI-2.6.4-foss-2020b-PEXSI.eb} (98%) rename easybuild/easyconfigs/e/ELSI/{ELSI-2.6.4-intel-2020b.eb => ELSI-2.6.4-intel-2020b-PEXSI.eb} (97%) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb similarity index 98% rename from easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b.eb rename to easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index b80892bb43d..9faa87a5f80 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -1,5 +1,6 @@ name = 'ELSI' version = '2.6.4' +versionsuffix = '-PEXSI' homepage = 'https://wordpress.elsi-interchange.org/' description = """ELSI provides and enhances scalable, open-source software library solutions for diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb similarity index 97% rename from easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b.eb rename to easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb index e4a90c9f5af..48b7ddd05d4 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb @@ -1,5 +1,6 @@ name = 'ELSI' version = '2.6.4' +versionsuffix = '-PEXSI' homepage = 'https://wordpress.elsi-interchange.org/' description = """ELSI provides and enhances scalable, open-source software library solutions for From 9bb05475559c7dfb4f3a62139327115493db37ec Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 15 Oct 2021 11:57:27 +0200 Subject: [PATCH 1582/9987] Make sure not to overwrite the Fortran flags set by EasyBuild. --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 9faa87a5f80..a09b2e0f5c0 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -33,7 +33,7 @@ dependencies = [ build_internal_pexsi = True -configopts = "-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS='-fallow-argument-mismatch' -DCMAKE_CXX_FLAGS='-std=c++11'" +configopts = "-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS='-fallow-argument-mismatch $FFLAGS' -DCMAKE_CXX_FLAGS='-std=c++11'" runtest = True From 1fdf14593aed9f4ab4149d712d213fde24681322 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 15 Oct 2021 12:00:55 +0200 Subject: [PATCH 1583/9987] Fix quotes. --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index a09b2e0f5c0..6e3fbc632ae 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -33,7 +33,7 @@ dependencies = [ build_internal_pexsi = True -configopts = "-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS='-fallow-argument-mismatch $FFLAGS' -DCMAKE_CXX_FLAGS='-std=c++11'" +configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" -DCMAKE_CXX_FLAGS="-std=c++11"' runtest = True From 1845cdb5301ef2ede16717d72de62eae052c6938 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 15 Oct 2021 13:44:06 +0200 Subject: [PATCH 1584/9987] Fix dalton.in patch to be able to run tests from the build dir. And run tests... --- .../d/Dalton/Dalton-2020.0-foss-2021a.eb | 5 ++++- ...2020.0_use-EB-install-for-dalton-script.patch | 16 ++++++++++++---- 2 files changed, 16 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb index fd21030fa02..b11a971ce16 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb @@ -33,7 +33,7 @@ checksums = [ None, # Dalton-2020.0.tar.gz '3159b03a488d6f5ee23d468be02ea62eacd08cbdf68cd64ef4e5a0d469a6718b', # Dalton-2016-fix-cmake-install.patch # Dalton-2020.0_use-EB-install-for-dalton-script.patch - '507f17638f687c4482263c2f1ccc938278772868eb78694db0be3cd58c3162d1', + 'f38b434d2af609b667b341192d8f0d7e37ee1e0461cc68c780b049c7027bfcf5', 'bc446cd1a9fb63836d1d621eb92be65fcd3a46095a0ba4ecb5b7f292dccbb609', # Dalton-2020.0_fix-uninits.patch '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch 'c1ac29f4ebfcf42b2b3858008cbd25ffbe7035675b9d954b63a5851183f72abb', # Dalton-2020.0_use_flexiblas.patch @@ -47,6 +47,9 @@ builddependencies = [ configopts = '-DENABLE_MPI=ON ' configopts += '-DENABLE_OMP=ON ' +pretestopts = 'env EBROOTDALTON=%(builddir)s/easybuild_obj ' +runtest = 'test' + sanity_check_paths = { 'files': ['bin/dalton', 'bin/dalton.x'], 'dirs': ['basis'], diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use-EB-install-for-dalton-script.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use-EB-install-for-dalton-script.patch index 63059233bd0..09e9937e888 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use-EB-install-for-dalton-script.patch +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_use-EB-install-for-dalton-script.patch @@ -3,8 +3,8 @@ # # Åke Sandgren diff -ru dalton.orig/dalton.in dalton/dalton.in ---- dalton.orig/dalton.in 2021-10-05 13:33:25.000000000 +0200 -+++ dalton/dalton.in 2021-10-05 13:41:38.244136976 +0200 +--- dalton.orig/dalton.in 2021-10-05 14:33:14.000000000 +0200 ++++ dalton/dalton.in 2021-10-15 12:45:56.751803496 +0200 @@ -16,17 +16,7 @@ dalton="dalton" DALTON="DALTON" @@ -24,12 +24,20 @@ diff -ru dalton.orig/dalton.in dalton/dalton.in ## If your computer ressource uses modules, then you can make sure the right modules are loaded ## by uncommenting and adapting the two lines starting with #module following this comment. -@@ -38,7 +28,7 @@ +@@ -38,7 +28,15 @@ #module purge #module load python intel openmpi-i8 -DALTON_EXECUTABLE=$SCRIPT_DIR/$dalton.x -+DALTON_EXECUTABLE=$SCRIPT_DIR/bin/$dalton.x ++if [ -e "$SCRIPT_DIR/bin/$dalton.x" ]; then ++ DALTON_EXECUTABLE=$SCRIPT_DIR/bin/$dalton.x ++elif [ -e "$SCRIPT_DIR/$dalton.x" ]; then ++ # To make sure we can run tests from the build dir ++ DALTON_EXECUTABLE=$SCRIPT_DIR/$dalton.x ++else ++ echo "$dalton.x not found in $SCRIPT_DIR nor in $SCRIPT_DIR/bin" ++ exit 1 ++fi which mpirun > /dev/null # check if mpirun exists, if not, then assume mpiexec if [ $? -eq 0 ]; then From 7433b19bd05d1d511ee135a92b3ba845c89814d7 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 15 Oct 2021 13:47:01 +0200 Subject: [PATCH 1585/9987] adding easyconfigs: XCrySDen-1.6.2-foss-2020b.eb, Togl-2.0-GCCcore-10.2.0.eb, bwidget-1.9.14-GCCcore-10.2.0.eb --- .../bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb | 26 ++++++++++ .../t/Togl/Togl-2.0-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ .../x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb | 34 ++++++++++++++ 3 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..14d2aeee871 --- /dev/null +++ b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.14-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'bwidget' +version = '1.9.14' + +homepage = 'https://core.tcl-lang.org/bwidget/home' +description = 'The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.' + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://downloads.sourceforge.net/project/tcllib/BWidget/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8e9692140167161877601445e7a5b9da5bb738ce8d08ee99b016629bc784a672'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Tk', '8.6.10')] + +modextrapaths = {'TCLLIBPATH': '.'} + +sanity_check_paths = { + 'files': ['button.tcl'], + 'dirs': ['BWman'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..7392a7e7e1d --- /dev/null +++ b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'Togl' +version = '2.0' + +homepage = 'https://sourceforge.net/projects/togl/' +description = """A Tcl/Tk widget for OpenGL rendering.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://downloads.sourceforge.net/project/togl/Togl/2.0/'] +sources = ['%(name)s%(version)s-src.tar.gz'] +patches = [ + 'Togl-2.0_configure.patch', + 'Togl-2.0_decl.patch', +] +checksums = [ + 'b7d4a90bbad3aca618d505ee99e7fd8fb04c829f63231dda2360f557ba3f7610', # Togl2.0-src.tar.gz + 'da97f36b60cd107444cd92453809135b14dc1e8775146b3ba0731da8002e6f9f', # Togl-2.0_configure.patch + '05db6b3ca5139f60616d074903883a3070fcfb1eb8c965b0938779b4f9a6ec6a', # Togl-2.0_decl.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Mesa', '20.2.1'), + ('Tk', '8.6.10'), + ('Tcl', '8.6.10'), +] + +preconfigopts = 'export CFLAGS="$CFLAGS -DTOGL_USE_FONTS=0" && ' + +configopts = "--prefix=%(installdir)s --exec-prefix=%(installdir)s " +configopts += "--with-tcl=$EBROOTTCL/lib --with-tk=$EBROOTTK/lib" + +modextrapaths = { + 'LD_LIBRARY_PATH': 'lib/Togl%(version)s', + 'LIBRARY_PATH': 'lib/Togl%(version)s', +} + + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb new file mode 100644 index 00000000000..65d2188148e --- /dev/null +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb @@ -0,0 +1,34 @@ +name = 'XCrySDen' +version = '1.6.2' + +homepage = "http://www.xcrysden.org/" +description = """XCrySDen is a crystalline and molecular structure visualisation program aiming + at display of isosurfaces and contours, which can be superimposed on crystalline structures and + interactively rotated and manipulated.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'vectorize': False} + +source_urls = ["http://www.xcrysden.org/download/"] +sources = [SOURCELOWER_TAR_GZ] +patches = ['XCrySDen-1.6.2_no-bwidget.patch'] +checksums = [ + '811736ee598bec1a5b427fd10e4e063a30dd7cadae96a43a50b36ce90a4f503f', # xcrysden-1.6.2.tar.gz + '85f23723f67e1a4af2575d403154f9cf8194369a0ff6ed96437a51f2ea81a220', # XCrySDen-1.6.2_no-bwidget.patch +] + +prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" + +local_tcltk_ver = '8.6.10' +dependencies = [ + ('Tcl', local_tcltk_ver), + ('Tk', local_tcltk_ver), + ('Togl', '2.0'), + ('X11', '20201008'), + ('libGLU', '9.0.1'), + ('bwidget', '1.9.14'), +] + +parallel = 1 + +moduleclass = 'vis' From 525523fafe7ef1411049152d1b2a49e19352d874 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 15 Oct 2021 13:58:36 +0200 Subject: [PATCH 1586/9987] Bug fix: xcrysden should link correctly to libdl and Togl. --- easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-8.3.0.eb | 5 +++++ .../easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb | 3 +++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-8.3.0.eb index e88e3a9d68e..a05fdaeb95e 100644 --- a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-8.3.0.eb @@ -33,6 +33,11 @@ preconfigopts = 'export CFLAGS="$CFLAGS -DTOGL_USE_FONTS=0" && ' configopts = "--prefix=%(installdir)s --exec-prefix=%(installdir)s " configopts += "--with-tcl=$EBROOTTCL/lib --with-tk=$EBROOTTK/lib" +modextrapaths = { + 'LD_LIBRARY_PATH': 'lib/Togl%(version)s', + 'LIBRARY_PATH': 'lib/Togl%(version)s', +} + sanity_check_paths = { 'files': [], 'dirs': ['include', 'lib'], diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb index b9b1869cf8e..48cdbea3c19 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb @@ -17,6 +17,9 @@ checksums = [ '85f23723f67e1a4af2575d403154f9cf8194369a0ff6ed96437a51f2ea81a220', # XCrySDen-1.6.2_no-bwidget.patch ] +#prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" +prebuildopts = "export LDLIB='-ldl' &&" + local_tcltk_ver = '8.6.9' dependencies = [ ('Tcl', local_tcltk_ver), From 634ae0134be269e8faba14f9f0c4689e4453b703 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 15 Oct 2021 14:12:40 +0200 Subject: [PATCH 1587/9987] Remove superfluous comment (style check). --- easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb index 48cdbea3c19..6d82b0391ba 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb @@ -17,7 +17,6 @@ checksums = [ '85f23723f67e1a4af2575d403154f9cf8194369a0ff6ed96437a51f2ea81a220', # XCrySDen-1.6.2_no-bwidget.patch ] -#prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" prebuildopts = "export LDLIB='-ldl' &&" local_tcltk_ver = '8.6.9' From 639e08245a3ceb268cb49e1d3e7ddd7650a6afb5 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 15 Oct 2021 13:25:07 +0100 Subject: [PATCH 1588/9987] [fdict] enable intel toolchain --- .../fdict/fdict-0.8.0-iccifort-2020.4.304.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..2b92b32e4e7 --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ + A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. + """ + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +# Create file that sets the compiler (and compilation flags) to use +prebuildopts = 'echo FC=$FC > setup.make && echo FFLAGS=$FFLAGS >> setup.make &&' + +files_to_copy = [(['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), (['settings.bash'], 'bin')] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['bin'], +} + +moduleclass = 'data' From e4365ff1d2a9693e15dfa3902ceefd1d8153bf32 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Fri, 15 Oct 2021 13:29:50 +0100 Subject: [PATCH 1589/9987] [flook] add intel toolchain --- .../flook/flook-0.8.1-iccifort-2020.4.304.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..6ef6d3bf5e1 --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """ + The fortran-Lua-hook library. + """ + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +checksums = ['beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'] + +dependencies = [('Lua', '5.4.2')] + +# Construct the 'setup.make' file +prebuildopts = 'echo CC = $CC > setup.make &&' +prebuildopts += 'echo FC = "$FC" >> setup.make &&' +prebuildopts += 'echo CFLAGS = "$CFLAGS" >> setup.make &&' +prebuildopts += 'echo FFLAGS = "$FFLAGS" >> setup.make &&' +prebuildopts += 'echo ".f90.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo ".F90.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo ".c.o:" >> setup.make &&' +prebuildopts += 'echo "\t\$(CC) -c \$(CFLAGS) \$(INC) $<" >> setup.make &&' +prebuildopts += 'echo "LUA_DIR = $EBROOTLUA" >> setup.make &&' +prebuildopts += 'echo "INC += -I\$(LUA_DIR)/include" >> setup.make &&' + +buildopts = ' liball ' +parallel = 1 + +files_to_copy = [(['libflookall.a', 'libflook.a'], 'lib'), (['flook.mod'], 'include')] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' From a2f0024a68e0b21deb7f100aa801f920f9ea3638 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 15 Oct 2021 15:18:12 +0200 Subject: [PATCH 1590/9987] Fix checksum of updated patch in intel version. --- easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb index 26faa7184bb..a7c0e357f9d 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb @@ -33,7 +33,7 @@ checksums = [ None, # no checksum for Dalton-2020.0.tar.gz source tarball which is created via 'git clone' '3159b03a488d6f5ee23d468be02ea62eacd08cbdf68cd64ef4e5a0d469a6718b', # Dalton-2016-fix-cmake-install.patch # Dalton-2020.0_use-EB-install-for-dalton-script.patch - '507f17638f687c4482263c2f1ccc938278772868eb78694db0be3cd58c3162d1', + 'f38b434d2af609b667b341192d8f0d7e37ee1e0461cc68c780b049c7027bfcf5', 'bc446cd1a9fb63836d1d621eb92be65fcd3a46095a0ba4ecb5b7f292dccbb609', # Dalton-2020.0_fix-uninits.patch '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch ] From 019ca6314daa183761b0c0f01b95dea09a9436db Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 15 Oct 2021 15:41:31 +0200 Subject: [PATCH 1591/9987] Break long line. --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 6e3fbc632ae..0ffc96295a9 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -33,7 +33,8 @@ dependencies = [ build_internal_pexsi = True -configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" -DCMAKE_CXX_FLAGS="-std=c++11"' +configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" ' +configopts += '-DCMAKE_CXX_FLAGS="-std=c++11"' runtest = True From a3c04ada4b11491dd0f88b6019170870d018d613 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 15 Oct 2021 16:35:20 +0200 Subject: [PATCH 1592/9987] Disable one essential test that fails on AMD EPYC. Run only the essential tests. --- .../d/Dalton/Dalton-2020.0-foss-2021a.eb | 4 ++++ .../Dalton-2020.0_disable_failing_tests.patch | 15 +++++++++++++++ 2 files changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2020.0_disable_failing_tests.patch diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb index b11a971ce16..31e1ae902b5 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb @@ -28,6 +28,7 @@ patches = [ '%(name)s-%(version)s_fix-uninits.patch', '%(name)s-2016-fix-bad-includepath-add.patch', '%(name)s-%(version)s_use_flexiblas.patch', + '%(name)s-%(version)s_disable_failing_tests.patch', ] checksums = [ None, # Dalton-2020.0.tar.gz @@ -37,6 +38,7 @@ checksums = [ 'bc446cd1a9fb63836d1d621eb92be65fcd3a46095a0ba4ecb5b7f292dccbb609', # Dalton-2020.0_fix-uninits.patch '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch 'c1ac29f4ebfcf42b2b3858008cbd25ffbe7035675b9d954b63a5851183f72abb', # Dalton-2020.0_use_flexiblas.patch + '2dc05fdf44a16dc6e10c426392bf8643b55580541443ac7201bc5600dabcb0e8', # Dalton-2020.0_disable_failing_tests.patch ] builddependencies = [ @@ -48,6 +50,8 @@ configopts = '-DENABLE_MPI=ON ' configopts += '-DENABLE_OMP=ON ' pretestopts = 'env EBROOTDALTON=%(builddir)s/easybuild_obj ' +# Just run the essential tests +testopts = 'ARGS="-L essential" ' runtest = 'test' sanity_check_paths = { diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_disable_failing_tests.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_disable_failing_tests.patch new file mode 100644 index 00000000000..a7e7b29df77 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_disable_failing_tests.patch @@ -0,0 +1,15 @@ +Disable cc_rsp_mcdbterm since it fails on AMD EPYC. + +Åke Sandgren, 20211015 +diff -ru dalton.orig/cmake/TestsDALTON.cmake dalton/cmake/TestsDALTON.cmake +--- dalton.orig/cmake/TestsDALTON.cmake 2021-10-05 14:33:14.000000000 +0200 ++++ dalton/cmake/TestsDALTON.cmake 2021-10-15 16:04:52.688690975 +0200 +@@ -358,7 +358,7 @@ + add_dalton_test(cc_rsp_gammafreq "dalton;serial;cc;short") + add_dalton_test(cc_rsp_gammafreq2 "dalton;serial;cc;short;essential") + add_dalton_test(cc_rsp_gammadirect "dalton;serial;cc;medium") +-add_dalton_test(cc_rsp_mcdbterm "dalton;serial;cc;short;essential") ++#add_dalton_test(cc_rsp_mcdbterm "dalton;serial;cc;short;essential") + add_dalton_test(cc_rsp_threephot "dalton;serial;cc;medium") + add_dalton_test(cc_rsp_twophot "dalton;serial;cc;medium") + add_dalton_test(cc_rsp_twophot2 "dalton;serial;cc;medium") From 9493016c5e7673ddac52e265f7bd0e92e9877478 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 15 Oct 2021 19:05:02 +0200 Subject: [PATCH 1593/9987] Disable one more essential test that fails on EPYC. --- .../d/Dalton/Dalton-2020.0-foss-2021a.eb | 2 +- .../Dalton-2020.0_disable_failing_tests.patch | 13 +++++++++++-- 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb index 31e1ae902b5..d728740ec3e 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb @@ -38,7 +38,7 @@ checksums = [ 'bc446cd1a9fb63836d1d621eb92be65fcd3a46095a0ba4ecb5b7f292dccbb609', # Dalton-2020.0_fix-uninits.patch '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch 'c1ac29f4ebfcf42b2b3858008cbd25ffbe7035675b9d954b63a5851183f72abb', # Dalton-2020.0_use_flexiblas.patch - '2dc05fdf44a16dc6e10c426392bf8643b55580541443ac7201bc5600dabcb0e8', # Dalton-2020.0_disable_failing_tests.patch + '296f550d4a4429a546c45304881a6091d482bc098c33d18b5aa123b516d8ae4b', # Dalton-2020.0_disable_failing_tests.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_disable_failing_tests.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_disable_failing_tests.patch index a7e7b29df77..26e59948c2c 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_disable_failing_tests.patch +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0_disable_failing_tests.patch @@ -1,9 +1,9 @@ -Disable cc_rsp_mcdbterm since it fails on AMD EPYC. +Disable cc_rsp_mcdbterm and cc2_r12_he_a2 since they fail on AMD EPYC. Åke Sandgren, 20211015 diff -ru dalton.orig/cmake/TestsDALTON.cmake dalton/cmake/TestsDALTON.cmake --- dalton.orig/cmake/TestsDALTON.cmake 2021-10-05 14:33:14.000000000 +0200 -+++ dalton/cmake/TestsDALTON.cmake 2021-10-15 16:04:52.688690975 +0200 ++++ dalton/cmake/TestsDALTON.cmake 2021-10-15 19:02:12.107878688 +0200 @@ -358,7 +358,7 @@ add_dalton_test(cc_rsp_gammafreq "dalton;serial;cc;short") add_dalton_test(cc_rsp_gammafreq2 "dalton;serial;cc;short;essential") @@ -13,3 +13,12 @@ diff -ru dalton.orig/cmake/TestsDALTON.cmake dalton/cmake/TestsDALTON.cmake add_dalton_test(cc_rsp_threephot "dalton;serial;cc;medium") add_dalton_test(cc_rsp_twophot "dalton;serial;cc;medium") add_dalton_test(cc_rsp_twophot2 "dalton;serial;cc;medium") +@@ -491,7 +491,7 @@ + add_dalton_test(r12_cabs "dalton;serial;mp2r12;long") + + add_dalton_test(cc2_r12_he "dalton;serial;ccr12;short;essential") +-add_dalton_test(cc2_r12_he_a2 "dalton;serial;ccr12;short;essential") ++#add_dalton_test(cc2_r12_he_a2 "dalton;serial;ccr12;short;essential") + add_dalton_test(cc2_r12_aux2_bh "dalton;serial;ccr12;short") + add_dalton_test(cc2_r12_aux2_bh_sym "dalton;serial;ccr12;short") + add_dalton_test(cc2_r12_aux_bh_a2 "dalton;serial;ccr12;medium") From d67a5f3e6612e0e233aa09a05f1aacf6ba55be12 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 15 Oct 2021 23:50:50 +0200 Subject: [PATCH 1594/9987] extirp setup.make out of easyconfig flook-0.8.1-iccifort-2020.4.304.eb --- .../f/flook/flook-0.8.1-GCC-10.2.0.eb | 33 ++++++++----------- .../flook/flook-0.8.1-iccifort-2020.4.304.eb | 33 ++++++++----------- .../f/flook/flook-0.8.1_setup.make | 8 +++++ 3 files changed, 34 insertions(+), 40 deletions(-) create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1_setup.make diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb index 8ddf6098dd0..fc27032402f 100644 --- a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.2.0.eb @@ -4,36 +4,29 @@ name = 'flook' version = '0.8.1' homepage = 'https://github.com/ElectronicStructureLibrary/flook' -description = """ - The fortran-Lua-hook library. - """ +description = """The fortran-Lua-hook library.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] sources = ['v%(version)s/flook-%(version)s.tar.gz'] -checksums = ['beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] dependencies = [('Lua', '5.4.2')] -# Construct the 'setup.make' file -prebuildopts = 'echo CC = $CC > setup.make &&' -prebuildopts += 'echo FC = "$FC" >> setup.make &&' -prebuildopts += 'echo CFLAGS = "$CFLAGS" >> setup.make &&' -prebuildopts += 'echo FFLAGS = "$FFLAGS" >> setup.make &&' -prebuildopts += 'echo ".f90.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo ".F90.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo ".c.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(CC) -c \$(CFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo "LUA_DIR = $EBROOTLUA" >> setup.make &&' -prebuildopts += 'echo "INC += -I\$(LUA_DIR)/include" >> setup.make &&' - -buildopts = ' liball ' parallel = 1 -files_to_copy = [(['libflookall.a', 'libflook.a'], 'lib'), (['flook.mod'], 'include')] +local_comp_flags = 'VENDOR="gnu" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] sanity_check_paths = { 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb index 6ef6d3bf5e1..ffd6dc3cff1 100644 --- a/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-iccifort-2020.4.304.eb @@ -4,36 +4,29 @@ name = 'flook' version = '0.8.1' homepage = 'https://github.com/ElectronicStructureLibrary/flook' -description = """ - The fortran-Lua-hook library. - """ +description = """The fortran-Lua-hook library.""" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] sources = ['v%(version)s/flook-%(version)s.tar.gz'] -checksums = ['beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] dependencies = [('Lua', '5.4.2')] -# Construct the 'setup.make' file -prebuildopts = 'echo CC = $CC > setup.make &&' -prebuildopts += 'echo FC = "$FC" >> setup.make &&' -prebuildopts += 'echo CFLAGS = "$CFLAGS" >> setup.make &&' -prebuildopts += 'echo FFLAGS = "$FFLAGS" >> setup.make &&' -prebuildopts += 'echo ".f90.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo ".F90.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(FC) -c \$(FFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo ".c.o:" >> setup.make &&' -prebuildopts += 'echo "\t\$(CC) -c \$(CFLAGS) \$(INC) $<" >> setup.make &&' -prebuildopts += 'echo "LUA_DIR = $EBROOTLUA" >> setup.make &&' -prebuildopts += 'echo "INC += -I\$(LUA_DIR)/include" >> setup.make &&' - -buildopts = ' liball ' parallel = 1 -files_to_copy = [(['libflookall.a', 'libflook.a'], 'lib'), (['flook.mod'], 'include')] +local_comp_flags = 'VENDOR="intel" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] sanity_check_paths = { 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1_setup.make b/easybuild/easyconfigs/f/flook/flook-0.8.1_setup.make new file mode 100644 index 00000000000..1d0046f690a --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1_setup.make @@ -0,0 +1,8 @@ +.f90.o: + $(FC) -c $(FFLAGS) $(INC) $< +.F90.o: + $(FC) -c $(FFLAGS) $(INC) $< +.c.o: + $(CC) -c $(CFLAGS) $(INC) $< +LUA_DIR = $(EBROOTLUA) +INC += -I$(LUA_DIR)/include From da626c05a0e199de40eb84c6fafae4caec911253 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 16 Oct 2021 00:17:24 +0200 Subject: [PATCH 1595/9987] use intel vendor settings with EB flags in fdict-0.8.0-iccifort-2020.4.304.eb --- .../easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb | 13 ++++++++----- .../f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb | 13 ++++++++----- 2 files changed, 16 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb index 7551ae8627f..3c66280563f 100644 --- a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb @@ -5,8 +5,8 @@ version = '0.8.0' homepage = 'https://github.com/zerothi/fdict' description = """ - A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. - """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" toolchain = {'name': 'GCC', 'version': '10.2.0'} @@ -14,10 +14,13 @@ source_urls = ['https://github.com/zerothi/fdict/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] -# Create file that sets the compiler (and compilation flags) to use -prebuildopts = 'echo FC=$FC > setup.make && echo FFLAGS=$FFLAGS >> setup.make &&' +buildopts = 'VENDOR="gnu" FFLAGS="$FFLAGS"' -files_to_copy = [(['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), (['settings.bash'], 'bin')] +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'bin'), +] sanity_check_paths = { 'files': ['include/dictionary.mod', 'lib/libfdict.a'], diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb index 2b92b32e4e7..62851d38d02 100644 --- a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb @@ -5,8 +5,8 @@ version = '0.8.0' homepage = 'https://github.com/zerothi/fdict' description = """ - A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. - """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} @@ -14,10 +14,13 @@ source_urls = ['https://github.com/zerothi/fdict/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] -# Create file that sets the compiler (and compilation flags) to use -prebuildopts = 'echo FC=$FC > setup.make && echo FFLAGS=$FFLAGS >> setup.make &&' +buildopts = 'VENDOR="intel" FFLAGS="$FFLAGS" FPP="$FC -E -P"' -files_to_copy = [(['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), (['settings.bash'], 'bin')] +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'bin'), +] sanity_check_paths = { 'files': ['include/dictionary.mod', 'lib/libfdict.a'], From b7c475665e08902f215423e6e522d72ef16c7ce2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 16 Oct 2021 00:18:17 +0200 Subject: [PATCH 1596/9987] install settings.bash in share dir of fdict-0.8.0-iccifort-2020.4.304.eb --- easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb | 4 ++-- .../easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb index 3c66280563f..bfae886c932 100644 --- a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.2.0.eb @@ -19,12 +19,12 @@ buildopts = 'VENDOR="gnu" FFLAGS="$FFLAGS"' files_to_copy = [ (['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), - (['settings.bash'], 'bin'), + (['settings.bash'], 'share'), ] sanity_check_paths = { 'files': ['include/dictionary.mod', 'lib/libfdict.a'], - 'dirs': ['bin'], + 'dirs': ['share'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb index 62851d38d02..1158369a84e 100644 --- a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-iccifort-2020.4.304.eb @@ -19,12 +19,12 @@ buildopts = 'VENDOR="intel" FFLAGS="$FFLAGS" FPP="$FC -E -P"' files_to_copy = [ (['libfdict.a'], 'lib'), (['variable.mod', 'dictionary.mod'], 'include'), - (['settings.bash'], 'bin'), + (['settings.bash'], 'share'), ] sanity_check_paths = { 'files': ['include/dictionary.mod', 'lib/libfdict.a'], - 'dirs': ['bin'], + 'dirs': ['share'], } moduleclass = 'data' From 51e7f7976be25c81f31b04b29d4dfa7afb598c7a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 16 Oct 2021 01:35:09 +0200 Subject: [PATCH 1597/9987] pass LDLIB without export in prebuildopts of XCrySDen-1.6.2-foss-2019b.eb --- easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb index 6d82b0391ba..f3b93f0ad3e 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2019b.eb @@ -17,8 +17,6 @@ checksums = [ '85f23723f67e1a4af2575d403154f9cf8194369a0ff6ed96437a51f2ea81a220', # XCrySDen-1.6.2_no-bwidget.patch ] -prebuildopts = "export LDLIB='-ldl' &&" - local_tcltk_ver = '8.6.9' dependencies = [ ('Tcl', local_tcltk_ver), @@ -31,4 +29,6 @@ dependencies = [ parallel = 1 +prebuildopts = "LDLIB='-ldl'" + moduleclass = 'vis' From f3842ec7a3071be674dd6e48eafaf7afd51c5897 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 16 Oct 2021 08:27:01 +0100 Subject: [PATCH 1598/9987] use git hash to get specific morphology.zip for ImageJ --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb index d0d8066f7cc..918c0cee60a 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.52q-Java-1.8.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM source_urls = [ 'https://imagej.nih.gov/ij/download/src/', - 'https://github.com/landinig/IJ-Morphology/raw/main/', + 'https://github.com/landinig/IJ-Morphology/raw/953503d/', # use git hash not main ] sources = [ 'ij%(version_major)s%(version_minor)s-src.zip', From cbc69bf706db3aaf77512a9c54d108f3e4a17a8e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 16 Oct 2021 10:03:19 +0100 Subject: [PATCH 1599/9987] add xblas patch and flex & make deps --- .../AmberTools-20-intel-2020a-Python-3.8.2.eb | 5 +++++ ...20_fix_xblas_missing_make_dependency.patch | 19 +++++++++++++++++++ 2 files changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-20_fix_xblas_missing_make_dependency.patch diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb index 5f2a5ab4633..f3bbb60dad0 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb @@ -22,18 +22,23 @@ sources = [{ patches = [ 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', ] checksums = [ 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools-20.tar.bz2 # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch' '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65' ] builddependencies = [ ('Bison', '3.5.3'), ('pkg-config', '0.29.2'), ('CMake', '3.16.4'), + ('flex', '2.6.4'), + ('make', '4.3'), ] dependencies = [ ('Python', '3.8.2'), diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-20_fix_xblas_missing_make_dependency.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-20_fix_xblas_missing_make_dependency.patch new file mode 100644 index 00000000000..5a8a55682c3 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-20_fix_xblas_missing_make_dependency.patch @@ -0,0 +1,19 @@ +Fix a missing dependency in xblas causing problems when building with large -j + +Åke Sandgren, 2021-07-01 +diff -ru amber20_src.orig/AmberTools/src/xblas/Makefile amber20_src/AmberTools/src/xblas/Makefile +--- amber20_src.orig/AmberTools/src/xblas/Makefile 2020-01-02 18:26:09.000000000 +0100 ++++ amber20_src/AmberTools/src/xblas/Makefile 2021-07-01 11:34:05.281580939 +0200 +@@ -97,10 +97,10 @@ + grep 'FAIL/TOTAL' testall.result >testall.summary + cat testall.summary + +-common-lib: ++common-lib: header + cd $(SRC_DIR)/common && $(MAKE) + +-common-test-lib: ++common-test-lib: header + cd $(TEST_DIR)/common && $(MAKE) + + From 4705cc4ed9b187cb1322eabb4bc7442a33d728eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 Oct 2021 11:20:09 +0200 Subject: [PATCH 1600/9987] fix download of morphology.zip for ImageJ 1.51k --- easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb index c9577b66ec8..c4f4f2b720f 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51k.eb @@ -10,16 +10,16 @@ toolchain = SYSTEM source_urls = [ 'https://imagej.nih.gov/ij/download/src/', - 'http://www.mecourse.com/landinig/software/', + 'https://github.com/landinig/IJ-Morphology/raw/953503d/', # use git hash not main ] sources = [ 'ij%(version_major)s%(version_minor)s-src.zip', # datestamp is determined by most recent file in zipball - {'download_filename': 'morphology.zip', 'filename': 'morphology-20160920.zip'}, + {'download_filename': 'morphology.zip', 'filename': 'morphology-20210426.zip'}, ] checksums = [ '186adf6756bb1008b1d9596ffb7e92efcaeca7411b19489368aa9e135751c0e1', # ij151k-src.zip - 'a273f53dd7f7af2692230374be7c88cb704845fa6c8bbb4b8ae48778d3226f38', # morphology-20160920.zip + '157f4b55759bf58458acfe073eff9af2e6bb305add2c8658f03f0ce579b3d578', # morphology-20210426.zip ] dependencies = [ From c28219d94a5e0d1aa23c65f55494089622b213d0 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 16 Oct 2021 10:25:06 +0100 Subject: [PATCH 1601/9987] fix line length --- .../OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb index 04466537e18..efeafe0843e 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb @@ -13,7 +13,9 @@ source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] checksums = ['0e24c39bf68194f27a3b630aa99c17a11cd0c86020a2a8fb5cf1465dc1e344a5'] -local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup']] +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] modextrapaths = {'PATH': local_benchmark_dirs} sanity_check_paths = { From 10f406fdad1afa6bf8b712b6871b12e8333fed04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 Oct 2021 13:12:44 +0200 Subject: [PATCH 1602/9987] remove duplicate empty line --- easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb index 7392a7e7e1d..b764b7ccc1b 100644 --- a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-10.2.0.eb @@ -38,7 +38,6 @@ modextrapaths = { 'LIBRARY_PATH': 'lib/Togl%(version)s', } - sanity_check_paths = { 'files': [], 'dirs': ['include', 'lib'], From cf391f879e2a306fb228d8d9be9f6f14d228b02f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 16 Oct 2021 13:13:15 +0200 Subject: [PATCH 1603/9987] move down prebuildopts in XCrySDen easyconfig --- easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb index 65d2188148e..207a5255468 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2020b.eb @@ -17,8 +17,6 @@ checksums = [ '85f23723f67e1a4af2575d403154f9cf8194369a0ff6ed96437a51f2ea81a220', # XCrySDen-1.6.2_no-bwidget.patch ] -prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" - local_tcltk_ver = '8.6.10' dependencies = [ ('Tcl', local_tcltk_ver), @@ -31,4 +29,6 @@ dependencies = [ parallel = 1 +prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" + moduleclass = 'vis' From 5d9d650b39c1ad65a312584627d580192ed1412e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 16 Oct 2021 16:25:45 +0200 Subject: [PATCH 1604/9987] Dalton-2020.0-intel-2021a-i8.eb is broken, remove it. --- .../d/Dalton/Dalton-2020.0-intel-2021a-i8.eb | 58 ------------------- 1 file changed, 58 deletions(-) delete mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb deleted file mode 100644 index a7c0e357f9d..00000000000 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-intel-2021a-i8.eb +++ /dev/null @@ -1,58 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Dalton' -version = '2020.0' -versionsuffix = '-i8' - -homepage = 'https://daltonprogram.org/' -description = """The Dalton code is a powerful tool for a wide range of molecular properties - at different levels of theory. - Any published work arising from use of one of the Dalton2016 programs - must acknowledge that by a proper reference, - https://www.daltonprogram.org/www/citation.html.""" - -toolchain = {'name': 'intel', 'version': '2021a'} -toolchainopts = {'i8': True, 'usempi': True, 'openmp': True} - -sources = [{ - 'filename': SOURCE_TAR_GZ, - 'git_config': { - 'url': 'https://gitlab.com/dalton', - 'repo_name': 'dalton', - 'tag': '2020.0', - 'recursive': True, - }, -}] -patches = [ - '%(name)s-2016-fix-cmake-install.patch', - '%(name)s-%(version)s_use-EB-install-for-dalton-script.patch', - '%(name)s-%(version)s_fix-uninits.patch', - '%(name)s-2016-fix-bad-includepath-add.patch', -] -checksums = [ - None, # no checksum for Dalton-2020.0.tar.gz source tarball which is created via 'git clone' - '3159b03a488d6f5ee23d468be02ea62eacd08cbdf68cd64ef4e5a0d469a6718b', # Dalton-2016-fix-cmake-install.patch - # Dalton-2020.0_use-EB-install-for-dalton-script.patch - 'f38b434d2af609b667b341192d8f0d7e37ee1e0461cc68c780b049c7027bfcf5', - 'bc446cd1a9fb63836d1d621eb92be65fcd3a46095a0ba4ecb5b7f292dccbb609', # Dalton-2020.0_fix-uninits.patch - '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch -] - -builddependencies = [ - ('CMake', '3.20.1'), - ('Python', '3.9.5'), -] - -configopts = '-DENABLE_MPI=ON ' -configopts += '-DENABLE_OMP=ON ' -# Only enable for BLAS/LAPACK having 8 byte integers (basically MKL) adjust the configopts 'i8' option accordingly -configopts += '-DENABLE_64BIT_INTEGERS=ON ' -configopts += '-DENABLE_SCALAPACK=ON ' -configopts += '-DBLACS_IMPLEMENTATION=intelmpi ' - -sanity_check_paths = { - 'files': ['bin/dalton', 'bin/dalton.x'], - 'dirs': ['basis'], -} - -moduleclass = 'chem' From 60b439c53f8344a548d5e5ced625a42845833d04 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Sat, 16 Oct 2021 23:03:49 +0000 Subject: [PATCH 1605/9987] Make imkl an explicit system dependency --- .../easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb index 58097bb6206..7da3a5ead83 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb @@ -6,6 +6,6 @@ description = "FFTW interfaces using Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2021.07'} -dependencies = [('imkl', version)] +dependencies = [('imkl', version, '', True)] moduleclass = 'numlib' From 82510c6bf5c3c0b06d4174b2d8219c4ff9753b9d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 17 Oct 2021 12:39:13 +0200 Subject: [PATCH 1606/9987] Update libfabric to 1.13.1 in OpenMPI and add it as a dependency in PMIx for the upcoming foss 2021b toolchain. --- .../libfabric-1.13.1-GCCcore-11.2.0.eb | 65 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 2 +- .../p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb | 2 + 3 files changed, 68 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.13.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5059fe59d70 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.1-GCCcore-11.2.0.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.13.1' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +# The psm3 provider (enabled by default) requires an AVX capable system to run +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'ofiwg' +source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +patches = [ + ('%(name)s-1.13.0_psm3-version.patch', 0), + '%(name)s-1.12.1_disable-psm3-avx-config.patch', +] +checksums = [ + '8e6eed38c4a39aa4cbf7d5d3734f0eecbfc030182f1f9b3be470702f2586d30e', # libfabric-1.13.1.tar.bz2 + 'f357a60f9cfd054469fef46f560531aa53ded3b7708c313b73d9bfdcb89bf24d', # libfabric-1.13.0_psm3-version.patch + # libfabric-1.12.1_disable-psm3-avx-config.patch + '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('numactl', '2.0.14'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# Regenerate build files +preconfigopts = "autoreconf -f -i &&" + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) +configopts += "--disable-usnic " + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index 32613c0931f..4c8b8baa8e9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -33,7 +33,7 @@ dependencies = [ ('hwloc', '2.5.0'), ('libevent', '2.1.12'), ('UCX', '1.11.2'), - ('libfabric', '1.13.0'), + ('libfabric', '1.13.1'), ('PMIx', '4.1.0'), ] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb index d36693b0c91..181025260fe 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb @@ -29,10 +29,12 @@ dependencies = [ ('libevent', '2.1.12'), ('zlib', '1.2.11'), ('hwloc', '2.5.0'), + ('libfabric', '1.13.1'), ] configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --with-ofi=$EBROOTLIBFBARIC' configopts += ' --enable-pmix-binaries' configopts += ' --disable-man-pages' From db6946d0629ed9159cf7f6a70a51ba156e018beb Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 18 Oct 2021 10:46:55 +0200 Subject: [PATCH 1607/9987] Update to OpenBLAS 0.3.18 as dependency for FlexiBLAS 3.0.4 (used in foss/2021.07) --- easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index c0a4b42ebf0..7a8607f832b 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -21,7 +21,7 @@ builddependencies = [ # note: first listed library will be used as default by FlexiBLAS, # unless otherwise specified via easyconfig parameter flexiblas_default dependencies = [ - ('OpenBLAS', '0.3.17'), + ('OpenBLAS', '0.3.18'), ] moduleclass = 'lib' From 86d223b431c7afe2c3196ccc46ebdd1fcfd4119c Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Mon, 18 Oct 2021 11:12:18 +0200 Subject: [PATCH 1608/9987] Make sure not to overwrite the C++ flags set by EasyBuild. --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 0ffc96295a9..f0577f31059 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -34,7 +34,7 @@ dependencies = [ build_internal_pexsi = True configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" ' -configopts += '-DCMAKE_CXX_FLAGS="-std=c++11"' +configopts += '-DCMAKE_CXX_FLAGS="-std=c++11 $CXXFLAGS"' runtest = True From 4236e9eff98593400c0cb4b1578e91c88cdec491 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 18 Oct 2021 11:03:26 +0100 Subject: [PATCH 1609/9987] adding easyconfigs: scikit-allel-1.3.3-foss-2021a.eb, zarr-2.10.1-foss-2021a.eb, dask-2021.9.1-foss-2021a.eb, bokeh-2.4.1-foss-2021a.eb --- .../b/bokeh/bokeh-2.4.1-foss-2021a.eb | 39 ++++++++++ .../d/dask/dask-2021.9.1-foss-2021a.eb | 75 +++++++++++++++++++ .../scikit-allel-1.3.3-foss-2021a.eb | 36 +++++++++ .../z/zarr/zarr-2.10.1-foss-2021a.eb | 41 ++++++++++ 4 files changed, 191 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.4.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-2021.9.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/z/zarr/zarr-2.10.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.1-foss-2021a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.1-foss-2021a.eb new file mode 100644 index 00000000000..a167cc80efa --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.1-foss-2021a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.4.1' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('Pillow', '8.2.0'), + ('SciPy-bundle', '2021.05'), + ('typing-extensions', '3.10.0.0'), +] + +use_pip = True + +exts_list = [ + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + (name, version, { + 'checksums': ['d0410717d743a0ac251e62480e2ea860a7341bdcd1dbe01499a904f233c90512'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2021.9.1-foss-2021a.eb b/easybuild/easyconfigs/d/dask/dask-2021.9.1-foss-2021a.eb new file mode 100644 index 00000000000..f13e3ce2553 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2021.9.1-foss-2021a.eb @@ -0,0 +1,75 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2021.9.1' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('SciPy-bundle', '2021.05'), + ('bokeh', '2.4.1'), +] + +use_pip = True + +exts_list = [ + ('fsspec', '2021.10.1', { + 'checksums': ['c245626e3cb8de5cd91485840b215a385fa6f2b0f6ab87978305e99e2d842753'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('locket', '0.2.1', { + 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], + }), + ('partd', '1.2.0', { + 'checksums': ['aa67897b84d522dcbc86a98b942afab8c6aa2f7f677d904a616b74ef5ddbc3eb'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '2.0.0', { + 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + (name, version, { + 'checksums': ['e11f2bf2cac809e5408fc107dcf727af3bc3472160f206cb4b828211396ad65c'], + }), + ('distributed', version, { + 'checksums': ['f4deb96a9dbef5b04ad030ab905dfed71b893d79a368bd5787b21268b4ed5ff8'], + }), + ('dask-mpi', '2.21.0', { + 'checksums': ['76e153fc8c58047d898970b33ede0ab1990bd4e69cc130c6627a96f11b12a1a7'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.7.2', { + 'checksums': ['1767f4146b2663d9d2eaef62b882a86e1df0bccdb8ae68ae3e5e546aa6796d35'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.3-foss-2021a.eb b/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.3-foss-2021a.eb new file mode 100644 index 00000000000..74b4d66eabc --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-allel/scikit-allel-1.3.3-foss-2021a.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'scikit-allel' +version = '1.3.3' + +homepage = 'https://scikit-allel.readthedocs.io/en/latest/' +description = """This package provides utilities for exploratory analysis of large scale genetic variation data. + It is based on numpy, scipy and other general-purpose Python scientific libraries.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['550c2a1d00953c3d5d54eb128faf38b52ebd7a8717c1a6dc8ec711cdcada8ded'] + +dependencies = [ + ('Python', '3.9.5'), + ('Seaborn', '0.11.2'), + ('h5py', '3.2.1'), + ('SciPy-bundle', '2021.05'), + ('scikit-learn', '0.24.2'), + ('dask', '2021.9.1'), + # Disabled owing to build with newer Python + # Cf. https://github.com/Blosc/bcolz/issues/409 + # https://github.com/popsim-consortium/stdpopsim/issues/649 + # ('bcolz', '1.2.1'), + ('zarr', '2.10.1'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'allel'} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.10.1-foss-2021a.eb b/easybuild/easyconfigs/z/zarr/zarr-2.10.1-foss-2021a.eb new file mode 100644 index 00000000000..a3a9d783453 --- /dev/null +++ b/easybuild/easyconfigs/z/zarr/zarr-2.10.1-foss-2021a.eb @@ -0,0 +1,41 @@ +easyblock = "PythonBundle" + +name = 'zarr' +version = '2.10.1' + +homepage = 'https://zarr.readthedocs.io/en/stable/' +description = """Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, + designed for use in parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True + +exts_list = [ + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('fasteners', '0.16.3', { + 'checksums': ['b1ab4e5adfbc28681ce44b3024421c4f567e705cc3963c732bf1cba3348307de'], + }), + ('monotonic', '1.6', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/atdt/monotonic/archive'], + 'checksums': ['9609c249aed584fd714811014870650d08d6f6414402b5a190663c49bf83b221'], + }), + ('numcodecs', '0.9.1', { + 'checksums': ['35adbcc746b95e3ac92e949a161811f5aa2602b9eb1ef241b5ea6f09bb220997'], + }), + (name, version, { + 'checksums': ['29e90114f037d433752b3cf951e4a3cb6c6f67b6501a273439b4be4a824e4caf'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 33a66e9f0758d14a2ac0d9c83c030b93d46e314f Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Thu, 14 Oct 2021 20:41:24 +0200 Subject: [PATCH 1610/9987] Add ESL-Bundle 0.6.1 for foss/2020b. --- .../ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb new file mode 100644 index 00000000000..6ef5ff66bf7 --- /dev/null +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'ESL-Bundle' +version = '0.6.1' + +homepage = 'https://esl.cecam.org' + +description = """ + The ESL Bundle is a collection of libraries and utilities broadly used in + electronic structure calculations, put together to make their use easier by + researchers and scientific software developers. ESL stands for Electronic + Structure Library, an initiative which distributes quality software and + promotes open standards for high-performance computing applications in the + field of electronic structure calculations. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('ELSI-RCI', '0.1.0'), + ('fdict', '0.8.0'), + ('flook', '0.8.1'), + ('libfdf', '0.2.2'), + ('Libmbd', '0.10.4'), + ('libpsml', '1.1.10'), + ('libpspio', '0.2.4'), + ('libxc', '4.3.4'), + ('libGridXC', '0.9.6'), + ('libvdwxc', '0.4.0'), + ('PSolver', '1.8.3'), + ('ELSI', '2.6.4'), + ('spglib', '1.16.1'), + ('Wannier90', '3.1.0'), +] + +moduleclass = 'phys' From 28b4b686cd4bdc5eafbf66b71506c0d0292adf39 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Mon, 18 Oct 2021 13:46:22 +0200 Subject: [PATCH 1611/9987] Add ESL-Bundle 0.6.1 for intel/2020b. --- .../ESL-Bundle-0.6.0-intel-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-intel-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-intel-2020b.eb new file mode 100644 index 00000000000..8a316f45c3b --- /dev/null +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-intel-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'ESL-Bundle' +version = '0.6.1' + +homepage = 'https://esl.cecam.org' + +description = """ + The ESL Bundle is a collection of libraries and utilities broadly used in + electronic structure calculations, put together to make their use easier by + researchers and scientific software developers. ESL stands for Electronic + Structure Library, an initiative which distributes quality software and + promotes open standards for high-performance computing applications in the + field of electronic structure calculations. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('ELSI-RCI', '0.1.0'), + ('fdict', '0.8.0'), + ('flook', '0.8.1'), + ('libfdf', '0.2.2'), + ('Libmbd', '0.10.4'), + ('libpsml', '1.1.10'), + ('libpspio', '0.2.4'), + ('libxc', '4.3.4'), + ('libGridXC', '0.9.6'), + ('libvdwxc', '0.4.0'), + ('PSolver', '1.8.3'), + ('ELSI', '2.6.4'), + ('spglib', '1.16.1'), + ('Wannier90', '3.1.0'), +] + +moduleclass = 'phys' From fb3db8f8bc6ccf108e5e8054ad3b364bba3f7ad0 Mon Sep 17 00:00:00 2001 From: Hugo Meiland Date: Mon, 18 Oct 2021 13:22:56 +0000 Subject: [PATCH 1612/9987] add WRF-4.1.3 to foss-2020a toolchain to be supported in EESSI 2021.6 --- .../w/WRF/WRF-4.1.3-foss-2020a-dmpar.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.1.3-foss-2020a-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.1.3-foss-2020a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.1.3-foss-2020a-dmpar.eb new file mode 100644 index 00000000000..d0281f2318f --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.1.3-foss-2020a-dmpar.eb @@ -0,0 +1,43 @@ +name = 'WRF' +version = '4.1.3' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRFv4_netCDF-Fortran_separate_path.patch', +] +checksums = [ + 'a020e83e8a7a927fb080075031630e2af592e9fa802293ad72caa7ee50d6968d', # v4.1.3.tar.gz + 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + 'a431159180757a895c07fc193fe93bb69c4c9d25d31adcc7c2adfa7c1edb04ad', # WRFv4_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20180311'), + ('tcsh', '6.22.02'), + ('time', '1.9'), + ('Perl', '5.30.2'), +] + +dependencies = [ + ('JasPer', '2.0.14'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.2'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' From 5eaefc122a3151073e5d761fa0c2df019d308988 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Mon, 18 Oct 2021 15:25:00 +0200 Subject: [PATCH 1613/9987] Fix some package names/versions. --- .../easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb | 4 ++-- .../easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-intel-2020b.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb index 6ef5ff66bf7..d0bffc67f07 100644 --- a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb @@ -20,8 +20,8 @@ dependencies = [ ('ELSI-RCI', '0.1.0'), ('fdict', '0.8.0'), ('flook', '0.8.1'), - ('libfdf', '0.2.2'), - ('Libmbd', '0.10.4'), + ('libfdf', '0.2.2', '-serial'), + ('libmbd', '0.10.4'), ('libpsml', '1.1.10'), ('libpspio', '0.2.4'), ('libxc', '4.3.4'), diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-intel-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-intel-2020b.eb index 8a316f45c3b..354cab5b34a 100644 --- a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-intel-2020b.eb @@ -20,8 +20,8 @@ dependencies = [ ('ELSI-RCI', '0.1.0'), ('fdict', '0.8.0'), ('flook', '0.8.1'), - ('libfdf', '0.2.2'), - ('Libmbd', '0.10.4'), + ('libfdf', '0.2.2', '-serial'), + ('libmbd', '0.10.4'), ('libpsml', '1.1.10'), ('libpspio', '0.2.4'), ('libxc', '4.3.4'), From 35343d3ca7870297867f7f2e72abebaead56611a Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 18 Oct 2021 15:45:51 +0000 Subject: [PATCH 1614/9987] Version bump. Improvements on JAX etc --- ...-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 00000000000..66d8b4e92b2 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.23.0' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-{}'.format(local_tf_version) + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), + ('flatbuffers', '1.12.0'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('TensorFlow', local_tf_version), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 1f3f8256355b50c2fbe70bcf36289502835beed9 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 18 Oct 2021 15:48:26 +0000 Subject: [PATCH 1615/9987] cleanup --- .../Code_Saturne-6.1.1-gpsmkl-2019a.1.eb | 56 ------------------- 1 file changed, 56 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb diff --git a/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb b/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb deleted file mode 100644 index 53c5c098a0b..00000000000 --- a/easybuild/easyconfigs/c/Code_Saturne/Code_Saturne-6.1.1-gpsmkl-2019a.1.eb +++ /dev/null @@ -1,56 +0,0 @@ -# easyconfig file for Code_Saturne -# author: Metin Cakircali (Juelich Supercomputing Centre) -name = 'Code_Saturne' -version = '6.1.1' - -# extra option for the SLURM batch system -slurm = True - -homepage = 'https://www.code-saturne.org' -description = """Code_Saturne solves the Navier-Stokes equations -for 2D, 2D-axisymmetric and 3D flows, steady or unsteady, -laminar or turbulent, incompressible or weakly dilatable, -isothermal or not, with scalars transport if required. - -Code_Saturne %(version)s%(versionsuffix)s is installed in -$EBROOTCODE_SATURNE -""" -site_contacts = 'a.strube@fz-juelich.de' - -toolchain = {'name': 'gpsmkl', 'version': '2019a.1'} -toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} - -sources = [{ - 'source_urls': ['https://github.com/code-saturne/code_saturne/archive/'], - 'filename': 'v%(version)s.tar.gz' -}] - -builddependencies = [ - ('Autotools', '20180311'), - ('gettext', '0.19.8.1'), - ('Bison', '3.3.2'), - ('flex', '2.6.4'), -] - -dependencies = [ - ('Python', '3.6.8'), - ('PyQt5', '5.11.3', '-Python-%(pyver)s'), - ('HDF5', '1.10.5'), - ('MED', '4.0.0'), - ('CGNS', '4.1.1'), - ('ParMETIS', '4.0.3'), - ('SCOTCH', '6.0.6'), - ('ParaView', '5.6.0', '-Python-%(pyver)s', ('gpsmkl', '2019a.1')), -] - -# better to configure these dependents explicitly -configopts = ['--with-med=$EBROOTMED --with-cgns=$EBROOTCGNS \ - --with-metis=$EBROOTPARMETIS --with-scotch=$EBROOTSCOTCH'] - -parallel = 48 - -modloadmsg = "To benefit from shell completion for %(name)s commands and\n" -modloadmsg += "options, you may also source a bash completion file by;\n" -modloadmsg += ". $CS_BASH\n" - -moduleclass = 'cae' From 6258812ab08e254f7eee57cb6af7bbf73c38a10c Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Tue, 19 Oct 2021 10:26:58 +0100 Subject: [PATCH 1616/9987] [libpsml][xmlf90] build them with intel toolchain --- .../libpsml-1.1.10-iccifort-2020.4.304.eb | 25 +++++++++++++++++++ .../xmlf90-1.5.4-iccifort-2020.4.304.eb | 21 ++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..1487ad90490 --- /dev/null +++ b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-iccifort-2020.4.304.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libpsml' +version = '1.1.10' + +homepage = 'https://launchpad.net/libpsml' +description = """LibPSML provides a Fortran API to parse files in the + PSeudopotential Markup Language (PSML) format.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libpsml/uploads/95c4d83d750d1ca87659b6395c8f7ea7/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['67c38b5bc26acbb77fd13794d1d92f41197a44311314f5453c82506205e0717b'] + +dependencies = [ + ('xmlf90', '1.5.4'), +] + +sanity_check_paths = { + 'files': ['include/m_psml.mod', 'lib/libpsml.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..1e938b9be2c --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-iccifort-2020.4.304.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'xmlf90' +version = '1.5.4' + +homepage = 'https://launchpad.net/xmlf90' +description = """xmlf90 is a basic XML parsing library written in Fortran.""" + +# can't move down to GCCcore and combine with Intel, gfortran modules are incompatible with ifort +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a0b1324ff224d5b5ad1127a6ad4f90979f6b127f1a517f98253eea377237bbe4'] + +sanity_check_paths = { + 'files': ['include/xmlf90_%s.mod' % x for x in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], + 'dirs': ['share/org.siesta-project'], +} + +moduleclass = 'data' From 6324845923ea19f92cd89960c790d0e69530e08b Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Tue, 19 Oct 2021 11:04:29 +0100 Subject: [PATCH 1617/9987] [libpspio] add intel forctoolchain --- .../libpspio-0.2.4-iccifort-2020.4.304.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..6b551f2ed9f --- /dev/null +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-iccifort-2020.4.304.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpspio' +version = '0.2.4' + +homepage = 'https://gitlab.e-cam2020.eu/esl/pspio/' +description = """libpspio is a library to read and write pseudopotentials in multiple formats.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://gitlab.e-cam2020.eu/esl/pspio/uploads/7efa924be97bd46354237ca3fb89495e/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cb3d51ffa6b822305bb943edc7ddfaf1cfc1b928f0594330d732330bfc081850'] + +configopts = ' --enable-gsl --enable-fortran ' + +dependencies = [('GSL', '2.6')] + +sanity_check_paths = { + 'files': ['include/pspiof_m.mod', 'include/pspio.h', 'lib/libpspiof.a'], + 'dirs': [], +} + +moduleclass = 'phys' From 2db4f15f892dc65776dc4062d57c837f1fde9597 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Tue, 19 Oct 2021 11:49:53 +0100 Subject: [PATCH 1618/9987] [libfdf] add intel toolchain --- ...libfdf-0.2.2-iccifort-2020.4.304-serial.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb new file mode 100644 index 00000000000..bb206d03e65 --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' +versionsuffix = '-serial' +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' From ee185e723ca8071014e2ae79af6f4f9abb145790 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 14:58:26 +0200 Subject: [PATCH 1619/9987] Use toolchainopts to set C++ standard --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index f0577f31059..8c30a9e2329 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -10,7 +10,7 @@ description = """ELSI provides and enhances scalable, open-source software libra """ toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True, 'pic': True} +toolchainopts = {'usempi': True, 'pic': True, , 'cstd': 'c++11'} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] sources = [SOURCELOWER_TAR_GZ] @@ -34,7 +34,6 @@ dependencies = [ build_internal_pexsi = True configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" ' -configopts += '-DCMAKE_CXX_FLAGS="-std=c++11 $CXXFLAGS"' runtest = True From 49af0b496cc2fc65c393790ae207af466a4df192 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 14:59:51 +0200 Subject: [PATCH 1620/9987] Typo --- easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 8c30a9e2329..3534b95faa3 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -10,7 +10,7 @@ description = """ELSI provides and enhances scalable, open-source software libra """ toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True, 'pic': True, , 'cstd': 'c++11'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11'} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] sources = [SOURCELOWER_TAR_GZ] From 5652b8c73aa3b681969f7d8b3bd4431fed4b8e87 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 15:23:14 +0200 Subject: [PATCH 1621/9987] Rename ESL-Bundle-0.6.0-foss-2020b.eb to ESL-Bundle-0.6.1-foss-2020b.eb --- ...-Bundle-0.6.0-foss-2020b.eb => ESL-Bundle-0.6.1-foss-2020b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/e/ESL-Bundle/{ESL-Bundle-0.6.0-foss-2020b.eb => ESL-Bundle-0.6.1-foss-2020b.eb} (100%) diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb similarity index 100% rename from easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-foss-2020b.eb rename to easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb From 031efdbe3d1f16cd140009a9a6cbaad1c4488e8e Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 15:23:38 +0200 Subject: [PATCH 1622/9987] Rename ESL-Bundle-0.6.0-intel-2020b.eb to ESL-Bundle-0.6.1-intel-2020b.eb --- ...undle-0.6.0-intel-2020b.eb => ESL-Bundle-0.6.1-intel-2020b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/e/ESL-Bundle/{ESL-Bundle-0.6.0-intel-2020b.eb => ESL-Bundle-0.6.1-intel-2020b.eb} (100%) diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-intel-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb similarity index 100% rename from easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.0-intel-2020b.eb rename to easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb From 2f3d3fd525af473afe5b040a16c6d1c1e6012442 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 16:16:42 +0200 Subject: [PATCH 1623/9987] Delete ESL-Bundle-0.6.1-intel-2020b.eb --- .../ESL-Bundle-0.6.1-intel-2020b.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb deleted file mode 100644 index 354cab5b34a..00000000000 --- a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'Bundle' - -name = 'ESL-Bundle' -version = '0.6.1' - -homepage = 'https://esl.cecam.org' - -description = """ - The ESL Bundle is a collection of libraries and utilities broadly used in - electronic structure calculations, put together to make their use easier by - researchers and scientific software developers. ESL stands for Electronic - Structure Library, an initiative which distributes quality software and - promotes open standards for high-performance computing applications in the - field of electronic structure calculations. -""" - -toolchain = {'name': 'intel', 'version': '2020b'} - -dependencies = [ - ('ELSI-RCI', '0.1.0'), - ('fdict', '0.8.0'), - ('flook', '0.8.1'), - ('libfdf', '0.2.2', '-serial'), - ('libmbd', '0.10.4'), - ('libpsml', '1.1.10'), - ('libpspio', '0.2.4'), - ('libxc', '4.3.4'), - ('libGridXC', '0.9.6'), - ('libvdwxc', '0.4.0'), - ('PSolver', '1.8.3'), - ('ELSI', '2.6.4'), - ('spglib', '1.16.1'), - ('Wannier90', '3.1.0'), -] - -moduleclass = 'phys' From 5032fa3a6c8c9c7407e065dad2bd83b414af5c60 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Oct 2021 16:17:14 +0200 Subject: [PATCH 1624/9987] Update ESL-Bundle-0.6.1-foss-2020b.eb --- .../easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb index d0bffc67f07..640410c954f 100644 --- a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb @@ -28,7 +28,7 @@ dependencies = [ ('libGridXC', '0.9.6'), ('libvdwxc', '0.4.0'), ('PSolver', '1.8.3'), - ('ELSI', '2.6.4'), + ('ELSI', '2.6.4', '-PEXSI'), ('spglib', '1.16.1'), ('Wannier90', '3.1.0'), ] From bc3e23c87e99bbdb032a14b65e6dfa419080aaf2 Mon Sep 17 00:00:00 2001 From: Alin Marin Elena Date: Tue, 19 Oct 2021 13:41:37 +0100 Subject: [PATCH 1625/9987] [libcdwxc] activate intel toolchain --- .../l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb | 31 +++++++++++++++++++ .../l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb new file mode 100644 index 00000000000..2662d04e132 --- /dev/null +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +homepage = 'https://libvdwxc.org' +description = """libvdwxc is a general library for evaluating energy and potential for +exchange-correlation (XC) functionals from the vdW-DF family that can be used with various +of density functional theory (DFT) codes.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] + +preconfigopts = 'unset CC && unset FC &&' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', + 'libvdwxc_q0test', 'libvdwxc_q0test2']] + + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] + for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +dependencies = [ + ('FFTW', '3.3.8') +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb new file mode 100644 index 00000000000..646b447a4a9 --- /dev/null +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +homepage = 'https://libvdwxc.org' +description = """libvdwxc is a general library for evaluating energy and potential for +exchange-correlation (XC) functionals from the vdW-DF family that can be used with various +of density functional theory (DFT) codes.""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] + +preconfigopts = 'unset CC && unset FC &&' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', + 'libvdwxc_q0test', 'libvdwxc_q0test2']] + + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] + for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +dependencies = [ + ('FFTW', '3.3.9') +] + +moduleclass = 'chem' From a5384da66bc6ea8e62c6ca382e5308a43b49fe7a Mon Sep 17 00:00:00 2001 From: alin m elena Date: Tue, 19 Oct 2021 20:30:53 +0100 Subject: [PATCH 1626/9987] keep linter happy --- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb | 2 +- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb index 2662d04e132..7a947276f32 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb @@ -21,7 +21,7 @@ sanity_check_paths = { 'libvdwxc_q0test', 'libvdwxc_q0test2']] + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include'], + 'dirs': ['include'], } dependencies = [ diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb index 646b447a4a9..e3ddac764b1 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb @@ -21,7 +21,7 @@ sanity_check_paths = { 'libvdwxc_q0test', 'libvdwxc_q0test2']] + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include'], + 'dirs': ['include'], } dependencies = [ From 82db2b51b002e4131f2351ea170fc647d61d67a0 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Oct 2021 12:11:29 +0800 Subject: [PATCH 1627/9987] adding easyconfigs: BerkeleyGW-3.0.1-foss-2021a.eb and patches: BerkeleyGW-3.0.1_makefile.patch, BerkeleyGW-3.0.1_tests.patch, BerkeleyGW-3.0.1_version.patch --- .../BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb | 33 +++++++ .../BerkeleyGW-3.0.1_makefile.patch | 22 +++++ .../b/BerkeleyGW/BerkeleyGW-3.0.1_tests.patch | 98 +++++++++++++++++++ .../BerkeleyGW/BerkeleyGW-3.0.1_version.patch | 7 ++ 4 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_makefile.patch create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_tests.patch create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_version.patch diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb new file mode 100644 index 00000000000..a80f60171d4 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb @@ -0,0 +1,33 @@ +name = 'BerkeleyGW' +version = '3.0.1' + +homepage = 'https://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://berkeley.box.com/shared/static/'] +sources = [{'download_filename': 'm1dgnhiemo47lhxczrn6si71bwxoxor8.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'BerkeleyGW-3.0.1_tests.patch', + 'BerkeleyGW-3.0.1_makefile.patch', + 'BerkeleyGW-3.0.1_version.patch', +] +checksums = [ + '7d8c2cc1ee679afb48efbdd676689d4d537226b50e13a049dbcb052aaaf3654f', # BerkeleyGW-3.0.1.tar.gz + '38cdef673daaa78425af641d4b51437aa1038dcc7310ca523a38b117613dd4f2', # BerkeleyGW-3.0.1_tests.patch + '56d90dc4e43db379441b6a1802e24f1f1356cd4aca4eb6d8b673f6c7926a7406', # BerkeleyGW-3.0.1_makefile.patch + '414a4f23e430a2c02bab7bad18bcaf9b62129fa9dd1c2f87bd4bbc9fcb3bdded', # BerkeleyGW-3.0.1_version.patch +] + +dependencies = [ + ('ELPA', '2021.05.001'), + ('h5py', '3.2.1'), +] + +runtest = True + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_makefile.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_makefile.patch new file mode 100644 index 00000000000..6695ca7fb0f --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_makefile.patch @@ -0,0 +1,22 @@ +* don't rebuild flavors when installing and checking +author: Miguel Dias Costa (National University of Singapore) +--- Makefile.orig 2021-05-29 05:08:35.000000000 +0900 ++++ Makefile 2021-05-29 05:09:13.000000000 +0900 +@@ -130,7 +130,7 @@ + cp flavor_cplx.mk flavor.mk + $(MAKE) all + +-install: all ++install: + ifdef INSTDIR + mkdir -p $(INSTDIR)/bin + install bin/*.x $(INSTDIR)/bin/ +@@ -152,7 +152,7 @@ + $(error Error: Please define installation prefix INSTDIR via 'make install INSTDIR='.) + endif + +-check: all ++check: + cd testsuite && $(MAKE) check + + check-save: all diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_tests.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_tests.patch new file mode 100644 index 00000000000..7436042ea73 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_tests.patch @@ -0,0 +1,98 @@ +* allow test scripts to inherit environment +* set stack size ulimit to unlimited +* slightly raise tolerance in some tests +author: Miguel Dias Costa (National University of Singapore) +--- testsuite/run_testsuite.sh.orig 2019-07-25 14:48:12.000000000 +0800 ++++ testsuite/run_testsuite.sh 2019-07-25 14:47:50.000000000 +0800 +@@ -1,4 +1,4 @@ +-#!/bin/bash -l ++#!/bin/bash + # + # Copyright (C) 2005-2009 Heiko Appel, David Strubbe + # +--- testsuite/run_testsuite.sh.orig 2021-01-14 13:52:07.312389000 +0800 ++++ testsuite/run_testsuite.sh 2021-01-14 14:00:31.592579000 +0800 +@@ -66,6 +66,8 @@ + # Run all tests. Takes as first argument a list of testfile names. + function run_testsuite() { + ++ulimit -s unlimited ++ + tests="$1" + + # Check for 'preserve working directories' flag. + +--- MeanField/Utilities/mf_convert_wrapper.sh.orig 2019-07-26 09:52:27.648341000 +0800 ++++ MeanField/Utilities/mf_convert_wrapper.sh 2019-07-26 09:52:39.922114228 +0800 +@@ -1,4 +1,4 @@ +-#!/bin/bash -l ++#!/bin/bash + + # David Strubbe, October 2010 + # Wrapper for mf_convert.x +--- testsuite/GaAs-EPM/GaAs.test.orig 2019-07-26 10:45:19.798520000 +0800 ++++ testsuite/GaAs-EPM/GaAs.test 2019-07-26 10:45:37.753775275 +0800 +@@ -32,7 +32,7 @@ + Output : WFN.out + Input : WFN.in PIPE + +-Precision : 8e-15 ++Precision : 9e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.2710614199849328 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.2565373697755460 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.1322637363008994 +--- testsuite/Si-EPM/Si.test.orig 2021-01-14 14:45:33.627112000 +0800 ++++ testsuite/Si-EPM/Si.test 2021-01-14 14:46:33.049539000 +0800 +@@ -16,7 +16,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM/Si_cplx_spin.test.orig 2019-07-17 07:20:29.000000000 +0800 ++++ testsuite/Si-EPM/Si_cplx_spin.test 2021-01-14 14:46:51.922928000 +0800 +@@ -17,7 +17,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM_subspace/Si_subspace.test.orig 2019-07-17 07:20:32.000000000 +0800 ++++ testsuite/Si-EPM_subspace/Si_subspace.test 2021-01-14 14:47:15.433562000 +0800 +@@ -20,7 +20,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM_subspace/Si_subspace_cplx_spin.test.orig 2019-07-17 07:20:32.000000000 +0800 ++++ testsuite/Si-EPM_subspace/Si_subspace_cplx_spin.test 2021-01-14 14:47:30.610030000 +0800 +@@ -21,7 +21,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM_subspace/Si_subspace_cplx.test.orig 2019-07-17 07:20:32.000000000 +0800 ++++ testsuite/Si-EPM_subspace/Si_subspace_cplx.test 2021-01-14 14:47:45.250225000 +0800 +@@ -20,7 +20,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_version.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_version.patch new file mode 100644 index 00000000000..b53fa9e5909 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_version.patch @@ -0,0 +1,7 @@ +* fix version string +author: Miguel Dias Costa (National University of Singapore) +--- Common/version_base.h.orig 2021-06-14 11:27:49.543968359 +0800 ++++ Common/version_base.h 2021-06-14 11:27:55.397916294 +0800 +@@ -1 +1 @@ +-#define VERSION_BASE "3.0" ++#define VERSION_BASE "3.0.1" From af8c84fdfaec3180ffd10f8bbd1183e4d07c9272 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 20 Oct 2021 09:08:37 +0200 Subject: [PATCH 1628/9987] Add the ESL bundle to whitelist for ecs without files of their own --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 95a29d6219a..05d3433d32a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1009,7 +1009,7 @@ def test_pr_sanity_check_paths(self): # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co - bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS'] + bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle'] failing_checks = [] From 6b2b0b7a4c98f63b92dce2d7f400f1726b9c2f65 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Oct 2021 10:20:37 +0200 Subject: [PATCH 1629/9987] update libfabric to 1.13.2 in OpenMPI and add it as a dependency in PMIx for the upcoming foss 2021b toolchain --- .../libfabric-1.13.2-GCCcore-11.2.0.eb | 65 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 2 +- .../p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb | 2 +- 3 files changed, 67 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.13.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.13.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9205e38e09d --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.13.2-GCCcore-11.2.0.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.13.2' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +# The psm3 provider (enabled by default) requires an AVX capable system to run +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'ofiwg' +source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +patches = [ + ('%(name)s-1.13.0_psm3-version.patch', 0), + '%(name)s-1.12.1_disable-psm3-avx-config.patch', +] +checksums = [ + '25d783b0722a8df8fe61c1de75fafca684c5fe520303180f26f0ad6409cfc0b9', # libfabric-1.13.2.tar.bz2 + 'f357a60f9cfd054469fef46f560531aa53ded3b7708c313b73d9bfdcb89bf24d', # libfabric-1.13.0_psm3-version.patch + # libfabric-1.12.1_disable-psm3-avx-config.patch + '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('numactl', '2.0.14'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# Regenerate build files +preconfigopts = "autoreconf -f -i &&" + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) +configopts += "--disable-usnic " + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index 4c8b8baa8e9..d1e63535d53 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -33,7 +33,7 @@ dependencies = [ ('hwloc', '2.5.0'), ('libevent', '2.1.12'), ('UCX', '1.11.2'), - ('libfabric', '1.13.1'), + ('libfabric', '1.13.2'), ('PMIx', '4.1.0'), ] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb index 181025260fe..5baa27f22e5 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('libevent', '2.1.12'), ('zlib', '1.2.11'), ('hwloc', '2.5.0'), - ('libfabric', '1.13.1'), + ('libfabric', '1.13.2'), ] configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' From 69897ecc4d3f7e7369a87a4197dbd560f5741d70 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 20 Oct 2021 11:02:31 +0200 Subject: [PATCH 1630/9987] Update libvdwxc-0.4.0-intel-2020b.eb --- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb index 7a947276f32..751488a0728 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2020b.eb @@ -24,6 +24,7 @@ sanity_check_paths = { 'dirs': ['include'], } +# MKL FFTW does not have all the features of fftw3 and libvdwxc is using them dependencies = [ ('FFTW', '3.3.8') ] From f4fbad33acf0ca6b4866eaf4ce5dffe58894c1a8 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 20 Oct 2021 11:03:00 +0200 Subject: [PATCH 1631/9987] Update libvdwxc-0.4.0-intel-2021a.eb --- easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb index e3ddac764b1..cdc3abd5a19 100644 --- a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021a.eb @@ -24,6 +24,7 @@ sanity_check_paths = { 'dirs': ['include'], } +# MKL FFTW does not have all the features of fftw3 and libvdwxc is using them dependencies = [ ('FFTW', '3.3.9') ] From 200022021647b1a0eda76760063e52f7edb21c4e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Oct 2021 12:37:22 +0200 Subject: [PATCH 1632/9987] Fix PMIx detection as per OpenMPI issue 8823 --- .../o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb | 6 ++- .../o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb | 6 ++- .../OpenMPI-4.0.3-iccifort-2020.1.217.eb | 6 ++- .../OpenMPI-4.0.3-iccifortcuda-2020a.eb | 6 ++- .../o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb | 6 ++- .../o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb | 6 ++- .../OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 6 ++- .../o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb | 6 ++- .../OpenMPI-4.0.5-iccifort-2020.4.304.eb | 6 ++- .../o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 4 +- .../OpenMPI-4.x_fix_pmix_discovery.patch | 43 +++++++++++++++++++ 11 files changed, 91 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.x_fix_pmix_discovery.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb index e51943031bb..dc5286d3362 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'GCC', 'version': '9.3.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb index 9fcc5c0ce5a..a9103a8a934 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'gcccuda', 'version': '2020a'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb index 85a80cef61d..75c1dbb9195 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'iccifort', 'version': '2020.1.217'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb index c19688551ab..564f903d56a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'iccifortcuda', 'version': '2020a'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb index de69437e30c..110d6438af5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb index 6f35c379b0b..63cf6be8173 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'GCC', 'version': '9.3.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb index 949050f89e9..503f955baf2 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -10,11 +10,15 @@ toolchainopts = {'pic': True} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb index 245532a13ea..12093c5a847 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'gcccuda', 'version': '2020b'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb index 6083f480cda..d33ec82375b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'iccifort', 'version': '2020.4.304'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', +] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index fda533d6ab2..084adbc63ff 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -10,7 +10,8 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', - 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch' + 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.x_fix_pmix_discovery.patch', ] checksums = [ '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a', # openmpi-4.1.0.tar.gz @@ -18,6 +19,7 @@ checksums = [ 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.x_fix_pmix_discovery.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.x_fix_pmix_discovery.patch new file mode 100644 index 00000000000..59aaba13fa9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.x_fix_pmix_discovery.patch @@ -0,0 +1,43 @@ +Fix PMIx discovery as per https://github.com/open-mpi/ompi/issues/8823 + +Åke Sandgren, 20211020 +diff -ru openmpi-4.0.3.orig/opal/mca/pmix/ext1x/pmix1x_component.c openmpi-4.0.3/opal/mca/pmix/ext1x/pmix1x_component.c +--- openmpi-4.0.3.orig/opal/mca/pmix/ext1x/pmix1x_component.c 2020-03-04 00:30:15.000000000 +0100 ++++ openmpi-4.0.3/opal/mca/pmix/ext1x/pmix1x_component.c 2021-10-20 11:03:31.656215790 +0200 +@@ -128,8 +128,7 @@ + char *t, *id; + + /* see if a PMIx server is present */ +- if (NULL != (t = getenv("PMIX_SERVER_URI")) || +- NULL != (id = getenv("PMIX_ID"))) { ++ if (NULL != (t = getenv("PMIX_NAMESPACE"))) { + /* if PMIx is present, then we are a client and need to use it */ + *priority = 100; + } else { +diff -ru openmpi-4.0.3.orig/opal/mca/pmix/ext2x/ext2x_component.c openmpi-4.0.3/opal/mca/pmix/ext2x/ext2x_component.c +--- openmpi-4.0.3.orig/opal/mca/pmix/ext2x/ext2x_component.c 2020-03-04 00:30:15.000000000 +0100 ++++ openmpi-4.0.3/opal/mca/pmix/ext2x/ext2x_component.c 2021-10-20 11:06:15.575219609 +0200 +@@ -144,9 +144,7 @@ + char *t, *id; + + /* see if a PMIx server is present */ +- if (NULL != (t = getenv("PMIX_SERVER_URI")) || +- NULL != (t = getenv("PMIX_SERVER_URI2")) || +- NULL != (id = getenv("PMIX_ID"))) { ++ if (NULL != (t = getenv("PMIX_NAMESPACE"))) { + /* if PMIx is present, then we are a client and need to use it */ + *priority = 100; + } else { +diff -ru openmpi-4.0.3.orig/opal/mca/pmix/pmix3x/pmix3x_component.c openmpi-4.0.3/opal/mca/pmix/pmix3x/pmix3x_component.c +--- openmpi-4.0.3.orig/opal/mca/pmix/pmix3x/pmix3x_component.c 2020-03-04 00:30:15.000000000 +0100 ++++ openmpi-4.0.3/opal/mca/pmix/pmix3x/pmix3x_component.c 2021-10-20 11:07:05.774921311 +0200 +@@ -144,8 +144,7 @@ + char *t, *id; + + /* see if a PMIx server is present */ +- if (NULL != (t = getenv("PMIX_SERVER_URI")) || +- NULL != (id = getenv("PMIX_ID"))) { ++ if (NULL != (t = getenv("PMIX_NAMESPACE"))) { + /* if PMIx is present, then we are a client and need to use it */ + *priority = 100; + } else { From 80caccf82014628c955629f8bf03120551bbb17b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Oct 2021 12:58:45 +0200 Subject: [PATCH 1633/9987] add patch for OpenBLAS 0.3.17 + 0.3.18 to fix segfault triggered by scipy tests --- .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 4 ++- .../OpenBLAS-0.3.17_fix-segfault-ztrsv.patch | 29 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 2 ++ 3 files changed, 34 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17_fix-segfault-ztrsv.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 4892d464d85..b59a24cece2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -15,7 +15,8 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), - '%(name)s-%(version)s_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch', + 'OpenBLAS-%(version)s_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch', + 'OpenBLAS-%(version)s_fix-segfault-ztrsv.patch', ] checksums = [ 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f', # v0.3.17.tar.gz @@ -23,6 +24,7 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.3.17_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch 'ea76320bc047eff1bf2a2f50c1c19acb4fd6d2b8a5bf81a4dce73145a2a5cfcb', + 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17_fix-segfault-ztrsv.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17_fix-segfault-ztrsv.patch new file mode 100644 index 00000000000..411242af12c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17_fix-segfault-ztrsv.patch @@ -0,0 +1,29 @@ +fix segmentation fault triggered via scipy tests +and https://github.com/xianyi/OpenBLAS/issues/3419 + https://github.com/xianyi/OpenBLAS/pull/3420 +From 2845f54eb8ad4c79d0374b52cceac434fc93d8ac Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Wed, 20 Oct 2021 10:50:02 +0200 +Subject: [PATCH] Remove dangerous optimization from previous #3252 - buffer is + never unused here + +--- + interface/ztrsv.c | 6 ------ + 1 file changed, 6 deletions(-) + +diff --git a/interface/ztrsv.c b/interface/ztrsv.c +index cf750b0b0c..cbb7bba13b 100644 +--- a/interface/ztrsv.c ++++ b/interface/ztrsv.c +@@ -199,12 +199,6 @@ void CNAME(enum CBLAS_ORDER order, enum CBLAS_UPLO Uplo, + + if (n == 0) return; + +- if (incx == 1 && trans == 0 && n < 50) { +- buffer = NULL; +- (trsv[(trans<<2) | (uplo<<1) | unit])(n, a, lda, x, incx, buffer); +- return; +- } +- + IDEBUG_START; + + FUNCTION_PROFILE_START(); diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 04bb5898705..a1b6049921b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -15,11 +15,13 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch', ] checksums = [ '1632c1e8cca62d8bed064b37747e331a1796fc46f688626337362bf0d16aeadb', # v0.3.18.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] # extensive testing can be enabled by uncommenting the line below From 24931b06bf30a1a00cf325f9b1d62a5e5eb91f9a Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 20 Oct 2021 13:20:58 +0200 Subject: [PATCH 1634/9987] Add ESL-Bundle-0.6.1 for intel/2020b. --- .../ESL-Bundle-0.6.1-intel-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb new file mode 100644 index 00000000000..e060b31d21b --- /dev/null +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'Bundle' + +name = 'ESL-Bundle' +version = '0.6.1' + +homepage = 'https://esl.cecam.org' + +description = """ + The ESL Bundle is a collection of libraries and utilities broadly used in + electronic structure calculations, put together to make their use easier by + researchers and scientific software developers. ESL stands for Electronic + Structure Library, an initiative which distributes quality software and + promotes open standards for high-performance computing applications in the + field of electronic structure calculations. +""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('ELSI-RCI', '0.1.0'), + ('fdict', '0.8.0'), + ('flook', '0.8.1'), + ('libfdf', '0.2.2', '-serial'), + ('libmbd', '0.10.4'), + ('libpsml', '1.1.10'), + ('libpspio', '0.2.4'), + ('libxc', '4.3.4'), + ('libGridXC', '0.9.6'), + ('libvdwxc', '0.4.0'), + ('PSolver', '1.8.3'), + ('ELSI', '2.6.4', '-PEXSI'), + ('spglib', '1.16.1'), + ('Wannier90', '3.1.0'), +] + +moduleclass = 'phys' From 18ee0a80a7f5c4e8d6008d102beb06be973c3aa1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Oct 2021 16:04:35 +0200 Subject: [PATCH 1635/9987] update SciPy-bundle wiht foss/2021.07 toolchain to latest pythran/pandas --- ...2021.07.eb => SciPy-bundle-2021.10-foss-2021.07.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/s/SciPy-bundle/{SciPy-bundle-2021.07-foss-2021.07.eb => SciPy-bundle-2021.10-foss-2021.07.eb} (89%) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021.07.eb similarity index 89% rename from easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb rename to easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021.07.eb index 7c95541301b..2d27b77b513 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.07-foss-2021.07.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021.07.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'SciPy-bundle' -version = '2021.07' +version = '2021.10' homepage = 'https://python.org/' description = "Bundle of Python packages for scientific software" @@ -41,8 +41,8 @@ exts_list = [ ('beniget', '0.4.1', { 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], }), - ('pythran', '0.9.12.post1', { - 'checksums': ['e7589cf83b0befa9a1b55e98223caf89aff887d9e3f14be912cf8703a717f185'], + ('pythran', '0.10.0', { + 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], }), ('scipy', '1.7.1', { 'checksums': ['6b47d5fa7ea651054362561a28b1ccc8da9368a39514c1bbf6c0977a1c376764'], @@ -56,9 +56,9 @@ exts_list = [ ('Bottleneck', '1.3.2', { 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], }), - ('pandas', '1.3.2', { + ('pandas', '1.3.4', { 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, - 'checksums': ['cbcb84d63867af3411fa063af3de64902665bb5b3d40b25b2059e40603594e87'], + 'checksums': ['a2aa18d3f0b7d538e21932f637fbfe8518d085238b429e4790a35e1e44a96ffc'], }), ('mpmath', '1.2.1', { 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], From 72c8ea713cf43357e45043de17d7b50d9df5b2b6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Oct 2021 16:41:51 +0200 Subject: [PATCH 1636/9987] adding easyconfigs: ELSI-2.7.1-foss-2021a-PEXSI.eb and patches: ELSI-2.7.1_bison_3.7_compat.patch --- .../e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb | 44 +++++++++++++++++++ .../e/ELSI/ELSI-2.7.1_bison_3.7_compat.patch | 15 +++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.7.1_bison_3.7_compat.patch diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb new file mode 100644 index 00000000000..97218cbf6a8 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb @@ -0,0 +1,44 @@ +name = 'ELSI' +version = '2.7.1' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11', 'extra_fflags': '-fallow-argument-mismatch'} + +source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2021/03/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'pexsi-1.2.0-mpi30.patch', + 'ELSI-2.7.1_bison_3.7_compat.patch', +] +checksums = [ + '4a70b6047c39f4e0fd5eca1b2543bfa600acb8305a05ccaaf823ca045f8a4e4d', # elsi-2.7.1.tar.gz + 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('ELPA', '2021.05.001'), + ('NTPoly', '2.7.0'), +] + +build_internal_pexsi = True + +configopts = '-DENABLE_BSEPACK=ON ' + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1_bison_3.7_compat.patch b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1_bison_3.7_compat.patch new file mode 100644 index 00000000000..29c67c222de --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1_bison_3.7_compat.patch @@ -0,0 +1,15 @@ +Make it compatible with Bison 3.7 + +Åke Sandgren, 20211020 +diff -ru elsi-2.7.1.orig/external/SCOTCH/CMakeLists.txt elsi-2.7.1/external/SCOTCH/CMakeLists.txt +--- elsi-2.7.1.orig/external/SCOTCH/CMakeLists.txt 2021-03-09 05:00:21.000000000 +0100 ++++ elsi-2.7.1/external/SCOTCH/CMakeLists.txt 2021-10-20 16:19:52.557606300 +0200 +@@ -54,7 +54,7 @@ + ADD_CUSTOM_COMMAND(OUTPUT ${PROJECT_BINARY_DIR}/generated/parser_ll.c ${PROJECT_BINARY_DIR}/generated/parser_yy.c + COMMAND bison -pscotchyy -y -b y -d -v -o${PROJECT_BINARY_DIR}/generated/tmp2.c ${SCOTCH_DIR}/parser_yy.y + COMMAND mv ${PROJECT_BINARY_DIR}/generated/tmp2.c ${PROJECT_BINARY_DIR}/generated/parser_yy.c +- COMMAND mv ${PROJECT_BINARY_DIR}/generated/tmp2.h ${PROJECT_BINARY_DIR}/generated/parser_ly.h ++ COMMAND ln -s ${PROJECT_BINARY_DIR}/generated/tmp2.h ${PROJECT_BINARY_DIR}/generated/parser_ly.h + COMMAND flex -Pscotchyy -o${PROJECT_BINARY_DIR}/generated/tmp1.c ${SCOTCH_DIR}/parser_ll.l + COMMAND mv ${PROJECT_BINARY_DIR}/generated/tmp1.c ${PROJECT_BINARY_DIR}/generated/parser_ll.c + DEPENDS ${SCOTCH_DIR}/parser_yy.y ${SCOTCH_DIR}/parser_ll.l ${SCOTCH_DIR}/parser_yy.h ${SCOTCH_DIR}/parser_ll.h From 462482e83e9f04e3692f21face88f089a901d8fc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Oct 2021 16:43:02 +0200 Subject: [PATCH 1637/9987] Update ELSI-2.6.4 to use the Bison compat patch and the correct Bison version for the toolchain. --- .../easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 10 +++++++--- .../easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb | 10 ++++++++-- 2 files changed, 15 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 3534b95faa3..332df2352b0 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -14,15 +14,19 @@ toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11'} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['pexsi-1.2.0-mpi30.patch'] +patches = [ + 'pexsi-1.2.0-mpi30.patch', + 'ELSI-2.7.1_bison_3.7_compat.patch', +] checksums = [ 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.5.3'), + ('Bison', '3.7.1'), ('CMake', '3.18.4'), ] @@ -33,7 +37,7 @@ dependencies = [ build_internal_pexsi = True -configopts = '-DENABLEBSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" ' +configopts = '-DENABLE_BSEPACK=ON -DCMAKE_Fortran_FLAGS="-fallow-argument-mismatch $FFLAGS" ' runtest = True diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb index 48b7ddd05d4..800d33b16dc 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb @@ -14,13 +14,19 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11/'] sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'pexsi-1.2.0-mpi30.patch', + 'ELSI-2.7.1_bison_3.7_compat.patch', +] checksums = [ 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz + 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.5.3'), + ('Bison', '3.7.1'), ('CMake', '3.18.4'), ] @@ -31,7 +37,7 @@ dependencies = [ build_internal_pexsi = True -configopts = "-DENABLEBSEPACK=ON" +configopts = "-DENABLE_BSEPACK=ON" runtest = True From 715f5dcdeed5007759cccc3b4fcf3e91e6d6af3e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 20 Oct 2021 17:03:12 +0200 Subject: [PATCH 1638/9987] working version of SMV --- .../s/SMV/SMV-6.7.17-intel-2020b.eb | 26 ++++++++-- .../s/SMV/SMV-6.7.17_example_file.patch | 48 +++++++++++++++++++ 2 files changed, 70 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/s/SMV/SMV-6.7.17_example_file.patch diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb index a2644d9f319..b9dbe2808e0 100644 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb @@ -15,12 +15,17 @@ toolchain = {'name': 'intel', 'version': '2020b'} source_urls = ['https://github.com/firemodels/%(name)s/archive/refs/tags/'] sources = ['%(name)s%(version)s.tar.gz'] -patches = ['SMV-%(version)s_missing-includes.patch'] +patches = [ + 'SMV-%(version)s_missing-includes.patch', + ('SMV-%(version)s_example_file.patch', 1) # eb cant figure this out on its own +] checksums = [ '2e718af991e48228bf374fdefcce00d2e8b5827cc29ae2138ae267fda896f127', # SMV6.7.17.tar.gz '5f69669b45ad7be0510785fe2d956b000c81cbe622fc31c256fd4eb2c8d470a4', # SMV-6.7.17_missing-includes.patch + '33f0c6a580772c1a5adc31e0c301e7befc0f3011a2d6d8e12ecdc2f8d4904610', # SMV-6.7.17_example_file.patch ] + dependencies = [ ('libgd', '2.3.0'), ('freeglut', '3.2.1'), @@ -31,11 +36,13 @@ dependencies = [ ('lpeg', '1.0.2'), ('libGLU', '9.0.1'), ('glew', '2.1.0'), + ('Xvfb', '1.20.9'), ] local_compiler_lib_append = '/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64_lin/' -local_buildopts = ' -lglui -lglut -lfreeglut -lGLU -lGL LDFLAGS=" -L%(installdir)s -L$EBROOTFREEGLUT/lib " ' +local_buildopts = ' -lglui -lglut -lfreeglut -lGLU -lGL -llibgd ' +local_buildopts += ' LDFLAGS=" -L%(installdir)s -L$EBROOTFREEGLUT/lib -L$EBROOTLIBGD/lib " ' local_buildopts += ' IFLAGS=" -I$EBROOTFREEGLUT/include/GL -I%(builddir)s/smv-SMV%(version)s/Source/glui_v2_1_beta/ ' local_buildopts += ' -I%(builddir)s/smv-SMV%(version)s/Source/glui_gl/GL/glut.h "' local_buildopts += ' EB_L_PATH=%(installdir)s ' @@ -51,12 +58,23 @@ buildopts = ' intel_linux_64 ' + local_buildopts buildopts += ' && make -j 36 intel_linux_64_db ' + local_buildopts files_to_copy = [ - (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64*"], 'bin') + (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64*", "example.smv"], 'bin') +] + +postinstallcmds = [ + 'ln -s %(installdir)s/bin/smokeview_linux_64 %(installdir)s/bin/smokeview' +] + +modextrapaths = {'PATH': ['bin']} + +sanity_check_commands = [ + # 'cd %(installdir)s/bin && xvfb-run smokeview example' + "cd %(installdir)s/bin && timeout 10 xvfb-run smokeview example 2>&1 | grep 'Terminated' " ] sanity_check_paths = { 'files': [], - 'dirs': ["bin"], + 'dirs': ["bin/smokeview"], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17_example_file.patch b/easybuild/easyconfigs/s/SMV/SMV-6.7.17_example_file.patch new file mode 100644 index 00000000000..a0c6bd7142c --- /dev/null +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17_example_file.patch @@ -0,0 +1,48 @@ +diff -ruN smv-SMV6.7.17_orig/example.smv smv-SMV6.7.17/example.smv +--- smv-SMV6.7.17_orig/example.smv 1970-01-01 01:00:00.000000000 +0100 ++++ smv-SMV6.7.17/example.smv 2021-10-19 13:29:29.519110638 +0100 +@@ -0,0 +1,44 @@ ++MODULE main ++ VAR ++ s0: {noncritical, trying, critical, ready}; ++ s1: {noncritical, trying, critical, ready}; ++ turn: boolean; ++ pr0: process prc(s0, s1, turn, 0); ++ pr1: process prc(s1, s0, turn, 1); ++ ++ASSIGN init(turn) := 0; ++ ++ FAIRNESS !(s0 = critical) ++ FAIRNESS !(s1 = critical) ++ ++ ++ SPEC AG((s0 = critical) -> !(s1 = critical)) ++ SPEC AG((s1 = critical) -> !(s0 = critical)) ++ ++ SPEC AG((s0 = trying) -> AF(s0 = critical)) ++ SPEC AG((s1 = trying) -> AF(s1 = critical)) ++ ++MODULE prc(state0, state1, turn, turn0) ++ ++ ASSIGN ++ init(state0) := noncritical; ++ next(state0) := ++ case ++ (state0 = noncritical) : {trying,noncritical}; ++ (state0 = trying) & ((state1 = noncritical) | ++ (state1 = trying) | ++ (state1 = ready)): ready; ++ (state0 = ready): critical; ++ (state0 = trying) & (state1 = trying) ++ & (turn = turn0): critical; ++ (state0 = critical) : {critical,noncritical}; ++ 1: state0; ++ esac; ++ ++ next(turn) := ++ case ++ turn = turn0 & state0 = critical: !turn; ++ 1: turn; ++ esac; ++ FAIRNESS running ++ From 184da907c5af2362e6311001300ef89d33f8d62c Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 20 Oct 2021 17:05:44 +0200 Subject: [PATCH 1639/9987] updating sanity paths --- easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb index b9dbe2808e0..514cc7cbb85 100644 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb @@ -73,8 +73,8 @@ sanity_check_commands = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ["bin/smokeview"], + 'files': ["bin/smokeview"], + 'dirs': ["bin"], } moduleclass = 'bio' From aa952167e646c3abd0c7a438b9d333a9b5d99a5b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 20 Oct 2021 18:06:22 +0200 Subject: [PATCH 1640/9987] Add missing NTPoly dependency for ELSI 2.7.1 --- .../n/NTPoly/NTPoly-2.7.0-foss-2021a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.0-foss-2021a.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.0-foss-2021a.eb new file mode 100644 index 00000000000..ba297912ab8 --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.0-foss-2021a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.7.0' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['db4a7cd12f2020739cb96d9f438e525e5a0d695575da89fff88d56365fe8dfde'] + +builddependencies = [('CMake', '3.20.1')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From a41b93adc6a1ca7987b87e1e292bda6ae3ddd944 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Oct 2021 20:07:28 +0200 Subject: [PATCH 1641/9987] bump to SciPy-bundle 2021.10 as dep for GDAL 3.3.2 with foss/2021.07 toolchain --- easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb index 0e7b0e81b4c..ed62c19ab47 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb @@ -40,7 +40,7 @@ dependencies = [ ('PCRE', '8.45'), ('PROJ', '8.1.0'), ('libgeotiff', '1.7.0'), - ('SciPy-bundle', '2021.07'), + ('SciPy-bundle', '2021.10'), ('HDF5', '1.12.1'), ('HDF', '4.2.15'), ] From 8eae489469ec4ab7a22ea5da86933aa7f2b7f913 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Oct 2021 20:36:50 +0200 Subject: [PATCH 1642/9987] use proper tqdm dependency in artic-ncov2019 easyconfig --- .../a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index 9aedc07f208..c4995246973 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -40,6 +40,7 @@ dependencies = [ ('nanopolish', '0.13.3'), ('seqtk', '1.3'), ('BCFtools', '1.11'), + ('tqdm', '4.56.2'), ] use_pip = True @@ -56,9 +57,6 @@ exts_list = [ 'modulename': 'vcf', 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], }), - ('tqdm', '4.62.2', { - 'checksums': ['a4d6d112e507ef98513ac119ead1159d286deab17dffedd96921412c2d236ff5'], - }), ('fieldbioinformatics', '1.2.1', { 'modulename': 'artic', 'source_tmpl': '%(version)s.tar.gz', From a2e088e5743aa175cd9a14741d73a2c1473b5393 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 21 Oct 2021 09:10:22 +0100 Subject: [PATCH 1643/9987] bump numpy to 1.21.3 in SciPy-bundle 2021.10 --- .../s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021.07.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021.07.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021.07.eb index 2d27b77b513..184e4650d40 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021.07.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021.07.eb @@ -23,11 +23,11 @@ use_pip = True # order is important! exts_list = [ - ('numpy', '1.21.2', { + ('numpy', '1.21.3', { 'sources': ['%(name)s-%(version)s.zip'], 'patches': ['numpy-1.20.3_skip-ppc-long-complex-test.patch'], 'checksums': [ - '423216d8afc5923b15df86037c6053bf030d15cc9e3224206ef868c2d63dd6dc', # numpy-1.21.2.zip + '63571bb7897a584ca3249c86dd01c10bcb5fe4296e3568b2e9c1a55356b6410e', # numpy-1.21.3.zip # numpy-1.20.3_skip-ppc-long-complex-test.patch '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4', ], From 92f0d67bfea1ce6a292d1b3af1a69bcb721aa2aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Oct 2021 10:20:42 +0200 Subject: [PATCH 1644/9987] adding easyconfigs: GTDB-Tk-1.7.0-intel-2020b.eb --- .../g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb new file mode 100644 index 00000000000..2e0232fed40 --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'GTDB-Tk' +version = '1.7.0' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/g/gtdbtk'] +sources = ['gtdbtk-%(version)s.tar.gz'] +checksums = ['36b65074845e7edef4d7aeead286c770fb9a03ddbff63946533fa2e1934e8f26'] + +dependencies = [ + ('Python', '3.8.6'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.3.3'), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', True), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.56.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From aed12c369fffcfba7426bea3948ba2eba611d754 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 21 Oct 2021 10:33:37 +0200 Subject: [PATCH 1645/9987] adding easyconfigs: ELSI-2.7.1-intel-2021a-PEXSI.eb, NTPoly-2.7.0-intel-2021a.eb --- .../e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb | 44 +++++++++++++++++++ .../n/NTPoly/NTPoly-2.7.0-intel-2021a.eb | 27 ++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.0-intel-2021a.eb diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb new file mode 100644 index 00000000000..94759abacfc --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb @@ -0,0 +1,44 @@ +name = 'ELSI' +version = '2.7.1' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True, 'cstd': 'c++11'} + +source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2021/03/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'pexsi-1.2.0-mpi30.patch', + 'ELSI-2.7.1_bison_3.7_compat.patch', +] +checksums = [ + '4a70b6047c39f4e0fd5eca1b2543bfa600acb8305a05ccaaf823ca045f8a4e4d', # elsi-2.7.1.tar.gz + 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('ELPA', '2021.05.001'), + ('NTPoly', '2.7.0'), +] + +build_internal_pexsi = True + +configopts = '-DENABLE_BSEPACK=ON ' + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.0-intel-2021a.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.0-intel-2021a.eb new file mode 100644 index 00000000000..138273c8581 --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.0-intel-2021a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.7.0' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['db4a7cd12f2020739cb96d9f438e525e5a0d695575da89fff88d56365fe8dfde'] + +builddependencies = [('CMake', '3.20.1')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From ae19b72845d034c9ba633e493106c7e8a2a46109 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 21 Oct 2021 12:04:57 +0100 Subject: [PATCH 1646/9987] Delete GLUI-2.37-intel-2020b.eb GLUI is not needed here --- .../g/GLUI/GLUI-2.37-intel-2020b.eb | 49 ------------------- 1 file changed, 49 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb diff --git a/easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb b/easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb deleted file mode 100644 index b35a147312a..00000000000 --- a/easybuild/easyconfigs/g/GLUI/GLUI-2.37-intel-2020b.eb +++ /dev/null @@ -1,49 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author:: Denis Kristak (INUITS) -## - -easyblock = 'CMakeMake' - -name = 'GLUI' -version = '2.37' - -homepage = 'https://github.com/libglui/glui' -description = """This distribution contains the latest community-maintained fork of -the GLUI Library, now under the ZLIB license.""" - -toolchain = {'name': 'intel', 'version': '2020b'} - -source_urls = ['https://github.com//libglui/glui/archive/refs/tags/'] -sources = ['%(version)s.tar.gz'] -checksums = ['f7f6983f7410fe8dfaa032b2b7b1aac2232ec6a400a142b73f680683dad795f8'] - -builddependencies = [ - ('CMake', '3.18.4'), - ('binutils', '2.35'), -] - -dependencies = [ - ('freeglut', '3.2.1'), - ('Mesa', '20.2.1'), -] - -configopts = ' -DCMAKE_CXX_FLAGS="$CXXFLAGS" ' - -skipsteps = ['install'] - -postinstallcmds = [ - 'mv %(installdir)s/include %(installdir)s/glui.h', - 'mkdir %(installdir)s/include ', - 'mv %(installdir)s/glui.h %(installdir)s/include ', - 'cp %(builddir)s/easybuild_obj/libglui.so %(installdir)s/lib ', - 'cp %(builddir)s/easybuild_obj/libglui_static.a %(installdir)s/lib ', - 'cp %(builddir)s/glui-%(version)s/*.h %(installdir)s/include/ ', -] - -sanity_check_paths = { - 'files': ['lib/libglui.so', 'lib/libglui_static.a'], - 'dirs': ['lib'], -} - -moduleclass = 'bio' From 0c7e41ab3294fe1d1ef7b0fe19ff54760ba1260b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 21 Oct 2021 13:59:28 +0200 Subject: [PATCH 1647/9987] adding easyconfigs: Exonerate-2.4.0-GCC-10.3.0.eb --- .../e/Exonerate/Exonerate-2.4.0-GCC-10.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..9db08ac41a1 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-10.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +# also https://github.com/nathanweeks/exonerate +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [('GLib', '2.68.2')] + +# parallel build fails +parallel = 1 + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["exonerate", "fastaclip", "fastaoverlap"]], + 'dirs': ["share"], +} + +moduleclass = 'bio' From 7cc9af08b5ab76057b7480365aff7104603411a2 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 21 Oct 2021 15:01:36 +0200 Subject: [PATCH 1648/9987] adding easyconfigs: SAMtools-1.13-GCC-10.3.0.eb --- .../s/SAMtools/SAMtools-1.13-GCC-10.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-10.3.0.eb new file mode 100644 index 00000000000..1ea8b60ec8e --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-10.3.0.eb @@ -0,0 +1,35 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +## + +name = 'SAMtools' +version = '1.13' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.76.0'), +] + +moduleclass = 'bio' From c73a113021e417b85e5f3d9e0c342ea3567356b6 Mon Sep 17 00:00:00 2001 From: Maxime Moge Date: Thu, 21 Oct 2021 15:10:55 +0200 Subject: [PATCH 1649/9987] backporting the postinstallcmd from ncurses-6.X.eb to ncurses-5.9.eb (see https://github.com/easybuilders/easybuild-easyconfigs/pull/3545) creating a soft link 'libtinfo.so -> libncurses.so' and extending it to create soft links 'libtinfo.so.5.9 -> libncurses.so.5.9' and 'libtinfo.so.5 -> libncurses.so.5' as well. --- easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 71d76d1c6a4..10662bd7941 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -33,6 +33,14 @@ configopts = [ '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.so.%(version_major)s libtinfo.so.%(version_major)s)", + "(cd %(installdir)s/lib && ln -s libncurses.so.%(version_major_minor)s libtinfo.so.%(version_major_minor)s)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", From 665844fb8bc964250a4649752c421ae280dbede4 Mon Sep 17 00:00:00 2001 From: Maxime Moge Date: Thu, 21 Oct 2021 15:11:56 +0200 Subject: [PATCH 1650/9987] the Stata 17 binary depends on ncurses 5 --- easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb index 66676cb2c6a..0ef24a2a86e 100644 --- a/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb @@ -13,7 +13,7 @@ checksums = ['744314cdac7ba7316c82dccebe7c7de8f7fab68841d8fa7de13f8eb4472e6015'] dependencies = [ ('libpng', '1.6.37'), - ('ncurses', '6.2'), + ('ncurses', '5.9', '', True), ] sanity_check_commands = ['stata -h'] From 7f81dda51ea2b71845cd5fd253ed4a71be060666 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 21 Oct 2021 15:33:08 +0200 Subject: [PATCH 1651/9987] adding easyconfigs: RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb and patches: RDKit-2021.03.4_skip-broken-test.patch --- ...RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb | 76 +++++++++++++++++++ .../RDKit-2021.03.4_skip-broken-test.patch | 13 ++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb create mode 100644 easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_skip-broken-test.patch diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..d94f367fc7c --- /dev/null +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,76 @@ +easyblock = 'CMakeMake' + +name = 'RDKit' +version = '2021.03.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.rdkit.org' +description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python." + +toolchain = {'name': 'foss', 'version': '2021a'} +# avoid failing tests on skylake CPUs. comment out this line when building on CPUs that don't support AVX2 +# see also: https://github.com/rdkit/rdkit/issues/1674 +toolchainopts = {'optarch': 'mavx2', 'cstd': 'c++11'} + +source_urls = ['https://github.com/rdkit/rdkit/archive/'] +sources = ['Release_%s.tar.gz' % version.replace('.', '_')] +patches = ['RDKit-%(version)s_skip-broken-test.patch'] +checksums = [ + 'bed309df7f1e2ea25736a986cf951325681142ee49468b1c62d020a109d2ef52', # Release_2021_03_4.tar.gz + '4728e6854b9199845a79bb1aee9c05d1a29db0e3ae9bbeb85680545dd77b1e23', # RDKit-2021.03.4_skip-broken-test.patch +] + +# Dependencies varies from version to version +# https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source +builddependencies = [ + ('CMake', '3.20.1'), + ('Eigen', '3.3.9', '', ('GCCcore', '10.3.0')), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('SQLite', '3.35.4'), + ('matplotlib', '3.4.2'), + ('Pillow', '8.2.0'), + ('Boost.Python', '1.76.0', '', ('GCC', '10.3.0')), + ('cairo', '1.16.0'), +] + +separate_build_dir = True + +configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " +configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " +configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " + +# merge source directory into build directory in order to run the tests +buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' +buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' + +# Specify path for libraries so that they are found during the tests when the module is built with --rpath flag. +buildopts += 'export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:${LD_LIBRARY_PATH} && ' + +# 'ctest' allows to pass additional arguments opposed to 'make test' +buildopts += 'ctest --output-on-failure' + +local_libs = ['Alignment', 'Catalogs', 'ChemicalFeatures', 'ChemReactions', 'ChemTransforms', 'coordgen', 'DataStructs', + 'Depictor', 'Descriptors', 'DistGeometry', 'DistGeomHelpers', 'EigenSolvers', 'FileParsers', + 'FilterCatalog', 'Fingerprints', 'FMCS', 'ForceFieldHelpers', 'ForceField', 'FragCatalog', 'GraphMol', + 'hc', 'InfoTheory', 'maeparser', 'MMPA', 'MolAlign', 'MolCatalog', 'MolChemicalFeatures', 'MolDraw2D', + 'MolHash', 'MolInterchange', 'MolStandardize', 'MolTransforms', 'Optimizer', 'PartialCharges', 'RDBoost', + 'RDGeneral', 'RDGeometryLib', 'RDStreams', 'ReducedGraphs', 'RGroupDecomposition', 'RingDecomposerLib', + 'ScaffoldNetwork', 'ShapeHelpers', 'SimDivPickers', 'SLNParse', 'SmilesParse', 'Subgraphs', + 'SubstructLibrary', 'SubstructMatch', 'Trajectory'] + +sanity_check_paths = { + 'files': ['lib/libRDKit%s.%s' % (x, SHLIB_EXT) for x in local_libs], + 'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'], +} + +sanity_check_commands = [ + "python -c 'import rdkit.rdBase'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_skip-broken-test.patch b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_skip-broken-test.patch new file mode 100644 index 00000000000..206f94fdba6 --- /dev/null +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_skip-broken-test.patch @@ -0,0 +1,13 @@ +skip broken test, see https://github.com/rdkit/rdkit/issues/3009 +author: Kenneth Hoste (HPC-UGent) +--- rdkit-Release_2021_03_4/Code/GraphMol/Wrap/rough_test.py.orig 2020-12-12 09:00:55.000000000 +0100 ++++ rdkit-Release_2021_03_4/Code/GraphMol/Wrap/rough_test.py 2021-01-05 11:43:13.850901127 +0100 +@@ -3945,7 +3945,7 @@ + self.assertEqual(v[0], 2) + self.assertEqual(v[1], 6) + +- def testCrambin(self): ++ def ignored_testCrambin(self): + crambinPdb = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FileParsers', 'test_data', + '1CRN.pdb') + crambin = Chem.MolFromPDBFile(crambinPdb) From 683851bfa9c553e7de2f2d4fc588a57bb0d9afb6 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 21 Oct 2021 16:05:00 +0200 Subject: [PATCH 1652/9987] Update RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb: correct checksum of patch file --- .../r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb index d94f367fc7c..63bccf2332b 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb @@ -17,7 +17,7 @@ sources = ['Release_%s.tar.gz' % version.replace('.', '_')] patches = ['RDKit-%(version)s_skip-broken-test.patch'] checksums = [ 'bed309df7f1e2ea25736a986cf951325681142ee49468b1c62d020a109d2ef52', # Release_2021_03_4.tar.gz - '4728e6854b9199845a79bb1aee9c05d1a29db0e3ae9bbeb85680545dd77b1e23', # RDKit-2021.03.4_skip-broken-test.patch + '45869e01461b66e42c9305f5e8a65f696417e4777c2da60ef81d1e26e57d1b2e', # RDKit-2021.03.4_skip-broken-test.patch ] # Dependencies varies from version to version From 340c4cb18488eade62e5da7699805aecf013a50f Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 21 Oct 2021 16:07:54 +0100 Subject: [PATCH 1653/9987] Update and rename SMV-6.7.17_example_file.patch to example.smv changing patchfile (which makes an example file) to the actual example file --- .../s/SMV/SMV-6.7.17_example_file.patch | 48 ------------------- easybuild/easyconfigs/s/SMV/example.smv | 43 +++++++++++++++++ 2 files changed, 43 insertions(+), 48 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SMV/SMV-6.7.17_example_file.patch create mode 100644 easybuild/easyconfigs/s/SMV/example.smv diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17_example_file.patch b/easybuild/easyconfigs/s/SMV/SMV-6.7.17_example_file.patch deleted file mode 100644 index a0c6bd7142c..00000000000 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17_example_file.patch +++ /dev/null @@ -1,48 +0,0 @@ -diff -ruN smv-SMV6.7.17_orig/example.smv smv-SMV6.7.17/example.smv ---- smv-SMV6.7.17_orig/example.smv 1970-01-01 01:00:00.000000000 +0100 -+++ smv-SMV6.7.17/example.smv 2021-10-19 13:29:29.519110638 +0100 -@@ -0,0 +1,44 @@ -+MODULE main -+ VAR -+ s0: {noncritical, trying, critical, ready}; -+ s1: {noncritical, trying, critical, ready}; -+ turn: boolean; -+ pr0: process prc(s0, s1, turn, 0); -+ pr1: process prc(s1, s0, turn, 1); -+ -+ASSIGN init(turn) := 0; -+ -+ FAIRNESS !(s0 = critical) -+ FAIRNESS !(s1 = critical) -+ -+ -+ SPEC AG((s0 = critical) -> !(s1 = critical)) -+ SPEC AG((s1 = critical) -> !(s0 = critical)) -+ -+ SPEC AG((s0 = trying) -> AF(s0 = critical)) -+ SPEC AG((s1 = trying) -> AF(s1 = critical)) -+ -+MODULE prc(state0, state1, turn, turn0) -+ -+ ASSIGN -+ init(state0) := noncritical; -+ next(state0) := -+ case -+ (state0 = noncritical) : {trying,noncritical}; -+ (state0 = trying) & ((state1 = noncritical) | -+ (state1 = trying) | -+ (state1 = ready)): ready; -+ (state0 = ready): critical; -+ (state0 = trying) & (state1 = trying) -+ & (turn = turn0): critical; -+ (state0 = critical) : {critical,noncritical}; -+ 1: state0; -+ esac; -+ -+ next(turn) := -+ case -+ turn = turn0 & state0 = critical: !turn; -+ 1: turn; -+ esac; -+ FAIRNESS running -+ diff --git a/easybuild/easyconfigs/s/SMV/example.smv b/easybuild/easyconfigs/s/SMV/example.smv new file mode 100644 index 00000000000..6d507ccb42f --- /dev/null +++ b/easybuild/easyconfigs/s/SMV/example.smv @@ -0,0 +1,43 @@ +MODULE main + VAR + s0: {noncritical, trying, critical, ready}; + s1: {noncritical, trying, critical, ready}; + turn: boolean; + pr0: process prc(s0, s1, turn, 0); + pr1: process prc(s1, s0, turn, 1); + +ASSIGN init(turn) := 0; + + FAIRNESS !(s0 = critical) + FAIRNESS !(s1 = critical) + + + SPEC AG((s0 = critical) -> !(s1 = critical)) + SPEC AG((s1 = critical) -> !(s0 = critical)) + + SPEC AG((s0 = trying) -> AF(s0 = critical)) + SPEC AG((s1 = trying) -> AF(s1 = critical)) + +MODULE prc(state0, state1, turn, turn0) + + ASSIGN + init(state0) := noncritical; + next(state0) := + case + (state0 = noncritical) : {trying,noncritical}; + (state0 = trying) & ((state1 = noncritical) | + (state1 = trying) | + (state1 = ready)): ready; + (state0 = ready): critical; + (state0 = trying) & (state1 = trying) + & (turn = turn0): critical; + (state0 = critical) : {critical,noncritical}; + 1: state0; + esac; + + next(turn) := + case + turn = turn0 & state0 = critical: !turn; + 1: turn; + esac; + FAIRNESS running From 95b7a6a32d0ae083f7bbddd2915933d6ea961800 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 21 Oct 2021 17:09:03 +0200 Subject: [PATCH 1654/9987] fixing of minor stuff from PR comments --- .../l/lpeg/lpeg-1.0.2-intel-2020b.eb | 9 --------- .../s/SMV/SMV-6.7.17-intel-2020b.eb | 20 +++++++++++-------- .../s/SMV/SMV-6.7.17_missing-includes.patch | 2 ++ 3 files changed, 14 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb b/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb index ecf73a8bb5e..3ee9b07e774 100644 --- a/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb +++ b/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb @@ -21,15 +21,6 @@ dependencies = [ ('Lua', '5.4.2'), ] -# list of all the libraries we need before installation: -# /user/gent/438/vsc43810/eb_inuits/210_smokeview/smv-SMV6.7.17/Build/LIBS/intel_linux_64/make_LIBS.make -# make sure to include those libraries in make commands when building SMV - -# shell script which runs makefile. actual smokeview: -# /user/gent/438/vsc43810/eb_inuits/210_smokeview/smv-SMV6.7.17/Build/smokeview/intel_linux_64/make_smokeview_db.sh - -# universal makefile for all OS - /user/gent/438/vsc43810/eb_inuits/210_smokeview/smv-SMV6.7.17/Build/smokeview/Makefile - files_to_copy = ['*'] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb index 514cc7cbb85..ca5ba00fcb2 100644 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb @@ -17,14 +17,19 @@ source_urls = ['https://github.com/firemodels/%(name)s/archive/refs/tags/'] sources = ['%(name)s%(version)s.tar.gz'] patches = [ 'SMV-%(version)s_missing-includes.patch', - ('SMV-%(version)s_example_file.patch', 1) # eb cant figure this out on its own + ('example.smv', '.'), # example file for sanity check ] checksums = [ '2e718af991e48228bf374fdefcce00d2e8b5827cc29ae2138ae267fda896f127', # SMV6.7.17.tar.gz - '5f69669b45ad7be0510785fe2d956b000c81cbe622fc31c256fd4eb2c8d470a4', # SMV-6.7.17_missing-includes.patch - '33f0c6a580772c1a5adc31e0c301e7befc0f3011a2d6d8e12ecdc2f8d4904610', # SMV-6.7.17_example_file.patch + '2b287f3e6ff368422684bd887568a369b9db3426a94efefcccc7680392b742ab', # SMV-6.7.17_missing-includes.patch + '1adf7dcc5293ec7a5f7ec01a828dec88b4ddd025505167b4e361d9450f66ea59', # example.smv ] +# checksums = [ +# '2e718af991e48228bf374fdefcce00d2e8b5827cc29ae2138ae267fda896f127', # SMV6.7.17.tar.gz +# '5f69669b45ad7be0510785fe2d956b000c81cbe622fc31c256fd4eb2c8d470a4', # SMV-6.7.17_missing-includes.patch +# '33f0c6a580772c1a5adc31e0c301e7befc0f3011a2d6d8e12ecdc2f8d4904610', # SMV-6.7.17_example_file.patch +# ] dependencies = [ ('libgd', '2.3.0'), @@ -39,7 +44,7 @@ dependencies = [ ('Xvfb', '1.20.9'), ] -local_compiler_lib_append = '/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64_lin/' +local_compiler_lib_append = '/compilers_and_libraries_$EBVERSIONICCIFORT/linux/compiler/lib/intel64_lin/' local_buildopts = ' -lglui -lglut -lfreeglut -lGLU -lGL -llibgd ' local_buildopts += ' LDFLAGS=" -L%(installdir)s -L$EBROOTFREEGLUT/lib -L$EBROOTLIBGD/lib " ' @@ -55,10 +60,10 @@ prebuildopts += "cd %(builddir)s/smv-SMV%(version)s/Build/smokeview/ && " prebuildopts += "export IFORT_COMPILER_LIB=$EBROOTICCIFORT%s && " % local_compiler_lib_append buildopts = ' intel_linux_64 ' + local_buildopts -buildopts += ' && make -j 36 intel_linux_64_db ' + local_buildopts +buildopts += ' && make -j %(parallel)s intel_linux_64_db ' + local_buildopts files_to_copy = [ - (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64*", "example.smv"], 'bin') + (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64*"], 'bin'), ] postinstallcmds = [ @@ -68,8 +73,7 @@ postinstallcmds = [ modextrapaths = {'PATH': ['bin']} sanity_check_commands = [ - # 'cd %(installdir)s/bin && xvfb-run smokeview example' - "cd %(installdir)s/bin && timeout 10 xvfb-run smokeview example 2>&1 | grep 'Terminated' " + "cd %(builddir)s/smv-SMV%(version)s && timeout 10 xvfb-run smokeview example 2>&1 | grep 'Terminated' ", ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17_missing-includes.patch b/easybuild/easyconfigs/s/SMV/SMV-6.7.17_missing-includes.patch index 5d6702a0958..f5a1c45d4a6 100644 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17_missing-includes.patch +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17_missing-includes.patch @@ -1,3 +1,5 @@ +author: Denis Kristak (Inuits) +correct relative paths in makefiles, add missing includes, prevent unnecessary SW from installing, fix compilation flags diff -ruN smv-SMV6.7.17_orig/Build/LIBS/intel_linux_64/make_LIBS.make smv-SMV6.7.17/Build/LIBS/intel_linux_64/make_LIBS.make --- smv-SMV6.7.17_orig/Build/LIBS/intel_linux_64/make_LIBS.make 2021-10-11 15:54:47.661332000 +0200 +++ smv-SMV6.7.17/Build/LIBS/intel_linux_64/make_LIBS.make 2021-10-14 13:59:41.548566000 +0200 From 194c7265aa887cd6d944e2bd3d7b9f6fc76da3d0 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 21 Oct 2021 17:10:13 +0200 Subject: [PATCH 1655/9987] fixing of minor stuff from PR comments --- easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb index ca5ba00fcb2..e4d034074f7 100644 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb @@ -25,12 +25,6 @@ checksums = [ '1adf7dcc5293ec7a5f7ec01a828dec88b4ddd025505167b4e361d9450f66ea59', # example.smv ] -# checksums = [ -# '2e718af991e48228bf374fdefcce00d2e8b5827cc29ae2138ae267fda896f127', # SMV6.7.17.tar.gz -# '5f69669b45ad7be0510785fe2d956b000c81cbe622fc31c256fd4eb2c8d470a4', # SMV-6.7.17_missing-includes.patch -# '33f0c6a580772c1a5adc31e0c301e7befc0f3011a2d6d8e12ecdc2f8d4904610', # SMV-6.7.17_example_file.patch -# ] - dependencies = [ ('libgd', '2.3.0'), ('freeglut', '3.2.1'), From aa5dcd9544be6b802e07737b726d35c70cba131c Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 21 Oct 2021 19:11:16 +0200 Subject: [PATCH 1656/9987] adding easyconfigs: Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb --- .../Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..db19965911d --- /dev/null +++ b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb @@ -0,0 +1,41 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'Binary' + +name = 'Rgurobi' +version = '9.1.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://www.gurobi.com' +description = """Gurobi Optimizer %(version_major_minor)s interface""" +# NOTE not in the license list of EB +# software_license = 'LGPL-2.1' + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['gurobi%(version)s_linux64.tar.gz'] +checksums = ['7f60bd675f79476bb2b32cd632aa1d470f8246f2b033b7652d8de86f6e7e429b'] + +dependencies = [ + ('R', '4.1.0'), + ('Gurobi', version), +] + +extract_sources = True +install_cmd = 'R CMD INSTALL R/gurobi_*.tar.gz --library=%(installdir)s --no-clean-on-error' + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['gurobi'], +} + +moduleclass = 'math' From c6f73f282a4635447ee28c952f7ea21814d09173 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 21 Oct 2021 20:01:26 +0200 Subject: [PATCH 1657/9987] Disable TestF90Callback since it fails with Intel. The produced Fortran code is incorrect. --- .../SciPy-bundle-2021.05-intel-2021a.eb | 3 +++ ...y-1.20.3_disable_fortran_callback_test.patch | 17 +++++++++++++++++ 2 files changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_disable_fortran_callback_test.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb index 7065c3550d1..bf9ae1e311a 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb @@ -25,6 +25,7 @@ exts_list = [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable-broken-override-test.patch', 'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch', + 'numpy-1.20.3_disable_fortran_callback_test.patch', ], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': [ @@ -34,6 +35,8 @@ exts_list = [ '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046', + # numpy-1.20.3_disable_fortran_callback_test.patch + '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', ], }), ('scipy', '1.6.3', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_disable_fortran_callback_test.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_disable_fortran_callback_test.patch new file mode 100644 index 00000000000..049735ff4f1 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.20.3_disable_fortran_callback_test.patch @@ -0,0 +1,17 @@ +Disable TestF90Callback which fails when compiling the resulting code with ifort. +The resulting code is incorrect Fortran. +See https://github.com/numpy/numpy/issues/20157 + +Åke Sandgren, 20211021 +diff -ru numpy-1.20.3.orig/numpy/f2py/tests/test_callback.py numpy-1.20.3/numpy/f2py/tests/test_callback.py +--- numpy-1.20.3.orig/numpy/f2py/tests/test_callback.py 2021-05-08 23:14:06.000000000 +0200 ++++ numpy-1.20.3/numpy/f2py/tests/test_callback.py 2021-10-21 19:05:32.463548952 +0200 +@@ -261,7 +261,7 @@ + options = ["-DF2PY_USE_PYTHON_TLS"] + + +-class TestF90Callback(util.F2PyTest): ++class Disabled_for_intel_TestF90Callback(util.F2PyTest): + + suffix = '.f90' + From 5c24d5ea2256f2e7318ae1e6b388e36832764027 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Oct 2021 21:45:14 +0200 Subject: [PATCH 1658/9987] add compiler/parallel/tcltk R libraries included in base installation to extensions in R 4.x easyconfigs using foss toolchain --- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 6 ++++++ 5 files changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index e4788de50ef..9afb0e13b61 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -77,15 +77,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 23 July 2020 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index d8bbd8572a8..3226ee0f4bc 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -74,15 +74,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 10 Nov 2020 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index e3dbbcb551d..26d6cbdb27b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -81,15 +81,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 08 Mar 2021 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9.1', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index d1f3feab30c..febdb0ca5e7 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -78,15 +78,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 07 Apr 2021 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9.1', { diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index 6a6012353a2..d50895fcfd0 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -79,15 +79,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 3rd June 2021 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9.1', { From 160327660dc30671f75904f97d0d1affc949e795 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Oct 2021 08:36:15 +0200 Subject: [PATCH 1659/9987] add compiler/parallel/tcltk R libraries included in base installation to extensions in R easyconfigs using fosscuda toolchain --- easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 6 ++++++ 6 files changed, 36 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb index 16cad3fccd8..df2b372cf23 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb @@ -72,15 +72,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on June 7, 2019 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index 5f8b881fea6..c455fc487cf 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -78,15 +78,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 16 December 2019 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb index e3624b70a79..4bd3700f409 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb @@ -87,15 +87,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 23 July 2020 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index 9e5053e29bb..d35824d64ba 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -83,15 +83,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 10 Nov 2020 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 9d9ad1166d3..9c612d32b95 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -85,15 +85,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 08 Mar 2021 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9.1', { diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index 2f1b150a616..d1e5430a104 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -88,15 +88,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 07 Apr 2021 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9.1', { From ce70ec01417069fade6fa48bf51de4efdf33bef0 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 22 Oct 2021 16:09:44 +0200 Subject: [PATCH 1660/9987] adding easyconfigs: HH-suite-3.3.0-gompic-2019b.eb --- .../h/HH-suite/HH-suite-3.3.0-gompic-2019b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b.eb diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b.eb new file mode 100644 index 00000000000..0f44de427d9 --- /dev/null +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b.eb @@ -0,0 +1,66 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Updated to use gompi-2020b toolchain: +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'HH-suite' +version = '3.3.0' + +homepage = 'https://github.com/soedinglab/hh-suite' +description = """The HH-suite is an open-source software package +for sensitive protein sequence searching based on the pairwise +alignment of hidden Markov models (HMMs).""" + +toolchain = {'name': 'gompic', 'version': '2019b'} + +source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +dependencies = [ + ('Perl', '5.30.0'), + ('Python', '3.7.4'), +] + +_binaries = [ + 'hhalign', 'hhalign_mpi', 'hhalign_omp', + 'hhblits', 'hhblits_mpi', 'hhblits_omp', + 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp', + 'hhmake', 'hhfilter', 'hhconsensus', +] + +_scriptfiles = [ + 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', +] + +fix_perl_shebang_for = ['scripts/*pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + ['scripts/%s' % y for y in _scriptfiles], + 'dirs': ['data', 'scripts'] +} + +modextrapaths = { + 'PATH': 'scripts', + 'PERL5LIB': 'scripts', +} + +moduleclass = 'bio' From f4bdb84221d56040210882c4d82f4c31dac4c3a4 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 22 Oct 2021 16:22:49 +0200 Subject: [PATCH 1661/9987] add python suffix --- ...mpic-2019b.eb => HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/h/HH-suite/{HH-suite-3.3.0-gompic-2019b.eb => HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb} (98%) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb similarity index 98% rename from easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b.eb rename to easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb index 0f44de427d9..8cd29719456 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb @@ -18,6 +18,7 @@ easyblock = 'CMakeMake' name = 'HH-suite' version = '3.3.0' +versionsuffix = '%(pyver)s' homepage = 'https://github.com/soedinglab/hh-suite' description = """The HH-suite is an open-source software package From 46339db1e79fd5f8135c98072c3f54bdba23924d Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 22 Oct 2021 16:24:53 +0200 Subject: [PATCH 1662/9987] add dash to suffix --- .../h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb index 8cd29719456..4ae863aca7f 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb @@ -18,7 +18,7 @@ easyblock = 'CMakeMake' name = 'HH-suite' version = '3.3.0' -versionsuffix = '%(pyver)s' +versionsuffix = '-%(pyver)s' homepage = 'https://github.com/soedinglab/hh-suite' description = """The HH-suite is an open-source software package From d253fc1ce1c315fe76abfe32593bcddf258c7d99 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 22 Oct 2021 16:20:00 +0100 Subject: [PATCH 1663/9987] adding easyconfigs: pygraphviz-1.7-foss-2020b.eb, pygraphviz-1.7-foss-2021a.eb --- .../p/pygraphviz/pygraphviz-1.7-foss-2020b.eb | 25 +++++++++++++++++++ .../p/pygraphviz/pygraphviz-1.7-foss-2021a.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb new file mode 100644 index 00000000000..d42c422ae7a --- /dev/null +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pygraphviz' +version = '1.7' + +homepage = 'https://pygraphviz.github.io/' +description = """PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. +With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz +graph data structure and layout algorithms.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_ZIP] +checksums = ['a7bec6609f37cf1e64898c59f075afd659106cf9356c5f387cecaa2e0cdb2304'] + +dependencies = [ + ('Python', '3.8.6'), + ('Graphviz', '2.47.0', '-Java-11'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2021a.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2021a.eb new file mode 100644 index 00000000000..e5f0bc1eece --- /dev/null +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.7-foss-2021a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pygraphviz' +version = '1.7' + +homepage = 'https://pygraphviz.github.io/' +description = """PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. +With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz +graph data structure and layout algorithms.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_ZIP] +checksums = ['a7bec6609f37cf1e64898c59f075afd659106cf9356c5f387cecaa2e0cdb2304'] + +dependencies = [ + ('Python', '3.9.5'), + ('Graphviz', '2.47.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From ea7b13002e0a336932c595f26a52cee0dff6cf9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Oct 2021 17:35:53 +0200 Subject: [PATCH 1664/9987] add compiler/parallel/tcltk R libraries included in base installation to extensions in R 3.5.x and 3.6.x easyconfigs --- .../easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb | 6 ++++++ .../easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb | 6 ++++++ 9 files changed, 54 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb index b5ababcb2d4..7c15c4437a8 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb @@ -70,15 +70,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on June 20 2018 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-7', { diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index ade3dc827cc..b13278061d0 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -71,15 +71,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on Aug 17, 2018 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-7', { diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 42f68a958e8..72905166d7d 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -69,15 +69,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on Aug 17, 2018 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-7', { diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb index 191e1926053..4fad425acdd 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb @@ -69,15 +69,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on Aug 17, 2018 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-7', { diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb index 305cfe5d42e..b3dfeeb1012 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb @@ -71,15 +71,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on June 7, 2019 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb index a60bcfdbb34..190263d2d3c 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb @@ -71,15 +71,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on June 7, 2019 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index fea6a7d1230..0bc641a52fc 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -77,15 +77,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 16 December 2019 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb index 368d1c5b59a..cabb0423e80 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb @@ -75,15 +75,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 16 December 2019 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { diff --git a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb index 152ea2ef921..dc8f3642b9a 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb @@ -71,15 +71,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 25 March 2020 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9', { From 43e748d5d83deab08cfc29024a59ce7e10e7e5d6 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Sat, 23 Oct 2021 02:07:25 +0000 Subject: [PATCH 1665/9987] {toolchain} intel/2021.09: change to SYSTEM imkl Plus imkl-FFTW dependency compiled with iimpi/2021.09 --- .../imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021.09.eb | 11 +++++++++++ .../i/imkl/imkl-2021.4.0-iimpi-2021.09.eb | 14 -------------- easybuild/easyconfigs/i/intel/intel-2021.09.eb | 3 ++- 3 files changed, 13 insertions(+), 15 deletions(-) create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021.09.eb delete mode 100644 easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iimpi-2021.09.eb diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021.09.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021.09.eb new file mode 100644 index 00000000000..198703d5040 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021.09.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2021.4.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2021.09'} + +dependencies = [('imkl', version, '', True)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iimpi-2021.09.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iimpi-2021.09.eb deleted file mode 100644 index 2e474b7e657..00000000000 --- a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iimpi-2021.09.eb +++ /dev/null @@ -1,14 +0,0 @@ -name = 'imkl' -version = '2021.4.0' - -homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' -description = "Intel oneAPI Math Kernel Library" - -toolchain = {'name': 'iimpi', 'version': '2021.09'} - -# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] -sources = ['l_onemkl_p_%(version)s.640_offline.sh'] -checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/intel/intel-2021.09.eb b/easybuild/easyconfigs/i/intel/intel-2021.09.eb index 34c8a44dfe7..0a18f57735a 100644 --- a/easybuild/easyconfigs/i/intel/intel-2021.09.eb +++ b/easybuild/easyconfigs/i/intel/intel-2021.09.eb @@ -15,7 +15,8 @@ dependencies = [ ('binutils', '2.37', '', ('GCCcore', local_gccver)), ('intel-compilers', local_comp_ver), ('impi', local_comp_ver, '', ('intel-compilers', local_comp_ver)), - ('imkl', local_comp_ver, '', ('iimpi', version)), + ('imkl', local_comp_ver, '', True), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), ] moduleclass = 'toolchain' From 717809a0538788289233170536cb91c275c06017 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 25 Oct 2021 09:52:41 +0200 Subject: [PATCH 1666/9987] actually add Python to versionsuffix --- .../h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb index 4ae863aca7f..f49756dd464 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2019b-Python-3.7.4.eb @@ -18,7 +18,7 @@ easyblock = 'CMakeMake' name = 'HH-suite' version = '3.3.0' -versionsuffix = '-%(pyver)s' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/soedinglab/hh-suite' description = """The HH-suite is an open-source software package From 26b61b8e50f28a3b21836c80914821517dd83ef8 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 25 Oct 2021 17:24:19 +0200 Subject: [PATCH 1667/9987] adding easyconfigs: OpenSceneGraph-3.6.5-foss-2021a.eb, DCMTK-3.6.6-GCCcore-10.3.0.eb --- .../d/DCMTK/DCMTK-3.6.6-GCCcore-10.3.0.eb | 37 ++++++++++++++ .../OpenSceneGraph-3.6.5-foss-2021a.eb | 48 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..434f78256f8 --- /dev/null +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'DCMTK' +version = '3.6.6' + +homepage = 'https://dicom.offis.de/dcmtk' +description = """DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. +It includes software for examining, constructing and converting DICOM image files, handling offline media, sending +and receiving images over a network connection, as well as demonstrative image storage and worklist servers.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dicom.offis.de/download/dcmtk/dcmtk%s/' % version.replace('.', '')] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['6859c62b290ee55677093cccfd6029c04186d91cf99c7642ae43627387f3458e'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1') +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.2.0'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.10'), + ('libiconv', '1.16'), +] + +sanity_check_paths = { + 'files': ['bin/dcmdump', 'bin/dcmj2pnm'], + 'dirs': ['lib'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb new file mode 100644 index 00000000000..e706cfc4035 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jiri Furst +### + +easyblock = 'CMakeMake' + +name = 'OpenSceneGraph' +version = '3.6.5' + +homepage = 'http://www.openscenegraph.org/' +description = """The OpenSceneGraph is an open source high performance 3D graphics toolkit, +used by application developers in fields such as visual simulation, games, virtual reality, +scientific visualization and modelling. Written entirely in Standard C++ and OpenGL it runs +on all Windows platforms, OSX, GNU/Linux, IRIX, Solaris, HP-Ux, AIX and FreeBSD operating +systems. The OpenSceneGraph is now well established as the world leading scene graph +technology, used widely in the vis-sim, space, scientific, oil-gas, games and virtual +reality industries.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_SOURCE] +sources = ['OpenSceneGraph-%(version)s.tar.gz'] +checksums = ['aea196550f02974d6d09291c5d83b51ca6a03b3767e234a8c0e21322927d1e12'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210518'), + ('Mesa', '21.1.1'), + ('GDAL', '3.3.0'), + ('DCMTK', '3.6.6'), + ('OpenEXR', '3.0.1'), + ('SDL2', '2.0.14'), + ('poppler', '21.06.1'), + ('librsvg', '2.51.2'), + ('giflib', '5.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/osgviewer', 'bin/present3D', 'bin/osgarchive'], +} + +moduleclass = 'vis' From ac2fabf2830b01274161c14842c03346b72c2a45 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Oct 2021 17:26:07 +0100 Subject: [PATCH 1668/9987] Fix spatstat.* downloads for Seurat/4.0.1 --- .../easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb index bddbf11b5e7..be3f28cdb22 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb @@ -25,18 +25,21 @@ exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} exts_list = [ ('spatstat.utils', '2.1-0', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.utils'], 'checksums': ['ed3569fea295b62396c49cdcfe476414b0b0f3e52044175532f316a402d3f8a1'], }), ('spatstat.data', '2.1-0', { 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], }), ('spatstat.geom', '2.0-1', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'], 'checksums': ['70ebfe115e733b2e6778baf6e2935861472154c0dd21f15a84ec2a61e0a3f6e4'], }), ('spatstat.sparse', '2.0-0', { 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], }), ('spatstat.core', '2.0-0', { + 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'], 'checksums': ['fde9a91bd32b7a3c8b25e802a16d470dcc919c24da5715149e1d91eeec119ba7'], }), (name, version, { From 066b02a94dda854319278930e7d665aa06ee4dc6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 26 Oct 2021 06:03:34 +0800 Subject: [PATCH 1669/9987] bring back explicit Python dependency --- .../easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb index a80f60171d4..9ac4cb09119 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb @@ -25,6 +25,7 @@ checksums = [ dependencies = [ ('ELPA', '2021.05.001'), + ('Python', '3.9.5'), ('h5py', '3.2.1'), ] From da542bd6bb0dcb11ecc207c9ebd0c956f3b70257 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Oct 2021 08:57:24 +0200 Subject: [PATCH 1670/9987] add extra numpy patch to SciPy-bundle 2021.05 to fix problem with tests --- .../s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb index 7065c3550d1..0691706c16f 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2021a.eb @@ -25,6 +25,7 @@ exts_list = [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable-broken-override-test.patch', 'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch', + 'numpy-1.20.3_fix-target-test-ccompiler-opt.patch', ], 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': [ @@ -34,6 +35,8 @@ exts_list = [ '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046', + # numpy-1.20.3_fix-target-test-ccompiler-opt.patch + '3d84e8b7d48387778974a5f6ae342a690ab5989547206b6add9d9667f8d7572a', ], }), ('scipy', '1.6.3', { From 8a7581786100136bc17fdb52edb5612e4a230b31 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Oct 2021 12:02:45 +0200 Subject: [PATCH 1671/9987] Add description to patch. --- .../abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch | 3 +++ .../a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch index be06bff30a3..d570e263954 100644 --- a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch @@ -1,3 +1,6 @@ +Author: Jakob Schiotz +Description: FFTW will use 1 thread instead of 12, unless the variable ABTEM_FFTW_THREADS is set. + --- abtem/device.py.orig 2021-09-13 20:15:59.190194233 +0200 +++ abtem/device.py 2021-09-13 20:17:43.763802138 +0200 @@ -3,13 +3,14 @@ diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb index bbc631dca58..5ed303535ea 100644 --- a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b24-fosscuda-2020b-ASE-3.22.0.eb @@ -19,7 +19,7 @@ patches = [ checksums = [ '503e7775f9764cf8298cbd2d06c4a36a9c83efbd84d58721eee638adfd1e626e', # abtem-1.0.0b24.tar.gz # abTEM-1.0.0b24-Make-FFTW-multithreading-optional.patch - '49eee97f444ff16b45745adcd70dbbf63d5ddb842d7d6539ec303f388b4293da', + '7aa081d6543bbec7024e2f4f166b9ea6ba62624fae465db04d231cce207b9b21', '0d4a0500e4947e4967858e6644969796d5bd76bc556a9c09fdc80461dcbcaed6', # abTEM-1.0.0b24-MTF-bug-fix-issue-53.patch ] From d7daa34912814e71e439c56002a517bff1cde4ec Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 26 Oct 2021 13:01:38 +0200 Subject: [PATCH 1672/9987] updating per review --- .../l/lpeg/lpeg-1.0.2-GCCcore-10.2.0.eb | 38 +++++++++ .../s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb | 78 +++++++++++++++++++ 2 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..00a0ab846ae --- /dev/null +++ b/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +## + +easyblock = 'MakeCp' + +name = 'lpeg' +version = '1.0.2' + +homepage = 'http://www.inf.puc-rio.br/~roberto/lpeg/' +description = """LPeg is a new pattern-matching library for Lua, based on Parsing Expression Grammars (PEGs).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://www.inf.puc-rio.br/~roberto/lpeg/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['48d66576051b6c78388faad09b70493093264588fcd0f258ddaab1cdd4a15ffe'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Lua', '5.4.2'), +] + +files_to_copy = [ + (['lpeg.so'], 'lib/'), + (['*.h'], 'include/'), +] + +sanity_check_paths = { + 'files': ["lib/lpeg.so"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..abdce7f5395 --- /dev/null +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb @@ -0,0 +1,78 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +## + +easyblock = 'MakeCp' + +name = 'SMV' # SmokeView +version = '6.7.17' + +homepage = 'https://github.com/firemodels/smv' +description = """Smokeview is a visualization program that displays output of FDS and CFAST simulations.""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/firemodels/%(name)s/archive/refs/tags/'] +sources = ['%(name)s%(version)s.tar.gz'] +patches = [ + 'SMV-%(version)s_missing-includes.patch', + ('example.smv', '.'), # example file for sanity check +] +checksums = [ + '2e718af991e48228bf374fdefcce00d2e8b5827cc29ae2138ae267fda896f127', # SMV6.7.17.tar.gz + '2b287f3e6ff368422684bd887568a369b9db3426a94efefcccc7680392b742ab', # SMV-6.7.17_missing-includes.patch + '1adf7dcc5293ec7a5f7ec01a828dec88b4ddd025505167b4e361d9450f66ea59', # example.smv +] + +dependencies = [ + ('libgd', '2.3.0'), + ('freeglut', '3.2.1'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('Lua', '5.4.2'), + ('lpeg', '1.0.2'), + ('libGLU', '9.0.1'), + ('glew', '2.1.0'), + ('Xvfb', '1.20.9'), +] + +local_compiler_lib_append = '/compilers_and_libraries_$EBVERSIONICCIFORT/linux/compiler/lib/intel64_lin/' + +local_buildopts = ' -lglui -lglut -lfreeglut -lGLU -lGL -llibgd ' +local_buildopts += ' LDFLAGS=" -L%(installdir)s -L$EBROOTFREEGLUT/lib -L$EBROOTLIBGD/lib " ' +local_buildopts += ' IFLAGS=" -I$EBROOTFREEGLUT/include/GL -I%(builddir)s/smv-SMV%(version)s/Source/glui_v2_1_beta/ ' +local_buildopts += ' -I%(builddir)s/smv-SMV%(version)s/Source/glui_gl/GL/glut.h "' +local_buildopts += ' EB_L_PATH=%(installdir)s ' +local_buildopts += ' CFLAGS="-Dpp_LINUX" ' + +prebuildopts = "cd %(builddir)s/smv-SMV%(version)s/Build/LIBS/intel_linux_64/ && " +prebuildopts += " make all -f make_LIBS.make " +prebuildopts += "SRCDIR=%(builddir)s/smv-SMV%(version)s/Source/ LIBDIR=%(installdir)s && " +prebuildopts += "cd %(builddir)s/smv-SMV%(version)s/Build/smokeview/ && " +prebuildopts += "export IFORT_COMPILER_LIB=$EBROOTICCIFORT%s && " % local_compiler_lib_append + +buildopts = ' intel_linux_64 ' + local_buildopts +buildopts += ' && make -j %(parallel)s intel_linux_64_db ' + local_buildopts + +files_to_copy = [ + (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64*"], 'bin'), +] + +postinstallcmds = [ + 'ln -s %(installdir)s/bin/smokeview_linux_64 %(installdir)s/bin/smokeview' +] + +modextrapaths = {'PATH': ['bin']} + +sanity_check_commands = [ + "cd %(builddir)s/smv-SMV%(version)s && timeout 10 xvfb-run smokeview example 2>&1 | grep 'Terminated' ", +] + +sanity_check_paths = { + 'files': ["bin/smokeview"], + 'dirs': ["bin"], +} + +moduleclass = 'bio' From 866805175b72a3aeb826a6012f9df9e2501f0ae8 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 26 Oct 2021 13:04:44 +0200 Subject: [PATCH 1673/9987] adding easyconfigs: FFTW-3.3.10-gompi-2021.07.eb, FFTW-3.3.10-iimpi-2021.09.eb --- .../f/FFTW/FFTW-3.3.10-gompi-2021.07.eb | 17 ++++++++++++ .../f/FFTW/FFTW-3.3.10-iimpi-2021.09.eb | 26 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-gompi-2021.07.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2021.09.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-gompi-2021.07.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-gompi-2021.07.eb new file mode 100644 index 00000000000..90d98e0e831 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-gompi-2021.07.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2021.07'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2021.09.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2021.09.eb new file mode 100644 index 00000000000..430b4b018f3 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2021.09.eb @@ -0,0 +1,26 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2021.09'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# https://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails on AMD systems when configuring with --enable-avx-128-fma, +# because Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' From 798f85c91c5b012a021d413a929a016897643391 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 26 Oct 2021 13:36:45 +0200 Subject: [PATCH 1674/9987] Added 'dirs' into sanity checks --- .../o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb index e706cfc4035..e06426c26f1 100644 --- a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb +++ b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb @@ -43,6 +43,7 @@ dependencies = [ sanity_check_paths = { 'files': ['bin/osgviewer', 'bin/present3D', 'bin/osgarchive'], + 'dirs': ['lib'] } moduleclass = 'vis' From b7c1ad949a02b83b8e0b017d752c189fd664dca5 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Oct 2021 15:54:01 +0200 Subject: [PATCH 1675/9987] Add sanity_pip_check to both .eb files. --- easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb | 1 + easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb index 37f0e99e6cf..9894375dcc0 100644 --- a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb @@ -32,6 +32,7 @@ dependencies = [ download_dep_fail = True use_pip = True +sanity_pip_check = True sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb index bfd19a0d087..73aa35a300a 100644 --- a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb @@ -32,6 +32,7 @@ dependencies = [ download_dep_fail = True use_pip = True +sanity_pip_check = True sanity_check_paths = { 'files': [], From 21cac071134c4b2a75a3aa87c706f4fdcaa97529 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Oct 2021 15:57:31 +0200 Subject: [PATCH 1676/9987] Add version suffix because of ASE dependency. --- .../pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb | 44 +++++++++++++++++++ ...pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb | 44 +++++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb create mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb new file mode 100644 index 00000000000..2e18fed82c8 --- /dev/null +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b-ASE-3.22.0.eb @@ -0,0 +1,44 @@ +easyblock = "PythonPackage" + +name = 'pyqstem' +version = '1.0.3' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/PyQSTEM' +description = """QSTEM is a program for quantitative image simulation in electron +microscopy, including TEM, STEM and CBED image simulation. + +This project interfaces the QSTEM code with Python and the Atomic +Simulation Environment (ASE) to provide a single environment for +building models, simulating and analysing images.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), +] +checksums = [ + '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz + # pyqstem-1.0.3-Remove-unused-scipy-import.patch + 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', +] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-image', '0.18.1'), + ('ASE', _aseversion), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb new file mode 100644 index 00000000000..b6a80dcfb0c --- /dev/null +++ b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b-ASE-3.22.0.eb @@ -0,0 +1,44 @@ +easyblock = "PythonPackage" + +name = 'pyqstem' +version = '1.0.3' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/PyQSTEM' +description = """QSTEM is a program for quantitative image simulation in electron +microscopy, including TEM, STEM and CBED image simulation. + +This project interfaces the QSTEM code with Python and the Atomic +Simulation Environment (ASE) to provide a single environment for +building models, simulating and analysing images.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), +] +checksums = [ + '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz + # pyqstem-1.0.3-Remove-unused-scipy-import.patch + 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', +] + +dependencies = [ + ('Python', '3.8.6'), + ('scikit-image', '0.18.1'), + ('ASE', _aseversion), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'phys' From a8c092a7c72944a2f5b9de5b7312b2874028548b Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Oct 2021 16:01:19 +0200 Subject: [PATCH 1677/9987] Remove old versions of files that were accidentally preserved. --- .../p/pyqstem/pyqstem-1.0.3-foss-2020b.eb | 42 ------------------- .../p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb | 42 ------------------- 2 files changed, 84 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb delete mode 100644 easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb deleted file mode 100644 index 9894375dcc0..00000000000 --- a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-foss-2020b.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = "PythonPackage" - -name = 'pyqstem' -version = '1.0.3' - -homepage = 'https://github.com/jacobjma/PyQSTEM' -description = """QSTEM is a program for quantitative image simulation in electron -microscopy, including TEM, STEM and CBED image simulation. - -This project interfaces the QSTEM code with Python and the Atomic -Simulation Environment (ASE) to provide a single environment for -building models, simulating and analysing images.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), -] -checksums = [ - '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz - # pyqstem-1.0.3-Remove-unused-scipy-import.patch - 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', -] - -dependencies = [ - ('Python', '3.8.6'), - ('scikit-image', '0.18.1'), - ('ASE', '3.22.0'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb deleted file mode 100644 index 73aa35a300a..00000000000 --- a/easybuild/easyconfigs/p/pyqstem/pyqstem-1.0.3-fosscuda-2020b.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = "PythonPackage" - -name = 'pyqstem' -version = '1.0.3' - -homepage = 'https://github.com/jacobjma/PyQSTEM' -description = """QSTEM is a program for quantitative image simulation in electron -microscopy, including TEM, STEM and CBED image simulation. - -This project interfaces the QSTEM code with Python and the Atomic -Simulation Environment (ASE) to provide a single environment for -building models, simulating and analysing images.""" - -toolchain = {'name': 'fosscuda', 'version': '2020b'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - ('pyqstem-1.0.3-Remove-unused-scipy-import.patch', 1), -] -checksums = [ - '612c4c95531ea9239c91e6f8b9e29a954ac873dd8584b6a57512dcfb6263ff0a', # pyqstem-1.0.3.tar.gz - # pyqstem-1.0.3-Remove-unused-scipy-import.patch - 'de1e6615057648c4d1f857f58d751699c1b292b4fe0c0f8b2f0b300e99f91d59', -] - -dependencies = [ - ('Python', '3.8.6'), - ('scikit-image', '0.18.1'), - ('ASE', '3.22.0'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'phys' From b0545c826a0bb72581d9599bf9892281d1feb52b Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 26 Oct 2021 17:06:08 +0200 Subject: [PATCH 1678/9987] adding easyconfigs: panaroo-1.2.8-foss-2020b.eb, MAFFT-7.475-GCC-10.2.0-with-extensions.eb, PRANK-170427-GCC-10.2.0.eb --- .../MAFFT-7.475-GCC-10.2.0-with-extensions.eb | 48 ++++++++++++++ .../p/PRANK/PRANK-170427-GCC-10.2.0.eb | 34 ++++++++++ .../p/panaroo/panaroo-1.2.8-foss-2020b.eb | 64 +++++++++++++++++++ 3 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-GCC-10.2.0-with-extensions.eb create mode 100644 easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-GCC-10.2.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-GCC-10.2.0-with-extensions.eb new file mode 100644 index 00000000000..70eb55dda67 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.475-GCC-10.2.0-with-extensions.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez (Swiss Institute of Bioinformatics, Biozentrum - University of Basel) +# 7.305 modified by: +# Adam Huffman (The Francis Crick Institute) +# 7.453 switch to Bundle by: +# Alex Domingo (Vrije Universiteit Brussel) + +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.475' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], + 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'checksums': ['bb6973ae089ea18cfbd3861a5b9d2c8b7e1543a1fdc78ac2d7cd8dbe3443f319'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft', 'libexec/mafft/mxscarnamod'], # mxscarnamod installed by MAFFT Extensions + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb new file mode 100644 index 00000000000..fccd68f1731 --- /dev/null +++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'PRANK' +version = '170427' + +homepage = 'http://wasabiapp.org/software/prank/' +description = """ PRANK is a probabilistic multiple alignment program for DNA, + codon and amino-acid sequences. PRANK is based on a novel algorithm that treats + insertions correctly and avoids over-estimation of the number of deletion events.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://wasabiapp.org/download/prank/'] +sources = ['%(namelower)s.source.%(version)s.tgz'] +checksums = ['623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859'] + +# PRANK uses MAFFT as external tool to contruct guide tree +dependencies = [('MAFFT', '7.475', '-with-extensions')] + +start_dir = 'src' + +files_to_copy = [(['prank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/prank'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb new file mode 100644 index 00000000000..1fcc48802c8 --- /dev/null +++ b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb @@ -0,0 +1,64 @@ +# Author: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'panaroo' +version = '1.2.8' + +homepage = 'https://gtonkinhill.github.io/panaroo/' +description = "A pangenome analysis pipeline." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('CD-HIT', '4.8.1'), + ('PRANK', '170427'), + ('Biopython', '1.78'), + ('SciPy-bundle', '2020.11'), + ('networkx', '2.5'), + ('edlib', '1.3.9'), + ('tqdm', '4.60.0'), + ('matplotlib', '3.3.3'), + ('scikit-learn', '0.23.2'), + ('plotly.py', '4.14.3'), + ('DendroPy', '4.5.2'), + ('pyfaidx', '0.5.9.5'), + ('prokka', '1.14.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} + +exts_list = [ + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), + ('argcomplete', '1.12.3', { + 'checksums': ['2c7dbffd8c045ea534921e63b0be6fe65e88599990d8dc408ac8c542b72a5445'], + }), + ('argh', '0.26.2', { + 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], + }), + ('gffutils', '0.10.1', { + 'checksums': ['a8fc39006d7aa353147238160640e2210b168f7849cb99896be3fc9441e351cb'], + }), + ('intbitset', '2.4.1', { + 'checksums': ['44bca80b8cc702d5a56f0686f2bb5e028ab4d0c2c1761941589d46b7fa2c701c'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/gtonkinhill/panaroo/archive/'], + 'checksums': ['af56fae581908a93b843a90471dc80d4ff7299afc9e66e22510233d1a76d00c5'], + }), +] + +sanity_check_commands = [ + "panaroo --version" +] + +moduleclass = 'bio' From 83654c893fd7e6f7599cf531571df48b22f13ef0 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Tue, 26 Oct 2021 16:09:42 +0100 Subject: [PATCH 1679/9987] Update freetype-2.6.5-foss-2016b.eb Source has moved. --- easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb index f59391c7f98..2aeb2e39e9e 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb @@ -8,7 +8,7 @@ description = """FreeType 2 is a software font engine that is designed to be sma toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = [GNU_SAVANNAH_SOURCE] +source_urls = ['https://download-mirror.savannah.gnu.org/releases/freetype/freetype-old/'] sources = [SOURCE_TAR_GZ] dependencies = [ From 93e85019ec80a67c5b8413c5fc75abb17220a910 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Tue, 26 Oct 2021 17:40:23 +0200 Subject: [PATCH 1680/9987] Fixed issues --- easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb index 1fcc48802c8..733968e1019 100644 --- a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb +++ b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.8-foss-2020b.eb @@ -18,7 +18,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('networkx', '2.5'), ('edlib', '1.3.9'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ('matplotlib', '3.3.3'), ('scikit-learn', '0.23.2'), ('plotly.py', '4.14.3'), @@ -30,10 +30,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = { - 'source_urls': [PYPI_SOURCE], -} - exts_list = [ ('sklearn', '0.0', { 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], From 009ed8efc677b758d96982c7b7d730e8bc1775e9 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Tue, 26 Oct 2021 16:42:01 +0100 Subject: [PATCH 1681/9987] Update freetype-2.6.5-foss-2016b.eb --- easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb index 2aeb2e39e9e..2488e2d0392 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://download-mirror.savannah.gnu.org/releases/freetype/freetype-old/'] sources = [SOURCE_TAR_GZ] +checksums = ['3bb24add9b9ec53636a63ea8e867ed978c4f8fdd8f1fa5ccfd41171163d4249a'] dependencies = [ ('libpng', '1.6.24'), From 50167aca55ea850983d3c177c83bf944b0e1204d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 26 Oct 2021 20:17:09 +0200 Subject: [PATCH 1682/9987] Patch GROMACS cpu detection to work with the CMake from 2019b toolchain --- .../g/GROMACS/GROMACS-2019.3-foss-2019b.eb | 4 +- .../GROMACS/GROMACS-2019.3-fosscuda-2019b.eb | 2 + .../GROMACS-2019_fix_cpu_detection.patch | 47 +++++++++++++++++++ 3 files changed, 52 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2019_fix_cpu_detection.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-foss-2019b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-foss-2019b.eb index 41bfe8d5061..6050943b9f4 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-foss-2019b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-foss-2019b.eb @@ -37,13 +37,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', 'GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch', + 'GROMACS-2019_fix_cpu_detection.patch', ] checksums = [ '4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573', # gromacs-2019.3.tar.gz # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', # GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch - '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06' + '727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06', + '6e305416773639e050f8cef6195e9de6f4555b213d093210bb0b2c0f37e9ef91', # GROMACS-2019_fix_cpu_detection.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-fosscuda-2019b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-fosscuda-2019b.eb index e7c29a6de9b..31b3d4f24d6 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-fosscuda-2019b.eb @@ -37,6 +37,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2019_fix_cpu_detection.patch', ] checksums = [ '4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573', # gromacs-2019.3.tar.gz @@ -44,6 +45,7 @@ checksums = [ '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', # GROMACS-2019_increase_test_timeout_for_GPU.patch '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + '6e305416773639e050f8cef6195e9de6f4555b213d093210bb0b2c0f37e9ef91', # GROMACS-2019_fix_cpu_detection.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019_fix_cpu_detection.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019_fix_cpu_detection.patch new file mode 100644 index 00000000000..abcb6023c92 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019_fix_cpu_detection.patch @@ -0,0 +1,47 @@ +There is a bug in the CPU detection when using CMake from 2019b toolchain. +Taking the diff between 2019 and 2019.4 makes the problem go away. + +Åke Sandgren, 20211026 +diff -ru gromacs-2019/cmake/gmxDetectCpu.cmake gromacs-2019.4/cmake/gmxDetectCpu.cmake +--- gromacs-2019/cmake/gmxDetectCpu.cmake 2017-07-23 18:42:23.000000000 +0200 ++++ gromacs-2019.4/cmake/gmxDetectCpu.cmake 2019-10-02 08:23:32.000000000 +0200 +@@ -1,7 +1,7 @@ + # + # This file is part of the GROMACS molecular simulation package. + # +-# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by ++# Copyright (c) 2012,2013,2014,2015,2016,2017,2019, by the GROMACS development team, led by + # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, + # and including many others, as listed in the AUTHORS file in the + # top-level source directory and at http://www.gromacs.org. +@@ -78,13 +78,13 @@ + # for x86 we need inline assembly to use cpuid + gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM) + if(GMX_X86_GCC_INLINE_ASM) +- set(GCC_INLINE_ASM_DEFINE "-DGMX_X86_GCC_INLINE_ASM=1") ++ set(GCC_INLINE_ASM_DEFINE -DGMX_X86_GCC_INLINE_ASM=1) + else() +- set(GCC_INLINE_ASM_DEFINE "-DGMX_X86_GCC_INLINE_ASM=0") ++ set(GCC_INLINE_ASM_DEFINE -DGMX_X86_GCC_INLINE_ASM=0) + endif() + +- set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${PROJECT_SOURCE_DIR}/src -DGMX_CPUINFO_STANDALONE ${GMX_STDLIB_CXX_FLAGS} -DGMX_TARGET_X86=${GMX_TARGET_X86_VALUE}") +- set(LINK_LIBRARIES "${GMX_STDLIB_LIBRARIES}") ++ set(_compile_definitions ${GCC_INLINE_ASM_DEFINE};-I${PROJECT_SOURCE_DIR}/src;-DGMX_CPUINFO_STANDALONE=1;-DGMX_TARGET_X86=${GMX_TARGET_X86_VALUE}) ++ set(LINK_LIBRARIES ${GMX_STDLIB_LIBRARIES}) + try_compile(CPU_DETECTION_COMPILED + "${PROJECT_BINARY_DIR}" + "${PROJECT_SOURCE_DIR}/src/gromacs/hardware/cpuinfo.cpp" +@@ -93,7 +93,11 @@ + OUTPUT_VARIABLE CPU_DETECTION_COMPILED_OUTPUT + COPY_FILE ${CPU_DETECTION_BINARY}) + if(NOT CPU_DETECTION_COMPILED AND NOT RUN_CPU_DETECTION_COMPILATION_QUIETLY) +- message(STATUS "Did not detect build CPU ${LOWERTYPE} - detection program did not compile") ++ if(GMX_TARGET_X86) ++ message(WARNING "CPU detection program did not compile on x86 host - this should never happen. It is VERY bad for performance, since you will lose all SIMD support. Please file a bug report.") ++ else() ++ message(WARNING "Did not detect build CPU ${LOWERTYPE} - detection program did not compile. Please file a bug report if this is a common platform.") ++ endif() + endif() + set(RUN_CPU_DETECTION_COMPILATION_QUIETLY TRUE CACHE INTERNAL "Keep quiet on any future compilation attempts") + endif() From d4e712279de8c726469d6cb82d0ef34c9636d4dc Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 26 Oct 2021 21:21:23 +0200 Subject: [PATCH 1683/9987] adding easyconfigs: matplotlib-3.4.2-intel-2021a.eb --- .../matplotlib-3.4.2-intel-2021a.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-intel-2021a.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-intel-2021a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-intel-2021a.eb new file mode 100644 index 00000000000..9ad30aad1b0 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-intel-2021a.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.4.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('cppy', '1.1.0') +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('libpng', '1.6.37'), + ('freetype', '2.10.4'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.2.0'), + ('Qhull', '2020.2') +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' setup.cfg.template >setup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['950a199911a8d94683a6b10321f9345d5a3a8433ec58b217ace979e18f16e248'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['d8d994cefdff9aaba45166eb3de4f5211adb4accac85cbf97137e98f26ea0219'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From e0cd6e67acc573287b911829929f5328e8868c66 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 27 Oct 2021 13:06:07 +0800 Subject: [PATCH 1684/9987] slightly relax a few more tests --- .../BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb | 2 +- .../b/BerkeleyGW/BerkeleyGW-3.0.1_tests.patch | 22 +++++++++++++++++++ 2 files changed, 23 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb index 9ac4cb09119..a0c6cb72f84 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2021a.eb @@ -18,7 +18,7 @@ patches = [ ] checksums = [ '7d8c2cc1ee679afb48efbdd676689d4d537226b50e13a049dbcb052aaaf3654f', # BerkeleyGW-3.0.1.tar.gz - '38cdef673daaa78425af641d4b51437aa1038dcc7310ca523a38b117613dd4f2', # BerkeleyGW-3.0.1_tests.patch + 'f66ff15e2b99de5e808f78a552985fda3181f35c25817de4ac7df4d8f7fddf5a', # BerkeleyGW-3.0.1_tests.patch '56d90dc4e43db379441b6a1802e24f1f1356cd4aca4eb6d8b673f6c7926a7406', # BerkeleyGW-3.0.1_makefile.patch '414a4f23e430a2c02bab7bad18bcaf9b62129fa9dd1c2f87bd4bbc9fcb3bdded', # BerkeleyGW-3.0.1_version.patch ] diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_tests.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_tests.patch index 7436042ea73..584d77d2361 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_tests.patch +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1_tests.patch @@ -96,3 +96,25 @@ author: Miguel Dias Costa (National University of Singapore) match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM/Si_hdf5_cplx_spin.test.orig 2021-10-27 09:15:36.543399656 +0800 ++++ testsuite/Si-EPM/Si_hdf5_cplx_spin.test 2021-10-27 09:16:19.549009302 +0800 +@@ -17,7 +17,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM/Si_hdf5.test.orig 2021-10-27 09:17:11.134541236 +0800 ++++ testsuite/Si-EPM/Si_hdf5.test 2021-10-27 09:17:28.086387460 +0800 +@@ -16,7 +16,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 From af0073ddf1f68813a394e81e3a0c0c88ac4c2eef Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 27 Oct 2021 10:28:46 +0200 Subject: [PATCH 1685/9987] add sanity_check_commands --- easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-10.3.0.eb | 3 +++ .../o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb | 6 ++++-- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-10.3.0.eb index 434f78256f8..e155a7482d9 100644 --- a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-10.3.0.eb @@ -34,4 +34,7 @@ sanity_check_paths = { 'dirs': ['lib'], } +sanity_check_commands = ['%s_tests | grep " 0 failed"' % x for x in [ + 'dcmdata', 'dcmect', 'dcmfg', 'dcmiod', 'dcmnet', 'dcmrt', 'dcmseg', 'dcmsr', 'dcmtls', 'ofstd']] + moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb index e06426c26f1..97d5359d7d8 100644 --- a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb +++ b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021a.eb @@ -42,8 +42,10 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['bin/osgviewer', 'bin/present3D', 'bin/osgarchive'], - 'dirs': ['lib'] + 'files': ['bin/%s' % x for x in ['osgarchive', 'osgconv', 'osgfilecache', 'osgversion', 'osgviewer', 'present3D']], + 'dirs': ['lib'], } +sanity_check_commands = ['osgversion'] + moduleclass = 'vis' From a2945d1e676bb6faa793ad3e28b9aecef48e4d5b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 27 Oct 2021 12:01:18 +0200 Subject: [PATCH 1686/9987] add sanity_check_command for PRANK --- easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb index fccd68f1731..ee59ac1eae1 100644 --- a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.2.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['prank -help'] + moduleclass = 'bio' From 3eada0db942b5a0f6217077571e4ac359138eba2 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 27 Oct 2021 12:45:39 +0200 Subject: [PATCH 1687/9987] adding easyconfigs: abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb, abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb and patches: abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch --- ...26-Make-FFTW-multithreading-optional.patch | 22 +++++++++++ .../abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb | 39 +++++++++++++++++++ ...bTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb | 39 +++++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch create mode 100644 easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb create mode 100644 easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch new file mode 100644 index 00000000000..3ada10d12d7 --- /dev/null +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch @@ -0,0 +1,22 @@ +Author: Jakob Schiotz +Description: FFTW will use 1 thread instead of 12, unless the variable ABTEM_FFTW_THREADS is set. + +--- abtem/device.py.orig 2021-10-27 12:36:41.043781555 +0200 ++++ abtem/device.py 2021-10-27 12:38:43.351586183 +0200 +@@ -2,13 +2,14 @@ + import numpy as np + import psutil + import pyfftw ++import os + + from abtem.cpu_kernels import abs2, complex_exponential, interpolate_radial_functions, sum_run_length_encoded + from abtem.interpolate import interpolate_bilinear_cpu + import numbers + + FFTW_EFFORT = 'FFTW_MEASURE' +-FFTW_THREADS = 12 ++FFTW_THREADS = int(os.getenv('ABTEM_FFTW_THREADS', '1')) + FFTW_TIMELIMIT = 600 + + try: # This should be the only place import cupy, to make it a non-essential dependency + \ No newline at end of file diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb new file mode 100644 index 00000000000..58040804add --- /dev/null +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-foss-2020b-ASE-3.22.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'abTEM' +version = '1.0.0b26' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/abTEM' +description = """abTEM provides a Python API for running simulations +of Transmission Electron Microscopy images.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch', +] +checksums = [ + '8a40b7ff5caeb5997924f43e981d5158159e521bda2abd4093c6f555661a4294', # abtem-1.0.0b26.tar.gz + # abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch + 'd0532bdde462591fe1a5202fc79ec7decef10207d3e622fa4b605b09ffe55adf', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('h5py', '3.1.0'), + ('numba', '0.53.1'), + ('pyFFTW', '0.12.0'), + ('tqdm', '4.56.2'), + ('imageio', '2.9.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb new file mode 100644 index 00000000000..24cc2f9f1fa --- /dev/null +++ b/easybuild/easyconfigs/a/abTEM/abTEM-1.0.0b26-fosscuda-2020b-ASE-3.22.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'abTEM' +version = '1.0.0b26' +_aseversion = '3.22.0' +versionsuffix = '-ASE-' + _aseversion + +homepage = 'https://github.com/jacobjma/abTEM' +description = """abTEM provides a Python API for running simulations +of Transmission Electron Microscopy images.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch', +] +checksums = [ + '8a40b7ff5caeb5997924f43e981d5158159e521bda2abd4093c6f555661a4294', # abtem-1.0.0b26.tar.gz + # abTEM-1.0.0b26-Make-FFTW-multithreading-optional.patch + 'd0532bdde462591fe1a5202fc79ec7decef10207d3e622fa4b605b09ffe55adf', +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('ASE', _aseversion), + ('h5py', '3.1.0'), + ('numba', '0.53.1'), + ('pyFFTW', '0.12.0'), + ('tqdm', '4.56.2'), + ('imageio', '2.9.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 5c3d1a9145c0ff233205a21e0ab08357860e5df7 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 27 Oct 2021 13:23:50 +0200 Subject: [PATCH 1688/9987] Add dependencies. --- .../i/imageio/imageio-2.9.0-foss-2020b.eb | 25 +++++++++++++++++++ .../p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb create mode 100755 easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb new file mode 100644 index 00000000000..51d59be8f6b --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.9.0-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.9.0' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow', '8.0.1'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb new file mode 100755 index 00000000000..09b5d4fc47a --- /dev/null +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.12.0-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pyFFTW' +version = '0.12.0' + +homepage = 'https://github.com/pyFFTW/pyFFTW' +description = """A pythonic wrapper around FFTW, the FFT library, presenting a unified interface + for all the supported transforms.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['60988e823ca75808a26fd79d88dbae1de3699e72a293f812aa4534f8a0a58cb0'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('FFTW', '3.3.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 4f246a9367389d90ccf312999f7c3914d20b2958 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 27 Oct 2021 15:40:52 +0200 Subject: [PATCH 1689/9987] promote foss/2021.07 to foss/2021b and update FFTW to 3.3.10 in foss/2021b --- ...021.07.eb => ELPA-2021.05.001-foss-2021b.eb} | 2 +- ...pi-2021.07.eb => FFTW-3.3.10-gompi-2021b.eb} | 2 +- .../f/FFTW/FFTW-3.3.9-gompi-2021.07.eb | 17 ----------------- .../f/foss/{foss-2021.07.eb => foss-2021b.eb} | 4 ++-- ...foss-2021.07.eb => GDAL-3.3.2-foss-2021b.eb} | 2 +- .../gompi/{gompi-2021.07.eb => gompi-2021b.eb} | 2 +- ...pi-2021.07.eb => HDF5-1.12.1-gompi-2021b.eb} | 2 +- ...1-foss-2021.07.eb => HPCG-3.1-foss-2021b.eb} | 2 +- ....3-foss-2021.07.eb => HPL-2.3-foss-2021b.eb} | 2 +- ....07.eb => imkl-FFTW-2021.4.0-gompi-2021b.eb} | 2 +- ...i-2021.07.eb => netCDF-4.8.1-gompi-2021b.eb} | 2 +- ...> OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb} | 2 +- ...-fb.eb => ScaLAPACK-2.1.0-gompi-2021b-fb.eb} | 2 +- ...07.eb => SciPy-bundle-2021.10-foss-2021b.eb} | 2 +- 14 files changed, 14 insertions(+), 31 deletions(-) rename easybuild/easyconfigs/e/ELPA/{ELPA-2021.05.001-foss-2021.07.eb => ELPA-2021.05.001-foss-2021b.eb} (96%) rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.10-gompi-2021.07.eb => FFTW-3.3.10-gompi-2021b.eb} (90%) delete mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.9-gompi-2021.07.eb rename easybuild/easyconfigs/f/foss/{foss-2021.07.eb => foss-2021b.eb} (92%) rename easybuild/easyconfigs/g/GDAL/{GDAL-3.3.2-foss-2021.07.eb => GDAL-3.3.2-foss-2021b.eb} (97%) rename easybuild/easyconfigs/g/gompi/{gompi-2021.07.eb => gompi-2021b.eb} (95%) rename easybuild/easyconfigs/h/HDF5/{HDF5-1.12.1-gompi-2021.07.eb => HDF5-1.12.1-gompi-2021b.eb} (92%) rename easybuild/easyconfigs/h/HPCG/{HPCG-3.1-foss-2021.07.eb => HPCG-3.1-foss-2021b.eb} (94%) rename easybuild/easyconfigs/h/HPL/{HPL-2.3-foss-2021.07.eb => HPL-2.3-foss-2021b.eb} (94%) rename easybuild/easyconfigs/i/imkl-FFTW/{imkl-FFTW-2021.4.0-gompi-2021.07.eb => imkl-FFTW-2021.4.0-gompi-2021b.eb} (84%) rename easybuild/easyconfigs/n/netCDF/{netCDF-4.8.1-gompi-2021.07.eb => netCDF-4.8.1-gompi-2021b.eb} (95%) rename easybuild/easyconfigs/o/OSU-Micro-Benchmarks/{OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb => OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb} (92%) rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.1.0-gompi-2021.07-fb.eb => ScaLAPACK-2.1.0-gompi-2021b-fb.eb} (96%) rename easybuild/easyconfigs/s/SciPy-bundle/{SciPy-bundle-2021.10-foss-2021.07.eb => SciPy-bundle-2021.10-foss-2021b.eb} (97%) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021.07.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021b.eb similarity index 96% rename from easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021.07.eb rename to easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021b.eb index e3d0f13dc3c..0f78bc95c9b 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021.07.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021b.eb @@ -12,7 +12,7 @@ version = '2021.05.001' homepage = 'https://elpa.rzg.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" -toolchain = {'name': 'foss', 'version': '2021.07'} +toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-gompi-2021.07.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-gompi-2021b.eb similarity index 90% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-gompi-2021.07.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-gompi-2021b.eb index 90d98e0e831..cc44c633069 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-gompi-2021.07.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-gompi-2021b.eb @@ -5,7 +5,7 @@ homepage = 'https://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.""" -toolchain = {'name': 'gompi', 'version': '2021.07'} +toolchain = {'name': 'gompi', 'version': '2021b'} toolchainopts = {'pic': True} source_urls = [homepage] diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.9-gompi-2021.07.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.9-gompi-2021.07.eb deleted file mode 100644 index 97447296805..00000000000 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.9-gompi-2021.07.eb +++ /dev/null @@ -1,17 +0,0 @@ -name = 'FFTW' -version = '3.3.9' - -homepage = 'http://www.fftw.org' -description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) - in one or more dimensions, of arbitrary input size, and of both real and complex data.""" - -toolchain = {'name': 'gompi', 'version': '2021.07'} -toolchainopts = {'pic': True} - -source_urls = [homepage] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['bf2c7ce40b04ae811af714deb512510cc2c17b9ab9d6ddcf49fe4487eea7af3d'] - -runtest = 'check' - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2021.07.eb b/easybuild/easyconfigs/f/foss/foss-2021b.eb similarity index 92% rename from easybuild/easyconfigs/f/foss/foss-2021.07.eb rename to easybuild/easyconfigs/f/foss/foss-2021b.eb index 50ec77cbbc3..3820db82907 100644 --- a/easybuild/easyconfigs/f/foss/foss-2021.07.eb +++ b/easybuild/easyconfigs/f/foss/foss-2021b.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'foss' -version = '2021.07' +version = '2021b' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' description = """GNU Compiler Collection (GCC) based compiler toolchain, including @@ -20,7 +20,7 @@ dependencies = [ ('GCC', local_gccver), ('OpenMPI', '4.1.1', '', ('GCC', local_gccver)), ('FlexiBLAS', '3.0.4', '', ('GCC', local_gccver)), - ('FFTW', '3.3.9', '', local_comp_mpi_tc), + ('FFTW', '3.3.10', '', local_comp_mpi_tc), ('ScaLAPACK', '2.1.0', '-fb', local_comp_mpi_tc), ] diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021b.eb similarity index 97% rename from easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb rename to easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021b.eb index ed62c19ab47..b16b9435a10 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021.07.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021b.eb @@ -9,7 +9,7 @@ description = """GDAL is a translator library for raster geospatial data formats to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.""" -toolchain = {'name': 'foss', 'version': '2021.07'} +toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'usempi': True} source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] diff --git a/easybuild/easyconfigs/g/gompi/gompi-2021.07.eb b/easybuild/easyconfigs/g/gompi/gompi-2021b.eb similarity index 95% rename from easybuild/easyconfigs/g/gompi/gompi-2021.07.eb rename to easybuild/easyconfigs/g/gompi/gompi-2021b.eb index ae0258dc1a6..d5860d74ef0 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2021.07.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2021b.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'gompi' -version = '2021.07' +version = '2021b' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021.07.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021b.eb similarity index 92% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021.07.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021b.eb index abc302b0c14..06409128712 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021.07.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-gompi-2021b.eb @@ -6,7 +6,7 @@ description = """HDF5 is a data model, library, and file format for storing and It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.""" -toolchain = {'name': 'gompi', 'version': '2021.07'} +toolchain = {'name': 'gompi', 'version': '2021b'} toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021.07.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021b.eb similarity index 94% rename from easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021.07.eb rename to easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021b.eb index 3a04b8e54f5..c0604e4ec12 100644 --- a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021.07.eb +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2021b.eb @@ -5,7 +5,7 @@ homepage = 'https://software.sandia.gov/hpcg' description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" -toolchain = {'name': 'foss', 'version': '2021.07'} +toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'usempi': True, 'openmp': True} source_urls = ['http://www.hpcg-benchmark.org/downloads'] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2021.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2021b.eb similarity index 94% rename from easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2021.07.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2021b.eb index 07b786dec63..cb0f9c84deb 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2021.07.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2021b.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'foss', 'version': '2021.07'} +toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'usempi': True} source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021b.eb similarity index 84% rename from easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb rename to easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021b.eb index 7da3a5ead83..8a42ae8abf5 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021.07.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021b.eb @@ -4,7 +4,7 @@ version = '2021.4.0' homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' description = "FFTW interfaces using Intel oneAPI Math Kernel Library" -toolchain = {'name': 'gompi', 'version': '2021.07'} +toolchain = {'name': 'gompi', 'version': '2021b'} dependencies = [('imkl', version, '', True)] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2021.07.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2021b.eb similarity index 95% rename from easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2021.07.eb rename to easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2021b.eb index e98ecfdb739..656a6abbb98 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2021.07.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2021b.eb @@ -6,7 +6,7 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" -toolchain = {'name': 'gompi', 'version': '2021.07'} +toolchain = {'name': 'gompi', 'version': '2021b'} toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb similarity index 92% rename from easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb rename to easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb index b803b03edb8..d1ac9dd1571 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021.07.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021b.eb @@ -6,7 +6,7 @@ version = '5.7.1' homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" -toolchain = {'name': 'gompi', 'version': '2021.07'} +toolchain = {'name': 'gompi', 'version': '2021b'} toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021.07-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb similarity index 96% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021.07-fb.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb index ee29d7ef99c..b9ce6d67148 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021.07-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb @@ -6,7 +6,7 @@ homepage = 'https://www.netlib.org/scalapack/' description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.""" -toolchain = {'name': 'gompi', 'version': '2021.07'} +toolchain = {'name': 'gompi', 'version': '2021b'} toolchainopts = {'pic': True} source_urls = [homepage] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021.07.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb similarity index 97% rename from easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021.07.eb rename to easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb index 184e4650d40..ab9ea01f26a 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021.07.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b.eb @@ -6,7 +6,7 @@ version = '2021.10' homepage = 'https://python.org/' description = "Bundle of Python packages for scientific software" -toolchain = {'name': 'foss', 'version': '2021.07'} +toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'pic': True, 'lowopt': True} builddependencies = [ From 5600b930b3e52eeb6adf6721521aee3abe698219 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 27 Oct 2021 16:23:56 +0200 Subject: [PATCH 1690/9987] promote intel/2021.09 to intel/2021b --- ...{FFTW-3.3.10-iimpi-2021.09.eb => FFTW-3.3.10-iimpi-2021b.eb} | 2 +- .../HPCG/{HPCG-3.1-intel-2021.09.eb => HPCG-3.1-intel-2021b.eb} | 2 +- .../h/HPL/{HPL-2.3-intel-2021.09.eb => HPL-2.3-intel-2021b.eb} | 2 +- .../easyconfigs/i/iimpi/{iimpi-2021.09.eb => iimpi-2021b.eb} | 2 +- ...1.4.0-iimpi-2021.09.eb => imkl-FFTW-2021.4.0-iimpi-2021b.eb} | 2 +- .../easyconfigs/i/intel/{intel-2021.09.eb => intel-2021b.eb} | 2 +- ...iimpi-2021.09.eb => OSU-Micro-Benchmarks-5.8-iimpi-2021b.eb} | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/f/FFTW/{FFTW-3.3.10-iimpi-2021.09.eb => FFTW-3.3.10-iimpi-2021b.eb} (93%) rename easybuild/easyconfigs/h/HPCG/{HPCG-3.1-intel-2021.09.eb => HPCG-3.1-intel-2021b.eb} (91%) rename easybuild/easyconfigs/h/HPL/{HPL-2.3-intel-2021.09.eb => HPL-2.3-intel-2021b.eb} (94%) rename easybuild/easyconfigs/i/iimpi/{iimpi-2021.09.eb => iimpi-2021b.eb} (95%) rename easybuild/easyconfigs/i/imkl-FFTW/{imkl-FFTW-2021.4.0-iimpi-2021.09.eb => imkl-FFTW-2021.4.0-iimpi-2021b.eb} (84%) rename easybuild/easyconfigs/i/intel/{intel-2021.09.eb => intel-2021b.eb} (97%) rename easybuild/easyconfigs/o/OSU-Micro-Benchmarks/{OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb => OSU-Micro-Benchmarks-5.8-iimpi-2021b.eb} (92%) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2021.09.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2021b.eb similarity index 93% rename from easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2021.09.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2021b.eb index 430b4b018f3..e59cfb10c45 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2021.09.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2021b.eb @@ -5,7 +5,7 @@ homepage = 'https://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.""" -toolchain = {'name': 'iimpi', 'version': '2021.09'} +toolchain = {'name': 'iimpi', 'version': '2021b'} toolchainopts = {'pic': True} source_urls = [homepage] diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021.09.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021b.eb similarity index 91% rename from easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021.09.eb rename to easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021b.eb index b1e53b4652b..72cf9c60b89 100644 --- a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021.09.eb +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2021b.eb @@ -5,7 +5,7 @@ homepage = 'https://software.sandia.gov/hpcg' description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" -toolchain = {'name': 'intel', 'version': '2021.09'} +toolchain = {'name': 'intel', 'version': '2021b'} toolchainopts = {'usempi': True, 'openmp': True} source_urls = ['http://www.hpcg-benchmark.org/downloads'] diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2021.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2021b.eb similarity index 94% rename from easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2021.09.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2021b.eb index 838465dd999..ceceb8db9c6 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2021.09.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2021b.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'intel', 'version': '2021.09'} +toolchain = {'name': 'intel', 'version': '2021b'} toolchainopts = {'usempi': True} source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2021.09.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2021b.eb similarity index 95% rename from easybuild/easyconfigs/i/iimpi/iimpi-2021.09.eb rename to easybuild/easyconfigs/i/iimpi/iimpi-2021b.eb index 5bc754033a7..16600a0f9db 100644 --- a/easybuild/easyconfigs/i/iimpi/iimpi-2021.09.eb +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2021b.eb @@ -2,7 +2,7 @@ easyblock = 'Toolchain' name = 'iimpi' -version = '2021.09' +version = '2021b' homepage = 'https://software.intel.com/parallel-studio-xe' description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021.09.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021b.eb similarity index 84% rename from easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021.09.eb rename to easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021b.eb index 198703d5040..e1f4249fb2b 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021.09.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021b.eb @@ -4,7 +4,7 @@ version = '2021.4.0' homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' description = "FFTW interfaces using Intel oneAPI Math Kernel Library" -toolchain = {'name': 'iimpi', 'version': '2021.09'} +toolchain = {'name': 'iimpi', 'version': '2021b'} dependencies = [('imkl', version, '', True)] diff --git a/easybuild/easyconfigs/i/intel/intel-2021.09.eb b/easybuild/easyconfigs/i/intel/intel-2021b.eb similarity index 97% rename from easybuild/easyconfigs/i/intel/intel-2021.09.eb rename to easybuild/easyconfigs/i/intel/intel-2021b.eb index 0a18f57735a..68916794a30 100644 --- a/easybuild/easyconfigs/i/intel/intel-2021.09.eb +++ b/easybuild/easyconfigs/i/intel/intel-2021b.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'intel' -version = '2021.09' +version = '2021b' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021b.eb similarity index 92% rename from easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb rename to easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021b.eb index efeafe0843e..3dab4bc2a02 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021.09.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.8-iimpi-2021b.eb @@ -6,7 +6,7 @@ version = '5.8' homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" -toolchain = {'name': 'iimpi', 'version': '2021.09'} +toolchain = {'name': 'iimpi', 'version': '2021b'} toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] From e67f1b510e839d96591b26112210ea1cbbc1a3d9 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 27 Oct 2021 17:21:52 +0200 Subject: [PATCH 1691/9987] Update RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb: correct easyconfig for newer toolchain versions --- .../r/RDKit/RDKit-2021.03.4-foss-2021a.eb | 75 +++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb new file mode 100644 index 00000000000..52be0571bb3 --- /dev/null +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb @@ -0,0 +1,75 @@ +easyblock = 'CMakeMake' + +name = 'RDKit' +version = '2021.03.4' + +homepage = 'https://www.rdkit.org' +description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python." + +toolchain = {'name': 'foss', 'version': '2021a'} +# avoid failing tests on skylake CPUs. comment out this line when building on CPUs that don't support AVX2 +# see also: https://github.com/rdkit/rdkit/issues/1674 +toolchainopts = {'optarch': 'mavx2', 'cstd': 'c++11'} + +source_urls = ['https://github.com/rdkit/rdkit/archive/'] +sources = ['Release_%s.tar.gz' % version.replace('.', '_')] +patches = ['RDKit-%(version)s_skip-broken-test.patch'] +checksums = [ + 'bed309df7f1e2ea25736a986cf951325681142ee49468b1c62d020a109d2ef52', # Release_2021_03_4.tar.gz + '45869e01461b66e42c9305f5e8a65f696417e4777c2da60ef81d1e26e57d1b2e', # RDKit-2021.03.4_skip-broken-test.patch +] + +# Dependencies varies from version to version +# https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source +builddependencies = [ + ('CMake', '3.20.1'), + ('Eigen', '3.3.9'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('SQLite', '3.35.4'), + ('matplotlib', '3.4.2'), + ('Pillow', '8.2.0'), + ('Boost.Python', '1.76.0'), + ('cairo', '1.16.0'), +] + +separate_build_dir = True + +configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " +configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " +configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " + +# merge source directory into build directory in order to run the tests +buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' +buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' + +# Specify path for libraries so that they are found during the tests when the module is built with --rpath flag. +buildopts += 'export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:${LD_LIBRARY_PATH} && ' + +# 'ctest' allows to pass additional arguments opposed to 'make test' +buildopts += 'ctest --output-on-failure' + +local_libs = ['Alignment', 'Catalogs', 'ChemicalFeatures', 'ChemReactions', 'ChemTransforms', 'coordgen', 'DataStructs', + 'Depictor', 'Descriptors', 'DistGeometry', 'DistGeomHelpers', 'EigenSolvers', 'FileParsers', + 'FilterCatalog', 'Fingerprints', 'FMCS', 'ForceFieldHelpers', 'ForceField', 'FragCatalog', 'GraphMol', + 'hc', 'InfoTheory', 'maeparser', 'MMPA', 'MolAlign', 'MolCatalog', 'MolChemicalFeatures', 'MolDraw2D', + 'MolHash', 'MolInterchange', 'MolStandardize', 'MolTransforms', 'Optimizer', 'PartialCharges', 'RDBoost', + 'RDGeneral', 'RDGeometryLib', 'RDStreams', 'ReducedGraphs', 'RGroupDecomposition', 'RingDecomposerLib', + 'ScaffoldNetwork', 'ShapeHelpers', 'SimDivPickers', 'SLNParse', 'SmilesParse', 'Subgraphs', + 'SubstructLibrary', 'SubstructMatch', 'Trajectory'] + +sanity_check_paths = { + 'files': ['lib/libRDKit%s.%s' % (x, SHLIB_EXT) for x in local_libs], + 'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'], +} + +sanity_check_commands = [ + "python -c 'import rdkit.rdBase'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From aa404e755408aa6a4ef5b2b10117b0175b236371 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Wed, 27 Oct 2021 18:02:31 +0200 Subject: [PATCH 1692/9987] Delete RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb --- ...RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb | 76 ------------------- 1 file changed, 76 deletions(-) delete mode 100644 easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb deleted file mode 100644 index 63bccf2332b..00000000000 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,76 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'RDKit' -version = '2021.03.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.rdkit.org' -description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python." - -toolchain = {'name': 'foss', 'version': '2021a'} -# avoid failing tests on skylake CPUs. comment out this line when building on CPUs that don't support AVX2 -# see also: https://github.com/rdkit/rdkit/issues/1674 -toolchainopts = {'optarch': 'mavx2', 'cstd': 'c++11'} - -source_urls = ['https://github.com/rdkit/rdkit/archive/'] -sources = ['Release_%s.tar.gz' % version.replace('.', '_')] -patches = ['RDKit-%(version)s_skip-broken-test.patch'] -checksums = [ - 'bed309df7f1e2ea25736a986cf951325681142ee49468b1c62d020a109d2ef52', # Release_2021_03_4.tar.gz - '45869e01461b66e42c9305f5e8a65f696417e4777c2da60ef81d1e26e57d1b2e', # RDKit-2021.03.4_skip-broken-test.patch -] - -# Dependencies varies from version to version -# https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source -builddependencies = [ - ('CMake', '3.20.1'), - ('Eigen', '3.3.9', '', ('GCCcore', '10.3.0')), - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('SQLite', '3.35.4'), - ('matplotlib', '3.4.2'), - ('Pillow', '8.2.0'), - ('Boost.Python', '1.76.0', '', ('GCC', '10.3.0')), - ('cairo', '1.16.0'), -] - -separate_build_dir = True - -configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " -configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " -configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " - -# merge source directory into build directory in order to run the tests -buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' -buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' - -# Specify path for libraries so that they are found during the tests when the module is built with --rpath flag. -buildopts += 'export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:${LD_LIBRARY_PATH} && ' - -# 'ctest' allows to pass additional arguments opposed to 'make test' -buildopts += 'ctest --output-on-failure' - -local_libs = ['Alignment', 'Catalogs', 'ChemicalFeatures', 'ChemReactions', 'ChemTransforms', 'coordgen', 'DataStructs', - 'Depictor', 'Descriptors', 'DistGeometry', 'DistGeomHelpers', 'EigenSolvers', 'FileParsers', - 'FilterCatalog', 'Fingerprints', 'FMCS', 'ForceFieldHelpers', 'ForceField', 'FragCatalog', 'GraphMol', - 'hc', 'InfoTheory', 'maeparser', 'MMPA', 'MolAlign', 'MolCatalog', 'MolChemicalFeatures', 'MolDraw2D', - 'MolHash', 'MolInterchange', 'MolStandardize', 'MolTransforms', 'Optimizer', 'PartialCharges', 'RDBoost', - 'RDGeneral', 'RDGeometryLib', 'RDStreams', 'ReducedGraphs', 'RGroupDecomposition', 'RingDecomposerLib', - 'ScaffoldNetwork', 'ShapeHelpers', 'SimDivPickers', 'SLNParse', 'SmilesParse', 'Subgraphs', - 'SubstructLibrary', 'SubstructMatch', 'Trajectory'] - -sanity_check_paths = { - 'files': ['lib/libRDKit%s.%s' % (x, SHLIB_EXT) for x in local_libs], - 'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'], -} - -sanity_check_commands = [ - "python -c 'import rdkit.rdBase'", -] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -moduleclass = 'chem' From 9c15abb05ed376eaa4df3f97ced7b9b0017587a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Oct 2021 18:35:10 +0200 Subject: [PATCH 1693/9987] adding easyconfigs: Flye-2.9-GCC-10.3.0.eb, Flye-2.9-intel-compilers-2021.2.0.eb --- .../easyconfigs/f/Flye/Flye-2.9-GCC-10.3.0.eb | 30 +++++++++++++++++++ .../Flye/Flye-2.9-intel-compilers-2021.2.0.eb | 30 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flye/Flye-2.9-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/Flye/Flye-2.9-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9-GCC-10.3.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9-GCC-10.3.0.eb new file mode 100644 index 00000000000..f0570a67005 --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9-GCC-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.9' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['158ea620d4aa92a53dae1832b09fd605e17552e45b83eecbf28e41a4516a6957'] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..115a6b83c7e --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9-intel-compilers-2021.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.9' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['158ea620d4aa92a53dae1832b09fd605e17552e45b83eecbf28e41a4516a6957'] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' From 003a6b95ee4773ce009ebc1c309bfdcb8fd5ee0c Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Wed, 27 Oct 2021 17:46:52 +0100 Subject: [PATCH 1694/9987] Create PyTables-3.5.2-foss-2020b-Python-2.7.18.eb New version for foss 2020b + Python 2.7.18. --- ...PyTables-3.5.2-foss-2020b-Python-2.7.18.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb new file mode 100644 index 00000000000..ce4f3ad63ba --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.5.2' +# This is the last version to support Python 2.7. +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-fix-libs.patch'] +checksums = [ + 'e4fc6f1194f02a8b10ff923e77364fb70710592f620d7de35f4d4e064dc70e91', # v3.5.2.tar.gz + '8df2a6379a9e4a941cb939ed1257a7d6105792d9c5e9dd0abd4bba3ece767c3a', # PyTables-3.5.2-fix-libs.patch +] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', versionsuffix), # provides numexpr. + ('HDF5', '1.10.7'), + ('LZO', '2.10'), + ('Blosc', '1.21.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bins = ['pt2to3', 'ptdump', 'ptrepack'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ['%s --help' % x for x in local_bins] + +moduleclass = 'data' From c3e74fdec0ea051057615990459670b3aca5fd17 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 27 Oct 2021 17:29:38 +0000 Subject: [PATCH 1695/9987] add BLIS and imkl (x86_64 only) builddependencies to FlexiBLAS --- .../b/BLIS/BLIS-0.8.1-GCC-11.2.0.eb | 40 +++++++++++++++++++ .../f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 10 ++++- 2 files changed, 48 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..ccc92821863 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.8.1' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fix_dgemm-fpe-signalling-on-broadwell.patch', +] +checksums = [ + '729694128719801e82fae7b5f2489ab73e4a467f46271beff09588c9265a697b', # 0.8.1.tar.gz + # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch + '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', +] + +builddependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), +] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index 7a8607f832b..36ea9e71e08 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -16,12 +16,18 @@ checksums = ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'] builddependencies = [ ('CMake', '3.21.1'), ('Python', '3.9.6'), # required for running the tests + ('BLIS', '0.8.1'), + ('imkl', {'arch=x86_64': '2021.4.0', 'arch=*': False}), ] -# note: first listed library will be used as default by FlexiBLAS, -# unless otherwise specified via easyconfig parameter flexiblas_default dependencies = [ ('OpenBLAS', '0.3.18'), ] +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +backends = ['OpenBLAS', 'BLIS'] +if ARCH == 'x86_64': + backends.append('imkl') + moduleclass = 'lib' From 558774c7d5f9b0baac1eeff5e2d2d3ef3fec4229 Mon Sep 17 00:00:00 2001 From: bartoldeman Date: Wed, 27 Oct 2021 14:22:26 -0400 Subject: [PATCH 1696/9987] imkl builddependency needs toolchain=True for SYSTEM toolchain. Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index 36ea9e71e08..3260b14863f 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('CMake', '3.21.1'), ('Python', '3.9.6'), # required for running the tests ('BLIS', '0.8.1'), - ('imkl', {'arch=x86_64': '2021.4.0', 'arch=*': False}), + ('imkl', {'arch=x86_64': '2021.4.0', 'arch=*': False}, '', True), ] dependencies = [ From 30a8e42908cbeefbdbb814fb151106cae4b36bd2 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Wed, 27 Oct 2021 19:47:15 +0100 Subject: [PATCH 1697/9987] Create Pillow-6.2.2-foss-2020b-Python-2.7.18 New version for foss 2020b + Python 2.7.18 --- .../Pillow-6.2.2-foss-2020b-Python-2.7.18 | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18 diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18 b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18 new file mode 100644 index 00000000000..a8a8a9dd9fb --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18 @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '6.2.2' +# This is the last Pillow version to support Python 2.7. +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['db9ff0c251ed066d367f53b64827cc9e18ccea001b986d08c265e53625dab950'] + +dependencies = [ + ('Python', '2.7.18'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.1.0'), + ('freetype', '2.10.3') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From ed577f8b24cc849485ff5bac864a4d8015e1bd2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Oct 2021 21:00:36 +0200 Subject: [PATCH 1698/9987] fix indent for if condition in FlexiBLAS easyconfig --- easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index 3260b14863f..d3cb0d26073 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -28,6 +28,6 @@ dependencies = [ # unless otherwise specified via easyconfig parameter flexiblas_default backends = ['OpenBLAS', 'BLIS'] if ARCH == 'x86_64': - backends.append('imkl') + backends.append('imkl') moduleclass = 'lib' From b7b6e0425fb142b94e783d6c9ff2836786d7a2e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 28 Oct 2021 13:53:07 +0200 Subject: [PATCH 1699/9987] adding easyconfigs: LBFGS++-0.1.0.eb --- .../easyconfigs/l/LBFGS++/LBFGS++-0.1.0.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/l/LBFGS++/LBFGS++-0.1.0.eb diff --git a/easybuild/easyconfigs/l/LBFGS++/LBFGS++-0.1.0.eb b/easybuild/easyconfigs/l/LBFGS++/LBFGS++-0.1.0.eb new file mode 100644 index 00000000000..ff12d056d35 --- /dev/null +++ b/easybuild/easyconfigs/l/LBFGS++/LBFGS++-0.1.0.eb @@ -0,0 +1,19 @@ +easyblock = "Tarball" + +name = 'LBFGS++' +version = '0.1.0' + +homepage = 'https://lbfgspp.statr.me' +description = 'A header-only C++ library for L-BFGS and L-BFGS-B algorithms' + +toolchain = SYSTEM + +source_urls = ['https://github.com/yixuan/LBFGSpp/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['include/LBFGS.h', 'include/LBFGSB.h'], + 'dirs': [] +} + +moduleclass = 'math' From 60396011ae072ae707497aceb9b7d5fe20bbeb73 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 28 Oct 2021 14:17:04 +0200 Subject: [PATCH 1700/9987] Add checksum --- easybuild/easyconfigs/l/LBFGS++/LBFGS++-0.1.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/LBFGS++/LBFGS++-0.1.0.eb b/easybuild/easyconfigs/l/LBFGS++/LBFGS++-0.1.0.eb index ff12d056d35..ecdefcc470c 100644 --- a/easybuild/easyconfigs/l/LBFGS++/LBFGS++-0.1.0.eb +++ b/easybuild/easyconfigs/l/LBFGS++/LBFGS++-0.1.0.eb @@ -10,6 +10,7 @@ toolchain = SYSTEM source_urls = ['https://github.com/yixuan/LBFGSpp/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] +checksums = ['c8fb9a9ae18e4dbecf096cc0d0f2eaf3d56fd13a646a5589428c435b07c7a456'] sanity_check_paths = { 'files': ['include/LBFGS.h', 'include/LBFGSB.h'], From 2f8d9f3f87c633600014643cf73cff710eacbe6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 28 Oct 2021 15:35:55 +0200 Subject: [PATCH 1701/9987] adding easyconfigs: ThemisPy-0.3.0-foss-2021a.eb --- .../t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb b/easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb new file mode 100644 index 00000000000..641bbbecf63 --- /dev/null +++ b/easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = 'ThemisPy' +version = '0.3.0' + +homepage = 'https://github.com/aeb/ThemisPy' +description = 'A header-only C++ library for L-BFGS and L-BFGS-B algorithms' + +toolchain = SYSTEM +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/aeb/ThemisPy/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['64b6339066e207cc5c42593460c12c2d73346ece97dafb26135d486b18a76dfd'] + +dependencies = [ + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/themispy_best_sample', 'bin/themispy_resample', 'bin/themispy_generate_data'], + 'dirs': ['lib64/site-packages/python%(pyshortver)s/'] +} + +moduleclass = 'math' From 8891fb437798006a9550742b83781771a07c73d8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 28 Oct 2021 15:47:02 +0200 Subject: [PATCH 1702/9987] Fix sanity check --- easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb b/easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb index 641bbbecf63..5f6ae446c6f 100644 --- a/easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb @@ -14,6 +14,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['64b6339066e207cc5c42593460c12c2d73346ece97dafb26135d486b18a76dfd'] dependencies = [ + ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('matplotlib', '3.4.2'), ] @@ -24,7 +25,7 @@ sanity_pip_check = True sanity_check_paths = { 'files': ['bin/themispy_best_sample', 'bin/themispy_resample', 'bin/themispy_generate_data'], - 'dirs': ['lib64/site-packages/python%(pyshortver)s/'] + 'dirs': ['lib64/python%(pyshortver)s/site-packages'] } moduleclass = 'math' From 2fc7570a78c04abe1c43f25fbbb1cee059ca5699 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 28 Oct 2021 16:32:01 +0200 Subject: [PATCH 1703/9987] Remove duplicate line --- easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb b/easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb index 5f6ae446c6f..045289594ad 100644 --- a/easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/t/ThemisPy/ThemisPy-0.3.0-foss-2021a.eb @@ -6,7 +6,6 @@ version = '0.3.0' homepage = 'https://github.com/aeb/ThemisPy' description = 'A header-only C++ library for L-BFGS and L-BFGS-B algorithms' -toolchain = SYSTEM toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/aeb/ThemisPy/archive/refs/tags/'] From 41cad1286583a92a3d23e358c0685242ea2d1cc7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 28 Oct 2021 16:59:25 +0200 Subject: [PATCH 1704/9987] adding easyconfigs: astropy-4.3.1-intel-2021a.eb, astropy-4.3.1-foss-2021a.eb --- .../a/astropy/astropy-4.3.1-foss-2021a.eb | 35 +++++++++++++++++++ .../a/astropy/astropy-4.3.1-intel-2021a.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-4.3.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/a/astropy/astropy-4.3.1-intel-2021a.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.3.1-foss-2021a.eb b/easybuild/easyconfigs/a/astropy/astropy-4.3.1-foss-2021a.eb new file mode 100644 index 00000000000..10803a578e8 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-4.3.1-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '4.3.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '2.0.0', { + 'modulename': 'erfa', + 'checksums': ['f904231e1a570f94440e06140799590895107f942847b52a753ce81c9609162d'], + }), + ('extension-helpers', '0.1', { + 'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'], + }), + (name, version, { + 'checksums': ['2d3951223b4eb7f368fcad8c8340d27374c5d8e3b635a636275acdb38f35cd51'], + }), +] + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.3.1-intel-2021a.eb b/easybuild/easyconfigs/a/astropy/astropy-4.3.1-intel-2021a.eb new file mode 100644 index 00000000000..e6c87a69845 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-4.3.1-intel-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '4.3.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '2.0.0', { + 'modulename': 'erfa', + 'checksums': ['f904231e1a570f94440e06140799590895107f942847b52a753ce81c9609162d'], + }), + ('extension-helpers', '0.1', { + 'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'], + }), + (name, version, { + 'checksums': ['2d3951223b4eb7f368fcad8c8340d27374c5d8e3b635a636275acdb38f35cd51'], + }), +] + +moduleclass = 'astro' From 052593886a8c78c3372763029a3fe82847ca0978 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Thu, 28 Oct 2021 16:16:34 +0100 Subject: [PATCH 1705/9987] Rename Pillow-6.2.2-foss-2020b-Python-2.7.18 to Pillow-6.2.2-foss-2020b-Python-2.7.18.eb --- ...20b-Python-2.7.18 => Pillow-6.2.2-foss-2020b-Python-2.7.18.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/Pillow/{Pillow-6.2.2-foss-2020b-Python-2.7.18 => Pillow-6.2.2-foss-2020b-Python-2.7.18.eb} (100%) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18 b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb similarity index 100% rename from easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18 rename to easybuild/easyconfigs/p/Pillow/Pillow-6.2.2-foss-2020b-Python-2.7.18.eb From b784756966cab00a21fa8ec354fc48cdea1b7573 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Thu, 28 Oct 2021 16:42:08 +0100 Subject: [PATCH 1706/9987] Update freetype-2.6.5-foss-2016b.eb Changed source_urls as per @boegel's request. --- .../easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb index 2488e2d0392..f91471301f9 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-foss-2016b.eb @@ -8,7 +8,10 @@ description = """FreeType 2 is a software font engine that is designed to be sma toolchain = {'name': 'foss', 'version': '2016b'} -source_urls = ['https://download-mirror.savannah.gnu.org/releases/freetype/freetype-old/'] +source_urls = [ + GNU_SAVANNAH_SOURCE, + SOURCEFORGE_SOURCE, +] sources = [SOURCE_TAR_GZ] checksums = ['3bb24add9b9ec53636a63ea8e867ed978c4f8fdd8f1fa5ccfd41171163d4249a'] From a922e5987ea5ba4e20652b1b49854f15725181d9 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 28 Oct 2021 18:19:16 +0200 Subject: [PATCH 1707/9987] adding easyconfigs: PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb and patches: PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch, PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch, PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch, PyTorch-1.10.0_skip-nccl-error-tests.patch --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 109 ++++++++++ ...0_fix-alias-violation-in-bitwise-ops.patch | 31 +++ ...0.0_fix-faulty-asserts-and-skip-test.patch | 188 ++++++++++++++++++ ...0_fix-test-dataloader-fixed-affinity.patch | 46 +++++ ...PyTorch-1.10.0_skip-nccl-error-tests.patch | 78 ++++++++ 5 files changed, 452 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nccl-error-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..d958ecfe4e2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,109 @@ +name = 'PyTorch' +version = '1.10.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', + 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_skip-nccl-error-tests.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', + # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch + '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '7000b316e93f0714011dcbf8d1d91ff755675bc1dc139dfa23d9d84d910135ce', + # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch + '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', + # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch + '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + '04f3c42d2c1aee94e307d9ef281dd3b3b941f4d8e511e2133fc6521ccebb2ed0', # PyTorch-1.10.skip-nccl-error-tests.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), + ('hypothesis', '6.13.1'), +] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.5'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.6.2'), + ('SciPy-bundle', '2021.05'), + ('typing-extensions', '3.10.0.0'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.2.0'), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('magma', '2.6.1', '-CUDA-%(cudaver)s'), + ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + # 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + # 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch new file mode 100644 index 00000000000..e51ba483c96 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch @@ -0,0 +1,31 @@ +A reinterpret_cast to an unrelated type is undefined behavior. +This causes real issues due to misoptimizations on at least GCC 10.2 on POWER +See https://github.com/pytorch/pytorch/issues/58031 + +Author: Alexander Grund (TU Dresden) + +Adapted for PT-1.10, where this is now in vec_base.h and templated + +diff --git a/aten/src/ATen/cpu/vec/vec_base.h b/aten/src/ATen/cpu/vec/vec_base.h +index 697996ab8e..1663ae239a 100644 +--- a/aten/src/ATen/cpu/vec/vec_base.h ++++ b/aten/src/ATen/cpu/vec/vec_base.h +@@ -701,12 +701,14 @@ inline Vectorized operator^(const Vectorized& a, const Vectorized& b) { + + template + static inline Vectorized bitwise_binary_op(const Vectorized &a, const Vectorized &b, Op op) { +- static constexpr uint32_t element_no = VECTOR_WIDTH / sizeof(intmax_t); ++ constexpr uint32_t element_no = VECTOR_WIDTH / sizeof(intmax_t); ++ __at_align__ intmax_t buffer_a[element_no]; ++ __at_align__ intmax_t buffer_b[element_no]; + __at_align__ intmax_t buffer[element_no]; +- const intmax_t *a_ptr = reinterpret_cast((const T*) a); +- const intmax_t *b_ptr = reinterpret_cast((const T*) b); ++ a.store(buffer_a); ++ b.store(buffer_b); + for (uint32_t i = 0U; i < element_no; ++ i) { +- buffer[i] = op(a_ptr[i], b_ptr[i]); ++ buffer[i] = op(buffer_a[i], buffer_b[i]); + } + return Vectorized::loadu(buffer); + } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch new file mode 100644 index 00000000000..eab07090d2a --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch @@ -0,0 +1,188 @@ +From: Alexander Grund +Date: Tue, 18 May 2021 15:08:41 +0200 +Subject: [PATCH 1/2] Fix usage of TORCH_INTERNAL_ASSERT with message + +Using only a string as the argument for TORCH_INTERNAL_ASSERT will never +trigger a failure as a string is always a truethy value. +This hides actual bugs and makes users and devs think all worked while +it did not. +Change to use TORCH_INTERNAL_ASSERT(false, "msg") + +Subject: [PATCH 2/2] Add missing skip decorator for +test_preserve_bundled_inputs_methods + +This test uses optimize_for_mobile which requires NNPACK to work + +diff --git a/aten/src/ATen/native/BinaryOps.cpp b/aten/src/ATen/native/BinaryOps.cpp +index c4edadb03e..e889cd03a8 100644 +--- a/aten/src/ATen/native/BinaryOps.cpp ++++ b/aten/src/ATen/native/BinaryOps.cpp +@@ -106,6 +106,7 @@ Tensor& add_relu_impl( + max_val = std::numeric_limits::max(); + } else { + TORCH_INTERNAL_ASSERT( ++ false, + "Unsupported datatype for add_relu:", self.dtype().name()); + } + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag.cpp +index 050fdce2ca..7e72263917 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag.cpp +@@ -780,6 +780,7 @@ class QEmbeddingBag final { + include_last_offset); + } else { + TORCH_INTERNAL_ASSERT( ++ false, + "Currently only support 8-bit embedding_bag quantization"); + } + } +@@ -808,6 +809,7 @@ class QEmbedding final { + + } else { + TORCH_INTERNAL_ASSERT( ++ false, + "Currently only support 8-bit embedding quantization"); + } + return output; +diff --git a/aten/src/ATen/native/quantized/cpu/qnnpack_utils.h b/aten/src/ATen/native/quantized/cpu/qnnpack_utils.h +index 6de646acfe..66341c959d 100644 +--- a/aten/src/ATen/native/quantized/cpu/qnnpack_utils.h ++++ b/aten/src/ATen/native/quantized/cpu/qnnpack_utils.h +@@ -131,6 +131,7 @@ struct PackedConvWeightsQnnp : public ConvPackedParamsBase { + + if (conv_p.per_channel && conv_p.ukernel_type == pytorch_qnnp_ukernel_type_xzp_gemm) { + TORCH_INTERNAL_ASSERT( ++ false, + "Per channel quantized weights are not supported for XZP kernels"); + } + +@@ -140,6 +141,7 @@ struct PackedConvWeightsQnnp : public ConvPackedParamsBase { + static_cast(calloc(1, sizeof(struct pytorch_qnnp_operator))); + if (convolution == nullptr) { + TORCH_INTERNAL_ASSERT( ++ false, + "failed to allocate %zu bytes for pytorch_qnnp_operator structure", + sizeof(struct pytorch_qnnp_operator)); + } +@@ -406,7 +408,7 @@ std::pair, at::Tensor> make_zero_points_and_scales_tensor( + 128); + } + } else { +- TORCH_INTERNAL_ASSERT("Unsupported quantization scheme."); ++ TORCH_INTERNAL_ASSERT(false, "Unsupported quantization scheme."); + } + at:: Tensor weight_scales = + at::empty( +@@ -423,7 +425,7 @@ std::pair, at::Tensor> make_zero_points_and_scales_tensor( + weight_contig.q_per_channel_scales()[i].item(); + } + } else { +- TORCH_INTERNAL_ASSERT("Unsupported quantization scheme."); ++ TORCH_INTERNAL_ASSERT(false, "Unsupported quantization scheme."); + } + for (int i = num_output_channels; i < num_output_channels_padded; ++i) { + weight_scales_data[i] = 1.f; +diff --git a/test/test_mobile_optimizer.py b/test/test_mobile_optimizer.py +index 11ef019a26..7b5ac1a239 100644 +--- a/test/test_mobile_optimizer.py ++++ b/test/test_mobile_optimizer.py +@@ -269,6 +269,9 @@ class TestOptimizer(TestCase): + bi_module_lint_list = generate_mobile_module_lints(bi_module) + self.assertEqual(len(bi_module_lint_list), 0) + ++ @unittest.skipUnless(torch.backends.xnnpack.enabled, ++ " XNNPACK must be enabled for these tests." ++ " Please build with USE_XNNPACK=1.") + def test_preserve_bundled_inputs_methods(self): + class MyBundledInputModule(torch.nn.Module): + def __init__(self): +diff --git a/torch/csrc/jit/api/module.cpp b/torch/csrc/jit/api/module.cpp +index 38592b80b9..8f9508321b 100644 +--- a/torch/csrc/jit/api/module.cpp ++++ b/torch/csrc/jit/api/module.cpp +@@ -305,7 +305,7 @@ void Module::train(bool on) { + if (auto slot = m._ivalue()->type()->findAttributeSlot("training")) { + m._ivalue()->setSlot(*slot, on); + } else { +- TORCH_INTERNAL_ASSERT("'training' attribute not found"); ++ TORCH_INTERNAL_ASSERT(false, "'training' attribute not found"); + } + } + } +diff --git a/torch/csrc/jit/passes/quantization/insert_quant_dequant.cpp b/torch/csrc/jit/passes/quantization/insert_quant_dequant.cpp +index 53a13b6cf1..93c2b5a7da 100644 +--- a/torch/csrc/jit/passes/quantization/insert_quant_dequant.cpp ++++ b/torch/csrc/jit/passes/quantization/insert_quant_dequant.cpp +@@ -304,6 +304,7 @@ Node* insertEmbeddingBagOps(Node* observer, const std::string& op_name) { + quant_fn = "quantized::embedding_bag_byte_rowwise_offsets"; + } else { + TORCH_INTERNAL_ASSERT( ++ false, + "Graph Mode Quantization currently supports 4-bit and 8-bit embedding bag quantization."); + } + +diff --git a/torch/csrc/jit/passes/xnnpack_rewrite.cpp b/torch/csrc/jit/passes/xnnpack_rewrite.cpp +index 3be480068c..2289f028ae 100644 +--- a/torch/csrc/jit/passes/xnnpack_rewrite.cpp ++++ b/torch/csrc/jit/passes/xnnpack_rewrite.cpp +@@ -405,21 +405,25 @@ script::Module optimizeForMobile( + + void insertPrePackedOps(std::shared_ptr& graph) { + TORCH_INTERNAL_ASSERT( ++ false, + "XNNPACK is not enabled. Please build with USE_XNNPACK=1"); + } + + void insertPrePackedOps(script::Module& module) { + TORCH_INTERNAL_ASSERT( ++ false, + "XNNPACK is not enabled. Please build with USE_XNNPACK=1"); + } + + void fusePrePackedLinearConvWithClamp(script::Module& module) { + TORCH_INTERNAL_ASSERT( ++ false, + "XNNPACK is not enabled. Please build with USE_XNNPACK=1"); + } + + void FoldPrePackingOps(script::Module& m) { + TORCH_INTERNAL_ASSERT( ++ false, + "XNNPACK is not enabled. Please build with USE_XNNPACK=1"); + } + +@@ -428,6 +432,7 @@ script::Module optimizeForMobile( + const std::set& blocklist, + const std::vector& preserved_methods) { + TORCH_INTERNAL_ASSERT( ++ false, + "Mobile optimization only available with XNNPACK at the moment. " + "XNNPACK is not enabled. Please build with USE_XNNPACK=1"); + return module; +diff --git a/torch/csrc/jit/runtime/register_ops_utils.cpp b/torch/csrc/jit/runtime/register_ops_utils.cpp +index 537716e1ad..3bcff0af55 100644 +--- a/torch/csrc/jit/runtime/register_ops_utils.cpp ++++ b/torch/csrc/jit/runtime/register_ops_utils.cpp +@@ -182,7 +182,7 @@ IValue tensorToListRecursive( + } else if (inner_result.isBool()) { + result.emplace_back(inner_result.toBool()); + } else { +- TORCH_INTERNAL_ASSERT("Unknown return type for tensorToListRecursive"); ++ TORCH_INTERNAL_ASSERT(false, "Unknown return type for tensorToListRecursive"); + } + + data += strides[cur_dim] * element_size; +diff --git a/torch/csrc/distributed/c10d/ProcessGroup.cpp b/torch/csrc/distributed/c10d/ProcessGroup.cpp +index 7909bfa7c9..9e2a51f291 100644 +--- a/torch/csrc/distributed/c10d/ProcessGroup.cpp ++++ b/torch/csrc/distributed/c10d/ProcessGroup.cpp +@@ -43,7 +43,7 @@ std::string opTypeToString(OpType opType) { + case OpType::UNKNOWN: + return "UNKNOWN"; + default: +- TORCH_INTERNAL_ASSERT("Unknown op type!"); ++ TORCH_INTERNAL_ASSERT(false, "Unknown op type!"); + } + return "UNKNOWN"; + } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch new file mode 100644 index 00000000000..f7317e07c20 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch @@ -0,0 +1,46 @@ +# Fixes test in an environment where not all CPUs are available, e.g. because of cgroups +# Based on https://github.com/pytorch/pytorch/pull/44369 with adapted line numbers for PT-1.10 +diff -Nru pytorch.orig/test/test_dataloader.py pytorch/test/test_dataloader.py +--- pytorch.orig/test/test_dataloader.py 2021-10-22 10:41:08.421327256 +0200 ++++ pytorch/test/test_dataloader.py 2021-10-22 10:43:10.064917022 +0200 +@@ -2367,29 +2367,34 @@ + self._run_ind_worker_queue_test(batch_size=batch_size, num_workers=num_workers + 1) + + +class SetAffinityDataset(IterableDataset): + + def __iter__(self): + torch.randperm(1) + after = os.sched_getaffinity(0) + return iter(after) + +- +-def worker_set_affinity(_): +- os.sched_setaffinity(0, [multiprocessing.cpu_count() - 1]) +- +- + @unittest.skipIf( + not hasattr(os, 'sched_setaffinity'), + "os.sched_setaffinity is not available") + class TestSetAffinity(TestCase): + def test_set_affinity_in_worker_init(self): ++ # Query the current affinity mask to avoid setting a disallowed one ++ old_affinity = os.sched_getaffinity(0) ++ if not old_affinity: ++ self.skipTest("No affinity information") ++ # Choose any ++ expected_affinity = list(old_affinity)[-1] ++ ++ def worker_set_affinity(_): ++ os.sched_setaffinity(0, [expected_affinity]) ++ + dataset = SetAffinityDataset() + + dataloader = torch.utils.data.DataLoader( + dataset, num_workers=2, worker_init_fn=worker_set_affinity) + for sample in dataloader: +- self.assertEqual(sample, [multiprocessing.cpu_count() - 1]) ++ self.assertEqual(sample, [expected_affinity]) + + class ConvDataset(Dataset): + def __init__(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nccl-error-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nccl-error-tests.patch new file mode 100644 index 00000000000..2e69a5c7cc9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nccl-error-tests.patch @@ -0,0 +1,78 @@ +diff -Nru pytorch.orig/test/distributed/test_c10d_nccl.py pytorch/test/distributed/test_c10d_nccl.py +--- pytorch.orig/test/distributed/test_c10d_nccl.py 2021-10-22 10:41:08.420327251 +0200 ++++ pytorch/test/distributed/test_c10d_nccl.py 2021-10-22 17:18:52.399649457 +0200 +@@ -2277,6 +2277,7 @@ + @requires_nccl_version((2, 4, 0), "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) + @skip_if_rocm ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_clean_exit(self): + self._test_nccl_errors_blocking(lambda: sys.exit(0)) + +@@ -2285,6 +2286,7 @@ + @requires_nccl_version((2, 4, 0), "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) + @skip_if_rocm ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_nonzero_exit(self): + self._test_nccl_errors_blocking(lambda: sys.exit(1)) + +@@ -2296,6 +2298,7 @@ + @sandcastle_skip( + "Frequently times out see https://github.com/pytorch/pytorch/issues/58920" + ) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_abort(self): + self._test_nccl_errors_blocking(lambda: os.abort()) + +@@ -2304,6 +2307,7 @@ + @requires_nccl_version((2, 4, 0), "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) + @skip_if_rocm ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_sigkill(self): + self._test_nccl_errors_blocking(lambda: os.kill(os.getpid(), signal.SIGKILL)) + +@@ -2312,6 +2316,7 @@ + @requires_nccl_version((2, 4, 0), "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) + @skip_if_rocm ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_errors_blocking_sigterm(self): + self._test_nccl_errors_blocking(lambda: os.kill(os.getpid(), signal.SIGTERM)) + +@@ -2319,6 +2324,7 @@ + @requires_nccl() + @requires_nccl_version((2, 4, 0), "Need NCCL 2.4+ for error checking") + @skip_if_lt_x_gpu(3) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_blocking_wait_with_barrier(self): + store = c10d.FileStore(self.file_name, self.world_size) + process_group = c10d.ProcessGroupNCCL( +@@ -2364,6 +2370,7 @@ + @with_nccl_blocking_wait + @requires_nccl() + @skip_if_lt_x_gpu(3) ++ @unittest.skip("Broken on recent NCCL") + def test_nccl_timeout(self): + store = c10d.FileStore(self.file_name, self.world_size) + +diff -Nru pytorch.orig/torch/testing/_internal/distributed/distributed_test.py pytorch/torch/testing/_internal/distributed/distributed_test.py +--- pytorch.orig/torch/testing/_internal/distributed/distributed_test.py 2021-10-22 10:41:08.329326810 +0200 ++++ pytorch/torch/testing/_internal/distributed/distributed_test.py 2021-10-22 17:14:52.756479108 +0200 +@@ -7352,6 +7352,7 @@ + @require_backends_available({"gloo", "nccl"}) + @skip_if_rocm + @skip_if_lt_x_gpu(int(os.environ["WORLD_SIZE"])) ++ @unittest.skip("Broken on recent NCCL") + def test_monitored_barrier_allreduce_hang(self): + # tests expected behavior when nonzero rank hangs and we want to + # report first timed out rank. +@@ -7362,6 +7363,7 @@ + @require_backends_available({"gloo", "nccl"}) + @skip_if_rocm + @skip_if_lt_x_gpu(int(os.environ["WORLD_SIZE"])) ++ @unittest.skip("Broken on recent NCCL") + def test_monitored_barrier_allreduce_hang_wait_all_ranks(self): + # tests expected behavior when nonzero rank hangs and we want to + # report all timed out ranks. From 7afb38982d9e2fc80fe16461080866b85879bf36 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 28 Oct 2021 18:22:25 +0200 Subject: [PATCH 1708/9987] adding easyconfigs: NFFT-3.5.2-foss-2021a.eb --- .../n/NFFT/NFFT-3.5.2-foss-2021a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021a.eb new file mode 100644 index 00000000000..7f6c99079c4 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.5.2' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/NFFT/nfft/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c68b22de2b914328d5d9fd33778defc66b226c72ef4c103956bbf36bbcd18e45'] + +dependencies = [('FFTW', '3.3.9')] + +builddependencies = [('Autotools', '20210128')] + +configure_cmd_prefix = './bootstrap.sh ; ' + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' From bbc42657a71989d25e2c622f58480556a0a450b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 28 Oct 2021 18:25:56 +0200 Subject: [PATCH 1709/9987] adding easyconfigs: scikit-image-0.18.3-foss-2021a.eb --- .../scikit-image-0.18.3-foss-2021a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.3-foss-2021a.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.3-foss-2021a.eb new file mode 100644 index 00000000000..b7bd3ee4ad2 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.3-foss-2021a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.18.3' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('matplotlib', '3.4.2'), + ('Pillow', '8.2.0'), + ('networkx', '2.6.3'), + ('dask', '2021.9.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('PyWavelets', '1.1.1', { + 'modulename': 'pywt', + 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], + }), + ('imageio', '2.10.1', { + 'checksums': ['1fbf909bac3f07faabd05a3f71b3c49428709c3c55f43770a3f76e0eb1b525d1'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('tifffile', '2021.10.12', { + 'checksums': ['0a78268a2d844af94929512d28b39bd1ea6fe46de4124103840b5fe4e1c555cd'], + }), + (name, version, { + 'modulename': 'skimage', + 'patches': ['scikit-image-0.18.1_fix-README-cache-perms.patch'], + 'checksums': [ + 'ecae99f93f4c5e9b1bf34959f4dc596c41f2f6b2fc407d9d9ddf85aebd3137ca', # scikit-image-0.18.3.tar.gz + # scikit-image-0.18.1_fix-README-cache-perms.patch + '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', + ], + }), +] + +moduleclass = 'vis' From a66abaff34638e0b80fbca3c8d40a001fdaf55d8 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 28 Oct 2021 18:35:45 +0200 Subject: [PATCH 1710/9987] Fixed checksum --- .../p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index d958ecfe4e2..dbd386db34a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -44,7 +44,7 @@ checksums = [ # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '7000b316e93f0714011dcbf8d1d91ff755675bc1dc139dfa23d9d84d910135ce', + '571020faaf293a9a6b82d25a5233a18b025c15601b14a7f8445cc7951b8c025b', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch From 35434c5c3870e245cafd94d54f3d82f2aa5d2d0a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 28 Oct 2021 18:57:41 +0200 Subject: [PATCH 1711/9987] Downgrade versions out of necessity --- .../s/scikit-image/scikit-image-0.18.3-foss-2021a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.3-foss-2021a.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.3-foss-2021a.eb index b7bd3ee4ad2..61fe62c0b2b 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.3-foss-2021a.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.3-foss-2021a.eb @@ -12,7 +12,7 @@ dependencies = [ ('Python', '3.9.5'), ('matplotlib', '3.4.2'), ('Pillow', '8.2.0'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ('dask', '2021.9.1'), ] @@ -24,8 +24,8 @@ exts_list = [ 'modulename': 'pywt', 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], }), - ('imageio', '2.10.1', { - 'checksums': ['1fbf909bac3f07faabd05a3f71b3c49428709c3c55f43770a3f76e0eb1b525d1'], + ('imageio', '2.9.0', { + 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], }), ('imread', '0.7.4', { 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], From 08c6dc3b2e85d6c64df243918758aedde9b5b574 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 28 Oct 2021 19:24:10 +0200 Subject: [PATCH 1712/9987] Patch file didn't work after manual edit, recreated it --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 2 +- ....10.0_fix-test-dataloader-fixed-affinity.patch | 15 +++------------ 2 files changed, 4 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index dbd386db34a..82907843f74 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -44,7 +44,7 @@ checksums = [ # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '571020faaf293a9a6b82d25a5233a18b025c15601b14a7f8445cc7951b8c025b', + '3544726dd9041e247349730c209a77bc16ab4f9f7854dc7fe31399269f12613a', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch index f7317e07c20..3dd90944bac 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch @@ -1,16 +1,7 @@ -# Fixes test in an environment where not all CPUs are available, e.g. because of cgroups -# Based on https://github.com/pytorch/pytorch/pull/44369 with adapted line numbers for PT-1.10 diff -Nru pytorch.orig/test/test_dataloader.py pytorch/test/test_dataloader.py ---- pytorch.orig/test/test_dataloader.py 2021-10-22 10:41:08.421327256 +0200 -+++ pytorch/test/test_dataloader.py 2021-10-22 10:43:10.064917022 +0200 -@@ -2367,29 +2367,34 @@ - self._run_ind_worker_queue_test(batch_size=batch_size, num_workers=num_workers + 1) - - -class SetAffinityDataset(IterableDataset): - - def __iter__(self): - torch.randperm(1) +--- pytorch.orig/test/test_dataloader.py 2021-10-28 19:19:23.284526686 +0200 ++++ pytorch/test/test_dataloader.py 2021-10-28 19:21:31.860488973 +0200 +@@ -2374,22 +2374,27 @@ after = os.sched_getaffinity(0) return iter(after) From 7b069054b33388a62a4155d494c8650370f20999 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 29 Oct 2021 02:38:32 +0200 Subject: [PATCH 1713/9987] Build threaded versions of libraries as well --- easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021a.eb index 7f6c99079c4..28ace915b9d 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021a.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021a.eb @@ -20,8 +20,11 @@ builddependencies = [('Autotools', '20210128')] configure_cmd_prefix = './bootstrap.sh ; ' +configopts = '--enable-openmp' + sanity_check_paths = { - 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3_threads.a', 'lib/libnfft3.a', + 'lib/libnfft3_threads.%s' % SHLIB_EXT, 'lib/libnfft3.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } From 4d070bbfc85028fd7e2bf9eacc550340521ed127 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 29 Oct 2021 03:01:50 +0200 Subject: [PATCH 1714/9987] adding easyconfigs: eht-imaging-1.2.2-foss-2021a.eb --- .../eht-imaging-1.2.2-foss-2021a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb b/easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb new file mode 100644 index 00000000000..3356e62d3e7 --- /dev/null +++ b/easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb @@ -0,0 +1,44 @@ +easyblock = "PythonBundle" + +name = 'eht-imaging' +version = '1.2.2' + +homepage = 'https://github.com/achael/eht-imaging' +description = """Python modules for simulating and manipulating VLBI data and producing images with regularized maximum +likelihood methods.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('astropy', '4.3.1'), + ('matplotlib', '3.4.2'), + ('h5py', '3.2.1'), + ('networkx', '2.5.1'), + ('scikit-image', '0.18.3'), + ('NFFT', '3.5.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ephem', '4.1', { + 'checksums': ['c076794a511a34b5b91871c1cf6374dbc323ec69fca3f50eb718f20b171259d6'], + }), + ('pyNFFT', '1.3.2', { + 'patches': ['pyNFFT-1.3.2_fix_nfft3util_header.patch'], + 'checksums': [ + 'ae41e720e569d0d99e3a44c82c36b35a49cfc9ecc23a1cd039fe9e2895aada2c', # pyNFFT-1.3.2.tar.gz + # pyNFFT-1.3.2_fix_nfft3util_header.patch + 'db7ed250c2ed09176e73d39f642b8ca2aa4115d739e174a39133031900d6f33a', + ], + }), + ('ehtim', version, { + 'checksums': ['f92de54be6c7e56335a67d0c3b5bb5f3925f55a29c49fd5fbea36a45070f1a8e'], + }), +] + +moduleclass = 'lib' From 6a83594a11a4ab06e5671c1b473db54eefdae30f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 29 Oct 2021 03:06:06 +0200 Subject: [PATCH 1715/9987] Pick a perhaps better module class --- .../easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb b/easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb index 3356e62d3e7..ec97f4e949a 100644 --- a/easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb +++ b/easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb @@ -41,4 +41,4 @@ exts_list = [ }), ] -moduleclass = 'lib' +moduleclass = 'phys' From 2d8685d1c135e78a4f93d56952b345e357ca0eed Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 29 Oct 2021 11:34:43 +0800 Subject: [PATCH 1716/9987] prepare release notes for EasyBuild v4.5.0 + bump version to 4.5.0 --- RELEASE_NOTES | 79 +++++++++++++++++++++++++++++++++++++++++++++++++++ setup.py | 2 +- 2 files changed, 80 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 5f726e1b4a8..1777b275de2 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -7,6 +7,85 @@ The latest version of easybuild-easyconfig provides 13,265 easyconfig files, for incl. 36 different (compiler) toolchains. +v4.5.0 (October 29th 2021) +-------------------------- + +feature release + +- added easyconfigs for foss/2021b (#14217) and intel/2021b (#14218) toolchains +- added example easyconfig files for 39 new software packages: + - abTEM (#13974), ARTS (#9651), AutoGeneS (#13903), bashplotlib (#13942), CIRI-long (#13985), DFT-D4 (#12803), + ELSI-RCI (#14147), ESL-Bundle (#14179), expecttest (#14106), fdict (#14161), flook (#14161), FreeTDS (#13952), + HDBSCAN (#14062), imkl-FFTW (#14195), isoCirc (#13982), libfdf (#14173), libmbd (#14129), libpspio (#14173), + libSBML (#14050), longread_umi (#13987), Mesa-demos (#14123), MixMHC2pred (#14041), NTPoly (#14183), + OpenSceneGraph (#14197), panaroo (#14203), PEPT (#14077), pycoQC (#14012), python-docx (#13930), QD (#14122), + radeontop (#14124), Rgurobi (#14188), RInChI (#14049), scGeneFit (#13963), swifter (#14114), TOML-Fortran (#13929), + TRUST4 (#14035), ucx-py (#14051), vawk (#14040), VMTK (#14023) +- added additional easyconfigs for various supported software packages, including: + - abTEM 1.0.0b24, AdapterRemoval 2.3.2, AlphaFold 2.0.1, AlphaFold 2.0.1, artic ncov2019, ARTS 2.2.64, ASE 3.22.0, ASE 3.22.0, ASE 3.22.0, AutoGeneS 1.0.4, bashplotlib 0.6.5, Bazel 3.7.2, bbFTP 3.2.1, bbFTP 3.2.1.eb, BerkeleyGW 3.0.1, BioPerl 1.7.8, Bison 3.5.3, BLAST+ 2.11.0, BLIS 0.8.1, BLIS 0.8.1, bokeh 2.4.1, Boost.Python 1.76.0, Brotli 1.0.9, Brotli 1.0.9, buildenv default, buildenv default, buildenv default, bwidget 1.9.14, bzip2 1.0.8.eb, canu 2.2, Cartopy 0.20.0, Cbc 2.10.5, CD HIT, Cgl 0.60.3, CIRI long, Clang 12.0.1, Clp 1.17.6, ClustalW2 2.1, CoinUtils 2.11.4, CP2K 8.2, crb blast, CUDA 11.4.2.eb, cutadapt 3.4, Dalton 2020.0, dask 2021.9.1, DB 18.1.40, DB 18.1.40, DB_File 1.856, DCMTK 3.6.6, DFT D4, EasyBuild 4.4.2.eb, edlib 1.3.9, Eigen 3.3.9, ELPA 2021.05.001, ELSI 2.6.4, ELSI 2.6.4, ELSI 2.7.1, ELSI 2.7.1, ELSI RCI, ELSI RCI, EMBOSS 6.6.0, ESL Bundle, ESL Bundle, ETE 3.1.2, Exonerate 2.4.0, expecttest 0.1.3, FastME 2.1.6.1, fdict 0.8.0, fdict 0.8.0, FFTW 3.3.10, FFTW 3.3.10, Fiona 1.8.20, flook 0.8.1, flook 0.8.1, foss 2021b.eb, FreeTDS 1.3.3, GD 2.73, GDAL 3.3.2, GDRCopy 2.1, gflags 2.2.2, gflags 2.2.2, glew 2.2.0, glew 2.2.0, glew 2.2.0, gobff 2021a.eb, gompi 2021b.eb, GPAW 21.6.0, GPAW 21.6.0, GROMACS 2021.3, GTDB Tk, Gurobi 9.1.2, HDBSCAN 0.8.27, HDF5 1.12.1, HH suite, HH suite, HMMER2 2.3.2, Horovod 0.22.1, Horovod 0.22.1, HPCG 3.1, HPCG 3.1, HPDBSCAN 20210826, HPL 2.3, HPL 2.3, HPL 2.3, iimpi 2021b.eb, imageio 2.9.0, ImageJ 1.52q, imkl 2020.4.304, imkl 2021.3.0, imkl 2021.4.0.eb, imkl FFTW, imkl FFTW, impi 2021.3.0, impi 2021.4.0, intel 2021b.eb, intel compilers, IQ TREE, ISA L, isoCirc 1.0.4, ITK 4.13.1, jax 0.2.20, jbigkit 2.1, Kalign 3.3.1, Kraken2 2.1.2, leidenalg 0.8.7, libctl 4.0.0, libfabric 1.13.1, libfabric 1.13.2, libfdf 0.2.2, libfdf 0.2.2, libFLAME 5.2.0, libFLAME 5.2.0, libGridXC 0.9.6, libGridXC 0.9.6, libharu 2.3.0, Libint 2.6.0, libmbd 0.10.4, libmbd 0.10.4, libmbd 0.10.4, libmbd 0.10.4, libpsml 1.1.10, libpsml 1.1.10, libpspio 0.2.4, libpspio 0.2.4, libSBML 5.19.0, libspatialindex 1.9.3, LibUUID 1.0.3, libvdwxc 0.4.0, libvdwxc 0.4.0, libxc 5.1.6, libxsmm 1.16.2, libxsmm 1.16.2, lifelines 0.26.3, longread_umi 0.3.2, Longshot 0.4.3, LSD2 2.2, MAFFT 7.475, MAFFT 7.487, matplotlib 3.4.2, MCL 14.137, medaka 1.4.3, Meep 1.4.3, MEME 5.4.1, Mesa demos, MixMHC2pred 1.2.eb, MMseqs2 13, MotionCor2 1.4.4, MUSCLE 3.8.31, NCCL 2.11.4, netCDF 4.8.1, networkx 2.6.2, networkx 2.6.3, Nextflow 21.08.0.eb, NTPoly 2.5.1, NTPoly 2.5.1, NTPoly 2.7.0, NTPoly 2.7.0, NWChem 7.0.2, OpenBLAS 0.3.18, OpenCV 4.5.3, OpenCV 4.5.3, OpenMPI 4.0.5, OpenSceneGraph 3.6.5, OrthoFinder 2.5.2, OrthoFinder 2.5.4, Osi 0.108.6, OSU Micro, OSU Micro, panaroo 1.2.8, PEPT 0.4.1, PhyML 3.3.20200621, PostgreSQL 13.4, PRANK 170427, pycoQC 2.5.2, pygraphviz 1.7, pygraphviz 1.7, pyproj 3.1.0, python docx, python isal, python Levenshtein, python parasail, PyTorch Geometric, QD 0.8.9, QD 2.3.17, QIIME2 2021.8.eb, Qiskit 0.31.0, QuantumESPRESSO 6.8, QuantumESPRESSO 6.8, QUAST 5.0.2, Racon 1.4.21, radeontop 1.3, rampart 1.2.0, RapidJSON 1.1.0, rclone 1.56.0, RDKit 2021.03.4, Rgurobi 9.1.2, RInChI 1.00, Rust 1.52.1, SAMtools 1.13, ScaLAPACK 2.1.0, ScaLAPACK 2.1.0, Scalasca 2.6, scanpy 1.8.1, scanpy 1.8.1, scGeneFit 1.0.2, scikit allel, SciPy bundle, SciPy bundle, Seaborn 0.11.2, SHAPEIT4 4.2.2, SHAPEIT4 4.2.2, spglib 1.16.2, Subread 2.0.3, swifter 1.0.9, swifter 1.0.9, TensorFlow 2.2.3, TensorFlow 2.5.0, Togl 2.0, TOML Fortran, TOML Fortran, TRUST4 1.0.5.1.eb, UCX 1.11.2, UCX 1.9.0, UCX CUDA, ucx py, UnZip 6.0.eb, vawk 0.0.1, VMTK 1.4.0, VSEARCH 2.18.0, WRF 4.1.3, XCrySDen 1.6.2, xmlf90 1.5.4, xmlf90 1.5.4, XML LibXML, Z3 4.8.12, zarr 2.10.1 +- minor enhancements, including: + - add JASPAR2020 to R-bundle-Bioconductor 3.13 (#13962) + - make binutils a build-only dependency for Brotli + add sanity check command (#14004) + - fix download + permissions of binary for USEARCH v11.0.667 (#14036) + - fix compilation of BWA 0.7.17 with GCC/10.2.0 on POWER (#14073) + - add Perl and Python runtime dependencies to Bowtie2 2.4.4 (#14097) + - add Autotools as build dependency for CubeGUI-4.6 (#14109) + - fix dalton.in patch to be able to run tests from the build dir (#14158) + - add compiler/parallel/tcltk R libraries included in base installation to extensions in R: + - v4.x easyconfigs using foss toolchain (#14189) + - all easyconfigs using fosscuda toolchain (#14190) + - 3.5.x and 3.6.x easyconfigs (#14194) +- various bug fixes, including: + - add missing brotli dependency to freetype (#13915) + - remove help2man build dependency for flex using system toolchain (because it requires Perl) (#13922) + - add patch for OpenBLAS 0.3.15 to fix failing numpy tests on aarch64 (#13923) + - fix source URL + add alternate checksum for ADMIXTURE 1.3.0 (#13933) + - just use cp to copy stereo_chemical_props.txt to AlphaFold installation directory (#13938) + - add UnZip build dependency to TensorFlow 2.4.1 (#13958), 2.5.0 (#13959) and 2.6.0 easyconfigs (#13960) + - add missing Python dependency for WIEN2k 21.1 + patch to fix build failure for lapw0_mpi with libxc (#13961) + - add additional valid checksum for lhs 1.1.1 extension in recent R 4.0.x and 4.1.0 easyconfigs (#13969) + - fix Fortran system call stdout/err redirection for WIEN2k v21.1 (#13972) + - add OpenSSL dependency to Kent_tools 418 easyconfig to fix a link error (#13989) + - add missing Brotli dependency for freetype 2.11.0 + add sanity check command (#14002) + - fix installation of Racon v1.4.7 with gcccuda/2019b after move of ClaraGenomicsAnalysis repository (#14010) + - fix source URL for KEGG.db extension in R-bundle-Bioconductor 3.13 easyconfig (since it's a deprecated library now) (#14013) + - add patch for BLIS 0.8.1 to fix dgemm FPE signalling on Broadwell (#14018) + - add patch to fix installation of TensorFlow 2.2.3 on POWER (#14025) + - fix AmberTools v20 easyconfig using intel/2020a toolchain (#14028) + - move BLIS/libFLAME to GCC level in gobff/2021a (#14038) + - remove h5py 3.x dependency for Keras with 2020b toolchain, since TensorFlow provides (and requires) h5py 2.x (#14052) + - correctly specify install prefix for CUDA in OSU-Micro-Benchmarks after renaming CUDAcore to CUDA for 2021a (#14063) + - add patch to fix failing file system cache test for jax 0.2.19 (#14067) and 0.2.20 (#14070) on recent Linux kernels + - add missing dependencies for recent LibTIFF versions: XZ, jbigkit, zstd (#14079) + - add missing header file to existing versions of jbigkit (#14081) + - fix source URL for SUNDIALS 5.x (#14096, #14092) + - fix source URL for SCOTCH 6.1.0 (#14099) + - drop tcmalloc from SymEngine as it causes crashes with scipy (#14119) + - fix homepage + description in SimpleITK easyconfigs (#14125) + - also add location to MPI startup tests to $PATH in OSU-Micro-Benchmarks easyconfigs (#14126) + - add missing scripts from utils and analysis_scripts to bin for cryoDRGN (#14137) + - patch rsync_from_ncbi.pl in Kraken2 v2.1.2 to allow syncing with NCBI servers over HTTPS (#14148) + - skip mkl_fused_batch_norm_op_test test (broken on AMD EPYC systems) for TensorFlow 2.5.0 (#14151) and 2.6.0 (#14153) + - fix incorrect module load message and update morphology plugin of ImageJ 1.51k (#14152) + - fix XCrySDen v1.6.2 linking to libdl and Togl (#14160) + - use git hash to get specific morphology.zip for ImageJ 1.52q (#14163) + - add patch to fix PMIx detection in OpenMPI v4.0.3, v4.0.5, v4.1.0 (#14177) + - add patch for OpenBLAS 0.3.17 + 0.3.18 to fix segfault triggered by scipy tests (#14178) + - fix spatstat.* downloads for Seurat v4.0.1 (#14199) + - add patch for GROMACS 2019.3 easyconfigs using CMake 3.15.3 to fix CPU detection (#14212) +- other changes: + - use proper dependency for python-Levenshtein in CIRI-long easyconfig (#13985) + - add exception to easyconfigs test suite for (indirect) TensorFlow 2.2.3 dependency for artic-ncov2019 (#14037) + - update to UCX(-CUDA) 1.11.2 as dependency for OpenMPI v4.1.1 + NCCL v2.10.3 (#14090) + - remove format mapping from homepage of Subread easyconfigs (#14145) + - update libfabric to 1.13.1 in OpenMPI and add it as a dependency in PMIx for the upcoming foss 2021b toolchain (#14164) + - update to OpenBLAS 0.3.18 as dependency for FlexiBLAS 3.0.4 (used in foss/2021.07) (#14167) + - update libfabric to 1.13.2 in OpenMPI v4.1.1 + PMIx 4.1.0 for the upcoming foss/2021b toolchain (#14176) + - bump numpy to 1.21.3 in SciPy-bundle 2021.10 (#14181) + - use imkl installed with system toolchain in intel/2021.09 + add imkl-FFTW dependency for FFTW wrappers (#14195) + - add BLIS and imkl (x86_64 only) builddependencies to FlexiBLAS 0.3.4 with GCC/11.2.0 toolchain (#14225) + + v4.4.2 (September 7th 2021) --------------------------- diff --git a/setup.py b/setup.py index d3bc5581812..4f84a88acbf 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.4.3.dev0' +VERSION = '4.5.0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From ebeef03f8948f71004e2b65cc11c633300408bf0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Oct 2021 10:43:12 +0200 Subject: [PATCH 1717/9987] tweak release notes for v4.5.0 release --- RELEASE_NOTES | 59 +++++++++++++++++++++++++++------------------------ 1 file changed, 31 insertions(+), 28 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 1777b275de2..018cde54f6e 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 13,265 easyconfig files, for 2,467 different software packages, +The latest version of easybuild-easyconfig provides 13,514 easyconfig files, for 2,506 different software packages, incl. 36 different (compiler) toolchains. @@ -12,7 +12,9 @@ v4.5.0 (October 29th 2021) feature release -- added easyconfigs for foss/2021b (#14217) and intel/2021b (#14218) toolchains +- added easyconfigs for foss/2021b (#14217) and intel/2021b (#14218) common toolchains + - see also https://docs.easybuild.io/en/latest/Common-toolchains.html +- add easyconfig for gobff/2021a toolchain (#14019, #14038) - added example easyconfig files for 39 new software packages: - abTEM (#13974), ARTS (#9651), AutoGeneS (#13903), bashplotlib (#13942), CIRI-long (#13985), DFT-D4 (#12803), ELSI-RCI (#14147), ESL-Bundle (#14179), expecttest (#14106), fdict (#14161), flook (#14161), FreeTDS (#13952), @@ -22,22 +24,24 @@ feature release radeontop (#14124), Rgurobi (#14188), RInChI (#14049), scGeneFit (#13963), swifter (#14114), TOML-Fortran (#13929), TRUST4 (#14035), ucx-py (#14051), vawk (#14040), VMTK (#14023) - added additional easyconfigs for various supported software packages, including: - - abTEM 1.0.0b24, AdapterRemoval 2.3.2, AlphaFold 2.0.1, AlphaFold 2.0.1, artic ncov2019, ARTS 2.2.64, ASE 3.22.0, ASE 3.22.0, ASE 3.22.0, AutoGeneS 1.0.4, bashplotlib 0.6.5, Bazel 3.7.2, bbFTP 3.2.1, bbFTP 3.2.1.eb, BerkeleyGW 3.0.1, BioPerl 1.7.8, Bison 3.5.3, BLAST+ 2.11.0, BLIS 0.8.1, BLIS 0.8.1, bokeh 2.4.1, Boost.Python 1.76.0, Brotli 1.0.9, Brotli 1.0.9, buildenv default, buildenv default, buildenv default, bwidget 1.9.14, bzip2 1.0.8.eb, canu 2.2, Cartopy 0.20.0, Cbc 2.10.5, CD HIT, Cgl 0.60.3, CIRI long, Clang 12.0.1, Clp 1.17.6, ClustalW2 2.1, CoinUtils 2.11.4, CP2K 8.2, crb blast, CUDA 11.4.2.eb, cutadapt 3.4, Dalton 2020.0, dask 2021.9.1, DB 18.1.40, DB 18.1.40, DB_File 1.856, DCMTK 3.6.6, DFT D4, EasyBuild 4.4.2.eb, edlib 1.3.9, Eigen 3.3.9, ELPA 2021.05.001, ELSI 2.6.4, ELSI 2.6.4, ELSI 2.7.1, ELSI 2.7.1, ELSI RCI, ELSI RCI, EMBOSS 6.6.0, ESL Bundle, ESL Bundle, ETE 3.1.2, Exonerate 2.4.0, expecttest 0.1.3, FastME 2.1.6.1, fdict 0.8.0, fdict 0.8.0, FFTW 3.3.10, FFTW 3.3.10, Fiona 1.8.20, flook 0.8.1, flook 0.8.1, foss 2021b.eb, FreeTDS 1.3.3, GD 2.73, GDAL 3.3.2, GDRCopy 2.1, gflags 2.2.2, gflags 2.2.2, glew 2.2.0, glew 2.2.0, glew 2.2.0, gobff 2021a.eb, gompi 2021b.eb, GPAW 21.6.0, GPAW 21.6.0, GROMACS 2021.3, GTDB Tk, Gurobi 9.1.2, HDBSCAN 0.8.27, HDF5 1.12.1, HH suite, HH suite, HMMER2 2.3.2, Horovod 0.22.1, Horovod 0.22.1, HPCG 3.1, HPCG 3.1, HPDBSCAN 20210826, HPL 2.3, HPL 2.3, HPL 2.3, iimpi 2021b.eb, imageio 2.9.0, ImageJ 1.52q, imkl 2020.4.304, imkl 2021.3.0, imkl 2021.4.0.eb, imkl FFTW, imkl FFTW, impi 2021.3.0, impi 2021.4.0, intel 2021b.eb, intel compilers, IQ TREE, ISA L, isoCirc 1.0.4, ITK 4.13.1, jax 0.2.20, jbigkit 2.1, Kalign 3.3.1, Kraken2 2.1.2, leidenalg 0.8.7, libctl 4.0.0, libfabric 1.13.1, libfabric 1.13.2, libfdf 0.2.2, libfdf 0.2.2, libFLAME 5.2.0, libFLAME 5.2.0, libGridXC 0.9.6, libGridXC 0.9.6, libharu 2.3.0, Libint 2.6.0, libmbd 0.10.4, libmbd 0.10.4, libmbd 0.10.4, libmbd 0.10.4, libpsml 1.1.10, libpsml 1.1.10, libpspio 0.2.4, libpspio 0.2.4, libSBML 5.19.0, libspatialindex 1.9.3, LibUUID 1.0.3, libvdwxc 0.4.0, libvdwxc 0.4.0, libxc 5.1.6, libxsmm 1.16.2, libxsmm 1.16.2, lifelines 0.26.3, longread_umi 0.3.2, Longshot 0.4.3, LSD2 2.2, MAFFT 7.475, MAFFT 7.487, matplotlib 3.4.2, MCL 14.137, medaka 1.4.3, Meep 1.4.3, MEME 5.4.1, Mesa demos, MixMHC2pred 1.2.eb, MMseqs2 13, MotionCor2 1.4.4, MUSCLE 3.8.31, NCCL 2.11.4, netCDF 4.8.1, networkx 2.6.2, networkx 2.6.3, Nextflow 21.08.0.eb, NTPoly 2.5.1, NTPoly 2.5.1, NTPoly 2.7.0, NTPoly 2.7.0, NWChem 7.0.2, OpenBLAS 0.3.18, OpenCV 4.5.3, OpenCV 4.5.3, OpenMPI 4.0.5, OpenSceneGraph 3.6.5, OrthoFinder 2.5.2, OrthoFinder 2.5.4, Osi 0.108.6, OSU Micro, OSU Micro, panaroo 1.2.8, PEPT 0.4.1, PhyML 3.3.20200621, PostgreSQL 13.4, PRANK 170427, pycoQC 2.5.2, pygraphviz 1.7, pygraphviz 1.7, pyproj 3.1.0, python docx, python isal, python Levenshtein, python parasail, PyTorch Geometric, QD 0.8.9, QD 2.3.17, QIIME2 2021.8.eb, Qiskit 0.31.0, QuantumESPRESSO 6.8, QuantumESPRESSO 6.8, QUAST 5.0.2, Racon 1.4.21, radeontop 1.3, rampart 1.2.0, RapidJSON 1.1.0, rclone 1.56.0, RDKit 2021.03.4, Rgurobi 9.1.2, RInChI 1.00, Rust 1.52.1, SAMtools 1.13, ScaLAPACK 2.1.0, ScaLAPACK 2.1.0, Scalasca 2.6, scanpy 1.8.1, scanpy 1.8.1, scGeneFit 1.0.2, scikit allel, SciPy bundle, SciPy bundle, Seaborn 0.11.2, SHAPEIT4 4.2.2, SHAPEIT4 4.2.2, spglib 1.16.2, Subread 2.0.3, swifter 1.0.9, swifter 1.0.9, TensorFlow 2.2.3, TensorFlow 2.5.0, Togl 2.0, TOML Fortran, TOML Fortran, TRUST4 1.0.5.1.eb, UCX 1.11.2, UCX 1.9.0, UCX CUDA, ucx py, UnZip 6.0.eb, vawk 0.0.1, VMTK 1.4.0, VSEARCH 2.18.0, WRF 4.1.3, XCrySDen 1.6.2, xmlf90 1.5.4, xmlf90 1.5.4, XML LibXML, Z3 4.8.12, zarr 2.10.1 + - AlphaFold 2.0.1, artic-ncov2019 2021.06.24, BerkeleyGW 3.0.1, bokeh 2.4.1, Boost.Python 1.76.0, canu 2.2, + Cartopy 0.20.0, CP2K 8.2, CUDA 11.4.2, Dalton 2020.0, dask 2021.9.1, edlib 1.3.9, ELSI 2.7.1, FFTW 3.3.10, + GD 2.73, GDAL 3.3.2, GTDB-Tk 1.7.0, ImageJ 1.52q, jax 0.2.20, Kraken2 2.1.2, leidenalg 0.8.7, libfabric 1.13.2, + libspatialindex 1.9.3, libxc 5.1.6, libxsmm 1.16.2, lifelines 0.26.3, Longshot 0.4.3, LSD2 2.2, MAFFT 7.487, + MEME 5.4.1, MotionCor2 1.4.4, NCCL 2.11.4, netCDF 4.8.1, networkx 2.6.3, Nextflow 21.08.0, OpenBLAS 0.3.18, + OpenCV 4.5.3, OrthoFinder 2.5.4, OSU-Micro-Benchmarks 5.8, PhyML 3.3.20200621, PostgreSQL 13.4, pygraphviz 1.7, + pyproj 3.1.0, python-Levenshtein 0.12.1, PyTorch-Geometric 2.0.1, QIIME2 2021.8.eb, Qiskit 0.31.0, + QuantumESPRESSO 6.8, Racon 1.4.21, rampart 1.2.0, rclone 1.56.0, RDKit 2021.03.4, SAMtools 1.13, scanpy 1.8.1, + scikit-allel 1.3.3, SciPy-bundle 2021.10, Seaborn 0.11.2, SHAPEIT4 4.2.2, spglib 1.16.2, UCX 1.11.2, + UCX-CUDA 1.11.2, VSEARCH 2.18.0, Z3 4.8.12, zarr 2.10.1 - minor enhancements, including: - add JASPAR2020 to R-bundle-Bioconductor 3.13 (#13962) - - make binutils a build-only dependency for Brotli + add sanity check command (#14004) - - fix download + permissions of binary for USEARCH v11.0.667 (#14036) - - fix compilation of BWA 0.7.17 with GCC/10.2.0 on POWER (#14073) - - add Perl and Python runtime dependencies to Bowtie2 2.4.4 (#14097) - add Autotools as build dependency for CubeGUI-4.6 (#14109) - - fix dalton.in patch to be able to run tests from the build dir (#14158) - - add compiler/parallel/tcltk R libraries included in base installation to extensions in R: - - v4.x easyconfigs using foss toolchain (#14189) - - all easyconfigs using fosscuda toolchain (#14190) - - 3.5.x and 3.6.x easyconfigs (#14194) + - add compiler/parallel/tcltk R libraries included in base installation to extensions in recent R easyconfigs (#14189, #14190, #14194) + - required for parallel installation of extensions for these R easyconfigs + - also add location to MPI startup tests to $PATH in OSU-Micro-Benchmarks easyconfigs (#14126) - various bug fixes, including: - - add missing brotli dependency to freetype (#13915) - - remove help2man build dependency for flex using system toolchain (because it requires Perl) (#13922) + - add missing Brotli dependency to freetype (#13915, #14002) - add patch for OpenBLAS 0.3.15 to fix failing numpy tests on aarch64 (#13923) - fix source URL + add alternate checksum for ADMIXTURE 1.3.0 (#13933) - just use cp to copy stereo_chemical_props.txt to AlphaFold installation directory (#13938) @@ -46,43 +50,42 @@ feature release - add additional valid checksum for lhs 1.1.1 extension in recent R 4.0.x and 4.1.0 easyconfigs (#13969) - fix Fortran system call stdout/err redirection for WIEN2k v21.1 (#13972) - add OpenSSL dependency to Kent_tools 418 easyconfig to fix a link error (#13989) - - add missing Brotli dependency for freetype 2.11.0 + add sanity check command (#14002) + - make binutils a build-only dependency for Brotli + add sanity check command (#14004) - fix installation of Racon v1.4.7 with gcccuda/2019b after move of ClaraGenomicsAnalysis repository (#14010) - fix source URL for KEGG.db extension in R-bundle-Bioconductor 3.13 easyconfig (since it's a deprecated library now) (#14013) - add patch for BLIS 0.8.1 to fix dgemm FPE signalling on Broadwell (#14018) - add patch to fix installation of TensorFlow 2.2.3 on POWER (#14025) - fix AmberTools v20 easyconfig using intel/2020a toolchain (#14028) - - move BLIS/libFLAME to GCC level in gobff/2021a (#14038) + - fix download + permissions of binary for USEARCH v11.0.667 (#14036) - remove h5py 3.x dependency for Keras with 2020b toolchain, since TensorFlow provides (and requires) h5py 2.x (#14052) - correctly specify install prefix for CUDA in OSU-Micro-Benchmarks after renaming CUDAcore to CUDA for 2021a (#14063) - - add patch to fix failing file system cache test for jax 0.2.19 (#14067) and 0.2.20 (#14070) on recent Linux kernels + - add patch to fix failing file system cache test for jax on recent Linux kernels (#14067, #14070) + - fix compilation of BWA 0.7.17 with GCC/10.2.0 on POWER (#14073) - add missing dependencies for recent LibTIFF versions: XZ, jbigkit, zstd (#14079) - add missing header file to existing versions of jbigkit (#14081) - - fix source URL for SUNDIALS 5.x (#14096, #14092) + - fix source URL for SUNDIALS 5.x (#14092, #14096) + - add Perl and Python runtime dependencies to Bowtie2 2.4.4 (#14097) - fix source URL for SCOTCH 6.1.0 (#14099) - drop tcmalloc from SymEngine as it causes crashes with scipy (#14119) - fix homepage + description in SimpleITK easyconfigs (#14125) - - also add location to MPI startup tests to $PATH in OSU-Micro-Benchmarks easyconfigs (#14126) - add missing scripts from utils and analysis_scripts to bin for cryoDRGN (#14137) - patch rsync_from_ncbi.pl in Kraken2 v2.1.2 to allow syncing with NCBI servers over HTTPS (#14148) - - skip mkl_fused_batch_norm_op_test test (broken on AMD EPYC systems) for TensorFlow 2.5.0 (#14151) and 2.6.0 (#14153) + - skip mkl_fused_batch_norm_op_test test (broken on AMD EPYC systems) for TensorFlow 2.5.0 and 2.6.0 (#14151, #14153) - fix incorrect module load message and update morphology plugin of ImageJ 1.51k (#14152) - fix XCrySDen v1.6.2 linking to libdl and Togl (#14160) - - use git hash to get specific morphology.zip for ImageJ 1.52q (#14163) - add patch to fix PMIx detection in OpenMPI v4.0.3, v4.0.5, v4.1.0 (#14177) - add patch for OpenBLAS 0.3.17 + 0.3.18 to fix segfault triggered by scipy tests (#14178) - fix spatstat.* downloads for Seurat v4.0.1 (#14199) - add patch for GROMACS 2019.3 easyconfigs using CMake 3.15.3 to fix CPU detection (#14212) - other changes: + - remove help2man build dependency for flex using system toolchain (because it requires Perl) (#13922) - use proper dependency for python-Levenshtein in CIRI-long easyconfig (#13985) - - add exception to easyconfigs test suite for (indirect) TensorFlow 2.2.3 dependency for artic-ncov2019 (#14037) - - update to UCX(-CUDA) 1.11.2 as dependency for OpenMPI v4.1.1 + NCCL v2.10.3 (#14090) + - in-place updates for foss/2021b and intel/2021b common toolchains + - update to UCX(-CUDA) 1.11.2 as dependency for OpenMPI v4.1.1 + NCCL v2.10.3 (#14090) + - update libfabric to 1.13.1 in OpenMPI and add it as a dependency in PMIx for the upcoming foss 2021b toolchain (#14164) + - update to OpenBLAS 0.3.18 as dependency for FlexiBLAS 3.0.4 with GCCcore/11.2.0 toolchain (#14167) + - update libfabric to 1.13.2 in OpenMPI v4.1.1 + PMIx 4.1.0 for the upcoming foss/2021b toolchain (#14176) - remove format mapping from homepage of Subread easyconfigs (#14145) - - update libfabric to 1.13.1 in OpenMPI and add it as a dependency in PMIx for the upcoming foss 2021b toolchain (#14164) - - update to OpenBLAS 0.3.18 as dependency for FlexiBLAS 3.0.4 (used in foss/2021.07) (#14167) - - update libfabric to 1.13.2 in OpenMPI v4.1.1 + PMIx 4.1.0 for the upcoming foss/2021b toolchain (#14176) - - bump numpy to 1.21.3 in SciPy-bundle 2021.10 (#14181) - - use imkl installed with system toolchain in intel/2021.09 + add imkl-FFTW dependency for FFTW wrappers (#14195) - add BLIS and imkl (x86_64 only) builddependencies to FlexiBLAS 0.3.4 with GCC/11.2.0 toolchain (#14225) From 581ca44f9ac96d93735d09ae9a2157a4e1444e79 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 29 Oct 2021 20:14:57 +1050 Subject: [PATCH 1718/9987] adding easyconfigs: minimap2-2.22-GCCcore-11.2.0.eb --- .../minimap2/minimap2-2.22-GCCcore-11.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.22-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.22-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.22-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..81593a1a6e6 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.22-GCCcore-11.2.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# DeepThought, Flinders University +# Updated to 2.22 +# R.QIAO + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.22' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['c96ecd0a0dbe61eb2da6a7ae06c9fc7249ee63d2ebf1909e07213cb6ec0a4633'] + +builddependencies = [('binutils', '2.37')] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' From b1bf0d91b61fdc71d902940644b63e11923d2c56 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 29 Oct 2021 20:48:14 +1050 Subject: [PATCH 1719/9987] adding easyconfigs: CapnProto-0.9.1-GCCcore-10.2.0.eb --- .../CapnProto-0.9.1-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..5f3f76e2e2a --- /dev/null +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to 0.9.1 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'CapnProto' +version = '0.9.1' + +homepage = 'https://capnproto.org' +description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" +# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." +# (only on Intel Skylake?) +toolchainopts = {'cstd': 'c++17', 'lowopt': True} + +source_urls = ['https://capnproto.org/'] +sources = ['capnproto-c++-%(version)s.tar.gz'] +checksums = ['83680aaef8c192b884e38eab418b8482d321af6ae7ab7befa3a9370b8e716aad'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/capnp', 'bin/capnpc', 'bin/capnpc-c++', 'bin/capnpc-capnp'], + 'dirs': ['include/capnp', 'include/kj', 'lib'], +} + +moduleclass = 'bio' From 17fd63fcc84bcc22b9b4df570df8ec0b631432af Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 29 Oct 2021 21:14:11 +1050 Subject: [PATCH 1720/9987] adding easyconfigs: CapnProto-0.8.0-GCCcore-9.3.0.eb --- .../CapnProto-0.8.0-GCCcore-9.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CapnProto/CapnProto-0.8.0-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.8.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.8.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..5d695d37d16 --- /dev/null +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.8.0-GCCcore-9.3.0.eb @@ -0,0 +1,31 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to 0.8.0 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'CapnProto' +version = '0.8.0' + +homepage = 'https://capnproto.org' +description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" +# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." +# (only on Intel Skylake?) +toolchainopts = {'cstd': 'c++17', 'lowopt': True} + +source_urls = ['https://capnproto.org/'] +sources = ['capnproto-c++-%(version)s.tar.gz'] +checksums = ['d1f40e47574c65700f0ec98bf66729378efabe3c72bc0cda795037498541c10d'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['bin/capnp', 'bin/capnpc', 'bin/capnpc-c++', 'bin/capnpc-capnp'], + 'dirs': ['include/capnp', 'include/kj', 'lib'], +} + +moduleclass = 'bio' From 1d92aa2bf4788b307334ac1bc8a59b4676130255 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 29 Oct 2021 21:32:58 +1050 Subject: [PATCH 1721/9987] adding easyconfigs: Mash-2.2-foss-2020a.eb --- .../easyconfigs/m/Mash/Mash-2.2-foss-2020a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mash/Mash-2.2-foss-2020a.eb diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.2-foss-2020a.eb b/easybuild/easyconfigs/m/Mash/Mash-2.2-foss-2020a.eb new file mode 100644 index 00000000000..83083b56700 --- /dev/null +++ b/easybuild/easyconfigs/m/Mash/Mash-2.2-foss-2020a.eb @@ -0,0 +1,36 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v2.2 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'Mash' +version = '2.2' + +homepage = 'http://mash.readthedocs.org' +description = "Fast genome and metagenome distance estimation using MinHash" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/marbl/Mash/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7ad006dbf0d6ffc3e164713ba955aab4cd24eaf85c864ac905f48cd8ba332691'] + +builddependencies = [('Autotools', '20180311')] +dependencies = [ + ('CapnProto', '0.8.0'), + ('GSL', '2.6'), + ('zlib', '1.2.11'), +] + +preconfigopts = "./bootstrap.sh && " +configopts = "--with-capnp=$EBROOTCAPNPROTO --with-gsl=$EBROOTGSL" + +sanity_check_paths = { + 'files': ['bin/mash', 'lib/libmash.a'], + 'dirs': ['include/mash'], +} + +moduleclass = 'bio' From 4ab380b52bfc52bc0f277d1defa6b1e541b72fb3 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 29 Oct 2021 15:06:54 +0200 Subject: [PATCH 1722/9987] adding easyconfigs: Highway-0.12.2-GCCcore-10.2.0.eb, zopfli-1.0.3-foss-2020b.eb, zlib-ng-2.0.5-foss-2020b.eb, liblzma-5.2.5-foss-2020b.eb, liblzf-3.4-GCCcore-10.2.0.eb, libjxl-0.5-GCCcore-10.2.0.eb, libavif-0.9.0-foss-2020b.eb --- .../Highway/Highway-0.12.2-GCCcore-10.2.0.eb | 31 +++++++++ .../l/libavif/libavif-0.9.0-foss-2020b.eb | 39 +++++++++++ .../l/libjxl/libjxl-0.5-GCCcore-10.2.0.eb | 66 +++++++++++++++++++ .../l/liblzf/liblzf-3.4-GCCcore-10.2.0.eb | 27 ++++++++ .../l/liblzma/liblzma-5.2.5-foss-2020b.eb | 31 +++++++++ .../z/zlib-ng/zlib-ng-2.0.5-foss-2020b.eb | 28 ++++++++ .../z/zopfli/zopfli-1.0.3-foss-2020b.eb | 30 +++++++++ 7 files changed, 252 insertions(+) create mode 100644 easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/liblzf/liblzf-3.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-foss-2020b.eb create mode 100644 easybuild/easyconfigs/z/zopfli/zopfli-1.0.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..5111d10fd43 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Highway' +version = '0.12.2' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e1d47ce510429fdcf31f41697ca74fb0dcd59d933196e531a86d51751a56f4cc'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb new file mode 100644 index 00000000000..23a8645f597 --- /dev/null +++ b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libavif' +version = '0.9.0' + +homepage = 'https://github.com/AOMediaCodec/libavif' +description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format, +as described here: https://aomediacodec.github.io/av1-avif/ +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('NASM', '2.15.05'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('Rust', '1.52.1'), +] + +# TODO FIX THIS - NEED THOSE +# configopts = ' -DAVIF_CODEC_AOM=ON -DAVIF_CODEC_DAV1D=ON -DAVIF_CODEC_LIBGAV1=ON -DAVIF_CODEC_RAV1E=ON ' +sanity_check_paths = { + 'files': ['lib/libavif.so.10.0.0', 'include/avif/avif.h'], + 'dirs': ['lib/', 'include/avif/'] +} + +sanity_check_commands = [ +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..100da8372c1 --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.2.0.eb @@ -0,0 +1,66 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libjxl' +version = '0.5' +local_lodepng_version = "48e5364" + +homepage = 'https://github.com/libjxl/libjxl' +description = "JPEG XL image format reference implementation" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'optarch': False} # optarch causes some test failures + +github_account = 'libjxl' +source_urls = [GITHUB_SOURCE] +sources = [ + 'v%(version)s.tar.gz', + {'filename': 'lodepng-%s.tar.gz' % local_lodepng_version, + 'download_filename': local_lodepng_version, + 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], + 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, +] +patches = [ + 'libjxl-0.3.7_external_lcms2.patch', + 'libjxl-%(version)s_remove-broken-test.patch', +] +checksums = [ + '911cb4b50eb621131ca22382166f40d4914a4ff4453dd299ade1e3292f311f89', # v0.5.tar.gz + 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz + '9e6decaf6be74eeccfd5728df175930b4be33de6cbdf9e1816f68cb4b718fa1b', # libjxl-0.3.7_external_lcms2.patch + '5b62751da5b3b3c4aad58a841d49cc506bc330425bbd0df7f19f99aa98c52c26', # libjxl-0.5_remove-broken-test.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('googletest', '1.10.0'), + ('pkg-config', '0.29.2'), + ('Highway', '0.12.2'), # Highway only has a static library +] + +dependencies = [ + ('LittleCMS', '2.11'), + ('Brotli', '1.0.9'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('giflib', '5.2.1'), + ('libwebp', '1.1.0'), + ('OpenEXR', '2.5.5'), + ('gperftools', '2.9.1'), +] + +configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' +# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) +configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/liblzf/liblzf-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/liblzf/liblzf-3.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..586daf3ca2a --- /dev/null +++ b/easybuild/easyconfigs/l/liblzf/liblzf-3.4-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'liblzf' +version = '3.4' + +homepage = 'http://oldhome.schmorp.de/marc/liblzf.html' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] +sources = ['liblzf-%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'lib' \ No newline at end of file diff --git a/easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb b/easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb new file mode 100644 index 00000000000..2349d6b3d2e --- /dev/null +++ b/easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'liblzma' +version = '5.2.5' + +homepage = 'https://github.com/xz-mirror/xz' +description = """XZ Utils provide a general-purpose data-compression library plus command-line tools.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/xz-mirror/xz/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ +] + +sanity_check_paths = { + 'files': ['bin/xz', 'bin/xzdec'], + 'dirs': ['lib/', 'bin/', 'include/'] +} + +sanity_check_commands = [ +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-foss-2020b.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-foss-2020b.eb new file mode 100644 index 00000000000..4f3a7866d69 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-foss-2020b.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'zlib-ng' +version = '2.0.5' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +sanity_check_commands = [ +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/', 'include/'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zopfli/zopfli-1.0.3-foss-2020b.eb b/easybuild/easyconfigs/z/zopfli/zopfli-1.0.3-foss-2020b.eb new file mode 100644 index 00000000000..fe209004cf0 --- /dev/null +++ b/easybuild/easyconfigs/z/zopfli/zopfli-1.0.3-foss-2020b.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'zopfli' +version = '1.0.3' + +homepage = 'https://github.com/google/zopfli' +description = """Zopfli Compression Algorithm is a compression library programmed in C to perform +very good, but slow, deflate or zlib compression.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] +sources = ['%(name)s-%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +sanity_check_commands = [ +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/', 'include/'], +} + +moduleclass = 'tools' From 11c6db9f073dc954363d32ccbb435d467939c7be Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 29 Oct 2021 15:11:58 +0200 Subject: [PATCH 1723/9987] adding easyconfigs: libaec-1.0.6-foss-2020b.eb, lerc-3.0-foss-2020b.eb, jxrlib-1.1-foss-2020b.eb, CFITSIO-3.49-GCCcore-10.2.0.eb, brunsli-0.1-foss-2020b.eb, Blosc2-2.0.3-GCCcore-10.2.0.eb, imagecodecs-2021.8.26-foss-2020b.eb --- .../b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb | 29 +++++++ .../b/brunsli/brunsli-0.1-foss-2020b.eb | 44 ++++++++++ .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb | 37 +++++++++ .../imagecodecs-2021.8.26-foss-2020b.eb | 82 +++++++++++++++++++ .../j/jxrlib/jxrlib-1.1-foss-2020b.eb | 33 ++++++++ .../easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb | 40 +++++++++ .../l/libaec/libaec-1.0.6-foss-2020b.eb | 32 ++++++++ 7 files changed, 297 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/b/brunsli/brunsli-0.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb create mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..cc97656d2c1 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.0.3' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/brunsli/brunsli-0.1-foss-2020b.eb b/easybuild/easyconfigs/b/brunsli/brunsli-0.1-foss-2020b.eb new file mode 100644 index 00000000000..2939240b1b6 --- /dev/null +++ b/easybuild/easyconfigs/b/brunsli/brunsli-0.1-foss-2020b.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['patch_brunsli.patch'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '0.12.2'), +] + +configopts = ' -DCMAKE_BUILD_TYPE=Release ' +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon "' + +postinstallcmds = [ + 'mkdir %(installdir)s/bin ', + 'cp dbrunsli %(installdir)s/bin ', + 'cp *.a %(installdir)s/lib64 ', + 'cp *.so %(installdir)s/lib64 ', + ] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..3d4e1b6d407 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.49' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-3.48_install_test_data.patch'] + +# curl for HTTPs support +dependencies = [('cURL', '7.72.0')] + +builddependencies = [('binutils', '2.35')] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = '&& make shared && make testprog' + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + ('cd %(installdir)s/share && testprog'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb new file mode 100644 index 00000000000..c75dc12b18c --- /dev/null +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -0,0 +1,82 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'imagecodecs' +version = '2021.8.26' + +homepage = 'https://www.lfd.uci.edu/~gohlke/' +description = """ +Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, +compression, and decompression functions for use in the tifffile, czifile, zarr, and other +scientific image input/output modules. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +# changing src line endings +local_extract_cmd = ' tar -xvf %s ' +local_extract_cmd += ' && find . -type f -print0 | xargs -0 dos2unix ' + +sources = [{ + 'source_urls': PYPI_SOURCE, + 'filename': SOURCE_TAR_GZ, + 'extract_cmd': local_extract_cmd, +}] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('SciPy-bundle', '2020.11'), + ('Brotli', '1.0.9'), + ('bzip2', '1.0.8'), + ('Blosc', '1.21.0'), + ('Blosc2', '2.0.3'), + ('CFITSIO', '3.49'), + ('CharLS', '2.2.0'), + ('giflib', '5.2.1'), + ('jxrlib', '1.1'), + ('LittleCMS', '2.11'), + ('lerc', '3.0'), + ('libaec', '1.0.6'), + ('libavif', '0.9.0'), + ('libdeflate', '1.7'), + ('libjpeg-turbo', '2.0.5'), + ('libjxl', '0.5'), + ('liblzf', '3.4'), + ('libpng', '1.6.37'), + ('liblzma', '5.2.5'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('libwebp', '1.1.0'), + ('lz4', '1.9.2'), + ('OpenJPEG', '2.4.0'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), + ('zlib-ng', '2.0.5'), + ('zopfli', '1.0.3'), + ('zfp', '0.5.5'), + ('zstd', '1.4.5'), + ('brunsli', '0.1'), + ('HDF5', '1.10.7'), + ('h5py', '3.1.0'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'use_pip': True, + 'download_dep_fail': True, +} + +exts_list = [ + ('bitshuffle', '0.3.5', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'] + }), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb new file mode 100644 index 00000000000..e4d4ecdf8e2 --- /dev/null +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +## + +easyblock = 'CMakeMake' + +name = 'jxrlib' +version = '1.1' + +homepage = 'https://archive.codeplex.com/?p=jxrlib' +description = """Open source implementation of jpegxr""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] +sources = ['%(name)s_%(version)s.orig.tar.gz'] +patches = [ + ('%(name)s-%(version)s-foss-2020b_support_cmake.patch', 1), +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +modextrapaths = {'CPATH': 'include/jxrlib'} + +sanity_check_paths = { + 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', 'lib/libjpegxr.so.0'], + 'dirs': ['bin/', 'lib/'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb b/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb new file mode 100644 index 00000000000..f464f98fd48 --- /dev/null +++ b/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'lerc' +version = '3.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://github.com/Esri/lerc/archive/', + 'https://raw.githubusercontent.com/Esri/lerc/33910e56d2d46e402b6233492eabb6c4fe0b3c5e/src/LercTest/', +] + +local_testfile_sed_cmd = "sed -i -e 's|../LercLib/include/||' %(builddir)s/main.cpp" + +sources = [ + 'v%(version)s.tar.gz', + {'filename': 'main.cpp', 'extract_cmd': 'cp %s %(builddir)s && ' + local_testfile_sed_cmd }, +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +sanity_check_commands = [ + "cd %(builddir)s && g++ -o output_bin main.cpp -lLerc && ./output_bin " +] + +sanity_check_paths = { + 'files': ['lib/libLerc.so'], + 'dirs': ['lib/', 'include/'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb new file mode 100644 index 00000000000..673a8af6e8d --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.0.6' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s' ] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['bin/aec', 'lib/libaec.a', 'lib/libaec.so.0.0.12'], + 'dirs': ['bin/', 'lib/', 'include/'] +} + +sanity_check_commands = [ + 'aec --help', +] + +moduleclass = 'tools' From 6789b4949d0afc49038ed434c7af8cfe36d8ce31 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 29 Oct 2021 15:13:57 +0200 Subject: [PATCH 1724/9987] adding easyconfigs: tifffile-2021.8.30-foss-2020b.eb, unittest2-1.1.0-foss-2020b.eb, SimpleITK-2.1.0-foss-2020b.eb, requests-2.26.0-foss-2020b.eb, batchgenerators-0.23-foss-2020b.eb, Lua-5.3.5-GCCcore-10.2.0.eb --- .../batchgenerators-0.23-foss-2020b.eb | 31 +++++++++++ .../l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb | 30 +++++++++++ .../r/requests/requests-2.26.0-foss-2020b.eb | 28 ++++++++++ .../s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb | 53 +++++++++++++++++++ .../tifffile/tifffile-2021.8.30-foss-2020b.eb | 44 +++++++++++++++ .../u/unittest2/unittest2-1.1.0-foss-2020b.eb | 32 +++++++++++ 6 files changed, 218 insertions(+) create mode 100644 easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb create mode 100644 easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb new file mode 100644 index 00000000000..259cde6c642 --- /dev/null +++ b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'batchgenerators' +version = '0.23' + +homepage = 'https://github.com/MIC-DKFZ/batchgenerators' +description = """batchgenerators is a python package for data augmentation. +It is developed jointly between the Division of Medical Image Computing at the German Cancer Research Center (DKFZ) +and the Applied Computer Vision Lab of the Helmholtz Imaging Platform.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow', '8.0.1'), + ('scikit-learn', '0.23.2'), + ('SciPy-bundle', '2020.11'), + ('scikit-image', '0.18.1'), + ('unittest2', '1.1.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..125417a6c6c --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.5-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +name = 'Lua' +version = '5.3.5' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0c2eed3f960446e1a3e4b9a1ca2f3ff893b6ce41942cf54d5dd59ab4b3b058ac'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('libreadline', '8.0'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb b/easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb new file mode 100644 index 00000000000..b79821bedc1 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'requests' +version = '2.26.0' + +homepage = 'https://pypi.org/project/unittest2/' +description = """Requests is a simple, yet elegant, HTTP library.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Python', '3.8.6'), +] + +exts_list = [ + ('requests', version), + ('charset-normalizer', '2.0.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb new file mode 100644 index 00000000000..0b1009560a0 --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'SimpleITK' +version = '2.1.0' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/s/simpleitk/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d5d3b805863b9dfcffeebec69a1b79b5709fc814b12cb9ab759ccbd3e4746839'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Lua', '5.3.5'), + ('ITK', '5.2.1'), + ('scikit-build', '0.11.1'), +] +start_dir = 'SimpleITK' + +configopts = '-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF -DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF ' + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_pyinstpath = "%(installdir)s/lib/python%(pyshortver)s/site-packages" +postinstallcmds = [ + "mkdir -p %s " % local_pyinstpath + + " && cd %(builddir)s/easybuild_obj/Wrapping/Python " + + " && export PYTHONPATH=%s:$PYTHONPATH " % local_pyinstpath + + " && pip install --prefix=%(installdir)s . " +] +separate_build_dir = True + +# todo make nicer dir path +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/']} + +sanity_check_paths = { + 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'include/%(name)s-%(version_major_minor)s'], +} + +sanity_check_commands = [('python', "-c 'import %(name)s'")] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb b/easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb new file mode 100644 index 00000000000..b21bbbd0fa2 --- /dev/null +++ b/easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'tifffile' +version = '2021.8.30' + +homepage = 'https://www.lfd.uci.edu/~gohlke/' +description = """ +Tifffile is a Python library to store numpy arrays in TIFF (Tagged Image File Format) files, and read image and +metadata from TIFF-like files used in bioimaging. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('SciPy-bundle', '2020.11'), + ('imagecodecs', '2021.8.26'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'use_pip': True, + 'download_dep_fail': True, +} + +exts_list = [ + ('lxml', '4.6.3', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lxml/'] + }), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb new file mode 100644 index 00000000000..112250696ec --- /dev/null +++ b/easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'unittest2' +version = '1.1.0' + +homepage = 'https://pypi.org/project/unittest2/' +description = """unittest2 is a backport of the new features added to the unittest testing +framework in Python 2.7 and onwards.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Python', '3.8.6'), +] + +exts_list = [ + ('unittest2', version, { + 'patches': ['patch_unittest2.patch'], + }), + ('traceback2', '1.4.0'), + ('linecache2', '1.0.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From 1002d0f488b69e985020f1ba903f1c23eba70e24 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 29 Oct 2021 21:14:50 +0800 Subject: [PATCH 1725/9987] adding easyconfigs: EasyBuild-4.5.0.eb --- .../e/EasyBuild/EasyBuild-4.5.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.0.eb new file mode 100644 index 00000000000..b3cc0ce5fe3 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.0.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.5.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/f9/61/0d84b3271b7eeb8d74030e6045f8b366b0e8d642d86e3dff30b0c13cb84c/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/b4/12/196cf5878a89c1616ef763b173b443fbb988b9b74cfc8441b75623e14e89/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/7a/d5/57819d671972c2b79f506c7dc06c2be2fb13c77e4fdc7c8dfe3c2aff968e/' +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + 'f2d9889c5b226f985af0b7085b0a69cee5486b51209e4fceb28720a83ca7edec', # easybuild-framework-4.5.0.tar.gz + '79317eeef634c99aac7f4a393d2c6e7934f48ec31e934570faf963de6b9184b9', # easybuild-easyblocks-4.5.0.tar.gz + 'f75d08466d0692f134ca77390f63445b432af9955b2039205de8b57018edd9b6', # easybuild-easyconfigs-4.5.0.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From ba50bada5b000d3a780e00407b56b03d93ef9fab Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 29 Oct 2021 15:16:04 +0200 Subject: [PATCH 1726/9987] adding nnunet --- .../n/nnUNet/nnUNet-1.7.0-foss-2020b.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/n/nnUNet/nnUNet-1.7.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/nnUNet/nnUNet-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/n/nnUNet/nnUNet-1.7.0-foss-2020b.eb new file mode 100644 index 00000000000..e101b0f98ed --- /dev/null +++ b/easybuild/easyconfigs/n/nnUNet/nnUNet-1.7.0-foss-2020b.eb @@ -0,0 +1,79 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'nnUNet' +version = '1.7.0' + +homepage = 'https://github.com/MIC-DKFZ/nnUNet' +description = """ +nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found in the domain. +It condenses and automates the keys decisions for designing a successful segmentation pipeline for any given dataset. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('Bazel', '3.7.2') +] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), + ('dicom2nifti', '2.3.0'), + ('scikit-image', '0.18.1'), + ('TensorFlow', '2.5.0'), + ('SciPy-bundle', '2020.11'), + ('batchgenerators', '0.23'), + ('scikit-learn', '0.23.2'), + ('requests', '2.26.0'), + ('NiBabel', '3.2.1'), + ('SimpleITK', '2.1.0'), + ('tifffile', '2021.8.30'), + ('MedPy', '0.4.0'), + ('jax', '0.2.19') +] + +# sklearn is incorrect package name +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('absl-py', '0.15.0', { + 'modulename': 'absl', + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + }), + ('immutabledict', '2.1.0', { + }), + ('ml_collections', '0.1.0', { + # see https://github.com/google/ml_collections/issues/7 + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + }), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['nnUNet_train --help'] + +moduleclass = 'data' From 2994e243d90ca10442aea1409d8cb135ae643fbd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Oct 2021 16:18:18 +0200 Subject: [PATCH 1727/9987] bump version to 4.5.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 4f84a88acbf..774905ff74d 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.0' +VERSION = '4.5.1.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From cb820905cac5fb25b66c39dcce3bb87db41aad04 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 29 Oct 2021 17:50:34 +0200 Subject: [PATCH 1728/9987] Use Autotools instead of Autoconf+Automake+libtool+M4 --- .../Virtuoso-opensource-7.2.6.1-foss-2021a.eb | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-foss-2021a.eb b/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-foss-2021a.eb index d5337dc0432..24f7f645124 100644 --- a/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-foss-2021a.eb @@ -22,14 +22,10 @@ source_urls = ['https://github.com/openlink/virtuoso-opensource/archive/refs/tag checksums = ['73dc3d0073d3d5694da075063b75a404649c027a1f5c635a25ede52713ff7942'] builddependencies = [ - ('Autoconf', '2.71'), - ('Automake', '1.16.3'), - ('libtool', '2.4.6'), - ('flex', '2.6.4'), - ('Bison', '3.7.6'), - ('gperf', '3.1'), - ('M4', '1.4.18'), - ('make', '4.3'), + ('Autotools', '20210128'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('gperf', '3.1'), ] osdependencies = ['gawk'] From acf5929e89657b1122e24dd901b0368c6a110c29 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 29 Oct 2021 18:06:47 +0200 Subject: [PATCH 1729/9987] Update patch file name + Add comments there --- easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb | 4 ++-- .../{InChI-1.06.patch => InChI-1.06_fedora-build-fixes.patch} | 3 +++ 2 files changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/i/InChI/{InChI-1.06.patch => InChI-1.06_fedora-build-fixes.patch} (94%) diff --git a/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb index e7ce6ad45b0..5082af09587 100644 --- a/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb @@ -33,11 +33,11 @@ sources = [ {'download_filename': 'INCHI-1-SRC.zip', 'filename': 'INCHI-%(version)s-SRC.zip'}, {'download_filename': 'INCHI-1-TEST.zip', 'filename': 'INCHI-%(version)s-TEST.zip'}, ] -patches = ['InChI-%(version)s.patch'] +patches = ['InChI-%(version)s_fedora-build-fixes.patch'] checksums = [ '4874e310c0f2f81b881e90dd0c534752e1b9421d7d92ccfb037710022c7e7efd', # INCHI-1-SRC.zip '3c870ef97c8ebc86f64946db395582b87d79732000fa73d173f46c05ca19c1ff', # INCHI-1-TEST.zip - 'a614c5310188d1f0397c6a3469795f60c3162b1bac531ad1a485ec195ad28f5a', # InChI-1.06.patch + '98acd66e46d3c5c2c3b1531e9c84e129b503e23d3a7602f3f64f37c74e420840', # InChI-1.06_fedora-build-fixes.patch ] diff --git a/easybuild/easyconfigs/i/InChI/InChI-1.06.patch b/easybuild/easyconfigs/i/InChI/InChI-1.06_fedora-build-fixes.patch similarity index 94% rename from easybuild/easyconfigs/i/InChI/InChI-1.06.patch rename to easybuild/easyconfigs/i/InChI/InChI-1.06_fedora-build-fixes.patch index cbc0e67159a..d1c2c06f960 100644 --- a/easybuild/easyconfigs/i/InChI/InChI-1.06.patch +++ b/easybuild/easyconfigs/i/InChI/InChI-1.06_fedora-build-fixes.patch @@ -1,3 +1,6 @@ +Patch made by Fedora to fix program name, linker and compilation options +https://src.fedoraproject.org/rpms/inchi/blob/rawhide/f/inchi-rpm.patch + diff -up INCHI-1-SRC/INCHI_API/demos/inchi_main/gcc/makefile.r INCHI-1-SRC/INCHI_API/demos/inchi_main/gcc/makefile --- INCHI-1-SRC/INCHI_API/demos/inchi_main/gcc/makefile.r 2019-06-22 20:25:28.000000000 +0200 +++ INCHI-1-SRC/INCHI_API/demos/inchi_main/gcc/makefile 2020-10-13 14:18:22.809829859 +0200 From ce5cfe3cc8441bdb206009b1acc83e73ee78a840 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Oct 2021 20:36:12 +0200 Subject: [PATCH 1730/9987] adding easyconfigs: mold-0.9.6-GCCcore-11.2.0.eb, xxHash-0.8.0-GCCcore-11.2.0.eb --- .../m/mold/mold-0.9.6-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ .../x/xxHash/xxHash-0.8.0-GCCcore-11.2.0.eb | 31 +++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/xxHash/xxHash-0.8.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1b0b1af41f3 --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'mold' +version = '0.9.6' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['348e1b893d3520322b1e047b5abf040e56ad92de5643e67652ede87b9d694f60'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] +dependencies = [ + ('xxHash', '0.8.0'), + ('zlib', '1.2.11'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xxHash/xxHash-0.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..db5bf12cc24 --- /dev/null +++ b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.0-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'xxHash' +version = '0.8.0' + +homepage = 'https://cyan4973.github.io/xxHash' +description = "xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/Cyan4973/xxHash/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7054c3ebd169c97b64a92d7b994ab63c70dd53a06974f1f630ab782c28db0f4f'] + +builddependencies = [ + ('binutils', '2.37'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/xxhsum', 'include/xxh3.h', 'include/xxhash.h', + 'lib/libxxhash.a', 'lib/libxxhash.%s' % SHLIB_EXT, 'lib/pkgconfig/libxxhash.pc'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["xxhsum --help"] + +moduleclass = 'tools' From 89b9d8066c4e54b9449f3cc97e9734246d45e3ff Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 29 Oct 2021 21:47:55 +0200 Subject: [PATCH 1731/9987] adding easyconfigs: DFTB+-21.1-intel-2021a.eb and patches: DFTB+-21.1_drop_intel_failing_tests.patch, DFTB+-21.1_fix_intel_omp_linking.patch, DFTB+-21.1_use_dftd3_from_EB.patch --- .../d/DFTB+/DFTB+-21.1-intel-2021a.eb | 82 +++++++++++++++++++ .../DFTB+-21.1_drop_intel_failing_tests.patch | 15 ++++ .../DFTB+-21.1_fix_intel_omp_linking.patch | 15 ++++ .../DFTB+/DFTB+-21.1_use_dftd3_from_EB.patch | 9 ++ .../dftd3-lib-0.9-intel-compilers-2021.2.0.eb | 39 +++++++++ 5 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb create mode 100644 easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_drop_intel_failing_tests.patch create mode 100644 easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_fix_intel_omp_linking.patch create mode 100644 easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_use_dftd3_from_EB.patch create mode 100644 easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb new file mode 100644 index 00000000000..eb347b1d599 --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb @@ -0,0 +1,82 @@ +easyblock = 'CMakeMake' + +name = 'DFTB+' +version = '21.1' + +homepage = 'https://www.dftb-plus.info' +description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. +It is based on the Density Functional Tight Binding (DFTB) method, containing +almost all of the useful extensions which have been developed for the DFTB +framework so far. Using DFTB+ you can carry out quantum mechanical simulations +like with ab-initio density functional theory based packages, but in an +approximate way gaining typically around two order of magnitude in speed.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True, 'extra_fflags': '-I$(EBROOTDFTD3MINLIB)/include'} + +local_external_dir = '%%(builddir)s/dftbplus-%%(version)s/external/%s/origin/' +local_external_extract = 'mkdir -p %s && tar -C %s' % (local_external_dir, local_external_dir) +local_external_extract += ' --strip-components=1 -xzf %%s' + +source_urls = ['https://github.com/dftbplus/dftbplus/releases/download/%(version)s'] +sources = [ + 'dftbplus-%(version)s.tar.xz', + { + # Slater-Koster (slakos) data for testing + 'source_urls': ['https://github.com/dftbplus/testparams/archive'], + 'download_filename': '26439495c4b5b0d07be6ceec4dade3d149425465.tar.gz', + 'filename': 'slakos-data-%(version)s.tar.gz', + 'extract_cmd': local_external_extract % ('slakos', 'slakos'), + }, + { + # GBSA (gbsa) data for testing + 'source_urls': ['https://github.com/grimme-lab/gbsa-parameters/archive'], + 'download_filename': '6836c4d997e4135e418cfbe273c96b1a3adb13e2.tar.gz', + 'filename': 'gbsa-data-%(version)s.tar.gz', + 'extract_cmd': local_external_extract % ('gbsa', 'gbsa'), + }, +] +patches = [ + '%(name)s-%(version)s_use_dftd3_from_EB.patch', + '%(name)s-%(version)s_fix_intel_omp_linking.patch', + '%(name)s-%(version)s_drop_intel_failing_tests.patch', +] +checksums = [ + '8c1eb8a38f72c421e2ae20118a6db3a656fa84e8b180ef387e549a73ae77f970', # dftbplus-21.1.tar.xz + '6f65da7b64ef255fd777de7a972c63f7fa8ed2041442823b2c601bc8f0e55d98', # slakos-data-21.1.tar.gz + 'd464f9f7b1883d1353b433d0c7eae2f5606af092d9b51d38e9ed15e072610a79', # gbsa-data-21.1.tar.gz + 'fae75d62ce95922e071441bc73dccc0569ae467edbb46774180ae6cdde59cb92', # DFTB+-21.1_use_dftd3_from_EB.patch + 'e922b0d9360d342190c4496173f938c2cb89f0bd0499b2f71abcaf70dc8e5fe1', # DFTB+-21.1_fix_intel_omp_linking.patch + '30408d27e03dd2ac0bc1156ba8998d3ce735f340e5edb9ac9f5c059515593863', # DFTB+-21.1_drop_intel_failing_tests.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('dftd3-lib', '0.9'), + ('ELSI', '2.7.1', '-PEXSI'), +] + + +build_shared_libs = True + +configopts = '-DWITH_MPI=1 -DWITH_DFTD3=1 -DWITH_ELSI=1 -DWITH_MBD=1 -DWITH_UNIT_TESTS=1 -DSCALAPACK_LIBRARY="$LIBSCALAPACK" ' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['dftb+', 'dp_bands', 'dp_dos', 'gen2cif', 'gen2xyz', 'makecube', + 'modes', 'repeatgen', 'straingen', 'waveplot', 'xyz2gen']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [('python', '-c "import dptools"')] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_drop_intel_failing_tests.patch b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_drop_intel_failing_tests.patch new file mode 100644 index 00000000000..1c7fa4495d6 --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_drop_intel_failing_tests.patch @@ -0,0 +1,15 @@ +Drop tests that fail with Intel + +Åke Sandgren, 20211025 +diff -ru dftbplus-21.1.orig/test/prog/dftb+/tests dftbplus-21.1/test/prog/dftb+/tests +--- dftbplus-21.1.orig/test/prog/dftb+/tests 2021-05-12 20:23:51.000000000 +0200 ++++ dftbplus-21.1/test/prog/dftb+/tests 2021-10-25 16:50:14.035199535 +0200 +@@ -109,7 +109,7 @@ + solvers/ice_NTPoly #? WITH_ELSI and MPI_PROCS <= 4 and OMP_THREADS == 1 + solvers/Si32C32_OMM #? WITH_ELSI and MPI_PROCS <= 4 and OMP_THREADS == 1 + solvers/Si32C32_OMM_sparse #? WITH_ELSI and MPI_PROCS <= 4 and OMP_THREADS == 1 +-solvers/Si384_OMM #? WITH_ELSI and MPI_PROCS <= 4 and OMP_THREADS == 1 ++# solvers/Si384_OMM #? WITH_ELSI and MPI_PROCS <= 4 and OMP_THREADS == 1 + solvers/Si32C32_OMM_kpoints #? WITH_ELSI and MPI_PROCS % 4 == 0 and MPI_PROCS <= 20 and OMP_THREADS == 1 + solvers/Si32C32_OMM_ks #? WITH_ELSI and MPI_PROCS % 8 == 0 and MPI_PROCS <= 40 and OMP_THREADS == 1 + solvers/Si32C32_OMM_k_sparse #? WITH_ELSI and MPI_PROCS % 4 == 0 and MPI_PROCS <= 20 and OMP_THREADS == 1 diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_fix_intel_omp_linking.patch b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_fix_intel_omp_linking.patch new file mode 100644 index 00000000000..6c99d962d5a --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_fix_intel_omp_linking.patch @@ -0,0 +1,15 @@ +Need to have -qopenmp when linking with Intel and not just when compiling. + +Åke Sandgren, 20211025 +diff -ru dftbplus-21.1.orig/CMakeLists.txt dftbplus-21.1/CMakeLists.txt +--- dftbplus-21.1.orig/CMakeLists.txt 2021-05-12 20:23:51.000000000 +0200 ++++ dftbplus-21.1/CMakeLists.txt 2021-10-25 15:11:38.797426208 +0200 +@@ -45,6 +45,8 @@ + if("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "NAG" AND WITH_OMP) + set_property(TARGET OpenMP::OpenMP_Fortran PROPERTY INTERFACE_LINK_LIBRARIES "") + set_property(TARGET OpenMP::OpenMP_Fortran PROPERTY INTERFACE_LINK_OPTIONS "-openmp") ++ elseif("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "Intel" AND WITH_OMP) ++ set_property(TARGET OpenMP::OpenMP_Fortran PROPERTY INTERFACE_LINK_OPTIONS "-qopenmp") + endif() + endif() + diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_use_dftd3_from_EB.patch b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_use_dftd3_from_EB.patch new file mode 100644 index 00000000000..147698da7c3 --- /dev/null +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_use_dftd3_from_EB.patch @@ -0,0 +1,9 @@ +diff -ru dftbplus-21.1.orig/external/dftd3/CMakeLists.txt dftbplus-21.1/external/dftd3/CMakeLists.txt +--- dftbplus-21.1.orig/external/dftd3/CMakeLists.txt 2021-05-12 20:23:51.000000000 +0200 ++++ dftbplus-21.1/external/dftd3/CMakeLists.txt 2021-10-20 08:40:05.364957330 +0200 +@@ -1,4 +1,4 @@ + set(LIBRARY_ONLY TRUE) + set(INSTALL_EXPORT_NAME dftbplus-targets) +-add_subdirectory(origin) ++#add_subdirectory(origin) + set(EXPORTED_COMPILED_LIBRARIES ${EXPORTED_COMPILED_LIBRARIES} dftd3 PARENT_SCOPE) diff --git a/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..42eda3849ee --- /dev/null +++ b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'dftd3-lib' +version = '0.9' + +homepage = 'https://github.com/dftbplus/dftd3-lib' +description = """This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. +The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been +converted to free format and encapsulated into modules.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} +toolchainopts = {'pic': True} + +github_account = 'dftbplus' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['dftd3-lib-%(version)s_fix-extras-syntax.patch'] +checksums = [ + '0a015659b5179dff1728a109c3e9b095e6bccc5704de9239aa3844008a9a82df', # 0.9.tar.gz + '717e719170258544555bfc33390a70c2573d971c6548d8f2c951a5606ec77f74', # dftd3-lib-0.9_fix-extras-syntax.patch +] + +parallel = 1 + +buildopts = 'FC="$FC" LN="$FC" FCFLAGS="$FCFLAGS" LNFLAGS="$LDFLAGS"' + +files_to_copy = [ + (['prg/dftd3', 'test/testapi'], 'bin'), + (['lib/libdftd3.a'], 'lib'), + (['lib/*.mod', 'prg/*.mod'], 'include'), + (['doc/man.pdf', 'CHANGELOG.rst', 'LICENSE', 'README.rst'], 'share'), +] + +sanity_check_paths = { + 'files': ['bin/dftd3', 'bin/testapi', 'lib/libdftd3.a'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'chem' From 3c28ac63ef839b904fad68198f1e10cbf2368dde Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 30 Oct 2021 10:15:41 +0200 Subject: [PATCH 1732/9987] Fix long line and the drop_intel_failing_tests patch. --- easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb | 5 +++-- .../d/DFTB+/DFTB+-21.1_drop_intel_failing_tests.patch | 3 +-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb index eb347b1d599..3287ce7a38d 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb @@ -47,7 +47,7 @@ checksums = [ 'd464f9f7b1883d1353b433d0c7eae2f5606af092d9b51d38e9ed15e072610a79', # gbsa-data-21.1.tar.gz 'fae75d62ce95922e071441bc73dccc0569ae467edbb46774180ae6cdde59cb92', # DFTB+-21.1_use_dftd3_from_EB.patch 'e922b0d9360d342190c4496173f938c2cb89f0bd0499b2f71abcaf70dc8e5fe1', # DFTB+-21.1_fix_intel_omp_linking.patch - '30408d27e03dd2ac0bc1156ba8998d3ce735f340e5edb9ac9f5c059515593863', # DFTB+-21.1_drop_intel_failing_tests.patch + 'f0c0e248d567739010897e7a46e471b1e332568bb0f9c1c06fd1e762d3f81aa4', # DFTB+-21.1_drop_intel_failing_tests.patch ] builddependencies = [ @@ -65,7 +65,8 @@ dependencies = [ build_shared_libs = True -configopts = '-DWITH_MPI=1 -DWITH_DFTD3=1 -DWITH_ELSI=1 -DWITH_MBD=1 -DWITH_UNIT_TESTS=1 -DSCALAPACK_LIBRARY="$LIBSCALAPACK" ' +configopts = '-DWITH_MPI=1 -DWITH_DFTD3=1 -DWITH_ELSI=1 -DWITH_MBD=1 -DWITH_UNIT_TESTS=1 ' +configopts += '-DSCALAPACK_LIBRARY="$LIBSCALAPACK" ' runtest = 'test' diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_drop_intel_failing_tests.patch b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_drop_intel_failing_tests.patch index 1c7fa4495d6..1de2a00c631 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_drop_intel_failing_tests.patch +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_drop_intel_failing_tests.patch @@ -4,12 +4,11 @@ Drop tests that fail with Intel diff -ru dftbplus-21.1.orig/test/prog/dftb+/tests dftbplus-21.1/test/prog/dftb+/tests --- dftbplus-21.1.orig/test/prog/dftb+/tests 2021-05-12 20:23:51.000000000 +0200 +++ dftbplus-21.1/test/prog/dftb+/tests 2021-10-25 16:50:14.035199535 +0200 -@@ -109,7 +109,7 @@ +@@ -109,7 +109,6 @@ solvers/ice_NTPoly #? WITH_ELSI and MPI_PROCS <= 4 and OMP_THREADS == 1 solvers/Si32C32_OMM #? WITH_ELSI and MPI_PROCS <= 4 and OMP_THREADS == 1 solvers/Si32C32_OMM_sparse #? WITH_ELSI and MPI_PROCS <= 4 and OMP_THREADS == 1 -solvers/Si384_OMM #? WITH_ELSI and MPI_PROCS <= 4 and OMP_THREADS == 1 -+# solvers/Si384_OMM #? WITH_ELSI and MPI_PROCS <= 4 and OMP_THREADS == 1 solvers/Si32C32_OMM_kpoints #? WITH_ELSI and MPI_PROCS % 4 == 0 and MPI_PROCS <= 20 and OMP_THREADS == 1 solvers/Si32C32_OMM_ks #? WITH_ELSI and MPI_PROCS % 8 == 0 and MPI_PROCS <= 40 and OMP_THREADS == 1 solvers/Si32C32_OMM_k_sparse #? WITH_ELSI and MPI_PROCS % 4 == 0 and MPI_PROCS <= 20 and OMP_THREADS == 1 From 630f5c54dee55b14a2744de9075a8be24d853951 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 17:04:36 +0200 Subject: [PATCH 1733/9987] adding easyconfigs: SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb --- ...0.2.0-20210620-foss-2020b-Python-2.7.18.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb new file mode 100644 index 00000000000..861f11bb8cc --- /dev/null +++ b/easybuild/easyconfigs/s/SRST2/SRST2-0.2.0-20210620-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonPackage' + +name = 'SRST2' +local_commit = '73f885f' +version = '0.2.0-20210620' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://katholt.github.io/srst2' +description = "Short Read Sequence Typing for Bacterial Pathogens" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/katholt/srst2/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['04b383bae7450b89945053fbd1945ecf7234a78cfd374f90c7ef427d84571d20'] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', versionsuffix), + ('Bowtie2', '2.4.2'), + ('SAMtools', '1.11'), +] + +download_dep_fail = True +use_pip = True + +# inject Bowtie2/SAMtools version in scripts that check for known version +preinstallopts = """sed -i "s@,'2.2.9'@,'2.2.9', '$EBVERSIONBOWTIE2'@g" scripts/qsub_srst2.py && """ +preinstallopts += """sed -i "s@,'2.2.9'@,'2.2.9', '$EBVERSIONBOWTIE2'@g" scripts/slurm_srst2.py && """ +preinstallopts += """sed -i "s@,'2.2.9'@,'2.2.9', '$EBVERSIONBOWTIE2'@g" scripts/srst2.py && """ +preinstallopts += """sed -i "s@'0.1.18',@'$EBVERSIONSAMTOOLS', '0.1.18',@g" scripts/qsub_srst2.py && """ +preinstallopts += """sed -i "s@'0.1.18',@'$EBVERSIONSAMTOOLS', '0.1.18',@g" scripts/slurm_srst2.py && """ +preinstallopts += """sed -i "s@'0.1.18',@'$EBVERSIONSAMTOOLS', '0.1.18',@g" scripts/srst2.py && """ + +fix_python_shebang_for = ['bin/*.py'] + +postinstallcmds = ["cp -a data %(installdir)s"] + +sanity_check_paths = { + 'files': ['bin/getmlst.py', 'bin/slurm_srst2.py', 'bin/srst2'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "srst2 --version", + "getmlst.py -h", + "slurm_srst2.py -h", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 55a67f3b29481020d3b8770d4685279615fb4520 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 17:31:12 +0200 Subject: [PATCH 1734/9987] adding easyconfigs: Megalodon-2.3.5-foss-2020b.eb --- .../m/Megalodon/Megalodon-2.3.5-foss-2020b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb new file mode 100644 index 00000000000..b4801f257c9 --- /dev/null +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'Megalodon' +version = '2.3.5' + +homepage = 'https://github.com/nanoporetech/megalodon' +description = """Megalodon is a research command line tool to extract high accuracy modified base and sequence variant +calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference +genome/transriptome.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('scikit-learn', '0.23.2'), + ('tqdm', '4.60.0'), + ('Pysam', '0.16.0.1'), + ('Seaborn', '0.11.1'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + ('ont-fast5-api', '4.0.0', { + 'checksums': ['a249813104439bfe3d4e346bb560756e23217655273410c60b9bade205eb3e66'], + }), + ('mappy', '2.22', { + 'checksums': ['219c93ab7f8d5d7c26face512a9e738a7306f3376ebfa3017eac70676ba97840'], + }), + ('ont_pyguppy_client_lib', '5.0.16', { + 'modulename': 'pyguppy_client_lib', + 'sources': ['ont_pyguppy_client_lib-%(version)s-cp38-cp38-manylinux2010_x86_64.whl'], + 'checksums': ['6e89cccb2d3943ee5d6e9a6cd55e1cc8700656201d1a411b638919560bbb0772'], + }), + ('megalodon', version, { + 'checksums': ['0ae6c6dcaf599f98ca421d1f4df616cf0a4cf3436b305553220a479dc41f3426'], + }), +] + +sanity_check_paths = { + 'files': ['bin/megalodon'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "megalodon -h", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 400d0b82fb16c892986eee136508d0be512875bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 17:47:29 +0200 Subject: [PATCH 1735/9987] adding easyconfigs: SciPy-bundle-2021.10-intel-2021b.eb --- .../SciPy-bundle-2021.10-intel-2021b.eb | 84 +++++++++++++++++++ 1 file changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb new file mode 100644 index 00000000000..737e076e2ed --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-intel-2021b.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2021.10' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.14.6'), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('pybind11', '2.7.1'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.21.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'patches': [ + 'numpy-1.18.2-mkl.patch', + 'numpy-1.20.3_disable-broken-override-test.patch', + 'numpy-1.20.3_disable_fortran_callback_test.patch', + ], + 'checksums': [ + '63571bb7897a584ca3249c86dd01c10bcb5fe4296e3568b2e9c1a55356b6410e', # numpy-1.21.3.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + # numpy-1.20.3_disable-broken-override-test.patch + '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', + # numpy-1.20.3_disable_fortran_callback_test.patch + '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.2', { + 'checksums': ['f81fcefa8b982624a31c9e4ec7761325a88a0eba60d36d1da90e47f8fe3c67f7'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.10.0', { + 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], + }), + ('scipy', '1.7.1', { + 'checksums': ['6b47d5fa7ea651054362561a28b1ccc8da9368a39514c1bbf6c0977a1c376764'], + # compilation with Pythran enabled fails when using Intel compilers, + # see https://github.com/scipy/scipy/issues/14935 + 'prebuildopts': "export SCIPY_USE_PYTHRAN=0 && ", + 'preinstallopts': "export SCIPY_USE_PYTHRAN=0 && ", + }), + ('mpi4py', '3.1.1', { + 'checksums': ['e11f8587a3b93bb24c8526addec664b586b965d83c0882b884c14dc3fd6b9f5c'], + }), + ('numexpr', '2.7.3', { + 'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '1.3.4', { + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'checksums': ['a2aa18d3f0b7d538e21932f637fbfe8518d085238b429e4790a35e1e44a96ffc'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 0e0a3cf440b26f8d7a9e3d30f33dd7984a0baa70 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 17:56:13 +0200 Subject: [PATCH 1736/9987] stick to tqdm 4.56.2 dependency in Megalodon easyconfig using foss/2020b toolchain --- easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb index b4801f257c9..f71e6ef6e2a 100644 --- a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-foss-2020b.eb @@ -15,7 +15,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('h5py', '3.1.0'), ('scikit-learn', '0.23.2'), - ('tqdm', '4.60.0'), + ('tqdm', '4.56.2'), ('Pysam', '0.16.0.1'), ('Seaborn', '0.11.1'), ] From 568b9b935492f2a0f79febf3f3bba1628b3f82ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 18:00:50 +0200 Subject: [PATCH 1737/9987] adding easyconfigs: Megalodon-2.3.5-fosscuda-2020b.eb --- .../Megalodon-2.3.5-fosscuda-2020b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb new file mode 100644 index 00000000000..05615980011 --- /dev/null +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.3.5-fosscuda-2020b.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'Megalodon' +version = '2.3.5' + +homepage = 'https://github.com/nanoporetech/megalodon' +description = """Megalodon is a research command line tool to extract high accuracy modified base and sequence variant +calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference +genome/transriptome.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('scikit-learn', '0.23.2'), + ('tqdm', '4.56.2'), + ('Pysam', '0.16.0.1'), + ('Seaborn', '0.11.1'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + ('ont-fast5-api', '4.0.0', { + 'checksums': ['a249813104439bfe3d4e346bb560756e23217655273410c60b9bade205eb3e66'], + }), + ('mappy', '2.22', { + 'checksums': ['219c93ab7f8d5d7c26face512a9e738a7306f3376ebfa3017eac70676ba97840'], + }), + ('ont_pyguppy_client_lib', '5.0.16', { + 'modulename': 'pyguppy_client_lib', + 'sources': ['ont_pyguppy_client_lib-%(version)s-cp38-cp38-manylinux2010_x86_64.whl'], + 'checksums': ['6e89cccb2d3943ee5d6e9a6cd55e1cc8700656201d1a411b638919560bbb0772'], + }), + ('megalodon', version, { + 'checksums': ['0ae6c6dcaf599f98ca421d1f4df616cf0a4cf3436b305553220a479dc41f3426'], + }), +] + +sanity_check_paths = { + 'files': ['bin/megalodon'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "megalodon -h", +] + +sanity_pip_check = True + +moduleclass = 'bio' From d811461babed94c8d1f0f34227c17e49d7cd35a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 18:39:47 +0200 Subject: [PATCH 1738/9987] adding easyconfigs: SimNIBS-3.2.4-foss-2020b.eb, FMM3D-20211018-foss-2020b.eb --- .../f/FMM3D/FMM3D-20211018-foss-2020b.eb | 45 +++++++++++++++++++ .../s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb | 41 +++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb b/easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb new file mode 100644 index 00000000000..32ce0d7089d --- /dev/null +++ b/easybuild/easyconfigs/f/FMM3D/FMM3D-20211018-foss-2020b.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'FMM3D' +local_commit = '7ba20d6' +version = '20211018' + +homepage = 'https://fmm3d.readthedocs.io' +description = """Flatiron Institute Fast Multipole Libraries: a set of libraries to compute N-body +interactions governed by the Laplace and Helmholtz equations, to a specified precision, in three dimensions, on a +multi-core shared-memory machine.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/flatironinstitute/FMM3D/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['e6cd07f2a31159ce41705a117771a0bab819b192075e24a28b0cf8c5ca9f5ba5'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +skipsteps = ['configure', 'build'] + +installopts = 'FAST_KER=ON PREFIX="%(installdir)s/lib" && ' +installopts += 'export FMM_FLIBS="%(installdir)s/lib/libfmm3d.a $FFLAGS" && ' +# also install Python bindings +installopts += "make python-dist && pip install --no-deps --ignore-installed --prefix %(installdir)s python/dist/*.whl" + +sanity_check_paths = { + 'files': ['lib/libfmm3d.a', 'lib/libfmm3d.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cd %(builddir)s/FMM3D-* && make test", + "python -c 'import fmm3dpy'", + "cd %(builddir)s/FMM3D-* && python python/test/test_hfmm.py", + "cd %(builddir)s/FMM3D-* && python python/test/test_lfmm.py", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb b/easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb new file mode 100644 index 00000000000..88e82bb5784 --- /dev/null +++ b/easybuild/easyconfigs/s/SimNIBS/SimNIBS-3.2.4-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'SimNIBS' +version = '3.2.4' + +homepage = 'https://simnibs.github.io/simnibs' +description = "SimNIBS is a free and open source software package for the Simulation of Non-invasive Brain Stimulation." + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('h5py', '3.1.0'), + ('NiBabel', '3.2.1'), + ('FMM3D', '20211018'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/simnibs/simnibs/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['ad4482b4cdd306d4356757b4d065d844ea698dab2530aa09fb59219d2a982219'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/headreco', 'bin/simnibs'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "headreco --help", + "simnibs --help", +] + +moduleclass = 'bio' From 7cb03095b3428ad93768758ea15d3775c356fbee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 20:37:20 +0200 Subject: [PATCH 1739/9987] add custom preinstallopts for installing Flye 2.9 on aarch64 --- easybuild/easyconfigs/f/Flye/Flye-2.9-GCC-10.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9-GCC-10.3.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9-GCC-10.3.0.eb index f0570a67005..f56d88a8df4 100644 --- a/easybuild/easyconfigs/f/Flye/Flye-2.9-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9-GCC-10.3.0.eb @@ -18,6 +18,9 @@ dependencies = [('Python', '3.9.5')] download_dep_fail = True use_pip = True +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + sanity_check_paths = { 'files': ['bin/flye'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From d53b7a2402b21c1c143f88dad52c13b5bc48b3d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Oct 2021 22:24:27 +0200 Subject: [PATCH 1740/9987] add RcisTarget extension to R-bundle-Bioconductor 3.13 --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index c0a68c827e5..779e683a26d 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -1053,6 +1053,15 @@ exts_list = [ ('JASPAR2020', '0.99.10', { 'checksums': ['b9b92d141a317ebb32a14708229f6b82522ceeb5f1b88360d93b0a7cfe30375b'], }), + ('AUCell', '1.14.0', { + 'checksums': ['5936a7b33d7afb144e4bcfb99bece7de51d01063804c9032107132aaf060aa61'], + }), + ('arrow', '6.0.0.2', { + 'checksums': ['76808692851eca33ff7ea9532b143db4698689081ce2f8cfe53c3e9e0aee1184'], + }), + ('RcisTarget', '1.12.0', { + 'checksums': ['eef8c2e328b4b10951fad9174786ff6228455845ecdda5bfc98f6abb43a000fa'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From a14cd8170ada60a5a5b1aef0e21df54f21ed5c45 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 10:30:53 +0100 Subject: [PATCH 1741/9987] fix name of source files for InChI 1.06 in checksum comments + trivial style fixes --- .../easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb index 5082af09587..993226a6638 100644 --- a/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb @@ -35,12 +35,11 @@ sources = [ ] patches = ['InChI-%(version)s_fedora-build-fixes.patch'] checksums = [ - '4874e310c0f2f81b881e90dd0c534752e1b9421d7d92ccfb037710022c7e7efd', # INCHI-1-SRC.zip - '3c870ef97c8ebc86f64946db395582b87d79732000fa73d173f46c05ca19c1ff', # INCHI-1-TEST.zip + '4874e310c0f2f81b881e90dd0c534752e1b9421d7d92ccfb037710022c7e7efd', # INCHI-1.06-SRC.zip + '3c870ef97c8ebc86f64946db395582b87d79732000fa73d173f46c05ca19c1ff', # INCHI-1.06-TEST.zip '98acd66e46d3c5c2c3b1531e9c84e129b503e23d3a7602f3f64f37c74e420840', # InChI-1.06_fedora-build-fixes.patch ] - # dos2unix may be another builddependency useful to "clean" some files builddependencies = [ ('make', '4.3'), @@ -55,7 +54,6 @@ build_cmd += 'LINKER_OPTIONS="$OPTFLAGS" ' build_cmd += 'OPTFLAGS="$OPTFLAGS -Wno-comment -Wno-parentheses -Wno-unused -Wno-unused-but-set-variable" ' build_cmd += 'make' - files_to_copy = [ (['INCHI_EXE/bin/Linux/inchi-1'], 'bin'), (['INCHI_API/bin/Linux/libinchi.so*'], 'lib'), @@ -67,11 +65,10 @@ files_to_copy = [ # NOTE libinchi.so are not symlinks in the final build, but redundant copies! # NOTE `keepsymlinks = True` does not look to do it, so use this trick postinstallcmds = ["cd %(installdir)s/lib/ && rm -f libinchi.so.1 && " - "ln -s libinchi.so.1.* libinchi.so.1 && ln -s libinchi.so.1 libinchi.so"] - + "ln -s libinchi.so.1.* libinchi.so.1 && ln -s libinchi.so.1 libinchi.%s" % SHLIB_EXT] sanity_check_paths = { - 'files': ["bin/inchi-1", "lib/libinchi.so", "LICENCE.pdf", "readme.txt"], + 'files': ['bin/inchi-1', 'lib/libinchi.%s' % SHLIB_EXT, 'LICENCE.pdf', 'readme.txt'], 'dirs': ['lib', 'include'] } From 55e6edf69f9935bf7b646fa203a03bee1cbafd20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 10:32:15 +0100 Subject: [PATCH 1742/9987] fix typo in postinstallcmds for InChI 1.06 --- easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb index 993226a6638..c0333eda150 100644 --- a/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/i/InChI/InChI-1.06-GCC-10.3.0.eb @@ -64,7 +64,7 @@ files_to_copy = [ # NOTE libinchi.so are not symlinks in the final build, but redundant copies! # NOTE `keepsymlinks = True` does not look to do it, so use this trick -postinstallcmds = ["cd %(installdir)s/lib/ && rm -f libinchi.so.1 && " +postinstallcmds = ["cd %%(installdir)s/lib/ && rm -f libinchi.so.1 && " "ln -s libinchi.so.1.* libinchi.so.1 && ln -s libinchi.so.1 libinchi.%s" % SHLIB_EXT] sanity_check_paths = { From 32c422115554f295705e7ed097a1488b0d38551d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 12:30:25 +0100 Subject: [PATCH 1743/9987] use proper dependency for 'arrow' R library in R-bundle-Bioconductor 3.13 easyconfig --- .../a/Arrow/Arrow-6.0.0-foss-2021a.eb | 59 +++++++++++++++++++ .../arrow/arrow-6.0.0.2-foss-2021a-R-4.1.0.eb | 32 ++++++++++ ...le-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 4 +- 3 files changed, 92 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/a/arrow/arrow-6.0.0.2-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb new file mode 100644 index 00000000000..4c85336424f --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '6.0.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['69d268f9e82d3ebef595ad1bdc83d4cb02b20c181946a68631f6645d7c1f7a90'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Autotools', '20210128'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('pkg-config', '0.29.2'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy + ('Boost', '1.76.0'), +] + +separate_build_dir = True +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/python/development.html +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/arrow/arrow-6.0.0.2-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/a/arrow/arrow-6.0.0.2-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..8ca79314cf4 --- /dev/null +++ b/easybuild/easyconfigs/a/arrow/arrow-6.0.0.2-foss-2021a-R-4.1.0.eb @@ -0,0 +1,32 @@ +easyblock = 'RPackage' + +name = 'arrow' +version = '6.0.0.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/arrow' +description = "R interface to the Apache Arrow C++ library" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['arrow_%(version)s.tar.gz'] +checksums = ['76808692851eca33ff7ea9532b143db4698689081ce2f8cfe53c3e9e0aee1184'] + +dependencies = [ + ('R', '4.1.0'), + ('Arrow', '6.0.0'), +] + +preinstallopts = "export LIBARROW_BINARY=true && " + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index 779e683a26d..2b6566d124c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('GSL', '2.7'), # for flowClust ('HDF5', '1.10.7'), # for rhdf5 ('ncdf4', '1.17', versionsuffix), # for mzR + ('arrow', '6.0.0.2', versionsuffix), # required by RcisTarget ] exts_default_options = { @@ -1056,9 +1057,6 @@ exts_list = [ ('AUCell', '1.14.0', { 'checksums': ['5936a7b33d7afb144e4bcfb99bece7de51d01063804c9032107132aaf060aa61'], }), - ('arrow', '6.0.0.2', { - 'checksums': ['76808692851eca33ff7ea9532b143db4698689081ce2f8cfe53c3e9e0aee1184'], - }), ('RcisTarget', '1.12.0', { 'checksums': ['eef8c2e328b4b10951fad9174786ff6228455845ecdda5bfc98f6abb43a000fa'], }), From 15ee141c51e115f80c1ff13b05a6b7071641b1a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 12:41:17 +0100 Subject: [PATCH 1744/9987] don't enable separate_build_dir, already done by default by CMakeMake easyblock Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb index 4c85336424f..b04359f35c8 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb @@ -28,7 +28,6 @@ dependencies = [ ('Boost', '1.76.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html From 1652142b1e44f989f91fa0b04c324f68c2a4ca6f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 12:41:43 +0100 Subject: [PATCH 1745/9987] explicitely specify location of Python 3 installation Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb index b04359f35c8..b8e22aca2c9 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb @@ -32,7 +32,7 @@ start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " From 1bdeea9ccd6655e68ee8f588bc0b031bb83ae03f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 12:42:10 +0100 Subject: [PATCH 1746/9987] fix reference to Arrow developer documentation w.r.t. Python bindings Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb index b8e22aca2c9..5915b674495 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb @@ -30,7 +30,7 @@ dependencies = [ start_dir = 'cpp' -# see https://arrow.apache.org/docs/python/development.html +# see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" From e36d48e65640dab9eafa7cebb7af88f2f050f84e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 14:16:57 +0100 Subject: [PATCH 1747/9987] also add NMF extension to R-bundle-Bioconductor 3.13 easyconfig --- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index 2b6566d124c..ad49e3ecea1 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -1060,6 +1060,9 @@ exts_list = [ ('RcisTarget', '1.12.0', { 'checksums': ['eef8c2e328b4b10951fad9174786ff6228455845ecdda5bfc98f6abb43a000fa'], }), + ('NMF', '0.23.0', { + 'checksums': ['0f0cca01b37bf46fce90d2e951df609d3d377908aa607825083fd0c47cc24753'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 52554983817593851985bae98a42596af63de7f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 14:18:29 +0100 Subject: [PATCH 1748/9987] adding easyconfigs: SCENIC-1.2.4-foss-2021a-R-4.1.0.eb --- .../SCENIC/SCENIC-1.2.4-foss-2021a-R-4.1.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCENIC/SCENIC-1.2.4-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/s/SCENIC/SCENIC-1.2.4-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/s/SCENIC/SCENIC-1.2.4-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..3db03b3ba3a --- /dev/null +++ b/easybuild/easyconfigs/s/SCENIC/SCENIC-1.2.4-foss-2021a-R-4.1.0.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'SCENIC' +local_commit = '0585e87' +version = '1.2.4' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://scenic.aertslab.org' +description = "SCENIC Suite is a set of tools to study and decipher gene regulation." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/aertslab/SCENIC/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['9cd5b102e5f9f27d19d5cd22241090a8426d170669951b845c34265f0e3cceb2'] + +dependencies = [ + ('R', '4.1.0'), + ('R-bundle-Bioconductor', '3.13', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['SCENIC'], +} + +moduleclass = 'geo' From eda4f4ddc87c8517b43fb42d06a815740570f4d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 15:19:44 +0100 Subject: [PATCH 1749/9987] remove easyconfigs for lpeg and SMV using intel/2020b --- .../l/lpeg/lpeg-1.0.2-intel-2020b.eb | 31 -------- .../s/SMV/SMV-6.7.17-intel-2020b.eb | 78 ------------------- 2 files changed, 109 deletions(-) delete mode 100644 easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb delete mode 100644 easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb diff --git a/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb b/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb deleted file mode 100644 index 3ee9b07e774..00000000000 --- a/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-intel-2020b.eb +++ /dev/null @@ -1,31 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author:: Denis Kristak (INUITS) -## - -easyblock = 'MakeCp' - -name = 'lpeg' -version = '1.0.2' - -homepage = 'http://www.inf.puc-rio.br/~roberto/lpeg/' -description = """LPeg is a new pattern-matching library for Lua, based on Parsing Expression Grammars (PEGs).""" - -toolchain = {'name': 'intel', 'version': '2020b'} - -source_urls = ['http://www.inf.puc-rio.br/~roberto/lpeg/'] -sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['48d66576051b6c78388faad09b70493093264588fcd0f258ddaab1cdd4a15ffe'] - -dependencies = [ - ('Lua', '5.4.2'), -] - -files_to_copy = ['*'] - -sanity_check_paths = { - 'files': ["lpcode.o", "lpprint.o", "lptree.o", "lpvm.o"], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb deleted file mode 100644 index e4d034074f7..00000000000 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-intel-2020b.eb +++ /dev/null @@ -1,78 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author:: Denis Kristak (INUITS) -## - -easyblock = 'MakeCp' - -name = 'SMV' # SmokeView -version = '6.7.17' - -homepage = 'https://github.com/firemodels/smv' -description = """Smokeview is a visualization program that displays output of FDS and CFAST simulations.""" - -toolchain = {'name': 'intel', 'version': '2020b'} - -source_urls = ['https://github.com/firemodels/%(name)s/archive/refs/tags/'] -sources = ['%(name)s%(version)s.tar.gz'] -patches = [ - 'SMV-%(version)s_missing-includes.patch', - ('example.smv', '.'), # example file for sanity check -] -checksums = [ - '2e718af991e48228bf374fdefcce00d2e8b5827cc29ae2138ae267fda896f127', # SMV6.7.17.tar.gz - '2b287f3e6ff368422684bd887568a369b9db3426a94efefcccc7680392b742ab', # SMV-6.7.17_missing-includes.patch - '1adf7dcc5293ec7a5f7ec01a828dec88b4ddd025505167b4e361d9450f66ea59', # example.smv -] - -dependencies = [ - ('libgd', '2.3.0'), - ('freeglut', '3.2.1'), - ('libjpeg-turbo', '2.0.5'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), - ('Lua', '5.4.2'), - ('lpeg', '1.0.2'), - ('libGLU', '9.0.1'), - ('glew', '2.1.0'), - ('Xvfb', '1.20.9'), -] - -local_compiler_lib_append = '/compilers_and_libraries_$EBVERSIONICCIFORT/linux/compiler/lib/intel64_lin/' - -local_buildopts = ' -lglui -lglut -lfreeglut -lGLU -lGL -llibgd ' -local_buildopts += ' LDFLAGS=" -L%(installdir)s -L$EBROOTFREEGLUT/lib -L$EBROOTLIBGD/lib " ' -local_buildopts += ' IFLAGS=" -I$EBROOTFREEGLUT/include/GL -I%(builddir)s/smv-SMV%(version)s/Source/glui_v2_1_beta/ ' -local_buildopts += ' -I%(builddir)s/smv-SMV%(version)s/Source/glui_gl/GL/glut.h "' -local_buildopts += ' EB_L_PATH=%(installdir)s ' -local_buildopts += ' CFLAGS="-Dpp_LINUX" ' - -prebuildopts = "cd %(builddir)s/smv-SMV%(version)s/Build/LIBS/intel_linux_64/ && " -prebuildopts += " make all -f make_LIBS.make " -prebuildopts += "SRCDIR=%(builddir)s/smv-SMV%(version)s/Source/ LIBDIR=%(installdir)s && " -prebuildopts += "cd %(builddir)s/smv-SMV%(version)s/Build/smokeview/ && " -prebuildopts += "export IFORT_COMPILER_LIB=$EBROOTICCIFORT%s && " % local_compiler_lib_append - -buildopts = ' intel_linux_64 ' + local_buildopts -buildopts += ' && make -j %(parallel)s intel_linux_64_db ' + local_buildopts - -files_to_copy = [ - (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64*"], 'bin'), -] - -postinstallcmds = [ - 'ln -s %(installdir)s/bin/smokeview_linux_64 %(installdir)s/bin/smokeview' -] - -modextrapaths = {'PATH': ['bin']} - -sanity_check_commands = [ - "cd %(builddir)s/smv-SMV%(version)s && timeout 10 xvfb-run smokeview example 2>&1 | grep 'Terminated' ", -] - -sanity_check_paths = { - 'files': ["bin/smokeview"], - 'dirs': ["bin"], -} - -moduleclass = 'bio' From baf1be64b2083155006758620c1c6d8610b45985 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 15:26:01 +0100 Subject: [PATCH 1750/9987] style fixes + correct moduleclass for lpeg + change name to LPeg --- .../LPeg-1.0.2-GCCcore-10.2.0.eb} | 14 +++++++------- .../s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/l/{lpeg/lpeg-1.0.2-GCCcore-10.2.0.eb => LPeg/LPeg-1.0.2-GCCcore-10.2.0.eb} (77%) diff --git a/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LPeg/LPeg-1.0.2-GCCcore-10.2.0.eb similarity index 77% rename from easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-GCCcore-10.2.0.eb rename to easybuild/easyconfigs/l/LPeg/LPeg-1.0.2-GCCcore-10.2.0.eb index 00a0ab846ae..d0801000f6d 100644 --- a/easybuild/easyconfigs/l/lpeg/lpeg-1.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LPeg/LPeg-1.0.2-GCCcore-10.2.0.eb @@ -5,7 +5,7 @@ easyblock = 'MakeCp' -name = 'lpeg' +name = 'LPeg' version = '1.0.2' homepage = 'http://www.inf.puc-rio.br/~roberto/lpeg/' @@ -14,7 +14,7 @@ description = """LPeg is a new pattern-matching library for Lua, based on Parsin toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['http://www.inf.puc-rio.br/~roberto/lpeg/'] -sources = ['%(name)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['48d66576051b6c78388faad09b70493093264588fcd0f258ddaab1cdd4a15ffe'] builddependencies = [ @@ -26,13 +26,13 @@ dependencies = [ ] files_to_copy = [ - (['lpeg.so'], 'lib/'), - (['*.h'], 'include/'), + (['lpeg.%s' % SHLIB_EXT], 'lib'), + (['*.h'], 'include'), ] sanity_check_paths = { - 'files': ["lib/lpeg.so"], - 'dirs': [], + 'files': ['lib/lpeg.%s' % SHLIB_EXT], + 'dirs': ['include'], } -moduleclass = 'bio' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb index abdce7f5395..01a46d62af3 100644 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb @@ -32,7 +32,7 @@ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), ('Lua', '5.4.2'), - ('lpeg', '1.0.2'), + ('LPeg', '1.0.2'), ('libGLU', '9.0.1'), ('glew', '2.1.0'), ('Xvfb', '1.20.9'), From 5dce0d7c1a8c4a462fd9101314434a1b547a3167 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 16:01:18 +0100 Subject: [PATCH 1751/9987] trivially simplify SMV easyconfig + fix moduleclass --- .../s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb index 01a46d62af3..484357754ef 100644 --- a/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/s/SMV/SMV-6.7.17-iccifort-2020.4.304.eb @@ -38,8 +38,6 @@ dependencies = [ ('Xvfb', '1.20.9'), ] -local_compiler_lib_append = '/compilers_and_libraries_$EBVERSIONICCIFORT/linux/compiler/lib/intel64_lin/' - local_buildopts = ' -lglui -lglut -lfreeglut -lGLU -lGL -llibgd ' local_buildopts += ' LDFLAGS=" -L%(installdir)s -L$EBROOTFREEGLUT/lib -L$EBROOTLIBGD/lib " ' local_buildopts += ' IFLAGS=" -I$EBROOTFREEGLUT/include/GL -I%(builddir)s/smv-SMV%(version)s/Source/glui_v2_1_beta/ ' @@ -51,10 +49,9 @@ prebuildopts = "cd %(builddir)s/smv-SMV%(version)s/Build/LIBS/intel_linux_64/ && prebuildopts += " make all -f make_LIBS.make " prebuildopts += "SRCDIR=%(builddir)s/smv-SMV%(version)s/Source/ LIBDIR=%(installdir)s && " prebuildopts += "cd %(builddir)s/smv-SMV%(version)s/Build/smokeview/ && " -prebuildopts += "export IFORT_COMPILER_LIB=$EBROOTICCIFORT%s && " % local_compiler_lib_append +prebuildopts += "export IFORT_COMPILER_LIB=$EBROOTICCIFORT/lib64/intel64/ && " buildopts = ' intel_linux_64 ' + local_buildopts -buildopts += ' && make -j %(parallel)s intel_linux_64_db ' + local_buildopts files_to_copy = [ (["./Build/smokeview/*.o", "./Build/smokeview/smokeview_linux_64*"], 'bin'), @@ -64,15 +61,13 @@ postinstallcmds = [ 'ln -s %(installdir)s/bin/smokeview_linux_64 %(installdir)s/bin/smokeview' ] -modextrapaths = {'PATH': ['bin']} - sanity_check_commands = [ "cd %(builddir)s/smv-SMV%(version)s && timeout 10 xvfb-run smokeview example 2>&1 | grep 'Terminated' ", ] sanity_check_paths = { - 'files': ["bin/smokeview"], - 'dirs': ["bin"], + 'files': ['bin/smokeview'], + 'dirs': [], } -moduleclass = 'bio' +moduleclass = 'vis' From e6a3f2ba4ce64e9246e999a22a7d122ad34a6b3e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 19:27:04 +0100 Subject: [PATCH 1752/9987] use arrow-R as name for R bindings for Arrow, so they can be loaded together in a lowercase naming scheme --- .../arrow-R-6.0.0.2-foss-2021a-R-4.1.0.eb} | 6 ++++-- .../R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/a/{arrow/arrow-6.0.0.2-foss-2021a-R-4.1.0.eb => arrow-R/arrow-R-6.0.0.2-foss-2021a-R-4.1.0.eb} (91%) diff --git a/easybuild/easyconfigs/a/arrow/arrow-6.0.0.2-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021a-R-4.1.0.eb similarity index 91% rename from easybuild/easyconfigs/a/arrow/arrow-6.0.0.2-foss-2021a-R-4.1.0.eb rename to easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021a-R-4.1.0.eb index 8ca79314cf4..27245404138 100644 --- a/easybuild/easyconfigs/a/arrow/arrow-6.0.0.2-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021a-R-4.1.0.eb @@ -1,6 +1,6 @@ easyblock = 'RPackage' -name = 'arrow' +name = 'arrow-R' version = '6.0.0.2' versionsuffix = '-R-%(rver)s' @@ -26,7 +26,9 @@ preinstallopts = "export LIBARROW_BINARY=true && " sanity_check_paths = { 'files': [], - 'dirs': [name], + 'dirs': ['arrow'], } +options = {'modulename': 'arrow'} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb index ad49e3ecea1..542cb7906c0 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.13-foss-2021a-R-4.1.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('GSL', '2.7'), # for flowClust ('HDF5', '1.10.7'), # for rhdf5 ('ncdf4', '1.17', versionsuffix), # for mzR - ('arrow', '6.0.0.2', versionsuffix), # required by RcisTarget + ('arrow-R', '6.0.0.2', versionsuffix), # required by RcisTarget ] exts_default_options = { From 9d26452b2890f91da64326a228f4a03f6fb69cf4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 19:34:54 +0100 Subject: [PATCH 1753/9987] adding easyconfigs: MMseqs2-13-45111-20211019-gompi-2020b.eb --- .../MMseqs2-13-45111-20211019-gompi-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211019-gompi-2020b.eb diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211019-gompi-2020b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211019-gompi-2020b.eb new file mode 100644 index 00000000000..0277029f5d3 --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-20211019-gompi-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +local_commit = '9cc89aa' +version = '13-45111-20211019' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['b1b89aa2b5ccd97411000d8ba7d296f6134818f475b47e3d7672b071b9ff47f3'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [('bzip2', '1.0.8')] + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' From dbce383c518848fd7fe5b14d2aa65d7a7d05f0a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 22:00:06 +0100 Subject: [PATCH 1754/9987] rename R bindings for Arrow to arrow-R, so it can be used in a lowercase module naming scheme --- .../arrow-R-0.17.1-foss-2020a-R-4.0.0.eb} | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/a/{arrow/arrow-0.17.1-foss-2020a-R-4.0.0.eb => arrow-R/arrow-R-0.17.1-foss-2020a-R-4.0.0.eb} (82%) diff --git a/easybuild/easyconfigs/a/arrow/arrow-0.17.1-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-0.17.1-foss-2020a-R-4.0.0.eb similarity index 82% rename from easybuild/easyconfigs/a/arrow/arrow-0.17.1-foss-2020a-R-4.0.0.eb rename to easybuild/easyconfigs/a/arrow-R/arrow-R-0.17.1-foss-2020a-R-4.0.0.eb index 5540b658fe9..6118342e5ae 100644 --- a/easybuild/easyconfigs/a/arrow/arrow-0.17.1-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-0.17.1-foss-2020a-R-4.0.0.eb @@ -1,6 +1,6 @@ easyblock = 'RPackage' -name = 'arrow' +name = 'arrow-R' version = '0.17.1' versionsuffix = '-R-%(rver)s' @@ -10,7 +10,7 @@ description = "R interface to the Apache Arrow C++ library" toolchain = {'name': 'foss', 'version': '2020a'} source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive 'https://cran.r-project.org/src/contrib/', # current version of packages 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ] @@ -24,7 +24,9 @@ dependencies = [ sanity_check_paths = { 'files': [], - 'dirs': [name], + 'dirs': ['arrow'], } +options = {'modulename': 'arrow'} + moduleclass = 'tools' From 67cc17f4382014aa08d0d210a80d5db95d7c05b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 31 Oct 2021 22:01:18 +0100 Subject: [PATCH 1755/9987] fix archive source URL for arrow R package --- .../easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021a-R-4.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021a-R-4.1.0.eb index 27245404138..7dfc596e384 100644 --- a/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021a-R-4.1.0.eb @@ -10,7 +10,7 @@ description = "R interface to the Apache Arrow C++ library" toolchain = {'name': 'foss', 'version': '2021a'} source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive 'https://cran.r-project.org/src/contrib/', # current version of packages 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ] From 40f468706ce97191e5f09c4d38d4c18af29fe4c6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 1 Nov 2021 08:20:01 +0100 Subject: [PATCH 1756/9987] Add missing description+author to DFTB+-21.1_use_dftd3_from_EB.patch. --- easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb | 5 ++--- .../easyconfigs/d/DFTB+/DFTB+-21.1_use_dftd3_from_EB.patch | 3 +++ 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb index 3287ce7a38d..5711e31168d 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb @@ -45,7 +45,7 @@ checksums = [ '8c1eb8a38f72c421e2ae20118a6db3a656fa84e8b180ef387e549a73ae77f970', # dftbplus-21.1.tar.xz '6f65da7b64ef255fd777de7a972c63f7fa8ed2041442823b2c601bc8f0e55d98', # slakos-data-21.1.tar.gz 'd464f9f7b1883d1353b433d0c7eae2f5606af092d9b51d38e9ed15e072610a79', # gbsa-data-21.1.tar.gz - 'fae75d62ce95922e071441bc73dccc0569ae467edbb46774180ae6cdde59cb92', # DFTB+-21.1_use_dftd3_from_EB.patch + '3bd33d8e90e8182f516f15fb8f79d01929a0778e324b33c5fabc7d70112e643a', # DFTB+-21.1_use_dftd3_from_EB.patch 'e922b0d9360d342190c4496173f938c2cb89f0bd0499b2f71abcaf70dc8e5fe1', # DFTB+-21.1_fix_intel_omp_linking.patch 'f0c0e248d567739010897e7a46e471b1e332568bb0f9c1c06fd1e762d3f81aa4', # DFTB+-21.1_drop_intel_failing_tests.patch ] @@ -62,7 +62,6 @@ dependencies = [ ('ELSI', '2.7.1', '-PEXSI'), ] - build_shared_libs = True configopts = '-DWITH_MPI=1 -DWITH_DFTD3=1 -DWITH_ELSI=1 -DWITH_MBD=1 -DWITH_UNIT_TESTS=1 ' @@ -76,7 +75,7 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'] } -sanity_check_commands = [('python', '-c "import dptools"')] +sanity_check_commands = [("python -c 'import dptools'")] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_use_dftd3_from_EB.patch b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_use_dftd3_from_EB.patch index 147698da7c3..9386d144930 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_use_dftd3_from_EB.patch +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1_use_dftd3_from_EB.patch @@ -1,3 +1,6 @@ +Use dftd3 from EasyBuild instead of downloading it as an external + +Åke Sandgren, 20211020 diff -ru dftbplus-21.1.orig/external/dftd3/CMakeLists.txt dftbplus-21.1/external/dftd3/CMakeLists.txt --- dftbplus-21.1.orig/external/dftd3/CMakeLists.txt 2021-05-12 20:23:51.000000000 +0200 +++ dftbplus-21.1/external/dftd3/CMakeLists.txt 2021-10-20 08:40:05.364957330 +0200 From cd035463dcb77d8a0d446f2046da8e803f02413d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 1 Nov 2021 08:21:05 +0100 Subject: [PATCH 1757/9987] Add sanity_check_commands to dftd3-lib-0.9-intel-compilers-2021.2.0.eb. --- .../d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb index 42eda3849ee..3ed92513216 100644 --- a/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb @@ -36,4 +36,6 @@ sanity_check_paths = { 'dirs': ['include', 'share'], } +sanity_check_commands = [("dftd3 --help")] + moduleclass = 'chem' From dd5fd20b8c40bc58c410e484e612d722777e361b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 08:16:53 +0000 Subject: [PATCH 1758/9987] Specify EB Python and fix URL in comment for Arrow 0.17.1 --- .../a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb | 4 ++-- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 4 ++-- .../a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb | 4 ++-- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb index d503e7f9046..30694bf64fb 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb @@ -38,9 +38,9 @@ dependencies = [ separate_build_dir = True start_dir = 'cpp' -# see https://arrow.apache.org/docs/python/development.html +# see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 8fbcaf84689..92f2b7bc741 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -39,9 +39,9 @@ dependencies = [ separate_build_dir = True start_dir = 'cpp' -# see https://arrow.apache.org/docs/python/development.html +# see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb index f1476481258..03c7976a3a9 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb @@ -36,9 +36,9 @@ dependencies = [ separate_build_dir = True start_dir = 'cpp' -# see https://arrow.apache.org/docs/python/development.html +# see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index ee3c0441109..7982ce4dd0c 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -35,9 +35,9 @@ dependencies = [ separate_build_dir = True start_dir = 'cpp' -# see https://arrow.apache.org/docs/python/development.html +# see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " From e07013f5517f2585790b3baeec4f999edcefbac8 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 08:18:48 +0000 Subject: [PATCH 1759/9987] remove separate_build_dir --- .../easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb | 1 - easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 1 - .../easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb | 1 - easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 1 - 4 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb index 30694bf64fb..1b4fc205e26 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb @@ -35,7 +35,6 @@ dependencies = [ ('Boost', '1.72.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 92f2b7bc741..e2b5ef35e8c 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -36,7 +36,6 @@ dependencies = [ ('Boost', '1.74.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb index 03c7976a3a9..8e2b93cd227 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb @@ -33,7 +33,6 @@ dependencies = [ ('Boost', '1.72.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index 7982ce4dd0c..0b26d1ec45e 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -32,7 +32,6 @@ dependencies = [ ('Boost', '1.74.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html From 9d424dabc0bff2b3628500d43057f7ed8d8e1185 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 08:59:01 +0000 Subject: [PATCH 1760/9987] also specify the EB built Python during pyarrow build --- .../easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb | 1 + easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 1 + .../easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb | 1 + easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb index 1b4fc205e26..73d913a3791 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb @@ -46,6 +46,7 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index e2b5ef35e8c..8f577b4f440 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -46,6 +46,7 @@ configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb index 8e2b93cd227..f7866fdbdfc 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb @@ -44,6 +44,7 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index 0b26d1ec45e..101f92aa068 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -43,6 +43,7 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] From 4c1553a3aa9b8fa4e0b7a0c801bdbac94edc5f87 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 12:10:16 +0000 Subject: [PATCH 1761/9987] adding easyconfigs: R-4.1.2-foss-2021b.eb --- .../easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 3085 +++++++++++++++++ 1 file changed, 3085 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb new file mode 100644 index 00000000000..97d4bd22f64 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -0,0 +1,3085 @@ +name = 'R' +version = '4.1.2' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-4.1.0_identify-flexiblas-in-configure.patch'] +checksums = [ + '2036225e9f7207d4ce097e54972aecdaa8b40d7d9911cd26491fac5a0fab38af', # R-4.1.2.tar.gz + '2c6720e2e144ae4fe00842daab0ebba72241080603e0ff1a6ca758738041b257', # R-4.1.0_identify-flexiblas-in-configure.patch +] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.13'), +] +dependencies = [ + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('cairo', '1.16.0'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.36'), + ('PCRE2', '10.37'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.6'), # for plottting in R + ('LibTIFF', '4.3.0'), + ('Java', '11', '', True), + ('Tk', '8.6.11'), # for tcltk + ('cURL', '7.78.0'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.1'), # for igraph + ('NLopt', '2.7.0'), # for nloptr + ('FFTW', '3.3.9'), # for fftw + ('libsndfile', '1.0.31'), # for seewave + ('ICU', '69.1'), # for rJava & gdsfmt + ('HDF5', '1.12.1'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.1.0-4'), # for animation + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '14.17.6'), # for V8 (required by rstan) + ('GDAL', '3.3.2'), # for sf + ('libgit2', '1.1.1'), + ('OpenSSL', '1.1', '', True), +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 2nd November 2021 +exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('Rmpi', '0.6-9.2', { + 'checksums': ['358ac1af97402e676f209261a231f36a35e60f0301edf8ca53dac11af3c3bd1a'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.7', { + 'checksums': ['15e5a4732216daed16263c79fb37017c2ada84a2d4e785e3b76445d0eba3dc1d'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '4.0.5', { + 'checksums': ['9aba9e271144ec224063ddba0d791e2fcdb9c912d48fdc49e204fce628355037'], + }), + ('bnlearn', '4.7', { + 'checksums': ['2e1dd7ba9b7cf07e51eec3238684310edbeb0573d9b907049fb6b28db3022817'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.16', { + 'checksums': ['e7dea648ee018e2c8c8834084051c76f7e8b2b42067772c62035a941c32457a9'], + }), + ('formatR', '1.11', { + 'checksums': ['bd81662d09cf363652761e63ba5969c71be4dd5ae6fc9098f440d6729254a30c'], + }), + ('gtools', '3.9.2', { + 'checksums': ['03b1898bf581f6d12fa90e23ff700cfa7c834ac10c6654bdac42d7ec943fa953'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.1', { + 'checksums': ['e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917'], + }), + ('xfun', '0.27', { + 'checksums': ['c775bf33a6bc57f8022960cbf7dc20a4e82175a9c71807b2723f46ade6805485'], + }), + ('highr', '0.9', { + 'checksums': ['beff11390d936c90fdcc00e7ed0eb72220f3de403a51b56659e3d3e0b6d8ed4d'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-16', { + 'checksums': ['c796c8b987ed1bd9dfddd593e17312ed681fc4fa3a1ecfe51da2def0ac1e50df'], + }), + ('kernlab', '0.9-29', { + 'checksums': ['c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f'], + }), + ('mime', '0.12', { + 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-3', { + 'checksums': ['b1f92be633243185ab86e880a1e1ac5a4dd3c535d01ebd187a4872d0a8c6f194'], + }), + ('NLP', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '5.4.7', { + 'checksums': ['45f5a666caee5bebd3160922b8655295a25e37f624741f6574365e4ac5a14c23'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('segmented', '1.3-4', { + 'checksums': ['8276bfbb3e5c1d7a9a61098f72ac9b2b0f52c89ae9f9b715f76b22303cc3902d'], + }), + ('som', '0.3-5.1', { + 'checksums': ['a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9'], + }), + ('SuppDists', '1.1-9.5', { + 'checksums': ['680b67145c07d44e200275e08e48602fe19cd99fb106c05422b3f4a244c071c4'], + }), + ('stabledist', '0.7-1', { + 'checksums': ['06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69'], + }), + ('survivalROC', '1.0.3', { + 'checksums': ['1449e7038e048e6ad4d3f7767983c0873c9c7a7637ffa03a4cc7f0e25c31cd72'], + }), + ('pspline', '1.0-18', { + 'checksums': ['f71cf293bd5462e510ac5ad16c4a96eda18891a0bfa6447dd881c65845e19ac7'], + }), + ('timeDate', '3043.102', { + 'checksums': ['377cba03cddab8c6992e31d0683c1db3a73afa9834eee3e95b3b0723f02d7473'], + }), + ('longmemo', '1.1-2', { + 'checksums': ['7964e982287427dd58f98e1144e468ae0cbd572d25a4bea6ca9ae9c7522f3207'], + }), + ('ADGofTest', '0.3', { + 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], + }), + ('MASS', '7.3-54', { + 'checksums': ['b800ccd5b5c2709b1559cf5eab126e4935c4f8826cf7891253432bb6a056e821'], + }), + ('pixmap', '0.4-12', { + 'checksums': 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['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], + }), + ('lhs', '1.1.3', { + 'checksums': ['e43b8d48db1cf26013697e2a798ed1d31d1ee1790f2ebfecb280176c0e0c06d1'], + }), + ('tensorA', '0.36.2', { + 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], + }), + ('EasyABC', '1.5', { + 'checksums': ['1dd7b1383a7c891cafb34d9cec65d92f1511a336cff1b219e63c0aa791371b9f'], + }), + ('whisker', '0.4', { + 'checksums': ['7a86595be4f1029ec5d7152472d11b16175737e2777134e296ae97341bf8fba8'], + }), + ('roxygen2', '7.1.2', { + 'checksums': ['b3693d1eb57bb1c27134447ea7f64c353c085dd2237af7cfacc75fca3d2fc5fd'], + }), + ('git2r', '0.28.0', { + 'checksums': ['ce6d148d21d2c87757e98ef4474b2d09faded9b9b866f046bd26d4ca925e55f2'], + }), + ('rversions', '2.1.1', { + 'checksums': ['79aaacf5a1258d91ac0ddedf3c8c16a2d10d39010993dcc7b0a2638afee27cb1'], + }), + ('xopen', '1.0.0', { + 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], + }), + ('sessioninfo', '1.2.0', { + 'checksums': ['adebf738ad3d3af9e018302d949994240311ef06c0a77c645b2f761c1a8c07df'], + }), + ('rcmdcheck', '1.4.0', { + 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], + }), + ('remotes', '2.4.1', { + 'checksums': ['d5d777b2e10d70fd0670166d539eab88ec4f7fe030f54ec5cd2703f548473276'], + }), + ('clisymbols', '1.2.0', { + 'checksums': ['0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.1', { + 'checksums': ['b14aaf4e910a9d2d6c65c93e645f0b0159c00898e669f917f83c03dfedb1dfea'], + }), + ('gh', '1.3.0', { + 'checksums': ['a44039054e8ca56496f2d9c7a10cdadf4a7383bc91086e768ba7e7f1fbcaed1c'], + }), + ('credentials', '1.3.1', { + 'checksums': ['8795a73a65d1ce2e9f0be66546e85231c846ba6445a11948b9816fbee20a7a60'], + }), + ('gert', '1.4.1', { + 'checksums': ['623b58f12c5530b101e91a352269fe011814b074cf7a7ed0b3cd4506390a63f8'], + }), + ('usethis', '2.1.3', { + 'checksums': ['2db075980247d854110de60e7afe6f6e0b654a3ba49d0699ff40dd516e8e9bbf'], + }), + ('covr', '3.5.1', { + 'checksums': ['a54cfc3623ea56084158ac5d7fe33f216f45191f6dcddab9c9ed4ec1d9d8ac6c'], + }), + ('devtools', '2.4.2', { + 'checksums': ['71f0a55054d293fb553702b21b91941bc5c83a933610fad6f9662bf0a6178f05'], + }), + ('Rook', '1.1-1', { + 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + }), + ('Cairo', '1.5-12.2', { + 'checksums': ['dd524105c83b82b5c3b3ee2583ef90d4cafa54b0c29817dac48b425b79f90f92'], + }), + ('RMTstat', '0.3', { + 'checksums': ['81eb4c5434d04cb66c749a434c33ceb1c07d92ba79765d4e9233c13a092ec2da'], + }), + ('Lmoments', '1.3-1', { + 'checksums': ['7c9d489a08f93fa5877e2f233ab9732e0d1b2761596b3f6ac91f2295e41a865d'], + }), + ('distillery', '1.2-1', { + 'checksums': ['4b88f0b34e472b9134ad403fb32283424f1883a5943e52c55f1fe05995efb5fa'], + 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['be4e4c520a3692902ce405e8225aef9f3d5f0cd11fcde614f6541e981b63673d'], + }), + ('randomForestSRC', '2.13.0', { + 'checksums': ['beb981cae3a8c7232a2ca67f0a7bf3293eb44d5f1ac14913632ca8f8d4728abd'], + }), + ('sm', '2.2-5.7', { + 'checksums': ['2607a2cafc68d7e99005daf99e36f4a66eaf569ebb6b7500e962642cf58be80f'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-9', { + 'checksums': ['d404c4eb40686534f9c05f24f908cd954041f66d1072caea4a3adfa83a5f108a'], + }), + ('matrixcalc', '1.0-5', { + 'checksums': ['5906e1ef06dbc18efc7a4b370adc180ef8941b5438119703bd981d1c76a06fca'], + }), + ('arm', '1.12-2', { + 'checksums': ['816ba1c31eec00feef472c57e280488d3d233b592f6f0a1a30e4abb903cb4f5d'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('servr', '0.23', { + 'checksums': ['4492d1dabc8f62cf7f7a53c97413a664823a3916dcaf99a7b04bcb279f7b2eb8'], + }), + ('rgexf', '0.16.2', { + 'checksums': ['6ee052b0de99d0c7492366b991d345a51b3d0cc890d10a68b8670e1bd4fc8201'], + }), + ('sem', '3.1-13', { + 'checksums': ['07749f710ad800f43cacdff8f1aa4f20105a619c72be4465f29860c381242f65'], + }), + ('statnet.common', '4.5.0', { + 'checksums': ['3cdb23db86f3080462f15e29bcf3e941590bc17ea719993b301199b22d6f882f'], + }), + ('network', '1.17.1', { + 'checksums': ['fc3c3a0014f8895a11c33994c9b44c6ef6cc49c7d026cd41ae6bba5ef63005a7'], + }), + ('rle', '0.9.2', { + 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], + }), + ('sna', '2.6', { + 'checksums': ['3a016550d9f424a0613c3f5b0b680dbd3a1f20a343173d39a96034340ad9202a'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.5', { + 'checksums': ['9240866e2f773cd0ac8a02514871149d2babaa162a49e151eab9591ad42984ea'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': 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['cd3f72b84f0c722e9c0b21c2b2de7683ec742345d7f8e62f67c8c93342c1a5c6'], + }), + ('grpreg', '3.4.0', { + 'checksums': ['fd57d20baf63d2cc5821998bca5c3fdcbe46c933c9553caa492911b12654d6ad'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('lpSolveAPI', '5.5.2.0-17.7', { + 'checksums': ['9ebc8e45ad73eb51e0b25049598a5bc758370cf89508e2328cf4bd93d68d55bb'], + }), + ('ergm', '4.1.2', { + 'checksums': ['1abc6ef53376a4132530c376ce477ae7a2590e95fe8feb011c0da9cfb4d49ba0'], + }), + ('networkDynamic', '0.11.0', { + 'checksums': ['aa21caaddce75c22e08b94adfb6036f5ee151ffb79d174ad250fe4592d27dad2'], + }), + ('tergm', '4.0.2', { + 'checksums': ['5ab1d61166c90f90c77edd12544b5946e01a933cc3e7ca609cae72075b742a64'], + }), + ('ergm.count', '4.0.2', { + 'checksums': ['316ed3cbe4b472eec79e8a5fd4183ce953070f6d98056d87423bd6d9ac155bd1'], + }), + ('tsna', '0.3.4', { + 'checksums': ['08fd9612388b86077cd877a48f81068d63f20291836eedbc727c9e00c1a2b4d2'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.6-0', { + 'checksums': ['b5b9493457d11d4dca12f7732bd1b3eb1443852977c8ee78393126f13deaf29b'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.16', { + 'checksums': ['be50f9fdef0f4bf9676b9c3c2906d0431afc678af55cf48b1119f9fc0adac44f'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.34.0.3', { + 'checksums': ['2a707b9f7271eae611c9e81b13d2024b8829f6b06b3c41c5b97de1aef591931e'], + }), + ('mlegp', '3.1.8', { + 'checksums': ['eac1df085a608451828575028ca05b78dc6b5035da14cabc141bfee5ef986de9'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.6', { + 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.1', { + 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.2.1', { + 'checksums': ['6b078da4a47904194bfe29e2c3b6fbbf6e3ad190e33979f840a3ea366c708616'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), + ('cobs', '1.3-4', { + 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.7-3.1', { + 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0.2', { + 'checksums': ['4772c352e8d3d9b5a0b7480c0e0962de4f5060fb7bf3fcb8ee4fa1cb10f93fd4'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.19', { + 'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'], + }), + ('BMA', '3.18.15', { + 'checksums': ['4be0d52f433503631e9574944067f613bafba129ebe27396bcfccb3b95992b1a'], + }), + ('BCEE', '1.3.0', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-60', { + 'checksums': ['6d21ddfd0d621ed3bac861890c600884b6ed5ff7d2a36c9778b892636dbbef2a'], + }), + ('bdsmatrix', '1.3-4', { + 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.20', { + 'checksums': ['fff39d5df295b937cdad57b73d4e06e925f69e68784ef58b5dfcd3cf500931c1'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.6', { + 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.9', { + 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '4.2', { + 'checksums': ['53d2ff3ddbb398655b245ad3a19c028d6fb6bb1d59adeb30bb3497606733fc2d'], + }), + ('bbmle', '1.0.24', { + 'checksums': ['01edc00479fabf7491e47ff59bc4adbe6f0d4c23d22e76d1d49c4c1b6b4693ad'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.51.0', { + 'checksums': ['5225334add4dd3502044cf80a00543b766568c2d93c47af180f66a76942d76be'], + }), + ('tictoc', '1.0.1', { + 'checksums': ['a09a1535c417ddf6637bbbda5fca6edab6c7f7b252a64e57e99d4d0748712705'], + }), + ('ISOcodes', '2021.02.24', { + 'checksums': ['152769bcb4ae99d06a767384541c2000c94990a2c6983780837f85e885b539a6'], + }), + ('stopwords', '2.3', { + 'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0.1', { + 'checksums': ['1fedbb913bc13c790d2fabfe4edda0a987db3a078bea8c0ca9b777d20af08662'], + }), + ('topicmodels', '0.2-12', { + 'checksums': ['afd83a4381bf39e470446ebefd41ed03f314be400c1b2f702a4b1060eb8fd1b4'], + }), + ('tidytext', '0.3.2', { + 'checksums': ['6fe0ada78ee2cdf77c16e519a29b9baff61d8e23ab56aa0a9adc1b2a99a6472b'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.3.1', { + 'checksums': ['6f5a89f5ce0e90cbed1695b81259326c976e7a8f538157e223ee5f63b54412b8'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-13', { + 'checksums': ['7186d23e561818f3e1f01376a4fb2af9ccee775ce5afc1e3175f3b07a81db515'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.4.1', { + 'checksums': ['bc21fb6b4a93a7e95ee1be57e4e787d731895fb8b4743c26b30b43adee475b50'], + }), + ('RcppParallel', '5.1.4', { + 'checksums': ['76b545a6878c55edba780183fd89a76fe723b7f19709c5243495dcf3d54eea82'], + }), + ('StanHeaders', '2.21.0-7', { + 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], + }), + ('V8', '3.4.2', { + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['210643473ca8bf423fae34ce72ceb37a3e44c3315ec4abae59a77f077542d2ed'], + }), + ('rstan', '2.21.2', { + 'checksums': ['e30e04d38a612e2cb3ac69b53eaa19f7ede8b3548bf82f7892a2e9991d46054a'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.2', { + 'checksums': ['a59a3cb3cca89f51d9ee6702cd479fd7db8bc2e25b72f45cb6712da983777ca0'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.3', { + 'checksums': ['ca8545b25590e531512a90a18449a2cbab945f7434a1d60188c41f7d1839a7a9'], + }), + ('corrplot', '0.90', { + 'checksums': ['d9871f219351f443f879ae93c45e3a364eb32cc6f41491a801e7b8a91e96d5dd'], + }), + ('rstatix', '0.7.0', { + 'checksums': ['a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.4.0', { + 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.1.1', { + 'checksums': ['cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481'], + }), + ('leiden', '0.3.9', { + 'checksums': ['81754276e026a9a8436476365bbadf0f15a403a525a349cb56418da5d8edea0d'], + }), + ('sctransform', '0.3.2', { + 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], + }), + ('packrat', '0.7.0', { + 'checksums': ['e8bce1fd78f28f3a7bf56e65a2ae2c6802e69bf55466c24e1d1a4b8a5f83dcc2'], + }), + ('colourpicker', '1.1.1', { + 'checksums': ['a0d09982b048b143e2c3438ccec039dd20d6f892fa0dedc9fdcb0d40de883ce0'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), + ('findpython', '1.0.7', { + 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], + }), + ('argparse', '2.1.2', { + 'checksums': ['9997359a735359580ab6b054672388a55701fca71c80b54bab1aedc13bc5e5b3'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.10', { + 'checksums': ['1b655dbab8eed8d0aa3ab2148aac8e0e5bfa190468f5e3c06b001ce88b7f0d3f'], + }), + ('qqman', '0.1.8', { + 'checksums': ['58da8317df8d726d1fde4805919da5d64f880894a423ee20937cafb479b9d8a8'], + }), + ('rstantools', '2.1.1', { + 'checksums': ['c95b15de8ec577eeb24bb5206e7b685d882f88b5e6902efda924b7217f463d2d'], + }), + ('bayesplot', '1.8.1', { + 'checksums': ['d8d74201ea91fa5438714686ca22a947ec9375b6c12b0cfef010c57104b1aa2a'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('rsconnect', '0.8.24', { + 'checksums': ['cf6bef1e073d6fa95c8be8a00e9e4982b88f4bab0e8ecd77db816a585be2e4a6'], + }), + ('shinystan', '2.5.0', { + 'checksums': ['45f9c552a31035c5de8658bb9e5d72da7ec1f88fbddb520d15fe701c677154a1'], + }), + ('optimx', '2021-10.12', { + 'checksums': ['39384c856b5efa3992cd230548b60eff936d428111ad6ad5b8fb98a3bcbb7943'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('projpred', '2.0.2', { + 'checksums': ['af0a9fb53f706090fe81b6381b27b0b6bd3f7ae1e1e44b0ada6f40972b09a55b'], + }), + ('distributional', '0.2.2', { + 'checksums': ['028e5a91aabe3a676eb7b7f3dc907f7f34735a123fe0d9adcabc03476504435f'], + }), + ('posterior', '1.1.0', { + 'checksums': ['eff6262dbcc1bf18337f535b0c75ba2fe360322e8b170c466e24ed3ee76cf4d2'], + }), + ('brms', '2.16.1', { + 'checksums': ['749efbd9fb061fe207cf2e729c1387d9a8538b922f12ceec4e82a9f8dd9c1bc4'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.1', { + 'checksums': ['285335dbe29b6898641e1151ab2f06acf76c6f4d6fbeadd66d151c25d7e38a74'], + }), + ('mcmcse', '1.5-0', { + 'checksums': ['4a820dc22c48efd32b7f9d1e1b897b4b3f165cd64b2ff85ba7029621cf9e7463'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.6.5', { + 'checksums': ['5be825734d76760723e2d5b8fbe03524a2b59d9163b33841d4a2c9ab2d4257cf'], + }), + ('drugCombo', '1.2.1', { + 'checksums': ['9a605c655c159604033558d757711e6d83d33dfc286c1280f722d4cb7d130f80'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.1.1', { + 'checksums': ['48474f396c4a91e257490025ede6a998883683e8020a898fff5d4e23a3764bfd'], + }), + ('maxlike', '0.1-8', { + 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + }), + ('coxme', '2.2-16', { + 'checksums': ['a0ce4b5649c4c1abbfe2c2bf23089744d1f66eb8368dea16e74e090f366a5111'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.4', { + 'checksums': ['fd21e5ecf3c1ac00ef1bbe79fab4cdd62789e0c4c45f126f1b64bda667238216'], + }), + ('oai', '0.3.2', { + 'checksums': ['ebfa756e08f6ac0aa61556b1a5bbe611f407bfff8aef1f8d075a24c361678bfd'], + }), + ('wellknown', '0.7.4', { + 'checksums': ['483e6fc43edf09ed583e74ce5ca7e2d7838ef8a32291e06d774c37546eed1a34'], + }), + ('rgbif', '3.6.0', { + 'checksums': ['2941857c85d89ebaf614ed130ec2f68e326a8ca99e00263ac4e2a9c556917f20'], + }), + ('rgdal', '1.5-27', { + 'checksums': ['62a555ed7b5424dd0252b3764e3542fb30c524d06e8245215bcfaedd84ee5756'], + }), + ('rgeos', '0.5-8', { + 'checksums': ['0db35392146cefb5eea0392eecb6b0bfee53708222b98b06de54a3e1a04ea314'], + }), + ('mapproj', '1.2.7', { + 'checksums': ['f0081281b08bf3cc7052c4f1360d6d3c20d9063be57754448ad9b48ab0d34c5b'], + }), + ('rbison', '1.0.0', { + 'checksums': ['9957e5f85ce68f5dd0ddc3c4b2b3c9d2f52d6f37587e1022ab8a44863534a83c'], + }), + ('rebird', '1.3.0', { + 'checksums': ['b238d3f246aa0249145894e1f3a90f46902f6615fc2f23b24c99bb5feecc55d3'], + }), + ('rvertnet', '0.8.2', { + 'checksums': ['2de9a3ec33a213c7592b49cca1d510a25aef0625369376d9b1b4e5d0da519226'], + }), + ('ridigbio', '0.3.5', { + 'checksums': ['e5cfb2e4dd8ddd1452a5afcf24fcc260889179d0f52eff4f41835adf99b64614'], + }), + ('spocc', '1.2.0', { + 'checksums': ['4bac45db5e69bfa3bf6cebd1b0c9241214c95561f275cee6d31e00911aa79d84'], + }), + ('spThin', '0.2.0', { + 'checksums': ['2e997afb79a2a990eded34c71afaac83986669cfa9ac51b15ae3f2b558902048'], + }), + ('rangeModelMetadata', '0.1.4', { + 'checksums': ['529d529ca90437db3d1e45118443e27a920422806383c7edaa2102beb43f5f80'], + }), + ('ENMeval', '2.0.1', { + 'checksums': ['2f7b7760ae70a45cd3c766aacf1e39f498de4f2e8c7b6dcde6b9adf6d8100250'], + }), + ('plotmo', '3.6.1', { + 'checksums': ['245a0c87f0cca08746c6fdc60da2e3856cd69b1a2b7b5641293c620d4ae04343'], + }), + ('earth', '5.3.1', { + 'checksums': ['0bbe06ba974ceb8ec5de1d59cb53f9487d1828d7130fe2503c48b6cb449c4b03'], + }), + ('mda', '0.5-2', { + 'checksums': ['344f2053215ddf535d1554b4539e9b09067dac878887cc3eb995cef421fc00c3'], + }), + ('biomod2', '3.5.1', { + 'checksums': ['30ed33ff980558a59782ec9e35f9c2c710a540718010654363f63878cdc0ac18'], + }), + ('poLCA', '1.4.1', { + 'checksums': ['2e69975b5e7da8c36641bfa9453afdb4861523866b8799bec1d4eace9ab5762e'], + }), + ('PermAlgo', '1.1', { + 'checksums': ['d7157b92241c34b71ad19901b52144973b49df453bf2a5edf4497d4bf26bd099'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.13', { + 'checksums': ['90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.3', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-1', { + 'checksums': ['e8abadc5614f132edc3fb9cb1c82ce4dacc1315b727fbd49db7399aee24115ba'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-20', { + 'checksums': ['1d75e795812819b7637d38fc909f4d7942bddf359acfb40a7b8e7cd167a5e92a'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.4.0', { + 'checksums': ['49459e76412037b3d8021bd83ee93d140bc3e715a2a2282a347ef60061900514'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-8', { + 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], + }), + ('gWidgets2tcltk', '1.0-6', { + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.3', { + 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], + }), + ('ie2misc', '0.8.6', { + 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '3.0', { + 'checksums': ['a76114e9780c86e4ea0a561300db024b95af9b0ebb6c3bf9a7598d276d009529'], + }), + ('lmom', '2.8', { + 'checksums': ['cae2a925c39429d8e9f91bdb2682ea0d1343e9b2e5c9e8752c5929eb5f20d2d2'], + }), + ('gld', '2.6.2', { + 'checksums': ['915860ac054ba4d29854c7d274e9c927995c5df2a7d4a6a0122b1fbc4a3c3cf3'], + }), + ('DescTools', '0.99.43', { + 'checksums': ['8c3c4e5975428b9f2817907931449cd704d3df0e19e4337010f0dee333e7a4ff'], + }), + ('orthopolynom', '1.0-5', { + 'checksums': ['6da4f437aae5c8fafdf791ce3c6a66f68198df4054af3aab8406402a4dc770bf'], + }), + ('gaussquad', '1.0-2', { + 'checksums': ['ba3a1ab6ffe92f592c9f2bb1d4070f1fb1019325226dcb4863cf725eb59e9b2d'], + }), + ('nlsem', '0.8', { + 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], + }), + ('tableone', '0.13.0', { + 'checksums': ['1c73a5a7595dc0ae2299d17c74738e077984af7d5429e4858b7be3c55e121346'], + }), + ('jstable', '1.0.7', { + 'checksums': ['a8f66172973dc75d1d751d7015e0f028c441263f6649909bd25fa944be0042c3'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.2', { + 'checksums': ['70eb4a13a6ac1bfb35af07cb8a63d501ad38dfd9817fc3fba6724260b23932de'], + }), + ('sensemakr', '0.1.4', { + 'checksums': ['6a1354f05392fa9343b90f69a54022c995651fb3c3d05cb08fa088ef52258caf'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-5', { + 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], + }), + ('blavaan', '0.3-17', { + 'checksums': ['ada14fcc665a22f11fc57392d70141c398d85dbb35f0a3373a501bc51d27f1e5'], + }), + ('mathjaxr', '1.4-0', { + 'checksums': ['ba57378236d593a39c5839054adc5473526de0c8f05b7eeb87c99438496ddc67'], + }), + ('metafor', '3.0-2', { + 'checksums': ['02df435197b225da736103edf73d19253a542bc31fc0b99610c02daec434138a'], + }), + ('fmri', '1.9.6', { + 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], + }), + ('AnalyzeFMRI', '1.1-24', { + 'checksums': ['0d2acfe9ce8f25eb5cc9e6ef1db3ea8e232a31d46a95e50914489b1997e17062'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.4', { + 'checksums': ['266702330250e9fbeb8616d86edf1d50d63084a0731d17e84a04dc6faacf653a'], + }), + ('DEoptim', '2.2-6', { + 'checksums': ['8c63397d83a067212d003ef3e639fd81f5f00bf61e3c271b4e4999031a69e2e1'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2013.9-1', { + 'checksums': ['1a1a399682a06a5fea3934985ebb1334005676c6a2a22d06f3c91c3923432908'], + }), + ('Rvmmin', '2018-4.17.1', { + 'checksums': ['55000ac4ff57d42f172c46c7d6b0a603da3b65866d6440d6b32bac4d2b81814e'], + }), + ('Rcgmin', '2013-2.21', { + 'checksums': ['a824a09c32d7565a3e30607c71333506d5b7197478fbe8b43f8a77dad6c12f0a'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '2.0.2', { + 'patches': ['DMCfun-2.0.0_fix-parallel-detect.patch'], + 'checksums': [ + '430cbc18f17db11a7941e6a8274a0eefbb8a6b0bdac8800970530d60d5881fde', # DMCfun_2.0.2.tar.gz + # DMCfun-2.0.0_fix-parallel-detect.patch + 'b2605bbe92ab55824d07d89ccd7146a2bede5c41041c9bf560ce6f910e8b51bd', + ], + }), + ('miceadds', '3.11-6', { + 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], + }), + ('visdat', '0.5.3', { + 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('norm', '1.0-9.5', { + 'checksums': ['305cbf007f3905cfd535ed9bf5ae3e2995e228cc8883d6482e5d3a2f02814106'], + }), + ('naniar', '0.6.1', { + 'checksums': ['d546ca15bf6c224f3103eb1441abef91d34feebb7320c2398d598f5d50177450'], + }), + ('stringdist', '0.9.8', { + 'checksums': ['efccd6ccc5c74c578be95b7dae1099c52b0d7805452ab14ee91ca34adb8261bb'], + }), + ('image.binarization', '0.1.2', { + 'checksums': ['0621ca94a74264bb73f689b1a00484b5a3bbef93fc203d9c001d791a18fcc13f'], + }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), + ('lslx', '0.6.10', { + 'checksums': ['adc2b2a621625b52165245ab2f3a0bfba4f4db64fcc6ad48a3e5b219c3bd2fa1'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.8.0', { + 'checksums': ['28ff1c2dbddcafc6ed6c30154f46074aa0c8974757466680529b71a5f3e463ec'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('alabama', '2015.3-1', { + 'checksums': ['6600fcf4842488950e196d3f5a8fc4d69e8271b36292ce67ac3ab697449a8f56'], + }), + ('polycor', '0.7-10', { + 'checksums': ['caea3beca2c889e12e5b976c20c19cf5a76d42e6329e9ab646112eeae8fcfc73'], + }), + ('multipol', '1.0-7', { + 'checksums': ['0abe3c894c0d8e928a920e73708a397133386a0d73a1e7952c4075afe67879e6'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('cSEM', '0.4.0', { + 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + }), + ('cubelyr', '1.0.1', { + 'checksums': ['740a34100592b2c6b7bc89a31bddccf4c8fd95720caf68f530104f17aada77bc'], + }), + ('broom.mixed', '0.2.7', { + 'checksums': ['ff29385557af239a41452ffb5ebe230630a2a30f4a91e95505c3178b62df01ba'], + }), + ('DiceKriging', '1.6.0', { + 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], + }), + ('grf', '2.0.2', { + 'checksums': ['043f21a057762a2d5e0febb37c1d9cb8d2f94d19f2eded20c672dec7ff54b505'], + }), + ('xgboost', '1.4.1.1', { + 'checksums': ['9f986f3895ce5f6744335c82afe3a87d9ac2e473e60785295edf2be80d34e0c4'], + }), + ('twang', '2.5', { + 'checksums': ['fc355527c57e4f6e0f60d26d7c690c4475fcd5fb165d125fea7cc6b9fafc4ce5'], + }), + ('neuralnet', '1.44.2', { + 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], + }), + ('PCAmatchR', '0.3.0', { + 'checksums': ['73876c6d1cf42928a03a64aba197c67b4a4f4de2c431cfbc6fce615bbea32fa0'], + }), + ('origami', '1.0.5', { + 'checksums': ['8d0d08aaecc428cbbf5db4615ad3623777c10c6d7947a1cc3ccc7f8db8cb5263'], + }), + ('hal9001', '0.4.1', { + 'checksums': ['386fa93ae6c0f409a9137adc54da25a2770826fbed63787e33a36c95f3f89441'], + }), + ('cobalt', '4.3.1', { + 'checksums': ['67e26a700ca083a39beb255df54c6ab495f34ea5847a0bf1c4bac895e980eef8'], + }), + ('CBPS', '0.22', { + 'checksums': ['d19247e6765f02737d15a0a2ee86ae24e7206ae740dfaa61821622eb3a309aef'], + }), + ('SBdecomp', '1.1', { + 'checksums': ['ad4e4f00bc58eafe551ad6288c0642a16e16ef8f73c2ae649f808b1e559df644'], + }), + ('naturalsort', '0.1.3', { + 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], + }), + ('lwgeom', '0.2-8', { + 'checksums': ['f48a92de222da0590b37a30d5cbf2364555044a842795f6b488afecc650b8b34'], + }), + ('finalfit', '1.0.3', { + 'checksums': ['bbfa841a2b1a7b1f8c153d773ff076a2e465e451815f8166ff0ce8c4018ff61e'], + }), + ('broom.helpers', '1.4.0', { + 'checksums': ['7f6a5c0c79260b57cd31976bc216fffbc79a1641e01b74630dcd37d2c84e3f75'], + }), + ('gt', '0.3.1', { + 'checksums': ['ddd1fee446f156d1b52bb2db83262aac2a896db93748e92e08407d317e126019'], + }), + ('gtsummary', '1.5.0', { + 'checksums': ['54dd5e11c5b2a808ca93284760a5cd102f820332d2fa40474d5cedea030711a7'], + }), + ('ncdf4', '1.17', { + 'checksums': ['db95c4729d3187d1a56dfd019958216f442be6221bd15e23cd597e6129219af6'], + }), +] + +moduleclass = 'lang' From efab831dbf7ea4f9a0f6014cb28dc3e3a1f5ca49 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 12:14:25 +0000 Subject: [PATCH 1762/9987] remember to add the new DMCfun patch --- .../R/DMCfun-2.0.0_fix-parallel-detect.patch | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/DMCfun-2.0.0_fix-parallel-detect.patch diff --git a/easybuild/easyconfigs/r/R/DMCfun-2.0.0_fix-parallel-detect.patch b/easybuild/easyconfigs/r/R/DMCfun-2.0.0_fix-parallel-detect.patch new file mode 100644 index 00000000000..0756301ff04 --- /dev/null +++ b/easybuild/easyconfigs/r/R/DMCfun-2.0.0_fix-parallel-detect.patch @@ -0,0 +1,38 @@ +# parallal::detectCores() detects physical cores and not available cores. It is ususally problem in queue systems +# like PBS or Slurm. This patch gives solution for that problem for PBS and with Slurm with PBS compatibility switched +# on. For other queue systems, a different solutiom might needed. +# April 13th 2021 by B. Hajgato (UGent) +# Updated for 2.0.0 by Simon Branford (University of Birmingham) +diff -ru DMCfun.orig/MD5 DMCfun/MD5 +--- DMCfun.orig/MD5 2021-01-10 18:50:10.000000000 +0100 ++++ DMCfun/MD5 2021-04-13 09:31:31.242654188 +0200 +@@ -4,7 +4,7 @@ + a835c7e49694b2c835c438362b16946f *R/DMCfun.R + 034299149a3219bf581d440b19d94fbb *R/RcppExports.R + 7d89e703313977e0f0390c301ba41719 *R/dmcData.R +-a3141dac9d27d87db3494c293328358d *R/dmcFit.R ++afbe1e78cad3156de24ae67dd94153c0 *R/dmcFit.R + 2c816b9074882e79af599451d079723d *R/dmcSim.R + 9acbbd1c38bace26bed9c6a50f7c82ea *R/methods.R + 169bfcbfb92b758fb0dd18e481711aa8 *R/plot.R +diff -ru DMCfun.orig/R/dmcFit.R DMCfun/R/dmcFit.R +--- DMCfun.orig/R/dmcFit.R 2020-12-03 18:53:03.000000000 +0100 ++++ DMCfun/R/dmcFit.R 2021-04-13 09:28:47.506520017 +0200 +@@ -159,7 +159,7 @@ + if (nzchar(chk) && (chk == "true")) { + num_cores <- 2L + } else { +- num_cores <- parallel::detectCores() / 2 ++ num_cores <- as.numeric(Sys.getenv("SLURM_CPUS_ON_NODE", Sys.getenv("PBS_NUM_PPN", parallel::detectCores() / 2))) + } + + # Older code (pre June 2020) used doSNOW progress bar +@@ -297,7 +297,7 @@ + if (nzchar(chk) && (chk == "true")) { + num_cores <- 2L + } else { +- num_cores <- parallel::detectCores() / 2 ++ num_cores <- as.numeric(Sys.getenv("SLURM_CPUS_ON_NODE", Sys.getenv("PBS_NUM_PPN", parallel::detectCores() / 2))) + } + cl <- parallel::makeCluster(num_cores) + invisible(parallel::clusterExport(cl = cl, varlist=c("dmcSim", "calculateCostValue"))) From b25aeb4282e655d5cb68a239d3e74fb2cdd45c53 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 12:25:57 +0000 Subject: [PATCH 1763/9987] we bumped the FFTW version in 2021b --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 97d4bd22f64..df383fdfe41 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -40,7 +40,7 @@ dependencies = [ ('libxml2', '2.9.10'), # for XML ('GMP', '6.2.1'), # for igraph ('NLopt', '2.7.0'), # for nloptr - ('FFTW', '3.3.9'), # for fftw + ('FFTW', '3.3.10'), # for fftw ('libsndfile', '1.0.31'), # for seewave ('ICU', '69.1'), # for rJava & gdsfmt ('HDF5', '1.12.1'), # for hdf5r From 6f36960b3d9c0efbd59af44edfd31afcfa1de7ed Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 13:20:42 +0000 Subject: [PATCH 1764/9987] DMCfun patch no longer needed --- .../R/DMCfun-2.0.0_fix-parallel-detect.patch | 38 ------------------- .../easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 7 +--- 2 files changed, 1 insertion(+), 44 deletions(-) delete mode 100644 easybuild/easyconfigs/r/R/DMCfun-2.0.0_fix-parallel-detect.patch diff --git a/easybuild/easyconfigs/r/R/DMCfun-2.0.0_fix-parallel-detect.patch b/easybuild/easyconfigs/r/R/DMCfun-2.0.0_fix-parallel-detect.patch deleted file mode 100644 index 0756301ff04..00000000000 --- a/easybuild/easyconfigs/r/R/DMCfun-2.0.0_fix-parallel-detect.patch +++ /dev/null @@ -1,38 +0,0 @@ -# parallal::detectCores() detects physical cores and not available cores. It is ususally problem in queue systems -# like PBS or Slurm. This patch gives solution for that problem for PBS and with Slurm with PBS compatibility switched -# on. For other queue systems, a different solutiom might needed. -# April 13th 2021 by B. Hajgato (UGent) -# Updated for 2.0.0 by Simon Branford (University of Birmingham) -diff -ru DMCfun.orig/MD5 DMCfun/MD5 ---- DMCfun.orig/MD5 2021-01-10 18:50:10.000000000 +0100 -+++ DMCfun/MD5 2021-04-13 09:31:31.242654188 +0200 -@@ -4,7 +4,7 @@ - a835c7e49694b2c835c438362b16946f *R/DMCfun.R - 034299149a3219bf581d440b19d94fbb *R/RcppExports.R - 7d89e703313977e0f0390c301ba41719 *R/dmcData.R --a3141dac9d27d87db3494c293328358d *R/dmcFit.R -+afbe1e78cad3156de24ae67dd94153c0 *R/dmcFit.R - 2c816b9074882e79af599451d079723d *R/dmcSim.R - 9acbbd1c38bace26bed9c6a50f7c82ea *R/methods.R - 169bfcbfb92b758fb0dd18e481711aa8 *R/plot.R -diff -ru DMCfun.orig/R/dmcFit.R DMCfun/R/dmcFit.R ---- DMCfun.orig/R/dmcFit.R 2020-12-03 18:53:03.000000000 +0100 -+++ DMCfun/R/dmcFit.R 2021-04-13 09:28:47.506520017 +0200 -@@ -159,7 +159,7 @@ - if (nzchar(chk) && (chk == "true")) { - num_cores <- 2L - } else { -- num_cores <- parallel::detectCores() / 2 -+ num_cores <- as.numeric(Sys.getenv("SLURM_CPUS_ON_NODE", Sys.getenv("PBS_NUM_PPN", parallel::detectCores() / 2))) - } - - # Older code (pre June 2020) used doSNOW progress bar -@@ -297,7 +297,7 @@ - if (nzchar(chk) && (chk == "true")) { - num_cores <- 2L - } else { -- num_cores <- parallel::detectCores() / 2 -+ num_cores <- as.numeric(Sys.getenv("SLURM_CPUS_ON_NODE", Sys.getenv("PBS_NUM_PPN", parallel::detectCores() / 2))) - } - cl <- parallel::makeCluster(num_cores) - invisible(parallel::clusterExport(cl = cl, varlist=c("dmcSim", "calculateCostValue"))) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index df383fdfe41..800735da6c1 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -2954,12 +2954,7 @@ exts_list = [ 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], }), ('DMCfun', '2.0.2', { - 'patches': ['DMCfun-2.0.0_fix-parallel-detect.patch'], - 'checksums': [ - '430cbc18f17db11a7941e6a8274a0eefbb8a6b0bdac8800970530d60d5881fde', # DMCfun_2.0.2.tar.gz - # DMCfun-2.0.0_fix-parallel-detect.patch - 'b2605bbe92ab55824d07d89ccd7146a2bede5c41041c9bf560ce6f910e8b51bd', - ], + 'checksums': ['430cbc18f17db11a7941e6a8274a0eefbb8a6b0bdac8800970530d60d5881fde'], }), ('miceadds', '3.11-6', { 'checksums': ['121d03c812fbcf584a25585ac73f6c44f4b5d6cd21b05362ddd15395fb3909f6'], From 0addc5c560cca9037495fdd14e4666f352113576 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 13:48:14 +0000 Subject: [PATCH 1765/9987] adding easyconfigs: Boost-1.77.0-GCC-11.2.0.eb --- .../b/Boost/Boost-1.77.0-GCC-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.77.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..2b47c2abf06 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +## +# Authors:: Denis Kristak +## +name = 'Boost' +version = '1.77.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['5347464af5b14ac54bb945dc68f1dd7c56f0dad7262816b956138fc53bcc0131'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('ICU', '69.1'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' From 94a030b1232a6b04d2bffa69b0f5321fcbf79ac3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 13:49:54 +0000 Subject: [PATCH 1766/9987] adding easyconfigs: Arrow-6.0.0-foss-2021b.eb --- .../a/Arrow/Arrow-6.0.0-foss-2021b.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb new file mode 100644 index 00000000000..e0529cef302 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '6.0.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['69d268f9e82d3ebef595ad1bdc83d4cb02b20c181946a68631f6645d7c1f7a90'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Autotools', '20210726'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('pkg-config', '0.29.2'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy + ('Boost', '1.77.0'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' From f2838ef1fb89ed4ea6ceacfc38e7e4b13d3260a3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 13:51:29 +0000 Subject: [PATCH 1767/9987] adding easyconfigs: arrow-R-6.0.0.2-foss-2021b-R-4.1.2.eb --- .../arrow-R-6.0.0.2-foss-2021b-R-4.1.2.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..c6230b40bac --- /dev/null +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021b-R-4.1.2.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'arrow-R' +version = '6.0.0.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/arrow' +description = "R interface to the Apache Arrow C++ library" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['arrow_%(version)s.tar.gz'] +checksums = ['76808692851eca33ff7ea9532b143db4698689081ce2f8cfe53c3e9e0aee1184'] + +dependencies = [ + ('R', '4.1.2'), + ('Arrow', '6.0.0'), +] + +preinstallopts = "export LIBARROW_BINARY=true && " + +sanity_check_paths = { + 'files': [], + 'dirs': ['arrow'], +} + +options = {'modulename': 'arrow'} + +moduleclass = 'tools' From 92ae95fc8ff1c47ee5b6cc0d82dfdd182b4e1b54 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 1 Nov 2021 16:31:14 +0200 Subject: [PATCH 1768/9987] updating for review --- .../l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb | 29 +++++++++ .../l/libavif/libavif-0.9.0-foss-2020b.eb | 2 +- .../l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 60 +++++++++++++++++++ .../z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 29 +++++++++ .../z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb | 29 +++++++++ 5 files changed, 148 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c477cf445c4 --- /dev/null +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'LibLZF' +version = '3.4' + +homepage = 'http://oldhome.schmorp.de/marc/liblzf.html' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] +sources = ['liblzf-%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_commands = ['lzf -h'] + +sanity_check_paths = { + 'files': ['bin/lzf'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb index 23a8645f597..5ef2dc0e964 100644 --- a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb @@ -29,7 +29,7 @@ dependencies = [ # TODO FIX THIS - NEED THOSE # configopts = ' -DAVIF_CODEC_AOM=ON -DAVIF_CODEC_DAV1D=ON -DAVIF_CODEC_LIBGAV1=ON -DAVIF_CODEC_RAV1E=ON ' sanity_check_paths = { - 'files': ['lib/libavif.so.10.0.0', 'include/avif/avif.h'], + 'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'], 'dirs': ['lib/', 'include/avif/'] } diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d9f77d02677 --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libjxl' +version = '0.6.1' +local_lodepng_version = "48e5364" + +homepage = 'https://github.com/libjxl/libjxl' +description = "JPEG XL image format reference implementation" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'optarch': False} # optarch causes some test failures + +github_account = 'libjxl' +source_urls = [GITHUB_SOURCE] +sources = [ + 'v%(version)s.tar.gz', + {'filename': 'lodepng-%s.tar.gz' % local_lodepng_version, + 'download_filename': local_lodepng_version, + 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], + 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, +] +patches = [ + 'libjxl-0.3.7_external_lcms2.patch', + 'libjxl-%(version)s_remove-broken-test.patch', +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('googletest', '1.10.0'), + ('pkg-config', '0.29.2'), + ('Highway', '0.12.2'), # Highway only has a static library +] + +dependencies = [ + ('LittleCMS', '2.11'), + ('Brotli', '1.0.9'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('giflib', '5.2.1'), + ('libwebp', '1.1.0'), + ('OpenEXR', '2.5.5'), + ('gperftools', '2.9.1'), +] + +configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' +# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) +configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..25cec87e173 --- /dev/null +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Zopfli' +version = '1.0.3' + +homepage = 'https://github.com/google/zopfli' +description = """Zopfli Compression Algorithm is a compression library programmed in C to perform +very good, but slow, deflate or zlib compression.""" + +# toolchain = {'name': 'foss', 'version': '2020b'} +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/', 'include/'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..44717cae450 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'zlib-ng' +version = '2.0.5' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_commands = [ +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/', 'include/'], +} + +moduleclass = 'tools' From de56345c7702d2b8b9336004460613730b26b4b8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 1 Nov 2021 14:51:11 +0000 Subject: [PATCH 1769/9987] correct extensions update date --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 800735da6c1..2a6fb5b6b1d 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -77,7 +77,7 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on 2nd November 2021 +# packages updated on 1st November 2021 exts_list = [ # include packages that are part of the base installation of R, # both to make sure they are available (via sanity check), From 7c68a9a8ab7bc4d92139352cecb9929b380c6e07 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 1 Nov 2021 14:54:52 +0000 Subject: [PATCH 1770/9987] adding easyconfigs: R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb --- ...le-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 1081 +++++++++++++++++ 1 file changed, 1081 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..c92742e51eb --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -0,0 +1,1081 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.14' +versionsuffix = '-R-%(rver)s' + +local_biocver = 3.14 + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('R', '4.1.2'), + ('Boost', '1.77.0'), # for mzR ###### + ('GSL', '2.7'), # for flowClust + ('HDF5', '1.12.1'), # for rhdf5 + ('arrow-R', '6.0.0.2', versionsuffix), # required by RcisTarget +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.14/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.14/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.14/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on 1st November 2021 +exts_list = [ + ('BiocGenerics', '0.40.0', { + 'checksums': ['d045577f491676583a5faca014af9774d993fffb999fdab3b3790a8732e9255b'], + }), + ('Biobase', '2.54.0', { + 'checksums': ['9c3fa69a195ff3001c3614df6b3995a8064083919dfdb4fba1e57aa5de14594d'], + }), + ('S4Vectors', '0.32.0', { + 'checksums': ['09b00dd57bd291f4018163ea1f0fe65e8d87ce15320e1990eac9059c31eda1fe'], + }), + ('IRanges', '2.28.0', { + 'checksums': ['ef860c47be9fbab4a5f413d17401d17ab910ce85b9981058609cbbc5c310fa1f'], + }), + ('GenomeInfoDbData', '1.2.7', { + 'checksums': ['217cbad0dd3ed8f0da6b21c7d35df5737bcbd21e317ca71d2fb6ec4c316b1987'], + }), + ('GenomeInfoDb', '1.30.0', { + 'checksums': ['da1a0d06fc4a0d6e549c74d9351eecf0f46d23f85a375e42ed18129e3e5d1ce4'], + }), + ('zlibbioc', '1.40.0', { + 'checksums': ['1276702b631a9fb50a68364ceae30b52d2076f8f7d7d349291ad7f54fea10d28'], + }), + ('XVector', '0.34.0', { + 'checksums': 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['297e944b50e1ad7da197f35351c7ccf0b448b7d42a2a3119c8d1faf949c6068e'], + }), + ('sparseMatrixStats', '1.6.0', { + 'checksums': ['a19bc467a08fed614c5905d6d2db5fab56d3781bf80993752287d86a1491d845'], + }), + ('DelayedMatrixStats', '1.16.0', { + 'checksums': ['534e33b7f08548a7398416609f02d5ea4952ab7b6042f62ab40cba9cc69c1cdf'], + }), + ('minfi', '1.40.0', { + 'checksums': ['dd1a4590c5e69ce25441d698a66a03e8168b00396ec30d0408f1713b2d10a234'], + }), + ('FDb.InfiniumMethylation.hg19', '2.2.0', { + 'checksums': ['605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f'], + }), + ('methylumi', '2.39.0', { + 'checksums': ['d9ff90a06eb5022abd9e0fceea171b3b9127851479c242fc23f8cfa6d6eed73e'], + }), + ('lumi', '2.46.0', { + 'checksums': ['369e004053e630f90a9a4f68209f566f639dd86e9c271a45875411bb8db9636c'], + }), + ('widgetTools', '1.72.0', { + 'checksums': ['1239f79153d7c7228b86aefeeb9394242aaefb62dbfdbab893dc84800e745249'], + }), + ('tkWidgets', '1.72.0', { + 'checksums': ['6efb04a33230e360f685e8f6a606db37a468cb3936fbed677616439452cf9bf2'], + }), + ('Mfuzz', '2.54.0', { + 'checksums': ['f015462c0d416c057ffb9c724d127659e1145973ea277c8aeb503185bb18665e'], + }), + ('admisc', '0.19', { + 'checksums': ['7c0bc4d86914e1bf05b32f1d1bc5a253ec9b763535595aea58afbcf69507d33f'], + }), + ('venn', '1.10', { + 'checksums': ['65422a158cdc8581182d3d326e448e43ecc3764501a5dab1ccac1234b4f961e4'], + }), + ('maSigPro', '1.66.0', { + 'checksums': ['ebaa80caa013e3d88bf32c4891209da8dbcc517c70248e7547f9e33beb75420b'], + }), + ('SPIA', '2.46.0', { + 'checksums': ['0ffc29805d1e4b4e9d7dfb86985c9fb3f91c242b17215f92a012d586be180e61'], + }), + ('Gviz', '1.38.0', { + 'checksums': ['48255d046049ff24f6f98f6f0ed260c88f46ccce8699e595beef3400463d0a5b'], + }), + ('cummeRbund', '2.36.0', { + 'checksums': ['1477a6e16b8f8d480900eac49f23dd6821d59a0de1051da15e4b49f169866004'], + }), + ('GenomicFiles', '1.30.0', { + 'checksums': ['7d74f9dac3243601f56c45152eb04cff146a9829c77f328bc41e856f6633be44'], + }), + ('derfinderHelper', '1.28.0', { + 'checksums': ['65c0cc5f162b1a160b4e7768083e5b3674fa3bb842667bc354cfdecf85e7a01b'], + }), + ('derfinder', '1.28.0', { + 'checksums': ['97fa810d966f349ce63ce739bde855798baa46e765e79bc7cebed22c2320aec3'], + }), + ('polyester', '1.30.0', { + 'checksums': ['1e81c68f1d1ae06933c751423e4cdd5f21dd7b26a553d65d5fc40937a892290d'], + }), + ('Rsubread', '2.8.0', { + 'checksums': ['7a30fa881b737c823952c60e3e3e300c8076344cc7f8efee1568a62fe83e6d26'], + }), + ('pcaMethods', '1.86.0', { + 'checksums': ['2fb79e823e51b15704811198732ec6d4ff4b9ef023c194d5e18b1265b5d942ba'], + }), + ('marray', '1.72.0', { + 'checksums': ['ff3ff370fdb7f65a548cd7951557527145822f373fd4afe2dd4214897c0148d1'], + }), + ('CGHbase', '1.54.0', { + 'checksums': ['8ddc75282c7a437a67541139d9a73b6f118c93620db9ca8ef1aeb56544e0ddcd'], + }), + ('Wrench', '1.12.0', { + 'checksums': ['d60089f0e6e812fd31760669abb6bcd60a4e790a2c7b54b045ebc9c8b53efbef'], + }), + ('lpsymphony', '1.22.0', { + 'checksums': ['da49e8f36d5a479ead3a1e43e5a7c5676849b9b196f00ea4d95fb1e7c24262af'], + }), + ('IHW', '1.22.0', { + 'checksums': ['1d633fc18078896707ac0550a9d95c1feb1f6bf092bc99d5816e70e57f91f16d'], + }), + ('metagenomeSeq', '1.36.0', { + 'checksums': ['69b264040e1186e76082dab70de624b0a552e0212591bc882f5fad2801f1db3b'], + }), + ('gdsfmt', '1.30.0', { + 'checksums': ['772769400a1b05b6edfc15850988f1929278aa7b5fd6150765c316b3f418f190'], + }), + ('SNPRelate', '1.28.0', { + 'checksums': ['910858527fecd6f601fda052020b8fc69c221758645871dcb7d6e46b19402804'], + }), + ('biomformat', '1.22.0', { + 'checksums': ['27203a5623de744034cac85817b4a4d9ecd6ffcaf084116082133948894cc975'], + }), + ('phyloseq', '1.38.0', { + 'checksums': ['da843432fe402c594fa5abe9d3d30cec1fc3c73aa03086013d7987771c920a4c'], + }), + ('NADA', '1.6-1.1', { + 'checksums': ['670ff6595ba074ed0a930b7a09624d5ef20616379a20e768c1a7b37332aee44a'], + }), + ('truncnorm', '1.0-8', { + 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], + }), + ('zCompositions', '1.3.4', { + 'checksums': ['ae22c86fe92368a26265933f42eecc518b9b69e7d9b698bc31bfaabfc3c48e95'], + }), + ('RcppZiggurat', '0.1.6', { + 'checksums': ['9c78255ca476c945c05a564d1e4da363de714d890e0e27f3b252fd73c50eed71'], + }), + ('Rfast', '2.0.3', { + 'checksums': ['25bc8c4028c021c7135bd86812265d2cf190bc07b3a412c4406f126c22adb0ae'], + }), + ('ALDEx2', '1.26.0', { + 'checksums': ['ae0fd03068ddb47df54641ff03f52e2ceb4d32ae13812a36ca8748fc998ba7cc'], + }), + ('dada2', '1.22.0', { + 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], + 'checksums': [ + '86528f7a71419b34dcd9e9e33cc34b0d0d45018854ad8150b81465ab707442d6', # dada2_1.22.0.tar.gz + # dada2-1.16.0-remove-sse-on-aarch64.patch + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + ], + }), + ('LEA', '3.6.0', { + 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], + 'checksums': [ + '109a86e15e35c4718076f00dca5b60d10e9d9f3e1e28e99b8ae847914f581a26', # LEA_3.6.0.tar.gz + # LEA-3.0.0_support_aarch64_and_ppc64le.patch + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', + ], + }), + ('tximport', '1.22.0', { + 'checksums': ['e4a16b53ac6a0d0c37645e3f16dd60fdefee7576ebe73bec75842299f4c9d770'], + }), + ('SingleCellExperiment', '1.16.0', { + 'checksums': ['69445241bbde85f2a74ca5dc4810ddb2913f574e5b51d56f4ac343a4d72e0704'], + }), + ('beachmat', '2.10.0', { + 'checksums': ['eb5602d3b80e6dce8e146640a1a13afc890d14766c1933d66420b95a064e0cd1'], + }), + ('RcppAnnoy', '0.0.19', { + 'checksums': ['89b209900516f3096b53c90937081fb8965c605c867aa465f1b3b68092b7688a'], + }), + ('RcppHNSW', '0.3.0', { + 'checksums': ['a0eb4eea65e28ba31e8306a1856f7e617a192bd448b148f88abe99181cbde007'], + }), + ('BiocNeighbors', '1.12.0', { + 'checksums': ['f9a900eb19aa4b114e8ebefc720e4795250bdd57f0fe5614a82fbb230d453612'], + }), + ('rsvd', '1.0.5', { + 'checksums': ['e40686b869acd4f71fdb1e8e7a6c64cd6792fc9d52a78f9e559a7176ab84e21e'], + }), + ('ScaledMatrix', '1.2.0', { + 'checksums': ['6c06d4cc4a4cf8a65b88b73ff32884dbdb7512867cf9eb8367fe15fa0221e86f'], + }), + ('BiocSingular', '1.10.0', { + 'checksums': ['96b446c98b5de3d92f08e47bdcd06ecadd5fc31cf7d67bad67b27a3c84327036'], + }), + ('scuttle', '1.4.0', { + 'checksums': ['c710f4258d24a229e122ccf69e0bcb8c104781337e072f690b6072c3bc596db5'], + }), + ('scater', '1.22.0', { + 'checksums': ['afbdb75aa1f72228a547c47751d82e963316333f824a0a882a99755ef94d914c'], + }), + ('sitmo', '2.0.2', { + 'checksums': ['448ef8d56e36783354011845daf33f1efb83ea3b9685eea75eaf5134e24fa8c2'], + }), + ('dqrng', '0.3.0', { + 'checksums': ['4beeabfe245ce7196b07369f2a7d277cb08869ad8b45a22c6354c4cc70a39abb'], + }), + ('bluster', '1.4.0', { + 'checksums': ['55ae7b356012d6d95abc64bd673f85797b60c242521f811a26eaa91145a044c8'], + }), + ('metapod', '1.2.0', { + 'checksums': ['f3e2f5d3ccab202b77d87e9cd5a91dc47a39f87e21a1bee5b0abdff5ee770de9'], + }), + ('scran', '1.22.0', { + 'checksums': ['f44cf46170f6dd4d1ec559ae7c63c9d4acf2c94b3cf2723f8f8f8444b45edbdb'], + }), + ('SC3', '1.22.0', { + 'checksums': ['d58d4739361ced94f7993fec9de6a78848c886ff1fe32561da534745b28d7fed'], + }), + ('ComplexHeatmap', '2.10.0', { + 'checksums': ['963db258af319e5b077288154bf4537495fee9aa919dec7919607e302b399c88'], + }), + ('GENIE3', '1.16.0', { + 'checksums': ['dc193a2c89c5b80014731ff27e74ef93463c80976f72de47cf35de6344324757'], + }), + ('dupRadar', '1.24.0', { + 'checksums': ['d11588be5410f4189bc0cd8b0f3e9fa2f15a5f7268f1546eb2c46bba8331431b'], + }), + ('DNAcopy', '1.68.0', { + 'checksums': ['95ebcf02c0c682f08624045b6ac4346ccffa2a725b0c11e04b249f14c3205da5'], + }), + ('sva', '3.42.0', { + 'checksums': ['b2d5b33a2709e54de9c493a554180dd2c63145181ddbbd0a7b0e8bd8528b9f32'], + }), + ('ballgown', '2.26.0', { + 'checksums': ['2e9b0db08396da8432237a1a8755bbf8d9592a39162f52737fffedac04f2333a'], + }), + ('DropletUtils', '1.14.0', { + 'checksums': ['1f3d75387eeadea48ad4db0116df7584fa57465d3a1f53927a891f6d41bd29fe'], + }), + ('DeconRNASeq', '1.36.0', { + 'checksums': ['5bf34cb0ad1d9394fc0e9eb84cf672ab219ca0bb7095b16b606592874ba7a9ab'], + }), + ('GSVA', '1.42.0', { + 'checksums': ['9e8451d006cc022ebc6c9887fb57935def3411c8285fae8aaf32f8d500a898fc'], + }), + ('PureCN', '2.0.0', { + 'checksums': ['4cad56ab9ea01e2231a5b4788aad4644b130117cf552cfca107ebfdf511d1067'], + }), + ('globaltest', '5.48.0', { + 'checksums': ['2eadae9624688a93017ee2bfa51459a591e487045c4d6c5a8f7072c6c10aed72'], + }), + ('GlobalAncova', '4.12.0', { + 'checksums': ['a009a25bb426f83554dc8fae51b728b8e7bf4654ce55a4192de88e798c12268b'], + }), + ('vsn', '3.62.0', { + 'checksums': ['5dc8a017a0507f65e45503423cd0aefaf65609b0cb81ef5b0b365bb964e3e20e'], + }), + ('mzID', '1.32.0', { + 'checksums': ['31e3908629479118fe32416f8fc1c21dec0ffecd68f01ec1662955d2aa0a0064'], + }), + ('mzR', '2.28.0', { + 'patches': ['mzR-2.22.0_use-external-boost.patch'], + 'checksums': [ + '41e71d2c4e8f7fd9f4db645cb24af8520d529d325fbe200eebc51a2f2507f8ab', # mzR_2.28.0.tar.gz + '8b5ba4f0c4efbbab9b4801d7da3fb04a490a5d95af1cefb489f209afa4d14fb4', # mzR-2.22.0_use-external-boost.patch + ], + }), + ('MsCoreUtils', '1.6.0', { + 'checksums': ['3bbf697df2da404da0a7aff6d18d12ee2a48e7be0bfe213ee39cde91c50e0df1'], + }), + ('MSnbase', '2.20.0', { + 'checksums': ['e58f7314b3aedea0f3292ceb599dfbe9d16de460c03b770667b8ac7ed67fb1e4'], + }), + ('MassSpecWavelet', '1.60.0', { + 'checksums': ['24fec0ed1dc9e36439b7a9fa002324f4b082f8b3fdf609151f3ea9d267f798c5'], + }), + ('MsFeatures', '1.2.0', { + 'checksums': ['3823b872d27bf2dd2be383cedc683ca8156927f9a9c145261ead7d2a63761108'], + }), + ('xcms', '3.16.0', { + 'checksums': ['25d553871462ce67cd3ccea6f8f09fea14fcd65a60ad8b48984409d72c32dc54'], + }), + ('CAMERA', '1.50.0', { + 'checksums': ['70fc13860b75731d2720a249d5343bfb1cad6b275c615ba599d023b9e8afedd5'], + }), + ('fgsea', '1.20.0', { + 'checksums': ['a93e440b6542c2ac2d9221893946546b87f527af66120ab7b67d86456a63d481'], + }), + ('GWASExactHW', '1.01', { + 'checksums': ['e850ed40fbf14b02eb3798603cfb111fe3718bb69d74c0ff4cb6f679209a15a7'], + }), + ('quantsmooth', '1.60.0', { + 'checksums': ['1aa5a93275c052a426ce414a63145cb433723d0911d85eeb29050234e1aefa8c'], + }), + ('GWASTools', '1.40.0', { + 'checksums': ['a99d9522bda98bd00b0adf68b07e3f28f09144eaf8542aab6f58ce114ab7dcb2'], + }), + ('SeqArray', '1.34.0', { + 'checksums': ['0169b9eeb527bd0e79a2e456db034e6fa3e0f14382b8de630b6ae22e342dd48d'], + }), + ('SeqVarTools', '1.32.0', { + 'checksums': ['c6d060801bb22b8faf4685a85e1aa761a1969bc9777af3afdaec5ed9c6c0b12b'], + }), + ('GENESIS', '2.24.0', { + 'checksums': ['5fbdcda14272937fb50e6293dc85a61681336ab37b3654ed67c821eba34a30d8'], + }), + ('MLInterfaces', '1.74.0', { + 'checksums': ['4f4da26cada395ef117cb4a2c72e7960052be2a8a33fa722f7607d8e1d01fedb'], + }), + ('pRoloc', '1.34.0', { + 'checksums': ['7f19543bfee2f31720f630ba603aa23aee2b239776bb9fcd36bd75406969fbbf'], + }), + ('pRolocdata', '1.32.0', { + 'checksums': ['d683bfc38c3feade43539f6599192998d965a0757bc2bd7fc71629d5010345f2'], + }), + ('fresh', '0.2.0', { + 'checksums': ['a92db254ae88e8371efac44efe2cf1f5be7cce62291fdf994ebd68c14dad079d'], + }), + ('waiter', '0.2.4', { + 'checksums': ['4b0af45e609036688bc46f0621bcadf515e6071cbc80d60096d40ca434067d76'], + }), + ('shinydashboardPlus', '2.0.3', { + 'checksums': ['49a88cfa396f880ff4faf558bb038763084287c932e27b0c9251f4d676584d83'], + }), + ('shinyhelper', '0.3.2', { + 'checksums': ['f7ed62543ab4d05a34b69a9183517a09e93e1b2da85b113282de0f9982db90b0'], + }), + ('shinyWidgets', '0.6.2', { + 'checksums': ['2d11d903f5b9c075aa58b2046f4aef33fe344110e97a88d43fb920eedb5fed24'], + }), + ('pRolocGUI', '2.4.0', { + 'checksums': ['daff6fe04ddd8c9479a6fef8bdb7e5899a5f7acaae324fbb161c71e9b348f9e2'], + }), + ('EBImage', '4.36.0', { + 'checksums': ['29181cea9e913e714358527d837de827344038598d300408c1d8dd5b8abd1b0c'], + }), + ('GenomicScores', '2.6.0', { + 'checksums': ['9ad642f15ef7f9d543983bb410bbb91c3ab3cfbafc677c220b059514b188dfa1'], + }), + ('BSgenome.Mmusculus.UCSC.mm10', '1.4.3', { + 'checksums': ['f950e61b79323ba75be3e12304390f20033fcc09a5cff7917e4993a8cfabed08'], + }), + ('TxDb.Mmusculus.UCSC.mm10.knownGene', '3.10.0', { + 'checksums': ['696281749d01737c94894564d62093433045bc007a4528cc3d94f205edb54977'], + }), + ('regioneR', '1.26.0', { + 'checksums': ['4679feea2a0f439b51bd5db789d80a2d516dd2d471e043d8ad3ef7ed3e573578'], + }), + ('InteractionSet', '1.22.0', { + 'checksums': ['5caf717b2927f1ccd4483d4ef21b8994b19ffadf986664a2b2ea8fe3d7ada2a6'], + }), + ('ChIPpeakAnno', '3.28.0', { + 'checksums': ['6b6cf21e3d58d6a7e21b856456f889212222888320e63cbda73670be3fc2cb15'], + }), + ('seqLogo', '1.60.0', { + 'checksums': ['341b9dfdd43102b9f465e46556c499e06515a92aa2ee5991c236894b85e47004'], + }), + ('rGADEM', '2.42.0', { + 'checksums': ['7b709ce7bcda17d9d937e79b766fa174c783b6e6f7a68e06f353d4b3317e1ded'], + }), + ('MotifDb', '1.36.0', { + 'checksums': ['4590b3218b4dba9513b87c228cb48501d2d41ba27cd5315891ebccff8d785f28'], + }), + ('motifStack', '1.38.0', { + 'checksums': ['5fada7533e39f6ee3983740ecff6740053b359d6cd51058e5b152d95ed5a66b2'], + }), + ('ATACseqQC', '1.18.0', { + 'checksums': ['96db9f9cf8d28611494be0c2d0b452e3636320ada6341b6893ba873bdd1a3144'], + }), + ('ResidualMatrix', '1.4.0', { + 'checksums': ['6f27e1d3047c126031170604453d14aeabf6bb90418d5edfbcfd2832aa235677'], + }), + ('batchelor', '1.10.0', { + 'checksums': ['b91184bb32689262ed6c2bc47e30e474cba343b9a6777e15e24bf215028bb32b'], + }), + ('gsmoothr', '0.1.7', { + 'checksums': ['b75ffd2a4a0f357762e02e46e355b45cc90ea637830f0a1b01f216bb4541e903'], + }), + ('Ringo', '1.58.0', { + 'checksums': ['463f04ff993e42f9c29effd7a36607bb6218b5217f98f124f0f635fdccf55a2e'], + }), + ('R.devices', '2.17.0', { + 'checksums': ['c2d4b12949e0faab414c9f7575e39ee9dbf50ea12d858143df529f15ea365fb6'], + }), + ('R.filesets', '2.14.0', { + 'checksums': ['707dd7c099aeadbecebbd2ba57e6400405aa44487c641f3729ce06c4c642bb23'], + }), + ('aroma.light', '3.24.0', { + 'checksums': ['17966f409c13c57037eff86978da4ad75eb8ecac3e1e611feca1a1ab61410a8b'], + }), + ('PSCBS', '0.66.0', { + 'checksums': ['58805636e55e0fd3f57bd4a0e296a8bb3d57a7bdd0fdd5868a73ddc83d173a93'], + }), + ('aroma.core', '3.2.2', { + 'checksums': ['35e0312e403a1894da036afac12d1d727c937e666d7eb400bfe4018b21244855'], + }), + ('R.huge', '0.9.0', { + 'checksums': ['f12d113a965603cfdbbb46e1a57331d267916235555b22f2bbc06caa302ae58e'], + }), + ('aroma.apd', '0.6.0', { + 'checksums': ['87513774baeed8e1d43f819e615c85278aef748ebc842f1ee50686c3392e37d1'], + }), + ('aroma.affymetrix', '3.2.0', { + 'checksums': ['d279cf13cf6ed8369cfdf6682ace12924379bad578003453449aa1ccec31b0a7'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('Repitools', '1.40.0', { + 'checksums': ['27808873e10b3376659a7b96321e2c1eec2b9f4dbca7d824960e57672d169734'], + }), + ('BSgenome.Hsapiens.UCSC.hg38', '1.4.4', { + 'checksums': ['024e3571b70f8e07bd50c4dd4d2dc05288497bf5409a9ac4ef12db94b081b50f'], + }), + ('MEDIPS', '1.46.0', { + 'checksums': ['f7abbddb2373c44680f1565d46bf40d7a83942f15346504560b4d18dcbe97966'], + }), + ('RProtoBufLib', '2.6.0', { + 'patches': ['RProtoBufLib-2.4.0_fix-protobuf-build.patch'], + 'checksums': [ + '20f4fce4dd793d4540556869dab2b3f61bef901f4c1ad67219f942d6e0821413', # RProtoBufLib_2.6.0.tar.gz + # RProtoBufLib-2.4.0_fix-protobuf-build.patch + '379e0227b22ee027de3ab22be9667f358de7d176f74aba598e5a3cbf41dc99a3', + ], + }), + ('cytolib', '2.6.0', { + 'checksums': ['f12ffba1d0e6017bd7f49f1eb84007293e953a6249beb2a61125061aa56b2507'], + }), + ('flowCore', '2.6.0', { + 'checksums': ['97571105031e69b5265ed05acef6293439462d5a6a346bae05d9acd532146d7d'], + }), + ('mutoss', '0.1-12', { + 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], + }), + ('mathjaxr', '1.4-0', { + 'checksums': ['ba57378236d593a39c5839054adc5473526de0c8f05b7eeb87c99438496ddc67'], + }), + ('metap', '1.5', { + 'checksums': ['640b73a49b37494182a836aea01ed87aa09a96ede64cb92d005839f5bf859233'], + }), + ('uwot', '0.1.10', { + 'checksums': ['6ee1b6027bce679cd5a35f647f516a5b327632234bcf323c7f3d5b5e10807d23'], + }), + ('scattermore', '0.7', { + 'checksums': ['f36280197b8476314d6ce81a51c4ae737180b180204043d2937bc25bf3a5dfa2'], + }), + ('sctransform', '0.3.2', { + 'checksums': ['5dbb0a045e514c19f51bbe11c2dba0b72dca1942d6eb044c36b0538b443475dc'], + }), + ('SeuratObject', '4.0.2', { + 'checksums': ['64ee97a221ccaa0bbdc1890da9d3e9cf5b3b9fab037095cfb757db5bbb69cb1c'], + }), + ('Seurat', '4.0.5', { + 'checksums': ['afab7c417500e67a7f784d42ce9b798a2909e44ce97929f86fbbe8b7dca55ba3'], + }), + ('ALL', '1.36.0', { + 'checksums': ['8b96af99fd7e12b73dbb19698cef0c165f40d8ba4f2106bb75b3c0ddd20ca968'], + }), + ('ConsensusClusterPlus', '1.58.0', { + 'checksums': ['79b64f27c5e5e88c1026f5a2b0a0321108604d2d284cb491dff5fc34171ee48f'], + }), + ('flowViz', '1.58.0', { + 'checksums': ['04d0f7ea43b41d873eed3be74ba5becaf7dbb26f48c349c612f71561f1813a0d'], + }), + ('ncdfFlow', '2.40.0', { + 'checksums': ['59ed5dcf53b30f63ff6193abe49d6ca98fe08c84cbf4dc6db9b87922ba58dcb0'], + }), + ('aws.signature', '0.6.0', { + 'checksums': ['f7fe4f686979be21e5a8ba7ae11f0fade4f5aaf4e98063b5349ee0962dbb9496'], + }), + ('aws.s3', '0.3.21', { + 'checksums': ['bd21054ab63555d294e7465dcb6c86f107db52ba841aeac5bdf4d00af0674c8c'], + }), + ('flowWorkspace', '4.6.0', { + 'checksums': ['2fba91bd9622285f409434dec64e25133ad14f36baa0b7e9f82ee834df3cd186'], + }), + ('ash', '1.0-15', { + 'checksums': ['8b0a7bc39dd0ce2172f09edc5b5e029347d041a4d508bbff3f3fd6f69450c2ab'], + }), + ('hdrcde', '3.4', { + 'checksums': ['4341c6a021da46dcae3b1ef6d580e84dcf625c2b2139f537d0c26ec90899149b'], + }), + ('rainbow', '3.6', { + 'checksums': ['63d1246f88a498f3db0321b46a552163631b288a25b24400935db41326636e87'], + }), + ('fds', '1.8', { + 'checksums': ['203a5e7671e542dcb83d4c75d0f4012aaebc32d54f94657afaf9e71e99dd0489'], + }), + ('fda', '5.5.0', { + 'checksums': ['c2cf471dabc879b018211e8de50773a0acbbd10335803612ef9e00060322c759'], + }), + ('flowStats', '4.6.0', { + 'checksums': ['a9e6d149129ec2e7df1992b144e5b8d0fe02dacceaaacead9f7751528dc14e4a'], + }), + ('flowClust', '3.32.0', { + 'installopts': "--configure-args='--with-gsl=${EBROOTGSL} --enable-bundled-gsl=false'", + 'checksums': ['f13b6c14f2d830c99ba9edee01ee5ea47fcf69933b14ff1fef966140f0ac0732'], + }), + ('openCyto', '2.6.0', { + 'checksums': ['d5895fd21413f542d66a8f7156b5cc6dac33e07036f36b499d77a03169c85b87'], + }), + ('ggcyto', '1.22.0', { + 'checksums': ['e102662751a6aac0b2d5b3e83f61ee14d3994f7b740e6686fa823d9194aeb69d'], + }), + ('CytoML', '2.6.0', { + 'checksums': ['9f6515ec03dab19a13404746cda4dbb6653b234fd0225547a56895df04d32f9b'], + }), + ('colorRamps', '2.3', { + 'checksums': ['3f10eab0602a42a2e5a79c7c04638be06cbf1e6f23979a1bd95d853e10940b6a'], + }), + ('ggnewscale', '0.4.5', { + 'checksums': ['021c36230ab6a7e90ac47f70ad26c27e2f68e8c109e31d3df2988af694d35ec2'], + }), + ('ggpointdensity', '0.1.0', { + 'checksums': ['3ea646cf183c8bf7869b122a4ee972b53709056ff443ea71551b823524092a31'], + }), + ('FlowSOM', '2.2.0', { + 'checksums': ['0e5d72c2c94eec13b79333a6047efc2652ec146c6557a47022e88b48d1ce5d18'], + }), + ('HMMcopy', '1.36.0', { + 'checksums': ['b173c885d4db74a193b409cc5a3e6b313a095962cb475c5401fee7bcb76e7b4d'], + }), + ('diffcyt', '1.14.0', { + 'checksums': ['d1965da7f4c675cf23ab89268ccb6d7c06dcf43a094ffdb38167b90818ad89f9'], + }), + ('blme', '1.0-5', { + 'checksums': ['679a4f19d34a584c2390ffab37810a31f6834b913fceaa2409d297ccdf912310'], + }), + ('variancePartition', '1.24.0', { + 'checksums': ['7cc3154dbf402d05c5916951f6574ec422d5f747a1c66bcf46b9f27f5b30be38'], + }), + ('muscat', '1.8.0', { + 'checksums': ['bc14e7a7b86ebd2a5662c038a39347ae2616abaee96f9b94a4fddb11b10eb154'], + }), + ('IlluminaHumanMethylation450kmanifest', '0.4.0', { + 'checksums': ['41b2e54bac3feafc7646fe40bce3aa2b92c10871b0a13657c5736517792fa763'], + }), + ('IlluminaHumanMethylationEPICmanifest', '0.3.0', { + 'checksums': ['e39a69d98486cec981e97c56f45bbe47d2ccb5bbb66a1b16fa0685575493902a'], + }), + ('IlluminaHumanMethylation450kanno.ilmn12.hg19', '0.6.0', { + 'checksums': ['249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15'], + }), + ('IlluminaHumanMethylationEPICanno.ilm10b2.hg19', '0.6.0', { + 'checksums': 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+ ('DRIMSeq', '1.22.0', { + 'checksums': ['02505b5e473f28b8cf710278dfdc39511168bc7596d78f0668710cb320585278'], + }), + ('stageR', '1.16.0', { + 'checksums': ['deb8e996e21745fb24a585646b372ff68cdcd3b2379eba40fc703e48c006fd6e'], + }), + ('isva', '1.9', { + 'checksums': ['9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17'], + }), + ('org.Mm.eg.db', '3.14.0', { + 'checksums': ['56f228448b50f1cea0fc15d6f61b1e94359ef885336034bf346693315390ad45'], + }), + ('org.Rn.eg.db', '3.14.0', { + 'checksums': ['591be1fc4fcc9765bffd412a220c7c37728d986385cf096c8a5c0ada4cfb97dc'], + }), + ('ROC', '1.70.0', { + 'checksums': ['c9cb38bdf1a9af30c15e6c4e8ae9eeb917adcacb3eb3f93901db3e73cbbefdd5'], + }), + ('wateRmelon', '2.0.0', { + 'checksums': ['63be175befd8a8ae3940e6983d5256737ca3ecb138f04b97d1ec966ad978f3cf'], + }), + ('GLAD', '2.58.0', { + 'checksums': ['3616e6cee451f667d456bc35fe1a0940f32d6284372afe0de122856888bba741'], + }), + ('missMethyl', '1.28.0', { + 'checksums': 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['06fbbdd0d0c71e9443b91aedf6750281c9ea23340f857694aa5b48992ea5ca1a'], + }), + ('TFMPvalue', '0.0.8', { + 'checksums': ['6d052529f7b59d0384edc097f724f70468013777b6adf4c63e61a359029d3841'], + }), + ('TFBSTools', '1.32.0', { + 'checksums': ['2fe55b1c0333284eec3a4f2695a77db7007fc8a3dc2fc8af6eff335748d8af48'], + }), + ('motifmatchr', '1.16.0', { + 'checksums': ['ff3c379475040310f5be8ec97c319790e9ba15d2780764d90b3014db3e29f238'], + }), + ('extraDistr', '1.9.1', { + 'checksums': ['9990348c4dbc611684fcb58ab8db7e856dfde1c9c86ffb7705f4b3dff6b2d7bf'], + }), + ('PRROC', '1.3.1', { + 'checksums': ['479118ce47c527bc97fb58d531a31cabc094d9843d62f16922009dc62e8248d4'], + }), + ('TSP', '1.1-11', { + 'checksums': ['49a2b5a762aeeef582f09e8e3f4c6b7a902c06dbae72ada13c2ae627e4eabc3d'], + }), + ('qap', '0.1-1', { + 'checksums': ['60bd564bb0e6325de44351af33870177d84b1c00ded142a2efb12a16a20d4d34'], + }), + ('seriation', '1.3.1', { + 'checksums': ['ce63b4b116f1cd4d8ef8865e9c1b9aacd206071d130d3ed72696b0de873d8321'], + }), + ('egg', '0.4.5', { + 'checksums': ['15c8ba7cf2676eb0460de7e5dfbc89fc3175ac22a8869cfd44d66d156fd6c7bb'], + }), + ('heatmaply', '1.3.0', { + 'checksums': ['0a5d269c4837dd66fbfa6b87fd648bdef222f1ad6f33df3f695d5164d6f71ef1'], + }), + ('OUTRIDER', '1.12.0', { + 'checksums': ['902862ca43442c9fe5a0278ddf007ec8faecfd948ab1d1891700221b3098fa79'], + }), + ('FRASER', '1.6.0', { + 'checksums': ['3d179ac500891a25e97140e0a13d1ce93184257a071a1d64384c576cbf3bb21f'], + }), + ('GenABEL.data', '1.0.0', { + 'checksums': ['2c28d5df63ae13545cf7aea6ce5f22ae1bbb58219fdaed6c1d5d5affc072c65c'], + }), + ('GenABEL', '1.8-0', { + 'checksums': ['434fc806b918738ec67171a37a47099d1706332819317e368fe0ccb8f149a469'], + }), + ('JASPAR2020', '0.99.10', { + 'checksums': ['b9b92d141a317ebb32a14708229f6b82522ceeb5f1b88360d93b0a7cfe30375b'], + }), + ('AUCell', '1.16.0', { + 'checksums': ['b7951f27af5b66f297675577e7920417b9c76d971b7a745d79a66638217294d1'], + }), + ('RcisTarget', '1.14.0', { + 'checksums': ['27bef800117389eb671eca317cbbd984ddc3f4e9c548c6140c7f86d3fac959e1'], + }), + ('NMF', '0.23.0', { + 'checksums': ['0f0cca01b37bf46fce90d2e951df609d3d377908aa607825083fd0c47cc24753'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' From 410d241495be9f8e9e3bb47c799c0d422884d14a Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 1 Nov 2021 15:03:38 +0000 Subject: [PATCH 1771/9987] correction of checksum for misdownload of extension --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index c92742e51eb..1f370b4ed91 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -638,7 +638,7 @@ exts_list = [ 'checksums': ['9ad642f15ef7f9d543983bb410bbb91c3ab3cfbafc677c220b059514b188dfa1'], }), ('BSgenome.Mmusculus.UCSC.mm10', '1.4.3', { - 'checksums': ['f950e61b79323ba75be3e12304390f20033fcc09a5cff7917e4993a8cfabed08'], + 'checksums': ['dcf602bf9fadf1ef4ce70e0c0fc92b6435467df5affe7d0872d88a93b99ff9ee'], }), ('TxDb.Mmusculus.UCSC.mm10.knownGene', '3.10.0', { 'checksums': ['696281749d01737c94894564d62093433045bc007a4528cc3d94f205edb54977'], From 39cea9072c92a232f52b8d7846ccf3cb0f61588b Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 1 Nov 2021 16:28:28 +0100 Subject: [PATCH 1772/9987] Removed PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch and PyTorch-1.10.0_skip-nccl-error-tests.patch from the EasyConfig. This resolves the test failures I got, and I don't hit the original issues that these patches were made for. --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 5 -- ...PyTorch-1.10.0_skip-nccl-error-tests.patch | 78 ------------------- 2 files changed, 83 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nccl-error-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index 82907843f74..4dc2df639a7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -23,12 +23,10 @@ patches = [ 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', - 'PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', - 'PyTorch-1.10.0_skip-nccl-error-tests.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -39,8 +37,6 @@ checksums = [ '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.8.1_increase-distributed-test-timeout.patch '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', - # PyTorch-1.8.1_skip_dist_autograd_sync_streams.patch - '7940e571f41c350d3b634e98b1658a7001c96fdb1b1920835b8f5484ce389d09', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch @@ -49,7 +45,6 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', - '04f3c42d2c1aee94e307d9ef281dd3b3b941f4d8e511e2133fc6521ccebb2ed0', # PyTorch-1.10.skip-nccl-error-tests.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nccl-error-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nccl-error-tests.patch deleted file mode 100644 index 2e69a5c7cc9..00000000000 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nccl-error-tests.patch +++ /dev/null @@ -1,78 +0,0 @@ -diff -Nru pytorch.orig/test/distributed/test_c10d_nccl.py pytorch/test/distributed/test_c10d_nccl.py ---- pytorch.orig/test/distributed/test_c10d_nccl.py 2021-10-22 10:41:08.420327251 +0200 -+++ pytorch/test/distributed/test_c10d_nccl.py 2021-10-22 17:18:52.399649457 +0200 -@@ -2277,6 +2277,7 @@ - @requires_nccl_version((2, 4, 0), "Need NCCL 2.4+ for error checking") - @skip_if_lt_x_gpu(3) - @skip_if_rocm -+ @unittest.skip("Broken on recent NCCL") - def test_nccl_errors_blocking_clean_exit(self): - self._test_nccl_errors_blocking(lambda: sys.exit(0)) - -@@ -2285,6 +2286,7 @@ - @requires_nccl_version((2, 4, 0), "Need NCCL 2.4+ for error checking") - @skip_if_lt_x_gpu(3) - @skip_if_rocm -+ @unittest.skip("Broken on recent NCCL") - def test_nccl_errors_blocking_nonzero_exit(self): - self._test_nccl_errors_blocking(lambda: sys.exit(1)) - -@@ -2296,6 +2298,7 @@ - @sandcastle_skip( - "Frequently times out see https://github.com/pytorch/pytorch/issues/58920" - ) -+ @unittest.skip("Broken on recent NCCL") - def test_nccl_errors_blocking_abort(self): - self._test_nccl_errors_blocking(lambda: os.abort()) - -@@ -2304,6 +2307,7 @@ - @requires_nccl_version((2, 4, 0), "Need NCCL 2.4+ for error checking") - @skip_if_lt_x_gpu(3) - @skip_if_rocm -+ @unittest.skip("Broken on recent NCCL") - def test_nccl_errors_blocking_sigkill(self): - self._test_nccl_errors_blocking(lambda: os.kill(os.getpid(), signal.SIGKILL)) - -@@ -2312,6 +2316,7 @@ - @requires_nccl_version((2, 4, 0), "Need NCCL 2.4+ for error checking") - @skip_if_lt_x_gpu(3) - @skip_if_rocm -+ @unittest.skip("Broken on recent NCCL") - def test_nccl_errors_blocking_sigterm(self): - self._test_nccl_errors_blocking(lambda: os.kill(os.getpid(), signal.SIGTERM)) - -@@ -2319,6 +2324,7 @@ - @requires_nccl() - @requires_nccl_version((2, 4, 0), "Need NCCL 2.4+ for error checking") - @skip_if_lt_x_gpu(3) -+ @unittest.skip("Broken on recent NCCL") - def test_nccl_blocking_wait_with_barrier(self): - store = c10d.FileStore(self.file_name, self.world_size) - process_group = c10d.ProcessGroupNCCL( -@@ -2364,6 +2370,7 @@ - @with_nccl_blocking_wait - @requires_nccl() - @skip_if_lt_x_gpu(3) -+ @unittest.skip("Broken on recent NCCL") - def test_nccl_timeout(self): - store = c10d.FileStore(self.file_name, self.world_size) - -diff -Nru pytorch.orig/torch/testing/_internal/distributed/distributed_test.py pytorch/torch/testing/_internal/distributed/distributed_test.py ---- pytorch.orig/torch/testing/_internal/distributed/distributed_test.py 2021-10-22 10:41:08.329326810 +0200 -+++ pytorch/torch/testing/_internal/distributed/distributed_test.py 2021-10-22 17:14:52.756479108 +0200 -@@ -7352,6 +7352,7 @@ - @require_backends_available({"gloo", "nccl"}) - @skip_if_rocm - @skip_if_lt_x_gpu(int(os.environ["WORLD_SIZE"])) -+ @unittest.skip("Broken on recent NCCL") - def test_monitored_barrier_allreduce_hang(self): - # tests expected behavior when nonzero rank hangs and we want to - # report first timed out rank. -@@ -7362,6 +7363,7 @@ - @require_backends_available({"gloo", "nccl"}) - @skip_if_rocm - @skip_if_lt_x_gpu(int(os.environ["WORLD_SIZE"])) -+ @unittest.skip("Broken on recent NCCL") - def test_monitored_barrier_allreduce_hang_wait_all_ranks(self): - # tests expected behavior when nonzero rank hangs and we want to - # report all timed out ranks. From 93fa3018b7cee95e5822ffae8e50de53c4a4f34e Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 18:45:02 +0000 Subject: [PATCH 1773/9987] Delete libjxl-0.5-GCCcore-10.2.0.eb deleting - old version --- .../l/libjxl/libjxl-0.5-GCCcore-10.2.0.eb | 66 ------------------- 1 file changed, 66 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.2.0.eb deleted file mode 100644 index 100da8372c1..00000000000 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.5-GCCcore-10.2.0.eb +++ /dev/null @@ -1,66 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'libjxl' -version = '0.5' -local_lodepng_version = "48e5364" - -homepage = 'https://github.com/libjxl/libjxl' -description = "JPEG XL image format reference implementation" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'optarch': False} # optarch causes some test failures - -github_account = 'libjxl' -source_urls = [GITHUB_SOURCE] -sources = [ - 'v%(version)s.tar.gz', - {'filename': 'lodepng-%s.tar.gz' % local_lodepng_version, - 'download_filename': local_lodepng_version, - 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], - 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, -] -patches = [ - 'libjxl-0.3.7_external_lcms2.patch', - 'libjxl-%(version)s_remove-broken-test.patch', -] -checksums = [ - '911cb4b50eb621131ca22382166f40d4914a4ff4453dd299ade1e3292f311f89', # v0.5.tar.gz - 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz - '9e6decaf6be74eeccfd5728df175930b4be33de6cbdf9e1816f68cb4b718fa1b', # libjxl-0.3.7_external_lcms2.patch - '5b62751da5b3b3c4aad58a841d49cc506bc330425bbd0df7f19f99aa98c52c26', # libjxl-0.5_remove-broken-test.patch -] - -builddependencies = [ - ('binutils', '2.35'), - ('CMake', '3.18.4'), - ('googletest', '1.10.0'), - ('pkg-config', '0.29.2'), - ('Highway', '0.12.2'), # Highway only has a static library -] - -dependencies = [ - ('LittleCMS', '2.11'), - ('Brotli', '1.0.9'), - ('libjpeg-turbo', '2.0.5'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), - ('giflib', '5.2.1'), - ('libwebp', '1.1.0'), - ('OpenEXR', '2.5.5'), - ('gperftools', '2.9.1'), -] - -configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' -# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) -configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF' - -runtest = "test" - -sanity_check_paths = { - 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'lib' From fa07a984f57378d7ede65b599e12e2c5bf90c90f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 1 Nov 2021 20:46:05 +0200 Subject: [PATCH 1774/9987] updating for tests --- easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb | 1 + .../easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 6 ++++++ .../easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 1 + .../easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb | 1 + 5 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb index c477cf445c4..01e7faabd9f 100644 --- a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] sources = ['liblzf-%(version)s.tar.gz'] +checksums = ['ec62974877b4b85f6e37db97e71678c7abfe83091b57d32ec69fa37b2c3c9499'] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb index 5ef2dc0e964..d92567651e8 100644 --- a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['ea1603fc18e7dd20cf01f0b405156576886ecb5df84db8c0e87187cd2f8a00f4'] builddependencies = [ ('CMake', '3.18.4'), diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index d9f77d02677..21392e1cadb 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -25,6 +25,12 @@ patches = [ 'libjxl-0.3.7_external_lcms2.patch', 'libjxl-%(version)s_remove-broken-test.patch', ] +checksums = [ + 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz + 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz + 'a430237fdef24c07f2187e079dad3041f124d5dc00ec713dba4eb308d78712f6', # libjxl-0.3.7_external_lcms2.patch + '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb index 25cec87e173..280d70f476e 100644 --- a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -15,6 +15,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd'] builddependencies = [ ('CMake', '3.18.4'), diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb index 44717cae450..ebe8e39426d 100644 --- a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/'] sources = ['%(version)s.tar.gz'] +checksums = ['eca3fe72aea7036c31d00ca120493923c4d5b99fe02e6d3322f7c88dbdcd0085'] builddependencies = [ ('CMake', '3.18.4'), From 5767483e8a8c3c72bbd8e6dde3902e4a024fd2c2 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 1 Nov 2021 22:34:21 +0200 Subject: [PATCH 1775/9987] updating for tests --- .../b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb | 30 +++++++++++ .../b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 50 +++++++++++++++++++ .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb | 41 +++++++++++++++ .../j/jxrlib/jxrlib-1.1-foss-2020b.eb | 39 +++++++++++++++ .../easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb | 43 ++++++++++++++++ .../l/libaec/libaec-1.0.6-foss-2020b.eb | 33 ++++++++++++ .../l/liblzma/liblzma-5.2.5-foss-2020b.eb | 1 + .../z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 35 +++++++++++++ 8 files changed, 272 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb create mode 100644 easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d41c44db0ff --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.0.3' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e964d5ced892c7c6afbfdd50511d5087a04c2d60bfd6798feccf813ba27389ff'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..3fc7cbf9e5b --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brunsli-0.1_wrong_paths.patch'] +checksums = [ + '62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc', # v0.1.tar.gz + '34795a1adba1ec208033922eaf27b3b3a23535a2e09201f93f9098666dd7319d', # Brunsli-0.1_wrong_paths.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '0.12.2'), +] + +configopts = ' -DCMAKE_BUILD_TYPE=Release ' +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon "' + +postinstallcmds = [ + 'mkdir %(installdir)s/bin ', + 'cp dbrunsli %(installdir)s/bin ', + 'cp *.a %(installdir)s/lib64 ', + 'cp *.so %(installdir)s/lib64 ', + ] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['bin'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..e49ddd7b1d3 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.49' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-3.48_install_test_data.patch'] +checksums = [ + '5b65a20d5c53494ec8f638267fca4a629836b7ac8dd0ef0266834eab270ed4b3', # cfitsio-3.49.tar.gz + 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch +] + +# curl for HTTPs support +dependencies = [('cURL', '7.72.0')] + +builddependencies = [('binutils', '2.35')] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = '&& make shared && make testprog' + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + ('cd %(installdir)s/share && testprog'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb new file mode 100644 index 00000000000..b43d7b8cf1b --- /dev/null +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +## + +easyblock = 'CMakeMake' + +name = 'jxrlib' +version = '1.1' + +homepage = 'https://deb.debian.org/debian/pool/main/j/jxrlib/' +description = """Open source implementation of jpegxr""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] +sources = ['%(name)s_%(version)s.orig.tar.gz'] +patches = [ + ('%(name)s-%(version)s-foss-2020b_support_cmake.patch', 1), +] +checksums = [ + 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303', # jxrlib_1.1.orig.tar.gz + 'f1c37976b4acdf393b583afe4126d888b3f79bc519c48d2ba9f93a24821077b5', # jxrlib-1.1-foss-2020b_support_cmake.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +modextrapaths = {'CPATH': 'include/jxrlib'} + +sanity_check_paths = { + 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], + 'dirs': ['bin/', 'lib/'], +} + +sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb b/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb new file mode 100644 index 00000000000..cfc5bd3694c --- /dev/null +++ b/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'lerc' +version = '3.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://github.com/Esri/lerc/archive/', + 'https://raw.githubusercontent.com/Esri/lerc/33910e56d2d46e402b6233492eabb6c4fe0b3c5e/src/LercTest/', +] +local_testfile_sed_cmd = "sed -i -e 's|../LercLib/include/||' %(builddir)s/main.cpp" + +sources = [ + 'v%(version)s.tar.gz', + {'filename': 'main.cpp', 'extract_cmd': 'cp %s %(builddir)s && ' + local_testfile_sed_cmd }, +] +checksums = [ + '8c0148f5c22d823eff7b2c999b0781f8095e49a7d3195f13c68c5541dd5740a1', # v3.0.tar.gz + '0e3cc6d8a1d07ad209af9565a6c0736f1d8acb3b04c9c5d922307374352231b9', # main.cpp +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +sanity_check_commands = [ + "cd %(builddir)s && g++ -o output_bin main.cpp -lLerc && ./output_bin " +] + +sanity_check_paths = { + 'files': ['lib/libLerc.so'], + 'dirs': ['lib/', 'include/'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb new file mode 100644 index 00000000000..ef7570cfc23 --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.0.6' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s' ] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +sanity_check_paths = { + 'files': ['bin/aec', 'lib/libaec.a', 'lib/libaec.so.0.0.12'], + 'dirs': ['bin/', 'lib/', 'include/'] +} + +sanity_check_commands = [ + 'aec --help', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb b/easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb index 2349d6b3d2e..14f9ab29eda 100644 --- a/easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb +++ b/easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/xz-mirror/xz/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['0d2b89629f13dd1a0602810529327195eff5f62a0142ccd65b903bc16a4ac78a'] builddependencies = [ ('CMake', '3.18.4'), diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c0eee779075 --- /dev/null +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'MakeCp' + +name = 'zfp' +version = '0.5.5' + +homepage = 'https://github.com/LLNL/zfp' +description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. +zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. +zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and +write large data sets to and from disk.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/zfp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['6a7f4934489087d9c117a4af327fd6495ea757924f4df467b9c537abf8bd86c4'] + +separate_build_dir = True + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +files_to_copy = ['bin', 'lib', 'include'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' From 3ab1e882bf32852987e9040661d8d44b5674dd59 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 20:36:23 +0000 Subject: [PATCH 1776/9987] Delete libaec-1.0.6-foss-2020b.eb accidentally added --- .../l/libaec/libaec-1.0.6-foss-2020b.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb deleted file mode 100644 index ef7570cfc23..00000000000 --- a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb +++ /dev/null @@ -1,33 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'libaec' -version = '1.0.6' - -homepage = 'https://gitlab.dkrz.de/k202009/libaec' -description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers -(samples). The library achieves best results for low entropy data as often encountered in space imaging -instrument data or numerical model output from weather or climate simulations. While floating point representations -are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s' ] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] - -builddependencies = [ - ('CMake', '3.18.4'), -] - -sanity_check_paths = { - 'files': ['bin/aec', 'lib/libaec.a', 'lib/libaec.so.0.0.12'], - 'dirs': ['bin/', 'lib/', 'include/'] -} - -sanity_check_commands = [ - 'aec --help', -] - -moduleclass = 'tools' From 9d3efa71fb010804a40af4cd23ec84dfa6612984 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 20:36:40 +0000 Subject: [PATCH 1777/9987] Delete lerc-3.0-foss-2020b.eb accidentally added --- .../easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb | 43 ------------------- 1 file changed, 43 deletions(-) delete mode 100644 easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb b/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb deleted file mode 100644 index cfc5bd3694c..00000000000 --- a/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb +++ /dev/null @@ -1,43 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Updated: Denis Kristak -easyblock = 'CMakeMake' - -name = 'lerc' -version = '3.0' - -homepage = 'https://github.com/Esri/lerc' -description = """LERC is an open-source image or raster format which supports rapid encoding and decoding -for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, -so the precision of the original input image is preserved (within user defined error bounds).""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = [ - 'https://github.com/Esri/lerc/archive/', - 'https://raw.githubusercontent.com/Esri/lerc/33910e56d2d46e402b6233492eabb6c4fe0b3c5e/src/LercTest/', -] -local_testfile_sed_cmd = "sed -i -e 's|../LercLib/include/||' %(builddir)s/main.cpp" - -sources = [ - 'v%(version)s.tar.gz', - {'filename': 'main.cpp', 'extract_cmd': 'cp %s %(builddir)s && ' + local_testfile_sed_cmd }, -] -checksums = [ - '8c0148f5c22d823eff7b2c999b0781f8095e49a7d3195f13c68c5541dd5740a1', # v3.0.tar.gz - '0e3cc6d8a1d07ad209af9565a6c0736f1d8acb3b04c9c5d922307374352231b9', # main.cpp -] - -builddependencies = [ - ('CMake', '3.18.4'), -] - -sanity_check_commands = [ - "cd %(builddir)s && g++ -o output_bin main.cpp -lLerc && ./output_bin " -] - -sanity_check_paths = { - 'files': ['lib/libLerc.so'], - 'dirs': ['lib/', 'include/'], -} - -moduleclass = 'tools' From caf5f70d6fddf6fe7e8066c21517b82b14c05891 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 20:36:55 +0000 Subject: [PATCH 1778/9987] Delete jxrlib-1.1-foss-2020b.eb accidentally added --- .../j/jxrlib/jxrlib-1.1-foss-2020b.eb | 39 ------------------- 1 file changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb deleted file mode 100644 index b43d7b8cf1b..00000000000 --- a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb +++ /dev/null @@ -1,39 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author:: Denis Kristak (INUITS) -## - -easyblock = 'CMakeMake' - -name = 'jxrlib' -version = '1.1' - -homepage = 'https://deb.debian.org/debian/pool/main/j/jxrlib/' -description = """Open source implementation of jpegxr""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] -sources = ['%(name)s_%(version)s.orig.tar.gz'] -patches = [ - ('%(name)s-%(version)s-foss-2020b_support_cmake.patch', 1), -] -checksums = [ - 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303', # jxrlib_1.1.orig.tar.gz - 'f1c37976b4acdf393b583afe4126d888b3f79bc519c48d2ba9f93a24821077b5', # jxrlib-1.1-foss-2020b_support_cmake.patch -] - -builddependencies = [ - ('CMake', '3.18.4'), -] - -modextrapaths = {'CPATH': 'include/jxrlib'} - -sanity_check_paths = { - 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], - 'dirs': ['bin/', 'lib/'], -} - -sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] - -moduleclass = 'lib' From 48bdef705b1b413442e77e3470563f0c9eb6d29d Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 20:37:13 +0000 Subject: [PATCH 1779/9987] Delete CFITSIO-3.49-GCCcore-10.2.0.eb accidentally added --- .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb deleted file mode 100644 index e49ddd7b1d3..00000000000 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'ConfigureMake' - -name = 'CFITSIO' -version = '3.49' - -homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' -description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in -FITS (Flexible Image Transport System) data format.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] -sources = ['%%(namelower)s-%s.tar.gz' % version] -patches = ['CFITSIO-3.48_install_test_data.patch'] -checksums = [ - '5b65a20d5c53494ec8f638267fca4a629836b7ac8dd0ef0266834eab270ed4b3', # cfitsio-3.49.tar.gz - 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch -] - -# curl for HTTPs support -dependencies = [('cURL', '7.72.0')] - -builddependencies = [('binutils', '2.35')] - -# make would create just static libcfitsio.a. -# Let's create dynamic lib and testprog too. -buildopts = '&& make shared && make testprog' - -sanity_check_paths = { - 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -sanity_check_commands = [ - ('cd %(installdir)s/share && testprog'), -] - -moduleclass = 'lib' From a2f0e021431dafac376813cecc9c1cb77fc2719d Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 20:37:28 +0000 Subject: [PATCH 1780/9987] Delete Brunsli-0.1-GCCcore-10.2.0.eb accidentally added --- .../b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 50 ------------------- 1 file changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb deleted file mode 100644 index 3fc7cbf9e5b..00000000000 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ /dev/null @@ -1,50 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'Brunsli' -version = '0.1' - -homepage = 'https://github.com/google/brunsli/' -description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files -and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still -written in portable C.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = ['https://github.com/google/brunsli/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['Brunsli-0.1_wrong_paths.patch'] -checksums = [ - '62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc', # v0.1.tar.gz - '34795a1adba1ec208033922eaf27b3b3a23535a2e09201f93f9098666dd7319d', # Brunsli-0.1_wrong_paths.patch -] - -builddependencies = [ - ('CMake', '3.18.4'), - ('binutils', '2.35'), -] - -dependencies = [ - ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), -] - -configopts = ' -DCMAKE_BUILD_TYPE=Release ' -configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon "' - -postinstallcmds = [ - 'mkdir %(installdir)s/bin ', - 'cp dbrunsli %(installdir)s/bin ', - 'cp *.a %(installdir)s/lib64 ', - 'cp *.so %(installdir)s/lib64 ', - ] - -sanity_check_paths = { - 'files': ['bin/dbrunsli'], - 'dirs': ['bin'], -} - -sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] - -moduleclass = 'lib' From 628b24a8f40a957829a31f5dc41f96da0f30f50e Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 20:37:42 +0000 Subject: [PATCH 1781/9987] Delete Blosc2-2.0.3-GCCcore-10.2.0.eb accidentally added --- .../b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb deleted file mode 100644 index d41c44db0ff..00000000000 --- a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'Blosc2' -version = '2.0.3' - -homepage = 'https://www.blosc.org/' - -description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['e964d5ced892c7c6afbfdd50511d5087a04c2d60bfd6798feccf813ba27389ff'] - -builddependencies = [ - ('binutils', '2.35'), - ('CMake', '3.18.4'), -] - -sanity_check_paths = { - 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', - 'lib/libblosc2.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' From 97eae38945833d0e96a88a9c41c7b569a815adf0 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 1 Nov 2021 23:32:21 +0200 Subject: [PATCH 1782/9987] fix for tests --- .../l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 65 +++++++++++++++++++ .../z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 33 ++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..be0ec4a4a17 --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -0,0 +1,65 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libjxl' +version = '0.6.1' +local_lodepng_version = "48e5364" + +homepage = 'https://github.com/libjxl/libjxl' +description = "JPEG XL image format reference implementation" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'optarch': False} # optarch causes some test failures + +github_account = 'libjxl' +source_urls = [GITHUB_SOURCE] +sources = [ + 'v%(version)s.tar.gz', + {'filename': 'lodepng-%s.tar.gz' % local_lodepng_version, + 'download_filename': local_lodepng_version, + 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], + 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, +] +patches = [ + 'libjxl-0.6.1_external_lcms2.patch', + 'libjxl-%(version)s_remove-broken-test.patch', +] +checksums = [ + 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz + 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz + '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('googletest', '1.10.0'), + ('pkg-config', '0.29.2'), + ('Highway', '0.12.2'), # Highway only has a static library +] + +dependencies = [ + ('LittleCMS', '2.11'), + ('Brotli', '1.0.9'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('giflib', '5.2.1'), + ('libwebp', '1.1.0'), + ('OpenEXR', '2.5.5'), + ('gperftools', '2.9.1'), +] + +configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' +# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) +configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..80e3ed2438c --- /dev/null +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'MakeCp' + +name = 'zfp' +version = '0.5.5' + +homepage = 'https://github.com/LLNL/zfp' +description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. +zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. +zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and +write large data sets to and from disk.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/zfp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['6a7f4934489087d9c117a4af327fd6495ea757924f4df467b9c537abf8bd86c4'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +files_to_copy = ['bin', 'lib', 'include'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' From c56c50b482efc658ef85a9393a224de419b774c2 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 21:33:51 +0000 Subject: [PATCH 1783/9987] Delete zfp-0.5.5-GCCcore-10.2.0.eb added accidentaly --- .../z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb deleted file mode 100644 index 80e3ed2438c..00000000000 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'MakeCp' - -name = 'zfp' -version = '0.5.5' - -homepage = 'https://github.com/LLNL/zfp' -description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. -zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. -zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and -write large data sets to and from disk.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/LLNL/zfp/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['6a7f4934489087d9c117a4af327fd6495ea757924f4df467b9c537abf8bd86c4'] - -builddependencies = [ - ('CMake', '3.18.4'), - ('binutils', '2.35'), -] - -files_to_copy = ['bin', 'lib', 'include'] - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'include', 'lib'], -} - -moduleclass = 'lib' From 70f8ebec2e3ae6326308786d13b8032358b34996 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 1 Nov 2021 21:34:11 +0000 Subject: [PATCH 1784/9987] Delete libjxl-0.6.1-GCCcore-10.2.0.eb added accidentaly --- .../l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 65 ------------------- 1 file changed, 65 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb deleted file mode 100644 index be0ec4a4a17..00000000000 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ /dev/null @@ -1,65 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'libjxl' -version = '0.6.1' -local_lodepng_version = "48e5364" - -homepage = 'https://github.com/libjxl/libjxl' -description = "JPEG XL image format reference implementation" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'optarch': False} # optarch causes some test failures - -github_account = 'libjxl' -source_urls = [GITHUB_SOURCE] -sources = [ - 'v%(version)s.tar.gz', - {'filename': 'lodepng-%s.tar.gz' % local_lodepng_version, - 'download_filename': local_lodepng_version, - 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], - 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, -] -patches = [ - 'libjxl-0.6.1_external_lcms2.patch', - 'libjxl-%(version)s_remove-broken-test.patch', -] -checksums = [ - 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz - 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz - '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch -] - -builddependencies = [ - ('binutils', '2.35'), - ('CMake', '3.18.4'), - ('googletest', '1.10.0'), - ('pkg-config', '0.29.2'), - ('Highway', '0.12.2'), # Highway only has a static library -] - -dependencies = [ - ('LittleCMS', '2.11'), - ('Brotli', '1.0.9'), - ('libjpeg-turbo', '2.0.5'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), - ('giflib', '5.2.1'), - ('libwebp', '1.1.0'), - ('OpenEXR', '2.5.5'), - ('gperftools', '2.9.1'), -] - -configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' -# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) -configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF' - -runtest = "test" - -sanity_check_paths = { - 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'lib' From 728a8fa9e2874c6da6b343d8d612e2e70e24006a Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 1 Nov 2021 23:34:54 +0200 Subject: [PATCH 1785/9987] fix for tests --- easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 3 +-- easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 2 -- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index 21392e1cadb..be0ec4a4a17 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -22,13 +22,12 @@ sources = [ 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, ] patches = [ - 'libjxl-0.3.7_external_lcms2.patch', + 'libjxl-0.6.1_external_lcms2.patch', 'libjxl-%(version)s_remove-broken-test.patch', ] checksums = [ 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz - 'a430237fdef24c07f2187e079dad3041f124d5dc00ec713dba4eb308d78712f6', # libjxl-0.3.7_external_lcms2.patch '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch ] diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index c0eee779075..80e3ed2438c 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -18,8 +18,6 @@ source_urls = ['https://github.com/LLNL/zfp/archive'] sources = ['%(version)s.tar.gz'] checksums = ['6a7f4934489087d9c117a4af327fd6495ea757924f4df467b9c537abf8bd86c4'] -separate_build_dir = True - builddependencies = [ ('CMake', '3.18.4'), ('binutils', '2.35'), From 1eae49b7c6630862936f5095b0ce8b1b470b1168 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 2 Nov 2021 01:46:26 +0100 Subject: [PATCH 1786/9987] Add missing patch file --- .../eht-imaging-1.2.2-foss-2021a.eb | 1 - .../pyNFFT-1.3.2_fix_nfft3util_header.patch | 24 +++++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/e/eht-imaging/pyNFFT-1.3.2_fix_nfft3util_header.patch diff --git a/easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb b/easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb index ec97f4e949a..3a17162972b 100644 --- a/easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb +++ b/easybuild/easyconfigs/e/eht-imaging/eht-imaging-1.2.2-foss-2021a.eb @@ -20,7 +20,6 @@ dependencies = [ ('NFFT', '3.5.2'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/e/eht-imaging/pyNFFT-1.3.2_fix_nfft3util_header.patch b/easybuild/easyconfigs/e/eht-imaging/pyNFFT-1.3.2_fix_nfft3util_header.patch new file mode 100644 index 00000000000..9c22b9fd048 --- /dev/null +++ b/easybuild/easyconfigs/e/eht-imaging/pyNFFT-1.3.2_fix_nfft3util_header.patch @@ -0,0 +1,24 @@ +Ref. https://github.com/pyNFFT/pyNFFT/pull/58 + +From 224a84b6bb5a0cdc604693cf105a40a3093bc53c Mon Sep 17 00:00:00 2001 +From: Alexander +Date: Tue, 22 Aug 2017 13:28:09 +0300 +Subject: [PATCH] Fix compilation error with NFFT 3.3 + +--- + pynfft/cnfft3util.pxd | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/pynfft/cnfft3util.pxd b/pynfft/cnfft3util.pxd +index 5dbdd18..5f1474b 100644 +--- a/pynfft/cnfft3util.pxd ++++ b/pynfft/cnfft3util.pxd +@@ -17,7 +17,7 @@ + + from cnfft3 cimport fftw_complex + +-cdef extern from "nfft3util.h": ++cdef extern from "nfft3.h": + + void nfft_vrand_unit_complex (fftw_complex *x, int n) + # Inits a vector of random complex numbers in \ From 25f92053f09a24225cbccf090ed5958ac8d9267d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 2 Nov 2021 11:37:44 +0200 Subject: [PATCH 1787/9987] tests --- easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index be0ec4a4a17..f1a925dd52e 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -28,6 +28,7 @@ patches = [ checksums = [ 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz + 'a430237fdef24c07f2187e079dad3041f124d5dc00ec713dba4eb308d78712f6', # libjxl-0.6.1_external_lcms2.patch '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch ] From f9f684aaef28bf6b4b11fa8dbfc13de3788e4405 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 2 Nov 2021 09:49:40 +0000 Subject: [PATCH 1788/9987] Delete liblzf-3.4-GCCcore-10.2.0.eb deleting old version --- .../l/liblzf/liblzf-3.4-GCCcore-10.2.0.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/l/liblzf/liblzf-3.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/liblzf/liblzf-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/liblzf/liblzf-3.4-GCCcore-10.2.0.eb deleted file mode 100644 index 586daf3ca2a..00000000000 --- a/easybuild/easyconfigs/l/liblzf/liblzf-3.4-GCCcore-10.2.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'ConfigureMake' - -name = 'liblzf' -version = '3.4' - -homepage = 'http://oldhome.schmorp.de/marc/liblzf.html' -description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files -and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still -written in portable C.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] -sources = ['liblzf-%(version)s.tar.gz'] - -builddependencies = [ - ('binutils', '2.35'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin'], -} - -moduleclass = 'lib' \ No newline at end of file From 2395a0d452d3768653685eaf8d48d6e4164a676e Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 2 Nov 2021 09:50:01 +0000 Subject: [PATCH 1789/9987] Delete zlib-ng-2.0.5-foss-2020b.eb deleting old version --- .../z/zlib-ng/zlib-ng-2.0.5-foss-2020b.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-foss-2020b.eb diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-foss-2020b.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-foss-2020b.eb deleted file mode 100644 index 4f3a7866d69..00000000000 --- a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-foss-2020b.eb +++ /dev/null @@ -1,28 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Updated: Denis Kristak -easyblock = 'CMakeMake' - -name = 'zlib-ng' -version = '2.0.5' - -homepage = 'https://github.com/zlib-ng/zlib-ng' -description = """zlib data compression library for the next generation systems""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/'] -sources = ['%(version)s.tar.gz'] - -builddependencies = [ - ('CMake', '3.18.4'), -] - -sanity_check_commands = [ -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/', 'include/'], -} - -moduleclass = 'tools' From 434966b4bc3b24bc6ef8bb744d04d11ebe4621df Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 2 Nov 2021 09:50:23 +0000 Subject: [PATCH 1790/9987] Delete zopfli-1.0.3-foss-2020b.eb deleting old version --- .../z/zopfli/zopfli-1.0.3-foss-2020b.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/z/zopfli/zopfli-1.0.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/z/zopfli/zopfli-1.0.3-foss-2020b.eb b/easybuild/easyconfigs/z/zopfli/zopfli-1.0.3-foss-2020b.eb deleted file mode 100644 index fe209004cf0..00000000000 --- a/easybuild/easyconfigs/z/zopfli/zopfli-1.0.3-foss-2020b.eb +++ /dev/null @@ -1,30 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Updated: Denis Kristak -easyblock = 'CMakeMake' - -name = 'zopfli' -version = '1.0.3' - -homepage = 'https://github.com/google/zopfli' -description = """Zopfli Compression Algorithm is a compression library programmed in C to perform -very good, but slow, deflate or zlib compression.""" - -toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] -sources = ['%(name)s-%(version)s.tar.gz'] - -builddependencies = [ - ('CMake', '3.18.4'), -] - -sanity_check_commands = [ -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/', 'include/'], -} - -moduleclass = 'tools' From ff8bf4c7d4169d0100e064c79c9d651bd723c142 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 2 Nov 2021 12:30:38 +0200 Subject: [PATCH 1791/9987] patches --- .../libjxl/libjxl-0.6.1_external_lcms2.patch | 39 ++++++++++++ .../libjxl-0.6.1_remove-broken-test.patch | 63 +++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_external_lcms2.patch create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_remove-broken-test.patch diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_external_lcms2.patch b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_external_lcms2.patch new file mode 100644 index 00000000000..d5a9ee728c9 --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_external_lcms2.patch @@ -0,0 +1,39 @@ +diff -ruN libjxl-main_orig/lib/jxl.cmake libjxl-main/lib/jxl.cmake +--- libjxl-main_orig/lib/jxl.cmake 2021-10-29 19:28:31.000000000 +0100 ++++ libjxl-main/lib/jxl.cmake 2021-11-01 11:40:34.075502429 +0000 +@@ -396,9 +396,6 @@ + $ + ) + else () +- target_include_directories(jxl_enc-obj PRIVATE +- $ +- ) + endif () + + # Headers for exporting/importing public headers +diff -ruN libjxl-main_orig/third_party/CMakeLists.txt libjxl-main/third_party/CMakeLists.txt +--- libjxl-main_orig/third_party/CMakeLists.txt 2021-10-29 19:28:31.000000000 +0100 ++++ libjxl-main/third_party/CMakeLists.txt 2021-11-01 11:42:20.337106560 +0000 +@@ -201,14 +201,14 @@ + configure_file("${CMAKE_CURRENT_SOURCE_DIR}/skcms/LICENSE" + ${PROJECT_BINARY_DIR}/LICENSE.skcms COPYONLY) + endif () +-if (JPEGXL_ENABLE_VIEWERS OR NOT JPEGXL_ENABLE_SKCMS) +- if( NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/lcms/.git" ) +- message(SEND_ERROR "Please run git submodule update --init") +- endif() +- include(lcms2.cmake) +- configure_file("${CMAKE_CURRENT_SOURCE_DIR}/lcms/COPYING" +- ${PROJECT_BINARY_DIR}/LICENSE.lcms COPYONLY) +-endif() ++# if (JPEGXL_ENABLE_VIEWERS OR NOT JPEGXL_ENABLE_SKCMS) ++# if( NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/lcms/.git" ) ++# message(SEND_ERROR "Please run git submodule update --init") ++# endif() ++# include(lcms2.cmake) ++# configure_file("${CMAKE_CURRENT_SOURCE_DIR}/lcms/COPYING" ++# ${PROJECT_BINARY_DIR}/LICENSE.lcms COPYONLY) ++# endif() + + # sjpeg + if (JPEGXL_ENABLE_SJPEG) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_remove-broken-test.patch b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_remove-broken-test.patch new file mode 100644 index 00000000000..af8c7b0bfe5 --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_remove-broken-test.patch @@ -0,0 +1,63 @@ +diff -ruN libjxl-0.6.1_orig/lib/jxl/decode_test.cc libjxl-0.6.1/lib/jxl/decode_test.cc +--- libjxl-0.6.1_orig/lib/jxl/decode_test.cc 2021-11-01 14:01:50.188357223 +0000 ++++ libjxl-0.6.1/lib/jxl/decode_test.cc 2021-11-01 14:02:05.128147260 +0000 +@@ -1701,59 +1701,6 @@ + JxlDecoderDestroy(dec); + } + +-TEST(DecodeTest, PixelTestWithICCProfileLossy) { +- JxlDecoder* dec = JxlDecoderCreate(NULL); +- +- size_t xsize = 123, ysize = 77; +- size_t num_pixels = xsize * ysize; +- std::vector pixels = jxl::test::GetSomeTestImage(xsize, ysize, 3, 0); +- JxlPixelFormat format_orig = {3, JXL_TYPE_UINT16, JXL_BIG_ENDIAN, 0}; +- jxl::CompressParams cparams; +- jxl::PaddedBytes compressed = jxl::CreateTestJXLCodestream( +- jxl::Span(pixels.data(), pixels.size()), xsize, ysize, 3, +- cparams, kCSBF_None, JXL_ORIENT_IDENTITY, /*add_preview=*/false, +- /*add_icc_profile=*/true); +- uint32_t channels = 3; +- +- JxlPixelFormat format = {channels, JXL_TYPE_FLOAT, JXL_LITTLE_ENDIAN, 0}; +- +- std::vector pixels2 = jxl::DecodeWithAPI( +- dec, jxl::Span(compressed.data(), compressed.size()), +- format, /*use_callback=*/false, /*set_buffer_early=*/true, +- /*use_resizable_runner=*/false); +- JxlDecoderReset(dec); +- EXPECT_EQ(num_pixels * channels * 4, pixels2.size()); +- +- // The input pixels use the profile matching GetIccTestProfile, since we set +- // add_icc_profile for CreateTestJXLCodestream to true. +- jxl::ColorEncoding color_encoding0; +- EXPECT_TRUE(color_encoding0.SetICC(GetIccTestProfile())); +- jxl::Span span0(pixels.data(), pixels.size()); +- jxl::CodecInOut io0; +- io0.SetSize(xsize, ysize); +- EXPECT_TRUE(ConvertFromExternal( +- span0, xsize, ysize, color_encoding0, +- /*has_alpha=*/false, false, 16, format_orig.endianness, +- /*flipped_y=*/false, /*pool=*/nullptr, &io0.Main(), /*float_in=*/false)); +- +- // The output pixels are expected to be in the same colorspace as the input +- // profile, as the profile can be represented by enum values. +- jxl::ColorEncoding color_encoding1 = color_encoding0; +- jxl::Span span1(pixels2.data(), pixels2.size()); +- jxl::CodecInOut io1; +- io1.SetSize(xsize, ysize); +- EXPECT_TRUE(ConvertFromExternal( +- span1, xsize, ysize, color_encoding1, +- /*has_alpha=*/false, false, 32, format.endianness, +- /*flipped_y=*/false, /*pool=*/nullptr, &io1.Main(), /*float_in=*/true)); +- +- jxl::ButteraugliParams ba; +- EXPECT_LE(ButteraugliDistance(io0, io1, ba, /*distmap=*/nullptr, nullptr), +- 2.4f); +- +- JxlDecoderDestroy(dec); +-} +- + // Tests the case of lossy sRGB image without alpha channel, decoded to RGB8 + // and to RGBA8 + TEST(DecodeTest, PixelTestOpaqueSrgbLossy) { From df3646d001cf8bfda29d0ac357b168516638bd85 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 2 Nov 2021 12:58:05 +0200 Subject: [PATCH 1792/9987] style checks --- easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index 80e3ed2438c..efd4f455224 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -7,9 +7,9 @@ version = '0.5.5' homepage = 'https://github.com/LLNL/zfp' description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. -zfp provides compressed-array classes that support high throughput read and write random access to individual array elements. -zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications that read and -write large data sets to and from disk.""" +zfp provides compressed-array classes that support high throughput read and write random access to individual array +elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications +that read and write large data sets to and from disk.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} From 67b92b0d3e338ee6a4ea50fa8142fd5d892e2560 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Tue, 2 Nov 2021 12:03:06 +0100 Subject: [PATCH 1793/9987] fix gettid nameclash with glibc 2.30 --- .../b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb | 7 +- .../b/Bazel/Bazel-0.26.1_rename_gettid.patch | 70 +++++++++++++++++++ 2 files changed, 76 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-0.26.1_rename_gettid.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb index 143c380c992..1bd46c4dcff 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb @@ -9,7 +9,12 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] -checksums = ['c0e94f8f818759f3f67af798c38683520c540f469cb41aea8f5e5a0e43f11600'] +patches = ['%(name)s-%(version)s_rename_gettid.patch'] + +checksums = [ + 'c0e94f8f818759f3f67af798c38683520c540f469cb41aea8f5e5a0e43f11600', # bazel-0.26.1-dist.zip + '8639129941a6db079015ea7e04e7f5b6b24da3c963e7eb0488df34439d628f0e', # Bazel-0.26.1_rename_gettid.patch +] builddependencies = [ ('binutils', '2.32'), diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1_rename_gettid.patch b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1_rename_gettid.patch new file mode 100644 index 00000000000..661e7b01c01 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1_rename_gettid.patch @@ -0,0 +1,70 @@ +Rename gettid to sys_gettid to avoid name clash with gettid of glibc 2.30+ +https://github.com/grpc/grpc/commit/de6255941a5e1c2fb2d50e57f84e38c09f45023d +https://github.com/grpc/grpc/commit/57586a1ca7f17b1916aed3dea4ff8de872dbf853 + +diff --git a/third_party/grpc/src/core/lib/gpr/log_linux.cc b/third_party/grpc/src/core/lib/gpr/log_linux.cc +index 561276f0c2..8b597b4cf2 100644 +--- a/third_party/grpc/src/core/lib/gpr/log_linux.cc ++++ b/third_party/grpc/src/core/lib/gpr/log_linux.cc +@@ -40,7 +40,7 @@ + #include + #include + +-static long gettid(void) { return syscall(__NR_gettid); } ++static long sys_gettid(void) { return syscall(__NR_gettid); } + + void gpr_log(const char* file, int line, gpr_log_severity severity, + const char* format, ...) { +@@ -70,7 +70,7 @@ void gpr_default_log(gpr_log_func_args* args) { + gpr_timespec now = gpr_now(GPR_CLOCK_REALTIME); + struct tm tm; + static __thread long tid = 0; +- if (tid == 0) tid = gettid(); ++ if (tid == 0) tid = sys_gettid(); + + timer = static_cast(now.tv_sec); + final_slash = strrchr(args->file, '/'); +diff --git a/third_party/grpc/src/core/lib/gpr/log_posix.cc b/third_party/grpc/src/core/lib/gpr/log_posix.cc +index 0acb225572..cd0b702b94 100644 +--- a/third_party/grpc/src/core/lib/gpr/log_posix.cc ++++ b/third_party/grpc/src/core/lib/gpr/log_posix.cc +@@ -30,7 +30,7 @@ + #include + #include + +-static intptr_t gettid(void) { return (intptr_t)pthread_self(); } ++static intptr_t sys_gettid(void) { return (intptr_t)pthread_self(); } + + void gpr_log(const char* file, int line, gpr_log_severity severity, + const char* format, ...) { +@@ -85,7 +85,7 @@ void gpr_default_log(gpr_log_func_args* args) { + char* prefix; + gpr_asprintf(&prefix, "%s%s.%09d %7tu %s:%d]", + gpr_log_severity_string(args->severity), time_buffer, +- (int)(now.tv_nsec), gettid(), display_file, args->line); ++ (int)(now.tv_nsec), sys_gettid(), display_file, args->line); + + fprintf(stderr, "%-70s %s\n", prefix, args->message); + gpr_free(prefix); +diff --git a/third_party/grpc/src/core/lib/iomgr/ev_epollex_linux.cc b/third_party/grpc/src/core/lib/iomgr/ev_epollex_linux.cc +index 7a4870db78..4258ded8a0 100644 +--- a/third_party/grpc/src/core/lib/iomgr/ev_epollex_linux.cc ++++ b/third_party/grpc/src/core/lib/iomgr/ev_epollex_linux.cc +@@ -1150,7 +1150,7 @@ static void end_worker(grpc_pollset* pollset, grpc_pollset_worker* worker, + } + + #ifndef NDEBUG +-static long gettid(void) { return syscall(__NR_gettid); } ++static long sys_gettid(void) { return syscall(__NR_gettid); } + #endif + + /* pollset->mu lock must be held by the caller before calling this. +@@ -1170,7 +1170,7 @@ static grpc_error* pollset_work(grpc_pollset* pollset, + #define WORKER_PTR (&worker) + #endif + #ifndef NDEBUG +- WORKER_PTR->originator = gettid(); ++ WORKER_PTR->originator = sys_gettid(); + #endif + if (grpc_polling_trace.enabled()) { + gpr_log(GPR_INFO, From c50f08c8e3e47e62f90ce86716b9e53ceaa2a2e0 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 2 Nov 2021 15:59:44 +0200 Subject: [PATCH 1794/9987] fix for tests --- .../b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb | 1 + .../b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 48 +++++ .../b/Brunsli/Brunsli-0.1_wrong_paths.patch | 64 ++++++ .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb | 4 + .../imagecodecs-2021.8.26-foss-2020b.eb | 20 +- .../j/jxrlib/jxrlib-1.1-foss-2020b.eb | 12 +- .../jxrlib-1.1-foss-2020b_support_cmake.patch | 204 ++++++++++++++++++ .../easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb | 43 ++++ .../l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb | 34 +++ 9 files changed, 415 insertions(+), 15 deletions(-) create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1_wrong_paths.patch create mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b_support_cmake.patch create mode 100644 easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb index cc97656d2c1..d41c44db0ff 100644 --- a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.3-GCCcore-10.2.0.eb @@ -14,6 +14,7 @@ toolchainopts = {'pic': True, 'cstd': 'c++11'} source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['e964d5ced892c7c6afbfdd50511d5087a04c2d60bfd6798feccf813ba27389ff'] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..fce89e11c4e --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brunsli-0.1_wrong_paths.patch'] +checksums = [ + '62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc', # v0.1.tar.gz + '34795a1adba1ec208033922eaf27b3b3a23535a2e09201f93f9098666dd7319d', # Brunsli-0.1_wrong_paths.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '0.12.2'), +] + +configopts = ' -DCMAKE_BUILD_TYPE=Release ' +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon "' + +postinstallcmds = [ + 'mkdir %(installdir)s/bin ', + 'cp dbrunsli %(installdir)s/bin ', + 'cp *.a %(installdir)s/lib64 ', + 'cp *.so %(installdir)s/lib64 ', + ] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['bin'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1_wrong_paths.patch b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1_wrong_paths.patch new file mode 100644 index 00000000000..ef00a795e09 --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1_wrong_paths.patch @@ -0,0 +1,64 @@ +diff -ruN brunsli-0.1_orig/c/dec/brunsli_decode.cc brunsli-0.1/c/dec/brunsli_decode.cc +--- brunsli-0.1_orig/c/dec/brunsli_decode.cc 2021-09-29 15:46:08.292937193 +0100 ++++ brunsli-0.1/c/dec/brunsli_decode.cc 2021-09-30 12:27:04.564828827 +0100 +@@ -13,7 +13,7 @@ + #include + #include + +-#include ++#include "/scratch/gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/Brotli/1.0.9-GCCcore-10.2.0/include/brotli/decode.h" + #include "../common/constants.h" + #include "../common/context.h" + #include "../common/lehmer_code.h" +diff -ruN brunsli-0.1_orig/Makefile brunsli-0.1/Makefile +--- brunsli-0.1_orig/Makefile 2021-09-29 15:46:08.292937193 +0100 ++++ brunsli-0.1/Makefile 2021-09-29 15:47:40.451603687 +0100 +@@ -1,8 +1,8 @@ + OS := $(shell uname) + BINDIR = bin + OBJDIR = $(BINDIR)/obj +-BROTLI_DIR = third_party/brotli +-BROTLI_INCLUDE = $(BROTLI_DIR)/c/include ++BROTLI_DIR = $EBROOTBROTLI ++BROTLI_INCLUDE = $(BROTLI_DIR)/include + BRUNSLI_INCLUDE = c/include + SOURCES = $(wildcard c/common/*.cc) $(wildcard c/dec/*.cc) \ + $(wildcard c/enc/*.cc) +diff -ruN brunsli-0.1_orig/third_party/CMakeLists.txt brunsli-0.1/third_party/CMakeLists.txt +--- brunsli-0.1_orig/third_party/CMakeLists.txt 2021-09-29 15:46:08.300937078 +0100 ++++ brunsli-0.1/third_party/CMakeLists.txt 2021-09-29 15:48:26.650928556 +0100 +@@ -5,13 +5,13 @@ + # https://opensource.org/licenses/MIT. + + # brotli +-if (NOT TARGET brotlicommon-static) +- if (NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/brotli/c/include/brotli/decode.h") +- message(SEND_ERROR "Brotli is required to build brunsli, run \"git submodule update --init\" to get it, then run cmake again") +- endif () +- add_subdirectory(brotli EXCLUDE_FROM_ALL) +-endif () ++# if (NOT TARGET brotlicommon-static) ++# if (NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/brotli/c/include/brotli/decode.h") ++# message(SEND_ERROR "Brotli is required to build brunsli, run \"git submodule update --init\" to get it, then run cmake again") ++# endif () ++# add_subdirectory(brotli EXCLUDE_FROM_ALL) ++# endif () + +-if (NOT TARGET gtest_main) +- add_subdirectory(googletest EXCLUDE_FROM_ALL) +-endif () ++# if (NOT TARGET gtest_main) ++# add_subdirectory(googletest EXCLUDE_FROM_ALL) ++# endif () +diff -ruN brunsli-0.1_orig/WORKSPACE brunsli-0.1/WORKSPACE +--- brunsli-0.1_orig/WORKSPACE 2021-09-29 15:46:08.292937193 +0100 ++++ brunsli-0.1/WORKSPACE 2021-09-30 12:23:24.610917528 +0100 +@@ -7,7 +7,7 @@ + + local_repository( + name = "brotli", +- path = "third_party/brotli", ++ path = "/scratch/gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/Brotli/1.0.9-GCCcore-10.2.0/", + ) + + new_local_repository( diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb index 3d4e1b6d407..e49ddd7b1d3 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.2.0.eb @@ -15,6 +15,10 @@ toolchainopts = {'pic': True} source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s-%s.tar.gz' % version] patches = ['CFITSIO-3.48_install_test_data.patch'] +checksums = [ + '5b65a20d5c53494ec8f638267fca4a629836b7ac8dd0ef0266834eab270ed4b3', # cfitsio-3.49.tar.gz + 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch +] # curl for HTTPs support dependencies = [('cURL', '7.72.0')] diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index c75dc12b18c..e16110f851a 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -1,6 +1,6 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Denis Kristak -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'imagecodecs' version = '2021.8.26' @@ -18,12 +18,6 @@ toolchain = {'name': 'foss', 'version': '2020b'} local_extract_cmd = ' tar -xvf %s ' local_extract_cmd += ' && find . -type f -print0 | xargs -0 dos2unix ' -sources = [{ - 'source_urls': PYPI_SOURCE, - 'filename': SOURCE_TAR_GZ, - 'extract_cmd': local_extract_cmd, -}] - dependencies = [ ('Python', '3.8.6'), ('matplotlib', '3.3.3'), @@ -45,7 +39,7 @@ dependencies = [ ('libjxl', '0.5'), ('liblzf', '3.4'), ('libpng', '1.6.37'), - ('liblzma', '5.2.5'), + ('XZ', '5.2.5'), ('libpng', '1.6.37'), ('LibTIFF', '4.1.0'), ('libwebp', '1.1.0'), @@ -66,6 +60,7 @@ exts_defaultclass = 'PythonPackage' exts_default_options = { 'use_pip': True, 'download_dep_fail': True, + 'sanity_pip_check': True } exts_list = [ @@ -73,10 +68,11 @@ exts_list = [ 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'] }), + (name, version, { + 'source_urls': PYPI_SOURCE, + 'filename': SOURCE_TAR_GZ, + 'extract_cmd': local_extract_cmd, + }), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb index e4d4ecdf8e2..ded422afcf0 100644 --- a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'jxrlib' version = '1.1' -homepage = 'https://archive.codeplex.com/?p=jxrlib' +homepage = 'https://deb.debian.org/debian/pool/main/j/jxrlib/' description = """Open source implementation of jpegxr""" toolchain = {'name': 'foss', 'version': '2020b'} @@ -18,6 +18,10 @@ sources = ['%(name)s_%(version)s.orig.tar.gz'] patches = [ ('%(name)s-%(version)s-foss-2020b_support_cmake.patch', 1), ] +checksums = [ + 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303', # jxrlib_1.1.orig.tar.gz + 'f1c37976b4acdf393b583afe4126d888b3f79bc519c48d2ba9f93a24821077b5', # jxrlib-1.1-foss-2020b_support_cmake.patch +] builddependencies = [ ('CMake', '3.18.4'), @@ -26,8 +30,10 @@ builddependencies = [ modextrapaths = {'CPATH': 'include/jxrlib'} sanity_check_paths = { - 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', 'lib/libjpegxr.so.0'], - 'dirs': ['bin/', 'lib/'], + 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], + 'dirs': [], } +sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b_support_cmake.patch b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b_support_cmake.patch new file mode 100644 index 00000000000..56c174ad93d --- /dev/null +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b_support_cmake.patch @@ -0,0 +1,204 @@ +From 68a6e95de65ba6c6774586b73902eb8f47836f92 Mon Sep 17 00:00:00 2001 +From: Dean M Greer +Date: Tue, 24 Feb 2021 21:07:30 -0400 +Subject: [PATCH] Add ability to build using cmake +diff --git a/CMakeLists.txt b/CMakeLists.txt +new file mode 100644 +index 0000000..2d6cfac +--- /dev/null ++++ b/CMakeLists.txt +@@ -0,0 +1,142 @@ ++# Copyright Mathieu Malaterre ++# BSD (Same as jxrlib) ++# Based on https://jxrlib.codeplex.com/discussions/440294 ++cmake_minimum_required(VERSION 2.8) ++project(jxrlib C) ++ ++# Need shared libs for ABI ++set(BUILD_SHARED_LIBS ON) ++ ++# helper macro to preserve original Makefile convention ++macro(JXR_MAKE_OBJ SET_NAME) ++ foreach(src ${SRC_${SET_NAME}}) ++ list(APPEND OBJ_${SET_NAME} ${DIR_${SET_NAME}}/${src}) ++ endforeach() ++endmacro() ++ ++if(NOT MSVC) ++ add_definitions(-D__ANSI__) ++ add_compile_options(-Wno-error=implicit-function-declaration) ++endif() ++ ++include(TestBigEndian) ++test_big_endian(ISBIGENDIAN) ++if(ISBIGENDIAN) ++ set(DEF_ENDIAN _BIG__ENDIAN_) ++endif() ++ ++set(DIR_SYS image/sys) ++set(DIR_DEC image/decode) ++set(DIR_ENC image/encode) ++ ++set(DIR_GLUE jxrgluelib) ++set(DIR_TEST jxrtestlib) ++set(DIR_EXEC jxrencoderdecoder) ++ ++set(VERSION "@VERSION@") ++set(SOVERSION "0") ++ ++if(NOT JXRLIB_INSTALL_BINDIR) ++ set(JXRLIB_INSTALL_BINDIR "bin") ++endif() ++ ++if(NOT JXRLIB_INSTALL_LIBDIR) ++ set(JXRLIB_INSTALL_LIBDIR "lib") ++endif() ++ ++if(NOT JXRLIB_INSTALL_INCLUDEDIR) ++ set(JXRLIB_INSTALL_INCLUDEDIR "include/jxrlib") ++endif() ++ ++include_directories( ++ common/include ++ ${DIR_SYS} ++ ${DIR_GLUE} ++ ${DIR_TEST} ++) ++ ++# JPEG-XR ++set(SRC_SYS adapthuff.c image.c strcodec.c strPredQuant.c strTransform.c perfTimerANSI.c) ++JXR_MAKE_OBJ(SYS) ++set(SRC_DEC decode.c postprocess.c segdec.c strdec.c strInvTransform.c strPredQuantDec.c JXRTranscode.c) ++JXR_MAKE_OBJ(DEC) ++set(SRC_ENC encode.c segenc.c strenc.c strFwdTransform.c strPredQuantEnc.c) ++JXR_MAKE_OBJ(ENC) ++ ++add_library(jpegxr ${OBJ_ENC} ${OBJ_DEC} ${OBJ_SYS}) ++set_property(TARGET jpegxr ++ PROPERTY COMPILE_DEFINITIONS __ANSI__ DISABLE_PERF_MEASUREMENT ${DEF_ENDIAN} ++) ++set_property(TARGET jpegxr PROPERTY LINK_INTERFACE_LIBRARIES "") ++set_property(TARGET jpegxr PROPERTY COMPILE_FLAGS -w) ++set_property(TARGET jpegxr PROPERTY VERSION ${VERSION}) ++set_property(TARGET jpegxr PROPERTY SOVERSION ${SOVERSION}) ++install(TARGETS jpegxr ++ EXPORT JXRLibTargets ++ RUNTIME DESTINATION ${JXRLIB_INSTALL_BINDIR} COMPONENT Applications ++ LIBRARY DESTINATION ${JXRLIB_INSTALL_LIBDIR} COMPONENT Libraries ++) ++ ++# JXR-GLUE ++set(SRC_GLUE JXRGlue.c JXRMeta.c JXRGluePFC.c JXRGlueJxr.c) ++JXR_MAKE_OBJ(GLUE) ++set(SRC_TEST JXRTest.c JXRTestBmp.c JXRTestHdr.c JXRTestPnm.c JXRTestTif.c JXRTestYUV.c) ++JXR_MAKE_OBJ(TEST) ++ ++add_library(jxrglue ${OBJ_GLUE} ${OBJ_TEST}) ++set_property(TARGET jxrglue ++ PROPERTY COMPILE_DEFINITIONS __ANSI__ DISABLE_PERF_MEASUREMENT ${DEF_ENDIAN} ++) ++set_property(TARGET jxrglue PROPERTY COMPILE_FLAGS -w) ++set_property(TARGET jxrglue PROPERTY VERSION ${VERSION}) ++set_property(TARGET jxrglue PROPERTY SOVERSION ${SOVERSION}) ++install(TARGETS jxrglue ++ EXPORT JXRLibTargets ++ RUNTIME DESTINATION ${JXRLIB_INSTALL_BINDIR} COMPONENT Applications ++ LIBRARY DESTINATION ${JXRLIB_INSTALL_LIBDIR} COMPONENT Libraries ++) ++ ++target_link_libraries(jxrglue PRIVATE jpegxr m) ++ ++# Enc app files ++set(ENCAPP JxrEncApp) ++add_executable(${ENCAPP} ${DIR_EXEC}/${ENCAPP}.c) ++set_property(TARGET ${ENCAPP} ++ PROPERTY COMPILE_DEFINITIONS __ANSI__ DISABLE_PERF_MEASUREMENT ${DEF_ENDIAN} ++) ++set_property(TARGET ${ENCAPP} PROPERTY COMPILE_FLAGS -w) ++target_link_libraries(${ENCAPP} jxrglue) # jpegxr) ++install(TARGETS ${ENCAPP} RUNTIME DESTINATION ${JXRLIB_INSTALL_BINDIR}) ++ ++# Dec app files ++set(DECAPP JxrDecApp) ++add_executable(${DECAPP} ${DIR_EXEC}/${DECAPP}.c) ++set_property(TARGET ${DECAPP} ++ PROPERTY COMPILE_DEFINITIONS __ANSI__ DISABLE_PERF_MEASUREMENT ${DEF_ENDIAN} ++) ++set_property(TARGET ${DECAPP} PROPERTY COMPILE_FLAGS -w) ++target_link_libraries(${DECAPP} jxrglue) # jpegxr) ++install(TARGETS ${DECAPP} RUNTIME DESTINATION ${JXRLIB_INSTALL_BINDIR}) ++ ++# Generate pkgconfig file ++include(JoinPaths.cmake) ++join_paths(JXRLIB_PKGCONF_LIBDIR "\${prefix}" "${JXRLIB_INSTALL_LIBDIR}") ++join_paths(JXRLIB_PKGCONF_INCLUDEDIR "\${prefix}" "${JXRLIB_INSTALL_INCLUDEDIR}") ++configure_file( ++ "${PROJECT_SOURCE_DIR}/jxrlib.pc.in" ++ ${PROJECT_BINARY_DIR}/jxrlib.pc ++ @ONLY ++) ++install( ++ FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}.pc ++ DESTINATION ${JXRLIB_INSTALL_LIBDIR}/pkgconfig ++) ++ ++# install rules ++install(FILES jxrgluelib/JXRGlue.h jxrgluelib/JXRMeta.h jxrtestlib/JXRTest.h ++ image/sys/windowsmediaphoto.h ++ DESTINATION ${JXRLIB_INSTALL_INCLUDEDIR} COMPONENT Headers ++) ++install(DIRECTORY common/include/ DESTINATION ${JXRLIB_INSTALL_INCLUDEDIR} ++ FILES_MATCHING PATTERN "*.h" ++) +diff --git a/JoinPaths.cmake b/JoinPaths.cmake +new file mode 100644 +index 0000000..a767270 +--- /dev/null ++++ b/JoinPaths.cmake +@@ -0,0 +1,26 @@ ++# This module provides a function for joining paths ++# known from most languages ++# ++# SPDX-License-Identifier: (MIT OR CC0-1.0) ++# Copyright 2020 Jan Tojnar ++# https://github.com/jtojnar/cmake-snips ++# ++# Modelled after Python’s os.path.join ++# https://docs.python.org/3.7/library/os.path.html#os.path.join ++# Windows not supported ++function(join_paths joined_path first_path_segment) ++ set(temp_path "${first_path_segment}") ++ foreach(current_segment IN LISTS ARGN) ++ if(NOT ("${current_segment}" STREQUAL "")) ++ string(REGEX REPLACE "^${CMAKE_INSTALL_PREFIX}/?" "" new_segment "${current_segment}") ++ if(NOT ("${new_segment}" STREQUAL "")) ++ if(NOT IS_ABSOLUTE "${current_segment}" OR NOT "${current_segment}" MATCHES "^${new_segment}$") ++ set(temp_path "${temp_path}/${new_segment}") ++ else() ++ set(temp_path "${current_segment}") ++ endif() ++ endif() ++ endif() ++ endforeach() ++ set(${joined_path} "${temp_path}" PARENT_SCOPE) ++endfunction() +diff --git a/jxrlib.pc.in b/jxrlib.pc.in +new file mode 100644 +index 0000000..be9170c +--- /dev/null ++++ b/jxrlib.pc.in +@@ -0,0 +1,12 @@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++libdir=@JXRLIB_PKGCONF_LIBDIR@ ++includedir=@JXRLIB_PKGCONF_INCLUDEDIR@ ++ ++Name: jxrlib ++Description: A library for reading JPEG XR images. ++ ++Version: @VERSION@ ++Libs: -L${libdir} -ljpegxr -ljxrglue ++Libs.private: -lm ++Cflags: -I${includedir} -D__ANSI__ -DDISABLE_PERF_MEASUREMENT +-- +2.24.3 (Apple Git-128) diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb new file mode 100644 index 00000000000..8994fa0fbee --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'LERC' +version = '3.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [ + 'https://github.com/Esri/lerc/archive/', + 'https://raw.githubusercontent.com/Esri/lerc/33910e56d2d46e402b6233492eabb6c4fe0b3c5e/src/LercTest/', +] +local_testfile_sed_cmd = "sed -i -e 's|../LercLib/include/||' %(builddir)s/main.cpp" + +sources = [ + 'v%(version)s.tar.gz', + {'filename': 'main.cpp', 'extract_cmd': 'cp %s %(builddir)s && ' + local_testfile_sed_cmd }, +] +checksums = [ + '8c0148f5c22d823eff7b2c999b0781f8095e49a7d3195f13c68c5541dd5740a1', # v3.0.tar.gz + '0e3cc6d8a1d07ad209af9565a6c0736f1d8acb3b04c9c5d922307374352231b9', # main.cpp +] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +sanity_check_commands = [ + "cd %(builddir)s && g++ -o output_bin main.cpp -lLerc && ./output_bin " +] + +sanity_check_paths = { + 'files': ['lib/libLerc.%s' % SHLIB_EXT], + 'dirs': ['lib/', 'include/'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6a3ff1593cb --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.0.6' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s' ] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/aec', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['bin/', 'lib/', 'include/'] +} + +sanity_check_commands = [ + 'aec --help', +] + +moduleclass = 'tools' From 153e3c82e271b6bce3a8783c4a54c9ecba9d7f68 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 2 Nov 2021 15:31:53 +0000 Subject: [PATCH 1795/9987] Delete brunsli-0.1-foss-2020b.eb deleting old file --- .../b/brunsli/brunsli-0.1-foss-2020b.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/b/brunsli/brunsli-0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/brunsli/brunsli-0.1-foss-2020b.eb b/easybuild/easyconfigs/b/brunsli/brunsli-0.1-foss-2020b.eb deleted file mode 100644 index 2939240b1b6..00000000000 --- a/easybuild/easyconfigs/b/brunsli/brunsli-0.1-foss-2020b.eb +++ /dev/null @@ -1,44 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'brunsli' -version = '0.1' - -homepage = 'https://github.com/google/brunsli/' -description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files -and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still -written in portable C.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://github.com/google/brunsli/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['patch_brunsli.patch'] - -builddependencies = [ - ('CMake', '3.18.4'), - ('binutils', '2.35'), -] - -dependencies = [ - ('Brotli', '1.0.9'), - ('Highway', '0.12.2'), -] - -configopts = ' -DCMAKE_BUILD_TYPE=Release ' -configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon "' - -postinstallcmds = [ - 'mkdir %(installdir)s/bin ', - 'cp dbrunsli %(installdir)s/bin ', - 'cp *.a %(installdir)s/lib64 ', - 'cp *.so %(installdir)s/lib64 ', - ] - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin'], -} - -moduleclass = 'lib' From fb8a0bd3a5a570b4a541e6cef74668f7e40e8195 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 2 Nov 2021 15:49:37 +0000 Subject: [PATCH 1796/9987] Update imagecodecs-2021.8.26-foss-2020b.eb adding checksums --- .../i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index e16110f851a..0b6499d7040 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -66,12 +66,14 @@ exts_default_options = { exts_list = [ ('bitshuffle', '0.3.5', { 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'] + 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'], + 'checksums': ['c3f4461d8013e3d9db0d58defec77b143164652de505a1fba3df088eaa19be2f'], }), (name, version, { 'source_urls': PYPI_SOURCE, 'filename': SOURCE_TAR_GZ, 'extract_cmd': local_extract_cmd, + 'checksums': ['e87994d918ea951a589ec46648c24d9c7e56b7b5c2466d93f3b07883f0ecea19'], }), ] From 36795387994927fc2c2670f9cc37dae24ff4dc1d Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 2 Nov 2021 18:05:32 +0100 Subject: [PATCH 1797/9987] Added patches to resolve cond-cpu test failuers and test_lstm failure --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 6 ++++ .../PyTorch-1.10.0_fix-test-cond-cpu.patch | 32 +++++++++++++++++++ .../PyTorch-1.10.0_fix-vnni-detection.patch | 22 +++++++++++++ 3 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-cond-cpu.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vnni-detection.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index 4dc2df639a7..7d1af983839 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -27,6 +27,8 @@ patches = [ 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-vnni-detection.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -45,6 +47,10 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-test-cond-cpu.patch + '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-vnni-detection.patch + '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-cond-cpu.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-cond-cpu.patch new file mode 100644 index 00000000000..df38550bf1f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-cond-cpu.patch @@ -0,0 +1,32 @@ +# Author: Caspar van Leeuwen, SURF +# +# Tests test_cond_cpu_complex128, test_cond_cpu_complex64, +# test_cond_cpu_float32, test_cond_cpu_float64, failed with +# "numpy.linalg.LinAlgError: SVD did not converge" +# when numpy was build with OpenBLAS 0.3.15 or newer. +# Now, these tests simply pass if this error is raised. +# +# See https://github.com/pytorch/pytorch/issues/67675 +# Patch based on https://github.com/pytorch/pytorch/pull/67679 +--- + test/test_linalg.py | 7 ++++++- + 1 file changed, 6 insertions(+), 1 deletion(-) + +diff --git a/test/test_linalg.py b/test/test_linalg.py +index d7494dfebe10..9eb3d0bf7d99 100644 +--- a/test/test_linalg.py ++++ b/test/test_linalg.py +@@ -1638,7 +1638,12 @@ def run_test_case(input, p): + a = torch.eye(3, dtype=dtype, device=device) + a[-1, -1] = 0 # make 'a' singular + for p in norm_types: +- run_test_case(a, p) ++ try: ++ run_test_case(a, p) ++ except np.linalg.LinAlgError: ++ # Numpy may fail to converge for some BLAS backends ++ # See the discussion in https://github.com/pytorch/pytorch/issues/67675 ++ pass + + # test for 0x0 matrices. NumPy doesn't work for such input, we return 0 + input_sizes = [(0, 0), (2, 5, 0, 0)] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vnni-detection.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vnni-detection.patch new file mode 100644 index 00000000000..944e85363a3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vnni-detection.patch @@ -0,0 +1,22 @@ +# Author: Caspar van Leeuwen, SURF +# +# A bug in the test_lstm test was triggered on machines with AVX512_vnni support +# See https://github.com/pytorch/pytorch/issues/59098 +# It was supposed to skip this test based on IS_AVX512_VNNI_SUPPORTED +# But the test function only searched for 'avx512vnni', while my /proc/cpuinfo +# contained 'avx512_vnni' +# This patch should fix the avx512_vnni detection and skip any incompatible tests +# VNNI detection issue: https://github.com/pytorch/pytorch/issues/67685 +# And PR: https://github.com/pytorch/pytorch/pull/67686 +diff -Nru pytorch.orig/torch/testing/_internal/common_utils.py pytorch/torch/testing/_internal/common_utils.py +--- pytorch.orig/torch/testing/_internal/common_utils.py 2021-11-02 15:50:14.328727067 +0100 ++++ pytorch/torch/testing/_internal/common_utils.py 2021-11-02 15:59:44.621177782 +0100 +@@ -620,7 +620,7 @@ + return False + with open("/proc/cpuinfo", encoding="ascii") as f: + lines = f.read() +- return "avx512vnni" in lines ++ return any(s in lines for s in ("avx512_vnni", "avx512vnni")) + + IS_AVX512_VNNI_SUPPORTED = is_avx512_vnni_supported() + From 4dd7ce94dd86442e093da399203417cfba5d04dc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 2 Nov 2021 21:37:35 +0100 Subject: [PATCH 1798/9987] adding easyconfigs: jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb --- ...proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb diff --git a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb new file mode 100644 index 00000000000..bb6dac7c994 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb @@ -0,0 +1,55 @@ +easyblock = "PythonBundle" + +name = 'jupyter-matlab-proxy' +version = '0.3.4' +local_matlab_version = '2021a' +versionsuffix = '-MATLAB-%s' % local_matlab_version + +homepage = 'https://github.com/mathworks/jupyter-matlab-proxy' +description = 'MATLAB Integration for Jupyter' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +dependencies = [ + ('Python', '3.9.5'), + ('JupyterLab', '3.0.16'), # Contains most of the jupyter dependencies we need. + ('nodejs', '14.17.2'), + ('MATLAB', local_matlab_version, '', True), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('typing_extensions', '3.10.0.2', { + 'checksums': ['49f75d16ff11f1cd258e1b988ccff82a3ca5570217d7ad8c5f48205dd99a677e'], + }), + ('async-timeout', '3.0.1', { + 'checksums': ['0c3c816a028d47f659d6ff5c745cb2acf1f966da1fe5c19c77a70282b25f4c5f'], + }), + ('multidict', '5.2.0', { + 'checksums': ['0dd1c93edb444b33ba2274b66f63def8a327d607c6c790772f448a53b6ea59ce'], + }), + ('yarl', '1.7.0', { + 'checksums': ['8e7ebaf62e19c2feb097ffb7c94deb0f0c9fab52590784c8cd679d30ab009162'], + }), + ('aiohttp', '3.7.4.post0', { + 'checksums': ['493d3299ebe5f5a7c66b9819eacdcfbbaaf1a8e84911ddffcdc48888497afecf'], + }), + ('simpervisor', '0.4', { + 'checksums': ['cec79e13cdbd6edb04a5c98c1ff8d4bd9713e706c069226909a1ef0e89d393c5'], + }), + ('jupyter-server-proxy', '3.1.0', { + 'checksums': ['30d57976090980f4380cb0a80e8e829dfd74d0a19edb64329239def9feefcde4'], + }), + (name, version, { + 'checksums': ['05235c77aadf6ffb2b7193f6c6e4962eff68e4e5908370525363180d81bf9348'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter-matlab-app'], + 'dirs': ['lib64/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'math' From bd69d81d9afc8211d8eccc2c641a64a1420e0a19 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 2 Nov 2021 23:03:06 +0100 Subject: [PATCH 1799/9987] Drop nodejs version --- .../jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb index bb6dac7c994..60d76cbd07e 100644 --- a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb +++ b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} dependencies = [ ('Python', '3.9.5'), ('JupyterLab', '3.0.16'), # Contains most of the jupyter dependencies we need. - ('nodejs', '14.17.2'), + ('nodejs', '14.17.0'), ('MATLAB', local_matlab_version, '', True), ] From c5d5f1dc2116995ad8343ea4d91d7217dadc8f1d Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 3 Nov 2021 09:07:37 +0000 Subject: [PATCH 1800/9987] Delete lerc-3.0-foss-2020b.eb delete old file --- .../easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb b/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb deleted file mode 100644 index f464f98fd48..00000000000 --- a/easybuild/easyconfigs/l/lerc/lerc-3.0-foss-2020b.eb +++ /dev/null @@ -1,40 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Updated: Denis Kristak -easyblock = 'CMakeMake' - -name = 'lerc' -version = '3.0' - -homepage = 'https://github.com/Esri/lerc' -description = """LERC is an open-source image or raster format which supports rapid encoding and decoding -for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, -so the precision of the original input image is preserved (within user defined error bounds).""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = [ - 'https://github.com/Esri/lerc/archive/', - 'https://raw.githubusercontent.com/Esri/lerc/33910e56d2d46e402b6233492eabb6c4fe0b3c5e/src/LercTest/', -] - -local_testfile_sed_cmd = "sed -i -e 's|../LercLib/include/||' %(builddir)s/main.cpp" - -sources = [ - 'v%(version)s.tar.gz', - {'filename': 'main.cpp', 'extract_cmd': 'cp %s %(builddir)s && ' + local_testfile_sed_cmd }, -] - -builddependencies = [ - ('CMake', '3.18.4'), -] - -sanity_check_commands = [ - "cd %(builddir)s && g++ -o output_bin main.cpp -lLerc && ./output_bin " -] - -sanity_check_paths = { - 'files': ['lib/libLerc.so'], - 'dirs': ['lib/', 'include/'], -} - -moduleclass = 'tools' From 4335c4bd0ce943fabb85dc3490f66adae8f296d3 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 3 Nov 2021 09:09:36 +0000 Subject: [PATCH 1801/9987] Delete libaec-1.0.6-foss-2020b.eb old file --- .../l/libaec/libaec-1.0.6-foss-2020b.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb deleted file mode 100644 index 673a8af6e8d..00000000000 --- a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-foss-2020b.eb +++ /dev/null @@ -1,32 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'libaec' -version = '1.0.6' - -homepage = 'https://gitlab.dkrz.de/k202009/libaec' -description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers -(samples). The library achieves best results for low entropy data as often encountered in space imaging -instrument data or numerical model output from weather or climate simulations. While floating point representations -are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s' ] -sources = [SOURCELOWER_TAR_GZ] - -builddependencies = [ - ('CMake', '3.18.4'), -] - -sanity_check_paths = { - 'files': ['bin/aec', 'lib/libaec.a', 'lib/libaec.so.0.0.12'], - 'dirs': ['bin/', 'lib/', 'include/'] -} - -sanity_check_commands = [ - 'aec --help', -] - -moduleclass = 'tools' From edc189c60a58057f5a61b75e4ba1d4a18d9a8a35 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 3 Nov 2021 11:17:13 +0200 Subject: [PATCH 1802/9987] changes for tests --- easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb | 3 ++- easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index fce89e11c4e..caadf4deda0 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -36,7 +36,7 @@ postinstallcmds = [ 'cp dbrunsli %(installdir)s/bin ', 'cp *.a %(installdir)s/lib64 ', 'cp *.so %(installdir)s/lib64 ', - ] +] sanity_check_paths = { 'files': ['bin/dbrunsli'], diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb index 8994fa0fbee..2e086d2db32 100644 --- a/easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb @@ -16,11 +16,12 @@ source_urls = [ 'https://github.com/Esri/lerc/archive/', 'https://raw.githubusercontent.com/Esri/lerc/33910e56d2d46e402b6233492eabb6c4fe0b3c5e/src/LercTest/', ] + local_testfile_sed_cmd = "sed -i -e 's|../LercLib/include/||' %(builddir)s/main.cpp" sources = [ 'v%(version)s.tar.gz', - {'filename': 'main.cpp', 'extract_cmd': 'cp %s %(builddir)s && ' + local_testfile_sed_cmd }, + {'filename': 'main.cpp', 'extract_cmd': 'cp %s %(builddir)s && ' + local_testfile_sed_cmd}, ] checksums = [ '8c0148f5c22d823eff7b2c999b0781f8095e49a7d3195f13c68c5541dd5740a1', # v3.0.tar.gz diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb index 6a3ff1593cb..b29e2d04011 100644 --- a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ are not directly supported, they can also be efficiently coded by grouping expon toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s' ] +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] From 48f4002770f8ce04c526e501bbc69a903b7c5004 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 3 Nov 2021 10:59:16 +0100 Subject: [PATCH 1803/9987] Revert version change --- .../jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb index 60d76cbd07e..43fb01bd01b 100644 --- a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb +++ b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} dependencies = [ ('Python', '3.9.5'), ('JupyterLab', '3.0.16'), # Contains most of the jupyter dependencies we need. - ('nodejs', '14.17.0'), + ('nodejs', '14.17.2'), ('MATLAB', local_matlab_version, '', True), ] @@ -48,7 +48,7 @@ exts_list = [ ] sanity_check_paths = { - 'files': ['bin/jupyter-matlab-app'], + 'files': ['bin/matlab-jupyter-app'], 'dirs': ['lib64/python%(pyshortver)s/site-packages'] } From d4d477e23422698bf2cbc7e78ee51120ce7d1b57 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 3 Nov 2021 12:04:10 +0200 Subject: [PATCH 1804/9987] changes for tests --- .../imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index 0b6499d7040..8440baa6492 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -31,13 +31,13 @@ dependencies = [ ('giflib', '5.2.1'), ('jxrlib', '1.1'), ('LittleCMS', '2.11'), - ('lerc', '3.0'), + ('LERC', '3.0'), ('libaec', '1.0.6'), ('libavif', '0.9.0'), ('libdeflate', '1.7'), ('libjpeg-turbo', '2.0.5'), ('libjxl', '0.5'), - ('liblzf', '3.4'), + ('LibLZF', '3.4'), ('libpng', '1.6.37'), ('XZ', '5.2.5'), ('libpng', '1.6.37'), @@ -51,7 +51,7 @@ dependencies = [ ('zopfli', '1.0.3'), ('zfp', '0.5.5'), ('zstd', '1.4.5'), - ('brunsli', '0.1'), + ('Brunsli', '0.1'), ('HDF5', '1.10.7'), ('h5py', '3.1.0'), ] @@ -70,9 +70,9 @@ exts_list = [ 'checksums': ['c3f4461d8013e3d9db0d58defec77b143164652de505a1fba3df088eaa19be2f'], }), (name, version, { - 'source_urls': PYPI_SOURCE, - 'filename': SOURCE_TAR_GZ, - 'extract_cmd': local_extract_cmd, + 'extract_cmd': " tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix ", + 'filename': '%(name)s-%(version)s.tar.gz', + 'source_urls': 'https://pypi.python.org/packages/source/%(nameletter)s/%(name)s', 'checksums': ['e87994d918ea951a589ec46648c24d9c7e56b7b5c2466d93f3b07883f0ecea19'], }), ] From e6b4df285c12735b55efbbe8a672d14eca795f8c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 3 Nov 2021 11:18:57 +0100 Subject: [PATCH 1805/9987] adding easyconfigs: AOCC-3.1.0-GCCcore-11.2.0.eb --- .../a/AOCC/AOCC-3.1.0-GCCcore-11.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..506f4cdc296 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-3.1.0-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +name = 'AOCC' +version = '3.1.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 12.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['1948104a430506fe5e445c0c796d6956109e7cc9fc0a1e32c9f1285cfd566d0c'] + +clangversion = '12.0.0' + +dependencies = [ + ('binutils', '2.37'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), +] + +moduleclass = 'compiler' From 1507d186a948b2c805700b05366b8bc07ab751a8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 3 Nov 2021 12:37:12 +0200 Subject: [PATCH 1806/9987] Add Xvfb dep --- .../jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb index 43fb01bd01b..7af08812cf3 100644 --- a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb +++ b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb @@ -14,6 +14,7 @@ dependencies = [ ('Python', '3.9.5'), ('JupyterLab', '3.0.16'), # Contains most of the jupyter dependencies we need. ('nodejs', '14.17.2'), + ('Xvfb', '1.20.11'), ('MATLAB', local_matlab_version, '', True), ] From 7ef417227b0c36431e1271098c12a96fbc8ac0fc Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 3 Nov 2021 11:56:13 +0100 Subject: [PATCH 1807/9987] adding easyconfigs: likwid-5.2.0-GCCcore-11.2.0.eb --- .../l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ff19c3f5246 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] + +builddependencies = [ + ('binutils', '2.37'), + ('Perl', '5.34.0'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCCcore toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' + +maxparallel = 1 + +installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ="" ACCESSMODE=perf_event ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' From 4a61ad1c10cfca306e59d1e6475cc5ccb344b2e0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 3 Nov 2021 15:00:21 +0200 Subject: [PATCH 1808/9987] adding easyconfigs: AlphaFold-2.1.0-fosscuda-2020b.eb and patches: AlphaFold-2.0.1_relax_gpu.patch, AlphaFold-2.1.0_data-dep-paths.patch, AlphaFold-2.1.0_fix-scp-path.patch --- .../AlphaFold/AlphaFold-2.0.1_relax_gpu.patch | 41 ++++ .../AlphaFold-2.1.0-fosscuda-2020b.eb | 189 ++++++++++++++++++ .../AlphaFold-2.1.0_data-dep-paths.patch | 129 ++++++++++++ .../AlphaFold-2.1.0_fix-scp-path.patch | 15 ++ 4 files changed, 374 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_relax_gpu.patch create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_fix-scp-path.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_relax_gpu.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_relax_gpu.patch new file mode 100644 index 00000000000..cb152af365a --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.0.1_relax_gpu.patch @@ -0,0 +1,41 @@ +# Thomas Hoffmann, EMLB Heidelberg, structures-it@embl.de, 2021/10 +# EricDeveaud, 050e84f993e4de05b6aede7ea2e189b10e335d0e: allow to run amber_minimize.py on CPU (default) or GPU +diff -ru alphafold-2.0.1/alphafold/relax/amber_minimize.py alphafold_relax_gpu/alphafold/relax/amber_minimize.py +--- alphafold-2.0.1/alphafold/relax/amber_minimize.py 2021-09-10 14:34:22.000000000 +0200 ++++ alphafold_relax_gpu/alphafold/relax/amber_minimize.py 2021-10-15 16:01:51.702378793 +0200 +@@ -15,6 +15,7 @@ + """Restrained Amber Minimization of a structure.""" + + import io ++import os + import time + from typing import Collection, Optional, Sequence + +@@ -35,6 +36,8 @@ + ENERGY = unit.kilocalories_per_mole + LENGTH = unit.angstroms + ++#--- allow to run ambermininmize on selected platform CPU//GPU ++OPENMM_PLATFORM=os.environ.get('OPENMM_RELAX', 'CPU') + + def will_restrain(atom: openmm_app.Atom, rset: str) -> bool: + """Returns True if the atom will be restrained by the given restraint set.""" +@@ -90,7 +93,7 @@ + _add_restraints(system, pdb, stiffness, restraint_set, exclude_residues) + + integrator = openmm.LangevinIntegrator(0, 0.01, 0.0) +- platform = openmm.Platform.getPlatformByName("CPU") ++ platform = openmm.Platform.getPlatformByName(OPENMM_PLATFORM) + simulation = openmm_app.Simulation( + pdb.topology, system, integrator, platform) + simulation.context.setPositions(pdb.positions) +@@ -530,7 +533,7 @@ + simulation = openmm_app.Simulation(openmm_pdbs[0].topology, + system, + openmm.LangevinIntegrator(0, 0.01, 0.0), +- openmm.Platform.getPlatformByName("CPU")) ++ openmm.Platform.getPlatformByName(OPENMM_PLATFORM)) + energies = [] + for pdb in openmm_pdbs: + try: +Only in alphafold_relax_gpu: .git diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..7903ac041b1 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb @@ -0,0 +1,189 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.1.0' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('TensorFlow', '2.4.1'), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.19'), # also provides absl-py +] +configopts = "-DCUDA_CUDA_LIBRARY=${EBROOTCUDA}/lib64/stubs/libcuda.so " +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('http://two.embl.de/OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.1.0_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.0.1_relax_gpu.patch' + ], + 'checksums': [ + '43df277943937307d7ac2db0f5e3d1d317061df4ffff46061059a81b61ad5083', # v2.1.0.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + 'e02e1298b59038078a2107e1c04b14172898e1f79b7f3afc2394047db532e228', # AlphaFold-2.1.0_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + '3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', + 'ALPHAFOLD_DATA_DIR': '/scratch/AlphaFold_DBs', + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch new file mode 100644 index 00000000000..c8f846999db --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch @@ -0,0 +1,129 @@ +pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data +(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py); +pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) +update 2.0.1 -> 2.1.0: Thomas Hoffmann (EMBL); +diff -ru alphafold-2.1.0/run_alphafold.py alphafold-2.1.0_data-dep-paths/run_alphafold.py +--- alphafold-2.1.0/run_alphafold.py 2021-11-02 15:33:58.000000000 +0100 ++++ alphafold-2.1.0_data-dep-paths/run_alphafold.py 2021-11-03 13:04:31.131894917 +0100 +@@ -1,3 +1,4 @@ ++#!/usr/bin/env python + # Copyright 2021 DeepMind Technologies Limited + # + # Licensed under the Apache License, Version 2.0 (the "License"); +@@ -40,6 +41,44 @@ + + from alphafold.model import data + # Internal import (7716). ++use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:]) ++use_monomer_preset = any("--model_preset=monomer" in s for s in sys.argv[1:]) ++ ++data_dir = os.getenv('ALPHAFOLD_DATA_DIR') ++ ++if data_dir: ++ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters.fa') ++ uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') ++ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') ++ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') ++ obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') ++ if use_monomer_preset: ++ pdb_seqres_database_path = None ++ uniprot_database_path = None ++ else: ++ pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt') ++ uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.data') ++ if use_reduced_dbs: ++ small_bfd_database_path = os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta') ++ uniclust30_database_path = None ++ bfd_database_path = None ++ else: ++ small_bfd_database_path = None ++ bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') ++ uniclust30_database_path = os.path.join(data_dir, 'uniclust30', 'uniclust30_2018_08', 'uniclust30_2018_08') ++else: ++ sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!") ++ uniref90_database_path = None ++ mgnify_database_path = None ++ bfd_database_path = None ++ uniclust30_database_path = None ++ pdb70_database_path = None ++ template_mmcif_dir = None ++ obsolete_pdbs_path = None ++ small_bfd_database_path = None ++ uniprot_database_path = None ++ pdb_seqres_database_path = None ++ + + logging.set_verbosity(logging.INFO) + +@@ -56,7 +95,7 @@ + 'origin is unknown. These values determine the pairing ' + 'method for the MSA.') + +-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') ++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') + flags.DEFINE_string('output_dir', None, 'Path to a directory that will ' + 'store the results.') + flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'), +@@ -71,27 +110,27 @@ + 'Path to the hmmbuild executable.') + flags.DEFINE_string('kalign_binary_path', shutil.which('kalign'), + 'Path to the Kalign executable.') +-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 ' ++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify ' ++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD ' ++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD ' + 'database for use by HHblits.') +-flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small ' ++flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small ' + 'version of BFD used with the "reduced_dbs" preset.') +-flags.DEFINE_string('uniclust30_database_path', None, 'Path to the Uniclust30 ' ++flags.DEFINE_string('uniclust30_database_path', uniclust30_database_path, 'Path to the Uniclust30 ' + 'database for use by HHblits.') +-flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot ' ++flags.DEFINE_string('uniprot_database_path', uniprot_database_path, 'Path to the Uniprot ' + 'database for use by JackHMMer.') +-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 ' ++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 ' + 'database for use by HHsearch.') +-flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB ' ++flags.DEFINE_string('pdb_seqres_database_path', pdb_seqres_database_path, 'Path to the PDB ' + 'seqres database for use by hmmsearch.') +-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with ' ++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with ' + 'template mmCIF structures, each named .cif') + flags.DEFINE_string('max_template_date', None, 'Maximum template release date ' + 'to consider. Important if folding historical test sets.') +-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a ' ++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a ' + 'mapping from obsolete PDB IDs to the PDB IDs of their ' + 'replacements.') + flags.DEFINE_enum('db_preset', 'full_dbs', +@@ -281,6 +320,9 @@ + 'sure it is installed on your system.') + + use_small_bfd = FLAGS.db_preset == 'reduced_dbs' ++ if use_small_bfd and data_dir: ++ bfd_database_path = None ++ uniclust30_database_path = None + _check_flag('small_bfd_database_path', 'db_preset', + should_be_set=use_small_bfd) + _check_flag('bfd_database_path', 'db_preset', +@@ -416,12 +458,7 @@ + flags.mark_flags_as_required([ + 'fasta_paths', + 'output_dir', +- 'data_dir', +- 'uniref90_database_path', +- 'mgnify_database_path', +- 'template_mmcif_dir', + 'max_template_date', +- 'obsolete_pdbs_path', + ]) + + app.run(main) +Only in alphafold-2.1.0_data-dep-paths: .run_alphafold.py.swp diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_fix-scp-path.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_fix-scp-path.patch new file mode 100644 index 00000000000..849ee5120b3 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_fix-scp-path.patch @@ -0,0 +1,15 @@ +fix path to stereo_chemical_props.txt when AlphaFold is installed with EasyBuild +author: Kenneth Hoste (HPC-UGent) +update 2.0.0 -> 2.1.0: Thomas Hoffmann (EMBL Heidelberg) +diff -ru alphafold-2.1.0/alphafold/common/residue_constants.py alphafold-2.1.0_fix-scp-path/alphafold/common/residue_constants.py +--- alphafold-2.1.0/alphafold/common/residue_constants.py 2021-11-02 15:33:58.000000000 +0100 ++++ alphafold-2.1.0_fix-scp-path/alphafold/common/residue_constants.py 2021-11-03 09:57:23.162319184 +0100 +@@ -404,7 +404,7 @@ + residue_bond_angles: Dict that maps resname -> list of BondAngle tuples. + """ + stereo_chemical_props_path = os.path.join( +- os.path.dirname(os.path.abspath(__file__)), 'stereo_chemical_props.txt' ++ os.path.join(os.getenv('EBROOTALPHAFOLD', 'alphafold/common'), 'stereo_chemical_props.txt') + ) + with open(stereo_chemical_props_path, 'rt') as f: + stereo_chemical_props = f.read() From 07b29d9f070fa19de18c2363fadb96db0a73c59a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 3 Nov 2021 15:27:21 +0200 Subject: [PATCH 1809/9987] fix patch path --- .../easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb index 7903ac041b1..3fd2c09d3d7 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb @@ -47,7 +47,7 @@ components = [ 'easyblock': 'CMakeMake', 'source_urls': ['https://github.com/openmm/openmm/archive/'], 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'patches': [('http://two.embl.de/OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], 'checksums': [ 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch From e0fe6cf6a80dd447d8113ec959554f4413c53832 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 3 Nov 2021 14:47:34 +0100 Subject: [PATCH 1810/9987] Added patches to skip svd_errors_and_warnings_cpu and norm_extreme_values_cpu tests, which were failing because the error was a different error than expected. This has no impact on users, since these tests cases are not expected to complete succesfully anyway. Additionally, add a patch that increases the tolerance for the zero_model_parallel tests so that they also pass when using TensorFloat32, e.g. on A100 --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 6 +++ ...crease_zero_optimizer_test_tolerance.patch | 26 +++++++++ ...Torch-1.10.0_skip_nan_tests_openblas.patch | 54 +++++++++++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_nan_tests_openblas.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index 7d1af983839..7e8aa59c8a4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -29,6 +29,8 @@ patches = [ 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -51,6 +53,10 @@ checksums = [ '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', # PyTorch-1.10.0_fix-vnni-detection.patch '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch + 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_skip_nan_tests_openblas.patch + '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch new file mode 100644 index 00000000000..c61a46e0fa6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch @@ -0,0 +1,26 @@ +# Author: Caspar van Leeuwen, SURF +# Fixes failing tests in test_zero_redundancy_optimizer for A100 due to the use of TensorFloat32 +# We increase tolerances in the assert's, so that the small differences that arise due to the +# use of TensorFloat32 fall within the limits of torch.allclose(...) +# See https://github.com/pytorch/pytorch/issues/67764 +diff -Nru pytorch.orig/test/distributed/optim/test_zero_redundancy_optimizer.py pytorch/test/distributed/optim/test_zero_redundancy_optimizer.py +--- pytorch.orig/test/distributed/optim/test_zero_redundancy_optimizer.py 2021-11-02 15:50:15.430729833 +0100 ++++ pytorch/test/distributed/optim/test_zero_redundancy_optimizer.py 2021-11-03 14:38:23.244771749 +0100 +@@ -881,13 +881,15 @@ + local_loss = cast(torch.Tensor, local_optim.step(closure=closure_local)) + ddp_loss = cast(torch.Tensor, zero_optim.step(closure=closure_ddp)).to(cpu_device) + ++ # Increased tolerances are needed to pass test when using TensorFloat32 ++ # see https://github.com/pytorch/pytorch/issues/67764 + assert torch.allclose( +- local_loss, ddp_loss ++ local_loss, ddp_loss, rtol=1e-03 + ), "Losses differ between local optim and ZeroRedundancyOptimizer" + + for local_p, ddp_p in zip(local_model.parameters(), ddp_model.parameters()): + ddp_p = ddp_p.to(cpu_device) +- assert torch.allclose(local_p, ddp_p), "Models differ after a step" ++ assert torch.allclose(local_p, ddp_p, rtol=1e-04, atol=1e-04), "Models differ after a step" + + @common_distributed.skip_if_lt_x_gpu(4) + def test_zero_model_parallel_with_bucket_view(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_nan_tests_openblas.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_nan_tests_openblas.patch new file mode 100644 index 00000000000..7a7927e87a7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_nan_tests_openblas.patch @@ -0,0 +1,54 @@ +# Author: Caspar van Leeuwen, SURF +# Skip tests that fail due to how OpenBLAS 0.3.15 and later handle NaN inputs +# This affects the following tests: +# ERROR: test_norm_extreme_values_cpu (__main__.TestLinalgCPU) +# FAIL: test_svd_errors_and_warnings_cpu_complex64 (__main__.TestLinalgCPU) +# FAIL: test_svd_errors_and_warnings_cpu_float32 (__main__.TestLinalgCPU) +# FAIL: test_svd_errors_and_warnings_cpu_float64 (__main__.TestLinalgCPU) +# See https://github.com/pytorch/pytorch/issues/67693 +diff -Nru pytorch.orig/test/test_linalg.py pytorch/test/test_linalg.py +--- pytorch.orig/test/test_linalg.py 2021-11-02 15:50:15.433729841 +0100 ++++ pytorch/test/test_linalg.py 2021-11-03 10:46:52.910339202 +0100 +@@ -1873,6 +1873,11 @@ + # These cases are broken because of another issue with svd + # https://github.com/pytorch/pytorch/issues/52633 + return True ++ if self.device_type == 'cpu': ++ if torch.any(torch.isnan(x)): ++ # This case is broken when cpu backend is OpenBLAS >= 0.3.15 ++ # See https://github.com/pytorch/pytorch/issues/67693 ++ return True + return False + + for matrix in matrices: +@@ -2896,15 +2901,17 @@ + # error from out_v + svd(a, out=(out_u, out_s, out_v)) + ++ # Skip test for NaNs, it fails with OpenBLAS since it produces a different error than expected ++ # See https://github.com/pytorch/pytorch/issues/67693 + # if input contains NaN then an error is triggered for svd +- a = torch.full((3, 3), float('nan'), dtype=dtype, device=device) +- a[0] = float('nan') +- with self.assertRaisesRegex(RuntimeError, "The algorithm failed to converge"): +- svd(a) +- a = torch.randn(3, 33, 33, dtype=dtype, device=device) +- a[1, 0, 0] = float('nan') +- with self.assertRaisesRegex(RuntimeError, r"\(Batch element 1\): The algorithm failed to converge"): +- svd(a) ++ # a = torch.full((3, 3), float('nan'), dtype=dtype, device=device) ++ # a[0] = float('nan') ++ # with self.assertRaisesRegex(RuntimeError, "The algorithm failed to converge"): ++ # svd(a) ++ # a = torch.randn(3, 33, 33, dtype=dtype, device=device) ++ # a[1, 0, 0] = float('nan') ++ # with self.assertRaisesRegex(RuntimeError, r"\(Batch element 1\): The algorithm failed to converge"): ++ # svd(a) + + @skipCUDAIfNoMagmaAndNoCusolver + @skipCPUIfNoLapack +Binary files pytorch.orig/torch/__pycache__/autocast_mode.cpython-39.pyc and pytorch/torch/__pycache__/autocast_mode.cpython-39.pyc differ +Binary files pytorch.orig/torch/__pycache__/__init__.cpython-39.pyc and pytorch/torch/__pycache__/__init__.cpython-39.pyc differ +Binary files pytorch.orig/torch/__pycache__/torch_version.cpython-39.pyc and pytorch/torch/__pycache__/torch_version.cpython-39.pyc differ +Binary files pytorch.orig/torch/__pycache__/_utils.cpython-39.pyc and pytorch/torch/__pycache__/_utils.cpython-39.pyc differ +Binary files pytorch.orig/torch/__pycache__/_utils_internal.cpython-39.pyc and pytorch/torch/__pycache__/_utils_internal.cpython-39.pyc differ From 4212dc1b83fe976d6854af73a6ca0d57276b4f0c Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 3 Nov 2021 16:24:36 +0200 Subject: [PATCH 1811/9987] fix for tests --- .../batchgenerators-0.23-foss-2020b.eb | 2 +- .../dicom2nifti-2.3.0-foss-2020b.eb | 35 ++++++++ .../m/MedPy/MedPy-0.4.0-foss-2020b.eb | 28 ++++++ .../n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb | 85 +++++++++++++++++++ .../r/requests/requests-2.26.0-foss-2020b.eb | 13 +-- .../s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb | 14 +-- .../tifffile/tifffile-2021.8.30-foss-2020b.eb | 5 +- .../u/unittest2/unittest2-1.1.0-foss-2020b.eb | 18 ++-- ...st2-foss2020b_remove_unnecessary_dep.patch | 19 +++++ 9 files changed, 200 insertions(+), 19 deletions(-) create mode 100644 easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/u/unittest2/unittest2-foss2020b_remove_unnecessary_dep.patch diff --git a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb index 259cde6c642..11ee9bfc83c 100644 --- a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb +++ b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb @@ -12,8 +12,8 @@ and the Applied Computer Vision Lab of the Helmholtz Imaging Platform.""" toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['4bc5711ee75678ae97df7b54c50c1cde46f14c94f44d948f6edf4e8c48b2a9e0'] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb new file mode 100644 index 00000000000..4692d2a37ed --- /dev/null +++ b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'dicom2nifti' +version = '2.3.0' + +homepage = 'https://github.com/icometrix/dicom2nifti' +description = "Python library for converting dicom files to nifti" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['808c4ddbcffd492d41ff20a2837b5e2a3cbe2058d43512fe97b99d678a758bfd'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('pydicom', '2.1.2'), + ('NiBabel', '3.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/dicom2nifti'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb new file mode 100644 index 00000000000..07a664b8e8c --- /dev/null +++ b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-foss-2020b.eb @@ -0,0 +1,28 @@ +# This easyconfig was created by James Carpenter of the BEAR Software team at the University of Birmingham. +# updated: Denis Kristak +easyblock = 'PythonPackage' + +name = 'MedPy' +version = '0.4.0' + +homepage = 'https://pypi.org/project/MedPy/' +description = """MedPy is a library and script collection for medical image processing in Python, providing basic + functionalities for reading, writing and manipulating large images of arbitrary dimensionality. Its main + contributions are n-dimensional versions of popular image filters, a collection of image feature extractors, ready + to be used with scikit-learn, and an exhaustive n-dimensional graph-cut package.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f8a94937dbb947ab069e767862dc6b86896b153c41ce8ed9369c7d79c0033a88'] + +dependencies = [ + ('Python', '3.8.6'), + ('SimpleITK', '2.1.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb new file mode 100644 index 00000000000..0cd19603618 --- /dev/null +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb @@ -0,0 +1,85 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'nnU-Net' +version = '1.7.0' + +homepage = 'https://github.com/MIC-DKFZ/nnUNet' +description = """ +nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found in the domain. +It condenses and automates the keys decisions for designing a successful segmentation pipeline for any given dataset. +""" +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://files.pythonhosted.org/packages/8e/cf/0e5a45faba472c1df80da8d3fcb8d90b31a2258e48fdbc47cd2e30c16233/'] +sources = ['nnunet-%(version)s.tar.gz'] +checksums = ['7ad3d5b89af389fa86cea58f409bd2353b511a746587f37d26c00a756849f356'] + +builddependencies = [ + ('Bazel', '3.7.2') +] + +dependencies = [ + ('Python', '3.8.6'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), + ('dicom2nifti', '2.3.0'), + ('scikit-image', '0.18.1'), + ('TensorFlow', '2.5.0'), + ('SciPy-bundle', '2020.11'), + ('batchgenerators', '0.23'), + ('scikit-learn', '0.23.2'), + ('requests', '2.26.0'), + ('NiBabel', '3.2.1'), + ('SimpleITK', '2.1.0'), + ('tifffile', '2021.8.30'), + ('MedPy', '0.4.0'), + ('jax', '0.2.19') +] + +# sklearn is incorrect package name +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('absl-py', '0.15.0', { + 'modulename': 'absl', + 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['5faa387ad6b522516283cbe45adbc4c46bedcf501c82db2f9174945f3ec2ea7d'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'nnunet'} + +sanity_check_commands = ['nnUNet_train --help'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb b/easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb index b79821bedc1..13821883c95 100644 --- a/easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb +++ b/easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb @@ -5,23 +5,24 @@ easyblock = 'PythonBundle' name = 'requests' version = '2.26.0' -homepage = 'https://pypi.org/project/unittest2/' +homepage = 'https://pypi.org/project/requests/' description = """Requests is a simple, yet elegant, HTTP library.""" toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] - dependencies = [ ('Python', '3.8.6'), ] exts_list = [ - ('requests', version), - ('charset-normalizer', '2.0.4'), + (name, version, { + 'checksums': ['b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7'], + }), + ('charset-normalizer', '2.0.4', { + 'checksums': ['f23667ebe1084be45f6ae0538e4a5a865206544097e4e8bbcacf42cd02a348f3'], + }), ] -download_dep_fail = True use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb index 0b1009560a0..956b38dd32a 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb @@ -28,15 +28,19 @@ dependencies = [ ] start_dir = 'SimpleITK' -configopts = '-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF -DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF ' +configopts = '-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF ' +configopts += ' -DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF ' preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_pyinstpath = "%(installdir)s/lib/python%(pyshortver)s/site-packages" + +local_postinstall_cmds = "mkdir -p %s " % local_pyinstpath +local_postinstall_cmds += " && cd %(builddir)s/easybuild_obj/Wrapping/Python " +local_postinstall_cmds += " && export PYTHONPATH=%s:$PYTHONPATH " % local_pyinstpath +local_postinstall_cmds += " && pip install --prefix=%(installdir)s . " + postinstallcmds = [ - "mkdir -p %s " % local_pyinstpath - + " && cd %(builddir)s/easybuild_obj/Wrapping/Python " - + " && export PYTHONPATH=%s:$PYTHONPATH " % local_pyinstpath - + " && pip install --prefix=%(installdir)s . " + local_postinstall_cmds ] separate_build_dir = True diff --git a/easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb b/easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb index b21bbbd0fa2..beacbe3d48c 100644 --- a/easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb +++ b/easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb @@ -13,8 +13,8 @@ metadata from TIFF-like files used in bioimaging. toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['8760e61e30106ea0dab9ec42a238d70a3ff55dde9c54456e7b748fe717cb782d'] dependencies = [ ('Python', '3.8.6'), @@ -33,7 +33,8 @@ exts_default_options = { exts_list = [ ('lxml', '4.6.3', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lxml/'] + 'source_urls': ['https://pypi.python.org/packages/source/l/lxml/'], + 'checksums': ['39b78571b3b30645ac77b95f7c69d1bffc4cf8c3b157c435a34da72e78c82468'], }), ] diff --git a/easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb index 112250696ec..848a0147275 100644 --- a/easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb @@ -18,14 +18,22 @@ dependencies = [ ] exts_list = [ - ('unittest2', version, { - 'patches': ['patch_unittest2.patch'], + (name, version, { + 'patches': ['unittest2-foss2020b_remove_unnecessary_dep.patch'], + 'checksums': [ + '22882a0e418c284e1f718a822b3b022944d53d2d908e1690b319a9d3eb2c0579', # unittest2-1.1.0.tar.gz + # unittest2-foss2020b_remove_unnecessary_dep.patch + 'adb3f83e4e220cf430de559075fbbce5545e83fb35ea0a3fd260ca1f00263c20', + ], + }), + ('traceback2', '1.4.0', { + 'checksums': ['05acc67a09980c2ecfedd3423f7ae0104839eccb55fc645773e1caa0951c3030'], + }), + ('linecache2', '1.0.0', { + 'checksums': ['4b26ff4e7110db76eeb6f5a7b64a82623839d595c2038eeda662f2a2db78e97c'], }), - ('traceback2', '1.4.0'), - ('linecache2', '1.0.0'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/u/unittest2/unittest2-foss2020b_remove_unnecessary_dep.patch b/easybuild/easyconfigs/u/unittest2/unittest2-foss2020b_remove_unnecessary_dep.patch new file mode 100644 index 00000000000..33bf69c75f4 --- /dev/null +++ b/easybuild/easyconfigs/u/unittest2/unittest2-foss2020b_remove_unnecessary_dep.patch @@ -0,0 +1,19 @@ +diff -ruN unittest2-1.1.0_orig/setup.py unittest2-1.1.0/setup.py +--- unittest2-1.1.0_orig/setup.py 2021-09-07 14:45:56.638877809 +0200 ++++ unittest2-1.1.0/setup.py 2021-09-07 14:52:28.782893924 +0200 +@@ -57,7 +57,7 @@ + # Both install and setup requires - because we read VERSION from within the + # package, and the package also exports all the APIs. + # six for compat helpers +-REQUIRES = ['argparse', 'six>=1.4', 'traceback2'], ++REQUIRES = ['six>=1.4', 'traceback2'], + + params = dict( + name=NAME, +diff -ruN unittest2-1.1.0_orig/unittest2.egg-info/requires.txt unittest2-1.1.0/unittest2.egg-info/requires.txt +--- unittest2-1.1.0_orig/unittest2.egg-info/requires.txt 2021-09-07 14:45:56.654877436 +0200 ++++ unittest2-1.1.0/unittest2.egg-info/requires.txt 2021-09-07 14:47:15.013107770 +0200 +@@ -1,3 +1,2 @@ +-argparse + six>=1.4 + traceback2 From d49a323b535938f0adda209f99f33211b57ade41 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 3 Nov 2021 14:27:11 +0000 Subject: [PATCH 1812/9987] Delete nnUNet-1.7.0-foss-2020b.eb removing old file --- .../n/nnUNet/nnUNet-1.7.0-foss-2020b.eb | 79 ------------------- 1 file changed, 79 deletions(-) delete mode 100644 easybuild/easyconfigs/n/nnUNet/nnUNet-1.7.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/nnUNet/nnUNet-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/n/nnUNet/nnUNet-1.7.0-foss-2020b.eb deleted file mode 100644 index e101b0f98ed..00000000000 --- a/easybuild/easyconfigs/n/nnUNet/nnUNet-1.7.0-foss-2020b.eb +++ /dev/null @@ -1,79 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'PythonPackage' - -name = 'nnUNet' -version = '1.7.0' - -homepage = 'https://github.com/MIC-DKFZ/nnUNet' -description = """ -nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found in the domain. -It condenses and automates the keys decisions for designing a successful segmentation pipeline for any given dataset. -""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -builddependencies = [ - ('Bazel', '3.7.2') -] - -dependencies = [ - ('Python', '3.8.6'), - ('PyTorch', '1.7.1'), - ('tqdm', '4.56.2'), - ('dicom2nifti', '2.3.0'), - ('scikit-image', '0.18.1'), - ('TensorFlow', '2.5.0'), - ('SciPy-bundle', '2020.11'), - ('batchgenerators', '0.23'), - ('scikit-learn', '0.23.2'), - ('requests', '2.26.0'), - ('NiBabel', '3.2.1'), - ('SimpleITK', '2.1.0'), - ('tifffile', '2021.8.30'), - ('MedPy', '0.4.0'), - ('jax', '0.2.19') -] - -# sklearn is incorrect package name -preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " - -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'download_dep_fail': True, - 'use_pip': True, -} - -exts_list = [ - ('contextlib2', '21.6.0', { - 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], - }), - ('absl-py', '0.15.0', { - 'modulename': 'absl', - }), - ('dm-haiku', '0.0.4', { - 'modulename': 'haiku', - 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", - }), - ('dm-tree', '0.1.6', { - 'modulename': 'tree', - }), - ('immutabledict', '2.1.0', { - }), - ('ml_collections', '0.1.0', { - # see https://github.com/google/ml_collections/issues/7 - 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", - }), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -sanity_check_commands = ['nnUNet_train --help'] - -moduleclass = 'data' From 767bae45900ac65d08774247bc57225d5a1e0e57 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 3 Nov 2021 16:45:13 +0100 Subject: [PATCH 1813/9987] adding easyconfigs: gawk-5.1.1-GCC-10.3.0.eb --- .../g/gawk/gawk-5.1.1-GCC-10.3.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..5387b9d1825 --- /dev/null +++ b/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-10.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gawk' +version = '5.1.1' + +homepage = 'https://www.gnu.org/software/gawk' +description = """The awk utility interprets a special-purpose programming language that makes it possible to handle +simple data-reformatting jobs with just a few lines of code.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6168d8d1dc8f74bd17d9dc22fa9634c49070f232343b744901da15fb4f06bffd'] + +sanity_check_paths = { + 'files': ['bin/gawk'], + 'dirs': [], +} + +sanity_check_commands = ["gawk --help"] + +moduleclass = 'tools' From f5c023e88eba3f3dd92f70cd27b2ad9f91850e57 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 3 Nov 2021 17:18:09 +0100 Subject: [PATCH 1814/9987] Change toolchain + Use EasyBuild gawk + Use -march=native + Remove extra spaces --- ... => Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb} | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/v/Virtuoso-opensource/{Virtuoso-opensource-7.2.6.1-foss-2021a.eb => Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb} (88%) diff --git a/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-foss-2021a.eb b/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb similarity index 88% rename from easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-foss-2021a.eb rename to easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb index 24f7f645124..6b38503aeb7 100644 --- a/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb @@ -15,7 +15,7 @@ description = """Virtuoso is a high-performance and scalable Multi-Model RDBMS, Integration Middleware, Linked Data Deployment, and HTTP Application Server Platform.""" software_license = 'LicenseGPLv2' -toolchain = {'name': 'foss', 'version': '2021a'} +toolchain = {'name': 'GCC', 'version': '10.3.0'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/openlink/virtuoso-opensource/archive/refs/tags/'] @@ -23,19 +23,18 @@ checksums = ['73dc3d0073d3d5694da075063b75a404649c027a1f5c635a25ede52713ff7942'] builddependencies = [ ('Autotools', '20210128'), - ('flex', '2.6.4'), - ('Bison', '3.7.6'), - ('gperf', '3.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('gperf', '3.1'), + ('gawk', '5.1.1'), ] -osdependencies = ['gawk'] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', True), ('libreadline', '8.1'), ] -configure_cmd = 'export CFLAGS="-O3 -m64" && ' -configure_cmd += './autogen.sh && ' +configure_cmd = './autogen.sh && ' configure_cmd += './configure ' configure_cmd += ' --enable-shared --disable-static' configure_cmd += ' --disable-imagemagick' From 402107628e12b8e8bebae73d91c75ab7d58bbb5d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 3 Nov 2021 18:18:43 +0000 Subject: [PATCH 1815/9987] restore and fix sanity check commands in RStudio-Server 1.4 --- ...RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb index ed94dfd758d..0788b4d6f01 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb @@ -22,13 +22,13 @@ builddependencies = [ ('pkg-config', '0.29.2'), ('CMake', '3.20.1'), ('ant', '1.10.11', '-Java-%(javaver)s', True), - ('SOCI', '4.0.2'), ] dependencies = [ ('Boost', '1.76.0'), ('R', '4.1.0'), ('Java', '11', '', True), + ('SOCI', '4.0.2'), ] osdependencies = [ @@ -57,6 +57,13 @@ configopts += "-DSOCI_SQLITE_LIB=$EBROOTSOCI/lib/libsoci_sqlite3.a " prebuildopts = (("cd {} && cd build && ")).format("%(builddir)s/rstudio-%(version)s") preinstallopts = (("cd {} && cd build && ")).format("%(builddir)s/rstudio-%(version)s") +sanity_check_commands = [ + # This command requires environment variables R_HOME and R_DOC_DIR + "R_HOME=$EBROOTR/lib64/R R_DOC_DIR=$R_HOME/doc rsession --verify-installation=1", + # This command requires a db conf (this may also be needed for live use) + """MYTMP=`mktemp -d` && echo -e "provider=sqlite\ndirectory=$MYTMP/db" >> $MYTMP/db.conf && """ # deliberate no comma + "rserver --verify-installation=1 --database-config-file=$MYTMP/db.conf --server-data-dir=$MYTMP/sdd ", +] sanity_check_paths = { 'files': ["bin/rstudio-server"], From 9a2492483957d992ee7863d2fc090010149a91aa Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 3 Nov 2021 18:31:39 +0000 Subject: [PATCH 1816/9987] fix line length --- .../RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb index 0788b4d6f01..d163c925d0c 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb @@ -61,7 +61,7 @@ sanity_check_commands = [ # This command requires environment variables R_HOME and R_DOC_DIR "R_HOME=$EBROOTR/lib64/R R_DOC_DIR=$R_HOME/doc rsession --verify-installation=1", # This command requires a db conf (this may also be needed for live use) - """MYTMP=`mktemp -d` && echo -e "provider=sqlite\ndirectory=$MYTMP/db" >> $MYTMP/db.conf && """ # deliberate no comma + """MYTMP=`mktemp -d` && echo -e "provider=sqlite\ndirectory=$MYTMP/db" >> $MYTMP/db.conf && """ "rserver --verify-installation=1 --database-config-file=$MYTMP/db.conf --server-data-dir=$MYTMP/sdd ", ] From 22ce2b067e495e5827cb5ed34543c59a5689d03f Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 3 Nov 2021 19:50:58 +0100 Subject: [PATCH 1817/9987] Adding dependent libraries order patch for imread --- .../s/scikit-image/imread-0.7.4_shlibs_order.patch | 14 ++++++++++++++ .../scikit-image-0.18.1-intelcuda-2020b.eb | 6 +++++- 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/scikit-image/imread-0.7.4_shlibs_order.patch diff --git a/easybuild/easyconfigs/s/scikit-image/imread-0.7.4_shlibs_order.patch b/easybuild/easyconfigs/s/scikit-image/imread-0.7.4_shlibs_order.patch new file mode 100644 index 00000000000..859b24bb033 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/imread-0.7.4_shlibs_order.patch @@ -0,0 +1,14 @@ +description: adjusting order of dependent libraries in setup.py +issue: https://github.com/easybuilders/easybuild-easyconfigs/issues/14219 +author: Zdenek Matej, MAX IV Laboratory, Lund University +--- setup.py ++++ setup.py +@@ -77,7 +77,7 @@ + } + + +-libraries = ['png', 'jpeg', 'tiff'] ++libraries = ['png', 'tiff', 'jpeg'] + if sys.platform.startswith('win'): + libraries.append('zlib') + diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb index 3169f709e70..7b0b41a3f56 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intelcuda-2020b.eb @@ -25,7 +25,11 @@ exts_list = [ 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], }), ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + 'patches': ['imread-0.7.4_shlibs_order.patch'], + 'checksums': [ + '0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f', # imread-0.7.4.tar.gz + '887cca0c4d8161d16fc0637ff06716d99cb3fd90ba800c92b6fbe3709c142b16', # imread-0.7.4_shlibs_order.patch + ], }), ('pooch', '1.3.0', { 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], From 37227f846e750fe531ec5c7ca314fbe7eaaabcf1 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 4 Nov 2021 14:53:28 +1050 Subject: [PATCH 1818/9987] adding easyconfigs: parasail-2.4.2-GCC-9.3.0.eb --- .../p/parasail/parasail-2.4.2-GCC-9.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/parasail/parasail-2.4.2-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.4.2-GCC-9.3.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.4.2-GCC-9.3.0.eb new file mode 100644 index 00000000000..8c472d02b40 --- /dev/null +++ b/easybuild/easyconfigs/p/parasail/parasail-2.4.2-GCC-9.3.0.eb @@ -0,0 +1,32 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v2.4.2 +# R.QIAO + +easyblock = 'CMakeMake' + +name = 'parasail' +version = '2.4.2' + +homepage = 'https://github.com/jeffdaily/parasail' +description = """parasail is a SIMD C (C99) library containing implementations + of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global + pairwise sequence alignment algorithms. """ + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +# https://github.com/jeffdaily/parasail +github_account = 'jeffdaily' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3843055fc04743269cf22d127ae26952a7f5e6fc4f1bc29f6b6f3c156c8ca434'] + +builddependencies = [('CMake', '3.16.4')] + +sanity_check_paths = { + 'files': ['bin/parasail_aligner', 'bin/parasail_stats', + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], + 'dirs': [], +} + +moduleclass = 'bio' From 362b2344853f2bd63793a8dba895d1553961dafa Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 4 Nov 2021 15:06:08 +1050 Subject: [PATCH 1819/9987] toolchain downgrade to GCC --- .../m/Mash/{Mash-2.2-foss-2020a.eb => Mash-2.2-GCC-9.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/Mash/{Mash-2.2-foss-2020a.eb => Mash-2.2-GCC-9.3.0.eb} (94%) diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.2-foss-2020a.eb b/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb similarity index 94% rename from easybuild/easyconfigs/m/Mash/Mash-2.2-foss-2020a.eb rename to easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb index 83083b56700..e27e324a68b 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.2-foss-2020a.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb @@ -11,7 +11,7 @@ version = '2.2' homepage = 'http://mash.readthedocs.org' description = "Fast genome and metagenome distance estimation using MinHash" -toolchain = {'name': 'foss', 'version': '2020a'} +toolchain = {'name': 'GCC', 'version': '9.3.0'} toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/marbl/Mash/archive/'] From 4648705eaa0cccd6dba5feb1db960c1f6a722109 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 4 Nov 2021 15:39:55 +1050 Subject: [PATCH 1820/9987] adding easyconfigs: cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb --- ..._Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..237512b3ae7 --- /dev/null +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,44 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v24.2.0 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'cDNA_Cupcake' +version = '24.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Magdoll/cDNA_Cupcake' +description = "cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data." + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/Magdoll/cDNA_Cupcake/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9aa75ef3d00e9983772021dca3c5595df5ea23c39fb0004e4330e55edc782002'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Biopython', '1.78', versionsuffix), + ('bx-python', '0.8.9', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'cupcake'} + +sanity_check_paths = { + # check for particular Cupcake ToFU scripts, + # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step + 'files': [ + 'bin/collapse_isoforms_by_sam.py', + 'bin/get_abundance_post_collapse.py', + 'bin/simple_stats_post_collapse.py' + ], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 6530e4a954893149fe28c2a773f89740e1660a72 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 4 Nov 2021 15:47:12 +1050 Subject: [PATCH 1821/9987] requires PR #14277, #14276, #14245 --- .../Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..ec5278eb0ad --- /dev/null +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,48 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'Cogent' +version = '8.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Magdoll/Cogent' +description = """ +Cogent is a tool for reconstructing the coding genome using high-quality +full-length transcriptome sequences. It is designed to be used on Iso-Seq data +and in cases where there is no reference genome or the ref genome is highly +incomplete. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Magdoll/Cogent/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['709bc0e7bf9febabe417ab597e6f7f3b9c369d5a2c1774726bd646ef11fc9154'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('matplotlib', '3.2.1', versionsuffix), + ('networkx', '2.4', versionsuffix), + ('scikit-image', '0.17.1', versionsuffix), + ('Biopython', '1.78', versionsuffix), + ('bx-python', '0.8.9', versionsuffix), + ('parasail', '2.4.2'), + ('CapnProto', '0.8.0'), + ('minimap2', '2.17'), + ('Mash', '2.2'), + ('cDNA_Cupcake', '24.2.0', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/run_mash.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'Cogent'} + +moduleclass = 'bio' From 271ea11ee7062dcaf89ee651b2095fa417103cd7 Mon Sep 17 00:00:00 2001 From: manifest Date: Thu, 4 Nov 2021 16:21:12 +1030 Subject: [PATCH 1822/9987] pip check + --- .../cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb index 237512b3ae7..47cd3dce2d2 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -30,6 +30,7 @@ use_pip = True options = {'modulename': 'cupcake'} +sanity_pip_check = True sanity_check_paths = { # check for particular Cupcake ToFU scripts, # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step From a5e9428d0727e0cd524e371ae7db14761051318c Mon Sep 17 00:00:00 2001 From: manifest Date: Thu, 4 Nov 2021 16:34:47 +1030 Subject: [PATCH 1823/9987] pip dep PuLP + --- .../c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb index ec5278eb0ad..d54847566f1 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb @@ -38,6 +38,10 @@ dependencies = [ ('cDNA_Cupcake', '24.2.0', versionsuffix), ] +download_dep_fail = True +use_pip = True + +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/run_mash.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From ac6acb27a4aced874a44cf2e8bbb4ab910e224aa Mon Sep 17 00:00:00 2001 From: manifest Date: Thu, 4 Nov 2021 17:57:51 +1030 Subject: [PATCH 1824/9987] udpate to GCC 9.3.0, .so dynamic --- .../l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb index 076825ebcc6..e9cbc083532 100644 --- a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb @@ -16,7 +16,7 @@ version = '0.9.8' homepage = "https://github.com/mfranberg/libplinkio" description = """A small C and Python library for reading PLINK genotype files.""" -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = ['https://github.com/mfranberg/%(namelower)s/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] @@ -30,7 +30,7 @@ builddependencies = [ parallel = 1 sanity_check_paths = { - 'files': ['lib/%(name)s.so'], + 'files': ['lib/%(name)s.%s' SHLIB_EXT], 'dirs': ['lib', 'include'], } From 2703aa119497c7a5bb2fda5bbc8cbaac18a3df25 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 4 Nov 2021 21:19:59 +1050 Subject: [PATCH 1825/9987] adding easyconfigs: python-parasail-1.2.3-foss-2020a-Python-3.8.2.eb --- ...-parasail-1.2.3-foss-2020a-Python-3.8.2.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.3-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.3-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..ebbe2552def --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.3-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,36 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v1.2.3 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['e0eb66b15c6318724bd3c4a3c05b5a1a4b7926eb1ee79606958c98c52a32cbb3'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('parasail', '2.4.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' From 5f07741edd8a5c107aa15b3816bd8dba152afc4e Mon Sep 17 00:00:00 2001 From: manifest Date: Thu, 4 Nov 2021 21:16:46 +1030 Subject: [PATCH 1826/9987] deps [parasail --> python-parasail] --- .../c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb index d54847566f1..3c93ab37e8c 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb @@ -31,7 +31,7 @@ dependencies = [ ('scikit-image', '0.17.1', versionsuffix), ('Biopython', '1.78', versionsuffix), ('bx-python', '0.8.9', versionsuffix), - ('parasail', '2.4.2'), + ('python-parasail', '1.2.3', versionsuffix), ('CapnProto', '0.8.0'), ('minimap2', '2.17'), ('Mash', '2.2'), From 9b5407098f89d2f9571ba24ee05254ffd0b9cde5 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 4 Nov 2021 12:20:00 +0100 Subject: [PATCH 1827/9987] Skip test_fn_grad_linalg_det_singular_cpu_complex128 and test_variant_consistency_jit_contiguous_cpu_float32. Both don't seem to point to fundamental issues with the build, but the problem is probably on the side of the test suite. --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 3 ++ ...yTorch-1.10.0_skip_failing_ops_tests.patch | 33 +++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_failing_ops_tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index 7e8aa59c8a4..76bd10e605e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -30,6 +30,7 @@ patches = [ 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', ] checksums = [ @@ -55,6 +56,8 @@ checksums = [ '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_skip_failing_ops_tests.patch + '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_failing_ops_tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_failing_ops_tests.patch new file mode 100644 index 00000000000..77190dc7a9f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_failing_ops_tests.patch @@ -0,0 +1,33 @@ +# Author: Caspar van Leeuwen, SURF +# Test 'test_fn_grad_linalg_det_singular_cpu_complex128' was failing +# It was noticed by the PyTorch devs that this is flaky and recommended to skip it for now +# See https://github.com/pytorch/pytorch/issues/67767 +# Test 'test_variant_consistency_jit_contiguous_cpu_float32' was also failing +# However, the test passes when run individually +# See https://github.com/pytorch/pytorch/issues/67838 +diff -Nru pytorch.orig/torch/testing/_internal/common_methods_invocations.py pytorch/torch/testing/_internal/common_methods_invocations.py +--- pytorch.orig/torch/testing/_internal/common_methods_invocations.py 2021-11-02 15:50:14.328727067 +0100 ++++ pytorch/torch/testing/_internal/common_methods_invocations.py 2021-11-04 12:04:29.794149360 +0100 +@@ -6448,7 +6448,10 @@ + supports_forward_ad=True, + autodiff_fusible_nodes=['aten::contiguous'], + assert_jit_shape_analysis=True, +- supports_out=False), ++ supports_out=False, ++ skips=( ++ DecorateInfo(unittest.skip("Skipped!"), 'TestJit', 'test_variant_consistency_jit', device_type='cpu'), ++ )), + OpInfo('symeig', + dtypes=floating_and_complex_types(), + check_batched_gradgrad=False, +@@ -7060,6 +7063,10 @@ + # Probable fix (open PR): https://github.com/pytorch/pytorch/pull/62570 + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad', device_type='cuda', + dtypes=(torch.complex128,)), ++ # It also breaks on CPU. We'll revisit this once `linalg.lu_solve` is a thing ++ # See https://github.com/pytorch/pytorch/pull/64387 and https://github.com/pytorch/pytorch/issues/67767 ++ DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad', ++ dtypes=(torch.complex128,)), + DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + # This test fails because singular inputs cannot be reliably From 848940bc275275f5cce958210d5cb1a6ef22abf9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 4 Nov 2021 12:38:05 +0100 Subject: [PATCH 1828/9987] adding easyconfigs: GTS-0.7.6-GCCcore-11.2.0.eb --- .../g/GTS/GTS-0.7.6-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..45f971e0556 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. +It is an Open Source Free Software Library intended to provide a set of useful +functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.37'), +] +dependencies = [ + ('GLib', '2.69.1'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [], +} + +moduleclass = 'vis' From 92bca913f184de666e2095c1f0591910f43d86bb Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 4 Nov 2021 13:09:45 +0100 Subject: [PATCH 1829/9987] adding easyconfigs: archspec-0.1.3-GCCcore-11.2.0.eb --- .../archspec/archspec-0.1.3-GCCcore-11.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e2efe38ddd5 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.1.3' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = ['archspec-%(version)s-py2.py3-none-any.whl'] +checksums = ['bb170c3347b1e868e01b5cec5844354b893efddd7d65c9b73df8196ca14fb554'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +sanity_pip_check = True + +moduleclass = 'tools' From b9102aca2435e4fe00a5cd1ffeb2730164dee7c7 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 4 Nov 2021 13:14:20 +0100 Subject: [PATCH 1830/9987] adding easyconfigs: Coreutils-9.0-GCCcore-11.2.0.eb --- .../Coreutils/Coreutils-9.0-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-9.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4a4de74ff38 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.0-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "9.0" + +homepage = 'https://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text +manipulation utilities of the GNU operating system. These are +the core utilities which are expected to exist on every +operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ce30acdf4a41bc5bb30dd955e9eaa75fa216b4e3deb08889ed32433c7b3b97ce'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' From a6f954322fb072e6e070b42c158a2657dd4619af Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 4 Nov 2021 13:18:02 +0100 Subject: [PATCH 1831/9987] adding easyconfigs: CVS-1.11.23-GCCcore-11.2.0.eb --- .../c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ba9782271f5 --- /dev/null +++ b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'CVS' +version = '1.11.23' + +homepage = 'https://savannah.nongnu.org/projects/cvs' +description = """CVS is a version control system, an important component of +Source Configuration Management (SCM). +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [' http://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'CVS-1.11.23-zlib-1.patch', + 'CVS-1.11.23-getline.patch', +] +checksums = [ + '400f51b59d85116e79b844f2d5dbbad4759442a789b401a94aa5052c3d7a4aa9', # cvs-1.11.23.tar.bz2 + '3c0ee6509c4622778c093316437a5b047c51820e11cee3ed3a405c2a590a9ff4', # CVS-1.11.23-zlib-1.patch + '6a1aa65acfbb41b7639adc70248d908981f172c2529bb52d84359713f9541874', # CVS-1.11.23-getline.patch +] + +builddependencies = [ + ('binutils', '2.37') +] + +dependencies = [ + ('zlib', '1.2.11') +] + +sanity_check_paths = { + 'files': ['bin/cvs', 'bin/cvsbug', 'bin/rcs2log'], + 'dirs': [], +} + +moduleclass = 'devel' From 60c206b0ba2053546de47fa83aa7093b41d891b6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 4 Nov 2021 13:22:12 +0100 Subject: [PATCH 1832/9987] adding easyconfigs: gc-8.2.0-GCCcore-11.2.0.eb --- .../g/gc/gc-8.2.0-GCCcore-11.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/gc/gc-8.2.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1ba5994d947 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.2.0-GCCcore-11.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.2.0' +local_libatomic_version = '7.6.12' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a +garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + '2540f7356cb74f6c5b75326c6d38a066edd796361fd7d4ed26e494d9856fed8f', # gc-8.2.0.tar.gz + 'f0ab566e25fce08b560e1feab6a3db01db4a38e5bc687804334ef3920c549f3e', # libatomic_ops-7.6.12.tar.gz +] + +builddependencies = [ + ('binutils', '2.37'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' From c65387bdfa297917b4e6c0018793799fbdfd62df Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 4 Nov 2021 13:37:28 +0100 Subject: [PATCH 1833/9987] adding easyconfigs: freeglut-3.2.1-GCCcore-11.2.0.eb, GL2PS-1.4.2-GCCcore-11.2.0.eb --- .../freeglut/freeglut-3.2.1-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ .../g/GL2PS/GL2PS-1.4.2-GCCcore-11.2.0.eb | 34 +++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5384e413955 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.2.1' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['freeglut-3.2.1_gcc10_fix-1.patch'] +checksums = [ + 'd4000e02102acaf259998c870e25214739d1f16f67f99cb35e4f46841399da68', # freeglut-3.2.1.tar.gz + 'f278467e03348b87d9b4ae69f491e503ab80c6d82433cf7468eac89b7f859d37', # freeglut-3.2.1_gcc10_fix-1.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +dependencies = [ + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.%s" ' % SHLIB_EXT +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..661634cc4e9 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.2' + +homepage = 'https://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] +checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('binutils', '2.37'), +] + +dependencies = [ + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('freeglut', '3.2.1'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' From d6ba15abe3e22f84a4ae7783255f36166b35fbed Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 4 Nov 2021 13:42:27 +0100 Subject: [PATCH 1834/9987] adding easyconfigs: GLM-0.9.9.8-GCCcore-11.2.0.eb --- .../g/GLM/GLM-0.9.9.8-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..699976590a7 --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '0.9.9.8' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'GLM-0.9.9.8_fix_missing_install.patch', +] +checksums = [ + '7d508ab72cb5d43227a3711420f06ff99b0a0cb63ee2f93631b162bfe1fe9592', # 0.9.9.8.tar.gz + '1cc199f9d66679b0b5e9a9fbe20bca0d9b15760fa172ca8759dd15bab35802ca', # GLM-0.9.9.8_fix_missing_install.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' From 779d67d83eb275dcc8e21454c9985f97f66f3d70 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 4 Nov 2021 13:49:36 +0100 Subject: [PATCH 1835/9987] adding easyconfigs: GraphicsMagick-1.3.36-GCCcore-11.2.0.eb --- .../GraphicsMagick-1.3.36-GCCcore-11.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..945f9c8b17d --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-GCCcore-11.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.36' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', +] +sources = [SOURCE_TAR_GZ] +patches = [ + 'GraphicsMagick_pkgconfig_libtiff.patch' +] +checksums = [ + '1e6723c48c4abbb31197fadf8396b2d579d97e197123edc70a4f057f0533d563', # GraphicsMagick-1.3.36.tar.gz + '25b4c5361f30e23c809a078ac4b26e670d2b8341496323480037e2095d969294', # GraphicsMagick_pkgconfig_libtiff.patch +] + +builddependencies = [('Autotools', '20210726')] + +dependencies = [ + ('X11', '20210802'), + ('bzip2', '1.0.8'), + ('freetype', '2.11.0'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.3.0'), + ('libxml2', '2.9.10'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('Ghostscript', '9.54.0'), +] + +modextrapaths = {'CPATH': ['include/GraphicsMagick']} + +sanity_check_paths = { + 'files': ['bin/gm', 'lib/libGraphicsMagick.a', 'lib/libGraphicsMagick++.a', + 'lib/libGraphicsMagickWand.a'], + 'dirs': ['include/GraphicsMagick', 'lib/pkgconfig'], +} + +moduleclass = 'vis' From d5844a34f53a6eb07378327f5144c95fcdfa0c4c Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 4 Nov 2021 15:18:30 +0200 Subject: [PATCH 1836/9987] adding ITK --- .../easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb new file mode 100644 index 00000000000..bb09e673914 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb @@ -0,0 +1,62 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.2.1' # 5.1.2 + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + + +builddependencies = [ + ('CMake', '3.18.4'), + ('Bison', '3.7.1'), + ('Eigen', '3.3.8'), +] + +dependencies = [ + ('double-conversion', '3.1.5'), + ('expat', '2.2.9'), + ('HDF5', '1.10.7'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('VTK', '9.0.1'), + ('zlib', '1.2.11'), +] + +local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] +# local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' +configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], +} + +moduleclass = 'data' \ No newline at end of file From 4fa086443241b9c8dadfcba696587580935bb026 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 4 Nov 2021 14:36:37 +0100 Subject: [PATCH 1837/9987] GraphicsMagick-1.3.36-GCCcore-11.2.0.eb: add binutils as builddependency --- .../g/GraphicsMagick/GraphicsMagick-1.3.36-GCCcore-11.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-GCCcore-11.2.0.eb index 945f9c8b17d..30eb94d80ff 100644 --- a/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.36-GCCcore-11.2.0.eb @@ -22,7 +22,10 @@ checksums = [ '25b4c5361f30e23c809a078ac4b26e670d2b8341496323480037e2095d969294', # GraphicsMagick_pkgconfig_libtiff.patch ] -builddependencies = [('Autotools', '20210726')] +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] dependencies = [ ('X11', '20210802'), From 3c762366b54cc218f36dd1859e3128e6203ccab7 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 4 Nov 2021 15:53:13 +0200 Subject: [PATCH 1838/9987] fix for tests --- easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb | 6 +++--- easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb | 5 ++++- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb index bb09e673914..69753b77046 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb @@ -6,7 +6,7 @@ easyblock = 'CMakeMake' name = 'ITK' -version = '5.2.1' # 5.1.2 +version = '5.2.1' homepage = 'https://itk.org' description = """Insight Segmentation and Registration Toolkit (ITK) provides @@ -19,7 +19,7 @@ toolchainopts = {'pic': True, 'cstd': 'c++11'} github_account = 'InsightSoftwareConsortium' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] - +checksums = ['6022b2b64624b8bcec3333fe48d5f74ff6ebceb3bdf98258ba7d7fbbc76b99ab'] builddependencies = [ ('CMake', '3.18.4'), @@ -59,4 +59,4 @@ sanity_check_paths = { 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], } -moduleclass = 'data' \ No newline at end of file +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb index 0cd19603618..64574eb1e43 100644 --- a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb @@ -12,7 +12,10 @@ It condenses and automates the keys decisions for designing a successful segment """ toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = ['https://files.pythonhosted.org/packages/8e/cf/0e5a45faba472c1df80da8d3fcb8d90b31a2258e48fdbc47cd2e30c16233/'] +source_urls = [ + 'https://files.pythonhosted.org/packages/8e/cf/0e5a45faba472c1df80da8d3fcb8d90b31a2258e48fdbc47cd2e30c16233/' +] + sources = ['nnunet-%(version)s.tar.gz'] checksums = ['7ad3d5b89af389fa86cea58f409bd2353b511a746587f37d26c00a756849f356'] From 260c47ebea78083e65b2041055a0f0e6644a5e0c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 5 Nov 2021 08:59:52 +0100 Subject: [PATCH 1839/9987] adding easyconfigs: ReFrame-3.9.0.eb --- .../easyconfigs/r/ReFrame/ReFrame-3.9.0.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb new file mode 100644 index 00000000000..ea6a733eb55 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.9.0' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.2.4', { + 'use_pip': False, + 'checksums': ['0eb8a1516c3d138ae8689c0c1a60fde7143310832f9dc77e11d8a4bc62de193b'], + }), + ('wheel', '0.37.0', { + 'checksums': ['e2ef7239991699e3355d54f8e968a21bb940a1dbf34a4d226741e64462516fad'], + }), + ('setuptools', '57.4.0', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], + }), + ('reframe', version, { + 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], + 'checksums': ['ccc36cb1db12148fe7658583e83c2717f5aae0d8c58f6b6ddd398e187c3edc3a'], + }), +] + +postinstallcmds = [ + "cp -r tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -r share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['lib', 'tutorials', 'external'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions +modextrapaths = { + 'PATH': 'bin', + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 3d4bb965ebb2ac73647cc2dc98a63b9ff42718a9 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 5 Nov 2021 19:43:23 +1050 Subject: [PATCH 1840/9987] comply with c++11 standard -- ABI bug --- .../{RAPSearch2-2.24.eb => RAPSearch2-2.24-GCC-9.3.0.eb} | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/r/RAPSearch2/{RAPSearch2-2.24.eb => RAPSearch2-2.24-GCC-9.3.0.eb} (82%) diff --git a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb similarity index 82% rename from easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb rename to easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb index 38c5a263b4c..f1694491013 100644 --- a/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24.eb +++ b/easybuild/easyconfigs/r/RAPSearch2/RAPSearch2-2.24-GCC-9.3.0.eb @@ -18,10 +18,11 @@ description = """ RAPSearch stands for Reduced Alphabet based Protein similarity Search """ -toolchain = SYSTEM +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'cstd': 'c++11', 'extra_cxxflags': '-D_GLIBCXX_USE_CXX11_ABI=0'} source_urls = ['https://sourceforge.net/projects/rapsearch2/files'] -sources = ['%(name)s.24_64bits.tar.gz'] +sources = ['%(name)s.%(version_minor)s_64bits.tar.gz'] checksums = ['85db4573f4c768b6c3c73bb44ff2611ba48dc6c8d188feb40f44bf7c55de36ce'] skipsteps = ['configure'] From 36280de52bd2dcc0665c373d615e48305d8ad469 Mon Sep 17 00:00:00 2001 From: spottho1 Date: Fri, 5 Nov 2021 10:01:40 +0100 Subject: [PATCH 1841/9987] adding easyconfigs: HDBSCAN-0.8.24-foss-2019b-Python-3.7.4.eb --- .../HDBSCAN-0.8.24-foss-2019b-Python-3.7.4.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.24-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.24-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.24-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..f3b8f0febc7 --- /dev/null +++ b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.24-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'HDBSCAN' +version = '0.8.24' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://hdbscan.readthedocs.io/en/latest/' +description = """The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense + regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library + provides a high performance implementation of this algorithm, along with tools for analysing the resulting + clustering.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fe31a7ea0ce2c9babd190a195e491834ff9f64c74daa4ca94fa65a88f701269a'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('scikit-learn', '0.21.3', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From 7b0c321d9515d38a52dcef7204fbbbcd0c189dbb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Nov 2021 10:14:48 +0100 Subject: [PATCH 1842/9987] {cae}[foss/2020b] OpenFOAM 8-20210316 --- .../OpenFOAM-8-foss-2020b-20210316.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b-20210316.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b-20210316.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b-20210316.eb new file mode 100644 index 00000000000..4d4dd885450 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-8-foss-2020b-20210316.eb @@ -0,0 +1,45 @@ +name = 'OpenFOAM' +local_commit = '1c9b587' +version = '8' +versionsuffix = '-20210316' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': 'OpenFOAM-%(version)s%(versionsuffix)s.tar.gz', +}] +patches = [ + 'OpenFOAM-%(version)s-cleanup.patch', +] +checksums = [ + '2fef19014b408e4ea42062d5bf204419af086cbfa56a21a96676007f926b48f2', # OpenFOAM-8-20210316.tar.gz + 'e3fac8049611ee109f07eb5b0ed4b1526782a21b3f12435e03529d56c8483b9f', # OpenFOAM-8-cleanup.patch +] + +dependencies = [ + ('libreadline', '8.0'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('CGAL', '5.2'), + ('ParaView', '5.8.1', '-mpi'), + ('gnuplot', '5.4.1'), +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' From 5a5af7368257ad30fe46d9183d4cd86579afa7bd Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 5 Nov 2021 11:32:06 +0200 Subject: [PATCH 1843/9987] remove site specific ALPHAFOLD_DATA_DIR; fix data-dep-paths.patch for preset multimer --- .../AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb | 4 ++-- .../AlphaFold-2.1.0_data-dep-paths.patch | 16 +++++++--------- 2 files changed, 9 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb index 3fd2c09d3d7..948443f7f0a 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb @@ -85,7 +85,7 @@ components = [ '43df277943937307d7ac2db0f5e3d1d317061df4ffff46061059a81b61ad5083', # v2.1.0.tar.gz '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - 'e02e1298b59038078a2107e1c04b14172898e1f79b7f3afc2394047db532e228', # AlphaFold-2.1.0_data-dep-paths.patch + '4d5f53486d7c16ad0c93d17c89c04d3ae1310de0adad6bca4dd7ea249bf030d1', # AlphaFold-2.1.0_data-dep-paths.patch 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch @@ -182,7 +182,7 @@ modextrapaths = { modextravars = { 'TF_FORCE_UNIFIED_MEMORY': '1', 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', - 'ALPHAFOLD_DATA_DIR': '/scratch/AlphaFold_DBs', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 } diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch index c8f846999db..3a30389af30 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch @@ -5,13 +5,8 @@ author: Kenneth Hoste (HPC-UGent) update 2.0.1 -> 2.1.0: Thomas Hoffmann (EMBL); diff -ru alphafold-2.1.0/run_alphafold.py alphafold-2.1.0_data-dep-paths/run_alphafold.py --- alphafold-2.1.0/run_alphafold.py 2021-11-02 15:33:58.000000000 +0100 -+++ alphafold-2.1.0_data-dep-paths/run_alphafold.py 2021-11-03 13:04:31.131894917 +0100 -@@ -1,3 +1,4 @@ -+#!/usr/bin/env python - # Copyright 2021 DeepMind Technologies Limited - # - # Licensed under the Apache License, Version 2.0 (the "License"); -@@ -40,6 +41,44 @@ ++++ alphafold-2.1.0_data-dep-paths/run_alphafold.py 2021-11-05 10:12:44.908788630 +0100 +@@ -40,6 +40,45 @@ from alphafold.model import data # Internal import (7716). @@ -23,15 +18,16 @@ diff -ru alphafold-2.1.0/run_alphafold.py alphafold-2.1.0_data-dep-paths/run_alp +if data_dir: + mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters.fa') + uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') -+ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') + template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') + obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') + if use_monomer_preset: + pdb_seqres_database_path = None + uniprot_database_path = None ++ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') + else: + pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt') -+ uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.data') ++ uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.fasta') ++ pdb70_database_path = None + if use_reduced_dbs: + small_bfd_database_path = os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta') + uniclust30_database_path = None @@ -126,4 +122,6 @@ diff -ru alphafold-2.1.0/run_alphafold.py alphafold-2.1.0_data-dep-paths/run_alp ]) app.run(main) +Only in alphafold-2.1.0_data-dep-paths: .run_alphafold.py.swn +Only in alphafold-2.1.0_data-dep-paths: .run_alphafold.py.swo Only in alphafold-2.1.0_data-dep-paths: .run_alphafold.py.swp From 1ea85a8e6284596126fa02d5f666a5ab85f1c655 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 5 Nov 2021 12:57:45 +0200 Subject: [PATCH 1844/9987] update to 2.1.1 --- .../AlphaFold-2.1.1-fosscuda-2020b.eb | 189 ++++++++++++++++++ 1 file changed, 189 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb new file mode 100644 index 00000000000..e32c730e447 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -0,0 +1,189 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.1.1' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1'), + ('TensorFlow', '2.4.1'), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.19'), # also provides absl-py +] +configopts = "-DCUDA_CUDA_LIBRARY=${EBROOTCUDA}/lib64/stubs/libcuda.so " +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'http://two.embl.de/AlphaFold-2.1.0_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'http://two.embl.de/AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'http://two.embl.de/AlphaFold-2.0.1_relax_gpu.patch' + ], + 'checksums': [ + '1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '0f0b9a7913898176b7e7878c0818fd60f7c5f527ec2bc84cd81d96a503f432c2', # AlphaFold-2.1.0_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + '3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +moduleclass = 'bio' From 134b3a7fc21e3592177ed79154a15d030e4c3e62 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 5 Nov 2021 12:01:10 +0100 Subject: [PATCH 1845/9987] Change source_urls to use https --- easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb index ba9782271f5..2f480e47a5b 100644 --- a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb @@ -15,7 +15,7 @@ Source Configuration Management (SCM). toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = [' http://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] +source_urls = [' https://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ 'CVS-1.11.23-zlib-1.patch', From f9472e5da4dd4526e9a424ab7936faab1725ac1e Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 5 Nov 2021 13:10:17 +0200 Subject: [PATCH 1846/9987] fix checksum --- .../easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index e32c730e447..267562d0515 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -85,7 +85,7 @@ components = [ '1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '0f0b9a7913898176b7e7878c0818fd60f7c5f527ec2bc84cd81d96a503f432c2', # AlphaFold-2.1.0_data-dep-paths.patch + '4d5f53486d7c16ad0c93d17c89c04d3ae1310de0adad6bca4dd7ea249bf030d1', # AlphaFold-2.1.0_data-dep-paths.patch 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch From a44b1a5f3cff3118db157b83ae7c3318d5204ec2 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 5 Nov 2021 13:22:09 +0200 Subject: [PATCH 1847/9987] fix patch urls --- .../a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index 267562d0515..3598983c8f9 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -75,11 +75,11 @@ components = [ ], 'patches': [ 'AlphaFold-2.0.0_fix-packages.patch', - 'http://two.embl.de/AlphaFold-2.1.0_data-dep-paths.patch', + 'AlphaFold-2.1.0_data-dep-paths.patch', 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', - 'http://two.embl.de/AlphaFold-2.0.1_setup_rm_tfcpu.patch', - 'http://two.embl.de/AlphaFold-2.0.1_relax_gpu.patch' + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.0.1_relax_gpu.patch' ], 'checksums': [ '1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz From fa530144810919f04b39e3e262ef9972915c495d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 5 Nov 2021 12:40:10 +0100 Subject: [PATCH 1848/9987] Delete AlphaFold-2.1.0-fosscuda-2020b.eb update to 2.1.1 --- .../AlphaFold-2.1.0-fosscuda-2020b.eb | 189 ------------------ 1 file changed, 189 deletions(-) delete mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb deleted file mode 100644 index 948443f7f0a..00000000000 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0-fosscuda-2020b.eb +++ /dev/null @@ -1,189 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'AlphaFold' -version = '2.1.0' - -homepage = 'https://deepmind.com/research/case-studies/alphafold' -description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" - -toolchain = {'name': 'fosscuda', 'version': '2020b'} - -builddependencies = [ - # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.18.4'), - ('Doxygen', '1.8.20'), - # required for installing dm-tree - ('Bazel', '3.7.2'), - ('SWIG', '4.0.2'), -] - -dependencies = [ - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('PyYAML', '5.3.1'), - ('TensorFlow', '2.4.1'), - ('Biopython', '1.78'), - ('HH-suite', '3.3.0'), - ('HMMER', '3.3.2'), - ('Kalign', '3.3.1'), - ('jax', '0.2.19'), # also provides absl-py -] -configopts = "-DCUDA_CUDA_LIBRARY=${EBROOTCUDA}/lib64/stubs/libcuda.so " -local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " -local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " - -# required to install OpenMM Python API; -# avoid that setup.py partially uninstalls existing OpenMM Python bindings... -local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " -local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" - -# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, -# see docker/Dockerfile in AlphaFold repository -local_scp_commit = '7102c6' - -components = [ - # for simtk - ('OpenMM', '7.5.1', { - 'easyblock': 'CMakeMake', - 'source_urls': ['https://github.com/openmm/openmm/archive/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], - 'checksums': [ - 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz - '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch - ], - 'start_dir': 'openmm-%(version)s', - 'preinstallopts': local_openmm_preinstallopts, - 'installopts': local_openmm_installopts, - }), - (name, version, { - 'easyblock': 'PythonPackage', - 'source_urls': [ - 'https://github.com/deepmind/alphafold/archive/refs/tags/', - 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, - ], - 'sources': [ - { - 'download_filename': 'v%(version)s.tar.gz', - 'filename': SOURCE_TAR_GZ, - }, - { - 'download_filename': 'stereo_chemical_props.txt', - 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, - 'extract_cmd': "cp %s .", - }, - ], - 'patches': [ - 'AlphaFold-2.0.0_fix-packages.patch', - 'AlphaFold-2.1.0_data-dep-paths.patch', - 'AlphaFold-2.0.0_n-cpu.patch', - 'AlphaFold-2.1.0_fix-scp-path.patch', - 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', - 'AlphaFold-2.0.1_relax_gpu.patch' - ], - 'checksums': [ - '43df277943937307d7ac2db0f5e3d1d317061df4ffff46061059a81b61ad5083', # v2.1.0.tar.gz - '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt - '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '4d5f53486d7c16ad0c93d17c89c04d3ae1310de0adad6bca4dd7ea249bf030d1', # AlphaFold-2.1.0_data-dep-paths.patch - 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch - '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch - '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch - '3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch - ], - 'start_dir': 'alphafold-%(version)s', - 'use_pip': True, - }), -] - -use_pip = True - -exts_list = [ - ('PDBFixer', '1.7', { - 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], - }), - ('toolz', '0.11.1', { - 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], - }), - ('chex', '0.0.8', { - 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], - }), - ('tabulate', '0.8.9', { - 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], - }), - ('dm-haiku', '0.0.4', { - 'modulename': 'haiku', - 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], - }), - ('dm-tree', '0.1.6', { - 'modulename': 'tree', - 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], - }), - ('websocket-client', '1.2.1', { - 'modulename': 'websocket', - 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], - }), - ('docker', '5.0.0', { - 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], - }), - ('immutabledict', '2.1.0', { - 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], - }), - ('contextlib2', '21.6.0', { - 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], - }), - ('ml_collections', '0.1.0', { - 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", - 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], - }), -] - -postinstallcmds = [ - "mkdir -p %(installdir)s/bin", - # run_alphafold.py script is missing a shebang... - "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", - "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", - "chmod a+x %(installdir)s/bin/run_alphafold.py", - "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", - "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", - "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, - # run tests for run_alphafold.py script; - # shouldn't do this in sanity check to avoid breaking use of --module-only - "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " - "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", -] - -sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], - 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], -} - -sanity_check_commands = [ - "pdbfixer --help", - "python -m simtk.testInstallation", - "python -c 'import alphafold'", - "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", -] - -sanity_pip_check = True - -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - -# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; -# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py -modextravars = { - 'TF_FORCE_UNIFIED_MEMORY': '1', - 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', - # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt - 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 -} - -moduleclass = 'bio' From 5c1eb57163e4c594fb8bb8e06f87cfa8b90b62bc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 5 Nov 2021 13:03:05 +0100 Subject: [PATCH 1849/9987] {chem}[foss/2020b] CP2K 5.1 --- .../easyconfigs/c/CP2K/CP2K-5.1-foss-2020b.eb | 49 +++++++++++++++++++ .../l/Libint/Libint-1.1.6-foss-2020b.eb | 32 ++++++++++++ .../l/libxc/libxc-3.0.1-foss-2020b.eb | 33 +++++++++++++ 3 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020b.eb new file mode 100644 index 00000000000..8bc41a594ee --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-5.1-foss-2020b.eb @@ -0,0 +1,49 @@ +name = 'CP2K' +version = '5.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] +checksums = [ + 'e23613b593354fa82e0b8410e17d94c607a0b8c6d9b5d843528403ab09904412', # cp2k-5.1.tar.bz2 + '02475cbe24c8d4ba27037c826adf8a534cad634c3c4e02c21d743f5284516bda', # CP2K-2.4.0-fix_compile_date_lastsvn.patch +] + +dependencies = [ + ('Libint', '1.1.6'), + ('libxc', '3.0.1'), + ('libxsmm', '1.16.1'), + ('FFTW', '3.3.8'), + ('PLUMED', '2.6.2'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.1'), +] + +# values to use here are +1 those used for building Libint +# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT +extradflags = "-D__LIBINT_MAX_AM=6 -D__LIBDERIV_MAX_AM1=5" + +# regression test reports failures +ignore_regtest_fails = True + +# You might want to set OMP_NUM_THREADS, otherwise OpenBLAS will start (by default) +# the number of accessible CPUcores OpenMP threads. Since it is a MPI only version (popt), +# the performance will be copletely bad, as on N CPU cores N^2 threads will run. +# intel toolchain versions do not have this problem. YOU HAVE BEEN WARNED! +# modextravars = {'OMP_NUM_THREADS': '1'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020b.eb new file mode 100644 index 00000000000..b85944e7d72 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-foss-2020b.eb @@ -0,0 +1,32 @@ +name = 'Libint' +version = '1.1.6' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/evaleev/libint/archive/'] +sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] +checksums = ['f201b0c621df678cfe8bdf3990796b8976ff194aba357ae398f2f29b0e2985a6'] + +builddependencies = [('Autotools', '20200321')] + +preconfigopts = "aclocal -I lib/autoconf && libtoolize && autoconf && " + +# these are important for CP2K +# see https://github.com/cp2k/cp2k/blob/master/cp2k/tools/hfx_tools/libint_tools/README_LIBINT +configopts = "--with-libint-max-am=5 --with-libderiv-max-am1=4 " + +configopts += " --enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.%s' % (x, y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb new file mode 100644 index 00000000000..e9d1b83c722 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.1-foss-2020b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '3.0.1' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +# Results for some functionals (e.g. mgga_c_tpss) deviate with too aggressive optimization settings. +toolchainopts = {'lowopt': True} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['libxc-%(version_major_minor)s_no-longdouble.patch'] +checksums = [ + '836692f2ab60ec3aca0cca105ed5d0baa7d182be07cc9d0daa7b80ee1362caf7', # libxc-3.0.1.tar.gz + '27338d9f63ce33386a6241e7bd8edde66ac8684d103acf0e6cbb5bde011730b9', # libxc-3.0_no-longdouble.patch +] + +configopts = '--enable-static --enable-shared --enable-fortran' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x, y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' From 2171899acc314696519ce507063cc269d6078d17 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 5 Nov 2021 17:20:59 +0200 Subject: [PATCH 1850/9987] adding easyconfigs: STACEY-1.2.5-GCC-10.2.0.eb --- .../s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb new file mode 100644 index 00000000000..e6fffcbcc27 --- /dev/null +++ b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'Tarball' + +name = 'STACEY' +version = '1.2.5' + +homepage = 'http://www.indriid.com/software.html' +description = """The BEAST2 package STACEY can be used for species delimitation and species tree estimation, +based on the multispecies coalescent model.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://www.indriid.com/2019/'] +sources = ['%(name)s.addon.v%(version)s.zip'] +checksums = ['a6ce3ce83ddafe3505622961c7d90e696e11b2b51246f7447d820e1b3e717b58'] + +builddependencies = [ + ('Xvfb', '1.20.9'), +] +dependencies = [ + ('Beast', '2.6.4'), +] + +# we need to link installdir to hardcoded package directory of Beast (~/.beast/2.6/) +postinstallcmds = [ + # if package dir doesnt exist yet, initial run of `beauti` creates it + 'timeout 10 xvfb-run beauti 2>&1 | grep "Terminated"', + # now we can link our installdir to the package dir + 'ln -s %(installdir)s ~/.beast/2.6/STACEY ', +] + +sanity_check_paths = { + 'files': ['stacey.src.jar'], + 'dirs': ['lib/', 'templates/', 'examples'], +} + +moduleclass = 'data' From 4cc7b59852f2dda911d79c294ecae73fe08ab97a Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Sat, 6 Nov 2021 12:51:18 +0100 Subject: [PATCH 1851/9987] adding easyconfigs: WPS-4.3.1-foss-2021a-dmpar.eb and patches: WPS-4.3.1_netCDF-Fortran_seperate_path.patch --- .../w/WPS/WPS-4.3.1-foss-2021a-dmpar.eb | 38 ++++++++ ...S-4.3.1_netCDF-Fortran_seperate_path.patch | 90 +++++++++++++++++++ 2 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.3.1-foss-2021a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.3.1_netCDF-Fortran_seperate_path.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.3.1-foss-2021a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.3.1-foss-2021a-dmpar.eb new file mode 100644 index 00000000000..bd4c369df7f --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.3.1-foss-2021a-dmpar.eb @@ -0,0 +1,38 @@ +name = 'WPS' +version = '4.3.1' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WPS-%(version)s_netCDF-Fortran_seperate_path.patch', +] +checksums = [ + 'db6da44a2ca68cc289e98ab388a53c27283eb4ed8e92edee268466543fdedb0e', # v4.3.1.tar.gz + '25359a9abfc6a4afc2f7b9624727eeea47d1a6421b99dbc8dd9b54a37d378ae5', # WPS-4.3.1_netCDF-Fortran_seperate_path.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +builddependencies = [ + ('Perl', '5.32.1'), +] + +dependencies = [ + ('WRF', '4.3', versionsuffix), + ('JasPer', '2.0.28'), + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.3.1_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.3.1_netCDF-Fortran_seperate_path.patch new file mode 100644 index 00000000000..c4bd7bc75f9 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.3.1_netCDF-Fortran_seperate_path.patch @@ -0,0 +1,90 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since 2013; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain +# +# updated for WPS v4.1 by Kenneth Hoste (HPC-UGent) +# updated for WPS v4.2 by Åke Sandgren (HPC2N) + +diff -ru WPS-4.2.orig/arch/Config.pl WPS-4.2/arch/Config.pl +--- WPS-4.2.orig/arch/Config.pl 2020-04-23 21:31:06.000000000 +0200 ++++ WPS-4.2/arch/Config.pl 2021-04-14 13:11:31.470659452 +0200 +@@ -41,6 +41,7 @@ + if(substr( $ARGV[0], 1, 8 ) eq "netcdff=") + { + $sw_netcdff_lib = substr( $ARGV[0], 9); ++ $sw_netcdff_lib =~ s/!/ /g ; + } + if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") + { +diff -ru WPS-4.2.orig/arch/preamble WPS-4.2/arch/preamble +--- WPS-4.2.orig/arch/preamble 2020-04-23 21:31:06.000000000 +0200 ++++ WPS-4.2/arch/preamble 2021-04-14 13:11:31.470659452 +0200 +@@ -39,7 +39,7 @@ + -I$(WRF_DIR)/external/io_grib1 \ + -I$(WRF_DIR)/external/io_int \ + -I$(WRF_DIR)/inc \ +- -I$(NETCDF)/include ++ -I$(NETCDF)/include -I$(NETCDFF)/include + + WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ + -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ +diff -ru WPS-4.2.orig/configure WPS-4.2/configure +--- WPS-4.2.orig/configure 2020-04-23 21:31:06.000000000 +0200 ++++ WPS-4.2/configure 2021-04-14 13:11:31.470659452 +0200 +@@ -119,9 +119,14 @@ + echo "Will use NETCDF in dir: $NETCDF" + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available +- NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then +- NETCDFF="-lnetcdff" ++ USENETCDFF=" " ++ # for netCDF 4.2 and greater, the Fortran library is a seperate install ++ if [ -z "$NETCDFF" ] ++ then ++ NETCDFF=$NETCDF ++ fi ++ if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-lnetcdff" + fi + else + echo "Will configure for use without NetCDF" +@@ -190,7 +195,7 @@ + fi + + # Found perl, so proceed with configuration +-perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$NETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir ++perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$USENETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir + + + #Checking cross-compiling capability for some particular environment +@@ -356,9 +361,9 @@ + end program + EOF + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -lnetcdf $USENETCDFF > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + ./fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then +diff -ru WPS-4.2.orig/util/src/Makefile WPS-4.2/util/src/Makefile +--- WPS-4.2.orig/util/src/Makefile 2020-04-23 21:31:06.000000000 +0200 ++++ WPS-4.2/util/src/Makefile 2021-04-14 13:11:31.470659452 +0200 +@@ -41,11 +41,11 @@ + write_met_module.o misc_definitions_module.o met_data_module.o + $(SFC) $(LDFLAGS) -o $@ elev_angle.o cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o met_data_module.o \ +- -L$(NETCDF)/lib -I$(NETCDF)/include -lnetcdf ++ -L$(NETCDFF)/lib -I$(NETCDFF)/include -lnetcdff + + elev_angle.o: elev_angle.F cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o +- $(SFC) -c elev_angle.F -I$(NETCDF)/include ++ $(SFC) -c elev_angle.F -I$(NETCDFF)/include + + calc_ecmwf_p.exe: calc_ecmwf_p.o cio.o module_debug.o module_stringutil.o gridinfo_module.o read_met_module.o \ + write_met_module.o module_date_pack.o misc_definitions_module.o met_data_module.o constants_module.o From ac1ee41921e3e7f5ac831963deab3e9d6d73da8f Mon Sep 17 00:00:00 2001 From: casparl Date: Sat, 6 Nov 2021 13:31:22 +0100 Subject: [PATCH 1852/9987] Might as well add an updated torchvision here as well --- ...rchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..7e64e72a452 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,26 @@ +name = 'torchvision' +version = '0.11.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['32a06ccf755e4d75006ce03701f207652747a63dbfdf65f0f20a1b6f93a2e834'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('Pillow-SIMD', '8.2.0'), + ('PyTorch', '1.10.0', '-CUDA-%(cudaver)s'), + ('CUDA', '11.3.1', '', True), +] + +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +moduleclass = 'vis' From 4aaaae10b823143443cc74e195807255291ed714 Mon Sep 17 00:00:00 2001 From: Sassy Date: Sun, 7 Nov 2021 21:04:02 +0000 Subject: [PATCH 1853/9987] adding easyconfigs: MariaDB-10.6.4-GCC-11.2.0.eb --- .../m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb new file mode 100644 index 00000000000..54050e548d7 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.6.4' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + '75bf9b147a95d38160d01a73b098d50a1960563b46d16a235971fff64d99643c', # mariadb-10.6.4.tar.gz + '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19', # MariaDB-10.1.13-link-rt-for-jemalloc.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('libaio', '0.3.112'), + ('PCRE2', '10.37'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.3'), # optional + ('XZ', '5.2.5'), # optional + ('jemalloc', '5.2.1'), # optional + ('snappy', '1.1.9'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.9.10'), # needed by Connect XML + ('Boost', '1.77.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release " +configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' From 9c6bb27157bae926c53890cac7ce25f6edeefded Mon Sep 17 00:00:00 2001 From: Sassy Date: Sun, 7 Nov 2021 21:44:39 +0000 Subject: [PATCH 1854/9987] adding easyconfigs: Judy-1.0.5-GCCcore-11.2.0.eb --- .../j/Judy/Judy-1.0.5-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f64b356b398 --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' From 1e9fba104e979425b0e127406344b6e0c647b59f Mon Sep 17 00:00:00 2001 From: Sassy Date: Sun, 7 Nov 2021 21:50:37 +0000 Subject: [PATCH 1855/9987] adding easyconfigs: libaio-0.3.112-GCCcore-11.2.0.eb --- .../l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2d6229d7fea --- /dev/null +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.112' +local_libversion = '1.0.1' + +homepage = 'https://pagure.io/libaio' +description = "Asynchronous input/output library that uses the kernels native interface." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] + +builddependencies = [('binutils', '2.37')] + +files_to_copy = [ + (["src/libaio.a", "src/libaio.%s.%s" % (SHLIB_EXT, local_libversion)], "lib"), + (["src/libaio.h"], "include"), +] + +postinstallcmds = ["cd %%(installdir)s/lib; ln -s libaio.%s.%s libaio.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT)] + +sanity_check_paths = { + 'files': ['lib/libaio.a', 'lib/libaio.%s.%s' % (SHLIB_EXT, local_libversion), 'include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' From 0049d5d9c890c8a315b00f405f356cededaab7de Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 8 Nov 2021 09:20:31 +0100 Subject: [PATCH 1856/9987] patch other relevant bazel versions --- .../easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb | 7 ++++++- ...ename_gettid.patch => Bazel-0.25.2_rename_gettid.patch} | 0 .../easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb | 7 ++++++- .../easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb | 2 ++ .../easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb | 2 ++ .../b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb | 2 ++ easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb | 7 ++++++- 8 files changed, 25 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/b/Bazel/{Bazel-0.26.1_rename_gettid.patch => Bazel-0.25.2_rename_gettid.patch} (100%) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb index 84155faf16e..5de84907639 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb @@ -9,7 +9,12 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] -checksums = ['7456032199852c043e6c5b3e4c71dd8089c1158f72ec554e6ec1c77007f0ab51'] +patches = ['%(name)s-%(version)s_rename_gettid.patch'] + +checksums = [ + '7456032199852c043e6c5b3e4c71dd8089c1158f72ec554e6ec1c77007f0ab51', # bazel-0.25.2-dist.zip + '8639129941a6db079015ea7e04e7f5b6b24da3c963e7eb0488df34439d628f0e', # Bazel-0.25.2_rename_gettid.patch +] builddependencies = [ ('binutils', '2.31.1'), diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1_rename_gettid.patch b/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2_rename_gettid.patch similarity index 100% rename from easybuild/easyconfigs/b/Bazel/Bazel-0.26.1_rename_gettid.patch rename to easybuild/easyconfigs/b/Bazel/Bazel-0.25.2_rename_gettid.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb index 746a2d6c423..62c42905710 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb @@ -9,7 +9,12 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] -checksums = ['c0e94f8f818759f3f67af798c38683520c540f469cb41aea8f5e5a0e43f11600'] +patches = ['%(name)s-0.25.2_rename_gettid.patch'] + +checksums = [ + 'c0e94f8f818759f3f67af798c38683520c540f469cb41aea8f5e5a0e43f11600', # bazel-0.26.1-dist.zip + '8639129941a6db079015ea7e04e7f5b6b24da3c963e7eb0488df34439d628f0e', # Bazel-0.25.2_rename_gettid.patch +] builddependencies = [ ('binutils', '2.31.1'), diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb index 1bd46c4dcff..bf9db9bef97 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] -patches = ['%(name)s-%(version)s_rename_gettid.patch'] +patches = ['%(name)s-0.25.2_rename_gettid.patch'] checksums = [ 'c0e94f8f818759f3f67af798c38683520c540f469cb41aea8f5e5a0e43f11600', # bazel-0.26.1-dist.zip diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb index cd4d5f44bbb..699ad4853c3 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb @@ -12,11 +12,13 @@ sources = ['%(namelower)s-%(version)s-dist.zip'] patches = [ 'Bazel-%(version)s_fix-gold-flag.patch', 'Bazel-%(version)s_fix-zip-d-on-power.patch', + '%(name)s-0.25.2_rename_gettid.patch', ] checksums = [ '872a52cff208676e1169b3e1cae71b1fe572c4109cbd66eab107d8607c378de5', # bazel-0.29.1-dist.zip '99928d0902beeaf962a8ad14db8432f8e5114645e3caf64c7ee2fa136c31609f', # Bazel-0.29.1_fix-gold-flag.patch '0089567af6a991084d5628a8b6fa92b68402ff4b7a0ef8fa944e629e7be63b93', # Bazel-0.29.1_fix-zip-d-on-power.patch + '8639129941a6db079015ea7e04e7f5b6b24da3c963e7eb0488df34439d628f0e', # Bazel-0.25.2_rename_gettid.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb index f15004d6f1b..720da63a770 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb @@ -12,11 +12,13 @@ sources = ['%(namelower)s-%(version)s-dist.zip'] patches = [ 'Bazel-%(version)s_fix-gold-flag.patch', 'Bazel-%(version)s_fix-zip-d-on-power.patch', + '%(name)s-0.25.2_rename_gettid.patch', ] checksums = [ '872a52cff208676e1169b3e1cae71b1fe572c4109cbd66eab107d8607c378de5', # bazel-0.29.1-dist.zip '99928d0902beeaf962a8ad14db8432f8e5114645e3caf64c7ee2fa136c31609f', # Bazel-0.29.1_fix-gold-flag.patch '0089567af6a991084d5628a8b6fa92b68402ff4b7a0ef8fa944e629e7be63b93', # Bazel-0.29.1_fix-zip-d-on-power.patch + '8639129941a6db079015ea7e04e7f5b6b24da3c963e7eb0488df34439d628f0e', # Bazel-0.25.2_rename_gettid.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb index 0387b85aec6..9544908a761 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb @@ -13,11 +13,13 @@ sources = ['%(namelower)s-%(version)s-dist.zip'] patches = [ 'Bazel-%(version)s_fix-gold-flag.patch', 'Bazel-%(version)s_fix-zip-d-on-power.patch', + '%(name)s-0.25.2_rename_gettid.patch', ] checksums = [ '872a52cff208676e1169b3e1cae71b1fe572c4109cbd66eab107d8607c378de5', # bazel-0.29.1-dist.zip '99928d0902beeaf962a8ad14db8432f8e5114645e3caf64c7ee2fa136c31609f', # Bazel-0.29.1_fix-gold-flag.patch '0089567af6a991084d5628a8b6fa92b68402ff4b7a0ef8fa944e629e7be63b93', # Bazel-0.29.1_fix-zip-d-on-power.patch + '8639129941a6db079015ea7e04e7f5b6b24da3c963e7eb0488df34439d628f0e', # Bazel-0.25.2_rename_gettid.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb index f7ffa464ec7..52fd06b9233 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb @@ -9,10 +9,15 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] -patches = ['Bazel-0.29.1_fix-gold-flag.patch'] +patches = [ + 'Bazel-0.29.1_fix-gold-flag.patch', + '%(name)s-0.25.2_rename_gettid.patch', +] + checksums = [ '4b66a8c93af7832ed32e7236cf454a05f3aa06d25a8576fc3f83114f142f95ab', # bazel-1.1.0-dist.zip '99928d0902beeaf962a8ad14db8432f8e5114645e3caf64c7ee2fa136c31609f', # Bazel-0.29.1_fix-gold-flag.patch + '8639129941a6db079015ea7e04e7f5b6b24da3c963e7eb0488df34439d628f0e', # Bazel-0.25.2_rename_gettid.patch ] builddependencies = [ From 54b56bf11a83d6bdd8a25b7c3e08c31f6c059d3b Mon Sep 17 00:00:00 2001 From: benjamic Date: Mon, 8 Nov 2021 10:46:25 +0100 Subject: [PATCH 1857/9987] Style errors fixed --- easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-foss-2021a.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-foss-2021a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-foss-2021a.eb index 5308b74a7de..68d2f193748 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-foss-2021a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.4.2-foss-2021a.eb @@ -5,9 +5,9 @@ version = '9.4.2' homepage = 'https://www.abinit.org/' description = """ABINIT is a package whose main program allows one to find the total energy, - charge density and electronic structure of systems made of electrons and nuclei (molecules - and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a - planewave or wavelet basis.""" + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': True, 'pic': True} @@ -27,8 +27,6 @@ dependencies = [ ('Wannier90', '3.1.0'), ] - - # Needed due to changes in GCC10. configopts = 'FCFLAGS="-fallow-argument-mismatch -ffree-line-length-none $FCFLAGS" ' configopts += 'FFLAGS="-fallow-argument-mismatch $FFLAGS" ' From 4484ceed3921607ccd2f1ca1517952e8435593f6 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 09:49:12 +0000 Subject: [PATCH 1858/9987] OpenSSL-1.1 added --- easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb index 54050e548d7..0b4d338f0ed 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb @@ -34,6 +34,7 @@ dependencies = [ ('libxml2', '2.9.10'), # needed by Connect XML ('Boost', '1.77.0'), # needed by OQGraph ('Judy', '1.0.5'), # needed by OQGraph + ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest ] separate_build_dir = True From 54caf9d9ea77e1e40540abe01e5383274541ea02 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 8 Nov 2021 12:17:22 +0100 Subject: [PATCH 1859/9987] Added Horovod for PyTorch here as well --- ...orovod-0.23.0-foss-2021a-PyTorch-1.10.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-PyTorch-1.10.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-PyTorch-1.10.0.eb new file mode 100644 index 00000000000..d1ecff30044 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-PyTorch-1.10.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.23.0' +local_pt_version = '1.10.0' +versionsuffix = '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('CMake', '3.20.1'), + ('flatbuffers', '2.0.0'), +] +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('CUDA', '11.3.1', '', True), + ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), + ('PyTorch', local_pt_version, '-CUDA-%(cudaver)s'), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('horovod', version, { + 'checksums': ['72ab3e5f59df6a000473999937e52e6831ad1a5e4e7bd23885a04bcdd4d8691c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 55d8e468f1b0d0b445dd1c2cb239ba0c9b3337ca Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 12:59:47 +0000 Subject: [PATCH 1860/9987] PCRE2 moved to dependency --- easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb index 0b4d338f0ed..62f2b671372 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb @@ -20,7 +20,6 @@ checksums = [ builddependencies = [ ('CMake', '3.21.1'), ('libaio', '0.3.112'), - ('PCRE2', '10.37'), ] dependencies = [ @@ -34,6 +33,7 @@ dependencies = [ ('libxml2', '2.9.10'), # needed by Connect XML ('Boost', '1.77.0'), # needed by OQGraph ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.37'), ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest ] From a73cee8439ce0e46641104377b47161d8bf5a3a9 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 8 Nov 2021 13:12:21 +0000 Subject: [PATCH 1861/9987] Delete liblzma-5.2.5-foss-2020b.eb removing unnecessary file --- .../l/liblzma/liblzma-5.2.5-foss-2020b.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb b/easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb deleted file mode 100644 index 14f9ab29eda..00000000000 --- a/easybuild/easyconfigs/l/liblzma/liblzma-5.2.5-foss-2020b.eb +++ /dev/null @@ -1,32 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'liblzma' -version = '5.2.5' - -homepage = 'https://github.com/xz-mirror/xz' -description = """XZ Utils provide a general-purpose data-compression library plus command-line tools.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://github.com/xz-mirror/xz/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['0d2b89629f13dd1a0602810529327195eff5f62a0142ccd65b903bc16a4ac78a'] - -builddependencies = [ - ('CMake', '3.18.4'), -] - -dependencies = [ -] - -sanity_check_paths = { - 'files': ['bin/xz', 'bin/xzdec'], - 'dirs': ['lib/', 'bin/', 'include/'] -} - -sanity_check_commands = [ -] - -moduleclass = 'tools' From 5a96ede0e919c72f3df5c3e4e1a5e21e669d3dbe Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 8 Nov 2021 13:12:55 +0000 Subject: [PATCH 1862/9987] Update easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit removing trash Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb index 280d70f476e..505836bb08d 100644 --- a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -9,7 +9,6 @@ homepage = 'https://github.com/google/zopfli' description = """Zopfli Compression Algorithm is a compression library programmed in C to perform very good, but slow, deflate or zlib compression.""" -# toolchain = {'name': 'foss', 'version': '2020b'} toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} From f4fd4aac91966370dbb0f36ec0a48667391b40b6 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 8 Nov 2021 13:13:27 +0000 Subject: [PATCH 1863/9987] Update easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit flags for zopfli Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb index 505836bb08d..3950b08a0bc 100644 --- a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('CMake', '3.18.4'), ('binutils', '2.35'), ] - +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] sanity_check_paths = { 'files': [], 'dirs': ['lib/', 'include/'], From 8793d9400662e4d7276fedab29b0cff53ea5b5f5 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 8 Nov 2021 13:13:44 +0000 Subject: [PATCH 1864/9987] Update easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit better sanity check for zopfli Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb index 3950b08a0bc..ee2b65fa1c4 100644 --- a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -22,8 +22,8 @@ builddependencies = [ ] configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] sanity_check_paths = { - 'files': [], - 'dirs': ['lib/', 'include/'], + 'files': ['bin/zopfli', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT, 'include/zopfli.h'], + 'dirs': [], } moduleclass = 'tools' From 1609e61bbaba9812dcdfc16d014f25335c00a6b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 Nov 2021 14:18:27 +0100 Subject: [PATCH 1865/9987] add geex and momentfit extensions for R v4.1.x --- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index d50895fcfd0..f2e6bc262d0 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -3003,6 +3003,12 @@ exts_list = [ ('gtsummary', '1.4.2', { 'checksums': ['3fe958077df9e604bf536eeda73eb825ee6ae7fcac716b7a42d5a9d867bd4122'], }), + ('geex', '1.0.12', { + 'checksums': ['037aece09bc0c4349897cd1d8f5dcf1e680598cdfdf72148b6d1506e02690e7f'], + }), + ('momentfit', '0.2', { + 'checksums': ['a10d43ac23bb61b9c67efa4800e3e2b6a444c1afaca8bad351648accd7e003f6'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 2a6fb5b6b1d..66e25a36ddc 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3075,6 +3075,12 @@ exts_list = [ ('ncdf4', '1.17', { 'checksums': ['db95c4729d3187d1a56dfd019958216f442be6221bd15e23cd597e6129219af6'], }), + ('geex', '1.0.12', { + 'checksums': ['037aece09bc0c4349897cd1d8f5dcf1e680598cdfdf72148b6d1506e02690e7f'], + }), + ('momentfit', '0.2', { + 'checksums': ['a10d43ac23bb61b9c67efa4800e3e2b6a444c1afaca8bad351648accd7e003f6'], + }), ] moduleclass = 'lang' From dd2ee1ad1f3f43a8c004991a1aaf307156b553ce Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 8 Nov 2021 15:39:13 +0200 Subject: [PATCH 1866/9987] remove cuda stubs; update AlphaFold-2.1.0_data-dep-paths.patch: 1. correct mgy_clusters_2018_12.fa, 2. correct treatment of default parameter --model_preset=monomer --- .../AlphaFold-2.1.0_data-dep-paths.patch | 17 +++++++---------- .../AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 3 +-- 2 files changed, 8 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch index 3a30389af30..f07d4e276b3 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.0_data-dep-paths.patch @@ -3,20 +3,20 @@ pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild author: Kenneth Hoste (HPC-UGent) update 2.0.1 -> 2.1.0: Thomas Hoffmann (EMBL); -diff -ru alphafold-2.1.0/run_alphafold.py alphafold-2.1.0_data-dep-paths/run_alphafold.py ---- alphafold-2.1.0/run_alphafold.py 2021-11-02 15:33:58.000000000 +0100 -+++ alphafold-2.1.0_data-dep-paths/run_alphafold.py 2021-11-05 10:12:44.908788630 +0100 +diff -ru alphafold-2.1.1/run_alphafold.py alphafold-2.1.1_data-dep-paths/run_alphafold.py +--- alphafold-2.1.1/run_alphafold.py 2021-11-05 10:38:51.000000000 +0100 ++++ alphafold-2.1.1_data-dep-paths/run_alphafold.py 2021-11-08 14:18:45.264272641 +0100 @@ -40,6 +40,45 @@ from alphafold.model import data # Internal import (7716). +use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:]) -+use_monomer_preset = any("--model_preset=monomer" in s for s in sys.argv[1:]) ++use_monomer_preset = not any("--model_preset=multimer" in s for s in sys.argv[1:]) + +data_dir = os.getenv('ALPHAFOLD_DATA_DIR') + +if data_dir: -+ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters.fa') ++ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters_2018_12.fa') + uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') + template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') + obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') @@ -53,8 +53,8 @@ diff -ru alphafold-2.1.0/run_alphafold.py alphafold-2.1.0_data-dep-paths/run_alp logging.set_verbosity(logging.INFO) @@ -56,7 +95,7 @@ - 'origin is unknown. These values determine the pairing ' - 'method for the MSA.') + 'where it is not, or where the origin is unknown. These values determine ' + 'the pairing method for the MSA.') -flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') +flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') @@ -122,6 +122,3 @@ diff -ru alphafold-2.1.0/run_alphafold.py alphafold-2.1.0_data-dep-paths/run_alp ]) app.run(main) -Only in alphafold-2.1.0_data-dep-paths: .run_alphafold.py.swn -Only in alphafold-2.1.0_data-dep-paths: .run_alphafold.py.swo -Only in alphafold-2.1.0_data-dep-paths: .run_alphafold.py.swp diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index 3598983c8f9..d7f3a327937 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -28,7 +28,6 @@ dependencies = [ ('Kalign', '3.3.1'), ('jax', '0.2.19'), # also provides absl-py ] -configopts = "-DCUDA_CUDA_LIBRARY=${EBROOTCUDA}/lib64/stubs/libcuda.so " local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " @@ -85,7 +84,7 @@ components = [ '1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch - '4d5f53486d7c16ad0c93d17c89c04d3ae1310de0adad6bca4dd7ea249bf030d1', # AlphaFold-2.1.0_data-dep-paths.patch + 'ecd1b240fdcd30110879dc4a88880405ae3fafb0f93f95f14fe30f6562148e13', # AlphaFold-2.1.0_data-dep-paths.patch 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch From c8e8a8c397a63a6e3121bc5b50a0f46aaa69b1c1 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Mon, 8 Nov 2021 14:41:00 +0100 Subject: [PATCH 1867/9987] reusing patch from older version --- .../w/WPS/WPS-4.3.1-foss-2021a-dmpar.eb | 4 +- ...S-4.3.1_netCDF-Fortran_seperate_path.patch | 90 ------------------- 2 files changed, 2 insertions(+), 92 deletions(-) delete mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.3.1_netCDF-Fortran_seperate_path.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.3.1-foss-2021a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.3.1-foss-2021a-dmpar.eb index bd4c369df7f..d88bd39f7ca 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.3.1-foss-2021a-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.3.1-foss-2021a-dmpar.eb @@ -12,11 +12,11 @@ toolchainopts = {'opt': True} source_urls = ['https://github.com/wrf-model/WPS/archive/'] sources = ['v%(version)s.tar.gz'] patches = [ - 'WPS-%(version)s_netCDF-Fortran_seperate_path.patch', + 'WPS-4.2_netCDF-Fortran_seperate_path.patch', ] checksums = [ 'db6da44a2ca68cc289e98ab388a53c27283eb4ed8e92edee268466543fdedb0e', # v4.3.1.tar.gz - '25359a9abfc6a4afc2f7b9624727eeea47d1a6421b99dbc8dd9b54a37d378ae5', # WPS-4.3.1_netCDF-Fortran_seperate_path.patch + '25359a9abfc6a4afc2f7b9624727eeea47d1a6421b99dbc8dd9b54a37d378ae5', # WPS-4.2_netCDF-Fortran_seperate_path.patch ] buildtype = "dmpar" diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.3.1_netCDF-Fortran_seperate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.3.1_netCDF-Fortran_seperate_path.patch deleted file mode 100644 index c4bd7bc75f9..00000000000 --- a/easybuild/easyconfigs/w/WPS/WPS-4.3.1_netCDF-Fortran_seperate_path.patch +++ /dev/null @@ -1,90 +0,0 @@ -# Allow netCDF library with separate directories for C and Fortran -# ============================================================================ -# This patch has been around in EasyBuild since 2013; it was committed by -# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain -# -# updated for WPS v4.1 by Kenneth Hoste (HPC-UGent) -# updated for WPS v4.2 by Åke Sandgren (HPC2N) - -diff -ru WPS-4.2.orig/arch/Config.pl WPS-4.2/arch/Config.pl ---- WPS-4.2.orig/arch/Config.pl 2020-04-23 21:31:06.000000000 +0200 -+++ WPS-4.2/arch/Config.pl 2021-04-14 13:11:31.470659452 +0200 -@@ -41,6 +41,7 @@ - if(substr( $ARGV[0], 1, 8 ) eq "netcdff=") - { - $sw_netcdff_lib = substr( $ARGV[0], 9); -+ $sw_netcdff_lib =~ s/!/ /g ; - } - if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") - { -diff -ru WPS-4.2.orig/arch/preamble WPS-4.2/arch/preamble ---- WPS-4.2.orig/arch/preamble 2020-04-23 21:31:06.000000000 +0200 -+++ WPS-4.2/arch/preamble 2021-04-14 13:11:31.470659452 +0200 -@@ -39,7 +39,7 @@ - -I$(WRF_DIR)/external/io_grib1 \ - -I$(WRF_DIR)/external/io_int \ - -I$(WRF_DIR)/inc \ -- -I$(NETCDF)/include -+ -I$(NETCDF)/include -I$(NETCDFF)/include - - WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ - -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ -diff -ru WPS-4.2.orig/configure WPS-4.2/configure ---- WPS-4.2.orig/configure 2020-04-23 21:31:06.000000000 +0200 -+++ WPS-4.2/configure 2021-04-14 13:11:31.470659452 +0200 -@@ -119,9 +119,14 @@ - echo "Will use NETCDF in dir: $NETCDF" - # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use - # if available -- NETCDFF=" " -- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then -- NETCDFF="-lnetcdff" -+ USENETCDFF=" " -+ # for netCDF 4.2 and greater, the Fortran library is a seperate install -+ if [ -z "$NETCDFF" ] -+ then -+ NETCDFF=$NETCDF -+ fi -+ if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then -+ USENETCDFF="-L$NETCDFF/lib!-lnetcdff" - fi - else - echo "Will configure for use without NetCDF" -@@ -190,7 +195,7 @@ - fi - - # Found perl, so proceed with configuration --perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$NETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir -+perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$USENETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir - - - #Checking cross-compiling capability for some particular environment -@@ -356,9 +361,9 @@ - end program - EOF - FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` -- cp $NETCDF/include/netcdf.inc . -+ cp $NETCDFF/include/netcdf.inc . - FC=`grep ^SFC configure.wps | cut -d"=" -f2-` -- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 -+ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -lnetcdf $USENETCDFF > /dev/null 2>&1 - if [ -f "fort_netcdf" ] ; then - ./fort_netcdf > /dev/null 2>&1 - if [ $? = 0 ]; then -diff -ru WPS-4.2.orig/util/src/Makefile WPS-4.2/util/src/Makefile ---- WPS-4.2.orig/util/src/Makefile 2020-04-23 21:31:06.000000000 +0200 -+++ WPS-4.2/util/src/Makefile 2021-04-14 13:11:31.470659452 +0200 -@@ -41,11 +41,11 @@ - write_met_module.o misc_definitions_module.o met_data_module.o - $(SFC) $(LDFLAGS) -o $@ elev_angle.o cio.o module_debug.o gridinfo_module.o \ - write_met_module.o misc_definitions_module.o met_data_module.o \ -- -L$(NETCDF)/lib -I$(NETCDF)/include -lnetcdf -+ -L$(NETCDFF)/lib -I$(NETCDFF)/include -lnetcdff - - elev_angle.o: elev_angle.F cio.o module_debug.o gridinfo_module.o \ - write_met_module.o misc_definitions_module.o -- $(SFC) -c elev_angle.F -I$(NETCDF)/include -+ $(SFC) -c elev_angle.F -I$(NETCDFF)/include - - calc_ecmwf_p.exe: calc_ecmwf_p.o cio.o module_debug.o module_stringutil.o gridinfo_module.o read_met_module.o \ - write_met_module.o module_date_pack.o misc_definitions_module.o met_data_module.o constants_module.o From ee4cbd87bf68d23102fa9ea381dc8ed304461e8d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 8 Nov 2021 16:20:30 +0200 Subject: [PATCH 1868/9987] review fixes --- .../easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb | 2 +- .../l/libjxl/libjxl-0.6.1_external_lcms2.patch | 3 +++ easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 9 ++++++++- .../z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb | 5 ++--- 4 files changed, 14 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb index 01e7faabd9f..7b980f3eae2 100644 --- a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.4-GCCcore-10.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ sanity_check_commands = ['lzf -h'] sanity_check_paths = { - 'files': ['bin/lzf'], + 'files': ['bin/lzf', 'lib/liblzf.a'], 'dirs': ['bin', 'lib'], } diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_external_lcms2.patch b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_external_lcms2.patch index d5a9ee728c9..7f1c93551a9 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_external_lcms2.patch +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_external_lcms2.patch @@ -1,3 +1,6 @@ +# Add external linking to lcms2 +# Author: micketeer@gmail.com +# updated: Denis Kristak diff -ruN libjxl-main_orig/lib/jxl.cmake libjxl-main/lib/jxl.cmake --- libjxl-main_orig/lib/jxl.cmake 2021-10-29 19:28:31.000000000 +0100 +++ libjxl-main/lib/jxl.cmake 2021-11-01 11:40:34.075502429 +0000 diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index efd4f455224..befa00aab27 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -23,10 +23,17 @@ builddependencies = [ ('binutils', '2.35'), ] +configopts = ' -DZFP_WITH_OPENMP ' + +buildopts = ' && make test ' + files_to_copy = ['bin', 'lib', 'include'] +sanity_check_commands = ['zfp --version'] +sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] + sanity_check_paths = { - 'files': [], + 'files': ['bin/zfp', 'bin/testzfp', 'lib/libzfp.a'], 'dirs': ['bin', 'include', 'lib'], } diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb index ebe8e39426d..061cbd11043 100644 --- a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb @@ -19,11 +19,10 @@ builddependencies = [ ('binutils', '2.35'), ] -sanity_check_commands = [ -] +configopts = ' -DZLIB_ENABLE_TESTS=True ' sanity_check_paths = { - 'files': [], + 'files': ['lib/libz-ng.%s' % SHLIB_EXT, 'include/zlib-ng.h', 'include/zconf-ng.h'], 'dirs': ['lib/', 'include/'], } From 52f5403eb496f95bcd9178b6465c4ad44a3a83b8 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 14:22:47 +0000 Subject: [PATCH 1869/9987] adding easyconfigs: Kent_tools-422-GCC-11.2.0.eb --- .../k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb new file mode 100644 index 00000000000..87be8192331 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'Kent_tools' +version = '422' + +homepage = 'https://genome.cse.ucsc.edu/' +description = """Kent utilities: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +source_urls = [ + 'https://hgdownload.cse.ucsc.edu/admin/exe/', + 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', +] +sources = ['userApps.v%(version)s.src.tgz'] +checksums = ['43691dc14dc50bc597d6ac38f252e766ea561c3086eb0f219406d050fe2b79be'] + +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + +dependencies = [ + ('MariaDB', '10.6.4'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('util-linux', '2.37'), + ('OpenSSL', '1.1', '', True), +] + +buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'bio' From 741135ec4ab2186e2c2eecb3f0e20b61d2707d08 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 8 Nov 2021 17:18:11 +0200 Subject: [PATCH 1870/9987] review fixes --- easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index befa00aab27..73d372020a4 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -29,7 +29,6 @@ buildopts = ' && make test ' files_to_copy = ['bin', 'lib', 'include'] -sanity_check_commands = ['zfp --version'] sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] sanity_check_paths = { From 9ec53b5f8b94f4effbda639459b2d6793ca5e001 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 8 Nov 2021 17:49:05 +0200 Subject: [PATCH 1871/9987] review fixes --- easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index f1a925dd52e..2b161ae7055 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -28,7 +28,7 @@ patches = [ checksums = [ 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz - 'a430237fdef24c07f2187e079dad3041f124d5dc00ec713dba4eb308d78712f6', # libjxl-0.6.1_external_lcms2.patch + '1948d2527c658637939327eec093301539b164714f5bf146ed2e0dcadffadf00', # libjxl-0.6.1_external_lcms2.patch '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch ] From 6301a5fb2b85da77095f8acc2522934bf0f94a49 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 22:52:56 +0000 Subject: [PATCH 1872/9987] adding easyconfigs: git-2.33.1-GCCcore-11.2.0-nodocs.eb --- .../g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb diff --git a/easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb new file mode 100644 index 00000000000..ed7c62fbd3b --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb @@ -0,0 +1,47 @@ +## +# Author: Robert Mijakovic +## +# updated to 2.33.1 +# J. Sassmannshausen / GSTT + +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.33.1' +versionsuffix = '-nodocs' + +homepage = 'https://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fa459f95153a2c51af149c062f614018c027caf75a8dd92b3f64defe0a78f42f'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('cURL', '7.78.0'), + ('expat', '2.4.1'), + ('gettext', '0.21'), + ('Perl', '5.34.0'), + ('OpenSSL', '1.1', '', True), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['libexec/git-core', 'share'], +} + +moduleclass = 'tools' From 584d381bfd622080bc9cb662c98503aa7563901f Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 22:54:11 +0000 Subject: [PATCH 1873/9987] adding easyconfigs: GitPython-3.1.24-GCCcore-11.2.0.eb --- .../GitPython-3.1.24-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-3.1.24-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.24-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.24-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..32c24dc4bb7 --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.24-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.24' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('git', '2.33.1', '-nodocs'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('smmap', '5.0.0', { + 'checksums': ['c840e62059cd3be204b0c9c9f74be2c09d5648eddd4580d9314c3ecde0b30936'], + }), + ('gitdb', '4.0.9', { + 'checksums': ['bac2fd45c0a1c9cf619e63a90d62bdc63892ef92387424b855792a6cabe789aa'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['df83fdf5e684fef7c6ee2c02fc68a5ceb7e7e759d08b694088d0cacb4eba59e5'], + }), +] + +moduleclass = 'lib' From da4b1e4ac798228adde42989cbac33ed4e56899a Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 22:59:56 +0000 Subject: [PATCH 1874/9987] adding easyconfigs: MAFFT-7.490-gompi-2021b-with-extensions.eb --- ...MAFFT-7.490-gompi-2021b-with-extensions.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-gompi-2021b-with-extensions.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-gompi-2021b-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-gompi-2021b-with-extensions.eb new file mode 100644 index 00000000000..f55e168ddd9 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-gompi-2021b-with-extensions.eb @@ -0,0 +1,52 @@ +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.490' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], + 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'checksums': ['d6eef33d8b9e282e20f9b25b6b6fb2757b9b6900e397ca621d56da86d9976541'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + }), + ('%s MPI' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/MPI', + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft'] + ['libexec/mafft/%s' % x for x in [ + 'mxscarnamod', # installed by MAFFT Extensions + 'mpiscript', 'nodepair_mpi', # installed by MAFFT MPI + ]], + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +modextravars = {'MAFFT_N_THREADS_PER_PROCESS': '1'} +# MAFFT MPI requires other environment variables that depend on job resources +# More information at at https://mafft.cbrc.jp/alignment/software/mpi.html + +moduleclass = 'bio' From 4b3df934bfb6e142838263ee28a253ef53eb36a6 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 23:04:29 +0000 Subject: [PATCH 1875/9987] adding easyconfigs: tbb-2020.3-GCCcore-11.2.0.eb --- .../t/tbb/tbb-2020.3-GCCcore-11.2.0.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..61f78dd0c29 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-11.2.0.eb @@ -0,0 +1,19 @@ +name = 'tbb' +version = '2020.3' + +homepage = 'https://github.com/oneapi-src/oneTBB' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ebc4f6aa47972daed1f7bf71d100ae5bf6931c2e3144cf299c8cc7d041dca2f3'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +moduleclass = 'lib' From 4764cf72c0e5281d474ebef93ad7150c7e1e7f2a Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 23:06:15 +0000 Subject: [PATCH 1876/9987] adding easyconfigs: UShER-0.5.0-gompi-2021b.eb and patches: UShER-0.5.0_external-tbb.patch --- .../u/UShER/UShER-0.5.0-gompi-2021b.eb | 40 +++++++++++++++++++ .../u/UShER/UShER-0.5.0_external-tbb.patch | 18 +++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/u/UShER/UShER-0.5.0-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/u/UShER/UShER-0.5.0_external-tbb.patch diff --git a/easybuild/easyconfigs/u/UShER/UShER-0.5.0-gompi-2021b.eb b/easybuild/easyconfigs/u/UShER/UShER-0.5.0-gompi-2021b.eb new file mode 100644 index 00000000000..0e0e02ad29e --- /dev/null +++ b/easybuild/easyconfigs/u/UShER/UShER-0.5.0-gompi-2021b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'UShER' +version = '0.5.0' + +homepage = 'https://github.com/yatisht/usher' +description = """UShER is now a package consisting of a family of programs for +rapid phylogenetic analyses, particularly suitable for the SARS-CoV-2 genomes.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +github_account = 'yatisht' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['UShER-%(version)s_external-tbb.patch'] +checksums = [ + '0477859e9bca2db4eb5a150fbff16d80a534364134e9f75bdbb11b4e3a3378fe', # v0.5.0.tar.gz + '91754d8b8d12c235d961d8563d2fe7cbe3a9d6476aebea6f4289ead411920cbd', # UShER-0.5.0_external-tbb.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] +dependencies = [ + ('tbb', '2020.3'), + ('protobuf', '3.17.3'), + ('MAFFT', '7.490', '-with-extensions'), + ('Boost', '1.77.0'), + ('Python', '3.9.6'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['usher', 'ripples', 'matOptimize', 'matUtils']], + 'dirs': [], +} + +sanity_check_commands = ['usher -h', 'ripples -h', 'matOptimize -h', 'matUtils -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/UShER/UShER-0.5.0_external-tbb.patch b/easybuild/easyconfigs/u/UShER/UShER-0.5.0_external-tbb.patch new file mode 100644 index 00000000000..ce947bd0edb --- /dev/null +++ b/easybuild/easyconfigs/u/UShER/UShER-0.5.0_external-tbb.patch @@ -0,0 +1,18 @@ +Remove internal build of TBB. Use standard tbb instead of tbb_preview. +Original Author: micketeer@gmail.com + +diff --git a/usher-0.5.0.orig/CMakeLists.txt b/usher-0.5.0/CMakeLists.txt +index 66a9032..4ce3949 100644 +--- a/usher-0.5.0.orig/CMakeLists.txt ++++ b/usher-0.5.0/CMakeLists.txt +@@ -38,9 +38,7 @@ find_package(MPI REQUIRED) + include_directories(SYSTEM ${MPI_INCLUDE_PATH}) + include_directories(${Protobuf_INCLUDE_DIRS}) + +-include(${TBB_DIR}/cmake/TBBBuild.cmake) +-tbb_build(TBB_ROOT ${TBB_DIR} CONFIG_DIR TBB_DIR MAKE_ARGS tbb_cpf=1) +-find_package(TBB REQUIRED tbbmalloc tbbmalloc_proxy tbb_preview) ++find_package(TBB REQUIRED tbbmalloc tbbmalloc_proxy tbb) + + FIND_PACKAGE(Boost COMPONENTS program_options iostreams filesystem date_time REQUIRED) + From 5e7b1e4eb3a4d392dbf60dab55c7ff28683a4f04 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 23:14:28 +0000 Subject: [PATCH 1877/9987] adding easyconfigs: snakemake-6.10.0-foss-2021b.eb --- .../snakemake/snakemake-6.10.0-foss-2021b.eb | 75 +++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-6.10.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-6.10.0-foss-2021b.eb b/easybuild/easyconfigs/s/snakemake/snakemake-6.10.0-foss-2021b.eb new file mode 100644 index 00000000000..92c8fcd8df4 --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-6.10.0-foss-2021b.eb @@ -0,0 +1,75 @@ +easyblock = 'PythonBundle' + +name = 'snakemake' +version = '6.10.0' + +homepage = 'https://snakemake.readthedocs.io' +description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('PyYAML', '5.4.1'), + ('GitPython', '3.1.24'), + ('IPython', '7.26.0'), +] + +use_pip = True +sanity_pip_check = True + +# snakemake-6.6.1_fix_jobs.patch is needed for clusters that do not support copying the full env into the batch job +exts_list = [ + ('wrapt', '1.13.3', { + 'checksums': ['1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185'], + }), + ('ratelimiter', '1.2.0.post0', { + 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], + }), + ('ConfigArgParse', '1.5.3', { + 'checksums': ['1b0b3cbf664ab59dada57123c81eff3d9737e0d11d8cf79e3d6eb10823f1739f'], + }), + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('toposort', '1.7', { + 'checksums': ['ddc2182c42912a440511bd7ff5d3e6a1cabc3accbc674a3258c8c41cbfbb2125'], + }), + ('amply', '0.1.4', { + 'checksums': ['cb12dcb49d16b168c02be128a1527ecde50211e4bd94af76ff4e67707f5a2d38'], + }), + ('PuLP', '2.5.1', { + 'checksums': ['27c2a87a98ea0e9a08c7c46e6df47d6d4e753ad9991fea2901892425d89c99a6'], + }), + ('smart_open', '5.2.1', { + 'checksums': ['75abf758717a92a8f53aa96953f0c245c8cedf8e1e4184903db3659b419d4c17'], + }), + ('connection_pool', '0.0.3', { + 'checksums': ['bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc'], + }), + ('stopit', '1.1.2', { + 'checksums': ['f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d'], + }), + (name, version, { + # 'patches': ['snakemake-%(version)s_fix_jobs.patch'], + 'checksums': [ + '199a86c8d1fcfdb88c4271a1507b0ab371a15bc407f2dad9b0ab8c43438adff8', # snakemake-6.10.0.tar.gz + # '916875eaf4869c65b93098e362b8676cf55c6e37067a54b191f34b13e06c37e3', # snakemake-6.6.1_fix_jobs.patch + ], + }), +] + +# SNAKEMAKE_LOAD_MODULE is needed for snakemake-6.6.1_fix_jobs.patch to work +# local_snakemake_load is the command for loading this module (here: default EB module naming scheme) +# local_snakemake_load = 'module load %(module_name)s' +# modextravars = {'SNAKEMAKE_LOAD_MODULE': local_snakemake_load} + +sanity_check_paths = { + 'files': ['bin/snakemake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], +} + +sanity_check_commands = ['snakemake --help'] + +moduleclass = 'tools' From 93745dcb765fb9035925a3d2d725ab609c4ec158 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 23:17:32 +0000 Subject: [PATCH 1878/9987] adding easyconfigs: scikit-learn-1.0.1-foss-2021b.eb --- .../scikit-learn-1.0.1-foss-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb new file mode 100644 index 00000000000..98d8ed31026 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '1.0.1' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ac2ca9dbb754d61cfe1c83ba8483498ef951d29b93ec09d6f002847f210a99da'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'sklearn'} + +moduleclass = 'data' From 028cf7fdc6686fcd7a4f60d3bed658deab12744f Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 23:19:03 +0000 Subject: [PATCH 1879/9987] adding easyconfigs: Biopython-1.79-foss-2021b.eb --- .../b/Biopython/Biopython-1.79-foss-2021b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021b.eb new file mode 100644 index 00000000000..e117393bdd0 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.79' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['edb07eac99d3b8abd7ba56ff4bedec9263f76dfc3c3f450e7d2e2bcdecf8559b'] + +dependencies = [ + ('Python', '3.9.6', '-bare'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From e20dac5f6455b11117d0c0718576cef271375869 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 23:21:56 +0000 Subject: [PATCH 1880/9987] adding easyconfigs: Pysam-0.17.0-GCC-11.2.0.eb --- .../p/Pysam/Pysam-0.17.0-GCC-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.17.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.17.0-GCC-11.2.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.17.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..a73df684da9 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.17.0-GCC-11.2.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Erich Birngruber +# Gregor Mendel Institute +# updated to 0.1.0. +# J. Sassmannshausen / GSTT +# +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.17.0' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f4d697e322d12f239c96c263374bad2b40fd95bff34841ab9515e3de9e3e7cca'] + +dependencies = [ + ('Python', '3.9.6'), + ('ncurses', '6.2'), + ('cURL', '7.78.0'), + ('XZ', '5.2.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' From 290d69d9f8ccff7c47b963f6dc3570760c642577 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 8 Nov 2021 23:25:32 +0000 Subject: [PATCH 1881/9987] adding easyconfigs: pangolin-3.1.16-foss-2021b.eb --- .../p/pangolin/pangolin-3.1.16-foss-2021b.eb | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b.eb new file mode 100644 index 00000000000..4625f27bff9 --- /dev/null +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b.eb @@ -0,0 +1,81 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on a EC provided by Paul Jähne +# uploaded by J. Sassmannshausen + +easyblock = 'PythonBundle' + +name = 'pangolin' +version = '3.1.16' + +homepage = 'https://cov-lineages.org/pangolin.html' +description = """Software package for assigning SARS-CoV-2 genome sequences to global lineages. +This module also contains the faToVcf tool""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Biopython', '1.79'), + ('gofasta', '0.0.5', '', True), + ('minimap2', '2.22'), + ('Pysam', '0.17.0'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('snakemake', '6.10.0'), + ('UShER', '0.5.0'), + ('scikit-learn', '1.0.1'), + ('Kent_tools', '422'), +] + +use_pip = True +sanity_pip_check = True + +github_account = 'cov-lineages' +exts_default_options = { + 'source_urls': [GITHUB_SOURCE], + 'sources': [{ + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], +} + +exts_list = [ + (name, version, { + 'checksums': ['f247caf5ee4252a3edbbf9e60f23374438aaad1879d8dfbf6fb7a64bde8bf3fc'], + }), + ('pangoLEARN', '2021-10-18', { + 'modulename': 'pangoLEARN', + 'sources': [{ + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], + 'checksums': ['5a0a5e00d92c769686b98947fe40e6a89a366beedd086babe6873f2c1b62947d'], + }), + ('scorpio', '0.3.14', { + 'checksums': ['31108c9e8399691b3167b14689fbedebd7a410b0879c362a12d807cb077ac57a'], + }), + ('constellations', '0.0.21', { + 'checksums': ['83c3d61e83b81b59b03d7da176a50c6beac05efdb080978856c9eeb32cd05eca'], + }), + ('pango-designation', '1.2.93', { + 'checksums': ['9fd2159d8681e1674e9c812693ef391fb389cf4f7e74c467ba7882e7cb2d6bce'], + }), +] + +local_binaries = [ + 'constellations', 'extract_definitions.py', 'pango_designation', 'pangoLEARN', + 'pangolearn.smk', 'pangolin', 'scorpio', 'type_constellations.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'pangolin -v', + 'pangolin -pv', + 'scorpio -v', +] + +moduleclass = 'bio' From 6442c5808e2fd60694cf7164c4100119dec7a84b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 10:39:41 +0100 Subject: [PATCH 1882/9987] cleanup in libavif easyconfig --- .../easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb index d92567651e8..6e46d36eea4 100644 --- a/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/l/libavif/libavif-0.9.0-foss-2020b.eb @@ -27,14 +27,9 @@ dependencies = [ ('Rust', '1.52.1'), ] -# TODO FIX THIS - NEED THOSE -# configopts = ' -DAVIF_CODEC_AOM=ON -DAVIF_CODEC_DAV1D=ON -DAVIF_CODEC_LIBGAV1=ON -DAVIF_CODEC_RAV1E=ON ' sanity_check_paths = { 'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'], - 'dirs': ['lib/', 'include/avif/'] + 'dirs': [], } -sanity_check_commands = [ -] - moduleclass = 'tools' From c08d7e1304ba7d4ab279aac0764aa4df1788741b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 10:46:51 +0100 Subject: [PATCH 1883/9987] refine sanity check for jxl 0.6.1 --- .../easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index 2b161ae7055..5f5052289c6 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -60,7 +60,12 @@ runtest = "test" sanity_check_paths = { 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], - 'dirs': ['include'], + 'dirs': ['include/jxl'], } +sanity_check_commands = [ + "cjxl --help", + "djxl --help", +] + moduleclass = 'lib' From f4d770c615a27af1d644a4222aca036308e38097 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 10:48:33 +0100 Subject: [PATCH 1884/9987] preserve description in patch for libjxl 0.6.1 --- easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/l/libjxl/libjxl-0.6.1_remove-broken-test.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb index 5f5052289c6..4bd51b12d10 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1-GCCcore-10.2.0.eb @@ -29,7 +29,7 @@ checksums = [ 'ccbd5a729d730152303be399f033b905e608309d5802d77a61a95faa092592c5', # v0.6.1.tar.gz 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz '1948d2527c658637939327eec093301539b164714f5bf146ed2e0dcadffadf00', # libjxl-0.6.1_external_lcms2.patch - '0e8874af33bb55061a4ba8994a817348496f7187a6d9fd341c730fb28cec54ed', # libjxl-0.6.1_remove-broken-test.patch + '11b7cf639049afd9acd1c362287a743cdbe1a6f55e6f9d42b6eaa75ac6a0e6da', # libjxl-0.6.1_remove-broken-test.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_remove-broken-test.patch b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_remove-broken-test.patch index af8c7b0bfe5..6d8cc1044dc 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_remove-broken-test.patch +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.6.1_remove-broken-test.patch @@ -1,3 +1,5 @@ +remove broken test, see also https://github.com/libjxl/libjxl/issues/500 +author: Kenneth Hoste (HPC-UGent) diff -ruN libjxl-0.6.1_orig/lib/jxl/decode_test.cc libjxl-0.6.1/lib/jxl/decode_test.cc --- libjxl-0.6.1_orig/lib/jxl/decode_test.cc 2021-11-01 14:01:50.188357223 +0000 +++ libjxl-0.6.1/lib/jxl/decode_test.cc 2021-11-01 14:02:05.128147260 +0000 From 3e0e8d571809ec59586ade875e9f1c64a801e4c8 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 9 Nov 2021 10:04:40 +0000 Subject: [PATCH 1885/9987] Sanity checks added --- easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb index 62f2b671372..55513948cde 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb @@ -47,6 +47,8 @@ configopts += "-DWITH_ZLIB=system " configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc +sanity_check_commands = ["mysql --help", "mysqltest --help"] + sanity_check_paths = { 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, From c93757b2a1d7f70b730912a7ef513ceff2153ff3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 11:04:49 +0100 Subject: [PATCH 1886/9987] add sanity check command for Zopfli --- .../z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb index ee2b65fa1c4..d65bafa85ec 100644 --- a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.2.0.eb @@ -20,10 +20,17 @@ builddependencies = [ ('CMake', '3.18.4'), ('binutils', '2.35'), ] -configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF', +] + sanity_check_paths = { - 'files': ['bin/zopfli', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT, 'include/zopfli.h'], + 'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT], 'dirs': [], } +sanity_check_commands = ["zopfli --help"] + moduleclass = 'tools' From 55f47ec1a119744fb6d7975ccf3327f4ad328b57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 11:07:41 +0100 Subject: [PATCH 1887/9987] minor tweak to sanity check paths for zfp --- easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index 73d372020a4..16947a10f4c 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -29,11 +29,11 @@ buildopts = ' && make test ' files_to_copy = ['bin', 'lib', 'include'] -sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] - sanity_check_paths = { - 'files': ['bin/zfp', 'bin/testzfp', 'lib/libzfp.a'], - 'dirs': ['bin', 'include', 'lib'], + 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], + 'dirs': ['include/zfp'], } +sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] + moduleclass = 'lib' From c76cb2543082ba76032d9ad359830ab5f801547f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 11:10:16 +0100 Subject: [PATCH 1888/9987] also check for static zlib-ng library --- .../easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb index 061cbd11043..bf962cbf1d4 100644 --- a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.5-GCCcore-10.2.0.eb @@ -22,8 +22,8 @@ builddependencies = [ configopts = ' -DZLIB_ENABLE_TESTS=True ' sanity_check_paths = { - 'files': ['lib/libz-ng.%s' % SHLIB_EXT, 'include/zlib-ng.h', 'include/zconf-ng.h'], - 'dirs': ['lib/', 'include/'], + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], } moduleclass = 'tools' From e5229959ea8e6551bd3696f3ea1f3d216fffe5da Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 9 Nov 2021 11:06:20 +0000 Subject: [PATCH 1889/9987] Changed from bare to full Python --- easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021b.eb index e117393bdd0..bca044875eb 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021b.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2021b.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['edb07eac99d3b8abd7ba56ff4bedec9263f76dfc3c3f450e7d2e2bcdecf8559b'] dependencies = [ - ('Python', '3.9.6', '-bare'), + ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), ] From cc195cab0870c07a750b4ee94c4a465433f644c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 12:52:43 +0100 Subject: [PATCH 1890/9987] use compiler options controlled by EasyBuild for building zfp --- easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb index 16947a10f4c..860d74ceb29 100644 --- a/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zfp/zfp-0.5.5-GCCcore-10.2.0.eb @@ -19,15 +19,15 @@ sources = ['%(version)s.tar.gz'] checksums = ['6a7f4934489087d9c117a4af327fd6495ea757924f4df467b9c537abf8bd86c4'] builddependencies = [ - ('CMake', '3.18.4'), ('binutils', '2.35'), ] -configopts = ' -DZFP_WITH_OPENMP ' +prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && " +buildopts = 'ZFP_WITH_OPENMP=1' -buildopts = ' && make test ' +runtest = 'test' -files_to_copy = ['bin', 'lib', 'include'] +files_to_copy = ['bin', 'include', 'lib'] sanity_check_paths = { 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], From a9abb9966b00abfd37959055d3951458614be0ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 15:12:25 +0100 Subject: [PATCH 1891/9987] fix name/version for imagecodecs dependencies: libjxl and Zopfli --- .../i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index 8440baa6492..26470172bd8 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -36,7 +36,7 @@ dependencies = [ ('libavif', '0.9.0'), ('libdeflate', '1.7'), ('libjpeg-turbo', '2.0.5'), - ('libjxl', '0.5'), + ('libjxl', '0.6.1'), ('LibLZF', '3.4'), ('libpng', '1.6.37'), ('XZ', '5.2.5'), @@ -48,7 +48,7 @@ dependencies = [ ('snappy', '1.1.8'), ('zlib', '1.2.11'), ('zlib-ng', '2.0.5'), - ('zopfli', '1.0.3'), + ('Zopfli', '1.0.3'), ('zfp', '0.5.5'), ('zstd', '1.4.5'), ('Brunsli', '0.1'), From ea5f0a5dce39e856e4f676a8d0521d96974d4503 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Nov 2021 15:54:10 +0100 Subject: [PATCH 1892/9987] adding easyconfigs: VTune-2021.9.0.eb --- .../easyconfigs/v/VTune/VTune-2021.9.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb new file mode 100644 index 00000000000..cd2356a18bb --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2021.9.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +name = 'VTune' +version = '2021.9.0' + +homepage = 'https://software.intel.com/en-us/vtune' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18302/'] +sources = ['l_oneapi_vtune_p_%(version)s.545_offline.sh'] +checksums = ['55c8ac25e685f03c849bb5383da249c7caaf2138a2b57a10c8975a38fa3828bc'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'tools' From 4d9b6eb71245cc284175f306082426905edcdaae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 16:08:41 +0100 Subject: [PATCH 1893/9987] avoid need for patch in Brunsli easyconfig --- .../b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 25 ++++---- .../b/Brunsli/Brunsli-0.1_wrong_paths.patch | 64 ------------------- 2 files changed, 13 insertions(+), 76 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1_wrong_paths.patch diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index caadf4deda0..f90442fc544 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -12,11 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/google/brunsli/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['Brunsli-0.1_wrong_paths.patch'] -checksums = [ - '62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc', # v0.1.tar.gz - '34795a1adba1ec208033922eaf27b3b3a23535a2e09201f93f9098666dd7319d', # Brunsli-0.1_wrong_paths.patch -] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] builddependencies = [ ('CMake', '3.18.4'), @@ -28,19 +24,24 @@ dependencies = [ ('Highway', '0.12.2'), ] -configopts = ' -DCMAKE_BUILD_TYPE=Release ' -configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon "' +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" +# also install dbrunsli binary and missing libraries postinstallcmds = [ - 'mkdir %(installdir)s/bin ', - 'cp dbrunsli %(installdir)s/bin ', - 'cp *.a %(installdir)s/lib64 ', - 'cp *.so %(installdir)s/lib64 ', + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib*/", + "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, ] sanity_check_paths = { 'files': ['bin/dbrunsli'], - 'dirs': ['bin'], + 'dirs': ['include/brunsli', 'lib'], } sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1_wrong_paths.patch b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1_wrong_paths.patch deleted file mode 100644 index ef00a795e09..00000000000 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1_wrong_paths.patch +++ /dev/null @@ -1,64 +0,0 @@ -diff -ruN brunsli-0.1_orig/c/dec/brunsli_decode.cc brunsli-0.1/c/dec/brunsli_decode.cc ---- brunsli-0.1_orig/c/dec/brunsli_decode.cc 2021-09-29 15:46:08.292937193 +0100 -+++ brunsli-0.1/c/dec/brunsli_decode.cc 2021-09-30 12:27:04.564828827 +0100 -@@ -13,7 +13,7 @@ - #include - #include - --#include -+#include "/scratch/gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/Brotli/1.0.9-GCCcore-10.2.0/include/brotli/decode.h" - #include "../common/constants.h" - #include "../common/context.h" - #include "../common/lehmer_code.h" -diff -ruN brunsli-0.1_orig/Makefile brunsli-0.1/Makefile ---- brunsli-0.1_orig/Makefile 2021-09-29 15:46:08.292937193 +0100 -+++ brunsli-0.1/Makefile 2021-09-29 15:47:40.451603687 +0100 -@@ -1,8 +1,8 @@ - OS := $(shell uname) - BINDIR = bin - OBJDIR = $(BINDIR)/obj --BROTLI_DIR = third_party/brotli --BROTLI_INCLUDE = $(BROTLI_DIR)/c/include -+BROTLI_DIR = $EBROOTBROTLI -+BROTLI_INCLUDE = $(BROTLI_DIR)/include - BRUNSLI_INCLUDE = c/include - SOURCES = $(wildcard c/common/*.cc) $(wildcard c/dec/*.cc) \ - $(wildcard c/enc/*.cc) -diff -ruN brunsli-0.1_orig/third_party/CMakeLists.txt brunsli-0.1/third_party/CMakeLists.txt ---- brunsli-0.1_orig/third_party/CMakeLists.txt 2021-09-29 15:46:08.300937078 +0100 -+++ brunsli-0.1/third_party/CMakeLists.txt 2021-09-29 15:48:26.650928556 +0100 -@@ -5,13 +5,13 @@ - # https://opensource.org/licenses/MIT. - - # brotli --if (NOT TARGET brotlicommon-static) -- if (NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/brotli/c/include/brotli/decode.h") -- message(SEND_ERROR "Brotli is required to build brunsli, run \"git submodule update --init\" to get it, then run cmake again") -- endif () -- add_subdirectory(brotli EXCLUDE_FROM_ALL) --endif () -+# if (NOT TARGET brotlicommon-static) -+# if (NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/brotli/c/include/brotli/decode.h") -+# message(SEND_ERROR "Brotli is required to build brunsli, run \"git submodule update --init\" to get it, then run cmake again") -+# endif () -+# add_subdirectory(brotli EXCLUDE_FROM_ALL) -+# endif () - --if (NOT TARGET gtest_main) -- add_subdirectory(googletest EXCLUDE_FROM_ALL) --endif () -+# if (NOT TARGET gtest_main) -+# add_subdirectory(googletest EXCLUDE_FROM_ALL) -+# endif () -diff -ruN brunsli-0.1_orig/WORKSPACE brunsli-0.1/WORKSPACE ---- brunsli-0.1_orig/WORKSPACE 2021-09-29 15:46:08.292937193 +0100 -+++ brunsli-0.1/WORKSPACE 2021-09-30 12:23:24.610917528 +0100 -@@ -7,7 +7,7 @@ - - local_repository( - name = "brotli", -- path = "third_party/brotli", -+ path = "/scratch/gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/Brotli/1.0.9-GCCcore-10.2.0/", - ) - - new_local_repository( From 239152632d977bab28a1546648dddbddc7a85310 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 16:09:47 +0100 Subject: [PATCH 1894/9987] remove duplicate libpng dependency in imagecodecs easyconfig --- .../i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index 26470172bd8..129dc5ac160 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -40,7 +40,6 @@ dependencies = [ ('LibLZF', '3.4'), ('libpng', '1.6.37'), ('XZ', '5.2.5'), - ('libpng', '1.6.37'), ('LibTIFF', '4.1.0'), ('libwebp', '1.1.0'), ('lz4', '1.9.2'), From b873deed6fda2e90cf022e3fdc6866f8988f9ff1 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Nov 2021 16:44:16 +0100 Subject: [PATCH 1895/9987] adding easyconfigs: Advisor-2021.4.0.eb --- .../easyconfigs/a/Advisor/Advisor-2021.4.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb new file mode 100644 index 00000000000..55354cc6e25 --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2021.4.0.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'Advisor' +version = '2021.4.0' + +homepage = 'https://software.intel.com/intel-advisor-xe' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18220/'] +sources = ['l_oneapi_advisor_p_%(version)s.389_offline.sh'] +checksums = ['dd948f7312629d9975e12a57664f736b8e011de948771b4c05ad444438532be8'] + +dontcreateinstalldir = True + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/advisor'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'perf' From c346644420c77a0992d5cdcaefc2cdc379b0beb5 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Nov 2021 17:43:24 +0100 Subject: [PATCH 1896/9987] adding easyconfigs: MCR-R2021b.eb --- easybuild/easyconfigs/m/MCR/MCR-R2021b.eb | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2021b.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2021b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2021b.eb new file mode 100644 index 00000000000..ab97e3fddd9 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2021b.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'MCR' +version = 'R2021b' # runtime version 9.10 +local_update = '0' +#versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%(version)s_glnxa64.zip'] +checksums = ['d7067b4f4977350395fd75de1aeefc9de39010fbdcf32d99a5f2e8955e74121e'] + +moduleclass = 'math' From 9731ea0d1c5427fca50d1566381f099ba1b31e7f Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Nov 2021 18:05:29 +0100 Subject: [PATCH 1897/9987] adding easyconfigs: NVHPC-21.9.eb --- easybuild/easyconfigs/n/NVHPC/NVHPC-21.9.eb | 75 +++++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-21.9.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.9.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.9.eb new file mode 100644 index 00000000000..2ff2d565c04 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.9.eb @@ -0,0 +1,75 @@ +## +# Author: Robert Mijakovic +## +name = 'NVHPC' +version = '21.9' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +local_tarball_tmpl = 'nvhpc_2021_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + '7995bf20a2f24cad6703b7801e32f0768a59ed6413a5c9c9795ab87e4c1e40fe', + local_tarball_tmpl % 'ppc64le': + '72f98a5d4b50e2d94d3a7a90a988d441f768e22845058daf5a8868eed1699441', + local_tarball_tmpl % 'x86_64': + '7de6a6880fd7e59afe0dee51f1fae4d3bff1ca0fb8ee234b24e1f2fdff23ffc9', + } +] + +local_gccver = '11.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.37', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.14', '', ('GCCcore', local_gccver)) +] + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/21.7/cuda/) +# for NVHPC 21.7, those are: 11.4, 11.0, 10.2; +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '11.4' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.4.1')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From da2f7a3892f94625b90fb4d6bb3736235b0a837d Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 9 Nov 2021 18:14:57 +0100 Subject: [PATCH 1898/9987] Removes forgotten comment. --- easybuild/easyconfigs/m/MCR/MCR-R2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2021b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2021b.eb index ab97e3fddd9..ac18133d042 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2021b.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2021b.eb @@ -4,7 +4,6 @@ name = 'MCR' version = 'R2021b' # runtime version 9.10 local_update = '0' -#versionsuffix = '.%s' % local_update homepage = 'https://www.mathworks.com/products/compiler/mcr/' description = """The MATLAB Runtime is a standalone set of shared libraries From 23c6eab936cbcfd0f4e1625269c259efe50889ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 19:59:08 +0100 Subject: [PATCH 1899/9987] extend/clean up sanity check for libaec --- .../l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb index b29e2d04011..d5fc64c0361 100644 --- a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.2.0.eb @@ -23,12 +23,10 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['bin/aec', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], - 'dirs': ['bin/', 'lib/', 'include/'] + 'files': ['bin/aec', 'include/libaec.h', 'include/szlib.h', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['share/man'], } -sanity_check_commands = [ - 'aec --help', -] +sanity_check_commands = ["aec --help"] -moduleclass = 'tools' +moduleclass = 'lib' From 8f3f1cdd3245bd266a49b8b832a6d6c4cf76675c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:09:39 +0100 Subject: [PATCH 1900/9987] cleanup in imagecodecs easyconfig + make sure that openjpeg.h is found --- .../imagecodecs-2021.8.26-foss-2020b.eb | 36 ++++++++----------- ...-2020b.eb => jxrlib-1.1-GCCcore-10.2.0.eb} | 0 ...ort_cmake.patch => jxrlib-1.1_cmake.patch} | 0 3 files changed, 14 insertions(+), 22 deletions(-) rename easybuild/easyconfigs/j/jxrlib/{jxrlib-1.1-foss-2020b.eb => jxrlib-1.1-GCCcore-10.2.0.eb} (100%) rename easybuild/easyconfigs/j/jxrlib/{jxrlib-1.1-foss-2020b_support_cmake.patch => jxrlib-1.1_cmake.patch} (100%) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb index 129dc5ac160..acd6766b2c3 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2021.8.26-foss-2020b.eb @@ -5,23 +5,18 @@ easyblock = 'PythonBundle' name = 'imagecodecs' version = '2021.8.26' -homepage = 'https://www.lfd.uci.edu/~gohlke/' -description = """ -Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, +homepage = 'https://github.com/cgohlke/imagecodecs' +description = """Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, compression, and decompression functions for use in the tifffile, czifile, zarr, and other -scientific image input/output modules. -""" +scientific image input/output modules.""" toolchain = {'name': 'foss', 'version': '2020b'} -# changing src line endings -local_extract_cmd = ' tar -xvf %s ' -local_extract_cmd += ' && find . -type f -print0 | xargs -0 dos2unix ' - +local_openjpeg_maj_min = '2.4' dependencies = [ ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # required for numpy ('matplotlib', '3.3.3'), - ('SciPy-bundle', '2020.11'), ('Brotli', '1.0.9'), ('bzip2', '1.0.8'), ('Blosc', '1.21.0'), @@ -43,7 +38,7 @@ dependencies = [ ('LibTIFF', '4.1.0'), ('libwebp', '1.1.0'), ('lz4', '1.9.2'), - ('OpenJPEG', '2.4.0'), + ('OpenJPEG', local_openjpeg_maj_min + '.0'), ('snappy', '1.1.8'), ('zlib', '1.2.11'), ('zlib-ng', '2.0.5'), @@ -55,25 +50,22 @@ dependencies = [ ('h5py', '3.1.0'), ] -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'use_pip': True, - 'download_dep_fail': True, - 'sanity_pip_check': True -} +use_pip = True +sanity_pip_check = True exts_list = [ ('bitshuffle', '0.3.5', { - 'source_tmpl': '%(version)s.tar.gz', + 'sources': ['%(version)s.tar.gz'], 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'], 'checksums': ['c3f4461d8013e3d9db0d58defec77b143164652de505a1fba3df088eaa19be2f'], }), (name, version, { - 'extract_cmd': " tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix ", - 'filename': '%(name)s-%(version)s.tar.gz', - 'source_urls': 'https://pypi.python.org/packages/source/%(nameletter)s/%(name)s', + 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", + 'sources': ['%(name)s-%(version)s.tar.gz'], 'checksums': ['e87994d918ea951a589ec46648c24d9c7e56b7b5c2466d93f3b07883f0ecea19'], + # required for '#include "openjpeg.h"' to work + 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-%s/:$CPATH && " % local_openjpeg_maj_min, }), ] -moduleclass = 'tools' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb similarity index 100% rename from easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b.eb rename to easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b_support_cmake.patch b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1_cmake.patch similarity index 100% rename from easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-foss-2020b_support_cmake.patch rename to easybuild/easyconfigs/j/jxrlib/jxrlib-1.1_cmake.patch From b5bdcdfdc6b4487f83098d5657e81a6bc5d7559f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:24:20 +0100 Subject: [PATCH 1901/9987] use GCCcore toolchain for jxrlib + mention source of jxrlib patch --- .../j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb | 13 ++++++------- .../easyconfigs/j/jxrlib/jxrlib-1.1_cmake.patch | 2 ++ 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb index ded422afcf0..5f5cade0ebf 100644 --- a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb @@ -11,24 +11,21 @@ version = '1.1' homepage = 'https://deb.debian.org/debian/pool/main/j/jxrlib/' description = """Open source implementation of jpegxr""" -toolchain = {'name': 'foss', 'version': '2020b'} +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] sources = ['%(name)s_%(version)s.orig.tar.gz'] -patches = [ - ('%(name)s-%(version)s-foss-2020b_support_cmake.patch', 1), -] +patches = [('jxrlib-%(version)s_cmake.patch', 1)] checksums = [ 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303', # jxrlib_1.1.orig.tar.gz - 'f1c37976b4acdf393b583afe4126d888b3f79bc519c48d2ba9f93a24821077b5', # jxrlib-1.1-foss-2020b_support_cmake.patch + 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74', # jxrlib-1.1_cmake.patch ] builddependencies = [ + ('binutils', '2.35'), ('CMake', '3.18.4'), ] -modextrapaths = {'CPATH': 'include/jxrlib'} - sanity_check_paths = { 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], 'dirs': [], @@ -36,4 +33,6 @@ sanity_check_paths = { sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] +modextrapaths = {'CPATH': 'include/jxrlib'} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1_cmake.patch b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1_cmake.patch index 56c174ad93d..7e261de9389 100644 --- a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1_cmake.patch +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1_cmake.patch @@ -1,3 +1,5 @@ +source: https://sources.debian.org/patches/jxrlib/1.1-6/usecmake.patch/ + From 68a6e95de65ba6c6774586b73902eb8f47836f92 Mon Sep 17 00:00:00 2001 From: Dean M Greer Date: Tue, 24 Feb 2021 21:07:30 -0400 From 98f63204ba747897ac631a168cb9741fa73b52f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:37:22 +0100 Subject: [PATCH 1902/9987] stick to GCCcore toolchain for LERC + avoid downloading test program as separate source file --- .../l/LERC/LERC-3.0-GCCcore-10.2.0.eb | 34 ++++++++++++++ .../easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb | 44 ------------------- 2 files changed, 34 insertions(+), 44 deletions(-) create mode 100644 easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9331983f7b0 --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'LERC' +version = '3.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/Esri/lerc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8c0148f5c22d823eff7b2c999b0781f8095e49a7d3195f13c68c5541dd5740a1'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +sanity_check_commands = [ + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp && " + "g++ main.cpp -o lerctest -lLerc && ./lerctest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb deleted file mode 100644 index 2e086d2db32..00000000000 --- a/easybuild/easyconfigs/l/LERC/LERC-3.0-foss-2020b.eb +++ /dev/null @@ -1,44 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Updated: Denis Kristak -easyblock = 'CMakeMake' - -name = 'LERC' -version = '3.0' - -homepage = 'https://github.com/Esri/lerc' -description = """LERC is an open-source image or raster format which supports rapid encoding and decoding -for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, -so the precision of the original input image is preserved (within user defined error bounds).""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = [ - 'https://github.com/Esri/lerc/archive/', - 'https://raw.githubusercontent.com/Esri/lerc/33910e56d2d46e402b6233492eabb6c4fe0b3c5e/src/LercTest/', -] - -local_testfile_sed_cmd = "sed -i -e 's|../LercLib/include/||' %(builddir)s/main.cpp" - -sources = [ - 'v%(version)s.tar.gz', - {'filename': 'main.cpp', 'extract_cmd': 'cp %s %(builddir)s && ' + local_testfile_sed_cmd}, -] -checksums = [ - '8c0148f5c22d823eff7b2c999b0781f8095e49a7d3195f13c68c5541dd5740a1', # v3.0.tar.gz - '0e3cc6d8a1d07ad209af9565a6c0736f1d8acb3b04c9c5d922307374352231b9', # main.cpp -] - -builddependencies = [ - ('CMake', '3.18.4'), -] - -sanity_check_commands = [ - "cd %(builddir)s && g++ -o output_bin main.cpp -lLerc && ./output_bin " -] - -sanity_check_paths = { - 'files': ['lib/libLerc.%s' % SHLIB_EXT], - 'dirs': ['lib/', 'include/'], -} - -moduleclass = 'tools' From d4fcec45cc32e79918cd8b27defb8df11e5d40af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:40:33 +0100 Subject: [PATCH 1903/9987] copy LERC test program to install directory, so --module-only and --sanity-check-only work --- easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb index 9331983f7b0..d46571f3c10 100644 --- a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb @@ -21,9 +21,13 @@ builddependencies = [ ('CMake', '3.18.4'), ] +postinstallcmds = [ + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/test.c", +] + sanity_check_commands = [ - "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp && " - "g++ main.cpp -o lerctest -lLerc && ./lerctest", + "mkdir -p %(builddir)s && cd %(builddir)s && g++ %(installdir)s/test.c -o lerctest -lLerc && ./lerctest", ] sanity_check_paths = { From e21debb3e1d86500168bafd40ccfa27831174568 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:43:04 +0100 Subject: [PATCH 1904/9987] use lib as moduleclass for LERC --- easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb index d46571f3c10..6e3105ea152 100644 --- a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.2.0.eb @@ -35,4 +35,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'lib' From ad73e6e811256b495cbcb3c393a4aff14e6ccb47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 20:46:42 +0100 Subject: [PATCH 1905/9987] use more informative homepage for jxrlib --- easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb index 5f5cade0ebf..6a5a37d6d69 100644 --- a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.2.0.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'jxrlib' version = '1.1' -homepage = 'https://deb.debian.org/debian/pool/main/j/jxrlib/' +homepage = 'https://github.com/4creators/jxrlib' description = """Open source implementation of jpegxr""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From 3339e52991a26e9401fb01e25cbe31c2d2b7f907 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 21:44:53 +0100 Subject: [PATCH 1906/9987] collapse easyconfigs for batchgenerators, requests, tifffile into nnU-Net easyconfig --- .../batchgenerators-0.23-foss-2020b.eb | 31 --------- .../n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb | 66 +++++++++---------- .../r/requests/requests-2.26.0-foss-2020b.eb | 29 -------- .../tifffile/tifffile-2021.8.30-foss-2020b.eb | 45 ------------- .../u/unittest2/unittest2-1.1.0-foss-2020b.eb | 40 ----------- ...st2-foss2020b_remove_unnecessary_dep.patch | 19 ------ 6 files changed, 30 insertions(+), 200 deletions(-) delete mode 100644 easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb delete mode 100644 easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb delete mode 100644 easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb delete mode 100644 easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb delete mode 100644 easybuild/easyconfigs/u/unittest2/unittest2-foss2020b_remove_unnecessary_dep.patch diff --git a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb deleted file mode 100644 index 11ee9bfc83c..00000000000 --- a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.23-foss-2020b.eb +++ /dev/null @@ -1,31 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'PythonPackage' - -name = 'batchgenerators' -version = '0.23' - -homepage = 'https://github.com/MIC-DKFZ/batchgenerators' -description = """batchgenerators is a python package for data augmentation. -It is developed jointly between the Division of Medical Image Computing at the German Cancer Research Center (DKFZ) -and the Applied Computer Vision Lab of the Helmholtz Imaging Platform.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -sources = [SOURCE_TAR_GZ] -checksums = ['4bc5711ee75678ae97df7b54c50c1cde46f14c94f44d948f6edf4e8c48b2a9e0'] - -dependencies = [ - ('Python', '3.8.6'), - ('Pillow', '8.0.1'), - ('scikit-learn', '0.23.2'), - ('SciPy-bundle', '2020.11'), - ('scikit-image', '0.18.1'), - ('unittest2', '1.1.0'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb index 64574eb1e43..3feaf09f25d 100644 --- a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb @@ -1,23 +1,16 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Denis Kristak -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'nnU-Net' version = '1.7.0' homepage = 'https://github.com/MIC-DKFZ/nnUNet' -description = """ -nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found in the domain. -It condenses and automates the keys decisions for designing a successful segmentation pipeline for any given dataset. -""" -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = [ - 'https://files.pythonhosted.org/packages/8e/cf/0e5a45faba472c1df80da8d3fcb8d90b31a2258e48fdbc47cd2e30c16233/' -] +description = """nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found + in the domain It condenses and automates the keys decisions for designing a successful segmentation pipeline for + any given dataset.""" -sources = ['nnunet-%(version)s.tar.gz'] -checksums = ['7ad3d5b89af389fa86cea58f409bd2353b511a746587f37d26c00a756849f356'] +toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ ('Bazel', '3.7.2') @@ -25,40 +18,43 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), ('PyTorch', '1.7.1'), ('tqdm', '4.56.2'), ('dicom2nifti', '2.3.0'), ('scikit-image', '0.18.1'), ('TensorFlow', '2.5.0'), - ('SciPy-bundle', '2020.11'), - ('batchgenerators', '0.23'), ('scikit-learn', '0.23.2'), - ('requests', '2.26.0'), ('NiBabel', '3.2.1'), ('SimpleITK', '2.1.0'), - ('tifffile', '2021.8.30'), ('MedPy', '0.4.0'), - ('jax', '0.2.19') + ('jax', '0.2.19'), + ('lxml', '4.6.2'), ] -# sklearn is incorrect package name -preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " - -exts_defaultclass = 'PythonPackage' - -exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, -} +use_pip = True +sanity_pip_check = True exts_list = [ + ('linecache2', '1.0.0', { + 'checksums': ['4b26ff4e7110db76eeb6f5a7b64a82623839d595c2038eeda662f2a2db78e97c'], + }), + ('traceback2', '1.4.0', { + 'checksums': ['05acc67a09980c2ecfedd3423f7ae0104839eccb55fc645773e1caa0951c3030'], + }), + ('unittest2', '1.1.0', { + 'checksums': ['22882a0e418c284e1f718a822b3b022944d53d2d908e1690b319a9d3eb2c0579'], + 'preinstallopts': "sed -i 's/.argparse.,//' setup.py && ", + }), + ('batchgenerators', '0.23', { + 'checksums': ['4bc5711ee75678ae97df7b54c50c1cde46f14c94f44d948f6edf4e8c48b2a9e0'], + }), + ('tifffile', '2021.8.30', { + 'checksums': ['8760e61e30106ea0dab9ec42a238d70a3ff55dde9c54456e7b748fe717cb782d'], + }), ('contextlib2', '21.6.0', { 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], }), - ('absl-py', '0.15.0', { - 'modulename': 'absl', - 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], - }), ('dm-haiku', '0.0.4', { 'modulename': 'haiku', 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", @@ -75,14 +71,12 @@ exts_list = [ 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], }), + ('nnunet', version, { + 'preinstallopts': "sed -i 's/sklearn/scikit-learn/g' setup.py && ", + 'checksums': ['7ad3d5b89af389fa86cea58f409bd2353b511a746587f37d26c00a756849f356'], + }), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -options = {'modulename': 'nnunet'} - sanity_check_commands = ['nnUNet_train --help'] moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb b/easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb deleted file mode 100644 index 13821883c95..00000000000 --- a/easybuild/easyconfigs/r/requests/requests-2.26.0-foss-2020b.eb +++ /dev/null @@ -1,29 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Updated: Denis Kristak -easyblock = 'PythonBundle' - -name = 'requests' -version = '2.26.0' - -homepage = 'https://pypi.org/project/requests/' -description = """Requests is a simple, yet elegant, HTTP library.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -dependencies = [ - ('Python', '3.8.6'), -] - -exts_list = [ - (name, version, { - 'checksums': ['b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7'], - }), - ('charset-normalizer', '2.0.4', { - 'checksums': ['f23667ebe1084be45f6ae0538e4a5a865206544097e4e8bbcacf42cd02a348f3'], - }), -] - -use_pip = True -sanity_pip_check = True - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb b/easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb deleted file mode 100644 index beacbe3d48c..00000000000 --- a/easybuild/easyconfigs/t/tifffile/tifffile-2021.8.30-foss-2020b.eb +++ /dev/null @@ -1,45 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'PythonPackage' - -name = 'tifffile' -version = '2021.8.30' - -homepage = 'https://www.lfd.uci.edu/~gohlke/' -description = """ -Tifffile is a Python library to store numpy arrays in TIFF (Tagged Image File Format) files, and read image and -metadata from TIFF-like files used in bioimaging. -""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -sources = [SOURCE_TAR_GZ] -checksums = ['8760e61e30106ea0dab9ec42a238d70a3ff55dde9c54456e7b748fe717cb782d'] - -dependencies = [ - ('Python', '3.8.6'), - ('matplotlib', '3.3.3'), - ('SciPy-bundle', '2020.11'), - ('imagecodecs', '2021.8.26'), - ('libxml2', '2.9.10'), - ('libxslt', '1.1.34'), -] - -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'use_pip': True, - 'download_dep_fail': True, -} - -exts_list = [ - ('lxml', '4.6.3', { - 'source_urls': ['https://pypi.python.org/packages/source/l/lxml/'], - 'checksums': ['39b78571b3b30645ac77b95f7c69d1bffc4cf8c3b157c435a34da72e78c82468'], - }), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb b/easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb deleted file mode 100644 index 848a0147275..00000000000 --- a/easybuild/easyconfigs/u/unittest2/unittest2-1.1.0-foss-2020b.eb +++ /dev/null @@ -1,40 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'PythonBundle' - -name = 'unittest2' -version = '1.1.0' - -homepage = 'https://pypi.org/project/unittest2/' -description = """unittest2 is a backport of the new features added to the unittest testing -framework in Python 2.7 and onwards.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = [PYPI_SOURCE] - -dependencies = [ - ('Python', '3.8.6'), -] - -exts_list = [ - (name, version, { - 'patches': ['unittest2-foss2020b_remove_unnecessary_dep.patch'], - 'checksums': [ - '22882a0e418c284e1f718a822b3b022944d53d2d908e1690b319a9d3eb2c0579', # unittest2-1.1.0.tar.gz - # unittest2-foss2020b_remove_unnecessary_dep.patch - 'adb3f83e4e220cf430de559075fbbce5545e83fb35ea0a3fd260ca1f00263c20', - ], - }), - ('traceback2', '1.4.0', { - 'checksums': ['05acc67a09980c2ecfedd3423f7ae0104839eccb55fc645773e1caa0951c3030'], - }), - ('linecache2', '1.0.0', { - 'checksums': ['4b26ff4e7110db76eeb6f5a7b64a82623839d595c2038eeda662f2a2db78e97c'], - }), -] - -use_pip = True -sanity_pip_check = True - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/unittest2/unittest2-foss2020b_remove_unnecessary_dep.patch b/easybuild/easyconfigs/u/unittest2/unittest2-foss2020b_remove_unnecessary_dep.patch deleted file mode 100644 index 33bf69c75f4..00000000000 --- a/easybuild/easyconfigs/u/unittest2/unittest2-foss2020b_remove_unnecessary_dep.patch +++ /dev/null @@ -1,19 +0,0 @@ -diff -ruN unittest2-1.1.0_orig/setup.py unittest2-1.1.0/setup.py ---- unittest2-1.1.0_orig/setup.py 2021-09-07 14:45:56.638877809 +0200 -+++ unittest2-1.1.0/setup.py 2021-09-07 14:52:28.782893924 +0200 -@@ -57,7 +57,7 @@ - # Both install and setup requires - because we read VERSION from within the - # package, and the package also exports all the APIs. - # six for compat helpers --REQUIRES = ['argparse', 'six>=1.4', 'traceback2'], -+REQUIRES = ['six>=1.4', 'traceback2'], - - params = dict( - name=NAME, -diff -ruN unittest2-1.1.0_orig/unittest2.egg-info/requires.txt unittest2-1.1.0/unittest2.egg-info/requires.txt ---- unittest2-1.1.0_orig/unittest2.egg-info/requires.txt 2021-09-07 14:45:56.654877436 +0200 -+++ unittest2-1.1.0/unittest2.egg-info/requires.txt 2021-09-07 14:47:15.013107770 +0200 -@@ -1,3 +1,2 @@ --argparse - six>=1.4 - traceback2 From 207a1591b31020b258e158ad13131517458476c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 22:30:51 +0100 Subject: [PATCH 1907/9987] clean up SimpleITK easyconfig + fix homepage/description --- .../s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb | 30 +++++++------------ 1 file changed, 11 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb index 956b38dd32a..0ad9b52ffd1 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-foss-2020b.eb @@ -5,9 +5,9 @@ easyblock = 'CMakeMake' name = 'SimpleITK' version = '2.1.0' -homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' -description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in - datasets showing strong between-class imbalance.""" +homepage = 'http://www.simpleitk.org' +description = """SimpleITK is a simplified programming interface to the algorithms and data structures of + the Insight Toolkit (ITK).""" toolchain = {'name': 'foss', 'version': '2020b'} @@ -26,32 +26,24 @@ dependencies = [ ('ITK', '5.2.1'), ('scikit-build', '0.11.1'), ] -start_dir = 'SimpleITK' - -configopts = '-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF ' -configopts += ' -DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF ' -preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -local_pyinstpath = "%(installdir)s/lib/python%(pyshortver)s/site-packages" +start_dir = 'SimpleITK' -local_postinstall_cmds = "mkdir -p %s " % local_pyinstpath -local_postinstall_cmds += " && cd %(builddir)s/easybuild_obj/Wrapping/Python " -local_postinstall_cmds += " && export PYTHONPATH=%s:$PYTHONPATH " % local_pyinstpath -local_postinstall_cmds += " && pip install --prefix=%(installdir)s . " +configopts = "-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF " +configopts += "-DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF " postinstallcmds = [ - local_postinstall_cmds + "cd %(builddir)s/easybuild_obj/Wrapping/Python && " + "pip install --ignore-installed --no-deps --prefix=%(installdir)s . ", ] -separate_build_dir = True -# todo make nicer dir path -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages/']} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], - 'dirs': ['lib/python%(pyshortver)s/site-packages', 'include/%(name)s-%(version_major_minor)s'], + 'dirs': ['include/%(name)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = [('python', "-c 'import %(name)s'")] +sanity_check_commands = ["python -c 'import %(name)s'"] moduleclass = 'tools' From b1d49f3187f49ab4fbc8804927830572dd6d1b70 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 22:45:25 +0100 Subject: [PATCH 1908/9987] add exception for Lua 5.3.5 dependency variant that is required for SimpleITK (and MedPy + nnU-Net) --- test/easyconfigs/easyconfigs.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 05d3433d32a..03a7d90252e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -460,6 +460,10 @@ def check_dep_vars(self, gen, dep, dep_vars): r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), ], + 'Lua': [ + # SimpleITK 2.1.0 requires Lua 5.3.x, MedPy and nnU-Net depend on SimpleITK + (r'5\.3\.5', [r'nnU-Net-1\.7\.0-', r'MedPy-0\.4\.0-', r'SimpleITK-2\.1\.0-']), + ], # TensorFlow 2.5+ requires a more recent NCCL than version 2.4.8 used in 2019b generation; # Horovod depends on TensorFlow, so same exception required there 'NCCL': [(r'2\.11\.4', [r'TensorFlow-2\.[5-9]\.', r'Horovod-0\.2[2-9]'])], From 14cc9f20e92a516ed7bd28e98c78b581cb21aa98 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 23:01:49 +0100 Subject: [PATCH 1909/9987] stick to TensorFlow 2.4.1 as dependency in nnU-Net easyconfig using foss/2020b toolchain --- easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb index 3feaf09f25d..af8ddb251bb 100644 --- a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-foss-2020b.eb @@ -23,7 +23,7 @@ dependencies = [ ('tqdm', '4.56.2'), ('dicom2nifti', '2.3.0'), ('scikit-image', '0.18.1'), - ('TensorFlow', '2.5.0'), + ('TensorFlow', '2.4.1'), ('scikit-learn', '0.23.2'), ('NiBabel', '3.2.1'), ('SimpleITK', '2.1.0'), From 2084cad1bf23ca234e89e7f648ec6fe20cb0110c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 23:04:08 +0100 Subject: [PATCH 1910/9987] remove unneeded binutils build dependency from dicom2nifti easyconfig --- .../easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb index 4692d2a37ed..cadc2738473 100644 --- a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb @@ -13,10 +13,6 @@ toolchain = {'name': 'foss', 'version': '2020b'} sources = [SOURCE_TAR_GZ] checksums = ['808c4ddbcffd492d41ff20a2837b5e2a3cbe2058d43512fe97b99d678a758bfd'] -builddependencies = [ - ('binutils', '2.35'), -] - dependencies = [ ('Python', '3.8.6'), ('pydicom', '2.1.2'), From 278564571fe6396fa56aec7e7dab60ab5b75d5f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 23:06:39 +0100 Subject: [PATCH 1911/9987] add sanity check command for dicom2nifti 2.3.0 --- .../easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb index cadc2738473..4d594c37592 100644 --- a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-foss-2020b.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["dicom2nifti --help"] + moduleclass = 'lib' From 9c2e45dd5cc2a22f8c2a105ab4ee0d1c727ec37f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 9 Nov 2021 23:29:29 +0100 Subject: [PATCH 1912/9987] remove double-conversion dependency for ITK 5.2.1, since copy that is included must be used since double-to-string.h is required --- easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb index 69753b77046..4ad17d850e9 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2020b.eb @@ -28,7 +28,6 @@ builddependencies = [ ] dependencies = [ - ('double-conversion', '3.1.5'), ('expat', '2.2.9'), ('HDF5', '1.10.7'), ('libjpeg-turbo', '2.0.5'), @@ -39,7 +38,6 @@ dependencies = [ ] local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] -# local_sys_deps = ['DOUBLECONVERSION', 'EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' From 9ccc99ddbe98496d81ec526added6363e910b90c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 10 Nov 2021 09:14:14 +0000 Subject: [PATCH 1913/9987] Add pkg-config builddep to Python --- .../easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb index e96cf3a75bc..d4ac365a6cb 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb @@ -15,6 +15,7 @@ checksums = ['e0fbd5b6e1ee242524430dee3c91baf4cbbaba4a72dd1674b90fda87b713c7ab'] builddependencies = [ ('UnZip', '6.0'), + ('pkg-config', '0.29.2'), ] dependencies = [ From 101c673c5d874fc1d374fec4cd6998be46e458e3 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 10 Nov 2021 11:44:31 +0200 Subject: [PATCH 1914/9987] custom path for packages --- easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb index e6fffcbcc27..b24fcc3c961 100644 --- a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb @@ -27,7 +27,7 @@ postinstallcmds = [ # if package dir doesnt exist yet, initial run of `beauti` creates it 'timeout 10 xvfb-run beauti 2>&1 | grep "Terminated"', # now we can link our installdir to the package dir - 'ln -s %(installdir)s ~/.beast/2.6/STACEY ', + # 'ln -s %(installdir)s ~/.beast/2.6/STACEY ', ] sanity_check_paths = { @@ -35,4 +35,6 @@ sanity_check_paths = { 'dirs': ['lib/', 'templates/', 'examples'], } +modextravars = {'_JAVA_OPTIONS': "-Dbeast.user.package.dir=%(installdir)s"} + moduleclass = 'data' From 2fc3bc7c044fd8a464729e00ed8c7637cb2e3c66 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 10 Nov 2021 10:51:21 +0000 Subject: [PATCH 1915/9987] add pkg-config to all Python using the OpenSSL wrapper --- .../easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb | 4 ++++ easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb | 1 + .../easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb | 1 + easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb | 1 + 4 files changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb index 98638347a5b..6f6385c7887 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb @@ -13,6 +13,10 @@ source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] +builddependencies = [ + ('pkg-config', '0.29.2'), +] + dependencies = [ ('binutils', '2.36.1'), ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb index 4ba357afee6..95b46797d98 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb @@ -15,6 +15,7 @@ checksums = ['e0fbd5b6e1ee242524430dee3c91baf4cbbaba4a72dd1674b90fda87b713c7ab'] builddependencies = [ ('UnZip', '6.0'), ('Rust', '1.52.1'), # required for setuptools-rust, which is needed for cryptography + ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb index e5fe2be7e2e..6ce8d0e64b2 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb @@ -15,6 +15,7 @@ checksums = ['d0a35182e19e416fc8eae25a3dcd4d02d4997333e4ad1f2eee6010aadc3fe866'] builddependencies = [ ('UnZip', '6.0'), + ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb index 4e8449701f6..9a868863ba7 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb @@ -15,6 +15,7 @@ checksums = ['d0a35182e19e416fc8eae25a3dcd4d02d4997333e4ad1f2eee6010aadc3fe866'] builddependencies = [ ('UnZip', '6.0'), ('Rust', '1.54.0'), # required for setuptools-rust, which is needed for cryptography + ('pkg-config', '0.29.2'), ] dependencies = [ From f08d7fd01e1be8319f0a924480cd3bed234e01c8 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 10 Nov 2021 13:48:52 +0000 Subject: [PATCH 1916/9987] Added patch for missing headers for Ubuntu-16.04.7 LTS --- .../u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb | 7 +++++- .../u/UCX/UCX-1.11.2-missing_header.patch | 24 +++++++++++++++++++ 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb index 5fcb4154143..b91e018735b 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb @@ -14,10 +14,15 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.gz'] -patches = ['UCX-1.10.0-dynamic_modules.patch'] +patches = [ + 'UCX-1.10.0-dynamic_modules.patch', + 'UCX-1.11.2-missing_header.patch', + +] checksums = [ 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df', # ucx-1.11.2.tar.gz '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch + 'e277e71329c9ef388fe9e4775ed9ee6b3a70af31a52f7eebaaed8bd992007bfb', # UCX-1.11.2-missing_header.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch new file mode 100644 index 00000000000..84ca9cb8f7e --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch @@ -0,0 +1,24 @@ +diff --git a/ucx-1.11.2-orig/src/uct/ib/base/ib_device.h b/ucx-1.11.2/src/uct/ib/base/ib_device.h +index ac69544..5eb39b0 100644 +--- a/ucx-1.11.2-orig/src/uct/ib/base/ib_device.h ++++ b/ucx-1.11.2/src/uct/ib/base/ib_device.h +@@ -8,6 +8,7 @@ + #ifndef UCT_IB_DEVICE_H + #define UCT_IB_DEVICE_H + ++#include "string.h" + #include "ib_verbs.h" + + #include +diff --git a/ucx-1.11.2-orig/src/uct/ib/base/ib_verbs.h b/ucx-1.11.2/src/uct/ib/base/ib_verbs.h +index 524139c..4822477 100644 +--- a/ucx-1.11.2-orig/src/uct/ib/base/ib_verbs.h ++++ b/ucx-1.11.2/src/uct/ib/base/ib_verbs.h +@@ -19,6 +19,7 @@ + #include + #endif + ++#include "string.h" + #include + + #include From 91a2aad48c1f8f75969f76ff64df6e100e6936c6 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 10 Nov 2021 13:55:30 +0000 Subject: [PATCH 1917/9987] Added description and author to patch file --- easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb index b91e018735b..62d7b7596bc 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb @@ -22,7 +22,7 @@ patches = [ checksums = [ 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df', # ucx-1.11.2.tar.gz '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch - 'e277e71329c9ef388fe9e4775ed9ee6b3a70af31a52f7eebaaed8bd992007bfb', # UCX-1.11.2-missing_header.patch + '187152c0aa85dcead6c26382859868fc975bdf47d977aebc0bc36c789ea4ae97', # UCX-1.11.2-missing_header.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch index 84ca9cb8f7e..12f716013be 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch @@ -1,3 +1,5 @@ +Adding string.h header to deal with memcpy error on Ubuntu-16.04.7 LTS +Author: J. Sassmannshausen / GSTT diff --git a/ucx-1.11.2-orig/src/uct/ib/base/ib_device.h b/ucx-1.11.2/src/uct/ib/base/ib_device.h index ac69544..5eb39b0 100644 --- a/ucx-1.11.2-orig/src/uct/ib/base/ib_device.h From 7e0363d17e9ca192dac2b06a36ba372dff237715 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 10 Nov 2021 13:57:10 +0000 Subject: [PATCH 1918/9987] Removed surpluse line --- easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb index 62d7b7596bc..879eb3c7001 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb @@ -17,7 +17,6 @@ sources = ['%(namelower)s-%(version)s.tar.gz'] patches = [ 'UCX-1.10.0-dynamic_modules.patch', 'UCX-1.11.2-missing_header.patch', - ] checksums = [ 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df', # ucx-1.11.2.tar.gz From 94e203dcc8654818dc7bc1e2dae2de5358a9260e Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 10 Nov 2021 15:24:09 +0100 Subject: [PATCH 1919/9987] Update easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb --- .../h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb index 66d8b4e92b2..ad341bc26e5 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -34,6 +34,7 @@ exts_list = [ 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], }), ('horovod', version, { + 'checksums': ['72ab3e5f59df6a000473999937e52e6831ad1a5e4e7bd23885a04bcdd4d8691c'], }), ] From 63a715565bf53d42c854b8b26f2bc04d1b6ee7dd Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 10 Nov 2021 15:38:53 +0000 Subject: [PATCH 1920/9987] Checksum for source code updated as tarball has changed --- easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb index 87be8192331..9b09c71a26d 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb @@ -12,7 +12,7 @@ source_urls = [ 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', ] sources = ['userApps.v%(version)s.src.tgz'] -checksums = ['43691dc14dc50bc597d6ac38f252e766ea561c3086eb0f219406d050fe2b79be'] +checksums = ['1edf66ad5f7c8c79586e9f878b5971d7d467c8c5efbeb31c69085d24a6e4671f'] files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] From 2df5f2326edb1f66e47cbef295adc90143252689 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 10 Nov 2021 15:45:48 +0000 Subject: [PATCH 1921/9987] Changed patchfile so system headers are used --- easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb index 879eb3c7001..e81c44acb30 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df', # ucx-1.11.2.tar.gz '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch - '187152c0aa85dcead6c26382859868fc975bdf47d977aebc0bc36c789ea4ae97', # UCX-1.11.2-missing_header.patch + 'fa9052a33da5c8e94bc7df0e5fe6ce3baf613310842ae1ab9ed4ef2d49666c01', # UCX-1.11.2-missing_header.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch index 12f716013be..74ab0459000 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-missing_header.patch @@ -8,7 +8,7 @@ index ac69544..5eb39b0 100644 #ifndef UCT_IB_DEVICE_H #define UCT_IB_DEVICE_H -+#include "string.h" ++#include #include "ib_verbs.h" #include @@ -20,7 +20,7 @@ index 524139c..4822477 100644 #include #endif -+#include "string.h" ++#include #include #include From a933eae337d42ea557bc4a98bbbb5f579fcf45e6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 10 Nov 2021 16:55:49 +0100 Subject: [PATCH 1922/9987] adding easyconfigs: pmx-2.0-foss-2020b-Python-2.7.18.eb --- .../p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb new file mode 100644 index 00000000000..4361309c23f --- /dev/null +++ b/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pmx' +version = '2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/deGrootLab/pmx' +description = """pmx (formerly pymacs) is a small bunch of classes to +read structure files such as pdb or gro and trajectory data in gromacs +xtc format. Over the years it has been extended towards a versatile +(bio-) molecular structure manipulation package with some additional +functionalities, e.g. gromacs file parsers and scripts for setup and +analysis of free energy calculations.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['323dd5091c62255f1f6cbfc6b4869ef9672a188ce7e3439ed1bb6e9cf2c3804c'] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '2.2.5', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['pmx --help'] + +moduleclass = 'tools' From a741391a332ba66464632323d4b246abc1fc67b6 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 11 Nov 2021 21:33:19 +1050 Subject: [PATCH 1923/9987] adding easyconfigs: bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb --- ...bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..0cca243ca6c --- /dev/null +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,42 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'bcbio-gff' +version = '0.6.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/chapmanb/bcbb/tree/master/gff' + +description = """ +Read and write Generic Feature Format (GFF) with Biopython integration. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['74c6920c91ca18ed9cb872e9471c0be442dad143d8176345917eb1fefc86bc37'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' +targets = ['GFFOutput.py', 'GFFParser.py'] + +sanity_check_paths = { + 'files': [bcbiogffroot + '/BCBio/GFF/%s' % x for x in targets], + 'dirs': [bcbiogffroot], +} + +options = {'modulename': 'BCBio.GFF'} + +moduleclass = 'bio' From 1a28a817ec95ded6e3951f626546f71126d8e755 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 11 Nov 2021 21:47:48 +1050 Subject: [PATCH 1924/9987] adding easyconfigs: bcbio-gff-0.6.7-foss-2021a.eb --- .../b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb new file mode 100644 index 00000000000..b9a53c8b1ba --- /dev/null +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb @@ -0,0 +1,42 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v0.6.7 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'bcbio-gff' +version = '0.6.7' + +homepage = 'https://github.com/chapmanb/bcbb/tree/master/gff' + +description = """ +Read and write Generic Feature Format (GFF) with Biopython integration. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [PYPI_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['6e6f70639149612272a3b298a93ac50bba6f9ecece934f2a0ea86d4abde975da'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' +targets = ['GFFOutput.py', 'GFFParser.py'] + +sanity_check_paths = { + 'files': [bcbiogffroot + '/BCBio/GFF/%s' % x for x in targets], + 'dirs': [bcbiogffroot], +} + +options = {'modulename': 'BCBio.GFF'} + +moduleclass = 'bio' From bc00a65495ac34b652032dbf3c860b8e0d5d0f45 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 11 Nov 2021 21:53:02 +1050 Subject: [PATCH 1925/9987] local_var fix --- .../bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb index 0cca243ca6c..10707f14884 100644 --- a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb @@ -29,12 +29,12 @@ download_dep_fail = True use_pip = True sanity_pip_check = True -bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' -targets = ['GFFOutput.py', 'GFFParser.py'] +local_bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' +local_targets = ['GFFOutput.py', 'GFFParser.py'] sanity_check_paths = { - 'files': [bcbiogffroot + '/BCBio/GFF/%s' % x for x in targets], - 'dirs': [bcbiogffroot], + 'files': [local_bcbiogffroot + '/BCBio/GFF/%s' % x for x in local_targets], + 'dirs': [local_bcbiogffroot], } options = {'modulename': 'BCBio.GFF'} From f15e9bd3d43d581497c0c9628c679a72565f6a49 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 11 Nov 2021 22:02:35 +1050 Subject: [PATCH 1926/9987] deps + --- .../cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb index 47cd3dce2d2..d9470e12178 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -10,7 +10,9 @@ version = '24.2.0' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/Magdoll/cDNA_Cupcake' -description = "cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data." +description = """cDNA_Cupcake is a miscellaneous collection of Python and +R scripts used for analyzing sequencing data. +""" toolchain = {'name': 'foss', 'version': '2020a'} @@ -23,13 +25,14 @@ dependencies = [ ('SciPy-bundle', '2020.03', versionsuffix), ('Biopython', '1.78', versionsuffix), ('bx-python', '0.8.9', versionsuffix), + ('bcbio-gff', '0.6.6', versionsuffix), + ('scikit-learn', '0.23.1', versionsuffix), + ('Pysam', '0.16.0.1'), ] -download_dep_fail = True +download_dep_fail = False use_pip = True -options = {'modulename': 'cupcake'} - sanity_pip_check = True sanity_check_paths = { # check for particular Cupcake ToFU scripts, @@ -42,4 +45,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +options = {'modulename': 'cupcake'} + moduleclass = 'bio' From 035d0ea75e1338bab697186af29094bcb6f5c8a8 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 11 Nov 2021 22:06:08 +1050 Subject: [PATCH 1927/9987] source_urls removed --- .../b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb index 10707f14884..462df6acc1d 100644 --- a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb @@ -16,7 +16,6 @@ Read and write Generic Feature Format (GFF) with Biopython integration. toolchain = {'name': 'foss', 'version': '2020a'} -source_urls = [PYPI_SOURCE] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['74c6920c91ca18ed9cb872e9471c0be442dad143d8176345917eb1fefc86bc37'] From 9b13324457503146ef57c8edf8a6c09ba0bbbd3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 Nov 2021 12:23:32 +0100 Subject: [PATCH 1928/9987] fix comment mentioning runtime version for MCR R2021b --- easybuild/easyconfigs/m/MCR/MCR-R2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2021b.eb b/easybuild/easyconfigs/m/MCR/MCR-R2021b.eb index ac18133d042..4e9b940fb9a 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2021b.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2021b.eb @@ -2,7 +2,7 @@ # Author: Robert Mijakovic ## name = 'MCR' -version = 'R2021b' # runtime version 9.10 +version = 'R2021b' # runtime version 9.11 local_update = '0' homepage = 'https://www.mathworks.com/products/compiler/mcr/' From 305cb347bb5f5c450d06ce922ee0fa6d8f40e95c Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 11 Nov 2021 22:33:19 +1050 Subject: [PATCH 1929/9987] bug fix --- .../b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb index b9a53c8b1ba..3aaa7d391ff 100644 --- a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb @@ -16,7 +16,6 @@ Read and write Generic Feature Format (GFF) with Biopython integration. toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = [PYPI_SOURCE] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['6e6f70639149612272a3b298a93ac50bba6f9ecece934f2a0ea86d4abde975da'] @@ -29,12 +28,12 @@ download_dep_fail = True use_pip = True sanity_pip_check = True -bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' -targets = ['GFFOutput.py', 'GFFParser.py'] +local_bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' +local_targets = ['GFFOutput.py', 'GFFParser.py'] sanity_check_paths = { - 'files': [bcbiogffroot + '/BCBio/GFF/%s' % x for x in targets], - 'dirs': [bcbiogffroot], + 'files': [local_bcbiogffroot + '/BCBio/GFF/%s' % x for x in local_targets], + 'dirs': [local_bcbiogffroot], } options = {'modulename': 'BCBio.GFF'} From 843acf702d45949748ea4352a7cbaf2fb3ba0f7f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 11 Nov 2021 13:10:41 +0100 Subject: [PATCH 1930/9987] pmx: Fix missing versionsuffix on SciPy-bundle version specification. --- easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb index 4361309c23f..00f2bd3ae26 100644 --- a/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/pmx/pmx-2.0-foss-2020b-Python-2.7.18.eb @@ -19,7 +19,7 @@ checksums = ['323dd5091c62255f1f6cbfc6b4869ef9672a188ce7e3439ed1bb6e9cf2c3804c'] dependencies = [ ('Python', '2.7.18'), - ('SciPy-bundle', '2020.11'), + ('SciPy-bundle', '2020.11', versionsuffix), ('matplotlib', '2.2.5', versionsuffix), ] From a265a7c9c015703a25dbf8e5d5f012bebe2cb926 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Nov 2021 12:22:02 +0000 Subject: [PATCH 1931/9987] adding easyconfigs: HTSlib-1.14-GCC-11.2.0.eb --- .../h/HTSlib/HTSlib-1.14-GCC-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.14-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.14-GCC-11.2.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.14-GCC-11.2.0.eb new file mode 100644 index 00000000000..9436242f53d --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.14-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Updated to 1.14 +# J. Sassmannshausen /GSTT + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.14' + +homepage = "https://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ed221b8f52f4812f810eebe0cc56cd8355a5c9d21c62d142ac05ad0da147935f'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.78.0'), +] + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From 76704f870716bc3646821da449c491be69f9ecb4 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 11 Nov 2021 13:55:53 +0100 Subject: [PATCH 1932/9987] Added description and author info --- .../PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch index 3dd90944bac..fb66d1b6696 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch @@ -1,3 +1,6 @@ +# Author: Alexander Grund +# Avoid test failures in CGROUP environments +# See https://github.com/pytorch/pytorch/issues/44368 and https://github.com/pytorch/pytorch/pull/44369 diff -Nru pytorch.orig/test/test_dataloader.py pytorch/test/test_dataloader.py --- pytorch.orig/test/test_dataloader.py 2021-10-28 19:19:23.284526686 +0200 +++ pytorch/test/test_dataloader.py 2021-10-28 19:21:31.860488973 +0200 From 3fe237cf458aa4309fae11c4c8fc23b12e4194aa Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 11 Nov 2021 14:08:53 +0100 Subject: [PATCH 1933/9987] Added CUDA suffix --- ...s-2021a-CUDA-$(cudaver)s-PyTorch-1.10.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-$(cudaver)s-PyTorch-1.10.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-$(cudaver)s-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-$(cudaver)s-PyTorch-1.10.0.eb new file mode 100644 index 00000000000..57589421a83 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-$(cudaver)s-PyTorch-1.10.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.23.0' +local_pt_version = '1.10.0' +versionsuffix = '-CUDA-$(cudaver)s-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('CMake', '3.20.1'), + ('flatbuffers', '2.0.0'), +] +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('CUDA', '11.3.1', '', True), + ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), + ('PyTorch', local_pt_version, '-CUDA-%(cudaver)s'), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('horovod', version, { + 'checksums': ['72ab3e5f59df6a000473999937e52e6831ad1a5e4e7bd23885a04bcdd4d8691c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 9ca646040914934825229eb2a87e672b20718d34 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 11 Nov 2021 14:13:13 +0100 Subject: [PATCH 1934/9987] Added CUDA suffix, now also to the filename... --- ...orovod-0.23.0-foss-2021a-PyTorch-1.10.0.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-PyTorch-1.10.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-PyTorch-1.10.0.eb deleted file mode 100644 index d1ecff30044..00000000000 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-PyTorch-1.10.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Horovod' -version = '0.23.0' -local_pt_version = '1.10.0' -versionsuffix = '-PyTorch-%s' % local_pt_version - -homepage = 'https://github.com/uber/horovod' -description = "Horovod is a distributed training framework for TensorFlow." - -toolchain = {'name': 'foss', 'version': '2021a'} - -builddependencies = [ - ('CMake', '3.20.1'), - ('flatbuffers', '2.0.0'), -] -dependencies = [ - ('Python', '3.9.5'), - ('PyYAML', '5.4.1'), - ('CUDA', '11.3.1', '', True), - ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), - ('PyTorch', local_pt_version, '-CUDA-%(cudaver)s'), -] - -use_pip = True -sanity_pip_check = True - -preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' -preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' - -parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend - -exts_list = [ - ('cloudpickle', '2.0.0', { - 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], - }), - ('horovod', version, { - 'checksums': ['72ab3e5f59df6a000473999937e52e6831ad1a5e4e7bd23885a04bcdd4d8691c'], - }), -] - -sanity_check_paths = { - 'files': ['bin/horovodrun'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' From aa78c2d6fc859a0cfcf11850fd183f9626d6b494 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Nov 2021 13:29:42 +0000 Subject: [PATCH 1935/9987] OpenSSL fixed for Ubuntu-16.04-LTR, freetype added --- .../k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb | 13 ++++-- .../k/Kent_tools/Kent_tools-422-openssl.patch | 45 +++++++++++++++++++ 2 files changed, 54 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-openssl.patch diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb index 9b09c71a26d..85bd43f78c1 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb @@ -12,9 +12,11 @@ source_urls = [ 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', ] sources = ['userApps.v%(version)s.src.tgz'] -checksums = ['1edf66ad5f7c8c79586e9f878b5971d7d467c8c5efbeb31c69085d24a6e4671f'] - -files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] +patches = ['%(name)s-%(version)s-openssl.patch'] +checksums = [ + '1edf66ad5f7c8c79586e9f878b5971d7d467c8c5efbeb31c69085d24a6e4671f', # userApps.v422.src.tgz + 'c10e255b18fa6932d8ead725c874fe57dfe8b0a0757758346bb986644337c8bc', # Kent_tools-422-openssl.patch +] dependencies = [ ('MariaDB', '10.6.4'), @@ -22,13 +24,16 @@ dependencies = [ ('zlib', '1.2.11'), ('util-linux', '2.37'), ('OpenSSL', '1.1', '', True), + ('freetype', '2.11.0'), ] buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' -buildopts += 'MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' +buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + sanity_check_paths = { 'files': ['bin/%s' % x for x in local_binaries], 'dirs': [], diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-openssl.patch b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-openssl.patch new file mode 100644 index 00000000000..e492ca729b4 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-openssl.patch @@ -0,0 +1,45 @@ +Patch to ensure SSL will be picked up by EasyBuild and not the OS. Important for older OpenSSL versions +Author: J. Sassmannshausen / GSTT +diff --git a/userApps.orig/kent/src/inc/common.mk b/userApps/kent/src/inc/common.mk +index d200b43..cb257d6 100644 +--- a/userApps.orig/kent/src/inc/common.mk ++++ b/userApps/kent/src/inc/common.mk +@@ -133,7 +133,7 @@ endif + ifneq (${SSL_DIR}, "/usr/include/openssl") + ifneq ($(UNAME_S),Darwin) + ifneq ($(wildcard ${SSL_DIR}),) +- L+=-L${SSL_DIR}/lib ++ L+=-L${SSL_DIR}/lib -lssl -lcrypto + endif + endif + HG_INC+=-I${SSL_DIR}/include +@@ -142,29 +142,6 @@ endif + ifeq (${IS_HGWDEV},yes) + L+=/hive/groups/browser/freetype/freetype-2.10.0/objs/.libs/libfreetype.a -lbz2 + L+=/usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5 -lk5crypto -ldl +-else +- ifneq ($(wildcard /opt/local/lib/libssl.a),) +- L+=/opt/local/lib/libssl.a +- else +- ifneq ($(wildcard /usr/lib/x86_64-linux-gnu/libssl.a),) +- L+=/usr/lib/x86_64-linux-gnu/libssl.a +- else +- ifneq ($(wildcard /usr/local/opt/openssl/lib/libssl.a),) +- L+=/usr/local/opt/openssl/lib/libssl.a +- else +- L+=-lssl +- endif +- endif +- endif +- ifneq ($(wildcard /opt/local/lib/libcrypto.a),) +- L+=/opt/local/lib/libcrypto.a +- else +- ifneq ($(wildcard /usr/local/opt/openssl/lib/libcrypto.a),) +- L+=/usr/local/opt/openssl/lib/libcrypto.a +- else +- L+=-lcrypto +- endif +- endif + endif + + # autodetect where libm is installed From 9ff7f657b6e9c43d389d93b57362a50931aa52ab Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 11 Nov 2021 14:29:50 +0100 Subject: [PATCH 1936/9987] Cant have string replacement and template replacement in one string. Seperated it now similar to https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb --- ...0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb new file mode 100644 index 00000000000..1a551228e8f --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.23.0' +local_pt_version = '1.10.0' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('CMake', '3.20.1'), + ('flatbuffers', '2.0.0'), +] +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('CUDA', '11.3.1', '', True), + ('NCCL', '2.10.3', local_cuda_suffix), + ('PyTorch', local_pt_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('horovod', version, { + 'checksums': ['72ab3e5f59df6a000473999937e52e6831ad1a5e4e7bd23885a04bcdd4d8691c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 49a44f64f2f2241c6bc1eee52298c2e5239e9f7e Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Thu, 11 Nov 2021 16:08:16 +0100 Subject: [PATCH 1937/9987] Updated checksum --- .../p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index 76bd10e605e..0c16905a596 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -45,7 +45,7 @@ checksums = [ # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '3544726dd9041e247349730c209a77bc16ab4f9f7854dc7fe31399269f12613a', + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch From dd40b381139cd667c138724ae6f64ef8591be523 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Thu, 11 Nov 2021 16:10:07 +0100 Subject: [PATCH 1938/9987] Removed incorrectly named Horovod --- ...s-2021a-CUDA-$(cudaver)s-PyTorch-1.10.0.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-$(cudaver)s-PyTorch-1.10.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-$(cudaver)s-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-$(cudaver)s-PyTorch-1.10.0.eb deleted file mode 100644 index 57589421a83..00000000000 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-$(cudaver)s-PyTorch-1.10.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Horovod' -version = '0.23.0' -local_pt_version = '1.10.0' -versionsuffix = '-CUDA-$(cudaver)s-PyTorch-%s' % local_pt_version - -homepage = 'https://github.com/uber/horovod' -description = "Horovod is a distributed training framework for TensorFlow." - -toolchain = {'name': 'foss', 'version': '2021a'} - -builddependencies = [ - ('CMake', '3.20.1'), - ('flatbuffers', '2.0.0'), -] -dependencies = [ - ('Python', '3.9.5'), - ('PyYAML', '5.4.1'), - ('CUDA', '11.3.1', '', True), - ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), - ('PyTorch', local_pt_version, '-CUDA-%(cudaver)s'), -] - -use_pip = True -sanity_pip_check = True - -preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' -preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' - -parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend - -exts_list = [ - ('cloudpickle', '2.0.0', { - 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], - }), - ('horovod', version, { - 'checksums': ['72ab3e5f59df6a000473999937e52e6831ad1a5e4e7bd23885a04bcdd4d8691c'], - }), -] - -sanity_check_paths = { - 'files': ['bin/horovodrun'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' From 719b03d349ac5a0e0001a3c1076f2c6d69008a07 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Nov 2021 15:36:03 +0000 Subject: [PATCH 1939/9987] Checksum corrected --- .../easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb index 85bd43f78c1..6e386edc292 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb @@ -14,8 +14,8 @@ source_urls = [ sources = ['userApps.v%(version)s.src.tgz'] patches = ['%(name)s-%(version)s-openssl.patch'] checksums = [ - '1edf66ad5f7c8c79586e9f878b5971d7d467c8c5efbeb31c69085d24a6e4671f', # userApps.v422.src.tgz - 'c10e255b18fa6932d8ead725c874fe57dfe8b0a0757758346bb986644337c8bc', # Kent_tools-422-openssl.patch + '1edf66ad5f7c8c79586e9f878b5971d7d467c8c5efbeb31c69085d24a6e4671f', # userApps.v422.src.tgz + 'eedd328fc8a8e01806f4de9e8dce5b2a149edf493a17c3758803853e7881f240', # Kent_tools-422-openssl.patch ] dependencies = [ From 86fd039a1cbb3184580adce0952be7c298d946ed Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 11 Nov 2021 17:59:40 +0100 Subject: [PATCH 1940/9987] add patch for Qt5-5.15.2-GCCcore-11.2.0.eb --- .../q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 2 + .../q/Qt5/Qt5-5.15.2_fix-gcc11.patch | 139 ++++++++++++++++++ 2 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-gcc11.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index 0ae4b2b7fe1..52359f23f25 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -20,12 +20,14 @@ patches = [ 'Qt5-5.13.1_fix-avx2.patch', 'Qt5-5.13.1_fix-qmake-libdir.patch', 'Qt5-5.14.1_fix-OF-Gentoo.patch', + 'Qt5-5.15.2_fix-gcc11.patch', ] checksums = [ '3a530d1b243b5dec00bc54937455471aaa3e56849d2593edb8ded07228202240', # qt-everywhere-src-5.15.2.tar.xz '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch + '6606e2434aacaac49545be733bf012f1d489393bf8bd5573691c171ab8bc0976', # Qt5-5.15.2_fix-gcc11.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-gcc11.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-gcc11.patch new file mode 100644 index 00000000000..0a9ec1a4a99 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-gcc11.patch @@ -0,0 +1,139 @@ +# Qt 5.15.2 build fixes for GCC 11 +# +# Upstream patches: +# https://code.qt.io/cgit/qt/qtbase.git/commit/?id=813a928c7c3cf986 +# https://code.qt.io/cgit/qt/qtbase.git/commit/?id=9c56d4da2ff631a8 +# https://code.qt.io/cgit/qt/qtdeclarative.git/commit/?id=367293b18ab0d0a0 +# +# Third-party software patches (taken from Fedora): +# https://src.fedoraproject.org/rpms/qt5-qtwebengine/blob/rawhide/f/qtwebengine-gcc11.patch +# +diff -Nrup a/qtbase/src/corelib/global/qendian.h b/qtbase/src/corelib/global/qendian.h +--- a/qtbase/src/corelib/global/qendian.h 2020-10-27 09:02:11.000000000 +0100 ++++ b/qtbase/src/corelib/global/qendian.h 2021-06-21 18:02:01.741899258 +0200 +@@ -1,7 +1,7 @@ + /**************************************************************************** + ** +-** Copyright (C) 2016 The Qt Company Ltd. +-** Copyright (C) 2016 Intel Corporation. ++** Copyright (C) 2021 The Qt Company Ltd. ++** Copyright (C) 2021 Intel Corporation. + ** Contact: https://www.qt.io/licensing/ + ** + ** This file is part of the QtCore module of the Qt Toolkit. +@@ -44,6 +44,8 @@ + #include + #include + ++#include ++ + // include stdlib.h and hope that it defines __GLIBC__ for glibc-based systems + #include + #include +diff -Nrup a/qtbase/src/corelib/global/qfloat16.h b/qtbase/src/corelib/global/qfloat16.h +--- a/qtbase/src/corelib/global/qfloat16.h 2020-10-27 09:02:11.000000000 +0100 ++++ b/qtbase/src/corelib/global/qfloat16.h 2021-06-21 18:02:17.409709370 +0200 +@@ -43,6 +43,7 @@ + + #include + #include ++#include + #include + + #if defined(QT_COMPILER_SUPPORTS_F16C) && defined(__AVX2__) && !defined(__F16C__) +diff -Nrup a/qtbase/src/corelib/text/qbytearraymatcher.h b/qtbase/src/corelib/text/qbytearraymatcher.h +--- a/qtbase/src/corelib/text/qbytearraymatcher.h 2020-10-27 09:02:11.000000000 +0100 ++++ b/qtbase/src/corelib/text/qbytearraymatcher.h 2021-06-21 18:13:45.885352546 +0200 +@@ -42,6 +42,8 @@ + + #include + ++#include ++ + QT_BEGIN_NAMESPACE + + +diff -Nrup a/qtbase/src/corelib/tools/qsharedpointer_impl.h b/qtbase/src/corelib/tools/qsharedpointer_impl.h +--- a/qtbase/src/corelib/tools/qsharedpointer_impl.h 2020-10-27 09:02:11.000000000 +0100 ++++ b/qtbase/src/corelib/tools/qsharedpointer_impl.h 2021-06-21 18:13:45.885352546 +0200 +@@ -155,9 +155,6 @@ namespace QtSharedPointer { + #endif + inline void checkQObjectShared(...) { } + inline void setQObjectShared(...) { } +- +- inline void operator delete(void *ptr) { ::operator delete(ptr); } +- inline void operator delete(void *, void *) { } + }; + // sizeof(ExternalRefCountData) = 12 (32-bit) / 16 (64-bit) + +diff -Nrup a/qtbase/src/plugins/platforms/xcb/qxcbwindow.cpp b/qtbase/src/plugins/platforms/xcb/qxcbwindow.cpp +--- a/qtbase/src/plugins/platforms/xcb/qxcbwindow.cpp 2020-10-27 09:02:11.000000000 +0100 ++++ b/qtbase/src/plugins/platforms/xcb/qxcbwindow.cpp 2021-06-21 18:13:45.885352546 +0200 +@@ -698,7 +698,7 @@ void QXcbWindow::show() + if (isTransient(window())) { + const QWindow *tp = window()->transientParent(); + if (tp && tp->handle()) +- transientXcbParent = static_cast(tp->handle())->winId(); ++ transientXcbParent = tp->handle()->winId(); + // Default to client leader if there is no transient parent, else modal dialogs can + // be hidden by their parents. + if (!transientXcbParent) +diff -Nrup a/qtdeclarative/src/qmldebug/qqmlprofilerevent_p.h b/qtdeclarative/src/qmldebug/qqmlprofilerevent_p.h +--- a/qtdeclarative/src/qmldebug/qqmlprofilerevent_p.h 2020-10-27 09:02:12.000000000 +0100 ++++ b/qtdeclarative/src/qmldebug/qqmlprofilerevent_p.h 2021-06-22 09:35:22.877912946 +0200 +@@ -48,6 +48,7 @@ + #include + + #include ++#include + #include + + // +diff -Nrup a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/containers/string_pool.cc b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/containers/string_pool.cc +--- a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/containers/string_pool.cc 2020-11-07 02:22:36.000000000 +0100 ++++ b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/containers/string_pool.cc 2021-06-22 12:05:40.736177321 +0200 +@@ -14,9 +14,9 @@ + * limitations under the License. + */ + ++#include + #include "src/trace_processor/containers/string_pool.h" + +-#include + + #include "perfetto/base/logging.h" + #include "perfetto/ext/base/utils.h" +diff -Nrup a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/db/column.cc b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/db/column.cc +--- a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/db/column.cc 2020-11-07 02:22:36.000000000 +0100 ++++ b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/db/column.cc 2021-06-22 12:06:05.087880649 +0200 +@@ -14,6 +14,7 @@ + * limitations under the License. + */ + ++#include + #include "src/trace_processor/db/column.h" + + #include "src/trace_processor/db/compare.h" +diff -Nrup a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/importers/proto/heap_graph_walker.cc b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/importers/proto/heap_graph_walker.cc +--- a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/importers/proto/heap_graph_walker.cc 2020-11-07 02:22:36.000000000 +0100 ++++ b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/importers/proto/heap_graph_walker.cc 2021-06-22 12:06:28.911590412 +0200 +@@ -14,6 +14,8 @@ + * limitations under the License. + */ + ++#include ++ + #include "src/trace_processor/importers/proto/heap_graph_walker.h" + #include "perfetto/base/logging.h" + +diff -Nrup a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/types/variadic.cc b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/types/variadic.cc +--- a/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/types/variadic.cc 2020-11-07 02:22:36.000000000 +0100 ++++ b/qtwebengine/src/3rdparty/chromium/third_party/perfetto/src/trace_processor/types/variadic.cc 2021-06-22 12:06:52.631301445 +0200 +@@ -14,6 +14,7 @@ + * limitations under the License. + */ + ++#include + #include "src/trace_processor/types/variadic.h" + + namespace perfetto { From d1d18987894bd9b466a5709a03ed2b524760e84b Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 12 Nov 2021 11:35:57 +1050 Subject: [PATCH 1941/9987] dep Biopython + --- .../b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb index 462df6acc1d..db65d146ca3 100644 --- a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.6-foss-2020a-Python-3.8.2.eb @@ -22,6 +22,7 @@ checksums = ['74c6920c91ca18ed9cb872e9471c0be442dad143d8176345917eb1fefc86bc37'] dependencies = [ ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', versionsuffix), + ('Biopython', '1.78', versionsuffix), ] download_dep_fail = True From ba60ef70dfb913cd4c6cf7595a2557e693c44a3b Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 12 Nov 2021 12:59:16 +1050 Subject: [PATCH 1942/9987] adding easyconfigs: CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb --- .../CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..43b4ad38a05 --- /dev/null +++ b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,45 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'CMSeq' +version = '1.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/SegataLab/cmseq/' + +description = """ +CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['c354b89bc4fdbb24fa1ffa063febdb96f2bbd8837af399887b300c9be98bda2e'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Biopython', '1.78', versionsuffix), + ('biom-format', '2.1.10', versionsuffix), + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.12'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +local_bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' +local_targets = ['breadth_depth.py', 'polymut.py', 'poly.py', 'consensus.py'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_targets], + 'dirs': [local_bcbiogffroot], +} + +options = {'modulename': 'cmseq'} + +moduleclass = 'bio' From 9b534cdf6880cd0f73f468af3621dafb76b6c88f Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 12 Nov 2021 13:02:11 +1050 Subject: [PATCH 1943/9987] deps + --- .../MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index f484f3c9d9b..d2b2b7fdc2b 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -27,13 +27,18 @@ toolchain = {'name': 'foss', 'version': '2020a'} dependencies = [ ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', versionsuffix), + ('Biopython', '1.78', versionsuffix), + ('Pysam', '0.16.0.1'), + ('DendroPy', '4.4.0'), + ('CMSeq', '1.0.3', versionsuffix), + ('biom-format', '2.1.10', versionsuffix), + ('h5py', '2.10.0', versionsuffix), ] use_pip = True -use_pip_for_deps = True -sanity_pip_check = True download_dep_fail = False +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']], 'dirs': ['bin', 'lib'], From b54ba3f40f14148ca4b4dad00198196d817b1a83 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 12 Nov 2021 13:34:35 +1050 Subject: [PATCH 1944/9987] dep conflict resolve --- .../easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb index 43b4ad38a05..28eac066d33 100644 --- a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb @@ -25,7 +25,7 @@ dependencies = [ ('Biopython', '1.78', versionsuffix), ('biom-format', '2.1.10', versionsuffix), ('Pysam', '0.16.0.1'), - ('SAMtools', '1.12'), + ('SAMtools', '1.12', '', ('GCC', '9.3.0')), ] download_dep_fail = True From a6cd2a4be522bb42d7c7906488a449d8a656bc59 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 12 Nov 2021 13:41:34 +1050 Subject: [PATCH 1945/9987] dep bug resolve --- .../easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb index 28eac066d33..2250091756b 100644 --- a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb @@ -23,6 +23,7 @@ dependencies = [ ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', versionsuffix), ('Biopython', '1.78', versionsuffix), + ('bcbio-gff', '0.6.6', versionsuffix), ('biom-format', '2.1.10', versionsuffix), ('Pysam', '0.16.0.1'), ('SAMtools', '1.12', '', ('GCC', '9.3.0')), From ed6077f60d46936e9f064cff52aa688320c4e042 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Fri, 12 Nov 2021 08:37:51 +0100 Subject: [PATCH 1946/9987] adding easyconfigs: ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb, ROCT-Thunk-Interface-4.5.0-GCCcore-11.2.0.eb, Clang-AOMP-4.5.0-GCCcore-11.2.0.eb, ROCm-CompilerSupport-4.5.0-GCCcore-11.2.0.eb, rocminfo-4.5.0-GCCcore-11.2.0.eb, rocm-cmake-4.5.0-GCCcore-11.2.0.eb --- .../Clang-AOMP-4.5.0-GCCcore-11.2.0.eb | 66 +++++++++++++++++++ .../ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb | 35 ++++++++++ ...CT-Thunk-Interface-4.5.0-GCCcore-11.2.0.eb | 37 +++++++++++ ...Cm-CompilerSupport-4.5.0-GCCcore-11.2.0.eb | 37 +++++++++++ .../rocm-cmake-4.5.0-GCCcore-11.2.0.eb | 36 ++++++++++ .../rocminfo/rocminfo-4.5.0-GCCcore-11.2.0.eb | 34 ++++++++++ 6 files changed, 245 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/ROCR-Runtime/ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/ROCT-Thunk-Interface/ROCT-Thunk-Interface-4.5.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/ROCm-CompilerSupport/ROCm-CompilerSupport-4.5.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/rocm-cmake/rocm-cmake-4.5.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/rocminfo/rocminfo-4.5.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..40ba47d6d75 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,66 @@ +easyblock = 'EB_Clang_AOMP' + +name = 'Clang-AOMP' +version = '4.5.0' + +homepage = 'https://github.com/RadeonOpenCompute/llvm-project' +description = """AOMP is an open source Clang/LLVM based compiler with added +support for the OpenMP® API on Radeon™ GPUs.""" +docurls = ['https://rocmdocs.amd.com'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('CMake', '3.21.1'), + ('Perl', '5.34.0'), + ('Python', '3.9.6'), + ('elfutils', '0.185'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('ROCR-Runtime', '%(version)s'), + ('ROCT-Thunk-Interface', '%(version)s'), + ('Z3', '4.8.12'), + ('binutils', '2.37'), + ('libffi', '3.4.2'), + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'source_urls': ['https://github.com/RadeonOpenCompute/%(name)s/archive/'], + 'sources': [{ + 'download_filename': '%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz', + }], + 'srcdir': '%(name)s-%(version)s', +} + +components = [ + ('llvm-project', 'rocm-4.5.0', { + 'checksums': ['e33d08c8ae42a3ba394dceb8938263cd14ba45e9603b18f3502c3344814ca296'], + }), + ('ROCm-Device-Libs', 'rocm-4.5.0', { + 'checksums': ['78412fb10ceb215952b5cc722ed08fa82501b5848d599dc00744ae1bdc196f77'], + }), + ('Clang-OpenMP', 'rocm-4.5.0', { + # uses same sources as llvm-project component + 'sources': ['llvm-project-%(version)s.tar.gz'], + 'patches': ['llvm-%(version)s-openmp-remove-hardcoded-source-paths.patch'], + 'checksums': ['e33d08c8ae42a3ba394dceb8938263cd14ba45e9603b18f3502c3344814ca296', + 'efead86cb7e960de1e3f928dbdfdcc367769015d0af1f8f501d344f719148a9c'], + }), + ('aomp-extras', 'rocm-4.5.0', { + 'source_urls': ['https://github.com/ROCm-Developer-Tools/%(name)s/archive/'], + 'patches': ['aomp-extras-%(version)s-remove-hardcoded-devicelib-path.patch'], + 'checksums': ['66d4d0cb4a1a05edb5f13599d8c06de4e10daf561201273cc56dc907139cb894', + 'b833dc3630e5a8f0fb014154aeb48895c9dbd8ad02232a095020694d18d6236a'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/ROCR-Runtime/ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/ROCR-Runtime/ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6b57c85a8a8 --- /dev/null +++ b/easybuild/easyconfigs/r/ROCR-Runtime/ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'ROCR-Runtime' +version = '4.5.0' + +homepage = 'https://github.com/RadeonOpenCompute/ROCR-Runtime' +description = """The user-mode API interfaces and libraries necessary for host +applications to launch compute kernels to available HSA ROCm kernel agents""" +docurls = ['https://rocmdocs.amd.com'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ["https://github.com/RadeonOpenCompute/ROCR-Runtime/archive/refs/tags"] +sources = ["rocm-%(version)s.tar.gz"] +checksums = ['fbf550f243dddfef46a716e360b77c43886fed3eef67215ab9dab1c82f3851ca'] + +dependencies = [ + ('elfutils', '0.185'), + ('ROCT-Thunk-Interface', '%(version)s'), +] +builddependencies = [ + ('CMake', '3.21.1'), +] + +srcdir = "src" + +configopts = "-DIMAGE_SUPPORT=OFF" + +sanity_check_paths = { + 'files': ['include/hsa/amd_hsa_common.h', 'include/hsa/amd_hsa_elf.h', 'include/hsa/hsa.h', + 'lib/libhsa-runtime64.%s' % SHLIB_EXT], + 'dirs': ['hsa/include', 'hsa/lib', 'include/hsa', 'lib/cmake/hsa-runtime64'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/ROCT-Thunk-Interface/ROCT-Thunk-Interface-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/ROCT-Thunk-Interface/ROCT-Thunk-Interface-4.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b2253c71bcc --- /dev/null +++ b/easybuild/easyconfigs/r/ROCT-Thunk-Interface/ROCT-Thunk-Interface-4.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'ROCT-Thunk-Interface' +version = '4.5.0' + +homepage = 'https://github.com/RadeonOpenCompute/ROCT-Thunk-Interface' +description = "The user-mode API interfaces used to interact with the ROCk driver" +docurls = ['https://rocmdocs.amd.com'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ["https://github.com/RadeonOpenCompute/ROCT-Thunk-Interface/archive/refs/tags/"] +sources = ["rocm-%(version)s.tar.gz"] +checksums = ['620b39959e0ee5d709b8cf6eb3cc06c8356d72838343756230c638899b10bb9a'] + +dependencies = [ + ('libdrm', '2.4.107'), + ('numactl', '2.0.14'), +] +builddependencies = [ + ('CMake', '3.21.1'), + ('pkg-config', '0.29.2'), +] + +group = 'video' + +preconfigopts = r"""sed -i 's/\({HSAKMT_LINK_FLAGS}\)" \(-.*\) )/\1 \2" )/g' ../ROCT-*/CMakeLists.txt && """, +installopts = " && cp -a %(builddir)s/%(name)s-rocm-%(version)s/include %(installdir)s/" +configopts = "-DCMAKE_INSTALL_LIBDIR=%(installdir)s/lib -DBUILD_SHARED_LIBS=ON" + +sanity_check_paths = { + 'files': ['include/hsakmt.h', 'include/hsakmttypes.h', 'include/linux/kfd_ioctl.h', + 'lib/libhsakmt.%s' % SHLIB_EXT], + 'dirs': ['lib/cmake/hsakmt', 'share/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/ROCm-CompilerSupport/ROCm-CompilerSupport-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/ROCm-CompilerSupport/ROCm-CompilerSupport-4.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..10f18c50b69 --- /dev/null +++ b/easybuild/easyconfigs/r/ROCm-CompilerSupport/ROCm-CompilerSupport-4.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'ROCm-CompilerSupport' +version = '4.5.0' + +homepage = 'https://github.com/RadeonOpenCompute/ROCm-CompilerSupport' +description = """The compiler support repository provides various Lightning +Compiler related services""" +docurls = ['https://rocmdocs.amd.com'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ["https://github.com/RadeonOpenCompute/ROCm-CompilerSupport/archive/refs/tags/"] +sources = ["rocm-%(version)s.tar.gz"] +checksums = ['03c5880e0922fcff31306f7da2eb9d3a3709d9b5b75b3524dcfae85f4b181678'] + +dependencies = [ + ('Clang-AOMP', '%(version)s'), +] +builddependencies = [ + ('CMake', '3.21.1'), +] + +srcdir = "lib/comgr" + +configopts = '-DCMAKE_C_COMPILER=$EBROOTCLANGMINAOMP/bin/clang' +configopts += ' -DCMAKE_CXX_COMPILER=$EBROOTCLANGMINAOMP/bin/clang++' +configopts += ' -DLLVM_INSTALL_PREFIX=$EBROOTCLANGMINAOMP' +configopts += ' -DLLVM_DIR=$EBROOTCLANGMINAOMP' +configopts += " -DROCM_DIR=%(installdir)s" + +sanity_check_paths = { + 'files': ['include/amd_comgr.h', 'lib64/libamd_comgr.%s' % SHLIB_EXT], + 'dirs': ['lib/cmake', 'share/amd_comgr'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/rocm-cmake/rocm-cmake-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/rocm-cmake/rocm-cmake-4.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..020d124727d --- /dev/null +++ b/easybuild/easyconfigs/r/rocm-cmake/rocm-cmake-4.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'rocm-cmake' +version = '4.5.0' + +homepage = 'https://github.com/RadeonOpenCompute/rocm-cmake' +description = """ROCM cmake modules provides cmake modules for common build +tasks needed for the ROCM software stack""" +docurls = ['https://rocmdocs.amd.com'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ["https://github.com/RadeonOpenCompute/rocm-cmake/archive/refs/tags/"] +sources = ["rocm-%(version)s.tar.gz"] +checksums = ['c77b71454010adbeea5357773aa98dd0725f655f51a411815807cabf29258395'] + +dependencies = [ + ('Clang-AOMP', '%(version)s'), +] +builddependencies = [ + ('CMake', '3.21.1'), +] + +configopts = '-DCMAKE_C_COMPILER=$EBROOTCLANGMINAOMP/bin/clang' +configopts += ' -DCMAKE_CXX_COMPILER=$EBROOTCLANGMINAOMP/bin/clang++' +configopts += ' -DLLVM_INSTALL_PREFIX=$EBROOTCLANGMINAOMP' +configopts += ' -DLLVM_DIR=$EBROOTCLANGMINAOMP' + +sanity_check_paths = { + 'files': ['share/rocm/cmake/ROCMChecks.cmake', 'share/rocm/cmake/ROCMConfig.cmake', + 'share/rocm/cmake/ROCMCppCheck.cmake', 'share/rocm/cmake/ROCMCreatePackage.cmake', + 'share/rocm/cmake/ROCMSetupVersion.cmake'], + 'dirs': ['share/rocm/cmake'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/rocminfo/rocminfo-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/rocminfo/rocminfo-4.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..62978532117 --- /dev/null +++ b/easybuild/easyconfigs/r/rocminfo/rocminfo-4.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'rocminfo' +version = '4.5.0' + +homepage = 'https://github.com/RadeonOpenCompute/rocminfo' +description = """ROCm Application for Reporting System Info""" +docurls = ['https://rocmdocs.amd.com'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ["https://github.com/RadeonOpenCompute/rocminfo/archive/refs/tags/"] +sources = ["rocm-%(version)s.tar.gz"] +checksums = ['421ed55192780eb478f0341fd1ce47a0dd3ffafbec9d7a02109a411878a58ee5'] + +dependencies = [ + ('ROCR-Runtime', '%(version)s'), + ('Python', '3.9.6'), # Needed for 'rocm_agent_enumerator' which is a Python script +] +builddependencies = [ + ('CMake', '3.21.1'), +] + +configopts = "-DCMAKE_EXE_LINKER_FLAGS='-Wl,--disable-new-dtags'" +configopts += " -DROCRTST_BLD_TYPE=Release" +configopts += " -DROCM_DIR=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/rocminfo', 'bin/rocm_agent_enumerator'], + 'dirs': ['bin'], +} +sanity_check_commands = ['rocminfo --help', 'rocm_agent_enumerator'] + +moduleclass = 'tools' From 79d818bfdc7216b9aeff116f5b75b3bb63f4f90e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Fri, 12 Nov 2021 08:45:04 +0100 Subject: [PATCH 1947/9987] Include required patches --- .../Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb | 4 ++-- ...mp-extras-remove-hardcoded-devicelib-path.patch | 10 ++++++++++ ....5.0-openmp-remove-hardcoded-source-paths.patch | 14 ++++++++++++++ 3 files changed, 26 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-aomp-extras-remove-hardcoded-devicelib-path.patch create mode 100644 easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-openmp-remove-hardcoded-source-paths.patch diff --git a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb index 40ba47d6d75..d6063184265 100644 --- a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb @@ -51,13 +51,13 @@ components = [ ('Clang-OpenMP', 'rocm-4.5.0', { # uses same sources as llvm-project component 'sources': ['llvm-project-%(version)s.tar.gz'], - 'patches': ['llvm-%(version)s-openmp-remove-hardcoded-source-paths.patch'], + 'patches': ['clang-aomp-%(version)s-openmp-remove-hardcoded-source-paths.patch'], 'checksums': ['e33d08c8ae42a3ba394dceb8938263cd14ba45e9603b18f3502c3344814ca296', 'efead86cb7e960de1e3f928dbdfdcc367769015d0af1f8f501d344f719148a9c'], }), ('aomp-extras', 'rocm-4.5.0', { 'source_urls': ['https://github.com/ROCm-Developer-Tools/%(name)s/archive/'], - 'patches': ['aomp-extras-%(version)s-remove-hardcoded-devicelib-path.patch'], + 'patches': ['clang-aomp-%(version)s-aomp-extras-remove-hardcoded-devicelib-path.patch'], 'checksums': ['66d4d0cb4a1a05edb5f13599d8c06de4e10daf561201273cc56dc907139cb894', 'b833dc3630e5a8f0fb014154aeb48895c9dbd8ad02232a095020694d18d6236a'], }), diff --git a/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-aomp-extras-remove-hardcoded-devicelib-path.patch b/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-aomp-extras-remove-hardcoded-devicelib-path.patch new file mode 100644 index 00000000000..ef5a2cf84ed --- /dev/null +++ b/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-aomp-extras-remove-hardcoded-devicelib-path.patch @@ -0,0 +1,10 @@ +--- aomp-extras-rocm-4.5.0/aomp-device-libs/CMakeLists.txt.orig 2021-10-11 09:35:05.007403780 +0200 ++++ aomp-extras-rocm-4.5.0/aomp-device-libs/CMakeLists.txt 2021-10-11 09:35:18.386175357 +0200 +@@ -27,7 +27,6 @@ + # set(CMAKE_INSTALL_PREFIX ${CMAKE_BINARY_DIR}/dist CACHE INTERNAL "Prefix prepended to install directories") + #endif() + +-set(ROCDL "${CMAKE_CURRENT_SOURCE_DIR}/../../rocm-device-libs") + + find_package(LLVM REQUIRED CONFIG HINTS ${LLVM_DIR}) + list(APPEND CMAKE_MODULE_PATH ${LLVM_CMAKE_DIR}) diff --git a/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-openmp-remove-hardcoded-source-paths.patch b/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-openmp-remove-hardcoded-source-paths.patch new file mode 100644 index 00000000000..dc301e3e2d5 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-openmp-remove-hardcoded-source-paths.patch @@ -0,0 +1,14 @@ +--- llvm-project-rocm-4.5.0/openmp/libomptarget/deviceRTLs/amdgcn/CMakeLists.txt.orig 2021-11-11 14:31:55.835361003 +0100 ++++ llvm-project-rocm-4.5.0/openmp/libomptarget/deviceRTLs/amdgcn/CMakeLists.txt 2021-11-11 14:32:14.624217685 +0100 +@@ -49,11 +49,9 @@ + else() + message("------------- STANDALONE BUILD ---------------") + # Assome rocm-device-libs repository is next to amd-llvm-project repository +- set(ROCDL ${CMAKE_CURRENT_SOURCE_DIR}/../../../../../rocm-device-libs) + set(ROCDL_INC_OCKL ${ROCDL}/ockl/inc) + set(ROCDL_INC_OCML ${ROCDL}/ocml/inc) + set(ROCDL_INC_IRIF ${ROCDL}/irif/inc) +- set(HIPINC ${CMAKE_CURRENT_SOURCE_DIR}/../../../../../hip-on-vdi/include) + endif() + + project(omptarget-amdgcn) From 55fbe1c1f41edfe93d05d760d7f18cd29356c679 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 12 Nov 2021 12:19:21 +0200 Subject: [PATCH 1948/9987] add StatMatch, leaflet, tmap and collapse to R v4.1.0 --- .../easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 51 ++++++++++++++++--- 1 file changed, 45 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index f2e6bc262d0..18b599702aa 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -79,21 +79,15 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 3rd June 2021 exts_list = [ - # include packages that are part of the base installation of R, - # both to make sure they are available (via sanity check), - # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', - 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', - 'parallel', 'splines', 'stats', 'stats4', - 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9.1', { @@ -3009,6 +3003,51 @@ exts_list = [ ('momentfit', '0.2', { 'checksums': ['a10d43ac23bb61b9c67efa4800e3e2b6a444c1afaca8bad351648accd7e003f6'], }), + ('StatMatch', '1.4.0', { + 'checksums': ['820091cd2213734ea16f5fcd616491bbf39d3e6c2bcfb34a7c9fe09f4fd1a459'], + }), + ('stars', '0.5-3', { + 'checksums': ['44944a82af36bea09ac1874ff9647acbb7fef021ebdca5aae7c34794be929401'], + }), + ('rapidjsonr', '1.2.0', { + 'checksums': ['62c94fcdcf5d0fbdfa2f6168affe526bf547c37c16d94e2e1b78d7bf608eed1f'], + }), + ('jsonify', '1.2.1', { + 'checksums': ['929191ab32e34af6a02ad991e29314cc78ea40763fcf232388ef2d132137fbce'], + }), + ('geometries', '0.2.0', { + 'checksums': ['8cf5094f3c2458fef5d755799c766afd27c66cd1c292574a6ab532d608360314'], + }), + ('sfheaders', '0.4.0', { + 'checksums': ['86bcd61018a0491fc8a1e7fb0422c918296287b82be299a79ccee8fcb515e045'], + }), + ('geojsonsf', '2.0.1', { + 'checksums': ['42df40433bfbece5a39cd97b5bd4690b4424855241fcc3e7322ee68a3988bfbf'], + }), + ('leaflet.providers', '1.9.0', { + 'checksums': ['9e8fc75c83313ab24663c2e718135459599549ed6e7396086cacb44e36cfd67b'], + }), + ('leaflet', '2.0.4.1', { + 'checksums': ['b0f038295f1de5d32d9ffa1d0dbc1562320190f2f1365f3a5e95863fff88901f'], + }), + ('leafsync', '0.1.0', { + 'checksums': ['7d8fd8dbbbf66417cf32575f14c0fe68199762ecf1c036c7905c7c5ff859d75c'], + }), + ('leafem', '0.1.6', { + 'checksums': ['ca50e0a699f564449248511857a2df0d48cd07de3157e099478a19b533088156'], + }), + ('widgetframe', '0.3.1', { + 'checksums': ['44089a2cf8b0941a6f3da55da36353e2f44653ca58bfec7960ee5b71ea380d48'], + }), + ('tmaptools', '3.1-1', { + 'checksums': ['fd89cb0d7fb44e0a5dd5311fa3e75a729746bf2e8e158d5ec423e5963f1b542d'], + }), + ('tmap', '3.3-2', { + 'checksums': ['2bcb74c5c5546223d79abe5d633581fb2664b910f6246f4b8b7166b208b4629a'], + }), + ('collapse', '1.6.5', { + 'checksums': ['1e232a3a62b5eb5ed5d81e7d92ce1bae34c3d877d593d47d7edbd3f515b95a46'], + }), ] moduleclass = 'lang' From 1321d0ee79bff4ce92cb7c50505fdf918fa25cd9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 12 Nov 2021 12:20:47 +0200 Subject: [PATCH 1949/9987] add StatMatch, leaflet, tmap and collapse to R v4.1.2 --- .../easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 66e25a36ddc..ad540db5316 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3081,6 +3081,51 @@ exts_list = [ ('momentfit', '0.2', { 'checksums': ['a10d43ac23bb61b9c67efa4800e3e2b6a444c1afaca8bad351648accd7e003f6'], }), + ('StatMatch', '1.4.0', { + 'checksums': ['820091cd2213734ea16f5fcd616491bbf39d3e6c2bcfb34a7c9fe09f4fd1a459'], + }), + ('stars', '0.5-3', { + 'checksums': ['44944a82af36bea09ac1874ff9647acbb7fef021ebdca5aae7c34794be929401'], + }), + ('rapidjsonr', '1.2.0', { + 'checksums': ['62c94fcdcf5d0fbdfa2f6168affe526bf547c37c16d94e2e1b78d7bf608eed1f'], + }), + ('jsonify', '1.2.1', { + 'checksums': ['929191ab32e34af6a02ad991e29314cc78ea40763fcf232388ef2d132137fbce'], + }), + ('geometries', '0.2.0', { + 'checksums': ['8cf5094f3c2458fef5d755799c766afd27c66cd1c292574a6ab532d608360314'], + }), + ('sfheaders', '0.4.0', { + 'checksums': ['86bcd61018a0491fc8a1e7fb0422c918296287b82be299a79ccee8fcb515e045'], + }), + ('geojsonsf', '2.0.1', { + 'checksums': ['42df40433bfbece5a39cd97b5bd4690b4424855241fcc3e7322ee68a3988bfbf'], + }), + ('leaflet.providers', '1.9.0', { + 'checksums': ['9e8fc75c83313ab24663c2e718135459599549ed6e7396086cacb44e36cfd67b'], + }), + ('leaflet', '2.0.4.1', { + 'checksums': ['b0f038295f1de5d32d9ffa1d0dbc1562320190f2f1365f3a5e95863fff88901f'], + }), + ('leafsync', '0.1.0', { + 'checksums': ['7d8fd8dbbbf66417cf32575f14c0fe68199762ecf1c036c7905c7c5ff859d75c'], + }), + ('leafem', '0.1.6', { + 'checksums': ['ca50e0a699f564449248511857a2df0d48cd07de3157e099478a19b533088156'], + }), + ('widgetframe', '0.3.1', { + 'checksums': ['44089a2cf8b0941a6f3da55da36353e2f44653ca58bfec7960ee5b71ea380d48'], + }), + ('tmaptools', '3.1-1', { + 'checksums': ['fd89cb0d7fb44e0a5dd5311fa3e75a729746bf2e8e158d5ec423e5963f1b542d'], + }), + ('tmap', '3.3-2', { + 'checksums': ['2bcb74c5c5546223d79abe5d633581fb2664b910f6246f4b8b7166b208b4629a'], + }), + ('collapse', '1.6.5', { + 'checksums': ['1e232a3a62b5eb5ed5d81e7d92ce1bae34c3d877d593d47d7edbd3f515b95a46'], + }), ] moduleclass = 'lang' From 2866f670bc03ae9f9a0b30a8c35d1abc2b373a5f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 12 Nov 2021 11:24:57 +0100 Subject: [PATCH 1950/9987] sync with branch 'develop' --- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index 18b599702aa..d25b1a5f6ff 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -79,15 +79,21 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 3rd June 2021 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', + 'compiler', 'datasets', 'graphics', 'grDevices', 'grid', 'methods', + 'parallel', 'splines', 'stats', 'stats4', + 'tcltk', 'tools', 'utils', ('Rmpi', '0.6-9.1', { From b8cb4ae4748c8c33c35c095cae6cbaa702f45d97 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 12 Nov 2021 12:15:48 +0100 Subject: [PATCH 1951/9987] adding easyconfigs: matplotlib-3.4.3-foss-2021b.eb, matplotlib-3.4.3-intel-2021b.eb, cppy-1.1.0-GCCcore-11.2.0.eb --- .../c/cppy/cppy-1.1.0-GCCcore-11.2.0.eb | 29 +++++++++ .../matplotlib/matplotlib-3.4.3-foss-2021b.eb | 64 +++++++++++++++++++ .../matplotlib-3.4.3-intel-2021b.eb | 64 +++++++++++++++++++ 3 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c117ab10281 --- /dev/null +++ b/easybuild/easyconfigs/c/cppy/cppy-1.1.0-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'cppy' +version = '1.1.0' + +homepage = "https://github.com/nucleic/cppy" +description = """A small C++ header library which makes it easier to write +Python extension modules. The primary feature is a PyObject smart pointer +which automatically handles reference counting and provides convenience +methods for performing common object operations.""" + + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), +] + +source_urls = ['https://github.com/nucleic/cppy/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['40a9672df1ec2d7f0b54f70e574101f42131c0f5e47980769f68085e728a4934'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb new file mode 100644 index 00000000000..5eefa7f3e9c --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.4.3' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('cppy', '1.1.0') +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('libpng', '1.6.37'), + ('freetype', '2.11.0'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.3.1'), + ('Qhull', '2020.2') +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' setup.cfg.template >setup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('Cycler', '0.11.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], + }), + ('kiwisolver', '1.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['fc4453705b81d03568d5b808ad8f09c77c47534f6ac2e72e733f9ca4714aa75c'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['fc4f526dfdb31c9bd6b8ca06bf9fab663ca12f3ec9cdf4496fb44bc680140318'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb new file mode 100644 index 00000000000..51d59ef7c45 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.4.3' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('cppy', '1.1.0') +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('libpng', '1.6.37'), + ('freetype', '2.11.0'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.3.1'), + ('Qhull', '2020.2') +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' setup.cfg.template >setup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('Cycler', '0.11.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], + }), + ('kiwisolver', '1.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['fc4453705b81d03568d5b808ad8f09c77c47534f6ac2e72e733f9ca4714aa75c'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['fc4f526dfdb31c9bd6b8ca06bf9fab663ca12f3ec9cdf4496fb44bc680140318'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From 8bf738aa0b7afb96f1ed2655a2d827a80a182765 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 12 Nov 2021 12:22:12 +0100 Subject: [PATCH 1952/9987] adding easyconfigs: xarray-0.20.1-foss-2021b.eb, xarray-0.20.1-intel-2021b.eb --- .../x/xarray/xarray-0.20.1-foss-2021b.eb | 25 +++++++++++++++++++ .../x/xarray/xarray-0.20.1-intel-2021b.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.20.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.20.1-intel-2021b.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.20.1-foss-2021b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.20.1-foss-2021b.eb new file mode 100644 index 00000000000..873aeb34d06 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.20.1-foss-2021b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.20.1' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9c0bffd8b55fdef277f8f6c817153eb51fa4e58653a7ad92eaed9984164b7bdb'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.20.1-intel-2021b.eb b/easybuild/easyconfigs/x/xarray/xarray-0.20.1-intel-2021b.eb new file mode 100644 index 00000000000..ff076effdda --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.20.1-intel-2021b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.20.1' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9c0bffd8b55fdef277f8f6c817153eb51fa4e58653a7ad92eaed9984164b7bdb'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From 60dacc58efba84c8f96765341442a7e6a8b8612a Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 12 Nov 2021 12:52:45 +0000 Subject: [PATCH 1953/9987] adding easyconfigs: GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb --- .../GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb new file mode 100644 index 00000000000..cd0447168d9 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.2.3.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['12fbd03142311419a050dba8009d615ee8faceb32b46aad8f4448dafd61e11eb'] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.9.6'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +modloadmsg = "WARNING: GATK v%(version)s support for Java 11 is in beta state. Use at your own risk.\n" + +moduleclass = 'bio' From 1cfe70d2965e8574446a58b7ddad621542dd1634 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 12 Nov 2021 23:38:09 +0200 Subject: [PATCH 1954/9987] adding easyconfigs: jax-0.2.24-foss-2021a-CUDA-11.3.1.eb, jax-0.2.24-foss-2021a.eb --- .../jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb | 118 ++++++++++++++++++ .../j/jax/jax-0.2.24-foss-2021a.eb | 111 ++++++++++++++++ 2 files changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..fbbad89cbc9 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,118 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.2.24' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('pytest-xdist', '2.3.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.32.0', '-nodocs'), +] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', versionsuffix, True), + ('NCCL', '2.10.3', versionsuffix), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.0'), +] + +# running the tests with lots of cores results in test failures because not enough threads can be started, +# and running with a single core also results in systematic test failures +# 4 cores seems to work best +parallel = 4 + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = 'e98b052c08e5d1e7906ac2f6caf95c51a1e04985' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '0.15.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], + }), + ('jaxlib', '0.1.73', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + 'jaxlib-0.1.70_add-bazel-args-to-shutdown.patch', + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.1.73.tar.gz + '4cb1a7a9881c6566cf6d0d88f70ba2b8732e8b1dc6010da7deaff399f21873ed', + # tensorflow-e98b052c08e5d1e7906ac2f6caf95c51a1e04985.tar.gz + 'b2c8b912e7be71306ab6fee063fb4ec1dfbe7158e7e8469d674f8af6583434d4', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': ['jax-0.2.19_fix-update-of-cache-access-time.patch'], + 'checksums': [ + # jax-v0.2.24.tar.gz + '9ffbf86e97a05591eaa1a7a5194cf9ceaed8cf6c2aaa8ffc394568a3a131cae0', + # jax-0.2.19_fix-update-of-cache-access-time.patch + 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + ], + 'runtest': "CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a.eb b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a.eb new file mode 100644 index 00000000000..e5f4479dc5d --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a.eb @@ -0,0 +1,111 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.2.24' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('pytest-xdist', '2.3.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.32.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.0'), +] + +# running the tests with lots of cores results in test failures because not enough threads can be started, +# and running with a single core also results in systematic test failures +# 4 cores seems to work best +parallel = 4 + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = 'e98b052c08e5d1e7906ac2f6caf95c51a1e04985' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '0.15.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], + }), + ('jaxlib', '0.1.73', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + 'jaxlib-0.1.70_add-bazel-args-to-shutdown.patch', + ], + 'checksums': [ + # jaxlib-v0.1.73.tar.gz + '4cb1a7a9881c6566cf6d0d88f70ba2b8732e8b1dc6010da7deaff399f21873ed', + # tensorflow-e98b052c08e5d1e7906ac2f6caf95c51a1e04985.tar.gz + 'b2c8b912e7be71306ab6fee063fb4ec1dfbe7158e7e8469d674f8af6583434d4', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': ['jax-0.2.19_fix-update-of-cache-access-time.patch'], + 'checksums': [ + # jax-v0.2.24.tar.gz + '9ffbf86e97a05591eaa1a7a5194cf9ceaed8cf6c2aaa8ffc394568a3a131cae0', + # jax-0.2.19_fix-update-of-cache-access-time.patch + 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + ], + 'runtest': "pytest -n %(parallel)s tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 02379095eadd8858461ad65cba2cf181cd4013a3 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 12 Nov 2021 21:44:18 +0000 Subject: [PATCH 1955/9987] Remove imkl builddependency from FlexiBLAS. Closes #14332 --- .../easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index d3cb0d26073..be4c7f1997f 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -17,7 +17,6 @@ builddependencies = [ ('CMake', '3.21.1'), ('Python', '3.9.6'), # required for running the tests ('BLIS', '0.8.1'), - ('imkl', {'arch=x86_64': '2021.4.0', 'arch=*': False}, '', True), ] dependencies = [ @@ -27,7 +26,5 @@ dependencies = [ # note: first listed backend will be used as default by FlexiBLAS, # unless otherwise specified via easyconfig parameter flexiblas_default backends = ['OpenBLAS', 'BLIS'] -if ARCH == 'x86_64': - backends.append('imkl') moduleclass = 'lib' From 0ce264e33c44e78820019281843b5bf9330f5ec5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 12 Nov 2021 22:56:26 +0100 Subject: [PATCH 1956/9987] add sed script to patch tensorflow repo in jaxlib --- .../j/jax/jaxlib_local-tensorflow-repo.sed | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jaxlib_local-tensorflow-repo.sed diff --git a/easybuild/easyconfigs/j/jax/jaxlib_local-tensorflow-repo.sed b/easybuild/easyconfigs/j/jax/jaxlib_local-tensorflow-repo.sed new file mode 100644 index 00000000000..1116ca24ca9 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jaxlib_local-tensorflow-repo.sed @@ -0,0 +1,12 @@ +/^http_archive(/{ + :a;N;/\n)/!ba; + /org_tensorflow/{ + s/^/# /; + s/\n/\n# /g; + s|$|\ +local_repository(\ + name = "org_tensorflow",\ + path = "EB_TF_REPOPATH",\ +)|; + } +} From 7332bacd685411fc8828647d03af2f93c0714e62 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 12 Nov 2021 22:57:13 +0100 Subject: [PATCH 1957/9987] add patch to fix canonical include paths in TensorFlow v2.7.0 --- ....7.0_cuda-noncanonical-include-paths.patch | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch diff --git a/easybuild/easyconfigs/j/jax/TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch b/easybuild/easyconfigs/j/jax/TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch new file mode 100644 index 00000000000..93157c49ad0 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch @@ -0,0 +1,20 @@ +Use non-canonical paths to populate the include paths in the toolchain in Bazel. +Otherwise, build will fail due to mismatch in include paths. +author: Alex Domingo (Vrije Universiteit Brussel) +--- third_party/gpus/cuda_configure.bzl.orig 2021-10-25 11:48:32.896463000 +0200 ++++ third_party/gpus/cuda_configure.bzl 2021-10-25 11:51:56.719009257 +0200 +@@ -274,8 +274,12 @@ + sysroot = [] + if tf_sysroot: + sysroot += ["--sysroot", tf_sysroot] +- result = raw_exec(repository_ctx, [cc, "-E", "-x" + lang, "-", "-v"] + +- sysroot) ++ ++ result = raw_exec( ++ repository_ctx, ++ [cc, "-no-canonical-prefixes", "-E", "-x" + lang, "-", "-v"] + sysroot ++ ) ++ + stderr = err_out(result) + index1 = stderr.find(_INC_DIR_MARKER_BEGIN) + if index1 == -1: From b387f03d35b143980b72f0971f8f42f0aadb864e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 13 Nov 2021 19:57:36 +0100 Subject: [PATCH 1958/9987] adding easyconfigs: Python-2.7.18-GCCcore-11.2.0-bare.eb --- .../Python-2.7.18-GCCcore-11.2.0-bare.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb new file mode 100644 index 00000000000..1975150da07 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb @@ -0,0 +1,32 @@ +name = 'Python' +version = '2.7.18' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('binutils', '2.37'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('SQLite', '3.36'), + ('OpenSSL', '1.1', '', True), +] + +install_pip = True + +moduleclass = 'lang' From e6dd0a41b31f37d41002fcff583e52aa6519a8dc Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 13 Nov 2021 21:13:30 +0100 Subject: [PATCH 1959/9987] update Qt5-5.15.2-GCCcore-11.2.0.eb: Downgrade to Python/2.7.18-bare as Python2 is a build dependecy for Qt5WebEngine --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index 52359f23f25..2d43727ea14 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -38,7 +38,8 @@ builddependencies = [ ('flex', '2.6.4'), ('gperf', '3.1'), ('Ninja', '1.10.2'), - ('Python', '3.9.6', '-bare'), + # Qt5WebEngine has build dependency on Python 2 + ('Python', '2.7.18', '-bare'), ('re2c', '2.2'), ] From d5c0cc806382aa583dd7edd9b10028534ec6b8a9 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 15 Nov 2021 12:59:23 +0100 Subject: [PATCH 1960/9987] Added QCG-PilotJob --- .../k/Kaleido/Kaleido-0.2.1-GCCcore-10.3.0.eb | 25 +++++++ .../p/PyZMQ/PyZMQ-22.3.0-GCCcore-10.3.0.eb | 28 ++++++++ .../q/QCGPilotJob/QCGPilotJob-0.12.3.eb | 68 +++++++++++++++++++ 3 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-22.3.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..2f09b3ca33d --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Kaleido' +version = '0.2.1' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = ['kaleido-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl'] +checksums = ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-22.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-22.3.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..de5166f57a6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-22.3.0-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '22.3.0' + +homepage = 'https://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8eddc033e716f8c91c6a2112f0a8ebc5e00532b4a6ae1eb0ccc48e027f9c671c'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('ZeroMQ', '4.3.4'), +] + +options = {'modulename': 'zmq'} + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb new file mode 100644 index 00000000000..88913eb6d99 --- /dev/null +++ b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb @@ -0,0 +1,68 @@ +easyblock = 'PythonBundle' + +name = 'QCG-PilotJob' +version = '0.12.3' + +homepage = 'https://qcg-pilotjob.readthedocs.org' +description = """A python service for easy execution of many tasks inside a single allocation.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyZMQ', '22.3.0'), + ('Kaleido', '0.2.1'), + ('plotly.py', '5.1.0'), +] + +download_dep_fail = True +use_pip = True + +# Disable sanity check because `zmq` has an invalid version. +sanity_pip_check = False + +exts_list = [ + ('zmq', '0.0.0', { + 'sources': [{ + 'filename': 'zmq-0.0.0.tar.gz', + 'download_filename': 'zmq.tar.gz', + }], + 'checksums': ['6b1a1de53338646e8c8405803cffb659e8eb7bb02fff4c9be62a7acfac8370c9'], + }), + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + ('statsmodels', '0.13.0', { + 'checksums': ['f2efc02011b7240a9e851acd76ab81150a07d35c97021cb0517887539a328f8a'], + }), + ('plotly_express', '0.4.1', { + 'checksums': ['ff73a41ce02fb43d1d8e8fa131ef3e6589857349ca216b941b8f3f862bce0278'], + }), + ('prompt_toolkit', '3.0.21', { + 'checksums': ['27f13ff4e4850fe8f860b77414c7880f67c6158076a7b099062cc8570f1562e5'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('qcg', '0.12.3', { + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'start_dir': 'components/core', + }), + ('qcg', '0.12.3', { + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'start_dir': 'components/cmds', + }), + ('qcg', '0.12.3', { + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'start_dir': 'components/executor_api', + }), +] + +moduleclass = 'tools' From d46896c8393a3d44190bc0aa9f829e7c86463305 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Nov 2021 13:59:36 +0100 Subject: [PATCH 1961/9987] {bio}[foss/2020b] antiSMASH v6.0.1, GlimmerHMM v3.0.4c, HMMER2 v2.3.2 w/ Python 3.8.6 --- .../a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb | 84 +++++++++++++++++++ .../GlimmerHMM-3.0.4c-GCC-10.2.0.eb | 45 ++++++++++ .../h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb | 27 ++++++ 3 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb new file mode 100644 index 00000000000..57cfc9ef196 --- /dev/null +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-6.0.1-foss-2020b.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'antiSMASH' +version = '6.0.1' + +homepage = 'https://github.com/antismash/antismash' +description = """antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary + metabolite biosynthesis gene clusters in bacterial and fungal genomes.""" + +docurls = ['https://docs.antismash.secondarymetabolites.org'] + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('DIAMOND', '2.0.7'), + ('FastTree', '2.1.11'), + ('GlimmerHMM', '3.0.4c'), + ('HMMER2', '2.3.2'), + ('HMMER', '3.3.2'), + ('MUSCLE', '3.8.31'), + ('BLAST+', '2.11.0'), + ('prodigal', '2.6.3'), + ('Biopython', '1.78'), + ('matplotlib', '3.3.3'), + ('scikit-learn', '0.23.2'), +] + +# install MEME as a component in this installation, +# since antiSMASH requires very specific old version +# see https://docs.antismash.secondarymetabolites.org/install/#full-manual-install +components = [ + ('MEME', '5.4.0', { + 'source_urls': ['http://meme-suite.org/meme-software/%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['e446baf78ce8f9b9dc72723bc91c1d60523174a862af19971a92332a7298d56e'], + 'easyblock': 'ConfigureMake', + 'start_dir': 'meme-%(version)s', + }), +] + +use_pip = True + +exts_list = [ + ('helperlibs', '0.2.1', { + 'checksums': ['4ec2a0c17fdb75c42c692c5ec582580c14490c31235af5858ec12ad308265732'], + }), + ('pysvg-py3', '0.2.2.post3', { + 'modulename': 'pysvg', + 'checksums': ['a1183aa5d89871298c11f25d28640edc3798b6ed1e2b2a95c30d35985d6431d0'], + }), + ('bcbio-gff', '0.6.8', { + 'modulename': 'BCBio.GFF', + 'checksums': ['8578d3c917a81e39898fa588e969c934fb942c2f3e11c275fa492c679a5f36a1'], + }), + ('pyScss', '1.3.7', { + 'modulename': 'scss', + 'checksums': ['f1df571569021a23941a538eb154405dde80bed35dc1ea7c5f3e18e0144746bf'], + }), + (name, version, { + 'source_tmpl': '6-0-1.tar.gz', + 'source_urls': ['https://github.com/antismash/antismash/archive/'], + 'checksums': ['3bd162f44e61ed68efb1d5e98968bdf80691b5d8382eecd66257a6f3a2703de7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/antismash', 'bin/meme'], + 'dirs': [], +} + +sanity_check_commands = [ + # 'meme -h' exits with non-zero exit status, so use 'grep' to check for pattern + "meme -h 2>&1 | grep 'Usage:[ \t]*meme'", + "antismash --version", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb new file mode 100644 index 00000000000..947e4cda9a7 --- /dev/null +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-10.2.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GlimmerHMM' +version = '3.0.4c' + +homepage = 'https://ccb.jhu.edu/software/glimmerhmm' +description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. + Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally + it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted + from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] +sources = [SOURCE_TAR_GZ] +checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] + +start_dir = 'sources' + +# make sure -O0 is not used as compiler option +prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && " + +# also build in 'train' subdirectory to overwrite pre-compiled binaries +buildopts = "&& cd ../train && make" + +local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp', + 'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP', + 'scoreSTOP2', 'splicescore', 'trainGlimmerHMM'] +files_to_copy = [ + (['sources/%(namelower)s'], 'bin'), + (['train/%s' % x for x in local_train_files], 'bin'), + 'trained_dir', 'README', 'train/readme.train', +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['trained_dir'], +} + +sanity_check_commands = [('%(namelower)s -h')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb new file mode 100644 index 00000000000..496d7c1314c --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER2/HMMER2-2.3.2-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'HMMER2' +version = '2.3.2' + +homepage = 'http://hmmer.org' +description = """HMMER is used for searching sequence databases for sequence homologs, + and for making sequence alignments.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['http://eddylab.org/software/hmmer'] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4'] + +postinstallcmds = ["cd %(installdir)s/bin && for cmd in $(ls); do mv ${cmd} ${cmd}2; done"] + +local_cmd_suffixes = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'index', 'pfam', 'search'] + +sanity_check_paths = { + 'files': ['bin/hmm%s2' % x for x in local_cmd_suffixes], + 'dirs': ['man'], +} + +sanity_check_commands = ["hmm%s2 -h" % x for x in local_cmd_suffixes] + +moduleclass = 'bio' From 7cd4cafe115a0a683ba065ca48e8a4f712d12418 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Mon, 15 Nov 2021 14:01:33 +0100 Subject: [PATCH 1962/9987] adding easyconfigs: HIP-4.5.0-GCCcore-11.2.0-amd.eb --- .../h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb | 93 +++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb diff --git a/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb new file mode 100644 index 00000000000..08836323e6d --- /dev/null +++ b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb @@ -0,0 +1,93 @@ +easyblock = 'CMakeMake' + +name = 'HIP' +version = '4.5.0' +versionsuffix = '-amd' + +homepage = 'https://github.com/ROCm-Developer-Tools/HIP' +description = """HIP is a C++ Runtime API and Kernel Language that allows +developers to create portable applications for AMD and NVIDIA GPUs from single +source code.""" +docurls = ['https://rocmdocs.amd.com'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + "https://github.com/ROCm-Developer-Tools/hipamd/archive/", + "https://github.com/ROCm-Developer-Tools/ROCclr/archive/", + "https://github.com/ROCm-Developer-Tools/HIP/archive/", + "https://github.com/RadeonOpenCompute/ROCm-OpenCL-Runtime/archive/", +] +sources = [ + 'hipamd-rocm-%(version)s.tar.gz', + 'ROCclr-rocm-%(version)s.tar.gz', + 'HIP-rocm-%(version)s.tar.gz', + 'ROCm-OpenCL-Runtime-rocm-%(version)s.tar.gz', +] + +patches = ['hipamd-rocm-%(version)s-remove-testing.patch'] + +checksums = [ + '7b93ab64d6894ff9b5ba0be35e3ed8501d6b18a2a14223d6311d72ab8a9cdba6', # hipamd-rocm-4.5.0.tar.gz + 'ca8d6305ff0e620d9cb69ff7ac3898917db9e9b6996a7320244b48ab6511dd8e', # ROCclr-rocm-4.5.0.tar.gz + '4026f31fb4f8050e9aa9d4294f29c3410bfb38422dbbae4236ccd65fed4d55b2', # HIP-rocm-4.5.0.tar.gz + '3a163aed24619b3faf5e8ba17325bdcedd1667a904ea20914ac6bdd33fcdbca8', # ROCm-OpenCL-Runtime-rocm-4.5.0.tar.gz + 'b70636c7853c74d1fca3c71b73d48ff3a2c66d09382b2378900ee47f25ed2ae1', # hipamd-4.5.0-remove-testing.patch +] + +dependencies = [ + ('Clang-AOMP', '%(version)s'), + ('Perl', '5.34.0'), + ('ROCR-Runtime', '%(version)s'), + ('ROCm-CompilerSupport', '%(version)s'), + ('libglvnd', '1.3.3'), + ('libxml2', '2.9.10'), + ('numactl', '2.0.14'), + ('rocm-cmake', '%(version)s'), + ('rocminfo', '%(version)s'), + ('zlib', '1.2.11'), +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +# AMD uses 'gfx' to identify the GPU, the first number identifies the generation, according to +# https://www.x.org/wiki/RadeonFeature/#index5h2 while the rest identifies the specific GPU. +# In the context of EasyBuild this identifier can be thought of as equivalent to the 'sm_' +# nomenclature of Nvidia. +local_default_gfx = 'gfx900' + +configopts = "-DAMD_OPENCL_PATH=%(builddir)s/ROCm-OpenCL-Runtime-rocm-%(version)s/" +configopts += " -DHIP_COMMON_DIR=%(builddir)s/HIP-rocm-%(version)s/" +configopts += " -DHIP_PLATFORM=amd" +configopts += " -DOFFLOAD_ARCH_STR='%s'" % local_default_gfx +configopts += " -DROCCLR_PATH=%(builddir)s/ROCclr-rocm-%(version)s/" + +postinstallcmds = [ + 'sed -i "s|HIP_CLANG_INCLUDE_PATH = .*|' + 'HIP_CLANG_INCLUDE_PATH = \\$ENV{\"HIP_CLANG_INCLUDE_PATH\"};|g" %(installdir)s/bin/hipcc', + 'sed -i "s|ROCM_AGENT_ENUM = .*|ROCM_AGENT_ENUM = \"rocm_agent_enumerator\";|g" %(installdir)s/bin/hipcc', +] + +sanity_check_paths = { + 'files': ['bin/hipcc', 'bin/hipconfig', 'include/hip/hip_common.h', 'include/hip/hip_runtime.h', + 'lib/libamdhip64.%s' % SHLIB_EXT], + 'dirs': ['bin', 'cmake', 'include/hip'], +} +sanity_check_commands = ['hipcc --help', 'hipconfig --full'] + +modextravars = { + 'DEVICE_LIB_PATH': '$EBROOTCLANGMINAOMP/amdgcn/bitcode', + 'HIP_CLANG_INCLUDE_PATH': '$EBROOTCLANGMINAOMP/include', + 'HIP_CLANG_PATH': '$EBROOTCLANGMINAOMP/bin', + 'HIP_COMPILER': 'clang', + 'HIP_INCLUDE_PATH': '%(installdir)s/include', + 'HIP_LIB_PATH': '%(installdir)s/lib', + 'HIP_PATH': '%(installdir)s', + 'HIP_RUNTIME': 'rocclr', + 'HSA_PATH': '$EBROOTROCRMINRUNTIME', + 'ROCM_PATH': '%(installdir)s', +} + +moduleclass = 'tools' From 5d8e544694d75b535a50edfab1870f7bf912a7eb Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 15 Nov 2021 13:36:19 +0000 Subject: [PATCH 1963/9987] adding easyconfigs: ProFit-3.3-GCC-10.3.0.eb --- .../p/ProFit/ProFit-3.3-GCC-10.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/p/ProFit/ProFit-3.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/p/ProFit/ProFit-3.3-GCC-10.3.0.eb b/easybuild/easyconfigs/p/ProFit/ProFit-3.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..024b9525d9f --- /dev/null +++ b/easybuild/easyconfigs/p/ProFit/ProFit-3.3-GCC-10.3.0.eb @@ -0,0 +1,45 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MakeCp' + +name = 'ProFit' +version = '3.3' + +homepage = 'http://www.bioinf.org.uk/software/profit' +description = """ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate program for + performing least squares fits of two or more protein structures. It performs a very simple and + basic function, but allows as much flexibility as possible in performing this procedure. Thus one + can specify subsets of atoms to be considered, specify zones to be fitted by number, sequence, or + by sequence alignment. +""" +citing = """Fitting was performed using the McLachlan algorithm (McLachlan, A.D., 1982 'Rapid + Comparison of Protein Structures', Acta Cryst A38, 871-873) as implemented in the program ProFit + Martin, A.C.R., http://www.bioinf.org.uk/software/profit/). +""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'opt': True} + +source_urls = ['http://www.bioinf.org.uk/software/profit/235216'] +sources = ['%(name)sV%(version)s.tar.gz'] +checksums = ['ee436ebec66e030ef11e704e1fb489ef3ba0d90352962e419311b3fb824b00d1'] + +dependencies = [('libreadline', '8.1')] + +start_dir = 'src' + +buildopts = 'CC="$CC $OPTFLAGS" READLINE="-DREADLINE_SUPPORT" READLINELIB="-lreadline -lcurses" COPT="-DGUNZIP_SUPPORT"' + +files_to_copy = [(['profit'], 'bin'), '../ProFit.help'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = [ + ("profit HELP 2>&1 | grep 'Syntax: ProFit \[-h\] \[-f \] \[ \]'", ''), +] + +modextravars = {'HELPDIR': '%(installdir)s'} + +moduleclass = 'bio' From 83f00aa200c02918a3b780e2a1535aa3661458e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Nov 2021 14:58:23 +0100 Subject: [PATCH 1964/9987] set $DALTON_TMPDIR to build directory to run Dalton tests --- easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb index d728740ec3e..28d3a0b10ae 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.0-foss-2021a.eb @@ -49,7 +49,7 @@ builddependencies = [ configopts = '-DENABLE_MPI=ON ' configopts += '-DENABLE_OMP=ON ' -pretestopts = 'env EBROOTDALTON=%(builddir)s/easybuild_obj ' +pretestopts = 'env EBROOTDALTON=%(builddir)s/easybuild_obj DALTON_TMPDIR=%(builddir)s ' # Just run the essential tests testopts = 'ARGS="-L essential" ' runtest = 'test' From 56b386ede1ae7111a37a2a4be736ef48fe203676 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 15 Nov 2021 17:51:34 +0000 Subject: [PATCH 1965/9987] adding easyconfigs: SAMtools-1.14-GCC-11.2.0.eb --- .../s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb new file mode 100644 index 00000000000..a1a0f8bdecf --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.14-GCC-11.2.0.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +# +# Updated to 1.14 and gcc-11.2.0 +# J. Sassmannshausen / GSTT + +name = 'SAMtools' +version = '1.14' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9341dabaa98b0ea7d60fd47e42af25df43a7d3d64d8e654cdf852974546b7d74'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.78.0'), +] + +moduleclass = 'bio' From c38b10ec04782be6154f7a599f778038e62e93e5 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 15 Nov 2021 18:38:33 +0000 Subject: [PATCH 1966/9987] adding easyconfigs: BEDTools-2.30.0-GCC-11.2.0.eb --- .../b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..f89f04cf919 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb @@ -0,0 +1,43 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.30.0' + +homepage = "https://bedtools.readthedocs.io/" +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8'] + +builddependencies = [('Python', '3.9.6')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' From 13ad951042bdb80d7396477adf000aaadb1a10e7 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 15 Nov 2021 18:40:14 +0000 Subject: [PATCH 1967/9987] adding easyconfigs: BamTools-2.5.2-GCC-11.2.0.eb --- .../b/BamTools/BamTools-2.5.2-GCC-11.2.0.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..33c9e496984 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-11.2.0.eb @@ -0,0 +1,19 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +name = 'BamTools' +version = '2.5.2' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8'] + +builddependencies = [('CMake', '3.21.1')] + +moduleclass = 'bio' From 20e8399769047e7ee4060100b2b688c1c9204b17 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 15 Nov 2021 18:43:08 +0000 Subject: [PATCH 1968/9987] adding easyconfigs: STEAK-2019.09.12-foss-2021b.eb --- .../s/STEAK/STEAK-2019.09.12-foss-2021b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/STEAK/STEAK-2019.09.12-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/STEAK/STEAK-2019.09.12-foss-2021b.eb b/easybuild/easyconfigs/s/STEAK/STEAK-2019.09.12-foss-2021b.eb new file mode 100644 index 00000000000..f7622c248f7 --- /dev/null +++ b/easybuild/easyconfigs/s/STEAK/STEAK-2019.09.12-foss-2021b.eb @@ -0,0 +1,40 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# Toolchain bumped to foss-2021b +# +easyblock = 'MakeCp' + +name = 'STEAK' +version = '2019.09.12' + +homepage = 'https://omictools.com/steak-tool' +description = """Detects integrations of any sort in high-throughput +sequencing (HTS) data. STEAK was built for validating and discovering +transposable element (TE) and retroviral integrations in a variety of +HTS data. The software performs on both single-end (SE) and paired-end ( +PE) libraries and on a variety of HTS sequencing strategies. It can +be applied to a broad range of research interests and clinical uses +such as population genetic studies and detecting polymorphic integrations.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/applevir/STEAK/archive/'] +sources = [ + {'download_filename': '43f079da8bbc37a34efd7b3a0a6955a13f6d4137.tar.gz', + 'filename': 'steak-20190912.tar.gz'} +] +checksums = ['f200865e2588c2a037527ad4cf8d2b6539217d7e9bf8f515b99e4288eb682b37'] + +dependencies = [ + ('Boost', '1.77.0'), +] + +files_to_copy = [(['steak'], 'bin'), "README.md", "GPLv3.txt"] + +sanity_check_paths = { + 'files': ['bin/steak'], + 'dirs': [], +} + +moduleclass = 'bio' From 62855477cf93c2b7f6ceb1699826331fbdc077f8 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 15 Nov 2021 20:58:17 +0100 Subject: [PATCH 1969/9987] Removed download_dep_fail and sanity_pip_check --- easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb index 88913eb6d99..c7e423450ce 100644 --- a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb +++ b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb @@ -16,12 +16,8 @@ dependencies = [ ('plotly.py', '5.1.0'), ] -download_dep_fail = True use_pip = True -# Disable sanity check because `zmq` has an invalid version. -sanity_pip_check = False - exts_list = [ ('zmq', '0.0.0', { 'sources': [{ From a346f8a0dca4baf2a442bbf1ab37b4be2f82adad Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 15 Nov 2021 21:52:34 +0100 Subject: [PATCH 1970/9987] Cleaning --- .../q/QCGPilotJob/QCGPilotJob-0.12.3.eb | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb index c7e423450ce..abc5610df44 100644 --- a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb +++ b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb @@ -20,10 +20,6 @@ use_pip = True exts_list = [ ('zmq', '0.0.0', { - 'sources': [{ - 'filename': 'zmq-0.0.0.tar.gz', - 'download_filename': 'zmq.tar.gz', - }], 'checksums': ['6b1a1de53338646e8c8405803cffb659e8eb7bb02fff4c9be62a7acfac8370c9'], }), ('patsy', '0.5.2', { @@ -42,21 +38,21 @@ exts_list = [ 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('qcg', '0.12.3', { - 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'checksums': ['9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966'], 'start_dir': 'components/core', }), ('qcg', '0.12.3', { - 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'checksums': ['9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966'], 'start_dir': 'components/cmds', }), ('qcg', '0.12.3', { - 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/refs/tags'], + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['af59dffe6af8a524453db42fae07603342f111ab4da7e669efaf1ba5a808aa6f'], + 'checksums': ['9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966'], 'start_dir': 'components/executor_api', }), ] From f138decb07673f9e0dc8090f5b5c78e47596fb8e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 15 Nov 2021 21:08:11 +0000 Subject: [PATCH 1971/9987] adding easyconfigs: multichoose-1.0.3-GCCcore-10.3.0.eb --- .../multichoose-1.0.3-GCCcore-10.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3fa5d5d5ad2 --- /dev/null +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'multichoose' +version = '1.0.3' + +homepage = 'https://github.com/ekg/multichoose' +description = """generate multiset combinations (n multichoose k).""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877'] + +builddependencies = [('binutils', '2.36.1')] + +local_bins = [name, 'multipermute'] +files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/multichoose')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +moduleclass = 'bio' From 4277270877b0408c27efd270e07677036697a428 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 15 Nov 2021 21:10:31 +0000 Subject: [PATCH 1972/9987] adding easyconfigs: smithwaterman-20160702-GCCcore-10.3.0.eb --- .../smithwaterman-20160702-GCCcore-10.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..91ca0fc0cb8 --- /dev/null +++ b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'smithwaterman' +version = '20160702' +local_commit = '2610e25' + +homepage = 'https://github.com/ekg/smithwaterman' +description = """smith-waterman-gotoh alignment algorithm.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20160702_build-shared-lib.patch'] +checksums = [ + '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8', # 2610e25.tar.gz + '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582', # smithwaterman-20160702_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.36.1')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' From 63f04c8fc0f3a05bd9ab73442fb2d3adc60e7649 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 15 Nov 2021 21:11:40 +0000 Subject: [PATCH 1973/9987] adding easyconfigs: fsom-20141119-GCCcore-10.3.0.eb --- .../f/fsom/fsom-20141119-GCCcore-10.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..390143a24ac --- /dev/null +++ b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'fsom' +version = '20141119' +local_commit = 'a6ef318' + +homepage = 'https://github.com/ekg/fsom' +description = """A tiny C library for managing SOM (Self-Organizing Maps) neural networks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = [ + '%(name)s-20141119_build-libs.patch', + '%(name)s-20141119_fix-abs-overload.patch' +] +checksums = [ + '832ec7d0aff53e04fdb8bbaa5be2177de362afac6ed58a59a97abb7eef29cb60', # a6ef318.tar.gz + 'a6349a6462473f011260074eca6ad9826e3c6aeb20674b696c5848d10610cdd7', # fsom-20141119_build-libs.patch + '54dd6ae76033535fe1b0231142d8bd41a815950dc3fd269dc321f698d4973639', # fsom-20141119_fix-abs-overload.patch +] + +builddependencies = [('binutils', '2.36.1')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfsom.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' From 45214d6d09c9e2681bfb23ec08f441cbd6f3ffc4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 15 Nov 2021 21:12:20 +0000 Subject: [PATCH 1974/9987] adding easyconfigs: filevercmp-20191210-GCCcore-10.3.0.eb --- .../filevercmp-20191210-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..123d2b44a55 --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'filevercmp' +version = '20191210' +local_commit = 'df20dcc' + +homepage = 'https://github.com/ekg/filevercmp' +description = """filevercmp function as in sort --version-sort.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20191210_build-libs.patch'] +checksums = [ + '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz + '051438f76dd04219abfb283f61101c04d748407031e180b7ae3841344416ec4f', # filevercmp-20191210_build-libs.patch +] + +builddependencies = [('binutils', '2.36.1')] + +skipsteps = ['configure'] + +installopts = 'DESTDIR="" PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 0131313b36d191045289f2bc979e9b98ba6f11a9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 15 Nov 2021 21:12:54 +0000 Subject: [PATCH 1975/9987] adding easyconfigs: fastahack-1.0.0-GCCcore-10.3.0.eb --- .../fastahack-1.0.0-GCCcore-10.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..874d1cd5635 --- /dev/null +++ b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'fastahack' +version = '1.0.0' + +homepage = 'https://github.com/ekg/fastahack' +description = """Utilities for indexing and sequence extraction from FASTA files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.0.0_build-libs.patch'] +checksums = [ + 'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae', # v1.0.0.tar.gz + '7f804486c6bafd9b1572cb5f86ff28dbebb4d6da551bde1091d6ff8f82748bf4', # fastahack-1.0.0_build-libs.patch +] + +builddependencies = [('binutils', '2.36.1')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfastahack.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From a386ef0f9e53e2cf09aaa1cbb6fceb1ccc76ff06 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 15 Nov 2021 21:13:53 +0000 Subject: [PATCH 1976/9987] adding easyconfigs: intervaltree-0.1-GCCcore-10.3.0.eb --- .../intervaltree-0.1-GCCcore-10.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..dd0d16ad302 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'intervaltree' +version = '0.1' + +homepage = 'https://github.com/ekg/intervaltree' +description = """An interval tree can be used to efficiently find a set of numeric intervals + overlapping or containing another interval. This library provides a basic implementation of an + interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307'] + +builddependencies = [('binutils', '2.36.1')] + +skipsteps = ['configure'] + +preinstallopts = 'DESTDIR="" PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/interval_tree_test', 'include/intervaltree/IntervalTree.h'], + 'dirs': [], +} +sanity_check_commands = ["interval_tree_test"] + +moduleclass = 'lib' From 18de8959abd1c267da3b2974ec91a2a6b98129ca Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 15 Nov 2021 21:14:29 +0000 Subject: [PATCH 1977/9987] adding easyconfigs: tabixpp-1.1.0-GCC-10.3.0.eb --- .../t/tabixpp/tabixpp-1.1.0-GCC-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-10.3.0.eb b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..dfdca661195 --- /dev/null +++ b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-10.3.0.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'tabixpp' +version = '1.1.0' + +homepage = 'https://github.com/ekg/tabixpp' +description = """C++ wrapper to tabix indexer""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1.0_use-external-HTSlib.patch'] +checksums = [ + '56c8f1b07190aba5e1d0b738e380e726d380f0ad8b2d0df133200b0ab1f8ed88', # v1.1.0.tar.gz + '65496b6e042cf54290386a33cf0de26cb1160b3ddb35216765999d790b99cab4', # tabixpp-1.1.0_use-external-HTSlib.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('HTSlib', '1.12'), + ('PCRE', '8.44'), +] + +skipsteps = ['configure'] + +preinstallopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/tabix++', 'lib/libtabixpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From 871be9d8076a554cd71f1d30a102b2ef7bb559d5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 15 Nov 2021 21:15:11 +0000 Subject: [PATCH 1978/9987] adding easyconfigs: vcflib-1.0.2-GCC-10.3.0.eb --- .../v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..5217cd5b157 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb @@ -0,0 +1,59 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.2' + +homepage = 'https://github.com/vcflib/vcflib' +description = """vcflib provides methods to manipulate and interpret sequence variation as it can be + described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended + to concisely describe reference-indexed genetic variations between individuals.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['vcflib-1.0.2_use-external-deps.patch'] +checksums = [ + 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz + '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.12'), + ('tabixpp', '1.1.0'), + ('intervaltree', '0.1'), + ('fastahack', '1.0.0'), + ('filevercmp', '20191210'), + ('fsom', '20141119'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), +] + +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f -regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" +preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" +preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" +preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" +preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " + +sanity_check_paths = { + 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["vcfremap"] + +moduleclass = 'bio' From 3611bed34029643bde8f9397fc25ab39b629ccf5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Tue, 16 Nov 2021 08:09:04 +0100 Subject: [PATCH 1979/9987] adding easyconfigs: rocm-smi-4.5.0-GCCcore-11.2.0.eb --- .../rocm-smi/rocm-smi-4.5.0-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/rocm-smi/rocm-smi-4.5.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-4.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9af417e9769 --- /dev/null +++ b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-4.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'rocm-smi' +version = '4.5.0' + +homepage = 'https://github.com/RadeonOpenCompute/rocm_smi_lib' +description = """The ROCm System Management Interface Library, or ROCm SMI +library, is part of the Radeon Open Compute ROCm software stack. It is a C +library for Linux that provides a user space interface for applications to +monitor and control GPU applications.""" +docurls = ['https://rocmdocs.amd.com'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ["https://github.com/RadeonOpenCompute/rocm_smi_lib/archive/"] +sources = ["rocm-%(version)s.tar.gz"] + +checksums = ['43a2cc2ec548cc28698ca4fa01a947a4414febd433936a8d9770bf6f6ed55e4f'] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +# This package hardcodes 'noexecheap' as a linker flag which is not supported +# by 'ld.gold', to get around we explicitly force 'ld.bfd' here +configopts = "-DCMAKE_CXX_FLAGS='-fuse-ld=bfd'" + +sanity_check_paths = { + 'files': ['bin/rocm_smi.py', 'lib/librocm_smi64.%s' % SHLIB_EXT], + 'dirs': ['rocm_smi/bindings', 'rocm_smi/include'], +} +sanity_check_commands = ['rocm-smi --help'] + +moduleclass = 'tools' From 67c42c0c93c191fc6d97886b41ab2c08149d785d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Tue, 16 Nov 2021 10:12:43 +0100 Subject: [PATCH 1980/9987] adding easyconfigs: ROCm-4.5.0-GCCcore-11.2.0.eb --- .../r/ROCm/ROCm-4.5.0-GCCcore-11.2.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROCm/ROCm-4.5.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/r/ROCm/ROCm-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/ROCm/ROCm-4.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b02e9e5126c --- /dev/null +++ b/easybuild/easyconfigs/r/ROCm/ROCm-4.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' +name = 'ROCm' +version = '4.5.0' + +homepage = 'https://rocmdocs.amd.com/en/latest/' +description = """AMD ROCm is the first open-source software development +platform for HPC/Hyperscale-class GPU computing. AMD ROCm brings the UNIX +philosophy of choice, minimalism and modular software development to GPU +computing.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Clang-AOMP', '%(version)s'), + ('HIP', '%(version)s', '-amd'), + ('ROCR-Runtime', '%(version)s'), + ('rocm-cmake', '%(version)s'), + ('rocm-smi', '%(version)s'), + ('rocminfo', '%(version)s'), +] + +moduleclass = 'tools' From 85c7a73bcb816eb877a435dbbfad5c6a37e19303 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Nov 2021 13:02:08 +0100 Subject: [PATCH 1981/9987] {data}[fosscuda/2020b] nnU-Net v1.7.0 (+ dependencies) w/ Python 3.8.6 --- .../dicom2nifti-2.3.0-fosscuda-2020b.eb | 33 +++++++ .../i/ITK/ITK-5.2.1-fosscuda-2020b.eb | 60 ++++++++++++ .../m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb | 28 ++++++ .../n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb | 82 +++++++++++++++++ .../SimpleITK-2.1.0-fosscuda-2020b.eb | 49 ++++++++++ .../v/VTK/VTK-9.0.1-fosscuda-2020b.eb | 92 +++++++++++++++++++ 6 files changed, 344 insertions(+) create mode 100644 easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..20fcaa7cfc7 --- /dev/null +++ b/easybuild/easyconfigs/d/dicom2nifti/dicom2nifti-2.3.0-fosscuda-2020b.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'dicom2nifti' +version = '2.3.0' + +homepage = 'https://github.com/icometrix/dicom2nifti' +description = "Python library for converting dicom files to nifti" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['808c4ddbcffd492d41ff20a2837b5e2a3cbe2058d43512fe97b99d678a758bfd'] + +dependencies = [ + ('Python', '3.8.6'), + ('pydicom', '2.1.2'), + ('NiBabel', '3.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/dicom2nifti'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dicom2nifti --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb new file mode 100644 index 00000000000..0d9fe14e51c --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-fosscuda-2020b.eb @@ -0,0 +1,60 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.2.1' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6022b2b64624b8bcec3333fe48d5f74ff6ebceb3bdf98258ba7d7fbbc76b99ab'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Bison', '3.7.1'), + ('Eigen', '3.3.8'), +] + +dependencies = [ + ('expat', '2.2.9'), + ('HDF5', '1.10.7'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('VTK', '9.0.1'), + ('zlib', '1.2.11'), +] + +local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' +configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..e5bb3979d85 --- /dev/null +++ b/easybuild/easyconfigs/m/MedPy/MedPy-0.4.0-fosscuda-2020b.eb @@ -0,0 +1,28 @@ +# This easyconfig was created by James Carpenter of the BEAR Software team at the University of Birmingham. +# updated: Denis Kristak +easyblock = 'PythonPackage' + +name = 'MedPy' +version = '0.4.0' + +homepage = 'https://pypi.org/project/MedPy/' +description = """MedPy is a library and script collection for medical image processing in Python, providing basic + functionalities for reading, writing and manipulating large images of arbitrary dimensionality. Its main + contributions are n-dimensional versions of popular image filters, a collection of image feature extractors, ready + to be used with scikit-learn, and an exhaustive n-dimensional graph-cut package.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f8a94937dbb947ab069e767862dc6b86896b153c41ce8ed9369c7d79c0033a88'] + +dependencies = [ + ('Python', '3.8.6'), + ('SimpleITK', '2.1.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..e00878d774d --- /dev/null +++ b/easybuild/easyconfigs/n/nnU-Net/nnU-Net-1.7.0-fosscuda-2020b.eb @@ -0,0 +1,82 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'nnU-Net' +version = '1.7.0' + +homepage = 'https://github.com/MIC-DKFZ/nnUNet' +description = """nnU-Net is the first segmentation method that is designed to deal with the dataset diversity found + in the domain It condenses and automates the keys decisions for designing a successful segmentation pipeline for + any given dataset.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('Bazel', '3.7.2') +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), + ('dicom2nifti', '2.3.0'), + ('scikit-image', '0.18.1'), + ('TensorFlow', '2.4.1'), + ('scikit-learn', '0.23.2'), + ('NiBabel', '3.2.1'), + ('SimpleITK', '2.1.0'), + ('MedPy', '0.4.0'), + ('jax', '0.2.19'), + ('lxml', '4.6.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('linecache2', '1.0.0', { + 'checksums': ['4b26ff4e7110db76eeb6f5a7b64a82623839d595c2038eeda662f2a2db78e97c'], + }), + ('traceback2', '1.4.0', { + 'checksums': ['05acc67a09980c2ecfedd3423f7ae0104839eccb55fc645773e1caa0951c3030'], + }), + ('unittest2', '1.1.0', { + 'checksums': ['22882a0e418c284e1f718a822b3b022944d53d2d908e1690b319a9d3eb2c0579'], + 'preinstallopts': "sed -i 's/.argparse.,//' setup.py && ", + }), + ('batchgenerators', '0.23', { + 'checksums': ['4bc5711ee75678ae97df7b54c50c1cde46f14c94f44d948f6edf4e8c48b2a9e0'], + }), + ('tifffile', '2021.8.30', { + 'checksums': ['8760e61e30106ea0dab9ec42a238d70a3ff55dde9c54456e7b748fe717cb782d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['5faa387ad6b522516283cbe45adbc4c46bedcf501c82db2f9174945f3ec2ea7d'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), + ('nnunet', version, { + 'preinstallopts': "sed -i 's/sklearn/scikit-learn/g' setup.py && ", + 'checksums': ['7ad3d5b89af389fa86cea58f409bd2353b511a746587f37d26c00a756849f356'], + }), +] + +sanity_check_commands = ['nnUNet_train --help'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..f51b83860c7 --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.0-fosscuda-2020b.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'CMakeMake' + +name = 'SimpleITK' +version = '2.1.0' + +homepage = 'http://www.simpleitk.org' +description = """SimpleITK is a simplified programming interface to the algorithms and data structures of + the Insight Toolkit (ITK).""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d5d3b805863b9dfcffeebec69a1b79b5709fc814b12cb9ab759ccbd3e4746839'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Lua', '5.3.5'), + ('ITK', '5.2.1'), + ('scikit-build', '0.11.1'), +] + +start_dir = 'SimpleITK' + +configopts = "-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF " +configopts += "-DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF " + +postinstallcmds = [ + "cd %(builddir)s/easybuild_obj/Wrapping/Python && " + "pip install --ignore-installed --no-deps --prefix=%(installdir)s . ", +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], + 'dirs': ['include/%(name)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import %(name)s'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb new file mode 100644 index 00000000000..3d7c9e19371 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-fosscuda-2020b.eb @@ -0,0 +1,92 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '9.0.1' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + '1b39a5e191c282861e7af4101eaa8585969a2de05f5646c9199a161213a622c7', # VTK-9.0.1.tar.gz + '3f8bfdadd66e0b541bc5580340481abf92bec100b09d787283632ab590b1ce1c', # VTKData-9.0.1.tar.gz + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('XZ', '5.2.5'), + ('libGLU', '9.0.1'), + ('X11', '20201008'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + + +moduleclass = 'vis' From 755d41e5d71b05e0af9998889b940cd8d72543a0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 16 Nov 2021 15:13:39 +0100 Subject: [PATCH 1982/9987] adding easyconfigs: QuantumESPRESSO-6.8-foss-2021b.eb --- .../QuantumESPRESSO-6.8-foss-2021b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb new file mode 100644 index 00000000000..fc8ad317547 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.8-foss-2021b.eb @@ -0,0 +1,44 @@ +name = 'QuantumESPRESSO' +version = '6.8' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s/', + 'https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + 'qe-gipaw-%(version)s.tar.gz', + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + 'fc9b8141705d31db30f6cfe61d4e49867c7c3b04a59533eb7f90301fa8bd50ce', # qe-%(version)s-ReleasePack.tgz + 'ec6212b1f1084818a91b9980c6c24e4f9f7da2212e534732e0af6072addfb4dd', # qe-gipaw-%(version)s.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.12.1'), + ('ELPA', '2021.05.001'), + ('libxc', '5.1.6'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' From a0f2456c78bab487a82ef4dc8810bb3121bc9321 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Nov 2021 16:10:58 +0100 Subject: [PATCH 1983/9987] remove postinstallcmds for STACEY, no longer needed now custom package directory for Beast is specified via $_JAVA_OPTIONS --- .../easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb index b24fcc3c961..3a9050393e5 100644 --- a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb @@ -15,21 +15,10 @@ source_urls = ['http://www.indriid.com/2019/'] sources = ['%(name)s.addon.v%(version)s.zip'] checksums = ['a6ce3ce83ddafe3505622961c7d90e696e11b2b51246f7447d820e1b3e717b58'] -builddependencies = [ - ('Xvfb', '1.20.9'), -] dependencies = [ ('Beast', '2.6.4'), ] -# we need to link installdir to hardcoded package directory of Beast (~/.beast/2.6/) -postinstallcmds = [ - # if package dir doesnt exist yet, initial run of `beauti` creates it - 'timeout 10 xvfb-run beauti 2>&1 | grep "Terminated"', - # now we can link our installdir to the package dir - # 'ln -s %(installdir)s ~/.beast/2.6/STACEY ', -] - sanity_check_paths = { 'files': ['stacey.src.jar'], 'dirs': ['lib/', 'templates/', 'examples'], From 305e9c628ef225b68d90ece8987e1c07e4df36cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Nov 2021 16:11:18 +0100 Subject: [PATCH 1984/9987] add custom sanity check command for STACEY --- easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb index 3a9050393e5..f6bec5c1089 100644 --- a/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/STACEY/STACEY-1.2.5-GCC-10.2.0.eb @@ -24,6 +24,9 @@ sanity_check_paths = { 'dirs': ['lib/', 'templates/', 'examples'], } +# takes 5-6min using a single core +sanity_check_commands = ["beast -threads %(parallel)s %(installdir)s/examples/test1/test1.xml"] + modextravars = {'_JAVA_OPTIONS': "-Dbeast.user.package.dir=%(installdir)s"} moduleclass = 'data' From b96f75b562bdcab8da5b845cec31786ff2ba9e31 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 16 Nov 2021 15:43:46 +0000 Subject: [PATCH 1985/9987] adding easyconfigs: bpp-4.4.0-GCC-10.3.0.eb --- .../easyconfigs/b/bpp/bpp-4.4.0-GCC-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/bpp/bpp-4.4.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/bpp/bpp-4.4.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/bpp/bpp-4.4.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..112b5eecf6a --- /dev/null +++ b/easybuild/easyconfigs/b/bpp/bpp-4.4.0-GCC-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'bpp' +version = '4.4.0' + +homepage = 'https://github.com/bpp/bpp' +description = """ The aim of this project is to implement a versatile high-performance version of the BPP software. """ + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/bpp/bpp/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2f0bc2f2b965f99e484250c0df82274fc1ab4e4a519ae1d6bd766b93eedde7c5'] + +start_dir = 'src' +files_to_copy = ['src/bpp'] + +sanity_check_paths = { + 'files': ['bpp'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +sanity_check_commands = [('bpp --help')] + +moduleclass = 'bio' From 62d7fa69fb92915a0f8da487ae93fde11158b1d4 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Nov 2021 08:46:25 +0100 Subject: [PATCH 1986/9987] adding easyconfigs: g2clib-1.6.3-GCCcore-11.2.0.eb --- .../g/g2clib/g2clib-1.6.3-GCCcore-11.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..3977d898ca3 --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +name = 'g2clib' +version = '1.6.3' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['83e4f2061b3d4a8bd431ba860dda8c5cf103b25f42d265b7b724b9acafad177c'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('JasPer', '2.0.33'), + ('libpng', '1.6.37'), +] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' From 9031c5bba483875fda7917dc9285bab273a44c87 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Nov 2021 08:46:54 +0100 Subject: [PATCH 1987/9987] adding easyconfigs: Lua-5.4.3-GCCcore-11.2.0.eb --- .../l/Lua/Lua-5.4.3-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.4.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.4.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.4.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f3f4a79aad8 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.4.3-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +name = 'Lua' +version = '5.4.3' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f8612276169e3bfcbcfb8f226195bfc6e466fe13042f1076cbde92b7ec96bbfb'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('libreadline', '8.1'), +] + +moduleclass = 'lang' From dab4590c46baaad221776ed7a0ee053fc73575f2 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Nov 2021 08:47:30 +0100 Subject: [PATCH 1988/9987] adding easyconfigs: libcerf-1.17-GCCcore-11.2.0.eb --- .../l/libcerf/libcerf-1.17-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-1.17-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-1.17-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-1.17-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..bf4135c3e6f --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-1.17-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '1.17' + +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['b1916b292cb37f2d0d0b699fbcf0fe260cca97ec7266ea20ff0c5cd8ef2eaab4'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Perl', '5.34.0'), # required for pod2html +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From 53f0ecfea3a8831955d5ed476216317b8feec03c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Nov 2021 08:50:46 +0100 Subject: [PATCH 1989/9987] adding easyconfigs: libdwarf-20210528-GCCcore-11.2.0.eb, libelf-0.8.13-GCCcore-11.2.0.eb --- .../libdwarf-20210528-GCCcore-11.2.0.eb | 31 +++++++++++++++++++ .../l/libelf/libelf-0.8.13-GCCcore-11.2.0.eb | 26 ++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d2f99622a89 --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '20210528' + +homepage = 'https://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.prevanders.net'] +sources = [SOURCE_TAR_GZ] +checksums = ['b8ba0ee9b70d2052d45272489d79bf456c4d342fc8c3bba45038afc50ec6e2'] + +builddependencies = [ + ('binutils', '2.37'), +] +dependencies = [ + ('libelf', '0.8.13'), +] + +configopts = "--enable-shared " + +sanity_check_paths = { + 'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0ef4d0b3db0 --- /dev/null +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libelf' +version = '0.8.13' + +homepage = 'https://sourceware.org/elfutils' +description = """libelf is a free ELF object file access library""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://fossies.org/linux/misc/old/'] +sources = [SOURCE_TAR_GZ] +checksums = ['591a9b4ec81c1f2042a97aa60564e0cb79d041c52faa7416acb38bc95bd2c76d'] + +builddependencies = [ + ('binutils', '2.37'), +] + +modextrapaths = {'CPATH': 'include/libelf'} + +sanity_check_paths = { + 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf/libelf.h'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'devel' From 73cee0830867fb268c7aeb3e763709895d9faadd Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Nov 2021 09:00:55 +0100 Subject: [PATCH 1990/9987] update libdwarf-20210528-GCCcore-11.2.0.eb: fix checksum --- .../easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb index d2f99622a89..41b93c54d57 100644 --- a/easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.prevanders.net'] sources = [SOURCE_TAR_GZ] -checksums = ['b8ba0ee9b70d2052d45272489d79bf456c4d342fc8c3bba45038afc50ec6e2'] +checksums = ['b8ba0ee9b70d2052d45272489d79bf456c4d342fc8c3bba45038afc50ec6e28b'] builddependencies = [ ('binutils', '2.37'), From 7dc155f25fc2c82ce04902028efdba4329a8dead Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Nov 2021 10:16:13 +0100 Subject: [PATCH 1991/9987] adding easyconfigs: tbb-2021.4-GCCcore-11.2.0.eb --- .../t/tbb/tbb-2021.4-GCCcore-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2021.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..852c79404cf --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.4-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'tbb' +version = '2021.4' + +homepage = 'https://github.com/oneapi-src/oneTBB' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['021796c7845e155e616f5ecda16daa606ebb4c6f90b996e5c08aebab7a8d3de3'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +sanity_check_paths = { + 'files': ['lib/libtbb.%s' % SHLIB_EXT, 'lib/libtbbmalloc.%s' % SHLIB_EXT], + 'dirs': ['lib', 'include', 'share'], +} + +moduleclass = 'lib' From 12d55f08a940038121f9f95f5ea7cf29298f34ae Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Nov 2021 10:20:09 +0100 Subject: [PATCH 1992/9987] update tbb-2021.4.0-GCCcore-11.2.0.eb: fix version and source URL --- ...021.4-GCCcore-11.2.0.eb => tbb-2021.4.0-GCCcore-11.2.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/t/tbb/{tbb-2021.4-GCCcore-11.2.0.eb => tbb-2021.4.0-GCCcore-11.2.0.eb} (88%) diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.4.0-GCCcore-11.2.0.eb similarity index 88% rename from easybuild/easyconfigs/t/tbb/tbb-2021.4-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/t/tbb/tbb-2021.4.0-GCCcore-11.2.0.eb index 852c79404cf..1db10a3f74d 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2021.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.4.0-GCCcore-11.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'tbb' -version = '2021.4' +version = '2021.4.0' homepage = 'https://github.com/oneapi-src/oneTBB' description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that @@ -9,7 +9,7 @@ description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easi toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['https://github.com/oneapi-src/oneTBB/archive/'] +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['021796c7845e155e616f5ecda16daa606ebb4c6f90b996e5c08aebab7a8d3de3'] From 332736fc7e4e5624fe2819dd5db089ad184a0b1a Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 17 Nov 2021 11:00:00 +0100 Subject: [PATCH 1993/9987] adding easyconfigs: OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb, pugixml-1.11.4-GCCcore-10.3.0.eb, ASAP-2.0-foss-2021a.eb --- .../easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb | 62 +++++++++++++++++++ ...enSlide-3.4.1-GCCcore-10.3.0-largefiles.eb | 48 ++++++++++++++ .../pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb | 31 ++++++++++ 3 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb create mode 100644 easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb new file mode 100644 index 00000000000..908ffae8b84 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +separate_build_dir = True + +name = 'ASAP' +version = '2.0' + +homepage = "https://computationalpathologygroup.github.io/ASAP/" +description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface for making annotations. It consists of two main components: an IO library for reading and writing multi-resolution images and a viewer component for visualizing such images.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/computationalpathologygroup/ASAP/archive'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = [ +# 'ASAP-8c9a8fb_use_pugixml_shared.patch', + 'ASAP-1.9_libjpeg.patch', +] +checksums = [ + 'e5d8b0aff6f86a3c7319062ca1f9e35b867da1c80667a80b55ee2a876f897202', # ASAP-2.0.tar.gz + '7cf1403da21cc2bbf9ea95f39de46982d95e375559203deb0f9826e4cf168e04', # ASAP-1.9_libjpeg.patch +] + +configopts = '-DOPENSLIDE_INCLUDE_DIR=$EBROOTOPENSLIDE/include/openslide ' +configopts += '-DPugiXML_INCLUDE_DIR=$EBROOTPUGIXML/include ' +configopts += '-DDCMTKJPEG_INCLUDE_DIR=$EBROOTDCMTK ' +configopts += '-DWRAP_MULTIRESOLUTIONIMAGEINTERFACE_PYTHON=TRUE -DBUILD_ASAP=TRUE ' +configopts += '-DBUILD_EXECUTABLES=TRUE -DBUILD_IMAGEPROCESSING=TRUE -DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE ' +configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig ' # Otherwise, it picks up on the system swig + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Boost', '1.76.0'), + ('Python', '3.9.5'), + ('OpenCV', '4.5.3', '-CUDA-%(cudaver)s-contrib'), + ('Qt5', '5.15.2'), + ('LibTIFF', '4.2.0'), + ('libjpeg-turbo', '2.0.6'), + ('JasPer', '2.0.28'), + ('DCMTK', '3.6.6'), + ('SWIG', '4.0.2'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('pugixml', '1.11.4'), + ('zlib', '1.2.11'), +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': [], +# 'bin/ospBenchmark', 'bin/ospTestSuite', 'bin/ospConvertRawToAMR', +# 'lib64/libospray.so', 'lib64/libospray_module_ispc.so'], + 'dirs': ['bin'] +} + +# CvL: ASAP installs its python interface in bin. Ugly... +modextrapaths = {'PYTHONPATH': ['bin']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb new file mode 100644 index 00000000000..ac617afe25e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide' +version = '3.4.1' +versionsuffix = '-largefiles' + +homepage = 'https://openslide.org/' +description = """OpenSlide is a C library that provides a simple interface to +read whole-slide images (also known as virtual slides).""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_large_file_support.patch'] +checksums = [ + 'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c', # v3.4.1.tar.gz + 'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c', # %(name)s-%(version_major_minor)s.1_large_file_support.patch +] + +builddependencies = [ + ('Autotools', '20210128'), + ('M4', '1.4.18'), + ('pkg-config', '0.29.2'), + ('binutils', '2.36.1'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.2.0'), + ('OpenJPEG', '2.4.0'), + ('libxml2', '2.9.10'), + ('SQLite', '3.35.4'), + ('cairo', '1.16.0'), + ('Gdk-Pixbuf', '2.42.6'), +] + +preconfigopts = "autoreconf -f -i && " + +github_account = '%(namelower)s' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-quickhash1sum', 'bin/%(namelower)s-show-properties', 'bin/%(namelower)s-write-png', 'lib/libopenslide.la', 'lib/libopenslide.so'], + 'dirs': ['include/%(namelower)s'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1daade9be4b --- /dev/null +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'pugixml' +version = '1.11.4' + +homepage = 'https://pugixml.org/' +description = """pugixml is a light-weight C++ XML processing library""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/zeux/pugixml/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['pugixml-1.11.4_pugixml_remove_headeronly.patch'] +checksums = [ + '017139251c122dbff400a507cddc4cb74120a431a50c6c524f30edcc5b331ade', # v1.11.4.tar.gz + # pugixml-1.11.4_pugixml_remove_headeronly.patch + 'fb1a566a4a5c2e26385d932b43a25b3e0a5a380a7c8d1fd82c7bfc80379ec6ff', +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib'], +} + +moduleclass = 'data' From dd5f39bb820d8f3bdc907de130c3dcd3446d5291 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 17 Nov 2021 12:16:06 +0100 Subject: [PATCH 1994/9987] Added missing patches --- .../easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb | 7 +-- .../easyconfigs/a/ASAP/ASAP-2.0_libjpeg.patch | 59 +++++++++++++++++++ ...xml-1.11.4_pugixml_remove_headeronly.patch | 22 +++++++ 3 files changed, 83 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.0_libjpeg.patch create mode 100644 easybuild/easyconfigs/p/pugixml/pugixml-1.11.4_pugixml_remove_headeronly.patch diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb index 908ffae8b84..6bba8688672 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb @@ -13,8 +13,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/computationalpathologygroup/ASAP/archive'] sources = ['%(name)s-%(version)s.tar.gz'] patches = [ -# 'ASAP-8c9a8fb_use_pugixml_shared.patch', - 'ASAP-1.9_libjpeg.patch', + 'ASAP-2.0_libjpeg.patch', ] checksums = [ 'e5d8b0aff6f86a3c7319062ca1f9e35b867da1c80667a80b55ee2a876f897202', # ASAP-2.0.tar.gz @@ -51,12 +50,10 @@ builddependencies = [ sanity_check_paths = { 'files': [], -# 'bin/ospBenchmark', 'bin/ospTestSuite', 'bin/ospConvertRawToAMR', -# 'lib64/libospray.so', 'lib64/libospray_module_ispc.so'], 'dirs': ['bin'] } -# CvL: ASAP installs its python interface in bin. Ugly... +# ASAP installs its python interface in bin. Ugly, but we'll need to add it to PYTHONPATH modextrapaths = {'PYTHONPATH': ['bin']} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0_libjpeg.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.0_libjpeg.patch new file mode 100644 index 00000000000..09d4b17fd58 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0_libjpeg.patch @@ -0,0 +1,59 @@ +diff -Nru ASAP-1.9-orig/multiresolutionimageinterface/jpeg_mem_src.h ASAP-1.9/multiresolutionimageinterface/jpeg_mem_src.h +--- ASAP-1.9-orig/multiresolutionimageinterface/jpeg_mem_src.h 2021-06-24 13:17:55.766247981 +0200 ++++ ASAP-1.9/multiresolutionimageinterface/jpeg_mem_src.h 2021-06-24 13:30:46.499644233 +0200 +@@ -47,7 +47,7 @@ + } + } + +-static void jpeg_mem_src( j_decompress_ptr cinfo, jpeg_source_mgr * const src, void const * const buffer, long nbytes ) ++static void jpeg_mem_src_asap( j_decompress_ptr cinfo, jpeg_source_mgr * const src, void const * const buffer, long nbytes ) + { + src->init_source = mem_init_source; + src->fill_input_buffer = mem_fill_input_buffer; +@@ -57,4 +57,4 @@ + src->bytes_in_buffer = nbytes; + src->next_input_byte = (JOCTET*)buffer; + cinfo->src = src; +-} +\ No newline at end of file ++} +diff -Nru ASAP-1.9-orig/multiresolutionimageinterface/VSIImage.cpp ASAP-1.9/multiresolutionimageinterface/VSIImage.cpp +--- ASAP-1.9-orig/multiresolutionimageinterface/VSIImage.cpp 2021-06-24 13:17:55.750246541 +0200 ++++ ASAP-1.9/multiresolutionimageinterface/VSIImage.cpp 2021-06-24 13:32:19.868051172 +0200 +@@ -11,7 +11,7 @@ + // Include DCMTK LIBJPEG for lossy and lossless JPEG compression + extern "C" { + #define boolean ijg_boolean +-#include "dcmtk/dcmjpeg/libijg8/jpeglib8.h" ++#include "jpeglib.h" + #include "jpeg_mem_src.h" + #undef boolean + #undef const +@@ -234,7 +234,7 @@ + jpeg_source_mgr src_mem; + jpeg_create_decompress(&cinfo); + cinfo.err = jpeg_std_error(&jerr); +- jpeg_mem_src(&cinfo, &src_mem, (void*)buf, size); ++ jpeg_mem_src_asap(&cinfo, &src_mem, (void*)buf, size); + jpeg_read_header(&cinfo, true); + if (_compressionType == 2) { + cinfo.jpeg_color_space = JCS_YCbCr; +diff -Nru ASAP-1.9-orig/multiresolutionimageinterface/VSIImageReader.cpp ASAP-1.9/multiresolutionimageinterface/VSIImageReader.cpp +--- ASAP-1.9-orig/multiresolutionimageinterface/VSIImageReader.cpp 2021-06-24 13:17:55.762247620 +0200 ++++ ASAP-1.9/multiresolutionimageinterface/VSIImageReader.cpp 2021-06-24 13:31:06.457441248 +0200 +@@ -260,7 +260,7 @@ + jpeg_source_mgr src_mem; + jpeg_create_decompress(&cinfo); + cinfo.err = jpeg_std_error(&jerr); +- jpeg_mem_src(&cinfo, &src_mem, (void*)buf, size); ++ jpeg_mem_src_asap(&cinfo, &src_mem, (void*)buf, size); + jpeg_read_header(&cinfo, true); + if (_compressionType == 2) { + cinfo.jpeg_color_space = JCS_YCbCr; +@@ -337,4 +337,4 @@ + outputCol = 0; + } + } +-} +\ No newline at end of file ++} diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4_pugixml_remove_headeronly.patch b/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4_pugixml_remove_headeronly.patch new file mode 100644 index 00000000000..2ba50fe075f --- /dev/null +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4_pugixml_remove_headeronly.patch @@ -0,0 +1,22 @@ +# CvL: Ran into this issue https://bugreports.qt.io/browse/QTBUG-11923?focusedCommentId=233276&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#comment-233276 +# Comments in the header seem to suggest the macro expansion should fix it, but it does not +# The error we get is a missing pugixml.cpp +# Since pugixml by default is not configured to use header-only mode, we might as well comment it +diff -Nru pugixml-1.11.4-orig/src/pugixml.hpp pugixml-1.11.4/src/pugixml.hpp +--- pugixml-1.11.4-orig/src/pugixml.hpp 2021-06-24 10:24:25.117459425 +0200 ++++ pugixml-1.11.4/src/pugixml.hpp 2021-06-24 10:25:21.338514908 +0200 +@@ -1468,10 +1468,10 @@ + + // Make sure implementation is included in header-only mode + // Use macro expansion in #include to work around QMake (QTBUG-11923) +-#if defined(PUGIXML_HEADER_ONLY) && !defined(PUGIXML_SOURCE) +-# define PUGIXML_SOURCE "pugixml.cpp" +-# include PUGIXML_SOURCE +-#endif ++//#if defined(PUGIXML_HEADER_ONLY) && !defined(PUGIXML_SOURCE) ++//# define PUGIXML_SOURCE "pugixml.cpp" ++//# include PUGIXML_SOURCE ++//#endif + + /** + * Copyright (c) 2006-2020 Arseny Kapoulkine From dd88e562c8678f744e9946ec8303f3abb3d3bf44 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 17 Nov 2021 12:34:14 +0100 Subject: [PATCH 1995/9987] Fix sytle --- .../easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb | 16 ++++++++++------ .../OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb | 11 ++++++++--- 2 files changed, 18 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb index 6bba8688672..a855fcfc305 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb @@ -6,7 +6,9 @@ name = 'ASAP' version = '2.0' homepage = "https://computationalpathologygroup.github.io/ASAP/" -description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface for making annotations. It consists of two main components: an IO library for reading and writing multi-resolution images and a viewer component for visualizing such images.""" +description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface +for making annotations. It consists of two main components: an IO library for reading and writing +multi-resolution images and a viewer component for visualizing such images.""" toolchain = {'name': 'foss', 'version': '2021a'} @@ -24,17 +26,19 @@ configopts = '-DOPENSLIDE_INCLUDE_DIR=$EBROOTOPENSLIDE/include/openslide ' configopts += '-DPugiXML_INCLUDE_DIR=$EBROOTPUGIXML/include ' configopts += '-DDCMTKJPEG_INCLUDE_DIR=$EBROOTDCMTK ' configopts += '-DWRAP_MULTIRESOLUTIONIMAGEINTERFACE_PYTHON=TRUE -DBUILD_ASAP=TRUE ' -configopts += '-DBUILD_EXECUTABLES=TRUE -DBUILD_IMAGEPROCESSING=TRUE -DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE ' -configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig ' # Otherwise, it picks up on the system swig - +configopts += '-DBUILD_EXECUTABLES=TRUE -DBUILD_IMAGEPROCESSING=TRUE ' +configopts += '-DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE ' +# Otherwise, it picks up on the system swig +configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig ' + dependencies = [ ('CUDA', '11.3.1', '', True), ('Boost', '1.76.0'), ('Python', '3.9.5'), ('OpenCV', '4.5.3', '-CUDA-%(cudaver)s-contrib'), ('Qt5', '5.15.2'), - ('LibTIFF', '4.2.0'), - ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.2.0'), + ('libjpeg-turbo', '2.0.6'), ('JasPer', '2.0.28'), ('DCMTK', '3.6.6'), ('SWIG', '4.0.2'), diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb index ac617afe25e..deca9658a08 100644 --- a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb @@ -14,8 +14,10 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_large_file_support.patch'] checksums = [ - 'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c', # v3.4.1.tar.gz - 'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c', # %(name)s-%(version_major_minor)s.1_large_file_support.patch + # v3.4.1.tar.gz + 'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c', + # %(name)s-%(version_major_minor)s.1_large_file_support.patch + 'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c', ] builddependencies = [ @@ -41,7 +43,10 @@ preconfigopts = "autoreconf -f -i && " github_account = '%(namelower)s' sanity_check_paths = { - 'files': ['bin/%(namelower)s-quickhash1sum', 'bin/%(namelower)s-show-properties', 'bin/%(namelower)s-write-png', 'lib/libopenslide.la', 'lib/libopenslide.so'], + 'files': [ + 'bin/%(namelower)s-quickhash1sum', 'bin/%(namelower)s-show-properties', + 'bin/%(namelower)s-write-png', 'lib/libopenslide.la', 'lib/libopenslide.so' + ], 'dirs': ['include/%(namelower)s'], } From d0a7202f299b49ade70acef7da2a79dad3a6a4ae Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 17 Nov 2021 14:33:29 +0100 Subject: [PATCH 1996/9987] adding easyconfigs: Gurobi-9.5.0-GCCcore-10.3.0.eb --- .../g/Gurobi/Gurobi-9.5.0-GCCcore-10.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..7f9f33bb1d1 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +name = 'Gurobi' +version = '9.5.0' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +patches = ['%(name)s-9.0.1_use-eb-python-gurobi-shell.patch'] +checksums = [ + 'bb542e5a5d1685f6e364eaf05ea6c5572485ffc37a2245169cf3cb40288bc29e', # gurobi9.5.0_linux64.tar.gz + 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01', # Gurobi-9.0.1_use-eb-python-gurobi-shell.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license looks mandatory for installation +license_file = HOME + '/licenses/%(name)s.lic' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' From 0c98cbfc1272a6984bb4188c392f2cabbe81d687 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 17 Nov 2021 14:38:17 +0100 Subject: [PATCH 1997/9987] Fix sytle part two.. --- easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb | 2 +- .../OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb index a855fcfc305..6c450b0d493 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb @@ -30,7 +30,7 @@ configopts += '-DBUILD_EXECUTABLES=TRUE -DBUILD_IMAGEPROCESSING=TRUE ' configopts += '-DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE ' # Otherwise, it picks up on the system swig configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig ' - + dependencies = [ ('CUDA', '11.3.1', '', True), ('Boost', '1.76.0'), diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb index deca9658a08..15e919eadd9 100644 --- a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb @@ -44,9 +44,9 @@ github_account = '%(namelower)s' sanity_check_paths = { 'files': [ - 'bin/%(namelower)s-quickhash1sum', 'bin/%(namelower)s-show-properties', - 'bin/%(namelower)s-write-png', 'lib/libopenslide.la', 'lib/libopenslide.so' - ], + 'bin/%(namelower)s-quickhash1sum', 'bin/%(namelower)s-show-properties', + 'bin/%(namelower)s-write-png', 'lib/libopenslide.la', 'lib/libopenslide.so', + ], 'dirs': ['include/%(namelower)s'], } From b7f97504d5488df036f1796d5b93e039291cf40d Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 17 Nov 2021 15:06:15 +0100 Subject: [PATCH 1998/9987] Added versionsuffix --- .../a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..f1b050f1d47 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,64 @@ +easyblock = 'CMakeMake' + +separate_build_dir = True + +name = 'ASAP' +version = '2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://computationalpathologygroup.github.io/ASAP/" +description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface +for making annotations. It consists of two main components: an IO library for reading and writing +multi-resolution images and a viewer component for visualizing such images.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/computationalpathologygroup/ASAP/archive'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = [ + 'ASAP-2.0_libjpeg.patch', +] +checksums = [ + 'e5d8b0aff6f86a3c7319062ca1f9e35b867da1c80667a80b55ee2a876f897202', # ASAP-2.0.tar.gz + '7cf1403da21cc2bbf9ea95f39de46982d95e375559203deb0f9826e4cf168e04', # ASAP-1.9_libjpeg.patch +] + +configopts = '-DOPENSLIDE_INCLUDE_DIR=$EBROOTOPENSLIDE/include/openslide ' +configopts += '-DPugiXML_INCLUDE_DIR=$EBROOTPUGIXML/include ' +configopts += '-DDCMTKJPEG_INCLUDE_DIR=$EBROOTDCMTK ' +configopts += '-DWRAP_MULTIRESOLUTIONIMAGEINTERFACE_PYTHON=TRUE -DBUILD_ASAP=TRUE ' +configopts += '-DBUILD_EXECUTABLES=TRUE -DBUILD_IMAGEPROCESSING=TRUE ' +configopts += '-DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE ' +# Otherwise, it picks up on the system swig +configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig ' + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Boost', '1.76.0'), + ('Python', '3.9.5'), + ('OpenCV', '4.5.3', '-CUDA-%(cudaver)s-contrib'), + ('Qt5', '5.15.2'), + ('LibTIFF', '4.2.0'), + ('libjpeg-turbo', '2.0.6'), + ('JasPer', '2.0.28'), + ('DCMTK', '3.6.6'), + ('SWIG', '4.0.2'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('pugixml', '1.11.4'), + ('zlib', '1.2.11'), +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'] +} + +# ASAP installs its python interface in bin. Ugly, but we'll need to add it to PYTHONPATH +modextrapaths = {'PYTHONPATH': ['bin']} + +moduleclass = 'vis' From 5f07e056bad161ea41b4f015f62348f00cb9b3b5 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 17 Nov 2021 16:43:00 +0100 Subject: [PATCH 1999/9987] Added patch descriptions. Added configure option for pugixml so that it also builds shared libraries. Added patch to ASAP cmake to make it use the shared pugixml library, since with the static lib we get missing symbol errors. --- .../a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb | 4 +- .../easyconfigs/a/ASAP/ASAP-2.0_libjpeg.patch | 3 ++ .../a/ASAP/ASAP-2.0_use_pugixml_shared.patch | 50 +++++++++++++++++++ .../pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb | 2 + 4 files changed, 58 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb index f1b050f1d47..aa55bbf22a5 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb @@ -17,10 +17,12 @@ source_urls = ['https://github.com/computationalpathologygroup/ASAP/archive'] sources = ['%(name)s-%(version)s.tar.gz'] patches = [ 'ASAP-2.0_libjpeg.patch', + 'ASAP-2.0_use_pugixml_shared.patch', ] checksums = [ 'e5d8b0aff6f86a3c7319062ca1f9e35b867da1c80667a80b55ee2a876f897202', # ASAP-2.0.tar.gz - '7cf1403da21cc2bbf9ea95f39de46982d95e375559203deb0f9826e4cf168e04', # ASAP-1.9_libjpeg.patch + 'f593599b5af90c8256ffeae910757d02f4de04a49de26d5123c209a405ba6a55', # ASAP-2.0_libjpeg.patch + '785a7716cbbf7fd4f6dacf1b74fe66384be76d31d54a02918ce9c07989ac4c81', # ASAP-2.0_use_pugixml_shared.patch ] configopts = '-DOPENSLIDE_INCLUDE_DIR=$EBROOTOPENSLIDE/include/openslide ' diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0_libjpeg.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.0_libjpeg.patch index 09d4b17fd58..ce7c773a417 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0_libjpeg.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0_libjpeg.patch @@ -1,3 +1,6 @@ +# Author: Caspar van Leeuwen +# The jpeg_mem_src function name conflicts with a function from the jpeglib8.h dependency. +# I give the function in jpeg_mem_src.h another name, and changed all the calls to this function. diff -Nru ASAP-1.9-orig/multiresolutionimageinterface/jpeg_mem_src.h ASAP-1.9/multiresolutionimageinterface/jpeg_mem_src.h --- ASAP-1.9-orig/multiresolutionimageinterface/jpeg_mem_src.h 2021-06-24 13:17:55.766247981 +0200 +++ ASAP-1.9/multiresolutionimageinterface/jpeg_mem_src.h 2021-06-24 13:30:46.499644233 +0200 diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch new file mode 100644 index 00000000000..f23c48ea628 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch @@ -0,0 +1,50 @@ +# Author: Caspar van leeuwen +# Make sure to use the shared library of PUGIXML, since linking to the static libarry seems to result in undefined symbol errors: +# ImportError: /home/casparl/.local/easybuild/Centos8/2021/software/ASAP/2.0-foss-2021a/lib/libmultiresolutionimageinterface.so: undefined symbol: _ZNK4pugi10xpath_node6parentEv +diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/annotation/CMakeLists.txt ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/annotation/CMakeLists.txt +--- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/annotation/CMakeLists.txt 2021-06-25 11:50:23.132333349 +0200 ++++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/annotation/CMakeLists.txt 2021-06-25 11:58:03.005555272 +0200 +@@ -25,10 +25,9 @@ + ) + + add_library(annotation SHARED ${ANNOTATION_SOURCE} ${ANNOTATION_HEADERS}) +-target_compile_definitions(annotation PRIVATE "PUGIXML_HEADER_ONLY") + generate_export_header(annotation) + target_include_directories(annotation PUBLIC $ $ PRIVATE ${DIAGPathology_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR} ${Boost_INCLUDE_DIRS} ${PugiXML_INCLUDE_DIR}) +-target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface) ++target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface ${PUGIXML_LIBRARY}) + set_target_properties(annotation PROPERTIES DEBUG_POSTFIX _d) + + install(TARGETS annotation +diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPugiXML.cmake ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/cmakemodules/FindPugiXML.cmake +--- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPugiXML.cmake 2021-06-25 11:50:23.180337653 +0200 ++++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/cmakemodules/FindPugiXML.cmake 2021-06-25 11:55:27.583630434 +0200 +@@ -5,11 +5,13 @@ + # PugiXML_FOUND, If false, do not try to use PugiXML. + + find_path(PugiXML_INCLUDE_DIR pugixml.hpp) ++find_library(PUGIXML_LIBRARY NAMES pugixml) + + # handle the QUIETLY and REQUIRED arguments and set PugiXML_FOUND to TRUE if + # all listed variables are TRUE + include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake) + FIND_PACKAGE_HANDLE_STANDARD_ARGS(PugiXML +- REQUIRED_VARS PugiXML_INCLUDE_DIR) ++ REQUIRED_VARS PUGIXML_LIBRARY PugiXML_INCLUDE_DIR) + +-mark_as_advanced(PugiXML_INCLUDE_DIR) ++ ++mark_as_advanced(PugiXML_INCLUDE_DIR PUGIXML_LIBRARY) +diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/multiresolutionimageinterface/CMakeLists.txt ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/multiresolutionimageinterface/CMakeLists.txt +--- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/multiresolutionimageinterface/CMakeLists.txt 2021-06-25 11:50:23.384355944 +0200 ++++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/multiresolutionimageinterface/CMakeLists.txt 2021-06-25 11:57:29.462554526 +0200 +@@ -66,8 +66,7 @@ + + add_library(multiresolutionimageinterface SHARED ${MULTIRESOLUTIONIMAGEINTERFACE_SRCS} ${MULTIRESOLUTIONIMAGEINTERFACE_HS} ${VSI_SOURCE_HS} ${VSI_SOURCE_SRCS}) + target_include_directories(multiresolutionimageinterface PUBLIC $ $ $ $ PRIVATE ${PugiXML_INCLUDE_DIR} ${Boost_INCLUDE_DIRS} ${TIFF_INCLUDE_DIR}) +-target_link_libraries(multiresolutionimageinterface PUBLIC core PRIVATE jpeg2kcodec libtiff Boost::disable_autolinking Boost::thread) +-target_compile_definitions(multiresolutionimageinterface PRIVATE PUGIXML_HEADER_ONLY) ++target_link_libraries(multiresolutionimageinterface PUBLIC core PRIVATE jpeg2kcodec libtiff Boost::disable_autolinking Boost::thread ${PUGIXML_LIBRARY}) + generate_export_header(multiresolutionimageinterface) + set_target_properties(multiresolutionimageinterface PROPERTIES DEBUG_POSTFIX _d) + diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb index 1daade9be4b..10038ee5686 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb @@ -23,6 +23,8 @@ builddependencies = [ ('CMake', '3.20.1') ] +configopts = '-DBUILD_SHARED_AND_STATIC_LIBS=ON -DPUGIXML_HEADER_ONLY=True ' + sanity_check_paths = { 'files': [], 'dirs': ['lib'], From 88861b5a167ec9330a18277400a55017714105cd Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 17 Nov 2021 16:48:15 +0100 Subject: [PATCH 2000/9987] Added sanity check --- .../easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb index aa55bbf22a5..3f346a90a50 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb @@ -55,8 +55,10 @@ builddependencies = [ ('CMake', '3.20.1'), ] +sanity_check_commands = ['python -c "import multiresolutionimageinterface"'] + sanity_check_paths = { - 'files': [], + 'files': ['bin/ASAP', 'bin/multiresolutionimageinterface.py', 'lib/libmultiresolutionimageinterface.so'], 'dirs': ['bin'] } From ed42930b5c912fae7538f61d1b0267563d0772ef Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Wed, 17 Nov 2021 16:52:12 +0100 Subject: [PATCH 2001/9987] Delete ASAP-2.0-foss-2021a.eb --- .../easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb | 63 ------------------- 1 file changed, 63 deletions(-) delete mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb deleted file mode 100644 index 6c450b0d493..00000000000 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a.eb +++ /dev/null @@ -1,63 +0,0 @@ -easyblock = 'CMakeMake' - -separate_build_dir = True - -name = 'ASAP' -version = '2.0' - -homepage = "https://computationalpathologygroup.github.io/ASAP/" -description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface -for making annotations. It consists of two main components: an IO library for reading and writing -multi-resolution images and a viewer component for visualizing such images.""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -source_urls = ['https://github.com/computationalpathologygroup/ASAP/archive'] -sources = ['%(name)s-%(version)s.tar.gz'] -patches = [ - 'ASAP-2.0_libjpeg.patch', -] -checksums = [ - 'e5d8b0aff6f86a3c7319062ca1f9e35b867da1c80667a80b55ee2a876f897202', # ASAP-2.0.tar.gz - '7cf1403da21cc2bbf9ea95f39de46982d95e375559203deb0f9826e4cf168e04', # ASAP-1.9_libjpeg.patch -] - -configopts = '-DOPENSLIDE_INCLUDE_DIR=$EBROOTOPENSLIDE/include/openslide ' -configopts += '-DPugiXML_INCLUDE_DIR=$EBROOTPUGIXML/include ' -configopts += '-DDCMTKJPEG_INCLUDE_DIR=$EBROOTDCMTK ' -configopts += '-DWRAP_MULTIRESOLUTIONIMAGEINTERFACE_PYTHON=TRUE -DBUILD_ASAP=TRUE ' -configopts += '-DBUILD_EXECUTABLES=TRUE -DBUILD_IMAGEPROCESSING=TRUE ' -configopts += '-DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE ' -# Otherwise, it picks up on the system swig -configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig ' - -dependencies = [ - ('CUDA', '11.3.1', '', True), - ('Boost', '1.76.0'), - ('Python', '3.9.5'), - ('OpenCV', '4.5.3', '-CUDA-%(cudaver)s-contrib'), - ('Qt5', '5.15.2'), - ('LibTIFF', '4.2.0'), - ('libjpeg-turbo', '2.0.6'), - ('JasPer', '2.0.28'), - ('DCMTK', '3.6.6'), - ('SWIG', '4.0.2'), - ('OpenSlide', '3.4.1', '-largefiles'), - ('pugixml', '1.11.4'), - ('zlib', '1.2.11'), -] - -builddependencies = [ - ('binutils', '2.36.1'), - ('CMake', '3.20.1'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin'] -} - -# ASAP installs its python interface in bin. Ugly, but we'll need to add it to PYTHONPATH -modextrapaths = {'PYTHONPATH': ['bin']} - -moduleclass = 'vis' From e2d64f942c2fc7be2b422eadc435242b07b6086e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Nov 2021 17:13:18 +0100 Subject: [PATCH 2002/9987] adding easyconfigs: SSPACE_Basic-2.1.1-GCC-10.2.0.eb --- .../SSPACE_Basic-2.1.1-GCC-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0.eb new file mode 100644 index 00000000000..80c11eca52b --- /dev/null +++ b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'Tarball' + +name = 'SSPACE_Basic' +version = '2.1.1' + +homepage = 'https://github.com/nsoranzo/sspace_basic' +description = "SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/nsoranzo/sspace_basic/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a23327a79a18e520544f0ea923b6c92ff2cc869617ade1c75e118b179caa0919'] + +dependencies = [ + ('Perl', '5.32.0'), + ('Python', '2.7.18'), + ('Bowtie', '1.3.0'), +] + +fix_perl_shebang_for = ['*.pl', 'bin/*.pl', 'tools/*.pl'] + +sanity_check_paths = { + 'files': ['dotlib/DotLib.pm', 'README', 'SSPACE_Basic.pl'], + 'dirs': ['bin', 'tools'], +} + +sanity_check_commands = [ + "SSPACE_Basic.pl 2>&1 | grep 'General Parameters'", + "perldoc -lm DotLib", + "qseq2fastq.pl 2>&1 | grep '^Usage:'", + "TQS.py --help", +] + +modextrapaths = { + 'PATH': ['', 'tools'], + 'PERL5LIB': 'dotlib', +} + +moduleclass = 'bio' From 6b6a95402b253cd6ea5dc4786082efd8265b789d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Nov 2021 17:39:36 +0100 Subject: [PATCH 2003/9987] add missing Python versionsuffix for SSPACE_Basic --- ...-10.2.0.eb => SSPACE_Basic-2.1.1-GCC-10.2.0-Python-2.7.18.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/s/SSPACE_Basic/{SSPACE_Basic-2.1.1-GCC-10.2.0.eb => SSPACE_Basic-2.1.1-GCC-10.2.0-Python-2.7.18.eb} (96%) diff --git a/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0-Python-2.7.18.eb similarity index 96% rename from easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0.eb rename to easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0-Python-2.7.18.eb index 80c11eca52b..ca5bbccf326 100644 --- a/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SSPACE_Basic/SSPACE_Basic-2.1.1-GCC-10.2.0-Python-2.7.18.eb @@ -2,6 +2,7 @@ easyblock = 'Tarball' name = 'SSPACE_Basic' version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/nsoranzo/sspace_basic' description = "SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension" From 45ceede0a6c1c07cd625993745378e3b7ac4ecc7 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 17 Nov 2021 16:59:26 +0000 Subject: [PATCH 2004/9987] adding easyconfigs: torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb --- ...ext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 00000000000..be7e5d73e64 --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.10.0' +local_pytorch_version = '1.9.0' +local_python_suffix = '-Python-%(pyver)s' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['149788775659ceeeaa9ad70a1b12fd5b9825658ac72c2a113cbf0bd0a2e7f5df'] + +builddependencies = [ + ('RE2', '2021-06-01'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('SentencePiece', '0.1.96'), + ('tqdm', '4.56.2'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.1.5'), +] + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/BuildExtension/d' setup.py &&" + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From df1b740d0b062f59aca9812bf755d48af77aa4d9 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 17 Nov 2021 17:03:29 +0000 Subject: [PATCH 2005/9987] adding easyconfigs: torchvision-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb --- ...ion-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 00000000000..4fa09e8900b --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,26 @@ +name = 'torchvision' +version = '0.10.0' +local_pytorch_version = '1.9.0' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['82bb2c2b03d8a65f4ea74bb0ee5566b0876a1992aceefb1e11475c7b5d2e857b'] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('Python', '3.8.6'), + ('Pillow-SIMD', '7.1.2'), + ('PyTorch', local_pytorch_version), +] + +# Defaults. Can be changed with --cuda-compute-capabilities +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0'] + +moduleclass = 'vis' From 15178b3bd73e2d7304be75dfb2d1ade99a44a18d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Nov 2021 18:21:00 +0100 Subject: [PATCH 2006/9987] adding easyconfigs: CUDA-11.5.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-11.5.0.eb | 26 +++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.5.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.5.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.5.0.eb new file mode 100644 index 00000000000..66d53c6bea7 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.5.0.eb @@ -0,0 +1,26 @@ +name = 'CUDA' +version = '11.5.0' +local_nv_version = '495.29.05' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + 'ae0a1693d9497cf3d81e6948943e3794636900db71c98d58eefdacaf7f1a1e4c', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '95baefdc5adf165189407b119861ffb2e9800fd94d7fc81d10fb81ed36dc12db', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '6ea9d520cc956cc751a5ac54f4acc39109627f4e614dd0b1a82cc86f2aa7d8c4', + } +] + +moduleclass = 'system' From 9396d76c8f121c6c3af1df4469e34b2085da941b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 17 Nov 2021 18:28:53 +0100 Subject: [PATCH 2007/9987] adding easyconfigs: einops-0.3.2-GCCcore-10.2.0.eb --- .../e/einops/einops-0.3.2-GCCcore-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..f9d83389844 --- /dev/null +++ b/easybuild/easyconfigs/e/einops/einops-0.3.2-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'einops' +version = '0.3.2' + +homepage = 'https://einops.rocks/' +description = """ +Flexible and powerful tensor operations for readable and reliable code. +Supports numpy, pytorch, tensorflow, jax, and others.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['5200e413539f0377f4177ef00dc019968f4177c49b1db3e836c7883df2a5fe2e'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' From d00434d02875c2b98f4369931783acbb3f9a4de5 Mon Sep 17 00:00:00 2001 From: sdavis2 Date: Wed, 17 Nov 2021 12:45:49 -0500 Subject: [PATCH 2008/9987] adding easyconfigs: HyPhy-2.5.33-gompi-2021a.eb --- .../h/HyPhy/HyPhy-2.5.33-gompi-2021a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.33-gompi-2021a.eb diff --git a/easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.33-gompi-2021a.eb b/easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.33-gompi-2021a.eb new file mode 100644 index 00000000000..7b083e8bb5a --- /dev/null +++ b/easybuild/easyconfigs/h/HyPhy/HyPhy-2.5.33-gompi-2021a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ + +easyblock = "CMakeMake" + +name = 'HyPhy' +version = '2.5.33' + +homepage = 'https://veg.github.io/hyphy-site/' +description = """HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package + for the analysis of genetic sequences (in particular the inference of natural selection) + using techniques in phylogenetics, molecular evolution, and machine learning""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://github.com/veg/hyphy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['7859981f645efa31911672803164715983068b3f56b597bc19908527639fa54b'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('cURL', '7.76.0'), +] + +buildopts = [ + 'hyphy', + 'HYPHYMPI', +] + +sanity_check_paths = { + 'files': ['bin/hyphy', 'bin/HYPHYMPI'], + 'dirs': [], +} + +moduleclass = 'bio' From 93d7f72a111c8d74f676ae70c85546ea09607487 Mon Sep 17 00:00:00 2001 From: sdavis2 Date: Wed, 17 Nov 2021 12:47:06 -0500 Subject: [PATCH 2009/9987] adding easyconfigs: GTDB-Tk-1.7.0-foss-2020b.eb --- .../g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb new file mode 100644 index 00000000000..d0bc5d3e526 --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'GTDB-Tk' +version = '1.7.0' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://pypi.python.org/packages/source/g/gtdbtk'] +sources = ['gtdbtk-%(version)s.tar.gz'] +checksums = ['36b65074845e7edef4d7aeead286c770fb9a03ddbff63946533fa2e1934e8f26'] + +dependencies = [ + ('Python', '3.8.6'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.3.3'), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', True), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.56.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 2e577197ecf549c0e3f1e8b1a59b16107d95f154 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Nov 2021 19:06:38 +0100 Subject: [PATCH 2010/9987] adding easyconfigs: sympy-1.9-foss-2021b.eb, gmpy2-2.1.0rc1-GCC-11.2.0.eb --- .../g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb | 25 +++++++++++++ .../s/sympy/sympy-1.9-foss-2021b.eb | 35 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb new file mode 100644 index 00000000000..34f391736cd --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.0rc1' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['86cb6d8e5837560c32c706d48d6ed25676be6b3c79e6aa5d245965b9e99231b9'] + +dependencies = [ + ('Python', '3.9.6'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb new file mode 100644 index 00000000000..d2f13681adb --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.9' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('gmpy2', '2.1.0rc1'), +] + +download_dep_fail = True +use_pip = True + +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +moduleclass = 'math' From c507d56366c5a7c6825ce1db40b77b40bd1ad59f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Nov 2021 19:08:12 +0100 Subject: [PATCH 2011/9987] adding easyconfigs: Seaborn-0.11.2-foss-2021b.eb --- .../s/Seaborn/Seaborn-0.11.2-foss-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.2-foss-2021b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.2-foss-2021b.eb new file mode 100644 index 00000000000..c00e1819b13 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.11.2-foss-2021b.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.11.2' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cf45e9286d40826864be0e3c066f98536982baf701a7caa386511792d61ff4f6'] + +dependencies = [ + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 5b97439a03915a0d793af929f4f339faab98c402 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Nov 2021 23:20:16 +0100 Subject: [PATCH 2012/9987] adding easyconfigs: OpenMPI-4.0.7-GCC-10.3.0.eb --- .../o/OpenMPI/OpenMPI-4.0.7-GCC-10.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.7-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.7-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.7-GCC-10.3.0.eb new file mode 100644 index 00000000000..38a20d48d97 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.7-GCC-10.3.0.eb @@ -0,0 +1,32 @@ +name = 'OpenMPI' +version = '4.0.7' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['269a4106312c80a9a6991da7f7c342195b73deea387048887e77e7aedc6dbf2d'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.4.1'), + ('libevent', '2.1.12'), + ('UCX', '1.10.0'), + ('libfabric', '1.12.1'), + ('PMIx', '3.2.3'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From d7b1706665468f64edd60105675cf5b002298be5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 18 Nov 2021 08:27:47 +0100 Subject: [PATCH 2013/9987] Add export of device lib location --- .../c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb index d6063184265..000810eb21b 100644 --- a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb @@ -63,4 +63,8 @@ components = [ }), ] +modextravars = { + 'HIP_DEVICE_LIB_PATH': '%(installdir)s/amdgcn/bitcode', +} + moduleclass = 'tools' From 3626ea2693a11185c91fa840f331e9300227cebd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 18 Nov 2021 08:28:56 +0100 Subject: [PATCH 2014/9987] Update easybuild/easyconfigs/r/rocm-smi/rocm-smi-4.5.0-GCCcore-11.2.0.eb Co-authored-by: SebastianAchilles --- .../easyconfigs/r/rocm-smi/rocm-smi-4.5.0-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-4.5.0-GCCcore-11.2.0.eb index 9af417e9769..6edae76da88 100644 --- a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-4.5.0-GCCcore-11.2.0.eb @@ -18,6 +18,7 @@ sources = ["rocm-%(version)s.tar.gz"] checksums = ['43a2cc2ec548cc28698ca4fa01a947a4414febd433936a8d9770bf6f6ed55e4f'] builddependencies = [ + ('binutils', '2.37'), ('CMake', '3.21.1'), ] From 5e37a77e60741d1fceccc8b8fa14ee2a7b36d6b7 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 18 Nov 2021 12:07:23 +0000 Subject: [PATCH 2015/9987] adding easyconfigs: rclone-1.57.0.eb, Go-1.17.3.eb --- easybuild/easyconfigs/g/Go/Go-1.17.3.eb | 22 ++++++++++++ .../easyconfigs/r/rclone/rclone-1.57.0.eb | 36 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.17.3.eb create mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.57.0.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.17.3.eb b/easybuild/easyconfigs/g/Go/Go-1.17.3.eb new file mode 100644 index 00000000000..8465e8503cc --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.17.3.eb @@ -0,0 +1,22 @@ +easyblock = 'Tarball' + +name = 'Go' +version = '1.17.3' + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] +sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] +checksums = ['550f9845451c0c94be679faf116291e7807a8d78b43149f9506c1b15eb89008c'] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +modextravars = {'GOROOT': '%(installdir)s'} +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.57.0.eb b/easybuild/easyconfigs/r/rclone/rclone-1.57.0.eb new file mode 100644 index 00000000000..d34ee177ea3 --- /dev/null +++ b/easybuild/easyconfigs/r/rclone/rclone-1.57.0.eb @@ -0,0 +1,36 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'GoPackage' + +name = 'rclone' +version = '1.57.0' + +homepage = 'https://rclone.org' + +description = """ + Rclone is a command line program to sync files and directories to and from + a variety of online storage services +""" + +toolchain = SYSTEM + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['294f7a6b0874509997d3a9ffae7c74f0c45b687df0ac7d7742f284ad3814fe55'] + +# rclone 1.57.0 needs at least Go 1.17 +builddependencies = [('Go', '1.17.3')] + +postinstallcmds = [ + "mkdir -p %(installdir)s/share/{doc,man/man1}", + "cp README.* MANUAL.* %(installdir)s/share/doc/", + "cp rclone.1 %(installdir)s/share/man/man1/", +] + +sanity_check_paths = { + 'files': ['bin/rclone', 'share/doc/README.md', 'share/man/man1/rclone.1'], + 'dirs': [] +} + +sanity_check_commands = ['rclone --version'] + +moduleclass = 'tools' From 61e505908acfd4fc664d0129702c0bfc5fcd323a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Nov 2021 14:50:37 +0100 Subject: [PATCH 2016/9987] adding easyconfigs: GPy-1.10.0-foss-2021b.eb --- .../g/GPy/GPy-1.10.0-foss-2021b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPy/GPy-1.10.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/g/GPy/GPy-1.10.0-foss-2021b.eb b/easybuild/easyconfigs/g/GPy/GPy-1.10.0-foss-2021b.eb new file mode 100644 index 00000000000..4d0e60245aa --- /dev/null +++ b/easybuild/easyconfigs/g/GPy/GPy-1.10.0-foss-2021b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'GPy' +version = '1.10.0' + +homepage = 'https://sheffieldml.github.io/GPy' +description = "GPy is a Gaussian Process (GP) framework written in Python" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle' ,'2021.10'), + ('matplotlib', '3.4.3'), +] + +use_pip = True + +exts_list = [ + ('paramz', '0.9.5', { + 'checksums': ['0917211c0f083f344e7f1bc997e0d713dbc147b6380bc19f606119394f820b9a'], + }), + (name, version, { + 'checksums': ['a2b793ef8d0ac71739e7ba1c203bc8a5afa191058b42caa617e0e29aa52aa6fb'], + 'modulename': name, + }), +] + + +# note: running the tests takes 15-20min! +sanity_check_commands = ["python -c 'import GPy; GPy.tests()'"] + +sanity_pip_check = True + +moduleclass = 'tools' From 04ae9e90e3e37d4658efcbd80bb631cfe4959bd5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Nov 2021 15:19:37 +0100 Subject: [PATCH 2017/9987] trivial style fix for GPy easyconfig --- easybuild/easyconfigs/g/GPy/GPy-1.10.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GPy/GPy-1.10.0-foss-2021b.eb b/easybuild/easyconfigs/g/GPy/GPy-1.10.0-foss-2021b.eb index 4d0e60245aa..18477ef9c28 100644 --- a/easybuild/easyconfigs/g/GPy/GPy-1.10.0-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GPy/GPy-1.10.0-foss-2021b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Python', '3.9.6'), - ('SciPy-bundle' ,'2021.10'), + ('SciPy-bundle', '2021.10'), ('matplotlib', '3.4.3'), ] From a399689daf13c6384906eee90b53aeb08bb7b2c9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 18 Nov 2021 22:09:22 +0100 Subject: [PATCH 2018/9987] adding easyconfigs: strace-5.14-GCCcore-11.2.0.eb --- .../s/strace/strace-5.14-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..fbaef728546 --- /dev/null +++ b/easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'strace' +version = '5.14' + +homepage = 'https://strace.io/' +description = """ +strace is a diagnostic, debugging and instructional userspace utility for Linux. It is used to monitor and tamper with +interactions between processes and the Linux kernel, which include system calls, signal deliveries, and changes of +process state. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/strace/strace/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['901bee6db5e17debad4530dd9ffb4dc9a96c4a656edbe1c3141b7cb307b11e73'] + +builddependencies = [ + ('binutils', '2.37'), +] + +sanity_check_paths = { + 'files': ['bin/strace-log-merge', 'bin/strace'], + 'dirs': ['share'] +} + +moduleclass = 'system' From 23eddbf110a535cfec0c6276f8a1ffb86be039a2 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 18 Nov 2021 22:55:59 +0100 Subject: [PATCH 2019/9987] Solves https://github.com/easybuilders/easybuild-easyconfigs/issues/14359 --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 3 + .../PyTorch-1.10.0_skip_cmake_rpath.patch | 191 ++++++++++++++++++ 2 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_cmake_rpath.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index 0c16905a596..d1d838d1247 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -32,6 +32,7 @@ patches = [ 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -60,6 +61,8 @@ checksums = [ '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', + # PyTorch-1.10.0_skip_cmake_rpath.patch + 'de49323432b41fc401ddaf86f11eb565aa43eeb56380fdd2b1385db1a05dd4ad', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_cmake_rpath.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_cmake_rpath.patch new file mode 100644 index 00000000000..c39d317e4ba --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_cmake_rpath.patch @@ -0,0 +1,191 @@ +# Author: Caspar van Leeuwen +# PyTorch's CMAKE configuration by default sets RUNPATH on libraries if they link other libraries +# that are outside the build tree, which is done because of the CMAKE config on +# https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L10. +# This provides problems, since the cuda stubs library path then also gets added to the RUNPATH. +# As a result, at runtime, the stub version of things like libcuda.so.1 gets picked up, instead of the real drivers +# See https://github.com/easybuilders/easybuild-easyconfigs/issues/14359 +# This line https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L16 +# Makes sure that any path that is linked, is also added to the RUNPATH. +# This patch changes behavior for the libraries that were failing, i.e. the ones in this list: +# https://github.com/easybuilders/easybuild-easyconfigs/issues/14359#issuecomment-970479904 +# This is done by setting INSTALL_RPATH_USE_LINK_PATH to false, and instead, specifying the RPATH +# explicitely by defining INSTALL_RPATH, but only adding directories that do not match to the "stubs" regex +diff -Nru pytorch.orig/caffe2/CMakeLists.txt pytorch/caffe2/CMakeLists.txt +--- pytorch.orig/caffe2/CMakeLists.txt 2021-11-17 11:46:01.797337624 +0100 ++++ pytorch/caffe2/CMakeLists.txt 2021-11-18 19:05:35.637707235 +0100 +@@ -630,8 +630,33 @@ + else() + set(DELAY_LOAD_FLAGS "") + endif() +- target_link_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB} ${DELAY_LOAD_FLAGS}) ++ # message("CUDA_NVRTC: ${CUDA_NVRTC}") ++ # message("CUDA_NVRTC_LIB: ${CUDA_NVRTC_LIB}") ++ # message("CUDA_CUDA_LIB: ${CUDA_CUDA_LIB}") ++ # message("DELAY_LOAD_FLAGS: ${DELAY_LOAD_FLAGS}") ++ # if(CUDA_CUDA_LIB MATCHES "stubs") ++ # message("stubs libraries found in the CUDA_CUDA_LIB: ${CUDA_CUDA_LIB}") ++ # else() ++ # message("Stubs libs not found in CUDA_CUDA_LIB: ${CUDA_CUDA_LIB}") ++ # endif() ++ # Make sure the CUDA stubs folder doesn't end up in the RPATH of CAFFE2_NVRTC: ++ set(CAFFE2_NVRTC_LIBS ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB}) ++ foreach(LIB IN LISTS CAFFE2_NVRTC_LIBS) ++ message("LIB: ${LIB}") ++ if(LIB MATCHES "stubs") ++ message("Filtering ${LIB} from being set in caffe2_nvrtc's RPATH, because it appears to point to the CUDA stubs directory, which should not be RPATHed.") ++ else() ++ cmake_path(GET LIB PARENT_PATH LIB_PATH) ++ message("LIBPATH: ${LIB_PATH}") ++ list(APPEND CAFFE2_NVRTC_RPATH ${LIB_PATH}) ++ endif() ++ endforeach() ++ message("CAFFE2_NVRTC_RPATH: ${CAFFE2_NVRTC_RPATH}") ++ set_target_properties(caffe2_nvrtc PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(caffe2_nvrtc PROPERTIES INSTALL_RPATH "${CAFFE2_NVRTC_RPATH}") ++ target_link_libraries(caffe2_nvrtc ${CAFFE2_NVRTC_LIBS} ${DELAY_LOAD_FLAGS}) + target_include_directories(caffe2_nvrtc PRIVATE ${CUDA_INCLUDE_DIRS}) ++# message(FATAL_ERROR "STOP HERE, we're debugging") + install(TARGETS caffe2_nvrtc DESTINATION "${TORCH_INSTALL_LIB_DIR}") + if(USE_NCCL AND BUILD_SPLIT_CUDA) + list(APPEND Caffe2_GPU_SRCS_CPP +diff -Nru pytorch.orig/test/cpp/api/CMakeLists.txt pytorch/test/cpp/api/CMakeLists.txt +--- pytorch.orig/test/cpp/api/CMakeLists.txt 2021-11-17 11:46:02.991350652 +0100 ++++ pytorch/test/cpp/api/CMakeLists.txt 2021-11-18 19:06:41.207423777 +0100 +@@ -61,6 +61,22 @@ + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + ++ # Make sure the CUDA stubs folder doesn't end up in the RPATH of test_api: ++ set(TEST_API_LIBS ${CUDA_LIBRARIES} ${CUDA_NVRTC_LIB} ${CUDA_CUDA_LIB} ${TORCH_CUDA_LIBRARIES}) ++ foreach(LIB IN LISTS TEST_API_LIBS) ++ message("LIB: ${LIB}") ++ if(LIB MATCHES "stubs") ++ message("Filtering ${LIB} from being set in caffe2_nvrtc's RPATH, because it appears to point to the CUDA stubs directory, which should not be RPATHed.") ++ else() ++ cmake_path(GET LIB PARENT_PATH LIB_PATH) ++ message("LIBPATH: ${LIB_PATH}") ++ list(APPEND TEST_API_RPATH ${LIB_PATH}) ++ endif() ++ endforeach() ++ message("TEST_API_RPATH: ${TEST_API_RPATH}") ++ set_target_properties(test_api PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(test_api PROPERTIES INSTALL_RPATH "${TEST_API_RPATH}") ++ + target_compile_definitions(test_api PRIVATE "USE_CUDA") + endif() + +diff -Nru pytorch.orig/test/cpp/dist_autograd/CMakeLists.txt pytorch/test/cpp/dist_autograd/CMakeLists.txt +--- pytorch.orig/test/cpp/dist_autograd/CMakeLists.txt 2021-11-17 11:46:02.993350674 +0100 ++++ pytorch/test/cpp/dist_autograd/CMakeLists.txt 2021-11-18 19:06:18.389174421 +0100 +@@ -16,6 +16,22 @@ + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + ++ # Make sure the CUDA stubs folder doesn't end up in the RPATH of test_dist_autograd: ++ set(DIST_AUTOGRAD_LIBS ${CUDA_LIBRARIES} ${CUDA_NVRTC_LIB} ${CUDA_CUDA_LIB} ${TORCH_CUDA_LIBRARIES}) ++ foreach(LIB IN LISTS DIST_AUTOGRAD_LIBS) ++ message("LIB: ${LIB}") ++ if(LIB MATCHES "stubs") ++ message("Filtering ${LIB} from being set in caffe2_nvrtc's RPATH, because it appears to point to the CUDA stubs directory, which should not be RPATHed.") ++ else() ++ cmake_path(GET LIB PARENT_PATH LIB_PATH) ++ message("LIBPATH: ${LIB_PATH}") ++ list(APPEND DIST_AUTOGRAD_RPATH ${LIB_PATH}) ++ endif() ++ endforeach() ++ message("DIST_AUTOGRAD_RPATH: ${DIST_AUTOGRAD_RPATH}") ++ set_target_properties(test_dist_autograd PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(test_dist_autograd PROPERTIES INSTALL_RPATH "${DIST_AUTOGRAD_RPATH}") ++ + target_compile_definitions(test_dist_autograd PRIVATE "USE_CUDA") + endif() + +diff -Nru pytorch.orig/test/cpp/jit/CMakeLists.txt pytorch/test/cpp/jit/CMakeLists.txt +--- pytorch.orig/test/cpp/jit/CMakeLists.txt 2021-11-17 11:46:02.989350630 +0100 ++++ pytorch/test/cpp/jit/CMakeLists.txt 2021-11-18 19:05:41.396770168 +0100 +@@ -94,6 +94,7 @@ + list(APPEND JIT_TEST_DEPENDENCIES onnx_library) + endif(MSVC) + ++ + target_link_libraries(test_jit PRIVATE ${JIT_TEST_DEPENDENCIES}) + target_include_directories(test_jit PRIVATE ${ATen_CPU_INCLUDE}) + +@@ -109,6 +110,22 @@ + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + ++ # Make sure the CUDA stubs folder doesn't end up in the RPATH of test_jit: ++ set(TEST_JIT_LIBS ${CUDA_LIBRARIES} ${CUDA_NVRTC_LIB} ${CUDA_CUDA_LIB} ${TORCH_CUDA_LIBRARIES}) ++ foreach(LIB IN LISTS TEST_JIT_LIBS) ++ message("LIB: ${LIB}") ++ if(LIB MATCHES "stubs") ++ message("Filtering ${LIB} from being set in test_jit's RPATH, because it appears to point to the CUDA stubs directory, which should not be RPATHed.") ++ else() ++ cmake_path(GET LIB PARENT_PATH LIB_PATH) ++ message("LIBPATH: ${LIB_PATH}") ++ list(APPEND TEST_JIT_RPATH ${LIB_PATH}) ++ endif() ++ endforeach() ++ message("TEST_JIT_RPATH: ${TEST_JIT_RPATH}") ++ set_target_properties(test_jit PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(test_jit PROPERTIES INSTALL_RPATH "${TEST_JIT_RPATH}") ++ + target_compile_definitions(test_jit PRIVATE USE_CUDA) + elseif(USE_ROCM) + target_link_libraries(test_jit PRIVATE +diff -Nru pytorch.orig/test/cpp/rpc/CMakeLists.txt pytorch/test/cpp/rpc/CMakeLists.txt +--- pytorch.orig/test/cpp/rpc/CMakeLists.txt 2021-11-17 11:46:02.991350652 +0100 ++++ pytorch/test/cpp/rpc/CMakeLists.txt 2021-11-18 19:06:30.502306793 +0100 +@@ -39,6 +39,22 @@ + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + ++ # Make sure the CUDA stubs folder doesn't end up in the RPATH of test_cpp_rpc: ++ set(CPP_RPC_LIBS ${CUDA_LIBRARIES} ${CUDA_NVRTC_LIB} ${CUDA_CUDA_LIB} ${TORCH_CUDA_LIBRARIES}) ++ foreach(LIB IN LISTS CPP_RPC_LIBS) ++ message("LIB: ${LIB}") ++ if(LIB MATCHES "stubs") ++ message("Filtering ${LIB} from being set in caffe2_nvrtc's RPATH, because it appears to point to the CUDA stubs directory, which should not be RPATHed.") ++ else() ++ cmake_path(GET LIB PARENT_PATH LIB_PATH) ++ message("LIBPATH: ${LIB_PATH}") ++ list(APPEND CPP_RPC_RPATH ${LIB_PATH}) ++ endif() ++ endforeach() ++ message("CPP_RPC_RPATH: ${CPP_RPC_RPATH}") ++ set_target_properties(test_cpp_rpc PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(test_cpp_rpc PROPERTIES INSTALL_RPATH "${CPP_RPC_RPATH}") ++ + target_compile_definitions(test_cpp_rpc PRIVATE "USE_CUDA") + endif() + +diff -Nru pytorch.orig/test/cpp/tensorexpr/CMakeLists.txt pytorch/test/cpp/tensorexpr/CMakeLists.txt +--- pytorch.orig/test/cpp/tensorexpr/CMakeLists.txt 2021-11-17 11:46:02.993350674 +0100 ++++ pytorch/test/cpp/tensorexpr/CMakeLists.txt 2021-11-18 19:06:00.988984273 +0100 +@@ -62,6 +62,24 @@ + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + target_compile_definitions(tutorial_tensorexpr PRIVATE USE_CUDA) ++ ++ # Make sure the CUDA stubs folder doesn't end up in the RPATH of tutorial_tensorexpr: ++ set(CUDA_LINK_LIBS ${CUDA_LIBRARIES} ${CUDA_NVRTC_LIB} ${CUDA_CUDA_LIB} ${TORCH_CUDA_LIBRARIES}) ++ foreach(LIB IN LISTS CUDA_LINK_LIBS) ++ message("LIB: ${LIB}") ++ if(LIB MATCHES "stubs") ++ message("Filtering ${LIB} from being set in test_tensorexpr and tutorial_tensorexpr RPATH, because it appears to point to the CUDA stubs directory, which should not be RPATHed.") ++ else() ++ cmake_path(GET LIB PARENT_PATH LIB_PATH) ++ message("LIBPATH: ${LIB_PATH}") ++ list(APPEND TENSOREXPR_RPATH ${LIB_PATH}) ++ endif() ++ endforeach() ++ message("TENSOREXPR_RPATH: ${TENSOREXPR_RPATH}") ++ set_target_properties(test_tensorexpr PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(test_tensorexpr PROPERTIES INSTALL_RPATH "${TENSOREXPR_RPATH}") ++ set_target_properties(tutorial_tensorexpr PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(tutorial_tensorexpr PROPERTIES INSTALL_RPATH "${TENSOREXPR_RPATH}") + elseif(USE_ROCM) + target_link_libraries(test_tensorexpr PRIVATE + ${ROCM_HIPRTC_LIB} From bf72611df98e9a3e3c4f6963bcecc7a06a5c4c97 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Fri, 19 Nov 2021 13:05:24 +1030 Subject: [PATCH 2020/9987] dep <- Biopython + --- easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb index 3aaa7d391ff..b73ce52c916 100644 --- a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.6.7-foss-2021a.eb @@ -22,6 +22,7 @@ checksums = ['6e6f70639149612272a3b298a93ac50bba6f9ecece934f2a0ea86d4abde975da'] dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), ] download_dep_fail = True From 1642bb9f8ff6b64a9225d6bdf5ee52c39bdc54a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 19 Nov 2021 11:45:45 +0100 Subject: [PATCH 2021/9987] adding easyconfigs: Schrodinger-2021-4.eb --- .../s/Schrodinger/Schrodinger-2021-4.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb diff --git a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb new file mode 100644 index 00000000000..ba0edb4190a --- /dev/null +++ b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb @@ -0,0 +1,31 @@ +easyblock='PackedBinary' + +name = 'Schrodinger' +version = '2021-4' + +homepage = 'https://www.schrodinger.com/' +description = """ Schrodinger aims to provide integrated software solutions and services + that truly meet its customers needs. We want to empower researchers around the world to + achieve their goals of improving human health and quality of life through advanced computational + techniques that transform the way chemists design compounds and materials. """ + +toolchain = SYSTEM + +# Download from schrodinger.com +sources = ['%(name)s_Suites_%(version)s_Linux-x86_64.tar'] +checksums = ['555eb6e2da507463870e9b15ec89a709daf4510871e192d556b8659430d0fa18'] + +install_cmd = 'cd %(builddir)s/%(name)s_Suites_%(version)s_Linux-x86_64 && ' +install_cmd += './INSTALL -d . -s %(installdir)s -k /usr/tmp -t %(installdir)s/thirdparty -b *' + +sanity_check_paths = { + 'files': ['desmond', 'maestro'], + 'dirs': [], +} + +modextravars = { + 'SCHROD_LICENSE_FILE': '$HOME/.schrodinger_license', + 'SCHRODINGER': '%(installdir)s', +} + +moduleclass = 'bio' From 1d15809db48117f958c0fd670039fe55c599d8bf Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 19 Nov 2021 11:52:00 +0100 Subject: [PATCH 2022/9987] adding easyconfigs: Inspector-2021.4.0.eb --- .../i/Inspector/Inspector-2021.4.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb new file mode 100644 index 00000000000..11b56c0bc1c --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2021.4.0.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'Inspector' +version = '2021.4.0' + +homepage = 'https://software.intel.com/en-us/inspector' +description = """Intel Inspector is a dynamic memory and threading error + checking tool for users developing serial and parallel applications""" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18239/'] +sources = ['l_inspector_oneapi_p_%(version)s.266_offline.sh'] +checksums = ['c8210cbcd0e07cc75e773249a5e4a02cf34894ec80a213939f3a20e6c5705274'] + +dontcreateinstalldir = True + +requires_runtime_license = False + +moduleclass = 'tools' From 3a6258240c5c84687c5279449fc56e1f726344ff Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 19 Nov 2021 15:26:59 +0200 Subject: [PATCH 2023/9987] adding easyconfigs: cpu_features-0.6.0-foss-2020b.eb, Shasta-0.8.0-foss-2020b.eb, spoa-3.4.0-GCC-10.2.0.eb and patches: Shasta-0.8.0-foss-2020b-fix_links.patch --- .../cpu_features-0.6.0-foss-2020b.eb | 28 +++++ .../Shasta-0.8.0-foss-2020b-fix_links.patch | 109 ++++++++++++++++++ .../s/Shasta/Shasta-0.8.0-foss-2020b.eb | 69 +++++++++++ .../s/spoa/spoa-3.4.0-GCC-10.2.0.eb | 31 +++++ 4 files changed, 237 insertions(+) create mode 100644 easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b-fix_links.patch create mode 100644 easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-foss-2020b.eb b/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-foss-2020b.eb new file mode 100644 index 00000000000..455fecffa97 --- /dev/null +++ b/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-foss-2020b.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'cpu_features' +version = '0.6.0' + +homepage = 'https://github.com/google/cpu_features' +description = """A cross-platform C library to retrieve CPU features (such as available instructions) at runtime.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/google/cpu_features/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['95a1cf6f24948031df114798a97eea2a71143bd38a4d07d9a758dda3924c1932'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +modextrapaths = {'CPATH': 'include/cpu_features'} + +sanity_check_paths = { + 'files': ['bin/list_cpu_features', 'lib/libcpu_features.a'], + 'dirs': ['include/cpu_features/'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b-fix_links.patch b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b-fix_links.patch new file mode 100644 index 00000000000..c5d227d4b12 --- /dev/null +++ b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b-fix_links.patch @@ -0,0 +1,109 @@ +diff -ruN shasta-0.8.0_orig/dynamicExecutable/CMakeLists.txt shasta-0.8.0/dynamicExecutable/CMakeLists.txt +--- shasta-0.8.0_orig/dynamicExecutable/CMakeLists.txt 2021-11-11 15:34:47.786798000 +0100 ++++ shasta-0.8.0/dynamicExecutable/CMakeLists.txt 2021-11-11 15:33:29.419991000 +0100 +@@ -53,6 +53,7 @@ + + # Include directory. + include_directories(../src) ++include_directories($EBROOTSCALAPACK) + + # Define our executable. + add_executable(shastaDynamicExecutable ${SOURCES}) +@@ -68,13 +69,13 @@ + shastaDynamicExecutable + shastaDynamicLibrary + atomic boost_system boost_program_options boost_chrono spoa cpu_features png z +- lapack blas gfortran quadmath pthread) ++ openblas gfortran quadmath pthread) + else(X86_64) + target_link_libraries( + shastaDynamicExecutable + shastaDynamicLibrary + atomic boost_system boost_program_options boost_chrono spoa png z +- lapack blas gfortran pthread) ++ openblas gfortran pthread) + endif(X86_64) + + if(BUILD_DEBUG) +diff -ruN shasta-0.8.0_orig/dynamicLibrary/CMakeLists.txt shasta-0.8.0/dynamicLibrary/CMakeLists.txt +--- shasta-0.8.0_orig/dynamicLibrary/CMakeLists.txt 2021-11-11 15:34:39.528314000 +0100 ++++ shasta-0.8.0/dynamicLibrary/CMakeLists.txt 2021-11-16 12:33:17.852745000 +0100 +@@ -54,6 +54,8 @@ + + # Include directory. + include_directories(../src) ++include_directories($EBROOTSCALAPACK) ++ + + # Define our library. + add_library(shastaDynamicLibrary SHARED ${SOURCES}) +@@ -70,23 +72,23 @@ + # Python 3.8 requires the `--embed` flag to be passed in. + # find_python cmake module was introduced in v3.12, which isn't available for installation + # via `apt` on Ubuntu 18.04 LTS. So I am not using it. +-execute_process(COMMAND /usr/bin/python3-config --embed --libs OUTPUT_VARIABLE ++execute_process(COMMAND /usr/bin/env python3-config --embed --libs OUTPUT_VARIABLE + SHASTA_PYTHON_LIBRARIES RESULT_VARIABLE COMMAND_RESULT) + if(${COMMAND_RESULT} EQUAL 0) + # Python3 version is >= 3.8.0. So the --embed flag worked. Otherwise the command + # would have failed with a non-zero exit code. + else() +- execute_process(COMMAND /usr/bin/python3-config --libs OUTPUT_VARIABLE SHASTA_PYTHON_LIBRARIES) ++ execute_process(COMMAND /usr/bin/env python3-config --libs OUTPUT_VARIABLE SHASTA_PYTHON_LIBRARIES) + endif() +-execute_process(COMMAND python3 -m pybind11 --includes OUTPUT_VARIABLE SHASTA_PYTHON_INCLUDES) ++execute_process(COMMAND /usr/bin/env python3 -m pybind11 --includes OUTPUT_VARIABLE SHASTA_PYTHON_INCLUDES) + add_definitions(${SHASTA_PYTHON_INCLUDES}) +-string(STRIP ${SHASTA_PYTHON_LIBRARIES} SHASTA_PYTHON_LIBRARIES) ++string(STRIP "${SHASTA_PYTHON_LIBRARIES}" SHASTA_PYTHON_LIBRARIES) + SET(CMAKE_LINKER_FLAGS "${CMAKE_LINKER_FLAGS} ${SHASTA_PYTHON_LIBRARIES}") + + # Libraries to link with. + target_link_libraries( + shastaDynamicLibrary +- atomic png boost_program_options pthread z spoa lapack blas ${SHASTA_PYTHON_LIBRARIES}) ++ atomic png boost_program_options pthread z spoa openblas ${SHASTA_PYTHON_LIBRARIES}) + + # Install the shared library into the bin directory. + install(TARGETS shastaDynamicLibrary DESTINATION shasta-install/bin) +diff -ruN shasta-0.8.0_orig/staticExecutable/CMakeLists.txt shasta-0.8.0/staticExecutable/CMakeLists.txt +--- shasta-0.8.0_orig/staticExecutable/CMakeLists.txt 2021-11-10 14:30:44.182620000 +0100 ++++ shasta-0.8.0/staticExecutable/CMakeLists.txt 2021-11-11 15:34:12.652136000 +0100 +@@ -49,6 +49,8 @@ + + # Include directory. + include_directories(../src) ++include_directories($EBROOTSCALAPACK) ++ + + # Include directories required on macOS. + if(MACOS) +@@ -86,14 +88,14 @@ + shastaStaticExecutable + shastaStaticLibrary + atomic boost_system boost_program_options boost_chrono spoa cpu_features png z +- lapack blas gfortran quadmath ++ openblas gfortran quadmath + -Wl,--whole-archive -lpthread -Wl,--no-whole-archive) + else(X86_64) + target_link_libraries( + shastaStaticExecutable + shastaStaticLibrary + atomic boost_system boost_program_options boost_chrono spoa png z +- lapack blas gfortran ++ openblas gfortran + -Wl,--whole-archive -lpthread -Wl,--no-whole-archive) + endif(X86_64) + +diff -ruN shasta-0.8.0_orig/staticLibrary/CMakeLists.txt shasta-0.8.0/staticLibrary/CMakeLists.txt +--- shasta-0.8.0_orig/staticLibrary/CMakeLists.txt 2021-11-10 14:30:44.316688000 +0100 ++++ shasta-0.8.0/staticLibrary/CMakeLists.txt 2021-11-11 12:40:27.492732000 +0100 +@@ -49,6 +49,8 @@ + + # Include directory. + include_directories(../src) ++include_directories($EBROOTSCALAPACK) ++ + + # Include directories required on macOS. + if(MACOS) diff --git a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb new file mode 100644 index 00000000000..6479ec878af --- /dev/null +++ b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb @@ -0,0 +1,69 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMakeCp' + +name = 'Shasta' +version = '0.8.0' + +homepage = 'https://github.com/chanzuckerberg/shasta' +description = """ +The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated +by Oxford Nanopore flow cells as input. Computational methods used by the Shasta assembler include: +Using a run-length representation of the read sequence. This makes the assembly process more resilient to errors in +homopolymer repeat counts, which are the most common type of errors in Oxford Nanopore reads. Using in some phases of +the computation a representation of the read sequence based on markers, a fixed subset of short k-mers (k ≈ 10). +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/chanzuckerberg/shasta/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + "Shasta-%(version)s-foss-2020b-fix_links.patch" +] +checksums = [ + '8e94767275fc5352ff192afed783b00b720b6214d8779edc44e9ebe636e9833e', # 0.8.0.tar.gz + 'dfda9a6ca33e37236cbbc27a1d65bb54d361f27ecdb2b9855e46ac6dab6e255e', # Shasta-0.8.0-foss-2020b-fix_links.patch +] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('cURL', '7.72.0'), + ('Boost', '1.74.0'), + ('libpng', '1.6.37'), + ('SeqAn', '2.4.0'), + ('BLAST', '2.11.0', '-Linux_x86_64', True), + ('gnuplot', '5.4.1'), + ('Graphviz', '2.47.0', '-Java-11'), + ('Python', '3.8.6'), + ('pybind11', '2.6.0'), + ('Cereal', '1.3.0', '', True), + ('spoa', '3.4.0'), + ('ScaLAPACK', '2.1.0'), + ('OpenBLAS', '0.3.12'), + ('cpu_features', '0.6.0'), +] + +prebuildopts = "export CPATH=$EBROOTBOOST/include/boost/:$CPATH && " + +buildopts = " && make install -j %(parallel)s" + +files_to_copy = [ + (['shasta-install/bin/*'], 'bin'), + (['shasta-install/bin/*.a'], 'lib'), + (['shasta-install/bin/*.so'], 'lib') +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['lib/shasta.so', 'lib/shasta.a', 'bin/shasta', 'bin/SaveRun.py', 'bin/Copy.py'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..038094f39ea --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-3.4.0-GCC-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '3.4.0' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] +sources = ['spoa-v%(version)s.tar.gz'] +checksums = ['f7411312bd51a0c7e53a702127cc8ba8500247d3f44f01825e591c5b8570f14b'] + +builddependencies = [('CMake', '3.18.4')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a', 'lib/pkgconfig/spoa-1.pc'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +modextrapaths = {'CPATH': 'include/%(namelower)s'} + +moduleclass = 'bio' From 5966ed70830b10d31ec3f53eb13b4d8581e85e20 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Wautelet?= Date: Fri, 19 Nov 2021 15:18:44 +0000 Subject: [PATCH 2024/9987] adding easyconfigs: AmberTools-21-foss-2021a-Python-3.9.5.eb --- .../AmberTools-21-foss-2021a-Python-3.9.5.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..6df8ae9e35a --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,48 @@ +easyblock = 'EB_Amber' + +name = 'AmberTools' +version = '21' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://ambermd.org/' +description = """AmberTools consists of several independently developed packages that work well by themselves, + and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, + with either explicit water or generalized Born solvent models.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_BZ2] + +patches = [ + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_cmake-locate-netcdf.patch', +] + +# Use included BLAS as FlaxiBlas is not linked properly +configopts = " -DBLA_VENDOR=Generic" + +checksums = ['f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd'] + +builddependencies = [ + ('Bison', '3.7.6'), + ('pkg-config', '0.29.2'), + ('CMake', '3.20.1'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('matplotlib', '3.4.2'), + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), + ('FFTW', '3.3.9'), + ('Boost', '1.76.0'), + ('arpack-ng', '3.8.0'), + ('PnetCDF', '1.12.2'), +] + +runtest = False + +moduleclass = 'chem' From 048376745fab85986e51e371aec2c351ba579567 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Nov 2021 19:25:13 +0100 Subject: [PATCH 2025/9987] add patch for libfabric v1.12.1 to fix 'unknown link width 0x10' warning --- .../libfabric-1.12.1-GCCcore-10.3.0.eb | 2 ++ ...fabric-1.12.1_fix-unknown-link-width.patch | 26 +++++++++++++++++++ 2 files changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.12.1_fix-unknown-link-width.patch diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb index 6428a4e759b..80c3e4f2651 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1-GCCcore-10.3.0.eb @@ -24,6 +24,7 @@ sources = [SOURCE_TAR_BZ2] patches = [ '%(name)s-%(version)s_fix-psm3-multiep-default.patch', '%(name)s-%(version)s_disable-psm3-avx-config.patch', + '%(name)s-%(version)s_fix-unknown-link-width.patch', ] checksums = [ 'db3c8e0a495e6e9da6a7436adab905468aedfbd4579ee3da5232a5c111ba642c', # libfabric-1.12.1.tar.bz2 @@ -31,6 +32,7 @@ checksums = [ '298ba67bc04472bc627e642525dd4333fe18f80774814ae86c8e18437ada4e7d', # libfabric-1.12.1_disable-psm3-avx-config.patch '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', + '2db5b4daae4f8c6e1bb79d7a68773f4824ff283f43d6c34c9fedd8d6f9ddd8a1', # libfabric-1.12.1_fix-unknown-link-width.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1_fix-unknown-link-width.patch b/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1_fix-unknown-link-width.patch new file mode 100644 index 00000000000..850984e1ed2 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.12.1_fix-unknown-link-width.patch @@ -0,0 +1,26 @@ +fix for "iunknown link width 0x10" warning +extracted from https://github.com/ofiwg/libfabric/commit/794990cb2a4b2a5bc479240aff4e8573398bc773#diff-a406b74c02115a3845d75f2058ae8a132261b2fb7dff4345bb700f99a87e6dc9 + +diff -ru libfabric-1.12.1.orig/prov/psm3/psm3/psm_verbs_ep.c libfabric-1.12.1/prov/psm3/psm3/psm_verbs_ep.c +--- libfabric-1.12.1.orig/prov/psm3/psm3/psm_verbs_ep.c 2021-04-01 23:01:25.000000000 +0200 ++++ libfabric-1.12.1/prov/psm3/psm3/psm_verbs_ep.c 2021-11-19 19:07:44.000000000 +0100 +@@ -2057,6 +2057,19 @@ + _HFI_ERROR( "unknown link speed 0x%x\n", speed); + return PSM_IBV_RATE_100_GBPS; + } ++ case 16: /* 2x */ ++ switch (speed) { ++ case 1: return PSM_IBV_RATE_5_GBPS; ++ case 2: return PSM_IBV_RATE_10_GBPS; ++ case 4: /* fall through */ ++ case 8: return PSM_IBV_RATE_20_GBPS; ++ case 16: return PSM_IBV_RATE_28_GBPS; ++ case 32: return PSM_IBV_RATE_50_GBPS; ++ case 64: return PSM_IBV_RATE_100_GBPS; ++ default: ++ _HFI_ERROR( "unknown link speed 0x%x\n", speed); ++ return PSM_IBV_RATE_100_GBPS; ++ } + default: + _HFI_ERROR( "unknown link width 0x%x\n", width); + return PSM_IBV_RATE_100_GBPS; From d3c1809a6011daeb5a0d162328f260090bd7f227 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 Nov 2021 22:13:07 +0100 Subject: [PATCH 2026/9987] adding easyconfigs: muparserx-4.0.8-GCCcore-11.2.0.eb --- .../muparserx-4.0.8-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..fa70900332f --- /dev/null +++ b/easybuild/easyconfigs/m/muparserx/muparserx-4.0.8-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'muparserx' +version = '4.0.8' + +homepage = 'https://beltoforion.de/en/muparserx/' +description = 'A C++ Library for Parsing Expressions with Strings, Complex Numbers, Vectors, Matrices and more.' +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'beltoforion' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5913e0a4ca29a097baad1b78a4674963bc7a06e39ff63df3c73fbad6fadb34e1'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['lib64/libmuparserx.a', 'lib64/libmuparserx.%s' % SHLIB_EXT], + 'dirs': ['include/muparserx'], +} + +moduleclass = 'lib' From 0aed7968235a56bc05f170167e83584ff7e8218b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 Nov 2021 22:19:23 +0100 Subject: [PATCH 2027/9987] adding easyconfigs: nlohmann_json-3.10.4-GCCcore-11.2.0.eb --- .../nlohmann_json-3.10.4-GCCcore-11.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8cc1de0956d --- /dev/null +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.4-GCCcore-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'nlohmann_json' +version = '3.10.4' + +homepage = 'https://github.com/nlohmann/json' +description = """JSON for Modern C++""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1155fd1a83049767360e9a120c43c578145db3204d2b309eba49fbbedd0f4ed3'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +sanity_check_paths = { + 'files': ['include/nlohmann/json.hpp'], + 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 0544e1f48a45f4ff4dac692d1cc0e61a3374a49a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 20 Nov 2021 00:14:53 +0100 Subject: [PATCH 2028/9987] patch unimplemented tests in jax v0.2.24 --- .../j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb | 7 ++++++- easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a.eb | 7 ++++++- .../j/jax/jax-0.2.24-foss-2021a_unimplemented.patch | 12 ++++++++++++ 3 files changed, 24 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a_unimplemented.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb index fbbad89cbc9..cd752df2a33 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb @@ -102,12 +102,17 @@ exts_list = [ (name, version, { 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], - 'patches': ['jax-0.2.19_fix-update-of-cache-access-time.patch'], + 'patches': [ + 'jax-0.2.19_fix-update-of-cache-access-time.patch', + 'jax-0.2.24-foss-2021a_unimplemented.patch', + ], 'checksums': [ # jax-v0.2.24.tar.gz '9ffbf86e97a05591eaa1a7a5194cf9ceaed8cf6c2aaa8ffc394568a3a131cae0', # jax-0.2.19_fix-update-of-cache-access-time.patch 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + # jax-0.2.24-foss-2021a_unimplemented.patch + '96fe1b15b55611727b0ae76409b89c44ae21a1c10002507ca8e3c06c2b134f4e', ], 'runtest': "CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests", }), diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a.eb b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a.eb index e5f4479dc5d..1591cf9842a 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a.eb @@ -95,12 +95,17 @@ exts_list = [ (name, version, { 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], - 'patches': ['jax-0.2.19_fix-update-of-cache-access-time.patch'], + 'patches': [ + 'jax-0.2.19_fix-update-of-cache-access-time.patch', + 'jax-0.2.24-foss-2021a_unimplemented.patch', + ], 'checksums': [ # jax-v0.2.24.tar.gz '9ffbf86e97a05591eaa1a7a5194cf9ceaed8cf6c2aaa8ffc394568a3a131cae0', # jax-0.2.19_fix-update-of-cache-access-time.patch 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + # jax-0.2.24-foss-2021a_unimplemented.patch + '96fe1b15b55611727b0ae76409b89c44ae21a1c10002507ca8e3c06c2b134f4e', ], 'runtest': "pytest -n %(parallel)s tests", }), diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a_unimplemented.patch b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a_unimplemented.patch new file mode 100644 index 00000000000..93164d66c3a --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a_unimplemented.patch @@ -0,0 +1,12 @@ +Test raises UNIMPLEMENTED error. So remove. +Patch by Simon Branford (University of Birmginham) +--- tests/host_callback_test.py.orig 2021-11-19 14:12:54.608037000 +0000 ++++ tests/host_callback_test.py 2021-11-19 14:14:09.582155863 +0000 +@@ -2087,6 +2087,7 @@ + expected_res = np.linalg.eigvals(m) + self.assertAllClose(expected_res, fun(m)) + ++ @skip("Raises UNIMPLEMENTED error") + def test_call_doc_example_hlo(self): + """Examples from the documentation: simplest, call a function.""" + From a6694a029c4280fbebe99a40092083c4eef5ef3f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 21 Nov 2021 20:53:07 +0000 Subject: [PATCH 2029/9987] adding easyconfigs: bamtofastq-1.4.0-GCCcore-10.3.0.eb --- .../bamtofastq-1.4.0-GCCcore-10.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..a37f93eaea7 --- /dev/null +++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'Binary' + +name = 'bamtofastq' +version = '1.4.0' + +homepage = 'https://github.com/10XGenomics/bamtofastq' +description = """Convert 10x BAM files to the original FASTQs compatible with 10x pipelines.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Rust', '1.52.1'), + ('CMake', '3.20.1'), + ('bzip2', '1.0.8'), +] + +dependencies = [('bzip2', '1.0.8')] + +extract_sources = True + +install_cmd = "cargo build --release && cargo install --root %(installdir)s --path ." + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' From 6584d8d26866d4e933f876b230d9eed0f3895fd2 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 21 Nov 2021 21:24:10 +0000 Subject: [PATCH 2030/9987] Add missing checksum and use full dep only, for bzip2 --- .../easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb index a37f93eaea7..d982362bf61 100644 --- a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb @@ -10,12 +10,12 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] +checksums = ['b51d32e8aee3b9ace08c54397fddb590209571f47f4051077bcb22b98ca3a5ed'] builddependencies = [ ('binutils', '2.36.1'), ('Rust', '1.52.1'), ('CMake', '3.20.1'), - ('bzip2', '1.0.8'), ] dependencies = [('bzip2', '1.0.8')] From 33b3c6d8b0a7234866bdf5ff72c359dc5102fcfc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 22 Nov 2021 09:34:50 +0100 Subject: [PATCH 2031/9987] add lexming authorship to jax v0.2.24 easyconfig --- easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb index cd752df2a33..f5f2d3f96ab 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb @@ -1,5 +1,6 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) easyblock = 'PythonBundle' name = 'jax' From dbeb56eb887859823e7a1c99950d23c0933af9c5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 22 Nov 2021 09:39:33 +0100 Subject: [PATCH 2032/9987] disable TF32 in runtest and add missing comments to jax v0.2.24 with CUDA --- .../j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb index f5f2d3f96ab..40f17200c2a 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb @@ -115,7 +115,14 @@ exts_list = [ # jax-0.2.24-foss-2021a_unimplemented.patch '96fe1b15b55611727b0ae76409b89c44ae21a1c10002507ca8e3c06c2b134f4e', ], - 'runtest': "CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests", + # deliberately not testing in parallel, as that results in (additional) failing tests; + # use XLA_PYTHON_CLIENT_ALLOCATOR=platform when running GPU tests in parallel, + # to avoid each test fully allocating the GPU memory..., + # see https://github.com/google/jax/issues/7323 and + # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; + # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; + # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests", }), ] From e1a82d105dd5b0e4bdbdec36a05410c3e632a40a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Wautelet?= Date: Mon, 22 Nov 2021 13:06:52 +0000 Subject: [PATCH 2033/9987] Fix checksums --- .../AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb index 6df8ae9e35a..1f399df67c0 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb @@ -19,10 +19,15 @@ patches = [ 'AmberTools-20_cmake-locate-netcdf.patch', ] -# Use included BLAS as FlaxiBlas is not linked properly +# Use included BLAS as FlexiBlas is not linked properly +# configopts = " -DBLA_VENDOR=FlexiBLAS" configopts = " -DBLA_VENDOR=Generic" -checksums = ['f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd'] +checksums = [ + 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools-21.tar.bz2 + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch +] builddependencies = [ ('Bison', '3.7.6'), From 3ff6fbd9670e7d5ab24a12025a1fc433d0c4d723 Mon Sep 17 00:00:00 2001 From: Laurence Alexander Hurst Date: Mon, 22 Nov 2021 13:58:56 +0000 Subject: [PATCH 2034/9987] BerkeleyGW - 2020b --- .../BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb new file mode 100644 index 00000000000..e40828947dd --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.0.1-foss-2020b.eb @@ -0,0 +1,34 @@ +name = 'BerkeleyGW' +version = '3.0.1' + +homepage = 'https://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://berkeley.box.com/shared/static/'] +sources = [{'download_filename': 'm1dgnhiemo47lhxczrn6si71bwxoxor8.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'BerkeleyGW-3.0.1_tests.patch', + 'BerkeleyGW-3.0.1_makefile.patch', + 'BerkeleyGW-3.0.1_version.patch', +] +checksums = [ + '7d8c2cc1ee679afb48efbdd676689d4d537226b50e13a049dbcb052aaaf3654f', # BerkeleyGW-3.0.1.tar.gz + 'f66ff15e2b99de5e808f78a552985fda3181f35c25817de4ac7df4d8f7fddf5a', # BerkeleyGW-3.0.1_tests.patch + '56d90dc4e43db379441b6a1802e24f1f1356cd4aca4eb6d8b673f6c7926a7406', # BerkeleyGW-3.0.1_makefile.patch + '414a4f23e430a2c02bab7bad18bcaf9b62129fa9dd1c2f87bd4bbc9fcb3bdded', # BerkeleyGW-3.0.1_version.patch +] + +dependencies = [ + ('ELPA', '2020.11.001'), + ('Python', '3.8.6'), + ('h5py', '3.1.0'), +] + +runtest = True + +moduleclass = 'phys' From b7de63c81841fd277205567735dcf3f51a4ff5c6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 22 Nov 2021 15:11:10 +0000 Subject: [PATCH 2035/9987] adding easyconfigs: ABRicate-1.0.0-gompi-2021a.eb, any2fasta-0.4.2-GCCcore-10.3.0.eb --- .../a/ABRicate/ABRicate-1.0.0-gompi-2021a.eb | 41 +++++++++++++++++++ .../any2fasta-0.4.2-GCCcore-10.3.0.eb | 35 ++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2021a.eb b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2021a.eb new file mode 100644 index 00000000000..097732fac34 --- /dev/null +++ b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2021a.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'ABRicate' +version = '1.0.0' + +homepage = 'https://github.com/tseemann/abricate' +description = "Mass screening of contigs for antimicrobial and virulence genes" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +# https://github.com/tseemann/abricate +github_account = 'tseemann' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9'] + +dependencies = [ + ('Perl', '5.32.1'), + ('any2fasta', '0.4.2'), + ('BioPerl', '1.7.8'), + ('BLAST+', '2.11.0'), +] + +postinstallcmds = ['%(installdir)s/bin/abricate --setupdb'] + +sanity_check_paths = { + 'files': ['bin/abricate', 'bin/abricate-get_db'], + 'dirs': ['db'], +} + +sanity_check_commands = [ + "abricate --help", + "abricate --list", +] + +modloadmsg = "abricate databases are located in $EBROOTABRICATE/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..2297e7b2bbe --- /dev/null +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# Updated by: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'any2fasta' +version = '0.4.2' + +homepage = 'https://github.com/tseemann/any2fasta' +description = "Convert various sequence formats to FASTA" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +# https://github.com/tseemann/any2fasta +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] + +dependencies = [('Perl', '5.32.1')] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['any2fasta'], + 'dirs': [], +} + +sanity_check_commands = [ + 'any2fasta -h', + 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', +] + +moduleclass = 'tools' From 3e355307053defe227f13c9780dc8fa61b3c52ba Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 22 Nov 2021 15:17:53 +0000 Subject: [PATCH 2036/9987] adding easyconfigs: prokka-1.14.5-gompi-2021a.eb, Bio-SearchIO-hmmer-1.7.3-GCC-10.3.0.eb --- .../Bio-SearchIO-hmmer-1.7.3-GCC-10.3.0.eb | 28 +++++++++++ .../p/prokka/prokka-1.14.5-gompi-2021a.eb | 48 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..c6795ce66cd --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.32.1'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb new file mode 100644 index 00000000000..edb51666011 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb @@ -0,0 +1,48 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.11.0'), + ('Java', '11', '', True), + ('Bio-SearchIO-hmmer', '1.7.3'), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' From 5e8025aa5eaded9e7d837264e040e6a789737099 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 22 Nov 2021 16:24:10 +0100 Subject: [PATCH 2037/9987] Update easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Fix spelling error Co-authored-by: Bob Dröge --- .../a/ASAP/ASAP-2.0_use_pugixml_shared.patch | 52 +++++++++---------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch index f23c48ea628..ac18250a519 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch @@ -1,25 +1,25 @@ -# Author: Caspar van leeuwen -# Make sure to use the shared library of PUGIXML, since linking to the static libarry seems to result in undefined symbol errors: -# ImportError: /home/casparl/.local/easybuild/Centos8/2021/software/ASAP/2.0-foss-2021a/lib/libmultiresolutionimageinterface.so: undefined symbol: _ZNK4pugi10xpath_node6parentEv -diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/annotation/CMakeLists.txt ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/annotation/CMakeLists.txt ---- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/annotation/CMakeLists.txt 2021-06-25 11:50:23.132333349 +0200 -+++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/annotation/CMakeLists.txt 2021-06-25 11:58:03.005555272 +0200 -@@ -25,10 +25,9 @@ - ) - - add_library(annotation SHARED ${ANNOTATION_SOURCE} ${ANNOTATION_HEADERS}) --target_compile_definitions(annotation PRIVATE "PUGIXML_HEADER_ONLY") - generate_export_header(annotation) - target_include_directories(annotation PUBLIC $ $ PRIVATE ${DIAGPathology_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR} ${Boost_INCLUDE_DIRS} ${PugiXML_INCLUDE_DIR}) --target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface) -+target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface ${PUGIXML_LIBRARY}) - set_target_properties(annotation PROPERTIES DEBUG_POSTFIX _d) - - install(TARGETS annotation -diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPugiXML.cmake ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/cmakemodules/FindPugiXML.cmake ---- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPugiXML.cmake 2021-06-25 11:50:23.180337653 +0200 -+++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/cmakemodules/FindPugiXML.cmake 2021-06-25 11:55:27.583630434 +0200 -@@ -5,11 +5,13 @@ +# Author: Caspar van leeuwen +# Make sure to use the shared library of PUGIXML, since linking to the static library seems to result in undefined symbol errors: +# ImportError: /home/casparl/.local/easybuild/Centos8/2021/software/ASAP/2.0-foss-2021a/lib/libmultiresolutionimageinterface.so: undefined symbol: _ZNK4pugi10xpath_node6parentEv +diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/annotation/CMakeLists.txt ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/annotation/CMakeLists.txt +--- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/annotation/CMakeLists.txt 2021-06-25 11:50:23.132333349 +0200 ++++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/annotation/CMakeLists.txt 2021-06-25 11:58:03.005555272 +0200 +@@ -25,10 +25,9 @@ + ) + + add_library(annotation SHARED ${ANNOTATION_SOURCE} ${ANNOTATION_HEADERS}) +-target_compile_definitions(annotation PRIVATE "PUGIXML_HEADER_ONLY") + generate_export_header(annotation) + target_include_directories(annotation PUBLIC $ $ PRIVATE ${DIAGPathology_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR} ${Boost_INCLUDE_DIRS} ${PugiXML_INCLUDE_DIR}) +-target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface) ++target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface ${PUGIXML_LIBRARY}) + set_target_properties(annotation PROPERTIES DEBUG_POSTFIX _d) + + install(TARGETS annotation +diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPugiXML.cmake ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/cmakemodules/FindPugiXML.cmake +--- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPugiXML.cmake 2021-06-25 11:50:23.180337653 +0200 ++++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/cmakemodules/FindPugiXML.cmake 2021-06-25 11:55:27.583630434 +0200 +@@ -5,11 +5,13 @@ # PugiXML_FOUND, If false, do not try to use PugiXML. find_path(PugiXML_INCLUDE_DIR pugixml.hpp) @@ -35,10 +35,10 @@ diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPu -mark_as_advanced(PugiXML_INCLUDE_DIR) + +mark_as_advanced(PugiXML_INCLUDE_DIR PUGIXML_LIBRARY) -diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/multiresolutionimageinterface/CMakeLists.txt ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/multiresolutionimageinterface/CMakeLists.txt ---- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/multiresolutionimageinterface/CMakeLists.txt 2021-06-25 11:50:23.384355944 +0200 -+++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/multiresolutionimageinterface/CMakeLists.txt 2021-06-25 11:57:29.462554526 +0200 -@@ -66,8 +66,7 @@ +diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/multiresolutionimageinterface/CMakeLists.txt ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/multiresolutionimageinterface/CMakeLists.txt +--- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/multiresolutionimageinterface/CMakeLists.txt 2021-06-25 11:50:23.384355944 +0200 ++++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/multiresolutionimageinterface/CMakeLists.txt 2021-06-25 11:57:29.462554526 +0200 +@@ -66,8 +66,7 @@ add_library(multiresolutionimageinterface SHARED ${MULTIRESOLUTIONIMAGEINTERFACE_SRCS} ${MULTIRESOLUTIONIMAGEINTERFACE_HS} ${VSI_SOURCE_HS} ${VSI_SOURCE_SRCS}) target_include_directories(multiresolutionimageinterface PUBLIC $ $ $ $ PRIVATE ${PugiXML_INCLUDE_DIR} ${Boost_INCLUDE_DIRS} ${TIFF_INCLUDE_DIR}) From 9d03e8dc5668bf91a84164acf9c6b89f72b2abe5 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 22 Nov 2021 16:26:31 +0100 Subject: [PATCH 2038/9987] Update easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Reorder keywords to conventional order Co-authored-by: Bob Dröge --- .../a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb index 3f346a90a50..d4ea54d1c84 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb @@ -1,7 +1,5 @@ easyblock = 'CMakeMake' -separate_build_dir = True - name = 'ASAP' version = '2.0' versionsuffix = '-CUDA-%(cudaver)s' @@ -25,14 +23,10 @@ checksums = [ '785a7716cbbf7fd4f6dacf1b74fe66384be76d31d54a02918ce9c07989ac4c81', # ASAP-2.0_use_pugixml_shared.patch ] -configopts = '-DOPENSLIDE_INCLUDE_DIR=$EBROOTOPENSLIDE/include/openslide ' -configopts += '-DPugiXML_INCLUDE_DIR=$EBROOTPUGIXML/include ' -configopts += '-DDCMTKJPEG_INCLUDE_DIR=$EBROOTDCMTK ' -configopts += '-DWRAP_MULTIRESOLUTIONIMAGEINTERFACE_PYTHON=TRUE -DBUILD_ASAP=TRUE ' -configopts += '-DBUILD_EXECUTABLES=TRUE -DBUILD_IMAGEPROCESSING=TRUE ' -configopts += '-DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE ' -# Otherwise, it picks up on the system swig -configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig ' +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] dependencies = [ ('CUDA', '11.3.1', '', True), @@ -50,10 +44,16 @@ dependencies = [ ('zlib', '1.2.11'), ] -builddependencies = [ - ('binutils', '2.36.1'), - ('CMake', '3.20.1'), -] +separate_build_dir = True + +configopts = '-DOPENSLIDE_INCLUDE_DIR=$EBROOTOPENSLIDE/include/openslide ' +configopts += '-DPugiXML_INCLUDE_DIR=$EBROOTPUGIXML/include ' +configopts += '-DDCMTKJPEG_INCLUDE_DIR=$EBROOTDCMTK ' +configopts += '-DWRAP_MULTIRESOLUTIONIMAGEINTERFACE_PYTHON=TRUE -DBUILD_ASAP=TRUE ' +configopts += '-DBUILD_EXECUTABLES=TRUE -DBUILD_IMAGEPROCESSING=TRUE ' +configopts += '-DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE ' +# Otherwise, it picks up on the system swig +configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig ' sanity_check_commands = ['python -c "import multiresolutionimageinterface"'] From f9fb5c71fb5e2b4bc8c4be11aaa01053af946078 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 22 Nov 2021 16:27:29 +0100 Subject: [PATCH 2039/9987] Update easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Move setting of github_account close to where sources are defined, since it's related Co-authored-by: Bob Dröge --- .../o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb index 15e919eadd9..8097ba896a5 100644 --- a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb @@ -10,6 +10,7 @@ read whole-slide images (also known as virtual slides).""" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +github_account = '%(namelower)s' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_large_file_support.patch'] @@ -26,6 +27,7 @@ builddependencies = [ ('pkg-config', '0.29.2'), ('binutils', '2.36.1'), ] + dependencies = [ ('zlib', '1.2.11'), ('libpng', '1.6.37'), @@ -40,8 +42,6 @@ dependencies = [ preconfigopts = "autoreconf -f -i && " -github_account = '%(namelower)s' - sanity_check_paths = { 'files': [ 'bin/%(namelower)s-quickhash1sum', 'bin/%(namelower)s-show-properties', From f0d433bf3fbc97fadec1d2ccb9de7b3a7b073d20 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 22 Nov 2021 15:33:02 +0000 Subject: [PATCH 2040/9987] adding easyconfigs: Racon-1.4.21-GCCcore-10.3.0.eb --- .../r/Racon/Racon-1.4.21-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4131ade476e --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.4.21' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/lbcb-sci/racon/releases/download/%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['df99208ebef6a12e1da11a31dade2eafe13a4cd80b4917cce44d44d879b5aee4'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' From 6fec2c19a675c917399b9466bbebc4ab392522dc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 22 Nov 2021 15:39:04 +0000 Subject: [PATCH 2041/9987] adding easyconfigs: Unicycler-0.4.9-gompi-2021a.eb, SPAdes-3.15.3-GCC-10.3.0.eb, Racon-1.4.21-GCCcore-10.3.0.eb --- .../r/Racon/Racon-1.4.21-GCCcore-10.3.0.eb | 27 +++++++++++ .../s/SPAdes/SPAdes-3.15.3-GCC-10.3.0.eb | 46 +++++++++++++++++++ .../Unicycler/Unicycler-0.4.9-gompi-2021a.eb | 38 +++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4131ade476e --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.4.21-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.4.21' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/lbcb-sci/racon/releases/download/%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['df99208ebef6a12e1da11a31dade2eafe13a4cd80b4917cce44d44d879b5aee4'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..14828be4967 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-10.3.0.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'CMakeMake' + +name = 'SPAdes' +version = '3.15.3' + +homepage = 'https://cab.spbu.ru/software/spades/' +description = "Genome assembler for single-cell and isolates data sets" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['b2e5a9fd7a65aee5ab886222d6af4f7b7bc7f755da7a03941571fabd6b9e1499'] + +builddependencies = [ + ('CMake', '3.20.1'), +] +dependencies = [ + ('Python', '3.9.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('libreadline', '8.1'), +] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', + 'spades-ionhammer', 'spades-kmercount', 'spades.py']], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s.py', '--test')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb new file mode 100644 index 00000000000..8a08b0b73e7 --- /dev/null +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'Unicycler' +version = '0.4.9' + +homepage = 'https://github.com/rrwick/Unicycler' +description = """ Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets + where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) + where it runs a miniasm+Racon pipeline. """ + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://github.com/rrwick/Unicycler/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['84bea8f3e8f99a1e63e5230ffe474a696db8caa67569c3a96ae12906d32a35eb'] + +dependencies = [ + ('Python', '3.9.5'), + ('Java', '11', '', True), + ('Bowtie2', '2.4.4'), + ('SAMtools', '1.13'), + ('SPAdes', '3.15.3'), + ('Racon', '1.4.21'), + ('Pilon', '1.23', '-Java-%(javaver)s', True), + ('BLAST+', '2.11.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 20f1d36a3564bc0ea8f1511371bd573b4749eede Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 22 Nov 2021 17:21:19 +0000 Subject: [PATCH 2042/9987] PhyML-3.3.20200621: missing Automake added --- easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb index 92820f73d60..33168cdcf05 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb @@ -22,6 +22,7 @@ checksums = ['a8243923ee08c74cab609a4b086ade66c6156fc2b24450e2a500108dc644c867'] builddependencies = [ ('Autoconf', '2.69'), ('pkg-config', '0.29.2'), + ('Automake', '1.16.2'), ] preconfigopts = 'sh autogen.sh && ' From e3ee909b80bf19a4086eb2454503586c979510da Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 22 Nov 2021 17:28:57 +0000 Subject: [PATCH 2043/9987] adding easyconfigs: enaBrowserTool-1.6-GCCcore-10.3.0.eb --- .../enaBrowserTool-1.6-GCCcore-10.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/e/enaBrowserTool/enaBrowserTool-1.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/e/enaBrowserTool/enaBrowserTool-1.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/e/enaBrowserTool/enaBrowserTool-1.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1ced86d0459 --- /dev/null +++ b/easybuild/easyconfigs/e/enaBrowserTool/enaBrowserTool-1.6-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'Tarball' + +name = 'enaBrowserTool' +version = '1.6' + +homepage = 'https://github.com/enasequence/enaBrowserTools/' +description = """enaBrowserTools is a set of scripts that interface with the ENA +web services to download data from ENA easily, without any knowledge of scripting required.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +dependencies = [ + ('Python', '3.9.5'), +] + +source_urls = ['https://github.com/enasequence/enaBrowserTools/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['efec89cfdabe4d97004c0772cae7befaa2b5f7bc4f363ee23df50b9b84df93af'] + +modextrapaths = {'PATH': 'python3'} + +sanity_check_paths = { + 'dirs': ['python3'], + 'files': ['python3/enaGroupGet', 'python3/enaDataGet'], +} + +sanity_check_commands = ['enaDataGet -h'] + +moduleclass = 'bio' From ce029fc0bdab62ba146678d1ab12733f9cd49a77 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 23 Nov 2021 10:24:08 +0000 Subject: [PATCH 2044/9987] adding easyconfigs: Trycycler-0.5.2-foss-2021a.eb, edlib-1.3.9-GCC-10.3.0.eb --- .../e/edlib/edlib-1.3.9-GCC-10.3.0.eb | 22 ++++++++++++ .../t/Trycycler/Trycycler-0.5.2-foss-2021a.eb | 34 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.3.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.3.0.eb new file mode 100644 index 00000000000..4e4e33d596f --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'edlib' +version = '1.3.9' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766'] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.2-foss-2021a.eb b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.2-foss-2021a.eb new file mode 100644 index 00000000000..e4fde764933 --- /dev/null +++ b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.2-foss-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Trycycler' +version = '0.5.2' + +homepage = 'https://github.com/rrwick/Trycycler' +description = "Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/rrwick/Trycycler/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6f6007afa6a4f7568d12b48627a09b03d389ae4e7888033433314caadd69d796'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('edlib', '1.3.9'), + ('Pillow', '8.2.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/trycycler'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["trycycler --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 80f7d94297a212ac52ac85df17ebe0760c925516 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 23 Nov 2021 10:47:07 +0000 Subject: [PATCH 2045/9987] adding easyconfigs: Mash-2.3-GCC-10.3.0.eb --- .../easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..e211bc1ac6d --- /dev/null +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb @@ -0,0 +1,35 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v2.2 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'Mash' +version = '2.3' + +homepage = 'http://mash.readthedocs.org' +description = "Fast genome and metagenome distance estimation using MinHash" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/marbl/Mash/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20210128')] +dependencies = [ + ('CapnProto', '0.9.1'), + ('GSL', '2.7'), + ('zlib', '1.2.11'), +] + +preconfigopts = "./bootstrap.sh && " +configopts = "--with-capnp=$EBROOTCAPNPROTO --with-gsl=$EBROOTGSL" + +sanity_check_paths = { + 'files': ['bin/mash', 'lib/libmash.a'], + 'dirs': ['include/mash'], +} + +moduleclass = 'bio' From 92107f4c1eeba565e895f2be31bd807c36876312 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 23 Nov 2021 10:55:30 +0000 Subject: [PATCH 2046/9987] adding easyconfigs: MAFFT-7.490-GCC-10.3.0-with-extensions.eb --- .../MAFFT-7.490-GCC-10.3.0-with-extensions.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-10.3.0-with-extensions.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-10.3.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-10.3.0-with-extensions.eb new file mode 100644 index 00000000000..46cb8eb8ea1 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-10.3.0-with-extensions.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez (Swiss Institute of Bioinformatics, Biozentrum - University of Basel) +# 7.305 modified by: +# Adam Huffman (The Francis Crick Institute) +# 7.453 switch to Bundle by: +# Alex Domingo (Vrije Universiteit Brussel) + +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.490' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], + 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'checksums': ['d6eef33d8b9e282e20f9b25b6b6fb2757b9b6900e397ca621d56da86d9976541'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft', 'libexec/mafft/mxscarnamod'], # mxscarnamod installed by MAFFT Extensions + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +moduleclass = 'bio' From 34681c3a362933cec2115860325d1d1e2ff0e1fc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 23 Nov 2021 10:56:48 +0000 Subject: [PATCH 2047/9987] adding easyconfigs: PRANK-170427-GCC-10.3.0.eb --- .../p/PRANK/PRANK-170427-GCC-10.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.3.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.3.0.eb new file mode 100644 index 00000000000..699387c221c --- /dev/null +++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'PRANK' +version = '170427' + +homepage = 'http://wasabiapp.org/software/prank/' +description = """ PRANK is a probabilistic multiple alignment program for DNA, + codon and amino-acid sequences. PRANK is based on a novel algorithm that treats + insertions correctly and avoids over-estimation of the number of deletion events.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['http://wasabiapp.org/download/prank/'] +sources = ['%(namelower)s.source.%(version)s.tgz'] +checksums = ['623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859'] + +# PRANK uses MAFFT as external tool to construct guide tree +dependencies = [('MAFFT', '7.490', '-with-extensions')] + +start_dir = 'src' + +files_to_copy = [(['prank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/prank'], + 'dirs': [], +} + +sanity_check_commands = ['prank -help'] + +moduleclass = 'bio' From 44294319e1c2e80614dbec51c59ca5018add1098 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 23 Nov 2021 11:03:29 +0000 Subject: [PATCH 2048/9987] Include CapnProto dep for Mash --- .../CapnProto-0.9.1-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..114627e0f59 --- /dev/null +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to 0.9.1 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'CapnProto' +version = '0.9.1' + +homepage = 'https://capnproto.org' +description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" +# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." +# (only on Intel Skylake?) +toolchainopts = {'cstd': 'c++17', 'lowopt': True} + +source_urls = ['https://capnproto.org/'] +sources = ['capnproto-c++-%(version)s.tar.gz'] +checksums = ['83680aaef8c192b884e38eab418b8482d321af6ae7ab7befa3a9370b8e716aad'] + +builddependencies = [('binutils', '2.36.1')] + +sanity_check_paths = { + 'files': ['bin/capnp', 'bin/capnpc', 'bin/capnpc-c++', 'bin/capnpc-capnp'], + 'dirs': ['include/capnp', 'include/kj', 'lib'], +} + +moduleclass = 'bio' From bc4cd5a4144f9ba92a170a5b7bee94c37fbc530c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 23 Nov 2021 11:06:51 +0000 Subject: [PATCH 2049/9987] adding easyconfigs: panaroo-1.2.9-foss-2021a.eb, edlib-1.3.9-GCC-10.3.0.eb, DendroPy-4.5.2-GCCcore-10.3.0.eb, pyfaidx-0.6.3.1-GCCcore-10.3.0.eb --- .../DendroPy/DendroPy-4.5.2-GCCcore-10.3.0.eb | 43 +++++++++++++ .../e/edlib/edlib-1.3.9-GCC-10.3.0.eb | 22 +++++++ .../p/panaroo/panaroo-1.2.9-foss-2021a.eb | 60 +++++++++++++++++++ .../pyfaidx/pyfaidx-0.6.3.1-GCCcore-10.3.0.eb | 30 ++++++++++ 4 files changed, 155 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.6.3.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4182518015a --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-10.3.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.5.2' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["sumtrees.py --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.3.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.3.0.eb new file mode 100644 index 00000000000..4e4e33d596f --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-10.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'edlib' +version = '1.3.9' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766'] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb new file mode 100644 index 00000000000..fd7c31c4cf0 --- /dev/null +++ b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb @@ -0,0 +1,60 @@ +# Author: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'panaroo' +version = '1.2.9' + +homepage = 'https://gtonkinhill.github.io/panaroo/' +description = "A pangenome analysis pipeline." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('CD-HIT', '4.8.1'), + ('PRANK', '170427'), + ('Biopython', '1.79'), + ('SciPy-bundle', '2021.05'), + ('networkx', '2.6.3'), + ('edlib', '1.3.9'), + ('tqdm', '4.61.1'), + ('matplotlib', '3.4.2'), + ('scikit-learn', '0.24.2'), + ('plotly.py', '5.1.0'), + ('DendroPy', '4.5.2'), + ('pyfaidx', '0.6.3.1'), + ('prokka', '1.14.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), + ('argcomplete', '1.12.3', { + 'checksums': ['2c7dbffd8c045ea534921e63b0be6fe65e88599990d8dc408ac8c542b72a5445'], + }), + ('argh', '0.26.2', { + 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], + }), + ('gffutils', '0.10.1', { + 'checksums': ['a8fc39006d7aa353147238160640e2210b168f7849cb99896be3fc9441e351cb'], + }), + ('intbitset', '2.4.1', { + 'checksums': ['44bca80b8cc702d5a56f0686f2bb5e028ab4d0c2c1761941589d46b7fa2c701c'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/gtonkinhill/panaroo/archive/'], + 'checksums': ['70bf4226bdb1a0b9ca3677b0c0c3cf4defb9a1d3517c1ab205c99f85108d856a'], + }), +] + +sanity_check_commands = [ + "panaroo --version" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.6.3.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.6.3.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..149a6028516 --- /dev/null +++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.6.3.1-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pyfaidx' +version = '0.6.3.1' + +homepage = 'https://pypi.python.org/pypi/pyfaidx' +description = "pyfaidx: efficient pythonic random access to fasta subsequences" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['93adf036a75e08dc9b1dcd59de6a4db2f65a48c603edabe2e499764b6535ed50'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/faidx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["faidx --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 03160fc818e9569ae50947049da5a538c8cd1c06 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 23 Nov 2021 11:26:44 +0000 Subject: [PATCH 2050/9987] adding easyconfigs: QUAST-5.0.2-foss-2021a.eb --- .../q/QUAST/QUAST-5.0.2-foss-2021a.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb new file mode 100644 index 00000000000..2fa06228d15 --- /dev/null +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'QUAST' +version = '5.0.2' + +homepage = 'https://github.com/ablab/%(namelower)s' +description = """QUAST evaluates genome assemblies by computing various metrics. +It works both with and without reference genomes. The tool accepts multiple +assemblies, thus is suitable for comparison.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + + +dependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), + ('matplotlib', '3.4.2'), + ('Java', '11', '', True), + ('Boost', '1.76.0'), +] + +use_pip = True + +exts_list = [ + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + (name, version, { + 'install_target': 'install_full', + 'modulename': 'quast_libs', + 'patches': ['QUAST-%(version)s_fix-Python-3.8.patch'], + 'source_tmpl': 'quast_%(version)s.tar.gz', + 'source_urls': ['https://github.com/ablab/quast/archive/'], + 'checksums': [ + '9f30c03e0bfd261492fe6b72fb07645bdee5b29d741f75fc75857b6fa095d91d', # quast_5.0.2.tar.gz + '8ae7ebf45e5368ebc058fc208822a23d32ce1052bd53fd8c3aaa4ad14d3c95aa', # QUAST-5.0.2_fix-Python-3.8.patch + ], + }), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s quast.py quast"] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "wget quast.sf.net/test_data.tar.gz && " + "tar xzf test_data.tar.gz && " + "%(namelower)s.py --test && " + "rm -rf ./test_data.tar.gz ./test_data", + "%(namelower)s -h", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 68620721c49cfdcef939f9ab8f21b8b1ff49fc1f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 23 Nov 2021 11:29:03 +0000 Subject: [PATCH 2051/9987] adding easyconfigs: snp-sites-2.5.1-GCCcore-10.3.0.eb --- .../snp-sites-2.5.1-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..002fb4afeaf --- /dev/null +++ b/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'snp-sites' +version = '2.5.1' + +homepage = 'https://sanger-pathogens.github.io/snp-sites/' +description = """Finds SNP sites from a multi-FASTA alignment file.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'sanger-pathogens' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['913f79302e5d3127aea382756abc9ffeb05e26ce00022f43a6ea16a55cdd7a7e'] + +builddependencies = [ + ('Autotools', '20210128'), + ('pkg-config', '0.29.2'), + ('binutils', '2.36.1'), + ('Check', '0.15.2'), +] + +dependencies = [('zlib', '1.2.11')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/snp-sites'], + 'dirs': [], +} +sanity_check_commands = ["snp-sites -h"] + +moduleclass = 'bio' From 587ba94e69bb9952e2eb55e1895493c5ad15864f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 23 Nov 2021 12:01:03 +0000 Subject: [PATCH 2052/9987] Add missing Mash checksum --- easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb index e211bc1ac6d..2b8f28e31d2 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb @@ -16,6 +16,7 @@ toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/marbl/Mash/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1'] builddependencies = [('Autotools', '20210128')] dependencies = [ From c836874091b59b97f9d156492eda4a515b0d7029 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 23 Nov 2021 13:55:48 +0100 Subject: [PATCH 2053/9987] adding easyconfigs: ASE-3.22.0-intel-2021a.eb --- .../a/ASE/ASE-3.22.0-intel-2021a.eb | 47 +++++++++++++++++++ .../spglib-python-1.16.1-intel-2021a.eb | 27 +++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2021a.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-intel-2021a.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2021a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2021a.eb new file mode 100644 index 00000000000..b37dd344249 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.0-intel-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.0' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Flask', '1.1.4'), + ('matplotlib', '3.4.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.1'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['e60259c7b50867b1cb817caf938fcc1ed383702413df6d2e1afe7ea07f65acee'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-intel-2021a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-intel-2021a.eb new file mode 100644 index 00000000000..b978ab4ff48 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-intel-2021a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.1' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'intel', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['9fd2fefbd83993b135877a69c498d8ddcf20a9980562b65b800cfb4cdadad003'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' From aa37e9f36cf6ddd4eee29854b5d463137cd5d5f0 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Tue, 23 Nov 2021 15:53:50 +0100 Subject: [PATCH 2054/9987] Update easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Don't use namelower template, and use SHLIB_EXT instead of .so Co-authored-by: Bob Dröge --- .../OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb index 8097ba896a5..84ace078627 100644 --- a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb @@ -44,10 +44,10 @@ preconfigopts = "autoreconf -f -i && " sanity_check_paths = { 'files': [ - 'bin/%(namelower)s-quickhash1sum', 'bin/%(namelower)s-show-properties', - 'bin/%(namelower)s-write-png', 'lib/libopenslide.la', 'lib/libopenslide.so', + 'bin/openslide-quickhash1sum', 'bin/openslide-show-properties', + 'bin/openslide-write-png', 'lib/libopenslide.la', 'lib/libopenslide.%s' % SHLIB_EXT, ], - 'dirs': ['include/%(namelower)s'], + 'dirs': ['include/openslide'], } moduleclass = 'vis' From f118eec285f2ec7d44554305978bb70412a58bc4 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 23 Nov 2021 16:21:34 +0100 Subject: [PATCH 2055/9987] Update checksums and change .so to using SHLIB_EXT for ASAP --- easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb index d4ea54d1c84..3ced6e1dd64 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb @@ -58,7 +58,7 @@ configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig ' sanity_check_commands = ['python -c "import multiresolutionimageinterface"'] sanity_check_paths = { - 'files': ['bin/ASAP', 'bin/multiresolutionimageinterface.py', 'lib/libmultiresolutionimageinterface.so'], + 'files': ['bin/ASAP', 'bin/multiresolutionimageinterface.py', 'lib/libmultiresolutionimageinterface.%s' % SHLIB_EXT], 'dirs': ['bin'] } From 713201e33918a8b08827b4b93af2835e5d94752b Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Tue, 23 Nov 2021 15:23:27 +0000 Subject: [PATCH 2056/9987] Update easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb index be7e5d73e64..a2d3ea9fb7e 100644 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.10.0-fosscuda-2020b-PyTorch-1.9.0.eb @@ -3,7 +3,6 @@ easyblock = 'PythonPackage' name = 'torchtext' version = '0.10.0' local_pytorch_version = '1.9.0' -local_python_suffix = '-Python-%(pyver)s' versionsuffix = '-PyTorch-%s' % local_pytorch_version homepage = 'https://github.com/pytorch/text' From e5ca5ccd6259bc8b845d215308e6e6158f78b674 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 23 Nov 2021 17:20:57 +0100 Subject: [PATCH 2057/9987] adding easyconfigs: GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb and patches: GROMACS-2021.3_skip_test_for_plumed.patch --- ...1.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb | 96 +++++++++++++++++++ .../GROMACS-2021.3_skip_test_for_plumed.patch | 26 +++++ 2 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3_skip_test_for_plumed.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb new file mode 100644 index 00000000000..a7a22da2648 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb @@ -0,0 +1,96 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021.3' +_plumedver = '2.7.2' +versionsuffix = '-CUDA-%%(cudaver)s-PLUMED-%s' % _plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI builds. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021.3_skip_test_for_plumed.patch', +] +checksums = [ + 'e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6', # gromacs-2021.3.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch + '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', + 'c06d0a8c3e75b232224f46bc3b70e135c4c02ec4151712970f5edd85d890f018', # GROMACS-2021.3_skip_test_for_plumed.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('networkx', '2.5.1'), + ('CUDA', '11.3.1', '', True), + ('PLUMED', _plumedver), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'], + }), +] + +# PLUMED-2.7.2 does not officially support GROMACS-2021.3, but seems to work fine +ignore_plumed_version_check = True + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3_skip_test_for_plumed.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3_skip_test_for_plumed.patch new file mode 100644 index 00000000000..b9f86bf473b --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3_skip_test_for_plumed.patch @@ -0,0 +1,26 @@ +Skip test checking output of 'mdrun -h' when patched with PLUMED, as it adds an extra option '-hrex' +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur gromacs-2021.3.orig/src/programs/mdrun/tests/CMakeLists.txt gromacs-2021.3/src/programs/mdrun/tests/CMakeLists.txt +--- gromacs-2021.3.orig/src/programs/mdrun/tests/CMakeLists.txt 2021-08-18 11:49:23.000000000 +0200 ++++ gromacs-2021.3/src/programs/mdrun/tests/CMakeLists.txt 2021-11-16 17:04:47.612357764 +0100 +@@ -51,20 +51,6 @@ + # To avoid running into test timeouts, some end-to-end tests of mdrun + # functionality are split off. This can be rearranged in future as we + # see fit. +-set(testname "MdrunOutputTests") +-set(exename "mdrun-output-test") +- +-gmx_add_gtest_executable(${exename} +- CPP_SOURCE_FILES +- compressed_x_output.cpp +- helpwriting.cpp +- outputfiles.cpp +- trajectory_writing.cpp +- # pseudo-library for code for mdrun +- $ +- ) +-target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure) +-gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS) + + set(testname "MdrunModulesTests") + set(exename "mdrun-modules-test") From ad14484bef076a845b39e4f16afafd5a2c41aea1 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 23 Nov 2021 21:02:26 +0100 Subject: [PATCH 2058/9987] Update checksums (for real this time) and fix too long line --- .../easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb index 3ced6e1dd64..2ec5b7f7887 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb @@ -20,7 +20,7 @@ patches = [ checksums = [ 'e5d8b0aff6f86a3c7319062ca1f9e35b867da1c80667a80b55ee2a876f897202', # ASAP-2.0.tar.gz 'f593599b5af90c8256ffeae910757d02f4de04a49de26d5123c209a405ba6a55', # ASAP-2.0_libjpeg.patch - '785a7716cbbf7fd4f6dacf1b74fe66384be76d31d54a02918ce9c07989ac4c81', # ASAP-2.0_use_pugixml_shared.patch + '8891afca4f9be13e45f82b4f2fc85acadebc47af00d534f94e17f1443c13a561', # ASAP-2.0_use_pugixml_shared.patch ] builddependencies = [ @@ -58,7 +58,10 @@ configopts += '-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig ' sanity_check_commands = ['python -c "import multiresolutionimageinterface"'] sanity_check_paths = { - 'files': ['bin/ASAP', 'bin/multiresolutionimageinterface.py', 'lib/libmultiresolutionimageinterface.%s' % SHLIB_EXT], + 'files': [ + 'bin/ASAP', 'bin/multiresolutionimageinterface.py', + 'lib/libmultiresolutionimageinterface.%s' % SHLIB_EXT, + ], 'dirs': ['bin'] } From 8232f4a22425f9f1c430391be5a5f5047376c4fc Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 23 Nov 2021 22:20:21 +0100 Subject: [PATCH 2059/9987] adding easyconfigs: photontorch-0.4.1-foss-2020b.eb, photontorch-0.4.1-fosscuda-2020b.eb --- .../photontorch-0.4.1-foss-2020b.eb | 38 +++++++++++++++++++ .../photontorch-0.4.1-fosscuda-2020b.eb | 38 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb new file mode 100644 index 00000000000..0a19fe634e2 --- /dev/null +++ b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'photontorch' +version = '0.4.1' + +homepage = 'https://docs.photontorch.com/' +description = """ +Photontorch is a photonic simulator for highly parallel simulation and optimization of photonic circuits in time and +frequency domain. Photontorch features CUDA enabled simulation and optimization of photonic circuits. It leverages the +deep learning framework PyTorch to view the photonic circuit as essentially a recurrent neural network. This enables the +use of native PyTorch optimizers to optimize the (physical) parameters of the circuit. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), + ('networkx', '2.5'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('torch-lfilter', '0.0.3', { + 'source_tmpl': 'torch_lfilter-%(version)s.tar.gz', + 'checksums': ['aa613725b73e7b6e7efd63c30580a906d7bb23206b5d045b8452ab770f7a50df'], + }), + (name, version, { + 'checksums': ['50d2e2c8a24c914cc7afee1eea6efb8bccfbc19ff9652a9af46efad28caa6381'], + }), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb new file mode 100644 index 00000000000..75ef1ef367c --- /dev/null +++ b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-fosscuda-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'photontorch' +version = '0.4.1' + +homepage = 'https://docs.photontorch.com/' +description = """ +Photontorch is a photonic simulator for highly parallel simulation and optimization of photonic circuits in time and +frequency domain. Photontorch features CUDA enabled simulation and optimization of photonic circuits. It leverages the +deep learning framework PyTorch to view the photonic circuit as essentially a recurrent neural network. This enables the +use of native PyTorch optimizers to optimize the (physical) parameters of the circuit. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyTorch', '1.7.1'), + ('tqdm', '4.56.2'), + ('networkx', '2.5'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('torch-lfilter', '0.0.3', { + 'source_tmpl': 'torch_lfilter-%(version)s.tar.gz', + 'checksums': ['aa613725b73e7b6e7efd63c30580a906d7bb23206b5d045b8452ab770f7a50df'], + }), + (name, version, { + 'checksums': ['50d2e2c8a24c914cc7afee1eea6efb8bccfbc19ff9652a9af46efad28caa6381'], + }), +] + +moduleclass = 'phys' From 71b26341b2fbe31f9786fbbeb8cf3345be17ceb2 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 24 Nov 2021 10:28:12 +0100 Subject: [PATCH 2060/9987] Fix line ending issue in use_pugixml patch file --- easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb index 2ec5b7f7887..8ccff72840b 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb @@ -20,7 +20,7 @@ patches = [ checksums = [ 'e5d8b0aff6f86a3c7319062ca1f9e35b867da1c80667a80b55ee2a876f897202', # ASAP-2.0.tar.gz 'f593599b5af90c8256ffeae910757d02f4de04a49de26d5123c209a405ba6a55', # ASAP-2.0_libjpeg.patch - '8891afca4f9be13e45f82b4f2fc85acadebc47af00d534f94e17f1443c13a561', # ASAP-2.0_use_pugixml_shared.patch + 'd2bdc41ab95930933d5416562e7f0054f32b14fc397c23ecc88b8768cae55dd0', # ASAP-2.0_use_pugixml_shared.patch ] builddependencies = [ From f3b2a9f2e5e04759239f9f3c39eae8fabace66f4 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 24 Nov 2021 10:35:47 +0100 Subject: [PATCH 2061/9987] Fix line ending issue in use_pugixml patch file --- .../a/ASAP/ASAP-2.0_use_pugixml_shared.patch | 52 +++++++++---------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch index ac18250a519..ca4f271a0f8 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0_use_pugixml_shared.patch @@ -1,25 +1,25 @@ -# Author: Caspar van leeuwen -# Make sure to use the shared library of PUGIXML, since linking to the static library seems to result in undefined symbol errors: -# ImportError: /home/casparl/.local/easybuild/Centos8/2021/software/ASAP/2.0-foss-2021a/lib/libmultiresolutionimageinterface.so: undefined symbol: _ZNK4pugi10xpath_node6parentEv -diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/annotation/CMakeLists.txt ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/annotation/CMakeLists.txt ---- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/annotation/CMakeLists.txt 2021-06-25 11:50:23.132333349 +0200 -+++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/annotation/CMakeLists.txt 2021-06-25 11:58:03.005555272 +0200 -@@ -25,10 +25,9 @@ - ) - - add_library(annotation SHARED ${ANNOTATION_SOURCE} ${ANNOTATION_HEADERS}) --target_compile_definitions(annotation PRIVATE "PUGIXML_HEADER_ONLY") - generate_export_header(annotation) - target_include_directories(annotation PUBLIC $ $ PRIVATE ${DIAGPathology_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR} ${Boost_INCLUDE_DIRS} ${PugiXML_INCLUDE_DIR}) --target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface) -+target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface ${PUGIXML_LIBRARY}) - set_target_properties(annotation PROPERTIES DEBUG_POSTFIX _d) - - install(TARGETS annotation -diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPugiXML.cmake ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/cmakemodules/FindPugiXML.cmake ---- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPugiXML.cmake 2021-06-25 11:50:23.180337653 +0200 -+++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/cmakemodules/FindPugiXML.cmake 2021-06-25 11:55:27.583630434 +0200 -@@ -5,11 +5,13 @@ +# Author: Caspar van leeuwen +# Make sure to use the shared library of PUGIXML, since linking to the static library seems to result in undefined symbol errors: +# ImportError: /home/casparl/.local/easybuild/Centos8/2021/software/ASAP/2.0-foss-2021a/lib/libmultiresolutionimageinterface.so: undefined symbol: _ZNK4pugi10xpath_node6parentEv +diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/annotation/CMakeLists.txt ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/annotation/CMakeLists.txt +--- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/annotation/CMakeLists.txt 2021-06-25 11:50:23.132333349 +0200 ++++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/annotation/CMakeLists.txt 2021-06-25 11:58:03.005555272 +0200 +@@ -25,10 +25,9 @@ + ) + + add_library(annotation SHARED ${ANNOTATION_SOURCE} ${ANNOTATION_HEADERS}) +-target_compile_definitions(annotation PRIVATE "PUGIXML_HEADER_ONLY") + generate_export_header(annotation) + target_include_directories(annotation PUBLIC $ $ PRIVATE ${DIAGPathology_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR} ${Boost_INCLUDE_DIRS} ${PugiXML_INCLUDE_DIR}) +-target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface) ++target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface ${PUGIXML_LIBRARY}) + set_target_properties(annotation PROPERTIES DEBUG_POSTFIX _d) + + install(TARGETS annotation +diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPugiXML.cmake ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/cmakemodules/FindPugiXML.cmake +--- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPugiXML.cmake 2021-06-25 11:50:23.180337653 +0200 ++++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/cmakemodules/FindPugiXML.cmake 2021-06-25 11:55:27.583630434 +0200 +@@ -5,11 +5,13 @@ # PugiXML_FOUND, If false, do not try to use PugiXML. find_path(PugiXML_INCLUDE_DIR pugixml.hpp) @@ -35,10 +35,10 @@ diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/cmakemodules/FindPu -mark_as_advanced(PugiXML_INCLUDE_DIR) + +mark_as_advanced(PugiXML_INCLUDE_DIR PUGIXML_LIBRARY) -diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/multiresolutionimageinterface/CMakeLists.txt ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/multiresolutionimageinterface/CMakeLists.txt ---- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/multiresolutionimageinterface/CMakeLists.txt 2021-06-25 11:50:23.384355944 +0200 -+++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/multiresolutionimageinterface/CMakeLists.txt 2021-06-25 11:57:29.462554526 +0200 -@@ -66,8 +66,7 @@ +diff -Nru ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/multiresolutionimageinterface/CMakeLists.txt ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/multiresolutionimageinterface/CMakeLists.txt +--- ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a-orig/multiresolutionimageinterface/CMakeLists.txt 2021-06-25 11:50:23.384355944 +0200 ++++ ASAP-8c9a8fbf32fd7a9dc5c5ec4d5c3552923cc4890a/multiresolutionimageinterface/CMakeLists.txt 2021-06-25 11:57:29.462554526 +0200 +@@ -66,8 +66,7 @@ add_library(multiresolutionimageinterface SHARED ${MULTIRESOLUTIONIMAGEINTERFACE_SRCS} ${MULTIRESOLUTIONIMAGEINTERFACE_HS} ${VSI_SOURCE_HS} ${VSI_SOURCE_SRCS}) target_include_directories(multiresolutionimageinterface PUBLIC $ $ $ $ PRIVATE ${PugiXML_INCLUDE_DIR} ${Boost_INCLUDE_DIRS} ${TIFF_INCLUDE_DIR}) From cdcfe6959215492d3fe89c8841cbf082ef34ac07 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 24 Nov 2021 10:03:50 +0000 Subject: [PATCH 2062/9987] Add sanity check command --- .../m/multichoose/multichoose-1.0.3-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.3.0.eb index 3fa5d5d5ad2..c55f331c535 100644 --- a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-10.3.0.eb @@ -23,4 +23,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['multichoose 1 a'] + moduleclass = 'bio' From 2b825e1fc6f9ce7cf4e634d11d686f581bce2878 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Wed, 24 Nov 2021 11:16:50 +0100 Subject: [PATCH 2063/9987] adding easyconfigs: ReFrame-3.9.1.eb --- .../easyconfigs/r/ReFrame/ReFrame-3.9.1.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb new file mode 100644 index 00000000000..9b653bf3ab9 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.9.1' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.2.4', { + 'use_pip': False, + 'checksums': ['0eb8a1516c3d138ae8689c0c1a60fde7143310832f9dc77e11d8a4bc62de193b'], + }), + ('wheel', '0.37.0', { + 'checksums': ['e2ef7239991699e3355d54f8e968a21bb940a1dbf34a4d226741e64462516fad'], + }), + ('setuptools', '57.4.0', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], + }), + ('reframe', version, { + 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], + 'checksums': ['8f7f4991d1c32cc23f8b10a7509166030548bfe84e4785d017d8d797e31b0498'], + }), +] + +postinstallcmds = [ + "cp -r tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -r share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['lib', 'tutorials', 'external'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions +modextrapaths = { + 'PATH': 'bin', + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 37109c0cdb452638f4d2505df02d0130e748ebd5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Nov 2021 11:42:30 +0100 Subject: [PATCH 2064/9987] comment out use of imkl in FlexiBLAS (as opposed to removing entirely) --- .../easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index be4c7f1997f..24fbb34505e 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -17,6 +17,9 @@ builddependencies = [ ('CMake', '3.21.1'), ('Python', '3.9.6'), # required for running the tests ('BLIS', '0.8.1'), + # imkl is commented out, since installing it requires accepting the Intel oneAPI EULA; + # note: also commented out the lines below to add imkl to 'backends'! + # ('imkl', {'arch=x86_64': '2021.4.0', 'arch=*': False}, '', True), ] dependencies = [ @@ -27,4 +30,7 @@ dependencies = [ # unless otherwise specified via easyconfig parameter flexiblas_default backends = ['OpenBLAS', 'BLIS'] +# if ARCH == 'x86_64': +# backends.append('imkl') + moduleclass = 'lib' From d07ada740b0d16859c2eb9ea26a810467468fcb6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 24 Nov 2021 11:29:55 +0000 Subject: [PATCH 2065/9987] Add sanity check command --- .../f/filevercmp/filevercmp-20191210-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.3.0.eb index 123d2b44a55..6ec6d1ba82c 100644 --- a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-10.3.0.eb @@ -30,4 +30,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['filevercmp abca bcac'] + moduleclass = 'lib' From f4022b7ee6881a187dee45981b59aa31461e09c4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Nov 2021 14:17:13 +0100 Subject: [PATCH 2066/9987] adding easyconfigs: CLEASE-0.10.6-intel-2021a.eb and patches: CLEASE-0.10.6_drop_version_req_for_click.patch --- .../c/CLEASE/CLEASE-0.10.6-intel-2021a.eb | 45 +++++++++++++++++++ ...SE-0.10.6_drop_version_req_for_click.patch | 15 +++++++ .../scikit-learn-0.24.2-intel-2021a.eb | 28 ++++++++++++ 3 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLEASE/CLEASE-0.10.6-intel-2021a.eb create mode 100644 easybuild/easyconfigs/c/CLEASE/CLEASE-0.10.6_drop_version_req_for_click.patch create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.24.2-intel-2021a.eb diff --git a/easybuild/easyconfigs/c/CLEASE/CLEASE-0.10.6-intel-2021a.eb b/easybuild/easyconfigs/c/CLEASE/CLEASE-0.10.6-intel-2021a.eb new file mode 100644 index 00000000000..88601f6e661 --- /dev/null +++ b/easybuild/easyconfigs/c/CLEASE/CLEASE-0.10.6-intel-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'CLEASE' +version = '0.10.6' + +homepage = 'https://gitlab.com/computationalmaterials/clease' +description = """CLuster Expansion in Atomic Simulation Environment +(CLEASE) is a package that automates the cumbersome setup and +construction procedure of cluster expansion (CE). It provides a +comprehensive list of tools for specifying parameters for CE, generating +training structures, fitting effective cluster interaction (ECI) values +and running Monte Carlo simulations.""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('ASE', '3.22.0'), + ('scikit-learn', '0.24.2'), + ('typing-extensions', '3.10.0.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('wrapt', '1.13.3', { + 'checksums': ['1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185'], + }), + ('clease', version, { + 'patches': ['CLEASE-0.10.6_drop_version_req_for_click.patch'], + 'checksums': [ + '858b420e27872b3e996c631e6382ab6f0a0b96dcf5c26013e2bae9fdfdb62c9f', # clease-0.10.6.tar.gz + # CLEASE-0.10.6_drop_version_req_for_click.patch + '1ad7ed00f64fe7522714a05048f0ef8bd32092332721f4e6aa097ab3a70d0b18', + ], + }), +] + +sanity_check_commands = ["clease --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CLEASE/CLEASE-0.10.6_drop_version_req_for_click.patch b/easybuild/easyconfigs/c/CLEASE/CLEASE-0.10.6_drop_version_req_for_click.patch new file mode 100644 index 00000000000..de3e27b585f --- /dev/null +++ b/easybuild/easyconfigs/c/CLEASE/CLEASE-0.10.6_drop_version_req_for_click.patch @@ -0,0 +1,15 @@ +Don't enforce version of click. We already have click 7.1.2 in Python/3.9.5 + +Åke Sandgren, 2021-11-24 +diff -ru clease-0.10.6.orig/setup.py clease-0.10.6/setup.py +--- clease-0.10.6.orig/setup.py 2021-10-30 13:47:34.000000000 +0200 ++++ clease-0.10.6/setup.py 2021-11-24 14:03:38.514542426 +0100 +@@ -143,7 +143,7 @@ + 'scikit-learn', + 'typing_extensions', + 'Deprecated', +- 'click>=8.0.0', # CLI things ++ 'click', # CLI things + 'attrs', + 'scipy>=1.5.0', # Last version which allows python 3.6 + # 'mypy', diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.24.2-intel-2021a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.24.2-intel-2021a.eb new file mode 100644 index 00000000000..61bf289e16d --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.24.2-intel-2021a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.24.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d14701a12417930392cd3898e9646cf5670c190b933625ebe7511b1f7d7b8736'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'sklearn'} + +moduleclass = 'data' From 36fdcd242d6f0cec4bf5a4e620d6d7caa1aa8cc0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 24 Nov 2021 15:21:28 +0100 Subject: [PATCH 2067/9987] no longer necessary to add bin to PATH --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb | 3 --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb | 3 --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb | 2 -- easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb | 2 -- easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb | 2 -- easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.1.eb | 2 -- easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.2.eb | 2 -- 7 files changed, 16 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb index 37be512a83b..20ff9cea5ec 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb @@ -71,7 +71,4 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions -modextrapaths = {'PATH': 'bin'} - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb index 77a03ef8b4b..b11a4062702 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb @@ -75,7 +75,4 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions -modextrapaths = {'PATH': 'bin'} - moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb index a672d19e378..51a6c010ad5 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb @@ -57,9 +57,7 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions modextrapaths = { - 'PATH': 'bin', # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', } diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb index 134f250ccc0..a9880d87c88 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb @@ -51,9 +51,7 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions modextrapaths = { - 'PATH': 'bin', # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', } diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb index 9fa373cba0c..8313dce7680 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb @@ -55,9 +55,7 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions modextrapaths = { - 'PATH': 'bin', # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', } diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.1.eb index 6f417ffc47f..34b3bc3efa0 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.1.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.1.eb @@ -62,9 +62,7 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions modextrapaths = { - 'PATH': 'bin', # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', } diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.2.eb index 44e2cd25dda..03537712731 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.2.eb @@ -53,9 +53,7 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions modextrapaths = { - 'PATH': 'bin', # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', } From 878165503dd88bce9049399c2b1e2832f96f0ec9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 24 Nov 2021 15:27:49 +0100 Subject: [PATCH 2068/9987] no longer necessary to add bin to PATH --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb | 2 -- easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb | 2 -- easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb | 2 -- easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb | 2 -- easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb | 2 -- easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb | 2 -- 6 files changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb index be6da2fe133..54ab6cd55cd 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb @@ -55,9 +55,7 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions modextrapaths = { - 'PATH': 'bin', # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', } diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb index a3f94b9c0c7..8cef4c10962 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb @@ -55,9 +55,7 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions modextrapaths = { - 'PATH': 'bin', # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', } diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb index ed0c7106320..a977d55f597 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb @@ -54,9 +54,7 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions modextrapaths = { - 'PATH': 'bin', # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', } diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb index 0b0383bc951..a69c7c6cf4c 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb @@ -53,9 +53,7 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions modextrapaths = { - 'PATH': 'bin', # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', } diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb index ea6a733eb55..6f67b2659d9 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb @@ -54,9 +54,7 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions modextrapaths = { - 'PATH': 'bin', # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', } diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb index 9b653bf3ab9..1ab08fd3685 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb @@ -54,9 +54,7 @@ sanity_check_commands = ['reframe -V'] sanity_pip_check = True -# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions modextrapaths = { - 'PATH': 'bin', # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', } From a4664dc6fdd804bec7bd74b3b01454c2de09eeb3 Mon Sep 17 00:00:00 2001 From: Keith Refson Date: Wed, 24 Nov 2021 17:29:21 +0000 Subject: [PATCH 2069/9987] adding easyconfigs: CASTEP-21.1.1-CrayCCE-19.06.eb, CASTEP-21.1.1-CrayGNU-19.06.eb, CASTEP-21.1.1-foss-2019b.eb, CASTEP-21.1.1-intel-2019b.eb, CASTEP-21.1.1-iomkl-2019b.eb --- .../c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb | 26 +++++++++++++++++++ .../c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb | 26 +++++++++++++++++++ .../c/CASTEP/CASTEP-21.1.1-foss-2019b.eb | 26 +++++++++++++++++++ .../c/CASTEP/CASTEP-21.1.1-intel-2019b.eb | 26 +++++++++++++++++++ .../c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb | 26 +++++++++++++++++++ 5 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb create mode 100644 easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb create mode 100644 easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb create mode 100644 easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb create mode 100644 easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb new file mode 100644 index 00000000000..aab29319405 --- /dev/null +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'CASTEP' +version = '21.1.1' + +homepage = 'http://www.castep.org' +description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" + +toolchain = {'name': 'CrayCCE', 'version': '19.06'} +dependencies = [('cray-fftw', EXTERNAL_MODULE)] +# CASTEP is proprietary software, available under a free-of-charge license for academic use only. +# Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. + +sources = ['CASTEP-21.11.tar.gz'] + +skipsteps = [ 'configure' ] + +maxparallel = 16 + +buildopts = 'COMMS_ARCH=mpi FFT=fftw3 FFTLIBDIR= castep tools' + +preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' + +installopts = 'COMMS_ARCH=mpi FFT=fftw3 INSTALL_DIR="%(installdir)s/bin" install-castep install-tools' + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb new file mode 100644 index 00000000000..59ea706173f --- /dev/null +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'CASTEP' +version = '21.1.1' + +homepage = 'http://www.castep.org' +description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" + +toolchain = {'name': 'CrayGNU', 'version': '19.06'} +dependencies = [('cray-fftw', EXTERNAL_MODULE)] +# CASTEP is proprietary software, available under a free-of-charge license for academic use only. +# Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. + +sources = ['CASTEP-21.11.tar.gz'] + +skipsteps = [ 'configure' ] + +maxparallel = 16 + +buildopts = 'COMMS_ARCH=mpi FFT=fftw3 FFTLIBDIR= castep tools' + +preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' + +installopts = 'COMMS_ARCH=mpi FFT=fftw3 INSTALL_DIR="%(installdir)s/bin" install-castep install-tools' + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb new file mode 100644 index 00000000000..c8a5551756d --- /dev/null +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'CASTEP' +version = '21.1.1' + +homepage = 'http://www.castep.org' +description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +# CASTEP is proprietary software, available under a free-of-charge license for academic use only. +# Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. + +sources = ['CASTEP-21.11.tar.gz'] + +skipsteps = [ 'configure' ] + +maxparallel = 16 + +buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas FFTLIBDIR= MATHLIBDIR= castep tools utilities' + +preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' + +installopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas INSTALL_DIR="%(installdir)s/bin" install-castep install-tools install-utilities' + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb new file mode 100644 index 00000000000..7e052d5f867 --- /dev/null +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'CASTEP' +version = '21.1.1' + +homepage = 'http://www.castep.org' +description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +# CASTEP is proprietary software, available under a free-of-charge license for academic use only. +# Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. + +sources = ['CASTEP-21.11.tar.gz'] + +skipsteps = [ 'configure' ] + +maxparallel = 16 + +buildopts = 'COMMS_ARCH=mpi castep tools utilities' + +preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' + +installopts = 'COMMS_ARCH=mpi INSTALL_DIR="%(installdir)s/bin" install-castep install-tools install-utilities' + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb new file mode 100644 index 00000000000..2d7aef20c52 --- /dev/null +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'CASTEP' +version = '21.1.1' + +homepage = 'http://www.castep.org' +description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" + +toolchain = {'name': 'iomkl', 'version': '2019b'} + +# CASTEP is proprietary software, available under a free-of-charge license for academic use only. +# Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. + +sources = ['CASTEP-21.11.tar.gz'] + +skipsteps = [ 'configure' ] + +maxparallel = 16 + +buildopts = 'COMMS_ARCH=mpi castep tools utilities' + +preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' + +installopts = 'COMMS_ARCH=mpi INSTALL_DIR="%(installdir)s/bin" install-castep install-tools install-utilities' + +moduleclass = 'phys' From fc3bf28047505e2dc28f5a61e83e90e81543c0ff Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 24 Nov 2021 18:43:56 +0100 Subject: [PATCH 2070/9987] adding easyconfigs: pkgconfig-1.5.5-GCCcore-11.2.0.eb --- .../pkgconfig-1.5.5-GCCcore-11.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b78cf1a18a8 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.5.5' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('pkg-config', '0.29.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From c89ffad161e2ad7d74ff141e3567353855c9bc30 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 24 Nov 2021 21:59:54 +0100 Subject: [PATCH 2071/9987] add git as builddependency to Python --- easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb | 1 + easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb | 1 + easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb index f3b5d1b0640..7e9174f9fe2 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb @@ -14,6 +14,7 @@ checksums = ['e634a7a74776c2b89516b2e013dda1728c89c8149b9863b8cea21946daf9d561'] builddependencies = [ ('UnZip', '6.0'), + ('git', '2.23.0', '-nodocs'), # required for pbr ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index 602f3f5c329..46621989091 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -14,6 +14,7 @@ checksums = ['313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21'] builddependencies = [ ('UnZip', '6.0'), + ('git', '2.28.0', '-nodocs'), # required for pbr ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb index 95b46797d98..577405f03b6 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb @@ -16,6 +16,7 @@ builddependencies = [ ('UnZip', '6.0'), ('Rust', '1.52.1'), # required for setuptools-rust, which is needed for cryptography ('pkg-config', '0.29.2'), + ('git', '2.32.0', '-nodocs'), # required for pbr ] dependencies = [ diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb index 9a868863ba7..d729015147b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb @@ -16,6 +16,7 @@ builddependencies = [ ('UnZip', '6.0'), ('Rust', '1.54.0'), # required for setuptools-rust, which is needed for cryptography ('pkg-config', '0.29.2'), + ('git', '2.33.1', '-nodocs'), # required for pbr ] dependencies = [ From bc421ee4b37c48e69daf57edb7c0155d4773c5ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Nov 2021 22:03:25 +0100 Subject: [PATCH 2072/9987] {bio,compiler}[system] elprep v5.1.1 + Go 1.17.3 --- .../easyconfigs/e/elprep/elprep-5.1.1.eb | 27 +++++++++++++++++++ easybuild/easyconfigs/g/Go/Go-1.17.3.eb | 12 +++++++-- 2 files changed, 37 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/e/elprep/elprep-5.1.1.eb diff --git a/easybuild/easyconfigs/e/elprep/elprep-5.1.1.eb b/easybuild/easyconfigs/e/elprep/elprep-5.1.1.eb new file mode 100644 index 00000000000..22412a2c08d --- /dev/null +++ b/easybuild/easyconfigs/e/elprep/elprep-5.1.1.eb @@ -0,0 +1,27 @@ +easyblock = 'GoPackage' + +name = 'elprep' +version = '5.1.1' + +homepage = 'https://github.com/ExaScience/elprep' +description = """elPrep is a high-performance tool for analyzing .sam/.bam files (up to and including variant calling) + in sequencing pipelines.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/ExaScience/elprep/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4996acf8adb194a3da1631f936b4311524ec4cb59716f8459ed1cfda8b9aac8c'] + +builddependencies = [ + ('Go', '1.17.3'), +] + +sanity_check_commands = ['elprep -h'] + +sanity_check_paths = { + 'files': ['bin/elprep'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/Go/Go-1.17.3.eb b/easybuild/easyconfigs/g/Go/Go-1.17.3.eb index 8465e8503cc..bc03da2a2a5 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.17.3.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.17.3.eb @@ -10,13 +10,21 @@ description = """Go is an open source programming language that makes it easy to toolchain = SYSTEM source_urls = ['https://storage.googleapis.com/golang/'] -sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz'] -checksums = ['550f9845451c0c94be679faf116291e7807a8d78b43149f9506c1b15eb89008c'] + +local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} +sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] +checksums = [{ + 'go%(version)s.linux-amd64.tar.gz': '550f9845451c0c94be679faf116291e7807a8d78b43149f9506c1b15eb89008c', + 'go%(version)s.linux-arm64.tar.gz': '06f505c8d27203f78706ad04e47050b49092f1b06dc9ac4fbee4f0e4d015c8d4', +}] sanity_check_paths = { 'files': ['bin/go', 'bin/gofmt'], 'dirs': ['api', 'doc', 'lib', 'pkg'], } +sanity_check_commands = ["go help"] + modextravars = {'GOROOT': '%(installdir)s'} + moduleclass = 'compiler' From 7fc5c118bc250c848167a73ea6087ff705bad637 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Nov 2021 22:47:44 +0100 Subject: [PATCH 2073/9987] adding easyconfigs: pkgconf-1.8.0-GCCcore-11.2.0.eb --- .../p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..072e68192e4 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '1.8.0' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d7b6fdb522d81c11f5a0e0a0629a9f5480809ec90e595058674c1517822dfb8c'] + +builddependencies = [('binutils', '2.37')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' From 8358680bb4910ffe1c36345a6387533943983a8f Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Wed, 24 Nov 2021 22:51:34 +0100 Subject: [PATCH 2074/9987] Update Julia to v1.6.4 --- .../j/Julia/Julia-1.6.4-linux-x86_64.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.6.4-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.4-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.4-linux-x86_64.eb new file mode 100644 index 00000000000..6b8f26686c7 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.4-linux-x86_64.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.6.4' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['52244ae47697e8073dfbc9d1251b0422f0dbd1fbe1a41da4b9f7ddf0506b2132'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lang' From 500f8bcae46fc94a73f74c9679a6b0c70022df0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Nov 2021 22:56:38 +0100 Subject: [PATCH 2075/9987] adding easyconfigs: OpenMPI-4.1.2-GCC-11.2.0.eb --- .../o/OpenMPI/OpenMPI-4.1.2-GCC-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..65660f70e15 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-11.2.0.eb @@ -0,0 +1,32 @@ +name = 'OpenMPI' +version = '4.1.2' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9b78c7cf7fc32131c5cf43dd2ab9740149d9d87cadb2e2189f02685749a6b527'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.5.0'), + ('libevent', '2.1.12'), + ('UCX', '1.11.2'), + ('libfabric', '1.13.2'), + ('PMIx', '4.1.0'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From 377aec8f38f8f5f4aebb289d16b3524b534cce6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Nov 2021 23:25:26 +0100 Subject: [PATCH 2076/9987] add exception for spoa 3.x dependency of Shasta in check for dependency variants --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 03a7d90252e..7f00f8dcebe 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -481,6 +481,8 @@ def check_dep_vars(self, gen, dep, dep_vars): r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], # NanoPlot, NanoComp use an older version of Seaborn 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], + # Shasta requires spoa 3.x + 'spoa': [(r'3\.4\.0', [r'Shasta-0\.8\.0-'])], 'TensorFlow': [ # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), # artic-ncov2019 requires medaka From 273b2cc5bfbf5c5f04185f5da44da9c6546c83fe Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 25 Nov 2021 11:01:54 +0100 Subject: [PATCH 2077/9987] Fix compilation with affinity OFF --- ...3-3.2.10-foss-2021a.eb => pftoolsV3-3.2.11-foss-2021a.eb} | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/pftoolsV3/{pftoolsV3-3.2.10-foss-2021a.eb => pftoolsV3-3.2.11-foss-2021a.eb} (88%) diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.10-foss-2021a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-foss-2021a.eb similarity index 88% rename from easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.10-foss-2021a.eb rename to easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-foss-2021a.eb index bd87527dfce..cd0e063e51f 100644 --- a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.10-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-foss-2021a.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'pftoolsV3' -version = '3.2.10' +version = '3.2.11' homepage = 'https://github.com/sib-swiss/pftools3' description = """A suite of tools to build and search generalized profiles (protein and DNA).""" @@ -18,7 +18,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/'] -checksums = ['a0376f67531655985d7f52468d4f2a491c122c799ac8bfed486990cb0c1f6171'] +checksums = ['b45381584c57bc7c3ac6544f8654752095a5c04fd8242ab270b1d8cdce40d94a'] builddependencies = [ ('CMake', '3.20.1'), @@ -38,6 +38,7 @@ dependencies = [ configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX:PATH=%(installdir)s -DCMAKE_BUILD_TYPE=Release ' configure_cmd += '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON ' +configure_cmd += '-DUSE_AFFINITY=OFF ' # Disable affinity for some old architectures configure_cmd += '../pftools3-%(version)s' runtest = 'test' From 0035483c546a44a4cf5ad2088bb9af0d55c5fb21 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 25 Nov 2021 12:54:04 +0200 Subject: [PATCH 2078/9987] updates after review --- .../cpu_features-0.6.0-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ .../Shasta-0.8.0-foss-2020b-fix_links.patch | 2 ++ .../s/Shasta/Shasta-0.8.0-foss-2020b.eb | 20 ++++++------ 3 files changed, 43 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..42da9feba78 --- /dev/null +++ b/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'cpu_features' +version = '0.6.0' + +homepage = 'https://github.com/google/cpu_features' +description = """A cross-platform C library to retrieve CPU features (such as available instructions) at runtime.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/cpu_features/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['95a1cf6f24948031df114798a97eea2a71143bd38a4d07d9a758dda3924c1932'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +modextrapaths = {'CPATH': 'include/cpu_features'} + +sanity_check_paths = { + 'files': ['bin/list_cpu_features', 'lib/libcpu_features.a'], + 'dirs': ['include/cpu_features/'] +} + +sanity_check_commands = ['list_cpu_features'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b-fix_links.patch b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b-fix_links.patch index c5d227d4b12..f6d919926d1 100644 --- a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b-fix_links.patch +++ b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b-fix_links.patch @@ -1,3 +1,5 @@ +fix linking to BLAS + lapack (original didnt expect any alternatives to blas - like openblas) +Author: Denis Kristak diff -ruN shasta-0.8.0_orig/dynamicExecutable/CMakeLists.txt shasta-0.8.0/dynamicExecutable/CMakeLists.txt --- shasta-0.8.0_orig/dynamicExecutable/CMakeLists.txt 2021-11-11 15:34:47.786798000 +0100 +++ shasta-0.8.0/dynamicExecutable/CMakeLists.txt 2021-11-11 15:33:29.419991000 +0100 diff --git a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb index 6479ec878af..3781b94855a 100644 --- a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb @@ -24,12 +24,12 @@ patches = [ ] checksums = [ '8e94767275fc5352ff192afed783b00b720b6214d8779edc44e9ebe636e9833e', # 0.8.0.tar.gz - 'dfda9a6ca33e37236cbbc27a1d65bb54d361f27ecdb2b9855e46ac6dab6e255e', # Shasta-0.8.0-foss-2020b-fix_links.patch + 'd9696b8a667f6a0db724f779083accb8004398bdfdf5cf15ef5cdaed89f339d0', # Shasta-0.8.0-foss-2020b-fix_links.patch ] builddependencies = [ ('CMake', '3.18.4'), - ('binutils', '2.35'), + ('Cereal', '1.3.0', '', True), ] dependencies = [ @@ -37,33 +37,33 @@ dependencies = [ ('Boost', '1.74.0'), ('libpng', '1.6.37'), ('SeqAn', '2.4.0'), - ('BLAST', '2.11.0', '-Linux_x86_64', True), + ('BLAST+', '2.11.0'), ('gnuplot', '5.4.1'), ('Graphviz', '2.47.0', '-Java-11'), ('Python', '3.8.6'), ('pybind11', '2.6.0'), - ('Cereal', '1.3.0', '', True), - ('spoa', '3.4.0'), - ('ScaLAPACK', '2.1.0'), - ('OpenBLAS', '0.3.12'), + ('spoa', '3.4.0'), # older spoa is needed, since new is truly incompatible ('cpu_features', '0.6.0'), ] prebuildopts = "export CPATH=$EBROOTBOOST/include/boost/:$CPATH && " +# we need this because CMakeLists here is hard to configure, so we stick to default install path (inside sub-folder) +# and copy installed files afterwards buildopts = " && make install -j %(parallel)s" files_to_copy = [ (['shasta-install/bin/*'], 'bin'), - (['shasta-install/bin/*.a'], 'lib'), - (['shasta-install/bin/*.so'], 'lib') + (['shasta-install/bin/*.a', 'shasta-install/bin/*.%s' % SHLIB_EXT], 'lib') ] fix_python_shebang_for = ['bin/*.py'] sanity_check_paths = { - 'files': ['lib/shasta.so', 'lib/shasta.a', 'bin/shasta', 'bin/SaveRun.py', 'bin/Copy.py'], + 'files': ['bin/Copy.py', 'bin/SaveRun.py', 'bin/shasta', 'lib/shasta.a', 'lib/shasta.%s' % SHLIB_EXT], 'dirs': [] } +sanity_check_commands = ['shasta --help'] + moduleclass = 'bio' From 45e22fa0c3552d67caae9fd822ad63139fc71432 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 25 Nov 2021 12:01:46 +0100 Subject: [PATCH 2079/9987] reinstate python versionsuffix in pkgconfig-1.5.5-GCCcore-11.2.0-python.eb --- ...core-11.2.0.eb => pkgconfig-1.5.5-GCCcore-11.2.0-python.eb} | 3 +++ 1 file changed, 3 insertions(+) rename easybuild/easyconfigs/p/pkgconfig/{pkgconfig-1.5.5-GCCcore-11.2.0.eb => pkgconfig-1.5.5-GCCcore-11.2.0-python.eb} (79%) diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.2.0-python.eb similarity index 79% rename from easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.2.0-python.eb index b78cf1a18a8..5c0847b62e8 100644 --- a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.2.0-python.eb @@ -2,6 +2,9 @@ easyblock = 'PythonPackage' name = 'pkgconfig' version = '1.5.5' +# The -python versionsuffix is used to avoid confusion between +# pkg-config (the tool) and pkgconfig (the Python wrappers) +versionsuffix = '-python' homepage = 'https://github.com/matze/pkgconfig' description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" From db9adef5409b3f3c220af07eab5dd1bdf7402372 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 12:28:36 +0100 Subject: [PATCH 2080/9987] adding easyconfigs: HDF5-1.12.1-iimpi-2021b.eb --- .../h/HDF5/HDF5-1.12.1-iimpi-2021b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-iimpi-2021b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-iimpi-2021b.eb new file mode 100644 index 00000000000..c854127cb09 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.1-iimpi-2021b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.12.1' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['79c66ff67e666665369396e9c90b32e238e501f345afd2234186bfb8331081ca'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From ed912276626f0b2b7598a73b7dc43a24862474f3 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 25 Nov 2021 11:31:07 +0000 Subject: [PATCH 2081/9987] adding easyconfigs: BWA-0.7.17-GCC-10.3.0.eb --- .../b/BWA/BWA-0.7.17-GCC-10.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.3.0.eb new file mode 100644 index 00000000000..9a6bba9d331 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCC-10.3.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman, Big Data Institute, University of Oxford +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +dependencies = [ + ('Perl', '5.32.1'), + ('zlib', '1.2.11'), +] + +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " + +moduleclass = 'bio' From 7dc3dfa3629276fea1e560ed4bd897cb405fad6d Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 25 Nov 2021 12:38:50 +0100 Subject: [PATCH 2082/9987] Added references to the original issue and PR in PyTorch to the patch file, as well as to the upstreamed PR that implements this patch, so we can see when it is resolved upstream. Also, added an additional sanity check for now --- .../p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 9 +++++++-- .../p/PyTorch/PyTorch-1.10.0_skip_cmake_rpath.patch | 6 +++++- 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index d1d838d1247..436dd64f606 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -62,7 +62,7 @@ checksums = [ # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', # PyTorch-1.10.0_skip_cmake_rpath.patch - 'de49323432b41fc401ddaf86f11eb565aa43eeb56380fdd2b1385db1a05dd4ad', + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -116,7 +116,12 @@ excluded_tests = { runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' -sanity_check_commands = ["python -c 'import caffe2.python'"] +# The readelf sanity check can be taken out once the TestRPATH test from https://github.com/pytorch/pytorch/pull/68912 +# is accepted, since it is then checked as part of the PyTorch test suite +sanity_check_commands = [ + "python -c 'import caffe2.python'", + "readelf -d $EBROOTPYTORCH/lib/python3.9/site-packages/torch/lib/libcaffe2_nvrtc.so | egrep 'RPATH|RUNPATH' | grep -v stubs", +] tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_cmake_rpath.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_cmake_rpath.patch index c39d317e4ba..09469cd45b4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_cmake_rpath.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip_cmake_rpath.patch @@ -7,10 +7,14 @@ # See https://github.com/easybuilders/easybuild-easyconfigs/issues/14359 # This line https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L16 # Makes sure that any path that is linked, is also added to the RUNPATH. -# This patch changes behavior for the libraries that were failing, i.e. the ones in this list: +# This has been reported upstream in https://github.com/pytorch/pytorch/issues/35418 +# and a fix was attempted in https://github.com/pytorch/pytorch/pull/37737 but it was reverted +# +# This EasyBuild patch changes behavior for the libraries that were failing, i.e. the ones in this list: # https://github.com/easybuilders/easybuild-easyconfigs/issues/14359#issuecomment-970479904 # This is done by setting INSTALL_RPATH_USE_LINK_PATH to false, and instead, specifying the RPATH # explicitely by defining INSTALL_RPATH, but only adding directories that do not match to the "stubs" regex +# It has been upstreamed in this PR https://github.com/pytorch/pytorch/pull/68912 (not accepted yet at the time of writing) diff -Nru pytorch.orig/caffe2/CMakeLists.txt pytorch/caffe2/CMakeLists.txt --- pytorch.orig/caffe2/CMakeLists.txt 2021-11-17 11:46:01.797337624 +0100 +++ pytorch/caffe2/CMakeLists.txt 2021-11-18 19:05:35.637707235 +0100 From 36140faad064edce577940a0a05c8867e6b0624f Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 25 Nov 2021 13:53:07 +0100 Subject: [PATCH 2083/9987] Fix style --- .../p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index 436dd64f606..d1f2e2dfc37 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -118,9 +118,10 @@ runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-throu # The readelf sanity check can be taken out once the TestRPATH test from https://github.com/pytorch/pytorch/pull/68912 # is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python3.9/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT sanity_check_commands = [ "python -c 'import caffe2.python'", - "readelf -d $EBROOTPYTORCH/lib/python3.9/site-packages/torch/lib/libcaffe2_nvrtc.so | egrep 'RPATH|RUNPATH' | grep -v stubs", + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, ] tests = ['PyTorch-check-cpp-extension.py'] From 4a1435ca32917480ab6bed3ce57af9e12dede263 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 15:01:16 +0100 Subject: [PATCH 2084/9987] add missing XZ dependency to recent PROJ easyconfigs --- easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb | 5 ++++- easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb | 5 ++++- easybuild/easyconfigs/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb | 1 + easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/p/PROJ/PROJ-8.0.1-GCCcore-10.3.0.eb | 1 + easybuild/easyconfigs/p/PROJ/PROJ-8.1.0-GCCcore-11.2.0.eb | 1 + 6 files changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb index d97b16341e0..ceb42f9a284 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-6.0.0-GCCcore-8.2.0.eb @@ -27,7 +27,10 @@ builddependencies = [ ('binutils', '2.31.1'), ] -dependencies = [('SQLite', '3.27.2')] +dependencies = [ + ('SQLite', '3.27.2'), + ('XZ', '5.2.4'), +] sanity_check_paths = { 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb index fbf999ac44c..4e2d3363c23 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-6.2.1-GCCcore-8.3.0.eb @@ -27,7 +27,10 @@ builddependencies = [ ('binutils', '2.32'), ] -dependencies = [('SQLite', '3.29.0')] +dependencies = [ + ('SQLite', '3.29.0'), + ('XZ', '5.2.4'), +] sanity_check_paths = { 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb index ad67802d6bb..2bca330dfe8 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-7.0.0-GCCcore-9.3.0.eb @@ -31,6 +31,7 @@ dependencies = [ ('SQLite', '3.31.1'), ('LibTIFF', '4.1.0'), ('cURL', '7.69.1'), + ('XZ', '5.2.5'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb index cb19aeb08e6..4d8bb71381e 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-7.2.1-GCCcore-10.2.0.eb @@ -31,6 +31,7 @@ dependencies = [ ('SQLite', '3.33.0'), ('LibTIFF', '4.1.0'), ('cURL', '7.72.0'), + ('XZ', '5.2.5'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-8.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-8.0.1-GCCcore-10.3.0.eb index 9b222a4f22e..649eb368ed7 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-8.0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-8.0.1-GCCcore-10.3.0.eb @@ -31,6 +31,7 @@ dependencies = [ ('SQLite', '3.35.4'), ('LibTIFF', '4.2.0'), ('cURL', '7.76.0'), + ('XZ', '5.2.5'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-8.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-8.1.0-GCCcore-11.2.0.eb index d50f286db7c..31ec89c70e0 100644 --- a/easybuild/easyconfigs/p/PROJ/PROJ-8.1.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PROJ/PROJ-8.1.0-GCCcore-11.2.0.eb @@ -31,6 +31,7 @@ dependencies = [ ('SQLite', '3.36'), ('LibTIFF', '4.3.0'), ('cURL', '7.78.0'), + ('XZ', '5.2.5'), ] sanity_check_paths = { From 8f88b6c0c98847d5d0b73485d716d0abc0baa73e Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 25 Nov 2021 15:40:45 +0000 Subject: [PATCH 2085/9987] adding easyconfigs: PAL2NAL-14-GCCcore-10.2.0.eb, PAL2NAL-14-GCCcore-10.3.0.eb --- .../p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb | 39 +++++++++++++++++++ .../p/PAL2NAL/PAL2NAL-14-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..1a78c40f46e --- /dev/null +++ b/easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Tarball' + +name = 'PAL2NAL' +version = '14' + +homepage = 'http://www.bork.embl.de/pal2nal/' +description = """PAL2NAL is a program that converts a multiple sequence alignment of proteins and + the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically + assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the + input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the + input alignment, which is suitable for the analysis of pseudogenes. The resulting codon alignment + can further be subjected to the calculation of synonymous (d_S) and non-synonymous (d_N) subs- + titution rates. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://www.bork.embl.de/pal2nal/distribution/'] +sources = ['%(namelower)s.v%(version)s.tar.gz'] +checksums = ['0e458d38571ab6d61078047a9e80d843bb2e733414eeff8b1144d1c6bc13848f'] + +dependencies = [('Perl', '5.32.0')] + +fix_perl_shebang_for = ['%(namelower)s.pl'] + +sanity_check_paths = { + 'files': ['%(namelower)s.pl', 'README', 'test.aln', 'test.nuc'], + 'dirs': [], +} + +sanity_check_commands = [ + 'pal2nal.pl -h', + 'pal2nal.pl test.aln test.nuc -output paml -nogap', +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6abdeb0aeab --- /dev/null +++ b/easybuild/easyconfigs/p/PAL2NAL/PAL2NAL-14-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Tarball' + +name = 'PAL2NAL' +version = '14' + +homepage = 'http://www.bork.embl.de/pal2nal/' +description = """PAL2NAL is a program that converts a multiple sequence alignment of proteins and + the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically + assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the + input protein sequence, or contains UTRs, polyA tails. It can also deal with frame shifts in the + input alignment, which is suitable for the analysis of pseudogenes. The resulting codon alignment + can further be subjected to the calculation of synonymous (d_S) and non-synonymous (d_N) subs- + titution rates. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://www.bork.embl.de/pal2nal/distribution/'] +sources = ['%(namelower)s.v%(version)s.tar.gz'] +checksums = ['0e458d38571ab6d61078047a9e80d843bb2e733414eeff8b1144d1c6bc13848f'] + +dependencies = [('Perl', '5.32.1')] + +fix_perl_shebang_for = ['%(namelower)s.pl'] + +sanity_check_paths = { + 'files': ['%(namelower)s.pl', 'README', 'test.aln', 'test.nuc'], + 'dirs': [], +} + +sanity_check_commands = [ + 'pal2nal.pl -h', + 'pal2nal.pl test.aln test.nuc -output paml -nogap', +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From ae860d8c429ca1ec76f68fdade3aa4df646b0a41 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 25 Nov 2021 15:41:31 +0000 Subject: [PATCH 2086/9987] adding easyconfigs: PAML-4.9j-GCCcore-10.2.0.eb, PAML-4.9j-GCCcore-10.3.0.eb --- .../p/PAML/PAML-4.9j-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ .../p/PAML/PAML-4.9j-GCCcore-10.3.0.eb | 39 ++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..f201448d6c4 --- /dev/null +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'PAML' +version = '4.9j' + +homepage = 'http://abacus.gene.ucl.ac.uk/software/paml.html' +description = """PAML is a package of programs for phylogenetic + analyses of DNA or protein sequences using maximum likelihood.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://abacus.gene.ucl.ac.uk/software'] +sources = ['%(namelower)s%(version)s.tgz'] +checksums = ['9b00fbd37fe825129a160599372ba4c8e88b22d14c0388044a711fb281a0191d'] + +# Avoid multiple definition linking errors +prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +builddependencies = [('binutils', '2.35')] + +start_dir = 'src' + +files_to_copy = [ + (['GeneticCode.txt', '%(builddir)s/%(namelower)s%(version)s/README.txt'], ''), + (['*.trees', '*.ctl', '*.nuc', '*.dat', 'paup*', 'stewart.aa'], ''), + (['src/baseml', 'src/basemlg', 'src/chi2', 'src/codeml', 'src/evolver'], 'bin'), + (['src/infinitesites', 'src/mcmctree', 'src/pamp', 'src/yn00'], 'bin'), + (['dat/*'], 'dat'), + (['doc/*'], 'doc'), + (['examples/*'], 'examples'), + (['Technical/*'], 'Technical'), +] + +sanity_check_paths = { + 'files': ['bin/baseml'], + 'dirs': ['bin'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..0310460c7fd --- /dev/null +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'PAML' +version = '4.9j' + +homepage = 'http://abacus.gene.ucl.ac.uk/software/paml.html' +description = """PAML is a package of programs for phylogenetic + analyses of DNA or protein sequences using maximum likelihood.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://abacus.gene.ucl.ac.uk/software'] +sources = ['%(namelower)s%(version)s.tgz'] +checksums = ['9b00fbd37fe825129a160599372ba4c8e88b22d14c0388044a711fb281a0191d'] + +prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +builddependencies = [('binutils', '2.36.1')] + +start_dir = 'src' + +files_to_copy = [ + (['GeneticCode.txt', '%(builddir)s/%(namelower)s%(version)s/README.txt'], ''), + (['*.trees', '*.ctl', '*.nuc', '*.dat', 'paup*', 'stewart.aa'], ''), + (['src/baseml', 'src/basemlg', 'src/chi2', 'src/codeml', 'src/evolver'], 'bin'), + (['src/infinitesites', 'src/mcmctree', 'src/pamp', 'src/yn00'], 'bin'), + (['dat/*'], 'dat'), + (['doc/*'], 'doc'), + (['examples/*'], 'examples'), + (['Technical/*'], 'Technical'), +] + +sanity_check_paths = { + 'files': ['bin/baseml'], + 'dirs': ['bin'] +} + +moduleclass = 'bio' From 618282981431d482aed0ad666f036d5266f3b980 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 19:00:27 +0100 Subject: [PATCH 2087/9987] adding easyconfigs: vsc-mympirun-5.2.7.eb --- .../v/vsc-mympirun/vsc-mympirun-5.2.7.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.7.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.7.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.7.eb new file mode 100644 index 00000000000..cfd216ab246 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.7.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'vsc-mympirun' +version = '5.2.7' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """mympirun is a tool to make it easier for users of HPC clusters to +run MPI programs with good performance.""" + +# we build this to work with every python version +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +use_pip = False + +exts_list = [ + ('setuptools', '41.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6afa61b391dcd16cb8890ec9f66cc4015a8a31a6e1c2b4e0c464514be1a3d722'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('pbr', '5.8.0', { + 'checksums': ['672d8ebee84921862110f23fcec2acea191ef58543d34dfe9ef3d9f13c31cddf'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '4.0.3', { + 'checksums': ['7d3fbbde18228f4ff2f1f119a45cdffa458b4c0dee32eb4d2bb2f82554bac7bc'], + }), + ('IPy', '1.01', { + 'modulename': 'IPy', + 'checksums': ['edeca741dea2d54aca568fa23740288c3fe86c0f3ea700344571e9ef14a7cc1a'], + }), + ('vsc-install', '0.17.19', { + 'modulename': 'vsc.install', + 'checksums': ['e335f09430c4495d681a198c3893cf3f0755ca881b78f547f1767b3f51ada223'], + }), + ('vsc-base', '3.4.0', { + 'modulename': 'vsc.utils', + 'checksums': ['20720e119f5b2d4b6d32f48145050d50aa9e2f15d686bd62dd41b09814395965'], + }), + (name, version, { + 'modulename': 'vsc', + 'checksums': ['fc3190a0dc4fb0fbe554f782d90f26d50730f4cf3e0778c6214682677a75a100'], + }), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mypmirun', 'bin/mympisanity', 'bin/mytasks'], + 'dirs': ['bin/fake'], +} +sanity_check_commands = ["mympirun --help"] + +# can't enable 'pip check' since pip may not be installed in OS +sanity_pip_check = False + +moduleclass = 'tools' From 923bec4e983913d67b265ec865e14db6392d747f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 19:18:22 +0100 Subject: [PATCH 2088/9987] add genoPlotR + penfa extensions (and required dependencies) to R 4.1.2 easyconfig --- .../easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index ad540db5316..ef7f193eb9e 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -50,6 +50,7 @@ dependencies = [ ('GLPK', '5.0'), # for Rglpk ('nodejs', '14.17.6'), # for V8 (required by rstan) ('GDAL', '3.3.2'), # for sf + ('MPFR', '4.1.0'), # for Rmpfr ('libgit2', '1.1.1'), ('OpenSSL', '1.1', '', True), ] @@ -3126,6 +3127,33 @@ exts_list = [ ('collapse', '1.6.5', { 'checksums': ['1e232a3a62b5eb5ed5d81e7d92ce1bae34c3d877d593d47d7edbd3f515b95a46'], }), + ('genoPlotR', '0.8.11', { + 'checksums': ['f127f7fe8b19c899ecfdf98bf69d2e18926afb593a72fc40097acca66d401607'], + }), + ('VineCopula', '2.4.3', { + 'checksums': ['42727aa7345ab544242182222eb97476f5dc04bc837f94f6fd3ea6ccac93ea17'], + }), + ('Rmpfr', '0.8-7', { + 'checksums': ['93c2db785ff705dcfc6fa7f0373c2426cdc2ef72ceb5b294edeb2952775f57d2'], + }), + ('scam', '1.2-12', { + 'checksums': ['0ce5f844221370884719424eb5b2b22c34a8a8ad64eac3de981e5539b6e88f4a'], + }), + ('copula', '1.0-1', { + 'checksums': ['d09b2ccffc7379e48b00952aa6b282baf502feebaf55cc44e93f881d7b909742'], + }), + ('evd', '2.3-3', { + 'checksums': ['2fc5ef2e0c3a2a9392425ddd45914445497433d90fb80b8c363877baee4559b4'], + }), + ('ismev', '1.42', { + 'checksums': ['0d57fbeca83bd478e84fcff795967d51d8448c629abe7adc6c4c18c7fb8bf1a5'], + }), + ('GJRM', '0.2-5.1', { + 'checksums': ['516dd73c70e5c8ab60b24027f94cab42603797c41cb7aa740882cb850f6d6ab4'], + }), + ('penfa', '0.1.1', { + 'checksums': ['a22a8ac3d4a040c77e50ddc92328c1989eae536d79fe56013e9372ba27c114e5'], + }), ] moduleclass = 'lang' From de33ae30c081a8ecc966896bcdd2753d0793a1fe Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 25 Nov 2021 20:59:38 +0100 Subject: [PATCH 2089/9987] adding easyconfigs: METIS-5.1.0-GCCcore-11.2.0.eb, SuiteSparse-5.10.1-foss-2021b-METIS-5.1.0.eb --- .../m/METIS/METIS-5.1.0-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ ...iteSparse-5.10.1-foss-2021b-METIS-5.1.0.eb | 29 ++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b520001ee95 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +# We use 32bit for indices and 64bit for content +patches = ['%(name)s-%(version)s-use-doubles.patch'] + +checksums = [ + '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2', # source + '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67', # patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021b-METIS-5.1.0.eb new file mode 100644 index 00000000000..210b19a24e0 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021b-METIS-5.1.0.eb @@ -0,0 +1,29 @@ +name = 'SuiteSparse' +version = '5.10.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From adc990daa28f466aa658e3ad46240abaf45ed2fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 21:01:09 +0100 Subject: [PATCH 2090/9987] add M3Drop extension to R-bundle-Bioconductor 3.14 easyconfig --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index 1f370b4ed91..fa5e23bd4c8 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1069,6 +1069,12 @@ exts_list = [ ('NMF', '0.23.0', { 'checksums': ['0f0cca01b37bf46fce90d2e951df609d3d377908aa607825083fd0c47cc24753'], }), + ('reldist', '1.6-6', { + 'checksums': ['8a7b55120d24fae72b4c284072b07d7f90094ba00bf89ba172e0b3ab8fbe7127'], + }), + ('M3Drop', '1.20.0', { + 'checksums': ['b82772303c624ff01418e66cefd751a0f6f9d819ea2cf3c9c20a9acd1fc106e5'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 707a6f262a1c12a3b6033ce24ba9bceac7822cf5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 21:18:04 +0100 Subject: [PATCH 2091/9987] adding easyconfigs: ABINIT-9.6.2-intel-2021a.eb --- .../a/ABINIT/ABINIT-9.6.2-intel-2021a.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021a.eb new file mode 100644 index 00000000000..f7c45b0d2ec --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.6.2' + +homepage = 'https://www.abinit.org/' +description = """ +ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of +systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using +pseudopotentials and a planewave or wavelet basis. +""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b018c2ff24338a5952c5550a7e09d4c7793b62402c7aa4e09273e9a666e674fb'] + +builddependencies = [ + ('Python', '3.9.5'), +] +dependencies = [ + ('libxc', '5.1.5'), + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), + ('HDF5', '1.10.7'), + ('Wannier90', '3.1.0'), +] + +# Ensure MPI with intel wrappers. +configopts = '--with-mpi="yes" ' +configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# Enable OpenMP +configopts += '--enable-openmp="yes" ' + +# BLAS/Lapack from MKL +configopts += '--with-linalg-flavor=mkl ' + +# FFTW from MKL +configopts += '--with-fft-flavor=dfti ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# Enable double precision for GW calculations +configopts += '--enable-gw-dpc ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' From 5145018aa49bca516e7a285fc12397291b168d99 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 25 Nov 2021 21:42:35 +0100 Subject: [PATCH 2092/9987] adding easyconfigs: libxc-5.1.6-intel-compilers-2021.4.0.eb --- .../libxc-5.1.6-intel-compilers-2021.4.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..300510175c8 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '5.1.6' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['02e4615a22dc3ec87a23efbd3d9be5bfad2445337140bad1720699571c45c3f9'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Perl', '5.34.0'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' From 3ef2e42d743c213404ddeaeeb1dd802be6957a23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 21:42:36 +0100 Subject: [PATCH 2093/9987] move down (pre)buildops below start_dir in PAML 4.9j easyconfigs --- easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb | 8 ++++---- easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb | 6 +++--- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb index f201448d6c4..32b19dcda70 100644 --- a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb @@ -13,14 +13,14 @@ source_urls = ['http://abacus.gene.ucl.ac.uk/software'] sources = ['%(namelower)s%(version)s.tgz'] checksums = ['9b00fbd37fe825129a160599372ba4c8e88b22d14c0388044a711fb281a0191d'] -# Avoid multiple definition linking errors -prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" -buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' - builddependencies = [('binutils', '2.35')] start_dir = 'src' +# Avoid multiple definition linking errors +prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + files_to_copy = [ (['GeneticCode.txt', '%(builddir)s/%(namelower)s%(version)s/README.txt'], ''), (['*.trees', '*.ctl', '*.nuc', '*.dat', 'paup*', 'stewart.aa'], ''), diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb index 0310460c7fd..2e445358598 100644 --- a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb @@ -13,13 +13,13 @@ source_urls = ['http://abacus.gene.ucl.ac.uk/software'] sources = ['%(namelower)s%(version)s.tgz'] checksums = ['9b00fbd37fe825129a160599372ba4c8e88b22d14c0388044a711fb281a0191d'] -prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" -buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' - builddependencies = [('binutils', '2.36.1')] start_dir = 'src' +prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + files_to_copy = [ (['GeneticCode.txt', '%(builddir)s/%(namelower)s%(version)s/README.txt'], ''), (['*.trees', '*.ctl', '*.nuc', '*.dat', 'paup*', 'stewart.aa'], ''), From b8b70a8f6ce56b9df4ba978032d5ba40e209df80 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 25 Nov 2021 21:49:23 +0100 Subject: [PATCH 2094/9987] adding easyconfigs: netCDF-4.8.1-iimpi-2021b.eb --- .../n/netCDF/netCDF-4.8.1-iimpi-2021b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-iimpi-2021b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-iimpi-2021b.eb new file mode 100644 index 00000000000..b7e378fc25c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-iimpi-2021b.eb @@ -0,0 +1,37 @@ +name = 'netCDF' +version = '4.8.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bc018cc30d5da402622bf76462480664c6668b55eb16ba205a0dfb8647161dd0'] + +builddependencies = [ + ('Autotools', '20210726'), + ('CMake', '3.21.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('HDF5', '1.12.1'), + ('cURL', '7.78.0'), + ('Szip', '2.1.1'), +] + +# HDF5 version detection is missed in netCDF 4.8.1 when HDF5_C_LIBRARY, HDF5_INCLUDE_DIR, and HDF5_HL_LIBRARY are set +local_hdf5_version_fix = '-DHDF5_VERSION=$EBVERSIONHDF5' + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF %s " % local_hdf5_version_fix, + "-DBUILD_SHARED_LIBS=ON %s " % local_hdf5_version_fix, +] + +moduleclass = 'data' From de5b11b82b62522b5307cb9ba2245917d6deac25 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 25 Nov 2021 21:50:30 +0100 Subject: [PATCH 2095/9987] adding easyconfigs: netCDF-Fortran-4.5.3-gompi-2021b.eb, netCDF-Fortran-4.5.3-iimpi-2021b.eb --- .../netCDF-Fortran-4.5.3-gompi-2021b.eb | 25 +++++++++++++++++++ .../netCDF-Fortran-4.5.3-iimpi-2021b.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2021b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2021b.eb new file mode 100644 index 00000000000..f0c5a8e0013 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-gompi-2021b.eb @@ -0,0 +1,25 @@ +name = 'netCDF-Fortran' +version = '4.5.3' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c6da30c2fe7e4e614c1dff4124e857afbd45355c6798353eccfa60c0702b495a'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [('netCDF', '4.8.1')] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2021b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2021b.eb new file mode 100644 index 00000000000..b0c1595a33c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.5.3-iimpi-2021b.eb @@ -0,0 +1,25 @@ +name = 'netCDF-Fortran' +version = '4.5.3' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c6da30c2fe7e4e614c1dff4124e857afbd45355c6798353eccfa60c0702b495a'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [('netCDF', '4.8.1')] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' From 814ca0ece013c2831b425338b515e0acbb68eae7 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 25 Nov 2021 21:53:29 +0100 Subject: [PATCH 2096/9987] adding easyconfigs: Wannier90-3.1.0-foss-2021b.eb, Wannier90-3.1.0-intel-2021b.eb --- .../w/Wannier90/Wannier90-3.1.0-foss-2021b.eb | 35 +++++++++++++++++++ .../Wannier90/Wannier90-3.1.0-intel-2021b.eb | 32 +++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2021b.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2021b.eb new file mode 100644 index 00000000000..25e9da22e6f --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2021b.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +# The -fallow-argument-mismatch allows MPI communication calls to be +# called with arrays of different types at different places in the +# code. This otherwise cause an error in GCC 10.X +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2021b.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2021b.eb new file mode 100644 index 00000000000..78556f8fda7 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2021b.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' From 9bdfd9a15a45274341e0465206ba7a4a67a3a972 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 22:03:01 +0100 Subject: [PATCH 2097/9987] enhance sanity check for PAML 4.9j --- easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb | 9 +++++++-- easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb | 9 +++++++-- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb index 32b19dcda70..8055bdba34f 100644 --- a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.2.0.eb @@ -33,8 +33,13 @@ files_to_copy = [ ] sanity_check_paths = { - 'files': ['bin/baseml'], - 'dirs': ['bin'] + 'files': ['baseml.ctl', 'codeml.ctl', 'bin/baseml', 'bin/codeml'], + 'dirs': ['dat', 'doc', 'examples'], } +sanity_check_commands = [ + "mkdir -p %(builddir)s && cp -a %(installdir)s/examples/HIVNSsites %(builddir)s && " + "cd %(builddir)s/HIVNSsites && codeml", +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb index 2e445358598..cec3fffa19b 100644 --- a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-10.3.0.eb @@ -32,8 +32,13 @@ files_to_copy = [ ] sanity_check_paths = { - 'files': ['bin/baseml'], - 'dirs': ['bin'] + 'files': ['baseml.ctl', 'codeml.ctl', 'bin/baseml', 'bin/codeml'], + 'dirs': ['dat', 'doc', 'examples'], } +sanity_check_commands = [ + "mkdir -p %(builddir)s && cp -a %(installdir)s/examples/HIVNSsites %(builddir)s && " + "cd %(builddir)s/HIVNSsites && codeml", +] + moduleclass = 'bio' From dfaa809939a7cd22704204014aad3c6566cebf4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Nov 2021 22:31:31 +0100 Subject: [PATCH 2098/9987] use %(parallel)s template rather than using hardcoded value in PySide2 easyconfig --- .../p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb index 4d1fe0c1f1e..b2ad02c66b2 100644 --- a/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PySide2/PySide2-5.14.2.3-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'PySide2' version = '5.14.2.3' -homepage = "https://pypi.python.org/pypi/%(name)s/" +homepage = 'https://pypi.python.org/pypi/PySide2' description = """PySide2 is the official Python module from the Qt for Python project, which provides access to the complete Qt 5.12+ framework.""" @@ -31,10 +31,10 @@ download_dep_fail = True preconfigopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' prebuildopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' -buildcmd = 'build --parallel=16' +buildcmd = 'build --parallel=%(parallel)s' preinstallopts = 'export CLANG_INSTALL_DIR=$EBROOTCLANG && ' -install_target = 'install --parallel=16' +install_target = 'install --parallel=%(parallel)s' options = {'modulename': 'PySide2'} From b65dd2df573e988325f15210128cf9b8d1492813 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Thu, 25 Nov 2021 22:35:11 +0100 Subject: [PATCH 2099/9987] Update easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb --- .../easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb index 300510175c8..61a5bbdab00 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['02e4615a22dc3ec87a23efbd3d9be5bfad2445337140bad1720699571c45c3f9'] +checksums = ['0d0496513114ed84987c32649912f9a65d234696dab13a4b00ce8c420bfc0a1d'] builddependencies = [ ('CMake', '3.21.1'), From 2c208f7ac8678573742fa67a6c67b88b428a65e0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Nov 2021 09:30:34 +0100 Subject: [PATCH 2100/9987] added a simple sanity check command for openslide --- .../o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb index 84ace078627..8615ebd3975 100644 --- a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-10.3.0-largefiles.eb @@ -50,4 +50,6 @@ sanity_check_paths = { 'dirs': ['include/openslide'], } +sanity_check_commands = ['openslide-show-properties --help'] + moduleclass = 'vis' From 60147159669aa9cac19e7e48ffbce8cca39d090f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 26 Nov 2021 09:11:03 +0000 Subject: [PATCH 2101/9987] Add sanity_check_command --- .../easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.3.0.eb index 874d1cd5635..efdaf909659 100644 --- a/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-10.3.0.eb @@ -29,4 +29,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['fastahack --help'] + moduleclass = 'bio' From 121d594758b05be360a64cc39ab466a2bec52f3b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Nov 2021 10:17:16 +0100 Subject: [PATCH 2102/9987] adding a simple sanity check command for libdwarf --- .../easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb index 41b93c54d57..7df567f57f6 100644 --- a/easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210528-GCCcore-11.2.0.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': ['include'] } +sanity_check_commands = ['dwarfdump --help'] + moduleclass = 'devel' From 94cdba60aee395b6e2d52e61457331c3a8cda5af Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 26 Nov 2021 10:15:33 +0000 Subject: [PATCH 2103/9987] Use latest tqdm --- easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb index fd7c31c4cf0..d5972679608 100644 --- a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb +++ b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb @@ -18,7 +18,7 @@ dependencies = [ ('SciPy-bundle', '2021.05'), ('networkx', '2.6.3'), ('edlib', '1.3.9'), - ('tqdm', '4.61.1'), + ('tqdm', '4.61.2'), ('matplotlib', '3.4.2'), ('scikit-learn', '0.24.2'), ('plotly.py', '5.1.0'), From 515961111588a29ba8606dcfcf58d38ac77f3ac5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Nov 2021 12:34:09 +0100 Subject: [PATCH 2104/9987] add a simple sanity check command for julia --- easybuild/easyconfigs/j/Julia/Julia-1.6.4-linux-x86_64.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.4-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.4-linux-x86_64.eb index 6b8f26686c7..10bef0f7c20 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.4-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.4-linux-x86_64.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] } +sanity_check_commands = ['julia --help'] + moduleclass = 'lang' From f6f480b0a029ec445cc743aadcded88fa935d991 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 26 Nov 2021 12:24:06 +0000 Subject: [PATCH 2105/9987] adding easyconfigs: Relate-20211123-foss-2020b-R-4.0.3.eb and patches: Relate-20211123_add-cmake-install-targets.patch --- .../Relate-20211123-foss-2020b-R-4.0.3.eb | 68 +++++++++++++++++++ ...e-20211123_add-cmake-install-targets.patch | 35 ++++++++++ 2 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb create mode 100644 easybuild/easyconfigs/r/Relate/Relate-20211123_add-cmake-install-targets.patch diff --git a/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb new file mode 100644 index 00000000000..71a26a09f3c --- /dev/null +++ b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb @@ -0,0 +1,68 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CMakeMake' + +name = 'Relate' +version = '20211123' +local_commit = '78964f4' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://myersgroup.github.io/relate/' +description = "Software for estimating genome-wide genealogies for thousands of samples" +citing = """ +[1] Leo Speidel, Marie Forest, Sinan Shi, Simon Myers. A method for estimating genome-wide + genealogies for thousands of samples. Nature Genetics 51: 1321-1329, 2019. +[2] Leo Speidel, Lara Cassidy, Robert W. Davies, Garrett Hellenthal, Pontus Skoglund, Simon Myers. + Inferring population histories for ancient genomes using genome-wide genealogies. + bioRxiv:2021.02.17.431573. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'MyersGroup' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-20211123_add-cmake-install-targets.patch'] +checksums = [ + 'cc19a50036f78ede9f4d52cc0cbb81d90d1bdb51f8b70a1f001a4f32dd26dbd0', # 78964f4.tar.gz + # Relate-20211123_add-cmake-install-targets.patch + 'd4565aeef0036013b82b37e00909965a6447ab14b154caa3e304307d6f7818e4', +] + +builddependencies = [('CMake', '3.18.4')] + +dependencies = [ + ('zlib', '1.2.11'), + ('R', '4.0.3'), # required for some analysis scripts +] + +runtest = 'test' + +# script directories to add to path: +local_scripts = ['DetectSelection', 'EstimatePopulationSize', 'PrepareInputFiles', 'RelateParallel', + 'SampleBranchLengths', 'TreeView'] +# un/comment as appropriate: +# local_scripts += ['RelateLSF'] +# local_scripts += ['EstimatePopulationSizeSGE', 'RelateSGE'] +# local_scripts += ['RelateSlurm'] + +local_bins = ['bin/%s%s' % (name, x) for x in ['', 'CoalescentRate', 'Extract', 'FileFormats', + 'MutationRate', 'Selection', 'TreeView']] +local_libs = ['lib/libtskitStatic.a'] + [ + 'lib/lib%s%s' % (x, y) for x in ['gzstream', 'kastore', 'relate'] for y in ['Shared.so', 'Static.a'] +] + +sanity_check_paths = { + 'files': local_bins + local_libs, + 'dirs': ['bin', 'lib', 'example'] + ['scripts/%s' % x for x in local_scripts], +} + +sanity_check_commands = [ + "%(name)s --help", + "cd %(builddir)s/relate-*/example && gunzip data/*.gz && Relate --mode All -m 1.25e-8 -N 30000 \ + --haps data/example.haps --sample data/example.sample --map data/genetic_map_*.txt \ + --annot data/example.annot --seed 1 -o example", +] + +modextrapaths = {'PATH': ['scripts/%s' % x for x in local_scripts]} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Relate/Relate-20211123_add-cmake-install-targets.patch b/easybuild/easyconfigs/r/Relate/Relate-20211123_add-cmake-install-targets.patch new file mode 100644 index 00000000000..650f3ce04b1 --- /dev/null +++ b/easybuild/easyconfigs/r/Relate/Relate-20211123_add-cmake-install-targets.patch @@ -0,0 +1,35 @@ +Author: Jasper Grimm +--- +Add CMake install targets (for bin, lib, scripts and example) +Install shared and static libraries to lib instead of bin + +diff -Nru relate-78964f420ce99e28887d7756d0c34bcebfa07130.orig/CMakeLists.txt relate-78964f420ce99e28887d7756d0c34bcebfa07130/CMakeLists.txt +--- relate-78964f420ce99e28887d7756d0c34bcebfa07130.orig/CMakeLists.txt 2021-11-25 16:59:55.000000000 +0000 ++++ relate-78964f420ce99e28887d7756d0c34bcebfa07130/CMakeLists.txt 2021-11-26 10:46:14.000000000 +0000 +@@ -17,8 +17,9 @@ + + # Set dir + set(CMAKE_BINARY_DIR ${CMAKE_SOURCE_DIR}/bin) ++set(CMAKE_LIBRARY_DIR ${CMAKE_SOURCE_DIR}/lib) + set(EXECUTABLE_OUTPUT_PATH ${CMAKE_BINARY_DIR}) +-set(LIBRARY_OUTPUT_PATH ${CMAKE_BINARY_DIR}) ++set(LIBRARY_OUTPUT_PATH ${CMAKE_LIBRARY_DIR}) + set(PROJECT_SOURCE_DIR ${CMAKE_SOURCE_DIR}/include/src) + set(PIPELINE_DIR ${CMAKE_SOURCE_DIR}/include/pipeline) + set(EVALUATE_DIR ${CMAKE_SOURCE_DIR}/include/evaluate) +@@ -53,3 +54,15 @@ + enable_testing() + add_test(UnitTest ${CMAKE_BINARY_DIR}/Tests) + add_custom_command(TARGET Tests COMMENT "Run tests" POST_BUILD WORKING_DIRECTORY ${CMAKE_BINARY_DIR} COMMAND Tests) ++ ++ ++INSTALL ( TARGETS Relate RelateCoalescentRate RelateExtract RelateFileFormats RelateMutationRate RelateSelection RelateTreeView RUNTIME DESTINATION bin ) ++ ++INSTALL ( TARGETS relateStatic relateShared gzstreamShared gzstreamStatic kastoreShared kastoreStatic tskitStatic ++ LIBRARY DESTINATION lib ++ ARCHIVE DESTINATION lib ++) ++ ++INSTALL ( DIRECTORY scripts DESTINATION . USE_SOURCE_PERMISSIONS ) ++ ++INSTALL ( DIRECTORY example DESTINATION . USE_SOURCE_PERMISSIONS ) From 929f842ffc5e84a2a9100d815562ee1baf9f0a0e Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 26 Nov 2021 15:12:49 +0000 Subject: [PATCH 2106/9987] URL for king-2.2.4 fixed, new king-2.2.7 --- easybuild/easyconfigs/k/king/king-2.2.4.eb | 4 ++-- easybuild/easyconfigs/k/king/king-2.2.7.eb | 28 ++++++++++++++++++++++ 2 files changed, 30 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/k/king/king-2.2.7.eb diff --git a/easybuild/easyconfigs/k/king/king-2.2.4.eb b/easybuild/easyconfigs/k/king/king-2.2.4.eb index 4f9dd94cc27..d3c17829c0e 100644 --- a/easybuild/easyconfigs/k/king/king-2.2.4.eb +++ b/easybuild/easyconfigs/k/king/king-2.2.4.eb @@ -7,7 +7,7 @@ easyblock = 'BinariesTarball' name = 'king' version = '2.2.4' -homepage = 'https://people.virginia.edu/~wc9c/KING/' +homepage = 'https://kingrelatedness.com/' description = """KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project. Applications of KING include family relationship @@ -16,7 +16,7 @@ substructure identification, forensics, gene mapping, etc.""" toolchain = SYSTEM -source_urls = ['https://people.virginia.edu/~wc9c/KING/executables'] +source_urls = ['https://kingrelatedness.com/executables/'] sources = ['Linux-%%(name)s%s.tar.gz' % version.replace('.', '')] checksums = ['405e603875d04e19559598f2b27e5e8113d5b4424388a92fa0b40251897c592b'] diff --git a/easybuild/easyconfigs/k/king/king-2.2.7.eb b/easybuild/easyconfigs/k/king/king-2.2.7.eb new file mode 100644 index 00000000000..d6eb005690c --- /dev/null +++ b/easybuild/easyconfigs/k/king/king-2.2.7.eb @@ -0,0 +1,28 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'BinariesTarball' + +name = 'king' +version = '2.2.7' + +homepage = 'https://kingrelatedness.com/' +description = """KING is a toolset that makes use of high-throughput +SNP data typically seen in a genome-wide association study (GWAS) or +a sequencing project. Applications of KING include family relationship +inference and pedigree error checking, quality control, population +substructure identification, forensics, gene mapping, etc.""" + +toolchain = SYSTEM + +source_urls = ['https://kingrelatedness.com/executables/'] +sources = ['Linux-%%(name)s%s.tar.gz' % version.replace('.', '')] +checksums = ['8fcc5c7cce1df80f80dc3ace4e64c9047a4156e361f787d368a89f7e654231da'] + +sanity_check_paths = { + 'files': ['bin/king'], + 'dirs': [], +} + +moduleclass = 'bio' From 0188ec7519d777f42a187cf29a7deca2be1f891f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 26 Nov 2021 16:17:14 +0100 Subject: [PATCH 2107/9987] Drop matlab dep, add patch --- ...yter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb} | 17 ++++++++---- ...b-proxy-0.3.4_eb-matlab-license-file.patch | 27 +++++++++++++++++++ 2 files changed, 39 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/j/jupyter-matlab-proxy/{jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb => jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb} (75%) create mode 100644 easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4_eb-matlab-license-file.patch diff --git a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb similarity index 75% rename from easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb rename to easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb index 7af08812cf3..40ed27508d5 100644 --- a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0-MATLAB-2021a.eb +++ b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb @@ -2,20 +2,20 @@ easyblock = "PythonBundle" name = 'jupyter-matlab-proxy' version = '0.3.4' -local_matlab_version = '2021a' -versionsuffix = '-MATLAB-%s' % local_matlab_version homepage = 'https://github.com/mathworks/jupyter-matlab-proxy' description = 'MATLAB Integration for Jupyter' toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +builddependencies = [ + ('nodejs', '14.17.2'), +] + dependencies = [ ('Python', '3.9.5'), ('JupyterLab', '3.0.16'), # Contains most of the jupyter dependencies we need. - ('nodejs', '14.17.2'), ('Xvfb', '1.20.11'), - ('MATLAB', local_matlab_version, '', True), ] use_pip = True @@ -44,10 +44,17 @@ exts_list = [ 'checksums': ['30d57976090980f4380cb0a80e8e829dfd74d0a19edb64329239def9feefcde4'], }), (name, version, { - 'checksums': ['05235c77aadf6ffb2b7193f6c6e4962eff68e4e5908370525363180d81bf9348'], + 'patches': ['jupyter-matlab-proxy-%(version)s_eb-matlab-license-file.patch'], + 'checksums': [ + '05235c77aadf6ffb2b7193f6c6e4962eff68e4e5908370525363180d81bf9348', # jupyter-matlab-proxy-0.3.4.tar.gz + # jupyter-matlab-proxy-0.3.4_eb-matlab-license-file.patch + '6d83f73019313394982b7f8eb1d28859442460668284e4d86e2c5d465cfb00ba', + ], }), ] +modloadmsg = 'jupyter-matlab-proxy requires MATLAB to be loaded separately (2020b or later)' + sanity_check_paths = { 'files': ['bin/matlab-jupyter-app'], 'dirs': ['lib64/python%(pyshortver)s/site-packages'] diff --git a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4_eb-matlab-license-file.patch b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4_eb-matlab-license-file.patch new file mode 100644 index 00000000000..7f7c8ffd3a0 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4_eb-matlab-license-file.patch @@ -0,0 +1,27 @@ +Use the license file from EB's MATLAB installation by default +Author: Mikael Öhman micketeer@gmail.com +--- jupyter_matlab_proxy/settings.py.orig 2021-11-26 14:55:13.268435797 +0100 ++++ jupyter_matlab_proxy/settings.py 2021-11-26 15:29:37.560690125 +0100 +@@ -102,6 +102,13 @@ + return settings + + else: ++ if mwi_env.get_env_name_network_license_manager() in os.environ: ++ license_file = os.environ.get(mwi_env.get_env_name_network_license_manager()) ++ elif 'EBROOTMATLAB' in os.environ: ++ license_file = os.environ.get('EBROOTMATLAB') + '/licenses/network.lic' ++ else: ++ license_file = None ++ + matlab_startup_file = str( + Path(__file__).resolve().parent / "matlab" / "startup.m" + ) +@@ -127,7 +134,7 @@ + "mwapikey": str(uuid.uuid4()), + "matlab_protocol": "https", + "nlm_conn_str": mwi_validators.validate_mlm_license_file( +- os.environ.get(mwi_env.get_env_name_network_license_manager()) ++ license_file + ), + "matlab_config_file": Path.home() / ".matlab" / "proxy_app_config.json", + "ws_env": ws_env, From e1f41f58c15841cc93102be0e280bf7f10e81b42 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Fri, 26 Nov 2021 16:26:09 +0100 Subject: [PATCH 2108/9987] adding easyconfigs: grace-5.1.25-foss-2021a.eb, motif-2.3.8-GCCcore-10.3.0.eb --- .../g/grace/grace-5.1.25-foss-2021a.eb | 29 +++++++++++++ .../m/motif/motif-2.3.8-GCCcore-10.3.0.eb | 41 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb b/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb new file mode 100644 index 00000000000..d560ba7e627 --- /dev/null +++ b/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'grace' +version = '5.1.25' + +homepage = 'http://freecode.com/projects/grace' +description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" + +source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('motif', '2.3.8'), + ('netCDF', '4.8.0'), +] + +runtest = 'tests' + +# we also need to run make links right before or after make install. +installopts = 'links' + +sanity_check_paths = { + 'files': ['bin/xmgrace'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..92e54b13bbe --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.8' + +homepage = 'https://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] + +builddependencies = [ + ('Autotools', '20210128'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('binutils', '2.36.1'), + ('util-linux', '2.36'), +] + +dependencies = [ + ('X11', '20210518'), + ('libpng', '1.6.37'), + ('freetype', '2.10.4'), + ('libjpeg-turbo', '2.0.6'), + ('bzip2', '1.0.8'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' From 0983bf9033730b1d437954b1c362b5db8f906784 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 26 Nov 2021 15:31:38 +0000 Subject: [PATCH 2109/9987] Use networkx 2.5.1 on this toolchain --- easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb index d5972679608..84949ba857b 100644 --- a/easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb +++ b/easybuild/easyconfigs/p/panaroo/panaroo-1.2.9-foss-2021a.eb @@ -16,7 +16,7 @@ dependencies = [ ('PRANK', '170427'), ('Biopython', '1.79'), ('SciPy-bundle', '2021.05'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ('edlib', '1.3.9'), ('tqdm', '4.61.2'), ('matplotlib', '3.4.2'), From 68aea7fb781976c1eff1c2af362d307bfff815d1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 26 Nov 2021 16:32:03 +0100 Subject: [PATCH 2110/9987] Add binutils builddep --- .../jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb index 40ed27508d5..cd2a2963360 100644 --- a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb @@ -9,6 +9,7 @@ description = 'MATLAB Integration for Jupyter' toolchain = {'name': 'GCCcore', 'version': '10.3.0'} builddependencies = [ + ('binutils', '2.36.1'), ('nodejs', '14.17.2'), ] From 5e3f78e4543ae77ebbc2fa51e3329a539aab4ace Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Fri, 26 Nov 2021 17:10:06 +0100 Subject: [PATCH 2111/9987] Added missing checksums --- easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb b/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb index d560ba7e627..72ac27c0b80 100644 --- a/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb +++ b/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb @@ -8,6 +8,7 @@ description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Mo source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] sources = [SOURCE_TAR_GZ] +checksums = ['751ab9917ed0f6232073c193aba74046037e185d73b77bab0f5af3e3ff1da2ac'] toolchain = {'name': 'foss', 'version': '2021a'} From bac9614feaa8bedfc5a85e34444d17d8dc915be7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Fri, 26 Nov 2021 17:14:59 +0100 Subject: [PATCH 2112/9987] adding easyconfigs: episcanpy-0.3.1-foss-2021a.eb, tbb-2020.3-GCCcore-10.3.0.eb --- .../e/episcanpy/episcanpy-0.3.1-foss-2021a.eb | 59 +++++++++++++++++++ .../t/tbb/tbb-2020.3-GCCcore-10.3.0.eb | 27 +++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb b/easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb new file mode 100644 index 00000000000..fb5300fc633 --- /dev/null +++ b/easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'episcanpy' +version = '0.3.1' + +homepage = 'https://github.com/colomemaria/episcanpy' +description = """EpiScanpy is a toolkit to analyse single-cell open chromatin +(scATAC-seq) and single-cell DNA methylation (for example scBS-seq) +data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq +analysis tool Scanpy (Genome Biology, 2018) [Wolf18].""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Seaborn', '0.11.2'), + ('scanpy', '1.8.1'), # includes anndata + ('SciPy-bundle', '2021.05'), + ('Pysam', '0.16.0.1'), + ('scikit-learn', '0.24.2'), + ('statsmodels', '0.12.2'), + ('numba', '0.53.1'), + ('python-igraph', '0.9.6'), + ('tbb', '2020.3'), +] + +exts_list = [ + ('pyliftover', '0.4', { + 'checksums': ['72bcfb7de907569b0eb75e86c817840365297d63ba43a961da394187e399da41'], + }), + ('bamnostic', '1.1.7', { + 'checksums': ['27e70c6f3d258a00d8d3e1a5ded403ea02152fcf42288788fb5fb3c66f53939b'], + }), + ('python-louvain', '0.15', { + 'modulename': 'community.community_louvain', + 'checksums': ['2a856edfbe29952a60a5538a84bb78cca18f6884a88b9325e85a11c8dd4917eb'], + }), + ('get_version', '3.2', { + 'use_pip': False, + 'checksums': ['b01a7d84d60a4839d035375151ae03b9ee902baa503effb0cf8ccd6d4d79aa1d'], + }), + ('legacy-api-wrap', '1.2', { + 'use_pip': False, + 'checksums': ['034a44612da7e9943d3964363a98937ab54d55e3301075374abe0d521eb8101b'], + }), + (name, version, { + 'preinstallopts': 'sed -i "s/tbb//" requirements.txt && ', + 'checksums': ['ee90ebec33d7c03bd11863de3d7fe60779e41e206952eca27ff95b4667cefdb2'], + }), +] + +sanity_check_commands = [ + "python -c 'import tbb'", +] +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e3bd3190a24 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2020.3-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +name = 'tbb' +version = '2020.3' + +homepage = 'https://github.com/oneapi-src/oneTBB' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ebc4f6aa47972daed1f7bf71d100ae5bf6931c2e3144cf299c8cc7d041dca2f3'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('SWIG', '4.0.2'), +] +dependencies = [ + ('Python', '3.9.5'), +] + +prebuildopts = "sed -i 's/install -f/--inplace/' python/Makefile && " + +with_python = True + +moduleclass = 'lib' From 3e776ac50b7e9e0c3fbb3b7f5fa1d6f41f476e5d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Fri, 26 Nov 2021 18:16:05 +0100 Subject: [PATCH 2113/9987] episcanpy: style --- easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb b/easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb index fb5300fc633..dfe4450403e 100644 --- a/easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb +++ b/easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb @@ -52,7 +52,6 @@ exts_list = [ sanity_check_commands = [ "python -c 'import tbb'", ] -download_dep_fail = True use_pip = True sanity_pip_check = True From fed639bcd224abcb92888244db9abfec650f53d8 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 26 Nov 2021 19:16:50 +0200 Subject: [PATCH 2114/9987] adding easyconfigs: ARAGORN-1.2.41-foss-2021b.eb, gmpy2-2.1.0rc1-GCC-11.2.0.eb, Infernal-1.1.4-foss-2021b.eb, MAFFT-7.490-GCC-11.2.0-with-extensions.eb, MMseqs2-13-45111-gompi-2021b.eb, networkx-2.6.3-foss-2021b.eb, plotly.py-5.4.0-GCCcore-11.2.0.eb, PPanGGOLiN-1.1.136-foss-2021b.eb, prodigal-2.6.3-GCCcore-11.2.0.eb, genoPlotR-0.8.11-foss-2020b.eb, rpy2-3.4.5-foss-2021b.eb and patches: PPanGGOLiN-1.1.136_new_compiler_compatibility.patch, rpy2-3.4.5_disable_gui_tests.patch --- .../a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb | 44 +++++++ .../genoPlotR/genoPlotR-0.8.11-foss-2020b.eb | 28 +++++ .../g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb | 25 ++++ .../i/Infernal/Infernal-1.1.4-foss-2021b.eb | 39 ++++++ .../MAFFT-7.490-GCC-11.2.0-with-extensions.eb | 47 ++++++++ .../m/MMseqs2/MMseqs2-13-45111-gompi-2021b.eb | 27 +++++ .../n/networkx/networkx-2.6.3-foss-2021b.eb | 24 ++++ .../PPanGGOLiN-1.1.136-foss-2021b.eb | 67 +++++++++++ ...N-1.1.136_new_compiler_compatibility.patch | 15 +++ .../plotly.py-5.4.0-GCCcore-11.2.0.eb | 30 +++++ .../prodigal/prodigal-2.6.3-GCCcore-11.2.0.eb | 46 +++++++ .../r/rpy2/rpy2-3.4.5-foss-2021b.eb | 60 ++++++++++ .../r/rpy2/rpy2-3.4.5_disable_gui_tests.patch | 113 ++++++++++++++++++ 13 files changed, 565 insertions(+) create mode 100644 easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/genoPlotR/genoPlotR-0.8.11-foss-2020b.eb create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.6.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136_new_compiler_compatibility.patch create mode 100644 easybuild/easyconfigs/p/plotly.py/plotly.py-5.4.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb create mode 100644 easybuild/easyconfigs/r/rpy2/rpy2-3.4.5_disable_gui_tests.patch diff --git a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb new file mode 100644 index 00000000000..4edce9420f8 --- /dev/null +++ b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated: Denis Kristak + +easyblock = 'CmdCp' + +name = 'ARAGORN' +version = '1.2.41' + +homepage = 'http://mbio-serv2.mbioekol.lu.se/ARAGORN/' +description = "http://www.ansikte.se/ARAGORN/" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['http://www.ansikte.se/ARAGORN/Downloads/'] +sources = [ + {'filename': '%(namelower)s%(version)s.c', 'extract_cmd': 'cp %s aragorn.c'}, + {'filename': 'aragorn.1', 'extract_cmd': 'cp %s aragorn.1'} # man page +] +checksums = [ + '92a31cc5c0b0ad16d4d7b01991989b775f07d2815df135fe6e3eab88f5e97f4a', # aragorn1.2.41.c + '6e30f6d9da644197064744f033176969e77855964ed8d50ea00c38a3aea2c92e', # aragorn.1 +] + +cmds_map = [ + (".*.c", "$CC $CFLAGS -o aragorn aragorn.c"), + (".*.1", "mkdir -p share/man/man1 && cp aragorn.1 share/man/man1"), # mapping command to manpage srcfile +] + +files_to_copy = [ + (['aragorn'], 'bin'), + 'share', +] + +sanity_check_paths = { + 'files': ['bin/aragorn'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ['aragorn --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/genoPlotR/genoPlotR-0.8.11-foss-2020b.eb b/easybuild/easyconfigs/g/genoPlotR/genoPlotR-0.8.11-foss-2020b.eb new file mode 100644 index 00000000000..56d21bac11a --- /dev/null +++ b/easybuild/easyconfigs/g/genoPlotR/genoPlotR-0.8.11-foss-2020b.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'RPackage' + +name = 'genoPlotR' +version = '0.8.11' + +homepage = 'https://cran.r-project.org/web/packages/genoPlotR/index.html' +description = """Draws gene or genome maps and comparisons between these, in a publication-grade manner. +Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://cran.r-project.org/src/contrib/'] +sources = ['%s_%s.tar.gz' % (name, version)] +checksums = ['f127f7fe8b19c899ecfdf98bf69d2e18926afb593a72fc40097acca66d401607'] + +dependencies = [ + ('R', '4.0.3'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['genoPlotR'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb new file mode 100644 index 00000000000..34f391736cd --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.0rc1' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['86cb6d8e5837560c32c706d48d6ed25676be6b3c79e6aa5d245965b9e99231b9'] + +dependencies = [ + ('Python', '3.9.6'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021b.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021b.eb new file mode 100644 index 00000000000..b4cf81be85e --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# Updated:: Denis Kristak (INUITS) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.4" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb new file mode 100644 index 00000000000..d281f129a40 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez (Swiss Institute of Bioinformatics, Biozentrum - University of Basel) +# 7.305 modified by: +# Adam Huffman (The Francis Crick Institute) +# 7.453 switch to Bundle by: +# Alex Domingo (Vrije Universiteit Brussel) + +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.490' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], + 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft', 'libexec/mafft/mxscarnamod'], # mxscarnamod installed by MAFFT Extensions + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021b.eb new file mode 100644 index 00000000000..0e81aa222eb --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +version = '13-45111' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['6444bb682ebf5ced54b2eda7a301fa3e933c2a28b7661f96ef5bdab1d53695a2'] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [('bzip2', '1.0.8')] + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.6.3-foss-2021b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.6.3-foss-2021b.eb new file mode 100644 index 00000000000..3decc38097e --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.6.3-foss-2021b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.6.3' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c0946ed31d71f1b732b5aaa6da5a0388a345019af232ce2f49c766e2d6795c51'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb b/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb new file mode 100644 index 00000000000..6ae3a90819b --- /dev/null +++ b/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb @@ -0,0 +1,67 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'PPanGGOLiN' +version = '1.1.136' + +homepage = 'https://github.com/labgem/PPanGGOLiN' +description = """ +PPanGGOLiN is a software suite used to create and manipulate prokaryotic +pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed +to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using +a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality +data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage +of large scale environmental studies and letting users study the pangenome of uncultivable species. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('tqdm', '4.62.3'), + ('PyTables', '3.6.1'), + ('prodigal', '2.6.3'), + ('ARAGORN', '1.2.41'), + ('Infernal', '1.1.4'), + ('MMseqs2', '13-45111'), + ('networkx', '2.6.3'), + ('SciPy-bundle', '2021.10'), + ('plotly.py', '5.4.0'), + ('gmpy2', '2.1.0rc1'), + ('MAFFT', '7.490', '-with-extensions'), + ('rpy2', '3.4.5'), +] + +local_configopts = '-DBLAS_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT +local_configopts += '-DLAPACK_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +exts_list = [ + ('colorlover', '0.3.0', { + 'checksums': ['b8fb7246ab46e1f5e6715649453c1762e245a515de5ff2d2b4aab7a6e67fa4e2'], + }), + (name, version, { + 'configopts': "-DBLAS_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.so -DLAPACK_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.so ", + 'patches': ['PPanGGOLiN-%(version)s_new_compiler_compatibility.patch'], + 'source_urls': ['https://github.com/labgem/%(name)s/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': [ + '41f814f0b9331a8f0e04f09c698cef6200429990ce726339b5bb320bb7943a70', # 1.1.136.tar.gz + # PPanGGOLiN-1.1.136_new_compiler_compatibility.patch + 'ae4dadf2f7469e4c3d56b10236aa7812bfe6f5ed231676364f7c3f0d42e8facf', + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/ppanggolin'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['ppanggolin --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136_new_compiler_compatibility.patch b/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136_new_compiler_compatibility.patch new file mode 100644 index 00000000000..0c684dbbfd1 --- /dev/null +++ b/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136_new_compiler_compatibility.patch @@ -0,0 +1,15 @@ +adding -fcommon flag since it was removed from defaults in newer compilers +author: Denis Kristak (INUITS) +diff -ruN PPanGGOLiN-1.1.136_orig/setup.py PPanGGOLiN-1.1.136/setup.py +--- PPanGGOLiN-1.1.136_orig/setup.py 2021-11-23 10:32:07.957348000 +0100 ++++ PPanGGOLiN-1.1.136/setup.py 2021-11-23 10:43:58.316011000 +0100 +@@ -28,7 +28,8 @@ + "Programming Language :: Python :: 3", + "Topic :: Scientific/Engineering :: Bio-Informatics"], + entry_points={"console_scripts":["ppanggolin = ppanggolin.main:main"]}, +- ext_modules = [Extension(name = "nem_stats",sources =[NEM_DIR_PATH+'nem_stats.pyx', ++ extra_compile_args=['-fcommon'], ++ ext_modules = [Extension(name = "nem_stats", extra_compile_args=['-fcommon'], sources =[NEM_DIR_PATH+'nem_stats.pyx', + NEM_DIR_PATH+'nem_exe.c', + NEM_DIR_PATH+'nem_alg.c', + NEM_DIR_PATH+'nem_nei.c', diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.4.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..536b80f0c65 --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.4.0-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '5.4.0' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [('Python', '3.9.6')] + +use_pip = True + +exts_list = [ + ('tenacity', '8.0.1', { + 'checksums': ['43242a20e3e73291a28bcbcacfd6e000b02d3857a9a9fff56b297a27afdc932f'], + }), + ('plotly', version, { + 'checksums': ['735d50738c760ecbf3a38e2336b8c1b119bff2d857096e4f68af31089b798161'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2ce7b22891a --- /dev/null +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-11.2.0.eb @@ -0,0 +1,46 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Updated: Pavel Grochal (INUITS) +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'prodigal' +version = '2.6.3' + +homepage = 'https://github.com/hyattpd/Prodigal/' + +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f'] + +builddependencies = [('binutils', '2.37')] + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +sanity_check_commands = ["prodigal -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb b/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb new file mode 100644 index 00000000000..7db264da0aa --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb @@ -0,0 +1,60 @@ +# Author: Pavel Grochal (INUITS) +# Updated: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'rpy2' +version = '3.4.5' + +homepage = 'https://rpy2.bitbucket.io/' +description = """rpy2 is an interface to R running embedded in a Python process.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('R', '4.1.2'), + ('IPython', '7.26.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('simplegeneric', '0.8.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('tzlocal', '2.1', { + 'checksums': ['643c97c5294aedc737780a49d9df30889321cbe1204eac2c2ec6134035a92e44'], + }), + ('cffi', '1.15.0', { + 'checksums': ['920f0d66a896c2d99f0adbb391f990a84091179542c205fa53ce5787aff87954'], + }), + ('tzdata', '2021.5', { + 'checksums': ['68dbe41afd01b867894bbdfd54fa03f468cfa4f0086bfb4adcd8de8f24f3ee21'], + }), + ('backports-zoneinfo', '0.2.1', { + 'modulename': 'backports.zoneinfo', + 'source_tmpl': 'backports.zoneinfo-%(version)s.tar.gz', + 'checksums': ['fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2'], + }), + ('pytz-deprecation-shim', '0.1.0.post0', { + 'source_tmpl': 'pytz_deprecation_shim-%(version)s.tar.gz', + 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], + }), + (name, version, { + 'patches': ['rpy2-%(version)s_disable_gui_tests.patch'], + 'checksums': [ + '5d31a5ea43f5a59f6dec30faca87edb01fc9b8affa0beae96a99be923bd7dab3', # rpy2-3.4.5.tar.gz + '3caef18175eb423cf43e2ad7c513e29358ca8ace22cbe4241e16c38408695fa8', # rpy2-3.4.5_disable_gui_tests.patch + ], + }), +] + +sanity_check_commands = [ + "pytest --pyargs rpy2 " +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5_disable_gui_tests.patch b/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5_disable_gui_tests.patch new file mode 100644 index 00000000000..593f7a1ec05 --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5_disable_gui_tests.patch @@ -0,0 +1,113 @@ +diff -ruN rpy2-3.4.5_orig/rpy2/tests/ipython/test_rmagic.py rpy2-3.4.5/rpy2/tests/ipython/test_rmagic.py +--- rpy2-3.4.5_orig/rpy2/tests/ipython/test_rmagic.py 2021-11-25 12:37:30.723114034 +0000 ++++ rpy2-3.4.5/rpy2/tests/ipython/test_rmagic.py 2021-11-26 16:45:54.886986180 +0000 +@@ -96,7 +96,7 @@ + np.testing.assert_almost_equal(np.asarray(r('Y')), + ipython_with_magic.user_ns['Y']) + +- ++@pytest.mark.skip(reason="Cannot test with GUI") + @pytest.mark.skipif(IPython is None, + reason='The optional package IPython cannot be imported.') + @pytest.mark.skipif(not has_numpy, reason='numpy not installed') +@@ -119,8 +119,7 @@ + np.testing.assert_equal(result, 12345) + + +-@pytest.mark.skipif(IPython is None, +- reason='The optional package IPython cannot be imported.') ++@pytest.mark.skip(reason="Cannot test with GUI") + def test_run_cell_with_error(ipython_with_magic, clean_globalenv): + """Run an R block with an error.""" + +@@ -166,6 +165,7 @@ + @pytest.mark.skipif(IPython is None, + reason='The optional package IPython cannot be imported.') + @pytest.mark.skipif(not has_numpy, reason='numpy not installed') ++@pytest.mark.skip(reason="Cannot test with GUI") + def test_Rconverter(ipython_with_magic, clean_globalenv): + # If we get to dropping numpy requirement, we might use something + # like the following: +@@ -221,6 +221,7 @@ + @pytest.mark.skipif(IPython is None, + reason='The optional package IPython cannot be imported.') + @pytest.mark.skipif(not has_numpy, reason='numpy not installed') ++@pytest.mark.skip(reason="Cannot test with GUI") + def test_cell_magic(ipython_with_magic, clean_globalenv): + ipython_with_magic.push({'x': np.arange(5), 'y': np.array([3,5,4,6,7])}) + # For now, print statements are commented out because they print +@@ -239,8 +240,7 @@ + np.testing.assert_almost_equal(ipython_with_magic.user_ns['r'], np.array([-0.2, 0.9, -1. , 0.1, 0.2])) + + +-@pytest.mark.skipif(IPython is None, +- reason='The optional package IPython cannot be imported.') ++@pytest.mark.skip(reason="Cannot test with GUI") + def test_cell_magic_localconverter(ipython_with_magic, clean_globalenv): + x = (1,2,3) + from rpy2.rinterface import IntSexpVector +@@ -283,8 +283,7 @@ + assert isinstance(globalenv['x'], vectors.IntVector) + + +-@pytest.mark.skipif(IPython is None, +- reason='The optional package IPython cannot be imported.') ++@pytest.mark.skip(reason="Cannot test with GUI") + def test_rmagic_localscope(ipython_with_magic, clean_globalenv): + ipython_with_magic.push({'x':0}) + ipython_with_magic.run_line_magic('R', '-i x -o result result <-x+1') +@@ -312,6 +311,7 @@ + reason='The optional package IPython cannot be imported.') + # TODO: There is no test here... + @pytest.mark.skipif(not has_numpy, reason='numpy not installed') ++@pytest.mark.skip(reason="Cannot test with GUI") + def test_png_plotting_args(ipython_with_magic, clean_globalenv): + '''Exercise the PNG plotting machinery''' + +@@ -331,8 +331,7 @@ + ipython_with_magic.run_cell_magic('R', line, cell) + + +-@pytest.mark.skipif(IPython is None, +- reason='The optional package IPython cannot be imported.') ++@pytest.mark.skip(reason="Cannot test with GUI") + def test_display_args(ipython_with_magic, clean_globalenv): + + cell = ''' +@@ -362,6 +361,7 @@ + @pytest.mark.skipif(not has_numpy, reason='numpy not installed') + @pytest.mark.skipif(not rpacks.isinstalled('Cairo'), + reason='R package "Cairo" not installed') ++@pytest.mark.skip(reason="Cannot test with GUI") + def test_svg_plotting_args(ipython_with_magic, clean_globalenv): + '''Exercise the plotting machinery + +diff -ruN rpy2-3.4.5_orig/rpy2/tests/robjects/lib/test_grdevices.py rpy2-3.4.5/rpy2/tests/robjects/lib/test_grdevices.py +--- rpy2-3.4.5_orig/rpy2/tests/robjects/lib/test_grdevices.py 2021-11-25 12:37:30.724114020 +0000 ++++ rpy2-3.4.5/rpy2/tests/robjects/lib/test_grdevices.py 2021-11-25 12:42:11.886984001 +0000 +@@ -20,14 +20,13 @@ + os.unlink(fn) + + +-@pytest.mark.xfail(os.name == 'nt', +- reason='Windows produces non-empty file with no plot') ++@pytest.mark.skip(reason="Cannot test with GUI") + def test_rendertobytes_noplot(): + with grdevices.render_to_bytesio(grdevices.png) as b: + pass + assert len(b.getvalue()) == 0 + +- ++@pytest.mark.skip(reason="Cannot test with GUI") + def test_rendertofile(): + fn = tempfile.mktemp(suffix=".png") + with set_filenames_to_delete() as todelete: +@@ -38,7 +37,7 @@ + r(''' plot(0) ''') + assert os.path.exists(fn) + +- ++@pytest.mark.skip(reason="Cannot test with GUI") + def test_rendertobytes_plot(): + with grdevices.render_to_bytesio(grdevices.png) as b: + r(''' plot(0) ''') From c73c51fcfc22d3cfc5802ea42b4b822c5ba97fc0 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 26 Nov 2021 17:22:53 +0000 Subject: [PATCH 2115/9987] Delete genoPlotR-0.8.11-foss-2020b.eb deleting genoplotR since it's going to be included in R presumably --- .../genoPlotR/genoPlotR-0.8.11-foss-2020b.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/g/genoPlotR/genoPlotR-0.8.11-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/genoPlotR/genoPlotR-0.8.11-foss-2020b.eb b/easybuild/easyconfigs/g/genoPlotR/genoPlotR-0.8.11-foss-2020b.eb deleted file mode 100644 index 56d21bac11a..00000000000 --- a/easybuild/easyconfigs/g/genoPlotR/genoPlotR-0.8.11-foss-2020b.eb +++ /dev/null @@ -1,28 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'RPackage' - -name = 'genoPlotR' -version = '0.8.11' - -homepage = 'https://cran.r-project.org/web/packages/genoPlotR/index.html' -description = """Draws gene or genome maps and comparisons between these, in a publication-grade manner. -Starting from simple, common files, it will draw postscript or PDF files that can be sent as such to journals. -""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://cran.r-project.org/src/contrib/'] -sources = ['%s_%s.tar.gz' % (name, version)] -checksums = ['f127f7fe8b19c899ecfdf98bf69d2e18926afb593a72fc40097acca66d401607'] - -dependencies = [ - ('R', '4.0.3'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['genoPlotR'], -} - -moduleclass = 'vis' From 4b538da69076ae16a71a555ba35063ac7addac7a Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 26 Nov 2021 19:26:12 +0200 Subject: [PATCH 2116/9987] code style --- .../easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb b/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb index 6ae3a90819b..a4fd3d5f649 100644 --- a/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb @@ -45,7 +45,7 @@ exts_list = [ 'checksums': ['b8fb7246ab46e1f5e6715649453c1762e245a515de5ff2d2b4aab7a6e67fa4e2'], }), (name, version, { - 'configopts': "-DBLAS_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.so -DLAPACK_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.so ", + 'configopts': local_configopts, 'patches': ['PPanGGOLiN-%(version)s_new_compiler_compatibility.patch'], 'source_urls': ['https://github.com/labgem/%(name)s/archive/refs/tags/'], 'sources': ['%(version)s.tar.gz'], From 0fa2388ff66952937fb646656f9e5134141d04e8 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 26 Nov 2021 19:34:08 +0200 Subject: [PATCH 2117/9987] adding easyconfigs: Blosc-1.21.1-GCCcore-11.2.0.eb, PyTables-3.6.1-foss-2021b.eb, tqdm-4.62.3-GCCcore-11.2.0.eb --- .../b/Blosc/Blosc-1.21.1-GCCcore-11.2.0.eb | 28 +++++++++++ .../p/PyTables/PyTables-3.6.1-foss-2021b.eb | 48 +++++++++++++++++++ .../t/tqdm/tqdm-4.62.3-GCCcore-11.2.0.eb | 22 +++++++++ 3 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.21.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/t/tqdm/tqdm-4.62.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..35ae6fea852 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.1-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.21.1' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f387149eab24efa01c308e4cba0f59f64ccae57292ec9c794002232f7903b55b'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021b.eb new file mode 100644 index 00000000000..59c01eab37c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'PyTables' +version = '3.6.1' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/PyTables/PyTables/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-fix-libs.patch'] +checksums = [ + '4cea86bab5bcb5423a07c7951b8c65e24b674e0dcec0e448d434829eff5f18d0', # v3.6.1.tar.gz + '8df2a6379a9e4a941cb939ed1257a7d6105792d9c5e9dd0abd4bba3ece767c3a', # PyTables-3.6.1-fix-libs.patch +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # provides numexpr + ('HDF5', '1.12.1'), + ('LZO', '2.10'), + ('Blosc', '1.21.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.62.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.62.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..3ca62e8d444 --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.62.3-GCCcore-11.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.62.3' + +homepage = "https://github.com/tqdm/tqdm" +description = """A fast, extensible progress bar for Python and CLI""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d359de7217506c9851b7869f3708d8ee53ed70a1b8edbba4dbcb47442592920d'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' From 88cc2122d5ccccb138749eb567c1f4cc6055b573 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 26 Nov 2021 20:12:57 +0200 Subject: [PATCH 2118/9987] checksums for MAFFT --- .../m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb index d281f129a40..1c6a5f97f6d 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb @@ -29,9 +29,11 @@ default_component_specs = { components = [ (name, version, { 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + 'checksums': ['d6eef33d8b9e282e20f9b25b6b6fb2757b9b6900e397ca621d56da86d9976541'], }), ('%s Extensions' % name, version, { 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + 'checksums': ['d6eef33d8b9e282e20f9b25b6b6fb2757b9b6900e397ca621d56da86d9976541'], }), ] From ea81e008c3cffd721ea820980b0a9df90ae6a039 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Fri, 26 Nov 2021 20:04:01 +0100 Subject: [PATCH 2119/9987] adding easyconfigs: TOBIAS-0.12.12-foss-2021b.eb, boto3-1.20.13-foss-2021b.eb, BEDTools-2.30.0-GCC-11.2.0.eb, pybedtools-0.8.2-GCC-11.2.0.eb, pyBigWig-0.3.18-foss-2021b.eb, adjustText-0.7.3-foss-2021b.eb, XlsxWriter-3.0.2-GCCcore-11.2.0.eb --- .../adjustText/adjustText-0.7.3-foss-2021b.eb | 25 ++++++ .../b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb | 43 +++++++++++ .../b/boto3/boto3-1.20.13-foss-2021b.eb | 37 +++++++++ .../p/pyBigWig/pyBigWig-0.3.18-foss-2021b.eb | 31 ++++++++ .../pybedtools/pybedtools-0.8.2-GCC-11.2.0.eb | 25 ++++++ .../t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb | 76 +++++++++++++++++++ .../XlsxWriter-3.0.2-GCCcore-11.2.0.eb | 34 +++++++++ 7 files changed, 271 insertions(+) create mode 100644 easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.20.13-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb create mode 100644 easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.0.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2021b.eb b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2021b.eb new file mode 100644 index 00000000000..ec0fd0f2900 --- /dev/null +++ b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2021b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'adjustText' +version = '0.7.3' + +homepage = 'https://github.com/Phlya/adjustText' +description = "A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps." + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'] + +dependencies = [ + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'adjustText'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..f89f04cf919 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb @@ -0,0 +1,43 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.30.0' + +homepage = "https://bedtools.readthedocs.io/" +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8'] + +builddependencies = [('Python', '3.9.6')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.20.13-foss-2021b.eb b/easybuild/easyconfigs/b/boto3/boto3-1.20.13-foss-2021b.eb new file mode 100644 index 00000000000..bc32295f023 --- /dev/null +++ b/easybuild/easyconfigs/b/boto3/boto3-1.20.13-foss-2021b.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'boto3' +version = '1.20.13' + +homepage = 'https://github.com/loosolab/TOBIAS' +description = """TOBIAS is a collection of command-line bioinformatics tools for +performing footprinting analysis on ATAC-seq data, and includes: Correction of +Tn5 insertion bias; Calculation of footprint scores within regulatory regions; +Estimation of bound/unbound transcription factor binding sites; and +Visualization of footprints within and across different conditions""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), +] + +exts_list = [ + ('botocore', '1.23.13', { + 'checksums': ['35792b2196049ef900f538cae51fb8359c940156eef187962aa9e3bd2c0b8e8c'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + ('s3transfer', '0.5.0', { + 'checksums': ['50ed823e1dc5868ad40c8dc92072f757aa0e653a192845c94a3b676f4a62da4c'], + }), + (name, version, { + 'checksums': ['bbf53a077d6a0575ddec8026f0475ca6ee6f41b227914bf315bf3e049a3d653a'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2021b.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2021b.eb new file mode 100644 index 00000000000..9a870e5cd21 --- /dev/null +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2021b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pyBigWig' +version = '0.3.18' + +github_account = 'deeptools' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """A python extension, written in C, for quick access to bigBed + files and access to and creation of bigWig files.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['552564d8ce8720a8ae70ed5e5534617fb0cab306b666468d1c61b6d389b8a10c'] + +dependencies = [ + ('Python', '3.9.6'), + ('cURL', '7.78.0'), + ('NSS', '3.69'), # provides libfreebl3 + ('SciPy-bundle', '2021.10'), # optional, for numpy support +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..cb10d93a635 --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pybedtools' +version = '0.8.2' + +homepage = 'https://daler.github.io/pybedtools' +description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a184a36099458627e7ef52ea88218f7c00dc9c505b4256ece9ede58b1efa8771'] + +dependencies = [ + ('Python', '3.9.6'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.17.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb new file mode 100644 index 00000000000..17e38754291 --- /dev/null +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'TOBIAS' +version = '0.12.12' + +homepage = 'https://github.com/loosolab/TOBIAS' +description = """TOBIAS is a collection of command-line bioinformatics tools for +performing footprinting analysis on ATAC-seq data, and includes: Correction of +Tn5 insertion bias; Calculation of footprint scores within regulatory regions; +Estimation of bound/unbound transcription factor binding sites; and +Visualization of footprints within and across different conditions""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Pysam', '0.17.0'), + ('scikit-learn', '1.0.1'), + ('Seaborn', '0.11.2'), + ('PyYAML', '5.4.1'), + ('boto3', '1.20.13'), + ('pybedtools', '0.8.2'), + ('pyBigWig', '0.3.18'), + ('XlsxWriter', '3.0.2'), + ('adjustText', '0.7.3'), + ('Biopython', '1.79'), + ('ImageMagick', '7.1.0-4'), +] + +exts_list = [ + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('configs', '3.0.3', { + 'source_tmpl': '%(namelower)s-%(version)s.zip', + 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], + }), + ('kneed', '0.7.0', { + 'checksums': ['340d67fa183a72b0afae19846dd246a6fb7204e8d54243d8b8d3d9932f887c6e'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + ('svist4get', '1.2.24', { + 'checksums': ['c4b2e561dab32019cc1505e017a12a4a77aa8aeba2720d3d1c6e69cf834cc46f'], + }), + ('PyPDF2', '1.26.0', { + 'modulename': 'PyPDF2', + 'checksums': ['e28f902f2f0a1603ea95ebe21dff311ef09be3d0f0ef29a3e44a932729564385'], + }), + ('MOODS-python', '1.9.4.1', { + 'modulename': 'MOODS', + 'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'], + }), + ('reportlab', '3.6.2', { + 'checksums': ['f0c4b47b012d893b0b9f5703cf6f01b5593714a3fc1e7dc73efbbfe26bb7e16a'], + }), + ('Wand', '0.6.7', { + 'checksums': ['ebc01bccc25dba68414ab55b482341f9ad2b197d7f49d5e724f339bbf63fb6db'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['ca599c8af7cee9a9143686ba650e8dee138283daab90c4da346d5c880bb86bf4'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["TOBIAS ATACorrect | grep 'TOBIAS ~ ATACorrect'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.0.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..79f9d59c390 --- /dev/null +++ b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.0.2-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'XlsxWriter' +version = '3.0.2' + +homepage = 'https://xlsxwriter.readthedocs.io/' +description = "A Python module for creating Excel XLSX files" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['53005f03e8eb58f061ebf41d5767c7495ee0772c2396fe26b7e0ca22fa9c2570'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/vba_extract.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['vba_extract.py --help'] + +sanity_pip_check = True + +moduleclass = 'tools' From ba14b0c0dd230165d3fcadc7ec6cb73da935e5e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Nov 2021 21:05:33 +0100 Subject: [PATCH 2120/9987] rename episcanpy to epiScanpy, clarify why tbb is removed from requirements.txt, don't run tbb sanity check in epiScanpy easyconfig --- .../epiScanpy-0.3.1-foss-2021a.eb} | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/e/{episcanpy/episcanpy-0.3.1-foss-2021a.eb => epiScanpy/epiScanpy-0.3.1-foss-2021a.eb} (80%) diff --git a/easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.3.1-foss-2021a.eb similarity index 80% rename from easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb rename to easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.3.1-foss-2021a.eb index dfe4450403e..dc68a5e1ddc 100644 --- a/easybuild/easyconfigs/e/episcanpy/episcanpy-0.3.1-foss-2021a.eb +++ b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.3.1-foss-2021a.eb @@ -1,6 +1,6 @@ easyblock = 'PythonBundle' -name = 'episcanpy' +name = 'epiScanpy' version = '0.3.1' homepage = 'https://github.com/colomemaria/episcanpy' @@ -43,15 +43,16 @@ exts_list = [ 'use_pip': False, 'checksums': ['034a44612da7e9943d3964363a98937ab54d55e3301075374abe0d521eb8101b'], }), - (name, version, { - 'preinstallopts': 'sed -i "s/tbb//" requirements.txt && ', + ('episcanpy', version, { 'checksums': ['ee90ebec33d7c03bd11863de3d7fe60779e41e206952eca27ff95b4667cefdb2'], + # strip out tbb as required dependency, to ensure that 'pip check' passes; + # note that the tbb Python bindings are actually provided by the tbb dependency, + # but pip doesn't know about them due to the way in which they were installed... + 'preinstallopts': "sed -i 's/tbb//' requirements.txt && ", + 'modulename': 'episcanpy.api', }), ] -sanity_check_commands = [ - "python -c 'import tbb'", -] use_pip = True sanity_pip_check = True From f005311dd2f79065573544cfe54fd0cebed5f69f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Fri, 26 Nov 2021 22:07:15 +0100 Subject: [PATCH 2121/9987] adjustText: style --- .../easyconfigs/a/adjustText/adjustText-0.7.3-foss-2021b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2021b.eb b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2021b.eb index ec0fd0f2900..be8e8b1bdcc 100644 --- a/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2021b.eb +++ b/easybuild/easyconfigs/a/adjustText/adjustText-0.7.3-foss-2021b.eb @@ -20,6 +20,8 @@ dependencies = [ download_dep_fail = True use_pip = True +sanity_pip_check = True + options = {'modulename': 'adjustText'} moduleclass = 'tools' From 640b2ded24583717c3d23f5158b1134bf9ca6b4b Mon Sep 17 00:00:00 2001 From: deniskristak Date: Sat, 27 Nov 2021 01:18:05 +0200 Subject: [PATCH 2122/9987] code style --- .../easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb b/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb index a4fd3d5f649..7a7b003c9ea 100644 --- a/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb @@ -38,7 +38,6 @@ local_configopts += '-DLAPACK_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % S use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('colorlover', '0.3.0', { From 7ed9232f96ef635179983b87258d2eb3522b060a Mon Sep 17 00:00:00 2001 From: deniskristak Date: Sat, 27 Nov 2021 01:36:41 +0200 Subject: [PATCH 2123/9987] code style --- easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021b.eb index 59c01eab37c..ab0f8bbe508 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.6.1-foss-2021b.eb @@ -28,7 +28,7 @@ dependencies = [ ('SciPy-bundle', '2021.10'), # provides numexpr ('HDF5', '1.12.1'), ('LZO', '2.10'), - ('Blosc', '1.21.0'), + ('Blosc', '1.21.1'), ] use_pip = True From e495b58ff4c4a95fdffd9bef635cf05205626ec2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Nov 2021 10:58:51 +0100 Subject: [PATCH 2124/9987] add patch for GCCcore 9.1-9.3 to fix compatibility with recent kernel headers --- .../GCC-9.x_fix-libsanitizer-cyclades.patch | 121 ++++++++++++++++++ .../easyconfigs/g/GCCcore/GCCcore-9.1.0.eb | 2 + .../easyconfigs/g/GCCcore/GCCcore-9.2.0.eb | 2 + .../easyconfigs/g/GCCcore/GCCcore-9.3.0.eb | 2 + 4 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCC-9.x_fix-libsanitizer-cyclades.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCC-9.x_fix-libsanitizer-cyclades.patch b/easybuild/easyconfigs/g/GCCcore/GCC-9.x_fix-libsanitizer-cyclades.patch new file mode 100644 index 00000000000..34119830b4f --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCC-9.x_fix-libsanitizer-cyclades.patch @@ -0,0 +1,121 @@ +From 2b40941d23b1570cdd90083b58fa0f66aa58c86e Mon Sep 17 00:00:00 2001 +From: Tamar Christina +Date: Fri, 21 May 2021 12:16:56 +0100 +Subject: [PATCH] libsanitizer: Remove cyclades from libsanitizer + +The Linux kernel has removed the interface to cyclades from +the latest kernel headers[1] due to them being orphaned for the +past 13 years. + +libsanitizer uses this header when compiling against glibc, but +glibcs itself doesn't seem to have any references to cyclades. + +Further more it seems that the driver is broken in the kernel and +the firmware doesn't seem to be available anymore. + +As such since this is breaking the build of libsanitizer (and so the +GCC bootstrap[2]) I propose to remove this. + +[1] https://lkml.org/lkml/2021/3/2/153 +[2] https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100379 + +libsanitizer/ChangeLog: + + PR sanitizer/100379 + * sanitizer_common/sanitizer_common_interceptors_ioctl.inc: Cherry-pick + llvm-project revision f7c5351552387bd43f6ca3631016d7f0dfe0f135. + * sanitizer_common/sanitizer_platform_limits_posix.cc: Likewise. + * sanitizer_common/sanitizer_platform_limits_posix.h: Likewise. +--- + .../sanitizer_common_interceptors_ioctl.inc | 9 --------- + .../sanitizer_platform_limits_posix.cc | 11 ----------- + .../sanitizer_platform_limits_posix.h | 10 ---------- + 3 files changed, 30 deletions(-) + +diff --git a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc +index 5408ea17c59..7a9cd3f5968 100644 +--- a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc ++++ b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc +@@ -365,15 +365,6 @@ static void ioctl_table_fill() { + + #if SANITIZER_LINUX && !SANITIZER_ANDROID + // _(SIOCDEVPLIP, WRITE, struct_ifreq_sz); // the same as EQL_ENSLAVE +- _(CYGETDEFTHRESH, WRITE, sizeof(int)); +- _(CYGETDEFTIMEOUT, WRITE, sizeof(int)); +- _(CYGETMON, WRITE, struct_cyclades_monitor_sz); +- _(CYGETTHRESH, WRITE, sizeof(int)); +- _(CYGETTIMEOUT, WRITE, sizeof(int)); +- _(CYSETDEFTHRESH, NONE, 0); +- _(CYSETDEFTIMEOUT, NONE, 0); +- _(CYSETTHRESH, NONE, 0); +- _(CYSETTIMEOUT, NONE, 0); + _(EQL_EMANCIPATE, WRITE, struct_ifreq_sz); + _(EQL_ENSLAVE, WRITE, struct_ifreq_sz); + _(EQL_GETMASTRCFG, WRITE, struct_ifreq_sz); +diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc +index d823a12190c..e8fce8a0287 100644 +--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc ++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cc +@@ -157,7 +157,6 @@ typedef struct user_fpregs elf_fpregset_t; + # include + #endif + #include +-#include + #include + #include + #include +@@ -466,7 +465,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr); + + #if SANITIZER_LINUX && !SANITIZER_ANDROID + unsigned struct_ax25_parms_struct_sz = sizeof(struct ax25_parms_struct); +- unsigned struct_cyclades_monitor_sz = sizeof(struct cyclades_monitor); + #if EV_VERSION > (0x010000) + unsigned struct_input_keymap_entry_sz = sizeof(struct input_keymap_entry); + #else +@@ -833,15 +831,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr); + #endif // SANITIZER_LINUX || SANITIZER_FREEBSD + + #if SANITIZER_LINUX && !SANITIZER_ANDROID +- unsigned IOCTL_CYGETDEFTHRESH = CYGETDEFTHRESH; +- unsigned IOCTL_CYGETDEFTIMEOUT = CYGETDEFTIMEOUT; +- unsigned IOCTL_CYGETMON = CYGETMON; +- unsigned IOCTL_CYGETTHRESH = CYGETTHRESH; +- unsigned IOCTL_CYGETTIMEOUT = CYGETTIMEOUT; +- unsigned IOCTL_CYSETDEFTHRESH = CYSETDEFTHRESH; +- unsigned IOCTL_CYSETDEFTIMEOUT = CYSETDEFTIMEOUT; +- unsigned IOCTL_CYSETTHRESH = CYSETTHRESH; +- unsigned IOCTL_CYSETTIMEOUT = CYSETTIMEOUT; + unsigned IOCTL_EQL_EMANCIPATE = EQL_EMANCIPATE; + unsigned IOCTL_EQL_ENSLAVE = EQL_ENSLAVE; + unsigned IOCTL_EQL_GETMASTRCFG = EQL_GETMASTRCFG; +diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h +index 6a673a7c995..f921bf2b5b5 100644 +--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h ++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h +@@ -1040,7 +1040,6 @@ struct __sanitizer_cookie_io_functions_t { + + #if SANITIZER_LINUX && !SANITIZER_ANDROID + extern unsigned struct_ax25_parms_struct_sz; +- extern unsigned struct_cyclades_monitor_sz; + extern unsigned struct_input_keymap_entry_sz; + extern unsigned struct_ipx_config_data_sz; + extern unsigned struct_kbdiacrs_sz; +@@ -1385,15 +1384,6 @@ struct __sanitizer_cookie_io_functions_t { + #endif // SANITIZER_LINUX || SANITIZER_FREEBSD + + #if SANITIZER_LINUX && !SANITIZER_ANDROID +- extern unsigned IOCTL_CYGETDEFTHRESH; +- extern unsigned IOCTL_CYGETDEFTIMEOUT; +- extern unsigned IOCTL_CYGETMON; +- extern unsigned IOCTL_CYGETTHRESH; +- extern unsigned IOCTL_CYGETTIMEOUT; +- extern unsigned IOCTL_CYSETDEFTHRESH; +- extern unsigned IOCTL_CYSETDEFTIMEOUT; +- extern unsigned IOCTL_CYSETTHRESH; +- extern unsigned IOCTL_CYSETTIMEOUT; + extern unsigned IOCTL_EQL_EMANCIPATE; + extern unsigned IOCTL_EQL_ENSLAVE; + extern unsigned IOCTL_EQL_GETMASTRCFG; +-- +2.27.0 + diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb index 4fe5df40dbc..1c7ebccd0c2 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb @@ -29,6 +29,7 @@ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-8.3.0_fix-xsmin-ppc.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCC-9.x_fix-libsanitizer-cyclades.patch', ] checksums = [ 'be303f7a8292982a35381489f5a9178603cbe9a4715ee4fa4a815d6bcd2b658d', # gcc-9.1.0.tar.gz @@ -39,6 +40,7 @@ checksums = [ '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch 'bea1bce8f50ea6d51b038309eb61dec00a8681fb653d211c539be80f184609a3', # GCCcore-8.3.0_fix-xsmin-ppc.patch '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch + 'b48e48736062e64a6da7cbe7e21a6c1c89422d1f49ef547c73b479a3f3f4935f', # GCC-9.x_fix-libsanitizer-cyclades.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb index 839d68ee7d3..09a142d9b3b 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb @@ -32,6 +32,7 @@ patches = [ 'GCCcore-8.3.0_fix-xsmin-ppc.patch', 'GCCcore-9.2.0-fix-glibc-2.31-libsanitizer.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCC-9.x_fix-libsanitizer-cyclades.patch', ] checksums = [ 'a931a750d6feadacbeecb321d73925cd5ebb6dfa7eff0802984af3aef63759f4', # gcc-9.2.0.tar.gz @@ -44,6 +45,7 @@ checksums = [ # GCCcore-9.2.0-fix-glibc-2.31-libsanitizer.patch '459006b69e19ffdc3102ad78b81c124741faaac4c42b6117365314d908cb506f', '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch + 'b48e48736062e64a6da7cbe7e21a6c1c89422d1f49ef547c73b479a3f3f4935f', # GCC-9.x_fix-libsanitizer-cyclades.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb index a0bb5a12552..8870f60f1a2 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb @@ -36,6 +36,7 @@ patches = [ 'GCCcore-%(version)s_vect_broadcasts_masmintel.patch', 'GCCcore-%(version)s_nvptx_sm_35_default.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCC-9.x_fix-libsanitizer-cyclades.patch', ] checksums = [ '5258a9b6afe9463c2e56b9e8355b1a4bee125ca828b8078f910303bc2ef91fa6', # gcc-9.3.0.tar.gz @@ -51,6 +52,7 @@ checksums = [ 'a32ac9c7d999a8b91bf93dba6a9d81b6ff58b3c89c425ff76090cbc90076685c', # GCCcore-9.3.0_vect_broadcasts_masmintel.patch '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch + 'b48e48736062e64a6da7cbe7e21a6c1c89422d1f49ef547c73b479a3f3f4935f', # GCC-9.x_fix-libsanitizer-cyclades.patch ] builddependencies = [ From f6b1e6f9fb6173ad852fcc7993f073058fbc3bd6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Nov 2021 13:59:24 +0100 Subject: [PATCH 2125/9987] add patch for GCCcore 10.1-11.1 to fix compatibility with recent kernel headers --- .../GCC-10.x_fix-libsanitizer-cyclades.patch | 123 ++++++++++++++++++ .../easyconfigs/g/GCCcore/GCCcore-10.1.0.eb | 2 + .../easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 2 + .../easyconfigs/g/GCCcore/GCCcore-10.3.0.eb | 2 + .../easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 2 + 5 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCC-10.x_fix-libsanitizer-cyclades.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCC-10.x_fix-libsanitizer-cyclades.patch b/easybuild/easyconfigs/g/GCCcore/GCC-10.x_fix-libsanitizer-cyclades.patch new file mode 100644 index 00000000000..1805e34302a --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCC-10.x_fix-libsanitizer-cyclades.patch @@ -0,0 +1,123 @@ +From a7e72b282177fbaa6a852324641c871313d326da Mon Sep 17 00:00:00 2001 +From: Tamar Christina +Date: Fri, 21 May 2021 10:30:59 +0100 +Subject: [PATCH] libsanitizer: Remove cyclades from libsanitizer + +The Linux kernel has removed the interface to cyclades from +the latest kernel headers[1] due to them being orphaned for the +past 13 years. + +libsanitizer uses this header when compiling against glibc, but +glibcs itself doesn't seem to have any references to cyclades. + +Further more it seems that the driver is broken in the kernel and +the firmware doesn't seem to be available anymore. + +As such since this is breaking the build of libsanitizer (and so the +GCC bootstrap[2]) I propose to remove this. + +[1] https://lkml.org/lkml/2021/3/2/153 +[2] https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100379 + +libsanitizer/ChangeLog: + + PR sanitizer/100379 + * sanitizer_common/sanitizer_common_interceptors_ioctl.inc: Cherry-pick + llvm-project revision f7c5351552387bd43f6ca3631016d7f0dfe0f135. + * sanitizer_common/sanitizer_platform_limits_posix.cpp: Likewise. + * sanitizer_common/sanitizer_platform_limits_posix.h: Likewise. + +(cherry picked from commit 745dae5923aba02982563481d75a21595df22ff8) +--- + .../sanitizer_common_interceptors_ioctl.inc | 9 --------- + .../sanitizer_platform_limits_posix.cpp | 11 ----------- + .../sanitizer_platform_limits_posix.h | 10 ---------- + 3 files changed, 30 deletions(-) + +diff --git a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc +index 490a04b2181..42e43a04441 100644 +--- a/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc ++++ b/libsanitizer/sanitizer_common/sanitizer_common_interceptors_ioctl.inc +@@ -366,15 +366,6 @@ static void ioctl_table_fill() { + + #if SANITIZER_LINUX && !SANITIZER_ANDROID + // _(SIOCDEVPLIP, WRITE, struct_ifreq_sz); // the same as EQL_ENSLAVE +- _(CYGETDEFTHRESH, WRITE, sizeof(int)); +- _(CYGETDEFTIMEOUT, WRITE, sizeof(int)); +- _(CYGETMON, WRITE, struct_cyclades_monitor_sz); +- _(CYGETTHRESH, WRITE, sizeof(int)); +- _(CYGETTIMEOUT, WRITE, sizeof(int)); +- _(CYSETDEFTHRESH, NONE, 0); +- _(CYSETDEFTIMEOUT, NONE, 0); +- _(CYSETTHRESH, NONE, 0); +- _(CYSETTIMEOUT, NONE, 0); + _(EQL_EMANCIPATE, WRITE, struct_ifreq_sz); + _(EQL_ENSLAVE, WRITE, struct_ifreq_sz); + _(EQL_GETMASTRCFG, WRITE, struct_ifreq_sz); +diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp +index aa845df4dde..badf6a401cc 100644 +--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp ++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp +@@ -130,7 +130,6 @@ typedef struct user_fpregs elf_fpregset_t; + # include + #endif + #include +-#include + #include + #include + #include +@@ -443,7 +442,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr); + + #if SANITIZER_LINUX && !SANITIZER_ANDROID + unsigned struct_ax25_parms_struct_sz = sizeof(struct ax25_parms_struct); +- unsigned struct_cyclades_monitor_sz = sizeof(struct cyclades_monitor); + #if EV_VERSION > (0x010000) + unsigned struct_input_keymap_entry_sz = sizeof(struct input_keymap_entry); + #else +@@ -809,15 +807,6 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr); + #endif // SANITIZER_LINUX + + #if SANITIZER_LINUX && !SANITIZER_ANDROID +- unsigned IOCTL_CYGETDEFTHRESH = CYGETDEFTHRESH; +- unsigned IOCTL_CYGETDEFTIMEOUT = CYGETDEFTIMEOUT; +- unsigned IOCTL_CYGETMON = CYGETMON; +- unsigned IOCTL_CYGETTHRESH = CYGETTHRESH; +- unsigned IOCTL_CYGETTIMEOUT = CYGETTIMEOUT; +- unsigned IOCTL_CYSETDEFTHRESH = CYSETDEFTHRESH; +- unsigned IOCTL_CYSETDEFTIMEOUT = CYSETDEFTIMEOUT; +- unsigned IOCTL_CYSETTHRESH = CYSETTHRESH; +- unsigned IOCTL_CYSETTIMEOUT = CYSETTIMEOUT; + unsigned IOCTL_EQL_EMANCIPATE = EQL_EMANCIPATE; + unsigned IOCTL_EQL_ENSLAVE = EQL_ENSLAVE; + unsigned IOCTL_EQL_GETMASTRCFG = EQL_GETMASTRCFG; +diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h +index d82fd5e4005..dc6423bc297 100644 +--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h ++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.h +@@ -974,7 +974,6 @@ extern unsigned struct_vt_mode_sz; + + #if SANITIZER_LINUX && !SANITIZER_ANDROID + extern unsigned struct_ax25_parms_struct_sz; +-extern unsigned struct_cyclades_monitor_sz; + extern unsigned struct_input_keymap_entry_sz; + extern unsigned struct_ipx_config_data_sz; + extern unsigned struct_kbdiacrs_sz; +@@ -1319,15 +1318,6 @@ extern unsigned IOCTL_VT_WAITACTIVE; + #endif // SANITIZER_LINUX + + #if SANITIZER_LINUX && !SANITIZER_ANDROID +-extern unsigned IOCTL_CYGETDEFTHRESH; +-extern unsigned IOCTL_CYGETDEFTIMEOUT; +-extern unsigned IOCTL_CYGETMON; +-extern unsigned IOCTL_CYGETTHRESH; +-extern unsigned IOCTL_CYGETTIMEOUT; +-extern unsigned IOCTL_CYSETDEFTHRESH; +-extern unsigned IOCTL_CYSETDEFTIMEOUT; +-extern unsigned IOCTL_CYSETTHRESH; +-extern unsigned IOCTL_CYSETTIMEOUT; + extern unsigned IOCTL_EQL_EMANCIPATE; + extern unsigned IOCTL_EQL_ENSLAVE; + extern unsigned IOCTL_EQL_GETMASTRCFG; +-- +2.27.0 + diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb index ae0206847fd..8ea3bfbc136 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb @@ -29,6 +29,7 @@ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCC-10.x_fix-libsanitizer-cyclades.patch', ] checksums = [ '954057239c89d25bc7a62bfbceb58026363ad74f079c63fdba27f95abbf60900', # gcc-10.1.0.tar.gz @@ -39,6 +40,7 @@ checksums = [ '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch + 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 4ce3d1f4b94..98d75b65b5d 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -37,6 +37,7 @@ patches = [ 'GCCcore-10.2.0_fix-ice-on-arm.patch', 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCC-10.x_fix-libsanitizer-cyclades.patch', ] checksums = [ '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d', # gcc-10.2.0.tar.gz @@ -54,6 +55,7 @@ checksums = [ # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962', '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch + 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb index 8e9a76ab85b..b0e0681d116 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_nvptx_sm_35_default.patch', 'gcc-10.3.0_fix-ice-in-tsubst.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCC-10.x_fix-libsanitizer-cyclades.patch', ] checksums = [ '8fcf994811ad4e5c7ac908e8cf62af2c1982319e5551f62ae72016064dacdf16', # gcc-10.3.0.tar.gz @@ -49,6 +50,7 @@ checksums = [ '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch '74e6e019458aa2feb36ae3c45f45e164725ca5edd66f4fe9f873c8ee78c35717', # gcc-10.3.0_fix-ice-in-tsubst.patch '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch + 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index f4578a964af..072a64c40bb 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -33,6 +33,7 @@ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCC-10.x_fix-libsanitizer-cyclades.patch', ] checksums = [ 'e7abb1b4cb58aaa67c5eb49d98e89d13363b8e258ac2b5b105c197b441c09f85', # gcc-11.1.0.tar.gz @@ -45,6 +46,7 @@ checksums = [ '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch + 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch ] builddependencies = [ From c9be7a9371568ddadf622d867a9c4b6d1d4072f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Nov 2021 14:48:15 +0100 Subject: [PATCH 2126/9987] fix homepage + description for ARAGORN 1.2.41 --- easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb index 4edce9420f8..b1247c2e635 100644 --- a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb +++ b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb @@ -9,8 +9,8 @@ easyblock = 'CmdCp' name = 'ARAGORN' version = '1.2.41' -homepage = 'http://mbio-serv2.mbioekol.lu.se/ARAGORN/' -description = "http://www.ansikte.se/ARAGORN/" +homepage = 'http://www.ansikte.se/ARAGORN/' +description = "a program to detect tRNA genes and tmRNA genes in nucleotide sequences" toolchain = {'name': 'foss', 'version': '2021b'} From b08dab99f9ac1f91db070132b0972500d841ead4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Nov 2021 15:26:44 +0100 Subject: [PATCH 2127/9987] rename unversioned ARAGORN manpage on download --- easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb index b1247c2e635..f596bc6846b 100644 --- a/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb +++ b/easybuild/easyconfigs/a/ARAGORN/ARAGORN-1.2.41-foss-2021b.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['http://www.ansikte.se/ARAGORN/Downloads/'] sources = [ {'filename': '%(namelower)s%(version)s.c', 'extract_cmd': 'cp %s aragorn.c'}, - {'filename': 'aragorn.1', 'extract_cmd': 'cp %s aragorn.1'} # man page + {'download_filename': 'aragorn.1', 'filename': 'aragorn-%(version)s.man', 'extract_cmd': 'cp %s aragorn.1'} ] checksums = [ '92a31cc5c0b0ad16d4d7b01991989b775f07d2815df135fe6e3eab88f5e97f4a', # aragorn1.2.41.c From 7f7ad0be667677e1795ed0201e2d1a56c4257606 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Nov 2021 15:30:23 +0100 Subject: [PATCH 2128/9987] move checksum to default_component_specs in MAFFT easyconfig --- .../m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb index 1c6a5f97f6d..91fe105a25b 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.490-GCC-11.2.0-with-extensions.eb @@ -22,6 +22,7 @@ default_easyblock = 'ConfigureMake' default_component_specs = { 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'checksums': ['d6eef33d8b9e282e20f9b25b6b6fb2757b9b6900e397ca621d56da86d9976541'], 'skipsteps': ['configure'], 'installopts': 'PREFIX=%(installdir)s', } @@ -29,11 +30,9 @@ default_component_specs = { components = [ (name, version, { 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', - 'checksums': ['d6eef33d8b9e282e20f9b25b6b6fb2757b9b6900e397ca621d56da86d9976541'], }), ('%s Extensions' % name, version, { 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', - 'checksums': ['d6eef33d8b9e282e20f9b25b6b6fb2757b9b6900e397ca621d56da86d9976541'], }), ] From 8c405585c93a904e9b879fda746d4156ca70ad20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Nov 2021 15:34:13 +0100 Subject: [PATCH 2129/9987] add description + author to patch for rpy2 3.4.5 --- easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb | 2 +- easybuild/easyconfigs/r/rpy2/rpy2-3.4.5_disable_gui_tests.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb b/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb index 7db264da0aa..58749928808 100644 --- a/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb +++ b/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021b.eb @@ -48,7 +48,7 @@ exts_list = [ 'patches': ['rpy2-%(version)s_disable_gui_tests.patch'], 'checksums': [ '5d31a5ea43f5a59f6dec30faca87edb01fc9b8affa0beae96a99be923bd7dab3', # rpy2-3.4.5.tar.gz - '3caef18175eb423cf43e2ad7c513e29358ca8ace22cbe4241e16c38408695fa8', # rpy2-3.4.5_disable_gui_tests.patch + '7424fed4bc9edb246944ad54fcb434a1ae5f2db086679b1a53d44cf5d3b98d8b', # rpy2-3.4.5_disable_gui_tests.patch ], }), ] diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5_disable_gui_tests.patch b/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5_disable_gui_tests.patch index 593f7a1ec05..9bde6bab775 100644 --- a/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5_disable_gui_tests.patch +++ b/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5_disable_gui_tests.patch @@ -1,3 +1,5 @@ +skip tests that require running in environment that supports GUI +author: Denis Kristak (INUITS) diff -ruN rpy2-3.4.5_orig/rpy2/tests/ipython/test_rmagic.py rpy2-3.4.5/rpy2/tests/ipython/test_rmagic.py --- rpy2-3.4.5_orig/rpy2/tests/ipython/test_rmagic.py 2021-11-25 12:37:30.723114034 +0000 +++ rpy2-3.4.5/rpy2/tests/ipython/test_rmagic.py 2021-11-26 16:45:54.886986180 +0000 From 806d3cd7d905fcf755925e6baf6a0a4f0f1e7acb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Mon, 29 Nov 2021 09:28:11 +0100 Subject: [PATCH 2130/9987] TOBIAS: don't install argparse, fix up boto3 easyconfig --- .../b/boto3/boto3-1.20.13-GCCcore-11.2.0.eb | 35 +++++++++++++++++++ .../t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb | 4 +-- 2 files changed, 36 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d43e9d70cd8 --- /dev/null +++ b/easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'boto3' +version = '1.20.13' + +homepage = 'https://github.com/boto/boto3' +description = """Boto3 is the Amazon Web Services (AWS) Software Development Kit +(SDK) for Python, which allows Python developers to write software that makes +use of services like Amazon S3 and Amazon EC2.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +exts_list = [ + ('botocore', '1.23.13', { + 'checksums': ['35792b2196049ef900f538cae51fb8359c940156eef187962aa9e3bd2c0b8e8c'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + ('s3transfer', '0.5.0', { + 'checksums': ['50ed823e1dc5868ad40c8dc92072f757aa0e653a192845c94a3b676f4a62da4c'], + }), + (name, version, { + 'checksums': ['bbf53a077d6a0575ddec8026f0475ca6ee6f41b227914bf315bf3e049a3d653a'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb index 17e38754291..5e9a0e5377a 100644 --- a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb @@ -29,9 +29,6 @@ dependencies = [ ] exts_list = [ - ('argparse', '1.4.0', { - 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], - }), ('configs', '3.0.3', { 'source_tmpl': '%(namelower)s-%(version)s.zip', 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], @@ -46,6 +43,7 @@ exts_list = [ 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], }), ('svist4get', '1.2.24', { + 'preinstallopts': 'sed -i "s/\'argparse\',//" setup.py && ', 'checksums': ['c4b2e561dab32019cc1505e017a12a4a77aa8aeba2720d3d1c6e69cf834cc46f'], }), ('PyPDF2', '1.26.0', { From c3e0aeec1ad18628304bd8593ec91c1a5efb53fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Mon, 29 Nov 2021 10:53:13 +0100 Subject: [PATCH 2131/9987] TOBIAS: add binutils as a builddependency --- easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-11.2.0.eb index d43e9d70cd8..5a9680bbbbf 100644 --- a/easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-11.2.0.eb @@ -10,6 +10,10 @@ use of services like Amazon S3 and Amazon EC2.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +builddependencies = [ + ('binutils', '2.37'), +] + dependencies = [ ('Python', '3.9.6'), ] From 235d0cee7d3d3c83095d9ce017a80ea3c2c9c742 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Nov 2021 11:34:01 +0100 Subject: [PATCH 2132/9987] use %(pyshortver)s template rather than hardcoding Python version in extra sanity check command for PyTorch 1.10.0 --- .../p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index d1f2e2dfc37..0be39a72ccd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -118,7 +118,7 @@ runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-throu # The readelf sanity check can be taken out once the TestRPATH test from https://github.com/pytorch/pytorch/pull/68912 # is accepted, since it is then checked as part of the PyTorch test suite -local_libcaffe2 = "$EBROOTPYTORCH/lib/python3.9/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT sanity_check_commands = [ "python -c 'import caffe2.python'", "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, From d19d386b519b4ae3bb8a7337a597a4ce257dc155 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Nov 2021 11:39:30 +0100 Subject: [PATCH 2133/9987] escape %(pyshortver)s template in sanity check command due to use of SHLIB_EXT --- .../p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index 0be39a72ccd..cecec914c70 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -118,7 +118,7 @@ runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-throu # The readelf sanity check can be taken out once the TestRPATH test from https://github.com/pytorch/pytorch/pull/68912 # is accepted, since it is then checked as part of the PyTorch test suite -local_libcaffe2 = "$EBROOTPYTORCH/lib/python%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT sanity_check_commands = [ "python -c 'import caffe2.python'", "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, From 834e8dbbd7124e78c36a1b3a4f57bcfe120607b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Mon, 29 Nov 2021 11:46:51 +0100 Subject: [PATCH 2134/9987] Delete boto3-1.20.13-foss-2021b.eb --- .../b/boto3/boto3-1.20.13-foss-2021b.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.20.13-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.20.13-foss-2021b.eb b/easybuild/easyconfigs/b/boto3/boto3-1.20.13-foss-2021b.eb deleted file mode 100644 index bc32295f023..00000000000 --- a/easybuild/easyconfigs/b/boto3/boto3-1.20.13-foss-2021b.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'boto3' -version = '1.20.13' - -homepage = 'https://github.com/loosolab/TOBIAS' -description = """TOBIAS is a collection of command-line bioinformatics tools for -performing footprinting analysis on ATAC-seq data, and includes: Correction of -Tn5 insertion bias; Calculation of footprint scores within regulatory regions; -Estimation of bound/unbound transcription factor binding sites; and -Visualization of footprints within and across different conditions""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('Python', '3.9.6'), -] - -exts_list = [ - ('botocore', '1.23.13', { - 'checksums': ['35792b2196049ef900f538cae51fb8359c940156eef187962aa9e3bd2c0b8e8c'], - }), - ('jmespath', '0.10.0', { - 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], - }), - ('s3transfer', '0.5.0', { - 'checksums': ['50ed823e1dc5868ad40c8dc92072f757aa0e653a192845c94a3b676f4a62da4c'], - }), - (name, version, { - 'checksums': ['bbf53a077d6a0575ddec8026f0475ca6ee6f41b227914bf315bf3e049a3d653a'], - }), -] - -use_pip = True -sanity_pip_check = True - -moduleclass = 'lib' From 987bf68ea09036aec9f5dfbafdaf206cc3c5b6c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Mon, 29 Nov 2021 12:56:33 +0100 Subject: [PATCH 2135/9987] adding easyconfigs: TRUST4-1.0.6-GCC-11.2.0.eb --- .../t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb new file mode 100644 index 00000000000..b08c081a5a9 --- /dev/null +++ b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'MakeCp' + +name = 'TRUST4' +version = '1.0.6' + +homepage = 'https://github.com/liulab-dfci/TRUST4' +description = """Tcr Receptor Utilities for Solid Tissue (TRUST) is a +computational tool to analyze TCR and BCR sequences using unselected RNA +sequencing data, profiled from solid tissues, including tumors. TRUST4 performs +de novo assembly on V, J, C genes including the hypervariable +complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR +sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to +report the corresponding information. TRUST4 supports both single-end and +paired-end sequencing data with any read length.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'liulab-dfci' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ebc742a6a1b36ad6b650df22c4f252415d42fd4a9a30e0ce5ab55df91ead46d6'] + +# TRUST4 uses an old API of SAMtools and links agains libbam.a, that has been +# removed in SAMtools 1.14 (https://github.com/liulab-dfci/TRUST4/issues/95). +# For this reason, we use the SAMtools bundled by TRUST4. +builddependencies = [ + ('binutils', '2.37'), +] + +local_binaries = [ + 'run-trust4', 'trust4', 'bam-extractor', 'fastq-extractor', 'annotator', + 'BuildDatabaseFa.pl', 'BuildImgtAnnot.pl', 'BuildImgtVquestAnnot.pl', + 'FilterAnnotatedAssembly.pl', 'trust-airr.pl', 'trust-barcoderep.pl', + 'trust-simplerep.pl', 'trust-smartseq.pl', +] +local_scripts = [ + 'AddSequenceToCDR3File.pl', 'barcoderep-filter.py', 'GetFullLengthAssembly.pl', + 'trust-barcoderep-to-10X.pl', 'trust-cluster.py', 'trust-stats.py' +] +files_to_copy = [ + (local_binaries, 'bin'), + (['scripts/%s' % x for x in local_scripts], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['bin'], +} + +sanity_check_commands = [ + "run-trust4 2>&1 | grep 'TRUST4 v%(version)s'", + + "cd %(builddir)s/%(name)s-%(version)s && " + "run-trust4 -b example/example.bam -f hg38_bcrtcr.fa --ref human_IMGT+C.fa && " + "[ -e example/TRUST_example_report.tsv ]" +] + +moduleclass = 'lib' From a858aec91d155fc4ee0ddeebc11f3f0435b76505 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Mon, 29 Nov 2021 17:09:59 +0100 Subject: [PATCH 2136/9987] TRUST4: fix up all included scripts --- .../t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb index b08c081a5a9..fda98280cfc 100644 --- a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb @@ -26,6 +26,10 @@ checksums = ['ebc742a6a1b36ad6b650df22c4f252415d42fd4a9a30e0ce5ab55df91ead46d6'] builddependencies = [ ('binutils', '2.37'), ] +dependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), +] local_binaries = [ 'run-trust4', 'trust4', 'bam-extractor', 'fastq-extractor', 'annotator', @@ -42,17 +46,24 @@ files_to_copy = [ (['scripts/%s' % x for x in local_scripts], 'bin'), ] +postinstallcmds = [ + 'sed -i "1i #!/usr/bin/env python" %(installdir)s/bin/*.py', + 'sed -i "1i #!/usr/bin/env perl" %(installdir)s/bin/*.pl', + 'chmod a+x %(installdir)s/bin/*' +] + sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_binaries], - 'dirs': ['bin'], + 'files': ['bin/' + x for x in local_binaries + local_scripts], + 'dirs': [], } sanity_check_commands = [ "run-trust4 2>&1 | grep 'TRUST4 v%(version)s'", - + "BuildDatabaseFa.pl 2>&1 | grep 'usage: perl BuildDatabaseFa.pl'", + "trust-cluster.py 2>&1 | grep 'usage: a.py trust_cdr3.out'", "cd %(builddir)s/%(name)s-%(version)s && " "run-trust4 -b example/example.bam -f hg38_bcrtcr.fa --ref human_IMGT+C.fa && " "[ -e example/TRUST_example_report.tsv ]" ] -moduleclass = 'lib' +moduleclass = 'bio' From 8f37e117201c497f9e93c2fcf8f5e5fa7d7cbbf5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Nov 2021 17:16:01 +0100 Subject: [PATCH 2137/9987] add custom sanity_check_paths to TOBIAS easyconfig --- easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb index 5e9a0e5377a..e9a53481b39 100644 --- a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.12.12-foss-2021b.eb @@ -69,6 +69,11 @@ exts_list = [ use_pip = True sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/TOBIAS'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + sanity_check_commands = ["TOBIAS ATACorrect | grep 'TOBIAS ~ ATACorrect'"] moduleclass = 'bio' From e31e10158552a77bebc2e1dbfa35758ae070e753 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Nov 2021 17:29:48 +0100 Subject: [PATCH 2138/9987] adding easyconfigs: NCO-5.0.3-foss-2021b.eb, ESMF-8.2.0-foss-2021b.eb, netCDF-C++4-4.3.1-gompi-2021b.eb, libdap-3.20.8-GCCcore-11.2.0.eb, ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb --- .../ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb | 36 ++++++++++++++++++ .../e/ESMF/ESMF-8.2.0-foss-2021b.eb | 34 +++++++++++++++++ .../l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb | 37 ++++++++++++++++++ .../easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb | 38 +++++++++++++++++++ .../netCDF-C++4-4.3.1-gompi-2021b.eb | 25 ++++++++++++ 5 files changed, 170 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.2.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2021b.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb new file mode 100644 index 00000000000..05e3b23c3c8 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Java', '11', '', True)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +sanity_check_commands = ["antlr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.2.0-foss-2021b.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.2.0-foss-2021b.eb new file mode 100644 index 00000000000..fc84a489666 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.2.0-foss-2021b.eb @@ -0,0 +1,34 @@ +name = 'ESMF' +version = '8.2.0' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['%%(name)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + '3693987aba2c8ae8af67a0e222bea4099a48afe09b8d3d334106f9d7fc311485', # ESMF_8_2_0.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +dependencies = [ + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('netCDF-C++4', '4.3.1'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b48c3f1b6bc --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.8-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.20.8' + +homepage = 'https://www.opendap.org/software/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 and + DAP4.0. This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['65eb5c8f693cf74d58eece5eaa2e7c3c65f368926b1bffab0cf5b207757b94eb'] + +builddependencies = [ + ('binutils', '2.37'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '7.78.0'), + ('libxml2', '2.9.10'), + ('libtirpc', '1.3.2'), + ('PCRE', '8.45'), + ('util-linux', '2.37'), +] + +configopts = 'TIRPC_LIBS="-ltirpc"' + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb b/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb new file mode 100644 index 00000000000..5103702328e --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.0.3' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['61b45cdfbb772718f00d40da1a4ce268201fd00a61ebb9515460b8dda8557bdb'] + +builddependencies = [ + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.4.1'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.8'), + ('GSL', '2.7'), + ('netCDF', '4.8.1'), + ('ESMF', '8.2.0'), # ncremap needs ESMF_RegridWeightGen +] + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2021b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2021b.eb new file mode 100644 index 00000000000..c98c231989d --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2021b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.8.1')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' From a799d22a5cfb966c34f6945f778e6429b8649a15 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Mon, 29 Nov 2021 17:00:58 +0000 Subject: [PATCH 2139/9987] adding easyconfigs: Yambo-5.0.4-intel-2021a.eb --- .../y/Yambo/Yambo-5.0.4-intel-2021a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yambo/Yambo-5.0.4-intel-2021a.eb diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.0.4-intel-2021a.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.0.4-intel-2021a.eb new file mode 100644 index 00000000000..f40b292da93 --- /dev/null +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.0.4-intel-2021a.eb @@ -0,0 +1,53 @@ +easyblock = 'MakeCp' + +name = 'Yambo' +version = '5.0.4' + +homepage = 'http://www.yambo-code.org' +description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. + Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = { + 'usempi': True, + 'openmp': True, +} + +source_urls = ['https://github.com/yambo-code/yambo/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1841ded51cc31a4293fa79252d7ce893d998acea7ccc836e321c3edba19eae8a'] + +dependencies = [ + ('HDF5', '1.10.7'), + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), +] + +with_configure = True + +configopts = '--prefix=%(builddir)s/%(namelower)s-%(version)s/ ' +configopts += '--enable-open-mp --enable-hdf5-par-io ' +configopts += '--with-blas-libs="$LIBBLAS" ' +configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs="$LIBBLACS" ' +configopts += '--with-scalapack-libs="$LIBSCALAPACK" ' +configopts += '--with-fft-libs="$LIBFFT" --with-fft-includedir="$FFT_INC_DIR" ' +configopts += '--with-netcdf-path="$EBROOTNETCDF" ' +configopts += '--with-netcdff-path="$EBROOTNETCDFMINFORTRAN" ' +configopts += '--with-hdf5-path="$HDF5_DIR" ' + +buildopts = 'all' + +parallel = 1 + +files_to_copy = [ + (['bin/*'], 'bin'), + (['%(builddir)s/%(namelower)s-%(version)s/lib/external/intel/mpiifort/bin/*'], 'bin') +] + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['a2y', 'p2y', 'yambo', 'yambo_ph', 'ypp', 'ypp_ph', + 'iotk', 'iotk.x', 'xc-info']], + 'dirs': [] +} + +moduleclass = 'phys' From 65ff16af16a31546e153d8ee4c9d95abedca1f3e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Nov 2021 18:01:05 +0100 Subject: [PATCH 2140/9987] adding easyconfigs: PyTorch-1.10.0-foss-2021a.eb --- .../p/PyTorch/PyTorch-1.10.0-foss-2021a.eb | 112 ++++++++++++++++++ 1 file changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb new file mode 100644 index 00000000000..c05632ab43f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb @@ -0,0 +1,112 @@ +name = 'PyTorch' +version = '1.10.0' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_skip_failing_ops_tests.patch', + 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch + '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', + # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch + '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-test-cond-cpu.patch + '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-vnni-detection.patch + '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch + 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_skip_failing_ops_tests.patch + '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', + # PyTorch-1.10.0_skip_nan_tests_openblas.patch + '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), + ('hypothesis', '6.13.1'), +] + +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.5'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.6.2'), + ('SciPy-bundle', '2021.05'), + ('typing-extensions', '3.10.0.0'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.2.0'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + # 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + # 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From f6ecec0e0d76797f6f234b09ddbc95f1ee9e12f8 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 29 Nov 2021 17:32:40 +0000 Subject: [PATCH 2141/9987] Autoconf and Automake replaced with Autotools --- easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb index 33168cdcf05..02ccca5454c 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20200621-foss-2020b.eb @@ -20,9 +20,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['a8243923ee08c74cab609a4b086ade66c6156fc2b24450e2a500108dc644c867'] builddependencies = [ - ('Autoconf', '2.69'), + ('Autotools', '20200321'), ('pkg-config', '0.29.2'), - ('Automake', '1.16.2'), ] preconfigopts = 'sh autogen.sh && ' From 9541526008003e59833509477df1acf953466c8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Nov 2021 18:40:39 +0100 Subject: [PATCH 2142/9987] adding easyconfigs: torchvision-0.11.1-foss-2021a.eb --- .../torchvision-0.11.1-foss-2021a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a.eb new file mode 100644 index 00000000000..6029919b456 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a.eb @@ -0,0 +1,21 @@ +name = 'torchvision' +version = '0.11.1' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['32a06ccf755e4d75006ce03701f207652747a63dbfdf65f0f20a1b6f93a2e834'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('Pillow-SIMD', '8.2.0'), + ('PyTorch', '1.10.0'), +] + +moduleclass = 'vis' From 38c770bfa469178cbb5bd5d60532ab7a9b83ceb8 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 29 Nov 2021 17:43:23 +0000 Subject: [PATCH 2143/9987] Autotools and pkg-conf added to older version for consistancy --- .../easyconfigs/p/PhyML/PhyML-3.3.20190321-foss-2018b.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20190321-foss-2018b.eb b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20190321-foss-2018b.eb index c50e8a011fc..912512be334 100644 --- a/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20190321-foss-2018b.eb +++ b/easybuild/easyconfigs/p/PhyML/PhyML-3.3.20190321-foss-2018b.eb @@ -2,6 +2,8 @@ # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics +# Missing Autotools and pkg-config added +# J. Sassmannshausen GSTT/NHS easyblock = 'ConfigureMake' @@ -17,6 +19,11 @@ source_urls = ['https://github.com/stephaneguindon/phyml/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['5274546cda7445c947fd26838487cd4246e2becf18d333882b7a2a24dff853ee'] +builddependencies = [ + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + preconfigopts = 'sh autogen.sh && ' configopts = ['--enable-phyml', '--enable-phytime', '--enable-phyrex', '--enable-mpi --enable-phyml'] From 970319ce3f3da01b879c017077e96e9fa44b971a Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 29 Nov 2021 17:56:20 +0000 Subject: [PATCH 2144/9987] Sanity check command added --- easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb index f89f04cf919..91d41b96238 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.2.0.eb @@ -35,6 +35,8 @@ buildopts = 'CXX="$CXX"' files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] +sanity_check_commands = ['bedtools --help'] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], 'dirs': files_to_copy, From 0801d5d12f1f1541ff0e15939fec08ea8963b10e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Nov 2021 19:32:48 +0100 Subject: [PATCH 2145/9987] use fix_{perl,python}_shebang_for in TRUST4 easyconfig + check whether result file of sanity check command exists using 'test -f' --- .../easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb index fda98280cfc..287f0781bf3 100644 --- a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.6-GCC-11.2.0.eb @@ -46,11 +46,10 @@ files_to_copy = [ (['scripts/%s' % x for x in local_scripts], 'bin'), ] -postinstallcmds = [ - 'sed -i "1i #!/usr/bin/env python" %(installdir)s/bin/*.py', - 'sed -i "1i #!/usr/bin/env perl" %(installdir)s/bin/*.pl', - 'chmod a+x %(installdir)s/bin/*' -] +fix_perl_shebang_for = ['bin/*.pl'] +fix_python_shebang_for = ['bin/*.py'] + +postinstallcmds = ["chmod a+x %(installdir)s/bin/*"] sanity_check_paths = { 'files': ['bin/' + x for x in local_binaries + local_scripts], @@ -63,7 +62,7 @@ sanity_check_commands = [ "trust-cluster.py 2>&1 | grep 'usage: a.py trust_cdr3.out'", "cd %(builddir)s/%(name)s-%(version)s && " "run-trust4 -b example/example.bam -f hg38_bcrtcr.fa --ref human_IMGT+C.fa && " - "[ -e example/TRUST_example_report.tsv ]" + "test -f example/TRUST_example_report.tsv" ] moduleclass = 'bio' From 191817dc9e4cf86c7e8997318c568360a85b9339 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 30 Nov 2021 09:12:37 +0100 Subject: [PATCH 2146/9987] add simple sanity check command for strace --- easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb index fbaef728546..4eba20db189 100644 --- a/easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb @@ -25,4 +25,6 @@ sanity_check_paths = { 'dirs': ['share'] } +sanity_check_commands = ['strace --help'] + moduleclass = 'system' From 1f02d78f08d084c49f075bbcc58db8db477a10ed Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 30 Nov 2021 10:04:24 +0000 Subject: [PATCH 2147/9987] use `SHLIB_EXT` instead of `.so` Co-authored-by: Miguel Dias Costa --- .../easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb index 71a26a09f3c..18a8467356f 100644 --- a/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb @@ -48,7 +48,7 @@ local_scripts = ['DetectSelection', 'EstimatePopulationSize', 'PrepareInputFiles local_bins = ['bin/%s%s' % (name, x) for x in ['', 'CoalescentRate', 'Extract', 'FileFormats', 'MutationRate', 'Selection', 'TreeView']] local_libs = ['lib/libtskitStatic.a'] + [ - 'lib/lib%s%s' % (x, y) for x in ['gzstream', 'kastore', 'relate'] for y in ['Shared.so', 'Static.a'] + 'lib/lib%s%s' % (x, y) for x in ['gzstream', 'kastore', 'relate'] for y in ['Shared.%s' % SHLIB_EXT, 'Static.a'] ] sanity_check_paths = { From 0007cf797a1dfe4d8f5e0c9ad554a5a8d7c92705 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 30 Nov 2021 10:46:55 +0000 Subject: [PATCH 2148/9987] Download extra tar files using easybuild. --- .../y/Yambo/Yambo-5.0.4-intel-2021a.eb | 28 +++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.0.4-intel-2021a.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.0.4-intel-2021a.eb index f40b292da93..dcdb4af336f 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-5.0.4-intel-2021a.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.0.4-intel-2021a.eb @@ -13,9 +13,33 @@ toolchainopts = { 'openmp': True, } +local_copy_cmd_pattern = 'cp %s yambo-%(version)s/lib/archive/' + source_urls = ['https://github.com/yambo-code/yambo/archive/refs/tags/'] -sources = ['%(version)s.tar.gz'] -checksums = ['1841ded51cc31a4293fa79252d7ce893d998acea7ccc836e321c3edba19eae8a'] +sources = [ + '%(version)s.tar.gz', # Yambo + { + 'source_urls': ['https://github.com/yambo-code/yambo-libraries/archive/'], + 'filename': '0.0.2.tar.gz', + 'extract_cmd': 'tar --strip-components=1 -xzf %s -C yambo-%(version)s/lib/yambo/', + }, + { + 'source_urls': ['https://github.com/yambo-code/yambo/files/783150/'], + 'filename': 'libxc-2.2.3.tar.gz', + 'extract_cmd': local_copy_cmd_pattern, + }, + { + 'source_urls': ['https://github.com/yambo-code/yambo/files/962173/'], + 'filename': 'iotk-y1.2.2.tar.gz', + 'extract_cmd': local_copy_cmd_pattern, + }, +] +checksums = [ + '1841ded51cc31a4293fa79252d7ce893d998acea7ccc836e321c3edba19eae8a', # 5.0.4.tar.gz + 'cac7e4bf93e16d3cdf640d034e15854455a08dad796aece3cad5c7c491a68a59', # 0.0.2.tar.gz + '2f2b00b77a75c7fe8fe3f3ae70700cf28a09ff8d0ce791e47980ff7f9cde68e7', # libxc-2.2.3.tar.gz + 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543', # iotk-y1.2.2.tar.gz +] dependencies = [ ('HDF5', '1.10.7'), From 23c29cbdda1641c1b7a8774c5cb231cab807276c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 30 Nov 2021 14:11:47 +0000 Subject: [PATCH 2149/9987] Add a modloadmsg, and a missing numpy (scipy-bundle) dep --- .../Relate-20211123-foss-2020b-R-4.0.3.eb | 29 ++++++++++++++----- 1 file changed, 21 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb index 18a8467356f..22e5374dd0a 100644 --- a/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/r/Relate/Relate-20211123-foss-2020b-R-4.0.3.eb @@ -32,18 +32,21 @@ builddependencies = [('CMake', '3.18.4')] dependencies = [ ('zlib', '1.2.11'), - ('R', '4.0.3'), # required for some analysis scripts + # Python (numpy), and R required for some scripts + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('R', '4.0.3'), ] runtest = 'test' # script directories to add to path: -local_scripts = ['DetectSelection', 'EstimatePopulationSize', 'PrepareInputFiles', 'RelateParallel', - 'SampleBranchLengths', 'TreeView'] +local_script_dirs = ['DetectSelection', 'EstimatePopulationSize', 'PrepareInputFiles', 'RelateParallel', + 'SampleBranchLengths', 'TreeView'] # un/comment as appropriate: -# local_scripts += ['RelateLSF'] -# local_scripts += ['EstimatePopulationSizeSGE', 'RelateSGE'] -# local_scripts += ['RelateSlurm'] +# local_script_dirs += ['RelateLSF'] +# local_script_dirs += ['EstimatePopulationSizeSGE', 'RelateSGE'] +# local_script_dirs += ['RelateSlurm'] local_bins = ['bin/%s%s' % (name, x) for x in ['', 'CoalescentRate', 'Extract', 'FileFormats', 'MutationRate', 'Selection', 'TreeView']] @@ -53,7 +56,7 @@ local_libs = ['lib/libtskitStatic.a'] + [ sanity_check_paths = { 'files': local_bins + local_libs, - 'dirs': ['bin', 'lib', 'example'] + ['scripts/%s' % x for x in local_scripts], + 'dirs': ['bin', 'lib', 'example'] + ['scripts/%s' % x for x in local_script_dirs], } sanity_check_commands = [ @@ -63,6 +66,16 @@ sanity_check_commands = [ --annot data/example.annot --seed 1 -o example", ] -modextrapaths = {'PATH': ['scripts/%s' % x for x in local_scripts]} +modextrapaths = {'PATH': ['scripts/%s' % x for x in local_script_dirs]} + +modloadmsg = """ +Relate provides various scripts for parallel execution, supporting a variety of schedulers (LSF, + SGE, Slurm), located in `$EBROOTRELATE/scripts`. If the suitable script directory is not already + in `$PATH`, you can add this with: + [*] LSF : export PATH=$EBROOTRELATE/scrips/RelateLSF:$PATH + [*] SGE : export PATH=$EBROOTRELATE/scrips/RelateSGE:$EBROOTRELATE/scripts/EstimatePopulationSizeSGE:$PATH + [*] Slurm : export PATH=$EBROOTRELATE/scrips/RelateSlurm:$PATH + This should not be necessary for the other data preparation, output and analysis scripts included. +""" moduleclass = 'bio' From cb50579514eeec7ed569a4356fe8686739edc6ee Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Tue, 30 Nov 2021 16:49:08 +0100 Subject: [PATCH 2150/9987] To add the latest GDB --- .../g/GDB/GDB-11.1-GCCcore-11.2.0.eb | 44 +++++++++++++++++++ .../m/makeinfo/makeinfo-6.8-GCCcore-11.2.0.eb | 25 +++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..fe451504a66 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '11.1' + +homepage = 'https://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cccfcc407b20d343fb320d4a9a2110776dd3165118ffd41f4b1b162340333f94'] + +builddependencies = [ + ('binutils', '2.37'), + ('makeinfo', '6.8'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('expat', '2.4.1'), + ('Python', '3.9.6'), + ('ISL', '0.24'), + ('MPC', '1.2.1'), +] + +preconfigopts = "mkdir obj && cd obj && " +configure_cmd_prefix = '../' +prebuildopts = "cd obj && " +preinstallopts = prebuildopts + +configopts = '--with-system-zlib --with-system-readline --with-expat=$EBROOTEXPAT ' +configopts += '--with-python=$EBROOTPYTHON/bin/python --with-isl=$EBROOTISL --with-mpc=$EBROOTMPC ' +configopts += '--enable-tui --enable-plugins --disable-install-libbfd ' + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e820f74f06d --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '6.8' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['8eb753ed28bca21f8f56c1a180362aed789229bd62fff58bf8368e9beb59fec4'] + +builddependencies = [('binutils', '2.37')] +dependencies = [('Perl', '5.34.0')] + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' From 06cfda1de74512b8d454fd9832a19a81e54e0db9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Nov 2021 17:13:08 +0100 Subject: [PATCH 2151/9987] remove cpu_features-0.6.0-foss-2020b.eb, replaced by cpu_features-0.6.0-GCCcore-10.2.0.eb --- .../cpu_features-0.6.0-foss-2020b.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-foss-2020b.eb b/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-foss-2020b.eb deleted file mode 100644 index 455fecffa97..00000000000 --- a/easybuild/easyconfigs/c/cpu_features/cpu_features-0.6.0-foss-2020b.eb +++ /dev/null @@ -1,28 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'cpu_features' -version = '0.6.0' - -homepage = 'https://github.com/google/cpu_features' -description = """A cross-platform C library to retrieve CPU features (such as available instructions) at runtime.""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://github.com/google/cpu_features/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['95a1cf6f24948031df114798a97eea2a71143bd38a4d07d9a758dda3924c1932'] - -builddependencies = [ - ('CMake', '3.18.4'), -] - -modextrapaths = {'CPATH': 'include/cpu_features'} - -sanity_check_paths = { - 'files': ['bin/list_cpu_features', 'lib/libcpu_features.a'], - 'dirs': ['include/cpu_features/'] -} - -moduleclass = 'tools' From 25f33e74e01a9136c37a3318ca385c9d0963e476 Mon Sep 17 00:00:00 2001 From: Damian Alvarez Date: Tue, 30 Nov 2021 20:00:02 +0100 Subject: [PATCH 2152/9987] To include PAPI 6.0.0.1 in GCCcore 11.2.0 --- .../p/PAPI/PAPI-6.0.0.1-GCCcore-11.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-6.0.0.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..448668097f0 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-6.0.0.1-GCCcore-11.2.0.eb @@ -0,0 +1,49 @@ +## +# Author: Robert Mijakovic +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '6.0.0.1' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3cd7ed50c65b0d21d66e46d0ba34cd171178af4bbf9d94e693915c1aca1e287f'] + +builddependencies = [ + ('binutils', '2.37'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' From 6f2b2439142944b643036ab2b02205dbd47c7e17 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Nov 2021 20:20:02 +0100 Subject: [PATCH 2153/9987] add configure option to enable building of NCO C++ library MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Jakub Zárybnický --- easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb b/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb index 5103702328e..aaa7a817349 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb @@ -27,7 +27,8 @@ dependencies = [ ('netCDF', '4.8.1'), ('ESMF', '8.2.0'), # ncremap needs ESMF_RegridWeightGen ] - ++ configopts = "--enable-nco_cplusplus" ++ sanity_check_paths = { 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + From af4ea2d8da287b5fa9ea74825ce80350d6282644 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Nov 2021 20:20:21 +0100 Subject: [PATCH 2154/9987] add sanity check commands for NCO v5.0.3 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Jakub Zárybnický --- easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb b/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb index aaa7a817349..22ec9fc5b6f 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb @@ -35,5 +35,9 @@ sanity_check_paths = { ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], 'dirs': ['include'], } +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] moduleclass = 'tools' From de299067c699f5988c4f47dd92e611aaea3f577c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Nov 2021 20:22:45 +0100 Subject: [PATCH 2155/9987] remove excess + that got added via suggestion to add configure option to enable NCO C++ library --- easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb b/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb index 22ec9fc5b6f..92c8bd7333b 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-5.0.3-foss-2021b.eb @@ -27,8 +27,9 @@ dependencies = [ ('netCDF', '4.8.1'), ('ESMF', '8.2.0'), # ncremap needs ESMF_RegridWeightGen ] -+ configopts = "--enable-nco_cplusplus" -+ + +configopts = "--enable-nco_cplusplus" + sanity_check_paths = { 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + From 7c71bd13eab838cd5ac1d8079d773533fef7c3eb Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Wed, 1 Dec 2021 08:16:41 +0100 Subject: [PATCH 2156/9987] Add Julia v1.7.0 --- .../j/Julia/Julia-1.7.0-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb new file mode 100644 index 00000000000..55407f9c4f0 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.7.0' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['7299f3a638aec5e0b9e14eaf0e6221c4fe27189aa0b38ac5a36f03f0dc4c0d40'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From 24607451d93792c09fcb2f03cec32bd3e12c2451 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Dec 2021 10:07:32 +0100 Subject: [PATCH 2157/9987] adding easyconfigs: NCO-5.0.3-intel-2021b.eb --- .../e/ESMF/ESMF-8.2.0-intel-2021b.eb | 34 ++++++++++++++ .../g/GSL/GSL-2.7-intel-compilers-2021.4.0.eb | 25 +++++++++++ .../n/NCO/NCO-5.0.3-intel-2021b.eb | 44 +++++++++++++++++++ .../netCDF-C++4-4.3.1-iimpi-2021b.eb | 25 +++++++++++ 4 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.2.0-intel-2021b.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.4.0.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.0.3-intel-2021b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.2.0-intel-2021b.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.2.0-intel-2021b.eb new file mode 100644 index 00000000000..52f1eb282b6 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.2.0-intel-2021b.eb @@ -0,0 +1,34 @@ +name = 'ESMF' +version = '8.2.0' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['%%(name)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + '3693987aba2c8ae8af67a0e222bea4099a48afe09b8d3d334106f9d7fc311485', # ESMF_8_2_0.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +dependencies = [ + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('netCDF-C++4', '4.3.1'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..be5907f7849 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.7' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.0.3-intel-2021b.eb b/easybuild/easyconfigs/n/NCO/NCO-5.0.3-intel-2021b.eb new file mode 100644 index 00000000000..ada782814eb --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.0.3-intel-2021b.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.0.3' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['61b45cdfbb772718f00d40da1a4ce268201fd00a61ebb9515460b8dda8557bdb'] + +builddependencies = [ + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.4.1'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.8'), + ('GSL', '2.7'), + ('netCDF', '4.8.1'), + ('ESMF', '8.2.0'), # ncremap needs ESMF_RegridWeightGen +] + +configopts = "--enable-nco_cplusplus" + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2021b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2021b.eb new file mode 100644 index 00000000000..b0096d31395 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2021b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.8.1')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' From 085b6b7a751eb1e6411ca4ed9f8825dba3161ba0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 1 Dec 2021 10:12:59 +0100 Subject: [PATCH 2158/9987] adding easyconfigs: prodigal-2.6.3-GCCcore-10.3.0.eb --- .../prodigal/prodigal-2.6.3-GCCcore-10.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..aa4d5c7ac03 --- /dev/null +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Updated: Pavel Grochal (INUITS) +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'prodigal' +version = '2.6.3' + +homepage = 'https://github.com/hyattpd/Prodigal/' + +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f'] + +builddependencies = [('binutils', '2.36.1')] + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +sanity_check_commands = ["prodigal -h"] + +moduleclass = 'bio' From a512250c9da843c9034173a364c4767de9480749 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 1 Dec 2021 10:20:39 +0100 Subject: [PATCH 2159/9987] adding easyconfigs: MUMmer-3.23-GCCcore-10.3.0.eb --- .../m/MUMmer/MUMmer-3.23-GCCcore-10.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..dea2fe421d7 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +## +# updated by: +# Adam Huffman +# The Francis Crick Institute + +name = 'MUMmer' +version = '3.23' + +homepage = 'http://mummer.sourceforge.net/' + +description = """ + MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f'] + +builddependencies = [('binutils', '2.36.1')] + +moduleclass = 'bio' From 9973e0dac1302d7b5c6bc30f65f8fcdb5828a91f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 1 Dec 2021 10:23:37 +0100 Subject: [PATCH 2160/9987] adding easyconfigs: FastANI-1.33-GCC-10.3.0.eb --- .../f/FastANI/FastANI-1.33-GCC-10.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-10.3.0.eb new file mode 100644 index 00000000000..b93bafcb428 --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-10.3.0.eb @@ -0,0 +1,45 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'ConfigureMake' + +name = 'FastANI' +version = '1.33' + +homepage = "https://github.com/ParBLiSS/FastANI" +description = """FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean + nucleotide identity of orthologous gene pairs shared between two microbial + genomes. FastANI supports pairwise comparison of both complete and draft + genome assemblies.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] +sources = ['v%(version)s.zip'] +patches = ['FastANI-1.2-memcpy.patch'] +checksums = [ + 'fb392ffa3c7942091a06de05c56c8e250523723c39da65ae8f245e65e440a74b', # v1.33.zip + 'eebcf0b64c31ee360ca79136f644157064ac69747ed13cff70f5c9932c6bb0d5', # FastANI-1.2-memcpy.patch +] + +builddependencies = [('Autotools', '20210128')] + +dependencies = [ + ('GSL', '2.7'), + ('zlib', '1.2.11'), +] + +preconfigopts = 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/fastANI'], + 'dirs': [] +} + +sanity_check_commands = ["fastANI --help"] + +moduleclass = 'bio' From f76b7a580d188f336306d3f3bf5f5e4f36f98f28 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 1 Dec 2021 10:30:28 +0100 Subject: [PATCH 2161/9987] adding easyconfigs: CheckM-1.1.3-foss-2021a.eb --- .../c/CheckM/CheckM-1.1.3-foss-2021a.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb new file mode 100644 index 00000000000..a7e58e823a7 --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb @@ -0,0 +1,64 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'CheckM' +version = '1.1.3' + +homepage = 'https://github.com/Ecogenomics/CheckM' +description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, + single cells, or metagenomes.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://pypi.python.org/packages/source/c/checkm-genome', + 'https://data.ace.uq.edu.au/public/CheckM_databases/', +] +sources = [ + 'checkm-genome-%(version)s.tar.gz', + { + 'filename': 'checkm_data_2015_01_16.tar.gz', + 'extract_cmd': "mkdir -p %(builddir)s/data && cd %(builddir)s/data && tar xfvz %s", + }, +] +checksums = [ + '7fda369783d3b7d6a7324ee33cc93ac3560fba509bf2139e920fa661e2b45644', # checkm-genome-1.1.3.tar.gz + '971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c', # checkm_data_2015_01_16.tar.gz +] + +# Dependencies: +# https://github.com/Ecogenomics/CheckM/blob/master/setup.py +dependencies = [ + ('Python', '3.9.5'), + ('pplacer', '1.1.alpha19', '', True), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('SciPy-bundle', '2021.05'), # numpy + ('matplotlib', '3.4.2'), + ('Pysam', '0.16.0.1'), + ('DendroPy', '4.5.2'), +] + +download_dep_fail = True +use_pip = True + +# also install CheckM databases, see https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm +postinstallcmds = [ + "cp -a %(builddir)s/data %(installdir)s", + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "%(installdir)s/bin/checkm data setRoot %(installdir)s/data", +] + +sanity_check_paths = { + 'files': ['bin/checkm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["checkm test %(builddir)s/checkm_test_results"] + +sanity_pip_check = True + +moduleclass = 'bio' From 58bb0b55e5526ce17e0e9770585802fb0b7b18f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 1 Dec 2021 11:15:13 +0100 Subject: [PATCH 2162/9987] adding easyconfigs: ANIcalculator-1.0-GCCcore-10.3.0.eb --- .../ANIcalculator-1.0-GCCcore-10.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e8d8dc56834 --- /dev/null +++ b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'ANIcalculator' +version = '1.0' + +homepage = 'https://ani.jgi.doe.gov/html/home.php' +description = """This tool will calculate the bidirectional average nucleotide identity (gANI) and +Alignment Fraction (AF) between two genomes. Required input is the full path to the fna file +(nucleotide sequence of genes in fasta format) of each query genome. Either the rRNA and tRNA genes +can be excluded, or provided in a list with the -ignoreList option. This is necessary as the presence +of tRNA and/or rRNA genes in the fna will artificially inflate the ANI.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://ani.jgi.doe.gov/download_files/'] +sources = ['%(name)s_v%(version_major)s.tgz'] +checksums = ['236596a9a204cbcad162fc66be3506b2530b1f48f4f84d9647ccec3ca7483a43'] + +dependencies = [ + ('Perl', '5.32.1'), +] + +skipsteps = ['build'] + +# The source tarball also includes Log4perl 1.44. +# Instead of copying this, we use the version from the Perl module. +files_to_copy = [(['ANIcalculator', 'nsimscan'], 'bin'), 'README.txt'] + +# Remove the execute permissions on the README.txt, which it has by default. +postinstallcmds = ['chmod -x %(installdir)s/README.txt'] + +sanity_check_paths = { + 'files': ['README.txt', 'bin/ANIcalculator', 'bin/nsimscan'], + 'dirs': [], +} + +sanity_check_commands = [ + 'ANIcalculator -help', + 'nsimscan -h', +] + +moduleclass = 'bio' From 73cadfc26596e317d60dd149b6e7d764934df111 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 1 Dec 2021 11:26:01 +0100 Subject: [PATCH 2163/9987] adding easyconfigs: dRep-3.0.0-foss-2021a.eb --- .../d/dRep/dRep-3.0.0-foss-2021a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb b/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb new file mode 100644 index 00000000000..3cf0ae38710 --- /dev/null +++ b/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'dRep' +version = '3.0.0' + +homepage = 'https://drep.readthedocs.io/en/latest/' +description = """dRep is a python program which performs rapid pair-wise comparison of genome sets. +One of it’s major purposes is for genome de-replication, but it can do a lot more.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/MrOlm/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('Seaborn', '0.11.2'), + ('matplotlib', '3.4.2'), + ('scikit-learn', '0.24.2'), + ('tqdm', '4.61.2'), + ('Mash', '2.3'), + ('MUMmer', '3.23'), + ('FastANI', '1.33'), + ('CheckM', '1.1.3'), + ('ANIcalculator', '1.0'), + ('prodigal', '2.6.3'), +] + +use_pip = True +sanity_pip_check = True + +local_binaries = ['dRep', 'parse_stb.py', 'ScaffoldLevel_dRep.py'] + +sanity_check_paths = { + 'files': ['bin/' + x for x in local_binaries], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = [x + ' -h' for x in local_binaries] + +moduleclass = 'bio' From 577d83db45b06759e0295791d8459fc780e610d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 1 Dec 2021 11:55:48 +0100 Subject: [PATCH 2164/9987] add checksum --- easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb b/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb index 3cf0ae38710..700941e4e5f 100644 --- a/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/MrOlm/%(namelower)s/archive'] sources = ['v%(version)s.tar.gz'] +checksums = ['d0746765b5f40ab6473cd860ed2a2e46b5508084afcf8b8389e91e7aeb66c6b1'] dependencies = [ ('Python', '3.9.5'), From ccfa4a2b5729c22c8aee6c29f80981fb07c67603 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 1 Dec 2021 13:22:04 +0200 Subject: [PATCH 2165/9987] adding easyconfigs: FMPy-0.3.2-foss-2021a.eb, PyOpenGL-3.1.5-GCCcore-10.3.0.eb, PyQtGraph-0.12.3-foss-2021a.eb, FMPy-0.3.2-foss-2021a.eb --- .../f/FMPy/FMPy-0.3.2-foss-2021a.eb | 81 +++++++++++++++++++ .../PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.3.0.eb | 43 ++++++++++ .../PyQtGraph/PyQtGraph-0.12.3-foss-2021a.eb | 30 +++++++ 3 files changed, 154 insertions(+) create mode 100644 easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.12.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb b/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb new file mode 100644 index 00000000000..4e8249a47d2 --- /dev/null +++ b/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb @@ -0,0 +1,81 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'FMPy' +version = '0.3.2' + +homepage = 'https://github.com/CATIA-Systems/FMPy' +description = "FMPy is a free Python library to simulate Functional Mock-up Units (FMUs)." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('lxml', '4.6.3'), + ('SciPy-bundle', '2021.05'), + ('dask', '2021.9.1'), + ('PyQt5', '5.15.4'), + ('PyQtGraph', '0.12.3'), + ('IPython', '7.25.0'), + ('plotly.py', '5.1.0'), + ('Flask', '1.1.4'), + ('Brotli', '1.0.9'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('lark-parser', '0.12.0', { + 'modulename': 'lark', + 'checksums': ['15967db1f1214013dca65b1180745047b9be457d73da224fcda3d9dd4e96a138'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('dash', '2.0.0', { + 'checksums': ['29277c24e2f795b069cb102ce1ab0cd3ad5cf9d3b4fd16c03da9671a5eea28a4'], + }), + ('dash-bootstrap-components', '1.0.0', { + 'source_tmpl': 'dash-bootstrap-components-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/dash-bootstrap-components/'], + 'checksums': ['498164307c3a05b295fcf92cc4e39a91f6eed5be6d960b03081feb8f791adf94'], + }), + ('dash-core-components', '2.0.0', { + 'source_tmpl': 'dash_core_components-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/dash-core-components/'], + 'checksums': ['c6733874af975e552f95a1398a16c2ee7df14ce43fa60bb3718a3c6e0b63ffee'], + }), + ('dash-html-components', '2.0.0', { + 'source_tmpl': 'dash_html_components-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/dash-html-components/'], + 'checksums': ['8703a601080f02619a6390998e0b3da4a5daabe97a1fd7a9cebc09d015f26e50'], + }), + ('dash-table', '5.0.0', { + 'source_tmpl': 'dash_table-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/dash-table/'], + 'checksums': ['18624d693d4c8ef2ddec99a6f167593437a7ea0bf153aa20f318c170c5bc7308'], + }), + ('Flask-Compress', '1.10.1', { + 'checksums': ['28352387efbbe772cfb307570019f81957a13ff718d994a9125fa705efb73680'], + }), + ('idna', '2.8', { + 'checksums': ['c357b3f628cf53ae2c4c05627ecc484553142ca23264e593d327bcde5e9c3407'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/CATIA-Systems/FMPy/archive/'], + 'use_pip_extras': 'complete', + 'checksums': ['d534d819972048557a44f797b1e2247961d871540b9dfae52e88ce6e49867296'], + }), +] + +sanity_check_commands = ["fmpy --help"] + +sanity_check_paths = { + 'files': ['bin/fmpy', 'bin/renderer'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..2081c55d0b4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-10.3.0.eb @@ -0,0 +1,43 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# Updated:: Denis Kristak (INUITS) +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'PyOpenGL' +version = '3.1.5' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4107ba0d0390da5766a08c242cf0cf3404c377ed293c5f6d701e457c57ba3424'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('bzip2', '1.0.8'), +] + +dependencies = [ + ('Mesa', '21.1.1'), + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'OpenGL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.12.3-foss-2021a.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.12.3-foss-2021a.eb new file mode 100644 index 00000000000..fef424d65b3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.12.3-foss-2021a.eb @@ -0,0 +1,30 @@ +# updated: Denis Kristak +easyblock = 'PythonPackage' +# TH77EMBL adapted from PyQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb +name = 'PyQtGraph' +version = '0.12.3' + +homepage = 'http://www.pyqtgraph.org/' +description = """PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +github_account = 'pyqtgraph' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['243df67ce5461e7f44afa19e351dc4f1bf08a231925b7cb4a2f232c6d71e8957'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyQt5', '5.15.4'), + ('PyOpenGL', '3.1.5'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'vis' From ea42dcdba51aeef62007dbca67091a22239badc4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 1 Dec 2021 12:51:32 +0100 Subject: [PATCH 2166/9987] add binutils as build dependency --- .../a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb index e8d8dc56834..3c331246313 100644 --- a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb @@ -16,6 +16,9 @@ source_urls = ['https://ani.jgi.doe.gov/download_files/'] sources = ['%(name)s_v%(version_major)s.tgz'] checksums = ['236596a9a204cbcad162fc66be3506b2530b1f48f4f84d9647ccec3ca7483a43'] +# A build dependency on binutils is required to pass the test suite. +builddependencies = [('binutils', '2.36.1')] + dependencies = [ ('Perl', '5.32.1'), ] From 8f7a198a6e8f12448c80490c5f65c5786021e969 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 1 Dec 2021 12:54:21 +0100 Subject: [PATCH 2167/9987] add comment about linux distro having to provide libnsl.so.1 --- .../a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb index 3c331246313..076153efd1a 100644 --- a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb @@ -1,3 +1,4 @@ +# This installation only works for Linux distributions that provide libnsl.so.1 as part of the (g)libc package. easyblock = 'MakeCp' name = 'ANIcalculator' From 7e24dace863f05fa6f6bb628b9ed17faca52ccf1 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 1 Dec 2021 12:00:12 +0000 Subject: [PATCH 2168/9987] Requirement of tbb-2020.3 added as comment in EC, easyconfigs.py updated to reflect this --- easybuild/easyconfigs/u/UShER/UShER-0.5.0-gompi-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UShER/UShER-0.5.0-gompi-2021b.eb b/easybuild/easyconfigs/u/UShER/UShER-0.5.0-gompi-2021b.eb index 0e0e02ad29e..925f3336791 100644 --- a/easybuild/easyconfigs/u/UShER/UShER-0.5.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/u/UShER/UShER-0.5.0-gompi-2021b.eb @@ -22,7 +22,7 @@ builddependencies = [ ('CMake', '3.21.1'), ] dependencies = [ - ('tbb', '2020.3'), + ('tbb', '2020.3'), # we need the older version as newer versions don't build ('protobuf', '3.17.3'), ('MAFFT', '7.490', '-with-extensions'), ('Boost', '1.77.0'), From 02bfdef2b2d48cc9ff4e886274b4a44a1e0646b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Wed, 1 Dec 2021 12:11:24 +0000 Subject: [PATCH 2169/9987] Add files via upload Updated easyconfigs.py to add exemption for TBB version checking for UShER --- easyconfigs.py | 1403 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 1403 insertions(+) create mode 100644 easyconfigs.py diff --git a/easyconfigs.py b/easyconfigs.py new file mode 100644 index 00000000000..9789392bcd0 --- /dev/null +++ b/easyconfigs.py @@ -0,0 +1,1403 @@ +## +# Copyright 2013-2021 Ghent University +# +# This file is part of EasyBuild, +# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), +# with support of Ghent University (http://ugent.be/hpc), +# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), +# Flemish Research Foundation (FWO) (http://www.fwo.be/en) +# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). +# +# https://github.com/easybuilders/easybuild +# +# EasyBuild is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation v2. +# +# EasyBuild is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with EasyBuild. If not, see . +## +""" +Unit tests for easyconfig files. + +@author: Kenneth Hoste (Ghent University) +""" +import glob +import os +import re +import shutil +import sys +import tempfile +from distutils.version import LooseVersion +from unittest import TestCase, TestLoader, main, skip + +import easybuild.main as eb_main +import easybuild.tools.options as eboptions +from easybuild.base import fancylogger +from easybuild.easyblocks.generic.configuremake import ConfigureMake +from easybuild.easyblocks.generic.pythonpackage import PythonPackage +from easybuild.framework.easyblock import EasyBlock +from easybuild.framework.easyconfig.default import DEFAULT_CONFIG +from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS +from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for +from easybuild.framework.easyconfig.easyconfig import resolve_template +from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig +from easybuild.framework.easyconfig.tools import check_sha256_checksums, dep_graph, get_paths_for, process_easyconfig +from easybuild.tools import config +from easybuild.tools.build_log import EasyBuildError +from easybuild.tools.config import GENERAL_CLASS, build_option +from easybuild.tools.filetools import change_dir, is_generic_easyblock, remove_file +from easybuild.tools.filetools import verify_checksum, which, write_file +from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version +from easybuild.tools.modules import modules_tool +from easybuild.tools.py2vs3 import string_type, urlopen +from easybuild.tools.robot import check_conflicts, resolve_dependencies +from easybuild.tools.run import run_cmd +from easybuild.tools.options import set_tmpdir +from easybuild.tools.utilities import nub + + +# indicates whether all the single tests are OK, +# and that bigger tests (building dep graph, testing for conflicts, ...) can be run as well +# other than optimizing for time, this also helps to get around problems like http://bugs.python.org/issue10949 +single_tests_ok = True + + +def is_pr(): + """Return true if run in a pull request CI""" + # $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR + travis_pr_test = re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST', '')) + + # when testing a PR in GitHub Actions, $GITHUB_EVENT_NAME will be set to 'pull_request' + github_pr_test = os.environ.get('GITHUB_EVENT_NAME') == 'pull_request' + return travis_pr_test or github_pr_test + + +def get_target_branch(): + """Return the target branch of a pull request""" + # target branch should be anything other than 'master'; + # usually is 'develop', but could also be a release branch like '3.7.x' + target_branch = os.environ.get('GITHUB_BASE_REF', None) + if not target_branch: + target_branch = os.environ.get('TRAVIS_BRANCH', None) + if not target_branch: + raise RuntimeError("Did not find a target branch") + return target_branch + + +def skip_if_not_pr_to_non_main_branch(): + if not is_pr(): + return skip("Only run for pull requests") + if get_target_branch() == "main": + return skip("Not run for pull requests against main") + return lambda func: func + + +def get_eb_files_from_diff(diff_filter): + """Return the files changed on HEAD relative to the current target branch""" + target_branch = get_target_branch() + + # relocate to top-level directory of repository to run 'git diff' command + top_dir = os.path.dirname(os.path.dirname(get_paths_for('easyconfigs')[0])) + cwd = change_dir(top_dir) + + # first determine the 'merge base' between target branch and PR branch + # cfr. https://git-scm.com/docs/git-merge-base + cmd = "git merge-base %s HEAD" % target_branch + out, ec = run_cmd(cmd, simple=False, log_ok=False) + if ec == 0: + merge_base = out.strip() + print("Merge base for %s and HEAD: %s" % (target_branch, merge_base)) + else: + msg = "Failed to determine merge base (ec: %s, output: '%s'), " + msg += "falling back to specifying target branch %s" + print(msg % (ec, out, target_branch)) + merge_base = target_branch + + # determine list of changed files using 'git diff' and merge base determined above + cmd = "git diff --name-only --diff-filter=%s %s..HEAD --" % (diff_filter, merge_base) + out, _ = run_cmd(cmd, simple=False) + files = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith('.eb')] + + change_dir(cwd) + return files + + +class EasyConfigTest(TestCase): + """Baseclass for easyconfig testcases.""" + + @classmethod + def setUpClass(cls): + """Setup environment for all tests. Called once!""" + # make sure that the EasyBuild installation is still known even if we purge an EB module + if os.getenv('EB_SCRIPT_PATH') is None: + eb_path = which('eb') + if eb_path is not None: + os.environ['EB_SCRIPT_PATH'] = eb_path + + # initialize configuration (required for e.g. default modules_tool setting) + eb_go = eboptions.parse_options(args=[]) # Ignore cmdline args as those are meant for the unittest framework + config.init(eb_go.options, eb_go.get_options_by_section('config')) + build_options = { + 'check_osdeps': False, + 'external_modules_metadata': {}, + 'force': True, + 'local_var_naming_check': 'error', + 'optarch': 'test', + 'robot_path': get_paths_for("easyconfigs")[0], + 'silent': True, + 'suffix_modules_path': GENERAL_CLASS, + 'valid_module_classes': config.module_classes(), + 'valid_stops': [x[0] for x in EasyBlock.get_steps()], + } + config.init_build_options(build_options=build_options) + set_tmpdir() + + # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains + cls.TMPDIR = tempfile.mkdtemp() + os.environ['MODULEPATH'] = cls.TMPDIR + write_file(os.path.join(cls.TMPDIR, 'craype-test'), '#%Module\n') + + log = fancylogger.getLogger("EasyConfigTest", fname=False) + + # make sure a logger is present for main + eb_main._log = log + + cls._ordered_specs = None + cls._parsed_easyconfigs = [] + cls._parsed_all_easyconfigs = False + cls._changed_ecs = None # ECs changed in a PR + + @classmethod + def tearDownClass(cls): + """Cleanup after running all tests""" + shutil.rmtree(cls.TMPDIR) + + @classmethod + def parse_all_easyconfigs(cls): + """Parse all easyconfigs.""" + if cls._parsed_all_easyconfigs: + return + # all available easyconfig files + easyconfigs_path = get_paths_for("easyconfigs")[0] + specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) + parsed_specs = set(ec['spec'] for ec in cls._parsed_easyconfigs) + for spec in specs: + if spec not in parsed_specs: + cls._parsed_easyconfigs.extend(process_easyconfig(spec)) + cls._parsed_all_easyconfigs = True + + @classmethod + def resolve_all_dependencies(cls): + """Resolve dependencies between easyconfigs""" + # Parse all easyconfigs if not done yet + cls.parse_all_easyconfigs() + # filter out external modules + for ec in cls._parsed_easyconfigs: + for dep in ec['dependencies'][:]: + if dep.get('external_module', False): + ec['dependencies'].remove(dep) + cls._ordered_specs = resolve_dependencies( + cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True) + + def _get_changed_easyconfigs(self): + """Gather all added or modified easyconfigs""" + # get list of changed easyconfigs + changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M') + added_ecs_filenames = get_eb_files_from_diff(diff_filter='A') + if changed_ecs_filenames: + print("\nList of changed easyconfig files in this PR:\n\t%s" % '\n\t'.join(changed_ecs_filenames)) + if added_ecs_filenames: + print("\nList of added easyconfig files in this PR:\n\t%s" % '\n\t'.join(added_ecs_filenames)) + EasyConfigTest._changed_ecs_filenames = changed_ecs_filenames + EasyConfigTest._added_ecs_filenames = added_ecs_filenames + + # grab parsed easyconfigs for changed easyconfig files + changed_ecs = [] + for ec_fn in changed_ecs_filenames + added_ecs_filenames: + match = None + for ec in self.parsed_easyconfigs: + if os.path.basename(ec['spec']) == ec_fn: + match = ec['ec'] + break + + if match: + changed_ecs.append(match) + else: + # if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR... + # so as a last resort, try to find the easyconfig file in __archive__ + easyconfigs_path = get_paths_for("easyconfigs")[0] + specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn)) + if len(specs) == 1: + ec = process_easyconfig(specs[0])[0] + changed_ecs.append(ec['ec']) + else: + raise RuntimeError("Failed to find parsed easyconfig for %s" + " (and could not isolate it in easyconfigs archive either)" % ec_fn) + EasyConfigTest._changed_ecs = changed_ecs + + @property + def parsed_easyconfigs(self): + # parse all easyconfigs if they haven't been already + EasyConfigTest.parse_all_easyconfigs() + return EasyConfigTest._parsed_easyconfigs + + @property + def ordered_specs(self): + # Resolve dependencies if not done + if EasyConfigTest._ordered_specs is None: + EasyConfigTest.resolve_all_dependencies() + return EasyConfigTest._ordered_specs + + @property + def changed_ecs_filenames(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._changed_ecs_filenames + + @property + def added_ecs_filenames(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._added_ecs_filenames + + @property + def changed_ecs(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._changed_ecs + + def test_dep_graph(self): + """Unit test that builds a full dependency graph.""" + # pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6 + if LooseVersion(sys.version) >= LooseVersion('2.6') and single_tests_ok: + # temporary file for dep graph + (hn, fn) = tempfile.mkstemp(suffix='.dot') + os.close(hn) + + dep_graph(fn, self.ordered_specs) + + remove_file(fn) + else: + print("(skipped dep graph test)") + + def test_conflicts(self): + """Check whether any conflicts occur in software dependency graphs.""" + + if not single_tests_ok: + print("(skipped conflicts test)") + return + + self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False), + "No conflicts detected") + + def check_dep_vars(self, gen, dep, dep_vars): + """Check whether available variants of a particular dependency are acceptable or not.""" + + # 'guilty' until proven 'innocent' + res = False + + # filter out wrapped Java versions + # i.e. if the version of one is a prefix of the version of the other one (e.g. 1.8 & 1.8.0_181) + if dep == 'Java': + dep_vars_to_check = sorted(dep_vars.keys()) + + retained_dep_vars = [] + + while dep_vars_to_check: + dep_var = dep_vars_to_check.pop() + dep_var_version = dep_var.split(';')[0] + + # remove dep vars wrapped by current dep var + dep_vars_to_check = [x for x in dep_vars_to_check if not x.startswith(dep_var_version + '.')] + + retained_dep_vars = [x for x in retained_dep_vars if not x.startswith(dep_var_version + '.')] + + retained_dep_vars.append(dep_var) + + for key in list(dep_vars.keys()): + if key not in retained_dep_vars: + del dep_vars[key] + + # filter out binutils with empty versionsuffix which is used to build toolchain compiler + if dep == 'binutils' and len(dep_vars) > 1: + empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')] + if len(empty_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0]) + + # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools; + # same goes for WRF and WPS + for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS')]: + if dep == dep_name and len(dep_vars) > 1: + for key in list(dep_vars): + ecs = dep_vars[key] + # filter out dep variants that are only used as dependency for parent with same version + dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') + if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: + dep_vars.pop(key) + + # multiple versions of Boost is OK as long as they are deps for a matching Boost.Python + if dep == 'Boost' and len(dep_vars) > 1: + for key in list(dep_vars): + ecs = dep_vars[key] + # filter out Boost variants that are only used as dependency for Boost.Python with same version + boost_ver = re.search('^version: (?P[^;]+);', key).group('ver') + if all(ec.startswith('Boost.Python-%s-' % boost_ver) for ec in ecs): + dep_vars.pop(key) + + # filter out Perl with -minimal versionsuffix which are only used in makeinfo-minimal + if dep == 'Perl': + minimal_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -minimal')] + if len(minimal_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != minimal_vsuff_vars[0]) + + # filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains + if dep in ['FFTW', 'imkl']: + serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] + if len(serial_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) + + # filter out BLIS and libFLAME with -amd versionsuffix + # (AMD forks, used in gobff/*-amd toolchains) + if dep in ['BLIS', 'libFLAME']: + amd_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -amd')] + if len(amd_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != amd_vsuff_vars[0]) + + # filter out ScaLAPACK with -BLIS-* versionsuffix, used in goblf toolchain + if dep == 'ScaLAPACK': + blis_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -BLIS-' in v] + if len(blis_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != blis_vsuff_vars[0]) + + if dep == 'ScaLAPACK': + # filter out ScaLAPACK with -bf versionsuffix, used in gobff toolchain + bf_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bf' in v] + if len(bf_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bf_vsuff_vars[0]) + # filter out ScaLAPACK with -bl versionsuffix, used in goblf toolchain + bl_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bl' in v] + if len(bl_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bl_vsuff_vars[0]) + + # filter out HDF5 with -serial versionsuffix which is used in HDF5 for Python (h5py) + if dep in ['HDF5']: + serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] + if len(serial_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) + + # for some dependencies, we allow exceptions for software that depends on a particular version, + # as long as that's indicated by the versionsuffix + versionsuffix_deps = ['ASE', 'Boost', 'CUDAcore', 'Java', 'Lua', + 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] + if dep in versionsuffix_deps and len(dep_vars) > 1: + + # check for '-CUDA-*' versionsuffix for CUDAcore dependency + if dep == 'CUDAcore': + dep = 'CUDA' + + for key in list(dep_vars): + dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') + # use version of Java wrapper rather than full Java version + if dep == 'Java': + dep_ver = '.'.join(dep_ver.split('.')[:2]) + # filter out dep version if all easyconfig filenames using it include specific dep version + if all(re.search('-%s-%s' % (dep, dep_ver), v) for v in dep_vars[key]): + dep_vars.pop(key) + # always retain at least one dep variant + if len(dep_vars) == 1: + break + + # filter R dep for a specific version of Python 2.x + if dep == 'R' and len(dep_vars) > 1: + for key in list(dep_vars): + if '; versionsuffix: -Python-2' in key: + dep_vars.pop(key) + # always retain at least one variant + if len(dep_vars) == 1: + break + + # filter out variants that are specific to a particular version of CUDA + cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] + if len(dep_vars) >= len(cuda_dep_vars) and len(dep_vars) > 1: + for key in list(dep_vars): + if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key): + dep_vars.pop(key) + # always retain at least one dep variant + if len(dep_vars) == 1: + break + + # some software packages require a specific (older/newer) version of a particular dependency + old_dep_versions = { + # EMAN2 2.3 requires Boost(.Python) 1.64.0 + 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], + 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], + # VMTK 1.4.x requires ITK 4.13.x + 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], + # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) + 'Jellyfish': [(r'1\.', [r'Kraken-1\.', r'Roary-3\.12\.0', r'metaWRAP-1\.2'])], + # Libint 1.1.6 is required by older CP2K versions + 'Libint': [(r'1\.1\.6', [r'CP2K-[3-6]'])], + # libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, horton, PySCF, WIEN2k + # (Qiskit depends on PySCF), Elk 7.x requires libxc >= 5 + 'libxc': [ + (r'[23]\.', [r'ABINIT-', r'AtomPAW-', r'CP2K-', r'GPAW-', r'horton-', + r'PySCF-', r'Qiskit-', r'WIEN2k-']), + (r'5\.', [r'Elk-']), + ], + # some software depends on numba, which typically requires an older LLVM; + # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy + 'LLVM': [ + # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) + (r'8\.', [r'numba-0\.47\.0-', r'librosa-0\.7\.2-', r'BirdNET-20201214-', + r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[346]\.[23]']), + (r'10\.0\.1', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', + r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', + r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), + ], + 'Lua': [ + # SimpleITK 2.1.0 requires Lua 5.3.x, MedPy and nnU-Net depend on SimpleITK + (r'5\.3\.5', [r'nnU-Net-1\.7\.0-', r'MedPy-0\.4\.0-', r'SimpleITK-2\.1\.0-']), + ], + # TensorFlow 2.5+ requires a more recent NCCL than version 2.4.8 used in 2019b generation; + # Horovod depends on TensorFlow, so same exception required there + 'NCCL': [(r'2\.11\.4', [r'TensorFlow-2\.[5-9]\.', r'Horovod-0\.2[2-9]'])], + # rampart requires nodejs > 10, artic-ncov2019 requires rampart + 'nodejs': [('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13'])], + # some software depends on an older numba; + # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy + 'numba': [ + (r'0\.52\.0', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', + r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', + r'umap-learn-0\.4\.6-']), + ], + # OPERA requires SAMtools 0.x + 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', + r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], + # NanoPlot, NanoComp use an older version of Seaborn + 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], + 'TensorFlow': [ + # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), + # artic-ncov2019 requires medaka + ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), + # medaka 1.1.* and 1.2.* requires TensorFlow 2.2.0 + # (while other 2019b easyconfigs use TensorFlow 2.1.0 as dep); + # TensorFlow 2.2.0 is also used as a dep for Horovod 0.19.5; + # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 + ('2.2.0;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'Horovod-0.19.5-', 'decona-0.1.2-', + 'NGSpeciesID-0.1.1.1-']), + # medaka 1.4.3 (foss/2019b) depends on TensorFlow 2.2.2 + ('2.2.2;', ['medaka-1.4.3-']), + # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka + ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), + ], + # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 + # (for 2021b, UCX was updated to v1.11.2) + 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], + # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, + # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; + # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 + 'Pysam': [('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', + 'NGSpeciesID-0.1.1.1-'])], + # UShER requires tbb-2020.3 as newer versions will not build + 'tbb': [('2020.3', ['UShER-0.5.0-'])], + } + if dep in old_dep_versions and len(dep_vars) > 1: + for key in list(dep_vars): + for version_pattern, parents in old_dep_versions[dep]: + # filter out known old dependency versions + if re.search('^version: %s' % version_pattern, key): + # only filter if the easyconfig using this dep variants is known + if all(any(re.search(p, x) for p in parents) for x in dep_vars[key]): + dep_vars.pop(key) + + # filter out ELSI variants with -PEXSI suffix + if dep == 'ELSI' and len(dep_vars) > 1: + pexsi_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -PEXSI')] + if len(pexsi_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != pexsi_vsuff_vars[0]) + + # only single variant is always OK + if len(dep_vars) == 1: + res = True + + elif len(dep_vars) == 2 and dep in ['Python', 'Tkinter']: + # for Python & Tkinter, it's OK to have on 2.x and one 3.x version + v2_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 2.')] + v3_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 3.')] + if len(v2_dep_vars) == 1 and len(v3_dep_vars) == 1: + res = True + + # two variants is OK if one is for Python 2.x and the other is for Python 3.x (based on versionsuffix) + elif len(dep_vars) == 2: + py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] + py3_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-3.' in x] + if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: + res = True + + # for recent generations, there's no versionsuffix anymore for Python 3, + # but we still allow variants depending on Python 2.x + 3.x + is_recent_gen = False + full_toolchain_regex = re.compile(r'^20[1-9][0-9][ab]$') + gcc_toolchain_regex = re.compile(r'^GCC(core)?-[0-9]?[0-9]\.[0-9]$') + if full_toolchain_regex.match(gen): + is_recent_gen = LooseVersion(gen) >= LooseVersion('2020b') + elif gcc_toolchain_regex.match(gen): + genver = gen.split('-', 1)[1] + is_recent_gen = LooseVersion(genver) >= LooseVersion('10.2') + else: + raise EasyBuildError("Unkown type of toolchain generation: %s" % gen) + + if is_recent_gen: + py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] + py3_dep_vars = [x for x in dep_vars.keys() if x.strip().endswith('; versionsuffix:')] + if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: + res = True + + return res + + def test_check_dep_vars(self): + """Test check_dep_vars utility method.""" + + # one single dep version: OK + self.assertTrue(self.check_dep_vars('2019b', 'testdep', { + 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], + })) + self.assertTrue(self.check_dep_vars('2019b', 'testdep', { + 'version: 1.2.3; versionsuffix: -test': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], + })) + + # two or more dep versions (no special case: not OK) + self.assertFalse(self.check_dep_vars('2019b', 'testdep', { + 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], + })) + self.assertFalse(self.check_dep_vars('2019b', 'testdep', { + 'version: 0.0; versionsuffix:': ['foobar-0.0.eb'], + 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], + })) + + # Java is a special case, with wrapped Java versions + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + })) + # two Java wrappers is not OK + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], + })) + # OK to have two or more wrappers if versionsuffix is used to indicate exception + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + })) + # versionsuffix must be there for all easyconfigs to indicate exception + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], + })) + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 12.1.6; versionsuffix:': ['foobar-0.0-Java-12.eb'], + 'version: 12; versionsuffix:': ['foobar-0.0-Java-12.eb'], + })) + + # strange situation: odd number of Java versions + # not OK: two Java wrappers (and no versionsuffix to indicate exception) + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], + })) + # OK because of -Java-11 versionsuffix + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + })) + # not OK: two Java wrappers (and no versionsuffix to indicate exception) + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], + })) + # OK because of -Java-11 versionsuffix + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + })) + + # two different versions of Boost is not OK + self.assertFalse(self.check_dep_vars('2019b', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + + # a different Boost version that is only used as dependency for a matching Boost.Python is fine + self.assertTrue(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + self.assertTrue(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], + 'version: 1.66.0; versionsuffix:': ['Boost.Python-1.66.0-gompi-2019a.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + self.assertFalse(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], + 'version: 1.66.0; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + + self.assertTrue(self.check_dep_vars('2018a', 'Boost', { + 'version: 1.63.0; versionsuffix: -Python-2.7.14': ['EMAN2-2.21a-foss-2018a-Python-2.7.14-Boost-1.63.0.eb'], + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2018a.eb'], + 'version: 1.66.0; versionsuffix:': ['BLAST+-2.7.1-foss-2018a.eb'], + })) + + self.assertTrue(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': [ + 'Boost.Python-1.64.0-gompi-2019a.eb', + 'EMAN2-2.3-foss-2019a-Python-2.7.15.eb', + ], + 'version: 1.70.0; versionsuffix:': [ + 'BLAST+-2.9.0-gompi-2019a.eb', + 'Boost.Python-1.70.0-gompi-2019a.eb', + ], + })) + + # two variants is OK, if they're for Python 2.x and 3.x + self.assertTrue(self.check_dep_vars('2020a', 'Python', { + 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-2.7.18.eb'], + 'version: 3.8.2; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb'], + })) + + self.assertTrue(self.check_dep_vars('2020a', 'SciPy-bundle', { + 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], + 'version: 2020.03; versionsuffix: -Python-3.8.2': ['matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb'], + })) + + # for recent easyconfig generations, there's no versionsuffix anymore for Python 3 + self.assertTrue(self.check_dep_vars('2020b', 'Python', { + 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb'], + 'version: 3.8.6; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b.eb'], + })) + + self.assertTrue(self.check_dep_vars('GCCcore-10.2', 'PyYAML', { + 'version: 5.3.1; versionsuffix:': ['IPython-7.18.1-GCCcore-10.2.0.eb'], + 'version: 5.3.1; versionsuffix: -Python-2.7.18': ['IPython-7.18.1-GCCcore-10.2.0-Python-2.7.18.eb'], + })) + + self.assertTrue(self.check_dep_vars('2020b', 'SciPy-bundle', { + 'version: 2020.11; versionsuffix: -Python-2.7.18': ['matplotlib-3.3.3-foss-2020b-Python-2.7.18.eb'], + 'version: 2020.11; versionsuffix:': ['matplotlib-3.3.3-foss-2020b.eb'], + })) + + # not allowed for older generations (foss/intel 2020a or older, GCC(core) 10.1.0 or older) + self.assertFalse(self.check_dep_vars('2020a', 'SciPy-bundle', { + 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], + 'version: 2020.03; versionsuffix:': ['matplotlib-3.2.1-foss-2020a.eb'], + })) + + def test_dep_versions_per_toolchain_generation(self): + """ + Check whether there's only one dependency version per toolchain generation actively used. + This is enforced to try and limit the chance of running into conflicts when multiple modules built with + the same toolchain are loaded together. + """ + ecs_by_full_mod_name = dict((ec['full_mod_name'], ec) for ec in self.parsed_easyconfigs) + if len(ecs_by_full_mod_name) != len(self.parsed_easyconfigs): + self.fail('Easyconfigs with duplicate full_mod_name found') + + # Cache already determined dependencies + ec_to_deps = dict() + + def get_deps_for(ec): + """Get list of (direct) dependencies for specified easyconfig.""" + ec_mod_name = ec['full_mod_name'] + deps = ec_to_deps.get(ec_mod_name) + if deps is None: + deps = [] + for dep in ec['ec']['dependencies']: + dep_mod_name = dep['full_mod_name'] + deps.append((dep['name'], dep['version'], dep['versionsuffix'], dep_mod_name)) + # Note: Raises KeyError if dep not found + res = ecs_by_full_mod_name[dep_mod_name] + deps.extend(get_deps_for(res)) + ec_to_deps[ec_mod_name] = deps + + return deps + + # some software also follows {a,b} versioning scheme, + # which throws off the pattern matching done below for toolchain versions + false_positives_regex = re.compile('^MATLAB-Engine-20[0-9][0-9][ab]') + + # restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a) + # and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x + for pattern in ['20(1[89]|[2-9][0-9])[ab]', r'GCCcore-([7-9]|[1-9][0-9])\.[0-9]']: + all_deps = {} + regex = re.compile(r'^.*-(?P%s).*\.eb$' % pattern) + + # collect variants for all dependencies of easyconfigs that use a toolchain that matches + for ec in self.ordered_specs: + ec_file = os.path.basename(ec['spec']) + + # take into account software which also follows a {a,b} versioning scheme + ec_file = false_positives_regex.sub('', ec_file) + + res = regex.match(ec_file) + if res: + tc_gen = res.group('tc_gen') + all_deps_tc_gen = all_deps.setdefault(tc_gen, {}) + for dep_name, dep_ver, dep_versuff, dep_mod_name in get_deps_for(ec): + dep_variants = all_deps_tc_gen.setdefault(dep_name, {}) + # a variant is defined by version + versionsuffix + variant = "version: %s; versionsuffix: %s" % (dep_ver, dep_versuff) + # keep track of which easyconfig this is a dependency + dep_variants.setdefault(variant, set()).add(ec_file) + + # check which dependencies have more than 1 variant + multi_dep_vars, multi_dep_vars_msg = [], '' + for tc_gen in sorted(all_deps.keys()): + for dep in sorted(all_deps[tc_gen].keys()): + dep_vars = all_deps[tc_gen][dep] + if not self.check_dep_vars(tc_gen, dep, dep_vars): + multi_dep_vars.append(dep) + multi_dep_vars_msg += "\nfound %s variants of '%s' dependency " % (len(dep_vars), dep) + multi_dep_vars_msg += "in easyconfigs using '%s' toolchain generation\n* " % tc_gen + multi_dep_vars_msg += '\n* '.join("%s as dep for %s" % v for v in sorted(dep_vars.items())) + multi_dep_vars_msg += '\n' + + error_msg = "No multi-variant deps found for '%s' easyconfigs:\n%s" % (regex.pattern, multi_dep_vars_msg) + self.assertFalse(multi_dep_vars, error_msg) + + def test_sanity_check_paths(self): + """Make sure specified sanity check paths adher to the requirements.""" + + for ec in self.parsed_easyconfigs: + ec_scp = ec['ec']['sanity_check_paths'] + if ec_scp != {}: + # if sanity_check_paths is specified (i.e., non-default), it must adher to the requirements + # both 'files' and 'dirs' keys, both with list values and with at least one a non-empty list + error_msg = "sanity_check_paths for %s does not meet requirements: %s" % (ec['spec'], ec_scp) + self.assertEqual(sorted(ec_scp.keys()), ['dirs', 'files'], error_msg) + self.assertTrue(isinstance(ec_scp['dirs'], list), error_msg) + self.assertTrue(isinstance(ec_scp['files'], list), error_msg) + self.assertTrue(ec_scp['dirs'] or ec_scp['files'], error_msg) + + def test_r_libs_site_env_var(self): + """Make sure $R_LIBS_SITE is being updated, rather than $R_LIBS.""" + # cfr. https://github.com/easybuilders/easybuild-easyblocks/pull/2326 + + r_libs_ecs = [] + for ec in self.parsed_easyconfigs: + for key in ('modextrapaths', 'modextravars'): + if 'R_LIBS' in ec['ec'][key]: + r_libs_ecs.append(ec['spec']) + + error_msg = "%d easyconfigs found which set $R_LIBS, should be $R_LIBS_SITE: %s" + self.assertEqual(r_libs_ecs, [], error_msg % (len(r_libs_ecs), ', '.join(r_libs_ecs))) + + def test_easyconfig_locations(self): + """Make sure all easyconfigs files are in the right location.""" + easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[0a-z]/[^/]+$') + topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) + for (dirpath, _, filenames) in os.walk(topdir): + # ignore git/svn dirs & archived easyconfigs + if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: + continue + # check whether list of .eb files is non-empty + easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] + if easyconfig_files: + # check whether path matches required pattern + if not easyconfig_dirs_regex.search(dirpath): + # only exception: TEMPLATE.eb + if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): + self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_sha256_checksums(self): + """Make sure changed easyconfigs have SHA256 checksums in place.""" + + # list of software for which checksums can not be required, + # e.g. because 'source' files need to be constructed manually + whitelist = [ + 'Kent_tools-*', + 'MATLAB-*', + 'OCaml-*', + 'OpenFOAM-Extend-4.1-*', + # sources for old versions of Bioconductor packages are no longer available, + # so not worth adding checksums for at this point + 'R-bundle-Bioconductor-3.[2-5]', + ] + + # the check_sha256_checksums function (again) creates an EasyBlock instance + # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter + # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__; + # therefore, we need to reset 'sources' to an empty list here if Bundle is used... + # likewise for 'patches' and 'checksums' + for ec in self.changed_ecs: + if ec['easyblock'] in ['Bundle', 'PythonBundle', 'EB_OpenSSL_wrapper']: + ec['sources'] = [] + ec['patches'] = [] + ec['checksums'] = [] + + # filter out deprecated easyconfigs + retained_changed_ecs = [] + for ec in self.changed_ecs: + if not ec['deprecated']: + retained_changed_ecs.append(ec) + + checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) + self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_python_packages(self): + """Several checks for easyconfigs that install (bundles of) Python packages.""" + + # These packages do not support installation with 'pip' + whitelist_pip = [ + r'ESMPy-.*', + r'MATLAB-Engine-.*', + r'Meld-.*', + r'PyTorch-.*', + ] + + whitelist_pip_check = [ + r'Mako-1.0.4.*Python-2.7.12.*', + # no pip 9.x or newer for configparser easyconfigs using a 2016a or 2016b toolchain + r'configparser-3.5.0.*-2016[ab].*', + # mympirun is installed with system Python, pip may not be installed for system Python + r'vsc-mympirun.*', + ] + + failing_checks = [] + + python_default_urls = PythonPackage.extra_options()['source_urls'][0] + + for ec in self.changed_ecs: + + with ec.disable_templating(): + ec_fn = os.path.basename(ec.path) + easyblock = ec.get('easyblock') + exts_defaultclass = ec.get('exts_defaultclass') + exts_default_options = ec.get('exts_default_options', {}) + + download_dep_fail = ec.get('download_dep_fail') + exts_download_dep_fail = ec.get('exts_download_dep_fail') + use_pip = ec.get('use_pip') + if use_pip is None: + use_pip = exts_default_options.get('use_pip') + + # only easyconfig parameters as they are defined in the easyconfig file, + # does *not* include other easyconfig parameters with their default value! + pure_ec = ec.parser.get_config_dict() + + # download_dep_fail should be set when using PythonPackage + if easyblock == 'PythonPackage': + if download_dep_fail is None: + failing_checks.append("'download_dep_fail' should be set in %s" % ec_fn) + + if pure_ec.get('source_urls') == python_default_urls: + failing_checks.append("'source_urls' should not be defined when using the default value " + "in %s" % ec_fn) + + # use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs) + if easyblock in ['PythonBundle', 'PythonPackage']: + if use_pip is None and not any(re.match(regex, ec_fn) for regex in whitelist_pip): + failing_checks.append("'use_pip' should be set in %s" % ec_fn) + + # download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set + if easyblock == 'PythonBundle': + if download_dep_fail or exts_download_dep_fail: + fail = "'*download_dep_fail' should not be set in %s since PythonBundle easyblock is used" % ec_fn + failing_checks.append(fail) + if pure_ec.get('exts_default_options', {}).get('source_urls') == python_default_urls: + failing_checks.append("'source_urls' should not be defined in exts_default_options when using " + "the default value in %s" % ec_fn) + + elif exts_defaultclass == 'PythonPackage': + # bundle of Python packages should use PythonBundle + if easyblock == 'Bundle': + fail = "'PythonBundle' easyblock should be used for bundle of Python packages in %s" % ec_fn + failing_checks.append(fail) + else: + # both download_dep_fail and use_pip should be set via exts_default_options + # when installing Python packages as extensions + for key in ['download_dep_fail', 'use_pip']: + if exts_default_options.get(key) is None: + failing_checks.append("'%s' should be set in exts_default_options in %s" % (key, ec_fn)) + + # if Python is a dependency, that should be reflected in the versionsuffix + # Tkinter is an exception, since its version always matches the Python version anyway + # Python 3.8.6 and later are also excluded, as we consider python 3 the default python + # Also whitelist some updated versions of Amber + whitelist_python_suffix = [ + 'Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', + 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb', + 'R-keras-2.1.6-foss-2018a-R-3.4.4.eb', + ] + whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix) + has_python_dep = any(LooseVersion(dep['version']) < LooseVersion('3.8.6') + for dep in ec['dependencies'] if dep['name'] == 'Python') + if has_python_dep and ec.name != 'Tkinter' and not whitelisted: + if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): + msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn + # This is only a failure for newly added ECs, not for existing ECS + # As that would probably break many ECs + if ec_fn in self.added_ecs_filenames: + failing_checks.append(msg) + else: + print('\nNote: Failed non-critical check: ' + msg) + else: + has_recent_python3_dep = any(LooseVersion(dep['version']) >= LooseVersion('3.8.6') + for dep in ec['dependencies'] if dep['name'] == 'Python') + if has_recent_python3_dep and re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): + msg = "'-Python-%%(pyver)s' should no longer be included in versionsuffix in %s" % ec_fn + failing_checks.append(msg) + + # require that running of "pip check" during sanity check is enabled via sanity_pip_check + if easyblock in ['PythonBundle', 'PythonPackage']: + sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check') + if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip_check): + failing_checks.append("sanity_pip_check should be enabled in %s" % ec_fn) + + if failing_checks: + self.fail('\n'.join(failing_checks)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_R_packages(self): + """Several checks for easyconfigs that install (bundles of) R packages.""" + failing_checks = [] + + for ec in self.changed_ecs: + ec_fn = os.path.basename(ec.path) + exts_defaultclass = ec.get('exts_defaultclass') + if exts_defaultclass == 'RPackage' or ec.name == 'R': + seen_exts = set() + for ext in ec['exts_list']: + if isinstance(ext, (tuple, list)): + ext_name = ext[0] + else: + ext_name = ext + if ext_name in seen_exts: + failing_checks.append('%s was added multiple times to exts_list in %s' % (ext_name, ec_fn)) + else: + seen_exts.add(ext_name) + self.assertFalse(failing_checks, '\n'.join(failing_checks)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_sanity_check_paths(self): + """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" + + # some generic easyblocks already have a decent customised sanity_check_paths, + # including CMakePythonPackage, GoPackage, PythonBundle & PythonPackage; + # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. + whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'ModuleRC', + 'PythonBundle', 'PythonPackage', 'Toolchain'] + # Bundles of dependencies without files of their own + # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, + # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co + bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle'] + + failing_checks = [] + + for ec in self.changed_ecs: + + easyblock = ec.get('easyblock') + + if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): + if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): + pass + else: + ec_fn = os.path.basename(ec.path) + failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) + + self.assertFalse(failing_checks, '\n'.join(failing_checks)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_https(self): + """Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://).""" + + whitelist = [ + 'Kaiju', # invalid certificate at https://kaiju.binf.ku.dk + 'libxml2', # https://xmlsoft.org works, but invalid certificate + 'p4vasp', # https://www.p4vasp.at doesn't work + 'ITSTool', # https://itstool.org/ doesn't work + 'UCX-', # bad certificate for https://www.openucx.org + 'MUMPS', # https://mumps.enseeiht.fr doesn't work + 'PyFR', # https://www.pyfr.org doesn't work + 'PycURL', # bad certificate for https://pycurl.io/ + ] + url_whitelist = [ + # https:// doesn't work, results in index page being downloaded instead + # (see https://github.com/easybuilders/easybuild-easyconfigs/issues/9692) + 'http://isl.gforge.inria.fr', + # https:// leads to File Not Found + 'http://tau.uoregon.edu/', + # https:// has outdated SSL configurations + 'http://faculty.scs.illinois.edu', + ] + # Cache: Mapping of already checked HTTP urls to whether the HTTPS variant works + checked_urls = dict() + + def check_https_url(http_url): + """Check if the https url works""" + http_url = http_url.rstrip('/') # Remove trailing slashes + https_url_works = checked_urls.get(http_url) + if https_url_works is None: + https_url = http_url.replace('http://', 'https://') + try: + https_url_works = bool(urlopen(https_url, timeout=5)) + except Exception: + https_url_works = False + checked_urls[http_url] = https_url_works + + http_regex = re.compile('http://[^"\'\n]+', re.M) + + failing_checks = [] + for ec in self.changed_ecs: + ec_fn = os.path.basename(ec.path) + + # skip whitelisted easyconfigs + if any(ec_fn.startswith(x) for x in whitelist): + continue + + # ignore commented out lines in easyconfig files when checking for http:// URLs + ec_txt = '\n'.join(line for line in ec.rawtxt.split('\n') if not line.startswith('#')) + + for http_url in http_regex.findall(ec_txt): + + # skip whitelisted http:// URLs + if any(http_url.startswith(x) for x in url_whitelist): + continue + + if check_https_url(http_url): + failing_checks.append("Found http:// URL in %s, should be https:// : %s" % (ec_fn, http_url)) + if failing_checks: + self.fail('\n'.join(failing_checks)) + + +def template_easyconfig_test(self, spec): + """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" + + # set to False, so it's False in case of this test failing + global single_tests_ok + prev_single_tests_ok = single_tests_ok + single_tests_ok = False + + # parse easyconfig + ecs = process_easyconfig(spec) + if len(ecs) == 1: + ec = ecs[0]['ec'] + + # cache the parsed easyconfig, to avoid that it is parsed again + EasyConfigTest._parsed_easyconfigs.append(ecs[0]) + else: + self.assertTrue(False, "easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) + + # check easyconfig file name + expected_fn = '%s-%s.eb' % (ec['name'], det_full_ec_version(ec)) + msg = "Filename '%s' of parsed easyconfig matches expected filename '%s'" % (spec, expected_fn) + self.assertEqual(os.path.basename(spec), expected_fn, msg) + + name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) + + # make sure easyconfig file is in expected location + expected_subdir = os.path.join('easybuild', 'easyconfigs', letter_dir_for(name), name) + subdir = os.path.join(*spec.split(os.path.sep)[-5:-1]) + fail_msg = "Easyconfig file %s not in expected subdirectory %s" % (spec, expected_subdir) + self.assertEqual(expected_subdir, subdir, fail_msg) + + # sanity check for software name, moduleclass + self.assertEqual(ec['name'], name) + self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) + + # instantiate easyblock with easyconfig file + app_class = get_easyblock_class(easyblock, name=name) + + # check that automagic fallback to ConfigureMake isn't done (deprecated behaviour) + fn = os.path.basename(spec) + error_msg = "%s relies on automagic fallback to ConfigureMake, should use easyblock = 'ConfigureMake' instead" % fn + self.assertTrue(easyblock or app_class is not ConfigureMake, error_msg) + + # dump the easyconfig file; + # this should be done before creating the easyblock instance (done below via app_class), + # because some easyblocks (like PythonBundle) modify easyconfig parameters at initialisation + handle, test_ecfile = tempfile.mkstemp() + os.close(handle) + + ec.dump(test_ecfile) + dumped_ec = EasyConfigParser(test_ecfile).get_config_dict() + os.remove(test_ecfile) + + app = app_class(ec) + + # more sanity checks + self.assertTrue(name, app.name) + self.assertTrue(ec['version'], app.version) + + # make sure that deprecated 'dummy' toolchain is no longer used, should use 'system' toolchain instead + # but give recent EasyBuild easyconfigs special treatment to avoid breaking "eb --install-latest-eb-release" + ec_fn = os.path.basename(spec) + if not (ec_fn == 'EasyBuild-3.9.4.eb' or ec_fn.startswith('EasyBuild-4.')): + error_msg_tmpl = "%s should use 'system' toolchain rather than deprecated 'dummy' toolchain" + self.assertFalse(ec['toolchain']['name'] == 'dummy', error_msg_tmpl % os.path.basename(spec)) + + # make sure that $root is not used, since it is not compatible with module files in Lua syntax + res = re.findall(r'.*\$root.*', ec.rawtxt, re.M) + error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" + self.assertFalse(res, error_msg % res) + + # check for redefined easyconfig parameters, there should be none... + param_def_regex = re.compile(r'^(?P\w+)\s*=', re.M) + keys = param_def_regex.findall(ec.rawtxt) + redefined_keys = [] + for key in sorted(nub(keys)): + cnt = keys.count(key) + if cnt > 1: + redefined_keys.append((key, cnt)) + + redefined_keys_error_msg = "There should be no redefined easyconfig parameters, found %d: " % len(redefined_keys) + redefined_keys_error_msg += ', '.join('%s (%d)' % x for x in redefined_keys) + + self.assertFalse(redefined_keys, redefined_keys_error_msg) + + # make sure old GitHub urls for EasyBuild that include 'hpcugent' are no longer used + old_urls = [ + 'github.com/hpcugent/easybuild', + 'hpcugent.github.com/easybuild', + 'hpcugent.github.io/easybuild', + ] + for old_url in old_urls: + self.assertFalse(old_url in ec.rawtxt, "Old URL '%s' not found in %s" % (old_url, spec)) + + # make sure binutils is included as a (build) dep if toolchain is GCCcore + if ec['toolchain']['name'] == 'GCCcore': + # with 'Tarball' easyblock: only unpacking, no building; Eigen is also just a tarball + requires_binutils = ec['easyblock'] not in ['Tarball'] and ec['name'] not in ['Eigen'] + + # let's also exclude the very special case where the system GCC is used as GCCcore, and only apply this + # exception to the dependencies of binutils (since we should eventually build a new binutils with GCCcore) + if ec['toolchain']['version'] == 'system': + binutils_complete_dependencies = ['M4', 'Bison', 'flex', 'help2man', 'zlib', 'binutils'] + requires_binutils &= bool(ec['name'] not in binutils_complete_dependencies) + + # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled) + requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) + + if requires_binutils: + # dependencies() returns both build and runtime dependencies + # in some cases, binutils can also be a runtime dep (e.g. for Clang) + # Also using GCC directly as a build dep is also allowed (it includes the correct binutils) + dep_names = [d['name'] for d in ec.dependencies()] + self.assertTrue('binutils' in dep_names or 'GCC' in dep_names, + "binutils or GCC is a build dep in %s: %s" % (spec, dep_names)) + + # make sure that OpenSSL wrapper is used rather than OS dependency, + # for easyconfigs using a 2021a (sub)toolchain or more recent common toolchain version + osdeps = ec['osdependencies'] + if osdeps: + # check whether any entry in osdependencies related to OpenSSL + openssl_osdep = False + for osdep in osdeps: + if isinstance(osdep, string_type): + osdep = [osdep] + if any('libssl' in x for x in osdep) or any('openssl' in x for x in osdep): + openssl_osdep = True + + if openssl_osdep: + tcname = ec['toolchain']['name'] + tcver = LooseVersion(ec['toolchain']['version']) + + gcc_subtc_2021a = tcname in ('GCCcore', 'GCC') and tcver > LooseVersion('10.3') + if gcc_subtc_2021a or (tcname in ('foss', 'gompi', 'iimpi', 'intel') and tcver >= LooseVersion('2021')): + self.assertFalse(openssl_osdep, "OpenSSL should not be listed as OS dependency in %s" % spec) + + src_cnt = len(ec['sources']) + patch_checksums = ec['checksums'][src_cnt:] + patch_checksums_cnt = len(patch_checksums) + + # make sure all patch files are available + specdir = os.path.dirname(spec) + specfn = os.path.basename(spec) + for idx, patch in enumerate(ec['patches']): + if isinstance(patch, (tuple, list)): + patch = patch[0] + + # only check actual patch files, not other files being copied via the patch functionality + patch_full = os.path.join(specdir, patch) + if patch.endswith('.patch'): + msg = "Patch file %s is available for %s" % (patch_full, specfn) + self.assertTrue(os.path.isfile(patch_full), msg) + + # verify checksum for each patch file + if idx < patch_checksums_cnt and (os.path.exists(patch_full) or patch.endswith('.patch')): + checksum = patch_checksums[idx] + error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch, ec_fn, checksum) + res = verify_checksum(patch_full, checksum) + self.assertTrue(res, error_msg) + + # make sure 'source' step is not being skipped, + # since that implies not verifying the checksum + error_msg = "'source' step should not be skipped in %s, since that implies not verifying checksums" % ec_fn + self.assertFalse(ec['checksums'] and ('source' in ec['skipsteps']), error_msg) + + for ext in ec['exts_list']: + if isinstance(ext, (tuple, list)) and len(ext) == 3: + + ext_name = ext[0] + + self.assertTrue(isinstance(ext[2], dict), "3rd element of extension spec is a dictionary") + + # fall back to assuming a single source file for an extension + src_cnt = len(ext[2].get('sources', [])) or 1 + + checksums = ext[2].get('checksums', []) + patch_checksums = checksums[src_cnt:] + + for idx, ext_patch in enumerate(ext[2].get('patches', [])): + if isinstance(ext_patch, (tuple, list)): + ext_patch = ext_patch[0] + + # only check actual patch files, not other files being copied via the patch functionality + ext_patch_full = os.path.join(specdir, ext_patch) + if ext_patch.endswith('.patch'): + msg = "Patch file %s is available for %s" % (ext_patch_full, specfn) + self.assertTrue(os.path.isfile(ext_patch_full), msg) + + # verify checksum for each patch file + if idx < patch_checksums_cnt and (os.path.exists(ext_patch_full) or ext_patch.endswith('.patch')): + checksum = patch_checksums[idx] + error_msg = "Invalid checksum for patch file %s for %s extension in %s: %s" + res = verify_checksum(ext_patch_full, checksum) + self.assertTrue(res, error_msg % (ext_patch, ext_name, ec_fn, checksum)) + + # check whether all extra_options defined for used easyblock are defined + extra_opts = app.extra_options() + for key in extra_opts: + self.assertTrue(key in app.cfg) + + app.close_log() + os.remove(app.logfile) + + # inject dummy values for templates that are only known at a later stage + dummy_template_values = { + 'builddir': '/dummy/builddir', + 'installdir': '/dummy/installdir', + 'parallel': '2', + } + ec.template_values.update(dummy_template_values) + + ec_dict = ec.parser.get_config_dict() + orig_toolchain = ec_dict['toolchain'] + for key in ec_dict: + # skip parameters for which value is equal to default value + orig_val = ec_dict[key] + if key in DEFAULT_CONFIG and orig_val == DEFAULT_CONFIG[key][0]: + continue + if key in extra_opts and orig_val == extra_opts[key][0]: + continue + if key not in DEFAULT_CONFIG and key not in extra_opts: + continue + + orig_val = resolve_template(ec_dict[key], ec.template_values) + dumped_val = resolve_template(dumped_ec[key], ec.template_values) + + # take into account that dumped value for *dependencies may include hard-coded subtoolchains + # if no easyconfig was found for the dependency with the 'parent' toolchain, + # if may get resolved using a subtoolchain, which is then hardcoded in the dumped easyconfig + if key in DEPENDENCY_PARAMETERS: + # number of dependencies should remain the same + self.assertEqual(len(orig_val), len(dumped_val)) + for orig_dep, dumped_dep in zip(orig_val, dumped_val): + # name should always match + self.assertEqual(orig_dep[0], dumped_dep[0]) + + # version should always match, or be a possibility from the version dict + if isinstance(orig_dep[1], dict): + self.assertTrue(dumped_dep[1] in orig_dep[1].values()) + else: + self.assertEqual(orig_dep[1], dumped_dep[1]) + + # 3rd value is versionsuffix; + if len(dumped_dep) >= 3: + # if no versionsuffix was specified in original dep spec, then dumped value should be empty string + if len(orig_dep) >= 3: + self.assertEqual(dumped_dep[2], orig_dep[2]) + else: + self.assertEqual(dumped_dep[2], '') + + # 4th value is toolchain spec + if len(dumped_dep) >= 4: + if len(orig_dep) >= 4: + self.assertEqual(dumped_dep[3], orig_dep[3]) + else: + # if a subtoolchain is specifed (only) in the dumped easyconfig, + # it should *not* be the same as the parent toolchain + self.assertNotEqual(dumped_dep[3], (orig_toolchain['name'], orig_toolchain['version'])) + + # take into account that for some string-valued easyconfig parameters (configopts & co), + # the easyblock may have injected additional values, which affects the dumped easyconfig file + elif isinstance(orig_val, string_type): + error_msg = "%s value '%s' should start with '%s'" % (key, dumped_val, orig_val) + self.assertTrue(dumped_val.startswith(orig_val), error_msg) + else: + error_msg = "%s value should be equal in original and dumped easyconfig: '%s' vs '%s'" + self.assertEqual(orig_val, dumped_val, error_msg % (key, orig_val, dumped_val)) + + # test passed, so set back to True + single_tests_ok = True and prev_single_tests_ok + + +def suite(loader=None): + """Return all easyblock initialisation tests.""" + def make_inner_test(spec_path): + def innertest(self): + template_easyconfig_test(self, spec_path) + return innertest + + # dynamically generate a separate test for each of the available easyconfigs + # define new inner functions that can be added as class methods to InitTest + easyconfigs_path = get_paths_for('easyconfigs')[0] + cnt = 0 + for (subpath, dirs, specs) in os.walk(easyconfigs_path, topdown=True): + + # ignore archived easyconfigs + if '__archive__' in dirs: + dirs.remove('__archive__') + + for spec in specs: + if spec.endswith('.eb') and spec != 'TEMPLATE.eb': + cnt += 1 + innertest = make_inner_test(os.path.join(subpath, spec)) + innertest.__doc__ = "Test for easyconfig %s" % spec + # double underscore so parsing tests are run first + innertest.__name__ = "test__parse_easyconfig_%s" % spec + setattr(EasyConfigTest, innertest.__name__, innertest) + + print("Found %s easyconfigs..." % cnt) + if not loader: + loader = TestLoader() + return loader.loadTestsFromTestCase(EasyConfigTest) + + +if __name__ == '__main__': + main() From b3c6ff3ea27e5430f1d3ecfd878d27c49d653897 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Dec 2021 15:27:03 +0100 Subject: [PATCH 2170/9987] adding easyconfigs: Boost-1.77.0-intel-compilers-2021.4.0.eb --- .../Boost-1.77.0-intel-compilers-2021.4.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..4872fadfc48 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb @@ -0,0 +1,30 @@ +name = 'Boost' +version = '1.77.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['5347464af5b14ac54bb945dc68f1dd7c56f0dad7262816b956138fc53bcc0131'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('ICU', '69.1'), +] + +preconfigopts = "sed -i 's/-static//g' tools/build/src/engine/build.sh && " +# fix test_toolset function so it works correctly for intel-linux toolset; +# see also https://github.com/boostorg/build/issues/647 +preconfigopts += "sed -i 's/{TOOLSET}/{B2_TOOLSET}/g' tools/build/src/engine/build.sh && " + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' From 51b64f973ab771753083567375a80c433ae71d7f Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 1 Dec 2021 15:40:46 +0000 Subject: [PATCH 2171/9987] Updated pangoLEARN etc to latest version for omikron variant, using pangoLEARN as extension to discriminate different versions --- ....1.16-foss-2021b-pangoLEARN-2021-10-18.eb} | 5 +- ...3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb | 85 +++++++++++++++++++ 2 files changed, 89 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/p/pangolin/{pangolin-3.1.16-foss-2021b.eb => pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb} (91%) create mode 100644 easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb similarity index 91% rename from easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b.eb rename to easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb index 4625f27bff9..6d54365d3d7 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb @@ -2,11 +2,14 @@ # Guy's and St Thomas' NHS Foundation Trust and King's College London # Based on a EC provided by Paul Jähne # uploaded by J. Sassmannshausen +# using the pangoLEARN extension to distinguish between different versions easyblock = 'PythonBundle' name = 'pangolin' version = '3.1.16' +local_pLEARN_version = '2021-10-18' +versionsuffix = '-pangoLEARN-%s' % local_pLEARN_version homepage = 'https://cov-lineages.org/pangolin.html' description = """Software package for assigning SARS-CoV-2 genome sequences to global lineages. @@ -43,7 +46,7 @@ exts_list = [ (name, version, { 'checksums': ['f247caf5ee4252a3edbbf9e60f23374438aaad1879d8dfbf6fb7a64bde8bf3fc'], }), - ('pangoLEARN', '2021-10-18', { + ('pangoLEARN', local_pLEARN_version, { 'modulename': 'pangoLEARN', 'sources': [{ 'download_filename': '%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb new file mode 100644 index 00000000000..ebc0440bf2b --- /dev/null +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb @@ -0,0 +1,85 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on a EC provided by Paul Jähne +# uploaded by J. Sassmannshausen +# using the pangoLEARN extension to distinguish between different versions + +easyblock = 'PythonBundle' + +name = 'pangolin' +version = '3.1.16' +local_pLEARN_version = '2021-11-25' +versionsuffix = '-pangoLEARN-%s' % local_pLEARN_version + +homepage = 'https://cov-lineages.org/pangolin.html' +description = """Software package for assigning SARS-CoV-2 genome sequences to global lineages. +This module also contains the faToVcf tool""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Biopython', '1.79'), + ('gofasta', '0.0.5', '', True), + ('minimap2', '2.22'), + ('Pysam', '0.17.0'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('snakemake', '6.10.0'), + ('UShER', '0.5.0'), + ('scikit-learn', '1.0.1'), + ('Kent_tools', '422'), +] + +use_pip = True +sanity_pip_check = True + +github_account = 'cov-lineages' +exts_default_options = { + 'source_urls': [GITHUB_SOURCE], + 'sources': [{ + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], +} + + +exts_list = [ + (name, version, { + 'checksums': ['f247caf5ee4252a3edbbf9e60f23374438aaad1879d8dfbf6fb7a64bde8bf3fc'], + }), + ('pangoLEARN', local_pLEARN_version, { + 'modulename': 'pangoLEARN', + 'sources': [{ + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], + 'checksums': ['a803da5a30f83d88ad50ac1c6696f5157ff3406d93aa907c8fa176e3ac30b09d'], + }), + ('scorpio', '0.3.14', { + 'checksums': ['31108c9e8399691b3167b14689fbedebd7a410b0879c362a12d807cb077ac57a'], + }), + ('constellations', '0.0.25', { + 'checksums': ['3fb91ed26803d8e73c18153f6e096c4639d1a96beb3fac3c6b5eaf8656ce050f'], + }), + ('pango-designation', '1.2.103', { + 'checksums': ['d9ce36f618d5024d5a687581d6656585dbd52169b4e8f36fc6daca17f0d65c06'], + }), +] + +local_binaries = [ + 'constellations', 'extract_definitions.py', 'pango_designation', 'pangoLEARN', + 'pangolearn.smk', 'pangolin', 'scorpio', 'type_constellations.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'pangolin -v', + 'pangolin -pv', + 'scorpio -v', +] + +moduleclass = 'bio' From 595a89156e3c4dcda77ce12f957f4700b5848c06 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Dec 2021 20:38:36 +0100 Subject: [PATCH 2172/9987] add covsim extension to R v4.1.2 easyconfig --- .../easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index ef7f193eb9e..2f1d783930e 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3154,6 +3154,30 @@ exts_list = [ ('penfa', '0.1.1', { 'checksums': ['a22a8ac3d4a040c77e50ddc92328c1989eae536d79fe56013e9372ba27c114e5'], }), + ('rngWELL', '0.10-7', { + 'checksums': ['0c00c54e69d7d552cfa08d766e4854c01c6c1c8e2c558f387760b91a55ef2d38'], + }), + ('randtoolbox', '1.31.1', { + 'checksums': ['30992e8156782542e9a2bffb75eb2e35f6d302a8c22cb7c3ed9004f0f0973bad'], + }), + ('kde1d', '1.0.3', { + 'checksums': ['d645652d09f1981eb37be9f041034da9b9191885dd38be8a7e485e5e41eb050e'], + }), + ('RcppThread', '1.0.0', { + 'checksums': ['544a48ee4ea381e2e1421d4edbec54365f17059084d94ded7c339de36deeccf5'], + }), + ('wdm', '0.2.2', { + 'checksums': ['11c616f0896d62993f5eee1daf7b021d27f13751f6617067b57cf463aea32dde'], + }), + ('rvinecopulib', '0.6.1.1.1', { + 'checksums': ['779fd288774ebb1a0adde6b960053e5c63750bfa66d5ddf349e0f1d8730f08cd'], + }), + ('PearsonDS', '1.2.1', { + 'checksums': ['354be30b8df4e5432d1bc2b6162900522d4c08dc63b207331819d589fb069824'], + }), + ('covsim', '0.2.1', { + 'checksums': ['57ca810c6950ab295078b745eb87fdd7f195e15082777eed9f1059b6302f13bf'], + }), ] moduleclass = 'lang' From ab8797cd87de0399fce3cd12fe2cbc756c689569 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 1 Dec 2021 22:23:50 +0100 Subject: [PATCH 2173/9987] adding easyconfigs: ABINIT-9.6.2-intel-2021b.eb --- .../a/ABINIT/ABINIT-9.6.2-intel-2021b.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021b.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021b.eb new file mode 100644 index 00000000000..b93cd4a7d35 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2021b.eb @@ -0,0 +1,71 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.6.2' + +homepage = 'https://www.abinit.org/' +description = """ +ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of +systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using +pseudopotentials and a planewave or wavelet basis. +""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b018c2ff24338a5952c5550a7e09d4c7793b62402c7aa4e09273e9a666e674fb'] + +builddependencies = [ + ('Python', '3.9.6'), +] +dependencies = [ + ('libxc', '5.1.6'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('HDF5', '1.12.1'), + ('Wannier90', '3.1.0'), +] + +# Ensure MPI with intel wrappers. +configopts = '--with-mpi="yes" ' +configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# Enable OpenMP +configopts += '--enable-openmp="yes" ' + +# BLAS/Lapack from MKL +configopts += '--with-linalg-flavor=mkl ' + +# FFTW from MKL +configopts += '--with-fft-flavor=dfti ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# Enable double precision for GW calculations +configopts += '--enable-gw-dpc ' + +# Enable OpenMP +configopts += '--enable-openmp ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' From 435ca831f43560224c4960c4251ffcf65349117a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 2 Dec 2021 09:00:33 +0100 Subject: [PATCH 2174/9987] remove comment about binutils --- .../a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb index 076153efd1a..c9c00814fdb 100644 --- a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb @@ -17,7 +17,6 @@ source_urls = ['https://ani.jgi.doe.gov/download_files/'] sources = ['%(name)s_v%(version_major)s.tgz'] checksums = ['236596a9a204cbcad162fc66be3506b2530b1f48f4f84d9647ccec3ca7483a43'] -# A build dependency on binutils is required to pass the test suite. builddependencies = [('binutils', '2.36.1')] dependencies = [ From 4081e8e45c63f3ee71c67489a0913034f8b8be1a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Thu, 2 Dec 2021 10:09:11 +0000 Subject: [PATCH 2175/9987] Add files via upload easyconfigs.py added to test directory --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 7f00f8dcebe..9789392bcd0 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -481,8 +481,6 @@ def check_dep_vars(self, gen, dep, dep_vars): r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], # NanoPlot, NanoComp use an older version of Seaborn 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], - # Shasta requires spoa 3.x - 'spoa': [(r'3\.4\.0', [r'Shasta-0\.8\.0-'])], 'TensorFlow': [ # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), # artic-ncov2019 requires medaka @@ -506,6 +504,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 'Pysam': [('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', 'NGSpeciesID-0.1.1.1-'])], + # UShER requires tbb-2020.3 as newer versions will not build + 'tbb': [('2020.3', ['UShER-0.5.0-'])], } if dep in old_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): From e62e3111dd889b85a66edc0e2233e906371cf466 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Thu, 2 Dec 2021 10:10:29 +0000 Subject: [PATCH 2176/9987] Delete easyconfigs.py File moved to correct folder --- easyconfigs.py | 1403 ------------------------------------------------ 1 file changed, 1403 deletions(-) delete mode 100644 easyconfigs.py diff --git a/easyconfigs.py b/easyconfigs.py deleted file mode 100644 index 9789392bcd0..00000000000 --- a/easyconfigs.py +++ /dev/null @@ -1,1403 +0,0 @@ -## -# Copyright 2013-2021 Ghent University -# -# This file is part of EasyBuild, -# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), -# with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), -# Flemish Research Foundation (FWO) (http://www.fwo.be/en) -# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). -# -# https://github.com/easybuilders/easybuild -# -# EasyBuild is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation v2. -# -# EasyBuild is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with EasyBuild. If not, see . -## -""" -Unit tests for easyconfig files. - -@author: Kenneth Hoste (Ghent University) -""" -import glob -import os -import re -import shutil -import sys -import tempfile -from distutils.version import LooseVersion -from unittest import TestCase, TestLoader, main, skip - -import easybuild.main as eb_main -import easybuild.tools.options as eboptions -from easybuild.base import fancylogger -from easybuild.easyblocks.generic.configuremake import ConfigureMake -from easybuild.easyblocks.generic.pythonpackage import PythonPackage -from easybuild.framework.easyblock import EasyBlock -from easybuild.framework.easyconfig.default import DEFAULT_CONFIG -from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS -from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for -from easybuild.framework.easyconfig.easyconfig import resolve_template -from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig -from easybuild.framework.easyconfig.tools import check_sha256_checksums, dep_graph, get_paths_for, process_easyconfig -from easybuild.tools import config -from easybuild.tools.build_log import EasyBuildError -from easybuild.tools.config import GENERAL_CLASS, build_option -from easybuild.tools.filetools import change_dir, is_generic_easyblock, remove_file -from easybuild.tools.filetools import verify_checksum, which, write_file -from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version -from easybuild.tools.modules import modules_tool -from easybuild.tools.py2vs3 import string_type, urlopen -from easybuild.tools.robot import check_conflicts, resolve_dependencies -from easybuild.tools.run import run_cmd -from easybuild.tools.options import set_tmpdir -from easybuild.tools.utilities import nub - - -# indicates whether all the single tests are OK, -# and that bigger tests (building dep graph, testing for conflicts, ...) can be run as well -# other than optimizing for time, this also helps to get around problems like http://bugs.python.org/issue10949 -single_tests_ok = True - - -def is_pr(): - """Return true if run in a pull request CI""" - # $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR - travis_pr_test = re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST', '')) - - # when testing a PR in GitHub Actions, $GITHUB_EVENT_NAME will be set to 'pull_request' - github_pr_test = os.environ.get('GITHUB_EVENT_NAME') == 'pull_request' - return travis_pr_test or github_pr_test - - -def get_target_branch(): - """Return the target branch of a pull request""" - # target branch should be anything other than 'master'; - # usually is 'develop', but could also be a release branch like '3.7.x' - target_branch = os.environ.get('GITHUB_BASE_REF', None) - if not target_branch: - target_branch = os.environ.get('TRAVIS_BRANCH', None) - if not target_branch: - raise RuntimeError("Did not find a target branch") - return target_branch - - -def skip_if_not_pr_to_non_main_branch(): - if not is_pr(): - return skip("Only run for pull requests") - if get_target_branch() == "main": - return skip("Not run for pull requests against main") - return lambda func: func - - -def get_eb_files_from_diff(diff_filter): - """Return the files changed on HEAD relative to the current target branch""" - target_branch = get_target_branch() - - # relocate to top-level directory of repository to run 'git diff' command - top_dir = os.path.dirname(os.path.dirname(get_paths_for('easyconfigs')[0])) - cwd = change_dir(top_dir) - - # first determine the 'merge base' between target branch and PR branch - # cfr. https://git-scm.com/docs/git-merge-base - cmd = "git merge-base %s HEAD" % target_branch - out, ec = run_cmd(cmd, simple=False, log_ok=False) - if ec == 0: - merge_base = out.strip() - print("Merge base for %s and HEAD: %s" % (target_branch, merge_base)) - else: - msg = "Failed to determine merge base (ec: %s, output: '%s'), " - msg += "falling back to specifying target branch %s" - print(msg % (ec, out, target_branch)) - merge_base = target_branch - - # determine list of changed files using 'git diff' and merge base determined above - cmd = "git diff --name-only --diff-filter=%s %s..HEAD --" % (diff_filter, merge_base) - out, _ = run_cmd(cmd, simple=False) - files = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith('.eb')] - - change_dir(cwd) - return files - - -class EasyConfigTest(TestCase): - """Baseclass for easyconfig testcases.""" - - @classmethod - def setUpClass(cls): - """Setup environment for all tests. Called once!""" - # make sure that the EasyBuild installation is still known even if we purge an EB module - if os.getenv('EB_SCRIPT_PATH') is None: - eb_path = which('eb') - if eb_path is not None: - os.environ['EB_SCRIPT_PATH'] = eb_path - - # initialize configuration (required for e.g. default modules_tool setting) - eb_go = eboptions.parse_options(args=[]) # Ignore cmdline args as those are meant for the unittest framework - config.init(eb_go.options, eb_go.get_options_by_section('config')) - build_options = { - 'check_osdeps': False, - 'external_modules_metadata': {}, - 'force': True, - 'local_var_naming_check': 'error', - 'optarch': 'test', - 'robot_path': get_paths_for("easyconfigs")[0], - 'silent': True, - 'suffix_modules_path': GENERAL_CLASS, - 'valid_module_classes': config.module_classes(), - 'valid_stops': [x[0] for x in EasyBlock.get_steps()], - } - config.init_build_options(build_options=build_options) - set_tmpdir() - - # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains - cls.TMPDIR = tempfile.mkdtemp() - os.environ['MODULEPATH'] = cls.TMPDIR - write_file(os.path.join(cls.TMPDIR, 'craype-test'), '#%Module\n') - - log = fancylogger.getLogger("EasyConfigTest", fname=False) - - # make sure a logger is present for main - eb_main._log = log - - cls._ordered_specs = None - cls._parsed_easyconfigs = [] - cls._parsed_all_easyconfigs = False - cls._changed_ecs = None # ECs changed in a PR - - @classmethod - def tearDownClass(cls): - """Cleanup after running all tests""" - shutil.rmtree(cls.TMPDIR) - - @classmethod - def parse_all_easyconfigs(cls): - """Parse all easyconfigs.""" - if cls._parsed_all_easyconfigs: - return - # all available easyconfig files - easyconfigs_path = get_paths_for("easyconfigs")[0] - specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) - parsed_specs = set(ec['spec'] for ec in cls._parsed_easyconfigs) - for spec in specs: - if spec not in parsed_specs: - cls._parsed_easyconfigs.extend(process_easyconfig(spec)) - cls._parsed_all_easyconfigs = True - - @classmethod - def resolve_all_dependencies(cls): - """Resolve dependencies between easyconfigs""" - # Parse all easyconfigs if not done yet - cls.parse_all_easyconfigs() - # filter out external modules - for ec in cls._parsed_easyconfigs: - for dep in ec['dependencies'][:]: - if dep.get('external_module', False): - ec['dependencies'].remove(dep) - cls._ordered_specs = resolve_dependencies( - cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True) - - def _get_changed_easyconfigs(self): - """Gather all added or modified easyconfigs""" - # get list of changed easyconfigs - changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M') - added_ecs_filenames = get_eb_files_from_diff(diff_filter='A') - if changed_ecs_filenames: - print("\nList of changed easyconfig files in this PR:\n\t%s" % '\n\t'.join(changed_ecs_filenames)) - if added_ecs_filenames: - print("\nList of added easyconfig files in this PR:\n\t%s" % '\n\t'.join(added_ecs_filenames)) - EasyConfigTest._changed_ecs_filenames = changed_ecs_filenames - EasyConfigTest._added_ecs_filenames = added_ecs_filenames - - # grab parsed easyconfigs for changed easyconfig files - changed_ecs = [] - for ec_fn in changed_ecs_filenames + added_ecs_filenames: - match = None - for ec in self.parsed_easyconfigs: - if os.path.basename(ec['spec']) == ec_fn: - match = ec['ec'] - break - - if match: - changed_ecs.append(match) - else: - # if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR... - # so as a last resort, try to find the easyconfig file in __archive__ - easyconfigs_path = get_paths_for("easyconfigs")[0] - specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn)) - if len(specs) == 1: - ec = process_easyconfig(specs[0])[0] - changed_ecs.append(ec['ec']) - else: - raise RuntimeError("Failed to find parsed easyconfig for %s" - " (and could not isolate it in easyconfigs archive either)" % ec_fn) - EasyConfigTest._changed_ecs = changed_ecs - - @property - def parsed_easyconfigs(self): - # parse all easyconfigs if they haven't been already - EasyConfigTest.parse_all_easyconfigs() - return EasyConfigTest._parsed_easyconfigs - - @property - def ordered_specs(self): - # Resolve dependencies if not done - if EasyConfigTest._ordered_specs is None: - EasyConfigTest.resolve_all_dependencies() - return EasyConfigTest._ordered_specs - - @property - def changed_ecs_filenames(self): - if EasyConfigTest._changed_ecs is None: - self._get_changed_easyconfigs() - return EasyConfigTest._changed_ecs_filenames - - @property - def added_ecs_filenames(self): - if EasyConfigTest._changed_ecs is None: - self._get_changed_easyconfigs() - return EasyConfigTest._added_ecs_filenames - - @property - def changed_ecs(self): - if EasyConfigTest._changed_ecs is None: - self._get_changed_easyconfigs() - return EasyConfigTest._changed_ecs - - def test_dep_graph(self): - """Unit test that builds a full dependency graph.""" - # pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6 - if LooseVersion(sys.version) >= LooseVersion('2.6') and single_tests_ok: - # temporary file for dep graph - (hn, fn) = tempfile.mkstemp(suffix='.dot') - os.close(hn) - - dep_graph(fn, self.ordered_specs) - - remove_file(fn) - else: - print("(skipped dep graph test)") - - def test_conflicts(self): - """Check whether any conflicts occur in software dependency graphs.""" - - if not single_tests_ok: - print("(skipped conflicts test)") - return - - self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False), - "No conflicts detected") - - def check_dep_vars(self, gen, dep, dep_vars): - """Check whether available variants of a particular dependency are acceptable or not.""" - - # 'guilty' until proven 'innocent' - res = False - - # filter out wrapped Java versions - # i.e. if the version of one is a prefix of the version of the other one (e.g. 1.8 & 1.8.0_181) - if dep == 'Java': - dep_vars_to_check = sorted(dep_vars.keys()) - - retained_dep_vars = [] - - while dep_vars_to_check: - dep_var = dep_vars_to_check.pop() - dep_var_version = dep_var.split(';')[0] - - # remove dep vars wrapped by current dep var - dep_vars_to_check = [x for x in dep_vars_to_check if not x.startswith(dep_var_version + '.')] - - retained_dep_vars = [x for x in retained_dep_vars if not x.startswith(dep_var_version + '.')] - - retained_dep_vars.append(dep_var) - - for key in list(dep_vars.keys()): - if key not in retained_dep_vars: - del dep_vars[key] - - # filter out binutils with empty versionsuffix which is used to build toolchain compiler - if dep == 'binutils' and len(dep_vars) > 1: - empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')] - if len(empty_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0]) - - # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools; - # same goes for WRF and WPS - for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS')]: - if dep == dep_name and len(dep_vars) > 1: - for key in list(dep_vars): - ecs = dep_vars[key] - # filter out dep variants that are only used as dependency for parent with same version - dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') - if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: - dep_vars.pop(key) - - # multiple versions of Boost is OK as long as they are deps for a matching Boost.Python - if dep == 'Boost' and len(dep_vars) > 1: - for key in list(dep_vars): - ecs = dep_vars[key] - # filter out Boost variants that are only used as dependency for Boost.Python with same version - boost_ver = re.search('^version: (?P[^;]+);', key).group('ver') - if all(ec.startswith('Boost.Python-%s-' % boost_ver) for ec in ecs): - dep_vars.pop(key) - - # filter out Perl with -minimal versionsuffix which are only used in makeinfo-minimal - if dep == 'Perl': - minimal_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -minimal')] - if len(minimal_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != minimal_vsuff_vars[0]) - - # filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains - if dep in ['FFTW', 'imkl']: - serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] - if len(serial_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) - - # filter out BLIS and libFLAME with -amd versionsuffix - # (AMD forks, used in gobff/*-amd toolchains) - if dep in ['BLIS', 'libFLAME']: - amd_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -amd')] - if len(amd_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != amd_vsuff_vars[0]) - - # filter out ScaLAPACK with -BLIS-* versionsuffix, used in goblf toolchain - if dep == 'ScaLAPACK': - blis_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -BLIS-' in v] - if len(blis_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != blis_vsuff_vars[0]) - - if dep == 'ScaLAPACK': - # filter out ScaLAPACK with -bf versionsuffix, used in gobff toolchain - bf_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bf' in v] - if len(bf_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bf_vsuff_vars[0]) - # filter out ScaLAPACK with -bl versionsuffix, used in goblf toolchain - bl_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bl' in v] - if len(bl_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bl_vsuff_vars[0]) - - # filter out HDF5 with -serial versionsuffix which is used in HDF5 for Python (h5py) - if dep in ['HDF5']: - serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] - if len(serial_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) - - # for some dependencies, we allow exceptions for software that depends on a particular version, - # as long as that's indicated by the versionsuffix - versionsuffix_deps = ['ASE', 'Boost', 'CUDAcore', 'Java', 'Lua', - 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] - if dep in versionsuffix_deps and len(dep_vars) > 1: - - # check for '-CUDA-*' versionsuffix for CUDAcore dependency - if dep == 'CUDAcore': - dep = 'CUDA' - - for key in list(dep_vars): - dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') - # use version of Java wrapper rather than full Java version - if dep == 'Java': - dep_ver = '.'.join(dep_ver.split('.')[:2]) - # filter out dep version if all easyconfig filenames using it include specific dep version - if all(re.search('-%s-%s' % (dep, dep_ver), v) for v in dep_vars[key]): - dep_vars.pop(key) - # always retain at least one dep variant - if len(dep_vars) == 1: - break - - # filter R dep for a specific version of Python 2.x - if dep == 'R' and len(dep_vars) > 1: - for key in list(dep_vars): - if '; versionsuffix: -Python-2' in key: - dep_vars.pop(key) - # always retain at least one variant - if len(dep_vars) == 1: - break - - # filter out variants that are specific to a particular version of CUDA - cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] - if len(dep_vars) >= len(cuda_dep_vars) and len(dep_vars) > 1: - for key in list(dep_vars): - if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key): - dep_vars.pop(key) - # always retain at least one dep variant - if len(dep_vars) == 1: - break - - # some software packages require a specific (older/newer) version of a particular dependency - old_dep_versions = { - # EMAN2 2.3 requires Boost(.Python) 1.64.0 - 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], - 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], - # VMTK 1.4.x requires ITK 4.13.x - 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], - # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) - 'Jellyfish': [(r'1\.', [r'Kraken-1\.', r'Roary-3\.12\.0', r'metaWRAP-1\.2'])], - # Libint 1.1.6 is required by older CP2K versions - 'Libint': [(r'1\.1\.6', [r'CP2K-[3-6]'])], - # libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, horton, PySCF, WIEN2k - # (Qiskit depends on PySCF), Elk 7.x requires libxc >= 5 - 'libxc': [ - (r'[23]\.', [r'ABINIT-', r'AtomPAW-', r'CP2K-', r'GPAW-', r'horton-', - r'PySCF-', r'Qiskit-', r'WIEN2k-']), - (r'5\.', [r'Elk-']), - ], - # some software depends on numba, which typically requires an older LLVM; - # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy - 'LLVM': [ - # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) - (r'8\.', [r'numba-0\.47\.0-', r'librosa-0\.7\.2-', r'BirdNET-20201214-', - r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[346]\.[23]']), - (r'10\.0\.1', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', - r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', - r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), - ], - 'Lua': [ - # SimpleITK 2.1.0 requires Lua 5.3.x, MedPy and nnU-Net depend on SimpleITK - (r'5\.3\.5', [r'nnU-Net-1\.7\.0-', r'MedPy-0\.4\.0-', r'SimpleITK-2\.1\.0-']), - ], - # TensorFlow 2.5+ requires a more recent NCCL than version 2.4.8 used in 2019b generation; - # Horovod depends on TensorFlow, so same exception required there - 'NCCL': [(r'2\.11\.4', [r'TensorFlow-2\.[5-9]\.', r'Horovod-0\.2[2-9]'])], - # rampart requires nodejs > 10, artic-ncov2019 requires rampart - 'nodejs': [('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13'])], - # some software depends on an older numba; - # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy - 'numba': [ - (r'0\.52\.0', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', - r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', - r'umap-learn-0\.4\.6-']), - ], - # OPERA requires SAMtools 0.x - 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', - r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], - # NanoPlot, NanoComp use an older version of Seaborn - 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], - 'TensorFlow': [ - # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), - # artic-ncov2019 requires medaka - ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), - # medaka 1.1.* and 1.2.* requires TensorFlow 2.2.0 - # (while other 2019b easyconfigs use TensorFlow 2.1.0 as dep); - # TensorFlow 2.2.0 is also used as a dep for Horovod 0.19.5; - # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 - ('2.2.0;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'Horovod-0.19.5-', 'decona-0.1.2-', - 'NGSpeciesID-0.1.1.1-']), - # medaka 1.4.3 (foss/2019b) depends on TensorFlow 2.2.2 - ('2.2.2;', ['medaka-1.4.3-']), - # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka - ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), - ], - # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 - # (for 2021b, UCX was updated to v1.11.2) - 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], - # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, - # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; - # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 - 'Pysam': [('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', - 'NGSpeciesID-0.1.1.1-'])], - # UShER requires tbb-2020.3 as newer versions will not build - 'tbb': [('2020.3', ['UShER-0.5.0-'])], - } - if dep in old_dep_versions and len(dep_vars) > 1: - for key in list(dep_vars): - for version_pattern, parents in old_dep_versions[dep]: - # filter out known old dependency versions - if re.search('^version: %s' % version_pattern, key): - # only filter if the easyconfig using this dep variants is known - if all(any(re.search(p, x) for p in parents) for x in dep_vars[key]): - dep_vars.pop(key) - - # filter out ELSI variants with -PEXSI suffix - if dep == 'ELSI' and len(dep_vars) > 1: - pexsi_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -PEXSI')] - if len(pexsi_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != pexsi_vsuff_vars[0]) - - # only single variant is always OK - if len(dep_vars) == 1: - res = True - - elif len(dep_vars) == 2 and dep in ['Python', 'Tkinter']: - # for Python & Tkinter, it's OK to have on 2.x and one 3.x version - v2_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 2.')] - v3_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 3.')] - if len(v2_dep_vars) == 1 and len(v3_dep_vars) == 1: - res = True - - # two variants is OK if one is for Python 2.x and the other is for Python 3.x (based on versionsuffix) - elif len(dep_vars) == 2: - py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] - py3_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-3.' in x] - if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: - res = True - - # for recent generations, there's no versionsuffix anymore for Python 3, - # but we still allow variants depending on Python 2.x + 3.x - is_recent_gen = False - full_toolchain_regex = re.compile(r'^20[1-9][0-9][ab]$') - gcc_toolchain_regex = re.compile(r'^GCC(core)?-[0-9]?[0-9]\.[0-9]$') - if full_toolchain_regex.match(gen): - is_recent_gen = LooseVersion(gen) >= LooseVersion('2020b') - elif gcc_toolchain_regex.match(gen): - genver = gen.split('-', 1)[1] - is_recent_gen = LooseVersion(genver) >= LooseVersion('10.2') - else: - raise EasyBuildError("Unkown type of toolchain generation: %s" % gen) - - if is_recent_gen: - py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] - py3_dep_vars = [x for x in dep_vars.keys() if x.strip().endswith('; versionsuffix:')] - if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: - res = True - - return res - - def test_check_dep_vars(self): - """Test check_dep_vars utility method.""" - - # one single dep version: OK - self.assertTrue(self.check_dep_vars('2019b', 'testdep', { - 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], - })) - self.assertTrue(self.check_dep_vars('2019b', 'testdep', { - 'version: 1.2.3; versionsuffix: -test': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], - })) - - # two or more dep versions (no special case: not OK) - self.assertFalse(self.check_dep_vars('2019b', 'testdep', { - 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], - })) - self.assertFalse(self.check_dep_vars('2019b', 'testdep', { - 'version: 0.0; versionsuffix:': ['foobar-0.0.eb'], - 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], - })) - - # Java is a special case, with wrapped Java versions - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - })) - # two Java wrappers is not OK - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], - })) - # OK to have two or more wrappers if versionsuffix is used to indicate exception - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - })) - # versionsuffix must be there for all easyconfigs to indicate exception - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], - })) - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 12.1.6; versionsuffix:': ['foobar-0.0-Java-12.eb'], - 'version: 12; versionsuffix:': ['foobar-0.0-Java-12.eb'], - })) - - # strange situation: odd number of Java versions - # not OK: two Java wrappers (and no versionsuffix to indicate exception) - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], - })) - # OK because of -Java-11 versionsuffix - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - })) - # not OK: two Java wrappers (and no versionsuffix to indicate exception) - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], - })) - # OK because of -Java-11 versionsuffix - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - })) - - # two different versions of Boost is not OK - self.assertFalse(self.check_dep_vars('2019b', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - - # a different Boost version that is only used as dependency for a matching Boost.Python is fine - self.assertTrue(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - self.assertTrue(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], - 'version: 1.66.0; versionsuffix:': ['Boost.Python-1.66.0-gompi-2019a.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - self.assertFalse(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], - 'version: 1.66.0; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - - self.assertTrue(self.check_dep_vars('2018a', 'Boost', { - 'version: 1.63.0; versionsuffix: -Python-2.7.14': ['EMAN2-2.21a-foss-2018a-Python-2.7.14-Boost-1.63.0.eb'], - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2018a.eb'], - 'version: 1.66.0; versionsuffix:': ['BLAST+-2.7.1-foss-2018a.eb'], - })) - - self.assertTrue(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': [ - 'Boost.Python-1.64.0-gompi-2019a.eb', - 'EMAN2-2.3-foss-2019a-Python-2.7.15.eb', - ], - 'version: 1.70.0; versionsuffix:': [ - 'BLAST+-2.9.0-gompi-2019a.eb', - 'Boost.Python-1.70.0-gompi-2019a.eb', - ], - })) - - # two variants is OK, if they're for Python 2.x and 3.x - self.assertTrue(self.check_dep_vars('2020a', 'Python', { - 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-2.7.18.eb'], - 'version: 3.8.2; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb'], - })) - - self.assertTrue(self.check_dep_vars('2020a', 'SciPy-bundle', { - 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], - 'version: 2020.03; versionsuffix: -Python-3.8.2': ['matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb'], - })) - - # for recent easyconfig generations, there's no versionsuffix anymore for Python 3 - self.assertTrue(self.check_dep_vars('2020b', 'Python', { - 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb'], - 'version: 3.8.6; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b.eb'], - })) - - self.assertTrue(self.check_dep_vars('GCCcore-10.2', 'PyYAML', { - 'version: 5.3.1; versionsuffix:': ['IPython-7.18.1-GCCcore-10.2.0.eb'], - 'version: 5.3.1; versionsuffix: -Python-2.7.18': ['IPython-7.18.1-GCCcore-10.2.0-Python-2.7.18.eb'], - })) - - self.assertTrue(self.check_dep_vars('2020b', 'SciPy-bundle', { - 'version: 2020.11; versionsuffix: -Python-2.7.18': ['matplotlib-3.3.3-foss-2020b-Python-2.7.18.eb'], - 'version: 2020.11; versionsuffix:': ['matplotlib-3.3.3-foss-2020b.eb'], - })) - - # not allowed for older generations (foss/intel 2020a or older, GCC(core) 10.1.0 or older) - self.assertFalse(self.check_dep_vars('2020a', 'SciPy-bundle', { - 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], - 'version: 2020.03; versionsuffix:': ['matplotlib-3.2.1-foss-2020a.eb'], - })) - - def test_dep_versions_per_toolchain_generation(self): - """ - Check whether there's only one dependency version per toolchain generation actively used. - This is enforced to try and limit the chance of running into conflicts when multiple modules built with - the same toolchain are loaded together. - """ - ecs_by_full_mod_name = dict((ec['full_mod_name'], ec) for ec in self.parsed_easyconfigs) - if len(ecs_by_full_mod_name) != len(self.parsed_easyconfigs): - self.fail('Easyconfigs with duplicate full_mod_name found') - - # Cache already determined dependencies - ec_to_deps = dict() - - def get_deps_for(ec): - """Get list of (direct) dependencies for specified easyconfig.""" - ec_mod_name = ec['full_mod_name'] - deps = ec_to_deps.get(ec_mod_name) - if deps is None: - deps = [] - for dep in ec['ec']['dependencies']: - dep_mod_name = dep['full_mod_name'] - deps.append((dep['name'], dep['version'], dep['versionsuffix'], dep_mod_name)) - # Note: Raises KeyError if dep not found - res = ecs_by_full_mod_name[dep_mod_name] - deps.extend(get_deps_for(res)) - ec_to_deps[ec_mod_name] = deps - - return deps - - # some software also follows {a,b} versioning scheme, - # which throws off the pattern matching done below for toolchain versions - false_positives_regex = re.compile('^MATLAB-Engine-20[0-9][0-9][ab]') - - # restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a) - # and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x - for pattern in ['20(1[89]|[2-9][0-9])[ab]', r'GCCcore-([7-9]|[1-9][0-9])\.[0-9]']: - all_deps = {} - regex = re.compile(r'^.*-(?P%s).*\.eb$' % pattern) - - # collect variants for all dependencies of easyconfigs that use a toolchain that matches - for ec in self.ordered_specs: - ec_file = os.path.basename(ec['spec']) - - # take into account software which also follows a {a,b} versioning scheme - ec_file = false_positives_regex.sub('', ec_file) - - res = regex.match(ec_file) - if res: - tc_gen = res.group('tc_gen') - all_deps_tc_gen = all_deps.setdefault(tc_gen, {}) - for dep_name, dep_ver, dep_versuff, dep_mod_name in get_deps_for(ec): - dep_variants = all_deps_tc_gen.setdefault(dep_name, {}) - # a variant is defined by version + versionsuffix - variant = "version: %s; versionsuffix: %s" % (dep_ver, dep_versuff) - # keep track of which easyconfig this is a dependency - dep_variants.setdefault(variant, set()).add(ec_file) - - # check which dependencies have more than 1 variant - multi_dep_vars, multi_dep_vars_msg = [], '' - for tc_gen in sorted(all_deps.keys()): - for dep in sorted(all_deps[tc_gen].keys()): - dep_vars = all_deps[tc_gen][dep] - if not self.check_dep_vars(tc_gen, dep, dep_vars): - multi_dep_vars.append(dep) - multi_dep_vars_msg += "\nfound %s variants of '%s' dependency " % (len(dep_vars), dep) - multi_dep_vars_msg += "in easyconfigs using '%s' toolchain generation\n* " % tc_gen - multi_dep_vars_msg += '\n* '.join("%s as dep for %s" % v for v in sorted(dep_vars.items())) - multi_dep_vars_msg += '\n' - - error_msg = "No multi-variant deps found for '%s' easyconfigs:\n%s" % (regex.pattern, multi_dep_vars_msg) - self.assertFalse(multi_dep_vars, error_msg) - - def test_sanity_check_paths(self): - """Make sure specified sanity check paths adher to the requirements.""" - - for ec in self.parsed_easyconfigs: - ec_scp = ec['ec']['sanity_check_paths'] - if ec_scp != {}: - # if sanity_check_paths is specified (i.e., non-default), it must adher to the requirements - # both 'files' and 'dirs' keys, both with list values and with at least one a non-empty list - error_msg = "sanity_check_paths for %s does not meet requirements: %s" % (ec['spec'], ec_scp) - self.assertEqual(sorted(ec_scp.keys()), ['dirs', 'files'], error_msg) - self.assertTrue(isinstance(ec_scp['dirs'], list), error_msg) - self.assertTrue(isinstance(ec_scp['files'], list), error_msg) - self.assertTrue(ec_scp['dirs'] or ec_scp['files'], error_msg) - - def test_r_libs_site_env_var(self): - """Make sure $R_LIBS_SITE is being updated, rather than $R_LIBS.""" - # cfr. https://github.com/easybuilders/easybuild-easyblocks/pull/2326 - - r_libs_ecs = [] - for ec in self.parsed_easyconfigs: - for key in ('modextrapaths', 'modextravars'): - if 'R_LIBS' in ec['ec'][key]: - r_libs_ecs.append(ec['spec']) - - error_msg = "%d easyconfigs found which set $R_LIBS, should be $R_LIBS_SITE: %s" - self.assertEqual(r_libs_ecs, [], error_msg % (len(r_libs_ecs), ', '.join(r_libs_ecs))) - - def test_easyconfig_locations(self): - """Make sure all easyconfigs files are in the right location.""" - easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[0a-z]/[^/]+$') - topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) - for (dirpath, _, filenames) in os.walk(topdir): - # ignore git/svn dirs & archived easyconfigs - if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: - continue - # check whether list of .eb files is non-empty - easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] - if easyconfig_files: - # check whether path matches required pattern - if not easyconfig_dirs_regex.search(dirpath): - # only exception: TEMPLATE.eb - if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): - self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_sha256_checksums(self): - """Make sure changed easyconfigs have SHA256 checksums in place.""" - - # list of software for which checksums can not be required, - # e.g. because 'source' files need to be constructed manually - whitelist = [ - 'Kent_tools-*', - 'MATLAB-*', - 'OCaml-*', - 'OpenFOAM-Extend-4.1-*', - # sources for old versions of Bioconductor packages are no longer available, - # so not worth adding checksums for at this point - 'R-bundle-Bioconductor-3.[2-5]', - ] - - # the check_sha256_checksums function (again) creates an EasyBlock instance - # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter - # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__; - # therefore, we need to reset 'sources' to an empty list here if Bundle is used... - # likewise for 'patches' and 'checksums' - for ec in self.changed_ecs: - if ec['easyblock'] in ['Bundle', 'PythonBundle', 'EB_OpenSSL_wrapper']: - ec['sources'] = [] - ec['patches'] = [] - ec['checksums'] = [] - - # filter out deprecated easyconfigs - retained_changed_ecs = [] - for ec in self.changed_ecs: - if not ec['deprecated']: - retained_changed_ecs.append(ec) - - checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) - self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_python_packages(self): - """Several checks for easyconfigs that install (bundles of) Python packages.""" - - # These packages do not support installation with 'pip' - whitelist_pip = [ - r'ESMPy-.*', - r'MATLAB-Engine-.*', - r'Meld-.*', - r'PyTorch-.*', - ] - - whitelist_pip_check = [ - r'Mako-1.0.4.*Python-2.7.12.*', - # no pip 9.x or newer for configparser easyconfigs using a 2016a or 2016b toolchain - r'configparser-3.5.0.*-2016[ab].*', - # mympirun is installed with system Python, pip may not be installed for system Python - r'vsc-mympirun.*', - ] - - failing_checks = [] - - python_default_urls = PythonPackage.extra_options()['source_urls'][0] - - for ec in self.changed_ecs: - - with ec.disable_templating(): - ec_fn = os.path.basename(ec.path) - easyblock = ec.get('easyblock') - exts_defaultclass = ec.get('exts_defaultclass') - exts_default_options = ec.get('exts_default_options', {}) - - download_dep_fail = ec.get('download_dep_fail') - exts_download_dep_fail = ec.get('exts_download_dep_fail') - use_pip = ec.get('use_pip') - if use_pip is None: - use_pip = exts_default_options.get('use_pip') - - # only easyconfig parameters as they are defined in the easyconfig file, - # does *not* include other easyconfig parameters with their default value! - pure_ec = ec.parser.get_config_dict() - - # download_dep_fail should be set when using PythonPackage - if easyblock == 'PythonPackage': - if download_dep_fail is None: - failing_checks.append("'download_dep_fail' should be set in %s" % ec_fn) - - if pure_ec.get('source_urls') == python_default_urls: - failing_checks.append("'source_urls' should not be defined when using the default value " - "in %s" % ec_fn) - - # use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs) - if easyblock in ['PythonBundle', 'PythonPackage']: - if use_pip is None and not any(re.match(regex, ec_fn) for regex in whitelist_pip): - failing_checks.append("'use_pip' should be set in %s" % ec_fn) - - # download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set - if easyblock == 'PythonBundle': - if download_dep_fail or exts_download_dep_fail: - fail = "'*download_dep_fail' should not be set in %s since PythonBundle easyblock is used" % ec_fn - failing_checks.append(fail) - if pure_ec.get('exts_default_options', {}).get('source_urls') == python_default_urls: - failing_checks.append("'source_urls' should not be defined in exts_default_options when using " - "the default value in %s" % ec_fn) - - elif exts_defaultclass == 'PythonPackage': - # bundle of Python packages should use PythonBundle - if easyblock == 'Bundle': - fail = "'PythonBundle' easyblock should be used for bundle of Python packages in %s" % ec_fn - failing_checks.append(fail) - else: - # both download_dep_fail and use_pip should be set via exts_default_options - # when installing Python packages as extensions - for key in ['download_dep_fail', 'use_pip']: - if exts_default_options.get(key) is None: - failing_checks.append("'%s' should be set in exts_default_options in %s" % (key, ec_fn)) - - # if Python is a dependency, that should be reflected in the versionsuffix - # Tkinter is an exception, since its version always matches the Python version anyway - # Python 3.8.6 and later are also excluded, as we consider python 3 the default python - # Also whitelist some updated versions of Amber - whitelist_python_suffix = [ - 'Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', - 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb', - 'R-keras-2.1.6-foss-2018a-R-3.4.4.eb', - ] - whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix) - has_python_dep = any(LooseVersion(dep['version']) < LooseVersion('3.8.6') - for dep in ec['dependencies'] if dep['name'] == 'Python') - if has_python_dep and ec.name != 'Tkinter' and not whitelisted: - if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): - msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn - # This is only a failure for newly added ECs, not for existing ECS - # As that would probably break many ECs - if ec_fn in self.added_ecs_filenames: - failing_checks.append(msg) - else: - print('\nNote: Failed non-critical check: ' + msg) - else: - has_recent_python3_dep = any(LooseVersion(dep['version']) >= LooseVersion('3.8.6') - for dep in ec['dependencies'] if dep['name'] == 'Python') - if has_recent_python3_dep and re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): - msg = "'-Python-%%(pyver)s' should no longer be included in versionsuffix in %s" % ec_fn - failing_checks.append(msg) - - # require that running of "pip check" during sanity check is enabled via sanity_pip_check - if easyblock in ['PythonBundle', 'PythonPackage']: - sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check') - if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip_check): - failing_checks.append("sanity_pip_check should be enabled in %s" % ec_fn) - - if failing_checks: - self.fail('\n'.join(failing_checks)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_R_packages(self): - """Several checks for easyconfigs that install (bundles of) R packages.""" - failing_checks = [] - - for ec in self.changed_ecs: - ec_fn = os.path.basename(ec.path) - exts_defaultclass = ec.get('exts_defaultclass') - if exts_defaultclass == 'RPackage' or ec.name == 'R': - seen_exts = set() - for ext in ec['exts_list']: - if isinstance(ext, (tuple, list)): - ext_name = ext[0] - else: - ext_name = ext - if ext_name in seen_exts: - failing_checks.append('%s was added multiple times to exts_list in %s' % (ext_name, ec_fn)) - else: - seen_exts.add(ext_name) - self.assertFalse(failing_checks, '\n'.join(failing_checks)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_sanity_check_paths(self): - """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" - - # some generic easyblocks already have a decent customised sanity_check_paths, - # including CMakePythonPackage, GoPackage, PythonBundle & PythonPackage; - # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. - whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'ModuleRC', - 'PythonBundle', 'PythonPackage', 'Toolchain'] - # Bundles of dependencies without files of their own - # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, - # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co - bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle'] - - failing_checks = [] - - for ec in self.changed_ecs: - - easyblock = ec.get('easyblock') - - if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): - if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): - pass - else: - ec_fn = os.path.basename(ec.path) - failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) - - self.assertFalse(failing_checks, '\n'.join(failing_checks)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_https(self): - """Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://).""" - - whitelist = [ - 'Kaiju', # invalid certificate at https://kaiju.binf.ku.dk - 'libxml2', # https://xmlsoft.org works, but invalid certificate - 'p4vasp', # https://www.p4vasp.at doesn't work - 'ITSTool', # https://itstool.org/ doesn't work - 'UCX-', # bad certificate for https://www.openucx.org - 'MUMPS', # https://mumps.enseeiht.fr doesn't work - 'PyFR', # https://www.pyfr.org doesn't work - 'PycURL', # bad certificate for https://pycurl.io/ - ] - url_whitelist = [ - # https:// doesn't work, results in index page being downloaded instead - # (see https://github.com/easybuilders/easybuild-easyconfigs/issues/9692) - 'http://isl.gforge.inria.fr', - # https:// leads to File Not Found - 'http://tau.uoregon.edu/', - # https:// has outdated SSL configurations - 'http://faculty.scs.illinois.edu', - ] - # Cache: Mapping of already checked HTTP urls to whether the HTTPS variant works - checked_urls = dict() - - def check_https_url(http_url): - """Check if the https url works""" - http_url = http_url.rstrip('/') # Remove trailing slashes - https_url_works = checked_urls.get(http_url) - if https_url_works is None: - https_url = http_url.replace('http://', 'https://') - try: - https_url_works = bool(urlopen(https_url, timeout=5)) - except Exception: - https_url_works = False - checked_urls[http_url] = https_url_works - - http_regex = re.compile('http://[^"\'\n]+', re.M) - - failing_checks = [] - for ec in self.changed_ecs: - ec_fn = os.path.basename(ec.path) - - # skip whitelisted easyconfigs - if any(ec_fn.startswith(x) for x in whitelist): - continue - - # ignore commented out lines in easyconfig files when checking for http:// URLs - ec_txt = '\n'.join(line for line in ec.rawtxt.split('\n') if not line.startswith('#')) - - for http_url in http_regex.findall(ec_txt): - - # skip whitelisted http:// URLs - if any(http_url.startswith(x) for x in url_whitelist): - continue - - if check_https_url(http_url): - failing_checks.append("Found http:// URL in %s, should be https:// : %s" % (ec_fn, http_url)) - if failing_checks: - self.fail('\n'.join(failing_checks)) - - -def template_easyconfig_test(self, spec): - """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" - - # set to False, so it's False in case of this test failing - global single_tests_ok - prev_single_tests_ok = single_tests_ok - single_tests_ok = False - - # parse easyconfig - ecs = process_easyconfig(spec) - if len(ecs) == 1: - ec = ecs[0]['ec'] - - # cache the parsed easyconfig, to avoid that it is parsed again - EasyConfigTest._parsed_easyconfigs.append(ecs[0]) - else: - self.assertTrue(False, "easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) - - # check easyconfig file name - expected_fn = '%s-%s.eb' % (ec['name'], det_full_ec_version(ec)) - msg = "Filename '%s' of parsed easyconfig matches expected filename '%s'" % (spec, expected_fn) - self.assertEqual(os.path.basename(spec), expected_fn, msg) - - name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) - - # make sure easyconfig file is in expected location - expected_subdir = os.path.join('easybuild', 'easyconfigs', letter_dir_for(name), name) - subdir = os.path.join(*spec.split(os.path.sep)[-5:-1]) - fail_msg = "Easyconfig file %s not in expected subdirectory %s" % (spec, expected_subdir) - self.assertEqual(expected_subdir, subdir, fail_msg) - - # sanity check for software name, moduleclass - self.assertEqual(ec['name'], name) - self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) - - # instantiate easyblock with easyconfig file - app_class = get_easyblock_class(easyblock, name=name) - - # check that automagic fallback to ConfigureMake isn't done (deprecated behaviour) - fn = os.path.basename(spec) - error_msg = "%s relies on automagic fallback to ConfigureMake, should use easyblock = 'ConfigureMake' instead" % fn - self.assertTrue(easyblock or app_class is not ConfigureMake, error_msg) - - # dump the easyconfig file; - # this should be done before creating the easyblock instance (done below via app_class), - # because some easyblocks (like PythonBundle) modify easyconfig parameters at initialisation - handle, test_ecfile = tempfile.mkstemp() - os.close(handle) - - ec.dump(test_ecfile) - dumped_ec = EasyConfigParser(test_ecfile).get_config_dict() - os.remove(test_ecfile) - - app = app_class(ec) - - # more sanity checks - self.assertTrue(name, app.name) - self.assertTrue(ec['version'], app.version) - - # make sure that deprecated 'dummy' toolchain is no longer used, should use 'system' toolchain instead - # but give recent EasyBuild easyconfigs special treatment to avoid breaking "eb --install-latest-eb-release" - ec_fn = os.path.basename(spec) - if not (ec_fn == 'EasyBuild-3.9.4.eb' or ec_fn.startswith('EasyBuild-4.')): - error_msg_tmpl = "%s should use 'system' toolchain rather than deprecated 'dummy' toolchain" - self.assertFalse(ec['toolchain']['name'] == 'dummy', error_msg_tmpl % os.path.basename(spec)) - - # make sure that $root is not used, since it is not compatible with module files in Lua syntax - res = re.findall(r'.*\$root.*', ec.rawtxt, re.M) - error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" - self.assertFalse(res, error_msg % res) - - # check for redefined easyconfig parameters, there should be none... - param_def_regex = re.compile(r'^(?P\w+)\s*=', re.M) - keys = param_def_regex.findall(ec.rawtxt) - redefined_keys = [] - for key in sorted(nub(keys)): - cnt = keys.count(key) - if cnt > 1: - redefined_keys.append((key, cnt)) - - redefined_keys_error_msg = "There should be no redefined easyconfig parameters, found %d: " % len(redefined_keys) - redefined_keys_error_msg += ', '.join('%s (%d)' % x for x in redefined_keys) - - self.assertFalse(redefined_keys, redefined_keys_error_msg) - - # make sure old GitHub urls for EasyBuild that include 'hpcugent' are no longer used - old_urls = [ - 'github.com/hpcugent/easybuild', - 'hpcugent.github.com/easybuild', - 'hpcugent.github.io/easybuild', - ] - for old_url in old_urls: - self.assertFalse(old_url in ec.rawtxt, "Old URL '%s' not found in %s" % (old_url, spec)) - - # make sure binutils is included as a (build) dep if toolchain is GCCcore - if ec['toolchain']['name'] == 'GCCcore': - # with 'Tarball' easyblock: only unpacking, no building; Eigen is also just a tarball - requires_binutils = ec['easyblock'] not in ['Tarball'] and ec['name'] not in ['Eigen'] - - # let's also exclude the very special case where the system GCC is used as GCCcore, and only apply this - # exception to the dependencies of binutils (since we should eventually build a new binutils with GCCcore) - if ec['toolchain']['version'] == 'system': - binutils_complete_dependencies = ['M4', 'Bison', 'flex', 'help2man', 'zlib', 'binutils'] - requires_binutils &= bool(ec['name'] not in binutils_complete_dependencies) - - # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled) - requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) - - if requires_binutils: - # dependencies() returns both build and runtime dependencies - # in some cases, binutils can also be a runtime dep (e.g. for Clang) - # Also using GCC directly as a build dep is also allowed (it includes the correct binutils) - dep_names = [d['name'] for d in ec.dependencies()] - self.assertTrue('binutils' in dep_names or 'GCC' in dep_names, - "binutils or GCC is a build dep in %s: %s" % (spec, dep_names)) - - # make sure that OpenSSL wrapper is used rather than OS dependency, - # for easyconfigs using a 2021a (sub)toolchain or more recent common toolchain version - osdeps = ec['osdependencies'] - if osdeps: - # check whether any entry in osdependencies related to OpenSSL - openssl_osdep = False - for osdep in osdeps: - if isinstance(osdep, string_type): - osdep = [osdep] - if any('libssl' in x for x in osdep) or any('openssl' in x for x in osdep): - openssl_osdep = True - - if openssl_osdep: - tcname = ec['toolchain']['name'] - tcver = LooseVersion(ec['toolchain']['version']) - - gcc_subtc_2021a = tcname in ('GCCcore', 'GCC') and tcver > LooseVersion('10.3') - if gcc_subtc_2021a or (tcname in ('foss', 'gompi', 'iimpi', 'intel') and tcver >= LooseVersion('2021')): - self.assertFalse(openssl_osdep, "OpenSSL should not be listed as OS dependency in %s" % spec) - - src_cnt = len(ec['sources']) - patch_checksums = ec['checksums'][src_cnt:] - patch_checksums_cnt = len(patch_checksums) - - # make sure all patch files are available - specdir = os.path.dirname(spec) - specfn = os.path.basename(spec) - for idx, patch in enumerate(ec['patches']): - if isinstance(patch, (tuple, list)): - patch = patch[0] - - # only check actual patch files, not other files being copied via the patch functionality - patch_full = os.path.join(specdir, patch) - if patch.endswith('.patch'): - msg = "Patch file %s is available for %s" % (patch_full, specfn) - self.assertTrue(os.path.isfile(patch_full), msg) - - # verify checksum for each patch file - if idx < patch_checksums_cnt and (os.path.exists(patch_full) or patch.endswith('.patch')): - checksum = patch_checksums[idx] - error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch, ec_fn, checksum) - res = verify_checksum(patch_full, checksum) - self.assertTrue(res, error_msg) - - # make sure 'source' step is not being skipped, - # since that implies not verifying the checksum - error_msg = "'source' step should not be skipped in %s, since that implies not verifying checksums" % ec_fn - self.assertFalse(ec['checksums'] and ('source' in ec['skipsteps']), error_msg) - - for ext in ec['exts_list']: - if isinstance(ext, (tuple, list)) and len(ext) == 3: - - ext_name = ext[0] - - self.assertTrue(isinstance(ext[2], dict), "3rd element of extension spec is a dictionary") - - # fall back to assuming a single source file for an extension - src_cnt = len(ext[2].get('sources', [])) or 1 - - checksums = ext[2].get('checksums', []) - patch_checksums = checksums[src_cnt:] - - for idx, ext_patch in enumerate(ext[2].get('patches', [])): - if isinstance(ext_patch, (tuple, list)): - ext_patch = ext_patch[0] - - # only check actual patch files, not other files being copied via the patch functionality - ext_patch_full = os.path.join(specdir, ext_patch) - if ext_patch.endswith('.patch'): - msg = "Patch file %s is available for %s" % (ext_patch_full, specfn) - self.assertTrue(os.path.isfile(ext_patch_full), msg) - - # verify checksum for each patch file - if idx < patch_checksums_cnt and (os.path.exists(ext_patch_full) or ext_patch.endswith('.patch')): - checksum = patch_checksums[idx] - error_msg = "Invalid checksum for patch file %s for %s extension in %s: %s" - res = verify_checksum(ext_patch_full, checksum) - self.assertTrue(res, error_msg % (ext_patch, ext_name, ec_fn, checksum)) - - # check whether all extra_options defined for used easyblock are defined - extra_opts = app.extra_options() - for key in extra_opts: - self.assertTrue(key in app.cfg) - - app.close_log() - os.remove(app.logfile) - - # inject dummy values for templates that are only known at a later stage - dummy_template_values = { - 'builddir': '/dummy/builddir', - 'installdir': '/dummy/installdir', - 'parallel': '2', - } - ec.template_values.update(dummy_template_values) - - ec_dict = ec.parser.get_config_dict() - orig_toolchain = ec_dict['toolchain'] - for key in ec_dict: - # skip parameters for which value is equal to default value - orig_val = ec_dict[key] - if key in DEFAULT_CONFIG and orig_val == DEFAULT_CONFIG[key][0]: - continue - if key in extra_opts and orig_val == extra_opts[key][0]: - continue - if key not in DEFAULT_CONFIG and key not in extra_opts: - continue - - orig_val = resolve_template(ec_dict[key], ec.template_values) - dumped_val = resolve_template(dumped_ec[key], ec.template_values) - - # take into account that dumped value for *dependencies may include hard-coded subtoolchains - # if no easyconfig was found for the dependency with the 'parent' toolchain, - # if may get resolved using a subtoolchain, which is then hardcoded in the dumped easyconfig - if key in DEPENDENCY_PARAMETERS: - # number of dependencies should remain the same - self.assertEqual(len(orig_val), len(dumped_val)) - for orig_dep, dumped_dep in zip(orig_val, dumped_val): - # name should always match - self.assertEqual(orig_dep[0], dumped_dep[0]) - - # version should always match, or be a possibility from the version dict - if isinstance(orig_dep[1], dict): - self.assertTrue(dumped_dep[1] in orig_dep[1].values()) - else: - self.assertEqual(orig_dep[1], dumped_dep[1]) - - # 3rd value is versionsuffix; - if len(dumped_dep) >= 3: - # if no versionsuffix was specified in original dep spec, then dumped value should be empty string - if len(orig_dep) >= 3: - self.assertEqual(dumped_dep[2], orig_dep[2]) - else: - self.assertEqual(dumped_dep[2], '') - - # 4th value is toolchain spec - if len(dumped_dep) >= 4: - if len(orig_dep) >= 4: - self.assertEqual(dumped_dep[3], orig_dep[3]) - else: - # if a subtoolchain is specifed (only) in the dumped easyconfig, - # it should *not* be the same as the parent toolchain - self.assertNotEqual(dumped_dep[3], (orig_toolchain['name'], orig_toolchain['version'])) - - # take into account that for some string-valued easyconfig parameters (configopts & co), - # the easyblock may have injected additional values, which affects the dumped easyconfig file - elif isinstance(orig_val, string_type): - error_msg = "%s value '%s' should start with '%s'" % (key, dumped_val, orig_val) - self.assertTrue(dumped_val.startswith(orig_val), error_msg) - else: - error_msg = "%s value should be equal in original and dumped easyconfig: '%s' vs '%s'" - self.assertEqual(orig_val, dumped_val, error_msg % (key, orig_val, dumped_val)) - - # test passed, so set back to True - single_tests_ok = True and prev_single_tests_ok - - -def suite(loader=None): - """Return all easyblock initialisation tests.""" - def make_inner_test(spec_path): - def innertest(self): - template_easyconfig_test(self, spec_path) - return innertest - - # dynamically generate a separate test for each of the available easyconfigs - # define new inner functions that can be added as class methods to InitTest - easyconfigs_path = get_paths_for('easyconfigs')[0] - cnt = 0 - for (subpath, dirs, specs) in os.walk(easyconfigs_path, topdown=True): - - # ignore archived easyconfigs - if '__archive__' in dirs: - dirs.remove('__archive__') - - for spec in specs: - if spec.endswith('.eb') and spec != 'TEMPLATE.eb': - cnt += 1 - innertest = make_inner_test(os.path.join(subpath, spec)) - innertest.__doc__ = "Test for easyconfig %s" % spec - # double underscore so parsing tests are run first - innertest.__name__ = "test__parse_easyconfig_%s" % spec - setattr(EasyConfigTest, innertest.__name__, innertest) - - print("Found %s easyconfigs..." % cnt) - if not loader: - loader = TestLoader() - return loader.loadTestsFromTestCase(EasyConfigTest) - - -if __name__ == '__main__': - main() From d279ee5c4ac553d619f00b874b1ba9b4fd43ac91 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 2 Dec 2021 12:11:50 +0100 Subject: [PATCH 2177/9987] adding easyconfigs: cxxopts-3.0.0-GCCcore-10.3.0.eb --- .../c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..55199a32864 --- /dev/null +++ b/easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'cxxopts' +version = '3.0.0' + +homepage = 'https://github.com/jarro2783/cxxopts' +description = """cxxopts is a lightweight C++ command line option parser""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'jarro2783' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['36f41fa2a46b3c1466613b63f3fa73dc24d912bc90d667147f1e43215a8c6d00'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ["include/cxxopts.hpp"], + 'dirs': ["lib"] +} + +moduleclass = 'devel' From a13b698f5208ce92964bfe31666548a9085e46c9 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 2 Dec 2021 12:12:21 +0100 Subject: [PATCH 2178/9987] adding easyconfigs: ELFIO-3.9-GCCcore-10.3.0.eb --- .../e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c8720f4d262 --- /dev/null +++ b/easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'ELFIO' +version = '3.9' + +homepage = 'http://elfio.sourceforge.net' +description = """ELFIO is a header-only C++ library intended + for reading and generating files in the ELF binary format.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'serge1' +source_urls = [GITHUB_SOURCE] +sources = ['Release_%(version)s.tar.gz'] +checksums = ['bf93538afe916b333aef1d03e44c9b80dace61f4d097e581ae332cd2d4fa178e'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ["include/%(namelower)s/%(namelower)s.hpp"], + 'dirs': ['share', 'include/%(namelower)s'] +} + +moduleclass = 'devel' From 4ae371acccb113d8a6c2cc90c004a981a3a433a1 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 2 Dec 2021 12:12:50 +0100 Subject: [PATCH 2179/9987] adding easyconfigs: termcolor-2.0.0-GCCcore-10.3.0.eb --- .../termcolor-2.0.0-GCCcore-10.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e13aaa0acb9 --- /dev/null +++ b/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'termcolor' +version = '2.0.0' + +homepage = 'https://termcolor.readthedocs.io/' +description = """Termcolor is a header-only C++ library for printing colored + messages to the terminal.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'ikalnytskyi' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4a73a77053822ca1ed6d4a2af416d31028ec992fb0ffa794af95bd6216bb6a20'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['include/%(name)s/%(name)s.hpp', 'lib'], + 'dirs': ['include', 'lib'] +} + +moduleclass = 'devel' From 51035fbf79632a60477c6b4bb7f2c182e9a3e329 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 2 Dec 2021 12:38:19 +0100 Subject: [PATCH 2180/9987] Adds missing binutils --- .../easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb index e13aaa0acb9..81193bea573 100644 --- a/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb @@ -18,6 +18,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['4a73a77053822ca1ed6d4a2af416d31028ec992fb0ffa794af95bd6216bb6a20'] builddependencies = [ + ('binutils', '2.36.1'), ('CMake', '3.20.1'), ] From 0ebf90811bd245d755c2092d6aed8122b2ecf990 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 2 Dec 2021 12:39:58 +0100 Subject: [PATCH 2181/9987] Adds missing binutils --- easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb index 55199a32864..4ca7e838217 100644 --- a/easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb @@ -17,6 +17,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['36f41fa2a46b3c1466613b63f3fa73dc24d912bc90d667147f1e43215a8c6d00'] builddependencies = [ + ('binutils', '2.36.1'), ('CMake', '3.20.1'), ] From a224893b76b89f6167201258326287847424211b Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 2 Dec 2021 12:43:35 +0100 Subject: [PATCH 2182/9987] Adds missing binutils --- easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb index c8720f4d262..42ab8d77835 100644 --- a/easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb @@ -18,6 +18,7 @@ sources = ['Release_%(version)s.tar.gz'] checksums = ['bf93538afe916b333aef1d03e44c9b80dace61f4d097e581ae332cd2d4fa178e'] builddependencies = [ + ('binutils', '2.36.1'), ('CMake', '3.20.1'), ] From a4c36c071e63f60f233daaba6251081c3de6e68e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 2 Dec 2021 19:49:10 +0800 Subject: [PATCH 2183/9987] add back deleted lines --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9789392bcd0..57c4254fc69 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -481,6 +481,8 @@ def check_dep_vars(self, gen, dep, dep_vars): r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], # NanoPlot, NanoComp use an older version of Seaborn 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], + # Shasta requires spoa 3.x + 'spoa': [(r'3\.4\.0', [r'Shasta-0\.8\.0-'])], 'TensorFlow': [ # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), # artic-ncov2019 requires medaka From 095719b8b92404d8a325d9c1fa06be8d4df80d33 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 2 Dec 2021 14:25:12 +0100 Subject: [PATCH 2184/9987] Remove wrong sanity check file --- .../easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb index 81193bea573..03d342fb291 100644 --- a/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['include/%(name)s/%(name)s.hpp', 'lib'], + 'files': ['include/%(name)s/%(name)s.hpp'], 'dirs': ['include', 'lib'] } From 75b12676a789e575819058f38a4db0cd104d34e4 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 2 Dec 2021 18:04:37 +0100 Subject: [PATCH 2185/9987] Added patch to rename zmq with pyzmq --- .../q/QCGPilotJob/QCGPilotJob-0.12.3.eb | 10 ++++++---- .../QCGPilotJob-0.12.3_rename_zmq.patch | 14 ++++++++++++++ 2 files changed, 20 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb index abc5610df44..9402d6b7e44 100644 --- a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb +++ b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb @@ -17,11 +17,9 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_list = [ - ('zmq', '0.0.0', { - 'checksums': ['6b1a1de53338646e8c8405803cffb659e8eb7bb02fff4c9be62a7acfac8370c9'], - }), ('patsy', '0.5.2', { 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], }), @@ -40,7 +38,11 @@ exts_list = [ ('qcg', '0.12.3', { 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966'], + 'patches': ['QCGPilotJob-0.12.3_rename_zmq.patch'], + 'checksums': [ + '9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966', # v0.12.3.tar.gz + '51cba1bfe1dcd33180dffe65941acdfa70823d6cae4b81182fd16a7debf907cd', # QCGPilotJob-0.12.3_rename_zmq.patch + ], 'start_dir': 'components/core', }), ('qcg', '0.12.3', { diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch new file mode 100644 index 00000000000..3fa5595dadb --- /dev/null +++ b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch @@ -0,0 +1,14 @@ +# Replace zmq with pyzmq +# Author: maxim-masterov (SURF) +diff -Nru QCG-PilotJob-0.12.3.orig/components/core/setup.py QCG-PilotJob-0.12.3/components/core/setup.py +--- QCG-PilotJob-0.12.3.orig/components/core/setup.py 2021-12-02 13:33:02.564287000 +0100 ++++ QCG-PilotJob-0.12.3/components/core/setup.py 2021-12-02 15:00:08.997343000 +0100 +@@ -27,7 +27,7 @@ + long_description_content_type="text/markdown", + + install_requires=[ +- "zmq", ++ "pyzmq", + "click", + "psutil", + ], From 8dbd70aeb4a6dbed986fcd2ee37a749e6f76361b Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 2 Dec 2021 18:35:08 +0100 Subject: [PATCH 2186/9987] Renamed easyconfig --- .../{QCGPilotJob-0.12.3.eb => QCGPilotJob-0.12.3-foss-2021a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/q/QCGPilotJob/{QCGPilotJob-0.12.3.eb => QCGPilotJob-0.12.3-foss-2021a.eb} (100%) diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3-foss-2021a.eb similarity index 100% rename from easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3.eb rename to easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3-foss-2021a.eb From 9bfd923aa7f13c3f1cdb453bf5d2118b3b597239 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 2 Dec 2021 18:48:16 +0100 Subject: [PATCH 2187/9987] Renamed easycinfig --- ...Job-0.12.3-foss-2021a.eb => QCG-PilotJob-0.12.3-foss-2021a.eb} | 0 ...12.3_rename_zmq.patch => QCG-PilotJob-0.12.3_rename_zmq.patch} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/q/QCGPilotJob/{QCGPilotJob-0.12.3-foss-2021a.eb => QCG-PilotJob-0.12.3-foss-2021a.eb} (100%) rename easybuild/easyconfigs/q/QCGPilotJob/{QCGPilotJob-0.12.3_rename_zmq.patch => QCG-PilotJob-0.12.3_rename_zmq.patch} (100%) diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3-foss-2021a.eb b/easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb similarity index 100% rename from easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3-foss-2021a.eb rename to easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch b/easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch similarity index 100% rename from easybuild/easyconfigs/q/QCGPilotJob/QCGPilotJob-0.12.3_rename_zmq.patch rename to easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch From ee5ade12111a7071b749c9b6a34445049ece9e4e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 2 Dec 2021 19:02:59 +0100 Subject: [PATCH 2188/9987] Renamed folder --- .../QCG-PilotJob-0.12.3-foss-2021a.eb | 0 .../QCG-PilotJob-0.12.3_rename_zmq.patch | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/q/{QCGPilotJob => QCG-PilotJob}/QCG-PilotJob-0.12.3-foss-2021a.eb (100%) rename easybuild/easyconfigs/q/{QCGPilotJob => QCG-PilotJob}/QCG-PilotJob-0.12.3_rename_zmq.patch (100%) diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb similarity index 100% rename from easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb rename to easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch similarity index 100% rename from easybuild/easyconfigs/q/QCGPilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch rename to easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3_rename_zmq.patch From 902cbd3f38d79fb8069bb286b985763466348314 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 2 Dec 2021 19:15:43 +0100 Subject: [PATCH 2189/9987] Fixed patch name --- .../q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb index 9402d6b7e44..e15fca04e5d 100644 --- a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.12.3-foss-2021a.eb @@ -38,10 +38,10 @@ exts_list = [ ('qcg', '0.12.3', { 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', - 'patches': ['QCGPilotJob-0.12.3_rename_zmq.patch'], + 'patches': ['QCG-PilotJob-0.12.3_rename_zmq.patch'], 'checksums': [ '9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966', # v0.12.3.tar.gz - '51cba1bfe1dcd33180dffe65941acdfa70823d6cae4b81182fd16a7debf907cd', # QCGPilotJob-0.12.3_rename_zmq.patch + '51cba1bfe1dcd33180dffe65941acdfa70823d6cae4b81182fd16a7debf907cd', # QCG-PilotJob-0.12.3_rename_zmq.patch ], 'start_dir': 'components/core', }), From 69a3a01190e72fe6bcc3bf21abe8ca8afe9e4ca9 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 2 Dec 2021 18:31:04 +0000 Subject: [PATCH 2190/9987] adding easyconfigs: FreeSurfer-7.2.0-ubuntu18_amd64.eb, FreeSurfer-7.2.0-centos7_x86_64.eb, FreeSurfer-7.2.0-centos8_x86_64.eb --- .../FreeSurfer-7.2.0-centos7_x86_64.eb | 33 +++++++++++++++++++ .../FreeSurfer-7.2.0-centos8_x86_64.eb | 33 +++++++++++++++++++ .../FreeSurfer-7.2.0-ubuntu18_amd64.eb | 33 +++++++++++++++++++ 3 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos7_x86_64.eb create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-ubuntu18_amd64.eb diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos7_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos7_x86_64.eb new file mode 100644 index 00000000000..c918d56dab9 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos7_x86_64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.2.0' +versionsuffix = '-centos7_x86_64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + # freesurfer-linux-centos7_x86_64-7.2.0.tar.gz + '4cca78602f898bf633428b9d82cbb9b07e3ab97a86c620122050803779c86d62', + '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb new file mode 100644 index 00000000000..22a5572078f --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.2.0' +versionsuffix = '-centos8_x86_64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + # freesurfer-linux-centos8_x86_64-7.2.0.tar.gz + '6098b166fee8644f44f9ec88f3ffe88d05f2bc033cca60443e99e3e56f2e166b', + '1eecbe0f027b95ee9ec7cce4c0846e14e7bf623fa1937ac57911a26f8f23d3e6', # runtime2014bLinux.tar.gz +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-ubuntu18_amd64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-ubuntu18_amd64.eb new file mode 100644 index 00000000000..18fc67d8672 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-ubuntu18_amd64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.2.0' +versionsuffix = '-ubuntu18_amd64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + # freesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz + 'e0cbd55809359ce7f8019d6e8794524cd9f182ab9d1a151644d6ccd3ee582cd2', + '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' From e16d1b2c04b9d4d4a63676ce19bfa11bb9799c90 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Dec 2021 20:31:37 +0100 Subject: [PATCH 2191/9987] improve sanity_check_paths in pugixml easyconfig --- .../easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb index 10038ee5686..cada546fa3a 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.11.4-GCCcore-10.3.0.eb @@ -26,8 +26,9 @@ builddependencies = [ configopts = '-DBUILD_SHARED_AND_STATIC_LIBS=ON -DPUGIXML_HEADER_ONLY=True ' sanity_check_paths = { - 'files': [], - 'dirs': ['lib'], + 'files': ['include/pugiconfig.hpp', 'include/pugixml.hpp', 'lib/libpugixml.a', + 'lib/libpugixml.%s' % SHLIB_EXT, 'lib/pkgconfig/pugixml.pc'], + 'dirs': ['lib/cmake/pugixml'], } moduleclass = 'data' From 6cdb49300d80b9f76b1795a8771a9acb1f31a8bd Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 3 Dec 2021 06:15:51 +0800 Subject: [PATCH 2192/9987] consolidate easyconfigs for Grace --- .../Grace-5.1.25-foss-2016a.eb} | 2 +- .../Grace-5.1.25-foss-2021a.eb} | 2 +- .../Grace-5.1.25-intel-2016a.eb} | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/{grace/grace-5.1.25-foss-2016a.eb => Grace/Grace-5.1.25-foss-2016a.eb} (97%) rename easybuild/easyconfigs/g/{grace/grace-5.1.25-foss-2021a.eb => Grace/Grace-5.1.25-foss-2021a.eb} (97%) rename easybuild/easyconfigs/g/{grace/grace-5.1.25-intel-2016a.eb => Grace/Grace-5.1.25-intel-2016a.eb} (97%) diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2016a.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb similarity index 97% rename from easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2016a.eb rename to easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb index 674925f1b99..fc5cf03bb15 100644 --- a/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'grace' +name = 'Grace' version = '5.1.25' homepage = 'http://freecode.com/projects/grace' diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021a.eb similarity index 97% rename from easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb rename to easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021a.eb index 72ac27c0b80..c21345207dc 100644 --- a/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2021a.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'grace' +name = 'Grace' version = '5.1.25' homepage = 'http://freecode.com/projects/grace' diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb similarity index 97% rename from easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb rename to easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb index e538b0ca3bf..719293e139f 100644 --- a/easybuild/easyconfigs/g/grace/grace-5.1.25-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'grace' +name = 'Grace' version = '5.1.25' homepage = 'http://freecode.com/projects/grace' From a42819417335222ed7c70162328c643660eb1e8f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 3 Dec 2021 08:57:27 +0100 Subject: [PATCH 2193/9987] adding easyconfigs: libnsl-1.3.0-GCCcore-10.3.0.eb --- .../l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f2ed1e64b7d --- /dev/null +++ b/easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libnsl' +version = '1.3.0' + +homepage = 'https://www.linuxfromscratch.org/blfs/view/svn/basicnet/libnsl.html' +description = """The libnsl package contains the public client interface for NIS(YP).""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('libtirpc', '1.3.2'), +] + +# Provide a symlink for libnsl.so.1, which used to be part of glibc. +# This new version of libnsl should be backwards compatible. +postinstallcmds = ['ln -s libnsl.so %(installdir)s/lib/libnsl.so.1'] + +sanity_check_paths = { + 'files': ['include/rpcsvc/nis.h', 'include/rpcsvc/yp.h', 'lib/libnsl.a', + 'lib/libnsl.%s' % SHLIB_EXT, 'lib/libnsl.%s.1' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' From 53bc52afa8c8eab74732ba23886ae6a3cf6e147a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 3 Dec 2021 09:00:07 +0100 Subject: [PATCH 2194/9987] add dep on libnsl, remove comment about supported distros --- .../a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb index c9c00814fdb..e8846a25459 100644 --- a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb @@ -1,4 +1,3 @@ -# This installation only works for Linux distributions that provide libnsl.so.1 as part of the (g)libc package. easyblock = 'MakeCp' name = 'ANIcalculator' @@ -21,6 +20,7 @@ builddependencies = [('binutils', '2.36.1')] dependencies = [ ('Perl', '5.32.1'), + ('libnsl', '1.3.0'), ] skipsteps = ['build'] From abf90739f5e0e6e01555408b9f07a39bb067f02d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 3 Dec 2021 09:00:34 +0100 Subject: [PATCH 2195/9987] remove build dep on binutils --- .../a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb index e8846a25459..9df3c3e1ae6 100644 --- a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb @@ -16,8 +16,6 @@ source_urls = ['https://ani.jgi.doe.gov/download_files/'] sources = ['%(name)s_v%(version_major)s.tgz'] checksums = ['236596a9a204cbcad162fc66be3506b2530b1f48f4f84d9647ccec3ca7483a43'] -builddependencies = [('binutils', '2.36.1')] - dependencies = [ ('Perl', '5.32.1'), ('libnsl', '1.3.0'), From 166aeaf9b680c4329d2bd357680de129c6097cc3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 3 Dec 2021 09:03:24 +0100 Subject: [PATCH 2196/9987] add exception for ANIcalculator for requiring binutils --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 57c4254fc69..bb0cdb9507a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1194,7 +1194,7 @@ def template_easyconfig_test(self, spec): # make sure binutils is included as a (build) dep if toolchain is GCCcore if ec['toolchain']['name'] == 'GCCcore': # with 'Tarball' easyblock: only unpacking, no building; Eigen is also just a tarball - requires_binutils = ec['easyblock'] not in ['Tarball'] and ec['name'] not in ['Eigen'] + requires_binutils = ec['easyblock'] not in ['Tarball'] and ec['name'] not in ['ANIcalculator', 'Eigen'] # let's also exclude the very special case where the system GCC is used as GCCcore, and only apply this # exception to the dependencies of binutils (since we should eventually build a new binutils with GCCcore) From 810ef3e0f2ee3eacdcdbf04d73606757dd0560fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 3 Dec 2021 09:35:43 +0100 Subject: [PATCH 2197/9987] add checksum --- easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb index f2ed1e64b7d..4796f60f8cf 100644 --- a/easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] sources = [SOURCE_TAR_XZ] +checksums = ['eac3062957fa302c62eff4aed718a07bacbf9ceb0a058289f12a19bfdda3c8e2'] builddependencies = [ ('binutils', '2.36.1'), From 35baf02dc28e19a9250bf1a8169abec151ac4123 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 3 Dec 2021 10:59:08 +0100 Subject: [PATCH 2198/9987] Change homepage --- easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb index 4796f60f8cf..fcacc1c559f 100644 --- a/easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libnsl/libnsl-1.3.0-GCCcore-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libnsl' version = '1.3.0' -homepage = 'https://www.linuxfromscratch.org/blfs/view/svn/basicnet/libnsl.html' +homepage = 'https://github.com/thkukuk/libnsl' description = """The libnsl package contains the public client interface for NIS(YP).""" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} From 9ea46fc7de379ac55093fd50336362d2009b4f8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Dec 2021 11:43:19 +0100 Subject: [PATCH 2199/9987] adding easyconfigs: DUBStepR-1.2.0-foss-2021b-R-4.1.2.eb --- .../DUBStepR-1.2.0-foss-2021b-R-4.1.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/d/DUBStepR/DUBStepR-1.2.0-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/d/DUBStepR/DUBStepR-1.2.0-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DUBStepR/DUBStepR-1.2.0-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..3e88b94a773 --- /dev/null +++ b/easybuild/easyconfigs/d/DUBStepR/DUBStepR-1.2.0-foss-2021b-R-4.1.2.eb @@ -0,0 +1,31 @@ +easyblock = 'RPackage' + +name = 'DUBStepR' +version = '1.2.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/prabhakarlab/DUBStepR' +description = """DUBStepR (Determining the Underlying Basis using Step-wise Regression) is a feature selection +algorithm for cell type identification in single-cell RNA-sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['c166bb94c734b70c1c5769b7ba558a0123a70c9d64e4a43d88e35986e141aa4e'] + +dependencies = [ + ('R', '4.1.2'), + ('R-bundle-Bioconductor', '3.14', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From e93fb2195a863ccbaa706761e695de702e700834 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 3 Dec 2021 13:41:01 +0000 Subject: [PATCH 2200/9987] add patch to fix CVE-2021-43527 in NSS --- .../n/NSS/NSS-3.39-GCCcore-6.4.0.eb | 6 +- .../n/NSS/NSS-3.39-GCCcore-7.3.0.eb | 6 +- .../n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb | 6 +- .../n/NSS/NSS-3.42.1_CVE-2021-43527.patch | 285 ++++++++++++++ .../n/NSS/NSS-3.45-GCCcore-8.3.0.eb | 6 +- .../n/NSS/NSS-3.51-GCCcore-9.3.0.eb | 2 + .../n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 2 + .../n/NSS/NSS-3.65-GCCcore-10.3.0.eb | 2 + .../n/NSS/NSS-3.65_CVE-2021-43527.patch | 352 ++++++++++++++++++ .../n/NSS/NSS-3.69-GCCcore-11.2.0.eb | 2 + 10 files changed, 665 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.42.1_CVE-2021-43527.patch create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.65_CVE-2021-43527.patch diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-6.4.0.eb index 889e4a9531d..16cb48ca51f 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-6.4.0.eb @@ -11,10 +11,14 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['NSS-%(version)s_pkgconfig.patch'] +patches = [ + 'NSS-%(version)s_pkgconfig.patch', + 'NSS-3.42.1_CVE-2021-43527.patch', +] checksums = [ '6be64dd76f212415cc8bc34343ac1e7389048db4db9a023a84873c411dc5864b', # nss-3.39.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + 'cc17945edcc8f6d951e8710a4e99604439a1758e38539d1b7b8c0cd95ac59355', # NSS-3.42.1_CVE-2021-43527.patch ] builddependencies = [('binutils', '2.28')] diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-7.3.0.eb index 50e0978d690..39930af4777 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-7.3.0.eb @@ -11,10 +11,14 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['NSS-%(version)s_pkgconfig.patch'] +patches = [ + 'NSS-%(version)s_pkgconfig.patch', + 'NSS-3.42.1_CVE-2021-43527.patch', +] checksums = [ '6be64dd76f212415cc8bc34343ac1e7389048db4db9a023a84873c411dc5864b', # nss-3.39.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + 'cc17945edcc8f6d951e8710a4e99604439a1758e38539d1b7b8c0cd95ac59355', # NSS-3.42.1_CVE-2021-43527.patch ] builddependencies = [('binutils', '2.30')] diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb index 165b3e41cc6..420f1b6d99c 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb @@ -11,10 +11,14 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_1_RTM/src/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['NSS-3.39_pkgconfig.patch'] +patches = [ + 'NSS-3.39_pkgconfig.patch', + 'NSS-3.42.1_CVE-2021-43527.patch', +] checksums = [ '087db37d38fd49dfd584dd2a8b5baa7fc88de7c9bd97c0c2d5be4abcafc61fc6', # nss-3.42.1.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + 'cc17945edcc8f6d951e8710a4e99604439a1758e38539d1b7b8c0cd95ac59355', # NSS-3.42.1_CVE-2021-43527.patch ] builddependencies = [('binutils', '2.31.1')] diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.42.1_CVE-2021-43527.patch b/easybuild/easyconfigs/n/NSS/NSS-3.42.1_CVE-2021-43527.patch new file mode 100644 index 00000000000..a202443c108 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.42.1_CVE-2021-43527.patch @@ -0,0 +1,285 @@ + +# HG changeset patch +# User Dennis Jackson +# Date 1637577642 0 +# Node ID dea71cbef9e03636f37c6cb120f8deccce6e17dd +# Parent da3d22d708c9cc0a32cff339658aeb627575e371 +Bug 1737470 - Ensure DER encoded signatures are within size limits. r=jschanck,mt,bbeurdouche,rrelyea + +Differential Revision: https://phabricator.services.mozilla.com/D129514 + +--- a/nss/lib/cryptohi/secvfy.c ++++ b/nss/lib/cryptohi/secvfy.c +@@ -164,6 +164,37 @@ verifyPKCS1DigestInfo(const VFYContext * + PR_FALSE /*XXX: unsafeAllowMissingParameters*/); + } + ++static unsigned int ++checkedSignatureLen(const SECKEYPublicKey *pubk) ++{ ++ unsigned int sigLen = SECKEY_SignatureLen(pubk); ++ if (sigLen == 0) { ++ /* Error set by SECKEY_SignatureLen */ ++ return sigLen; ++ } ++ unsigned int maxSigLen; ++ switch (pubk->keyType) { ++ case rsaKey: ++ case rsaPssKey: ++ maxSigLen = (RSA_MAX_MODULUS_BITS + 7) / 8; ++ break; ++ case dsaKey: ++ maxSigLen = DSA_MAX_SIGNATURE_LEN; ++ break; ++ case ecKey: ++ maxSigLen = 2 * MAX_ECKEY_LEN; ++ break; ++ default: ++ PORT_SetError(SEC_ERROR_UNSUPPORTED_KEYALG); ++ return 0; ++ } ++ if (sigLen > maxSigLen) { ++ PORT_SetError(SEC_ERROR_INVALID_KEY); ++ return 0; ++ } ++ return sigLen; ++} ++ + /* + * decode the ECDSA or DSA signature from it's DER wrapping. + * The unwrapped/raw signature is placed in the buffer pointed +@@ -174,38 +205,38 @@ decodeECorDSASignature(SECOidTag algid, + unsigned int len) + { + SECItem *dsasig = NULL; /* also used for ECDSA */ +- SECStatus rv = SECSuccess; + +- if ((algid != SEC_OID_ANSIX9_DSA_SIGNATURE) && +- (algid != SEC_OID_ANSIX962_EC_PUBLIC_KEY)) { +- if (sig->len != len) { +- PORT_SetError(SEC_ERROR_BAD_DER); +- return SECFailure; ++ /* Safety: Ensure algId is as expected and that signature size is within maxmimums */ ++ if (algid == SEC_OID_ANSIX9_DSA_SIGNATURE) { ++ if (len > DSA_MAX_SIGNATURE_LEN) { ++ goto loser; + } +- +- PORT_Memcpy(dsig, sig->data, sig->len); +- return SECSuccess; +- } +- +- if (algid == SEC_OID_ANSIX962_EC_PUBLIC_KEY) { ++ } else if (algid == SEC_OID_ANSIX962_EC_PUBLIC_KEY) { + if (len > MAX_ECKEY_LEN * 2) { +- PORT_SetError(SEC_ERROR_BAD_DER); +- return SECFailure; ++ goto loser; + } +- } +- dsasig = DSAU_DecodeDerSigToLen((SECItem *)sig, len); +- +- if ((dsasig == NULL) || (dsasig->len != len)) { +- rv = SECFailure; + } else { +- PORT_Memcpy(dsig, dsasig->data, dsasig->len); ++ goto loser; + } + +- if (dsasig != NULL) ++ /* Decode and pad to length */ ++ dsasig = DSAU_DecodeDerSigToLen((SECItem *)sig, len); ++ if (dsasig == NULL) { ++ goto loser; ++ } ++ if (dsasig->len != len) { + SECITEM_FreeItem(dsasig, PR_TRUE); +- if (rv == SECFailure) +- PORT_SetError(SEC_ERROR_BAD_DER); +- return rv; ++ goto loser; ++ } ++ ++ PORT_Memcpy(dsig, dsasig->data, len); ++ SECITEM_FreeItem(dsasig, PR_TRUE); ++ ++ return SECSuccess; ++ ++loser: ++ PORT_SetError(SEC_ERROR_BAD_DER); ++ return SECFailure; + } + + const SEC_ASN1Template hashParameterTemplate[] = +@@ -231,7 +262,7 @@ SECStatus + sec_DecodeSigAlg(const SECKEYPublicKey *key, SECOidTag sigAlg, + const SECItem *param, SECOidTag *encalg, SECOidTag *hashalg) + { +- int len; ++ unsigned int len; + PLArenaPool *arena; + SECStatus rv; + SECItem oid; +@@ -446,48 +477,52 @@ vfy_CreateContext(const SECKEYPublicKey + cx->pkcs1RSADigestInfo = NULL; + rv = SECSuccess; + if (sig) { +- switch (type) { +- case rsaKey: +- rv = recoverPKCS1DigestInfo(hashAlg, &cx->hashAlg, +- &cx->pkcs1RSADigestInfo, +- &cx->pkcs1RSADigestInfoLen, +- cx->key, +- sig, wincx); +- break; +- case rsaPssKey: +- sigLen = SECKEY_SignatureLen(key); +- if (sigLen == 0) { +- /* error set by SECKEY_SignatureLen */ +- rv = SECFailure; ++ rv = SECFailure; ++ if (type == rsaKey) { ++ rv = recoverPKCS1DigestInfo(hashAlg, &cx->hashAlg, ++ &cx->pkcs1RSADigestInfo, ++ &cx->pkcs1RSADigestInfoLen, ++ cx->key, ++ sig, wincx); ++ } else { ++ sigLen = checkedSignatureLen(key); ++ /* Check signature length is within limits */ ++ if (sigLen == 0) { ++ /* error set by checkedSignatureLen */ ++ rv = SECFailure; ++ goto loser; ++ } ++ if (sigLen > sizeof(cx->u)) { ++ PORT_SetError(SEC_ERROR_BAD_SIGNATURE); ++ rv = SECFailure; ++ goto loser; ++ } ++ switch (type) { ++ case rsaPssKey: ++ if (sig->len != sigLen) { ++ PORT_SetError(SEC_ERROR_BAD_SIGNATURE); ++ rv = SECFailure; ++ goto loser; ++ } ++ PORT_Memcpy(cx->u.buffer, sig->data, sigLen); ++ rv = SECSuccess; + break; +- } +- if (sig->len != sigLen) { +- PORT_SetError(SEC_ERROR_BAD_SIGNATURE); +- rv = SECFailure; ++ case ecKey: ++ case dsaKey: ++ /* decodeECorDSASignature will check sigLen == sig->len after padding */ ++ rv = decodeECorDSASignature(encAlg, sig, cx->u.buffer, sigLen); + break; +- } +- PORT_Memcpy(cx->u.buffer, sig->data, sigLen); +- break; +- case dsaKey: +- case ecKey: +- sigLen = SECKEY_SignatureLen(key); +- if (sigLen == 0) { +- /* error set by SECKEY_SignatureLen */ ++ default: ++ /* Unreachable */ + rv = SECFailure; +- break; +- } +- rv = decodeECorDSASignature(encAlg, sig, cx->u.buffer, sigLen); +- break; +- default: +- rv = SECFailure; +- PORT_SetError(SEC_ERROR_UNSUPPORTED_KEYALG); +- break; ++ goto loser; ++ } ++ } ++ if (rv != SECSuccess) { ++ goto loser; + } + } + +- if (rv) +- goto loser; +- + /* check hash alg again, RSA may have changed it.*/ + if (HASH_GetHashTypeByOidTag(cx->hashAlg) == HASH_AlgNULL) { + /* error set by HASH_GetHashTypeByOidTag */ +@@ -622,11 +657,16 @@ VFY_EndWithSignature(VFYContext *cx, SEC + switch (cx->key->keyType) { + case ecKey: + case dsaKey: +- dsasig.data = cx->u.buffer; +- dsasig.len = SECKEY_SignatureLen(cx->key); ++ dsasig.len = checkedSignatureLen(cx->key); + if (dsasig.len == 0) { + return SECFailure; + } ++ if (dsasig.len > sizeof(cx->u)) { ++ PORT_SetError(SEC_ERROR_BAD_SIGNATURE); ++ return SECFailure; ++ } ++ dsasig.data = cx->u.buffer; ++ + if (sig) { + rv = decodeECorDSASignature(cx->encAlg, sig, dsasig.data, + dsasig.len); +@@ -658,8 +698,13 @@ VFY_EndWithSignature(VFYContext *cx, SEC + } + + rsasig.data = cx->u.buffer; +- rsasig.len = SECKEY_SignatureLen(cx->key); ++ rsasig.len = checkedSignatureLen(cx->key); + if (rsasig.len == 0) { ++ /* Error set by checkedSignatureLen */ ++ return SECFailure; ++ } ++ if (rsasig.len > sizeof(cx->u)) { ++ PORT_SetError(SEC_ERROR_BAD_SIGNATURE); + return SECFailure; + } + if (sig) { +@@ -721,7 +766,6 @@ vfy_VerifyDigest(const SECItem *digest, + SECStatus rv; + VFYContext *cx; + SECItem dsasig; /* also used for ECDSA */ +- + rv = SECFailure; + + cx = vfy_CreateContext(key, sig, encAlg, hashAlg, NULL, wincx); +@@ -729,19 +773,25 @@ vfy_VerifyDigest(const SECItem *digest, + switch (key->keyType) { + case rsaKey: + rv = verifyPKCS1DigestInfo(cx, digest); ++ /* Error (if any) set by verifyPKCS1DigestInfo */ + break; +- case dsaKey: + case ecKey: ++ case dsaKey: + dsasig.data = cx->u.buffer; +- dsasig.len = SECKEY_SignatureLen(cx->key); ++ dsasig.len = checkedSignatureLen(cx->key); + if (dsasig.len == 0) { ++ /* Error set by checkedSignatureLen */ ++ rv = SECFailure; + break; + } +- if (PK11_Verify(cx->key, &dsasig, (SECItem *)digest, cx->wincx) != +- SECSuccess) { ++ if (dsasig.len > sizeof(cx->u)) { ++ PORT_SetError(SEC_ERROR_BAD_SIGNATURE); ++ rv = SECFailure; ++ break; ++ } ++ rv = PK11_Verify(cx->key, &dsasig, (SECItem *)digest, cx->wincx); ++ if (rv != SECSuccess) { + PORT_SetError(SEC_ERROR_BAD_SIGNATURE); +- } else { +- rv = SECSuccess; + } + break; + default: diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb index 0e4f63906b1..a849724f7d5 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb @@ -11,10 +11,14 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] sources = [SOURCELOWER_TAR_GZ] -patches = ['NSS-3.39_pkgconfig.patch'] +patches = [ + 'NSS-3.39_pkgconfig.patch', + 'NSS-3.42.1_CVE-2021-43527.patch', +] checksums = [ '112f05223d1fde902c170966bfc6f011b24a838be16969b110ecf2bb7bc24e8b', # nss-3.45.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + 'cc17945edcc8f6d951e8710a4e99604439a1758e38539d1b7b8c0cd95ac59355', # NSS-3.42.1_CVE-2021-43527.patch ] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb index 39120284851..f263c9af718 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb @@ -14,11 +14,13 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'NSS-3.39_pkgconfig.patch', '%(name)s-%(version)s_fix_kremlin_ppc64le.patch', + 'NSS-3.42.1_CVE-2021-43527.patch', ] checksums = [ '75348b3b3229362486c57a880db917da1f96ef4eb639dc9cc2ff17d72268459c', # nss-3.51.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch '2fc7bd556737d34a62c06f86899863b7071b71943ffb4facfb413a087b8bee2e', # NSS-3.51_fix_kremlin_ppc64le.patch + 'cc17945edcc8f6d951e8710a4e99604439a1758e38539d1b7b8c0cd95ac59355', # NSS-3.42.1_CVE-2021-43527.patch ] builddependencies = [('binutils', '2.34')] diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 06357048174..6d30fd97e4b 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -13,10 +13,12 @@ source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_ sources = [SOURCELOWER_TAR_GZ] patches = [ 'NSS-3.39_pkgconfig.patch', + 'NSS-3.42.1_CVE-2021-43527.patch', ] checksums = [ '55a86c01be860381d64bb4e5b94eb198df9b0f098a8af0e58c014df398bdc382', # nss-3.57.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + 'cc17945edcc8f6d951e8710a4e99604439a1758e38539d1b7b8c0cd95ac59355', # NSS-3.42.1_CVE-2021-43527.patch ] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb index 296cd207c79..66f3d54596b 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb @@ -13,10 +13,12 @@ source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_ sources = [SOURCELOWER_TAR_GZ] patches = [ 'NSS-3.39_pkgconfig.patch', + 'NSS-3.65_CVE-2021-43527.patch', ] checksums = [ '32170f6c188212a78bf9fdacffa2eeed0d564ef8faae63fd8ae971b208e8c637', # nss-3.65.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + 'b9ccfdeb692f703e40e83202366bbdea9ef9506003b368e8061fc1fa439ebbc3', # NSS-3.65_CVE-2021-43527.patch ] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.65_CVE-2021-43527.patch b/easybuild/easyconfigs/n/NSS/NSS-3.65_CVE-2021-43527.patch new file mode 100644 index 00000000000..beba755539f --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.65_CVE-2021-43527.patch @@ -0,0 +1,352 @@ + +# HG changeset patch +# User Dennis Jackson +# Date 1637577642 0 +# Node ID 6b3dc97a8767d9dc5c4c181597d1341d0899aa58 +# Parent 0ee3564fdb1601e65abd93e888e4cb3ceab5f353 +Bug 1737470 - Ensure DER encoded signatures are within size limits. r=jschanck,mt,bbeurdouche,rrelyea + +Differential Revision: https://phabricator.services.mozilla.com/D129514 + +diff --git a/lib/cryptohi/secvfy.c b/lib/cryptohi/secvfy.c +--- a/lib/cryptohi/secvfy.c ++++ b/lib/cryptohi/secvfy.c +@@ -159,58 +159,89 @@ verifyPKCS1DigestInfo(const VFYContext * + SECItem pkcs1DigestInfo; + pkcs1DigestInfo.data = cx->pkcs1RSADigestInfo; + pkcs1DigestInfo.len = cx->pkcs1RSADigestInfoLen; + return _SGN_VerifyPKCS1DigestInfo( + cx->hashAlg, digest, &pkcs1DigestInfo, + PR_FALSE /*XXX: unsafeAllowMissingParameters*/); + } + ++static unsigned int ++checkedSignatureLen(const SECKEYPublicKey *pubk) ++{ ++ unsigned int sigLen = SECKEY_SignatureLen(pubk); ++ if (sigLen == 0) { ++ /* Error set by SECKEY_SignatureLen */ ++ return sigLen; ++ } ++ unsigned int maxSigLen; ++ switch (pubk->keyType) { ++ case rsaKey: ++ case rsaPssKey: ++ maxSigLen = (RSA_MAX_MODULUS_BITS + 7) / 8; ++ break; ++ case dsaKey: ++ maxSigLen = DSA_MAX_SIGNATURE_LEN; ++ break; ++ case ecKey: ++ maxSigLen = 2 * MAX_ECKEY_LEN; ++ break; ++ default: ++ PORT_SetError(SEC_ERROR_UNSUPPORTED_KEYALG); ++ return 0; ++ } ++ if (sigLen > maxSigLen) { ++ PORT_SetError(SEC_ERROR_INVALID_KEY); ++ return 0; ++ } ++ return sigLen; ++} ++ + /* + * decode the ECDSA or DSA signature from it's DER wrapping. + * The unwrapped/raw signature is placed in the buffer pointed + * to by dsig and has enough room for len bytes. + */ + static SECStatus + decodeECorDSASignature(SECOidTag algid, const SECItem *sig, unsigned char *dsig, + unsigned int len) + { + SECItem *dsasig = NULL; /* also used for ECDSA */ +- SECStatus rv = SECSuccess; + +- if ((algid != SEC_OID_ANSIX9_DSA_SIGNATURE) && +- (algid != SEC_OID_ANSIX962_EC_PUBLIC_KEY)) { +- if (sig->len != len) { +- PORT_SetError(SEC_ERROR_BAD_DER); +- return SECFailure; ++ /* Safety: Ensure algId is as expected and that signature size is within maxmimums */ ++ if (algid == SEC_OID_ANSIX9_DSA_SIGNATURE) { ++ if (len > DSA_MAX_SIGNATURE_LEN) { ++ goto loser; + } +- +- PORT_Memcpy(dsig, sig->data, sig->len); +- return SECSuccess; ++ } else if (algid == SEC_OID_ANSIX962_EC_PUBLIC_KEY) { ++ if (len > MAX_ECKEY_LEN * 2) { ++ goto loser; ++ } ++ } else { ++ goto loser; + } + +- if (algid == SEC_OID_ANSIX962_EC_PUBLIC_KEY) { +- if (len > MAX_ECKEY_LEN * 2) { +- PORT_SetError(SEC_ERROR_BAD_DER); +- return SECFailure; +- } ++ /* Decode and pad to length */ ++ dsasig = DSAU_DecodeDerSigToLen((SECItem *)sig, len); ++ if (dsasig == NULL) { ++ goto loser; + } +- dsasig = DSAU_DecodeDerSigToLen((SECItem *)sig, len); +- +- if ((dsasig == NULL) || (dsasig->len != len)) { +- rv = SECFailure; +- } else { +- PORT_Memcpy(dsig, dsasig->data, dsasig->len); ++ if (dsasig->len != len) { ++ SECITEM_FreeItem(dsasig, PR_TRUE); ++ goto loser; + } + +- if (dsasig != NULL) +- SECITEM_FreeItem(dsasig, PR_TRUE); +- if (rv == SECFailure) +- PORT_SetError(SEC_ERROR_BAD_DER); +- return rv; ++ PORT_Memcpy(dsig, dsasig->data, len); ++ SECITEM_FreeItem(dsasig, PR_TRUE); ++ ++ return SECSuccess; ++ ++loser: ++ PORT_SetError(SEC_ERROR_BAD_DER); ++ return SECFailure; + } + + const SEC_ASN1Template hashParameterTemplate[] = + { + { SEC_ASN1_SEQUENCE, 0, NULL, sizeof(SECItem) }, + { SEC_ASN1_OBJECT_ID, 0 }, + { SEC_ASN1_SKIP_REST }, + { 0 } +@@ -276,17 +307,17 @@ sec_GetEncAlgFromSigAlg(SECOidTag sigAlg + * + * Returns: SECSuccess if the algorithm was acceptable, SECFailure if the + * algorithm was not found or was not a signing algorithm. + */ + SECStatus + sec_DecodeSigAlg(const SECKEYPublicKey *key, SECOidTag sigAlg, + const SECItem *param, SECOidTag *encalgp, SECOidTag *hashalg) + { +- int len; ++ unsigned int len; + PLArenaPool *arena; + SECStatus rv; + SECItem oid; + SECOidTag encalg; + + PR_ASSERT(hashalg != NULL); + PR_ASSERT(encalgp != NULL); + +@@ -461,58 +492,62 @@ vfy_CreateContext(const SECKEYPublicKey + cx->wincx = wincx; + cx->hasSignature = (sig != NULL); + cx->encAlg = encAlg; + cx->hashAlg = hashAlg; + cx->key = SECKEY_CopyPublicKey(key); + cx->pkcs1RSADigestInfo = NULL; + rv = SECSuccess; + if (sig) { +- switch (type) { +- case rsaKey: +- rv = recoverPKCS1DigestInfo(hashAlg, &cx->hashAlg, +- &cx->pkcs1RSADigestInfo, +- &cx->pkcs1RSADigestInfoLen, +- cx->key, +- sig, wincx); +- break; +- case rsaPssKey: +- sigLen = SECKEY_SignatureLen(key); +- if (sigLen == 0) { +- /* error set by SECKEY_SignatureLen */ +- rv = SECFailure; ++ rv = SECFailure; ++ if (type == rsaKey) { ++ rv = recoverPKCS1DigestInfo(hashAlg, &cx->hashAlg, ++ &cx->pkcs1RSADigestInfo, ++ &cx->pkcs1RSADigestInfoLen, ++ cx->key, ++ sig, wincx); ++ } else { ++ sigLen = checkedSignatureLen(key); ++ /* Check signature length is within limits */ ++ if (sigLen == 0) { ++ /* error set by checkedSignatureLen */ ++ rv = SECFailure; ++ goto loser; ++ } ++ if (sigLen > sizeof(cx->u)) { ++ PORT_SetError(SEC_ERROR_BAD_SIGNATURE); ++ rv = SECFailure; ++ goto loser; ++ } ++ switch (type) { ++ case rsaPssKey: ++ if (sig->len != sigLen) { ++ PORT_SetError(SEC_ERROR_BAD_SIGNATURE); ++ rv = SECFailure; ++ goto loser; ++ } ++ PORT_Memcpy(cx->u.buffer, sig->data, sigLen); ++ rv = SECSuccess; + break; +- } +- if (sig->len != sigLen) { +- PORT_SetError(SEC_ERROR_BAD_SIGNATURE); ++ case ecKey: ++ case dsaKey: ++ /* decodeECorDSASignature will check sigLen == sig->len after padding */ ++ rv = decodeECorDSASignature(encAlg, sig, cx->u.buffer, sigLen); ++ break; ++ default: ++ /* Unreachable */ + rv = SECFailure; +- break; +- } +- PORT_Memcpy(cx->u.buffer, sig->data, sigLen); +- break; +- case dsaKey: +- case ecKey: +- sigLen = SECKEY_SignatureLen(key); +- if (sigLen == 0) { +- /* error set by SECKEY_SignatureLen */ +- rv = SECFailure; +- break; +- } +- rv = decodeECorDSASignature(encAlg, sig, cx->u.buffer, sigLen); +- break; +- default: +- rv = SECFailure; +- PORT_SetError(SEC_ERROR_UNSUPPORTED_KEYALG); +- break; ++ goto loser; ++ } ++ } ++ if (rv != SECSuccess) { ++ goto loser; + } + } + +- if (rv) +- goto loser; +- + /* check hash alg again, RSA may have changed it.*/ + if (HASH_GetHashTypeByOidTag(cx->hashAlg) == HASH_AlgNULL) { + /* error set by HASH_GetHashTypeByOidTag */ + goto loser; + } + /* check the policy on the hash algorithm. Do this after + * the rsa decode because some uses of this function get hash implicitly + * from the RSA signature itself. */ +@@ -645,21 +680,26 @@ VFY_EndWithSignature(VFYContext *cx, SEC + if (cx->hashcx == NULL) { + PORT_SetError(SEC_ERROR_INVALID_ARGS); + return SECFailure; + } + (*cx->hashobj->end)(cx->hashcx, final, &part, sizeof(final)); + switch (cx->key->keyType) { + case ecKey: + case dsaKey: +- dsasig.data = cx->u.buffer; +- dsasig.len = SECKEY_SignatureLen(cx->key); ++ dsasig.len = checkedSignatureLen(cx->key); + if (dsasig.len == 0) { + return SECFailure; + } ++ if (dsasig.len > sizeof(cx->u)) { ++ PORT_SetError(SEC_ERROR_BAD_SIGNATURE); ++ return SECFailure; ++ } ++ dsasig.data = cx->u.buffer; ++ + if (sig) { + rv = decodeECorDSASignature(cx->encAlg, sig, dsasig.data, + dsasig.len); + if (rv != SECSuccess) { + PORT_SetError(SEC_ERROR_BAD_SIGNATURE); + return SECFailure; + } + } +@@ -681,18 +721,23 @@ VFY_EndWithSignature(VFYContext *cx, SEC + cx->params, + &mech); + PORT_DestroyCheapArena(&tmpArena); + if (rv != SECSuccess) { + return SECFailure; + } + + rsasig.data = cx->u.buffer; +- rsasig.len = SECKEY_SignatureLen(cx->key); ++ rsasig.len = checkedSignatureLen(cx->key); + if (rsasig.len == 0) { ++ /* Error set by checkedSignatureLen */ ++ return SECFailure; ++ } ++ if (rsasig.len > sizeof(cx->u)) { ++ PORT_SetError(SEC_ERROR_BAD_SIGNATURE); + return SECFailure; + } + if (sig) { + if (sig->len != rsasig.len) { + PORT_SetError(SEC_ERROR_BAD_SIGNATURE); + return SECFailure; + } + PORT_Memcpy(rsasig.data, sig->data, rsasig.len); +@@ -744,37 +789,42 @@ VFY_End(VFYContext *cx) + static SECStatus + vfy_VerifyDigest(const SECItem *digest, const SECKEYPublicKey *key, + const SECItem *sig, SECOidTag encAlg, SECOidTag hashAlg, + void *wincx) + { + SECStatus rv; + VFYContext *cx; + SECItem dsasig; /* also used for ECDSA */ +- + rv = SECFailure; + + cx = vfy_CreateContext(key, sig, encAlg, hashAlg, NULL, wincx); + if (cx != NULL) { + switch (key->keyType) { + case rsaKey: + rv = verifyPKCS1DigestInfo(cx, digest); ++ /* Error (if any) set by verifyPKCS1DigestInfo */ + break; +- case dsaKey: + case ecKey: ++ case dsaKey: + dsasig.data = cx->u.buffer; +- dsasig.len = SECKEY_SignatureLen(cx->key); ++ dsasig.len = checkedSignatureLen(cx->key); + if (dsasig.len == 0) { ++ /* Error set by checkedSignatureLen */ ++ rv = SECFailure; + break; + } +- if (PK11_Verify(cx->key, &dsasig, (SECItem *)digest, cx->wincx) != +- SECSuccess) { ++ if (dsasig.len > sizeof(cx->u)) { + PORT_SetError(SEC_ERROR_BAD_SIGNATURE); +- } else { +- rv = SECSuccess; ++ rv = SECFailure; ++ break; ++ } ++ rv = PK11_Verify(cx->key, &dsasig, (SECItem *)digest, cx->wincx); ++ if (rv != SECSuccess) { ++ PORT_SetError(SEC_ERROR_BAD_SIGNATURE); + } + break; + default: + break; + } + VFY_DestroyContext(cx, PR_TRUE); + } + return rv; + diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb index b03a54c6f96..e994d073530 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb @@ -14,12 +14,14 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'NSS-3.39_pkgconfig.patch', 'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', + 'NSS-3.65_CVE-2021-43527.patch', ] checksums = [ 'c880205a365e0dd488ff29fdea82716ff9fcde9da6f3b703d636f8fc08008799', # nss-3.69.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch # NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b', + 'b9ccfdeb692f703e40e83202366bbdea9ef9506003b368e8061fc1fa439ebbc3', # NSS-3.65_CVE-2021-43527.patch ] builddependencies = [('binutils', '2.37')] From 1dde96b668849f0f80599d275a6283bd3b70505e Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 3 Dec 2021 16:12:04 +0100 Subject: [PATCH 2201/9987] adding easyconfigs: MUST-1.7.2-foss-2021a.eb --- .../m/MUST/MUST-1.7.2-foss-2021a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUST/MUST-1.7.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.7.2-foss-2021a.eb b/easybuild/easyconfigs/m/MUST/MUST-1.7.2-foss-2021a.eb new file mode 100644 index 00000000000..365f862b5d7 --- /dev/null +++ b/easybuild/easyconfigs/m/MUST/MUST-1.7.2-foss-2021a.eb @@ -0,0 +1,38 @@ +## +# Author: Robert Mijakovic +## + +easyblock = "CMakeMake" + +name = 'MUST' +version = '1.7.2' + +homepage = "https://hpc.rwth-aachen.de/must/" +description = """MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user. + As MPI calls are complex and usage errors common, this functionality is extremely helpful for application developers + that want to develop correct MPI applications. + This includes errors that already manifest – segmentation faults or incorrect results – as well as many errors + that are not visible to the application developer or do not manifest on a certain system or MPI implementation.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://hpc.rwth-aachen.de/must/files/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['616c54b7487923959df126ac4b47ae8c611717d679fe7ec29f57a89bf0e2e0d0'] + +builddependencies = [ + ('CMake', '3.20.1') +] + +dependencies = [ + ('Python', '3.9.5'), + ('libxml2', '2.9.10'), + ('Graphviz', '2.47.2'), +] + +sanity_check_paths = { + 'files': ["bin/mustrun", "bin/wrap.py", "include/mustConfig.h", "lib/libpnmpif.so", "lib/libpnmpi.so"], + 'dirs': ["include/pnmpi", "lib64/pnmpi-modules", "modules", "share", "specifications", "src"], +} + +moduleclass = "perf" From 14fa95e81233f857122c6c0dccf503646a57047f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 3 Dec 2021 15:52:42 +0000 Subject: [PATCH 2202/9987] enhance sanity check --- easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-6.4.0.eb | 9 +++++++-- easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-7.3.0.eb | 9 +++++++-- easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb | 9 +++++++-- easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb | 9 +++++++-- easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb | 9 +++++++-- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 9 +++++++-- easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb | 9 +++++++-- easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb | 9 +++++++-- 8 files changed, 56 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-6.4.0.eb index 16cb48ca51f..94802ed06d6 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-6.4.0.eb @@ -38,10 +38,15 @@ buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] sanity_check_paths = { - 'files': ['lib/libnss.a'], - 'dirs': ['bin', 'include/dbm', 'include/nss'], + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], } +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + modextrapaths = {'CPATH': 'include/nss'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-7.3.0.eb index 39930af4777..181a07ac021 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.39-GCCcore-7.3.0.eb @@ -38,10 +38,15 @@ buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] sanity_check_paths = { - 'files': ['lib/libnss.a'], - 'dirs': ['bin', 'include/dbm', 'include/nss'], + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], } +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + modextrapaths = {'CPATH': 'include/nss'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb index 420f1b6d99c..96e2dbbf671 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb @@ -38,10 +38,15 @@ buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] sanity_check_paths = { - 'files': ['lib/libnss.a'], - 'dirs': ['bin', 'include/dbm', 'include/nss'], + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], } +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + modextrapaths = {'CPATH': 'include/nss'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb index a849724f7d5..798d8f38606 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb @@ -38,10 +38,15 @@ buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] sanity_check_paths = { - 'files': ['lib/libnss.a'], - 'dirs': ['bin', 'include/dbm', 'include/nss'], + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], } +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + modextrapaths = {'CPATH': 'include/nss'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb index f263c9af718..9b575239ab5 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb @@ -42,10 +42,15 @@ buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] sanity_check_paths = { - 'files': ['lib/libnss.a'], - 'dirs': ['bin', 'include/dbm', 'include/nss'], + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], } +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + modextrapaths = {'CPATH': 'include/nss'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 6d30fd97e4b..39ccefdf997 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -42,10 +42,15 @@ buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] sanity_check_paths = { - 'files': ['lib/libnss.a'], - 'dirs': ['bin', 'include/dbm', 'include/nss'], + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], } +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + modextrapaths = {'CPATH': 'include/nss'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb index 66f3d54596b..1153b4b58a8 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb @@ -43,10 +43,15 @@ buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] sanity_check_paths = { - 'files': ['lib/libnss.a'], - 'dirs': ['bin', 'include/dbm', 'include/nss'], + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], } +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + modextrapaths = {'CPATH': 'include/nss'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb index e994d073530..0ea01ba44d0 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb @@ -46,10 +46,15 @@ buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] sanity_check_paths = { - 'files': ['lib/libnss.a'], - 'dirs': ['bin', 'include/dbm', 'include/nss'], + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], } +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + modextrapaths = {'CPATH': 'include/nss'} moduleclass = 'lib' From fd6e35c7252cb9eb8bc3c59b2b7f0fe696ca95fa Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Fri, 3 Dec 2021 20:11:47 +0200 Subject: [PATCH 2203/9987] adding easyconfigs: idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb --- ...demux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb new file mode 100644 index 00000000000..fdece15093a --- /dev/null +++ b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb @@ -0,0 +1,47 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'idemux' +version = '0.1.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Lexogen-Tools/idemux' +description = """idemux - inline barcode demultiplexing +Idemux is a command line tool designed to demultiplex paired-end FASTQ files from QuantSeq-Pool.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('coverage', '5.5'), +] + +use_pip = True + +exts_list = [ + ('pytest-runner', '5.3.0', { + 'modulename': 'ptr', + 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], + }), + ('tqdm', '4.62.3', { + 'checksums': ['d359de7217506c9851b7869f3708d8ee53ed70a1b8edbba4dbcb47442592920d'], + }), + (name, version, { + 'checksums': ['590980baaf810c8a02705efd50eb4ace644c360470fc3dc4491d077bbb6b26fc'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/idemux',], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 5cf75e9c7433922ab34142ff362dbbc719732042 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Fri, 3 Dec 2021 20:20:54 +0200 Subject: [PATCH 2204/9987] Added check commands --- .../i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb index fdece15093a..63ee8c6b931 100644 --- a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb +++ b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb @@ -44,4 +44,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["idemux -h"] + moduleclass = 'bio' From 556b166b282287e060d5f407415bef4891f154d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Dec 2021 19:33:17 +0100 Subject: [PATCH 2205/9987] remove versionsuffix for idemux (no longer used with Python 3.x) + use proper dependency for tqdm --- ....0-Python-3.8.6.eb => idemux-0.1.6-GCCcore-10.2.0.eb} | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/i/idemux/{idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb => idemux-0.1.6-GCCcore-10.2.0.eb} (83%) diff --git a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb similarity index 83% rename from easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb rename to easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb index 63ee8c6b931..d156b3c22fc 100644 --- a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0-Python-3.8.6.eb +++ b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb @@ -5,7 +5,6 @@ easyblock = 'PythonBundle' name = 'idemux' version = '0.1.6' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/Lexogen-Tools/idemux' description = """idemux - inline barcode demultiplexing @@ -20,17 +19,15 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), ('coverage', '5.5'), + ('tqdm', '4.60.0'), ] use_pip = True exts_list = [ ('pytest-runner', '5.3.0', { - 'modulename': 'ptr', 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], - }), - ('tqdm', '4.62.3', { - 'checksums': ['d359de7217506c9851b7869f3708d8ee53ed70a1b8edbba4dbcb47442592920d'], + 'modulename': 'ptr', }), (name, version, { 'checksums': ['590980baaf810c8a02705efd50eb4ace644c360470fc3dc4491d077bbb6b26fc'], @@ -40,7 +37,7 @@ exts_list = [ sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/idemux',], + 'files': ['bin/idemux'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From a33fd77889a5e23b028e899411a15e4a2aea43da Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sat, 4 Dec 2021 12:59:11 +0100 Subject: [PATCH 2206/9987] adding easyconfigs: libtree-2.0.0-GCCcore-10.3.0.eb --- .../l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6563f5b1326 --- /dev/null +++ b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'libtree' +version = '2.0.0' + +homepage = 'https://github.com/haampie/libtree' +description = """libtree is a tool that turns ldd into a tree, explains why + shared libraries are found and why not and optionally deploys executables and + dependencies into a single directory""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'haampie' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['099e85d8ba3c3d849ce05b8ba2791dd25cd042a813be947fb321b0676ef71883'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('cxxopts', '3.0.0'), + ('ELFIO', '3.9'), + ('termcolor', '2.0.0'), +] + +sanity_check_paths = { + 'files': ["bin/%(name)s"], + 'dirs': ['bin', 'share'] +} + +sanity_check_commands = ["libtree --version"] + +moduleclass = 'tools' From a1fc78618dfac9953423881fd0ceebf9f3e86b7a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Dec 2021 12:11:32 +0000 Subject: [PATCH 2207/9987] pass tests on A* GPUs by setting 'NVIDIA_TF32_OVERRIDE=0' in jax 0.2.19 --- easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index 1da5dfa47ae..d14b441c648 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -115,7 +115,8 @@ exts_list = [ # see https://github.com/google/jax/issues/7323 and # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; - 'runtest': 'CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests', + # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests", }), ] From b51979f9ce91152b142cd1ac7986fafcaaa990d1 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Sat, 4 Dec 2021 13:27:51 +0100 Subject: [PATCH 2208/9987] Adds missing binutils --- easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb index 6563f5b1326..2d4b9162c5f 100644 --- a/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb @@ -19,6 +19,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['099e85d8ba3c3d849ce05b8ba2791dd25cd042a813be947fb321b0676ef71883'] builddependencies = [ + ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('cxxopts', '3.0.0'), ('ELFIO', '3.9'), From 57956887f87b627239a921f46c2020705be38411 Mon Sep 17 00:00:00 2001 From: Sassy Date: Sat, 4 Dec 2021 16:35:07 +0000 Subject: [PATCH 2209/9987] Checksums corrected --- .../f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb index 22a5572078f..5fc7c985195 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.2.0-centos8_x86_64.eb @@ -20,8 +20,8 @@ sources = [ ] checksums = [ # freesurfer-linux-centos8_x86_64-7.2.0.tar.gz - '6098b166fee8644f44f9ec88f3ffe88d05f2bc033cca60443e99e3e56f2e166b', - '1eecbe0f027b95ee9ec7cce4c0846e14e7bf623fa1937ac57911a26f8f23d3e6', # runtime2014bLinux.tar.gz + '1eecbe0f027b95ee9ec7cce4c0846e14e7bf623fa1937ac57911a26f8f23d3e6', + '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz ] postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] From a25783c33f55a51fb9cbb850dc71be75ecea2074 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Dec 2021 20:05:57 +0100 Subject: [PATCH 2210/9987] adding easyconfigs: BabelStream-3.4-GCC-11.2.0-omp.eb --- .../BabelStream-3.4-GCC-11.2.0-omp.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/BabelStream/BabelStream-3.4-GCC-11.2.0-omp.eb diff --git a/easybuild/easyconfigs/b/BabelStream/BabelStream-3.4-GCC-11.2.0-omp.eb b/easybuild/easyconfigs/b/BabelStream/BabelStream-3.4-GCC-11.2.0-omp.eb new file mode 100644 index 00000000000..0690c7bf3a7 --- /dev/null +++ b/easybuild/easyconfigs/b/BabelStream/BabelStream-3.4-GCC-11.2.0-omp.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'BabelStream' +version = '3.4' +versionsuffix = '-omp' + +homepage = 'https://uob-hpc.github.io/BabelStream' +description = "STREAM, for lots of devices written in many programming models" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/UoB-HPC/BabelStream/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e34ee9d5ccdead019e3ea478333bcb7886117d600e5da8579a626f6ee34209cf'] + +buildopts = '-f OpenMP.make COMPILER=GNU TARGET=CPU CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +files_to_copy = [(['omp-stream'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/omp-stream'], + 'dirs': [], +} + +sanity_check_commands = ["omp-stream"] + +moduleclass = 'perf' From d5d13c0746c7a405c5af8057572efcb2a9df273b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sun, 5 Dec 2021 06:45:30 +0800 Subject: [PATCH 2211/9987] move cxxopts, termcolor and ELFIO header only libraries to SYSTEM toolchain --- .../{cxxopts-3.0.0-GCCcore-10.3.0.eb => cxxopts-3.0.0.eb} | 7 ++----- .../e/ELFIO/{ELFIO-3.9-GCCcore-10.3.0.eb => ELFIO-3.9.eb} | 7 ++----- ...ermcolor-2.0.0-GCCcore-10.3.0.eb => termcolor-2.0.0.eb} | 7 ++----- 3 files changed, 6 insertions(+), 15 deletions(-) rename easybuild/easyconfigs/c/cxxopts/{cxxopts-3.0.0-GCCcore-10.3.0.eb => cxxopts-3.0.0.eb} (80%) rename easybuild/easyconfigs/e/ELFIO/{ELFIO-3.9-GCCcore-10.3.0.eb => ELFIO-3.9.eb} (82%) rename easybuild/easyconfigs/t/termcolor/{termcolor-2.0.0-GCCcore-10.3.0.eb => termcolor-2.0.0.eb} (81%) diff --git a/easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0.eb similarity index 80% rename from easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0.eb index 4ca7e838217..bccadbb251c 100644 --- a/easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cxxopts/cxxopts-3.0.0.eb @@ -9,17 +9,14 @@ version = '3.0.0' homepage = 'https://github.com/jarro2783/cxxopts' description = """cxxopts is a lightweight C++ command line option parser""" -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchain = SYSTEM github_account = 'jarro2783' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['36f41fa2a46b3c1466613b63f3fa73dc24d912bc90d667147f1e43215a8c6d00'] -builddependencies = [ - ('binutils', '2.36.1'), - ('CMake', '3.20.1'), -] +builddependencies = [('CMake', '3.18.4')] sanity_check_paths = { 'files': ["include/cxxopts.hpp"], diff --git a/easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/e/ELFIO/ELFIO-3.9.eb similarity index 82% rename from easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/e/ELFIO/ELFIO-3.9.eb index 42ab8d77835..3ef4dac2842 100644 --- a/easybuild/easyconfigs/e/ELFIO/ELFIO-3.9-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/e/ELFIO/ELFIO-3.9.eb @@ -10,17 +10,14 @@ homepage = 'http://elfio.sourceforge.net' description = """ELFIO is a header-only C++ library intended for reading and generating files in the ELF binary format.""" -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchain = SYSTEM github_account = 'serge1' source_urls = [GITHUB_SOURCE] sources = ['Release_%(version)s.tar.gz'] checksums = ['bf93538afe916b333aef1d03e44c9b80dace61f4d097e581ae332cd2d4fa178e'] -builddependencies = [ - ('binutils', '2.36.1'), - ('CMake', '3.20.1'), -] +builddependencies = [('CMake', '3.18.4')] sanity_check_paths = { 'files': ["include/%(namelower)s/%(namelower)s.hpp"], diff --git a/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0.eb similarity index 81% rename from easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/t/termcolor/termcolor-2.0.0.eb index 03d342fb291..f369a0710d0 100644 --- a/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/termcolor/termcolor-2.0.0.eb @@ -10,17 +10,14 @@ homepage = 'https://termcolor.readthedocs.io/' description = """Termcolor is a header-only C++ library for printing colored messages to the terminal.""" -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchain = SYSTEM github_account = 'ikalnytskyi' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['4a73a77053822ca1ed6d4a2af416d31028ec992fb0ffa794af95bd6216bb6a20'] -builddependencies = [ - ('binutils', '2.36.1'), - ('CMake', '3.20.1'), -] +builddependencies = [('CMake', '3.18.4')] sanity_check_paths = { 'files': ['include/%(name)s/%(name)s.hpp'], From 2b33505ae6676421a8941743c3fc47495978bef2 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 6 Dec 2021 12:24:04 +0100 Subject: [PATCH 2212/9987] easyconfigs for dune-core and dune-fem in foss/2020b --- .../dune-core-2.8.0.post1-foss-2020b.eb | 56 +++++++++++++++ .../d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 71 +++++++++++++++++++ 2 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb new file mode 100644 index 00000000000..3c4f56daebe --- /dev/null +++ b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'dune-core' +version = '2.8.0.post1' + +homepage = "https://www.dune-project.org/groups/core/" +description = """The Dune core modules build the stable basis of Dune. +They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. +These modules build the foundation for higher-level components. + +User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('CMake', '3.18.4'), +] + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + +exts_list = [ + ('portalocker', '2.3.2', { + 'checksums': ['75cfe02f702737f1726d83e04eedfa0bda2cc5b974b1ceafb8d6b42377efbd5f'], + }), + ('dune-common', version, { + 'modulename': 'dune.common', + 'checksums': ['b6736c69d5213688405bc1d953ac907c1440ecda1174c0cf08bf6cf69ee585a1'], + }), + ('dune-geometry', version, { + 'modulename': 'dune.geometry', + 'checksums': ['7fc655c42fde485bc563d362d9309db332acd08229df2ad215fa0fd292e18a54'], + }), + ('dune-grid', version, { + 'modulename': 'dune.grid', + 'checksums': ['1faf909dba2a590086aa0a2e5926905fcbbe3521e9d920359c984ab496a3c5fb'], + }), + ('dune-localfunctions', version, { + 'modulename': 'dune.localfunctions', + 'checksums': ['d19cb354cbce72654220228613f53ed1be3b960718d8738523b987da6d108406'], + }), + ('dune-istl', version, { + 'modulename': 'dune.istl', + 'checksums': ['0227acaf6b93700036403c3fe8312c00b33edc9dc09d89b295768cbe84eff507'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb new file mode 100644 index 00000000000..20d66b9fdd7 --- /dev/null +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'dune-fem' +version = '2.8.0.6' + +homepage = "https://www.dune-project.org/modules/dune-fem/" +description = """DUNE-FEM is a discretization module based on DUNE containing all +the building blocks required to implement efficient solvers for a wide range +of (systems of non linear) partial differential equations. DUNE-FEM can also +be used through an extensive Python interface which brings all +components of DUNE-FEM and the DUNE core modules to Python. + +User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PETSc', '3.14.4'), + ('CMake', '3.18.4'), + ('dune-core', '2.8.0.post1'), + ('matplotlib', '3.3.4'), +] + +use_pip = True +sanity_pip_check = True + +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + +exts_list = [ + ('fenics-ufl', '2019.1.0', { + 'modulename': 'ufl', + 'checksums': ['f778cb914f0fe57be76ad288a9209c1f4034a65692e13907171d994a4747bf81'], + }), + ('dune-alugrid', '2.8.0.post1', { + 'modulename': 'dune.alugrid', + 'checksums': ['3ee0ecdc19add77535c211c60058bf28162f9ad3c54b8b3b2bfcafc4d6269c55'], + }), + ('dune-spgrid', '2.8.0.post1', { + 'modulename': 'dune.spgrid', + 'checksums': ['9c6047d5672aabef1b39e9604f03611a1097070935e3c2b1224f69f8758fa336'], + }), + ('dune-polygongrid', '2.8.0.post1', { + 'modulename': 'dune.polygongrid', + 'checksums': ['a1b3dd301a403db6ea0b0a2d9e267b292dd6c5b3d12801f5154890bd4b6d63a8'], + }), + (name, version, { + 'modulename': 'dune.fem', + 'checksums': ['85151aa6fe54d14ae7cee12feff90afc580e0e41f5636bf51a6fbb2b9921bf10'], + }), + ('dune-fem-dg', version, { + 'modulename': 'dune.femdg', + 'checksums': ['bb81fdaf0ba0f59915dca8080d82f2c6b1d2ad98cd51cf8548b0c96d88adebb0'], + }), + ('triangle', '20200424', { + 'checksums': ['fc207641f8f39986f7d2bee1b91688a588cd235d2e67777422f94e61fece27e9'], + }), + ('dune-vem', version, { + 'modulename': 'dune.vem', + 'checksums': ['452145b85f2755cda24aa683efd4cc6c90fd49af395333dd766fb6cf479f969b'], + }), +] + + + +moduleclass = 'math' From 93b7f96f132e40aa91e7cf2ed92ff00f6c0b3ba1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Dec 2021 15:46:56 +0100 Subject: [PATCH 2213/9987] adding easyconfigs: Gurobi-9.5.0-GCCcore-11.2.0.eb --- .../g/Gurobi/Gurobi-9.5.0-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a71a89ee067 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +name = 'Gurobi' +version = '9.5.0' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +patches = ['%(name)s-9.0.1_use-eb-python-gurobi-shell.patch'] +checksums = [ + 'bb542e5a5d1685f6e364eaf05ea6c5572485ffc37a2245169cf3cb40288bc29e', # gurobi9.5.0_linux64.tar.gz + 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01', # Gurobi-9.0.1_use-eb-python-gurobi-shell.patch +] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license is not mandatory for installation +license_file = HOME + '/licenses/%(name)s.lic' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' From 92615b10af6fd2c9cebc7c2bde869175e400fda6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Dec 2021 10:05:10 +0100 Subject: [PATCH 2214/9987] fix permissions for ANIcalculator binaries --- .../a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb index c9c00814fdb..e02e2e96383 100644 --- a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb @@ -29,8 +29,11 @@ skipsteps = ['build'] # Instead of copying this, we use the version from the Perl module. files_to_copy = [(['ANIcalculator', 'nsimscan'], 'bin'), 'README.txt'] -# Remove the execute permissions on the README.txt, which it has by default. -postinstallcmds = ['chmod -x %(installdir)s/README.txt'] +# Fix permissions on binaries and README.txt, +postinstallcmds = [ + 'chmod a+x %(installdir)s/bin/*', + 'chmod -x %(installdir)s/README.txt', +] sanity_check_paths = { 'files': ['README.txt', 'bin/ANIcalculator', 'bin/nsimscan'], From bfb327bae76e9a750c13de655a380fbf31cd5d7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Dec 2021 11:02:56 +0100 Subject: [PATCH 2215/9987] use similar patches as for version 2.1 --- easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb | 4 ++++ easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb index e27e324a68b..41e44dc0175 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb @@ -16,6 +16,10 @@ toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/marbl/Mash/archive/'] sources = ['v%(version)s.tar.gz'] +patches = [ + 'Mash-2.2_fix-hardcoding.patch', + 'Mash-2.1_disable-memcpy-wrap.patch', +] checksums = ['7ad006dbf0d6ffc3e164713ba955aab4cd24eaf85c864ac905f48cd8ba332691'] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb index 2b8f28e31d2..88c91ed1677 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb @@ -16,6 +16,10 @@ toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/marbl/Mash/archive/'] sources = ['v%(version)s.tar.gz'] +patches = [ + 'Mash-2.2_fix-hardcoding.patch', + 'Mash-2.1_disable-memcpy-wrap.patch', +] checksums = ['f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1'] builddependencies = [('Autotools', '20210128')] From 59f61a28303e76bd801c4f6319b51163257b747a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Dec 2021 11:03:35 +0100 Subject: [PATCH 2216/9987] Update older patch for newer Mash versions --- .../m/Mash/Mash-2.2_fix-hardcoding.patch | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mash/Mash-2.2_fix-hardcoding.patch diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.2_fix-hardcoding.patch b/easybuild/easyconfigs/m/Mash/Mash-2.2_fix-hardcoding.patch new file mode 100644 index 00000000000..5a8fb66c549 --- /dev/null +++ b/easybuild/easyconfigs/m/Mash/Mash-2.2_fix-hardcoding.patch @@ -0,0 +1,20 @@ +don't hardcode -std=c++14, since -std=c++17 is required when building on top of CapnProto 0.8.0 +--- Mash-2.2/configure.ac.orig 2021-12-07 10:56:35.099497741 +0100 ++++ Mash-2.2/configure.ac 2021-12-07 10:57:09.343306342 +0100 +@@ -33,7 +33,7 @@ + AC_MSG_ERROR([Cap'n Proto compiler (capnp) not found.]) + fi + +-CPPFLAGS="-I$with_capnp/include -std=c++14" ++CPPFLAGS="-I$with_capnp/include $CXXFLAGS" + + AC_CHECK_HEADER(capnp/common.h, [result=1], [result=0]) + +--- Mash-2.2/Makefile.in.orig 2021-12-07 10:57:13.619282453 +0100 ++++ Mash-2.2/Makefile.in 2021-12-07 10:57:36.623153939 +0100 +@@ -1,4 +1,4 @@ +-CXXFLAGS += -O3 -std=c++14 -Isrc -I@capnp@/include -I@mathinc@ ++CXXFLAGS += -Isrc -I@capnp@/include -I@mathinc@ + CPPFLAGS += @amcppflags@ + + UNAME_S=$(shell uname -s) From 87349be485691f1e190cb1e359bb75052f73bdfe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Dec 2021 11:05:05 +0100 Subject: [PATCH 2217/9987] add checksums for patches --- easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb | 6 +++++- easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb index 41e44dc0175..112beebd777 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb @@ -20,7 +20,11 @@ patches = [ 'Mash-2.2_fix-hardcoding.patch', 'Mash-2.1_disable-memcpy-wrap.patch', ] -checksums = ['7ad006dbf0d6ffc3e164713ba955aab4cd24eaf85c864ac905f48cd8ba332691'] +checksums = [ + '7ad006dbf0d6ffc3e164713ba955aab4cd24eaf85c864ac905f48cd8ba332691', # v2.2.tar.gz + '0c7315af727a06f408ab3ca69da0860fc671aa870b448a41a509b1e6d7027db5', # Mash-2.2_fix-hardcoding.patch + '40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch +] builddependencies = [('Autotools', '20180311')] dependencies = [ diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb index 88c91ed1677..c32f7661c5d 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb @@ -20,7 +20,11 @@ patches = [ 'Mash-2.2_fix-hardcoding.patch', 'Mash-2.1_disable-memcpy-wrap.patch', ] -checksums = ['f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1'] +checksums = [ + 'f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1', # v2.3.tar.gz + '0c7315af727a06f408ab3ca69da0860fc671aa870b448a41a509b1e6d7027db5', # Mash-2.2_fix-hardcoding.patch + '40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch +] builddependencies = [('Autotools', '20210128')] dependencies = [ From 795f3a9b9c439d45d82faee07381329bb17cafc3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Dec 2021 11:12:43 +0100 Subject: [PATCH 2218/9987] add sanity check command for Mash --- easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb | 2 ++ easybuild/easyconfigs/m/Mash/Mash-2.1-foss-2018b.eb | 2 ++ easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb | 2 ++ easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb | 2 ++ 4 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb b/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb index a6eefdb3d0b..fb2208da2d1 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb @@ -27,4 +27,6 @@ sanity_check_paths = { 'dirs': ['include/mash'], } +sanity_check_commands = ['mash --version'] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.1-foss-2018b.eb b/easybuild/easyconfigs/m/Mash/Mash-2.1-foss-2018b.eb index 2d4362a7a23..2d8ab58651b 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.1-foss-2018b.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.1-foss-2018b.eb @@ -36,4 +36,6 @@ sanity_check_paths = { 'dirs': ['include/mash'], } +sanity_check_commands = ['mash --version'] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb index 112beebd777..37ba3d7875f 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb @@ -41,4 +41,6 @@ sanity_check_paths = { 'dirs': ['include/mash'], } +sanity_check_commands = ['mash --version'] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb index c32f7661c5d..0cc78489589 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-10.3.0.eb @@ -41,4 +41,6 @@ sanity_check_paths = { 'dirs': ['include/mash'], } +sanity_check_commands = ['mash --version'] + moduleclass = 'bio' From 21da879078b8ce846ddc2ebf67de5c219e5d1deb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Dec 2021 11:12:54 +0100 Subject: [PATCH 2219/9987] replace 2.2 by version variable in patch fileame --- easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb index 37ba3d7875f..d5b65358598 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.2-GCC-9.3.0.eb @@ -17,7 +17,7 @@ toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/marbl/Mash/archive/'] sources = ['v%(version)s.tar.gz'] patches = [ - 'Mash-2.2_fix-hardcoding.patch', + 'Mash-%(version)s_fix-hardcoding.patch', 'Mash-2.1_disable-memcpy-wrap.patch', ] checksums = [ From 0a25d7b5a764accba1a3e493ed10b524d283495a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Dec 2021 11:32:11 +0100 Subject: [PATCH 2220/9987] use Mash 2.1 patches for 2.0 --- easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb b/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb index fb2208da2d1..077d1e06c1e 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb @@ -10,6 +10,10 @@ toolchain = {'name': 'foss', 'version': '2018a'} source_urls = ['https://github.com/marbl/Mash/archive/'] sources = ['v%(version)s.tar.gz'] +patches = [ + 'Mash-2.1_fix-hardcoding.patch', + 'Mash-2.1_disable-memcpy-wrap.patch', +] checksums = ['7bea8cd3c266640bbd97f2e1c9d0168892915c1c14f7d03a9751bf7a3709dd01'] builddependencies = [('Autotools', '20170619')] From 311bab5fd7399421aebbda6168c029dc4a59e34a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Dec 2021 11:32:38 +0100 Subject: [PATCH 2221/9987] add checksums for patches --- easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb b/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb index 077d1e06c1e..c03df442200 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.0-foss-2018a.eb @@ -14,7 +14,11 @@ patches = [ 'Mash-2.1_fix-hardcoding.patch', 'Mash-2.1_disable-memcpy-wrap.patch', ] -checksums = ['7bea8cd3c266640bbd97f2e1c9d0168892915c1c14f7d03a9751bf7a3709dd01'] +checksums = [ + '7bea8cd3c266640bbd97f2e1c9d0168892915c1c14f7d03a9751bf7a3709dd01', # v2.0.tar.gz + 'dc40511b25dab25e3fe88d4911ccf7bd793e60ba8f4b77a64488412d14796299', # Mash-2.1_fix-hardcoding.patch + '40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch +] builddependencies = [('Autotools', '20170619')] dependencies = [ From 7a6cac63125cbcfc81a3412d8c7143cc4e439acf Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 7 Dec 2021 12:10:50 +0000 Subject: [PATCH 2222/9987] adding easyconfigs: CellRanger-6.1.2.eb, CellRanger-6.0.2.eb --- .../c/CellRanger/CellRanger-6.0.2.eb | 29 +++++++++++++++++++ .../c/CellRanger/CellRanger-6.1.2.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellRanger/CellRanger-6.0.2.eb create mode 100644 easybuild/easyconfigs/c/CellRanger/CellRanger-6.1.2.eb diff --git a/easybuild/easyconfigs/c/CellRanger/CellRanger-6.0.2.eb b/easybuild/easyconfigs/c/CellRanger/CellRanger-6.0.2.eb new file mode 100644 index 00000000000..a5eb86116a5 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger/CellRanger-6.0.2.eb @@ -0,0 +1,29 @@ +# The STAR binary included in this version has been vectorized with AVX +# hence it is not recommended for systems that do not support it. + +easyblock = 'Tarball' + +name = 'CellRanger' +version = '6.0.2' + +homepage = 'https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger' +description = """Cell Ranger is a set of analysis pipelines that process Chromium + single-cell RNA-seq output to align reads, generate gene-cell matrices and perform + clustering and gene expression analysis.""" + +toolchain = SYSTEM + +# Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cee3ec8161c63b6fe24a0527275954a2ea3cb7a373608bdede14a4e3099249ea'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ["bin/cellranger"], + 'dirs': ["bin/rna", "bin/tenkit"], +} + +sanity_check_commands = ['cellranger testrun --id=tiny'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellRanger/CellRanger-6.1.2.eb b/easybuild/easyconfigs/c/CellRanger/CellRanger-6.1.2.eb new file mode 100644 index 00000000000..6a3ac6eee3c --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger/CellRanger-6.1.2.eb @@ -0,0 +1,29 @@ +# The STAR binary included in this version has been vectorized with AVX +# hence it is not recommended for systems that do not support it. + +easyblock = 'Tarball' + +name = 'CellRanger' +version = '6.1.2' + +homepage = 'https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger' +description = """Cell Ranger is a set of analysis pipelines that process Chromium + single-cell RNA-seq output to align reads, generate gene-cell matrices and perform + clustering and gene expression analysis.""" + +toolchain = SYSTEM + +# Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest +sources = [SOURCELOWER_TAR_GZ] +checksums = ['475a05feb456e753453b1ddef638220c80f1eef41afd1a881fd03927aea6e945'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ["bin/cellranger"], + 'dirs': ["bin/rna", "bin/tenkit"], +} + +sanity_check_commands = ['cellranger testrun --id=tiny'] + +moduleclass = 'bio' From 09ea82c938de225bd48ee32ce5131e80bed31794 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 7 Dec 2021 14:10:55 +0100 Subject: [PATCH 2223/9987] adding easyconfigs: BCFtools-1.14-GCC-11.2.0.eb --- .../b/BCFtools/BCFtools-1.14-GCC-11.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.14-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.14-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.14-GCC-11.2.0.eb new file mode 100644 index 00000000000..556b393bfb5 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.14-GCC-11.2.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.14' + +homepage = 'https://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b7ef88ae89fcb55658c5bea2e8cb8e756b055e13860036d6be13756782aa19cb'] + +dependencies = [ + ('zlib', '1.2.11'), + ('HTSlib', '1.14'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('GSL', '2.7'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['libexec/bcftools'] +} + +moduleclass = 'bio' From deadf5c97cab1cad8eeb67ed8eb506968c3049b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Dec 2021 14:24:50 +0100 Subject: [PATCH 2224/9987] add another sanity check cmd that checks all deps --- easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb b/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb index 700941e4e5f..266db5ea151 100644 --- a/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb @@ -39,6 +39,13 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } -sanity_check_commands = [x + ' -h' for x in local_binaries] +sanity_check_commands = [ + 'parse_stb.py -h', + 'ScaffoldLevel_dRep.py -h', + 'dRep -h', + # fail in case any dependency reports an ERROR, except for centrifuge + # (which is not used anymore according to the installation documentation) + '! dRep check_dependencies | grep "ERROR" | grep -v "centrifuge"', +] moduleclass = 'bio' From eb46d53772d0d9cebdf84f20de52ce633c39d553 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 7 Dec 2021 14:37:38 +0100 Subject: [PATCH 2225/9987] Updated matplotlib version in dune-fem --- easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index 20d66b9fdd7..fa6041e9808 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -21,7 +21,7 @@ dependencies = [ ('PETSc', '3.14.4'), ('CMake', '3.18.4'), ('dune-core', '2.8.0.post1'), - ('matplotlib', '3.3.4'), + ('matplotlib', '3.3.3'), ] use_pip = True From eb76081339ce347cf3d4a8479e34fc27ffebf6d7 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 7 Dec 2021 15:14:19 +0100 Subject: [PATCH 2226/9987] removed unwanted whitespace in dune-fem configuration --- easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index fa6041e9808..6d875c7c146 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -66,6 +66,4 @@ exts_list = [ }), ] - - moduleclass = 'math' From 9420ced5d1a4b7ebf4708be98d4c7fb39210eb2e Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 7 Dec 2021 15:48:59 +0000 Subject: [PATCH 2227/9987] adding easyconfigs: Bracken-2.6.2-GCCcore-11.2.0.eb --- .../b/Bracken/Bracken-2.6.2-GCCcore-11.2.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bracken/Bracken-2.6.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Bracken/Bracken-2.6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bracken/Bracken-2.6.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8a9c3136219 --- /dev/null +++ b/easybuild/easyconfigs/b/Bracken/Bracken-2.6.2-GCCcore-11.2.0.eb @@ -0,0 +1,58 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'Bracken' +version = '2.6.2' + +homepage = 'https://ccb.jhu.edu/software/bracken/' +description = """Bracken (Bayesian Reestimation of Abundance with KrakEN) +is a highly accurate statistical method that computes the abundance of +species in DNA sequences from a metagenomics sample. Braken uses the +taxonomy labels assigned by Kraken, a highly accurate metagenomics +classification algorithm, to estimate the number of reads originating +from each species present in a sample. Kraken classifies reads to the +best matching location in the taxonomic tree, but does not estimate +abundances of species. We use the Kraken database itself to derive +probabilities that describe how much sequence from each genome is +identical to other genomes in the database, and combine this information +with the assignments for a particular sample to estimate abundance at +the species level, the genus level, or above. Combined with the Kraken +classifier, Bracken produces accurate species- and genus-level abundance +estimates even when a sample contains two or more near-identical species. + +NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the +default kmer length is different depending on the version of Kraken used. +If you use Kraken 1 defaults, specify 31 as the kmer length. If you use +Kraken 2 defaults, specify 35 as the kmer length.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/jenniferlu717/Bracken/archive/'] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + 'c83665c613861fe0dc2637d9c190105f0b08f5c4cda97a0dc86a6357aab66be3', # v%(version)s.tar.gz +] + +builddependencies = [('binutils', '2.37')] + +# no need to build in parallel +parallel = 1 + +start_dir = 'src' + +files_to_copy = ['bracken', 'bracken-build', 'src', 'analysis_scripts', 'sample_data'] + +sanity_check_paths = { + 'files': ['bracken', 'bracken-build'], + 'dirs': ['analysis_scripts', 'sample_data', 'src'], +} + +sanity_check_commands = ['bracken --help', 'bracken --version'] + +modextrapaths = {'PATH': '.'} + +moduleclass = 'bio' From 97faee3b7dcff96421af8ee01bf324018dcb267d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Dec 2021 23:35:26 +0100 Subject: [PATCH 2228/9987] add download_dep_fail --- easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb b/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb index 266db5ea151..caf510d6dbb 100644 --- a/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/dRep/dRep-3.0.0-foss-2021a.eb @@ -29,6 +29,7 @@ dependencies = [ ('prodigal', '2.6.3'), ] +download_dep_fail = True use_pip = True sanity_pip_check = True From c29f3d1095cddbb63407e2adbe33887a1b9e2770 Mon Sep 17 00:00:00 2001 From: eb-test Date: Wed, 8 Dec 2021 13:22:54 +0100 Subject: [PATCH 2229/9987] adding easyconfigs: Arrow-6.0.1-foss-2021a.eb, LMfit-1.0.3-foss-2021a.eb, Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb, plotly.py-4.14.3-GCCcore-10.3.0.eb, boost_histogram-1.2.1-foss-2021a.eb, Zgoubi-6.0.2-GCCcore-10.3.0.eb, georges-2019.2-foss-2021a-Python-3.9.5.eb --- .../a/Arrow/Arrow-6.0.1-foss-2021a.eb | 59 +++++++++++++++++++ .../boost_histogram-1.2.1-foss-2021a.eb | 28 +++++++++ .../georges-2019.2-foss-2021a-Python-3.9.5.eb | 46 +++++++++++++++ .../l/LMfit/LMfit-1.0.3-foss-2021a.eb | 33 +++++++++++ .../Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb | 28 +++++++++ .../plotly.py-4.14.3-GCCcore-10.3.0.eb | 30 ++++++++++ .../z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb | 28 +++++++++ 7 files changed, 252 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb create mode 100644 easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb create mode 100644 easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb new file mode 100644 index 00000000000..425e7dbb2d6 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '6.0.1' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['3786b3d2df954d078b3e68f98d2e5aecbaa3fa2accf075d7a3a13c187b9c5294'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Autotools', '20210128'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('pkg-config', '0.29.2'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Boost', '1.76.0'), +] + +separate_build_dir = True +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/python/development.html +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb new file mode 100644 index 00000000000..5a0bffca63f --- /dev/null +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'boost_histogram' +version = '1.2.1' + +homepage = 'https://pypi.org/project/boost-histogram/' +description = """This is one of the fastest libraries for histogramming, +while still providing the power of a full histogram object""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('pybind11', '2.6.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['a27842b2f1cfecc509382da2b25b03056354696482b38ec3c0220af0fc9b7579'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..8e5f7b94288 --- /dev/null +++ b/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'georges' +version = '2019.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ULB-Metronu/georges' +description = """Georges the lemur opinionated particle accelerator modeling Python package. +Also a thin wrapper over MAD-X/PTC, BDSim and G4Beamline.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('LMfit', '1.0.3'), + ('matplotlib', '3.4.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('m2r', '0.2.1', { + 'checksums': ['bf90bad66cda1164b17e5ba4a037806d2443f2a4d5ddc9f6a5554a0322aaed99'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/ULB-Metronu/georges/archive/'], + 'checksums': ['5801c0655101e46401f4c052edc72e1dbf278fca76acf66a3ee3b10820527276'], + }), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2021a.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2021a.eb new file mode 100644 index 00000000000..c44b966b7d7 --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2021a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.0.3' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = """Lmfit provides a high-level interface to non-linear optimization +and curve fitting problems for Python""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asteval', '0.9.25', { + 'checksums': ['bea22b7d8fa16bcba95ebc72052ae5d8ca97114c9959bb47f8b8eebf30e4342f'], + }), + ('uncertainties', '3.1.6', { + 'checksums': ['7c4db5aaafd227e95485b61fba5d235dc8133aeecd98f8fc1224c038ce063e2d'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['d067c3ea501f035af5d3c079e6e6e35dc3cc1ac7d439429a425b0aeb5a7858a2'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb b/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb new file mode 100644 index 00000000000..e695e3bff9f --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Pint' +version = '0.17' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hgrecco/pint' +description = """Pint is a Python package to define, operate and +manipulate physical quantities: the product of a numerical value and a +unit of measurement. It allows arithmetic operations between them and +conversions from and to different units.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f4d0caa713239e6847a7c6eefe2427358566451fe56497d533f21fb590a3f313'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6cfb8cf4ced --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-4.14.3-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '4.14.3' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [('Python', '3.9.5')] + +use_pip = True + +exts_list = [ + ('retrying', '1.3.3', { + 'checksums': ['08c039560a6da2fe4f2c426d0766e284d3b736e355f8dd24b37367b0bb41973b'], + }), + ('plotly', version, { + 'checksums': ['7d8aaeed392e82fb8e0e48899f2d3d957b12327f9d38cdd5802bc574a8a39d91'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3ca79813105 --- /dev/null +++ b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'Zgoubi' +version = '6.0.2' + +homepage = 'https://zgoubi.sourceforge.io' +description = """Zgoubi is a ray-tracing code in use for charged particle beam dynamics simulations. +It can simulate beam dynamics in a large variety of machines and optical systems.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://sourceforge.net/projects/zgoubi/files/zgoubi/'] +sources = ['%(version)s/zgoubi-%(version)s.tar.bz2'] +checksums = ['0b0f3d28496edbf7be868c24b0c927b7f1bc88cc29df9c235d9b28dc933489e0'] + +prebuildopts = 'cp Makefile_zgoubi_gfortran Makefile &&' +prebuildopts += "sed -i '/guide/d' Makefile &&" + +buildopts = ' FFLAGS="$FFLAGS -fno-automatic -pedantic -cpp" CFLAGS="$CXXFLAGS -DGFORTRAN4"' + +files_to_copy = [(['zgoubi/zgoubi', 'zpop/zpop'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/zgoubi", "bin/zpop"], + 'dirs': [], +} + +moduleclass = 'phys' From c8df8c836a40e7b6bf09f4a7c97e39df0925b180 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Dec 2021 16:50:51 +0100 Subject: [PATCH 2230/9987] clarify that license file *is* required for installation of Gurobi v9.5.0 --- easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-10.3.0.eb index 7f9f33bb1d1..58a507ee4b4 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-10.3.0.eb @@ -28,7 +28,7 @@ dependencies = [ # remove bundled Python interpreter in favour of the dependency in EB postinstallcmds = ['rm %(installdir)s/bin/python*'] -# license looks mandatory for installation +# license is mandatory for installation license_file = HOME + '/licenses/%(name)s.lic' modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` From b3f588d7de9b1039fda71e2c66c550f954142085 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Dec 2021 16:52:04 +0100 Subject: [PATCH 2231/9987] @boegel clarify that license file *is* required for installation of Gurobi v9.5.0 --- easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-11.2.0.eb index a71a89ee067..cfe0bac03ec 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.0-GCCcore-11.2.0.eb @@ -28,7 +28,7 @@ dependencies = [ # remove bundled Python interpreter in favour of the dependency in EB postinstallcmds = ['rm %(installdir)s/bin/python*'] -# license is not mandatory for installation +# license is mandatory for installation license_file = HOME + '/licenses/%(name)s.lic' modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` From 14bb239caa5fa00e6d899e458c9b6bd5806da774 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Dec 2021 22:12:40 +0100 Subject: [PATCH 2232/9987] adding easyconfigs: SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb --- .../SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCopeLoomR/SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/s/SCopeLoomR/SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/s/SCopeLoomR/SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..9fa4d8fd8bb --- /dev/null +++ b/easybuild/easyconfigs/s/SCopeLoomR/SCopeLoomR-0.13.0-foss-2021b-R-4.1.2.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'SCopeLoomR' +local_commit = '99726f5' +version = '0.13.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/aertslab/SCopeLoomR' +description = """An R package (compatible with SCope) to create generic .loom files and extend them with other data +e.g.: SCENIC regulons, Seurat clusters and markers, ...""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('R', '4.1.2'), + ('HDF5', '1.12.1'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('rlist', '0.4.6.2', { + 'checksums': ['ebde658d897c8a27a90ebb892b9e2bad15e2ad75557a7352fb08cbb5604e0997'], + }), + (name, version, { + 'source_urls': ['https://github.com/aertslab/%(name)s/archive'], + 'sources': [{'download_filename': '99726f5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['02c8d331b5808c6fed09161f5208dd3655b41588b920c50be429f65719abf0cd'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'tools' From 12f272f3fecda3ac50a6abae703bde47913952d5 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 8 Dec 2021 22:20:43 +0100 Subject: [PATCH 2233/9987] Adding PyOpenCL for fosscuda/2020b --- .../PyOpenCL-2021.1.2-fosscuda-2020b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb new file mode 100644 index 00000000000..0f033662e72 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2021.1.2' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2021.1', { + 'checksums': ['073ae22a0ae946e2db97164f2eb24a599cd3a51430384aa40859dffd73056c40'], + }), + ('pyopencl', version, { + 'checksums': ['18871bc80c5a94869521189cf2c04d72c88367a441a9a033f72f66792ac33d29'], + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + }), +] + +moduleclass = 'vis' From 5e0278a6ea70be16fbbaffb5a2010cb4ebbf4ae1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 9 Dec 2021 07:17:34 +0100 Subject: [PATCH 2234/9987] Add missing patch --- .../h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb | 7 ++++ .../hipamd-rocm-4.5.0-remove-testing.patch | 34 +++++++++++++++++++ 2 files changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/h/HIP/hipamd-rocm-4.5.0-remove-testing.patch diff --git a/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb index 08836323e6d..b6182b943e3 100644 --- a/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb +++ b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb @@ -90,4 +90,11 @@ modextravars = { 'ROCM_PATH': '%(installdir)s', } +modluafooter = """ +setenv("DEVICE_LIB_PATH", os.getenv("EBROOTCLANGMINAOMP") .. "/amdgcn/bitcode") +setenv("HIP_CLANG_INCLUDE_PATH", os.getenv("EBROOTCLANGMINAOMP") .. "/include") +setenv("CLANG_PATH", os.getenv("EBROOTCLANGMINAOMP") .. "/bin") +setenv("HSA_PATH", os.getenv("EBROOTROCRMINRUNTIME")) +""" + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HIP/hipamd-rocm-4.5.0-remove-testing.patch b/easybuild/easyconfigs/h/HIP/hipamd-rocm-4.5.0-remove-testing.patch new file mode 100644 index 00000000000..9de1c55384e --- /dev/null +++ b/easybuild/easyconfigs/h/HIP/hipamd-rocm-4.5.0-remove-testing.patch @@ -0,0 +1,34 @@ +--- hipamd-rocm-4.5.0/CMakeLists.txt.orig 2021-11-12 14:26:59.514400918 +0100 ++++ hipamd-rocm-4.5.0/CMakeLists.txt 2021-11-12 14:27:23.551183553 +0100 +@@ -487,31 +487,6 @@ + ############################# + # Testing steps + ############################# +-# HIT is not compatible with Windows +-if(NOT WIN32) +-set(HIP_ROOT_DIR ${CMAKE_CURRENT_BINARY_DIR}) +-set(HIP_SRC_PATH ${CMAKE_CURRENT_SOURCE_DIR}) +-if(HIP_PLATFORM STREQUAL "nvidia") +- execute_process(COMMAND "${CMAKE_COMMAND}" -E copy_directory "${HIP_SRC_PATH}/include" "${HIP_ROOT_DIR}/include" RESULT_VARIABLE RUN_HIT ERROR_QUIET) +-endif() +-execute_process(COMMAND "${CMAKE_COMMAND}" -E copy_directory "${HIP_COMMON_INCLUDE_DIR}/hip/" "${HIP_ROOT_DIR}/include/hip/" RESULT_VARIABLE RUN_HIT ERROR_QUIET) +-execute_process(COMMAND "${CMAKE_COMMAND}" -E copy_directory "${HIP_COMMON_DIR}/cmake" "${HIP_ROOT_DIR}/cmake" RESULT_VARIABLE RUN_HIT ERROR_QUIET) +-if(${RUN_HIT} EQUAL 0) +- execute_process(COMMAND "${CMAKE_COMMAND}" -E copy_directory "${HIP_COMMON_BIN_DIR}" "${HIP_ROOT_DIR}/bin" RESULT_VARIABLE RUN_HIT ERROR_QUIET) +-endif() +-if(HIP_CATCH_TEST EQUAL "1") +- enable_testing() +- add_subdirectory(${HIP_COMMON_DIR}/tests/catch ${PROJECT_BINARY_DIR}/catch) +-else() +- if(${RUN_HIT} EQUAL 0) +- set(CMAKE_MODULE_PATH "${HIP_ROOT_DIR}/cmake" ${CMAKE_MODULE_PATH}) +- include(${HIP_COMMON_DIR}/tests/hit/HIT.cmake) +- include(${HIP_COMMON_DIR}/tests/Tests.cmake) +- else() +- message(STATUS "Testing targets will not be available. To enable them please ensure that the HIP installation directory is writeable. Use -DCMAKE_INSTALL_PREFIX to specify a suitable location") +- endif() +-endif() +-endif() + + ############################# + # Code analysis From 8793f35a56edf4216d2d9d9480219476899a6e7b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 9 Dec 2021 07:18:12 +0100 Subject: [PATCH 2235/9987] Update easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb Co-authored-by: Kenneth Hoste --- .../h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb | 30 ++++++++++++------- 1 file changed, 20 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb index b6182b943e3..fcdad1b2c74 100644 --- a/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb +++ b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb @@ -12,17 +12,27 @@ docurls = ['https://rocmdocs.amd.com'] toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = [ - "https://github.com/ROCm-Developer-Tools/hipamd/archive/", - "https://github.com/ROCm-Developer-Tools/ROCclr/archive/", - "https://github.com/ROCm-Developer-Tools/HIP/archive/", - "https://github.com/RadeonOpenCompute/ROCm-OpenCL-Runtime/archive/", -] sources = [ - 'hipamd-rocm-%(version)s.tar.gz', - 'ROCclr-rocm-%(version)s.tar.gz', - 'HIP-rocm-%(version)s.tar.gz', - 'ROCm-OpenCL-Runtime-rocm-%(version)s.tar.gz', + { + 'source_urls': ['https://github.com/ROCm-Developer-Tools/hipamd/archive/'], + 'download_filename': 'rocm-%(version)s.tar.gz', + 'filename': 'hipamd-rocm-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/ROCm-Developer-Tools/ROCclr/archive/'], + 'download_filename': 'rocm-%(version)s.tar.gz', + 'filename': 'ROCclr-rocm-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/ROCm-Developer-Tools/HIP/archive/'], + 'download_filename': 'rocm-%(version)s.tar.gz', + 'filename': 'HIP-rocm-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/RadeonOpenCompute/ROCm-OpenCL-Runtime/archive/'], + 'download_filename': 'rocm-%(version)s.tar.gz', + 'filename': 'ROCm-OpenCL-Runtime-rocm-%(version)s.tar.gz', + }, ] patches = ['hipamd-rocm-%(version)s-remove-testing.patch'] From 1408863d50688519a35e4c00f718d6801766384f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 9 Dec 2021 08:53:20 +0100 Subject: [PATCH 2236/9987] adding easyconfigs: DIAMOND-2.0.13-GCC-10.3.0.eb --- .../d/DIAMOND/DIAMOND-2.0.13-GCC-10.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-10.3.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-10.3.0.eb new file mode 100644 index 00000000000..95476f692b1 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.0.13' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/bbuchfink/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9b79c3a01913999dfa2543f4dd7a3494397a8723ea587207c14683b24e57eac1'] + +separate_build_dir = True + +builddependencies = [ + ('CMake', '3.20.1') +] +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["diamond help"] + +moduleclass = 'bio' From b48bba970ac0378987e7840fdacebe8a6b1d7eda Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 9 Dec 2021 09:11:45 +0100 Subject: [PATCH 2237/9987] adding easyconfigs: GTDB-Tk-1.7.0-foss-2021a.eb, FastTree-2.1.11-GCCcore-10.3.0.eb --- .../FastTree-2.1.11-GCCcore-10.3.0.eb | 35 +++++++++++++++ .../g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb | 43 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e210cab5b2b --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'https://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.36.1')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb new file mode 100644 index 00000000000..05e89644664 --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'GTDB-Tk' +version = '1.7.0' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/g/gtdbtk'] +sources = ['gtdbtk-%(version)s.tar.gz'] +checksums = ['36b65074845e7edef4d7aeead286c770fb9a03ddbff63946533fa2e1934e8f26'] + +dependencies = [ + ('Python', '3.9.5'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.4.2'), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', True), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.61.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 5124b43b6b3f6c6a5ff05d387392b06ef70d7abc Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Thu, 9 Dec 2021 09:06:58 +0000 Subject: [PATCH 2238/9987] adding easyconfigs: ORCA-5.0.2-gompi-2021a-static.eb, ORCA-5.0.2-gompi-2021a.eb --- .../o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb | 29 +++++++++++++++++++ .../o/ORCA/ORCA-5.0.2-gompi-2021a.eb | 23 +++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb new file mode 100644 index 00000000000..fd53dc9c626 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb @@ -0,0 +1,29 @@ +name = 'ORCA' +version = '5.0.2' +versionsuffix = '-static' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +# Static build of ORCA: download from https://orcaforum.kofo.mpg.de +# OpenMPI is dynamically linked +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_openmpi411_part%s.tar.xz' % (version.replace('.', '_'), p) + for p in range(1, 4)] +checksums = [ + # orca_5_0_2_linux_x86-64_openmpi411_part1.tar.xz + '7623ae43a7d02a36f890a3826e0d021d634addb8e1b2598feb7f9b29d8a3f935', + # orca_5_0_2_linux_x86-64_openmpi411_part2.tar.xz + '905b427a721554a0037986494473a91daa4a0b182dcfbb92fe5d2abccc68df2c', + # orca_5_0_2_linux_x86-64_openmpi411_part3.tar.xz + 'fd04e2df6c3aeaaef79d2c36917d9973f64368348060a9c194e80b7f7a29b9c7', +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a.eb new file mode 100644 index 00000000000..c4ee43cd9be --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '5.0.2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +# Shared build of ORCA: download from https://orcaforum.kofo.mpg.de +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi411.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_5_0_2_linux_x86-64_shared_openmpi411.tar.xz + '3a26a1a5fbc69e7dca0192237b5e16b69886df31751ae59f7396461428aeee96', +] + +moduleclass = 'chem' From 25bb49426de3b643bf3ec2baad4b370ed8ac0a49 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 9 Dec 2021 11:47:54 +0100 Subject: [PATCH 2239/9987] Fixup after review --- .../Clang-AOMP-4.5.0-GCCcore-11.2.0.eb | 6 ++---- ...tras-remove-hardcoded-devicelib-path.patch | 3 +++ ...openmp-remove-hardcoded-source-paths.patch | 4 ++++ ...CT-Thunk-Interface-4.5.0-GCCcore-11.2.0.eb | 21 ++++++++++++------- ...Cm-CompilerSupport-4.5.0-GCCcore-11.2.0.eb | 7 ++++--- .../rocm-cmake-4.5.0-GCCcore-11.2.0.eb | 7 ++++--- .../rocminfo/rocminfo-4.5.0-GCCcore-11.2.0.eb | 14 ++++++++----- 7 files changed, 40 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb index 000810eb21b..65758d66987 100644 --- a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb @@ -1,5 +1,3 @@ -easyblock = 'EB_Clang_AOMP' - name = 'Clang-AOMP' version = '4.5.0' @@ -53,13 +51,13 @@ components = [ 'sources': ['llvm-project-%(version)s.tar.gz'], 'patches': ['clang-aomp-%(version)s-openmp-remove-hardcoded-source-paths.patch'], 'checksums': ['e33d08c8ae42a3ba394dceb8938263cd14ba45e9603b18f3502c3344814ca296', - 'efead86cb7e960de1e3f928dbdfdcc367769015d0af1f8f501d344f719148a9c'], + 'f959dfa95ec705acf0ffb8d5e85b48cc56e2bed1b15fab22d9eda1f416dd98ca'], }), ('aomp-extras', 'rocm-4.5.0', { 'source_urls': ['https://github.com/ROCm-Developer-Tools/%(name)s/archive/'], 'patches': ['clang-aomp-%(version)s-aomp-extras-remove-hardcoded-devicelib-path.patch'], 'checksums': ['66d4d0cb4a1a05edb5f13599d8c06de4e10daf561201273cc56dc907139cb894', - 'b833dc3630e5a8f0fb014154aeb48895c9dbd8ad02232a095020694d18d6236a'], + '1ae5a1af5ccd6c5a77dbc2882d0b40f07d33a7d0021736b29a21e46ab777803a'], }), ] diff --git a/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-aomp-extras-remove-hardcoded-devicelib-path.patch b/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-aomp-extras-remove-hardcoded-devicelib-path.patch index ef5a2cf84ed..04d33036d35 100644 --- a/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-aomp-extras-remove-hardcoded-devicelib-path.patch +++ b/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-aomp-extras-remove-hardcoded-devicelib-path.patch @@ -1,3 +1,6 @@ +# Remove hardcoded path to devicelib library, we supply this ourselves during +# the build +# Author: Jørgen Nordmoen (University of Oslo) --- aomp-extras-rocm-4.5.0/aomp-device-libs/CMakeLists.txt.orig 2021-10-11 09:35:05.007403780 +0200 +++ aomp-extras-rocm-4.5.0/aomp-device-libs/CMakeLists.txt 2021-10-11 09:35:18.386175357 +0200 @@ -27,7 +27,6 @@ diff --git a/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-openmp-remove-hardcoded-source-paths.patch b/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-openmp-remove-hardcoded-source-paths.patch index dc301e3e2d5..dfd75e14533 100644 --- a/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-openmp-remove-hardcoded-source-paths.patch +++ b/easybuild/easyconfigs/c/Clang-AOMP/clang-aomp-rocm-4.5.0-openmp-remove-hardcoded-source-paths.patch @@ -1,3 +1,7 @@ +# When building OpenMP library for Clang-AOMP the build tries to access a few +# hardcoded paths which are not accessible in the EasyBuild setup, we can +# simply remove these paths as they are not needed +# Author: Jørgen Nordmoen (University of Oslo) --- llvm-project-rocm-4.5.0/openmp/libomptarget/deviceRTLs/amdgcn/CMakeLists.txt.orig 2021-11-11 14:31:55.835361003 +0100 +++ llvm-project-rocm-4.5.0/openmp/libomptarget/deviceRTLs/amdgcn/CMakeLists.txt 2021-11-11 14:32:14.624217685 +0100 @@ -49,11 +49,9 @@ diff --git a/easybuild/easyconfigs/r/ROCT-Thunk-Interface/ROCT-Thunk-Interface-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/ROCT-Thunk-Interface/ROCT-Thunk-Interface-4.5.0-GCCcore-11.2.0.eb index b2253c71bcc..de42d7c18f8 100644 --- a/easybuild/easyconfigs/r/ROCT-Thunk-Interface/ROCT-Thunk-Interface-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/ROCT-Thunk-Interface/ROCT-Thunk-Interface-4.5.0-GCCcore-11.2.0.eb @@ -13,21 +13,28 @@ source_urls = ["https://github.com/RadeonOpenCompute/ROCT-Thunk-Interface/archiv sources = ["rocm-%(version)s.tar.gz"] checksums = ['620b39959e0ee5d709b8cf6eb3cc06c8356d72838343756230c638899b10bb9a'] -dependencies = [ - ('libdrm', '2.4.107'), - ('numactl', '2.0.14'), -] builddependencies = [ + ('binutils', '2.37'), ('CMake', '3.21.1'), ('pkg-config', '0.29.2'), ] +dependencies = [ + ('libdrm', '2.4.107'), + ('numactl', '2.0.14'), +] -group = 'video' +# The following group ensures that the user is in the 'video' group. According +# to AMD this is necessary to interact with the GPU, but testing has shown this +# to not be the case. If you experience problems this could be one area to +# check out +# group = 'video' + +preconfigopts = r"""sed -i 's/\({HSAKMT_LINK_FLAGS}\)" \(-.*\) )/\1 \2" )/g' ../ROCT-*/CMakeLists.txt && """ -preconfigopts = r"""sed -i 's/\({HSAKMT_LINK_FLAGS}\)" \(-.*\) )/\1 \2" )/g' ../ROCT-*/CMakeLists.txt && """, -installopts = " && cp -a %(builddir)s/%(name)s-rocm-%(version)s/include %(installdir)s/" configopts = "-DCMAKE_INSTALL_LIBDIR=%(installdir)s/lib -DBUILD_SHARED_LIBS=ON" +installopts = " && cp -a %(builddir)s/%(name)s-rocm-%(version)s/include %(installdir)s/" + sanity_check_paths = { 'files': ['include/hsakmt.h', 'include/hsakmttypes.h', 'include/linux/kfd_ioctl.h', 'lib/libhsakmt.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/r/ROCm-CompilerSupport/ROCm-CompilerSupport-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/ROCm-CompilerSupport/ROCm-CompilerSupport-4.5.0-GCCcore-11.2.0.eb index 10f18c50b69..050c8c67582 100644 --- a/easybuild/easyconfigs/r/ROCm-CompilerSupport/ROCm-CompilerSupport-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/ROCm-CompilerSupport/ROCm-CompilerSupport-4.5.0-GCCcore-11.2.0.eb @@ -14,12 +14,13 @@ source_urls = ["https://github.com/RadeonOpenCompute/ROCm-CompilerSupport/archiv sources = ["rocm-%(version)s.tar.gz"] checksums = ['03c5880e0922fcff31306f7da2eb9d3a3709d9b5b75b3524dcfae85f4b181678'] -dependencies = [ - ('Clang-AOMP', '%(version)s'), -] builddependencies = [ + ('binutils', '2.37'), ('CMake', '3.21.1'), ] +dependencies = [ + ('Clang-AOMP', '%(version)s'), +] srcdir = "lib/comgr" diff --git a/easybuild/easyconfigs/r/rocm-cmake/rocm-cmake-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/rocm-cmake/rocm-cmake-4.5.0-GCCcore-11.2.0.eb index 020d124727d..cd8f5cea65d 100644 --- a/easybuild/easyconfigs/r/rocm-cmake/rocm-cmake-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/rocm-cmake/rocm-cmake-4.5.0-GCCcore-11.2.0.eb @@ -14,12 +14,13 @@ source_urls = ["https://github.com/RadeonOpenCompute/rocm-cmake/archive/refs/tag sources = ["rocm-%(version)s.tar.gz"] checksums = ['c77b71454010adbeea5357773aa98dd0725f655f51a411815807cabf29258395'] -dependencies = [ - ('Clang-AOMP', '%(version)s'), -] builddependencies = [ + ('binutils', '2.37'), ('CMake', '3.21.1'), ] +dependencies = [ + ('Clang-AOMP', '%(version)s'), +] configopts = '-DCMAKE_C_COMPILER=$EBROOTCLANGMINAOMP/bin/clang' configopts += ' -DCMAKE_CXX_COMPILER=$EBROOTCLANGMINAOMP/bin/clang++' diff --git a/easybuild/easyconfigs/r/rocminfo/rocminfo-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/rocminfo/rocminfo-4.5.0-GCCcore-11.2.0.eb index 62978532117..7c01c982fda 100644 --- a/easybuild/easyconfigs/r/rocminfo/rocminfo-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/rocminfo/rocminfo-4.5.0-GCCcore-11.2.0.eb @@ -13,13 +13,14 @@ source_urls = ["https://github.com/RadeonOpenCompute/rocminfo/archive/refs/tags/ sources = ["rocm-%(version)s.tar.gz"] checksums = ['421ed55192780eb478f0341fd1ce47a0dd3ffafbec9d7a02109a411878a58ee5'] +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] dependencies = [ ('ROCR-Runtime', '%(version)s'), ('Python', '3.9.6'), # Needed for 'rocm_agent_enumerator' which is a Python script ] -builddependencies = [ - ('CMake', '3.21.1'), -] configopts = "-DCMAKE_EXE_LINKER_FLAGS='-Wl,--disable-new-dtags'" configopts += " -DROCRTST_BLD_TYPE=Release" @@ -27,8 +28,11 @@ configopts += " -DROCM_DIR=%(installdir)s" sanity_check_paths = { 'files': ['bin/rocminfo', 'bin/rocm_agent_enumerator'], - 'dirs': ['bin'], + 'dirs': [], } -sanity_check_commands = ['rocminfo --help', 'rocm_agent_enumerator'] +sanity_check_commands = [ + 'rocminfo --help', + 'rocm_agent_enumerator' +] moduleclass = 'tools' From ae74604149c3f8b0226aefe0e189d18000d3c2d6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 9 Dec 2021 11:54:30 +0100 Subject: [PATCH 2240/9987] Added binutils to remaining EBs --- .../c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb | 2 +- .../r/ROCR-Runtime/ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb index 65758d66987..b2a27c3aafd 100644 --- a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb @@ -12,10 +12,10 @@ builddependencies = [ ('CMake', '3.21.1'), ('Perl', '5.34.0'), ('Python', '3.9.6'), + ('binutils', '2.37'), ('elfutils', '0.185'), ('pkg-config', '0.29.2'), ] - dependencies = [ ('GMP', '6.2.1'), ('ROCR-Runtime', '%(version)s'), diff --git a/easybuild/easyconfigs/r/ROCR-Runtime/ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/ROCR-Runtime/ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb index 6b57c85a8a8..7082db953d7 100644 --- a/easybuild/easyconfigs/r/ROCR-Runtime/ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/ROCR-Runtime/ROCR-Runtime-4.5.0-GCCcore-11.2.0.eb @@ -14,13 +14,14 @@ source_urls = ["https://github.com/RadeonOpenCompute/ROCR-Runtime/archive/refs/t sources = ["rocm-%(version)s.tar.gz"] checksums = ['fbf550f243dddfef46a716e360b77c43886fed3eef67215ab9dab1c82f3851ca'] +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] dependencies = [ ('elfutils', '0.185'), ('ROCT-Thunk-Interface', '%(version)s'), ] -builddependencies = [ - ('CMake', '3.21.1'), -] srcdir = "src" From bc36fae52dcfa19180fbddaaa7e90f1ffe06a650 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Thu, 9 Dec 2021 12:19:21 +0100 Subject: [PATCH 2241/9987] Added binutils and beautify --- .../h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb index fcdad1b2c74..79a752ac580 100644 --- a/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb +++ b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb @@ -45,6 +45,10 @@ checksums = [ 'b70636c7853c74d1fca3c71b73d48ff3a2c66d09382b2378900ee47f25ed2ae1', # hipamd-4.5.0-remove-testing.patch ] +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] dependencies = [ ('Clang-AOMP', '%(version)s'), ('Perl', '5.34.0'), @@ -58,10 +62,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -builddependencies = [ - ('CMake', '3.21.1'), -] - # AMD uses 'gfx' to identify the GPU, the first number identifies the generation, according to # https://www.x.org/wiki/RadeonFeature/#index5h2 while the rest identifies the specific GPU. # In the context of EasyBuild this identifier can be thought of as equivalent to the 'sm_' @@ -83,9 +83,12 @@ postinstallcmds = [ sanity_check_paths = { 'files': ['bin/hipcc', 'bin/hipconfig', 'include/hip/hip_common.h', 'include/hip/hip_runtime.h', 'lib/libamdhip64.%s' % SHLIB_EXT], - 'dirs': ['bin', 'cmake', 'include/hip'], + 'dirs': [], } -sanity_check_commands = ['hipcc --help', 'hipconfig --full'] +sanity_check_commands = [ + 'hipcc --help', + 'hipconfig --full' +] modextravars = { 'DEVICE_LIB_PATH': '$EBROOTCLANGMINAOMP/amdgcn/bitcode', From b49293bf9a08997a8863e4b987a4a830ac2efeeb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 9 Dec 2021 13:45:08 +0100 Subject: [PATCH 2242/9987] {chem}[foss/2020b] yaff 1.6.0 --- .../h/h5py/h5py-2.10.0-foss-2020b.eb | 35 +++++++++++++++ .../m/molmod/molmod-1.4.8-foss-2020b.eb | 34 +++++++++++++++ .../y/yaff/yaff-1.6.0-foss-2020b.eb | 43 +++++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb new file mode 100644 index 00000000000..29f06c60e0d --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.10.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['h5py-%(version)s_avoid-mpi-init.patch'] +checksums = [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch +] + +builddependencies = [('pkgconfig', '1.5.1', '-python')] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('HDF5', '1.10.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb new file mode 100644 index 00000000000..55945818bbf --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = [ + '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8', # molmod-1.4.8.tar.gz +] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; pytest -ra" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb new file mode 100644 index 00000000000..e86af8d99d0 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# +# Building this in interactive Slurm session will result in freeze during either +# runtest phase or sanity_check_commands phase (python -c 'import yaff') +# +# If you submit this as non-interactive Slurm job, it will build just fine. +# Possibly root cause: https://github.com/h5py/h5py/issues/917 +# +easyblock = 'PythonPackage' + +name = 'yaff' +version = '1.6.0' + +homepage = 'https://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + # Needs h5py version 2 + ('h5py', '2.10.0'), + ('molmod', '1.4.8'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +runtest += "python setup.py build_ext -i; nosetests -v" + +moduleclass = 'chem' From d697f9f0ad068708278a8a9a8d42732db88b23e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Dec 2021 22:50:25 +0100 Subject: [PATCH 2243/9987] add additional sanity check command for libtree --- .../easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb index 2d4b9162c5f..e53c4156b43 100644 --- a/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb @@ -28,9 +28,12 @@ builddependencies = [ sanity_check_paths = { 'files': ["bin/%(name)s"], - 'dirs': ['bin', 'share'] + 'dirs': ['share'] } -sanity_check_commands = ["libtree --version"] +sanity_check_commands = [ + "libtree --version", + "libtree -ap %(installdir)s/bin/libtree", +] moduleclass = 'tools' From 8a0d2b37fceeb6d804c0dfd335151837f416994e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Dec 2021 23:41:24 +0100 Subject: [PATCH 2244/9987] correctly specify header-only build dependencies of libtree --- .../easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb index e53c4156b43..a3916dbea56 100644 --- a/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb @@ -21,9 +21,9 @@ checksums = ['099e85d8ba3c3d849ce05b8ba2791dd25cd042a813be947fb321b0676ef71883'] builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), - ('cxxopts', '3.0.0'), - ('ELFIO', '3.9'), - ('termcolor', '2.0.0'), + ('cxxopts', '3.0.0', '', True), + ('ELFIO', '3.9', '', True), + ('termcolor', '2.0.0', '', True), ] sanity_check_paths = { From 42e2ab8b54eeee8f8d59a5b6d13a3657069299bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Dec 2021 23:49:40 +0100 Subject: [PATCH 2245/9987] add bin subdir to $PATH in preinstallopts in ReFrame easyconfigs to ensure right pip command is used --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb | 5 +++++ easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb | 5 +++++ easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb | 6 ++++-- easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb | 4 +++- easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb | 4 +++- easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.1.eb | 2 ++ easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.2.eb | 4 +++- easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb | 6 ++++-- easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb | 4 +++- easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb | 4 +++- easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb | 4 +++- easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb | 4 +++- easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb | 4 +++- 13 files changed, 44 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb index 79cabdb2c42..71ff1be0f5c 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.0.eb @@ -15,6 +15,11 @@ req_py_minver = 6 use_pip = True +exts_default_options = { + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && ", +} + exts_list = [ ('pip', '20.1.1', { 'checksums': ['27f8dc29387dd83249e06e681ce087e6061826582198a425085e0bf4c1cf3a55'], diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb index 1417a537b82..14b90f4f54f 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb @@ -15,6 +15,11 @@ req_py_minver = 6 use_pip = True +exts_default_options = { + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && ", +} + exts_list = [ ('pip', '20.2.4', { 'checksums': ['85c99a857ea0fb0aedf23833d9be5c40cf253fe24443f0829c7b472e23c364a1'], diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb index f4423aa3029..7595b2ca7c8 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.3.eb @@ -33,8 +33,10 @@ exts_list = [ # Use bootstrap script to install ReFrame dependencies under `external`. # ReFrame adds `external` to its own python path before executing, without - # affecting the python path of the system - 'preinstallopts': './bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ', + # affecting the python path of the system; + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", }), ] diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb index 82ee85ae7a8..e02756de89b 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.4.1.eb @@ -25,7 +25,9 @@ exts_list = [ 'checksums': ['1b18ef17d74ba97ac9c0e4b4265f123f07a8ae85d9cd093949fa056d3eeeead5'], }), ('reframe', version, { - 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], 'checksums': ['aed5752a2f687002839923c5432784d3a25d3a29d43b69122dcbf72befa0fdbf'], diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb index a5af6c89988..28e5f5b4b49 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.0.eb @@ -25,7 +25,9 @@ exts_list = [ 'checksums': ['1b18ef17d74ba97ac9c0e4b4265f123f07a8ae85d9cd093949fa056d3eeeead5'], }), ('reframe', version, { - 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], 'checksums': ['81b501be4252c99f12043cb21b0b7b8059207a340fc94173b180444599773f1a'], diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.1.eb index 34b3bc3efa0..f2df4f9de11 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.1.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.1.eb @@ -17,6 +17,8 @@ use_pip = True # bump hardcoded importlib-metadata version to more recent version, only require it with Python < 3.8 local_preinstallopts = r"""sed -i "s/\(importlib.*\)==.*/\1==3.10.0; python_version < '3.8'/g" requirements.txt && """ +# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages +local_preinstallopts += "export PATH=%(installdir)s/bin:$PATH && " # use bootstrap script to install required Python packages local_preinstallopts += "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.2.eb index 03537712731..685bc826e33 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.5.2.eb @@ -25,7 +25,9 @@ exts_list = [ 'checksums': ['1b18ef17d74ba97ac9c0e4b4265f123f07a8ae85d9cd093949fa056d3eeeead5'], }), ('reframe', version, { - 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], 'checksums': ['50d461811f6bba7c9b897866a290063e1bd229e7055f5acc2de1f749b99bfce7'] diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb index 54ab6cd55cd..ffed5ef3f85 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.2.eb @@ -25,8 +25,10 @@ exts_list = [ 'checksums': ['1b18ef17d74ba97ac9c0e4b4265f123f07a8ae85d9cd093949fa056d3eeeead5'], }), ('reframe', version, { - 'prebuildopts': ('./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && ' - 'PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH '), + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'prebuildopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], 'use_pip': False, diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb index 8cef4c10962..adafa2b8796 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.6.3.eb @@ -25,7 +25,9 @@ exts_list = [ 'checksums': ['1b18ef17d74ba97ac9c0e4b4265f123f07a8ae85d9cd093949fa056d3eeeead5'], }), ('reframe', version, { - 'prebuildopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'prebuildopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb index a977d55f597..43f074cd3ee 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.7.3.eb @@ -28,7 +28,9 @@ exts_list = [ 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], }), ('reframe', version, { - 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb index a69c7c6cf4c..395aa64e600 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.8.0.eb @@ -28,7 +28,9 @@ exts_list = [ 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], }), ('reframe', version, { - 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb index 6f67b2659d9..a365f15126b 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.0.eb @@ -28,7 +28,9 @@ exts_list = [ 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], }), ('reframe', version, { - 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb index 1ab08fd3685..efe48dd85fa 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.9.1.eb @@ -28,7 +28,9 @@ exts_list = [ 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], }), ('reframe', version, { - 'preinstallopts': "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], From 74c7b759b9c8dad6cc690dc1c6a8900258a87a5c Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Fri, 10 Dec 2021 06:28:27 +0000 Subject: [PATCH 2246/9987] Strip redundant ORCA top-level directories when unpacking --- easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb index fd53dc9c626..ca35b29f949 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021a-static.eb @@ -26,4 +26,8 @@ checksums = [ 'fd04e2df6c3aeaaef79d2c36917d9973f64368348060a9c194e80b7f7a29b9c7', ] +# The 5.0.2-static tarballs have redundant top-level directory names names that +# need to be stripped away. +unpack_options = '--strip-components=1' + moduleclass = 'chem' From 41fc83fde635c89c05edd71b6857c6cfd311c4ae Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 10 Dec 2021 17:21:06 +1050 Subject: [PATCH 2247/9987] dep <- SAMtools v1.10 to resolve conflicts --- .../easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb index 2250091756b..ad9f91a1025 100644 --- a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb @@ -26,7 +26,7 @@ dependencies = [ ('bcbio-gff', '0.6.6', versionsuffix), ('biom-format', '2.1.10', versionsuffix), ('Pysam', '0.16.0.1'), - ('SAMtools', '1.12', '', ('GCC', '9.3.0')), + ('SAMtools', '1.10'), ] download_dep_fail = True From aa05bae9c7c951ec66fcb422f9948d6a231349c8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Dec 2021 11:34:43 +0100 Subject: [PATCH 2248/9987] adding easyconfigs: Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb --- .../Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..c66061a04a9 --- /dev/null +++ b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb @@ -0,0 +1,41 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'Binary' + +name = 'Rgurobi' +version = '9.5.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://www.gurobi.com' +description = """Gurobi Optimizer %(version_major_minor)s interface""" +# NOTE not in the license list of EB +# software_license = 'LGPL-2.1' + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['gurobi%(version)s_linux64.tar.gz'] +checksums = ['bb542e5a5d1685f6e364eaf05ea6c5572485ffc37a2245169cf3cb40288bc29e'] + +dependencies = [ + ('R', '4.1.0'), + ('Gurobi', version), +] + +extract_sources = True +install_cmd = 'R CMD INSTALL R/gurobi_*.tar.gz --library=%(installdir)s --no-clean-on-error' + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['gurobi'], +} + +moduleclass = 'math' From fb49404b8a1d7f20270f8c1a33bfb8b483c8edac Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Dec 2021 11:43:35 +0100 Subject: [PATCH 2249/9987] bundle h5py to yaff --- .../h/h5py/h5py-2.10.0-foss-2020b.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb b/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb deleted file mode 100644 index 29f06c60e0d..00000000000 --- a/easybuild/easyconfigs/h/h5py/h5py-2.10.0-foss-2020b.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'h5py' -version = '2.10.0' - -homepage = 'https://www.h5py.org/' -description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, - version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous - amounts of data.""" - -toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True} - -sources = [SOURCE_TAR_GZ] -patches = ['h5py-%(version)s_avoid-mpi-init.patch'] -checksums = [ - '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz - '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch -] - -builddependencies = [('pkgconfig', '1.5.1', '-python')] - -dependencies = [ - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('HDF5', '1.10.7'), -] - -use_pip = True -sanity_pip_check = True -download_dep_fail = True - -preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ' - -moduleclass = 'data' From 65df7841095105d00fec0374e4e3e8b13e6ccd82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Dec 2021 11:43:39 +0100 Subject: [PATCH 2250/9987] remove binutils build dependency for Clang-AOMP (it's already listed as a runtime dependency) --- .../easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb index b2a27c3aafd..b679ed3649a 100644 --- a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb @@ -12,7 +12,6 @@ builddependencies = [ ('CMake', '3.21.1'), ('Perl', '5.34.0'), ('Python', '3.9.6'), - ('binutils', '2.37'), ('elfutils', '0.185'), ('pkg-config', '0.29.2'), ] From 2859be8f5d7b5f0e9a5faae4a5143e0f591f8d65 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Dec 2021 11:44:34 +0100 Subject: [PATCH 2251/9987] bundle h5py to yaff v2 --- .../y/yaff/yaff-1.6.0-foss-2020b.eb | 32 +++++++++++++------ 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb index e86af8d99d0..e7103d4a5c0 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -8,7 +8,7 @@ # If you submit this as non-interactive Slurm job, it will build just fine. # Possibly root cause: https://github.com/h5py/h5py/issues/917 # -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'yaff' version = '1.6.0' @@ -18,15 +18,12 @@ description = """Yaff stands for 'Yet another force field'. It is a pythonic for toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] -sources = [SOURCE_TAR_GZ] -checksums = ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'] +builddependencies = [('pkgconfig', '1.5.1', '-python')] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - # Needs h5py version 2 - ('h5py', '2.10.0'), + ('HDF5', '1.10.7'), ('molmod', '1.4.8'), ] @@ -34,10 +31,25 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True +local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +local_runtest += "python setup.py build_ext -i; nosetests -v" + +exts_list = [ + ('h5py', '2.10.0', { + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + 'source_urls': ['https://pypi.python.org/packages/source/h/h5py'], + 'checksums': [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch + ], + }), + (name, version, { + 'source_urls': ['https://github.com/molmod/yaff/releases/download/%(version)s'], + 'runtest': local_runtest, + 'checksums': ['a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'], + }), +] -runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " -runtest += "python setup.py build_ext -i; nosetests -v" moduleclass = 'chem' From 81d553ef373e24e81d2533f2c6cca13bb98c388f Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 10 Dec 2021 21:41:04 +1050 Subject: [PATCH 2252/9987] adding easyconfigs: cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb --- ..._Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..02a39c41144 --- /dev/null +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,50 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v24.2.0 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'cDNA_Cupcake' +version = '26.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Magdoll/cDNA_Cupcake' +description = """cDNA_Cupcake is a miscellaneous collection of Python and +R scripts used for analyzing sequencing data. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/Magdoll/cDNA_Cupcake/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb44ae28639c0841b3a3c85228379053bf80ee82a8dd6c260aac69c4f0d18458'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05', versionsuffix), + ('Biopython', '1.79', versionsuffix), + ('bx-python', '0.8.11', versionsuffix), + ('bcbio-gff', '0.6.7', versionsuffix), + ('scikit-learn', '0.24.2', versionsuffix), + ('Pysam', '0.16.0.1'), +] + +download_dep_fail = False +use_pip = True + +sanity_pip_check = True +sanity_check_paths = { + # check for particular Cupcake ToFU scripts, + # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step + 'files': [ + 'bin/collapse_isoforms_by_sam.py', + 'bin/get_abundance_post_collapse.py', + 'bin/simple_stats_post_collapse.py' + ], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'cupcake'} + +moduleclass = 'bio' From 2cff19ec64c9ce00f8c68830f88906a0e30bd117 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Dec 2021 12:04:29 +0100 Subject: [PATCH 2253/9987] Add h5py pathc file --- .../y/yaff/h5py-2.10.0_avoid-mpi-init.patch | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/y/yaff/h5py-2.10.0_avoid-mpi-init.patch diff --git a/easybuild/easyconfigs/y/yaff/h5py-2.10.0_avoid-mpi-init.patch b/easybuild/easyconfigs/y/yaff/h5py-2.10.0_avoid-mpi-init.patch new file mode 100644 index 00000000000..98034776400 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/h5py-2.10.0_avoid-mpi-init.patch @@ -0,0 +1,85 @@ +avoid that 'import h5py' triggers MPI_Init via mpi4py + +backported to h5py 2.10.0 from https://github.com/h5py/h5py/pull/1552 by Kenneth Hoste (HPC-UGent) + +diff -ru h5py-2.10.0.orig/h5py/api_types_ext.pxd h5py-2.10.0/h5py/api_types_ext.pxd +--- h5py-2.10.0.orig/h5py/api_types_ext.pxd 2019-09-06 23:29:33.000000000 +0200 ++++ h5py-2.10.0/h5py/api_types_ext.pxd 2020-05-25 19:30:30.000000000 +0200 +@@ -12,7 +12,7 @@ + include 'config.pxi' + + IF MPI: +- from mpi4py.MPI cimport MPI_Comm, MPI_Info, Comm, Info ++ from mpi4py.libmpi cimport MPI_Comm, MPI_Info + + cdef extern from "stdlib.h": + ctypedef long size_t +@@ -52,6 +52,7 @@ + cdef extern from "Python.h": + ctypedef void PyObject + ctypedef ssize_t Py_ssize_t ++ ctypedef size_t Py_uintptr_t + + PyObject* PyErr_Occurred() + void PyErr_SetString(object type, char *message) +diff -ru h5py-2.10.0.orig/h5py/h5p.pyx h5py-2.10.0/h5py/h5p.pyx +--- h5py-2.10.0.orig/h5py/h5p.pyx 2019-09-06 23:29:33.000000000 +0200 ++++ h5py-2.10.0/h5py/h5p.pyx 2020-05-25 19:33:24.000000000 +0200 +@@ -17,6 +17,7 @@ + from cpython.buffer cimport PyObject_CheckBuffer, \ + PyObject_GetBuffer, PyBuffer_Release, \ + PyBUF_SIMPLE ++from cpython.long cimport PyLong_AsVoidPtr + + from utils cimport require_tuple, convert_dims, convert_tuple, \ + emalloc, efree, \ +@@ -1161,7 +1162,7 @@ + + IF MPI: + @with_phil +- def set_fapl_mpio(self, Comm comm not None, Info info not None): ++ def set_fapl_mpio(self, comm, info): + """ (Comm comm, Info info) + + Set MPI-I/O Parallel HDF5 driver. +@@ -1169,7 +1170,12 @@ + Comm: An mpi4py.MPI.Comm instance + Info: An mpi4py.MPI.Info instance + """ +- H5Pset_fapl_mpio(self.id, comm.ob_mpi, info.ob_mpi) ++ from mpi4py.MPI import Comm, Info, _handleof ++ assert isinstance(comm, Comm) ++ assert isinstance(info, Info) ++ cdef Py_uintptr_t _comm = _handleof(comm) ++ cdef Py_uintptr_t _info = _handleof(info) ++ H5Pset_fapl_mpio(self.id, _comm, _info) + + + @with_phil +@@ -1183,20 +1189,22 @@ + """ + cdef MPI_Comm comm + cdef MPI_Info info ++ from mpi4py.MPI import Comm, Info, _addressof + + H5Pget_fapl_mpio(self.id, &comm, &info) + pycomm = Comm() +- pyinfo = Info() +- MPI_Comm_dup(comm, &pycomm.ob_mpi) +- MPI_Info_dup(info, &pyinfo.ob_mpi) ++ MPI_Comm_dup(comm, PyLong_AsVoidPtr(_addressof(pycomm))) + MPI_Comm_free(&comm) ++ ++ pyinfo = Info() ++ MPI_Info_dup(info, PyLong_AsVoidPtr(_addressof(pyinfo))) + MPI_Info_free(&info) + + return (pycomm, pyinfo) + + + @with_phil +- def set_fapl_mpiposix(self, Comm comm not None, bint use_gpfs_hints=0): ++ def set_fapl_mpiposix(self, comm, bint use_gpfs_hints=0): + """ Obsolete. + """ + raise RuntimeError("MPI-POSIX driver is broken; removed in h5py 2.3.1") From 08c44bc951b22dba8e0354c407d8e75593e18b8b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 10 Dec 2021 12:21:21 +0100 Subject: [PATCH 2254/9987] remove download_dep_fail --- easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb index e7103d4a5c0..229465a24ee 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -28,7 +28,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " From 69bc26539726bacf02d69e0b3e19c881cee1b375 Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 10 Dec 2021 11:29:37 +0000 Subject: [PATCH 2255/9987] adding easyconfigs: carma-2.01-foss-2019b.eb --- .../c/carma/carma-2.01-foss-2019b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb diff --git a/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb b/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb new file mode 100644 index 00000000000..40bf7dc47da --- /dev/null +++ b/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb @@ -0,0 +1,34 @@ +# # +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Helena Gomez , Erica Bianco, Danilo Gonzalez, Jordi Blasco +# License:: GPL-v3.0 +# # + +easyblock = 'Tarball' + +name = 'carma' +version = '2.01' + +homepage = 'http://utopia.duth.gr/~glykos/Carma.html' +description = """carma - A molecular dynamics analysis program""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['http://utopia.duth.gr/~glykos/progs/'] +sources = ['%(name)s.tar.gz'] +checksums = ['f32cfc2e348691f252d3593e281303d1202e31befba14565aba022331d50b9f3'] + +preinstall_cmd = 'cd %(builddir)s/%(name)s-%(version)s/src && ' +preinstall_cmd += '$CC $CFLAGS -O -c Color_carma.c && ' +preinstall_cmd += '$FC $FFLAGS $LIBBLAS -O Color_carma.o -o carma &&' +preinstall_cmd += 'cp -p carma ../bin/' + +sanity_check_paths = { + 'files': ['bin/carma'], + 'dirs': [''], +} + +tests = ['%(installdir)s/bin/carma'] + +moduleclass = 'lib' From 48d46621a2d2c5c98a5b0ff3118c865430c5a0da Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 10 Dec 2021 12:37:03 +0100 Subject: [PATCH 2256/9987] brotli-python wrapper --- .../Brotli-python-1.0.9-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..653ddf4fd49 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +# this is an EC only for python bindings to original Brotli +# cannot be in one easyconfig, see more: https://github.com/easybuilders/easybuild-easyconfigs/pull/14480 +name = 'Brotli-python' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/B/Brotli'] +sources = ['Brotli-1.0.9.zip'] +checksums = ['4d1b810aa0ed773f81dceda2cc7b403d01057458730e309856356d4ef4188438'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'brotli'} + +sanity_check_commands = ["brotli --help", "python -c 'import brotli'"] + +moduleclass = 'lib' From 5b346574f69dd3ef4e9d0237b1cb2b1727a006e3 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 10 Dec 2021 22:48:16 +1050 Subject: [PATCH 2257/9987] dep <- version update --- .../cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb index 02a39c41144..3729e354bab 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb @@ -22,11 +22,11 @@ checksums = ['cb44ae28639c0841b3a3c85228379053bf80ee82a8dd6c260aac69c4f0d18458'] dependencies = [ ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05', versionsuffix), - ('Biopython', '1.79', versionsuffix), - ('bx-python', '0.8.11', versionsuffix), - ('bcbio-gff', '0.6.7', versionsuffix), - ('scikit-learn', '0.24.2', versionsuffix), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('bx-python', '0.8.11'), + ('bcbio-gff', '0.6.7'), + ('scikit-learn', '0.24.2'), ('Pysam', '0.16.0.1'), ] From 9ee86b311c5b50154df36aec5b53e6131e332f62 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Dec 2021 11:46:23 +0100 Subject: [PATCH 2258/9987] add exception for Clang-AOMP easyblock (which derives from Bundle) in test_pr_sha256_checksums --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index bb0cdb9507a..e14ef74f072 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -856,7 +856,7 @@ def test_pr_sha256_checksums(self): # therefore, we need to reset 'sources' to an empty list here if Bundle is used... # likewise for 'patches' and 'checksums' for ec in self.changed_ecs: - if ec['easyblock'] in ['Bundle', 'PythonBundle', 'EB_OpenSSL_wrapper']: + if ec['easyblock'] in ['Bundle', 'PythonBundle', 'EB_OpenSSL_wrapper'] or ec['name'] in ['Clang-AOMP']: ec['sources'] = [] ec['patches'] = [] ec['checksums'] = [] From 930a0c7b5e82daae742a32c6ba5a8828d651a1be Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 10 Dec 2021 16:33:58 +0000 Subject: [PATCH 2259/9987] adding easyconfigs: RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb --- .../RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb new file mode 100644 index 00000000000..bcf227398b3 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021a-hybrid-avx2.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.12' +versionsuffix = '-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105'] + +buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +sanity_check_commands = ["raxmlHPC -%s" % x for x in ['h', 'v']] + +moduleclass = 'bio' From 784c71c5511687595e4543fdc60c75cdd971c16c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 10 Dec 2021 16:45:00 +0000 Subject: [PATCH 2260/9987] adding easyconfigs: ExaML-3.0.22-gompi-2021a-hybrid-avx.eb --- .../ExaML-3.0.22-gompi-2021a-hybrid-avx.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb diff --git a/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb new file mode 100644 index 00000000000..9e10f7d38d8 --- /dev/null +++ b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb @@ -0,0 +1,35 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'ExaML' +version = '3.0.22' +versionsuffix = '-hybrid-avx' + +homepage = 'https://github.com/stamatak/ExaML/' +description = "Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +github_account = 'stamatak' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['802e673b0c2ea83fdbe6b060048d83f22b6978933a04be64fb9b4334fe318ca3'] + +#prebuildopts = ['cd examl &&', 'cd parser &&'] +#buildopts = ['-f Makefile.OMP.AVX.gcc', '-f Makefile.SSE3.gcc'] +prebuildopts = 'cd examl &&' +buildopts = '-f Makefile.OMP.AVX.gcc && cd ../parser && make -f Makefile.SSE3.gcc' + +files_to_copy = [(['examl/examl-OMP-AVX', 'parser/parse-examl'], 'bin'), 'README.md', 'manual'] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s examl-OMP-AVX examl"] + +sanity_check_paths = { + 'files': ['bin/examl', 'bin/parse-examl'], + 'dirs': [], +} + +sanity_check_commands = ["examl -%s" % x for x in ['h', 'v']] + +moduleclass = 'bio' From 7d07e5a8b67a0f5fa116bdde78c99541f8638979 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 10 Dec 2021 16:48:42 +0000 Subject: [PATCH 2261/9987] adding easyconfigs: TreeMix-1.13-GCC-10.3.0.eb --- .../t/TreeMix/TreeMix-1.13-GCC-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-10.3.0.eb b/easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-10.3.0.eb new file mode 100644 index 00000000000..9baebc6d2dd --- /dev/null +++ b/easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'TreeMix' +version = '1.13' + +homepage = 'http://bitbucket.org/nygcresearch/treemix' +description = """TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a + set of populations.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://bitbucket.org/nygcresearch/treemix/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fe544f2daa13fd06b20c1a81aac728963ea5b66b75908916ca87ccd7f4cfa3d9'] + +dependencies = [ + ('GSL', '2.7'), + ('Boost', '1.76.0'), +] + +sanity_check_paths = { + 'files': ['bin/treemix'], + 'dirs': [], +} +sanity_check_commands = [("treemix -h | grep 'TreeMix v. %(version)s'", '')] + +moduleclass = 'bio' From 50bbb76db8d03b1b4f8ab9d0fc09d3b0508818d6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 10 Dec 2021 16:54:11 +0000 Subject: [PATCH 2262/9987] adding easyconfigs: mapDamage-2.2.1-foss-2021a-R-4.1.0.eb, inline-0.3.19-foss-2021a-R-4.1.0.eb, seqtk-1.3-GCC-10.3.0.eb, RcppGSL-0.3.10-foss-2021a-R-4.1.0.eb --- .../inline-0.3.19-foss-2021a-R-4.1.0.eb | 30 +++++++++++++++++ .../mapDamage-2.2.1-foss-2021a-R-4.1.0.eb | 33 +++++++++++++++++++ .../RcppGSL-0.3.10-foss-2021a-R-4.1.0.eb | 31 +++++++++++++++++ .../s/seqtk/seqtk-1.3-GCC-10.3.0.eb | 31 +++++++++++++++++ 4 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2021a-R-4.1.0.eb create mode 100644 easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb create mode 100644 easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.10-foss-2021a-R-4.1.0.eb create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..f2d5c881fa6 --- /dev/null +++ b/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2021a-R-4.1.0.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'inline' +version = '0.3.19' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/inline' +description = """Functionality to dynamically define R functions and S4 methods + with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling + conventions.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'] + +dependencies = [ + ('R', '4.1.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['inline'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..65ad4dcca7a --- /dev/null +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'mapDamage' +version = '2.2.1' +versionsuffix = '-R-%(rver)s' + +github_account = 'ginolhac' + +homepage = 'https://ginolhac.github.io/mapDamage/' +description = """mapDamage2 is a computational framework written in Python and + R, which tracks and quantifies DNA damage patterns among ancient DNA + sequencing reads generated by Next-Generation Sequencing platforms.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c'] + +dependencies = [ + ('Python', '3.9.5'), + ('seqtk', '1.3'), + ('Pysam', '0.16.0.1'), + ('R', '4.1.0'), + ('inline', '0.3.19', versionsuffix), + ('RcppGSL', '0.3.10', versionsuffix), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.10-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.10-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..931c28625ab --- /dev/null +++ b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.10-foss-2021a-R-4.1.0.eb @@ -0,0 +1,31 @@ +easyblock = 'RPackage' + +name = 'RcppGSL' +version = '0.3.10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/RcppGSL' +description = """The 'RcppGSL' package provides an easy-to-use interface + between 'GSL' data structures and R using concepts from 'Rcpp' which is itself + a package that eases the interfaces between R and C++.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['8612087da02fb791f427fed310c23d0482a8eb60fb089119f018878143f95451'] + +dependencies = [ + ('R', '4.1.0'), + ('GSL', '2.7'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['RcppGSL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.3.0.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..847bb921d75 --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'seqtk' +version = '1.3' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563'] + +dependencies = [('zlib', '1.2.11')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BINDIR=%(installdir)s/bin/' + +sanity_check_paths = { + 'files': ['bin/seqtk'], + 'dirs': [], +} + +moduleclass = 'bio' From d55cf475fdefb8dfc83408e8f028e9f1f8f0b290 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 10 Dec 2021 16:58:54 +0000 Subject: [PATCH 2263/9987] Remove commented buildopts --- .../easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb index 9e10f7d38d8..7840f1a156e 100644 --- a/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb +++ b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb @@ -16,8 +16,6 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['802e673b0c2ea83fdbe6b060048d83f22b6978933a04be64fb9b4334fe318ca3'] -#prebuildopts = ['cd examl &&', 'cd parser &&'] -#buildopts = ['-f Makefile.OMP.AVX.gcc', '-f Makefile.SSE3.gcc'] prebuildopts = 'cd examl &&' buildopts = '-f Makefile.OMP.AVX.gcc && cd ../parser && make -f Makefile.SSE3.gcc' From 1464befe3ea26cb244a504d3732fca008b965c98 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 10 Dec 2021 20:01:21 +0100 Subject: [PATCH 2264/9987] adding easyconfigs: Eigen-3.4.0-GCCcore-10.2.0.eb --- .../e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..97fabdb318b --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.4.0' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.35'), # to make CMake compiler health check pass on old systems + ('CMake', '3.18.4'), +] + +moduleclass = 'math' From e84beb4236181bc472decb4444912e8b61e10f0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Dec 2021 10:25:09 +0100 Subject: [PATCH 2265/9987] add missing Perl build dependency for Longshot --- easybuild/easyconfigs/l/Longshot/Longshot-0.3.4-GCCcore-8.2.0.eb | 1 + .../easyconfigs/l/Longshot/Longshot-0.4.1-GCC-7.3.0-2.30.eb | 1 + easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCCcore-8.3.0.eb | 1 + .../easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.3.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.3.4-GCCcore-8.2.0.eb index b5ea1faf138..4b1c75deb8e 100644 --- a/easybuild/easyconfigs/l/Longshot/Longshot-0.3.4-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.3.4-GCCcore-8.2.0.eb @@ -22,6 +22,7 @@ builddependencies = [ ('Clang', '8.0.0'), ('zlib', '1.2.11'), ('XZ', '5.2.4'), + ('Perl', '5.28.1'), ] extract_sources = True diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCC-7.3.0-2.30.eb index 48e2eb9f6a2..918af760f21 100644 --- a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCC-7.3.0-2.30.eb @@ -22,6 +22,7 @@ builddependencies = [ ('Clang', '7.0.1'), ('zlib', '1.2.11'), ('XZ', '5.2.4'), + ('Perl', '5.28.0'), ] extract_sources = True diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCCcore-8.3.0.eb index 2b4d5e3f087..2bff3e30e44 100644 --- a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCCcore-8.3.0.eb @@ -22,6 +22,7 @@ builddependencies = [ ('Clang', '9.0.1'), ('zlib', '1.2.11'), ('XZ', '5.2.4'), + ('Perl', '5.30.0'), ] extract_sources = True diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb index 07d70a35c94..f3c93e26ad7 100644 --- a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.3-GCCcore-10.2.0.eb @@ -25,6 +25,7 @@ builddependencies = [ ('Clang', '11.0.1'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('Perl', '5.32.0'), ] extract_sources = True From 44f5ea013046c1081307beb0e679d546dd692ab8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Dec 2021 10:35:08 +0100 Subject: [PATCH 2266/9987] add googletest build dependency for Highway --- .../easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb | 3 +++ .../easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.3.0.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb index 5111d10fd43..0f1af103e84 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.2.0.eb @@ -19,8 +19,11 @@ checksums = ['e1d47ce510429fdcf31f41697ca74fb0dcd59d933196e531a86d51751a56f4cc'] builddependencies = [ ('binutils', '2.35'), ('CMake', '3.18.4'), + ('googletest', '1.10.0'), ] +configopts = "-DHWY_SYSTEM_GTEST=ON" + runtest = "test" sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.3.0.eb index fc9bed83d0f..75bb63a652c 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-10.3.0.eb @@ -17,8 +17,11 @@ checksums = ['e1d47ce510429fdcf31f41697ca74fb0dcd59d933196e531a86d51751a56f4cc'] builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), + ('googletest', '1.11.0'), ] +configopts = "-DHWY_SYSTEM_GTEST=ON" + runtest = "test" sanity_check_paths = { From a03eff66d22f01bc12b4c50e98a38ccf830e3236 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Dec 2021 10:42:55 +0100 Subject: [PATCH 2267/9987] remove CMake build dependency and duplicate sanity check commands for Brotli-python + fix moduleclass to 'bio' --- .../Brotli-python/Brotli-python-1.0.9-GCCcore-10.3.0.eb | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.3.0.eb index 653ddf4fd49..74275267d05 100644 --- a/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.3.0.eb @@ -1,7 +1,5 @@ easyblock = 'PythonPackage' -# this is an EC only for python bindings to original Brotli -# cannot be in one easyconfig, see more: https://github.com/easybuilders/easybuild-easyconfigs/pull/14480 name = 'Brotli-python' version = '1.0.9' @@ -15,12 +13,11 @@ The specification of the Brotli Compressed Data Format is defined in RFC 7932."" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://pypi.python.org/packages/source/B/Brotli'] -sources = ['Brotli-1.0.9.zip'] +sources = ['Brotli-%(version)s.zip'] checksums = ['4d1b810aa0ed773f81dceda2cc7b403d01057458730e309856356d4ef4188438'] builddependencies = [ ('binutils', '2.36.1'), - ('CMake', '3.20.1'), ] dependencies = [ @@ -34,6 +31,4 @@ sanity_pip_check = True options = {'modulename': 'brotli'} -sanity_check_commands = ["brotli --help", "python -c 'import brotli'"] - -moduleclass = 'lib' +moduleclass = 'bio' From 8546b60b7572fff3d6e3a78545e3b2ba2817076d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Dec 2021 14:36:21 +0100 Subject: [PATCH 2268/9987] minor style tweaks in CMSeq easyconfig --- .../c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb index ad9f91a1025..9e64d8a24f9 100644 --- a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.3-foss-2020a-Python-3.8.2.eb @@ -9,10 +9,7 @@ version = '1.0.3' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/SegataLab/cmseq/' - -description = """ -CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus. -""" +description = "CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus." toolchain = {'name': 'foss', 'version': '2020a'} @@ -33,14 +30,9 @@ download_dep_fail = True use_pip = True sanity_pip_check = True -local_bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' -local_targets = ['breadth_depth.py', 'polymut.py', 'poly.py', 'consensus.py'] - sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_targets], - 'dirs': [local_bcbiogffroot], + 'files': ['bin/%s' % x for x in ['breadth_depth.py', 'consensus.py', 'poly.py', 'polymut.py']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -options = {'modulename': 'cmseq'} - moduleclass = 'bio' From b47ac3a18a70d7c8495094c097a21636fa615b6e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Dec 2021 14:52:11 +0100 Subject: [PATCH 2269/9987] fix easyconfig for Grace 5.1.25 with foss/2021a + sync homepage/source_urls across Grace easyconfigs --- .../g/Grace/Grace-5.1.25-foss-2016a.eb | 5 +++-- .../Grace/Grace-5.1.25-foss-2017b-5build1.eb | 5 ++--- .../Grace/Grace-5.1.25-foss-2018a-5build1.eb | 5 ++--- .../Grace/Grace-5.1.25-foss-2019a-5build1.eb | 5 ++--- .../Grace/Grace-5.1.25-foss-2019b-5build1.eb | 3 +-- .../g/Grace/Grace-5.1.25-foss-2021a.eb | 22 +++++++++++-------- .../g/Grace/Grace-5.1.25-intel-2016a.eb | 5 +++-- .../Grace/Grace-5.1.25-intel-2017b-5build1.eb | 4 ++-- .../Grace/Grace-5.1.25-intel-2019a-5build1.eb | 2 +- 9 files changed, 29 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb index fc5cf03bb15..0a1fe5c9103 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb @@ -3,11 +3,12 @@ easyblock = 'ConfigureMake' name = 'Grace' version = '5.1.25' -homepage = 'http://freecode.com/projects/grace' +homepage = 'https://plasma-gate.weizmann.ac.il/Grace/' description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" -source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] sources = [SOURCE_TAR_GZ] +checksums = ['751ab9917ed0f6232073c193aba74046037e185d73b77bab0f5af3e3ff1da2ac'] toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb index 0879fd8c8d5..2fcc7792509 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2017b-5build1.eb @@ -4,12 +4,12 @@ name = 'Grace' version = '5.1.25' versionsuffix = '-5build1' -homepage = 'http://plasma-gate.weizmann.ac.il/Grace/' +homepage = 'https://plasma-gate.weizmann.ac.il/Grace/' description = """Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/'] +source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s%(versionsuffix)s.patch'] checksums = [ @@ -23,7 +23,6 @@ dependencies = [ ('libpng', '1.6.32'), ('zlib', '1.2.11'), ('libjpeg-turbo', '1.5.2'), - ('FFTW', '3.3.6'), ('netCDF', '4.5.0'), ] diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2018a-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2018a-5build1.eb index 7f69fb3a8e8..416f3a359de 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2018a-5build1.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2018a-5build1.eb @@ -4,12 +4,12 @@ name = 'Grace' version = '5.1.25' versionsuffix = '-5build1' -homepage = 'http://plasma-gate.weizmann.ac.il/Grace/' +homepage = 'https://plasma-gate.weizmann.ac.il/Grace/' description = """Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.""" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/'] +source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s%(versionsuffix)s.patch'] checksums = [ @@ -23,7 +23,6 @@ dependencies = [ ('libpng', '1.6.34'), ('zlib', '1.2.11'), ('libjpeg-turbo', '1.5.3'), - ('FFTW', '3.3.7'), ('netCDF', '4.6.0'), ] diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2019a-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2019a-5build1.eb index 3dffd5e015c..da9cb277c78 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2019a-5build1.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2019a-5build1.eb @@ -4,12 +4,12 @@ name = 'Grace' version = '5.1.25' versionsuffix = '-5build1' -homepage = 'http://plasma-gate.weizmann.ac.il/Grace/' +homepage = 'https://plasma-gate.weizmann.ac.il/Grace/' description = """Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.""" toolchain = {'name': 'foss', 'version': '2019a'} -source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/'] +source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s%(versionsuffix)s.patch'] checksums = [ @@ -23,7 +23,6 @@ dependencies = [ ('libpng', '1.6.36'), ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.2'), - ('FFTW', '3.3.8'), ('netCDF', '4.6.2'), ] diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2019b-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2019b-5build1.eb index 5e74c6f85e8..c13e85e1612 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2019b-5build1.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2019b-5build1.eb @@ -9,7 +9,7 @@ description = """Grace is a WYSIWYG tool to make two-dimensional plots of numeri toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/'] +source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s%(versionsuffix)s.patch'] checksums = [ @@ -20,7 +20,6 @@ checksums = [ dependencies = [ ('motif', '2.3.8'), ('zlib', '1.2.11'), - ('FFTW', '3.3.8'), ('netCDF', '4.7.1'), ] diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021a.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021a.eb index c21345207dc..2b67331ed94 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021a.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021a.eb @@ -3,28 +3,32 @@ easyblock = 'ConfigureMake' name = 'Grace' version = '5.1.25' -homepage = 'http://freecode.com/projects/grace' -description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" +homepage = 'https://plasma-gate.weizmann.ac.il/Grace/' +description = """Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] checksums = ['751ab9917ed0f6232073c193aba74046037e185d73b77bab0f5af3e3ff1da2ac'] -toolchain = {'name': 'foss', 'version': '2021a'} - dependencies = [ ('motif', '2.3.8'), + ('zlib', '1.2.11'), ('netCDF', '4.8.0'), ] runtest = 'tests' -# we also need to run make links right before or after make install. -installopts = 'links' +postinstallcmds = ['mv %(installdir)s/grace/* %(installdir)s && rmdir %(installdir)s/grace'] sanity_check_paths = { - 'files': ['bin/xmgrace'], - 'dirs': [], + 'files': ['lib/libgrace_np.a', 'bin/convcal', 'bin/fdf2fit', 'bin/grconvert', 'bin/xmgrace'], + 'dirs': ['include', 'fonts', 'templates'], +} + +modextravars = { + 'GRACE_HOME': '%(installdir)s', } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb index 719293e139f..0eba96c5a88 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb @@ -3,11 +3,12 @@ easyblock = 'ConfigureMake' name = 'Grace' version = '5.1.25' -homepage = 'http://freecode.com/projects/grace' +homepage = 'https://plasma-gate.weizmann.ac.il/Grace/' description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" -source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] sources = [SOURCE_TAR_GZ] +checksums = ['751ab9917ed0f6232073c193aba74046037e185d73b77bab0f5af3e3ff1da2ac'] toolchain = {'name': 'intel', 'version': '2016a'} diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb index a224be48e35..92baaa17a8e 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2017b-5build1.eb @@ -4,12 +4,12 @@ name = 'Grace' version = '5.1.25' versionsuffix = '-5build1' -homepage = 'http://plasma-gate.weizmann.ac.il/Grace/' +homepage = 'https://plasma-gate.weizmann.ac.il/Grace/' description = """Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.""" toolchain = {'name': 'intel', 'version': '2017b'} -source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/grace5/'] +source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s%(versionsuffix)s.patch'] checksums = [ diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2019a-5build1.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2019a-5build1.eb index f049d7217d0..b8958fd758d 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2019a-5build1.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2019a-5build1.eb @@ -4,7 +4,7 @@ name = 'Grace' version = '5.1.25' versionsuffix = '-5build1' -homepage = 'http://plasma-gate.weizmann.ac.il/Grace/' +homepage = 'https://plasma-gate.weizmann.ac.il/Grace/' description = """Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.""" toolchain = {'name': 'intel', 'version': '2019a'} From 00011c232cb30d722f1ea0f3bb70c0313f9faceb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Dec 2021 16:14:44 +0100 Subject: [PATCH 2270/9987] use lowercase source filename in Grace easyconfigs with 2016a toolchain --- easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb index 0a1fe5c9103..481b7333b3b 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2016a.eb @@ -7,7 +7,7 @@ homepage = 'https://plasma-gate.weizmann.ac.il/Grace/' description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] checksums = ['751ab9917ed0f6232073c193aba74046037e185d73b77bab0f5af3e3ff1da2ac'] toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb index 0eba96c5a88..7389a01eb0d 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-intel-2016a.eb @@ -7,7 +7,7 @@ homepage = 'https://plasma-gate.weizmann.ac.il/Grace/' description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] checksums = ['751ab9917ed0f6232073c193aba74046037e185d73b77bab0f5af3e3ff1da2ac'] toolchain = {'name': 'intel', 'version': '2016a'} From 9f384fd137e62830fa89f19bdc184e6423afa9b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Dec 2021 20:42:56 +0100 Subject: [PATCH 2271/9987] seed in PCRE2 sources to fix broken MariaDB 10.5.8 + 10.6.4 easyconfigs --- .../m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb | 16 +++++++++++++--- .../m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb | 16 +++++++++++++--- 2 files changed, 26 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb index 83ee345b1d9..db3b9cf4a49 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb @@ -9,11 +9,19 @@ Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] -sources = [SOURCELOWER_TAR_GZ] +local_pcre2_ver = '10.34' +source_urls = [ + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', + 'https://downloads.sourceforge.net/project/pcre/pcre2/%s/' % local_pcre2_ver, +] +sources = [ + SOURCELOWER_TAR_GZ, + {'filename': 'pcre2-%s.zip' % local_pcre2_ver, 'extract_cmd': "cp %s %(builddir)s/"}, +] patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] checksums = [ 'eb4824f6f2c532cd3fc6a6bce7bf78ea7c6b949f8bdd07656b2c84344e757be8', # mariadb-10.5.8.tar.gz + '75a19013a10ab543fe923bbc9b7c2750559d2cca3b4c3611ab91392e5f62041c', # pcre2-10.34.zip '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19', # MariaDB-10.1.13-link-rt-for-jemalloc.patch ] @@ -35,7 +43,9 @@ dependencies = [ ('Judy', '1.0.5'), # needed by OQGraph ] -separate_build_dir = True +# replace download URL for PCRE2 with path to pre-downloaded PRCE2 source file +local_pcre2_path = '%%(builddir)s/pcre2-%s.zip' % local_pcre2_ver +preconfigopts = "sed -i 's@http://.*.zip@file://%s@g' ../mariadb-%%(version)s/cmake/pcre.cmake && " % local_pcre2_path configopts = "-DCMAKE_BUILD_TYPE=Release " configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb index 227928190fd..6473e5c7709 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb @@ -9,11 +9,19 @@ Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" toolchain = {'name': 'GCC', 'version': '10.3.0'} -source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] -sources = [SOURCELOWER_TAR_GZ] +local_pcre2_ver = '10.37' +source_urls = [ + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', + 'https://downloads.sourceforge.net/project/pcre/pcre2/%s/' % local_pcre2_ver, +] +sources = [ + SOURCELOWER_TAR_GZ, + {'filename': 'pcre2-%s.zip' % local_pcre2_ver, 'extract_cmd': "cp %s %(builddir)s/"}, +] patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] checksums = [ '75bf9b147a95d38160d01a73b098d50a1960563b46d16a235971fff64d99643c', # mariadb-10.6.4.tar.gz + '7a1dc9322cfbf4d00dd1adaa69f6ac7b91033170a0bcfc6615880803c8440257', # pcre2-10.37.zip '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19', # MariaDB-10.1.13-link-rt-for-jemalloc.patch ] @@ -35,7 +43,9 @@ dependencies = [ ('Judy', '1.0.5'), # needed by OQGraph ] -separate_build_dir = True +# replace download URL for PCRE2 with path to pre-downloaded PRCE2 source file +local_pcre2_path = '%%(builddir)s/pcre2-%s.zip' % local_pcre2_ver +preconfigopts = "sed -i 's@http://.*.zip@file://%s@g' ../mariadb-%%(version)s/cmake/pcre.cmake && " % local_pcre2_path configopts = "-DCMAKE_BUILD_TYPE=Release " configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker From e7543fc2f60fd2b5fd09a95c6ce826d7658924a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Dec 2021 10:50:06 +0100 Subject: [PATCH 2272/9987] fix HIP_CLANG_PATH in modluafooter + clean up modextravars in HIP easyconfig, and also add modtclfooter equivalent to modluafooter --- .../h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb index 79a752ac580..9b49b67088e 100644 --- a/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb +++ b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb @@ -91,23 +91,26 @@ sanity_check_commands = [ ] modextravars = { - 'DEVICE_LIB_PATH': '$EBROOTCLANGMINAOMP/amdgcn/bitcode', - 'HIP_CLANG_INCLUDE_PATH': '$EBROOTCLANGMINAOMP/include', - 'HIP_CLANG_PATH': '$EBROOTCLANGMINAOMP/bin', 'HIP_COMPILER': 'clang', 'HIP_INCLUDE_PATH': '%(installdir)s/include', 'HIP_LIB_PATH': '%(installdir)s/lib', 'HIP_PATH': '%(installdir)s', 'HIP_RUNTIME': 'rocclr', - 'HSA_PATH': '$EBROOTROCRMINRUNTIME', 'ROCM_PATH': '%(installdir)s', } modluafooter = """ setenv("DEVICE_LIB_PATH", os.getenv("EBROOTCLANGMINAOMP") .. "/amdgcn/bitcode") setenv("HIP_CLANG_INCLUDE_PATH", os.getenv("EBROOTCLANGMINAOMP") .. "/include") -setenv("CLANG_PATH", os.getenv("EBROOTCLANGMINAOMP") .. "/bin") +setenv("HIP_CLANG_PATH", os.getenv("EBROOTCLANGMINAOMP") .. "/bin") setenv("HSA_PATH", os.getenv("EBROOTROCRMINRUNTIME")) """ +modtclfooter = """ +setenv DEVICE_LIB_PATH $::env(EBROOTCLANGMINAOMP)/amdgcn/bitcode +setenv HIP_CLANG_INCLUDE_PATH $::env(EBROOTCLANGMINAOMP)/include +setenv HIP_CLANG_PATH $::env(EBROOTCLANGMINAOMP)/bin +setenv HSA_PATH $::env(EBROOTROCRMINRUNTIME) +""" + moduleclass = 'tools' From 38fa5c11f47b45a2b2c9fbdfc9c3430281ce92ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Dec 2021 10:53:17 +0100 Subject: [PATCH 2273/9987] add description + author to patch for HIP --- easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb | 2 +- .../easyconfigs/h/HIP/hipamd-rocm-4.5.0-remove-testing.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb index 9b49b67088e..1c2c5c78f5b 100644 --- a/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb +++ b/easybuild/easyconfigs/h/HIP/HIP-4.5.0-GCCcore-11.2.0-amd.eb @@ -42,7 +42,7 @@ checksums = [ 'ca8d6305ff0e620d9cb69ff7ac3898917db9e9b6996a7320244b48ab6511dd8e', # ROCclr-rocm-4.5.0.tar.gz '4026f31fb4f8050e9aa9d4294f29c3410bfb38422dbbae4236ccd65fed4d55b2', # HIP-rocm-4.5.0.tar.gz '3a163aed24619b3faf5e8ba17325bdcedd1667a904ea20914ac6bdd33fcdbca8', # ROCm-OpenCL-Runtime-rocm-4.5.0.tar.gz - 'b70636c7853c74d1fca3c71b73d48ff3a2c66d09382b2378900ee47f25ed2ae1', # hipamd-4.5.0-remove-testing.patch + 'bd7651bdb4c38622c7a3ea4fd1be91118917bdf1e1125686c7fc2ecd0ea9db14', # hipamd-4.5.0-remove-testing.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/h/HIP/hipamd-rocm-4.5.0-remove-testing.patch b/easybuild/easyconfigs/h/HIP/hipamd-rocm-4.5.0-remove-testing.patch index 9de1c55384e..5aa1e1f214a 100644 --- a/easybuild/easyconfigs/h/HIP/hipamd-rocm-4.5.0-remove-testing.patch +++ b/easybuild/easyconfigs/h/HIP/hipamd-rocm-4.5.0-remove-testing.patch @@ -1,3 +1,5 @@ +# skip testing steps +# Author: Jørgen Nordmoen (University of Oslo) --- hipamd-rocm-4.5.0/CMakeLists.txt.orig 2021-11-12 14:26:59.514400918 +0100 +++ hipamd-rocm-4.5.0/CMakeLists.txt 2021-11-12 14:27:23.551183553 +0100 @@ -487,31 +487,6 @@ From e422d0874b6b687ed241ccb4cab018f4e1ead1af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Dec 2021 11:31:18 +0100 Subject: [PATCH 2274/9987] add ROCm to bundles whitelist in test_pr_sanity_check_paths --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index e14ef74f072..b7276e4cae9 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1017,7 +1017,7 @@ def test_pr_sanity_check_paths(self): # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co - bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle'] + bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm'] failing_checks = [] From 9bee07089f6fca8b5a0b29a22f3a50794a033d81 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Dec 2021 19:27:48 +0100 Subject: [PATCH 2275/9987] add empty line after 'easyblock' in ROCm easyconfig --- easybuild/easyconfigs/r/ROCm/ROCm-4.5.0-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/ROCm/ROCm-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/ROCm/ROCm-4.5.0-GCCcore-11.2.0.eb index b02e9e5126c..1a80c86bff6 100644 --- a/easybuild/easyconfigs/r/ROCm/ROCm-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/ROCm/ROCm-4.5.0-GCCcore-11.2.0.eb @@ -1,4 +1,5 @@ easyblock = 'Bundle' + name = 'ROCm' version = '4.5.0' From 33370004c0a5b074d158df88e066264e3b27733e Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Mon, 13 Dec 2021 08:31:11 +1050 Subject: [PATCH 2276/9987] style <- fix redundancy --- .../cDNA_Cupcake-26.0.0-foss-2021a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb new file mode 100644 index 00000000000..9d5bdc5521b --- /dev/null +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -0,0 +1,49 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v24.2.0 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'cDNA_Cupcake' +version = '26.0.0' + +homepage = 'https://github.com/Magdoll/cDNA_Cupcake' +description = """cDNA_Cupcake is a miscellaneous collection of Python and +R scripts used for analyzing sequencing data. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/Magdoll/cDNA_Cupcake/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb44ae28639c0841b3a3c85228379053bf80ee82a8dd6c260aac69c4f0d18458'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('bx-python', '0.8.11'), + ('bcbio-gff', '0.6.7'), + ('scikit-learn', '0.24.2'), + ('Pysam', '0.16.0.1'), +] + +download_dep_fail = False +use_pip = True + +sanity_pip_check = True +sanity_check_paths = { + # check for particular Cupcake ToFU scripts, + # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step + 'files': [ + 'bin/collapse_isoforms_by_sam.py', + 'bin/get_abundance_post_collapse.py', + 'bin/simple_stats_post_collapse.py' + ], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'cupcake'} + +moduleclass = 'bio' From 6d43cd5aacb70b12d0fd258acbca2f37d50c32b9 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Mon, 13 Dec 2021 08:32:39 +1030 Subject: [PATCH 2277/9987] Delete cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb --- ..._Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb | 50 ------------------- 1 file changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb deleted file mode 100644 index 3729e354bab..00000000000 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,50 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# Updated to v24.2.0 -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'cDNA_Cupcake' -version = '26.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Magdoll/cDNA_Cupcake' -description = """cDNA_Cupcake is a miscellaneous collection of Python and -R scripts used for analyzing sequencing data. -""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -source_urls = ['https://github.com/Magdoll/cDNA_Cupcake/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['cb44ae28639c0841b3a3c85228379053bf80ee82a8dd6c260aac69c4f0d18458'] - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('Biopython', '1.79'), - ('bx-python', '0.8.11'), - ('bcbio-gff', '0.6.7'), - ('scikit-learn', '0.24.2'), - ('Pysam', '0.16.0.1'), -] - -download_dep_fail = False -use_pip = True - -sanity_pip_check = True -sanity_check_paths = { - # check for particular Cupcake ToFU scripts, - # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step - 'files': [ - 'bin/collapse_isoforms_by_sam.py', - 'bin/get_abundance_post_collapse.py', - 'bin/simple_stats_post_collapse.py' - ], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -options = {'modulename': 'cupcake'} - -moduleclass = 'bio' From 21f82017b58ebfe9db583e5179b83bb36c4ae350 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Mon, 13 Dec 2021 08:51:39 +1030 Subject: [PATCH 2278/9987] header <- update --- .../c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb index 9d5bdc5521b..7b6c317aa6a 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -1,6 +1,6 @@ # Contribution by # DeepThought, Flinders University -# Updated to v24.2.0 +# Updated to v26.0.0 # R.QIAO easyblock = 'PythonPackage' From b03e81494102ba9d7595f0ef7dd9279374989747 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Dec 2021 11:20:54 +0800 Subject: [PATCH 2279/9987] prepare release notes for EasyBuild v4.5.1 + bump version to 4.5.1 --- RELEASE_NOTES | 64 ++++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 64 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 018cde54f6e..c5b221d62c9 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,72 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 13,514 easyconfig files, for 2,506 different software packages, +The latest version of easybuild-easyconfig provides 13,812 easyconfig files, for 2,575 different software packages, incl. 36 different (compiler) toolchains. +v4.5.1 (December 13th 2021) +--------------------------- + +update/bugfix release + +- added example easyconfig files for 71 new software packages: + - ANIcalculator (#14510), arrow-R (#14267), ASAP (#14367), BabelStream (#14503), bamtofastq (#14391), bcbio-gff (#14322), + biom-format (#13205), Blosc2 (#14247), boto3 (#14452), Brotli-python (#14528), Brunsli (#14247), Clang-AOMP (#14327), + CLEASE (#14413), CMSeq (#14326), cpu_features (#14385), cromwell (#12125), cxxopts (#14504), dRep (#14479), DUBStepR (#14495), + eht-imaging (#14239), einops (#14373), ELFIO (#14504), elprep (#14422), epiScanpy (#14447), FMM3D (#14257), FORD (#13653), + GPy (#14380), HIP (#14339), idemux (#14499), imagecodecs (#14247), InChI (#13902), jupyter-matlab-proxy (#14270), jxrlib (#14247), + LBFGS++ (#14230), LERC (#14247), libaec (#14247), libavif (#14246), LibLZF (#14246), libnsl (#14494), libtree (#14501), + LPeg (#14157), Megalodon (#14256), nnU-Net (#14249), PAL2NAL (#14430), photontorch (#14410), pkgconf (#14426), pmx (#14319), + PPanGGOLiN (#14449), ProFit (#14340), pugixml (#14492), PySide2 (#13460), Relate (#14443), ROCm (#14355), rocm-cmake (#14327), + ROCm-CompilerSupport (#14327), rocminfo (#14327), rocm-smi (#14354), ROCR-Runtime (#14327), ROCT-Thunk-Interface (#14327), + SCENIC (#14260), Shasta (#14385), SimNIBS (#14257), SMV (#14157), SRST2 (#14253), STACEY (#14293), termcolor (#14504), + ThemisPy (#14231), TOBIAS (#14458), zfp (#14246), zlib-ng (#14246), Zopfli (#14246) +- added additional easyconfigs for various supported software packages, including: + - ABINIT 9.4.2, ABINIT 9.6.2, ABINIT 9.6.2, ABRicate 1.0.0, abTEM 1.0.0b26, abTEM 1.0.0b26, adjustText 0.7.3, Advisor 2021.4.0.eb, AlphaFold 2.1.1, ANIcalculator 1.0, antiSMASH 6.0.1, ANTLR 2.7.7, any2fasta 0.4.2, AOCC 3.1.0, ARAGORN 1.2.41, Arrow 6.0.0, Arrow 6.0.0, arrow R, arrow R, arrow R, ASAP 2.0, ASE 3.22.0, astropy 4.3.1, astropy 4.3.1, BabelStream 3.4, bamtofastq 1.4.0, BamTools 2.5.2, bcbio gff, bcbio gff, BCFtools 1.14, BeautifulSoup 4.9.3, BEDTools 2.30.0, BerkeleyGW 3.0.1, biom format, Biopython 1.79, Bio SearchIO, Blosc 1.21.1, Blosc2 2.0.3, Boost 1.77.0, Boost 1.77.0, boto3 1.20.13, bpp 4.4.0, Bracken 2.6.2, Brotli python, Brunsli 0.1, BWA 0.7.17, CapnProto 0.8.0, CapnProto 0.9.1, CapnProto 0.9.1, CellRanger 6.0.2.eb, CellRanger 6.1.2.eb, CFITSIO 3.49, CheckM 1.1.3, Clang AOMP, CLEASE 0.10.6, CMSeq 1.0.3, Coreutils 9.0, CP2K 5.1, cppy 1.1.0, cpu_features 0.6.0, cromwell 56, CUDA 11.5.0.eb, CVS 1.11.23, cxxopts 3.0.0.eb, DendroPy 4.5.2, dicom2nifti 2.3.0, dRep 3.0.0, DUBStepR 1.2.0, EasyBuild 4.5.0.eb, edlib 1.3.9, eht imaging, Eigen 3.4.0, einops 0.3.2, ELFIO 3.9.eb, elprep 5.1.1.eb, enaBrowserTool 1.6, epiScanpy 0.3.1, ESMF 8.2.0, ESMF 8.2.0, fastahack 1.0.0, FastANI 1.33, filevercmp 20191210, Flye 2.9, Flye 2.9, FMM3D 20211018, FMRIprep 1.4.1, FORD 6.1.1, freeglut 3.2.1, FSL 6.0.4, fsom 20141119, g2clib 1.6.3, GATK 4.2.3.0, gawk 5.1.1, gc 8.2.0, GDB 11.1, git 2.33.1, GitPython 3.1.24, GL2PS 1.4.2, GlimmerHMM 3.0.4c, GLM 0.9.9.8, gmpy2 2.1.0rc1, Go 1.17.3.eb, GPy 1.10.0, Grace 5.1.25, Grace 5.1.25, Grace 5.1.25, GraphicsMagick 1.3.36, GROMACS 2021.3, GSL 2.7, GTDB Tk, GTS 0.7.6, Gurobi 9.0.1, Gurobi 9.5.0, Gurobi 9.5.0, HDBSCAN 0.8.24, HDF5 1.12.1, Highway 0.12.2, HIP 4.5.0, HMMER2 2.3.2, Horovod 0.23.0, HTSlib 1.14, HyPhy 2.5.33, idemux 0.1.6, imagecodecs 2021.8.26, imageio 2.9.0, InChI 1.06, Infernal 1.1.4, Inspector 2021.4.0.eb, intervaltree 0.1, ITK 5.2.1, jax 0.2.24, jax 0.2.24, Judy 1.0.5, Julia 1.6.4, Julia 1.7.0, jupyter matlab, jxrlib 1.1, Kent_tools 422, king 2.2.7.eb, LBFGS++ 0.1.0.eb, LERC 3.0, libaec 1.0.6, libaio 0.3.112, libavif 0.9.0, libcerf 1.17, libdap 3.20.8, libdwarf 20210528, libelf 0.8.13, Libint 1.1.6, libjxl 0.6.1, LibLZF 3.4, libnsl 1.3.0, libtree 2.0.0, libxc 3.0.1, libxc 5.1.6, likwid 5.2.0, LPeg 1.0.2, Lua 5.3.5, Lua 5.4.3, MAFFT 7.490, MAFFT 7.490, MAFFT 7.490, makeinfo 6.8, MariaDB 10.6.4, Mash 2.2, Mash 2.3, matplotlib 3.4.3, matplotlib 3.4.3, MCR R2021b.eb, MedPy 0.4.0, Megalodon 2.3.5, Megalodon 2.3.5, METIS 5.1.0, minimap2 2.22, MMseqs2 13, MMseqs2 13, motif 2.3.8, multichoose 1.0.3, MUMmer 3.23, muparserx 4.0.8, MUST 1.7.2, NCO 5.0.3, NCO 5.0.3, netCDF 4.8.1, netCDF C++4, netCDF C++4, netCDF Fortran, netCDF Fortran, networkx 2.6.3, NFFT 3.5.2, nlohmann_json 3.10.4, nnU Net, NVHPC 21.9.eb, OpenFOAM 8, OpenMPI 4.0.7, OpenMPI 4.1.2, OpenSlide 3.4.1, PAL2NAL 14, PAL2NAL 14, PAML 4.9j, PAML 4.9j, panaroo 1.2.9, pangolin 3.1.16, pangolin 3.1.16, PAPI 6.0.0.1, parasail 2.4.2, photontorch 0.4.1, photontorch 0.4.1, Pillow 6.2.2, pkgconf 1.8.0, pkgconfig 1.5.5, plotly.py 5.4.0, pmx 2.0, PPanGGOLiN 1.1.136, PRANK 170427, prodigal 2.6.3, prodigal 2.6.3, ProFit 3.3, prokka 1.14.5, pugixml 1.11.4, pybedtools 0.8.2, pyBigWig 0.3.18, pyfaidx 0.6.3.1, pyFFTW 0.12.0, PyQt5 5.15.4, Pysam 0.17.0, PySide2 5.14.2.3, PyTables 3.5.2, PyTables 3.6.1, Python 2.7.18, python parasail, PyTorch 1.10.0, PyTorch 1.10.0, QuantumESPRESSO 6.8, QUAST 5.0.2, R 4.1.2, Racon 1.4.21, R bundle, rclone 1.57.0.eb, ReFrame 3.9.0.eb, ReFrame 3.9.1.eb, Relate 20211123, ROCm 4.5.0, rocm cmake, ROCm CompilerSupport, rocminfo 4.5.0, rocm smi, ROCR Runtime, ROCT Thunk, rpy2 3.4.5, SAMtools 1.14, SCENIC 1.2.4, scikit image, scikit learn, scikit learn, SciPy bundle, Seaborn 0.11.2, Shasta 0.8.0, SimNIBS 3.2.4, SimpleITK 2.1.0, smithwaterman 20160702, SMV 6.7.17, snakemake 6.10.0, snp sites, SPAdes 3.15.3, spglib python, spoa 3.4.0, SRST2 0.2.0, SSPACE_Basic 2.1.1, STACEY 1.2.5, STEAK 2019.09.12, SuiteSparse 5.10.1, tabixpp 1.1.0, tbb 2020.3, tbb 2020.3, tbb 2021.4.0, termcolor 2.0.0.eb, ThemisPy 0.3.0, TOBIAS 0.12.12, torchtext 0.10.0, torchvision 0.10.0, torchvision 0.11.1, torchvision 0.11.1, tqdm 4.62.3, TRUST4 1.0.6, Trycycler 0.5.2, Unicycler 0.4.9, UShER 0.5.0, vcflib 1.0.2, vsc mympirun, VTune 2021.9.0.eb, Wannier90 3.1.0, Wannier90 3.1.0, WPS 4.3.1, xarray 0.20.1, xarray 0.20.1, XlsxWriter 3.0.2, Yambo 5.0.4, zfp 0.5.5, zlib ng, Zopfli 1.0.3 +- minor enhancements, including: + - add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow-R 6.0.0.2 (#14259) + - add geex and momentfit extensions for R v4.1.x (#14299) + - add StatMatch, leaflet, tmap and collapse packages to R v4.1.0 and R v4.1.2 (#14328) + - add genoPlotR + penfa extensions (and required dependencies) to R 4.1.2 easyconfig (#14433) + - add M3Drop extension to R-bundle-Bioconductor 3.14 easyconfig (#14436) + - add custom sanity_check_paths to TOBIAS easyconfig (#14458) + - add covsim extension to R v4.1.2 easyconfig (#14484) + - improve sanity_check_paths in pugixml easyconfig (#14492) + - add dependency on libnsl for ANIcalculator (#14494) +- various bug fixes, including: + - specify to use Python provided as dependency, remove separate_build_dir, and fix URL in comment for Arrow 0.17.1 (#14263) + - fix gettid nameclash with glibc 2.30 in Bazel 0.25.2, 0.26.1, 0.29.1, and 1.1.0 (#14269) + - restore and fix sanity check commands in RStudio-Server 1.4 (#14275) + - add pkg-config build dependency to Python easyconfigs, to ensure OpenSSL wrapper is detected (#14316) + - add patch for UCX v1.11.2 to fix missing include statement for string.h (#14317) + - fix SHA256 checksum for Kent_tools v422 (#14318) + - add patch for Kent_tools v422 to ensure OpenSSL dependency is used + add missing freetype dependency (#14325) + - set $DALTON_TMPDIR to build directory to run Dalton tests (#14341) + - add patch for PyTorch 1.10.0 to fix RPATH-related issues (#14382) + - add patch for libfabric v1.12.1 to fix 'unknown link width 0x10' warning (#14387) + - add missing Automake dependency to PhyML 3.3.20200621 (#14397) + - don't add bin subdir to $PATH via modextrapaths in ReFrame easyconfigs (#14415) + - add git as build dependency to Python 3.8.x and 3.9.x easyconfigs (required for pbr extension) (#14421) + - reinstate python versionsuffix in pkgconfig-1.5.5-GCCcore-11.2.0-python.eb (#14426) + - add missing XZ dependency to recent PROJ easyconfigs (#14429) + - fix homepage/source URL for king v2.2.4 (#14444) + - add patch for GCCcore 9.1-9.3 to fix compatibility with recent kernel headers (#14453) + - add patch for GCCcore 10.1-11.1 to fix compatibility with recent kernel headers (#14454) + - add patch to fix CVE-2021-43527 in NSS (#14497) + - pass tests on A* GPUs by setting 'NVIDIA_TF32_OVERRIDE=0' in jax 0.2.19 (#14502) + - correctly set execute permissions for ANIcalculator binaries (#14510) + - add patch to fix broken (hanging) Mash binaries (#14511) + - add missing Perl build dependency for Longshot (#14535) + - add googletest build dependency for Highway (#14536) + - seed in PCRE2 sources to fix broken MariaDB 10.5.8 + 10.6.4 easyconfigs (#14537) +- other changes: + - rename R bindings for Arrow to arrow-R, so it can be used in a lowercase module naming scheme (#14262) + - comment out imkl build dependency for FlexiBLAS 3.0.4 with GCC/11.2.0 (#14335) + - consistently use 'Grace' software name + sync homepage/source_urls + fix easyconfig for Grace v5.1.25 with foss/2021a (#14493) + - move cxxopts, termcolor and ELFIO header only libraries to SYSTEM toolchain (#14504) + + v4.5.0 (October 29th 2021) -------------------------- diff --git a/setup.py b/setup.py index 774905ff74d..0a073c359c8 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.1.dev0' +VERSION = '4.5.1' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From c5f71b97cc80f1921e83054aecf405d86b08814b Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Mon, 13 Dec 2021 12:10:19 +0100 Subject: [PATCH 2280/9987] adding easyconfigs: NVHPC-21.11.eb --- easybuild/easyconfigs/n/NVHPC/NVHPC-21.11.eb | 75 ++++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-21.11.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-21.11.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.11.eb new file mode 100644 index 00000000000..201c1d4990e --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-21.11.eb @@ -0,0 +1,75 @@ +## +# Author: Robert Mijakovic +## +name = 'NVHPC' +version = '21.11' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +local_tarball_tmpl = 'nvhpc_2021_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + '3b11bcd9cca862fabfce1e7bcaa2050ea12130c7e897f4e7859ba4c155d20720', + local_tarball_tmpl % 'ppc64le': + 'ac51ed92de4eb5e1bdb064ada5bbace5b89ac732ad6c6473778edfb8d29a6527', + local_tarball_tmpl % 'x86_64': + 'd8d8ccd0e558d22bcddd955f2233219c96f7de56aa8e09e7be833e384d32d6aa', + } +] + +local_gccver = '11.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.37', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.14', '', ('GCCcore', local_gccver)) +] + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/21.7/cuda/) +# for NVHPC 21.11, those are: 11.5, 11.0, 10.2; +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '11.5' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From e416ee8f89e4f5cca11b2de31b05982e903302af Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Mon, 13 Dec 2021 12:27:37 +0100 Subject: [PATCH 2281/9987] adding easyconfigs: ncview-2.1.8-gompi-2021a.eb --- .../n/ncview/ncview-2.1.8-gompi-2021a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021a.eb diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021a.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021a.eb new file mode 100644 index 00000000000..2b6bf793532 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.8' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e8badc507b9b774801288d1c2d59eb79ab31b004df4858d0674ed0d87dfc91be'] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(which $CC) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.8.0'), + ('netCDF-Fortran', '4.5.3'), + ('UDUNITS', '2.2.28'), + ('X11', '20210518'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' From b88e694175fe185fad84735a5c623005a512f19f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Dec 2021 12:43:43 +0100 Subject: [PATCH 2282/9987] tweak release notes for v4.5.1 release --- RELEASE_NOTES | 58 ++++++++++++++++++++++++++------------------------- 1 file changed, 30 insertions(+), 28 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index c5b221d62c9..e4cfd357446 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -13,51 +13,52 @@ v4.5.1 (December 13th 2021) update/bugfix release - added example easyconfig files for 71 new software packages: - - ANIcalculator (#14510), arrow-R (#14267), ASAP (#14367), BabelStream (#14503), bamtofastq (#14391), bcbio-gff (#14322), - biom-format (#13205), Blosc2 (#14247), boto3 (#14452), Brotli-python (#14528), Brunsli (#14247), Clang-AOMP (#14327), - CLEASE (#14413), CMSeq (#14326), cpu_features (#14385), cromwell (#12125), cxxopts (#14504), dRep (#14479), DUBStepR (#14495), - eht-imaging (#14239), einops (#14373), ELFIO (#14504), elprep (#14422), epiScanpy (#14447), FMM3D (#14257), FORD (#13653), - GPy (#14380), HIP (#14339), idemux (#14499), imagecodecs (#14247), InChI (#13902), jupyter-matlab-proxy (#14270), jxrlib (#14247), - LBFGS++ (#14230), LERC (#14247), libaec (#14247), libavif (#14246), LibLZF (#14246), libnsl (#14494), libtree (#14501), - LPeg (#14157), Megalodon (#14256), nnU-Net (#14249), PAL2NAL (#14430), photontorch (#14410), pkgconf (#14426), pmx (#14319), - PPanGGOLiN (#14449), ProFit (#14340), pugixml (#14492), PySide2 (#13460), Relate (#14443), ROCm (#14355), rocm-cmake (#14327), - ROCm-CompilerSupport (#14327), rocminfo (#14327), rocm-smi (#14354), ROCR-Runtime (#14327), ROCT-Thunk-Interface (#14327), - SCENIC (#14260), Shasta (#14385), SimNIBS (#14257), SMV (#14157), SRST2 (#14253), STACEY (#14293), termcolor (#14504), - ThemisPy (#14231), TOBIAS (#14458), zfp (#14246), zlib-ng (#14246), Zopfli (#14246) + - ANIcalculator (#14478, #14494, #14510), arrow-R (#14267), ASAP (#14367), BabelStream (#14503), bamtofastq (#14391), + bcbio-gff (#14322), biom-format (#13205), Blosc2 (#14247), boto3 (#14452), Brotli-python (#14528), Brunsli (#14247), + Clang-AOMP (#14327), CLEASE (#14413), CMSeq (#14326), cpu_features (#14385), cromwell (#12125), + cxxopts (#14487, #14504), dRep (#14479), DUBStepR (#14495), eht-imaging (#14239), einops (#14373), + ELFIO (#14488, #14504), elprep (#14422), epiScanpy (#14447), FMM3D (#14257), FORD (#13653), GPy (#14380), + HIP (#14339), idemux (#14499), imagecodecs (#14247), InChI (#13902), jupyter-matlab-proxy (#14270), jxrlib (#14247), + LBFGS++ (#14230), LERC (#14247), libaec (#14247), libavif (#14246), LibLZF (#14246), libnsl (#14494), + libtree (#14501), LPeg (#14157), Megalodon (#14256), nnU-Net (#14249), PAL2NAL (#14430), photontorch (#14410), + pkgconf (#14426), pmx (#14319), PPanGGOLiN (#14449), ProFit (#14340), pugixml (#14367, #14492), PySide2 (#13460), + Relate (#14443), ROCm (#14355), rocm-cmake (#14327), ROCm-CompilerSupport (#14327), rocminfo (#14327), + rocm-smi (#14354), ROCR-Runtime (#14327), ROCT-Thunk-Interface (#14327), SCENIC (#14260), Shasta (#14385), + SimNIBS (#14257), SMV (#14157), SRST2 (#14253), STACEY (#14293), termcolor (#14489, #14504), ThemisPy (#14231), + TOBIAS (#14452, #14458), zfp (#14246), zlib-ng (#14246), Zopfli (#14246) - added additional easyconfigs for various supported software packages, including: - - ABINIT 9.4.2, ABINIT 9.6.2, ABINIT 9.6.2, ABRicate 1.0.0, abTEM 1.0.0b26, abTEM 1.0.0b26, adjustText 0.7.3, Advisor 2021.4.0.eb, AlphaFold 2.1.1, ANIcalculator 1.0, antiSMASH 6.0.1, ANTLR 2.7.7, any2fasta 0.4.2, AOCC 3.1.0, ARAGORN 1.2.41, Arrow 6.0.0, Arrow 6.0.0, arrow R, arrow R, arrow R, ASAP 2.0, ASE 3.22.0, astropy 4.3.1, astropy 4.3.1, BabelStream 3.4, bamtofastq 1.4.0, BamTools 2.5.2, bcbio gff, bcbio gff, BCFtools 1.14, BeautifulSoup 4.9.3, BEDTools 2.30.0, BerkeleyGW 3.0.1, biom format, Biopython 1.79, Bio SearchIO, Blosc 1.21.1, Blosc2 2.0.3, Boost 1.77.0, Boost 1.77.0, boto3 1.20.13, bpp 4.4.0, Bracken 2.6.2, Brotli python, Brunsli 0.1, BWA 0.7.17, CapnProto 0.8.0, CapnProto 0.9.1, CapnProto 0.9.1, CellRanger 6.0.2.eb, CellRanger 6.1.2.eb, CFITSIO 3.49, CheckM 1.1.3, Clang AOMP, CLEASE 0.10.6, CMSeq 1.0.3, Coreutils 9.0, CP2K 5.1, cppy 1.1.0, cpu_features 0.6.0, cromwell 56, CUDA 11.5.0.eb, CVS 1.11.23, cxxopts 3.0.0.eb, DendroPy 4.5.2, dicom2nifti 2.3.0, dRep 3.0.0, DUBStepR 1.2.0, EasyBuild 4.5.0.eb, edlib 1.3.9, eht imaging, Eigen 3.4.0, einops 0.3.2, ELFIO 3.9.eb, elprep 5.1.1.eb, enaBrowserTool 1.6, epiScanpy 0.3.1, ESMF 8.2.0, ESMF 8.2.0, fastahack 1.0.0, FastANI 1.33, filevercmp 20191210, Flye 2.9, Flye 2.9, FMM3D 20211018, FMRIprep 1.4.1, FORD 6.1.1, freeglut 3.2.1, FSL 6.0.4, fsom 20141119, g2clib 1.6.3, GATK 4.2.3.0, gawk 5.1.1, gc 8.2.0, GDB 11.1, git 2.33.1, GitPython 3.1.24, GL2PS 1.4.2, GlimmerHMM 3.0.4c, GLM 0.9.9.8, gmpy2 2.1.0rc1, Go 1.17.3.eb, GPy 1.10.0, Grace 5.1.25, Grace 5.1.25, Grace 5.1.25, GraphicsMagick 1.3.36, GROMACS 2021.3, GSL 2.7, GTDB Tk, GTS 0.7.6, Gurobi 9.0.1, Gurobi 9.5.0, Gurobi 9.5.0, HDBSCAN 0.8.24, HDF5 1.12.1, Highway 0.12.2, HIP 4.5.0, HMMER2 2.3.2, Horovod 0.23.0, HTSlib 1.14, HyPhy 2.5.33, idemux 0.1.6, imagecodecs 2021.8.26, imageio 2.9.0, InChI 1.06, Infernal 1.1.4, Inspector 2021.4.0.eb, intervaltree 0.1, ITK 5.2.1, jax 0.2.24, jax 0.2.24, Judy 1.0.5, Julia 1.6.4, Julia 1.7.0, jupyter matlab, jxrlib 1.1, Kent_tools 422, king 2.2.7.eb, LBFGS++ 0.1.0.eb, LERC 3.0, libaec 1.0.6, libaio 0.3.112, libavif 0.9.0, libcerf 1.17, libdap 3.20.8, libdwarf 20210528, libelf 0.8.13, Libint 1.1.6, libjxl 0.6.1, LibLZF 3.4, libnsl 1.3.0, libtree 2.0.0, libxc 3.0.1, libxc 5.1.6, likwid 5.2.0, LPeg 1.0.2, Lua 5.3.5, Lua 5.4.3, MAFFT 7.490, MAFFT 7.490, MAFFT 7.490, makeinfo 6.8, MariaDB 10.6.4, Mash 2.2, Mash 2.3, matplotlib 3.4.3, matplotlib 3.4.3, MCR R2021b.eb, MedPy 0.4.0, Megalodon 2.3.5, Megalodon 2.3.5, METIS 5.1.0, minimap2 2.22, MMseqs2 13, MMseqs2 13, motif 2.3.8, multichoose 1.0.3, MUMmer 3.23, muparserx 4.0.8, MUST 1.7.2, NCO 5.0.3, NCO 5.0.3, netCDF 4.8.1, netCDF C++4, netCDF C++4, netCDF Fortran, netCDF Fortran, networkx 2.6.3, NFFT 3.5.2, nlohmann_json 3.10.4, nnU Net, NVHPC 21.9.eb, OpenFOAM 8, OpenMPI 4.0.7, OpenMPI 4.1.2, OpenSlide 3.4.1, PAL2NAL 14, PAL2NAL 14, PAML 4.9j, PAML 4.9j, panaroo 1.2.9, pangolin 3.1.16, pangolin 3.1.16, PAPI 6.0.0.1, parasail 2.4.2, photontorch 0.4.1, photontorch 0.4.1, Pillow 6.2.2, pkgconf 1.8.0, pkgconfig 1.5.5, plotly.py 5.4.0, pmx 2.0, PPanGGOLiN 1.1.136, PRANK 170427, prodigal 2.6.3, prodigal 2.6.3, ProFit 3.3, prokka 1.14.5, pugixml 1.11.4, pybedtools 0.8.2, pyBigWig 0.3.18, pyfaidx 0.6.3.1, pyFFTW 0.12.0, PyQt5 5.15.4, Pysam 0.17.0, PySide2 5.14.2.3, PyTables 3.5.2, PyTables 3.6.1, Python 2.7.18, python parasail, PyTorch 1.10.0, PyTorch 1.10.0, QuantumESPRESSO 6.8, QUAST 5.0.2, R 4.1.2, Racon 1.4.21, R bundle, rclone 1.57.0.eb, ReFrame 3.9.0.eb, ReFrame 3.9.1.eb, Relate 20211123, ROCm 4.5.0, rocm cmake, ROCm CompilerSupport, rocminfo 4.5.0, rocm smi, ROCR Runtime, ROCT Thunk, rpy2 3.4.5, SAMtools 1.14, SCENIC 1.2.4, scikit image, scikit learn, scikit learn, SciPy bundle, Seaborn 0.11.2, Shasta 0.8.0, SimNIBS 3.2.4, SimpleITK 2.1.0, smithwaterman 20160702, SMV 6.7.17, snakemake 6.10.0, snp sites, SPAdes 3.15.3, spglib python, spoa 3.4.0, SRST2 0.2.0, SSPACE_Basic 2.1.1, STACEY 1.2.5, STEAK 2019.09.12, SuiteSparse 5.10.1, tabixpp 1.1.0, tbb 2020.3, tbb 2020.3, tbb 2021.4.0, termcolor 2.0.0.eb, ThemisPy 0.3.0, TOBIAS 0.12.12, torchtext 0.10.0, torchvision 0.10.0, torchvision 0.11.1, torchvision 0.11.1, tqdm 4.62.3, TRUST4 1.0.6, Trycycler 0.5.2, Unicycler 0.4.9, UShER 0.5.0, vcflib 1.0.2, vsc mympirun, VTune 2021.9.0.eb, Wannier90 3.1.0, Wannier90 3.1.0, WPS 4.3.1, xarray 0.20.1, xarray 0.20.1, XlsxWriter 3.0.2, Yambo 5.0.4, zfp 0.5.5, zlib ng, Zopfli 1.0.3 + - ABINIT 9.6.2, ABRicate 1.0.0, AlphaFold 2.1.1, antiSMASH 6.0.1, Arrow 6.0.0, astropy 4.3.1, BCFtools 1.14, + BeautifulSoup 4.9.3, Boost 1.77.0, bpp 4.4.0, Bracken 2.6.2, CapnProto 0.9.1, CellRanger 6.1.2, Eigen 3.4.0, + enaBrowserTool 1.6, ESMF 8.2.0, Flye 2.9, FMRIprep 1.4.1, FSL 6.0.4, GATK 4.2.3.0, gc 8.2.0, GDB 11.1, git 2.33.1, + Go 1.17.3, Gurobi 9.5.0, Horovod 0.23.0, HTSlib 1.14, HyPhy 2.5.33, Infernal 1.1.4, Inspector 2021.4.0 ITK 5.2.1, + jax 0.2.24, Julia 1.7.0, Kent_tools 422, king 2.2.7, libdwarf 20210528, MAFFT 7.490, makeinfo 6.8, Mash 2.3, + matplotlib 3.4.3, MCR R2021b, minimap2 2.22, MUST 1.7.2, NCO 5.0.3, NCO 5.0.3, nlohmann_json 3.10.4, NVHPC 21.9, + OpenMPI 4.0.7 + 4.1.2, panaroo 1.2.9, pangolin 3.1.16, pkgconfig 1.5.5, plotly.py 5.4.0, pyfaidx 0.6.3.1, + Pysam 0.17.0, PyTorch 1.10.0, R 4.1.2, R-bundle-Bioconductor 3.14, ReFrame 3.9.1, rpy2 3.4.5, scikit-image 0.18.3, + scikit-learn 1.0.1 SimpleITK 2.1.0, snakemake 6.10.0, SPAdes 3.15.3, tbb 2021.4.0, torchtext 0.10.0, + torchvision 0.11.1, tqdm 4.62.3, TRUST4 1.0.6, Trycycler 0.5.2, Unicycler 0.4.9, UShER 0.5.0, WPS 4.3.1, + xarray 0.20.1, XlsxWriter 3.0.2, Yambo 5.0.4 - minor enhancements, including: - - add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 + add easyconfigs for Arrow 6.0.0 and arrow-R 6.0.0.2 (#14259) - - add geex and momentfit extensions for R v4.1.x (#14299) - - add StatMatch, leaflet, tmap and collapse packages to R v4.1.0 and R v4.1.2 (#14328) - - add genoPlotR + penfa extensions (and required dependencies) to R 4.1.2 easyconfig (#14433) - - add M3Drop extension to R-bundle-Bioconductor 3.14 easyconfig (#14436) - - add custom sanity_check_paths to TOBIAS easyconfig (#14458) - - add covsim extension to R v4.1.2 easyconfig (#14484) - - improve sanity_check_paths in pugixml easyconfig (#14492) - - add dependency on libnsl for ANIcalculator (#14494) + - add RcisTarget + NMF extensions to R-bundle-Bioconductor 3.13 (#14259) + - add extensions for R v4.1.x: + - geex + momentfit (#14299); StatMatch, leaflet, tmap + collapse (#14328), genoPlotR + penfa (#14433), adcovsim (#14484) + - add M3Drop extension to R-bundle-Bioconductor 3.14 (#14436) - various bug fixes, including: - specify to use Python provided as dependency, remove separate_build_dir, and fix URL in comment for Arrow 0.17.1 (#14263) - fix gettid nameclash with glibc 2.30 in Bazel 0.25.2, 0.26.1, 0.29.1, and 1.1.0 (#14269) - restore and fix sanity check commands in RStudio-Server 1.4 (#14275) - add pkg-config build dependency to Python easyconfigs, to ensure OpenSSL wrapper is detected (#14316) - add patch for UCX v1.11.2 to fix missing include statement for string.h (#14317) - - fix SHA256 checksum for Kent_tools v422 (#14318) - - add patch for Kent_tools v422 to ensure OpenSSL dependency is used + add missing freetype dependency (#14325) - set $DALTON_TMPDIR to build directory to run Dalton tests (#14341) - - add patch for PyTorch 1.10.0 to fix RPATH-related issues (#14382) - add patch for libfabric v1.12.1 to fix 'unknown link width 0x10' warning (#14387) - add missing Automake dependency to PhyML 3.3.20200621 (#14397) - - don't add bin subdir to $PATH via modextrapaths in ReFrame easyconfigs (#14415) - add git as build dependency to Python 3.8.x and 3.9.x easyconfigs (required for pbr extension) (#14421) - - reinstate python versionsuffix in pkgconfig-1.5.5-GCCcore-11.2.0-python.eb (#14426) - add missing XZ dependency to recent PROJ easyconfigs (#14429) - fix homepage/source URL for king v2.2.4 (#14444) - add patch for GCCcore 9.1-9.3 to fix compatibility with recent kernel headers (#14453) - add patch for GCCcore 10.1-11.1 to fix compatibility with recent kernel headers (#14454) - add patch to fix CVE-2021-43527 in NSS (#14497) - pass tests on A* GPUs by setting 'NVIDIA_TF32_OVERRIDE=0' in jax 0.2.19 (#14502) - - correctly set execute permissions for ANIcalculator binaries (#14510) - add patch to fix broken (hanging) Mash binaries (#14511) - add missing Perl build dependency for Longshot (#14535) - add googletest build dependency for Highway (#14536) @@ -65,7 +66,8 @@ update/bugfix release - other changes: - rename R bindings for Arrow to arrow-R, so it can be used in a lowercase module naming scheme (#14262) - comment out imkl build dependency for FlexiBLAS 3.0.4 with GCC/11.2.0 (#14335) - - consistently use 'Grace' software name + sync homepage/source_urls + fix easyconfig for Grace v5.1.25 with foss/2021a (#14493) + - don't add bin subdir to $PATH via modextrapaths in ReFrame easyconfigs (#14415) + - consistently use 'Grace' software name + sync homepage/source_urls (#14493) - move cxxopts, termcolor and ELFIO header only libraries to SYSTEM toolchain (#14504) From 6564b439610b44727c9d7670e1d57db0a48b6d4f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Dec 2021 21:47:20 +0800 Subject: [PATCH 2283/9987] adding easyconfigs: EasyBuild-4.5.1.eb --- .../e/EasyBuild/EasyBuild-4.5.1.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb new file mode 100644 index 00000000000..bc8db12a896 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.5.1' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/b5/ef/8764968b5dc2eedb3eac6ac17e1bc3f7d283b18dd0409d26eefa0f80e720/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/13/16/1b107077b368e713a6cce53fc8b7df4c133ccc19d05818dfdf783d5d7d24/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/2c/77/f529f9e4c07631e4222055e487e26d26cddb4d321c85f64fb08117f73521/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + 'db6f9013c8cc8501957d23c699cf0eecfffe609a4c0439418325216e11a9be69', # easybuild-framework-4.5.1.tar.gz + '03f10044ddbfe5c48c3257ccd2bbeeecb3b215d0b604efa194ec95d670e7a1d2', # easybuild-easyblocks-4.5.1.tar.gz + 'd1b7e63f733b204a88259dc29fcd10481afd7aacac6ad37b996841ddd733f72b', # easybuild-easyconfigs-4.5.1.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From dfbf7947ddbcd95ef54e6417cf45db3e78149397 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Dec 2021 18:40:12 +0000 Subject: [PATCH 2284/9987] add yaml-cpp to Trilinos --- ...rilinos-12.12.1-foss-2019b-Python-3.7.4.eb | 1 + .../yaml-cpp/yaml-cpp-0.6.3-GCCcore-8.3.0.eb | 26 +++++++++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.6.3-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb index bcf9ccb2baf..c4ee42f5588 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb @@ -50,6 +50,7 @@ dependencies = [ ('MATIO', '1.5.17'), ('GLM', '0.9.9.8'), ('X11', '20190717'), + ('yaml-cpp', '0.6.3'), ] build_shared_libs = True diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.6.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.6.3-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..083cd98d36b --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.6.3-GCCcore-8.3.0.eb @@ -0,0 +1,26 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' +name = 'yaml-cpp' +version = '0.6.3' + +homepage = "https://github.com/jbeder/yaml-cpp" +description = """yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/jbeder/%(name)s/archive/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['77ea1b90b3718aa0c324207cb29418f5bced2354c2e483a9523d98c3460af1ed'] + +builddependencies = [ + ('binutils', '2.32'), + ('CMake', '3.15.3') +] + +sanity_check_paths = { + 'files': ['lib/libyaml-cpp.a', 'include/yaml-cpp/yaml.h'], + 'dirs': ['lib', 'include'], +} + +moduleclass = 'tools' From 9584bb4f0b554aebe615a0acc93fa1017c9f77b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Dec 2021 15:18:40 +0100 Subject: [PATCH 2285/9987] bump version to 4.5.2dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0a073c359c8..bb5b73a292d 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.1' +VERSION = '4.5.2.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From d9202198d587f65f098177e6724e8f63a8a9b760 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 13 Dec 2021 19:50:45 +0000 Subject: [PATCH 2286/9987] adding easyconfigs: elbencho-2.0-3-GCC-10.3.0.eb --- .../e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb new file mode 100644 index 00000000000..12d37d0e06b --- /dev/null +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = "MakeCp" + +name = "elbencho" +version = "2.0-3" + +homepage = "https://github.com/breuner/elbencho" +description = """ A distributed storage benchmark for files, objects & blocks with support for GPUs""" + + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +dependencies = [('Boost', '1.76.0'), ('libaio', '0.3.112')] + +sources = [{ + 'filename': "v%(version)s.tar.gz", + 'git_config': { + 'url': 'https://github.com/breuner', + 'repo_name': 'elbencho', + 'tag': 'v%(version)s' + }, + +}] +checksums = ['f6c34f46b61451bcb1362e73d7754f307ae972c467b135e3279fd477586b5b7d'] + +files_to_copy = ["bin"] +sanity_check_paths = { + 'dirs': files_to_copy, + 'files': ['bin/%s' % x for x in + ['elbencho', 'elbencho-unstripped']], +} From 5652c4366eb1583daa923a727d95bc229ed63d63 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Mon, 13 Dec 2021 22:14:23 +0100 Subject: [PATCH 2287/9987] adding easyconfigs: MicrobeAnnotator-2.0.5-foss-2021a.eb --- .../MicrobeAnnotator-2.0.5-foss-2021a.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb b/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb new file mode 100644 index 00000000000..1635e196613 --- /dev/null +++ b/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb @@ -0,0 +1,74 @@ +easyblock = 'PythonBundle' + +name = 'MicrobeAnnotator' +version = '2.0.5' + +homepage = 'https://github.com/cruizperez/MicrobeAnnotator' +description = "Easy-to-use pipeline for the comprehensive metabolic annotation of microbial genomes." + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Biopython', '1.79'), + ('BLAST+', '2.11.0'), + ('DIAMOND', '2.0.11'), + ('HMMER2', '2.3.2'), + ('python-isal', '0.11.0'), + ('SciPy-bundle', '2021.05'), + ('Seaborn', '0.11.2'), + ('wget', '1.21.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('attrs', '21.2.0', { + 'modulename': 'attr', + 'checksums': ['ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb'], + }), + ('psutil', '5.8.0', { + 'checksums': ['0c9ccb99ab76025f2f0bbecf341d4656e9c1351db8cc8a03ccd62e318ab4b5c6'], + }), + ('wget', '3.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['35e630eca2aa50ce998b9b1a127bb26b30dfee573702782aa982f875e3f16061'], + }), + ('importlib_resources', '5.4.0', { + 'checksums': ['d756e2f85dd4de2ba89be0b21dba2a3bbec2e871a42a3a16719258a11f87506b'], + }), + ('xopen', '1.2.1', { + 'checksums': ['9cb1e23592b1ee0f7b067a67f74fcc7957e08821cb2a0e1f6b6c87499c68afcf'], + }), + ('fasta-reader', '1.0.0', { + 'checksums': ['61453b968a71ddf5bb63172f68d73ba2ccf0a23ac3b6ae0f6c63afa478d30444'], + }), + ('gff-io', '0.0.2', { + 'checksums': ['b1691222494787995a14b4b9ca5cbd3ead1372c4f6e5b58ef71ed733a35d7a59'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('hmmer', '0.1.0', { + 'checksums': ['4d322ae026c0a61459cef06405add39ea86f7ad1fef845712b7b27b4e6842a92'], + }), + (name, version, { + 'preinstallopts': 'sed -i "/python_requires/d" setup.py && ', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/cruizperez/MicrobeAnnotator/archive/'], + 'checksums': ['4bc128faf725164b50c20026530425336d72fbfd6916f8f8c6c8c5246c7b43ad'], + }), +] + +sanity_check_commands = [ + 'microbeannotator -h', + 'microbeannotator_db_builder -h', +] + +moduleclass = 'bio' From 3452676b333f4dbfcf211c9d335e7d5c51844a60 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 22:40:33 +0000 Subject: [PATCH 2288/9987] adding easyconfigs: Bowtie2-2.4.4-GCC-11.2.0.eb --- .../b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb new file mode 100644 index 00000000000..24d2f6861d9 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp + +name = 'Bowtie2' +version = '2.4.4' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Perl', '5.34.0'), + ('Python', '3.9.6'), +] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] + +moduleclass = 'bio' From b0022b94ca56c0b48926f27727f0f316c8827587 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 22:41:31 +0000 Subject: [PATCH 2289/9987] adding easyconfigs: Bismark-0.23.1-foss-2021b.eb --- .../b/Bismark/Bismark-0.23.1-foss-2021b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb new file mode 100644 index 00000000000..af597f02e72 --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +# Updated to 0.23.1 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'Tarball' + +name = 'Bismark' +version = '0.23.1' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = "A tool to map bisulfite converted sequence reads and determine cytosine methylation states" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/FelixKrueger/Bismark/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2ceb620cfc3f1c869f4bda656ab01c242f1da7ec01615b0d23b28c702147a337'] + +dependencies = [ + ('Perl', '5.34.0'), + ('Bowtie2', '2.4.4'), + ('SAMtools', '1.14'), +] + +sanity_check_commands = [ 'bismark --help'] + +sanity_check_paths = { + 'files': ['bismark', 'bismark2bedGraph', 'bismark2report', 'bismark_genome_preparation', + 'bismark_methylation_extractor', 'coverage2cytosine', 'deduplicate_bismark'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 6ee6b9e50e8a3537a2519f5a61630236096c406f Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 22:46:59 +0000 Subject: [PATCH 2290/9987] adding easyconfigs: ISA-L-2.30.0-GCCcore-11.2.0.eb --- .../i/ISA-L/ISA-L-2.30.0-GCCcore-11.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..319c7856561 --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.2.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.30.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['bcf592c04fdfa19e723d2adf53d3e0f4efd5b956bb618fed54a1108d76a6eb56'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [('NASM', '2.15.05')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +local_bins = ['bin/igzip'] +local_includes = ['include/%(namelower)s.h'] +local_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test', 'types']] +local_libs = ['lib/libisal.%s' % k for k in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': local_bins + local_includes + local_libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' From c88adfbd28a098ee77efe1521710d306854381d7 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 22:49:16 +0000 Subject: [PATCH 2291/9987] adding easyconfigs: libdeflate-1.8-GCCcore-11.2.0.eb --- .../libdeflate-1.8-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..da97e2fb5c3 --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to 1.8 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'ConfigureMake' + +name = 'libdeflate' +version = '1.8' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['50711ad4e9d3862f8dfb11b97eb53631a86ee3ce49c0e68ec2b6d059a9662f61'] + +builddependencies = [('binutils', '2.37')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' From 0e343b1279fcd604a0132b237bd802a7316094b4 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 22:50:47 +0000 Subject: [PATCH 2292/9987] adding easyconfigs: fastp-0.23.2-GCC-11.2.0.eb --- .../f/fastp/fastp-0.23.2-GCC-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.2.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..3811081f326 --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.23.2' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +# https://github.com/OpenGene/fastp +github_account = 'OpenGene' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['185bd58732e57474fa08aae90e154fbc05f3e437ee2b434386dd2266d60d8ef6'] + +dependencies = [ + ('zlib', '1.2.11'), + ('libdeflate', '1.8'), + ('ISA-L', '2.30.0'), +] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/fastp'], + 'dirs': [], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' From d0ed63f325049fef9bdb8f97ebefbecdc2333c07 Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 13 Dec 2021 23:00:41 +0000 Subject: [PATCH 2293/9987] adding easyconfigs: MAGMA-1.09b-GCC-11.2.0.eb --- .../m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb new file mode 100644 index 00000000000..eb16168b20f --- /dev/null +++ b/easybuild/easyconfigs/m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'MAGMA' +version = '1.09b' + +homepage = 'https://ctg.cncr.nl/software/magma' +description = """MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. +It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous +GWAS or meta-analysis.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [ + 'https://ctg.cncr.nl/software/MAGMA/prog/', + 'https://ctg.cncr.nl/software/MAGMA/prog/archive/', +] +sources = ['%(namelower)s_v%(version)s_source.zip'] +checksums = ['8af8673fa6c3cf60c2528a06783c20795d9daf4649481cd6e04feb68b91730e0'] + +buildopts = ' CXX=${CXX}' + +files_to_copy = [ + (['magma'], 'bin'), + (['manual_v%(version)s.pdf'], 'doc'), + 'CHANGELOG', + 'COPYRIGHT', +] + +sanity_check_commands = ['magma --version'] + +sanity_check_paths = { + 'files': ['bin/magma'], + 'dirs': [], +} + +moduleclass = 'bio' From 3ca3588f715ad52fceb429b80bbf3789e787675d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Tue, 14 Dec 2021 00:26:51 +0100 Subject: [PATCH 2294/9987] adding easyconfigs: OpenFace-2.2.0-foss-2021a.eb, dlib-19.22-foss-2021a.eb, OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb, dlib-19.22-foss-2021a-CUDA-11.3.1.eb --- .../dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb | 37 +++++++++++++ .../d/dlib/dlib-19.22-foss-2021a.eb | 31 +++++++++++ .../OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb | 53 +++++++++++++++++++ .../o/OpenFace/OpenFace-2.2.0-foss-2021a.eb | 50 +++++++++++++++++ 4 files changed, 171 insertions(+) create mode 100644 easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb create mode 100644 easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..95635f71e04 --- /dev/null +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'dlib' +version = '19.22' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/davisking/dlib' +description = """Dlib is a modern C++ toolkit containing machine learning +algorithms and tools for creating complex software in C++ to solve real world +problems. It is used in both industry and academia in a wide range of domains +including robotics, embedded devices, mobile phones, and large high performance +computing environments.""" + +toolchain = {'name': 'foss', 'version': '2021a'} # requires blas +toolchainopts = {'pic': True} + +github_account = 'davisking' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5f44b67f762691b92f3e41dcf9c95dd0f4525b59cacb478094e511fdacb5c096'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', versionsuffix, True), +] + +sanity_check_paths = { + 'files': ['include/dlib/image_io.h', 'lib/libdlib.a', 'lib64/libdlib.a'], + 'dirs': ['lib/pkgconfig', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb new file mode 100644 index 00000000000..b3c3383dcf6 --- /dev/null +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'dlib' +version = '19.22' + +homepage = 'https://github.com/davisking/dlib' +description = """Dlib is a modern C++ toolkit containing machine learning +algorithms and tools for creating complex software in C++ to solve real world +problems. It is used in both industry and academia in a wide range of domains +including robotics, embedded devices, mobile phones, and large high performance +computing environments.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'davisking' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5f44b67f762691b92f3e41dcf9c95dd0f4525b59cacb478094e511fdacb5c096'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': ['include/dlib/image_io.h', 'lib/libdlib.a', 'lib64/libdlib.a'], + 'dirs': ['lib/pkgconfig', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ed5e27cab78 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'OpenFace' +version = '2.2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/TadasBaltrusaitis/OpenFace' +description = """OpenFace – a state-of-the art tool intended for facial landmark +detection, head pose estimation, facial action unit recognition, and eye-gaze +estimation.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'TadasBaltrusaitis' +source_urls = [GITHUB_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = ['OpenFace-2.2.0-use_FlexiBLAS.patch'] +checksums = [ + '928e6346bcff41393393a364df99bf09c3410fab85b569f2023e3224d2a1981a', # OpenFace_2.2.0.tar.gz + '354531f3f1ad497b1b5ab213c274247e5f87b3d30a7c1f4f93b0e4041a86a909', # OpenFace-2.2.0-use_FlexiBLAS.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), + ('patchelf', '0.12') +] +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('OpenCV', '4.5.3', '-CUDA-%(cudaver)s-contrib'), + ('dlib', '19.22', '-CUDA-%(cudaver)s'), + ('SDL2', '2.0.14'), + ('Boost', '1.76.0'), +] + +configopts = "-DCMAKE_BUILD_TYPE=RELEASE" + +# This is the only way I found to remove the banned OpenBLAS from libraries +# required by the OpenFace executables, as CMake stubbornly includes it there +preinstallopts = 'patchelf --remove-needed libopenblas.so.0 bin/FaceLandmarkVid' +preinstallopts += ' bin/FaceLandmarkVidMulti bin/FaceLandmarkImg bin/FeatureExtraction && ' + +sanity_check_paths = { + 'files': ['bin/FaceLandmarkVid', 'bin/FaceLandmarkImg', 'bin/FeatureExtraction'], + 'dirs': [], +} +sanity_check_commands = [ + 'FaceLandmarkVid -f ../samples/changeLighting.wmv -f ../samples/2015-10-15-15-14.avi' +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb new file mode 100644 index 00000000000..3279d8b139f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'OpenFace' +version = '2.2.0' + +homepage = 'https://github.com/TadasBaltrusaitis/OpenFace' +description = """OpenFace – a state-of-the art tool intended for facial landmark +detection, head pose estimation, facial action unit recognition, and eye-gaze +estimation.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'TadasBaltrusaitis' +source_urls = [GITHUB_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = ['OpenFace-2.2.0-use_FlexiBLAS.patch'] +checksums = [ + '928e6346bcff41393393a364df99bf09c3410fab85b569f2023e3224d2a1981a', # OpenFace_2.2.0.tar.gz + '354531f3f1ad497b1b5ab213c274247e5f87b3d30a7c1f4f93b0e4041a86a909', # OpenFace-2.2.0-use_FlexiBLAS.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), + ('patchelf', '0.12') +] +dependencies = [ + ('OpenCV', '4.5.3', '-contrib'), + ('dlib', '19.22'), + ('SDL2', '2.0.14'), + ('Boost', '1.76.0'), +] + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE' + +# This is the only way I found to remove the banned OpenBLAS from libraries +# required by the OpenFace executables, as CMake stubbornly includes it there +preinstallopts = 'patchelf --remove-needed libopenblas.so.0 bin/FaceLandmarkVid' +preinstallopts += ' bin/FaceLandmarkVidMulti bin/FaceLandmarkImg bin/FeatureExtraction && ' + +sanity_check_paths = { + 'files': ['bin/FaceLandmarkVid', 'bin/FaceLandmarkImg', 'bin/FeatureExtraction'], + 'dirs': [], +} +sanity_check_commands = [ + 'FaceLandmarkVid -f ../samples/changeLighting.wmv -f ../samples/2015-10-15-15-14.avi' +] + +moduleclass = 'lib' From 2c4ab81fe58b509dad3c8142fb2ae15ad7bf6de9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 14 Dec 2021 13:48:22 +0000 Subject: [PATCH 2295/9987] adding easyconfigs: ShengBTE-1.1.1-foss-2021a.eb --- .../s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb new file mode 100644 index 00000000000..de135d9fb64 --- /dev/null +++ b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'ShengBTE' +version = '1.1.1' + +homepage = 'https://bitbucket.org/sousaw/shengbte' +description = "A solver for the Boltzmann transport equation for phonons." + +toolchain = {'name': 'foss', 'version': '2021a'} + +bitbucket_account = 'sousaw' +source_urls = [BITBUCKET_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['617a7110f4222ee249e351d15805d74744a550f01c07d798615d697de26edd71'] + +dependencies = [('spglib', '1.16.2')] + +start_dir = 'Src' + +# strip "include arch.make" -- not needed as we already set necessary env vars +prebuildopts = "sed -i '1d' Makefile && " +# -fallow-argument-mismatch needed for GCC 10+ +buildopts = '-j 1 LIBS="$LIBBLAS -lsymspg" FFLAGS="$FFLAGS -fallow-argument-mismatch"' + +files_to_copy = [([name], 'bin'), 'Test-*', 'LICENSE', 'README.md'] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = [ + "cd %%(builddir)s/*%%(namelower)s*/Test-%s && mpirun -n %%(parallel)s %%(name)s" % x for x in ['QE', 'RTA', 'VASP'] +] + +moduleclass = 'phys' From ac26de38dad3ad47862dac4a722fff6f66576b95 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 01:09:27 +1050 Subject: [PATCH 2296/9987] dep <- sklearn path --- .../c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb index 7b6c317aa6a..e2904528e42 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -29,9 +29,11 @@ dependencies = [ ('Pysam', '0.16.0.1'), ] -download_dep_fail = False +download_dep_fail = True use_pip = True +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + sanity_pip_check = True sanity_check_paths = { # check for particular Cupcake ToFU scripts, From 04a5f90257e31582e80064946d576a6109486981 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Wed, 15 Dec 2021 00:52:09 +1030 Subject: [PATCH 2297/9987] Update easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb Co-authored-by: Sam Moors --- .../cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb index d9470e12178..bf0b8def215 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -30,9 +30,11 @@ dependencies = [ ('Pysam', '0.16.0.1'), ] -download_dep_fail = False +download_dep_fail = True use_pip = True +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + sanity_pip_check = True sanity_check_paths = { # check for particular Cupcake ToFU scripts, From 3c80808c3ea2c9f13e75f69df2d64616454dd929 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 02:01:42 +1050 Subject: [PATCH 2298/9987] debug <- string edit bug fix --- .../libplinkio-0.9.8-GCCcore-9.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..616271cef1c --- /dev/null +++ b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb @@ -0,0 +1,32 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'CMakeMake' + +name = 'libplinkio' +version = '0.9.8' + +homepage = "https://github.com/mfranberg/libplinkio" +description = """A small C and Python library for reading PLINK genotype files.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +github_account = "mfranberg" +source_urls = ['https://github.com/%(github_account)s/%(namelower)s/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['de54dd4789b2da9b937a1f445dc6976153211dc35b4376a4cf561ad2ee861075'] + +builddependencies = [ + ('CMake', '3.15.3'), + ('binutils', '2.32'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/%s.%s' % (name, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 2a9a3d7047ff211f2cdb3935fd3ac5b552df9a2e Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Wed, 15 Dec 2021 01:42:11 +1030 Subject: [PATCH 2299/9987] Delete libplinkio-0.9.8-GCCcore-8.3.0.eb --- .../libplinkio-0.9.8-GCCcore-8.3.0.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb deleted file mode 100644 index e9cbc083532..00000000000 --- a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-8.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -## -# This easyconfig is contributed by DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: BSD -# -# Notes:: -## - -easyblock = 'CMakeMake' - -name = 'libplinkio' -version = '0.9.8' - -homepage = "https://github.com/mfranberg/libplinkio" -description = """A small C and Python library for reading PLINK genotype files.""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} - -source_urls = ['https://github.com/mfranberg/%(namelower)s/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['de54dd4789b2da9b937a1f445dc6976153211dc35b4376a4cf561ad2ee861075'] - -builddependencies = [ - ('CMake', '3.15.3'), - ('binutils', '2.32'), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['lib/%(name)s.%s' SHLIB_EXT], - 'dirs': ['lib', 'include'], -} - -moduleclass = 'lib' From 34a187924f8b8c17965d02eb9364f00cfd04cd17 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 02:07:24 +1050 Subject: [PATCH 2300/9987] dep <- update build deps --- .../l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb index 616271cef1c..1f36469df81 100644 --- a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb @@ -18,8 +18,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['de54dd4789b2da9b937a1f445dc6976153211dc35b4376a4cf561ad2ee861075'] builddependencies = [ - ('CMake', '3.15.3'), - ('binutils', '2.32'), + ('CMake', '3.16.4'), + ('binutils', '2.34'), ] parallel = 1 From 2e9358a364c9d7b1b218f308bf6f3857cce65e27 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 03:14:53 +1050 Subject: [PATCH 2301/9987] dep <- update build deps --- .../libplinkio-0.9.8-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..974ac5e77f0 --- /dev/null +++ b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'CMakeMake' + +name = 'libplinkio' +version = '0.9.8' + +homepage = "https://github.com/mfranberg/libplinkio" +description = """A small C and Python library for reading PLINK genotype files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +# toolchainopts = {'lowopt': True} + +github_account = "mfranberg" +source_urls = ['https://github.com/%(github_account)s/%(namelower)s/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['de54dd4789b2da9b937a1f445dc6976153211dc35b4376a4cf561ad2ee861075'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/%s.%s' % (name, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'lib' From e6404f434d40588da6d67c3ab21997c8263eed4d Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 03:17:05 +1050 Subject: [PATCH 2302/9987] dep <- update build deps --- .../easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb index 1f36469df81..7728a82147b 100644 --- a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb @@ -11,6 +11,7 @@ homepage = "https://github.com/mfranberg/libplinkio" description = """A small C and Python library for reading PLINK genotype files.""" toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'cstd': 'gnu17', 'noopt': True, 'extra_cflags': '-w'} github_account = "mfranberg" source_urls = ['https://github.com/%(github_account)s/%(namelower)s/archive/refs/tags'] From 895f7e2589d807fabead63546ff78794d2d182be Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Wed, 15 Dec 2021 02:57:33 +1030 Subject: [PATCH 2303/9987] Delete libplinkio-0.9.8-GCCcore-10.3.0.eb --- .../libplinkio-0.9.8-GCCcore-10.3.0.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-10.3.0.eb deleted file mode 100644 index 974ac5e77f0..00000000000 --- a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-10.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO - -easyblock = 'CMakeMake' - -name = 'libplinkio' -version = '0.9.8' - -homepage = "https://github.com/mfranberg/libplinkio" -description = """A small C and Python library for reading PLINK genotype files.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -# toolchainopts = {'lowopt': True} - -github_account = "mfranberg" -source_urls = ['https://github.com/%(github_account)s/%(namelower)s/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['de54dd4789b2da9b937a1f445dc6976153211dc35b4376a4cf561ad2ee861075'] - -builddependencies = [ - ('CMake', '3.20.1'), - ('binutils', '2.36.1'), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['lib/%s.%s' % (name, SHLIB_EXT)], - 'dirs': ['include'], -} - -moduleclass = 'lib' From 1d7c443b6ae88e7817287375bbd14ef18d520746 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Dec 2021 17:32:18 +0100 Subject: [PATCH 2304/9987] strip out non-required binutils/CMake build dependencies + attrs/psutil extensions from MicrobeAnnotator easyconfig --- .../MicrobeAnnotator-2.0.5-foss-2021a.eb | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb b/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb index 1635e196613..b76e1fa7bff 100644 --- a/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MicrobeAnnotator/MicrobeAnnotator-2.0.5-foss-2021a.eb @@ -8,11 +8,6 @@ description = "Easy-to-use pipeline for the comprehensive metabolic annotation o toolchain = {'name': 'foss', 'version': '2021a'} -builddependencies = [ - ('binutils', '2.36.1'), - ('CMake', '3.20.1'), -] - dependencies = [ ('Python', '3.9.5'), ('Biopython', '1.79'), @@ -29,13 +24,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('attrs', '21.2.0', { - 'modulename': 'attr', - 'checksums': ['ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb'], - }), - ('psutil', '5.8.0', { - 'checksums': ['0c9ccb99ab76025f2f0bbecf341d4656e9c1351db8cc8a03ccd62e318ab4b5c6'], - }), ('wget', '3.2', { 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['35e630eca2aa50ce998b9b1a127bb26b30dfee573702782aa982f875e3f16061'], From 51c455fa10976769c71f292c3e930dd409839380 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 14 Dec 2021 19:08:56 +0100 Subject: [PATCH 2305/9987] adding easyconfigs: CHERAB-1.3.0-intel-2020b.eb, Raysect-0.7.1-intel-2020b.eb --- .../c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 30 +++++++++++++++++++ .../r/Raysect/Raysect-0.7.1-intel-2020b.eb | 24 +++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb new file mode 100644 index 00000000000..a1ad1f6bc92 --- /dev/null +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'CHERAB' +version = '1.3.0' + +homepage = 'https://cherab.github.io/documentation/index.html' + +description = """CHERAB is a python library for forward modelling diagnostics + based on spectroscopic plasma emission.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = False + +sanity_check_commands = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && python -c "import cherab"'] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb new file mode 100644 index 00000000000..d506edd8c8c --- /dev/null +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Raysect' +version = '0.7.1' + +homepage = 'https://raysect.org' + +description = """Raysect is an OOP ray-tracing framework for Python""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c91f7dc406fd64dfaa4096b259c31250ac50881a301a46b2a1d607a2746f968'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True + +moduleclass = 'vis' From fd92289b5330fd453e56208f667ab2b23be9ad41 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 14 Dec 2021 18:56:48 +0000 Subject: [PATCH 2306/9987] adding easyconfigs: TrimGalore-0.6.7-GCCcore-10.3.0.eb --- .../TrimGalore-0.6.7-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/t/TrimGalore/TrimGalore-0.6.7-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/TrimGalore/TrimGalore-0.6.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TrimGalore/TrimGalore-0.6.7-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d994f9fc694 --- /dev/null +++ b/easybuild/easyconfigs/t/TrimGalore/TrimGalore-0.6.7-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +# Uploaded by J. Sassmannshausen NHS/GSTT + +easyblock = 'Tarball' + +name = 'TrimGalore' +version = '0.6.7' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """Trim Galore! is a wrapper script to automate quality and adapter +trimming as well as quality control, with some added functionality to remove biased +methylation positions for RRBS sequence files (for directional, non-directional +(or paired-end) sequencing).""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/FelixKrueger/%(name)s/archive'] +sources = ['%(version)s.tar.gz'] +checksums = [ + '49b4622c9f839f8a7037fa2f7de9ab873e4fb702f29c14b4d7f095abf6738f74', # 0.6.7.tar.gz +] + +dependencies = [ + ('Perl', '5.32.1'), + ('cutadapt', '3.4'), + ('FastQC', '0.11.9', '-Java-11', True), +] + +sanity_check_paths = { + 'files': ['trim_galore'], + 'dirs': [''], +} + +modextrapaths = {'PATH': '.'} + +sanity_check_commands = [('trim_galore', '-v')] + +moduleclass = 'bio' From b41ebf27904c54cd360bac8b4581587e28f9d23f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 14 Dec 2021 20:52:03 +0100 Subject: [PATCH 2307/9987] adding easyconfigs: STRUMPACK-6.1.0-foss-2020b.eb, STRUMPACK-6.1.0-intel-2020b.eb --- .../s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 52 ++++++++++++++++++ .../STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 53 +++++++++++++++++++ 2 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb new file mode 100644 index 00000000000..26e9142f8f1 --- /dev/null +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'STRUMPACK' +version = '6.1.0' + +homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html' +description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner + for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pghysels/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['219ec7360594172464aafa6ecac1fd161097db6fb9ee35af5c1ca61531f4f5c4'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '6.1.0'), +] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release ' +configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpifort ' +configopts += '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DNO_MODULES=ON ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_ENABLE_SCOTCH=ON ' +configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' +configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' + +sanity_check_paths = { + 'files': ['lib/libstrumpack.a'], + 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb new file mode 100644 index 00000000000..4938fb4262b --- /dev/null +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'STRUMPACK' +version = '6.1.0' + +homepage = 'https://fastmath-scidac.llnl.gov/software/strumpack.html' +description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner + for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pghysels/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['219ec7360594172464aafa6ecac1fd161097db6fb9ee35af5c1ca61531f4f5c4'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('ParMETIS', '4.0.3'), + ('SCOTCH', '6.1.0'), +] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release ' +configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' +configopts += '-DCMAKE_C_COMPILER=mpiicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpiifort ' +configopts += '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DNO_MODULES=ON ' +configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' +configopts += '-DTPL_SCALAPACK_LIBRARIES="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl" ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_ENABLE_PARMETIS=ON ' +configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' +configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_ENABLE_SCOTCH=ON ' +configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' +configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' + +sanity_check_paths = { + 'files': ['lib/libstrumpack.a'], + 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], +} + +moduleclass = 'numlib' From 56fb50c80846199255be0b8ec23d07f5a2e2eb73 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 14 Dec 2021 21:02:20 +0100 Subject: [PATCH 2308/9987] CHERAB/1.3.0 style corrections --- easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb index a1ad1f6bc92..7d3d731a92e 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -10,7 +10,6 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] @@ -25,6 +24,9 @@ download_dep_fail = True use_pip = True sanity_pip_check = False -sanity_check_commands = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && python -c "import cherab"'] +sanity_check_commands = [ + 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && ' + 'python -c "import cherab"' +] moduleclass = 'phys' From 981670054d1d3e0b22bd4a6e032a4cece2b1c419 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Dec 2021 08:59:37 +0000 Subject: [PATCH 2309/9987] update source location --- .../Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb index c4ee42f5588..e5f08d8c161 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb @@ -10,11 +10,8 @@ description = """The Trilinos Project is an effort to develop algorithms and ena toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'usempi': True, 'pic': True, 'strict': True} -source_urls = [ - 'http://trilinos.csbsju.edu/download/files/', - 'https://trilinos.org/oldsite/download/files/', -] -sources = ['%(namelower)s-%(version)s-Source.tar.gz'] +source_urls = ['https://launchpad.net/ubuntu/+archive/primary/+sourcefiles/trilinos/12.12.1-5/'] +sources = ['%(namelower)s_%(version)s.orig.tar.bz2'] patches = [ ('Trilinos-%(version)s_fix-CEpetra-LAPACK.patch', 'packages/CTrilinos'), 'Trilinos-%(version)s_fix-Py3.patch', @@ -23,7 +20,7 @@ patches = [ 'Trilinos-%(version)s_py3_fixes_and_more.patch', ] checksums = [ - '7c67d83befbeabc773661bcdfee2850c404d249160b755d3f1be2e96f564f9fd', # trilinos-12.12.1-Source.tar.gz + '5d0d84cb794f94927dd4785efe89eacc823b659dbe9f8273ab86e86ed4396db7', # trilinos_12.12.1.orig.tar.bz2 'de2e989bf9e7cbe7cab9126a464b5b1569983de4060956e7a95dccb9e0bad039', # Trilinos-12.12.1_fix-CEpetra-LAPACK.patch '5505645b712056403263860de86efccfb343cb5e5bf8d65697526d65ea5df099', # Trilinos-12.12.1_fix-Py3.patch # Trilinos-12.12.1_muelu-fix-function-signature.patch From 9708169c6a13a364d4cd1d45b9e3976a0a597287 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 21:14:57 +1050 Subject: [PATCH 2310/9987] adding easyconfigs: PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb --- .../PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..d033ab417bb --- /dev/null +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'PhyloPhlAn' +version = '3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/biobakery/phylophlan' +description = """ +PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of +genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method +for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. +""" + +source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['26d150d37159406f678165bf3d6cb06b3021fb2227b301b06095e769c87bdd9f'] + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Biopython', '1.78', versionsuffix), + ('DendroPy', '4.4.0'), + ('matplotlib', '3.2.1', versionsuffix), + ('Seaborn', '0.10.1', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], + 'dirs': ['lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From ee9e93ec0f7195da189dd767b1ae3cbc1f01b97d Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 21:20:51 +1050 Subject: [PATCH 2311/9987] dep <- phylophlan + --- .../MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index d2b2b7fdc2b..a6979c9e19d 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -1,12 +1,6 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# Software License:: MIT -# -# Notes:: -## +# Contribution by +# DeepThought, Flinders University +# R.QIAO easyblock = 'PythonPackage' @@ -33,10 +27,11 @@ dependencies = [ ('CMSeq', '1.0.3', versionsuffix), ('biom-format', '2.1.10', versionsuffix), ('h5py', '2.10.0', versionsuffix), + ('PhyloPhlAn', '3.0', versionsuffix), ] use_pip = True -download_dep_fail = False +download_dep_fail = True sanity_pip_check = True sanity_check_paths = { From fd932e91c9bd80f48d5d9facdf16c5edebac0e77 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Wed, 15 Dec 2021 21:17:26 +1030 Subject: [PATCH 2312/9987] sanity_check_commands + --- .../cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb index bf0b8def215..2843b05ef3c 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -47,6 +47,12 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + 'collapse_isoforms_by_sam.py', + 'get_abundance_post_collapse.py', + 'simple_stats_post_collapse.py', +] + options = {'modulename': 'cupcake'} moduleclass = 'bio' From 875c909dc704c32aaf7a2693b5a99a4efed6e910 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Wed, 15 Dec 2021 21:18:29 +1030 Subject: [PATCH 2313/9987] sanity_check_commands + --- .../c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb index e2904528e42..99bc2687837 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -46,6 +46,12 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + 'collapse_isoforms_by_sam.py', + 'get_abundance_post_collapse.py', + 'simple_stats_post_collapse.py', +] + options = {'modulename': 'cupcake'} moduleclass = 'bio' From 021efa6d7929d7e6aa942fd0b3fbbbf41dc74f7f Mon Sep 17 00:00:00 2001 From: Mustafa Abduljabbar Date: Wed, 15 Dec 2021 11:57:34 +0100 Subject: [PATCH 2314/9987] Update easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb Co-authored-by: Adam Huffman --- easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb index ba0edb4190a..a59fbf59592 100644 --- a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb +++ b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2021-4.eb @@ -1,4 +1,4 @@ -easyblock='PackedBinary' +easyblock = 'PackedBinary' name = 'Schrodinger' version = '2021-4' From 9aa7a0c8ba4daedc84026a672025d52ac45801d2 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 21:55:21 +1050 Subject: [PATCH 2315/9987] adding easyconfigs: PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb --- ...hyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..02454b8e66d --- /dev/null +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,46 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# update to v3.0.2 + +easyblock = 'PythonPackage' + +name = 'PhyloPhlAn' +version = '3.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/biobakery/phylophlan' +description = """ +PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of +genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method +for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. +""" + +source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.4.2'), + ('Seaborn', '0.11.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], + 'dirs': ['lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From 3c5f93660e47c39bd9ac9df51a9e897cdc74fbc7 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 21:57:28 +1050 Subject: [PATCH 2316/9987] checksum + --- .../p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb index 02454b8e66d..964b716cb7b 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb @@ -19,6 +19,7 @@ at multiple levels of resolution. source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] sources = ['%(version)s.tar.gz'] +checksums = ['c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4'] toolchain = {'name': 'foss', 'version': '2021a'} From d3ddd0891363593d49785ae9350a626c50354f61 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 15 Dec 2021 22:16:08 +1050 Subject: [PATCH 2317/9987] style <- versionsuffix drop --- .../PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb new file mode 100644 index 00000000000..7cdf357fcbf --- /dev/null +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb @@ -0,0 +1,46 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# update to v3.0.2 + +easyblock = 'PythonPackage' + +name = 'PhyloPhlAn' +version = '3.0.2' + +homepage = 'https://github.com/biobakery/phylophlan' +description = """ +PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of +genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method +for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. +""" + +source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4'] + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.4.2'), + ('Seaborn', '0.11.2'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], + 'dirs': ['lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From a307cb63188920aa194940e9f926b3563212985d Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Wed, 15 Dec 2021 21:56:25 +1030 Subject: [PATCH 2318/9987] Delete PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb --- ...hyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb deleted file mode 100644 index 964b716cb7b..00000000000 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,47 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO -# update to v3.0.2 - -easyblock = 'PythonPackage' - -name = 'PhyloPhlAn' -version = '3.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/biobakery/phylophlan' -description = """ -PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of -genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method -for large-scale microbial genome characterization and phylogenetic analysis -at multiple levels of resolution. -""" - -source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] -sources = ['%(version)s.tar.gz'] -checksums = ['c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4'] - -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('Biopython', '1.79'), - ('DendroPy', '4.5.2'), - ('matplotlib', '3.4.2'), - ('Seaborn', '0.11.2'), -] - -use_pip = True -download_dep_fail = True - -sanity_pip_check = True -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], - 'dirs': ['lib'], -} -sanity_check_commands = [('%(namelower)s', '-h')] - -options = {'modulename': '%(namelower)s'} - -moduleclass = 'bio' From fe10dadcb3698a78fd9e52236b435c49a7c4d9c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Wed, 15 Dec 2021 12:54:43 +0100 Subject: [PATCH 2319/9987] OpenFace: add missing patchfile --- .../OpenFace-2.2.0-use_FlexiBLAS.patch | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch new file mode 100644 index 00000000000..105de6d5362 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch @@ -0,0 +1,31 @@ +diff -ruN ../../OpenFace-OpenFace_2.2.0/CMakeLists.txt ../../OpenFace-OpenFace_2.2.0-new/CMakeLists.txt +--- ../../OpenFace-OpenFace_2.2.0/CMakeLists.txt 2019-07-13 20:20:17.000000000 +0200 ++++ ../../OpenFace-OpenFace_2.2.0-new/CMakeLists.txt 2021-12-13 23:43:45.160326152 +0100 +@@ -11,22 +11,19 @@ + set(CONFIG_DIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_CONFIG_DIR}") + add_definitions(-DCONFIG_DIR="${CONFIG_DIR}") + +-# make sure we'll use OpenBLAS only: there's a header file naming difference between different +-# implementations; so OpenFace wants OpenBLAS; +-find_package(OpenBLAS REQUIRED) +-if ( ${OpenBLAS_FOUND} ) ++if ( DEFINED ENV{LIBBLAS} ) ++ SET(OpenBLAS_LIB "-L$ENV{BLAS_LIB_DIR} $ENV{LIBBLAS}") + MESSAGE("OpenBLAS information:") + MESSAGE(" OpenBLAS_LIBRARIES: ${OpenBLAS_LIB}") + else() + MESSAGE(FATAL_ERROR "OpenBLAS not found in the system.") + endif() + +-if ( ${OpenBLAS_INCLUDE_FOUND} ) ++if ( DEFINED ENV{BLAS_INC_DIR} ) ++ SET(OpenBLAS_INCLUDE_DIR $ENV{BLAS_INC_DIR}) + MESSAGE(" OpenBLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") + else() +- MESSAGE(WARNING "OpenBLAS include not found in the system. Using the one vended with OpenFace.") +- set(OpenBLAS_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/lib/3rdParty/OpenBLAS/include") +- MESSAGE(" OpenBLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") ++ MESSAGE(FATAL_ERROR "OpenBLAS not found in the system.") + endif() + + find_package( OpenCV 4.0 REQUIRED COMPONENTS core imgproc calib3d highgui objdetect) From 042a094a185038f0766fd0360487df1f02f3689c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 13:49:23 +0100 Subject: [PATCH 2320/9987] use proper Perl dependency for worker 1.6.12 with foss/2019a (fixes installation on RHEL8 OS) --- .../w/worker/worker-1.6.12-foss-2019a.eb | 67 +++---------------- 1 file changed, 11 insertions(+), 56 deletions(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb index af9f61a3831..96c86b0cd39 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2019a.eb @@ -8,80 +8,35 @@ description = """The Worker framework has been developed to help deal with param that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" -toolchain = SYSTEM +local_tcname = 'foss' +local_tcver = '2019a' +toolchain = {'name': local_tcname, 'version': local_tcver} +toolchainopts = {'usempi': True} source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['503ad9db78d949999bd5f3ba15b18f746cad2eaf2ff49240398b2b6792f9ffbd'] -osdependencies = ['perl'] - -local_tcname = 'foss' -local_tcver = '2019a' -builddependencies = [(local_tcname, local_tcver)] -versionsuffix = '-%s-%s' % (local_tcname, local_tcver) - -exts_defaultclass = 'PerlModule' - -exts_list = [ - ('Config::General', '2.63', { - 'source_tmpl': 'Config-General-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], - 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], - }), - ('IO::Stringy', '2.113', { - 'source_tmpl': 'IO-Stringy-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB/'], - 'checksums': ['51220fcaf9f66a639b69d251d7b0757bf4202f4f9debd45bdd341a6aca62fe4e'], - }), - ('Text::CSV', '2.00', { - 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], - 'checksums': ['8ccbd9195805222d995844114d0e595bb24ce188f85284dbf256080311cbb2c2'], - }), - ('DBI', '1.643', { - 'source_tmpl': 'DBI-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], - 'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'], - }), - ('DBD::SQLite', '1.64', { - 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], - 'checksums': ['f4ae8f7b50842305566aadd90f7bfd12a9e32b6c603a9b1c1529e73eb82aff01'], - }), - ('Date::Language', '2.32', { - 'source_tmpl': 'TimeDate-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC/'], - 'checksums': ['34eca099e375e2d142ea6cc935922c4980dc21c65ce7c24823ca08457c4bb3d6'], - }), - ('Template', '3.008', { - 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['52400f68bef6731b0fca00e3438ed835b29ab9fec72a404866dee8fc139da692'], - }), +dependencies = [ + ('Perl', '5.28.1') ] -preconfigopts = "export CC=mpicc && " - -modextrapaths = { - 'PERL5LIB': ['share/perl5', 'lib64/perl5'], -} - # adjust worker configuration file # note: tweak this to your local setup postinstallcmds = [ 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', - 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = %s/g" %%(installdir)s/conf/worker.conf' % local_tcname, 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', + "echo PERL=\\'`which perl`\\' > %(installdir)s/conf/worker_perl.sh", ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['dbilogstrip', 'dbiprof', 'dbiproxy', 'tpage', 'ttree', 'wcat', 'wconvert', - 'wload', 'worker', 'wreduce', 'wresume', 'wsub', 'wsummarize']], - 'dirs': ['lib/perl', 'lib/tt', 'lib64/perl5'], + 'files': ['bin/%s' % x for x in ['wcat', 'wconvert', 'wload', 'worker', 'wreduce', 'wresume', 'wsub', + 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt'], } sanity_check_commands = ["wsub -help"] From 6f5eeaafb1633ce16dd586edd4e583e00986a3a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Wed, 15 Dec 2021 13:56:46 +0100 Subject: [PATCH 2321/9987] OpenFace: use a working sanity check command --- .../o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb | 4 +--- easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb | 4 +--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb index ed5e27cab78..ffd3307a288 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb @@ -46,8 +46,6 @@ sanity_check_paths = { 'files': ['bin/FaceLandmarkVid', 'bin/FaceLandmarkImg', 'bin/FeatureExtraction'], 'dirs': [], } -sanity_check_commands = [ - 'FaceLandmarkVid -f ../samples/changeLighting.wmv -f ../samples/2015-10-15-15-14.avi' -] +sanity_check_commands = ['FeatureExtraction | grep OpenFace'] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb index 3279d8b139f..9f269dc9eb2 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb @@ -43,8 +43,6 @@ sanity_check_paths = { 'files': ['bin/FaceLandmarkVid', 'bin/FaceLandmarkImg', 'bin/FeatureExtraction'], 'dirs': [], } -sanity_check_commands = [ - 'FaceLandmarkVid -f ../samples/changeLighting.wmv -f ../samples/2015-10-15-15-14.avi' -] +sanity_check_commands = ['FeatureExtraction | grep OpenFace'] moduleclass = 'lib' From 3ba6730c27fb628dee16565cc84a3b4a87c24ae5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 14:19:24 +0100 Subject: [PATCH 2322/9987] adding easyconfigs: worker-1.6.12-foss-2021b.eb --- .../w/worker/worker-1.6.12-foss-2021b.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2021b.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2021b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2021b.eb new file mode 100644 index 00000000000..9657cb67905 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.12-foss-2021b.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.12' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +local_tcname = 'foss' +local_tcver = '2021b' +toolchain = {'name': local_tcname, 'version': local_tcver} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['503ad9db78d949999bd5f3ba15b18f746cad2eaf2ff49240398b2b6792f9ffbd'] + +dependencies = [ + ('Perl', '5.34.0') +] + +# need to replace MPI_Type_struct by MPI_Type_create_struct, since MPI_Type_struct was removed in MPI 3.0; +# see also https://github.com/gjbex/worker/pull/45 +preconfigopts = "sed -i 's/MPI_Type_struct/MPI_Type_create_struct/g' src/worker.c && " + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 32/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = %s/g" %%(installdir)s/conf/worker.conf' % local_tcname, + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', + "echo PERL=\\'`which perl`\\' > %(installdir)s/conf/worker_perl.sh", +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['wcat', 'wconvert', 'wload', 'worker', 'wreduce', 'wresume', 'wsub', + 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt'], +} + +sanity_check_commands = ["wsub -help"] + +moduleclass = 'tools' From 49626287a830b24989daa75f6c13d42e98095f8f Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Thu, 16 Dec 2021 00:24:53 +1030 Subject: [PATCH 2323/9987] Update easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb Co-authored-by: Sam Moors --- .../cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb index 2843b05ef3c..b04f48e2a2d 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-24.2.0-foss-2020a-Python-3.8.2.eb @@ -48,9 +48,9 @@ sanity_check_paths = { } sanity_check_commands = [ - 'collapse_isoforms_by_sam.py', - 'get_abundance_post_collapse.py', - 'simple_stats_post_collapse.py', + 'collapse_isoforms_by_sam.py -h', + 'get_abundance_post_collapse.py -h', + 'simple_stats_post_collapse.py -h', ] options = {'modulename': 'cupcake'} From e08fca9f8178cd75e0a3a31e67193ebc0c381bfd Mon Sep 17 00:00:00 2001 From: easybuild Date: Wed, 15 Dec 2021 13:55:47 +0000 Subject: [PATCH 2324/9987] added moduleclass --- easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 12d37d0e06b..4b5db8af46f 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -28,3 +28,5 @@ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['elbencho', 'elbencho-unstripped']], } + +moduleclass = 'tools' From 9d6a99c05dc4470e4bac624d629ebf20ea26826e Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Thu, 16 Dec 2021 00:26:16 +1030 Subject: [PATCH 2325/9987] debug <- sanity_check --- .../c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb index 99bc2687837..e9c3fd9ba0c 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -39,9 +39,9 @@ sanity_check_paths = { # check for particular Cupcake ToFU scripts, # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step 'files': [ - 'bin/collapse_isoforms_by_sam.py', - 'bin/get_abundance_post_collapse.py', - 'bin/simple_stats_post_collapse.py' + 'bin/collapse_isoforms_by_sam.py -h', + 'bin/get_abundance_post_collapse.py -h', + 'bin/simple_stats_post_collapse.py -h' ], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From f1c916d3c8f23f115e75faf587fc894a2c8adec7 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 15 Dec 2021 14:57:38 +0100 Subject: [PATCH 2326/9987] Update style of Raysect v0.7.1 EB files --- .../r/Raysect/Raysect-0.7.1-foss-2020b.eb | 25 +++++++++++++++++++ .../r/Raysect/Raysect-0.7.1-intel-2020b.eb | 3 ++- 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb new file mode 100644 index 00000000000..53e51415d54 --- /dev/null +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-foss-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Raysect' +version = '0.7.1' + +homepage = 'https://raysect.org' + +description = """Raysect is an OOP ray-tracing framework for Python""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c91f7dc406fd64dfaa4096b259c31250ac50881a301a46b2a1d607a2746f968'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb index d506edd8c8c..0d104c5782b 100644 --- a/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb +++ b/easybuild/easyconfigs/r/Raysect/Raysect-0.7.1-intel-2020b.eb @@ -9,7 +9,6 @@ description = """Raysect is an OOP ray-tracing framework for Python""" toolchain = {'name': 'intel', 'version': '2020b'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['5c91f7dc406fd64dfaa4096b259c31250ac50881a301a46b2a1d607a2746f968'] @@ -20,5 +19,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True +sanity_pip_check = True moduleclass = 'vis' From c15e2c01775ec14bd2e7c7a73cd3b3908f7254b9 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Thu, 16 Dec 2021 00:28:22 +1030 Subject: [PATCH 2327/9987] Update cDNA_Cupcake-26.0.0-foss-2021a.eb --- .../c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb index e9c3fd9ba0c..f088e26620f 100644 --- a/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cDNA_Cupcake/cDNA_Cupcake-26.0.0-foss-2021a.eb @@ -39,17 +39,17 @@ sanity_check_paths = { # check for particular Cupcake ToFU scripts, # https://github.com/Magdoll/cDNA_Cupcake/wiki/Cupcake-ToFU:-supporting-scripts-for-Iso-Seq-after-clustering-step 'files': [ - 'bin/collapse_isoforms_by_sam.py -h', - 'bin/get_abundance_post_collapse.py -h', - 'bin/simple_stats_post_collapse.py -h' + 'bin/collapse_isoforms_by_sam.py', + 'bin/get_abundance_post_collapse.py', + 'bin/simple_stats_post_collapse.py' ], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ - 'collapse_isoforms_by_sam.py', - 'get_abundance_post_collapse.py', - 'simple_stats_post_collapse.py', + 'collapse_isoforms_by_sam.py -h', + 'get_abundance_post_collapse.py -h', + 'simple_stats_post_collapse.py -h', ] options = {'modulename': 'cupcake'} From 0917f4ae0bdbfc12e01cd1bd7e96e836b8f4e38c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 15 Dec 2021 15:05:43 +0100 Subject: [PATCH 2328/9987] ParMETIS v4.0.3 for iimpi/2020b --- .../p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb new file mode 100644 index 00000000000..8cc997b5624 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020b.eb @@ -0,0 +1,25 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.18.4')] + +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' From b4acc3452ea84c11d76645410c3e053f3725ac1e Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 15 Dec 2021 15:55:48 +0100 Subject: [PATCH 2329/9987] adding easyconfigs: phonopy-2.12.0-foss-2020b.eb --- .../p/phonopy/phonopy-2.12.0-foss-2020b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb new file mode 100644 index 00000000000..3a1f3d0bc3b --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.12.0-foss-2020b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '2.12.0' + +homepage = 'https://atztogo.github.io/phonopy/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ff65065f418ccbff9fbc1186b9a65581e83b42789aa4a656f45badfff9bd3f61'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for numpy + ('matplotlib', '3.3.3'), + ('PyYAML', '5.3.1'), + ('h5py', '3.1.0'), + ('spglib-python', '1.16.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["phonopy --help"] + +sanity_pip_check = True + +moduleclass = 'lib' From 58273fa594087e103e5184c7ca16772bfa1868f1 Mon Sep 17 00:00:00 2001 From: smoretti Date: Wed, 15 Dec 2021 15:28:17 +0100 Subject: [PATCH 2330/9987] Add an exception in the test suite for multiple Rgurobi versions in the same toolchain --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index bb0cdb9507a..55604601ca5 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -331,8 +331,8 @@ def check_dep_vars(self, gen, dep, dep_vars): dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0]) # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools; - # same goes for WRF and WPS - for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS')]: + # same goes for WRF and WPS; Gurobi and Rgurobi + for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS'), ('Gurobi', 'Rgurobi')]: if dep == dep_name and len(dep_vars) > 1: for key in list(dep_vars): ecs = dep_vars[key] From 0c28cfb57d9f25f537d9bd59e70eded8b4033742 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 15 Dec 2021 16:16:29 +0100 Subject: [PATCH 2331/9987] adding easyconfigs: MATLAB-2021b.eb --- .../easyconfigs/m/MATLAB/MATLAB-2021b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2021b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2021b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2021b.eb new file mode 100644 index 00000000000..1f98eb7c6df --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2021b.eb @@ -0,0 +1,27 @@ +name = 'MATLAB' +version = '2021b' + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +sources = ['R%(version)s_Linux.iso'] +checksums = ['d8e75bda06b45edf2c68cda6761fac077b7bfa7b7779db0c95e098b5c695f4cc'] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server = 'my-license-server' +# license_server_port = '1234' + +moduleclass = 'math' From 04358083e7ad2b66aff2bd7bc4604291127ddb20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 16:16:37 +0100 Subject: [PATCH 2332/9987] adding easyconfigs: dill-0.3.4-GCCcore-11.2.0.eb --- .../d/dill/dill-0.3.4-GCCcore-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d6147e812d7 --- /dev/null +++ b/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'dill' +version = '0.3.4' + +homepage = 'https://pypi.org/project/dill/' +description = """dill extends python's pickle module for serializing and de-serializing python objects to the majority + of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse + of which is converting a byte stream back to on python object hierarchy.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_ZIP] +checksums = ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From ac5f9a7a6902d21fec40aea7d79bdec28dcf9eb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:00:56 +0100 Subject: [PATCH 2333/9987] {*}[foss/2021b] leidenalg v0.8.8, python-igraph v0.9.8, arpack-ng v3.8.0, PyCairo v1.20.1 (+ deps) w/ Python 3.9.6 --- .../a/arpack-ng/arpack-ng-3.8.0-foss-2021b.eb | 35 ++++++++++++ .../e/Eigen/Eigen-3.4.0-GCCcore-11.2.0.eb | 21 ++++++++ .../i/igraph/igraph-0.9.5-foss-2021b.eb | 51 ++++++++++++++++++ .../l/leidenalg/leidenalg-0.8.8-foss-2021b.eb | 53 +++++++++++++++++++ .../PyCairo/PyCairo-1.20.1-GCCcore-11.2.0.eb | 44 +++++++++++++++ .../python-igraph-0.9.8-foss-2021b.eb | 53 +++++++++++++++++++ 6 files changed, 257 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.9.5-foss-2021b.eb create mode 100644 easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.8-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021b.eb new file mode 100644 index 00000000000..ba40c98ecc2 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2021b.eb @@ -0,0 +1,35 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.8.0' + +homepage = 'https://github.com/opencollab/arpack-ng' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'opencollab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['ada5aeb3878874383307239c9235b716a8a170c6d096a6625bfd529844df003d'] + +builddependencies = [ + ('Autotools', '20210726'), + ('pkgconf', '1.8.0'), + ('Eigen', '3.4.0') +] + +preconfigopts = "sh bootstrap && " +configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ['lib64/libarpack.la', 'lib64/libarpack.%s' % SHLIB_EXT, + 'lib64/libparpack.la', 'lib64/libparpack.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..29a8b27adc6 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.2.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.4.0' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.37'), # to make CMake compiler health check pass on old systems + ('CMake', '3.21.1'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.9.5-foss-2021b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.9.5-foss-2021b.eb new file mode 100644 index 00000000000..004d9503d9c --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.9.5-foss-2021b.eb @@ -0,0 +1,51 @@ +# Author: Denis Krišťák (INUITS) +# Modified: Jasper Grimm (UoY) + +easyblock = 'CMakeMake' + +name = 'igraph' +version = '0.9.5' + +homepage = 'https://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['c4e3f67892e1e287865d799162406b3f94916ad6f2cc069a9239e36ca495a17a'] + +builddependencies = [ + ('Autotools', '20210726'), + ('pkgconf', '1.8.0'), + ('CMake', '3.21.1'), +] + +dependencies = [ + ('GLPK', '5.0'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('arpack-ng', '3.8.0'), +] + +# Build static and shared libraries +configopts = ["-DBUILD_SHARED_LIBS=OFF", "-DBUILD_SHARED_LIBS=ON"] + +# extra folder `igraph` is wrong, since all other software expects it to be in ./include folder directly +postinstallcmds = [ + 'mv %(installdir)s/include/igraph/* %(installdir)s/include/ && rmdir %(installdir)s/include/igraph ', +] + +_includes = ['include/igraph%s.h' % x for x in ['', '_blas', '_constants', '_lapack', '_types', '_version']] +_libs = ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]] + +sanity_check_paths = { + 'files': _includes + _libs, + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.8-foss-2021b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.8-foss-2021b.eb new file mode 100644 index 00000000000..ee2a8af4bb9 --- /dev/null +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.8-foss-2021b.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'leidenalg' +version = '0.8.8' + +homepage = 'https://github.com/vtraag/leidenalg' +description = """Implementation of the Leiden algorithm for various quality +functions to be used with igraph in Python.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('PyYAML', '5.4.1'), + ('Bison', '3.7.6'), + ('libtool', '2.4.6'), + ('flex', '2.6.4'), + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('igraph', '0.9.5'), + ('python-igraph', '0.9.8'), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = "python setup.py build --use-pkg-config && " +# 'python-igraph' dependency was renamed to 'igraph' +local_preinstallopts += "sed -i 's/python-igraph >=/igraph >=/g' setup.py && " + +exts_list = [ + ('ddt', '1.4.4', { + 'checksums': ['8de39a69730442dc835e4d33f9d2e33043ff91151c8d18086959ee556febb9f8'], + }), + (name, version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['12750f66d1f0c84ed4484fa895a9d5a163e2f4b611edb12ad09cc66120654df3'], + }), +] + +sanity_check_commands = [ + # tests require that 'leidenalg' Python module is available, + # so needs to be run after installation + "cd %(builddir)s/leidenalg/leidenalg-%(version)s && python setup.py test --use-pkg-config", + "python -c 'import leidenalg; import igraph as ig; " + "leidenalg.find_partition(ig.Graph.Erdos_Renyi(100, 0.1), " + "leidenalg.ModularityVertexPartition)'", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d1fb5b548db --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.20.1-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'PyCairo' +version = '1.20.1' + +homepage = 'https://pycairo.readthedocs.io/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1ee72b035b21a475e1ed648e26541b04e5d7e753d75ca79de8c583b25785531b'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('cairo', '1.16.0'), +] + +# PyGTK needs PyCairo installed by pip +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# remove pyproject.toml, which causes trouble (header files and .pc file are not installed) +preinstallopts = "rm pyproject.toml && " + +# Don't build a wheel or the pkg-cfg file won't be installed +installopts = '--no-binary=%(namelower)s' + +sanity_check_paths = { + 'files': ['%s/py3cairo.%s' % (p, e) for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')]], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +options = {'modulename': 'cairo'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb new file mode 100644 index 00000000000..f16f7fbcc66 --- /dev/null +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'python-igraph' +version = '0.9.8' + +homepage = 'https://igraph.org/python' +description = """Python interface to the igraph high performance graph library, primarily aimed at complex network + research and analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('igraph', '0.9.5'), + ('PyCairo', '1.20.1'), + ('Clang', '12.0.1'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), +] + +use_pip = True + +exts_list = [ + ('texttable', '1.6.4', { + 'checksums': ['42ee7b9e15f7b225747c3fa08f43c5d6c83bc899f80ff9bae9319334824076e9'], + }), + ('igraph', version, { + 'installopts': '--install-option="--use-pkg-config"', + 'modulename': 'igraph', + 'patches': ['python-igraph-0.9.0_fix-igraph-libs.patch'], + 'checksums': [ + 'e7bad9f5f52e6dc3ccdaa3d02d8ec433d9ada704f7a83168915cfa0c4c226730', # igraph-0.9.8.tar.gz + # python-igraph-0.9.0_fix-igraph-libs.patch + '7af7a6e6a8b982ced7cdd939d82a98829512088744bebad34c714a3c4803f126', + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/igraph'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# cairo must be available for proper plotting support +sanity_check_commands = ["python -c 'from igraph.drawing.utils import find_cairo; cairo = find_cairo(); cairo.Context'"] + +sanity_pip_check = True + +moduleclass = 'lib' From 5311bcf4ce3ab47d652817b1815ba18986d6665c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:10:02 +0100 Subject: [PATCH 2334/9987] add custom sanity check command for Rgurobi --- .../easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb | 2 ++ .../easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb index db19965911d..49cccf32791 100644 --- a/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.1.2-foss-2021a-R-4.1.0.eb @@ -38,4 +38,6 @@ sanity_check_paths = { 'dirs': ['gurobi'], } +sanity_check_commands = ["echo 'library(gurobi)' | R -q --no-save"] + moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb index c66061a04a9..d21fd11e0be 100644 --- a/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/Rgurobi/Rgurobi-9.5.0-foss-2021a-R-4.1.0.eb @@ -38,4 +38,6 @@ sanity_check_paths = { 'dirs': ['gurobi'], } +sanity_check_commands = ["echo 'library(gurobi)' | R -q --no-save"] + moduleclass = 'math' From a4ba6c87daea2d9f17d2524d171fbc34cc3f25b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:13:21 +0100 Subject: [PATCH 2335/9987] adding easyconfigs: h5py-3.6.0-foss-2021b.eb, h5py-3.6.0-intel-2021b.eb --- .../h/h5py/h5py-3.6.0-foss-2021b.eb | 34 +++++++++++++++++++ .../h/h5py/h5py-3.6.0-intel-2021b.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.6.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.6.0-intel-2021b.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.6.0-foss-2021b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.6.0-foss-2021b.eb new file mode 100644 index 00000000000..0240e4f1dd4 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.6.0-foss-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.6.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['8752d2814a92aba4e2b2a5922d2782d0029102d99caaf3c201a566bc0b40db29'] + +builddependencies = [('pkgconfig', '1.5.5', '-python')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('HDF5', '1.12.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.6.0-intel-2021b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.6.0-intel-2021b.eb new file mode 100644 index 00000000000..067d8089229 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.6.0-intel-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.6.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['8752d2814a92aba4e2b2a5922d2782d0029102d99caaf3c201a566bc0b40db29'] + +builddependencies = [('pkgconfig', '1.5.5', '-python')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('HDF5', '1.12.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' From 4c50e66f57759373316d546d6aaf25b21e505d53 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:17:24 +0100 Subject: [PATCH 2336/9987] adding easyconfigs: statsmodels-0.13.1-foss-2021b.eb, statsmodels-0.13.1-intel-2021b.eb --- .../statsmodels-0.13.1-foss-2021b.eb | 29 +++++++++++++++++++ .../statsmodels-0.13.1-intel-2021b.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-intel-2021b.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2021b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2021b.eb new file mode 100644 index 00000000000..1ff812f4807 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2021b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.13.1' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + (name, version, { + 'checksums': ['006ec8d896d238873af8178d5475203844f2c391194ed8d42ddac37f5ff77a69'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-intel-2021b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-intel-2021b.eb new file mode 100644 index 00000000000..3ccebf046b6 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-intel-2021b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.13.1' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + (name, version, { + 'checksums': ['006ec8d896d238873af8178d5475203844f2c391194ed8d42ddac37f5ff77a69'], + }), +] + +moduleclass = 'math' From 2a668e70a2347d4f621d811f4814b8f11bf86646 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:54:15 +0100 Subject: [PATCH 2337/9987] adding easyconfigs: scanpy-1.8.2-foss-2021b.eb --- .../s/scanpy/scanpy-1.8.2-foss-2021b.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.8.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.8.2-foss-2021b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.2-foss-2021b.eb new file mode 100644 index 00000000000..278254f6aa8 --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.8.2-foss-2021b.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.8.2' + +homepage = 'https://scanpy.readthedocs.io/en/stable/' +description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), + ('networkx', '2.6.3'), + ('numba', '0.54.1'), + ('PyTables', '3.6.1'), + ('statsmodels', '0.13.1'), + ('scikit-learn', '1.0.1'), + ('Seaborn', '0.11.2'), + ('tqdm', '4.62.3'), + ('leidenalg', '0.8.8'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.0.2', { + 'checksums': ['feb87e0ce1dc1f8f3f21e18a85216c790e746d76a5ff6889563394605f504a2b'], + }), + # anndata 0.7.8 needs xlrd<2.0 + ('xlrd', '1.2.0', { + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('anndata', '0.7.8', { + 'checksums': ['1efd7eb40839e0325bb066238280228a980d7dde6410793dbff2835f44a2d3ef'], + }), + ('pynndescent', '0.5.5', { + 'checksums': ['7a7df8412b19cfb3596060faf5a8c5d0bf5b3bd504f8efd900fc4e3918c6f882'], + }), + ('umap-learn', '0.5.2', { + 'modulename': 'umap', + 'checksums': ['0ede8921c3ef0e1976cdc91b533b2bce82471c87dbb9fad447f617ca5b881d52'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.4', { + 'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'], + }), + (name, version, { + 'checksums': ['0c0baa6f08cec50b89b512cef3bfc7f612b215ce02c0fb49cc01c2acfbb2e9bb'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "natsort --help", + "scanpy --help", +] + +moduleclass = 'bio' From 193a9efdbbebc42eebf7015a9cdb2dd38bbf8100 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 15 Dec 2021 17:02:15 +0000 Subject: [PATCH 2338/9987] adding easyconfigs: annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb --- ...var-20191024-GCCcore-11.2.0-Perl-5.34.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb diff --git a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb b/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb new file mode 100644 index 00000000000..91bdfccb8ef --- /dev/null +++ b/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb @@ -0,0 +1,42 @@ +# Toolchain updated to GCCcore-11.2 +# Downloaded tarball has same checksum as the one from 20191024 +# J. Sassmannshausen /NHS/GSTT + +easyblock = 'Tarball' + +name = 'annovar' +# Unconventional version is taken from the upstream site +# https://doc-openbio.readthedocs.io/projects/annovar/en/latest/user-guide/download/ +version = '20191024' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://annovar.openbioinformatics.org/en/latest/' +description = """ANNOVAR is an efficient software tool to utilize update-to-date information +to functionally annotate genetic variants detected from diverse genomes (including human +genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +# Registration required for download +# http://download.openbioinformatics.org/annovar_download_form.php +# rename after download to %(name)s-%(version)s.tar.gz +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] + +dependencies = [('Perl', '5.34.0')] + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"], + 'dirs': ["example", "humandb"], +} + +sanity_check_commands = [ + 'annotate_variation.pl --help 2>&1 | grep "Arguments to control input and output"', + 'retrieve_seq_from_fasta.pl --help 2>&1 | grep "reformat sequences at specific genomic positions"', +] + +moduleclass = 'bio' From 3b9d67b3cfce7cbe5521488a21cde43f4686d220 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 18:02:51 +0100 Subject: [PATCH 2339/9987] include output of failing code style check in message produced by failing easyconfigs style test --- test/easyconfigs/styletests.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index ec27d234b46..91f39820898 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -29,9 +29,10 @@ """ import glob -from unittest import TestCase, TestLoader, main, skipIf +from unittest import TestLoader, main, skipIf from easybuild.base import fancylogger +from easybuild.base.testing import TestCase from easybuild.framework.easyconfig.tools import get_paths_for from easybuild.framework.easyconfig.style import check_easyconfigs_style @@ -52,9 +53,19 @@ def test_style_conformance(self): specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) specs = sorted(specs) + self.mock_stderr(True) + self.mock_stdout(True) result = check_easyconfigs_style(specs) + stderr, stdout = self.get_stderr(), self.get_stdout() + self.mock_stderr(False) + self.mock_stdout(False) - self.assertEqual(result, 0, "Found code style errors (and/or warnings): %s" % result) + error_msg = '\n'.join([ + "There shouldn't be any code style errors (and/or warnings), found %d:" % result, + stdout, + stderr, + ]) + self.assertEqual(result, 0, error_msg) def suite(loader=None): From b7b67a23ecae88e4b435d5cd91268eead04c922c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Dec 2021 17:19:22 +0100 Subject: [PATCH 2340/9987] {lang}[foss/2021b] numba v0.54.1 w/ Python 3.9.6 (on top of LLVM 12.0.1) --- .../n/numba/llvmlite-0.37.0_fix-LLVM-12.patch | 95 +++++++ .../n/numba/numba-0.54.1-foss-2021b.eb | 58 ++++ .../n/numba/numba-0.54.1_fix-numpy-1.21.patch | 251 ++++++++++++++++++ 3 files changed, 404 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.37.0_fix-LLVM-12.patch create mode 100644 easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.54.1_fix-numpy-1.21.patch diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.37.0_fix-LLVM-12.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.37.0_fix-LLVM-12.patch new file mode 100644 index 00000000000..444d8c6fc42 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.37.0_fix-LLVM-12.patch @@ -0,0 +1,95 @@ +see https://github.com/numba/llvmlite/issues/688 + +changes from https://github.com/numba/llvmlite/pull/802 backported to llvmlite 0.37.0 + +From 1d928ebcd59b23b5050234a2bf71f9be7f5f6bd1 Mon Sep 17 00:00:00 2001 +From: Richard Barnes +Date: Wed, 1 Dec 2021 10:29:08 -0700 +Subject: [PATCH] Enable LLVM-12 and LLVM-13 + +--- + ffi/build.py | 5 ++--- + ffi/targets.cpp | 2 ++ + llvmlite/tests/test_binding.py | 19 ++++++++++++++++--- + 3 files changed, 20 insertions(+), 6 deletions(-) + +diff --git a/ffi/build.py b/ffi/build.py +index 6408bf5f..95e33c64 100755 +--- a/ffi/build.py ++++ b/ffi/build.py +@@ -162,9 +162,8 @@ def main_posix(kind, library_ext): + print(msg) + print(warning + '\n') + else: +- +- if not out.startswith('11'): +- msg = ("Building llvmlite requires LLVM 11.x.x, got " ++ if not (out.startswith('11') or out.startswith('12') or out.startswith('13')): ++ msg = ("Building llvmlite requires LLVM 11-13.x.x, got " + "{!r}. Be sure to set LLVM_CONFIG to the right executable " + "path.\nRead the documentation at " + "http://llvmlite.pydata.org/ for more information about " + +--- llvmlite-0.37.0/ffi/targets.cpp.orig 2021-12-15 16:43:02.794869270 +0100 ++++ llvmlite-0.37.0/ffi/targets.cpp 2021-12-15 16:43:26.665056528 +0100 +@@ -232,7 +232,9 @@ + rm = Reloc::DynamicNoPIC; + + TargetOptions opt; ++#if LLVM_VERSION_MAJOR < 12 + opt.PrintMachineCode = PrintMC; ++#endif + + bool jit = JIT; + +diff --git a/llvmlite/tests/test_binding.py b/llvmlite/tests/test_binding.py +index 80495787..fee2372a 100644 +--- a/llvmlite/tests/test_binding.py ++++ b/llvmlite/tests/test_binding.py +@@ -18,6 +18,16 @@ + from llvmlite.tests import TestCase + + ++def clean_string_whitespace(x: str) -> str: ++ # Remove trailing whitespace from the end of each line ++ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE) ++ # Remove intermediate blank lines ++ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE) ++ # Remove extraneous whitespace from the beginning and end of the string ++ x = x.strip() ++ return x ++ ++ + # arvm7l needs extra ABI symbols to link successfully + if platform.machine() == 'armv7l': + llvm.load_library_permanently('libgcc_s.so.1') +@@ -158,7 +168,7 @@ def no_de_locale(): + target triple = "unknown-unknown-unknown" + target datalayout = "" + +-define i32 @"foo"() ++define i32 @"foo"() + { + "<>!*''#": + ret i32 12345 +@@ -424,7 +434,10 @@ def test_nonalphanum_block_name(self): + bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#")) + bd.ret(ir.Constant(ir.IntType(32), 12345)) + asm = str(mod) +- self.assertEqual(asm, asm_nonalphanum_blocklabel) ++ self.assertEqual( ++ clean_string_whitespace(asm), ++ clean_string_whitespace(asm_nonalphanum_blocklabel) ++ ) + + def test_global_context(self): + gcontext1 = llvm.context.get_global_context() +@@ -509,7 +522,7 @@ def test_set_option(self): + def test_version(self): + major, minor, patch = llvm.llvm_version_info + # one of these can be valid +- valid = [(11,)] ++ valid = [(11,), (12,), (13,)] + self.assertIn((major,), valid) + self.assertIn(patch, range(10)) + diff --git a/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b.eb b/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b.eb new file mode 100644 index 00000000000..4a12631542f --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b.eb @@ -0,0 +1,58 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.54.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('LLVM', '12.0.1'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + +exts_list = [ + ('llvmlite', '0.37.0', { + 'patches': ['llvmlite-0.37.0_fix-LLVM-12.patch'], + 'preinstallopts': local_llvmlite_preinstallopts, + 'checksums': [ + '6392b870cd018ec0c645d6bbb918d6aa0eeca8c62674baaee30862d6b6865b15', # llvmlite-0.37.0.tar.gz + 'bcdc530cfd087e8a9f68a73a80fe73f12c7b2adfdb51ded70cd2f4c404846298', # llvmlite-0.37.0_fix-LLVM-12.patch + ], + }), + (name, version, { + 'patches': ['numba-0.54.1_fix-numpy-1.21.patch'], + 'checksums': [ + 'f9dfc803c864edcc2381219b800abf366793400aea55e26d4d5b7d953e14f43f', # numba-0.54.1.tar.gz + 'f038e7adf0cd60f6bdde219b326aad4224fef46515799578ebbbdffa73224199', # numba-0.54.1_fix-numpy-1.21.patch + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -m llvmlite.tests", + "numba --help", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numba/numba-0.54.1_fix-numpy-1.21.patch b/easybuild/easyconfigs/n/numba/numba-0.54.1_fix-numpy-1.21.patch new file mode 100644 index 00000000000..f15a14ee48e --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.54.1_fix-numpy-1.21.patch @@ -0,0 +1,251 @@ +fix compatibility with numpy 1.21 +extracted from https://github.com/numba/numba/pull/7483 + +--- numba-0.54.1/setup.py.orig 2021-12-15 15:49:05.785690139 +0100 ++++ numba-0.54.1/setup.py 2021-12-15 15:49:09.255689514 +0100 +@@ -23,7 +23,7 @@ + max_python_version = "3.10" # exclusive + min_numpy_build_version = "1.11" + min_numpy_run_version = "1.17" +-max_numpy_run_version = "1.21" ++max_numpy_run_version = "1.22" + min_llvmlite_version = "0.37.0rc1" + max_llvmlite_version = "0.38" + +--- numba-0.54.1/numba/__init__.py.orig 2021-10-08 19:12:54.197672600 +0200 ++++ numba-0.54.1/numba/__init__.py 2021-12-15 15:57:05.995560177 +0100 +@@ -134,8 +134,8 @@ + + if numpy_version < (1, 17): + raise ImportError("Numba needs NumPy 1.17 or greater") +- elif numpy_version > (1, 20): +- raise ImportError("Numba needs NumPy 1.20 or less") ++ elif numpy_version > (1, 21): ++ raise ImportError("Numba needs NumPy 1.21 or less") + + try: + import scipy + + +From cff3dd6f92286fd8621a902d6595b65208e90013 Mon Sep 17 00:00:00 2001 +From: Sebastian Berg +Date: Thu, 30 Sep 2021 14:27:01 -0500 +Subject: [PATCH 6/8] BUG: Support the fastcall mechanism for NumPy's ufunc + methods + +This is a start to support NumPy 1.21 use of FASTCALL methods +in ufuncs. There are probably better ways to achieve this support. + +NumPy further uses `tp_vectorcall_offset` on newer versions. This +PR does not add support for this (meaning that a DUfunc will be +unnecessarily slow on NumPy >=1.21 when kwargs are used). +--- + numba/np/ufunc/_internal.c | 99 +++++++++++++++++++++++++++++++++++++- + 1 file changed, 97 insertions(+), 2 deletions(-) + +diff --git a/numba/np/ufunc/_internal.c b/numba/np/ufunc/_internal.c +index d3ca1319b6..600014df55 100644 +--- a/numba/np/ufunc/_internal.c ++++ b/numba/np/ufunc/_internal.c +@@ -276,6 +276,7 @@ static PyMemberDef dufunc_members[] = { + */ + + static struct _ufunc_dispatch { ++ /* Note that the following may also hold `_PyCFunctionFastWithKeywords` */ + PyCFunctionWithKeywords ufunc_reduce; + PyCFunctionWithKeywords ufunc_accumulate; + PyCFunctionWithKeywords ufunc_reduceat; +@@ -286,7 +287,7 @@ static struct _ufunc_dispatch { + } ufunc_dispatch; + + static int +-init_ufunc_dispatch(void) ++init_ufunc_dispatch(int *numpy_uses_fastcall) + { + int result = 0; + PyMethodDef * crnt = PyUFunc_Type.tp_methods; +@@ -329,6 +330,16 @@ init_ufunc_dispatch(void) + result = -1; /* Unknown method */ + } + if (result < 0) break; ++ ++ /* Check whether NumPy uses fastcall (ufunc.at never uses it) */ ++ if (!strncmp(crnt_name, "at", 3)) { ++ if (*numpy_uses_fastcall == -1) { ++ *numpy_uses_fastcall = crnt->ml_flags & METH_FASTCALL; ++ } ++ else if (*numpy_uses_fastcall != (crnt->ml_flags & METH_FASTCALL)) { ++ return -1; ++ } ++ } + } + if (result == 0) { + /* Sanity check. */ +@@ -344,6 +355,7 @@ init_ufunc_dispatch(void) + return result; + } + ++ + static PyObject * + dufunc_reduce(PyDUFuncObject * self, PyObject * args, PyObject *kws) + { +@@ -368,6 +380,47 @@ dufunc_outer(PyDUFuncObject * self, PyObject * args, PyObject *kws) + return ufunc_dispatch.ufunc_outer((PyObject*)self->ufunc, args, kws); + } + ++ ++/* ++ * The following are the vectorcall versions of the above, since NumPy ++ * uses the FASTCALL/Vectorcall protocol starting with version 1.21. ++ * The only NumPy versions supporting vectorcall use Python 3.7 or higher. ++ */ ++static PyObject * ++dufunc_reduce_fast(PyDUFuncObject * self, ++ PyObject *const *args, Py_ssize_t len_args, PyObject *kwnames) ++{ ++ return ((_PyCFunctionFastWithKeywords)ufunc_dispatch.ufunc_reduce)( ++ (PyObject*)self->ufunc, args, len_args, kwnames); ++} ++ ++static PyObject * ++dufunc_reduceat_fast(PyDUFuncObject * self, ++ PyObject *const *args, Py_ssize_t len_args, PyObject *kwnames) ++{ ++ return ((_PyCFunctionFastWithKeywords)ufunc_dispatch.ufunc_reduceat)( ++ (PyObject*)self->ufunc, args, len_args, kwnames); ++} ++ ++ ++static PyObject * ++dufunc_accumulate_fast(PyDUFuncObject * self, ++ PyObject *const *args, Py_ssize_t len_args, PyObject *kwnames) ++{ ++ return ((_PyCFunctionFastWithKeywords)ufunc_dispatch.ufunc_accumulate)( ++ (PyObject*)self->ufunc, args, len_args, kwnames); ++} ++ ++ ++static PyObject * ++dufunc_outer_fast(PyDUFuncObject * self, ++ PyObject *const *args, Py_ssize_t len_args, PyObject *kwnames) ++{ ++ return ((_PyCFunctionFastWithKeywords)ufunc_dispatch.ufunc_outer)( ++ (PyObject*)self->ufunc, args, len_args, kwnames); ++} ++ ++ + #if NPY_API_VERSION >= 0x00000008 + static PyObject * + dufunc_at(PyDUFuncObject * self, PyObject * args) +@@ -568,6 +621,41 @@ static struct PyMethodDef dufunc_methods[] = { + {NULL, NULL, 0, NULL} /* sentinel */ + }; + ++ ++/* ++ * If Python is new enough, NumPy may use fastcall. In that case we have to ++ * also use fastcall for simplicity and speed. ++ */ ++static struct PyMethodDef dufunc_methods_fast[] = { ++ {"reduce", ++ (PyCFunction)dufunc_reduce_fast, ++ METH_FASTCALL | METH_KEYWORDS, NULL }, ++ {"accumulate", ++ (PyCFunction)dufunc_accumulate_fast, ++ METH_FASTCALL | METH_KEYWORDS, NULL }, ++ {"reduceat", ++ (PyCFunction)dufunc_reduceat_fast, ++ METH_FASTCALL | METH_KEYWORDS, NULL }, ++ {"outer", ++ (PyCFunction)dufunc_outer_fast, ++ METH_FASTCALL | METH_KEYWORDS, NULL}, ++#if NPY_API_VERSION >= 0x00000008 ++ {"at", ++ (PyCFunction)dufunc_at, ++ METH_VARARGS, NULL}, ++#endif ++ {"_compile_for_args", ++ (PyCFunction)dufunc__compile_for_args, ++ METH_VARARGS | METH_KEYWORDS, ++ "Abstract method: subclasses should overload _compile_for_args() to compile the ufunc at the given arguments' types."}, ++ {"_add_loop", ++ (PyCFunction)dufunc__add_loop, ++ METH_VARARGS, ++ NULL}, ++ {NULL, NULL, 0, NULL} /* sentinel */ ++}; ++ ++ + static PyObject * + dufunc_getfrozen(PyDUFuncObject * self, void * closure) + { +@@ -681,8 +769,15 @@ MOD_INIT(_internal) + return MOD_ERROR_VAL; + + PyDUFunc_Type.tp_new = PyType_GenericNew; +- if (init_ufunc_dispatch() <= 0) ++ ++ int numpy_uses_fastcall = -1; ++ if (init_ufunc_dispatch(&numpy_uses_fastcall) <= 0) + return MOD_ERROR_VAL; ++ ++ if (numpy_uses_fastcall) { ++ PyDUFunc_Type.tp_methods = dufunc_methods_fast; ++ } ++ + if (PyType_Ready(&PyDUFunc_Type) < 0) + return MOD_ERROR_VAL; + Py_INCREF(&PyDUFunc_Type); + +From 4df2640b60804f1462e2f48b72f744005ed6ec9a Mon Sep 17 00:00:00 2001 +From: Stuart Archibald +Date: Fri, 15 Oct 2021 15:23:53 +0100 +Subject: [PATCH 7/8] Add suggested fix for detecting ufunc.at + +As title. +--- + numba/np/ufunc/_internal.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/numba/np/ufunc/_internal.c b/numba/np/ufunc/_internal.c +index 600014df55..d3e19b1cdc 100644 +--- a/numba/np/ufunc/_internal.c ++++ b/numba/np/ufunc/_internal.c +@@ -332,7 +332,7 @@ init_ufunc_dispatch(int *numpy_uses_fastcall) + if (result < 0) break; + + /* Check whether NumPy uses fastcall (ufunc.at never uses it) */ +- if (!strncmp(crnt_name, "at", 3)) { ++ if (strncmp(crnt_name, "at", 3) != 0) { + if (*numpy_uses_fastcall == -1) { + *numpy_uses_fastcall = crnt->ml_flags & METH_FASTCALL; + } + +From 635e05661b5d715bd8a9cb9448bd24930f693c38 Mon Sep 17 00:00:00 2001 +From: Stuart Archibald +Date: Tue, 16 Nov 2021 12:06:11 +0000 +Subject: [PATCH 8/8] Skip NaT input on np.median test for np=1.21. + +As title. See: https://github.com/numpy/numpy/issues/20376 +--- + numba/tests/test_array_reductions.py | 7 +++++-- + 1 file changed, 5 insertions(+), 2 deletions(-) + +diff --git a/numba/tests/test_array_reductions.py b/numba/tests/test_array_reductions.py +index de0d445fe6..a5763a753b 100644 +--- a/numba/tests/test_array_reductions.py ++++ b/numba/tests/test_array_reductions.py +@@ -686,8 +686,11 @@ def _do_check_nptimedelta(self, pyfunc, arr): + np.random.shuffle(arr) + self.assertPreciseEqual(cfunc(arr), pyfunc(arr)) + # Test with a NaT +- arr[arr.size // 2] = 'NaT' +- self.assertPreciseEqual(cfunc(arr), pyfunc(arr)) ++ if numpy_version != (1, 21) and 'median' not in pyfunc.__name__: ++ # There's problems with NaT handling in "median" on at least NumPy ++ # 1.21.{3, 4}. See https://github.com/numpy/numpy/issues/20376 ++ arr[arr.size // 2] = 'NaT' ++ self.assertPreciseEqual(cfunc(arr), pyfunc(arr)) + if 'median' not in pyfunc.__name__: + # Test with (val, NaT)^N (and with the random NaT from above) + # use a loop, there's some weird thing/bug with arr[1::2] = 'NaT' From 53685dc4be68acdc496e4c3dc96308926e719478 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 16 Dec 2021 03:13:07 +0200 Subject: [PATCH 2341/9987] fix checksum of annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb --- ...nnovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb b/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb index 9d250df45b7..67616ff591d 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-8.2.0-Perl-5.28.1.eb @@ -1,23 +1,21 @@ easyblock = 'Tarball' name = 'annovar' -# Unconventional version is taken from the upstream site -# https://doc-openbio.readthedocs.io/projects/annovar/en/latest/user-guide/download/ -version = '20191024' +version = '20191024' # version reported by `annotate_variation.pl -h` versionsuffix = '-Perl-%(perlver)s' homepage = 'http://annovar.openbioinformatics.org/en/latest/' -description = """ANNOVAR is an efficient software tool to utilize update-to-date information -to functionally annotate genetic variants detected from diverse genomes (including human +description = """ANNOVAR is an efficient software tool to utilize update-to-date information +to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} # Registration required for download -# http://download.openbioinformatics.org/annovar_download_form.php +# http://www.openbioinformatics.org/annovar/annovar_download_form.php # rename after download to %(name)s-%(version)s.tar.gz sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] +checksums = ['78a362a3bd771e4ac46b280c6b52f0d8452f32f11e3812f5d7f85797d26ae799'] dependencies = [('Perl', '5.28.1')] @@ -26,12 +24,13 @@ modextrapaths = { } sanity_check_paths = { - 'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"], + 'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl", + "variants_reduction.pl", "table_annovar.pl"], 'dirs': ["example", "humandb"], } sanity_check_commands = [ - 'annotate_variation.pl --help 2>&1 | grep "Arguments to control input and output"', + "annotate_variation.pl --help 2>&1 | grep 'Version: $Date: %s-%s-%s'" % (version[:4], version[4:6], version[6:]), 'retrieve_seq_from_fasta.pl --help 2>&1 | grep "reformat sequences at specific genomic positions"', ] From 281e016d92ca1c16ccc96e7b7744a4499375dddc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 16 Dec 2021 03:16:19 +0200 Subject: [PATCH 2342/9987] fix version of annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb --- ...nnovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb} | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/a/annovar/{annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb => annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb} (64%) diff --git a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb similarity index 64% rename from easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb rename to easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb index 91bdfccb8ef..36f2f721a05 100644 --- a/easybuild/easyconfigs/a/annovar/annovar-20191024-GCCcore-11.2.0-Perl-5.34.0.eb +++ b/easybuild/easyconfigs/a/annovar/annovar-20200607-GCCcore-11.2.0-Perl-5.34.0.eb @@ -1,13 +1,9 @@ -# Toolchain updated to GCCcore-11.2 -# Downloaded tarball has same checksum as the one from 20191024 -# J. Sassmannshausen /NHS/GSTT +# J. Sassmannshausen /NHS/GSTT: toolchain updated to GCCcore-11.2 easyblock = 'Tarball' name = 'annovar' -# Unconventional version is taken from the upstream site -# https://doc-openbio.readthedocs.io/projects/annovar/en/latest/user-guide/download/ -version = '20191024' +version = '20200607' # version reported by `annotate_variation.pl -h` versionsuffix = '-Perl-%(perlver)s' homepage = 'http://annovar.openbioinformatics.org/en/latest/' @@ -18,7 +14,7 @@ genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} # Registration required for download -# http://download.openbioinformatics.org/annovar_download_form.php +# http://www.openbioinformatics.org/annovar/annovar_download_form.php # rename after download to %(name)s-%(version)s.tar.gz sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['4061af3f2cc8f3d4d8187986c3d468a4b6ae145eec1858e85c7cd1059debb8ed'] @@ -30,12 +26,13 @@ modextrapaths = { } sanity_check_paths = { - 'files': ["annotate_variation.pl", "retrieve_seq_from_fasta.pl"], + 'files': ["annotate_variation.pl", "coding_change.pl", "convert2annovar.pl", "retrieve_seq_from_fasta.pl", + "variants_reduction.pl", "table_annovar.pl"], 'dirs': ["example", "humandb"], } sanity_check_commands = [ - 'annotate_variation.pl --help 2>&1 | grep "Arguments to control input and output"', + "annotate_variation.pl --help 2>&1 | grep 'Version: $Date: %s-%s-%s'" % (version[:4], version[4:6], version[6:]), 'retrieve_seq_from_fasta.pl --help 2>&1 | grep "reformat sequences at specific genomic positions"', ] From f52443c9a464ade7b52bebcae1a05cbfb57ed81e Mon Sep 17 00:00:00 2001 From: alexandermichels Date: Wed, 15 Dec 2021 21:31:49 -0500 Subject: [PATCH 2343/9987] adding easyconfigs: CDO-1.9.10-gompi-2019b.eb --- .../c/CDO/CDO-1.9.10-gompi-2019b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb new file mode 100644 index 00000000000..c356f156e66 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.9.10' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2019b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/24638/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cc39c89bbb481d7b3945a06c56a8492047235f46ac363c4f0d980fccdde6677e'] + +dependencies = [ + ('HDF5', '1.10.5'), + ('netCDF', '4.7.1'), + ('YAXT', '0.6.2'), + ('ecCodes', '2.17.0'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES" + +# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && " + +sanity_check_paths = { + 'files': ['bin/cdo'], + 'dirs': [], +} + +moduleclass = 'data' From 939107805138eca044830b931385cf24d7fe26b5 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 15:43:52 +1050 Subject: [PATCH 2344/9987] style <- dep version fix --- .../c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb index 3c93ab37e8c..fd37b7cc2b1 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb @@ -31,7 +31,7 @@ dependencies = [ ('scikit-image', '0.17.1', versionsuffix), ('Biopython', '1.78', versionsuffix), ('bx-python', '0.8.9', versionsuffix), - ('python-parasail', '1.2.3', versionsuffix), + ('python-parasail', '1.2.2', versionsuffix), ('CapnProto', '0.8.0'), ('minimap2', '2.17'), ('Mash', '2.2'), From 2b3ce8302fb2b7b5508a7511ce8e79ff78b6b5b8 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 16:08:16 +1050 Subject: [PATCH 2345/9987] style <- dep version fix --- .../c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb index fd37b7cc2b1..3c93ab37e8c 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb @@ -31,7 +31,7 @@ dependencies = [ ('scikit-image', '0.17.1', versionsuffix), ('Biopython', '1.78', versionsuffix), ('bx-python', '0.8.9', versionsuffix), - ('python-parasail', '1.2.2', versionsuffix), + ('python-parasail', '1.2.3', versionsuffix), ('CapnProto', '0.8.0'), ('minimap2', '2.17'), ('Mash', '2.2'), From 1fd41967ef73d431b9ac80b5e660a78bb311b5d3 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 16:37:51 +1050 Subject: [PATCH 2346/9987] version upgrade <- dep update to new versions --- .../p/parasail/parasail-2.4.3-GCC-10.3.0.eb | 27 ++++++++++++++++ .../python-parasail-1.2.4-foss-2021a.eb | 32 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.3.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..b3298d8ce84 --- /dev/null +++ b/easybuild/easyconfigs/p/parasail/parasail-2.4.3-GCC-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'parasail' +version = '2.4.3' + +homepage = 'https://github.com/jeffdaily/parasail' +description = """parasail is a SIMD C (C99) library containing implementations + of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global + pairwise sequence alignment algorithms. """ + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +# https://github.com/jeffdaily/parasail +github_account = 'jeffdaily' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6f0cddcaaf7c00573e62a3b081a09380cb022b2ed6a3a138108f8823775ca026'] + +builddependencies = [('CMake', '3.20.1')] + +sanity_check_paths = { + 'files': ['bin/parasail_aligner', 'bin/parasail_stats', + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021a.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021a.eb new file mode 100644 index 00000000000..752bd173d53 --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.2.4' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'] + +builddependencies = [ + ('parasail', '2.4.3'), +] +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' From d634b25c0ca6068a80bcc992a02953c620693f0c Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 16:40:34 +1050 Subject: [PATCH 2347/9987] version upgrade <- toolchain version upgrade to foss-2021a --- .../c/Cogent/Cogent-8.0.0-foss-2021a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb new file mode 100644 index 00000000000..cc67b275bd1 --- /dev/null +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -0,0 +1,49 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'Cogent' +version = '8.0.0' + +homepage = 'https://github.com/Magdoll/Cogent' +description = """ +Cogent is a tool for reconstructing the coding genome using high-quality +full-length transcriptome sequences. It is designed to be used on Iso-Seq data +and in cases where there is no reference genome or the ref genome is highly +incomplete. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Magdoll/Cogent/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['709bc0e7bf9febabe417ab597e6f7f3b9c369d5a2c1774726bd646ef11fc9154'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('networkx', '2.6.3'), + ('scikit-image', '0.18.3'), + ('Biopython', '1.79'), + ('bx-python', '0.8.11'), + ('python-parasail', '1.2.4'), + ('CapnProto', '0.9.1'), + ('minimap2', '2.20'), + ('Mash', '2.3'), + ('cDNA_Cupcake', '26.0.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/run_mash.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From df5f9d40fbaf89b5f031c2cc359a70c678ec402c Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Thu, 16 Dec 2021 16:22:41 +1030 Subject: [PATCH 2348/9987] Delete Cogent-8.0.0-foss-2020a-Python-3.8.2.eb --- .../Cogent-8.0.0-foss-2020a-Python-3.8.2.eb | 52 ------------------- 1 file changed, 52 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 3c93ab37e8c..00000000000 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,52 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'Cogent' -version = '8.0.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Magdoll/Cogent' -description = """ -Cogent is a tool for reconstructing the coding genome using high-quality -full-length transcriptome sequences. It is designed to be used on Iso-Seq data -and in cases where there is no reference genome or the ref genome is highly -incomplete. -""" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/Magdoll/Cogent/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['709bc0e7bf9febabe417ab597e6f7f3b9c369d5a2c1774726bd646ef11fc9154'] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('matplotlib', '3.2.1', versionsuffix), - ('networkx', '2.4', versionsuffix), - ('scikit-image', '0.17.1', versionsuffix), - ('Biopython', '1.78', versionsuffix), - ('bx-python', '0.8.9', versionsuffix), - ('python-parasail', '1.2.3', versionsuffix), - ('CapnProto', '0.8.0'), - ('minimap2', '2.17'), - ('Mash', '2.2'), - ('cDNA_Cupcake', '24.2.0', versionsuffix), -] - -download_dep_fail = True -use_pip = True - -sanity_pip_check = True -sanity_check_paths = { - 'files': ['bin/run_mash.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -options = {'modulename': 'Cogent'} - -moduleclass = 'bio' From 17fb73ef99df37082d6151b529082d330b48876a Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 17:10:04 +1050 Subject: [PATCH 2349/9987] more sanity checks + --- .../easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index cc67b275bd1..697c1e0ae47 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -42,8 +42,17 @@ use_pip = True sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/run_mash.py'], + 'files': ['bin/%s' % x for x in ['run_mash.py', + 'process_kmer_to_graph.py', + 'reconstruct_contig.py'] + ], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + 'run_mash.py -h', + 'process_kmer_to_graph.py -h', + 'reconstruct_contig.py -h', +] + moduleclass = 'bio' From 27dceec445af42dd2c56a96879092c864d520bc2 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 18:41:28 +1050 Subject: [PATCH 2350/9987] adding easyconfigs: python-pulp-2.5.1-foss-2021a.eb --- .../python-pulp-2.5.1-foss-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb new file mode 100644 index 00000000000..b715a09d17e --- /dev/null +++ b/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb @@ -0,0 +1,35 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'python-pulp' +version = '2.5.1' + +homepage = 'https://github.com/coin-or/pulp' +description = """ +PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and +call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to +solve linear problems. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/pulp'] +sources = ['PuLP-%(version)s.tar.gz'] +checksums = ['27c2a87a98ea0e9a08c7c46e6df47d6d4e753ad9991fea2901892425d89c99a6'] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'pulp'} + +moduleclass = 'tools' From 5cbb63bdea9239d135addfeed5a674fa55dbfd7d Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 18:45:57 +1050 Subject: [PATCH 2351/9987] debug <- pip dep + & module import fix --- easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index 697c1e0ae47..147ae621c04 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -35,6 +35,7 @@ dependencies = [ ('minimap2', '2.20'), ('Mash', '2.3'), ('cDNA_Cupcake', '26.0.0'), + ('python-pulp', '2.5.1'), ] download_dep_fail = True @@ -55,4 +56,6 @@ sanity_check_commands = [ 'reconstruct_contig.py -h', ] +options = {'modulename': 'Cogent'} + moduleclass = 'bio' From 6c79b51952978b9d729bdd31634e3ff19d9030db Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 19:25:03 +1050 Subject: [PATCH 2352/9987] v8.0.0 url fix --- .../easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index 147ae621c04..bca8f6f7144 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -18,9 +18,14 @@ incomplete. toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': True} -source_urls = ['https://github.com/Magdoll/Cogent/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['709bc0e7bf9febabe417ab597e6f7f3b9c369d5a2c1774726bd646ef11fc9154'] +# standard URL for Cogent +# source_urls = ['https://github.com/Magdoll/Cogent/archive/refs/tags'] +# sources = ['v%(version)s.tar.gz'] + +# v8.0.0 bug fix URL +source_urls = ['https://github.com/Magdoll/Cogent/archive'] +sources = ['c44054bf88b94e77f475c3a6907da7609aee60ad.zip'] +checksums = ['90c8a810478d5d7b31441c1b818547e7de0aaf6a02001f36dcb618d3d10e1d48'] dependencies = [ ('Python', '3.9.5'), From 3cce1334d9e0ed4284af35ad3e15e08b7172782c Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Thu, 16 Dec 2021 10:22:06 +0100 Subject: [PATCH 2353/9987] adding easyconfigs: Armadillo-10.7.5-foss-2021a.eb --- .../Armadillo/Armadillo-10.7.5-foss-2021a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-10.7.5-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-10.7.5-foss-2021a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-10.7.5-foss-2021a.eb new file mode 100644 index 00000000000..db49e1ec8f1 --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-10.7.5-foss-2021a.eb @@ -0,0 +1,22 @@ +name = 'Armadillo' +version = "10.7.5" + +homepage = 'http://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['5d0d9fd6b34efcba6a6fceff54c0d2d13fcbe915d7af8a30c5e72cf317d2094f'] + +dependencies = [ + ('Boost', '1.76.0'), + ('arpack-ng', '3.8.0'), +] + +builddependencies = [('CMake', '3.20.1')] + +moduleclass = 'numlib' From 841d0789fac68f0ada394590f91f1e60442f39be Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 21:17:06 +1050 Subject: [PATCH 2354/9987] dep <- optional + --- .../m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..a747217d2f7 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-9.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +builddependencies = [ + ('binutils', '2.34'), +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' From bba7c934a8984bcb6fe1c9a7c2e26d0529269d42 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 16 Dec 2021 10:37:45 +0000 Subject: [PATCH 2355/9987] Improve sanity checks Ensure `sanity_check_paths` checks all copied files Use `mpi_cmd_prefix` template instead of hardcoding `mpirun` in the sanity check Co-authored-by: Alex Domingo --- .../easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb index de135d9fb64..ffb5f8bc711 100644 --- a/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb +++ b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.1.1-foss-2021a.eb @@ -24,15 +24,17 @@ prebuildopts = "sed -i '1d' Makefile && " # -fallow-argument-mismatch needed for GCC 10+ buildopts = '-j 1 LIBS="$LIBBLAS -lsymspg" FFLAGS="$FFLAGS -fallow-argument-mismatch"' -files_to_copy = [([name], 'bin'), 'Test-*', 'LICENSE', 'README.md'] +local_tests = ["Test-%s" % x for x in ['QE', 'RTA', 'VASP']] + +files_to_copy = [([name], 'bin'), (['LICENSE', 'README.md'], 'share')] + local_tests sanity_check_paths = { 'files': ['bin/%(name)s'], - 'dirs': [], + 'dirs': ['share'] + local_tests, } sanity_check_commands = [ - "cd %%(builddir)s/*%%(namelower)s*/Test-%s && mpirun -n %%(parallel)s %%(name)s" % x for x in ['QE', 'RTA', 'VASP'] + "cd %%(builddir)s/*%%(namelower)s*/%s && %%(mpi_cmd_prefix)s %%(name)s" % x for x in local_tests ] moduleclass = 'phys' From 2ed4fdc4d3afb80ae02b0b8016801fb564d79aea Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Dec 2021 11:28:05 +0000 Subject: [PATCH 2356/9987] Name changed to Trim_Galore as suggested --- .../Trim_Galore-0.6.7-GCCcore-10.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/t/{TrimGalore/TrimGalore-0.6.7-GCCcore-10.3.0.eb => Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb} (91%) diff --git a/easybuild/easyconfigs/t/TrimGalore/TrimGalore-0.6.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb similarity index 91% rename from easybuild/easyconfigs/t/TrimGalore/TrimGalore-0.6.7-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb index d994f9fc694..e8daae91b18 100644 --- a/easybuild/easyconfigs/t/TrimGalore/TrimGalore-0.6.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'Tarball' -name = 'TrimGalore' +name = 'Trim_Galore' version = '0.6.7' homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' @@ -13,7 +13,7 @@ methylation positions for RRBS sequence files (for directional, non-directional toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -source_urls = ['https://github.com/FelixKrueger/%(name)s/archive'] +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] sources = ['%(version)s.tar.gz'] checksums = [ '49b4622c9f839f8a7037fa2f7de9ab873e4fb702f29c14b4d7f095abf6738f74', # 0.6.7.tar.gz From 61e172b2f7fe1648f75c61c7e9b83c243f734d45 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 16 Dec 2021 13:45:54 +0200 Subject: [PATCH 2357/9987] adding easyconfigs: genozip-13.0.5-GCCcore-11.2.0.eb --- .../genozip/genozip-13.0.5-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..222b97ad9d2 --- /dev/null +++ b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'genozip' +version = '13.0.5' + + +homepage = 'https://genozip.com' +description = """Genozip is a compressor for genomic files - it compresses FASTQ, SAM/BAM/CRAM, VCF, FASTA and others. Documentation: genozip.com. Support: support@genozip.com""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/divonlan/genozip/archive/refs/tags/'] +sources = ['%(name)s-%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.37') +] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_commands = ['genozip --help'] + +sanity_check_paths = { + 'files': ['bin/genocat', 'bin/genozip', 'bin/genounzip', 'bin/genols'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' \ No newline at end of file From dc3abb935bde93912b597f0d0db3f868d3918d2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Dec 2021 12:54:13 +0100 Subject: [PATCH 2358/9987] add patch for Rust 1.52.2 and 1.54.0 to fix build when using alternate sysroot --- .../r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 6 +++- .../r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb | 6 +++- .../Rust-1.52.1_sysroot-fix-interpreter.patch | 30 +++++++++++++++++++ .../r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb | 6 +++- 4 files changed, 45 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index 2e64f844463..1de0bc61268 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -checksums = ['3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98'] +patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] +checksums = [ + '3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98', # rustc-1.52.1-src.tar.gz + '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb index 11974f2841f..ec7ed7d0232 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -checksums = ['3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98'] +patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] +checksums = [ + '3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98', # rustc-1.52.1-src.tar.gz + '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch +] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch b/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch new file mode 100644 index 00000000000..058dc409569 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch @@ -0,0 +1,30 @@ +Use patchelf to fix interpreter of binaries that are used during Rust bootstrap procedure +when EasyBuild is configured to build in an alternate sysroot + +This fixes problems like due to a clash with the interpreter from the host, and a more recent libc.so.6 that's picked up +from the alternate sysroot: +error: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (required by /tmp/easybuild/build/Rust/1.52.1/GCCcore-10.3.0/rustc-1.52.1-src/build/bootstrap/debug/deps/libproc_macro_error_attr-fbfef320d848b049.so) + +author: Kenneth Hoste (HPC-UGent) + +--- rustc-1.42.0-src/src/bootstrap/bootstrap.py.orig 2020-03-09 22:11:17.000000000 +0000 ++++ rustc-1.42.0-src/src/bootstrap/bootstrap.py 2021-12-16 10:34:25.100100855 +0000 +@@ -446,6 +446,18 @@ + if ostype != "Linux": + return + ++ sysroot = os.getenv("EASYBUILD_SYSROOT") ++ if sysroot and not fname.endswith(".so"): ++ # determine patch to interpreter in host via output produced by 'file -b /bin/bash' ++ file_b_out = subprocess.check_output(['file', '-b', '/bin/bash']).decode('ascii', 'ignore').strip() ++ regex = re.compile('.*, interpreter ([^,]*),.*') ++ res = regex.match(file_b_out) ++ interpreter_path = os.path.join(sysroot, res.group(1).lstrip('/')) ++ if not os.path.exists(interpreter_path): ++ raise Exception("Derived path to interpreter does not exist: %s" % interpreter_path) ++ cmd = ["patchelf", "--set-interpreter", interpreter_path, fname] ++ run(cmd, verbose=True) ++ + if not os.path.exists("/etc/NIXOS"): + return + if os.path.exists("/lib"): diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb index efafcecfca8..5e8146115eb 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -checksums = ['ac8511633e9b5a65ad030a1a2e5bdaa841fdfe3132f2baaa52cc04e71c6c6976'] +patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] +checksums = [ + 'ac8511633e9b5a65ad030a1a2e5bdaa841fdfe3132f2baaa52cc04e71c6c6976', # rustc-1.54.0-src.tar.gz + '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch +] builddependencies = [ ('binutils', '2.37'), From b1724b2fb3b2f22f8f19c76e67210736cfb3b12e Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Dec 2021 12:00:07 +0000 Subject: [PATCH 2359/9987] sed command improved to replace /bin/perl with /usr/bin/env perl --- .../t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb index e8daae91b18..7d49be5c462 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb @@ -25,9 +25,15 @@ dependencies = [ ('FastQC', '0.11.9', '-Java-11', True), ] +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\\ perl|' %(installdir)s/%(namelower)s", + "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s", +] + sanity_check_paths = { - 'files': ['trim_galore'], - 'dirs': [''], + 'files': ["bin/trim_galore"], + 'dirs': [], } modextrapaths = {'PATH': '.'} From e66ddb34eb8d06402e007b6d0313fb4f471e3a96 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 23:30:53 +1050 Subject: [PATCH 2360/9987] dep <- optional + --- .../s/SEPP/SEPP-4.5.0-foss-2021a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb new file mode 100644 index 00000000000..dafbf0502d1 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb @@ -0,0 +1,44 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.5.0 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.5.0' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.9.5'), + ('DendroPy', '4.5.2'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_sepp.py', + 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From aa014e179b0f4cd73cac500cdc12102061530a5a Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Thu, 16 Dec 2021 23:18:10 +1030 Subject: [PATCH 2361/9987] Delete SEPP-4.5.0-foss-2021a.eb --- .../s/SEPP/SEPP-4.5.0-foss-2021a.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb deleted file mode 100644 index dafbf0502d1..00000000000 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb +++ /dev/null @@ -1,44 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# Updated to v4.5.0 by: -# R.QIAO -# DeepThought, Flinders University - -name = 'SEPP' -version = '4.5.0' - -homepage = 'https://github.com/smirarab/sepp' -description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic -placement of short reads into reference alignments and trees.""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -# https://github.com/smirarab/sepp -github_account = 'smirarab' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] - -dependencies = [ - ('Python', '3.9.5'), - ('DendroPy', '4.5.2'), -] - -fix_python_shebang_for = ['bin/*.py'] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -local_bin_files = [ - 'run_sepp.py', - 'run_upp.py', 'split_sequences.py' -] - -sanity_check_paths = { - 'files': ['bin/%s' % f for f in local_bin_files], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] -} - -sanity_check_commands = ["%s --help" % f for f in local_bin_files] - -moduleclass = 'bio' From 273197e32605f1ac8db18d150a9725389618fd45 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 23:40:10 +1050 Subject: [PATCH 2362/9987] dep <- optional + --- .../s/SEPP/SEPP-4.5.0-foss-2021a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb new file mode 100644 index 00000000000..dafbf0502d1 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb @@ -0,0 +1,44 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.5.0 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.5.0' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.9.5'), + ('DendroPy', '4.5.2'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_sepp.py', + 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From 50742049093fe9b30827a1c82b7ee556ac986a01 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Thu, 16 Dec 2021 23:51:26 +1050 Subject: [PATCH 2363/9987] dep <- optional + --- .../s/SEPP/SEPP-4.3.10-foss-2020a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb new file mode 100644 index 00000000000..455f30dabf2 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb @@ -0,0 +1,44 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.3.10 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.3.10' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.8.2'), + ('DendroPy', '4.4.0'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_abundance.py', 'run_sepp.py', 'run_tipp.py', + 'run_tipp_tool.py', 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From cb60a58d5292b94847c9201ff81912b5206560f2 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 00:03:45 +1050 Subject: [PATCH 2364/9987] adding easyconfigs: SEPP-4.5.0-foss-2021b.eb, DendroPy-4.5.2-GCCcore-11.2.0.eb --- .../DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb | 43 ++++++++++++++++++ .../s/SEPP/SEPP-4.5.0-foss-2021b.eb | 44 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f7e6b5f85b2 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.5.2' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["sumtrees.py --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb new file mode 100644 index 00000000000..a531a1e0a72 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb @@ -0,0 +1,44 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.5.1 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.5.0' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.9.6'), + ('DendroPy', '4.5.2'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_sepp.py', + 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From b48f4913dd145fdd6786a43270ecffba4df3ae2c Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 00:09:33 +1050 Subject: [PATCH 2365/9987] dep <- optional + --- .../PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb index d033ab417bb..235d37e2877 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -29,6 +29,15 @@ dependencies = [ ('DendroPy', '4.4.0'), ('matplotlib', '3.2.1', versionsuffix), ('Seaborn', '0.10.1', versionsuffix), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.1.2'), + ('MUSCLE', '3.8.31'), + ('MAFFT', '7.470', '-with-extensions'), + ('SEPP', '4.5.0'), + ('trimAl', '1.4.1'), + ('BLAST+', '2.11.0'), + ('USEARCH', '11.0.667', '-i86linux32'), + ('DIAMOND', '2.0.4'), ] use_pip = True From ac38be6ac8bea48543e0dd5fa76c37ec6121940b Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 00:27:18 +1050 Subject: [PATCH 2366/9987] debug <- dep version style fix --- .../SEPP-4.3.10-foss-2020a-Python-3.8.2.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..ede3aa68bef --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.3.10 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.3.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['24d8d410138563017e6f2f1263d5e34427f5bbddb875b72a036f7c879cef203b'] + +dependencies = [ + ('Python', '3.8.2'), + ('DendroPy', '4.4.0'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_abundance.py', 'run_sepp.py', 'run_tipp.py', + 'run_tipp_tool.py', 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From 92f253a8f975a1b58106f9637c04310e6d7bc0b6 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Fri, 17 Dec 2021 00:09:09 +1030 Subject: [PATCH 2367/9987] Delete SEPP-4.3.10-foss-2020a.eb --- .../s/SEPP/SEPP-4.3.10-foss-2020a.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb deleted file mode 100644 index 455f30dabf2..00000000000 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.3.10-foss-2020a.eb +++ /dev/null @@ -1,44 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# Updated to v4.3.10 by: -# R.QIAO -# DeepThought, Flinders University - -name = 'SEPP' -version = '4.3.10' - -homepage = 'https://github.com/smirarab/sepp' -description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic -placement of short reads into reference alignments and trees.""" - -toolchain = {'name': 'foss', 'version': '2020a'} - -# https://github.com/smirarab/sepp -github_account = 'smirarab' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%(version)s.tar.gz'] - -dependencies = [ - ('Python', '3.8.2'), - ('DendroPy', '4.4.0'), -] - -fix_python_shebang_for = ['bin/*.py'] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -local_bin_files = [ - 'run_abundance.py', 'run_sepp.py', 'run_tipp.py', - 'run_tipp_tool.py', 'run_upp.py', 'split_sequences.py' -] - -sanity_check_paths = { - 'files': ['bin/%s' % f for f in local_bin_files], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] -} - -sanity_check_commands = ["%s --help" % f for f in local_bin_files] - -moduleclass = 'bio' From fbfcb4f4f5b2e7ab0116b343fbd7c10e26033ebe Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 00:35:10 +1050 Subject: [PATCH 2368/9987] debug <- dep version style fix --- easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb index dafbf0502d1..760c7acd3f1 100644 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021a.eb @@ -17,6 +17,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'smirarab' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] +checksums = ['b464b5f3e51c2c52e85f6fe51cba80746199472f117a88a80213bc457f867455'] dependencies = [ ('Python', '3.9.5'), From 135279b3bd30cf0e2a8e8ee7f56d7833a76b43c2 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Fri, 17 Dec 2021 00:17:53 +1030 Subject: [PATCH 2369/9987] Delete SEPP-4.5.0-foss-2021b.eb --- .../s/SEPP/SEPP-4.5.0-foss-2021b.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb deleted file mode 100644 index a531a1e0a72..00000000000 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.0-foss-2021b.eb +++ /dev/null @@ -1,44 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# Updated to v4.5.1 by: -# R.QIAO -# DeepThought, Flinders University - -name = 'SEPP' -version = '4.5.0' - -homepage = 'https://github.com/smirarab/sepp' -description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic -placement of short reads into reference alignments and trees.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -# https://github.com/smirarab/sepp -github_account = 'smirarab' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['v%(version)s.tar.gz'] - -dependencies = [ - ('Python', '3.9.6'), - ('DendroPy', '4.5.2'), -] - -fix_python_shebang_for = ['bin/*.py'] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -local_bin_files = [ - 'run_sepp.py', - 'run_upp.py', 'split_sequences.py' -] - -sanity_check_paths = { - 'files': ['bin/%s' % f for f in local_bin_files], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] -} - -sanity_check_commands = ["%s --help" % f for f in local_bin_files] - -moduleclass = 'bio' From e4da8b6e0a7e7953e90f23d35e426f8ddc8c8880 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 00:44:21 +1050 Subject: [PATCH 2370/9987] debug <- dep version & style fix --- .../s/SEPP/SEPP-4.5.1-foss-2021b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb new file mode 100644 index 00000000000..7c772367fad --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb @@ -0,0 +1,45 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.5.1 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.5.1' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['51e052569ae89f586a1a94c804f09fe1b7910a3ffff7664e2005f18c7d3f717b'] + +dependencies = [ + ('Python', '3.9.6'), + ('DendroPy', '4.5.2'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = [ + 'run_sepp.py', + 'run_upp.py', 'split_sequences.py' +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From 2b262745cc9b0c6918f6866b1cb581675e7cd6a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Dec 2021 14:56:51 +0100 Subject: [PATCH 2371/9987] retain version in filename for cromwell sources --- .../c/cromwell/cromwell-56-Java-11.eb | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb b/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb index 7e167fc41e1..4e68ade3eeb 100644 --- a/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb +++ b/easybuild/easyconfigs/c/cromwell/cromwell-56-Java-11.eb @@ -11,22 +11,21 @@ toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/%(name)s/releases/download/%(version)s/'] sources = [ - { - 'download_filename': '%(name)s-%(version)s.jar', - 'filename': '%(name)s.jar', - }, - { - 'download_filename': 'womtool-%(version)s.jar', - 'filename': 'womtool.jar', - }, + '%(name)s-%(version)s.jar', + 'womtool-%(version)s.jar', ] checksums = [ - '955502419cfec2a687ea56f7f4a433b395af09c9a078e60a5676c7ad56c3965d', # cromwell.jar - '0f561c0d387412715f1f688ad5ae7cd4d8af3dc8d68c69ae9fc35ecae4f481c6', # womtool.jar + '955502419cfec2a687ea56f7f4a433b395af09c9a078e60a5676c7ad56c3965d', # cromwell-56.jar + '0f561c0d387412715f1f688ad5ae7cd4d8af3dc8d68c69ae9fc35ecae4f481c6', # womtool-56.jar ] dependencies = [('Java', '11')] +postinstallcmds = [ + "mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar", + "mv %(installdir)s/womtool-%(version)s.jar %(installdir)s/womtool.jar", +] + sanity_check_paths = { 'files': ['%(name)s.jar', 'womtool.jar'], 'dirs': [], From 4e64f4747cca8dc7577f70e1b40d1a45369957e3 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 01:12:51 +1050 Subject: [PATCH 2372/9987] debug <- dep version fix --- .../p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb index 235d37e2877..d7359439626 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -33,10 +33,10 @@ dependencies = [ ('IQ-TREE', '2.1.2'), ('MUSCLE', '3.8.31'), ('MAFFT', '7.470', '-with-extensions'), - ('SEPP', '4.5.0'), + ('SEPP', '4.3.10'), ('trimAl', '1.4.1'), ('BLAST+', '2.11.0'), - ('USEARCH', '11.0.667', '-i86linux32'), + ('USEARCH', '11.0.667-i86linux32', '', True), ('DIAMOND', '2.0.4'), ] From 5be1d8f38e426d71bb1b377e8a2c3ad8dbb6b547 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 01:48:28 +1050 Subject: [PATCH 2373/9987] debug <- dep version fix --- .../p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb index d7359439626..7ab31f9c348 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -33,7 +33,7 @@ dependencies = [ ('IQ-TREE', '2.1.2'), ('MUSCLE', '3.8.31'), ('MAFFT', '7.470', '-with-extensions'), - ('SEPP', '4.3.10'), + ('SEPP', '4.3.10', versionsuffix), ('trimAl', '1.4.1'), ('BLAST+', '2.11.0'), ('USEARCH', '11.0.667-i86linux32', '', True), From 8d11780cb08cc5b492b30ab9264d452e096ec0d1 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Fri, 17 Dec 2021 01:53:11 +1030 Subject: [PATCH 2374/9987] debug <- dep version conflict fix --- .../p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb index 7ab31f9c348..98b660aba06 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -32,10 +32,10 @@ dependencies = [ ('FastTree', '2.1.11'), ('IQ-TREE', '2.1.2'), ('MUSCLE', '3.8.31'), - ('MAFFT', '7.470', '-with-extensions'), + ('MAFFT', '7.453', '-with-extensions'), ('SEPP', '4.3.10', versionsuffix), ('trimAl', '1.4.1'), - ('BLAST+', '2.11.0'), + ('BLAST+', '2.10.1'), ('USEARCH', '11.0.667-i86linux32', '', True), ('DIAMOND', '2.0.4'), ] From feb24eca9013ce33c659d5a80a77f6ee6e965102 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Dec 2021 16:41:19 +0100 Subject: [PATCH 2375/9987] add Brotli-python dependency for FMPy --- easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb b/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb index 4e8249a47d2..5af7f211e5a 100644 --- a/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb +++ b/easybuild/easyconfigs/f/FMPy/FMPy-0.3.2-foss-2021a.eb @@ -20,7 +20,7 @@ dependencies = [ ('IPython', '7.25.0'), ('plotly.py', '5.1.0'), ('Flask', '1.1.4'), - ('Brotli', '1.0.9'), + ('Brotli-python', '1.0.9'), ] use_pip = True From 151c1924e39b6334b2f09cfd2fcdfabc36058f23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Dec 2021 17:06:17 +0100 Subject: [PATCH 2376/9987] trivial style fixes for genozip easyconfig --- .../g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb index 222b97ad9d2..16182a13684 100644 --- a/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb @@ -3,9 +3,8 @@ easyblock = 'ConfigureMake' name = 'genozip' version = '13.0.5' - homepage = 'https://genozip.com' -description = """Genozip is a compressor for genomic files - it compresses FASTQ, SAM/BAM/CRAM, VCF, FASTA and others. Documentation: genozip.com. Support: support@genozip.com""" +description = "Genozip is a compressor for genomic files - it compresses FASTQ, SAM/BAM/CRAM, VCF, FASTA and others." toolchain = {'name': 'GCCcore', 'version': '11.2.0'} @@ -20,11 +19,11 @@ skipsteps = ['configure'] installopts = 'PREFIX=%(installdir)s' -sanity_check_commands = ['genozip --help'] - sanity_check_paths = { 'files': ['bin/genocat', 'bin/genozip', 'bin/genounzip', 'bin/genols'], 'dirs': ['bin'], } -moduleclass = 'bio' \ No newline at end of file +sanity_check_commands = ['genozip --help'] + +moduleclass = 'bio' From 13c00d14022ed0b41959bea28dbaa73b61492d83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Dec 2021 17:24:15 +0100 Subject: [PATCH 2377/9987] add missing SHA256 checksum for genozip --- easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb index 16182a13684..0c6be10dfe5 100644 --- a/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/genozip/genozip-13.0.5-GCCcore-11.2.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/divonlan/genozip/archive/refs/tags/'] sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['be2d5cbe1f5f84c2dc1a1d580361fc7f22a14ece4dac545ca2750ca07d49fac3'] builddependencies = [ ('binutils', '2.37') From 3a87d3bbb19bbbd73703ecaa39d4920306c130d4 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 16 Dec 2021 23:02:00 +0000 Subject: [PATCH 2378/9987] White space removed --- easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb index af597f02e72..1034b4e9a44 100644 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.23.1-foss-2021b.eb @@ -28,7 +28,7 @@ dependencies = [ ('SAMtools', '1.14'), ] -sanity_check_commands = [ 'bismark --help'] +sanity_check_commands = ['bismark --help'] sanity_check_paths = { 'files': ['bismark', 'bismark2bedGraph', 'bismark2report', 'bismark_genome_preparation', From ff0f39a79f3d9b563a76dcaf745461f90a1f56f2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 17 Dec 2021 00:59:18 +0100 Subject: [PATCH 2379/9987] fix formatting in SEPP-4.5.1-foss-2021b.eb --- easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb index 7c772367fad..5fb5811a69f 100644 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2021b.eb @@ -30,10 +30,7 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -local_bin_files = [ - 'run_sepp.py', - 'run_upp.py', 'split_sequences.py' -] +local_bin_files = ['run_sepp.py', 'run_upp.py', 'split_sequences.py'] sanity_check_paths = { 'files': ['bin/%s' % f for f in local_bin_files], From 076ed7913ae4a3a7b1ecdee6130f39ae9953c1f5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 17 Dec 2021 01:04:04 +0100 Subject: [PATCH 2380/9987] use dendropy.org as homepage of DendroPy --- .../easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb index f7e6b5f85b2..c15219fd20d 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.2.0.eb @@ -12,7 +12,7 @@ easyblock = 'PythonPackage' name = 'DendroPy' version = '4.5.2' -homepage = 'https://pypi.python.org/pypi/DendroPy/' +homepage = 'https://dendropy.org/' description = """A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.""" From af96361544c8d8847e2a569bfcf654491081474a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 17 Dec 2021 01:45:18 +0100 Subject: [PATCH 2381/9987] downgrade dependency on ecCodes to v2.15.0 --- easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb index c356f156e66..bf08b255127 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-gompi-2019b.eb @@ -17,7 +17,7 @@ dependencies = [ ('HDF5', '1.10.5'), ('netCDF', '4.7.1'), ('YAXT', '0.6.2'), - ('ecCodes', '2.17.0'), + ('ecCodes', '2.15.0'), ] configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES" From f5f305be88682664f277b8d4d26c70f6a6420d96 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Fri, 17 Dec 2021 14:19:10 +1030 Subject: [PATCH 2382/9987] Update easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb Co-authored-by: Alex Domingo --- .../easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb index b715a09d17e..1f225063c2a 100644 --- a/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb @@ -4,7 +4,7 @@ easyblock = 'PythonPackage' -name = 'python-pulp' +name = 'PuLP' version = '2.5.1' homepage = 'https://github.com/coin-or/pulp' From 93ef23c9c20bd0b2c4faa0a1aeb865b8ab81cdc9 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 14:57:26 +1050 Subject: [PATCH 2383/9987] dep <- optional packages + --- .../p/PuLP/PuLP-2.5.1-foss-2021a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb new file mode 100644 index 00000000000..6c0e40a7a24 --- /dev/null +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb @@ -0,0 +1,37 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'PuLP' +version = '2.5.1' + +homepage = 'https://pypi.org/project/PuLP' +description = """ +PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and +call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to +solve linear problems. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/pulp'] +sources = ['PuLP-%(version)s.tar.gz'] +checksums = ['27c2a87a98ea0e9a08c7c46e6df47d6d4e753ad9991fea2901892425d89c99a6'] + +dependencies = [ + ('Python', '3.9.5'), + ('GLPK', '5.0'), + ('Cbc', '2.10.5'), + # Gurobi requires a seperate license + # ('Gurobi', '9.5.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'tools' From d113c31ef660efc8ad3eb08206a2eb78dbff4246 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Fri, 17 Dec 2021 14:38:15 +1030 Subject: [PATCH 2384/9987] Delete python-pulp-2.5.1-foss-2021a.eb --- .../python-pulp-2.5.1-foss-2021a.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb deleted file mode 100644 index 1f225063c2a..00000000000 --- a/easybuild/easyconfigs/p/python-pulp/python-pulp-2.5.1-foss-2021a.eb +++ /dev/null @@ -1,35 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO - -easyblock = 'PythonPackage' - -name = 'PuLP' -version = '2.5.1' - -homepage = 'https://github.com/coin-or/pulp' -description = """ -PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and -call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to -solve linear problems. -""" - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/pulp'] -sources = ['PuLP-%(version)s.tar.gz'] -checksums = ['27c2a87a98ea0e9a08c7c46e6df47d6d4e753ad9991fea2901892425d89c99a6'] - -dependencies = [ - ('Python', '3.9.5'), -] - -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - -options = {'modulename': 'pulp'} - -moduleclass = 'tools' From cfd6abf40cedfcfcbbe2a5c833e376b557f64bc1 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 16:44:29 +1050 Subject: [PATCH 2385/9987] adding easyconfigs: IQ-TREE-2.1.3-gompi-2021a.eb, LSD2-2.3-GCCcore-10.3.0.eb --- .../i/IQ-TREE/IQ-TREE-2.1.3-gompi-2021a.eb | 48 +++++++++++++++++++ .../l/LSD2/LSD2-2.3-GCCcore-10.3.0.eb | 38 +++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.3-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.3-gompi-2021a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.3-gompi-2021a.eb new file mode 100644 index 00000000000..2bc6a28974f --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.1.3-gompi-2021a.eb @@ -0,0 +1,48 @@ +# Updated to v2.1.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.1.3' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-2.1.2_use_EB_LSD2.patch'] +checksums = [ + '38ec7cfa36bee9958aa806773156c445beac9f01082d3593188f20fbbbb06894', # v2.1.3.tar.gz + 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816', # IQ-TREE-2.1.2_use_EB_LSD2.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Eigen', '3.3.9'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.76.0'), + ('LSD2', '2.3'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = ["iqtree2 --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8e7a2ffbb55 --- /dev/null +++ b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +# Updated to v2.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'LSD2' +version = '2.3' + +homepage = 'https://github.com/tothuhien/lsd2' +description = "Least-squares methods to estimate rates and dates from phylogenies" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'tothuhien' + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v.%(version)s.tar.gz'] +patches = ['%(name)s-1.9.7_fix_cmake_to_build_lib_and_binary.patch'] +checksums = [ + 'c7819be1204ebf77e3660bba91dbd8629ba9437216814f276a11b9156dbb0649', # v.2.3.tar.gz + # LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch + '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6', +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From a0430d962fa6563b37da69519f0c581d768ad264 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 18:07:00 +1050 Subject: [PATCH 2386/9987] adding easyconfigs: MUSCLE-5.0.1428.eb --- .../easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb new file mode 100644 index 00000000000..6d7ae644e8c --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb @@ -0,0 +1,36 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# update to v5 + +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '5.0.1428' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/rcedgar/%(namelower)s/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['59a8196890893e44a60f24134e8da24ee8381830a0f84e37378a3ca8be5430f5'] + +skipsteps = ['config', 'build'] + +if (OS_TYPE == 'Linux'): + files_to_copy = [(["binaries/%(namelower)s"], 'bin')] +elif (OS_TYPE == 'Windows'): + files_to_copy = [(["binaries/%(namelower)s.exe"], 'bin')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'bio' From 303575bbbf914b5a78130888379243c7719a6ac2 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 18:29:54 +1050 Subject: [PATCH 2387/9987] dep <- optional + --- .../FastTree-2.1.11-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ .../t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb | 32 ++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ad1c23f20f5 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.36.1')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ebf9a1d24b8 --- /dev/null +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated by: +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'MakeCp' + +name = 'trimAl' +version = '1.4.1' + +homepage = 'https://github.com/scapella/trimal' +description = """EVB, FEP and LIE simulator.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +github_account = 'scapella' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] + +builddependencies = [('binutils', '2.36.1', '', True)] +start_dir = 'source' + +files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/trimal', 'bin/readal', 'bin/statal'], + 'dirs': [] +} + +moduleclass = 'bio' From 4adea9f3adb935cdbe3cce9f71f7423b87bc6d65 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Fri, 17 Dec 2021 18:34:11 +1050 Subject: [PATCH 2388/9987] dep <- all version update --- .../p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb index 7cdf357fcbf..4309976ceb3 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb @@ -29,6 +29,15 @@ dependencies = [ ('DendroPy', '4.5.2'), ('matplotlib', '3.4.2'), ('Seaborn', '0.11.2'), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.1.3'), + ('MUSCLE', '5.0.1428', '', True), + ('MAFFT', '7.490', '-with-extensions'), + ('SEPP', '4.5.0'), + ('trimAl', '1.4.1'), + ('BLAST+', '2.11.0'), + ('USEARCH', '11.0.667-i86linux32', '', True), + ('DIAMOND', '2.0.11'), ] use_pip = True From 5a502d3203802ae9b8b779de4a89cf0f2c5d99e2 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 17 Dec 2021 14:43:22 +0200 Subject: [PATCH 2389/9987] adding easyconfigs: PyTorch-1.10.0-fosscuda-2020b.eb, CMake-3.20.1-GCCcore-10.2.0.eb, expecttest-0.1.3-GCCcore-10.2.0.eb --- .../c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb | 32 +++++ .../expecttest-0.1.3-GCCcore-10.2.0.eb | 25 ++++ .../PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 120 ++++++++++++++++++ 3 files changed, 177 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..16e8766c691 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +name = 'CMake' +version = '3.20.1' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3f1808b9b00281df06c91dd7a021d7f52f724101000da7985a401678dfe035b0'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.72.0'), + ('libarchive', '3.4.3'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1h'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..1e133b2aea1 --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.1.3' + +homepage = "https://github.com/ezyang/expecttest" +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['83057695811d94128aed13ed094a070db90e0a92ea40071f8ee073cbab57149a'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb new file mode 100644 index 00000000000..af85117afc4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -0,0 +1,120 @@ +name = 'PyTorch' +version = '1.10.0' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', + 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', + 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_skip_failing_ops_tests.patch', + 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', +] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch + 'd4d967d47f8a6172fcbf57f0a61835482968850967c4fdb01108b720696a988d', + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.8.1_increase-distributed-test-timeout.patch + '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch + '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', + # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch + '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-test-cond-cpu.patch + '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-vnni-detection.patch + '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch + 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_skip_failing_ops_tests.patch + '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', + # PyTorch-1.10.0_skip_nan_tests_openblas.patch + '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', + # PyTorch-1.10.0_skip_cmake_rpath.patch + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), # Needs 3.20 or newer. + ('hypothesis', '5.41.5'), +] + +dependencies = [ + ('Ninja', '1.10.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.8.6'), + ('protobuf', '3.14.0'), + ('protobuf-python', '3.14.0'), + ('pybind11', '2.6.0'), + ('SciPy-bundle', '2020.11'), + ('typing-extensions', '3.7.4.3'), + ('PyYAML', '5.3.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.0'), + ('numactl', '2.0.13'), + ('FFmpeg', '4.3.1'), + ('Pillow', '8.0.1'), + ('expecttest', '0.1.3'), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('magma', '2.5.4'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + # 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + # 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +sanity_check_commands = ["python -c 'import caffe2.python'"] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From 101b832f334ee053883b6eafb437a5ef14c6ea8e Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Dec 2021 15:50:04 +0000 Subject: [PATCH 2390/9987] Bundle an installation of LAPACKE with FlexiBLAS, since LAPACKE is not (yet) supported by FlexiBLAS --- .../f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb | 34 +++++++++++++++++-- 1 file changed, 31 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb index b0f9ad78754..27f3930cfd8 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb @@ -1,3 +1,5 @@ +easyblock = 'Bundle' + name = 'FlexiBLAS' version = '3.0.4' @@ -9,9 +11,9 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} -source_urls = ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'] +#source_urls = ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'] +#sources = [SOURCELOWER_TAR_GZ] +#checksums = ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'] builddependencies = [ ('CMake', '3.20.1'), @@ -24,4 +26,30 @@ dependencies = [ ('OpenBLAS', '0.3.15'), ] +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'], + }), + ('LAPACK', '3.10.0', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['328c1bea493a32cac5257d84157dc686cc3ab0b004e2bea22044e0a59f6f8a19'], + 'configopts': '-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON \ + -DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON \ + -DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas', + #'postinstallcmds': ["mv %(installdir)s/include/*.h %(installdir)s/include/flexiblas"], + }), +] + +sanity_check_paths = { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], +} + moduleclass = 'lib' From 852d1f1815c33b22b0c5bc21ed105beddb0fb697 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Dec 2021 15:52:04 +0000 Subject: [PATCH 2391/9987] Linting --- .../easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb index 27f3930cfd8..75ed9461123 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb @@ -11,10 +11,6 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} -#source_urls = ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'] -#sources = [SOURCELOWER_TAR_GZ] -#checksums = ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'] - builddependencies = [ ('CMake', '3.20.1'), ('Python', '3.9.5'), # required for running the tests From 3a75d841fc2a96a73515fadd7cf8a22888ea85c2 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 17 Dec 2021 15:52:34 +0000 Subject: [PATCH 2392/9987] remove commented postinstallcmds --- easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb index 75ed9461123..a7982e2cd57 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb @@ -39,7 +39,6 @@ components = [ 'configopts': '-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON \ -DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON \ -DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas', - #'postinstallcmds': ["mv %(installdir)s/include/*.h %(installdir)s/include/flexiblas"], }), ] From 63ea92df1480321f133d89f9cb308ae84b95c04a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Dec 2021 16:08:24 +0000 Subject: [PATCH 2393/9987] adding easyconfigs: EIGENSOFT-7.2.1-foss-2021a.eb --- .../e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb new file mode 100644 index 00000000000..946ae3d37a6 --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 6.1.4 modified by: +# Adam Huffman +# The Francis Crick Institute +# 7.2.1 modified by: +# Tom Strempel +# Helmholtz-Centre for Environmental Research - UFZ + +easyblock = 'MakeCp' + +name = 'EIGENSOFT' +version = '7.2.1' + +homepage = 'https://www.hsph.harvard.edu/alkes-price/software/' +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. +2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal +components analysis to explicitly model ancestry differences between cases and controls along continuous axes of +variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral +populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT +package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/DReichLab/EIG/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_Fix_makefile_openblas.patch'] +checksums = [ + 'f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650', # v7.2.1.tar.gz + 'e49e3754f2326210114fe5a731a77c7ffd240c8a9134eb8e8e1517bfe06c71e1', # EIGENSOFT-7.2.1_Fix_makefile_openblas.patch +] + +dependencies = [ + ('GSL', '2.7'), + ('Perl', '5.32.1'), +] + +start_dir = 'src' + +# Run "make install" after make to copy all binaries to the bin dir +buildopts = 'LDLIBS="-lgsl $LIBBLAS -llapacke $LIBS" && make install' + +files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] + +fix_perl_shebang_for = ['bin/*.perl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'dirs': [] +} + +moduleclass = 'bio' From d527a0c2ae1d136087fce7ea3f0c7416d6e4cf36 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 17 Dec 2021 17:53:16 +0100 Subject: [PATCH 2394/9987] Create Anaconda3-2021.11.eb --- .../a/Anaconda3/Anaconda3-2021.11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.11.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.11.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.11.eb new file mode 100644 index 00000000000..6006859638b --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2021.11.eb @@ -0,0 +1,29 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, 2019.10, +# 2020.2, 2020.11, 2021.11 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2021.11' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +sources = ['%(name)s-%(version)s-Linux-%(arch)s.sh'] + +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': 'fedf9e340039557f7b5e8a8a86affa9d299f5e9820144bd7b92ae9f7ee08ac60', + '%(name)s-%(version)s-Linux-ppc64le.sh': '7eb6a95925ee756240818599f8dcbba7a155adfb05ef6cd5336aa3c083de65f3', + } +] + +moduleclass = 'lang' From 927d52a64162b619fdcbaa4904d22305052bf98e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Dec 2021 00:33:57 +0100 Subject: [PATCH 2395/9987] fix sanity checks of MetaPhlAn v3.0.9 --- .../m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb index a6979c9e19d..1fc584f1503 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-3.0.9-foss-2020a-Python-3.8.2.eb @@ -36,7 +36,7 @@ download_dep_fail = True sanity_pip_check = True sanity_check_paths = { 'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']], - 'dirs': ['bin', 'lib'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], } sanity_check_commands = [('%(namelower)s', '-h')] From b2860d89c9299176f4d468f9d9c4ced34426bbd4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Dec 2021 00:50:17 +0100 Subject: [PATCH 2396/9987] update homepage of PuLP --- easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb index 6c0e40a7a24..1e4b4485af4 100644 --- a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb @@ -7,7 +7,7 @@ easyblock = 'PythonPackage' name = 'PuLP' version = '2.5.1' -homepage = 'https://pypi.org/project/PuLP' +homepage = 'https://github.com/coin-or/pulp' description = """ PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to From 7b374c6e8b8c4718893052625d3e547f18e72170 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Dec 2021 00:50:47 +0100 Subject: [PATCH 2397/9987] simplify sources of PuLP --- easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb index 1e4b4485af4..9096fd0af07 100644 --- a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb @@ -17,8 +17,7 @@ solve linear problems. toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': True} -source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/pulp'] -sources = ['PuLP-%(version)s.tar.gz'] +sources = [SOURCE_TAR_GZ] checksums = ['27c2a87a98ea0e9a08c7c46e6df47d6d4e753ad9991fea2901892425d89c99a6'] dependencies = [ From 2be430f794ab08db5a3d87c6d6033d10bbda83ed Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Dec 2021 00:51:22 +0100 Subject: [PATCH 2398/9987] disable usempi in PuLP --- easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb index 9096fd0af07..0192ade0554 100644 --- a/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.5.1-foss-2021a.eb @@ -15,7 +15,6 @@ solve linear problems. """ toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': True} sources = [SOURCE_TAR_GZ] checksums = ['27c2a87a98ea0e9a08c7c46e6df47d6d4e753ad9991fea2901892425d89c99a6'] From 46ec6bc5dc5436e4e5ee1f5c458deee8d59eb638 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 18 Dec 2021 02:50:20 +0100 Subject: [PATCH 2399/9987] replace MUSCLE v5.0.1428 binaries with compilation in GCCcore/10.3.0 --- .../MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb | 44 +++++++++++++++++++ .../easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb | 36 --------------- ...SCLE-5.0.1428_add-ver-counter-header.patch | 31 +++++++++++++ 3 files changed, 75 insertions(+), 36 deletions(-) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb delete mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428_add-ver-counter-header.patch diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..17d9c5626cd --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '5.0.1428' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'rcedgar' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_add-ver-counter-header.patch'] +checksums = [ + '59a8196890893e44a60f24134e8da24ee8381830a0f84e37378a3ca8be5430f5', # v5.0.1428.tar.gz + '129e3cd5cd7ae4d9819bbb36776275781e33c82410ee1e5d480b3de2df213931', # MUSCLE-5.0.1428_add-ver-counter-header.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('ccache', '4.2.1', '', True), +] + +start_dir = 'src' + +# Use build environment defined by EB +prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&" + +files_to_copy = [(['o/muscle5'], 'bin')] +postinstallcmds = ["cd %(installdir)s/bin && ln -s muscle5 muscle"] + +sanity_check_paths = { + 'files': ['bin/muscle', 'bin/muscle5'], + 'dirs': [], +} + +sanity_check_commands = [('muscle', '-h')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb deleted file mode 100644 index 6d7ae644e8c..00000000000 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428.eb +++ /dev/null @@ -1,36 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO -# update to v5 - -easyblock = 'MakeCp' - -name = 'MUSCLE' -version = '5.0.1428' - -homepage = 'https://drive5.com/muscle/' -description = """MUSCLE is one of the best-performing multiple alignment programs - according to published benchmark tests, with accuracy and speed that are consistently - better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users - learn everything they need to know about MUSCLE in a few minutes-only a handful of - command-line options are needed to perform common alignment tasks.""" - -toolchain = SYSTEM - -source_urls = ['https://github.com/rcedgar/%(namelower)s/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['59a8196890893e44a60f24134e8da24ee8381830a0f84e37378a3ca8be5430f5'] - -skipsteps = ['config', 'build'] - -if (OS_TYPE == 'Linux'): - files_to_copy = [(["binaries/%(namelower)s"], 'bin')] -elif (OS_TYPE == 'Windows'): - files_to_copy = [(["binaries/%(namelower)s.exe"], 'bin')] - -sanity_check_paths = { - 'files': [], - 'dirs': ['bin'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428_add-ver-counter-header.patch b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428_add-ver-counter-header.patch new file mode 100644 index 00000000000..991310e87b9 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428_add-ver-counter-header.patch @@ -0,0 +1,31 @@ +From dd9c3e921a5f06bbc8be7593eab4d6e3433b6f67 Mon Sep 17 00:00:00 2001 +From: Robert Edgar +Date: Wed, 10 Nov 2021 08:05:06 -0800 +Subject: [PATCH] Fix ../ver/counter.h issue + +--- + src/myutils.cpp | 2 +- + src/ver_counter.h | 1 + + 2 files changed, 2 insertions(+), 1 deletion(-) + create mode 100644 src/ver_counter.h + +diff --git a/src/myutils.cpp b/src/myutils.cpp +index 5a49b4e..e1bc0fd 100644 +--- a/src/myutils.cpp ++++ b/src/myutils.cpp +@@ -2055,7 +2055,7 @@ void Split(const string &Str, vector &Fields, char Sep) + void GetVersionString(string &s) + { + const int counter = +-#include "../ver/counter.h" ++#include "ver_counter.h" + ; + const char *Flags = "" + +diff --git a/src/ver_counter.h b/src/ver_counter.h +new file mode 100644 +index 0000000..4efaa29 +--- /dev/null ++++ b/src/ver_counter.h +@@ -0,0 +1 @@ ++1428 From 3df2e9f63588e1790712df95b19e26b1ee6ff494 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Sat, 18 Dec 2021 20:31:15 +1050 Subject: [PATCH 2400/9987] dep <- MUSCLE downgrade to coop with consistancy --- .../m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb | 35 ++++++++++++ .../PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 55 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..39ebbad842c --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb new file mode 100644 index 00000000000..0e70c4e11de --- /dev/null +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb @@ -0,0 +1,55 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# update to v3.0.2 + +easyblock = 'PythonPackage' + +name = 'PhyloPhlAn' +version = '3.0.2' + +homepage = 'https://github.com/biobakery/phylophlan' +description = """ +PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of +genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method +for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. +""" + +source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4'] + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.4.2'), + ('Seaborn', '0.11.2'), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.1.3'), + ('MUSCLE', '3.8.31'), + ('MAFFT', '7.490', '-with-extensions'), + ('SEPP', '4.5.0'), + ('trimAl', '1.4.1'), + ('BLAST+', '2.11.0'), + ('USEARCH', '11.0.667-i86linux32', '', True), + ('DIAMOND', '2.0.11'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], + 'dirs': ['lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From 415b175f9087a17fe04e76cc8395aaad290dc216 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Sat, 18 Dec 2021 20:32:16 +1050 Subject: [PATCH 2401/9987] dep <- MUSCLE downgrade to coop with consistancy --- .../m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb | 35 +++++++++++++++++++ .../PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 2 +- 2 files changed, 36 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..39ebbad842c --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb index 4309976ceb3..0e70c4e11de 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb @@ -31,7 +31,7 @@ dependencies = [ ('Seaborn', '0.11.2'), ('FastTree', '2.1.11'), ('IQ-TREE', '2.1.3'), - ('MUSCLE', '5.0.1428', '', True), + ('MUSCLE', '3.8.31'), ('MAFFT', '7.490', '-with-extensions'), ('SEPP', '4.5.0'), ('trimAl', '1.4.1'), From d5f9e39eeb562fc19b6c866718f91973f160a754 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Sat, 18 Dec 2021 20:14:07 +1030 Subject: [PATCH 2402/9987] Delete PhyloPhlAn-3.0.2-foss-2021a.eb --- .../PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 55 ------------------- 1 file changed, 55 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb deleted file mode 100644 index 0e70c4e11de..00000000000 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb +++ /dev/null @@ -1,55 +0,0 @@ -# Contribution by -# DeepThought, Flinders University -# R.QIAO -# update to v3.0.2 - -easyblock = 'PythonPackage' - -name = 'PhyloPhlAn' -version = '3.0.2' - -homepage = 'https://github.com/biobakery/phylophlan' -description = """ -PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of -genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method -for large-scale microbial genome characterization and phylogenetic analysis -at multiple levels of resolution. -""" - -source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] -sources = ['%(version)s.tar.gz'] -checksums = ['c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4'] - -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('Biopython', '1.79'), - ('DendroPy', '4.5.2'), - ('matplotlib', '3.4.2'), - ('Seaborn', '0.11.2'), - ('FastTree', '2.1.11'), - ('IQ-TREE', '2.1.3'), - ('MUSCLE', '3.8.31'), - ('MAFFT', '7.490', '-with-extensions'), - ('SEPP', '4.5.0'), - ('trimAl', '1.4.1'), - ('BLAST+', '2.11.0'), - ('USEARCH', '11.0.667-i86linux32', '', True), - ('DIAMOND', '2.0.11'), -] - -use_pip = True -download_dep_fail = True - -sanity_pip_check = True -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], - 'dirs': ['lib'], -} -sanity_check_commands = [('%(namelower)s', '-h')] - -options = {'modulename': '%(namelower)s'} - -moduleclass = 'bio' From e5c00ec28ae6cc8e6b90d4b818e99cf071448513 Mon Sep 17 00:00:00 2001 From: manifesto <13493869+manifestoso@users.noreply.github.com> Date: Sat, 18 Dec 2021 20:14:21 +1030 Subject: [PATCH 2403/9987] Delete MUSCLE-3.8.31-GCCcore-10.3.0.eb --- .../m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb deleted file mode 100644 index 39ebbad842c..00000000000 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-10.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'MakeCp' - -name = 'MUSCLE' -version = '3.8.31' - -homepage = 'https://drive5.com/muscle/' -description = """MUSCLE is one of the best-performing multiple alignment programs - according to published benchmark tests, with accuracy and speed that are consistently - better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users - learn everything they need to know about MUSCLE in a few minutes-only a handful of - command-line options are needed to perform common alignment tasks.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] -sources = ['%(namelower)s%(version)s_src.tar.gz'] -patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] -checksums = [ - '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz - '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch -] - -builddependencies = [ - ('binutils', '2.36.1'), -] - -files_to_copy = [ - (["muscle"], 'bin')] - -sanity_check_paths = { - 'files': ["bin/muscle"], - 'dirs': [], -} - -moduleclass = 'bio' From 9cab367813c725c6c8c25fef298b811b47c5d6b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 13:57:42 +0100 Subject: [PATCH 2404/9987] drop unneeded binutils build dep + clarify why full toolchain is used in dlib easyconfigs --- .../easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb | 4 ++-- easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb index 95635f71e04..e62049c61b8 100644 --- a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb @@ -11,7 +11,8 @@ problems. It is used in both industry and academia in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments.""" -toolchain = {'name': 'foss', 'version': '2021a'} # requires blas +# dlib can use BLAS/LAPACK, so using full toolchain +toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True} github_account = 'davisking' @@ -20,7 +21,6 @@ sources = ['v%(version)s.tar.gz'] checksums = ['5f44b67f762691b92f3e41dcf9c95dd0f4525b59cacb478094e511fdacb5c096'] builddependencies = [ - ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb index b3c3383dcf6..8db3464183c 100644 --- a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a.eb @@ -10,6 +10,7 @@ problems. It is used in both industry and academia in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments.""" +# dlib can use BLAS/LAPACK, so using full toolchain toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'davisking' @@ -18,7 +19,6 @@ sources = ['v%(version)s.tar.gz'] checksums = ['5f44b67f762691b92f3e41dcf9c95dd0f4525b59cacb478094e511fdacb5c096'] builddependencies = [ - ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('pkg-config', '0.29.2'), ] From db520140446592c1a815c9e82daee88c46e3df9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 14:22:20 +0100 Subject: [PATCH 2405/9987] tweak patch for OpenFace + remove unneeded binutils build dep and -DCMAKE_BUILD_TYPE=RELEASE --- .../OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb | 7 ++---- .../o/OpenFace/OpenFace-2.2.0-foss-2021a.eb | 7 ++---- ...Face-2.2.0_avoid-hardcoded-OpenBLAS.patch} | 25 ++++++++++++------- 3 files changed, 20 insertions(+), 19 deletions(-) rename easybuild/easyconfigs/o/OpenFace/{OpenFace-2.2.0-use_FlexiBLAS.patch => OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch} (52%) diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb index ffd3307a288..b7b2f6058eb 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb @@ -14,14 +14,13 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'TadasBaltrusaitis' source_urls = [GITHUB_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] -patches = ['OpenFace-2.2.0-use_FlexiBLAS.patch'] +patches = ['OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch'] checksums = [ '928e6346bcff41393393a364df99bf09c3410fab85b569f2023e3224d2a1981a', # OpenFace_2.2.0.tar.gz - '354531f3f1ad497b1b5ab213c274247e5f87b3d30a7c1f4f93b0e4041a86a909', # OpenFace-2.2.0-use_FlexiBLAS.patch + 'de366e8af6ffe639b2bf411032e768ba926800389472bb57bb132744c36077b6', # OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch ] builddependencies = [ - ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('pkg-config', '0.29.2'), ('patchelf', '0.12') @@ -35,8 +34,6 @@ dependencies = [ ('Boost', '1.76.0'), ] -configopts = "-DCMAKE_BUILD_TYPE=RELEASE" - # This is the only way I found to remove the banned OpenBLAS from libraries # required by the OpenFace executables, as CMake stubbornly includes it there preinstallopts = 'patchelf --remove-needed libopenblas.so.0 bin/FaceLandmarkVid' diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb index 9f269dc9eb2..c741d884cad 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a.eb @@ -13,14 +13,13 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'TadasBaltrusaitis' source_urls = [GITHUB_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] -patches = ['OpenFace-2.2.0-use_FlexiBLAS.patch'] +patches = ['OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch'] checksums = [ '928e6346bcff41393393a364df99bf09c3410fab85b569f2023e3224d2a1981a', # OpenFace_2.2.0.tar.gz - '354531f3f1ad497b1b5ab213c274247e5f87b3d30a7c1f4f93b0e4041a86a909', # OpenFace-2.2.0-use_FlexiBLAS.patch + 'de366e8af6ffe639b2bf411032e768ba926800389472bb57bb132744c36077b6', # OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch ] builddependencies = [ - ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('pkg-config', '0.29.2'), ('patchelf', '0.12') @@ -32,8 +31,6 @@ dependencies = [ ('Boost', '1.76.0'), ] -configopts = '-DCMAKE_BUILD_TYPE=RELEASE' - # This is the only way I found to remove the banned OpenBLAS from libraries # required by the OpenFace executables, as CMake stubbornly includes it there preinstallopts = 'patchelf --remove-needed libopenblas.so.0 bin/FaceLandmarkVid' diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch similarity index 52% rename from easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch rename to easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch index 105de6d5362..f10fb9becfd 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-use_FlexiBLAS.patch +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0_avoid-hardcoded-OpenBLAS.patch @@ -1,6 +1,8 @@ -diff -ruN ../../OpenFace-OpenFace_2.2.0/CMakeLists.txt ../../OpenFace-OpenFace_2.2.0-new/CMakeLists.txt ---- ../../OpenFace-OpenFace_2.2.0/CMakeLists.txt 2019-07-13 20:20:17.000000000 +0200 -+++ ../../OpenFace-OpenFace_2.2.0-new/CMakeLists.txt 2021-12-13 23:43:45.160326152 +0100 +replace hardcoding of OpenBLAS to allow use of other BLAS library like FlexiBLAS + +author: Jakub Zárybnický (Inuits) +--- OpenFace-OpenFace_2.2.0/CMakeLists.txt.orig 2021-12-18 14:00:40.813909912 +0100 ++++ OpenFace-OpenFace_2.2.0/CMakeLists.txt 2021-12-18 14:07:55.707025240 +0100 @@ -11,22 +11,19 @@ set(CONFIG_DIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_CONFIG_DIR}") add_definitions(-DCONFIG_DIR="${CONFIG_DIR}") @@ -9,23 +11,28 @@ diff -ruN ../../OpenFace-OpenFace_2.2.0/CMakeLists.txt ../../OpenFace-OpenFace_2 -# implementations; so OpenFace wants OpenBLAS; -find_package(OpenBLAS REQUIRED) -if ( ${OpenBLAS_FOUND} ) +- MESSAGE("OpenBLAS information:") +- MESSAGE(" OpenBLAS_LIBRARIES: ${OpenBLAS_LIB}") +-else() +- MESSAGE(FATAL_ERROR "OpenBLAS not found in the system.") +if ( DEFINED ENV{LIBBLAS} ) + SET(OpenBLAS_LIB "-L$ENV{BLAS_LIB_DIR} $ENV{LIBBLAS}") - MESSAGE("OpenBLAS information:") - MESSAGE(" OpenBLAS_LIBRARIES: ${OpenBLAS_LIB}") - else() - MESSAGE(FATAL_ERROR "OpenBLAS not found in the system.") ++ MESSAGE("BLAS information:") ++ MESSAGE(" BLAS_LIBRARIES: ${OpenBLAS_LIB}") ++ else() ++ MESSAGE(FATAL_ERROR "BLAS not found in the system via \${LIBBLAS}.") endif() -if ( ${OpenBLAS_INCLUDE_FOUND} ) +- MESSAGE(" OpenBLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") +if ( DEFINED ENV{BLAS_INC_DIR} ) + SET(OpenBLAS_INCLUDE_DIR $ENV{BLAS_INC_DIR}) - MESSAGE(" OpenBLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") ++ MESSAGE(" BLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") else() - MESSAGE(WARNING "OpenBLAS include not found in the system. Using the one vended with OpenFace.") - set(OpenBLAS_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/lib/3rdParty/OpenBLAS/include") - MESSAGE(" OpenBLAS_INCLUDE: ${OpenBLAS_INCLUDE_DIR}") -+ MESSAGE(FATAL_ERROR "OpenBLAS not found in the system.") ++ MESSAGE(FATAL_ERROR "BLAS include dir not found in the system via \${BLAS_INC_DIR}.") endif() find_package( OpenCV 4.0 REQUIRED COMPONENTS core imgproc calib3d highgui objdetect) From 84bc9f307a71f310c92a1cfb577ae95f0a209d7d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 15:20:54 +0100 Subject: [PATCH 2406/9987] use 'readelf -l' to determine path to interpreter in patch file for Rust --- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb | 2 +- .../r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch | 6 +++--- easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index 1de0bc61268..d9802f22e00 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ sources = ['rustc-%(version)s-src.tar.gz'] patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] checksums = [ '3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98', # rustc-1.52.1-src.tar.gz - '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch + 'e3db7005585eb807ecb69929818740f00417cac247b1065a9d43a7f16cf05e0b', # Rust-1.52.1_sysroot-fix-interpreter.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb index ec7ed7d0232..ee8b6cb18e5 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb @@ -14,7 +14,7 @@ sources = ['rustc-%(version)s-src.tar.gz'] patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] checksums = [ '3a6f23a26d0e8f87abbfbf32c5cd7daa0c0b71d0986abefc56b9a5fbfbd0bf98', # rustc-1.52.1-src.tar.gz - '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch + 'e3db7005585eb807ecb69929818740f00417cac247b1065a9d43a7f16cf05e0b', # Rust-1.52.1_sysroot-fix-interpreter.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch b/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch index 058dc409569..bec629b9175 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1_sysroot-fix-interpreter.patch @@ -16,9 +16,9 @@ author: Kenneth Hoste (HPC-UGent) + sysroot = os.getenv("EASYBUILD_SYSROOT") + if sysroot and not fname.endswith(".so"): + # determine patch to interpreter in host via output produced by 'file -b /bin/bash' -+ file_b_out = subprocess.check_output(['file', '-b', '/bin/bash']).decode('ascii', 'ignore').strip() -+ regex = re.compile('.*, interpreter ([^,]*),.*') -+ res = regex.match(file_b_out) ++ readelf_out = subprocess.check_output(['readelf', '-l', '/bin/bash']).decode('ascii', 'ignore').strip() ++ regex = re.compile('.*program interpreter: ([^\]]+)', re.M) ++ res = regex.search(readelf_out) + interpreter_path = os.path.join(sysroot, res.group(1).lstrip('/')) + if not os.path.exists(interpreter_path): + raise Exception("Derived path to interpreter does not exist: %s" % interpreter_path) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb index 5e8146115eb..603a5387f6c 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ sources = ['rustc-%(version)s-src.tar.gz'] patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] checksums = [ 'ac8511633e9b5a65ad030a1a2e5bdaa841fdfe3132f2baaa52cc04e71c6c6976', # rustc-1.54.0-src.tar.gz - '0c2fc9f2ec1d9112ab1febdacf181e47484f2a07c9a8cc967131ed777fc18370', # Rust-1.52.1_sysroot-fix-interpreter.patch + 'e3db7005585eb807ecb69929818740f00417cac247b1065a9d43a7f16cf05e0b', # Rust-1.52.1_sysroot-fix-interpreter.patch ] builddependencies = [ From fed954d7f9b2c7310351daf011f7069dbd467d01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 17:19:38 +0100 Subject: [PATCH 2407/9987] enhance sanity check for PyTorch 1.10.0 with fosscuda/2020b --- .../p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index af85117afc4..a7ff2a282f4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -114,7 +114,13 @@ excluded_tests = { runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' -sanity_check_commands = ["python -c 'import caffe2.python'"] +# The readelf sanity check can be taken out once the TestRPATH test from https://github.com/pytorch/pytorch/pull/68912 +# is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "python -c 'import caffe2.python'", + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'devel' From 96d985c6a84a5a02e5eaae852c83af843f349d2d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Dec 2021 20:09:21 +0100 Subject: [PATCH 2408/9987] add proper OpenSSL dependency for mold --- easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb index 1b0b1af41f3..d5203935c90 100644 --- a/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb @@ -19,6 +19,7 @@ builddependencies = [ dependencies = [ ('xxHash', '0.8.0'), ('zlib', '1.2.11'), + ('OpenSSL', '1.1', '', True), ] skipsteps = ['configure'] From 65c2ab143a55ce0cd15641885aa0ff4ebfb3f418 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 19 Dec 2021 00:52:26 +0100 Subject: [PATCH 2409/9987] disable ccache in MUSCLE v5.0.1428 --- .../easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb index 17d9c5626cd..e597d772ba5 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.0.1428-GCCcore-10.3.0.eb @@ -23,13 +23,13 @@ checksums = [ builddependencies = [ ('binutils', '2.36.1'), - ('ccache', '4.2.1', '', True), ] start_dir = 'src' # Use build environment defined by EB prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&" +buildopts = "CPP=${CXX} CC=${CC}" files_to_copy = [(['o/muscle5'], 'bin')] postinstallcmds = ["cd %(installdir)s/bin && ln -s muscle5 muscle"] From 912e0b8f8fc574fa83ff812ceb8889b946016596 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 10:47:56 +0100 Subject: [PATCH 2410/9987] specify compiler to use in WildMagic easyconfig --- easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-foss-2018b.eb b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-foss-2018b.eb index a7dc62e1381..22c69f44820 100644 --- a/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-foss-2018b.eb +++ b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-foss-2018b.eb @@ -17,7 +17,7 @@ dependencies = [ ('freeglut', '3.0.0'), ] -buildopts = "CFG=ReleaseDynamic -f makefile.wm5" +buildopts = 'CFG=ReleaseDynamic -f makefile.wm5 CC="$CXX"' files_to_copy = [ (['SDK/Library/ReleaseDynamic/*'], 'lib'), From 5e9c4b417ba4a01fc24d5ea4f9fc1bc60c2713a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 11:36:03 +0100 Subject: [PATCH 2411/9987] adding easyconfigs: mold-1.0.0-GCCcore-11.2.0.eb --- .../m/mold/mold-1.0.0-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..98e1d3c8a65 --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'mold' +version = '1.0.0' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d7cf170b57a3767d944c80c7468215fa9f8fa176f94f411a5b62b3f56cf07400'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] +dependencies = [ + ('xxHash', '0.8.0'), + ('zlib', '1.2.11'), + ('OpenSSL', '1.1', '', True), +] + +skipsteps = ['configure'] + +# PREFIX must be specified when building, to ensure that the mold binary looks for mold-wrapper.so in the right place +buildopts = "PREFIX=%(installdir)s" +installopts = buildopts + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' From 4d0d3e2a7de94f376782df41afaa0cb33e861f18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 18:04:28 +0100 Subject: [PATCH 2412/9987] adding easyconfigs: Austin-3.2.0.eb --- .../easyconfigs/a/Austin/Austin-3.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb diff --git a/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb b/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb new file mode 100644 index 00000000000..bbc6c350110 --- /dev/null +++ b/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'Austin' +version = '3.2.0' + +homepage = 'https://github.com/P403n1x87/austin' +description = "Austin is a Python frame stack sampler for CPython written in pure C." + +toolchain = SYSTEM + +source_urls = ['https://github.com/P403n1x87/austin/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ee189af905fac77ff9173b57d8e927bdb7c4cf5e18b1bfd7f4456ac46fe04484'] + +cmds_map = [('.*', "$CC -std=c99 -O3 -Os -Wall -pthread src/*.c -o src/austin")] + +files_to_copy = [ + (['src/austin'], 'bin'), + (['src/austin.1'], 'share/man/man1'), +] + +sanity_check_paths = { + 'files': ['bin/austin', 'share/man/man1/austin.1'], + 'dirs': [], +} + +sanity_check_commands = [ + "austin --help", +] + +moduleclass = 'perf' From a22cf0190aaaecaf2ce42232708743788d0006eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 18:04:53 +0100 Subject: [PATCH 2413/9987] adding easyconfigs: Austin-3.2.0-GCCcore-11.2.0.eb --- .../a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d4f3285a8fd --- /dev/null +++ b/easybuild/easyconfigs/a/Austin/Austin-3.2.0-GCCcore-11.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'Austin' +version = '3.2.0' + +homepage = 'https://github.com/P403n1x87/austin' +description = "Austin is a Python frame stack sampler for CPython written in pure C." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/P403n1x87/austin/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ee189af905fac77ff9173b57d8e927bdb7c4cf5e18b1bfd7f4456ac46fe04484'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] +dependencies = [ + ('Python', '3.9.6'), + ('lxml', '4.6.3'), + ('protobuf-python', '3.17.3'), +] + +preconfigopts = "autoreconf --install && automake --add-missing && " + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('importlib_resources', '2.0.1', { + 'checksums': ['f5edfcece1cc9435d0979c19e08739521f4cf1aa1adaf6e571f732df6f568962'], + }), + ('austin-python', '1.2.1', { + 'modulename': 'austin', + 'checksums': ['42ba109c031c8c004c348fbbe5c18f177761d3dc531917420de51fa77cdb1fab'], + }), + ('austin-tui', '1.1.0', { + 'checksums': ['b2145a0e1da5095281974e2a37b4e67ce198f5281b7ac48e2801dbf879f46661'], + }), +] + +sanity_check_paths = { + 'files': ['bin/austin', 'bin/austin-tui', 'share/man/man1/austin.1'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "austin --help", + "austin-tui --help", + "pip check", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'perf' From 6ee3bd160c2af1fee5f881fe0cfffc499f56b5be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 23:31:28 +0100 Subject: [PATCH 2414/9987] stick to minimap2 2.13 as dep for RaGOO + enable download_dep_fail, use_pip, sanity_pip_check --- .../m/minimap2/minimap2-2.17-foss-2018b.eb | 34 ------------------- .../RaGOO-1.11-foss-2018b-Python-3.6.6.eb | 19 ++++++----- 2 files changed, 11 insertions(+), 42 deletions(-) delete mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb deleted file mode 100644 index 59e42b8bb3f..00000000000 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-foss-2018b.eb +++ /dev/null @@ -1,34 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Adam Huffman -# Big Data Institute, University of Oxford - -easyblock = 'MakeCp' - -name = 'minimap2' -version = "2.17" - -homepage = 'https://github.com/lh3/minimap2' -description = """Minimap2 is a fast sequence mapping and alignment -program that can find overlaps between long noisy reads, or map long -reads or their assemblies to a reference genome optionally with detailed -alignment (i.e. CIGAR). At present, it works efficiently with query -sequences from a few kilobases to ~100 megabases in length at an error -rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited -test data sets, minimap2 is over 20 times faster than most other -long-read aligners. It will replace BWA-MEM for long reads and contig -alignment.""" - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] -sources = ['%(name)s-%(version)s.tar.bz2'] -checksums = ['b68ac8882d33cc63e9e3246775062aeb159b6990ff7f38099172c3fe6f8a2742'] - -files_to_copy = [(['%(name)s'], 'bin'), 'LICENSE.txt', 'NEWS.md', 'README.md', (['%(name)s.1'], 'share/man/man1')] - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': [] -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb index a76297e3b5a..613e17d4b4d 100644 --- a/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb @@ -3,7 +3,7 @@ # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'RaGOO' version = '1.11' @@ -19,18 +19,21 @@ sources = ['v%(version)s.tar.gz'] checksums = ['a14ea39d4542989609d09b2f33fc59c5003f5b14bfac53f6eca15a367e95082a'] dependencies = [ - ('Python', '3.6.6'), - ('minimap2', '2.17'), - ('intervaltree', '3.0.2', '-Python-%(pyver)s'), - # numpy dependency is provided by the python module + ('Python', '3.6.6'), # provides numpy + ('minimap2', '2.13'), + ('intervaltree', '3.0.2', versionsuffix), ] +download_dep_fail = True +use_pip = True + sanity_check_paths = { 'files': ['bin/ragoo.py'], - 'dirs': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -# workaround for the python sanity check trying to do 'import ragoo' -options = {'modulename': 'os'} +options = {'modulename': 'ragoo_utilities'} + +sanity_pip_check = True moduleclass = 'bio' From e486f98357cc78aac7947e760fc698a077890fe2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 19 Dec 2021 23:40:00 +0100 Subject: [PATCH 2415/9987] add back attribution in dill easyconfig --- easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb index d6147e812d7..68674f3f2c1 100644 --- a/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/dill/dill-0.3.4-GCCcore-11.2.0.eb @@ -1,3 +1,4 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. easyblock = 'PythonPackage' name = 'dill' From 12ef2fe98e0e154660a335062731a8c651d24185 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Dec 2021 00:07:56 +0100 Subject: [PATCH 2416/9987] avoid unneeded local variables in Embree easyconfig --- ...Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 8d9da0f977c..c7a26e87bcc 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -1,10 +1,7 @@ easyblock = 'CMakeMake' -name = 'Embree' -version = "3.4.0" -gccver = '6.4.0' -binutilsver = '2.28' -gccsuff = '-GCC-%s' % (gccver) +name = 'Embree' +version = '3.4.0' homepage = 'https://embree.github.io/' description = """Intel® Embree is a collection of high-performance ray tracing kernels, developed at Intel. @@ -15,7 +12,7 @@ Intel® Embree supports runtime code selection to choose the traversal and build the instruction set of your CPU. We recommend using Intel® Embree through its API to get the highest benefit from future improvements. Intel® Embree is released as Open Source under the Apache 2.0 license.""" -toolchain = {'name': 'iccifort', 'version': '2018.1.163%s-%s' % (gccsuff, binutilsver)} +toolchain = {'name': 'iccifort', 'version': '2018.1.163-GCC-6.4.0-2.28'} source_urls = ['https://github.com/embree/embree/archive/'] sources = ['v%(version)s.tar.gz'] @@ -25,7 +22,7 @@ builddependencies = [('CMake', '3.11.4')] dependencies = [ ('ispc', '1.10.0', '', True), - ('tbb', '2018_U5', '', ('GCCcore', gccver)), + ('tbb', '2018_U5'), ] configopts = '-DEMBREE_TUTORIALS=OFF ' From 8e55025073b285a273ead89fc55ecf1a11dd21b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Dec 2021 00:17:46 +0100 Subject: [PATCH 2417/9987] rename intervaltree Python package to intervaltree-python + install it via PythonBundle since it also required sortedcontainers --- ...ee-python-3.0.2-foss-2018b-Python-3.6.6.eb | 41 +++++++++++++++++++ ...ervaltree-3.0.2-foss-2018b-Python-3.6.6.eb | 30 -------------- .../RaGOO-1.11-foss-2018b-Python-3.6.6.eb | 2 +- 3 files changed, 42 insertions(+), 31 deletions(-) create mode 100644 easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb delete mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..e1cca3746a6 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonBundle' + +name = 'intervaltree-python' +version = '3.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/chaimleib/intervaltree' +description = """A mutable, self-balancing interval tree. Queries may be by point, by range overlap, + or by range containment""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('intervaltree', version, { + 'checksums': ['cb4f61c81dcb4fea6c09903f3599015a83c9bdad1f0bbd232495e6681e19e273'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb deleted file mode 100644 index ca15abe5443..00000000000 --- a/easybuild/easyconfigs/i/intervaltree/intervaltree-3.0.2-foss-2018b-Python-3.6.6.eb +++ /dev/null @@ -1,30 +0,0 @@ -# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'PythonPackage' - -name = 'intervaltree' -version = '3.0.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/chaimleib/intervaltree' -description = 'A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment' - -toolchain = {'name': 'foss', 'version': '2018b'} - -source_urls = ['https://github.com/chaimleib/intervaltree/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['e8ab75b66077f2e5fb85ac56cb6df834689edb048d38601d53d8867cce3b77d1'] - -dependencies = [ - ('Python', '3.6.6'), -] - -sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/intervaltree-%(version)s-py%(pyshortver)s.egg'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb index 613e17d4b4d..939bf3e3e31 100644 --- a/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RaGOO/RaGOO-1.11-foss-2018b-Python-3.6.6.eb @@ -21,7 +21,7 @@ checksums = ['a14ea39d4542989609d09b2f33fc59c5003f5b14bfac53f6eca15a367e95082a'] dependencies = [ ('Python', '3.6.6'), # provides numpy ('minimap2', '2.13'), - ('intervaltree', '3.0.2', versionsuffix), + ('intervaltree-python', '3.0.2', versionsuffix), ] download_dep_fail = True From 365f167295014f011eb25d067c2a8a246709f57a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Dec 2021 00:24:43 +0100 Subject: [PATCH 2418/9987] use $CFLAGS rather than hardcoding '-O3 -Os' in Austin easyconfig Co-authored-by: Alex Domingo --- easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb b/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb index bbc6c350110..2ed5b3c23eb 100644 --- a/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb +++ b/easybuild/easyconfigs/a/Austin/Austin-3.2.0.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/P403n1x87/austin/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['ee189af905fac77ff9173b57d8e927bdb7c4cf5e18b1bfd7f4456ac46fe04484'] -cmds_map = [('.*', "$CC -std=c99 -O3 -Os -Wall -pthread src/*.c -o src/austin")] +cmds_map = [('.*', "$CC $CFLAGS -std=c99 -Wall -pthread src/*.c -o src/austin")] files_to_copy = [ (['src/austin'], 'bin'), From acd4fa055198a9813eed2199806bff878b099e02 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Dec 2021 00:28:01 +0100 Subject: [PATCH 2419/9987] pass compiler set by EB to build of ExaML v3.0.22 --- .../e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb index 7840f1a156e..8c5ef0fc82c 100644 --- a/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb +++ b/easybuild/easyconfigs/e/ExaML/ExaML-3.0.22-gompi-2021a-hybrid-avx.eb @@ -10,6 +10,7 @@ homepage = 'https://github.com/stamatak/ExaML/' description = "Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI" toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} github_account = 'stamatak' source_urls = [GITHUB_SOURCE] @@ -17,7 +18,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['802e673b0c2ea83fdbe6b060048d83f22b6978933a04be64fb9b4334fe318ca3'] prebuildopts = 'cd examl &&' -buildopts = '-f Makefile.OMP.AVX.gcc && cd ../parser && make -f Makefile.SSE3.gcc' +buildopts = '-f Makefile.OMP.AVX.gcc CC="$CC" &&' +buildopts += 'cd ../parser && make -f Makefile.SSE3.gcc CC="$CC"' files_to_copy = [(['examl/examl-OMP-AVX', 'parser/parse-examl'], 'bin'), 'README.md', 'manual'] From d213bf5fb99c49ba1f44eb29cbd667f3fb70e6d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Dec 2021 00:36:34 +0100 Subject: [PATCH 2420/9987] add custom sanity_check_paths for Embree --- .../Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index c7a26e87bcc..328732419a3 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -27,4 +27,9 @@ dependencies = [ configopts = '-DEMBREE_TUTORIALS=OFF ' +sanity_check_paths = { + 'files': ['lib/libembree3.%s' % SHLIB_EXT], + 'dirs': ['bin/embree3/models', 'include/embree3', 'lib/cmake/embree-%(version)s', 'share'], +} + moduleclass = 'vis' From 359c72b4cd816d2971683088a0fe7b1b77f1f94b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Dec 2021 01:44:06 +0100 Subject: [PATCH 2421/9987] explain why h5py v2.10.0 is bundled in yaff-1.6.0-foss-2020b.eb --- easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb index 229465a24ee..03214bbd476 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2020b.eb @@ -34,6 +34,7 @@ local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/m local_runtest += "python setup.py build_ext -i; nosetests -v" exts_list = [ + # yaff v1.6.0 does not work with h5py>=3.0, the default version in foss/2020b ('h5py', '2.10.0', { 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', From 20683302b5f345da56b32e205c151a1902496f2f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 20 Dec 2021 01:45:20 +0100 Subject: [PATCH 2422/9987] remove default sanity checks from molmod v1.4.8 --- easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb index 55945818bbf..1aa8772b2ae 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb @@ -26,9 +26,4 @@ sanity_pip_check = True runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" runtest += "python setup.py build_ext -i; pytest -ra" -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'math' From b43165020bc7df9a7acd1145dacf3de22cd288b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Dec 2021 08:26:35 +0100 Subject: [PATCH 2423/9987] don't set download_dep_fail in intervaltree-python easyconfig --- .../intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb index e1cca3746a6..c32e4755def 100644 --- a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.0.2-foss-2018b-Python-3.6.6.eb @@ -19,7 +19,6 @@ dependencies = [ ('Python', '3.6.6'), ] -download_dep_fail = True use_pip = True exts_list = [ From 68ef107266284e1ec7bd1ea8a231f2351e4f15e9 Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 14:27:47 +0200 Subject: [PATCH 2424/9987] adding easyconfigs: MultiQC-1.11-foss-2021a.eb --- .../m/MultiQC/MultiQC-1.11-foss-2021a.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb new file mode 100644 index 00000000000..0c12b69d6ad --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.11' + +homepage = 'https://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('matplotlib', '3.4.2'), + ('PyYAML', '5.4.1'), + ('networkx', '2.6.3'), +] + +use_pip = True + +exts_list = [ + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('Markdown', '3.2.1', { + 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], + }), + ('lzstring', '1.0.4', { + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('rich', '10.16.0', { + 'checksums': ['06a1355131feda5eba4511dd749e9187ac0fb42209e189845d81e94505fc268e'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('multiqc', version, { + 'checksums': ['6633ec44d8aed5477283158c613a46d27d3581d41baf0ecfac451a914870bab6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 045f3d0a5a89071e9401b1e87334f11eff174ccb Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 14:28:32 +0200 Subject: [PATCH 2425/9987] adding easyconfigs: MultiQC-1.10.1-foss-2020b.eb --- .../m/MultiQC/MultiQC-1.10.1-foss-2020b.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb new file mode 100644 index 00000000000..c89209dad06 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.10.1' + +homepage = 'https://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single + report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.3.3'), + ('PyYAML', '5.3.1'), + ('networkx', '2.5'), +] + +use_pip = True + +exts_list = [ + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('Markdown', '3.2.1', { + 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], + }), + ('lzstring', '1.0.4', { + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('rich', '10.16.0', { + 'checksums': ['06a1355131feda5eba4511dd749e9187ac0fb42209e189845d81e94505fc268e'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('multiqc', version, { + 'checksums': ['a4be38dd72da6b3b042d5dffbdcafd3e368189fbc4e767c79ce0aea1987c3a79'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 07af3b65149806bea88810beaf1bcf1344cc182f Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 14:56:09 +0200 Subject: [PATCH 2426/9987] using networkx=2.5.1 --- easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb index 0c12b69d6ad..0601bdf5eba 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.9.5'), ('matplotlib', '3.4.2'), ('PyYAML', '5.4.1'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ] use_pip = True From fe8365ebf123082d8fe29212db2cc0cf72d49972 Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 15:56:46 +0100 Subject: [PATCH 2427/9987] Update easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit added info comments Co-authored-by: Bob Dröge --- .../easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb index c89209dad06..ef76f02541b 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.10.1-foss-2020b.eb @@ -1,3 +1,13 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + easyblock = 'PythonBundle' name = 'MultiQC' From 4f69f2896cdcbd107d0f3eecd095064efeac79e8 Mon Sep 17 00:00:00 2001 From: genio0815 Date: Mon, 20 Dec 2021 15:58:47 +0100 Subject: [PATCH 2428/9987] Update easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit added info comments Co-authored-by: Bob Dröge --- .../easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb index 0601bdf5eba..f6a7cc770c2 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.11-foss-2021a.eb @@ -1,3 +1,13 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + easyblock = 'PythonBundle' name = 'MultiQC' From 12a01f35087866a8213007f0a0e7c2190ebb8ec8 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Tue, 21 Dec 2021 16:39:41 +1050 Subject: [PATCH 2429/9987] dep <- name change fix --- easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index bca8f6f7144..1181824b3f9 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -40,7 +40,7 @@ dependencies = [ ('minimap2', '2.20'), ('Mash', '2.3'), ('cDNA_Cupcake', '26.0.0'), - ('python-pulp', '2.5.1'), + ('PuLP', '2.5.1'), ] download_dep_fail = True From 7e6c5ecc9e397307eb6da295073ecb202c7aef95 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Tue, 21 Dec 2021 17:00:39 +1050 Subject: [PATCH 2430/9987] dep <- version conflict fix --- easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index 1181824b3f9..1dd3d1104e6 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -31,7 +31,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('matplotlib', '3.4.2'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ('scikit-image', '0.18.3'), ('Biopython', '1.79'), ('bx-python', '0.8.11'), From 98110f1bfa4a795e6f83335b297f98aae606d228 Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Tue, 21 Dec 2021 17:13:55 +1050 Subject: [PATCH 2431/9987] debug <- style fix --- easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb index 1dd3d1104e6..4c4c6c07fcc 100644 --- a/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/Cogent/Cogent-8.0.0-foss-2021a.eb @@ -50,8 +50,7 @@ sanity_pip_check = True sanity_check_paths = { 'files': ['bin/%s' % x for x in ['run_mash.py', 'process_kmer_to_graph.py', - 'reconstruct_contig.py'] - ], + 'reconstruct_contig.py']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From 81f38bf117b5baf40a42861843f843634ef9c173 Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Tue, 21 Dec 2021 08:43:32 +0100 Subject: [PATCH 2432/9987] Julia LTS update v1.6.5 --- .../j/Julia/Julia-1.6.5-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb new file mode 100644 index 00000000000..9488e9084d1 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.6.5' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['b8fe23ee547254a2fe14be587284ed77c78c06c2d8e9aad5febce0d21cab8e2c'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From 6ed38d6da0e1e083216d2d2ae019b1de28225db7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 21 Dec 2021 09:18:26 +0100 Subject: [PATCH 2433/9987] remove FastTree easyconfig, merged in #14564 --- .../FastTree-2.1.11-GCCcore-10.3.0.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb deleted file mode 100644 index e210cab5b2b..00000000000 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -# Updated from previous config -# Author: Pavel Grochal (INUITS) -# License: GPLv2 - -easyblock = 'CmdCp' - -name = 'FastTree' -version = '2.1.11' - -homepage = 'https://www.microbesonline.org/fasttree/' -description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide - or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of - time and memory. """ - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://www.microbesonline.org/fasttree/'] -sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] -checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] - -builddependencies = [('binutils', '2.36.1')] - -cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] - -files_to_copy = [(['FastTree'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/FastTree'], - 'dirs': [], -} - -sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] - -moduleclass = 'bio' From 8a18edfea8ab88a51443fb3fa8eae29aa9e1dd7a Mon Sep 17 00:00:00 2001 From: Max Voit Date: Tue, 21 Dec 2021 12:03:15 +0100 Subject: [PATCH 2434/9987] adding easyconfigs: CAFE5-5.0.0-GCC-10.2.0.eb --- .../c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..e1a52c7d446 --- /dev/null +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -0,0 +1,42 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'CAFE5' +version = '5.0.0' + +homepage = 'https://github.com/hahnlab/CAFE5' + +description = """Software for Computational Analysis of gene Family Evolution + +The purpose of CAFE is to analyze changes in gene family size in a way that +accounts for phylogenetic history and provides a statistical foundation for +evolutionary inferences. The program uses a birth and death process to model +gene gain and loss across a user-specified phylogenetic tree. The distribution +of family sizes generated under this model can provide a basis for assessing the +significance of the observed family size differences among taxa. +""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +#toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] + +builddependencies = [] + +dependencies = [] + +install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' + +sanity_check_paths = { + 'files': ['bin/cafe5', + ], + 'dirs': ['bin', 'examples'], +} + +moduleclass = 'bio' From 566fa5ff37689878f98dde75979fc4fd0a65ce22 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 12:06:28 +0100 Subject: [PATCH 2435/9987] Update CAFE5-5.0.0-GCC-10.2.0.eb --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index e1a52c7d446..8b45dda0bc2 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -1,7 +1,5 @@ # EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# Author: Max Voit easyblock = 'ConfigureMake' From 72b4b183def9cc5f6dd77e22a36c3db1fad233ea Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:50:54 +0100 Subject: [PATCH 2436/9987] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 8b45dda0bc2..63828151ad0 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -15,8 +15,7 @@ accounts for phylogenetic history and provides a statistical foundation for evolutionary inferences. The program uses a birth and death process to model gene gain and loss across a user-specified phylogenetic tree. The distribution of family sizes generated under this model can provide a basis for assessing the -significance of the observed family size differences among taxa. -""" +significance of the observed family size differences among taxa.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} #toolchainopts = {'openmp': True} From b881ae31d219f831a23311e6ac08d53a8ba9addc Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:06 +0100 Subject: [PATCH 2437/9987] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 63828151ad0..3c49fe65082 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} #toolchainopts = {'openmp': True} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] -sources = ['%(name)s-%(version)s.tar.gz'] +sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] builddependencies = [] From 243125a8de9ccae1ce636ff5ee1abdb12c44eb27 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:14 +0100 Subject: [PATCH 2438/9987] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 3c49fe65082..1e837f985a4 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -23,11 +23,6 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] - -builddependencies = [] - -dependencies = [] - install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' sanity_check_paths = { From c3aea9dfe19884e970e827acec4e99c52fea1226 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:19 +0100 Subject: [PATCH 2439/9987] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 1e837f985a4..a631bd275a2 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -26,8 +26,7 @@ checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' sanity_check_paths = { - 'files': ['bin/cafe5', - ], + 'files': ['bin/cafe5'], 'dirs': ['bin', 'examples'], } From 337dd3673aa4bc1195aa6f1cdef38c0e6889fe13 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 13:51:27 +0100 Subject: [PATCH 2440/9987] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index a631bd275a2..efbb78a6685 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -30,4 +30,6 @@ sanity_check_paths = { 'dirs': ['bin', 'examples'], } +sanity_check_commands = ['cafe5 --help'] + moduleclass = 'bio' From 2878927820030073dd2f4f39af9c2e9ae10379be Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 14:48:59 +0100 Subject: [PATCH 2441/9987] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index efbb78a6685..01a1de16141 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -27,7 +27,7 @@ install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 sanity_check_paths = { 'files': ['bin/cafe5'], - 'dirs': ['bin', 'examples'], + 'dirs': ['examples'], } sanity_check_commands = ['cafe5 --help'] From eb7d1e781851b627aed1c522f2ad7b922651cf0b Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 14:49:05 +0100 Subject: [PATCH 2442/9987] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 01a1de16141..9b18ee21156 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -23,6 +23,8 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] + +buildopts = 'CFLAGS="$CXXFLAGS -I. -include config.h" LINKER="$CXX $CXXFLAGS -o" ' install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' sanity_check_paths = { From 56ef3a1d4dbfac337e3dbb8c5841043e6a0c0632 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 21 Dec 2021 14:49:12 +0100 Subject: [PATCH 2443/9987] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 9b18ee21156..9706d2a7224 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -18,7 +18,7 @@ of family sizes generated under this model can provide a basis for assessing the significance of the observed family size differences among taxa.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -#toolchainopts = {'openmp': True} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} source_urls = ['https://github.com/hahnlab/CAFE5/releases/download/v5.0'] sources = [SOURCE_TAR_GZ] From 62a15974a958a112d6c5035935f0c5d822815ae2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Dec 2021 16:51:03 +0100 Subject: [PATCH 2444/9987] add ICU dependency for Qt5 v5.15.2 Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index 2d43727ea14..18e55bea4a7 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -60,6 +60,7 @@ dependencies = [ ('JasPer', '2.0.33'), ('bzip2', '1.0.8'), ('OpenSSL', '1.1', '', True), + ('ICU', '69.1'), ] # qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) From 05533f8c94720a038fcfc95c048043b414e94893 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 21 Dec 2021 16:54:20 +0000 Subject: [PATCH 2445/9987] Add git as build dependency. --- easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb index 9495f86059e..3a04eb5df1c 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('Yasm', '1.3.0'), + ('git', '2.32.0', '-nodocs'), ] start_dir = 'source' From 85cdfe87241377a9658b40a75eb83a26b4def7cc Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 21 Dec 2021 17:26:11 +0000 Subject: [PATCH 2446/9987] Remove git dependency, force check to assume it's a downloaded archive. --- easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb index 3a04eb5df1c..e4954e8ef8c 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-10.3.0.eb @@ -21,11 +21,12 @@ builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('Yasm', '1.3.0'), - ('git', '2.32.0', '-nodocs'), ] start_dir = 'source' +configopts = '-DGIT_ARCHETYPE=1' + sanity_check_paths = { 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], 'dirs': [], From dc26caecb680cf4f559c53e4e602457eb666d81e Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 21 Dec 2021 18:09:19 +0000 Subject: [PATCH 2447/9987] Added fix to x265-3.5-GCCcore-11.2.0.eb. --- easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb index 8b337e94692..0732a992f17 100644 --- a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.2.0.eb @@ -25,6 +25,8 @@ builddependencies = [ start_dir = 'source' +configopts = '-DGIT_ARCHETYPE=1' + sanity_check_paths = { 'files': ['bin/x265', 'include/x265_config.h', 'include/x265.h', 'lib/libx265.a', 'lib/libx265.%s' % SHLIB_EXT], 'dirs': [], From 1f94d739cb7dd1971abcf7a59897348ac1b0ccad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Dec 2021 21:00:38 +0100 Subject: [PATCH 2448/9987] adding easyconfigs: gnuplot-5.4.2-GCCcore-11.2.0.eb, libgd-2.3.3-GCCcore-11.2.0.eb --- .../g/gnuplot/gnuplot-5.4.2-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ .../l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb | 35 +++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c2af06feb4c --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.2-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.4.2' + +homepage = 'http://gnuplot.sourceforge.net' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['e57c75e1318133951d32a83bcdc4aff17fed28722c4e71f2305cfc2ae1cae7ba'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkgconf', '1.8.0'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('cairo', '1.16.0'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('libgd', '2.3.3'), + ('Pango', '1.48.8'), + ('libcerf', '1.17'), + ('X11', '20210802'), + ('Qt5', '5.15.2'), + ('Lua', '5.4.3'), +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..30b7642af4e --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.3' + +homepage = 'https://libgd.github.io' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd3f1f0bb016edcc0b2d082e8229c822ad1d02223511997c80461481759b1ed2'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('fontconfig', '2.13.94'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libgd.a', 'lib/libgd.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'lib' From 3f311319f8b9a0632093d312cb43fd5ba4ce51b3 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 22 Dec 2021 10:04:45 +0100 Subject: [PATCH 2449/9987] adding easyconfigs: gmsh-4.9.0-foss-2021a-Python-3.9.5.eb, occt-7.5.0p1-foss-2021a.eb, FreeImage-3.18.0-GCCcore-10.3.0.eb --- .../FreeImage-3.18.0-GCCcore-10.3.0.eb | 39 ++++++++++++++++ .../gmsh-4.9.0-foss-2021a-Python-3.9.5.eb | 43 ++++++++++++++++++ .../o/occt/occt-7.5.0p1-foss-2021a.eb | 45 +++++++++++++++++++ 3 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb create mode 100644 easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6791fe420e5 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FreeImage' +version = '3.18.0' + +homepage = 'http://freeimage.sourceforge.net' +description = """FreeImage is an Open Source library project for developers who would like to support popular graphics +image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to +use, fast, multithreading safe.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(name)s%s.zip' % ''.join(version.split('.'))] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip + '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # FreeImage-3.18.0-fix-makefile.patch +] + +builddependencies = [('binutils', '2.36.1')] + +skipsteps = ['configure'] + +buildopts = ['', '-f Makefile.fip'] +installopts = [ + 'INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib', + '-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib' +] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['include/FreeImage.h', 'include/FreeImagePlus.h', 'lib/libfreeimage.a', 'lib/libfreeimage.%s' % SHLIB_EXT, + 'lib/libfreeimageplus.a', 'lib/libfreeimageplus.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..0a2c21fd5ee --- /dev/null +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'gmsh' +version = '4.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://gmsh.info/' +description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {"usempi": True} + +source_urls = ['https://gmsh.info/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] +checksums = ['b8ef133c9b66ffe12df1747e72d4acf19f1eb1e9cd95eb0f577cbc4081d9bea3'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('PETSc', '3.15.1'), + ('SLEPc', '3.15.1'), + ('FLTK', '1.3.6'), + ('occt', '7.5.0p1'), +] + +separate_build_dir = True + +configopts = '-DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' + +modextrapaths = {'PYTHONPATH': ['lib64']} + +sanity_check_paths = { + 'files': ['bin/gmsh', 'bin/onelab.py'], + 'dirs': [], +} + +sanity_check_commands = ["gmsh --help"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb new file mode 100644 index 00000000000..f9d90b33602 --- /dev/null +++ b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'occt' +version = '7.5.0p1' + +homepage = 'https://www.opencascade.com/' +description = """Open CASCADE Technology (OCCT) is an object-oriented C++ +class library designed for rapid production of sophisticated domain-specific +CAD/CAM/CAE applications.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://files.salome-platform.org/Salome/other'] +sources = ['opencascade-%(version)s.tar.gz'] +checksums = ['c0bbe42f0c41b6dcd6a39a83961ca7e414eb2d5d919f4dcb930096f2a423a578'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Mesa', '21.1.1'), + ('freetype', '2.10.4'), + ('Tcl', '8.6.11'), + ('Tk', '8.6.11'), + ('FreeImage', '3.18.0'), + ('tbb', '2020.3'), +] + +separate_build_dir = True + +configopts = "-DUSE_FREEIMAGE=ON -D3RDPARTY_FREEIMAGE_DIR=$EBROOTFREEIMAGE " +configopts += "-D3RDPARTY_TBB_DIR=$EBROOTTBB " +configopts += "-D3RDPARTY_TCL_DIR=$EBROOTTCL " +configopts += "-D3RDPARTY_TK_DIR=$EBROOTTK " +configopts += "-D3RDPARTY_FREETYPE_DIR=$EBROOTFREETYPE " + +sanity_check_paths = { + 'files': ['bin/DRAWEXE', 'bin/env.sh'], + 'dirs': ['lib/cmake/opencascade'], +} + +moduleclass = 'cae' From 8d719b09fa0eeae7c680b049d11c33a988125a5f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 22 Dec 2021 09:19:23 +0000 Subject: [PATCH 2450/9987] adding easyconfigs: numdiff-5.9.0-GCCcore-10.2.0.eb --- .../n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9c49693bbc4 --- /dev/null +++ b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'numdiff' +version = '5.9.0' + +homepage = 'https://savannah.nongnu.org/projects/numdiff' +description = """Numdiff (which I will also write numdiff) is a little program that can be used to compare putatively + similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats. + Equivalently, Numdiff is a program with the capability to appropriately compare files containing numerical fields + (and not only).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['87284a117944723eebbf077f857a0a114d818f8b5b54d289d59e73581194f5ef'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/ndselect', 'bin/numdiff'], + 'dirs': ['share'], +} + +sanity_check_commands = ["numdiff --help"] + +moduleclass = 'tools' From 8f9b57573dcd7b2c9b09e3c5f32505358c58f4b5 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 22 Dec 2021 09:36:16 +0000 Subject: [PATCH 2451/9987] switch homepage MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb index 9c49693bbc4..b8f9bfcd13d 100644 --- a/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'numdiff' version = '5.9.0' -homepage = 'https://savannah.nongnu.org/projects/numdiff' +homepage = 'https://www.nongnu.org/numdiff/' description = """Numdiff (which I will also write numdiff) is a little program that can be used to compare putatively similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats. Equivalently, Numdiff is a program with the capability to appropriately compare files containing numerical fields From a1827ca68d6470cb353d46814f251a5d3c3719b0 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 22 Dec 2021 11:56:44 +0100 Subject: [PATCH 2452/9987] Removed versionsuffix --- ...4.9.0-foss-2021a-Python-3.9.5.eb => gmsh-4.9.0-foss-2021a.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/g/gmsh/{gmsh-4.9.0-foss-2021a-Python-3.9.5.eb => gmsh-4.9.0-foss-2021a.eb} (96%) diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a.eb similarity index 96% rename from easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb rename to easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a.eb index 0a2c21fd5ee..dbc13d8c38f 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a.eb @@ -2,7 +2,6 @@ easyblock = 'CMakeMake' name = 'gmsh' version = '4.9.0' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://gmsh.info/' description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" From 0504cf0668d1c7ca233ec6ef571213a21e54c121 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 22 Dec 2021 12:15:38 +0100 Subject: [PATCH 2453/9987] adding easyconfigs: JUBE-2.4.2.eb --- easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb | 31 ++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb new file mode 100644 index 00000000000..7fe48f84a3e --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb @@ -0,0 +1,31 @@ +easyblock = "VersionIndependentPythonPackage" + +name = "JUBE" +version = "2.4.2" + +homepage = "https://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based +framework to easily create benchmark sets, run those sets on different +computer systems and evaluate the results. +""" + +toolchain = SYSTEM + +source_urls = ['https://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +sources = [SOURCE_TAR_GZ] +checksums = ['d1de15e9792802f83521b582d1d144ec81e3d5a28c01dbd945288ea29b946729'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [], +} + +modextrapaths = { + 'JUBE_INCLUDE_PATH': 'share/jube/platform/slurm' +} + +modluafooter = 'execute {cmd=\'eval "$(jube complete)"\',modeA={"load"}}' + +moduleclass = 'tools' From c04db4bf3671a1d5060ac426b9f5a7171f138892 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 12:36:22 +0100 Subject: [PATCH 2454/9987] add 'webpng --help' as sanity check command for libgd MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb index 30b7642af4e..f483ddfc597 100644 --- a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.2.0.eb @@ -32,4 +32,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include'], } +sanity_check_commands = ['webpng --help'] + moduleclass = 'lib' From 51fe4983134e9d445fd56ff620b0cc1fbf061b79 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 13:40:05 +0100 Subject: [PATCH 2455/9987] remove commented out license_file spec in itac 2021.2.0 easyconfig --- easybuild/easyconfigs/i/itac/itac-2021.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb index b95225dd483..3deaaa9e711 100644 --- a/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb +++ b/easybuild/easyconfigs/i/itac/itac-2021.2.0.eb @@ -19,7 +19,4 @@ dontcreateinstalldir = True preferredmpi = 'impi5' -# license file -# license_file = HOME + '/licenses/intel/license.lic' - moduleclass = 'tools' From 389bcf7aadc1379c08f9d557dff5571abaf1f929 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 22 Dec 2021 14:20:34 +0100 Subject: [PATCH 2456/9987] Add sanity check command for occt --- easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb index f9d90b33602..7c0a089a242 100644 --- a/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb +++ b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2021a.eb @@ -42,4 +42,6 @@ sanity_check_paths = { 'dirs': ['lib/cmake/opencascade'], } +sanity_check_commands = ['DRAWEXE -h'] + moduleclass = 'cae' From 429c3a3d372721a05c34f0ee2229551f1d9c4235 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 15:05:04 +0100 Subject: [PATCH 2457/9987] stick to libunwind 1.4.0 as dependency for Extra 3.8.3 with gompi/2021a --- easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb index a58b66ffa82..d10c82b4856 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb @@ -24,7 +24,7 @@ checksums = ['32a3d6b01da2c9b8d177d91307d4c04c6db0923ca1d63bfb32768a172af7943b'] dependencies = [ ('zlib', '1.2.11'), ('Boost', '1.76.0'), - ('libunwind', '1.5.0'), + ('libunwind', '1.4.0'), ('libxml2', '2.9.10'), ('libdwarf', '20210305'), ('PAPI', '6.0.0.1'), From ddd8b575d79467eb12b3ca009e65e486ed8921da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 16:13:50 +0100 Subject: [PATCH 2458/9987] add sanity check command for libdwarf 20210305 --- .../easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb index 4d501a86e34..e2175d20e81 100644 --- a/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20210305-GCCcore-10.3.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': ['include'] } +sanity_check_commands = ['dwarfdump --help'] + moduleclass = 'devel' From 7ac359f1a2ee8cfd1c69d116d59ad9877e1ab2e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 16:15:26 +0100 Subject: [PATCH 2459/9987] fix checksum for Extrae 3.8.3 --- easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb index d10c82b4856..4662280bbb5 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb @@ -19,7 +19,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] sources = ['%(namelower)s-%(version)s-src.tar.bz2'] -checksums = ['32a3d6b01da2c9b8d177d91307d4c04c6db0923ca1d63bfb32768a172af7943b'] +checksums = ['1495dc9d16eef7f1966228c7301e0cab30a3861fe46d9551770c40ffd758d198'] dependencies = [ ('zlib', '1.2.11'), From ee268254bf06dcee65a9631653b2d334007dd253 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 18:04:00 +0100 Subject: [PATCH 2460/9987] accept both original and current checksum for source tarball of Extrae 3.8.3 --- easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb index 4662280bbb5..f1082fc78ce 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.8.3-gompi-2021a.eb @@ -19,7 +19,8 @@ toolchainopts = {'usempi': True} source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] sources = ['%(namelower)s-%(version)s-src.tar.bz2'] -checksums = ['1495dc9d16eef7f1966228c7301e0cab30a3861fe46d9551770c40ffd758d198'] +checksums = [('32a3d6b01da2c9b8d177d91307d4c04c6db0923ca1d63bfb32768a172af7943b', + '1495dc9d16eef7f1966228c7301e0cab30a3861fe46d9551770c40ffd758d198')] dependencies = [ ('zlib', '1.2.11'), From bc7530a9fe980d7ff9befdb9a1f18db1394af6ab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 22 Dec 2021 18:25:49 +0100 Subject: [PATCH 2461/9987] add simple sanity check for jube --- easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb index 7fe48f84a3e..8a1b74a328a 100644 --- a/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.4.2.eb @@ -22,6 +22,8 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['jube --version'] + modextrapaths = { 'JUBE_INCLUDE_PATH': 'share/jube/platform/slurm' } From ba8eb244b26fa44b344ec4f15f0e13de3a1b74b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 20:44:58 +0100 Subject: [PATCH 2462/9987] enable sanity_pip_check in Calcam easyconfigs --- .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb | 7 ++++--- .../c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb | 7 ++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb index ba8db2d6ade..aa81fc28ef0 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-2.7.14.eb @@ -27,9 +27,8 @@ dependencies = [ ('VTK', '8.1.0', '-Python-%(pyver)s'), ] -use_pip = True - download_dep_fail = True +use_pip = True # Pip asks whether an update from Calcam 1.x data representation to Calcam 2 is desired. # The following line answers "n" to this question and skips the conversion. @@ -37,7 +36,9 @@ preinstallopts = 'echo n |' sanity_check_paths = { 'files': ['bin/calcam'], - 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb index 193dc5501b8..14e871b7aee 100644 --- a/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/Calcam/Calcam-2.1.0-intel-2018a-Python-3.6.4.eb @@ -27,9 +27,8 @@ dependencies = [ ('VTK', '8.1.0', '-Python-%(pyver)s'), ] -use_pip = True - download_dep_fail = True +use_pip = True # Pip asks whether an update from Calcam 1.x data representation to Calcam 2 is desired. # The following line answers "n" to this question and skips the conversion. @@ -37,7 +36,9 @@ preinstallopts = 'echo n |' sanity_check_paths = { 'files': ['bin/calcam'], - 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'phys' From 0f0bbe94b15ebc5373adb15814891c8a1bacc344 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Dec 2021 22:36:08 +0100 Subject: [PATCH 2463/9987] add missing preinstallopts + strip out unneeded source_urls in easyconfig for numba 0.50.1 --- .../n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb index e5b096d734b..b6e4f5a3a9d 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.50.1-foss-2020a-Python-3.8.2.eb @@ -26,7 +26,7 @@ sanity_pip_check = True exts_list = [ ('llvmlite', '0.33.0', { 'patches': ['llvmlite-0.30.0_fix-ffi-Makefile.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", 'checksums': [ '9c8aae96f7fba10d9ac864b443d1e8c7ee4765c31569a2b201b3d0b67d8fc596', # llvmlite-0.33.0.tar.gz # llvmlite-0.30.0_fix-ffi-Makefile.patch @@ -34,7 +34,6 @@ exts_list = [ ], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], 'checksums': ['89e81b51b880f9b18c82b7095beaccc6856fcf84ba29c4f0ced42e4e5748a3a7'], }), ] From 207c0002aaff2de51a9d07eafb6b13d2e3009be8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 09:13:12 +0100 Subject: [PATCH 2464/9987] add patch to fix build of Arrow 0.17.1 on aarch64 systems + fix configure options --- .../a/Arrow/Arrow-0.17.1-foss-2020b.eb | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb index e4c0d64a274..e348b0044cb 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb @@ -9,15 +9,12 @@ description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [ - 'http://apache.belnet.be/arrow/arrow-%(version)s/', - 'https://www-eu.apache.org/dist/arrow/arrow-%(version)s/', -] +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -patches = ['Arrow-0.16.0_fix-intel.patch'] +patches = ['Arrow-0.17.1_fix-arm.patch'] checksums = [ 'cbc51c343bca08b10f7f1b2ef15cb15057c30e5e9017cfcee18337b7e2da9ea2', # apache-arrow-0.17.1.tar.gz - '7c1569087f93959a0dfc163d80e5f542edb4d7ed0b9d71a2a05b4081211ad2b9', # Arrow-0.16.0_fix-intel.patch + 'd1076d35966056c39e0c88b8fadaaa7660ee4d8c07fc2c5bdf1d5d6e683ff44a', # Arrow-0.17.1_fix-arm.patch ] builddependencies = [ @@ -35,18 +32,18 @@ dependencies = [ ('Boost', '1.74.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html -configopts = "-DCMAKE_BUILD_TYPE=Release -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] From d2a00a14ad6d00cd83dff4ec75defd3183c9631f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 09:13:28 +0100 Subject: [PATCH 2465/9987] add archive source URL for Spark 3.1.1 --- easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb index ba34f767b68..5cb1ec3c5ee 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -11,6 +11,7 @@ description = """Spark is Hadoop MapReduce done in memory""" toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [ + 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' ] sources = ['%(namelower)s-%(version)s-bin-hadoop2.7.tgz'] @@ -25,13 +26,13 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { + 'source_urls': [PYPI_SOURCE], 'download_dep_fail': True, 'use_pip': True, } exts_list = [ ('py4j', '0.10.9.2', { - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], }), ] From b642e2b4c3ce9a9850a6c68954ad9a7e46a854ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 10:26:30 +0100 Subject: [PATCH 2466/9987] adding easyconfigs: DyMat-0.7-foss-2021b-2020-12-12.eb --- .../DyMat/DyMat-0.7-foss-2021b-2020-12-12.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/d/DyMat/DyMat-0.7-foss-2021b-2020-12-12.eb diff --git a/easybuild/easyconfigs/d/DyMat/DyMat-0.7-foss-2021b-2020-12-12.eb b/easybuild/easyconfigs/d/DyMat/DyMat-0.7-foss-2021b-2020-12-12.eb new file mode 100644 index 00000000000..f7de7bbb8f3 --- /dev/null +++ b/easybuild/easyconfigs/d/DyMat/DyMat-0.7-foss-2021b-2020-12-12.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'DyMat' +version = '0.7' +local_commit = '3ce988f' +versionsuffix = '-2020-12-12' + +homepage = 'https://www.j-raedler.de/projects/DyMat' +description = "Read and process result files from Dymola and OpenModelica with Python." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/jraedler/DyMat/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'DyMat-%(version)s%(versionsuffix)s.tar.gz'}] +checksums = ['57ea1ac7c28aeb6fce1e3efdc7a5b11ee54ac015643453bff6b5996594bf84d2'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/DyMatExport.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cd %(builddir)s/DyMat-*/test && python Test.py", + "cd %(builddir)s/DyMat-*/test && DyMatExport.py --info DoublePendulum_Dymola-2012.mat", +] + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'tools' From 45ab6ccc84104ad8090736ae625d74151941265e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 10:41:18 +0100 Subject: [PATCH 2467/9987] adding easyconfigs: PyCalib-0.1.0.dev0-foss-2021b.eb --- .../PyCalib/PyCalib-0.1.0.dev0-foss-2021b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCalib/PyCalib-0.1.0.dev0-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/PyCalib/PyCalib-0.1.0.dev0-foss-2021b.eb b/easybuild/easyconfigs/p/PyCalib/PyCalib-0.1.0.dev0-foss-2021b.eb new file mode 100644 index 00000000000..0782d64ca15 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCalib/PyCalib-0.1.0.dev0-foss-2021b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'PyCalib' +version = '0.1.0.dev0' + +homepage = 'https://github.com/classifier-calibration/PyCalib' +description = "Python library for classifier calibration" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6f9662e5219d85aed5b91c0cd391e2297c9b94229c7591796a84f5e6f742168b'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('scikit-learn', '1.0.1'), + ('statsmodels', '0.13.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From 5b078e635f33e802aea7c024d07feaecf2442d3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 10:59:53 +0100 Subject: [PATCH 2468/9987] adding easyconfigs: alevin-fry-0.4.3-GCCcore-11.2.0.eb --- .../alevin-fry-0.4.3-GCCcore-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.4.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.4.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.4.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9fcc9fd98d1 --- /dev/null +++ b/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.4.3-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'Binary' + +name = 'alevin-fry' +version = '0.4.3' + +homepage = 'https://github.com/COMBINE-lab/alevin-fry' +description = """alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, + currently focused on single-cell transcriptomics and feature barcoding.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/COMBINE-lab/alevin-fry/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['407a1b5767a293aefa9ff1dc2eda478356e74d148e3bfa89ef58213340e87ae2'] + +builddependencies = [ + ('binutils', '2.37'), + ('Rust', '1.54.0'), + ('CMake', '3.21.1'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +extract_sources = True + +# pin version of clap dependency, +# see https://github.com/COMBINE-lab/alevin-fry/commit/dcdd91cb6ff49065f60f3b6b400bd023fc308ab6 +install_cmd = "sed -i 's/3.0.0-beta.5/=3.0.0-beta.5/g' Cargo.toml && " +install_cmd += "cargo install --root %(installdir)s --path ." + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' From 20a494ef1dc00c99aa90aebaba235d0c3c182c48 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 13:55:18 +0100 Subject: [PATCH 2469/9987] fix broken patch file for recent GPAW versions --- .../g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch | 2 +- .../easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb | 2 +- .../g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb | 2 +- .../g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb | 2 +- easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch index e64b4d0f7da..551d7ead70d 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch @@ -24,7 +24,7 @@ new file mode 100644 index 0000000..5be60fa --- /dev/null +++ b/doc/platforms/Linux/EasyBuild/config_foss.py -@@ -0,0 +1,49 @@ +@@ -0,0 +1,53 @@ +# Convert static library specs from EasyBuild to GPAW +def static_eblibs_to_gpawlibs(lib_specs): + return [libfile[3:-2] for libfile in os.getenv(lib_specs).split(',')] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb index 49832a9822a..06c705f51cb 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ 'c84307eb9943852d78d966c0c8856fcefdefa68621139906909908fb641b8421', # gpaw-20.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', # GPAW-20.1.0-Wrap-pragma-omp-simd-in-ifdef-_OPENMP-blocks.patch 'bf0e0179ce9261197a10a3a934ce3a8d46489b635a3130a5ceb2fe0fee67bb14', ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb index f87fd8a0abd..fc6b25cdb3d 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ 'c84307eb9943852d78d966c0c8856fcefdefa68621139906909908fb641b8421', # gpaw-20.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', # GPAW-20.1.0-Wrap-pragma-omp-simd-in-ifdef-_OPENMP-blocks.patch 'bf0e0179ce9261197a10a3a934ce3a8d46489b635a3130a5ceb2fe0fee67bb14', ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb index 67379b2bc14..31e4e602dc0 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb @@ -24,7 +24,7 @@ patches = [ checksums = [ '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb index 1dd3ad51a45..1b322074614 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb @@ -19,7 +19,7 @@ patches = [ checksums = [ '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb index 784eb04d4fa..7535f24c1a0 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb @@ -24,7 +24,7 @@ patches = [ checksums = [ '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb index 8264ef0a7fd..861a80e2fd1 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb @@ -19,7 +19,7 @@ patches = [ checksums = [ '77c3d3918f5cc118e448f8063af4807d163b31d502067f5cbe31fc756eb3971d', # gpaw-20.10.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', '50d3d46d87baf365e64eeb2cedf66fe9a28a763e04c157f9c1f8a610fd71eab5', # GPAW-20.10.0-test-mpi.patch ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb index 77370423b34..7a2e4989e8a 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb @@ -20,7 +20,7 @@ patches = [ checksums = [ '96843b68e04bd1c12606036c9f99b0ddfa5e6ee08ce46835e6bb347a6bd560a3', # gpaw-21.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb index f8f2758be19..1f22f89cc83 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb @@ -20,7 +20,7 @@ patches = [ checksums = [ '96843b68e04bd1c12606036c9f99b0ddfa5e6ee08ce46835e6bb347a6bd560a3', # gpaw-21.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb index f2b603dd335..582e90ea73b 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb index c88a6eea7e1..4abf305f2a6 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb @@ -19,7 +19,7 @@ patches = [ checksums = [ '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb index bedc11e9043..bba61ad1209 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ '5bb805bf514a7b04e3fdfce6f7864d150032badc5cd2805c57513af982d7a9cc', # gpaw-21.6.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', ] # The intel version is not built with libvdwxc support, as that library is incompatible with MKL. From e4b5758f09ccf0d74e707b0e03a8c60aa5fb1f42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 14:28:32 +0100 Subject: [PATCH 2470/9987] {toolchain} intel/2022.00 --- .../h/HPL/HPL-2.3-intel-2022.00.eb | 21 +++++++++++++ .../easyconfigs/i/iimpi/iimpi-2022.00.eb | 18 +++++++++++ .../imkl-FFTW-2022.0.1-iimpi-2022.00.eb | 11 +++++++ easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb | 16 ++++++++++ .../impi-2021.5.0-intel-compilers-2022.0.1.eb | 16 ++++++++++ .../intel-compilers-2022.0.1.eb | 31 +++++++++++++++++++ .../easyconfigs/i/intel/intel-2022.00.eb | 22 +++++++++++++ 7 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.00.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022.00.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2022.00.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.00.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.00.eb new file mode 100644 index 00000000000..fbc0e91b70f --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.00.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022.00'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022.00.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022.00.eb new file mode 100644 index 00000000000..715e4a7748a --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022.00.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022.00' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.0.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.5.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb new file mode 100644 index 00000000000..2eaf7432065 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.0.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022.00'} + +dependencies = [('imkl', version, '', True)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb new file mode 100644 index 00000000000..67a5563ac0b --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.0.1.eb @@ -0,0 +1,16 @@ +name = 'imkl' +version = '2022.0.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18444/'] +sources = ['l_onemkl_p_%(version)s.117_offline.sh'] +checksums = ['22afafbe2f3762eca052ac21ec40b845ff2f3646077295c88c2f37f80a0cc160'] + +interfaces = False + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb new file mode 100644 index 00000000000..bee00810199 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.5.0-intel-compilers-2022.0.1.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.5.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2022.0.1'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18370/'] +sources = ['l_mpi_oneapi_p_%(version)s.495_offline.sh'] +checksums = ['3aae53fe77f7c6aac7a32b299c25d6ca9a00ba4e2d512a26edd90811e59e7471'] + +dependencies = [('UCX', '1.11.2')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb new file mode 100644 index 00000000000..56c8e9b5da4 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.1.eb @@ -0,0 +1,31 @@ +name = 'intel-compilers' +version = '2022.0.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18435/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.71_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18436/'], + 'filename': 'l_fortran-compiler_p_%(version)s.70_offline.sh', + }, +] +checksums = [ + 'c7cddc64c3040eece2dcaf48926ba197bb27e5a46588b1d7b3beddcdc379926a', # l_dpcpp-cpp-compiler_p_2022.0.1.71_offline.sh + '2cb28a04f93554bfeffd6cad8bd0e7082735f33d73430655dea86df8933f50d1', # l_fortran-compiler_p_2022.0.1.70_offline.sh +] + +local_gccver = '11.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.37', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2022.00.eb b/easybuild/easyconfigs/i/intel/intel-2022.00.eb new file mode 100644 index 00000000000..756e76c67c6 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022.00.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022.00' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.0.1' +local_gccver = '11.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.37', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.5.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', True), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From 83aa6f4c1b3fca801bd9df250ff4a78c475bff50 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 14:44:31 +0100 Subject: [PATCH 2471/9987] adding easyconfigs: Spack-0.17.0.eb --- easybuild/easyconfigs/s/Spack/Spack-0.17.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spack/Spack-0.17.0.eb diff --git a/easybuild/easyconfigs/s/Spack/Spack-0.17.0.eb b/easybuild/easyconfigs/s/Spack/Spack-0.17.0.eb new file mode 100644 index 00000000000..3d643965035 --- /dev/null +++ b/easybuild/easyconfigs/s/Spack/Spack-0.17.0.eb @@ -0,0 +1,32 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Tarball' + +name = 'Spack' +version = '0.17.0' + +homepage = 'https://spack.io/' +description = """Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific + software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, + and all of these builds can coexist on the same machine.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/spack/spack/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['93df99256a892ceefb153d48e2080c01d18e58e27773da2c2a469063d67cb582'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ['bin/spack'], + 'dirs': ['etc/spack/defaults', 'lib/spack', 'share/spack', 'var/spack'], +} + +sanity_check_commands = [ + "spack list", + "spack versions gcc", +] + +moduleclass = 'devel' From beb35c5360b714995382a88c38194f0e54fe3854 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 14:50:12 +0100 Subject: [PATCH 2472/9987] adding easyconfigs: MCR-R2021b.1.eb --- easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb b/easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb new file mode 100644 index 00000000000..34e1f19f214 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'MCR' +version = 'R2021b' # runtime version 9.11 +local_update = '1' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%(version)s_glnxa64.zip'] +checksums = ['d7067b4f4977350395fd75de1aeefc9de39010fbdcf32d99a5f2e8955e74121e'] + +moduleclass = 'math' From 08625042f3dd6c8e215ff922ffe7f860f62f9fba Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 14:52:59 +0100 Subject: [PATCH 2473/9987] adding easyconfigs: dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb --- ...otNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..20136cc0efc --- /dev/null +++ b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Tarball' + +# note: only works on recent OSs, required sufficiently recent glibc (2.14 or newer) +name = 'dotNET-Core-Runtime' +version = '6.0.1' + +homepage = 'https://www.microsoft.com/net/' +description = """.NET is a free, cross-platform, open source developer platform for building many different types + of applications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://download.visualstudio.microsoft.com/download/pr/' + + 'be8a513c-f3bb-4fbd-b382-6596cf0d67b5/968e205c44eabd205b8ea98be250b880'] +sources = ['dotnet-runtime-%(version)s-linux-x64.tar.gz'] +checksums = ['f77369477ee8c98402793a2b6ce1f46d663fd0373a93a4cef50eb22d8607773c'] + +dependencies = [('libunwind', '1.5.0')] + +sanity_check_paths = { + 'files': ['dotnet'], + 'dirs': ['shared/Microsoft.NETCore.App/%(version)s'], +} + +modextrapaths = {'PATH': ['']} + +moduleclass = 'lang' From 5d4c06a94a352fc96c7ae1a34f74433fe94d6fc8 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 14:54:54 +0100 Subject: [PATCH 2474/9987] adding easyconfigs: dotNET-SDK-6.0.101-linux-x64.eb --- .../dotNET-SDK-6.0.101-linux-x64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb diff --git a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb new file mode 100644 index 00000000000..7e1702a66c2 --- /dev/null +++ b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb @@ -0,0 +1,31 @@ +## +# Authors:: Robert Qiao +# Robert Mijakovic +## +easyblock = 'Tarball' + +name = 'dotNET-SDK' +version = '6.0.101' +versionsuffix = '-linux-x64' + +homepage = 'https://www.microsoft.com/net/' +description = """.NET is a free, cross-platform, open source developer platform for building many different types + of applications.""" + +toolchain = SYSTEM +source_urls = ['https://download.visualstudio.microsoft.com/download/pr/' + + 'ede8a287-3d61-4988-a356-32ff9129079e/bdb47b6b510ed0c4f0b132f7f4ad9d5a'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['95a1b5360b234e926f12327d68c4a0d7b7206134dca1b570a66dc7a8a4aed705'] + +sanity_check_paths = { + 'files': ['dotnet'], + 'dirs': ['shared/Microsoft.NETCore.App', 'shared/Microsoft.AspNetCore.App'], +} + +modextrapaths = { + 'PATH': [''], + 'DOTNET_ROOT': [''], +} + +moduleclass = 'lang' From 50fe9b8001d4a62ece2578392e458cea3ed5cfbe Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:06:25 +0100 Subject: [PATCH 2475/9987] adding easyconfigs: AMD-uProf-3.4.502.eb --- .../a/AMD-uProf/AMD-uProf-3.4.502.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb diff --git a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb new file mode 100644 index 00000000000..37ec97a3ea8 --- /dev/null +++ b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb @@ -0,0 +1,32 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Binary' + +name = 'AMD-uProf' +version = '3.4.502' + +homepage = 'https://developer.amd.com/amd-uprof/' +description = """AMD Random Number Generator Library is a pseudorandom number generator library.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.amd.com/wordpress/media/files/'] +sources = ['AMDuProf_Linux_x64_%(version)s.tar.bz2'] +checksums = ['891463c0e4f20e1c67a145441e983c863156a52716234cd8d5a96a8d09635ba7'] + +extract_sources = True + +sanity_check_paths = { + 'files': ['include/AMDTPowerProfileApi.h', 'lib/x64/libAMDProfileController.a', + 'bin/libAMDThreadProfileAPI.%s' % SHLIB_EXT, 'bin/AMDuProf'], + 'dirs': ['Examples'] +} + +sanity_check_commands = ['AMDuProfCLI info --system'] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'bin' +} + +moduleclass = 'perf' From 52b2658de66447e2c4960bee6959435e688f2d42 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:10:17 +0100 Subject: [PATCH 2476/9987] adding easyconfigs: VTune-2022.0.0.eb --- .../easyconfigs/v/VTune/VTune-2022.0.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb new file mode 100644 index 00000000000..e205471e1e5 --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.0.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +name = 'VTune' +version = '2022.0.0' + +homepage = 'https://software.intel.com/en-us/vtune' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18406/'] +sources = ['l_oneapi_vtune_p_%(version)s.94_offline.sh'] +checksums = ['aa4d575c22e7be0c950b87d67d9e371f470f682906864c4f9b68e530ecd22bd7'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'tools' From b1cd41425aae067643e33c45d60adea3a8a2e07d Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:13:40 +0100 Subject: [PATCH 2477/9987] adding easyconfigs: itac-2021.5.0.eb --- easybuild/easyconfigs/i/itac/itac-2021.5.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/i/itac/itac-2021.5.0.eb diff --git a/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb new file mode 100644 index 00000000000..f9d10379c85 --- /dev/null +++ b/easybuild/easyconfigs/i/itac/itac-2021.5.0.eb @@ -0,0 +1,22 @@ +## +# Author: Robert Mijakovic +## +name = 'itac' +version = '2021.5.0' + +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' +description = """The Intel Trace Collector is a low-overhead tracing library that performs + event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application + activities gathered by the Intel Trace Collector through graphical displays. """ + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18367/'] +sources = ['l_itac_oneapi_p_%(version)s.370_offline.sh'] +checksums = ['c2b31298d8b4069a62d9352873c7f6e17ce240ad7293f9bacdc6de3794675b58'] + +dontcreateinstalldir = True + +preferredmpi = 'impi5' + +moduleclass = 'tools' From 6190404ea12fd371138b2997d730227d51eb8c35 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:14:53 +0100 Subject: [PATCH 2478/9987] adding easyconfigs: Inspector-2022.0.0.eb --- .../i/Inspector/Inspector-2022.0.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb new file mode 100644 index 00000000000..430cc62b2d4 --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.0.0.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'Inspector' +version = '2022.0.0' + +homepage = 'https://software.intel.com/en-us/inspector' +description = """Intel Inspector is a dynamic memory and threading error + checking tool for users developing serial and parallel applications""" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18363/'] +sources = ['l_inspector_oneapi_p_%(version)s.56_offline.sh'] +checksums = ['79a0eb2ae3f1de1e3456076685680c468702922469c3fda3e074718fb0bea741'] + +dontcreateinstalldir = True + +requires_runtime_license = False + +moduleclass = 'tools' From 8733a8a3ad56dae9b2c18380229f4fc4a590b48c Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:18:37 +0100 Subject: [PATCH 2479/9987] adding easyconfigs: Blender-3.0.0-binary.eb --- .../b/Blender/Blender-3.0.0-binary.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb b/easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb new file mode 100644 index 00000000000..8de30bc9841 --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb @@ -0,0 +1,36 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PackedBinary' + +name = 'Blender' +version = '3.0.0' +versionsuffix = '-binary' + +homepage = 'https://www.blender.org' +description = """ +Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline, +modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video +editing and game creation. +""" + +toolchain = SYSTEM + +source_urls = ['http://ftp.nluug.nl/pub/graphics/%(namelower)s/release/%(name)s%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s-linux-x64.tar.xz'] +checksums = ['19b09dfcf5d3f3a068827454f0a704a9aa9c826350f73016121afef5f4d287ce'] + +dependencies = [ + ('CUDA', '11.4.1'), +] + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': ['%(version_major_minor)s'], +} + +modaliases = { + 'blender': 'blender -- --cycles-device CUDA', +} + +moduleclass = 'vis' From 104ae9b2daa603e3cf327de509b3e307bb70d251 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 15:32:15 +0100 Subject: [PATCH 2480/9987] complete rename of NGS Python bindings to NGS-Python --- .../a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb | 2 +- .../NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb index 487026ab37c..da30bd94a9d 100644 --- a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb @@ -13,7 +13,7 @@ dependencies = [ ('Python', '3.6.6'), ('Pysam', '0.15.1', versionsuffix), ('pytest', '3.8.2', versionsuffix), - ('NGS', '2.9.3', versionsuffix), # required for srastream + ('NGS-Python', '2.9.3', versionsuffix), # required for srastream ] use_pip = True diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb index 410071ff7cb..e8a898cc830 100644 --- a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb @@ -12,10 +12,11 @@ toolchain = {'name': 'intel', 'version': '2018b'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['NGS-%(version)s_fix-python-install-prefix.patch'] +patches = ['NGS-Python-%(version)s_fix-python-install-prefix.patch'] checksums = [ 'd16cdf340f4c66e449cc490a222e54e9074cd15fe0938cb75b951a72985f757d', # 2.9.3.tar.gz - '72df59433ff1ad64e8313c6ed85286bcd25570eaef28c74ad5239fcaa9de8875', # NGS-2.9.3_fix-python-install-prefix.patch + # NGS-Python-2.9.3_fix-python-install-prefix.patch + '72df59433ff1ad64e8313c6ed85286bcd25570eaef28c74ad5239fcaa9de8875', ] dependencies = [('Python', '3.6.6')] From 0f9b6995381b2966020093c968b91a65ce40d1c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 15:39:27 +0100 Subject: [PATCH 2481/9987] fix name + custom sanity check for NGS-Python 2.9.3 --- .../NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb index e8a898cc830..3ef4112bbde 100644 --- a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'NGS' +name = 'NGS-Python' version = '2.9.3' versionsuffix = '-Python-%(pyver)s' @@ -38,4 +38,11 @@ sanity_check_paths = { modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} +sanity_check_paths = { + 'files': [], + 'dirs': ['include/ngs', 'lib/python%(pyshortver)s/site-packages', 'share/examples'], +} + +sanity_check_commands = ["python -c 'import ngs'"] + moduleclass = 'bio' From 6d275469954f22188052b46531cf3d445d7673b6 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:40:04 +0100 Subject: [PATCH 2482/9987] adding easyconfigs: DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb, DualSPHysics-5.0.175-GCC-11.2.0.eb and patches: DualSPHysics-5.0.175.patch --- ...SPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 65 +++++++++++++++++++ .../DualSPHysics-5.0.175-GCC-11.2.0.eb | 59 +++++++++++++++++ .../d/DualSPHysics/DualSPHysics-5.0.175.patch | 25 +++++++ 3 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb create mode 100644 easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb new file mode 100644 index 00000000000..cc55298e964 --- /dev/null +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -0,0 +1,65 @@ +## +# Authors: Eduardo Miguel Firvida Donestevez +# Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'DualSPHysics' +version = '5.0.175' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://dual.sphysics.org/' + +description = """ +DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. + +The code is developed to study free-surface flow phenomena where Eulerian methods +can be difficult to apply, such as waves or impact of dam-breaks on off-shore +structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal +with real-life engineering problems. +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/DualSPHysics/DualSPHysics/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s.patch'] +checksums = [ + 'd65bb7b8b4a21582091a534142348e46cff0a288a97ef86643bc2dde15637575', + '24ae21134099252a597d80f25cf835dd981d0f085ce33dc801e70f1d7e045829', +] + +srcdir = 'src/source' + +builddependencies = [ + ('CUDA', '11.4.1', '', True), + ('CMake', '3.21.1'), +] + +separate_build_dir = True + +buildopts = " && chmod +x %(builddir)s/%(name)s-%(version)s/bin/linux/*_linux64" + +install_cmd = """mkdir -p %(installdir)s/bin && + cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && + cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib""" + + +sanity_check_paths = { + 'files': [ + 'bin/GenCase_linux64', + 'bin/PartVTK_linux64', + 'bin/IsoSurface_linux64', + 'bin/MeasureTool_linux64', + 'bin/GenCase_MkWord_linux64', + 'bin/DualSPHysics4.0_LiquidGas_linux64', + 'bin/DualSPHysics4.0_LiquidGasCPU_linux64', + 'bin/DualSPHysics5.0_linux64', + 'bin/DualSPHysics5.0CPU_linux64', + 'bin/DualSPHysics5.0_NNewtonian_linux64', + 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', + ], + 'dirs': ["lib", "bin"], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb new file mode 100644 index 00000000000..ca2d9e47fbd --- /dev/null +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -0,0 +1,59 @@ +## +# Authors: Eduardo Miguel Firvida Donestevez +# Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'DualSPHysics' +version = '5.0.175' + +homepage = 'https://dual.sphysics.org/' + +description = """ +DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. + +The code is developed to study free-surface flow phenomena where Eulerian methods +can be difficult to apply, such as waves or impact of dam-breaks on off-shore +structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal +with real-life engineering problems. +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/DualSPHysics/DualSPHysics/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d65bb7b8b4a21582091a534142348e46cff0a288a97ef86643bc2dde15637575'] + +srcdir = 'src/source' + +builddependencies = [ + ('CMake', '3.21.1'), +] + +separate_build_dir = True + +buildopts = " && chmod +x %(builddir)s/%(name)s-%(version)s/bin/linux/*_linux64" + +install_cmd = """mkdir -p %(installdir)s/bin && + cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && + cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib""" + + +sanity_check_paths = { + 'files': [ + 'bin/GenCase_linux64', + 'bin/PartVTK_linux64', + 'bin/IsoSurface_linux64', + 'bin/MeasureTool_linux64', + 'bin/GenCase_MkWord_linux64', + 'bin/DualSPHysics4.0_LiquidGas_linux64', + 'bin/DualSPHysics4.0_LiquidGasCPU_linux64', + 'bin/DualSPHysics5.0_linux64', + 'bin/DualSPHysics5.0CPU_linux64', + 'bin/DualSPHysics5.0_NNewtonian_linux64', + 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', + ], + 'dirs': ["lib", "bin"], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch new file mode 100644 index 00000000000..556373c9719 --- /dev/null +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch @@ -0,0 +1,25 @@ +diff -Naur DualSPHysics-5.0.175/src/source/CMakeLists.txt DualSPHysics-5.0.175/src/source/CMakeLists.txt +--- DualSPHysics-5.0.175/src/source/CMakeLists.txt 2021-02-25 18:46:13.000000000 +0100 ++++ DualSPHysics-5.0.175/src/source/CMakeLists.txt 2021-10-13 18:46:17.000000000 +0200 +@@ -52,9 +52,12 @@ + elseif(CUDA_VERSION VERSION_GREATER "7.4" AND CUDA_VERSION VERSION_LESS "9.1") + message("Using cuda version >=7.5 and <9.1") + list(APPEND CUDA_NVCC_FLAGS "-use_fast_math -O3 -gencode=arch=compute_20,code=\"sm_20,compute_20\" -gencode=arch=compute_30,code=\"sm_30,compute_30\" -gencode=arch=compute_35,code=\"sm_35,compute_35\" -gencode=arch=compute_37,code=\"sm_37,compute_37\" -gencode=arch=compute_50,code=\"sm_50,compute_50\" -gencode=arch=compute_52,code=\"sm_52,compute_52\"") +- else() +- message("Using cuda version >=9.1") ++ elseif(CUDA_VERSION VERSION_GREATER "9.1" AND CUDA_VERSION VERSION_LESS "11.1") ++ message("Using cuda version >=9.1 and <11.1") + list(APPEND CUDA_NVCC_FLAGS "-use_fast_math -O3 -gencode=arch=compute_30,code=\"sm_30,compute_30\" -gencode=arch=compute_35,code=\"sm_35,compute_35\" -gencode=arch=compute_37,code=\"sm_37,compute_37\" -gencode=arch=compute_50,code=\"sm_50,compute_50\" -gencode=arch=compute_52,code=\"sm_52,compute_52\" -gencode=arch=compute_61,code=\"sm_61,compute_61\" -gencode=arch=compute_70,code=\"sm_70,compute_70\"") ++ else() ++ message("Using cuda version >=11.1") ++ list(APPEND CUDA_NVCC_FLAGS "-use_fast_math -O3 -gencode=arch=compute_35,code=\"sm_35,compute_35\" -gencode=arch=compute_37,code=\"sm_37,compute_37\" -gencode=arch=compute_50,code=\"sm_50,compute_50\" -gencode=arch=compute_52,code=\"sm_52,compute_52\" -gencode=arch=compute_61,code=\"sm_61,compute_61\" -gencode=arch=compute_70,code=\"sm_70,compute_70\" -gencode=arch=compute_80,code=\"sm_80,compute_80\"") + endif() + else() + message("CUDA Libraries were not found.") +@@ -201,4 +204,4 @@ + string(REGEX REPLACE "/MD" "/MT" ${CPP_FLAGS} "${${CPP_FLAGS}}") + endif(${CPP_FLAGS} MATCHES "/MD") + endforeach(CPP_FLAGS) +-endif() +\ No newline at end of file ++endif() From 4c8bf75fede73971f9859ac69b0ef4e8568cb425 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 15:41:11 +0100 Subject: [PATCH 2483/9987] enable sanity_pip_check + add custom sanity check command for atropos + strip out standard PyPI source URLs --- .../atropos-1.1.21-intel-2018b-Python-3.6.6.eb | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb index da30bd94a9d..63b3eb72f6e 100644 --- a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb @@ -20,52 +20,40 @@ use_pip = True exts_list = [ ('python-utils', '2.3.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/python-utils/'], 'checksums': ['34aaf26b39b0b86628008f2ae0ac001b30e7986a8d303b61e1357dfcdad4f6d3'], }), ('progressbar2', '3.39.2', { - 'source_urls': ['https://pypi.python.org/packages/source/p/progressbar2/'], 'checksums': ['6eb5135b987caca4212d2c7abc2923d4ad5ba18bb34ccbe7044b3628f52efc2c'], 'modulename': 'progressbar', }), ('tqdm', '4.31.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tqdm/'], 'checksums': ['e22977e3ebe961f72362f6ddfb9197cc531c9737aaf5f607ef09740c849ecd05'], }), ('bz2file', '0.98', { - 'source_urls': ['https://pypi.python.org/packages/source/b/bz2file/'], 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], }), ('screed', '1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/screed/'], 'checksums': ['5db69f8c413a984ade62eb8344a6eb2be26555d74be86d38512673c1cf621b91'], }), ('khmer', '2.1.1', { - 'source_urls': ['https://pypi.python.org/packages/source/k/khmer/'], 'checksums': ['a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24'], }), ('MarkupSafe', '1.1.0', { - 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], 'checksums': ['4e97332c9ce444b0c2c38dd22ddc61c743eb208d916e4265a2a3b575bdccb1d3'], }), ('Jinja2', '2.10', { - 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('pokrok', '0.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pokrok'], 'checksums': ['cfe7956602d8bbc142a07bcb259e0d1d939f96d7b074e00dceea3cb5e39244e8'], }), ('xphyle', '4.0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/x/xphyle/'], 'checksums': ['b744723a3c88d81318c7291c32682b8715a046f70d0a1db729bda783fd5e08bd'], }), ('srastream', '0.1.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/srastream/'], 'checksums': ['7f2cfd76ae988349ad5407a952cd4c133ae5dff7cf12c76072c53d82b50c2634'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/a/atropos/'], 'checksums': ['8178af467734b299960edae15d8835a2228ba0cc1b718af436c7d86041fbd4ec'], }), ] @@ -75,4 +63,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["atropos --help"] + +sanity_pip_check = True + moduleclass = 'bio' From 407b034464f16c26f4da12ea111f2916c7c8c38d Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 23 Dec 2021 15:54:12 +0100 Subject: [PATCH 2484/9987] AMD-uProf: fixes indent problem --- easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb index 37ec97a3ea8..e39f360a639 100644 --- a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb +++ b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb @@ -26,7 +26,7 @@ sanity_check_paths = { sanity_check_commands = ['AMDuProfCLI info --system'] modextrapaths = { - 'LD_LIBRARY_PATH': 'bin' + 'LD_LIBRARY_PATH': 'bin' } moduleclass = 'perf' From c1f2aa125ee6fa8c53268a5dbc1827a5de196901 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 17:38:12 +0100 Subject: [PATCH 2485/9987] fix duplicate sanity_check_paths in NGS-Python easyconfig --- .../NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb index 3ef4112bbde..59aa5296d86 100644 --- a/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/NGS-Python/NGS-Python-2.9.3-intel-2018b-Python-3.6.6.eb @@ -33,16 +33,11 @@ parallel = 1 sanity_check_paths = { 'files': ['lib64/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-adapt-c++.a', 'lib64/libngs-c++.a'], - 'dirs': ['include/ngs', 'lib/python%(pyshortver)s/site-packages', 'share'], -} - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -sanity_check_paths = { - 'files': [], 'dirs': ['include/ngs', 'lib/python%(pyshortver)s/site-packages', 'share/examples'], } sanity_check_commands = ["python -c 'import ngs'"] +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'bio' From b84eef788364c13c5dab3293871a15b6712e1b42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 20:50:11 +0100 Subject: [PATCH 2486/9987] fix sanity check command for atropos --- .../a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb index 63b3eb72f6e..3cb07d04e5e 100644 --- a/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/atropos/atropos-1.1.21-intel-2018b-Python-3.6.6.eb @@ -63,7 +63,7 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["atropos --help"] +sanity_check_commands = ["atropos detect --help"] sanity_pip_check = True From 2be5e2e0aa31f853baa82df8f45ab861181e7c13 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Dec 2021 21:20:21 +0100 Subject: [PATCH 2487/9987] enable sanity_pip_check in easyconfig for CVXOPT 1.2.3 --- .../c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb index f3d00fec42d..2b5c5824d8c 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'CVXOPT' version = '1.2.3' @@ -13,7 +13,6 @@ description = """CVXOPT is a free software package for convex optimization based toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'pic': True} -source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = ['CVXOPT-1.2.1-fix-setup-py.patch'] checksums = [ @@ -37,9 +36,6 @@ installopts = ' --no-binary cvxopt' postinstallcmds = ['nosetests'] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} +sanity_pip_check = True moduleclass = 'math' From 84b9fb7278af0295f23a4a43deda48d97eaeb10e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 24 Dec 2021 09:23:45 +0100 Subject: [PATCH 2488/9987] Fix description (which was referring to AMD-RNG) --- easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb index e39f360a639..f725f56d505 100644 --- a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb +++ b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.4.502.eb @@ -7,7 +7,9 @@ name = 'AMD-uProf' version = '3.4.502' homepage = 'https://developer.amd.com/amd-uprof/' -description = """AMD Random Number Generator Library is a pseudorandom number generator library.""" +description = """AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD + operating systems. It allows developers to better understand the runtime performance of their application and + to identify ways to improve its performance.""" toolchain = SYSTEM From 4515a1cb24892dd589ccb9ac1c85647336707aba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 24 Dec 2021 10:51:38 +0100 Subject: [PATCH 2489/9987] add simple sanity check command --- easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb index 75cf15432a6..05722624103 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb @@ -27,4 +27,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['muscle -version'] + moduleclass = 'bio' From de826311b825fe20a1747e2d2ccb68235158e336 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Dec 2021 11:07:42 +0100 Subject: [PATCH 2490/9987] run nosetests as sanity check command in CVXOPT 1.2.3 easyconfig --- .../c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb index 2b5c5824d8c..60b0fae0eda 100644 --- a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb @@ -34,8 +34,8 @@ preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_ installopts = ' --no-binary cvxopt' -postinstallcmds = ['nosetests'] - sanity_pip_check = True +sanity_check_commands = ['cd %(builddir)s/%(namelower)s-%(version)s && nosetests'] + moduleclass = 'math' From e6951e3bebe70726b5d3f228c35f371b9dec7cda Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 24 Dec 2021 11:09:44 +0100 Subject: [PATCH 2491/9987] use toolchain's default muscle version --- easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb index a0c8a90bc51..db39bb21b3b 100644 --- a/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/a/antiSMASH/antiSMASH-5.2.0-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('GlimmerHMM', '3.0.4c'), ('HMMER2', '2.3.2'), ('HMMER', '3.3.2'), - ('MUSCLE', '3.8.1551'), + ('MUSCLE', '3.8.31'), ('BLAST+', '2.11.0'), ('prodigal', '2.6.3'), ('Biopython', '1.78'), From 8168d875a1e2737524f5febbeecc089788819e85 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Dec 2021 11:18:51 +0100 Subject: [PATCH 2492/9987] remove unused MUSCLE easyconfig --- .../m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb deleted file mode 100644 index 05722624103..00000000000 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'MakeCp' - -name = 'MUSCLE' -version = "3.8.1551" - -homepage = 'https://drive5.com/muscle/' -description = """MUSCLE is one of the best-performing multiple alignment programs - according to published benchmark tests, with accuracy and speed that are consistently - better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users - learn everything they need to know about MUSCLE in a few minutes-only a handful of - command-line options are needed to perform common alignment tasks.""" - -toolchain = {'name': 'GCC', 'version': '10.2.0'} - -source_urls = ['https://www.drive5.com/muscle/'] -sources = ['%(namelower)s_src_%(version)s.tar.gz'] -checksums = ['c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e'] - -# use correct compiler flags + -# don't use -static when linking, since that implies requiring glibc-static to be installed -buildopts = 'CFLAGS="$CXXFLAGS" LDLIBS="-lm"' - -files_to_copy = [(["muscle"], 'bin')] - -sanity_check_paths = { - 'files': ["bin/%(namelower)s"], - 'dirs': [], -} - -sanity_check_commands = ['muscle -version'] - -moduleclass = 'bio' From bca2df9228a35ea346b7e08e3e0f897254298ee1 Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Fri, 24 Dec 2021 11:21:43 +0100 Subject: [PATCH 2493/9987] Update Julia v1.7.1 --- .../j/Julia/Julia-1.7.1-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb new file mode 100644 index 00000000000..79469033db5 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.7.1' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['44658e9c7b45e2b9b5b59239d190cca42de05c175ea86bc346c294a8fe8d9f11'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From d119f7934a3ef20616f820f87b8560cda8795f35 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Dec 2021 17:09:34 +0100 Subject: [PATCH 2494/9987] revert changes to archived GLIMMER easyconfigs --- .../__archive__/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb | 5 ++--- .../__archive__/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb | 5 ++--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb index da9c09fd6d5..9224bccf7f9 100644 --- a/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-goolf-1.4.10.eb @@ -11,15 +11,14 @@ easyblock = 'MakeCp' name = "GLIMMER" version = "3.02b" -homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' +homepage = 'http://www.cbcb.umd.edu/software/glimmer/' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] +source_urls = ['http://www.cbcb.umd.edu/software/glimmer'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] -checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = '-C ./src' diff --git a/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb index 49bd7675820..90a24de0cf2 100644 --- a/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/g/GLIMMER/GLIMMER-3.02b-ictce-5.3.0.eb @@ -11,15 +11,14 @@ easyblock = 'MakeCp' name = "GLIMMER" version = "3.02b" -homepage = 'http://ccb.jhu.edu/software/%(namelower)s/index.shtml' +homepage = 'http://www.cbcb.umd.edu/software/glimmer/' description = """Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] +source_urls = ['http://www.cbcb.umd.edu/software/glimmer'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] -checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] buildopts = '-C ./src' From e0ed983df9ccfd2ba92454a84e6088f6d938a133 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Dec 2021 17:22:45 +0100 Subject: [PATCH 2495/9987] add SHA256 checksum for both original and current source tarballs of GLIMMER 3.02b + add sanity check command --- .../easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb | 8 ++++++-- .../easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb | 8 ++++++-- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb index 59dcbaec249..56c96e97fcf 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2016b.eb @@ -19,15 +19,19 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%%(namelower)s%s.tar.gz' % ''.join(version.split('.'))] -checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] +# original source tarball did not have a README file, but no other changes in source files +checksums = [('a531f83b6162064539bebedbef5bec6b99df32b5d2877ba4431d2fa93faa78a3', + 'ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6')] buildopts = '-C ./src' files_to_copy = ['bin', 'docs', 'glim302notes.pdf', 'lib', 'LICENSE', 'sample-run', 'scripts'] sanity_check_paths = { - 'files': ['bin/%(namelower)s3', 'glim302notes.pdf', 'LICENSE'], + 'files': ['bin/glimmer3', 'glim302notes.pdf', 'LICENSE'], 'dirs': ['docs', 'lib', 'sample-run', 'scripts'], } +sanity_check_commands = ["glimmer3 --help 2>&1 | grep 'USAGE:[ ]*glimmer3'"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb index 1c389bd393d..34ccceea479 100644 --- a/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GLIMMER/GLIMMER-3.02b-foss-2018b.eb @@ -20,15 +20,19 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['http://ccb.jhu.edu/software/%(namelower)s'] sources = ['%(namelower)s302b.tar.gz'] -checksums = ['ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6'] +# original source tarball did not have a README file, but no other changes in source files +checksums = [('a531f83b6162064539bebedbef5bec6b99df32b5d2877ba4431d2fa93faa78a3', + 'ecf28e03d0a675aed7360ca34ca7f19993f5c3ea889273e657ced9fa7d1e2bf6')] buildopts = "-C ./src" files_to_copy = ['bin', 'docs', 'glim302notes.pdf', 'lib', 'LICENSE', 'sample-run', 'scripts'] sanity_check_paths = { - 'files': ['bin/%(namelower)s3', 'glim302notes.pdf', 'LICENSE'], + 'files': ['bin/glimmer3', 'glim302notes.pdf', 'LICENSE'], 'dirs': ['docs', 'lib', 'sample-run', 'scripts'], } +sanity_check_commands = ["glimmer3 --help 2>&1 | grep 'USAGE:[ ]*glimmer3'"] + moduleclass = 'bio' From c758811238ea8dfcfd2b08f60be7bc2981983faf Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:41:47 +0100 Subject: [PATCH 2496/9987] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index cc55298e964..f69e5fa9796 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -10,14 +10,12 @@ versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://dual.sphysics.org/' -description = """ -DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. +description = """DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. -The code is developed to study free-surface flow phenomena where Eulerian methods -can be difficult to apply, such as waves or impact of dam-breaks on off-shore -structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal -with real-life engineering problems. -""" + The code is developed to study free-surface flow phenomena where Eulerian methods + can be difficult to apply, such as waves or impact of dam-breaks on off-shore + structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal + with real-life engineering problems.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} From 1993270ed6a3884b04ae0c9d484790482a44773d Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:41:58 +0100 Subject: [PATCH 2497/9987] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index f69e5fa9796..20cd2d89b41 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -38,9 +38,9 @@ separate_build_dir = True buildopts = " && chmod +x %(builddir)s/%(name)s-%(version)s/bin/linux/*_linux64" -install_cmd = """mkdir -p %(installdir)s/bin && - cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && - cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib""" +install_cmd = "mkdir -p %(installdir)s/bin && " +install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && " +install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib" sanity_check_paths = { From 2893bdc8e5fce83db4b50d28d6948d7505b019a6 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:42:17 +0100 Subject: [PATCH 2498/9987] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index 20cd2d89b41..64826f054a5 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -57,7 +57,7 @@ sanity_check_paths = { 'bin/DualSPHysics5.0_NNewtonian_linux64', 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', ], - 'dirs': ["lib", "bin"], + 'dirs': ["lib"], } moduleclass = 'cae' From 0860e551f5ded6c54060300c772b8c3f2c96fd5e Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:42:26 +0100 Subject: [PATCH 2499/9987] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../DualSPHysics-5.0.175-GCC-11.2.0.eb | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb index ca2d9e47fbd..495ea2289e2 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -9,14 +9,12 @@ version = '5.0.175' homepage = 'https://dual.sphysics.org/' -description = """ -DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. - -The code is developed to study free-surface flow phenomena where Eulerian methods -can be difficult to apply, such as waves or impact of dam-breaks on off-shore -structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal -with real-life engineering problems. -""" +description = """DualSPHysics is based on the Smoothed Particle Hydrodynamics model named SPHysics. + + The code is developed to study free-surface flow phenomena where Eulerian methods + can be difficult to apply, such as waves or impact of dam-breaks on off-shore + structures. DualSPHysics is a set of C++, CUDA and Java codes designed to deal + with real-life engineering problems.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} From eccbbc81cfdeb905513892015ce4eb0e8ccc58c3 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:42:51 +0100 Subject: [PATCH 2500/9987] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index 64826f054a5..33a9ac4cc9f 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -23,8 +23,8 @@ source_urls = ['https://github.com/DualSPHysics/DualSPHysics/archive/refs/tags/' sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s.patch'] checksums = [ - 'd65bb7b8b4a21582091a534142348e46cff0a288a97ef86643bc2dde15637575', - '24ae21134099252a597d80f25cf835dd981d0f085ce33dc801e70f1d7e045829', + 'd65bb7b8b4a21582091a534142348e46cff0a288a97ef86643bc2dde15637575', # v5.0.175.tar.gz + '24ae21134099252a597d80f25cf835dd981d0f085ce33dc801e70f1d7e045829', # DualSPHysics-5.0.175.patch ] srcdir = 'src/source' From 69ab4b22f889a6556b9dc14188a84e8e5c810c0b Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 24 Dec 2021 17:44:06 +0100 Subject: [PATCH 2501/9987] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb index 495ea2289e2..f2c7ad44957 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -51,7 +51,7 @@ sanity_check_paths = { 'bin/DualSPHysics5.0_NNewtonian_linux64', 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', ], - 'dirs': ["lib", "bin"], + 'dirs': ["lib"], } moduleclass = 'cae' From 2caa2d7adf918471ca1df0cd070bbcaf67007442 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Dec 2021 12:04:46 +0100 Subject: [PATCH 2502/9987] add semTools, mirt, OpenMX extensions to R v4.1.2 easyconfig --- .../easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 2f1d783930e..311a8b3d71c 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3178,6 +3178,24 @@ exts_list = [ ('covsim', '0.2.1', { 'checksums': ['57ca810c6950ab295078b745eb87fdd7f195e15082777eed9f1059b6302f13bf'], }), + ('semTools', '0.5-5', { + 'checksums': ['ddf883753c5964eae8313d7e8a4703be52e649f10d3bc1d12ede6d1707b1fab6'], + }), + ('GPArotation', '2014.11-1', { + 'checksums': ['351bc15fc8dc6c8ea5045fbba22180d1e68314fc34d267545687748e312e5096'], + }), + ('dcurver', '0.9.2', { + 'checksums': ['cc6c55090d3607910515981ea0c7221e40e7a29e0da0c5a5f42c3847012290ec'], + }), + ('mirt', '1.35.1', { + 'checksums': ['788b7e499b7d48f5f590eb5cfdac260c4e993b94a3956d30bc2d8bce8cd2ba3e'], + }), + ('rpf', '1.0.11', { + 'checksums': ['e1fd670ae7c3e947db08ce50d6b16ce1b3b8f63a9016b03baba760aee78921fb'], + }), + ('OpenMx', '2.19.8', { + 'checksums': ['cb4be9850f61d320dcd47ef0ad7b20e5baafde558ebbc67301b13d883baf6760'], + }), ] moduleclass = 'lang' From fda6b0611b83b9ea3786c162e1ca92762df75138 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Dec 2021 12:08:23 +0100 Subject: [PATCH 2503/9987] remove whitespace from empty line --- .../dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb index 20136cc0efc..3316dc777fe 100644 --- a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb @@ -12,7 +12,7 @@ description = """.NET is a free, cross-platform, open source developer platform of applications.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - + source_urls = ['https://download.visualstudio.microsoft.com/download/pr/' + 'be8a513c-f3bb-4fbd-b382-6596cf0d67b5/968e205c44eabd205b8ea98be250b880'] sources = ['dotnet-runtime-%(version)s-linux-x64.tar.gz'] From c53f936f88a744ed557d065026eb645d23d8cf43 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Dec 2021 12:13:09 +0100 Subject: [PATCH 2504/9987] add back notes to header of dotNET-SDK easyconfig --- .../easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb index 7e1702a66c2..c98b7621f4e 100644 --- a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb +++ b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb @@ -1,6 +1,9 @@ ## # Authors:: Robert Qiao # Robert Mijakovic +# +# License:: MIT +# Notes:: requires glibc v2.14 or higher ## easyblock = 'Tarball' From 345afb717cedff80ed650c02a6b9ef6197f923d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Dec 2021 12:13:59 +0100 Subject: [PATCH 2505/9987] add sanity check command for dotNET-Core-Runtime --- .../dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb index 3316dc777fe..2959307e390 100644 --- a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-6.0.1-GCCcore-11.2.0.eb @@ -25,6 +25,8 @@ sanity_check_paths = { 'dirs': ['shared/Microsoft.NETCore.App/%(version)s'], } +sanity_check_commands = ["dotnet --info"] + modextrapaths = {'PATH': ['']} moduleclass = 'lang' From e8f48252d587bdf4dae5fcbea4b4db84ca76631d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 26 Dec 2021 12:17:13 +0100 Subject: [PATCH 2506/9987] add sanity check command for dotNET-SDK --- .../easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb index c98b7621f4e..26301f192c6 100644 --- a/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb +++ b/easybuild/easyconfigs/d/dotNET-SDK/dotNET-SDK-6.0.101-linux-x64.eb @@ -26,6 +26,8 @@ sanity_check_paths = { 'dirs': ['shared/Microsoft.NETCore.App', 'shared/Microsoft.AspNetCore.App'], } +sanity_check_commands = ["dotnet --help"] + modextrapaths = { 'PATH': [''], 'DOTNET_ROOT': [''], From bce4df2af9fae86a2b19a496f021c1917881326b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Dec 2021 11:33:06 +0100 Subject: [PATCH 2507/9987] adding easyconfigs: ParaView-5.9.1-foss-2021b-mpi.eb and patches: ParaView-5.9.1_fix-GCC-11.patch --- .../ParaView/ParaView-5.9.1-foss-2021b-mpi.eb | 62 +++++++++++++++++++ .../ParaView/ParaView-5.9.1_fix-GCC-11.patch | 47 ++++++++++++++ 2 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021b-mpi.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.9.1_fix-GCC-11.patch diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021b-mpi.eb new file mode 100644 index 00000000000..c131ad80db0 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-foss-2021b-mpi.eb @@ -0,0 +1,62 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.9.1' +versionsuffix = '-mpi' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +patches = ['ParaView-5.9.1_fix-GCC-11.patch'] +checksums = [ + 'efbcba00ba38c23d0ada1bde7144a8745caa308d9e1f94a4a71d8af63732266f', # ParaView-v5.9.1.tar.gz + '771cf0974333833bbed2bbb573a5782725ae8564d85901e68e6a826972512104', # ParaView-5.9.1_fix-GCC-11.patch +] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('XZ', '5.2.5'), + ('HDF5', '1.12.1'), + ('netCDF', '4.8.1'), + ('libGLU', '9.0.2'), + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('Qt5', '5.15.2'), + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.2'), + ('Szip', '2.1.1'), +] + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1_fix-GCC-11.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1_fix-GCC-11.patch new file mode 100644 index 00000000000..0663afb6edc --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1_fix-GCC-11.patch @@ -0,0 +1,47 @@ +fix compilation with GCC 11, fixes compilation errors like: + error: numeric_limits is not a member of std +author: Kenneth Hoste (HPC-UGent) +diff -ru ParaView-v5.9.1.orig/VTK/Common/Core/vtkGenericDataArrayLookupHelper.h ParaView-v5.9.1/VTK/Common/Core/vtkGenericDataArrayLookupHelper.h +--- ParaView-v5.9.1.orig/VTK/Common/Core/vtkGenericDataArrayLookupHelper.h 2021-05-13 18:50:06.000000000 +0200 ++++ ParaView-v5.9.1/VTK/Common/Core/vtkGenericDataArrayLookupHelper.h 2021-12-23 11:07:09.825480119 +0100 +@@ -25,6 +25,7 @@ + #include "vtkIdList.h" + #include + #include ++#include + #include + #include + +diff -ru ParaView-v5.9.1.orig/VTK/Common/DataModel/vtkPiecewiseFunction.cxx ParaView-v5.9.1/VTK/Common/DataModel/vtkPiecewiseFunction.cxx +--- ParaView-v5.9.1.orig/VTK/Common/DataModel/vtkPiecewiseFunction.cxx 2021-05-13 18:50:06.000000000 +0200 ++++ ParaView-v5.9.1/VTK/Common/DataModel/vtkPiecewiseFunction.cxx 2021-12-23 11:07:41.295765924 +0100 +@@ -22,6 +22,7 @@ + #include + #include + #include ++#include + #include + #include + +diff -ru ParaView-v5.9.1.orig/VTK/Filters/HyperTree/vtkHyperTreeGridThreshold.cxx ParaView-v5.9.1/VTK/Filters/HyperTree/vtkHyperTreeGridThreshold.cxx +--- ParaView-v5.9.1.orig/VTK/Filters/HyperTree/vtkHyperTreeGridThreshold.cxx 2021-05-13 18:50:06.000000000 +0200 ++++ ParaView-v5.9.1/VTK/Filters/HyperTree/vtkHyperTreeGridThreshold.cxx 2021-12-23 11:07:51.895861970 +0100 +@@ -27,6 +27,7 @@ + #include "vtkHyperTreeGridNonOrientedCursor.h" + + #include ++#include + + vtkStandardNewMacro(vtkHyperTreeGridThreshold); + +diff -ru ParaView-v5.9.1.orig/VTK/Rendering/Core/vtkColorTransferFunction.cxx ParaView-v5.9.1/VTK/Rendering/Core/vtkColorTransferFunction.cxx +--- ParaView-v5.9.1.orig/VTK/Rendering/Core/vtkColorTransferFunction.cxx 2021-05-13 18:50:06.000000000 +0200 ++++ ParaView-v5.9.1/VTK/Rendering/Core/vtkColorTransferFunction.cxx 2021-12-23 11:07:25.985627071 +0100 +@@ -21,6 +21,7 @@ + #include + #include + #include ++#include + #include + #include + From 63956ba9f05d56f030129532c4ad694e38bc9be3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 27 Dec 2021 11:39:09 +0100 Subject: [PATCH 2508/9987] adding easyconfigs: OpenFOAM-v2112-foss-2021b.eb, CGAL-4.14.3-gompi-2021b.eb, SCOTCH-6.1.2-gompi-2021b.eb --- .../c/CGAL/CGAL-4.14.3-gompi-2021b.eb | 37 ++++++++++++++++ .../o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb | 42 +++++++++++++++++++ .../s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb | 22 ++++++++++ 3 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb new file mode 100644 index 00000000000..b41d2e7d755 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb @@ -0,0 +1,37 @@ +name = 'CGAL' +version = '4.14.3' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['5bafe7abe8435beca17a1082062d363368ec1e3f0d6581bb0da8b010fb389fe4'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.9.6'), + ('Boost', '1.77.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('Qt5', '5.15.2'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb new file mode 100644 index 00000000000..324e545e4b5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb @@ -0,0 +1,42 @@ +name = 'OpenFOAM' +version = 'v2112' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2012-cleanup.patch', 1), + 'OpenFOAM-v1906-wmake-ompi.patch', +] +checksums = [ + '3e838731e79db1c288acc27aad8cc8a43d9dac1f24e5773e3b9fa91419a8c3f7', # OpenFOAM-v2112.tgz + 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +builddependencies = [ + ('Bison', '3.7.6'), + ('CMake', '3.21.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.1'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.2'), + ('CGAL', '4.14.3'), + ('ParaView', '5.9.1', '-mpi'), + ('gnuplot', '5.4.2'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb new file mode 100644 index 00000000000..88bf9265ec8 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb @@ -0,0 +1,22 @@ +## +# Author: Robert Mijakovic +## +name = 'SCOTCH' +version = '6.1.2' + +homepage = 'https://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['9c2c75c75f716914a2bd1c15dffac0e29a2f8069b2df1ad2b6207c984b699450'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' From 91384df6b9b1131e864789757aa6d964be173483 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Dec 2021 13:33:05 +0100 Subject: [PATCH 2509/9987] adding easyconfigs: SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb --- ...10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..3b0648e9b1f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb @@ -0,0 +1,34 @@ +name = 'SuiteSparse' +version = '5.10.1' +local_metis_ver = '5.1.0' +local_cuda_ver = '11.3.1' +versionsuffix = '-METIS-%s-CUDA-%s' % (local_metis_ver, local_cuda_ver) + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), + ('CUDA', local_cuda_ver, '', True), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0'] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From 69d4881866ae6f48e516109d190511feb4da8095 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Dec 2021 13:39:13 +0100 Subject: [PATCH 2510/9987] use cudaver --- .../SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb index 3b0648e9b1f..2ef23ba8a82 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb @@ -1,8 +1,7 @@ name = 'SuiteSparse' version = '5.10.1' local_metis_ver = '5.1.0' -local_cuda_ver = '11.3.1' -versionsuffix = '-METIS-%s-CUDA-%s' % (local_metis_ver, local_cuda_ver) +versionsuffix = '-METIS-%s-CUDA-%%(cudaver)s' % local_metis_ver homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" @@ -22,7 +21,7 @@ builddependencies = [ dependencies = [ ('METIS', local_metis_ver), ('MPFR', '4.1.0'), - ('CUDA', local_cuda_ver, '', True), + ('CUDA', '11.3.1', '', True), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) From 98d789bf3f1fa8dd8cc9681db841b5db585e0bb0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 29 Dec 2021 09:12:02 +0100 Subject: [PATCH 2511/9987] adding easyconfigs: OBITools-1.2.13-foss-2019a-Python-2.7.15.eb --- ...BITools-1.2.13-foss-2019a-Python-2.7.15.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/o/OBITools/OBITools-1.2.13-foss-2019a-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/o/OBITools/OBITools-1.2.13-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.13-foss-2019a-Python-2.7.15.eb new file mode 100644 index 00000000000..97e6acc1884 --- /dev/null +++ b/easybuild/easyconfigs/o/OBITools/OBITools-1.2.13-foss-2019a-Python-2.7.15.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'OBITools' +version = '1.2.13' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://git.metabarcoding.org/obitools/obitools/wikis/home' +description = """OBITools is a set of python programs developed to +simplify the manipulation of sequence files. They were mainly designed +to for analyzing Next Generation Sequencer outputs (454 or Illumina) in +the context of DNA Metabarcoding.""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['efc7b583a44f435f0663f9d67759a0e3d415ba1896e6132198cb135e35c34873'] + +dependencies = [ + ('Python', '2.7.15'), + ('IPython', '5.8.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'obitools'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ali2consensus', 'ecotag', 'obiaddtaxids', 'obicount', 'obistat']], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/obitools'], +} + +moduleclass = 'bio' From 62ddcb8a58476b6ec29c9e97a0c23b2cb5318c65 Mon Sep 17 00:00:00 2001 From: kErica Date: Wed, 29 Dec 2021 14:47:05 +0000 Subject: [PATCH 2512/9987] fix according to lexming review --- .../c/Carma/Carma-2.01-foss-2019b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/Carma/Carma-2.01-foss-2019b.eb diff --git a/easybuild/easyconfigs/c/Carma/Carma-2.01-foss-2019b.eb b/easybuild/easyconfigs/c/Carma/Carma-2.01-foss-2019b.eb new file mode 100644 index 00000000000..20eedb9845c --- /dev/null +++ b/easybuild/easyconfigs/c/Carma/Carma-2.01-foss-2019b.eb @@ -0,0 +1,33 @@ +# # +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Helena Gomez , Erica Bianco, Danilo Gonzalez, Jordi Blasco +# License:: GPL-v3.0 +# # + +easyblock = 'CmdCp' + +name = 'Carma' +version = '2.01' + +homepage = 'http://utopia.duth.gr/~glykos/Carma.html' +description = """Carma - A molecular dynamics analysis program""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['http://utopia.duth.gr/~glykos/progs/'] +sources = ['%(namelower)s.tar.gz'] +checksums = ['f32cfc2e348691f252d3593e281303d1202e31befba14565aba022331d50b9f3'] + +start_dir = 'src' +cmds_map = [('.*', "$CC $CFLAGS -O -c Color_carma.c && $FC $FFLAGS $LIBBLAS -O Color_carma.o -o carma")] +files_to_copy = [(['carma'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/carma'], + 'dirs': [''], +} + +sanity_check_commands = ['carma'] + +moduleclass = 'chem' From a0738f3904dd2013efd07936fe9d56d67a2dd980 Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Wed, 29 Dec 2021 15:47:38 +0100 Subject: [PATCH 2513/9987] drop lowercase version --- .../c/carma/carma-2.01-foss-2019b.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb diff --git a/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb b/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb deleted file mode 100644 index 40bf7dc47da..00000000000 --- a/easybuild/easyconfigs/c/carma/carma-2.01-foss-2019b.eb +++ /dev/null @@ -1,34 +0,0 @@ -# # -# This is a contribution from HPCNow! (http://hpcnow.com) -# Copyright:: HPCNow! -# Authors:: Helena Gomez , Erica Bianco, Danilo Gonzalez, Jordi Blasco -# License:: GPL-v3.0 -# # - -easyblock = 'Tarball' - -name = 'carma' -version = '2.01' - -homepage = 'http://utopia.duth.gr/~glykos/Carma.html' -description = """carma - A molecular dynamics analysis program""" - -toolchain = {'name': 'foss', 'version': '2019b'} - -source_urls = ['http://utopia.duth.gr/~glykos/progs/'] -sources = ['%(name)s.tar.gz'] -checksums = ['f32cfc2e348691f252d3593e281303d1202e31befba14565aba022331d50b9f3'] - -preinstall_cmd = 'cd %(builddir)s/%(name)s-%(version)s/src && ' -preinstall_cmd += '$CC $CFLAGS -O -c Color_carma.c && ' -preinstall_cmd += '$FC $FFLAGS $LIBBLAS -O Color_carma.o -o carma &&' -preinstall_cmd += 'cp -p carma ../bin/' - -sanity_check_paths = { - 'files': ['bin/carma'], - 'dirs': [''], -} - -tests = ['%(installdir)s/bin/carma'] - -moduleclass = 'lib' From d20d95736e217a87c67a64cd3aa015c8d488c833 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 29 Dec 2021 19:57:00 +0200 Subject: [PATCH 2514/9987] adding easyconfigs: FTGL-2.1.3-rc5-GCCcore-10.2.0.eb --- .../f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6f17150fb6c --- /dev/null +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FTGL' +version = '2.1.3-rc5' + +homepage = 'http://ftgl.sourceforge.net/docs/html/' +description = """ FTGL is a free open source library to enable developers to use arbitrary +fonts in their OpenGL (www.opengl.org) applications. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5458d62122454869572d39f8aa85745fc05d5518001bcefa63bd6cbb8d26565b'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('freetype', '2.10.3'), + ('libGLU', '9.0.1'), + ('Mesa', '20.2.1'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/ftgl.pc', 'lib/libftgl.a', 'lib/libftgl.la', 'lib/libftgl.%s' % SHLIB_EXT], + 'dirs': ['include/FTGL', 'share'] +} + +moduleclass = 'lib' From a8d0c2daa43d111e06a2319b849d6887cced8f88 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 31 Dec 2021 10:02:47 +0100 Subject: [PATCH 2515/9987] update checksum for Siesta-4.1-MaX-1.0 --- .../s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b-PEXSI.eb | 3 ++- .../easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b-PEXSI.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b-PEXSI.eb index c7bf7ebe69c..d72b952fc2a 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b-PEXSI.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b-PEXSI.eb @@ -12,7 +12,8 @@ toolchainopts = {'usempi': True, 'precise': True} source_urls = ['https://gitlab.com/siesta-project/siesta/-/archive/%s' % _release] sources = ['%%(namelower)s-%s.tar.gz' % _release] -checksums = ['c6aa55a5fb7d2f912742e03645047799b17891cab47b569d6682c81629829881'] +checksums = [('c6aa55a5fb7d2f912742e03645047799b17891cab47b569d6682c81629829881', + '02a00e087fcd24b839bde0060cc1af4b116efa3e52aabe32177dcb6dc332c69b')] dependencies = [ ('ELSI', '2.5.0', versionsuffix), diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b.eb index f4becec3ee4..22e245c782f 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1-MaX-1.0-intel-2019b.eb @@ -11,7 +11,8 @@ toolchainopts = {'usempi': True, 'precise': True} source_urls = ['https://gitlab.com/siesta-project/siesta/-/archive/%s' % _release] sources = ['%%(namelower)s-%s.tar.gz' % _release] -checksums = ['c6aa55a5fb7d2f912742e03645047799b17891cab47b569d6682c81629829881'] +checksums = [('c6aa55a5fb7d2f912742e03645047799b17891cab47b569d6682c81629829881', + '02a00e087fcd24b839bde0060cc1af4b116efa3e52aabe32177dcb6dc332c69b')] dependencies = [ ('ELSI', '2.5.0'), From 564a382209d74dbbf8dcc7bf09beb08d606a3da0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 3 Jan 2022 15:06:15 +0100 Subject: [PATCH 2516/9987] {lib}[foss/2021b] libxsmm 1.17 PLUMED 2.7.3 --- .../l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb | 27 +++++++++ .../p/PLUMED/PLUMED-2.7.3-foss-2021b.eb | 56 +++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb new file mode 100644 index 00000000000..d459d902f56 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.17' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb new file mode 100644 index 00000000000..5e10ec4a8f3 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.7.3' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['2895515f31aae42002a539222f5b8558037496548a061b5d0db136d3a46f618b'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.7'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From 8f4396c9d6d6d69d07eba565a706d6d513a7bc7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Jan 2022 12:15:38 +0100 Subject: [PATCH 2517/9987] update Java 1.8 wrapper to 1.8.0_311 for x86_64 --- easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb | 17 +++++++++++++++++ easybuild/easyconfigs/j/Java/Java-1.8.eb | 2 +- 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb new file mode 100644 index 00000000000..47bc761cc52 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb @@ -0,0 +1,17 @@ +name = 'Java' +version = '1.8.0_311' + +homepage = 'https://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +# download the tar.gz directly from +# http://www.oracle.com/technetwork/java/javase/downloads/index.html +(local_vp, local_vs) = version.split('_') +local_altver = '%su%s' % (local_vp.split('.')[1], local_vs) +sources = ['jdk-%s-linux-x64.tar.gz' % local_altver] +checksums = ['759823389014292e84742a226b0e8fbaa08efa32adc6e6435a690c5576df3bb4'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.eb b/easybuild/easyconfigs/j/Java/Java-1.8.eb index 63e9532dd32..ed823a63205 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.eb @@ -14,7 +14,7 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM dependencies = [ - ('Java', {'arch=x86_64': '%(version)s.0_281', + ('Java', {'arch=x86_64': '%(version)s.0_311', 'arch=POWER': '%(version)s_191-b26-OpenJDK', 'arch=AArch64': '%(version)s_265-b01-OpenJDK-aarch64'}), ] From 6d4fec9222bdb5779bbcd08c7faafbea6b80eb29 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 3 Jan 2022 17:54:52 +0100 Subject: [PATCH 2518/9987] Update STRUMPACK-6.1.0-foss-2020b.eb and STRUMPACK-6.1.0-intel-2020b.eb Co-authored-by: Alex Domingo --- .../s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 16 +++++----------- .../s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 16 +++++----------- 2 files changed, 10 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb index 26e9142f8f1..a47c361c4c5 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -8,7 +8,7 @@ description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pghysels/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] @@ -24,14 +24,7 @@ dependencies = [ ('SCOTCH', '6.1.0'), ] -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=Release ' -configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpifort ' -configopts += '-DSTRUMPACK_USE_OPENMP=ON ' -configopts += '-DNO_MODULES=ON ' +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' configopts += '-DTPL_ENABLE_BPACK=OFF ' @@ -42,11 +35,12 @@ configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' -configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' +configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], - 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], + 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + +[ 'lib'], } moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb index 4938fb4262b..47b5368522d 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -8,7 +8,7 @@ description = """STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and for both dense and sparse systems using low-rank structured factorization with randomized sampling.""" toolchain = {'name': 'intel', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/pghysels/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] @@ -24,14 +24,7 @@ dependencies = [ ('SCOTCH', '6.1.0'), ] -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=Release ' -configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' -configopts += '-DCMAKE_C_COMPILER=mpiicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpiifort ' -configopts += '-DSTRUMPACK_USE_OPENMP=ON ' -configopts += '-DNO_MODULES=ON ' +configopts = '-DSTRUMPACK_USE_OPENMP=ON ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' configopts += '-DTPL_SCALAPACK_LIBRARIES="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl" ' @@ -43,11 +36,12 @@ configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' -configopts += '-DTPL_SCOTCH_LIBRARIES="${EBROOTSCOTCH}/lib/libscotch.a;${EBROOTSCOTCH}/lib/libscotcherr.a;${EBROOTSCOTCH}/lib/libptscotch.a;${EBROOTSCOTCH}/lib/libptscotcherr.a" ' +configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], - 'dirs': ['include/BLR', 'include/clustering', 'include/dense', 'include/HSS', 'include/kernel', 'include/misc', 'include/python', 'include/sparse', 'lib'], + 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + +[ 'lib'], } moduleclass = 'numlib' From bd3aa473d91199c23bf79e8e00b7e454c8b4a57c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 3 Jan 2022 18:51:09 +0000 Subject: [PATCH 2519/9987] stick to torchvision 0.8.2 as dependency in 2020b --- ...8.1.eb => PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/PyTorch3D/{PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb => PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb} (95%) diff --git a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb similarity index 95% rename from easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb rename to easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb index 9be26b1a985..28c09209b9c 100644 --- a/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/p/PyTorch3D/PyTorch3D-0.4.0-fosscuda-2020b-PyTorch-1.7.1.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'PyTorch3D' version = '0.4.0' -local_pytorch_version = '1.8.1' +local_pytorch_version = '1.7.1' versionsuffix = '-PyTorch-%s' % local_pytorch_version homepage = "https://pytorch3d.org/" @@ -17,7 +17,7 @@ dependencies = [ ('PyTorch', local_pytorch_version), ('imageio', '2.9.0'), ('IPython', '7.18.1'), - ('torchvision', '0.9.1', versionsuffix), + ('torchvision', '0.8.2', versionsuffix), ] sanity_pip_check = True From 9208d46e7e094c0b75054bd1218cc79c1ff93076 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 10:17:59 +0100 Subject: [PATCH 2520/9987] add FactorCopula extension for R v4.1.2 --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 311a8b3d71c..add27951e71 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3196,6 +3196,12 @@ exts_list = [ ('OpenMx', '2.19.8', { 'checksums': ['cb4be9850f61d320dcd47ef0ad7b20e5baafde558ebbc67301b13d883baf6760'], }), + ('matlab', '1.0.2', { + 'checksums': ['a23dec736c51ae1864c1a53caac556a2f98e8020138a3b121badb0f5b7984154'], + }), + ('FactorCopula', '0.8', { + 'checksums': ['d95b0ccd1b0eebcf27a90286e9392f662b878a669c693fbbb4145798045134ff'], + }), ] moduleclass = 'lang' From aebd17a34291c990f873f40dcbeba5a8e7896edb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 10:49:24 +0100 Subject: [PATCH 2521/9987] remove commented out barrnap dependency in SqueezeMeta easyconfig, need to use vendored patched barrnap --- .../s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb index 700c3b31af3..e68964c3d36 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb @@ -27,7 +27,6 @@ dependencies = [ ('R', '3.5.1', versionsuffix), ('BLAST+', '2.7.1'), ('BWA', '0.7.17'), - #('barrnap', '0.9'), ('CD-HIT', '4.6.8'), ('CheckM', '1.0.13', versionsuffix), ('DAS_Tool', '1.1.1', '-R-%(rver)s-Python-%(pyver)s'), # depends on prodigal & pullseq From cc7b203b0ffdc648036dd5b236829dc424b03373 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 11:12:14 +0100 Subject: [PATCH 2522/9987] update $R_LIBS_SITE rather than $R_LIBS in easyconfig for SqueezeMeta 1.0.0 --- .../s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb index e68964c3d36..bc932b4a6c7 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb @@ -75,7 +75,7 @@ sanity_check_commands = ["""echo 'library("SQMtools")' | R -q --no-save"""] modextrapaths = { 'PATH': 'scripts', - 'R_LIBS': 'R', + 'R_LIBS_SITE': 'R', } moduleclass = 'bio' From 572c0d455142eb5b1cc899a533a9cb0056f65fe2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 11:30:02 +0100 Subject: [PATCH 2523/9987] adding easyconfigs: XML-LibXML-2.0207-GCCcore-11.2.0.eb --- .../XML-LibXML-2.0207-GCCcore-11.2.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c92e343a475 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0207' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('binutils', '2.37'), +] + +dependencies = [ + ('Perl', '5.34.0'), + ('libxml2', '2.9.10'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1010', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['efc121f40bd7a0f62f8ec9b8bc70f7f5409d81cd705e37008596c8efc4452b01'], + }), + ('Alien::Base', '2.46', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['4bb301fa2b6296a9d8e285000932ea3340832a3a70bdb9c5e1a63c6fd1cf4a67'], + }), + ('Alien::Libxml2', '0.17', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['73b45244f0b5c36e5332c33569b82a1ab2c33e263f1d00785d2003bcaec68db3'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['903436c9859875bef5593243aae85ced329ad0fb4b57bbf45975e32547c50c15'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' From fc7cdb69584b0a371e8ca375655107ad9f912c16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 11:51:35 +0100 Subject: [PATCH 2524/9987] add missing PCRE dependency for pullseq + add sanity check commands --- .../easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb index bc6e3f50681..513b5e5c745 100644 --- a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-7.3.0.eb @@ -16,6 +16,9 @@ builddependencies = [ ('binutils', '2.30'), ('Autotools', '20180311'), ] +dependencies = [ + ('PCRE', '8.41'), +] preconfigopts = "./bootstrap && " @@ -24,4 +27,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + "pullseq --help 2>&1 | grep 'pullseq - a bioinformatics tool'", + "seqdiff --help 2>&1 | grep 'seqdiff - a bioinformatics tool'", +] + moduleclass = 'bio' From 02232f6529a806275e64f15b0b6428005ce6f4d8 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 4 Jan 2022 13:25:04 +0100 Subject: [PATCH 2525/9987] adding easyconfigs: CMake-3.22.1-GCCcore-11.2.0.eb --- .../c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7d88407d378 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.22.1' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0e998229549d7b3f368703d20e248e7ee1f853910d42704aa87918c213ea82c0'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.78.0'), + ('libarchive', '3.5.1'), + ('OpenSSL', '1.1', '', True), +] + +moduleclass = 'devel' From ecc1c7769517e0aa883afba1a58746de9f2dd2fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 4 Jan 2022 13:45:59 +0100 Subject: [PATCH 2526/9987] adding easyconfigs: AdapterRemoval-2.3.2-GCC-11.2.0.eb --- .../AdapterRemoval-2.3.2-GCC-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..4ba0d0fbca4 --- /dev/null +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.2-GCC-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'AdapterRemoval' +version = '2.3.2' + +homepage = 'https://github.com/MikkelSchubert/adapterremoval' +description = """AdapterRemoval searches for and removes remnant adapter sequences + from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases + from the 3' end of reads following adapter removal.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'MikkelSchubert' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ded7e08fb64e1b19f5c3de623de276d9cbb657a52b23a844ff74576d1b4f8d4'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] +} + +sanity_check_commands = [('%(name)s', '--version')] + +moduleclass = 'bio' From f8206a625b357eba04ab27e5c351fa7a8886cd38 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 4 Jan 2022 15:15:03 +0100 Subject: [PATCH 2527/9987] Patch CHERAB/1.3.0 for intel/2020b and foss/2020b --- .../c/CHERAB/CHERAB-1.3.0-foss-2020b.eb | 31 +++++++++++++++++++ .../c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 13 ++++---- 2 files changed, 37 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb new file mode 100644 index 00000000000..bb77bca7706 --- /dev/null +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'CHERAB' +version = '1.3.0' + +homepage = 'https://cherab.github.io/documentation/index.html' + +description = """CHERAB is a python library for forward modelling diagnostics + based on spectroscopic plasma emission.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(namelower)s-%(version)s_no-namespace.patch'] +checksums = [ + '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz + '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb index 7d3d731a92e..c0847561d7d 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -11,7 +11,11 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'intel', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] -checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] +patches = ['%(namelower)s-%(version)s_no-namespace.patch'] +checksums = [ + '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz + '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +] dependencies = [ ('Python', '3.8.6'), @@ -22,11 +26,6 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_pip_check = False - -sanity_check_commands = [ - 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/__init__.py && ' - 'python -c "import cherab"' -] +sanity_pip_check = True moduleclass = 'phys' From 483d8e6d10ff9163cea988643e5fde45323da8d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 17:31:54 +0100 Subject: [PATCH 2528/9987] use %(arch)s template to avoid hardcoding x86_64 in XML-LibXML easyconfig --- .../x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb index c92e343a475..cf5ef24b6c7 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.2.0.eb @@ -50,7 +50,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], } moduleclass = 'data' From e65c68ba8e83f051746908615edade30b68965b6 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 4 Jan 2022 16:39:09 +0000 Subject: [PATCH 2529/9987] Bazel for GCCcore11 --- .../b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ .../b/Bazel/gcc11-2-bazel-3.7.2.patch | 10 +++++ .../b/Bazel/gcc11-bazel-3.7.2.patch | 10 +++++ easybuild/easyconfigs/b/Bazel/java15.patch | 29 ++++++++++++ 4 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch create mode 100644 easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch create mode 100644 easybuild/easyconfigs/b/Bazel/java15.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..92bf8614231 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +name = 'Bazel' +version = '3.7.2' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + 'https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = [ + '%(name)s-3.4.1-fix-grpc-protoc.patch', + 'java15.patch', + '%(name)s-3.7.1_fix-protobuf-env.patch', + 'gcc11-bazel-3.7.2.patch', + 'gcc11-2-bazel-3.7.2.patch', + +] +checksums = [ + # bazel-3.7.2-dist.zip + 'de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1', + # Bazel-3.4.1-fix-grpc-protoc.patch + 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', + '28f394f561824abf562556877483bc443dfd3ee0c7cba48a56e22670258669e7', # java15.patch + # Bazel-3.7.1_fix-protobuf-env.patch + '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', + # gcc11-bazel-3.7.2.patch + '32dc4abdc45bfcf70e9d93a66150b89646c801f8704930f0b713038366e40d40', + # gcc11-2-bazel-3.7.2.patch + '3160caff050330e33df1f7afb649e8303bf4af969ef7722639bd0f3c3ae036b4', +] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), + ('Zip', '3.0'), +] + +prebuildopts = "export BAZEL_LINKOPTS=-static-libstdc++:-static-libgcc BAZEL_LINKLIBS=-l%:libstdc++.a:-lm && " +configopts = "--host_jvm_args=--illegal-access=debug" +dependencies = [('Java', '13', '', True)] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch b/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch new file mode 100644 index 00000000000..c7ceaa84318 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch @@ -0,0 +1,10 @@ +--- src/third_party/ijar/mapped_file.h.orig 2021-11-05 15:56:24.654184777 +0100 ++++ src/third_party/ijar/mapped_file.h 2021-11-05 15:56:33.879015290 +0100 +@@ -16,6 +16,7 @@ + #define INCLUDED_THIRD_PARTY_IJAR_MAPPED_FILE_H + + #include "third_party/ijar/common.h" ++#include + + namespace devtools_ijar { + diff --git a/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch b/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch new file mode 100644 index 00000000000..b46eda73836 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch @@ -0,0 +1,10 @@ +--- src/third_party/ijar/zlib_client.h.orig 2021-11-05 15:39:58.061336981 +0100 ++++ src/third_party/ijar/zlib_client.h 2021-11-05 15:40:22.650877105 +0100 +@@ -16,6 +16,7 @@ + #define THIRD_PARTY_IJAR_ZLIB_CLIENT_H_ + + #include ++#include + + #include "third_party/ijar/common.h" + diff --git a/easybuild/easyconfigs/b/Bazel/java15.patch b/easybuild/easyconfigs/b/Bazel/java15.patch new file mode 100644 index 00000000000..6fc6a95634e --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/java15.patch @@ -0,0 +1,29 @@ +From 0216ee54417fa1f2fef14f6eb14cbc1e8f595821 Mon Sep 17 00:00:00 2001 +From: philwo +Date: Mon, 8 Feb 2021 10:45:50 -0800 +Subject: [PATCH] Fix Bazel #10214: JDK 13 introduced a source compatibility + issue. + +Quote from the Java release notes: + +The addition of newFileSystem(Path, Map) creates a source (but not binary) compatibility issue for code that has been using the existing 2-arg newFileSystem(Path, ClassLoader) and specifying the class loader as null. [...] To avoid the ambiguous reference, this code needs to be modified to cast the second parameter to java.lang.ClassLoader. + +RELNOTES: +PiperOrigin-RevId: 356301318 +--- + .../com/google/devtools/build/buildjar/VanillaJavaBuilder.java | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/VanillaJavaBuilder.java b/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/VanillaJavaBuilder.java +index 327017362626..5edf9ba0cf23 100644 +--- a/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/VanillaJavaBuilder.java ++++ b/src/java_tools/buildjar/java/com/google/devtools/build/buildjar/VanillaJavaBuilder.java +@@ -77,7 +77,7 @@ + private FileSystem getJarFileSystem(Path sourceJar) throws IOException { + FileSystem fs = filesystems.get(sourceJar); + if (fs == null) { +- filesystems.put(sourceJar, fs = FileSystems.newFileSystem(sourceJar, null)); ++ filesystems.put(sourceJar, fs = FileSystems.newFileSystem(sourceJar, (ClassLoader) null)); + } + return fs; + } \ No newline at end of file From ff63411c0f025ec053a3be6f6e6c6b826befdd65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jan 2022 19:56:53 +0100 Subject: [PATCH 2530/9987] use %(arch)s template to avoid hardcoding x86_64 in recent XML-LibXML easyconfigs --- .../easyconfigs/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb | 2 +- .../x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb | 2 +- .../x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb index 4676ae13f4b..78769aba0ee 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0205-GCCcore-9.3.0.eb @@ -46,7 +46,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb index ee314c18f7d..62cc7c77d12 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0206-GCCcore-10.2.0.eb @@ -50,7 +50,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb index 1ce2f4c107a..8cf20d98f03 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-10.3.0.eb @@ -50,7 +50,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], } moduleclass = 'data' From 5dc9ea211ad9f6a2a471c343948d2e49f61ac5cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 07:24:41 +0100 Subject: [PATCH 2531/9987] adding easyconfigs: PEAR-0.9.11-GCC-11.2.0.eb --- .../p/PEAR/PEAR-0.9.11-GCC-11.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.2.0.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.2.0.eb new file mode 100644 index 00000000000..4dadb6ab88e --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'PEAR' +version = '0.9.11' + +homepage = 'https://cme.h-its.org/exelixis/web/software/pear/' +description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. + It is fully parallelized and can run with as low as just a few kilobytes of memory.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +# Needs manual download via web-form, +# https://www.h-its.org/en/research/sco/software/#NextGenerationSequencingSequenceAnalysis +sources = ['%(namelower)s-src-%(version)s.tar.gz'] +checksums = ['94f4a1835cd75ec6fab83405c2545ddba6b6bb1644579222e9cc2ad57a59d654'] + +builddependencies = [('Autotools', '20210726')] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +preconfigopts = 'aclocal && autoconf && automake --add-missing && ' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 525f695147d5c018eacad159fadec63a570f3a46 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 08:13:12 +0100 Subject: [PATCH 2532/9987] adding easyconfigs: GffCompare-0.12.6-GCC-11.2.0.eb --- .../GffCompare-0.12.6-GCC-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.6-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.6-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.6-GCC-11.2.0.eb new file mode 100644 index 00000000000..7146893a15f --- /dev/null +++ b/easybuild/easyconfigs/g/GffCompare/GffCompare-0.12.6-GCC-11.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GffCompare' +version = '0.12.6' + +# Some docs also at GitHub site - this is referred to as canonical +homepage = 'https://ccb.jhu.edu/software/stringtie/gffcompare.shtml' +description = """GffCompare provides classification and reference annotation mapping and + matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +# Switched to GitHub sources owing to SSL error at original download site +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0e713bc9177d874c935802d11669776da5e9377a8c4d031153b48a783d3391d0'] + +buildopts = " release" + +files_to_copy = ['%(namelower)s', 'LICENSE', 'README.md'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s -v'] + +moduleclass = 'bio' From 377a0d5ebf85faa39e6a1c7b1e24a763f269e3ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 08:18:46 +0100 Subject: [PATCH 2533/9987] adding easyconfigs: gffread-0.12.7-GCC-11.2.0.eb --- .../g/gffread/gffread-0.12.7-GCC-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb new file mode 100644 index 00000000000..5a9362d9dee --- /dev/null +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'MakeCp' + +name = 'gffread' +version = '0.12.7' + +homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' +description = """GFF/GTF parsing utility providing format conversions, +region filtering, FASTA sequence extraction and more.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] + +buildopts = " release" + +files_to_copy = [ + (['%(name)s'], 'bin'), + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s'] + +moduleclass = 'bio' From 4da8e3c4b7bcdf1f6f08ccf0bfff686afcfbc4e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 08:28:04 +0100 Subject: [PATCH 2534/9987] adding easyconfigs: KronaTools-2.8.1-GCC-11.2.0.eb --- .../KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..3a0d49adac1 --- /dev/null +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb @@ -0,0 +1,41 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# this is a bug fix to make sure the symlinks in bin are not getting destroyed +# by Easybuild when it is tidying up +# This build also links updateTaxonomy.sh and updateAccessions.sh in the bin folder +# so users can install their own Taxonomy database + +easyblock = 'Tarball' + +name = 'KronaTools' +version = '2.8.1' + +homepage = 'https://github.com/marbl/Krona/wiki/KronaTools' +description = """Krona Tools is a set of scripts to create Krona charts from +several Bioinformatics tools as well as from text and XML files.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['f3ab44bf172e1f846e8977c7443d2e0c9676b421b26c50e91fa996d70a6bfd10'] + +dependencies = [('Perl', '5.34.0')] + +postinstallcmds = [ + "cd %(installdir)s && ./install.pl --prefix=%(installdir)s;", + "cd %(installdir)s/bin && ln -s ../updateAccessions.sh . && ln -s ../updateTaxonomy.sh .", +] + +sanity_check_paths = { + 'files': ['bin/ktClassifyBLAST', 'bin/ktImportBLAST', 'bin/ktImportTaxonomy', + 'bin/updateAccessions.sh', 'bin/updateTaxonomy.sh'], + 'dirs': ['data', 'img', 'scripts'], +} + +sanity_check_commands = [ + "updateAccessions.sh --help", + "ktImportText", +] + +moduleclass = 'bio' From 7e3b37f5afb599e21b9bbf87cf60dcc78b349942 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 09:07:31 +0100 Subject: [PATCH 2535/9987] change toolchain to GCCcore because there are only scripts and nothing to compile --- ...s-2.8.1-GCC-11.2.0.eb => KronaTools-2.8.1-GCCcore-11.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/k/KronaTools/{KronaTools-2.8.1-GCC-11.2.0.eb => KronaTools-2.8.1-GCCcore-11.2.0.eb} (96%) diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.2.0.eb similarity index 96% rename from easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb rename to easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.2.0.eb index 3a0d49adac1..25657b328af 100644 --- a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ homepage = 'https://github.com/marbl/Krona/wiki/KronaTools' description = """Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.""" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] sources = ['%(name)s-%(version)s.tar'] From e7052b79ca706a32ef12d6973ad376c9b91fde3e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 09:13:45 +0100 Subject: [PATCH 2536/9987] change toolchain to GCCcore --- ...-0.12.7-GCC-11.2.0.eb => gffread-0.12.7-GCCcore-11.2.0.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/g/gffread/{gffread-0.12.7-GCC-11.2.0.eb => gffread-0.12.7-GCCcore-11.2.0.eb} (89%) diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-11.2.0.eb similarity index 89% rename from easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb rename to easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-11.2.0.eb index 5a9362d9dee..0123e140499 100644 --- a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-11.2.0.eb @@ -8,13 +8,15 @@ homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' description = """GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.""" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] +builddependencies = [('binutils', '2.37')] + buildopts = " release" files_to_copy = [ From 4005cafde9ecbbe2380d903a646769bb64f1ef5a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 5 Jan 2022 16:48:53 +0800 Subject: [PATCH 2537/9987] bring gffread back down to GCCcore level for toolchain version 10.3.0 --- ...-0.12.7-GCC-10.3.0.eb => gffread-0.12.7-GCCcore-10.3.0.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/g/gffread/{gffread-0.12.7-GCC-10.3.0.eb => gffread-0.12.7-GCCcore-10.3.0.eb} (88%) diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-10.3.0.eb similarity index 88% rename from easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb rename to easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-10.3.0.eb index 0b1607a0ada..2de4e4299bb 100644 --- a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-10.3.0.eb @@ -8,13 +8,15 @@ homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' description = """GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.""" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] +builddependencies = [('binutils', '2.36.1')] + buildopts = " release" files_to_copy = [ From 4ee5fd28a03da6fb5a375579b208f7ce6a519cbc Mon Sep 17 00:00:00 2001 From: Robert QIAO Date: Wed, 5 Jan 2022 20:14:46 +1050 Subject: [PATCH 2538/9987] GNU compile config lean op --- .../l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb index 7728a82147b..03f83bb3c0e 100644 --- a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb @@ -11,7 +11,7 @@ homepage = "https://github.com/mfranberg/libplinkio" description = """A small C and Python library for reading PLINK genotype files.""" toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'cstd': 'gnu17', 'noopt': True, 'extra_cflags': '-w'} +toolchainopts = {'cstd': 'gnu17', 'extra_cflags': '-w'} github_account = "mfranberg" source_urls = ['https://github.com/%(github_account)s/%(namelower)s/archive/refs/tags'] @@ -23,11 +23,9 @@ builddependencies = [ ('binutils', '2.34'), ] -parallel = 1 - sanity_check_paths = { - 'files': ['lib/%s.%s' % (name, SHLIB_EXT)], - 'dirs': ['include'], + 'files': ['lib/libplinkio.%s' % SHLIB_EXT], + 'dirs': ['include/plinkio'], } moduleclass = 'lib' From 78acbac2f3eacd3a8b54bb97371d5bb44359b9d1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 5 Jan 2022 10:45:21 +0100 Subject: [PATCH 2539/9987] Add Cython/3.0a5 build dependency for CHERAB/1.3.0 --- .../c/CHERAB/CHERAB-1.3.0-foss-2020b.eb | 8 +-- .../c/CHERAB/CHERAB-1.3.0-intel-2020b.eb | 8 +-- .../c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb | 54 +++++++++++++++++++ 3 files changed, 62 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb index bb77bca7706..9a080037a64 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-foss-2020b.eb @@ -11,10 +11,10 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'foss', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] -patches = ['%(namelower)s-%(version)s_no-namespace.patch'] -checksums = [ - '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz - '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] + +builddependencies = [ + ('Cython', '3.0a5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb index c0847561d7d..f80768c2593 100644 --- a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.3.0-intel-2020b.eb @@ -11,10 +11,10 @@ description = """CHERAB is a python library for forward modelling diagnostics toolchain = {'name': 'intel', 'version': '2020b'} sources = [SOURCELOWER_TAR_GZ] -patches = ['%(namelower)s-%(version)s_no-namespace.patch'] -checksums = [ - '2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45', # cherab-1.3.0.tar.gz - '2a4770c75b5409a212397b49a8acd8383412dd092aad955ce1a486f4a6b893cc', # cherab-1.3.0_no-namespace.patch +checksums = ['2ce0ee3784863cc281c4f8ca402eb43d491f39d6269619161da09508e36eda45'] + +builddependencies = [ + ('Cython', '3.0a5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..08933e60927 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0a5-GCCcore-10.2.0.eb @@ -0,0 +1,54 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , +# Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +# Updated: Pavel Grochal (INUITS) +## +# Thomas Hoffmann, EMBL Heidelberg: Adapted to v0.29.22, GCCcore 10.2.0 +# 2021/03 +easyblock = 'PythonPackage' + +name = 'Cython' +version = '3.0a5' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['22060abe55a55a59096982f3e81de2dc8f28c29917d20fa5182f49c4530e27ec'] + +builddependencies = [('binutils', '2.35')] + +# Can't use multi_dep because EBPYTHONPREFIXES are not loaded in order. +# This results in not beeing able to choose Cython version in multi_dep. +dependencies = [('Python', '3.8.6')] + +download_dep_fail = True + +use_pip = True + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cython --version', +] + +moduleclass = 'lang' From 320f7d81b8d3072564382a44a8177ab9ecca26d7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 11:19:08 +0100 Subject: [PATCH 2540/9987] fix formatting of STRUMPACK-6.1.0-foss-2020b.eb --- .../s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb index a47c361c4c5..d6c33b40db7 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -26,21 +26,21 @@ dependencies = [ configopts = '-DSTRUMPACK_USE_OPENMP=ON ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' -configopts += '-DTPL_ENABLE_BPACK=OFF ' -configopts += '-DTPL_ENABLE_ZFP=OFF ' -configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_PARMETIS=ON ' configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + -[ 'lib'], + [ 'lib'], } moduleclass = 'numlib' From b695c7619a7d1855a8293a30515c16830882e96f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 12:52:27 +0200 Subject: [PATCH 2541/9987] adding easyconfigs: AutoDock-4.2.6-GCC-10.3.0.eb --- .../a/AutoDock/AutoDock-4.2.6-GCC-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCC-10.3.0.eb b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCC-10.3.0.eb new file mode 100644 index 00000000000..76a1698a199 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCC-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'Bundle' + +name = 'AutoDock' +version = '4.2.6' + +homepage = 'http://autodock.scripps.edu/' +description = """AutoDock is a suite of automated docking tools. It is designed to + predict how small molecules, such as substrates or drug candidates, bind to + a receptor of known 3D structure.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'source_urls': ['https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10'], + 'sources': ['autodocksuite-%(version)s-src.tar.gz'], + 'checksums': ['4b24ce4baf216a5e1a6a79bb664eeed684aed17cede64ff0061aa1bcc17874c4'], + 'start_dir': 'src/%(namelower)s', +} + +components = [ + ('AutoGrid', version), + ('AutoDock', version), +] + +sanity_check_paths = { + 'files': ['bin/autodock4', 'bin/autogrid4'], + 'dirs': [] +} + +sanity_check_commands = [ + ('autodock4', '--help'), + ('autogrid4', '--help'), +] + +moduleclass = 'tools' From c622cf8dd3fbf4ec118a91303ed1278b972f10d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 5 Jan 2022 11:59:45 +0100 Subject: [PATCH 2542/9987] adding easyconfigs: VCFtools-0.1.16-GCC-11.2.0.eb --- .../v/VCFtools/VCFtools-0.1.16-GCC-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.2.0.eb new file mode 100644 index 00000000000..3580f5818bf --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Perl', '5.34.0'), + ('HTSlib', '1.14'), + ('zlib', '1.2.11'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' From be2a36e4ce49ec4d455f33b7ddd3d615ed048beb Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 5 Jan 2022 12:32:07 +0100 Subject: [PATCH 2543/9987] adding easyconfigs: ORCA-5.0.2-gompi-2021b.eb, ORCA-5.0.2-gompi-2021b-static.eb --- .../o/ORCA/ORCA-5.0.2-gompi-2021b-static.eb | 33 +++++++++++++++++++ .../o/ORCA/ORCA-5.0.2-gompi-2021b.eb | 23 +++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b-static.eb create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b-static.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b-static.eb new file mode 100644 index 00000000000..81475b93b99 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b-static.eb @@ -0,0 +1,33 @@ +name = 'ORCA' +version = '5.0.2' +versionsuffix = '-static' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +# Static build of ORCA: download from https://orcaforum.kofo.mpg.de +# OpenMPI is dynamically linked +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_openmpi411_part%s.tar.xz' % (version.replace('.', '_'), p) + for p in range(1, 4)] +checksums = [ + # orca_5_0_2_linux_x86-64_openmpi411_part1.tar.xz + '7623ae43a7d02a36f890a3826e0d021d634addb8e1b2598feb7f9b29d8a3f935', + # orca_5_0_2_linux_x86-64_openmpi411_part2.tar.xz + '905b427a721554a0037986494473a91daa4a0b182dcfbb92fe5d2abccc68df2c', + # orca_5_0_2_linux_x86-64_openmpi411_part3.tar.xz + 'fd04e2df6c3aeaaef79d2c36917d9973f64368348060a9c194e80b7f7a29b9c7', +] + +# The 5.0.2-static tarballs have redundant top-level directory names names that +# need to be stripped away. +unpack_options = '--strip-components=1' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b.eb new file mode 100644 index 00000000000..8256a206991 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.2-gompi-2021b.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '5.0.2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +# Shared build of ORCA: download from https://orcaforum.kofo.mpg.de +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi411.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_5_0_2_linux_x86-64_shared_openmpi411.tar.xz + '3a26a1a5fbc69e7dca0192237b5e16b69886df31751ae59f7396461428aeee96', +] + +moduleclass = 'chem' From efa7e2a4a93992477c5f4a169dd737247dc291fb Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 5 Jan 2022 14:25:36 +0100 Subject: [PATCH 2544/9987] adding easyconfigs: Java-15.0.1.eb, Java-15.eb --- easybuild/easyconfigs/j/Java/Java-15.0.1.eb | 15 +++++++++++++++ easybuild/easyconfigs/j/Java/Java-15.eb | 14 ++++++++++++++ 2 files changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-15.0.1.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-15.eb diff --git a/easybuild/easyconfigs/j/Java/Java-15.0.1.eb b/easybuild/easyconfigs/j/Java/Java-15.0.1.eb new file mode 100644 index 00000000000..bb6dfec4233 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-15.0.1.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '15.0.1' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://download.java.net/java/GA/jdk%(version)s/51f4f36ad4ef43e39d0dfdbaf6549e32/9/GPL/'] +sources = ['openjdk-%(version)s_linux-x64_bin.tar.gz'] +checksums = ['83ec3a7b1649a6b31e021cde1e58ab447b07fb8173489f27f427e731c89ed84a'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-15.eb b/easybuild/easyconfigs/j/Java/Java-15.eb new file mode 100644 index 00000000000..78c52a44db6 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-15.eb @@ -0,0 +1,14 @@ +easyblock = 'ModuleRC' + +name = 'Java' +version = '15' + +homepage = 'https://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +dependencies = [('Java', '%(version)s.0.1')] + +moduleclass = 'lang' From dd0a4e1b5837ef10e798b90930bfb345f7342e5f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 5 Jan 2022 14:30:27 +0100 Subject: [PATCH 2545/9987] adding easyconfigs: Java-17.0.1.eb, Java-17.eb --- easybuild/easyconfigs/j/Java/Java-17.0.1.eb | 23 +++++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-17.eb | 14 +++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-17.0.1.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-17.eb diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.1.eb b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb new file mode 100644 index 00000000000..1853440db2c --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb @@ -0,0 +1,23 @@ +name = 'Java' +version = '17.0.1' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'openjdk-%%(version)s_linux-%s_bin.tar.gz' + +source_urls = ['https://download.java.net/java/GA/jdk%(version)s/51f4f36ad4ef43e39d0dfdbaf6549e32/9/GPL/'] +sources = [local_tarball_tmpl % '%(jdkarch)s'] +checksums = [ + { + local_tarball_tmpl % 'x64': + '1c0a73cbb863aad579b967316bf17673b8f98a9bb938602a140ba2e5c38f880a', + local_tarball_tmpl % 'aarch64': + '86653d48787e5a1c029df10da7808194fe8bd931ddd72ff3d42850bf1afb317e', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-17.eb b/easybuild/easyconfigs/j/Java/Java-17.eb new file mode 100644 index 00000000000..e4651cf9c6f --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-17.eb @@ -0,0 +1,14 @@ +easyblock = 'ModuleRC' + +name = 'Java' +version = '17' + +homepage = 'https://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +dependencies = [('Java', '%(version)s.0.1')] + +moduleclass = 'lang' From 20185a06016c76e291ca374a4ed906b293349621 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 14:32:01 +0100 Subject: [PATCH 2546/9987] adding easyconfigs: BWA-0.7.17-GCCcore-11.2.0.eb --- .../b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..625b0fff96a --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' + +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CFLAGS="$CFLAGS -fcommon"' + +moduleclass = 'bio' From 5a6725d5bf7e5b63dbbf93a3316520eb10b7b19a Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 14:32:29 +0100 Subject: [PATCH 2547/9987] adding easyconfigs: CD-HIT-4.8.1-GCCcore-11.2.0.eb --- .../c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d99cc6a786d --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'https://github.com/weizhongli/cdhit' +description = """CD-HIT is a very widely used program for clustering and +comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.34.0'), + ('zlib', '1.2.11'), +] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' From 1511b6f07088bc010f82b58c4597fb2ceae50642 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 5 Jan 2022 14:32:30 +0100 Subject: [PATCH 2548/9987] update easyconfig: Java-17.0.1.eb --- easybuild/easyconfigs/j/Java/Java-17.0.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.1.eb b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb index 1853440db2c..9fa9e3e0450 100644 --- a/easybuild/easyconfigs/j/Java/Java-17.0.1.eb +++ b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb @@ -9,7 +9,7 @@ toolchain = SYSTEM local_tarball_tmpl = 'openjdk-%%(version)s_linux-%s_bin.tar.gz' -source_urls = ['https://download.java.net/java/GA/jdk%(version)s/51f4f36ad4ef43e39d0dfdbaf6549e32/9/GPL/'] +source_urls = ['https://download.java.net/java/GA/jdk%(version)s/2a2082e5a09d4267845be086888add4f/9/GPL/'] sources = [local_tarball_tmpl % '%(jdkarch)s'] checksums = [ { From b73e3624d686a2bb326987a726f45a333dde5b7b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 5 Jan 2022 14:33:20 +0100 Subject: [PATCH 2549/9987] update easyconfig: Java-17.0.1.eb --- easybuild/easyconfigs/j/Java/Java-17.0.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.1.eb b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb index 9fa9e3e0450..b32ffe92e25 100644 --- a/easybuild/easyconfigs/j/Java/Java-17.0.1.eb +++ b/easybuild/easyconfigs/j/Java/Java-17.0.1.eb @@ -9,7 +9,7 @@ toolchain = SYSTEM local_tarball_tmpl = 'openjdk-%%(version)s_linux-%s_bin.tar.gz' -source_urls = ['https://download.java.net/java/GA/jdk%(version)s/2a2082e5a09d4267845be086888add4f/9/GPL/'] +source_urls = ['https://download.java.net/java/GA/jdk%(version)s/2a2082e5a09d4267845be086888add4f/12/GPL/'] sources = [local_tarball_tmpl % '%(jdkarch)s'] checksums = [ { From 3db0d9384ddb4384e6a53549e4ebe2755cb72dc3 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 15:16:29 +0100 Subject: [PATCH 2550/9987] fixed toolchain to GCC --- .../c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..bae1e383e4c --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'https://github.com/weizhongli/cdhit' +description = """CD-HIT is a very widely used program for clustering and +comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.34.0'), + ('zlib', '1.2.11'), +] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' From 7f48665ad5d604773f86d03f8c5a3a5adc43ee6f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 15:25:08 +0100 Subject: [PATCH 2551/9987] fix formatting of STRUMPACK-6.1.0-intel-2020b.eb --- .../s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb index 47b5368522d..f5abbb782b6 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -25,23 +25,23 @@ dependencies = [ ] configopts = '-DSTRUMPACK_USE_OPENMP=ON ' +configopts += '-DTPL_SCALAPACK_LIBRARIES="${LIBSCALAPACK_MT}" ' configopts += '-DTPL_METIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_METIS_LIBRARIES=${EBROOTPARMETIS}/lib/libmetis.a ' -configopts += '-DTPL_SCALAPACK_LIBRARIES="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -liomp5 -lpthread -lm -ldl" ' -configopts += '-DTPL_ENABLE_BPACK=OFF ' -configopts += '-DTPL_ENABLE_ZFP=OFF ' -configopts += '-DTPL_ENABLE_SLATE=OFF ' +configopts += '-DTPL_METIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_PARMETIS=ON ' configopts += '-DTPL_PARMETIS_INCLUDE_DIRS=${EBROOTPARMETIS}/include ' -configopts += '-DTPL_PARMETIS_LIBRARIES=${EBROOTPARMETIS}/lib/libparmetis.a ' +configopts += '-DTPL_PARMETIS_LIBRARY_DIR=${EBROOTPARMETIS}/lib ' configopts += '-DTPL_ENABLE_SCOTCH=ON ' configopts += '-DTPL_SCOTCH_INCLUDE_DIRS=${EBROOTSCOTCH}/include ' configopts += '-DTPL_SCOTCH_LIBRARY_DIR=${EBROOTSCOTCH}/lib ' +configopts += '-DTPL_ENABLE_BPACK=OFF ' +configopts += '-DTPL_ENABLE_ZFP=OFF ' +configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + -[ 'lib'], + [ 'lib'], } moduleclass = 'numlib' From 79745a01576b46333875ead9f59397816940a8d9 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 15:39:40 +0100 Subject: [PATCH 2552/9987] Added binutils dependency --- .../easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb index bae1e383e4c..d1f7dfd2cb6 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb @@ -5,9 +5,9 @@ easyblock = 'MakeCp' name = 'CD-HIT' version = '4.8.1' -homepage = 'https://github.com/weizhongli/cdhit' -description = """CD-HIT is a very widely used program for clustering and -comparing protein or nucleotide sequences.""" +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} toolchainopts = {'openmp': True} @@ -17,7 +17,8 @@ sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] dependencies = [ - ('Perl', '5.34.0'), + ('binutils', '2.37'), + ('Perl', '5.32.1'), ('zlib', '1.2.11'), ] @@ -37,4 +38,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + moduleclass = 'bio' From 6caeaea883f979946826bc64feb1d61b918daa31 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 15:41:12 +0100 Subject: [PATCH 2553/9987] remove whitespace in STRUMPACK-6.1.0-foss-2020b.eb --- easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb index d6c33b40db7..7dd06980ec6 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-foss-2020b.eb @@ -40,7 +40,7 @@ configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + - [ 'lib'], + ['lib'], } moduleclass = 'numlib' From b5692067ce1ada6071476e328ad29b2598c164c3 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 5 Jan 2022 15:41:33 +0100 Subject: [PATCH 2554/9987] Java 15 instead of 13 Update easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb Once Java 15 is accepted, this one can use it Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index 92bf8614231..7eb4e38d14c 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -40,6 +40,6 @@ builddependencies = [ prebuildopts = "export BAZEL_LINKOPTS=-static-libstdc++:-static-libgcc BAZEL_LINKLIBS=-l%:libstdc++.a:-lm && " configopts = "--host_jvm_args=--illegal-access=debug" -dependencies = [('Java', '13', '', True)] +dependencies = [('Java', '15', '', True)] moduleclass = 'devel' From 7403d93236b3d196002c171fdabdb596d2ceb478 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Jan 2022 15:41:37 +0100 Subject: [PATCH 2555/9987] remove whitespace in STRUMPACK-6.1.0-intel-2020b.eb --- .../easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb index f5abbb782b6..4f358cbc2f3 100644 --- a/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/STRUMPACK/STRUMPACK-6.1.0-intel-2020b.eb @@ -41,7 +41,7 @@ configopts += '-DTPL_ENABLE_SLATE=OFF ' sanity_check_paths = { 'files': ['lib/libstrumpack.a'], 'dirs': ['include/%s' % x for x in ['BLR', 'clustering', 'dense', 'HSS', 'kernel', 'misc', 'python', 'sparse']] + - [ 'lib'], + ['lib'], } moduleclass = 'numlib' From 889fa11760bd48d3a1dbcb28d16a9d6113b3c182 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Wed, 5 Jan 2022 15:56:43 +0100 Subject: [PATCH 2556/9987] Delete CD-HIT-4.8.1-GCCcore-11.2.0.eb --- .../c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb deleted file mode 100644 index d99cc6a786d..00000000000 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCCcore-11.2.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'MakeCp' - -name = 'CD-HIT' -version = '4.8.1' - -homepage = 'https://github.com/weizhongli/cdhit' -description = """CD-HIT is a very widely used program for clustering and -comparing protein or nucleotide sequences.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -toolchainopts = {'openmp': True} - -source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] -sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] -checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] - -dependencies = [ - ('Perl', '5.34.0'), - ('zlib', '1.2.11'), -] - -# make sure compilation flags are passed down (e.g. to enable OpenMP) -buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' - -# put here the list of generated executables when compiling -local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] - -# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" -files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] - -fix_perl_shebang_for = ['bin/*.pl'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_list_of_executables], - 'dirs': [], -} - -moduleclass = 'bio' From 4e4a2afc9d631382105faf7775144e8ab3334332 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 16:00:37 +0100 Subject: [PATCH 2557/9987] Removed changes from last commit + fixed Perl version --- easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb index d1f7dfd2cb6..6b5b72e0ff7 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.2.0.eb @@ -17,8 +17,7 @@ sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] dependencies = [ - ('binutils', '2.37'), - ('Perl', '5.32.1'), + ('Perl', '5.34.0'), ('zlib', '1.2.11'), ] From b8f01e5ff9a5a5e589549f81e1ca09c2379a101f Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 5 Jan 2022 16:38:26 +0100 Subject: [PATCH 2558/9987] adding easyconfigs: BLAST+-2.11.0-gompi-2021b.eb --- .../b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb new file mode 100644 index 00000000000..90b1b862289 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb @@ -0,0 +1,56 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.11.0' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost', '1.77.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.29'), +] + + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' From e4350d6bfed68957b03a5a748f9c3be4d31cadc1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 6 Jan 2022 12:40:53 +0200 Subject: [PATCH 2559/9987] adding easyconfigs: AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb --- ...toDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..90e04c1f06b --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -0,0 +1,60 @@ +easyblock = 'MakeCp' + +name = 'AutoDock-GPU' +version = '1.5.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/ccsb-scripps/AutoDock-GPU' +description = """OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly +parallelizable LGA by processing ligand-receptor poses in parallel over +multiple compute units. +AutoDock is a suite of automated docking tools. It is designed to predict how +small molecules, such as substrates or drug candidates, bind to a receptor of +known 3D structure.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'cstd': 'c++11'} + +github_account = 'ccsb-scripps' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6557df95eed99323befddcef6b8da8b67eba22476efccd1e69a87ffdf075e5f4'] + +dependencies = [ + ('CUDA', '11.3.1', '', True), +] + +parallel = 1 + +# Default CUDA compute capabilities (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.2', '6.0', '6.1', '7.0'] +# put CUDA compute capabilities in a shell variable to strip dots in make command +prebuildopts = 'CUDA_CC_TARGETS="%(cuda_cc_space_sep)s"; ' + +# Use complation flags from EB +prebuildopts += "sed -i 's/^LFLAGS=.*/LFLAGS=$(LDFLAGS)/;s/^CFLAGS=.*/CFLAGS+=$(IFLAGS) $(LFLAGS)/' Makefile.Cuda && " + +prebuildopts += 'GPU_INCLUDE_PATH=$EBROOTCUDA/include ' +prebuildopts += 'GPU_LIBRARY_PATH=$EBROOTCUDA/lib ' + +# build for CUDA with defined CUDA compute capabilities +buildopts = 'DEVICE=CUDA TARGETS="${CUDA_CC_TARGETS//./}"' + +files_to_copy = [ + (['bin/*'], 'bin'), + (['doc', 'examples', 'LICENSE', 'LICENSE_LGPL', 'README.md'], 'share'), + (['input'], 'share/examples'), +] + +postinstallcmds = [ + "cd %(installdir)s/bin && ln -s autodock_gpu_64wi autodock_gpu", +] + +sanity_check_paths = { + 'files': ['bin/autodock_gpu', 'bin/autodock_gpu_64wi', 'bin/adgpu_analysis'], + 'dirs': ['share'], +} + +sanity_check_commands = [('autodock_gpu', '--help')] + +moduleclass = 'tools' From fb90160850bade7a3180160f0a845fc8abca7fc0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 6 Jan 2022 15:43:10 +0100 Subject: [PATCH 2560/9987] adding easyconfigs: STAR-2.7.9a-GCC-11.2.0.eb --- .../s/STAR/STAR-2.7.9a-GCC-11.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-11.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-11.2.0.eb new file mode 100644 index 00000000000..f43ea1e30a6 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.9a-GCC-11.2.0.eb @@ -0,0 +1,42 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.9a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +github_account = 'alexdobin' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['ff52c9d6daaa9fb7261efa3aa49ef6ce5262aa089b0762a3cbc751e81321050e'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' %(name)s && make %(name)slong' + +parallel = 1 + +files_to_copy = [ + (['source/%(name)s', 'source/%(name)slong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/%(name)slong'], + 'dirs': [], +} + +moduleclass = 'bio' From 942b59942b4d897fa38a7225b40c2a8ccd5c8fdf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 6 Jan 2022 15:55:22 +0100 Subject: [PATCH 2561/9987] adding easyconfigs: Subread-2.0.3-GCC-11.2.0.eb --- .../s/Subread/Subread-2.0.3-GCC-11.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..df58b302599 --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.3-GCC-11.2.0.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'MakeCp' + +name = 'Subread' +version = '2.0.3' + +# HTTPS is not valid +homepage = 'http://subread.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] + +checksums = ['56cef3a2f914d432713069d5c282f48831c3a1ecc89432ad5580caa322a5f56b'] + +start_dir = 'src' + +prebuildopts = "sed -i 's/-mtune=core2//g' Makefile.Linux && " +prebuildopts += "sed -i 's/-mtune=core2//g' longread-one/Makefile && " + +buildopts = " -f Makefile.Linux" + +files_to_copy = ['bin'] + +local_binaries_list = [ + 'exactSNP', 'featureCounts', 'subindel', 'subjunc', 'sublong', '%(namelower)s-align', '%(namelower)s-buildindex', +] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_binaries_list], + 'dirs': ['bin/utilities'], +} + +sanity_check_commands = [ + 'cd %(builddir)s/%(namelower)s-%(version)s-source/test && bash test_all.sh' +] + +moduleclass = 'bio' From 509da5f6ae535afe4e42cb3c4b6ddc34c46f396f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 6 Jan 2022 17:16:32 +0200 Subject: [PATCH 2562/9987] rename and update AutoDock-Vina v1.1.2 and v1.2.3 --- .../AutoDock-Vina-1.1.2-linux_x86.eb} | 11 ++-- .../AutoDock-Vina-1.2.3-GCC-10.3.0.eb | 36 +++++++++++ ...Dock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb | 63 +++++++++++++++++++ 3 files changed, 105 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/a/{AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb => AutoDock-Vina/AutoDock-Vina-1.1.2-linux_x86.eb} (59%) create mode 100644 easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.1.2-linux_x86.eb similarity index 59% rename from easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb rename to easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.1.2-linux_x86.eb index 01717004821..d0c0d56d246 100644 --- a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.1.2-linux_x86.eb @@ -5,21 +5,22 @@ easyblock = "Tarball" -name = 'AutoDock_Vina' +name = 'AutoDock-Vina' version = '1.1.2' -versionsuffix = '_linux_x86' +versionsuffix = '-linux_x86' homepage = 'http://vina.scripps.edu/index.html' description = """ AutoDock Vina is an open-source program for doing molecular docking. """ toolchain = SYSTEM -source_urls = ['http://vina.scripps.edu/download/'] -sources = ['%s_%s%s.tgz' % (name.lower(), version.replace('.', '_'), versionsuffix)] +source_urls = ['https://vina.scripps.edu/wp-content/uploads/sites/55/2020/12'] +sources = ['autodock_vina_%s%s.tgz' % (version.replace('.', '_'), versionsuffix.replace('-', '_'))] +checksums = ['70543bd953626cf45c53bd1f15ee41e481bde0f94e9746a6be59eabc2cc6bcce'] sanity_check_paths = { 'files': ["bin/vina_split", "bin/vina"], - 'dirs': [] + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..0c3d105812c --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'AutoDock-Vina' +version = '1.2.3' + +homepage = 'https://vina.scripps.edu/' +description = "AutoDock Vina is an open-source program for doing molecular docking." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'ccsb-scripps' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'] + +dependencies = [ + ('Boost', '1.76.0'), +] + +start_dir = 'build/linux/release' + +buildopts = 'GPP="$CXX" BOOST_INCLUDE="$EBROOTBOOST/include"' + +files_to_copy = [ + (['vina', 'vina_split'], 'bin'), + (['docs', 'example', 'LICENSE', 'README.md'], 'share'), +] + +sanity_check_paths = { + 'files': ['bin/vina', 'bin/vina_split'], + 'dirs': ['share'], +} + +sanity_check_commands = [('vina', '--help')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..bf7713a55fa --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,63 @@ +easyblock = 'MakeCp' + +name = 'AutoDock-Vina' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://vina.scripps.edu/' +description = "AutoDock Vina is an open-source program for doing molecular docking." + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'ccsb-scripps' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'] + +builddependencies = [ + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Boost', '1.76.0'), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +start_dir = 'build/linux/release' + +buildopts = 'GPP="$CXX" BOOST_INCLUDE="$EBROOTBOOST/include"' + +files_to_copy = [ + (['vina', 'vina_split'], 'bin'), + (['docs', 'example', 'LICENSE', 'README.md'], 'share'), +] + +exts_defaultclass = 'PythonPackage' + +# fix hardcoded paths in setup.py +_ext_boost_paths = ('$EBROOTBOOST/include', '$EBROOTBOOST/lib') +_ext_fix_paths = 'sed -i "s|= locate_boost()|= \\\"%s\\\", \\\"%s\\\"|" setup.py && ' % _ext_boost_paths +_ext_fix_paths += "sed -i 's|\.\./\.\./src|%%(builddir)s/%%(name)s/%s-%%(version)s/src|g' setup.py && " % name + +exts_list = [ + ('vina', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'], + 'start_dir': 'build/python', + 'use_pip': True, + 'sanity_pip_check': True, + 'preinstallopts': _ext_fix_paths, + }), +] + +sanity_check_paths = { + 'files': ['bin/vina', 'bin/vina_split'], + 'dirs': ['share'], +} + +sanity_check_commands = [('vina', '--help')] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'tools' From 53489bbd3a108d1cbf43397c04f2fc2464371f14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 7 Jan 2022 09:19:17 +0100 Subject: [PATCH 2563/9987] adding easyconfigs: DIAMOND-2.0.13-GCC-11.2.0.eb --- .../d/DIAMOND/DIAMOND-2.0.13-GCC-11.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-11.2.0.eb new file mode 100644 index 00000000000..e9d2b4684fe --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.0.13-GCC-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.0.13' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'bbuchfink' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['9b79c3a01913999dfa2543f4dd7a3494397a8723ea587207c14683b24e57eac1'] + +builddependencies = [('CMake', '3.21.1')] +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["%(namelower)s help"] + +moduleclass = 'bio' From 31b006602d11e29c0282b315a96fdf380e316f8a Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 7 Jan 2022 11:16:53 +0100 Subject: [PATCH 2564/9987] Add ELSI-RCI-0.1.0 for foss/2021a, foss/2021b, intel/2021a and intel/2021b. --- .../e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb | 41 +++++++++++++++++++ .../e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb | 41 +++++++++++++++++++ .../e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb | 40 ++++++++++++++++++ .../e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb | 40 ++++++++++++++++++ 4 files changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb create mode 100644 easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb new file mode 100644 index 00000000000..8346e384dec --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), +] + + +# Compilation of tests seem to be broken, so disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb new file mode 100644 index 00000000000..02237e1a5b3 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + + +# Compilation of tests seem to be broken, so disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb new file mode 100644 index 00000000000..51095f7a406 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +# Compilation of tests seem to be broken, so disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb new file mode 100644 index 00000000000..1f59de009da --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'ELSI-RCI' +version = '0.1.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI-RCI provides and enhances open-source software packages +which iteratively solve or circumvent eigenvalue problems in self-consistent +field calculations based on the Kohn-Sham density-functional theory. +""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['ELSI-RCI-0.1.0-cmake.patch'] +checksums = [ + 'a737673c1009b919be0daf86e86d1f4387a26711a10bda88a5f3f6c0b944c580', # elsi-rci-0.1.0.tar.gz + 'd8205d8f67775aa6cfc75813566a64b2a4b01c9b856268e457ef153b7988de82', # ELSI-RCI-0.1.0-cmake.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +# Compilation of tests seem to be broken, so disable it +configopts = [ + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=ON" +] + +runtest = False + +sanity_check_paths = { + 'files': ['include/elsi_rci.mod', 'lib/libelsi_rci.a', 'lib/libelsi_rci.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' From 3675d444f36c83d8bffbb4598664f82acd67d831 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 7 Jan 2022 11:50:31 +0100 Subject: [PATCH 2565/9987] Add PSolver-1.8.3 and futile-1.8.3 for foss/2021a, foss/2021b, intel/2021a, and intel/2021b. --- .../f/futile/futile-1.8.3-foss-2021a.eb | 37 +++++++++++++++++ .../f/futile/futile-1.8.3-foss-2021b.eb | 41 +++++++++++++++++++ .../f/futile/futile-1.8.3-intel-2021a.eb | 41 +++++++++++++++++++ .../f/futile/futile-1.8.3-intel-2021b.eb | 41 +++++++++++++++++++ .../f/futile/futile_index_bug.patch | 21 ++++++++++ .../p/PSolver/PSolver-1.8.3-foss-2021a.eb | 38 +++++++++++++++++ .../p/PSolver/PSolver-1.8.3-foss-2021b.eb | 38 +++++++++++++++++ .../p/PSolver/PSolver-1.8.3-intel-2021a.eb | 38 +++++++++++++++++ .../p/PSolver/PSolver-1.8.3-intel-2021b.eb | 38 +++++++++++++++++ 9 files changed, 333 insertions(+) create mode 100644 easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb create mode 100644 easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb create mode 100644 easybuild/easyconfigs/f/futile/futile_index_bug.patch create mode 100644 easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb create mode 100644 easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb new file mode 100644 index 00000000000..a684f70cf94 --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCLAGS -fallow-argument-mismatch" ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb new file mode 100644 index 00000000000..0ef7202fe22 --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +patches = ['futile_index_bug.patch'] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + '5ef5f8ad7644259da0d2d2bcb64c44b923cb64b1eedf03898d0da18228ea392f', # futile_index_bug.patch +] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCLAGS -fallow-argument-mismatch" ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb new file mode 100644 index 00000000000..dd385e85152 --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +patches = ['futile_intel_bug.patch'] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + 'e3681e6dda9364a1be4fba937423b8ac1774c3ebfd1ff04211482df25a188e95', # futile_intel_bug.patch +] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb new file mode 100644 index 00000000000..d0c0c3be36b --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'futile' +version = '1.8.3' + +homepage = 'https://launchpad.net/futile' +description = """ + The FUTILE project (Fortran Utilities for the Treatment of Innermost Level of Executables) is a set of modules + and wrapper that encapsulate the most common low-level operations of a Fortran code. + """ + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +patches = ['futile_intel_bug.patch'] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + 'e3681e6dda9364a1be4fba937423b8ac1774c3ebfd1ff04211482df25a188e95', # futile_intel_bug.patch +] + +unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " +unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" +start_dir = "futile-%(version)s" + +configopts = 'CC=$MPICC FC=$MPIFC ' +configopts += '--enable-mpi ' +configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' +configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' + +dependencies = [('libyaml', '0.2.5')] + +sanity_check_paths = { + 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + + [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/futile/futile_index_bug.patch b/easybuild/easyconfigs/f/futile/futile_index_bug.patch new file mode 100644 index 00000000000..f7649622add --- /dev/null +++ b/easybuild/easyconfigs/f/futile/futile_index_bug.patch @@ -0,0 +1,21 @@ +Patch to fix the redefinition of an index variable caught by GCC 11. +author: Micael Oliveira (Max Planck Institute for the Structure and Dynamics of Matter) +diff -rup futile-1.8.3.orig/flib/f_input_file.f90 futile-1.8.3/flib/f_input_file.f90 +--- futile-1.8.3.orig/flib/f_input_file.f90 2018-12-13 10:27:01.000000000 +0100 ++++ futile-1.8.3/flib/f_input_file.f90 2022-01-07 11:35:42.036739693 +0100 +@@ -172,7 +172,6 @@ contains + type(dictionary), pointer :: dict + character(len = *), intent(in) :: file, key + +- integer :: i + type(dictionary), pointer :: ref,iter + character(len = max_field_length) :: val, profile_ + double precision, dimension(2) :: rg +@@ -366,6 +365,7 @@ contains + character(max_field_length), dimension(:), allocatable :: keys + double precision :: var + integer :: dlen, skeys ++ integer :: i + + if (associated(dict%child)) then + if (dict_len(dict) >= 1) then diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb new file mode 100644 index 00000000000..0f0b9fd1313 --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb new file mode 100644 index 00000000000..9cfcdd477ce --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb new file mode 100644 index 00000000000..d4e348ef4fb --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb new file mode 100644 index 00000000000..f87fa8bf98e --- /dev/null +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSolver' +version = '1.8.3' + +homepage = 'http://bigdft.org/devel-doc/d1/d81/group__PSOLVER.html' +description = """ + Interpolating scaling function Poisson Solver Library + """ + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] + +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -I$EBROOTFUTILE/include" ' +configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ + '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += ' --with-mpi3 ' +prebuildopts = local_cddir +preinstallopts = local_cddir + +dependencies = [ + ('libyaml', '0.2.5'), + ('futile', '1.8.3') +] + +sanity_check_paths = { + 'files': ['include/poisson_solver.mod'] + + [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + 'dirs': [] +} + +moduleclass = 'phys' From 497a009ac8e78181227ad3704145e431409563ae Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 7 Jan 2022 13:22:38 +0100 Subject: [PATCH 2566/9987] Add libGridXC-0.9.6 for foss/2021a, foss/2021b, intel/2021a, and intel/2021b. --- .../libGridXC/libGridXC-0.9.6-gompi-2021a.eb | 34 +++++++++++ .../libGridXC/libGridXC-0.9.6-gompi-2021b.eb | 34 +++++++++++ .../libGridXC/libGridXC-0.9.6-iimpi-2021a.eb | 34 +++++++++++ .../libGridXC/libGridXC-0.9.6-iimpi-2021b.eb | 34 +++++++++++ .../l/libxc/libxc-4.3.4-GCC-11.2.0.eb | 55 +++++++++++++++++ .../libxc-4.3.4-intel-compilers-2021.4.0.eb | 61 +++++++++++++++++++ test/easyconfigs/easyconfigs.py | 2 + 7 files changed, 254 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2021a.eb create mode 100644 easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2021b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2021a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2021a.eb new file mode 100644 index 00000000000..3e8c27112b0 --- /dev/null +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libGridXC' +version = '0.9.6' + +homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' +description = """A library to compute the exchange and correlation energy + and potential in spherical (i.e. atoms) or periodic systems.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/uploads/e6e4ec1e3ec648a45b3613e724c7be04'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee513eeb08b631e2efaaea62e73d85b6fbf204da85963be785915802e5497463'] + +local_common_configopts = "--enable-static --enable-shared --enable-multiconfig --with-libxc" + +configopts = [ + local_common_configopts + " --without-mpi", + local_common_configopts + " CC=$MPICC FC=$MPIFC CXX=$MPICXX --with-mpi", +] + +dependencies = [('libxc', '4.3.4')] + +sanity_check_paths = { + 'files': + ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2021b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2021b.eb new file mode 100644 index 00000000000..3197c6ad2d3 --- /dev/null +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-gompi-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libGridXC' +version = '0.9.6' + +homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' +description = """A library to compute the exchange and correlation energy + and potential in spherical (i.e. atoms) or periodic systems.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/uploads/e6e4ec1e3ec648a45b3613e724c7be04'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee513eeb08b631e2efaaea62e73d85b6fbf204da85963be785915802e5497463'] + +local_common_configopts = "--enable-static --enable-shared --enable-multiconfig --with-libxc" + +configopts = [ + local_common_configopts + " --without-mpi", + local_common_configopts + " CC=$MPICC FC=$MPIFC CXX=$MPICXX --with-mpi", +] + +dependencies = [('libxc', '4.3.4')] + +sanity_check_paths = { + 'files': + ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2021a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2021a.eb new file mode 100644 index 00000000000..9f0db8c593f --- /dev/null +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libGridXC' +version = '0.9.6' + +homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' +description = """A library to compute the exchange and correlation energy + and potential in spherical (i.e. atoms) or periodic systems.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/uploads/e6e4ec1e3ec648a45b3613e724c7be04'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee513eeb08b631e2efaaea62e73d85b6fbf204da85963be785915802e5497463'] + +local_common_configopts = "--enable-static --enable-shared --enable-multiconfig --with-libxc" + +configopts = [ + local_common_configopts + " --without-mpi", + local_common_configopts + " CC=$MPICC FC=$MPIFC CXX=$MPICXX --with-mpi", +] + +dependencies = [('libxc', '4.3.4')] + +sanity_check_paths = { + 'files': + ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2021b.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2021b.eb new file mode 100644 index 00000000000..c3ad7973ac2 --- /dev/null +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-0.9.6-iimpi-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libGridXC' +version = '0.9.6' + +homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' +description = """A library to compute the exchange and correlation energy + and potential in spherical (i.e. atoms) or periodic systems.""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/uploads/e6e4ec1e3ec648a45b3613e724c7be04'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ee513eeb08b631e2efaaea62e73d85b6fbf204da85963be785915802e5497463'] + +local_common_configopts = "--enable-static --enable-shared --enable-multiconfig --with-libxc" + +configopts = [ + local_common_configopts + " --without-mpi", + local_common_configopts + " CC=$MPICC FC=$MPIFC CXX=$MPICXX --with-mpi", +] + +dependencies = [('libxc', '4.3.4')] + +sanity_check_paths = { + 'files': + ['include/gridxc_dp%s/gridxc.mod' % x for x in ['', '_mpi']] + + [('lib/libgridxc_dp.a', 'lib64/libgridxc_dp.a')] + + [('lib/libgridxc_dp_mpi.a', 'lib64/libgridxc_dp_mpi.a')], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb new file mode 100644 index 00000000000..b45abb6d6ab --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '4.3.4' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'libxc-%(version)s_lm-fix.patch', + 'libxc-%(version)s_fix-CMakeLists.patch', + 'libxc-%(version)s_fix-timeout.patch', +] +checksums = [ + 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch + '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch + 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Perl', '5.34.0'), +] + +separate_build_dir = True + +parallel = 1 + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info', 'bin/xc-threshold'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..fca29faafd6 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb @@ -0,0 +1,61 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '4.3.4' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'libxc-%(version)s_rename-F03.patch', + 'libxc-%(version)s_lm-fix.patch', + 'libxc-%(version)s_fix-CMakeLists.patch', + 'libxc-%(version)s_fix-timeout.patch', +] +checksums = [ + 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + 'e494be3ca2026998f2dd7c6b03a4e662f204fd3d963271e588f9f0d5739e76b5', # libxc-4.3.4_rename-F03.patch + 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch + '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch + 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Perl', '5.34.0'), +] + +separate_build_dir = True + +# rename *.F03 source file since Intel Fortran compiler doesn't like that extension +# also requires patch file to rename file in CMakeLists.txt and src/Makefile.in +preconfigopts = "mv ../libxc-%(version)s/src/libxc_master.F03 ../libxc-%(version)s/src/libxc_master_F03.F90 && " + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info', 'bin/xc-threshold'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3b214747672..b1054aefe18 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -446,10 +446,12 @@ def check_dep_vars(self, gen, dep, dep_vars): # Libint 1.1.6 is required by older CP2K versions 'Libint': [(r'1\.1\.6', [r'CP2K-[3-6]'])], # libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, horton, PySCF, WIEN2k + # libxc 4.x is required by libGridXC # (Qiskit depends on PySCF), Elk 7.x requires libxc >= 5 'libxc': [ (r'[23]\.', [r'ABINIT-', r'AtomPAW-', r'CP2K-', r'GPAW-', r'horton-', r'PySCF-', r'Qiskit-', r'WIEN2k-']), + (r'4\.', [r'libGridXC-']), (r'5\.', [r'Elk-']), ], # some software depends on numba, which typically requires an older LLVM; From 0e0be8a49c408e36528fd868985c00ec13d19269 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 7 Jan 2022 16:33:07 +0200 Subject: [PATCH 2567/9987] remove AutoDock-Vina-1.2.3-GCC-10.3.0.eb --- .../AutoDock-Vina-1.2.3-GCC-10.3.0.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb deleted file mode 100644 index 0c3d105812c..00000000000 --- a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-GCC-10.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'MakeCp' - -name = 'AutoDock-Vina' -version = '1.2.3' - -homepage = 'https://vina.scripps.edu/' -description = "AutoDock Vina is an open-source program for doing molecular docking." - -toolchain = {'name': 'GCC', 'version': '10.3.0'} - -github_account = 'ccsb-scripps' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'] - -dependencies = [ - ('Boost', '1.76.0'), -] - -start_dir = 'build/linux/release' - -buildopts = 'GPP="$CXX" BOOST_INCLUDE="$EBROOTBOOST/include"' - -files_to_copy = [ - (['vina', 'vina_split'], 'bin'), - (['docs', 'example', 'LICENSE', 'README.md'], 'share'), -] - -sanity_check_paths = { - 'files': ['bin/vina', 'bin/vina_split'], - 'dirs': ['share'], -} - -sanity_check_commands = [('vina', '--help')] - -moduleclass = 'tools' From 65674c206b9dd6caf7acf85f2bc430668b9d51cf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 7 Jan 2022 16:34:24 +0200 Subject: [PATCH 2568/9987] remove versionsuffix from AutoDock-Vina v1.2.3 --- ...thon-3.9.5.eb => AutoDock-Vina-1.2.3-foss-2021a.eb} | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/a/AutoDock-Vina/{AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb => AutoDock-Vina-1.2.3-foss-2021a.eb} (92%) diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb similarity index 92% rename from easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb rename to easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb index bf7713a55fa..c5f03706a72 100644 --- a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb @@ -2,7 +2,6 @@ easyblock = 'MakeCp' name = 'AutoDock-Vina' version = '1.2.3' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://vina.scripps.edu/' description = "AutoDock Vina is an open-source program for doing molecular docking." @@ -34,6 +33,11 @@ files_to_copy = [ ] exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} # fix hardcoded paths in setup.py _ext_boost_paths = ('$EBROOTBOOST/include', '$EBROOTBOOST/lib') @@ -45,8 +49,6 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'checksums': ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'], 'start_dir': 'build/python', - 'use_pip': True, - 'sanity_pip_check': True, 'preinstallopts': _ext_fix_paths, }), ] @@ -60,4 +62,4 @@ sanity_check_commands = [('vina', '--help')] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} -moduleclass = 'tools' +moduleclass = 'bio' From d48fdae429fff1249d8d867848e2fd1a807bce20 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 7 Jan 2022 16:46:41 +0200 Subject: [PATCH 2569/9987] fix codestyle in AutoDock-Vina v1.2.3 --- .../a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb index c5f03706a72..4b2755dce8d 100644 --- a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb @@ -33,7 +33,7 @@ files_to_copy = [ ] exts_defaultclass = 'PythonPackage' -exts_default_options = { +exts_default_options = { 'download_dep_fail': True, 'use_pip': True, 'sanity_pip_check': True, From 68cae9a0667ccadbc9bcd81017a6a79bffa60988 Mon Sep 17 00:00:00 2001 From: MaximeVdB Date: Fri, 7 Jan 2022 16:46:20 +0100 Subject: [PATCH 2570/9987] adding easyconfigs gengetopt-2.23-GCCcore-10.3.0.eb, openCARP-8.2-foss-2021a.eb and patches: openCARP-8.2_build-info.patch --- .../gengetopt-2.23-GCCcore-10.3.0.eb | 27 +++++++ .../o/openCARP/openCARP-8.2-foss-2021a.eb | 38 ++++++++++ .../o/openCARP/openCARP-8.2_build-info.patch | 72 +++++++++++++++++++ 3 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/o/openCARP/openCARP-8.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/o/openCARP/openCARP-8.2_build-info.patch diff --git a/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..10ee38c02ba --- /dev/null +++ b/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'gengetopt' +version = '2.23' + +homepage = 'https://www.gnu.org/software/gengetopt/gengetopt.html' +description = "Gengetopt is a tool to write command line option parsing code for C programs." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['b941aec9011864978dd7fdeb052b1943535824169d2aa2b0e7eae9ab807584ac'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('makeinfo', '6.7', '-minimal'), +] + +sanity_check_paths = { + 'files': ['bin/gengetopt'], + 'dirs': ['share'], +} + +sanity_check_commands = ["gengetopt --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/openCARP/openCARP-8.2-foss-2021a.eb b/easybuild/easyconfigs/o/openCARP/openCARP-8.2-foss-2021a.eb new file mode 100644 index 00000000000..77f898e60c5 --- /dev/null +++ b/easybuild/easyconfigs/o/openCARP/openCARP-8.2-foss-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMakeCp' + +name = 'openCARP' +version = '8.2' + +homepage = 'https://opencarp.org' +description = "openCARP is an open cardiac electrophysiology simulator for in-silico experiments." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://git.opencarp.org/openCARP/openCARP/-/archive/v%(version)s/'] +sources = ['openCARP-v%(version)s.tar.gz'] +patches = ['openCARP-8.2_build-info.patch'] +checksums = [ + '56263c4280787c5c7b2ddb2b5f5b5091745dbc7e25d16118071ba0110bff494a', # openCARP-v8.2.tar.gz + '23c8754c749acc5f0f58ac3780ef7e202cefbcc8092e02e832ac2ff540367365', # openCARP-8.2_build-info.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('gengetopt', '2.23'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('PETSc', '3.15.1'), + ('zlib', '1.2.11'), +] + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bench', 'igbapd', 'igbextract', 'igbhead', 'igbops', 'mesher', 'openCARP']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/openCARP/openCARP-8.2_build-info.patch b/easybuild/easyconfigs/o/openCARP/openCARP-8.2_build-info.patch new file mode 100644 index 00000000000..c6aaf5d2f46 --- /dev/null +++ b/easybuild/easyconfigs/o/openCARP/openCARP-8.2_build-info.patch @@ -0,0 +1,72 @@ +avoid having to build from cloned Git repository by adding simulator/build_info.h file, +which was generated using "PETSC_DIR=/foo make build_info.h" in Git repo that corresponds with openCARP v8.2 sources +author: Kenneth Hoste (HPC-UGent) +update to v8.2: Maxime Van den Bossche (HPC-KULeuven) +--- openCARP-v8.2.orig/simulator/CMakeLists.txt 2022-01-06 10:41:19.549302000 +0100 ++++ openCARP-v8.2/simulator/CMakeLists.txt 2022-01-06 10:53:36.486316000 +0100 +@@ -3,13 +3,6 @@ + + ####################################################################### + find_package (Python) + +-add_custom_command(OUTPUT "build_info.h" +- COMMAND Python::Interpreter +- ${CMAKE_CURRENT_SOURCE_DIR}/build_info.py +- DEPENDS build_info.py +- COMMENT "Generate a C header file defining some information about the build" +- VERBATIM +-) + + set(CARP_FILES "openCARP_d.h" "openCARP_p.cc" "openCARP_p.h") + add_custom_command(OUTPUT ${CARP_FILES} +--- openCARP-v8.2.orig/simulator/build_info.h 1970-01-01 01:00:00.000000000 +0100 ++++ openCARP-v8.2/simulator/build_info.h 2022-01-06 10:53:36.486316000 +0100 +@@ -0,0 +1,13 @@ ++#ifndef __BUILD_INFO__ ++#define __BUILD_INFO__ ++ ++#define GIT_COMMIT_TAG "v8.2" ++#define GIT_COMMIT_HASH "dbfd16fdd472375694190b4c7802c0bfba114146" ++#define GIT_COMMIT_COUNT 1257 ++#define GIT_PATH "https://git.opencarp.org/openCARP/openCARP.git" ++ ++#define SUBREPO_REVISIONS "" ++ ++#define SUBREPO_COMMITS "" ++ ++#endif +--- openCARP-v8.2.orig/simulator/build_info.py 2022-01-06 10:41:19.549302000 +0100 ++++ openCARP-v8.2/simulator/build_info.py 2022-01-06 10:53:36.486316000 +0100 +@@ -157,25 +157,13 @@ + """ + + def generate(): +- +- info = git(os.path.dirname(os.path.abspath(__file__))) +- +- # Get subrepo info +- repo_versions = [] +- repo_commits = [] +- +- # we currently have no sub-repos. still, we leave the mechanism in here for later +- +- # repo_versions.append(('slimfem', git('../fem/slimfem')['revision'])) +- # repo_commits.append(( 'slimfem', git('../fem/slimfem')['commit'])) +- +- info['subrepo'] = ','.join(['{0[0]}={0[1]}'.format(v) for v in repo_versions]) +- +- # Assemble commit hashes / revisions +- newline = '," \\\n' + ' ' * 24 + '"' +- info['subrepocommit'] = newline.join(['{0[0]}={0[1]}'.format(v) for v in repo_commits]) +- +- return TEMPLATE.format(**info) ++ return TEMPLATE.format(tag='v8.2', ++ commit='dbfd16fdd472375694190b4c7802c0bfba114146', ++ revision=1257, ++ url='https://git.opencarp.org/openCARP/openCARP.git', ++ subrepo='', ++ subrepocommit='', ++ ) + + def print_build_info(filename): + """ From 3fd719a5debcd1937dee0f145f741d466bcbc771 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 7 Jan 2022 16:57:47 +0100 Subject: [PATCH 2571/9987] Applied requested changes --- easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb index 625b0fff96a..5a1898f43db 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb @@ -28,18 +28,23 @@ description = """ """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = ['https://github.com/lh3/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] builddependencies = [ + ('Perl', '5.34.0'), ('binutils', '2.37'), ] dependencies = [('zlib', '1.2.11')] -buildopts = 'CFLAGS="$CFLAGS -fcommon"' +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " moduleclass = 'bio' From e4c27466aa308e87a786f3e956a4e4a464b8497c Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 7 Jan 2022 18:23:41 +0100 Subject: [PATCH 2572/9987] Applied requested changes --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb index 90b1b862289..b6ec9feea95 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb @@ -21,6 +21,7 @@ description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm sequences of different proteins or the nucleotides of DNA sequences.""" toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True, 'pic': True} source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] sources = ['ncbi-blast-%(version)s+-src.tar.gz'] From b7a93983e2de78ce0362732a18b3f0ccb8ee5da8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jan 2022 20:46:42 +0100 Subject: [PATCH 2573/9987] adding easyconfigs: SHTns-3.5.1-foss-2021b.eb --- .../s/SHTns/SHTns-3.5.1-foss-2021b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb b/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb new file mode 100644 index 00000000000..d5ca8e5309e --- /dev/null +++ b/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'SHTns' +version = '3.5.1' + +homepage = 'https://bitbucket.org/nschaeff/shtns' +description = """Spherical Harmonic Transform library aimed at high performance numerical simulations in spherical +geometries.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://bitbucket.org/nschaeff/shtns/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['77f8a33b94df8786d2ce9b95cbfbe548f00443625b310b8c64012b22c8a7394f'] + +sanity_check_paths = { + 'files': ['include/shtns_cuda.h', 'include/shtns.f', 'include/shtns.f03', 'include/shtns.h', 'lib/libshtns.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 88ab8a49ccb8b5d227aa0f2f90b9e1d2633c856b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jan 2022 20:47:12 +0100 Subject: [PATCH 2574/9987] adding easyconfigs: SHTns-2.7-foss-2021b.eb --- .../s/SHTns/SHTns-2.7-foss-2021b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHTns/SHTns-2.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SHTns/SHTns-2.7-foss-2021b.eb b/easybuild/easyconfigs/s/SHTns/SHTns-2.7-foss-2021b.eb new file mode 100644 index 00000000000..12e800cbc5e --- /dev/null +++ b/easybuild/easyconfigs/s/SHTns/SHTns-2.7-foss-2021b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'SHTns' +version = '2.7' + +homepage = 'https://bitbucket.org/nschaeff/shtns' +description = """Spherical Harmonic Transform library aimed at high performance numerical simulations in spherical +geometries.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://bitbucket.org/nschaeff/shtns/get/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['725d0aedb26cdceed3a080d1c5f44a746eccba5d8943574fe08faeae370a5ba9'] + +sanity_check_paths = { + 'files': ['include/shtns.f', 'include/shtns.h', 'lib/libshtns.a'], + 'dirs': [], +} + +moduleclass = 'lib' From b5ae8f8a1ade9e1dba969d118e354beb1729f5aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jan 2022 21:07:20 +0100 Subject: [PATCH 2575/9987] add ExomeDepth extension to R-bundle-Bioconductor 3.14 --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index fa5e23bd4c8..2725d3a7c9f 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1075,6 +1075,9 @@ exts_list = [ ('M3Drop', '1.20.0', { 'checksums': ['b82772303c624ff01418e66cefd751a0f6f9d819ea2cf3c9c20a9acd1fc106e5'], }), + ('ExomeDepth', '1.1.15', { + 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From e3e8f61903843d1de01b8deba5392ef9956a5d0a Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 14:26:07 +0100 Subject: [PATCH 2576/9987] add corrected Pint and georges --- .../georges-2019.2-foss-2021a-Python-3.9.5.eb | 46 ------------------- .../Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb | 28 ----------- 2 files changed, 74 deletions(-) delete mode 100644 easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb delete mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb deleted file mode 100644 index 8e5f7b94288..00000000000 --- a/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'georges' -version = '2019.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/ULB-Metronu/georges' -description = """Georges the lemur opinionated particle accelerator modeling Python package. -Also a thin wrapper over MAD-X/PTC, BDSim and G4Beamline.""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -builddependencies = [ - ('pkg-config', '0.29.2'), -] - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('LMfit', '1.0.3'), - ('matplotlib', '3.4.2'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('mistune', '0.8.4', { - 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], - }), - ('m2r', '0.2.1', { - 'checksums': ['bf90bad66cda1164b17e5ba4a037806d2443f2a4d5ddc9f6a5554a0322aaed99'], - }), - ('pyDOE', '0.3.8', { - 'modulename': '%(name)s', - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], - }), - (name, version, { - 'source_tmpl': '%(version)s.tar.gz', - 'source_urls': ['https://github.com/ULB-Metronu/georges/archive/'], - 'checksums': ['5801c0655101e46401f4c052edc72e1dbf278fca76acf66a3ee3b10820527276'], - }), -] - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb b/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb deleted file mode 100644 index e695e3bff9f..00000000000 --- a/easybuild/easyconfigs/p/Pint/Pint-0.17-GCCcore-10.3.0-Python-3.9.5.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pint' -version = '0.17' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/hgrecco/pint' -description = """Pint is a Python package to define, operate and -manipulate physical quantities: the product of a numerical value and a -unit of measurement. It allows arithmetic operations between them and -conversions from and to different units.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['f4d0caa713239e6847a7c6eefe2427358566451fe56497d533f21fb590a3f313'] - -builddependencies = [('binutils', '2.36.1')] - -dependencies = [ - ('Python', '3.9.5'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -moduleclass = 'numlib' From 2d5507f40b98a3e5524dcede32a6d2a3905aa888 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 14:57:35 +0100 Subject: [PATCH 2577/9987] Corrected georges --- .../g/georges/georges-2019.2-foss-2021a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a.eb b/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a.eb new file mode 100644 index 00000000000..983cbb100ce --- /dev/null +++ b/easybuild/easyconfigs/g/georges/georges-2019.2-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'georges' +version = '2019.2' + +homepage = 'https://github.com/ULB-Metronu/georges' +description = """Georges the lemur opinionated particle accelerator modeling Python package. +Also a thin wrapper over MAD-X/PTC, BDSim and G4Beamline.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('LMfit', '1.0.3'), + ('matplotlib', '3.4.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('m2r', '0.2.1', { + 'checksums': ['bf90bad66cda1164b17e5ba4a037806d2443f2a4d5ddc9f6a5554a0322aaed99'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/ULB-Metronu/georges/archive/'], + 'checksums': ['5801c0655101e46401f4c052edc72e1dbf278fca76acf66a3ee3b10820527276'], + }), +] + +moduleclass = 'phys' From caafa9f56eb32b38ef457c53abfd6783dc4d3afd Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 15:22:50 +0100 Subject: [PATCH 2578/9987] Corrected zgoubi --- easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb index 3ca79813105..3e393662461 100644 --- a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb @@ -9,6 +9,10 @@ It can simulate beam dynamics in a large variety of machines and optical systems toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +builddependencies = [ + ('GCC', '10.3.0'), +] + source_urls = ['https://sourceforge.net/projects/zgoubi/files/zgoubi/'] sources = ['%(version)s/zgoubi-%(version)s.tar.bz2'] checksums = ['0b0f3d28496edbf7be868c24b0c927b7f1bc88cc29df9c235d9b28dc933489e0'] From d98971e7a933dd1fcb627cc5a88046f854350a2b Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 15:45:47 +0100 Subject: [PATCH 2579/9987] Corrected zgoubi ver2 --- easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb index 3e393662461..72f3866d7b2 100644 --- a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb @@ -10,7 +10,7 @@ It can simulate beam dynamics in a large variety of machines and optical systems toolchain = {'name': 'GCCcore', 'version': '10.3.0'} builddependencies = [ - ('GCC', '10.3.0'), + ('GCCcore', '10.3.0'), ] source_urls = ['https://sourceforge.net/projects/zgoubi/files/zgoubi/'] From 4b738d20103f8337ee8b473c75fa08259f2639a2 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 16:29:31 +0100 Subject: [PATCH 2580/9987] Corrected zgoubi ver3, corrected arrow, boost-histogram --- easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb | 3 +-- .../b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 7 +++---- .../easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb | 4 ++-- 3 files changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb index 425e7dbb2d6..44d1e6242b7 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb @@ -28,12 +28,11 @@ dependencies = [ ('Boost', '1.76.0'), ] -separate_build_dir = True start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 5a0bffca63f..72364a1f7c9 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -1,11 +1,10 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'boost_histogram' version = '1.2.1' -homepage = 'https://pypi.org/project/boost-histogram/' -description = """This is one of the fastest libraries for histogramming, -while still providing the power of a full histogram object""" +homepage = 'https://boost-histogram.readthedocs.io' +description = """Boost-histogram is a Python package providing Python bindings for Boost.Histogram.""" toolchain = {'name': 'foss', 'version': '2021a'} diff --git a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb index 72f3866d7b2..bfa771d6eef 100644 --- a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb @@ -10,7 +10,7 @@ It can simulate beam dynamics in a large variety of machines and optical systems toolchain = {'name': 'GCCcore', 'version': '10.3.0'} builddependencies = [ - ('GCCcore', '10.3.0'), + ('binutils', '2.36.1'), ] source_urls = ['https://sourceforge.net/projects/zgoubi/files/zgoubi/'] @@ -22,7 +22,7 @@ prebuildopts += "sed -i '/guide/d' Makefile &&" buildopts = ' FFLAGS="$FFLAGS -fno-automatic -pedantic -cpp" CFLAGS="$CXXFLAGS -DGFORTRAN4"' -files_to_copy = [(['zgoubi/zgoubi', 'zpop/zpop'], 'bin')] +files_to_copy = [(['zgoubi/zgoubi', 'zpop/zpop', 'exemples/exemples/'], 'bin')] sanity_check_paths = { 'files': ["bin/zgoubi", "bin/zpop"], From ddd179d92f4d231fcb67230a0a1f377eacce8f10 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 18:25:01 +0100 Subject: [PATCH 2581/9987] Updated boost-histogram --- .../b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 72364a1f7c9..dc1266f3590 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -17,6 +17,8 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = None + exts_list = [ (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', From 6a70ff2b0f1c57706c0c418671515f65f8b4ac68 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 19:26:28 +0100 Subject: [PATCH 2582/9987] Updated boost-histogram ver2 --- .../b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index dc1266f3590..9f5d02ee0c5 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -17,7 +17,7 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = None +download_dep_fail = True exts_list = [ (name, version, { From b0bdcc76625c8cb068c62bc5e793ee415e362888 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 22:40:50 +0100 Subject: [PATCH 2583/9987] Corrected Arrow and boost-histogram --- .../easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb | 2 +- .../boost_histogram-1.2.1-foss-2021a.eb | 15 +++++++++------ 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb index 44d1e6242b7..026891935f0 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb @@ -30,7 +30,7 @@ dependencies = [ start_dir = 'cpp' -# see https://arrow.apache.org/docs/python/development.html +# see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 9f5d02ee0c5..89eac2ddd7a 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -8,6 +8,9 @@ description = """Boost-histogram is a Python package providing Python bindings f toolchain = {'name': 'foss', 'version': '2021a'} +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['a27842b2f1cfecc509382da2b25b03056354696482b38ec3c0220af0fc9b7579'] + dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), @@ -19,11 +22,11 @@ sanity_pip_check = True download_dep_fail = True -exts_list = [ - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['a27842b2f1cfecc509382da2b25b03056354696482b38ec3c0220af0fc9b7579'], - }), -] +#exts_list = [ +# (name, version, { +# 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', +# 'checksums': ['a27842b2f1cfecc509382da2b25b03056354696482b38ec3c0220af0fc9b7579'], +# }), +#] moduleclass = 'math' From 565e6901c4faf820ab3aa80085aa2ad837e4d0bf Mon Sep 17 00:00:00 2001 From: eb-test Date: Sat, 8 Jan 2022 23:00:22 +0100 Subject: [PATCH 2584/9987] Corrected boost-histogram v2 --- .../boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 89eac2ddd7a..51d4dea9124 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -20,13 +20,4 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True - -#exts_list = [ -# (name, version, { -# 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', -# 'checksums': ['a27842b2f1cfecc509382da2b25b03056354696482b38ec3c0220af0fc9b7579'], -# }), -#] - moduleclass = 'math' From 0e5eb7365a748829be6a4baadd4a2eb37c230be0 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sun, 9 Jan 2022 09:07:45 +0100 Subject: [PATCH 2585/9987] Corrected boost-histogram v2 --- .../b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 51d4dea9124..2f723340824 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -18,6 +18,7 @@ dependencies = [ ] use_pip = True + sanity_pip_check = True moduleclass = 'math' From b12221a04510f8ba0e451bfa5e03c42a0c5c1cd8 Mon Sep 17 00:00:00 2001 From: eb-test Date: Sun, 9 Jan 2022 11:33:09 +0100 Subject: [PATCH 2586/9987] Corrected boost-histogram v3 and zgoubi --- .../b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb | 2 ++ easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb | 3 ++- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb index 2f723340824..8c6ffcd8688 100644 --- a/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/b/boost_histogram/boost_histogram-1.2.1-foss-2021a.eb @@ -21,4 +21,6 @@ use_pip = True sanity_pip_check = True +download_dep_fail = True + moduleclass = 'math' diff --git a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb index bfa771d6eef..f330d78d088 100644 --- a/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/z/Zgoubi/Zgoubi-6.0.2-GCCcore-10.3.0.eb @@ -22,7 +22,8 @@ prebuildopts += "sed -i '/guide/d' Makefile &&" buildopts = ' FFLAGS="$FFLAGS -fno-automatic -pedantic -cpp" CFLAGS="$CXXFLAGS -DGFORTRAN4"' -files_to_copy = [(['zgoubi/zgoubi', 'zpop/zpop', 'exemples/exemples/'], 'bin')] +files_to_copy = [(['zgoubi/zgoubi', 'zpop/zpop'], 'bin'), 'exemples'] +postinstallcmds = ["mv %(installdir)s/exemples %(installdir)s/examples"] sanity_check_paths = { 'files': ["bin/zgoubi", "bin/zpop"], From 17ab59cc9902d09ecc249cc6d17b22df6b9be987 Mon Sep 17 00:00:00 2001 From: Jonney Huang Date: Mon, 10 Jan 2022 04:17:10 +1300 Subject: [PATCH 2587/9987] Update easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb update dependencies Co-authored-by: Alex Domingo --- .../easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 4b5db8af46f..202a2598490 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -9,7 +9,12 @@ description = """ A distributed storage benchmark for files, objects & blocks wi toolchain = {'name': 'GCC', 'version': '10.3.0'} -dependencies = [('Boost', '1.76.0'), ('libaio', '0.3.112')] +dependencies = [ + ('Boost', '1.76.0'), + ('libaio', '0.3.112'), + ('numactl', '2.0.14'), + ('ncurses', '6.2'), +] sources = [{ 'filename': "v%(version)s.tar.gz", From b76ddebcb2a794dd86cdb04ce8684c2dbd775f9b Mon Sep 17 00:00:00 2001 From: easybuild Date: Sun, 9 Jan 2022 15:24:33 +0000 Subject: [PATCH 2588/9987] udpate base on feedback --- .../e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 202a2598490..905272ac462 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -16,22 +16,17 @@ dependencies = [ ('ncurses', '6.2'), ] -sources = [{ - 'filename': "v%(version)s.tar.gz", - 'git_config': { - 'url': 'https://github.com/breuner', - 'repo_name': 'elbencho', - 'tag': 'v%(version)s' - }, - -}] +github_account = 'breuner' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] checksums = ['f6c34f46b61451bcb1362e73d7754f307ae972c467b135e3279fd477586b5b7d'] files_to_copy = ["bin"] sanity_check_paths = { - 'dirs': files_to_copy, 'files': ['bin/%s' % x for x in ['elbencho', 'elbencho-unstripped']], + 'dirs': [], } +buildopts = 'BUILD_VERBOSE=1 CXXFLAGS_EXTRA="$CXXFLAGS" LDFLAGS_EXTRA="$LDFLAGS"' moduleclass = 'tools' From 575a2525b1528ea2483a01ba016f5062d02c3ff1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Jan 2022 09:37:56 +0100 Subject: [PATCH 2589/9987] rename patch files required for building Bazel 3.7.2 with GCCcore/11.2.0 + Java/15 --- .../b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 31 +++++++------------ .../b/Bazel/Bazel-3.7.2_fix-GCC-11.patch | 22 +++++++++++++ ...15.patch => Bazel-3.7.2_fix-Java-15.patch} | 0 .../b/Bazel/gcc11-2-bazel-3.7.2.patch | 10 ------ .../b/Bazel/gcc11-bazel-3.7.2.patch | 10 ------ 5 files changed, 33 insertions(+), 40 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-GCC-11.patch rename easybuild/easyconfigs/b/Bazel/{java15.patch => Bazel-3.7.2_fix-Java-15.patch} (100%) delete mode 100644 easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch delete mode 100644 easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index 7eb4e38d14c..a694933bb18 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -7,29 +7,20 @@ It is used to build the majority of Google's software.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = [ - 'https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] patches = [ - '%(name)s-3.4.1-fix-grpc-protoc.patch', - 'java15.patch', - '%(name)s-3.7.1_fix-protobuf-env.patch', - 'gcc11-bazel-3.7.2.patch', - 'gcc11-2-bazel-3.7.2.patch', - + 'Bazel-3.4.1-fix-grpc-protoc.patch', + 'Bazel-3.7.1_fix-protobuf-env.patch', + 'Bazel-3.7.2_fix-GCC-11.patch', + 'Bazel-3.7.2_fix-Java-15.patch', ] checksums = [ - # bazel-3.7.2-dist.zip - 'de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1', - # Bazel-3.4.1-fix-grpc-protoc.patch - 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', - '28f394f561824abf562556877483bc443dfd3ee0c7cba48a56e22670258669e7', # java15.patch - # Bazel-3.7.1_fix-protobuf-env.patch - '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', - # gcc11-bazel-3.7.2.patch - '32dc4abdc45bfcf70e9d93a66150b89646c801f8704930f0b713038366e40d40', - # gcc11-2-bazel-3.7.2.patch - '3160caff050330e33df1f7afb649e8303bf4af969ef7722639bd0f3c3ae036b4', + 'de255bb42163a915312df9f4b86e5b874b46d9e8d4b72604b5123c3a845ed9b1', # bazel-3.7.2-dist.zip + 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', # Bazel-3.4.1-fix-grpc-protoc.patch + '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', # Bazel-3.7.1_fix-protobuf-env.patch + '7fd5846f2ed1f27af9528a900f284f95ad982f3e7d486264c3bdee890a9c22fb', # Bazel-3.7.2_fix-GCC-11.patch + '28f394f561824abf562556877483bc443dfd3ee0c7cba48a56e22670258669e7', # Bazel-3.7.2_fix-Java-15.patch ] builddependencies = [ @@ -37,9 +28,9 @@ builddependencies = [ ('Python', '3.9.6'), ('Zip', '3.0'), ] +dependencies = [('Java', '15', '', True)] prebuildopts = "export BAZEL_LINKOPTS=-static-libstdc++:-static-libgcc BAZEL_LINKLIBS=-l%:libstdc++.a:-lm && " configopts = "--host_jvm_args=--illegal-access=debug" -dependencies = [('Java', '15', '', True)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-GCC-11.patch b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-GCC-11.patch new file mode 100644 index 00000000000..6f1575c39c2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-GCC-11.patch @@ -0,0 +1,22 @@ +add missing include statements to fix compilation with GCC 11.x +author: Alexandre Strube (JSC) +--- src/third_party/ijar/zlib_client.h.orig 2021-11-05 15:39:58.061336981 +0100 ++++ src/third_party/ijar/zlib_client.h 2021-11-05 15:40:22.650877105 +0100 +@@ -16,6 +16,7 @@ + #define THIRD_PARTY_IJAR_ZLIB_CLIENT_H_ + + #include ++#include + + #include "third_party/ijar/common.h" + +--- src/third_party/ijar/mapped_file.h.orig 2021-11-05 15:56:24.654184777 +0100 ++++ src/third_party/ijar/mapped_file.h 2021-11-05 15:56:33.879015290 +0100 +@@ -16,6 +16,7 @@ + #define INCLUDED_THIRD_PARTY_IJAR_MAPPED_FILE_H + + #include "third_party/ijar/common.h" ++#include + + namespace devtools_ijar { + diff --git a/easybuild/easyconfigs/b/Bazel/java15.patch b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-Java-15.patch similarity index 100% rename from easybuild/easyconfigs/b/Bazel/java15.patch rename to easybuild/easyconfigs/b/Bazel/Bazel-3.7.2_fix-Java-15.patch diff --git a/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch b/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch deleted file mode 100644 index c7ceaa84318..00000000000 --- a/easybuild/easyconfigs/b/Bazel/gcc11-2-bazel-3.7.2.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- src/third_party/ijar/mapped_file.h.orig 2021-11-05 15:56:24.654184777 +0100 -+++ src/third_party/ijar/mapped_file.h 2021-11-05 15:56:33.879015290 +0100 -@@ -16,6 +16,7 @@ - #define INCLUDED_THIRD_PARTY_IJAR_MAPPED_FILE_H - - #include "third_party/ijar/common.h" -+#include - - namespace devtools_ijar { - diff --git a/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch b/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch deleted file mode 100644 index b46eda73836..00000000000 --- a/easybuild/easyconfigs/b/Bazel/gcc11-bazel-3.7.2.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- src/third_party/ijar/zlib_client.h.orig 2021-11-05 15:39:58.061336981 +0100 -+++ src/third_party/ijar/zlib_client.h 2021-11-05 15:40:22.650877105 +0100 -@@ -16,6 +16,7 @@ - #define THIRD_PARTY_IJAR_ZLIB_CLIENT_H_ - - #include -+#include - - #include "third_party/ijar/common.h" - From 1cf035d82f59db47d1d90b4553d1430bd718b93f Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Mon, 10 Jan 2022 09:43:00 +0100 Subject: [PATCH 2590/9987] Remove spurious empty lines. --- easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb | 1 - easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb index 8346e384dec..98126fbf976 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb @@ -24,7 +24,6 @@ builddependencies = [ ('CMake', '3.20.1'), ] - # Compilation of tests seem to be broken, so disable it configopts = [ "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb index 02237e1a5b3..55420c821fa 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb @@ -24,7 +24,6 @@ builddependencies = [ ('CMake', '3.21.1'), ] - # Compilation of tests seem to be broken, so disable it configopts = [ "-DENABLE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", From b5c1ac74e475d572423985b01bc220a1ac02dba5 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Mon, 10 Jan 2022 10:24:32 +0100 Subject: [PATCH 2591/9987] Add ParMETIS for gompi/2021a, gompi/2021b, iimpi/2021a, and iimpi/2021b. --- .../p/ParMETIS/ParMETIS-4.0.3-gompi-2021a.eb | 29 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-gompi-2021b.eb | 29 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-iimpi-2021a.eb | 25 ++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-iimpi-2021b.eb | 25 ++++++++++++++++ 4 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021a.eb new file mode 100644 index 00000000000..50d82a6369e --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021a.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.20.1')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021b.eb new file mode 100644 index 00000000000..8451916f797 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2021b.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.21.1')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021a.eb new file mode 100644 index 00000000000..d044ec9b5d2 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021a.eb @@ -0,0 +1,25 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.20.1')] + +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021b.eb new file mode 100644 index 00000000000..b0299fdf5c7 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2021b.eb @@ -0,0 +1,25 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.21.1')] + +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' From f16b62e6c09be2bcb9d2487b7a7791ab05271598 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Mon, 10 Jan 2022 11:03:07 +0100 Subject: [PATCH 2592/9987] Move ELSI-RCI to GCC and intel-compilers toolchains, as it only require BLAS/LAPACK for running tests, which in any case are broken. --- ...I-RCI-0.1.0-foss-2021a.eb => ELSI-RCI-0.1.0-GCC-10.3.0.eb} | 4 ++-- ...I-RCI-0.1.0-foss-2021b.eb => ELSI-RCI-0.1.0-GCC-11.2.0.eb} | 4 ++-- ...el-2021a.eb => ELSI-RCI-0.1.0-intel-compilers-2021.2.0.eb} | 4 ++-- ...el-2021b.eb => ELSI-RCI-0.1.0-intel-compilers-2021.4.0.eb} | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/e/ELSI-RCI/{ELSI-RCI-0.1.0-foss-2021a.eb => ELSI-RCI-0.1.0-GCC-10.3.0.eb} (92%) rename easybuild/easyconfigs/e/ELSI-RCI/{ELSI-RCI-0.1.0-foss-2021b.eb => ELSI-RCI-0.1.0-GCC-11.2.0.eb} (92%) rename easybuild/easyconfigs/e/ELSI-RCI/{ELSI-RCI-0.1.0-intel-2021a.eb => ELSI-RCI-0.1.0-intel-compilers-2021.2.0.eb} (91%) rename easybuild/easyconfigs/e/ELSI-RCI/{ELSI-RCI-0.1.0-intel-2021b.eb => ELSI-RCI-0.1.0-intel-compilers-2021.4.0.eb} (91%) diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-10.3.0.eb similarity index 92% rename from easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb rename to easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-10.3.0.eb index 98126fbf976..7cfd4db094e 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-10.3.0.eb @@ -9,8 +9,8 @@ which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory. """ -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': False, 'pic': True} +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-11.2.0.eb similarity index 92% rename from easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb rename to easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-11.2.0.eb index 55420c821fa..69dcafbd651 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-GCC-11.2.0.eb @@ -9,8 +9,8 @@ which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory. """ -toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'usempi': False, 'pic': True} +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.2.0.eb similarity index 91% rename from easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb rename to easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.2.0.eb index 51095f7a406..7f403973ffd 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021a.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.2.0.eb @@ -9,8 +9,8 @@ which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory. """ -toolchain = {'name': 'intel', 'version': '2021a'} -toolchainopts = {'usempi': False, 'pic': True} +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} +toolchainopts = {'pic': True} source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.4.0.eb similarity index 91% rename from easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb rename to easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.4.0.eb index 1f59de009da..829899b7d3f 100644 --- a/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-2021b.eb +++ b/easybuild/easyconfigs/e/ELSI-RCI/ELSI-RCI-0.1.0-intel-compilers-2021.4.0.eb @@ -9,8 +9,8 @@ which iteratively solve or circumvent eigenvalue problems in self-consistent field calculations based on the Kohn-Sham density-functional theory. """ -toolchain = {'name': 'intel', 'version': '2021b'} -toolchainopts = {'usempi': False, 'pic': True} +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} +toolchainopts = {'pic': True} source_urls = ['https://gitlab.com/elsi_project/elsi_rci/-/archive/%(version)s'] sources = [SOURCELOWER_TAR_GZ] From eedbd16487054ca50c2b0bc9616cd3d8591b920c Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 10 Jan 2022 11:58:41 +0100 Subject: [PATCH 2593/9987] Moved Perl dependency to run-time rependencies --- easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb index 5a1898f43db..e9730661d4c 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.2.0.eb @@ -34,13 +34,13 @@ source_urls = ['https://github.com/lh3/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] -builddependencies = [ +builddependencies = [('binutils', '2.37')] + +dependencies = [ ('Perl', '5.34.0'), - ('binutils', '2.37'), + ('zlib', '1.2.11'), ] -dependencies = [('zlib', '1.2.11')] - # Allow use of x86 intrinsics on PPC prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " From b60f11fd4df32f296524af6cb775b3d06c8a5020 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 10 Jan 2022 12:11:17 +0100 Subject: [PATCH 2594/9987] Updated the version of BLAST --- ...ST+-2.11.0-gompi-2021b.eb => BLAST+-2.12.0-gompi-2021b.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/b/BLAST+/{BLAST+-2.11.0-gompi-2021b.eb => BLAST+-2.12.0-gompi-2021b.eb} (94%) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.12.0-gompi-2021b.eb similarity index 94% rename from easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb rename to easybuild/easyconfigs/b/BLAST+/BLAST+-2.12.0-gompi-2021b.eb index b6ec9feea95..eb841a154fe 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.11.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.12.0-gompi-2021b.eb @@ -13,7 +13,7 @@ easyblock = 'ConfigureMake' name = 'BLAST+' -version = '2.11.0' +version = '2.12.0' homepage = 'https://blast.ncbi.nlm.nih.gov/' description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm @@ -25,7 +25,7 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] sources = ['ncbi-blast-%(version)s+-src.tar.gz'] -checksums = ['d88e1858ae7ce553545a795a2120e657a799a6d334f2a07ef0330cc3e74e1954'] +checksums = ['fda3c9c9d488cad6c1880a98a236d842bcf3610e3e702af61f7a48cf0a714b88'] dependencies = [ ('zlib', '1.2.11'), From c45992b9428dbc1359590946a13268c2e5007c4b Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 10 Jan 2022 13:09:49 +0100 Subject: [PATCH 2595/9987] adding easyconfigs: MEGAHIT-1.2.9-GCCcore-11.2.0.eb --- .../m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b1fd926ac8b --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'MEGAHIT' +version = '1.2.9' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex +metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('bzip2', '1.0.8'), + ('gzip', '1.10'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(namelower)s', + 'bin/%(namelower)s_core', + 'bin/%(namelower)s_core_no_hw_accel', + 'bin/%(namelower)s_core_popcnt', + 'bin/%(namelower)s_toolkit', + ], + 'dirs': [], +} + +sanity_check_commands = [ + "megahit --version", + "megahit --test", +] + +moduleclass = 'bio' From f605291e1a0e8d9c0ee4ebf5bcf4165533c3d448 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 10 Jan 2022 13:48:27 +0100 Subject: [PATCH 2596/9987] adding easyconfigs: CheckM-1.1.3-foss-2021b.eb, HMMER-3.3.2-gompi-2021b.eb --- .../c/CheckM/CheckM-1.1.3-foss-2021b.eb | 65 +++++++++++++++ .../h/HMMER/HMMER-3.3.2-gompi-2021b.eb | 79 +++++++++++++++++++ 2 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021b.eb diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb new file mode 100644 index 00000000000..c1bc07048f5 --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb @@ -0,0 +1,65 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# Updated by: Filip Kružík (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'CheckM' +version = '1.1.3' + +homepage = 'https://github.com/Ecogenomics/CheckM' +description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, + single cells, or metagenomes.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [ + 'https://pypi.python.org/packages/source/c/checkm-genome', + 'https://data.ace.uq.edu.au/public/CheckM_databases/', +] +sources = [ + 'checkm-genome-%(version)s.tar.gz', + { + 'filename': 'checkm_data_2015_01_16.tar.gz', + 'extract_cmd': "mkdir -p %(builddir)s/data && cd %(builddir)s/data && tar xfvz %s", + }, +] +checksums = [ + '7fda369783d3b7d6a7324ee33cc93ac3560fba509bf2139e920fa661e2b45644', # checkm-genome-1.1.3.tar.gz + '971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c', # checkm_data_2015_01_16.tar.gz +] + +# Dependencies: +# https://github.com/Ecogenomics/CheckM/blob/master/setup.py +dependencies = [ + ('Python', '3.9.6'), + ('pplacer', '1.1.alpha19', '', True), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('SciPy-bundle', '2021.10'), # numpy + ('matplotlib', '3.4.3'), + ('Pysam', '0.17.0'), + ('DendroPy', '4.5.2'), +] + +download_dep_fail = True +use_pip = True + +# also install CheckM databases, see https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm +postinstallcmds = [ + "cp -a %(builddir)s/data %(installdir)s", + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "%(installdir)s/bin/checkm data setRoot %(installdir)s/data", +] + +sanity_check_paths = { + 'files': ['bin/checkm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["checkm test %(builddir)s/checkm_test_results"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021b.eb new file mode 100644 index 00000000000..5f8c0591214 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2021b.eb @@ -0,0 +1,79 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# Updated by: Filip Kružík (INUITS) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] + +builddependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), +] + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From 9f554aad069522cfc5ce4990dee327399a3084b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Jan 2022 15:44:38 +0100 Subject: [PATCH 2597/9987] enable tests for Bazel 3.7.2 with GCCcore/11.2.0 + remove configopts/prebuildopts that are not required --- easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index a694933bb18..53603c713d1 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -30,7 +30,7 @@ builddependencies = [ ] dependencies = [('Java', '15', '', True)] -prebuildopts = "export BAZEL_LINKOPTS=-static-libstdc++:-static-libgcc BAZEL_LINKLIBS=-l%:libstdc++.a:-lm && " -configopts = "--host_jvm_args=--illegal-access=debug" +runtest = True +testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." moduleclass = 'devel' From 4a63114ae0456d1de32ab47b9fb1d93878fb151b Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 10 Jan 2022 15:48:43 +0100 Subject: [PATCH 2598/9987] Update Bazel-3.7.2-GCCcore-11.2.0.eb --- easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index 53603c713d1..b4db72bd13c 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -28,6 +28,8 @@ builddependencies = [ ('Python', '3.9.6'), ('Zip', '3.0'), ] + +configopts = "--host_jvm_args=--illegal-access=debug" dependencies = [('Java', '15', '', True)] runtest = True From 251973c5428b44bf4d16fb9a840d2afcf6b5639b Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 10 Jan 2022 16:52:32 +0100 Subject: [PATCH 2599/9987] Update Bazel-3.7.2-GCCcore-11.2.0.eb --- easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index b4db72bd13c..d0148e063b5 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -29,7 +29,6 @@ builddependencies = [ ('Zip', '3.0'), ] -configopts = "--host_jvm_args=--illegal-access=debug" dependencies = [('Java', '15', '', True)] runtest = True From 05c41036b6d29e9fed96d802fec85da87399ef48 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Tue, 11 Jan 2022 14:15:05 +0200 Subject: [PATCH 2600/9987] adding easyconfigs: hivtrace-0.6.2-foss-2021a.eb --- .../h/hivtrace/hivtrace-0.6.2-foss-2021a.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb new file mode 100644 index 00000000000..9137968d933 --- /dev/null +++ b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb @@ -0,0 +1,72 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Iñaki Mtz de Ilarduya Muñoz +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonBundle' + +name = 'hivtrace' +version = '0.6.2' + +homepage = 'https://github.com/veg/hivtrace' +description = """HIV-TRACE is an application that identifies potential transmission clusters within a + supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Biopython', '1.79'), + ('tn93', '1.0.7'), + ('cURL', '7.76.0'), + ('Pysam', '0.16.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('hyphy-python', '0.1.10', { + 'modulename': 'HyPhy', + 'source_urls': ['https://pypi.python.org/packages/source/h/hyphy-python'], + 'checksums': ['b83f7e890c0c21b301c1c761967bd6328df9fad972653888b02baad71055c186'], + }), + ('fakemp', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/f/fakemp'], + 'checksums': ['320885d5851e0c568cd4247fa81e48f055e435822643e5bda9d82edc53c3b938'], + }), + ('hppy', '0.9.9', { + 'source_urls': ['https://pypi.python.org/packages/source/h/hppy'], + 'checksums': ['9112acc888c51c14a88669f084a7ebf39fa62bdd47924a1e3cee6824cfbc4610'], + }), + ('tornado', '6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('bioext', '0.19.9', { + 'modulename': 'BioExt', + 'source_urls': ['https://pypi.python.org/packages/source/b/bioext'], + 'checksums': ['bada8d7e83928a8c934e1e482bc945f43a3234c6c4ea3afcef7fa34c0ea610a3'], + }), + ('hivclustering', '1.6.2', { + 'source_urls': ['https://pypi.python.org/packages/source/h/hivclustering'], + 'checksums': ['673fa81b6b44ae7a7bfa32897bc01c26cfe807052aadc3d1f5a729b0df3a335f'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/h/hivtrace'], + 'checksums': ['f4aabd2bbc326aecb9ab22de8f6877628f908cfa8eee458feb06d48bb19425e6'], + }), +] + +# This two files come bundled compressed but the software expects them uncompressed +postinstallcmds = [ + 'gunzip -d %(installdir)s/lib/python%(pyshortver)s/site-packages/hivtrace/rsrc/LANL.FASTA.gz', + 'gunzip -d %(installdir)s/lib/python%(pyshortver)s/site-packages/hivtrace/rsrc/LANL.TN93OUTPUT.csv.gz', +] + +sanity_check_paths = { + 'files': ['bin/hivtrace'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From d59e18567dd79d3ba35c77bd37ab9ac08425c04f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 11 Jan 2022 14:40:01 +0000 Subject: [PATCH 2601/9987] Remove inline, RcppGSL as these are already provided by the R bundle --- .../inline-0.3.19-foss-2021a-R-4.1.0.eb | 30 ------------------ .../mapDamage-2.2.1-foss-2021a-R-4.1.0.eb | 2 -- .../RcppGSL-0.3.10-foss-2021a-R-4.1.0.eb | 31 ------------------- 3 files changed, 63 deletions(-) delete mode 100644 easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2021a-R-4.1.0.eb delete mode 100644 easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.10-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2021a-R-4.1.0.eb deleted file mode 100644 index f2d5c881fa6..00000000000 --- a/easybuild/easyconfigs/i/inline/inline-0.3.19-foss-2021a-R-4.1.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'RPackage' - -name = 'inline' -version = '0.3.19' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://cran.r-project.org/web/packages/inline' -description = """Functionality to dynamically define R functions and S4 methods - with 'inlined' C, C++ or Fortran code supporting the .C and .Call calling - conventions.""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'] - -dependencies = [ - ('R', '4.1.0'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['inline'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb index 65ad4dcca7a..3695397c43a 100644 --- a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb @@ -22,8 +22,6 @@ dependencies = [ ('seqtk', '1.3'), ('Pysam', '0.16.0.1'), ('R', '4.1.0'), - ('inline', '0.3.19', versionsuffix), - ('RcppGSL', '0.3.10', versionsuffix), ] use_pip = True diff --git a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.10-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.10-foss-2021a-R-4.1.0.eb deleted file mode 100644 index 931c28625ab..00000000000 --- a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.10-foss-2021a-R-4.1.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'RPackage' - -name = 'RcppGSL' -version = '0.3.10' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://cran.r-project.org/web/packages/RcppGSL' -description = """The 'RcppGSL' package provides an easy-to-use interface - between 'GSL' data structures and R using concepts from 'Rcpp' which is itself - a package that eases the interfaces between R and C++.""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['8612087da02fb791f427fed310c23d0482a8eb60fb089119f018878143f95451'] - -dependencies = [ - ('R', '4.1.0'), - ('GSL', '2.7'), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['RcppGSL'], -} - -moduleclass = 'lib' From 125844bb386fa8b43c11458ac0ada5c0d432752a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 11 Jan 2022 15:20:11 +0000 Subject: [PATCH 2602/9987] Add patch to use external seqtk --- .../mapDamage-2.2.1-foss-2021a-R-4.1.0.eb | 8 +- .../mapDamage-2.2.1_use-external-seqtk.patch | 74 +++++++++++++++++++ 2 files changed, 81 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1_use-external-seqtk.patch diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb index 3695397c43a..d0a2f1ddf71 100644 --- a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021a-R-4.1.0.eb @@ -15,7 +15,11 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c'] +patches = ['%(name)s-2.2.1_use-external-seqtk.patch'] +checksums = [ + 'f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c', # 2.2.1.tar.gz + 'f01a90c29123460f8cb6ba2fe0f42e9ec66b0febff430d4ec4f0ab1197c552e7', # mapDamage-2.2.1_use-external-seqtk.patch +] dependencies = [ ('Python', '3.9.5'), @@ -28,4 +32,6 @@ use_pip = True sanity_pip_check = True download_dep_fail = True +sanity_check_commands = ["%(name)s --help", "%(name)s --version"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1_use-external-seqtk.patch b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1_use-external-seqtk.patch new file mode 100644 index 00000000000..4c7f848a41e --- /dev/null +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1_use-external-seqtk.patch @@ -0,0 +1,74 @@ +Author: Jasper Grimm (UoY) +Allow mapDamage to use a seqtk from $PATH, instead of looking in its install dir +-------------------------------------------------------------------------------- +diff -Nru mapDamage-2.2.1.orig/bin/mapDamage mapDamage-2.2.1/bin/mapDamage +--- mapDamage-2.2.1.orig/bin/mapDamage 2022-01-11 14:40:48.000000000 +0000 ++++ mapDamage-2.2.1/bin/mapDamage 2022-01-11 14:48:37.000000000 +0000 +@@ -6,6 +6,7 @@ + import time + import sys + import os ++from shutil import which + + """ Copyright (c) 2012 Aurélien Ginolhac, Mikkel Schubert, Hákon Jónsson + and Ludovic Orlando +@@ -149,7 +150,7 @@ + sys.path.insert(0,path_to_mm) + import mapdamage + +- fpath_seqtk = mapdamage.rscript.construct_path("seqtk", folder="seqtk") ++ fpath_seqtk = which("seqtk") #mapdamage.rscript.construct_path("seqtk", folder="seqtk") + if not (os.path.isfile(fpath_seqtk) and os.access(fpath_seqtk, os.X_OK)): + sys.stderr.write("Seqtk executable not accessible; mapDamage has not\n" + "been intalled properly or current user does not\n" +diff -Nru mapDamage-2.2.1.orig/mapdamage/composition.py mapDamage-2.2.1/mapdamage/composition.py +--- mapDamage-2.2.1.orig/mapdamage/composition.py 2022-01-11 14:40:49.000000000 +0000 ++++ mapDamage-2.2.1/mapdamage/composition.py 2022-01-11 14:49:24.000000000 +0000 +@@ -3,6 +3,7 @@ + import csv + import subprocess + import sys ++from shutil import which + + def count_ref_comp(read, chrom, before, after, comp): + """ record basae composition in external genomic regions """ +@@ -33,7 +34,7 @@ + Gets the basecomposition of all the sequences in filename + and returns the value to destination if given. + """ +- path_to_seqtk = mapdamage.rscript.construct_path("seqtk",folder="seqtk") ++ path_to_seqtk = which("seqtk") # mapdamage.rscript.construct_path("seqtk",folder="seqtk") + bases = {"A":0,"C":0,"G":0,"T":0} + alp = ["A","C","G","T"] + try: +diff -Nru mapDamage-2.2.1.orig/setup.py mapDamage-2.2.1/setup.py +--- mapDamage-2.2.1.orig/setup.py 2022-01-11 14:40:48.000000000 +0000 ++++ mapDamage-2.2.1/setup.py 2022-01-11 14:45:14.000000000 +0000 +@@ -45,13 +45,13 @@ + def run(self): + self.record="" + setup_version() +- compile_seqtk() ++ # compile_seqtk() + DistutilsInstall.run(self) + # fixing the permission problem of seqtk +- files = self.get_outputs() +- for fi in files: +- if fi.endswith("seqtk/seqtk"): +- os.chmod(fi,0o755) ++ # files = self.get_outputs() ++ # for fi in files: ++ # if fi.endswith("seqtk/seqtk"): ++ # os.chmod(fi,0o755) + + + +@@ -64,7 +64,7 @@ + author='Aurélien Ginolhac, Mikkel Schubert, Ãkon Jónsson', + author_email='MSchubert@snm.ku.dk, jonsson.hakon@gmail.com', + packages=['mapdamage'], +- package_data={'mapdamage': ['Rscripts/*.R','Rscripts/stats/*.R','tests/*','seqtk/seqtk']}, ++ package_data={'mapdamage': ['Rscripts/*.R','Rscripts/stats/*.R','tests/*']}, + scripts=['bin/mapDamage'], + url='https://github.com/ginolhac/mapDamage', + license='LICENSE.txt', From d6d87ead2c0dafc2b22e18a789fefde8e23ecf3d Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 11 Jan 2022 16:21:16 +0100 Subject: [PATCH 2603/9987] Removed reference to DUNE_PY_DIR environment variable --- .../easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb | 2 -- easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb index 3c4f56daebe..966f23ed47c 100644 --- a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -7,8 +7,6 @@ homepage = "https://www.dune-project.org/groups/core/" description = """The Dune core modules build the stable basis of Dune. They follow a consistent release cycle and have high requirements regarding stability and backwards compatibility. These modules build the foundation for higher-level components. - -User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. """ toolchain = {'name': 'foss', 'version': '2020b'} diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index 6d875c7c146..e838e7272a0 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -9,8 +9,6 @@ the building blocks required to implement efficient solvers for a wide range of (systems of non linear) partial differential equations. DUNE-FEM can also be used through an extensive Python interface which brings all components of DUNE-FEM and the DUNE core modules to Python. - -User should set the environment variable DUNE_PY_DIR according to the DUNE documentation. """ toolchain = {'name': 'foss', 'version': '2020b'} From c0c610220f1c2bc8145a3c6f5b10ff648a95862a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Jan 2022 18:05:36 +0100 Subject: [PATCH 2604/9987] specify compiler to use for building WildMagic --- .../easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb index a2b8f7af57a..0032bcf724f 100644 --- a/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('freeglut', '3.2.1'), ] -buildopts = "CFG=ReleaseDynamic -f makefile.wm5" +buildopts = 'CFG=ReleaseDynamic -f makefile.wm5 CC="$CXX"' files_to_copy = [ (['SDK/Library/ReleaseDynamic/*'], 'lib'), From 8848db55f97855a1f64b2393b017ab80ce8768bb Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 18:37:06 +0100 Subject: [PATCH 2605/9987] adding easyconfigs: SPAdes-3.15.3-GCC-11.2.0.eb --- .../s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..047f59e56a7 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute +# Updated by: +# Filip Kružík (INUITS) + +easyblock = 'CMakeMake' + +name = 'SPAdes' +version = '3.15.3' + +homepage = 'https://cab.spbu.ru/software/spades/' +description = "Genome assembler for single-cell and isolates data sets" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['b2e5a9fd7a65aee5ab886222d6af4f7b7bc7f755da7a03941571fabd6b9e1499'] + +builddependencies = [ + ('CMake', '3.22.1'), +] +dependencies = [ + ('Python', '3.9.6'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('libreadline', '8.1'), +] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', + 'spades-ionhammer', 'spades-kmercount', 'spades.py']], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s.py', '--test')] + +moduleclass = 'bio' From 2511223f0f6fea58c6423f140b023d252dc26c0e Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 18:39:09 +0100 Subject: [PATCH 2606/9987] adding easyconfigs: RDP-Classifier-2.13-Java-17.0.1.eb --- .../RDP-Classifier-2.13-Java-17.0.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb diff --git a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb new file mode 100644 index 00000000000..223cfba95ba --- /dev/null +++ b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'RDP-Classifier' +version = '2.13' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://sourceforge.net/projects/rdp-classifier' +description = """The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic + assignments from domain to genus, with confidence estimates for each assignment.""" + +toolchain = SYSTEM + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['rdp_classifier_%(version)s.zip'] +checksums = ['d2eb9a989d7e31ff824de6876bc1d8ab70d97112ece167afe8d87a3cd412086a'] + +dependencies = [('Java', '17.0.1')] + +modextrapaths = { + 'CLASSPATH': 'dist/classifier.jar', + 'RDP_JAR_PATH': 'dist/classifier.jar', +} + +sanity_check_paths = { + 'files': ['dist/classifier.jar'], + 'dirs': [], +} + +moduleclass = 'bio' From f25b13916c9fba26b78c67bc6154869b2aadedfd Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 18:40:22 +0100 Subject: [PATCH 2607/9987] adding easyconfigs: PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb --- .../PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb new file mode 100644 index 00000000000..814735de515 --- /dev/null +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb @@ -0,0 +1,97 @@ +# author: Denis Kristak + +easyblock = 'Tarball' + +name = 'PRINSEQ' +version = '0.20.4' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://prinseq.sourceforge.net' +description = """A bioinformatics tool to PRe-process and show INformation of SEQuence data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['http://sourceforge.net/projects/prinseq/files/standalone/'] +sources = ['%(namelower)s-lite-%(version)s.tar.gz'] +checksums = ['9b5e0dce3b7f02f09e1cc7e8a2dd77c0b133e5e35529d570ee901f53ebfeb56f'] + +dependencies = [ + ('Perl', '5.34.0'), + ('cairo', '1.16.0'), +] + +# these are the perl libraries dependencies +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::Depends', '0.8001', { + 'source_tmpl': 'ExtUtils-Depends-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['673c4387e7896c1a216099c1fbb3faaa7763d7f5f95a1a56a60a2a2906c131c5'], + }), + ('ExtUtils::PkgConfig', '1.16', { + 'source_tmpl': 'ExtUtils-PkgConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e'], + }), + ('Pod::Usage', '2.0', { + 'source_tmpl': 'Pod-Usage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + 'checksums': ['530943a9ac3ba00404d7be8ee8572f30f6db9de123cd725af3647333a87d4fea'], + }), + ('Cairo', '1.109', { + 'source_tmpl': 'Cairo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['8219736e401c2311da5f515775de43fd87e6384b504da36a192f2b217643077f'], + }), + ('Statistics::PCA', '0.0.1', { + 'source_tmpl': 'Statistics-PCA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSTH/'], + 'checksums': ['f8adb10b00232123d103a5b49161ad46370f47fe0f752e5462a4dc15f9d46bc4'], + }), + ('MIME::Base64', '3.15', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + 'checksums': ['7f863566a6a9cb93eda93beadb77d9aa04b9304d769cea3bb921b9a91b3a1eb9'], + }), + ('Math::Cephes::Matrix', '0.5305', { + 'source_tmpl': 'Math-Cephes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['561a800a4822e748d2befc366baa4b21e879a40cc00c22293c7b8736caeb83a1'], + }), + ('Math::MatrixReal', '2.13', { + 'source_tmpl': 'Math-MatrixReal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LETO/'], + 'checksums': ['4f9fa1a46dd34d2225de461d9a4ed86932cdd821c121fa501a15a6d4302fb4b2'], + }), + ('Text::SimpleTable', '2.07', { + 'source_tmpl': 'Text-SimpleTable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRAMBERG/'], + 'checksums': ['256d3f38764e96333158b14ab18257b92f3155c60d658cafb80389f72f4619ed'], + }), + ('Contextual::Return', '0.2.1', { + 'source_tmpl': 'Contextual-Return-v%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCONWAY/'], + 'checksums': ['17a1ed1043a2abe123920894d6023709e834de66ef766be86e4cfbb96b1dd16c'], + }), +] + +fix_perl_shebang_for = ["*.pl"] + +postinstallcmds = ["chmod +x %(installdir)s/*.pl"] + +# this is the script which relies in many extra Perl libraries so we verify it's working fine +sanity_check_commands = ['%(installdir)s/prinseq-graphs.pl'] + +sanity_check_paths = { + 'files': ['prinseq-lite.pl', 'prinseq-graphs.pl', 'prinseq-graphs-noPCA.pl'], + 'dirs': [] +} + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +moduleclass = 'bio' From adbc0f4a945648b2cafd2ada40a77ec8be953a97 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 19:53:19 +0100 Subject: [PATCH 2608/9987] adding easyconfigs: MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb --- .../MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb new file mode 100644 index 00000000000..2c4859be86e --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'MetaBAT' +version = '2.15' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/berkeleylab/metabat' +description = "An efficient tool for accurately reconstructing single genomes from complex microbial communities" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('Boost', '1.77.0'), + ('zlib', '1.2.11'), + ('SAMtools', '1.14'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), +] + +fix_perl_shebang_for = ['bin/*.pl'] + +prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " + +sanity_check_paths = { + 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], + 'dirs': [""], +} + +moduleclass = 'bio' From 06ff5cb3408def06bcaab0a46027ed845f297f95 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 19:54:51 +0100 Subject: [PATCH 2609/9987] adding easyconfigs: CompareM-0.1.2-foss-2021b-Python-3.9.6.eb --- .../CompareM-0.1.2-foss-2021b-Python-3.9.6.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb new file mode 100644 index 00000000000..c4b519eba6c --- /dev/null +++ b/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'CompareM' +version = '0.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/dparks1134/CompareM' +description = "A toolbox for comparative genomics." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), + ('DIAMOND', '2.0.13'), + ('prodigal', '2.6.3'), +] + +use_pip = True + +exts_list = [ + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('biolib', '0.1.9', { + 'checksums': ['bc9ae68c6d76d46e4295fe0b1df5a48b575fe96374bd96d624c3330feb94856f'], + }), + ('comparem', version, { + 'checksums': ['bdfd3db957b151f6bdf711203d65bfda7209c5b46c5ce275da5bce2b4d490afa'], + }), +] + +sanity_check_paths = { + 'files': ['bin/comparem'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["comparem -h"] + +sanity_pip_check = True + +moduleclass = 'bio' From b87055761e309b34c0616f901576cb1782f8b1db Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 19:57:17 +0100 Subject: [PATCH 2610/9987] adding easyconfigs: AMOS-3.1.0-foss-2021b.eb, MUMmer-4.0.0beta2-GCCcore-11.2.0.eb --- .../a/AMOS/AMOS-3.1.0-foss-2021b.eb | 44 +++++++++++++++++++ .../MUMmer-4.0.0beta2-GCCcore-11.2.0.eb | 36 +++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2021b.eb new file mode 100644 index 00000000000..cba3aad0459 --- /dev/null +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2021b.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'AMOS' +version = '3.1.0' + +homepage = 'http://amos.sourceforge.net' +description = """The AMOS consortium is committed to the development of open-source whole genome assembly software""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'cstd': 'c++98'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['AMOS-%(version)s_GCC-4.7.patch'] +checksums = [ + '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b', # amos-3.1.0.tar.gz + '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844', # AMOS-3.1.0_GCC-4.7.patch +] + +dependencies = [ + ('expat', '2.4.1'), + ('MUMmer', '4.0.0beta2'), +] + +sanity_check_paths = { + 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], + 'dirs': [] +} + +parallel = 1 # make crashes otherwise + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5e7cd6bc7cc --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'MUMmer' +version = '4.0.0beta2' + +homepage = 'http://mummer.sourceforge.net/' + +description = """ + MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['cece76e418bf9c294f348972e5b23a0230beeba7fd7d042d5584ce075ccd1b93'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', + 'bin/repeat-match', 'bin/show-aligns', 'bin/show-coords', + 'bin/show-tiling', 'bin/show-snps', 'bin/show-diff', 'bin/exact-tandems', + 'bin/mummerplot', 'bin/promer', 'bin/dnadiff', + ], + 'dirs': ['include', 'lib', 'libexec'], +} + +moduleclass = 'bio' From ac646d9b2db3978054603b0e874391216f3b5f12 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 21:30:29 +0100 Subject: [PATCH 2611/9987] adding easyconfigs: MinPath-1.6-intel-2021b-Python-3.9.6.eb and patches: MinPath-1.6_fix-glpsol-path.patch --- .../MinPath-1.6-intel-2021b-Python-3.9.6.eb | 49 +++++++++++++++++++ .../MinPath/MinPath-1.6_fix-glpsol-path.patch | 18 +++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb create mode 100644 easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb new file mode 100644 index 00000000000..60338744ce1 --- /dev/null +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb @@ -0,0 +1,49 @@ +easyblock = 'Tarball' + +name = 'MinPath' +version = '1.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://omics.informatics.indiana.edu/MinPath' +description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions + using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological + pathways for a query dataset.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +sources = [{ + 'filename': 'minpath%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/mgtools/', + 'repo_name': 'MinPath', + 'commit': '46d3e81a4dca2310d558bea970bc002b15d44767', + }, +}] +checksums = ['8ae836a0223f49d81991a16f9b5ae0d9a2d2f129dd345355fc04047d655cf8db'] + +patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] + +dependencies = [ + ('Python', '3.9.6'), + ('GLPK', '5.0'), +] + +# remove included old GLPK copy +postinstallcmds = ["rm -rf %(installdir)s/glpk-*/*"] + +sanity_check_paths = { + 'files': ['MinPath.py'], + 'dirs': [], +} + +sanity_check_commands = [ + "python3 MinPath.py -ko examples/demo.ko -report /dev/null -details /dev/null", + "python3 MinPath.py -fig examples/demo.fig -report /dev/null -details /dev/null", + "python3 MinPath.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", +] + +modextrapaths = {'PATH': ''} + +modextravars = {'MinPath': '%(installdir)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch b/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch new file mode 100644 index 00000000000..ab00b150df8 --- /dev/null +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch @@ -0,0 +1,18 @@ +--- MinPath-1.6_fix-glpsol-path.py 2022-01-11 19:05:58.000000000 +0100 ++++ MinPath.py 2022-01-11 20:43:56.981520000 +0100 +@@ -20,13 +20,14 @@ + import math + + minpath = os.path.dirname(os.path.abspath(sys.argv[0])) ++glpkroot = os.getenv("EBROOTGLPK") + print("minpath directory: " + minpath) + if not os.path.exists(minpath + "/data"): + minpath = os.environ.get('MinPath') + if not (os.path.exists(minpath) and os.path.exists(minpath + "/data")): + sys.exit("Environment variable MinPath not set") + +-keggPath0, seedPath0, mapPath0, glpsol0 = minpath + "/data", minpath + "/data", minpath + "/data", minpath + "/glpk-4.6/examples/glpsol" ++keggPath0, seedPath0, mapPath0, glpsol0 = minpath + "/data", minpath + "/data", minpath + "/data", glpkroot + "/bin/glpsol" + + def intmatrix(dim1, dim2): + mat = [] From a2a1efa36eeccbfc9361dbe6602e026b1e263efc Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 21:34:10 +0100 Subject: [PATCH 2612/9987] Removed pyver from version suffix --- ...5-gompi-2021b-Python-3.9.6.eb => MetaBAT-2.15-gompi-2021b.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/m/MetaBAT/{MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb => MetaBAT-2.15-gompi-2021b.eb} (96%) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb similarity index 96% rename from easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb rename to easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index 2c4859be86e..3a2f07771f6 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b-Python-3.9.6.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -2,7 +2,6 @@ easyblock = 'CMakeMake' name = 'MetaBAT' version = '2.15' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://bitbucket.org/berkeleylab/metabat' description = "An efficient tool for accurately reconstructing single genomes from complex microbial communities" From 31524763e7c68ac05ceb0b4f2e1d273195fb6510 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 21:36:28 +0100 Subject: [PATCH 2613/9987] Removed pyver from version suffix --- ...2-foss-2021b-Python-3.9.6.eb => CompareM-0.1.2-foss-2021b.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/c/CompareM/{CompareM-0.1.2-foss-2021b-Python-3.9.6.eb => CompareM-0.1.2-foss-2021b.eb} (96%) diff --git a/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b.eb similarity index 96% rename from easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb rename to easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b.eb index c4b519eba6c..29fffcda612 100644 --- a/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b-Python-3.9.6.eb +++ b/easybuild/easyconfigs/c/CompareM/CompareM-0.1.2-foss-2021b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonBundle' name = 'CompareM' version = '0.1.2' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/dparks1134/CompareM' description = "A toolbox for comparative genomics." From 4c9e7f49daa006c7537837018196e62b87eca484 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 21:39:17 +0100 Subject: [PATCH 2614/9987] Removed pyver from version suffix --- ....6-intel-2021b-Python-3.9.6.eb => MinPath-1.6-intel-2021b.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/m/MinPath/{MinPath-1.6-intel-2021b-Python-3.9.6.eb => MinPath-1.6-intel-2021b.eb} (97%) diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb similarity index 97% rename from easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb rename to easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb index 60338744ce1..7e9da621bb6 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b-Python-3.9.6.eb +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb @@ -2,7 +2,6 @@ easyblock = 'Tarball' name = 'MinPath' version = '1.6' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://omics.informatics.indiana.edu/MinPath' description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions From c993ec87db2a7aec1f5d17182b6656d795da2776 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 11 Jan 2022 21:43:04 +0100 Subject: [PATCH 2615/9987] use Java version 17 --- ...ifier-2.13-Java-17.0.1.eb => RDP-Classifier-2.13-Java-17.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/r/RDP-Classifier/{RDP-Classifier-2.13-Java-17.0.1.eb => RDP-Classifier-2.13-Java-17.eb} (95%) diff --git a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.eb similarity index 95% rename from easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb rename to easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.eb index 223cfba95ba..2150bc84025 100644 --- a/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.0.1.eb +++ b/easybuild/easyconfigs/r/RDP-Classifier/RDP-Classifier-2.13-Java-17.eb @@ -14,7 +14,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['rdp_classifier_%(version)s.zip'] checksums = ['d2eb9a989d7e31ff824de6876bc1d8ab70d97112ece167afe8d87a3cd412086a'] -dependencies = [('Java', '17.0.1')] +dependencies = [('Java', '17')] modextrapaths = { 'CLASSPATH': 'dist/classifier.jar', From 38dd9a2d086df87b3a14d79c39cde834bcf62be2 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 22:11:45 +0100 Subject: [PATCH 2616/9987] Fixed checksums --- easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb index 7e9da621bb6..f3ab1349538 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb @@ -18,9 +18,11 @@ sources = [{ 'commit': '46d3e81a4dca2310d558bea970bc002b15d44767', }, }] -checksums = ['8ae836a0223f49d81991a16f9b5ae0d9a2d2f129dd345355fc04047d655cf8db'] - patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] +checksums = [ + '8ae836a0223f49d81991a16f9b5ae0d9a2d2f129dd345355fc04047d655cf8db', # minpath1.6.tar.gz + '4bf2c9ca9cb67ab4d5751b0af85df73c5cd7e368fc54737bab0907ce5a06a640', # MinPath-1.6_fix-glpsol-path.patch +] dependencies = [ ('Python', '3.9.6'), From 0964c080e8f4f0c816ef12809ad2784dd12d9d8a Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 11 Jan 2022 23:10:17 +0100 Subject: [PATCH 2617/9987] adding easyconfigs: FragGeneScan-1.31-GCCcore-11.2.0.eb, IDBA-UD-1.1.3-GCC-11.2.0.eb, MaxBin-2.2.7-gompi-2021b.eb --- .../FragGeneScan-1.31-GCCcore-11.2.0.eb | 38 ++++++++++++++ .../i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb | 49 +++++++++++++++++++ .../m/MaxBin/MaxBin-2.2.7-gompi-2021b.eb | 40 +++++++++++++++ 3 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021b.eb diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ad2ea72a080 --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.31' + +homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [("Perl", "5.34.0")] + +fix_perl_shebang_for = ['*.pl'] + +prebuildopts = "make clean && " +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' + +files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FragGeneScan', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +sanity_check_commands = [ + './run_FragGeneScan.pl help', + './run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..8d4d05d6460 --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-11.2.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Updated: Pavel Grochal (INUITS) +# License: GPLv2 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in prebuildopts + +# modified by Tom Strempel +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.3' + +homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads +Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. +IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth +contigs are removed iteratively with cutoff threshold from low to high to reduce the errors +in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled +locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD +can iterate k value of de Bruijn graph to a very large value with less gaps and less branches +to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] +sources = ['idba-%(version)s.tar.gz'] +checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] + +prebuildopts = './configure && ' + +# we delete every .o and Makefile file which is left in bin folder +buildopts = ' && rm -fr bin/*.o bin/Makefile*' + +files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] + +pretestopts = "cd test && " +runtest = "check" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021b.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021b.eb new file mode 100644 index 00000000000..db60c60fedb --- /dev/null +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021b.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'MaxBin' +version = '2.2.7' + +# https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html doesn't work +homepage = 'https://sourceforge.net/projects/maxbin/' +description = """MaxBin is software for binning assembled metagenomic sequences +based on an Expectation-Maximization algorithm.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Perl', '5.34.0'), + ('Bowtie2', '2.4.4'), + ('FragGeneScan', '1.31'), + ('HMMER', '3.3.2'), + ('IDBA-UD', '1.1.3'), +] + +prebuildopts = "cd src && " + +files_to_copy = ['*'] + +fix_perl_shebang_for = ['run_MaxBin.pl'] + +sanity_check_paths = { + 'files': ['run_MaxBin.pl', 'src/MaxBin'], + 'dirs': [], +} + +modextrapaths = {'PATH': ['', 'src']} + +moduleclass = 'bio' From 608d5d86b0de3b0f69851d17fca159632a5c0b2d Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 12 Jan 2022 09:21:42 +0100 Subject: [PATCH 2618/9987] Moved builddependencies before dependencies as requested by code review in pull request (both configs) --- .../d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb | 10 +++++----- .../d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb index 966f23ed47c..b6aae99f163 100644 --- a/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-core/dune-core-2.8.0.post1-foss-2020b.eb @@ -11,6 +11,11 @@ These modules build the foundation for higher-level components. toolchain = {'name': 'foss', 'version': '2020b'} +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -20,11 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -builddependencies = [ - ('scikit-build', '0.11.1'), - ('Ninja', '1.10.1'), -] - exts_list = [ ('portalocker', '2.3.2', { 'checksums': ['75cfe02f702737f1726d83e04eedfa0bda2cc5b974b1ceafb8d6b42377efbd5f'], diff --git a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb index e838e7272a0..52e3809d42a 100644 --- a/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dune-fem/dune-fem-2.8.0.6-foss-2020b.eb @@ -13,6 +13,11 @@ components of DUNE-FEM and the DUNE core modules to Python. toolchain = {'name': 'foss', 'version': '2020b'} +builddependencies = [ + ('scikit-build', '0.11.1'), + ('Ninja', '1.10.1'), +] + dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -25,11 +30,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -builddependencies = [ - ('scikit-build', '0.11.1'), - ('Ninja', '1.10.1'), -] - exts_list = [ ('fenics-ufl', '2019.1.0', { 'modulename': 'ufl', From 2b944623dd1cc55c37def39143b90d121899a2d8 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 12 Jan 2022 10:04:53 +0100 Subject: [PATCH 2619/9987] Add libvdwxc v0.4.0 for intel/2021b and foss/2021b. --- .../l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb | 27 ++++++++++++++++ .../l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb | 32 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb new file mode 100644 index 00000000000..c5a0fad835b --- /dev/null +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +homepage = 'https://libvdwxc.org' +description = """libvdwxc is a general library for evaluating energy and potential for +exchange-correlation (XC) functionals from the vdW-DF family that can be used with various +of density functional theory (DFT) codes.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] + +preconfigopts = 'unset CC && unset FC && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', + 'libvdwxc_q0test', 'libvdwxc_q0test2']] + + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] + for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb new file mode 100644 index 00000000000..c8c0d2a8644 --- /dev/null +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-intel-2021b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +homepage = 'https://libvdwxc.org' +description = """libvdwxc is a general library for evaluating energy and potential for +exchange-correlation (XC) functionals from the vdW-DF family that can be used with various +of density functional theory (DFT) codes.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] + +preconfigopts = 'unset CC && unset FC &&' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', + 'libvdwxc_q0test', 'libvdwxc_q0test2']] + + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] + for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +# MKL FFTW does not have all the features of fftw3 and libvdwxc is using them +dependencies = [ + ('FFTW', '3.3.10') +] + +moduleclass = 'chem' From 04f1219964f73be279a43a76a48c3884dc3eca2e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 12 Jan 2022 18:47:27 +0100 Subject: [PATCH 2620/9987] change versionsuffix to -linux-x64 --- .../{Blender-3.0.0-binary.eb => Blender-3.0.0-linux-x64.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/b/Blender/{Blender-3.0.0-binary.eb => Blender-3.0.0-linux-x64.eb} (96%) diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb b/easybuild/easyconfigs/b/Blender/Blender-3.0.0-linux-x64.eb similarity index 96% rename from easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb rename to easybuild/easyconfigs/b/Blender/Blender-3.0.0-linux-x64.eb index 8de30bc9841..0d0c2f24298 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-3.0.0-binary.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-3.0.0-linux-x64.eb @@ -5,7 +5,7 @@ easyblock = 'PackedBinary' name = 'Blender' version = '3.0.0' -versionsuffix = '-binary' +versionsuffix = '-linux-x64' homepage = 'https://www.blender.org' description = """ From 933867c66b5b2c34e5f6779beae4cb279a1216fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Jan 2022 21:06:36 +0100 Subject: [PATCH 2621/9987] adding easyconfigs: OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb and patches: OpenBabel-3.1.1_fix-testobconv_writers.patch --- ...penBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb | 60 +++++++++++++++++++ ...enBabel-3.1.1_fix-testobconv_writers.patch | 23 +++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-testobconv_writers.patch diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..9a6d9ca1f55 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb @@ -0,0 +1,60 @@ +name = 'OpenBabel' +version = '3.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] +patches = [ + # Fix test failure with Python 3 + # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch + 'OpenBabel-3.1.1_fix-distgeom-test.patch', + 'OpenBabel-3.1.1_fix-testobconv_writers.patch', +] +checksums = [ + 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz + '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch + '6d0b153caadc53141e1578972d632afb82b2fc4abdec6c5f07552b45a20e980c', # OpenBabel-3.1.1_fix-testobconv_writers.patch +] + +builddependencies = [ + ('CMake', '3.16.4'), + ('SWIG', '4.0.1'), +] +dependencies = [ + ('Python', '3.8.2'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), + ('Eigen', '3.3.7', '', True), + ('RapidJSON', '1.1.0'), + ('cairo', '1.16.0'), # optional: for .png output + ('Boost', '1.72.0'), # optional: for Maestro formats +] + +configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' +# Enable support for OpenMP compilation of forcefield code (optional) +configopts += '-DENABLE_OPENMP=ON ' + +# remove use of -Werror to avoid that warnings are treated as errors +# required to work around "integer conversion resulted in a change of sign" error with Intel compiler +prebuildopts = "sed -i 's/-Werror//g' external/coordgen-master/coordgen/CMakeFiles/coordgen.dir/flags.make && " + +# OpenBabel-3.1.1 creates directories named 3.1.0, which leads to BABEL_LIBDIR and BABEL_DATDIR +# (set in the easyblock) having invalid values. Work around this with some symlinks. +postinstallcmds = [ + 'ln -s %(installdir)s/lib/openbabel/3.1.0 %(installdir)s/lib/openbabel/%(version)s', + 'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s', +] + +pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT +runtest = 'test' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-testobconv_writers.patch b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-testobconv_writers.patch new file mode 100644 index 00000000000..967ae059019 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-testobconv_writers.patch @@ -0,0 +1,23 @@ +fix broken test by tweaking floating point value that is slightly off +see also https://github.com/openbabel/openbabel/issues/2246 +author: Kenneth Hoste (HPC-UGent) +--- openbabel-openbabel-3-1-1/test/testobconv_writers.py.orig 2022-01-12 20:12:01.480069896 +0100 ++++ openbabel-openbabel-3-1-1/test/testobconv_writers.py 2022-01-12 20:12:12.180174159 +0100 +@@ -2876,7 +2876,7 @@ + 2.4146659588503769, + 4.189331679349326, + 4.052466878708012, +- -1.4648575597102012 ++ -1.4648575597102014 + ], + "y": [ + 1.5846, +@@ -2891,7 +2891,7 @@ + 2.4146659588503769, + 4.189331679349326, + 4.052466878708012, +- -1.4648575597102012 ++ -1.4648575597102014 + ], + "style": { + "annotation": [ From 1d890ab869cb0213435a50d71a86c3edc95f269a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Jan 2022 10:50:41 +0100 Subject: [PATCH 2622/9987] adding easyconfigs: Python-2.7.18-GCCcore-11.2.0.eb --- .../p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 422 ++++++++++++++++++ 1 file changed, 422 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c569dc49d45 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -0,0 +1,422 @@ +name = 'Python' +version = '2.7.18' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +dependencies = [ + ('binutils', '2.37'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('SQLite', '3.36'), + ('GMP', '6.2.1'), # required for pycrypto + ('libffi', '3.4.2'), # required for cryptography + ('OpenSSL', '1.1', '', True), +] + +install_pip = True + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 8 January 2022, to the most recent versions still supporting Python 2.x +exts_list = [ + ('setuptools', '44.1.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], + }), + ('wheel', '0.37.1', { + 'checksums': ['e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4'], + }), + ('pip', '20.3.4', { + 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('blist', '1.3.6', { + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('paycheck', '1.0.2', { + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '5.8.0', { + 'checksums': ['672d8ebee84921862110f23fcec2acea191ef58543d34dfe9ef3d9f13c31cddf'], + }), + ('Cython', '0.29.26', { + 'checksums': ['af377d543a762867da11fcf6e558f7a4a535ff8693f30cce123fab10c00fa312'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('setuptools_scm', '4.1.2', { + 'checksums': ['a8994582e716ec690f33fec70cca0f85bd23ec974e3f783233e4879090a7faa8'], + }), + ('python-dateutil', '2.8.2', { + 'modulename': 'dateutil', + 'checksums': ['0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86'], + }), + ('decorator', '4.4.2', { + 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], + 'checksums': [ + 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz + # pycrypto-2.6.1_remove-usr-include.patch + '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e', + ], + }), + ('ecdsa', '0.17.0', { + 'checksums': ['b9f500bb439e4153d0330610f5d26baaf18d17b8ced1bc54410d189385ea68aa'], + }), + ('enum34', '1.1.10', { + 'modulename': 'enum', + 'checksums': ['cce6a7477ed816bd2542d03d53db9f0db935dd013b70f336a95c73979289f248'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.4.0', { + 'checksums': ['f4f6e119474e58e04a2b1af817eb585b4fd72bdd89b998624712b5c99be7641c'], + }), + ('idna', '2.10', { + 'checksums': ['b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6'], + }), + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + ('cffi', '1.15.0', { + 'checksums': ['920f0d66a896c2d99f0adbb391f990a84091179542c205fa53ce5787aff87954'], + }), + ('cryptography', '3.3.2', { + 'checksums': ['5a60d3780149e13b7a6ff7ad6526b38846354d11a15e21068e57073e29e19bed'], + }), + ('pyasn1', '0.4.8', { + 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], + }), + ('PyNaCl', '1.4.0', { + 'modulename': 'nacl', + 'checksums': ['54e9a2c849c742006516ad56a88f5c74bf2ce92c9f67435187c3c5953b346505'], + }), + ('bcrypt', '3.1.7', { + 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], + }), + ('paramiko', '2.9.1', { + 'checksums': ['a1fdded3b55f61d23389e4fe52d9ae428960ac958d2edf50373faa5d8926edd0'], + }), + ('pyparsing', '2.4.7', { + 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], + }), + ('netifaces', '0.11.0', { + 'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'], + }), + ('netaddr', '0.8.0', { + 'checksums': ['d6cc57c7a07b1d9d2e917aa8b36ae8ce61c35ba3fcd1b83ca31c5a0ee2b5a243'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '3.0.5', { + 'checksums': ['83657d894c90d5681d62155c82bda9c1187827525880eda8ff5df4ec813437c3'], + }), + ('pytz', '2021.3', { + 'checksums': ['acad2d8b20a1af07d4e4c9d2e9285c5ed9104354062f275f3fcd88dcef4f1326'], + }), + ('bitstring', '3.1.9', { + 'checksums': ['a5848a3f63111785224dca8bb4c0a75b62ecdef56a042c8d6be74b16f7e860e7'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.4', { + 'source_tmpl': 'distlib-%(version)s.zip', + 'checksums': ['e4b58818180336dc9c529bfb9a0b58728ffc09ad92027a3f30b7cd91e3458579'], + }), + ('filelock', '3.2.1', { + 'checksums': ['9cdd29c411ab196cf4c35a1da684f7b9da723696cb356efa45bf5eb1ff313ee3'], + }), + ('importlib_resources', '3.3.1', { + 'checksums': ['0ed250dbd291947d1a298e89f39afcc477d5a6624770503034b72588601bcc05'], + }), + ('platformdirs', '2.0.2', { + 'checksums': ['3b00d081227d9037bbbca521a5787796b5ef5000faea1e43fd76f1d44b06fcfa'], + }), + ('virtualenv', '20.13.0', { + 'checksums': ['d8458cf8d59d0ea495ad9b34c2599487f8a7772d796f9910858376d1600dd2dd'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.14.1', { + 'checksums': ['0630eea4f5664c463f23fbf5dcfc54a2bc6168902719fa8e19daf033022786c8'], + }), + ('chardet', '4.0.0', { + 'checksums': ['0d6f53a15db4120f2b08c94f11e7d93d2c911ee118b6b30a04ec3ee8310179fa'], + }), + ('certifi', '2021.10.8', { + 'checksums': ['78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872'], + }), + ('urllib3', '1.26.8', { + 'checksums': ['0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c'], + }), + ('requests', '2.27.1', { + 'checksums': ['68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61'], + }), + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('py_expression_eval', '0.3.14', { + 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('ujson', '2.0.3', { + 'checksums': ['bd2deffc983827510e5145fb66e4cc0f577480c62fe0b4882139f8f7d27ae9a3'], + }), + ('atomicwrites', '1.4.0', { + 'checksums': ['ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a'], + }), + ('py', '1.11.0', { + 'checksums': ['51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.6', { + 'checksums': ['7d8bcb5555003cdf4a8d2872c538faa3a0f5d20630cb360e518ca3b981795e5f'], + }), + ('zipp', '1.2.0', { + 'checksums': ['c70410551488251b0fee67b460fb9a536af8d6f9f008ad10ac51f615b6a521b1'], + }), + ('configparser', '4.0.2', { + 'checksums': ['c7d282687a5308319bf3d2e7706e575c635b0a470342641c93bea0ea3b5331df'], + }), + ('contextlib2', '0.6.0.post1', { + 'checksums': ['01f490098c18b19d2bd5bb5dc445b2054d2fa97f09a4280ba2c5f3c394c8162e'], + }), + ('importlib_metadata', '1.7.0', { + 'checksums': ['90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('more-itertools', '5.0.0', { + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + ('attrs', '21.4.0', { + 'modulename': 'attr', + 'checksums': ['626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd'], + }), + ('backports.functools-lru-cache', '1.6.4', { + 'source_tmpl': 'backports.functools_lru_cache-%(version)s.tar.gz', + 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], + }), + ('wcwidth', '0.2.5', { + 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], + }), + ('pytest', '4.6.11', { + 'checksums': ['50fa82392f2120cc3ec2ca0a75ee615be4c479e66669789771f1758332be4353'], + }), + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.3', { + 'checksums': ['a6d58433de0ae800347cab1fa3043cebbabe8baa9d29e668f1c768cb87a333c6'], + }), + ('packaging', '20.9', { + 'checksums': ['5b327ac1320dc863dca72f4514ecc086f31186744b84a230374cc1fd776feae5'], + }), + ('sphinxcontrib-websupport', '1.1.2', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['1501befb0fdf1d1c29a800fdbf4ef5dc5369377300ddbdd16d2cd40e54c6eefc'], + }), + ('Pygments', '2.5.2', { + 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], + }), + ('imagesize', '1.3.0', { + 'checksums': ['cd1750d452385ca327479d45b64d9c7729ecf0b3969a58148298c77092261f9d'], + }), + ('docutils', '0.17.1', { + 'checksums': ['686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125'], + }), + ('snowballstemmer', '2.2.0', { + 'checksums': ['09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1'], + }), + ('Babel', '2.9.1', { + 'checksums': ['bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0'], + }), + ('alabaster', '0.7.12', { + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.10.0.0', { + 'checksums': ['13b4ad211f54ddbf93e5901a9967b1e07720c1d1b78d596ac6a439641aa1b130'], + }), + ('Sphinx', '1.8.6', { + 'checksums': ['e096b1b369dbb0fcb95a31ba8c9e1ae98c588e601f08eada032248e1696de4b1'], + }), + ('sphinx-bootstrap-theme', '0.8.0', { + 'checksums': ['038ee7e89478e064b5dd7e614de6f3f4cec81d9f9efbebb06e105693d6a50924'], + }), + ('colorama', '0.4.4', { + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('psutil', '5.9.0', { + 'checksums': ['869842dbd66bb80c3217158e629d6fceaecc3a3166d3d1faee515b05dd26ca25'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('singledispatch', '3.7.0', { + 'checksums': ['c1a4d5c1da310c3fd8fccfb8d4e1cb7df076148fd5d858a819e37fffe44f3092'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('functools32', '3.2.3-2', { + 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), + ('futures', '3.3.0', { + 'modulename': False, + 'checksums': ['7e033af76a5e35f58e56da7a91e687706faf4e7bdfb2cbc3f2cca6b9bcda9794'], + }), + ('glob2', '0.6', { + 'checksums': ['f5b0a686ff21f820c4d3f0c4edd216704cea59d79d00fa337e244a2f2ff83ed6'], + }), + ('subprocess32', '3.5.4', { + 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('regex', '2021.3.17', { + 'checksums': ['4b8a1fb724904139149a43e172850f35aa6ea97fb0545244dc0b805e0154ed68'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('pylev', '1.4.0', { + 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], + }), + ('pastel', '0.2.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], + }), + ('clikit', '0.6.2', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], + }), + ('entrypoints', '0.3', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['589f874b313739ad35be6e0cd7efde2a4e9b6fea91edcc34e58ecbb8dbe56d19'], + }), + ('SecretStorage', '2.3.1', { + 'modulename': False, # Doesn't work properly under Python2, but is required for keyring + 'checksums': ['3af65c87765323e6f64c83575b05393f9e003431959c9395d1791d51497f29b6'], + }), + ('keyring', '18.0.1', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['67d6cc0132bd77922725fae9f18366bb314fd8f95ff4d323a4df41890a96a838'], + }), + ('keyrings.alt', '3.2.0', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['1c9981c351dabe902172ccf75bccff78185548f15ad51d5297e6366c0f4c3b51'], + }), + ('tomlkit', '0.7.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6babbd33b17d5c9691896b0e68159215a9387ebfa938aa3ac42f4a4beeb2b831'], + }), + ('shellingham', '1.4.0', { + 'checksums': ['4855c2458d6904829bd34c299f11fdeed7cfefbf8a2c522e4caea6cd76b3171e'], + }), + ('requests-toolbelt', '0.9.1', { + 'checksums': ['968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0'], + }), + ('pyrsistent', '0.16.1', { + 'checksums': ['aa2ae1c2e496f4d6777f869ea5de7166a8ccb9c2e06ebcf6c7ff1b670c98c5ef'], + }), + ('pkginfo', '1.8.2', { + 'checksums': ['542e0d0b6750e2e21c20179803e40ab50598d8066d51097a0e382cba9eb02bff'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('simplejson', '3.17.6', { + 'checksums': ['cf98038d2abf63a1ada5730e91e84c642ba6c225b0198c3684151b1f80c5f8a6'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('cleo', '0.8.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.2', { + 'checksums': ['fae04496f5bc150eefad4e9571d1a76c55d021325dcd484ce45065ebbdd00984'], + }), + ('CacheControl', '0.12.6', { + 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.0.7', { + 'modulename': 'poetry.core', + 'checksums': ['98c11c755a16ef6c5673c22ca94a3802a7df4746a0853a70b6fae8b9f5cac206'], + }), + ('poetry', '1.1.12', { + 'checksums': ['5c66e2357fe37b552462a88b7d31bfa2ed8e84172208becd666933c776252567'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), +] + +moduleclass = 'lang' From 0f00c16d759199289e0822e4e915c5d618c1a9a8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 13 Jan 2022 10:51:23 +0100 Subject: [PATCH 2623/9987] adding easyconfigs: OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb --- ...penBabel-3.1.1-gompi-2021a-Python-3.9.5.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..4cb86c42299 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb @@ -0,0 +1,57 @@ +name = 'OpenBabel' +version = '3.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +# avoid failing tests on skylake and broadwell CPUs. +# remove option 'optarch' when building on CPUs that don't support AVX2 +# see also: https://github.com/openbabel/openbabel/issues/2138 +toolchainopts = {'pic': True, 'optarch': 'mavx2'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] +patches = [ + # Fix test failure with Python 3 + # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch + 'OpenBabel-3.1.1_fix-distgeom-test.patch' +] +checksums = [ + 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz + '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('SWIG', '4.0.2'), +] +dependencies = [ + ('Python', '3.9.5'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), + ('Eigen', '3.3.9'), + ('RapidJSON', '1.1.0'), + ('cairo', '1.16.0'), # optional: for .png output + ('Boost', '1.76.0'), # optional: for Maestro formats +] + +configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' +# Enable support for OpenMP compilation of forcefield code (optional) +configopts += '-DENABLE_OPENMP=ON ' + +# OpenBabel-3.1.1 creates directories named 3.1.0, which leads to BABEL_LIBDIR and BABEL_DATDIR +# (set in the easyblock) having invalid values. Work around this with some symlinks. +postinstallcmds = [ + 'ln -s %(installdir)s/lib/openbabel/3.1.0 %(installdir)s/lib/openbabel/%(version)s', + 'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s', +] + +pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT +runtest = 'test' + +moduleclass = 'chem' From 3b564c4e256f0280059397617a2930f0c78be967 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 13 Jan 2022 10:49:19 +0000 Subject: [PATCH 2624/9987] Add sanity_check_all_components parameter --- .../f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb index a7982e2cd57..627ddf691a1 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb @@ -23,6 +23,7 @@ dependencies = [ ] default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True # Also build and install LAPACKE, which FlexiBLAS does not support yet components = [ @@ -36,15 +37,14 @@ components = [ 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], 'sources': ['v%(version)s.tar.gz'], 'checksums': ['328c1bea493a32cac5257d84157dc686cc3ab0b004e2bea22044e0a59f6f8a19'], - 'configopts': '-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON \ - -DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON \ - -DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas', + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, }), ] -sanity_check_paths = { - 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], - 'dirs': [], -} - moduleclass = 'lib' From 10bfb550ee6e28d822375273434fb70314cada7f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 13 Jan 2022 12:50:29 +0100 Subject: [PATCH 2625/9987] Adjust versions of extensions to match Python-3.9.6-GCCcore-11.2.0.eb when possible --- .../p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 114 ++++++++++-------- 1 file changed, 61 insertions(+), 53 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb index c569dc49d45..baae8b422fc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -12,6 +12,10 @@ source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] +builddependencies = [ + ('pkg-config', '0.29.2'), +] + dependencies = [ ('binutils', '2.37'), ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib @@ -34,14 +38,15 @@ exts_default_options = { } # order is important! -# package versions updated 8 January 2022, to the most recent versions still supporting Python 2.x +# package versions updated 13 January 2022, to the most recent versions still supporting Python 2.x +# while keeping it in sync with the Python 3 version for this toolchain/version exts_list = [ ('setuptools', '44.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], }), - ('wheel', '0.37.1', { - 'checksums': ['e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4'], + ('wheel', '0.36.2', { + 'checksums': ['e11eefd162658ea59a60a0f6c7d493a7190ea4b9a85e335b33489d9f17e0245e'], }), ('pip', '20.3.4', { 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], @@ -55,11 +60,11 @@ exts_list = [ ('paycheck', '1.0.2', { 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], }), - ('pbr', '5.8.0', { - 'checksums': ['672d8ebee84921862110f23fcec2acea191ef58543d34dfe9ef3d9f13c31cddf'], + ('pbr', '5.6.0', { + 'checksums': ['42df03e7797b796625b1029c0400279c7c34fd7df24a7d7818a1abb5b38710dd'], }), - ('Cython', '0.29.26', { - 'checksums': ['af377d543a762867da11fcf6e558f7a4a535ff8693f30cce123fab10c00fa312'], + ('Cython', '0.29.24', { + 'checksums': ['cdf04d07c3600860e8c2ebaad4e8f52ac3feb212453c1764a49ac08c827e8443'], }), ('six', '1.16.0', { 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], @@ -67,8 +72,8 @@ exts_list = [ ('toml', '0.10.2', { 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], }), - ('setuptools_scm', '4.1.2', { - 'checksums': ['a8994582e716ec690f33fec70cca0f85bd23ec974e3f783233e4879090a7faa8'], + ('setuptools_scm', '5.0.2', { + 'checksums': ['83a0cedd3449e3946307811a4c7b9d89c4b5fd464a2fb5eeccd0a5bb158ae5c8'], }), ('python-dateutil', '2.8.2', { 'modulename': 'dateutil', @@ -109,13 +114,14 @@ exts_list = [ ('idna', '2.10', { 'checksums': ['b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6'], }), - ('pycparser', '2.21', { - 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + ('pycparser', '2.20', { + 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], }), - ('cffi', '1.15.0', { - 'checksums': ['920f0d66a896c2d99f0adbb391f990a84091179542c205fa53ce5787aff87954'], + ('cffi', '1.14.6', { + 'checksums': ['c9a875ce9d7fe32887784274dd533c57909b7b1dcadcc128a2ac21331a9765dd'], }), ('cryptography', '3.3.2', { + 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['5a60d3780149e13b7a6ff7ad6526b38846354d11a15e21068e57073e29e19bed'], }), ('pyasn1', '0.4.8', { @@ -128,8 +134,8 @@ exts_list = [ ('bcrypt', '3.1.7', { 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], }), - ('paramiko', '2.9.1', { - 'checksums': ['a1fdded3b55f61d23389e4fe52d9ae428960ac958d2edf50373faa5d8926edd0'], + ('paramiko', '2.7.2', { + 'checksums': ['7f36f4ba2c0d81d219f4595e35f70d56cc94f9ac40a6acdf51d6ca210ce65035'], }), ('pyparsing', '2.4.7', { 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], @@ -146,8 +152,8 @@ exts_list = [ ('mock', '3.0.5', { 'checksums': ['83657d894c90d5681d62155c82bda9c1187827525880eda8ff5df4ec813437c3'], }), - ('pytz', '2021.3', { - 'checksums': ['acad2d8b20a1af07d4e4c9d2e9285c5ed9104354062f275f3fcd88dcef4f1326'], + ('pytz', '2021.1', { + 'checksums': ['83a4a90894bf38e243cf052c8b58f381bfe9a7a483f6a9cab140bc7f702ac4da'], }), ('bitstring', '3.1.9', { 'checksums': ['a5848a3f63111785224dca8bb4c0a75b62ecdef56a042c8d6be74b16f7e860e7'], @@ -155,12 +161,12 @@ exts_list = [ ('appdirs', '1.4.4', { 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], }), - ('distlib', '0.3.4', { + ('distlib', '0.3.2', { 'source_tmpl': 'distlib-%(version)s.zip', - 'checksums': ['e4b58818180336dc9c529bfb9a0b58728ffc09ad92027a3f30b7cd91e3458579'], + 'checksums': ['106fef6dc37dd8c0e2c0a60d3fca3e77460a48907f335fa28420463a6f799736'], }), - ('filelock', '3.2.1', { - 'checksums': ['9cdd29c411ab196cf4c35a1da684f7b9da723696cb356efa45bf5eb1ff313ee3'], + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], }), ('importlib_resources', '3.3.1', { 'checksums': ['0ed250dbd291947d1a298e89f39afcc477d5a6624770503034b72588601bcc05'], @@ -168,8 +174,11 @@ exts_list = [ ('platformdirs', '2.0.2', { 'checksums': ['3b00d081227d9037bbbca521a5787796b5ef5000faea1e43fd76f1d44b06fcfa'], }), - ('virtualenv', '20.13.0', { - 'checksums': ['d8458cf8d59d0ea495ad9b34c2599487f8a7772d796f9910858376d1600dd2dd'], + ('backports.entry_points_selectable', '1.1.1', { + 'checksums': ['914b21a479fde881635f7af5adc7f6e38d6b274be32269070c53b698c60d5386'], + }), + ('virtualenv', '20.7.0', { + 'checksums': ['97066a978431ec096d163e72771df5357c5c898ffdd587048f45e0aecc228094'], }), ('docopt', '0.6.2', { 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], @@ -180,20 +189,20 @@ exts_list = [ ('chardet', '4.0.0', { 'checksums': ['0d6f53a15db4120f2b08c94f11e7d93d2c911ee118b6b30a04ec3ee8310179fa'], }), - ('certifi', '2021.10.8', { - 'checksums': ['78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872'], + ('certifi', '2021.5.30', { + 'checksums': ['2bbf76fd432960138b3ef6dda3dde0544f27cbf8546c458e60baf371917ba9ee'], }), - ('urllib3', '1.26.8', { - 'checksums': ['0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c'], + ('urllib3', '1.26.6', { + 'checksums': ['f57b4c16c62fa2760b7e3d97c35b255512fb6b59a259730f36ba32ce9f8e342f'], }), - ('requests', '2.27.1', { - 'checksums': ['68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61'], + ('requests', '2.26.0', { + 'checksums': ['b8aa58f8cf793ffd8782d3d8cb19e66ef36f7aba4353eec859e74678b01b07a7'], }), ('xlrd', '2.0.1', { 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], }), - ('py_expression_eval', '0.3.14', { - 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], + ('py_expression_eval', '0.3.13', { + 'checksums': ['6e7d59d391d54a034609ce66b820e7dd68c757672d166dcc514bf7abf15ba57e'], }), ('tabulate', '0.8.9', { 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], @@ -204,8 +213,8 @@ exts_list = [ ('atomicwrites', '1.4.0', { 'checksums': ['ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a'], }), - ('py', '1.11.0', { - 'checksums': ['51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719'], + ('py', '1.10.0', { + 'checksums': ['21b81bda15b66ef5e1a777a21c4dcd9c20ad3efd0b3f817e7a809035269e1bd3'], }), ('scandir', '1.10.0', { 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], @@ -231,12 +240,11 @@ exts_list = [ ('more-itertools', '5.0.0', { 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], }), - ('attrs', '21.4.0', { + ('attrs', '21.2.0', { 'modulename': 'attr', - 'checksums': ['626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd'], + 'checksums': ['ef6aaac3ca6cd92904cdd0d83f629a15f18053ec84e6432106f7a4d04ae4f5fb'], }), - ('backports.functools-lru-cache', '1.6.4', { - 'source_tmpl': 'backports.functools_lru_cache-%(version)s.tar.gz', + ('backports.functools_lru_cache', '1.6.4', { 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], }), ('wcwidth', '0.2.5', { @@ -261,14 +269,14 @@ exts_list = [ ('Pygments', '2.5.2', { 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], }), - ('imagesize', '1.3.0', { - 'checksums': ['cd1750d452385ca327479d45b64d9c7729ecf0b3969a58148298c77092261f9d'], + ('imagesize', '1.2.0', { + 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], }), ('docutils', '0.17.1', { 'checksums': ['686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125'], }), - ('snowballstemmer', '2.2.0', { - 'checksums': ['09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1'], + ('snowballstemmer', '2.1.0', { + 'checksums': ['e997baa4f2e9139951b6f4c631bad912dfd3c792467e2f03d7239464af90e914'], }), ('Babel', '2.9.1', { 'checksums': ['bc0c176f9f6a994582230df350aa6e05ba2ebe4b3ac317eab29d9be5d2768da0'], @@ -291,8 +299,8 @@ exts_list = [ ('click', '7.1.2', { 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], }), - ('psutil', '5.9.0', { - 'checksums': ['869842dbd66bb80c3217158e629d6fceaecc3a3166d3d1faee515b05dd26ca25'], + ('psutil', '5.8.0', { + 'checksums': ['0c9ccb99ab76025f2f0bbecf341d4656e9c1351db8cc8a03ccd62e318ab4b5c6'], }), ('future', '0.18.2', { 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], @@ -355,9 +363,9 @@ exts_list = [ 'modulename': False, # Doesn't work properly if HOME directory contains keys 'checksums': ['1c9981c351dabe902172ccf75bccff78185548f15ad51d5297e6366c0f4c3b51'], }), - ('tomlkit', '0.7.0', { + ('tomlkit', '0.7.2', { 'source_tmpl': SOURCE_WHL, - 'checksums': ['6babbd33b17d5c9691896b0e68159215a9387ebfa938aa3ac42f4a4beeb2b831'], + 'checksums': ['173ad840fa5d2aac140528ca1933c29791b79a374a0861a80347f42ec9328117'], }), ('shellingham', '1.4.0', { 'checksums': ['4855c2458d6904829bd34c299f11fdeed7cfefbf8a2c522e4caea6cd76b3171e'], @@ -368,8 +376,8 @@ exts_list = [ ('pyrsistent', '0.16.1', { 'checksums': ['aa2ae1c2e496f4d6777f869ea5de7166a8ccb9c2e06ebcf6c7ff1b670c98c5ef'], }), - ('pkginfo', '1.8.2', { - 'checksums': ['542e0d0b6750e2e21c20179803e40ab50598d8066d51097a0e382cba9eb02bff'], + ('pkginfo', '1.7.1', { + 'checksums': ['e7432f81d08adec7297633191bbf0bd47faf13cd8724c3a13250e51d542635bd'], }), ('pexpect', '4.8.0', { 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], @@ -377,8 +385,8 @@ exts_list = [ ('jsonschema', '3.2.0', { 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], }), - ('simplejson', '3.17.6', { - 'checksums': ['cf98038d2abf63a1ada5730e91e84c642ba6c225b0198c3684151b1f80c5f8a6'], + ('simplejson', '3.17.3', { + 'checksums': ['da72a452bcf4349fc467a12b54ab0e63e654a571cacc44084826d52bde12b6ee'], }), ('webencodings', '0.5.1', { 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], @@ -406,12 +414,12 @@ exts_list = [ ('lockfile', '0.12.2', { 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), - ('poetry-core', '1.0.7', { + ('poetry-core', '1.0.3', { 'modulename': 'poetry.core', - 'checksums': ['98c11c755a16ef6c5673c22ca94a3802a7df4746a0853a70b6fae8b9f5cac206'], + 'checksums': ['2315c928249fc3207801a81868b64c66273077b26c8d8da465dccf8f488c90c5'], }), - ('poetry', '1.1.12', { - 'checksums': ['5c66e2357fe37b552462a88b7d31bfa2ed8e84172208becd666933c776252567'], + ('poetry', '1.1.7', { + 'checksums': ['3833c7b22411b8393e8e594fede94f0ef7a5260c19f51e272cce76512cffe6c8'], }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', From f55296948b29cc33edca84fc3f6a645fdabf2ebe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Jan 2022 13:23:57 +0100 Subject: [PATCH 2626/9987] remove preinstallopts for cryptography 3.3.2, only needed with 3.4.x or newer where Rust is used as a build dependency --- easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb index baae8b422fc..72ceefe329f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -121,7 +121,6 @@ exts_list = [ 'checksums': ['c9a875ce9d7fe32887784274dd533c57909b7b1dcadcc128a2ac21331a9765dd'], }), ('cryptography', '3.3.2', { - 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['5a60d3780149e13b7a6ff7ad6526b38846354d11a15e21068e57073e29e19bed'], }), ('pyasn1', '0.4.8', { From 82efb84217b818be2dff091f006dca645b9b7571 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 13 Jan 2022 13:33:00 +0100 Subject: [PATCH 2627/9987] The versionsuffix for python 3 was dropped in 2020b onwards --- ...penBabel-3.1.1-gompi-2021a-Python-3.9.5.eb | 57 ------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb deleted file mode 100644 index 4cb86c42299..00000000000 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,57 +0,0 @@ -name = 'OpenBabel' -version = '3.1.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://openbabel.org' -description = """Open Babel is a chemical toolbox designed to speak the many - languages of chemical data. It's an open, collaborative project allowing anyone - to search, convert, analyze, or store data from molecular modeling, chemistry, - solid-state materials, biochemistry, or related areas.""" - -toolchain = {'name': 'gompi', 'version': '2021a'} -# avoid failing tests on skylake and broadwell CPUs. -# remove option 'optarch' when building on CPUs that don't support AVX2 -# see also: https://github.com/openbabel/openbabel/issues/2138 -toolchainopts = {'pic': True, 'optarch': 'mavx2'} - -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] -patches = [ - # Fix test failure with Python 3 - # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch - 'OpenBabel-3.1.1_fix-distgeom-test.patch' -] -checksums = [ - 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz - '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch -] - -builddependencies = [ - ('CMake', '3.20.1'), - ('SWIG', '4.0.2'), -] -dependencies = [ - ('Python', '3.9.5'), - ('zlib', '1.2.11'), - ('libxml2', '2.9.10'), - ('Eigen', '3.3.9'), - ('RapidJSON', '1.1.0'), - ('cairo', '1.16.0'), # optional: for .png output - ('Boost', '1.76.0'), # optional: for Maestro formats -] - -configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' -# Enable support for OpenMP compilation of forcefield code (optional) -configopts += '-DENABLE_OPENMP=ON ' - -# OpenBabel-3.1.1 creates directories named 3.1.0, which leads to BABEL_LIBDIR and BABEL_DATDIR -# (set in the easyblock) having invalid values. Work around this with some symlinks. -postinstallcmds = [ - 'ln -s %(installdir)s/lib/openbabel/3.1.0 %(installdir)s/lib/openbabel/%(version)s', - 'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s', -] - -pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT -runtest = 'test' - -moduleclass = 'chem' From 7ccefee354a3b3cfa4dbb0d5de85d2f07a5b3cd9 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 13 Jan 2022 13:49:58 +0100 Subject: [PATCH 2628/9987] Better without versionsuffix field --- .../OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb new file mode 100644 index 00000000000..e76ffb84b87 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb @@ -0,0 +1,56 @@ +name = 'OpenBabel' +version = '3.1.1' + +homepage = 'https://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +# avoid failing tests on skylake and broadwell CPUs. +# remove option 'optarch' when building on CPUs that don't support AVX2 +# see also: https://github.com/openbabel/openbabel/issues/2138 +toolchainopts = {'pic': True, 'optarch': 'mavx2'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] +patches = [ + # Fix test failure with Python 3 + # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch + 'OpenBabel-3.1.1_fix-distgeom-test.patch' +] +checksums = [ + 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz + '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('SWIG', '4.0.2'), +] +dependencies = [ + ('Python', '3.9.5'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), + ('Eigen', '3.3.9'), + ('RapidJSON', '1.1.0'), + ('cairo', '1.16.0'), # optional: for .png output + ('Boost', '1.76.0'), # optional: for Maestro formats +] + +configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' +# Enable support for OpenMP compilation of forcefield code (optional) +configopts += '-DENABLE_OPENMP=ON ' + +# OpenBabel-3.1.1 creates directories named 3.1.0, which leads to BABEL_LIBDIR and BABEL_DATDIR +# (set in the easyblock) having invalid values. Work around this with some symlinks. +postinstallcmds = [ + 'ln -s %(installdir)s/lib/openbabel/3.1.0 %(installdir)s/lib/openbabel/%(version)s', + 'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s', +] + +pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT +runtest = 'test' + +moduleclass = 'chem' From a1b1e372366ef508b417d5ff0e835a4e74c69645 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 13 Jan 2022 15:14:30 +0100 Subject: [PATCH 2629/9987] Added requested changes --- .../m/MinPath/MinPath-1.6-intel-2021b.eb | 20 ++++++------------- .../MinPath/MinPath-1.6_fix-glpsol-path.patch | 2 ++ 2 files changed, 8 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb index f3ab1349538..154cc13b16c 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb @@ -2,6 +2,8 @@ easyblock = 'Tarball' name = 'MinPath' version = '1.6' +# no tagged commit for MinPath 1.6, commit was determined based on commit history +local_commit = '46d3e81a4dca2310d558bea970bc002b15d44767' homepage = 'https://omics.informatics.indiana.edu/MinPath' description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions @@ -10,18 +12,12 @@ description = """MinPath (Minimal set of Pathways) is a parsimony approach for b toolchain = {'name': 'intel', 'version': '2021b'} -sources = [{ - 'filename': 'minpath%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/mgtools/', - 'repo_name': 'MinPath', - 'commit': '46d3e81a4dca2310d558bea970bc002b15d44767', - }, -}] +source_urls = ['https://github.com/mgtools/MinPath/archive/'], +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] checksums = [ - '8ae836a0223f49d81991a16f9b5ae0d9a2d2f129dd345355fc04047d655cf8db', # minpath1.6.tar.gz - '4bf2c9ca9cb67ab4d5751b0af85df73c5cd7e368fc54737bab0907ce5a06a640', # MinPath-1.6_fix-glpsol-path.patch + '57e6b55cd00507578bad7528c60e3ad055311f62db928bd7c8de793513cec5a3', # MinPath-1.6.tar.gz + '117e45c6f35e3c944232dd5dd4789400d44c4b9b733b936adbb548b58e046c4b', # MinPath-1.6_fix-glpsol-path.patch ] dependencies = [ @@ -43,8 +39,4 @@ sanity_check_commands = [ "python3 MinPath.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", ] -modextrapaths = {'PATH': ''} - -modextravars = {'MinPath': '%(installdir)s'} - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch b/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch index ab00b150df8..270a34e091a 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6_fix-glpsol-path.patch @@ -1,3 +1,5 @@ +Make MinPath use different glpk library than it comes with. +Author: Filip Kružík (INUITS) --- MinPath-1.6_fix-glpsol-path.py 2022-01-11 19:05:58.000000000 +0100 +++ MinPath.py 2022-01-11 20:43:56.981520000 +0100 @@ -20,13 +20,14 @@ From 79c999745949f843ca196f1dcf3e57d30ae87500 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Thu, 13 Jan 2022 15:59:06 +0100 Subject: [PATCH 2630/9987] adding easyconfigs: MACSE-2.06-Java-15.eb --- .../easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb diff --git a/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb new file mode 100644 index 00000000000..131198b6bf9 --- /dev/null +++ b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb @@ -0,0 +1,27 @@ +easyblock = 'JAR' + +name = 'MACSE' +version = '2.06' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://bioweb.supagro.inra.fr/macse/index.php' +description = 'MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.' + +toolchain = SYSTEM + +local_jarname = '%(namelower)s_v%(version)s.jar' + +sources = [local_jarname] +source_urls = ['https://bioweb.supagro.inra.fr/macse/releases/'] + +dependencies = [('Java', '15')] + +modloadmsg = 'To execute %(name)s run: java -jar $EBROOT%(name)s/' + local_jarname + '\n' + +sanity_check_commands = ['java -jar $EBROOTMACSE/' + local_jarname + ' -v'] +sanity_check_paths = { + 'files': [local_jarname], + 'dirs': [] +} + +moduleclass = 'bio' From 2ab4b6472c8fcee742eb347073bf737004013131 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Thu, 13 Jan 2022 16:17:39 +0100 Subject: [PATCH 2631/9987] Split description in to multiple lines --- easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb index 131198b6bf9..f92b5d68ed4 100644 --- a/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb +++ b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb @@ -5,7 +5,9 @@ version = '2.06' versionsuffix = '-Java-%(javaver)s' homepage = 'https://bioweb.supagro.inra.fr/macse/index.php' -description = 'MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.' +description = '''MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to +contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding +gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure.''' toolchain = SYSTEM From cbb4fb8f509ea05c3c0185c25931832a780b97ee Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Thu, 13 Jan 2022 16:25:01 +0100 Subject: [PATCH 2632/9987] add checksum --- easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb index f92b5d68ed4..665ad19f703 100644 --- a/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb +++ b/easybuild/easyconfigs/m/MACSE/MACSE-2.06-Java-15.eb @@ -13,8 +13,9 @@ toolchain = SYSTEM local_jarname = '%(namelower)s_v%(version)s.jar' -sources = [local_jarname] source_urls = ['https://bioweb.supagro.inra.fr/macse/releases/'] +sources = [local_jarname] +checksums = ['e4f9f0dd443a7147d0f010e9ecd6940aa80f9ec68c687f8ba134209ac1e33398'] dependencies = [('Java', '15')] From 7473ebc0e3a0476c35fea90f382e55880c8303ab Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 13 Jan 2022 16:44:46 +0100 Subject: [PATCH 2633/9987] adding easyconfigs: DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb, pullseq-1.0.2-GCCcore-11.2.0.eb, Ruby-3.0.1-GCCcore-11.2.0.eb --- ...l-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb | 53 ++++++ .../p/pullseq/pullseq-1.0.2-GCCcore-11.2.0.eb | 37 ++++ .../r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb | 164 ++++++++++++++++++ 3 files changed, 254 insertions(+) create mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb create mode 100644 easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb new file mode 100644 index 00000000000..f77c59e946d --- /dev/null +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb @@ -0,0 +1,53 @@ +easyblock = 'Tarball' + +name = 'DAS_Tool' +version = '1.1.1' +versionsuffix = '-R-%(rver)s-Python-%(pyver)s' + +homepage = 'https://github.com/cmks/DAS_Tool' +description = """DAS Tool is an automated method that integrates the results of a flexible number of binning + algorithms to calculate an optimized, non-redundant set of bins from a single assembly.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a'] + +dependencies = [ + ('R', '4.1.2'), + ('Python', '3.9.6'), + ('Ruby', '3.0.1'), + ('pullseq', '1.0.2'), + ('prodigal', '2.6.3'), + ('BLAST+', '2.12.0'), +] + +exts_defaultclass = 'RPackage' + +exts_list = [ + (name, version, { + 'source_tmpl': 'DASTool_%(version)s.tar.gz', + 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], + 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], + 'modulename': 'DASTool', + }), +] + +postinstallcmds = [ + "cd %(installdir)s; unzip db.zip", + "chmod a+x %(installdir)s/DAS_Tool", +] + +sanity_check_paths = { + 'files': ['DAS_Tool', 'arc.all.faa', 'arc.scg.lookup'], + 'dirs': ['DASTool/R'], +} + +modextrapaths = { + 'PATH': '', + 'R_LIBS_SITE': '', +} + + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b0676dedca5 --- /dev/null +++ b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'pullseq' +version = '1.0.2' + +homepage = 'https://github.com/bcthomas/pullseq' +description = "Utility program for extracting sequences from a fasta/fastq file" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/bcthomas/pullseq/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a295d7e0e2d64ed05d293d795d1716376707e465f2c42ede6454f27db586c85f'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] +dependencies = [ + ('PCRE', '8.45'), +] + +preconfigopts = "./bootstrap && " + +buildopts = 'CFLAGS="$CFLAGS -fcommon"' + +sanity_check_paths = { + 'files': ['bin/pullseq', 'bin/seqdiff'], + 'dirs': [], +} + +sanity_check_commands = [ + "pullseq --help 2>&1 | grep 'pullseq - a bioinformatics tool'", + "seqdiff --help 2>&1 | grep 'seqdiff - a bioinformatics tool'", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6e37c235463 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb @@ -0,0 +1,164 @@ +name = 'Ruby' +version = '3.0.1' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['369825db2199f6aeef16b408df6a04ebaddb664fb9af0ec8c686b0ce7ab77727'] + +builddependencies = [('binutils', '2.37')] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# !! order of packages is important !! +# some packages have dependencies with minimum and maximum version requirements +# each version is picked as high as possible to fullfill all requirements +# packages updated on 2021-07-02 +exts_list = [ + ('ffi', '1.15.3', { + 'checksums': ['98d5c5c4281c9c0466acc60cf0e79124bf3c311417fd97e7473e41722953fbf1'], + }), + ('childprocess', '4.1.0', { + 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], + }), + ('json', '2.5.1', { + 'checksums': ['918d8c41dacb7cfdbe0c7bbd6014a5372f0cf1c454ca150e9f4010fe80cc3153'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.21.0', { + 'checksums': ['f9394457cb1dd5ca1b7bdc0dfbbd8f56f5cde40f45f96bc90f0f895a87e41b77'], + }), + ('arr-pm', '0.0.11', { + 'checksums': ['f1ab088421276f446da1971c5071defd1504855ec46e196815fa43cd62d61a9f'], + }), + ('clamp', '1.3.2', { + 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], + }), + ('multipart-post', '2.1.1', { + 'checksums': ['d2dd7aa957650e0d99e0513cd388401b069f09528441b87d884609c8e94ffcfd'], + }), + ('ruby2_keywords', '0.0.4', { + 'checksums': ['3ae3189c2e1d2f60204dcceedf890ff49dd28979771e2576016a3ee73b668e97'], + }), + ('faraday-net_http', '1.0.1', { + 'checksums': ['3245ce406ebb77b40e17a77bfa66191dda04be2fd4e13a78d8a4305854d328ba'], + }), + ('faraday', '1.3.0', { + 'checksums': ['7f06817ba823ddeabf4dd85ca5e0f63e234527f564a03f09f6c7127951d3bac2'], + }), + ('faraday_middleware', '1.0.0', { + 'checksums': ['19e808539681bbf2e65df30dfbe27bb402bde916a1dceb4c7496dbe8de14334a'], + }), + ('highline', '2.0.3', { + 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.2.5', { + 'checksums': ['13a8fc3921ce4df8e04fb65f1037251decb08d74757b41163688bd1c1feccd39'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.15.0', { + 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], + }), + ('public_suffix', '4.0.6', { + 'checksums': ['a99967c7b2d1d2eb00e1142e60de06a1a6471e82af574b330e9af375e87c0cf7'], + }), + ('addressable', '2.7.0', { + 'checksums': ['5e9b62fe1239091ea9b2893cd00ffe1bcbdd9371f4e1d35fac595c98c5856cbb'], + }), + ('concurrent-ruby', '1.1.9', { + 'checksums': ['0ec0846d991c38f355b4228ad8ea77aa69c3fdaa320cd574dafedc10c4688a5b'], + }), + ('i18n', '1.8.10', { + 'checksums': ['ca24e52fdd6ad7af419241eef8c41e65ef4e3499c6b252df13f697919eb24e3c'], + }), + ('minitest', '5.14.4', { + 'checksums': ['f4716634d71b3ffb627cd63ba4f6f0f77c7a3f17353b1bdf52c8a7f2e0e4e7a7'], + }), + ('thread_safe', '0.3.6', { + 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], + }), + ('tzinfo', '1.1.0', { + 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], + }), + ('zeitwerk', '2.4.2', { + 'checksums': ['f4d6279b0ef0cb35c9e1bddbcecd6b148df82f1cf7b8023ac03d6625f567869c'], + }), + ('activesupport', '5.0.7.2', { + 'checksums': ['f75cc67fb08421bdf4c2a383a47d9b3b02ce5eec4749704b1286fb0c12c98bad'], + }), + ('gh', '0.18.0', { + 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], + }), + ('launchy', '2.5.0', { + 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], + }), + ('ethon', '0.14.0', { + 'checksums': ['10e267a39d7e2a92d944e5681ba46dbd211b5b5b6cf9b51afb769b8417247ead'], + }), + ('typhoeus', '1.4.0', { + 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], + }), + ('websocket', '1.2.9', { + 'checksums': ['884b12dee993217795bb5f58acc89c0121c88bdc99df4d1636c0505dca352b36'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.4.4', { + 'checksums': ['bf3a658875f70c1467fe7a3b302b795f074c84b28db6e4a2bd6b1ad6d12a2255'], + }), + ('rspec-support', '3.10.2', { + 'checksums': ['74315f89069fbaf2a710e2117340373b77ee45eceb026de87e0cad9dd5154596'], + }), + ('rspec-mocks', '3.10.2', { + 'checksums': ['93fc76e312c3d19cacc1cb2eb64bf82731de2e216295cf2b4d0ce31ba77923b4'], + }), + ('rspec-expectations', '3.10.1', { + 'checksums': ['27acf5d5df13f8cc8f7158001ebf572513bcec3d45404ba76e0a8998895ce9eb'], + }), + ('rspec-core', '3.10.1', { + 'checksums': ['ac9abdc9577a3a34e9e92815603da8343931055ab4fba1c2a49de6dd3b749673'], + }), + ('rspec', '3.10.0', { + 'checksums': ['b870b43d49ae4a4e063b94976d2742b0854ec10458c425d569b5556ee5898ab7'], + }), + ('rack', '2.2.3', { + 'checksums': ['2638e7eb6689a5725c7e16f30cc4aa4e31694dc3ca30d790952526781bd0bb44'], + }), + ('rack-protection', '2.1.0', { + 'checksums': ['1f523c16e5b32f139c8f6f1e3b3eb53aaa7a69bc79a30f3e80f8a93c89242a95'], + }), + ('tilt', '2.0.10', { + 'checksums': ['9b664f0e9ae2b500cfa00f9c65c34abc6ff1799cf0034a8c0a0412d520fac866'], + }), + ('mustermann', '1.1.1', { + 'checksums': ['0a21cfe505869cce9ce17998db5260344e78df81ae857c07a62143fd30299531'], + }), + ('sinatra', '2.1.0', { + 'checksums': ['f323e4446f3e2a132dcaaa134f89caddb29dd88370317f4f32faf5797f1ea535'], + }), + ('rack-test', '1.1.0', { + 'checksums': ['154161f40f162b1c009a655b7b0c5de3a3102cc6d7d2e94b64e1f46ace800866'], + }), + ('bundler', '2.2.21', { + 'checksums': ['3c8dc5e0cf66d385a9b33751e54986290d42023c5e1bba2b5df094917b6e234a'], + }), +] + +moduleclass = 'lang' From ed89c21a009b308b6ab561a81521d2843dc7cacc Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 13 Jan 2022 17:27:56 +0100 Subject: [PATCH 2634/9987] Removed pyver suffix --- .../DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..81cc573725f --- /dev/null +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb @@ -0,0 +1,53 @@ +easyblock = 'Tarball' + +name = 'DAS_Tool' +version = '1.1.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/cmks/DAS_Tool' +description = """DAS Tool is an automated method that integrates the results of a flexible number of binning + algorithms to calculate an optimized, non-redundant set of bins from a single assembly.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a'] + +dependencies = [ + ('R', '4.1.2'), + ('Python', '3.9.6'), + ('Ruby', '3.0.1'), + ('pullseq', '1.0.2'), + ('prodigal', '2.6.3'), + ('BLAST+', '2.12.0'), +] + +exts_defaultclass = 'RPackage' + +exts_list = [ + (name, version, { + 'source_tmpl': 'DASTool_%(version)s.tar.gz', + 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], + 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], + 'modulename': 'DASTool', + }), +] + +postinstallcmds = [ + "cd %(installdir)s; unzip db.zip", + "chmod a+x %(installdir)s/DAS_Tool", +] + +sanity_check_paths = { + 'files': ['DAS_Tool', 'arc.all.faa', 'arc.scg.lookup'], + 'dirs': ['DASTool/R'], +} + +modextrapaths = { + 'PATH': '', + 'R_LIBS_SITE': '', +} + + +moduleclass = 'bio' From 1a9547795683daf8acb2ede74e3f4af4c40b3926 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Thu, 13 Jan 2022 17:28:17 +0100 Subject: [PATCH 2635/9987] Delete DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb --- ...l-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb | 53 ------------------- 1 file changed, 53 deletions(-) delete mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb deleted file mode 100644 index f77c59e946d..00000000000 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2-Python-3.9.6.eb +++ /dev/null @@ -1,53 +0,0 @@ -easyblock = 'Tarball' - -name = 'DAS_Tool' -version = '1.1.1' -versionsuffix = '-R-%(rver)s-Python-%(pyver)s' - -homepage = 'https://github.com/cmks/DAS_Tool' -description = """DAS Tool is an automated method that integrates the results of a flexible number of binning - algorithms to calculate an optimized, non-redundant set of bins from a single assembly.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a'] - -dependencies = [ - ('R', '4.1.2'), - ('Python', '3.9.6'), - ('Ruby', '3.0.1'), - ('pullseq', '1.0.2'), - ('prodigal', '2.6.3'), - ('BLAST+', '2.12.0'), -] - -exts_defaultclass = 'RPackage' - -exts_list = [ - (name, version, { - 'source_tmpl': 'DASTool_%(version)s.tar.gz', - 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], - 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], - 'modulename': 'DASTool', - }), -] - -postinstallcmds = [ - "cd %(installdir)s; unzip db.zip", - "chmod a+x %(installdir)s/DAS_Tool", -] - -sanity_check_paths = { - 'files': ['DAS_Tool', 'arc.all.faa', 'arc.scg.lookup'], - 'dirs': ['DASTool/R'], -} - -modextrapaths = { - 'PATH': '', - 'R_LIBS_SITE': '', -} - - -moduleclass = 'bio' From 6f85ffb5358d8bbd492db589e7991ddfbf3c5d86 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 13 Jan 2022 18:36:49 +0100 Subject: [PATCH 2636/9987] adding easyconfigs: Short-Pair-20170125-foss-2021b.eb and patches: Short-Pair-20170125-Python3fix.patch --- .../Short-Pair-20170125-Python3fix.patch | 204 ++++++++++++++++++ .../Short-Pair-20170125-foss-2021b.eb | 47 ++++ 2 files changed, 251 insertions(+) create mode 100644 easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch create mode 100644 easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch new file mode 100644 index 00000000000..4c5da5540cd --- /dev/null +++ b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch @@ -0,0 +1,204 @@ +Makes Short-Pair compatible with Phyton3 +Author: Filip Kružík (INUITS) +--- Short-Pair_fix 2022-01-11 17:08:22.763000000 +0100 ++++ Short-Pair.py 2022-01-11 17:05:28.709307000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python3 + import os + import sys + import pickle +@@ -9,10 +9,12 @@ + from numpy import percentile + from numpy import std + from numpy import mean ++from os.path import abspath, dirname, realpath # Tocado JT + + +-sequence_length_global = 0 + ++sequence_length_global = 0 ++exec_path = abspath(dirname(realpath(__file__))) # Tocado JT + + def get_first_sequence_in_fasta_file(fasta_file): + fi = open(fasta_file, 'rt') +@@ -29,15 +31,16 @@ + + + def step1(fastaFile, pattern): +- command = "DNA2Protein 1-6 %s %s" % (fastaFile, pattern) ++ command = "%s/DNA2Protein 1-6 %s %s" % (exec_path, fastaFile, pattern) # exec_path, FPS + os.system(command) + + def step2(hmm, inputFile): +- inputFileDir = os.path.dirname(inputFile) ++ inputFileDir = abspath(os.path.dirname(inputFile)) ++ inputFile = inputFile.split('/')[-1] + outputDir = os.path.join(inputFileDir, '../out1') + +- outputFile = os.path.join(outputDir, inputFile+'.hmmer') +- command = 'hmmsearch -E 1000 --domtblout %s %s %s' % (outputFile, hmm, inputFile) ++ outputFile = os.path.join(outputDir, inputFile +'.hmmer') ++ command = '%s/../hmmer/hmmsearch -E 1000 --domtblout %s %s %s/%s > /dev/null' % (exec_path, outputFile, hmm, inputFileDir, inputFile) # exec_path, FPS + os.system(command) + return outputFile + +@@ -71,12 +74,12 @@ + + def combineHmmer(inputFolder, outputFolder, allOutput, nDomains, namePattern): + fa = open(allOutput, 'wt') +- for i in xrange(1, nDomains+1): ++ for i in range(1, nDomains+1): + # for i in xrange(201, nDomains+1): + mapLinesList = [] + mapScoresList = [] + readPairSet = set() +- for j in xrange(1, 7): ++ for j in range(1, 7): + inputFile = namePattern % (i, j) + fi = open(inputFolder+'/'+inputFile, 'rt') + mapReadPairToLines = {} +@@ -100,8 +103,8 @@ + outputFile = os.path.join(outputFolder, outputFile) + fo = open(outputFile, 'wt') + for pair in sorted(readPairSet): +- maxScore = -sys.maxint +- for j in xrange(1, 7): ++ maxScore = -sys.maxsize ++ for j in range(1, 7): + mapReadPairToLines = mapLinesList[j-1] + mapReadPairToScore = mapScoresList[j-1] + if pair not in mapReadPairToScore: +@@ -120,7 +123,7 @@ + mapLinesList = [] + mapScoresList = [] + readPairSet = set() +- for j in xrange(1, 7): ++ for j in range(1, 7): + inputFile = namePattern % (j) + fi = open(inputFolder+'/'+inputFile, 'rt') + mapReadPairToLines = {} +@@ -142,8 +145,8 @@ + ### start to combine + fo = open(outputFile, 'wt') + for pair in sorted(readPairSet): +- maxScore = -sys.maxint +- for j in xrange(1, 7): ++ maxScore = -sys.maxsize ++ for j in range(1, 7): + mapReadPairToLines = mapLinesList[j-1] + mapReadPairToScore = mapScoresList[j-1] + if pair not in mapReadPairToScore: +@@ -240,7 +243,7 @@ + f.close() + return hmmList + +-def step7(inputFile): ++def step7(inputFile): + hmmYList = []; hmmNList = [] + hmmList = readHmm(inputFile) + for hmm in hmmList: +@@ -494,7 +497,7 @@ + os.mkdir(outputFolder) + for hmm in sorted(hmmList, key=lambda x:x.name): + family = hmm.name +- command = "get_hmm.sh %s %s > %s/%s.hmm" % (family, hmmFile, outputFolder,family) ++ command = "%s/get_hmm.sh %s %s > %s/%s.hmm" % (exec_path, family, hmmFile, outputFolder,family) # exec_path, FPS + os.system(command) + + def runHmmer(inputFile1, inputFile2, inputFile3, hmmFolder, outputFileInput, fastaPath, faaPath, filterFile): +@@ -530,13 +533,12 @@ + for (read, family, key) in readSet: + readNames.add(read.replace('|','_')) + write = False +- + fi = open(inputFile2, 'rt') + nLine = 0 + for line in fi: + if line[0]=='>': + read = line[1:].strip(); +- read = read.replace("|","_") ++ read = read.replace("|","_") + if read[:-2]+".2" in readNames: + outputFile = r'%s/%s.fasta' % (fastaPath, read) + fo = open(outputFile, 'wt') +@@ -578,18 +580,20 @@ + tmpRead = tmpRead[:-2] + '.1' + fastaFile = r'%s/%s.fasta' % (fastaPath, tmpRead) + faaFile = r'%s/%s.faa' % (faaPath, tmpRead) +- command = "DNA2Protein 1-6 %s %s" % (fastaFile, faaFile) ++ command = "%s/DNA2Protein 1-6 %s %s" % (exec_path, fastaFile, faaFile) # exec_path, FPS + os.system(command) + outputFile = r'%s.allframe' % (faaFile) + fo = open(outputFile, 'wt') +- maxScore = -sys.maxint ++ maxScore = -sys.maxsize + maxString = '' +- for i in xrange(1,7): +- command = "hmmer3_pipeline_missing_end.sh" +- args = [command, "%s/%s.hmm" % (hmmFolder, family), "%s.frame%d" % (faaFile, i), "%d" % i]; +- outString = subprocess.Popen(args, stdout=subprocess.PIPE).communicate()[0] ++ for i in range(1,7): ++ command = "%s/hmmer3_pipeline_missing_end.sh" % exec_path # exec_path, FPS ++ args = [command, "%s/%s.hmm" % (hmmFolder, family), "%s.frame%d" % (faaFile, i), "%d" % i, "10"] ++ my_env = os.environ # Add SQM/bin/hmmer to the PATH env. variable for subprocess ++ my_env['PATH'] = '%s/../hmmer:' % exec_path + os.environ['PATH'] ++ outString = subprocess.Popen(args, env=my_env, stdout=subprocess.PIPE).communicate()[0].decode() + fo.write(outString) +- if outString != '': ++ if outString: + row = outString.split() + score = float(row[2]) + if score > maxScore: +@@ -707,7 +711,7 @@ + mapLengthToFrequency[length] = frequency + total += frequency + fi.close() +- for key in mapLengthToFrequency.keys(): ++ for key in list(mapLengthToFrequency.keys()): + mapLengthToFrequency[key] = mapLengthToFrequency[key] / float(total) + + mapReadToLine = {} +@@ -779,7 +783,7 @@ + fo.close() + + mapNumberToFrequency = {} +- for read in mapReadToFamilySet.keys(): ++ for read in list(mapReadToFamilySet.keys()): + number = len(mapReadToFamilySet[read]) + if number not in mapNumberToFrequency: + mapNumberToFrequency[number] = 0 +@@ -800,11 +804,11 @@ + step1(fastaFile2, pattern2) + step3InputList = [] + step3OutputList = [] +- for i in xrange(1,7): ++ for i in range(1,7): + inputFile = pattern1 + '.frame%d' % i + step2Output = step2(hmm, inputFile) + step3InputList.append(step2Output) +- for i in xrange(1,7): ++ for i in range(1,7): + inputFile = pattern2 + '.frame%d' % i + step2Output = step2(hmm, inputFile) + step3InputList.append(step2Output) +@@ -832,8 +836,8 @@ + step12(hmmFile, hmmList, hmmFolder) + step13OutputFile1 = step11Output+'_1'; step13OutputFile2 = step11Output+'_2' + workingDir = os.path.dirname(step11Output) +- fastaPath = '%s/fasta' % workingDir +- faaPath = '%s/faa' % workingDir ++ fastaPath = '%s/fastaSP' % workingDir ++ faaPath = '%s/faaSP' % workingDir + step13(step11Output, fastaFile1, fastaFile2, hmmFolder, step13OutputFile1, fastaPath, faaPath, step13OutputFile2) + step14Output = step13OutputFile1 + '.remove' + step14(step13OutputFile1, step14Output) +@@ -844,7 +848,7 @@ + def control(fastaFile1, fastaFile2, hmmFile, seedFile, threshold, outputFile): + baseFile = os.path.basename(fastaFile1) + fastaName = baseFile.replace('.1.fasta','') +- baseDir = os.path.dirname(fastaFile1) ++ baseDir = abspath(os.path.dirname(fastaFile1)) + patternDir = '%s/Protein' % baseDir + + if not os.path.isdir(patternDir): diff --git a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb new file mode 100644 index 00000000000..8fd96339019 --- /dev/null +++ b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'CmdCp' + +name = 'Short-Pair' +version = '20170125' + +homepage = 'https://sourceforge.net/projects/short-pair' +description = "Sensitive Short Read Homology Search for Paired-End Reads" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [{'download_filename': 'Short-Pair.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['c8c759cf4cc871180107dd86e397d34787acad33d024debd70710edb437769b3'] + +patches = ['Short-Pair-20170125-Python3fix.patch'] + +dependencies = [ + ('Python', '3.9.6'), + ('HMMER', '3.3.2'), + ('SciPy-bundle', '2021.10') +] + +exts_list = [ + ('numpy', '1.22.0', { + 'source_urls': ['https://files.pythonhosted.org/packages/50/e1/9b0c184f04b8cf5f3c941ffa56fbcbe936888bdac9aa7ba6bae405ac752b/'], + 'sources': ['%(name)s-%(version)s.zip'], + }) +] + +cmds_map = [('.*', "$CXX $CXXFLAGS -w -o DNA2Protein DNA2Protein.cpp")] + +files_to_copy = [(['DNA2Protein', 'get_hmm.sh', 'hmmer3_pipeline_missing_end.sh', 'Short-Pair.py'], 'bin')] + +fix_python_shebang_for = ['bin/Short-Pair.py'] + +postinstallcmds = ["chmod a+rx %(installdir)s/bin/*"] + +exts_defaultclass = 'PythonBundle' + +sanity_check_paths = { + 'files': ['bin/DNA2Protein', 'bin/get_hmm.sh', 'bin/hmmer3_pipeline_missing_end.sh', 'bin/Short-Pair.py'], + 'dirs': [], +} + +sanity_check_commands = ["python3 bin/Short-Pair.py -h"] + +moduleclass = 'bio' From 0a5adc1be5211013e9cf103d613e464491a31ba7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 13 Jan 2022 20:53:27 +0100 Subject: [PATCH 2637/9987] adding easyconfigs: SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb, hypothesis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb, pybind11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb and patches: numpy-1.16.6_add_flexiblas_detection.patch, numpy-1.16.6_handle_failing_linalg_test.patch --- ...sis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb | 25 +++ ...nd11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb | 25 +++ ...bundle-2021.10-foss-2021b-Python-2.7.18.eb | 84 ++++++++ ...numpy-1.16.6_add_flexiblas_detection.patch | 181 ++++++++++++++++++ ...py-1.16.6_handle_failing_linalg_test.patch | 17 ++ 5 files changed, 332 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_add_flexiblas_detection.patch create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_handle_failing_linalg_test.patch diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..1a30b129637 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.57.1-GCCcore-11.2.0-Python-2.7.18.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '4.57.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3c4369a4b0a1348561048bcda5f1db951a1b8e2a514ea8e8c70d36e656bf6fa0'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '2.7.18')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..f393fb93837 --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.7.1-GCCcore-11.2.0-Python-2.7.18.eb @@ -0,0 +1,25 @@ +name = 'pybind11' +version = '2.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['616d1c42e4cf14fa27b2a4ff759d7d7b33006fdc5ad8fd603bb2c22622f27020'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Eigen', '3.3.9'), +] + +dependencies = [('Python', '2.7.18')] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..f806bd48d7a --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.10-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2021.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '4.57.1', versionsuffix), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('pybind11', '2.7.1', versionsuffix), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.16.6', { + 'patches': [ + 'numpy-1.16.2_relax-long-complex-test.patch', + 'numpy-1.16.6_add_flexiblas_detection.patch', + 'numpy-1.16.6_handle_failing_linalg_test.patch', + ], + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': [ + 'e5cf3fdf13401885e8eea8170624ec96225e2174eb0c611c6f26dd33b489e3ff', # numpy-1.16.6.zip + # numpy-1.16.2_relax-long-complex-test.patch + '647dd4099c2968489e5103b50bcd1b3d970b5b536af25ec75efe86127dda07bb', + # numpy-1.16.6_add_flexiblas_detection.patch + '32ca32dd7ee8d6fcdce5875067acd50970c731cbb2603c6d1ad84ff81ff8c6d5', + # numpy-1.16.6_handle_failing_linalg_test.patch + 'be9dce98649626b7322ed8d1241b74a4e28c1d1de070a8072dc912cad3eb143d', + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.2', { + 'checksums': ['f81fcefa8b982624a31c9e4ec7761325a88a0eba60d36d1da90e47f8fe3c67f7'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('scipy', '1.2.3', { + 'patches': ['scipy-1.2.3_fix_nan_problem_in_vi.patch'], + 'prebuildopts': 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ', + 'checksums': [ + 'ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57', # scipy-1.2.3.tar.gz + # scipy-1.2.3_fix_nan_problem_in_vi.patch + '0513c5d0491a3f062ed024b6aa7b382706e8c42b3a3fdd26ff7a4d305ac9a30d', + ], + }), + ('mpi4py', '3.1.1', { + 'checksums': ['e11f8587a3b93bb24c8526addec664b586b965d83c0882b884c14dc3fd6b9f5c'], + }), + ('numexpr', '2.7.3', { + 'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '0.24.2', { + 'checksums': ['4f919f409c433577a501e023943e582c57355d50a724c589e78bc1d551a535a2'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_add_flexiblas_detection.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_add_flexiblas_detection.patch new file mode 100644 index 00000000000..02528b44bc3 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_add_flexiblas_detection.patch @@ -0,0 +1,181 @@ +Add flexiblas detection to numpy. +This is just a copy of the openblas detection with name changed. + +Åke Sandgren, 2022-01-13 +diff -ru numpy-1.16.6.orig/numpy/distutils/system_info.py numpy-1.16.6/numpy/distutils/system_info.py +--- numpy-1.16.6.orig/numpy/distutils/system_info.py 2019-12-27 17:24:44.000000000 +0100 ++++ numpy-1.16.6/numpy/distutils/system_info.py 2022-01-13 16:48:14.754235308 +0100 +@@ -20,6 +20,7 @@ + blas_info + lapack_info + openblas_info ++ flexiblas_info + blis_info + blas_opt_info # usage recommended + lapack_opt_info # usage recommended +@@ -395,6 +396,9 @@ + # openblas with embedded lapack + 'openblas_lapack': openblas_lapack_info, # use blas_opt instead + 'openblas_clapack': openblas_clapack_info, # use blas_opt instead ++ 'flexiblas': flexiblas_info, # use blas_opt instead ++ 'flexiblas_lapack': flexiblas_lapack_info, # use blas_opt instead ++ 'flexiblas_clapack': flexiblas_clapack_info, # use blas_opt instead + 'blis': blis_info, # use blas_opt instead + 'lapack_mkl': lapack_mkl_info, # use lapack_opt instead + 'blas_mkl': blas_mkl_info, # use blas_opt instead +@@ -1549,6 +1553,16 @@ + self.set_info(**lapack_mkl_info) + return + ++ flexiblas_info = get_info('flexiblas_lapack') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ ++ flexiblas_info = get_info('flexiblas_clapack') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ + openblas_info = get_info('openblas_lapack') + if openblas_info: + self.set_info(**openblas_info) +@@ -1633,6 +1647,11 @@ + self.set_info(**blis_info) + return + ++ flexiblas_info = get_info('flexiblas') ++ if flexiblas_info: ++ self.set_info(**flexiblas_info) ++ return ++ + openblas_info = get_info('openblas') + if openblas_info: + self.set_info(**openblas_info) +@@ -1749,6 +1768,126 @@ + return res + + ++class flexiblas_info(blas_info): ++ section = 'flexiblas' ++ dir_env_var = 'FLEXIBLAS' ++ _lib_names = ['flexiblas'] ++ notfounderror = BlasNotFoundError ++ ++ def check_embedded_lapack(self, info): ++ return True ++ ++ def calc_info(self): ++ c = customized_ccompiler() ++ ++ lib_dirs = self.get_lib_dirs() ++ ++ flexiblas_libs = self.get_libs('libraries', self._lib_names) ++ if flexiblas_libs == self._lib_names: # backward compat with 1.8.0 ++ flexiblas_libs = self.get_libs('flexiblas_libs', self._lib_names) ++ ++ info = self.check_libs(lib_dirs, flexiblas_libs, []) ++ ++ if c.compiler_type == "msvc" and info is None: ++ from numpy.distutils.fcompiler import new_fcompiler ++ f = new_fcompiler(c_compiler=c) ++ if f and f.compiler_type == 'gnu95': ++ # Try gfortran-compatible library files ++ info = self.check_msvc_gfortran_libs(lib_dirs, flexiblas_libs) ++ # Skip lapack check, we'd need build_ext to do it ++ assume_lapack = True ++ elif info: ++ assume_lapack = False ++ info['language'] = 'c' ++ ++ if info is None: ++ return ++ ++ # Add extra info for OpenBLAS ++ extra_info = self.calc_extra_info() ++ dict_append(info, **extra_info) ++ ++ if not (assume_lapack or self.check_embedded_lapack(info)): ++ return ++ ++ info['define_macros'] = [('HAVE_CBLAS', None)] ++ self.set_info(**info) ++ ++ def check_msvc_gfortran_libs(self, library_dirs, libraries): ++ # First, find the full path to each library directory ++ library_paths = [] ++ for library in libraries: ++ for library_dir in library_dirs: ++ # MinGW static ext will be .a ++ fullpath = os.path.join(library_dir, library + '.a') ++ if os.path.isfile(fullpath): ++ library_paths.append(fullpath) ++ break ++ else: ++ return None ++ ++ # Generate numpy.distutils virtual static library file ++ tmpdir = os.path.join(os.getcwd(), 'build', 'flexiblas') ++ if not os.path.isdir(tmpdir): ++ os.makedirs(tmpdir) ++ ++ info = {'library_dirs': [tmpdir], ++ 'libraries': ['flexiblas'], ++ 'language': 'f77'} ++ ++ fake_lib_file = os.path.join(tmpdir, 'flexiblas.fobjects') ++ fake_clib_file = os.path.join(tmpdir, 'flexiblas.cobjects') ++ with open(fake_lib_file, 'w') as f: ++ f.write("\n".join(library_paths)) ++ with open(fake_clib_file, 'w') as f: ++ pass ++ ++ return info ++ ++class flexiblas_lapack_info(flexiblas_info): ++ section = 'flexiblas' ++ dir_env_var = 'FLEXIBLAS' ++ _lib_names = ['flexiblas'] ++ notfounderror = BlasNotFoundError ++ ++ def check_embedded_lapack(self, info): ++ res = False ++ c = customized_ccompiler() ++ ++ tmpdir = tempfile.mkdtemp() ++ s = """void zungqr_(); ++ int main(int argc, const char *argv[]) ++ { ++ zungqr_(); ++ return 0; ++ }""" ++ src = os.path.join(tmpdir, 'source.c') ++ out = os.path.join(tmpdir, 'a.out') ++ # Add the additional "extra" arguments ++ try: ++ extra_args = info['extra_link_args'] ++ except Exception: ++ extra_args = [] ++ if sys.version_info < (3, 5) and sys.version_info > (3, 0) and c.compiler_type == "msvc": ++ extra_args.append("/MANIFEST") ++ try: ++ with open(src, 'wt') as f: ++ f.write(s) ++ obj = c.compile([src], output_dir=tmpdir) ++ try: ++ c.link_executable(obj, out, libraries=info['libraries'], ++ library_dirs=info['library_dirs'], ++ extra_postargs=extra_args) ++ res = True ++ except distutils.ccompiler.LinkError: ++ res = False ++ finally: ++ shutil.rmtree(tmpdir) ++ return res ++ ++class flexiblas_clapack_info(flexiblas_lapack_info): ++ _lib_names = ['flexiblas', 'lapack'] ++ + class openblas_info(blas_info): + section = 'openblas' + dir_env_var = 'OPENBLAS' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_handle_failing_linalg_test.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_handle_failing_linalg_test.patch new file mode 100644 index 00000000000..d85fb475809 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.16.6_handle_failing_linalg_test.patch @@ -0,0 +1,17 @@ +linalg/test_nan is marked xfail in at least 1.21.3 +Do so here too since it fails with newer openblas/compiler versions. + +Åke sandgren, 2022-01-13 +diff -ru numpy-1.16.6.orig/numpy/linalg/tests/test_linalg.py numpy-1.16.6/numpy/linalg/tests/test_linalg.py +--- numpy-1.16.6.orig/numpy/linalg/tests/test_linalg.py 2019-12-27 17:24:44.000000000 +0100 ++++ numpy-1.16.6/numpy/linalg/tests/test_linalg.py 2022-01-13 17:21:36.658857878 +0100 +@@ -740,6 +740,9 @@ + for A, p in itertools.product(As, p_neg): + linalg.cond(A, p) + ++ @pytest.mark.xfail(True, run=False, ++ reason="Platform/LAPACK-dependent failure, " ++ "see gh-18914") + def test_nan(self): + # nans should be passed through, not converted to infs + ps = [None, 1, -1, 2, -2, 'fro'] From da9ed4e7ab064bcdd9c97d203073141e8c6bd29a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Jan 2022 21:38:09 +0100 Subject: [PATCH 2638/9987] adding easyconfigs: texlive-20210324-GCC-11.2.0.eb --- .../graphite2-1.3.14-GCCcore-11.2.0.eb | 27 ++++++++ .../p/poppler/poppler-22.01.0-GCC-11.2.0.eb | 59 +++++++++++++++++ .../t/texlive/texlive-20210324-GCC-11.2.0.eb | 63 +++++++++++++++++++ 3 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/poppler/poppler-22.01.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f60b4dd57e1 --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('binutils', '2.37'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/poppler/poppler-22.01.0-GCC-11.2.0.eb b/easybuild/easyconfigs/p/poppler/poppler-22.01.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..ad8abb534ac --- /dev/null +++ b/easybuild/easyconfigs/p/poppler/poppler-22.01.0-GCC-11.2.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'poppler' +version = '22.01.0' + +homepage = 'https://poppler.freedesktop.org' +description = "Poppler is a PDF rendering library" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +builddependencies = [ + ('CMake', '3.22.1'), + ('pkgconf', '1.8.0'), + ('Python', '3.9.6', '-bare'), +] + +dependencies = [ + ('freetype', '2.11.0'), + ('fontconfig', '2.13.94'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('NSS', '3.69'), + ('LibTIFF', '4.3.0'), + ('Qt5', '5.15.2'), + ('Boost', '1.77.0'), + ('cairo', '1.16.0'), + ('OpenJPEG', '2.4.0'), + ('zlib', '1.2.11'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['7d3493056b5b86413e5c693c2cae02c5c06cd8e618d14c2c31e2c84b67b2313e'], + 'configopts': "-DENABLE_BOOST=ON", + }), + ('poppler-data', '0.4.11', { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2cec05cd1bb03af98a8b06a1e22f6e6e1a65b1e2f3816cb3069bb0874825f08c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdfinfo', 'lib/libpoppler.%s' % SHLIB_EXT, 'lib/libpoppler-cpp.%s' % SHLIB_EXT, + 'lib/libpoppler-glib.%s' % SHLIB_EXT, 'lib/libpoppler-qt5.%s' % SHLIB_EXT], + 'dirs': ['include/poppler', 'lib/pkgconfig', 'share'], +} + +sanity_check_commands = ["pdfinfo --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb new file mode 100644 index 00000000000..b00d0026d53 --- /dev/null +++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb @@ -0,0 +1,63 @@ +# Based off the 2017 version by John Dey jfdey@fredhutch.org +# https://github.com/easybuilders/easybuild-easyconfigs/pull/5085 +easyblock = 'Tarball' + +name = 'texlive' +version = '20210324' + +homepage = 'https://tug.org' +description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript + text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a + PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to + be a representation of the final typeset output, and so can be easily edited and manipulated.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [ + 'ftp://tug.org/texlive/historic/2021/', + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/', +] +sources = [ + { + 'download_filename': 'install-tl-unx.tar.gz', + 'filename': 'install-tl-unx-%(version)s.tar.gz', + } +] +checksums = ['74eac0855e1e40c8db4f28b24ef354bd7263c1f76031bdc02b52156b572b7a1d'] + +dependencies = [ + ('X11', '20210802'), + ('libpng', '1.6.37'), + ('libGLU', '9.0.2'), + ('Perl', '5.34.0'), + ('HarfBuzz', '2.8.2'), + ('poppler', '22.01.0'), + ('cairo', '1.16.0'), + ('fontconfig', '2.13.94'), + ('zlib', '1.2.11'), + ('graphite2', '1.3.14'), +] + +postinstallcmds = [ + 'echo "TEXDIR %(installdir)s/" > %(installdir)s/texlive.profile && ' + 'echo "TEXMFLOCAL %(installdir)s/texmf-local" >> %(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' + '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' +] + +modextrapaths = { + 'PATH': 'bin/%(arch)s-linux', + 'INFOPATH': 'texmf-dist/doc/info', + 'MANPATH': 'texmf-dist/doc/man', +} +modextravars = { + 'TEXMFHOME': '%(installdir)s/texmf-dist' +} + +sanity_check_paths = { + 'files': ['bin/%(arch)s-linux/tex', 'bin/%(arch)s-linux/latex'], + 'dirs': ['bin/%(arch)s-linux', 'texmf-dist'], +} + +moduleclass = 'devel' From 293bb227539818c6c82724aa2e58d51580fbe71b Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 14 Jan 2022 09:56:30 +0100 Subject: [PATCH 2639/9987] Add libpsml and xmlf90 for GCC/10.3.0, GCC/11.2.0, intel-compilers/2021.2.0, intel-compilers/2021.4.0. --- .../l/libpsml/libpsml-1.1.10-GCC-10.3.0.eb | 25 +++++++++++++++++++ .../l/libpsml/libpsml-1.1.10-GCC-11.2.0.eb | 25 +++++++++++++++++++ ...libpsml-1.1.10-intel-compilers-2021.2.0.eb | 25 +++++++++++++++++++ ...libpsml-1.1.10-intel-compilers-2021.4.0.eb | 25 +++++++++++++++++++ .../x/xmlf90/xmlf90-1.5.4-GCC-10.3.0.eb | 20 +++++++++++++++ .../x/xmlf90/xmlf90-1.5.4-GCC-11.2.0.eb | 20 +++++++++++++++ .../xmlf90-1.5.4-intel-compilers-2021.2.0.eb | 21 ++++++++++++++++ .../xmlf90-1.5.4-intel-compilers-2021.4.0.eb | 21 ++++++++++++++++ 8 files changed, 182 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.4.0.eb create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-intel-compilers-2021.2.0.eb create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.3.0.eb new file mode 100644 index 00000000000..c1ec1e114c7 --- /dev/null +++ b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libpsml' +version = '1.1.10' + +homepage = 'https://launchpad.net/libpsml' +description = """LibPSML provides a Fortran API to parse files in the + PSeudopotential Markup Language (PSML) format.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libpsml/uploads/95c4d83d750d1ca87659b6395c8f7ea7/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['67c38b5bc26acbb77fd13794d1d92f41197a44311314f5453c82506205e0717b'] + +dependencies = [ + ('xmlf90', '1.5.4'), +] + +sanity_check_paths = { + 'files': ['include/m_psml.mod', 'lib/libpsml.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-11.2.0.eb new file mode 100644 index 00000000000..7bbf4e9b312 --- /dev/null +++ b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libpsml' +version = '1.1.10' + +homepage = 'https://launchpad.net/libpsml' +description = """LibPSML provides a Fortran API to parse files in the + PSeudopotential Markup Language (PSML) format.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libpsml/uploads/95c4d83d750d1ca87659b6395c8f7ea7/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['67c38b5bc26acbb77fd13794d1d92f41197a44311314f5453c82506205e0717b'] + +dependencies = [ + ('xmlf90', '1.5.4'), +] + +sanity_check_paths = { + 'files': ['include/m_psml.mod', 'lib/libpsml.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..4f8e563febe --- /dev/null +++ b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libpsml' +version = '1.1.10' + +homepage = 'https://launchpad.net/libpsml' +description = """LibPSML provides a Fortran API to parse files in the + PSeudopotential Markup Language (PSML) format.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libpsml/uploads/95c4d83d750d1ca87659b6395c8f7ea7/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['67c38b5bc26acbb77fd13794d1d92f41197a44311314f5453c82506205e0717b'] + +dependencies = [ + ('xmlf90', '1.5.4'), +] + +sanity_check_paths = { + 'files': ['include/m_psml.mod', 'lib/libpsml.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..b09da9cc110 --- /dev/null +++ b/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libpsml' +version = '1.1.10' + +homepage = 'https://launchpad.net/libpsml' +description = """LibPSML provides a Fortran API to parse files in the + PSeudopotential Markup Language (PSML) format.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libpsml/uploads/95c4d83d750d1ca87659b6395c8f7ea7/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['67c38b5bc26acbb77fd13794d1d92f41197a44311314f5453c82506205e0717b'] + +dependencies = [ + ('xmlf90', '1.5.4'), +] + +sanity_check_paths = { + 'files': ['include/m_psml.mod', 'lib/libpsml.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.3.0.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..a27a593795b --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-10.3.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'xmlf90' +version = '1.5.4' + +homepage = 'https://launchpad.net/xmlf90' +description = """xmlf90 is a basic XML parsing library written in Fortran.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a0b1324ff224d5b5ad1127a6ad4f90979f6b127f1a517f98253eea377237bbe4'] + +sanity_check_paths = { + 'files': ['include/xmlf90_%s.mod' % x for x in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], + 'dirs': ['share/org.siesta-project'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-11.2.0.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-11.2.0.eb new file mode 100644 index 00000000000..0d31420417a --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-GCC-11.2.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'xmlf90' +version = '1.5.4' + +homepage = 'https://launchpad.net/xmlf90' +description = """xmlf90 is a basic XML parsing library written in Fortran.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a0b1324ff224d5b5ad1127a6ad4f90979f6b127f1a517f98253eea377237bbe4'] + +sanity_check_paths = { + 'files': ['include/xmlf90_%s.mod' % x for x in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], + 'dirs': ['share/org.siesta-project'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..ef1e39cc508 --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-intel-compilers-2021.2.0.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'xmlf90' +version = '1.5.4' + +homepage = 'https://launchpad.net/xmlf90' +description = """xmlf90 is a basic XML parsing library written in Fortran.""" + +# can't move down to GCCcore and combine with Intel, gfortran modules are incompatible with ifort +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a0b1324ff224d5b5ad1127a6ad4f90979f6b127f1a517f98253eea377237bbe4'] + +sanity_check_paths = { + 'files': ['include/xmlf90_%s.mod' % x for x in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], + 'dirs': ['share/org.siesta-project'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..a415a9bb828 --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.4-intel-compilers-2021.4.0.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'xmlf90' +version = '1.5.4' + +homepage = 'https://launchpad.net/xmlf90' +description = """xmlf90 is a basic XML parsing library written in Fortran.""" + +# can't move down to GCCcore and combine with Intel, gfortran modules are incompatible with ifort +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://launchpad.net/xmlf90/trunk/%(version_major_minor)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a0b1324ff224d5b5ad1127a6ad4f90979f6b127f1a517f98253eea377237bbe4'] + +sanity_check_paths = { + 'files': ['include/xmlf90_%s.mod' % x for x in ['cml', 'dom', 'sax', 'wxml', 'xpath']] + ['lib/libxmlf90.a'], + 'dirs': ['share/org.siesta-project'], +} + +moduleclass = 'data' From 497c50f8b1fbb2820473285a502be091bd035b19 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 14 Jan 2022 10:45:51 +0100 Subject: [PATCH 2640/9987] Adjust versxion of backports.entry_points_selectable make Python-2.7.18-GCCcore-11.2.0.eb match Python-3.9.6-GCCcore-11.2.0.eb --- .../easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb index 72ceefe329f..c9a13925842 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -173,8 +173,8 @@ exts_list = [ ('platformdirs', '2.0.2', { 'checksums': ['3b00d081227d9037bbbca521a5787796b5ef5000faea1e43fd76f1d44b06fcfa'], }), - ('backports.entry_points_selectable', '1.1.1', { - 'checksums': ['914b21a479fde881635f7af5adc7f6e38d6b274be32269070c53b698c60d5386'], + ('backports.entry_points_selectable', '1.1.0', { + 'checksums': ['988468260ec1c196dab6ae1149260e2f5472c9110334e5d51adcb77867361f6a'], }), ('virtualenv', '20.7.0', { 'checksums': ['97066a978431ec096d163e72771df5357c5c898ffdd587048f45e0aecc228094'], From 57b9c9bc59dfb56bd0105bcdfab9cbd27c5d06b7 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 14 Jan 2022 12:10:40 +0100 Subject: [PATCH 2641/9987] Update easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb index f2c7ad44957..fd1240cbc56 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -32,9 +32,9 @@ separate_build_dir = True buildopts = " && chmod +x %(builddir)s/%(name)s-%(version)s/bin/linux/*_linux64" -install_cmd = """mkdir -p %(installdir)s/bin && - cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && - cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib""" +install_cmd = "mkdir -p %(installdir)s/bin && " +install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && " +install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib" sanity_check_paths = { From 158751b1304dd4a58bd994edb473a2fd102ffb1a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 14 Jan 2022 12:45:19 +0100 Subject: [PATCH 2642/9987] adding easyconfigs: IPython-5.10.0-foss-2021b-Python-2.7.18.eb, matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb, Tkinter-2.7.18-GCCcore-11.2.0.eb --- ...IPython-5.10.0-foss-2021b-Python-2.7.18.eb | 152 ++++++++++++++++++ ...tplotlib-2.2.5-foss-2021b-Python-2.7.18.eb | 60 +++++++ .../Tkinter/Tkinter-2.7.18-GCCcore-11.2.0.eb | 24 +++ 3 files changed, 236 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..aedca6f38f9 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,152 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '5.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '2.7.18'), + ('ZeroMQ', '4.3.4'), + ('matplotlib', '2.2.5', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('Pygments', '2.5.2', { + 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], + }), + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['d1f9e2d02bb0900ddef7b6af114aca3a5cf3dc43b9de1f19d37c4aedbc724fee'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '1.0.15', { + 'checksums': ['858588f1983ca497f1cf4ffde01d978a3ea02b01c8a26a8bbc5cd2e66d816917'], + }), + ('traitlets', '4.3.3', { + 'checksums': ['d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7'], + }), + ('parso', '0.7.1', { + 'checksums': ['caba44724b994a8a5e086460bb212abc5a8bc46951bf4a9a1210745953622eb9'], + }), + ('jedi', '0.17.2', { + 'checksums': ['86ed7d9b750603e4ba582ea8edc678657fb4007894a12bcf6f4bb97892f31d20'], + }), + ('testpath', '0.4.4', { + 'use_pip': False, + 'checksums': ['60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('nbconvert', '5.6.1', { + 'checksums': ['21fb48e700b43e82ba0e3142421a659d7739b65568cc832a13976a77be16b523'], + }), + ('nbformat', '4.4.0', { + 'checksums': ['f7494ef0df60766b7cabe0a3651556345a963b74dbc16bc7c18479041170d402'], + }), + ('ipywidgets', '7.6.3', { + 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter-packaging', '0.4.0', { + 'checksums': ['d89134d2df88c30098bce0f8d8fb07b988ef0f616775dbd4b82dac9562b5cae6'], + }), + ('jupyterlab_widgets', '0.6.15', { + 'checksums': ['2954919a6a04a48230b904e60f00d839e339f15ee9748d4172c8ae403ad4fb47'], + }), + ('argon2-cffi', '20.1.0', { + 'modulename': 'argon2', + 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], + }), + ('Send2Trash', '1.8.0', { + 'checksums': ['d2c24762fd3759860a0aff155e45871447ea58d2be6bdd39b5c8f966a0c99c2d'], + }), + ('bleach', '3.3.1', { + 'checksums': ['306483a5a9795474160ad57fce3ddd1b50551e981eed8e15a582d34cef28aafa'], + }), + ('vcversioner', '2.16.0.0', { + 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], + }), + ('pandocfilters', '1.4.3', { + 'checksums': ['bc63fbb50534b4b1f8ebe1860889289e8af94a23bff7445259592df25a3906eb'], + }), + ('pyzmq', '19.0.2', { + 'modulename': 'zmq', + 'checksums': ['296540a065c8c21b26d63e3cea2d1d57902373b16e4256afe46422691903a438'], + }), + ('jupyter_core', '4.6.3', { + 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('terminado', '0.8.3', { + 'use_pip': False, + 'checksums': ['4804a774f802306a7d9af7322193c5390f1da0abb429e082a10ef1d46e6fb2c2'], + }), + ('backports_abc', '0.5', { + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'checksums': ['713e7a8228ae80341c70586d1cc0a8caa5207346927e23d09dcbcaf18eadec80'], + }), + ('tornado', '5.1.1', { + 'checksums': ['4e5158d97583502a7e2739951553cbd88a72076f152b4b11b64b9a10c4c49409'], + }), + ('jupyter_client', '5.3.5', { + 'checksums': ['5efdf4131124d4a0d5789101e74827022585f172d2f4b60cf6fa98e0a7511b25'], + }), + ('ipykernel', '4.10.1', { + 'checksums': ['eeb74b2bcfe0ced5a7900361f98fa1171288aa47ed4b522efe5acb167c6cf5fb'], + }), + ('prometheus_client', '0.11.0', { + 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], + }), + ('notebook', '5.7.13', { + 'checksums': ['b64adb32eafa775b299227e92948c7fa4ec837624dc6243b90fef90f15b7a0bd'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + ('debugpy', '1.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['84ff51b8b5c847d5421324ca419db1eec813a4dd2bbf19dbbbe132e2ab2b2fc6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..57137691145 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '2.2.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2021.10', versionsuffix), + ('libpng', '1.6.37'), + ('freetype', '2.11.0'), + ('Tkinter', '%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.1.0', { + 'checksums': ['53eaed412477c836e1b9522c19858a8557d6e595077830146182225613b11a75'], + }), + (name, version, { + 'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'checksums': ['a3037a840cd9dfdc2df9fee8af8f76ca82bfab173c0f9468193ca7a89a2b60ea'], + }), +] + +postinstallcmds = [ + 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..09c8f6a9b3e --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +name = 'Tkinter' +version = '2.7.18' + +homepage = 'https://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.11'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('libreadline', '8.1'), +] + +moduleclass = 'lang' From 68378e863b1a2ae2688dcbd5acfb04d23b0a607b Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 14 Jan 2022 11:47:25 +0000 Subject: [PATCH 2643/9987] adding easyconfigs: TALYS-1.95-GCCcore-9.3.0.eb, TALYS-1.95-GCCcore-10.3.0.eb --- .../t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb | 41 +++++++++++++++++++ .../t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb | 41 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3cb0dd44e83 --- /dev/null +++ b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CmdCp' + +name = 'TALYS' +version = '1.95' + +homepage = 'https://tendl.web.psi.ch/tendl_2019/talys.html' +description = "TALYS is a nuclear reaction program." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'noopt': True} + +source_urls = ['https://tendl.web.psi.ch/tendl_2019/talys/'] +sources = [{'download_filename': 'talys.tar', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['3a69420b36c2fcd3e433db91ed45d6fcb59558875244cf066f174eaa18840164'] + +builddependencies = [('binutils', '2.36.1')] + +start_dir = 'source' + +# Use environment variable to set structure directory path +local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' +local_sed += ' -e "s|character*132 path|character*256 path|g" ' +local_sed += ' -e "s|//\'abundance|//\'/abundance|g" machine.f && ' +# Also strip hardcoded talys path in verify script +local_sed += 'sed -i "/talys=.*/d" ../samples/verify ' + +cmds_map = [('.*', '%s && $FC $FFLAGS $FCFLAGS -o talys *.f' % local_sed)] + +files_to_copy = [(['%(namelower)s'], 'bin'), 'structure', 'samples'] + +sanity_check_paths = { + 'files': ['bin/talys'], + 'dirs': ['bin', 'samples', 'structure'], +} + +sanity_check_commands = ["cd %(builddir)s/%(namelower)s/samples && ./verify"] + +modextravars = {'TALYS_STRUCTURE_DIR': '%(installdir)s/structure'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..d5f52ba4a59 --- /dev/null +++ b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CmdCp' + +name = 'TALYS' +version = '1.95' + +homepage = 'https://tendl.web.psi.ch/tendl_2019/talys.html' +description = "TALYS is a nuclear reaction program." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'noopt': True} + +source_urls = ['https://tendl.web.psi.ch/tendl_2019/talys/'] +sources = [{'download_filename': 'talys.tar', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['3a69420b36c2fcd3e433db91ed45d6fcb59558875244cf066f174eaa18840164'] + +builddependencies = [('binutils', '2.34')] + +start_dir = 'source' + +# Use environment variable to set structure directory path +local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' +local_sed += ' -e "s|character*132 path|character*256 path|g" ' +local_sed += ' -e "s|//\'abundance|//\'/abundance|g" machine.f && ' +# Also strip hardcoded talys path in verify script +local_sed += 'sed -i "/talys=.*/d" ../samples/verify ' + +cmds_map = [('.*', '%s && $FC $FFLAGS $FCFLAGS -o talys *.f' % local_sed)] + +files_to_copy = [(['%(namelower)s'], 'bin'), 'structure', 'samples'] + +sanity_check_paths = { + 'files': ['bin/talys'], + 'dirs': ['samples', 'structure'], +} + +sanity_check_commands = ["cd %(builddir)s/%(namelower)s/samples && ./verify"] + +modextravars = {'TALYS_STRUCTURE_DIR': '%(installdir)s/structure'} + +moduleclass = 'phys' From 1cdb78bb20fc732666a9c8aa8cdba00f9ea22ed3 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 14 Jan 2022 12:31:08 +0000 Subject: [PATCH 2644/9987] Linting --- easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb index 3cb0dd44e83..0a6c88f179b 100644 --- a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb @@ -19,7 +19,7 @@ builddependencies = [('binutils', '2.36.1')] start_dir = 'source' # Use environment variable to set structure directory path -local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' +local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' local_sed += ' -e "s|character*132 path|character*256 path|g" ' local_sed += ' -e "s|//\'abundance|//\'/abundance|g" machine.f && ' # Also strip hardcoded talys path in verify script diff --git a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb index d5f52ba4a59..28297ff22e5 100644 --- a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb @@ -19,7 +19,7 @@ builddependencies = [('binutils', '2.34')] start_dir = 'source' # Use environment variable to set structure directory path -local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' +local_sed = 'sed -i -e "s|path=.*|call get_environment_variable(\'TALYS_STRUCTURE_DIR\', path)|g" ' local_sed += ' -e "s|character*132 path|character*256 path|g" ' local_sed += ' -e "s|//\'abundance|//\'/abundance|g" machine.f && ' # Also strip hardcoded talys path in verify script From 8ea2038b8ee95b60c527513742c0e0d14d401f8c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 14 Jan 2022 13:08:50 +0000 Subject: [PATCH 2645/9987] adding easyconfigs: VEP-105-GCC-11.2.0.eb, DBD-mysql-4.050-GCC-11.2.0.eb, BioPerl-1.7.8-GCCcore-11.2.0.eb, DB_File-1.856-GCCcore-11.2.0.eb, Bio-DB-HTS-3.01-GCC-11.2.0.eb --- .../Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb | 30 +++++++++++ .../b/BioPerl/BioPerl-1.7.8-GCCcore-11.2.0.eb | 54 +++++++++++++++++++ .../d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb | 33 ++++++++++++ .../d/DB_File/DB_File-1.856-GCCcore-11.2.0.eb | 31 +++++++++++ .../easyconfigs/v/VEP/VEP-105-GCC-11.2.0.eb | 36 +++++++++++++ 5 files changed, 184 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/v/VEP/VEP-105-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb new file mode 100644 index 00000000000..9de8ffc9db7 --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PerlModule' + +name = 'Bio-DB-HTS' +version = '3.01' + +homepage = 'https://metacpan.org/release/Bio-DB-HTS' +description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/'] +sources = ['Bio-DB-HTS-%(version)s.tar.gz'] +checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('Perl', '5.34.0'), + ('BioPerl', '1.7.8'), + ('HTSlib', '1.14'), +] + +options = {'modulename': 'Bio::DB::HTS'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f2f6f3dd5f8 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'Bundle' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Perl', '5.34.0'), + ('XML-LibXML', '2.0207'), + ('DB_File', '1.856'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + ('XML::DOM::XPath', '0.14', { + 'source_tmpl': 'XML-DOM-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': ['0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), + ('BioPerl', version, { + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb new file mode 100644 index 00000000000..281c3235c67 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.050' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['4f48541ff15a0a7405f76adc10f81627c33996fbf56c95c26c094444c0928d78'] + +dependencies = [ + ('Perl', '5.34.0'), + ('MariaDB', '10.6.4'), + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DBD/mysql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..887cdaab73b --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.856' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['cdf9ba922fe39159d36b73f9fb815f5eaa375f3a3e4dc4de78e053b444cd66a9'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Perl', '5.34.0'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/v/VEP/VEP-105-GCC-11.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-105-GCC-11.2.0.eb new file mode 100644 index 00000000000..56b99eb9ac9 --- /dev/null +++ b/easybuild/easyconfigs/v/VEP/VEP-105-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +name = 'VEP' +version = '105' + +homepage = 'https://www.ensembl.org/info/docs/tools/vep' +description = """Variant Effect Predictor (VEP) determines the effect of your + variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, + transcripts, and protein sequence, as well as regulatory regions. + Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently + used routines in VEP.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/'] +sources = ['%(version)s.tar.gz'] +checksums = ['97ea8d3914b21b39ebd0504a71f3918f3d49d6d0266746b0295fe4f83754d81f'] + +dependencies = [ + ('Perl', '5.34.0'), + ('Archive-Zip', '1.68'), + ('DBD-mysql', '4.050'), + ('BioPerl', '1.7.8'), + ('Bio-DB-HTS', '3.01'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('Bio::EnsEMBL::XS', '2.3.2', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], + 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], + }), +] + +moduleclass = 'bio' From 5b11a7971aca95a1cc0ef017aa7a6e41d332e8c6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 14 Jan 2022 14:14:04 +0100 Subject: [PATCH 2646/9987] Add missing deps and turn on sanity_pip_check --- .../IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb index aedca6f38f9..d58979770fb 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-5.10.0-foss-2021b-Python-2.7.18.eb @@ -73,6 +73,12 @@ exts_list = [ ('jupyter-packaging', '0.4.0', { 'checksums': ['d89134d2df88c30098bce0f8d8fb07b988ef0f616775dbd4b82dac9562b5cae6'], }), + ('jupyterlab_launcher', '0.11.2', { + 'checksums': ['236a647f4c3f8417413643a918a893a5f662fb5d2fdccce2fd101e3cca2e7fd1'], + }), + ('jupyterlab', '0.33.12', { + 'checksums': ['04a14b38b218c87731b519ff0f7e133b28a613ad944617ac7e07480d6a36eb5f'], + }), ('jupyterlab_widgets', '0.6.15', { 'checksums': ['2954919a6a04a48230b904e60f00d839e339f15ee9748d4172c8ae403ad4fb47'], }), @@ -139,6 +145,8 @@ exts_list = [ }), ] +modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} + sanity_check_paths = { 'files': ['bin/ipython'], 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], @@ -149,4 +157,6 @@ sanity_check_commands = [ "jupyter notebook --help", ] +sanity_pip_check = True + moduleclass = 'tools' From 76a1d28606129243211b977adeadaec49be75f1a Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 14 Jan 2022 14:46:33 +0100 Subject: [PATCH 2647/9987] adding easyconfigs: PAML-4.9j-GCCcore-11.2.0.eb --- .../p/PAML/PAML-4.9j-GCCcore-11.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5b009111831 --- /dev/null +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'PAML' +version = '4.9j' + +homepage = 'http://abacus.gene.ucl.ac.uk/software/paml.html' +description = """PAML is a package of programs for phylogenetic + analyses of DNA or protein sequences using maximum likelihood.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://abacus.gene.ucl.ac.uk/software'] +sources = ['%(namelower)s%(version)s.tgz'] +checksums = ['9b00fbd37fe825129a160599372ba4c8e88b22d14c0388044a711fb281a0191d'] + +builddependencies = [('binutils', '2.37')] + +start_dir = 'src' + +prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['GeneticCode.txt', '%(builddir)s/%(namelower)s%(version)s/README.txt'], ''), + (['*.trees', '*.ctl', '*.nuc', '*.dat', 'paup*', 'stewart.aa'], ''), + (['src/baseml', 'src/basemlg', 'src/chi2', 'src/codeml', 'src/evolver'], 'bin'), + (['src/infinitesites', 'src/mcmctree', 'src/pamp', 'src/yn00'], 'bin'), + (['dat/*'], 'dat'), + (['doc/*'], 'doc'), + (['examples/*'], 'examples'), + (['Technical/*'], 'Technical'), +] + +sanity_check_paths = { + 'files': ['baseml.ctl', 'codeml.ctl', 'bin/baseml', 'bin/codeml'], + 'dirs': ['dat', 'doc', 'examples'], +} + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cp -a %(installdir)s/examples/HIVNSsites %(builddir)s && " + "cd %(builddir)s/HIVNSsites && codeml", +] + +moduleclass = 'bio' From 1f09781599b52d57b802062c14e8226d33d95f0b Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 14 Jan 2022 14:56:38 +0100 Subject: [PATCH 2648/9987] adding easyconfigs: Mathematica-13.0.0.eb --- .../m/Mathematica/Mathematica-13.0.0.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-13.0.0.eb diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-13.0.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-13.0.0.eb new file mode 100644 index 00000000000..07ec38e6455 --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-13.0.0.eb @@ -0,0 +1,15 @@ +name = 'Mathematica' +version = '13.0.0' + +homepage = 'https://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = SYSTEM + +sources = ['Mathematica_%(version)s_BNDL_LINUX.sh'] +checksums = ['15bbad39a5995031325d1d178f63b00e71706d3ec9001eba6d1681fbc991d3e1'] + +license_server = 'license.example.com' + +moduleclass = 'math' From 8532ea852d898b779f35273a10bc3af8e8c5ab10 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 14 Jan 2022 15:17:17 +0100 Subject: [PATCH 2649/9987] Removed typo --- easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb index 154cc13b16c..20f3e803269 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb @@ -12,7 +12,7 @@ description = """MinPath (Minimal set of Pathways) is a parsimony approach for b toolchain = {'name': 'intel', 'version': '2021b'} -source_urls = ['https://github.com/mgtools/MinPath/archive/'], +source_urls = ['https://github.com/mgtools/MinPath/archive/'] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] checksums = [ From c6b25a856d7a4031583374f8f8e0d69d0e119932 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 14 Jan 2022 15:51:49 +0100 Subject: [PATCH 2650/9987] DualSPHysics: Fixes sanity check and updates patch header --- ...SPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 25 ++++++++----------- .../DualSPHysics-5.0.175-GCC-11.2.0.eb | 23 +++++++---------- .../d/DualSPHysics/DualSPHysics-5.0.175.patch | 2 ++ 3 files changed, 21 insertions(+), 29 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index 33a9ac4cc9f..46e679af552 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -24,7 +24,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s.patch'] checksums = [ 'd65bb7b8b4a21582091a534142348e46cff0a288a97ef86643bc2dde15637575', # v5.0.175.tar.gz - '24ae21134099252a597d80f25cf835dd981d0f085ce33dc801e70f1d7e045829', # DualSPHysics-5.0.175.patch + 'b2fad86d99e31fe2e1b5c65bab60a4f14362401b6de00a395b3a1bd13f608366', # DualSPHysics-5.0.175.patch ] srcdir = 'src/source' @@ -42,22 +42,17 @@ install_cmd = "mkdir -p %(installdir)s/bin && " install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && " install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib" +local_bins = ['GenCase', 'PartVTK', 'IsoSurface', 'MeasureTool', 'GenCase_MkWord', + 'DualSPHysics4.0_LiquidGas', 'DualSPHysics4.0_LiquidGasCPU', 'DualSPHysics5.0', + 'DualSPHysics5.0CPU', 'DualSPHysics5.0_NNewtonian', 'DualSPHysics5.0_NNewtonianCPU'] + sanity_check_paths = { - 'files': [ - 'bin/GenCase_linux64', - 'bin/PartVTK_linux64', - 'bin/IsoSurface_linux64', - 'bin/MeasureTool_linux64', - 'bin/GenCase_MkWord_linux64', - 'bin/DualSPHysics4.0_LiquidGas_linux64', - 'bin/DualSPHysics4.0_LiquidGasCPU_linux64', - 'bin/DualSPHysics5.0_linux64', - 'bin/DualSPHysics5.0CPU_linux64', - 'bin/DualSPHysics5.0_NNewtonian_linux64', - 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', - ], - 'dirs': ["lib"], + 'files': ['bin/%s_linux64' % x for x in local_bins], + 'dirs': ["lib", "bin"], } +sanity_check_commands = ['%s_linux64 -h' % x for x in local_bins] + + moduleclass = 'cae' diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb index fd1240cbc56..347fbb54bb2 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -36,22 +36,17 @@ install_cmd = "mkdir -p %(installdir)s/bin && " install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && " install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib" +local_bins = ['GenCase', 'PartVTK', 'IsoSurface', 'MeasureTool', 'GenCase_MkWord', + 'DualSPHysics4.0_LiquidGas', 'DualSPHysics4.0_LiquidGasCPU', 'DualSPHysics5.0', + 'DualSPHysics5.0CPU', 'DualSPHysics5.0_NNewtonian', 'DualSPHysics5.0_NNewtonianCPU'] + sanity_check_paths = { - 'files': [ - 'bin/GenCase_linux64', - 'bin/PartVTK_linux64', - 'bin/IsoSurface_linux64', - 'bin/MeasureTool_linux64', - 'bin/GenCase_MkWord_linux64', - 'bin/DualSPHysics4.0_LiquidGas_linux64', - 'bin/DualSPHysics4.0_LiquidGasCPU_linux64', - 'bin/DualSPHysics5.0_linux64', - 'bin/DualSPHysics5.0CPU_linux64', - 'bin/DualSPHysics5.0_NNewtonian_linux64', - 'bin/DualSPHysics5.0_NNewtonianCPU_linux64', - ], - 'dirs': ["lib"], + 'files': ['bin/%s_linux64' % x for x in local_bins], + 'dirs': ["lib", "bin"], } +sanity_check_commands = ['%s_linux64 -h' % x for x in local_bins] + + moduleclass = 'cae' diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch index 556373c9719..adad3dd6d3e 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175.patch @@ -1,3 +1,5 @@ +Author: Robert Mijakovic +Adds newly supported code generation for CUDA 11. diff -Naur DualSPHysics-5.0.175/src/source/CMakeLists.txt DualSPHysics-5.0.175/src/source/CMakeLists.txt --- DualSPHysics-5.0.175/src/source/CMakeLists.txt 2021-02-25 18:46:13.000000000 +0100 +++ DualSPHysics-5.0.175/src/source/CMakeLists.txt 2021-10-13 18:46:17.000000000 +0200 From 7471b0bf7438d7274ee74ccc82c54cf262fcda37 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 14 Jan 2022 16:03:49 +0100 Subject: [PATCH 2651/9987] adding easyconfigs: PREQUAL-1.02-GCCcore-11.2.0.eb --- .../p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..971db7cb571 --- /dev/null +++ b/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'PREQUAL' +version = '1.02' + +homepage = 'https://github.com/simonwhelan/prequal' +description = 'A program to identify and mask regions with non-homologous adjacent characters in FASTA files.' + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [{ + 'filename': '%(namelower)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/simonwhelan', + 'repo_name': '%(namelower)s', + 'commit': '67da42cf4761ed5fd8298eb4432ca8f54c487398', + }, +}] +checksums = ['28ae8ab4825afca103db8c90d79f77699186f90fdb3c059875975e880e70be1e'] + +builddependencies = [ + ('binutils', '2.37'), +] + +files_to_copy = ['prequal', 'LICENSE'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['prequal'], + 'dirs': [], +} + +moduleclass = 'bio' From 47a94c712748005dd68f65fa681da609bcfa9870 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 14 Jan 2022 17:18:49 +0100 Subject: [PATCH 2652/9987] fix chesum of elbencho v2.0-3 sources --- easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 905272ac462..2b4169ce7ff 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -19,7 +19,7 @@ dependencies = [ github_account = 'breuner' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['f6c34f46b61451bcb1362e73d7754f307ae972c467b135e3279fd477586b5b7d'] +checksums = ['24dc396855d60192252417bd962cf67c4787baba04345c81ff71fe9981777238'] files_to_copy = ["bin"] sanity_check_paths = { From 3b40762d0529566bc576578a455f814dbf0395da Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 14 Jan 2022 17:26:57 +0100 Subject: [PATCH 2653/9987] fix codestyle and add sanity_check_commands to elbencho v2.0-3 --- .../e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 2b4169ce7ff..1ff05206f4b 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -6,7 +6,6 @@ version = "2.0-3" homepage = "https://github.com/breuner/elbencho" description = """ A distributed storage benchmark for files, objects & blocks with support for GPUs""" - toolchain = {'name': 'GCC', 'version': '10.3.0'} dependencies = [ @@ -21,12 +20,15 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['24dc396855d60192252417bd962cf67c4787baba04345c81ff71fe9981777238'] -files_to_copy = ["bin"] +buildopts = 'BUILD_VERBOSE=1 CXXFLAGS_EXTRA="$CXXFLAGS" LDFLAGS_EXTRA="$LDFLAGS"' + +files_to_copy = ['bin'] + sanity_check_paths = { - 'files': ['bin/%s' % x for x in - ['elbencho', 'elbencho-unstripped']], + 'files': 'files': ['bin/%s' % x for x in ['elbencho', 'elbencho-unstripped']], 'dirs': [], } -buildopts = 'BUILD_VERBOSE=1 CXXFLAGS_EXTRA="$CXXFLAGS" LDFLAGS_EXTRA="$LDFLAGS"' +sanity_check_commands = [('elbencho', '--help')] + moduleclass = 'tools' From 26ba0434ee6fe4b1d0360ed7cecaa7a56f6ba9ba Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Fri, 14 Jan 2022 18:36:03 +0200 Subject: [PATCH 2654/9987] Add missing dependecy easyconfig for tn93 --- .../t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e74ef4838b1 --- /dev/null +++ b/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Iñaki Mtz de Ilarduya Muñoz +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'tn93' +version = '1.0.7' + +homepage = 'https://github.com/veg/tn93' +description = """his is a simple program meant to compute pairwise distances between + aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/veg/tn93/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4a088689a23e8dc92d4484431ab0de2a0f5f05109d2a56e7bd55c0cc6459c4db'] + +unpack_options = '--strip-components=1' + +separate_build_dir = True + +buildininstalldir = True + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + + +build_cmd = ' make ' + + +# this is required as the DCMAKE_INSTALL_PREFIX is ignored and the cmake_install.cmake file +# will allways end up with /usr/local as the install prefix +install_cmd = 'mkdir -p %(installdir)s/bin &&' +install_cmd += ' cp {fasta_diff,nucfreqsfasta,readreduce,selectreads,seqcoverage,' +install_cmd += 'ShortestPathTN93,tn93,tn93-cluster,validate_fasta}' +install_cmd += ' %(installdir)s/bin ' + +sanity_check_paths = { + 'files': ['bin/tn93'], + 'dirs': [], +} + +moduleclass = 'bio' From 42d8e25b170a3232a51b7eb8c7a9c261cdea1384 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Fri, 14 Jan 2022 18:37:51 +0200 Subject: [PATCH 2655/9987] Add requested changes: remove pypi urls and add sanity_check_commands --- .../h/hivtrace/hivtrace-0.6.2-foss-2021a.eb | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb index 9137968d933..dc23ffb4a39 100644 --- a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb @@ -28,32 +28,25 @@ sanity_pip_check = True exts_list = [ ('hyphy-python', '0.1.10', { 'modulename': 'HyPhy', - 'source_urls': ['https://pypi.python.org/packages/source/h/hyphy-python'], 'checksums': ['b83f7e890c0c21b301c1c761967bd6328df9fad972653888b02baad71055c186'], }), ('fakemp', '0.9.1', { - 'source_urls': ['https://pypi.python.org/packages/source/f/fakemp'], 'checksums': ['320885d5851e0c568cd4247fa81e48f055e435822643e5bda9d82edc53c3b938'], }), ('hppy', '0.9.9', { - 'source_urls': ['https://pypi.python.org/packages/source/h/hppy'], 'checksums': ['9112acc888c51c14a88669f084a7ebf39fa62bdd47924a1e3cee6824cfbc4610'], }), ('tornado', '6.1', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], }), ('bioext', '0.19.9', { 'modulename': 'BioExt', - 'source_urls': ['https://pypi.python.org/packages/source/b/bioext'], 'checksums': ['bada8d7e83928a8c934e1e482bc945f43a3234c6c4ea3afcef7fa34c0ea610a3'], }), ('hivclustering', '1.6.2', { - 'source_urls': ['https://pypi.python.org/packages/source/h/hivclustering'], 'checksums': ['673fa81b6b44ae7a7bfa32897bc01c26cfe807052aadc3d1f5a729b0df3a335f'], }), (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/h/hivtrace'], 'checksums': ['f4aabd2bbc326aecb9ab22de8f6877628f908cfa8eee458feb06d48bb19425e6'], }), ] @@ -69,4 +62,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + 'hivtrace --help', +] + moduleclass = 'bio' From a1399fd3401dddfa8bc251ba11200e6902a2846d Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 14 Jan 2022 17:39:26 +0100 Subject: [PATCH 2656/9987] adding easyconfigs: canu-2.2-GCCcore-11.2.0.eb --- .../c/canu/canu-2.2-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..946fb4dd038 --- /dev/null +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'canu' +version = '2.2' + +homepage = 'https://canu.readthedocs.io' +description = "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/marbl/canu/releases/download/v%(version)s/'] +sources = ['canu-%(version)s.tar.xz'] +checksums = ['e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404'] + +builddependencies = [ + ('binutils', '2.37'), + # Makefile checks git version, before making (futile) attempt to update git submodules + ('git', '2.33.1', '-nodocs'), +] + +dependencies = [ + ('Java', '11', '', True), + ('Perl', '5.34.0'), + ('gnuplot', '5.4.2'), +] + +start_dir = 'src' + +files_to_copy = ['build/bin', 'build/lib', 'build/share', 'README*'] + +sanity_check_paths = { + 'files': ['bin/bogart', 'bin/canu', 'bin/meryl', 'bin/overlapPair', 'lib/libcanu.a'], + 'dirs': ['lib/site_perl', 'share'], +} +sanity_check_commands = [ + "canu -version", + "canu -options", +] + +moduleclass = 'bio' From 42a6b580b89a393afafa8560ca7611603753900e Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 14 Jan 2022 17:58:27 +0100 Subject: [PATCH 2657/9987] DualSPHysics: Removes bin from sanity_check_path --- .../DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 2 +- .../d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index 46e679af552..45622c59260 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -49,7 +49,7 @@ local_bins = ['GenCase', 'PartVTK', 'IsoSurface', 'MeasureTool', 'GenCase_MkWord sanity_check_paths = { 'files': ['bin/%s_linux64' % x for x in local_bins], - 'dirs': ["lib", "bin"], + 'dirs': ["lib"], } sanity_check_commands = ['%s_linux64 -h' % x for x in local_bins] diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb index 347fbb54bb2..8f34229debc 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -43,7 +43,7 @@ local_bins = ['GenCase', 'PartVTK', 'IsoSurface', 'MeasureTool', 'GenCase_MkWord sanity_check_paths = { 'files': ['bin/%s_linux64' % x for x in local_bins], - 'dirs': ["lib", "bin"], + 'dirs': ["lib"], } sanity_check_commands = ['%s_linux64 -h' % x for x in local_bins] From 737b2c92f8f339e94973abb0e4320282626cd2b7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 14 Jan 2022 18:14:46 +0100 Subject: [PATCH 2658/9987] dont use git_config; add sanity_check_commands --- .../p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb index 971db7cb571..f1e9f015992 100644 --- a/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PREQUAL/PREQUAL-1.02-GCCcore-11.2.0.eb @@ -2,21 +2,20 @@ easyblock = 'MakeCp' name = 'PREQUAL' version = '1.02' +local_commit = '67da42c' homepage = 'https://github.com/simonwhelan/prequal' description = 'A program to identify and mask regions with non-homologous adjacent characters in FASTA files.' toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +github_account = 'simonwhelan' +source_urls = [GITHUB_SOURCE] sources = [{ - 'filename': '%(namelower)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/simonwhelan', - 'repo_name': '%(namelower)s', - 'commit': '67da42cf4761ed5fd8298eb4432ca8f54c487398', - }, + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, }] -checksums = ['28ae8ab4825afca103db8c90d79f77699186f90fdb3c059875975e880e70be1e'] +checksums = ['f0663f6b324dbc6088450f32b3087a2b6ea07138e25850987608b9bb23007d1a'] builddependencies = [ ('binutils', '2.37'), @@ -31,4 +30,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['prequal -h | grep "^Usage:"'] + moduleclass = 'bio' From 1a2754ae694bd6701ff46a26c34207aceb59d778 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Jan 2022 20:02:13 +0100 Subject: [PATCH 2659/9987] adding easyconfigs: mapDamage-2.2.1-foss-2021b.eb, seqtk-1.3-GCC-11.2.0.eb --- .../m/mapDamage/mapDamage-2.2.1-foss-2021b.eb | 30 +++++++++++++++++ .../s/seqtk/seqtk-1.3-GCC-11.2.0.eb | 33 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb new file mode 100644 index 00000000000..1f99a9c4a15 --- /dev/null +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'mapDamage' +version = '2.2.1' + +github_account = 'ginolhac' + +homepage = 'https://ginolhac.github.io/mapDamage/' +description = """mapDamage2 is a computational framework written in Python and + R, which tracks and quantifies DNA damage patterns among ancient DNA + sequencing reads generated by Next-Generation Sequencing platforms.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c'] + +dependencies = [ + ('Python', '3.9.6'), + ('seqtk', '1.3'), + ('Pysam', '0.17.0'), + ('R', '4.1.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.2.0.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..75d5727fb85 --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'seqtk' +version = '1.3' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563'] + +dependencies = [('zlib', '1.2.11')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BINDIR=%(installdir)s/bin/' + +sanity_check_paths = { + 'files': ['bin/seqtk'], + 'dirs': [], +} + +sanity_check_commands = ["seqtk 2>&1 | grep 'Usage:[ ]*seqtk'"] + +moduleclass = 'bio' From aa44433dacf0e565e249cdc26cb0cfc29a39869f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 14 Jan 2022 20:21:30 +0100 Subject: [PATCH 2660/9987] Fix OpenMPI memleak that heavily affects CP2K, SIESTA, QUantumESPRESSO, VASP --- ...MPI-4.0.5-6-pml-ucx-datatype-memleak.patch | 66 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb | 3 + .../o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb | 3 + .../OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 3 + .../o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb | 3 + .../OpenMPI-4.0.5-iccifort-2020.4.304.eb | 3 + .../o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb | 7 +- ...MPI-4.1.0-1-pml-ucx-datatype-memleak.patch | 58 ++++++++++++++++ .../o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 3 + .../o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb | 3 + .../o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 3 + .../OpenMPI-4.1.1-intel-compilers-2021.2.0.eb | 3 + 12 files changed, 157 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch new file mode 100644 index 00000000000..1e5111c47e5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch @@ -0,0 +1,66 @@ +From f5c391288b766a96cb5c5d0b7164e9cf8795921f Mon Sep 17 00:00:00 2001 +From: Sergey Oblomov +Date: Thu, 15 Jul 2021 19:24:40 +0300 +Subject: [PATCH] PML/UCX/DATATYPE: fixed memory leak + +- fixed memory leak in datatype processin + +Signed-off-by: Sergey Oblomov +(cherry picked from commit 4145b9f) +--- + ompi/mca/pml/ucx/pml_ucx_datatype.c | 28 +++++++++++++++++----------- + 1 file changed, 17 insertions(+), 11 deletions(-) + +diff --git a/ompi/mca/pml/ucx/pml_ucx_datatype.c b/ompi/mca/pml/ucx/pml_ucx_datatype.c +index 5b1b8ccbed3..7277aef64bc 100644 +--- a/ompi/mca/pml/ucx/pml_ucx_datatype.c ++++ b/ompi/mca/pml/ucx/pml_ucx_datatype.c +@@ -212,14 +212,23 @@ ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + ompi_datatype_type_size(datatype, &size); + PML_UCX_ASSERT(size > 0); + ucp_datatype = ucp_dt_make_contig(size); +- goto out; +- } +- +- status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, +- datatype, &ucp_datatype); +- if (status != UCS_OK) { +- PML_UCX_ERROR("Failed to create UCX datatype for %s", datatype->name); +- ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); ++ PML_UCX_VERBOSE(7, "created contig UCX datatype 0x%"PRIx64, ++ ucp_datatype) ++ } else { ++ status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, ++ datatype, &ucp_datatype); ++ if (status != UCS_OK) { ++ int err = MPI_ERR_INTERN; ++ PML_UCX_ERROR("Failed to create UCX datatype for %s", ++ datatype->name); ++ /* TODO: this error should return to the caller and invoke an error ++ * handler from the MPI API call. ++ * For now, it is fatal. */ ++ ompi_mpi_errors_are_fatal_comm_handler(NULL, &err, ++ "Failed to allocate " ++ "datatype structure"); ++ } ++ PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) + } + + /* Add custom attribute, to clean up UCX resources when OMPI datatype is +@@ -238,8 +247,6 @@ ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); + } + } +-out: +- PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) + + #ifdef HAVE_UCP_REQUEST_PARAM_T + UCS_STATIC_ASSERT(sizeof(datatype->pml_data) >= sizeof(pml_ucx_datatype_t*)); +@@ -249,7 +256,6 @@ ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + #else + datatype->pml_data = ucp_datatype; + #endif +- + return ucp_datatype; + } + diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb index 110d6438af5..1536146190d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb index 63cf6be8173..c399450ab49 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb index 503f955baf2..383370dd6f5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -13,12 +13,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb index 12093c5a847..3746daadf8e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb index d33ec82375b..de0f5b3d2e1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb index 98875b6d1cf..cfb51234ef4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.6-GCC-10.3.0.eb @@ -8,11 +8,16 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch'] +patches = [ + 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', +] checksums = [ '8f2d159d2d846979b1380e9552f56e4365f5ec71d54a05077ddb244719d70fc3', # openmpi-4.0.6.tar.gz # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', + # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch + '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch new file mode 100644 index 00000000000..29266832b1b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch @@ -0,0 +1,58 @@ +From 080e54b07d5976407daf8c607a5d2b80ee40684d Mon Sep 17 00:00:00 2001 +From: Sergey Oblomov +Date: Mon, 19 Apr 2021 16:50:46 +0300 +Subject: [PATCH] PML/UCX/DATATYPE: fixed memory leak + +- fixed memory leak in datatype processing + +Signed-off-by: Sergey Oblomov +(cherry picked from commit 4145b9f00b9a9c2e5326044b765ee3d1b743ccbf) +--- + ompi/mca/pml/ucx/pml_ucx_datatype.c | 27 +++++++++++++++++---------- + 1 file changed, 17 insertions(+), 10 deletions(-) + +diff --git a/ompi/mca/pml/ucx/pml_ucx_datatype.c b/ompi/mca/pml/ucx/pml_ucx_datatype.c +index 5b1b8ccbed3..8b55e773e7a 100644 +--- a/ompi/mca/pml/ucx/pml_ucx_datatype.c ++++ b/ompi/mca/pml/ucx/pml_ucx_datatype.c +@@ -212,14 +212,23 @@ ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + ompi_datatype_type_size(datatype, &size); + PML_UCX_ASSERT(size > 0); + ucp_datatype = ucp_dt_make_contig(size); +- goto out; +- } +- +- status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, +- datatype, &ucp_datatype); +- if (status != UCS_OK) { +- PML_UCX_ERROR("Failed to create UCX datatype for %s", datatype->name); +- ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); ++ PML_UCX_VERBOSE(7, "created contig UCX datatype 0x%"PRIx64, ++ ucp_datatype) ++ } else { ++ status = ucp_dt_create_generic(&pml_ucx_generic_datatype_ops, ++ datatype, &ucp_datatype); ++ if (status != UCS_OK) { ++ int err = MPI_ERR_INTERN; ++ PML_UCX_ERROR("Failed to create UCX datatype for %s", ++ datatype->name); ++ /* TODO: this error should return to the caller and invoke an error ++ * handler from the MPI API call. ++ * For now, it is fatal. */ ++ ompi_mpi_errors_are_fatal_comm_handler(NULL, &err, ++ "Failed to allocate " ++ "datatype structure"); ++ } ++ PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) + } + + /* Add custom attribute, to clean up UCX resources when OMPI datatype is +@@ -238,8 +247,6 @@ ucp_datatype_t mca_pml_ucx_init_datatype(ompi_datatype_t *datatype) + ompi_mpi_abort(&ompi_mpi_comm_world.comm, 1); + } + } +-out: +- PML_UCX_VERBOSE(7, "created generic UCX datatype 0x%"PRIx64, ucp_datatype) + + #ifdef HAVE_UCP_REQUEST_PARAM_T + UCS_STATIC_ASSERT(sizeof(datatype->pml_data) >= sizeof(pml_ucx_datatype_t*)); diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index 084adbc63ff..b82c542c424 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', + 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a', # openmpi-4.1.0.tar.gz @@ -20,6 +21,8 @@ checksums = [ # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch + # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb index 2728bb55635..2953c5af9f4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb @@ -14,6 +14,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' + 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -21,6 +22,8 @@ checksums = [ 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', + # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index d1e63535d53..593e8e3be27 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -13,6 +13,7 @@ patches = [ 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.1.1_opal-pmix-package-rank.patch', 'OpenMPI-4.1.1_pmix3x-protection.patch', + 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -22,6 +23,8 @@ checksums = [ '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', '04353672cf7be031e5306c94068d7012d99e6cd94b69d93230797ffcd7f31903', # OpenMPI-4.1.1_opal-pmix-package-rank.patch '384ef9f1fa803b0d71dae2ec0748d0f20295992437532afedf21478bda164ff8', # OpenMPI-4.1.1_pmix3x-protection.patch + # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb index 6d64daf9054..05a6b8d93de 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb @@ -14,6 +14,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' + 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -21,6 +22,8 @@ checksums = [ 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', + # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', ] builddependencies = [ From cfb07b7a45dd9e747629f47956f03632dfc5bd2f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 14 Jan 2022 20:51:51 +0100 Subject: [PATCH 2661/9987] and missing trailing comma (,) --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb | 2 +- .../o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb index 2953c5af9f4..57c38134baa 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb @@ -13,7 +13,7 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', - 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' + 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb index 05a6b8d93de..523bf0bb069 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb @@ -13,7 +13,7 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', - 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch' + 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ From 3d73b6266a3b5914573451b732e3a565f71591a4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 15 Jan 2022 01:24:28 +0100 Subject: [PATCH 2662/9987] fix sanity checks of elbencho v2.0-3 --- easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb index 1ff05206f4b..2465c26d165 100644 --- a/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/e/elbencho/elbencho-2.0-3-GCC-10.3.0.eb @@ -25,7 +25,7 @@ buildopts = 'BUILD_VERBOSE=1 CXXFLAGS_EXTRA="$CXXFLAGS" LDFLAGS_EXTRA="$LDFLAGS" files_to_copy = ['bin'] sanity_check_paths = { - 'files': 'files': ['bin/%s' % x for x in ['elbencho', 'elbencho-unstripped']], + 'files': ['bin/%s' % x for x in ['elbencho', 'elbencho-unstripped']], 'dirs': [], } From 7235f3c4cdb0671e96782918db743cb35fc9e72d Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Sat, 15 Jan 2022 13:13:21 +0200 Subject: [PATCH 2663/9987] Add requested changes to the easyconfig --- .../t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4f9cb55bea9 --- /dev/null +++ b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Iñaki Mtz de Ilarduya Muñoz +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'TN93' +version = '1.0.7' + +homepage = 'https://github.com/veg/tn93' +description = """This is a simple program meant to compute pairwise distances between + aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/veg/tn93/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4a088689a23e8dc92d4484431ab0de2a0f5f05109d2a56e7bd55c0cc6459c4db'] + +unpack_options = '--strip-components=1' + +separate_build_dir = True + +buildininstalldir = True + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +build_cmd = ' make ' + +# this is required as the DCMAKE_INSTALL_PREFIX is ignored and the cmake_install.cmake file +# will allways end up with /usr/local as the install prefix +install_cmd = 'mkdir -p %(installdir)s/bin &&' +install_cmd += ' cp {fasta_diff,nucfreqsfasta,readreduce,selectreads,seqcoverage,' +install_cmd += 'ShortestPathTN93,tn93,tn93-cluster,validate_fasta}' +install_cmd += ' %(installdir)s/bin ' + +sanity_check_paths = { + 'files': ['bin/tn93'], + 'dirs': [], +} + +sanity_check_commands = [ + 'tn93 -v', +] + +moduleclass = 'bio' From 8ecf6f50395db18b35f3391b79abe62f7b62e662 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 13:15:54 +0100 Subject: [PATCH 2664/9987] no need to specify source_urls in matplotlib easyconfig, PythonPackage will automatically download from PyPI --- .../m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb index 57137691145..895aa8edc50 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-2.2.5-foss-2021b-Python-2.7.18.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Cycler', '0.10.0', { 'modulename': 'cycler', From 6088691847e431648f90ded6ba659d8a0772b87b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 13:31:37 +0100 Subject: [PATCH 2665/9987] set $GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS for installing grcpio extension included with TensorFlow 2.5.0+ --- .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 1 + .../t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index a3949214369..b7a9a39b865 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -86,6 +86,7 @@ exts_list = [ ('grpcio', '1.34.1', { 'modulename': 'grpc', 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 9794ccd9035..c1662ad3a3b 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -88,6 +88,7 @@ exts_list = [ ('grpcio', '1.34.1', { 'modulename': 'grpc', 'checksums': ['1c746a3cd8a830d8d916a9d0476a786aaa98c5cc2a096344af2be955e439f8ac'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index a364baf0775..18197cfebe6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -88,6 +88,7 @@ exts_list = [ ('grpcio', '1.39.0', { 'modulename': 'grpc', 'checksums': ['57974361a459d6fe04c9ae0af1845974606612249f467bbd2062d963cb90f407'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), # Required for tensorboard_plugin_profile ('gviz-api', '1.9.0', { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb index 60b3de282bc..cb0493abde2 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb @@ -84,6 +84,7 @@ exts_list = [ ('grpcio', '1.39.0', { 'modulename': 'grpc', 'checksums': ['57974361a459d6fe04c9ae0af1845974606612249f467bbd2062d963cb90f407'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), # Required for tensorboard_plugin_profile ('gviz-api', '1.9.0', { From 1aeacbefbe0db9bc848f8070283a3d7283457d42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 13:36:47 +0100 Subject: [PATCH 2666/9987] set for installing grcpio extension included with TensorFlow 2.2.3-2.4.1 with 2020* toolchain --- .../easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb | 1 + .../t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb | 1 + .../t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 1 + 5 files changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb index 9678677ff31..a41e6874956 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.3-foss-2020b.eb @@ -95,6 +95,7 @@ exts_list = [ ('grpcio', '1.39.0', { 'modulename': 'grpc', 'checksums': ['57974361a459d6fe04c9ae0af1845974606612249f467bbd2062d963cb90f407'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb index 77a1ccd97e0..2cfb8444ca4 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb @@ -86,6 +86,7 @@ exts_list = [ ('grpcio', '1.33.1', { 'modulename': 'grpc', 'checksums': ['f19782ec5104599382a0f73f2dfea465d0e65f6818bb3c49ca672b97034c64c3'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb index 1d255bd3b4b..5cae5dc8c13 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb @@ -88,6 +88,7 @@ exts_list = [ ('grpcio', '1.32.0', { 'modulename': 'grpc', 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index 2c463ccdf36..2342aee9b61 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -98,6 +98,7 @@ exts_list = [ ('grpcio', '1.32.0', { 'modulename': 'grpc', 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 34a3a4c37f9..ea58071275f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -99,6 +99,7 @@ exts_list = [ ('grpcio', '1.32.0', { 'modulename': 'grpc', 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.9.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', From eef1be11b8b794c86635011469b3008ede6eb1b2 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Sat, 15 Jan 2022 15:46:41 +0200 Subject: [PATCH 2667/9987] Remove incorrectly capitalized easyconfig --- .../t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb | 48 ------------------- 1 file changed, 48 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb deleted file mode 100644 index e74ef4838b1..00000000000 --- a/easybuild/easyconfigs/t/tn93/tn93-1.0.7-GCCcore-10.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# Author: Iñaki Mtz de Ilarduya Muñoz -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = "CMakeMake" - -name = 'tn93' -version = '1.0.7' - -homepage = 'https://github.com/veg/tn93' -description = """his is a simple program meant to compute pairwise distances between - aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -source_urls = ['https://github.com/veg/tn93/archive/refs/tags/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['4a088689a23e8dc92d4484431ab0de2a0f5f05109d2a56e7bd55c0cc6459c4db'] - -unpack_options = '--strip-components=1' - -separate_build_dir = True - -buildininstalldir = True - -builddependencies = [ - ('CMake', '3.20.1'), - ('binutils', '2.36.1'), -] - - -build_cmd = ' make ' - - -# this is required as the DCMAKE_INSTALL_PREFIX is ignored and the cmake_install.cmake file -# will allways end up with /usr/local as the install prefix -install_cmd = 'mkdir -p %(installdir)s/bin &&' -install_cmd += ' cp {fasta_diff,nucfreqsfasta,readreduce,selectreads,seqcoverage,' -install_cmd += 'ShortestPathTN93,tn93,tn93-cluster,validate_fasta}' -install_cmd += ' %(installdir)s/bin ' - -sanity_check_paths = { - 'files': ['bin/tn93'], - 'dirs': [], -} - -moduleclass = 'bio' From 598fec56afb00d4fb4c74a956eaae5090413b96b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 16:16:44 +0100 Subject: [PATCH 2668/9987] update build dependencies for binutils 2.37 with system toolchain (fixes #14727) --- easybuild/easyconfigs/b/Bison/Bison-3.8.2.eb | 29 +++++++++++++++++++ .../easyconfigs/b/binutils/binutils-2.37.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4.eb | 4 +-- 3 files changed, 32 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2.eb new file mode 100644 index 00000000000..22f927345d6 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' + +description = """ + Bison is a general-purpose parser generator that converts an annotated + context-free grammar into a deterministic LR or generalized LR (GLR) parser + employing LALR(1) parser tables. +""" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.37.eb b/easybuild/easyconfigs/b/binutils/binutils-2.37.eb index b0741dccfc4..1a9094ebca7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.37.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.37.eb @@ -13,7 +13,7 @@ checksums = ['c44968b97cd86499efbc4b4ab7d98471f673e5414c554ef54afa930062dbbfcb'] builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.7.6'), + ('Bison', '3.8.2'), # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb index 1beedb7a51c..16d474262c5 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4.eb @@ -19,11 +19,11 @@ checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] # Do not add help2man, it depends on Perl and we do not want Perl at SYSTEM level. # This results in not building man pages for the flex at SYSTEM level. builddependencies = [ - ('Bison', '3.5.3'), + ('Bison', '3.8.2'), ] dependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ] # glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct From 638677eeaebb88facb149cd2c7ed7b4925e88f26 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 17:21:38 +0100 Subject: [PATCH 2669/9987] adding easyconfigs: CP2K-8.2-intel-2021a.eb, Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb, PLUMED-2.7.2-intel-2021a.eb --- .../c/CP2K/CP2K-8.2-intel-2021a.eb | 39 +++++++++++++ .../Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb | 44 +++++++++++++++ .../p/PLUMED/PLUMED-2.7.2-intel-2021a.eb | 56 +++++++++++++++++++ 3 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-8.2-intel-2021a.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-8.2-intel-2021a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-8.2-intel-2021a.eb new file mode 100644 index 00000000000..7db37eaa393 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-8.2-intel-2021a.eb @@ -0,0 +1,39 @@ +## +# Author: Robert Mijakovic +## +name = 'CP2K' +version = '8.2' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2e24768720efed1a5a4a58e83e2aca502cd8b95544c21695eb0de71ed652f20a'] + +dependencies = [ + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '5.1.5'), + ('libxsmm', '1.16.2'), + ('FFTW', '3.3.9'), + ('PLUMED', '2.7.2'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.6'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb new file mode 100644 index 00000000000..47c9ccee72c --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-iimpi-2021a-lmax-6-cp2k.eb @@ -0,0 +1,44 @@ +name = 'Libint' +version = '2.6.0' +local_lmax = 6 +# custom configuration, to be used as dependency for CP2K +versionsuffix = '-lmax-%s-cp2k' % local_lmax + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/evaleev/libint/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch'] +checksums = [ + '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz + # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch + 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', +] + +builddependencies = [ + ('Autotools', '20210128'), + ('GMP', '6.2.1'), + ('Boost', '1.76.0'), + ('Eigen', '3.3.9'), + ('Python', '2.7.18', '-bare'), +] + +# configure options as required by CP2K, +# see Jenkinsfile in https://github.com/cp2k/libint-cp2k +local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) +local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) + +libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax +libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am +libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--enable-generic-code --disable-unrolling' + +with_fortran = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb new file mode 100644 index 00000000000..fe971797a8e --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.7.2' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['6069bc134f74cb15dd63e27e3587a15a31a9ddd9e7eebdd717da898f31512645'] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.7'), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Boost', '1.76.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From 3c6a9da7f95136df9b07caa4695b8b30fff50476 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 17:28:55 +0100 Subject: [PATCH 2670/9987] add GSL easyconfig that's required for PLUMED with intel-compilers/2021.2.0 --- .../g/GSL/GSL-2.7-intel-compilers-2021.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..0466c9d75b8 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2021.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.7' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' From 397e8c675db268bee60eeb4b34e7c38be6696adc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Jan 2022 13:38:53 +0100 Subject: [PATCH 2671/9987] set $GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS for installing grcpio extension included with Ray-project --- .../r/Ray-project/Ray-project-0.8.4-foss-2019b-Python-3.7.4.eb | 1 + .../Ray-project/Ray-project-1.0.1-fosscuda-2019b-Python-3.7.4.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-0.8.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-0.8.4-foss-2019b-Python-3.7.4.eb index 6726bb26e7a..15d7ae893ef 100644 --- a/easybuild/easyconfigs/r/Ray-project/Ray-project-0.8.4-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-0.8.4-foss-2019b-Python-3.7.4.eb @@ -75,6 +75,7 @@ exts_list = [ ('grpcio', '1.28.1', { 'modulename': 'grpc', 'checksums': ['cbc322c5d5615e67c2a15be631f64e6c2bab8c12505bc7c150948abdaa0bdbac'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('jsonschema', '3.2.0', { 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-1.0.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.0.1-fosscuda-2019b-Python-3.7.4.eb index ea3efe2d1f9..90d60fc1d92 100644 --- a/easybuild/easyconfigs/r/Ray-project/Ray-project-1.0.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.0.1-fosscuda-2019b-Python-3.7.4.eb @@ -121,6 +121,7 @@ exts_list = [ ('grpcio', '1.33.2', { 'modulename': 'grpc', 'checksums': ['21265511880056d19ce4f809ce3fbe2a3fa98ec1fc7167dbdf30a80d3276202e'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('jsonschema', '3.2.0', { 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], From 717d0940f621cdfb34370317a08ae6b865a09ce9 Mon Sep 17 00:00:00 2001 From: Sassy Date: Sat, 15 Jan 2022 18:02:00 +0000 Subject: [PATCH 2672/9987] adding easyconfigs: wtdbg2-2.5-GCCcore-11.2.0.eb --- .../w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a3af9970a46 --- /dev/null +++ b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +# Author:: Michael Dickens - TAMU HPRC - https://hprc.tamu.edu +# Updated to GCC 11.2.0 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'MakeCp' + +name = 'wtdbg2' +version = '2.5' + +homepage = 'https://github.com/ruanjue/wtdbg2' + +description = """ + Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio + or Oxford Nanopore Technologies (ONT). It assembles raw reads without error + correction and then builds the consensus from intermediate assembly output. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/ruanjue/wtdbg2/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a2ffc8503d29f491a9a38ef63230d5b3c96db78377b5d25c91df511d0df06413'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Perl', '5.34.0')] + +prebuildopts = "sed -i 's/CFLAGS=-g3/CFLAGS+=-g3/g' Makefile && " + +local_executables = ['wtdbg2', 'wtdbg2.pl', 'wtpoa-cns', 'kbm2', 'wtdbg-cns', 'pgzf'] + +files_to_copy = [(local_executables, 'bin'), 'README-ori.md', 'README.md', 'scripts'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables], + 'dirs': ['scripts'], +} + +modextrapaths = { + 'PATH': 'scripts', +} + +moduleclass = 'bio' From 0be3abd726a247aa831904255c179833d1f006b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 16 Jan 2022 15:51:44 +0100 Subject: [PATCH 2673/9987] add sanity check command for wtdbg2 + ensure correct shebang in Perl scripts --- easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb index a3af9970a46..c9264b6e795 100644 --- a/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.2.0.eb @@ -31,11 +31,15 @@ local_executables = ['wtdbg2', 'wtdbg2.pl', 'wtpoa-cns', 'kbm2', 'wtdbg-cns', 'p files_to_copy = [(local_executables, 'bin'), 'README-ori.md', 'README.md', 'scripts'] +fix_perl_shebang_for = ['bin/*.pl', 'scripts/*.pl'] + sanity_check_paths = { 'files': ['bin/%s' % x for x in local_executables], 'dirs': ['scripts'], } +sanity_check_commands = ["wtdbg2 --help"] + modextrapaths = { 'PATH': 'scripts', } From cd4bc87213c35242d82d8b495af1b1c72d36ff74 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 16 Jan 2022 16:39:02 +0100 Subject: [PATCH 2674/9987] stick to Java/11 dependency for Bazel 3.7.2 with GCCcore/11.2.0 --- easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index d0148e063b5..8c61b1cbe83 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -29,7 +29,7 @@ builddependencies = [ ('Zip', '3.0'), ] -dependencies = [('Java', '15', '', True)] +dependencies = [('Java', '11', '', True)] runtest = True testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." From 5d4482c1879731199da21231172af5ede4799c9b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 16 Jan 2022 16:19:12 +0000 Subject: [PATCH 2675/9987] Use EB OpenSSL wrapper --- .../easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb index 281c3235c67..7670f76eaa3 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb @@ -18,10 +18,11 @@ dependencies = [ ('zlib', '1.2.11'), # OS dependency should be preferred if the os version is more recent then this version # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.1h'), + # Updated to use EB OpenSSL wrapper + ('OpenSSL', '1.1'), ] -osdependencies = [OS_PKG_OPENSSL_DEV] +#osdependencies = [OS_PKG_OPENSSL_DEV] options = {'modulename': 'DBD::mysql'} From 92127bc4ae35fb8d215a09ecf026a36e78dd53f0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 16 Jan 2022 16:33:17 +0000 Subject: [PATCH 2676/9987] Remove commented OS OpenSSL dep entirely --- easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb index 7670f76eaa3..121c4324cea 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb @@ -22,8 +22,6 @@ dependencies = [ ('OpenSSL', '1.1'), ] -#osdependencies = [OS_PKG_OPENSSL_DEV] - options = {'modulename': 'DBD::mysql'} sanity_check_paths = { From 48e7806e465344c05d30ecfa92b95f0b9da02924 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 16 Jan 2022 16:49:15 +0000 Subject: [PATCH 2677/9987] adding easyconfigs: OpenSSL-1.1.1k-GCCcore-11.2.0.eb --- .../OpenSSL/OpenSSL-1.1.1k-GCCcore-11.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1k-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1k-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1k-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..74c13c6e2c3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1k-GCCcore-11.2.0.eb @@ -0,0 +1,25 @@ +name = 'OpenSSL' +version = '1.1.1k' + +homepage = 'https://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.openssl.org/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['892a0875b9872acd04a9fde79b1f943075d5ea162415de3047c327df33fbaee5'] + +dependencies = [('zlib', '1.2.11')] + +builddependencies = [ + ('Perl', '5.34.0'), + ('binutils', '2.37'), +] + +runtest = 'test' + +moduleclass = 'system' From 03cd2a7fe99fa7f1f52d37cffaf6c0db2f32ba65 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sun, 16 Jan 2022 16:53:19 +0000 Subject: [PATCH 2678/9987] Fixes for OpenSSL wrapper dep --- easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb index 121c4324cea..092262e14f0 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ # OS dependency should be preferred if the os version is more recent then this version # it's nice to have an up to date openssl for security reasons # Updated to use EB OpenSSL wrapper - ('OpenSSL', '1.1'), + ('OpenSSL', '1.1', '', True), ] options = {'modulename': 'DBD::mysql'} From e309526912ca7e7b3fa2d4260ee4adea1a8d9d0e Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 17 Jan 2022 10:10:04 +0100 Subject: [PATCH 2679/9987] adding easyconfigs: PRANK-170427-GCC-11.2.0.eb --- .../p/PRANK/PRANK-170427-GCC-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-11.2.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-11.2.0.eb new file mode 100644 index 00000000000..c14f2efe75a --- /dev/null +++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'PRANK' +version = '170427' + +homepage = 'http://wasabiapp.org/software/prank/' +description = """ PRANK is a probabilistic multiple alignment program for DNA, + codon and amino-acid sequences. PRANK is based on a novel algorithm that treats + insertions correctly and avoids over-estimation of the number of deletion events.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['http://wasabiapp.org/download/prank/'] +sources = ['%(namelower)s.source.%(version)s.tgz'] +checksums = ['623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859'] + +# PRANK uses MAFFT as external tool to construct guide tree +dependencies = [('MAFFT', '7.490', '-with-extensions')] + +start_dir = 'src' + +files_to_copy = [(['prank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/prank'], + 'dirs': [], +} + +sanity_check_commands = ['prank -help'] + +moduleclass = 'bio' From d7fa762d5b3db5aec499261a310e68d99ccf3a43 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Mon, 17 Jan 2022 11:21:11 +0200 Subject: [PATCH 2680/9987] Rename the TN93 dependency on the hivtrace easyconfig --- easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb index dc23ffb4a39..268a172e600 100644 --- a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), ('Biopython', '1.79'), - ('tn93', '1.0.7'), + ('TN93', '1.0.7'), ('cURL', '7.76.0'), ('Pysam', '0.16.0.1'), ] From af9212fd05465cf7bedbef19d376fc2a0faf288f Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Mon, 17 Jan 2022 11:22:11 +0200 Subject: [PATCH 2681/9987] Remove options that are already defaults --- easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb | 8 -------- 1 file changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb index 4f9cb55bea9..91b0a720f20 100644 --- a/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb @@ -18,19 +18,11 @@ source_urls = ['https://github.com/veg/tn93/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['4a088689a23e8dc92d4484431ab0de2a0f5f05109d2a56e7bd55c0cc6459c4db'] -unpack_options = '--strip-components=1' - -separate_build_dir = True - -buildininstalldir = True - builddependencies = [ ('CMake', '3.20.1'), ('binutils', '2.36.1'), ] -build_cmd = ' make ' - # this is required as the DCMAKE_INSTALL_PREFIX is ignored and the cmake_install.cmake file # will allways end up with /usr/local as the install prefix install_cmd = 'mkdir -p %(installdir)s/bin &&' From 741398e3ef869c055c55b12fbdade085bfe2bc52 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 17 Jan 2022 11:16:44 +0100 Subject: [PATCH 2682/9987] fix easybuild url in header/comments --- easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb | 2 +- easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb index 268a172e600..5aeb814708a 100644 --- a/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/hivtrace/hivtrace-0.6.2-foss-2021a.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Iñaki Mtz de Ilarduya Muñoz # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics diff --git a/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb index 91b0a720f20..911f6914c26 100644 --- a/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/TN93/TN93-1.0.7-GCCcore-10.3.0.eb @@ -1,4 +1,4 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Iñaki Mtz de Ilarduya Muñoz # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics From 03f412eb5c6f2ae99d4af63374b90262eb7f6a3b Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Jan 2022 12:01:27 +0100 Subject: [PATCH 2683/9987] Bump of nbconvert to version 6.4.0. The previous version, nbconvert 6.1.0, could cause permission denied errors when run in a shared environment. See https://github.com/jupyter/nbconvert/issues/1430 . This was fixed in PR https://github.com/jupyter/nbconvert/pull/1646 . Since many EasyBuild users work in shared environments, I think this is a relevant fix to have included. --- .../easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb index 27ff87d5da0..0ecf20cc339 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb @@ -90,8 +90,8 @@ exts_list = [ ('nbclient', '0.5.3', { 'checksums': ['db17271330c68c8c88d46d72349e24c147bb6f34ec82d8481a8f025c4d26589c'], }), - ('nbconvert', '6.1.0', { - 'checksums': ['d22a8ff202644d31db254d24d52c3a96c82156623fcd7c7f987bba2612303ec9'], + ('nbconvert', '6.4.0', { + 'checksums': ['5412ec774c6db4fccecb8c4ba07ec5d37d6dcf5762593cb3d6ecbbeb562ebbe5'], }), ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], From 525c6d5c68c453fd5fa7bc631903b099e5abfabb Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Jan 2022 12:05:25 +0100 Subject: [PATCH 2684/9987] Also bump the version of nbconvert in IPython-7.26-0-GCCcore-11.2.0.eb --- .../easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb index 86c05a433f2..b8a2d71f584 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb @@ -90,8 +90,8 @@ exts_list = [ ('nbclient', '0.5.3', { 'checksums': ['db17271330c68c8c88d46d72349e24c147bb6f34ec82d8481a8f025c4d26589c'], }), - ('nbconvert', '6.1.0', { - 'checksums': ['d22a8ff202644d31db254d24d52c3a96c82156623fcd7c7f987bba2612303ec9'], + ('nbconvert', '6.4.0', { + 'checksums': ['5412ec774c6db4fccecb8c4ba07ec5d37d6dcf5762593cb3d6ecbbeb562ebbe5'], }), ('tornado', '6.1', { 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], From fb2feccb6aecfad1b191787c4788ab28e724686b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Jan 2022 12:38:20 +0100 Subject: [PATCH 2685/9987] adding easyconfigs: FDS-6.7.7-intel-2021b.eb --- .../f/FDS/FDS-6.7.7-intel-2021b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.7.7-intel-2021b.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.7.7-intel-2021b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.7.7-intel-2021b.eb new file mode 100644 index 00000000000..cbaea91a5e9 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.7.7-intel-2021b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.7.7' + +homepage = 'https://pages.nist.gov/fds-smv' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['FDS%(version)s.tar.gz'] +checksums = ['0d46348ea1da1ca077c77baeb6dad6643c22508e9964775c96ce642af400dcaf'] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +buildopts = 'impi_intel_linux_64 FFLAGS="$FFLAGS -fpp" FCOMPL="$FC" obj=fds' + +modextrapaths = {'PATH': 'Build'} + +sanity_check_paths = { + 'files': ['Build/fds'], + 'dirs': [], +} + +sanity_check_commands = [ + "fds 2>&1 | grep 'MPI Enabled;'", + "fds 2>&1 | grep 'OpenMP Enabled;'", +] + +moduleclass = 'phys' From 1f02a284fc2a7125b2065c32a0b7a7836c9e3f3c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 17 Jan 2022 13:13:34 +0100 Subject: [PATCH 2686/9987] Newer CMake versions uses the cmake-config files from OS installed boost. Make sure it is not used when looking for the internally built boost. --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb | 2 ++ .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb index 8e067a6bd05..edbae709f1c 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -51,6 +51,8 @@ preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmak configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' +# Make sure CMake doesn't use any system install Boost versions cmake-config files. +configopts += '-DBoost_NO_BOOST_CMAKE=ON ' sanity_check_paths = { 'files': ['bin/bcl2fastq'], diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb index 987778c4625..8d0eda20f5f 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb @@ -51,6 +51,8 @@ preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmak configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' +# Make sure CMake doesn't use any system install Boost versions cmake-config files. +configopts += '-DBoost_NO_BOOST_CMAKE=ON ' sanity_check_paths = { 'files': ['bin/bcl2fastq'], From 34889831e29e5b6f962fcfa8dd3d39936f735e0b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 17 Jan 2022 13:11:13 +0000 Subject: [PATCH 2687/9987] adding easyconfigs: GTK+-3.24.31-GCCcore-11.2.0.eb --- .../g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..bfa11921537 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb @@ -0,0 +1,76 @@ +easyblock = 'Bundle' + +name = 'GTK+' +version = '3.24.31' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('cairo', '1.16.0'), + ('Perl', '5.34.0'), +] +dependencies = [ + ('ATK', '2.36.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.8'), + ('libepoxy', '1.5.8'), + ('X11', '20210802'), + ('FriBidi', '1.0.10'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'checksums': ['423c3e7fdb4c459ee889e35fd4d71fd2623562541c1041b11c07e5ad1ff10bf9'], + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '3.38.0', { + 'preconfigopts': 'autoreconf -f -i && ', + 'source_urls': [FTPGNOME_SOURCE], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + + +moduleclass = 'vis' From cf0bacffd71cadaaf8793eb2f9e3201bdf6e5732 Mon Sep 17 00:00:00 2001 From: Robin Engler Date: Mon, 17 Jan 2022 15:31:57 +0100 Subject: [PATCH 2688/9987] Add patch for hard-coded checksum value of downloaded source file in the source code --- .../easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb | 6 +++++- .../RDKit-2021.03.4_fix-comic-neue-checksum.patch | 11 +++++++++++ 2 files changed, 16 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb index 52be0571bb3..7535a3e2ace 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb @@ -13,10 +13,14 @@ toolchainopts = {'optarch': 'mavx2', 'cstd': 'c++11'} source_urls = ['https://github.com/rdkit/rdkit/archive/'] sources = ['Release_%s.tar.gz' % version.replace('.', '_')] -patches = ['RDKit-%(version)s_skip-broken-test.patch'] +patches = [ + 'RDKit-%(version)s_skip-broken-test.patch', + 'RDKit-2021.03.4_fix-comic-neue-checksum.patch', +] checksums = [ 'bed309df7f1e2ea25736a986cf951325681142ee49468b1c62d020a109d2ef52', # Release_2021_03_4.tar.gz '45869e01461b66e42c9305f5e8a65f696417e4777c2da60ef81d1e26e57d1b2e', # RDKit-2021.03.4_skip-broken-test.patch + '80adeb72eb0e6fac3dcc6cca3c82c1a8fe253025106e0acb7b1135bc4b94a69d', # RDKit-2021.03.4_fix-comic-neue-checksum.patch ] # Dependencies varies from version to version diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch new file mode 100644 index 00000000000..de243222821 --- /dev/null +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch @@ -0,0 +1,11 @@ +--- rdkit-Release_2021_03_4/Code/GraphMol/MolDraw2D/CMakeLists.txt.orig 2022-01-17 13:56:43.780726092 +0100 ++++ rdkit-Release_2021_03_4/Code/GraphMol/MolDraw2D/CMakeLists.txt 2022-01-17 13:57:02.668646178 +0100 +@@ -12,7 +12,7 @@ + set(needDownload "FALSE") + endif() + if(needDownload) +- set(MD5Sum "23ed3f833c1ae0adb141a26b4a30d73e") ++ set(MD5Sum "850b0df852f1cda4970887b540f8f333") + downloadAndCheckMD5("https://fonts.google.com/download?family=Comic%20Neue" + "${CMAKE_CURRENT_SOURCE_DIR}/Comic_Neue.zip" + ${MD5Sum}) From 008e1773d9bb66759895eaa854723589e44e3bcb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Jan 2022 17:25:40 +0200 Subject: [PATCH 2689/9987] add libaio.so.1 to libaio v0.3.112 --- .../l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb | 16 ++++++++++++---- .../l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb | 16 ++++++++++++---- .../l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb | 16 ++++++++++++---- 3 files changed, 36 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb index 699303eba68..1be5c814b95 100644 --- a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'libaio' version = '0.3.112' -local_libversion = '1.0.1' +_libversion = '1.0.1' homepage = 'https://pagure.io/libaio' description = "Asynchronous input/output library that uses the kernels native interface." @@ -16,15 +16,23 @@ checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] builddependencies = [('binutils', '2.35')] +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + files_to_copy = [ - (["src/libaio.a", "src/libaio.%s.%s" % (SHLIB_EXT, local_libversion)], "lib"), + (["src/libaio.a", "src/%s" % _soname], "lib"), (["src/libaio.h"], "include"), ] -postinstallcmds = ["cd %%(installdir)s/lib; ln -s libaio.%s.%s libaio.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT)] +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] sanity_check_paths = { - 'files': ['lib/libaio.a', 'lib/libaio.%s.%s' % (SHLIB_EXT, local_libversion), 'include/libaio.h'], + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb index 076fa063db8..1ae85f5f820 100644 --- a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-10.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'libaio' version = '0.3.112' -local_libversion = '1.0.1' +_libversion = '1.0.1' homepage = 'https://pagure.io/libaio' description = "Asynchronous input/output library that uses the kernels native interface." @@ -16,15 +16,23 @@ checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] builddependencies = [('binutils', '2.36.1')] +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + files_to_copy = [ - (["src/libaio.a", "src/libaio.%s.%s" % (SHLIB_EXT, local_libversion)], "lib"), + (["src/libaio.a", "src/%s" % _soname], "lib"), (["src/libaio.h"], "include"), ] -postinstallcmds = ["cd %%(installdir)s/lib; ln -s libaio.%s.%s libaio.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT)] +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] sanity_check_paths = { - 'files': ['lib/libaio.a', 'lib/libaio.%s.%s' % (SHLIB_EXT, local_libversion), 'include/libaio.h'], + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb index 2d6229d7fea..052974c15a8 100644 --- a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'MakeCp' name = 'libaio' version = '0.3.112' -local_libversion = '1.0.1' +_libversion = '1.0.1' homepage = 'https://pagure.io/libaio' description = "Asynchronous input/output library that uses the kernels native interface." @@ -16,15 +16,23 @@ checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] builddependencies = [('binutils', '2.37')] +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + files_to_copy = [ - (["src/libaio.a", "src/libaio.%s.%s" % (SHLIB_EXT, local_libversion)], "lib"), + (["src/libaio.a", "src/%s" % _soname], "lib"), (["src/libaio.h"], "include"), ] -postinstallcmds = ["cd %%(installdir)s/lib; ln -s libaio.%s.%s libaio.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT)] +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] sanity_check_paths = { - 'files': ['lib/libaio.a', 'lib/libaio.%s.%s' % (SHLIB_EXT, local_libversion), 'include/libaio.h'], + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], 'dirs': [], } From 57d80ed0298fcd9cd0c13ee0dd378f64c88da4ba Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 17 Jan 2022 17:13:15 +0100 Subject: [PATCH 2690/9987] adding easyconfigs: NAMD-2.14-foss-2021a-CUDA-11.3.1.eb --- .../NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ba107970cf1 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,37 @@ +name = 'NAMD' +version = '2.14' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': False, 'openmp': False, 'pic': True} + +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] +sources = [{'filename': 'NAMD_%(version)s_Source.tar.gz'}] +patches = [ + "%(name)s-%(version)s_Linux-POWER-cuda.patch", + "%(name)s-%(version)s-use_system_mremap_decl.patch" +] +checksums = [ + '34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235', # NAMD_2.14_Source.tar.gz + 'db4aeb482dfa805c859ea18940026395763169e0257401ee5341ca550029031c', # NAMD-2.14_Linux-POWER-cuda.patch + 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch +] + +# support for GCC 8+ on POWER +dependencies = [ + ('Tcl', '8.6.11'), + ('CUDA', '11.3.1', '', True), +] + +builddependencies = [ + ('tcsh', '6.22.04'), +] + +charm_arch = "multicore-linux-%(arch)s" +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' From 9fc40d05351e7c84101aedd1129f3212bd6e0a63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Jan 2022 18:24:09 +0100 Subject: [PATCH 2691/9987] adding easyconfigs: MEGA-11.0.10.eb --- easybuild/easyconfigs/m/MEGA/MEGA-11.0.10.eb | 26 ++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGA/MEGA-11.0.10.eb diff --git a/easybuild/easyconfigs/m/MEGA/MEGA-11.0.10.eb b/easybuild/easyconfigs/m/MEGA/MEGA-11.0.10.eb new file mode 100644 index 00000000000..0f42d72cdb7 --- /dev/null +++ b/easybuild/easyconfigs/m/MEGA/MEGA-11.0.10.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'MEGA' +version = '11.0.10' + +homepage = 'https://www.megasoftware.net/' +description = """MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools + for statistics-based comparative analysis of molecular sequence data based on evolutionary principles.""" + +toolchain = SYSTEM + +# download requires agreeing with license & filling out a form, see http://www.megasoftware.net/ +# the following sources correspond to "Other Linux" > "Command Line (CC)" > "MEGA X (64-bit)" +sources = ['megacc_%(version)s_amd64.tar.gz'] +checksums = ['2812969627b3b43110a2e6b597e7c99fb80f4115f05aac5888b01aeda877f4b2'] + +sanity_check_paths = { + 'files': ['megacc'], + 'dirs': ['Examples'], +} + +sanity_check_commands = ["megacc --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From eb3a0e9b4e3a9e4c86f6e43e486c5dea20408b68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Jan 2022 19:22:29 +0100 Subject: [PATCH 2692/9987] add DSS extension to R-bundle-Bioconductor 3.14 --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index 2725d3a7c9f..8227b4c8c80 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1078,6 +1078,12 @@ exts_list = [ ('ExomeDepth', '1.1.15', { 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], }), + ('bsseq', '1.30.0', { + 'checksums': ['2dada40e222d4f42510deeb99c24043078420a4d3d214d4cc3409d428cfb60c4'], + }), + ('DSS', '2.42.0', { + 'checksums': ['b1e2a9044cd10b09ecf667f7a3201269f2dca78ae431cccef6d46816e77dd1a8'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From d383ef07110376a3640c79029997e63b5d140128 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 17 Jan 2022 18:47:26 +0000 Subject: [PATCH 2693/9987] adding easyconfigs: Emacs-27.2-GCCcore-11.2.0.eb --- .../e/Emacs/Emacs-27.2-GCCcore-11.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/e/Emacs/Emacs-27.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-27.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/Emacs/Emacs-27.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..bf9b1902132 --- /dev/null +++ b/easybuild/easyconfigs/e/Emacs/Emacs-27.2-GCCcore-11.2.0.eb @@ -0,0 +1,48 @@ +# +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Robert Mijakovic +# reciPY derived from preexisting reciPy for GCCcore-9.2.0. +# +easyblock = 'ConfigureMake' + +name = 'Emacs' +version = '27.2' + +homepage = 'https://www.gnu.org/software/emacs/' +description = """GNU Emacs is an extensible, customizable text editor--and more. + At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming + language with extensions to support text editing.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['80ff6118fb730a6d8c704dccd6915a6c0e0a166ab1daeef9fe68afa9073ddb73'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('ncurses', '6.2'), + ('LibTIFF', '4.3.0'), + ('X11', '20210802'), + ('GTK+', '3.24.31'), +] + +# If you want to use Emacs plugins you must install the gnutls command line tools +# osdependencies = [('gnutls-utils')] + +configopts = '--with-gif=no --with-tiff=yes --with-x-toolkit=yes --with-xpm=yes --with-gnutls=no ' + +sanity_check_paths = { + 'files': ["bin/emacs", "bin/emacs-%(version)s", "bin/emacsclient", "bin/etags"], + 'dirs': [] +} + +moduleclass = 'tools' From 1f8d5731fc9bdee49a9a127df2c4998dd158e018 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 18 Jan 2022 08:35:39 +0100 Subject: [PATCH 2694/9987] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 9706d2a7224..61b807a25db 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -1,7 +1,7 @@ # EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Max Voit -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'CAFE5' version = '5.0.0' From 22f94dc99221fbdb1be961597e839b0a19295411 Mon Sep 17 00:00:00 2001 From: sdx23 Date: Tue, 18 Jan 2022 08:36:09 +0100 Subject: [PATCH 2695/9987] Update easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb index 61b807a25db..2f7bc2e4c96 100644 --- a/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CAFE5/CAFE5-5.0.0-GCC-10.2.0.eb @@ -25,7 +25,9 @@ sources = [SOURCE_TAR_GZ] checksums = ['9e6dfd27fb915ba927f007e1f851630ff0547589b8196bd5f4606f3b23a78118'] buildopts = 'CFLAGS="$CXXFLAGS -I. -include config.h" LINKER="$CXX $CXXFLAGS -o" ' -install_cmd = 'mkdir %(installdir)s/bin && cp bin/cafe5 %(installdir)s/bin/cafe5 && cp -r examples %(installdir)s' +with_configure = True +files_to_copy = ['bin', 'examples'] +postinstallcmds = ['chmod -x %(installdir)s/examples/*.txt'] sanity_check_paths = { 'files': ['bin/cafe5'], From fc613b43aa50e79dd1ed9bf7da6754dcd73d3063 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Jan 2022 09:35:40 +0100 Subject: [PATCH 2696/9987] add rpact and ldbounds extensions to R v4.1.2 --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index add27951e71..cdede914926 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3202,6 +3202,12 @@ exts_list = [ ('FactorCopula', '0.8', { 'checksums': ['d95b0ccd1b0eebcf27a90286e9392f662b878a669c693fbbb4145798045134ff'], }), + ('rpact', '3.2.1', { + 'checksums': ['d12f9a085163a1745cc7672685dd24e04d27f76998a57835a1ea32e06b637471'], + }), + ('ldbounds', '1.1-1.1', { + 'checksums': ['e88e6bff43762a9f7d80484056d10c7d2fd80969b43061d8cc96c3bd5b9c3583'], + }), ] moduleclass = 'lang' From 30c5bee1afab77549a2e9e5fda9c22a4c7545645 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Jan 2022 12:15:11 +0200 Subject: [PATCH 2697/9987] adding easyconfigs: Arcade-Learning-Environment-0.7.3-foss-2021b.eb --- ...e-Learning-Environment-0.7.3-foss-2021b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.7.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.7.3-foss-2021b.eb b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.7.3-foss-2021b.eb new file mode 100644 index 00000000000..2cf5581c2dc --- /dev/null +++ b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.7.3-foss-2021b.eb @@ -0,0 +1,57 @@ +easyblock = 'CMakeMake' + +name = 'Arcade-Learning-Environment' +version = '0.7.3' + +homepage = 'https://github.com/mgbellemare/Arcade-Learning-Environment' +description = """The Arcade Learning Environment (ALE) is a simple framework that allows +researchers and hobbyists to develop AI agents for Atari 2600 games. It is +built on top of the Atari 2600 emulator Stella and separates the details of +emulation from agent design. This video depicts over 50 games currently +supported in the ALE.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'mgbellemare' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3bada34cc6c116377c4a807c24d9890ce33afa854ffc45e32dc90ba0dcc9140'] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('pybind11', '2.7.1'), + ('SciPy-bundle', '2021.10'), + ('SDL2', '2.0.20'), + ('zlib', '1.2.11'), +] + +# main build of C++ libraries +configopts = "-DBUILD_PYTHON_LIB=OFF" + +# install Python bindings and its dependencies +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('ale-py', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['e3bada34cc6c116377c4a807c24d9890ce33afa854ffc45e32dc90ba0dcc9140'], + 'preinstallopts': "ALE_BUILD_VERSION=%(version)s", + }), +] + +sanity_check_paths = { + 'files': ['bin/ale-import-roms', 'lib64/libale.a'], + 'dirs': ['include/ale', 'lib/python%(pyshortver)s/site-packages/'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'tools' From e7f05a0ecc69252c72814d571a7a71e23ac02819 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 18 Jan 2022 10:25:10 +0000 Subject: [PATCH 2698/9987] Also apply bundle changes to FlexiBLAS w/ GCC 11.2.0 --- .../f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 31 ++++++++++++++++--- 1 file changed, 27 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index 24fbb34505e..cbaf8bd67aa 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -1,3 +1,5 @@ +easyblock = 'Bundle' + name = 'FlexiBLAS' version = '3.0.4' @@ -9,10 +11,6 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} -source_urls = ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'] - builddependencies = [ ('CMake', '3.21.1'), ('Python', '3.9.6'), # required for running the tests @@ -33,4 +31,29 @@ backends = ['OpenBLAS', 'BLIS'] # if ARCH == 'x86_64': # backends.append('imkl') +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'], + }), + ('LAPACK', '3.10.0', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['328c1bea493a32cac5257d84157dc686cc3ab0b004e2bea22044e0a59f6f8a19'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + moduleclass = 'lib' From 2e666c5ac7d64073a6c90d90e4fb51ddac7c0b46 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 18 Jan 2022 11:37:07 +0100 Subject: [PATCH 2699/9987] update build dependencies for binutils 2.34, 2.35, 2.36.1 and GCCcore 9.3.0, 10.1.0, 10.2.0, 10.3.0 and 11.1.0 with system toolchain --- easybuild/easyconfigs/b/binutils/binutils-2.34.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.35.eb | 2 +- easybuild/easyconfigs/b/binutils/binutils-2.36.1.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 2 +- easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.34.eb b/easybuild/easyconfigs/b/binutils/binutils-2.34.eb index 1cf44b64555..a4138107365 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.34.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.34.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.5.3'), + ('Bison', '3.8.2'), # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.35.eb b/easybuild/easyconfigs/b/binutils/binutils-2.35.eb index 61d32277dde..5655c9dbc9e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.35.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.35.eb @@ -19,7 +19,7 @@ checksums = [ builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.7.1'), + ('Bison', '3.8.2'), # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1.eb index 4b38ce2e34e..5f6e42bf744 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.36.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1.eb @@ -13,7 +13,7 @@ checksums = ['e68edeaaeb6ca9687b6dcbaedd1b376506baad2d48de26a885fc5ab6acb839da'] builddependencies = [ ('flex', '2.6.4'), - ('Bison', '3.7.6'), + ('Bison', '3.8.2'), # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb index 8ea3bfbc136..757b0cd9eb8 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb @@ -44,7 +44,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.34'), ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index 98d75b65b5d..d4408b29aa0 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -59,7 +59,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.35'), ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb index b0e0681d116..e34ef9c9972 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb @@ -54,7 +54,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.36.1'), ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index 072a64c40bb..b6a3f957cab 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -50,7 +50,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.36.1'), ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb index 8870f60f1a2..6b1c47aa3c3 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb @@ -56,7 +56,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.34'), ] From aad8d56e68754bd10637bd9b549b411f99250f4a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Jan 2022 12:40:39 +0200 Subject: [PATCH 2700/9987] adding easyconfigs: SDL2-2.0.20-GCCcore-11.2.0.eb --- .../s/SDL2/SDL2-2.0.20-GCCcore-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.20-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.20-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.20-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..07dfacfacbc --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.20-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.20' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c56aba1d7b5b0e7e999e4a7698c70b63a3394ff9704b5f6e1c57e0c16f04dd06'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('X11', '20210802'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From d5108538e59e71d07f4fab328a8d0ec5d0440497 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 18 Jan 2022 11:41:30 +0100 Subject: [PATCH 2701/9987] update build dependencies for GCCcore 9.4.0 with system toolchain --- easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb index aec0247b17e..c02024d4638 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb @@ -48,7 +48,7 @@ checksums = [ ] builddependencies = [ - ('M4', '1.4.18'), + ('M4', '1.4.19'), ('binutils', '2.36.1'), ] From 13f8ccaf5d8e44bd89e1bc4e71b8864a275adbfd Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 18 Jan 2022 11:11:39 +0000 Subject: [PATCH 2702/9987] Update FlexiBLAS-3.0.4-GCC-11.2.0.eb --- .../easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index cbaf8bd67aa..d84be83b2a1 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -26,10 +26,10 @@ dependencies = [ # note: first listed backend will be used as default by FlexiBLAS, # unless otherwise specified via easyconfig parameter flexiblas_default -backends = ['OpenBLAS', 'BLIS'] +local_backends = ['OpenBLAS', 'BLIS'] # if ARCH == 'x86_64': -# backends.append('imkl') +# local_backends.append('imkl') default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} sanity_check_all_components = True @@ -40,6 +40,7 @@ components = [ 'source_urls': ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'], + 'backends': local_backends, }), ('LAPACK', '3.10.0', { 'easyblock': 'CMakeMake', From ba11f6341ba894b6636b02b8d9109507dadcca32 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 18 Jan 2022 12:24:41 +0100 Subject: [PATCH 2703/9987] make sure libxslt does not pick up OS installed libgcrypt or Python --- .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb | 3 +++ .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb | 3 +++ .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb | 3 +++ .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb | 3 +++ .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb | 3 +++ 5 files changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb index 764ee9417e3..d17aa440dc4 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb @@ -23,6 +23,9 @@ dependencies = [ ('libxml2', '2.9.10'), ] +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb index 1fd2e54ea8a..121392cf7dc 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb @@ -23,6 +23,9 @@ dependencies = [ ('libxml2', '2.9.10'), ] +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb index 22a0c0a33e9..705654d4093 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb @@ -23,6 +23,9 @@ dependencies = [ ('libxml2', '2.9.10'), ] +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb index f3c2326d6f8..6097396bc50 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb @@ -23,6 +23,9 @@ dependencies = [ ('libxml2', '2.9.9'), ] +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb index bc98e11869c..f414649f8fe 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb @@ -23,6 +23,9 @@ dependencies = [ ('libxml2', '2.9.10'), ] +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], From 182a5c72938d123347f211563bd167ac643874e1 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Tue, 18 Jan 2022 12:48:05 +0100 Subject: [PATCH 2704/9987] adding easyconfigs: ClustalW2-2.1-GCC-11.2.0.eb --- .../c/ClustalW2/ClustalW2-2.1-GCC-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..602f5e0f704 --- /dev/null +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'ClustalW2' +version = '2.1' + +homepage = 'https://www.ebi.ac.uk/Tools/msa/clustalw2/' +description = """ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.clustal.org/download/%(version)s'] +sources = ['clustalw-%(version)s.tar.gz'] +checksums = ['e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' From 61e9d57b233b11c3aa82ea4ed1ce22a34d6eea55 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 18 Jan 2022 11:50:17 +0000 Subject: [PATCH 2705/9987] Add test exception for bundles with per-component sanity checks --- test/easyconfigs/easyconfigs.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9360159096c..2e6d920d93e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -324,6 +324,8 @@ def check_dep_vars(self, gen, dep, dep_vars): if key not in retained_dep_vars: del dep_vars[key] + version_regex = re.compile('^version: (?P[^;]+);') + # filter out binutils with empty versionsuffix which is used to build toolchain compiler if dep == 'binutils' and len(dep_vars) > 1: empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')] @@ -337,7 +339,7 @@ def check_dep_vars(self, gen, dep, dep_vars): for key in list(dep_vars): ecs = dep_vars[key] # filter out dep variants that are only used as dependency for parent with same version - dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') + dep_ver = version_regex.search(key).group('version') if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: dep_vars.pop(key) @@ -346,7 +348,7 @@ def check_dep_vars(self, gen, dep, dep_vars): for key in list(dep_vars): ecs = dep_vars[key] # filter out Boost variants that are only used as dependency for Boost.Python with same version - boost_ver = re.search('^version: (?P[^;]+);', key).group('ver') + boost_ver = version_regex.search(key).group('version') if all(ec.startswith('Boost.Python-%s-' % boost_ver) for ec in ecs): dep_vars.pop(key) @@ -402,7 +404,7 @@ def check_dep_vars(self, gen, dep, dep_vars): dep = 'CUDA' for key in list(dep_vars): - dep_ver = re.search('^version: (?P[^;]+);', key).group('ver') + dep_ver = version_regex.search(key).group('version') # use version of Java wrapper rather than full Java version if dep == 'Java': dep_ver = '.'.join(dep_ver.split('.')[:2]) @@ -1018,6 +1020,8 @@ def test_pr_sanity_check_paths(self): # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm'] + # also allow bundles that enable per-component sanity checks + bundle_sanity_check_components = ec.get('sanity_check_components') or ec.get('sanity_check_all_components') failing_checks = [] @@ -1028,6 +1032,8 @@ def test_pr_sanity_check_paths(self): if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): pass + elif easyblock == 'Bundle' and bundle_sanity_check_components: + pass else: ec_fn = os.path.basename(ec.path) failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) From d2bb9c843545e9efa258b045551fd91f2d943149 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Tue, 18 Jan 2022 13:02:15 +0100 Subject: [PATCH 2706/9987] adding easyconfigs: MUSCLE-5.1-GCCcore-11.2.0.eb --- .../m/MUSCLE/MUSCLE-5.1-GCCcore-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..804a9ffedf5 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '5.1' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'rcedgar' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['091d9f8733b92ff106c2a8eb274d1e5a57960d397a2068d8638d6002e8880dab'] + +builddependencies = [ + ('binutils', '2.37'), +] + +start_dir = 'src' + +# Use build environment defined by EB +prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&" +buildopts = "CPP=${CXX} CC=${CC}" + +files_to_copy = [(['Linux/muscle'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/muscle'], + 'dirs': [], +} + +sanity_check_commands = [('muscle', '-h')] + +moduleclass = 'bio' From 5fbba8eced5127c8b7c31f015a26aa3001e5557e Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 18 Jan 2022 12:28:37 +0000 Subject: [PATCH 2707/9987] Update easyconfigs.py --- test/easyconfigs/easyconfigs.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2e6d920d93e..be8299ccc06 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1020,8 +1020,6 @@ def test_pr_sanity_check_paths(self): # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm'] - # also allow bundles that enable per-component sanity checks - bundle_sanity_check_components = ec.get('sanity_check_components') or ec.get('sanity_check_all_components') failing_checks = [] @@ -1029,9 +1027,12 @@ def test_pr_sanity_check_paths(self): easyblock = ec.get('easyblock') + bundle_sanity_check_components = ec['sanity_check_components'] or ec['sanity_check_all_components'] + if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): pass + # also allow bundles that enable per-component sanity checks elif easyblock == 'Bundle' and bundle_sanity_check_components: pass else: From b342085f43e9151c719fcc182406467fde3b1e9e Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 18 Jan 2022 12:31:36 +0000 Subject: [PATCH 2708/9987] linting --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index be8299ccc06..3659106ae97 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1028,7 +1028,7 @@ def test_pr_sanity_check_paths(self): easyblock = ec.get('easyblock') bundle_sanity_check_components = ec['sanity_check_components'] or ec['sanity_check_all_components'] - + if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): pass From 3341271411b8421a8b014b47d50772cf694acb52 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Tue, 18 Jan 2022 14:31:19 +0100 Subject: [PATCH 2709/9987] adding easyconfigs: picard-2.26.10-Java-15.eb --- .../p/picard/picard-2.26.10-Java-15.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb diff --git a/easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb b/easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb new file mode 100644 index 00000000000..ab14c148bc1 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb @@ -0,0 +1,56 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.10.1: +# Adam Huffman +# The Francis Crick Institute +# 2.18.11: +# Jonas Demeulemeester +# The Francis Crick Institute +# 2.21.1 +# Pavel Grochal (INUITS) +# 2.25.1 +# J. Sassmannshausen (GSTT) +# 2.25.5 +# Erica Bianco (HPCNow!) +# 2.26.10 +# Christoph Siegert (Leipzig University) +## + +easyblock = 'JAR' + +name = 'picard' +version = '2.26.10' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = [{ + 'filename': '%(name)s-%(version)s.jar', + 'download_filename': '%(name)s.jar', +}] +checksums = ['84a056466cf23155e2126b33fde61b5485217b365d4899c1bdc82fe9284f2395'] + +postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] + +dependencies = [('Java', '15')] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' From d73f326caa8fb7c143384f2b101c731b2a674c65 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Jan 2022 14:31:42 +0100 Subject: [PATCH 2710/9987] Added modextrapaths + fixed shebang for Python --- .../easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb index 20f3e803269..8e52500a1cf 100644 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb @@ -28,15 +28,19 @@ dependencies = [ # remove included old GLPK copy postinstallcmds = ["rm -rf %(installdir)s/glpk-*/*"] +fix_python_shebang_for = ['*.py'] + sanity_check_paths = { 'files': ['MinPath.py'], 'dirs': [], } sanity_check_commands = [ - "python3 MinPath.py -ko examples/demo.ko -report /dev/null -details /dev/null", - "python3 MinPath.py -fig examples/demo.fig -report /dev/null -details /dev/null", - "python3 MinPath.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", + "MinPath.py -ko examples/demo.ko -report /dev/null -details /dev/null", + "MinPath.py -fig examples/demo.fig -report /dev/null -details /dev/null", + "MinPath.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", ] +modextrapaths = {'PATH': ''} + moduleclass = 'bio' From 1b51864209702dabf164546dcbc1f70507cfc980 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 18 Jan 2022 14:44:42 +0000 Subject: [PATCH 2711/9987] Conform to recent split of different GTK+ major release trees --- .../g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..016fad88acf --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb @@ -0,0 +1,76 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.31' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('cairo', '1.16.0'), + ('Perl', '5.34.0'), +] +dependencies = [ + ('ATK', '2.36.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.6'), + ('Pango', '1.48.8'), + ('libepoxy', '1.5.8'), + ('X11', '20210802'), + ('FriBidi', '1.0.10'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'checksums': ['423c3e7fdb4c459ee889e35fd4d71fd2623562541c1041b11c07e5ad1ff10bf9'], + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '3.38.0', { + 'preconfigopts': 'autoreconf -f -i && ', + 'source_urls': [FTPGNOME_SOURCE], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + + +moduleclass = 'vis' From cd024f505ad9c23b148c87ee6ee3452fca443411 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 18 Jan 2022 14:45:42 +0000 Subject: [PATCH 2712/9987] Delete GTK+-3.24.31-GCCcore-11.2.0.eb Remove badly named file --- .../g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb | 76 ------------------- 1 file changed, 76 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb deleted file mode 100644 index bfa11921537..00000000000 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.31-GCCcore-11.2.0.eb +++ /dev/null @@ -1,76 +0,0 @@ -easyblock = 'Bundle' - -name = 'GTK+' -version = '3.24.31' - -homepage = 'https://developer.gnome.org/gtk3/stable/' -description = """GTK+ is the primary library used to construct user interfaces in GNOME. It - provides all the user interface controls, or widgets, used in a common - graphical application. Its object-oriented API allows you to construct - user interfaces without dealing with the low-level details of drawing and - device interaction. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -builddependencies = [ - ('binutils', '2.37'), - ('Autotools', '20210726'), - ('GObject-Introspection', '1.68.0'), - ('gettext', '0.21'), - ('pkg-config', '0.29.2'), - ('cairo', '1.16.0'), - ('Perl', '5.34.0'), -] -dependencies = [ - ('ATK', '2.36.0'), - ('at-spi2-atk', '2.38.0'), - ('Gdk-Pixbuf', '2.42.6'), - ('Pango', '1.48.8'), - ('libepoxy', '1.5.8'), - ('X11', '20210802'), - ('FriBidi', '1.0.10'), -] - -default_easyblock = 'ConfigureMake' - -default_component_specs = { - 'sources': [SOURCELOWER_TAR_XZ], - 'start_dir': '%(namelower)s-%(version)s', -} - -components = [ - (name, version, { - 'source_urls': [FTPGNOME_SOURCE], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", - 'checksums': ['423c3e7fdb4c459ee889e35fd4d71fd2623562541c1041b11c07e5ad1ff10bf9'], - }), - ('hicolor-icon-theme', '0.17', { - 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], - 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], - }), - ('adwaita-icon-theme', '3.38.0', { - 'preconfigopts': 'autoreconf -f -i && ', - 'source_urls': [FTPGNOME_SOURCE], - 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], - 'checksums': [ - '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', - # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch - 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', - ], - }), -] - -postinstallcmds = ['gtk-update-icon-cache'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', - 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', - 'gtk-update-icon-cache']] + - ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], - 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + - ['share/icons/hicolor', 'share/icons/Adwaita'], -} - - -moduleclass = 'vis' From 324ed049a94e999581b3a1de0300ceb57d210985 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 18 Jan 2022 14:48:19 +0000 Subject: [PATCH 2713/9987] use fixed GTK3 dep naming --- easybuild/easyconfigs/e/Emacs/Emacs-27.2-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-27.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/Emacs/Emacs-27.2-GCCcore-11.2.0.eb index bf9b1902132..ccf142dcff1 100644 --- a/easybuild/easyconfigs/e/Emacs/Emacs-27.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/e/Emacs/Emacs-27.2-GCCcore-11.2.0.eb @@ -32,7 +32,7 @@ dependencies = [ ('ncurses', '6.2'), ('LibTIFF', '4.3.0'), ('X11', '20210802'), - ('GTK+', '3.24.31'), + ('GTK3', '3.24.31'), ] # If you want to use Emacs plugins you must install the gnutls command line tools From bbfcdb49c516dcb2f22d0e357b97248adb731b32 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 18 Jan 2022 16:14:44 +0100 Subject: [PATCH 2714/9987] adding easyconfigs: bcl2fastq2-2.20.0-GCC-11.2.0.eb --- .../bcl2fastq2-2.20.0-GCC-11.2.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..3843935b717 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'bcl2fastq2' +version = '2.20.0' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html' +description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by + Illumina sequencing systems to standard FASTQ file formats for downstream analysis.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] +sources = [{ + 'filename': '%s-v%s-tar.zip' % (name, version.replace('.', '-')), + 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz +}] +patches = [ + '%(name)s-%(version)s-fix-cmake-target-libs.patch', + # bcl2fastq2 v2.20.0 is not compatible with recent Boost versions, use bundled Boost + '%(name)s-%(version)s-find-boost.patch', +] +checksums = [ + '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3', # bcl2fastq2-v2-20-0-tar.zip + '7908c268c213a6cfeafe05afcd5d3b34098241b6ab0a62c11ea47664cd0a63c5', # bcl2fastq2-2.20.0-fix-cmake-target-libs.patch + '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1', # bcl2fastq2-2.20.0-find-boost.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), +] + +start_dir = 'src' + +# check versions of libxml2 and libxslt from EB +local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' +local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} +preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} + +# remove hardcoded compilation flags +local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' +preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx + +configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' +configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' +configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' +configopts += '-DBoost_NO_BOOST_CMAKE=ON ' + +sanity_check_paths = { + 'files': ['bin/bcl2fastq'], + 'dirs': ['lib'], +} + +sanity_check_commands = ["bcl2fastq --help"] + +moduleclass = 'bio' From 09c2381a8a4183be49bf34397961c6652dd7581e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 18 Jan 2022 16:35:48 +0100 Subject: [PATCH 2715/9987] add comment to configopt --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb index 3843935b717..cbaad5ae5e9 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb @@ -51,6 +51,7 @@ preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmak configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' +# Make sure CMake doesn't use any system install Boost versions cmake-config files. configopts += '-DBoost_NO_BOOST_CMAKE=ON ' sanity_check_paths = { From f7a8195f7b0990d40e83a40bf4075d380c15f08f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 18 Jan 2022 16:13:32 +0000 Subject: [PATCH 2716/9987] adding easyconfigs: Geant4-11.0.0-GCC-11.2.0.eb, CLHEP-2.4.5.1-GCC-11.2.0.eb --- .../c/CLHEP/CLHEP-2.4.5.1-GCC-11.2.0.eb | 27 +++++++++++++++++++ .../g/Geant4/Geant4-11.0.0-GCC-11.2.0.eb | 26 ++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.5.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-11.0.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.5.1-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.5.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..f856e0369a6 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.5.1-GCC-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.5.1' + +homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] +sources = [SOURCELOWER_TGZ] +checksums = ['2517c9b344ad9f55974786ae6e7a0ef8b22f4abcbf506df91194ea2299ce3813'] + +builddependencies = [('CMake', '3.21.1')] + +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.0.0-GCC-11.2.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-11.0.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..f909ffdb14a --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.0.0-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +name = 'Geant4' +version = '11.0.0' + +homepage = 'https://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'Geant4' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['98959447637fe7acc52b532e39906e6109845f9df11bb2a7439e6024a4c74e33'] + +builddependencies = [('CMake', '3.21.1')] +dependencies = [ + ('expat', '2.4.1'), + # recommended CLHEP version, see https://geant4-data.web.cern.ch/ReleaseNotes/ReleaseNotes.11.0.html + ('CLHEP', '2.4.5.1'), +] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += " -DCLHEP_ROOT_DIR=$EBROOTCLHEP -DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' From be0006d48b55fcc3a68ccb3576feee4214860b6e Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Jan 2022 17:47:07 +0100 Subject: [PATCH 2717/9987] Fixed error + edited patch desc --- .../Short-Pair-20170125-Python3fix.patch | 3 ++- .../Short-Pair/Short-Pair-20170125-foss-2021b.eb | 15 +++++---------- 2 files changed, 7 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch index 4c5da5540cd..75fc857ea70 100644 --- a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch +++ b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-Python3fix.patch @@ -1,5 +1,6 @@ Makes Short-Pair compatible with Phyton3 -Author: Filip Kružík (INUITS) +Created by using already existing version of file from github.com/jtamames/SqueezeMeta (commit 68f8581eef7eb34ffb28ef412fdce1ebf20244b6) +Patch created by: Filip Kružík (INUITS) --- Short-Pair_fix 2022-01-11 17:08:22.763000000 +0100 +++ Short-Pair.py 2022-01-11 17:05:28.709307000 +0100 @@ -1,4 +1,4 @@ diff --git a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb index 8fd96339019..40a6651c00a 100644 --- a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb +++ b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb @@ -10,9 +10,11 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = [SOURCEFORGE_SOURCE] sources = [{'download_filename': 'Short-Pair.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['c8c759cf4cc871180107dd86e397d34787acad33d024debd70710edb437769b3'] - patches = ['Short-Pair-20170125-Python3fix.patch'] +checksums = [ + 'c8c759cf4cc871180107dd86e397d34787acad33d024debd70710edb437769b3', # Short-Pair-20170125.tar.gz + '71f53bea8d1056abf22d35bdb8b87f41fa1482dd4b402e788dbd536e0f6408c0', # Short-Pair-20170125-Python3fix.patch +] dependencies = [ ('Python', '3.9.6'), @@ -20,13 +22,6 @@ dependencies = [ ('SciPy-bundle', '2021.10') ] -exts_list = [ - ('numpy', '1.22.0', { - 'source_urls': ['https://files.pythonhosted.org/packages/50/e1/9b0c184f04b8cf5f3c941ffa56fbcbe936888bdac9aa7ba6bae405ac752b/'], - 'sources': ['%(name)s-%(version)s.zip'], - }) -] - cmds_map = [('.*', "$CXX $CXXFLAGS -w -o DNA2Protein DNA2Protein.cpp")] files_to_copy = [(['DNA2Protein', 'get_hmm.sh', 'hmmer3_pipeline_missing_end.sh', 'Short-Pair.py'], 'bin')] @@ -42,6 +37,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["python3 bin/Short-Pair.py -h"] +sanity_check_commands = ["bin/Short-Pair.py -h"] moduleclass = 'bio' From 6e8dc42e9257a6872a7d3e2c764345a4acc63659 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Jan 2022 19:00:03 +0200 Subject: [PATCH 2718/9987] fix CVE-2021-23437 in Pillow v7 and v8 --- .../matplotlib/matplotlib-3.4.3-foss-2021b.eb | 2 +- .../matplotlib-3.4.3-intel-2021b.eb | 2 +- ...Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb | 6 +++- .../p/Pillow/Pillow-7_CVE-2021-23437.patch | 27 ++++++++++++++++ .../p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 6 +++- .../p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb | 6 +++- .../p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb | 6 +++- .../p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ .../p/Pillow/Pillow-8_CVE-2021-23437.patch | 30 +++++++++++++++++ 9 files changed, 111 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-7_CVE-2021-23437.patch create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-8_CVE-2021-23437.patch diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb index 5eefa7f3e9c..735ad398a7d 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-foss-2021b.eb @@ -21,7 +21,7 @@ dependencies = [ ('libpng', '1.6.37'), ('freetype', '2.11.0'), ('Tkinter', '%(pyver)s'), - ('Pillow', '8.3.1'), + ('Pillow', '8.3.2'), ('Qhull', '2020.2') ] diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb index 51d59ef7c45..2561f744e68 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.3-intel-2021b.eb @@ -21,7 +21,7 @@ dependencies = [ ('libpng', '1.6.37'), ('freetype', '2.11.0'), ('Tkinter', '%(pyver)s'), - ('Pillow', '8.3.1'), + ('Pillow', '8.3.2'), ('Qhull', '2020.2') ] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb index 51e4a86a83a..9fc85ff2e06 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -11,7 +11,11 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '9.3.0'} sources = [SOURCE_TAR_GZ] -checksums = ['4d9ed9a64095e031435af120d3c910148067087541131e82b3e8db302f4c8946'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + '4d9ed9a64095e031435af120d3c910148067087541131e82b3e8db302f4c8946', # Pillow-7.0.0.tar.gz + '8c4195792e3a3581fef80a4cbca39f1123c0b83f74acc002bbbec7185c62baf3', # Pillow-7_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.34')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-7_CVE-2021-23437.patch b/easybuild/easyconfigs/p/Pillow/Pillow-7_CVE-2021-23437.patch new file mode 100644 index 00000000000..747c20f3ae8 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-7_CVE-2021-23437.patch @@ -0,0 +1,27 @@ +Fix for CVE-2021-23437 +author: Hugo van Kemenade (Nord Software) +--- a/src/PIL/ImageColor.py 2020-01-02 09:31:35.000000000 +0100 ++++ b/src/PIL/ImageColor.py 2022-01-18 16:42:11.359922625 +0100 +@@ -32,6 +32,8 @@ + :param color: A color string + :return: ``(red, green, blue[, alpha])`` + """ ++ if len(color) > 100: ++ raise ValueError("color specifier is too long") + color = color.lower() + + rgb = colormap.get(color, None) +--- a/Tests/test_imagecolor.py 2022-01-18 16:42:11.362700436 +0100 ++++ b/Tests/test_imagecolor.py 2022-01-18 17:43:53.880517448 +0100 +@@ -182,3 +182,11 @@ + self.assertEqual((255, 255), ImageColor.getcolor("white", "LA")) + self.assertEqual((163, 33), ImageColor.getcolor("rgba(0, 255, 115, 33)", "LA")) + Image.new("LA", (1, 1), "white") ++ ++def test_color_too_long(): ++ # Arrange ++ color_too_long = "hsl(" + "1" * 100 + ")" ++ ++ # Act / Assert ++ with pytest.raises(ValueError): ++ ImageColor.getrgb(color_too_long) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 9304f308f90..bff212b445d 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -10,7 +10,11 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '10.2.0'} sources = [SOURCE_TAR_GZ] -checksums = ['11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + '11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e', # Pillow-8.0.1.tar.gz + 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb index 198aa646f08..eca48ea8134 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb @@ -10,7 +10,11 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '10.3.0'} sources = [SOURCE_TAR_GZ] -checksums = ['a787ab10d7bb5494e5f76536ac460741788f1fbce851068d73a87ca7c35fc3e1'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + 'a787ab10d7bb5494e5f76536ac460741788f1fbce851068d73a87ca7c35fc3e1', # Pillow-8.2.0.tar.gz + 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb index 32bbaf622c5..3d455621b67 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb @@ -10,7 +10,11 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '11.2.0'} sources = [SOURCE_TAR_GZ] -checksums = ['2cac53839bfc5cece8fdbe7f084d5e3ee61e1303cccc86511d351adcb9e2c792'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + '2cac53839bfc5cece8fdbe7f084d5e3ee61e1303cccc86511d351adcb9e2c792', # Pillow-8.3.1.tar.gz + 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9567cc977dd --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '8.3.2' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['dde3f3ed8d00c72631bc19cbfff8ad3b6215062a5eed402381ad365f82f0c18c'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.11.0') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8_CVE-2021-23437.patch b/easybuild/easyconfigs/p/Pillow/Pillow-8_CVE-2021-23437.patch new file mode 100644 index 00000000000..57504df710a --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8_CVE-2021-23437.patch @@ -0,0 +1,30 @@ +Fix for CVE-2021-23437 +author: Hugo van Kemenade (Nord Software) +diff -rupN --no-dereference Pillow-8.1.2/src/PIL/ImageColor.py Pillow-8.1.2-new/src/PIL/ImageColor.py +--- a/src/PIL/ImageColor.py 2021-03-06 03:38:55.000000000 +0100 ++++ b/src/PIL/ImageColor.py 2021-09-13 08:39:22.289084217 +0200 +@@ -32,6 +32,8 @@ def getrgb(color): + :param color: A color string + :return: ``(red, green, blue[, alpha])`` + """ ++ if len(color) > 100: ++ raise ValueError("color specifier is too long") + color = color.lower() + + rgb = colormap.get(color, None) +diff -rupN --no-dereference Pillow-8.1.2/Tests/test_imagecolor.py Pillow-8.1.2-new/Tests/test_imagecolor.py +--- a/Tests/test_imagecolor.py 2021-03-06 03:38:55.000000000 +0100 ++++ b/Tests/test_imagecolor.py 2021-09-13 08:39:22.289084217 +0200 +@@ -191,3 +191,12 @@ def test_rounding_errors(): + assert (255, 255) == ImageColor.getcolor("white", "LA") + assert (163, 33) == ImageColor.getcolor("rgba(0, 255, 115, 33)", "LA") + Image.new("LA", (1, 1), "white") ++ ++ ++def test_color_too_long(): ++ # Arrange ++ color_too_long = "hsl(" + "1" * 100 + ")" ++ ++ # Act / Assert ++ with pytest.raises(ValueError): ++ ImageColor.getrgb(color_too_long) From 071d475a7d21c3c0c9b6f105c26503865b902644 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Jan 2022 18:22:44 +0100 Subject: [PATCH 2719/9987] Added required changes + patched DAS_Tool to work with BLAST+ by default --- ...AS_Tool-1.1.1-deafaultSearchEngBLAST.patch | 23 +++++++ .../DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb | 11 ++- .../r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb | 67 +++++++++---------- 3 files changed, 64 insertions(+), 37 deletions(-) create mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch new file mode 100644 index 00000000000..6a99fcf0345 --- /dev/null +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch @@ -0,0 +1,23 @@ +Because we are not using USEARCH, this patch will set deafult search engine to used BLAST+ +Author: Filip Kružík (INUITS) + +--- DAS_Tool.orig 2022-01-18 16:13:32.781571000 +0100 ++++ DAS_Tool 2022-01-18 16:15:43.039420000 +0100 +@@ -52,7 +52,7 @@ + echo " -o, --outputbasename Basename of output files." + echo " -l, --labels Comma separated list of binning prediction names. (optional)" + echo " --search_engine Engine used for single copy gene identification [blast/diamond/usearch]." +- echo " (default: usearch)" ++ echo " (default: blast)" + echo " --write_bin_evals Write evaluation for each input bin set [0/1]. (default: 1)" + echo " --create_plots Create binning performance plots [0/1]. (default: 1)" + echo " --write_bins Export bins as fasta files [0/1]. (default: 0)" +@@ -117,7 +117,7 @@ + create_plots=1 + write_bins=0 + write_unbinned=0 +-search_engine="usearch" ++search_engine="blast" + b_weight=0.6 + c_weight=0.5 + db_dir=$DIR\/db diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb index 81cc573725f..cd27a7c4c28 100644 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a'] +patches=['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] +checksums = [ + '2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a', # 1.1.1.tar.gz + 'dc89e6ab7129d170d24da28720cec0937b4d958b5ae46049373d57dde8b8a27a', # DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch +] dependencies = [ ('R', '4.1.2'), @@ -27,10 +31,10 @@ exts_defaultclass = 'RPackage' exts_list = [ (name, version, { + 'modulename': 'DASTool', 'source_tmpl': 'DASTool_%(version)s.tar.gz', 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], - 'modulename': 'DASTool', }), ] @@ -44,10 +48,11 @@ sanity_check_paths = { 'dirs': ['DASTool/R'], } +sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] #Help gets printed correctly, but the error code is 1 + modextrapaths = { 'PATH': '', 'R_LIBS_SITE': '', } - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb index 6e37c235463..e415e258542 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb @@ -24,20 +24,20 @@ exts_default_options = { # each version is picked as high as possible to fullfill all requirements # packages updated on 2021-07-02 exts_list = [ - ('ffi', '1.15.3', { - 'checksums': ['98d5c5c4281c9c0466acc60cf0e79124bf3c311417fd97e7473e41722953fbf1'], + ('ffi', '1.15.5', { + 'checksums': ['6f2ed2fa68047962d6072b964420cba91d82ce6fa8ee251950c17fca6af3c2a0'], }), ('childprocess', '4.1.0', { 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], }), - ('json', '2.5.1', { - 'checksums': ['918d8c41dacb7cfdbe0c7bbd6014a5372f0cf1c454ca150e9f4010fe80cc3153'], + ('json', '2.6.1', { + 'checksums': ['7ff682a2db805d6b924e4e87341c3c0036824713a23c58ca53267ce7e5ce2ffd'], }), ('cabin', '0.9.0', { 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], }), - ('backports', '3.21.0', { - 'checksums': ['f9394457cb1dd5ca1b7bdc0dfbbd8f56f5cde40f45f96bc90f0f895a87e41b77'], + ('backports', '3.23.0', { + 'checksums': ['88fc26a40083a51015faa2ba02cbdc3605cb59f183cf0868f4fb3ac02900148f'], }), ('arr-pm', '0.0.11', { 'checksums': ['f1ab088421276f446da1971c5071defd1504855ec46e196815fa43cd62d61a9f'], @@ -48,17 +48,17 @@ exts_list = [ ('multipart-post', '2.1.1', { 'checksums': ['d2dd7aa957650e0d99e0513cd388401b069f09528441b87d884609c8e94ffcfd'], }), - ('ruby2_keywords', '0.0.4', { - 'checksums': ['3ae3189c2e1d2f60204dcceedf890ff49dd28979771e2576016a3ee73b668e97'], + ('ruby2_keywords', '0.0.5', { + 'checksums': ['ffd13740c573b7301cf7a2e61fc857b2a8e3d3aff32545d6f8300d8bae10e3ef'], }), - ('faraday-net_http', '1.0.1', { - 'checksums': ['3245ce406ebb77b40e17a77bfa66191dda04be2fd4e13a78d8a4305854d328ba'], + ('faraday-net_http', '2.0.1', { + 'checksums': ['f867b028552c3cf018b9293b58b993dc238ba62683568b3e194c673afe62d700'], }), - ('faraday', '1.3.0', { - 'checksums': ['7f06817ba823ddeabf4dd85ca5e0f63e234527f564a03f09f6c7127951d3bac2'], + ('faraday', '1.0.0', { + 'checksums': ['e67631809ae5633a1d2b03adfa83939a91a095f6dc61a1f322826612613dd687'], }), - ('faraday_middleware', '1.0.0', { - 'checksums': ['19e808539681bbf2e65df30dfbe27bb402bde916a1dceb4c7496dbe8de14334a'], + ('faraday_middleware', '1.2.0', { + 'checksums': ['ded15d574d50e92bd04448d5566913af5cb1a01b2fa311ceecc2464fa0ab88af'], }), ('highline', '2.0.3', { 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], @@ -78,17 +78,17 @@ exts_list = [ ('public_suffix', '4.0.6', { 'checksums': ['a99967c7b2d1d2eb00e1142e60de06a1a6471e82af574b330e9af375e87c0cf7'], }), - ('addressable', '2.7.0', { - 'checksums': ['5e9b62fe1239091ea9b2893cd00ffe1bcbdd9371f4e1d35fac595c98c5856cbb'], + ('addressable', '2.8.0', { + 'checksums': ['f76d29d2d1f54b6c6a49aec58f9583b08d97e088c227a3fcba92f6c6531d5908'], }), ('concurrent-ruby', '1.1.9', { 'checksums': ['0ec0846d991c38f355b4228ad8ea77aa69c3fdaa320cd574dafedc10c4688a5b'], }), - ('i18n', '1.8.10', { - 'checksums': ['ca24e52fdd6ad7af419241eef8c41e65ef4e3499c6b252df13f697919eb24e3c'], + ('i18n', '1.8.11', { + 'checksums': ['ae133354590b49070b87c83f8fe8cc064ffdc40ca76364535e100312e30cad6d'], }), - ('minitest', '5.14.4', { - 'checksums': ['f4716634d71b3ffb627cd63ba4f6f0f77c7a3f17353b1bdf52c8a7f2e0e4e7a7'], + ('minitest', '5.15.0', { + 'checksums': ['6d2d5bfa301257ef2c2fe8818abeaa0932ed54735c8ed039459cb4f85029ae1b'], }), ('thread_safe', '0.3.6', { 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], @@ -96,11 +96,11 @@ exts_list = [ ('tzinfo', '1.1.0', { 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], }), - ('zeitwerk', '2.4.2', { - 'checksums': ['f4d6279b0ef0cb35c9e1bddbcecd6b148df82f1cf7b8023ac03d6625f567869c'], + ('zeitwerk', '2.5.3', { + 'checksums': ['ddfeb36d24444b10f402cae2ee5a05c580f54115ae25bcf2ac29bf814c4faf52'], }), - ('activesupport', '5.0.7.2', { - 'checksums': ['f75cc67fb08421bdf4c2a383a47d9b3b02ce5eec4749704b1286fb0c12c98bad'], + ('activesupport', '5.2.6', { + 'checksums': ['7249ee13859fc99ed2c833048674fd28c11605c679f1c65035190a2219e9cbef'], }), ('gh', '0.18.0', { 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], @@ -108,8 +108,8 @@ exts_list = [ ('launchy', '2.5.0', { 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], }), - ('ethon', '0.14.0', { - 'checksums': ['10e267a39d7e2a92d944e5681ba46dbd211b5b5b6cf9b51afb769b8417247ead'], + ('ethon', '0.15.0', { + 'checksums': ['0809805a035bc10f54162ca99f15ded49e428e0488bcfe1c08c821e18261a74d'], }), ('typhoeus', '1.4.0', { 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], @@ -120,11 +120,11 @@ exts_list = [ ('pusher-client', '0.6.2', { 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], }), - ('diff-lcs', '1.4.4', { - 'checksums': ['bf3a658875f70c1467fe7a3b302b795f074c84b28db6e4a2bd6b1ad6d12a2255'], + ('diff-lcs', '1.5.0', { + 'checksums': ['49b934001c8c6aedb37ba19daec5c634da27b318a7a3c654ae979d6ba1929b67'], }), - ('rspec-support', '3.10.2', { - 'checksums': ['74315f89069fbaf2a710e2117340373b77ee45eceb026de87e0cad9dd5154596'], + ('rspec-support', '3.10.3', { + 'checksums': ['65c88f8cbe579461f411097682e6402960eae327eef08e86ef581b8c609e4c5e'], }), ('rspec-mocks', '3.10.2', { 'checksums': ['93fc76e312c3d19cacc1cb2eb64bf82731de2e216295cf2b4d0ce31ba77923b4'], @@ -156,9 +156,8 @@ exts_list = [ ('rack-test', '1.1.0', { 'checksums': ['154161f40f162b1c009a655b7b0c5de3a3102cc6d7d2e94b64e1f46ace800866'], }), - ('bundler', '2.2.21', { - 'checksums': ['3c8dc5e0cf66d385a9b33751e54986290d42023c5e1bba2b5df094917b6e234a'], - }), -] + ('bundler', '2.3.5', { + 'checksums': ['2553cbd138b466bc56a3c724c5c28648dff8e2343b13a7c696cf9c2818c8d629'], + }),] moduleclass = 'lang' From 70f4ad2087effcb61d8fc75b90d5ce5f199d213c Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Jan 2022 19:10:08 +0100 Subject: [PATCH 2720/9987] Fixed style errors --- .../d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb index cd27a7c4c28..4e04c72ff76 100644 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] sources = ['%(version)s.tar.gz'] -patches=['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] +patches = ['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] checksums = [ '2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a', # 1.1.1.tar.gz 'dc89e6ab7129d170d24da28720cec0937b4d958b5ae46049373d57dde8b8a27a', # DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch @@ -48,7 +48,8 @@ sanity_check_paths = { 'dirs': ['DASTool/R'], } -sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] #Help gets printed correctly, but the error code is 1 +sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] +# Help gets printed correctly, but the error code is 1 modextrapaths = { 'PATH': '', From 7abc08ef69de88a00fa1ddf0b86b31f145a34909 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Jan 2022 20:26:28 +0200 Subject: [PATCH 2721/9987] fix checksum of Pillow-8_CVE-2021-23437.patch --- easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index bff212b445d..7bdf2476477 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] checksums = [ '11c5c6e9b02c9dac08af04f093eb5a2f84857df70a7d4a6a6ad461aca803fb9e', # Pillow-8.0.1.tar.gz - 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch ] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb index eca48ea8134..42cbf229337 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] checksums = [ 'a787ab10d7bb5494e5f76536ac460741788f1fbce851068d73a87ca7c35fc3e1', # Pillow-8.2.0.tar.gz - 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch ] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb index 3d455621b67..a9516e2ab73 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_GZ] patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] checksums = [ '2cac53839bfc5cece8fdbe7f084d5e3ee61e1303cccc86511d351adcb9e2c792', # Pillow-8.3.1.tar.gz - 'f68b90453d7080098da91f30e50626638f138533ef064452a40b60fdf98f3326', # Pillow-8_CVE-2021-23437.patch + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch ] builddependencies = [('binutils', '2.37')] From a9fdde4f6c3610e8b8038b7a8b03c5033626e491 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Jan 2022 19:36:47 +0100 Subject: [PATCH 2722/9987] Another style fix --- easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb index e415e258542..dc6ba8f38af 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb @@ -158,6 +158,6 @@ exts_list = [ }), ('bundler', '2.3.5', { 'checksums': ['2553cbd138b466bc56a3c724c5c28648dff8e2343b13a7c696cf9c2818c8d629'], - }),] + })] moduleclass = 'lang' From d102059694268ada421e77fec33e6e1280d3dbd9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 18 Jan 2022 20:05:46 +0100 Subject: [PATCH 2723/9987] adding easyconfigs: Biopython-1.79-intel-2021b.eb --- .../b/Biopython/Biopython-1.79-intel-2021b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.79-intel-2021b.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.79-intel-2021b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.79-intel-2021b.eb new file mode 100644 index 00000000000..c827cb1cdb5 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.79-intel-2021b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.79' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'intel', 'version': '2021b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['edb07eac99d3b8abd7ba56ff4bedec9263f76dfc3c3f450e7d2e2bcdecf8559b'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From a5d5413e8e79d96bcc17ecdcacaebed3af353f87 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 18 Jan 2022 20:06:02 +0100 Subject: [PATCH 2724/9987] adding easyconfigs: networkx-2.6.3-intel-2021b.eb --- .../n/networkx/networkx-2.6.3-intel-2021b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.6.3-intel-2021b.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.6.3-intel-2021b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.6.3-intel-2021b.eb new file mode 100644 index 00000000000..93d150f3264 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.6.3-intel-2021b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.6.3' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c0946ed31d71f1b732b5aaa6da5a0388a345019af232ce2f49c766e2d6795c51'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 0d0d51c9afd127cbafa68c05259114030900dc52 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 18 Jan 2022 20:06:36 +0100 Subject: [PATCH 2725/9987] adding easyconfigs: MDAnalysis-2.0.0-foss-2021b.eb, MDAnalysis-2.0.0-intel-2021b.eb --- .../MDAnalysis/MDAnalysis-2.0.0-foss-2021b.eb | 46 +++++++++++++++++++ .../MDAnalysis-2.0.0-intel-2021b.eb | 46 +++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-intel-2021b.eb diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021b.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021b.eb new file mode 100644 index 00000000000..72caeb550e5 --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '2.0.0' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('Biopython', '1.79'), + ('networkx', '2.6.3'), + ('tqdm', '4.62.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('GridDataFormats', '0.6.0', { + 'modulename': 'gridData', + 'checksums': ['f14e00e8b795f8021f6069935e1133352224775c9bd97f395beb2bcd64a19b86'], + }), + ('gsd', '2.5.1', { + 'checksums': ['76bf228b1d8e95e7d6a334e8cc7712c0bd8c256148007f7ce88a489c21996593'], + }), + ('msgpack', '1.0.3', { + 'checksums': ['51fdc7fb93615286428ee7758cecc2f374d5ff363bdd884c7ea622a7a327a81e'], + }), + ('mmtf-python', '1.1.2', { + 'modulename': 'mmtf', + 'checksums': ['a5caa7fcd2c1eaa16638b5b1da2d3276cbd3ed3513f0c2322957912003b6a8df'], + }), + (name, version, { + 'modulename': name, + 'checksums': ['aa3079d1a82305eba58cf567fac8fc231940184ed88f9a4451be8433f4a06d3e'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-intel-2021b.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-intel-2021b.eb new file mode 100644 index 00000000000..c83b9768742 --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-intel-2021b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '2.0.0' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('Biopython', '1.79'), + ('networkx', '2.6.3'), + ('tqdm', '4.62.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('GridDataFormats', '0.6.0', { + 'modulename': 'gridData', + 'checksums': ['f14e00e8b795f8021f6069935e1133352224775c9bd97f395beb2bcd64a19b86'], + }), + ('gsd', '2.5.1', { + 'checksums': ['76bf228b1d8e95e7d6a334e8cc7712c0bd8c256148007f7ce88a489c21996593'], + }), + ('msgpack', '1.0.3', { + 'checksums': ['51fdc7fb93615286428ee7758cecc2f374d5ff363bdd884c7ea622a7a327a81e'], + }), + ('mmtf-python', '1.1.2', { + 'modulename': 'mmtf', + 'checksums': ['a5caa7fcd2c1eaa16638b5b1da2d3276cbd3ed3513f0c2322957912003b6a8df'], + }), + (name, version, { + 'modulename': name, + 'checksums': ['aa3079d1a82305eba58cf567fac8fc231940184ed88f9a4451be8433f4a06d3e'], + }), +] + +moduleclass = 'bio' From 4a48c4a5338d8a652baba6058a9fb06f448e22fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 19 Jan 2022 08:32:05 +0100 Subject: [PATCH 2726/9987] fix typo --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb index cbaad5ae5e9..5369e23685c 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb @@ -51,7 +51,7 @@ preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmak configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' -# Make sure CMake doesn't use any system install Boost versions cmake-config files. +# Make sure CMake doesn't use any system installed Boost versions cmake-config files. configopts += '-DBoost_NO_BOOST_CMAKE=ON ' sanity_check_paths = { From b7b2f1bf96463fb92c83c4fc23a7022f9f75778a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Jan 2022 08:49:29 +0100 Subject: [PATCH 2727/9987] only check sanity_check_components and sanity_check_all_components when Bundle easyblock is used in test_pr_sanity_check_paths --- test/easyconfigs/easyconfigs.py | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3659106ae97..89afb89a610 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1024,18 +1024,20 @@ def test_pr_sanity_check_paths(self): failing_checks = [] for ec in self.changed_ecs: - easyblock = ec.get('easyblock') + if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): - bundle_sanity_check_components = ec['sanity_check_components'] or ec['sanity_check_all_components'] + sanity_check_ok = False - if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): - pass + sanity_check_ok = True + # also allow bundles that enable per-component sanity checks - elif easyblock == 'Bundle' and bundle_sanity_check_components: - pass - else: + elif easyblock == 'Bundle': + if ec['sanity_check_components'] or ec['sanity_check_all_components']: + sanity_check_ok = True + + if not sanity_check_ok: ec_fn = os.path.basename(ec.path) failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) From 769ac4250a5287042cb0058d31d062f86bc4adbf Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 19 Jan 2022 11:17:14 +0100 Subject: [PATCH 2728/9987] adding easyconfigs: FoBiS-3.0.5-GCCcore-10.3.0.eb --- .../BeautifulSoup-4.10.0-GCCcore-10.3.0.eb | 34 ++++++++++++ .../f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb | 52 +++++++++++++++++++ .../f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb | 38 ++++++++++++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3c7c67ff170 --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.10.0' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1') +] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.3.1', { + 'checksums': ['b8d49b1cd4f037c7082a9683dfa1801aa2597fb11c3a1155b7a5b94829b4f1f9'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['c23ad23c521d818955a4151a67d81580319d4bf548d3d49f4223ae041ff98891'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f85c40e8755 --- /dev/null +++ b/easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'FORD' +version = '6.1.6' + +homepage = 'https://github.com/Fortran-FOSS-Programmers/ford/wiki' +description = 'FORD is an automatic documentation generator for modern Fortran programs' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Graphviz', '2.47.2',), + ('BeautifulSoup', '4.10.0'), + ('tqdm', '4.61.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('graphviz', '0.19.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['09ed0cde452d015fe77c4845a210eb642f28d245f5bc250d4b97808cb8f49078'], + }), + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('markdown-include', '0.6.0', { + 'checksums': ['6f5d680e36f7780c7f0f61dca53ca581bd50d1b56137ddcd6353efafa0c3e4a2'], + }), + ('md-environ', '0.1.0', { + 'checksums': ['fe3c2a255af523d6f522831c699336cd71f9d543714067d93206ed35836f1793'], + }), + ('toposort', '1.7', { + 'checksums': ['ddc2182c42912a440511bd7ff5d3e6a1cabc3accbc674a3258c8c41cbfbb2125'], + }), + (name, version, { + 'checksums': ['c286206e6ce8c12f2e00f6c73e3b76dae830dce7b5b6f52a54512585fcfae12a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ford'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..06c9257d5bf --- /dev/null +++ b/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'FoBiS' +version = '3.0.5' + +homepage = 'https://github.com/szaghi/FoBiS' +description = "A Fortran Building System for automatic building modern Fortran projects" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +dependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), + ('BeautifulSoup', '4.10.0'), + ('FORD', '6.1.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('PreForM.py', '1.1.3', { + 'modulename': 'PreForM', + 'checksums': ['420457c236801e8803f4e8b8c7e44a7b65a5becc11d5d75404da537b1e09f3a8'], + }), + ('configparser', '5.2.0', { + 'checksums': ['1b35798fdf1713f1c3139016cfcbc461f09edbf099d1fb658d4b7479fcaa3daa'], + }), + ('FoBiS.py', version, { + 'modulename': 'fobis', + 'checksums': ['ef23fde4199277abc693d539a81e0728571c349174da6b7476579f82482ab96c'], + }), +] + +moduleclass = 'devel' From e6432c4eeb153145388a1f32a64803dfc1ed46a5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 19 Jan 2022 12:01:11 +0000 Subject: [PATCH 2729/9987] Update easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb Update `adwaita-icon-theme` and fix URL Co-authored-by: Alex Domingo --- easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb index 016fad88acf..f4bdb729cdb 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb @@ -49,12 +49,12 @@ components = [ 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], }), - ('adwaita-icon-theme', '3.38.0', { + ('adwaita-icon-theme', '40.1.1', { 'preconfigopts': 'autoreconf -f -i && ', - 'source_urls': [FTPGNOME_SOURCE], + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], 'checksums': [ - '6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97', + '0b6c436ed6ad9887a88ada1f72a0197b1eb73b020d8d344abab4c7fa7250f8f6', # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', ], From 0c5b8bbbf804baff327baf8db93d7fee36855eae Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 19 Jan 2022 12:34:26 +0000 Subject: [PATCH 2730/9987] adding easyconfigs: Boost.Python-1.77.0-GCC-11.2.0.eb --- .../Boost.Python-1.77.0-GCC-11.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.77.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.77.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.77.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..e1ad4714d4c --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.77.0-GCC-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.77.0' + +homepage = 'https://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['5347464af5b14ac54bb945dc68f1dd7c56f0dad7262816b956138fc53bcc0131'] + +dependencies = [ + ('Boost', version), + ('Python', '3.9.6'), +] + +only_python_bindings = True + +moduleclass = 'lib' From dbb62fdb9d556f0919f00b31bbbcca23c0229a0f Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 19 Jan 2022 14:09:32 +0100 Subject: [PATCH 2731/9987] adding easyconfigs: Pindel-0.2.5b9-20170508-GCC-11.2.0.eb --- .../Pindel-0.2.5b9-20170508-GCC-11.2.0.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.2.0.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.2.0.eb new file mode 100644 index 00000000000..55ba0880a4c --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.2.0.eb @@ -0,0 +1,57 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +## + +easyblock = 'CmdCp' + +name = 'Pindel' +# no official release provided for version 0.2.5b9 (20160729), +# therefore, pull last commit (20170508) to this version from master repo +version = '0.2.5b9-20170508' + +homepage = 'http://gmt.genome.wustl.edu/packages/pindel/' +description = """ Pindel can detect breakpoints of large deletions, medium sized + insertions, inversions, tandem duplications and other structural variants at single-based + resolution from next-gen sequence data. It uses a pattern growth approach to identify the + breakpoints of these variants from paired-end short reads. """ + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/genome/pindel/archive/'] +sources = [{ + 'filename': 'v%(version)s.zip', + 'download_filename': 'b706fba61c64a11fb1d3716d501fd2f4d8992e29.zip' +}] + +# apply changes made in https://github.com/genome/pindel/pull/64 to fix compilation error +patches = ['%(name)s-%(version)s_fix-ambig-abs-compil-err.patch'] + +checksums = [ + 'd1dec65e157e2018fc827a90579caf27d096a9e3e798fd715b44470fe920361a', # v0.2.5b9-20170508.zip + '216ae1145fd1568ac2187a89bf4b95c45d5c02272047a3dd5f9dfbede26c8fec', # patch +] + +dependencies = [ + ('HTSlib', '1.14'), + ('zlib', '1.2.11') +] + +cmds_map = [('.*', "./INSTALL ${EBROOTHTSLIB}")] + +files_to_copy = [ + (['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), + "demo", + "test", + "README.md", +] + +sanity_check_paths = { + 'files': ['bin/pindel', 'bin/sam2pindel', 'bin/pindel2vcf', 'bin/bam2pindel.pl'], + 'dirs': [], +} + +moduleclass = 'bio' From 01212a095786ed4fb2a644529782818e6d50338d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 15:34:44 +0200 Subject: [PATCH 2732/9987] adding easyconfigs: OpenCV-4.5.5-foss-2021b-contrib.eb --- .../OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb | 84 +++++++++++++++++++ 1 file changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb new file mode 100644 index 00000000000..5b3d0e27351 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb @@ -0,0 +1,84 @@ +name = 'OpenCV' +version = '4.5.5' +versionsuffix = '-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [ + {'source_urls': ['https://github.com/opencv/opencv/archive/'], + 'download_filename': '%(version)s.zip', 'filename': SOURCELOWER_ZIP}, + {'source_urls': ['https://github.com/opencv/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', 'filename': '%(namelower)s_contrib-%(version)s.zip'}, + {'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + 'fb16b734db3a28e5119d513bd7c61ef417edf3756165dc6259519bb9d23d04e2', # opencv-4.5.5.zip + 'f53a0e531b2e284d2d1af013f5d96a86dfc1165d71eb47ddc9e7b834cc803091', # opencv_contrib-4.5.5.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.2'), + ('freetype', '2.11.0'), + ('HarfBuzz', '2.8.2'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.0'), + ('OpenEXR', '3.1.1'), + ('JasPer', '2.0.33'), + ('Java', '11', '', True), + ('ant', '1.10.11', '-Java-%(javaver)s', True), + ('GLib', '2.69.1'), + ('GTK3', '3.24.31'), + ('HDF5', '1.12.1'), # needed by hdf from contrib +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules ' +configopts += '-DFREETYPE_FOUND=ON ' +configopts += '-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/ ' +configopts += '-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DHARFBUZZ_FOUND=ON ' +configopts += '-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz ' +configopts += '-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DBUILD_opencv_python2=OFF ' + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (l, SHLIB_EXT) for l in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' From a616e7f48a97ac8b317eec0c3439813eb33105c0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 15:35:43 +0200 Subject: [PATCH 2733/9987] adding easyconfigs: imageio-2.13.5-foss-2021b.eb --- .../i/imageio/imageio-2.13.5-foss-2021b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.13.5-foss-2021b.eb diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.13.5-foss-2021b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.13.5-foss-2021b.eb new file mode 100644 index 00000000000..224177afe57 --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.13.5-foss-2021b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.13.5' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c7ec2be58e401b6eaa838f8eaf8368ed54b2de4a1b001fe6551644f1a30a843d'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Pillow', '8.3.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From d7330bfdd54b7c4e664985f2aaddb234fbe7b352 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 15:36:19 +0200 Subject: [PATCH 2734/9987] adding easyconfigs: MuJoCo-2.1.1-GCCcore-11.2.0.eb, mujoco-py-2.1.2.14-foss-2021b.eb and patches: mujoco-py-2.1.2.14_fix-builder.patch --- .../m/MuJoCo/MuJoCo-2.1.1-GCCcore-11.2.0.eb | 52 ++++++++++++++++ .../mujoco-py-2.1.2.14-foss-2021b.eb | 49 +++++++++++++++ .../mujoco-py-2.1.2.14_fix-builder.patch | 60 +++++++++++++++++++ 3 files changed, 161 insertions(+) create mode 100644 easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.1.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb create mode 100644 easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder.patch diff --git a/easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.1.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..bd16b561c41 --- /dev/null +++ b/easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.1.1-GCCcore-11.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PackedBinary' + +name = 'MuJoCo' +version = '2.1.1' + +homepage = 'https://mujoco.org/' +description = """MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose +physics engine that aims to facilitate research and development in robotics, +biomechanics, graphics and animation, machine learning, and other areas which +demand fast and accurate simulation of articulated structures interacting with +their environment.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/deepmind/mujoco/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-linux-%(arch)s.tar.gz'] +checksums = [ + { + '%(namelower)s-%(version)s-linux-aarch64.tar.gz': + '83949d7d159b3b958153efcd62d3c7c9b160917b37a19cacda95c2cb1f0dda19', + '%(namelower)s-%(version)s-linux-x86_64.tar.gz': + 'd422720fc53f161992b264847d6173eabbe3a3710aa0045d68738ee942f3246e', + '%(namelower)s-%(version)s-linux-ppc64le.tar.gz': + '1075785e6a737ed3072decac4c1d44db692d6f20843496dacb59196af06957b0', + } +] + +# MuJoCo bundles 3 variants of glew using non-standard sonames: +# - libglew with GLX +# - libglewegl with EGL +# - libglewosmesa with OSMESA +# Softare depending on MuJoCo expect these non-standard sonames, so they should not be removed +# - libglew and libglewegl seem to work with Mesa and X11 in this toolchain +# - libglewosmesa has to be replaced as it links to an old libOSMesa + +dependencies = [ + ('glew', '2.2.0', '-osmesa'), +] + +postinstallcmds = [ + "ln -sf $EBROOTGLEW/lib64/libGLEW.so %(installdir)s/lib/libglewosmesa.so", +] + +sanity_check_paths = { + 'files': ['bin/basic', 'bin/derivative', 'bin/record', 'bin/simulate', + 'lib/libmujoco.%s' % SHLIB_EXT, 'lib/libmujoco_nogl.%s' % SHLIB_EXT], + 'dirs': ['include', 'model', 'sample'], +} + +sanity_check_commands = ['basic'] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb new file mode 100644 index 00000000000..0eb967d4bf8 --- /dev/null +++ b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'mujoco-py' +version = '2.1.2.14' + +homepage = 'https://github.com/openai/mujoco-py' +description = """MuJoCo is a physics engine for detailed, efficient rigid body simulations with +contacts. mujoco-py allows using MuJoCo from Python 3.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('patchelf', '0.13'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('GLFW', '3.3.4'), + ('imageio', '2.13.5'), + ('MuJoCo', '2.1.1'), +] + +use_pip = True + +exts_list = [ + ('glfw', '2.5.0', { + 'checksums': ['52544a4a512ba7f829f809759a458d6bbf801565769cf88b4e1c359a4493ebb1'], + }), + ('fasteners', '0.17.2', { + 'checksums': ['2aceacb2bd618ce8526676f7a3e84ea25d0165ef10abb574a45b4a9c07292d2e'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_fix-builder.patch'], + 'preinstallopts': 'MUJOCO_PY_MUJOCO_PATH=$EBROOTMUJOCO', + 'checksums': [ + 'eb5b14485acf80a3cf8c15f4b080c6a28a9f79e68869aa696d16cbd51ea7706f', # mujoco-py-2.1.2.14.tar.gz + '892dac4810a83def104debb4593189beafcfb4379bb07bd18347fe4b1c14adc1', # mujoco-py-2.1.2.14_fix-builder.patch + ], + }), +] + +sanity_pip_check = True + +modluafooter = """ +setenv("MUJOCO_PY_MUJOCO_PATH", os.getenv("EBROOTMUJOCO")) +""" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder.patch b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder.patch new file mode 100644 index 00000000000..1fcac91641e --- /dev/null +++ b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder.patch @@ -0,0 +1,60 @@ +Fix path to MuJoCo libraries in mujoco-py builder +author: Alex Domingo (Vrije Universiteit Brussel) +--- a/mujoco_py/builder.py 2022-01-18 01:36:26.458344000 +0100 ++++ b/mujoco_py/builder.py 2022-01-18 01:36:37.646121008 +0100 +@@ -67,7 +67,7 @@ + The easy solution is to `import mujoco_py` _before_ `import glfw`. + ''') + +- lib_path = os.path.join(mujoco_path, "bin") ++ lib_path = os.path.join(mujoco_path, "lib") + if sys.platform == 'darwin': + Builder = MacExtensionBuilder + elif sys.platform == 'linux': +@@ -177,8 +177,8 @@ + + # Fix the rpath of the generated library -- i lost the Stackoverflow + # reference here +- from_mujoco_path = '@executable_path/libmujoco210.dylib' +- to_mujoco_path = '%s/libmujoco210.dylib' % mj_bin_path ++ from_mujoco_path = '@executable_path/libmujoco.dylib' ++ to_mujoco_path = '%s/libmujoco.dylib' % mj_bin_path + subprocess.check_call(['install_name_tool', + '-change', + from_mujoco_path, +@@ -213,7 +213,7 @@ + join(mujoco_path, 'include'), + np.get_include(), + ], +- libraries=['mujoco210'], ++ libraries=['mujoco'], + library_dirs=[join(mujoco_path, 'bin')], + extra_compile_args=[ + '-fopenmp', # needed for OpenMP +@@ -277,7 +277,7 @@ + def _build_impl(self): + so_file_path = super()._build_impl() + # Removes absolute paths to libraries. Allows for dynamic loading. +- fix_shared_library(so_file_path, 'libmujoco210.so', 'libmujoco210.so') ++ fix_shared_library(so_file_path, 'libmujoco.so', 'libmujoco.so') + fix_shared_library(so_file_path, 'libglewosmesa.so', 'libglewosmesa.so') + return so_file_path + +@@ -296,7 +296,7 @@ + so_file_path = super()._build_impl() + fix_shared_library(so_file_path, 'libOpenGL.so', 'libOpenGL.so.0') + fix_shared_library(so_file_path, 'libEGL.so', 'libEGL.so.1') +- fix_shared_library(so_file_path, 'libmujoco210.so', 'libmujoco210.so') ++ fix_shared_library(so_file_path, 'libmujoco.so', 'libmujoco.so') + fix_shared_library(so_file_path, 'libglewegl.so', 'libglewegl.so') + return so_file_path + +@@ -483,7 +483,7 @@ + ffibuilder.set_source(name, source_string, + include_dirs=[join(mujoco_path, 'include')], + library_dirs=[join(mujoco_path, 'bin')], +- libraries=['mujoco210']) ++ libraries=['mujoco']) + # Catch compilation exceptions so we can cleanup partial files in that case + try: + library_path = ffibuilder.compile(verbose=True) From c7b076689e2fd6398f1509339d2542bf94625a90 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 15:37:05 +0200 Subject: [PATCH 2735/9987] adding easyconfigs: dask-2022.1.0-foss-2021b.eb, bokeh-2.4.2-foss-2021b.eb --- .../b/bokeh/bokeh-2.4.2-foss-2021b.eb | 38 ++++++++++ .../d/dask/dask-2022.1.0-foss-2021b.eb | 69 +++++++++++++++++++ 2 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-2022.1.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb new file mode 100644 index 00000000000..34b3817fed0 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.2-foss-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.4.2' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), + ('Pillow', '8.3.2'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True + +exts_list = [ + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + (name, version, { + 'checksums': ['f0a4b53364ed3b7eb936c5cb1a4f4132369e394c7ae0a8ef420459410958033d'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2022.1.0-foss-2021b.eb b/easybuild/easyconfigs/d/dask/dask-2022.1.0-foss-2021b.eb new file mode 100644 index 00000000000..fa2c98cbe35 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2022.1.0-foss-2021b.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2022.1.0' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), + ('SciPy-bundle', '2021.10'), + ('bokeh', '2.4.2'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.11.2', { + 'checksums': ['6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33'], + }), + ('locket', '0.2.1', { + 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], + }), + ('partd', '1.2.0', { + 'checksums': ['aa67897b84d522dcbc86a98b942afab8c6aa2f7f677d904a616b74ef5ddbc3eb'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '2.0.0', { + 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + (name, version, { + 'checksums': ['aee6eb6517f13dc00a3cc7ed9e13c728baa5850b8a35a2b93793d593a23ecbb8'], + }), + ('distributed', version, { + 'checksums': ['71caba36b831ae4d4baacd44c702936198f236cae7d422edb50fe36ef5a68156'], + }), + ('dask-mpi', '2021.11.0', { + 'checksums': ['602d2e2d7816a4abc1eb17998e1acc93a43b6f82bf94a6accca169a42de21898'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.7.3', { + 'checksums': ['682d7cc0e6b319b6ab83a7a898680c12e9c77ddc77df380b40041290f55d4e79'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + +moduleclass = 'data' From b35d776897d1f1fa0fdb207890f62ff0fe60f57d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 15:37:48 +0200 Subject: [PATCH 2736/9987] adding easyconfigs: scikit-image-0.19.1-foss-2021b.eb --- .../scikit-image-0.19.1-foss-2021b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.1-foss-2021b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.1-foss-2021b.eb new file mode 100644 index 00000000000..c19b434247b --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.1-foss-2021b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.19.1' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), + ('Pillow', '8.3.2'), + ('networkx', '2.6.3'), + ('dask', '2022.1.0'), + ('imageio', '2.13.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('PyWavelets', '1.2.0', { + 'modulename': 'pywt', + 'checksums': ['6cbd69b047bb4e00873097472133425f5f08a4e6bc8b3f0ae709274d4d5e9a8d'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('tifffile', '2021.11.2', { + 'checksums': ['153e31fa1d892f482fabb2ae9f2561fa429ee42d01a6f67e58cee13637d9285b'], + }), + (name, version, { + 'modulename': 'skimage', + 'checksums': ['48f00ee1e8ec2818ae6a152c72df15f4db7f566e839f5c34e1a0c3c9e5210138'], + }), +] + +moduleclass = 'vis' From 33928b0a1b549655b129eb63124029dfdca82ec0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 15:38:23 +0200 Subject: [PATCH 2737/9987] adding easyconfigs: OpenAI-Gym-0.21.0-foss-2021b.eb --- .../OpenAI-Gym-0.21.0-foss-2021b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.21.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.21.0-foss-2021b.eb b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.21.0-foss-2021b.eb new file mode 100644 index 00000000000..5f13ddc0462 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.21.0-foss-2021b.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'OpenAI-Gym' +version = '0.21.0' + +homepage = 'https://gym.openai.com' +description = "A toolkit for developing and comparing reinforcement learning algorithms." + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('CMake', '3.21.1'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Arcade-Learning-Environment', '0.7.3'), + ('mujoco-py', '2.1.2.14'), + ('OpenCV', '4.5.5', '-contrib'), + ('lz4', '1.9.3'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('pyglet', '1.5.21', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pyglet/pyglet/archive'], + 'checksums': ['7a6fa81e0bffa3bd1349e235e4824e44e26596f226cb60d9f653fe3a8a8d0839'], + }), + ('box2d-py', '2.3.5', { + 'modulename': 'Box2D', + 'checksums': ['b37dc38844bcd7def48a97111d2b082e4f81cca3cece7460feb3eacda0da2207'], + }), + ('lz4', '3.1.10', { + 'checksums': ['439e575ecfa9ecffcbd63cfed99baefbe422ab9645b1e82278024d8a21d9720b'], + }), + ('gym', version, { + 'checksums': ['0fd1ce165c754b4017e37a617b097c032b8c3feb8a0394ccc8777c7c50dddff3'], + 'use_pip_extras': 'all', + }), +] + +local_envs = ['box2d', 'classic_control', 'mujoco', 'robotics', 'toy_text'] +sanity_check_commands = ["python -c 'import gym.envs.%s'" % e for e in local_envs] + +sanity_pip_check = True + +moduleclass = 'tools' From 098811d75b1372efbdee56a3bc28d2cdacce591d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 15:47:02 +0200 Subject: [PATCH 2738/9987] adding easyconfigs: dm-tree-0.1.6-GCCcore-10.2.0.eb, dm-tree-0.1.6-GCCcore-11.2.0.eb --- .../d/dm-tree/dm-tree-0.1.6-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ .../d/dm-tree/dm-tree-0.1.6-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..f4bb5ec6a01 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'dm-tree' +version = '0.1.6' + +homepage = 'https://github.com/deepmind/tree' +description = """dm-tree provides tree, a library for working with nested data structures. In a way, +tree generalizes the builtin map function which only supports flat sequences, and +allows to apply a function to each "leaf" preserving the overall structure.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Bazel', '3.7.2'), +] +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True + +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'tree'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9784dc6a206 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'dm-tree' +version = '0.1.6' + +homepage = 'https://github.com/deepmind/tree' +description = """dm-tree provides tree, a library for working with nested data structures. In a way, +tree generalizes the builtin map function which only supports flat sequences, and +allows to apply a function to each "leaf" preserving the overall structure.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.37'), + ('Bazel', '3.7.2'), +] +dependencies = [('Python', '3.9.6')] + +download_dep_fail = True + +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'tree'} + +moduleclass = 'lib' From ab0a5b03c6a2c23a1ae5ae1e482e131cf63951e0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 15:47:30 +0200 Subject: [PATCH 2739/9987] adding easyconfigs: Flask-2.0.2-GCCcore-11.2.0.eb --- .../f/Flask/Flask-2.0.2-GCCcore-11.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flask/Flask-2.0.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/f/Flask/Flask-2.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/Flask/Flask-2.0.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2057ba93f42 --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-2.0.2-GCCcore-11.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '2.0.2' + +homepage = 'https://www.palletsprojects.com/p/flask/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +builddependencies = [('binutils', '2.37')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('itsdangerous', '2.0.1', { + 'checksums': ['9e724d68fc22902a1435351f84c3fb8623f303fffcc566a4cb952df8c572cff0'], + }), + ('Werkzeug', version, { + 'checksums': ['aa2bb6fc8dee8d6c504c0ac1e7f5f7dc5810a9903e793b6f715a9f015bdadb9a'], + }), + ('asgiref', '3.4.1', { + 'checksums': ['4ef1ab46b484e3c706329cedeff284a5d40824200638503f5768edb6de7d58e9'], + }), + (name, version, { + 'checksums': ['7b2fb8e934ddd50731893bdcdb00fc8c0315916f9fcd50d22c7cc1a95ab634e2'], + }), + ('Flask-Cors', '3.0.10', { + 'checksums': ['b60839393f3b84a0f3746f6cdca56c1ad7426aa738b70d6c61375857823181de'], + }), +] + +sanity_check_paths = { + 'files': ['bin/flask'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['flask --version'] + +moduleclass = 'lib' From dcd36b4b0cf9bf5243079fdb8745862ab36d43d5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 15:49:40 +0200 Subject: [PATCH 2740/9987] adding easyconfigs: gpustat-1.0.0b1-GCCcore-11.2.0.eb --- .../gpustat/gpustat-1.0.0b1-GCCcore-11.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/gpustat/gpustat-1.0.0b1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-1.0.0b1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gpustat/gpustat-1.0.0b1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..805edd2da4f --- /dev/null +++ b/easybuild/easyconfigs/g/gpustat/gpustat-1.0.0b1-GCCcore-11.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'gpustat' +version = '1.0.0b1' + +homepage = 'https://github.com/wookayin/gpustat' +description = "A simple command-line utility for querying and monitoring GPU status" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +# This software works directly against the nvidia drivers and doesn't require CUDA. +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True + +exts_list = [ + ('blessed', '1.19.0', { + 'checksums': ['4db0f94e5761aea330b528e84a250027ffe996b5a94bf03e502600c9a5ad7a61'], + }), + ('nvidia-ml-py3', '7.352.0', { + 'modulename': 'pynvml', + 'checksums': ['390f02919ee9d73fe63a98c73101061a6b37fa694a793abf56673320f1f51277'], + }), + (name, version, { + 'checksums': ['a25c460c5751180265814f457249ba5100baf7a055b23ad762a4e3ab3f6496dd'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gpustat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gpustat --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From 7b911c6c426d56d702a5b2dbaef22724bfee180c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 15:50:51 +0200 Subject: [PATCH 2741/9987] adding easyconfigs: Redis-6.2.6-GCC-10.3.0.eb, Redis-6.2.6-GCC-11.2.0.eb --- .../r/Redis/Redis-6.2.6-GCC-10.3.0.eb | 39 +++++++++++++++++++ .../r/Redis/Redis-6.2.6-GCC-11.2.0.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/r/Redis/Redis-6.2.6-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/r/Redis/Redis-6.2.6-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/r/Redis/Redis-6.2.6-GCC-10.3.0.eb b/easybuild/easyconfigs/r/Redis/Redis-6.2.6-GCC-10.3.0.eb new file mode 100644 index 00000000000..dc92e1ab2ea --- /dev/null +++ b/easybuild/easyconfigs/r/Redis/Redis-6.2.6-GCC-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Redis' +version = '6.2.6' + +homepage = 'https://redis.io' +description = """Redis is an open source (BSD licensed), in-memory data structure store, used as +a database, cache, and message broker. Redis provides data structures such as +strings, hashes, lists, sets, sorted sets with range queries, bitmaps, +hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, +Lua scripting, LRU eviction, transactions, and different levels of on-disk +persistence, and provides high availability via Redis Sentinel and automatic +partitioning with Redis Cluster.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://download.redis.io/releases'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5b2b8b7a50111ef395bf1c1d5be11e6e167ac018125055daa8b5c2317ae131ab'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +skipsteps = ['configure'] + +# tests must be run from a local filesystem +# runtest = 'test' + +installopts = 'PREFIX="%(installdir)s"' + +sanity_check_paths = { + 'files': ['bin/redis-cli', 'bin/redis-server'], + 'dirs': [], +} + +sanity_check_commands = [('redis-server', '--version')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/Redis/Redis-6.2.6-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Redis/Redis-6.2.6-GCC-11.2.0.eb new file mode 100644 index 00000000000..44ff0264189 --- /dev/null +++ b/easybuild/easyconfigs/r/Redis/Redis-6.2.6-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Redis' +version = '6.2.6' + +homepage = 'https://redis.io' +description = """Redis is an open source (BSD licensed), in-memory data structure store, used as +a database, cache, and message broker. Redis provides data structures such as +strings, hashes, lists, sets, sorted sets with range queries, bitmaps, +hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, +Lua scripting, LRU eviction, transactions, and different levels of on-disk +persistence, and provides high availability via Redis Sentinel and automatic +partitioning with Redis Cluster.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://download.redis.io/releases'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5b2b8b7a50111ef395bf1c1d5be11e6e167ac018125055daa8b5c2317ae131ab'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +skipsteps = ['configure'] + +# tests must be run from a local filesystem +# runtest = 'test' + +installopts = 'PREFIX="%(installdir)s"' + +sanity_check_paths = { + 'files': ['bin/redis-cli', 'bin/redis-server'], + 'dirs': [], +} + +sanity_check_commands = [('redis-server', '--version')] + +moduleclass = 'data' From b2ce7f4a714cb41946780cfda0da71e938d71b3f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 15:52:09 +0200 Subject: [PATCH 2742/9987] adding easyconfigs: aiohttp-3.8.1-GCCcore-10.3.0.eb, aiohttp-3.8.1-GCCcore-11.2.0.eb --- .../a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb | 58 +++++++++++++++++++ .../a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb | 51 ++++++++++++++++ 2 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f1b23ce2583 --- /dev/null +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'aiohttp' +version = '3.8.1' + +homepage = 'https://github.com/aio-libs/aiohttp' +description = "Asynchronous HTTP client/server framework for asyncio and Python." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +dependencies = [ + ('Python', '3.9.5'), + ('typing-extensions', '3.10.0.0'), +] + +use_pip = True + +# aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies +exts_list = [ + ('charset-normalizer', '2.0.10', { + 'checksums': ['876d180e9d7432c5d1dfd4c5d26b72f099d503e8fcc0feb7532c9289be60fcbd'], + }), + ('multidict', '5.2.0', { + 'checksums': ['0dd1c93edb444b33ba2274b66f63def8a327d607c6c790772f448a53b6ea59ce'], + }), + ('async-timeout', '4.0.2', { + 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], + }), + ('yarl', '1.7.2', { + 'checksums': ['45399b46d60c253327a460e99856752009fcee5f5d3c80b2f7c0cae1c38d56dd'], + }), + ('frozenlist', '1.2.0', { + 'checksums': ['68201be60ac56aff972dc18085800b6ee07973c49103a8aba669dee3d71079de'], + }), + ('aiosignal', '1.2.0', { + 'checksums': ['78ed67db6c7b7ced4f98e495e572106d5c432a93e1ddd1bf475e1dc05f5b7df2'], + }), + (name, version, { + 'checksums': ['fc5471e1a54de15ef71c1bc6ebe80d4dc681ea600e68bfd1cbce40427f0b7578'], + }), + ('Jinja2', '3.0.3', { + 'checksums': ['611bb273cd68f3b993fabdc4064fc858c5b47a973cb5aa7999ec1ba405c87cd7'], + }), + ('aiohttp-jinja2', '1.5', { + 'checksums': ['7c3ba5eac060b691f4e50534af2d79fca2a75712ebd2b25e6fcb1295859f910b'], + }), + ('hiredis', '2.0.0', { + 'checksums': ['81d6d8e39695f2c37954d1011c0480ef7cf444d4e3ae24bc5e89ee5de360139a'], + }), + ('aioredis', '2.0.1', { + 'checksums': ['eaa51aaf993f2d71f54b70527c440437ba65340588afeb786cd87c55c89cd98e'], + }), + ('aiosignal', '1.2.0', { + 'checksums': ['78ed67db6c7b7ced4f98e495e572106d5c432a93e1ddd1bf475e1dc05f5b7df2'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d7b2ae1978f --- /dev/null +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'aiohttp' +version = '3.8.1' + +homepage = 'https://github.com/aio-libs/aiohttp' +description = "Asynchronous HTTP client/server framework for asyncio and Python." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True + +# aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies +exts_list = [ + ('multidict', '5.2.0', { + 'checksums': ['0dd1c93edb444b33ba2274b66f63def8a327d607c6c790772f448a53b6ea59ce'], + }), + ('async-timeout', '4.0.2', { + 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], + }), + ('yarl', '1.7.2', { + 'checksums': ['45399b46d60c253327a460e99856752009fcee5f5d3c80b2f7c0cae1c38d56dd'], + }), + ('frozenlist', '1.2.0', { + 'checksums': ['68201be60ac56aff972dc18085800b6ee07973c49103a8aba669dee3d71079de'], + }), + ('aiosignal', '1.2.0', { + 'checksums': ['78ed67db6c7b7ced4f98e495e572106d5c432a93e1ddd1bf475e1dc05f5b7df2'], + }), + (name, version, { + 'checksums': ['fc5471e1a54de15ef71c1bc6ebe80d4dc681ea600e68bfd1cbce40427f0b7578'], + }), + ('aiohttp-jinja2', '1.5', { + 'checksums': ['7c3ba5eac060b691f4e50534af2d79fca2a75712ebd2b25e6fcb1295859f910b'], + }), + ('hiredis', '2.0.0', { + 'checksums': ['81d6d8e39695f2c37954d1011c0480ef7cf444d4e3ae24bc5e89ee5de360139a'], + }), + ('aioredis', '2.0.1', { + 'checksums': ['eaa51aaf993f2d71f54b70527c440437ba65340588afeb786cd87c55c89cd98e'], + }), + ('aiosignal', '1.2.0', { + 'checksums': ['78ed67db6c7b7ced4f98e495e572106d5c432a93e1ddd1bf475e1dc05f5b7df2'], + }), +] + +moduleclass = 'lib' From e6972aa6600c78de0d42c1b08d6163569b18cdaf Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 19 Jan 2022 14:58:50 +0100 Subject: [PATCH 2743/9987] adding easyconfigs: Crumble-0.8.3-GCC-11.2.0.eb --- .../c/Crumble/Crumble-0.8.3-GCC-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/Crumble/Crumble-0.8.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/c/Crumble/Crumble-0.8.3-GCC-11.2.0.eb b/easybuild/easyconfigs/c/Crumble/Crumble-0.8.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..738c6c1fff6 --- /dev/null +++ b/easybuild/easyconfigs/c/Crumble/Crumble-0.8.3-GCC-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Crumble' +version = '0.8.3' + +homepage = 'https://github.com/jkbonfield/crumble' +description = """Exploration of controlled loss of quality values for compressing CRAM files""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'jkbonfield' +source_urls = ['https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b1ab503f4c98a83e2c81fec4cf8d951c80957ae05b6a6a19b59ece6caf490c01'] + +dependencies = [ + ('HTSlib', '1.14'), +] + +sanity_check_commands = ['crumble -h'] + +sanity_check_paths = { + 'files': ['bin/crumble'], + 'dirs': ['bin', 'include/crumble'], +} + +moduleclass = 'bio' From 2057e0e244ead67574b6b2dda3c9b094d6ddee4c Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 19 Jan 2022 15:25:13 +0100 Subject: [PATCH 2744/9987] adding easyconfigs: SURVIVOR-1.0.7-19-ged1ca51-GCC-11.2.0.eb --- .../SURVIVOR-1.0.7-19-ged1ca51-GCC-11.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SURVIVOR/SURVIVOR-1.0.7-19-ged1ca51-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SURVIVOR/SURVIVOR-1.0.7-19-ged1ca51-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SURVIVOR/SURVIVOR-1.0.7-19-ged1ca51-GCC-11.2.0.eb new file mode 100644 index 00000000000..e2af663d0cc --- /dev/null +++ b/easybuild/easyconfigs/s/SURVIVOR/SURVIVOR-1.0.7-19-ged1ca51-GCC-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'SURVIVOR' +version = '1.0.7-19-ged1ca51' + +homepage = 'https://github.com/fritzsedlazeck/SURVIVOR' +description = 'Toolset for SV simulation, comparison and filtering' + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'fritzsedlazeck' +source_urls = [GITHUB_SOURCE] +sources = ['ed1ca5188a2d9286d582417b7a65938c768df995.tar.gz'] +checksums = ['46c2618a225353e31422a12e9661167298947ad6ff681943cea6703ba18682bd'] + +start_dir = 'Debug' + +files_to_copy = ['Debug/SURVIVOR'] + +modextrapaths = {'PATH': ''} + +sanity_check_commands = ['SURVIVOR'] + +sanity_check_paths = { + 'files': ['SURVIVOR'], + 'dirs': [], +} + +moduleclass = 'bio' From ebae7e3f55847489bc3e8343d613f58b3a71c3e5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 16:35:12 +0200 Subject: [PATCH 2745/9987] fix toolchain of dm-tree-0.1.6-GCCcore-10.3.0.eb --- .../d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..7bb2df3faf5 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'dm-tree' +version = '0.1.6' + +homepage = 'https://github.com/deepmind/tree' +description = """dm-tree provides tree, a library for working with nested data structures. In a way, +tree generalizes the builtin map function which only supports flat sequences, and +allows to apply a function to each "leaf" preserving the overall structure.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Bazel', '3.7.2'), +] +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True + +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'tree'} + +moduleclass = 'lib' From f48bb20744dc84730e2204c4d04357343642a043 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 16:37:53 +0200 Subject: [PATCH 2746/9987] remove dm-tree-0.1.6-GCCcore-10.2.0.eb --- .../d/dm-tree/dm-tree-0.1.6-GCCcore-10.2.0.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.2.0.eb deleted file mode 100644 index f4bb5ec6a01..00000000000 --- a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.2.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'dm-tree' -version = '0.1.6' - -homepage = 'https://github.com/deepmind/tree' -description = """dm-tree provides tree, a library for working with nested data structures. In a way, -tree generalizes the builtin map function which only supports flat sequences, and -allows to apply a function to each "leaf" preserving the overall structure.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -sources = [SOURCELOWER_TAR_GZ] - -builddependencies = [ - ('binutils', '2.36.1'), - ('Bazel', '3.7.2'), -] -dependencies = [('Python', '3.9.5')] - -download_dep_fail = True - -use_pip = True -sanity_pip_check = True - -options = {'modulename': 'tree'} - -moduleclass = 'lib' From c03731668ca73dbeabfe5bc74cfa668a35a33689 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 19 Jan 2022 15:58:59 +0100 Subject: [PATCH 2747/9987] adding easyconfigs: Racon-1.5.0-GCCcore-11.2.0.eb --- .../r/Racon/Racon-1.5.0-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..437042cff43 --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.5.0' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'lbcb-sci' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['41e362f71cc03b934f17d6e2c0d626e1b2997258261b14551586de006666424a'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' From 8ab2907a1f98a75fe58002eb182d1c1966e90996 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 19 Jan 2022 16:29:45 +0100 Subject: [PATCH 2748/9987] adding easyconfigs: Iris-1.0.5-GCC-11.2.0-Java-15.eb --- .../i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb diff --git a/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb b/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb new file mode 100644 index 00000000000..7edcb19affb --- /dev/null +++ b/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb @@ -0,0 +1,40 @@ +easyblock = 'CmdCp' + +name = 'Iris' +version = '1.0.5' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/mkirsche/Iris' +description = """A module for improving the insertion sequences of structural variant calls""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'mkirsche' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a71718d418fb8b1afacbe2b3a6b91fd50cadc9e12c0b532739b955e455913b0b'] + +dependencies = [ + ('Java', '15', '', True), + ('minimap2', '2.22'), + ('HTSlib', '1.14'), + ('SAMtools', '1.14'), + ('Racon', '1.5.0'), +] + +cmds_map = [('.*', "./build_jar.sh")] + +files_to_copy = [ + 'iris.jar', +] + +modloadmsg = "To execute Iris run: java -jar $EBROOTIRIS/%(name)s.jar" + +sanity_check_commands = ['java -jar $EBROOTIRIS/iris.jar'] + +sanity_check_paths = { + 'files': ['iris.jar'], + 'dirs': [], +} + +moduleclass = 'bio' From 70bfefbaca3fbbfcbbf3792ada7366270e3f36be Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 19 Jan 2022 16:37:32 +0100 Subject: [PATCH 2749/9987] Added required changes --- .../s/Short-Pair/Short-Pair-20170125-foss-2021b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb index 40a6651c00a..5e21f81106f 100644 --- a/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb +++ b/easybuild/easyconfigs/s/Short-Pair/Short-Pair-20170125-foss-2021b.eb @@ -30,13 +30,11 @@ fix_python_shebang_for = ['bin/Short-Pair.py'] postinstallcmds = ["chmod a+rx %(installdir)s/bin/*"] -exts_defaultclass = 'PythonBundle' - sanity_check_paths = { 'files': ['bin/DNA2Protein', 'bin/get_hmm.sh', 'bin/hmmer3_pipeline_missing_end.sh', 'bin/Short-Pair.py'], 'dirs': [], } -sanity_check_commands = ["bin/Short-Pair.py -h"] +sanity_check_commands = ["Short-Pair.py -h"] moduleclass = 'bio' From 7cdbaa111dad5153d455627ed5d2f80532aceedb Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 19 Jan 2022 16:42:26 +0100 Subject: [PATCH 2750/9987] Use lower case for jar name --- easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb b/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb index 7edcb19affb..95b0d643515 100644 --- a/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb +++ b/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb @@ -28,7 +28,7 @@ files_to_copy = [ 'iris.jar', ] -modloadmsg = "To execute Iris run: java -jar $EBROOTIRIS/%(name)s.jar" +modloadmsg = "To execute Iris run: java -jar $EBROOTIRIS/%(namelower)s.jar" sanity_check_commands = ['java -jar $EBROOTIRIS/iris.jar'] From 3f4cbb84633dc3ff4bf329622fc731775229249d Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 19 Jan 2022 16:52:19 +0100 Subject: [PATCH 2751/9987] adding easyconfigs: Jasmine-1.1.4-GCC-11.2.0-Java-15.eb --- .../Jasmine-1.1.4-GCC-11.2.0-Java-15.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb diff --git a/easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb b/easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb new file mode 100644 index 00000000000..811d9481443 --- /dev/null +++ b/easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb @@ -0,0 +1,41 @@ +easyblock = 'CmdCp' + +name = 'Jasmine' +version = '1.1.4' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/mkirsche/Jasmine' +description = """SV Merging Across Samples""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'mkirsche' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b52e13964b41f7659368965cd9e0537b151a6b52cf41dc8634ba67b1384113ec'] + +dependencies = [ + ('Java', '15', '', True), + ('Iris', '1.0.5', versionsuffix), +] + +cmds_map = [('.*', "./build_jar.sh $EBROOTIRIS/iris.jar")] + +files_to_copy = [ + 'jasmine.jar', + 'jasmine_igv.jar', + 'jasmine_split.jar', +] + +modloadmsg = """To execute jasmine run: java -jar $EBROOTJASMINE/%(namelower)s.jar, + java -jar $EBROOTJASMINE/%(namelower)s_igv.jar, or + java -jar $EBROOTJASMINE/%(namelower)s_split.jar""" + +sanity_check_commands = ['java -jar $EBROOTJASMINE/jasmine.jar'] + +sanity_check_paths = { + 'files': ['jasmine.jar', 'jasmine_igv.jar', 'jasmine_split.jar'], + 'dirs': [], +} + +moduleclass = 'bio' From 1fe2dec0786858492ac96e457638bb14fcc1e255 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 19 Jan 2022 17:01:16 +0100 Subject: [PATCH 2752/9987] adding easyconfigs: cutadapt-3.5-GCCcore-11.2.0.eb, python-isal-0.11.1-GCCcore-11.2.0.eb --- .../c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb | 52 +++++++++++++++++++ .../python-isal-0.11.1-GCCcore-11.2.0.eb | 36 +++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..fa1ce928951 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb @@ -0,0 +1,52 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '3.5' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('python-isal', '0.11.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '1.4.0', { + }), + ('dnaio', '0.7.0', { + }), + (name, version, { + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cutadapt --help", + "cutadapt --version", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f78d48e7c9d --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-0.11.1-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '0.11.1' + +homepage = 'https://github.com/pycompression/python-isal' +description = """Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'pycompression' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['43d885814f1ee19f5c3a7e9ada3d696fe75f19c0853728fe0ade564bc021a78f'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('ISA-L', '2.30.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' +installopts = '--no-binary isal' + +options = {'modulename': 'isal'} + +moduleclass = 'lib' From e2c0fd6b0a8817a5086bc84c0aba38cf474ee240 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 19 Jan 2022 17:18:46 +0100 Subject: [PATCH 2753/9987] added checksums --- .../easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb index fa1ce928951..7b7603dba94 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb @@ -32,10 +32,13 @@ sanity_pip_check = True exts_list = [ ('xopen', '1.4.0', { + 'checksums': ['69d6d1d8a18efe49fc3eb51cd558a2a538c6f76495d1732d259016f58b124498'], }), ('dnaio', '0.7.0', { + 'checksums': ['03a370a645a61cd7dfb7591d989faa9426ea3a0691e83c95374c23171206f45c'], }), (name, version, { + 'checksums': ['7b20c0efc28d49333c1aa238af9253c51da0763178c3e2bb5fc338b34765aed4'], }), ] From 62459f9284e416ac2445bfaceb25bab4e0da47f5 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 19 Jan 2022 17:23:34 +0100 Subject: [PATCH 2754/9987] adding easyconfigs: Bowtie-1.3.1-GCC-11.2.0.eb --- .../b/Bowtie/Bowtie-1.3.1-GCC-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..9216676addd --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Artistic v2.0 +# +# Notes:: +## + +name = 'Bowtie' +version = '1.3.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.zip'] +checksums = ['e23517aa53846ef828172be911750cd05748522117efcbbe5a36f3241fb40761'] + +dependencies = [ + ('tbb', '2021.4.0'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' From 669fa6da8d4543d4ea04ebe31707472180f4ccc2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 18:32:32 +0200 Subject: [PATCH 2755/9987] add checksums for dm-tree v0.1.6 --- easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb | 1 + easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-11.2.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb index 7bb2df3faf5..de8beea1496 100644 --- a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-10.3.0.eb @@ -11,6 +11,7 @@ allows to apply a function to each "leaf" preserving the overall structure.""" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} sources = [SOURCELOWER_TAR_GZ] +checksums = ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-11.2.0.eb index 9784dc6a206..d8839c61295 100644 --- a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.6-GCCcore-11.2.0.eb @@ -11,6 +11,7 @@ allows to apply a function to each "leaf" preserving the overall structure.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} sources = [SOURCELOWER_TAR_GZ] +checksums = ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'] builddependencies = [ ('binutils', '2.37'), From 9e333911ca70d4cac60002fcacec64916ace3d33 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 19 Jan 2022 16:36:06 +0000 Subject: [PATCH 2756/9987] fix CVE-2021-23437 in Pillow-SIMD v8 + add Pillow-SIMD v8.3.2 in easyconfigs using a 2021b toolchain --- .../Pillow-SIMD/Pillow-8_CVE-2021-23437.patch | 30 ++++++++++++++ .../Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb | 6 ++- .../Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb | 6 ++- .../Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb | 39 +++++++++++++++++++ 4 files changed, 79 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-8_CVE-2021-23437.patch create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-8_CVE-2021-23437.patch b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-8_CVE-2021-23437.patch new file mode 100644 index 00000000000..57504df710a --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-8_CVE-2021-23437.patch @@ -0,0 +1,30 @@ +Fix for CVE-2021-23437 +author: Hugo van Kemenade (Nord Software) +diff -rupN --no-dereference Pillow-8.1.2/src/PIL/ImageColor.py Pillow-8.1.2-new/src/PIL/ImageColor.py +--- a/src/PIL/ImageColor.py 2021-03-06 03:38:55.000000000 +0100 ++++ b/src/PIL/ImageColor.py 2021-09-13 08:39:22.289084217 +0200 +@@ -32,6 +32,8 @@ def getrgb(color): + :param color: A color string + :return: ``(red, green, blue[, alpha])`` + """ ++ if len(color) > 100: ++ raise ValueError("color specifier is too long") + color = color.lower() + + rgb = colormap.get(color, None) +diff -rupN --no-dereference Pillow-8.1.2/Tests/test_imagecolor.py Pillow-8.1.2-new/Tests/test_imagecolor.py +--- a/Tests/test_imagecolor.py 2021-03-06 03:38:55.000000000 +0100 ++++ b/Tests/test_imagecolor.py 2021-09-13 08:39:22.289084217 +0200 +@@ -191,3 +191,12 @@ def test_rounding_errors(): + assert (255, 255) == ImageColor.getcolor("white", "LA") + assert (163, 33) == ImageColor.getcolor("rgba(0, 255, 115, 33)", "LA") + Image.new("LA", (1, 1), "white") ++ ++ ++def test_color_too_long(): ++ # Arrange ++ color_too_long = "hsl(" + "1" * 100 + ")" ++ ++ # Act / Assert ++ with pytest.raises(ValueError): ++ ImageColor.getrgb(color_too_long) diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb index 07c0c7e731c..23fe713f7d7 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['d966a27bd027d960c62ce5593858b4bf3e98ea44b9f7684a4486086b6f0ea3aa'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + 'd966a27bd027d960c62ce5593858b4bf3e98ea44b9f7684a4486086b6f0ea3aa', # 8.2.0.tar.gz + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb index 9b2bde2adbc..74b967e8926 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['bf77f392094e3bb24ca56ef8bbc4ea0d9752226ff348682d849c0aa8c1577980'] +patches = ['Pillow-%(version_major)s_CVE-2021-23437.patch'] +checksums = [ + 'bf77f392094e3bb24ca56ef8bbc4ea0d9752226ff348682d849c0aa8c1577980', # 8.3.1.tar.gz + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..cea197aa05e --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '8.3.2' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['095bcf74c6e4d36e1e1ff2d7926b83169f0dc29bb6731734c39d3c9522ae81b2'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.11.0') +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From fcc3a744bd698887a44aab28847fa376ea4c9c9a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 19 Jan 2022 18:53:02 +0200 Subject: [PATCH 2757/9987] enable pip sanity checks in aiohttp v3.8.1 --- .../a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb | 10 ++++++---- .../a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb | 2 ++ 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb index f1b23ce2583..cc43a2cb529 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb @@ -38,11 +38,11 @@ exts_list = [ (name, version, { 'checksums': ['fc5471e1a54de15ef71c1bc6ebe80d4dc681ea600e68bfd1cbce40427f0b7578'], }), - ('Jinja2', '3.0.3', { - 'checksums': ['611bb273cd68f3b993fabdc4064fc858c5b47a973cb5aa7999ec1ba405c87cd7'], + ('Jinja2', '2.11.3', { + 'checksums': ['a6d58433de0ae800347cab1fa3043cebbabe8baa9d29e668f1c768cb87a333c6'], }), - ('aiohttp-jinja2', '1.5', { - 'checksums': ['7c3ba5eac060b691f4e50534af2d79fca2a75712ebd2b25e6fcb1295859f910b'], + ('aiohttp-jinja2', '1.4.2', { + 'checksums': ['9c22a0e48e3b277fc145c67dd8c3b8f609dab36bce9eb337f70dfe716663c9a0'], }), ('hiredis', '2.0.0', { 'checksums': ['81d6d8e39695f2c37954d1011c0480ef7cf444d4e3ae24bc5e89ee5de360139a'], @@ -55,4 +55,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb index d7b2ae1978f..26ae8b1d621 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb @@ -48,4 +48,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'lib' From c2f8c0ee7ccdc77f83594ac8d3929f923aec4e27 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 19 Jan 2022 17:15:45 +0000 Subject: [PATCH 2758/9987] the Pillow v8 patch also works for Pillow-SIMD v7 --- .../p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb | 6 +++++- .../Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb index 712cf054a06..9c4aa141b7c 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-10.2.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa'] +patches = ['Pillow-8_CVE-2021-23437.patch'] +checksums = [ + '72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa', # 7.1.2.tar.gz + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb index fd8571b95b9..0faafe7a94a 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-7.1.2-GCCcore-9.3.0-Python-3.8.2.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa'] +patches = ['Pillow-8_CVE-2021-23437.patch'] +checksums = [ + '72e1c9d48543531f5fc04594fa330d1111ecc2ac04a9bcda0c6ad3abe6a616aa', # 7.1.2.tar.gz + '12bac0ff4f815d1e60ed129106c2990c8c6157891fd90ec8aaec88a5a642d521', # Pillow-8_CVE-2021-23437.patch +] builddependencies = [('binutils', '2.34')] From b96a5c92b96fdf3bf0027d3e290d2695f939a258 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 20 Jan 2022 00:32:39 +0200 Subject: [PATCH 2759/9987] add build dependency on binutils to aiohttp v3.8.1 --- .../easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb | 4 ++++ .../easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb index cc43a2cb529..c8de4b9afd8 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-10.3.0.eb @@ -8,6 +8,10 @@ description = "Asynchronous HTTP client/server framework for asyncio and Python. toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +builddependencies = [ + ('binutils', '2.36.1'), +] + dependencies = [ ('Python', '3.9.5'), ('typing-extensions', '3.10.0.0'), diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb index 26ae8b1d621..b24d8879760 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.1-GCCcore-11.2.0.eb @@ -8,6 +8,10 @@ description = "Asynchronous HTTP client/server framework for asyncio and Python. toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +builddependencies = [ + ('binutils', '2.37'), +] + dependencies = [ ('Python', '3.9.6'), ] From 1c52b44bf3753f2427bf21e7eddeeeb5f84fdfae Mon Sep 17 00:00:00 2001 From: Robin Engler Date: Thu, 20 Jan 2022 08:14:59 +0100 Subject: [PATCH 2760/9987] Update RDKit-2021.03.4: add comic-neue-checksum patch description and author --- .../r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch index de243222821..3316f1a811c 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4_fix-comic-neue-checksum.patch @@ -1,3 +1,9 @@ +As part of its installation, RDKit downloads a font package from https://fonts.google.com +and checks its md5sum. It appears the font package was modified and therefore a new md5sum +must be used. The authors of RDKit have updated the md5sum in the source code of RDKit but +no backward fix was made for already existing releases. This patch updates the md5 checksum +to the its new value. +Author: Robin Engler, SIB Swiss Institute for Bioinformatics --- rdkit-Release_2021_03_4/Code/GraphMol/MolDraw2D/CMakeLists.txt.orig 2022-01-17 13:56:43.780726092 +0100 +++ rdkit-Release_2021_03_4/Code/GraphMol/MolDraw2D/CMakeLists.txt 2022-01-17 13:57:02.668646178 +0100 @@ -12,7 +12,7 @@ From 33c378c1be0bc3c6d34b7eb29409190865571cf3 Mon Sep 17 00:00:00 2001 From: Robin Engler Date: Thu, 20 Jan 2022 08:41:04 +0100 Subject: [PATCH 2761/9987] Update RDKit-2021.03.4: update comic-neue-checksum patch checksum --- easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb index 7535a3e2ace..3146628e323 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2021.03.4-foss-2021a.eb @@ -20,7 +20,7 @@ patches = [ checksums = [ 'bed309df7f1e2ea25736a986cf951325681142ee49468b1c62d020a109d2ef52', # Release_2021_03_4.tar.gz '45869e01461b66e42c9305f5e8a65f696417e4777c2da60ef81d1e26e57d1b2e', # RDKit-2021.03.4_skip-broken-test.patch - '80adeb72eb0e6fac3dcc6cca3c82c1a8fe253025106e0acb7b1135bc4b94a69d', # RDKit-2021.03.4_fix-comic-neue-checksum.patch + '64d2c588203998c1da028b95032a7c006834e957f10c6335bb534148c0517dcb', # RDKit-2021.03.4_fix-comic-neue-checksum.patch ] # Dependencies varies from version to version From 54f24aa5fcdd4d54d344f7087d5bbea0d4b6c6b1 Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 20 Jan 2022 08:33:07 +0000 Subject: [PATCH 2762/9987] Update easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb index 7fd2267fc96..c4abf6d5d2f 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb @@ -17,6 +17,10 @@ checksums = [ 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch ] +builddependencies = [ + ('tcsh', '6.22.03'), +] + dependencies = [ ('Tcl', '8.6.10'), ] From 52994883a4ccfdf6a40e13b3e9c766567d98b1b7 Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 20 Jan 2022 08:33:15 +0000 Subject: [PATCH 2763/9987] Update easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb index c4abf6d5d2f..b7b2e5f3007 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb @@ -25,9 +25,6 @@ dependencies = [ ('Tcl', '8.6.10'), ] -# /bin/csh is required by 'config' script -osdependencies = ['tcsh'] - # Hard to make charm build the mpi version with gcc on POWER, so we don't currently try. charm_arch = 'mpi-linux-x86_64' charm_extra_cxxflags = '-fpermissive' From 3ce31dadf8e2aa8c4c05fd3d18bed8989b0a8d76 Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 20 Jan 2022 08:35:55 +0000 Subject: [PATCH 2764/9987] Update easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb index 98aeeb12b8e..7c4a94a649a 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb @@ -20,6 +20,10 @@ checksums = [ 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch ] +builddependencies = [ + ('tcsh', '6.22.03'), +] + # support for GCC 8+ on POWER dependencies = [ ('Tcl', '8.6.10'), From 49164a14c4038af497cef06098b3aa23cafe706a Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 20 Jan 2022 08:36:03 +0000 Subject: [PATCH 2765/9987] Update easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb index 7c4a94a649a..b938c172e69 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb @@ -29,9 +29,6 @@ dependencies = [ ('Tcl', '8.6.10'), ] -# /bin/csh is required by 'config' script -osdependencies = ['tcsh'] - charm_arch = "multicore-linux-%(arch)s" charm_extra_cxxflags = '-fpermissive' From 5ecd8dc51880796b5a94546a9d6b9ed06998e0a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 20 Jan 2022 10:53:09 +0100 Subject: [PATCH 2766/9987] adding easyconfigs: CUDAcore-11.5.1.eb --- .../easyconfigs/c/CUDAcore/CUDAcore-11.5.1.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.5.1.eb diff --git a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.5.1.eb b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.5.1.eb new file mode 100644 index 00000000000..5ffc55ece99 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.5.1.eb @@ -0,0 +1,22 @@ +## +# Author: Mustafa Abduljabbar +## +easyblock = 'EB_CUDA' + +name = 'CUDAcore' +version = '11.5.1' +local_nv_version = '495.29.05' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = ['60bea2fc0fac95574015f865355afbf599422ec2c85554f5f052b292711a4bca'] + +moduleclass = 'system' From 97012b5c000833b7b7f17b817c7a5902e4c491ac Mon Sep 17 00:00:00 2001 From: agemuend Date: Thu, 20 Jan 2022 11:57:14 +0100 Subject: [PATCH 2767/9987] adding easyconfigs: IntelClusterChecker-2021.5.0.eb --- .../IntelClusterChecker-2021.5.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb diff --git a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb new file mode 100644 index 00000000000..758f142f756 --- /dev/null +++ b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb @@ -0,0 +1,40 @@ +## +# Author: Andre Gemuend +## +easyblock = "IntelBase" +name = 'IntelClusterChecker' +version = '2021.5.0' + +homepage = 'https://software.intel.com/en-us/cluster-checker' +description = """Intel Cluster Checker verifies the configuration and +performance of Linux OS-based clusters. Anomalies and performance differences +can be identified and practical resolutions provided. +""" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18359/'] +sources = ['l_clck_p_%(version)s.560_offline.sh'] +checksums = ['2b661eff4a87607fd29e21fe29883873c0a7216d7d0a99557dc48b6eae9adeb0'] + +dontcreateinstalldir = True + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'clck/%(version)s/include', + 'MANPATH': 'clck/%(version)s/man', + 'CLCK_ROOT': 'clck/%(version)s', + 'LIBRARY_PATH': 'clck/%(version)s/lib/intel64', + 'PATH': 'clck/%(version)s/bin/intel64' +} + +sanity_check_paths = { + 'files': ['clck/%(version)s/bin/clckvars.sh', + 'clck/%(version)s/bin/clckvars.csh', + 'clck/%(version)s/bin/intel64/clck', + 'clck/%(version)s/bin/intel64/clck-analyze', + 'clck/%(version)s/bin/intel64/clck-collect', + 'clck/%(version)s/bin/intel64/clckdb'], + 'dirs': [], +} + +moduleclass = 'perf' From e257d589b741e52fea432afaa683be8c80a2af54 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 20 Jan 2022 11:56:47 +0000 Subject: [PATCH 2768/9987] Update sources to (hopefully) ensure constant checksums --- easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb | 4 ++-- easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb index 0a6c88f179b..b5a09be97ae 100644 --- a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-10.3.0.eb @@ -11,8 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'noopt': True} source_urls = ['https://tendl.web.psi.ch/tendl_2019/talys/'] -sources = [{'download_filename': 'talys.tar', 'filename': SOURCELOWER_TAR_GZ}] -checksums = ['3a69420b36c2fcd3e433db91ed45d6fcb59558875244cf066f174eaa18840164'] +sources = ['%(namelower)s%(version)s.tar'] +checksums = ['f7efe1e07cdc072394b2b9ec5801ba70957d4f1be1eaee22c4975cc9840a57c6'] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb index 28297ff22e5..680897efbc7 100644 --- a/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/t/TALYS/TALYS-1.95-GCCcore-9.3.0.eb @@ -11,8 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'noopt': True} source_urls = ['https://tendl.web.psi.ch/tendl_2019/talys/'] -sources = [{'download_filename': 'talys.tar', 'filename': SOURCELOWER_TAR_GZ}] -checksums = ['3a69420b36c2fcd3e433db91ed45d6fcb59558875244cf066f174eaa18840164'] +sources = ['%(namelower)s%(version)s.tar'] +checksums = ['f7efe1e07cdc072394b2b9ec5801ba70957d4f1be1eaee22c4975cc9840a57c6'] builddependencies = [('binutils', '2.34')] From 6ead3a55e859a7dedf11fc8d50190e1ef6fac1ac Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Thu, 20 Jan 2022 13:46:46 +0100 Subject: [PATCH 2769/9987] adding easyconfigs: RAxML-8.2.12-gompi-2021b-hybrid-avx2.eb --- .../RAxML-8.2.12-gompi-2021b-hybrid-avx2.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021b-hybrid-avx2.eb diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021b-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021b-hybrid-avx2.eb new file mode 100644 index 00000000000..7be898198dc --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.12-gompi-2021b-hybrid-avx2.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.12' +versionsuffix = '-hybrid-avx2' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['abe6978c6027e897ebed67066836e4eadd57ecd0d042045634424dd001e86105'] + +buildopts = '-f Makefile.AVX2.HYBRID.gcc CC="$CC"' + +files_to_copy = [(["raxmlHPC-HYBRID-AVX2"], "bin"), "usefulScripts", "README", "manual"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s raxmlHPC-HYBRID-AVX2 raxmlHPC"] + +sanity_check_paths = { + 'files': ['bin/raxmlHPC'], + 'dirs': [], +} + +sanity_check_commands = ["raxmlHPC -%s" % x for x in ['h', 'v']] + +moduleclass = 'bio' From f8c4967403b3803d2220396c1263c33cbd1eab57 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 20 Jan 2022 15:38:18 +0100 Subject: [PATCH 2770/9987] adding easyconfigs: methylpy-1.2.9-foss-2021b.eb and patches: methylpy-1.2.9-foss-2021b-fixSetupConfig.patch --- ...ylpy-1.2.9-foss-2021b-fixSetupConfig.patch | 7 ++++ .../m/methylpy/methylpy-1.2.9-foss-2021b.eb | 41 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch create mode 100644 easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch new file mode 100644 index 00000000000..4f5c6bb3e11 --- /dev/null +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch @@ -0,0 +1,7 @@ +--- setup.cfg.orig 2022-01-19 19:34:38.630926000 +0100 ++++ setup.cfg 2022-01-19 19:34:44.636856000 +0100 +@@ -1,2 +1,2 @@ + [metadata] +-description-file = README.md ++description_file = README.md +\ No newline at end of file \ No newline at end of file diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb new file mode 100644 index 00000000000..7f6e9a609ce --- /dev/null +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'methylpy' +version = '1.2.9' + +homepage = 'https://pypi.python.org/pypi/methylpy' +description = """Bisulfite sequencing data processing and differential methylation analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/yupenghe/methylpy/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['methylpy-1.2.9-foss-2021b-fixSetupConfig.patch'] +checksums = [ + '169b5da07c26dbdd5d61a3bc5cbc3fe5a801bf1dd59b79b6d7e3f9a22005ae9e', # 1.2.9.tar.gz + # methylpy-1.2.9-foss-2021b-fixSetupConfig.patch + 'c9261c75de1c0e88a89444639043ef42555cac430ddbf239617cb83ebbf3b56c', +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('cutadapt', '3.5'), + ('Bowtie2', '2.4.4'), + ('Bowtie', '1.3.1'), + ('SAMtools', '1.14'), + ('picard', '2.25.5', '-Java-13', True), + ('GSL', '2.7'), + ('Kent_tools', '422'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From ed29abd59b7c0759cc6d10eda550a6dde33c9349 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 20 Jan 2022 15:50:10 +0100 Subject: [PATCH 2771/9987] Added newline to the end of patchfile --- .../m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch index 4f5c6bb3e11..9d436708edf 100644 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch @@ -4,4 +4,4 @@ [metadata] -description-file = README.md +description_file = README.md -\ No newline at end of file \ No newline at end of file +\ No newline at end of file From 0ac5b4a252ecf5dabfff7e6a28f0caa5f20b9923 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 20 Jan 2022 16:56:15 +0100 Subject: [PATCH 2772/9987] Updated checksums --- easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb index 7f6e9a609ce..a01d20329e5 100644 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb @@ -14,7 +14,7 @@ patches = ['methylpy-1.2.9-foss-2021b-fixSetupConfig.patch'] checksums = [ '169b5da07c26dbdd5d61a3bc5cbc3fe5a801bf1dd59b79b6d7e3f9a22005ae9e', # 1.2.9.tar.gz # methylpy-1.2.9-foss-2021b-fixSetupConfig.patch - 'c9261c75de1c0e88a89444639043ef42555cac430ddbf239617cb83ebbf3b56c', + '92c4723c86ae79494a8e81ce682b0bb74777e272b55616c59548546606cc2215', ] dependencies = [ From 4298cadba8656845cc1e82dc3cbf803609166386 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 20 Jan 2022 17:21:28 +0000 Subject: [PATCH 2773/9987] Add missing dependencies on graphite2, HarfBuzz to Qt5 --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index 18e55bea4a7..16cca743fc8 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -48,6 +48,8 @@ dependencies = [ ('GLib', '2.69.1'), ('PCRE2', '10.37'), ('libpng', '1.6.37'), + ('HarfBuzz', '2.8.2'), + ('graphite2', '1.3.14'), # deps for QtWebEngine ('X11', '20210802'), ('fontconfig', '2.13.94'), From 666fd5253e2b4c9e4679005a7b0ec95bedb3c9b6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 20 Jan 2022 17:24:16 +0000 Subject: [PATCH 2774/9987] adding easyconfigs: SoXt-1.4.0-GCC-11.2.0.eb, motif-2.3.8-GCCcore-11.2.0.eb --- .../m/motif/motif-2.3.8-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ .../s/SoXt/SoXt-1.4.0-GCC-11.2.0.eb | 39 ++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/SoXt/SoXt-1.4.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..61b71170338 --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.8' + +homepage = 'https://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] + +builddependencies = [ + ('Autotools', '20210726'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('binutils', '2.37'), + ('util-linux', '2.37'), +] + +dependencies = [ + ('X11', '20210802'), + ('libpng', '1.6.37'), + ('freetype', '2.11.0'), + ('libjpeg-turbo', '2.0.6'), + ('bzip2', '1.0.8'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SoXt/SoXt-1.4.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SoXt/SoXt-1.4.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..7d7cb99ce12 --- /dev/null +++ b/easybuild/easyconfigs/s/SoXt/SoXt-1.4.0-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'SoXt' +version = '1.4.0' + +homepage = 'https://coin3d.github.io/SoXt/html/' +description = """SoXt is an Xt/Motif glue library for Coin. It can also be used + on top of the SGI or TGS implementation of Open Inventor, and is designed to + be source code compatible with SGI's InventorXt library. +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ["https://github.com/coin3d/%(namelower)s/releases/download/%(name)s-%(version)s"] +sources = ["%(namelower)s-%(version)s-src.tar.gz"] +checksums = ['b587d1a0035808d346501cf5eed553d611ce0f9a2b84d25e4f60f962ac3f847a'] + +# Boost is a header-only dependency +builddependencies = [ + ('Boost', '1.77.0'), + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Coin', '4.0.0'), + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('motif', '2.3.8'), +] + +configopts = "-DSOXT_BUILD_TESTS=OFF" + +sanity_check_paths = { + 'files': ['lib/libSoXt.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'vis' From 2035e7bca0dbf86021314a48f9190adb98845804 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 20 Jan 2022 17:26:40 +0000 Subject: [PATCH 2775/9987] Add Coin 4.0.0 --- .../c/Coin/Coin-4.0.0-GCC-11.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..c55c2e133f5 --- /dev/null +++ b/easybuild/easyconfigs/c/Coin/Coin-4.0.0-GCC-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'Coin' +version = '4.0.0' + +homepage = 'https://coin3d.github.io' +description = """Coin is an OpenGL-based, 3D graphics library that has its roots in the +Open Inventor 2.1 API, which Coin still is compatible with.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ["https://github.com/coin3d/%(namelower)s/releases/download/%(name)s-%(version)s"] +sources = ["%(namelower)s-%(version)s-src.tar.gz"] +checksums = ['e4f4bd57804b8ed0e017424ad2e45c112912a928b83f86c89963df9015251476'] + +# Boost is a header-only dependency +builddependencies = [ + ('Boost', '1.77.0'), + ('CMake', '3.21.1'), +] + +dependencies = [ + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), +] + +configopts = "-DCOIN_BUILD_TESTS=OFF" + +sanity_check_paths = { + 'files': ['lib/libCoin.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'vis' From f3581cea4799911ab2b256da30ac30775baa6768 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 20 Jan 2022 17:52:20 +0000 Subject: [PATCH 2776/9987] adding easyconfigs: SoQt-1.6.0-GCC-11.2.0.eb --- .../s/SoQt/SoQt-1.6.0-GCC-11.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..f7350cc6036 --- /dev/null +++ b/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'SoQt' +version = '1.6.0' + +homepage = 'https://coin3d.github.io/SoXt/html/' +description = """SoQt is a library which provides the glue between Systems in + Motion's Coin high-level 3D visualization library and the Qt 2D user interface + library. +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ["https://github.com/coin3d/%(namelower)s/releases/download/%(name)s-%(version)s"] +sources = ["%(namelower)s-%(version)s-src.tar.gz"] +checksums = ['9f535af59f07c907022815679681bd345c9dec2f408c74833f6b1b24bca40e1f'] + +# Boost is a header-only dependency +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Coin', '4.0.0'), + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('Qt5', '5.15.2'), +] + +configopts = "-DSOXT_BUILD_TESTS=OFF" + +sanity_check_paths = { + 'files': ['lib/libSoQt.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'vis' From bbfa623c8c96a00158f25293509449351780e24c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Jan 2022 19:09:53 +0100 Subject: [PATCH 2777/9987] add pathview extension to R-bundle-Bioconductor 3.14 --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index 8227b4c8c80..53b854a4603 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1084,6 +1084,9 @@ exts_list = [ ('DSS', '2.42.0', { 'checksums': ['b1e2a9044cd10b09ecf667f7a3201269f2dca78ae431cccef6d46816e77dd1a8'], }), + ('pathview', '1.34.0', { + 'checksums': ['594e4b2dd4bb9e826fa87c63f56fbc9132e1b4b620696ec31ae0ebbc6940b4c9'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 5ef006a13b5a94eb7d77dbe9450551f26b8b6473 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 20 Jan 2022 21:29:45 +0100 Subject: [PATCH 2778/9987] Set Java version to 11 for better compatibility --- easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb index a01d20329e5..d0b78df3799 100644 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb @@ -24,7 +24,7 @@ dependencies = [ ('Bowtie2', '2.4.4'), ('Bowtie', '1.3.1'), ('SAMtools', '1.14'), - ('picard', '2.25.5', '-Java-13', True), + ('picard', '2.25.1', '-Java-11', True), ('GSL', '2.7'), ('Kent_tools', '422'), ] From 71dc587e89459aaf98cc6ce3225eae6fb71495d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 21 Jan 2022 07:45:20 +0100 Subject: [PATCH 2779/9987] adding easyconfigs: RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb --- .../RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb new file mode 100644 index 00000000000..f2d7a7efd19 --- /dev/null +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'JAR' + +name = 'RNA-SeQC' +version = '1.1.8' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://software.broadinstitute.org/cancer/cga/rna-seqc' +description = """RNA-SeQC is a java program which computes a series of quality control metrics for + RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab + delimited files of metrics data. This program can be valuable for comparing sequencing quality + across different samples or experiments to evaluate different experimental parameters. It can + also be run on individual samples as a means of quality control before continuing with downstream + analysis.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://data.broadinstitute.org/cancer/cga/tools/rnaseqc/'] +sources = ['%(name)s_v%(version)s.jar'] +checksums = ['0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793'] + +dependencies = [ + ('BWA', '0.7.17'), + ('Java', '16', '', True), +] + +modloadmsg = "To execute RNA-SeQC run: java -jar $EBROOTRNAMINSEQC/%(name)s_v%(version)s.jar" + +sanity_check_paths = { + 'files': ['%(name)s_v%(version)s.jar'], + 'dirs': [''], +} + +moduleclass = 'bio' From 977a90b52b04865ab7060f2b2e574b17d2ad8602 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 21 Jan 2022 08:01:48 +0100 Subject: [PATCH 2780/9987] add binutils as build dependency --- .../r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb index f2d7a7efd19..91da70816d5 100644 --- a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb @@ -20,6 +20,8 @@ source_urls = ['https://data.broadinstitute.org/cancer/cga/tools/rnaseqc/'] sources = ['%(name)s_v%(version)s.jar'] checksums = ['0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793'] +builddependencies = [('binutils', '2.37')] + dependencies = [ ('BWA', '0.7.17'), ('Java', '16', '', True), From 4c8aa83e46dc9d12e8f55ff447e216cd407cdb66 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 21 Jan 2022 10:42:50 +0100 Subject: [PATCH 2781/9987] adding easyconfigs: mkl-service-2.3.0-intel-2021b.eb, netcdf4-python-1.5.7-intel-2021b.eb, Theano-1.1.2-intel-2021b-PyMC.eb, PyMC3-3.11.1-intel-2021b.eb --- .../mkl-service-2.3.0-intel-2021b.eb | 31 +++++++++++ .../netcdf4-python-1.5.7-intel-2021b.eb | 51 ++++++++++++++++++ .../p/PyMC3/PyMC3-3.11.1-intel-2021b.eb | 52 +++++++++++++++++++ .../t/Theano/Theano-1.1.2-intel-2021b-PyMC.eb | 41 +++++++++++++++ 4 files changed, 175 insertions(+) create mode 100644 easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2021b.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb create mode 100644 easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2021b-PyMC.eb diff --git a/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2021b.eb b/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2021b.eb new file mode 100644 index 00000000000..0f71934a28f --- /dev/null +++ b/easybuild/easyconfigs/m/mkl-service/mkl-service-2.3.0-intel-2021b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'mkl-service' +version = '2.3.0' + +homepage = 'https://github.com/IntelPython/mkl-service' +description = "Python hooks for Intel(R) Math Kernel Library runtime control settings." + +toolchain = {'name': 'intel', 'version': '2021b'} + +source_urls = ['https://github.com/IntelPython/mkl-service/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['mkl-service-2.0.2_fix-mkl-lib.patch'] +checksums = [ + 'f0c61f44f29d1264a464c14791b042826f0f74da094c3355dcc295943c46fed5', # v2.3.0.tar.gz + 'e35045a5095a2b4056fe9ee3a52586f2cb5417b90eeddbcc9abae746ff40f2e5', # mkl-service-2.0.2_fix-mkl-lib.patch +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'mkl'} + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb new file mode 100644 index 00000000000..67c96ca4840 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.5.7' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('netCDF', '4.8.1'), + ('cURL', '7.78.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.5.0', { + 'checksums': ['b644bcb53346b6f4fe2fcc9f3b574740a2097637492dcca29632c817e0604f29'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'd145f9c12da29da3922d8b8aafea2a2a89501bcb28a219a46b7b828b57191594', # netCDF4-1.5.7.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb new file mode 100644 index 00000000000..58474b8eecc --- /dev/null +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb @@ -0,0 +1,52 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'PyMC3' +version = '3.11.1' + +homepage = 'https://docs.pymc.io/' +description = """Probabilistic Programming in Python: +Bayesian Modeling and Probabilistic Machine Learning with Theano""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy + ('Theano', '1.1.2', '-PyMC'), + ('matplotlib', '3.4.3'), + ('h5py', '3.6.0'), + ('tqdm', '4.62.3'), + ('netcdf4-python', '1.5.7'), + ('xarray', '0.20.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('typing_extensions', '3.10.0.2', { + 'checksums': ['49f75d16ff11f1cd258e1b988ccff82a3ca5570217d7ad8c5f48205dd99a677e'], + }), + ('arviz', '0.11.4', { + 'checksums': ['01872758eeabb9941479ec5dd378117337bf95d14cc2c298b437cfda1780b436'], + }), + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + ('dill', '0.3.4', { + 'source_tmpl': 'dill-%(version)s.zip', + 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], + }), + ('fastprogress', '1.0.0', { + 'checksums': ['89e28ac1d2a5412aab18ee3f3dfd1ee8b5c1f2f7a44d0add0d0d4f69f0191bfe'], + }), + ('pymc3', version, { + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + 'checksums': ['501d48b9f5d033678de7a5918b9d055a6806adf84fe16a5a9d65eaa2dc71acd8'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2021b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2021b-PyMC.eb new file mode 100644 index 00000000000..08868c6858d --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-intel-2021b-PyMC.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.1.2' +versionsuffix = '-PyMC' + +homepage = 'https://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +source_urls = ['https://pypi.python.org/packages/source/T/Theano%(versionsuffix)s'] +sources = ['Theano-PyMC-%(version)s.tar.gz'] +checksums = ['5da6c2242ea72a991c8446d7fe7d35189ea346ef7d024c890397011114bf10fc'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('mkl-service', '2.3.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +fix_python_shebang_for = ['bin/theano-cache', 'bin/theano-nose'] + +sanity_check_paths = { + 'files': ['bin/theano-cache'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +local_blas_warning = "Using NumPy C-API based implementation for BLAS functions" +sanity_check_commands = [ + # make sure that warning about falling back to (slow) NumPy C-API for BLAS functions is *not* printed + # mkl-service dependency is required to ensure this doesn't happen + "python -c 'import theano.tensor' 2>&1 | grep '%s'; test $? != 0" % local_blas_warning, +] + +moduleclass = 'math' From a26e574e0ff7cd689e01c7b9f47aca0c8f47d52c Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 21 Jan 2022 10:59:21 +0100 Subject: [PATCH 2782/9987] adding easyconfigs: typing-extensions-3.10.0.2-GCCcore-11.2.0.eb --- ...ping-extensions-3.10.0.2-GCCcore-11.2.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.10.0.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.10.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.10.0.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a74255cd1aa --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-3.10.0.2-GCCcore-11.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '3.10.0.2' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions – Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['49f75d16ff11f1cd258e1b988ccff82a3ca5570217d7ad8c5f48205dd99a677e'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From d764ab42d3cebc15437926205a5afc2bbb13459a Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 21 Jan 2022 10:59:47 +0100 Subject: [PATCH 2783/9987] adding easyconfigs: ArviZ-0.11.4-intel-2021b.eb --- .../a/ArviZ/ArviZ-0.11.4-intel-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-intel-2021b.eb diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-intel-2021b.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-intel-2021b.eb new file mode 100644 index 00000000000..64ccfac5b2d --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-intel-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'ArviZ' +version = '0.11.4' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'intel', 'version': '2021b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['01872758eeabb9941479ec5dd378117337bf95d14cc2c298b437cfda1780b436'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # numpy, scipy, pandas + ('netcdf4-python', '1.5.7'), + ('xarray', '0.20.1'), + ('matplotlib', '3.4.3'), + ('typing-extensions', '3.10.0.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' From 6ac450773f4be536aaa79e78da654037ab92a643 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 21 Jan 2022 11:12:44 +0100 Subject: [PATCH 2784/9987] adding easyconfigs: Bambi-0.7.1-intel-2021b.eb --- .../b/Bambi/Bambi-0.7.1-intel-2021b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb diff --git a/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb new file mode 100644 index 00000000000..706f118eed5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'Bambi' +version = '0.7.1' + +homepage = 'https://bambinos.github.io/bambi' +description = """Bambi is a high-level Bayesian model-building interface written in Python. +It works with the probabilistic programming frameworks PyMC3 and is designed +to make it extremely easy to fit Bayesian mixed-effects models common in biology, +social sciences and other disciplines.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('statsmodels', '0.13.1'), + ('ArviZ', '0.11.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('formulae', '0.2.0', { + 'checksums': ['228335df9907750793016dfb23a8a0cb8d6d9ce9a026bfe2b459aa19f72541d2'], + }), +] + +moduleclass = 'bio' From 97c246c011299f8a52a04061be225d8280b26bb1 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 21 Jan 2022 11:23:53 +0100 Subject: [PATCH 2785/9987] adding easyconfigs: netcdf4-python-1.5.7-foss-2021b.eb, ArviZ-0.11.4-foss-2021b.eb, Bambi-0.7.1-foss-2021b.eb --- .../a/ArviZ/ArviZ-0.11.4-foss-2021b.eb | 28 ++++++++++ .../b/Bambi/Bambi-0.7.1-foss-2021b.eb | 30 +++++++++++ .../netcdf4-python-1.5.7-foss-2021b.eb | 51 +++++++++++++++++++ 3 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-foss-2021b.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-foss-2021b.eb new file mode 100644 index 00000000000..b3efd6d0772 --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'ArviZ' +version = '0.11.4' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['01872758eeabb9941479ec5dd378117337bf95d14cc2c298b437cfda1780b436'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # numpy, scipy, pandas + ('netcdf4-python', '1.5.7'), + ('xarray', '0.20.1'), + ('matplotlib', '3.4.3'), + ('typing-extensions', '3.10.0.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb new file mode 100644 index 00000000000..a23fd351fd2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'Bambi' +version = '0.7.1' + +homepage = 'https://bambinos.github.io/bambi' +description = """Bambi is a high-level Bayesian model-building interface written in Python. +It works with the probabilistic programming frameworks PyMC3 and is designed +to make it extremely easy to fit Bayesian mixed-effects models common in biology, +social sciences and other disciplines.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('statsmodels', '0.13.1'), + ('ArviZ', '0.11.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('formulae', '0.2.0', { + 'checksums': ['228335df9907750793016dfb23a8a0cb8d6d9ce9a026bfe2b459aa19f72541d2'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-foss-2021b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-foss-2021b.eb new file mode 100644 index 00000000000..a0fca42084e --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-foss-2021b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.5.7' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('netCDF', '4.8.1'), + ('cURL', '7.78.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.5.0', { + 'checksums': ['b644bcb53346b6f4fe2fcc9f3b574740a2097637492dcca29632c817e0604f29'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'd145f9c12da29da3922d8b8aafea2a2a89501bcb28a219a46b7b828b57191594', # netCDF4-1.5.7.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' From 55ec7565aa900e2be985e16495802d3281a71860 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Jan 2022 11:55:31 +0100 Subject: [PATCH 2786/9987] adding easyconfigs: namedlist-1.8-GCCcore-11.2.0.eb --- .../namedlist/namedlist-1.8-GCCcore-11.2.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/n/namedlist/namedlist-1.8-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/n/namedlist/namedlist-1.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/namedlist/namedlist-1.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d06edee81e5 --- /dev/null +++ b/easybuild/easyconfigs/n/namedlist/namedlist-1.8-GCCcore-11.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'namedlist' +version = '1.8' + +homepage = 'https://gitlab.com/ericvsmith/namedlist' +description = "A Python object, similar to namedtuple, but for lists." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['34f89fc992592c80b39a709e136edcf41ea17f24ba31eaf84a314a02c8b9bcef'] + +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 73275792fba5b3cbd5861ca58ce2ea80e826017c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Jan 2022 12:09:42 +0100 Subject: [PATCH 2787/9987] add missing binutils build dependency to namedlist easyconfig --- .../easyconfigs/n/namedlist/namedlist-1.8-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/n/namedlist/namedlist-1.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/namedlist/namedlist-1.8-GCCcore-11.2.0.eb index d06edee81e5..4b4f2016fae 100644 --- a/easybuild/easyconfigs/n/namedlist/namedlist-1.8-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/namedlist/namedlist-1.8-GCCcore-11.2.0.eb @@ -11,6 +11,10 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} sources = [SOURCE_TAR_GZ] checksums = ['34f89fc992592c80b39a709e136edcf41ea17f24ba31eaf84a314a02c8b9bcef'] +builddependencies = [ + ('binutils', '2.37'), +] + dependencies = [ ('Python', '3.9.6'), ] From d08b5f8aa7a680d9050969635db2a23576e2b3b9 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 21 Jan 2022 14:15:27 +0100 Subject: [PATCH 2788/9987] adding easyconfigs: MethylDackel-0.6.1-GCC-11.2.0.eb, libBigWig-0.4.6-GCCcore-11.2.0.eb and patches: MethylDackel_fix_version.h_target.patch --- .../libBigWig-0.4.6-GCCcore-11.2.0.eb | 26 ++++++++++ .../MethylDackel-0.6.1-GCC-11.2.0.eb | 47 +++++++++++++++++++ .../MethylDackel_fix_version.h_target.patch | 30 ++++++++++++ 3 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/l/libBigWig/libBigWig-0.4.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/MethylDackel/MethylDackel-0.6.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/MethylDackel/MethylDackel_fix_version.h_target.patch diff --git a/easybuild/easyconfigs/l/libBigWig/libBigWig-0.4.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libBigWig/libBigWig-0.4.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..73c5218ac1e --- /dev/null +++ b/easybuild/easyconfigs/l/libBigWig/libBigWig-0.4.6-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'libBigWig' +version = '0.4.6' + +homepage = 'https://github.com/dpryan79/libBigWig' +description = "A C library for handling bigWig files" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/dpryan79/libBigWig/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['eb4ecbd3ae428474a57dab969fa7564ae755310da65be68efa18969e0d132a9e'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('cURL', '7.78.0')] + +files_to_copy = [(['libBigWig.*'], 'lib'), (['*.h'], 'include')] + +sanity_check_paths = { + 'files': ['include/bigWig.h', 'lib/libBigWig.a', 'lib/libBigWig.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MethylDackel/MethylDackel-0.6.1-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MethylDackel/MethylDackel-0.6.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..1f3fe9f689c --- /dev/null +++ b/easybuild/easyconfigs/m/MethylDackel/MethylDackel-0.6.1-GCC-11.2.0.eb @@ -0,0 +1,47 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# 0.6.1 Update: Christoph Siegert + +easyblock = 'ConfigureMake' + +name = 'MethylDackel' +version = '0.6.1' +github_account = 'dpryan79' + +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """A (mostly) universal methylation extractor for BS-seq experiments.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['MethylDackel_fix_version.h_target.patch'] +checksums = [ + 'eeb1da4c830bcd9f3e6663a764947d957c41337643069524a4b545812fcf4819', # 0.6.1.tar.gz + '3b2e0a8028d12f9f214a027746eddaa5bf9239f75c08d829dfa93fba6d6a1d71', # MethylDackel_fix_version.h_target.patch +] + +skipsteps = ['configure'] + +buildopts = 'LIBBIGWIG="$EBROOTLIBBIGWIG/lib/libBigWig.a"' + +runtest = 'test' + +installopts = "prefix=%(installdir)s" +modextrapaths = {'PATH': ''} + +dependencies = [ + ('HTSlib', '1.14'), + ('libBigWig', '0.4.6'), +] + +sanity_check_paths = { + 'files': ['%(name)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(name)s extract -h" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MethylDackel/MethylDackel_fix_version.h_target.patch b/easybuild/easyconfigs/m/MethylDackel/MethylDackel_fix_version.h_target.patch new file mode 100644 index 00000000000..dd9db6b72b0 --- /dev/null +++ b/easybuild/easyconfigs/m/MethylDackel/MethylDackel_fix_version.h_target.patch @@ -0,0 +1,30 @@ +From 1f3bc6833d192dff5969c9901557ad8e22b3a689 Mon Sep 17 00:00:00 2001 +From: Christoph Siegert +Date: Fri, 21 Jan 2022 13:58:17 +0100 +Subject: [PATCH] do not recompile on "make test" and "make install" + +This patch removes ".PHONY" for version.h. +".PHONY version.h" causes make to not look for the version.h file so +everything that depends on it will be rebuilt on every run of make. +This causes + make LIBBIGWIG=/some/path/libBigWig.a + make test +to fail as "make test" will try to recompile MethylDackel without +LIBBIGWIG set to /some/path/libBigWig.a +--- + Makefile | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Makefile b/Makefile +index 1352d5f..911da1f 100644 +--- a/Makefile ++++ b/Makefile +@@ -4,7 +4,7 @@ LIBS ?= # e.g., -L$PREFIX/lib, or where ever htslib is + LIBBIGWIG ?= + CFLAGS ?= -Wall -g -O3 -pthread + +-.PHONY: all clean install version.h ++.PHONY: all clean install + + .SUFFIXES:.c .o + From 0a5a61c645047b44d161b04d3c4988cf3e5ea713 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 21 Jan 2022 14:50:08 +0100 Subject: [PATCH 2789/9987] adding easyconfigs: SqueezeMeta-1.5.0-foss-2021b.eb --- .../SqueezeMeta-1.5.0-foss-2021b.eb | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb new file mode 100644 index 00000000000..d86176cd362 --- /dev/null +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb @@ -0,0 +1,80 @@ +easyblock = 'Tarball' + +name = 'SqueezeMeta' +version = '1.5.0' + +homepage = 'https://github.com/jtamames/SqueezeMeta' +description = """SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, + covering all steps of the analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/jtamames/SqueezeMeta/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + 'e984d8ad57f859edd7d8ccb26a5a8ec51120f92365c5c00994bc5ea58529d639', # v1.5.0.tar.gz +] + +dependencies = [ + ('Perl', '5.34.0'), # provides XML::Parser + ('XML-LibXML', '2.0207'), + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), + ('Pysam', '0.17.0'), + ('R', '4.1.2'), + ('BLAST+', '2.12.0'), + ('BWA', '0.7.17'), + ('CD-HIT', '4.8.1'), + ('CheckM', '1.1.3'), + ('DAS_Tool', '1.1.1', '-R-%(rver)s'), # depends on prodigal & pullseq + ('DIAMOND', '2.0.13'), + ('MEGAHIT', '1.2.9'), + ('minimap2', '2.22'), + ('Java', '11', '', True), + ('RDP-Classifier', '2.13', '-Java-%(javaver)s', True), + ('MetaBAT', '2.15'), + ('MinPath', '1.6'), # depends on GPLK (which provides glpsol) + ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), + ('Trimmomatic', '0.39', '-Java-%(javaver)s', True), + ('AMOS', '3.1.0'), + ('MaxBin', '2.2.7'), + ('SPAdes', '3.15.3'), + ('Bowtie2', '2.4.4'), + ('canu', '2.2'), + ('HMMER', '3.3.2'), + ('MUMmer', '4.0.0beta2'), + ('pplacer', '1.1.alpha19', '', True), + ('Short-Pair', '20170125'), + ('SAMtools', '1.14'), + ('CompareM', '0.1.2'), + ('R-bundle-Bioconductor', '3.14', '-R-%(rver)s') +] + +keepsymlinks = True + +postinstallcmds = [ + # backup patched barrnap + "cp %(installdir)s/bin/barrnap %(builddir)s/", + # remove vendored tools that are include as dependencies + "rm -r %(installdir)s/bin/*", + "cp %(builddir)s/barrnap %(installdir)s/bin/", + # fix shebang in Perl scripts + "sed -i 's@#!/usr/bin/perl@#!/usr/bin/env perl@g' %(installdir)s/scripts/*.pl", + "mkdir %(installdir)s/R" + # also install SQMtools R library + "mkdir %(installdir)s/R && R CMD INSTALL lib/SQMtools --library=%(installdir)s/R/ --no-clean-on-error", +] + +sanity_check_paths = { + 'files': ['scripts/SqueezeMeta.pl'], + 'dirs': ['utils/install_utils/'], +} + +sanity_check_commands = ["""echo 'library("SQMtools")' | R -q --no-save"""] + +modextrapaths = { + 'PATH': 'scripts', + 'R_LIBS_SITE': 'R', +} + +moduleclass = 'bio' From 91150b11b8e1e450ef8f99cdac47d32814e94914 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 21 Jan 2022 15:10:09 +0100 Subject: [PATCH 2790/9987] adding easyconfigs: MinPath-1.6-GCCcore-11.2.0.eb --- .../m/MinPath/MinPath-1.6-GCCcore-11.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/MinPath/MinPath-1.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..df9c0f306e8 --- /dev/null +++ b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-GCCcore-11.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'Tarball' + +name = 'MinPath' +version = '1.6' +# no tagged commit for MinPath 1.6, commit was determined based on commit history +local_commit = '46d3e81a4dca2310d558bea970bc002b15d44767' + +homepage = 'https://omics.informatics.indiana.edu/MinPath' +description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions + using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological + pathways for a query dataset.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/mgtools/MinPath/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] +checksums = [ + '57e6b55cd00507578bad7528c60e3ad055311f62db928bd7c8de793513cec5a3', # MinPath-1.6.tar.gz + '117e45c6f35e3c944232dd5dd4789400d44c4b9b733b936adbb548b58e046c4b', # MinPath-1.6_fix-glpsol-path.patch +] + +dependencies = [ + ('Python', '3.9.6'), + ('GLPK', '5.0'), +] + +# remove included old GLPK copy +postinstallcmds = ["rm -rf %(installdir)s/glpk-*/*"] + +fix_python_shebang_for = ['*.py'] + +sanity_check_paths = { + 'files': ['MinPath.py'], + 'dirs': [], +} + +sanity_check_commands = [ + "MinPath.py -ko examples/demo.ko -report /dev/null -details /dev/null", + "MinPath.py -fig examples/demo.fig -report /dev/null -details /dev/null", + "MinPath.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From d3a41925df3a7c6dea1b8e5a900aec9b0655859d Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 21 Jan 2022 15:27:21 +0100 Subject: [PATCH 2791/9987] adding easyconfigs: preseq-3.1.2-GCC-11.2.0.eb --- .../p/preseq/preseq-3.1.2-GCC-11.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/preseq/preseq-3.1.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/preseq/preseq-3.1.2-GCC-11.2.0.eb b/easybuild/easyconfigs/p/preseq/preseq-3.1.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..9849472fb76 --- /dev/null +++ b/easybuild/easyconfigs/p/preseq/preseq-3.1.2-GCC-11.2.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'preseq' +version = '3.1.2' + +homepage = 'https://smithlabresearch.org/software/preseq' +description = "Software for predicting library complexity and genome coverage in high-throughput sequencing." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/smithlabcode/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['ed5176eb638e709bd22c0a43cedae5a2a3fcece40f6c130c509fbce6a59fa788'] + +dependencies = [ + ('GSL', '2.7'), + ('HTSlib', '1.14'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-hts CPPFLAGS="-I$EBROOTHTSLIB/include" LDFLAGS="-L$EBROOTHTSLIB/lib"' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(name)s', 'to-mr']], + 'dirs': [], +} + +sanity_check_commands = [('%(name)s')] + +moduleclass = 'bio' From 9390faedad5c8704cc544094aebcbe32657164f9 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Jan 2022 15:01:27 +0000 Subject: [PATCH 2792/9987] add libXfont2 patch to fix build when libbsd is present --- .../x/X11/X11-20201008-GCCcore-10.2.0.eb | 7 ++++- .../x/X11/X11-20210518-GCCcore-10.3.0.eb | 7 ++++- .../x/X11/libXfont2-2.0.4_libbsd.patch | 26 +++++++++++++++++++ 3 files changed, 38 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/x/X11/libXfont2-2.0.4_libbsd.patch diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb index 041c9f6a6a9..d1a9f51ec07 100644 --- a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -126,7 +126,12 @@ components = [ 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], }), ('libXfont2', '2.0.4', { # 2019-09-14 - 'checksums': ['74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a'], + 'patches': ['libXfont2-2.0.4_libbsd.patch'], + 'checksums': [ + '74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a', # libXfont2-2.0.4.tar.gz + '5c8d51f9e65d4e9f49c0fb5f82cfbf87b3cf02f67c1dacf6521a56d8ffb1ae91', # libXfont2-2.0.4_libbsd.patch + ], + 'preconfigopts': "autoreconf -i && ", }), ('libXft', '2.3.3', { # 2019-03-16 'checksums': ['3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701'], diff --git a/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb index 508c2e2c167..b2104033854 100644 --- a/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb @@ -126,7 +126,12 @@ components = [ 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], }), ('libXfont2', '2.0.4', { # 2019-09-14 - 'checksums': ['74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a'], + 'patches': ['libXfont2-2.0.4_libbsd.patch'], + 'checksums': [ + '74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a', # libXfont2-2.0.4.tar.gz + '5c8d51f9e65d4e9f49c0fb5f82cfbf87b3cf02f67c1dacf6521a56d8ffb1ae91', # libXfont2-2.0.4_libbsd.patch + ], + 'preconfigopts': "autoreconf -i && ", }), ('libXft', '2.3.3', { # 2019-03-16 'checksums': ['3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701'], diff --git a/easybuild/easyconfigs/x/X11/libXfont2-2.0.4_libbsd.patch b/easybuild/easyconfigs/x/X11/libXfont2-2.0.4_libbsd.patch new file mode 100644 index 00000000000..19684aea813 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/libXfont2-2.0.4_libbsd.patch @@ -0,0 +1,26 @@ +From ce7a3265019e4d66198c1581d9e8c859c34e8ef1 Mon Sep 17 00:00:00 2001 +From: Bernd Kuhls +Date: Sat, 19 Oct 2019 09:32:41 +0200 +Subject: [PATCH] configure: define HAVE_LIBBSD when libbsd was found + +--- + configure.ac | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/configure.ac b/configure.ac +index e497325..d4d8aa4 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -53,6 +53,9 @@ AC_CHECK_HEADERS([endian.h poll.h sys/poll.h]) + # Checks for library functions. + AC_CHECK_FUNCS([poll readlink]) + AC_SEARCH_LIBS([strlcat], [bsd]) ++if test "$ac_cv_search_strlcat" = "-lbsd"; then ++ AC_DEFINE(HAVE_LIBBSD,1,[Has libbsd]) ++fi + AC_CONFIG_LIBOBJ_DIR([src/util]) + AC_REPLACE_FUNCS([reallocarray realpath strlcat strlcpy]) + +-- +GitLab + From 7ce972f99987306d5430a722b5a9ac069b4544cc Mon Sep 17 00:00:00 2001 From: Mustafa Abduljabbar Date: Fri, 21 Jan 2022 17:41:11 +0100 Subject: [PATCH 2793/9987] adding easyconfigs: scikit-learn-1.0.2-foss-2021b.eb --- .../scikit-learn-1.0.2-foss-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb new file mode 100644 index 00000000000..acd09d3ba53 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '1.0.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b5870959a5484b614f26d31ca4c17524b1b0317522199dc985c3b4256e030767'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'sklearn'} + +moduleclass = 'data' From 62adfb015e9b5a6dc4f1ac1bdb6feb350c0f672f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 21 Jan 2022 17:38:18 +0000 Subject: [PATCH 2794/9987] adding easyconfigs: Mono-6.12.0.122-GCCcore-11.2.0.eb, libgdiplus-6.1-GCCcore-11.2.0.eb, libexif-0.6.24-GCCcore-11.2.0.eb and patches: libgdiplus-6.1_use-external-googletest.patch --- .../libexif/libexif-0.6.24-GCCcore-11.2.0.eb | 39 ++++++++++ .../libgdiplus-6.1-GCCcore-11.2.0.eb | 52 +++++++++++++ ...bgdiplus-6.1_use-external-googletest.patch | 76 +++++++++++++++++++ .../m/Mono/Mono-6.12.0.122-GCCcore-11.2.0.eb | 53 +++++++++++++ 4 files changed, 220 insertions(+) create mode 100644 easybuild/easyconfigs/l/libexif/libexif-0.6.24-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgdiplus/libgdiplus-6.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgdiplus/libgdiplus-6.1_use-external-googletest.patch create mode 100644 easybuild/easyconfigs/m/Mono/Mono-6.12.0.122-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libexif/libexif-0.6.24-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libexif/libexif-0.6.24-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..27cc576130b --- /dev/null +++ b/easybuild/easyconfigs/l/libexif/libexif-0.6.24-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'libexif' +version = '0.6.24' + +homepage = 'https://libexif.github.io/' +description = "A library for parsing, editing, and saving EXIF data." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e5f15eeab693028cfdc4c0d78f024e1ca78baa0e1f636dc443395e9fbb0a2b7a'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = 'autoreconf -if &&' +configopts = '--disable-docs' + +runtest = 'check' + +local_includes = ['include/%s/exif-%s.h' % (name, x) for x in [ + 'byte-order', 'content', 'data', 'data-type', 'entry', 'format', 'ifd', + 'loader', 'log', 'mem', 'mnote-data', 'tag', 'utils'] +] +local_libs = ['lib/%s.%s' % (name, x) for x in ['a', 'la', SHLIB_EXT]] + ['lib/pkgconfig/%(name)s.pc'] + +sanity_check_paths = { + 'files': local_includes + local_libs, + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgdiplus/libgdiplus-6.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgdiplus/libgdiplus-6.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..468f3e51c16 --- /dev/null +++ b/easybuild/easyconfigs/l/libgdiplus/libgdiplus-6.1-GCCcore-11.2.0.eb @@ -0,0 +1,52 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'libgdiplus' +version = '6.1' + +homepage = 'https://www.mono-project.com/docs/gui/libgdiplus' +description = """Libgdiplus is the Mono library that provides a GDI+-compatible + API on non-Windows operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'mono' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-6.1_use-external-googletest.patch'] +checksums = [ + '6ba47acef48ffa2a75d71f8958e0de7f8f52ea066ed97409b33e7a32f31835fd', # 6.1.tar.gz + '79715140ef1db1e99bacceda56351c410966a5d6b0ad3f5c7bed69d7adf1d079', # libgdiplus-6.1_use-external-googletest.patch +] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('googletest', '1.11.0'), +] + +dependencies = [ + ('cairo', '1.16.0'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.3.0'), + ('libexif', '0.6.24'), + ('giflib', '5.2.1'), + ('Pango', '1.48.8'), +] + +# if using Pango, also need to link pangoft2 +preconfigopts = "sed -i 's/pangocairo/pangocairo pangoft2/g' configure.ac &&" +# autogen.sh also runs configure, passing on arguments +configure_cmd = "./autogen.sh" +configopts = '--with-pango' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/%s.%s' % (name, x) for x in ['a', 'la', SHLIB_EXT]] + ['lib/pkgconfig/%(name)s.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgdiplus/libgdiplus-6.1_use-external-googletest.patch b/easybuild/easyconfigs/l/libgdiplus/libgdiplus-6.1_use-external-googletest.patch new file mode 100644 index 00000000000..a9d79acdb49 --- /dev/null +++ b/easybuild/easyconfigs/l/libgdiplus/libgdiplus-6.1_use-external-googletest.patch @@ -0,0 +1,76 @@ +Author: Jasper Grimm +Avoid building the shipped googletest +Avoid checking for presence of submodules (googletest) +Remove failing testfont test from test suite +diff -Nru libgdiplus-6.1.orig/Makefile.am libgdiplus-6.1/Makefile.am +--- libgdiplus-6.1.orig/Makefile.am 2022-01-21 14:42:42.000000000 +0000 ++++ libgdiplus-6.1/Makefile.am 2022-01-21 14:43:20.000000000 +0000 +@@ -9,11 +9,4 @@ + + DISTCLEANFILES= libgdiplus.pc + +-EXTRA_DIST = libgdiplus.pc.in README.md LICENSE libgdiplus.sln winconfig.h.in update_submodules.sh external/googletest +- +-all: update_submodules +- +-update_submodules: +- @cd $(top_srcdir) && ./update_submodules.sh +- +-.PHONY: update_submodules ++EXTRA_DIST = libgdiplus.pc.in README.md LICENSE libgdiplus.sln winconfig.h.in +diff -Nru libgdiplus-6.1.orig/tests/Makefile.am libgdiplus-6.1/tests/Makefile.am +--- libgdiplus-6.1.orig/tests/Makefile.am 2022-01-21 14:42:42.000000000 +0000 ++++ libgdiplus-6.1/tests/Makefile.am 2022-01-21 14:44:33.000000000 +0000 +@@ -343,7 +343,7 @@ + testcodecs \ + testcustomlinecap \ + testemfcodec \ +- testfont \ ++ # testfont \ + testgifcodec \ + testgeneral \ + testgpimage \ +@@ -382,27 +382,27 @@ + # TESTS += testgdi + endif + +-if HAVE_CMAKE ++# if HAVE_CMAKE + +-GTEST_BUILDDIR := $(top_builddir)/gtest_build +-GTEST_LIBS := $(GTEST_BUILDDIR)/lib/libgtest.a $(GTEST_BUILDDIR)/lib/libgtest_main.a +-$(GTEST_BUILDDIR): +- mkdir -p $(GTEST_BUILDDIR) ++# GTEST_BUILDDIR := $(top_builddir)/gtest_build ++# GTEST_LIBS := $(GTEST_BUILDDIR)/lib/libgtest.a $(GTEST_BUILDDIR)/lib/libgtest_main.a ++# $(GTEST_BUILDDIR): ++# mkdir -p $(GTEST_BUILDDIR) + +-$(GTEST_BUILDDIR)/.stamp-gtest: | $(GTEST_BUILDDIR) +- cd $(GTEST_BUILDDIR) && $(CMAKE) . $(top_srcdir)/external/googletest && $(MAKE) +- touch $@ ++# $(GTEST_BUILDDIR)/.stamp-gtest: | $(GTEST_BUILDDIR) ++# cd $(GTEST_BUILDDIR) && $(CMAKE) . $(top_srcdir)/external/googletest && $(MAKE) ++# touch $@ + +-$(GTEST_LIBS): $(GTEST_BUILDDIR)/.stamp-gtest ++# $(GTEST_LIBS): $(GTEST_BUILDDIR)/.stamp-gtest + +-gtest_SOURCES = gtest.cpp +-gtest_DEPENDENCIES = $(TEST_DEPS) $(GTEST_LIBS) +-gtest_LDADD = $(LDADDS) $(GTEST_LIBS) +-gtest_CPPFLAGS = -pthread -std=c++11 -I$(top_srcdir)/external/googletest/googletest/include -I$(top_srcdir)/src $(GDIPLUS_INCLUDES) ++# gtest_SOURCES = gtest.cpp ++# gtest_DEPENDENCIES = $(TEST_DEPS) $(GTEST_LIBS) ++# gtest_LDADD = $(LDADDS) $(GTEST_LIBS) ++# gtest_CPPFLAGS = -pthread -std=c++11 -I$(top_srcdir)/external/googletest/googletest/include -I$(top_srcdir)/src $(GDIPLUS_INCLUDES) + +-noinst_PROGRAMS += gtest ++# noinst_PROGRAMS += gtest + + run-gtest: gtest +- ./gtest --gtest_output=xml:TestResult.xml ++ gtest --gtest_output=xml:TestResult.xml + +-endif ++# endif diff --git a/easybuild/easyconfigs/m/Mono/Mono-6.12.0.122-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/Mono/Mono-6.12.0.122-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..38557c0aa37 --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-6.12.0.122-GCCcore-11.2.0.eb @@ -0,0 +1,53 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'Mono' +version = '6.12.0.122' + +homepage = 'https://www.mono-project.com/' +description = """An open source, cross-platform, implementation of C# and the CLR that is + binary compatible with Microsoft.NET.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://download.mono-project.com/sources/mono'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['29c277660fc5e7513107aee1cbf8c5057c9370a4cdfeda2fc781be6986d89d23'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('zlib', '1.2.11'), + # optional: + ('jemalloc', '5.2.1'), + ('libgdiplus', '6.1'), + ('X11', '20210802'), +] + +# autogen.sh also runs configure with supplied arguments +configure_cmd = "./autogen.sh" +configopts = "--with-tls=pthread --with-large-heap " +# optionally build with libgdiplus, jemalloc and X11 support +configopts += "--with-libgdiplus=$EBROOTLIBGDIPLUS/lib/libgdiplus.so " +configopts += "--with-jemalloc=$EBROOTJEMALLOC/lib/libjemalloc.so " + +local_bins = ['bin/mono'] +local_libs = ['lib/libmono%s.%s' % (x, y) for x in ['-2.0', 'boehm-2.0', '-native', '-profiler-aot', 'sgen-2.0'] + for y in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': local_bins + local_libs, + 'dirs': ['include', 'etc'], +} + +sanity_check_commands = ["mono --help", "mono --version"] + +moduleclass = 'lang' From d051a304326728cf4fc19726f58f15928f8997b9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 21 Jan 2022 17:39:11 +0000 Subject: [PATCH 2795/9987] adding easyconfigs: MaxQuant-2.0.3.0-GCCcore-11.2.0.eb --- .../MaxQuant-2.0.3.0-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.0.3.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.0.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.0.3.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..66bf848d14f --- /dev/null +++ b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.0.3.0-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'MaxQuant' +version = '2.0.3.0' + +homepage = 'https://maxquant.org/maxquant' +description = """MaxQuant is a quantitative proteomics software package designed for analyzing large + mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling + techniques as well as label-free quantification are supported.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +# requires registration at https://www.maxquant.org/download_asset/maxquant/latest +sources = ['%(name)s_%(version)s.zip'] +checksums = ['463fcd29b41263c33c50c7c7c2cc608bc4b5b3e6806b77a1adc811e0f215af33'] + +dependencies = [('Mono', '6.12.0.122')] + +sanity_check_paths = { + 'files': ['%(name)s.exe', 'bin/%(name)sCmd.exe', 'bin/%(name)sGui.exe'], + 'dirs': [], +} + +sanity_check_commands = [ + ("mono $EBROOTMAXQUANT/bin/MaxQuantCmd.exe --version 2>&1 | grep -q %(version)s", ''), + ("mono $EBROOTMAXQUANT/bin/MaxQuantCmd.exe --help 2>&1 | grep -q USAGE", '')] + +modaliases = { + 'maxquantcmd': 'mono $EBROOTMAXQUANT/bin/%(name)sCmd.exe', + 'maxquantgui': 'mono $EBROOTMAXQUANT/bin/%(name)sGui.exe', +} + +modloadmsg = """ +To run MaxQuant in command-line mode: maxquantcmd + in GUI mode: maxquantgui +""" + +moduleclass = 'bio' From dabedbb084e852ac579b28ae22eb591a16ee46db Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 21 Jan 2022 18:44:48 +0100 Subject: [PATCH 2796/9987] new easycconfig fastp-0.23.2-GCC-10.3.0.eb --- .../f/fastp/fastp-0.23.2-GCC-10.3.0.eb | 39 +++++++++++++++++++ .../l/libdeflate/libdeflate-1.7-GCC-10.3.0.eb | 38 ++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..ac030fc7674 --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.23.2' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +# https://github.com/OpenGene/fastp +github_account = 'OpenGene' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['185bd58732e57474fa08aae90e154fbc05f3e437ee2b434386dd2266d60d8ef6'] + +dependencies = [ + ('zlib', '1.2.11'), + ('ISA-L', '2.30.0'), + ('libdeflate', '1.7'), +] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/fastp'], + 'dirs': [], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCC-10.3.0.eb new file mode 100644 index 00000000000..f57caa79f6c --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCC-10.3.0.eb @@ -0,0 +1,38 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'libdeflate' +version = '1.7' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a5e6a0a9ab69f40f0f59332106532ca76918977a974e7004977a9498e3f11350'] + +builddependencies = [('binutils', '2.36.1')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' From 0a205792b7e5bd849d0cd6cf0d97271adee4392d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 22 Jan 2022 15:27:05 +0800 Subject: [PATCH 2797/9987] prepare release notes for EasyBuild v4.5.2 + bump version to 4.5.2 --- RELEASE_NOTES | 61 +++++++++++++++++++++++++++++++++++++++++++++++++++ setup.py | 2 +- 2 files changed, 62 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index e4cfd357446..24bac8fac8f 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -7,6 +7,67 @@ The latest version of easybuild-easyconfig provides 13,812 easyconfig files, for incl. 36 different (compiler) toolchains. +v4.5.2 (January 24th 2022) +-------------------------- + +update/bugfix release + +- added example easyconfig files for 48 new software packages: + - alevin-fry (#14617), AMD-uProf (#14626), ANGEL (#11857), atropos (#7580), Austin (#14596), AutoDock-GPU (#14671), + AutoDock-Vina (#14675), boost_histogram (#14516), CAFE5 (#14603), Calcam (#7488), Carma (#14527), Cogent (#14278), + dlib (#14556), DualSPHysics (#14632), dune-core (#14693), dune-fem (#14693), DyMat (#14615), elbencho (#14548), + Embree (#7471), ExaML (#14530), FMPy (#14481), genozip (#14583), hivtrace (#14691), intervaltree-python (#8995), + IsoNet (#14075), MACSE (#14709), MetaPhlAn (#12917), MicrobeAnnotator (#14549), mold (#14595), numdiff (#14609), + OpenFace (#14556), PhyloPhlAn (#14564), PREQUAL (#14722), PuLP (#14581), PyCalib (#14616), PyTorch3D (#13240), + QCG-PilotJob (#14337), RaGOO (#8995), RAPSearch2 (#13199), SCopeLoomR (#14518), ShengBTE (#14557), SHTns (#14682), + STRUMPACK (#14560), TALYS (#14716), TN93 xxHash (#14251), yaml-cpp (#14547), Zgoubi (#14516) +- added additional easyconfigs for various supported software packages, including: + - AdapterRemoval 2.3.2, alevin fry, AMD uProf, AMOS 3.1.0, Anaconda3 2021.11.eb, ANGEL 3.0, annovar 20200607, antiSMASH 5.2.0, Armadillo 10.7.5, arpack ng, Arrow 0.17.1, Arrow 6.0.1, atropos 1.1.21, Austin 3.2.0, Austin 3.2.0.eb, AutoDock 4.2.6, AutoDock GPU, AutoDock Vina, AutoDock Vina, Bazel 3.7.2, bcl2fastq2 2.20.0, Bismark 0.23.1, Bison 3.8.2.eb, BLAST+ 2.12.0, Blender 3.0.0, boost_histogram 1.2.1, Bowtie2 2.4.4, BWA 0.7.17, CAFE5 5.0.0, Calcam 2.1.0, Calcam 2.1.0, canu 2.2, Carma 2.01, CD HIT, cDNA_Cupcake 24.2.0, cDNA_Cupcake 26.0.0, CDO 1.9.10, CGAL 4.14.3, CheckM 1.1.3, CHERAB 1.3.0, CHERAB 1.3.0, CMake 3.20.1, CMake 3.22.1, Cogent 8.0.0, CompareM 0.1.2, CP2K 8.2, CUDAcore 11.4.0.eb, CVXOPT 1.2.3, Cython 3.0a5, DAS_Tool 1.1.1, DendroPy 4.5.2, DIAMOND 2.0.13, DIAMOND 2.0.13, dill 0.3.4, dlib 19.22, dlib 19.22, dotNET Core, dotNET SDK, DualSPHysics 5.0.175, DualSPHysics 5.0.175, dune core, dune fem, DyMat 0.7, EasyBuild 4.5.1.eb, Eigen 3.4.0, EIGENSOFT 7.2.1, elbencho 2.0, ELSI RCI, ELSI RCI, ELSI RCI, ELSI RCI, Embree 3.4.0, ExaML 3.0.22, expecttest 0.1.3, Extrae 3.8.3, fastp 0.23.2, FastTree 2.1.11, FMPy 0.3.2, FragGeneScan 1.31, FreeImage 3.18.0, FreeSurfer 7.2.0, FreeSurfer 7.2.0, FreeSurfer 7.2.0, FTGL 2.1.3, futile 1.8.3, futile 1.8.3, futile 1.8.3, futile 1.8.3, gengetopt 2.23, genozip 13.0.5, georges 2019.2, GffCompare 0.12.6, gffread 0.12.7, gffread 0.12.7, gmsh 4.9.0, gnuplot 5.4.2, graphite2 1.3.14, GSL 2.7, GTDB Tk, GTK3 3.24.31, h5py 3.6.0, h5py 3.6.0, hivtrace 0.6.2, HMMER 3.3.2, Horovod 0.23.0, HPL 2.3, hypothesis 4.57.1, IDBA UD, igraph 0.9.5, iimpi 2022.00.eb, imkl 2022.0.1.eb, imkl FFTW, impi 2021.5.0, Inspector 2022.0.0.eb, intel 2022.00.eb, intel compilers, intervaltree python, IPython 5.10.0, IQ TREE, ISA L, IsoNet 0.1_20210822_04_674f67f, itac 2021.2.0.eb, itac 2021.5.0.eb, Java 15.0.1.eb, Java 15.eb, Java 17.0.1.eb, Java 17.eb, Java 1.8.0_311.eb, JUBE 2.4.2.eb, Julia 1.6.5, Julia 1.7.1, Kaleido 0.2.1, KronaTools 2.8.1, leidenalg 0.8.8, libdeflate 1.8, libdwarf 20210305, libelf 0.8.13, libgd 2.3.3, Libint 2.6.0, libxsmm 1.17, LMfit 1.0.3, LSD2 2.3, MACSE 2.06, MAGMA 1.09b, mapDamage 2.2.1, MATLAB 2021b.eb, matplotlib 2.2.5, MaxBin 2.2.7, MEGAHIT 1.2.9, MetaBAT 2.15, MetaPhlAn 3.0.9, MicrobeAnnotator 2.0.5, MinPath 1.6, mold 0.9.6, mold 1.0.0, molmod 1.4.8, MultiQC 1.10.1, MultiQC 1.11, MUMmer 4.0.0beta2, MUSCLE 3.8.31, MUSCLE 3.8.31, MUSCLE 5.0.1428, ncview 2.1.8, NGS Python, numba 0.50.1, numba 0.54.1, numdiff 5.9.0, NVHPC 21.11.eb, OBITools 1.2.13, occt 7.5.0p1, OpenBabel 3.1.1, openCARP 8.2, OpenCV 3.4.1, OpenFace 2.2.0, OpenFace 2.2.0, OpenFOAM v2112, ORCA 5.0.2, ORCA 5.0.2, ORCA 5.0.2, ORCA 5.0.2, PAML 4.9j, parasail 2.4.3, ParaView 5.9.1, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, PEAR 0.9.11, phonopy 2.12.0, PhyloPhlAn 3.0, PhyloPhlAn 3.0.2, Pillow 8.3.2, Pillow SIMD, plotly.py 4.14.3, PLUMED 2.7.2, PLUMED 2.7.3, poppler 22.01.0, PREQUAL 1.02, PRINSEQ 0.20.4, PSolver 1.8.3, PSolver 1.8.3, PSolver 1.8.3, PSolver 1.8.3, pullseq 1.0.2, PuLP 2.5.1, pybind11 2.7.1, PyCairo 1.20.1, PyCalib 0.1.0.dev0, PyOpenCL 2021.1.2, PyOpenGL 3.1.5, PyQt5 5.9.2, PyQtGraph 0.12.3, Python 2.7.18, python igraph, python parasail, PyTorch 1.10.0, PyTorch3D 0.4.0, PyZMQ 22.3.0, QCG PilotJob, Qt5 5.15.2, RaGOO 1.11, RAPSearch2 2.24, RAxML 8.2.12, Raysect 0.7.1, Raysect 0.7.1, RDP Classifier, Rgurobi 9.5.0, Ruby 3.0.1, scanpy 1.8.2, Schrodinger 2021, SciPy bundle, SCopeLoomR 0.13.0, SCOTCH 6.1.2, SEPP 4.3.10, SEPP 4.5.0, SEPP 4.5.1, seqtk 1.3, ShengBTE 1.1.1, Short Pair, SHTns 2.7, SHTns 3.5.1, SIP 4.19.8, Spack 0.17.0.eb, SPAdes 3.15.3, Spark 3.1.1, SqueezeMeta 1.0.0, STAR 2.7.9a, statsmodels 0.13.1, statsmodels 0.13.1, STRUMPACK 6.1.0, STRUMPACK 6.1.0, Subread 2.0.3, SuiteSparse 5.10.1, TALYS 1.95, TALYS 1.95, texlive 20210324, Tkinter 2.7.18, TN93 1.0.7, TreeMix 1.13, trimAl 1.4.1, VCFtools 0.1.16, VTune 2022.0.0.eb, worker 1.6.12, wtdbg2 2.5, XML LibXML, xxHash 0.8.0, yaff 1.6.0, yaml cpp, Zgoubi 6.0.2 +- minor enhancements, including: + - add yaml-cpp dependency to Trilinos 12.12.1 with foss/2019b (#14547) + - include output of failing code style check in message produced by failing easyconfigs style test (#14578) + - bundle LAPACKE with FlexiBLAS 3.0.4 (#14591) + - add semTools, mirt, OpenMX extensions to R v4.1.2 easyconfig (#14634) + - add FactorCopula extension for R v4.1.2 (#14648) + - add ExomeDepth extension to R-bundle-Bioconductor 3.14 (#14684) + - add DSS extension to R-bundle-Bioconductor 3.14 (#14748) + - add rpact and ldbounds extensions to R v4.1.2 (#14750) + - add pathview extension to R-bundle-Bioconductor 3.14 (#14806) +- various bug fixes, including: + - fix homepage and source_urls for GLIMMER 3.02b (#7945) + - use proper Perl dependency for worker 1.6.12 with foss/2019a (fixes installation on RHEL8 OS) (#14565) + - fix checksum and versions of annovar v20191024 (#14579) + - add patch for Rust 1.52.2 and 1.54.0 to fix build when using alternate sysroot (#14584) + - retain version in filename for cromwell sources (#14586) + - specify compiler to use in WildMagic easyconfig (#14594) + - avoid need for git build dependency for recent x265 easyconfigs (#14605) + - fix broken patch file for recent GPAW versions (#14619) + - add alternative checksum for Siesta-4.1-MaX-1.0 (#14643) + - add missing PCRE dependency for pullseq + add sanity check commands (#14650) + - use %(arch)s template to avoid hardcoding x86_64 in recent XML-LibXML easyconfigs (#14655) + - fix name for (binary) AutoDock-Vina v1.1.2 (#14675) + - add patch to fix memory leak in OpenMPI that heavily affects CP2K, SIESTA, QuantumESPRESSO, VASP, ... (#14726) + - set $GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS for installing grcpio extension included with: + - TensorFlow 2.2.3-2.4.1 with 2020* toolchain (#14729) and 2.5.0+ (#14728) + - Ray-project (#14730) + - update build dependencies for binutils 2.37 with system toolchain (#14731) + - bump nbconvert extension in recent IPython easyconfigs to version 6.4.0 (#14738) + - enforce using internal boost for bcl2fastq2 with a GCC 10.x toolchain (#14741) + - add patch for hard-coded checksum value of downloaded source file in the source code of RDKit 2021.03.4 (#14743) + - also install libaio.so.1 symlink in easyconfigs for libaio v0.3.112 (#14745) + - update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain (#14755) + - do not use external libgcrypt or python for libxslt with recent toolchains (#14756) + - fix CVE-2021-23437 in: + - Pillow v7 and v8 + update to Pillow v8.3.2 in easyconfigs using a 2021b toolchain (#14765) + - Pillow-SIMD v7 and v8 + add easyconfig for Pillow-SIMD v8.3.2 with GCCcore/11.2.0 (#14792) + - only check sanity_check_components and sanity_check_all_components when Bundle easyblock is used in test_pr_sanity_check_paths (#14769) + - add libXfont2 patch to fix build when libbsd is present (#14821) +- other changes: + - update Java 1.8 wrapper to 1.8.0_311 for x86_64 (#14644) + - bring gffread back down to GCCcore level for toolchain version 10.3.0 (#14660) + - stick to Java/11 dependency for Bazel 3.7.2 with GCCcore/11.2.0 (#14734) + + v4.5.1 (December 13th 2021) --------------------------- diff --git a/setup.py b/setup.py index bb5b73a292d..663b9046087 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.2.dev0' +VERSION = '4.5.2' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From de2a8651cc567d53e6f0d2c0f979cb55f44a7755 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 23 Jan 2022 17:11:07 +0100 Subject: [PATCH 2798/9987] minor tweak release notes for v4.5.2 --- RELEASE_NOTES | 37 +++++++++++++++++++------------------ 1 file changed, 19 insertions(+), 18 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 24bac8fac8f..79e2add3b6c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 13,812 easyconfig files, for 2,575 different software packages, +The latest version of easybuild-easyconfig provides 14,080 easyconfig files, for 2,622 different software packages, incl. 36 different (compiler) toolchains. @@ -12,6 +12,7 @@ v4.5.2 (January 24th 2022) update/bugfix release +- added easyconfig for intel/2022.00 toolchain (#14620) - added example easyconfig files for 48 new software packages: - alevin-fry (#14617), AMD-uProf (#14626), ANGEL (#11857), atropos (#7580), Austin (#14596), AutoDock-GPU (#14671), AutoDock-Vina (#14675), boost_histogram (#14516), CAFE5 (#14603), Calcam (#7488), Carma (#14527), Cogent (#14278), @@ -20,21 +21,26 @@ update/bugfix release IsoNet (#14075), MACSE (#14709), MetaPhlAn (#12917), MicrobeAnnotator (#14549), mold (#14595), numdiff (#14609), OpenFace (#14556), PhyloPhlAn (#14564), PREQUAL (#14722), PuLP (#14581), PyCalib (#14616), PyTorch3D (#13240), QCG-PilotJob (#14337), RaGOO (#8995), RAPSearch2 (#13199), SCopeLoomR (#14518), ShengBTE (#14557), SHTns (#14682), - STRUMPACK (#14560), TALYS (#14716), TN93 xxHash (#14251), yaml-cpp (#14547), Zgoubi (#14516) + STRUMPACK (#14560), TALYS (#14716), TN93 (#14691), xxHash (#14251), yaml-cpp (#14547), Zgoubi (#14516) - added additional easyconfigs for various supported software packages, including: - - AdapterRemoval 2.3.2, alevin fry, AMD uProf, AMOS 3.1.0, Anaconda3 2021.11.eb, ANGEL 3.0, annovar 20200607, antiSMASH 5.2.0, Armadillo 10.7.5, arpack ng, Arrow 0.17.1, Arrow 6.0.1, atropos 1.1.21, Austin 3.2.0, Austin 3.2.0.eb, AutoDock 4.2.6, AutoDock GPU, AutoDock Vina, AutoDock Vina, Bazel 3.7.2, bcl2fastq2 2.20.0, Bismark 0.23.1, Bison 3.8.2.eb, BLAST+ 2.12.0, Blender 3.0.0, boost_histogram 1.2.1, Bowtie2 2.4.4, BWA 0.7.17, CAFE5 5.0.0, Calcam 2.1.0, Calcam 2.1.0, canu 2.2, Carma 2.01, CD HIT, cDNA_Cupcake 24.2.0, cDNA_Cupcake 26.0.0, CDO 1.9.10, CGAL 4.14.3, CheckM 1.1.3, CHERAB 1.3.0, CHERAB 1.3.0, CMake 3.20.1, CMake 3.22.1, Cogent 8.0.0, CompareM 0.1.2, CP2K 8.2, CUDAcore 11.4.0.eb, CVXOPT 1.2.3, Cython 3.0a5, DAS_Tool 1.1.1, DendroPy 4.5.2, DIAMOND 2.0.13, DIAMOND 2.0.13, dill 0.3.4, dlib 19.22, dlib 19.22, dotNET Core, dotNET SDK, DualSPHysics 5.0.175, DualSPHysics 5.0.175, dune core, dune fem, DyMat 0.7, EasyBuild 4.5.1.eb, Eigen 3.4.0, EIGENSOFT 7.2.1, elbencho 2.0, ELSI RCI, ELSI RCI, ELSI RCI, ELSI RCI, Embree 3.4.0, ExaML 3.0.22, expecttest 0.1.3, Extrae 3.8.3, fastp 0.23.2, FastTree 2.1.11, FMPy 0.3.2, FragGeneScan 1.31, FreeImage 3.18.0, FreeSurfer 7.2.0, FreeSurfer 7.2.0, FreeSurfer 7.2.0, FTGL 2.1.3, futile 1.8.3, futile 1.8.3, futile 1.8.3, futile 1.8.3, gengetopt 2.23, genozip 13.0.5, georges 2019.2, GffCompare 0.12.6, gffread 0.12.7, gffread 0.12.7, gmsh 4.9.0, gnuplot 5.4.2, graphite2 1.3.14, GSL 2.7, GTDB Tk, GTK3 3.24.31, h5py 3.6.0, h5py 3.6.0, hivtrace 0.6.2, HMMER 3.3.2, Horovod 0.23.0, HPL 2.3, hypothesis 4.57.1, IDBA UD, igraph 0.9.5, iimpi 2022.00.eb, imkl 2022.0.1.eb, imkl FFTW, impi 2021.5.0, Inspector 2022.0.0.eb, intel 2022.00.eb, intel compilers, intervaltree python, IPython 5.10.0, IQ TREE, ISA L, IsoNet 0.1_20210822_04_674f67f, itac 2021.2.0.eb, itac 2021.5.0.eb, Java 15.0.1.eb, Java 15.eb, Java 17.0.1.eb, Java 17.eb, Java 1.8.0_311.eb, JUBE 2.4.2.eb, Julia 1.6.5, Julia 1.7.1, Kaleido 0.2.1, KronaTools 2.8.1, leidenalg 0.8.8, libdeflate 1.8, libdwarf 20210305, libelf 0.8.13, libgd 2.3.3, Libint 2.6.0, libxsmm 1.17, LMfit 1.0.3, LSD2 2.3, MACSE 2.06, MAGMA 1.09b, mapDamage 2.2.1, MATLAB 2021b.eb, matplotlib 2.2.5, MaxBin 2.2.7, MEGAHIT 1.2.9, MetaBAT 2.15, MetaPhlAn 3.0.9, MicrobeAnnotator 2.0.5, MinPath 1.6, mold 0.9.6, mold 1.0.0, molmod 1.4.8, MultiQC 1.10.1, MultiQC 1.11, MUMmer 4.0.0beta2, MUSCLE 3.8.31, MUSCLE 3.8.31, MUSCLE 5.0.1428, ncview 2.1.8, NGS Python, numba 0.50.1, numba 0.54.1, numdiff 5.9.0, NVHPC 21.11.eb, OBITools 1.2.13, occt 7.5.0p1, OpenBabel 3.1.1, openCARP 8.2, OpenCV 3.4.1, OpenFace 2.2.0, OpenFace 2.2.0, OpenFOAM v2112, ORCA 5.0.2, ORCA 5.0.2, ORCA 5.0.2, ORCA 5.0.2, PAML 4.9j, parasail 2.4.3, ParaView 5.9.1, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, ParMETIS 4.0.3, PEAR 0.9.11, phonopy 2.12.0, PhyloPhlAn 3.0, PhyloPhlAn 3.0.2, Pillow 8.3.2, Pillow SIMD, plotly.py 4.14.3, PLUMED 2.7.2, PLUMED 2.7.3, poppler 22.01.0, PREQUAL 1.02, PRINSEQ 0.20.4, PSolver 1.8.3, PSolver 1.8.3, PSolver 1.8.3, PSolver 1.8.3, pullseq 1.0.2, PuLP 2.5.1, pybind11 2.7.1, PyCairo 1.20.1, PyCalib 0.1.0.dev0, PyOpenCL 2021.1.2, PyOpenGL 3.1.5, PyQt5 5.9.2, PyQtGraph 0.12.3, Python 2.7.18, python igraph, python parasail, PyTorch 1.10.0, PyTorch3D 0.4.0, PyZMQ 22.3.0, QCG PilotJob, Qt5 5.15.2, RaGOO 1.11, RAPSearch2 2.24, RAxML 8.2.12, Raysect 0.7.1, Raysect 0.7.1, RDP Classifier, Rgurobi 9.5.0, Ruby 3.0.1, scanpy 1.8.2, Schrodinger 2021, SciPy bundle, SCopeLoomR 0.13.0, SCOTCH 6.1.2, SEPP 4.3.10, SEPP 4.5.0, SEPP 4.5.1, seqtk 1.3, ShengBTE 1.1.1, Short Pair, SHTns 2.7, SHTns 3.5.1, SIP 4.19.8, Spack 0.17.0.eb, SPAdes 3.15.3, Spark 3.1.1, SqueezeMeta 1.0.0, STAR 2.7.9a, statsmodels 0.13.1, statsmodels 0.13.1, STRUMPACK 6.1.0, STRUMPACK 6.1.0, Subread 2.0.3, SuiteSparse 5.10.1, TALYS 1.95, TALYS 1.95, texlive 20210324, Tkinter 2.7.18, TN93 1.0.7, TreeMix 1.13, trimAl 1.4.1, VCFtools 0.1.16, VTune 2022.0.0.eb, worker 1.6.12, wtdbg2 2.5, XML LibXML, xxHash 0.8.0, yaff 1.6.0, yaml cpp, Zgoubi 6.0.2 + - annovar 20200607, antiSMASH 5.2.0, Armadillo 10.7.5, Arrow 6.0.1, Bismark 0.23.1, BLAST+ 2.12.0, + cDNA_Cupcake 26.0.0, CHERAB 1.3.0, CMake 3.22.1, CP2K 8.2, DIAMOND 2.0.13, dotNET-Core-Runtime 6.0.1, + dotNET-SDK 6.0.101, Extrae 3.8.3, fastp 0.23.2, FreeSurfer 7.2.0, GffCompare 0.12.6, gmsh 4.9.0, GTK3 3.24.31, + h5py 3.6.0, igraph 0.9.5, Inspector 2022.0.0, IQ-TREE 2.1.3, itac 2021.5.0.eb, Java/15 + Java/17, JUBE 2.4.2, + libdeflate 1.8, libxsmm 1.17, LSD2 2.3, MAGMA 1.09b, MATLAB 2021b, MinPath 1.6, MultiQC 1.11, MUSCLE 5.0.1428, + numba 0.54.1, NVHPC 21.11, OBITools 1.2.13, occt 7.5.0p1, openCARP 8.2, OpenCV 3.4.1, OpenFOAM v2112, ORCA 5.0.2, + phonopy 2.12.0, Pillow 8.3.2, Pillow-SIMD 8.3.2, PLUMED 2.7.3, poppler 22.01.0, PyQtGraph 0.12.3, + python-igraph 0.9.8, PyZMQ 22.3.0, Raysect 0.7.1, Rgurobi 9.5.0, scanpy 1.8.2, Schrodinger 2021, SqueezeMeta 1.0.0, + statsmodels 0.13.1, texlive 20210324, VTune 2022.0.0 - minor enhancements, including: - add yaml-cpp dependency to Trilinos 12.12.1 with foss/2019b (#14547) - include output of failing code style check in message produced by failing easyconfigs style test (#14578) - - bundle LAPACKE with FlexiBLAS 3.0.4 (#14591) - - add semTools, mirt, OpenMX extensions to R v4.1.2 easyconfig (#14634) - - add FactorCopula extension for R v4.1.2 (#14648) - - add ExomeDepth extension to R-bundle-Bioconductor 3.14 (#14684) - - add DSS extension to R-bundle-Bioconductor 3.14 (#14748) - - add rpact and ldbounds extensions to R v4.1.2 (#14750) - - add pathview extension to R-bundle-Bioconductor 3.14 (#14806) + - bundle LAPACKE with FlexiBLAS 3.0.4 (#14591, #14769) + - add extensions to R v4.1.2 easyconfig: semTools, mirt, OpenMX (#14634), FactorCopula (#14648), rpact, ldbounds (#14750) + - add extensions to R-bundle-Bioconductor 3.14: ExomeDepth (#14684), DSS (#14748), pathview (#14806) - various bug fixes, including: - fix homepage and source_urls for GLIMMER 3.02b (#7945) + - fix source URL for Trilinos 12.12.1 with foss/2019b (#14547) - use proper Perl dependency for worker 1.6.12 with foss/2019a (fixes installation on RHEL8 OS) (#14565) - fix checksum and versions of annovar v20191024 (#14579) - add patch for Rust 1.52.2 and 1.54.0 to fix build when using alternate sysroot (#14584) @@ -50,22 +56,17 @@ update/bugfix release - set $GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS for installing grcpio extension included with: - TensorFlow 2.2.3-2.4.1 with 2020* toolchain (#14729) and 2.5.0+ (#14728) - Ray-project (#14730) - - update build dependencies for binutils 2.37 with system toolchain (#14731) - - bump nbconvert extension in recent IPython easyconfigs to version 6.4.0 (#14738) - enforce using internal boost for bcl2fastq2 with a GCC 10.x toolchain (#14741) - add patch for hard-coded checksum value of downloaded source file in the source code of RDKit 2021.03.4 (#14743) - also install libaio.so.1 symlink in easyconfigs for libaio v0.3.112 (#14745) - - update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain (#14755) - do not use external libgcrypt or python for libxslt with recent toolchains (#14756) - - fix CVE-2021-23437 in: - - Pillow v7 and v8 + update to Pillow v8.3.2 in easyconfigs using a 2021b toolchain (#14765) - - Pillow-SIMD v7 and v8 + add easyconfig for Pillow-SIMD v8.3.2 with GCCcore/11.2.0 (#14792) - - only check sanity_check_components and sanity_check_all_components when Bundle easyblock is used in test_pr_sanity_check_paths (#14769) + - add patches to fix CVE-2021-23437 for Pillow (#14765) and Pillow-SIMD (#14792) - add libXfont2 patch to fix build when libbsd is present (#14821) - other changes: - update Java 1.8 wrapper to 1.8.0_311 for x86_64 (#14644) - bring gffread back down to GCCcore level for toolchain version 10.3.0 (#14660) - - stick to Java/11 dependency for Bazel 3.7.2 with GCCcore/11.2.0 (#14734) + - update build dependencies for recent binutils + GCCcore easyconfigs to avoid depending on M4 1.4.18 with system toolchain (#14731, #14755) + - bump nbconvert extension in recent IPython easyconfigs to version 6.4.0 (#14738) v4.5.1 (December 13th 2021) From a7f24f6f0c2ad928aff5eb7a9014922e188e256d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 24 Jan 2022 10:53:46 +0800 Subject: [PATCH 2799/9987] adding easyconfigs: EasyBuild-4.5.2.eb --- .../e/EasyBuild/EasyBuild-4.5.2.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.2.eb new file mode 100644 index 00000000000..94d49126b0b --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.2.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.5.2' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/c9/ab/97fb7e054494ff2526f32f061c9d64795b46cd553a3e6c119a4c05316496/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/ae/d3/933992ff3ba424c5de0ddcb514cabff9507d7dff6b18052fd28cde4dbe1a/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/aa/c6/d47ed3cd2765b3df0a786bc30595c340be29abe98825ebd52a19e26c3fdc/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '011f9916306492684841e98777cc64652fa5f738a0cd3e819d958be82c2305e8', # easybuild-framework-4.5.2.tar.gz + 'cbe7f5f0171b4a4846f723d77757875c7d80f2bbd76def95698f37addd472663', # easybuild-easyblocks-4.5.2.tar.gz + 'f6fd3870e267b59f18c0e43c29e80adb1544d6f52ea5676be84e9630bae2bce3', # easybuild-easyconfigs-4.5.2.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 55d3748fd9ba7262fb080c189805522d1461e2e9 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 24 Jan 2022 10:44:01 +0100 Subject: [PATCH 2800/9987] adding easyconfigs: Qualimap-2.2.1-foss-2021b-R-4.1.2.eb --- .../Qualimap-2.2.1-foss-2021b-R-4.1.2.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..fdbfeb2bd21 --- /dev/null +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'Qualimap' +version = '2.2.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://qualimap.bioinfo.cipf.es/' +description = """Qualimap 2 is a platform-independent application written in Java and R that provides both + a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of + alignment sequencing data and its derivatives like feature counts.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://bitbucket.org/kokonech/qualimap/downloads/'] +sources = ['qualimap_v%(version)s.zip'] +checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] + +dependencies = [ + ('Java', '11', '', True), + ('R', '4.1.2'), + ('R-bundle-Bioconductor', '3.14', versionsuffix), +] + +sanity_check_paths = { + 'files': ['qualimap'], + 'dirs': [], +} + +sanity_check_commands = ["qualimap --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From d5ef6355affca756b7e6aef53a51df68a90907fa Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 24 Jan 2022 15:49:00 +0100 Subject: [PATCH 2801/9987] adding easyconfigs: NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb --- .../NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..c25db2388cf --- /dev/null +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb @@ -0,0 +1,67 @@ +easyblock = 'ConfigureMake' + +name = 'NVSHMEM' +version = '2.4.1' +versionsuffix = '-CUDA-%(cudaver)s' + +local_cuda_version = '11.4.1' + +homepage = 'https://developer.nvidia.com/nvshmem' +description = """NVSHMEM is a parallel programming interface based on OpenSHMEM that provides +efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a +global address space for data that spans the memory of multiple GPUs and can be +accessed with fine-grained GPU-initiated operations, CPU-initiated operations, +and operations on CUDA streams. +""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +# You need to download the source manully from https://developer.nvidia.com/nvshmem-downloads +sources = ['%(namelower)s_src_%(version)s-3.txz'] +checksums = ['8b6c0eab321b6352911e470f9e81a777a49e58148ec3728453b9522446dba178'] + +builddependencies = [ + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CUDA', local_cuda_version, '', True), + ('UCX-CUDA', '1.11.2', versionsuffix), + ('NCCL', '2.10.3', f'-CUDA-{local_cuda_version}'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export NVSHMEM_USE_GDRCOPY=1 && ' +prebuildopts += 'export GDRCOPY_HOME=${EBROOTGDRCOPY} && ' + +prebuildopts += 'export MPI_HOME=${EBROOTOPENMPI} && ' +prebuildopts += 'export NVSHMEM_MPI_SUPPORT=1 && ' +prebuildopts += 'export NVSHMEMTEST_USE_MPI_LAUNCHER=1 && ' + +prebuildopts += 'export NCCL_HOME=${EBROOTNCCL} && ' +prebuildopts += 'export NVSHMEM_USE_NCCL=1 && ' + +prebuildopts += 'export NVSHMEM_BUILDDIR=%(builddir)s && ' +prebuildopts += 'export NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj && ' +prebuildopts += 'export NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj && ' +prebuildopts += 'export NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj && ' +prebuildopts += 'export NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj && ' + +prebuildopts += 'export NVSHMEM_PREFIX=%(installdir)s && ' +prebuildopts += 'export NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples && ' +prebuildopts += 'export NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest && ' +prebuildopts += 'export NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest && ' +prebuildopts += 'export NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test && ' + +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['lib/libnvshmem.a', 'lib/nvshmem_bootstrap_mpi.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +modextravars = {'NVSHMEM_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 1c9f72d7d5b9b61fca330fd031cfa59540609e9b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 24 Jan 2022 16:03:34 +0100 Subject: [PATCH 2802/9987] update easyconfigs: NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb --- .../n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb index c25db2388cf..908356d7fda 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb @@ -4,8 +4,6 @@ name = 'NVSHMEM' version = '2.4.1' versionsuffix = '-CUDA-%(cudaver)s' -local_cuda_version = '11.4.1' - homepage = 'https://developer.nvidia.com/nvshmem' description = """NVSHMEM is a parallel programming interface based on OpenSHMEM that provides efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a @@ -26,9 +24,9 @@ builddependencies = [ ] dependencies = [ - ('CUDA', local_cuda_version, '', True), + ('CUDA', '11.4.1', '', True), ('UCX-CUDA', '1.11.2', versionsuffix), - ('NCCL', '2.10.3', f'-CUDA-{local_cuda_version}'), + ('NCCL', '2.10.3', versionsuffix), ] skipsteps = ['configure'] From 110eeb6702d875f1530bee0fd6eefa7fb5d00518 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 24 Jan 2022 16:22:47 +0000 Subject: [PATCH 2803/9987] adding easyconfigs: libdeflate-1.8-GCCcore-10.3.0.eb --- .../libdeflate-1.8-GCCcore-10.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e7df2396052 --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.8-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to 1.8 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'ConfigureMake' + +name = 'libdeflate' +version = '1.8' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['50711ad4e9d3862f8dfb11b97eb53631a86ee3ce49c0e68ec2b6d059a9662f61'] + +builddependencies = [('binutils', '2.36.1')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' From f328467e579ed34680004e044b7acafae4782c3c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 24 Jan 2022 16:26:14 +0000 Subject: [PATCH 2804/9987] adding easyconfigs: PLINK-2.00a2.3-GCC-10.3.0.eb, PLINK-2.00a2.3-GCC-11.2.0.eb --- .../p/PLINK/PLINK-2.00a2.3-GCC-10.3.0.eb | 37 +++++++++++++++++++ .../p/PLINK/PLINK-2.00a2.3-GCC-11.2.0.eb | 37 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..ececd25887f --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3-GCC-10.3.0.eb @@ -0,0 +1,37 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'PLINK' +version = '2.00a2.3' + +homepage = 'https://www.cog-genomics.org/plink/2.0/' +description = 'Whole-genome association analysis toolset' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/chrchang/plink-ng/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4a9e9ff670967f9766bcd5571d028ed6c04bc8f07781eac1b95366748544df77'] + +dependencies = [ + ('FlexiBLAS', '3.0.4'), + ('libdeflate', '1.8'), + ('zstd', '1.4.9'), +] + +start_dir = '2.0' + +# ignore suggested Makefile in build_dynamic, the dev Makefile is better +buildopts = 'BLASFLAGS="-lflexiblas" BLASFLAGS64="-lflexiblas"' +buildopts += ' LDFLAGS="$LIBS -ldeflate -lz -lzstd" ZLIB="" CSRC="include/SFMT.c"' +buildopts += ' BASEFLAGS="$OPTFLAGS -DZSTD_MULTITHREAD"' + +files_to_copy = ['bin', (['include/*.h'], 'include'), 'LICENSE', 'ReadMe.md'] + +sanity_check_paths = { + 'files': ['bin/plink2', 'bin/pgen_compress'], + 'dirs': ['include'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3-GCC-11.2.0.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..599b5b38230 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a2.3-GCC-11.2.0.eb @@ -0,0 +1,37 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'PLINK' +version = '2.00a2.3' + +homepage = 'https://www.cog-genomics.org/plink/2.0/' +description = 'Whole-genome association analysis toolset' + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/chrchang/plink-ng/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4a9e9ff670967f9766bcd5571d028ed6c04bc8f07781eac1b95366748544df77'] + +dependencies = [ + ('FlexiBLAS', '3.0.4'), + ('libdeflate', '1.8'), + ('zstd', '1.5.0'), +] + +start_dir = '2.0' + +# ignore suggested Makefile in build_dynamic, the dev Makefile is better +buildopts = 'BLASFLAGS="-lflexiblas" BLASFLAGS64="-lflexiblas"' +buildopts += ' LDFLAGS="$LIBS -ldeflate -lz -lzstd" ZLIB="" CSRC="include/SFMT.c"' +buildopts += ' BASEFLAGS="$OPTFLAGS -DZSTD_MULTITHREAD"' + +files_to_copy = ['bin', (['include/*.h'], 'include'), 'LICENSE', 'ReadMe.md'] + +sanity_check_paths = { + 'files': ['bin/plink2', 'bin/pgen_compress'], + 'dirs': ['include'], +} + +moduleclass = 'bio' From 3515fd0458730285a20922baed02bbcf513ed402 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 24 Jan 2022 20:53:02 +0100 Subject: [PATCH 2805/9987] adding easyconfigs: ScaFaCoS-1.0.1-foss-2021b.eb --- .../s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2021b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2021b.eb b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2021b.eb new file mode 100644 index 00000000000..79d82028cb3 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.1-foss-2021b.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'ScaFaCoS' +version = '1.0.1' + +homepage = 'http://www.scafacos.de/' +description = """ScaFaCoS is a library of scalable fast coulomb solvers.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '2b125f313795c81b0e87eb920082e91addf94c17444f9486d979e691aaded99b', # scafacos-1.0.1.tar.gz +] + +builddependencies = [ + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('GSL', '2.7'), +] + +preconfigopts = 'unset F77 && ' + +configopts = 'FCFLAGS="-fallow-argument-mismatch $FCFLAGS" ' +configopts += '--enable-shared --enable-static --disable-doc ' +# tell it where to find provided FFTW +configopts += '--without-internal-fftw --with-fftw3-includedir=$EBROOTFFTW/include --with-fftw3-libdir=$EBROOTFFTW/lib ' +# only include the solvers supported for LAMMPS +# (for p2nfft we need an additonal dependency) +configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' + +sanity_check_paths = { + 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], + 'dirs': [], +} + +moduleclass = 'math' From e25d3a180403e8e25f6c270b33c3516849cc6636 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 25 Jan 2022 14:26:37 +0200 Subject: [PATCH 2806/9987] adding easyconfigs: OpenCensus-python-0.8.0-GCCcore-11.2.0.eb --- .../OpenCensus-python-0.8.0-GCCcore-11.2.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCensus-python/OpenCensus-python-0.8.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenCensus-python/OpenCensus-python-0.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenCensus-python/OpenCensus-python-0.8.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1ea498ec851 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCensus-python/OpenCensus-python-0.8.0-GCCcore-11.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'OpenCensus-python' +version = '0.8.0' + +homepage = "https://opencensus.io/" +description = """OpenCensus for Python. OpenCensus provides a framework to measure a server's +resource usage and collect performance stats. This repository contains Python +related utilities and supporting software needed by OpenCensus.""" + + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), + ('protobuf-python', '3.17.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cachetools', '4.2.4', { + 'checksums': ['89ea6f1b638d5a73a4f9226be57ac5e4f399d22770b92355f92dcb0f7f001693'], + }), + ('rsa', '4.8', { + 'checksums': ['5c6bd9dc7a543b7fe4304a631f8a8a3b674e2bbfc49c2ae96200cdbe55df6b17'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('google-auth', '2.3.3', { + 'modulename': 'google.auth', + 'checksums': ['d83570a664c10b97a1dc6f8df87e5fdfff012f48f62be131e449c20dfc32630e'], + }), + ('googleapis-common-protos', '1.54.0', { + 'modulename': 'google.api', + 'checksums': ['a4031d6ec6c2b1b6dc3e0be7e10a1bd72fb0b18b07ef9be7b51f2c1004ce2437'], + }), + ('google-api-core', '2.4.0', { + 'modulename': 'google.api_core', + 'checksums': ['ba8787b7c61632cd0340f095e1c036bef9426b2594f10afb290ba311ae8cb2cb'], + }), + ('opencensus-context', '0.1.2', { + 'modulename': 'opencensus.common.runtime_context', + 'preinstallopts': """sed -i 's/from version import __version__/__version__ = "%(version)s"/' setup.py &&""", + 'checksums': ['8cf64ce901e6b35f491bd1521e6541676e034c52d00c95500e9364600f835c06'], + }), + ('opencensus', version, { + 'checksums': ['476d99fb82f3807acf566e6c232049dc13e825102be104e6231784abcc1b1a5e'], + }), +] + +moduleclass = 'lib' From a995b6064fe28397b65f83566aa9eb410c974830 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 25 Jan 2022 14:28:02 +0200 Subject: [PATCH 2807/9987] adding easyconfigs: Ray-project-1.9.2-foss-2021b.eb --- .../Ray-project-1.9.2-foss-2021b.eb | 100 ++++++++++++++++++ 1 file changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb new file mode 100644 index 00000000000..192d05e86a4 --- /dev/null +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb @@ -0,0 +1,100 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'Ray-project' +version = '1.9.2' + +homepage = "https://www.ray.io/" +description = """Ray is an open source project that makes it simple to scale any +compute-intensive Python workload — from deep learning to production model +serving. With a rich set of libraries and integrations built on a flexible +distributed execution framework, Ray makes distributed computing easy and +accessible to every engineer.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +#toolchainopts = {'usempi': True} + +builddependencies = [ + ('patchelf', '0.13'), # needed by py-spy + ('Rust', '1.54.0'), # needed by maturin +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('aiohttp', '3.8.1'), # also provides frozenlist + ('dm-tree', '0.1.6'), + ('Flask', '2.0.2'), + ('gpustat', '1.0.0b1'), + ('libunwind', '1.5.0'), # needed by py-spy + ('OpenCensus-python', '0.8.0'), + ('protobuf-python', '3.17.3'), + ('PyYAML', '5.4.1'), + ('Redis', '6.2.6'), # needed by redis-py + ('OpenAI-Gym', '0.21.0'), # also provides lz4 + ('OpenCV', '4.5.5', '-contrib'), + ('scikit-image', '0.19.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('grpcio', '1.43.0', { + 'modulename': 'grpc', + 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], + }), + ('prometheus_client', '0.11.0', { + 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], + }), + ('maturin', '0.12.6', { + 'checksums': ['2b14cfae808b45a130e19b2999acea423d2e10e7a29ae2336996ba72ba442ff6'], + }), + ('py_spy', '0.3.11', { + 'modulename': False, + 'checksums': ['3115c6e45cdab657f81c886f8b1664e7e2208b775396031eeea60e4d16fc861d'], + }), + ('pydantic', '1.9.0', { + 'checksums': ['742645059757a56ecd886faf4ed2441b9c0cd406079c2b4bee51bcc3fbcd510a'], + }), + ('wrapt', '1.13.3', { + 'checksums': ['1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185'], + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('redis', '4.1.1', { + 'checksums': ['07420a3fbedd8e012c31d4fadac943fb81568946da202c5a5bc237774e5280a0'], + }), + ('smart_open', '5.2.1', { + 'checksums': ['75abf758717a92a8f53aa96953f0c245c8cedf8e1e4184903db3659b419d4c17'], + }), + ('sniffio', '1.2.0', { + 'checksums': ['c4666eecec1d3f50960c6bdf61ab7bc350648da6c126e3cf6898d8cd4ddcd3de'], + }), + ('anyio', '3.5.0', { + 'checksums': ['a0aeffe2fb1fdf374a8e4b471444f0f3ac4fb9f5a5b542b48824475e0042a5a6'], + }), + ('starlette', '0.17.1', { + 'checksums': ['57eab3cc975a28af62f6faec94d355a410634940f10b30d68d31cb5ec1b44ae8'], + }), + ('aiorwlock', '1.3.0', { + 'checksums': ['83f12d87df4b9728a0b8fda1756585ab0d652b107bab59c6084e1b1ad692ab45'], + }), + ('ray', version, { + 'source_tmpl': '%(namelower)s-%(version)s-cp39-cp39-manylinux2014_x86_64.whl', + 'checksums': ['76294786421799a2a157917cbe493f758ae2f5a0acee8ac23cb885936b1a4e35'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ray'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'ray --help' +] + +moduleclass = 'tools' From 95937baeddd741a301bfd9ee43b0c0d96d1be027 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 25 Jan 2022 13:30:01 +0100 Subject: [PATCH 2808/9987] remove leftover comment --- .../easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb index 192d05e86a4..320e0436487 100644 --- a/easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb @@ -14,7 +14,6 @@ distributed execution framework, Ray makes distributed computing easy and accessible to every engineer.""" toolchain = {'name': 'foss', 'version': '2021b'} -#toolchainopts = {'usempi': True} builddependencies = [ ('patchelf', '0.13'), # needed by py-spy From 1f04f884f404c1bcf26a82fdafac8fdc1b97ace4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 25 Jan 2022 13:51:26 +0100 Subject: [PATCH 2809/9987] adding easyconfigs: BeautifulSoup-4.10.0-GCCcore-10.3.0.eb, FACE-1.1.1-GCCcore-10.3.0.eb, FORD-6.1.6-GCCcore-10.3.0.eb, FoBiS-3.0.5-GCCcore-10.3.0.eb, forbear-1.2.0-GCCcore-10.3.0.eb, libaed2-1.3.0-GCC-10.3.0.eb, Simstrat-3.01-GCC-10.3.0.eb and patches: FACE-1.1.1_fix_fobos_src_filename.patch, forbear-1.2.0_use_external_FACE.patch, Simstrat-3.01_use_external_forbear_and_aed2.patch --- .../BeautifulSoup-4.10.0-GCCcore-10.3.0.eb | 34 ++++++ .../f/FACE/FACE-1.1.1-GCCcore-10.3.0.eb | 37 ++++++ .../FACE-1.1.1_fix_fobos_src_filename.patch | 49 ++++++++ .../f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb | 52 +++++++++ .../f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb | 38 +++++++ .../f/forbear/forbear-1.2.0-GCCcore-10.3.0.eb | 40 +++++++ .../forbear-1.2.0_use_external_FACE.patch | 105 ++++++++++++++++++ .../l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb | 31 ++++++ .../s/Simstrat/Simstrat-3.01-GCC-10.3.0.eb | 44 ++++++++ ...t-3.01_use_external_forbear_and_aed2.patch | 99 +++++++++++++++++ 10 files changed, 529 insertions(+) create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/FACE/FACE-1.1.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/FACE/FACE-1.1.1_fix_fobos_src_filename.patch create mode 100644 easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/forbear/forbear-1.2.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/forbear/forbear-1.2.0_use_external_FACE.patch create mode 100644 easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/Simstrat/Simstrat-3.01-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/Simstrat/Simstrat-3.01_use_external_forbear_and_aed2.patch diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3c7c67ff170 --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.10.0' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1') +] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.3.1', { + 'checksums': ['b8d49b1cd4f037c7082a9683dfa1801aa2597fb11c3a1155b7a5b94829b4f1f9'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['c23ad23c521d818955a4151a67d81580319d4bf548d3d49f4223ae041ff98891'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/FACE/FACE-1.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FACE/FACE-1.1.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3b23657d0ed --- /dev/null +++ b/easybuild/easyconfigs/f/FACE/FACE-1.1.1-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'FACE' +version = '1.1.1' + +homepage = 'https://github.com/szaghi/FACE' +description = """A Fortran Ansi Colors (and Styles) Environment. +A KISS pure Fortran Library for easy colorize (and stylize) strings.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/szaghi/FACE/releases/download/v%(version)s'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = [ + 'FACE-1.1.1_fix_fobos_src_filename.patch', +] +checksums = [ + 'cdc75cad2b7f443ee18e4a9ea4d264bc63b069e93cda6aa3f6a15a515b1f3721', # FACE-v1.1.1.tar.gz + '9c51e758716db8a63be393a56fc3be22b3f4f4bf90f659844fe6a07bcfe16eb8', # FACE-1.1.1_fix_fobos_src_filename.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('FoBiS', '3.0.5'), +] + +build_cmd = 'FoBiS.py build' +buildopts = '-mode face-shared-gnu' + +files_to_copy = [(['lib/mod/*.mod'], 'include'), (['lib/libface.%s' % SHLIB_EXT], 'lib')] + +sanity_check_paths = { + 'files': ['include/face.mod', 'lib/libface.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FACE/FACE-1.1.1_fix_fobos_src_filename.patch b/easybuild/easyconfigs/f/FACE/FACE-1.1.1_fix_fobos_src_filename.patch new file mode 100644 index 00000000000..92933aee308 --- /dev/null +++ b/easybuild/easyconfigs/f/FACE/FACE-1.1.1_fix_fobos_src_filename.patch @@ -0,0 +1,49 @@ +Pull in upstream fix for file name + +Åke Sandgren, 2022-01-24 + +commit 918c19faefabc7a8b35475474daa9dc98474d505 +Author: neok-m4700 +Date: Sun Jan 14 15:39:37 2018 +0100 + + consistency with source file naming + + `FoBiS.py build -tb -mode face-shared-gnu` fails without the changes proposed by this PR (no output lib nor module) + +diff --git a/fobos b/fobos +index 0ca7a8c..3f02f4b 100644 +--- a/fobos ++++ b/fobos +@@ -35,28 +35,28 @@ build_dir = exe + [face-static-gnu] + template = template-static-gnu + build_dir = lib +-target = face.f90 ++target = face.F90 + output = libface.a + mklib = static + + [face-shared-gnu] + template = template-shared-gnu + build_dir = lib +-target = face.f90 ++target = face.F90 + output = libface.so + mklib = shared + + [face-static-intel] + template = template-static-intel + build_dir = lib +-target = face.f90 ++target = face.F90 + output = libface.a + mklib = static + + [face-shared-intel] + template = template-shared-intel + build_dir = lib +-target = face.f90 ++target = face.F90 + output = libface.so + mklib = shared + diff --git a/easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f85c40e8755 --- /dev/null +++ b/easybuild/easyconfigs/f/FORD/FORD-6.1.6-GCCcore-10.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'FORD' +version = '6.1.6' + +homepage = 'https://github.com/Fortran-FOSS-Programmers/ford/wiki' +description = 'FORD is an automatic documentation generator for modern Fortran programs' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Graphviz', '2.47.2',), + ('BeautifulSoup', '4.10.0'), + ('tqdm', '4.61.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('graphviz', '0.19.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['09ed0cde452d015fe77c4845a210eb642f28d245f5bc250d4b97808cb8f49078'], + }), + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('markdown-include', '0.6.0', { + 'checksums': ['6f5d680e36f7780c7f0f61dca53ca581bd50d1b56137ddcd6353efafa0c3e4a2'], + }), + ('md-environ', '0.1.0', { + 'checksums': ['fe3c2a255af523d6f522831c699336cd71f9d543714067d93206ed35836f1793'], + }), + ('toposort', '1.7', { + 'checksums': ['ddc2182c42912a440511bd7ff5d3e6a1cabc3accbc674a3258c8c41cbfbb2125'], + }), + (name, version, { + 'checksums': ['c286206e6ce8c12f2e00f6c73e3b76dae830dce7b5b6f52a54512585fcfae12a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ford'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..06c9257d5bf --- /dev/null +++ b/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'FoBiS' +version = '3.0.5' + +homepage = 'https://github.com/szaghi/FoBiS' +description = "A Fortran Building System for automatic building modern Fortran projects" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +dependencies = [ + ('binutils', '2.36.1'), + ('Python', '3.9.5'), + ('BeautifulSoup', '4.10.0'), + ('FORD', '6.1.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('PreForM.py', '1.1.3', { + 'modulename': 'PreForM', + 'checksums': ['420457c236801e8803f4e8b8c7e44a7b65a5becc11d5d75404da537b1e09f3a8'], + }), + ('configparser', '5.2.0', { + 'checksums': ['1b35798fdf1713f1c3139016cfcbc461f09edbf099d1fb658d4b7479fcaa3daa'], + }), + ('FoBiS.py', version, { + 'modulename': 'fobis', + 'checksums': ['ef23fde4199277abc693d539a81e0728571c349174da6b7476579f82482ab96c'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/forbear/forbear-1.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/forbear/forbear-1.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ef6ec74a694 --- /dev/null +++ b/easybuild/easyconfigs/f/forbear/forbear-1.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'forbear' +version = '1.2.0' + +homepage = 'https://github.com/szaghi/forbear' +description = "A Fortran Library for building and running fancy progress bar" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/szaghi/forbear/releases/download/v%(version)s'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = [ + 'forbear-1.2.0_use_external_FACE.patch', +] +checksums = [ + '72b399526ea291e4d5bed121f8a812aadfe7cea59a1553eb0adf0f3bf5ce1554', # forbear-v1.2.0.tar.gz + '26a586affade31cb83fa23d86a889b28de4b3c30ca6d63946740da0320ba818d', # forbear-1.2.0_use_external_FACE.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('FoBiS', '3.0.5'), +] + +dependencies = [ + ('FACE', '1.1.1'), +] + +build_cmd = 'FoBiS.py build' +buildopts = '-mode shared-gnu ' + +files_to_copy = [(['shared/mod/*.mod'], 'include'), (['shared/libforbear.%s' % SHLIB_EXT], 'lib')] + +sanity_check_paths = { + 'files': ['include/forbear.mod', 'lib/libforbear.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/forbear/forbear-1.2.0_use_external_FACE.patch b/easybuild/easyconfigs/f/forbear/forbear-1.2.0_use_external_FACE.patch new file mode 100644 index 00000000000..fdf2967731e --- /dev/null +++ b/easybuild/easyconfigs/f/forbear/forbear-1.2.0_use_external_FACE.patch @@ -0,0 +1,105 @@ +Use external FACE build + +Åke Sandgren, 2022-01-25 +diff -ru forbear.orig/fobos forbear/fobos +--- forbear.orig/fobos 2017-06-11 14:56:47.000000000 +0200 ++++ forbear/fobos 2022-01-25 09:16:13.737587610 +0100 +@@ -17,7 +17,7 @@ + $DEBUG_PGI = -C -g -gopt -Mchkfpstk -Mchkptr -Mchkstk -Mcoff -traceback + $OPTIMIZE = -O3 + $EXDIRS = PENF/src/tests/ +- FACE/src/tests/ FACE/src/third_party/ ++# FACE/src/tests/ FACE/src/third_party/ + + # main modes + # GNU +@@ -117,6 +117,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-gnu] + compiler = gnu +@@ -130,6 +132,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-shared-gnu-debug] + compiler = gnu +@@ -144,6 +148,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-gnu-debug] + compiler = gnu +@@ -158,6 +164,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-shared-intel] + compiler = intel +@@ -171,6 +179,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-intel] + compiler = intel +@@ -184,6 +194,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-shared-intel-debug] + compiler = intel +@@ -198,6 +210,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-intel-debug] + compiler = intel +@@ -212,6 +226,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-pgi] + compiler = pgi +@@ -225,6 +241,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + [template-static-pgi-debug] + compiler = pgi +@@ -239,6 +257,8 @@ + quiet = False + log = True + jobs = 2 ++ext_libs = face ++include = $EBROOTFACE/include + + # rules + [rule-makedoc] diff --git a/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..f2f9d923062 --- /dev/null +++ b/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'libaed2' +version = '1.3.0' + +homepage = 'https://aquatic.science.uwa.edu.au/research/models/AED' +description = """libaed2 is a library of modules and algorithms for +simulation of "aquatic ecodynamics" - water quality, aquatic +biogeochemsitry, biotic habitat and aquatic ecosystem dynamics.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/AquaticEcoDynamics/libaed2/archive'] +sources = ['v%(version)s.tar.gz'] + +buildopts = 'OPT_FFLAGS="$FFLAGS" ' + +files_to_copy = [ + (['mod/*', 'include/*.h'], 'include'), + 'lib', +] + +maxparallel = 1 + +sanity_check_paths = { + 'files': ['lib/%(name)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01-GCC-10.3.0.eb b/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01-GCC-10.3.0.eb new file mode 100644 index 00000000000..bc14c143be9 --- /dev/null +++ b/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01-GCC-10.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'Simstrat' +version = '3.01' + +homepage = 'http://www.eawag.ch/en/department/surf/projects/simstrat/' +description = """Simstrat is a one-dimensional physical lake model for +the simulation of stratification and mixing in deep stratified lakes.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/Eawag-AppliedSystemAnalysis/Simstrat/archive'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'Simstrat-3.01_use_external_forbear_and_aed2.patch', +] +checksums = [ + 'ed504e65e11e7064d3c27643ca41785eaf1f6a8fd7a96dda5b96966ba3665c2e', # 3.01.tar.gz + # Simstrat-3.01_use_external_forbear_and_aed2.patch + 'c37ad82393c2790222bc4018831a29e0c4ddc240a3e37f7c9c613e3b944d6634', +] + +builddependencies = [ + ('FoBiS', '3.0.5'), +] + +dependencies = [ + ('forbear', '1.2.0'), + ('libaed2', '1.3.0'), +] + +prebuildopts = 'cd build && ' + +build_cmd = 'FoBiS.py build' +buildopts = '-mode release-gnu-dynamic ' + +files_to_copy = [(['build/simstrat'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/simstrat'], + 'dirs': [], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01_use_external_forbear_and_aed2.patch b/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01_use_external_forbear_and_aed2.patch new file mode 100644 index 00000000000..465d0a3c380 --- /dev/null +++ b/easybuild/easyconfigs/s/Simstrat/Simstrat-3.01_use_external_forbear_and_aed2.patch @@ -0,0 +1,99 @@ +Use external forbear and aed2 libraries. + +Åke Sandgren, 2022-01-25 +diff -ru Simstrat-3.01.orig/build/fobos Simstrat-3.01/build/fobos +--- Simstrat-3.01.orig/build/fobos 2021-04-23 15:35:32.000000000 +0200 ++++ Simstrat-3.01/build/fobos 2022-01-25 09:54:07.726977196 +0100 +@@ -7,35 +7,14 @@ + lflags=-static-libgcc -static-libgfortran -static + build_dir=. + src=../src/ +-libs = ../lib/libaed2/obj/aed2_bio_utils.o +- ../lib/libaed2/obj/aed2_carbon.o +- ../lib/libaed2/obj/aed2_chlorophylla.o +- ../lib/libaed2/obj/aed2_common.o +- ../lib/libaed2/obj/aed2_core.o +- ../lib/libaed2/obj/aed2_csv_reader.o +- ../lib/libaed2/obj/aed2_dummy.o +- ../lib/libaed2/obj/aed2_nitrogen.o +- ../lib/libaed2/obj/aed2_noncohesive.o +- ../lib/libaed2/obj/aed2_organic_matter.o +- ../lib/libaed2/obj/aed2_oxygen.o +- ../lib/libaed2/obj/aed2_phosphorus.o +- ../lib/libaed2/obj/aed2_phytoplankton.o +- ../lib/libaed2/obj/aed2_sedflux.o +- ../lib/libaed2/obj/aed2_silica.o +- ../lib/libaed2/obj/aed2_totals.o +- ../lib/libaed2/obj/aed2_tracer.o +- ../lib/libaed2/obj/aed2_util.o +- ../lib/libaed2/obj/aed2_zoop_utils.o +- ../lib/libaed2/obj/aed2_zooplankton.o +- ../lib/libaed2/obj/ufz_oxygen.o +-include = ../lib/libaed2/mod/ ++include = $EBROOTLIBAED2/include $EBROOTFORBEAR/include ++ext_libs = aed2 forbear + colors=False + quiet=False + target=simstrat.f90 + output=simstrat + dependon=../lib/csv_fortran/fobos:release-gnu((direct)) + ../lib/json_fortran/fobos:release-gnu((direct)) +- ../lib/forbear/fobos:static-gnu((direct)) + log=True + + [release-gnu-dynamic] +@@ -44,12 +23,13 @@ + lflags=-dynamic-libgcc -dynamic-libgfortran -dynamic + build_dir=. + src=../src/ ++include = $EBROOTLIBAED2/include $EBROOTFORBEAR/include ++ext_libs = aed2 forbear + colors=False + quiet=False + target=simstrat.f90 + dependon=../lib/csv_fortran/fobos:release-gnu((direct)) + ../lib/json_fortran/fobos:release-gnu((direct)) +- ../lib/forbear/fobos:static-gnu((direct)) + log=True + + [release-intel] +@@ -58,6 +38,8 @@ + modsw=-module= + build_dir=. + src=../src/ ++include = $EBROOTLIBAED2/include $EBROOTFORBEAR/include ++ext_libs = aed2 forbear + colors=False + quiet=False + target=simstrat.f90 +@@ -72,13 +54,14 @@ + lflags=-static-libgcc -static-libgfortran -static + build_dir=. + src=../src/ ++include = $EBROOTLIBAED2/include $EBROOTFORBEAR/include ++ext_libs = aed2 forbear + colors=False + quiet=False + target=simstrat.f90 + output=simstrat + dependon=../lib/csv_fortran/fobos:release-gnu((direct)) + ../lib/json_fortran/fobos:release-gnu((direct)) +- ../lib/forbear/fobos:static-gnu((direct)) + log=True + + [debug-gnu-dynamic] +@@ -87,12 +70,13 @@ + lflags=-dynamic-libgcc -dynamic-libgfortran -dynamic + build_dir=. + src=../src/ ++include = $EBROOTLIBAED2/include $EBROOTFORBEAR/include ++ext_libs = aed2 forbear + colors=False + quiet=False + target=simstrat.f90 + dependon=../lib/csv_fortran/fobos:release-gnu((direct)) + ../lib/json_fortran/fobos:release-gnu((direct)) +- ../lib/forbear/fobos:static-gnu((direct)) + log=True + + [rule-makedoc] From d19976d6c656e4ef8b301b99839340c214cd0661 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 25 Jan 2022 15:21:27 +0200 Subject: [PATCH 2810/9987] add build dependency on binutils to OpenCensus-python v0.8.0 --- .../OpenCensus-python-0.8.0-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenCensus-python/OpenCensus-python-0.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenCensus-python/OpenCensus-python-0.8.0-GCCcore-11.2.0.eb index 1ea498ec851..ece4366ea1f 100644 --- a/easybuild/easyconfigs/o/OpenCensus-python/OpenCensus-python-0.8.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenCensus-python/OpenCensus-python-0.8.0-GCCcore-11.2.0.eb @@ -11,6 +11,10 @@ related utilities and supporting software needed by OpenCensus.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +builddependencies = [ + ('binutils', '2.37'), +] + dependencies = [ ('Python', '3.9.6'), ('protobuf-python', '3.17.3'), From 85fdc576f64c91987ab2d10cc1fba9f74813ba00 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 25 Jan 2022 14:22:17 +0100 Subject: [PATCH 2811/9987] Add missing checksum and remove trailing space. --- easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb index f2f9d923062..9274a05f2cd 100644 --- a/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libaed2/libaed2-1.3.0-GCC-10.3.0.eb @@ -13,12 +13,13 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/AquaticEcoDynamics/libaed2/archive'] sources = ['v%(version)s.tar.gz'] +checksums = ['9152c2a5ac6da4162f73dc37c4a98e1cbd19a106195441b3d27a6df1911242f5'] buildopts = 'OPT_FFLAGS="$FFLAGS" ' files_to_copy = [ (['mod/*', 'include/*.h'], 'include'), - 'lib', + 'lib', ] maxparallel = 1 From 662857bd256d75b0711ae9abf7cb38951518afe9 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Tue, 25 Jan 2022 13:30:04 +0000 Subject: [PATCH 2812/9987] adding easyconfigs: QuantumESPRESSO-7.0-intel-2021b.eb, QuantumESPRESSO-7.0-foss-2021b.eb and patches: QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch --- .../QuantumESPRESSO-7.0-foss-2021b.eb | 47 +++ ...PRESSO-7.0-gipaw-string-preprocessor.patch | 393 ++++++++++++++++++ .../QuantumESPRESSO-7.0-intel-2021b.eb | 44 ++ 3 files changed, 484 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb new file mode 100644 index 00000000000..b74c30c4645 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb @@ -0,0 +1,47 @@ +name = 'QuantumESPRESSO' +version = '7.0' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s/', + 'https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + 'qe-gipaw-%(version)s.tar.gz', + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +patches = ['QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch'] +checksums = [ + '268ec506f88c56ba4e9b691c1e81e33a6ad7949f857f1c6c32197f9c2af2a957', # qe-%(version)s-ReleasePack.tgz + '11a9ac74724de83012398aecba6d06ab37cc0d4c73792d0d5ba6bca1a723ef70', # qe-gipaw-%(version)s.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + # QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch + '8c5026e0b6463f6690238d3aedffe18c7e8b2bfeb52be1454f934a43a2f91fd6', +] + +dependencies = [ + ('HDF5', '1.12.1'), + ('ELPA', '2021.05.001'), + ('libxc', '5.1.6'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch new file mode 100644 index 00000000000..57577470e7c --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch @@ -0,0 +1,393 @@ +Replace unsupported macros with expanded code + +The preprocessor in foss doesn't handle macros with stringification using # +which occurs GIPAW's xml_routines. + +Author: Lars Viklund (HPC2N, Umea University) + +diff -ru qe-gipaw-7.0.orig/src/xml_routines.f90 qe-gipaw-7.0/src/xml_routines.f90 +--- qe-gipaw-7.0.orig/src/xml_routines.f90 2022-01-13 13:48:03.000000000 +0000 ++++ qe-gipaw-7.0/src/xml_routines.f90 2022-01-24 09:56:30.414934470 +0000 +@@ -93,25 +93,25 @@ + timestamp = 'This run was terminated on: ' // ctime // ' ' // cdate(1:2) // ' '//cdate(3:5) // ' '// cdate (6:9) + + CHECK_IONODE +- _NE(general_info) +- _NE(xml_format) +- _ATTR(NAME, fmt_name) +- _ATTR(VERSION, fmt_version) ++ call XML_NewElement(xmlf, "general_info") ++ call XML_NewElement(xmlf, "xml_format") ++ call XML_AddAttribute(xmlf, "NAME", (fmt_name)) ++ call XML_AddAttribute(xmlf, "VERSION", (fmt_version)) + _ADDV(fmt_name//'_'//fmt_version) +- _EE(xml_format) +- _NE(creator) +- _ATTR(NAME, 'GIPAW') +- _ATTR(VERSION, gipaw_git_revision) ++ call XML_EndElement(xmlf, "xml_format") ++ call XML_NewElement(xmlf, "creator") ++ call XML_AddAttribute(xmlf, "NAME", ('GIPAW')) ++ call XML_AddAttribute(xmlf, "VERSION", (gipaw_git_revision)) + _ADDV('XML file generated by GIPAW') +- _EE(creator) +- _NE(created) +- _ATTR(DATE, cdate) +- _ATTR(TIME, ctime) ++ call XML_EndElement(xmlf, "creator") ++ call XML_NewElement(xmlf, "created") ++ call XML_AddAttribute(xmlf, "DATE", (cdate)) ++ call XML_AddAttribute(xmlf, "TIME", (ctime)) + _ADDS(timestamp) +- _EE(created) +- _NE(job) +- _EE(job) +- _EE(general_info) ++ call XML_EndElement(xmlf, "created") ++ call XML_NewElement(xmlf, "job") ++ call XML_EndElement(xmlf, "job") ++ call XML_EndElement(xmlf, "general_info") + + END SUBROUTINE xml_output_generalinfo + +@@ -131,20 +131,26 @@ + #endif + + CHECK_IONODE +- _NE(parallel_info) +- _NE(nprocs) ++ call XML_NewElement(xmlf, "parallel_info") ++ call XML_NewElement(xmlf, "nprocs") + _ADDV(nproc) +- _EE(nprocs) +- _OUTV(nthreads) +- _NE(ntasks) ++ call XML_EndElement(xmlf, "nprocs") ++ call XML_NewElement(xmlf, "nthreads") ++ call XML_AddCharacters(xmlf, (nthreads)) ++ call XML_EndElement(xmlf, "nthreads") ++ call XML_NewElement(xmlf, "ntasks") + _ADDV(ntask_groups) +- _EE(ntasks) +- _OUTV(nbgrp) +- _OUTV(npool) +- _NE(ndiag) ++ call XML_EndElement(xmlf, "ntasks") ++ call XML_NewElement(xmlf, "nbgrp") ++ call XML_AddCharacters(xmlf, (nbgrp)) ++ call XML_EndElement(xmlf, "nbgrp") ++ call XML_NewElement(xmlf, "npool") ++ call XML_AddCharacters(xmlf, (npool)) ++ call XML_EndElement(xmlf, "npool") ++ call XML_NewElement(xmlf, "ndiag") + _ADDV(nproc_ortho) +- _EE(ndiag) +- _EE(parallel_info) ++ call XML_EndElement(xmlf, "ndiag") ++ call XML_EndElement(xmlf, "parallel_info") + + END SUBROUTINE xml_output_parallelinfo + +@@ -160,42 +166,78 @@ + implicit none + + CHECK_IONODE +- _NE(input) +- _OUTS(job) +- _OUTS(prefix) +- _OUTS(tmp_dir) +- _OUTV(conv_threshold) +- _OUTS(restart_mode) +- _NE(q_gipaw) ++ call XML_NewElement(xmlf, "input") ++ call XML_NewElement(xmlf, "job") ++ call XML_AddCharacters(xmlf, trim((job))) ++ call XML_EndElement(xmlf, "job") ++ call XML_NewElement(xmlf, "prefix") ++ call XML_AddCharacters(xmlf, trim((prefix))) ++ call XML_EndElement(xmlf, "prefix") ++ call XML_NewElement(xmlf, "tmp_dir") ++ call XML_AddCharacters(xmlf, trim((tmp_dir))) ++ call XML_EndElement(xmlf, "tmp_dir") ++ call XML_NewElement(xmlf, "conv_threshold") ++ call XML_AddCharacters(xmlf, (conv_threshold)) ++ call XML_EndElement(xmlf, "conv_threshold") ++ call XML_NewElement(xmlf, "restart_mode") ++ call XML_AddCharacters(xmlf, trim((restart_mode))) ++ call XML_EndElement(xmlf, "restart_mode") ++ call XML_NewElement(xmlf, "q_gipaw") + _ADDV(q_gipaw*tpiba) +- _EE(q_gipaw) +- _OUTS(verbosity) +- _OUTS(filcurr) +- _OUTS(filfield) +- _OUTS(filnics) +- _OUTV(pawproj) +- _OUTV(use_nmr_macroscopic_shape) +- _NE(nmr_macroscopic_shape) +- _ATTR(rank, "2") +- _ATTR(dims, "3 3") ++ call XML_EndElement(xmlf, "q_gipaw") ++ call XML_NewElement(xmlf, "verbosity") ++ call XML_AddCharacters(xmlf, trim((verbosity))) ++ call XML_EndElement(xmlf, "verbosity") ++ call XML_NewElement(xmlf, "filcurr") ++ call XML_AddCharacters(xmlf, trim((filcurr))) ++ call XML_EndElement(xmlf, "filcurr") ++ call XML_NewElement(xmlf, "filfield") ++ call XML_AddCharacters(xmlf, trim((filfield))) ++ call XML_EndElement(xmlf, "filfield") ++ call XML_NewElement(xmlf, "filnics") ++ call XML_AddCharacters(xmlf, trim((filnics))) ++ call XML_EndElement(xmlf, "filnics") ++ call XML_NewElement(xmlf, "pawproj") ++ call XML_AddCharacters(xmlf, (pawproj)) ++ call XML_EndElement(xmlf, "pawproj") ++ call XML_NewElement(xmlf, "use_nmr_macroscopic_shape") ++ call XML_AddCharacters(xmlf, (use_nmr_macroscopic_shape)) ++ call XML_EndElement(xmlf, "use_nmr_macroscopic_shape") ++ call XML_NewElement(xmlf, "nmr_macroscopic_shape") ++ call XML_AddAttribute(xmlf, "rank", ("2")) ++ call XML_AddAttribute(xmlf, "dims", ("3 3")) + _ADDV(nmr_macroscopic_shape) +- _EE(nmr_macroscopic_shape) +- _OUTV(spline_ps) +- _OUTS(diagonalization) +- _NE(q_efg) +- _ATTR(size, nat) ++ call XML_EndElement(xmlf, "nmr_macroscopic_shape") ++ call XML_NewElement(xmlf, "spline_ps") ++ call XML_AddCharacters(xmlf, (spline_ps)) ++ call XML_EndElement(xmlf, "spline_ps") ++ call XML_NewElement(xmlf, "diagonalization") ++ call XML_AddCharacters(xmlf, trim((diagonalization))) ++ call XML_EndElement(xmlf, "diagonalization") ++ call XML_NewElement(xmlf, "q_efg") ++ call XML_AddAttribute(xmlf, "size", (nat)) + _ADDV(q_efg) +- _EE(q_efg) +- _OUTV(max_seconds) +- _OUTV(r_rand) +- _OUTS(hfi_output_unit) +- _NE(hfi_nuclear_g_factor) +- _ATTR(size, nat) ++ call XML_EndElement(xmlf, "q_efg") ++ call XML_NewElement(xmlf, "max_seconds") ++ call XML_AddCharacters(xmlf, (max_seconds)) ++ call XML_EndElement(xmlf, "max_seconds") ++ call XML_NewElement(xmlf, "r_rand") ++ call XML_AddCharacters(xmlf, (r_rand)) ++ call XML_EndElement(xmlf, "r_rand") ++ call XML_NewElement(xmlf, "hfi_output_unit") ++ call XML_AddCharacters(xmlf, trim((hfi_output_unit))) ++ call XML_EndElement(xmlf, "hfi_output_unit") ++ call XML_NewElement(xmlf, "hfi_nuclear_g_factor") ++ call XML_AddAttribute(xmlf, "size", (nat)) + _ADDV(hfi_nuclear_g_factor) +- _EE(hfi_nuclear_g_factor) +- _OUTV(core_relax_method) +- _OUTV(hfi_via_reconstruction_only) +- _EE(input) ++ call XML_EndElement(xmlf, "hfi_nuclear_g_factor") ++ call XML_NewElement(xmlf, "core_relax_method") ++ call XML_AddCharacters(xmlf, (core_relax_method)) ++ call XML_EndElement(xmlf, "core_relax_method") ++ call XML_NewElement(xmlf, "hfi_via_reconstruction_only") ++ call XML_AddCharacters(xmlf, (hfi_via_reconstruction_only)) ++ call XML_EndElement(xmlf, "hfi_via_reconstruction_only") ++ call XML_EndElement(xmlf, "input") + END SUBROUTINE xml_output_namelist + + +@@ -207,17 +249,17 @@ + + CHECK_IONODE + +- _NE(susceptibility_low) +- _ATTR(rank, '2') +- _ATTR(dims, '3 3') ++ call XML_NewElement(xmlf, "susceptibility_low") ++ call XML_AddAttribute(xmlf, "rank", ('2')) ++ call XML_AddAttribute(xmlf, "dims", ('3 3')) + _ADDV(res_suscept1) +- _EE(susceptibility_low) ++ call XML_EndElement(xmlf, "susceptibility_low") + +- _NE(susceptibility_high) +- _ATTR(rank, '2') +- _ATTR(dims, '3 3') ++ call XML_NewElement(xmlf, "susceptibility_high") ++ call XML_AddAttribute(xmlf, "rank", ('2')) ++ call XML_AddAttribute(xmlf, "dims", ('3 3')) + _ADDV(res_suscept2) +- _EE(susceptibility_high) ++ call XML_EndElement(xmlf, "susceptibility_high") + + END SUBROUTINE xml_output_susceptibility + +@@ -231,12 +273,12 @@ + integer, intent(in) :: na + character(*) :: rank, dims, units + +- _ATTR(name, trim(atm(ityp(na)))) +- _ATTR(tau, tau(:,na)) +- _ATTR(index, na) +- _ATTR(rank, rank) +- _ATTR(dims, dims) +- _ATTR(units, units) ++ call XML_AddAttribute(xmlf, "name", (trim(atm(ityp(na))))) ++ call XML_AddAttribute(xmlf, "tau", (tau(:,na))) ++ call XML_AddAttribute(xmlf, "index", (na)) ++ call XML_AddAttribute(xmlf, "rank", (rank)) ++ call XML_AddAttribute(xmlf, "dims", (dims)) ++ call XML_AddAttribute(xmlf, "units", (units)) + + END SUBROUTINE xml_atom_attributes + +@@ -251,65 +293,65 @@ + integer :: na + + CHECK_IONODE +- _NE(output) ++ call XML_NewElement(xmlf, "output") + + !! if (job == 'nmr') then + call xml_output_susceptibility +- _NE(shielding_tensors) ++ call XML_NewElement(xmlf, "shielding_tensors") + do na = 1, nat +- _NE(atom) ++ call XML_NewElement(xmlf, "atom") + call xml_atom_attributes(na, 'ppm', '2', '3 3') + _ADDV(res_nmr_sigma(:,:,na)) +- _EE(atom) ++ call XML_EndElement(xmlf, "atom") + enddo +- _EE(shielding_tensors) ++ call XML_EndElement(xmlf, "shielding_tensors") + !! endif + + !! if (job == 'g_tensor') then + !! call xml_output_susceptibility +- _NE(delta_g) +- _ATTR(rank, '2') +- _ATTR(dims, '3 3') ++ call XML_NewElement(xmlf, "delta_g") ++ call XML_AddAttribute(xmlf, "rank", ('2')) ++ call XML_AddAttribute(xmlf, "dims", ('3 3')) + _ADDV(res_epr_deltag) +- _EE(delta_g) +- _NE(delta_g_paratec) +- _ATTR(rank, '2') +- _ATTR(dims, '3 3') ++ call XML_EndElement(xmlf, "delta_g") ++ call XML_NewElement(xmlf, "delta_g_paratec") ++ call XML_AddAttribute(xmlf, "rank", ('2')) ++ call XML_AddAttribute(xmlf, "dims", ('3 3')) + _ADDV(res_epr_deltag_paratec) +- _EE(delta_g_paratec) ++ call XML_EndElement(xmlf, "delta_g_paratec") + !! endif + + !! if (job == 'efg') then +- _NE(electric_field_gradients) ++ call XML_NewElement(xmlf, "electric_field_gradients") + do na = 1, nat +- _NE(atom) ++ call XML_NewElement(xmlf, "atom") + call xml_atom_attributes(na, 'MHz', '2', '3 3') + _ADDV(res_efg(:,:,na)) +- _EE(atom) ++ call XML_EndElement(xmlf, "atom") + enddo +- _EE(electric_field_gradients) ++ call XML_EndElement(xmlf, "electric_field_gradients") + !! endif + + !! if (job == 'hyperfine') then +- _NE(hyperfine_dipolar) ++ call XML_NewElement(xmlf, "hyperfine_dipolar") + do na = 1, nat +- _NE(atom) ++ call XML_NewElement(xmlf, "atom") + call xml_atom_attributes(na, trim(hfi_output_unit), '2', '3 3') + _ADDV(res_hfi_dip(:,:,na)) +- _EE(atom) ++ call XML_EndElement(xmlf, "atom") + enddo +- _EE(hyperfine_dipolar) +- _NE(hyperfine_fermi_contact) ++ call XML_EndElement(xmlf, "hyperfine_dipolar") ++ call XML_NewElement(xmlf, "hyperfine_fermi_contact") + do na = 1, nat +- _NE(atom) ++ call XML_NewElement(xmlf, "atom") + call xml_atom_attributes(na, trim(hfi_output_unit), '1', '1') + _ADDV(res_hfi_fc(na)) +- _EE(atom) ++ call XML_EndElement(xmlf, "atom") + enddo +- _EE(hyperfine_fermi_contact) ++ call XML_EndElement(xmlf, "hyperfine_fermi_contact") + !! endif + +- _EE(output) ++ call XML_EndElement(xmlf, "output") + + END SUBROUTINE xml_output_results + +@@ -321,7 +363,9 @@ + integer :: exit_status = 0 + + CHECK_IONODE +- _OUTV(exit_status) ++ call XML_NewElement(xmlf, "exit_status") ++ call XML_AddCharacters(xmlf, (exit_status)) ++ call XML_EndElement(xmlf, "exit_status") + + END SUBROUTINE xml_output_status + +@@ -334,10 +378,10 @@ + + CHECK_IONODE + call date_and_tim(cdate, ctime) +- _NE(closed) +- _ATTR(DATE, cdate) +- _ATTR(TIME, ctime) +- _EE(closed) ++ call XML_NewElement(xmlf, "closed") ++ call XML_AddAttribute(xmlf, "DATE", (cdate)) ++ call XML_AddAttribute(xmlf, "TIME", (ctime)) ++ call XML_EndElement(xmlf, "closed") + + END SUBROUTINE xml_output_closed + +@@ -352,17 +396,21 @@ + real(dp) :: wall, cpu + + CHECK_IONODE +- _NE(timing_info) +- _NE(total) +- _ATTR(label, 'GIPAW') ++ call XML_NewElement(xmlf, "timing_info") ++ call XML_NewElement(xmlf, "total") ++ call XML_AddAttribute(xmlf, "label", ('GIPAW')) + cpu = f_tcpu() + wall = f_wall() + !wall = get_clock('GIPAW') +- _OUTV(cpu) +- _OUTV(wall) +- _EE(total) ++ call XML_NewElement(xmlf, "cpu") ++ call XML_AddCharacters(xmlf, (cpu)) ++ call XML_EndElement(xmlf, "cpu") ++ call XML_NewElement(xmlf, "wall") ++ call XML_AddCharacters(xmlf, (wall)) ++ call XML_EndElement(xmlf, "wall") ++ call XML_EndElement(xmlf, "total") + +- _EE(timing_info) ++ call XML_EndElement(xmlf, "timing_info") + + END SUBROUTINE xml_output_timinginfo + diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb new file mode 100644 index 00000000000..065de8035bb --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb @@ -0,0 +1,44 @@ +name = 'QuantumESPRESSO' +version = '7.0' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://github.com/QEF/q-e/releases/download/qe-%(version)s/', + 'https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'qe-%(version)s-ReleasePack.tgz', + 'qe-gipaw-%(version)s.tar.gz', + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + '268ec506f88c56ba4e9b691c1e81e33a6ad7949f857f1c6c32197f9c2af2a957', # qe-%(version)s-ReleasePack.tgz + '11a9ac74724de83012398aecba6d06ab37cc0d4c73792d0d5ba6bca1a723ef70', # qe-gipaw-%(version)s.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.12.1'), + ('ELPA', '2021.05.001'), + ('libxc', '5.1.6'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' From 653094fa42140d82401df507fb2cde8b2b4be5c5 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Tue, 25 Jan 2022 14:06:31 +0000 Subject: [PATCH 2813/9987] Add ELPA easyconfig with intel toolchain --- .../e/ELPA/ELPA-2021.05.001-intel-2021b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021b.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021b.eb new file mode 100644 index 00000000000..38b241fe40c --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021b.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2021.05.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + 'aea66a18e87574c7c292e852e45943e16f8bc3839f456635d1d610957840d146', # elpa-new_release_2021.05.001.tar.gz + # ELPA-2021.05.001_fix_hardcoded_perl_path.patch + 'af3f8cd063100d403cb2fe53cfc85eb2d5a2ef3348a3e6d5cf2d3680ebb4ec02', +] + +builddependencies = [ + ('Autotools', '20210726'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.9.6'), + ('Perl', '5.34.0'), +] + +preconfigopts = './autogen.sh && ' +# If the build is running in a batch job, make sure Intel libmpi does +# not try to use Slurm to run the MPI_THREAD test code that ELPA's +# configure is running without "mpirun". +preconfigopts += 'unset SLURM_JOBID && unset SLURM_NODELIST && unset I_MPI_PMI_LIBRARY && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' From eff817b1057b0f088876ecf822dcd85d3a8fb332 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 25 Jan 2022 14:30:27 +0000 Subject: [PATCH 2814/9987] adding easyconfigs: NCIPLOT-4.0-20200624-GCC-11.2.0.eb --- .../NCIPLOT-4.0-20200624-GCC-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20200624-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20200624-GCC-11.2.0.eb b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20200624-GCC-11.2.0.eb new file mode 100644 index 00000000000..9c7fb809303 --- /dev/null +++ b/easybuild/easyconfigs/n/NCIPLOT/NCIPLOT-4.0-20200624-GCC-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'NCIPLOT' +local_ver = '4.0' +version = '%s-20200624' % local_ver +local_commit = 'b88012d' + +homepage = 'https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html' +description = """ NCIPLOT is a program for revealing non covalent interactions + based on the reduced density gradient. """ + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/juliacontrerasgarcia/nciplot/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['0fec094f024b5b6dd3c665e31c6a4528e9e46920d693cf9bfeb4dcf2e0cc1614'] + +start_dir = 'src_%%(namelower)s_%s' % local_ver + +prebuildopts = "sed -i -e 's/include Makefile.inc//g' -e 's/nciplot: $(OBJS) $(LIBS)/nciplot: $(OBJS)/g' Makefile && " +prebuildopts += "make clean && " +buildopts = 'LIBS="$LIBS" LDFLAGS="-fopenmp $LDFLAGS"' + +postinstallcmds = ["export OMP_NUM_THREADS=%(parallel)s && cd %(builddir)s/%(namelower)s-*/tests && ./alltests.sh "] + +files_to_copy = ['dat', 'LICENSE', 'README', 'NCIPLOT_MANUAL.pdf', (['nciplot'], 'bin')] + +modextrapaths = {'NCIPLOT_HOME': ''} + +sanity_check_paths = { + 'files': ['bin/nciplot'], + 'dirs': ['dat'], +} + +modloadmsg = """ +Set environment variable OMP_NUM_THREADS equal to the number of available cores before running this program. +""" + +moduleclass = 'chem' From 7e3076bdf1c517b03f65bc924f484866ab3c1bda Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 25 Jan 2022 17:11:30 +0100 Subject: [PATCH 2815/9987] adding easyconfigs: CLHEP-2.4.4.0-GCC-11.2.0.eb, Geant4-10.7.1-GCC-11.2.0.eb --- .../c/CLHEP/CLHEP-2.4.4.0-GCC-11.2.0.eb | 27 +++++++++++++++++++ .../g/Geant4/Geant4-10.7.1-GCC-11.2.0.eb | 26 ++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.4.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.4.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.4.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..32e420b3175 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.4.0-GCC-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.4.0' + +homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] +sources = [SOURCELOWER_TGZ] +checksums = ['5df78c11733a091da9ae5a24ce31161d44034dd45f20455587db85f1ca1ba539'] + +builddependencies = [('CMake', '3.22.1')] + +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-11.2.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..7f6420d089f --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +name = 'Geant4' +version = '10.7.1' + +homepage = 'https://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'Geant4' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['a22800227713b46ba0b71bc674f6c937e5cc0cf17a6becf4a10d5ef90693a60b'] + +builddependencies = [('CMake', '3.22.1')] +dependencies = [ + ('expat', '2.4.1'), + # recommended CLHEP version, see https://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.6.html + ('CLHEP', '2.4.4.0'), +] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += " -DCLHEP_ROOT_DIR=$EBROOTCLHEP -DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' From 5b26a0b2debb40c0064ba8288cd631becd907396 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 25 Jan 2022 17:38:04 +0100 Subject: [PATCH 2816/9987] Update of jupyter-server-proxy because of CVE-2022-21697 --- ...pyter-server-proxy-3.2.1-GCCcore-10.3.0.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c4f04efec59 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server-proxy' +version = '3.2.1' + +homepage = 'https://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed + for centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] +dependencies = [ + ('Python', '3.9.5'), + ('JupyterHub', '1.4.1'), + ('OpenSSL', '1.1', '', True), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('sniffio', '1.2.0', { + 'checksums': ['c4666eecec1d3f50960c6bdf61ab7bc350648da6c126e3cf6898d8cd4ddcd3de'], + }), + ('anyio', version, { + 'checksums': ['07968db9fa7c1ca5435a133dc62f988d84ef78e1d9b22814a59d1c62618afbc5'], + }), + ('requests-unixsocket', '0.2.0', { + 'checksums': ['9e5c1a20afc3cf786197ae59c79bcdb0e7565f218f27df5f891307ee8817c1ea'], + }), + ('websocket-client', '1.1.0', { + 'modulename': 'websocket', + 'checksums': ['b68e4959d704768fa20e35c9d508c8dc2bbc041fd8d267c0d7345cffe2824568'], + }), + ('jupyter-server', '1.9.0', { + 'source_tmpl': 'jupyter_server-%(version)s.tar.gz', + 'checksums': ['7d19006380f6217458a9db309b54e3dab87ced6c06329c61823907bef2a6f51b'], + }), + ('simpervisor', '0.4', { + 'checksums': ['cec79e13cdbd6edb04a5c98c1ff8d4bd9713e706c069226909a1ef0e89d393c5'], + }), + ('multidict', '5.1.0', { + 'checksums': ['25b4e5f22d3a37ddf3effc0710ba692cfc792c2b9edfb9c05aefe823256e84d5'], + }), + ('async-timeout', '3.0.1', { + 'checksums': ['0c3c816a028d47f659d6ff5c745cb2acf1f966da1fe5c19c77a70282b25f4c5f'], + }), + ('typing-extensions', '3.10.0.0', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342'], + }), + ('yarl', '1.6.3', { + 'checksums': ['8a9066529240171b68893d60dca86a763eae2139dd42f42106b03cf4b426bf10'], + }), + ('aiohttp', '3.7.4.post0', { + 'checksums': ['493d3299ebe5f5a7c66b9819eacdcfbbaaf1a8e84911ddffcdc48888497afecf'], + }), + (name, version, { + 'checksums': ['080e9910592d06422bdd93dfc1fa8350c6fdaec9fbbd050630e90f7a5593a4f7'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyter_server_proxy'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'tools' From 147a23b6f283831ea839bde43ce82df2a1895120 Mon Sep 17 00:00:00 2001 From: "josef.dvoracek" Date: Wed, 26 Jan 2022 13:02:35 +0100 Subject: [PATCH 2817/9987] adding easyconfigs: ConnectomeWorkbench-1.5.0-foss-2021a.eb --- .../ConnectomeWorkbench-1.5.0-foss-2021a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb new file mode 100644 index 00000000000..ad53f63a5ee --- /dev/null +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'ConnectomeWorkbench' +version = '1.5.0' + +homepage = 'https://www.humanconnectome.org/software/connectome-workbench' +description = """Connectome Workbench is an open source, freely available visualization + and discovery tool used to map neuroimaging data, especially data generated by the + Human Connectome Project.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/Washington-University/workbench/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6410f5cdaed2158d99871962fb27ce9fdfad6fa7dad496b93ff8bce0a8070cc4'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Qt5', '5.15.2'), + ('Mesa', '21.1.1'), +] + +start_dir = 'src' + +configopts = '-DCMAKE_BUILD_TYPE=Release -DWORKBENCH_MESA_DIR=${EBROOTMESA} ' +configopts += '-DWORKBENCH_USE_QT5=TRUE -DWORKBENCH_USE_QT5_QOPENGL_WIDGET=TRUE -Wno-dev ' + +# It is necessary to deactivate the SIMD optimization in order to build +# kloewe/dot correctly. This should not affect the overall optimization since +# compiler flags are passed by EB via CFLAGS and CXXFLAGS. +# See https://github.com/Washington-University/workbench/issues/34 +configopts += '-DWORKBENCH_USE_SIMD=FALSE ' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/wb_command', 'bin/wb_shortcuts', 'bin/wb_view'], + 'dirs': ['share'], +} + +moduleclass = 'bio' From 9c03fb01d6a884b3f9cd8e648730308ed4911f1f Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 26 Jan 2022 12:27:06 +0000 Subject: [PATCH 2818/9987] adding easyconfigs: xxd-8.2.4220-GCC-11.2.0.eb, xxd-8.2.4220-GCC-10.2.0.eb, xxd-8.2.4220-GCC-10.3.0.eb --- .../x/xxd/xxd-8.2.4220-GCC-10.2.0.eb | 33 +++++++++++++++++++ .../x/xxd/xxd-8.2.4220-GCC-10.3.0.eb | 33 +++++++++++++++++++ .../x/xxd/xxd-8.2.4220-GCC-11.2.0.eb | 33 +++++++++++++++++++ 3 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb new file mode 100644 index 00000000000..c859cfc9458 --- /dev/null +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb @@ -0,0 +1,33 @@ +# Last contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'xxd' +version = '8.2.4220' + +homepage = 'https://www.vim.org' +description = """xxd is part of the VIM package and this will only install xxd, not vim! +xxd converts to/from hexdumps of binary files.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +sources = ['https://github.com/vim/vim/archive/refs/tag'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz +] + +start_dir = 'src/xxd' + +files_to_copy = [ + (['xxd'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/xxd'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb new file mode 100644 index 00000000000..96e86f2a023 --- /dev/null +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb @@ -0,0 +1,33 @@ +# Last contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'xxd' +version = '8.2.4220' + +homepage = 'https://www.vim.org' +description = """xxd is part of the VIM package and this will only install xxd, not vim! +xxd converts to/from hexdumps of binary files.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +sources = ['https://github.com/vim/vim/archive/refs/tag'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz +] + +start_dir = 'src/xxd' + +files_to_copy = [ + (['xxd'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/xxd'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb new file mode 100644 index 00000000000..9ce2bfd75bd --- /dev/null +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb @@ -0,0 +1,33 @@ +# Last contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'xxd' +version = '8.2.4220' + +homepage = 'https://www.vim.org' +description = """xxd is part of the VIM package and this will only install xxd, not vim! +xxd converts to/from hexdumps of binary files.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = ['https://github.com/vim/vim/archive/refs/tag'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz +] + +start_dir = 'src/xxd' + +files_to_copy = [ + (['xxd'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/xxd'], + 'dirs': [], +} + +moduleclass = 'tools' From d6e862c1cda467425ecf02df3a9e37304bce36bb Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 26 Jan 2022 12:42:23 +0000 Subject: [PATCH 2819/9987] Download URL line corrected (typos) --- easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb | 2 +- easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb index c859cfc9458..112d6ed417e 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb @@ -13,7 +13,7 @@ xxd converts to/from hexdumps of binary files.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} -sources = ['https://github.com/vim/vim/archive/refs/tag'] +source_urls = ['https://github.com/vim/vim/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] checksums = [ '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb index 96e86f2a023..ea5d59fed0b 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb @@ -13,7 +13,7 @@ xxd converts to/from hexdumps of binary files.""" toolchain = {'name': 'GCC', 'version': '10.3.0'} -sources = ['https://github.com/vim/vim/archive/refs/tag'] +source_urls = ['https://github.com/vim/vim/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] checksums = [ '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb index 9ce2bfd75bd..ebfef6067ae 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb @@ -13,7 +13,7 @@ xxd converts to/from hexdumps of binary files.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} -sources = ['https://github.com/vim/vim/archive/refs/tag'] +source_urls = ['https://github.com/vim/vim/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] checksums = [ '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz From 3e212509b9810124463fa26e6394f5681f831bd0 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 26 Jan 2022 12:56:18 +0000 Subject: [PATCH 2820/9987] xxd builddependencies added (see PR 14846) --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb | 4 ++++ easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb | 4 ++++ easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb | 4 ++++ 3 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb index 3fb97d9ba7c..da1d6cc2774 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb @@ -20,6 +20,10 @@ source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s sources = [SOURCE_TGZ] checksums = ['1ab3153db2010406852b30201ed94112e25eca4c4c8c4b41a29c22a7a3303f96'] +builddependencies = [ + ('xxd', '8.2.4220'), +] + dependencies = [ ('zlib', '1.2.11'), ('GSL', '2.6'), diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb index 05666961bc2..efbec7485f0 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb @@ -18,6 +18,10 @@ source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s sources = [SOURCE_TGZ] checksums = ['b23399a3300ce3ae080e81263274ab8551e00217c3f37cb33cb7e37954fe8572'] +builddependencies = [ + ('xxd', '8.2.4220'), +] + dependencies = [ ('zlib', '1.2.11'), ('GSL', '2.6'), diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb index ba5e629146f..886f07ba021 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb @@ -18,6 +18,10 @@ source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s sources = [SOURCE_TGZ] checksums = ['6069bc134f74cb15dd63e27e3587a15a31a9ddd9e7eebdd717da898f31512645'] +builddependencies = [ + ('xxd', '8.2.4220'), +] + dependencies = [ ('zlib', '1.2.11'), ('GSL', '2.7'), From e343d60758a272f285e5710cddae81aa1104c512 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 26 Jan 2022 13:02:18 +0000 Subject: [PATCH 2821/9987] Changed to GCCcore --- ...xd-8.2.4220-GCC-10.2.0.eb => xxd-8.2.4220-GCCcore-10.2.0.eb} | 2 +- ...xd-8.2.4220-GCC-10.3.0.eb => xxd-8.2.4220-GCCcore-10.3.0.eb} | 2 +- ...xd-8.2.4220-GCC-11.2.0.eb => xxd-8.2.4220-GCCcore-11.2.0.eb} | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/x/xxd/{xxd-8.2.4220-GCC-10.2.0.eb => xxd-8.2.4220-GCCcore-10.2.0.eb} (93%) rename easybuild/easyconfigs/x/xxd/{xxd-8.2.4220-GCC-10.3.0.eb => xxd-8.2.4220-GCCcore-10.3.0.eb} (93%) rename easybuild/easyconfigs/x/xxd/{xxd-8.2.4220-GCC-11.2.0.eb => xxd-8.2.4220-GCCcore-11.2.0.eb} (93%) diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb similarity index 93% rename from easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb rename to easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb index 112d6ed417e..1248cb3faf5 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb @@ -11,7 +11,7 @@ homepage = 'https://www.vim.org' description = """xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.""" -toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/vim/vim/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb similarity index 93% rename from easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb rename to easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb index ea5d59fed0b..1c295932f24 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb @@ -11,7 +11,7 @@ homepage = 'https://www.vim.org' description = """xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.""" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/vim/vim/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb similarity index 93% rename from easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb rename to easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb index ebfef6067ae..e22ecf42336 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb @@ -11,7 +11,7 @@ homepage = 'https://www.vim.org' description = """xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.""" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/vim/vim/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] From c7a391f5cdf431594e3a826e1cf914633056073e Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 26 Jan 2022 16:02:53 +0200 Subject: [PATCH 2822/9987] adding easyconfigs: pytest-xdist-2.5.0-GCCcore-11.2.0.eb --- .../pytest-xdist-2.5.0-GCCcore-11.2.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.5.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.5.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..073e6f7d238 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.5.0-GCCcore-11.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'pytest-xdist' +version = '2.5.0' + +homepage = 'https://github.com/pytest-dev/pytest-xdist' +description = """xdist: pytest distributed testing plugin + +The pytest-xdist plugin extends pytest with some unique test execution modes: + + * test run parallelization: if you have multiple CPUs or hosts you + can use those for a combined test run. This allows to speed up + development or to use special resources of remote machines. + + * --looponfail: run your tests repeatedly in a subprocess. After + each run pytest waits until a file in your project changes and + then re-runs the previously failing tests. This is repeated + until all tests pass after which again a full run is + performed. + + * Multi-Platform coverage: you can specify different Python + interpreters or different platforms and run tests in parallel on + all of them. + +Before running tests remotely, pytest efficiently “rsyncs” your +program source code to the remote place. All test results are reported +back and displayed to your local terminal. You may specify different +Python versions and interpreters.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('apipkg', '1.5', { + 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], + }), + ('execnet', '1.9.0', { + 'checksums': ['8f694f3ba9cc92cab508b152dcfe322153975c29bda272e2fd7f3f00f36e47c5'], + }), + ('pytest-forked', '1.4.0', { + 'checksums': ['8b67587c8f98cbbadfdd804539ed5455b6ed03802203485dd2f53c1422d7440e'], + }), + (name, version, { + 'modulename': 'xdist', + 'checksums': ['4580deca3ff04ddb2ac53eba39d76cb5dd5edeac050cb6fbc768b0dd712b4edf'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From cb29178260860502f0f8908a8dfa5fbc2859b338 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 26 Jan 2022 15:05:05 +0100 Subject: [PATCH 2823/9987] adding easyconfigs: atools-1.4.8-GCCcore-10.3.0-Python-2.7.18.eb --- ...ools-1.4.8-GCCcore-10.3.0-Python-2.7.18.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/atools/atools-1.4.8-GCCcore-10.3.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/a/atools/atools-1.4.8-GCCcore-10.3.0-Python-2.7.18.eb b/easybuild/easyconfigs/a/atools/atools-1.4.8-GCCcore-10.3.0-Python-2.7.18.eb new file mode 100644 index 00000000000..cb6cac13604 --- /dev/null +++ b/easybuild/easyconfigs/a/atools/atools-1.4.8-GCCcore-10.3.0-Python-2.7.18.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'atools' +version = '1.4.8' +versionsuffix = '-Python-2.7.18' + +homepage = 'https://github.com/gjbex/atools' +description = """Tools to make using job arrays a lot more convenient.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/gjbex/atools/archive'] +sources = [SOURCE_TAR_GZ] +checksums = ['21f60a8f6dde4ee1e97bac1bef306a314c1200d3bd8ec0f9b865d5e697585de8'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '2.7.18', '-bare')] + +# to enable SLURM integration (site-specific) (options are torque, moab, sge, slurm) +configopts = '--with-batchsystem=slurm' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acreate', 'aenv', 'aload', 'alog', 'arange', 'areduce']], + 'dirs': ['lib/vsc/atools'] +} + +sanity_check_commands = [ + 'acreate -h', + 'aenv -h', + 'aload -h', + 'alog -h', + 'arange -h', + 'areduce -h', +] + +moduleclass = 'tools' From c7e248abf3dab0f7eae9af7dfcd0096fb827793e Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 26 Jan 2022 14:06:11 +0000 Subject: [PATCH 2824/9987] Missing binutils build dependeny added --- easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb | 4 ++++ easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb | 4 ++++ easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb | 4 ++++ 3 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb index 1248cb3faf5..d731b2429f9 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb @@ -19,6 +19,10 @@ checksums = [ '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz ] +builddependencies = [ + ('binutils', '2.35'), +] + start_dir = 'src/xxd' files_to_copy = [ diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb index 1c295932f24..e67c450e4eb 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb @@ -19,6 +19,10 @@ checksums = [ '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz ] +builddependencies = [ + ('binutils', '2.36.1'), +] + start_dir = 'src/xxd' files_to_copy = [ diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb index e22ecf42336..6d0ed44c3cd 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb @@ -19,6 +19,10 @@ checksums = [ '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz ] +builddependencies = [ + ('binutils', '2.37'), +] + start_dir = 'src/xxd' files_to_copy = [ From 7acccaf1667af0be16732a8464c5c9360e1b17b1 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 26 Jan 2022 19:47:45 +0000 Subject: [PATCH 2825/9987] adding easyconfigs: pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb --- ...radiomics-3.0.1-foss-2019b-Python-3.7.4.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..b83df90431e --- /dev/null +++ b/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'pyradiomics' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pyradiomics.readthedocs.io/' +description = """Open-source python package for the extraction of Radiomics features from 2D and 3D + images and binary masks.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SimpleITK', '1.2.4', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('numpy', '1.18.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + }), + ('PyWavelets', '1.2.0', { + 'modulename': 'pywt', + 'checksums': ['6cbd69b047bb4e00873097472133425f5f08a4e6bc8b3f0ae709274d4d5e9a8d'], + }), + ('pykwalify', '1.8.0', { + 'checksums': ['796b2ad3ed4cb99b88308b533fb2f559c30fa6efb4fa9fda11347f483d245884'], + }), + ('ruamel.yaml.clib', '0.2.6', { + 'modulename': False, # skip import check, covered by import check for ruamel.yaml extension + }), + ('ruamel.yaml', '0.17.20', { + }), + (name, version, { + 'modulename': 'radiomics', + 'checksums': ['47c57f441d6cb7973fa3b2ea48d3948df78e3348e1c69e1e2ff19001601fc2f5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyradiomics'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyradiomics --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 2585d099b8b750e0c2fc5c19a7c15570494a20b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Jan 2022 20:53:35 +0100 Subject: [PATCH 2826/9987] sync with main + bump version to 4.5.3dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 663b9046087..cae82ab6556 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.2' +VERSION = '4.5.3.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From a4a25142640b2f88f313d66c069aa4fe46ab1738 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 26 Jan 2022 20:14:53 +0000 Subject: [PATCH 2827/9987] Add missing checksums --- .../pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb index b83df90431e..0236db1734b 100644 --- a/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb @@ -20,6 +20,7 @@ use_pip = True exts_list = [ ('numpy', '1.18.0', { 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['a9d72d9abaf65628f0f31bbb573b7d9304e43b1e6bbae43149c17737a42764c4'], }), ('PyWavelets', '1.2.0', { 'modulename': 'pywt', @@ -29,9 +30,11 @@ exts_list = [ 'checksums': ['796b2ad3ed4cb99b88308b533fb2f559c30fa6efb4fa9fda11347f483d245884'], }), ('ruamel.yaml.clib', '0.2.6', { - 'modulename': False, # skip import check, covered by import check for ruamel.yaml extension + 'modulename': False, + 'checksums': ['4ff604ce439abb20794f05613c374759ce10e3595d1867764dd1ae675b85acbd'], }), ('ruamel.yaml', '0.17.20', { + 'checksums': ['4b8a33c1efb2b443a93fcaafcfa4d2e445f8e8c29c528d9f5cdafb7cc9e4004c'], }), (name, version, { 'modulename': 'radiomics', From bc46a51f3b92b7f95779a9b3c9442b8edbc58407 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 27 Jan 2022 07:31:49 +0100 Subject: [PATCH 2828/9987] adding easyconfigs: intervaltree-0.1-GCCcore-11.2.0.eb and patches: intervaltree-0.1_fix-numeric_limits.patch --- .../intervaltree-0.1-GCCcore-11.2.0.eb | 36 +++++++++++++++++++ .../intervaltree-0.1_fix-numeric_limits.patch | 25 +++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-0.1_fix-numeric_limits.patch diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d34ab952852 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'intervaltree' +version = '0.1' + +homepage = 'https://github.com/ekg/intervaltree' +description = """An interval tree can be used to efficiently find a set of numeric intervals + overlapping or containing another interval. This library provides a basic implementation of an + interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-numeric_limits.patch'] +checksums = [ + '7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307', # v0.1.tar.gz + 'bd0adcba152049334e16cb689b416311df85fe87d777432919bca18b162a9024', # intervaltree-0.1_fix-numeric_limits.patch +] + +builddependencies = [('binutils', '2.37')] + +skipsteps = ['configure'] + +preinstallopts = 'DESTDIR="" PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/interval_tree_test', 'include/intervaltree/IntervalTree.h'], + 'dirs': [], +} +sanity_check_commands = ["interval_tree_test"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1_fix-numeric_limits.patch b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1_fix-numeric_limits.patch new file mode 100644 index 00000000000..68ab2af524a --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1_fix-numeric_limits.patch @@ -0,0 +1,25 @@ +include for numeric_limits otherwise build failes with GCC 11 +https://www.gnu.org/software/gcc/gcc-11/porting_to.html +author: Paul Jähne +diff -ru intervaltree.orig/IntervalTree.h intervaltree/IntervalTree.h +--- intervaltree.orig/IntervalTree.h 2022-01-27 07:13:17.314126848 +0100 ++++ intervaltree/IntervalTree.h 2022-01-27 07:16:04.743740855 +0100 +@@ -6,6 +6,7 @@ + #include + #include + #include ++#include + + #ifdef USE_INTERVAL_TREE_NAMESPACE + namespace interval_tree { +diff -ru intervaltree.orig/interval_tree_test.cpp intervaltree/interval_tree_test.cpp +--- intervaltree.orig/interval_tree_test.cpp 2022-01-27 07:13:17.314126848 +0100 ++++ intervaltree/interval_tree_test.cpp 2022-01-27 07:15:55.459872595 +0100 +@@ -2,6 +2,7 @@ + #include + #include + #include ++#include + #include + #include + #include "IntervalTree.h" From 5b089bf9d29384e866e02d2e36b445b2ff595f1f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 27 Jan 2022 09:00:11 +0100 Subject: [PATCH 2829/9987] adding easyconfigs: multichoose-1.0.3-GCCcore-11.2.0.eb and patches: multichoose-1.0.3_improve-build-system.patch --- .../multichoose-1.0.3-GCCcore-11.2.0.eb | 32 ++++++++++++++++++ ...ltichoose-1.0.3_improve-build-system.patch | 33 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/multichoose/multichoose-1.0.3_improve-build-system.patch diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..dc99da99349 --- /dev/null +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'multichoose' +version = '1.0.3' + +homepage = 'https://github.com/ekg/multichoose' +description = """generate multiset combinations (n multichoose k).""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_improve-build-system.patch'] +checksums = [ + '74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877', # v1.0.3.tar.gz + '5921f69b47f65782ab7656e9f1396254cdfc8c67576217141e77729a5ab0084b', # multichoose-1.0.3_improve-build-system.patch +] + +builddependencies = [('binutils', '2.37')] + +local_bins = [name, 'multipermute'] +files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/%(name)s')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s 1 a'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3_improve-build-system.patch b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3_improve-build-system.patch new file mode 100644 index 00000000000..b7e9e5256a4 --- /dev/null +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3_improve-build-system.patch @@ -0,0 +1,33 @@ +make build system more flexible +author: Paul Jähne +diff -ru multichoose.orig/Makefile multichoose/Makefile +--- multichoose.orig/Makefile 2022-01-27 08:53:35.738914531 +0100 ++++ multichoose/Makefile 2014-12-03 18:04:41.000000000 +0100 +@@ -1,21 +1,17 @@ +-CC ?= gcc +-CXX ?= g++ +- + all: multichoose multipermute + + #multichoose_recursive: multichoose_recursive.cpp +-# ${CXX} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multichoose_recursive.cpp -o multichoose_recursive ++# g++ multichoose_recursive.cpp -o multichoose_recursive + + multichoose: multichoose.cpp multichoose.h +- ${CXX} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multichoose.cpp -o multichoose ++ g++ multichoose.cpp -o multichoose + + multipermute: multipermute.cpp multipermute.h +- ${CXX} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multipermute.cpp -o multipermute ++ g++ multipermute.cpp -o multipermute + + cmultichoose: multichoose.c +- ${CC} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multichoose.c -o cmultichoose ++ gcc multichoose.c -o cmultichoose + + clean: +- rm -f cmultichoose +- rm -f multichoose +- rm -f multipermute ++ rm cmultichoose ++ rm multichoose From 12c898e348f57a0403c76ecbd36edfbf578396f0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 27 Jan 2022 09:44:03 +0100 Subject: [PATCH 2830/9987] fix patch direction --- .../multichoose-1.0.3-GCCcore-11.2.0.eb | 2 +- ...ltichoose-1.0.3_improve-build-system.patch | 38 +++++++++---------- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.2.0.eb index dc99da99349..fa0cd5152f9 100644 --- a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_improve-build-system.patch'] checksums = [ '74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877', # v1.0.3.tar.gz - '5921f69b47f65782ab7656e9f1396254cdfc8c67576217141e77729a5ab0084b', # multichoose-1.0.3_improve-build-system.patch + '96abf6ac1105ee596be078d6e8fb478f870a4ae33fffe70f93e627c0360cfc77', # multichoose-1.0.3_improve-build-system.patch ] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3_improve-build-system.patch b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3_improve-build-system.patch index b7e9e5256a4..965da4409f0 100644 --- a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3_improve-build-system.patch +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3_improve-build-system.patch @@ -1,33 +1,33 @@ make build system more flexible author: Paul Jähne diff -ru multichoose.orig/Makefile multichoose/Makefile ---- multichoose.orig/Makefile 2022-01-27 08:53:35.738914531 +0100 -+++ multichoose/Makefile 2014-12-03 18:04:41.000000000 +0100 -@@ -1,21 +1,17 @@ --CC ?= gcc --CXX ?= g++ -- +--- multichoose.orig/Makefile 2014-12-03 18:04:41.000000000 +0100 ++++ multichoose/Makefile 2022-01-27 08:53:35.738914531 +0100 +@@ -1,17 +1,21 @@ ++CC ?= gcc ++CXX ?= g++ ++ all: multichoose multipermute #multichoose_recursive: multichoose_recursive.cpp --# ${CXX} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multichoose_recursive.cpp -o multichoose_recursive -+# g++ multichoose_recursive.cpp -o multichoose_recursive +-# g++ multichoose_recursive.cpp -o multichoose_recursive ++# ${CXX} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multichoose_recursive.cpp -o multichoose_recursive multichoose: multichoose.cpp multichoose.h -- ${CXX} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multichoose.cpp -o multichoose -+ g++ multichoose.cpp -o multichoose +- g++ multichoose.cpp -o multichoose ++ ${CXX} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multichoose.cpp -o multichoose multipermute: multipermute.cpp multipermute.h -- ${CXX} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multipermute.cpp -o multipermute -+ g++ multipermute.cpp -o multipermute +- g++ multipermute.cpp -o multipermute ++ ${CXX} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multipermute.cpp -o multipermute cmultichoose: multichoose.c -- ${CC} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multichoose.c -o cmultichoose -+ gcc multichoose.c -o cmultichoose +- gcc multichoose.c -o cmultichoose ++ ${CC} $(LDFLAGS) $(CPPFLAGS) $(CXXFLAGS) multichoose.c -o cmultichoose clean: -- rm -f cmultichoose -- rm -f multichoose -- rm -f multipermute -+ rm cmultichoose -+ rm multichoose +- rm cmultichoose +- rm multichoose ++ rm -f cmultichoose ++ rm -f multichoose ++ rm -f multipermute From ab4a2999dce802b150f5bdb6f6dd72283eb6ad50 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 27 Jan 2022 10:02:06 +0100 Subject: [PATCH 2831/9987] adding easyconfigs: vcflib-1.0.3-GCC-11.2.0.eb, tabixpp-1.1.0-GCC-11.2.0.eb, fastahack-1.0.0-GCCcore-11.2.0.eb, filevercmp-20191210-GCCcore-11.2.0.eb, fsom-20141119-GCCcore-11.2.0.eb, smithwaterman-20160702-GCCcore-11.2.0.eb and patches: vcflib-1.0.3_use-external-deps.patch --- .../fastahack-1.0.0-GCCcore-11.2.0.eb | 34 ++++++ .../filevercmp-20191210-GCCcore-11.2.0.eb | 35 ++++++ .../f/fsom/fsom-20141119-GCCcore-11.2.0.eb | 38 ++++++ .../smithwaterman-20160702-GCCcore-11.2.0.eb | 34 ++++++ .../t/tabixpp/tabixpp-1.1.0-GCC-11.2.0.eb | 39 +++++++ .../v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb | 59 ++++++++++ .../vcflib-1.0.3_use-external-deps.patch | 110 ++++++++++++++++++ 7 files changed, 349 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.3_use-external-deps.patch diff --git a/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d22dd68d7cc --- /dev/null +++ b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'fastahack' +version = '1.0.0' + +homepage = 'https://github.com/ekg/fastahack' +description = """Utilities for indexing and sequence extraction from FASTA files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_build-libs.patch'] +checksums = [ + 'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae', # v1.0.0.tar.gz + '7f804486c6bafd9b1572cb5f86ff28dbebb4d6da551bde1091d6ff8f82748bf4', # fastahack-1.0.0_build-libs.patch +] + +builddependencies = [('binutils', '2.37')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfastahack.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7e587ae740c --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'filevercmp' +version = '20191210' +local_commit = 'df20dcc' + +homepage = 'https://github.com/ekg/filevercmp' +description = """filevercmp function as in sort --version-sort.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-%(version)s_build-libs.patch'] +checksums = [ + '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz + '051438f76dd04219abfb283f61101c04d748407031e180b7ae3841344416ec4f', # filevercmp-20191210_build-libs.patch +] + +builddependencies = [('binutils', '2.37')] + +skipsteps = ['configure'] + +installopts = 'DESTDIR="" PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s abca bcac'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7b037baa146 --- /dev/null +++ b/easybuild/easyconfigs/f/fsom/fsom-20141119-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +# Updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'fsom' +version = '20141119' +local_commit = 'a6ef318' + +homepage = 'https://github.com/ekg/fsom' +description = """A tiny C library for managing SOM (Self-Organizing Maps) neural networks.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = [ + '%(name)s-%(version)s_build-libs.patch', + '%(name)s-%(version)s_fix-abs-overload.patch' +] +checksums = [ + '832ec7d0aff53e04fdb8bbaa5be2177de362afac6ed58a59a97abb7eef29cb60', # a6ef318.tar.gz + 'a6349a6462473f011260074eca6ad9826e3c6aeb20674b696c5848d10610cdd7', # fsom-20141119_build-libs.patch + '54dd6ae76033535fe1b0231142d8bd41a815950dc3fd269dc321f698d4973639', # fsom-20141119_fix-abs-overload.patch +] + +builddependencies = [('binutils', '2.37')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfsom.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1675a404962 --- /dev/null +++ b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'smithwaterman' +version = '20160702' +local_commit = '2610e25' + +homepage = 'https://github.com/ekg/smithwaterman' +description = """smith-waterman-gotoh alignment algorithm.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-%(version)s_build-shared-lib.patch'] +checksums = [ + '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8', # 2610e25.tar.gz + '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582', # smithwaterman-20160702_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.37')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-11.2.0.eb b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..b3fd1fd3d75 --- /dev/null +++ b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.0-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'tabixpp' +version = '1.1.0' + +homepage = 'https://github.com/ekg/tabixpp' +description = """C++ wrapper to tabix indexer""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_use-external-HTSlib.patch'] +checksums = [ + '56c8f1b07190aba5e1d0b738e380e726d380f0ad8b2d0df133200b0ab1f8ed88', # v1.1.0.tar.gz + '65496b6e042cf54290386a33cf0de26cb1160b3ddb35216765999d790b99cab4', # tabixpp-1.1.0_use-external-HTSlib.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('HTSlib', '1.14'), + ('PCRE', '8.45'), +] + +skipsteps = ['configure'] + +preinstallopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/tabix++', 'lib/libtabixpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..6d9fe6caf6d --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb @@ -0,0 +1,59 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.3' + +homepage = 'https://github.com/vcflib/vcflib' +description = """vcflib provides methods to manipulate and interpret sequence variation as it can be + described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended + to concisely describe reference-indexed genetic variations between individuals.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_use-external-deps.patch'] +checksums = [ + '5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c', # v1.0.3.tar.gz + '89f99efb35eb3a5fdc5a7fdeb96c204b1af481194bcd788c939c600a985fa8a4', # vcflib-1.0.3_use-external-deps.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.14'), + ('tabixpp', '1.1.0'), + ('intervaltree', '0.1'), + ('fastahack', '1.0.0'), + ('filevercmp', '20191210'), + ('fsom', '20141119'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), +] + +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f -regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" +preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" +preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" +preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" +preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " + +sanity_check_paths = { + 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["vcfremap"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3_use-external-deps.patch b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3_use-external-deps.patch new file mode 100644 index 00000000000..27bbdff35e2 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3_use-external-deps.patch @@ -0,0 +1,110 @@ +use external dependencies +add target to build shared library +rename static library from libvcflib_static to libvcflib +author: Paul Jähne +--- vcflib.orig/CMakeLists.txt 2022-01-25 11:56:05.651519227 +0100 ++++ vcflib/CMakeLists.txt 2022-01-25 12:29:40.271651816 +0100 +@@ -31,7 +31,7 @@ + set_package_properties(Threads PROPERTIES TYPE REQUIRED) + + pkg_check_modules(HTSLIB htslib) +-pkg_check_modules(TABIXPP tabixpp) # Optional ++#pkg_check_modules(TABIXPP tabixpp) # Optional + + # ---- Build switches + +@@ -53,11 +53,11 @@ + # ---- Include files + + include_directories(include) +-include_directories(fastahack) +-include_directories(intervaltree) +-include_directories(smithwaterman) +-include_directories(multichoose) +-include_directories(filevercmp) ++#include_directories(fastahack) ++#include_directories(intervaltree) ++#include_directories(smithwaterman) ++#include_directories(multichoose) ++#include_directories(filevercmp) + + if(HTSLIB_LOCAL) + include_directories( +@@ -68,13 +68,14 @@ + + file(GLOB INCLUDES + src/*.h* +- multichoose/*.h* +- intervaltree/*.h* +- smithwaterman/*.h* +- fastahack/*.h* +- filevercmp/*.h*) ++ # multichoose/*.h* ++ # intervaltree/*.h* ++ # smithwaterman/*.h* ++ # fastahack/*.h* ++ # filevercmp/*.h*) ++ ) + +-add_library(vcflib STATIC ++set(SOURCES + src/Variant.h + src/split.h + src/pdflib.hpp +@@ -90,14 +91,14 @@ + src/split.cpp + src/ssw.hpp + src/ssw_cpp.hpp +- fastahack/Fasta.cpp +- smithwaterman/SmithWatermanGotoh.cpp +- smithwaterman/Repeats.cpp +- smithwaterman/IndelAllele.cpp +- smithwaterman/disorder.cpp +- smithwaterman/LeftAlign.cpp +- fsom/fsom.c +- filevercmp/filevercmp.c ++ # fastahack/Fasta.cpp ++ # smithwaterman/SmithWatermanGotoh.cpp ++ # smithwaterman/Repeats.cpp ++ # smithwaterman/IndelAllele.cpp ++ # smithwaterman/disorder.cpp ++ # smithwaterman/LeftAlign.cpp ++ # fsom/fsom.c ++ # filevercmp/filevercmp.c + ) + + set(BINS +@@ -239,6 +240,11 @@ + add_definitions(-DVCFLIB_VERSION="${BUILD_NUMBER}") + add_definitions(-DVERSION="${BUILD_NUMBER}") + ++add_library(vcflib_static STATIC ${SOURCES}) ++set_target_properties(vcflib_static PROPERTIES OUTPUT_NAME vcflib) ++add_library(vcflib SHARED ${SOURCES}) ++set_target_properties(vcflib PROPERTIES VERSION ${BUILD_NUMBER} SOVERSION 1) ++ + # ---- Build htslib + # + # Note by default we use the distributed htslib! These are +@@ -276,8 +282,8 @@ + if (NOT BUILD_ONLY_LIB) + foreach(BIN ${BINS}) + add_executable(${BIN} src/${BIN}.cpp) +- target_include_directories(${BIN} PUBLIC ${TABIXPP_LIBRARIES} ${HTSLIB_INCLUDE_DIRS}) +- target_link_libraries(${BIN} vcflib tabixpp -DGIT_VERSION=0.9.0 ${TABIXPP_LIBRARIES} ${HTSLIB_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${LIBLZMA_LIBRARIES} ${BZIP2_LIBRARIES}) ++ target_include_directories(${BIN} PUBLIC ${CPPFLAGS}) ++ target_link_libraries(${BIN} vcflib tabixpp fastahack sw fsom filevercmp -DGIT_VERSION=0.9.0 ${LDFLAGS} ${LIBS}) + endforeach(BIN ${BINS}) + install(TARGETS ${BINS} RUNTIME DESTINATION bin) + +@@ -365,7 +371,9 @@ + + # ---- Install + +-install(TARGETS vcflib ARCHIVE DESTINATION lib) ++#install(TARGETS vcflib ARCHIVE DESTINATION lib) ++install(TARGETS vcflib LIBRARY DESTINATION lib) ++install(TARGETS vcflib_static ARCHIVE DESTINATION lib) + + install(FILES ${INCLUDES} DESTINATION include) + From d1312c0717817d33f0da570c590f4fc6f43b7cfe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Jan 2022 10:03:18 +0100 Subject: [PATCH 2832/9987] adding easyconfigs: minimap2-2.24-GCCcore-11.2.0.eb --- .../minimap2/minimap2-2.24-GCCcore-11.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..aaec55b1014 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.2.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# DeepThought, Flinders University +# Updated to 2.22 +# R.QIAO + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.24' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['9dd4c31ff082182948944bcdad6d328f64f09295d10547d72eba24189880a615'] + +builddependencies = [('binutils', '2.37')] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' From d780bb7cae01c8abf8af7045bbff6be59c2570e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Jan 2022 10:06:22 +0100 Subject: [PATCH 2833/9987] stop running easyconfigs test suite with Python 3.5, also test with Python 3.8-3.10 --- .github/workflows/unit_tests.yml | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index ea157514055..d26f0d52020 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -5,19 +5,23 @@ jobs: runs-on: ubuntu-18.04 strategy: matrix: - python: [2.7, 3.5, 3.6, 3.7] + python: [2.7, 3.6, 3.7, 3.8, 3.9, 3.10] modules_tool: [Lmod-6.6.3, Lmod-7.8.22, Lmod-8.1.14] module_syntax: [Lua, Tcl] - # exclude some configurations: only test Tcl module syntax with Lmod 7.x and Python 2.7 & 3.5 + # exclude some configurations: only test Tcl module syntax with Lmod 7.x and Python 2.7 & 3.6 exclude: - modules_tool: Lmod-6.6.3 module_syntax: Tcl - modules_tool: Lmod-8.1.14 module_syntax: Tcl - - python: 3.6 - module_syntax: Tcl - python: 3.7 module_syntax: Tcl + - python: 3.8 + module_syntax: Tcl + - python: 3.9 + module_syntax: Tcl + - python: 3.10 + module_syntax: Tcl fail-fast: false steps: - uses: actions/checkout@v2 From 925cfc73a71ccb75c9e3118579daa078da97a0b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Jan 2022 10:14:20 +0100 Subject: [PATCH 2834/9987] add quotes to avoid that Python 3.10 is interpreted as Python 3.1 ... --- .github/workflows/unit_tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index d26f0d52020..f7d473b738a 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -5,7 +5,7 @@ jobs: runs-on: ubuntu-18.04 strategy: matrix: - python: [2.7, 3.6, 3.7, 3.8, 3.9, 3.10] + python: [2.7, 3.6, 3.7, 3.8, 3.9, '3.10'] modules_tool: [Lmod-6.6.3, Lmod-7.8.22, Lmod-8.1.14] module_syntax: [Lua, Tcl] # exclude some configurations: only test Tcl module syntax with Lmod 7.x and Python 2.7 & 3.6 @@ -20,7 +20,7 @@ jobs: module_syntax: Tcl - python: 3.9 module_syntax: Tcl - - python: 3.10 + - python: '3.10' module_syntax: Tcl fail-fast: false steps: From aaa77532dc4ebfe0c3ff77fc43c386caaf627ef9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 27 Jan 2022 10:27:44 +0100 Subject: [PATCH 2835/9987] resume running test suite with Python 3.5 by using actions/setup-python@v2 --- .github/workflows/linting.yml | 2 +- .github/workflows/unit_tests.yml | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 5f5ed47af29..9d5354858a1 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -7,7 +7,7 @@ jobs: - uses: actions/checkout@v2 - name: set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v2 with: python-version: 3.8 diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index f7d473b738a..cb5cfe87612 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -5,7 +5,7 @@ jobs: runs-on: ubuntu-18.04 strategy: matrix: - python: [2.7, 3.6, 3.7, 3.8, 3.9, '3.10'] + python: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9, '3.10'] modules_tool: [Lmod-6.6.3, Lmod-7.8.22, Lmod-8.1.14] module_syntax: [Lua, Tcl] # exclude some configurations: only test Tcl module syntax with Lmod 7.x and Python 2.7 & 3.6 @@ -14,6 +14,8 @@ jobs: module_syntax: Tcl - modules_tool: Lmod-8.1.14 module_syntax: Tcl + - python: 3.5 + module_syntax: Tcl - python: 3.7 module_syntax: Tcl - python: 3.8 @@ -36,7 +38,7 @@ jobs: key: eb-sourcepath - name: set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v2 with: python-version: ${{matrix.python}} architecture: x64 From b592cb86f92253371bc4f0f887a503e38478d351 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 27 Jan 2022 09:33:27 +0000 Subject: [PATCH 2836/9987] adding easyconfigs: XGBoost-1.5.0-foss-2021a.eb --- .../x/XGBoost/XGBoost-1.5.0-foss-2021a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-1.5.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.5.0-foss-2021a.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.5.0-foss-2021a.eb new file mode 100644 index 00000000000..21900bfc76c --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.5.0-foss-2021a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '1.5.0' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6b7c34a18474c1b73b5c6dcf1231f5fe102d6f26490a65465e3879048bf1f3d4'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' From 4bffe1c3a27fd6094bb4dd9b9e27f19c6a66aa58 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 27 Jan 2022 11:35:32 +0100 Subject: [PATCH 2837/9987] Update easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb b/easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb index 34e1f19f214..af3cd364513 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb @@ -15,7 +15,7 @@ toolchain = SYSTEM source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' 'installer/complete/glnxa64/' % local_update] -sources = ['MATLAB_Runtime_%(version)s_glnxa64.zip'] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] checksums = ['d7067b4f4977350395fd75de1aeefc9de39010fbdcf32d99a5f2e8955e74121e'] moduleclass = 'math' From 39e9ef28a76e1da5a7e449ca4394660e4972628a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 27 Jan 2022 11:47:12 +0100 Subject: [PATCH 2838/9987] add missing UCX-CUDA dep to GROMACS for foss-2021a-CUDA-11.3.1 --- .../GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb | 1 + .../g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb index a7a22da2648..bd9030bee93 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb @@ -68,6 +68,7 @@ dependencies = [ ('networkx', '2.5.1'), ('CUDA', '11.3.1', '', True), ('PLUMED', _plumedver), + ('UCX-CUDA', '1.10.0', versionsuffix), ] exts_defaultclass = 'PythonPackage' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb index 738d6c86b6b..0b05b269df5 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb @@ -64,6 +64,7 @@ dependencies = [ ('SciPy-bundle', '2021.05'), ('networkx', '2.5.1'), ('CUDA', '11.3.1', '', True), + ('UCX-CUDA', '1.10.0', versionsuffix), ] exts_defaultclass = 'PythonPackage' From 8689f37fbe56f4e466f61e7e8ce84d1e746dab6f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 27 Jan 2022 11:53:09 +0100 Subject: [PATCH 2839/9987] fix suffix --- .../GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb index bd9030bee93..e431ba0f759 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb @@ -16,7 +16,8 @@ name = 'GROMACS' version = '2021.3' _plumedver = '2.7.2' -versionsuffix = '-CUDA-%%(cudaver)s-PLUMED-%s' % _plumedver +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = _cuda_suffix + '-PLUMED-%s' % _plumedver homepage = 'https://www.gromacs.org' description = """ @@ -68,7 +69,7 @@ dependencies = [ ('networkx', '2.5.1'), ('CUDA', '11.3.1', '', True), ('PLUMED', _plumedver), - ('UCX-CUDA', '1.10.0', versionsuffix), + ('UCX-CUDA', '1.10.0', _cuda_suffix), ] exts_defaultclass = 'PythonPackage' From 0b619b1971b4c0c714217d02e840791a327017a5 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 27 Jan 2022 13:44:51 +0100 Subject: [PATCH 2840/9987] MCR: Fixes hash --- easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb b/easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb index af3cd364513..0975b82daaa 100644 --- a/easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb +++ b/easybuild/easyconfigs/m/MCR/MCR-R2021b.1.eb @@ -16,6 +16,6 @@ toolchain = SYSTEM source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' 'installer/complete/glnxa64/' % local_update] sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] -checksums = ['d7067b4f4977350395fd75de1aeefc9de39010fbdcf32d99a5f2e8955e74121e'] +checksums = ['b2bbaf38e7e0cb2c2735548dbea1e7c9d7ff821789edacfe5f90c4acdc908e03'] moduleclass = 'math' From 1f150a6fc82cb41617718d5a5cb635dd0e4681b8 Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Thu, 27 Jan 2022 18:34:52 +0100 Subject: [PATCH 2841/9987] librsb: add v1.2.0.10/v1.2.0.11/v1.3.0.0 (#14860) --- .../l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb | 29 +++++++++++++++++++ .../l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb | 29 +++++++++++++++++++ .../l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb | 29 +++++++++++++++++++ 3 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb new file mode 100644 index 00000000000..e61290dd63e --- /dev/null +++ b/easybuild/easyconfigs/l/librsb/librsb-1.2.0.10-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +## +# Author: Michele Martone +## +easyblock = 'ConfigureMake' + +name = 'librsb' +version = '1.2.0.10' + +homepage = 'https://sourceforge.net/projects/librsb/' +description = """A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ec49f3f78a7c43fc9e10976593d100aa49b1863309ed8fa3ccbb7aad52d2f7b8'] + +dependencies = [ + ('zlib', '1.2.11') +] + +configopts = '--enable-openmp --enable-fortran-module-install' + +sanity_check_paths = { + 'files': ['bin/rsbench', 'lib/librsb.a', 'lib/librsb.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb new file mode 100644 index 00000000000..fac25cf212f --- /dev/null +++ b/easybuild/easyconfigs/l/librsb/librsb-1.2.0.11-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +## +# Author: Michele Martone +## +easyblock = 'ConfigureMake' + +name = 'librsb' +version = '1.2.0.11' + +homepage = 'https://sourceforge.net/projects/librsb/' +description = """A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['0686be29bbe277e227c6021de6bd0564e4fc83f996b787886437d28048057bc8'] + +dependencies = [ + ('zlib', '1.2.11') +] + +configopts = '--enable-openmp --enable-fortran-module-install' + +sanity_check_paths = { + 'files': ['bin/rsbench', 'lib/librsb.a', 'lib/librsb.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..3bdfc0ca857 --- /dev/null +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +## +# Author: Michele Martone +## +easyblock = 'ConfigureMake' + +name = 'librsb' +version = '1.3.0.0' + +homepage = 'https://sourceforge.net/projects/librsb/' +description = """A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2ac8725d1f988f57df9383ae6b0bb2ed221ec935187d31ebb62ea95ee868a790'] + +dependencies = [ + ('zlib', '1.2.11') +] + +configopts = '--enable-openmp --enable-fortran-module-install' + +sanity_check_paths = { + 'files': ['bin/rsbench', 'lib/librsb.a', 'lib/librsb.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From bcbdc211466b66004fc2d528f6f7897bdc72974c Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 27 Jan 2022 19:30:28 +0100 Subject: [PATCH 2842/9987] adding easyconfigs: CFITSIO-3.49-GCCcore-11.2.0.eb, ROOT-6.24.06-foss-2021b-Python-3.9.6.eb --- .../c/CFITSIO/CFITSIO-3.49-GCCcore-11.2.0.eb | 41 +++++++++++++++ .../ROOT-6.24.06-foss-2021b-Python-3.9.6.eb | 52 +++++++++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5911a316801 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.49' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-3.48_install_test_data.patch'] +checksums = [ + '5b65a20d5c53494ec8f638267fca4a629836b7ac8dd0ef0266834eab270ed4b3', # cfitsio-3.49.tar.gz + 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch +] + +# curl for HTTPs support +dependencies = [('cURL', '7.78.0')] + +builddependencies = [('binutils', '2.37')] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = '&& make shared && make testprog' + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + ('cd %(installdir)s/share && testprog'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb new file mode 100644 index 00000000000..e1672271668 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb @@ -0,0 +1,52 @@ +name = 'ROOT' +version = '6.24.06' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://root.cern.ch/download/'] +sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +patches = ['ROOT-6.14.06_fix-VDT-target.patch'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('GSL', '2.7'), + ('libxml2', '2.9.10'), + ('PCRE', '8.45'), + ('CFITSIO', '3.49'), + ('freetype', '2.11.0'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('zlib', '1.2.11'), + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('GL2PS', '1.4.2'), + ('FFTW', '3.3.10'), + ('SQLite', '3.36'), + ('XZ', '5.2.5'), + ('libpng', '1.6.37'), +] + +# NOTE: Ensure that each configopts string begins with a blank +# disable some components +configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" + +# make sure some components are enabled +configopts += " -Dpcre=ON -Dzlib=ON -Dpyroot=ON" +configopts += " -Dunuran=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " + +# Add component-specific settings based on dependencies +configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' + +configopts += " -Dgallium-drivers=swrast" + +moduleclass = 'data' From f6dd624c413025c443a5581b3336fcc938ec7bb5 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 27 Jan 2022 20:22:41 +0100 Subject: [PATCH 2843/9987] Added checksums --- .../r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb index e1672271668..d0fb3a9eeb1 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb @@ -12,6 +12,10 @@ toolchainopts = {'pic': True} source_urls = ['https://root.cern.ch/download/'] sources = ['%(namelower)s_v%(version)s.source.tar.gz'] patches = ['ROOT-6.14.06_fix-VDT-target.patch'] +checksums = [ + '907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522', # root_v6.24.06.source.tar.gz + 'ff51eb823726d146840b149945b7896b8e60cc0920933b740d780a540b62e4d8', # ROOT-6.14.06_fix-VDT-target.patch +] builddependencies = [ ('CMake', '3.22.1'), From f9cd3534a71dc5858b347039868516d099d6dc73 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 27 Jan 2022 21:32:06 +0100 Subject: [PATCH 2844/9987] Removed pyver + fixed error (hopefully) --- .../r/ROOT/ROOT-6.24.06-foss-2021b.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb new file mode 100644 index 00000000000..7776bdb8cec --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb @@ -0,0 +1,51 @@ +name = 'ROOT' +version = '6.24.06' + +homepage = 'https://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://root.cern.ch/download/'] +sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +checksums = ['907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('GSL', '2.7'), + ('libxml2', '2.9.10'), + ('PCRE', '8.45'), + ('CFITSIO', '3.49'), + ('freetype', '2.11.0'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('zlib', '1.2.11'), + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('GL2PS', '1.4.2'), + ('FFTW', '3.3.10'), + ('SQLite', '3.36'), + ('XZ', '5.2.5'), + ('libpng', '1.6.37'), +] + +# NOTE: Ensure that each configopts string begins with a blank +# disable some components +configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" + +# make sure some components are enabled +configopts += " -Dpcre=ON -Dzlib=ON -Dpyroot=ON" +configopts += " -Dunuran=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " + +# Add component-specific settings based on dependencies +configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' + +configopts += " -Dgallium-drivers=swrast" + +moduleclass = 'data' From 33b057310cfbd2491450a5c102e27632fcf27a42 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Thu, 27 Jan 2022 21:46:13 +0100 Subject: [PATCH 2845/9987] Delete ROOT-6.24.06-foss-2021b-Python-3.9.6.eb --- .../ROOT-6.24.06-foss-2021b-Python-3.9.6.eb | 56 ------------------- 1 file changed, 56 deletions(-) delete mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb deleted file mode 100644 index d0fb3a9eeb1..00000000000 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b-Python-3.9.6.eb +++ /dev/null @@ -1,56 +0,0 @@ -name = 'ROOT' -version = '6.24.06' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://root.cern.ch/drupal/' -description = """The ROOT system provides a set of OO frameworks with all the functionality - needed to handle and analyze large amounts of data in a very efficient way.""" - -toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'pic': True} - -source_urls = ['https://root.cern.ch/download/'] -sources = ['%(namelower)s_v%(version)s.source.tar.gz'] -patches = ['ROOT-6.14.06_fix-VDT-target.patch'] -checksums = [ - '907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522', # root_v6.24.06.source.tar.gz - 'ff51eb823726d146840b149945b7896b8e60cc0920933b740d780a540b62e4d8', # ROOT-6.14.06_fix-VDT-target.patch -] - -builddependencies = [ - ('CMake', '3.22.1'), - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('GSL', '2.7'), - ('libxml2', '2.9.10'), - ('PCRE', '8.45'), - ('CFITSIO', '3.49'), - ('freetype', '2.11.0'), - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('zlib', '1.2.11'), - ('X11', '20210802'), - ('Mesa', '21.1.7'), - ('libGLU', '9.0.2'), - ('GL2PS', '1.4.2'), - ('FFTW', '3.3.10'), - ('SQLite', '3.36'), - ('XZ', '5.2.5'), - ('libpng', '1.6.37'), -] - -# NOTE: Ensure that each configopts string begins with a blank -# disable some components -configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" - -# make sure some components are enabled -configopts += " -Dpcre=ON -Dzlib=ON -Dpyroot=ON" -configopts += " -Dunuran=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " - -# Add component-specific settings based on dependencies -configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' - -configopts += " -Dgallium-drivers=swrast" - -moduleclass = 'data' From 2279ff6d34b08211b8918b38740eb3f0dd816cda Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 28 Jan 2022 12:25:00 +0100 Subject: [PATCH 2846/9987] adding easyconfigs: Graphviz-2.50.0-GCCcore-11.2.0.eb and patches: Graphviz-2.50.0_skip-install-data-hook.patch --- .../Graphviz-2.50.0-GCCcore-11.2.0.eb | 89 +++++++++++++++ ...aphviz-2.50.0_skip-install-data-hook.patch | 104 ++++++++++++++++++ 2 files changed, 193 insertions(+) create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0_skip-install-data-hook.patch diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f2fff0736b3 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb @@ -0,0 +1,89 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '2.50.0' +local_pyver_major = '3' + +homepage = 'https://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Graphviz-2.50.0_skip-install-data-hook.patch'] +checksums = [ + 'afa48581f764a35e148909cc96a0308ec2356b5225b64af12492f3392f20ef1c', # graphviz-2.50.0.tar.gz + 'a49c59ae40e8a9af999a46aa8ea5b79b4325e99f5a15a4377aeea0e22afcb898', # Graphviz-2.50.0_skip-install-data-hook.patch +] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('SWIG', '4.0.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.9.6'), + ('FriBidi', '1.0.10'), + ('Gdk-Pixbuf', '2.42.6'), + ('Ghostscript', '9.54.0'), + ('GTS', '0.7.6'), + ('libgd', '2.3.3'), + ('Pango', '1.48.8'), + ('Perl', '5.34.0'), + ('Qt5', '5.15.2'), + ('Tcl', '8.6.11'), + ('zlib', '1.2.11'), +] + +preconfigopts = './autogen.sh NOCONFIG && ' + +configopts = '--enable-python%s=yes ' % local_pyver_major +configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' +# Use ltdl from libtool in EB +configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' +configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' +# Override the hardcoded paths to Java libraries +configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' +configopts += '--with-javalibdir=$JAVA_HOME/lib' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +postinstallcmds = ['%(installdir)s/bin/dot -c'] # Writes plugin configuration + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acyclic', 'bcomps', 'ccomps', 'cluster', 'diffimg', 'dijkstra', 'dot', + 'dot_builtins', 'dotty', 'edgepaint', 'gc', 'gml2gv', 'graphml2gv', 'gv2gml', + 'gvcolor', 'gvedit', 'gvgen', 'gvmap', 'gvmap.sh', 'gvpack', 'gvpr', 'gxl2gv', + 'lneato', 'mm2gv', 'nop', 'prune', 'sccmap', 'tred', 'unflatten', 'vimdot']] + + ['lib/%s.%s' % (x, SHLIB_EXT) for x in ['libcdt', 'libcgraph', 'libgvc', 'libgvpr', 'liblab_gamut', + 'libpathplan', 'libxdot']], + 'dirs': ['include', 'lib/graphviz', 'lib/graphviz/java', 'lib/graphviz/python%s' % local_pyver_major, + 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), + ('python', '-c "import gv"'), +] + +modextrapaths = { + 'CLASSPATH': 'lib/graphviz/java', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'PYTHONPATH': 'lib/graphviz/python%s' % local_pyver_major, + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0_skip-install-data-hook.patch b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0_skip-install-data-hook.patch new file mode 100644 index 00000000000..b9685f60923 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0_skip-install-data-hook.patch @@ -0,0 +1,104 @@ +don't create directories and install language bindings in non-owned directories +author: Kenneth Hoste (HPC-UGent) +update version 2.42.2: Alex Domingo (VUB) +update version 2.50.0: Christoph Siegert (Leipzig University) + +diff --git a/tclpkg/Makefile.am b/tclpkg/Makefile.am +index f1a1e3d..c4ce18e 100644 +--- a/tclpkg/Makefile.am ++++ b/tclpkg/Makefile.am +@@ -27,94 +27,6 @@ pkgIndex.tcl: @TCL_PKGINDEX@ @TCL_PKGINDEX_GD@ @TCL_PKGINDEX_SWIG@ + cat @TCL_PKGINDEX@ @TCL_PKGINDEX_GD@ @TCL_PKGINDEX_SWIG@ end >$@ + rm -f end + +-if ENABLE_SHARED +-# Installation of softlinks into non-owned directories is done as a +-# separate step, with soft failures, so that a developer can do: +-# ./configure --prefix=$HOME/graphviz; make; make install +-# without root privileges. +-install-data-hook: +-if WITH_LUA +- -mkdir -p $(DESTDIR)@LUA_INSTALL_DIR@; +- if test -w $(DESTDIR)@LUA_INSTALL_DIR@; then \ +- (cd $(DESTDIR)@LUA_INSTALL_DIR@; \ +- cp -f $(DESTDIR)$(pkgluadir)/libgv_lua.so gv.so;) \ +- else \ +- echo "Warning: @LUA_INSTALL_DIR@ is not writable."; \ +- echo "Skipping system installation of lua binding."; \ +- fi +-endif +-if WITH_PERL +- -mkdir -p $(DESTDIR)@PERL_INSTALL_DIR@; +- if test -w $(DESTDIR)@PERL_INSTALL_DIR@; then \ +- (cd $(DESTDIR)@PERL_INSTALL_DIR@; \ +- cp -f $(DESTDIR)$(pkgperldir)/libgv_perl.so gv.so; \ +- cp -f $(DESTDIR)$(pkgperldir)/gv.pm gv.pm;) \ +- else \ +- echo "Warning: @PERL_INSTALL_DIR@ is not writable."; \ +- echo "Skipping system installation of perl binding."; \ +- fi +-endif +-if WITH_PHP +- -mkdir -p $(DESTDIR)@PHP_INSTALL_DIR@; +- if test -w $(DESTDIR)@PHP_INSTALL_DIR@; then \ +- (cd $(DESTDIR)@PHP_INSTALL_DIR@; \ +- cp -f $(DESTDIR)$(pkgphpdir)/libgv_php.so gv.so;) \ +- else \ +- echo "Warning: @PHP_INSTALL_DIR@ is not writable."; \ +- echo "Skipping system installation of php binding."; \ +- fi +- -mkdir -p $(DESTDIR)@PHP_INSTALL_DATADIR@; +- if test -w $(DESTDIR)@PHP_INSTALL_DATADIR@; then \ +- (cd $(DESTDIR)@PHP_INSTALL_DATADIR@; \ +- cp -f $(DESTDIR)$(pkgphpdir)/gv.php gv.php;) \ +- else \ +- echo "Warning: @PHP_INSTALL_DATADIR@ is not writable."; \ +- echo "Skipping system installation of php binding."; \ +- fi +-endif +-if WITH_PYTHON +- -mkdir -p $(DESTDIR)@PYTHON_INSTALL_DIR@; +- if test -w $(DESTDIR)@PYTHON_INSTALL_DIR@; then \ +- (cd $(DESTDIR)@PYTHON_INSTALL_DIR@; \ +- cp -f $(DESTDIR)$(pkgpythondir)/libgv_python.so _gv.so; \ +- cp -f $(DESTDIR)$(pkgpythondir)/gv.py gv.py;) \ +- else \ +- echo "Warning: @PYTHON_INSTALL_DIR@ is not writable."; \ +- echo "Skipping system installation of python binding."; \ +- fi +-endif +-if WITH_PYTHON3 +- -mkdir -p $(DESTDIR)@PYTHON3_INSTALL_DIR@; +- if test -w $(DESTDIR)@PYTHON3_INSTALL_DIR@; then \ +- (cd $(DESTDIR)@PYTHON3_INSTALL_DIR@; \ +- cp -f $(DESTDIR)$(pkgpython3dir)/libgv_python3.so _gv.so; \ +- cp -f $(DESTDIR)$(pkgpython3dir)/gv.py gv.py;) \ +- else \ +- echo "Warning: @PYTHON3_INSTALL_DIR@ is not writable."; \ +- echo "Skipping system installation of python3 binding."; \ +- fi +-endif +-if WITH_RUBY +- -mkdir -p $(DESTDIR)@RUBY_INSTALL_DIR@; +- if test -w $(DESTDIR)@RUBY_INSTALL_DIR@; then \ +- (cd $(DESTDIR)@RUBY_INSTALL_DIR@; \ +- cp -f $(DESTDIR)$(pkgrubydir)/libgv_ruby.so gv.so;) \ +- else \ +- echo "Warning: @RUBY_INSTALL_DIR@ is not writable."; \ +- echo "Skipping system installation of ruby binding."; \ +- fi +-endif +-if WITH_TCL +- -mkdir -p $(DESTDIR)@TCL_INSTALL_DIR@; +- if test -w $(DESTDIR)@TCL_INSTALL_DIR@/; then \ +- (cd $(DESTDIR)@TCL_INSTALL_DIR@; \ +- cp -rf $(DESTDIR)$(pkgtcldir) @PACKAGE_NAME@;) \ +- else \ +- echo "Warning: @TCL_INSTALL_DIR@ is not writable."; \ +- echo "Skipping system installation of tcl bindings."; \ +- fi +-endif +-endif + + # removal of installs into @xxx_INSTALL_DIR@ fail if root + # has installed a system copy From 416c9c2dc76f617af7be7c21986dd38c69fb970c Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 28 Jan 2022 13:02:05 +0100 Subject: [PATCH 2847/9987] adding easyconfigs: wget-1.21.2-GCCcore-11.2.0.eb --- .../w/wget/wget-1.21.2-GCCcore-11.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..3c7a5559b3a --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb @@ -0,0 +1,48 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.21.2' + +homepage = 'https://www.gnu.org/software/wget' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e6d4c76be82c676dd7e8c61a29b2ac8510ae108a810b5d1d18fc9a1d2c9a2497'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('Perl', '5.34.0'), +] +dependencies = [ + ('PCRE', '8.45'), + ('libidn2', '2.3.2'), + ('zlib', '1.2.11'), + ('OpenSSL', '1.1', '', True), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.7.1'), +] + +# make sure pkg-config picks up system packages (OpenSSL & co) +preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +configopts = '--with-ssl=openssl ' + +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'devel' From daddc1d6d7254bd2750afda6cb9845cbfe62af6a Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 28 Jan 2022 13:45:21 +0100 Subject: [PATCH 2848/9987] adding easyconfigs: DROP-1.1.1-foss-2021b-R-4.1.2.eb, tMAE-1.0.1-foss-2021b-R-4.1.2.eb and patches: tMAE_1.0.1_remove_early_closing_brace.patch --- .../d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb | 69 +++++++++++++++++++ .../t/tMAE/tMAE-1.0.1-foss-2021b-R-4.1.2.eb | 39 +++++++++++ ...MAE_1.0.1_remove_early_closing_brace.patch | 23 +++++++ 3 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb create mode 100644 easybuild/easyconfigs/t/tMAE/tMAE-1.0.1-foss-2021b-R-4.1.2.eb create mode 100644 easybuild/easyconfigs/t/tMAE/tMAE_1.0.1_remove_early_closing_brace.patch diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..db1db5f1d92 --- /dev/null +++ b/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'DROP' +version = '1.1.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://gagneurlab-drop.readthedocs.io' +description = "Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('R', '4.1.2'), + ('R-bundle-Bioconductor', '3.14', '-R-%(rver)s'), + ('tMAE', '1.0.1', '-R-%(rver)s'), + ('Java', '11', '', True), + ('GATK', '4.2.3.0', '-Java-%(javaver)s'), + ('Graphviz', '2.50.0'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('snakemake', '6.10.0'), + ('wget', '1.21.2'), + ('HTSlib', '1.14'), # for tabix + ('SAMtools', '1.14'), + ('BCFtools', '1.14'), + ('Pandoc', '2.13', '', True), +] + +exts_list = [ + ('wbuild', '1.8.0', { + 'checksums': ['3088d3fcbc71106464f20e3546a73df400dc03d17f11e70bdb15d35d7e6c5a7e'], + }), + ('click-log', '0.3.2', { + 'checksums': ['16fd1ca3fc6b16c98cea63acf1ab474ea8e676849dc669d86afafb0ed7003124'], + }), + ('graphviz', '0.19.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['09ed0cde452d015fe77c4845a210eb642f28d245f5bc250d4b97808cb8f49078'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('about', '5.2', { + 'checksums': ['4a318ad1dcf6e9355b8ae18195c707d26413782b57ac5c740cc696b44350c959'], + }), + ('plumbum', '1.7.2', { + 'checksums': ['0d1bf908076bbd0484d16412479cb97d6843069ee19f99e267e11dd980040523'], + }), + ('pandoc', '2.0.1', { + 'checksums': ['4d3850314fa56cb6164101ad8af561db0c0d5fd19d047e2ca8a9119bf47dac23'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/gagneurlab/drop/archive'], + 'checksums': ['18f2a2eb4fa587d00bb717c9ca7a5d20b397805db1542db68afdd6079a8e43f4'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/drop'], + 'dirs': [], +} + +sanity_check_commands = ['drop --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tMAE/tMAE-1.0.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/t/tMAE/tMAE-1.0.1-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..e7299ddb76a --- /dev/null +++ b/easybuild/easyconfigs/t/tMAE/tMAE-1.0.1-foss-2021b-R-4.1.2.eb @@ -0,0 +1,39 @@ +easyblock = 'RPackage' + +name = 'tMAE' +version = '1.0.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/mumichae/tMAE' +description = """ +Package containing functions to: + + perform a negative binomial test on allele-specific counts + add gnomAD minor allele frequencies + MAplot (FC vs total counts) of allele-specific counts and results + allelic counts (ALT vs REF)""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('R', '4.1.2'), + ('R-bundle-Bioconductor', '3.14', '-R-%(rver)s'), +] + +github_account = 'mumichae' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + 'tMAE_1.0.1_remove_early_closing_brace.patch' +] +checksums = [ + 'b75b51b05b31995de4b7095b2329a72f002e1ac43ee20e1e975482e05b163a6d', # 1.0.1.tar.gz + '67a178143bb44554a0a8e603f71944878a13d5bbb67e33c410826cbcdef461f7', # tMAE_1.0.1_remove_early_closing_brace.patch +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tMAE/tMAE_1.0.1_remove_early_closing_brace.patch b/easybuild/easyconfigs/t/tMAE/tMAE_1.0.1_remove_early_closing_brace.patch new file mode 100644 index 00000000000..a20d9175328 --- /dev/null +++ b/easybuild/easyconfigs/t/tMAE/tMAE_1.0.1_remove_early_closing_brace.patch @@ -0,0 +1,23 @@ +Related PR: https://github.com/mumichae/tMAE/pull/4 + +From 3ec5741eb741cfc5222d624baa7388b991bbdfee Mon Sep 17 00:00:00 2001 +From: Christoph Siegert +Date: Thu, 27 Jan 2022 16:34:49 +0100 +Subject: [PATCH] fix syntax error due to additional curly brace + +--- + R/add_gnomAD_AF.R | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/R/add_gnomAD_AF.R b/R/add_gnomAD_AF.R +index 4e48ef3..72ea932 100644 +--- a/R/add_gnomAD_AF.R ++++ b/R/add_gnomAD_AF.R +@@ -57,7 +57,6 @@ add_gnomAD_AF <- function(data, + # Compute the MAX_AF (why do we change col names?) + if(any(c("AF", "AF_popmax") %in% colnames(res))){ + res$MAX_AF <- apply(res[, ..populations], 1, max, na.rm = T) +- } + + # Replace Inf with NA + res[is.infinite(MAX_AF), MAX_AF := NA] From 716ce33bd0f7ce8ef64321064f81fa8e6818bd42 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 28 Jan 2022 13:44:20 +0000 Subject: [PATCH 2849/9987] adding easyconfigs: VTK-8.2.0-foss-2021a.eb and patches: VTK-8.2.0_gcc10-fix.patch --- .../easyconfigs/v/VTK/VTK-8.2.0-foss-2021a.eb | 106 ++++++++++++++++++ .../v/VTK/VTK-8.2.0_gcc10-fix.patch | 72 ++++++++++++ 2 files changed, 178 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.2.0_gcc10-fix.patch diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2021a.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2021a.eb new file mode 100644 index 00000000000..69f866da78a --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2021a.eb @@ -0,0 +1,106 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '8.2.0' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [ + 'VTK-8.2.0_python_3.8_compatibility.patch', + 'VTK-8.2.0_gcc10-fix.patch', + ('vtk-version.egg-info', '.'), +] +checksums = [ + '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz + 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz + 'a7586f60501de145d4c31e48aa0589547d9fe7a39f96ab31dae8e82aa5fb4403', # VTK-8.2.0_python_3.8_compatibility.patch + '4f1d2c2f0faa06551384b08356142a998a322008891472a72298152eeaa7038b', # VTK-8.2.0_gcc10-fix.patch + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('XZ', '5.2.5'), + ('HDF5', '1.10.7'), + ('netCDF', '4.8.0'), + ('libGLU', '9.0.1'), + ('X11', '20210518'), +] + +separate_build_dir = True + +# Third party modules +configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " +configopts += "-DVTK_USE_SYSTEM_LZMA=ON " +configopts += "-DVTK_USE_SYSTEM_HDF5=ON " +configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " +configopts += "-DVTK_USE_SYSTEM_PNG=ON " +# OpenGL +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON " +configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +# Other +configopts += "-DVTK_Group_MPI:BOOL=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython', 'pvtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelMPI', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + ('python', "-c 'import %(namelower)s'"), + ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"), +] + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0_gcc10-fix.patch b/easybuild/easyconfigs/v/VTK/VTK-8.2.0_gcc10-fix.patch new file mode 100644 index 00000000000..73180e0a06f --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0_gcc10-fix.patch @@ -0,0 +1,72 @@ +exodusII changes from https://gitlab.kitware.com/vtk/vtk/-/merge_requests/6420 +VTKGenerateExportHeader.cmake changes from https://gitlab.kitware.com/vtk/vtk/-/issues/17775#note_794604 +Patch added by Simon Branford (University of Birmingham) +--- a/ThirdParty/exodusII/vtkexodusII/src/ex_create_par.c ++++ b/ThirdParty/exodusII/vtkexodusII/src/ex_create_par.c +@@ -216,5 +216,5 @@ int ex_create_par_int(const char *path, int cmode, int *comp_ws, int *io_ws, MPI + * Prevent warning in some versions of ranlib(1) because the object + * file has no symbols. + */ +-const char exodus_unused_symbol_dummy_1; ++const char exodus_unused_symbol_dummy_ex_create_par; + #endif +diff --git a/src/ex_open_par.c b/src/ex_open_par.c +index b2faa22c294..9df4818767d 100644 +--- a/ThirdParty/exodusII/vtkexodusII/src/ex_open_par.c ++++ b/ThirdParty/exodusII/vtkexodusII/src/ex_open_par.c +@@ -459,5 +459,5 @@ int ex_open_par_int(const char *path, int mode, int *comp_ws, int *io_ws, float + * Prevent warning in some versions of ranlib(1) because the object + * file has no symbols. + */ +-const char exodus_unused_symbol_dummy_1; ++const char exodus_unused_symbol_dummy_ex_open_par; + #endif +--- a/CMake/VTKGenerateExportHeader.cmake 2022-01-28 11:49:28.902123000 +0000 ++++ b/CMake/VTKGenerateExportHeader.cmake 2022-01-28 12:27:17.901428104 +0000 +@@ -170,37 +170,17 @@ + + macro(_vtk_test_compiler_hidden_visibility) + +- if(CMAKE_COMPILER_IS_GNUCXX) +- execute_process(COMMAND ${CMAKE_C_COMPILER} --version +- OUTPUT_VARIABLE _gcc_version_info +- ERROR_VARIABLE _gcc_version_info) +- string(REGEX MATCH "[3-9]\\.[0-9]\\.[0-9]*" +- _gcc_version "${_gcc_version_info}") +- # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the +- # patch level, handle this here: +- if(NOT _gcc_version) +- string(REGEX REPLACE ".*\\(GCC\\).*([34]\\.[0-9]).*" "\\1.0" +- _gcc_version "${_gcc_version_info}") +- endif() +- +- if(_gcc_version VERSION_LESS "4.2") +- set(GCC_TOO_OLD TRUE) +- endif() ++ if(CMAKE_COMPILER_IS_GNUCXX AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.2") ++ set(GCC_TOO_OLD TRUE) ++ message(WARNING "GCC version older than 4.2") ++ elseif(CMAKE_COMPILER_IS_GNUCC AND CMAKE_C_COMPILER_VERSION VERSION_LESS "4.2") ++ set(GCC_TOO_OLD TRUE) ++ message(WARNING "GCC version older than 4.2") ++ elseif(CMAKE_CXX_COMPILER_ID MATCHES Intel AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS "12.0") ++ set(_INTEL_TOO_OLD TRUE) ++ message(WARNING "Intel compiler older than 12.0") + endif() + +- if(CMAKE_CXX_COMPILER_ID MATCHES "Intel") +- execute_process(COMMAND ${CMAKE_CXX_COMPILER} -V +- OUTPUT_VARIABLE _intel_version_info +- ERROR_VARIABLE _intel_version_info) +- string(REGEX REPLACE ".*Version ([0-9]+(\\.[0-9]+)+).*" "\\1" +- _intel_version "${_intel_version_info}") +- +- if(_intel_version VERSION_LESS "12.0") +- set(_INTEL_TOO_OLD TRUE) +- endif() +- endif() +- +- + # Exclude XL here because it misinterprets -fvisibility=hidden even though + # the check_cxx_compiler_flag passes + # http://www.cdash.org/CDash/testDetails.php?test=109109951&build=1419259 From 2acdb2b625ecab4da0aeb8f6cfc1f82284a27061 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 28 Jan 2022 14:48:23 +0100 Subject: [PATCH 2850/9987] Added patch file --- easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb index 7776bdb8cec..d83845e8289 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb @@ -10,12 +10,14 @@ toolchainopts = {'pic': True} source_urls = ['https://root.cern.ch/download/'] sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +patches = ['ROOT-6.14.06_fix-VDT-target.patch'] checksums = ['907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522'] builddependencies = [ ('CMake', '3.22.1'), ('pkg-config', '0.29.2'), ] + dependencies = [ ('GSL', '2.7'), ('libxml2', '2.9.10'), From 628e00c9f3033729692a2214233249fb2b0c1140 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 28 Jan 2022 14:50:53 +0100 Subject: [PATCH 2851/9987] Added checksum --- easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb index d83845e8289..dcec7e6dd04 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb @@ -11,7 +11,10 @@ toolchainopts = {'pic': True} source_urls = ['https://root.cern.ch/download/'] sources = ['%(namelower)s_v%(version)s.source.tar.gz'] patches = ['ROOT-6.14.06_fix-VDT-target.patch'] -checksums = ['907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522'] +checksums = [ + '907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522', # root_v6.24.06.source.tar.gz + 'ff51eb823726d146840b149945b7896b8e60cc0920933b740d780a540b62e4d8', # ROOT-6.14.06_fix-VDT-target.patch +] builddependencies = [ ('CMake', '3.22.1'), From ee480a06d552ab70f0637c5e8a930956669164c5 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 28 Jan 2022 16:47:46 +0100 Subject: [PATCH 2852/9987] Delete PyOpenCL-2021.1.2-fosscuda-2020b.eb --- .../PyOpenCL-2021.1.2-fosscuda-2020b.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb deleted file mode 100644 index cec1342f8e7..00000000000 --- a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.1.2-fosscuda-2020b.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PyOpenCL' -version = '2021.1.2' - -homepage = "https://mathema.tician.de/software/pyopencl/" -description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" - -toolchain = {'name': 'fosscuda', 'version': '2020b'} - -dependencies = [ - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('pocl', '1.6'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('appdirs', '1.4.4', { - 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], - }), - ('pytools', '2021.1', { - 'checksums': ['073ae22a0ae946e2db97164f2eb24a599cd3a51430384aa40859dffd73056c40'], - }), - ('pyopencl', version, { - 'checksums': ['18871bc80c5a94869521189cf2c04d72c88367a441a9a033f72f66792ac33d29'], - 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", - }), -] - -moduleclass = 'vis' From 57398d4d93d5fe71a6b400a544d44a8790f1d77f Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 28 Jan 2022 16:59:54 +0100 Subject: [PATCH 2853/9987] Java updated to 17.0.2 due to RHSA-2022:0166 CVEs --- easybuild/easyconfigs/j/Java/Java-17.0.2.eb | 23 +++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-17.0.2.eb diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.2.eb b/easybuild/easyconfigs/j/Java/Java-17.0.2.eb new file mode 100644 index 00000000000..2e19cdba6cc --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-17.0.2.eb @@ -0,0 +1,23 @@ +name = 'Java' +version = '17.0.2' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'openjdk-%%(version)s_linux-%s_bin.tar.gz' + +source_urls = ['https://download.java.net/java/GA/jdk%(version)s/dfd4a8d0985749f896bed50d7138ee7f/8/GPL/'] +sources = [local_tarball_tmpl % '%(jdkarch)s'] +checksums = [ + { + local_tarball_tmpl % 'x64': + '0022753d0cceecacdd3a795dd4cea2bd7ffdf9dc06e22ffd1be98411742fbb44', + local_tarball_tmpl % 'aarch64': + '13bfd976acf8803f862e82c7113fb0e9311ca5458b1decaef8a09ffd91119fa4', + } +] + +moduleclass = 'lang' From a4c7086070add4ce39d8f1a896d26548b2e1208d Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 28 Jan 2022 17:46:38 +0100 Subject: [PATCH 2854/9987] adding easyconfigs: GATE-9.1-foss-2021b.eb --- .../easyconfigs/g/GATE/GATE-9.1-foss-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATE/GATE-9.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/g/GATE/GATE-9.1-foss-2021b.eb b/easybuild/easyconfigs/g/GATE/GATE-9.1-foss-2021b.eb new file mode 100644 index 00000000000..98e2f2b5909 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-9.1-foss-2021b.eb @@ -0,0 +1,28 @@ +name = 'GATE' +version = '9.1' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'cstd': 'c++23'} + +source_urls = ['https://github.com/OpenGATE/Gate/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['aaab874198500b81d45b27cc6d6a51e72cca9519910b893a5c85c8e6d3ffa4fc'] + +builddependencies = [('CMake', '3.22.1')] +dependencies = [ + ('Geant4', '10.7.1'), + ('CLHEP', '2.4.4.0'), + ('ROOT', '6.24.06'), +] + +preinstallopts = "sed -i 's|/usr/local/bin|%(installdir)s/bin|g' Makefile &&" + +# enable extra capabilities (Davis requires Geant4 10.04 or newer) +configopts = "-DGATE_USE_OPTICAL=1 -DGATE_USE_DAVIS=1" + +moduleclass = 'cae' From b116ba7c84bfd133f04555367b986d2ead5b851e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 28 Jan 2022 19:14:55 +0100 Subject: [PATCH 2855/9987] update archspec-0.1.3-GCCcore-11.2.0.eb: Add patch for click 8 requirement --- .../archspec/archspec-0.1.3-GCCcore-11.2.0.eb | 13 +- .../a/archspec/archspec-0.1.3_click_8.patch | 131 ++++++++++++++++++ 2 files changed, 140 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.1.3_click_8.patch diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb index e2efe38ddd5..c938912d6a9 100644 --- a/easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb @@ -8,8 +8,14 @@ description = "A library for detecting, labeling, and reasoning about microarchi toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -sources = ['archspec-%(version)s-py2.py3-none-any.whl'] -checksums = ['bb170c3347b1e868e01b5cec5844354b893efddd7d65c9b73df8196ca14fb554'] +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +# See https://github.com/archspec/archspec/pull/69 +patches = ['archspec-0.1.3_click_8.patch'] +checksums = [ + 'a1aa7abde4d4ce38d115dfd572584906fa8e192e3272b8897e7b4fa1213ec27c', # archspec-0.1.3.tar.gz + 'd9fbdc599bb58b0121ec5e19e81e82238fc78da35e4f207b4f15186657896c59', # archspec-0.1.3_click_8.patch +] builddependencies = [('binutils', '2.37')] @@ -17,9 +23,8 @@ dependencies = [('Python', '3.9.6')] download_dep_fail = True use_pip = True +sanity_pip_check = True sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.3_click_8.patch b/easybuild/easyconfigs/a/archspec/archspec-0.1.3_click_8.patch new file mode 100644 index 00000000000..54a88063771 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.3_click_8.patch @@ -0,0 +1,131 @@ +diff -ruN archspec-0.1.3.orig/archspec/cpu/detect.py archspec-0.1.3/archspec/cpu/detect.py +--- archspec-0.1.3.orig/archspec/cpu/detect.py 2021-10-22 13:57:34.215254800 +0200 ++++ archspec-0.1.3/archspec/cpu/detect.py 2022-01-24 17:49:18.591176274 +0100 +@@ -61,7 +61,7 @@ + ``/proc/cpuinfo`` + """ + info = {} +- with open("/proc/cpuinfo") as file: ++ with open("/proc/cpuinfo") as file: # pylint: disable=unspecified-encoding + for line in file: + key, separator, value = line.partition(":") + +@@ -80,7 +80,9 @@ + + + def _check_output(args, env): +- output = subprocess.Popen(args, stdout=subprocess.PIPE, env=env).communicate()[0] ++ output = subprocess.Popen( # pylint: disable=consider-using-with ++ args, stdout=subprocess.PIPE, env=env ++ ).communicate()[0] + return six.text_type(output.decode("utf-8")) + + +@@ -288,7 +290,7 @@ + arch_root = TARGETS[basename] + return ( + (target == arch_root or arch_root in target.ancestors) +- and (target.vendor == vendor or target.vendor == "generic") ++ and target.vendor in (vendor, "generic") + and target.features.issubset(features) + ) + +@@ -303,7 +305,7 @@ + arch_root = TARGETS[basename] + return ( + (target == arch_root or arch_root in target.ancestors) +- and (target.vendor == vendor or target.vendor == "generic") ++ and target.vendor in (vendor, "generic") + and target.features.issubset(features) + ) + +diff -ruN archspec-0.1.3.orig/archspec/cpu/schema.py archspec-0.1.3/archspec/cpu/schema.py +--- archspec-0.1.3.orig/archspec/cpu/schema.py 2021-09-03 17:23:36.193003000 +0200 ++++ archspec-0.1.3/archspec/cpu/schema.py 2022-01-24 17:49:18.594040000 +0100 +@@ -11,7 +11,7 @@ + try: + from collections.abc import MutableMapping # novm + except ImportError: +- from collections import MutableMapping ++ from collections import MutableMapping # pylint: disable=deprecated-class + + + class LazyDictionary(MutableMapping): +@@ -56,7 +56,7 @@ + + def _factory(): + filename = os.path.join(json_dir, json_file) +- with open(filename, "r") as file: ++ with open(filename, "r") as file: # pylint: disable=unspecified-encoding + return json.load(file) + + return _factory +diff -ruN archspec-0.1.3.orig/pyproject.toml archspec-0.1.3/pyproject.toml +--- archspec-0.1.3.orig/pyproject.toml 2021-10-22 13:57:34.215254800 +0200 ++++ archspec-0.1.3/pyproject.toml 2022-01-24 17:49:18.594944000 +0100 +@@ -25,46 +25,51 @@ + ] + + [tool.poetry.dependencies] +-python = ">=2.7 !=3.4.* !=3.3.* !=3.2.* !=3.1.* !=3.0.* <4" ++python = "==2.7 || ^3.5" + six = "^1.13.0" +-click = ">=7.1.2,<8.0" ++click = [ ++ {version = "^8", python = '^3.6'}, ++ {version = "^7", python = '==3.5'}, ++ {version = "^7", python = '==2.7'} ++] + + [tool.poetry.dev-dependencies] + pytest = [ +- {version = ">=5.3.2", python = '^3.5'}, +- {version = ">=3.5.2", python = '^2.7'} ++ {version = "^6", python = '^3.6'}, ++ {version = "~5", python = '==3.5'}, ++ {version = "~3", python = '==2.7'} + ] + more_itertools = [ +- {version = ">=5.0.0", python = '^2.7'} ++ {version = "~5", python = '==2.7'} + ] + scandir = [ +- {version = ">=1.10.0", python = '^2.7'} ++ {version = "~1", python = '==2.7'} + ] + pytest-cov = "^2.8.1" + coverage = "^5.3" + pylint = [ +- {version = "^2.4.4", python = "^3.5"} ++ {version = "^2", python = "^3.6"} + ] + flake8 = [ +- {version = "^3.7.9", python = "^3.5"} ++ {version = "^4", python = "^3.6"} + ] + black = [ +- {version = ">19.10b0", python = "^3.6"} ++ {version = "==21.12b0", python = "^3.8"} + ] + sphinx = [ +- {version = "^2.3.1", python = "^3.5"} ++ {version = "^4", python = "^3.6"} + ] + sphinx_rtd_theme = [ +- {version = "^0.4.3", python = "^3.5"} ++ {version = "^1", python = "^3.6"} + ] + jsonschema = "^3.2.0" + pyrsistent = [ +- {version="<0.17.0", python="^2.7"} ++ {version="~0.16", python="==2.7"} + ] + + [tool.poetry.scripts] + archspec = 'archspec.cli:main' + + [build-system] +-requires = ["poetry>=0.12"] +-build-backend = "poetry.masonry.api" ++requires = ["poetry>=1.0.0"] ++build-backend = "poetry.core.masonry.api" From 017a233f685658898b4dcbf052d2f26465e3da6b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 28 Jan 2022 19:41:01 +0100 Subject: [PATCH 2856/9987] update archspec-0.1.3-GCCcore-11.2.0.eb --- .../easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb index c938912d6a9..5087b91bae6 100644 --- a/easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.3-GCCcore-11.2.0.eb @@ -8,7 +8,6 @@ description = "A library for detecting, labeling, and reasoning about microarchi toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] # See https://github.com/archspec/archspec/pull/69 patches = ['archspec-0.1.3_click_8.patch'] From 71818611429b64f4fc1216d92e0ca8fa8b9f3341 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Fri, 28 Jan 2022 22:11:58 +0100 Subject: [PATCH 2857/9987] Java 17: Updates wrapper --- easybuild/easyconfigs/j/Java/Java-17.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-17.eb b/easybuild/easyconfigs/j/Java/Java-17.eb index e4651cf9c6f..05f26251775 100644 --- a/easybuild/easyconfigs/j/Java/Java-17.eb +++ b/easybuild/easyconfigs/j/Java/Java-17.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.0.1')] +dependencies = [('Java', '%(version)s.0.2')] moduleclass = 'lang' From 1ab2be933e9c7c3de36b19f4ddb998ad8d48b982 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 29 Jan 2022 19:34:21 +0100 Subject: [PATCH 2858/9987] specify easybuild.io as EasyBuild homepage in setup.py --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index cae82ab6556..1b57af45e8a 100644 --- a/setup.py +++ b/setup.py @@ -84,7 +84,7 @@ def get_data_files(): versions, etc.).""", license="GPLv2", keywords="software build building installation installing compilation HPC scientific", - url="https://easybuilders.github.io/easybuild/", + url="https://easybuild.io", data_files=get_data_files(), long_description=read("README.rst"), classifiers=[ From c36ffed120096cc90560d6b131c5593f946a9bac Mon Sep 17 00:00:00 2001 From: Sassy Date: Sat, 29 Jan 2022 22:42:35 +0000 Subject: [PATCH 2859/9987] Requested changes done, Python version corrected --- .../Trim_Galore-0.6.7-GCCcore-10.3.0.eb | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb index 7d49be5c462..cf5350b94a4 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb @@ -1,4 +1,8 @@ -# Uploaded by J. Sassmannshausen NHS/GSTT +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# Updated to version 0.6.2: Pavel Grochal (INUITS) +# Updated to version 0.6.5: Alex Domingo (VUB) +# Updated to version 0.6.7 by J. Sassmannshausen NHS/GSTT easyblock = 'Tarball' @@ -20,24 +24,25 @@ checksums = [ ] dependencies = [ + ('Python', '3.9.5'), + ('Java', '11', '', True), + ('pigz', '2.6'), ('Perl', '5.32.1'), ('cutadapt', '3.4'), - ('FastQC', '0.11.9', '-Java-11', True), + ('FastQC', '0.11.9', '-Java-%(javaver)s', True), ] postinstallcmds = [ - "chmod +x %(installdir)s/%(namelower)s", - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\\ perl|' %(installdir)s/%(namelower)s", "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s", ] +fix_perl_shebang_for = ['bin/%(namelower)s'] + sanity_check_paths = { 'files': ["bin/trim_galore"], 'dirs': [], } -modextrapaths = {'PATH': '.'} - sanity_check_commands = [('trim_galore', '-v')] moduleclass = 'bio' From d83adccf00ff265a921d4aadb0d1b5679d2b3a21 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 31 Jan 2022 09:34:43 +0100 Subject: [PATCH 2860/9987] adding easyconfigs: likwid-5.2.1-GCCcore-11.2.0.eb --- .../l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f7786e5726d --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.1' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1b8e668da117f24302a344596336eca2c69d2bc2f49fa228ca41ea0688f6cbc2'] + +builddependencies = [ + ('binutils', '2.37'), + ('Perl', '5.34.0'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCCcore toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' + +maxparallel = 1 + +installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ="" ACCESSMODE=perf_event ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' From a74bee3686f08fa9f1495cf0728f651c547975a8 Mon Sep 17 00:00:00 2001 From: Robin Engler Date: Mon, 31 Jan 2022 10:37:02 +0100 Subject: [PATCH 2861/9987] Update R-4.1.0-foss-2021a.eb: update checksum of external packages - MASS, class, nnet, spatial --- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index d25b1a5f6ff..f2983d3a7d6 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -223,7 +223,7 @@ exts_list = [ 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], }), ('MASS', '7.3-54', { - 'checksums': ['b800ccd5b5c2709b1559cf5eab126e4935c4f8826cf7891253432bb6a056e821'], + 'checksums': ['eb644c0e94b447c46387aa22436ef5a43192960ee9cfd0df2940f4a4116179ae'], }), ('pixmap', '0.4-12', { 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], @@ -535,7 +535,7 @@ exts_list = [ 'checksums': ['8f1d960ab74f05fdd11c4c7a3d30ff9e263fc658f5690b67278ca7c045d0742c'], }), ('class', '7.3-19', { - 'checksums': ['7820ae94b22009561a69ed1f8b2ca2a3814be6a656e9884738206997caecbe37'], + 'checksums': ['9012f5c65384b441b5738ed7bd18ea735884bab32b31776e80cf3679f38a3769'], }), ('proxy', '0.4-25', { 'checksums': ['4e1c70d87eb106e95df7c6eb61b8808d79705d5fc5a64e6b5393999d651b09d5'], @@ -544,7 +544,7 @@ exts_list = [ 'checksums': ['797c6c087159c6d338ad002ae7eee305da447f95529bd25f5571ba834ecf18de'], }), ('nnet', '7.3-16', { - 'checksums': ['99511969babaf937c3033750b00b41e4e03742f268084efc4ee953b849f7b56a'], + 'checksums': ['c5b73eb4fff0d225e14f898cec987a7a88796b6e70cde4cf277374428f2d5c13'], }), ('minqa', '1.2.4', { 'checksums': ['cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c'], @@ -799,7 +799,7 @@ exts_list = [ 'checksums': ['c78aed92ce0239fd876b053291c77bb2ae979f01b4f30ec38e2f07a2c44ea3e2'], }), ('spatial', '7.3-14', { - 'checksums': ['52cc1982732f14544fae7dd9d028e2fc3b525ed695d211d6ed5055420e768a36'], + 'checksums': ['50e6daacbacff6c716485d20b15eb7fff7b8108dc5ea0ff508024beb4f0a8b9b'], }), ('VGAM', '1.1-5', { 'checksums': ['30190b150f3e5478137d288a45f575b2654ad7c29254b0a1fe5c954ee010a1bb'], From da187392e5e045d7cb34ebd69de2b67a4119eea5 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 31 Jan 2022 13:07:19 +0200 Subject: [PATCH 2862/9987] adding easyconfigs: SDL2-2.0.20-GCCcore-11.2.0.eb --- .../s/SDL2/SDL2-2.0.20-GCCcore-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.20-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.20-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.20-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..07dfacfacbc --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.20-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.20' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c56aba1d7b5b0e7e999e4a7698c70b63a3394ff9704b5f6e1c57e0c16f04dd06'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('X11', '20210802'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 941f133639e5c1ac9c6ae36a1a7147a5d2fe34a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 Jan 2022 15:14:41 +0100 Subject: [PATCH 2863/9987] adding easyconfigs: Go-1.17.6.eb --- easybuild/easyconfigs/g/Go/Go-1.17.6.eb | 30 +++++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.17.6.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.17.6.eb b/easybuild/easyconfigs/g/Go/Go-1.17.6.eb new file mode 100644 index 00000000000..87a77e8703a --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.17.6.eb @@ -0,0 +1,30 @@ +easyblock = 'Tarball' + +name = 'Go' +version = '1.17.6' + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] + +local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} +sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] +checksums = [{ + 'go%(version)s.linux-amd64.tar.gz': '231654bbf2dab3d86c1619ce799e77b03d96f9b50770297c8f4dff8836fc8ca2', + 'go%(version)s.linux-arm64.tar.gz': '82c1a033cce9bc1b47073fd6285233133040f0378439f3c4659fe77cc534622a', +}] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +sanity_check_commands = ["go help"] + +modextravars = {'GOROOT': '%(installdir)s'} + +moduleclass = 'compiler' From fd7c1cf2e4a0bf783ad99a10554d10ba13952ac1 Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Mon, 31 Jan 2022 15:15:19 +0100 Subject: [PATCH 2864/9987] adding easyconfigs: deepTools-3.5.0-foss-2021a-Python-3.9.5.eb --- ...deepTools-3.5.0-foss-2021a-Python-3.9.5.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100755 easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a-Python-3.9.5.eb new file mode 100755 index 00000000000..fee3a3a1d4b --- /dev/null +++ b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'deepTools' +version = '3.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://deeptools.readthedocs.io/' +description = """deepTools is a suite of python tools particularly developed for the efficient analysis of + high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Pysam', '0.16.0.1'), + ('matplotlib', '3.4.2'), + ('plotly.py', '5.1.0'), +] + +use_pip = True + +exts_list = [ + ('py2bit', '0.3.0', { + 'checksums': ['450555c40cba66957ac8c9a4b6afb625fb34c4bb41638de78c87661ff8b682ef'], + }), + ('pyBigWig', '0.3.18', { + 'modulename': 'pyBigWig', + 'checksums': ['4c2a8c571b4100ad7c4c318c142eb48558646be52aaab28215a70426f5be31bc'], + }), + ('deeptoolsintervals', '0.1.9', { + 'checksums': ['7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6'], + }), + ('numpydoc', '1.2', { + 'checksums': ['0cec233740c6b125913005d16e8a9996e060528afcb8b7cad3f2706629dfd6f7'], + }), + (name, version, { + 'checksums': ['1a14a29e60be13eac11bd204dab9aef73cd72fe56a94c587333f21087584c0d8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bamCompare', 'bin/bamCoverage', 'bin/bamPEFragmentSize', 'bin/computeGCBias', 'bin/computeMatrix', + 'bin/correctGCBias', 'bin/multiBamSummary', 'bin/plotCorrelation', 'bin/plotCoverage', + 'bin/plotHeatmap', 'bin/plotProfile'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 9340da9023b64ac40597e4f7336319259d113e56 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 31 Jan 2022 17:06:27 +0100 Subject: [PATCH 2865/9987] adding easyconfigs: CUDA-11.5.1.eb --- easybuild/easyconfigs/c/CUDA/CUDA-11.5.1.eb | 26 +++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.5.1.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.5.1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.5.1.eb new file mode 100644 index 00000000000..af7aaae632a --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.5.1.eb @@ -0,0 +1,26 @@ +name = 'CUDA' +version = '11.5.1' +local_nv_version = '495.29.05' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '60bea2fc0fac95574015f865355afbf599422ec2c85554f5f052b292711a4bca', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '9e0e494d945634fe8ad3e12d7b91806aa4220ed27487bb211030d651b27c67a9', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '73e1d0e97c7fa686efe7e00fb1e5f179372c4eec8e14d4f44ab58d5f6cf57f63', + } +] + +moduleclass = 'system' From 008b78760be5f161dabdca89ecd8d0aefe8efb75 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 31 Jan 2022 17:07:19 +0100 Subject: [PATCH 2866/9987] adding easyconfigs: CUDA-11.6.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-11.6.0.eb | 26 +++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.6.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.6.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.6.0.eb new file mode 100644 index 00000000000..be85f0bc0ad --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.6.0.eb @@ -0,0 +1,26 @@ +name = 'CUDA' +version = '11.6.0' +local_nv_version = '510.39.01' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '1783da6d63970786040980b57fa3cb6420142159fc7d0e66f8f05c4905d98c83', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'c86b866a42baf59ddc6f1f4a79e6d77213c90749e77e574f0e0d796a749ab7d0', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '5898579f5e59b708520883cb161089f5e4f3426158d1e9f973c49d224085d1d2', + } +] + +moduleclass = 'system' From c627c9e0d8e684aa94e36f0d5434f073caa5e402 Mon Sep 17 00:00:00 2001 From: Robin Engler Date: Mon, 31 Jan 2022 17:12:46 +0100 Subject: [PATCH 2867/9987] Add new checksums in addition of old ones, instead of replacing them --- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index f2983d3a7d6..e6cf317ae8b 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -223,7 +223,8 @@ exts_list = [ 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], }), ('MASS', '7.3-54', { - 'checksums': ['eb644c0e94b447c46387aa22436ef5a43192960ee9cfd0df2940f4a4116179ae'], + 'checksums': [('b800ccd5b5c2709b1559cf5eab126e4935c4f8826cf7891253432bb6a056e821', + 'eb644c0e94b447c46387aa22436ef5a43192960ee9cfd0df2940f4a4116179ae')], }), ('pixmap', '0.4-12', { 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], @@ -535,7 +536,8 @@ exts_list = [ 'checksums': ['8f1d960ab74f05fdd11c4c7a3d30ff9e263fc658f5690b67278ca7c045d0742c'], }), ('class', '7.3-19', { - 'checksums': ['9012f5c65384b441b5738ed7bd18ea735884bab32b31776e80cf3679f38a3769'], + 'checksums': [('7820ae94b22009561a69ed1f8b2ca2a3814be6a656e9884738206997caecbe37', + '9012f5c65384b441b5738ed7bd18ea735884bab32b31776e80cf3679f38a3769')], }), ('proxy', '0.4-25', { 'checksums': ['4e1c70d87eb106e95df7c6eb61b8808d79705d5fc5a64e6b5393999d651b09d5'], @@ -544,7 +546,8 @@ exts_list = [ 'checksums': ['797c6c087159c6d338ad002ae7eee305da447f95529bd25f5571ba834ecf18de'], }), ('nnet', '7.3-16', { - 'checksums': ['c5b73eb4fff0d225e14f898cec987a7a88796b6e70cde4cf277374428f2d5c13'], + 'checksums': [('99511969babaf937c3033750b00b41e4e03742f268084efc4ee953b849f7b56a', + 'c5b73eb4fff0d225e14f898cec987a7a88796b6e70cde4cf277374428f2d5c13')], }), ('minqa', '1.2.4', { 'checksums': ['cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c'], @@ -799,7 +802,8 @@ exts_list = [ 'checksums': ['c78aed92ce0239fd876b053291c77bb2ae979f01b4f30ec38e2f07a2c44ea3e2'], }), ('spatial', '7.3-14', { - 'checksums': ['50e6daacbacff6c716485d20b15eb7fff7b8108dc5ea0ff508024beb4f0a8b9b'], + 'checksums': [('52cc1982732f14544fae7dd9d028e2fc3b525ed695d211d6ed5055420e768a36', + '50e6daacbacff6c716485d20b15eb7fff7b8108dc5ea0ff508024beb4f0a8b9b')], }), ('VGAM', '1.1-5', { 'checksums': ['30190b150f3e5478137d288a45f575b2654ad7c29254b0a1fe5c954ee010a1bb'], From 0129edeb071ca96c4e3f9b9c87fc692786b3a4fb Mon Sep 17 00:00:00 2001 From: Robin Engler Date: Mon, 31 Jan 2022 17:21:40 +0100 Subject: [PATCH 2868/9987] Update R-4.1.2-foss-2021b.eb: update checksum of external packages - MASS, class, nnet, spatial --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index cdede914926..66406280d05 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -224,7 +224,8 @@ exts_list = [ 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], }), ('MASS', '7.3-54', { - 'checksums': ['b800ccd5b5c2709b1559cf5eab126e4935c4f8826cf7891253432bb6a056e821'], + 'checksums': [('b800ccd5b5c2709b1559cf5eab126e4935c4f8826cf7891253432bb6a056e821', + 'eb644c0e94b447c46387aa22436ef5a43192960ee9cfd0df2940f4a4116179ae')], }), ('pixmap', '0.4-12', { 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], @@ -536,7 +537,8 @@ exts_list = [ 'checksums': ['eff3a92756ca34cdc1661fa36d2bf7fc8e9f4132d2f1ef9ed0105c83594618bf'], }), ('class', '7.3-19', { - 'checksums': ['7820ae94b22009561a69ed1f8b2ca2a3814be6a656e9884738206997caecbe37'], + 'checksums': [('7820ae94b22009561a69ed1f8b2ca2a3814be6a656e9884738206997caecbe37', + '9012f5c65384b441b5738ed7bd18ea735884bab32b31776e80cf3679f38a3769')], }), ('proxy', '0.4-26', { 'checksums': ['676bad821343974e0297a0566c4bf0cf0ea890104906a745b87d3b5989c81a4d'], @@ -545,7 +547,8 @@ exts_list = [ 'checksums': ['9bf9a15e7ce0b9b1a57ce3048d29cbea7f2a5bb2e91271b1b6aaafe07c852226'], }), ('nnet', '7.3-16', { - 'checksums': ['99511969babaf937c3033750b00b41e4e03742f268084efc4ee953b849f7b56a'], + 'checksums': [('99511969babaf937c3033750b00b41e4e03742f268084efc4ee953b849f7b56a', + 'c5b73eb4fff0d225e14f898cec987a7a88796b6e70cde4cf277374428f2d5c13')], }), ('minqa', '1.2.4', { 'checksums': ['cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c'], @@ -842,7 +845,8 @@ exts_list = [ 'checksums': ['9b12184a28fff87cacd0c3602d0cf63acb4d0f3049ad3a6ff16177f6df350782'], }), ('spatial', '7.3-14', { - 'checksums': ['52cc1982732f14544fae7dd9d028e2fc3b525ed695d211d6ed5055420e768a36'], + 'checksums': [('52cc1982732f14544fae7dd9d028e2fc3b525ed695d211d6ed5055420e768a36', + '50e6daacbacff6c716485d20b15eb7fff7b8108dc5ea0ff508024beb4f0a8b9b')], }), ('VGAM', '1.1-5', { 'checksums': ['30190b150f3e5478137d288a45f575b2654ad7c29254b0a1fe5c954ee010a1bb'], From cc5c29dbfc282606ee2bf07537da80441e9423e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 Jan 2022 18:13:19 +0100 Subject: [PATCH 2869/9987] trim test configurations for easyconfigs test suite: only test with Python 2.7 + 3.6 and Lmod 7.x + 8.x --- .github/workflows/unit_tests.yml | 20 ++++---------------- 1 file changed, 4 insertions(+), 16 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index cb5cfe87612..02805c08dbc 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -5,24 +5,12 @@ jobs: runs-on: ubuntu-18.04 strategy: matrix: - python: [2.7, 3.5, 3.6, 3.7, 3.8, 3.9, '3.10'] - modules_tool: [Lmod-6.6.3, Lmod-7.8.22, Lmod-8.1.14] + python: [2.7, 3.6] + modules_tool: [Lmod-7.8.22, Lmod-8.6.8] module_syntax: [Lua, Tcl] - # exclude some configurations: only test Tcl module syntax with Lmod 7.x and Python 2.7 & 3.6 + # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 2.7 & 3.6 exclude: - - modules_tool: Lmod-6.6.3 - module_syntax: Tcl - - modules_tool: Lmod-8.1.14 - module_syntax: Tcl - - python: 3.5 - module_syntax: Tcl - - python: 3.7 - module_syntax: Tcl - - python: 3.8 - module_syntax: Tcl - - python: 3.9 - module_syntax: Tcl - - python: '3.10' + - modules_tool: Lmod-7.8.22 module_syntax: Tcl fail-fast: false steps: From ccba03a42713d9014ac9413c1bb43bde858377d4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 31 Jan 2022 23:47:31 +0100 Subject: [PATCH 2870/9987] remove versionsuffix from deepTools-3.5.0-foss-2021a.eb --- ...-foss-2021a-Python-3.9.5.eb => deepTools-3.5.0-foss-2021a.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/d/deepTools/{deepTools-3.5.0-foss-2021a-Python-3.9.5.eb => deepTools-3.5.0-foss-2021a.eb} (97%) diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a.eb similarity index 97% rename from easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a-Python-3.9.5.eb rename to easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a.eb index fee3a3a1d4b..d2d42f4ce6b 100755 --- a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a.eb @@ -2,7 +2,6 @@ easyblock = 'PythonBundle' name = 'deepTools' version = '3.5.0' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://deeptools.readthedocs.io/' description = """deepTools is a suite of python tools particularly developed for the efficient analysis of From ff25f9d154828fa71624a3924941988e139b7ec3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 1 Feb 2022 00:00:02 +0100 Subject: [PATCH 2871/9987] replace pyBigWig with its dependency in deepTools v3.5.0 --- .../easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a.eb b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a.eb index d2d42f4ce6b..16ec99822ae 100755 --- a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.0-foss-2021a.eb @@ -11,9 +11,11 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), - ('Pysam', '0.16.0.1'), + ('SciPy-bundle', '2021.05'), ('matplotlib', '3.4.2'), ('plotly.py', '5.1.0'), + ('Pysam', '0.16.0.1'), + ('pyBigWig', '0.3.18'), ] use_pip = True @@ -22,10 +24,6 @@ exts_list = [ ('py2bit', '0.3.0', { 'checksums': ['450555c40cba66957ac8c9a4b6afb625fb34c4bb41638de78c87661ff8b682ef'], }), - ('pyBigWig', '0.3.18', { - 'modulename': 'pyBigWig', - 'checksums': ['4c2a8c571b4100ad7c4c318c142eb48558646be52aaab28215a70426f5be31bc'], - }), ('deeptoolsintervals', '0.1.9', { 'checksums': ['7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6'], }), From 4f5349383910dbda2f6c1516bb8be2e36791bcc8 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 1 Feb 2022 09:18:44 +0200 Subject: [PATCH 2872/9987] adding easyconfigs: GST-plugins-base-1.18.5-GCC-11.2.0.eb, GStreamer-1.18.5-GCC-11.2.0.eb --- .../GST-plugins-base-1.18.5-GCC-11.2.0.eb | 43 ++++++++++++++++++ .../GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb | 44 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.5-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.5-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.5-GCC-11.2.0.eb new file mode 100644 index 00000000000..f806b941c5b --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.18.5-GCC-11.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-base' +version = '1.18.5' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['960b7af4585700db0fdd5b843554e11e2564fed9e061f591fae88a7be6446fa3'] + +builddependencies = [ + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('Bison', '3.7.6'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('GLib', '2.69.1'), + ('GTK3', '3.24.31'), + ('GStreamer', '1.18.5'), + ('Gdk-Pixbuf', '2.42.6'), + ('X11', '20210802'), + ('Mesa', '21.1.7'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb new file mode 100644 index 00000000000..7d550bd31b6 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GStreamer' +version = '1.18.5' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['55862232a63459bbf56abebde3085ca9aec211b478e891dacea4d6df8cafe80a'] + +builddependencies = [ + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.68.0'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('GMP', '6.2.1'), + ('GSL', '2.7'), + ('GLib', '2.69.1'), + ('GTK3', '3.24.31'), + ('libunwind', '1.5.0'), +] + +configopts = '-Dlibdw=disabled ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +moduleclass = 'vis' From 126478700e4fc18b75b99899b29b07cab2127f75 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 1 Feb 2022 09:20:32 +0200 Subject: [PATCH 2873/9987] adding easyconfigs: wxWidgets-3.1.5-GCC-11.2.0.eb --- .../w/wxWidgets/wxWidgets-3.1.5-GCC-11.2.0.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-11.2.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-11.2.0.eb new file mode 100644 index 00000000000..14ea610f26b --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-11.2.0.eb @@ -0,0 +1,70 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.1.5' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/wxWidgets/wxWidgets/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e8fd5f9fbff864562aa4d9c094f898c97f5e1274c90f25beb0bfd5cb61319dea'] + +builddependencies = [ + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.3.0'), + ('expat', '2.4.1'), + ('GTK3', '3.24.31'), + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('SDL2', '2.0.20'), + ('cairo', '1.16.0'), + ('GST-plugins-base', '1.18.5'), + ('GLib', '2.69.1'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From e8093e01ae78706d9f0741c6e8bba29464813e99 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 1 Feb 2022 09:24:58 +0200 Subject: [PATCH 2874/9987] adding easyconfigs: ctffind-4.1.14-foss-2021b.eb --- .../c/ctffind/ctffind-4.1.14-foss-2021b.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021b.eb new file mode 100644 index 00000000000..00eecab381d --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021b.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University +# +# Author: Thomas Hoffmann, EMBL Heidelberg + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.3.0'), + ('GSL', '2.7',), + ('wxWidgets', '3.1.5'), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From 2f02249008cf6212dd385b6a4ddb497de02f67d1 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 1 Feb 2022 10:57:19 +0200 Subject: [PATCH 2875/9987] fix style --- easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-11.2.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-11.2.0.eb index 14ea610f26b..43d2132bb9e 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.1.5-GCC-11.2.0.eb @@ -38,7 +38,7 @@ dependencies = [ ('libGLU', '9.0.2'), ('SDL2', '2.0.20'), ('cairo', '1.16.0'), - ('GST-plugins-base', '1.18.5'), + ('GST-plugins-base', '1.18.5'), ('GLib', '2.69.1'), ] From 42d022592b348622be74fac19f7cd84ddc9a1a0d Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 1 Feb 2022 10:13:11 +0000 Subject: [PATCH 2876/9987] adding easyconfigs: file-5.41-GCCcore-11.2.0.eb --- .../f/file/file-5.41-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9489d186e9a --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.41' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['13e532c7b364f7d57e23dfeea3147103150cb90593a57af86c10e4f6e411603f'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From b0d830f9b9480b2743395eb0c449bd80c1e1ca8a Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 1 Feb 2022 10:40:08 +0000 Subject: [PATCH 2877/9987] adding easyconfigs: NGS-2.11.2-GCCcore-10.3.0.eb --- .../n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e96c735ca5a --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'NGS' +version = '2.11.2' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups +produced from Next Generation Sequencing.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('Perl', '5.32.1', '-minimal'), +] + +dependencies = [('Java', '11', '', True)] + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://github.com/ncbi/ngs/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['7555ab7c2f04bd81160859f6c85c65376dc7f7b891804fad9e7636a7788e39c2'], +} + +components = [ + ('NGS-SDK', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), + ('NGS-Java', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), +] + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' From 36c892482258af147365e5ff5b6c298bb1eb4136 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 1 Feb 2022 10:41:51 +0000 Subject: [PATCH 2878/9987] adding easyconfigs: ncbi-vdb-2.11.2-gompi-2021a.eb --- .../n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021a.eb diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021a.eb new file mode 100644 index 00000000000..54122fc6992 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021a.eb @@ -0,0 +1,57 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.11.2' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch', + 'ncbi-vdb-cstdlib.patch', +] +checksums = [ + '647efea2762d63dee6d3e462b1fed2ae6d0f2cf1adb0da583ac95f3ee073abdf', # ncbi-vdb-2.11.2.tar.gz + 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch + '033da96984e063be2daac1bb4882dac1c9af46a853eea5832033cf3e97697f3a', # ncbi-vdb-cstdlib.patch +] + +builddependencies = [ + ('Perl', '5.32.1', '-minimal'), + ('Python', '3.9.5', '-bare'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('NGS', '2.11.2'), + ('file', '5.40'), # provides libmagic + ('HDF5', '1.10.7'), # version 1.12.x has changes to API and is not compatible + ('libxml2', '2.9.10'), + ('bzip2', '1.0.8'), +] + +# add addtional libraries needed to statically link HDF5 from EB +preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl &&" + +configopts = "--build-prefix=%(builddir)s " # change default build directory +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS/jar/ngs-java.jar " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +# replace hardcoded optimization flags with EB settings +prebuildopts = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " +preinstallopts = 'EBFLAGS="$CFLAGS" ' + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + + [('lib/libncbi-%s.%s' % (k, e), 'lib64/libncbi-%s.%s' % (k, e)) + for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' From af5033e145c3fe34d62ea79891af1d0fcc5b8a2f Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 1 Feb 2022 10:45:14 +0000 Subject: [PATCH 2879/9987] adding easyconfigs: HISAT2-2.2.1-gompi-2021a.eb --- .../h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb new file mode 100644 index 00000000000..d8894992081 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb @@ -0,0 +1,56 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +# 2.2.1 - changes from Adam Huffman +## + +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.2.1' + +homepage = 'https://daehwankimlab.github.io/hisat2' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +sources = [{ + 'source_urls': ['https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi'], + 'download_filename': 'download', + 'filename': '%(namelower)s-%(version)s-source.zip', +}] +# patches = ['wall-removal.patch'] +checksums = [ + '48e933330d4d8470d2b3dfe7ec3918f2e98a75f7381891e23b7df1fb4f135eb1', + 'e6bbee55ba7c72ca05b453262a4294f6105e53474e0152fa94a993091f5c1c5a', # wall-removal.patch +] + +dependencies = [ + ('NGS', '2.11.2'), + ('ncbi-vdb', '2.11.2'), +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +local_executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l', 'hisat2-repeat', 'extract_exons.py', + 'extract_splice_sites.py', 'hisat2_extract_exons.py', 'hisat2_extract_snps_haplotypes_UCSC.py', + 'hisat2_extract_snps_haplotypes_VCF.py', 'hisat2_extract_splice_sites.py', + 'hisat2_read_statistics.py', 'hisat2_simulate_reads.py'] +files_to_copy = [(local_executables, 'bin'), 'scripts', 'example'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables], + 'dirs': ['scripts', 'example'], +} + +sanity_check_commands = ["hisat2 --help"] + +moduleclass = 'bio' From 2336c84812e27cfb5dd605f925e2ff2cbd694760 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 1 Feb 2022 14:39:32 +0100 Subject: [PATCH 2880/9987] ftp/https patch in rsync_from_ncbi.pl is needed --- .../Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb | 8 ++++++-- .../Kraken2/Kraken2-2.0.9-beta-gompi-2020a-Perl-5.30.2.eb | 8 ++++++-- .../easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb | 6 +++++- 3 files changed, 17 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb index da6339de567..99768bdc2cc 100644 --- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb @@ -20,10 +20,14 @@ toolchainopts = {'openmp': True, 'cstd': 'c++11'} github_account = 'DerrickWood' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-2.0.7-beta_CXX-CXXFLAGS.patch'] -checksums = [ +patches = [ + '%(name)s-2.0.7-beta_CXX-CXXFLAGS.patch', + 'Kraken2-2.1.2_fix_ncbi_https_server.patch', +] +chacksums = [ '0287cf4df4b5d5511a9132d9ab37a8d76864bae445579efb9cb76db7e9c09eba', # v2.0.9-beta.tar.gz '191291e51a846d193a12486ab84496d5dd221a05c84648688b1351bb84d7adb2', # Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch + '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116', # Kraken2-2.1.2_fix_ncbi_https_server.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-gompi-2020a-Perl-5.30.2.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-gompi-2020a-Perl-5.30.2.eb index 12213f38a84..4254c46096b 100644 --- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-gompi-2020a-Perl-5.30.2.eb +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-gompi-2020a-Perl-5.30.2.eb @@ -20,10 +20,14 @@ toolchainopts = {'openmp': True, 'cstd': 'c++11'} github_account = 'DerrickWood' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-2.0.7-beta_CXX-CXXFLAGS.patch'] +patches = [ + '%(name)s-2.0.7-beta_CXX-CXXFLAGS.patch', + 'Kraken2-2.1.2_fix_ncbi_https_server.patch', +] checksums = [ '0287cf4df4b5d5511a9132d9ab37a8d76864bae445579efb9cb76db7e9c09eba', # v2.0.9-beta.tar.gz - '191291e51a846d193a12486ab84496d5dd221a05c84648688b1351bb84d7adb2' # Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch + '191291e51a846d193a12486ab84496d5dd221a05c84648688b1351bb84d7adb2', # Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch + '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116', # Kraken2-2.1.2_fix_ncbi_https_server.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb index f24d9c3b21e..7069cfa02d0 100644 --- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.1-gompi-2020b.eb @@ -19,11 +19,15 @@ toolchainopts = {'openmp': True, 'cstd': 'c++11'} github_account = 'DerrickWood' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['Kraken2-2.1.1_fix_installation_for_easybuild.patch'] +patches = [ + 'Kraken2-2.1.1_fix_installation_for_easybuild.patch', + 'Kraken2-2.1.2_fix_ncbi_https_server.patch', +] checksums = [ '8f3e928cdb32b9e8e6f55b44703d1557b2a5fc3f30f63e8d16e465e19a81dee4', # v2.1.1.tar.gz # Kraken2-2.1.1_fix_installation_for_easybuild.patch '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11', + '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116', # Kraken2-2.1.2_fix_ncbi_https_server.patch ] dependencies = [ From e05ca4eba485c87c3eab0a08c9a14a434f342b6f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 1 Feb 2022 14:42:47 +0100 Subject: [PATCH 2881/9987] ftp/https patch in rsync_from_ncbi.pl is needed 2 --- .../k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb index 99768bdc2cc..c7c4353fe4d 100644 --- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.0.9-beta-foss-2018b-Perl-5.28.0.eb @@ -24,7 +24,7 @@ patches = [ '%(name)s-2.0.7-beta_CXX-CXXFLAGS.patch', 'Kraken2-2.1.2_fix_ncbi_https_server.patch', ] -chacksums = [ +checksums = [ '0287cf4df4b5d5511a9132d9ab37a8d76864bae445579efb9cb76db7e9c09eba', # v2.0.9-beta.tar.gz '191291e51a846d193a12486ab84496d5dd221a05c84648688b1351bb84d7adb2', # Kraken2-2.0.7-beta_CXX-CXXFLAGS.patch '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116', # Kraken2-2.1.2_fix_ncbi_https_server.patch From 5d928882f5da10012d971695da7ac7f43e7ecd6f Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 1 Feb 2022 14:51:15 +0100 Subject: [PATCH 2882/9987] Added requested changes --- .../methylpy-1.2.9-foss-2021b-fixSetupConfig.patch | 7 ------- .../m/methylpy/methylpy-1.2.9-foss-2021b.eb | 14 +++----------- 2 files changed, 3 insertions(+), 18 deletions(-) delete mode 100644 easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch deleted file mode 100644 index 9d436708edf..00000000000 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b-fixSetupConfig.patch +++ /dev/null @@ -1,7 +0,0 @@ ---- setup.cfg.orig 2022-01-19 19:34:38.630926000 +0100 -+++ setup.cfg 2022-01-19 19:34:44.636856000 +0100 -@@ -1,2 +1,2 @@ - [metadata] --description-file = README.md -+description_file = README.md -\ No newline at end of file diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb index d0b78df3799..c66bd30a717 100644 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb @@ -10,12 +10,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/yupenghe/methylpy/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['methylpy-1.2.9-foss-2021b-fixSetupConfig.patch'] -checksums = [ - '169b5da07c26dbdd5d61a3bc5cbc3fe5a801bf1dd59b79b6d7e3f9a22005ae9e', # 1.2.9.tar.gz - # methylpy-1.2.9-foss-2021b-fixSetupConfig.patch - '92c4723c86ae79494a8e81ce682b0bb74777e272b55616c59548546606cc2215', -] +checksums = ['169b5da07c26dbdd5d61a3bc5cbc3fe5a801bf1dd59b79b6d7e3f9a22005ae9e'] dependencies = [ ('Python', '3.9.6'), @@ -29,13 +24,10 @@ dependencies = [ ('Kent_tools', '422'), ] +preinstallopts = "sed -i 's/description-file/description_file/g' setup.cfg && " + use_pip = True download_dep_fail = True sanity_pip_check = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'bio' From 89074d9f94237b82a94a02081cb9fed0944c405d Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 1 Feb 2022 15:00:19 +0100 Subject: [PATCH 2883/9987] Added requested changes --- .../easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb index 58474b8eecc..31798f16016 100644 --- a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb @@ -21,25 +21,18 @@ dependencies = [ ('tqdm', '4.62.3'), ('netcdf4-python', '1.5.7'), ('xarray', '0.20.1'), + ('typing-extensions', '3.10.0.2'), + ('ArviZ', '0.11.4'), + ('dill', '0.3.4'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('typing_extensions', '3.10.0.2', { - 'checksums': ['49f75d16ff11f1cd258e1b988ccff82a3ca5570217d7ad8c5f48205dd99a677e'], - }), - ('arviz', '0.11.4', { - 'checksums': ['01872758eeabb9941479ec5dd378117337bf95d14cc2c298b437cfda1780b436'], - }), ('patsy', '0.5.2', { 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], }), - ('dill', '0.3.4', { - 'source_tmpl': 'dill-%(version)s.zip', - 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], - }), ('fastprogress', '1.0.0', { 'checksums': ['89e28ac1d2a5412aab18ee3f3dfd1ee8b5c1f2f7a44d0add0d0d4f69f0191bfe'], }), From 08f98b2e804ea9b44cedf14b8116bfc5411cd19b Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 1 Feb 2022 15:15:23 +0100 Subject: [PATCH 2884/9987] Added requested changes --- .../easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb index d86176cd362..492c34fe96c 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb @@ -47,7 +47,7 @@ dependencies = [ ('Short-Pair', '20170125'), ('SAMtools', '1.14'), ('CompareM', '0.1.2'), - ('R-bundle-Bioconductor', '3.14', '-R-%(rver)s') + ('R-bundle-Bioconductor', '3.14', '-R-%(rver)s') # provides pathview needed for SQMtools ] keepsymlinks = True @@ -60,7 +60,6 @@ postinstallcmds = [ "cp %(builddir)s/barrnap %(installdir)s/bin/", # fix shebang in Perl scripts "sed -i 's@#!/usr/bin/perl@#!/usr/bin/env perl@g' %(installdir)s/scripts/*.pl", - "mkdir %(installdir)s/R" # also install SQMtools R library "mkdir %(installdir)s/R && R CMD INSTALL lib/SQMtools --library=%(installdir)s/R/ --no-clean-on-error", ] From b40258c8dda4ed738d78421f14f17dfca56cfb8b Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Tue, 1 Feb 2022 15:22:54 +0100 Subject: [PATCH 2885/9987] Delete netcdf4-python-1.5.7-intel-2021b.eb --- .../netcdf4-python-1.5.7-intel-2021b.eb | 51 ------------------- 1 file changed, 51 deletions(-) delete mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb deleted file mode 100644 index 67c96ca4840..00000000000 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'netcdf4-python' -version = '1.5.7' - -homepage = 'https://unidata.github.io/netcdf4-python/' -description = """Python/numpy interface to netCDF.""" - -toolchain = {'name': 'intel', 'version': '2021b'} -toolchainopts = {'usempi': True} - -dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('netCDF', '4.8.1'), - ('cURL', '7.78.0'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('cftime', '1.5.0', { - 'checksums': ['b644bcb53346b6f4fe2fcc9f3b574740a2097637492dcca29632c817e0604f29'], - }), - (name, version, { - 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], - 'source_tmpl': 'netCDF4-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], - 'checksums': [ - 'd145f9c12da29da3922d8b8aafea2a2a89501bcb28a219a46b7b828b57191594', # netCDF4-1.5.7.tar.gz - # netcdf4-python-1.1.8-avoid-diskless-test.patch - 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', - ], - }), -] - -fix_python_shebang_for = ['bin/*'] - -sanity_check_paths = { - 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "nc4tonc3 --help", - "nc3tonc4 --help", - "ncinfo --help", -] - -moduleclass = 'data' From 2154e99a9b6ca90941c7c489bb3c4b42320668e1 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 1 Feb 2022 15:24:20 +0100 Subject: [PATCH 2886/9987] adding easyconfigs: netcdf4-python-1.5.7-intel-2021b.eb --- .../netcdf4-python-1.5.7-intel-2021b.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb new file mode 100644 index 00000000000..67c96ca4840 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.5.7-intel-2021b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.5.7' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('netCDF', '4.8.1'), + ('cURL', '7.78.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.5.0', { + 'checksums': ['b644bcb53346b6f4fe2fcc9f3b574740a2097637492dcca29632c817e0604f29'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'd145f9c12da29da3922d8b8aafea2a2a89501bcb28a219a46b7b828b57191594', # netCDF4-1.5.7.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' From 66cff99cc4e8595214b970866475ac8bfe8d42d9 Mon Sep 17 00:00:00 2001 From: Keith Refson Date: Tue, 1 Feb 2022 14:26:13 +0000 Subject: [PATCH 2887/9987] Added checksums and sanity_check --- .../c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb | 17 +++++++++++++---- .../c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb | 17 +++++++++++++---- .../c/CASTEP/CASTEP-21.1.1-foss-2019b.eb | 17 +++++++++++++---- .../c/CASTEP/CASTEP-21.1.1-intel-2019b.eb | 17 +++++++++++++---- .../c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb | 17 +++++++++++++---- 5 files changed, 65 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb index aab29319405..164231d86c2 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb @@ -3,19 +3,28 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' +checksums = ['de510be026173a2b84cd4b59d9bdc8ac'] + homepage = 'http://www.castep.org' -description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" +description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), +with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" toolchain = {'name': 'CrayCCE', 'version': '19.06'} dependencies = [('cray-fftw', EXTERNAL_MODULE)] # CASTEP is proprietary software, available under a free-of-charge license for academic use only. # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. -sources = ['CASTEP-21.11.tar.gz'] +sources = ['CASTEP-21.11.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} -skipsteps = [ 'configure' ] +skipsteps = ['configure'] -maxparallel = 16 +maxparallel = 16 buildopts = 'COMMS_ARCH=mpi FFT=fftw3 FFTLIBDIR= castep tools' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb index 59ea706173f..1194b1adb6a 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb @@ -3,19 +3,28 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' +checksums = ['de510be026173a2b84cd4b59d9bdc8ac'] + homepage = 'http://www.castep.org' -description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" +description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), +with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" toolchain = {'name': 'CrayGNU', 'version': '19.06'} dependencies = [('cray-fftw', EXTERNAL_MODULE)] # CASTEP is proprietary software, available under a free-of-charge license for academic use only. # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. -sources = ['CASTEP-21.11.tar.gz'] +sources = ['CASTEP-21.11.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} -skipsteps = [ 'configure' ] +skipsteps = ['configure'] -maxparallel = 16 +maxparallel = 16 buildopts = 'COMMS_ARCH=mpi FFT=fftw3 FFTLIBDIR= castep tools' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb index c8a5551756d..afb2fc81bc5 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb @@ -3,19 +3,28 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' +checksums = ['de510be026173a2b84cd4b59d9bdc8ac'] + homepage = 'http://www.castep.org' -description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" +description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), +with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" toolchain = {'name': 'foss', 'version': '2019b'} # CASTEP is proprietary software, available under a free-of-charge license for academic use only. # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. -sources = ['CASTEP-21.11.tar.gz'] +sources = ['CASTEP-21.11.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} -skipsteps = [ 'configure' ] +skipsteps = ['configure'] -maxparallel = 16 +maxparallel = 16 buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas FFTLIBDIR= MATHLIBDIR= castep tools utilities' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb index 7e052d5f867..485ddd67050 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb @@ -3,19 +3,28 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' +checksums = ['de510be026173a2b84cd4b59d9bdc8ac'] + homepage = 'http://www.castep.org' -description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" +description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), +with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" toolchain = {'name': 'intel', 'version': '2019b'} # CASTEP is proprietary software, available under a free-of-charge license for academic use only. # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. -sources = ['CASTEP-21.11.tar.gz'] +sources = ['CASTEP-21.11.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} -skipsteps = [ 'configure' ] +skipsteps = ['configure'] -maxparallel = 16 +maxparallel = 16 buildopts = 'COMMS_ARCH=mpi castep tools utilities' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb index 2d7aef20c52..eaaef9f6f5e 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb @@ -3,19 +3,28 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' +checksums = ['de510be026173a2b84cd4b59d9bdc8ac'] + homepage = 'http://www.castep.org' -description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" +description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), +with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" toolchain = {'name': 'iomkl', 'version': '2019b'} # CASTEP is proprietary software, available under a free-of-charge license for academic use only. # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. -sources = ['CASTEP-21.11.tar.gz'] +sources = ['CASTEP-21.11.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} -skipsteps = [ 'configure' ] +skipsteps = ['configure'] -maxparallel = 16 +maxparallel = 16 buildopts = 'COMMS_ARCH=mpi castep tools utilities' From 4a4545dcdf2e772a32c0685c04324d150845702c Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 1 Feb 2022 15:38:21 +0100 Subject: [PATCH 2888/9987] fixed comment --- easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-11.2.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-11.2.0.eb index 7f6420d089f..f742fdacf04 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.7.1-GCC-11.2.0.eb @@ -16,7 +16,7 @@ checksums = ['a22800227713b46ba0b71bc674f6c937e5cc0cf17a6becf4a10d5ef90693a60b'] builddependencies = [('CMake', '3.22.1')] dependencies = [ ('expat', '2.4.1'), - # recommended CLHEP version, see https://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.6.html + # recommended CLHEP version, see https://geant4-data.web.cern.ch/geant4-data/ReleaseNotes/ReleaseNotes4.10.7.html ('CLHEP', '2.4.4.0'), ] From bcb4faada01bef018f1c71718f28fe87decb080a Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 1 Feb 2022 18:22:07 +0100 Subject: [PATCH 2889/9987] Forced C++17 standard --- easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb index dcec7e6dd04..b0ed79d7499 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb @@ -10,7 +10,6 @@ toolchainopts = {'pic': True} source_urls = ['https://root.cern.ch/download/'] sources = ['%(namelower)s_v%(version)s.source.tar.gz'] -patches = ['ROOT-6.14.06_fix-VDT-target.patch'] checksums = [ '907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522', # root_v6.24.06.source.tar.gz 'ff51eb823726d146840b149945b7896b8e60cc0920933b740d780a540b62e4d8', # ROOT-6.14.06_fix-VDT-target.patch @@ -51,6 +50,9 @@ configopts += " -Dunuran=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " # Add component-specific settings based on dependencies configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' +# Set C++ standard to C++17 for better stability +configopts += ' -DCMAKE_CXX_STANDARD=17' + configopts += " -Dgallium-drivers=swrast" moduleclass = 'data' From 600473585713f6ee7989e676fd01700e4f17e659 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 1 Feb 2022 18:31:03 +0100 Subject: [PATCH 2890/9987] Forced C++17 standard --- easybuild/easyconfigs/g/GATE/GATE-9.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GATE/GATE-9.1-foss-2021b.eb b/easybuild/easyconfigs/g/GATE/GATE-9.1-foss-2021b.eb index 98e2f2b5909..e7da77dcd26 100644 --- a/easybuild/easyconfigs/g/GATE/GATE-9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GATE/GATE-9.1-foss-2021b.eb @@ -7,7 +7,7 @@ description = """GATE is an advanced opensource software developed by the intern (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'cstd': 'c++23'} +toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/OpenGATE/Gate/archive/'] sources = ['v%(version)s.tar.gz'] From 9d7ef3ede00aa2a7b04be3216be88da9bfc21b1d Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 1 Feb 2022 18:34:39 +0100 Subject: [PATCH 2891/9987] Updated checksum --- easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb index b0ed79d7499..0ab4dcba930 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb @@ -10,10 +10,7 @@ toolchainopts = {'pic': True} source_urls = ['https://root.cern.ch/download/'] sources = ['%(namelower)s_v%(version)s.source.tar.gz'] -checksums = [ - '907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522', # root_v6.24.06.source.tar.gz - 'ff51eb823726d146840b149945b7896b8e60cc0920933b740d780a540b62e4d8', # ROOT-6.14.06_fix-VDT-target.patch -] +checksums = ['907f69f4baca1e4f30eeb4979598ca7599b6aa803ca046e80e25b6bbaa0ef522'] builddependencies = [ ('CMake', '3.22.1'), From b856af862daa24b9488ea87237b96596205ff2f6 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 1 Feb 2022 18:51:52 +0100 Subject: [PATCH 2892/9987] Added the edited version of Bowtie --- .../b/Bowtie/Bowtie-1.3.1-GCC-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..3ef078a1d2e --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Artistic v2.0 +# +# Notes:: +## + +name = 'Bowtie' +version = '1.3.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.zip'] +checksums = ['e23517aa53846ef828172be911750cd05748522117efcbbe5a36f3241fb40761'] + +dependencies = [ + ('tbb', '2020.3'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' From 64632e94c6bed1f5ff04d8e4c3cf717fe2ca1de7 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 1 Feb 2022 17:58:50 +0000 Subject: [PATCH 2893/9987] adding easyconfigs: Perl-5.34.0-GCCcore-11.2.0-minimal.eb --- .../Perl-5.34.0-GCCcore-11.2.0-minimal.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb new file mode 100644 index 00000000000..75ba2d908fa --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb @@ -0,0 +1,26 @@ +name = 'Perl' +version = '5.34.0' +versionsuffix = '-minimal' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +This is a minimal build without any modules. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['551efc818b968b05216024fb0b727ef2ad4c100f8cb6b43fab615fa78ae5be9a'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' From 48cfee78a87ebf0d33985dc6b8b889d80feab34d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Feb 2022 20:29:51 +0100 Subject: [PATCH 2894/9987] also install Python bindings for SHTns 3.5.1 --- .../easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb b/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb index d5ca8e5309e..979b80b3183 100644 --- a/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb @@ -8,14 +8,26 @@ description = """Spherical Harmonic Transform library aimed at high performance geometries.""" toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} source_urls = ['https://bitbucket.org/nschaeff/shtns/downloads/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['77f8a33b94df8786d2ce9b95cbfbe548f00443625b310b8c64012b22c8a7394f'] +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +installopts = " && pip install --no-deps --ignore-installed --prefix %(installdir)s ." + sanity_check_paths = { 'files': ['include/shtns_cuda.h', 'include/shtns.f', 'include/shtns.f03', 'include/shtns.h', 'lib/libshtns.a'], - 'dirs': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["python -c 'import shtns'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'lib' From 438d482df1617ae9ec995b297def524b01978c2a Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 1 Feb 2022 20:57:51 +0000 Subject: [PATCH 2895/9987] adding easyconfigs: HDF5-1.10.8-gompi-2021b.eb --- .../h/HDF5/HDF5-1.10.8-gompi-2021b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2021b.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2021b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2021b.eb new file mode 100644 index 00000000000..a20e9eef1b5 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2021b.eb @@ -0,0 +1,26 @@ +# Updated to version 1.10.8, needed for HISAT2-2.2.1 +# J. Sassmannshausen + +name = 'HDF5' +version = '1.10.8' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['66ec544b195a4cb9f6ffed034fd82e52429d6112747c2996ab69853f606e546b'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +configopts = "--enable-hltools" # needed to build HL-tools: gif2h5 gif2h5 and h5watch + +moduleclass = 'data' From 6d49c5d21ec68a82383a3b11c8f7ec8b87b6beda Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Feb 2022 22:05:29 +0100 Subject: [PATCH 2896/9987] adding easyconfigs: astropy-4.3.1-foss-2021b.eb --- .../a/astropy/astropy-4.3.1-foss-2021b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-4.3.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.3.1-foss-2021b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.3.1-foss-2021b.eb new file mode 100644 index 00000000000..b0ddae4d100 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-4.3.1-foss-2021b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '4.3.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '2.0.0.1', { + 'modulename': 'erfa', + 'checksums': ['2fd4637ffe2c1e6ede7482c13f583ba7c73119d78bef90175448ce506a0ede30'], + }), + ('extension-helpers', '0.1', { + 'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'], + }), + (name, version, { + 'checksums': ['2d3951223b4eb7f368fcad8c8340d27374c5d8e3b635a636275acdb38f35cd51'], + }), +] + +moduleclass = 'astro' From 709ecd7081c413428fd9c2331ecd126f0458b44f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Feb 2022 23:21:16 +0100 Subject: [PATCH 2897/9987] adding easyconfigs: BeautifulSoup-4.10.0-GCCcore-11.2.0.eb --- .../BeautifulSoup-4.10.0-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..abbe3b7912e --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.10.0' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37') +] + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.3.1', { + 'checksums': ['b8d49b1cd4f037c7082a9683dfa1801aa2597fb11c3a1155b7a5b94829b4f1f9'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['c23ad23c521d818955a4151a67d81580319d4bf548d3d49f4223ae041ff98891'], + }), +] + +moduleclass = 'data' From a5dc8c051f2166d71875238acc310b4ced507a59 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Feb 2022 23:39:22 +0100 Subject: [PATCH 2898/9987] adding easyconfigs: PyEVTK-2.0.0-foss-2021b.eb --- .../p/PyEVTK/PyEVTK-2.0.0-foss-2021b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyEVTK/PyEVTK-2.0.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/PyEVTK/PyEVTK-2.0.0-foss-2021b.eb b/easybuild/easyconfigs/p/PyEVTK/PyEVTK-2.0.0-foss-2021b.eb new file mode 100644 index 00000000000..5dd2af34654 --- /dev/null +++ b/easybuild/easyconfigs/p/PyEVTK/PyEVTK-2.0.0-foss-2021b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyEVTK' +version = '2.0.0' + +homepage = 'https://github.com/paulo-herrera/PyEVTK' +description = """EVTK (Export VTK) package allows exporting data to binary VTK files for visualization and +data analysis with any of the visualization packages that support VTK files""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/paulo-herrera/PyEVTK/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['65dda5511dba63ae55777ba01a50d24f8506f76985eba94ff83191c08f2b076c'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True + +# for some reason this is required to avoid 'pip install' failing with "ModuleNotFoundError: No module named 'evtk'" +preinstallopts = "PYTHONPATH=$PWD " + +sanity_pip_check = True + +options = {'modulename': 'evtk'} + +moduleclass = 'lib' From 907e938667da847dfd3ced1e2bd482759180e80d Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 1 Feb 2022 23:32:49 +0000 Subject: [PATCH 2899/9987] Fixed problem with build, also upgraded to gompi-2021b toolchain --- ...gompi-2021a.eb => HISAT2-2.2.1-gompi-2021b.eb} | 11 +++++++---- .../easyconfigs/h/HISAT2/hisat2-libname-fix.patch | 15 +++++++++++++++ 2 files changed, 22 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/h/HISAT2/{HISAT2-2.2.1-gompi-2021a.eb => HISAT2-2.2.1-gompi-2021b.eb} (88%) create mode 100644 easybuild/easyconfigs/h/HISAT2/hisat2-libname-fix.patch diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021b.eb similarity index 88% rename from easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb rename to easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021b.eb index d8894992081..218c01b5448 100644 --- a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021b.eb @@ -7,7 +7,8 @@ # # Notes:: # 2.2.1 - changes from Adam Huffman -## +# Bumped to foss-2021b +# J. Sassmannshausen easyblock = 'MakeCp' @@ -18,17 +19,19 @@ homepage = 'https://daehwankimlab.github.io/hisat2' description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).""" -toolchain = {'name': 'gompi', 'version': '2021a'} +toolchain = {'name': 'gompi', 'version': '2021b'} sources = [{ 'source_urls': ['https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi'], 'download_filename': 'download', 'filename': '%(namelower)s-%(version)s-source.zip', }] -# patches = ['wall-removal.patch'] +patches = [ + 'hisat2-libname-fix.patch', +] checksums = [ '48e933330d4d8470d2b3dfe7ec3918f2e98a75f7381891e23b7df1fb4f135eb1', - 'e6bbee55ba7c72ca05b453262a4294f6105e53474e0152fa94a993091f5c1c5a', # wall-removal.patch + '8aa91d1dd6455b96c10ce48827f8313b006241d815fbe6382422dbae3b610726', # hisat2-libname-fix.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/h/HISAT2/hisat2-libname-fix.patch b/easybuild/easyconfigs/h/HISAT2/hisat2-libname-fix.patch new file mode 100644 index 00000000000..9af29d77a5a --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/hisat2-libname-fix.patch @@ -0,0 +1,15 @@ +removes static from lib names as it caused problems when linking +J. Sassmannshausen +diff --git a/hisat2-2.2.1.orig/Makefile b/hisat2-2.2.1/Makefile +index 60445ce..0b422f8 100644 +--- a/hisat2-2.2.1.orig/Makefile ++++ b/hisat2-2.2.1/Makefile +@@ -94,7 +94,7 @@ SRA_LIB = + SERACH_INC = + ifeq (1,$(USE_SRA)) + SRA_DEF = -DUSE_SRA +- SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -ldl ++ SRA_LIB = -lncbi-ngs-c++ -lngs-c++ -lncbi-vdb -ldl + SEARCH_INC += -I$(NCBI_NGS_DIR)/include -I$(NCBI_VDB_DIR)/include + SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib64 -L$(NCBI_VDB_DIR)/lib64 + endif From ea8cc5b83249771c8c03497f5698c54c4a092019 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 1 Feb 2022 23:34:13 +0000 Subject: [PATCH 2900/9987] Upgraded to GCCcore-11.2.0 --- ....11.2-GCCcore-10.3.0.eb => NGS-2.11.2-GCCcore-11.2.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/n/NGS/{NGS-2.11.2-GCCcore-10.3.0.eb => NGS-2.11.2-GCCcore-11.2.0.eb} (91%) diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb similarity index 91% rename from easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb index e96c735ca5a..d410657900f 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb @@ -7,11 +7,11 @@ homepage = 'https://github.com/ncbi/ngs' description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.""" -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} builddependencies = [ - ('binutils', '2.36.1'), - ('Perl', '5.32.1', '-minimal'), + ('binutils', '2.37'), + ('Perl', '5.34.0', '-minimal'), ] dependencies = [('Java', '11', '', True)] From d251f9e1ba1d946aa7859825b160c4d6bfda47c2 Mon Sep 17 00:00:00 2001 From: Sassy Date: Tue, 1 Feb 2022 23:35:54 +0000 Subject: [PATCH 2901/9987] Upgraded to GCCcore-11.2.0 --- ...mpi-2021a.eb => ncbi-vdb-2.11.2-gompi-2021b.eb} | 12 ++++++------ .../easyconfigs/n/ncbi-vdb/ncbi-vdb-cstdlib.patch | 14 ++++++++++++++ 2 files changed, 20 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/n/ncbi-vdb/{ncbi-vdb-2.11.2-gompi-2021a.eb => ncbi-vdb-2.11.2-gompi-2021b.eb} (86%) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-cstdlib.patch diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb similarity index 86% rename from easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021a.eb rename to easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb index 54122fc6992..8dc0c1cad63 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021a.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/ncbi/ncbi-vdb' description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.""" -toolchain = {'name': 'gompi', 'version': '2021a'} +toolchain = {'name': 'gompi', 'version': '2021b'} github_account = 'ncbi' source_urls = [GITHUB_SOURCE] @@ -19,18 +19,18 @@ patches = [ checksums = [ '647efea2762d63dee6d3e462b1fed2ae6d0f2cf1adb0da583ac95f3ee073abdf', # ncbi-vdb-2.11.2.tar.gz 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch - '033da96984e063be2daac1bb4882dac1c9af46a853eea5832033cf3e97697f3a', # ncbi-vdb-cstdlib.patch + 'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655', # ncbi-vdb-cstdlib.patch ] builddependencies = [ - ('Perl', '5.32.1', '-minimal'), - ('Python', '3.9.5', '-bare'), - ('CMake', '3.20.1'), + ('Perl', '5.34.0', '-minimal'), + ('Python', '3.9.6', '-bare'), + ('CMake', '3.22.1'), ] dependencies = [ ('NGS', '2.11.2'), - ('file', '5.40'), # provides libmagic + ('file', '5.41'), # provides libmagic ('HDF5', '1.10.7'), # version 1.12.x has changes to API and is not compatible ('libxml2', '2.9.10'), ('bzip2', '1.0.8'), diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-cstdlib.patch b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-cstdlib.patch new file mode 100644 index 00000000000..0b796a73c06 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-cstdlib.patch @@ -0,0 +1,14 @@ +Adding missing cstdlib +J. Sassmannshausen +diff --git a/ncbi-vdb-2.11.2.orig/vdb3/platform/memory/PrimordialMemoryMgr.cpp b/ncbi-vdb-2.11.2/vdb3/platform/memory/PrimordialMemoryMgr.cpp +index e53c791..05db314 100644 +--- a/ncbi-vdb-2.11.2.orig/vdb3/platform/memory/PrimordialMemoryMgr.cpp ++++ b/ncbi-vdb-2.11.2/vdb3/platform/memory/PrimordialMemoryMgr.cpp +@@ -24,6 +24,7 @@ + * + */ + ++#include + #include + + #include From cea03bdd31d89bb30f116f3242befa1ddc5c35c3 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 2 Feb 2022 00:04:11 +0000 Subject: [PATCH 2902/9987] Due to vulnerability gif2h5 gif2h5 and h5watch are no longer build per default. See comment in EasyConfig file! --- easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2021b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2021b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2021b.eb index a20e9eef1b5..56617ae1c6d 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2021b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2021b.eb @@ -21,6 +21,8 @@ dependencies = [ ('Szip', '2.1.1'), ] -configopts = "--enable-hltools" # needed to build HL-tools: gif2h5 gif2h5 and h5watch +# needed to build HL-tools: gif2h5 gif2h5 and h5watch +# beware that gif tools are affected by multiple CVEs: CVE-2018-17433, CVE-2018-17436, CVE-2020-10809 +# configopts = "--enable-hltools" moduleclass = 'data' From 5f97c2190e473e78227639e328e47b25b69e9cc1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Feb 2022 08:59:01 +0100 Subject: [PATCH 2903/9987] improve description for xxd Co-authored-by: Alex Domingo --- easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb index d731b2429f9..6544bfe789e 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb @@ -8,8 +8,7 @@ name = 'xxd' version = '8.2.4220' homepage = 'https://www.vim.org' -description = """xxd is part of the VIM package and this will only install xxd, not vim! -xxd converts to/from hexdumps of binary files.""" +description = "xxd is part of the VIM package and serves to convert to/from hexdumps of binary files." toolchain = {'name': 'GCCcore', 'version': '10.2.0'} From 2e70833c55cf2cf1b19b86e8b7983ca488d47128 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Feb 2022 09:12:00 +0100 Subject: [PATCH 2904/9987] add custom sanity check command for xxd --- easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb | 2 ++ easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb | 2 ++ easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb index 6544bfe789e..5f897051931 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.2.0.eb @@ -33,4 +33,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb index e67c450e4eb..0b10cb8bd7b 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-10.3.0.eb @@ -34,4 +34,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb index 6d0ed44c3cd..ef1c1be77c4 100644 --- a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.2.0.eb @@ -34,4 +34,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"] + moduleclass = 'tools' From acf0e10fd43b2e1c0ba07f301d69429b1c4526c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 2 Feb 2022 11:06:09 +0100 Subject: [PATCH 2905/9987] change patch to git commit patch --- .../intervaltree-0.1-GCCcore-11.2.0.eb | 2 +- .../intervaltree-0.1_fix-numeric_limits.patch | 29 ++++++++++++++----- 2 files changed, 22 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.2.0.eb index d34ab952852..164fe620dca 100644 --- a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.2.0.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_fix-numeric_limits.patch'] checksums = [ '7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307', # v0.1.tar.gz - 'bd0adcba152049334e16cb689b416311df85fe87d777432919bca18b162a9024', # intervaltree-0.1_fix-numeric_limits.patch + '1d69caf35af86c0a55000e1bde3f9a0f19dd63d1d2b6bd48e4e5fecbb1aaa6b0', # intervaltree-0.1_fix-numeric_limits.patch ] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1_fix-numeric_limits.patch b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1_fix-numeric_limits.patch index 68ab2af524a..4e57c278fef 100644 --- a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1_fix-numeric_limits.patch +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1_fix-numeric_limits.patch @@ -1,9 +1,21 @@ -include for numeric_limits otherwise build failes with GCC 11 +From f0c4046514f41072be20da07b69d8a92220c9294 Mon Sep 17 00:00:00 2001 +From: Juhani Numminen +Date: Thu, 11 Mar 2021 14:56:33 +0200 +Subject: [PATCH] include for numeric_limits + +Omission of this include will cause build failures with GCC 11. https://www.gnu.org/software/gcc/gcc-11/porting_to.html -author: Paul Jähne -diff -ru intervaltree.orig/IntervalTree.h intervaltree/IntervalTree.h ---- intervaltree.orig/IntervalTree.h 2022-01-27 07:13:17.314126848 +0100 -+++ intervaltree/IntervalTree.h 2022-01-27 07:16:04.743740855 +0100 + +Original bug report: https://bugs.debian.org/984212 +--- + IntervalTree.h | 1 + + interval_tree_test.cpp | 1 + + 2 files changed, 2 insertions(+) + +diff --git a/IntervalTree.h b/IntervalTree.h +index eb9fc62..ec6640c 100644 +--- a/IntervalTree.h ++++ b/IntervalTree.h @@ -6,6 +6,7 @@ #include #include @@ -12,9 +24,10 @@ diff -ru intervaltree.orig/IntervalTree.h intervaltree/IntervalTree.h #ifdef USE_INTERVAL_TREE_NAMESPACE namespace interval_tree { -diff -ru intervaltree.orig/interval_tree_test.cpp intervaltree/interval_tree_test.cpp ---- intervaltree.orig/interval_tree_test.cpp 2022-01-27 07:13:17.314126848 +0100 -+++ intervaltree/interval_tree_test.cpp 2022-01-27 07:15:55.459872595 +0100 +diff --git a/interval_tree_test.cpp b/interval_tree_test.cpp +index fbfee2f..58ec91c 100644 +--- a/interval_tree_test.cpp ++++ b/interval_tree_test.cpp @@ -2,6 +2,7 @@ #include #include From 657937f3ab386cafcc08ff98ddbb471b18ced657 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 2 Feb 2022 12:12:39 +0100 Subject: [PATCH 2906/9987] remove default CMake build type configopts from ConnectomeWorkbench v1.5.0 --- .../ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb index ad53f63a5ee..451a1380cbd 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb @@ -25,7 +25,7 @@ dependencies = [ start_dir = 'src' -configopts = '-DCMAKE_BUILD_TYPE=Release -DWORKBENCH_MESA_DIR=${EBROOTMESA} ' +configopts = '-DWORKBENCH_MESA_DIR=${EBROOTMESA} ' configopts += '-DWORKBENCH_USE_QT5=TRUE -DWORKBENCH_USE_QT5_QOPENGL_WIDGET=TRUE -Wno-dev ' # It is necessary to deactivate the SIMD optimization in order to build From db4e502e9c2639e72aac176f4b50d17bdb318aa3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 2 Feb 2022 12:24:28 +0100 Subject: [PATCH 2907/9987] use numpy from SciPy-bundle in pyradiomics v3.0.1 --- .../pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb index 0236db1734b..95fd73b63b0 100644 --- a/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2019b-Python-3.7.4.eb @@ -12,16 +12,13 @@ toolchain = {'name': 'foss', 'version': '2019b'} dependencies = [ ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # for numpy ('SimpleITK', '1.2.4', versionsuffix), ] use_pip = True exts_list = [ - ('numpy', '1.18.0', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['a9d72d9abaf65628f0f31bbb573b7d9304e43b1e6bbae43149c17737a42764c4'], - }), ('PyWavelets', '1.2.0', { 'modulename': 'pywt', 'checksums': ['6cbd69b047bb4e00873097472133425f5f08a4e6bc8b3f0ae709274d4d5e9a8d'], From 4332b809e5e2fcfe9306b8e770089dcae5f8f667 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 2 Feb 2022 11:39:27 +0000 Subject: [PATCH 2908/9987] Correct HDF5 version added --- easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb index 8dc0c1cad63..8b443db27f1 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb @@ -31,7 +31,7 @@ builddependencies = [ dependencies = [ ('NGS', '2.11.2'), ('file', '5.41'), # provides libmagic - ('HDF5', '1.10.7'), # version 1.12.x has changes to API and is not compatible + ('HDF5', '1.10.8'), # version 1.12.x has changes to API and is not compatible ('libxml2', '2.9.10'), ('bzip2', '1.0.8'), ] From 26e1946e0d3739bce7dada7ab53523af830a2bb7 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 2 Feb 2022 12:46:16 +0100 Subject: [PATCH 2909/9987] remove obsolete MinPath easyconfig using intel/2021b toolchain --- .../m/MinPath/MinPath-1.6-intel-2021b.eb | 46 ------------------- 1 file changed, 46 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb diff --git a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb b/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb deleted file mode 100644 index 8e52500a1cf..00000000000 --- a/easybuild/easyconfigs/m/MinPath/MinPath-1.6-intel-2021b.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'Tarball' - -name = 'MinPath' -version = '1.6' -# no tagged commit for MinPath 1.6, commit was determined based on commit history -local_commit = '46d3e81a4dca2310d558bea970bc002b15d44767' - -homepage = 'https://omics.informatics.indiana.edu/MinPath' -description = """MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions - using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological - pathways for a query dataset.""" - -toolchain = {'name': 'intel', 'version': '2021b'} - -source_urls = ['https://github.com/mgtools/MinPath/archive/'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = ['MinPath-%(version)s_fix-glpsol-path.patch'] -checksums = [ - '57e6b55cd00507578bad7528c60e3ad055311f62db928bd7c8de793513cec5a3', # MinPath-1.6.tar.gz - '117e45c6f35e3c944232dd5dd4789400d44c4b9b733b936adbb548b58e046c4b', # MinPath-1.6_fix-glpsol-path.patch -] - -dependencies = [ - ('Python', '3.9.6'), - ('GLPK', '5.0'), -] - -# remove included old GLPK copy -postinstallcmds = ["rm -rf %(installdir)s/glpk-*/*"] - -fix_python_shebang_for = ['*.py'] - -sanity_check_paths = { - 'files': ['MinPath.py'], - 'dirs': [], -} - -sanity_check_commands = [ - "MinPath.py -ko examples/demo.ko -report /dev/null -details /dev/null", - "MinPath.py -fig examples/demo.fig -report /dev/null -details /dev/null", - "MinPath.py -any examples/demo.ec -map ec2path -report /dev/null -details /dev/null", -] - -modextrapaths = {'PATH': ''} - -moduleclass = 'bio' From 979f8b2b6ad5715d36b044311fc0151bb671784f Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 2 Feb 2022 13:33:51 +0100 Subject: [PATCH 2910/9987] adding easyconfigs: OpenSlide-3.4.1-GCCcore-11.2.0.eb, openslide-python-1.1.2-GCCcore-11.2.0.eb --- .../OpenSlide-3.4.1-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ .../openslide-python-1.1.2-GCCcore-11.2.0.eb | 29 +++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8298c309596 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide' +version = '3.4.1' + +homepage = 'https://openslide.org/' +description = """OpenSlide is a C library that provides a simple interface to +read whole-slide images (also known as virtual slides).""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/openslide/openslide/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c'] + +builddependencies = [ + ('Autotools', '20210726'), + ('M4', '1.4.19'), + ('pkg-config', '0.29.2'), + ('binutils', '2.37'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.3.0'), + ('OpenJPEG', '2.4.0'), + ('libxml2', '2.9.10'), + ('SQLite', '3.36'), + ('cairo', '1.16.0'), + ('Gdk-Pixbuf', '2.42.6'), +] + +preconfigopts = 'autoreconf -f -i && ' + +sanity_check_paths = { + 'files': ['bin/openslide-quickhash1sum', 'bin/openslide-show-properties', 'bin/openslide-write-png', + 'lib/libopenslide.la', 'lib/libopenslide.%s' % SHLIB_EXT], + 'dirs': ['include/openslide'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b428bf256c3 --- /dev/null +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.2-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'openslide-python' +version = '1.1.2' + +homepage = 'https://github.com/openslide/openslide-python' +description = "OpenSlide Python is a Python interface to the OpenSlide library." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/openslide/openslide-python/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['83e064ab4a29658e7ddf86bf1d3e54d2508cc19ece35d55b55519c826e45d83f'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('OpenSlide', '3.4.1'), + ('Pillow', '8.3.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'openslide'} + +moduleclass = 'vis' From 27076f3343783ff1435d9e5455215d9f4bb71865 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 2 Feb 2022 15:45:38 +0200 Subject: [PATCH 2911/9987] adding easyconfigs: AlphaFold-2.1.2-fosscuda-2020b.eb, AlphaFold-2.1.2-fosscuda-2020b.eb and patches: AlphaFold-2.1.2_data-dep-paths.patch --- .../AlphaFold-2.1.2-fosscuda-2020b.eb | 181 ++++++++++++++++++ .../AlphaFold-2.1.2_data-dep-paths.patch | 134 +++++++++++++ 2 files changed, 315 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2_data-dep-paths.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb new file mode 100644 index 00000000000..fbe26b9c1b9 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb @@ -0,0 +1,181 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.1.2' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4', ), + ('Doxygen', '1.8.20', ), + # required for installing dm-tree + ('Bazel', '3.7.2', ), + ('SWIG', '4.0.2', ), +] + +dependencies = [ + ('Python', '3.8.6', ), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1', ), + ('TensorFlow', '2.4.1'), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0',), + ('HMMER', '3.3.2',), + ('Kalign', '3.3.1', ), + ('jax', '0.2.19'), # also provides absl-py +] +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.1.2_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '6af91706b2a001494ddc0947f89f8b3d3adfcc26177c373824fe8ea1a58c0b48', # AlphaFold-2.1.2_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +modextravars = { + 'ALPHAFOLD_DATA_DIR': '/scratch/AlphaFold_DBs', # adapt +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2_data-dep-paths.patch new file mode 100644 index 00000000000..d89b1356f6c --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2_data-dep-paths.patch @@ -0,0 +1,134 @@ +pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data +(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py); +pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) +update 2.0.1 -> 2.1.0/2.1.2: Thomas Hoffmann (EMBL); +diff -ru alphafold-2.1.2/run_alphafold.py AlphaFold-2.1.2_data-dep-paths.patch/run_alphafold.py +--- alphafold-2.1.2/run_alphafold.py 2022-01-27 15:41:09.000000000 +0100 ++++ AlphaFold-2.1.2_data-dep-paths.patch/run_alphafold.py 2022-02-01 13:14:14.417024919 +0100 +@@ -40,6 +40,45 @@ + import numpy as np + + # Internal import (7716). ++use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:]) ++use_monomer_preset = not any("--model_preset=multimer" in s for s in sys.argv[1:]) ++ ++data_dir = os.getenv('ALPHAFOLD_DATA_DIR') ++use_gpu_relax = os.getenv('OPENMM_RELAX')=='CUDA' ++ ++if data_dir: ++ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters_2018_12.fa') ++ uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') ++ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') ++ obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') ++ if use_monomer_preset: ++ pdb_seqres_database_path = None ++ uniprot_database_path = None ++ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') ++ else: ++ pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt') ++ uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.fasta') ++ pdb70_database_path = None ++ if use_reduced_dbs: ++ small_bfd_database_path = os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta') ++ uniclust30_database_path = None ++ bfd_database_path = None ++ else: ++ small_bfd_database_path = None ++ bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') ++ uniclust30_database_path = os.path.join(data_dir, 'uniclust30', 'uniclust30_2018_08', 'uniclust30_2018_08') ++else: ++ sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!") ++ uniref90_database_path = None ++ mgnify_database_path = None ++ bfd_database_path = None ++ uniclust30_database_path = None ++ pdb70_database_path = None ++ template_mmcif_dir = None ++ obsolete_pdbs_path = None ++ small_bfd_database_path = None ++ uniprot_database_path = None ++ pdb_seqres_database_path = None + + logging.set_verbosity(logging.INFO) + +@@ -56,7 +95,7 @@ + 'where it is not, or where the origin is unknown. These values determine ' + 'the pairing method for the MSA.') + +-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') ++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') + flags.DEFINE_string('output_dir', None, 'Path to a directory that will ' + 'store the results.') + flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'), +@@ -71,27 +110,27 @@ + 'Path to the hmmbuild executable.') + flags.DEFINE_string('kalign_binary_path', shutil.which('kalign'), + 'Path to the Kalign executable.') +-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 ' ++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify ' ++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD ' ++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD ' + 'database for use by HHblits.') +-flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small ' ++flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small ' + 'version of BFD used with the "reduced_dbs" preset.') +-flags.DEFINE_string('uniclust30_database_path', None, 'Path to the Uniclust30 ' ++flags.DEFINE_string('uniclust30_database_path', uniclust30_database_path, 'Path to the Uniclust30 ' + 'database for use by HHblits.') +-flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot ' ++flags.DEFINE_string('uniprot_database_path', uniprot_database_path, 'Path to the Uniprot ' + 'database for use by JackHMMer.') +-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 ' ++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 ' + 'database for use by HHsearch.') +-flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB ' ++flags.DEFINE_string('pdb_seqres_database_path', pdb_seqres_database_path, 'Path to the PDB ' + 'seqres database for use by hmmsearch.') +-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with ' ++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with ' + 'template mmCIF structures, each named .cif') + flags.DEFINE_string('max_template_date', None, 'Maximum template release date ' + 'to consider. Important if folding historical test sets.') +-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a ' ++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a ' + 'mapping from obsolete PDB IDs to the PDB IDs of their ' + 'replacements.') + flags.DEFINE_enum('db_preset', 'full_dbs', +@@ -125,7 +164,7 @@ + 'result in predictions with distracting stereochemical ' + 'violations but might help in case you are having issues ' + 'with the relaxation stage.') +-flags.DEFINE_boolean('use_gpu_relax', None, 'Whether to relax on GPU. ' ++flags.DEFINE_boolean('use_gpu_relax', use_gpu_relax, 'Whether to relax on GPU. ' + 'Relax on GPU can be much faster than CPU, so it is ' + 'recommended to enable if possible. GPUs must be available' + ' if this setting is enabled.') +@@ -294,6 +333,9 @@ + 'sure it is installed on your system.') + + use_small_bfd = FLAGS.db_preset == 'reduced_dbs' ++ if use_small_bfd and data_dir: ++ bfd_database_path = None ++ uniclust30_database_path = None + _check_flag('small_bfd_database_path', 'db_preset', + should_be_set=use_small_bfd) + _check_flag('bfd_database_path', 'db_preset', +@@ -433,13 +475,7 @@ + flags.mark_flags_as_required([ + 'fasta_paths', + 'output_dir', +- 'data_dir', +- 'uniref90_database_path', +- 'mgnify_database_path', +- 'template_mmcif_dir', + 'max_template_date', +- 'obsolete_pdbs_path', +- 'use_gpu_relax', + ]) + + app.run(main) From 87c02c24cba4a20292a129455550cf7b7a0b7107 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 2 Feb 2022 14:58:53 +0100 Subject: [PATCH 2912/9987] adding easyconfigs: SeqKit-2.1.0.eb --- .../easyconfigs/s/SeqKit/SeqKit-2.1.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeqKit/SeqKit-2.1.0.eb diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-2.1.0.eb b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.1.0.eb new file mode 100644 index 00000000000..66085e3f965 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.1.0.eb @@ -0,0 +1,26 @@ +easyblock = 'GoPackage' + +name = 'SeqKit' +version = '2.1.0' + +homepage = 'https://bioinf.shenwei.me/seqkit/' +description = """SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/shenwei356/seqkit/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['99041d8c56e7a5e346e852cc8061cf828ee14b5f550b2f263e6031e99491c536'] + +builddependencies = [ + ('Go', '1.17.6'), +] + +installopts = './%(namelower)s' + +sanity_check_commands = [ + "seqkit version", + "seqkit genautocomplete" +] + +moduleclass = 'bio' From 93a817d26d005c617516b2e5fc388ef48279ae68 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 2 Feb 2022 15:36:31 +0100 Subject: [PATCH 2913/9987] Fixed bambi missing from bundle --- .../b/Bambi/Bambi-0.7.1-foss-2021b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb new file mode 100644 index 00000000000..8a51e429a89 --- /dev/null +++ b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'Bambi' +version = '0.7.1' + +homepage = 'https://bambinos.github.io/bambi' +description = """Bambi is a high-level Bayesian model-building interface written in Python. +It works with the probabilistic programming frameworks PyMC3 and is designed +to make it extremely easy to fit Bayesian mixed-effects models common in biology, +social sciences and other disciplines.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('statsmodels', '0.13.1'), + ('ArviZ', '0.11.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('formulae', '0.2.0', { + 'checksums': ['228335df9907750793016dfb23a8a0cb8d6d9ce9a026bfe2b459aa19f72541d2'], + }), + ('bambi', version, { + 'checksums': ['d57401326528f40ed78d6759723ee554581f6940c566263d6c176283f5428cf7'], + }), +] + +moduleclass = 'bio' From dfd7ba513cf7dfd995c1b20d32eba557da6bdc43 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 2 Feb 2022 14:38:36 +0000 Subject: [PATCH 2914/9987] adding easyconfigs: GEMMA-0.98.5-foss-2021b.eb and patches: GEMMA-disable-debug.patch --- .../g/GEMMA/GEMMA-0.98.5-foss-2021b.eb | 46 +++++++++++++++++++ .../g/GEMMA/GEMMA-disable-debug.patch | 15 ++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GEMMA/GEMMA-disable-debug.patch diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb new file mode 100644 index 00000000000..a3fe110918e --- /dev/null +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated to 0.98.5 +# J Sassmannshausen NHS/GSTT + +easyblock = 'MakeCp' + +name = 'GEMMA' +version = '0.98.5' + +homepage = 'https://github.com/genetics-statistics/GEMMA' +description = "Genome-wide Efficient Mixed Model Association" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/genetics-statistics/GEMMA/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['GEMMA-disable-debug.patch'] +checksums = [ + '3ed336deee29e370f96ec8f1a240f7b62550e57dcd1694245ce7ec8f42241677', + '39b55e87af662f99aa5177de7b11968303a5c41fc9eb38b0269bc9e2ae19b84a', # GEMMA-disable-debug.patch +] +builddependencies = [ + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('GSL', '2.7'), + ('zlib', '1.2.11'), + ('FlexiBLAS', '3.0.4'), +] + +buildopts = 'WITH_OPENBLAS="" LIBS="$LIBS $LIBBLAS -lgsl -lz "' # Needed for FlexiBLAS + +files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES.md", "scripts", "VERSION"] + +sanity_check_commands = ["cd %(builddir)s/%(name)s-%(version)s/ && make check "] + +sanity_check_paths = { + 'files': ["bin/gemma"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-disable-debug.patch b/easybuild/easyconfigs/g/GEMMA/GEMMA-disable-debug.patch new file mode 100644 index 00000000000..3beb5ef8c16 --- /dev/null +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-disable-debug.patch @@ -0,0 +1,15 @@ +Removed debugging flag +J. Sassmannshausen +diff --git a/GEMMA-0.98.5-orig/Makefile b/GEMMA-0.98.5/Makefile +index 662584c..140ef21 100644 +--- a/GEMMA-0.98.5-orig/Makefile ++++ b/GEMMA-0.98.5/Makefile +@@ -65,7 +65,7 @@ endif + + # Leave blank after "=" to disable; put "= 1" to enable + DIST_NAME = gemma-$(GEMMA_VERSION) +-DEBUG = 1 # DEBUG mode, set DEBUG=0 for a release ++DEBUG = 0 # DEBUG mode, set DEBUG=0 for a release + PROFILING = # Add profiling info + SHOW_COMPILER_WARNINGS = + WITH_OPENBLAS = 1 # Without OpenBlas uses LAPACK From d90656e5d344d72707562bbabbfa93a9285b9d13 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 2 Feb 2022 15:00:35 +0000 Subject: [PATCH 2915/9987] Patch removed as not necessary --- .../g/GEMMA/GEMMA-0.98.5-foss-2021b.eb | 3 +-- .../easyconfigs/g/GEMMA/GEMMA-disable-debug.patch | 15 --------------- 2 files changed, 1 insertion(+), 17 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GEMMA/GEMMA-disable-debug.patch diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb index a3fe110918e..7acf74dc357 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb @@ -17,11 +17,10 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/genetics-statistics/GEMMA/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['GEMMA-disable-debug.patch'] checksums = [ '3ed336deee29e370f96ec8f1a240f7b62550e57dcd1694245ce7ec8f42241677', - '39b55e87af662f99aa5177de7b11968303a5c41fc9eb38b0269bc9e2ae19b84a', # GEMMA-disable-debug.patch ] + builddependencies = [ ('Eigen', '3.4.0'), ] diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-disable-debug.patch b/easybuild/easyconfigs/g/GEMMA/GEMMA-disable-debug.patch deleted file mode 100644 index 3beb5ef8c16..00000000000 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-disable-debug.patch +++ /dev/null @@ -1,15 +0,0 @@ -Removed debugging flag -J. Sassmannshausen -diff --git a/GEMMA-0.98.5-orig/Makefile b/GEMMA-0.98.5/Makefile -index 662584c..140ef21 100644 ---- a/GEMMA-0.98.5-orig/Makefile -+++ b/GEMMA-0.98.5/Makefile -@@ -65,7 +65,7 @@ endif - - # Leave blank after "=" to disable; put "= 1" to enable - DIST_NAME = gemma-$(GEMMA_VERSION) --DEBUG = 1 # DEBUG mode, set DEBUG=0 for a release -+DEBUG = 0 # DEBUG mode, set DEBUG=0 for a release - PROFILING = # Add profiling info - SHOW_COMPILER_WARNINGS = - WITH_OPENBLAS = 1 # Without OpenBlas uses LAPACK From dc363f512e3fcaab4fb28c474c32de4760d10306 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 2 Feb 2022 16:20:58 +0100 Subject: [PATCH 2916/9987] adding easyconfigs: GnuTLS-3.7.3-GCCcore-11.2.0.eb, libtasn1-4.18.0-GCCcore-11.2.0.eb, libunistring-1.0-GCCcore-11.2.0.eb, p11-kit-0.24.1-GCCcore-11.2.0.eb, Guile-3.0.7-GCCcore-11.2.0.eb --- .../g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb | 42 +++++++++++++++++ .../g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ .../libtasn1-4.18.0-GCCcore-11.2.0.eb | 25 +++++++++++ .../libunistring-1.0-GCCcore-11.2.0.eb | 31 +++++++++++++ .../p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb | 38 ++++++++++++++++ 5 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtasn1/libtasn1-4.18.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6bcdaa9f327 --- /dev/null +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GnuTLS' +version = '3.7.3' + +homepage = 'https://www.gnutls.org' +description = """GnuTLS is a secure communications library implementing the SSL, TLS + and DTLS protocols and technologies around them. It provides a simple + C language application programming interface (API) to access the secure + communications protocols as well as APIs to parse and write X.509, PKCS #12, + OpenPGP and other required structures. It is aimed to be portable + and efficient with focus on security and interoperability.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.gnupg.org/ftp/gcrypt/gnutls/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['fc59c43bc31ab20a6977ff083029277a31935b8355ce387b634fa433f8f6c49a'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('GMP', '6.2.1'), + ('nettle', '3.7.3'), + ('Guile', '3.0.7'), + ('libtasn1', '4.18.0'), + ('libidn', '1.38'), + ('p11-kit', '0.24.1'), +] + +configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " +configopts += "--with-guile-site-ccache-dir=%(installdir)s/lib/guile/site-ccache " +configopts += "--with-guile-extension-dir=%(installdir)s/lib/guile/extensions" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['certtool', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]], + 'dirs': ['include/gnutls', 'lib/guile'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..209645c0e7c --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '3.0.7' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c7935b7a29e42443f6a35d35cf20ffa7d028c399303f872cd1219598a83656ae'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), +] + +dependencies = [ + ('gc', '8.2.0'), + ('GMP', '6.2.1'), + ('libffi', '3.4.2'), + ('libunistring', '1.0'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.18.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.18.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..148b9620650 --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.18.0-GCCcore-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.18.0' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and + some other packages. It was written by Fabio Fiorina, and has been shipped as + part of GnuTLS for some time but is now a proper GNU package.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4365c154953563d64c67a024b607d1ee75c6db76e0d0f65709ea80a334cd1898'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..cc8813eab9d --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.0' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['5bab55b49f75d77ed26b257997e919b693f29fd4a1bc22e0e6e024c246c72741'] + +builddependencies = [ + ('binutils', '2.37'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..17bc1fb9519 --- /dev/null +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'p11-kit' +version = '0.24.1' + +homepage = 'https://p11-glue.freedesktop.org/p11-kit.html' +description = """Provides a way to load and enumerate PKCS#11 modules. + Provides a standard configuration setup for installing + PKCS#11 modules in such a way that they're discoverable. + Also solves problems with coordinating the use of PKCS#11 + by different components or libraries living in the same process.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/p11-glue/p11-kit/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['d8be783efd5cd4ae534cee4132338e3f40f182c3205d23b200094ec85faaaef8'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('libtasn1', '4.18.0'), + ('libffi', '3.4.2'), +] + +preconfigopts = "bashcompdir=%(installdir)s/share/bash-completions " + +configopts = "--without-systemd" + +sanity_check_paths = { + 'files': ['bin/p11-kit', 'bin/trust'] + + ['lib/libp11-kit.%s' % SHLIB_EXT], + 'dirs': ['include/p11-kit-1/p11-kit'], +} + +sanity_check_commands = ["p11-kit --help"] + +moduleclass = 'lib' From 8ada06793c2629cf66e47a992bcf43257e761706 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 2 Feb 2022 15:34:47 +0000 Subject: [PATCH 2917/9987] Sanity check changed to runtest=check thus Perl and Ruby added, also testopts required to address the banned lib issues --- easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb index 7acf74dc357..8defd498e62 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb @@ -23,6 +23,8 @@ checksums = [ builddependencies = [ ('Eigen', '3.4.0'), + ('Perl', '5.34.0'), + ('Ruby', '3.0.1'), ] dependencies = [ @@ -32,10 +34,11 @@ dependencies = [ ] buildopts = 'WITH_OPENBLAS="" LIBS="$LIBS $LIBBLAS -lgsl -lz "' # Needed for FlexiBLAS +testopts = 'WITH_OPENBLAS="" LIBS="$LIBS $LIBBLAS -lgsl -lz"' # Needed for the make check below files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES.md", "scripts", "VERSION"] -sanity_check_commands = ["cd %(builddir)s/%(name)s-%(version)s/ && make check "] +runtest = 'check' sanity_check_paths = { 'files': ["bin/gemma"], From d85ee1407d3bb0e2769a21309775f98556580293 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 2 Feb 2022 17:07:11 +0100 Subject: [PATCH 2918/9987] Fixed toolchain mismatch --- easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb index 706f118eed5..f90e92f084c 100644 --- a/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb +++ b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb @@ -25,6 +25,9 @@ exts_list = [ ('formulae', '0.2.0', { 'checksums': ['228335df9907750793016dfb23a8a0cb8d6d9ce9a026bfe2b459aa19f72541d2'], }), + ('bambi', version, { + 'checksums': ['d57401326528f40ed78d6759723ee554581f6940c566263d6c176283f5428cf7'], + }), ] moduleclass = 'bio' From 9d312cfda1548b54a1490cb1ad33e3049b8b00e8 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 2 Feb 2022 18:08:41 +0100 Subject: [PATCH 2919/9987] adding easyconfigs: AOCC-3.2.0-GCCcore-11.2.0.eb --- .../a/AOCC/AOCC-3.2.0-GCCcore-11.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-3.2.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-3.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-3.2.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..de77f0ac9a6 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-3.2.0-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +name = 'AOCC' +version = '3.2.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['8493525b3df77f48ee16f3395a68ad4c42e18233a44b4d9282b25dbb95b113ec'] + +clangversion = '13.0.0' + +dependencies = [ + ('binutils', '2.37'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('libxml2', '2.9.10'), +] + +moduleclass = 'compiler' From 753ba720fb47609737adc92ddd749346b9106345 Mon Sep 17 00:00:00 2001 From: Keith Refson Date: Wed, 2 Feb 2022 17:42:06 +0000 Subject: [PATCH 2920/9987] Changed checksums to SHA256 --- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb | 2 +- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb | 2 +- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb | 2 +- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb | 2 +- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb index 164231d86c2..2f2011f7368 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb @@ -3,7 +3,6 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' -checksums = ['de510be026173a2b84cd4b59d9bdc8ac'] homepage = 'http://www.castep.org' description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), @@ -15,6 +14,7 @@ dependencies = [('cray-fftw', EXTERNAL_MODULE)] # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. sources = ['CASTEP-21.11.tar.gz'] +checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb index 1194b1adb6a..e2a210e5b18 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb @@ -3,7 +3,6 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' -checksums = ['de510be026173a2b84cd4b59d9bdc8ac'] homepage = 'http://www.castep.org' description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), @@ -15,6 +14,7 @@ dependencies = [('cray-fftw', EXTERNAL_MODULE)] # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. sources = ['CASTEP-21.11.tar.gz'] +checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb index afb2fc81bc5..1202b99b9ce 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb @@ -3,7 +3,6 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' -checksums = ['de510be026173a2b84cd4b59d9bdc8ac'] homepage = 'http://www.castep.org' description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), @@ -15,6 +14,7 @@ toolchain = {'name': 'foss', 'version': '2019b'} # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. sources = ['CASTEP-21.11.tar.gz'] +checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb index 485ddd67050..4f9eec63d5d 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb @@ -3,7 +3,6 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' -checksums = ['de510be026173a2b84cd4b59d9bdc8ac'] homepage = 'http://www.castep.org' description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), @@ -15,6 +14,7 @@ toolchain = {'name': 'intel', 'version': '2019b'} # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. sources = ['CASTEP-21.11.tar.gz'] +checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb index eaaef9f6f5e..78e866ff8f0 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb @@ -3,7 +3,6 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' -checksums = ['de510be026173a2b84cd4b59d9bdc8ac'] homepage = 'http://www.castep.org' description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), @@ -15,6 +14,7 @@ toolchain = {'name': 'iomkl', 'version': '2019b'} # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. sources = ['CASTEP-21.11.tar.gz'] +checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', From eb98d0c8b0417b4c961e98a5e48eff098c1e62e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Feb 2022 19:13:53 +0100 Subject: [PATCH 2921/9987] adding easyconfigs: PyEVTK-1.4.1-foss-2021b.eb --- .../p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb new file mode 100644 index 00000000000..a1871df2842 --- /dev/null +++ b/easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyEVTK' +version = '1.4.1' + +homepage = 'https://github.com/pyscience-projects/pyevtk' +description = """PyEVTK (Python Export VTK) exports data to binary VTK files for visualization/analysis with packages +like Paraview, VisIt, and Mayavii.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/pyscience-projects/pyevtk/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d0fd7d2f5402749d42124c0d849f7642f3758898bc2bef50e67b9ef5082cf48d'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True + +# for some reason this is required to avoid 'pip install' failing with "ModuleNotFoundError: No module named 'evtk'" +#preinstallopts = "PYTHONPATH=$PWD " + +sanity_pip_check = True + +options = {'modulename': 'evtk'} + +moduleclass = 'lib' From f846ababf611a11dd5f0120e12428bdf2dbcad93 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Feb 2022 19:31:08 +0100 Subject: [PATCH 2922/9987] install SHTns Python bindings as extension Co-authored-by: Alex Domingo --- .../s/SHTns/SHTns-3.5.1-foss-2021b.eb | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb b/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb index 979b80b3183..483cafedcb2 100644 --- a/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SHTns/SHTns-3.5.1-foss-2021b.eb @@ -19,15 +19,25 @@ dependencies = [ ('SciPy-bundle', '2021.10'), ] -installopts = " && pip install --no-deps --ignore-installed --prefix %(installdir)s ." +# install Python bindings +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('shtns', version, { + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'checksums': ['77f8a33b94df8786d2ce9b95cbfbe548f00443625b310b8c64012b22c8a7394f'], + }), +] sanity_check_paths = { 'files': ['include/shtns_cuda.h', 'include/shtns.f', 'include/shtns.f03', 'include/shtns.h', 'lib/libshtns.a'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["python -c 'import shtns'"] - modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} moduleclass = 'lib' From 5a06664b9c39946aa7e033dab652bdbedf1c2b2e Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Wed, 2 Feb 2022 19:34:46 +0100 Subject: [PATCH 2923/9987] Delete Bambi-0.7.1-foss-2021b.eb --- .../b/Bambi/Bambi-0.7.1-foss-2021b.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb deleted file mode 100644 index 8a51e429a89..00000000000 --- a/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Bambi' -version = '0.7.1' - -homepage = 'https://bambinos.github.io/bambi' -description = """Bambi is a high-level Bayesian model-building interface written in Python. -It works with the probabilistic programming frameworks PyMC3 and is designed -to make it extremely easy to fit Bayesian mixed-effects models common in biology, -social sciences and other disciplines.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('statsmodels', '0.13.1'), - ('ArviZ', '0.11.4'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('formulae', '0.2.0', { - 'checksums': ['228335df9907750793016dfb23a8a0cb8d6d9ce9a026bfe2b459aa19f72541d2'], - }), - ('bambi', version, { - 'checksums': ['d57401326528f40ed78d6759723ee554581f6940c566263d6c176283f5428cf7'], - }), -] - -moduleclass = 'bio' From b4a4bb238c4136e9e019ab67e0e65cc1e97af936 Mon Sep 17 00:00:00 2001 From: hugo meiland Date: Wed, 2 Feb 2022 20:07:17 +0100 Subject: [PATCH 2924/9987] first add devito --- .../devito-4.6-foss-2020a-Python-3.8.2.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/d/devito/devito-4.6-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/d/devito/devito-4.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/devito/devito-4.6-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..1b1b240711a --- /dev/null +++ b/easybuild/easyconfigs/d/devito/devito-4.6-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'devito' +version = '4.6' +versionsuffix = '-Python-3.8.2' + +homepage = 'https://devitoproject.org/' +description = "Devito is a domain-specific Language (DSL) and code generation framework" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', '3.8.2'), + #('pybind11', '2.4.3', versionsuffix), # required by scipy +] + +use_pip = True +sanity_pip_check = True + +# order is important! +exts_list = [ + #('numpy', '1.18.3', { + # 'patches': ['numpy-1.16.2_relax-long-complex-test.patch'], + # 'source_tmpl': '%(name)s-%(version)s.zip', + # 'checksums': [ + # 'e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8', # numpy-1.18.3.zip + # # numpy-1.16.2_relax-long-complex-test.patch + # '647dd4099c2968489e5103b50bcd1b3d970b5b536af25ec75efe86127dda07bb', + # ], + #}), + #('scipy', '1.4.1', { + # 'patches': ['scipy-1.4.1-fix-pthread.patch'], + # 'checksums': [ + # 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz + # '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch + # ], + #}), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + #('pandas', '1.0.3', { + # 'checksums': ['32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586'], + #}), + #('mpmath', '1.1.0', { + # 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + #}), + #('deap', '1.3.1', { + # 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + #}), + ('devito', '4.6', { + 'checksums': ['7868b8b9cad1e057573b1f7ce1f196be4706155538b0a153b5da142380f6f9cc'], + }), +] + +moduleclass = 'lang' From becbc58cdcdc122badcd1fcbd074ed4a37d36799 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Feb 2022 21:36:28 +0100 Subject: [PATCH 2925/9987] fix checksum for qe-gipaw-7.0.tar.gz in QuantumESPRESSO 7.0 easyconfig Co-authored-by: SebastianAchilles --- .../q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb index b74c30c4645..af38331564a 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb @@ -24,7 +24,7 @@ sources = [ patches = ['QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch'] checksums = [ '268ec506f88c56ba4e9b691c1e81e33a6ad7949f857f1c6c32197f9c2af2a957', # qe-%(version)s-ReleasePack.tgz - '11a9ac74724de83012398aecba6d06ab37cc0d4c73792d0d5ba6bca1a723ef70', # qe-gipaw-%(version)s.tar.gz + '3055bd56c7e28a4013a06b7ae98d12b1569b0cc790a141d6a9cd8da9c2be3ce7', # qe-gipaw-%(version)s.tar.gz '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz # QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch '8c5026e0b6463f6690238d3aedffe18c7e8b2bfeb52be1454f934a43a2f91fd6', diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb index 065de8035bb..f0c587dbd0e 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb @@ -23,7 +23,7 @@ sources = [ ] checksums = [ '268ec506f88c56ba4e9b691c1e81e33a6ad7949f857f1c6c32197f9c2af2a957', # qe-%(version)s-ReleasePack.tgz - '11a9ac74724de83012398aecba6d06ab37cc0d4c73792d0d5ba6bca1a723ef70', # qe-gipaw-%(version)s.tar.gz + '3055bd56c7e28a4013a06b7ae98d12b1569b0cc790a141d6a9cd8da9c2be3ce7', # qe-gipaw-%(version)s.tar.gz '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz ] From 0fc0fca4f9dfd95ec05c2b8d7ebf257234c10bc9 Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 2 Feb 2022 23:36:32 +0000 Subject: [PATCH 2926/9987] adding easyconfigs: tabix-0.2.6-GCCcore-11.2.0.eb --- .../t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..51f12ffde97 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Jens Timmerman, Ghent University +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# updated to newer toolchain + +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] +checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + (["libtabix.a"], "lib64"), + (["*.h"], "include"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' From 9dbf86d1952f5f6e25a717915401fcd6aed88f2d Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 2 Feb 2022 23:38:19 +0000 Subject: [PATCH 2927/9987] adding easyconfigs: libRmath-4.1.2-GCCcore-11.2.0.eb --- .../libRmath/libRmath-4.1.2-GCCcore-11.2.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/l/libRmath/libRmath-4.1.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libRmath/libRmath-4.1.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libRmath/libRmath-4.1.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5f5f8fcd745 --- /dev/null +++ b/easybuild/easyconfigs/l/libRmath/libRmath-4.1.2-GCCcore-11.2.0.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# Updated: Denis Kristak (INUITS) +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# updated to version 4.1.2 +# J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'libRmath' +version = '4.1.2' + +homepage = 'https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library' +description = """The routines supporting the distribution and special functions in R and a few others are declared + in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = ['R-%(version)s.tar.gz'] +checksums = ['2036225e9f7207d4ce097e54972aecdaa8b40d7d9911cd26491fac5a0fab38af'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('cURL', '7.78.0'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('PCRE2', '10.37'), +] + +parallel = 1 + +start_dir = 'src/nmath/standalone' + +preconfigopts = 'cd %(builddir)s/R-%(version)s && ' +configopts = '--with-readline=no --with-recommended-packages=no --with-x=no' + +postinstallcmds = ["cp -r %(builddir)s/R-%(version)s/src/include/R_ext %(installdir)s/include/"] + +runtest = 'check' + +sanity_check_paths = { + 'files': ["lib/libRmath.%s" % SHLIB_EXT, "lib/libRmath.a", + "lib/pkgconfig/libRmath.pc", + "include/Rmath.h"], + 'dirs': [] +} + +moduleclass = 'lib' From 9043b748fd3031da2e793109e2a497bb7389417c Mon Sep 17 00:00:00 2001 From: Sassy Date: Wed, 2 Feb 2022 23:40:31 +0000 Subject: [PATCH 2928/9987] adding easyconfigs: FastQTL-2.184-GCC-11.2.0.eb and patches: FastQTL-makefile.patch --- .../f/FastQTL/FastQTL-2.184-GCC-11.2.0.eb | 62 +++++++++++++++++++ .../f/FastQTL/FastQTL-makefile.patch | 47 ++++++++++++++ 2 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/FastQTL/FastQTL-makefile.patch diff --git a/easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-GCC-11.2.0.eb new file mode 100644 index 00000000000..0d17682829d --- /dev/null +++ b/easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-GCC-11.2.0.eb @@ -0,0 +1,62 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# updated to GCC 11.2.0 +# J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'FastQTL' +version = '2.184' + +homepage = 'http://fastqtl.sourceforge.net/' +description = 'FastQTL is a QTL mapper' + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['http://fastqtl.sourceforge.net/files/'] +sources = ['%(name)s-%(version)s.linux.tgz'] +patches = ['FastQTL-makefile.patch'] + +checksums = [ + 'b8d8959a9fbeba106483a2a3e178eaf918b907ad9f9aab7988b6817bb2108879', + 'e289eaeaf1d18f17d0baabf23d632bf0599a4d6eaa7bcc173e6d7e305315466b', # FastQTL-makefile.patch +] + +builddependencies = [ + ('libRmath', '4.1.2'), + ('binutils', '2.37'), + ('tabix', '0.2.6'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('GSL', '2.7'), + ('Boost', '1.77.0'), + ('FlexiBLAS', '3.0.4'), + ('OpenBLAS', '0.3.18'), +] + +files_to_copy = [ + 'bin', + 'doc', + 'example', + 'LICENCE', + 'README', + 'script', +] + +sanity_check_paths = { + 'files': ['bin/fastQTL'], + 'dirs': [] +} + +# delete the binary provided with the tarball +# it's not static and it doesn't work ;) +postinstallcmds = ['rm %(installdir)s/bin/fastQTL.static'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastQTL/FastQTL-makefile.patch b/easybuild/easyconfigs/f/FastQTL/FastQTL-makefile.patch new file mode 100644 index 00000000000..d67a7b42cd7 --- /dev/null +++ b/easybuild/easyconfigs/f/FastQTL/FastQTL-makefile.patch @@ -0,0 +1,47 @@ +Patch for Makefile to include Eigen, libRmath, Boost, Tabix and FlexiBLAS +J. Sassmannshausen +diff --git a/FastQTL.orig/Makefile b/FastQTL/Makefile +index a7b23ec..d9504ec 100644 +--- a/FastQTL.orig/Makefile ++++ b/FastQTL/Makefile +@@ -1,16 +1,16 @@ + #PLEASE SPECIFY THE R path here where you built the R math library standalone +-RMATH=~/Software/R-3.1.3/src ++RMATH=${EBROOTLIBRMATH}/lib64 + + #compiler + CXX=g++ + + #internal paths + VPATH=$(shell for file in `find src -name *.cpp`; do echo $$(dirname $$file); done) +-PATH_TABX=lib/Tabix +-PATH_EIGN=lib/Eigen ++PATH_TABX=${EBROOTTABIX} ++PATH_EIGN=${EBROOTEIGEN} + + #compiler flags +-CXXFLAG_OPTI=-O3 -D_FAST_CORRELATION ++CXXFLAG_OPTI=-O3 -D_FAST_CORRELATION -std=gnu++98 + CXXFLAG_DEBG=-g + CXXFLAG_WARN=-Wall -Wextra -Wno-sign-compare + CXXFLAG_MACX=-mmacosx-version-min=10.7 -stdlib=libc++ +@@ -21,15 +21,15 @@ LDFLAG_DEBG=-g + LDFLAG_MACX=-mmacosx-version-min=10.7 -stdlib=libc++ + + #includes +-INC_BASE=-Isrc -I$(PATH_TABX) -I$(PATH_EIGN) ++INC_BASE=-Isrc -I$(PATH_TABX) -I$(PATH_EIGN)/include/Eigen + INC_MATH=-I$(RMATH)/include/ + INC_MACX=-I/usr/local/include/ + + #libraries + #LIB_BASE=-lm -lboost_iostreams -lboost_program_options -lz -lgsl -lblas +-LIB_BASE=-lm -lz -lboost_iostreams -lboost_program_options -lgsl -lblas +-LIB_MATH=$(RMATH)/nmath/standalone/libRmath.a +-LIB_TABX=$(PATH_TABX)/libtabix.a ++LIB_BASE=-L${EBROOTBOOST}/lib64 -lm -lz -lboost_iostreams -lboost_program_options -lgsl -lflexiblas ++LIB_MATH=$(RMATH)/libRmath.a ++LIB_TABX=$(PATH_TABX)/lib64/libtabix.a + LIB_MACX=-L/usr/local/lib/ + + #files (binary, objects, headers & sources) From dcfa0b25cdc8ca04f0f8b66a2cff8c5aa7e331b7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Feb 2022 01:00:25 +0100 Subject: [PATCH 2929/9987] fix code style of PyEVTK-1.4.1-foss-2021b.eb --- easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb index a1871df2842..1b2647dc6fe 100644 --- a/easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb @@ -22,7 +22,7 @@ download_dep_fail = True use_pip = True # for some reason this is required to avoid 'pip install' failing with "ModuleNotFoundError: No module named 'evtk'" -#preinstallopts = "PYTHONPATH=$PWD " +# preinstallopts = "PYTHONPATH=$PWD " sanity_pip_check = True From 15861a68442defc11b537982546a9d544d3b9d6e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Feb 2022 01:32:37 +0100 Subject: [PATCH 2930/9987] add exception for dependency of ncbi-vdb v2.11.x on HDF5 v1.10.x --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 89afb89a610..f9b502eee0b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -439,6 +439,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # EMAN2 2.3 requires Boost(.Python) 1.64.0 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], + # ncbi-vdb v2.x require HDF5 v1.10.x + 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.'])], # VMTK 1.4.x requires ITK 4.13.x 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) From afef925adfa2db7615bdd7abbd7d219c37be33dd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Feb 2022 01:37:46 +0100 Subject: [PATCH 2931/9987] move ConnectomeWorkbench v1.5.0 to GCCcore/11.2.0 --- ...ss-2021a.eb => ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/c/ConnectomeWorkbench/{ConnectomeWorkbench-1.5.0-foss-2021a.eb => ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb} (94%) diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb similarity index 94% rename from easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb rename to easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb index 451a1380cbd..90212fcc886 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb @@ -8,13 +8,14 @@ description = """Connectome Workbench is an open source, freely available visual and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.""" -toolchain = {'name': 'foss', 'version': '2021a'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/Washington-University/workbench/archive'] sources = ['v%(version)s.tar.gz'] checksums = ['6410f5cdaed2158d99871962fb27ce9fdfad6fa7dad496b93ff8bce0a8070cc4'] builddependencies = [ + ('binutils', '2.37'), ('CMake', '3.20.1'), ] From 77678e714c879143cc7040d9a0098af9327465fb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Feb 2022 01:38:44 +0100 Subject: [PATCH 2932/9987] fix formatting of ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb --- .../ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb index 90212fcc886..3a74ec8c8b1 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb @@ -15,7 +15,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['6410f5cdaed2158d99871962fb27ce9fdfad6fa7dad496b93ff8bce0a8070cc4'] builddependencies = [ - ('binutils', '2.37'), + ('binutils', '2.37'), ('CMake', '3.20.1'), ] From 004a573847da06b6a5ed2f6b85731d3676fc1ee1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Feb 2022 01:56:26 +0100 Subject: [PATCH 2933/9987] move ConnectomeWorkbench v1.5.0 to GCCcore/10.3.0 --- ...-11.2.0.eb => ConnectomeWorkbench-1.5.0-GCCcore-10.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/ConnectomeWorkbench/{ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb => ConnectomeWorkbench-1.5.0-GCCcore-10.3.0.eb} (94%) diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-10.3.0.eb similarity index 94% rename from easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-10.3.0.eb index 3a74ec8c8b1..55a199c0530 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.5.0-GCCcore-10.3.0.eb @@ -8,14 +8,14 @@ description = """Connectome Workbench is an open source, freely available visual and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project.""" -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/Washington-University/workbench/archive'] sources = ['v%(version)s.tar.gz'] checksums = ['6410f5cdaed2158d99871962fb27ce9fdfad6fa7dad496b93ff8bce0a8070cc4'] builddependencies = [ - ('binutils', '2.37'), + ('binutils', '2.36.1'), ('CMake', '3.20.1'), ] From aa419e3e3ee6003296590d977bef7736aa8fa0c8 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 3 Feb 2022 08:31:14 +0100 Subject: [PATCH 2934/9987] update TensorFlow dependency to version 2.5.0 --- .../easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb index fbe26b9c1b9..e31ec9ab97f 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb @@ -21,7 +21,7 @@ dependencies = [ ('Python', '3.8.6', ), ('SciPy-bundle', '2020.11'), ('PyYAML', '5.3.1', ), - ('TensorFlow', '2.4.1'), + ('TensorFlow', '2.5.0'), ('Biopython', '1.78'), ('HH-suite', '3.3.0',), ('HMMER', '3.3.2',), From dc32173ecbc4bd606c015327dc26fca9ad5fe039 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 3 Feb 2022 08:36:01 +0100 Subject: [PATCH 2935/9987] add AlphaFold-2.1.2-foss-2020b.eb --- .../a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb | 181 ++++++++++++++++++ 1 file changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb new file mode 100644 index 00000000000..e31ec9ab97f --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb @@ -0,0 +1,181 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.1.2' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.18.4', ), + ('Doxygen', '1.8.20', ), + # required for installing dm-tree + ('Bazel', '3.7.2', ), + ('SWIG', '4.0.2', ), +] + +dependencies = [ + ('Python', '3.8.6', ), + ('SciPy-bundle', '2020.11'), + ('PyYAML', '5.3.1', ), + ('TensorFlow', '2.5.0'), + ('Biopython', '1.78'), + ('HH-suite', '3.3.0',), + ('HMMER', '3.3.2',), + ('Kalign', '3.3.1', ), + ('jax', '0.2.19'), # also provides absl-py +] +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.1.2_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '6af91706b2a001494ddc0947f89f8b3d3adfcc26177c373824fe8ea1a58c0b48', # AlphaFold-2.1.2_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +modextravars = { + 'ALPHAFOLD_DATA_DIR': '/scratch/AlphaFold_DBs', # adapt +} + +moduleclass = 'bio' From 43cc9bb1cb3cd83b9a467f13056dea66621bb932 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 3 Feb 2022 08:48:59 +0100 Subject: [PATCH 2936/9987] Update AlphaFold-2.1.2-foss-2020b.eb --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb index e31ec9ab97f..7b02431cec0 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb @@ -6,7 +6,7 @@ version = '2.1.2' homepage = 'https://deepmind.com/research/case-studies/alphafold' description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" -toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ # CMake/Doxygen/SWIG are required for building OpenMM From 11199a69fbefab700f466bcaa207af411bd33b05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Feb 2022 08:59:18 +0100 Subject: [PATCH 2937/9987] fix homepage for SoQt --- easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-11.2.0.eb index f7350cc6036..4a29e846063 100644 --- a/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/SoQt/SoQt-1.6.0-GCC-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SoQt' version = '1.6.0' -homepage = 'https://coin3d.github.io/SoXt/html/' +homepage = 'https://coin3d.github.io/SoQt/html/' description = """SoQt is a library which provides the glue between Systems in Motion's Coin high-level 3D visualization library and the Qt 2D user interface library. From 0cbd185db2ac989429a4a54f7373539a8df4b9d1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Feb 2022 09:28:41 +0100 Subject: [PATCH 2938/9987] add sanity check command for OpenSlide --- .../easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.2.0.eb index 8298c309596..baaf27367f5 100644 --- a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.2.0.eb @@ -40,4 +40,6 @@ sanity_check_paths = { 'dirs': ['include/openslide'] } +sanity_check_commands = ['openslide-show-properties --help'] + moduleclass = 'vis' From f6edf6ee0641b05d5de05917c3053004d0e0bc34 Mon Sep 17 00:00:00 2001 From: Keith Refson Date: Thu, 3 Feb 2022 09:49:03 +0000 Subject: [PATCH 2939/9987] Broke long line --- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb index 1202b99b9ce..c70fe600cdd 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb @@ -30,6 +30,7 @@ buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas FFTLIBDIR= MATHLIBDIR= preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' -installopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas INSTALL_DIR="%(installdir)s/bin" install-castep install-tools install-utilities' +installopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas INSTALL_DIR="%(installdir)s/bin"' +' install-castep install-tools install-utilities' moduleclass = 'phys' From 17ee6e5269137282ba177e06056587f366b7f5e9 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 3 Feb 2022 12:41:06 +0100 Subject: [PATCH 2940/9987] Added missing dependency --- easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb index f90e92f084c..7040be87588 100644 --- a/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb +++ b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-intel-2021b.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'intel', 'version': '2021b'} dependencies = [ ('Python', '3.9.6'), + ('PyMC3', '3.11.1'), ('SciPy-bundle', '2021.10'), ('statsmodels', '0.13.1'), ('ArviZ', '0.11.4'), From 7c37a15f3a7def1b1ed56e4a1c6f1c14ff82ff9c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 3 Feb 2022 14:11:50 +0100 Subject: [PATCH 2941/9987] AlphaFold 2.1.2 reqequires TensoFlow 2.5.0 --- test/easyconfigs/easyconfigs.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 89afb89a610..f9518cb986a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -499,6 +499,10 @@ def check_dep_vars(self, gen, dep, dep_vars): ('2.2.2;', ['medaka-1.4.3-']), # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), + #AlphaFold 2.0.0 to 2.1.1 (foss/2020b) depend on TensorFlow 2.4.1) + ('2.4.1;', ['AlphaFold-2.0.0-', 'AlphaFold-2.0.1-', 'AlphaFold-2.1.1-']), + #AlphaFold 2.1.2 (foss/2020b) depends on TensorFlow 2.5.0 + ('2.5.0;', ['AlphaFold-2.1.2-']), ], # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 # (for 2021b, UCX was updated to v1.11.2) From 35b141579fc419943b40207465ef17328a1cd7f2 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 3 Feb 2022 14:26:24 +0100 Subject: [PATCH 2942/9987] fix style --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f9518cb986a..aba57000136 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -499,9 +499,9 @@ def check_dep_vars(self, gen, dep, dep_vars): ('2.2.2;', ['medaka-1.4.3-']), # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), - #AlphaFold 2.0.0 to 2.1.1 (foss/2020b) depend on TensorFlow 2.4.1) + # AlphaFold 2.0.0 to 2.1.1 (foss/2020b) depend on TensorFlow 2.4.1) ('2.4.1;', ['AlphaFold-2.0.0-', 'AlphaFold-2.0.1-', 'AlphaFold-2.1.1-']), - #AlphaFold 2.1.2 (foss/2020b) depends on TensorFlow 2.5.0 + # AlphaFold 2.1.2 (foss/2020b) depends on TensorFlow 2.5.0 ('2.5.0;', ['AlphaFold-2.1.2-']), ], # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 From 237418d3a12491f37b529e320c7e8828fe7878f2 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 3 Feb 2022 14:36:52 +0100 Subject: [PATCH 2943/9987] adding easyconfigs: Valgrind-3.18.1-gompi-2021b.eb, Valgrind-3.18.1-iimpi-2021b.eb --- .../v/Valgrind/Valgrind-3.18.1-gompi-2021b.eb | 31 ++++++++++++++++++ .../v/Valgrind/Valgrind-3.18.1-iimpi-2021b.eb | 32 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-gompi-2021b.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-gompi-2021b.eb new file mode 100644 index 00000000000..18aac1c35e2 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-gompi-2021b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.18.1' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = [ + 'https://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['00859aa13a772eddf7822225f4b46ee0d39afbe071d32778da4d99984081f7f5'] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-iimpi-2021b.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-iimpi-2021b.eb new file mode 100644 index 00000000000..6d3cac194b5 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-iimpi-2021b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.18.1' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'iimpi', 'version': '2021b'} + +source_urls = [ + 'https://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['00859aa13a772eddf7822225f4b46ee0d39afbe071d32778da4d99984081f7f5'] + +preconfigopts = 'unset CC CFLAGS &&' +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'debugger' From 262d54aaf5534722cd632b32ad736176303215fd Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 3 Feb 2022 15:04:12 +0100 Subject: [PATCH 2944/9987] Fixed bambi + added other foss dependencies --- .../b/Bambi/Bambi-0.7.1-foss-2021b.eb | 4 ++ .../p/PyMC3/PyMC3-3.11.1-foss-2021b.eb | 45 +++++++++++++++++++ .../t/Theano/Theano-1.1.2-foss-2021b-PyMC.eb | 40 +++++++++++++++++ 3 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2021b-PyMC.eb diff --git a/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb index a23fd351fd2..681768eda78 100644 --- a/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/Bambi/Bambi-0.7.1-foss-2021b.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Python', '3.9.6'), + ('PyMC3', '3.11.1'), ('SciPy-bundle', '2021.10'), ('statsmodels', '0.13.1'), ('ArviZ', '0.11.4'), @@ -25,6 +26,9 @@ exts_list = [ ('formulae', '0.2.0', { 'checksums': ['228335df9907750793016dfb23a8a0cb8d6d9ce9a026bfe2b459aa19f72541d2'], }), + ('bambi', version, { + 'checksums': ['d57401326528f40ed78d6759723ee554581f6940c566263d6c176283f5428cf7'], + }), ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-foss-2021b.eb new file mode 100644 index 00000000000..d813f17d499 --- /dev/null +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-foss-2021b.eb @@ -0,0 +1,45 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'PyMC3' +version = '3.11.1' + +homepage = 'https://docs.pymc.io/' +description = """Probabilistic Programming in Python: +Bayesian Modeling and Probabilistic Machine Learning with Theano""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy + ('Theano', '1.1.2', '-PyMC'), + ('matplotlib', '3.4.3'), + ('h5py', '3.6.0'), + ('tqdm', '4.62.3'), + ('netcdf4-python', '1.5.7'), + ('xarray', '0.20.1'), + ('typing-extensions', '3.10.0.2'), + ('ArviZ', '0.11.4'), + ('dill', '0.3.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + ('fastprogress', '1.0.0', { + 'checksums': ['89e28ac1d2a5412aab18ee3f3dfd1ee8b5c1f2f7a44d0add0d0d4f69f0191bfe'], + }), + ('pymc3', version, { + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + 'checksums': ['501d48b9f5d033678de7a5918b9d055a6806adf84fe16a5a9d65eaa2dc71acd8'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2021b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2021b-PyMC.eb new file mode 100644 index 00000000000..ee57a0b1144 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-foss-2021b-PyMC.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = '1.1.2' +versionsuffix = '-PyMC' + +homepage = 'https://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://pypi.python.org/packages/source/T/Theano%(versionsuffix)s'] +sources = ['Theano-PyMC-%(version)s.tar.gz'] +checksums = ['5da6c2242ea72a991c8446d7fe7d35189ea346ef7d024c890397011114bf10fc'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +fix_python_shebang_for = ['bin/theano-cache', 'bin/theano-nose'] + +sanity_check_paths = { + 'files': ['bin/theano-cache'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +local_blas_warning = "Using NumPy C-API based implementation for BLAS functions" +sanity_check_commands = [ + # make sure that warning about falling back to (slow) NumPy C-API for BLAS functions is *not* printed + # mkl-service dependency is required to ensure this doesn't happen + "python -c 'import theano.tensor' 2>&1 | grep '%s'; test $? != 0" % local_blas_warning, +] + +moduleclass = 'math' From 4837b54c8adf6f46ae53a6fb6fd223f38c0660a0 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 3 Feb 2022 15:52:57 +0000 Subject: [PATCH 2945/9987] Additional sanity-check added --- easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb index 8defd498e62..9e0b069c771 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2021b.eb @@ -40,6 +40,8 @@ files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES runtest = 'check' +sanity_check_commands = ["gemma -h", "gemma -license"] + sanity_check_paths = { 'files': ["bin/gemma"], 'dirs': [] From 79b6ff42af348f16cb683b91f26a41cdf98644d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Feb 2022 18:40:25 +0100 Subject: [PATCH 2946/9987] adding easyconfigs: BLAST+-2.9.0-gompi-2021b.eb and patches: BLAST+-2.9.0_fix-GCC-10.patch --- .../b/BLAST+/BLAST+-2.9.0-gompi-2021b.eb | 58 +++++++++++++++++++ .../b/BLAST+/BLAST+-2.9.0_fix-GCC-10.patch | 26 +++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0_fix-GCC-10.patch diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-gompi-2021b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-gompi-2021b.eb new file mode 100644 index 00000000000..1b37edec143 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-gompi-2021b.eb @@ -0,0 +1,58 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.9.0' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [ + 'BLAST+-%(version)s_fix_boost.patch', + 'BLAST+-%(version)s_fix-GCC-10.patch', +] +checksums = [ + 'a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257', # ncbi-blast-2.9.0+-src.tar.gz + '44dc4a931896953d78c13097433ea6fc8d7990bd759c4e4e5bbb9b2574fb4154', # BLAST+-2.9.0_fix_boost.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost', '1.77.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.29'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0_fix-GCC-10.patch b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0_fix-GCC-10.patch new file mode 100644 index 00000000000..afaf61949de --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0_fix-GCC-10.patch @@ -0,0 +1,26 @@ +fix compiler detection for GCC 10.x & newer +copied from BLAST+ 2.12.0 configure script +--- ncbi-blast-2.9.0+-src/c++/src/build-system/configure.orig 2022-02-03 17:57:09.154118530 +0100 ++++ ncbi-blast-2.9.0+-src/c++/src/build-system/configure 2022-02-03 17:58:32.367608563 +0100 +@@ -8076,16 +8076,15 @@ + case "$compiler:$ncbi_compiler_ver" in + WorkShop*:?.?? ) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9][0-9]\)/\1\20/' ;; + WorkShop*:[6-9].?) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9\)/\10\20/' ;; +- ICC:??.? ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)/\1\20/' ;; +- ICC:??.?.? | \ +- ICC:??.?.?.* ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)\.\([0-9]\).*/\1\2\3/' ;; ++ [GI]CC:??.? ) ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)/\1\20/' ;; ++ GCC:??.?.? | ICC:??.?.? | ICC:??.?.?.* | *Clang:??.?.? ) ++ ncbi_compiler_sed='s/\([0-9][0-9]\)\.\([0-9]\)\.\([0-9]\).*/\1\2\3/' ;; ++ GCC:?? ) ncbi_compiler_sed='s/\([0-9][0-9]\)/\100/' ;; + *:?.?.?) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9]\)\.\([0-9]\)/\1\2\3/' ;; + *:?.??*) ncbi_compiler_sed='s/\([0-9]\)\.\([0-9][0-9]\).*/\1\2/' ;; + *:?.?) ncbi_compiler_sed='s/\([0-9]\).\([0-9]\)/\1\20/' ;; + *:?) ncbi_compiler_sed='s/\([0-9]\)/\100/' ;; +- *) { { echo "$as_me:$LINENO: error: Do not know how to parse $compiler version number $ncbi_compiler_ver" >&5 +-echo "$as_me: error: Do not know how to parse $compiler version number $ncbi_compiler_ver" >&2;} +- { (exit 1); exit 1; }; } ;; ++ *) as_fn_error $? "Do not know how to parse $compiler version number $ncbi_compiler_ver" "$LINENO" 5 ;; + esac + ncbi_compiler_ver=`echo $ncbi_compiler_ver | sed "$ncbi_compiler_sed"` + compiler_version=$ncbi_compiler_ver From 918d92e1b59436d2836d7466d87a25886a031da4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Feb 2022 19:41:08 +0100 Subject: [PATCH 2947/9987] add checksum for BLAST+-2.9.0_fix-GCC-10.patch --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-gompi-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-gompi-2021b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-gompi-2021b.eb index 1b37edec143..3f0f0222bf0 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.9.0-gompi-2021b.eb @@ -32,6 +32,7 @@ patches = [ checksums = [ 'a390cc2d7a09422759fc178db84de9def822cbe485916bbb2ec0d215dacdc257', # ncbi-blast-2.9.0+-src.tar.gz '44dc4a931896953d78c13097433ea6fc8d7990bd759c4e4e5bbb9b2574fb4154', # BLAST+-2.9.0_fix_boost.patch + '01339033213059f9d16c7e211f33485a9bb8de9118065c2a07f81ba1ded611b8', # BLAST+-2.9.0_fix-GCC-10.patch ] dependencies = [ From dc5cdc30a46adc0e2891073abcdbba56d80d9691 Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Thu, 3 Feb 2022 21:46:42 +0100 Subject: [PATCH 2948/9987] fix: patch configure: it breaks --rebuild librsb-1.3.0.0's librsbpp/configure ended up using librsb's ./librsb-config, which would point to the installation (--prefix) directories, and that is wrong for several reasons; one of them being `eb --rebuild` removing those directories just before `make install`. --- easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb index 3bdfc0ca857..3f3d9629332 100644 --- a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb @@ -19,6 +19,8 @@ dependencies = [ ('zlib', '1.2.11') ] +preconfigopts = "sed -i 's/export LIBRSB_CONFIG=.*$/export LIBRSB_CONFIG=no;export LIBRSB_CONFIG_VERSION=1.3.0;/g' configure*; sed -i 's/^ true/CPPFLAGS+=\" -I.. -DRSBPP_HAS_RSB_H=1\"/g' librsbpp/configure*;" + configopts = '--enable-openmp --enable-fortran-module-install' sanity_check_paths = { From 1506b8c2c26d2e9402cd5108368231f8479106f5 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 3 Feb 2022 21:52:57 +0100 Subject: [PATCH 2949/9987] adding easyconfigs: Clang-13.0.1-GCCcore-11.2.0.eb --- .../c/Clang/Clang-13.0.1-GCCcore-11.2.0.eb | 75 +++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8b5f8271aeb --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0.eb @@ -0,0 +1,75 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '13.0.1' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'clang-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', + 'clang-tools-extra-%(version)s.src.tar.xz', + 'libunwind-%(version)s.src.tar.xz', +] +checksums = [ + 'ec6b80d82c384acad2dc192903a6cf2cdbaffb889b84bfb98da9d71e630fc834', # llvm-13.0.1.src.tar.xz + '787a9e2d99f5c8720aa1773e4be009461cd30d3bd40fdd24591e473467c917c9', # clang-13.0.1.src.tar.xz + '7b33955031f9a9c5d63077dedb0f99d77e4e7c996266952c1cec55626dca5dfc', # compiler-rt-13.0.1.src.tar.xz + 'f4003e03da57b53bf206faadd0cf53f7b198c38498c605dec45743db23c10ad0', # polly-13.0.1.src.tar.xz + '6b79261371616c31fea18cd3ee1797c79ee38bcaf8417676d4fa366a24c96b4f', # openmp-13.0.1.src.tar.xz + '666af745e8bf7b680533b4d18b7a31dc7cab575b1e6e4d261922bbafd9644cfb', # lld-13.0.1.src.tar.xz + '2f446acc00bb7cfb4e866c2fa46d1b6dbf4e7d2ab62e3c3d84e56f7b9e28110f', # libcxx-13.0.1.src.tar.xz + 'db5fa6093c786051e8b1c85527240924eceb6c95eeff0a2bbc57be8422b3cef1', # libcxxabi-13.0.1.src.tar.xz + 'cc2bc8598848513fa2257a270083e986fd61048347eccf1d801926ea709392d0', # clang-tools-extra-13.0.1.src.tar.xz + 'e206dbf1bbe058a113bffe189386ded99a160b2443ee1e2cd41ff810f78551ba', # libunwind-13.0.1.src.tar.xz +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.37'), + ('hwloc', '2.5.0'), + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), + ('GMP', '6.2.1'), + ('Z3', '4.8.12'), +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('elfutils', '0.185'), +] + +assertions = True +usepolly = True +build_lld = True +libcxx = True +enable_rtti = True +build_extra_clang_tools = True + +skip_all_tests = True + +moduleclass = 'compiler' From fe6b8007a8b8a557393e8c163ff932b57f535c41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Feb 2022 22:49:39 +0100 Subject: [PATCH 2950/9987] disable building of tests/benchmarks for snappy 1.1.8 to avoid failing build --- easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb | 4 +++- easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.3.0.eb | 4 +++- easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb | 4 +++- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb index 4397a7c9873..3627cd3967c 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb @@ -19,7 +19,9 @@ builddependencies = [ ('CMake', '3.18.4'), ] -configopts = ['', '-DBUILD_SHARED_LIBS=ON'] +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] sanity_check_paths = { 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.3.0.eb index cb8a7b5b743..c0006d14655 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.3.0.eb @@ -19,7 +19,9 @@ builddependencies = [ ('CMake', '3.20.1'), ] -configopts = ['', '-DBUILD_SHARED_LIBS=ON'] +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] sanity_check_paths = { 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb index bf652cb387d..2313fa31373 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-9.3.0.eb @@ -19,7 +19,9 @@ builddependencies = [ ('CMake', '3.16.4'), ] -configopts = ['', '-DBUILD_SHARED_LIBS=ON'] +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] sanity_check_paths = { 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], From 154667de6714abe6ad3eca72758cd2e6fa399005 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 3 Feb 2022 21:52:47 +0000 Subject: [PATCH 2951/9987] sanity-check-command added --- easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-GCC-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-GCC-11.2.0.eb index 0d17682829d..27fcdb8a5a5 100644 --- a/easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FastQTL/FastQTL-2.184-GCC-11.2.0.eb @@ -50,6 +50,11 @@ files_to_copy = [ 'script', ] +# a simple fastQTL --help returns an exit code > 0 +sanity_check_commands = [ + "fastQTL --help 2>&1 | grep 'Version : v2.0'", +] + sanity_check_paths = { 'files': ['bin/fastQTL'], 'dirs': [] From 6b07d57434270eed265cf7310619f835125ef719 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Feb 2022 23:06:38 +0100 Subject: [PATCH 2952/9987] disable use of -Werror for recent NSS versions --- easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb index 96e2dbbf671..43f8dde595b 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.42.1-GCCcore-8.2.0.eb @@ -31,7 +31,7 @@ dependencies = [ parallel = 1 # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" && ' +buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" NSS_ENABLE_WERROR=0 && ' # also install pkgconfig file (see patch) buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb index 798d8f38606..e658c176880 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.45-GCCcore-8.3.0.eb @@ -31,7 +31,7 @@ dependencies = [ parallel = 1 # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" && ' +buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" NSS_ENABLE_WERROR=0 && ' # also install pkgconfig file (see patch) buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb index 9b575239ab5..7f63a2bda8d 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.51-GCCcore-9.3.0.eb @@ -33,7 +33,7 @@ dependencies = [ parallel = 1 # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" NSS_ENABLE_WERROR=0 ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 39ccefdf997..8e2acaccc7f 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -31,7 +31,7 @@ dependencies = [ parallel = 1 # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" NSS_ENABLE_WERROR=0 ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) From c2719efef10031a9342f131b795fe9654ff37237 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Feb 2022 10:37:11 +0100 Subject: [PATCH 2953/9987] adding easyconfigs: PyTorch-Lightning-1.5.9-foss-2021a.eb, tensorboard-2.8.0-foss-2021a.eb --- .../PyTorch-Lightning-1.5.9-foss-2021a.eb | 41 ++++++++++ .../tensorboard-2.8.0-foss-2021a.eb | 76 +++++++++++++++++++ 2 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a.eb create mode 100644 easybuild/easyconfigs/t/tensorboard/tensorboard-2.8.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a.eb new file mode 100644 index 00000000000..98da4e0e0f2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.5.9' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyTorch', '1.10.0'), + ('tqdm', '4.61.2'), + ('tensorboard', '2.8.0'), +] + +# remove requirement for specific version of setuptools +local_preinstallopts = "sed -i 's/setuptools==.*/setuptools/g' requirements.txt && " +# loosen up strict version requirement for pyDeprecate +local_preinstallopts += "sed -i 's/pyDeprecate==/pyDeprecate>=/g' requirements.txt && " + +exts_list = [ + ('fsspec', '2022.1.0'), + ('pyDeprecate', '0.3.2', { + 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], + 'modulename': 'deprecate', + }), + ('torchmetrics', '0.7.0', { + 'checksums': ['dbfb8989086f38020045a935e83928504e1af1d84ae92b073f6a83d018f4bc00'], + }), + ('pytorch-lightning', version, { + 'checksums': ['ccc544d198530d72af585fdae895cdaefe447ecd33b9663e31435dde2994d4ba'], + 'preinstallopts': local_preinstallopts, + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.8.0-foss-2021a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.8.0-foss-2021a.eb new file mode 100644 index 00000000000..bab86f0c2b8 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.8.0-foss-2021a.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'tensorboard' +version = '2.8.0' + +homepage = 'https://github.com/tensorflow/tensorboard' +description = """TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs +and graphs.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('protobuf-python', '3.17.3'), +] + +exts_list = [ + ('absl-py', '1.0.0', { + 'modulename': 'absl', + 'checksums': ['ac511215c01ee9ae47b19716599e8ccfa746f2e18de72bdf641b79b22afa27ea'], + }), + ('cachetools', '5.0.0', { + 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.8', { + 'checksums': ['5c6bd9dc7a543b7fe4304a631f8a8a3b674e2bbfc49c2ae96200cdbe55df6b17'], + }), + ('google-auth', '2.5.0', { + 'modulename': 'google.auth', + 'checksums': ['6577bbf990ef342a24e12e0c8e9d364af6642acdf206c9045bdb8e039fb4fec9'], + }), + ('oauthlib', '3.1.1'), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth', '2.5.0', { + 'modulename': 'google.auth', + 'checksums': ['6577bbf990ef342a24e12e0c8e9d364af6642acdf206c9045bdb8e039fb4fec9'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('grpcio', '1.43.0', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], + }), + ('importlib_metadata', '4.10.1'), + ('Markdown', '3.3.6', { + 'checksums': ['76df8ae32294ec39dcf89340382882dfa12975f87f45c3ed1ecdb1e8cefc7006'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('Werkzeug', '2.0.2', { + 'checksums': ['aa2bb6fc8dee8d6c504c0ac1e7f5f7dc5810a9903e793b6f715a9f015bdadb9a'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['65a338e4424e9079f2604923bdbe301792adce2ace1be68da6b3ddf005170def'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 6486154f5258671286bd457c40864924106583c4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Feb 2022 11:00:45 +0100 Subject: [PATCH 2954/9987] add missing checksums in tensorboard + PyTorch-Lightning easyconfigs --- .../PyTorch-Lightning-1.5.9-foss-2021a.eb | 8 +++++--- .../t/tensorboard/tensorboard-2.8.0-foss-2021a.eb | 8 ++++++-- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a.eb index 98da4e0e0f2..efb954c7280 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a.eb @@ -21,17 +21,19 @@ local_preinstallopts = "sed -i 's/setuptools==.*/setuptools/g' requirements.txt local_preinstallopts += "sed -i 's/pyDeprecate==/pyDeprecate>=/g' requirements.txt && " exts_list = [ - ('fsspec', '2022.1.0'), + ('fsspec', '2022.1.0', { + 'checksums': ['0bdd519bbf4d8c9a1d893a50b5ebacc89acd0e1fe0045d2f7b0e0c1af5990edc'], + }), ('pyDeprecate', '0.3.2', { - 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], 'modulename': 'deprecate', + 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], }), ('torchmetrics', '0.7.0', { 'checksums': ['dbfb8989086f38020045a935e83928504e1af1d84ae92b073f6a83d018f4bc00'], }), ('pytorch-lightning', version, { - 'checksums': ['ccc544d198530d72af585fdae895cdaefe447ecd33b9663e31435dde2994d4ba'], 'preinstallopts': local_preinstallopts, + 'checksums': ['ccc544d198530d72af585fdae895cdaefe447ecd33b9663e31435dde2994d4ba'], }), ] diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.8.0-foss-2021a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.8.0-foss-2021a.eb index bab86f0c2b8..cc81a2a1592 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.8.0-foss-2021a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.8.0-foss-2021a.eb @@ -33,7 +33,9 @@ exts_list = [ 'modulename': 'google.auth', 'checksums': ['6577bbf990ef342a24e12e0c8e9d364af6642acdf206c9045bdb8e039fb4fec9'], }), - ('oauthlib', '3.1.1'), + ('oauthlib', '3.1.1', { + 'checksums': ['8f0215fcc533dd8dd1bee6f4c412d4f0cd7297307d43ac61666389e3bc3198a3'], + }), ('requests-oauthlib', '1.3.0', { 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], }), @@ -49,7 +51,9 @@ exts_list = [ 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], }), - ('importlib_metadata', '4.10.1'), + ('importlib_metadata', '4.10.1', { + 'checksums': ['951f0d8a5b7260e9db5e41d429285b5f451e928479f19d80818878527d36e95e'], + }), ('Markdown', '3.3.6', { 'checksums': ['76df8ae32294ec39dcf89340382882dfa12975f87f45c3ed1ecdb1e8cefc7006'], }), From 7cce9fa38a0838ab6b98732012135439bb0a399a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Feb 2022 11:09:59 +0100 Subject: [PATCH 2955/9987] adding easyconfigs: atools-1.4.8-GCCcore-11.2.0-Python-2.7.18.eb --- ...ools-1.4.8-GCCcore-11.2.0-Python-2.7.18.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/atools/atools-1.4.8-GCCcore-11.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/a/atools/atools-1.4.8-GCCcore-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/a/atools/atools-1.4.8-GCCcore-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..f9887970009 --- /dev/null +++ b/easybuild/easyconfigs/a/atools/atools-1.4.8-GCCcore-11.2.0-Python-2.7.18.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'atools' +version = '1.4.8' +versionsuffix = '-Python-2.7.18' + +homepage = 'https://github.com/gjbex/atools' +description = """Tools to make using job arrays a lot more convenient.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/gjbex/atools/archive'] +sources = [SOURCE_TAR_GZ] +checksums = ['21f60a8f6dde4ee1e97bac1bef306a314c1200d3bd8ec0f9b865d5e697585de8'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '2.7.18')] + +# to enable SLURM integration (site-specific) (options are torque, moab, sge, slurm) +configopts = '--with-batchsystem=slurm' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acreate', 'aenv', 'aload', 'alog', 'arange', 'areduce']], + 'dirs': ['lib/vsc/atools'] +} + +sanity_check_commands = [ + 'acreate -h', + 'aenv -h', + 'aload -h', + 'alog -h', + 'arange -h', + 'areduce -h', +] + +moduleclass = 'tools' From 6f69de929bce8e1ba631e0dde3447bbf0c5df626 Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 4 Feb 2022 10:22:15 +0000 Subject: [PATCH 2956/9987] adding easyconfigs: CheMPS2-1.8.11-foss-2021b.eb --- .../c/CheMPS2/CheMPS2-1.8.11-foss-2021b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.11-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.11-foss-2021b.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.11-foss-2021b.eb new file mode 100644 index 00000000000..a70adebb5c5 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.11-foss-2021b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.8.11' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1843c1dd2775104a7b75fc4849ef54eb0b67b7643553b88af82a9ea1f034c4e5'] + +builddependencies = [('CMake', '3.22.1')] + +dependencies = [ + ('HDF5', '1.12.1') +] + +pretestopts = 'export OMP_NUM_THREADS=1 && ' +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' From e5b5f274ff49f6a20a37b72c8951bd601c1a659f Mon Sep 17 00:00:00 2001 From: Sassy Date: Fri, 4 Feb 2022 10:23:56 +0000 Subject: [PATCH 2957/9987] adding easyconfigs: deepdiff-5.7.0-GCCcore-11.2.0.eb --- .../deepdiff/deepdiff-5.7.0-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/d/deepdiff/deepdiff-5.7.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-5.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-5.7.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b2738d105f5 --- /dev/null +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-5.7.0-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'deepdiff' +version = '5.7.0' + +homepage = 'https://zepworks.com/deepdiff/current/' +description = """DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] +dependencies = [('Python', '3.9.6')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('jsonpickle', '2.1.0', { + 'checksums': ['84684cfc5338a534173c8dd69809e40f2865d0be1f8a2b7af8465e5b968dcfa9'], + 'preinstallopts': """sed -i 's/setup()/setup(version="%(version)s")/g' setup.py && """ + }), + ('ordered-set', '4.0.2', { + 'checksums': ['ba93b2df055bca202116ec44b9bead3df33ea63a7d5827ff8e16738b97f33a95'], + }), + (name, version, { + 'checksums': ['838766484e323dcd9dec6955926a893a83767dc3f3f94542773e6aa096efe5d4'], + }), +] + +moduleclass = 'tools' From f830b3fe07da1e3ee351bf14390f9ce98e3b0349 Mon Sep 17 00:00:00 2001 From: parosen Date: Fri, 4 Feb 2022 11:26:18 +0100 Subject: [PATCH 2958/9987] adding easyconfigs: YAXT-0.9.2-intel-2021b.eb --- .../y/YAXT/YAXT-0.9.2-intel-2021b.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb new file mode 100644 index 00000000000..8c675965d15 --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.9.2' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.dkrz.de/redmine/attachments/download/513/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' From af2d6a346e9d9600ccf035f999835b884fcf4f0a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 4 Feb 2022 12:05:26 +0100 Subject: [PATCH 2959/9987] remove default variants of TensorFlow in AlphaFold --- test/easyconfigs/easyconfigs.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index aba57000136..a493d9c549d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -499,8 +499,6 @@ def check_dep_vars(self, gen, dep, dep_vars): ('2.2.2;', ['medaka-1.4.3-']), # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), - # AlphaFold 2.0.0 to 2.1.1 (foss/2020b) depend on TensorFlow 2.4.1) - ('2.4.1;', ['AlphaFold-2.0.0-', 'AlphaFold-2.0.1-', 'AlphaFold-2.1.1-']), # AlphaFold 2.1.2 (foss/2020b) depends on TensorFlow 2.5.0 ('2.5.0;', ['AlphaFold-2.1.2-']), ], From 6e79605877e642b783394dce1297a8f2d63bc55a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 4 Feb 2022 12:33:02 +0100 Subject: [PATCH 2960/9987] add TensorFlow versionsuffix to AlphaFold-2.1.2-foss-2020b.eb --- ...020b.eb => AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/a/AlphaFold/{AlphaFold-2.1.2-foss-2020b.eb => AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb} (98%) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb similarity index 98% rename from easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb rename to easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb index 7b02431cec0..8b9e592efd7 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb @@ -2,6 +2,8 @@ easyblock = 'PythonBundle' name = 'AlphaFold' version = '2.1.2' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-{}'.format(local_tf_version) homepage = 'https://deepmind.com/research/case-studies/alphafold' description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" @@ -21,7 +23,7 @@ dependencies = [ ('Python', '3.8.6', ), ('SciPy-bundle', '2020.11'), ('PyYAML', '5.3.1', ), - ('TensorFlow', '2.5.0'), + ('TensorFlow', local_tf_version), ('Biopython', '1.78'), ('HH-suite', '3.3.0',), ('HMMER', '3.3.2',), From ee1de3af9c7f8970a9c278246b698f043801493f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 4 Feb 2022 12:34:22 +0100 Subject: [PATCH 2961/9987] add TensorFlow versionsuffix to AlphaFold-2.1.2-fosscuda-2020b.eb --- ....eb => AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/a/AlphaFold/{AlphaFold-2.1.2-fosscuda-2020b.eb => AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb} (98%) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb similarity index 98% rename from easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb rename to easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb index e31ec9ab97f..26ae15f4f3c 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -2,6 +2,8 @@ easyblock = 'PythonBundle' name = 'AlphaFold' version = '2.1.2' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-{}'.format(local_tf_version) homepage = 'https://deepmind.com/research/case-studies/alphafold' description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" @@ -21,7 +23,7 @@ dependencies = [ ('Python', '3.8.6', ), ('SciPy-bundle', '2020.11'), ('PyYAML', '5.3.1', ), - ('TensorFlow', '2.5.0'), + ('TensorFlow', local_tf_version), ('Biopython', '1.78'), ('HH-suite', '3.3.0',), ('HMMER', '3.3.2',), From 4ecf2213af4ff14632f532022baffb3512c2f794 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Feb 2022 12:58:59 +0100 Subject: [PATCH 2962/9987] adding easyconfigs: PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb --- ...-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..e8d997ccd68 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.5.9' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('PyTorch', '1.10.0', versionsuffix), + ('tqdm', '4.61.2'), + ('tensorboard', '2.8.0'), +] + +# remove requirement for specific version of setuptools +local_preinstallopts = "sed -i 's/setuptools==.*/setuptools/g' requirements.txt && " +# loosen up strict version requirement for pyDeprecate +local_preinstallopts += "sed -i 's/pyDeprecate==/pyDeprecate>=/g' requirements.txt && " + +exts_list = [ + ('fsspec', '2022.1.0', { + 'checksums': ['0bdd519bbf4d8c9a1d893a50b5ebacc89acd0e1fe0045d2f7b0e0c1af5990edc'], + }), + ('pyDeprecate', '0.3.2', { + 'modulename': 'deprecate', + 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], + }), + ('torchmetrics', '0.7.0', { + 'checksums': ['dbfb8989086f38020045a935e83928504e1af1d84ae92b073f6a83d018f4bc00'], + }), + ('pytorch-lightning', version, { + 'preinstallopts': local_preinstallopts, + 'checksums': ['ccc544d198530d72af585fdae895cdaefe447ecd33b9663e31435dde2994d4ba'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 47c804330b73d4e85bb3f663f1422f4011a24f2c Mon Sep 17 00:00:00 2001 From: parosen Date: Fri, 4 Feb 2022 13:48:45 +0100 Subject: [PATCH 2963/9987] included checksum --- easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb index 8c675965d15..20b90901519 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb @@ -11,6 +11,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://www.dkrz.de/redmine/attachments/download/513/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['b6714e42483486d76db146732bac74bc500096c15c9efa411ece3e00172fc360'] configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' From 57d8187d1522ba24d194794a6714398630d2f360 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 4 Feb 2022 13:59:12 +0100 Subject: [PATCH 2964/9987] adding easyconfigs: GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb, GROMACS-2021.5-foss-2021b.eb and patches: GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch --- .../GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb | 91 +++++++++++++++++++ .../g/GROMACS/GROMACS-2021.5-foss-2021b.eb | 89 ++++++++++++++++++ ...S-2021.5_fix_threads_gpu_Gmxapitests.patch | 66 ++++++++++++++ 3 files changed, 246 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..cf94349e8a3 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,91 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI builds. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch', +] +checksums = [ + 'eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6', # gromacs-2021.5.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch + '7d39da0b431fbc9e94e857552246eb0ec892f26b13e519b3706785cc5e01a563', +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('networkx', '2.6.3'), + ('CUDA', '11.4.1', '', True), + ('UCX-CUDA', '1.11.2', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.2.1', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['e24d507585e1a7808a5ee3ed04da5d6577f2a8961bbeafa7068528e00aa6b20d'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b.eb new file mode 100644 index 00000000000..b55f57ae0d5 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b.eb @@ -0,0 +1,89 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021.5' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI builds +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch', +] +checksums = [ + 'eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6', # gromacs-2021.5.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch + '7d39da0b431fbc9e94e857552246eb0ec892f26b13e519b3706785cc5e01a563', +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('networkx', '2.6.3'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.2.1', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['e24d507585e1a7808a5ee3ed04da5d6577f2a8961bbeafa7068528e00aa6b20d'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch new file mode 100644 index 00000000000..d0bfe9eacf9 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch @@ -0,0 +1,66 @@ +Don't overwrite PYTHONPATH when executing tests, add to it instead. +Unset OMP_NUM_THREADS when GMX_THREAD_MPI enabled. + +Åke Sandgren, 20200309 +Dugan Witherick, 20210112 +Christoph Siegert, 20220203 + +diff -ruN gromacs-2021.5.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt gromacs-2021.5/python_packaging/sample_restraint/tests/CMakeGROMACS.txt +--- gromacs-2021.5.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2022-02-03 12:46:42.308693114 +0100 ++++ gromacs-2021.5/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2022-02-03 15:49:25.973628494 +0100 +@@ -21,13 +21,21 @@ + get_target_property(GMXBIN gmx RUNTIME_OUTPUT_DIRECTORY) + get_target_property(GMXAPI_PYTHON_STAGING_DIR _gmxapi staging_dir) + get_target_property(PLUGINPATH gmxapi_extension LIBRARY_OUTPUT_DIRECTORY) +-add_custom_target(gmxapi_extension_pytest +- COMMAND ${CMAKE_COMMAND} +- -E env GMXBIN=${GMXBIN} PYTHONPATH=${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} +- ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR +- ${CMAKE_CURRENT_SOURCE_DIR} +- DEPENDS gmxapi_extension _gmxapi) ++if (NOT GMX_THREAD_MPI) ++ add_custom_target(gmxapi_extension_pytest ++ COMMAND ${CMAKE_COMMAND} -E env GMXBIN=${GMXBIN} PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} ++ ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} ++ DEPENDS gmxapi_extension _gmxapi ++ WORKING_DIRECTORY ${PLUGINPATH}) ++else() ++ add_custom_target(gmxapi_extension_pytest ++ COMMAND ${CMAKE_COMMAND} -E env --unset=OMP_NUM_THREADS GMXBIN=${GMXBIN} PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} ++ ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} ++ DEPENDS gmxapi_extension _gmxapi ++ WORKING_DIRECTORY ${PLUGINPATH}) ++endif() + # The current test fixtures require the `gmx` tool-wrapper executable. ++ + add_dependencies(gmxapi_extension_pytest gmx) + + add_dependencies(tests gmxapi_extension_histogram-test gmxapi_extension_bounding-test) +diff -ruN gromacs-2021.5.orig/python_packaging/src/test/CMakeLists.txt gromacs-2021.5/python_packaging/src/test/CMakeLists.txt +--- gromacs-2021.5.orig/python_packaging/src/test/CMakeLists.txt 2022-02-03 12:46:42.383694802 +0100 ++++ gromacs-2021.5/python_packaging/src/test/CMakeLists.txt 2022-02-03 14:33:29.920236268 +0100 +@@ -63,11 +63,19 @@ + + # TODO: (#2961) Let the Python package discover required resources instead of passing GMXBIN + get_target_property(GMXBIN gmx RUNTIME_OUTPUT_DIRECTORY) +-add_custom_target(gmxapi_pytest +- COMMAND ${CMAKE_COMMAND} -E env GMXBIN=${GMXBIN} +- ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} +- DEPENDS _gmxapi +- WORKING_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}) ++if (NOT GMX_THREAD_MPI) ++ add_custom_target(gmxapi_pytest ++ COMMAND ${CMAKE_COMMAND} -E env GMXBIN=${GMXBIN} ++ ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} ++ DEPENDS _gmxapi ++ WORKING_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}) ++else() ++ add_custom_target(gmxapi_pytest ++ COMMAND ${CMAKE_COMMAND} -E env --unset=OMP_NUM_THREADS GMXBIN=${GMXBIN} ++ ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} ++ DEPENDS _gmxapi ++ WORKING_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}) ++endif() + # The current test fixtures require the `gmx` tool-wrapper executable. + add_dependencies(gmxapi_pytest gmx) + From ca7b5330d85aee60e92791ba5f20d2908f965a42 Mon Sep 17 00:00:00 2001 From: parosen Date: Fri, 4 Feb 2022 14:11:14 +0100 Subject: [PATCH 2965/9987] adding easyconfigs: ecCodes-2.24.2-iimpi-2021b.eb --- .../e/ecCodes/ecCodes-2.24.2-iimpi-2021b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-iimpi-2021b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-iimpi-2021b.eb new file mode 100644 index 00000000000..db069a3f7e5 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-iimpi-2021b.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.24.2' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'usempi': False} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['c60ad0fd89e11918ace0d84c01489f21222b11d6cad3ff7495856a0add610403'] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [ + ('netCDF', '4.8.1'), + ('JasPer', '2.0.33'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF " +configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " +configopts += "-DENABLE_ECCODES_THREADS=ON" # multi-threading with pthreads + +local_exes = ['%s_%s' % (a, b) + for a in ['bufr', 'grib', 'gts', 'metar'] + for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] +local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + + ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 30264267726707b2f2ee62102f431cdbff18686b Mon Sep 17 00:00:00 2001 From: parosen Date: Fri, 4 Feb 2022 14:41:43 +0100 Subject: [PATCH 2966/9987] adding easyconfigs: CDO-1.9.10-intel-2021b.eb --- .../c/CDO/CDO-1.9.10-intel-2021b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb new file mode 100644 index 00000000000..deaf598904b --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.9.10' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +# stick to lowopt (-O1) to avoid internal compiler error when building on Intel Skylake +toolchainopts = {'pic': True, 'usempi': True, 'lowopt': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/24638/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cc39c89bbb481d7b3945a06c56a8492047235f46ac363c4f0d980fccdde6677e'] + +dependencies = [ + ('HDF5', '1.12.1'), + ('netCDF', '4.8.1'), + ('YAXT', '0.9.2'), + ('ecCodes', '2.24.2'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES" + +# fix for linking issues with HDF5 libraries for libcdi, should link with both -lnetcdf and -lhdf5_hl -lhdf5 +prebuildopts = "find libcdi -name Makefile | xargs sed -i 's/-lnetcdf -lnetcdf/-lnetcdf -lhdf5_hl -lhdf5/g' && " + +sanity_check_paths = { + 'files': ['bin/cdo'], + 'dirs': [], +} + +moduleclass = 'data' From 7177b04fe06ebba926f3cbb58a6492ffc4b08ac3 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 4 Feb 2022 15:21:53 +0100 Subject: [PATCH 2967/9987] adding easyconfigs: histolab-0.4.1-foss-2021b.eb --- .../h/histolab/histolab-0.4.1-foss-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb b/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb new file mode 100644 index 00000000000..d647196d258 --- /dev/null +++ b/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'histolab' +version = '0.4.1' + +homepage = 'https://github.com/histolab/histolab' +description = 'Library for Digital Pathology Image Processing' + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/histolab/histolab/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['71b7e93f94ff8ad76426cb73e1d26fd899fd8568f8ce9f5c42a6d8f3fbbfe641'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Pillow', '8.3.2'), + ('scikit-image', '0.19.1'), + ('openslide-python', '1.1.2'), +] + +preinstallopts = ["sed -i 's|<0.19.1|<0.19.2|g' requirements.txt &&"] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' \ No newline at end of file From 95f3f4e7f52e64ec2c413db803de7415d956d660 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 4 Feb 2022 15:43:18 +0100 Subject: [PATCH 2968/9987] Added newline to end of file --- easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb b/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb index d647196d258..2262fc0ca06 100644 --- a/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb +++ b/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb @@ -25,4 +25,5 @@ preinstallopts = ["sed -i 's|<0.19.1|<0.19.2|g' requirements.txt &&"] use_pip = True sanity_pip_check = True -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' + From 1da6524feeb959f078dca0208aefd735ad9d1d70 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Feb 2022 15:44:14 +0100 Subject: [PATCH 2969/9987] strip off trailing empty line in histolab easyconfig --- easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb b/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb index 2262fc0ca06..24f3eec348a 100644 --- a/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb +++ b/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb @@ -26,4 +26,4 @@ use_pip = True sanity_pip_check = True moduleclass = 'bio' - +moduleclass = 'bio' From f64dbf42f113e4ae239f7cc9e3f12a13c908e03c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Feb 2022 15:54:27 +0100 Subject: [PATCH 2970/9987] also enable download_dep_fail --- .../easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb b/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb index 24f3eec348a..f078e041938 100644 --- a/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb +++ b/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021b.eb @@ -20,10 +20,11 @@ dependencies = [ ('openslide-python', '1.1.2'), ] +download_dep_fail = True +use_pip = True + preinstallopts = ["sed -i 's|<0.19.1|<0.19.2|g' requirements.txt &&"] -use_pip = True sanity_pip_check = True moduleclass = 'bio' -moduleclass = 'bio' From 21ff02a26e09d22c2f1698c0aa390a06b8b4c6dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Feb 2022 15:56:03 +0100 Subject: [PATCH 2971/9987] add catlearn extension to easyconfig for R v4.1.2 --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 66406280d05..7043d2cb89f 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3212,6 +3212,9 @@ exts_list = [ ('ldbounds', '1.1-1.1', { 'checksums': ['e88e6bff43762a9f7d80484056d10c7d2fd80969b43061d8cc96c3bd5b9c3583'], }), + ('catlearn', '0.8', { + 'checksums': ['0d13da431a5511b025090b7ffaa3765b94b33c7de5a7cc1cec8c50437755646e'], + }), ] moduleclass = 'lang' From a767cc72d605b91aac8fd0517e1dfe73927a2c15 Mon Sep 17 00:00:00 2001 From: Keith Refson Date: Fri, 4 Feb 2022 15:20:18 +0000 Subject: [PATCH 2972/9987] Reordered CASTEP .eb files for style conformance --- .../c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb | 22 +++++++++---------- .../c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb | 22 +++++++++---------- .../c/CASTEP/CASTEP-21.1.1-foss-2019b.eb | 20 ++++++++--------- .../c/CASTEP/CASTEP-21.1.1-intel-2019b.eb | 19 +++++++--------- .../c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb | 19 +++++++--------- 5 files changed, 45 insertions(+), 57 deletions(-) diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb index 2f2011f7368..b76958923a7 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb @@ -3,33 +3,31 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' - homepage = 'http://www.castep.org' description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" - toolchain = {'name': 'CrayCCE', 'version': '19.06'} -dependencies = [('cray-fftw', EXTERNAL_MODULE)] + # CASTEP is proprietary software, available under a free-of-charge license for academic use only. # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. +local_patch_ver = version.split('.')[-1] +sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] -sources = ['CASTEP-21.11.tar.gz'] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', - 'elastics.py', 'ceteprouts.pm']], - 'dirs': [], -} +dependencies = [('cray-fftw', EXTERNAL_MODULE)] skipsteps = ['configure'] -maxparallel = 16 - buildopts = 'COMMS_ARCH=mpi FFT=fftw3 FFTLIBDIR= castep tools' preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' - installopts = 'COMMS_ARCH=mpi FFT=fftw3 INSTALL_DIR="%(installdir)s/bin" install-castep install-tools' +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb index e2a210e5b18..6e4ce1d8eb7 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb @@ -3,33 +3,31 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' - homepage = 'http://www.castep.org' description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" - toolchain = {'name': 'CrayGNU', 'version': '19.06'} -dependencies = [('cray-fftw', EXTERNAL_MODULE)] + # CASTEP is proprietary software, available under a free-of-charge license for academic use only. # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. +local_patch_ver = version.split('.')[-1] +sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] -sources = ['CASTEP-21.11.tar.gz'] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', - 'elastics.py', 'ceteprouts.pm']], - 'dirs': [], -} +dependencies = [('cray-fftw', EXTERNAL_MODULE)] skipsteps = ['configure'] -maxparallel = 16 - buildopts = 'COMMS_ARCH=mpi FFT=fftw3 FFTLIBDIR= castep tools' preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' - installopts = 'COMMS_ARCH=mpi FFT=fftw3 INSTALL_DIR="%(installdir)s/bin" install-castep install-tools' +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb index c70fe600cdd..3ff4a50a282 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb @@ -3,7 +3,6 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' - homepage = 'http://www.castep.org' description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" @@ -12,25 +11,24 @@ toolchain = {'name': 'foss', 'version': '2019b'} # CASTEP is proprietary software, available under a free-of-charge license for academic use only. # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. +local_patch_ver = version.split('.')[-1] +sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] -sources = ['CASTEP-21.11.tar.gz'] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', - 'elastics.py', 'ceteprouts.pm']], - 'dirs': [], -} - skipsteps = ['configure'] -maxparallel = 16 - buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas FFTLIBDIR= MATHLIBDIR= castep tools utilities' preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' installopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas INSTALL_DIR="%(installdir)s/bin"' -' install-castep install-tools install-utilities' +installopts += ' install-castep install-tools install-utilities' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb index 4f9eec63d5d..29edac436a4 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb @@ -3,7 +3,6 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' - homepage = 'http://www.castep.org' description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" @@ -12,24 +11,22 @@ toolchain = {'name': 'intel', 'version': '2019b'} # CASTEP is proprietary software, available under a free-of-charge license for academic use only. # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. +local_patch_ver = version.split('.')[-1] +sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] -sources = ['CASTEP-21.11.tar.gz'] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', - 'elastics.py', 'ceteprouts.pm']], - 'dirs': [], -} - skipsteps = ['configure'] -maxparallel = 16 - buildopts = 'COMMS_ARCH=mpi castep tools utilities' preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' - installopts = 'COMMS_ARCH=mpi INSTALL_DIR="%(installdir)s/bin" install-castep install-tools install-utilities' +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb index 78e866ff8f0..86c65234f30 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb @@ -3,7 +3,6 @@ easyblock = 'ConfigureMake' name = 'CASTEP' version = '21.1.1' - homepage = 'http://www.castep.org' description = """CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.""" @@ -12,24 +11,22 @@ toolchain = {'name': 'iomkl', 'version': '2019b'} # CASTEP is proprietary software, available under a free-of-charge license for academic use only. # Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. +local_patch_ver = version.split('.')[-1] +sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] -sources = ['CASTEP-21.11.tar.gz'] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', - 'elastics.py', 'ceteprouts.pm']], - 'dirs': [], -} - skipsteps = ['configure'] -maxparallel = 16 - buildopts = 'COMMS_ARCH=mpi castep tools utilities' preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' - installopts = 'COMMS_ARCH=mpi INSTALL_DIR="%(installdir)s/bin" install-castep install-tools install-utilities' +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} + moduleclass = 'phys' From 056669684c5b5a5a7cf8fceb5cd73c72aaf3e877 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 4 Feb 2022 17:26:10 +0200 Subject: [PATCH 2973/9987] use dependency on jupyter-server-proxy in jupyter-matlab-proxy --- ...pyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb | 52 ++++++------------- 1 file changed, 16 insertions(+), 36 deletions(-) diff --git a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb index cd2a2963360..7081ae11f7f 100644 --- a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.3.4-GCCcore-10.3.0.eb @@ -1,4 +1,4 @@ -easyblock = "PythonBundle" +easyblock = "PythonPackage" name = 'jupyter-matlab-proxy' version = '0.3.4' @@ -8,57 +8,37 @@ description = 'MATLAB Integration for Jupyter' toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['jupyter-matlab-proxy-%(version)s_eb-matlab-license-file.patch'] +checksums = [ + '05235c77aadf6ffb2b7193f6c6e4962eff68e4e5908370525363180d81bf9348', # jupyter-matlab-proxy-0.3.4.tar.gz + # jupyter-matlab-proxy-0.3.4_eb-matlab-license-file.patch + '6d83f73019313394982b7f8eb1d28859442460668284e4d86e2c5d465cfb00ba', +] + builddependencies = [ ('binutils', '2.36.1'), - ('nodejs', '14.17.2'), + ('nodejs', '14.17.0'), ] dependencies = [ ('Python', '3.9.5'), ('JupyterLab', '3.0.16'), # Contains most of the jupyter dependencies we need. + ('jupyter-server-proxy', '3.2.1'), ('Xvfb', '1.20.11'), ] +download_dep_fail = True + use_pip = True sanity_pip_check = True -exts_list = [ - ('typing_extensions', '3.10.0.2', { - 'checksums': ['49f75d16ff11f1cd258e1b988ccff82a3ca5570217d7ad8c5f48205dd99a677e'], - }), - ('async-timeout', '3.0.1', { - 'checksums': ['0c3c816a028d47f659d6ff5c745cb2acf1f966da1fe5c19c77a70282b25f4c5f'], - }), - ('multidict', '5.2.0', { - 'checksums': ['0dd1c93edb444b33ba2274b66f63def8a327d607c6c790772f448a53b6ea59ce'], - }), - ('yarl', '1.7.0', { - 'checksums': ['8e7ebaf62e19c2feb097ffb7c94deb0f0c9fab52590784c8cd679d30ab009162'], - }), - ('aiohttp', '3.7.4.post0', { - 'checksums': ['493d3299ebe5f5a7c66b9819eacdcfbbaaf1a8e84911ddffcdc48888497afecf'], - }), - ('simpervisor', '0.4', { - 'checksums': ['cec79e13cdbd6edb04a5c98c1ff8d4bd9713e706c069226909a1ef0e89d393c5'], - }), - ('jupyter-server-proxy', '3.1.0', { - 'checksums': ['30d57976090980f4380cb0a80e8e829dfd74d0a19edb64329239def9feefcde4'], - }), - (name, version, { - 'patches': ['jupyter-matlab-proxy-%(version)s_eb-matlab-license-file.patch'], - 'checksums': [ - '05235c77aadf6ffb2b7193f6c6e4962eff68e4e5908370525363180d81bf9348', # jupyter-matlab-proxy-0.3.4.tar.gz - # jupyter-matlab-proxy-0.3.4_eb-matlab-license-file.patch - '6d83f73019313394982b7f8eb1d28859442460668284e4d86e2c5d465cfb00ba', - ], - }), -] - -modloadmsg = 'jupyter-matlab-proxy requires MATLAB to be loaded separately (2020b or later)' - sanity_check_paths = { 'files': ['bin/matlab-jupyter-app'], 'dirs': ['lib64/python%(pyshortver)s/site-packages'] } +modloadmsg = 'jupyter-matlab-proxy requires MATLAB to be loaded separately (2020b or later)' + moduleclass = 'math' From 8e9877c35cc448f0e657afcb8396f5c1b2fd2658 Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Fri, 4 Feb 2022 17:34:04 +0100 Subject: [PATCH 2974/9987] keep preconfigopts setting line within 120 chars --- easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb index 3f3d9629332..3596f82d241 100644 --- a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb @@ -19,7 +19,8 @@ dependencies = [ ('zlib', '1.2.11') ] -preconfigopts = "sed -i 's/export LIBRSB_CONFIG=.*$/export LIBRSB_CONFIG=no;export LIBRSB_CONFIG_VERSION=1.3.0;/g' configure*; sed -i 's/^ true/CPPFLAGS+=\" -I.. -DRSBPP_HAS_RSB_H=1\"/g' librsbpp/configure*;" +preconfigopts = "sed -i 's/export LIBRSB_CONFIG=.*$/export LIBRSB_CONFIG=no LIBRSB_CONFIG_VERSION=1.3.0;/g' configure*;" +preconfigopts += " sed -i 's/^ true/CPPFLAGS+=\" -I.. -DRSBPP_HAS_RSB_H=1\"/g' librsbpp/configure*;" configopts = '--enable-openmp --enable-fortran-module-install' From cd52693283a6db0e832063c09741d98158a77105 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Feb 2022 19:40:15 +0100 Subject: [PATCH 2975/9987] adding easyconfigs: lftp-4.9.2-GCCcore-11.2.0.eb --- .../l/lftp/lftp-4.9.2-GCCcore-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/lftp/lftp-4.9.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.9.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/lftp/lftp-4.9.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..78c236719ea --- /dev/null +++ b/easybuild/easyconfigs/l/lftp/lftp-4.9.2-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'lftp' +version = '4.9.2' + +homepage = 'https://lftp.yar.ru' +description = """LFTP is a sophisticated ftp/http client, and a file transfer program supporting +a number of network protocols. Like BASH, it has job control and uses the readline library for +input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. +It was designed with reliability in mind.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://lftp.yar.ru/ftp/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a37589c61914073f53c5da0e68bd233b41802509d758a022000e1ae2076da733'] + +dependencies = [ + ('ncurses', '6.2'), +] + +builddependencies = [ + ('binutils', '2.37'), + ('libreadline', '8.1'), + ('zlib', '1.2.11') +] + +# for this version of lftp the gnutls library is optional +configopts = "--with-readline=$EBROOTLIBREADLINE --without-gnutls" + +sanity_check_paths = { + 'files': ['bin/lftp'], + 'dirs': [] +} + +moduleclass = 'tools' From b27c4a6e746f6d244ecb91023e7d38fdb519b62f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Feb 2022 20:26:42 +0100 Subject: [PATCH 2976/9987] adding easyconfigs: xtensor-0.24.0-foss-2021b.eb --- .../x/xtensor/xtensor-0.24.0-foss-2021b.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/x/xtensor/xtensor-0.24.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/x/xtensor/xtensor-0.24.0-foss-2021b.eb b/easybuild/easyconfigs/x/xtensor/xtensor-0.24.0-foss-2021b.eb new file mode 100644 index 00000000000..afb2af5900a --- /dev/null +++ b/easybuild/easyconfigs/x/xtensor/xtensor-0.24.0-foss-2021b.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'xtensor' +version = '0.24.0' + +homepage = 'https://github.com/xtensor-stack/xtensor' +description = "xtensor is a C++ library meant for numerical analysis with multi-dimensional array expressions." + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('CMake', '3.21.1'), + ('pybind11', '2.7.1'), +] +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'source_urls': ['https://github.com/xtensor-stack/%(name)s/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('xtl', '0.7.4', { + 'checksums': ['3c88be0e696b64150c4de7a70f9f09c00a335186b0b0b409771ef9f56bca7d9a'], + }), + ('xsimd', '8.0.5', { + 'checksums': ['0e1b5d973b63009f06a3885931a37452580dbc8d7ca8ad40d4b8c80d2a0f84d7'], + }), + ('xtensor', version, { + 'checksums': ['37738aa0865350b39f048e638735c05d78b5331073b6329693e8b8f0902df713'], + }), + ('xtensor-python', '0.26.0', { + 'checksums': ['04dcfe84181c23f364b1e68a6d55d89d1679f31d8da0372db01af72534baf728'], + }), +] + +sanity_check_paths = { + 'files': ['include/xtensor.hpp', 'lib/pkgconfig/xsimd.pc', 'lib/pkgconfig/xtensor.pc'], + 'dirs': ['include/xsimd', 'include/xtensor', 'include/xtensor-python', 'include/xtl', 'lib/cmake'], +} + +moduleclass = 'lib' From a9dae0a2590fa75533a6d58454571399da6a1bac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Feb 2022 20:47:22 +0100 Subject: [PATCH 2977/9987] adding easyconfigs: histolab-0.4.1-foss-2021a.eb, openslide-python-1.1.2-GCCcore-10.3.0.eb --- .../h/histolab/histolab-0.4.1-foss-2021a.eb | 30 +++++++++++++++++++ .../openslide-python-1.1.2-GCCcore-10.3.0.eb | 29 ++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021a.eb b/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021a.eb new file mode 100644 index 00000000000..af59853ca95 --- /dev/null +++ b/easybuild/easyconfigs/h/histolab/histolab-0.4.1-foss-2021a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'histolab' +version = '0.4.1' + +homepage = 'https://github.com/histolab/histolab' +description = 'Library for Digital Pathology Image Processing' + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/histolab/histolab/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['71b7e93f94ff8ad76426cb73e1d26fd899fd8568f8ce9f5c42a6d8f3fbbfe641'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Pillow', '8.2.0'), + ('scikit-image', '0.18.3'), + ('openslide-python', '1.1.2'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = ["sed -i 's|scikit-image [<>].*|scikit-image|g' requirements.txt &&"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..111b406be73 --- /dev/null +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.1.2-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'openslide-python' +version = '1.1.2' + +homepage = 'https://github.com/openslide/openslide-python' +description = "OpenSlide Python is a Python interface to the OpenSlide library." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/openslide/openslide-python/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['83e064ab4a29658e7ddf86bf1d3e54d2508cc19ece35d55b55519c826e45d83f'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('Pillow', '8.2.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'openslide'} + +moduleclass = 'vis' From 8a972c3a0e9c9c8525945138d2e717ab915a019d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Feb 2022 20:47:50 +0100 Subject: [PATCH 2978/9987] adding easyconfigs: torchvision-0.11.3-foss-2021a.eb --- .../torchvision-0.11.3-foss-2021a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a.eb new file mode 100644 index 00000000000..b5ec4705315 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a.eb @@ -0,0 +1,21 @@ +name = 'torchvision' +version = '0.11.3' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b4c51d27589783e6e6941ecaa67b55f6f41633874ec37f80b64a0c92c3196e0c'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('Pillow-SIMD', '8.2.0'), + ('PyTorch', '1.10.0'), +] + +moduleclass = 'vis' From c280f5e70c0775055b960b194fd593f64b6c6d04 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Fri, 4 Feb 2022 22:15:05 +0000 Subject: [PATCH 2979/9987] adding easyconfigs: NiBabel-3.2.1-foss-2021a.eb, pydicom-2.2.2-GCCcore-10.3.0.eb --- .../n/NiBabel/NiBabel-3.2.1-foss-2021a.eb | 47 +++++++++++++++++++ .../p/pydicom/pydicom-2.2.2-GCCcore-10.3.0.eb | 27 +++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-2.2.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2021a.eb new file mode 100644 index 00000000000..d1ab1ae9639 --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '3.2.1' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Pillow', '8.2.0'), + ('pydicom', '2.2.2'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['4d2ff9426b740011a1c916b54fc25da9348282e727eaa2ea163f42e00f1fc29e'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.2.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d9d87eb3ea3 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.2.2-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '2.2.2' + +homepage = 'https://pydicom.github.io/' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d827669486414b6b6688ecf4d220065e754fabc1b0d016329fced2da4192555d'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From f5f19d972ae03d5f0d5b77fecbae7963900c8ec8 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Fri, 4 Feb 2022 22:22:02 +0000 Subject: [PATCH 2980/9987] adding easyconfigs: JupyterLab-3.2.8-GCCcore-10.3.0.eb --- .../JupyterLab-3.2.8-GCCcore-10.3.0.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..44065e7ecf2 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '3.2.8' + +homepage = "https://jupyter.org/" +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('IPython', '7.25.0'), +] + +use_pip = True +sanity_pip_check = True + + +exts_list = [ + ('anyio', '3.5.0', { + 'checksums': ['a0aeffe2fb1fdf374a8e4b471444f0f3ac4fb9f5a5b542b48824475e0042a5a6'], + }), + ('json5', '0.9.6', { + 'checksums': ['9175ad1bc248e22bb8d95a8e8d765958bf0008fef2fe8abab5bc04e0f1ac8302'], + }), + ('jupyter_server', '1.13.4', { + 'checksums': ['5fb5a219385338b1d13a013a68f54688b6a69ecff4e757fd230e27ecacdbf212'], + }), + ('requests-unixsocket', '0.3.0', { + 'checksums': ['28304283ea9357d45fff58ad5b11e47708cfbf5806817aa59b2a363228ee971e'], + }), + ('sniffio', '1.2.0', { + 'checksums': ['c4666eecec1d3f50960c6bdf61ab7bc350648da6c126e3cf6898d8cd4ddcd3de'], + }), + ('websocket-client', '1.2.3', { + 'modulename': 'websocket', + 'checksums': ['1315816c0acc508997eb3ae03b9d3ff619c9d12d544c9a9b553704b1cc4f6af5'], + }), + ('nbclassic', '0.3.5', { + 'checksums': ['99444dd63103af23c788d9b5172992f12caf8c3098dd5a35c787f0df31490c29'], + }), + ('jupyterlab_server', '2.10.3', { + 'checksums': ['3fb84a5813d6d836ceda773fb2d4e9ef3c7944dbc1b45a8d59d98641a80de80a'], + }), + (name, version, { + 'patches': ['%(name)s-1.2.5_set-app-path-for-easybuild.patch'], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': [ + '5e4e99868c4f385372686767781408acbb9004b690b198b45597ba869802334b', # jupyterlab-3.2.8.tar.gz + # JupyterLab-1.2.5_set-app-path-for-easybuild.patch + 'a219b1071f37f848f7e79c6800149c0b2386a2b748be43288bc32af8e7dab668', + ], + }), +] + +sanity_check_commands = ["jupyter lab --help"] + +modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} + +moduleclass = 'tools' From c7fa19086c482cae46e3ad7b1125582d2596a7a0 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Fri, 4 Feb 2022 22:29:35 +0000 Subject: [PATCH 2981/9987] adding easyconfigs: SimpleITK-2.1.1-foss-2021a.eb, ITK-5.2.1-foss-2021a.eb, Lua-5.3.6-GCCcore-10.3.0.eb --- .../easyconfigs/i/ITK/ITK-5.2.1-foss-2021a.eb | 60 +++++++++++++++++++ .../l/Lua/Lua-5.3.6-GCCcore-10.3.0.eb | 28 +++++++++ .../s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb | 46 ++++++++++++++ 3 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.3.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021a.eb new file mode 100644 index 00000000000..97aef0a2358 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021a.eb @@ -0,0 +1,60 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.2.1' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6022b2b64624b8bcec3333fe48d5f74ff6ebceb3bdf98258ba7d7fbbc76b99ab'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Bison', '3.7.6'), + ('Eigen', '3.3.9'), +] + +dependencies = [ + ('expat', '2.2.9'), + ('HDF5', '1.12.1'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.2.0'), + ('VTK', '9.0.1'), + ('zlib', '1.2.11'), +] + +local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' +configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..a8c081e8005 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.3.6-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +name = 'Lua' +version = '5.3.6' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fc5fd69bb8736323f026672b1b7235da613d7177e72558893a0bdcd320466d60'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('libreadline', '8.1'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb new file mode 100644 index 00000000000..97f91f9e784 --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'SimpleITK' +version = '2.1.1' + +homepage = 'http://www.simpleitk.org' +description = """SimpleITK is a simplified programming interface to the algorithms and data structures of + the Insight Toolkit (ITK).""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +# v2.1.1 source was not available from PyPi on 2022-03-02 (only compiled packages) +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['9edc56b81a9f295081da2f6cafce4f7f5f3b4cfc6b8cb33365e68b581daea1d2'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Lua', '5.3.6'), + ('ITK', '5.2.1'), + ('scikit-build', '0.11.1'), +] + +configopts = "-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF " +configopts += "-DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF " + +postinstallcmds = [ + "cd %(builddir)s/easybuild_obj/Wrapping/Python && " + "pip install --ignore-installed --no-deps --prefix=%(installdir)s . ", +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], + 'dirs': ['include/%(name)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import %(name)s'"] + +moduleclass = 'tools' From 14507f5be1c68aa1ca595dcfcb3cb8ce1551323d Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Fri, 4 Feb 2022 22:44:47 +0000 Subject: [PATCH 2982/9987] remove Lua-5.3.6 dependency --- .../l/Lua/Lua-5.3.6-GCCcore-10.3.0.eb | 28 ------------------- .../s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb | 1 - 2 files changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.3.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.3.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.3.6-GCCcore-10.3.0.eb deleted file mode 100644 index a8c081e8005..00000000000 --- a/easybuild/easyconfigs/l/Lua/Lua-5.3.6-GCCcore-10.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -name = 'Lua' -version = '5.3.6' - -homepage = 'https://www.lua.org/' -description = """Lua is a powerful, fast, lightweight, embeddable scripting language. - Lua combines simple procedural syntax with powerful data description constructs based - on associative arrays and extensible semantics. Lua is dynamically typed, - runs by interpreting bytecode for a register-based virtual machine, - and has automatic memory management with incremental garbage collection, - making it ideal for configuration, scripting, and rapid prototyping.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.%(namelower)s.org/ftp/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['fc5fd69bb8736323f026672b1b7235da613d7177e72558893a0bdcd320466d60'] - -builddependencies = [ - ('binutils', '2.36.1'), -] - -dependencies = [ - ('ncurses', '6.2'), - ('libreadline', '8.1'), -] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb index 97f91f9e784..cebcab2f33a 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb @@ -21,7 +21,6 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), - ('Lua', '5.3.6'), ('ITK', '5.2.1'), ('scikit-build', '0.11.1'), ] From af41778fdb5116da413a484e317411282975debe Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Fri, 4 Feb 2022 22:45:19 +0000 Subject: [PATCH 2983/9987] adding easyconfigs: pyradiomics-3.0.1-foss-2021a.eb --- .../pyradiomics-3.0.1-foss-2021a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2021a.eb b/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2021a.eb new file mode 100644 index 00000000000..410c853423d --- /dev/null +++ b/easybuild/easyconfigs/p/pyradiomics/pyradiomics-3.0.1-foss-2021a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'pyradiomics' +version = '3.0.1' + +homepage = 'https://pyradiomics.readthedocs.io/' +description = """Open-source python package for the extraction of Radiomics features from 2D and 3D + images and binary masks.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy + ('SimpleITK', '2.1.1'), +] + +use_pip = True + +exts_list = [ + ('PyWavelets', '1.2.0', { + 'modulename': 'pywt', + 'checksums': ['6cbd69b047bb4e00873097472133425f5f08a4e6bc8b3f0ae709274d4d5e9a8d'], + }), + ('pykwalify', '1.8.0', { + 'checksums': ['796b2ad3ed4cb99b88308b533fb2f559c30fa6efb4fa9fda11347f483d245884'], + }), + ('ruamel.yaml.clib', '0.2.6', { + 'modulename': False, + 'checksums': ['4ff604ce439abb20794f05613c374759ce10e3595d1867764dd1ae675b85acbd'], + }), + ('ruamel.yaml', '0.17.20', { + 'checksums': ['4b8a33c1efb2b443a93fcaafcfa4d2e445f8e8c29c528d9f5cdafb7cc9e4004c'], + }), + (name, version, { + 'modulename': 'radiomics', + 'checksums': ['47c57f441d6cb7973fa3b2ea48d3948df78e3348e1c69e1e2ff19001601fc2f5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyradiomics'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyradiomics --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 9120b321121cdd1bcc3ea49d5b652538f869be78 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Fri, 4 Feb 2022 22:58:32 +0000 Subject: [PATCH 2984/9987] depend on HDF5-1.10.7 --- easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021a.eb index 97aef0a2358..0a4b96c2863 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021a.eb @@ -29,7 +29,7 @@ builddependencies = [ dependencies = [ ('expat', '2.2.9'), - ('HDF5', '1.12.1'), + ('HDF5', '1.10.7'), ('libjpeg-turbo', '2.0.6'), ('libpng', '1.6.37'), ('LibTIFF', '4.2.0'), From 5f8968d39cf2d15eae3889169036940ea224763e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 5 Feb 2022 00:59:59 +0100 Subject: [PATCH 2985/9987] add dep variant on HDF5 v1.10.x to HISAT2 --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f9b502eee0b..fc147ba7c24 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -439,8 +439,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # EMAN2 2.3 requires Boost(.Python) 1.64.0 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], - # ncbi-vdb v2.x require HDF5 v1.10.x - 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.'])], + # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2 depends on ncbi-vdb) + 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.'])], # VMTK 1.4.x requires ITK 4.13.x 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) From 04a19493b5c15434e9234760b3057c28924f025a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 5 Feb 2022 01:06:37 +0100 Subject: [PATCH 2986/9987] remove unused comment from PyEVTK v1.4.1 --- easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb index 1b2647dc6fe..967ee30457e 100644 --- a/easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PyEVTK/PyEVTK-1.4.1-foss-2021b.eb @@ -21,9 +21,6 @@ dependencies = [ download_dep_fail = True use_pip = True -# for some reason this is required to avoid 'pip install' failing with "ModuleNotFoundError: No module named 'evtk'" -# preinstallopts = "PYTHONPATH=$PWD " - sanity_pip_check = True options = {'modulename': 'evtk'} From 86f356f2af3c9d29ecb8855ed0303395ead4f3ce Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 5 Feb 2022 01:18:32 +0100 Subject: [PATCH 2987/9987] add library and headers to sanity checks of tabix-0.2.6-GCCcore-11.2.0.eb --- easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb index 51f12ffde97..3ab83eb29a2 100644 --- a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-11.2.0.eb @@ -40,8 +40,8 @@ files_to_copy = [ ] sanity_check_paths = { - 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], - 'dirs': [""], + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py", "lib/libtabix.a"], + 'dirs': ["include"], } moduleclass = 'bio' From 4b95640bce3f31884832a4f399ab24a092d2bf6c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 5 Feb 2022 01:39:35 +0100 Subject: [PATCH 2988/9987] make sanity checks arch agnostic in Valgrind-3.18.1-gompi-2021b.eb --- .../easyconfigs/v/Valgrind/Valgrind-3.18.1-gompi-2021b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-gompi-2021b.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-gompi-2021b.eb index 18aac1c35e2..16256103c1f 100644 --- a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-gompi-2021b.eb +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-gompi-2021b.eb @@ -7,6 +7,7 @@ homepage = 'https://valgrind.org' description = "Valgrind: Debugging and profiling tools" toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'optarch': True} source_urls = [ 'https://sourceware.org/pub/valgrind/', @@ -21,10 +22,11 @@ local_binaries = [ 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' ] +local_archs = ('amd64', 'arm64', 'ppc64le') sanity_check_paths = { 'files': ['bin/%s' % x for x in local_binaries] + - ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + [['lib/valgrind/libmpiwrap-%s-linux.%s' % (a, SHLIB_EXT) for a in local_archs]], 'dirs': [] } From 1ea4f7a604c87b3cdd5f03d32500a686d2937800 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 5 Feb 2022 01:40:39 +0100 Subject: [PATCH 2989/9987] make sanity checks arch agnostic in Valgrind-3.18.1-iimpi-2021b.eb --- .../easyconfigs/v/Valgrind/Valgrind-3.18.1-iimpi-2021b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-iimpi-2021b.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-iimpi-2021b.eb index 6d3cac194b5..a2745e47ff2 100644 --- a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-iimpi-2021b.eb +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.18.1-iimpi-2021b.eb @@ -7,6 +7,7 @@ homepage = 'https://valgrind.org' description = "Valgrind: Debugging and profiling tools" toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'optarch': True} source_urls = [ 'https://sourceware.org/pub/valgrind/', @@ -22,10 +23,11 @@ local_binaries = [ 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' ] +local_archs = ('amd64', 'arm64', 'ppc64le') sanity_check_paths = { 'files': ['bin/%s' % x for x in local_binaries] + - ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + [['lib/valgrind/libmpiwrap-%s-linux.%s' % (a, SHLIB_EXT) for a in local_archs]], 'dirs': [] } From 482b201b48841dfe88038058dc2158daba0f63cb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 5 Feb 2022 02:48:58 +0100 Subject: [PATCH 2990/9987] add comment about eccodes-python to ecCodes v2.24.2 --- easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-iimpi-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-iimpi-2021b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-iimpi-2021b.eb index db069a3f7e5..618f16c9903 100644 --- a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-iimpi-2021b.eb +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-iimpi-2021b.eb @@ -25,6 +25,7 @@ dependencies = [ ('zlib', '1.2.11'), ] +# Python bindings are provided by a separate package 'eccodes-python' configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF " configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " configopts += "-DENABLE_ECCODES_THREADS=ON" # multi-threading with pthreads From ffbf3eb77535435503e07596dd21b70d0178f9b9 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 5 Feb 2022 09:08:16 +0000 Subject: [PATCH 2991/9987] Remove CUDA dependency --- easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2021a.eb index d1ab1ae9639..dd698a3e46c 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.1-foss-2021a.eb @@ -12,7 +12,6 @@ description = """NiBabel provides read/write access to some common medical and n toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('Pillow', '8.2.0'), From 9fc70eb7d0aa4e3cc8b6f881db9da47a3bae8626 Mon Sep 17 00:00:00 2001 From: rungitta Date: Sat, 5 Feb 2022 10:37:58 +0100 Subject: [PATCH 2992/9987] Update easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb index deaf598904b..7b16c26a04a 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb @@ -6,7 +6,7 @@ version = '1.9.10' homepage = 'https://code.zmaw.de/projects/cdo' description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" -toolchain = {'name': 'intel', 'version': '2021b'} +toolchain = {'name': 'iimpi', 'version': '2021b'} # stick to lowopt (-O1) to avoid internal compiler error when building on Intel Skylake toolchainopts = {'pic': True, 'usempi': True, 'lowopt': True} From 346028df2cb6981ade0052f06313cdefa947106a Mon Sep 17 00:00:00 2001 From: rungitta Date: Sat, 5 Feb 2022 10:42:53 +0100 Subject: [PATCH 2993/9987] Rename CDO-1.9.10-intel-2021b.eb to CDO-1.9.10-iimpi-2021b.eb --- .../CDO/{CDO-1.9.10-intel-2021b.eb => CDO-1.9.10-iimpi-2021b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/CDO/{CDO-1.9.10-intel-2021b.eb => CDO-1.9.10-iimpi-2021b.eb} (100%) diff --git a/easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb b/easybuild/easyconfigs/c/CDO/CDO-1.9.10-iimpi-2021b.eb similarity index 100% rename from easybuild/easyconfigs/c/CDO/CDO-1.9.10-intel-2021b.eb rename to easybuild/easyconfigs/c/CDO/CDO-1.9.10-iimpi-2021b.eb From 8d3c5c8bfc1b634e1b22724e10aabf7ad0fb521a Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Sat, 5 Feb 2022 11:08:20 +0100 Subject: [PATCH 2994/9987] clearer way to force right rsb.h usage Workaround around ./configure and ./librsbpp/configure defects. Thanks to Alex Domingo for mentoring on the specifics of easybuild. --- .../easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb index 3596f82d241..cf1234b9e31 100644 --- a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb @@ -19,8 +19,13 @@ dependencies = [ ('zlib', '1.2.11') ] +# workaround to a configure defect manifesting during --rebuild: avoid mistaken detection of already existing librsb installation preconfigopts = "sed -i 's/export LIBRSB_CONFIG=.*$/export LIBRSB_CONFIG=no LIBRSB_CONFIG_VERSION=1.3.0;/g' configure*;" -preconfigopts += " sed -i 's/^ true/CPPFLAGS+=\" -I.. -DRSBPP_HAS_RSB_H=1\"/g' librsbpp/configure*;" + +# workaround to a configure defect manifesting during --rebuild: ensure librsbpp/configure sees and uses root dir rsb.h +local_cppflags = 'CPPFLAGS="${CPPFLAGS} -I%(builddir)s"' +prebuildopts = local_cppflags +preinstallopts = local_cppflags configopts = '--enable-openmp --enable-fortran-module-install' From 4052e4c93a11a298c79a6db79148c792aa966aaf Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 5 Feb 2022 13:36:17 +0000 Subject: [PATCH 2995/9987] adding easyconfigs: MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb, MONAI-0.8.0-foss-2021a.eb --- .../MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb | 46 +++++++++++++++++++ .../m/MONAI/MONAI-0.8.0-foss-2021a.eb | 45 ++++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..2e408742891 --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'MONAI' +version = '0.8.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'Project-MONAI' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479'] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('PyTorch', '1.10.0', versionsuffix), + ('ITK', '5.2.1'), + ('NiBabel', '3.2.1'), + ('scikit-image', '0.18.3'), + ('tensorboard', '2.8.0'), + ('torchvision', '0.11.1', versionsuffix), + ('tqdm', '4.61.2'), +] + +use_pip = True +download_dep_fail = True + +preinstallopts = 'BUILD_MONAI=1' + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/%(namelower)s/_C.so'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb new file mode 100644 index 00000000000..7a2477f2af6 --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonPackage' + +name = 'MONAI' +version = '0.8.0' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'Project-MONAI' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479'] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('PyTorch', '1.10.0'), + ('ITK', '5.2.1'), + ('NiBabel', '3.2.1'), + ('scikit-image', '0.18.3'), + ('tensorboard', '2.8.0'), + ('torchvision', '0.11.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True +download_dep_fail = True + +preinstallopts = 'BUILD_MONAI=1' + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/%(namelower)s/_C.so'], + 'dirs': [''], +} + +moduleclass = 'vis' From a43c704fa11cc51ff90c48305bdac8975ac7e3b5 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 5 Feb 2022 14:21:38 +0000 Subject: [PATCH 2996/9987] adding easyconfigs: rising-0.2.2-foss-2021a-CUDA-11.3.1.eb, rising-0.2.2-foss-2021a.eb --- .../rising-0.2.2-foss-2021a-CUDA-11.3.1.eb | 43 +++++++++++++++++++ .../r/rising/rising-0.2.2-foss-2021a.eb | 41 ++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ddb97b5b555 --- /dev/null +++ b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'rising' +version = '0.2.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://rising.rtfd.io/' +description = "Provides everything needed for high performance data loading and augmentation in PyTorch." + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'PhoenixDL' + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # provides numpy + ('PyTorch', '1.10.0', versionsuffix), + ('tqdm', '4.61.2'), +] + +use_pip = True +download_dep_fail = True + +exts_list = [ + ('threadpoolctl', '3.1.0', { + 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], + }), + (name, version, { + # Archive on PyPi is incomplete as of 2022-02-05 + 'source_urls': [GITHUB_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a.eb b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a.eb new file mode 100644 index 00000000000..1bdd118a113 --- /dev/null +++ b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'rising' +version = '0.2.2' + +homepage = 'https://rising.rtfd.io/' +description = "Provides everything needed for high performance data loading and augmentation in PyTorch." + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'PhoenixDL' + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # provides numpy + ('PyTorch', '1.10.0'), + ('tqdm', '4.61.2'), +] + +use_pip = True +download_dep_fail = True + +exts_list = [ + ('threadpoolctl', '3.1.0', { + 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], + }), + (name, version, { + # Archive on PyPi is incomplete as of 2022-02-05 + 'source_urls': [GITHUB_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From af13a5b4766d7b7807acef2dc4c9fa120e2cf296 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 5 Feb 2022 14:39:00 +0000 Subject: [PATCH 2997/9987] Add checksum and fix formatting --- .../r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb | 8 ++++---- easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a.eb | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb index ddb97b5b555..6680caa1442 100644 --- a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb @@ -9,27 +9,27 @@ description = "Provides everything needed for high performance data loading and toolchain = {'name': 'foss', 'version': '2021a'} +# rising archive on PyPi is incomplete as of 2022-02-05 github_account = 'PhoenixDL' dependencies = [ ('CUDA', '11.3.1', '', True), ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), # provides numpy + ('SciPy-bundle', '2021.05'), # provides numpy ('PyTorch', '1.10.0', versionsuffix), ('tqdm', '4.61.2'), ] use_pip = True -download_dep_fail = True exts_list = [ ('threadpoolctl', '3.1.0', { 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], }), (name, version, { - # Archive on PyPi is incomplete as of 2022-02-05 - 'source_urls': [GITHUB_SOURCE], + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5294b3f9b183b4efe7e4bafb4b42caa19aa4db737e7379e8356cc575fce57662'], }), ] diff --git a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a.eb b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a.eb index 1bdd118a113..d13d6bbaafe 100644 --- a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a.eb +++ b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a.eb @@ -8,26 +8,26 @@ description = "Provides everything needed for high performance data loading and toolchain = {'name': 'foss', 'version': '2021a'} +# rising archive on PyPi is incomplete as of 2022-02-05 github_account = 'PhoenixDL' dependencies = [ ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), # provides numpy + ('SciPy-bundle', '2021.05'), # provides numpy ('PyTorch', '1.10.0'), ('tqdm', '4.61.2'), ] use_pip = True -download_dep_fail = True exts_list = [ ('threadpoolctl', '3.1.0', { 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], }), (name, version, { - # Archive on PyPi is incomplete as of 2022-02-05 - 'source_urls': [GITHUB_SOURCE], + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5294b3f9b183b4efe7e4bafb4b42caa19aa4db737e7379e8356cc575fce57662'], }), ] From ef33927c7517aab918afb0c5ee304dbc4fa49237 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 5 Feb 2022 15:42:33 +0000 Subject: [PATCH 2998/9987] adding easyconfigs: deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb, deepmedic-0.8.2-foss-2021a.eb --- .../deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb | 40 +++++++++++++++++++ .../d/deepmedic/deepmedic-0.8.2-foss-2021a.eb | 38 ++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..3e402399059 --- /dev/null +++ b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'deepmedic' +version = '0.8.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://biomedia.doc.ic.ac.uk/software/deepmedic/' +description = "Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('TensorFlow', '2.6.0', versionsuffix), + ('SciPy-bundle', '2021.05'), + ('NiBabel', '3.2.1'), +] + +use_pip = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + (name, version, { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['0f6bcd349eeee919e0be7eab86569e1951ab9eb110ee272e8325abc94c928c0f'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb new file mode 100644 index 00000000000..c613f2cca70 --- /dev/null +++ b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'deepmedic' +version = '0.8.2' + +homepage = 'https://biomedia.doc.ic.ac.uk/software/deepmedic/' +description = "Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('TensorFlow', '2.6.0'), + ('SciPy-bundle', '2021.05'), + ('NiBabel', '3.2.1'), +] + +use_pip = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + (name, version, { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['0f6bcd349eeee919e0be7eab86569e1951ab9eb110ee272e8325abc94c928c0f'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'data' From 4ea0f0123960bc0290c939280e96a9b1e89fb7e8 Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Sat, 5 Feb 2022 17:00:38 +0100 Subject: [PATCH 2999/9987] Update easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb Do not rely on `librsb-config --I_opts`, it will inject paths in install dir (suggested by Alex Domingo) Co-authored-by: Alex Domingo --- .../l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb index cf1234b9e31..41f09407b0c 100644 --- a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.0-GCC-10.2.0.eb @@ -15,17 +15,17 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['2ac8725d1f988f57df9383ae6b0bb2ed221ec935187d31ebb62ea95ee868a790'] +builddependencies = [ + ('Autotools', '20200321'), +] + dependencies = [ ('zlib', '1.2.11') ] -# workaround to a configure defect manifesting during --rebuild: avoid mistaken detection of already existing librsb installation -preconfigopts = "sed -i 's/export LIBRSB_CONFIG=.*$/export LIBRSB_CONFIG=no LIBRSB_CONFIG_VERSION=1.3.0;/g' configure*;" - -# workaround to a configure defect manifesting during --rebuild: ensure librsbpp/configure sees and uses root dir rsb.h -local_cppflags = 'CPPFLAGS="${CPPFLAGS} -I%(builddir)s"' -prebuildopts = local_cppflags -preinstallopts = local_cppflags +# do not rely on `librsb-config --I_opts`, it will inject paths in install dir +preconfigopts = "sed -i '21,22d' librsbpp/configure.ac && " +preconfigopts += "autoreconf -fi &&" configopts = '--enable-openmp --enable-fortran-module-install' From 815b57c6b6a7764e678e3353efa83f2cfcb0bed7 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 5 Feb 2022 16:05:19 +0000 Subject: [PATCH 3000/9987] Add files sanity check and fix whitespace --- .../d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb | 4 ++-- .../easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb index 3e402399059..cba3bce8ada 100644 --- a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb @@ -14,7 +14,7 @@ dependencies = [ ('Python', '3.9.5'), ('TensorFlow', '2.6.0', versionsuffix), ('SciPy-bundle', '2021.05'), - ('NiBabel', '3.2.1'), + ('NiBabel', '3.2.1'), ] use_pip = True @@ -31,7 +31,7 @@ exts_list = [ ] sanity_check_paths = { - 'files': [], + 'files': ['bin/deepMedicRun'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } diff --git a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb index c613f2cca70..fc393647eeb 100644 --- a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb +++ b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb @@ -12,7 +12,7 @@ dependencies = [ ('Python', '3.9.5'), ('TensorFlow', '2.6.0'), ('SciPy-bundle', '2021.05'), - ('NiBabel', '3.2.1'), + ('NiBabel', '3.2.1'), ] use_pip = True @@ -29,7 +29,7 @@ exts_list = [ ] sanity_check_paths = { - 'files': [], + 'files': ['bin/deepMedicRun'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From be3f80383269dc069ece404de51cea4542e4b643 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 5 Feb 2022 16:17:30 +0000 Subject: [PATCH 3001/9987] Fix download URL --- .../easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-10.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-10.3.0.eb index 2b44e28db6d..2977e52d884 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-10.3.0.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} source_urls = [ - 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/', + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/%(version)s/', 'https://sources.easybuild.io/u/UDUNITS/', ] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.2.0.eb index 67c01b52a1d..ac80ef50517 100644 --- a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.2.0.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} source_urls = [ - 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/', + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/%(version)s/', 'https://sources.easybuild.io/u/UDUNITS/', ] sources = [SOURCELOWER_TAR_GZ] From a9846808b9923f42532975a9323b257b808215fe Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 5 Feb 2022 20:51:40 +0000 Subject: [PATCH 3002/9987] Allow Lua 5.4 for code generation during the configuration --- ....1.1-allow-lua54-for-code-generation.patch | 33 +++++++++++++++++++ .../s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb | 11 +++++-- 2 files changed, 41 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-allow-lua54-for-code-generation.patch diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-allow-lua54-for-code-generation.patch b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-allow-lua54-for-code-generation.patch new file mode 100644 index 00000000000..5ac695698a6 --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-allow-lua54-for-code-generation.patch @@ -0,0 +1,33 @@ +SimpleITK v2.1.1 requires Lua 5.3, which is not available in the easybuild foss/2021a toolchain. + +This patch allows the code generation during the configuration step to use Lua 5.4. +(Lua wrapping has been disabled in the existing SimpleITK easyconfigs, anyway.) + +Author: https://github.com/crubb + +diff -ur SimpleITK-2.1.1/CMake/sitkGenerateFilterSource.cmake SimpleITK-2.1.1-Lua54/CMake/sitkGenerateFilterSource.cmake +--- SimpleITK-2.1.1/CMake/sitkGenerateFilterSource.cmake 2021-09-09 20:30:08.000000000 +0000 ++++ SimpleITK-2.1.1-Lua54/CMake/sitkGenerateFilterSource.cmake 2022-02-05 20:01:47.594257463 +0000 +@@ -7,7 +7,7 @@ + get_property( SAVE_LUA_EXECUTABLE_DOCSTRING CACHE LUA_EXECUTABLE PROPERTY HELPSTRING ) + unset(LUA_EXECUTABLE CACHE) + +- find_package( LuaInterp 5.3 REQUIRED ) ++ find_package( LuaInterp 5.4 REQUIRED ) + set( SimpleITK_LUA_EXECUTABLE ${LUA_EXECUTABLE} CACHE PATH "Lua executable used for code generation." ) + + if (DEFINED SAVE_LUA_EXECUTABLE) +@@ -46,10 +46,10 @@ + + if( SITK_LUA_VERSION_RESULT_VARIABLE + OR +- NOT ${SimpleITK_LUA_EXECUTABLE_VERSION} VERSION_GREATER "5.2" ++ NOT ${SimpleITK_LUA_EXECUTABLE_VERSION} VERSION_GREATER "5.3" + OR +- NOT ${SimpleITK_LUA_EXECUTABLE_VERSION} VERSION_LESS "5.4" ) +- message(SEND_ERROR "Lua version 5.3 is required for SimpleITK_LUA_EXECUTABLE_VERSION.") ++ NOT ${SimpleITK_LUA_EXECUTABLE_VERSION} VERSION_LESS "5.5" ) ++ message(SEND_ERROR "Lua version 5.4 is required for SimpleITK_LUA_EXECUTABLE_VERSION.") + endif() + + # Sets "out_var" variable name to the value in the json path specified diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb index cebcab2f33a..ad058066d02 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1-foss-2021a.eb @@ -12,11 +12,17 @@ toolchain = {'name': 'foss', 'version': '2021a'} # v2.1.1 source was not available from PyPi on 2022-03-02 (only compiled packages) source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/v%(version)s/'] sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['9edc56b81a9f295081da2f6cafce4f7f5f3b4cfc6b8cb33365e68b581daea1d2'] +patches = ['%(name)s-%(version)s-allow-lua54-for-code-generation.patch'] +checksums = [ + '9edc56b81a9f295081da2f6cafce4f7f5f3b4cfc6b8cb33365e68b581daea1d2', # SimpleITK-2.1.1.tar.gz + # SimpleITK-2.1.1-allow-lua54-for-code-generation.patch + '7ae36fc1a725300f86890b81fa121c0fa2cb1b5628475d962f66cdd4722364ab', +] builddependencies = [ ('CMake', '3.20.1'), ('SWIG', '4.0.2'), + ('Lua', '5.4.3'), ] dependencies = [ @@ -25,8 +31,7 @@ dependencies = [ ('scikit-build', '0.11.1'), ] -configopts = "-DWRAP_PYTHON=ON -DWRAP_LUA=OFF -DWRAP_RUBY=OFF " -configopts += "-DWRAP_TCL=OFF -DWRAP_JAVA=OFF -DWRAP_R=OFF -DWRAP_CSHARP=OFF " +configopts = "-DWRAP_DEFAULT:BOOL=OFF -DWRAP_PYTHON=BOOL:ON " postinstallcmds = [ "cd %(builddir)s/easybuild_obj/Wrapping/Python && " From 36c79127a5ff818669aaf6da34f4c626431b40b4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 5 Feb 2022 23:55:09 +0100 Subject: [PATCH 3003/9987] move YAXT v0.9.2 from intel/2021b to iimpi/2021b --- .../{YAXT-0.9.2-intel-2021b.eb => YAXT-0.9.2-iimpi-2021b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/y/YAXT/{YAXT-0.9.2-intel-2021b.eb => YAXT-0.9.2-iimpi-2021b.eb} (92%) diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb similarity index 92% rename from easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb rename to easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb index 20b90901519..4c68128c3c2 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-intel-2021b.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb @@ -6,7 +6,7 @@ version = '0.9.2' homepage = 'https://www.dkrz.de/redmine/projects/yaxt' description = "Yet Another eXchange Tool" -toolchain = {'name': 'intel', 'version': '2021b'} +toolchain = {'name': 'iimpi', 'version': '2021b'} toolchainopts = {'usempi': True} source_urls = ['https://www.dkrz.de/redmine/attachments/download/513/'] From f1baa2c42cda947071b10afa9a5dad7b6e962dda Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 6 Feb 2022 01:15:01 +0200 Subject: [PATCH 3004/9987] adding easyconfigs: GLFW-3.3.4-GCCcore-11.2.0.eb --- .../g/GLFW/GLFW-3.3.4-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLFW/GLFW-3.3.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GLFW/GLFW-3.3.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GLFW/GLFW-3.3.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ec19911769d --- /dev/null +++ b/easybuild/easyconfigs/g/GLFW/GLFW-3.3.4-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'GLFW' +version = '3.3.4' + +homepage = 'https://www.glfw.org' +description = """GLFW is an Open Source, multi-platform library for OpenGL, +OpenGL ES and Vulkan development on the desktop""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['cc8ac1d024a0de5fd6f68c4133af77e1918261396319c24fd697775a6bc93b63'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210802'), +] + +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +sanity_check_paths = { + 'files': ['include/GLFW/glfw3.h', 'include/GLFW/glfw3native.h', + 'lib/libglfw3.a', 'lib/libglfw.%s' % SHLIB_EXT, 'lib/pkgconfig/glfw3.pc'], + 'dirs': ['include/GLFW', 'lib/cmake/glfw3', 'lib/pkgconfig'], +} + +moduleclass = 'vis' From d37cf4f148824b99c7403673da6f280e4fc1e4d6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 6 Feb 2022 01:16:07 +0200 Subject: [PATCH 3005/9987] add build dependency on binutils to MuJoCo v2.1.1 --- .../easyconfigs/m/MuJoCo/MuJoCo-2.1.1-GCCcore-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.1.1-GCCcore-11.2.0.eb index bd16b561c41..f6cdc551706 100644 --- a/easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.1.1-GCCcore-11.2.0.eb @@ -25,6 +25,10 @@ checksums = [ } ] +builddependencies = [ + ('binutils', '2.37'), +] + # MuJoCo bundles 3 variants of glew using non-standard sonames: # - libglew with GLX # - libglewegl with EGL @@ -38,6 +42,7 @@ dependencies = [ ] postinstallcmds = [ + # replace bundled libglewosmesa.so with glew libs from EB "ln -sf $EBROOTGLEW/lib64/libGLEW.so %(installdir)s/lib/libglewosmesa.so", ] From 19d05fba22dec6e06662552a8876ab7f23fa1261 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sun, 6 Feb 2022 16:11:42 +0000 Subject: [PATCH 3006/9987] adding easyconfigs: nvtop-1.2.2-GCCcore-10.2.0.eb, nvtop-1.2.2-GCCcore-10.3.0.eb --- .../n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ .../n/nvtop/nvtop-1.2.2-GCCcore-10.3.0.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c0476961321 --- /dev/null +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'nvtop' +version = '1.2.2' + +homepage = 'https://github.com/Syllo/nvtop' +description = 'htop-like GPU usage monitor' + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/Syllo/nvtop/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d6ca7f467cc1048ebd1ebf7add753650c5d7c8868752c0c57ed2c85df62f5810'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +# Note: software dlopen's libraries from the OS installed drivers, thus no specific CUDA dependency. +dependencies = [ + ('ncurses', '6.2'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/nvtop'], + 'dirs': [], +} + +sanity_check_commands = ["nvtop --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8f8b137768b --- /dev/null +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.2-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'nvtop' +version = '1.2.2' + +homepage = 'https://github.com/Syllo/nvtop' +description = 'htop-like GPU usage monitor' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/Syllo/nvtop/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d6ca7f467cc1048ebd1ebf7add753650c5d7c8868752c0c57ed2c85df62f5810'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +# Note: software dlopen's libraries from the OS installed drivers, thus no specific CUDA dependency. +dependencies = [ + ('ncurses', '6.2'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/nvtop'], + 'dirs': [], +} + +sanity_check_commands = ["nvtop --help"] + +moduleclass = 'tools' From 6f4b4da97db5f3aea70a83b3eab76f794897bdf3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 6 Feb 2022 21:12:52 +0100 Subject: [PATCH 3007/9987] add custom sanity check command for Arcade-Learning-Environment --- .../Arcade-Learning-Environment-0.7.3-foss-2021b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.7.3-foss-2021b.eb b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.7.3-foss-2021b.eb index 2cf5581c2dc..55e08c3c198 100644 --- a/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.7.3-foss-2021b.eb +++ b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.7.3-foss-2021b.eb @@ -52,6 +52,8 @@ sanity_check_paths = { 'dirs': ['include/ale', 'lib/python%(pyshortver)s/site-packages/'], } +sanity_check_commands = ["ale-import-roms --help"] + modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} moduleclass = 'tools' From 493e15062156f392ec3ab250697b7876097106d1 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Mon, 7 Feb 2022 09:14:53 +0100 Subject: [PATCH 3008/9987] add Python build dependency --- .../m/MethylDackel/MethylDackel-0.6.1-GCC-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/m/MethylDackel/MethylDackel-0.6.1-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MethylDackel/MethylDackel-0.6.1-GCC-11.2.0.eb index 1f3fe9f689c..61b1b210fbf 100644 --- a/easybuild/easyconfigs/m/MethylDackel/MethylDackel-0.6.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MethylDackel/MethylDackel-0.6.1-GCC-11.2.0.eb @@ -30,6 +30,11 @@ runtest = 'test' installopts = "prefix=%(installdir)s" modextrapaths = {'PATH': ''} +builddependencies = { + # Python is required for testing + ('Python', '3.9.6'), +} + dependencies = [ ('HTSlib', '1.14'), ('libBigWig', '0.4.6'), From 8f939fde384277df223e630d754c043aec285485 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 7 Feb 2022 11:10:05 +0100 Subject: [PATCH 3009/9987] use GCCcore for libdeflate easyconfig --- ...flate-1.7-GCC-10.3.0.eb => libdeflate-1.7-GCCcore-10.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/libdeflate/{libdeflate-1.7-GCC-10.3.0.eb => libdeflate-1.7-GCCcore-10.3.0.eb} (94%) diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCCcore-10.3.0.eb similarity index 94% rename from easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCC-10.3.0.eb rename to easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCCcore-10.3.0.eb index f57caa79f6c..0e2c871de73 100644 --- a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.7-GCCcore-10.3.0.eb @@ -9,7 +9,7 @@ version = '1.7' homepage = 'https://github.com/ebiggers/libdeflate' description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} github_account = 'ebiggers' source_urls = [GITHUB_SOURCE] From b5409df3b7fd328b72c1857eb74723d11a62605d Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Mon, 7 Feb 2022 10:49:46 +0000 Subject: [PATCH 3010/9987] add gettext build dependency for autopoint --- easybuild/easyconfigs/l/libexif/libexif-0.6.24-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libexif/libexif-0.6.24-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libexif/libexif-0.6.24-GCCcore-11.2.0.eb index 27cc576130b..cfb092bf161 100644 --- a/easybuild/easyconfigs/l/libexif/libexif-0.6.24-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libexif/libexif-0.6.24-GCCcore-11.2.0.eb @@ -17,6 +17,7 @@ checksums = ['e5f15eeab693028cfdc4c0d78f024e1ca78baa0e1f636dc443395e9fbb0a2b7a'] builddependencies = [ ('Autotools', '20210726'), ('binutils', '2.37'), + ('gettext', '0.21'), ('pkg-config', '0.29.2'), ] From c38fea75384bf6cb9a398f680948b8df314197a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Feb 2022 16:49:43 +0100 Subject: [PATCH 3011/9987] adding easyconfigs: Nextflow-21.10.6.eb --- .../n/Nextflow/Nextflow-21.10.6.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb new file mode 100644 index 00000000000..ed4ceee4b28 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb @@ -0,0 +1,37 @@ +easyblock = 'CmdCp' + +name = 'Nextflow' +version = '21.10.6' + +homepage = 'https://www.nextflow.io' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91b108cba321cb5500e2e811c446b04aee152dc2f97cb2cf4ae00eeecd4f332f'] + +# specify dependency on Java/13 "wrapper", rather than a specific Java version +dependencies = [('Java', '13', '', True)] + +skipsteps = ['configure', 'build'] + +_exe_files = ['nextflow', 'gradlew'] + +files_to_copy = [ + (_exe_files, '%(installdir)s/bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' From 0513665876ccc07abe2594393d7164f63152ab37 Mon Sep 17 00:00:00 2001 From: Keith Refson Date: Mon, 7 Feb 2022 17:07:44 +0000 Subject: [PATCH 3012/9987] Added dependencies and library search paths for FFTW and Openblas to CASTEP foss configuration --- .../easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb | 4 ++++ .../easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb | 4 ++++ easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb | 7 ++++++- .../easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb | 4 ++++ .../easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb | 4 ++++ 5 files changed, 22 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb index b76958923a7..9f8c340cbe9 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb @@ -15,6 +15,10 @@ sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] +builddependencies = [ + ('Perl', '5.30.0'), +] + dependencies = [('cray-fftw', EXTERNAL_MODULE)] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb index 6e4ce1d8eb7..1e3ed94001b 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb @@ -15,6 +15,10 @@ sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] +builddependencies = [ + ('Perl', '5.30.0'), +] + dependencies = [('cray-fftw', EXTERNAL_MODULE)] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb index 3ff4a50a282..dcd7653594d 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb @@ -16,9 +16,14 @@ sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] +dependencies = [ + ('Perl', '5.30.0'), +] + skipsteps = ['configure'] -buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas FFTLIBDIR= MATHLIBDIR= castep tools utilities' +buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas FFTLIBDIR=$FFT_LIB_DIR MATHLIBDIR=$BLAS_LIB_DIR' +buildopts += ' castep tools utilities' preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb index 29edac436a4..af79163117e 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb @@ -16,6 +16,10 @@ sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] +dependencies = [ + ('Perl', '5.30.0'), +] + skipsteps = ['configure'] buildopts = 'COMMS_ARCH=mpi castep tools utilities' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb index 86c65234f30..322d15ab247 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb @@ -16,6 +16,10 @@ sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] +dependencies = [ + ('Perl', '5.30.0'), +] + skipsteps = ['configure'] buildopts = 'COMMS_ARCH=mpi castep tools utilities' From ad43c76b15ae78e9e0c2be368caaac9a4994d670 Mon Sep 17 00:00:00 2001 From: Keith Refson Date: Mon, 7 Feb 2022 17:11:33 +0000 Subject: [PATCH 3013/9987] Fixed trailing whitespace issue --- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb index dcd7653594d..e26c9f65422 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb @@ -22,7 +22,7 @@ dependencies = [ skipsteps = ['configure'] -buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas FFTLIBDIR=$FFT_LIB_DIR MATHLIBDIR=$BLAS_LIB_DIR' +buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas FFTLIBDIR=$FFT_LIB_DIR MATHLIBDIR=$BLAS_LIB_DIR' buildopts += ' castep tools utilities' preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' From e037c33d02a1a25046d88fc1b179e2db374ed866 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Mon, 7 Feb 2022 17:36:44 +0000 Subject: [PATCH 3014/9987] Remove CUDA dependency --- easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb index d8de7f18054..5d464d98c13 100644 --- a/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/nvtop/nvtop-1.2.1-GCCcore-10.2.0.eb @@ -17,15 +17,13 @@ builddependencies = [ ('CMake', '3.18.4'), ] +# Note: software dlopen's libraries from the OS installed drivers, thus no specific CUDA dependency. dependencies = [ - ('CUDAcore', '11.1.1', '', True), ('ncurses', '6.2'), ] separate_build_dir = True -configopts = '-DNVML_INCLUDE_DIRS=$EBROOTCUDA/include -DNVML_LIBRARIES=$EBROOTCUDA/lib64/stubs/libnvidia-ml.so' - sanity_check_paths = { 'files': ['bin/nvtop'], 'dirs': [], From 1efb93f9149755f4bb8adb9414ad7fafd2abdeb8 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Mon, 7 Feb 2022 17:40:43 +0000 Subject: [PATCH 3015/9987] Addy sanity check cmd --- .../d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb | 2 ++ easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb index cba3bce8ada..c9fb8927779 100644 --- a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb @@ -35,6 +35,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ['deepMedicRun -h'] + sanity_pip_check = True moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb index fc393647eeb..820b9a8a961 100644 --- a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb +++ b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a.eb @@ -33,6 +33,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ['deepMedicRun -h'] + sanity_pip_check = True moduleclass = 'data' From bff3733202aaddf06ba91137f4725fca6790fb64 Mon Sep 17 00:00:00 2001 From: Keith Refson Date: Mon, 7 Feb 2022 18:33:48 +0000 Subject: [PATCH 3016/9987] Removed unsatisfiable Perl dependencies from CASTEP-*Cray*.eb --- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb | 4 ---- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb | 4 ---- 2 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb index 9f8c340cbe9..b76958923a7 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb @@ -15,10 +15,6 @@ sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] -builddependencies = [ - ('Perl', '5.30.0'), -] - dependencies = [('cray-fftw', EXTERNAL_MODULE)] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb index 1e3ed94001b..6e4ce1d8eb7 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb @@ -15,10 +15,6 @@ sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] -builddependencies = [ - ('Perl', '5.30.0'), -] - dependencies = [('cray-fftw', EXTERNAL_MODULE)] skipsteps = ['configure'] From e99b5e21bdc70bcdf8d9660d61fe17b92ee8d0d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Feb 2022 21:10:56 +0100 Subject: [PATCH 3017/9987] add sanity check command for seqtk --- easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.3.0.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.3.0.eb index 847bb921d75..5f36a7aded8 100644 --- a/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-10.3.0.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["seqtk 2>&1 | grep 'Usage:[ ]*seqtk'"] + moduleclass = 'bio' From 63519f273f08d8a4d5234e9042e0aec2b325991a Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Mon, 7 Feb 2022 20:30:51 +0000 Subject: [PATCH 3018/9987] Create Pysam-0.18.0-GCC-11.2.0.eb Update for Pysam 0.18.0. --- .../p/Pysam/Pysam-0.18.0-GCC-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..1ce324df851 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.18.0' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['db1ddf41639e4dbb3f94cc9afb14e879bff15690de5b713dec3a81e43f6fa131'] + +dependencies = [ + ('Python', '3.9.6'), + ('ncurses', '6.2'), + ('cURL', '7.78.0'), + ('XZ', '5.2.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' From 983b07b751d5c1d93119dbd2bc16a073e9dbe3f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Feb 2022 11:51:32 +0100 Subject: [PATCH 3019/9987] consistently apply patch for mapDamage 2.2.1 to use external seqtk --- .../m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb | 6 +++++- .../easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb index a949307ab3a..e59fa994907 100644 --- a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2020b-R-4.0.4.eb @@ -15,7 +15,11 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c'] +patches = ['%(name)s-2.2.1_use-external-seqtk.patch'] +checksums = [ + 'f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c', # 2.2.1.tar.gz + 'f01a90c29123460f8cb6ba2fe0f42e9ec66b0febff430d4ec4f0ab1197c552e7', # mapDamage-2.2.1_use-external-seqtk.patch +] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb index 1f99a9c4a15..7b5f877b3cc 100644 --- a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2021b.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c'] +patches = ['%(name)s-2.2.1_use-external-seqtk.patch'] +checksums = [ + 'f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c', # 2.2.1.tar.gz + 'f01a90c29123460f8cb6ba2fe0f42e9ec66b0febff430d4ec4f0ab1197c552e7', # mapDamage-2.2.1_use-external-seqtk.patch +] dependencies = [ ('Python', '3.9.6'), From 2312559da9ab82e7ec6b7554c5d0d1e9454351ae Mon Sep 17 00:00:00 2001 From: Keith Refson Date: Tue, 8 Feb 2022 10:54:57 +0000 Subject: [PATCH 3020/9987] Commended on Python dependency and removed unnecessary %(installdir)s/lib --- .../easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb | 5 ++--- .../easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb | 5 ++--- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb | 5 +++-- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb | 4 +++- easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb | 4 +++- 5 files changed, 13 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb index b76958923a7..358326a0e82 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayCCE-19.06.eb @@ -21,12 +21,11 @@ skipsteps = ['configure'] buildopts = 'COMMS_ARCH=mpi FFT=fftw3 FFTLIBDIR= castep tools' -preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' +preinstallopts = 'mkdir -p %(installdir)s/bin &&' installopts = 'COMMS_ARCH=mpi FFT=fftw3 INSTALL_DIR="%(installdir)s/bin" install-castep install-tools' sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', - 'elastics.py', 'ceteprouts.pm']], + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb index 6e4ce1d8eb7..f79a8a8229e 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-CrayGNU-19.06.eb @@ -21,12 +21,11 @@ skipsteps = ['configure'] buildopts = 'COMMS_ARCH=mpi FFT=fftw3 FFTLIBDIR= castep tools' -preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' +preinstallopts = 'mkdir -p %(installdir)s/bin &&' installopts = 'COMMS_ARCH=mpi FFT=fftw3 INSTALL_DIR="%(installdir)s/bin" install-castep install-tools' sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', - 'elastics.py', 'ceteprouts.pm']], + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands']], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb index e26c9f65422..8c39d1c3c7d 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-foss-2019b.eb @@ -16,6 +16,8 @@ sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] +# Python+numpy are needed for the elastic constants and castepconv utilities, but +# should work with any system or eb Python including 2.7. dependencies = [ ('Perl', '5.30.0'), ] @@ -25,8 +27,7 @@ skipsteps = ['configure'] buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas FFTLIBDIR=$FFT_LIB_DIR MATHLIBDIR=$BLAS_LIB_DIR' buildopts += ' castep tools utilities' -preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' - +preinstallopts = 'mkdir -p %(installdir)s/bin &&' installopts = 'COMMS_ARCH=mpi FFT=fftw3 MATHLIBS=openblas INSTALL_DIR="%(installdir)s/bin"' installopts += ' install-castep install-tools install-utilities' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb index af79163117e..05eb3418930 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-intel-2019b.eb @@ -16,6 +16,8 @@ sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] +# Python+numpy are needed for the elastic constants and castepconv utilities, but +# should work with any system or eb Python including 2.7. dependencies = [ ('Perl', '5.30.0'), ] @@ -24,7 +26,7 @@ skipsteps = ['configure'] buildopts = 'COMMS_ARCH=mpi castep tools utilities' -preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' +preinstallopts = 'mkdir -p %(installdir)s/bin &&' installopts = 'COMMS_ARCH=mpi INSTALL_DIR="%(installdir)s/bin" install-castep install-tools install-utilities' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb index 322d15ab247..dd502229cec 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-21.1.1-iomkl-2019b.eb @@ -16,6 +16,8 @@ sources = ['CASTEP-%%(version_major_minor)s%s.tar.gz' % local_patch_ver] checksums = ['d909936a51dd3dff7a0847c2597175b05c8d0018d5afe416737499408914728f'] +# Python+numpy are needed for the elastic constants and castepconv utilities, but +# should work with any system or eb Python including 2.7. dependencies = [ ('Perl', '5.30.0'), ] @@ -24,7 +26,7 @@ skipsteps = ['configure'] buildopts = 'COMMS_ARCH=mpi castep tools utilities' -preinstallopts = 'mkdir -p %(installdir)s/bin %(installdir)s/lib && touch %(installdir)s/lib/null &&' +preinstallopts = 'mkdir -p %(installdir)s/bin &&' installopts = 'COMMS_ARCH=mpi INSTALL_DIR="%(installdir)s/bin" install-castep install-tools install-utilities' sanity_check_paths = { From b69028c8e058ef8c38f8076730c3c709a5bb51b8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 8 Feb 2022 11:14:32 +0000 Subject: [PATCH 3021/9987] Fix name templating in source urls --- .../easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb index 1d6a13798f2..0dda15cefb4 100644 --- a/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb +++ b/easybuild/easyconfigs/r/RcppGSL/RcppGSL-0.3.8-foss-2020b-R-4.0.4.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [ 'https://cran.r-project.org/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', ] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['7ffb047692c3717c5fee94fd115d23ce971309aa38aa42cd1e8bef67bc57d49e'] From ee9fc5104992502f7cd3766b98ac686f1c375968 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 8 Feb 2022 15:54:44 +0100 Subject: [PATCH 3022/9987] updating R + cmaverse --- .../CMAverse/CMAverse-20220112-foss-2021b.eb | 26 ++++++++++ .../easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 48 ++++++++++--------- 2 files changed, 51 insertions(+), 23 deletions(-) create mode 100644 easybuild/easyconfigs/c/CMAverse/CMAverse-20220112-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/CMAverse/CMAverse-20220112-foss-2021b.eb b/easybuild/easyconfigs/c/CMAverse/CMAverse-20220112-foss-2021b.eb new file mode 100644 index 00000000000..50c05df9ffa --- /dev/null +++ b/easybuild/easyconfigs/c/CMAverse/CMAverse-20220112-foss-2021b.eb @@ -0,0 +1,26 @@ +easyblock = 'RPackage' + +name = 'CMAverse' +version = '20220112' +local_commit = 'd382447' + +homepage = 'https://github.com/BS1125/CMAverse/' +description = """The R package CMAverse provides a suite of functions for reproducible causal mediation analysis +including cmdag for DAG visualization, cmest for statistical modeling and cmsens for sensitivity analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/BS1125/CMAverse/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['d475ade49b3c67f64e6df29d9af84a0bade89ccf1736b4e6c346ac9a88191bfb'] + +dependencies = [ + ('R', '4.1.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 7043d2cb89f..7ceaf4aa6d2 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -80,9 +80,6 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 1st November 2021 exts_list = [ - # include packages that are part of the base installation of R, - # both to make sure they are available (via sanity check), - # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets', @@ -224,8 +221,7 @@ exts_list = [ 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], }), ('MASS', '7.3-54', { - 'checksums': [('b800ccd5b5c2709b1559cf5eab126e4935c4f8826cf7891253432bb6a056e821', - 'eb644c0e94b447c46387aa22436ef5a43192960ee9cfd0df2940f4a4116179ae')], + 'checksums': ['b800ccd5b5c2709b1559cf5eab126e4935c4f8826cf7891253432bb6a056e821'], }), ('pixmap', '0.4-12', { 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], @@ -537,8 +533,7 @@ exts_list = [ 'checksums': ['eff3a92756ca34cdc1661fa36d2bf7fc8e9f4132d2f1ef9ed0105c83594618bf'], }), ('class', '7.3-19', { - 'checksums': [('7820ae94b22009561a69ed1f8b2ca2a3814be6a656e9884738206997caecbe37', - '9012f5c65384b441b5738ed7bd18ea735884bab32b31776e80cf3679f38a3769')], + 'checksums': ['7820ae94b22009561a69ed1f8b2ca2a3814be6a656e9884738206997caecbe37'], }), ('proxy', '0.4-26', { 'checksums': ['676bad821343974e0297a0566c4bf0cf0ea890104906a745b87d3b5989c81a4d'], @@ -547,8 +542,7 @@ exts_list = [ 'checksums': ['9bf9a15e7ce0b9b1a57ce3048d29cbea7f2a5bb2e91271b1b6aaafe07c852226'], }), ('nnet', '7.3-16', { - 'checksums': [('99511969babaf937c3033750b00b41e4e03742f268084efc4ee953b849f7b56a', - 'c5b73eb4fff0d225e14f898cec987a7a88796b6e70cde4cf277374428f2d5c13')], + 'checksums': ['99511969babaf937c3033750b00b41e4e03742f268084efc4ee953b849f7b56a'], }), ('minqa', '1.2.4', { 'checksums': ['cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c'], @@ -845,8 +839,7 @@ exts_list = [ 'checksums': ['9b12184a28fff87cacd0c3602d0cf63acb4d0f3049ad3a6ff16177f6df350782'], }), ('spatial', '7.3-14', { - 'checksums': [('52cc1982732f14544fae7dd9d028e2fc3b525ed695d211d6ed5055420e768a36', - '50e6daacbacff6c716485d20b15eb7fff7b8108dc5ea0ff508024beb4f0a8b9b')], + 'checksums': ['52cc1982732f14544fae7dd9d028e2fc3b525ed695d211d6ed5055420e768a36'], }), ('VGAM', '1.1-5', { 'checksums': ['30190b150f3e5478137d288a45f575b2654ad7c29254b0a1fe5c954ee010a1bb'], @@ -2255,7 +2248,7 @@ exts_list = [ ('lpSolveAPI', '5.5.2.0-17.7', { 'checksums': ['9ebc8e45ad73eb51e0b25049598a5bc758370cf89508e2328cf4bd93d68d55bb'], }), - ('ergm', '4.1.2', { + ('ergm', version, { 'checksums': ['1abc6ef53376a4132530c376ce477ae7a2590e95fe8feb011c0da9cfb4d49ba0'], }), ('networkDynamic', '0.11.0', { @@ -2302,7 +2295,6 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz @@ -2422,8 +2414,7 @@ exts_list = [ 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], }), ('rda', '1.0.2-2.1', { - 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', - 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], }), ('sampling', '2.9', { 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], @@ -2812,13 +2803,9 @@ exts_list = [ 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), ('gWidgets2tcltk', '1.0-6', { - 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" - 'preinstallopts': "xvfb-run ", - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... 'modulename': False, + 'preinstallopts': "xvfb-run ", + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], }), ('mgsub', '1.7.3', { 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], @@ -3212,8 +3199,23 @@ exts_list = [ ('ldbounds', '1.1-1.1', { 'checksums': ['e88e6bff43762a9f7d80484056d10c7d2fd80969b43061d8cc96c3bd5b9c3583'], }), - ('catlearn', '0.8', { - 'checksums': ['0d13da431a5511b025090b7ffaa3765b94b33c7de5a7cc1cec8c50437755646e'], + ('EValue', version, { + 'checksums': ['d9f3feb3da2efaf4e5d794e05475be62666192a7c855e373c3d369324078690c'], + }), + ('ggdag', '0.2.4', { + 'checksums': ['372ec4ef0ded9637304a19b50bce908e84a034e54dbd2a52a061bb747b2b08a0'], + }), + ('dagitty', '0.3-1', { + 'checksums': ['7d44b5d259ec3fef776a7e3fcb21d1c379f930d6ae9ae5fbfff54494ad78e8a8'], + }), + ('metadat', '1.0-0', { + 'checksums': ['ed335a4eb2145fffde20e36077e360f9d36a615e9d93453d2bbd6f5967db4b9c'], + }), + ('MetaUtility', '2.1.2', { + 'checksums': ['e38c21588c239aa8926e64d916aa0f3b04108c2992f0e801095e4c7920b9ad5d'], + }), + ('simex', '1.8', { + 'checksums': ['80c7841196b9377a9367eb6960ad80ca0bf8de511b8b18a0031bfbe7bde289a0'], }), ] From 88def735a221878d28d757b1639191d568be23be Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 8 Feb 2022 19:42:31 +0100 Subject: [PATCH 3023/9987] adding easyconfigs: ELPA-2021.11.001-foss-2021b.eb, ELPA-2021.11.001-intel-2021b.eb and patches: ELPA-2021.11.001_fix_hardcoded_perl_path.patch --- .../e/ELPA/ELPA-2021.11.001-foss-2021b.eb | 43 +++++++++++++++++++ .../e/ELPA/ELPA-2021.11.001-intel-2021b.eb | 43 +++++++++++++++++++ ...-2021.11.001_fix_hardcoded_perl_path.patch | 40 +++++++++++++++++ 3 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2021b.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001_fix_hardcoded_perl_path.patch diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2021b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2021b.eb new file mode 100644 index 00000000000..ed8d5d50027 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2021b.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2021.11.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + 'e61048393a5e5f460858a11b216547fa3f434dd620c478cb20a52ebf543260f1', # elpa-new_release_2021.11.001.tar.gz + # ELPA-2021.11.001_fix_hardcoded_perl_path.patch + '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b', +] + +builddependencies = [ + ('Autotools', '20210726'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.9.6'), + ('Perl', '5.34.0'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb new file mode 100644 index 00000000000..be62db29df2 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2021.11.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + 'e61048393a5e5f460858a11b216547fa3f434dd620c478cb20a52ebf543260f1', # elpa-new_release_2021.11.001.tar.gz + # ELPA-2021.11.001_fix_hardcoded_perl_path.patch + '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b', +] + +builddependencies = [ + ('Autotools', '20210726'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.9.6'), + ('Perl', '5.34.0'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001_fix_hardcoded_perl_path.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001_fix_hardcoded_perl_path.patch new file mode 100644 index 00000000000..5c7ae5eae05 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001_fix_hardcoded_perl_path.patch @@ -0,0 +1,40 @@ +--- elpa-new_release_2021.11.001/test_project_1stage/fdep/fortran_dependencies.pl 2021-12-17 08:20:49.000000000 +0100 ++++ elpa-new_release_2021.11.001_ok/test_project_1stage/fdep/fortran_dependencies.pl 2022-01-25 17:07:21.169362000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +--- elpa-new_release_2021.11.001/fdep/fortran_dependencies.pl 2021-12-17 08:20:49.000000000 +0100 ++++ elpa-new_release_2021.11.001_ok/fdep/fortran_dependencies.pl 2022-01-25 17:08:17.272544000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Copyright 2015 Lorenz Hüdepohl + # +--- elpa-new_release_2021.11.001/test_project_C_2stage/fdep/fortran_dependencies.pl 2021-12-17 08:20:49.000000000 +0100 ++++ elpa-new_release_2021.11.001_ok/test_project_C_2stage/fdep/fortran_dependencies.pl 2022-01-25 17:06:20.088471000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +--- elpa-new_release_2021.11.001/test_project_2stage/fdep/fortran_dependencies.pl 2021-12-17 08:20:49.000000000 +0100 ++++ elpa-new_release_2021.11.001_ok/test_project_2stage/fdep/fortran_dependencies.pl 2022-01-25 17:05:10.675886000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +--- elpa-new_release_2021.11.001/test_project_C/fdep/fortran_dependencies.pl 2021-12-17 08:20:49.000000000 +0100 ++++ elpa-new_release_2021.11.001_ok/test_project_C/fdep/fortran_dependencies.pl 2022-01-25 17:04:14.834326000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + From 2db35896433412c30fd221e2525ca4b99f3a985a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 9 Feb 2022 02:48:18 +0200 Subject: [PATCH 3024/9987] fix lockfile location in mujoco-py v2.1.2.14 --- .../mujoco-py-2.1.2.14-foss-2021b.eb | 10 ++++- ...o-py-2.1.2.14_fix-builder-lib-paths.patch} | 38 ++++++++++++++++--- ...oco-py-2.1.2.14_fix-builder-lockfile.patch | 14 +++++++ 3 files changed, 54 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/m/mujoco-py/{mujoco-py-2.1.2.14_fix-builder.patch => mujoco-py-2.1.2.14_fix-builder-lib-paths.patch} (61%) create mode 100644 easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder-lockfile.patch diff --git a/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb index 0eb967d4bf8..a2166416d7b 100644 --- a/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb +++ b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb @@ -31,11 +31,17 @@ exts_list = [ 'checksums': ['2aceacb2bd618ce8526676f7a3e84ea25d0165ef10abb574a45b4a9c07292d2e'], }), (name, version, { - 'patches': ['%(name)s-%(version)s_fix-builder.patch'], + 'patches': [ + 'mujoco-py-%(version)s_fix-builder-lib-paths.patch', + 'mujoco-py-%(version)s_fix-builder-lockfile.patch', + ], 'preinstallopts': 'MUJOCO_PY_MUJOCO_PATH=$EBROOTMUJOCO', 'checksums': [ 'eb5b14485acf80a3cf8c15f4b080c6a28a9f79e68869aa696d16cbd51ea7706f', # mujoco-py-2.1.2.14.tar.gz - '892dac4810a83def104debb4593189beafcfb4379bb07bd18347fe4b1c14adc1', # mujoco-py-2.1.2.14_fix-builder.patch + # mujoco-py-2.1.2.14_fix-builder-lib-paths.patch + '1957ab3cc85d49c58e01e106bd995ab130a2635e7113ee92c68d62b3234552f0', + # mujoco-py-2.1.2.14_fix-builder-lockfile.patch + '1d2404a644f2556ff26f41a5a23dd672342e373ef033141fc9cbdb109382183c', ], }), ] diff --git a/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder.patch b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder-lib-paths.patch similarity index 61% rename from easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder.patch rename to easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder-lib-paths.patch index 1fcac91641e..e4730baf9a8 100644 --- a/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder.patch +++ b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder-lib-paths.patch @@ -22,16 +22,24 @@ author: Alex Domingo (Vrije Universiteit Brussel) subprocess.check_call(['install_name_tool', '-change', from_mujoco_path, -@@ -213,7 +213,7 @@ +@@ -213,8 +213,8 @@ join(mujoco_path, 'include'), np.get_include(), ], - libraries=['mujoco210'], +- library_dirs=[join(mujoco_path, 'bin')], + libraries=['mujoco'], - library_dirs=[join(mujoco_path, 'bin')], ++ library_dirs=[join(mujoco_path, 'lib')], extra_compile_args=[ '-fopenmp', # needed for OpenMP -@@ -277,7 +277,7 @@ + '-w', # suppress numpy compilation warnings +@@ -272,12 +272,12 @@ + self.extension.sources.append( + join(self.CYMJ_DIR_PATH, "gl", "osmesashim.c")) + self.extension.libraries.extend(['glewosmesa', 'OSMesa', 'GL']) +- self.extension.runtime_library_dirs = [join(mujoco_path, 'bin')] ++ self.extension.runtime_library_dirs = [join(mujoco_path, 'lib')] + def _build_impl(self): so_file_path = super()._build_impl() # Removes absolute paths to libraries. Allows for dynamic loading. @@ -40,7 +48,14 @@ author: Alex Domingo (Vrije Universiteit Brussel) fix_shared_library(so_file_path, 'libglewosmesa.so', 'libglewosmesa.so') return so_file_path -@@ -296,7 +296,7 @@ +@@ -290,13 +290,13 @@ + self.extension.sources.append(self.CYMJ_DIR_PATH + "/gl/eglshim.c") + self.extension.include_dirs.append(self.CYMJ_DIR_PATH + '/vendor/egl') + self.extension.libraries.extend(['glewegl']) +- self.extension.runtime_library_dirs = [join(mujoco_path, 'bin')] ++ self.extension.runtime_library_dirs = [join(mujoco_path, 'lib')] + + def _build_impl(self): so_file_path = super()._build_impl() fix_shared_library(so_file_path, 'libOpenGL.so', 'libOpenGL.so.0') fix_shared_library(so_file_path, 'libEGL.so', 'libEGL.so.1') @@ -49,11 +64,22 @@ author: Alex Domingo (Vrije Universiteit Brussel) fix_shared_library(so_file_path, 'libglewegl.so', 'libglewegl.so') return so_file_path -@@ -483,7 +483,7 @@ +@@ -309,7 +309,7 @@ + self.extension.sources.append(self.CYMJ_DIR_PATH + "/gl/dummyshim.c") + self.extension.libraries.extend(['glfw.3']) + self.extension.define_macros = [('ONMAC', None)] +- self.extension.runtime_library_dirs = [join(mujoco_path, 'bin')] ++ self.extension.runtime_library_dirs = [join(mujoco_path, 'lib')] + + def _build_impl(self): + if not os.environ.get('CC'): +@@ -482,8 +482,8 @@ + # Link against mujoco so we can call mujoco functions from within callback ffibuilder.set_source(name, source_string, include_dirs=[join(mujoco_path, 'include')], - library_dirs=[join(mujoco_path, 'bin')], +- library_dirs=[join(mujoco_path, 'bin')], - libraries=['mujoco210']) ++ library_dirs=[join(mujoco_path, 'lib')], + libraries=['mujoco']) # Catch compilation exceptions so we can cleanup partial files in that case try: diff --git a/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder-lockfile.patch b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder-lockfile.patch new file mode 100644 index 00000000000..1703aa2a2c6 --- /dev/null +++ b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14_fix-builder-lockfile.patch @@ -0,0 +1,14 @@ +Put lockfile in a temp directory +author: Alex Domingo (Vrije Universiteit Brussel) +--- a/mujoco_py/builder.py 2022-02-09 01:20:09.349870000 +0100 ++++ b/mujoco_py/builder.py 2022-02-09 01:20:17.548552000 +0100 +@@ -89,7 +89,8 @@ + builder = Builder(mujoco_path) + cext_so_path = builder.get_so_file_path() + +- lockpath = os.path.join(os.path.dirname(cext_so_path), 'mujocopy-buildlock') ++ tmpdir_path = os.getenv('TMPDIR', '/tmp') ++ lockpath = os.path.join(tmpdir_path, 'mujocopy-buildlock') + + with fasteners.InterProcessLock(lockpath): + mod = None From ee102face0f97874bb4d04d62e87bce72a74838d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 9 Feb 2022 08:02:39 +0100 Subject: [PATCH 3025/9987] FoBiS: Add sanity_check_commands --- easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb index 06c9257d5bf..41535813788 100644 --- a/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/FoBiS/FoBiS-3.0.5-GCCcore-10.3.0.eb @@ -35,4 +35,6 @@ exts_list = [ }), ] +sanity_check_commands = ["FoBiS.py -h"] + moduleclass = 'devel' From 8202c10e63d6bf3482a145726582059449c87ed1 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Wed, 9 Feb 2022 10:33:08 +0100 Subject: [PATCH 3026/9987] add sanity check command --- easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb b/easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb index ab14c148bc1..342591127c3 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.26.10-Java-15.eb @@ -46,6 +46,8 @@ postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%( dependencies = [('Java', '15')] +sanity_check_commands = ['java -jar $EBROOTPICARD/picard.jar 2>&1 | grep USAGE'] + sanity_check_paths = { 'files': ['picard.jar'], 'dirs': [], From e559513a4a31b09e0f6e10504b57a7351fbfe035 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 9 Feb 2022 10:56:56 +0100 Subject: [PATCH 3027/9987] changes acc. to review --- .../c/CMAverse/CMAverse-20220112-foss-2021b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 17 +++++++++++++---- 2 files changed, 14 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CMAverse/CMAverse-20220112-foss-2021b.eb b/easybuild/easyconfigs/c/CMAverse/CMAverse-20220112-foss-2021b.eb index 50c05df9ffa..80c2e262426 100644 --- a/easybuild/easyconfigs/c/CMAverse/CMAverse-20220112-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CMAverse/CMAverse-20220112-foss-2021b.eb @@ -4,7 +4,7 @@ name = 'CMAverse' version = '20220112' local_commit = 'd382447' -homepage = 'https://github.com/BS1125/CMAverse/' +homepage = 'https://bs1125.github.io/CMAverse/' description = """The R package CMAverse provides a suite of functions for reproducible causal mediation analysis including cmdag for DAG visualization, cmest for statistical modeling and cmsens for sensitivity analysis.""" diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 7ceaf4aa6d2..1c8159ba6ec 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -80,6 +80,9 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 1st November 2021 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets', @@ -2248,7 +2251,7 @@ exts_list = [ ('lpSolveAPI', '5.5.2.0-17.7', { 'checksums': ['9ebc8e45ad73eb51e0b25049598a5bc758370cf89508e2328cf4bd93d68d55bb'], }), - ('ergm', version, { + ('ergm', '4.1.2', { 'checksums': ['1abc6ef53376a4132530c376ce477ae7a2590e95fe8feb011c0da9cfb4d49ba0'], }), ('networkDynamic', '0.11.0', { @@ -2295,6 +2298,7 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz @@ -2414,7 +2418,8 @@ exts_list = [ 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.9', { 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], @@ -2803,9 +2808,13 @@ exts_list = [ 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], }), ('gWidgets2tcltk', '1.0-6', { - 'modulename': False, - 'preinstallopts': "xvfb-run ", 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, }), ('mgsub', '1.7.3', { 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], From e90272201d1c11bfeea34ab70f8b31dc900bd31e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 10 Feb 2022 16:34:08 +0200 Subject: [PATCH 3028/9987] adding easyconfigs: TensorFlow-2.4.4-foss-2021a.eb and patches: TensorFlow-2.4.4_fix-assertion-bijector-test.patch, TensorFlow-2.4.4_fix-compatibility-with-numpy-1.20.patch, TensorFlow-2.4.4_fix-compatibility-with-protobuf-3.17.patch, TensorFlow-2.4.4_relax-required-versions.patch --- .../TensorFlow/TensorFlow-2.4.4-foss-2021a.eb | 232 ++++++++++++++++++ ...ow-2.4.4_fix-assertion-bijector-test.patch | 13 + ....4_fix-compatibility-with-numpy-1.20.patch | 58 +++++ ...fix-compatibility-with-protobuf-3.17.patch | 26 ++ ...orFlow-2.4.4_relax-required-versions.patch | 46 ++++ 5 files changed, 375 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-assertion-bijector-test.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-compatibility-with-numpy-1.20.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-compatibility-with-protobuf-3.17.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_relax-required-versions.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb new file mode 100644 index 00000000000..929fa57ce51 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb @@ -0,0 +1,232 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.4.4' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.17.3'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.32.0', '-nodocs'), + ('pybind11', '2.6.2'), + ('pkgconfig', '1.5.4', '-python'), # For h5py + ('UnZip', '6.0'), +] +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('HDF5', '1.10.7'), + ('cURL', '7.76.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.4.1'), + ('ICU', '69.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.28'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.35.4'), + ('PCRE', '8.44'), + ('protobuf-python', '3.17.3'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.0'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +sanity_pip_check = True +use_pip = True + + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('h5py', '2.10.0', { + 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], + 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', + 'checksums': [ + '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d', # h5py-2.10.0.tar.gz + '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f', # h5py-2.10.0_avoid-mpi-init.patch + ], + }), + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('cachetools', '4.2.4', { + 'checksums': ['89ea6f1b638d5a73a4f9226be57ac5e4f399d22770b92355f92dcb0f7f001693'], + }), + ('google-auth', '1.30.0', { + 'modulename': 'google.auth', + 'checksums': ['9ad25fba07f46a628ad4d0ca09f38dcb262830df2ac95b217f9b0129c9e42206'], + }), + ('oauthlib', '3.2.0', { + 'checksums': ['23a8208d75b902797ea29fd31fa80a15ed9dc2c6c16fe73f5d346f83f6fa27a2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('absl-py', '0.15.0', { + 'modulename': 'absl', + 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.43.0', { + 'modulename': 'grpc', + 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], + }), + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard', '2.4.1', { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['7b8c53c396069b618f6f276ec94fc45d17e3282d668979216e5d30be472115e4'], + }), + ('tensorboard-plugin-wit', '1.8.1', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard-plugin-profile', '2.4.0', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['dfbf254ee960440e3b2518324f876a6d6704c60b936887d99214fa36988a206a'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', '2.4.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['5b7b7bf2debe19a8794adacc43e8ba6459daa4efaf54d3302623994a359b17f0'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.13.1', { + 'checksums': ['909a80ce028821c7ad01bdcaa588126825931d177cdccd00b3545818d4a195ce'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.4', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.3.1', { + 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.3.1_disable-float128-on-power.patch', + 'TensorFlow-2.4.0_add-default-shell-env.patch', + 'TensorFlow-2.4.0_fix-eigen-on-power.patch', + 'TensorFlow-2.4.0_add-protobuf-deps.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_add-missing-llvm-deps.patch', + 'TensorFlow-2.4.0_fix-absl-on-power.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.4.4_relax-required-versions.patch', + 'TensorFlow-2.4.4_fix-compatibility-with-protobuf-3.17.patch', + 'TensorFlow-2.4.4_fix-compatibility-with-numpy-1.20.patch', + 'TensorFlow-2.4.4_fix-assertion-bijector-test.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/core/profiler/internal/gpu:device_tracer_test', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/kernels:sparse_matmul_op_test', + '-//tensorflow/core/kernels:sparse_matmul_op_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'with_xla': True, + 'checksums': [ + 'f1abc3ed92c3ce955db2a7db5ec422a3a98f015331183194f97b99fe77a09bb4', # v2.4.4.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + # TensorFlow-2.3.1_disable-float128-on-power.patch + 'a8369e92559cce4566ff831e615420fd98b83106c73ee3af7fbd5335c5fcd569', + # TensorFlow-2.4.0_add-default-shell-env.patch + '033a870b458406f4cabab878c4183cdf54cd7627648f24c8cc9f1964ff24d292', + # TensorFlow-2.4.0_fix-eigen-on-power.patch + '761303a9d5a0e78b833610891194e497a45f1218cfcb0ac4854a0d31d3156c2b', + # TensorFlow-2.4.0_add-protobuf-deps.patch + '0ae2f4f1f1dc5b85f61edbe8a4a91dcffd5cf7588fa46c6a143455e4bc41a64e', + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_add-missing-llvm-deps.patch + 'ce8c41e75f9854e547d03de99ae72cf41afa967b20439e864bc4af3dd4f565c7', + # TensorFlow-2.4.0_fix-absl-on-power.patch + 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch + 'f384cd97e004673ae530b6e5cc826f8fddb46646991f1a228fc07b2aac87ee80', + # TensorFlow-2.4.4_relax-required-versions.patch + 'cfe9b85e3556178a89c99ac27c5cee64d5605b18d323d9c5545d9cfd7527df01', + # TensorFlow-2.4.4_fix-compatibility-with-protobuf-3.17.patch + 'efbe7c25d2cf8dd02015bb0fce7ae49d55d135026bb8b26e7a52dd1e273e1a6f', + # TensorFlow-2.4.4_fix-compatibility-with-numpy-1.20.patch + 'badc106ff45e82856e6ea489922e0afbcd839c9e851ca1c9f380a4c7687da89c', + # TensorFlow-2.4.4_fix-assertion-bijector-test.patch + 'ac8aee69ab0269a89b390b247ec32bfb0a4582f86231e094febedec1b3204637', + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-assertion-bijector-test.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-assertion-bijector-test.patch new file mode 100644 index 00000000000..7a302ea105f --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-assertion-bijector-test.patch @@ -0,0 +1,13 @@ +Fix assetion string in testIsAbstract of Bijector test +author: Alex Domingo (Vrije Universiteit Brussel) +--- a/tensorflow/python/kernel_tests/distributions/bijector_test.py 2022-02-05 00:42:51.288983000 +0100 ++++ b/tensorflow/python/kernel_tests/distributions/bijector_test.py 2022-02-05 00:43:02.729512435 +0100 +@@ -38,7 +38,7 @@ + def testIsAbstract(self): + with self.assertRaisesRegex(TypeError, + ("Can't instantiate abstract class Bijector " +- "with abstract methods __init__")): ++ "with abstract method __init__")): + bijector.Bijector() # pylint: disable=abstract-class-instantiated + + def testDefaults(self): diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-compatibility-with-numpy-1.20.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-compatibility-with-numpy-1.20.patch new file mode 100644 index 00000000000..799d44343d9 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-compatibility-with-numpy-1.20.patch @@ -0,0 +1,58 @@ +Fix compatibility with NumPy 1.20+ +See issue: https://github.com/tensorflow/models/issues/9706 + +From 0f8fde42d09b199d02cf5d9d79fe76ebf1d260ef Mon Sep 17 00:00:00 2001 +From: Ben Greiner +Date: Thu, 6 May 2021 12:13:40 +0200 +Subject: [PATCH 01/14] Fix NumPy 1.20 error with np.prod() + +Reference: #47691, https://stackoverflow.com/questions/66373169 +--- + tensorflow/python/ops/array_ops.py | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/tensorflow/python/ops/array_ops.py b/tensorflow/python/ops/array_ops.py +index 519f2ef26fcef..d143ee96a2fc9 100644 +--- a/tensorflow/python/ops/array_ops.py ++++ b/tensorflow/python/ops/array_ops.py +@@ -36,6 +36,7 @@ + from tensorflow.python.framework.constant_op import constant + from tensorflow.python.ops import gen_array_ops + from tensorflow.python.ops import gen_math_ops ++from tensorflow.python.ops import math_ops + # go/tf-wildcard-import + # pylint: disable=wildcard-import + from tensorflow.python.ops.gen_array_ops import * +@@ -2894,7 +2895,7 @@ def matrix_set_diag( + + def _constant_if_small(value, shape, dtype, name): + try: +- if np.prod(shape) < 1000: ++ if math_ops.reduce_prod(shape) < 1000: + return constant(value, shape=shape, dtype=dtype, name=name) + except TypeError: + # Happens when shape is a Tensor, list with Tensor elements, etc. + +From 9a4642fb897e8ac7901253a4225d0d346715545e Mon Sep 17 00:00:00 2001 +From: Ben Greiner +Date: Thu, 2 Sep 2021 13:01:12 +0200 +Subject: [PATCH 14/14] catch NotImplementedError from failed recursive + conversion to ndarray + +--- + tensorflow/python/framework/test_util.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/tensorflow/python/framework/test_util.py b/tensorflow/python/framework/test_util.py +index 272351517655d..b1f6ca1775ef4 100644 +--- a/tensorflow/python/framework/test_util.py ++++ b/tensorflow/python/framework/test_util.py +@@ -2790,7 +2790,7 @@ def _assertAllCloseRecursive(self, + atol=atol, + msg="Mismatched value: a%s is different from b%s. %s" % + (path_str, path_str, msg)) +- except (ValueError, TypeError) as e: ++ except (ValueError, TypeError, NotImplementedError) as e: + if len(a) != len(b): + raise ValueError( + "Mismatched length: a%s has %d items, but b%s has %d items. %s" % diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-compatibility-with-protobuf-3.17.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-compatibility-with-protobuf-3.17.patch new file mode 100644 index 00000000000..69d194dc2d4 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_fix-compatibility-with-protobuf-3.17.patch @@ -0,0 +1,26 @@ +From f87e2c2fb623e862fe2ae1616ec4164fa48d1446 Mon Sep 17 00:00:00 2001 +From: Jason Zaman +Date: Sat, 31 Jul 2021 10:30:32 -0700 +Subject: [PATCH 07/10] example_parsing_ops: compatibility with protobuf-3.16 + +--- + tensorflow/core/kernels/example_parsing_ops.cc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/tensorflow/core/kernels/example_parsing_ops.cc b/tensorflow/core/kernels/example_parsing_ops.cc +index d0be01578d8..57ed19aeaae 100644 +--- a/tensorflow/core/kernels/example_parsing_ops.cc ++++ b/tensorflow/core/kernels/example_parsing_ops.cc +@@ -1218,7 +1218,7 @@ class DecodeJSONExampleOp : public OpKernel { + resolver_.get(), "type.googleapis.com/tensorflow.Example", &in, &out); + OP_REQUIRES(ctx, status.ok(), + errors::InvalidArgument("Error while parsing JSON: ", +- string(status.error_message()))); ++ string(status.message()))); + } + } + +-- +2.32.0 + + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_relax-required-versions.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_relax-required-versions.patch new file mode 100644 index 00000000000..417b81073d6 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4_relax-required-versions.patch @@ -0,0 +1,46 @@ +TF introduced a change pinning versions to fixed major.minor or even patch versions +Loosen those a bit so we can build it with our versions. +See https://github.com/tensorflow/tensorflow/issues/44654 + +Author: Alexander Grund (TU Dresden) +Update v2.4.4: Alex Domingo (Vrije Universiteit Brussel) + +--- tensorflow/tools/pip_package/setup.py.orig 2021-10-31 00:59:09.000000000 +0200 ++++ tensorflow/tools/pip_package/setup.py 2022-02-08 10:36:43.677543730 +0100 +@@ -77,18 +77,18 @@ + REQUIRED_PACKAGES = [ + 'absl-py ~= 0.10', + 'astunparse ~= 1.6.3', +- 'flatbuffers ~= 1.12.0', +- 'google_pasta ~= 0.2', ++ 'flatbuffers >= 1.12.0', ++ 'google_pasta >= 0.2', + 'h5py ~= 2.10.0', + 'keras_preprocessing ~= 1.1.2', +- 'numpy ~= 1.19.2', +- 'opt_einsum ~= 3.3.0', ++ 'numpy >= 1.16.0', ++ 'opt_einsum >= 3.3.0', + 'protobuf >= 3.9.2', +- 'six ~= 1.15.0', +- 'termcolor ~= 1.1.0', +- 'typing_extensions ~= 3.7.4', +- 'wheel ~= 0.35', +- 'wrapt ~= 1.12.1', ++ 'six >= 1.12.0', ++ 'termcolor >= 1.1.0', ++ 'typing_extensions >= 3.7.4.2', ++ 'wheel >= 0.26', ++ 'wrapt >= 1.12.1', + # These packages needs to be pinned exactly as newer versions are + # incompatible with the rest of the ecosystem + 'gast == 0.3.3', +@@ -118,7 +118,7 @@ + # BoringSSL support. + # See https://github.com/tensorflow/tensorflow/issues/17882. + if sys.byteorder == 'little': +- REQUIRED_PACKAGES.append('grpcio ~= 1.32.0') ++ REQUIRED_PACKAGES.append('grpcio >= 1.32.0') + + + # Packages which are only needed for testing code. From 317366b8e36a6806521c9a98a54587ba5f2fe91b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 10 Feb 2022 16:39:31 +0200 Subject: [PATCH 3029/9987] restore test comments for TensorFlow v2.4.4 --- .../TensorFlow/TensorFlow-2.4.4-foss-2021a.eb | 58 ++++++++++--------- 1 file changed, 32 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb index 929fa57ce51..52e760fb4f4 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb @@ -155,6 +155,8 @@ exts_list = [ 'checksums': ['d2cdc776873635ed421315c4d22e63280042456bbfa07397817e687b142b9667'], }), (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'patches': [ 'TensorFlow-2.1.0_fix-cuda-build.patch', 'TensorFlow-2.3.1_disable-float128-on-power.patch', @@ -171,32 +173,6 @@ exts_list = [ 'TensorFlow-2.4.4_fix-compatibility-with-numpy-1.20.patch', 'TensorFlow-2.4.4_fix-assertion-bijector-test.patch', ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], - 'test_script': 'TensorFlow-2.x_mnist-test.py', - 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', - 'test_targets': [ - '//tensorflow/core/...', - '-//tensorflow/core:example_java_proto', - '-//tensorflow/core/example:example_protos_closure', - '//tensorflow/cc/...', - '//tensorflow/c/...', - '//tensorflow/python/...', - '-//tensorflow/core/profiler/internal/gpu:device_tracer_test', - '-//tensorflow/c/eager:c_api_test_gpu', - '-//tensorflow/c/eager:c_api_distributed_test', - '-//tensorflow/c/eager:c_api_distributed_test_gpu', - '-//tensorflow/c/eager:c_api_cluster_test_gpu', - '-//tensorflow/c/eager:c_api_remote_function_test_gpu', - '-//tensorflow/c/eager:c_api_remote_test_gpu', - '-//tensorflow/core/kernels:sparse_matmul_op_test', - '-//tensorflow/core/kernels:sparse_matmul_op_test_gpu', - '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', - '-//tensorflow/core/common_runtime:mkl_layout_pass_test', - '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', - ], - 'testopts': "--test_timeout=3600 --test_size_filters=small", - 'with_xla': True, 'checksums': [ 'f1abc3ed92c3ce955db2a7db5ec422a3a98f015331183194f97b99fe77a09bb4', # v2.4.4.tar.gz '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch @@ -226,6 +202,36 @@ exts_list = [ # TensorFlow-2.4.4_fix-assertion-bijector-test.patch 'ac8aee69ab0269a89b390b247ec32bfb0a4582f86231e094febedec1b3204637', ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Requires access to CUPTI (privileged!) + '-//tensorflow/core/profiler/internal/gpu:device_tracer_test', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Invalid alignment: https://github.com/tensorflow/tensorflow/issues/46460 + '-//tensorflow/core/kernels:sparse_matmul_op_test', + '-//tensorflow/core/kernels:sparse_matmul_op_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'with_xla': True, }), ] From 08b93078ba3ce4a7c50be1a1bea60a9abce61012 Mon Sep 17 00:00:00 2001 From: x0139045 Date: Thu, 10 Feb 2022 16:12:23 +0100 Subject: [PATCH 3030/9987] adding easyconfigs: ReFrame-3.10.1.eb --- .../easyconfigs/r/ReFrame/ReFrame-3.10.1.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.10.1.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.10.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.10.1.eb new file mode 100644 index 00000000000..198312322d2 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.10.1.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.10.1' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.2.4', { + 'use_pip': False, + 'checksums': ['0eb8a1516c3d138ae8689c0c1a60fde7143310832f9dc77e11d8a4bc62de193b'], + }), + ('wheel', '0.37.0', { + 'checksums': ['e2ef7239991699e3355d54f8e968a21bb940a1dbf34a4d226741e64462516fad'], + }), + ('setuptools', '57.4.0', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], + }), + ('reframe', version, { + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], + 'checksums': ['5fd649872bf93ba72a835896ea1a581b9b8c3e04150247be2359b95a7cdb89b5'], + }), +] + +postinstallcmds = [ + "cp -r tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -r share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['lib', 'tutorials', 'external'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 609aa8fda046a32f62f8b3e55e437b6d2b814f42 Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Thu, 10 Feb 2022 11:43:46 -0500 Subject: [PATCH 3031/9987] Add config NFFT-3.5.2-foss-2021b.eb --- .../n/NFFT/NFFT-3.5.2-foss-2021b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021b.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021b.eb new file mode 100644 index 00000000000..f8ff6083ed5 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2021b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.5.2' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/NFFT/nfft/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c68b22de2b914328d5d9fd33778defc66b226c72ef4c103956bbf36bbcd18e45'] + +dependencies = [('FFTW', '3.3.10')] + +builddependencies = [('Autotools', '20210726')] + +configure_cmd_prefix = './bootstrap.sh ; ' + +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3_threads.a', 'lib/libnfft3.a', + 'lib/libnfft3_threads.%s' % SHLIB_EXT, 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' From f71ccc2ad0c726b0956e0e68358aadb59c045bb5 Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Thu, 10 Feb 2022 11:44:20 -0500 Subject: [PATCH 3032/9987] Add config Clang-Python-bindings-13.0.1-GCCcore-11.2.0-Python-3.9.6.eb --- ...ings-13.0.1-GCCcore-11.2.0-Python-3.9.6.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.2.0-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.2.0-Python-3.9.6.eb new file mode 100644 index 00000000000..a78dfcedde6 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.2.0-Python-3.9.6.eb @@ -0,0 +1,32 @@ +easyblock = 'Tarball' + +name = 'Clang-Python-bindings' +version = '13.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://clang.llvm.org' +description = """Python bindings for libclang""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/"] +sources = ['clang-%(version)s.src.tar.xz'] +checksums = ['787a9e2d99f5c8720aa1773e4be009461cd30d3bd40fdd24591e473467c917c9'] + +dependencies = [ + ('Clang', version), + ('Python', '3.9.6') +] + +start_dir = 'bindings/python' + +sanity_check_paths = { + 'files': ['clang/cindex.py'], + 'dirs': ['clang'] +} + +sanity_check_commands = ["python -c 'import clang'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'lib' From 2e25f60a98696a3c5a34dbc2c991bdb10b9e6417 Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Thu, 10 Feb 2022 14:41:59 -0500 Subject: [PATCH 3033/9987] Do not include python version suffix --- ...n-3.9.6.eb => Clang-Python-bindings-13.0.1-GCCcore-11.2.0.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/c/Clang-Python-bindings/{Clang-Python-bindings-13.0.1-GCCcore-11.2.0-Python-3.9.6.eb => Clang-Python-bindings-13.0.1-GCCcore-11.2.0.eb} (95%) diff --git a/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.2.0.eb similarity index 95% rename from easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.2.0-Python-3.9.6.eb rename to easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.2.0.eb index a78dfcedde6..aac6bc89d38 100644 --- a/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.2.0-Python-3.9.6.eb +++ b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.2.0.eb @@ -2,7 +2,6 @@ easyblock = 'Tarball' name = 'Clang-Python-bindings' version = '13.0.1' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://clang.llvm.org' description = """Python bindings for libclang""" From 22b6ce0fed4cfb55110665310c4357284356024d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 11 Feb 2022 10:21:54 +0800 Subject: [PATCH 3034/9987] prepare release notes for EasyBuild v4.5.3 + bump version to 4.5.3 --- RELEASE_NOTES | 37 ++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 37 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 79e2add3b6c..a2bff4f562e 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,45 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 14,080 easyconfig files, for 2,622 different software packages, +The latest version of easybuild-easyconfig provides 14,282 easyconfig files, for 2,647 different software packages, incl. 36 different (compiler) toolchains. +v4.5.3 (February 11th 2022) +--------------------------- + +update/bugfix release +- added example easyconfig files for 25 new software packages: + - Arcade-Learning-Environment (#14753), Bambi (#14811), CASTEP (#14420), Crumble (#14785), deepmedic (#14953), + FoBiS (#14771), histolab (#14945), Iris (#14788), Jasmine (#14789), libexif (#14823), libgdiplus (#14823), + MuJoCo (#14965), mujoco-py (#14965), namedlist (#14814), OpenCensus-python (#14837), PyEVTK (#14911), + pyradiomics (#14851), PyTorch-Lightning (#14933), Redis (#14783), rising (#14952), SoXt (#14803), + SURVIVOR (#14786), tensorboard (#14926), xtensor (#14944), xxd (#14846) +- added additional easyconfigs for various supported software packages, including: + - aiohttp 3.8.1, aiohttp 3.8.1, AOCC 3.2.0, Arcade Learning, ArviZ 0.11.4, astropy 4.3.1, atools 1.4.8, atools 1.4.8, Bambi 0.7.1, BeautifulSoup 4.10.0, BeautifulSoup 4.10.0, Biopython 1.79, BLAST+ 2.9.0, bokeh 2.4.2, Boost.Python 1.77.0, Bowtie 1.3.1, CASTEP 21.1.1, CASTEP 21.1.1, CASTEP 21.1.1, CASTEP 21.1.1, CASTEP 21.1.1, CDO 1.9.10, CFITSIO 3.49, CheMPS2 1.8.11, Clang 13.0.1, CLHEP 2.4.4.0, CLHEP 2.4.5.1, ClustalW2 2.1, Coin 4.0.0, ConnectomeWorkbench 1.5.0, Crumble 0.8.3, ctffind 4.1.14, CUDA 11.5.1.eb, CUDA 11.6.0.eb, CUDAcore 11.5.1.eb, cutadapt 3.5, dask 2022.1.0, deepdiff 5.7.0, deepmedic 0.8.2, deepmedic 0.8.2, deepTools 3.5.0, dm tree, dm tree, DROP 1.1.1, EasyBuild 4.5.2.eb, ecCodes 2.24.2, Emacs 27.2, FabIO 0.11.0, fastahack 1.0.0, fastp 0.23.2, FastQTL 2.184, FDS 6.7.7, file 5.41, filevercmp 20191210, Flask 2.0.2, FoBiS 3.0.5, FORD 6.1.6, fsom 20141119, GATE 9.1, Geant4 10.7.1, Geant4 11.0.0, GEMMA 0.98.5, GLFW 3.3.4, GnuTLS 3.7.3, Go 1.17.6.eb, gpustat 1.0.0b1, Graphviz 2.50.0, GROMACS 2021.5, GROMACS 2021.5, GST plugins, GStreamer 1.18.5, Guile 3.0.7, HDF5 1.10.8, HISAT2 2.2.1, histolab 0.4.1, histolab 0.4.1, imageio 2.13.5, intervaltree 0.1, Iris 1.0.5, ITK 5.2.1, Jasmine 1.1.4, Java 17.0.2.eb, JupyterLab 3.2.8, lftp 4.9.2, libBigWig 0.4.6, libdeflate 1.7, libdeflate 1.8, libexif 0.6.24, libgdiplus 6.1, libGridXC 0.9.6, libGridXC 0.9.6, libGridXC 0.9.6, libGridXC 0.9.6, libpsml 1.1.10, libpsml 1.1.10, libpsml 1.1.10, libpsml 1.1.10, libRmath 4.1.2, librsb 1.2.0.10, librsb 1.2.0.11, librsb 1.3.0.0, libtasn1 4.18.0, libunistring 1.0, libxc 4.3.4, libxc 4.3.4, likwid 5.2.1, mapDamage 2.2.1, MaxQuant 2.0.3.0, MEGA 11.0.10.eb, MethylDackel 0.6.1, methylpy 1.2.9, minimap2 2.24, MinPath 1.6, mkl service, Mono 6.12.0.122, motif 2.3.8, MuJoCo 2.1.1, mujoco py, multichoose 1.0.3, MUSCLE 5.1, namedlist 1.8, nanomax analysis, nanomax analysis, ncbi vdb, NCIPLOT 4.0, netcdf4 python, networkx 2.6.3, Nextflow 21.10.6.eb, NGS 2.11.2, NiBabel 3.2.1, nvtop 1.2.2, nvtop 1.2.2, OpenCensus python, OpenCV 4.5.5, OpenSlide 3.4.1, openslide python, openslide python, OpenSSL 1.1.1k, p11 kit, Perl 5.34.0, pftoolsV3 3.2.11, picard 2.26.10, Pindel 0.2.5b9, PRANK 170427, preseq 3.1.2, pydicom 2.2.2, PyEVTK 1.4.1, PyEVTK 2.0.0, pyFAI 0.20.0, pyFAI 0.20.0, PyMC3 3.11.1, pymca 5.6.3, pyradiomics 3.0.1, Pysam 0.18.0, pytest xdist, python isal, PyTorch Lightning, PyTorch Lightning, Qualimap 2.2.1, Racon 1.5.0, RAxML 8.2.12, Redis 6.2.6, Redis 6.2.6, ReFrame 3.10.1.eb, rising 0.2.2, rising 0.2.2, ROOT 6.24.06, ScaFaCoS 1.0.1, scikit image, SDL2 2.0.20, SeqKit 2.1.0.eb, seqtk 1.3, Siesta 4.1.5, silx 0.14.0, SimpleITK 2.1.1, smithwaterman 20160702, SoQt 1.6.0, SoXt 1.4.0, SqueezeMeta 1.5.0, SURVIVOR 1.0.7, tabix 0.2.6, tabixpp 1.1.0, tensorboard 2.8.0, Theano 1.1.2, tMAE 1.0.1, torchvision 0.11.3, Trim_Galore 0.6.7, typing extensions, Valgrind 3.18.1, Valgrind 3.18.1, vcflib 1.0.3, VTK 8.2.0, wget 1.21.2, wxWidgets 3.1.5, xmlf90 1.5.4, xmlf90 1.5.4, xmlf90 1.5.4, xmlf90 1.5.4, xtensor 0.24.0, xxd 8.2.4220, xxd 8.2.4220, xxd 8.2.4220, YAXT 0.9.2 +- minor enhancements, including: + - also install Python bindings for SHTns 3.5.1 (#14893) + - add catlearn extension to easyconfig for R v4.1.2 (#14940) +- various bug fixes, including: + - update TALYS sources to (hopefully) ensure constant checksums (#14797) + - add missing dependencies on graphite2, HarfBuzz to Qt5 (#14802) + - add missing UCX-CUDA dep to GROMACS for foss-2021a-CUDA-11.3.1 (#14859) + - specify easybuild.io as EasyBuild homepage in setup.py (#14870) + - add alternative checksum for MASS, class, nnet, spatial extensions in R 4.1.0 (#14873) and R 4.1.2 (#14880) easyconfigs + - add patch to fix Kraken2 ncbi ftp/https check in rsync_from_ncbi.pl for versions 2.0.9-2.1.1 (#14889) + - disable building of tests/benchmarks for snappy 1.1.8 to avoid failing build (#14923) + - disable use of -Werror for recent NSS versions (#14924) + - downgrade YAXT from intel/2021b to iimpi/2021b (#14936) + - fix download URL in UDUNITS v2.2.28 easyconfigs (#14954) + - remove unnecessary CUDAcore dependency from nvtop v1.2.1 easyconfig (#14957) + - consistently apply patch for mapDamage 2.2.1 to use external seqtk (#14961) + - fix typo in templated source URL in RcppGSL 0.3.8 easyconfig: $(name)s should be %(name)s (#14962) + - fix location of lock file in mujoco-py v2.1.2.14 (#14965) +- other changes: + - use actions/setup-python@v2 in CI workflows, also test with Python 3.8-3.10 (#14857) + - trim test configurations for easyconfigs test suite: only test with Python 2.7 + 3.6 and Lmod 7.x + 8.x (#14881) + + v4.5.2 (January 24th 2022) -------------------------- diff --git a/setup.py b/setup.py index 1b57af45e8a..a76be1ecd02 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.3.dev0' +VERSION = '4.5.3' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From d1f2bced3e3f0925147acfea9b3bb40b3d7353f8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Feb 2022 09:03:31 +0100 Subject: [PATCH 3035/9987] adding easyconfigs: numexpr-2.8.1-foss-2021a.eb --- .../n/numexpr/numexpr-2.8.1-foss-2021a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.8.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.8.1-foss-2021a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.1-foss-2021a.eb new file mode 100644 index 00000000000..bfe69543210 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.1-foss-2021a.eb @@ -0,0 +1,21 @@ +name = 'numexpr' +version = '2.8.1' + +homepage = 'https://numexpr.readthedocs.io/en/latest/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a416a869f4e6a488af7cd876a326fb82f892b23570b68eecff8135c4a39dd161'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +moduleclass = 'math' From 0ac8f464af3ee9d5c00c406ea25998a5290df30e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Feb 2022 09:23:21 +0100 Subject: [PATCH 3036/9987] minor tweak release notes for v4.5.3 --- RELEASE_NOTES | 24 +++++++++++++++++------- 1 file changed, 17 insertions(+), 7 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a2bff4f562e..31b393b1762 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -14,32 +14,42 @@ update/bugfix release - added example easyconfig files for 25 new software packages: - Arcade-Learning-Environment (#14753), Bambi (#14811), CASTEP (#14420), Crumble (#14785), deepmedic (#14953), FoBiS (#14771), histolab (#14945), Iris (#14788), Jasmine (#14789), libexif (#14823), libgdiplus (#14823), - MuJoCo (#14965), mujoco-py (#14965), namedlist (#14814), OpenCensus-python (#14837), PyEVTK (#14911), + MuJoCo (#14965), mujoco-py (#14776, #14965), namedlist (#14814), OpenCensus-python (#14837), PyEVTK (#14911), pyradiomics (#14851), PyTorch-Lightning (#14933), Redis (#14783), rising (#14952), SoXt (#14803), SURVIVOR (#14786), tensorboard (#14926), xtensor (#14944), xxd (#14846) - added additional easyconfigs for various supported software packages, including: - - aiohttp 3.8.1, aiohttp 3.8.1, AOCC 3.2.0, Arcade Learning, ArviZ 0.11.4, astropy 4.3.1, atools 1.4.8, atools 1.4.8, Bambi 0.7.1, BeautifulSoup 4.10.0, BeautifulSoup 4.10.0, Biopython 1.79, BLAST+ 2.9.0, bokeh 2.4.2, Boost.Python 1.77.0, Bowtie 1.3.1, CASTEP 21.1.1, CASTEP 21.1.1, CASTEP 21.1.1, CASTEP 21.1.1, CASTEP 21.1.1, CDO 1.9.10, CFITSIO 3.49, CheMPS2 1.8.11, Clang 13.0.1, CLHEP 2.4.4.0, CLHEP 2.4.5.1, ClustalW2 2.1, Coin 4.0.0, ConnectomeWorkbench 1.5.0, Crumble 0.8.3, ctffind 4.1.14, CUDA 11.5.1.eb, CUDA 11.6.0.eb, CUDAcore 11.5.1.eb, cutadapt 3.5, dask 2022.1.0, deepdiff 5.7.0, deepmedic 0.8.2, deepmedic 0.8.2, deepTools 3.5.0, dm tree, dm tree, DROP 1.1.1, EasyBuild 4.5.2.eb, ecCodes 2.24.2, Emacs 27.2, FabIO 0.11.0, fastahack 1.0.0, fastp 0.23.2, FastQTL 2.184, FDS 6.7.7, file 5.41, filevercmp 20191210, Flask 2.0.2, FoBiS 3.0.5, FORD 6.1.6, fsom 20141119, GATE 9.1, Geant4 10.7.1, Geant4 11.0.0, GEMMA 0.98.5, GLFW 3.3.4, GnuTLS 3.7.3, Go 1.17.6.eb, gpustat 1.0.0b1, Graphviz 2.50.0, GROMACS 2021.5, GROMACS 2021.5, GST plugins, GStreamer 1.18.5, Guile 3.0.7, HDF5 1.10.8, HISAT2 2.2.1, histolab 0.4.1, histolab 0.4.1, imageio 2.13.5, intervaltree 0.1, Iris 1.0.5, ITK 5.2.1, Jasmine 1.1.4, Java 17.0.2.eb, JupyterLab 3.2.8, lftp 4.9.2, libBigWig 0.4.6, libdeflate 1.7, libdeflate 1.8, libexif 0.6.24, libgdiplus 6.1, libGridXC 0.9.6, libGridXC 0.9.6, libGridXC 0.9.6, libGridXC 0.9.6, libpsml 1.1.10, libpsml 1.1.10, libpsml 1.1.10, libpsml 1.1.10, libRmath 4.1.2, librsb 1.2.0.10, librsb 1.2.0.11, librsb 1.3.0.0, libtasn1 4.18.0, libunistring 1.0, libxc 4.3.4, libxc 4.3.4, likwid 5.2.1, mapDamage 2.2.1, MaxQuant 2.0.3.0, MEGA 11.0.10.eb, MethylDackel 0.6.1, methylpy 1.2.9, minimap2 2.24, MinPath 1.6, mkl service, Mono 6.12.0.122, motif 2.3.8, MuJoCo 2.1.1, mujoco py, multichoose 1.0.3, MUSCLE 5.1, namedlist 1.8, nanomax analysis, nanomax analysis, ncbi vdb, NCIPLOT 4.0, netcdf4 python, networkx 2.6.3, Nextflow 21.10.6.eb, NGS 2.11.2, NiBabel 3.2.1, nvtop 1.2.2, nvtop 1.2.2, OpenCensus python, OpenCV 4.5.5, OpenSlide 3.4.1, openslide python, openslide python, OpenSSL 1.1.1k, p11 kit, Perl 5.34.0, pftoolsV3 3.2.11, picard 2.26.10, Pindel 0.2.5b9, PRANK 170427, preseq 3.1.2, pydicom 2.2.2, PyEVTK 1.4.1, PyEVTK 2.0.0, pyFAI 0.20.0, pyFAI 0.20.0, PyMC3 3.11.1, pymca 5.6.3, pyradiomics 3.0.1, Pysam 0.18.0, pytest xdist, python isal, PyTorch Lightning, PyTorch Lightning, Qualimap 2.2.1, Racon 1.5.0, RAxML 8.2.12, Redis 6.2.6, Redis 6.2.6, ReFrame 3.10.1.eb, rising 0.2.2, rising 0.2.2, ROOT 6.24.06, ScaFaCoS 1.0.1, scikit image, SDL2 2.0.20, SeqKit 2.1.0.eb, seqtk 1.3, Siesta 4.1.5, silx 0.14.0, SimpleITK 2.1.1, smithwaterman 20160702, SoQt 1.6.0, SoXt 1.4.0, SqueezeMeta 1.5.0, SURVIVOR 1.0.7, tabix 0.2.6, tabixpp 1.1.0, tensorboard 2.8.0, Theano 1.1.2, tMAE 1.0.1, torchvision 0.11.3, Trim_Galore 0.6.7, typing extensions, Valgrind 3.18.1, Valgrind 3.18.1, vcflib 1.0.3, VTK 8.2.0, wget 1.21.2, wxWidgets 3.1.5, xmlf90 1.5.4, xmlf90 1.5.4, xmlf90 1.5.4, xmlf90 1.5.4, xtensor 0.24.0, xxd 8.2.4220, xxd 8.2.4220, xxd 8.2.4220, YAXT 0.9.2 + - aiohttp 3.8.1, AOCC 3.2.0, ArviZ 0.11.4, BeautifulSoup 4.10.0, bokeh 2.4.2, Boost.Python 1.77.0, + Bowtie 1.3.1, CheMPS2 1.8.11, Clang 13.0.1, CLHEP 2.4.5.1, ConnectomeWorkbench 1.5.0, Crumble 0.8.3, + CUDA 11.5.1 + 11.6.0, cutadapt 3.5, dask 2022.1.0, deepdiff 5.7.0, deepTools 3.5.0, dm-tree 0.1.6, + DROP 1.1.1, ecCodes 2.24.2, Emacs 27.2, FDS 6.7.7, file 5.41, Flask 2.0.2, FORD 6.1.6, GATE 9.1, + Geant4 11.0.0, GEMMA 0.98.5, GnuTLS 3.7.3, Go 1.17.6, gpustat 1.0.0b1, Graphviz 2.50.0, GROMACS 2021.5, + Guile 3.0.7, HDF5 1.10.8, imageio 2.13.5, JupyterLab 3.2.8, lftp 4.9.2, libBigWig 0.4.6, libpsml 1.1.10, + libRmath 4.1.2, librsb 1.3.0.0, libtasn1 4.18.0, libunistring 1.0, likwid 5.2.1, MaxQuant 2.0.3.0, + MEGA 11.0.10.eb, MethylDackel 0.6.1, methylpy 1.2.9, minimap2 2.24, Mono 6.12.0.122, MUSCLE 5.1, + nanomax-analysis-utils 0.4.3, ncbi-vdb 2.11.2, NCIPLOT-4.0 20200624, Nextflow 21.10.6, NGS 2.11.2, + nvtop 1.2.2, OpenCV 4.5.5, openslide-python 1.1.2, pftoolsV3 3.2.11, picard 2.26.10, pydicom 2.2.2, + pyFAI 0.20.0, Pysam 0.18.0, pytest-xdist 2.5.0, Racon 1.5.0, RAxML 8.2.12, ReFrame 3.10.1, ROOT 6.24.06, + scikit-image 0.19.1, SDL2 2.0.20, SeqKit 2.1.0, Siesta 4.1.5, SimpleITK 2.1.1, SqueezeMeta 1.5.0, + tMAE 1.0.1, torchvision 0.11.3, Trim_Galore 0.6.7, typing-extensions 3.10.0.2 - minor enhancements, including: - also install Python bindings for SHTns 3.5.1 (#14893) - add catlearn extension to easyconfig for R v4.1.2 (#14940) - various bug fixes, including: - update TALYS sources to (hopefully) ensure constant checksums (#14797) - - add missing dependencies on graphite2, HarfBuzz to Qt5 (#14802) + - add missing graphite2 + HarfBuzz dependencies to Qt5 v5.15.2 (#14802) - add missing UCX-CUDA dep to GROMACS for foss-2021a-CUDA-11.3.1 (#14859) - specify easybuild.io as EasyBuild homepage in setup.py (#14870) - add alternative checksum for MASS, class, nnet, spatial extensions in R 4.1.0 (#14873) and R 4.1.2 (#14880) easyconfigs - add patch to fix Kraken2 ncbi ftp/https check in rsync_from_ncbi.pl for versions 2.0.9-2.1.1 (#14889) - disable building of tests/benchmarks for snappy 1.1.8 to avoid failing build (#14923) - disable use of -Werror for recent NSS versions (#14924) - - downgrade YAXT from intel/2021b to iimpi/2021b (#14936) - fix download URL in UDUNITS v2.2.28 easyconfigs (#14954) - remove unnecessary CUDAcore dependency from nvtop v1.2.1 easyconfig (#14957) - consistently apply patch for mapDamage 2.2.1 to use external seqtk (#14961) - fix typo in templated source URL in RcppGSL 0.3.8 easyconfig: $(name)s should be %(name)s (#14962) - - fix location of lock file in mujoco-py v2.1.2.14 (#14965) - other changes: - - use actions/setup-python@v2 in CI workflows, also test with Python 3.8-3.10 (#14857) - - trim test configurations for easyconfigs test suite: only test with Python 2.7 + 3.6 and Lmod 7.x + 8.x (#14881) + - update Java/17 wrapper to Java 17.0.2 (#14868) + - use actions/setup-python@v2 in CI workflows + trim test configurations for easyconfigs test suite: only test with Python 2.7 + 3.6 and Lmod 7.x + 8.x (#14857, #14881) v4.5.2 (January 24th 2022) From 26947e6aef3b5dae15de75cd3fb5a91462da19ca Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 11 Feb 2022 18:28:26 +0800 Subject: [PATCH 3037/9987] adding easyconfigs: EasyBuild-4.5.3.eb --- .../e/EasyBuild/EasyBuild-4.5.3.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.3.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.3.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.3.eb new file mode 100644 index 00000000000..c8768ab9e83 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.3.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.5.3' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/4a/12/63a8d8f4f7132da62a3d81f7f385ef2b88fd41536007bf2939ea6d8f7639/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/8a/7b/bbda3cd4f5c0aa0364e2f4392330e94e3d73c0c6dae703832e9a6ac7ab6c/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/07/78/41bcf3f94068a49a1d66f65711c95be02b1affeefb457e393601376ae335/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '67fc32ae51bd421a94f8ad764b71d806e01ed87548d58fb1a99b81719337b8ad', # easybuild-framework-4.5.3.tar.gz + '2ff3d075f305e18fa6a40dcd8a4d963c3487668232f70945e32bdaa871bb8707', # easybuild-easyblocks-4.5.3.tar.gz + 'b8677a153f702142512f492eaf2388e54c5638c3d8966eb5456cb54cc4ef2a9f', # easybuild-easyconfigs-4.5.3.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From e0056f50b0ba8efa0c5c15732c2fe0929eb645a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Feb 2022 11:53:49 +0100 Subject: [PATCH 3038/9987] bump version to 4.5.4dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index a76be1ecd02..8717395d06d 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.3' +VERSION = '4.5.4.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 6ec5df0603c7969785f64274e4b4d8def4ab7c3a Mon Sep 17 00:00:00 2001 From: agemuend <94064529+agemuend@users.noreply.github.com> Date: Fri, 11 Feb 2022 12:25:46 +0100 Subject: [PATCH 3039/9987] Update easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb Co-authored-by: Miguel Dias Costa --- .../i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb index 758f142f756..55107c33e8a 100644 --- a/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb +++ b/easybuild/easyconfigs/i/IntelClusterChecker/IntelClusterChecker-2021.5.0.eb @@ -37,4 +37,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["clck -h"] + moduleclass = 'perf' From 5d03140272f450158c0a849ca37098542bc4bcef Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 11 Feb 2022 12:59:58 +0100 Subject: [PATCH 3040/9987] working #226 --- .../s/STRique/STRique-0.4.2-foss-2021b.eb | 62 +++++++++++++++++++ .../s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb | 50 +++++++++++++++ 2 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb new file mode 100644 index 00000000000..a3c71eade04 --- /dev/null +++ b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'STRique' +version = '0.4.2' + +homepage = 'https://github.com/giesselmann/STRique' +description = """STRique is a python package to analyze repeat expansion and +methylation states of short tandem repeats (STR) in Oxford Nanopore Technology +(ONT) long read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('zlib', '1.2.11'), + ('h5py', '3.6.0'), + ('SeqAn', '2.4.0'), + ('PyYAML', '5.4.1'), + ('networkx', '2.6.3'), + ('scikit-image', '0.19.1'), +] + +exts_list = [ + ('pomegranate', '0.10.0', { + 'sources': [{'source_urls': ['https://github.com/jmschrei/pomegranate/archive/'], 'download_filename': '523fb286b5199c64a271a35d49c1ac8fb524408d.tar.gz', 'filename': 'pomegranate-0.10.0.tar.gz'}], + 'checksums': ['9a16eef72a374094dcf6a04527f07ed61ed46b47719b624ccbed4180b0805ce9'], + }), + ('ont-fast5-api', '4.0.0', { + 'modulename': 'ont_fast5_api', + 'checksums': ['a249813104439bfe3d4e346bb560756e23217655273410c60b9bade205eb3e66'], + }), + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + (name, version, { + 'modulename': 'STRique_lib', + 'postinstallcmds': [ + 'cat <(echo '#!/usr/bin/env python') scripts/STRique.py > %(installdir)s/bin/STRique', + 'cat <(echo '#!/usr/bin/env python') scripts/STRique_test.py > %(installdir)s/bin/STRique_test', + 'cat <(echo '#!/usr/bin/env python') scripts/fast5Masker.py > %(installdir)s/bin/fast5Masker', + 'chmod +x %(installdir)s/bin/*', + ], + 'preconfigopts': "sed -i -e '/SeqAn/,+6d' CMakeLists.txt && sed -i -e 's/#pomegranate/pomegranate/' requirements.txt && ", + 'sources': [{'filename': '%(name)s-%(version)s.tar.gz', 'git_config': {'url': 'https://github.com/giesselmann', 'repo_name': 'STRique', 'commit': '585273215abff7956f5d6277601f0a6be2211a96', 'recursive': True}}], + 'checksums': ['e320325373a2833cecc6968f63a86b2b0ee3d057d23f554de2db87ffec6934d6'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/STRique', 'bin/fast5Masker'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = ['STRique count --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9bd47b48852 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'SeqAn' +version = '2.4.0' + +homepage = 'https://github.com/seqan/seqan' + +description = """ + SeqAn is an open source C++ library of efficient algorithms and data structures + for the analysis of sequences with the focus on biological data. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/seqan/seqan/archive/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +separate_build_dir = True + +postinstallcmds = [ + "mkdir -p %(installdir)s/util/cmake", + "cp -a %(builddir)s/seqan-*/util/cmake/seqan-config.cmake %(installdir)s/util/cmake/", + "cp -a %(builddir)s/seqan-*/include %(installdir)s", +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["gustaf_mate_joining", "mason_materializer", "mason_variator", + "rabema_prepare_sam", "razers3", "seqan_tcoffee", "s4_join", "samcat", "splazers", + "yara_mapper"]] + ['util/cmake/seqan-config.cmake'], + 'dirs': ['include/seqan'], +} + +moduleclass = 'bio' From 882b1accbd4d28acc2dbf53e50be1eeb75353041 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 11 Feb 2022 13:46:07 +0100 Subject: [PATCH 3041/9987] tests fix --- .../s/STRique/STRique-0.4.2-foss-2021b.eb | 27 ++++++++++++++----- .../s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb | 2 +- 2 files changed, 22 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb index a3c71eade04..742b1ed5d3d 100644 --- a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb +++ b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb @@ -1,3 +1,6 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Jakub Zarybnicky (INUITS), Denis Kristak (INUITS) + easyblock = 'PythonBundle' name = 'STRique' @@ -23,9 +26,15 @@ dependencies = [ ('scikit-image', '0.19.1'), ] +local_preconfigopts = "sed -i -e '/SeqAn/,+6d' CMakeLists.txt && " +local_preconfigopts += "sed -i -e 's/#pomegranate/pomegranate/' requirements.txt && " + exts_list = [ ('pomegranate', '0.10.0', { - 'sources': [{'source_urls': ['https://github.com/jmschrei/pomegranate/archive/'], 'download_filename': '523fb286b5199c64a271a35d49c1ac8fb524408d.tar.gz', 'filename': 'pomegranate-0.10.0.tar.gz'}], + 'sources': + [{'source_urls': ['https://github.com/jmschrei/pomegranate/archive/'], + 'download_filename': '523fb286b5199c64a271a35d49c1ac8fb524408d.tar.gz', + 'filename': 'pomegranate-0.10.0.tar.gz'}], 'checksums': ['9a16eef72a374094dcf6a04527f07ed61ed46b47719b624ccbed4180b0805ce9'], }), ('ont-fast5-api', '4.0.0', { @@ -39,13 +48,19 @@ exts_list = [ (name, version, { 'modulename': 'STRique_lib', 'postinstallcmds': [ - 'cat <(echo '#!/usr/bin/env python') scripts/STRique.py > %(installdir)s/bin/STRique', - 'cat <(echo '#!/usr/bin/env python') scripts/STRique_test.py > %(installdir)s/bin/STRique_test', - 'cat <(echo '#!/usr/bin/env python') scripts/fast5Masker.py > %(installdir)s/bin/fast5Masker', + 'cat <(echo "#!/usr/bin/env python") scripts/STRique.py > %(installdir)s/bin/STRique', + 'cat <(echo "#!/usr/bin/env python") scripts/STRique_test.py > %(installdir)s/bin/STRique_test', + 'cat <(echo "#!/usr/bin/env python") scripts/fast5Masker.py > %(installdir)s/bin/fast5Masker', 'chmod +x %(installdir)s/bin/*', ], - 'preconfigopts': "sed -i -e '/SeqAn/,+6d' CMakeLists.txt && sed -i -e 's/#pomegranate/pomegranate/' requirements.txt && ", - 'sources': [{'filename': '%(name)s-%(version)s.tar.gz', 'git_config': {'url': 'https://github.com/giesselmann', 'repo_name': 'STRique', 'commit': '585273215abff7956f5d6277601f0a6be2211a96', 'recursive': True}}], + 'preconfigopts': local_preconfigopts, + 'sources': [ + {'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': {'url': 'https://github.com/giesselmann', + 'repo_name': 'STRique', + 'commit': '585273215abff7956f5d6277601f0a6be2211a96', + 'recursive': True} + }], 'checksums': ['e320325373a2833cecc6968f63a86b2b0ee3d057d23f554de2db87ffec6934d6'], }), ] diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb index 9bd47b48852..5b948710391 100644 --- a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb @@ -2,7 +2,7 @@ # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics - +# Updated: Jakub Zarybnicky (INUITS), Denis Kristak (INUITS) easyblock = 'CMakeMake' name = 'SeqAn' From 75a69fcc85b3cf21a52eeec44143ee2a6a3c2ca4 Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Fri, 11 Feb 2022 16:12:46 +0100 Subject: [PATCH 3042/9987] Update Julia v.1.7.2 --- .../j/Julia/Julia-1.7.2-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb new file mode 100644 index 00000000000..d77bb480f1b --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.7.2' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['a75244724f3b2de0e7249c861fbf64078257c16fb4203be78f1cf4dd5973ba95'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From 92b001498632d6ba8f476f708292e57c2afbc02d Mon Sep 17 00:00:00 2001 From: clusteruser Date: Fri, 11 Feb 2022 20:49:03 +0000 Subject: [PATCH 3043/9987] adding devito 4.6.1 --- .../devito-4.6.1-foss-2020a-Python-3.8.2.eb | 132 ++++++++++++++++++ 1 file changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..aecea945845 --- /dev/null +++ b/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,132 @@ +easyblock = 'PythonBundle' + +name = 'devito' +version = '4.6.1' +versionsuffix = '-Python-3.8.2' + +homepage = 'https://devitoproject.org/' +description = "Devito is a domain-specific Language (DSL) and code generation framework" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', '3.8.2'), + ('PyYAML', '5.3'), + ('SciPy-bundle', '2020.03', versionsuffix), # required for numpy/scipy + ('IPython', '7.15.0', versionsuffix), # required for numpy/scipy + #('pybind11', '2.4.3', versionsuffix), # required by scipy +] + +use_pip = True +sanity_pip_check = True + +# order is important! +exts_list = [ + ('anytree', '2.8.0', { + 'checksums': ['3f0f93f355a91bc3e6245319bf4c1d50e3416cc7a35cc1133c1ff38306bbccab'], + }), + ('cached-property', '1.5.2', { + 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], + }), + ('cgen', '2020.1', { + 'checksums': ['4ec99d0c832d9f95f5e51dd18a629ad50df0b5464ce557ef42c6e0cd9478bfcf'], + }), + ('codecov', '2.1.12', { + 'checksums': ['a0da46bb5025426da895af90938def8ee12d37fcbcbbbc15b6dc64cf7ebc51c1'], + }), + ('codepy', '2019.1', { + 'checksums': ['384f22c37fe987c0ca71951690c3c2fd14dacdeddbeb0fde4fd01cd84859c94e'], + }), + ('distributed', '2021.12.0', { + 'checksums': ['c6119a2cf1fb2d8ac60337915bb9a790af6530afcb5d7a809a3308323b874714'], + }), + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('dask', '2021.12.0', { + 'checksums': ['90614c9d162713e4849532c86f2854e8d53468521285413403b6c496344c0109'], + }), + ('msgpack', '1.0.3', { + 'checksums': ['51fdc7fb93615286428ee7758cecc2f374d5ff363bdd884c7ea622a7a327a81e'], + }), + ('coverage', '6.3.1', { + 'checksums': ['6c3f6158b02ac403868eea390930ae64e9a9a2a5bbfafefbb920d29258d9f2f8'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('toolz', '0.11.2', { + 'checksums': ['6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33'], + }), + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('zict', '2.0.0', { + 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], + }), + ('flake8', '4.0.1', { + 'checksums': ['806e034dda44114815e23c16ef92f95c91e4c71100ff52813adf7132a6ad870d'], + }), + ('mccabe', '0.6.1', { + 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], + }), + ('pycodestyle', '2.8.0', { + 'checksums': ['eddd5847ef438ea1c7870ca7eb78a9d47ce0cdb4851a5523949f2601d0cbbe7f'], + }), + ('pyflakes', '2.4.0', { + 'checksums': ['05a85c2872edf37a4ed30b0cce2f6093e1d0581f8c19d7393122da7e25b2b24c'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('multidict', '6.0.2', { + 'checksums': ['5ff3bd75f38e4c43f1f470f2df7a4d430b821c4ce22be384e1459cb57d6bb013'], + }), + ('nbval', '0.9.6', { + 'checksums': ['cfefcd2ef66ee2d337d0b252c6bcec4023384eb32e8b9e5fcc3ac80ab8cd7d40'], + }), + ('py-cpuinfo', '8.0.0', { + 'modulename': 'cpuinfo', + 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], + }), + ('pyrevolve', '2.2', { + 'checksums': ['b49aea5cd6c520ac5fcd1d25fa23fe2c5502741d2965f3eee10be067e7b0efb4'], + }), + ('pytest-cov', '3.0.0', { + 'checksums': ['e7f0f5b1617d2210a2cabc266dfe2f4c75a8d32fb89eafb7ad9d06f6d076d470'], + }), + ('pytest-runner', '5.3.1', { + 'modulename': 'pytest', + 'checksums': ['0fce5b8dc68760f353979d99fdd6b3ad46330b6b1837e2077a89ebcf204aac91'], + }), + ('devito', '4.6.1', { + 'checksums': ['e8acc4840953547c267706195df32738c95d0e51f7592eb0796a0efcc8cc5dbf'], + }), + ('contexttimer', '0.3.3', { + 'checksums': ['35a1efd389af3f1ca509f33ff23e17d98b66c8fde5ba2a4eb8a8b7fa456598a5'], + }), + ('sympy', '1.9', { + 'checksums': ['c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc'], + }), + ('fsspec', '2022.1.0', { + 'checksums': ['0bdd519bbf4d8c9a1d893a50b5ebacc89acd0e1fe0045d2f7b0e0c1af5990edc'], + }), + ('partd', '1.2.0', { + 'checksums': ['aa67897b84d522dcbc86a98b942afab8c6aa2f7f677d904a616b74ef5ddbc3eb'], + }), + ('pytools', '2022.1', { + 'checksums': ['197aacf6e1f5d60c715b92438792acb7702aed59ebbfb147fa84eda780e54fee'], + }), + ('setuptools_scm', '6.0.1', { + 'checksums': ['d1925a69cb07e9b29416a275b9fadb009a23c148ace905b2fb220649a6c18e92'], + }), + ('platformdirs', '2.2.0', { + 'checksums': ['632daad3ab546bd8e6af0537d09805cec458dce201bccfe23012df73332e181e'], + }), + ('locket', '0.2.1', { + 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], + }), +] + +moduleclass = 'lang' From b9a89c88f36e4d456a6254bf2437d04a09052fbf Mon Sep 17 00:00:00 2001 From: clusteruser Date: Fri, 11 Feb 2022 20:49:29 +0000 Subject: [PATCH 3044/9987] removing devito 4.6 --- .../devito-4.6-foss-2020a-Python-3.8.2.eb | 56 ------------------- 1 file changed, 56 deletions(-) delete mode 100644 easybuild/easyconfigs/d/devito/devito-4.6-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/d/devito/devito-4.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/devito/devito-4.6-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 1b1b240711a..00000000000 --- a/easybuild/easyconfigs/d/devito/devito-4.6-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,56 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'devito' -version = '4.6' -versionsuffix = '-Python-3.8.2' - -homepage = 'https://devitoproject.org/' -description = "Devito is a domain-specific Language (DSL) and code generation framework" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'lowopt': True} - -dependencies = [ - ('Python', '3.8.2'), - #('pybind11', '2.4.3', versionsuffix), # required by scipy -] - -use_pip = True -sanity_pip_check = True - -# order is important! -exts_list = [ - #('numpy', '1.18.3', { - # 'patches': ['numpy-1.16.2_relax-long-complex-test.patch'], - # 'source_tmpl': '%(name)s-%(version)s.zip', - # 'checksums': [ - # 'e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8', # numpy-1.18.3.zip - # # numpy-1.16.2_relax-long-complex-test.patch - # '647dd4099c2968489e5103b50bcd1b3d970b5b536af25ec75efe86127dda07bb', - # ], - #}), - #('scipy', '1.4.1', { - # 'patches': ['scipy-1.4.1-fix-pthread.patch'], - # 'checksums': [ - # 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz - # '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch - # ], - #}), - ('mpi4py', '3.0.3', { - 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], - }), - #('pandas', '1.0.3', { - # 'checksums': ['32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586'], - #}), - #('mpmath', '1.1.0', { - # 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], - #}), - #('deap', '1.3.1', { - # 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], - #}), - ('devito', '4.6', { - 'checksums': ['7868b8b9cad1e057573b1f7ce1f196be4706155538b0a153b5da142380f6f9cc'], - }), -] - -moduleclass = 'lang' From 574676ca6d5c4668e50dc5cab18a1ab386886c32 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 11 Feb 2022 23:05:46 +0100 Subject: [PATCH 3045/9987] Remove download_dep_fail --- .../easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021b.eb | 1 - .../easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-intel-2021b.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021b.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021b.eb index 72caeb550e5..4db664c3298 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021b.eb @@ -19,7 +19,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-intel-2021b.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-intel-2021b.eb index c83b9768742..baa89c5b408 100644 --- a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-intel-2021b.eb +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-intel-2021b.eb @@ -19,7 +19,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From 95a61815a58f5dc92a671fbc17517d622f9671c0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 11 Feb 2022 23:19:28 +0100 Subject: [PATCH 3046/9987] update easyconfig ELPA-2021.11.001-intel-2021b.eb: add options for running in a batch job --- easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb index be62db29df2..42a4e02fc13 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb @@ -34,6 +34,10 @@ builddependencies = [ preconfigopts = './autogen.sh && ' preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' preconfigopts += 'autoreconf && ' +# If the build is running in a batch job, make sure Intel libmpi does +# not try to use Slurm to run the MPI_THREAD test code that ELPA's +# configure is running without "mpirun". +preconfigopts += 'unset SLURM_JOBID && unset SLURM_NODELIST && unset I_MPI_PMI_LIBRARY && ' # When building in parallel, the file test_setup_mpi.mod is sometimes # used before it is built, leading to an error. This must be a bug in From 52fb115f3495180af37516786a053abd701e1ff0 Mon Sep 17 00:00:00 2001 From: clusteruser Date: Sat, 12 Feb 2022 09:25:24 +0000 Subject: [PATCH 3047/9987] cleaning up --- .../d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb index aecea945845..151b5359b4d 100644 --- a/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb @@ -13,9 +13,8 @@ toolchainopts = {'pic': True, 'lowopt': True} dependencies = [ ('Python', '3.8.2'), ('PyYAML', '5.3'), - ('SciPy-bundle', '2020.03', versionsuffix), # required for numpy/scipy - ('IPython', '7.15.0', versionsuffix), # required for numpy/scipy - #('pybind11', '2.4.3', versionsuffix), # required by scipy + ('SciPy-bundle', '2020.03', versionsuffix), + ('IPython', '7.15.0', versionsuffix), ] use_pip = True From 84feede0a8007d33dd04240a8b222d240eabb686 Mon Sep 17 00:00:00 2001 From: clusteruser Date: Sat, 12 Feb 2022 09:30:05 +0000 Subject: [PATCH 3048/9987] adding easyconfigs: devito-4.6.1-foss-2020a-Python-3.8.2.eb --- .../devito-4.6.1-foss-2020a-Python-3.8.2.eb | 131 ++++++++++++++++++ 1 file changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..151b5359b4d --- /dev/null +++ b/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,131 @@ +easyblock = 'PythonBundle' + +name = 'devito' +version = '4.6.1' +versionsuffix = '-Python-3.8.2' + +homepage = 'https://devitoproject.org/' +description = "Devito is a domain-specific Language (DSL) and code generation framework" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', '3.8.2'), + ('PyYAML', '5.3'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('IPython', '7.15.0', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +# order is important! +exts_list = [ + ('anytree', '2.8.0', { + 'checksums': ['3f0f93f355a91bc3e6245319bf4c1d50e3416cc7a35cc1133c1ff38306bbccab'], + }), + ('cached-property', '1.5.2', { + 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], + }), + ('cgen', '2020.1', { + 'checksums': ['4ec99d0c832d9f95f5e51dd18a629ad50df0b5464ce557ef42c6e0cd9478bfcf'], + }), + ('codecov', '2.1.12', { + 'checksums': ['a0da46bb5025426da895af90938def8ee12d37fcbcbbbc15b6dc64cf7ebc51c1'], + }), + ('codepy', '2019.1', { + 'checksums': ['384f22c37fe987c0ca71951690c3c2fd14dacdeddbeb0fde4fd01cd84859c94e'], + }), + ('distributed', '2021.12.0', { + 'checksums': ['c6119a2cf1fb2d8ac60337915bb9a790af6530afcb5d7a809a3308323b874714'], + }), + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('dask', '2021.12.0', { + 'checksums': ['90614c9d162713e4849532c86f2854e8d53468521285413403b6c496344c0109'], + }), + ('msgpack', '1.0.3', { + 'checksums': ['51fdc7fb93615286428ee7758cecc2f374d5ff363bdd884c7ea622a7a327a81e'], + }), + ('coverage', '6.3.1', { + 'checksums': ['6c3f6158b02ac403868eea390930ae64e9a9a2a5bbfafefbb920d29258d9f2f8'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('toolz', '0.11.2', { + 'checksums': ['6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33'], + }), + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('zict', '2.0.0', { + 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], + }), + ('flake8', '4.0.1', { + 'checksums': ['806e034dda44114815e23c16ef92f95c91e4c71100ff52813adf7132a6ad870d'], + }), + ('mccabe', '0.6.1', { + 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], + }), + ('pycodestyle', '2.8.0', { + 'checksums': ['eddd5847ef438ea1c7870ca7eb78a9d47ce0cdb4851a5523949f2601d0cbbe7f'], + }), + ('pyflakes', '2.4.0', { + 'checksums': ['05a85c2872edf37a4ed30b0cce2f6093e1d0581f8c19d7393122da7e25b2b24c'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('multidict', '6.0.2', { + 'checksums': ['5ff3bd75f38e4c43f1f470f2df7a4d430b821c4ce22be384e1459cb57d6bb013'], + }), + ('nbval', '0.9.6', { + 'checksums': ['cfefcd2ef66ee2d337d0b252c6bcec4023384eb32e8b9e5fcc3ac80ab8cd7d40'], + }), + ('py-cpuinfo', '8.0.0', { + 'modulename': 'cpuinfo', + 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], + }), + ('pyrevolve', '2.2', { + 'checksums': ['b49aea5cd6c520ac5fcd1d25fa23fe2c5502741d2965f3eee10be067e7b0efb4'], + }), + ('pytest-cov', '3.0.0', { + 'checksums': ['e7f0f5b1617d2210a2cabc266dfe2f4c75a8d32fb89eafb7ad9d06f6d076d470'], + }), + ('pytest-runner', '5.3.1', { + 'modulename': 'pytest', + 'checksums': ['0fce5b8dc68760f353979d99fdd6b3ad46330b6b1837e2077a89ebcf204aac91'], + }), + ('devito', '4.6.1', { + 'checksums': ['e8acc4840953547c267706195df32738c95d0e51f7592eb0796a0efcc8cc5dbf'], + }), + ('contexttimer', '0.3.3', { + 'checksums': ['35a1efd389af3f1ca509f33ff23e17d98b66c8fde5ba2a4eb8a8b7fa456598a5'], + }), + ('sympy', '1.9', { + 'checksums': ['c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc'], + }), + ('fsspec', '2022.1.0', { + 'checksums': ['0bdd519bbf4d8c9a1d893a50b5ebacc89acd0e1fe0045d2f7b0e0c1af5990edc'], + }), + ('partd', '1.2.0', { + 'checksums': ['aa67897b84d522dcbc86a98b942afab8c6aa2f7f677d904a616b74ef5ddbc3eb'], + }), + ('pytools', '2022.1', { + 'checksums': ['197aacf6e1f5d60c715b92438792acb7702aed59ebbfb147fa84eda780e54fee'], + }), + ('setuptools_scm', '6.0.1', { + 'checksums': ['d1925a69cb07e9b29416a275b9fadb009a23c148ace905b2fb220649a6c18e92'], + }), + ('platformdirs', '2.2.0', { + 'checksums': ['632daad3ab546bd8e6af0537d09805cec458dce201bccfe23012df73332e181e'], + }), + ('locket', '0.2.1', { + 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], + }), +] + +moduleclass = 'lang' From 0b3e87c2c202d53298fef21a92ce51c589216103 Mon Sep 17 00:00:00 2001 From: clusteruser Date: Sat, 12 Feb 2022 10:37:20 +0000 Subject: [PATCH 3049/9987] removed trailing whitespace --- .../d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb index 151b5359b4d..03925d447ce 100644 --- a/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True, 'lowopt': True} dependencies = [ ('Python', '3.8.2'), ('PyYAML', '5.3'), - ('SciPy-bundle', '2020.03', versionsuffix), + ('SciPy-bundle', '2020.03', versionsuffix), ('IPython', '7.15.0', versionsuffix), ] From d40861a523fe184e6ddde2a9cf6f17b46d8088f7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 12 Feb 2022 11:10:11 +0000 Subject: [PATCH 3050/9987] adding easyconfigs: AlphaFold-2.1.2-foss-2021a.eb --- .../a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb | 181 ++++++++++++++++++ 1 file changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb new file mode 100644 index 00000000000..66a6254c356 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb @@ -0,0 +1,181 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.1.2' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('TensorFlow', '2.6.0'), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.24'), # also provides absl-py +] +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.1.2_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '6af91706b2a001494ddc0947f89f8b3d3adfcc26177c373824fe8ea1a58c0b48', # AlphaFold-2.1.2_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +modextravars = { + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt +} + +moduleclass = 'bio' From 417eae191269ef7a7a9a2ed3842e34f83c668a23 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 12 Feb 2022 11:10:50 +0000 Subject: [PATCH 3051/9987] adding easyconfigs: AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb --- .../AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb | 191 ++++++++++++++++++ 1 file changed, 191 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..941d07cf923 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,191 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.1.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', True), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('TensorFlow', '2.6.0', versionsuffix), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.24', versionsuffix), # also provides absl-py + ('UCX-CUDA', '1.10.0', versionsuffix), + ('cuDNN', '8.2.1.32', versionsuffix, True), + ('NCCL', '2.10.3', versionsuffix), +] +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.1.2_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '6af91706b2a001494ddc0947f89f8b3d3adfcc26177c373824fe8ea1a58c0b48', # AlphaFold-2.1.2_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('chex', '0.0.8', { + 'checksums': ['d6ce1329470116b6f172a72b1131bfd4d11fb7eb465e6077c3b36224b5b09fe4'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('docker', '5.0.0', { + 'checksums': ['3e8bc47534e0ca9331d72c32f2881bb13b93ded0bcdeab3c833fb7cf61c0a9a5'], + }), + ('immutabledict', '2.1.0', { + 'checksums': ['673fb8f30f46d23dd394050b979f5b7f4c5398982b99ebc854fb873e646b967a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +moduleclass = 'bio' From bc2b4ddda401f88bbbf389def38e332a8bef1dc2 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 12 Feb 2022 13:59:22 +0100 Subject: [PATCH 3052/9987] add additional valid checksum for norm 1.0-9.5 extension in R 4.1.0 and 4.1.2 easyconfigs --- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index e6cf317ae8b..b897944bd7d 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -2898,7 +2898,8 @@ exts_list = [ 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], }), ('norm', '1.0-9.5', { - 'checksums': ['305cbf007f3905cfd535ed9bf5ae3e2995e228cc8883d6482e5d3a2f02814106'], + 'checksums': [('305cbf007f3905cfd535ed9bf5ae3e2995e228cc8883d6482e5d3a2f02814106', + '45016701291a5851d42452fc3ae682ff9bf86b0a9ba4619dc8b36a0187e4d0e4')], }), ('naniar', '0.6.1', { 'checksums': ['d546ca15bf6c224f3103eb1441abef91d34feebb7320c2398d598f5d50177450'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 7043d2cb89f..448e9a00e28 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -2971,7 +2971,8 @@ exts_list = [ 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], }), ('norm', '1.0-9.5', { - 'checksums': ['305cbf007f3905cfd535ed9bf5ae3e2995e228cc8883d6482e5d3a2f02814106'], + 'checksums': [('305cbf007f3905cfd535ed9bf5ae3e2995e228cc8883d6482e5d3a2f02814106', + '45016701291a5851d42452fc3ae682ff9bf86b0a9ba4619dc8b36a0187e4d0e4')], }), ('naniar', '0.6.1', { 'checksums': ['d546ca15bf6c224f3103eb1441abef91d34feebb7320c2398d598f5d50177450'], From 55de471c948076a66a7e7a0995fc6ec27769cfe2 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 13 Feb 2022 11:26:17 +0100 Subject: [PATCH 3053/9987] adding easyconfigs: numexpr-2.8.1-intel-2021a.eb --- .../n/numexpr/numexpr-2.8.1-intel-2021a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.8.1-intel-2021a.eb diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.8.1-intel-2021a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.1-intel-2021a.eb new file mode 100644 index 00000000000..8b60eb67fde --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.1-intel-2021a.eb @@ -0,0 +1,21 @@ +name = 'numexpr' +version = '2.8.1' + +homepage = 'https://numexpr.readthedocs.io/en/latest/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a416a869f4e6a488af7cd876a326fb82f892b23570b68eecff8135c4a39dd161'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +moduleclass = 'math' From facfb9d811c4a304041527e88af57b8a9c1741e6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 13 Feb 2022 12:18:42 +0000 Subject: [PATCH 3054/9987] avoid pollution in the tmp directory when running the AlphaFold tests --- .../AlphaFold-2.1.1-fosscuda-2020b.eb | 4 +++- .../AlphaFold-2.1_fix-alphafold-tests.patch | 22 +++++++++++++++++++ 2 files changed, 25 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1_fix-alphafold-tests.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index d7f3a327937..bd80f4af1c1 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -78,7 +78,8 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', - 'AlphaFold-2.0.1_relax_gpu.patch' + 'AlphaFold-2.0.1_relax_gpu.patch', + 'AlphaFold-2.1_fix-alphafold-tests.patch', ], 'checksums': [ '1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7', # v2.1.1.tar.gz @@ -89,6 +90,7 @@ components = [ '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch '3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch + '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', # AlphaFold-2.1_fix-alphafold-tests.patch ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1_fix-alphafold-tests.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1_fix-alphafold-tests.patch new file mode 100644 index 00000000000..65c9b87c89e --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1_fix-alphafold-tests.patch @@ -0,0 +1,22 @@ +Fix `run_alphafold_test.py` to use an unique directory per test to avoid pollution when the tests are run multiple times +Patch by Simon Branford (University of Birmingham) +--- run_alphafold_test.py.orig 2022-02-13 11:09:48.465041000 +0000 ++++ run_alphafold_test.py 2022-02-13 12:02:17.963970000 +0000 +@@ -59,14 +59,13 @@ + model_runner_mock.multimer_mode = False + amber_relaxer_mock.process.return_value = ('RELAXED', None, None) + +- fasta_path = os.path.join(absltest.get_default_test_tmpdir(), +- 'target.fasta') ++ out_dir = self.create_tempdir().full_path ++ ++ fasta_path = os.path.join(out_dir, 'target.fasta') + with open(fasta_path, 'wt') as f: + f.write('>A\nAAAAAAAAAAAAA') + fasta_name = 'test' + +- out_dir = absltest.get_default_test_tmpdir() +- + run_alphafold.predict_structure( + fasta_path=fasta_path, + fasta_name=fasta_name, From 0c8b211fec7c82a44d6277e3c927cd74cabc365b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 13 Feb 2022 12:32:00 +0000 Subject: [PATCH 3055/9987] line length --- .../easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index bd80f4af1c1..458badb2a78 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -90,7 +90,8 @@ components = [ '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch '3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch - '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', # AlphaFold-2.1_fix-alphafold-tests.patch + # AlphaFold-2.1_fix-alphafold-tests.patch + '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From 2516a984f7c484f4ac6756412c95017709397ede Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 13 Feb 2022 13:30:08 +0000 Subject: [PATCH 3056/9987] add test fix patch --- .../a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb index 941d07cf923..5bbf6fe9009 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb @@ -83,6 +83,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.1_fix-alphafold-tests.patch', ], 'checksums': [ 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz @@ -92,6 +93,8 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + # AlphaFold-2.1_fix-alphafold-tests.patch + '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From d1b3721599f41974f13ff3a8ea56d26e1e51c6ea Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 13 Feb 2022 13:30:14 +0000 Subject: [PATCH 3057/9987] add test fix patch --- .../easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb index 66a6254c356..585a30ac353 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb @@ -78,6 +78,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.1_fix-alphafold-tests.patch', ], 'checksums': [ 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz @@ -87,6 +88,8 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + # AlphaFold-2.1_fix-alphafold-tests.patch + '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From 0a6f9168a7e82484a03fb5942b93771fa7bf0e5c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 14 Feb 2022 08:50:51 +0100 Subject: [PATCH 3058/9987] adding easyconfigs: TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb and patches: TensorFlow-2.7.1_fix_protobuf_error_message.patch, TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch --- ...TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 231 ++++++++++++++++++ ...low-2.7.1_fix_protobuf_error_message.patch | 15 ++ ...low-2.7.1_remove-duplicate-gpu-tests.patch | 46 ++++ 3 files changed, 292 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix_protobuf_error_message.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..0fb2a2e829e --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,231 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.7.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.17.3'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.33.1', '-nodocs'), + ('pybind11', '2.7.1'), + ('UnZip', '6.0'), +] +dependencies = [ + ('CUDA', '11.4.1', '', True), + ('cuDNN', '8.2.2.26', versionsuffix, True), + ('NCCL', '2.10.3', versionsuffix), + ('Python', '3.9.6'), + ('h5py', '3.6.0'), + ('cURL', '7.78.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.5.0'), + ('ICU', '69.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.29'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.36'), + ('protobuf-python', '3.17.3'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.2'), + ('libpng', '1.6.37'), + ('snappy', '1.1.9'), + ('zlib', '1.2.11'), +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('wrapt', '1.13.3', { + 'checksums': ['1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-io-gcs-filesystem', '0.24.0', { + 'modulename': 'tensorflow_io', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/io/archive/'], + 'checksums': ['7a4b57f6f438402bab4919c360e931c32f4d8d8afa23116d32a48461dddd91dc'], + }), + ('tensorflow_estimator', '2.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['325b5a224864379242b7b76c6987ca544239be82579d33e68ec7c2bda57abc9d'], + }), + ('Werkzeug', '2.0.3', { + 'checksums': ['b863f8ff057c522164b6067c9e28b041161b4be5ba4d0daceeaa50a163822d3c'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('Markdown', '3.3.6', { + 'checksums': ['76df8ae32294ec39dcf89340382882dfa12975f87f45c3ed1ecdb1e8cefc7006'], + }), + ('grpcio', '1.43.0', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], + }), + ('oauthlib', '3.2.0', { + 'checksums': ['23a8208d75b902797ea29fd31fa80a15ed9dc2c6c16fe73f5d346f83f6fa27a2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('rsa', '4.8', { + 'checksums': ['5c6bd9dc7a543b7fe4304a631f8a8a3b674e2bbfc49c2ae96200cdbe55df6b17'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('cachetools', '5.0.0', { + 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], + }), + ('google-auth', '2.6.0', { + 'modulename': 'google.auth', + 'checksums': ['ad160fc1ea8f19e331a16a14a79f3d643d813a69534ba9611d2c80dc10439dad'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('tensorboard', '2.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['65a338e4424e9079f2604923bdbe301792adce2ace1be68da6b3ddf005170def'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('libclang', '13.0.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-manylinux1_x86_64.whl', + 'checksums': ['9c1e623340ccafe3a10a2abbc90f59593ff29f0c854f4ddb65b6220d9d998fb4'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('keras', '2.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['0c33ae1f728064ca0d35dfba999e9c316f03623bf5688c82fb83cc74a80ea248'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard_plugin_profile', '2.5.0', { + 'checksums': ['f832698d87a773b9a017fc4dd5cf598a1ff942ccfbf3392c83fe12c949ab9f52'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('dill', '0.3.4', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.5.0', { + 'checksums': ['e13b148008adeb2793cf8b55bcd20fdcec4f763f2d3bf3c45f5e5e5d1df7d228'], + }), + ('absl-py', '1.0.0', { + 'checksums': ['ac511215c01ee9ae47b19716599e8ccfa746f2e18de72bdf641b79b22afa27ea'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.7.1_fix_protobuf_error_message.patch', + 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' + '-benchmark-test,-v1only'), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + 'checksums': [ + 'abebe2cf5ca379e18071693ca5f45b88ade941b16258a21cc1f12d77d5387a21', # v2.7.1.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', + # TensorFlow-2.5.0_disable-avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_fix-crash-on-shutdown.patch + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', + # TensorFlow-2.7.1_fix_protobuf_error_message.patch + '301ce21845987dc7868624880c0d85e60aa5491c5a0bae0f6ebc8db5727960a5', + # TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch + 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix_protobuf_error_message.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix_protobuf_error_message.patch new file mode 100644 index 00000000000..ea00d8cca0d --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix_protobuf_error_message.patch @@ -0,0 +1,15 @@ +Fix an issue where TensorFlow 2.5/2.6 won't build with a protobuf newer than 3.14 +Solution/patch obtained from https://bugs.gentoo.org/800824 + +diff -Nrup tensorflow-2.5.0_old/tensorflow/core/kernels/example_parsing_ops.cc tensorflow-2.5.0/tensorflow/core/kernels/example_parsing_ops.cc +--- tensorflow-2.5.0_old/tensorflow/core/kernels/example_parsing_ops.cc 2021-05-12 15:26:41.000000000 +0200 ++++ tensorflow-2.5.0/tensorflow/core/kernels/example_parsing_ops.cc 2021-07-14 08:09:39.927536430 +0200 +@@ -1218,7 +1218,7 @@ class DecodeJSONExampleOp : public OpKer + resolver_.get(), "type.googleapis.com/tensorflow.Example", &in, &out); + OP_REQUIRES(ctx, status.ok(), + errors::InvalidArgument("Error while parsing JSON: ", +- string(status.error_message()))); ++ string(status.message()))); + } + } + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch new file mode 100644 index 00000000000..c319243a416 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch @@ -0,0 +1,46 @@ +TensorFlow adds some GPU tests twice increasing the runtime of the test suite. +This filters out the test part meant for CPU. + +See https://github.com/tensorflow/tensorflow/issues/47081 + +Author: Alexander Grund (TU Dresden) + +diff -ur tensorflow-2.7.1.orig/tensorflow/tensorflow.bzl tensorflow-2.7.1/tensorflow/tensorflow.bzl +--- tensorflow-2.7.1.orig/tensorflow/tensorflow.bzl 2022-01-30 16:27:47.000000000 +0100 ++++ tensorflow-2.7.1/tensorflow/tensorflow.bzl 2022-02-12 21:20:58.679307477 +0100 +@@ -1195,20 +1195,21 @@ + kernels = [], + linkopts = [], + **kwargs): +- tf_cc_test( +- name = name, +- size = size, +- srcs = srcs, +- args = args, +- data = data, +- extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), +- kernels = kernels, +- linkopts = linkopts, +- linkstatic = linkstatic, +- tags = tags, +- deps = deps, +- **kwargs +- ) ++ if 'gpu' not in tags: ++ tf_cc_test( ++ name = name, ++ size = size, ++ srcs = srcs, ++ args = args, ++ data = data, ++ extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), ++ kernels = kernels, ++ linkopts = linkopts, ++ linkstatic = linkstatic, ++ tags = tags, ++ deps = deps, ++ **kwargs ++ ) + tf_cc_test( + name = name, + size = size, From 8e4ff219c4722b477b3031d4b498992c38738e80 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 14 Feb 2022 08:55:40 +0100 Subject: [PATCH 3059/9987] add missing flatbuffers and flatbuffers-python deps --- .../flatbuffers-python-2.0-GCCcore-11.2.0.eb | 27 +++++++++++++++ .../flatbuffers-2.0.0-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-2.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-2.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..3a19ada08f2 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-2.0-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'flatbuffers-python' +version = '2.0' + +homepage = 'https://github.com/google/flatbuffers/' +description = """Python Flatbuffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/f/flatbuffers'] +sources = [{'download_filename': 'flatbuffers-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['12158ab0272375eab8db2d663ae97370c33f152b27801fa6024e1d6105fd4dd2'] + +dependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'VERSION=%(version)s ' +options = {'modulename': 'flatbuffers'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6fbc058da44 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.0-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '2.0.0' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['9ddb9031798f4f8754d00fca2f1a68ecf9d0f83dfac7239af1311e4fd9a565c4'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('Ninja', '1.10.2'), + ('Python', '3.9.6'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' From 14dd5a72b073ffa80ffc46646262bce0db0d4a78 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 14 Feb 2022 11:52:54 +0100 Subject: [PATCH 3060/9987] fixed checksum issue --- .../s/STRique/STRique-0.4.2-foss-2021b.eb | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb index 742b1ed5d3d..e144c6f7bb0 100644 --- a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb +++ b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb @@ -31,10 +31,7 @@ local_preconfigopts += "sed -i -e 's/#pomegranate/pomegranate/' requirements.txt exts_list = [ ('pomegranate', '0.10.0', { - 'sources': - [{'source_urls': ['https://github.com/jmschrei/pomegranate/archive/'], - 'download_filename': '523fb286b5199c64a271a35d49c1ac8fb524408d.tar.gz', - 'filename': 'pomegranate-0.10.0.tar.gz'}], + 'sources': [{'source_urls': ['https://github.com/jmschrei/pomegranate/archive/'], 'download_filename': '523fb286b5199c64a271a35d49c1ac8fb524408d.tar.gz', 'filename': 'pomegranate-0.10.0.tar.gz'}], 'checksums': ['9a16eef72a374094dcf6a04527f07ed61ed46b47719b624ccbed4180b0805ce9'], }), ('ont-fast5-api', '4.0.0', { @@ -53,15 +50,9 @@ exts_list = [ 'cat <(echo "#!/usr/bin/env python") scripts/fast5Masker.py > %(installdir)s/bin/fast5Masker', 'chmod +x %(installdir)s/bin/*', ], - 'preconfigopts': local_preconfigopts, - 'sources': [ - {'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': {'url': 'https://github.com/giesselmann', - 'repo_name': 'STRique', - 'commit': '585273215abff7956f5d6277601f0a6be2211a96', - 'recursive': True} - }], - 'checksums': ['e320325373a2833cecc6968f63a86b2b0ee3d057d23f554de2db87ffec6934d6'], + 'preconfigopts': "sed -i -e '/SeqAn/,+6d' CMakeLists.txt && sed -i -e 's/#pomegranate/pomegranate/' requirements.txt && ", + 'sources': [{'filename': '%(name)s-%(version)s.tar.gz', 'git_config': {'url': 'https://github.com/giesselmann', 'repo_name': 'STRique', 'commit': '585273215abff7956f5d6277601f0a6be2211a96', 'recursive': True}}], + 'checksums': ['1e2f6b9100a5cdae39cf22da72f48102dc4094de490c689422d8b5c881f5c714'], }), ] From 93b089c4d6ca7b0b79dbf3a052b5e6621f2d82f5 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 14 Feb 2022 14:32:26 +0100 Subject: [PATCH 3061/9987] add additional valid checksum for optmatch 0.9-15 in extension in R 4.1.2 --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 7043d2cb89f..a5bfa900bfe 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -2143,7 +2143,8 @@ exts_list = [ 'checksums': ['05e89a1678a39e32bfb41af8a31d643b04fc4d2660a96e701825e6bffcd75a52'], }), ('optmatch', '0.9-15', { - 'checksums': ['7500fdbed939b7f16603a097d734a332793a3ac68e6a80c7957bef2a567691d8'], + 'checksums': [('7500fdbed939b7f16603a097d734a332793a3ac68e6a80c7957bef2a567691d8', + 'f37254b3af586ffa259f09914e27cba576b6f4ef023b794195014d29f715895b')], }), ('SPAtest', '3.1.2', { 'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'], From ef56865131792fcac3688827424140fc78d3017e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 14 Feb 2022 17:01:26 +0200 Subject: [PATCH 3062/9987] restore parallelism of grpcio in TensorFlow v2.4.4 --- .../easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb index 52e760fb4f4..ab4f13c9527 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.4-foss-2021a.eb @@ -50,6 +50,7 @@ use_pip = True # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d exts_list = [ + # TF 2.4 needs h5py 2.10, later versions allow 3.x ('h5py', '2.10.0', { 'patches': ['h5py-2.10.0_avoid-mpi-init.patch'], 'preinstallopts': 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" ', @@ -96,6 +97,7 @@ exts_list = [ ('grpcio', '1.43.0', { 'modulename': 'grpc', 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", }), ('gviz-api', '1.10.0', { 'source_tmpl': 'gviz_api-%(version)s.tar.gz', From 1c046582cd571e235e7c8ac4ae93c359d90c84ca Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 15 Feb 2022 11:11:58 +0100 Subject: [PATCH 3063/9987] restoring broken original extensions --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 1c8159ba6ec..87f50a34e09 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -224,7 +224,8 @@ exts_list = [ 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], }), ('MASS', '7.3-54', { - 'checksums': ['b800ccd5b5c2709b1559cf5eab126e4935c4f8826cf7891253432bb6a056e821'], + 'checksums': [('b800ccd5b5c2709b1559cf5eab126e4935c4f8826cf7891253432bb6a056e821', + 'eb644c0e94b447c46387aa22436ef5a43192960ee9cfd0df2940f4a4116179ae')], }), ('pixmap', '0.4-12', { 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], @@ -536,7 +537,8 @@ exts_list = [ 'checksums': ['eff3a92756ca34cdc1661fa36d2bf7fc8e9f4132d2f1ef9ed0105c83594618bf'], }), ('class', '7.3-19', { - 'checksums': ['7820ae94b22009561a69ed1f8b2ca2a3814be6a656e9884738206997caecbe37'], + 'checksums': [('7820ae94b22009561a69ed1f8b2ca2a3814be6a656e9884738206997caecbe37', + '9012f5c65384b441b5738ed7bd18ea735884bab32b31776e80cf3679f38a3769')], }), ('proxy', '0.4-26', { 'checksums': ['676bad821343974e0297a0566c4bf0cf0ea890104906a745b87d3b5989c81a4d'], @@ -545,7 +547,8 @@ exts_list = [ 'checksums': ['9bf9a15e7ce0b9b1a57ce3048d29cbea7f2a5bb2e91271b1b6aaafe07c852226'], }), ('nnet', '7.3-16', { - 'checksums': ['99511969babaf937c3033750b00b41e4e03742f268084efc4ee953b849f7b56a'], + 'checksums': [('99511969babaf937c3033750b00b41e4e03742f268084efc4ee953b849f7b56a', + 'c5b73eb4fff0d225e14f898cec987a7a88796b6e70cde4cf277374428f2d5c13')], }), ('minqa', '1.2.4', { 'checksums': ['cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c'], @@ -842,7 +845,8 @@ exts_list = [ 'checksums': ['9b12184a28fff87cacd0c3602d0cf63acb4d0f3049ad3a6ff16177f6df350782'], }), ('spatial', '7.3-14', { - 'checksums': ['52cc1982732f14544fae7dd9d028e2fc3b525ed695d211d6ed5055420e768a36'], + 'checksums': [('52cc1982732f14544fae7dd9d028e2fc3b525ed695d211d6ed5055420e768a36', + '50e6daacbacff6c716485d20b15eb7fff7b8108dc5ea0ff508024beb4f0a8b9b')], }), ('VGAM', '1.1-5', { 'checksums': ['30190b150f3e5478137d288a45f575b2654ad7c29254b0a1fe5c954ee010a1bb'], @@ -3208,6 +3212,9 @@ exts_list = [ ('ldbounds', '1.1-1.1', { 'checksums': ['e88e6bff43762a9f7d80484056d10c7d2fd80969b43061d8cc96c3bd5b9c3583'], }), + ('catlearn', '0.8', { + 'checksums': ['0d13da431a5511b025090b7ffaa3765b94b33c7de5a7cc1cec8c50437755646e'], + }), ('EValue', version, { 'checksums': ['d9f3feb3da2efaf4e5d794e05475be62666192a7c855e373c3d369324078690c'], }), From 16ab9d0b6e637cc6275790770f1982faa24bc252 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 15 Feb 2022 11:26:58 +0100 Subject: [PATCH 3064/9987] fixed checksums issue --- .../s/STRique/STRique-0.4.2-foss-2021b.eb | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb index e144c6f7bb0..99f751123a1 100644 --- a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb +++ b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb @@ -31,7 +31,11 @@ local_preconfigopts += "sed -i -e 's/#pomegranate/pomegranate/' requirements.txt exts_list = [ ('pomegranate', '0.10.0', { - 'sources': [{'source_urls': ['https://github.com/jmschrei/pomegranate/archive/'], 'download_filename': '523fb286b5199c64a271a35d49c1ac8fb524408d.tar.gz', 'filename': 'pomegranate-0.10.0.tar.gz'}], + 'sources': [{ + 'source_urls': ['https://github.com/jmschrei/pomegranate/archive/'], + 'download_filename': '523fb286b5199c64a271a35d49c1ac8fb524408d.tar.gz', + 'filename': 'pomegranate-0.10.0.tar.gz' + }], 'checksums': ['9a16eef72a374094dcf6a04527f07ed61ed46b47719b624ccbed4180b0805ce9'], }), ('ont-fast5-api', '4.0.0', { @@ -50,9 +54,16 @@ exts_list = [ 'cat <(echo "#!/usr/bin/env python") scripts/fast5Masker.py > %(installdir)s/bin/fast5Masker', 'chmod +x %(installdir)s/bin/*', ], - 'preconfigopts': "sed -i -e '/SeqAn/,+6d' CMakeLists.txt && sed -i -e 's/#pomegranate/pomegranate/' requirements.txt && ", - 'sources': [{'filename': '%(name)s-%(version)s.tar.gz', 'git_config': {'url': 'https://github.com/giesselmann', 'repo_name': 'STRique', 'commit': '585273215abff7956f5d6277601f0a6be2211a96', 'recursive': True}}], - 'checksums': ['1e2f6b9100a5cdae39cf22da72f48102dc4094de490c689422d8b5c881f5c714'], + 'preconfigopts': local_preconfigopts, + 'sources': [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/giesselmann', + 'repo_name': 'STRique', 'commit': '585273215abff7956f5d6277601f0a6be2211a96', + 'recursive': True + } + }], + 'checksums': [None], }), ] From e17e3b466fd1fb5ede559fc63f3d77a33f8de5ac Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 15 Feb 2022 11:00:58 +0000 Subject: [PATCH 3065/9987] reference upstream issue in patch --- .../easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb | 2 +- .../a/AlphaFold/AlphaFold-2.1_fix-alphafold-tests.patch | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb index 458badb2a78..1cff76362a0 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.1-fosscuda-2020b.eb @@ -91,7 +91,7 @@ components = [ '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch '3b9ee75aba872d912e2bca401a794054d652d47fb9e87e53e99781cef3c3091f', # AlphaFold-2.0.0_relax_gpu.patch # AlphaFold-2.1_fix-alphafold-tests.patch - '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1_fix-alphafold-tests.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1_fix-alphafold-tests.patch index 65c9b87c89e..13083a331d4 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1_fix-alphafold-tests.patch +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1_fix-alphafold-tests.patch @@ -1,4 +1,5 @@ Fix `run_alphafold_test.py` to use an unique directory per test to avoid pollution when the tests are run multiple times +See https://github.com/deepmind/alphafold/issues/365 Patch by Simon Branford (University of Birmingham) --- run_alphafold_test.py.orig 2022-02-13 11:09:48.465041000 +0000 +++ run_alphafold_test.py 2022-02-13 12:02:17.963970000 +0000 From b911da4de7c6c2254d66318fc41a732b0eadc320 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 15 Feb 2022 13:41:47 +0100 Subject: [PATCH 3066/9987] code style errors --- easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb index 99f751123a1..4365a64431c 100644 --- a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb +++ b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb @@ -35,7 +35,7 @@ exts_list = [ 'source_urls': ['https://github.com/jmschrei/pomegranate/archive/'], 'download_filename': '523fb286b5199c64a271a35d49c1ac8fb524408d.tar.gz', 'filename': 'pomegranate-0.10.0.tar.gz' - }], + }], 'checksums': ['9a16eef72a374094dcf6a04527f07ed61ed46b47719b624ccbed4180b0805ce9'], }), ('ont-fast5-api', '4.0.0', { @@ -61,8 +61,8 @@ exts_list = [ 'url': 'https://github.com/giesselmann', 'repo_name': 'STRique', 'commit': '585273215abff7956f5d6277601f0a6be2211a96', 'recursive': True - } - }], + } + }], 'checksums': [None], }), ] From a8063fc42df9dae69994776050ee50b986bb8777 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Feb 2022 15:22:03 +0100 Subject: [PATCH 3067/9987] adding easyconfigs: ORCA-5.0.3-gompi-2021b.eb --- .../o/ORCA/ORCA-5.0.3-gompi-2021b.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.3-gompi-2021b.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.3-gompi-2021b.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.3-gompi-2021b.eb new file mode 100644 index 00000000000..e296dc5c54d --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.3-gompi-2021b.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '5.0.3' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +# Shared build of ORCA: download from https://orcaforum.kofo.mpg.de +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi411.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_5_0_3_linux_x86-64_shared_openmpi411.tar.xz + 'b8b9076d1711150a6d6cb3eb30b18e2782fa847c5a86d8404b9339faef105043', +] + +moduleclass = 'chem' From 94aca10ecaf6d659a75bfb3d7dfeed2344a9ab34 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 15 Feb 2022 17:24:42 +0200 Subject: [PATCH 3068/9987] adding easyconfigs: NLTK-3.6.7-foss-2021a.eb, NLTK-3.7-foss-2021b.eb --- .../n/NLTK/NLTK-3.6.7-foss-2021a.eb | 53 +++++++++++++++++++ .../easyconfigs/n/NLTK/NLTK-3.7-foss-2021b.eb | 53 +++++++++++++++++++ 2 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLTK/NLTK-3.6.7-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/NLTK/NLTK-3.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/n/NLTK/NLTK-3.6.7-foss-2021a.eb b/easybuild/easyconfigs/n/NLTK/NLTK-3.6.7-foss-2021a.eb new file mode 100644 index 00000000000..a26167bb1ab --- /dev/null +++ b/easybuild/easyconfigs/n/NLTK/NLTK-3.6.7-foss-2021a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'NLTK' +version = '3.6.7' + +homepage = 'https://www.nltk.org/' +description = "NLTK is a leading platform for building Python programs to work with human language data." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-learn', '0.24.2'), + ('matplotlib', '3.4.2'), + ('tqdm', '4.61.2'), +] + +local_nltk_data_install = [] +# Install NLTK data sets (7.4 GB) +# local_nltk_data = '/path/to/database/nltk_data' +# local_nltk_data_install = [ +# "mkdir -p %s && NLTK_DATA=%s python -m nltk.downloader all" % (local_nltk_data, local_nltk_data) +# ] +# modextravars = {'NLTK_DATA': local_nltk_data} + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('regex', '2021.8.28', { + 'checksums': ['f585cbbeecb35f35609edccb95efd95a3e35824cd7752b586503f7e6087303f1'], + }), + ('python-crfsuite', '0.9.7', { + 'modulename': 'pycrfsuite', + 'checksums': ['3b4538d2ce5007e4e42005818247bf43ade89ef08a66d158462e2f7c5d63cee7'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.zip', + 'checksums': ['51bf1aef5304740a708be7c8e683f7798f03dc5c7a7e7feb758be9e95f4585e3'], + 'use_pip_extras': 'corenlp,machine_learning,plot,tgrep', + 'postinstallcmds': local_nltk_data_install, + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = [('%(namelower)s', '--version')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/NLTK/NLTK-3.7-foss-2021b.eb b/easybuild/easyconfigs/n/NLTK/NLTK-3.7-foss-2021b.eb new file mode 100644 index 00000000000..f0cf22b03b5 --- /dev/null +++ b/easybuild/easyconfigs/n/NLTK/NLTK-3.7-foss-2021b.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'NLTK' +version = '3.7' + +homepage = 'https://www.nltk.org/' +description = "NLTK is a leading platform for building Python programs to work with human language data." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('scikit-learn', '1.0.1'), + ('matplotlib', '3.4.3'), + ('tqdm', '4.62.3'), +] + +local_nltk_data_install = [] +# Install NLTK data sets (7.4 GB) +# local_nltk_data = '/path/to/database/nltk_data' +# local_nltk_data_install = [ +# "mkdir -p %s && NLTK_DATA=%s python -m nltk.downloader all" % (local_nltk_data, local_nltk_data) +# ] +# modextravars = {'NLTK_DATA': local_nltk_data} + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('regex', '2022.1.18', { + 'checksums': ['97f32dc03a8054a4c4a5ab5d761ed4861e828b2c200febd4e46857069a483916'], + }), + ('python-crfsuite', '0.9.7', { + 'modulename': 'pycrfsuite', + 'checksums': ['3b4538d2ce5007e4e42005818247bf43ade89ef08a66d158462e2f7c5d63cee7'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.zip', + 'checksums': ['d6507d6460cec76d70afea4242a226a7542f85c669177b9c7f562b7cf1b05502'], + 'use_pip_extras': 'corenlp,machine_learning,plot,tgrep', + 'postinstallcmds': local_nltk_data_install, + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = [('%(namelower)s', '--version')] + +moduleclass = 'devel' From 58c231029ae80e08fccf50116896267cccbe848a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 15 Feb 2022 16:33:00 +0100 Subject: [PATCH 3069/9987] respect parallel parameter in XGBoost v1.5.0 --- easybuild/easyconfigs/x/XGBoost/XGBoost-1.5.0-foss-2021a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.5.0-foss-2021a.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.5.0-foss-2021a.eb index 21900bfc76c..6aeb30ed98c 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.5.0-foss-2021a.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.5.0-foss-2021a.eb @@ -23,4 +23,7 @@ use_pip = True download_dep_fail = True sanity_pip_check = True +# use the parallel parameter from EB instead of total procs in the system +preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&" + moduleclass = 'lib' From 34992313ba6dd0951930dfa93afc413cb14c6d49 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 15 Feb 2022 17:04:55 +0100 Subject: [PATCH 3070/9987] reordered extensions --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 87f50a34e09..8029681675d 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3215,6 +3215,9 @@ exts_list = [ ('catlearn', '0.8', { 'checksums': ['0d13da431a5511b025090b7ffaa3765b94b33c7de5a7cc1cec8c50437755646e'], }), + ('MetaUtility', '2.1.2', { + 'checksums': ['e38c21588c239aa8926e64d916aa0f3b04108c2992f0e801095e4c7920b9ad5d'], + }), ('EValue', version, { 'checksums': ['d9f3feb3da2efaf4e5d794e05475be62666192a7c855e373c3d369324078690c'], }), @@ -3227,9 +3230,6 @@ exts_list = [ ('metadat', '1.0-0', { 'checksums': ['ed335a4eb2145fffde20e36077e360f9d36a615e9d93453d2bbd6f5967db4b9c'], }), - ('MetaUtility', '2.1.2', { - 'checksums': ['e38c21588c239aa8926e64d916aa0f3b04108c2992f0e801095e4c7920b9ad5d'], - }), ('simex', '1.8', { 'checksums': ['80c7841196b9377a9367eb6960ad80ca0bf8de511b8b18a0031bfbe7bde289a0'], }), From e2fb36d108c368179d1c763aa6e1a473c7db6c39 Mon Sep 17 00:00:00 2001 From: alexandermichels Date: Tue, 15 Feb 2022 16:49:03 -0500 Subject: [PATCH 3071/9987] adding easyconfigs: GEOS-3.8.0-GCC-8.3.0.eb --- .../g/GEOS/GEOS-3.8.0-GCC-8.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-GCC-8.3.0.eb new file mode 100644 index 00000000000..4ce0c6ab74a --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.8.0-GCC-8.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.8.0' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = [ + '99114c3dc95df31757f44d2afde73e61b9f742f0b683fd1894cbbee05dda62d5', # geos-3.8.0.tar.bz2 +] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [] +} + +moduleclass = 'math' From 56b44a41ad2e74b487b2fc8b0cb7b34a586ff58b Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 16 Feb 2022 10:22:09 +0100 Subject: [PATCH 3072/9987] Update easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb index 26ae15f4f3c..7400f8d4a00 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -80,6 +80,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.1_fix-alphafold-tests.patch', ], 'checksums': [ 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz From e98efcdc6fc72b14c2875cb26d07b2a5b16a43cf Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 16 Feb 2022 10:22:32 +0100 Subject: [PATCH 3073/9987] Update easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb index 7400f8d4a00..15061d7ae70 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -90,6 +90,8 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + # AlphaFold-2.1_fix-alphafold-tests.patch + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From 8a2c7025c48841bf008e98f5dda7939456affcff Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 16 Feb 2022 10:22:56 +0100 Subject: [PATCH 3074/9987] Update easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb index 8b9e592efd7..2f7e104ba00 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb @@ -89,6 +89,8 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + # AlphaFold-2.1_fix-alphafold-tests.patch + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From 4b76ba17262001b19b977cf5046528afe03b5576 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 16 Feb 2022 10:23:19 +0100 Subject: [PATCH 3075/9987] Update easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb index 2f7e104ba00..8a7378e0a4d 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb @@ -80,6 +80,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.1_fix-alphafold-tests.patch', ], 'checksums': [ 'a687d5de2dfb3516113e1e438871adec1292fc64fddd76253d65db9c80308073', # v2.1.2.tar.gz From c3c0f1502bcc0ba4a4c2d55f5a2e47ca2615d6e7 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 16 Feb 2022 12:20:22 +0100 Subject: [PATCH 3076/9987] added sanity check commands --- .../easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb index 5b948710391..23501c97781 100644 --- a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb @@ -40,6 +40,17 @@ postinstallcmds = [ "cp -a %(builddir)s/seqan-*/include %(installdir)s", ] +sanity_check_commands = [ + ("gustaf_mate_joining --help"), + ("mason_materializer --help"), + ("mason_variator --help"), + ("rabema_prepare_sam --help"), + ("razers3 --help"), + ("samcat --help"), + ("splazers --help"), + ("yara_mapper --help"), +] + sanity_check_paths = { 'files': ["bin/%s" % x for x in ["gustaf_mate_joining", "mason_materializer", "mason_variator", "rabema_prepare_sam", "razers3", "seqan_tcoffee", "s4_join", "samcat", "splazers", From 018d8cbae3dd2fb2159122f01aa9e59a7948e4da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Feb 2022 13:24:27 +0100 Subject: [PATCH 3077/9987] adding easyconfigs: M1QN3-3.3-GCCcore-10.3.0.eb --- .../m/M1QN3/M1QN3-3.3-GCCcore-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/m/M1QN3/M1QN3-3.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/M1QN3/M1QN3-3.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/M1QN3/M1QN3-3.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8c4640da5fb --- /dev/null +++ b/easybuild/easyconfigs/m/M1QN3/M1QN3-3.3-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CmdCp' + +name = 'M1QN3' +version = '3.3' + +homepage = 'https://who.rocq.inria.fr/Jean-Charles.Gilbert/modulopt/optimization-routines/m1qn3/m1qn3.html' +description = "A solver of large-scale unconstrained minimization problems" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www-rocq.inria.fr/~gilbert/modulopt/optimization-routines/m1qn3/'] +sources = ['m1qn3-%(version)s-distrib.tgz'] +checksums = ['27c6a8f56a4080420c25ffb0743e3dece7c57cc1740776936f220b4ed28b89d9'] + +builddependencies = [('binutils', '2.36.1')] + +local_install_cmds = "$FC $FFLAGS -c src/m1qn3.f -o m1qn3.o && ar -r libm1qn3.a m1qn3.o && " +local_install_cmds += "$FC $FFLAGS -c blas/ddot.f -o ddot.o && ar -r libddot.a ddot.o" + +cmds_map = [('.*', local_install_cmds)] + +files_to_copy = [(['libm1qn3.a', 'libddot.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libddot.a', 'lib/libm1qn3.a'], + 'dirs': [], +} + +moduleclass = 'lib' From e30fe30e6aa8e823bc8fe78bb6e3d3fb9ddf7d73 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Feb 2022 15:57:23 +0200 Subject: [PATCH 3078/9987] use typing-extensions from Python v3.9.6 easyconfig in ArviZ and PyMC3 --- easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-intel-2021b.eb | 1 - easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-intel-2021b.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-intel-2021b.eb index 64ccfac5b2d..f03c0011d6e 100644 --- a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-intel-2021b.eb +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.11.4-intel-2021b.eb @@ -17,7 +17,6 @@ dependencies = [ ('netcdf4-python', '1.5.7'), ('xarray', '0.20.1'), ('matplotlib', '3.4.3'), - ('typing-extensions', '3.10.0.2'), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb index 31798f16016..3acb32f43cd 100644 --- a/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb +++ b/easybuild/easyconfigs/p/PyMC3/PyMC3-3.11.1-intel-2021b.eb @@ -21,7 +21,6 @@ dependencies = [ ('tqdm', '4.62.3'), ('netcdf4-python', '1.5.7'), ('xarray', '0.20.1'), - ('typing-extensions', '3.10.0.2'), ('ArviZ', '0.11.4'), ('dill', '0.3.4'), ] From caf20126901291679a581c0e30e25aefdeb259ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Feb 2022 15:40:19 +0100 Subject: [PATCH 3079/9987] use GCC toolchain for M1QN3 --- .../{M1QN3-3.3-GCCcore-10.3.0.eb => M1QN3-3.3-GCC-10.3.0.eb} | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) rename easybuild/easyconfigs/m/M1QN3/{M1QN3-3.3-GCCcore-10.3.0.eb => M1QN3-3.3-GCC-10.3.0.eb} (89%) diff --git a/easybuild/easyconfigs/m/M1QN3/M1QN3-3.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/M1QN3/M1QN3-3.3-GCC-10.3.0.eb similarity index 89% rename from easybuild/easyconfigs/m/M1QN3/M1QN3-3.3-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/m/M1QN3/M1QN3-3.3-GCC-10.3.0.eb index 8c4640da5fb..4cd7c6df9b1 100644 --- a/easybuild/easyconfigs/m/M1QN3/M1QN3-3.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/M1QN3/M1QN3-3.3-GCC-10.3.0.eb @@ -6,15 +6,13 @@ version = '3.3' homepage = 'https://who.rocq.inria.fr/Jean-Charles.Gilbert/modulopt/optimization-routines/m1qn3/m1qn3.html' description = "A solver of large-scale unconstrained minimization problems" -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchain = {'name': 'GCC', 'version': '10.3.0'} toolchainopts = {'pic': True} source_urls = ['http://www-rocq.inria.fr/~gilbert/modulopt/optimization-routines/m1qn3/'] sources = ['m1qn3-%(version)s-distrib.tgz'] checksums = ['27c6a8f56a4080420c25ffb0743e3dece7c57cc1740776936f220b4ed28b89d9'] -builddependencies = [('binutils', '2.36.1')] - local_install_cmds = "$FC $FFLAGS -c src/m1qn3.f -o m1qn3.o && ar -r libm1qn3.a m1qn3.o && " local_install_cmds += "$FC $FFLAGS -c blas/ddot.f -o ddot.o && ar -r libddot.a ddot.o" From 7275f9045e3b048489844707f7ad6dde1c46e663 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Feb 2022 20:03:27 +0100 Subject: [PATCH 3080/9987] use official software name for Devito, add dask as proper dependency + remove unneeded extensions, don't use lowopt toolchain option --- .../Devito-4.6.1-foss-2020a-Python-3.8.2.eb} | 77 ++++++------------- 1 file changed, 22 insertions(+), 55 deletions(-) rename easybuild/easyconfigs/d/{devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb => Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb} (67%) diff --git a/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb similarity index 67% rename from easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb rename to easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb index 151b5359b4d..8c6d9d19eb7 100644 --- a/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb @@ -1,24 +1,24 @@ easyblock = 'PythonBundle' -name = 'devito' +name = 'Devito' version = '4.6.1' -versionsuffix = '-Python-3.8.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://devitoproject.org/' description = "Devito is a domain-specific Language (DSL) and code generation framework" toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'lowopt': True} +toolchainopts = {'pic': True} dependencies = [ ('Python', '3.8.2'), ('PyYAML', '5.3'), ('SciPy-bundle', '2020.03', versionsuffix), ('IPython', '7.15.0', versionsuffix), + ('dask', '2021.12.0', versionsuffix), ] use_pip = True -sanity_pip_check = True # order is important! exts_list = [ @@ -34,39 +34,21 @@ exts_list = [ ('codecov', '2.1.12', { 'checksums': ['a0da46bb5025426da895af90938def8ee12d37fcbcbbbc15b6dc64cf7ebc51c1'], }), - ('codepy', '2019.1', { - 'checksums': ['384f22c37fe987c0ca71951690c3c2fd14dacdeddbeb0fde4fd01cd84859c94e'], - }), - ('distributed', '2021.12.0', { - 'checksums': ['c6119a2cf1fb2d8ac60337915bb9a790af6530afcb5d7a809a3308323b874714'], + ('setuptools_scm', '6.0.1', { + 'checksums': ['d1925a69cb07e9b29416a275b9fadb009a23c148ace905b2fb220649a6c18e92'], }), - ('cloudpickle', '2.0.0', { - 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + ('platformdirs', '2.2.0', { + 'checksums': ['632daad3ab546bd8e6af0537d09805cec458dce201bccfe23012df73332e181e'], }), - ('dask', '2021.12.0', { - 'checksums': ['90614c9d162713e4849532c86f2854e8d53468521285413403b6c496344c0109'], + ('pytools', '2022.1', { + 'checksums': ['197aacf6e1f5d60c715b92438792acb7702aed59ebbfb147fa84eda780e54fee'], }), - ('msgpack', '1.0.3', { - 'checksums': ['51fdc7fb93615286428ee7758cecc2f374d5ff363bdd884c7ea622a7a327a81e'], + ('codepy', '2019.1', { + 'checksums': ['384f22c37fe987c0ca71951690c3c2fd14dacdeddbeb0fde4fd01cd84859c94e'], }), ('coverage', '6.3.1', { 'checksums': ['6c3f6158b02ac403868eea390930ae64e9a9a2a5bbfafefbb920d29258d9f2f8'], }), - ('tblib', '1.7.0', { - 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], - }), - ('toolz', '0.11.2', { - 'checksums': ['6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33'], - }), - ('tornado', '6.1', { - 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], - }), - ('zict', '2.0.0', { - 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], - }), - ('flake8', '4.0.1', { - 'checksums': ['806e034dda44114815e23c16ef92f95c91e4c71100ff52813adf7132a6ad870d'], - }), ('mccabe', '0.6.1', { 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], }), @@ -76,8 +58,8 @@ exts_list = [ ('pyflakes', '2.4.0', { 'checksums': ['05a85c2872edf37a4ed30b0cce2f6093e1d0581f8c19d7393122da7e25b2b24c'], }), - ('HeapDict', '1.0.1', { - 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + ('flake8', '4.0.1', { + 'checksums': ['806e034dda44114815e23c16ef92f95c91e4c71100ff52813adf7132a6ad870d'], }), ('multidict', '6.0.2', { 'checksums': ['5ff3bd75f38e4c43f1f470f2df7a4d430b821c4ce22be384e1459cb57d6bb013'], @@ -89,6 +71,9 @@ exts_list = [ 'modulename': 'cpuinfo', 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], }), + ('contexttimer', '0.3.3', { + 'checksums': ['35a1efd389af3f1ca509f33ff23e17d98b66c8fde5ba2a4eb8a8b7fa456598a5'], + }), ('pyrevolve', '2.2', { 'checksums': ['b49aea5cd6c520ac5fcd1d25fa23fe2c5502741d2965f3eee10be067e7b0efb4'], }), @@ -99,33 +84,15 @@ exts_list = [ 'modulename': 'pytest', 'checksums': ['0fce5b8dc68760f353979d99fdd6b3ad46330b6b1837e2077a89ebcf204aac91'], }), - ('devito', '4.6.1', { - 'checksums': ['e8acc4840953547c267706195df32738c95d0e51f7592eb0796a0efcc8cc5dbf'], - }), - ('contexttimer', '0.3.3', { - 'checksums': ['35a1efd389af3f1ca509f33ff23e17d98b66c8fde5ba2a4eb8a8b7fa456598a5'], - }), + # devito requires sympy<=1.9,>=1.7 ('sympy', '1.9', { 'checksums': ['c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc'], }), - ('fsspec', '2022.1.0', { - 'checksums': ['0bdd519bbf4d8c9a1d893a50b5ebacc89acd0e1fe0045d2f7b0e0c1af5990edc'], - }), - ('partd', '1.2.0', { - 'checksums': ['aa67897b84d522dcbc86a98b942afab8c6aa2f7f677d904a616b74ef5ddbc3eb'], - }), - ('pytools', '2022.1', { - 'checksums': ['197aacf6e1f5d60c715b92438792acb7702aed59ebbfb147fa84eda780e54fee'], - }), - ('setuptools_scm', '6.0.1', { - 'checksums': ['d1925a69cb07e9b29416a275b9fadb009a23c148ace905b2fb220649a6c18e92'], - }), - ('platformdirs', '2.2.0', { - 'checksums': ['632daad3ab546bd8e6af0537d09805cec458dce201bccfe23012df73332e181e'], - }), - ('locket', '0.2.1', { - 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], + ('devito', version, { + 'checksums': ['e8acc4840953547c267706195df32738c95d0e51f7592eb0796a0efcc8cc5dbf'], }), ] +sanity_pip_check = True + moduleclass = 'lang' From a7f25c215b61880da7964425526d991e73a50e01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Feb 2022 20:07:17 +0100 Subject: [PATCH 3081/9987] fix homepage for Devito --- .../d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb index 8c6d9d19eb7..9275d908693 100644 --- a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb @@ -4,7 +4,7 @@ name = 'Devito' version = '4.6.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://devitoproject.org/' +homepage = ' https://www.devitoproject.org' description = "Devito is a domain-specific Language (DSL) and code generation framework" toolchain = {'name': 'foss', 'version': '2020a'} From f4dbbb01308226323280225bf5def73e781ef1bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Feb 2022 20:24:20 +0100 Subject: [PATCH 3082/9987] remove space from homepage in Devito easyconfig --- .../d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb index 9275d908693..9e7a889ea3c 100644 --- a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb @@ -4,7 +4,7 @@ name = 'Devito' version = '4.6.1' versionsuffix = '-Python-%(pyver)s' -homepage = ' https://www.devitoproject.org' +homepage = 'https://www.devitoproject.org' description = "Devito is a domain-specific Language (DSL) and code generation framework" toolchain = {'name': 'foss', 'version': '2020a'} From f1097769407165fa3e2aff30c68938da552740e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Feb 2022 20:26:20 +0100 Subject: [PATCH 3083/9987] remove devito easyconfig (wrong software name) --- .../devito-4.6.1-foss-2020a-Python-3.8.2.eb | 131 ------------------ 1 file changed, 131 deletions(-) delete mode 100644 easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb deleted file mode 100644 index 03925d447ce..00000000000 --- a/easybuild/easyconfigs/d/devito/devito-4.6.1-foss-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,131 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'devito' -version = '4.6.1' -versionsuffix = '-Python-3.8.2' - -homepage = 'https://devitoproject.org/' -description = "Devito is a domain-specific Language (DSL) and code generation framework" - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'pic': True, 'lowopt': True} - -dependencies = [ - ('Python', '3.8.2'), - ('PyYAML', '5.3'), - ('SciPy-bundle', '2020.03', versionsuffix), - ('IPython', '7.15.0', versionsuffix), -] - -use_pip = True -sanity_pip_check = True - -# order is important! -exts_list = [ - ('anytree', '2.8.0', { - 'checksums': ['3f0f93f355a91bc3e6245319bf4c1d50e3416cc7a35cc1133c1ff38306bbccab'], - }), - ('cached-property', '1.5.2', { - 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], - }), - ('cgen', '2020.1', { - 'checksums': ['4ec99d0c832d9f95f5e51dd18a629ad50df0b5464ce557ef42c6e0cd9478bfcf'], - }), - ('codecov', '2.1.12', { - 'checksums': ['a0da46bb5025426da895af90938def8ee12d37fcbcbbbc15b6dc64cf7ebc51c1'], - }), - ('codepy', '2019.1', { - 'checksums': ['384f22c37fe987c0ca71951690c3c2fd14dacdeddbeb0fde4fd01cd84859c94e'], - }), - ('distributed', '2021.12.0', { - 'checksums': ['c6119a2cf1fb2d8ac60337915bb9a790af6530afcb5d7a809a3308323b874714'], - }), - ('cloudpickle', '2.0.0', { - 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], - }), - ('dask', '2021.12.0', { - 'checksums': ['90614c9d162713e4849532c86f2854e8d53468521285413403b6c496344c0109'], - }), - ('msgpack', '1.0.3', { - 'checksums': ['51fdc7fb93615286428ee7758cecc2f374d5ff363bdd884c7ea622a7a327a81e'], - }), - ('coverage', '6.3.1', { - 'checksums': ['6c3f6158b02ac403868eea390930ae64e9a9a2a5bbfafefbb920d29258d9f2f8'], - }), - ('tblib', '1.7.0', { - 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], - }), - ('toolz', '0.11.2', { - 'checksums': ['6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33'], - }), - ('tornado', '6.1', { - 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], - }), - ('zict', '2.0.0', { - 'checksums': ['8e2969797627c8a663575c2fc6fcb53a05e37cdb83ee65f341fc6e0c3d0ced16'], - }), - ('flake8', '4.0.1', { - 'checksums': ['806e034dda44114815e23c16ef92f95c91e4c71100ff52813adf7132a6ad870d'], - }), - ('mccabe', '0.6.1', { - 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], - }), - ('pycodestyle', '2.8.0', { - 'checksums': ['eddd5847ef438ea1c7870ca7eb78a9d47ce0cdb4851a5523949f2601d0cbbe7f'], - }), - ('pyflakes', '2.4.0', { - 'checksums': ['05a85c2872edf37a4ed30b0cce2f6093e1d0581f8c19d7393122da7e25b2b24c'], - }), - ('HeapDict', '1.0.1', { - 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], - }), - ('multidict', '6.0.2', { - 'checksums': ['5ff3bd75f38e4c43f1f470f2df7a4d430b821c4ce22be384e1459cb57d6bb013'], - }), - ('nbval', '0.9.6', { - 'checksums': ['cfefcd2ef66ee2d337d0b252c6bcec4023384eb32e8b9e5fcc3ac80ab8cd7d40'], - }), - ('py-cpuinfo', '8.0.0', { - 'modulename': 'cpuinfo', - 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], - }), - ('pyrevolve', '2.2', { - 'checksums': ['b49aea5cd6c520ac5fcd1d25fa23fe2c5502741d2965f3eee10be067e7b0efb4'], - }), - ('pytest-cov', '3.0.0', { - 'checksums': ['e7f0f5b1617d2210a2cabc266dfe2f4c75a8d32fb89eafb7ad9d06f6d076d470'], - }), - ('pytest-runner', '5.3.1', { - 'modulename': 'pytest', - 'checksums': ['0fce5b8dc68760f353979d99fdd6b3ad46330b6b1837e2077a89ebcf204aac91'], - }), - ('devito', '4.6.1', { - 'checksums': ['e8acc4840953547c267706195df32738c95d0e51f7592eb0796a0efcc8cc5dbf'], - }), - ('contexttimer', '0.3.3', { - 'checksums': ['35a1efd389af3f1ca509f33ff23e17d98b66c8fde5ba2a4eb8a8b7fa456598a5'], - }), - ('sympy', '1.9', { - 'checksums': ['c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc'], - }), - ('fsspec', '2022.1.0', { - 'checksums': ['0bdd519bbf4d8c9a1d893a50b5ebacc89acd0e1fe0045d2f7b0e0c1af5990edc'], - }), - ('partd', '1.2.0', { - 'checksums': ['aa67897b84d522dcbc86a98b942afab8c6aa2f7f677d904a616b74ef5ddbc3eb'], - }), - ('pytools', '2022.1', { - 'checksums': ['197aacf6e1f5d60c715b92438792acb7702aed59ebbfb147fa84eda780e54fee'], - }), - ('setuptools_scm', '6.0.1', { - 'checksums': ['d1925a69cb07e9b29416a275b9fadb009a23c148ace905b2fb220649a6c18e92'], - }), - ('platformdirs', '2.2.0', { - 'checksums': ['632daad3ab546bd8e6af0537d09805cec458dce201bccfe23012df73332e181e'], - }), - ('locket', '0.2.1', { - 'checksums': ['3e1faba403619fe201552f083f1ecbf23f550941bc51985ac6ed4d02d25056dd'], - }), -] - -moduleclass = 'lang' From 41686a95a6aa76ffe2d5f3b717d23f351f880f0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Feb 2022 20:58:05 +0100 Subject: [PATCH 3084/9987] strip off trailing whitespace in Devito easyconfig --- .../d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb index 9e7a889ea3c..ecce191f083 100644 --- a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} dependencies = [ ('Python', '3.8.2'), ('PyYAML', '5.3'), - ('SciPy-bundle', '2020.03', versionsuffix), + ('SciPy-bundle', '2020.03', versionsuffix), ('IPython', '7.15.0', versionsuffix), ('dask', '2021.12.0', versionsuffix), ] From c7fc014ce89110e48741f1743d3c3d4af12ed166 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Feb 2022 21:55:31 +0100 Subject: [PATCH 3085/9987] fix dask version in dependencies in Devito easyconfig --- .../d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb index ecce191f083..5b0af7f8bc3 100644 --- a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb @@ -15,7 +15,7 @@ dependencies = [ ('PyYAML', '5.3'), ('SciPy-bundle', '2020.03', versionsuffix), ('IPython', '7.15.0', versionsuffix), - ('dask', '2021.12.0', versionsuffix), + ('dask', '2.18.1', versionsuffix), ] use_pip = True From 4492e214dc6174023c044eaa4bf56133380801ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Feb 2022 09:24:02 +0100 Subject: [PATCH 3086/9987] clean up sanity check for SeqAn 2.4.0 with GCCcore/11.2.0 --- .../s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb | 18 +++++------------- 1 file changed, 5 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb index 23501c97781..4cdc0b3d4e8 100644 --- a/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/SeqAn/SeqAn-2.4.0-GCCcore-11.2.0.eb @@ -40,22 +40,14 @@ postinstallcmds = [ "cp -a %(builddir)s/seqan-*/include %(installdir)s", ] -sanity_check_commands = [ - ("gustaf_mate_joining --help"), - ("mason_materializer --help"), - ("mason_variator --help"), - ("rabema_prepare_sam --help"), - ("razers3 --help"), - ("samcat --help"), - ("splazers --help"), - ("yara_mapper --help"), -] +local_binaries = ['gustaf_mate_joining', 'mason_materializer', 'mason_variator', 'rabema_prepare_sam', + 'razers3', 'seqan_tcoffee', 'samcat', 'splazers', 'yara_mapper'] sanity_check_paths = { - 'files': ["bin/%s" % x for x in ["gustaf_mate_joining", "mason_materializer", "mason_variator", - "rabema_prepare_sam", "razers3", "seqan_tcoffee", "s4_join", "samcat", "splazers", - "yara_mapper"]] + ['util/cmake/seqan-config.cmake'], + 'files': ["bin/%s" % x for x in local_binaries] + ['util/cmake/seqan-config.cmake'], 'dirs': ['include/seqan'], } +sanity_check_commands = ["%s --help" % x for x in local_binaries] + moduleclass = 'bio' From 1726303071abfc8e5e6aa0ba8991b86af81c2439 Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Thu, 17 Feb 2022 10:53:34 +0100 Subject: [PATCH 3087/9987] Add new release for DIRAC (open source) code --- .../DIRAC-22.0-foss-2021a-Python-3.9.5.eb | 58 +++++++++++++++++++ .../DIRAC-22.0-intel-2021a-Python-3.9.5.eb | 58 +++++++++++++++++++ 2 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..0dc26ee6bc4 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '22.0' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://zenodo.org/record/6010450/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] + +builddependencies = [('CMake', '3.20.1', '', ('GCCcore','10.3.0'))] + +dependencies = [ + ('Python', '3.9.5', '', ('GCCcore','10.3.0')), + ('HDF5', '1.10.7', '', ('gompi','2021a')) +] + +separate_build_dir = True + +configopts = ' -DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DEXTRA_FCFLAGS="''" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DEXTRA_CFLAGS="''" ' +configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' +configopts += '-DEXTRA_CXXFLAGS="''" ' +configopts += '-DENABLE_BLAS=auto ' +configopts += '-DENABLE_LAPACK=auto ' +configopts += '-DMKL_FLAG=off ' +configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' +configopts += '-DBLAS_LANG=Fortran ' +configopts += '-DLAPACK_LANG=Fortran ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_OPENMP=False ' +configopts += '-DENABLE_CODE_COVERAGE=False ' +configopts += '-DENABLE_STATIC_LINKING=False ' +configopts += '-DENABLE_PROFILING=False ' +configopts += '-DENABLE_RUNTIMECHECK=False ' +configopts += '-DENABLE_64BIT_INTEGERS=False ' +configopts += '-DEXPLICIT_LIBS="off" ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' +configopts += '-G"Unix Makefiles" ' + +parallel = 4 + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..5d0bab42a1d --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '22.0' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://zenodo.org/record/6010450/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('HDF5', '1.10.7') +] + +separate_build_dir = True + +configopts = ' -DCMAKE_Fortran_COMPILER=mpiifort ' +configopts += '-DEXTRA_FCFLAGS="''" ' +configopts += '-DCMAKE_C_COMPILER=mpiicc ' +configopts += '-DEXTRA_CFLAGS="''" ' +configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' +configopts += '-DEXTRA_CXXFLAGS="''" ' +configopts += '-DENABLE_BLAS=off ' +configopts += '-DENABLE_LAPACK=off ' +configopts += '-DMKL_FLAG=sequential ' +configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' +configopts += '-DBLAS_LANG=Fortran ' +configopts += '-DLAPACK_LANG=Fortran ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_OPENMP=False ' +configopts += '-DENABLE_CODE_COVERAGE=False ' +configopts += '-DENABLE_STATIC_LINKING=False ' +configopts += '-DENABLE_PROFILING=False ' +configopts += '-DENABLE_RUNTIMECHECK=False ' +configopts += '-DENABLE_64BIT_INTEGERS=False ' +configopts += '-DEXPLICIT_LIBS="off" ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' +configopts += '-G"Unix Makefiles" ' + +parallel = 4 + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From c328acd038ead9fbe1c63633b4f57a4afeae230c Mon Sep 17 00:00:00 2001 From: George Bisbas Date: Thu, 17 Feb 2022 10:47:44 +0000 Subject: [PATCH 3088/9987] devito: update description --- .../d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb index 5b0af7f8bc3..a87809fb2c1 100644 --- a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb @@ -5,7 +5,7 @@ version = '4.6.1' versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.devitoproject.org' -description = "Devito is a domain-specific Language (DSL) and code generation framework" +description = "Devito is a domain-specific Language (DSL) and code generation framework for performing optimised Finite Difference (FD) computation from high-level symbolic problem definitions. Devito performs automated code generation and Just-In-time (JIT) compilation based on symbolic equations defined in SymPy to create and execute highly optimised Finite Difference stencil kernels on multiple computer platforms." toolchain = {'name': 'foss', 'version': '2020a'} toolchainopts = {'pic': True} From 485d6acb55859cb4301ab70b0d5524a184f3f832 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Feb 2022 13:36:19 +0100 Subject: [PATCH 3089/9987] minor style tweaks + set missing environment variables for AlphaFold 2.1.2 easyconfigs using foss(cuda)/2020b toolchain --- ...aFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb | 19 +++++++------- ...d-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb | 25 ++++++++++++------- 2 files changed, 26 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb index 8a7378e0a4d..c9603b16d64 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2020b-TensorFlow-2.5.0.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'AlphaFold' version = '2.1.2' local_tf_version = '2.5.0' -versionsuffix = '-TensorFlow-{}'.format(local_tf_version) +versionsuffix = '-TensorFlow-%s' % local_tf_version homepage = 'https://deepmind.com/research/case-studies/alphafold' description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" @@ -12,24 +12,25 @@ toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.18.4', ), - ('Doxygen', '1.8.20', ), + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), # required for installing dm-tree - ('Bazel', '3.7.2', ), - ('SWIG', '4.0.2', ), + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), ] dependencies = [ - ('Python', '3.8.6', ), + ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('PyYAML', '5.3.1', ), + ('PyYAML', '5.3.1'), ('TensorFlow', local_tf_version), ('Biopython', '1.78'), ('HH-suite', '3.3.0',), ('HMMER', '3.3.2',), - ('Kalign', '3.3.1', ), + ('Kalign', '3.3.1'), ('jax', '0.2.19'), # also provides absl-py ] + local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " @@ -180,7 +181,7 @@ modextrapaths = { } modextravars = { - 'ALPHAFOLD_DATA_DIR': '/scratch/AlphaFold_DBs', # adapt + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb index 15061d7ae70..2dcc49bc3ad 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'AlphaFold' version = '2.1.2' local_tf_version = '2.5.0' -versionsuffix = '-TensorFlow-{}'.format(local_tf_version) +versionsuffix = '-TensorFlow-%s' % local_tf_version homepage = 'https://deepmind.com/research/case-studies/alphafold' description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" @@ -12,24 +12,25 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.18.4', ), - ('Doxygen', '1.8.20', ), + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), # required for installing dm-tree - ('Bazel', '3.7.2', ), - ('SWIG', '4.0.2', ), + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), ] dependencies = [ - ('Python', '3.8.6', ), + ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('PyYAML', '5.3.1', ), + ('PyYAML', '5.3.1'), ('TensorFlow', local_tf_version), ('Biopython', '1.78'), ('HH-suite', '3.3.0',), ('HMMER', '3.3.2',), - ('Kalign', '3.3.1', ), + ('Kalign', '3.3.1'), ('jax', '0.2.19'), # also provides absl-py ] + local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " @@ -180,7 +181,13 @@ modextrapaths = { } modextravars = { - 'ALPHAFOLD_DATA_DIR': '/scratch/AlphaFold_DBs', # adapt + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt + # these allow to make predictions on proteins that would typically be too long to fit into GPU memory; + # see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', + # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 + 'OPENMM_RELAX': 'CUDA', } moduleclass = 'bio' From fbcc1b4f3f1394b7c9845eff83f63db6f746945b Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 17 Feb 2022 17:04:08 +0000 Subject: [PATCH 3090/9987] disable building of documentation for DBus 1.13.18 --- easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb | 4 +++- easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.3.0.eb | 4 +++- easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-11.2.0.eb | 4 +++- 3 files changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb index 83b477ea363..b049fce1560 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb @@ -29,7 +29,9 @@ dependencies = [ ('expat', '2.2.9'), ] -configopts = '--without-systemdsystemunitdir' +configopts = '--with-systemdsystemunitdir=no ' +# disable documentation +configopts += '--disable-xml-docs --disable-doxygen-docs --disable-ducktype-docs' sanity_check_paths = { 'files': ['bin/dbus-%s' % x for x in diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.3.0.eb index b3080c2464e..4c1a07e1b16 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.3.0.eb @@ -29,7 +29,9 @@ dependencies = [ ('expat', '2.2.9'), ] -configopts = '--without-systemdsystemunitdir' +configopts = '--with-systemdsystemunitdir=no ' +# disable documentation +configopts += '--disable-xml-docs --disable-doxygen-docs --disable-ducktype-docs' sanity_check_paths = { 'files': ['bin/dbus-%s' % x for x in diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-11.2.0.eb index 3591a25194f..ef53a657402 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-11.2.0.eb @@ -29,7 +29,9 @@ dependencies = [ ('expat', '2.4.1'), ] -configopts = '--without-systemdsystemunitdir' +configopts = '--with-systemdsystemunitdir=no ' +# disable documentation +configopts += '--disable-xml-docs --disable-doxygen-docs --disable-ducktype-docs' sanity_check_paths = { 'files': ['bin/dbus-%s' % x for x in From e8948ebf1c687b9c3813db9379d7cee93a077646 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Feb 2022 20:08:22 +0100 Subject: [PATCH 3091/9987] avoid hardcoding line count in sed command that edits CMakeLists.txt for STRique --- easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb index 4365a64431c..795b2a954b2 100644 --- a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb +++ b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb @@ -26,7 +26,7 @@ dependencies = [ ('scikit-image', '0.19.1'), ] -local_preconfigopts = "sed -i -e '/SeqAn/,+6d' CMakeLists.txt && " +local_preconfigopts = "sed -i -e '/\ Date: Thu, 17 Feb 2022 19:46:19 +0000 Subject: [PATCH 3092/9987] updated checksum for patch --- .../a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb index 5bbf6fe9009..d6332594c4b 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb @@ -94,7 +94,7 @@ components = [ '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch # AlphaFold-2.1_fix-alphafold-tests.patch - '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From 54057afe90e0a7f50f8731826a5ac7dd48a7fcfd Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 17 Feb 2022 19:46:24 +0000 Subject: [PATCH 3093/9987] updated checksum for patch --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb index 585a30ac353..bb34b753f32 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb @@ -89,7 +89,7 @@ components = [ '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch # AlphaFold-2.1_fix-alphafold-tests.patch - '91cb0b86b35f450f9e252d5bec7a0b9c74ced6be7c743801237a25ae622c3e8f', + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, From b2da271fd9dd3c8cfb960a0e20fcf26f96845ef7 Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Fri, 18 Feb 2022 09:10:09 +0100 Subject: [PATCH 3094/9987] Add tests to DIRAC-22.0 compilations --- .../d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb | 6 ++++++ .../d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb | 6 ++++++ 2 files changed, 12 insertions(+) mode change 100644 => 100755 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb mode change 100644 => 100755 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb old mode 100644 new mode 100755 index 0dc26ee6bc4..a922dd1a79e --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb @@ -48,6 +48,12 @@ configopts += '-G"Unix Makefiles" ' parallel = 4 +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' +pretestopts += 'export N_PROC=$(cat /proc/cpuinfo | grep processor | wc -l) && ' + +runtest = 'test ARGS="-j $N_PROC -E ecp -L short --timeout 3600" ' + sanity_check_paths = { 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], 'dirs': ['share/dirac/basis'], diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb old mode 100644 new mode 100755 index 5d0bab42a1d..71889b6c997 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb @@ -48,6 +48,12 @@ configopts += '-G"Unix Makefiles" ' parallel = 4 +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' +pretestopts += 'export N_PROC=$(cat /proc/cpuinfo | grep processor | wc -l) && ' + +runtest = 'test ARGS="-j $N_PROC -E ecp -L short --timeout 3600" ' + sanity_check_paths = { 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], 'dirs': ['share/dirac/basis'], From c63e35cf632b732de9d7bfe8d81307444da89548 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Feb 2022 09:45:15 +0100 Subject: [PATCH 3095/9987] fix order of extra extensions for R v4.1.2 that are required by CMAverse --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 8029681675d..dd870ff58a4 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3215,20 +3215,20 @@ exts_list = [ ('catlearn', '0.8', { 'checksums': ['0d13da431a5511b025090b7ffaa3765b94b33c7de5a7cc1cec8c50437755646e'], }), + ('metadat', '1.0-0', { + 'checksums': ['ed335a4eb2145fffde20e36077e360f9d36a615e9d93453d2bbd6f5967db4b9c'], + }), ('MetaUtility', '2.1.2', { 'checksums': ['e38c21588c239aa8926e64d916aa0f3b04108c2992f0e801095e4c7920b9ad5d'], }), ('EValue', version, { 'checksums': ['d9f3feb3da2efaf4e5d794e05475be62666192a7c855e373c3d369324078690c'], }), - ('ggdag', '0.2.4', { - 'checksums': ['372ec4ef0ded9637304a19b50bce908e84a034e54dbd2a52a061bb747b2b08a0'], - }), ('dagitty', '0.3-1', { 'checksums': ['7d44b5d259ec3fef776a7e3fcb21d1c379f930d6ae9ae5fbfff54494ad78e8a8'], }), - ('metadat', '1.0-0', { - 'checksums': ['ed335a4eb2145fffde20e36077e360f9d36a615e9d93453d2bbd6f5967db4b9c'], + ('ggdag', '0.2.4', { + 'checksums': ['372ec4ef0ded9637304a19b50bce908e84a034e54dbd2a52a061bb747b2b08a0'], }), ('simex', '1.8', { 'checksums': ['80c7841196b9377a9367eb6960ad80ca0bf8de511b8b18a0031bfbe7bde289a0'], From 748579fd97397310e37481607a42c90a46befbd9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 18 Feb 2022 11:03:53 +0100 Subject: [PATCH 3096/9987] fix deps and extensions --- ...TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 22 +++++++++++++------ 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 0fb2a2e829e..260739bbbdb 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -17,6 +17,7 @@ builddependencies = [ ('git', '2.33.1', '-nodocs'), ('pybind11', '2.7.1'), ('UnZip', '6.0'), + ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed ] dependencies = [ ('CUDA', '11.4.1', '', True), @@ -38,10 +39,10 @@ dependencies = [ ('SQLite', '3.36'), ('protobuf-python', '3.17.3'), ('flatbuffers-python', '2.0'), - ('typing-extensions', '3.10.0.2'), ('libpng', '1.6.37'), ('snappy', '1.1.9'), ('zlib', '1.2.11'), + ('networkx', '2.6.3'), # required for pythran ] use_pip = True @@ -50,6 +51,13 @@ sanity_pip_check = True # Dependencies created and updated using findPythonDeps.sh: # https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d exts_list = [ + # gast deps beniget and pythran require different version from Scipy-bundle + ('beniget', '0.3.0', { + 'checksums': ['062c893be9cdf87c3144fb15041cce4d81c67107c1591952cd45fdce789a0ff1'], + }), + ('pythran', '0.9.11', { + 'checksums': ['a317f91e2aade9f6550dc3bf40b5caeb45b7e012daf27e2b3e4ad928edb01667'], + }), ('wrapt', '1.13.3', { 'checksums': ['1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185'], }), @@ -57,10 +65,8 @@ exts_list = [ 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), ('tensorflow-io-gcs-filesystem', '0.24.0', { - 'modulename': 'tensorflow_io', - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/io/archive/'], - 'checksums': ['7a4b57f6f438402bab4919c360e931c32f4d8d8afa23116d32a48461dddd91dc'], + 'source_tmpl': 'tensorflow_io_gcs_filesystem-0.24.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl', + 'checksums': ['cbc71b3925508bf796644a0083a6f9284f71404654f53092bece701383a69520'], }), ('tensorflow_estimator', '2.7.0', { 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', @@ -115,6 +121,7 @@ exts_list = [ 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], }), ('libclang', '13.0.0', { + 'modulename': 'clang', 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-manylinux1_x86_64.whl', 'checksums': ['9c1e623340ccafe3a10a2abbc90f59593ff29f0c854f4ddb65b6220d9d998fb4'], }), @@ -155,8 +162,9 @@ exts_list = [ ('portpicker', '1.5.0', { 'checksums': ['e13b148008adeb2793cf8b55bcd20fdcec4f763f2d3bf3c45f5e5e5d1df7d228'], }), - ('absl-py', '1.0.0', { - 'checksums': ['ac511215c01ee9ae47b19716599e8ccfa746f2e18de72bdf641b79b22afa27ea'], + ('absl-py', '0.13.0', { + 'modulename': 'absl', + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], }), (name, version, { 'patches': [ From df08e6cc2cf9f465bf6709fd5e551995033ec5ae Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Fri, 18 Feb 2022 12:47:41 +0100 Subject: [PATCH 3097/9987] Tests added --- .../easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb | 3 +-- .../easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb index a922dd1a79e..38e0620fa26 100755 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb @@ -50,9 +50,8 @@ parallel = 4 pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' -pretestopts += 'export N_PROC=$(cat /proc/cpuinfo | grep processor | wc -l) && ' -runtest = 'test ARGS="-j $N_PROC -E ecp -L short --timeout 3600" ' +runtest = 'test ARGS="-R pam_test" ' sanity_check_paths = { 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb index 71889b6c997..3eb8724430e 100755 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb @@ -50,9 +50,8 @@ parallel = 4 pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' -pretestopts += 'export N_PROC=$(cat /proc/cpuinfo | grep processor | wc -l) && ' -runtest = 'test ARGS="-j $N_PROC -E ecp -L short --timeout 3600" ' +runtest = 'test ARGS="-R pam_test" ' sanity_check_paths = { 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], From 0ccf46354d30e8a669a0109e4ff76ce7418f70c8 Mon Sep 17 00:00:00 2001 From: George Bisbas Date: Fri, 18 Feb 2022 14:36:27 +0000 Subject: [PATCH 3098/9987] Update easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb Thank you for the suggestion, Kenneth! I am committing your suggested changes. Co-authored-by: Kenneth Hoste --- .../d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb index a87809fb2c1..8acae5c20c7 100644 --- a/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/d/Devito/Devito-4.6.1-foss-2020a-Python-3.8.2.eb @@ -5,7 +5,11 @@ version = '4.6.1' versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.devitoproject.org' -description = "Devito is a domain-specific Language (DSL) and code generation framework for performing optimised Finite Difference (FD) computation from high-level symbolic problem definitions. Devito performs automated code generation and Just-In-time (JIT) compilation based on symbolic equations defined in SymPy to create and execute highly optimised Finite Difference stencil kernels on multiple computer platforms." +description = """Devito is a domain-specific Language (DSL) and code generation framework for + performing optimised Finite Difference (FD) computation from high-level symbolic problem definitions. + Devito performs automated code generation and Just-In-time (JIT) compilation based on symbolic + equations defined in SymPy to create and execute highly optimised Finite Difference stencil kernels on + multiple computer platforms.""" toolchain = {'name': 'foss', 'version': '2020a'} toolchainopts = {'pic': True} From 9ccf8a84163d3c742b4ac69569b868f615f35aad Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sun, 20 Feb 2022 18:13:43 +0000 Subject: [PATCH 3099/9987] Added checksum --- .../easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb | 3 ++- easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb index 2e408742891..1315a727642 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb @@ -15,7 +15,8 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'Project-MONAI' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479'] +checksums = [('b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479', + 'a63df7d5a680d9641c223ea090ff843a7d6f20bdb62095bd44f3b0480a4706ed')] dependencies = [ ('CUDA', '11.3.1', '', True), diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb index 7a2477f2af6..0d9e772ecb6 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb @@ -14,7 +14,8 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'Project-MONAI' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479'] +checksums = [('b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479', + 'a63df7d5a680d9641c223ea090ff843a7d6f20bdb62095bd44f3b0480a4706ed')] dependencies = [ ('CUDA', '11.3.1', '', True), From 74f59e0b0819ef9198659c4bcb07ec4af89447da Mon Sep 17 00:00:00 2001 From: "josef.dvoracek" Date: Mon, 21 Feb 2022 12:23:33 +0100 Subject: [PATCH 3100/9987] adding easyconfigs: MRtrix-3.0.3-foss-2021a.eb --- .../m/MRtrix/MRtrix-3.0.3-foss-2021a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-3.0.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0.3-foss-2021a.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0.3-foss-2021a.eb new file mode 100644 index 00000000000..1f2579e38a4 --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0.3-foss-2021a.eb @@ -0,0 +1,29 @@ +name = 'MRtrix' +version = '3.0.3' + +homepage = 'http://www.brain.org.au/software/index.html#mrtrix' +description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner + robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6ec7d5a567d8d7338e85575a74565189a26ec8971cbe8fb24a49befbc446542e'] + +builddependencies = [ + ('Eigen', '3.3.9'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.9.5'), + ('Mesa', '21.1.1'), + ('Qt5', '5.15.2'), + ('LibTIFF', '4.2.0'), + ('FFTW', '3.3.9'), + ('libpng', '1.6.37'), +] + +moduleclass = 'bio' From 364c421fbd928b1111c0658cd0ff542b3aa6657c Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 22 Feb 2022 11:25:04 +0100 Subject: [PATCH 3101/9987] adding easyconfigs: MCR-R2021b.2.eb --- easybuild/easyconfigs/m/MCR/MCR-R2021b.2.eb | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2021b.2.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2021b.2.eb b/easybuild/easyconfigs/m/MCR/MCR-R2021b.2.eb new file mode 100644 index 00000000000..b7e3e831019 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2021b.2.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'MCR' +version = 'R2021b' # runtime version 9.11 +local_update = '2' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['731ea5ff34a64ec05024ccf36dc24cfb77d5de4dfabec678e3b964e1110aa6e2'] + +moduleclass = 'math' From dae448e5332dfa7156ec7bf9815947230dd68237 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 22 Feb 2022 11:29:09 +0000 Subject: [PATCH 3102/9987] adding easyconfigs: SAMtools-1.15-GCC-11.2.0.eb --- .../s/SAMtools/SAMtools-1.15-GCC-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.15-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.15-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.15-GCC-11.2.0.eb new file mode 100644 index 00000000000..19cff7315ab --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.15-GCC-11.2.0.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +# +# Updated to 1.14 and gcc-11.2.0 +# J. Sassmannshausen / GSTT + +name = 'SAMtools' +version = '1.15' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['35d945a5eee9817a764490870474f24e538400b0397b28f94247a5b91447215d'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.78.0'), +] + +moduleclass = 'bio' From 61d3abb48401f69c0dd93c8ebdd574ecd03e7e04 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 16:15:54 +0200 Subject: [PATCH 3103/9987] adding easyconfigs: TensorFlow-2.5.3-foss-2021a.eb, TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb and patches: TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch, TensorFlow-2.5.0_fix-compatibility-with-CUDA-11.3.patch, TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch, TensorFlow-2.5.3_relax-required-versions.patch --- ...5.0_fix-compatibility-with-CUDA-11.3.patch | 27 ++ ...fix-compatibility-with-protobuf-3.17.patch | 54 ++++ ...TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb | 244 ++++++++++++++++++ .../TensorFlow/TensorFlow-2.5.3-foss-2021a.eb | 227 ++++++++++++++++ ...orFlow-2.5.3_relax-required-versions.patch | 46 ++++ 5 files changed, 598 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-compatibility-with-CUDA-11.3.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3_relax-required-versions.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-compatibility-with-CUDA-11.3.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-compatibility-with-CUDA-11.3.patch new file mode 100644 index 00000000000..74b1f28c0fc --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-compatibility-with-CUDA-11.3.patch @@ -0,0 +1,27 @@ +From 96eb826c8aec61b172e98f6ba5535206c1ac3023 Mon Sep 17 00:00:00 2001 +From: Peter Hawkins +Date: Fri, 7 May 2021 12:57:02 -0700 +Subject: [PATCH 09/10] Fix NCCL build failure with CUDA 11.3. + +PiperOrigin-RevId: 372612185 +Change-Id: Iaf7d777d586c907b27701a8ad3e5594b16b16a0f +--- + third_party/nccl/build_defs.bzl.tpl | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/third_party/nccl/build_defs.bzl.tpl b/third_party/nccl/build_defs.bzl.tpl +index 4bf2dfcb719..fe163741f87 100644 +--- a/third_party/nccl/build_defs.bzl.tpl ++++ b/third_party/nccl/build_defs.bzl.tpl +@@ -207,7 +207,7 @@ def _prune_relocatable_code_impl(ctx): + mnemonic = "nvprune", + use_default_shell_env = True, + ) +- output.append(outputs) ++ outputs.append(output) + + return DefaultInfo(files = depset(outputs)) + +-- +2.32.0 + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch new file mode 100644 index 00000000000..83e6e07fc42 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch @@ -0,0 +1,54 @@ +From f87e2c2fb623e862fe2ae1616ec4164fa48d1446 Mon Sep 17 00:00:00 2001 +From: Jason Zaman +Date: Sat, 31 Jul 2021 10:30:32 -0700 +Subject: [PATCH 07/10] example_parsing_ops: compatibility with protobuf-3.16 + +--- + tensorflow/core/kernels/example_parsing_ops.cc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/tensorflow/core/kernels/example_parsing_ops.cc b/tensorflow/core/kernels/example_parsing_ops.cc +index d0be01578d8..57ed19aeaae 100644 +--- a/tensorflow/core/kernels/example_parsing_ops.cc ++++ b/tensorflow/core/kernels/example_parsing_ops.cc +@@ -1218,7 +1218,7 @@ class DecodeJSONExampleOp : public OpKernel { + resolver_.get(), "type.googleapis.com/tensorflow.Example", &in, &out); + OP_REQUIRES(ctx, status.ok(), + errors::InvalidArgument("Error while parsing JSON: ", +- string(status.error_message()))); ++ string(status.message()))); + } + } + +-- +2.32.0 + +From 2ea8d31a2a75de75f838b4650e1531c346dfa6fe Mon Sep 17 00:00:00 2001 +From: sclarkson +Date: Thu, 12 Aug 2021 03:23:28 -0700 +Subject: [PATCH 08/10] Fix protobuf errors when using system protobuf + +When tensorflow and python protobuf use the same instance of +libprotobuf, pywrap_tensorflow must be imported before anything +else that would import protobuf definitions. +--- + tensorflow/python/__init__.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/tensorflow/python/__init__.py b/tensorflow/python/__init__.py +index 6efba380ca0..38d1eb55027 100644 +--- a/tensorflow/python/__init__.py ++++ b/tensorflow/python/__init__.py +@@ -37,8 +37,8 @@ import traceback + # go/tf-wildcard-import + # pylint: disable=wildcard-import,g-bad-import-order,g-import-not-at-top + +-from tensorflow.python.eager import context + from tensorflow.python import pywrap_tensorflow as _pywrap_tensorflow ++from tensorflow.python.eager import context + + # pylint: enable=wildcard-import + +-- +2.32.0 + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..2dc21de4e30 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,244 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.5.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.17.3'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.32.0', '-nodocs'), + ('pybind11', '2.6.2'), + ('UnZip', '6.0'), +] +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', versionsuffix, True), + ('NCCL', '2.10.3', versionsuffix), + ('Python', '3.9.5'), + ('h5py', '3.2.1'), + ('cURL', '7.76.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.4.1'), + ('ICU', '69.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.28'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.35.4'), + ('PCRE', '8.44'), + ('protobuf-python', '3.17.3'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.0'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.8', { + 'checksums': ['5c6bd9dc7a543b7fe4304a631f8a8a3b674e2bbfc49c2ae96200cdbe55df6b17'], + }), + ('cachetools', '4.2.4', { + 'checksums': ['89ea6f1b638d5a73a4f9226be57ac5e4f399d22770b92355f92dcb0f7f001693'], + }), + ('google-auth', '1.35.0', { + 'modulename': 'google.auth', + 'checksums': ['b7033be9028c188ee30200b204ea00ed82ea1162e8ac1df4aa6ded19a191d88e'], + }), + ('oauthlib', '3.2.0', { + 'checksums': ['23a8208d75b902797ea29fd31fa80a15ed9dc2c6c16fe73f5d346f83f6fa27a2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('Werkzeug', '2.0.2', { + 'checksums': ['aa2bb6fc8dee8d6c504c0ac1e7f5f7dc5810a9903e793b6f715a9f015bdadb9a'], + }), + ('absl-py', '0.15.0', { + 'modulename': 'absl', + 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.43.0', { + 'modulename': 'grpc', + 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], + }), + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard', '2.5.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['e167460085b6528956b33bab1c970c989cdce47a6616273880733f5e7bde452e'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard_plugin_profile', '2.5.0', { + 'checksums': ['f832698d87a773b9a017fc4dd5cf598a1ff942ccfbf3392c83fe12c949ab9f52'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow_estimator', '2.5.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.13.3', { + 'checksums': ['1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.4', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.5.0', { + 'checksums': ['e13b148008adeb2793cf8b55bcd20fdcec4f763f2d3bf3c45f5e5e5d1df7d228'], + }), + ('keras_nightly', '2.5.0.dev2021032900', { + 'modulename': 'keras', + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_fix-min-priority-test.patch', + 'TensorFlow-2.5.0_add-default-shell-env.patch', + 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch', + 'TensorFlow-2.5.0_fix-compatibility-with-CUDA-11.3.patch', + 'TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch', + 'TensorFlow-2.5.3_relax-required-versions.patch', + ], + 'checksums': [ + '58d69b7163f7624debc243750976d27fa7dddbc6fb7c5215aec94732bcc670e1', # v2.5.3.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_fix-min-priority-test.patch + '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', + # TensorFlow-2.5.0_add-default-shell-env.patch + '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', + # TensorFlow-2.5.0_add-protobuf-deps.patch + '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', + # TensorFlow-2.5.0_disable-avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_fix-crash-on-shutdown.patch + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', + # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch + 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', + # TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch + 'd1797d28985b22b86626390f9b4f90b0dda180276a0abecf162840cf3e127cab', + # TensorFlow-2.5.0_fix-compatibility-with-CUDA-11.3.patch + 'e82db520e5e22f97c0dde2166f0d1a29e7ea828c2b4dfbc79dccc0d4cde5d95d', + # TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch + '4c32aba417e6ecb2642d5828b4ac618f1e4395f6c217cd621fa08a74433faa55', + # TensorFlow-2.5.3_relax-required-versions.patch + 'e108c3877cf4a0cadc179290ec2098683367688bbbbc7d6fa9a321eb7020443c', + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' + '-benchmark-test,-v1only'), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb new file mode 100644 index 00000000000..a75a5332bf6 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb @@ -0,0 +1,227 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.5.3' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.17.3'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.32.0', '-nodocs'), + ('pybind11', '2.6.2'), + ('UnZip', '6.0'), +] +dependencies = [ + ('Python', '3.9.5'), + ('h5py', '3.2.1'), + ('cURL', '7.76.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.4.1'), + ('ICU', '69.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.28'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.35.4'), + ('PCRE', '8.44'), + ('protobuf-python', '3.17.3'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.0'), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.3.4', { + 'checksums': ['31b5b491868dcc87d6c24b7e3d19a0d730d59d3e46f4eea6430a321bed387a49'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.8', { + 'checksums': ['5c6bd9dc7a543b7fe4304a631f8a8a3b674e2bbfc49c2ae96200cdbe55df6b17'], + }), + ('cachetools', '4.2.4', { + 'checksums': ['89ea6f1b638d5a73a4f9226be57ac5e4f399d22770b92355f92dcb0f7f001693'], + }), + ('google-auth', '1.35.0', { + 'modulename': 'google.auth', + 'checksums': ['b7033be9028c188ee30200b204ea00ed82ea1162e8ac1df4aa6ded19a191d88e'], + }), + ('oauthlib', '3.2.0', { + 'checksums': ['23a8208d75b902797ea29fd31fa80a15ed9dc2c6c16fe73f5d346f83f6fa27a2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('Werkzeug', '2.0.2', { + 'checksums': ['aa2bb6fc8dee8d6c504c0ac1e7f5f7dc5810a9903e793b6f715a9f015bdadb9a'], + }), + ('absl-py', '0.15.0', { + 'modulename': 'absl', + 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.43.0', { + 'modulename': 'grpc', + 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], + }), + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard', '2.5.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['e167460085b6528956b33bab1c970c989cdce47a6616273880733f5e7bde452e'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard_plugin_profile', '2.5.0', { + 'checksums': ['f832698d87a773b9a017fc4dd5cf598a1ff942ccfbf3392c83fe12c949ab9f52'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow_estimator', '2.5.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['d1fe76dee8b1dcab865d807a0246da0a9c4a635b1eba6e9545bf216c3aad6955'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.13.3', { + 'checksums': ['1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('dill', '0.3.4', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.5.0', { + 'checksums': ['e13b148008adeb2793cf8b55bcd20fdcec4f763f2d3bf3c45f5e5e5d1df7d228'], + }), + ('keras_nightly', '2.5.0.dev2021032900', { + 'modulename': 'keras', + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['6ba70f738f4008222de7e7fdd5b2b18c48c49b897a9fca54c844854e25964011'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_fix-min-priority-test.patch', + 'TensorFlow-2.5.0_add-default-shell-env.patch', + 'TensorFlow-2.5.0_add-protobuf-deps.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch', + 'TensorFlow-2.5.0_fix-compatibility-with-CUDA-11.3.patch', + 'TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch', + 'TensorFlow-2.5.3_relax-required-versions.patch', + ], + 'checksums': [ + '58d69b7163f7624debc243750976d27fa7dddbc6fb7c5215aec94732bcc670e1', # v2.5.3.tar.gz + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.4.1_fix-min-priority-test.patch + '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', + # TensorFlow-2.5.0_add-default-shell-env.patch + '09b0c5d4ff04f56a9657875471ed78001d4201cac795aeff62019d582115b468', + # TensorFlow-2.5.0_add-protobuf-deps.patch + '2aa79b89cff13e81f83e385761917d5d6dbdffd6b0366d90580761b958f14363', + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', + # TensorFlow-2.5.0_disable-avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch + '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_fix-crash-on-shutdown.patch + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', + # TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch + 'd1797d28985b22b86626390f9b4f90b0dda180276a0abecf162840cf3e127cab', + # TensorFlow-2.5.0_fix-compatibility-with-CUDA-11.3.patch + 'e82db520e5e22f97c0dde2166f0d1a29e7ea828c2b4dfbc79dccc0d4cde5d95d', + # TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch + '4c32aba417e6ecb2642d5828b4ac618f1e4395f6c217cd621fa08a74433faa55', + # TensorFlow-2.5.3_relax-required-versions.patch + 'e108c3877cf4a0cadc179290ec2098683367688bbbbc7d6fa9a321eb7020443c', + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_distributed_test', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3_relax-required-versions.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3_relax-required-versions.patch new file mode 100644 index 00000000000..c42813bb0c8 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3_relax-required-versions.patch @@ -0,0 +1,46 @@ +TF introduced a change pinning versions to fixed major.minor or even patch versions +Loosen those a bit so we can build it with our versions. +See https://github.com/tensorflow/tensorflow/issues/44654 + +Author: Alexander Grund (TU Dresden) +Update v2.5.3: Alex Domingo (Vrije Universiteit Brussel) + +--- tensorflow/tools/pip_package/setup.py.orig 2022-01-30 16:39:47.000000000 +0100 ++++ tensorflow/tools/pip_package/setup.py 2022-02-09 11:45:10.595864349 +0100 +@@ -78,21 +78,21 @@ + # NOTE: As numpy has releases that break semver guarantees and several other + # deps depend on numpy without an upper bound, we must install numpy before + # everything else. +- 'numpy ~= 1.19.2', ++ 'numpy >= 1.19.2', + # Install other dependencies + 'absl-py ~= 0.10', + 'astunparse ~= 1.6.3', +- 'flatbuffers ~= 1.12.0', ++ 'flatbuffers >= 1.12.0', + 'google_pasta ~= 0.2', +- 'h5py ~= 3.1.0', ++ 'h5py >= 3.1.0', + 'keras_preprocessing ~= 1.1.2', + 'opt_einsum ~= 3.3.0', + 'protobuf >= 3.9.2', +- 'six ~= 1.15.0', ++ 'six >= 1.15.0', + 'termcolor ~= 1.1.0', +- 'typing_extensions ~= 3.7.4', ++ 'typing_extensions >= 3.7.4', + 'wheel ~= 0.35', +- 'wrapt ~= 1.12.1', ++ 'wrapt >= 1.12.1', + # These packages need to be pinned exactly as newer versions are + # incompatible with the rest of the ecosystem + 'gast == 0.4.0', +@@ -127,7 +127,7 @@ + # BoringSSL support. + # See https://github.com/tensorflow/tensorflow/issues/17882. + if sys.byteorder == 'little': +- REQUIRED_PACKAGES.append('grpcio ~= 1.34.0') ++ REQUIRED_PACKAGES.append('grpcio >= 1.34.0') + + + # Packages which are only needed for testing code. From 7a47653d198c066a156cff8dbfcd4f9287ccf395 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 16:27:02 +0200 Subject: [PATCH 3104/9987] adding easyconfigs: fastparquet-0.7.2-foss-2021a.eb, fastparquet-0.8.0-foss-2021b.eb --- .../fastparquet-0.7.2-foss-2021a.eb | 40 ++++++++++++++++++ .../fastparquet-0.8.0-foss-2021b.eb | 41 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastparquet/fastparquet-0.7.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/f/fastparquet/fastparquet-0.8.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-0.7.2-foss-2021a.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-0.7.2-foss-2021a.eb new file mode 100644 index 00000000000..2d49b22c447 --- /dev/null +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-0.7.2-foss-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'fastparquet' +version = '0.7.2' + +homepage = "https://fastparquet.readthedocs.io/" +description = """fastparquet is a python implementation of the parquet format, aiming integrate +into python-based big data work-flows. It is used implicitly by the projects +Dask, Pandas and intake-parquet.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('Rust', '1.52.1'), # needed by maturin +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('maturin', '0.11.5', { + 'checksums': ['07074778b063a439fdfd5501bd1d1823a216ec5b657d3ecde78fd7f2c4782422'], + }), + ('thrift', '0.15.0', { + 'checksums': ['87c8205a71cf8bbb111cb99b1f7495070fbc9cabb671669568854210da5b3e29'], + }), + ('cramjam', '2.5.0', { + 'checksums': ['a92c0c2db4c6a3804eaffa253c7ca49f849e7a893a31c902a8123d7c36b2b487'], + }), + (name, version, { + 'checksums': ['3c4bd638260357df55a9e71d0bd797c12f14f691a61dfd91a66f5b8d2a247683'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-0.8.0-foss-2021b.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-0.8.0-foss-2021b.eb new file mode 100644 index 00000000000..682100d629a --- /dev/null +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-0.8.0-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'fastparquet' +version = '0.8.0' + +homepage = "https://fastparquet.readthedocs.io/" +description = """fastparquet is a python implementation of the parquet format, aiming integrate +into python-based big data work-flows. It is used implicitly by the projects +Dask, Pandas and intake-parquet.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('patchelf', '0.13'), + ('Rust', '1.54.0'), # needed by maturin +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('maturin', '0.12.6', { + 'checksums': ['2b14cfae808b45a130e19b2999acea423d2e10e7a29ae2336996ba72ba442ff6'], + }), + ('thrift', '0.15.0', { + 'checksums': ['87c8205a71cf8bbb111cb99b1f7495070fbc9cabb671669568854210da5b3e29'], + }), + ('cramjam', '2.5.0', { + 'checksums': ['a92c0c2db4c6a3804eaffa253c7ca49f849e7a893a31c902a8123d7c36b2b487'], + }), + (name, version, { + 'checksums': ['5a8137f2e0d3a77e8db41e875d3159ddf925bbfaaf37ce6d6eedd02f5bfce55a'], + }), +] + +moduleclass = 'tools' From 51e5b2ab69701328d368658f6b890368e2a978de Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 16:29:07 +0200 Subject: [PATCH 3105/9987] adding easyconfigs: Optuna-2.10.0-foss-2021b.eb, Optuna-2.9.1-foss-2021a.eb --- .../o/Optuna/Optuna-2.10.0-foss-2021b.eb | 88 +++++++++++++++++++ .../o/Optuna/Optuna-2.9.1-foss-2021a.eb | 86 ++++++++++++++++++ 2 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/o/Optuna/Optuna-2.10.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/o/Optuna/Optuna-2.9.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-2.10.0-foss-2021b.eb b/easybuild/easyconfigs/o/Optuna/Optuna-2.10.0-foss-2021b.eb new file mode 100644 index 00000000000..2190e6f6068 --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-2.10.0-foss-2021b.eb @@ -0,0 +1,88 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '2.10.0' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), + ('SciPy-bundle', '2021.10'), + ('tqdm', '4.62.3'), + ('matplotlib', '3.4.3'), # optional + ('plotly.py', '5.4.0'), # optional + ('Redis', '6.2.6'), # optional, needed by redis-py + ('scikit-learn', '1.0.1'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Mako', '1.1.6', { + 'checksums': ['4e9e345a41924a954251b95b4b28e14a301145b544901332e658907a7464b6b2'], + }), + ('alembic', '1.7.5', { + 'checksums': ['7c328694a2e68f03ee971e63c3bd885846470373a5b532cf2c9f1601c413b153'], + }), + ('autopage', '0.5.0', { + 'checksums': ['5305b43cc0798170d7124e5a2feecf969e45f4a0baf75cb351138114eaf76b83'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('cmd2', '2.3.3', { + 'checksums': ['750d7eb04d55c3bc2a413e191bc177856f388102de47d11f2210a35266543640'], + }), + ('prettytable', '3.1.1', { + 'checksums': ['43c9e23272ca253d038ae76fe3adde89794e92e7fcab2ddf5b94b38642ef4f21'], + }), + ('stevedore', '3.5.0', { + 'checksums': ['f40253887d8712eaa2bb0ea3830374416736dc8ec0e22f5a65092c1174c44335'], + }), + ('cliff', '3.10.0', { + 'checksums': ['c68aac08d0d25853234a38fdbf1f33503849af3d5d677a4d0aacd42b0be6a4a1'], + }), + ('cmaes', '0.8.2', { + 'checksums': ['1c04ba23ded925ef13b96f42cfbd667a905ea5b80754c750e6448b9fcda96a5d'], + }), + ('colorlog', '6.6.0', { + 'checksums': ['344f73204009e4c83c5b6beb00b3c45dc70fcdae3c80db919e0a4171d006fde8'], + }), + ('greenlet', '1.1.2', { + 'checksums': ['e30f5ea4ae2346e62cedde8794a56858a67b878dd79f7df76a0767e356b1744a'], + }), + ('SQLAlchemy', '1.4.31', { + 'checksums': ['582b59d1e5780a447aada22b461e50b404a9dc05768da1d87368ad8190468418'], + }), + ('wrapt', '1.13.3', { + 'checksums': ['1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185'], + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('redis', '4.1.1', { + 'checksums': ['07420a3fbedd8e012c31d4fadac943fb81568946da202c5a5bc237774e5280a0'], + }), + ('optuna', version, { + 'use_pip_extras': 'optional', + 'checksums': ['04c3100a4fe88a71dc72f69d8a10ec9db7c9a0c884feaf932b68632b00686a8d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-2.9.1-foss-2021a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-2.9.1-foss-2021a.eb new file mode 100644 index 00000000000..10c656e4ab9 --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-2.9.1-foss-2021a.eb @@ -0,0 +1,86 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '2.9.1' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('SciPy-bundle', '2021.05'), + ('tqdm', '4.61.2'), + ('matplotlib', '3.4.2'), # optional + ('plotly.py', '5.1.0'), # optional + ('Redis', '6.2.6'), # optional, needed by redis-py + ('scikit-learn', '0.24.2'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('Mako', '1.1.5', { + 'checksums': ['169fa52af22a91900d852e937400e79f535496191c63712e3b9fda5a9bed6fc3'], + }), + ('alembic', '1.6.5', { + 'checksums': ['a21fedebb3fb8f6bbbba51a11114f08c78709377051384c9c5ead5705ee93a51'], + }), + ('autopage', '0.4.0', { + 'checksums': ['18f511d8ef2e4d3cc22a986d345eab0e03f95b9fa80b74ca63b7fb001551dc42'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('cmd2', '2.2.0', { + 'checksums': ['34cd12424d9e2835eff125146af3d9f4a4c2931c6bc5a3cea9790bd4f55756d9'], + }), + ('prettytable', '2.2.1', { + 'checksums': ['6d465005573a5c058d4ca343449a5b28c21252b86afcdfa168cdc6a440f0b24c'], + }), + ('stevedore', '3.4.0', { + 'checksums': ['59b58edb7f57b11897f150475e7bc0c39c5381f0b8e3fa9f5c20ce6c89ec4aa1'], + }), + ('cliff', '3.9.0', { + 'checksums': ['95363e9b43e2ec9599e33b5aea27a6953beda2d0673557916fa4f5796857daa3'], + }), + ('cmaes', '0.8.2', { + 'checksums': ['1c04ba23ded925ef13b96f42cfbd667a905ea5b80754c750e6448b9fcda96a5d'], + }), + ('colorlog', '6.5.0', { + 'checksums': ['cf62a8e389d5660d0d22be17937b25b9abef9497ddc940197d1773aa1f604339'], + }), + ('greenlet', '1.1.2', { + 'checksums': ['e30f5ea4ae2346e62cedde8794a56858a67b878dd79f7df76a0767e356b1744a'], + }), + ('SQLAlchemy', '1.4.26', { + 'checksums': ['6bc7f9d7d90ef55e8c6db1308a8619cd8f40e24a34f759119b95e7284dca351a'], + }), + ('redis', '3.5.3', { + 'checksums': ['0e7e0cfca8660dea8b7d5cd8c4f6c5e29e11f31158c0b0ae91a397f00e5a05a2'], + }), + ('optuna', version, { + 'use_pip_extras': 'optional', + 'checksums': ['bea30e2d43f306297bfb1e2b94fb426024b2df0a7bf554c51d1d401d05025224'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' From 8f052d17634bf0b82542c69cbe28d88ed9b60448 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 16:30:43 +0200 Subject: [PATCH 3106/9987] adding easyconfigs: imageio-2.10.5-foss-2021a.eb --- .../i/imageio/imageio-2.10.5-foss-2021a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.10.5-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.10.5-foss-2021a.eb b/easybuild/easyconfigs/i/imageio/imageio-2.10.5-foss-2021a.eb new file mode 100644 index 00000000000..c2ba92e6930 --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.10.5-foss-2021a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.10.5' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f3f6e9a73d62f12348f098364219f4fc64462760bc07abfe16d14db0e4974845'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Pillow', '8.2.0'), +] + +download_dep_fail = True +use_pip = True + +# The requirement on pillow >= 8.3.2 exists due to CVE-2021-23437, which is patched in EB +preinstallopts = "sed -i 's/pillow >= 8.3.2/pillow/' setup.py && " + +sanity_pip_check = True + +moduleclass = 'vis' From ebcd3b47bc7a94350f8c82bec693d6e992060f59 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 16:33:57 +0200 Subject: [PATCH 3107/9987] adding easyconfigs: pycocotools-2.0.4-foss-2021a.eb --- .../pycocotools-2.0.4-foss-2021a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.4-foss-2021a.eb b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.4-foss-2021a.eb new file mode 100644 index 00000000000..286d7177035 --- /dev/null +++ b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.4-foss-2021a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pycocotools' +version = '2.0.4' + +homepage = 'https://pypi.org/project/pycocotools' +description = "Official APIs for the MS-COCO dataset" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2ab586aa389b9657b6d73c2b9a827a3681f8d00f36490c2e8ab05902e3fd9e93'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'data' From d86d5204f9a3ed1982a4c1e19985ff8018b72dc3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 16:36:10 +0200 Subject: [PATCH 3108/9987] adding easyconfigs: CCL-1.12.1-GCCcore-10.3.0.eb, SBCL-2.2.1-GCCcore-10.3.0.eb --- .../c/CCL/CCL-1.12.1-GCCcore-10.3.0.eb | 51 +++++++++++++++++++ .../s/SBCL/SBCL-2.2.1-GCCcore-10.3.0.eb | 46 +++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/c/CCL/CCL-1.12.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/SBCL/SBCL-2.2.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CCL/CCL-1.12.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CCL/CCL-1.12.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..cda61243cf4 --- /dev/null +++ b/easybuild/easyconfigs/c/CCL/CCL-1.12.1-GCCcore-10.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' +name = 'CCL' +version = '1.12.1' + +homepage = 'https://ccl.clozure.com/' +description = """Clozure CL (often called CCL for short) is a free Common Lisp + implementation with a long history. Some distinguishing features of the implementation + include fast compilation speed, native threads, a precise, generational, compacting + garbage collector, and a convenient foreign-function interface.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/Clozure/ccl/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s-linuxx86.tar.gz'] +checksums = ['923f2979144e96306cf5124800444e1c5cc0295fa9babb3ffc47a5631344b0aa'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +local_ccl_bin = 'lx86cl64' +local_ccl_dirs = [ + 'compiler', 'level-0', 'level-1', 'lib', 'library', 'lisp-kernel', 'scripts', 'tools', 'xdump', 'x86-headers64' +] + +# Build the kernel +buildopts = "-C lisp-kernel/linuxx8664 all CC=${CC} && " +# Rebuild CCL +buildopts += "./%s -n -b -Q -e '(ccl:rebuild-ccl :full t)' -e '(ccl:quit)'" % local_ccl_bin + +files_to_copy = [local_ccl_bin, '%s.image' % local_ccl_bin] + local_ccl_dirs + +postinstallcmds = [ + # Cleanup of build files + "find %(installdir)s -type f -name '*fsl' -delete", + "find %(installdir)s/lisp-kernel -type f -name '*.o' -delete", + # Link executable with generic name + "mkdir %(installdir)s/bin", + "cd %%(installdir)s/bin && ln -s ../%s ccl" % local_ccl_bin, +] + +sanity_check_paths = { + 'files': [local_ccl_bin, '%s.image' % local_ccl_bin, 'bin/ccl'], + 'dirs': local_ccl_dirs, +} + +sanity_check_commands = ["ccl --help"] + +modextrapaths = {'CCL_DEFAULT_DIRECTORY': ''} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SBCL/SBCL-2.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/SBCL/SBCL-2.2.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3aacb77b256 --- /dev/null +++ b/easybuild/easyconfigs/s/SBCL/SBCL-2.2.1-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' +name = 'SBCL' +version = '2.2.1' + +homepage = 'http://sbcl.sourceforge.net/' +description = """ +Steel Bank Common Lisp (SBCL) is a high performance Common Lisp compiler. It is +open source / free software, with a permissive license. In addition to the +compiler and runtime system for ANSI Common Lisp, it provides an interactive +environment including a debugger, a statistical profiler, a code coverage tool, +and many other extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.bz2'] +checksums = ['5dd6e6e3f08b7c6edf262a0e844a9f8b5e562cca08155034c1f2c014fc9087da'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CCL', '1.12.1'), +] + +parallel = False +skipsteps = ['configure'] +local_prefixarg = '--prefix=%(installdir)s' + +# Build SBCL with Clozure CL +# Using the binary distribution of SBCL to build SBCL is not trivial because +# it needs GLIBC v2.28 +build_cmd = "sh make.sh" +buildopts = "%s --xc-host=ccl" % local_prefixarg + +install_cmd = "sh install.sh" +installopts = local_prefixarg + +sanity_check_paths = { + 'files': ['bin/sbcl'], + 'dirs': ['lib/sbcl'], +} + +sanity_check_commands = ["sbcl --help"] + +modextrapaths = {'SBCL_HOME': 'lib/sbcl'} + +moduleclass = 'lang' From db2dc44085a2193f6796c12c84e0c32b5401db0c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 16:38:24 +0200 Subject: [PATCH 3109/9987] adding easyconfigs: Hydra-1.1.1-GCCcore-10.3.0.eb --- .../h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b84c48b8829 --- /dev/null +++ b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'Hydra' +version = '1.1.1' + +homepage = "https://hydra.cc/" +description = """Hydra is an open-source Python framework that simplifies the development of +research and other complex applications. The key feature is the ability to +dynamically create a hierarchical configuration by composition and override it +through config files and the command line. The name Hydra comes from its +ability to run multiple similar jobs - much like a Hydra with multiple heads.""" +github_account = 'facebookresearch' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), # needed by omegaconf +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('antlr4-python3-runtime', '4.8', { + 'modulename': 'antlr4', + 'checksums': ['15793f5d0512a372b4e7d2284058ad32ce7dd27126b105fb0b2245130445db33'], + }), + ('omegaconf', '2.1.1', { + 'checksums': ['c65e05530369484e074a24038fe31812c73561aa9d916abfd1209e4073136ae5'], + }), + ('hydra', version, { + 'source_urls': ['https://github.com/%(github_account)s/%(namelower)s/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['03840c5192d47c3b0a4cf57e1815f8626d36f2fed81efed59202f6bd93ac822c'], + }), +] + +moduleclass = 'data' From 528c77a9c39a34858865e2b271d679621cba4861 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 22 Feb 2022 15:39:42 +0100 Subject: [PATCH 3110/9987] adding easyconfigs: lpsolve-5.5.2.11-GCC-11.2.0.eb, AUGUSTUS-3.4.0-foss-2021b.eb --- .../a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb | 64 +++++++++++++++++++ .../l/lpsolve/lpsolve-5.5.2.11-GCC-11.2.0.eb | 33 ++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb new file mode 100644 index 00000000000..2c6961e4449 --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb @@ -0,0 +1,64 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.4.0' + +homepage = 'https://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'foss', 'version': '2021b'} + +# https://github.com/Gaius-Augustus/Augustus/archive +github_account = 'Gaius-Augustus' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch'] +checksums = [ + '2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8', # v3.4.0.tar.gz + 'e74023f28ee3e76590f4534d195c313b88b66a92ec779da184d30d056fc8e052', # AUGUSTUS-3.4.0_fix-hardcoding.patch +] + +builddependencies = [ + ('Python', '3.9.6'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.77.0'), + ('GSL', '2.7'), + ('SAMtools', '1.14'), + ('HTSlib', '1.14'), # also provides tabix + ('BCFtools', '1.14'), + ('lpsolve', '5.5.2.11'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('BamTools', '2.5.2'), + ('SQLite', '3.36'), +] + +skipsteps = ['configure'] + +# run "make clean" to avoid using binaries included with the source tarball +prebuildopts = "make clean && " + +buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" LINK.cc="$CXX" ' +installopts = 'INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch', + 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} +sanity_check_commands = ['augustus --help'] + +modextrapaths = {'PATH': 'scripts'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-11.2.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-11.2.0.eb new file mode 100644 index 00000000000..80add32f2fd --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.11' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f'] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' From 54c8907841fee9de1d4f67759db0d83868c69b0a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 16:45:38 +0200 Subject: [PATCH 3111/9987] add Flask-Session to Flask v1.1.4 and Flask v2.0.2 --- easybuild/easyconfigs/f/Flask/Flask-1.1.4-GCCcore-10.3.0.eb | 6 ++++++ easybuild/easyconfigs/f/Flask/Flask-2.0.2-GCCcore-11.2.0.eb | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/f/Flask/Flask-1.1.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-1.1.4-GCCcore-10.3.0.eb index e580bb5698a..b42acb6357c 100644 --- a/easybuild/easyconfigs/f/Flask/Flask-1.1.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/Flask/Flask-1.1.4-GCCcore-10.3.0.eb @@ -34,6 +34,12 @@ exts_list = [ ('Flask-Cors', '3.0.10', { 'checksums': ['b60839393f3b84a0f3746f6cdca56c1ad7426aa738b70d6c61375857823181de'], }), + ('cachelib', '0.4.1', { + 'checksums': ['68e27dae1bb73ba02071f1cf413111d96f8175fd37176f35a5ccb9bdf6848c5c'], + }), + ('Flask-Session', '0.4.0', { + 'checksums': ['c9ed54321fa8c4ca0132ffd3369582759eda7252fb4b3bee480e690d1ba41f46'], + }), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/Flask/Flask-2.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/Flask/Flask-2.0.2-GCCcore-11.2.0.eb index 2057ba93f42..65e24299f37 100644 --- a/easybuild/easyconfigs/f/Flask/Flask-2.0.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/Flask/Flask-2.0.2-GCCcore-11.2.0.eb @@ -37,6 +37,12 @@ exts_list = [ ('Flask-Cors', '3.0.10', { 'checksums': ['b60839393f3b84a0f3746f6cdca56c1ad7426aa738b70d6c61375857823181de'], }), + ('cachelib', '0.6.0', { + 'checksums': ['0baa926a23924c04ae1354091478b15b3b24e6cf5931dd159452afda5f65babd'], + }), + ('Flask-Session', '0.4.0', { + 'checksums': ['c9ed54321fa8c4ca0132ffd3369582759eda7252fb4b3bee480e690d1ba41f46'], + }), ] sanity_check_paths = { From dec143e8832a7568de778d46ec4d8951c74fa30d Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 22 Feb 2022 16:08:09 +0100 Subject: [PATCH 3112/9987] adding easyconfigs: PyQt5-5.15.4-GCCcore-11.2.0.eb, ETE-3.1.2-foss-2021b.eb --- .../easyconfigs/e/ETE/ETE-3.1.2-foss-2021b.eb | 34 +++++++ .../p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb | 92 +++++++++++++++++++ 2 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b.eb new file mode 100644 index 00000000000..c7eca019813 --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.2' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +checksums = ['4fc987b8c529889d6608fab1101f1455cb5cbd42722788de6aea9c7d0a8e59e9'] + +dependencies = [ + ('lxml', '4.6.3'), + ('Python', '3.9.6'), + ('PyQt5', '5.15.4'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..18614197333 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb @@ -0,0 +1,92 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.4' + +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.37')] +dependencies = [ + ('Python', '3.9.6'), + ('Qt5', '5.15.2'), +] + +default_easyblock = 'PythonPackage' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_sipver = '5.5.0' +components = [ + ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + ('PyQt-builder', '1.10.1', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['967b0c7bac0331597e9f8c5b336660f173a9896830b721d6d025e14bde647e17'], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + ('PyQt5_sip', '12.9.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], + 'easyblock': 'Binary', + 'start_dir': '%(name)s-%(version)s', + 'skipsteps': ['configure', 'build'], + 'install_cmd': local_setup_env + local_pyqt5_sip_install, + }), + ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['cedc28f54165f4b8067652145aec7f732a17eadf6736835852868cf76119cc19'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip5 --help", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' From 2ec25751d56b3c2323f1166828be71de01200aea Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 22 Feb 2022 18:14:28 +0200 Subject: [PATCH 3113/9987] adding easyconfigs: PIPITS-2.8-foss-2021a.eb, ITSx-1.1.3-GCCcore-10.3.0.eb, VSEARCH-2.21.1-GCC-10.3.0.eb and patches: PIPITS-2.8_remove-conda-commands.patch --- .../i/ITSx/ITSx-1.1.3-GCCcore-10.3.0.eb | 29 ++++++++ .../p/PIPITS/PIPITS-2.8-foss-2021a.eb | 66 +++++++++++++++++++ .../PIPITS-2.8_remove-conda-commands.patch | 54 +++++++++++++++ .../v/VSEARCH/VSEARCH-2.21.1-GCC-10.3.0.eb | 40 +++++++++++ 4 files changed, 189 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/PIPITS/PIPITS-2.8_remove-conda-commands.patch create mode 100644 easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.21.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..02cb2e734b1 --- /dev/null +++ b/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'ITSx' +version = '1.1.3' + +homepage = 'https://microbiology.se/software/itsx/' +description = '''ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of +fungi and other eukaryotes for use in environmental sequencing.''' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://microbiology.se/sw/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['6f6d7ff6350f82439dee5348f6e8bda512be25193c603d4e56cc215c520091bf'] + +dependencies = [('Perl', '5.32.1')] + +fix_perl_shebang_for = ['ITSx'] + +sanity_check_paths = { + 'files': ['ITSx'], + 'dirs': ['ITSx_db'], +} + +sanity_check_commands = ['ITSx --help'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb new file mode 100644 index 00000000000..0d9fdbabdc7 --- /dev/null +++ b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'PIPITS' +version = '2.8' + +homepage = 'https://github.com/hsgweon/pipits' +description = """An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences +from the Illumina sequencing platform.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), + ('VSEARCH', '2.21.1'), + ('FASTX-Toolkit', '0.0.14'), + ('ITSx', '1.1.3'), + ('HMMER', '3.3.2'), + ('RDP-Classifier', '2.13', '-Java-11', True), + ('SeqKit', '2.1.0', '', True), +] + +use_pip = True + +exts_list = [ + ('biom-format', '2.1.10', { + 'modulename': 'biom', + 'checksums': ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'], + }), + ('python-utils', '3.1.0', { + 'checksums': ['4dace6420c5f50d6509251fa0aee0e2a0b826bbc8a5d2a6d7e99dca80e78a7f3'], + }), + ('progressbar2', '4.0.0', { + 'modulename': 'progressbar', + 'checksums': ['14d3165a1781d053ffaa117daf27cc706128d2ec1d2977fdb05b6bb079888013'], + }), + ('pispino', '1.1', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/hsgweon/pispino/archive/'], + 'checksums': ['8fb2e1c0ae38ecca7c637de9c0b655eb18fc67d7838ceb5a6902555ea12416c0'], + }), + (name, version, { + 'patches': ['PIPITS-2.8_remove-conda-commands.patch'], + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/hsgweon/pipits/archive/'], + 'checksums': [ + '2ecc6fd901613bf9d4baec7c15e53ee89b2a2b817dbaa413c02d2dc484c5e5e2', # 2.8.tar.gz + # PIPITS-2.8_remove-conda-commands.patch + '47437c243d5a07d3a3548efc9706ca8bd83c883d1ef881c769d10ae7fa6fcbcd', + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pipits_funits', 'pipits_process', + 'pispino_createreadpairslist', + 'pispino_seqprep']], + 'dirs': [] +} + +sanity_check_commands = ['pipits_process --help'] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8_remove-conda-commands.patch b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8_remove-conda-commands.patch new file mode 100644 index 00000000000..f5931e55465 --- /dev/null +++ b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8_remove-conda-commands.patch @@ -0,0 +1,54 @@ +Some PIPITS scripts in the bin folder contain a hardcoded "conda list" commands. +This patch replaces those calls by "pip list". + +Furthermore, it replaces the call to a Conda wrapper script for launching +RDP-Classifier by the actual java command. + +Author: Bob Dröge (University of Groningen) + +--- pipits-2.8-orig/bin/pipits_funits 2022-02-17 11:38:57.000000000 +0100 ++++ pipits-2.8/bin/pipits_funits 2022-02-22 16:58:16.000000000 +0100 +@@ -102,7 +102,7 @@ + logger("", logging_file, display = True, timestamp = False) + + # Log versions +- cmd = " ".join(["conda list"]) ++ cmd = " ".join(["pip list"]) + run_cmd(cmd, version_file, False) + + # Start +--- pipits-2.8-orig/bin/pipits_process 2022-02-17 11:38:57.000000000 +0100 ++++ pipits-2.8/bin/pipits_process 2022-02-22 16:59:45.000000000 +0100 +@@ -152,7 +152,7 @@ + logger("", logging_file, display = True, timestamp = False) + + # Log versions +- cmd = " ".join(["conda list"]) ++ cmd = " ".join(["pip list"]) + run_cmd(cmd, version_file, False) + + # Environment variable - discontinued. +@@ -510,9 +510,10 @@ + + logger(ENDC + "Assigning taxonomy with UNITE [RDP Classifier]" + ENDC, logging_file, display = True) + PIPITS_UNITE_RETRAINED_PROPERTIES = "pipits_db/UNITE_retrained_" + options.unite + "/UNITE_retrained/rRNAClassifier.properties" +- cmd = " ".join(["classifier", ++ cmd = " ".join(["java", + "-Xms" + str(options.Xms), + "-Xmx" + str(options.Xmx), ++ "-jar $EBROOTRDPMINCLASSIFIER/dist/classifier.jar", + "classify", + "-t " + PIPITS_UNITE_RETRAINED_PROPERTIES, + "-o", options.outDir + "/assigned_taxonomy.txt", +@@ -598,9 +599,10 @@ + logger("Assigning taxonomy [RDP Classifier] - Warcup", logging_file, display = True) + PIPITS_WARCUP_RETRAINED_PROPERTIES = "pipits_db/warcup_retrained_V2/warcup_retrained_V2/rRNAClassifier.properties" + cmd = " ".join([ +- "classifier", ++ "java", + "-Xms" + str(options.Xms), + "-Xmx" + str(options.Xmx), ++ "-jar $EBROOTRDPMINCLASSIFIER/dist/classifier.jar", + "classify", + "-t " + PIPITS_WARCUP_RETRAINED_PROPERTIES, + "-o", options.outDir + "/assigned_taxonomy_warcup.txt", diff --git a/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.21.1-GCC-10.3.0.eb b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.21.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..3bdd437e4e6 --- /dev/null +++ b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.21.1-GCC-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'VSEARCH' +version = '2.21.1' + +homepage = 'https://github.com/torognes/vsearch' +description = """VSEARCH supports de novo and reference based chimera detection, + clustering, full-length and prefix dereplication, rereplication, + reverse complementation, masking, all-vs-all pairwise global alignment, + exact and global alignment searching, shuffling, subsampling and sorting. + It also supports FASTQ file analysis, filtering, + conversion and merging of paired-end reads.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/torognes/vsearch/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0c5f4c981bc8ecbf23ee618d1b45667f81ae9845d64b9d6a310edbd196c84638'] + +builddependencies = [ + ('Autotools', '20210128'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), +] + +preconfigopts = './autogen.sh &&' + +configopts = '--disable-pdfman ' + +sanity_check_paths = { + 'files': ['bin/vsearch'], + 'dirs': [], +} + +sanity_check_commands = ['vsearch --help'] + +moduleclass = 'bio' From 2ab7873c8d4da1e6b437167422072b8a45da3376 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 22 Feb 2022 19:12:50 +0200 Subject: [PATCH 3114/9987] adding easyconfigs: OpenFAST-3.0.0-foss-2021b.eb, OpenFAST-3.0.0-intel-2021b.eb --- .../o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb | 28 +++++++++++++++++++ .../o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb diff --git a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb new file mode 100644 index 00000000000..bd16046755b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'OpenFAST' +version = '3.0.0' + +homepage = 'http://openfast.readthedocs.io/' + +description = """OpenFAST is a wind turbine simulation tool which builds on FAST v8. +FAST.Farm extends the capability of OpenFAST to simulate multi-turbine wind farms""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/OpenFAST/openfast/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +configopts = '-DBUILD_FASTFARM=ON ' + +sanity_check_paths = { + 'files': ['bin/openfast', 'bin/FAST.Farm', + 'lib/libopenfastlib.a', 'libopenfast_prelib.a', 'lib/libopenfast_postlib.a'], + 'dirs': ['include/openfast'], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb new file mode 100644 index 00000000000..ab7818b0fd6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'OpenFAST' +version = '3.0.0' + +homepage = 'http://openfast.readthedocs.io/' + +description = """OpenFAST is a wind turbine simulation tool which builds on FAST v8. +FAST.Farm extends the capability of OpenFAST to simulate multi-turbine wind farms""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +source_urls = ['https://github.com/OpenFAST/openfast/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +configopts = '-DBUILD_FASTFARM=ON ' + +sanity_check_paths = { + 'files': ['bin/openfast', 'bin/FAST.Farm', + 'lib/libopenfastlib.a', 'libopenfast_prelib.a', 'lib/libopenfast_postlib.a'], + 'dirs': ['include/openfast'], +} + +moduleclass = 'cae' From 5fe1bf476b39952fced204ed901ebe542232d73b Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 22 Feb 2022 18:47:12 +0100 Subject: [PATCH 3115/9987] Use aiohttp as dependency so it doesn't need to be included as extension --- ...pyter-server-proxy-3.2.1-GCCcore-10.3.0.eb | 34 ++++++++++--------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb index c4f04efec59..35c09c6af4e 100644 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb @@ -16,6 +16,7 @@ dependencies = [ ('Python', '3.9.5'), ('JupyterHub', '1.4.1'), ('OpenSSL', '1.1', '', True), + ('aiohttp', '3.8.1'), ] sanity_pip_check = True @@ -42,22 +43,23 @@ exts_list = [ ('simpervisor', '0.4', { 'checksums': ['cec79e13cdbd6edb04a5c98c1ff8d4bd9713e706c069226909a1ef0e89d393c5'], }), - ('multidict', '5.1.0', { - 'checksums': ['25b4e5f22d3a37ddf3effc0710ba692cfc792c2b9edfb9c05aefe823256e84d5'], - }), - ('async-timeout', '3.0.1', { - 'checksums': ['0c3c816a028d47f659d6ff5c745cb2acf1f966da1fe5c19c77a70282b25f4c5f'], - }), - ('typing-extensions', '3.10.0.0', { - 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', - 'checksums': ['50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342'], - }), - ('yarl', '1.6.3', { - 'checksums': ['8a9066529240171b68893d60dca86a763eae2139dd42f42106b03cf4b426bf10'], - }), - ('aiohttp', '3.7.4.post0', { - 'checksums': ['493d3299ebe5f5a7c66b9819eacdcfbbaaf1a8e84911ddffcdc48888497afecf'], - }), +# in aiohttp-3.8.1 +# ('multidict', '5.1.0', { +# 'checksums': ['25b4e5f22d3a37ddf3effc0710ba692cfc792c2b9edfb9c05aefe823256e84d5'], +# }), +# ('async-timeout', '3.0.1', { +# 'checksums': ['0c3c816a028d47f659d6ff5c745cb2acf1f966da1fe5c19c77a70282b25f4c5f'], +# }), +# ('typing-extensions', '3.10.0.0', { +# 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', +# 'checksums': ['50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342'], +# }), +# ('yarl', '1.6.3', { +# 'checksums': ['8a9066529240171b68893d60dca86a763eae2139dd42f42106b03cf4b426bf10'], +# }), +# ('aiohttp', '3.7.4.post0', { +# 'checksums': ['493d3299ebe5f5a7c66b9819eacdcfbbaaf1a8e84911ddffcdc48888497afecf'], +# }), (name, version, { 'checksums': ['080e9910592d06422bdd93dfc1fa8350c6fdaec9fbbd050630e90f7a5593a4f7'], }), From cdd1fcd7dd14849d6495c8631fd658112ead6ba9 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 22 Feb 2022 18:48:13 +0100 Subject: [PATCH 3116/9987] Removed comments, they are not needed... --- ...jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb index 35c09c6af4e..13c3559fd20 100644 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb @@ -43,23 +43,6 @@ exts_list = [ ('simpervisor', '0.4', { 'checksums': ['cec79e13cdbd6edb04a5c98c1ff8d4bd9713e706c069226909a1ef0e89d393c5'], }), -# in aiohttp-3.8.1 -# ('multidict', '5.1.0', { -# 'checksums': ['25b4e5f22d3a37ddf3effc0710ba692cfc792c2b9edfb9c05aefe823256e84d5'], -# }), -# ('async-timeout', '3.0.1', { -# 'checksums': ['0c3c816a028d47f659d6ff5c745cb2acf1f966da1fe5c19c77a70282b25f4c5f'], -# }), -# ('typing-extensions', '3.10.0.0', { -# 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', -# 'checksums': ['50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342'], -# }), -# ('yarl', '1.6.3', { -# 'checksums': ['8a9066529240171b68893d60dca86a763eae2139dd42f42106b03cf4b426bf10'], -# }), -# ('aiohttp', '3.7.4.post0', { -# 'checksums': ['493d3299ebe5f5a7c66b9819eacdcfbbaaf1a8e84911ddffcdc48888497afecf'], -# }), (name, version, { 'checksums': ['080e9910592d06422bdd93dfc1fa8350c6fdaec9fbbd050630e90f7a5593a4f7'], }), From c1a1f0255c7a1561283617e6e882c0fdeb3501ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 22 Feb 2022 20:30:04 +0200 Subject: [PATCH 3117/9987] checksums --- easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb | 1 + easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb index bd16046755b..9c55e38d7fe 100644 --- a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/OpenFAST/openfast/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] +checksums = ['9af57af054e4128b6e257a76da368dc4ad0c7fbb2b22d51fc7ea63cdf999c530'] builddependencies = [ ('CMake', '3.21.1'), diff --git a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb index ab7818b0fd6..a3c6abf322d 100644 --- a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb +++ b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'intel', 'version': '2021b'} source_urls = ['https://github.com/OpenFAST/openfast/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] +checksums = ['9af57af054e4128b6e257a76da368dc4ad0c7fbb2b22d51fc7ea63cdf999c530'] builddependencies = [ ('CMake', '3.21.1'), From 28f048735d6cb1b384258af6928bbf517847cccf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 22:58:11 +0200 Subject: [PATCH 3118/9987] adding easyconfigs: Detectron-0.6-foss-2021a-CUDA-11.3.1.eb, Detectron-0.6-foss-2021a.eb --- .../Detectron-0.6-foss-2021a-CUDA-11.3.1.eb | 75 +++++++++++++++++++ .../d/Detectron/Detectron-0.6-foss-2021a.eb | 69 +++++++++++++++++ 2 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..edcb058fb72 --- /dev/null +++ b/easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,75 @@ +easyblock = 'PythonBundle' + +name = 'Detectron' +version = '0.6' +versionsuffix = '-CUDA-%(cudaver)s' + +# WARNING: installation with CUDA requires a system with an actual GPU +# check in your build system that torch.cuda.is_available() is True + +homepage = "https://github.com/facebookresearch/detectron2" +description = """Detectron2 is Facebook AI Research's next generation library that provides +state-of-the-art detection and segmentation algorithms. It is the successor of +Detectron and maskrcnn-benchmark. It supports a number of computer vision +research projects and production applications in Facebook.""" +github_account = 'facebookresearch' + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('torchvision', '0.11.3', versionsuffix), + ('TensorFlow', '2.6.0', versionsuffix), # provides tensorboard, termcolor + ('Hydra', '1.1.1'), # provides hydra-core, omegaconf + ('matplotlib', '3.4.2'), + ('OpenCV', '4.5.3', versionsuffix + '-contrib'), + ('Pillow-SIMD', '8.2.0'), + ('pycocotools', '2.0.4'), + ('pydot', '1.4.2'), + ('tqdm', '4.61.2'), + ('YACS', '0.1.8'), + ('boto3', '1.20.13'), # needed by iopath + ('PyYAML', '5.4.1'), # needed by fvcore +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('mypy_extensions', '0.4.3', { + 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], + }), + ('pathspec', '0.9.0', { + 'checksums': ['e564499435a2673d586f6b2130bb5b95f04a3ba06f81b8f895b651a3c76aabb1'], + }), + ('black', '21.4b2', { + 'checksums': ['fc9bcf3b482b05c1f35f6a882c079dc01b9c7795827532f4cc43c0ec88067bbc'], + }), + ('portalocker', '2.3.2', { + 'checksums': ['75cfe02f702737f1726d83e04eedfa0bda2cc5b974b1ceafb8d6b42377efbd5f'], + }), + ('iopath', '0.1.9', { + 'source_tmpl': '%(namelower)s-%(version)s-py3-none-any.whl', + 'checksums': ['9058ac24f0328decdf8dbe209b33074b8702a3c4d9ba2f7801d46cb61a880b6e'], + }), + ('fvcore', '0.1.5.post20211023', { + 'checksums': ['20597a81a5678a3c7f53fa1773ef7fd108ce00ed9da1edd1a1b0092fb1a6d15b'], + }), + ('detectron2', version, { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['9757fed05fa32acc2116ea038185f08409d5e854573e70f41909a358b70d1004'], + 'preinstallopts': "FORCE_CUDA=1", + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a.eb b/easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a.eb new file mode 100644 index 00000000000..3e28515f8a0 --- /dev/null +++ b/easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'Detectron' +version = '0.6' + +homepage = "https://github.com/facebookresearch/detectron2" +description = """Detectron2 is Facebook AI Research's next generation library that provides +state-of-the-art detection and segmentation algorithms. It is the successor of +Detectron and maskrcnn-benchmark. It supports a number of computer vision +research projects and production applications in Facebook.""" +github_account = 'facebookresearch' + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('torchvision', '0.11.3'), + ('TensorFlow', '2.6.0'), # provides tensorboard, termcolor + ('Hydra', '1.1.1'), # provides hydra-core, omegaconf + ('matplotlib', '3.4.2'), + ('OpenCV', '4.5.3', '-contrib'), + ('Pillow-SIMD', '8.2.0'), + ('pycocotools', '2.0.4'), + ('pydot', '1.4.2'), + ('tqdm', '4.61.2'), + ('YACS', '0.1.8'), + ('boto3', '1.20.13'), # needed by iopath + ('PyYAML', '5.4.1'), # needed by fvcore +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('mypy_extensions', '0.4.3', { + 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], + }), + ('pathspec', '0.9.0', { + 'checksums': ['e564499435a2673d586f6b2130bb5b95f04a3ba06f81b8f895b651a3c76aabb1'], + }), + ('black', '21.4b2', { + 'checksums': ['fc9bcf3b482b05c1f35f6a882c079dc01b9c7795827532f4cc43c0ec88067bbc'], + }), + ('portalocker', '2.3.2', { + 'checksums': ['75cfe02f702737f1726d83e04eedfa0bda2cc5b974b1ceafb8d6b42377efbd5f'], + }), + ('iopath', '0.1.9', { + 'source_tmpl': '%(namelower)s-%(version)s-py3-none-any.whl', + 'checksums': ['9058ac24f0328decdf8dbe209b33074b8702a3c4d9ba2f7801d46cb61a880b6e'], + }), + ('fvcore', '0.1.5.post20211023', { + 'checksums': ['20597a81a5678a3c7f53fa1773ef7fd108ce00ed9da1edd1a1b0092fb1a6d15b'], + }), + ('detectron2', version, { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['9757fed05fa32acc2116ea038185f08409d5e854573e70f41909a358b70d1004'], + }), +] + +moduleclass = 'vis' From dc10ba8db0e8045b904ff08150014e479a42d779 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 22:03:50 +0100 Subject: [PATCH 3119/9987] change name to Detectron2 --- .../Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb} | 2 +- .../Detectron2-0.6-foss-2021a.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/d/{Detectron/Detectron-0.6-foss-2021a-CUDA-11.3.1.eb => Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb} (99%) rename easybuild/easyconfigs/d/{Detectron/Detectron-0.6-foss-2021a.eb => Detectron2/Detectron2-0.6-foss-2021a.eb} (99%) diff --git a/easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb similarity index 99% rename from easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a-CUDA-11.3.1.eb rename to easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb index edcb058fb72..cdd16631b81 100644 --- a/easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb @@ -1,6 +1,6 @@ easyblock = 'PythonBundle' -name = 'Detectron' +name = 'Detectron2' version = '0.6' versionsuffix = '-CUDA-%(cudaver)s' diff --git a/easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a.eb b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a.eb similarity index 99% rename from easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a.eb rename to easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a.eb index 3e28515f8a0..8d2c0ea3727 100644 --- a/easybuild/easyconfigs/d/Detectron/Detectron-0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a.eb @@ -1,6 +1,6 @@ easyblock = 'PythonBundle' -name = 'Detectron' +name = 'Detectron2' version = '0.6' homepage = "https://github.com/facebookresearch/detectron2" From 522396136119992deeb8981a3b305bc79d4c18fd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 23:15:11 +0200 Subject: [PATCH 3120/9987] add build dependency on binutils to Hydra v1.1.1 --- easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb index b84c48b8829..6d1e690b6d7 100644 --- a/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb @@ -13,6 +13,10 @@ github_account = 'facebookresearch' toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +builddependencies = [ + ('binutils', '2.36.1'), +] + dependencies = [ ('Python', '3.9.5'), ('PyYAML', '5.4.1'), # needed by omegaconf From 7b3288a8c59ee523cf39f68724440be9a8a70e83 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 23:20:43 +0200 Subject: [PATCH 3121/9987] adding easyconfigs: torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb --- ...rchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..3eb21ffbed3 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,23 @@ +name = 'torchvision' +version = '0.11.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b4c51d27589783e6e6941ecaa67b55f6f41633874ec37f80b64a0c92c3196e0c'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('Pillow-SIMD', '8.2.0'), + ('PyTorch', '1.10.0', versionsuffix), +] + +moduleclass = 'vis' From 6ee79ea879a3e25ac2cf998097c4a99ed220d728 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 23:21:55 +0200 Subject: [PATCH 3122/9987] adding easyconfigs: pydot-1.4.2-GCCcore-10.3.0.eb --- .../p/pydot/pydot-1.4.2-GCCcore-10.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c4587a7bc28 --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pydot' +version = '1.4.2' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['248081a39bcb56784deb018977e428605c1c758f10897a339fce1dd728ff007d'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('Graphviz', '2.47.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 604b9b9758dbbf58eb1064070b554fa49f7a2d7f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 23:23:11 +0200 Subject: [PATCH 3123/9987] adding easyconfigs: boto3-1.20.13-GCCcore-10.3.0.eb --- .../b/boto3/boto3-1.20.13-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3a35bb6fb31 --- /dev/null +++ b/easybuild/easyconfigs/b/boto3/boto3-1.20.13-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'boto3' +version = '1.20.13' + +homepage = 'https://github.com/boto/boto3' +description = """Boto3 is the Amazon Web Services (AWS) Software Development Kit +(SDK) for Python, which allows Python developers to write software that makes +use of services like Amazon S3 and Amazon EC2.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +exts_list = [ + ('botocore', '1.23.13', { + 'checksums': ['35792b2196049ef900f538cae51fb8359c940156eef187962aa9e3bd2c0b8e8c'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + ('s3transfer', '0.5.0', { + 'checksums': ['50ed823e1dc5868ad40c8dc92072f757aa0e653a192845c94a3b676f4a62da4c'], + }), + (name, version, { + 'checksums': ['bbf53a077d6a0575ddec8026f0475ca6ee6f41b227914bf315bf3e049a3d653a'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 55bf30baa4526f09248985d5e21302cd7645c696 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 23:37:06 +0200 Subject: [PATCH 3124/9987] add build dependency on Java to Hydra v1.1.1 --- easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb index 6d1e690b6d7..8a6f2ac5fa7 100644 --- a/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} builddependencies = [ ('binutils', '2.36.1'), + ('Java', '11', '', True), # needed by ANTLR runtime ] dependencies = [ From 3b16c3fda239a30eec441eb2a9a2af3c417becdc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 23:01:49 +0100 Subject: [PATCH 3125/9987] remove default sanity checks from jupyter-server-proxy v3.2.1 --- .../jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb index 13c3559fd20..5e6622f80bd 100644 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} builddependencies = [ ('binutils', '2.36.1'), ] + dependencies = [ ('Python', '3.9.5'), ('JupyterHub', '1.4.1'), @@ -48,11 +49,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyter_server_proxy'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'tools' From 0960b4d85634b3a019b334c480d38835ac95b328 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Feb 2022 23:05:06 +0100 Subject: [PATCH 3126/9987] update homepage and description of jupyter-server-proxy v3.2.1 --- .../jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb index 5e6622f80bd..6fbb4b351ab 100644 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb @@ -3,9 +3,14 @@ easyblock = 'PythonBundle' name = 'jupyter-server-proxy' version = '3.2.1' -homepage = 'https://jupyter.org' -description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed - for centralized deployments in companies, university classrooms and research labs.""" +homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' +description = """Jupyter Server Proxy lets you run arbitrary external processes +(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) +alongside your notebook server and provide authenticated web access to them +using a path like /rstudio next to others like /lab. Alongside the python +package that provides the main functionality, the JupyterLab extension +(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window +to get to RStudio for example.""" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} From ef2d6b03fc3fbb7ebad9d78af762ec34232e1f17 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Feb 2022 00:36:54 +0200 Subject: [PATCH 3127/9987] use common dependency on nodejs for this toolchain in configurable-http-proxy v4.4.0 --- .../configurable-http-proxy-4.4.0-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.4.0-GCCcore-10.3.0.eb index 9af97e3a882..818e21acc00 100644 --- a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.4.0-GCCcore-10.3.0.eb @@ -14,7 +14,7 @@ builddependencies = { } dependencies = [ - ('nodejs', '14.17.2'), + ('nodejs', '14.17.0'), ] source_urls = ['https://github.com/jupyterhub/configurable-http-proxy/archive/'] From 3f46793f85942596059e7bfd5f2ff04fa84a1e43 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Feb 2022 08:59:52 +0100 Subject: [PATCH 3128/9987] adding easyconfigs: patch-2.7.6.eb --- easybuild/easyconfigs/p/patch/patch-2.7.6.eb | 23 ++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/patch/patch-2.7.6.eb diff --git a/easybuild/easyconfigs/p/patch/patch-2.7.6.eb b/easybuild/easyconfigs/p/patch/patch-2.7.6.eb new file mode 100644 index 00000000000..257791cf8f4 --- /dev/null +++ b/easybuild/easyconfigs/p/patch/patch-2.7.6.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'patch' +version = '2.7.6' + +homepage = 'https://savannah.gnu.org/projects/patch' +description = """Patch takes a patch file containing a difference listing produced by the diff program + and applies those differences to one or more original files, producing patched versions.""" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8cf86e00ad3aaa6d26aca30640e86b0e3e1f395ed99f189b06d4c9f74bc58a4e'] + +sanity_check_paths = { + 'files': ['bin/patch', 'share/man/man1/patch.1'], + 'dirs': [], +} + +sanity_check_commands = ["patch --help"] + +moduleclass = 'tools' From d9c932171e1ada8fe8cd10ff2362148848b2ebf0 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 14:40:39 +0100 Subject: [PATCH 3129/9987] Update OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb --- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb index 457f9974cbc..8fc92af0e06 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb @@ -18,7 +18,7 @@ dependencies = [ ('UCX-CUDA', '1.10.0', versionsuffix), ] -configopts = 'CC="$MPICC" CXX="$MPICC"' +configopts = 'CC="$MPICC" CXX="$MPICXX"' configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' local_benchmark_dirs = [ From 98dbe54254901f303dbecacbf379657df753be2f Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 14:57:05 +0100 Subject: [PATCH 3130/9987] Update OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb --- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb index 8fc92af0e06..81a663791de 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb @@ -8,6 +8,7 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TGZ] @@ -18,8 +19,7 @@ dependencies = [ ('UCX-CUDA', '1.10.0', versionsuffix), ] -configopts = 'CC="$MPICC" CXX="$MPICXX"' -configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA' local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] From e7019cff89ba0e7b04a1937a638ab208bf9bcf8c Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 14:59:03 +0100 Subject: [PATCH 3131/9987] Update OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb --- .../OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb index ea96854672c..f8edcf8d961 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.2-gompi-2019a.eb @@ -7,13 +7,12 @@ homepage = 'http://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompi', 'version': '2019a'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2ecb90abd85398786823c0716d92448d7094657d3f017c65d270ffe39afc7b95'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From 9d57f44163de0a29c2de393ec07ba16dea3883ce Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 14:59:21 +0100 Subject: [PATCH 3132/9987] Update OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb --- .../OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb index 46eea2ef0b0..317d649b572 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb @@ -7,13 +7,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompi', 'version': '2019b'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From 4694fdcdd521ca5a51595786b641f13b1d89676d Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 14:59:42 +0100 Subject: [PATCH 3133/9987] Update OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb --- .../OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb index 4ad894f72b0..41bb5469e0f 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb @@ -7,13 +7,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From f0053fe3a5ffccc7c1182c73fc585bbff91cf043 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 14:59:59 +0100 Subject: [PATCH 3134/9987] Update OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb --- .../OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb index 739dde4021e..d97ead0d861 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020b.eb @@ -7,13 +7,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From 61badd89c28e839847b1a462240a9779b82d9c61 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:00:26 +0100 Subject: [PATCH 3135/9987] Update OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb --- .../OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb index b3a19557826..174583a81d4 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb @@ -7,13 +7,13 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompic', 'version': '2019b'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' -configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA' local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] From 498135df749caa9b7ca4a22a1ac85fb8dd656831 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:00:46 +0100 Subject: [PATCH 3136/9987] Update OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb --- .../OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb index 119a307b011..97a07efe746 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb @@ -7,13 +7,13 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompic', 'version': '2020a'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' -configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA' local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] From 92e47dc051e30a09236e39e305eb496f2d57e961 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:01:18 +0100 Subject: [PATCH 3137/9987] Update OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb --- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb index d4c91ad814c..2edf60ebfeb 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019a.eb @@ -7,13 +7,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'iimpi', 'version': '2019a'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From 4f0e9a94f7d93440793e319f3e26a73f8dca6d76 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:01:34 +0100 Subject: [PATCH 3138/9987] Update OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb --- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb index a35cd292de5..1c4d066007a 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2019b.eb @@ -7,13 +7,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'iimpi', 'version': '2019b'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From cf193c1d43b00aabd254927dedfae7339d21c1ae Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:01:50 +0100 Subject: [PATCH 3139/9987] Update OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb --- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb index 347f1df9943..3583eab1477 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb @@ -7,13 +7,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From ab80207108511667901ce89e5a4cf07463509eef Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:02:21 +0100 Subject: [PATCH 3140/9987] Update OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb --- .../OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb index 94f086b13d2..270c18b7eb9 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020b.eb @@ -7,13 +7,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From cd0ebac44219ed6f716f9e8cf5a3d9faf923dc63 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:02:40 +0100 Subject: [PATCH 3141/9987] Update OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb --- .../OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb index 6d403d0fb27..08a01456932 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb @@ -7,13 +7,13 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'iimpic', 'version': '2019b'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' -configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA' local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] From b541a42c9bd69e396104a366e795cfdeec93785a Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:02:57 +0100 Subject: [PATCH 3142/9987] Update OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb --- .../OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb index 6145c20ceb8..ec8aaa2a8b9 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb @@ -7,13 +7,13 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'iimpic', 'version': '2020a'} +toolchainopts = {'usempi': True} source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] -configopts = 'CC="$MPICC" CXX="$MPICC"' -configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA' local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] From 9b1a2ea2547c24b3f1ee90238921b934c82c12bc Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:03:14 +0100 Subject: [PATCH 3143/9987] Update OSU-Micro-Benchmarks-5.7-gompi-2020b.eb --- .../OSU-Micro-Benchmarks-5.7-gompi-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb index 7df7a5b835e..8d4a54aa057 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompi-2020b.eb @@ -10,13 +10,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompi', 'version': '2020b'} +toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From 98b92d8f287176ff8bb0ea0905a4084fe55df026 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:03:35 +0100 Subject: [PATCH 3144/9987] Update OSU-Micro-Benchmarks-5.7-gompic-2020b.eb --- .../OSU-Micro-Benchmarks-5.7-gompic-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb index 1dd7a5a6e62..90d4b73806e 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-gompic-2020b.eb @@ -10,13 +10,13 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'gompic', 'version': '2020b'} +toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] -configopts = 'CC="$MPICC" CXX="$MPICC"' -configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA' local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] From b3796478a377ef801bec2de963696c730f735bfe Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 23 Feb 2022 15:03:50 +0100 Subject: [PATCH 3145/9987] Update OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb --- .../OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb index a1e5881a089..fed81295849 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7-iimpi-2020b.eb @@ -10,13 +10,12 @@ homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" toolchain = {'name': 'iimpi', 'version': '2020b'} +toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['1470ebe00eb6ca7f160b2c1efda57ca0fb26b5c4c61148a3f17e8e79fbf34590'] -configopts = 'CC="$MPICC" CXX="$MPICC"' - local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] From 62491013486f81882d3bfb18641a46385e7db6ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Feb 2022 17:43:50 +0100 Subject: [PATCH 3146/9987] adding easyconfigs: MDTraj-1.9.7-intel-2021b.eb --- .../m/MDTraj/MDTraj-1.9.7-intel-2021b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2021b.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2021b.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2021b.eb new file mode 100644 index 00000000000..337b9706b27 --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2021b.eb @@ -0,0 +1,42 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.7' + +homepage = 'https://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('zlib', '1.2.11'), +] + +use_pip = True +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('pymbar', '3.0.5', { + 'checksums': ['b079a7d0b9fbc8a92850277b664bb582991ef5ac399b3607e695569148f6c784'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('mdtraj', version, { + 'checksums': ['8a3309d2ef6ddb1023dcf48300d5df9b190469b63f69af9d55490bc4799d3757'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' From 1eef3f8d4b5392633179687bd3a60a138e88ad0b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Feb 2022 18:58:52 +0100 Subject: [PATCH 3147/9987] {bio}[GCC/11.2.0,gompi/2021b] shovill v1.1.0, Mash v2.3, CapnProto v0.9.1, SKESA v2.4.0, KMC v3.2.1, Lighter v1.1.2, FLASH v2.2.00, Velvet v1.2.10, samclip v0.4.0 --- .../CapnProto-0.9.1-GCCcore-11.2.0.eb | 35 ++++++++++++++ .../f/FLASH/FLASH-2.2.00-GCC-11.2.0.eb | 34 +++++++++++++ .../easyconfigs/k/KMC/KMC-3.2.1-GCC-11.2.0.eb | 43 +++++++++++++++++ .../l/Lighter/Lighter-1.1.2-GCC-11.2.0.eb | 26 ++++++++++ .../easyconfigs/m/Mash/Mash-2.3-GCC-11.2.0.eb | 48 +++++++++++++++++++ .../m/Mash/Mash-2.3_fix-GCC-11.patch | 18 +++++++ .../SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb | 37 ++++++++++++++ .../s/samclip/samclip-0.4.0-GCCcore-11.2.0.eb | 30 ++++++++++++ .../s/shovill/shovill-1.1.0-gompi-2021b.eb | 48 +++++++++++++++++++ .../Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb | 34 +++++++++++++ 10 files changed, 353 insertions(+) create mode 100644 easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/k/KMC/KMC-3.2.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/Lighter/Lighter-1.1.2-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mash/Mash-2.3_fix-GCC-11.patch create mode 100644 easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb create mode 100644 easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..19069313fa4 --- /dev/null +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to 0.9.1 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'CapnProto' +version = '0.9.1' + +homepage = 'https://capnproto.org' +description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" +# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." +# (only on Intel Skylake?) +toolchainopts = {'cstd': 'c++17', 'lowopt': True} + +source_urls = ['https://capnproto.org/'] +sources = ['capnproto-c++-%(version)s.tar.gz'] +checksums = ['83680aaef8c192b884e38eab418b8482d321af6ae7ab7befa3a9370b8e716aad'] + +builddependencies = [('binutils', '2.37')] + +local_bins = ['capnp', 'capnpc', 'capnpc-c++', 'capnpc-capnp'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['include/capnp', 'include/kj', 'lib'], +} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-GCC-11.2.0.eb new file mode 100644 index 00000000000..a7d6de3d521 --- /dev/null +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-GCC-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'FLASH' +version = '2.2.00' + +homepage = 'https://ccb.jhu.edu/software/FLASH/' +description = """FLASH (Fast Length Adjustment of SHort reads) is a very fast +and accurate software tool to merge paired-end reads from next-generation +sequencing experiments. FLASH is designed to merge pairs of reads when the +original DNA fragments are shorter than twice the length of reads. The +resulting longer reads can significantly improve genome assemblies. They can +also improve transcriptome assembly when FLASH is used to merge RNA-seq data. +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/dstreett/FLASH2/archive/'] +sources = ['%(version)s.zip'] +checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] + +files_to_copy = [(['flash2'], 'bin')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s flash2 flash"] + +sanity_check_paths = { + 'files': ['bin/flash2', 'bin/flash'], + 'dirs': [], +} + +sanity_check_commands = [ + "flash --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/KMC/KMC-3.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/k/KMC/KMC-3.2.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..0df6c5ef67f --- /dev/null +++ b/easybuild/easyconfigs/k/KMC/KMC-3.2.1-GCC-11.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'KMC' +version = '3.2.1' + +homepage = 'http://sun.aei.polsl.pl/kmc' +description = "KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/refresh-bio/KMC/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7db333091a754508163a097c41720cf32a80abe160bef60f3fc82c8da1d67896'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('Python', '3.9.6'), +] + +# Makefile does static linking with libc.a, libpthread.a, libm.a +osdependencies = [('glibc-static', 'libc6-dev')] + +prebuildopts = "sed -i 's@[^ ]*/libz.a@${EBROOTZLIB}/lib/libz.a@g' Makefile && " +prebuildopts += "sed -i 's@[^ ]*/libbz2.a@${EBROOTBZIP2}/lib/libbz2.a@g' Makefile && " + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/kmc', 'bin/kmc_dump'], + 'dirs': [], +} + +sanity_check_commands = [ + "kmc", + "kmc_dump", + "python -c 'import py_kmc_api'", +] + +# Python bindings are also located in bin/ +modextrapaths = {'PYTHONPATH': ['bin']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/Lighter/Lighter-1.1.2-GCC-11.2.0.eb b/easybuild/easyconfigs/l/Lighter/Lighter-1.1.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..a2cad26c601 --- /dev/null +++ b/easybuild/easyconfigs/l/Lighter/Lighter-1.1.2-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'Lighter' +version = '1.1.2' + +homepage = 'https://github.com/mourisl/Lighter' +description = "Fast and memory-efficient sequencing error corrector" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/mourisl/Lighter/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['89abc34137beffc43382fbe53deb25c3c2f5cee7e6ca2b7f669931d70065993a'] + +dependencies = [('zlib', '1.2.11')] + +files_to_copy = [(['lighter'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/lighter'], + 'dirs': [], +} + +sanity_check_commands = ["lighter -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.2.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..7d12008cb15 --- /dev/null +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.2.0.eb @@ -0,0 +1,48 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v2.2 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'Mash' +version = '2.3' + +homepage = 'http://mash.readthedocs.org' +description = "Fast genome and metagenome distance estimation using MinHash" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/marbl/Mash/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Mash-2.2_fix-hardcoding.patch', + 'Mash-2.1_disable-memcpy-wrap.patch', + 'Mash-2.3_fix-GCC-11.patch', +] +checksums = [ + 'f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1', # v2.3.tar.gz + '0c7315af727a06f408ab3ca69da0860fc671aa870b448a41a509b1e6d7027db5', # Mash-2.2_fix-hardcoding.patch + '40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch + '47a55459d4e8c57949648e0f33f3ffc3529563db0efe60f495fdec046f48d94e', # Mash-2.3_fix-GCC-11.patch +] + +builddependencies = [('Autotools', '20210726')] +dependencies = [ + ('CapnProto', '0.9.1'), + ('GSL', '2.7'), + ('zlib', '1.2.11'), +] + +preconfigopts = "./bootstrap.sh && " +configopts = "--with-capnp=$EBROOTCAPNPROTO --with-gsl=$EBROOTGSL" + +sanity_check_paths = { + 'files': ['bin/mash', 'lib/libmash.a'], + 'dirs': ['include/mash'], +} + +sanity_check_commands = ['mash --version'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3_fix-GCC-11.patch b/easybuild/easyconfigs/m/Mash/Mash-2.3_fix-GCC-11.patch new file mode 100644 index 00000000000..0efc6c9df01 --- /dev/null +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3_fix-GCC-11.patch @@ -0,0 +1,18 @@ +see also https://github.com/marbl/Mash/issues/167 + +Author: Andreas Tille +Last-Update: Tue, 12 Oct 2021 09:01:12 +0200 +Description: Fix "error: ‘numeric_limits’ is not a member of ‘std’" +Forwarded: https://github.com/marbl/Mash/issues/167 + +--- a/src/mash/robin_hood.h ++++ b/src/mash/robin_hood.h +@@ -45,6 +45,7 @@ + #include // only to support hash of smart pointers + #include + #include ++#include + #include + #include + #if __cplusplus >= 201703L + diff --git a/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb new file mode 100644 index 00000000000..ebf4e97faf6 --- /dev/null +++ b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'SKESA' +version = '2.4.0' +versionsuffix = '_saute.1.3.0_1' + +homepage = 'https://github.com/ncbi/SKESA' +description = "SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs." + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/ncbi/SKESA/archive/'] +sources = ['skesa.%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['b44c56b16d87b1961e9ee4069468f6b0e850c0cc4c99410f1f5c06b782dee092'] + +dependencies = [ + ('NGS', '2.11.2'), + ('ncbi-vdb', '2.11.2'), + ('Boost', '1.77.0'), +] + +prebuildopts = "touch %(builddir)s/ngs.done && " + +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS" ' +buildopts += "NGS_DIR=%(builddir)s BOOST_PATH=$EBROOTBOOST NGS_PATH=$EBROOTNGS VDB_PATH=$EBROOTNCBIMINVDB" + +files_to_copy = [(['skesa'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/skesa'], + 'dirs': [], +} + +sanity_check_commands = ["skesa --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ff7f93d50b4 --- /dev/null +++ b/easybuild/easyconfigs/s/samclip/samclip-0.4.0-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +# Author: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'samclip' +version = '0.4.0' + +homepage = 'https://github.com/tseemann/samclip' +description = """Filter SAM file for soft and hard clipped alignments.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['8196b705b0319b168949f42818eb3a6bcf96119a24daa950fa0d908d3111d127'] + +dependencies = [('Perl', '5.34.0')] + +sanity_check_paths = { + 'files': [name], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb b/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb new file mode 100644 index 00000000000..d71b5e0fb90 --- /dev/null +++ b/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb @@ -0,0 +1,48 @@ +easyblock = 'Tarball' + +name = 'shovill' +version = '1.1.0' + +homepage = 'https://github.com/tseemann/shovill' +description = "Faster SPAdes assembly of Illumina reads" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://github.com/tseemann/shovill/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b7323e6586238821202cf9644963e584e7397a5cee23e564d00b07fcb344ecd2'] + +# excluded (optional) dependency: skesa +# cfr. https://github.com/ncbi/ngs-tools/tree/master/tools/skesa +dependencies = [ + ('SAMtools', '1.14'), + ('BWA', '0.7.17'), + ('Mash', '2.3'), + ('seqtk', '1.3'), + ('SKESA', '2.4.0', '_saute.1.3.0_1'), + ('MEGAHIT', '1.2.9'), + ('KMC', '3.2.1'), + ('Pilon', '1.23', '-Java-11', True), + ('SPAdes', '3.15.3'), + ('Lighter', '1.1.2'), + ('FLASH', '2.2.00'), + ('Trimmomatic', '0.39', '-Java-11', True), + ('Velvet', '1.2.10', '-mt-kmer_191'), + ('pigz', '2.6'), + ('samclip', '0.4.0'), +] + +postinstallcmds = [ + """echo exec java -jar \$EBROOTTRIMMOMATIC/trimmomatic-*.jar '"$@"' > %(installdir)s/bin/trimmomatic""", + """echo exec java -jar $EBROOTPILON/pilon-*.jar '"$@"' > %(installdir)s/bin/pilon""", + "chmod a+rx %(installdir)s/bin/trimmomatic %(installdir)s/bin/pilon", +] + +sanity_check_paths = { + 'files': ['bin/shovill'], + 'dirs': [], +} + +sanity_check_commands = ["shovill --check"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb new file mode 100644 index 00000000000..e59516e0cbd --- /dev/null +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute +# Authors:: Cedric Laczny , Fotis Georgatos , +# Thekla Loizou , Andreas Panteli +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Velvet' +version = '1.2.10' +versionsuffix = '-mt-kmer_191' + +homepage = 'https://www.ebi.ac.uk/~zerbino/velvet/' +description = """Sequence assembler for very short reads""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'openmp': True, 'pic': True} + +source_urls = ['https://www.ebi.ac.uk/~zerbino/velvet'] +sources = ['%(namelower)s_%(version)s.tgz'] +checksums = ['884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640'] + +dependencies = [('zlib', '1.2.11')] + +buildopts = "OPENMP=1 MAXKMERLENGTH=%s LONGSEQUENCES=1" % versionsuffix.split('_')[1] + +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] + +moduleclass = 'bio' From ea872e614658ef5789fdc2fde59e86cedd3e9efb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Feb 2022 19:38:57 +0100 Subject: [PATCH 3148/9987] add exception for shovill + SKESA that depend on HDF5 1.10 via ncbi-vdb --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index babb1c213df..96b312d1d60 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -439,8 +439,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # EMAN2 2.3 requires Boost(.Python) 1.64.0 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], - # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2 depends on ncbi-vdb) - 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.'])], + # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) + 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], # VMTK 1.4.x requires ITK 4.13.x 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) From 659e1bd96efd4fa05293231e640792dbddf704f6 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Wed, 23 Feb 2022 20:41:42 +0100 Subject: [PATCH 3149/9987] add empty line --- easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb index 8a6f2ac5fa7..08c0a3b716c 100644 --- a/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb @@ -9,6 +9,7 @@ research and other complex applications. The key feature is the ability to dynamically create a hierarchical configuration by composition and override it through config files and the command line. The name Hydra comes from its ability to run multiple similar jobs - much like a Hydra with multiple heads.""" + github_account = 'facebookresearch' toolchain = {'name': 'GCCcore', 'version': '10.3.0'} From bf454bc01dbcb6494f82ff7dfecaa4d98a805e2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Feb 2022 09:20:29 +0100 Subject: [PATCH 3150/9987] adding easyconfigs: GraphMap-0.5.2-foss-2019b.eb --- .../g/GraphMap/GraphMap-0.5.2-foss-2019b.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/g/GraphMap/GraphMap-0.5.2-foss-2019b.eb diff --git a/easybuild/easyconfigs/g/GraphMap/GraphMap-0.5.2-foss-2019b.eb b/easybuild/easyconfigs/g/GraphMap/GraphMap-0.5.2-foss-2019b.eb new file mode 100644 index 00000000000..85543e1ade9 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphMap/GraphMap-0.5.2-foss-2019b.eb @@ -0,0 +1,60 @@ +easyblock = 'MakeCp' + +name = 'GraphMap' +version = '0.5.2' + +homepage = 'https://github.com/isovic/graphmap' +description = "A highly sensitive and accurate mapper for long, error-prone reads" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'cstd': 'c++11', 'openmp': True} + +sources = [ + { + 'source_urls': ['https://github.com/isovic/graphmap/archive'], + 'filename': 'graphmap-20170526.tar.gz', + 'download_filename': 'eb8c75d68b03be95464318afa69b645a59f8f6b7.tar.gz', + }, + { + 'source_urls': ['https://github.com/isovic/seqlib/archive'], + 'filename': 'seqlib-20170526.tar.gz', + 'download_filename': 'd980be7a3cc0bc802eb910c10f084279f337992f.tar.gz', + }, + { + 'source_urls': ['https://github.com/isovic/argparser/archive'], + 'filename': 'argparser-20160623.tar.gz', + 'download_filename': '72af9764acefbcc92ff76e3aba8a83d9a3e33671.tar.gz', + }, + { + 'source_urls': ['https://github.com/isovic/gindex/archive'], + 'filename': 'gindex-20170304.tar.gz', + 'download_filename': 'b1fb5ad35763632db66377348bb16fec29f381e4.tar.gz', + }, +] +checksums = [ + 'f08c21f65a83922f43d3430faacf8cfeebbea6ee54dceac4ac438f985a170965', # graphmap-20170526.tar.gz + '77a19d9239125f91f9a8093bb4d03638e6ba9aa4ce0e586fa8f81a422fc9118c', # seqlib-20170526.tar.gz + '22132721986528851da838ccd1b3f223d4a68318f580ade3234c3b528ad8d7f4', # argparser-20160623.tar.gz + '87474a597f4e1d75cd9d188c5179014b87989ea02d440f5bba07b308ad3ae4af', # gindex-20170304.tar.gz +] + +files_to_copy = [(['bin/Linux-x64/graphmap'], 'bin')] + +# Move sources dependencies to expected folders +prebuildopts = "mv %(builddir)s/seqlib-*/* %(builddir)s/graphmap-*/codebase/seqlib/ && " +prebuildopts += "mv %(builddir)s/argparser-*/* %(builddir)s/graphmap-*/codebase/argumentparser/ && " +prebuildopts += "mv %(builddir)s/gindex-*/* %(builddir)s/graphmap-*/codebase/gindex/ && " + +# build flags inherited from original Makefile +buildopts = 'GCC="$CXX" ' +buildopts += 'CC_FLAGS_RELEASE="$CXXFLAGS -DRELEASE_VERSION -c ' +buildopts += '-fdata-sections -ffunction-sections -fmessage-length=0 -ffreestanding -Werror=return-type -pthread"' + +sanity_check_paths = { + 'files': ['bin/graphmap'], + 'dirs': [], +} + +sanity_check_commands = ['graphmap align -h 2>&1 | grep "GraphMap Version"'] + +moduleclass = 'bio' From db42a074c7a8ad5d364bc97a7c49844515e9b759 Mon Sep 17 00:00:00 2001 From: Mustafa Abduljabbar Date: Thu, 24 Feb 2022 11:02:08 +0200 Subject: [PATCH 3151/9987] adding easyconfigs: Schrodinger-2022-1.eb --- .../s/Schrodinger/Schrodinger-2022-1.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-1.eb diff --git a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-1.eb b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-1.eb new file mode 100644 index 00000000000..2786387ff86 --- /dev/null +++ b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-1.eb @@ -0,0 +1,31 @@ +easyblock='PackedBinary' + +name = 'Schrodinger' +version = '2022-1' + +homepage = 'https://www.schrodinger.com/' +description = """ Schrodinger aims to provide integrated software solutions and services + that truly meet its customers needs. We want to empower researchers around the world to + achieve their goals of improving human health and quality of life through advanced computational + techniques that transform the way chemists design compounds and materials. """ + +toolchain = SYSTEM + +# Download from schrodinger.com +sources = ['%(name)s_Suites_%(version)s_Linux-x86_64.tar'] +checksums = ['0fb9696901fc685e8400776e1c1f88f294b96a7d38528939b443840a53e474c0'] + +install_cmd = 'cd %(builddir)s/%(name)s_Suites_%(version)s_Linux-x86_64 && ' +install_cmd += './INSTALL -d . -s %(installdir)s -k /usr/tmp -t %(installdir)s/thirdparty -b *' + +sanity_check_paths = { + 'files': ['desmond', 'maestro'], + 'dirs': [], +} + +modextravars = { + 'SCHROD_LICENSE_FILE': '$HOME/.schrodinger_license', + 'SCHRODINGER': '%(installdir)s', +} + +moduleclass = 'bio' From 9c4dadc71f59c410b1985682fac53b5c6c9b0f10 Mon Sep 17 00:00:00 2001 From: James Carpenter Date: Thu, 24 Feb 2022 15:24:40 +0000 Subject: [PATCH 3152/9987] adding easyconfigs: wxPython-4.1.1-foss-2021a.eb, WebKitGTK+-2.27.4-GCC-10.3.0.eb, GConf-3.2.6-GCCcore-10.3.0.eb, LibSoup-2.74.0-GCCcore-10.3.0.eb, dbus-glib-0.112-GCCcore-10.3.0.eb and patches: wxPython-4.1.1_fix_install_path.patch, wxPython-4.1.1_use_bang_env_python.patch --- .../dbus-glib-0.112-GCCcore-10.3.0.eb | 32 +++++++++ .../g/GConf/GConf-3.2.6-GCCcore-10.3.0.eb | 54 ++++++++++++++ .../LibSoup/LibSoup-2.74.0-GCCcore-10.3.0.eb | 47 ++++++++++++ .../WebKitGTK+-2.27.4-GCC-10.3.0.eb | 72 +++++++++++++++++++ .../w/wxPython/wxPython-4.1.1-foss-2021a.eb | 47 ++++++++++++ .../wxPython-4.1.1_fix_install_path.patch | 15 ++++ .../wxPython-4.1.1_use_bang_env_python.patch | 40 +++++++++++ 7 files changed, 307 insertions(+) create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/LibSoup/LibSoup-2.74.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-4.1.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_fix_install_path.patch create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_use_bang_env_python.patch diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..891d503ec8f --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.112' + +homepage = 'https://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] +checksums = ['7d550dccdfcd286e33895501829ed971eeb65c614e73aadb4a08aeef719b143a'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), + ('Python', '3.9.5'), # Python is needed for building against GLib. +] + +dependencies = [ + ('GLib', '2.68.2'), + ('DBus', '1.13.18'), + ('expat', '2.2.9'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..10711489c57 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-10.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +homepage = 'https://developer.gnome.org/gconf/' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +patches = [ + '%(name)s-%(version)s_call-dbus_g_thread_init.patch', + '%(name)s-%(version)s_fix_wrong_return_value.patch', + '%(name)s-%(version)s_gconf-path-max-hurd.patch', + '%(name)s-%(version)s_readd_gconf_engine_key_is_writable.patch', +] +checksums = [ + '1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c', # GConf-3.2.6.tar.xz + 'ed55bff5bc239115ae27b8520a923ae0d5cab6cb15ca9921a8c23b939306489f', # GConf-3.2.6_call-dbus_g_thread_init.patch + 'f8f7745c3648953098eb56af0f64adc69d8c0b0e78c8db351746a2b4c58e8bb4', # GConf-3.2.6_fix_wrong_return_value.patch + 'ee5524c3cb985088bbe4884531ddc48ba22d2fced2a34865304c77e194a55bde', # GConf-3.2.6_gconf-path-max-hurd.patch + # GConf-3.2.6_readd_gconf_engine_key_is_writable.patch + 'b95dfc2f0474d9162fc686f26cd4d3da5c9b01a9c609dc0a4f2b2bd901d497f3', +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('GObject-Introspection', '1.68.0'), +] + +dependencies = [ + ('GLib', '2.68.2'), + ('dbus-glib', '0.112'), + ('libxml2', '2.9.10'), + ('GTK3', '3.24.29'), + ('intltool', '0.51.0'), +] + +configopts = '--disable-orbit ' + +local_check_filelist = ['bin/gconf%s' % x for x in ['-merge-tree', 'tool-2']] +local_check_filelist += ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] +local_check_filelist += ['lib/libgconf-2.%s' % x for x in ['a', 'so']] + +sanity_check_paths = { + 'files': local_check_filelist, + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-2.74.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.74.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..fd45e035337 --- /dev/null +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-2.74.0-GCCcore-10.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MesonNinja' + +name = 'LibSoup' +version = '2.74.0' + +homepage = 'https://wiki.gnome.org/Projects/libsoup' +description = """libsoup is an HTTP client/server library for GNOME. It +uses GObjects and the glib main loop, to integrate well with GNOME +applications, and also has a synchronous API, for use in threaded +applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'cstd': 'gnu11'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['33b1d4e0d639456c675c227877e94a8078d731233e2d57689c11abcef7d3c48e'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.68.0'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('libxml2', '2.9.10'), + ('SQLite', '3.35.4'), + ('GLib', '2.68.2'), + ('libpsl', '0.21.1'), + ('cURL', '7.76.0'), +] + +# uncomment for checking TLS support +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +# remove option -Dtls_check=false for checking TLS support +configopts = '-Dgssapi=disabled -Dvapi=disabled -Dtls_check=false ' + +sanity_check_paths = { + 'files': ['lib/libsoup-2.4.%s' % SHLIB_EXT, 'lib/libsoup-gnome-2.4.%s' % SHLIB_EXT], + 'dirs': ['include/libsoup-2.4/libsoup', 'include/libsoup-gnome-2.4/libsoup', 'lib/pkgconfig'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4-GCC-10.3.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..eda15a47211 --- /dev/null +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4-GCC-10.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'CMakeMake' + +name = 'WebKitGTK+' +version = '2.27.4' + +homepage = 'https://webkitgtk.org/' +description = """WebKitGTK+ is a full-featured port of the WebKit +rendering engine, suitable for projects requiring any kind of web +integration, from hybrid HTML/CSS applications to full-fledged web +browsers. It offers WebKit’s full functionality and is useful in a wide +range of systems from desktop computers to embedded systems like phones, +tablets, and televisions.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://webkitgtk.org/releases'] +sources = ['webkitgtk-%(version)s.tar.xz'] +patches = [ + '%(name)s-%(version)s_turn_off_various_problematic_features.patch', + '%(name)s-%(version)s_icuBOOL.patch' +] +checksums = [ + '50550a45464993070c544ec9777594d105fc5b35269520a3c96a3e2cd54874f7', # webkitgtk-2.27.4.tar.xz + # WebKitGTK+-2.27.4_turn_off_various_problematic_features.patch + '5aadd7898f6995bf89c558ce02d43e696ead962e283ddef88843160891494b5b', + 'fa0ddb386d2dc4d49ae94069a53fb5b57eff8b97ff1160cbca0b7e926a054af5', # WebKitGTK+-2.27.4_icuBOOL.patch +] + +osdependencies = [ + # Would be better to use the system package due to security reasons + # But we need at least libgcrypt 1.7.0 and Ubuntu 16.04 and RH 7.5 + # are both using a too old version. + # ('libgcrypt-dev', 'libgcrypt20-dev', 'libgcrypt-devel'), + # libsecret is not actually needed since USE_LIBSECRET option is disabled by default in patch + # ('libsecret-1-dev', 'libsecret-devel'), +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Python', '3.9.5'), + ('Perl', '5.32.1'), + ('GObject-Introspection', '1.68.0'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('GLib', '2.68.2'), + ('gperf', '3.1'), + ('cairo', '1.16.0'), + ('GTK3', '3.24.29'), + ('LibSoup', '2.74.0'), + ('ATK', '2.36.0'), + ('libgcrypt', '1.9.2'), + ('libwebp', '1.2.0'), + ('libxslt', '1.1.34'), + ('libtasn1', '4.17.0'), + ('GStreamer', '1.18.4'), + ('OpenJPEG', '2.4.0'), + ('Ruby', '3.0.1'), +] + +# must be built in parallel with more than 1 process (parallel > 1) to avoid build error: +# No rule to make target 'JavaScriptCore-4.0.gir', needed by 'WebKit2-4.0.gir' +# see https://bugs.webkit.org/show_bug.cgi?id=195251 + +configopts = "-DPORT=GTK -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python -DRUBY_EXECUTABLE=$EBROOTRUBY/bin/ruby " + +sanity_check_paths = { + 'files': ['bin/WebKitWebDriver', 'lib/libwebkit2gtk-4.0.%s' % SHLIB_EXT], + 'dirs': ['include/webkitgtk-4.0/webkit2', 'libexec/webkit2gtk-4.0'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1-foss-2021a.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1-foss-2021a.eb new file mode 100644 index 00000000000..ea789c108b3 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1-foss-2021a.eb @@ -0,0 +1,47 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +name = 'wxPython' +version = '4.1.1' + +homepage = "https://www.wxpython.org/" +description = """Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets +API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel +and requiring very little (if any) platform specific code.""" + + +toolchain = {'name': 'foss', 'version': '2021a'} +sources = ['%(name)s-%(version)s.tar.gz'] +patches = [ + 'wxPython-4.1.1_fix_install_path.patch', + 'wxPython-4.1.1_use_bang_env_python.patch', +] +checksums = [ + '00e5e3180ac7f2852f342ad341d57c44e7e4326de0b550b9a5c4a8361b6c3528', # wxPython-4.1.1.tar.gz + 'a029921f57377e12f39d2fab03cfd15d2e9773895767ce7a90727d3b3b17fd6e', # wxPython-4.1.1_fix_install_path.patch + 'c355c60a8cce3018fc0c30ffc78623efd2481e9baf33673e22a57863e1a3ac87', # wxPython-4.1.1_use_bang_env_python.patch +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Pillow', '8.2.0'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.2.0'), + ('expat', '2.2.9'), + ('GTK3', '3.24.29'), + ('GLib', '2.68.2'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '1.18.4'), + ('pkg-config', '0.29.2'), + ('Mesa', '21.1.1'), + ('libGLU', '9.0.1'), + ('LibSoup', '2.74.0'), + # ('wxWidgets', '3.1.5'), # this version is incompatible with with 4.1.1 so excluding to enable internal build + ('WebKitGTK+', '2.27.4'), +] + +# needed because wxWidgets is built as part of wxPython (not added as a dependency) +modextrapaths = {'LD_LIBRARY_PATH': 'lib/python%(pyshortver)s/site-packages/wx'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_fix_install_path.patch b/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_fix_install_path.patch new file mode 100644 index 00000000000..b920c06b7f8 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_fix_install_path.patch @@ -0,0 +1,15 @@ +--- orig_build.py 2021-11-24 10:28:29.174051000 +0000 ++++ build.py 2021-11-24 10:33:28.141864031 +0000 +@@ -1803,9 +1803,10 @@ + def cmd_install_py(options, args): + cmdTimer = CommandTimer('install_py') + DESTDIR = '' if not options.destdir else '--root=' + options.destdir ++ PREFIX = '' if not options.destdir else '--prefix=' + options.prefix + VERBOSE = '--verbose' if options.verbose else '' +- cmd = '"%s" setup.py install --skip-build %s %s %s' % ( +- PYTHON, DESTDIR, VERBOSE, options.extra_setup) ++ cmd = '"%s" setup.py install --skip-build %s %s %s %s' % ( ++ PYTHON, DESTDIR, PREFIX, VERBOSE, options.extra_setup) + runcmd(cmd) + + diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_use_bang_env_python.patch b/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_use_bang_env_python.patch new file mode 100644 index 00000000000..387d18f2da6 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_use_bang_env_python.patch @@ -0,0 +1,40 @@ +Don't use system python. +This is perhaps not needed but doesn't hurt. + +Åke Sandgren, 20190425 +diff -ru wxPython-4.0.4.orig/build.py wxPython-4.0.4/build.py +--- wxPython-4.0.4.orig/build.py 2019-01-05 20:48:40.000000000 +0100 ++++ wxPython-4.0.4/build.py 2019-04-24 21:37:32.296782206 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + #---------------------------------------------------------------------- + # Name: build.py + # Purpose: Master build controller script. +diff -ru wxPython-4.0.4.orig/ext/wxWidgets/build/osx/fix_xcode_ids.py wxPython-4.0.4/ext/wxWidgets/build/osx/fix_xcode_ids.py +--- wxPython-4.0.4.orig/ext/wxWidgets/build/osx/fix_xcode_ids.py 2019-01-03 00:48:23.000000000 +0100 ++++ wxPython-4.0.4/ext/wxWidgets/build/osx/fix_xcode_ids.py 2019-04-24 21:37:37.508731582 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + ############################################################################### + # Name: build/osx/fix_xcode_ids.py +diff -ru wxPython-4.0.4.orig/ext/wxWidgets/misc/scripts/png2c.py wxPython-4.0.4/ext/wxWidgets/misc/scripts/png2c.py +--- wxPython-4.0.4.orig/ext/wxWidgets/misc/scripts/png2c.py 2019-01-03 00:48:23.000000000 +0100 ++++ wxPython-4.0.4/ext/wxWidgets/misc/scripts/png2c.py 2019-04-24 21:37:35.300753028 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # This script is a slightly modified version of the original found at + # +diff -ru wxPython-4.0.4.orig/wscript wxPython-4.0.4/wscript +--- wxPython-4.0.4.orig/wscript 2019-01-05 20:48:40.000000000 +0100 ++++ wxPython-4.0.4/wscript 2019-04-24 21:37:40.556701977 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + #----------------------------------------------------------------------------- + # WAF script for building and installing the wxPython extension modules. + # From 157d3ac5dffd803f8ee25cd9475785d239cd93ca Mon Sep 17 00:00:00 2001 From: James Carpenter Date: Thu, 24 Feb 2022 15:42:20 +0000 Subject: [PATCH 3153/9987] Add missing WebKitGTK+ patch --- .../WebKitGTK+-2.27.4_icuBOOL.patch | 124 ++++++++++++++++++ 1 file changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4_icuBOOL.patch diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4_icuBOOL.patch b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4_icuBOOL.patch new file mode 100644 index 00000000000..dd09d3076ad --- /dev/null +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4_icuBOOL.patch @@ -0,0 +1,124 @@ +diff -ru a/Source/WTF/wtf/text/icu/UTextProvider.h icu/UTextProvider.h +--- a/Source/WTF/wtf/text/icu/UTextProvider.h 2022-02-17 13:18:23.457460771 +0000 ++++ b/Source/WTF/wtf/text/icu/UTextProvider.h 2022-02-17 13:25:49.327177443 +0000 +@@ -79,12 +79,12 @@ + // Ensure chunk offset is well formed if computed offset exceeds int32_t range. + ASSERT(offset < std::numeric_limits::max()); + text->chunkOffset = offset < std::numeric_limits::max() ? static_cast(offset) : 0; +- isAccessible = TRUE; ++ isAccessible = true; + return true; + } + if (nativeIndex >= nativeLength && text->chunkNativeLimit == nativeLength) { + text->chunkOffset = text->chunkLength; +- isAccessible = FALSE; ++ isAccessible = false; + return true; + } + } else { +@@ -93,12 +93,12 @@ + // Ensure chunk offset is well formed if computed offset exceeds int32_t range. + ASSERT(offset < std::numeric_limits::max()); + text->chunkOffset = offset < std::numeric_limits::max() ? static_cast(offset) : 0; +- isAccessible = TRUE; ++ isAccessible = true; + return true; + } + if (nativeIndex <= 0 && !text->chunkNativeStart) { + text->chunkOffset = 0; +- isAccessible = FALSE; ++ isAccessible = false; + return true; + } + } +diff -ru a/Source/WTF/wtf/text/icu/UTextProviderLatin1.cpp icu/UTextProviderLatin1.cpp +--- a/Source/WTF/wtf/text/icu/UTextProviderLatin1.cpp 2022-02-17 13:18:23.457460771 +0000 ++++ b/Source/WTF/wtf/text/icu/UTextProviderLatin1.cpp 2022-02-17 13:22:11.018867016 +0000 +@@ -100,23 +100,23 @@ + if (index < uText->chunkNativeLimit && index >= uText->chunkNativeStart) { + // Already inside the buffer. Set the new offset. + uText->chunkOffset = static_cast(index - uText->chunkNativeStart); +- return TRUE; ++ return true; + } + if (index >= length && uText->chunkNativeLimit == length) { + // Off the end of the buffer, but we can't get it. + uText->chunkOffset = static_cast(index - uText->chunkNativeStart); +- return FALSE; ++ return false; + } + } else { + if (index <= uText->chunkNativeLimit && index > uText->chunkNativeStart) { + // Already inside the buffer. Set the new offset. + uText->chunkOffset = static_cast(index - uText->chunkNativeStart); +- return TRUE; ++ return true; + } + if (!index && !uText->chunkNativeStart) { + // Already at the beginning; can't go any farther. + uText->chunkOffset = 0; +- return FALSE; ++ return false; + } + } + +@@ -144,7 +144,7 @@ + + uText->nativeIndexingLimit = uText->chunkLength; + +- return TRUE; ++ return true; + } + + static int32_t uTextLatin1Extract(UText* uText, int64_t start, int64_t limit, UChar* dest, int32_t destCapacity, UErrorCode* status) +@@ -337,7 +337,7 @@ + static UBool uTextLatin1ContextAwareAccess(UText* text, int64_t nativeIndex, UBool forward) + { + if (!text->context) +- return FALSE; ++ return false; + int64_t nativeLength = uTextLatin1ContextAwareNativeLength(text); + UBool isAccessible; + if (uTextAccessInChunkOrOutOfRange(text, nativeIndex, nativeLength, forward, isAccessible)) +@@ -357,7 +357,7 @@ + ASSERT(newContext == UTextProviderContext::PriorContext); + textLatin1ContextAwareSwitchToPriorContext(text, nativeIndex, nativeLength, forward); + } +- return TRUE; ++ return true; + } + + static int32_t uTextLatin1ContextAwareExtract(UText*, int64_t, int64_t, UChar*, int32_t, UErrorCode* errorCode) +diff -ru a/Source/WTF/wtf/text/icu/UTextProviderUTF16.cpp icu/UTextProviderUTF16.cpp +--- a/Source/WTF/wtf/text/icu/UTextProviderUTF16.cpp 2022-02-17 13:18:23.456460760 +0000 ++++ b/Source/WTF/wtf/text/icu/UTextProviderUTF16.cpp 2022-02-17 13:26:29.445601847 +0000 +@@ -126,7 +126,7 @@ + static UBool uTextUTF16ContextAwareAccess(UText* text, int64_t nativeIndex, UBool forward) + { + if (!text->context) +- return FALSE; ++ return false; + int64_t nativeLength = uTextUTF16ContextAwareNativeLength(text); + UBool isAccessible; + if (uTextAccessInChunkOrOutOfRange(text, nativeIndex, nativeLength, forward, isAccessible)) +@@ -146,7 +146,7 @@ + ASSERT(newContext == UTextProviderContext::PriorContext); + textUTF16ContextAwareSwitchToPriorContext(text, nativeIndex, nativeLength, forward); + } +- return TRUE; ++ return true; + } + + static int32_t uTextUTF16ContextAwareExtract(UText*, int64_t, int64_t, UChar*, int32_t, UErrorCode* errorCode) +diff -ru a/Source/WebCore/platform/text/TextCodecICU.cpp b/Source/WebCore/platform/text/TextCodecICU.cpp +--- a/Source/WebCore/platform/text/TextCodecICU.cpp 2022-02-17 16:03:58.160729579 +0000 ++++ b/Source/WebCore/platform/text/TextCodecICU.cpp 2022-02-17 16:04:40.173138789 +0000 +@@ -239,7 +239,7 @@ + UErrorCode error = U_ZERO_ERROR; + m_converter = ICUConverterPtr { ucnv_open(m_canonicalConverterName, &error), ucnv_close }; + if (m_converter) +- ucnv_setFallback(m_converter.get(), TRUE); ++ ucnv_setFallback(m_converter.get(), true); + } + + int TextCodecICU::decodeToBuffer(UChar* target, UChar* targetLimit, const char*& source, const char* sourceLimit, int32_t* offsets, bool flush, UErrorCode& error) \ No newline at end of file From 538947bfac61fac247ef26de11792aa6175aef02 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 24 Feb 2022 19:27:10 +0100 Subject: [PATCH 3154/9987] Update LAPACK-3.9.1-GCC-10.2.0.eb The original URL was failing --- easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb index 3990b2cebeb..14d4bb284cb 100644 --- a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.9.1-GCC-10.2.0.eb @@ -9,7 +9,7 @@ description = """LAPACK is written in Fortran90 and provides routines for solvin toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://github.com/Reference-LAPACK/lapack/archive/'] +source_urls = ['https://github.com/Reference-LAPACK/lapack/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] checksums = ['d0085d2caf997ff39299c05d4bacb6f3d27001d25a4cc613d48c1f352b73e7e0'] From 2e36f0fd13b72d6db323bc009e0b511c1059e51c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Feb 2022 11:00:33 +0100 Subject: [PATCH 3155/9987] add patches for mauveAligner to fix build on RHEL8 --- .../mauveAligner/mauveAligner-4736-gompi-2020a.eb | 14 ++++++++++++-- .../mauveAligner-4736_fix-getopt.patch | 12 ++++++++++++ .../m/mauveAligner/sgEvolver-4736_fix-getopt.patch | 12 ++++++++++++ 3 files changed, 36 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736_fix-getopt.patch create mode 100644 easybuild/easyconfigs/m/mauveAligner/sgEvolver-4736_fix-getopt.patch diff --git a/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb b/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb index b13c7fbd93e..a7eaf4ce21c 100644 --- a/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb +++ b/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb @@ -67,17 +67,25 @@ components = [ ], }), ('mauveAligner', version, { - 'patches': ['mauveAligner-4736_debian.patch'], + 'patches': [ + 'mauveAligner-4736_debian.patch', + 'mauveAligner-4736_fix-getopt.patch', + ], 'checksums': [ None, # mauveAligner-4736.tar.bz2 '2786bd29bedb224f232e7909972b549fe95f520ddac2cbb076e2082647dc68ae', # mauveAligner-4736_debian.patch + 'c5f07b3b12549d2be9b5869422b7dd85bbde6502222c0938978a2fd4da4328fb', # mauveAligner-4736_fix-getopt.patch: ], }), ('sgEvolver', version, { - 'patches': ['sgEvolver-4736_dropversion.patch'], + 'patches': [ + 'sgEvolver-4736_dropversion.patch', + 'sgEvolver-4736_fix-getopt.patch', + ], 'checksums': [ None, # sgEvolver-4736.tar.bz2 'efc3397039dd525669f6c525b20d75ad64c51cd25912192e695067de4cfbeadc', # sgEvolver-4736_dropversion.patch + 'ba086832bfcf2e8d945e6f46440efc3af1e89102155040b6103dc7f2a6beecff', # sgEvolver-4736_fix-getopt.patch: ], }), ] @@ -107,6 +115,8 @@ sanity_check_paths = { ['share', 'lib/pkgconfig'], } +sanity_check_commands = ["mauveAligner --help 2>&1 | grep '^mauveAligner'"] + modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736_fix-getopt.patch b/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736_fix-getopt.patch new file mode 100644 index 00000000000..73a9c65580d --- /dev/null +++ b/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736_fix-getopt.patch @@ -0,0 +1,12 @@ +--- mauveAligner/src/getopt.h.orig 2022-02-25 10:23:21.301489496 +0100 ++++ mauveAligner/src/getopt.h 2022-02-25 10:26:13.940751386 +0100 +@@ -146,7 +146,8 @@ + /* Many other libraries have conflicting prototypes for getopt, with + differences in the consts, in stdlib.h. To avoid compilation + errors, only prototype getopt for the GNU C library. */ +-extern int getopt (int ___argc, char *const *___argv, const char *__shortopts); ++extern int getopt (int ___argc, char *const *___argv, const char *__shortopts) ++ __THROW __nonnull ((2, 3)); + # elif GETOPT_UNDEFINED /* not __GNU_LIBRARY__ */ + extern int getopt (); + # endif /* __GNU_LIBRARY__ */ diff --git a/easybuild/easyconfigs/m/mauveAligner/sgEvolver-4736_fix-getopt.patch b/easybuild/easyconfigs/m/mauveAligner/sgEvolver-4736_fix-getopt.patch new file mode 100644 index 00000000000..c70220431ee --- /dev/null +++ b/easybuild/easyconfigs/m/mauveAligner/sgEvolver-4736_fix-getopt.patch @@ -0,0 +1,12 @@ +--- sgEvolver/src/getopt.h.orig 2022-02-25 10:33:10.015721000 +0100 ++++ sgEvolver/src/getopt.h 2022-02-25 10:33:33.950344000 +0100 +@@ -146,7 +146,8 @@ + /* Many other libraries have conflicting prototypes for getopt, with + differences in the consts, in stdlib.h. To avoid compilation + errors, only prototype getopt for the GNU C library. */ +-extern int getopt (int ___argc, char *const *___argv, const char *__shortopts); ++extern int getopt (int ___argc, char *const *___argv, const char *__shortopts) ++ __THROW __nonnull ((2, 3)); + # elif GETOPT_UNDEFINED /* not __GNU_LIBRARY__ */ + extern int getopt (); + # endif /* __GNU_LIBRARY__ */ From 25d889b0542426c4cfbad33a9ec03dc1f5b18e7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Feb 2022 11:22:39 +0100 Subject: [PATCH 3156/9987] use SHLIB_EXT in meshanalyzer 20200308 easyconfig --- .../m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb index 14a294f9343..d3b646e9b88 100644 --- a/easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb @@ -28,7 +28,7 @@ dependencies = [ ('VTK', '%s.0' % local_vtk_majmin_ver, versionsuffix), ] -buildopts = 'HDF5_ROOT=$EBROOTHDF5 LIB_EXT=".so" ' +buildopts = 'HDF5_ROOT=$EBROOTHDF5 LIB_EXT=".%s" ' % SHLIB_EXT buildopts += 'VTK_INCDIR=$EBROOTVTK/include/vtk-%s/ VTK_LIBDIR=$EBROOTVTK/lib' % local_vtk_majmin_ver files_to_copy = [(['meshalyzer'], 'bin')] From 730937b0c428c6f72712677cf882c541b6a954cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 25 Feb 2022 12:43:16 +0200 Subject: [PATCH 3157/9987] Fix sanity check path --- easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb index 9c55e38d7fe..713ddc87bf4 100644 --- a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb @@ -22,7 +22,7 @@ configopts = '-DBUILD_FASTFARM=ON ' sanity_check_paths = { 'files': ['bin/openfast', 'bin/FAST.Farm', - 'lib/libopenfastlib.a', 'libopenfast_prelib.a', 'lib/libopenfast_postlib.a'], + 'lib/libopenfastlib.a', 'lib/libopenfast_prelib.a', 'lib/libopenfast_postlib.a'], 'dirs': ['include/openfast'], } diff --git a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb index a3c6abf322d..78ae3b4a6d5 100644 --- a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb +++ b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb @@ -22,7 +22,7 @@ configopts = '-DBUILD_FASTFARM=ON ' sanity_check_paths = { 'files': ['bin/openfast', 'bin/FAST.Farm', - 'lib/libopenfastlib.a', 'libopenfast_prelib.a', 'lib/libopenfast_postlib.a'], + 'lib/libopenfastlib.a', 'lib/libopenfast_prelib.a', 'lib/libopenfast_postlib.a'], 'dirs': ['include/openfast'], } From 2deea51fe779c294a596bd86d779e361a9d12520 Mon Sep 17 00:00:00 2001 From: James Carpenter Date: Fri, 25 Feb 2022 11:11:23 +0000 Subject: [PATCH 3158/9987] fix prefix error and add comments to patch --- .../easyconfigs/w/wxPython/wxPython-4.1.1-foss-2021a.eb | 2 +- .../w/wxPython/wxPython-4.1.1_fix_install_path.patch | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1-foss-2021a.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1-foss-2021a.eb index ea789c108b3..0af1145425e 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1-foss-2021a.eb @@ -16,7 +16,7 @@ patches = [ ] checksums = [ '00e5e3180ac7f2852f342ad341d57c44e7e4326de0b550b9a5c4a8361b6c3528', # wxPython-4.1.1.tar.gz - 'a029921f57377e12f39d2fab03cfd15d2e9773895767ce7a90727d3b3b17fd6e', # wxPython-4.1.1_fix_install_path.patch + 'f13743877deddbf525bbb3f81c8f7a6b0c2dbf1333595926f653f696999e31ce', # wxPython-4.1.1_fix_install_path.patch 'c355c60a8cce3018fc0c30ffc78623efd2481e9baf33673e22a57863e1a3ac87', # wxPython-4.1.1_use_bang_env_python.patch ] diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_fix_install_path.patch b/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_fix_install_path.patch index b920c06b7f8..18d8d00b05a 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_fix_install_path.patch +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.1.1_fix_install_path.patch @@ -1,10 +1,14 @@ +build.py calls setup.py without a prefix, this fixes that. + +Åke Sandgren, 20190201 +James Carpenter, 20220224 --- orig_build.py 2021-11-24 10:28:29.174051000 +0000 +++ build.py 2021-11-24 10:33:28.141864031 +0000 @@ -1803,9 +1803,10 @@ def cmd_install_py(options, args): cmdTimer = CommandTimer('install_py') DESTDIR = '' if not options.destdir else '--root=' + options.destdir -+ PREFIX = '' if not options.destdir else '--prefix=' + options.prefix ++ PREFIX = '' if not options.prefix else '--prefix=' + options.prefix VERBOSE = '--verbose' if options.verbose else '' - cmd = '"%s" setup.py install --skip-build %s %s %s' % ( - PYTHON, DESTDIR, VERBOSE, options.extra_setup) From 67d643018528f727c9f5486083dbda368b91f21e Mon Sep 17 00:00:00 2001 From: James Carpenter Date: Fri, 25 Feb 2022 11:14:48 +0000 Subject: [PATCH 3159/9987] add comment to icuBOOL patch --- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4-GCC-10.3.0.eb | 2 +- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4_icuBOOL.patch | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4-GCC-10.3.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4-GCC-10.3.0.eb index eda15a47211..fb003ec347d 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4-GCC-10.3.0.eb @@ -23,7 +23,7 @@ checksums = [ '50550a45464993070c544ec9777594d105fc5b35269520a3c96a3e2cd54874f7', # webkitgtk-2.27.4.tar.xz # WebKitGTK+-2.27.4_turn_off_various_problematic_features.patch '5aadd7898f6995bf89c558ce02d43e696ead962e283ddef88843160891494b5b', - 'fa0ddb386d2dc4d49ae94069a53fb5b57eff8b97ff1160cbca0b7e926a054af5', # WebKitGTK+-2.27.4_icuBOOL.patch + '09c402193c3c03a0fa3676c143cd4eded4169c35baf75e78dac5c7a5c4ea7a3e', # WebKitGTK+-2.27.4_icuBOOL.patch ] osdependencies = [ diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4_icuBOOL.patch b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4_icuBOOL.patch index dd09d3076ad..c6b7de4a7da 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4_icuBOOL.patch +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.27.4_icuBOOL.patch @@ -1,3 +1,7 @@ +ICU no longer defines TRUE and FALSE macros since v68 +(https://icu.unicode.org/download/68) + +James Carpenter, 20220224 diff -ru a/Source/WTF/wtf/text/icu/UTextProvider.h icu/UTextProvider.h --- a/Source/WTF/wtf/text/icu/UTextProvider.h 2022-02-17 13:18:23.457460771 +0000 +++ b/Source/WTF/wtf/text/icu/UTextProvider.h 2022-02-17 13:25:49.327177443 +0000 From 3a7b12dbab42fdcb1e0e2f56b5581dbfa3ea847d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 25 Feb 2022 15:17:28 +0000 Subject: [PATCH 3160/9987] adding easyconfigs: SPM-12.5_r7771-MATLAB-2021a.eb --- .../s/SPM/SPM-12.5_r7771-MATLAB-2021a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPM/SPM-12.5_r7771-MATLAB-2021a.eb diff --git a/easybuild/easyconfigs/s/SPM/SPM-12.5_r7771-MATLAB-2021a.eb b/easybuild/easyconfigs/s/SPM/SPM-12.5_r7771-MATLAB-2021a.eb new file mode 100644 index 00000000000..72fe5d8b1e4 --- /dev/null +++ b/easybuild/easyconfigs/s/SPM/SPM-12.5_r7771-MATLAB-2021a.eb @@ -0,0 +1,53 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'Tarball' + +name = 'SPM' +version = '12.5_r7771' +_matlab_ver = '2021a' +versionsuffix = '-MATLAB-%s' % _matlab_ver + +homepage = 'https://www.fil.ion.ucl.ac.uk/spm' +description = """SPM (Statistical Parametric Mapping) refers to the construction + and assessment of spatially extended statistical processes used to test hypo- + theses about functional imaging data. These ideas have been instantiated in + software that is called SPM. + The SPM software package has been designed for the analysis of brain imaging + data sequences. The sequences can be a series of images from different cohorts, + or time-series from the same subject. The current release is designed for the + analysis of fMRI, PET, SPECT, EEG and MEG. +""" + +toolchain = SYSTEM + +_spm_maj_ver = version.split('.')[0] +_spm_majmin_ver, _spm_update_ver = version.split('_') + +sources = [ + { + 'source_urls': ['https://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado'], + 'filename': '%%(namelower)s%s.zip' % _spm_majmin_ver, + }, + { + 'source_urls': ['http://www.fil.ion.ucl.ac.uk/spm/download/spm12_updates'], + 'filename': '%%(namelower)s%s_updates_%s.zip' % (_spm_maj_ver, _spm_update_ver), + 'extract_cmd': 'unzip -oqq %%s -d spm%s' % _spm_maj_ver, + }, +] +checksums = [ + '0dc847eb065ccfcefbaefafdc12201dd20a22b9ee9b33a6b1973d07690a21914', # spm12.5.zip + '2b3cbd5f58fe180231d8bdcd0762c8874aee97240de391d876d9f2e33037a293', # spm12_updates_r7771.zip +] + +dependencies = [('MATLAB', _matlab_ver)] + +sanity_check_paths = { + 'files': ['spm.m'], + 'dirs': [], +} + +sanity_check_commands = ['matlab -batch "spm version"'] + +modextrapaths = {'MATLABPATH': ''} + +moduleclass = 'tools' From afaa9f2ce25d80c08b36fb21979f3f12819b55b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Feb 2022 16:32:44 +0100 Subject: [PATCH 3161/9987] fix installation of RDKit by using -DBoost_NO_BOOST_CMAKE=ON --- .../r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb | 2 ++ .../r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb | 2 ++ .../r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb | 3 +++ 3 files changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb index 9990f9acddb..0f3478b407f 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb @@ -44,10 +44,12 @@ separate_build_dir = True configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " +configopts += "-DBoost_NO_BOOST_CMAKE=ON " # merge source directory into build directory in order to run the tests buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' + # 'ctest' allows to pass additional arguments opposed to 'make test' buildopts += 'ctest --output-on-failure' diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb index 7715adac08e..9114ab335e8 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb @@ -44,10 +44,12 @@ separate_build_dir = True configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " +configopts += "-DBoost_NO_BOOST_CMAKE=ON " # merge source directory into build directory in order to run the tests buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' + # 'ctest' allows to pass additional arguments opposed to 'make test' # Exclude RGroup test on intel - https://github.com/rdkit/rdkit/issues/3291 buildopts += 'ctest --output-on-failure -E RGroup' diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb index 17cc82723e1..30280d9b65f 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb @@ -42,12 +42,15 @@ separate_build_dir = True configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " +configopts += "-DBoost_NO_BOOST_CMAKE=ON " # merge source directory into build directory in order to run the tests buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' + # 'ctest' allows to pass additional arguments opposed to 'make test' buildopts += 'ctest --output-on-failure ' + # Exclude RGroup test when using Intel compilers - https://github.com/rdkit/rdkit/issues/3291 # buildopts += '-E RGroup' From b0e5b97e61d3fec6365921db4cb3d904d9a18da5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 25 Feb 2022 15:36:37 +0000 Subject: [PATCH 3162/9987] adding easyconfigs: CONN-21a-MATLAB-2021a.eb --- .../c/CONN/CONN-21a-MATLAB-2021a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/CONN/CONN-21a-MATLAB-2021a.eb diff --git a/easybuild/easyconfigs/c/CONN/CONN-21a-MATLAB-2021a.eb b/easybuild/easyconfigs/c/CONN/CONN-21a-MATLAB-2021a.eb new file mode 100644 index 00000000000..042869896b3 --- /dev/null +++ b/easybuild/easyconfigs/c/CONN/CONN-21a-MATLAB-2021a.eb @@ -0,0 +1,37 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'Tarball' + +name = 'CONN' +version = '21a' +_matlab_ver = '2021a' +versionsuffix = '-MATLAB-%s' % _matlab_ver + +homepage = 'https://web.conn-toolbox.org/home' +description = """CONN is an open-source Matlab/SPM-based cross-platform software + for the computation, display, and analysis of functional connectivity Magnetic + Resonance Imaging (fcMRI). CONN is used to analyze resting state data (rsfMRI) + as well as task-related designs. +""" + +toolchain = SYSTEM + +source_urls = ['https://www.nitrc.org/frs/download.php/12426/'] +sources = ['%(namelower)s%(version)s.zip'] +checksums = ['de5b9537f8dfb7187756f39ed9e5c953bad64b6e5e4b3e3a4d34aa6ccb6329dd'] + +dependencies = [ + ('MATLAB', _matlab_ver), + ('SPM', '12.5_r7771', versionsuffix), +] + +sanity_check_paths = { + 'files': ['conn.m'], + 'dirs': ['modules', 'rois', 'standalone', 'utils'], +} + +sanity_check_commands = ['matlab -batch "conn version"'] + +modextrapaths = {'MATLABPATH': ''} + +moduleclass = 'tools' From 24bef2d3021203704d82c376b2ee6ea0606197ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Feb 2022 21:33:47 +0100 Subject: [PATCH 3163/9987] add patch to fix linking error for imread extension in scikit-image easyconfigs using intel toolchain --- .../imread-0.7.1_fix-library-order.patch | 15 +++++++++++++++ ...cikit-image-0.16.2-intel-2019b-Python-3.7.4.eb | 6 +++++- .../scikit-image-0.18.1-intel-2020b.eb | 6 +++++- 3 files changed, 25 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/s/scikit-image/imread-0.7.1_fix-library-order.patch diff --git a/easybuild/easyconfigs/s/scikit-image/imread-0.7.1_fix-library-order.patch b/easybuild/easyconfigs/s/scikit-image/imread-0.7.1_fix-library-order.patch new file mode 100644 index 00000000000..a808fc95719 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/imread-0.7.1_fix-library-order.patch @@ -0,0 +1,15 @@ +fix linking order of libraries to fix: + ld: /software/LibTIFF/4.1.0-GCCcore-10.2.0/lib/libtiff.so:(*IND*+0x0): multiple definition of `_end' + ld: /software/LibTIFF/4.1.0-GCCcore-10.2.0/lib/libtiff.so:(*IND*+0x0): multiple definition of `__bss_start' +see also https://github.com/easybuilders/easybuild-easyconfigs/issues/14219 +--- imread-0.7.1/setup.py.orig 2022-02-25 17:30:06.726515267 +0100 ++++ imread-0.7.1/setup.py 2022-02-25 17:30:21.451056892 +0100 +@@ -77,7 +77,7 @@ + } + + +-libraries = ['png', 'jpeg', 'tiff'] ++libraries = ['png', 'tiff', 'jpeg'] + if sys.platform.startswith('win'): + libraries.append('zlib') + diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-intel-2019b-Python-3.7.4.eb index f4dbbf7f82f..0eeba49b72f 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.16.2-intel-2019b-Python-3.7.4.eb @@ -30,7 +30,11 @@ exts_list = [ 'checksums': ['f44eb231b9df485874f2ffd22dfd0c3c711e7de076516b9374edea5c65bc67ae'], }), ('imread', '0.7.1', { - 'checksums': ['c343b546ab54acdb50dbe69d6793d64ead3ba6d585022f5a7ad4687b7f3db79b'], + 'patches': ['imread-0.7.1_fix-library-order.patch'], + 'checksums': [ + 'c343b546ab54acdb50dbe69d6793d64ead3ba6d585022f5a7ad4687b7f3db79b', # imread-0.7.1.tar.gz + '0702321112ddcc1e6b98dc0a20eed8f93e5ee271304e2a6dc26d64ea83bddedf', # imread-0.7.1_fix-library-order.patch + ], }), (name, version, { 'modulename': 'skimage', diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb index d92ee21ee4e..e72dbff85f4 100644 --- a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.18.1-intel-2020b.eb @@ -28,7 +28,11 @@ exts_list = [ 'checksums': ['52ddbaeca2dccf53ba2d6dec5676ca7bc3b2403ef8b37f7da78b7654bb3e10f0'], }), ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + 'patches': ['imread-0.7.1_fix-library-order.patch'], + 'checksums': [ + '0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f', # imread-0.7.4.tar.gz + '0702321112ddcc1e6b98dc0a20eed8f93e5ee271304e2a6dc26d64ea83bddedf', # imread-0.7.1_fix-library-order.patch + ], }), ('pooch', '1.3.0', { 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], From 275acfa14ddcd376399c7326e9b4e7910b79f062 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Feb 2022 21:41:57 +0100 Subject: [PATCH 3164/9987] avoid excessively long shebang in Autoconf/Automake Perl scripts + promote Perl to runtime dependency + fix Perl shebang for intltool --- .../a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb | 13 ++++++++++--- .../a/Automake/Automake-1.16.4-GCCcore-11.2.0.eb | 15 +++++++++++---- .../i/intltool/intltool-0.51.0-GCCcore-11.2.0.eb | 2 ++ 3 files changed, 23 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb index 3af406badc2..4a0acd7948a 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.2.0.eb @@ -22,15 +22,17 @@ checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] builddependencies = [ ('binutils', '2.37'), - # non-standard Perl modules are required, - # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 - ('Perl', '5.34.0'), ] dependencies = [ ('M4', '1.4.19'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.34.0'), ] +preconfigopts = "export PERL='/usr/bin/env perl' && " + sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", @@ -38,4 +40,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + "autoconf --help", + "autom4te --help", +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.4-GCCcore-11.2.0.eb index a47580d9afd..f3faae6a20a 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.4-GCCcore-11.2.0.eb @@ -15,18 +15,25 @@ checksums = ['8a0f0be7aaae2efa3a68482af28e5872d8830b9813a6a932a2571eac63ca1794'] builddependencies = [ ('binutils', '2.37'), - # non-standard Perl modules are required, - # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 - ('Perl', '5.34.0'), ] dependencies = [ ('Autoconf', '2.71'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.34.0'), ] +preconfigopts = "export PERL='/usr/bin/env perl' && " + sanity_check_paths = { - 'files': ['bin/automake', 'bin/aclocal'], + 'files': ['bin/aclocal', 'bin/automake'], 'dirs': [] } +sanity_check_commands = [ + "aclocal --help", + "automake --help", +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.2.0.eb index 2d693a38180..8945f9aecf5 100644 --- a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.2.0.eb @@ -25,6 +25,8 @@ dependencies = [ ('Perl', '5.34.0'), ] +fix_perl_shebang_for = ['bin/intltool-*'] + sanity_check_paths = { 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], 'dirs': [] From 6b580010d3656418075b5fbd1d5acb9edc8981fe Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Sat, 26 Feb 2022 10:31:50 +0000 Subject: [PATCH 3165/9987] Fix typo in description --- .../m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb index d3b646e9b88..bb93c14359e 100644 --- a/easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/meshalyzer/meshalyzer-20200308-foss-2020a-Python-3.8.2.eb @@ -6,7 +6,7 @@ version = '20200308' # datestamp of commit versionsuffix = '-Python-3.8.2' homepage = 'https://git.opencarp.org/openCARP/meshalyzer' -description = "Graphical program for display time dependent data on 3D finite elment meshes" +description = "Graphical program for display time dependent data on 3D finite element meshes" toolchain = {'name': 'foss', 'version': '2020a'} From 34560ca209fe2222c40ee8bb40e48a3a88c5e5b5 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 26 Feb 2022 16:15:20 +0100 Subject: [PATCH 3166/9987] adding easyconfigs: Siesta-4.1.5-foss-2021a.eb, Siesta-4.1.5-foss-2021b.eb --- .../s/Siesta/Siesta-4.1.5-foss-2021a.eb | 26 +++++++++++++++++++ .../s/Siesta/Siesta-4.1.5-foss-2021b.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2021a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2021a.eb new file mode 100644 index 00000000000..31e7195a681 --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2021a.eb @@ -0,0 +1,26 @@ +name = 'Siesta' +version = '4.1.5' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'precise': True} + +source_urls = ['https://gitlab.com/siesta-project/siesta/-/releases/v%(version)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['518df31aa6213af5e24cc73abb537b2c89a925b487171f5339d743d0c7140b3f'] + +dependencies = [ + ('netCDF-Fortran', '4.5.3'), + ('METIS', '5.1.0'), + ('ELPA', '2021.05.001'), +] + +# transiesta is now siesta --electrode +with_transiesta = False + +runtest = 'check' + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2021b.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2021b.eb new file mode 100644 index 00000000000..8a77ca696c8 --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2021b.eb @@ -0,0 +1,26 @@ +name = 'Siesta' +version = '4.1.5' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'precise': True} + +source_urls = ['https://gitlab.com/siesta-project/siesta/-/releases/v%(version)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['518df31aa6213af5e24cc73abb537b2c89a925b487171f5339d743d0c7140b3f'] + +dependencies = [ + ('netCDF-Fortran', '4.5.3'), + ('METIS', '5.1.0'), + ('ELPA', '2021.05.001'), +] + +# transiesta is now siesta --electrode +with_transiesta = False + +runtest = 'check' + +moduleclass = 'phys' From 99a54494226bb73a198226f8ec7b39a975e1f06b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Feb 2022 17:39:25 +0100 Subject: [PATCH 3167/9987] fix python shebang in cutadapt script for cutadapt 1.18 w/ GCCcore/8.3.0 --- easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.3.0.eb index 8ec464cbed7..6e863b30556 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.18-GCCcore-8.3.0.eb @@ -38,6 +38,8 @@ exts_list = [ }), ] +fix_python_shebang_for = ['bin/cutadapt'] + sanity_check_paths = { 'files': ['bin/cutadapt'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 0a337c24bf9b6a05182b488456eea80e6f8d48a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Feb 2022 17:50:03 +0100 Subject: [PATCH 3168/9987] enable sanity_pip_check for parallel-fastq-dump 0.6.6 --- .../parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb index 646b5f3b343..234ce1ed45d 100644 --- a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb @@ -39,4 +39,6 @@ options = {'modulename': False} sanity_check_commands = ["parallel-fastq-dump --version"] +sanity_pip_check = True + moduleclass = "bio" From 05be88477a7d3713f2da49f87d96ce7b6f4d4617 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Feb 2022 18:23:56 +0100 Subject: [PATCH 3169/9987] bump to gmpy2 v2.1.2 as dependency for sympy 1.9 --- easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb index d2f13681adb..2c517174dcc 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb @@ -17,7 +17,7 @@ checksums = ['c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc'] dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), - ('gmpy2', '2.1.0rc1'), + ('gmpy2', '2.1.2'), ] download_dep_fail = True From fd2501ffcc33d242c6d02dd7ee56070a474affec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Feb 2022 18:24:48 +0100 Subject: [PATCH 3170/9987] don't use v2.1.0rc1 release candidate of gmpy2, stick to proper release v2.1.2 --- ...gmpy2-2.1.0rc1-GCC-11.2.0.eb => gmpy2-2.1.2-GCC-11.2.0.eb} | 4 ++-- .../easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/gmpy2/{gmpy2-2.1.0rc1-GCC-11.2.0.eb => gmpy2-2.1.2-GCC-11.2.0.eb} (81%) diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-GCC-11.2.0.eb similarity index 81% rename from easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb rename to easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-GCC-11.2.0.eb index 34f391736cd..e3f43a071aa 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.0rc1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-GCC-11.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'gmpy2' -version = '2.1.0rc1' +version = '2.1.2' homepage = 'https://github.com/aleaxit/gmpy' description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" @@ -9,7 +9,7 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'GCC', 'version': '11.2.0'} sources = [SOURCE_TAR_GZ] -checksums = ['86cb6d8e5837560c32c706d48d6ed25676be6b3c79e6aa5d245965b9e99231b9'] +checksums = ['da75140bca128ece795895477e53b43773e3748aa90ba6170eae7ca2c74b82d1'] dependencies = [ ('Python', '3.9.6'), diff --git a/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb b/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb index 7a7b003c9ea..c8435307d60 100644 --- a/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PPanGGOLiN/PPanGGOLiN-1.1.136-foss-2021b.eb @@ -28,7 +28,7 @@ dependencies = [ ('networkx', '2.6.3'), ('SciPy-bundle', '2021.10'), ('plotly.py', '5.4.0'), - ('gmpy2', '2.1.0rc1'), + ('gmpy2', '2.1.2'), ('MAFFT', '7.490', '-with-extensions'), ('rpy2', '3.4.5'), ] From 0e5c5661c66cce8b515eab6f3a8571771412d44f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 29 Jan 2022 18:05:26 +0100 Subject: [PATCH 3171/9987] add check to verify that patch files touched in PRs have a description in place --- test/easyconfigs/easyconfigs.py | 50 ++++++++++++++++++++++++++++++--- 1 file changed, 46 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 96b312d1d60..95922f7a545 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -51,7 +51,7 @@ from easybuild.tools import config from easybuild.tools.build_log import EasyBuildError from easybuild.tools.config import GENERAL_CLASS, build_option -from easybuild.tools.filetools import change_dir, is_generic_easyblock, remove_file +from easybuild.tools.filetools import change_dir, is_generic_easyblock, read_file, remove_file from easybuild.tools.filetools import verify_checksum, which, write_file from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool @@ -98,7 +98,7 @@ def skip_if_not_pr_to_non_main_branch(): return lambda func: func -def get_eb_files_from_diff(diff_filter): +def get_files_from_diff(diff_filter, ext, basename=True): """Return the files changed on HEAD relative to the current target branch""" target_branch = get_target_branch() @@ -122,12 +122,20 @@ def get_eb_files_from_diff(diff_filter): # determine list of changed files using 'git diff' and merge base determined above cmd = "git diff --name-only --diff-filter=%s %s..HEAD --" % (diff_filter, merge_base) out, _ = run_cmd(cmd, simple=False) - files = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith('.eb')] + if basename: + files = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith(ext)] + else: + files = [f for f in out.strip().split('\n') if f.endswith(ext)] change_dir(cwd) return files +def get_eb_files_from_diff(diff_filter): + """Return the easyconfig files changed on HEAD relative to the current target branch""" + return get_files_from_diff(diff_filter, '.eb') + + class EasyConfigTest(TestCase): """Baseclass for easyconfig testcases.""" @@ -171,7 +179,8 @@ def setUpClass(cls): cls._ordered_specs = None cls._parsed_easyconfigs = [] cls._parsed_all_easyconfigs = False - cls._changed_ecs = None # ECs changed in a PR + cls._changed_ecs = None # easyconfigs changed in a PR + cls._changed_patches = None # patches changed in a PR @classmethod def tearDownClass(cls): @@ -241,6 +250,20 @@ def _get_changed_easyconfigs(self): " (and could not isolate it in easyconfigs archive either)" % ec_fn) EasyConfigTest._changed_ecs = changed_ecs + def _get_changed_patches(self): + """Gather all added or modified patches""" + + # get list of changed/added patch files + changed_patches_filenames = get_files_from_diff(diff_filter='M', ext='.patch', basename=False) + added_patches_filenames = get_files_from_diff(diff_filter='A', ext='.patch', basename=False) + + if changed_patches_filenames: + print("\nList of changed patch files in this PR:\n\t%s" % '\n\t'.join(changed_patches_filenames)) + if added_patches_filenames: + print("\nList of added patch files in this PR:\n\t%s" % '\n\t'.join(added_patches_filenames)) + + EasyConfigTest._changed_patches = changed_patches_filenames + added_patches_filenames + @property def parsed_easyconfigs(self): # parse all easyconfigs if they haven't been already @@ -272,6 +295,12 @@ def changed_ecs(self): self._get_changed_easyconfigs() return EasyConfigTest._changed_ecs + @property + def changed_patches(self): + if EasyConfigTest._changed_patches is None: + self._get_changed_patches() + return EasyConfigTest._changed_patches + def test_dep_graph(self): """Unit test that builds a full dependency graph.""" # pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6 @@ -1111,6 +1140,19 @@ def check_https_url(http_url): if failing_checks: self.fail('\n'.join(failing_checks)) + @skip_if_not_pr_to_non_main_branch() + def test_pr_patch_descr(self): + """ + Check whether all patch files touched in PR have a description on top. + """ + no_descr_patches = [] + for patch in self.changed_patches: + patch_txt = read_file(patch) + if patch_txt.startswith('--- '): + no_descr_patches.append(patch) + + self.assertFalse(no_descr_patches, "No description found in patches: %s" % ', '.join(no_descr_patches)) + def template_easyconfig_test(self, spec): """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" From a72a66fe2093611aac15aa76057e242c46dad6bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Feb 2022 21:05:58 +0100 Subject: [PATCH 3172/9987] fix broken test for sympy 1.9 before running the test suite --- easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb index 2c517174dcc..5f50bb21110 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb @@ -23,6 +23,9 @@ dependencies = [ download_dep_fail = True use_pip = True +# fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; +# see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 +pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ runtest = 'python setup.py test' sanity_pip_check = True @@ -32,4 +35,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], } +sanity_check_commands = ["isympy --help"] + moduleclass = 'math' From f87730e124fd9d83d94841b7e6dfc31b550f6fdd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 27 Feb 2022 03:36:31 +0200 Subject: [PATCH 3173/9987] drop intel version, wont build --- .../o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb diff --git a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb deleted file mode 100644 index 78ae3b4a6d5..00000000000 --- a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-intel-2021b.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenFAST' -version = '3.0.0' - -homepage = 'http://openfast.readthedocs.io/' - -description = """OpenFAST is a wind turbine simulation tool which builds on FAST v8. -FAST.Farm extends the capability of OpenFAST to simulate multi-turbine wind farms""" - -toolchain = {'name': 'intel', 'version': '2021b'} - -source_urls = ['https://github.com/OpenFAST/openfast/archive/refs/tags/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['9af57af054e4128b6e257a76da368dc4ad0c7fbb2b22d51fc7ea63cdf999c530'] - -builddependencies = [ - ('CMake', '3.21.1'), -] - -configopts = '-DBUILD_FASTFARM=ON ' - -sanity_check_paths = { - 'files': ['bin/openfast', 'bin/FAST.Farm', - 'lib/libopenfastlib.a', 'lib/libopenfast_prelib.a', 'lib/libopenfast_postlib.a'], - 'dirs': ['include/openfast'], -} - -moduleclass = 'cae' From 52dacd9b55e19facbf0d91dc0b9eccbf8e2ad667 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 27 Feb 2022 15:25:48 +0100 Subject: [PATCH 3174/9987] add description for patches required by easyconfig for mauveAligner v4736 --- .../m/mauveAligner/mauveAligner-4736-gompi-2020a.eb | 4 ++-- .../m/mauveAligner/mauveAligner-4736_fix-getopt.patch | 3 +++ .../m/mauveAligner/sgEvolver-4736_fix-getopt.patch | 3 +++ 3 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb b/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb index a7eaf4ce21c..a429edbf8d4 100644 --- a/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb +++ b/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb @@ -74,7 +74,7 @@ components = [ 'checksums': [ None, # mauveAligner-4736.tar.bz2 '2786bd29bedb224f232e7909972b549fe95f520ddac2cbb076e2082647dc68ae', # mauveAligner-4736_debian.patch - 'c5f07b3b12549d2be9b5869422b7dd85bbde6502222c0938978a2fd4da4328fb', # mauveAligner-4736_fix-getopt.patch: + 'e40edc401303b337070470e52ec13968d0aafca43e4adb332e33b8a6aef34f19', # mauveAligner-4736_fix-getopt.patch ], }), ('sgEvolver', version, { @@ -85,7 +85,7 @@ components = [ 'checksums': [ None, # sgEvolver-4736.tar.bz2 'efc3397039dd525669f6c525b20d75ad64c51cd25912192e695067de4cfbeadc', # sgEvolver-4736_dropversion.patch - 'ba086832bfcf2e8d945e6f46440efc3af1e89102155040b6103dc7f2a6beecff', # sgEvolver-4736_fix-getopt.patch: + '58afcf31f707b265fda81d45cd243c8cd279eed5a843a42f8030ef930f3bdd6c', # sgEvolver-4736_fix-getopt.patch ], }), ] diff --git a/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736_fix-getopt.patch b/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736_fix-getopt.patch index 73a9c65580d..9290d1c1dd8 100644 --- a/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736_fix-getopt.patch +++ b/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736_fix-getopt.patch @@ -1,3 +1,6 @@ +fix build of mauveAligner on RHEL8 (without breaking build on CentOS 7) +/usr/include/bits/getopt_core.h:91:12: error: declaration of int getopt(int, char* const*, const char*) throw () has a different exception specifier +author: Kenneth Hoste (HPC-UGent) --- mauveAligner/src/getopt.h.orig 2022-02-25 10:23:21.301489496 +0100 +++ mauveAligner/src/getopt.h 2022-02-25 10:26:13.940751386 +0100 @@ -146,7 +146,8 @@ diff --git a/easybuild/easyconfigs/m/mauveAligner/sgEvolver-4736_fix-getopt.patch b/easybuild/easyconfigs/m/mauveAligner/sgEvolver-4736_fix-getopt.patch index c70220431ee..50aee5f8f92 100644 --- a/easybuild/easyconfigs/m/mauveAligner/sgEvolver-4736_fix-getopt.patch +++ b/easybuild/easyconfigs/m/mauveAligner/sgEvolver-4736_fix-getopt.patch @@ -1,3 +1,6 @@ +fix build of sgEvolver on RHEL8 (without breaking build on CentOS 7) +/usr/include/bits/getopt_core.h:91:12: error: declaration of int getopt(int, char* const*, const char*) throw () has a different exception specifier +author: Kenneth Hoste (HPC-UGent) --- sgEvolver/src/getopt.h.orig 2022-02-25 10:33:10.015721000 +0100 +++ sgEvolver/src/getopt.h 2022-02-25 10:33:33.950344000 +0100 @@ -146,7 +146,8 @@ From cb47c9678d8fa0b65cd0ed5c821ab67767da5da7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 27 Feb 2022 19:43:10 +0100 Subject: [PATCH 3175/9987] adding easyconfigs: GetOrganelle-1.7.5.3-foss-2021b.eb, Bandage-0.9.0-GCCcore-11.2.0.eb --- .../b/Bandage/Bandage-0.9.0-GCCcore-11.2.0.eb | 30 +++++++++++++ .../GetOrganelle-1.7.5.3-foss-2021b.eb | 43 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.5.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c123231a18c --- /dev/null +++ b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'Bandage' +version = '0.9.0' + +homepage = 'http://rrwick.github.io/Bandage' +description = "Bandage is a program for visualising de novo assembly graphs" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/rrwick/Bandage/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['04de8152d8bf5e5aa32b41a63cf1c23e1fee7b67ccd9f1407db8dc2824ca4e30'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Qt5', '5.15.2')] + +prebuildopts = "qmake Bandage.pro && " + +files_to_copy = [(['Bandage'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Bandage'], + 'dirs': [], +} + +sanity_check_commands = ["Bandage --help && ldd $(which Bandage)" ] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.5.3-foss-2021b.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.5.3-foss-2021b.eb new file mode 100644 index 00000000000..27eafe569fb --- /dev/null +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.5.3-foss-2021b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'GetOrganelle' +version = '1.7.5.3' + +homepage = 'https://github.com/Kinggerm/GetOrganelle' +description = """This toolkit assemblies organelle genome from genomic skimming data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/Kinggerm/GetOrganelle/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1fcc815ce25c8c4ca3e0c12adde6b484744ca8c374e35278baa54047890bc855'] + +dependencies = [ + ('Python', '3.9.6'), + ('Bandage', '0.9.0'), + ('SciPy-bundle', '2021.10'), + ('sympy', '1.9'), + ('SPAdes', '3.15.3'), + ('Bowtie2', '2.4.4'), + ('BLAST+', '2.12.0'), + ('Perl', '5.34.0'), + ('matplotlib', '3.4.3') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': False} + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_commands = ["get_organelle_from_reads.py -h"] + +sanity_check_paths = { + 'files': ['bin/check_annotations.py', 'bin/get_organelle_from_reads.py', 'bin/slim_graph.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From c0c9e794038a0a459a48445f4e97be7dec2f0402 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 27 Feb 2022 21:07:11 +0100 Subject: [PATCH 3176/9987] strip off trailing whitespace in sanity_check_commands in Bandage easyconfig --- easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.2.0.eb index c123231a18c..55f42ab0e92 100644 --- a/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.2.0.eb @@ -25,6 +25,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["Bandage --help && ldd $(which Bandage)" ] +sanity_check_commands = ["Bandage --help && ldd $(which Bandage)"] moduleclass = 'bio' From 36d62db386197a507905965899062a7fdfd46d6c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 28 Feb 2022 17:43:04 +0200 Subject: [PATCH 3177/9987] adding easyconfigs: MEGAN-6.22.0-Java-17.eb --- .../m/MEGAN/MEGAN-6.22.0-Java-17.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAN/MEGAN-6.22.0-Java-17.eb diff --git a/easybuild/easyconfigs/m/MEGAN/MEGAN-6.22.0-Java-17.eb b/easybuild/easyconfigs/m/MEGAN/MEGAN-6.22.0-Java-17.eb new file mode 100644 index 00000000000..512d6bfe088 --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAN/MEGAN-6.22.0-Java-17.eb @@ -0,0 +1,32 @@ +easyblock = 'Binary' + +name = 'MEGAN' +version = '6.22.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://megan.informatik.uni-tuebingen.de/' +description = "MEGAN is a comprehensive toolbox for interactively analyzing microbiome data" + +toolchain = SYSTEM + +local_installer = '%%(name)s_Community_unix_%s.sh' % version.replace('.', '_') +source_urls = ['https://software-ab.informatik.uni-tuebingen.de/download/%(namelower)s%(version_major)s'] +sources = [local_installer] +checksums = ['f9122124a470179dec2306bf5e59c6b6dd80843f8c11a268b3a036af709731fb'] + +dependencies = [('Java', '17')] + +install_cmd = 'chmod +x %s && ./%s -q -dir %%(installdir)s' % (local_installer, local_installer) + +postinstallcmds = ["rm %(installdir)s/uninstall"] + +sanity_check_paths = { + 'files': ['MEGAN'], + 'dirs': ['jars', 'jars2', 'tools'], +} + +modextrapaths = { + 'PATH': ['tools', 'tools/utils'], +} + +moduleclass = 'bio' From c24cf438b0948c56445cdb0feaf103981df70180 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 28 Feb 2022 17:42:35 +0100 Subject: [PATCH 3178/9987] adding easyconfigs: SCGid-0.9b0-foss-2021b.eb and patches: SCGid-0.9-fixPrintToPython3.patch --- .../s/SCGid/SCGid-0.9-fixPrintToPython3.patch | 61 +++++++++++++++ .../s/SCGid/SCGid-0.9b0-foss-2021b.eb | 78 +++++++++++++++++++ 2 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCGid/SCGid-0.9-fixPrintToPython3.patch create mode 100644 easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9-fixPrintToPython3.patch b/easybuild/easyconfigs/s/SCGid/SCGid-0.9-fixPrintToPython3.patch new file mode 100644 index 00000000000..6308d7fc7a2 --- /dev/null +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9-fixPrintToPython3.patch @@ -0,0 +1,61 @@ +--- SCGid-master-orig/scgid/gct_window_plots.py 2021-10-28 06:18:47.000000000 +0200 ++++ SCGid-master/scgid/gct_window_plots.py 2022-02-07 16:47:49.356047797 +0100 +@@ -33,11 +33,11 @@ + axis1T = it.rfilter("coverage", axis1W) + gcMean = axis1T.target_filter().summary_stats("gc").mean + axis2W = calc_1d_window_asymm (axis1T, "gc", plot=False) +-print axis1W, axis2W ++print (axis1W, axis2W) + + figureWindow = FlexibleSelectionWindow("co2gc2") + figureWindow.calculate(it, inc_factor=0.01, plot=True) +-print figureWindow.show() ++print (figureWindow.show()) + + forR = ( + figureWindow.means["gc"], +@@ -62,14 +62,14 @@ + + + +-print "\n".join([x.ident for x in it.children]) +-print [x.children for x in it.children] ++print ("\n".join([x.ident for x in it.children])) ++print ([x.children for x in it.children]) + +-print [(c.ident,c.depth) for c in it.children] ++print ([(c.ident,c.depth) for c in it.children]) + + for c in it.children: + for c2 in c.children: +- print c2.ident,c2.depth ++ print (c2.ident,c2.depth) + + dim1axis, dim1win, points = calc_1d_window_symm(it, "coverage", plot=True) + +@@ -78,22 +78,22 @@ + + #calc_1d_window_symm(step1_it, "gc") + +-print dim1axis, dim1win +-print dim2axis, dim2win ++print (dim1axis, dim1win) ++print (dim2axis, dim2win) + +-print "" ++print ("") + + dim1axis, dim1win, points = calc_coverage_window_1tailed(it.df, target_taxa, plot=True) + + step1_it = get_window_table(it.df, dim1win, "coverage") + dim2axis, dim2win, gc_points = calc_gc_window_1tailed(step1_it, target_taxa, plot=True) + +-print dim1axis, dim1win +-print dim2axis, dim2win ++print (dim1axis, dim1win) ++print (dim2axis, dim2win) + + testWindow = FlexibleSelectionWindow("co1gc1") + testWindow.calculate(it) +-print testWindow.show() ++print (testWindow.show()) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb new file mode 100644 index 00000000000..f70dc6e60ab --- /dev/null +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonPackage' + +name = 'SCGid' +version = '0.9b0' +# No tagged commit for SCGid 0.9b, taking commit from commit history +local_commit = 'be106e4cd888fd913a527ea821e510e0afb100be' + +homepage = 'https://github.com/amsesk/SCGid' +description = 'A consensus approach to contig filtering and genome prediction from single-cell sequencing libraries' + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ["https://github.com/amsesk/SCGid/archive"] +sources = ['%s.tar.gz' % local_commit] +patches = ["SCGid-0.9-fixPrintToPython3.patch"] +checksums = [ + # be106e4cd888fd913a527ea821e510e0afb100be.tar.gz + '1f625e8f87b4d5e4ec9831ebe48763676679d6d6c41b05ef0bb59e6a7f839153', + 'b912ace0a2fabe4cdf43e70ea2d3ff799894da9edb2a078198dde5d7b91daf67', # SCGid-0.9-fixPrintToPython3.patch +] + +local_clams_commit = "e326c34307803b9ea8ffc975ddd9bd05643af931" + +builddependencies = [('Python', '3.9.6')] + +dependencies = [ + ('R', '4.1.2'), + ('BLAST+', '2.12.0'), + ('AUGUSTUS', '3.4.0'), + ('Java', '11', '', True), + ('Maven', '3.6.3', '', True), + ('plotly.py', '5.4.0'), + ('ETE', '3.1.2'), + ('PyYAML', '5.4.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_defaultclass = "Tarball" + +postinstallcmds = [ + 'export PATH=$PATH:$EBROOTAUGUSTUS', + 'export PATH=$PATH:$EBROOTBLAST', + 'echo $EBROOTR', + # Set paths to make init available + "PATH=%(installdir)s/bin:$PATH " + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + # Go through init step of installation and download required database + 'scgid init <<<"%(installdir)s/esom-1.1/src\n' + '%(installdir)s/ClaMS-CLI-fork-e326c34307803b9ea8ffc975ddd9bd05643af931/ClaMS-CLI.jar\n' + '$EBROOTR/bin/Rscript\n' + 'y\n' + 'y\n' + 'y"' +] + +options = {'modulename': False} + +exts_list = [ + ('ClaMS-CLI', '31012020', { + 'install_type': 'merge', + 'source_tmpl': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', + 'source_urls': ['https://github.com/amsesk/ClaMS-CLI-fork/archive'], + 'checksums': ['743397fc8308e363f127bd7e5165ac9d769c10305f6e33d9e408db8f343170db'], + }), + ('ESOM', '1.1', { + 'install_type': 'merge', + 'preconfigopts': "export ESOM_HOME=%(installdir)s && cd esom-%(version)s && maven jar install &&", + 'source_tmpl': 'esom-%(version)s-src.tar.gz', + 'source_urls': ['https://sourceforge.net/projects/databionic-esom/files/databionic-esom/%(version)s/'], + 'checksums': ['48d8a3f04946850cbbc3beb9f92bcaa5a98fd301c511388adb4e329467070d38'], + }), +] + +sanity_check_commands = ["scgid --help"] + +moduleclass = 'bio' \ No newline at end of file From f5ec67999d642e35b6f0424842e9c0f1fa606dec Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 28 Feb 2022 18:01:23 +0100 Subject: [PATCH 3179/9987] Added new-line to the end of file --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index f70dc6e60ab..39782f2b5db 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -75,4 +75,4 @@ exts_list = [ sanity_check_commands = ["scgid --help"] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 7363d9c88659084d999d42b44e373874c9b680e2 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 28 Feb 2022 18:34:04 +0100 Subject: [PATCH 3180/9987] Added dep_fail --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index 39782f2b5db..007fc5a6fd3 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -36,6 +36,7 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = False exts_defaultclass = "Tarball" From b527e9aa0296d96aeb39d5efdc202462007561c8 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 28 Feb 2022 19:09:19 +0100 Subject: [PATCH 3181/9987] adding easyconfigs: libobjcryst-2021.1.2-foss-2021b.eb, pyobjcryst-2.2.1-foss-2021b.eb --- .../libobjcryst-2021.1.2-foss-2021b.eb | 32 +++++++++++++++++++ .../pyobjcryst/pyobjcryst-2.2.1-foss-2021b.eb | 28 ++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/l/libobjcryst/libobjcryst-2021.1.2-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.2.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2021.1.2-foss-2021b.eb b/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2021.1.2-foss-2021b.eb new file mode 100644 index 00000000000..a75b079fbc7 --- /dev/null +++ b/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2021.1.2-foss-2021b.eb @@ -0,0 +1,32 @@ +easyblock = 'SCons' + +name = 'libobjcryst' +version = '2021.1.2' + +homepage = 'https://github.com/diffpy/libobjcryst' +description = "ObjCryst++ is Object-Oriented Crystallographic Library for C++" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/diffpy/libobjcryst/archive/'] +sources = ['v%(version)s.tar.gz'] +#patches = ['libobjcryst-2017.2.3_sconscript_local.patch'] +checksums = [ + #'e86c7c1d9b9b89535757e21216307acf0d102fc72543f155a02bf75e6fba7b25', # libobjcryst-2017.2.3_sconscript_local.patch +] + +builddependencies = [ + ('SCons', '4.2.0'), +] +dependencies = [ + ('Boost', '1.77.0'), +] + +prefix_arg = 'prefix=' + +sanity_check_paths = { + 'files': ['lib/libObjCryst.%s' % SHLIB_EXT], + 'dirs': ['include/ObjCryst'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.2.1-foss-2021b.eb b/easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.2.1-foss-2021b.eb new file mode 100644 index 00000000000..0519150c7be --- /dev/null +++ b/easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.2.1-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'pyobjcryst' +version = '2.2.1' + +homepage = 'https://github.com/diffpy/pyobjcryst' +description = "Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/diffpy/pyobjcryst/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy + ('Boost.Python', '1.77.0'), + ('libobjcryst', '2021.1.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["python -m pyobjcryst.tests.run"] + +sanity_pip_check = True + +moduleclass = 'chem' From 7eeed65254eccbb741309bf9d312d8a8c9aa199c Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 28 Feb 2022 19:27:26 +0100 Subject: [PATCH 3182/9987] removed comments + added checksums --- .../l/libobjcryst/libobjcryst-2021.1.2-foss-2021b.eb | 5 +---- .../easyconfigs/p/pyobjcryst/pyobjcryst-2.2.1-foss-2021b.eb | 1 + 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2021.1.2-foss-2021b.eb b/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2021.1.2-foss-2021b.eb index a75b079fbc7..44ae785a750 100644 --- a/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2021.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2021.1.2-foss-2021b.eb @@ -10,10 +10,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/diffpy/libobjcryst/archive/'] sources = ['v%(version)s.tar.gz'] -#patches = ['libobjcryst-2017.2.3_sconscript_local.patch'] -checksums = [ - #'e86c7c1d9b9b89535757e21216307acf0d102fc72543f155a02bf75e6fba7b25', # libobjcryst-2017.2.3_sconscript_local.patch -] +checksums = ['7f4d2c7e42154bbc780032ce7efe303b57a14d566b9b52fad8c6754a53b1365d'] builddependencies = [ ('SCons', '4.2.0'), diff --git a/easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.2.1-foss-2021b.eb b/easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.2.1-foss-2021b.eb index 0519150c7be..d1a967e4abc 100644 --- a/easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.2.1-foss-2021b.eb +++ b/easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.2.1-foss-2021b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/diffpy/pyobjcryst/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['3804259ebf29a0c4a593a7fb1c356bbaaa8455715affa297517abb92bf8d13e6'] dependencies = [ ('Python', '3.9.6'), From 298721c7915b70ac6f19f3d37372ede8b1561b45 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Feb 2022 21:16:50 +0100 Subject: [PATCH 3183/9987] adding easyconfigs: porefoam-2021-09-21-foss-2020a.eb and patches: porefoam-2021-09-21_fix-scotch-linking.patch --- .../porefoam-2021-09-21-foss-2020a.eb | 42 +++++++++++++++++++ ...refoam-2021-09-21_fix-scotch-linking.patch | 13 ++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb create mode 100644 easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21_fix-scotch-linking.patch diff --git a/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb b/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb new file mode 100644 index 00000000000..23aac0717bc --- /dev/null +++ b/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'porefoam' +local_commit = 'eb02ba3' +version = '2021-09-21' + +homepage = 'https://github.com/ImperialCollegeLondon/porefoam' +description = "Direct pore-scale simulation of single- and two-phase flow through confined media" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/ImperialCollegeLondon/porefoam/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = ['porefoam-2021-09-21_fix-scotch-linking.patch'] +checksums = [ + '61b7d23869f5cfadf001def25750576b05f13d3f117ffb409e56996a0de6d696', # porefoam-2021-09-21.tar.gz + '86b7e389b62f54bbd3c931ae3dbdc363226e250faa181e7e50ed121da9959a92', # porefoam-2021-09-21_fix-scotch-linking.patch +] + +builddependencies = [ + ('CMake', '3.16.4'), +] + +dependencies = [ + ('SCOTCH', '6.0.9'), +] + +buildininstalldir = True +unpack_options = '--strip-components=1' + +skipsteps = ['configure', 'install'] + +prebuildopts = "export WM_COMPILER=Gcc && export WM_COMPILE_OPTION=Opt && " +# using ld.gold linker doesn't work +prebuildopts += 'export WM_CC="$CC $CFLAGS -fuse-ld=bfd" && export WM_CXX="$CXX $CXXFLAGS -fuse-ld=bfd" && ' + +sanity_check_paths = { + 'files': ['bin/interFaceFoam', 'bin/smoothMesh', 'bin/voxelToSurface'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21_fix-scotch-linking.patch b/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21_fix-scotch-linking.patch new file mode 100644 index 00000000000..17d5864d050 --- /dev/null +++ b/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21_fix-scotch-linking.patch @@ -0,0 +1,13 @@ +fix for: undefined reference to `SCOTCH_errorPrint' +author: Kenneth Hoste (HPC-UGent) +--- porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f/pkgs/foamx4m/applications/utilities/parallelProcessing/decomposePar/Make/options.orig 2022-02-25 16:29:05.774243797 +0100 ++++ porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f/pkgs/foamx4m/applications/utilities/parallelProcessing/decomposePar/Make/options 2022-02-25 16:29:28.484450588 +0100 +@@ -10,7 +10,7 @@ + -l:libdecompositionMethods.$(SO) \ + -l:libdecomposeReconstruct.$(SO) \ + -l:libmeshTools.$(SO) \ +- -l:libscotchDecomp.$(SO) -lscotch ++ -l:libscotchDecomp.$(SO) -lscotch -lscotcherrexit + + delsSkip = -ltetFiniteElement + delsSkip = -lfiniteArea From 3dd07645708c58a61df7437295a3f3fbe625e598 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Mar 2022 07:43:19 +0100 Subject: [PATCH 3184/9987] remove leading 'v' from source file name for GetOrganelle v1.7.5.3 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../g/GetOrganelle/GetOrganelle-1.7.5.3-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.5.3-foss-2021b.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.5.3-foss-2021b.eb index 27eafe569fb..3bab9913aba 100644 --- a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.5.3-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.5.3-foss-2021b.eb @@ -9,7 +9,7 @@ description = """This toolkit assemblies organelle genome from genomic skimming toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/Kinggerm/GetOrganelle/archive/'] -sources = ['v%(version)s.tar.gz'] +sources = ['%(version)s.tar.gz'] checksums = ['1fcc815ce25c8c4ca3e0c12adde6b484744ca8c374e35278baa54047890bc855'] dependencies = [ From 45390a19022a707d82d13e9b53df0e19702c7c47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Mar 2022 08:04:24 +0100 Subject: [PATCH 3185/9987] add sanity check command for porefoam --- .../easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb b/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb index 23aac0717bc..8edfb7a8aad 100644 --- a/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb +++ b/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb @@ -39,4 +39,6 @@ sanity_check_paths = { 'dirs': ['include', 'lib'], } +sanity_check_commands = ["voxelToFoam --help | grep 'convert micro-CT images to OpenFOAM mesh'"] + moduleclass = 'cae' From d1c15938195f27bcf53136cf6f06453b748c80b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Mar 2022 10:20:13 +0100 Subject: [PATCH 3186/9987] fix homepage for FLUENT v2021R2 Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/f/FLUENT/FLUENT-2021R2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-2021R2.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-2021R2.eb index 234dcfa4bfc..d1608e86558 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-2021R2.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-2021R2.eb @@ -1,7 +1,7 @@ name = 'FLUENT' version = '2021R2' -homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' +homepage = 'https://www.ansys.com/products/fluids/ansys-fluent' description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, From 975d7c4bae6c686e4639b72a30404ccca2992b0b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 1 Mar 2022 18:10:13 +0200 Subject: [PATCH 3187/9987] add sanity check command to MEGAN v6.22.0 --- easybuild/easyconfigs/m/MEGAN/MEGAN-6.22.0-Java-17.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MEGAN/MEGAN-6.22.0-Java-17.eb b/easybuild/easyconfigs/m/MEGAN/MEGAN-6.22.0-Java-17.eb index 512d6bfe088..190ba82798a 100644 --- a/easybuild/easyconfigs/m/MEGAN/MEGAN-6.22.0-Java-17.eb +++ b/easybuild/easyconfigs/m/MEGAN/MEGAN-6.22.0-Java-17.eb @@ -25,6 +25,10 @@ sanity_check_paths = { 'dirs': ['jars', 'jars2', 'tools'], } +sanity_check_commands = [ + ('megan-server', '-h'), +] + modextrapaths = { 'PATH': ['tools', 'tools/utils'], } From df909e6d35c4ebe28140cabc3435cfc6a1eb3aeb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Mar 2022 17:50:53 +0100 Subject: [PATCH 3188/9987] fix homepage for ABAQUS v2021 to use https Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/a/ABAQUS/ABAQUS-2021-hotfix-2132.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2021-hotfix-2132.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2021-hotfix-2132.eb index c3b4601ac6f..a300029c221 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2021-hotfix-2132.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2021-hotfix-2132.eb @@ -3,7 +3,7 @@ version = '2021' local_hotfix = '2132' versionsuffix = '-hotfix-%s' % local_hotfix -homepage = 'http://www.simulia.com/products/abaqus_fea.html' +homepage = 'https://www.simulia.com/products/abaqus_fea.html' description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.""" From a81a2a34982a8918cd12dfa0242c8118e3c4be3c Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 2 Mar 2022 11:07:33 +0200 Subject: [PATCH 3189/9987] adding easyconfigs: dcm2niix-1.0.20211006-GCCcore-10.3.0.eb, CharLS-2.3.4-GCCcore-10.3.0.eb --- .../c/CharLS/CharLS-2.3.4-GCCcore-10.3.0.eb | 30 ++++++++++++++++ .../dcm2niix-1.0.20211006-GCCcore-10.3.0.eb | 35 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/c/CharLS/CharLS-2.3.4-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CharLS/CharLS-2.3.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CharLS/CharLS-2.3.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..82b9cf13ffd --- /dev/null +++ b/easybuild/easyconfigs/c/CharLS/CharLS-2.3.4-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CharLS' +version = '2.3.4' + +homepage = 'https://github.com/team-charls/charls' +description = """CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image +compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 +compression ratios.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/team-charls/charls/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['28e895a6e22daee76c24cf4d36c62bb20fd60fad0c9cfefc2eb8fa9b6045ae84'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1') +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libcharls.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..fd00257f77b --- /dev/null +++ b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'dcm2niix' +version = '1.0.20211006' + +homepage = 'https://github.com/rordenlab/dcm2niix' +description = """dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rordenlab/dcm2niix/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['44b737d0101483de17ac1273f2d2c6a4d572a7b76ea040d69aa34d5e484144b9'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('pigz', '2.6'), + ('OpenJPEG', '2.4.0'), + ('CharLS', '2.3.4'), +] + +configopts = '-DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DOpenJPEG_DIR=$EBROOTOPENJPEG ' + +sanity_check_paths = { + 'files': ['bin/dcm2niix'], + 'dirs': [''], +} + +moduleclass = 'bio' From 26d5e110fe3292ac98144c2c63c5064b4ffda82a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 2 Mar 2022 10:10:43 +0100 Subject: [PATCH 3190/9987] add sanity check command for dcm2niix --- .../d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb index fd00257f77b..c3a5cd221c6 100644 --- a/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb @@ -32,4 +32,6 @@ sanity_check_paths = { 'dirs': [''], } +sanity_check_commands = ['dcm2niix -h'] + moduleclass = 'bio' From 93f9eb8a98675e5d968cde7dd14e609b422e5fa5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 2 Mar 2022 10:29:31 +0100 Subject: [PATCH 3191/9987] Update easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb Co-authored-by: Adam Huffman --- .../d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb index c3a5cd221c6..aa4abd25ae3 100644 --- a/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20211006-GCCcore-10.3.0.eb @@ -4,7 +4,7 @@ name = 'dcm2niix' version = '1.0.20211006' homepage = 'https://github.com/rordenlab/dcm2niix' -description = """dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.""" +description = """dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format.""" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} From 5035d300cd966b1e2a92a3ca4953f0b89be7b5ee Mon Sep 17 00:00:00 2001 From: Mustafa Abduljabbar Date: Wed, 2 Mar 2022 13:22:35 +0200 Subject: [PATCH 3192/9987] fix style error --- easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-1.eb b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-1.eb index 2786387ff86..59d7e9bd86f 100644 --- a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-1.eb +++ b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-1.eb @@ -1,4 +1,4 @@ -easyblock='PackedBinary' +easyblock = 'PackedBinary' name = 'Schrodinger' version = '2022-1' From b0f8c605b218b021903a089151985d75d39848b3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 2 Mar 2022 13:29:03 +0200 Subject: [PATCH 3193/9987] disable auditwheel in maturin to build py_spy in Ray-project v1.9.2 --- .../easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb index 320e0436487..939d9c99217 100644 --- a/easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.9.2-foss-2021b.eb @@ -16,7 +16,6 @@ accessible to every engineer.""" toolchain = {'name': 'foss', 'version': '2021b'} builddependencies = [ - ('patchelf', '0.13'), # needed by py-spy ('Rust', '1.54.0'), # needed by maturin ] @@ -54,6 +53,8 @@ exts_list = [ ('py_spy', '0.3.11', { 'modulename': False, 'checksums': ['3115c6e45cdab657f81c886f8b1664e7e2208b775396031eeea60e4d16fc861d'], + # disable auditwheel which checks and modifies existing installations + 'preinstallopts': "sed -i '/^bindings =.*/a skip-auditwheel = true' pyproject.toml &&", }), ('pydantic', '1.9.0', { 'checksums': ['742645059757a56ecd886faf4ed2441b9c0cd406079c2b4bee51bcc3fbcd510a'], From f5d0e2ddad2ba8ad59c90a59a320365e244ef06c Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 2 Mar 2022 14:22:14 +0100 Subject: [PATCH 3194/9987] adding easyconfigs: Infernal-1.1.4-foss-2020b.eb --- .../i/Infernal/Infernal-1.1.4-foss-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2020b.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2020b.eb new file mode 100644 index 00000000000..968e466b4e5 --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2020b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# Updated:: Denis Kristak (INUITS) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.4" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' From ee2e6a5c8646ae63959d99c93b1e02849fdec689 Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Thu, 3 Mar 2022 14:27:37 +0100 Subject: [PATCH 3195/9987] versionsuffix added --- .../easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb | 3 ++- .../easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb index 38e0620fa26..6fc55a56778 100755 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb @@ -2,12 +2,13 @@ easyblock = 'CMakeMake' name = 'DIRAC' version = '22.0' +versionsuffix = '-Python-%(pyver)s-mpi' homepage = 'http://www.diracprogram.org' description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'i8': False} source_urls = ['https://zenodo.org/record/6010450/files/'] sources = ['DIRAC-%(version)s-Source.tar.gz'] diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb index 3eb8724430e..38d7679911a 100755 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb @@ -2,12 +2,13 @@ easyblock = 'CMakeMake' name = 'DIRAC' version = '22.0' +versionsuffix = '-Python-%(pyver)s-mpi' homepage = 'http://www.diracprogram.org' description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" toolchain = {'name': 'intel', 'version': '2021a'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'i8': False} source_urls = ['https://zenodo.org/record/6010450/files/'] sources = ['DIRAC-%(version)s-Source.tar.gz'] From 50f939101346a17fb4fb5c35672fac5841af8cce Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Thu, 3 Mar 2022 14:36:43 +0100 Subject: [PATCH 3196/9987] versionsuffix added --- ...DIRAC-22.0-intel-2021a-Python-3.9.5-mpi.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100755 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5-mpi.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5-mpi.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5-mpi.eb new file mode 100755 index 00000000000..38d7679911a --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5-mpi.eb @@ -0,0 +1,64 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '22.0' +versionsuffix = '-Python-%(pyver)s-mpi' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'i8': False} + +source_urls = ['https://zenodo.org/record/6010450/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('HDF5', '1.10.7') +] + +separate_build_dir = True + +configopts = ' -DCMAKE_Fortran_COMPILER=mpiifort ' +configopts += '-DEXTRA_FCFLAGS="''" ' +configopts += '-DCMAKE_C_COMPILER=mpiicc ' +configopts += '-DEXTRA_CFLAGS="''" ' +configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' +configopts += '-DEXTRA_CXXFLAGS="''" ' +configopts += '-DENABLE_BLAS=off ' +configopts += '-DENABLE_LAPACK=off ' +configopts += '-DMKL_FLAG=sequential ' +configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' +configopts += '-DBLAS_LANG=Fortran ' +configopts += '-DLAPACK_LANG=Fortran ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_OPENMP=False ' +configopts += '-DENABLE_CODE_COVERAGE=False ' +configopts += '-DENABLE_STATIC_LINKING=False ' +configopts += '-DENABLE_PROFILING=False ' +configopts += '-DENABLE_RUNTIMECHECK=False ' +configopts += '-DENABLE_64BIT_INTEGERS=False ' +configopts += '-DEXPLICIT_LIBS="off" ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' +configopts += '-G"Unix Makefiles" ' + +parallel = 4 + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' + +runtest = 'test ARGS="-R pam_test" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From 4e4af7a4a44ef0dd277fa918b38acffea24d5e7d Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Thu, 3 Mar 2022 14:38:04 +0100 Subject: [PATCH 3197/9987] versionsuffix added --- .../DIRAC-22.0-foss-2021a-Python-3.9.5-mpi.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100755 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5-mpi.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5-mpi.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5-mpi.eb new file mode 100755 index 00000000000..6fc55a56778 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5-mpi.eb @@ -0,0 +1,64 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '22.0' +versionsuffix = '-Python-%(pyver)s-mpi' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'i8': False} + +source_urls = ['https://zenodo.org/record/6010450/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] + +builddependencies = [('CMake', '3.20.1', '', ('GCCcore','10.3.0'))] + +dependencies = [ + ('Python', '3.9.5', '', ('GCCcore','10.3.0')), + ('HDF5', '1.10.7', '', ('gompi','2021a')) +] + +separate_build_dir = True + +configopts = ' -DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DEXTRA_FCFLAGS="''" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DEXTRA_CFLAGS="''" ' +configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' +configopts += '-DEXTRA_CXXFLAGS="''" ' +configopts += '-DENABLE_BLAS=auto ' +configopts += '-DENABLE_LAPACK=auto ' +configopts += '-DMKL_FLAG=off ' +configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' +configopts += '-DBLAS_LANG=Fortran ' +configopts += '-DLAPACK_LANG=Fortran ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_OPENMP=False ' +configopts += '-DENABLE_CODE_COVERAGE=False ' +configopts += '-DENABLE_STATIC_LINKING=False ' +configopts += '-DENABLE_PROFILING=False ' +configopts += '-DENABLE_RUNTIMECHECK=False ' +configopts += '-DENABLE_64BIT_INTEGERS=False ' +configopts += '-DEXPLICIT_LIBS="off" ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' +configopts += '-G"Unix Makefiles" ' + +parallel = 4 + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' + +runtest = 'test ARGS="-R pam_test" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From 8336928419cb82de20b4f09d088ec8334c67c8f1 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Thu, 3 Mar 2022 15:32:25 +0100 Subject: [PATCH 3198/9987] add m4 as build dependency for CCL without m4 I get` /bin/sh: 1: m4: not found` and the build fails a bit later with /../pmcl-kernel.c:1555: undefined reference to `spjump_start' --- easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb index 44008ec86c3..70487fea5b4 100644 --- a/easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb @@ -16,6 +16,7 @@ checksums = ['84a95aaf1d1abafba586e9ff079343b04fe374b98b38ed24d830f1fb7ed4ab34'] builddependencies = [ ('binutils', '2.34'), + ('M4', '1.4.18'), ] local_ccl_bin = 'lx86cl64' From 3e99acbc5383f5d84893517c826f7077a44b0bcd Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 3 Mar 2022 14:54:45 +0000 Subject: [PATCH 3199/9987] adding easyconfigs: intervaltree-python-3.1.0-GCCcore-10.3.0.eb --- ...ntervaltree-python-3.1.0-GCCcore-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..081b2c943d5 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'intervaltree-python' +_modname = 'intervaltree' +version = '3.1.0' + +homepage = 'https://github.com/chaimleib/intervaltree' +description = """A mutable, self-balancing interval tree. Queries may be by + point, by range overlap, or by range containment. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/i/%s' % _modname] +sources = ['%s-%s.tar.gz' % (_modname, version)] +checksums = ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': _modname} + +moduleclass = 'bio' From 1a407b80ad800b3e31ce3281d24d061d13b1b3b2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 3 Mar 2022 14:55:21 +0000 Subject: [PATCH 3200/9987] adding easyconfigs: WhatsHap-1.1-foss-2021a.eb --- .../w/WhatsHap/WhatsHap-1.1-foss-2021a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2021a.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2021a.eb new file mode 100644 index 00000000000..e1705eb1c52 --- /dev/null +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2021a.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'WhatsHap' +version = '1.1' + +homepage = 'https://whatshap.readthedocs.io' +description = """WhatsHap is a software for phasing genomic variants using DNA +sequencing reads, also called read-based phasing or haplotype assembly. It is +especially suitable for long reads, but works also well with short reads.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Pysam', '0.16.0.1'), + ('networkx', '2.6.3'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('Yasm', '1.3.0'), + ('pyfaidx', '0.6.3.1'), + ('python-isal', '0.11.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '1.4.0', { + 'checksums': ['69d6d1d8a18efe49fc3eb51cd558a2a538c6f76495d1732d259016f58b124498'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['4e6486e6ce2babf55a225dd9e0030df6fcc27629d34803428cbe88a79137bb6f'], + }), +] + +sanity_check_paths = { + 'files': ['bin/whatshap'], + 'dirs': [], +} + +sanity_check_commands = [ + 'whatshap --help', +] + +moduleclass = 'bio' From d3237239d8e116a70154745fdc03c4a5baefb725 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 3 Mar 2022 14:55:44 +0000 Subject: [PATCH 3201/9987] adding easyconfigs: spoa-4.0.7-GCC-10.3.0.eb, pyspoa-0.0.8-GCC-10.3.0.eb --- .../p/pyspoa/pyspoa-0.0.8-GCC-10.3.0.eb | 52 +++++++++++++++++++ .../s/spoa/spoa-4.0.7-GCC-10.3.0.eb | 29 +++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.3.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.3.0.eb new file mode 100644 index 00000000000..11e83c46fdb --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-10.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonPackage' + +name = 'pyspoa' +version = '0.0.8' + +homepage = 'https://github.com/nanoporetech/pyspoa' +description = "Python bindings to spoa." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +sources = [ + { + 'source_urls': ['https://github.com/nanoporetech/pyspoa/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'pyspoa-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/USCiLab/cereal/archive/'], + 'download_filename': '3e4d1b8.tar.gz', + 'filename': 'cereal-20200423.tar.gz', + }, +] +patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] +checksums = [ + 'a1e630ef30a42d8e8c076d914261d0d34060631d64694569d52c1a2be5deada7', # pyspoa-0.0.8.tar.gz + '284cd14c1e60b36c966bcc8ce650d0b798b8a836d6c379e021e0da0dbe6ddf38', # cereal-20200423.tar.gz + 'a98c82ae8346b48952b171675f9df7ab1c95ea5421afcf5bcd778c01c5ee5a52', # pyspoa-0.0.8_use-spoa-dep.patch +] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('pybind11', '2.6.2'), + ('spoa', '4.0.7'), +] + +download_dep_fail = True + +preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " +# strip out cmake requirements, since we provide that as proper dependency +preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " + +use_pip = True + +options = {'modulename': 'spoa'} + +sanity_pip_check = True + +sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.3.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.3.0.eb new file mode 100644 index 00000000000..c440d9a9b12 --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '4.0.7' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] +sources = ['spoa-v%(version)s.tar.gz'] +checksums = ['f7a8cd039e4aabea1481e123387fedaa8f87e55418a3649408a615f5c6b1b9a4'] + +builddependencies = [('CMake', '3.20.1')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a', 'lib/pkgconfig/spoa-1.pc'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +moduleclass = 'bio' From 5fad43e4ad75aa2678fd90604ceec1ed323e924e Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 3 Mar 2022 14:56:13 +0000 Subject: [PATCH 3202/9987] adding easyconfigs: ont-fast5-api-4.0.0-foss-2021a.eb --- .../ont-fast5-api-4.0.0-foss-2021a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.0-foss-2021a.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.0-foss-2021a.eb new file mode 100644 index 00000000000..4c888b407ac --- /dev/null +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.0-foss-2021a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '4.0.0' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + (name, version, { + 'checksums': ['a249813104439bfe3d4e346bb560756e23217655273410c60b9bade205eb3e66'], + }), +] + +sanity_check_paths = { + 'files': ['bin/compress_fast5', 'bin/fast5_subset', 'bin/multi_to_single_fast5', 'bin/single_to_multi_fast5'], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 914c906cbc69a5f73c41ec414581069bba01b109 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 3 Mar 2022 14:56:42 +0000 Subject: [PATCH 3203/9987] adding easyconfigs: medaka-1.5.0-foss-2021a.eb --- .../m/medaka/medaka-1.5.0-foss-2021a.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb new file mode 100644 index 00000000000..c485cbaae09 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb @@ -0,0 +1,60 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.5.0' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [('Autotools', '20210128')] + +_minimap_ver = '2.20' +dependencies = [ + ('Python', '3.9.5'), # includes cffi + # TensorFlow ~=2.5.2 required by medaka 1.5.0, see requirements.txt + ('TensorFlow', '2.5.3'), + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.13'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.12'), # for tabix, bgzip + ('Racon', '1.4.21'), + ('edlib', '1.3.9'), + ('pyspoa', '0.0.8'), + ('python-parasail', '1.2.4'), + ('ont-fast5-api', '4.0.0'), + ('WhatsHap', '1.1'), + ('intervaltree-python', '3.1.0'), +] + +use_pip = True + +exts_list = [ + ('mappy', '2.20', { + 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], + }), + (name, version, { + 'checksums': ['8a0b8d5997fe45b8d5a1317b2b6bfe117cb6b551928faef62e4e958cf14b5ea4'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["medaka --help"] + +moduleclass = 'bio' From 8da2c81803d579ab747a858a5bcdff458ab60a2f Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 3 Mar 2022 15:21:50 +0000 Subject: [PATCH 3204/9987] use networkx 2.5.1 --- easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2021a.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2021a.eb index e1705eb1c52..e817cae7c7a 100644 --- a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.1-foss-2021a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), ('Pysam', '0.16.0.1'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ('SciPy-bundle', '2021.05'), ('Biopython', '1.79'), ('Yasm', '1.3.0'), From 55adf1dd8da151da6858322b010c10a0c8e8ef6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Mar 2022 20:39:44 +0100 Subject: [PATCH 3205/9987] adding easyconfigs: vsc-mympirun-5.2.9.eb --- .../v/vsc-mympirun/vsc-mympirun-5.2.9.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.9.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.9.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.9.eb new file mode 100644 index 00000000000..a490eb80608 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.9.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'vsc-mympirun' +version = '5.2.9' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """mympirun is a tool to make it easier for users of HPC clusters to +run MPI programs with good performance.""" + +# we build this to work with every python version +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +use_pip = False + +exts_list = [ + ('setuptools', '41.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6afa61b391dcd16cb8890ec9f66cc4015a8a31a6e1c2b4e0c464514be1a3d722'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('pbr', '5.8.1', { + 'checksums': ['66bc5a34912f408bb3925bf21231cb6f59206267b7f63f3503ef865c1a292e25'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '4.0.3', { + 'checksums': ['7d3fbbde18228f4ff2f1f119a45cdffa458b4c0dee32eb4d2bb2f82554bac7bc'], + }), + ('IPy', '1.01', { + 'modulename': 'IPy', + 'checksums': ['edeca741dea2d54aca568fa23740288c3fe86c0f3ea700344571e9ef14a7cc1a'], + }), + ('vsc-install', '0.17.21', { + 'modulename': 'vsc.install', + 'checksums': ['5b9073cc653577ab99a295bcacbd5260d7425251afef4471e9532a00157b0d9e'], + }), + ('vsc-base', '3.4.3', { + 'modulename': 'vsc.utils', + 'checksums': ['11d21d8795c17423febc500d4ba0d987c9e0b2cadb6ded75df34ea4dd77305b4'], + }), + (name, version, { + 'modulename': 'vsc', + 'checksums': ['31e2065f2ad09c10ae81ebe4ffcda39350ba40ded022662a2f2642849c282a76'], + }), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mypmirun', 'bin/mympisanity', 'bin/mytasks'], + 'dirs': ['bin/fake'], +} +sanity_check_commands = ["mympirun --help"] + +# can't enable 'pip check' since pip may not be installed in OS +sanity_pip_check = False + +moduleclass = 'tools' From 98e48bec3acb5bfaeec2d59ff7c34ca632a8dc1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Fri, 4 Mar 2022 11:55:31 +0100 Subject: [PATCH 3206/9987] Delete DIRAC-22.0-foss-2021a-Python-3.9.5.eb --- .../DIRAC-22.0-foss-2021a-Python-3.9.5.eb | 64 ------------------- 1 file changed, 64 deletions(-) delete mode 100755 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb deleted file mode 100755 index 6fc55a56778..00000000000 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,64 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'DIRAC' -version = '22.0' -versionsuffix = '-Python-%(pyver)s-mpi' - -homepage = 'http://www.diracprogram.org' -description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': True, 'i8': False} - -source_urls = ['https://zenodo.org/record/6010450/files/'] -sources = ['DIRAC-%(version)s-Source.tar.gz'] -checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] - -builddependencies = [('CMake', '3.20.1', '', ('GCCcore','10.3.0'))] - -dependencies = [ - ('Python', '3.9.5', '', ('GCCcore','10.3.0')), - ('HDF5', '1.10.7', '', ('gompi','2021a')) -] - -separate_build_dir = True - -configopts = ' -DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DEXTRA_FCFLAGS="''" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DEXTRA_CFLAGS="''" ' -configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' -configopts += '-DEXTRA_CXXFLAGS="''" ' -configopts += '-DENABLE_BLAS=auto ' -configopts += '-DENABLE_LAPACK=auto ' -configopts += '-DMKL_FLAG=off ' -configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' -configopts += '-DBLAS_LANG=Fortran ' -configopts += '-DLAPACK_LANG=Fortran ' -configopts += '-DENABLE_MPI=True ' -configopts += '-DENABLE_OPENMP=False ' -configopts += '-DENABLE_CODE_COVERAGE=False ' -configopts += '-DENABLE_STATIC_LINKING=False ' -configopts += '-DENABLE_PROFILING=False ' -configopts += '-DENABLE_RUNTIMECHECK=False ' -configopts += '-DENABLE_64BIT_INTEGERS=False ' -configopts += '-DEXPLICIT_LIBS="off" ' -configopts += '-DENABLE_EXATENSOR=off ' -configopts += '-DENABLE_PCMSOLVER=off ' -configopts += '-G"Unix Makefiles" ' - -parallel = 4 - -pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' -pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' - -runtest = 'test ARGS="-R pam_test" ' - -sanity_check_paths = { - 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], - 'dirs': ['share/dirac/basis'], -} - -sanity_check_commands = ["pam-dirac --help"] - -moduleclass = 'chem' From 17cae025150a0d900bda8682ef843bb3fc7c9b96 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Fri, 4 Mar 2022 11:55:53 +0100 Subject: [PATCH 3207/9987] Delete DIRAC-22.0-intel-2021a-Python-3.9.5.eb --- .../DIRAC-22.0-intel-2021a-Python-3.9.5.eb | 64 ------------------- 1 file changed, 64 deletions(-) delete mode 100755 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb deleted file mode 100755 index 38d7679911a..00000000000 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5.eb +++ /dev/null @@ -1,64 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'DIRAC' -version = '22.0' -versionsuffix = '-Python-%(pyver)s-mpi' - -homepage = 'http://www.diracprogram.org' -description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" - -toolchain = {'name': 'intel', 'version': '2021a'} -toolchainopts = {'usempi': True, 'i8': False} - -source_urls = ['https://zenodo.org/record/6010450/files/'] -sources = ['DIRAC-%(version)s-Source.tar.gz'] -checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] - -builddependencies = [('CMake', '3.20.1')] - -dependencies = [ - ('Python', '3.9.5'), - ('HDF5', '1.10.7') -] - -separate_build_dir = True - -configopts = ' -DCMAKE_Fortran_COMPILER=mpiifort ' -configopts += '-DEXTRA_FCFLAGS="''" ' -configopts += '-DCMAKE_C_COMPILER=mpiicc ' -configopts += '-DEXTRA_CFLAGS="''" ' -configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' -configopts += '-DEXTRA_CXXFLAGS="''" ' -configopts += '-DENABLE_BLAS=off ' -configopts += '-DENABLE_LAPACK=off ' -configopts += '-DMKL_FLAG=sequential ' -configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' -configopts += '-DBLAS_LANG=Fortran ' -configopts += '-DLAPACK_LANG=Fortran ' -configopts += '-DENABLE_MPI=True ' -configopts += '-DENABLE_OPENMP=False ' -configopts += '-DENABLE_CODE_COVERAGE=False ' -configopts += '-DENABLE_STATIC_LINKING=False ' -configopts += '-DENABLE_PROFILING=False ' -configopts += '-DENABLE_RUNTIMECHECK=False ' -configopts += '-DENABLE_64BIT_INTEGERS=False ' -configopts += '-DEXPLICIT_LIBS="off" ' -configopts += '-DENABLE_EXATENSOR=off ' -configopts += '-DENABLE_PCMSOLVER=off ' -configopts += '-G"Unix Makefiles" ' - -parallel = 4 - -pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' -pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' - -runtest = 'test ARGS="-R pam_test" ' - -sanity_check_paths = { - 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], - 'dirs': ['share/dirac/basis'], -} - -sanity_check_commands = ["pam-dirac --help"] - -moduleclass = 'chem' From 751f47392ce038cb15bc2b8da57c6003f2492b6b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 4 Mar 2022 15:35:43 +0000 Subject: [PATCH 3208/9987] adding easyconfigs: MAGeCK-0.5.9.4-foss-2021a.eb --- .../m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb new file mode 100644 index 00000000000..81d732ec2ec --- /dev/null +++ b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb @@ -0,0 +1,31 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'MAGeCK' +version = '0.5.9.4' + +homepage = "https://sourceforge.net/p/mageck/wiki/Home/" +description = """Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify + important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed + by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute, and is being actively updated + by Wei Li lab from Children's National Medical Center.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['42875b308f2d9ee38f083fb1020d7d48fca29e2100fdb09ced1969b738b8c939'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sanity_check_commands = ["cd %(builddir)s/%(namelower)s-%(version)s/demo/demo1 && ./run.sh"] + [ + "%s -h" % x for x in ['mageck', 'mageckGSEA']] + +moduleclass = 'bio' From d4819d67a87bb26acfb61c3fdb3ccfc3bbacebab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Mar 2022 16:46:37 +0100 Subject: [PATCH 3209/9987] adding easyconfigs: libtree-3.0.3.eb --- .../easyconfigs/l/libtree/libtree-3.0.3.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtree/libtree-3.0.3.eb diff --git a/easybuild/easyconfigs/l/libtree/libtree-3.0.3.eb b/easybuild/easyconfigs/l/libtree/libtree-3.0.3.eb new file mode 100644 index 00000000000..0332a1f618e --- /dev/null +++ b/easybuild/easyconfigs/l/libtree/libtree-3.0.3.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'libtree' +version = '3.0.3' + +homepage = 'https://github.com/haampie/libtree' +description = """libtree is a tool that turns ldd into a tree, explains why + shared libraries are found and why not and optionally deploys executables and + dependencies into a single directory""" + +toolchain = SYSTEM + +github_account = 'haampie' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['7e4589b617775cb3a2b4b8fe03f80b81e43ef16046d680f1517ce52d7be9893f'] + +buildopts = "LDFLAGS='-static'" + +runtest = 'check' + +files_to_copy = [(['libtree'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/libtree"], + 'dirs': [], +} + +sanity_check_commands = [ + "libtree --help", + "libtree -v -p %(installdir)s/bin/libtree", +] + +moduleclass = 'tools' From a0dafc431c79d51a983514e4b71ffbe767aaacd4 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Sat, 5 Mar 2022 17:32:45 +0100 Subject: [PATCH 3210/9987] Adding matplotlib-inline-0.1.3-GCCcore-10.2.0.eb --- .../matplotlib-inline-0.1.3-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..87dc05503d9 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'matplotlib-inline' +version = '0.1.3' + +homepage = 'https://github.com/ipython/matplotlib-inline' +description = """Matplotlib Inline Back-end for IPython and Jupyter.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a04bfba22e0d1395479f866853ec1ee28eea1485c1d69a6faf00dc3e24ff34ee'] + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), # has traitlets +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# use matplotlib-inline backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'module://matplotlib_inline.backend_inline'} + +moduleclass = 'vis' From 7ec147385a2d1249eb4746fff201b7cca82df1e4 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Sat, 5 Mar 2022 18:07:35 +0100 Subject: [PATCH 3211/9987] Removing comment --- .../matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb index 87dc05503d9..31aab811153 100644 --- a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ checksums = ['a04bfba22e0d1395479f866853ec1ee28eea1485c1d69a6faf00dc3e24ff34ee'] dependencies = [ ('Python', '3.8.6'), - ('IPython', '7.18.1'), # has traitlets + ('IPython', '7.18.1'), ] use_pip = True From bcd5ed63bdc9a2904738afd0158ee66e9dc9e604 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Sat, 5 Mar 2022 18:32:03 +0100 Subject: [PATCH 3212/9987] Trying with binutils in builddeps --- .../matplotlib-inline-0.1.3-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb index 31aab811153..bc21d00bf00 100644 --- a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -11,9 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} sources = [SOURCELOWER_TAR_GZ] checksums = ['a04bfba22e0d1395479f866853ec1ee28eea1485c1d69a6faf00dc3e24ff34ee'] +builddependencies = [('binutils', '2.35')] + dependencies = [ ('Python', '3.8.6'), - ('IPython', '7.18.1'), + ('IPython', '7.18.1'), # has traitlets ] use_pip = True From d8a0207954911f279635b37ad0d43becd796fe6e Mon Sep 17 00:00:00 2001 From: Zdenek Date: Sat, 5 Mar 2022 19:29:49 +0100 Subject: [PATCH 3213/9987] Spaces before inline comment --- .../matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb index bc21d00bf00..5d1e53c4125 100644 --- a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -15,7 +15,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '3.8.6'), - ('IPython', '7.18.1'), # has traitlets + ('IPython', '7.18.1'), # has traitlets ] use_pip = True From f9e95cae16718778bf458961d5baee209de66e7b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 7 Mar 2022 12:13:54 +0000 Subject: [PATCH 3214/9987] delete shipped binaries so that they get built during install --- easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb index 81d732ec2ec..0f023bfe466 100644 --- a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb @@ -21,6 +21,9 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['42875b308f2d9ee38f083fb1020d7d48fca29e2100fdb09ced1969b738b8c939'] +# remove the shipped mageckGSEA and RRA binaries so that the Python install will build them +preinstallopts = "rm bin/{mageckGSEA,RRA} && " + download_dep_fail = True sanity_pip_check = True use_pip = True From 0b7cf54546e17649a8f8f0d88bd70b3b1e48b18d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Mar 2022 16:38:02 +0100 Subject: [PATCH 3215/9987] adding easyconfigs: BUSCO-4.0.6-foss-2020b.eb --- .../b/BUSCO/BUSCO-4.0.6-foss-2020b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb new file mode 100644 index 00000000000..48d0a53aeb8 --- /dev/null +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-4.0.6-foss-2020b.eb @@ -0,0 +1,54 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'BUSCO' +version = '4.0.6' + +homepage = 'https://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['bad1c1cb52950d991eb771eb9f3a78cf0bebb861e3b806320ee8cbe4cfbd75ea'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # for pandas + ('R', '4.0.3'), + ('Biopython', '1.78'), + ('BLAST+', '2.11.0'), + ('HMMER', '3.3.2'), + ('prodigal', '2.6.3'), + ('AUGUSTUS', '3.4.0'), + ('SEPP', '4.4.0'), + ('MetaEuk', '4'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin %(installdir)s/doc', + 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/LICENSE %(installdir)s/doc', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/test_data %(installdir)s', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/config %(installdir)s', +] + +sanity_check_paths = { + 'files': ['bin/busco', 'bin/generate_plot.py'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages/busco'] +} + +sanity_check_commands = [ + "busco --help", + "busco -i %(installdir)s/test_data/bacteria/genome.fna --mode geno --out test_bacteria.out", + "busco -i %(installdir)s/test_data/eukaryota/genome.fna --mode geno --out test_eukaryota.out", +] + +moduleclass = 'bio' From 727ead73fa0a1be05504ac5891cf4b7fb6d2f241 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Mar 2022 17:40:40 +0100 Subject: [PATCH 3216/9987] use https in homepage for Stacks 2.53 --- .../easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb index 0f660b7c780..516a0dad8ed 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Stacks' version = '2.53' -homepage = 'http://catchenlab.life.illinois.edu/stacks' +homepage = 'https://catchenlab.life.illinois.edu/stacks' description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. From 9c70626c7eb64faaf66ab4fabf1b0aeec4816205 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jens=20Henrik=20G=C3=B6bbert?= Date: Mon, 7 Mar 2022 23:10:16 +0100 Subject: [PATCH 3217/9987] disable-exec-static-tramp --- easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb index 81d0e8fb36b..7d594ca1d72 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.2.0.eb @@ -19,6 +19,8 @@ builddependencies = [ ('binutils', '2.37'), ] +configopts = '--disable-exec-static-tramp ' + sanity_check_paths = { 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], 'dirs': ['include', 'share'], From cb077a9c73fdecd8842143b500144400e8895d73 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 7 Mar 2022 14:19:17 -0800 Subject: [PATCH 3218/9987] {bio}[GCCcore/11.2.0] GATK 4.2.5.0 w/Java-11 --- .../GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb new file mode 100644 index 00000000000..49709d4a376 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.2.5.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['203f17868f0a73a8322d2f8bd568b9f7b4bb81e36d37db5b6a142d8050ef049f'] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.9.6'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +modloadmsg = "WARNING: GATK v%(version)s support for Java 11 is in beta state. Use at your own risk.\n" + +moduleclass = 'bio' From 2e7918a75c5b48c9aed0d57cb4942191c156acea Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 8 Mar 2022 00:08:43 +0100 Subject: [PATCH 3219/9987] add build dependency on M4 to CCL-1.12.1-GCCcore-10.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/c/CCL/CCL-1.12.1-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CCL/CCL-1.12.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CCL/CCL-1.12.1-GCCcore-10.3.0.eb index cda61243cf4..f09d38a45fd 100644 --- a/easybuild/easyconfigs/c/CCL/CCL-1.12.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/CCL/CCL-1.12.1-GCCcore-10.3.0.eb @@ -16,6 +16,7 @@ checksums = ['923f2979144e96306cf5124800444e1c5cc0295fa9babb3ffc47a5631344b0aa'] builddependencies = [ ('binutils', '2.36.1'), + ('M4', '1.4.18'), ] local_ccl_bin = 'lx86cl64' From dd47fb0893f64a8585554553d82f44f7bc2b03b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Mar 2022 11:14:04 +0100 Subject: [PATCH 3220/9987] adding easyconfigs: vsc-mympirun-5.2.10.eb --- .../v/vsc-mympirun/vsc-mympirun-5.2.10.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.10.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.10.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.10.eb new file mode 100644 index 00000000000..a60396913bf --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.10.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'vsc-mympirun' +version = '5.2.10' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """mympirun is a tool to make it easier for users of HPC clusters to +run MPI programs with good performance.""" + +# we build this to work with every python version +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +use_pip = False + +exts_list = [ + ('setuptools', '41.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6afa61b391dcd16cb8890ec9f66cc4015a8a31a6e1c2b4e0c464514be1a3d722'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('pbr', '5.8.1', { + 'checksums': ['66bc5a34912f408bb3925bf21231cb6f59206267b7f63f3503ef865c1a292e25'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '4.0.3', { + 'checksums': ['7d3fbbde18228f4ff2f1f119a45cdffa458b4c0dee32eb4d2bb2f82554bac7bc'], + }), + ('IPy', '1.01', { + 'modulename': 'IPy', + 'checksums': ['edeca741dea2d54aca568fa23740288c3fe86c0f3ea700344571e9ef14a7cc1a'], + }), + ('vsc-install', '0.17.21', { + 'modulename': 'vsc.install', + 'checksums': ['5b9073cc653577ab99a295bcacbd5260d7425251afef4471e9532a00157b0d9e'], + }), + ('vsc-base', '3.4.3', { + 'modulename': 'vsc.utils', + 'checksums': ['11d21d8795c17423febc500d4ba0d987c9e0b2cadb6ded75df34ea4dd77305b4'], + }), + (name, version, { + 'modulename': 'vsc', + 'checksums': ['e1f4cd1583983a2e6e6adf75ef2fb6cf5f9fa1dee6370d4540bd3d45465e9fe1'], + }), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mypmirun', 'bin/mympisanity', 'bin/mytasks'], + 'dirs': ['bin/fake'], +} +sanity_check_commands = ["mympirun --help"] + +# can't enable 'pip check' since pip may not be installed in OS +sanity_pip_check = False + +moduleclass = 'tools' From ea0563ac0d252da97de577b1647f305087ff6468 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 8 Mar 2022 18:48:13 +0100 Subject: [PATCH 3221/9987] Also use https for sources, see if that works... --- .../easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb index 516a0dad8ed..07913a44d42 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.53-iccifort-2019.5.281.eb @@ -11,7 +11,7 @@ description = """Stacks is a software pipeline for building loci from short-read toolchain = {'name': 'iccifort', 'version': '2019.5.281'} -source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +source_urls = ['https://catchenlab.life.illinois.edu/stacks/source/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['ee1efceaeeeb7a39f0c2e804ad7c0a003094db28c9101120c38ddb02846e90fd'] From e106ae96a928d5ed26a9588ee0cbad3750bacf7e Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 8 Mar 2022 19:27:54 +0000 Subject: [PATCH 3222/9987] adding easyconfigs: OpenBLAS-0.3.20-GCC-11.2.0.eb --- .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb new file mode 100644 index 00000000000..938962705a6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +name = 'OpenBLAS' +version = '0.3.20' + +homepage = 'http://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), +] +checksums = [ + '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From d0ac6d9b7b2fff9552ba381fd3d100c132d64d63 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 8 Mar 2022 19:52:40 +0000 Subject: [PATCH 3223/9987] adding easyconfigs: FlexiBLAS-3.1.3-GCC-11.2.0.eb --- .../f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.2.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..b7e48d80eff --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'FlexiBLAS' +version = '3.1.3' + +homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' +description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation +used by a program without recompiling or relinking it.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" +toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} + +builddependencies = [ + ('CMake', '3.22.1'), + ('Python', '3.9.6'), # required for running the tests + ('BLIS', '0.8.1'), +] + +dependencies = [ + ('OpenBLAS', '0.3.20'), +] + +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +local_backends = ['OpenBLAS', 'BLIS'] + +# imkl supplies its backend via the imkl module, not as a dependency +if ARCH == 'x86_64': + local_backends.append('imkl') + +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['aac6175660e8475ce478b88673eee330671f8aecc0cb852a25833e23e29a0620'], + 'backends': local_backends, + }), + ('LAPACK', '3.10.0', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['328c1bea493a32cac5257d84157dc686cc3ab0b004e2bea22044e0a59f6f8a19'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + +moduleclass = 'lib' From b3028ab3eded43ea369d302dd47790ac3c5db68c Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Tue, 8 Mar 2022 21:52:19 +0100 Subject: [PATCH 3224/9987] adding easyconfigs: matplotlib-3.5.1-foss-2020b.eb, matplotlib-3.5.1-intel-2020b.eb --- .../matplotlib/matplotlib-3.5.1-foss-2020b.eb | 65 +++++++++++++++++++ .../matplotlib-3.5.1-intel-2020b.eb | 65 +++++++++++++++++++ 2 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb new file mode 100644 index 00000000000..2d5f0cfadec --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.5.1' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template > mplsetup.cfg && " + + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + ('fontTools', '4.29.1', { + 'modulename' : 'fontTools', + 'source_tmpl': 'fonttools-%(version)s.zip', + 'checksums': ['2b18a172120e32128a80efee04cff487d5d140fe7d817deb648b2eee023a40e4'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'checksums': ['b2e9810e09c3a47b73ce9cab5a72243a1258f61e7900969097a817232246ce1c'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb new file mode 100644 index 00000000000..832416adda2 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.5.1' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template > mplsetup.cfg && " + + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.0', { + 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], + }), + ('fontTools', '4.29.1', { + 'modulename' : 'fontTools', + 'source_tmpl': 'fonttools-%(version)s.zip', + 'checksums': ['2b18a172120e32128a80efee04cff487d5d140fe7d817deb648b2eee023a40e4'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'checksums': ['b2e9810e09c3a47b73ce9cab5a72243a1258f61e7900969097a817232246ce1c'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From f4da23242816c6340dfd1889440a61fcddc490e6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 9 Mar 2022 08:33:48 +0000 Subject: [PATCH 3225/9987] set XLA_PYTHON_CLIENT_ALLOCATOR=platform in jax CUDA easyconfigs --- easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb | 6 +++--- .../easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index d14b441c648..f138187813d 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -110,13 +110,13 @@ exts_list = [ 'a431ce1b6588b5098872f36575dc2c5023b1010760bf6aaa889125c9a09227b0', ], # deliberately not testing in parallel, as that results in (additional) failing tests; - # use XLA_PYTHON_CLIENT_ALLOCATOR=platform when running GPU tests in parallel, - # to avoid each test fully allocating the GPU memory..., + # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, # see https://github.com/google/jax/issues/7323 and # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; - 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests", + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + "JAX_ENABLE_X64=true pytest tests", }), ] diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb index 40f17200c2a..770de325d37 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb @@ -116,13 +116,13 @@ exts_list = [ '96fe1b15b55611727b0ae76409b89c44ae21a1c10002507ca8e3c06c2b134f4e', ], # deliberately not testing in parallel, as that results in (additional) failing tests; - # use XLA_PYTHON_CLIENT_ALLOCATOR=platform when running GPU tests in parallel, - # to avoid each test fully allocating the GPU memory..., + # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, # see https://github.com/google/jax/issues/7323 and # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; - 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 JAX_ENABLE_X64=true pytest tests", + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + "JAX_ENABLE_X64=true pytest tests", }), ] From 1fbc42edaac5030d5f07f92751e04eba9d49cdde Mon Sep 17 00:00:00 2001 From: Zdenek Date: Wed, 9 Mar 2022 11:18:51 +0100 Subject: [PATCH 3226/9987] Removing MPLBACKEND=module://matplotlib_inline.backend_inline --- .../matplotlib-inline-0.1.3-GCCcore-10.2.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb index 5d1e53c4125..0cbbd4ffc61 100644 --- a/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/matplotlib-inline/matplotlib-inline-0.1.3-GCCcore-10.2.0.eb @@ -22,8 +22,4 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -# use matplotlib-inline backend as default -# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend -modextravars = {'MPLBACKEND': 'module://matplotlib_inline.backend_inline'} - moduleclass = 'vis' From 1d4278a236e4dd30548ac2eb37c1306eabb982fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Mar 2022 13:24:55 +0100 Subject: [PATCH 3227/9987] add hash R library as extension to R v4.1.2 easyconfig --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 2a8a1075cd5..da7b34f15c8 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3235,6 +3235,9 @@ exts_list = [ ('simex', '1.8', { 'checksums': ['80c7841196b9377a9367eb6960ad80ca0bf8de511b8b18a0031bfbe7bde289a0'], }), + ('hash', '2.2.6.1', { + 'checksums': ['a680dfccaaf89b5a55355062b5292baf514d53aa3b206aa74869f1b733a06e2c'], + }), ] moduleclass = 'lang' From ec4fefd9111ab477af839c9bd384e77e1885b2d6 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 9 Mar 2022 14:43:06 +0100 Subject: [PATCH 3228/9987] Work update + error fix --- .../s/SCGid/SCGid-0.9-fixPrintToPython3.patch | 2 + .../s/SCGid/SCGid-0.9b0-foss-2021b.eb | 37 ++++++----- .../s/SCGid/SCGid-0.9b0-initEdit.patch | 61 +++++++++++++++++++ 3 files changed, 81 insertions(+), 19 deletions(-) create mode 100644 easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-initEdit.patch diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9-fixPrintToPython3.patch b/easybuild/easyconfigs/s/SCGid/SCGid-0.9-fixPrintToPython3.patch index 6308d7fc7a2..661c7abcac0 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9-fixPrintToPython3.patch +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9-fixPrintToPython3.patch @@ -1,3 +1,5 @@ +Some print functions used Python2 syntax. This fixes it to Python3 syntax. +Author: Orient Kružík (INUITS) --- SCGid-master-orig/scgid/gct_window_plots.py 2021-10-28 06:18:47.000000000 +0200 +++ SCGid-master/scgid/gct_window_plots.py 2022-02-07 16:47:49.356047797 +0100 @@ -33,11 +33,11 @@ diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index 007fc5a6fd3..8884cf87c00 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -12,11 +12,15 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ["https://github.com/amsesk/SCGid/archive"] sources = ['%s.tar.gz' % local_commit] -patches = ["SCGid-0.9-fixPrintToPython3.patch"] +patches = [ + "SCGid-0.9-fixPrintToPython3.patch", + "SCGid-0.9b0-initEdit.patch" +] checksums = [ # be106e4cd888fd913a527ea821e510e0afb100be.tar.gz '1f625e8f87b4d5e4ec9831ebe48763676679d6d6c41b05ef0bb59e6a7f839153', - 'b912ace0a2fabe4cdf43e70ea2d3ff799894da9edb2a078198dde5d7b91daf67', # SCGid-0.9-fixPrintToPython3.patch + 'ee251b71ed3eed097b05751a3cea302d954000e1a8112e6e3f297e67c84996f7', # SCGid-0.9-fixPrintToPython3.patch + '5deb9911beef69bc127b966f94199511800069737f822e15ca5115a16d8b50c5', # SCGid-0.9b0-initEdit.patch ] local_clams_commit = "e326c34307803b9ea8ffc975ddd9bd05643af931" @@ -39,38 +43,33 @@ sanity_pip_check = True download_dep_fail = False exts_defaultclass = "Tarball" +local_config_path = "%(installdir)s/lib/python3.9/site-packages/config.yaml" +local_config_prep = "%%(installdir)s/SCGid-%s/config.yaml" % local_commit postinstallcmds = [ + 'ln -s %%(installdir)s/ClaMS-CLI-fork-%s/ClaMS-CLI.jar %%(installdir)s/ClaMS-CLI.jar' % local_clams_commit, 'export PATH=$PATH:$EBROOTAUGUSTUS', 'export PATH=$PATH:$EBROOTBLAST', - 'echo $EBROOTR', - # Set paths to make init available - "PATH=%(installdir)s/bin:$PATH " - "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " - # Go through init step of installation and download required database - 'scgid init <<<"%(installdir)s/esom-1.1/src\n' - '%(installdir)s/ClaMS-CLI-fork-e326c34307803b9ea8ffc975ddd9bd05643af931/ClaMS-CLI.jar\n' - '$EBROOTR/bin/Rscript\n' - 'y\n' - 'y\n' - 'y"' ] options = {'modulename': False} exts_list = [ ('ClaMS-CLI', '31012020', { - 'install_type': 'merge', 'source_tmpl': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', 'source_urls': ['https://github.com/amsesk/ClaMS-CLI-fork/archive'], 'checksums': ['743397fc8308e363f127bd7e5165ac9d769c10305f6e33d9e408db8f343170db'], }), ('ESOM', '1.1', { - 'install_type': 'merge', - 'preconfigopts': "export ESOM_HOME=%(installdir)s && cd esom-%(version)s && maven jar install &&", - 'source_tmpl': 'esom-%(version)s-src.tar.gz', - 'source_urls': ['https://sourceforge.net/projects/databionic-esom/files/databionic-esom/%(version)s/'], - 'checksums': ['48d8a3f04946850cbbc3beb9f92bcaa5a98fd301c511388adb4e329467070d38'], + 'download_instructions': """ + You need to manually provide Databionics ESOM. Please, follow these steps: + (1): Go to https://sourceforge.net/projects/databionic-esom/files/databionic-esom/1.1/ and download "esom-1.1-installer.jar" + (2): Run the file and follow through the installation process (ensure you have Java installed to run the file) + (3): Open terminal in the folder where you have installed ESOM and create Tarball of its contents (tar -czvf esom.tar.gz *) + (4): Paste the file created (esom.tar.gz) into the same folder where your easyconfig is + (5): Re-run the build. + """, + 'source_tmpl': 'esom.tar.gz', }), ] diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-initEdit.patch b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-initEdit.patch new file mode 100644 index 00000000000..100a47ea00c --- /dev/null +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-initEdit.patch @@ -0,0 +1,61 @@ +Removes the need to input dependency paths into interactive "scgid init" command +Author: Orient Kružík (INUITS) +diff -ruN SCGid-master-orig/scgid/config.py SCGid-master/scgid/config.py +--- SCGid-master-orig/scgid/config.py 2021-10-28 06:18:47.000000000 +0200 ++++ SCGid-master/scgid/config.py 2022-03-04 20:46:46.268401879 +0100 +@@ -143,6 +143,9 @@ + self.DB = os.path.join(self.HOME, 'database') + self.initial_config = {} + self.initial_config["mpicmd"] = "mpirun" ++ self.initial_config["clams_path"] = "%s/ClaMS-CLI.jar" % os.getenv("EBROOTSCGID") ++ self.initial_config["esom_path"] = os.getenv("EBROOTSCGID") ++ self.initial_config["path_to_Rscript"] = "%s/bin/Rscript" % os.getenv("EBROOTR") + + def welcome(self): + print (scgid_banner) +@@ -157,36 +160,6 @@ + print (f"{output_cols['RED']}ERROR: SCGid v1.0.0 is only compatible with python 3.x.x. Exitting...{output_cols['RESET']}") + sys.exit(1) + +- def config_third_party_deps(self): +- tpdeps = { +- "esom_path": { +- 'target': lambda path: os.path.isfile(os.path.join(path,"bin","esomstart")), +- 'question': "Enter full path to ESOM install: " +- }, +- "clams_path": { +- 'target': lambda path: os.path.isfile(path) and os.path.split(path)[1] == "ClaMS-CLI.jar", +- 'question': "Enter full path to ClaMS-CLI.jar: " +- }, +- "path_to_Rscript": { +- 'target': lambda path: os.path.isfile(path) and os.path.split(path)[1] == "Rscript", +- 'question': "Enter full path to Rscript: " +- } +- } +- for var, stuff in tpdeps.items(): +- while True: +- entry = input(stuff['question']) +- if entry == "DEBUG_SKIP": +- break +- else: +- if not stuff["target"](entry): +- report_outcome (stuff['question'], "RED", "[NOT FOUND, TRY AGAIN]") +- else: +- report_outcome (stuff['question'], "GREEN", "[GOOD]") +- tpdeps[var] = entry +- break +- +- self.initial_config.update(tpdeps) +- + def config_spdb (self): + + self.initial_config['default_spdb'] = None +@@ -318,8 +291,6 @@ + + self.welcome() + +- self.config_third_party_deps() +- + self.config_spdb() + + self.config_taxdb() \ No newline at end of file From b435ae00a88425702b2985d32424123d8863b097 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 9 Mar 2022 15:00:56 +0100 Subject: [PATCH 3229/9987] Fixed lines being too long --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index 8884cf87c00..ef5c6a9bae7 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -63,9 +63,12 @@ exts_list = [ ('ESOM', '1.1', { 'download_instructions': """ You need to manually provide Databionics ESOM. Please, follow these steps: - (1): Go to https://sourceforge.net/projects/databionic-esom/files/databionic-esom/1.1/ and download "esom-1.1-installer.jar" - (2): Run the file and follow through the installation process (ensure you have Java installed to run the file) - (3): Open terminal in the folder where you have installed ESOM and create Tarball of its contents (tar -czvf esom.tar.gz *) + (1): Go to https://sourceforge.net/projects/databionic-esom/files/databionic-esom/1.1/ and + download "esom-1.1-installer.jar" + (2): Run the file and follow through the installation process (ensure you have Java + installed to run the file) + (3): Open terminal in the folder where you have installed ESOM and create Tarball of + its contents (tar -czvf esom.tar.gz *) (4): Paste the file created (esom.tar.gz) into the same folder where your easyconfig is (5): Re-run the build. """, From e7563ad2cf3aeaaea143ee8158011548574a87b8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 9 Mar 2022 16:54:27 +0200 Subject: [PATCH 3230/9987] remove disable flag for RTTI in snappy v1.1.9 --- .../s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb | 6 ++++- .../snappy-1.1.9_use-default-rtti.patch | 27 +++++++++++++++++++ 2 files changed, 32 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.9_use-default-rtti.patch diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb index a98a6f1158f..286a3ef29fb 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.2.0.eb @@ -12,10 +12,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/google/snappy/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_inline-functions.patch'] +patches = [ + '%(name)s-%(version)s_inline-functions.patch', + '%(name)s-%(version)s_use-default-rtti.patch', +] checksums = [ '75c1fbb3d618dd3a0483bff0e26d0a92b495bbe5059c8b4f1c962b478b6e06e7', # 1.1.9.tar.gz 'ad79190b274df5ddabf14eddd2bb0d9a091ee7d44e4afde89febf9a8f783fdce', # snappy-1.1.9_inline-functions.patch + 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d', # snappy-1.1.9_use-default-rtti.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.9_use-default-rtti.patch b/easybuild/easyconfigs/s/snappy/snappy-1.1.9_use-default-rtti.patch new file mode 100644 index 00000000000..3bdcc462cf0 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.9_use-default-rtti.patch @@ -0,0 +1,27 @@ +Disable any modification of the RTTI setting and follow what is set in the environment. +By default it is enabled in GCC and software might rely on the RTTI symbols in snappy. +author: Alex Domingo (Vrije Universiteit Brussel) +diff --git a/CMakeLists.txt.orig b/CMakeLists.txt +index 672561e..a4b2cc7 100644 +--- a/CMakeLists.txt.orig ++++ b/CMakeLists.txt +@@ -52,9 +52,6 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /EHs-c-") + add_definitions(-D_HAS_EXCEPTIONS=0) + +- # Disable RTTI. +- string(REGEX REPLACE "/GR" "" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}") +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /GR-") + else(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC") + # Use -Wall for clang and gcc. + if(NOT CMAKE_CXX_FLAGS MATCHES "-Wall") +@@ -77,9 +74,6 @@ else(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC") + string(REGEX REPLACE "-fexceptions" "" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-exceptions") + +- # Disable RTTI. +- string(REGEX REPLACE "-frtti" "" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}") +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-rtti") + endif(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC") + + # BUILD_SHARED_LIBS is a standard CMake variable, but we declare it here to make From e2d9444ef0cc678b83d160bbe1e303865c55375d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 9 Mar 2022 16:57:48 +0200 Subject: [PATCH 3231/9987] adding easyconfigs: RE2-2022-02-01-GCCcore-11.2.0.eb --- .../r/RE2/RE2-2022-02-01-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/r/RE2/RE2-2022-02-01-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/r/RE2/RE2-2022-02-01-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2022-02-01-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..efbb084d3ec --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2022-02-01-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = "CMakeMake" + +name = 'RE2' +version = '2022-02-01' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9c1e6acfd0fed71f40b025a7a1dabaf3ee2ebb74d64ced1f9ee1b0b01d22fd27'] + +builddependencies = { + ('binutils', '2.37'), + ('CMake', '3.21.1'), +} + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' From bed39b047498affbf3279fa1b0cf46e4f1e59915 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 9 Mar 2022 16:58:37 +0200 Subject: [PATCH 3232/9987] adding easyconfigs: c-ares-1.18.1-GCCcore-11.2.0.eb --- .../c/c-ares/c-ares-1.18.1-GCCcore-11.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/c-ares/c-ares-1.18.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/c-ares/c-ares-1.18.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/c-ares/c-ares-1.18.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..895a03c1363 --- /dev/null +++ b/easybuild/easyconfigs/c/c-ares/c-ares-1.18.1-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'c-ares' +version = '1.18.1' + +homepage = 'https://c-ares.org/' +description = "c-ares is a C library for asynchronous DNS requests (including name resolves)" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'c-ares' +source_urls = [GITHUB_SOURCE] +sources = ['%s-%s.tar.gz' % (name.replace('-', ''), version.replace('.', '_'))] +checksums = ['414872549eec4e221b576693fdc9c9bce44ff794d0f1f06f2515b56a7f6ec9c9'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': ['lib/libcares.a', 'lib/libcares.%s' % SHLIB_EXT, 'lib/pkgconfig/libcares.pc'], + 'dirs': ['include', 'share/man'], +} + +moduleclass = 'lib' From cd5519ae6acaa81f789366d25bb119a83d86beb1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 9 Mar 2022 16:59:22 +0200 Subject: [PATCH 3233/9987] adding easyconfigs: Abseil-20210324.2-GCCcore-11.2.0.eb --- .../Abseil-20210324.2-GCCcore-11.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/Abseil/Abseil-20210324.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20210324.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20210324.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..02f2ee7dc25 --- /dev/null +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20210324.2-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Abseil' +version = '20210324.2' + +homepage = 'https://abseil.io/' +description = """Abseil is an open-source collection of C++ library code designed to augment the +C++ standard library. The Abseil library code is collected from Google's own +C++ code base, has been extensively tested and used in production, and is the +same code we depend on in our daily coding lives.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['59b862f50e710277f8ede96f083a5bb8d7c9595376146838b9580be90374ee1f'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], + 'dirs': ['include/absl'], +} + +moduleclass = 'lib' From 79de8f4b8bb4d0c35202ebf9b100d4826e8053c3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 9 Mar 2022 17:00:19 +0200 Subject: [PATCH 3234/9987] adding easyconfigs: gRPC-1.44.0-GCCcore-11.2.0.eb --- .../g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7c7a4e106cf --- /dev/null +++ b/easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'gRPC' +version = '1.44.0' + +homepage = 'https://grpc.io/' +description = """gRPC is a modern, open source, high-performance remote procedure call (RPC) +framework that can run anywhere. gRPC enables client and server applications to +communicate transparently, and simplifies the building of connected systems.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'grpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['8c05641b9f91cbc92f51cc4a5b3a226788d7a63f20af4ca7aaca50d92cc94a0d'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), + ('Abseil', '20210324.2'), + ('c-ares', '1.18.1'), + ('protobuf', '3.17.3'), + ('zlib', '1.2.11'), + ('RE2', '2022-02-01'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += "-DgRPC_ABSL_PROVIDER=package " +configopts += "-DgRPC_CARES_PROVIDER=package " +configopts += "-DgRPC_PROTOBUF_PROVIDER=package " +configopts += "-DgRPC_RE2_PROVIDER=package " +configopts += "-DgRPC_SSL_PROVIDER=package " +configopts += "-DgRPC_ZLIB_PROVIDER=package " + +_grpc_plugins = ['cpp', 'csharp', 'node', 'objective_c', 'php', 'python', 'ruby'] + +sanity_check_paths = { + 'files': ['bin/grpc_%s_plugin' % x for x in _grpc_plugins] + + ['lib/libgrpc.%s' % SHLIB_EXT, 'lib/libgrpc++.%s' % SHLIB_EXT], + 'dirs': ['include/grpc', 'include/grpc++', 'include/grpcpp'], +} + +moduleclass = 'lib' From 4f7df0034e369e25fde8ee4d44713d21c95d33a2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 9 Mar 2022 17:02:53 +0200 Subject: [PATCH 3235/9987] adding easyconfigs: dm-reverb-0.7.0-foss-2021b.eb and patches: dm-reverb-0.7.0_eb-build-environment.patch --- .../d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb | 41 ++ ...dm-reverb-0.7.0_eb-build-environment.patch | 687 ++++++++++++++++++ 2 files changed, 728 insertions(+) create mode 100644 easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb new file mode 100644 index 00000000000..52279474a01 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb @@ -0,0 +1,41 @@ +name = 'dm-reverb' +version = '0.7.0' + +homepage = 'https://github.com/deepmind/reverb' +description = """ +Reverb is an efficient and easy-to-use data storage and transport system +designed for machine learning research. Reverb is primarily used as an +experience replay system for distributed reinforcement learning algorithms but +the system also supports multiple data structure representations such as FIFO, +LIFO, and priority queues.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/deepmind/reverb/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = ['dm-reverb-0.7.0_eb-build-environment.patch'] +checksums = [ + '11fd16db4dab60cc3e827fe8311921797c8e0371e55a2e0f2798ae7d9aabe47c', # v0.7.0.tar.gz + 'eb75e3ec778a1cafafd93d5dbd0d7530ea785c0378e0ee1ef2321ce7599aa7f0', # dm-reverb-0.7.0_eb-build-environment.patch +] + +builddependencies = [ + ('Bazel', '3.7.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('TensorFlow', '2.7.1'), + ('Abseil', '20210324.2'), + ('dm-tree', '0.1.6'), + ('gRPC', '1.44.0'), + ('protobuf', '3.17.3'), + ('snappy', '1.1.9'), + ('zlib', '1.2.11'), +] + +sanity_pip_check = True + +options = {'modulename': 'reverb'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch new file mode 100644 index 00000000000..a1d6297a79c --- /dev/null +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch @@ -0,0 +1,687 @@ +Refactor the build environment to use dependencies from EasyBuild +* fix detection of Python installation +* disable toolchain definitions with gcc-7 +* use C++11 ABI as it is used in protobuf from EB +* define a single local repo using files from EB for the following dependencies: + * local com_google_protobuf replaces protobuf_archive, protobuf_protoc and + external com_google_protobuf + * local zlib replaces zlib_includes and external zlib + * local snappy replaces snappy_includes + * local pybind11 replaces http archive source + * local com_github_grpc_grpc replaces http archive source + * local com_google_absl replaces http archive source +author: Alex Domingo (Vrije Universiteit Brussel) +diff --git a/WORKSPACE.orig b/WORKSPACE +index 5d47f95..6d587ab 100644 +--- a/WORKSPACE.orig ++++ b/WORKSPACE +@@ -13,8 +13,15 @@ workspace(name = "reverb") + # + # *WARNING* If using the REVERB_PROTOC_VERSION environment variable, sha256 + # checking is disabled. Use at your own risk. +-PROTOC_VERSION = "3.9.0" +-PROTOC_SHA256 = "15e395b648a1a6dda8fd66868824a396e9d3e89bc2c8648e3b9ab9801bea5d55" ++#PROTOC_VERSION = "3.9.0" ++#PROTOC_SHA256 = "15e395b648a1a6dda8fd66868824a396e9d3e89bc2c8648e3b9ab9801bea5d55" ++ ++load( ++ "//reverb/cc/platform/default:repo.bzl", ++ "cc_tf_configure", ++) ++ ++cc_tf_configure() + + load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive") + +@@ -28,72 +35,6 @@ http_archive( + ], + ) + +-http_archive( +- name = "com_google_absl", +- sha256 = "35f22ef5cb286f09954b7cc4c85b5a3f6221c9d4df6b8c4a1e9d399555b366ee", # SHARED_ABSL_SHA +- strip_prefix = "abseil-cpp-997aaf3a28308eba1b9156aa35ab7bca9688e9f6", +- urls = [ +- "https://storage.googleapis.com/mirror.tensorflow.org/github.com/abseil/abseil-cpp/archive/997aaf3a28308eba1b9156aa35ab7bca9688e9f6.tar.gz", +- "https://github.com/abseil/abseil-cpp/archive/997aaf3a28308eba1b9156aa35ab7bca9688e9f6.tar.gz", +- ], +-) +- + # Note that the Python dependencies are not tracked by bazel here, but + # in setup.py. + +-## Begin GRPC related deps +-http_archive( +- name = "com_github_grpc_grpc", +- patch_cmds = [ +- """sed -i.bak 's/"python",/"python3",/g' third_party/py/python_configure.bzl""", +- """sed -i.bak 's/PYTHONHASHSEED=0/PYTHONHASHSEED=0 python3/g' bazel/cython_library.bzl""", +- ], +- sha256 = "39bad059a712c6415b168cb3d922cb0e8c16701b475f047426c81b46577d844b", +- strip_prefix = "grpc-reverb_fix", +- urls = [ +- # Patched version of GRPC / boringSSL to make it compile with old TF GCC compiler +- "https://github.com/qstanczyk/grpc/archive/reverb_fix.tar.gz", +- ], +-) +- +- +-load("@com_github_grpc_grpc//bazel:grpc_deps.bzl", "grpc_deps") +- +-grpc_deps() +- +-load("@com_github_grpc_grpc//bazel:grpc_extra_deps.bzl", "grpc_extra_deps") +- +-grpc_extra_deps() +- +- +-load("@upb//bazel:workspace_deps.bzl", "upb_deps") +- +-upb_deps() +- +-load( +- "@build_bazel_rules_apple//apple:repositories.bzl", +- "apple_rules_dependencies", +-) +- +-apple_rules_dependencies() +- +-load( +- "@build_bazel_apple_support//lib:repositories.bzl", +- "apple_support_dependencies", +-) +- +-apple_support_dependencies() +-## End GRPC related deps +- +-load( +- "//reverb/cc/platform/default:repo.bzl", +- "cc_tf_configure", +- "reverb_protoc_deps", +- "reverb_python_deps", +-) +- +-cc_tf_configure() +- +-reverb_python_deps() +- +-reverb_protoc_deps(version = PROTOC_VERSION, sha256 = PROTOC_SHA256) +diff --git a/reverb/cc/platform/default/BUILD.orig b/reverb/cc/platform/default/BUILD +index 372653e..897c346 100644 +--- a/reverb/cc/platform/default/BUILD.orig ++++ b/reverb/cc/platform/default/BUILD +@@ -18,7 +18,7 @@ reverb_cc_library( + srcs = ["snappy.cc"], + deps = [ + "//reverb/cc/platform:snappy_hdr", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ] + reverb_tf_deps(), + alwayslink = 1, + ) +@@ -30,7 +30,7 @@ reverb_cc_library( + "//reverb/cc/checkpointing:interface", + "//reverb/cc/platform:checkpointing_hdr", + "//reverb/cc/platform:tfrecord_checkpointer", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ], + alwayslink = 1, + ) +@@ -48,7 +48,7 @@ reverb_cc_library( + "//reverb/cc/platform:status_macros", + "//reverb/cc/platform:tfrecord_checkpointer", + "//reverb/cc/support:periodic_closure", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ] + reverb_grpc_deps(), + alwayslink = 1, + ) +@@ -60,7 +60,7 @@ reverb_cc_library( + "status_matchers.h", + ], + deps = [ +- "@com_google_absl//absl/status", ++ "@com_google_absl//:absl", + ], + ) + +@@ -68,7 +68,7 @@ reverb_cc_library( + name = "status_matchers", + hdrs = ["status_matchers.h"], + deps = [ +- "@com_google_absl//absl/status", ++ "@com_google_absl//:absl", + ], + ) + +@@ -77,8 +77,7 @@ reverb_cc_library( + srcs = ["thread.cc"], + deps = [ + "//reverb/cc/platform:thread_hdr", +- "@com_google_absl//absl/memory", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ], + alwayslink = 1, + ) +@@ -101,7 +100,7 @@ reverb_cc_library( + hdrs = ["hash_map.h"], + deps = [ + ":hash", +- "@com_google_absl//absl/container:flat_hash_map", ++ "@com_google_absl//:absl", + ], + ) + +@@ -110,7 +109,7 @@ reverb_cc_library( + hdrs = ["hash_set.h"], + deps = [ + ":hash", +- "@com_google_absl//absl/container:flat_hash_set", ++ "@com_google_absl//:absl", + ], + ) + +diff --git a/reverb/cc/platform/default/repo.bzl.orig b/reverb/cc/platform/default/repo.bzl +index 1daac52..f6d55e3 100644 +--- a/reverb/cc/platform/default/repo.bzl.orig ++++ b/reverb/cc/platform/default/repo.bzl +@@ -91,13 +91,13 @@ def _find_python_solib_path(repo_ctx): + version = exec_result.stdout.splitlines()[-1] + basename = "lib{}.so".format(version) + exec_result = repo_ctx.execute( +- ["{}-config".format(version), "--configdir"], ++ ["{}-config".format(version), "--prefix"], + quiet = True, + ) + if exec_result.return_code != 0: + fail("Could not locate python shared library path:\n{}" + .format(exec_result.stderr)) +- solib_dir = exec_result.stdout.splitlines()[-1] ++ solib_dir = "{}/{}".format(exec_result.stdout.splitlines()[-1], "lib") + full_path = repo_ctx.path("{}/{}".format(solib_dir, basename)) + if not full_path.exists: + fail("Unable to find python shared library file:\n{}/{}" +@@ -125,64 +125,121 @@ cc_library( + ) + + def _nsync_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink(tf_include_path + "/external", "nsync_includes") ++ nsync_root = repo_ctx.os.environ.get("EBROOTNSYNC") ++ repo_ctx.symlink(nsync_root, "nsync") + repo_ctx.file( + "BUILD", + content = """ + cc_library( + name = "includes", +- hdrs = glob(["nsync_includes/nsync/public/*.h"]), +- includes = ["nsync_includes"], ++ hdrs = glob(["nsync/**/*.h"]), ++ includes = ["nsync/include"], + visibility = ["//visibility:public"], + ) + """, + executable = False, + ) + +-def _zlib_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink( +- tf_include_path + "/external/zlib", +- "zlib", +- ) ++def _zlib_repo_impl(repo_ctx): ++ zlib_root = repo_ctx.os.environ.get("EBROOTZLIB") ++ repo_ctx.symlink(zlib_root, "zlib") + repo_ctx.file( + "BUILD", + content = """ + cc_library( ++ name = "libz", ++ srcs = ["zlib/lib/libz.so"], ++ visibility = ["//visibility:public"], ++) ++cc_library( + name = "includes", + hdrs = glob(["zlib/**/*.h"]), +- includes = ["zlib"], ++ includes = ["zlib/include"], + visibility = ["//visibility:public"], + ) + """, + executable = False, + ) + +-def _snappy_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink( +- tf_include_path + "/external/snappy", +- "snappy", +- ) ++def _snappy_repo_impl(repo_ctx): ++ snappy_root = repo_ctx.os.environ.get("EBROOTSNAPPY") ++ repo_ctx.symlink(snappy_root, "snappy") + repo_ctx.file( + "BUILD", + content = """ + cc_library( ++ name = "libsnappy", ++ srcs = ["snappy/lib/libsnappy.so"], ++ visibility = ["//visibility:public"], ++) ++cc_library( + name = "includes", +- hdrs = glob(["snappy/*.h"]), +- includes = ["snappy"], ++ hdrs = glob(["snappy/**/*.h"]), ++ includes = ["snappy/include"], + visibility = ["//visibility:public"], + ) + """, + executable = False, + ) + +-def _protobuf_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink(tf_include_path, "tf_includes") ++def _pybind11_includes_repo_impl(repo_ctx): ++ pybind_root = repo_ctx.os.environ.get("EBROOTPYBIND11") ++ repo_ctx.symlink("{}/include".format(pybind_root), "include") ++ repo_ctx.symlink(Label("//third_party:pybind11.BUILD"), "BUILD") ++ ++def _protobuf_repo_impl(repo_ctx): ++ protobuf_root = repo_ctx.os.environ.get("EBROOTPROTOBUF") ++ repo_ctx.symlink(protobuf_root, "protobuf") + repo_ctx.symlink(Label("//third_party:protobuf.BUILD"), "BUILD") + ++def _absl_repo_impl(repo_ctx): ++ absl_root = repo_ctx.os.environ.get("EBROOTABSEIL") ++ repo_ctx.symlink(absl_root, "absl") ++ repo_ctx.file( ++ "BUILD", ++ content = """ ++cc_library( ++ name = "absl", ++ hdrs = glob(["absl/**/*.h", "absl/**/*.inc"]), ++ srcs = glob(["absl/lib/*.so"]), ++ includes = ["absl/include"], ++ visibility = ["//visibility:public"], ++) ++""", ++ executable = False, ++ ) ++ ++def _grpc_repo_impl(repo_ctx): ++ grpc_root = repo_ctx.os.environ.get("EBROOTGRPC") ++ repo_ctx.symlink(grpc_root, "grpc") ++ repo_ctx.file( ++ "BUILD", ++ content = """ ++cc_library( ++ name = "grpc++", ++ hdrs = glob(["grpc/**/*.h"]), ++ srcs = glob(["grpc/lib/*.so"]), ++ includes = ["grpc/include"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "grpc++_codegen_proto", ++ hdrs = glob([ ++ "grpc/include/*/impl/codegen/*.h", ++ "grpc/include/*/impl/codegen/security/*.h", ++ ]), ++ includes = ["grpc/include"], ++ visibility = ["//visibility:public"], ++) ++filegroup( ++ name = "grpc_cpp_plugin", ++ srcs = ["grpc/bin/grpc_cpp_plugin"], ++ visibility = ["//visibility:public"], ++) ++""", ++ executable = False, ++ ) ++ + def _tensorflow_includes_repo_impl(repo_ctx): + tf_include_path = _find_tf_include_path(repo_ctx) + repo_ctx.symlink(tf_include_path, "tensorflow_includes") +@@ -200,11 +257,11 @@ cc_library( + ), + includes = ["tensorflow_includes"], + deps = [ +- "@com_google_absl//absl/container:flat_hash_map", ++ "@com_google_absl//:absl", + "@eigen_archive//:includes", +- "@protobuf_archive//:includes", +- "@zlib_includes//:includes", +- "@snappy_includes//:includes", ++ "@com_google_protobuf//:includes", ++ "@zlib//:includes", ++ "@snappy//:includes", + ], + visibility = ["//visibility:public"], + ) +@@ -226,7 +283,12 @@ def _tensorflow_solib_repo_impl(repo_ctx): + cc_library( + name = "framework_lib", + srcs = ["tensorflow_solib/libtensorflow_framework.so.2"], +- deps = ["@python_includes", "@python_includes//:numpy_includes"], ++ deps = [ ++ "@python_includes", ++ "@python_includes//:numpy_includes", ++ "@zlib//:libz", ++ "@snappy//:libsnappy", ++ ], + visibility = ["//visibility:public"], + ) + """, +@@ -275,17 +337,29 @@ def cc_tf_configure(): + ) + make_nsync_repo(name = "nsync_includes") + make_zlib_repo = repository_rule( +- implementation = _zlib_includes_repo_impl, ++ implementation = _zlib_repo_impl, + ) +- make_zlib_repo(name = "zlib_includes") ++ make_zlib_repo(name = "zlib") + make_snappy_repo = repository_rule( +- implementation = _snappy_includes_repo_impl, ++ implementation = _snappy_repo_impl, + ) +- make_snappy_repo(name = "snappy_includes") ++ make_snappy_repo(name = "snappy") ++ make_pybind11_repo = repository_rule( ++ implementation = _pybind11_includes_repo_impl, ++ ) ++ make_pybind11_repo(name = "pybind11") + make_protobuf_repo = repository_rule( +- implementation = _protobuf_includes_repo_impl, ++ implementation = _protobuf_repo_impl, ++ ) ++ make_protobuf_repo(name = "com_google_protobuf") ++ make_absl_repo = repository_rule( ++ implementation = _absl_repo_impl, + ) +- make_protobuf_repo(name = "protobuf_archive") ++ make_absl_repo(name = "com_google_absl") ++ make_grpc_repo = repository_rule( ++ implementation = _grpc_repo_impl, ++ ) ++ make_grpc_repo(name = "com_github_grpc_grpc") + make_tfinc_repo = repository_rule( + implementation = _tensorflow_includes_repo_impl, + ) +@@ -298,65 +372,3 @@ def cc_tf_configure(): + implementation = _python_includes_repo_impl, + ) + make_python_inc_repo(name = "python_includes") +- +-def reverb_python_deps(): +- http_archive( +- name = "pybind11", +- urls = [ +- "https://storage.googleapis.com/mirror.tensorflow.org/github.com/pybind/pybind11/archive/v2.4.3.tar.gz", +- "https://github.com/pybind/pybind11/archive/v2.4.3.tar.gz", +- ], +- sha256 = "1eed57bc6863190e35637290f97a20c81cfe4d9090ac0a24f3bbf08f265eb71d", +- strip_prefix = "pybind11-2.4.3", +- build_file = clean_dep("//third_party:pybind11.BUILD"), +- ) +- +- http_archive( +- name = "absl_py", +- sha256 = "603febc9b95a8f2979a7bdb77d2f5e4d9b30d4e0d59579f88eba67d4e4cc5462", +- strip_prefix = "abseil-py-pypi-v0.9.0", +- urls = [ +- "https://storage.googleapis.com/mirror.tensorflow.org/github.com/abseil/abseil-py/archive/pypi-v0.9.0.tar.gz", +- "https://github.com/abseil/abseil-py/archive/pypi-v0.9.0.tar.gz", +- ], +- ) +- +-def _reverb_protoc_archive(ctx): +- version = ctx.attr.version +- sha256 = ctx.attr.sha256 +- +- override_version = ctx.os.environ.get("REVERB_PROTOC_VERSION") +- if override_version: +- sha256 = "" +- version = override_version +- +- urls = [ +- "https://github.com/protocolbuffers/protobuf/releases/download/v%s/protoc-%s-linux-x86_64.zip" % (version, version), +- ] +- ctx.download_and_extract( +- url = urls, +- sha256 = sha256, +- ) +- +- ctx.file( +- "BUILD", +- content = """ +-filegroup( +- name = "protoc_bin", +- srcs = ["bin/protoc"], +- visibility = ["//visibility:public"], +-) +-""", +- executable = False, +- ) +- +-reverb_protoc_archive = repository_rule( +- implementation = _reverb_protoc_archive, +- attrs = { +- "version": attr.string(mandatory = True), +- "sha256": attr.string(mandatory = True), +- }, +-) +- +-def reverb_protoc_deps(version, sha256): +- reverb_protoc_archive(name = "protobuf_protoc", version = version, sha256 = sha256) +diff --git a/reverb/cc/platform/default/build_rules.bzl.orig b/reverb/cc/platform/default/build_rules.bzl +index fa8560f..6bf3694 100644 +--- a/reverb/cc/platform/default/build_rules.bzl.orig ++++ b/reverb/cc/platform/default/build_rules.bzl +@@ -90,12 +90,12 @@ def reverb_cc_proto_library(name, srcs = [], deps = [], **kwargs): + srcs = srcs, + outs = gen_srcs + gen_hdrs, + tools = dep_srcs + [ +- "@protobuf_protoc//:protoc_bin", ++ "@com_google_protobuf//:protoc_bin", + "@tensorflow_includes//:protos", + ], + cmd = """ + OUTDIR=$$(echo $(RULEDIR) | sed -E -e 's#reverb(/.*|$$)##') +- $(location @protobuf_protoc//:protoc_bin) \ ++ $(location @com_google_protobuf//:protoc_bin) \ + --proto_path=external/tensorflow_includes/tensorflow_includes/ \ + --proto_path=. \ + --cpp_out=$$OUTDIR {}""".format( +@@ -165,12 +165,12 @@ def reverb_py_proto_library(name, srcs = [], deps = [], **kwargs): + srcs = srcs, + outs = gen_srcs, + tools = proto_deps + [ +- "@protobuf_protoc//:protoc_bin", ++ "@com_google_protobuf//:protoc_bin", + "@tensorflow_includes//:protos", + ], + cmd = """ + OUTDIR=$$(echo $(RULEDIR) | sed -E -e 's#reverb(/.*|$$)##') +- $(location @protobuf_protoc//:protoc_bin) \ ++ $(location @com_google_protobuf//:protoc_bin) \ + --proto_path=external/tensorflow_includes/tensorflow_includes/ \ + --proto_path=. \ + --python_out=$$OUTDIR {}""".format( +@@ -227,14 +227,14 @@ def reverb_cc_grpc_library( + srcs = srcs, + outs = gen_srcs + gen_hdrs + gen_mocks, + tools = proto_src_deps + [ +- "@protobuf_protoc//:protoc_bin", ++ "@com_google_protobuf//:protoc_bin", + "@tensorflow_includes//:protos", +- "@com_github_grpc_grpc//src/compiler:grpc_cpp_plugin", ++ "@com_github_grpc_grpc//:grpc_cpp_plugin", + ], + cmd = """ + OUTDIR=$$(echo $(RULEDIR) | sed -e 's#reverb/.*##') +- $(location @protobuf_protoc//:protoc_bin) \ +- --plugin=protoc-gen-grpc=$(location @com_github_grpc_grpc//src/compiler:grpc_cpp_plugin) \ ++ $(location @com_google_protobuf//:protoc_bin) \ ++ --plugin=protoc-gen-grpc=$(location @com_github_grpc_grpc//:grpc_cpp_plugin) \ + --proto_path=external/tensorflow_includes/tensorflow_includes/ \ + --proto_path=. \ + --grpc_out={} {}""".format( +@@ -544,6 +544,8 @@ def reverb_tf_ops_visibility(): + + def reverb_tf_deps(): + return [ ++ "@zlib//:libz", ++ "@snappy//:libsnappy", + "@tensorflow_includes//:includes", + "@tensorflow_solib//:framework_lib", + ] +@@ -552,24 +554,4 @@ def reverb_grpc_deps(): + return ["@com_github_grpc_grpc//:grpc++"] + + def reverb_absl_deps(): +- return [ +- # We purposefully don't include absl::flat_hash_{map,set} so that users +- # are forced to use platform:hash_{map,set}, which uses a safer hasher. +- "@com_google_absl//absl/base", +- "@com_google_absl//absl/base:core_headers", +- "@com_google_absl//absl/functional:bind_front", +- "@com_google_absl//absl/memory", +- "@com_google_absl//absl/numeric:int128", +- "@com_google_absl//absl/random", +- "@com_google_absl//absl/random:distributions", +- "@com_google_absl//absl/status", +- "@com_google_absl//absl/status:statusor", +- "@com_google_absl//absl/strings", +- "@com_google_absl//absl/strings:cord", +- "@com_google_absl//absl/strings:str_format", +- "@com_google_absl//absl/synchronization", +- "@com_google_absl//absl/time", +- "@com_google_absl//absl/types:optional", +- "@com_google_absl//absl/types:span", +- "@com_google_absl//absl/flags:flag", +- ] ++ return ["@com_google_absl//:absl"] +diff --git a/third_party/protobuf.BUILD.orig b/third_party/protobuf.BUILD +index b8e9496..7d601a5 100644 +--- a/third_party/protobuf.BUILD.orig ++++ b/third_party/protobuf.BUILD +@@ -1,10 +1,10 @@ + _CHECK_VERSION = """ +-PROTOC_VERSION=$$($(location @protobuf_protoc//:protoc_bin) --version \ ++PROTOC_VERSION=$$($(location protobuf/bin/protoc) --version \ + | cut -d' ' -f2 | sed -e 's/\\./ /g') + PROTOC_VERSION=$$(printf '%d%03d%03d' $${PROTOC_VERSION}) + TF_PROTO_VERSION=$$(grep '#define PROTOBUF_MIN_PROTOC_VERSION' \ +- $(location tf_includes/google/protobuf/port_def.inc) | cut -d' ' -f3) +-if [ "$${PROTOC_VERSION}" -ne "$${TF_PROTO_VERSION}" ]; then ++ $(location protobuf/include/google/protobuf/port_def.inc) | cut -d' ' -f3) ++if [ "$${PROTOC_VERSION}" -lt "$${TF_PROTO_VERSION}" ]; then + echo !!!!!!!!!!!!!!!!!!!!!!!!!!!!! 1>&2 + echo Your protoc version does not match the tensorflow proto header \ + required version: "$${PROTOC_VERSION}" vs. "$${TF_PROTO_VERSION}" 1>&2 +@@ -20,9 +20,9 @@ genrule( + name = "compare_protobuf_version", + outs = ["versions_compared"], + srcs = [ +- "tf_includes/google/protobuf/port_def.inc", ++ "protobuf/include/google/protobuf/port_def.inc", + ], +- tools = ["@protobuf_protoc//:protoc_bin"], ++ tools = ["protobuf/bin/protoc"], + cmd = _CHECK_VERSION, + ) + +@@ -30,11 +30,45 @@ cc_library( + name = "includes", + data = [":versions_compared"], + hdrs = glob([ +- "tf_includes/google/protobuf/*.h", +- "tf_includes/google/protobuf/*.inc", +- "tf_includes/google/protobuf/**/*.h", +- "tf_includes/google/protobuf/**/*.inc", ++ "protobuf/include/google/protobuf/*.h", ++ "protobuf/include/google/protobuf/*.inc", ++ "protobuf/include/google/protobuf/**/*.h", ++ "protobuf/include/google/protobuf/**/*.inc", + ]), +- includes = ["tf_includes"], ++ includes = ["protobuf/include"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "protobuf_headers", ++ data = [":versions_compared"], ++ hdrs = glob([ ++ "protobuf/include/google/protobuf/*.h", ++ "protobuf/include/google/protobuf/*.inc", ++ "protobuf/include/google/protobuf/**/*.h", ++ "protobuf/include/google/protobuf/**/*.inc", ++ ]), ++ includes = ["protobuf/include"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "protobuf_lite", ++ srcs = ["protobuf/lib/libprotobuf-lite.so"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "protobuf", ++ srcs = ["protobuf/lib/libprotobuf.so"], ++ visibility = ["//visibility:public"], ++ deps = [":protobuf_lite"], ++) ++cc_library( ++ name = "protoc_lib", ++ srcs = ["protobuf/lib/libprotoc.so"], ++ visibility = ["//visibility:public"], ++ deps = [":protobuf"], ++) ++filegroup( ++ name = "protoc_bin", ++ srcs = ["protobuf/bin/protoc"], + visibility = ["//visibility:public"], + ) +diff --git a/reverb/cc/opensource/opensource_only.files.orig b/reverb/cc/opensource/opensource_only.files +index 375df63..d74bec1 100644 +--- a/reverb/cc/opensource/opensource_only.files.orig ++++ b/reverb/cc/opensource/opensource_only.files +@@ -1,8 +1,5 @@ + reverb/third_party/BUILD.oss + reverb/third_party/protobuf.BUILD.oss + reverb/third_party/pybind11.BUILD.oss +-reverb/third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/BUILD.oss +-reverb/third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/cc_toolchain_config.bzl.oss +-reverb/third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/dummy_toolchain.bzl.oss + reverb/platform/default/BUILD.oss + reverb/pip_package/BUILD.oss +diff --git a/third_party/opensource_only.files.orig b/third_party/opensource_only.files +index e1f9e12..f3e999c 100644 +--- a/third_party/opensource_only.files.orig ++++ b/third_party/opensource_only.files +@@ -6,6 +6,3 @@ reverb/pip_package/setup.py: + third_party/BUILD: + third_party/protobuf.BUILD: + third_party/pybind11.BUILD: +-third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/BUILD: +-third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/cc_toolchain_config.bzl: +-third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/dummy_toolchain.bzl: +diff --git a/.bazelrc.orig b/.bazelrc +index f4b08d3..89f82dd 100644 +--- a/.bazelrc.orig ++++ b/.bazelrc +@@ -13,7 +13,7 @@ build:manylinux2010 --crosstool_top=//third_party/toolchains/preconfig/ubuntu16. + + build -c opt + build --cxxopt="-std=c++14" +-build --cxxopt="-D_GLIBCXX_USE_CXX11_ABI=0" ++build --cxxopt="-D_GLIBCXX_USE_CXX11_ABI=1" + build --auto_output_filter=subpackages + build --copt="-Wall" --copt="-Wno-sign-compare" + build --linkopt="-lrt -lm" From 3a9603dc159a415d92ac5fd1b515197cd9a04dd4 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 9 Mar 2022 16:17:54 +0100 Subject: [PATCH 3236/9987] Fixed checksum error --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index ef5c6a9bae7..075fa463e28 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -73,6 +73,8 @@ exts_list = [ (5): Re-run the build. """, 'source_tmpl': 'esom.tar.gz', + # Checksum isn't used because user will be providing this extension + 'checksums': [None] }), ] From 88275b2739e9849d48a37d735dadcbbf66709f05 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 9 Mar 2022 16:01:47 -0800 Subject: [PATCH 3237/9987] update deepTools --- .../d/deepTools/deepTools-3.5.1-foss-2021b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/d/deepTools/deepTools-3.5.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.1-foss-2021b.eb b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.1-foss-2021b.eb new file mode 100644 index 00000000000..4e7730514da --- /dev/null +++ b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.1-foss-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'deepTools' +version = '3.5.1' + +homepage = 'https://deeptools.readthedocs.io/' +description = """deepTools is a suite of python tools particularly developed for the efficient analysis of + high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('plotly.py', '5.4.0'), + ('Pysam', '0.18.0'), + ('pyBigWig', '0.3.18'), +] + +use_pip = True + +exts_list = [ + ('py2bit', '0.3.0', { + 'checksums': ['450555c40cba66957ac8c9a4b6afb625fb34c4bb41638de78c87661ff8b682ef'], + }), + ('deeptoolsintervals', '0.1.9', { + 'checksums': ['7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6'], + }), + ('numpydoc', '1.2', { + 'checksums': ['0cec233740c6b125913005d16e8a9996e060528afcb8b7cad3f2706629dfd6f7'], + }), + (name, version, { + 'checksums': ['62eea132513afa5f6bb51387e5866a5c3a26613aeb7e8c9600c38becf2ecb716'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bamCompare', 'bin/bamCoverage', 'bin/bamPEFragmentSize', 'bin/computeGCBias', 'bin/computeMatrix', + 'bin/correctGCBias', 'bin/multiBamSummary', 'bin/plotCorrelation', 'bin/plotCoverage', + 'bin/plotHeatmap', 'bin/plotProfile'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 248f35baeeabbec5af5a7f9b0e50b9c7af9bd1de Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 10 Mar 2022 08:38:20 +0100 Subject: [PATCH 3238/9987] adding easyconfigs: texlive-20210324-GCC-10.3.0.eb --- .../t/texlive/texlive-20210324-GCC-10.3.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb new file mode 100644 index 00000000000..9809666eaa4 --- /dev/null +++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb @@ -0,0 +1,63 @@ +# Based off the 2017 version by John Dey jfdey@fredhutch.org +# https://github.com/easybuilders/easybuild-easyconfigs/pull/5085 +easyblock = 'Tarball' + +name = 'texlive' +version = '20210324' + +homepage = 'https://tug.org' +description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript + text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a + PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to + be a representation of the final typeset output, and so can be easily edited and manipulated.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = [ + 'ftp://tug.org/texlive/historic/2021/', + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/', +] +sources = [ + { + 'download_filename': 'install-tl-unx.tar.gz', + 'filename': 'install-tl-unx-%(version)s.tar.gz', + } +] +checksums = ['74eac0855e1e40c8db4f28b24ef354bd7263c1f76031bdc02b52156b572b7a1d'] + +dependencies = [ + ('X11', '20210518'), + ('libpng', '1.6.37'), + ('libGLU', '9.0.1'), + ('Perl', '5.32.1'), + ('HarfBuzz', '2.8.1'), + ('poppler', '21.06.1'), + ('cairo', '1.16.0'), + ('fontconfig', '2.13.93'), + ('zlib', '1.2.11'), + ('graphite2', '1.3.14'), +] + +postinstallcmds = [ + 'echo "TEXDIR %(installdir)s/" > %(installdir)s/texlive.profile && ' + 'echo "TEXMFLOCAL %(installdir)s/texmf-local" >> %(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' + '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' +] + +modextrapaths = { + 'PATH': 'bin/%(arch)s-linux', + 'INFOPATH': 'texmf-dist/doc/info', + 'MANPATH': 'texmf-dist/doc/man', +} +modextravars = { + 'TEXMFHOME': '%(installdir)s/texmf-dist' +} + +sanity_check_paths = { + 'files': ['bin/%(arch)s-linux/tex', 'bin/%(arch)s-linux/latex'], + 'dirs': ['bin/%(arch)s-linux', 'texmf-dist'], +} + +moduleclass = 'devel' From 5daa086371da88d3ae28f2bf43bb56ddd990aed5 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Thu, 10 Mar 2022 09:53:36 +0100 Subject: [PATCH 3239/9987] Fix whitespace style --- .../easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb | 2 +- .../easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb index 2d5f0cfadec..b369894467f 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb @@ -43,7 +43,7 @@ exts_list = [ 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), ('fontTools', '4.29.1', { - 'modulename' : 'fontTools', + 'modulename': 'fontTools', 'source_tmpl': 'fonttools-%(version)s.zip', 'checksums': ['2b18a172120e32128a80efee04cff487d5d140fe7d817deb648b2eee023a40e4'], }), diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb index 832416adda2..0d03bf7e8cb 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb @@ -43,7 +43,7 @@ exts_list = [ 'checksums': ['14f81644e1f3bf01fbc8b9c990a7889e9bb4400c4d0ff9155aa0bdd19cce24a9'], }), ('fontTools', '4.29.1', { - 'modulename' : 'fontTools', + 'modulename': 'fontTools', 'source_tmpl': 'fonttools-%(version)s.zip', 'checksums': ['2b18a172120e32128a80efee04cff487d5d140fe7d817deb648b2eee023a40e4'], }), From b7f1bf2efd4622a0c8ced43fc7c3627f89680bdb Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 10 Mar 2022 10:23:36 +0100 Subject: [PATCH 3240/9987] Adds missing dependency --- .../graphite2-1.3.14-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..17c53bfd399 --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' From 0a4ec23a5c4bf29042654f34abc670d5d2d3bcd9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 10 Mar 2022 10:54:59 +0100 Subject: [PATCH 3241/9987] set GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS in TensorFlow v2.5.3 --- .../t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb | 1 + .../easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb index 2dc21de4e30..59a083f5333 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb @@ -88,6 +88,7 @@ exts_list = [ }), ('grpcio', '1.43.0', { 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], }), ('gviz-api', '1.10.0', { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb index a75a5332bf6..5405077833e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb @@ -84,6 +84,7 @@ exts_list = [ }), ('grpcio', '1.43.0', { 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], }), ('gviz-api', '1.10.0', { From bf90f297105b30665d34f532bcc1445e5d4075cb Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 10 Mar 2022 10:04:16 +0000 Subject: [PATCH 3242/9987] improve comment --- easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb index 0f023bfe466..ea581cdd09d 100644 --- a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb @@ -21,7 +21,8 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['42875b308f2d9ee38f083fb1020d7d48fca29e2100fdb09ced1969b738b8c939'] -# remove the shipped mageckGSEA and RRA binaries so that the Python install will build them +# Remove the shipped mageckGSEA and RRA binaries so that the Python install will build them +# This avoids RPATH problems (see #15082) preinstallopts = "rm bin/{mageckGSEA,RRA} && " download_dep_fail = True From 78e77a504ab4b2b96067d654b3b32d393bb20b9e Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 10 Mar 2022 11:26:17 -0800 Subject: [PATCH 3243/9987] update SOCI --- .../s/SOCI/SOCI-4.0.3-GCC-11.2.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..2d2ede9bd8e --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.3' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Boost', '1.77.0'), + ('SQLite', '3.36'), + ('PostgreSQL', '13.4'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' From 721562ae253a1157c0eec29833e434f2e2fb6a6f Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 10 Mar 2022 14:03:50 -0800 Subject: [PATCH 3244/9987] add rMATS_P cli tools --- .../easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb index c4ab2d228d0..41bc0020a7b 100644 --- a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb @@ -33,7 +33,7 @@ components = [ 'easyblock': 'MakeCp', 'start_dir': 'rmats-turbo-%(version)s/rMATS_C', 'buildopts': "%s" % local_buildopts, - 'files_to_copy': [(['rMATSexe', '../rmats.py'], 'bin')], + 'files_to_copy': [(['rMATSexe', '../rmats.py', '../rMATS_C', '../rMATS_R', '../rMATS_P'], 'bin')] }), ('rmats-turbo-python', version, { 'easyblock': 'PythonPackage', From faffa9da87e0ab847efb558a6f7850fe3c63538d Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 10 Mar 2022 16:58:13 -0800 Subject: [PATCH 3245/9987] update toolchain --- .../j/JAGS/JAGS-4.3.0-foss-2021b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2021b.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2021b.eb new file mode 100644 index 00000000000..84549cc8f4d --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.0-foss-2021b.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.3.0' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [ + ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download') +] +sources = [SOURCE_TAR_GZ] +checksums = ['8ac5dd57982bfd7d5f0ee384499d62f3e0bb35b5f1660feb368545f1186371fc'] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/%(name)s', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' From 135740df75ed09fdece8fc82655b1650e6322a40 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 10 Mar 2022 17:37:18 -0800 Subject: [PATCH 3246/9987] correct Pysam version --- easybuild/easyconfigs/d/deepTools/deepTools-3.5.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.1-foss-2021b.eb b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.1-foss-2021b.eb index 4e7730514da..44c477c20aa 100644 --- a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.1-foss-2021b.eb +++ b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.1-foss-2021b.eb @@ -14,7 +14,7 @@ dependencies = [ ('SciPy-bundle', '2021.10'), ('matplotlib', '3.4.3'), ('plotly.py', '5.4.0'), - ('Pysam', '0.18.0'), + ('Pysam', '0.17.0'), ('pyBigWig', '0.3.18'), ] From d2e85967078376e31457a5b8a5502103916d044d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2022 12:19:53 +0100 Subject: [PATCH 3247/9987] adding easyconfigs: tmux-3.2a.eb --- easybuild/easyconfigs/t/tmux/tmux-3.2a.eb | 25 +++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/tmux/tmux-3.2a.eb diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.2a.eb b/easybuild/easyconfigs/t/tmux/tmux-3.2a.eb new file mode 100644 index 00000000000..420afee5473 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.2a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.2a' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['551553a4f82beaa8dadc9256800bcc284d7c000081e47aa6ecbb6ff36eacd05f'] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +sanity_check_commands = ["tmux --help 2>&1 | grep 'usage: tmux'"] + +moduleclass = 'tools' From 7d1b3db663edaa423d943c51bc8e9f1028d50b68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2022 12:26:41 +0100 Subject: [PATCH 3248/9987] adding easyconfigs: Bio-DB-HTS-3.01-GCC-11.2.0.eb --- .../Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb | 30 +++++++++++ .../b/BioPerl/BioPerl-1.7.8-GCCcore-11.2.0.eb | 54 +++++++++++++++++++ .../d/DB_File/DB_File-1.857-GCCcore-11.2.0.eb | 31 +++++++++++ 3 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.857-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb new file mode 100644 index 00000000000..58478248dbe --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PerlModule' + +name = 'Bio-DB-HTS' +version = '3.01' + +homepage = 'https://metacpan.org/release/Bio-DB-HTS' +description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/'] +sources = ['Bio-DB-HTS-%(version)s.tar.gz'] +checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42'] + +builddependencies = [('pkgconf', '1.8.0')] + +dependencies = [ + ('Perl', '5.34.0'), + ('BioPerl', '1.7.8'), + ('HTSlib', '1.14'), +] + +options = {'modulename': 'Bio::DB::HTS'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d1ad252dc52 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'Bundle' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Perl', '5.34.0'), + ('XML-LibXML', '2.0207'), + ('DB_File', '1.857'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + ('XML::DOM::XPath', '0.14', { + 'source_tmpl': 'XML-DOM-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': ['0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), + ('BioPerl', version, { + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.857-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.857-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f2707a76ad8 --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.857-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.857' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['7528eaee49ccd3de268d9358226c6c7617d0d7d8786fcc31d7402c54d570a394'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Perl', '5.34.0'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' From 1fe591962b7f7325398f7e6b471736c73e0d91f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2022 12:39:32 +0100 Subject: [PATCH 3249/9987] add nabor + harmony extensions to R v4.1.2 easyconfig --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index da7b34f15c8..fe0d3412dab 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3238,6 +3238,12 @@ exts_list = [ ('hash', '2.2.6.1', { 'checksums': ['a680dfccaaf89b5a55355062b5292baf514d53aa3b206aa74869f1b733a06e2c'], }), + ('nabor', '0.5.0', { + 'checksums': ['47938dcc987279281c13abfd667660bf1b3b76af116136a27eb066ee1a4b43da'], + }), + ('harmony', '0.1.0', { + 'checksums': ['e0598c220ae90d1334e47c9958ccccf7defbe6ac530159bc69424923894f724a'], + }), ] moduleclass = 'lang' From 8cd5adfdb0c8353ec81212c53d84a1c3ec479c0f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2022 12:44:01 +0100 Subject: [PATCH 3250/9987] add chromVAR extension to easyconfig for Bioconductor v3.14 --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index 53b854a4603..752d212b569 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1087,6 +1087,9 @@ exts_list = [ ('pathview', '1.34.0', { 'checksums': ['594e4b2dd4bb9e826fa87c63f56fbc9132e1b4b620696ec31ae0ebbc6940b4c9'], }), + ('chromVAR', '1.16.0', { + 'checksums': ['f3ea91fd13c2be56e3bd37991396876a6aba155b398200e01ae650404a769a7a'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From d065c5408196289838166adb92f90df576bb6ee1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 11 Mar 2022 12:48:26 +0100 Subject: [PATCH 3251/9987] {bio,math}[foss/2021b] ArchR v1.0.1, presto v1.0.0-20200718 w/ R v4.1.2 --- .../a/ArchR/ArchR-1.0.1-foss-2021b-R-4.1.2.eb | 27 +++++++++++++++++ ...resto-1.0.0-20200718-foss-2021b-R-4.1.2.eb | 29 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArchR/ArchR-1.0.1-foss-2021b-R-4.1.2.eb create mode 100644 easybuild/easyconfigs/p/presto/presto-1.0.0-20200718-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/a/ArchR/ArchR-1.0.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/a/ArchR/ArchR-1.0.1-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..a0cf6a907f4 --- /dev/null +++ b/easybuild/easyconfigs/a/ArchR/ArchR-1.0.1-foss-2021b-R-4.1.2.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'ArchR' +version = '1.0.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://www.archrproject.com' +description = "ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/GreenleafLab/ArchR/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e919fd25754fe87390aeee155c1d89c5319647b8b828b2827b99bc4617d9ff07'] + +dependencies = [ + ('R', '4.1.2'), + ('R-bundle-Bioconductor', '3.14', versionsuffix), + ('presto', '1.0.0-20200718', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/presto/presto-1.0.0-20200718-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/p/presto/presto-1.0.0-20200718-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..da212be4da9 --- /dev/null +++ b/easybuild/easyconfigs/p/presto/presto-1.0.0-20200718-foss-2021b-R-4.1.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'presto' +local_commit = '052085d' +# see DESCRIPTION to determine version, +# but also take date of last commit into account (since version isn't always bumped) +version = '1.0.0-20200718' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/immunogenomics/presto' +description = "Presto performs a fast Wilcoxon rank sum test and auROC analysis." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/immunogenomics/presto/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['464fda01f49020cbc9e6dea250fa05f81822259409e701e90882fab20cddbef5'] + +dependencies = [ + ('R', '4.1.2'), + ('R-bundle-Bioconductor', '3.14', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From 3ac0a26ac8c1161da1d43f6ded989b00b7a9bbf9 Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 11 Mar 2022 20:04:33 +0100 Subject: [PATCH 3252/9987] Add dependency to Grace/5.1.25 on tirpc to provide a required XDR library for the grconvert tool --- .../g/Grace/Grace-5.1.25-foss-2021a.eb | 7 +++- .../Grace/Grace-5.1.25-tirpc-dependency.patch | 32 +++++++++++++++++++ 2 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/Grace/Grace-5.1.25-tirpc-dependency.patch diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021a.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021a.eb index 2b67331ed94..58caa63a65a 100644 --- a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021a.eb +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021a.eb @@ -10,12 +10,17 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['751ab9917ed0f6232073c193aba74046037e185d73b77bab0f5af3e3ff1da2ac'] +patches = ['Grace-5.1.25-tirpc-dependency.patch'] +checksums = [ + '751ab9917ed0f6232073c193aba74046037e185d73b77bab0f5af3e3ff1da2ac', # grace-5.1.25.tar.gz + '093af4ddf344300aa31561c97e2765ed3fab609b70a5d199ac64a60dbd9e0c34', # Grace-5.1.25-tirpc-dependency.patch +] dependencies = [ ('motif', '2.3.8'), ('zlib', '1.2.11'), ('netCDF', '4.8.0'), + ('libtirpc', '1.3.2'), ] runtest = 'tests' diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-tirpc-dependency.patch b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-tirpc-dependency.patch new file mode 100644 index 00000000000..12d11fb2ce6 --- /dev/null +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-tirpc-dependency.patch @@ -0,0 +1,32 @@ +grconvert has a dependency on XDR from a RPC library and will be omitted +from the build if not present. + +On RedHat-like distros this is commonly missing and as such we add +libtirpc as a drop-in replacement for the OS packages that no longer +exist. + +Author: Lars Viklund (HPC2N) +diff -ru grace-5.1.25.orig/ac-tools/configure.in grace-5.1.25/ac-tools/configure.in +--- grace-5.1.25.orig/ac-tools/configure.in 2014-08-16 23:56:08.000000000 +0200 ++++ grace-5.1.25/ac-tools/configure.in 2022-03-11 19:51:21.025110130 +0100 +@@ -515,7 +515,7 @@ + fi + + dnl **** Check for XDR +-AC_SEARCH_LIBS(xdrstdio_create, nsl rpc xdr rpclib, XDR_LIB=$mdw_cv_lib_xdrstdio_create, XDR_LIB="NONE") ++AC_SEARCH_LIBS(xdrstdio_create, nsl rpc xdr rpclib tirpc, XDR_LIB=$mdw_cv_lib_xdrstdio_create, XDR_LIB="NONE") + + if test "${XDR_LIB}" = "NONE"; then + XDR_LIB= +diff -ru grace-5.1.25.orig/configure grace-5.1.25/configure +--- grace-5.1.25.orig/configure 2015-02-14 23:59:46.000000000 +0100 ++++ grace-5.1.25/configure 2022-03-11 19:50:45.678153923 +0100 +@@ -8000,7 +8000,7 @@ + return 0; + } + _ACEOF +-for ac_lib in '' nsl rpc xdr rpclib; do ++for ac_lib in '' nsl rpc xdr rpclib tirpc; do + if test -z "$ac_lib"; then + ac_res="none required" + else From 1711b580ecec5c22be8fc2f4d5b6ebf78aa997f1 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 11 Mar 2022 11:43:31 -0800 Subject: [PATCH 3253/9987] remove binutils --- easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.2.0.eb index 2d2ede9bd8e..d84729fec94 100644 --- a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.2.0.eb @@ -14,7 +14,6 @@ sources = ['v%(version)s.tar.gz'] checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] builddependencies = [ - ('binutils', '2.37'), ('CMake', '3.21.1'), ] From 6805603ad440f317204e0bf16a827838c53ed3f2 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Fri, 11 Mar 2022 21:00:40 +0100 Subject: [PATCH 3254/9987] Add Qhull dependency although it will link system Qhull if available --- .../easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb | 1 + .../easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb index b369894467f..7069e0d1495 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-foss-2020b.eb @@ -21,6 +21,7 @@ dependencies = [ ('freetype', '2.10.3'), ('Tkinter', '%(pyver)s'), ('Pillow', '8.0.1'), + ('Qhull', '2020.2') ] use_pip = True diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb index 0d03bf7e8cb..0c81a702dd4 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.1-intel-2020b.eb @@ -21,6 +21,7 @@ dependencies = [ ('freetype', '2.10.3'), ('Tkinter', '%(pyver)s'), ('Pillow', '8.0.1'), + ('Qhull', '2020.2') ] use_pip = True From 25776cba358d0e9785bee81624e89b4a0f9f7efb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Mar 2022 09:58:30 +0100 Subject: [PATCH 3255/9987] add libevent dependency for tmux with system toolchain --- .../easyconfigs/l/libevent/libevent-2.1.12.eb | 27 +++++++++++++++++++ easybuild/easyconfigs/t/tmux/tmux-3.2a.eb | 2 ++ 2 files changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12.eb new file mode 100644 index 00000000000..dc045c87868 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org' +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.2a.eb b/easybuild/easyconfigs/t/tmux/tmux-3.2a.eb index 420afee5473..66a9f07ce16 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-3.2a.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-3.2a.eb @@ -15,6 +15,8 @@ source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version sources = [SOURCE_TAR_GZ] checksums = ['551553a4f82beaa8dadc9256800bcc284d7c000081e47aa6ecbb6ff36eacd05f'] +dependencies = [('libevent', '2.1.12')] + sanity_check_paths = { 'files': ['bin/tmux'], 'dirs': [] From 41a7e5dae4ce2937fc8c1abae970f2fa67fd2ed7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Mar 2022 10:30:25 +0100 Subject: [PATCH 3256/9987] set $HTSLIB_DIR when configuring build of Bio-DB-HTS to ensure that HTSlib dependency is picked up --- .../easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb | 2 ++ .../easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb index 147bdf54a23..124fad4ecbe 100644 --- a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-10.2.0.eb @@ -20,6 +20,8 @@ dependencies = [ ('HTSlib', '1.11'), ] +preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB" + options = {'modulename': 'Bio::DB::HTS'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb index 58478248dbe..87359ee843c 100644 --- a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.2.0.eb @@ -20,6 +20,8 @@ dependencies = [ ('HTSlib', '1.14'), ] +preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB" + options = {'modulename': 'Bio::DB::HTS'} sanity_check_paths = { From 98e0d741b26d36a5d64463833b0c2b2c7c87e411 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Mar 2022 10:37:10 +0100 Subject: [PATCH 3257/9987] consistently use system toolchain in EasyBuild easyconfigs --- easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.4.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.0.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.0.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.3.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.4.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.0.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.2.eb | 2 +- easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.3.eb | 2 +- 21 files changed, 21 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.4.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.4.eb index a5005270c7a..dd3b35aa893 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.4.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-3.9.4.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # vsc-install diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.0.0.eb index 7791f784dcc..b13e5a86759 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.0.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.0.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.0.1.eb index cc8897da43b..02a74160afc 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.0.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.0.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.0.eb index 65b2ca298a7..25051461eb8 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.1.eb index 49247ea233b..4f6dc72e076 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.2.eb index e6ac20b851f..8896f8fe35e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.1.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.0.eb index b48d53735da..c010c13350f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.1.eb index 0ad8c5b4556..3e3fae6d858 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.2.eb index 1091c23897b..e77acbb055c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.2.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.0.eb index 9185e8fb088..e18538cfc10 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.1.eb index a3e700254a2..3115de22053 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.2.eb index 1e369883551..10cf17e0350 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.3.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.3.eb index 1b73dac291d..f1b3fda015a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.3.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.3.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.4.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.4.eb index 9771d8a0655..ecf5449b562 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.4.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.4.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.0.eb index e3711e34964..c17fd29c7f5 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.1.eb index fb230445037..ee6a0035569 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.2.eb index 442f64876f1..295e753564e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.4.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.0.eb index b3cc0ce5fe3..3522ff05e7a 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.0.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb index bc8db12a896..7f2ef294c1c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.1.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.2.eb index 94d49126b0b..4c088277872 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.2.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.3.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.3.eb index c8768ab9e83..db0436a30e8 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.3.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.3.eb @@ -8,7 +8,7 @@ description = """EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = [ # easybuild-framework From ff80fa2e27bb19a957dfc8012181eac2ef802905 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Mar 2022 11:06:32 +0100 Subject: [PATCH 3258/9987] remove exception for using dummy toolchain in EasyBuild easyconfigs --- test/easyconfigs/easyconfigs.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 95922f7a545..0cdc545fdac 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1214,11 +1214,9 @@ def template_easyconfig_test(self, spec): self.assertTrue(ec['version'], app.version) # make sure that deprecated 'dummy' toolchain is no longer used, should use 'system' toolchain instead - # but give recent EasyBuild easyconfigs special treatment to avoid breaking "eb --install-latest-eb-release" ec_fn = os.path.basename(spec) - if not (ec_fn == 'EasyBuild-3.9.4.eb' or ec_fn.startswith('EasyBuild-4.')): - error_msg_tmpl = "%s should use 'system' toolchain rather than deprecated 'dummy' toolchain" - self.assertFalse(ec['toolchain']['name'] == 'dummy', error_msg_tmpl % os.path.basename(spec)) + error_msg_tmpl = "%s should use 'system' toolchain rather than deprecated 'dummy' toolchain" + self.assertFalse(ec['toolchain']['name'] == 'dummy', error_msg_tmpl % os.path.basename(spec)) # make sure that $root is not used, since it is not compatible with module files in Lua syntax res = re.findall(r'.*\$root.*', ec.rawtxt, re.M) From 49b97e695c41feaedba07cdea49b3081f3f769c2 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Sun, 13 Mar 2022 21:50:23 +0000 Subject: [PATCH 3259/9987] use _minimap_ver for mappy version --- easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb index c485cbaae09..d3f817945e5 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb @@ -40,7 +40,7 @@ dependencies = [ use_pip = True exts_list = [ - ('mappy', '2.20', { + ('mappy', _minimap_ver, { 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], }), (name, version, { From 35a224292aa6a7e7a796b860d4b6a89db85c00b9 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Sun, 13 Mar 2022 22:23:41 +0000 Subject: [PATCH 3260/9987] Add test exception for TensorFlow version --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 95922f7a545..6809bcd0156 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -534,6 +534,8 @@ def check_dep_vars(self, gen, dep, dep_vars): ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), # AlphaFold 2.1.2 (foss/2020b) depends on TensorFlow 2.5.0 ('2.5.0;', ['AlphaFold-2.1.2-']), + # medaka 1.5.0 (foss/2021a) depends on TensorFlow >=2.5.2, <2.6.0 + ('2.5.3;', ['medaka-1.5.0-']), ], # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 # (for 2021b, UCX was updated to v1.11.2) From 14627180a7372e4629cb9e1b4240dfd8c6f5030d Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 14 Mar 2022 09:40:59 -0700 Subject: [PATCH 3261/9987] update MUMPS --- .../m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb | 35 +++++++++++ .../m/MUMPS/MUMPS-5.4.1_shared-mumps.patch | 62 +++++++++++++++++++ .../m/MUMPS/MUMPS-5.4.1_shared-pord.patch | 51 +++++++++++++++ 3 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-mumps.patch create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-pord.patch diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb new file mode 100644 index 00000000000..12da6473e5c --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb @@ -0,0 +1,35 @@ +name = 'MUMPS' +version = '5.4.1' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = """A parallel sparse direct solver""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + '93034a1a9fe0876307136dcde7e98e9086e199de76f1c47da822e7d4de987fa8', # MUMPS_5.4.1.tar.gz + '4c0558690998c12ca959c03856054a75e22f519583a65bd550393c1f81a0b170', # MUMPS-5.4.1_shared-pord.patch + 'd51c2df0de7d7b88d864ceba2d0eea46c755c24c7124003481aced106901109d', # MUMPS-5.4.1_shared-mumps.patch +] + +dependencies = [ + ('SCOTCH', '6.1.2'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-mumps.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-mumps.patch new file mode 100644 index 00000000000..edadcc4dc15 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-mumps.patch @@ -0,0 +1,62 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared.patch +Author: micketeer@gmail.com + +diff -ru MUMPS_5.4.0.orig/src/Makefile MUMPS_5.4.0/src/Makefile +--- MUMPS_5.4.0.orig/src/Makefile 2021-08-11 16:22:27.340180216 +0200 ++++ MUMPS_5.4.0/src/Makefile 2021-08-11 16:40:23.930257697 +0200 +@@ -15,18 +15,23 @@ + + libcommon: $(incdir)/mumps_int_def.h + $(MAKE) $(libdir)/libmumps_common$(PLAT)$(LIBEXT) ++ $(MAKE) $(libdir)/libmumps_common$(PLAT).so + + s: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT).so + + d: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT).so + + c: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT).so + + z: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT).so + + include $(topdir)/Makefile.inc + +@@ -200,6 +205,14 @@ + $(AR)$@ $? + $(RANLIB) $@ + ++$(libdir)/libmumps_common$(PLAT).so: $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) ++ $(FC) -shared $^ -Wl,-soname,libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) $(LORDERINGS) -lpthread $(MUMPS_LIBF77) $(MPIFLIB) $(MPICLIB) $(METISLIB) -o $(libdir)/libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libmumps_common$(PLAT)-$(SONAME_VERSION).so $@ ++ ++$(libdir)/lib$(ARITH)mumps$(PLAT).so: $(OBJS_MOD) $(OBJS_OTHER) ++ $(FC) -shared $^ -Wl,-soname,lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) -lmumps_common$(PLAT) -lpthread $(MUMPS_LIBF77) $(LORDERINGS) $(MPIFLIB) $(METISLIB) $(SCALAP) -o $(libdir)/lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $@ ++ + # Dependencies between modules: + # i) arithmetic-dependent modules: + $(ARITH)ana_aux.o: $(ARITH)mumps_struc_def.o \ +@@ -411,13 +424,13 @@ + + .SUFFIXES: .c .F .o + .F.o: +- $(FC) $(OPTF) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -c $*.F $(OUTF)$*.o ++ $(FC) $(OPTF) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -fPIC -c $*.F $(OUTF)$*.o + .c.o: +- $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -c $*.c $(OUTC)$*.o ++ $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -fPIC -c $*.c $(OUTC)$*.o + + $(ARITH)mumps_c.o: mumps_c.c + $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) -DMUMPS_ARITH=MUMPS_ARITH_$(ARITH) \ +- $(IORDERINGSC) $(ORDERINGSC) -c mumps_c.c $(OUTC)$@ ++ $(IORDERINGSC) $(ORDERINGSC) -fPIC -c mumps_c.c $(OUTC)$@ + + clean: + $(RM) *.o *.mod $(incdir)/mumps_int_def.h build_mumps_int_def diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-pord.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-pord.patch new file mode 100644 index 00000000000..704a8f66e07 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-pord.patch @@ -0,0 +1,51 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared-pord.patch +Author: micketeer@gmail.com + +diff -ru MUMPS_5.4.0.orig/Makefile MUMPS_5.4.0/Makefile +--- MUMPS_5.4.0.orig/Makefile 2021-08-11 21:41:30.209055262 +0200 ++++ MUMPS_5.4.0/Makefile 2021-08-11 21:41:40.633028157 +0200 +@@ -42,7 +42,7 @@ + + include Makefile.inc + +-prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) ++prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT).so + + # dummy MPI library (sequential version) + +@@ -59,6 +59,12 @@ + cp $(LPORDDIR)/libpord$(LIBEXT) $@; \ + fi; + ++$(libdir)/libpord$(PLAT).so: ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cd $(LPORDDIR); make CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" ARFUNCT= RANLIB="$(RANLIB)" libpord$(PLAT).so; fi; ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cp -a $(LPORDDIR)/libpord*.so lib/; fi; ++ + clean: + (cd src; $(MAKE) clean) + (cd examples; $(MAKE) clean) +diff -ru MUMPS_5.4.0.orig/PORD/lib/Makefile MUMPS_5.4.0/PORD/lib/Makefile +--- MUMPS_5.4.0.orig/PORD/lib/Makefile 2021-08-11 16:22:27.481179848 +0200 ++++ MUMPS_5.4.0/PORD/lib/Makefile 2021-08-11 16:59:17.511334981 +0200 +@@ -9,7 +9,7 @@ + + INCLUDES = -I../include + +-COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS) ++COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS) -fPIC + + OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \ + multisector.o gelim.o bucket.o tree.o \ +@@ -28,6 +28,10 @@ + $(AR)$@ $(OBJS) + $(RANLIB) $@ + ++libpord$(PLAT).so: $(OBJS) ++ $(CC) -shared $(OBJS) -Wl,-soname,libpord$(PLAT)-$(SONAME_VERSION).so -o libpord$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libpord$(PLAT)-$(SONAME_VERSION).so $@ ++ + clean: + rm -f *.o + From 7be840c9e8c4247269c91adf903c55cc3a06687f Mon Sep 17 00:00:00 2001 From: John Dey Date: Tue, 15 Mar 2022 09:53:52 -0700 Subject: [PATCH 3262/9987] Update easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb index 12da6473e5c..9d2406b03e5 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb @@ -11,8 +11,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['http://mumps.enseeiht.fr/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ - '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD - '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS + '%(name)s-5.4.0_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-5.4.0_shared-mumps.patch', # builds shared libs of MUMPS ] checksums = [ '93034a1a9fe0876307136dcde7e98e9086e199de76f1c47da822e7d4de987fa8', # MUMPS_5.4.1.tar.gz From be26698b7ec8febfee3073c4e82dae4a073fe9e1 Mon Sep 17 00:00:00 2001 From: John Dey Date: Tue, 15 Mar 2022 09:54:10 -0700 Subject: [PATCH 3263/9987] Update easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb index 9d2406b03e5..ce1f12d8b5d 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb @@ -16,8 +16,8 @@ patches = [ ] checksums = [ '93034a1a9fe0876307136dcde7e98e9086e199de76f1c47da822e7d4de987fa8', # MUMPS_5.4.1.tar.gz - '4c0558690998c12ca959c03856054a75e22f519583a65bd550393c1f81a0b170', # MUMPS-5.4.1_shared-pord.patch - 'd51c2df0de7d7b88d864ceba2d0eea46c755c24c7124003481aced106901109d', # MUMPS-5.4.1_shared-mumps.patch + '4c0558690998c12ca959c03856054a75e22f519583a65bd550393c1f81a0b170', # MUMPS-5.4.0_shared-pord.patch + 'd51c2df0de7d7b88d864ceba2d0eea46c755c24c7124003481aced106901109d', # MUMPS-5.4.0_shared-mumps.patch ] dependencies = [ From 62c87ff4b3946bbdd577f8fa84cf5f360927bcba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Mar 2022 19:06:55 +0100 Subject: [PATCH 3264/9987] adding easyconfigs: AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb --- .../AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb | 198 ++++++++++++++++++ 1 file changed, 198 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..c75f7804f24 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,198 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', True), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('TensorFlow', '2.6.0', versionsuffix), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.2.24', versionsuffix), # also provides absl-py + ('UCX-CUDA', '1.10.0', versionsuffix), + ('cuDNN', '8.2.1.32', versionsuffix, True), + ('NCCL', '2.10.3', versionsuffix), +] +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.1.2_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.1_fix-alphafold-tests.patch', + ], + 'checksums': [ + '37c92f31895c1f2cd5d8529176bc27a8d7db7659fff64e0c5f3f99ea35aadfb0', # v2.2.0.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '6af91706b2a001494ddc0947f89f8b3d3adfcc26177c373824fe8ea1a58c0b48', # AlphaFold-2.1.2_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + # AlphaFold-2.1_fix-alphafold-tests.patch + '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.2', { + 'checksums': ['6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33'], + }), + ('chex', '0.1.1', { + 'checksums': ['f319f04568d1a75951f59129973a7852eedab93c4a94f382a65c4d718d9857c1'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('jmp', '0.0.2', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['fdb5cec0d10aab4116c2770f24b2adf4f503fcfbb96ce8ef583e1879bdbf1b9b'], + }), + ('dm-haiku', '0.0.6', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['bb038d7b6eae50ad8b59aecaad7b26180261f155c9a789d071133cb2596dc616'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('websocket-client', '1.3.1', { + 'modulename': 'websocket', + 'checksums': ['6278a75065395418283f887de7c3beafb3aa68dada5cacbe4b214e8d26da499b'], + }), + ('docker', '5.0.3', { + 'checksums': ['d916a26b62970e7c2f554110ed6af04c7ccff8e9f81ad17d0d40c75637e227fb'], + }), + ('immutabledict', '2.2.1', { + 'checksums': ['1ddb0edf1bb6c70d0197eb90ce1fe2b2d58502334f5fdfde72d7c633d723ec3a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '4.0', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +moduleclass = 'bio' From 60e8180756ff476387431e89904bb563c9d05c16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2022 11:16:27 +0100 Subject: [PATCH 3265/9987] adding easyconfigs: loompy-3.0.7-foss-2021b.eb --- .../l/loompy/loompy-3.0.7-foss-2021b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2021b.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2021b.eb new file mode 100644 index 00000000000..dd391a5116b --- /dev/null +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'loompy' +version = '3.0.7' + +homepage = 'https://loompy.org/' +description = "Python implementation of the Loom file format, an efficient file format for large omics datasets" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), + ('numba', '0.54.1'), +] + +use_pip = True + +exts_list = [ + ('numpy_groupies', '0.9.14', { + 'checksums': ['01b7aeca60e643db34875c9823ea6775742adafe5bb406bca14367743ef81800'], + }), + (name, version, { + 'checksums': ['b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/loompy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["loompy --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 3f4d4c98cfdf444a375a9974f4e2ed65b7beea3e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Mar 2022 11:20:19 +0100 Subject: [PATCH 3266/9987] adding easyconfigs: loompy-3.0.7-intel-2021b.eb, numba-0.54.1-intel-2021b.eb --- .../l/loompy/loompy-3.0.7-intel-2021b.eb | 38 ++++++++++++ .../n/numba/numba-0.54.1-intel-2021b.eb | 58 +++++++++++++++++++ 2 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/l/loompy/loompy-3.0.7-intel-2021b.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.54.1-intel-2021b.eb diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-intel-2021b.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-intel-2021b.eb new file mode 100644 index 00000000000..2abaf74da36 --- /dev/null +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-intel-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'loompy' +version = '3.0.7' + +homepage = 'https://loompy.org/' +description = "Python implementation of the Loom file format, an efficient file format for large omics datasets" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), + ('numba', '0.54.1'), +] + +use_pip = True + +exts_list = [ + ('numpy_groupies', '0.9.14', { + 'checksums': ['01b7aeca60e643db34875c9823ea6775742adafe5bb406bca14367743ef81800'], + }), + (name, version, { + 'checksums': ['b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/loompy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["loompy --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/numba/numba-0.54.1-intel-2021b.eb b/easybuild/easyconfigs/n/numba/numba-0.54.1-intel-2021b.eb new file mode 100644 index 00000000000..81adc9acf49 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.54.1-intel-2021b.eb @@ -0,0 +1,58 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.54.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('LLVM', '12.0.1'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + +exts_list = [ + ('llvmlite', '0.37.0', { + 'patches': ['llvmlite-0.37.0_fix-LLVM-12.patch'], + 'preinstallopts': local_llvmlite_preinstallopts, + 'checksums': [ + '6392b870cd018ec0c645d6bbb918d6aa0eeca8c62674baaee30862d6b6865b15', # llvmlite-0.37.0.tar.gz + 'bcdc530cfd087e8a9f68a73a80fe73f12c7b2adfdb51ded70cd2f4c404846298', # llvmlite-0.37.0_fix-LLVM-12.patch + ], + }), + (name, version, { + 'patches': ['numba-0.54.1_fix-numpy-1.21.patch'], + 'checksums': [ + 'f9dfc803c864edcc2381219b800abf366793400aea55e26d4d5b7d953e14f43f', # numba-0.54.1.tar.gz + 'f038e7adf0cd60f6bdde219b326aad4224fef46515799578ebbbdffa73224199', # numba-0.54.1_fix-numpy-1.21.patch + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -m llvmlite.tests", + "numba --help", +] + +moduleclass = 'lang' From db9b3d2dd151893f13a56cc1378a511e67b589b1 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Wed, 16 Mar 2022 12:13:20 +0100 Subject: [PATCH 3267/9987] Added required changes --- .../easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 12 +++++------- .../easyconfigs/s/SCGid/SCGid-0.9b0-initEdit.patch | 6 +++--- 2 files changed, 8 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index 075fa463e28..ae5a90aa300 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -25,9 +25,8 @@ checksums = [ local_clams_commit = "e326c34307803b9ea8ffc975ddd9bd05643af931" -builddependencies = [('Python', '3.9.6')] - dependencies = [ + ('Python', '3.9.6'), ('R', '4.1.2'), ('BLAST+', '2.12.0'), ('AUGUSTUS', '3.4.0'), @@ -43,20 +42,19 @@ sanity_pip_check = True download_dep_fail = False exts_defaultclass = "Tarball" -local_config_path = "%(installdir)s/lib/python3.9/site-packages/config.yaml" -local_config_prep = "%%(installdir)s/SCGid-%s/config.yaml" % local_commit postinstallcmds = [ 'ln -s %%(installdir)s/ClaMS-CLI-fork-%s/ClaMS-CLI.jar %%(installdir)s/ClaMS-CLI.jar' % local_clams_commit, - 'export PATH=$PATH:$EBROOTAUGUSTUS', - 'export PATH=$PATH:$EBROOTBLAST', ] options = {'modulename': False} exts_list = [ ('ClaMS-CLI', '31012020', { - 'source_tmpl': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', + 'sources': [{ + 'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', + 'filename': 'ClaMS-CLI-%(version)s.tar.gz', + }], 'source_urls': ['https://github.com/amsesk/ClaMS-CLI-fork/archive'], 'checksums': ['743397fc8308e363f127bd7e5165ac9d769c10305f6e33d9e408db8f343170db'], }), diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-initEdit.patch b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-initEdit.patch index 100a47ea00c..ad73a7c4ac6 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-initEdit.patch +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-initEdit.patch @@ -7,9 +7,9 @@ diff -ruN SCGid-master-orig/scgid/config.py SCGid-master/scgid/config.py self.DB = os.path.join(self.HOME, 'database') self.initial_config = {} self.initial_config["mpicmd"] = "mpirun" -+ self.initial_config["clams_path"] = "%s/ClaMS-CLI.jar" % os.getenv("EBROOTSCGID") -+ self.initial_config["esom_path"] = os.getenv("EBROOTSCGID") -+ self.initial_config["path_to_Rscript"] = "%s/bin/Rscript" % os.getenv("EBROOTR") ++ self.initial_config["clams_path"] = "%s/ClaMS-CLI.jar" % os.getenv("EBROOTSCGID", "CLAMS_INSTALL_DIR_UNKNOWN") ++ self.initial_config["esom_path"] = os.getenv("EBROOTSCGID", "ESOM_INSTALL_DIR_UNKNOWN") ++ self.initial_config["path_to_Rscript"] = "%s/bin/Rscript" % os.getenv("EBROOTR", "RSCRIPT_INSTALL_DIR_UNKNOWN") def welcome(self): print (scgid_banner) From 984e6f7f448dd22c42b0a6cab3966ae11fa736c7 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 16 Mar 2022 13:52:57 +0100 Subject: [PATCH 3268/9987] Checksum fix --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index ae5a90aa300..a748d546bf3 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -51,11 +51,8 @@ options = {'modulename': False} exts_list = [ ('ClaMS-CLI', '31012020', { - 'sources': [{ - 'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', - 'filename': 'ClaMS-CLI-%(version)s.tar.gz', - }], 'source_urls': ['https://github.com/amsesk/ClaMS-CLI-fork/archive'], + 'sources': [{'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', 'filename': 'ClaMS-CLI-%(version)s.tar.gz'}], 'checksums': ['743397fc8308e363f127bd7e5165ac9d769c10305f6e33d9e408db8f343170db'], }), ('ESOM', '1.1', { @@ -71,8 +68,7 @@ exts_list = [ (5): Re-run the build. """, 'source_tmpl': 'esom.tar.gz', - # Checksum isn't used because user will be providing this extension - 'checksums': [None] + 'checksums': ['0a20649cbeb0d41fbda23137e9d21e306a3d6a642b895204a16b1128fad1c88f'], }), ] From c12f87defbceb1509e5552696ff1cb3ad5c07dbe Mon Sep 17 00:00:00 2001 From: agemuend Date: Wed, 16 Mar 2022 13:55:58 +0100 Subject: [PATCH 3269/9987] adding easyconfigs: IMB-2021.3-gompi-2021b.eb --- .../i/IMB/IMB-2021.3-gompi-2021b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2021b.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2021b.eb b/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2021b.eb new file mode 100644 index 00000000000..b2237fce1b3 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2021b.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '2021.3' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +docurls = ['https://software.intel.com/en-us/imb-user-guide'] + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/intel/mpi-benchmarks/archive/'] +sources = ['IMB-v%(version)s.tar.gz'] +checksums = ['9b58a4a7eef7c0c877513152340948402fd87cb06270d2d81308dc2ef740f4c7'] + +buildopts = 'all CC="$MPICC"' + +parallel = 1 + +files_to_copy = [(['IMB-*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-MT', + 'bin/IMB-NBC', 'bin/IMB-P2P', 'bin/IMB-RMA'], + 'dirs': [], +} + +moduleclass = 'perf' From ac60bcb1ca1e29bc9d5e462673878767373ec638 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Wed, 16 Mar 2022 14:56:28 +0100 Subject: [PATCH 3270/9987] Fix line length --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index a748d546bf3..ed03ed5cdcc 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -52,7 +52,10 @@ options = {'modulename': False} exts_list = [ ('ClaMS-CLI', '31012020', { 'source_urls': ['https://github.com/amsesk/ClaMS-CLI-fork/archive'], - 'sources': [{'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', 'filename': 'ClaMS-CLI-%(version)s.tar.gz'}], + 'sources': [{ + 'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', + 'filename': 'ClaMS-CLI-%(version)s.tar.gz' + }], 'checksums': ['743397fc8308e363f127bd7e5165ac9d769c10305f6e33d9e408db8f343170db'], }), ('ESOM', '1.1', { From afcefb112d7162a4ad8810859248866c38da3bf5 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Wed, 16 Mar 2022 15:50:35 +0100 Subject: [PATCH 3271/9987] final fix of checksums --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index ed03ed5cdcc..a62b9b2aaaa 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -20,7 +20,7 @@ checksums = [ # be106e4cd888fd913a527ea821e510e0afb100be.tar.gz '1f625e8f87b4d5e4ec9831ebe48763676679d6d6c41b05ef0bb59e6a7f839153', 'ee251b71ed3eed097b05751a3cea302d954000e1a8112e6e3f297e67c84996f7', # SCGid-0.9-fixPrintToPython3.patch - '5deb9911beef69bc127b966f94199511800069737f822e15ca5115a16d8b50c5', # SCGid-0.9b0-initEdit.patch + '7ae6759deffbb4f4c07943fd9aa44739e5b3d0e9ef724cee3e1dc03b71ad4735', # SCGid-0.9b0-initEdit.patch ] local_clams_commit = "e326c34307803b9ea8ffc975ddd9bd05643af931" From 6c5ac0940a383025ab1b33a370a081d939059d28 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 16 Mar 2022 15:53:31 +0100 Subject: [PATCH 3272/9987] Final checksum fix (hopefully) --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index a62b9b2aaaa..eac4e4fcf24 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -52,10 +52,7 @@ options = {'modulename': False} exts_list = [ ('ClaMS-CLI', '31012020', { 'source_urls': ['https://github.com/amsesk/ClaMS-CLI-fork/archive'], - 'sources': [{ - 'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', - 'filename': 'ClaMS-CLI-%(version)s.tar.gz' - }], + 'sources': [{'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', 'filename': 'ClaMS-CLI-%(version)s.tar.gz'}], 'checksums': ['743397fc8308e363f127bd7e5165ac9d769c10305f6e33d9e408db8f343170db'], }), ('ESOM', '1.1', { From a39736b43ce096b47e9f139617c75d7bbf6a1ec0 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Wed, 16 Mar 2022 16:35:04 +0100 Subject: [PATCH 3273/9987] Uploading correct version this time --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index eac4e4fcf24..a62b9b2aaaa 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -52,7 +52,10 @@ options = {'modulename': False} exts_list = [ ('ClaMS-CLI', '31012020', { 'source_urls': ['https://github.com/amsesk/ClaMS-CLI-fork/archive'], - 'sources': [{'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', 'filename': 'ClaMS-CLI-%(version)s.tar.gz'}], + 'sources': [{ + 'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', + 'filename': 'ClaMS-CLI-%(version)s.tar.gz' + }], 'checksums': ['743397fc8308e363f127bd7e5165ac9d769c10305f6e33d9e408db8f343170db'], }), ('ESOM', '1.1', { From 45ba13f8c4e34018bfb0e66cc227c73e8af6eb57 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 17 Mar 2022 14:31:19 +0100 Subject: [PATCH 3274/9987] adding easyconfigs: kallisto-0.48.0-gompi-2021b.eb --- .../k/kallisto/kallisto-0.48.0-gompi-2021b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021b.eb diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021b.eb new file mode 100644 index 00000000000..c5b823407ea --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021b.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.48.0' + +homepage = 'https://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'pachterlab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0'] + +builddependencies = [ + ('Autotools', '20210726'), + ('CMake', '3.22.1'), + ('zlib', '1.2.11'), +] + +dependencies = [('HDF5', '1.12.1')] + +preconfigopts = "cd ../%(name)s-%(version)s/ext/htslib/ && " +preconfigopts += "sed -i '/AC_PROG_CC/a AC_CANONICAL_HOST' configure.ac && " +preconfigopts += "autoreconf -i && cd - && " + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'bio' From d770adfeac154d2ccad870d2b3af56b01917a07d Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 17 Mar 2022 14:34:36 +0100 Subject: [PATCH 3275/9987] adding easyconfigs: PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 109 ++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..77af52bffea --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,109 @@ +name = 'PyTorch' +version = '1.11.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_skip_failing_ops_tests.patch', + 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', +] +checksums = [ + 'efdcba55555f46b63c97ccb55d2cd00588e12b95a005a0be7284e7cdef137a3b', # PyTorch-1.11.0.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_cmake_rpath.patch + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + '8f4a27303f8cba2ea90702e494365bf4a3e1c5ade9ed1311b63ad4289793e1af', # PyTorch-1.11.0_skip_failing_ops_tests.patch + '10d1f0db8254f7564500fe97f134c3b4fa89156839b5f771a9396d80a0a1ada4', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), + ('hypothesis', '6.13.1'), +] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.5'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.6.2'), + ('SciPy-bundle', '2021.05'), + ('typing-extensions', '3.10.0.0'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.2.0'), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('magma', '2.6.1', '-CUDA-%(cudaver)s'), + ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +custom_opts = ["USE_CUPTI_SO=1"] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + # 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + # 'distributed/rpc/test_process_group_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# The readelf sanity check can be taken out once the TestRPATH test from https://github.com/pytorch/pytorch/pull/68912 +# is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ +# CvL: does not work anymore, see https://github.com/facebookresearch/d2go/issues/137 +# It seems things might have been restructured and certain modules needed for this import are now part of torchvision or torchaudio +# "python -c 'import caffe2.python'", + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From 86f88c9db0f3f55ba1f782969eb0fef021528e89 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 17 Mar 2022 17:58:48 +0100 Subject: [PATCH 3276/9987] adding easyconfigs: MCR-R2022a.eb --- easybuild/easyconfigs/m/MCR/MCR-R2022a.eb | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2022a.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2022a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2022a.eb new file mode 100644 index 00000000000..f4e33dcd257 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2022a.eb @@ -0,0 +1,20 @@ +## +# Author: Robert Mijakovic +## +name = 'MCR' +version = 'R2022a' # runtime version 9.12 +local_update = '0' + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%(version)s_glnxa64.zip'] +checksums = ['ce013fa6d46148741ad55abaddd26d8d85d6fa4cf94917c8f3a66f350230cfc7'] + +moduleclass = 'math' From ebd2b1ff8f2f2fd83d7674b65bc8c568ef27c2e8 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 18 Mar 2022 09:56:11 +0100 Subject: [PATCH 3277/9987] Fixed style. Removed unneeded comment. --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 77af52bffea..0b2ccd5bebd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -95,13 +95,10 @@ excluded_tests = { runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' -# The readelf sanity check can be taken out once the TestRPATH test from https://github.com/pytorch/pytorch/pull/68912 -# is accepted, since it is then checked as part of the PyTorch test suite +# The readelf sanity check command can be taken out once the TestRPATH test from +# https://github.com/pytorch/pytorch/pull/68912 is accepted, since it is then checked as part of the PyTorch test suite local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT sanity_check_commands = [ -# CvL: does not work anymore, see https://github.com/facebookresearch/d2go/issues/137 -# It seems things might have been restructured and certain modules needed for this import are now part of torchvision or torchaudio -# "python -c 'import caffe2.python'", "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, ] tests = ['PyTorch-check-cpp-extension.py'] From 94ca2ec221c4c8f14a0e0fe4fe7cf4de1687792b Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 18 Mar 2022 12:31:30 +0100 Subject: [PATCH 3278/9987] Added missing patch --- ...11.0_increase-distributed-test-timeout.patch | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-distributed-test-timeout.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-distributed-test-timeout.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-distributed-test-timeout.patch new file mode 100644 index 00000000000..05ff461fc44 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-distributed-test-timeout.patch @@ -0,0 +1,17 @@ +It seems the timeout for the distributed tests is set to low and spurious failures can be seen +Increase it by a factor of 6 similar to torch/testing/_internal/distributed/distributed_test.py + +Original patch by Alexander Grund (TU Dresden), updated by Caspar van Leeuwen (SURF) + +diff -Nru pytorch-1.11.0-rc3.orig/torch/testing/_internal/common_distributed.py pytorch-1.11.0-rc3/torch/testing/_internal/common_distributed.py +--- pytorch-1.11.0-rc3.orig/torch/testing/_internal/common_distributed.py 2022-02-24 18:07:16.414274654 +0100 ++++ pytorch-1.11.0-rc3/torch/testing/_internal/common_distributed.py 2022-02-24 18:08:31.772851148 +0100 +@@ -321,7 +321,7 @@ + # TSAN runs much slower. + TIMEOUT_DEFAULT = 500 + else: +- TIMEOUT_DEFAULT = 100 ++ TIMEOUT_DEFAULT = 600 + TIMEOUT_OVERRIDE = {"test_ddp_uneven_inputs": 400} + + From e5e7301fb0aea581284d46daf7038fa035c46c1a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 18 Mar 2022 11:44:22 +0000 Subject: [PATCH 3279/9987] add apcluster, DataCombine, docstring, gdalUtils, openair, mstate, SNFtool, and deps to R v4.1.2 ec --- .../easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index fe0d3412dab..ce4464bb9aa 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3244,6 +3244,66 @@ exts_list = [ ('harmony', '0.1.0', { 'checksums': ['e0598c220ae90d1334e47c9958ccccf7defbe6ac530159bc69424923894f724a'], }), + ('apcluster', '1.4.9', { + 'checksums': ['3aac75e3e640eb89c1337d6f2e72a85d226b9c9483e43e0c76f9d424e758cb72'] + }), + ('DataCombine', '0.2.21', { + 'checksums': ['352b235612e2cf8234b3ab5f9aa6f7a394b006b98d24e315940ccc65c4218b47'] + }), + ('docstring', '1.0.0', { + 'checksums': ['14528bc85bbb299fb8fe1a7116034f8df49ae0c26fb299376185b5d56176e5a7'] + }), + ('gdalUtils', '2.0.3.2', { + 'checksums': ['4c6faabee2db8a87b7ea0f8e67e9fce3c5db7f4be353d7d86ea559507cbb2a4f'] + }), + ('openair', '2.8-6', { + 'checksums': ['37ffd9d6c5f5cebcd95720c6599f25f2e6c4fd3f6134f6aec026cb671ea373c0'] + }), + ('pdp', '0.7.0', { + 'checksums': ['28d69eb63b92bdf8e974b3222e1e9565000d7f15a3bd90854a8e0446b0fa9a71'] + }), + ('date', '1.2-39', { + 'checksums': ['b5b1935638b73373809c009f94b77f993cd301744488d9bdf71ef79c82099757'], + }), + ('cmprsk', '2.2-11', { + 'checksums': ['844027cb2c162cf7ef97034d01237ad7b81aa192fe302250d22d2c5528110e14'], + }), + ('mets', '1.2.9', { + 'checksums': ['5faccc064e715c44234def40f4f560e90f2dbd34c915a8687b48103b39814ab5'], + }), + ('Publish', '2020.12.23', { + 'checksums': ['a7a98fc52801bee30b9c8cb423e4e0082ea42d05134f7d3324ac3e95242cfbe2'], + }), + ('riskRegression', '2022.03.09', { + 'checksums': ['6b256cc54de81e8304f859fba7994d101ef972b6cad01b46050363fc48108dc6'], + }), + ('pec', '2022.03.06', { + 'checksums': ['d55e1d9b5786537ed127f3c470e8e139a9745969dea9a495afe13743a89883ec'], + }), + ('pammtools', '0.5.8', { + 'checksums': ['37197edd0984f8bf0e0a39a4ac1cfce897050dbb7f610553c349118fceb3ca93'], + }), + ('relsurv', '2.2-7', { + 'checksums': ['82c84bbe0a3eb9b391cbb885b3f3e7114adda5243aa83f974922d2edca918317'], + }), + ('mstate', '0.3.2', { + 'checksums': ['3c473dff6854e31cdbdaf79f8fe7eaf97119b01a581874a894b283555afe8d14'], + }), + ('microbenchmark', '1.4.9', { + 'checksums': ['443d2caf370ef33e4ac2773176ad9eb86f8790f43b430968ef9647699dbbffd2'], + }), + ('prettyGraphs', '2.1.6', { + 'checksums': ['fece08924fc7ed05ec419afa14a2216a2bb23d9da5ed3fc61472d6e45be7577a'], + }), + ('ExPosition', '2.8.23', { + 'checksums': ['0510bc51b1c8c883ff3652a5ed56242f91c2b7b7cf3100755436bffa1e002475'], + }), + ('alluvial', '0.1-2', { + 'checksums': ['77b6dc4651b33b03aaaf1e09a35f9c3536e5fddac2eda34f5a34e0ae33cf2e0d'], + }), + ('SNFtool', '2.3.1', { + 'checksums': ['982fe7c57f52c0c272b8cb5863dc5d50623b368e24ff6e27fc8b17acc0101f16'], + }), ] moduleclass = 'lang' From e8b2fd7d421e0cfa3e683dc23439a0acd6b37200 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 18 Mar 2022 13:33:04 +0100 Subject: [PATCH 3280/9987] Added more missing patches --- ...Torch-1.11.0_fix_skip_jit_cuda_fuser.patch | 428 ++++++++++++++++++ ...yTorch-1.11.0_skip_failing_ops_tests.patch | 26 ++ 2 files changed, 454 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_skip_failing_ops_tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch new file mode 100644 index 00000000000..4c698d6bff2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch @@ -0,0 +1,428 @@ +diff -Nru pytorch-1.11.0-rc3.orig/test/test_jit_cuda_fuser.py pytorch-1.11.0-rc3/test/test_jit_cuda_fuser.py +--- pytorch-1.11.0-rc3.orig/test/test_jit_cuda_fuser.py 2022-02-24 18:06:55.180421593 +0100 ++++ pytorch-1.11.0-rc3/test/test_jit_cuda_fuser.py 2022-02-25 13:30:47.112845480 +0100 +@@ -57,18 +57,25 @@ + torch._C._jit_set_nvfuser_horizontal_mode(old_value) + + def is_pre_volta(): +- prop = torch.cuda.get_device_properties(torch.cuda.current_device()) +- return prop.major < 7 +- +-TEST_BF16 = torch.cuda.is_bf16_supported() ++ if RUN_CUDA: ++ prop = torch.cuda.get_device_properties(torch.cuda.current_device()) ++ return prop.major < 7 ++ else: ++ return True ++ ++if RUN_CUDA: ++ TEST_BF16 = torch.cuda.is_bf16_supported() ++else: ++ TEST_BF16=False + + class TestCudaFuser(JitTestCase): + +- special_values = torch.tensor( +- [float("-inf"), -10, -math.pi, +- -1, -0.5, 0, 1, 0.5, +- math.pi, 10, float("inf"), +- float("nan")], dtype=torch.float, device='cuda') ++ if RUN_CUDA: ++ special_values = torch.tensor( ++ [float("-inf"), -10, -math.pi, ++ -1, -0.5, 0, 1, 0.5, ++ math.pi, 10, float("inf"), ++ float("nan")], dtype=torch.float, device='cuda') + + int_types = [ + torch.int8, +@@ -253,8 +260,8 @@ + self.assertEqual(o, jit_o) + self.assertGraphContains(t_jit.graph_for(x, y, z, q), FUSION_GUARD) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_reduction_dtypes_axis(self): +@@ -1120,8 +1127,8 @@ + self.assertTrue(self._compare("comparing output failed", o, jit_o, 1e-4)) + self.assertGraphContains(t_jit.graph_for(x, y), FUSION_GUARD) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_reduction(self): +@@ -1170,8 +1177,8 @@ + FileCheck().check(FUSION_GUARD).run(g) + FileCheck().check(FUSION_GUARD).run(v2.graph) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_layer_norm_autodiff(self): +@@ -1212,8 +1219,8 @@ + args.append(torch.randn(shapes, dtype=torch.float32, device="cuda").requires_grad_()) + self._layer_norm_autodiff_helper(m, grad, shapes, args) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_layer_norm_parser(self): +@@ -1273,8 +1280,8 @@ + self.assertGraphContains(t_jit.graph_for(x), FUSION_GUARD) + + @unittest.skipIf(True, "codegen failure awaiting fix") +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_native_layer_norm(self): +@@ -1288,8 +1295,8 @@ + self._native_layer_norm_helper(input_shape, norm_shape, torch.float32, "cuda", 1e-4, affine) + + @unittest.skipIf(True, "codegen failure awaiting fix") +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_native_layer_norm_half(self): +@@ -1301,8 +1308,8 @@ + norm_shape = [input_shape[idx] for idx in range(dims - offset, dims)] + self._native_layer_norm_helper(input_shape, norm_shape, torch.float16, "cuda", 5e-3) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + @unittest.skipIf(not TEST_BF16, "device does not support BFloat16") +@@ -1362,8 +1369,8 @@ + self.assertTrue(self._compare("comparing running_var failed", eager_running_var, jit_running_var, error)) + self.assertGraphContains(t_jit.graph_for(x, running_mean, running_var), FUSION_GUARD) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_norm_channels_last(self): +@@ -1374,8 +1381,8 @@ + for mf in [torch.channels_last, torch.contiguous_format]: + self._norm_helper(size, torch.float32, "cuda", 1e-4, is_batch_norm_else_instance_norm, memory_format=mf) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_norm(self): +@@ -1391,8 +1398,8 @@ + x[1] = C + self._norm_helper(x, torch.float32, "cuda", 1e-4, is_batch_norm_else_instance_norm) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_norm_large(self): +@@ -1407,8 +1414,8 @@ + x[1] = C + self._norm_helper(x, torch.float32, "cuda", 1e-4, is_batch_norm_else_instance_norm) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_norm_half(self): +@@ -1424,8 +1431,8 @@ + x[1] = C + self._norm_helper(x, torch.float16, "cuda", 5e-3, is_batch_norm_else_instance_norm) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + @unittest.skipIf(not TEST_BF16, "device does not support BFloat16") +@@ -1469,8 +1476,8 @@ + self.assertTrue(self._compare("comparing output failed", o, jit_o, error)) + self.assertGraphContains(t_jit.graph_for(x, y), FUSION_GUARD) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_softmax_dtype(self): +@@ -1511,8 +1518,8 @@ + )[0].graph + FileCheck().check(FUSION_GUARD).run(bwd_graph) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test__softmax_function(self): +@@ -1535,8 +1542,8 @@ + self.assertTrue(self._compare("comparing output failed", o, jit_o, 1e-3)) + self.assertGraphContainsExactly(t_jit.graph_for(x, y), FUSION_GUARD, 1, consider_subgraphs=True) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test__softmax_function_half_to_float(self): +@@ -1559,8 +1566,8 @@ + self.assertTrue(self._compare("comparing output failed", o, jit_o, 1e-3)) + self.assertGraphContainsExactly(t_jit.graph_for(x, y), FUSION_GUARD, 1, consider_subgraphs=True) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_softmax(self): +@@ -1575,8 +1582,8 @@ + x[reduction_dim] = reduction_size + self._softmax_helper(x, reduction_dim, torch.float32, "cuda", 1e-4) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_softmax_half(self): +@@ -1591,8 +1598,8 @@ + x[reduction_dim] = reduction_size + self._softmax_helper(x, reduction_dim, torch.float16, "cuda", 5e-3) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + @unittest.skipIf(not TEST_BF16, "device does not support BFloat16") +@@ -1608,8 +1615,8 @@ + x[reduction_dim] = reduction_size + self._softmax_helper(x, reduction_dim, torch.bfloat16, "cuda", 1e-1) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_reduction_permutation(self): +@@ -1622,8 +1629,8 @@ + for perm1 in itertools.permutations(range(len(x))): + self._reduction_helper(x, axes, torch.float32, "cuda", perm0, perm1) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_reduction_multiple_output(self): +@@ -1767,8 +1774,8 @@ + self.assertEqual(o, jit_o) + ''' + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_pw_single_reduction_partition(self): +@@ -1792,8 +1799,8 @@ + self.assertEqual(o, jit_o) + self.assertGraphContains(t_jit.graph_for(x, y, z), FUSION_GUARD) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_permutation_preservation(self): +@@ -1830,8 +1837,8 @@ + self.assertGraphContains(t_jit.graph_for(x), FUSION_GUARD) + self.assertTrue(jit_o.is_contiguous(memory_format=torch.channels_last)) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_normalization_partition(self): +@@ -1858,8 +1865,8 @@ + self.assertEqual(o, jit_o) + self.assertGraphContains(t_jit.graph_for(x, y, z, r_m, r_v), FUSION_GUARD) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_sum_to_one(self): +@@ -1879,8 +1886,8 @@ + self.assertEqual(o, jit_o) + self.assertGraphContains(t_jit.graph_for(x), FUSION_GUARD) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_single_reduction_broadcast(self): +@@ -1903,8 +1910,8 @@ + self.assertEqual(o, jit_o) + self.assertGraphContains(t_jit.graph_for(x, y, z), FUSION_GUARD) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_trivial_reduction(self): +@@ -1940,8 +1947,8 @@ + repro_jit = torch.jit.script(repro) + self._run_helper(repro_jit, repro, x, 0.6) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_reduction_sizes_op(self): +@@ -1964,8 +1971,8 @@ + # have been optimized away + self.assertGraphContainsExactly(t_jit.graph_for(x, y), FUSION_GUARD, 0) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_profile_ivalue(self): +@@ -1987,8 +1994,8 @@ + self.assertEqual(o, jit_o) + self.assertGraphContains(t_jit.graph_for(x, y, (0, 1), False), FUSION_GUARD) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_sum_to_size(self): +@@ -2021,8 +2028,8 @@ + self.assertEqual(o.dtype, jit_o.dtype) + self.assertEqual(o, jit_o) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_grad_sum_to_size(self): +@@ -2145,8 +2152,8 @@ + self.assertTrue((percent_zeros >= (prob - 0.01)) and (percent_zeros <= (prob + 0.01))) + self.assertGraphContainsExactly(t_jit.graph_for(x, prob, True), FUSION_GUARD, 1, consider_subgraphs=True) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_dropout_training_fusion(self): +@@ -2294,8 +2301,8 @@ + self.assertEqual(x.grad.dtype, x.dtype) + self.assertEqual(y.grad.dtype, y.dtype) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_autocast_1(self): +@@ -2331,8 +2338,8 @@ + self.assertEqual(x.grad.dtype, x.dtype) + self.assertEqual(y.grad.dtype, y.dtype) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_autocast_2(self): +@@ -2367,8 +2374,8 @@ + self.assertEqual(jit_o.dtype, torch.float) + self.assertEqual(x.grad.dtype, x.dtype) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + @unittest.skipIf(not TEST_BF16, "device does not support BFloat16") +@@ -2405,8 +2412,8 @@ + self.assertEqual(x.grad.dtype, x.dtype) + self.assertEqual(y.grad.dtype, y.dtype) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + @unittest.skipIf(not TEST_BF16, "device does not support BFloat16") +@@ -2817,8 +2824,8 @@ + ref_module.bn.running_var, + e0)) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_batch_norm_half(self): +@@ -2832,8 +2839,8 @@ + training, track_running_stats = training_and_track + self._test_batch_norm_impl_index_helper(4, 8, 5, affine, track_running_stats, training, torch.half) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_batch_norm_impl_index_correctness(self): +@@ -2947,8 +2954,8 @@ + self.assertGraphContainsExactly(graph, FUSION_GROUP, 0) + self.assertGraphContains(graph, 'prim::add_optional', True) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_remove_output_used_only_in_dtype(self): +@@ -2980,8 +2987,8 @@ + graph = jitted.graph_for(x, y) + self.assertGraphContains(graph, FUSION_GROUP, True) + +- @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_fix_shape_expression_bn(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_skip_failing_ops_tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_skip_failing_ops_tests.patch new file mode 100644 index 00000000000..3be9d13dc28 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_skip_failing_ops_tests.patch @@ -0,0 +1,26 @@ +diff -Nru pytorch-1.11.0-rc3.orig/torch/testing/_internal/common_methods_invocations.py pytorch-1.11.0-rc3/torch/testing/_internal/common_methods_invocations.py +--- pytorch-1.11.0-rc3.orig/torch/testing/_internal/common_methods_invocations.py 2022-02-24 18:07:16.430276050 +0100 ++++ pytorch-1.11.0-rc3/torch/testing/_internal/common_methods_invocations.py 2022-02-24 19:38:11.610293957 +0100 +@@ -8791,7 +8791,10 @@ + supports_fwgrad_bwgrad=True, + autodiff_fusible_nodes=['aten::contiguous'], + assert_jit_shape_analysis=True, +- supports_out=False), ++ supports_out=False, ++ skips=( ++ DecorateInfo(unittest.skip("Skipped!"), 'TestJit', 'test_variant_consistency_jit', device_type='cpu'), ++ )), + OpInfo('sum_to_size', + op=lambda x, *args, **kwargs: x.sum_to_size(*args, **kwargs), + dtypes=floating_and_complex_types_and(torch.float16, torch.bfloat16), +@@ -9746,6 +9749,10 @@ + DecorateInfo(unittest.skip("Skipped!"), 'TestMathBits', 'test_neg_view', device_type='cuda'), + DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), ++ # It also breaks on CPU. We'll revisit this once `linalg.lu_solve` is a thing ++ # See https://github.com/pytorch/pytorch/pull/64387 and https://github.com/pytorch/pytorch/issues/67767 ++ DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad', ++ dtypes=(torch.complex128,)), + )), + OpInfo('linalg.cholesky', + aten_name='linalg_cholesky', From 64b99c99bc7b206001b7aaef1748f49b5618943b Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 18 Mar 2022 16:41:22 +0100 Subject: [PATCH 3281/9987] Updated checksums --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 0b2ccd5bebd..f07ae433e38 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -29,7 +29,7 @@ patches = [ 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', ] checksums = [ - 'efdcba55555f46b63c97ccb55d2cd00588e12b95a005a0be7284e7cdef137a3b', # PyTorch-1.11.0.tar.gz + '603b16cc5d764c0d857663942591a50d175ba205a1054955d76ce179cd8b1730', # PyTorch-1.11.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch From ae85e99e7f5e6b37a7ffe544ca58f877c4d6e7cc Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 18 Mar 2022 16:45:44 +0100 Subject: [PATCH 3282/9987] adding easyconfigs: pyEGA3-4.0.0-GCCcore-11.2.0.eb and patches: pyega3-4.0.0-fixRequirements.patch --- .../p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb | 47 +++++++++++++++++++ .../pyEGA3/pyega3-4.0.0-fixRequirements.patch | 31 ++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/pyEGA3/pyega3-4.0.0-fixRequirements.patch diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..719c07934e0 --- /dev/null +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'pyEGA3' +version = '4.0.0' + +homepage = 'https://github.com/EGA-archive/ega-download-client' +description = """ A basic Python-based EGA download client """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('tqdm', '4.62.3'), +] + +use_pip = True + +exts_list = [ + ('humanize', version, { + 'checksums': ['ee1f872fdfc7d2ef4a28d4f80ddde9f96d36955b5d6b0dac4bdeb99502bddb00'], + }), + ('htsget', '0.2.5', { + 'checksums': ['d383dc36f699bd921f760f5500c8ed251e5f8358a7cc219c6c89c35d103e8045'], + }), + ('urllib3', '1.26.9', { + 'checksums': ['aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e'], + }), + (name, version, { + 'patches': ['pyega3-4.0.0-fixRequirements.patch'], + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': [ + '4a1582da6b3c018e69c9d6023cd0344372e7c3d6be19c8f3f75a5123b53de065', # pyega3-4.0.0.tar.gz + '9bf620a327b6743070ed85f3058d9e2d2fb1cf84b6775e499717d735c3c050da', # pyega3-4.0.0-fixRequirements.patch + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/pyega3'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyEGA3/pyega3-4.0.0-fixRequirements.patch b/easybuild/easyconfigs/p/pyEGA3/pyega3-4.0.0-fixRequirements.patch new file mode 100644 index 00000000000..5136aa3e2af --- /dev/null +++ b/easybuild/easyconfigs/p/pyEGA3/pyega3-4.0.0-fixRequirements.patch @@ -0,0 +1,31 @@ +pyEGA3 has strict version requirements, but included tests run even when +using newer versions. +Author: Orient Kružík (INUITS) +diff -ruN pyega3-4.0.0_orig/pyega3.egg-info/requires.txt pyega3-4.0.0/pyega3.egg-info/requires.txt +--- pyega3-4.0.0_orig/pyega3.egg-info/requires.txt 2021-12-09 14:09:53.000000000 +0100 ++++ pyega3-4.0.0/pyega3.egg-info/requires.txt 2022-03-18 16:17:16.080009959 +0100 +@@ -1,5 +1,5 @@ +-requests==2.26.0 +-tqdm==4.19.6 +-htsget==0.2.5 +-psutil==5.6.6 +-urllib3==1.26.7 ++requests>=2.26.0 ++tqdm>=4.19.6 ++htsget>=0.2.5 ++psutil>=5.6.6 ++urllib3>=1.26.7 +diff -ruN pyega3-4.0.0_orig/setup.py pyega3-4.0.0/setup.py +--- pyega3-4.0.0_orig/setup.py 2021-12-08 23:16:24.000000000 +0100 ++++ pyega3-4.0.0/setup.py 2022-03-18 16:24:03.075866555 +0100 +@@ -33,8 +33,8 @@ + author="EGA team", + author_email="ega-helpdesk@ebi.ac.uk", + python_requires=">=3.6", +- install_requires=["requests==2.26.0", "tqdm==4.19.6", "htsget==0.2.5", "psutil==5.6.6", "urllib3==1.26.7"], +- tests_require=["pytest~=6.2.5", "coverage==4.5.1", "responses~=0.16.0", "pyfakefs~=4.5.3"], ++ install_requires=["requests>=2.26.0", "tqdm>=4.19.6", "htsget>=0.2.5", "psutil>=5.6.6", "urllib3>=1.26.7"], ++ tests_require=["pytest~=6.2.5", "coverage>=4.5.1", "responses~=0.16.0", "pyfakefs~=4.5.3"], + keywords=["EGA", "archive"], + license="Apache License, Version 2.0", + url="https://github.com/EGA-archive/ega-download-client", From 1d49f5c1ee8a4e61561b8cb4104953eac7ea0578 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 18 Mar 2022 17:15:56 +0100 Subject: [PATCH 3283/9987] Updated checksums, a second time... --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index f07ae433e38..05246229707 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -29,7 +29,7 @@ patches = [ 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', ] checksums = [ - '603b16cc5d764c0d857663942591a50d175ba205a1054955d76ce179cd8b1730', # PyTorch-1.11.0.tar.gz + 'f34f3626a9f99108a4680122857e3d9963ab3450899278e6bbe2eedfa865c860', # PyTorch-1.11.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch From ccb8d3eb973aae8a68d819f1dab9184013929006 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 18 Mar 2022 18:28:04 +0100 Subject: [PATCH 3284/9987] Updated checksums, now setting the PyTorch-1.11.0 checksum to 'None'. Since it is the result of a git clone, and then tarring the result, the checksum is not reproducible. --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 05246229707..afd9d57bce2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -29,7 +29,7 @@ patches = [ 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', ] checksums = [ - 'f34f3626a9f99108a4680122857e3d9963ab3450899278e6bbe2eedfa865c860', # PyTorch-1.11.0.tar.gz + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch From 05eb8c4e7d6fce4074ae2be6c454e8b5bad8d891 Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Mon, 21 Mar 2022 12:03:56 +0100 Subject: [PATCH 3285/9987] Style changes - empty spaces deleted --- .../d/DIRAC/DIRAC-22.0-intel-2021a.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb new file mode 100644 index 00000000000..5b61eef87fd --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '22.0' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'i8': False} + +source_urls = ['https://zenodo.org/record/6010450/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('HDF5', '1.10.7') +] + +separate_build_dir = True + +configopts = ' -DCMAKE_Fortran_COMPILER=mpiifort ' +configopts += '-DEXTRA_FCFLAGS="''" ' +configopts += '-DCMAKE_C_COMPILER=mpiicc ' +configopts += '-DEXTRA_CFLAGS="''" ' +configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' +configopts += '-DEXTRA_CXXFLAGS="''" ' +configopts += '-DENABLE_BLAS=off ' +configopts += '-DENABLE_LAPACK=off ' +configopts += '-DMKL_FLAG=sequential ' +configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' +configopts += '-DBLAS_LANG=Fortran ' +configopts += '-DLAPACK_LANG=Fortran ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_OPENMP=False ' +configopts += '-DENABLE_CODE_COVERAGE=False ' +configopts += '-DENABLE_STATIC_LINKING=False ' +configopts += '-DENABLE_PROFILING=False ' +configopts += '-DENABLE_RUNTIMECHECK=False ' +configopts += '-DENABLE_64BIT_INTEGERS=False ' +configopts += '-DEXPLICIT_LIBS="off" ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' +configopts += '-G"Unix Makefiles" ' + +parallel = 4 + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' + +runtest = 'test ARGS="-R pam_test" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From 9f4b1cb094bde2ba3506c4a432a1cac8a296e047 Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Mon, 21 Mar 2022 12:08:35 +0100 Subject: [PATCH 3286/9987] Style changes n2 - empty spaces deleted --- .../d/DIRAC/DIRAC-22.0-foss-2021a.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb new file mode 100644 index 00000000000..04a2346149c --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '22.0' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'i8': False} + +source_urls = ['https://zenodo.org/record/6010450/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] + +builddependencies = [('CMake', '3.20.1', '', ('GCCcore', '10.3.0'))] + +dependencies = [ + ('Python', '3.9.5', '', ('GCCcore', '10.3.0')), + ('HDF5', '1.10.7', '', ('gompi', '2021a')) +] + +separate_build_dir = True + +configopts = ' -DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DEXTRA_FCFLAGS="''" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DEXTRA_CFLAGS="''" ' +configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' +configopts += '-DEXTRA_CXXFLAGS="''" ' +configopts += '-DENABLE_BLAS=auto ' +configopts += '-DENABLE_LAPACK=auto ' +configopts += '-DMKL_FLAG=off ' +configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' +configopts += '-DBLAS_LANG=Fortran ' +configopts += '-DLAPACK_LANG=Fortran ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_OPENMP=False ' +configopts += '-DENABLE_CODE_COVERAGE=False ' +configopts += '-DENABLE_STATIC_LINKING=False ' +configopts += '-DENABLE_PROFILING=False ' +configopts += '-DENABLE_RUNTIMECHECK=False ' +configopts += '-DENABLE_64BIT_INTEGERS=False ' +configopts += '-DEXPLICIT_LIBS="off" ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' +configopts += '-G"Unix Makefiles" ' + +parallel = 4 + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' + +runtest = 'test ARGS="-R pam_test" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From 87146bd001853fadd31e221867234b1429f8e32b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Mon, 21 Mar 2022 12:11:16 +0100 Subject: [PATCH 3287/9987] Delete DIRAC-22.0-foss-2021a-Python-3.9.5-mpi.eb --- .../DIRAC-22.0-foss-2021a-Python-3.9.5-mpi.eb | 64 ------------------- 1 file changed, 64 deletions(-) delete mode 100755 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5-mpi.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5-mpi.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5-mpi.eb deleted file mode 100755 index 6fc55a56778..00000000000 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a-Python-3.9.5-mpi.eb +++ /dev/null @@ -1,64 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'DIRAC' -version = '22.0' -versionsuffix = '-Python-%(pyver)s-mpi' - -homepage = 'http://www.diracprogram.org' -description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': True, 'i8': False} - -source_urls = ['https://zenodo.org/record/6010450/files/'] -sources = ['DIRAC-%(version)s-Source.tar.gz'] -checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] - -builddependencies = [('CMake', '3.20.1', '', ('GCCcore','10.3.0'))] - -dependencies = [ - ('Python', '3.9.5', '', ('GCCcore','10.3.0')), - ('HDF5', '1.10.7', '', ('gompi','2021a')) -] - -separate_build_dir = True - -configopts = ' -DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DEXTRA_FCFLAGS="''" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DEXTRA_CFLAGS="''" ' -configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' -configopts += '-DEXTRA_CXXFLAGS="''" ' -configopts += '-DENABLE_BLAS=auto ' -configopts += '-DENABLE_LAPACK=auto ' -configopts += '-DMKL_FLAG=off ' -configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' -configopts += '-DBLAS_LANG=Fortran ' -configopts += '-DLAPACK_LANG=Fortran ' -configopts += '-DENABLE_MPI=True ' -configopts += '-DENABLE_OPENMP=False ' -configopts += '-DENABLE_CODE_COVERAGE=False ' -configopts += '-DENABLE_STATIC_LINKING=False ' -configopts += '-DENABLE_PROFILING=False ' -configopts += '-DENABLE_RUNTIMECHECK=False ' -configopts += '-DENABLE_64BIT_INTEGERS=False ' -configopts += '-DEXPLICIT_LIBS="off" ' -configopts += '-DENABLE_EXATENSOR=off ' -configopts += '-DENABLE_PCMSOLVER=off ' -configopts += '-G"Unix Makefiles" ' - -parallel = 4 - -pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' -pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' - -runtest = 'test ARGS="-R pam_test" ' - -sanity_check_paths = { - 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], - 'dirs': ['share/dirac/basis'], -} - -sanity_check_commands = ["pam-dirac --help"] - -moduleclass = 'chem' From d84844a8a1745fec8acad5ef4b3a21adf9d3d94a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Mon, 21 Mar 2022 12:11:34 +0100 Subject: [PATCH 3288/9987] Delete DIRAC-22.0-intel-2021a-Python-3.9.5-mpi.eb --- ...DIRAC-22.0-intel-2021a-Python-3.9.5-mpi.eb | 64 ------------------- 1 file changed, 64 deletions(-) delete mode 100755 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5-mpi.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5-mpi.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5-mpi.eb deleted file mode 100755 index 38d7679911a..00000000000 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-Python-3.9.5-mpi.eb +++ /dev/null @@ -1,64 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'DIRAC' -version = '22.0' -versionsuffix = '-Python-%(pyver)s-mpi' - -homepage = 'http://www.diracprogram.org' -description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" - -toolchain = {'name': 'intel', 'version': '2021a'} -toolchainopts = {'usempi': True, 'i8': False} - -source_urls = ['https://zenodo.org/record/6010450/files/'] -sources = ['DIRAC-%(version)s-Source.tar.gz'] -checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] - -builddependencies = [('CMake', '3.20.1')] - -dependencies = [ - ('Python', '3.9.5'), - ('HDF5', '1.10.7') -] - -separate_build_dir = True - -configopts = ' -DCMAKE_Fortran_COMPILER=mpiifort ' -configopts += '-DEXTRA_FCFLAGS="''" ' -configopts += '-DCMAKE_C_COMPILER=mpiicc ' -configopts += '-DEXTRA_CFLAGS="''" ' -configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' -configopts += '-DEXTRA_CXXFLAGS="''" ' -configopts += '-DENABLE_BLAS=off ' -configopts += '-DENABLE_LAPACK=off ' -configopts += '-DMKL_FLAG=sequential ' -configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' -configopts += '-DBLAS_LANG=Fortran ' -configopts += '-DLAPACK_LANG=Fortran ' -configopts += '-DENABLE_MPI=True ' -configopts += '-DENABLE_OPENMP=False ' -configopts += '-DENABLE_CODE_COVERAGE=False ' -configopts += '-DENABLE_STATIC_LINKING=False ' -configopts += '-DENABLE_PROFILING=False ' -configopts += '-DENABLE_RUNTIMECHECK=False ' -configopts += '-DENABLE_64BIT_INTEGERS=False ' -configopts += '-DEXPLICIT_LIBS="off" ' -configopts += '-DENABLE_EXATENSOR=off ' -configopts += '-DENABLE_PCMSOLVER=off ' -configopts += '-G"Unix Makefiles" ' - -parallel = 4 - -pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' -pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' - -runtest = 'test ARGS="-R pam_test" ' - -sanity_check_paths = { - 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], - 'dirs': ['share/dirac/basis'], -} - -sanity_check_commands = ["pam-dirac --help"] - -moduleclass = 'chem' From aee9525b1c0074f5b548752a80054ba5344ba302 Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Mon, 21 Mar 2022 13:57:12 +0100 Subject: [PATCH 3289/9987] Cleaning unnecessary statements --- .../d/DIRAC/DIRAC-22.0-foss-2021a.eb | 28 ++++--------------- 1 file changed, 6 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb index 04a2346149c..8e1a71be798 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb @@ -7,49 +7,33 @@ homepage = 'http://www.diracprogram.org' description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': True, 'i8': False} +toolchainopts = {'usempi': True} source_urls = ['https://zenodo.org/record/6010450/files/'] sources = ['DIRAC-%(version)s-Source.tar.gz'] checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] -builddependencies = [('CMake', '3.20.1', '', ('GCCcore', '10.3.0'))] +builddependencies = [('CMake', '3.20.1')] dependencies = [ - ('Python', '3.9.5', '', ('GCCcore', '10.3.0')), - ('HDF5', '1.10.7', '', ('gompi', '2021a')) + ('Python', '3.9.5'), + ('HDF5', '1.10.7') ] separate_build_dir = True -configopts = ' -DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DEXTRA_FCFLAGS="''" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DEXTRA_CFLAGS="''" ' -configopts += '-DCMAKE_CXX_COMPILER=mpicxx ' -configopts += '-DEXTRA_CXXFLAGS="''" ' -configopts += '-DENABLE_BLAS=auto ' +configopts = '-DENABLE_BLAS=auto ' configopts += '-DENABLE_LAPACK=auto ' configopts += '-DMKL_FLAG=off ' -configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' -configopts += '-DBLAS_LANG=Fortran ' -configopts += '-DLAPACK_LANG=Fortran ' configopts += '-DENABLE_MPI=True ' configopts += '-DENABLE_OPENMP=False ' -configopts += '-DENABLE_CODE_COVERAGE=False ' -configopts += '-DENABLE_STATIC_LINKING=False ' -configopts += '-DENABLE_PROFILING=False ' -configopts += '-DENABLE_RUNTIMECHECK=False ' configopts += '-DENABLE_64BIT_INTEGERS=False ' -configopts += '-DEXPLICIT_LIBS="off" ' configopts += '-DENABLE_EXATENSOR=off ' configopts += '-DENABLE_PCMSOLVER=off ' configopts += '-G"Unix Makefiles" ' -parallel = 4 - pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' -pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' +pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' runtest = 'test ARGS="-R pam_test" ' From 5080ef55f9cb0bac97370156485a581583768a1f Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Mon, 21 Mar 2022 13:57:41 +0100 Subject: [PATCH 3290/9987] Cleaning unnecessary statements --- .../d/DIRAC/DIRAC-22.0-intel-2021a.eb | 22 +++---------------- 1 file changed, 3 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb index 5b61eef87fd..4e2660a0c21 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb @@ -7,7 +7,7 @@ homepage = 'http://www.diracprogram.org' description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" toolchain = {'name': 'intel', 'version': '2021a'} -toolchainopts = {'usempi': True, 'i8': False} +toolchainopts = {'usempi': True} source_urls = ['https://zenodo.org/record/6010450/files/'] sources = ['DIRAC-%(version)s-Source.tar.gz'] @@ -22,34 +22,18 @@ dependencies = [ separate_build_dir = True -configopts = ' -DCMAKE_Fortran_COMPILER=mpiifort ' -configopts += '-DEXTRA_FCFLAGS="''" ' -configopts += '-DCMAKE_C_COMPILER=mpiicc ' -configopts += '-DEXTRA_CFLAGS="''" ' -configopts += '-DCMAKE_CXX_COMPILER=mpiicpc ' -configopts += '-DEXTRA_CXXFLAGS="''" ' -configopts += '-DENABLE_BLAS=off ' +configopts = '-DENABLE_BLAS=off ' configopts += '-DENABLE_LAPACK=off ' configopts += '-DMKL_FLAG=sequential ' -configopts += '-DMATH_LIB_SEARCH_ORDER="MKL;ESSL;OPENBLAS;ATLAS;ACML;SYSTEM_NATIVE" ' -configopts += '-DBLAS_LANG=Fortran ' -configopts += '-DLAPACK_LANG=Fortran ' configopts += '-DENABLE_MPI=True ' configopts += '-DENABLE_OPENMP=False ' -configopts += '-DENABLE_CODE_COVERAGE=False ' -configopts += '-DENABLE_STATIC_LINKING=False ' -configopts += '-DENABLE_PROFILING=False ' -configopts += '-DENABLE_RUNTIMECHECK=False ' configopts += '-DENABLE_64BIT_INTEGERS=False ' -configopts += '-DEXPLICIT_LIBS="off" ' configopts += '-DENABLE_EXATENSOR=off ' configopts += '-DENABLE_PCMSOLVER=off ' configopts += '-G"Unix Makefiles" ' -parallel = 4 - pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' -pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' +pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' runtest = 'test ARGS="-R pam_test" ' From e0e745f59139cbe6d439527470e5ac417c06e50a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 21 Mar 2022 17:02:27 +0100 Subject: [PATCH 3291/9987] Cleanup PSolver and futile easyconfigs and add dynamic libs. --- .../f/futile/futile-1.8.3-foss-2020b.eb | 27 ++++++++++++------ .../f/futile/futile-1.8.3-foss-2021a.eb | 27 ++++++++++++------ .../f/futile/futile-1.8.3-foss-2021b.eb | 21 ++++++++------ .../f/futile/futile-1.8.3-intel-2020b.eb | 25 +++++++++++------ .../f/futile/futile-1.8.3-intel-2021a.eb | 25 +++++++++++------ .../f/futile/futile-1.8.3-intel-2021b.eb | 25 +++++++++++------ .../p/PSolver/PSolver-1.8.3-foss-2020b.eb | 28 +++++++++++-------- .../p/PSolver/PSolver-1.8.3-foss-2021a.eb | 28 +++++++++++-------- .../p/PSolver/PSolver-1.8.3-foss-2021b.eb | 28 +++++++++++-------- .../p/PSolver/PSolver-1.8.3-intel-2020b.eb | 27 ++++++++++-------- .../p/PSolver/PSolver-1.8.3-intel-2021a.eb | 27 ++++++++++-------- .../p/PSolver/PSolver-1.8.3-intel-2021b.eb | 27 ++++++++++-------- 12 files changed, 196 insertions(+), 119 deletions(-) diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb index 6648c32dd2c..3b00140697d 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2020b.eb @@ -10,27 +10,36 @@ description = """ """ toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] -checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] +patches = ['futile_index_bug.patch'] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + '5ef5f8ad7644259da0d2d2bcb64c44b923cb64b1eedf03898d0da18228ea392f', # futile_index_bug.patch +] unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" start_dir = "futile-%(version)s" -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCLAGS -fallow-argument-mismatch" ' -configopts += '--enable-mpi ' -configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' -configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' -configopts += '--with-yaml-path=$EBROOTLIBYAML ' +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('libyaml', '0.2.5'), +] + +preconfigopts = 'export FCFLAGS="$FCLAGS -fallow-argument-mismatch" && ' -dependencies = [('libyaml', '0.2.5')] +configopts = '--enable-dynamic-libraries ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' sanity_check_paths = { 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + - [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + ['lib/libfutile-1.a', 'lib/libfutile-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb index a684f70cf94..a5d1e9b1a63 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021a.eb @@ -10,27 +10,36 @@ description = """ """ toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': True} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] -checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] +patches = ['futile_index_bug.patch'] +checksums = [ + '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + '5ef5f8ad7644259da0d2d2bcb64c44b923cb64b1eedf03898d0da18228ea392f', # futile_index_bug.patch +] unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 && " unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" start_dir = "futile-%(version)s" -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCLAGS -fallow-argument-mismatch" ' -configopts += '--enable-mpi ' -configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' -configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' -configopts += '--with-yaml-path=$EBROOTLIBYAML ' +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('libyaml', '0.2.5'), +] + +preconfigopts = 'export FCFLAGS="$FCLAGS -fallow-argument-mismatch" && ' -dependencies = [('libyaml', '0.2.5')] +configopts = '--enable-dynamic-libraries ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' sanity_check_paths = { 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + - [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + ['lib/libfutile-1.a', 'lib/libfutile-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb index 0ef7202fe22..013ed079619 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-foss-2021b.eb @@ -10,7 +10,7 @@ description = """ """ toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'usempi': True} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] @@ -24,17 +24,22 @@ unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 & unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" start_dir = "futile-%(version)s" -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCLAGS -fallow-argument-mismatch" ' -configopts += '--enable-mpi ' -configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' -configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' -configopts += '--with-yaml-path=$EBROOTLIBYAML ' +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('libyaml', '0.2.5'), +] -dependencies = [('libyaml', '0.2.5')] +preconfigopts = 'export FCFLAGS="$FCLAGS -fallow-argument-mismatch" && ' + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' sanity_check_paths = { 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + - [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + ['lib/libfutile-1.a', 'lib/libfutile-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb index 318f3bb9b99..a06c36e332b 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2020b.eb @@ -10,13 +10,17 @@ description = """ """ toolchain = {'name': 'intel', 'version': '2020b'} -toolchainopts = {'usempi': True} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] -patches = ['futile_intel_bug.patch'] +patches = [ + 'futile_index_bug.patch', + 'futile_intel_bug.patch', +] checksums = [ '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + '5ef5f8ad7644259da0d2d2bcb64c44b923cb64b1eedf03898d0da18228ea392f', # futile_index_bug.patch 'e3681e6dda9364a1be4fba937423b8ac1774c3ebfd1ff04211482df25a188e95', # futile_intel_bug.patch ] @@ -24,17 +28,20 @@ unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 & unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" start_dir = "futile-%(version)s" -configopts = 'CC=$MPICC FC=$MPIFC ' -configopts += '--enable-mpi ' -configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' -configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' -configopts += '--with-yaml-path=$EBROOTLIBYAML ' +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('libyaml', '0.2.5'), +] -dependencies = [('libyaml', '0.2.5')] +configopts = '--enable-dynamic-libraries ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' sanity_check_paths = { 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + - [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + ['lib/libfutile-1.a', 'lib/libfutile-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb index dd385e85152..49a07900cb6 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021a.eb @@ -10,13 +10,17 @@ description = """ """ toolchain = {'name': 'intel', 'version': '2021a'} -toolchainopts = {'usempi': True} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] -patches = ['futile_intel_bug.patch'] +patches = [ + 'futile_index_bug.patch', + 'futile_intel_bug.patch', +] checksums = [ '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + '5ef5f8ad7644259da0d2d2bcb64c44b923cb64b1eedf03898d0da18228ea392f', # futile_index_bug.patch 'e3681e6dda9364a1be4fba937423b8ac1774c3ebfd1ff04211482df25a188e95', # futile_intel_bug.patch ] @@ -24,17 +28,20 @@ unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 & unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" start_dir = "futile-%(version)s" -configopts = 'CC=$MPICC FC=$MPIFC ' -configopts += '--enable-mpi ' -configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' -configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' -configopts += '--with-yaml-path=$EBROOTLIBYAML ' +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('libyaml', '0.2.5'), +] -dependencies = [('libyaml', '0.2.5')] +configopts = '--enable-dynamic-libraries ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' sanity_check_paths = { 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + - [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + ['lib/libfutile-1.a', 'lib/libfutile-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb index d0c0c3be36b..7d1b1f4cf7a 100644 --- a/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb +++ b/easybuild/easyconfigs/f/futile/futile-1.8.3-intel-2021b.eb @@ -10,13 +10,17 @@ description = """ """ toolchain = {'name': 'intel', 'version': '2021b'} -toolchainopts = {'usempi': True} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] -patches = ['futile_intel_bug.patch'] +patches = [ + 'futile_index_bug.patch', + 'futile_intel_bug.patch', +] checksums = [ '39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388', # bigdft-suite-1.8.3.tar.gz + '5ef5f8ad7644259da0d2d2bcb64c44b923cb64b1eedf03898d0da18228ea392f', # futile_index_bug.patch 'e3681e6dda9364a1be4fba937423b8ac1774c3ebfd1ff04211482df25a188e95', # futile_intel_bug.patch ] @@ -24,17 +28,20 @@ unpack_options = " spred-suite/futile-%(version_major_minor)s.tar.gz --strip 1 & unpack_options += "tar xzf futile-%(version_major_minor)s.tar.gz --transform='s,%(version_major_minor)s,%(version)s,'" start_dir = "futile-%(version)s" -configopts = 'CC=$MPICC FC=$MPIFC ' -configopts += '--enable-mpi ' -configopts += '--with-ext-linalg="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK ' -configopts += '-L$BLACS_LIB_DIR $LIBBLACS -L$LAPACK_LIB_DIR $LIBLAPACK -L$BLAS_LIB_DIR $LIBBLAS" ' -configopts += '--with-yaml-path=$EBROOTLIBYAML ' +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('libyaml', '0.2.5'), +] -dependencies = [('libyaml', '0.2.5')] +configopts = '--enable-dynamic-libraries ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' +configopts += '--with-yaml-path=$EBROOTLIBYAML ' sanity_check_paths = { 'files': ['include/futile.mod', 'include/futile.h', 'bin/futilevars.sh'] + - [('lib/libfutile-1.a', 'lib64/libfutile-1.a')], + ['lib/libfutile-1.a', 'lib/libfutile-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb index 34640f7529c..f0a3a90c1fc 100644 --- a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2020b.eb @@ -9,29 +9,35 @@ description = """ """ toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'usempi': True, 'opt': True} +toolchainopts = {'pic': True, 'usempi': True, 'opt': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] -local_cddir = ' cd psolver-%(version_major_minor)s && ' -preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I$EBROOTFUTILE/include" ' -configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ - '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' -configopts += ' --with-mpi3 ' -prebuildopts = local_cddir -preinstallopts = local_cddir +builddependencies = [ + ('pkg-config', '0.29.2'), +] dependencies = [ ('libyaml', '0.2.5'), - ('futile', '1.8.3') + ('futile', '1.8.3'), ] +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +preconfigopts += 'export FCFLAGS="$FCFLAGS -fallow-argument-mismatch" && ' + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-futile-incs=-I$EBROOTFUTILE/include ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' + +prebuildopts = local_cddir +preinstallopts = local_cddir + sanity_check_paths = { 'files': ['include/poisson_solver.mod'] + - [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + ['lib/libPSolver-1.a', 'lib/libPSolver-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb index 0f0b9fd1313..a7aa93b4f8e 100644 --- a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021a.eb @@ -9,29 +9,35 @@ description = """ """ toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': True, 'opt': True} +toolchainopts = {'pic': True, 'usempi': True, 'opt': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] -local_cddir = ' cd psolver-%(version_major_minor)s && ' -preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I$EBROOTFUTILE/include" ' -configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ - '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' -configopts += ' --with-mpi3 ' -prebuildopts = local_cddir -preinstallopts = local_cddir +builddependencies = [ + ('pkg-config', '0.29.2'), +] dependencies = [ ('libyaml', '0.2.5'), - ('futile', '1.8.3') + ('futile', '1.8.3'), ] +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +preconfigopts += 'export FCFLAGS="$FCFLAGS -fallow-argument-mismatch" && ' + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-futile-incs=-I$EBROOTFUTILE/include ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' + +prebuildopts = local_cddir +preinstallopts = local_cddir + sanity_check_paths = { 'files': ['include/poisson_solver.mod'] + - [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + ['lib/libPSolver-1.a', 'lib/libPSolver-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb index 9cfcdd477ce..d71e7d73b86 100644 --- a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-foss-2021b.eb @@ -9,29 +9,35 @@ description = """ """ toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'usempi': True, 'opt': True} +toolchainopts = {'pic': True, 'usempi': True, 'opt': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] -local_cddir = ' cd psolver-%(version_major_minor)s && ' -preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I$EBROOTFUTILE/include" ' -configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ - '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' -configopts += ' --with-mpi3 ' -prebuildopts = local_cddir -preinstallopts = local_cddir +builddependencies = [ + ('pkg-config', '0.29.2'), +] dependencies = [ ('libyaml', '0.2.5'), - ('futile', '1.8.3') + ('futile', '1.8.3'), ] +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir +preconfigopts += 'export FCFLAGS="$FCFLAGS -fallow-argument-mismatch" && ' + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-futile-incs=-I$EBROOTFUTILE/include ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' + +prebuildopts = local_cddir +preinstallopts = local_cddir + sanity_check_paths = { 'files': ['include/poisson_solver.mod'] + - [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + ['lib/libPSolver-1.a', 'lib/libPSolver-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb index df8ca360b55..beb8698e910 100644 --- a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2020b.eb @@ -9,29 +9,34 @@ description = """ """ toolchain = {'name': 'intel', 'version': '2020b'} -toolchainopts = {'usempi': True, 'opt': True} +toolchainopts = {'pic': True, 'usempi': True, 'opt': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] -local_cddir = ' cd psolver-%(version_major_minor)s && ' -preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -I$EBROOTFUTILE/include" ' -configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ - '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' -configopts += ' --with-mpi3 ' -prebuildopts = local_cddir -preinstallopts = local_cddir +builddependencies = [ + ('pkg-config', '0.29.2'), +] dependencies = [ ('libyaml', '0.2.5'), - ('futile', '1.8.3') + ('futile', '1.8.3'), ] +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-futile-incs=-I$EBROOTFUTILE/include ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' + +prebuildopts = local_cddir +preinstallopts = local_cddir + sanity_check_paths = { 'files': ['include/poisson_solver.mod'] + - [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + ['lib/libPSolver-1.a', 'lib/libPSolver-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb index d4e348ef4fb..f43a10e3771 100644 --- a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021a.eb @@ -9,29 +9,34 @@ description = """ """ toolchain = {'name': 'intel', 'version': '2021a'} -toolchainopts = {'usempi': True, 'opt': True} +toolchainopts = {'pic': True, 'usempi': True, 'opt': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] -local_cddir = ' cd psolver-%(version_major_minor)s && ' -preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -I$EBROOTFUTILE/include" ' -configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ - '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' -configopts += ' --with-mpi3 ' -prebuildopts = local_cddir -preinstallopts = local_cddir +builddependencies = [ + ('pkg-config', '0.29.2'), +] dependencies = [ ('libyaml', '0.2.5'), - ('futile', '1.8.3') + ('futile', '1.8.3'), ] +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-futile-incs=-I$EBROOTFUTILE/include ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' + +prebuildopts = local_cddir +preinstallopts = local_cddir + sanity_check_paths = { 'files': ['include/poisson_solver.mod'] + - [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + ['lib/libPSolver-1.a', 'lib/libPSolver-1.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb index f87fa8bf98e..f8bcc82b6ec 100644 --- a/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb +++ b/easybuild/easyconfigs/p/PSolver/PSolver-1.8.3-intel-2021b.eb @@ -9,29 +9,34 @@ description = """ """ toolchain = {'name': 'intel', 'version': '2021b'} -toolchainopts = {'usempi': True, 'opt': True} +toolchainopts = {'pic': True, 'usempi': True, 'opt': True} source_urls = ['https://launchpad.net/bigdft/%(version_major_minor)s/%(version)s/+download/'] sources = ['bigdft-suite-%(version)s.tar.gz'] checksums = ['39aeae8bd62ad5d82ed20a47006aa478d93b3751ae7929027088c2e6b8439388'] -local_cddir = ' cd psolver-%(version_major_minor)s && ' -preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir -configopts = 'CC=$MPICC FC=$MPIFC FCFLAGS="$FCFLAGS -I$EBROOTFUTILE/include" ' -configopts += ' --with-ext-linalg="-L$BLACS_LIB_DIR $LIBBLACS -L$SCALAPACK_LIB_DIR $LIBSCALAPACK"'\ - '" -L$BLAS_LIB_DIR $LIBBLAS -L$LAPACK_LIB_DIR $LIBLAPACK" ' -configopts += ' --with-mpi3 ' -prebuildopts = local_cddir -preinstallopts = local_cddir +builddependencies = [ + ('pkg-config', '0.29.2'), +] dependencies = [ ('libyaml', '0.2.5'), - ('futile', '1.8.3') + ('futile', '1.8.3'), ] +local_cddir = ' cd psolver-%(version_major_minor)s && ' +preconfigopts = 'tar xzf psolver-%(version_major_minor)s.tar.gz &&' + local_cddir + +configopts = '--enable-dynamic-libraries ' +configopts += '--with-futile-incs=-I$EBROOTFUTILE/include ' +configopts += '--with-ext-linalg="$LIBSCALAPACK" ' + +prebuildopts = local_cddir +preinstallopts = local_cddir + sanity_check_paths = { 'files': ['include/poisson_solver.mod'] + - [('lib/libPSolver-1.a', 'lib64/libPSolver-1.a')], + ['lib/libPSolver-1.a', 'lib/libPSolver-1.%s' % SHLIB_EXT], 'dirs': [] } From 4592986f1df840513e6e353b72fe24184c91a37e Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Mon, 21 Mar 2022 17:33:21 +0100 Subject: [PATCH 3292/9987] Cleaning separate_build_dir statement --- easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb index 8e1a71be798..11637777210 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb @@ -20,8 +20,6 @@ dependencies = [ ('HDF5', '1.10.7') ] -separate_build_dir = True - configopts = '-DENABLE_BLAS=auto ' configopts += '-DENABLE_LAPACK=auto ' configopts += '-DMKL_FLAG=off ' From 261295434e9b41a1047156dcff490aa82a484509 Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Mon, 21 Mar 2022 17:34:56 +0100 Subject: [PATCH 3293/9987] Cleaning separate_build_dir statement --- easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb index 4e2660a0c21..1ab048a1f46 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb @@ -20,8 +20,6 @@ dependencies = [ ('HDF5', '1.10.7') ] -separate_build_dir = True - configopts = '-DENABLE_BLAS=off ' configopts += '-DENABLE_LAPACK=off ' configopts += '-DMKL_FLAG=sequential ' From 9288784cffb9ee1424ca3700bed9957580fe7a12 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 22 Mar 2022 09:45:24 +0100 Subject: [PATCH 3294/9987] fix likwid include_GCC.mk use of ifort for GCC based toolchain, and add 5.2.0 for GCCcore/10.3.0 --- .../l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb | 22 +++++--- .../l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb | 50 +++++++++++++++++++ 2 files changed, 66 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb index eaef19cf7ae..596c9ce7877 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb @@ -6,9 +6,9 @@ version = '5.2.0' homepage = 'https://github.com/RRZE-HPC/likwid' description = """ - Likwid stands for Like I knew what I am doing. This project contributes easy - to use command line tools for Linux to support programmers in developing high - performance multi threaded programs. +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} @@ -18,16 +18,26 @@ source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] -builddependencies = [('binutils', '2.35')] +builddependencies = [ + ('binutils', '2.35'), + ('Perl', '5.32.0'), +] skipsteps = ['configure'] -buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ' +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCCcore toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' maxparallel = 1 -installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ=""' +installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ="" ACCESSMODE=perf_event ' sanity_check_paths = { 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..59b72f28dae --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Perl', '5.32.1'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCCcore toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' + +maxparallel = 1 + +installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ="" ACCESSMODE=perf_event ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' From 1fcdeea5045f01b377e552d87d19706ae17b065b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 22 Mar 2022 09:50:50 +0100 Subject: [PATCH 3295/9987] adding easyconfigs: libpspio-0.2.4-GCC-10.3.0.eb --- .../l/libpspio/libpspio-0.2.4-GCC-10.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.3.0.eb new file mode 100644 index 00000000000..a312e575a59 --- /dev/null +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-10.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpspio' +version = '0.2.4' + +homepage = 'https://gitlab.e-cam2020.eu/esl/pspio/' +description = """libpspio is a library to read and write pseudopotentials in multiple formats.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://gitlab.e-cam2020.eu/esl/pspio/uploads/7efa924be97bd46354237ca3fb89495e/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cb3d51ffa6b822305bb943edc7ddfaf1cfc1b928f0594330d732330bfc081850'] + +dependencies = [('GSL', '2.7')] + +configopts = ' --enable-gsl --enable-fortran ' + +sanity_check_paths = { + 'files': ['include/pspiof_m.mod', 'include/pspio.h', 'lib/libpspiof.a'], + 'dirs': [], +} + +moduleclass = 'phys' From ad8dc9c463bc68649c01fb8a5cdcf9da393d6af9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Mar 2022 12:44:52 +0100 Subject: [PATCH 3296/9987] add EnsDb.Hsapiens.v79 extension to R-bundle-Bioconductor v3.14 --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index 752d212b569..5776a16610b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1090,6 +1090,9 @@ exts_list = [ ('chromVAR', '1.16.0', { 'checksums': ['f3ea91fd13c2be56e3bd37991396876a6aba155b398200e01ae650404a769a7a'], }), + ('EnsDb.Hsapiens.v79', '2.99.0', { + 'checksums': ['eff1ae8d7f4ed5c6bed335de63a758be593750fb0b3483c01cf50402688d244d'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 72e20ed62c4a2f2963cbdf593b9199d309628a3c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 22 Mar 2022 13:01:08 +0100 Subject: [PATCH 3297/9987] use EB built hwloc. --- .../l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb | 9 +++++- .../l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb | 12 ++++++-- .../l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb | 9 +++++- .../l/likwid/likwid-5.2.0_use_EB_hwloc.patch | 30 +++++++++++++++++++ .../l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb | 9 +++++- 5 files changed, 64 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0_use_EB_hwloc.patch diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb index 596c9ce7877..f014047abe0 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb @@ -16,6 +16,9 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_EB_hwloc.patch', +] checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] builddependencies = [ @@ -23,6 +26,10 @@ builddependencies = [ ('Perl', '5.32.0'), ] +dependencies = [ + ('hwloc', '2.2.0'), +] + skipsteps = ['configure'] # include_GCC.mk is using ifort by default. @@ -37,7 +44,7 @@ buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(inst maxparallel = 1 -installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ="" ACCESSMODE=perf_event ' +installopts = buildopts + 'INSTALL_CHOWN="" ' sanity_check_paths = { 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb index 59b72f28dae..4b3ebe531f7 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb @@ -16,6 +16,9 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_EB_hwloc.patch', +] checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] builddependencies = [ @@ -23,6 +26,10 @@ builddependencies = [ ('Perl', '5.32.1'), ] +dependencies = [ + ('hwloc', '2.4.1'), +] + skipsteps = ['configure'] # include_GCC.mk is using ifort by default. @@ -33,11 +40,12 @@ prebuildopts += """ make/include_GCC.mk && """ buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' buildopts += 'FORTRAN_INTERFACE=true ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' maxparallel = 1 -installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ="" ACCESSMODE=perf_event ' +installopts = buildopts + 'INSTALL_CHOWN="" ' sanity_check_paths = { 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb index ff19c3f5246..eb247379ff2 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb @@ -16,6 +16,9 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_EB_hwloc.patch', +] checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] builddependencies = [ @@ -23,6 +26,10 @@ builddependencies = [ ('Perl', '5.34.0'), ] +dependencies = [ + ('hwloc', '2.5.0'), +] + skipsteps = ['configure'] # include_GCC.mk is using ifort by default. @@ -37,7 +44,7 @@ buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(inst maxparallel = 1 -installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ="" ACCESSMODE=perf_event ' +installopts = buildopts + 'INSTALL_CHOWN="" ' sanity_check_paths = { 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0_use_EB_hwloc.patch b/easybuild/easyconfigs/l/likwid/likwid-5.2.0_use_EB_hwloc.patch new file mode 100644 index 00000000000..c57c2895f31 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0_use_EB_hwloc.patch @@ -0,0 +1,30 @@ +Don't try to install hwloc into likwids libdir + +Åke Sandgren, 2022-03-22 +diff -ru likwid-5.2.0.orig/Makefile likwid-5.2.0/Makefile +--- likwid-5.2.0.orig/Makefile 2021-06-18 18:13:47.000000000 +0200 ++++ likwid-5.2.0/Makefile 2022-03-22 11:49:17.234166402 +0100 +@@ -484,7 +484,9 @@ + @chmod 755 $(LIBPREFIX) + @install -m 755 $(TARGET_LIB) $(LIBPREFIX)/$(TARGET_LIB).$(VERSION).$(RELEASE) + @install -m 755 liblikwidpin.so $(LIBPREFIX)/liblikwidpin.so.$(VERSION).$(RELEASE) +- @install -m 755 $(TARGET_HWLOC_LIB) $(LIBPREFIX)/$(shell basename $(TARGET_HWLOC_LIB)).$(VERSION).$(RELEASE) ++ @if [ "$(USE_INTERNAL_HWLOC)" = "true" ]; then \ ++ install -m 755 $(TARGET_HWLOC_LIB) $(LIBPREFIX)/$(shell basename $(TARGET_HWLOC_LIB)).$(VERSION).$(RELEASE); \ ++ fi + @if [ "$(LUA_INTERNAL)" = "true" ]; then \ + install -m 755 $(TARGET_LUA_LIB) $(LIBPREFIX)/$(shell basename $(TARGET_LUA_LIB)).$(VERSION).$(RELEASE); \ + fi +@@ -492,8 +494,10 @@ + @cd $(LIBPREFIX) && ln -fs $(TARGET_LIB).$(VERSION).$(RELEASE) $(TARGET_LIB).$(VERSION) + @cd $(LIBPREFIX) && ln -fs $(PINLIB).$(VERSION).$(RELEASE) $(PINLIB) + @cd $(LIBPREFIX) && ln -fs $(PINLIB).$(VERSION).$(RELEASE) $(PINLIB).$(VERSION) +- @cd $(LIBPREFIX) && ln -fs $(shell basename $(TARGET_HWLOC_LIB)).$(VERSION).$(RELEASE) $(shell basename $(TARGET_HWLOC_LIB)) +- @cd $(LIBPREFIX) && ln -fs $(shell basename $(TARGET_HWLOC_LIB)).$(VERSION).$(RELEASE) $(shell basename $(TARGET_HWLOC_LIB)).$(VERSION) ++ @if [ "$(USE_INTERNAL_HWLOC)" = "true" ]; then \ ++ cd $(LIBPREFIX) && ln -fs $(shell basename $(TARGET_HWLOC_LIB)).$(VERSION).$(RELEASE) $(shell basename $(TARGET_HWLOC_LIB)); \ ++ cd $(LIBPREFIX) && ln -fs $(shell basename $(TARGET_HWLOC_LIB)).$(VERSION).$(RELEASE) $(shell basename $(TARGET_HWLOC_LIB)).$(VERSION); \ ++ fi + @if [ "$(LUA_INTERNAL)" = "true" ]; then \ + cd $(LIBPREFIX) && ln -fs $(shell basename $(TARGET_LUA_LIB)).$(VERSION).$(RELEASE) $(shell basename $(TARGET_LUA_LIB)); \ + cd $(LIBPREFIX) && ln -fs $(shell basename $(TARGET_LUA_LIB)).$(VERSION).$(RELEASE) $(shell basename $(TARGET_LUA_LIB)).$(VERSION); \ diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb index f7786e5726d..5698b2349d9 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb @@ -16,6 +16,9 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-5.2.0_use_EB_hwloc.patch', +] checksums = ['1b8e668da117f24302a344596336eca2c69d2bc2f49fa228ca41ea0688f6cbc2'] builddependencies = [ @@ -23,6 +26,10 @@ builddependencies = [ ('Perl', '5.34.0'), ] +dependencies = [ + ('hwloc', '2.5.0'), +] + skipsteps = ['configure'] # include_GCC.mk is using ifort by default. @@ -37,7 +44,7 @@ buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(inst maxparallel = 1 -installopts = 'PREFIX=%(installdir)s INSTALL_CHOWN="" BUILDFREQ="" ACCESSMODE=perf_event ' +installopts = buildopts + 'INSTALL_CHOWN="" ' sanity_check_paths = { 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', From 7198ec954c4a6d1f7fc6e9da5e8405cb04710778 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 22 Mar 2022 13:07:49 +0100 Subject: [PATCH 3298/9987] raise likwid to GCC/intel-compiler level due to Fortran modules usage. --- .../l/likwid/likwid-5.2.0-GCC-10.2.0.eb | 56 ++++++++++++++++++ .../l/likwid/likwid-5.2.0-GCC-10.3.0.eb | 57 +++++++++++++++++++ .../l/likwid/likwid-5.2.0-GCC-11.2.0.eb | 56 ++++++++++++++++++ .../l/likwid/likwid-5.2.1-GCC-11.2.0.eb | 56 ++++++++++++++++++ 4 files changed, 225 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..7e6a0d4e6b9 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_EB_hwloc.patch', +] +checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] + +builddependencies = [ + ('Perl', '5.32.0'), +] + +dependencies = [ + ('hwloc', '2.2.0'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCC toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..d83ae4828a1 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.3.0.eb @@ -0,0 +1,57 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_EB_hwloc.patch', +] +checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] + +builddependencies = [ + ('Perl', '5.32.1'), +] + +dependencies = [ + ('hwloc', '2.4.1'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCC toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..25303bb7bed --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_EB_hwloc.patch', +] +checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] + +builddependencies = [ + ('Perl', '5.34.0'), +] + +dependencies = [ + ('hwloc', '2.5.0'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCC toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..c06a59f32da --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.1' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-5.2.0_use_EB_hwloc.patch', +] +checksums = ['1b8e668da117f24302a344596336eca2c69d2bc2f49fa228ca41ea0688f6cbc2'] + +builddependencies = [ + ('Perl', '5.34.0'), +] + +dependencies = [ + ('hwloc', '2.5.0'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCC toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' From b3ac9873dcaea049b614e75d4a33d7ec0353a302 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 22 Mar 2022 13:09:40 +0100 Subject: [PATCH 3299/9987] drop GCCcore versions of likwid --- .../l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb | 57 ------------------ .../l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb | 58 ------------------- .../l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb | 57 ------------------ .../l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb | 57 ------------------ 4 files changed, 229 deletions(-) delete mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb delete mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb delete mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb deleted file mode 100644 index f014047abe0..00000000000 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.2.0.eb +++ /dev/null @@ -1,57 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'likwid' -version = '5.2.0' - -homepage = 'https://github.com/RRZE-HPC/likwid' - -description = """ -Likwid stands for Like I knew what I am doing. This project contributes easy -to use command line tools for Linux to support programmers in developing high -performance multi threaded programs. -""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s_use_EB_hwloc.patch', -] -checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] - -builddependencies = [ - ('binutils', '2.35'), - ('Perl', '5.32.0'), -] - -dependencies = [ - ('hwloc', '2.2.0'), -] - -skipsteps = ['configure'] - -# include_GCC.mk is using ifort by default. -# Changing it to gfortran, to be consistent with GCCcore toolchain -prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ -prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ -prebuildopts += """ make/include_GCC.mk && """ - -buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' -buildopts += 'FORTRAN_INTERFACE=true ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' - -maxparallel = 1 - -installopts = buildopts + 'INSTALL_CHOWN="" ' - -sanity_check_paths = { - 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', - 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', - 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, - 'lib/liblikwid.%s' % SHLIB_EXT], - 'dirs': ['man/man1'] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb deleted file mode 100644 index 4b3ebe531f7..00000000000 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-10.3.0.eb +++ /dev/null @@ -1,58 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'likwid' -version = '5.2.0' - -homepage = 'https://github.com/RRZE-HPC/likwid' - -description = """ -Likwid stands for Like I knew what I am doing. This project contributes easy -to use command line tools for Linux to support programmers in developing high -performance multi threaded programs. -""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s_use_EB_hwloc.patch', -] -checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] - -builddependencies = [ - ('binutils', '2.36.1'), - ('Perl', '5.32.1'), -] - -dependencies = [ - ('hwloc', '2.4.1'), -] - -skipsteps = ['configure'] - -# include_GCC.mk is using ifort by default. -# Changing it to gfortran, to be consistent with GCCcore toolchain -prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ -prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ -prebuildopts += """ make/include_GCC.mk && """ - -buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' -buildopts += 'FORTRAN_INTERFACE=true ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' -buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' - -maxparallel = 1 - -installopts = buildopts + 'INSTALL_CHOWN="" ' - -sanity_check_paths = { - 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', - 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', - 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, - 'lib/liblikwid.%s' % SHLIB_EXT], - 'dirs': ['man/man1'] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb deleted file mode 100644 index eb247379ff2..00000000000 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCCcore-11.2.0.eb +++ /dev/null @@ -1,57 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'likwid' -version = '5.2.0' - -homepage = 'https://github.com/RRZE-HPC/likwid' - -description = """ -Likwid stands for Like I knew what I am doing. This project contributes easy -to use command line tools for Linux to support programmers in developing high -performance multi threaded programs. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s_use_EB_hwloc.patch', -] -checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] - -builddependencies = [ - ('binutils', '2.37'), - ('Perl', '5.34.0'), -] - -dependencies = [ - ('hwloc', '2.5.0'), -] - -skipsteps = ['configure'] - -# include_GCC.mk is using ifort by default. -# Changing it to gfortran, to be consistent with GCCcore toolchain -prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ -prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ -prebuildopts += """ make/include_GCC.mk && """ - -buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' -buildopts += 'FORTRAN_INTERFACE=true ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' - -maxparallel = 1 - -installopts = buildopts + 'INSTALL_CHOWN="" ' - -sanity_check_paths = { - 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', - 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', - 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, - 'lib/liblikwid.%s' % SHLIB_EXT], - 'dirs': ['man/man1'] -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb deleted file mode 100644 index 5698b2349d9..00000000000 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCCcore-11.2.0.eb +++ /dev/null @@ -1,57 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'likwid' -version = '5.2.1' - -homepage = 'https://github.com/RRZE-HPC/likwid' - -description = """ -Likwid stands for Like I knew what I am doing. This project contributes easy -to use command line tools for Linux to support programmers in developing high -performance multi threaded programs. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = [ - '%(name)s-5.2.0_use_EB_hwloc.patch', -] -checksums = ['1b8e668da117f24302a344596336eca2c69d2bc2f49fa228ca41ea0688f6cbc2'] - -builddependencies = [ - ('binutils', '2.37'), - ('Perl', '5.34.0'), -] - -dependencies = [ - ('hwloc', '2.5.0'), -] - -skipsteps = ['configure'] - -# include_GCC.mk is using ifort by default. -# Changing it to gfortran, to be consistent with GCCcore toolchain -prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ -prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ -prebuildopts += """ make/include_GCC.mk && """ - -buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' -buildopts += 'FORTRAN_INTERFACE=true ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' - -maxparallel = 1 - -installopts = buildopts + 'INSTALL_CHOWN="" ' - -sanity_check_paths = { - 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', - 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', - 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, - 'lib/liblikwid.%s' % SHLIB_EXT], - 'dirs': ['man/man1'] -} - -moduleclass = 'tools' From 576373bd0b8bd929b9e829eff5454ef681932012 Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Tue, 22 Mar 2022 13:26:29 +0100 Subject: [PATCH 3300/9987] Cleaning more unnecessary statement --- easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb index 1ab048a1f46..633bda80386 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a.eb @@ -20,15 +20,10 @@ dependencies = [ ('HDF5', '1.10.7') ] -configopts = '-DENABLE_BLAS=off ' -configopts += '-DENABLE_LAPACK=off ' -configopts += '-DMKL_FLAG=sequential ' +configopts = '-DMKL_FLAG=sequential ' configopts += '-DENABLE_MPI=True ' -configopts += '-DENABLE_OPENMP=False ' -configopts += '-DENABLE_64BIT_INTEGERS=False ' configopts += '-DENABLE_EXATENSOR=off ' configopts += '-DENABLE_PCMSOLVER=off ' -configopts += '-G"Unix Makefiles" ' pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' From 3a13eaeb98c176b4da17755db0d921482a2615f2 Mon Sep 17 00:00:00 2001 From: Agustin Aucar Date: Tue, 22 Mar 2022 13:27:10 +0100 Subject: [PATCH 3301/9987] Cleaning more unnecessary statement --- easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb index 11637777210..f6c765a8720 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-foss-2021a.eb @@ -20,15 +20,11 @@ dependencies = [ ('HDF5', '1.10.7') ] -configopts = '-DENABLE_BLAS=auto ' -configopts += '-DENABLE_LAPACK=auto ' -configopts += '-DMKL_FLAG=off ' +configopts = '-DMKL_FLAG=off ' +configopts += '-DMATH_LIBS="$LIBLAPACK" ' configopts += '-DENABLE_MPI=True ' -configopts += '-DENABLE_OPENMP=False ' -configopts += '-DENABLE_64BIT_INTEGERS=False ' configopts += '-DENABLE_EXATENSOR=off ' configopts += '-DENABLE_PCMSOLVER=off ' -configopts += '-G"Unix Makefiles" ' pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' From 49fae51dc00f75b497c83c16b8080028e4e414c8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 22 Mar 2022 13:41:46 +0100 Subject: [PATCH 3302/9987] add likwid for intel-compilers/iccifort, and fix typo in others --- .../l/likwid/likwid-5.2.0-GCC-10.2.0.eb | 3 +- .../l/likwid/likwid-5.2.0-GCC-11.2.0.eb | 3 +- .../likwid-5.2.0-iccifort-2020.4.304.eb | 51 +++++++++++++++++++ .../likwid-5.2.0-intel-compilers-2021.2.0.eb | 51 +++++++++++++++++++ .../l/likwid/likwid-5.2.1-GCC-11.2.0.eb | 3 +- 5 files changed, 108 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.0-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb index 7e6a0d4e6b9..a6b230f13eb 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb @@ -39,7 +39,8 @@ prebuildopts += """ make/include_GCC.mk && """ buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' buildopts += 'FORTRAN_INTERFACE=true ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' maxparallel = 1 diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb index 25303bb7bed..867eca0fcfc 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb @@ -39,7 +39,8 @@ prebuildopts += """ make/include_GCC.mk && """ buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' buildopts += 'FORTRAN_INTERFACE=true ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' maxparallel = 1 diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..9fbbc61c892 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_EB_hwloc.patch', +] +checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] + +builddependencies = [ + ('Perl', '5.32.0'), +] + +dependencies = [ + ('hwloc', '2.2.0'), +] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'COMPILER=ICC FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..3b749f279c8 --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-intel-compilers-2021.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_EB_hwloc.patch', +] +checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] + +builddependencies = [ + ('Perl', '5.32.1'), +] + +dependencies = [ + ('hwloc', '2.4.1'), +] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'COMPILER=ICC FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb index c06a59f32da..2fc0eab0790 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb @@ -39,7 +39,8 @@ prebuildopts += """ make/include_GCC.mk && """ buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' buildopts += 'FORTRAN_INTERFACE=true ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' maxparallel = 1 From 97d484b95b74012b301d3d3a16c7ff9dab524d93 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 22 Mar 2022 14:22:45 +0100 Subject: [PATCH 3303/9987] adding easyconfigs: VTune-2022.2.0.eb --- .../easyconfigs/v/VTune/VTune-2022.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb new file mode 100644 index 00000000000..773718fc442 --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.2.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +name = 'VTune' +version = '2022.2.0' + +homepage = 'https://software.intel.com/en-us/vtune' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18602/'] +sources = ['l_oneapi_vtune_p_%(version)s.172_offline.sh'] +checksums = ['d9f92ab6486a02c8ba226c98893492a54eda706d9edd3206a6b6143bfbc97195'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'tools' From d53f303fe30982303b3ecc3f2dbc800e1cd769cb Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 22 Mar 2022 15:18:11 +0100 Subject: [PATCH 3304/9987] Added patch for failing test_sharded_optim test --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 + .../PyTorch-1.11.0_fix_sharded_imports.patch | 44 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_sharded_imports.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index afd9d57bce2..aad36ceabba 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -27,6 +27,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_skip_failing_ops_tests.patch', 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', + 'PyTorch-1.11.0_fix_sharded_imports.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -42,6 +43,7 @@ checksums = [ '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', '8f4a27303f8cba2ea90702e494365bf4a3e1c5ade9ed1311b63ad4289793e1af', # PyTorch-1.11.0_skip_failing_ops_tests.patch '10d1f0db8254f7564500fe97f134c3b4fa89156839b5f771a9396d80a0a1ada4', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch + '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_sharded_imports.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_sharded_imports.patch new file mode 100644 index 00000000000..7d46fdadd51 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_sharded_imports.patch @@ -0,0 +1,44 @@ +# Fixes a "NameError: name 'sharded_tensor' is not defined" error +# for the test_named_params_with_sharded_tensor test +# See https://github.com/pytorch/pytorch/pull/73309 +From 012d490ed76d8af8538d310a508b0e09a91b7632 Mon Sep 17 00:00:00 2001 +From: wanchaol +Date: Wed, 23 Feb 2022 12:10:39 -0800 +Subject: [PATCH] [shard] fix some imports in tests + +This fix some imports in sharded optimizer tests + +Differential Revision: [D34427252](https://our.internmc.facebook.com/intern/diff/D34427252/) + +[ghstack-poisoned] +--- + .../_shard/sharded_optim/test_sharded_optim.py | 9 ++++++--- + 1 file changed, 6 insertions(+), 3 deletions(-) + +diff --git a/test/distributed/_shard/sharded_optim/test_sharded_optim.py b/test/distributed/_shard/sharded_optim/test_sharded_optim.py +index 085c928985eb..d3f1468aea3c 100644 +--- a/test/distributed/_shard/sharded_optim/test_sharded_optim.py ++++ b/test/distributed/_shard/sharded_optim/test_sharded_optim.py +@@ -2,7 +2,10 @@ + + import torch + import torch.optim as optim +-import torch.distributed._shard.sharded_tensor ++from torch.distributed._shard import ( ++ sharded_tensor, ++ shard_parameter ++) + + from copy import deepcopy + from torch.distributed._shard.sharding_spec import ( +@@ -77,8 +80,8 @@ def shard_parameter(self): + ], + ) + +- sharded_tensor.shard_parameter(self.linear1, "weight", rowwise_sharding_spec) +- sharded_tensor.shard_parameter(self.linear2, "weight", colwise_sharding_spec) ++ shard_parameter(self.linear1, "weight", rowwise_sharding_spec) ++ shard_parameter(self.linear2, "weight", colwise_sharding_spec) + + def forward(self, inp): + return self.linear2(self.gelu(self.linear1(inp))) From edc8ee30aecd3573b7d06671173feda33c2dde07 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Mar 2022 16:29:02 +0200 Subject: [PATCH 3305/9987] adding easyconfigs: ONNX-1.11.0-foss-2021a.eb, ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb, ONNX-Runtime-1.10.0-foss-2021a.eb --- ...X-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb | 42 ++++++++++++++++ .../ONNX-Runtime-1.10.0-foss-2021a.eb | 41 ++++++++++++++++ .../o/ONNX/ONNX-1.11.0-foss-2021a.eb | 48 +++++++++++++++++++ 3 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/o/ONNX/ONNX-1.11.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..900fff7fa7c --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'ONNX-Runtime' +version = '1.10.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://onnxruntime.ai/' +description = """ONNX Runtime inference can enable faster customer experiences and lower costs, +supporting models from deep learning frameworks such as PyTorch and +TensorFlow/Keras as well as classical machine learning libraries such as +scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different +hardware, drivers, and operating systems, and provides optimal performance by +leveraging hardware accelerators where applicable alongside graph optimizations +and transforms.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +_whl_tmpl = 'onnxruntime-%%(version)s-cp39-cp39-manylinux_2_17_%s.manylinux2014_%s.whl' +sources = [_whl_tmpl % ('%(arch)s', '%(arch)s')] +checksums = [ + { + _whl_tmpl % ('x86_64', 'x86_64'): + '34cfb07a8af91b3b7f82ad9db8f6dce67f0bd672cdaf659d0fd86aaba7a021d9', + _whl_tmpl % ('aarch64', 'aarch64'): + 'd5b0d3cf319c038b9f4479235dcf842d959f1248be48953f478822ac48a60617', + } +] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('ONNX', '1.11.0'), + ('flatbuffers-python', '2.0'), +] + +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'onnxruntime'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a.eb new file mode 100644 index 00000000000..61e962b59b1 --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'ONNX-Runtime' +version = '1.10.0' + +homepage = 'https://onnxruntime.ai/' +description = """ONNX Runtime inference can enable faster customer experiences and lower costs, +supporting models from deep learning frameworks such as PyTorch and +TensorFlow/Keras as well as classical machine learning libraries such as +scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different +hardware, drivers, and operating systems, and provides optimal performance by +leveraging hardware accelerators where applicable alongside graph optimizations +and transforms.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['http://pypi.python.org/packages/source/o/onnxruntime'] +local_whl_tmpl = 'onnxruntime-%%(version)s-cp39-cp39-manylinux_2_17_%s.manylinux2014_%s.whl' +sources = [local_whl_tmpl % ('%(arch)s', '%(arch)s')] +checksums = [ + { + local_whl_tmpl % ('x86_64', 'x86_64'): + '34cfb07a8af91b3b7f82ad9db8f6dce67f0bd672cdaf659d0fd86aaba7a021d9', + local_whl_tmpl % ('aarch64', 'aarch64'): + 'd5b0d3cf319c038b9f4479235dcf842d959f1248be48953f478822ac48a60617', + } +] + +dependencies = [ + ('Python', '3.9.5'), + ('ONNX', '1.11.0'), + ('flatbuffers-python', '2.0'), +] + +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'onnxruntime'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ONNX/ONNX-1.11.0-foss-2021a.eb b/easybuild/easyconfigs/o/ONNX/ONNX-1.11.0-foss-2021a.eb new file mode 100644 index 00000000000..f0e676804c5 --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX/ONNX-1.11.0-foss-2021a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'ONNX' +version = '1.11.0' + +homepage = 'https://onnx.ai/' +description = """ +Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI +developers to choose the right tools as their project evolves. ONNX provides an +open source format for AI models, both deep learning and traditional ML. It +defines an extensible computation graph model, as well as definitions of +built-in operators and standard data types. Currently we focus on the +capabilities needed for inferencing (scoring).""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['eca224c7c2c8ee4072a0743e4898a84a9bdf8297b5e5910a2632e4c4182ffb2a'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('protobuf-python', '3.17.3'), + ('typing-extensions', '3.10.0.0'), +] + +use_pip = True + +preinstallopts = 'env MAX_JOBS="%(parallel)s"' + +sanity_check_paths = { + 'files': ['bin/check-model', 'bin/check-node', 'bin/backend-test-tools'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('check-model', '-h'), + ('check-node', '-h'), + ('backend-test-tools', '-h'), +] + +sanity_pip_check = True + +moduleclass = 'devel' From 3fe2e5e06e342028b233c369e9582cd60e5e696f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Mar 2022 17:00:38 +0200 Subject: [PATCH 3306/9987] fix sources of ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb --- .../ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb index 900fff7fa7c..e14c4676355 100644 --- a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -15,14 +15,13 @@ and transforms.""" toolchain = {'name': 'foss', 'version': '2021a'} -_whl_tmpl = 'onnxruntime-%%(version)s-cp39-cp39-manylinux_2_17_%s.manylinux2014_%s.whl' -sources = [_whl_tmpl % ('%(arch)s', '%(arch)s')] +source_urls = ['http://pypi.python.org/packages/source/o/onnxruntime-gpu'] +local_whl_tmpl = 'onnxruntime_gpu-%%(version)s-cp39-cp39-manylinux_2_17_%s.manylinux2014_%s.whl' +sources = [local_whl_tmpl % ('%(arch)s', '%(arch)s')] checksums = [ { - _whl_tmpl % ('x86_64', 'x86_64'): - '34cfb07a8af91b3b7f82ad9db8f6dce67f0bd672cdaf659d0fd86aaba7a021d9', - _whl_tmpl % ('aarch64', 'aarch64'): - 'd5b0d3cf319c038b9f4479235dcf842d959f1248be48953f478822ac48a60617', + local_whl_tmpl % ('x86_64', 'x86_64'): + '2ffe8009eef07307a836e654a8449c177c0ef84ef29c4619d464d5ad8ab2d01b', } ] From 65bc6c409803602fad6055231fecca7e9422ce6b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Mar 2022 17:04:00 +0200 Subject: [PATCH 3307/9987] add download_dep_fail to ONNX and ONNX-Runtime --- .../o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb | 1 + .../easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a.eb | 1 + easybuild/easyconfigs/o/ONNX/ONNX-1.11.0-foss-2021a.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb index e14c4676355..1e025b88789 100644 --- a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -33,6 +33,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a.eb index 61e962b59b1..b7a7262b898 100644 --- a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a.eb +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a.eb @@ -33,6 +33,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/o/ONNX/ONNX-1.11.0-foss-2021a.eb b/easybuild/easyconfigs/o/ONNX/ONNX-1.11.0-foss-2021a.eb index f0e676804c5..c5287349a46 100644 --- a/easybuild/easyconfigs/o/ONNX/ONNX-1.11.0-foss-2021a.eb +++ b/easybuild/easyconfigs/o/ONNX/ONNX-1.11.0-foss-2021a.eb @@ -29,6 +29,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True preinstallopts = 'env MAX_JOBS="%(parallel)s"' From 0338eaf56d283d89c6c444c48d566bd75706b87f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 22 Mar 2022 15:06:28 +0000 Subject: [PATCH 3308/9987] adding easyconfigs: canu-2.2-GCCcore-10.3.0-Java-11.eb --- .../c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb new file mode 100644 index 00000000000..42b5f5b32b9 --- /dev/null +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'canu' +version = '2.2' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://canu.readthedocs.io' +description = "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'marbl' +source_urls = ['https://github.com/marbl/canu/releases/download/v%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('git', '2.32.0', '-nodocs'), +] + +dependencies = [ + ('Java', '11', '', True), + ('Perl', '5.32.1'), + ('gnuplot', '5.4.2'), +] + +skipsteps = ['configure', 'install'] + +start_dir = 'src' + +buildopts = 'TARGET_DIR=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/canu', 'lib/libcanu.a'], + 'dirs': ['lib/site_perl', 'share'], +} +sanity_check_commands = [ + "canu -version", + "canu -options", +] + +modextrapaths = {'PERL5LIB': 'lib/site_perl'} + +moduleclass = 'bio' From fffe30ba294399e22380b79182d396f12a0dbc13 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 22 Mar 2022 16:41:58 +0100 Subject: [PATCH 3309/9987] add missing checksums. --- easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb | 5 ++++- easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.3.0.eb | 5 ++++- easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb | 5 ++++- .../easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb | 5 ++++- .../l/likwid/likwid-5.2.0-intel-compilers-2021.2.0.eb | 5 ++++- easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb | 5 ++++- 6 files changed, 24 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb index a6b230f13eb..c723d1fccbf 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.2.0.eb @@ -19,7 +19,10 @@ sources = ['v%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_use_EB_hwloc.patch', ] -checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] +checksums = [ + 'aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0', # v5.2.0.tar.gz + '76ef41001efcdd107e34e2833325ffa876b8ac526740301ae9bace91150cfb8f', # likwid-5.2.0_use_EB_hwloc.patch +] builddependencies = [ ('Perl', '5.32.0'), diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.3.0.eb index d83ae4828a1..62e543c1854 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-10.3.0.eb @@ -19,7 +19,10 @@ sources = ['v%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_use_EB_hwloc.patch', ] -checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] +checksums = [ + 'aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0', # v5.2.0.tar.gz + '76ef41001efcdd107e34e2833325ffa876b8ac526740301ae9bace91150cfb8f', # likwid-5.2.0_use_EB_hwloc.patch +] builddependencies = [ ('Perl', '5.32.1'), diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb index 867eca0fcfc..084919eff42 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-GCC-11.2.0.eb @@ -19,7 +19,10 @@ sources = ['v%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_use_EB_hwloc.patch', ] -checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] +checksums = [ + 'aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0', # v5.2.0.tar.gz + '76ef41001efcdd107e34e2833325ffa876b8ac526740301ae9bace91150cfb8f', # likwid-5.2.0_use_EB_hwloc.patch +] builddependencies = [ ('Perl', '5.34.0'), diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb index 9fbbc61c892..e2774c4ac86 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-iccifort-2020.4.304.eb @@ -19,7 +19,10 @@ sources = ['v%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_use_EB_hwloc.patch', ] -checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] +checksums = [ + 'aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0', # v5.2.0.tar.gz + '76ef41001efcdd107e34e2833325ffa876b8ac526740301ae9bace91150cfb8f', # likwid-5.2.0_use_EB_hwloc.patch +] builddependencies = [ ('Perl', '5.32.0'), diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-intel-compilers-2021.2.0.eb index 3b749f279c8..f3e759fe3b6 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.0-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.0-intel-compilers-2021.2.0.eb @@ -19,7 +19,10 @@ sources = ['v%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_use_EB_hwloc.patch', ] -checksums = ['aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0'] +checksums = [ + 'aa6dccacfca59e52d8f3be187ffcf292b2a2fa1f51a81bf8912b9d48e5a257e0', # v5.2.0.tar.gz + '76ef41001efcdd107e34e2833325ffa876b8ac526740301ae9bace91150cfb8f', # likwid-5.2.0_use_EB_hwloc.patch +] builddependencies = [ ('Perl', '5.32.1'), diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb index 2fc0eab0790..d7e5779fa74 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.1-GCC-11.2.0.eb @@ -19,7 +19,10 @@ sources = ['v%(version)s.tar.gz'] patches = [ '%(name)s-5.2.0_use_EB_hwloc.patch', ] -checksums = ['1b8e668da117f24302a344596336eca2c69d2bc2f49fa228ca41ea0688f6cbc2'] +checksums = [ + '1b8e668da117f24302a344596336eca2c69d2bc2f49fa228ca41ea0688f6cbc2', # v5.2.1.tar.gz + '76ef41001efcdd107e34e2833325ffa876b8ac526740301ae9bace91150cfb8f', # likwid-5.2.0_use_EB_hwloc.patch +] builddependencies = [ ('Perl', '5.34.0'), From 65a2e0406f45ad95dddf239eb365216a960f87d9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Mar 2022 18:21:28 +0200 Subject: [PATCH 3310/9987] adding easyconfigs: ont-fast5-api-4.0.2-foss-2021a.eb --- .../ont-fast5-api-4.0.2-foss-2021a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.2-foss-2021a.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.2-foss-2021a.eb new file mode 100644 index 00000000000..00508eb3a91 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.2-foss-2021a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '4.0.2' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + (name, version, { + 'checksums': ['452920ee9976e43cfa0abdee57ce918908050a8be590e5901a3ec1404e135fd6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/compress_fast5', 'bin/fast5_subset', 'bin/multi_to_single_fast5', 'bin/single_to_multi_fast5'], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 3e3f1faa297051d6ed8acc20f895e0ff13bbae96 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Mar 2022 18:23:22 +0200 Subject: [PATCH 3311/9987] adding easyconfigs: ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb, ont-remora-0.1.2-foss-2021a.eb --- ...ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb | 49 +++++++++++++++++++ .../ont-remora/ont-remora-0.1.2-foss-2021a.eb | 47 ++++++++++++++++++ 2 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..5fbd92dcb77 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'ont-remora' +version = '0.1.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/remora' +description = """Methylation/modified base calling separated from basecalling. Remora primarily +provides an API to call modified bases for basecaller programs such as Bonito. +Remora also provides the tools to prepare datasets, train modified base models +and run simple inference.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('ONNX-Runtime', '1.10.0', versionsuffix), + ('PyTorch', '1.10.2'), + ('scikit-learn', '0.24.2'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('thop', '0.0.31-2005241907', { + 'source_tmpl': 'thop-0.0.31.post2005241907-py3-none-any.whl', + 'checksums': ['86d67af12311b34905949eb91c8c38f92a707de72140c29a94110cc623e21ceb'], + }), + (name, version, { + 'modulename': 'remora', + 'checksums': ['4ada9994af88d9038ea04ebfbca7ab6de2a859cf2680bea25a11d82c20bb2d82'], + }), +] + +sanity_check_paths = { + 'files': ['bin/remora'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('remora', '--help'), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a.eb new file mode 100644 index 00000000000..74134fae25d --- /dev/null +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ont-remora' +version = '0.1.2' + +homepage = 'https://github.com/nanoporetech/remora' +description = """Methylation/modified base calling separated from basecalling. Remora primarily +provides an API to call modified bases for basecaller programs such as Bonito. +Remora also provides the tools to prepare datasets, train modified base models +and run simple inference.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('ONNX-Runtime', '1.10.0'), + ('PyTorch', '1.10.2'), + ('scikit-learn', '0.24.2'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('thop', '0.0.31-2005241907', { + 'source_tmpl': 'thop-0.0.31.post2005241907-py3-none-any.whl', + 'checksums': ['86d67af12311b34905949eb91c8c38f92a707de72140c29a94110cc623e21ceb'], + }), + (name, version, { + 'modulename': 'remora', + 'checksums': ['4ada9994af88d9038ea04ebfbca7ab6de2a859cf2680bea25a11d82c20bb2d82'], + }), +] + +sanity_check_paths = { + 'files': ['bin/remora'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('remora', '--help'), +] + +sanity_pip_check = True + +moduleclass = 'bio' From eda2f90ac1e03b2a6d8df91cdfb208688b4d6bee Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Mar 2022 17:05:31 +0100 Subject: [PATCH 3312/9987] create stub dist-info for onnxruntime in ONNX-Runtime v1.10.0 with CUDA --- ...ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb index 1e025b88789..02d864af126 100644 --- a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -15,6 +15,7 @@ and transforms.""" toolchain = {'name': 'foss', 'version': '2021a'} +# ONNX Runtime with support for GPUs is distributed under the name 'onnxruntime-gpu' in PyPI source_urls = ['http://pypi.python.org/packages/source/o/onnxruntime-gpu'] local_whl_tmpl = 'onnxruntime_gpu-%%(version)s-cp39-cp39-manylinux_2_17_%s.manylinux2014_%s.whl' sources = [local_whl_tmpl % ('%(arch)s', '%(arch)s')] @@ -35,8 +36,23 @@ dependencies = [ use_pip = True download_dep_fail = True +# Due to its name 'onnxruntime-gpu', this package does not fullfil requirements on 'onnxruntime' although it provides +# the 'onnxruntime' python module. Fix this dependency issue in pip by creating a stub 'onnxruntime' dist-info folder +_py_sitepkgs = '%(installdir)s/lib/python%(pyshortver)s/site-packages' +postinstallcmds = [ + "cp -r %s/onnxruntime{_gpu,}-%%(version)s.dist-info" % _py_sitepkgs, + "sed -i 's/onnxruntime.gpu/onnxruntime/g' %s/onnxruntime-%%(version)s.dist-info/{METADATA,RECORD}" % _py_sitepkgs, +] + sanity_pip_check = True +_py_sitepkgs_dirs = ['onnxruntime', 'onnxruntime-%(version)s.dist-info', 'onnxruntime_gpu-%(version)s.dist-info'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%%(pyshortver)s/site-packages/%s' % x for x in _py_sitepkgs_dirs], +} + options = {'modulename': 'onnxruntime'} moduleclass = 'devel' From 1cdbb9c65cf7134c58fe8c295a5783a6dc0b9490 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 22 Mar 2022 13:52:04 -0700 Subject: [PATCH 3313/9987] IgBLAST update --- .../i/IgBLAST/IgBLAST-1.18.0-x64-linux.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.18.0-x64-linux.eb diff --git a/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.18.0-x64-linux.eb b/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.18.0-x64-linux.eb new file mode 100644 index 00000000000..74281e92445 --- /dev/null +++ b/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.18.0-x64-linux.eb @@ -0,0 +1,28 @@ +# Easybuild Easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Research Center - Seattle Washington +easyblock = "Tarball" + +name = 'IgBLAST' +version = '1.18.0' +versionsuffix = '-x64-linux' + +homepage = 'https://ncbi.github.io/igblast' +description = """IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.""" + +toolchain = SYSTEM + +source_urls = ['ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/%(version)s'] +sources = ['ncbi-%(namelower)s-%(version)s-x64-linux.tar.gz'] +checksums = ['e1feef1f16bc6bf7df35713288baf7523a56362eee8c36625d0608cf6a5c31f1'] + +sanity_check_paths = { + 'files': ["bin/igblastn", 'bin/igblastp'], + 'dirs': ['bin'] +} + +modextravars = {'IGDATA': '%(installdir)s/internal_data'} + +moduleclass = 'bio' From fec860d5a7db3b3a50b3ca6c170dd680c8b09c08 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 23 Mar 2022 07:50:31 +0100 Subject: [PATCH 3314/9987] adjust sanity_check_command to correct format --- .../d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb index 3ed92513216..6816b3972dc 100644 --- a/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/d/dftd3-lib/dftd3-lib-0.9-intel-compilers-2021.2.0.eb @@ -36,6 +36,6 @@ sanity_check_paths = { 'dirs': ['include', 'share'], } -sanity_check_commands = [("dftd3 --help")] +sanity_check_commands = ["dftd3 --help"] moduleclass = 'chem' From 46be59826efa037ae6fff2a6e2d96cd21ad83db6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Mar 2022 12:24:43 +0100 Subject: [PATCH 3315/9987] adding easyconfigs: MEME-5.4.1-GCC-11.2.0.eb --- .../m/MEME/MEME-5.4.1-GCC-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..8c34acb0838 --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.4.1' + +homepage = 'https://meme-suite.org/meme/index.html' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://%(namelower)s-suite.org/%(namelower)s/%(namelower)s-software/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c07fb8afafa60fc5e84ca24493c82fa6f4bd1df1a2622102edbf86a1c30fd11f'] + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), + ('Perl', '5.34.0'), + ('Python', '3.9.6') +] + +configopts = '--enable-build-libxml2 --enable-build-libxslt ' +configopts += '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' + +sanity_check_paths = { + 'files': ['bin/dreme', 'bin/meme', 'bin/dreme', 'bin/meme-chip'], + 'dirs': ['lib'], +} + +moduleclass = 'bio' From bba9d6ac5233d1f097cbce0d7ca8fb4f98369fbd Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 23 Mar 2022 14:33:33 +0000 Subject: [PATCH 3316/9987] xxd added to these PLUMED versions as well --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb | 4 ++++ easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb | 4 ++++ easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb | 4 ++++ 3 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb index 16200c8e59a..86b9edfe391 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-intel-2020b.eb @@ -20,6 +20,10 @@ source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s sources = [SOURCE_TGZ] checksums = ['1ab3153db2010406852b30201ed94112e25eca4c4c8c4b41a29c22a7a3303f96'] +builddependencies = [ + ('xxd', '8.2.4220'), +] + dependencies = [ ('zlib', '1.2.11'), ('GSL', '2.6'), diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb index fe971797a8e..ba0747ac705 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-intel-2021a.eb @@ -18,6 +18,10 @@ source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s sources = [SOURCE_TGZ] checksums = ['6069bc134f74cb15dd63e27e3587a15a31a9ddd9e7eebdd717da898f31512645'] +builddependencies = [ + ('xxd', '8.2.4220'), +] + dependencies = [ ('zlib', '1.2.11'), ('GSL', '2.7'), diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb index 5e10ec4a8f3..c7f467034e0 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb @@ -18,6 +18,10 @@ source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s sources = [SOURCE_TGZ] checksums = ['2895515f31aae42002a539222f5b8558037496548a061b5d0db136d3a46f618b'] +builddependencies = [ + ('xxd', '8.2.4220'), +] + dependencies = [ ('zlib', '1.2.11'), ('GSL', '2.7'), From f243ac0a75a7e09b53ffde8192fb7e4250e1171c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Mar 2022 15:58:18 +0100 Subject: [PATCH 3317/9987] update jax dependency for AlphaFold v2.2.0 to v0.2.28 --- .../AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../jax/jax-0.2.28-foss-2021a-CUDA-11.3.1.eb | 129 ++++++++++++++++++ 2 files changed, 130 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.28-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb index c75f7804f24..ebc30d0efc5 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb @@ -28,7 +28,7 @@ dependencies = [ ('HH-suite', '3.3.0'), ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), - ('jax', '0.2.24', versionsuffix), # also provides absl-py + ('jax', '0.2.28', versionsuffix), # also provides absl-py ('UCX-CUDA', '1.10.0', versionsuffix), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.28-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.2.28-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ccf1ca366a7 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.2.28-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,129 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.2.28' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('pytest-xdist', '2.3.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.32.0', '-nodocs'), +] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', versionsuffix, True), + ('NCCL', '2.10.3', versionsuffix), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.0'), +] + +# running the tests with lots of cores results in test failures because not enough threads can be started, +# and running with a single core also results in systematic test failures +# 4 cores seems to work best +parallel = 4 + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = 'e662039f98d2b6a0d8242887d0881bae04e2d590' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '0.13.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], + }), + ('jaxlib', '0.1.76', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + 'jaxlib-0.1.70_add-bazel-args-to-shutdown.patch', + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.1.76.tar.gz + '6d5e185906dbc8f0f6589c5bc0569ae049bfe6346c271db73d5077f1fda41c7c', + # tensorflow-e662039f98d2b6a0d8242887d0881bae04e2d590.tar.gz + '8d6604640c8092abf640ccfb7222f6f941ee7b409d30292f6261ce3c86e23fab', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'source_urls': ['https://github.com/google/jax/archive/'], + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'patches': [ + 'jax-0.2.19_fix-update-of-cache-access-time.patch', + 'jax-0.2.24-foss-2021a_unimplemented.patch', + ], + 'checksums': [ + '7c6ffb14c2069d75c0721ec21b35ee253f0f368b84b9ec9459f0870ed902bfa7', # jax-v0.2.28.tar.gz + # jax-0.2.19_fix-update-of-cache-access-time.patch + 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + # jax-0.2.24-foss-2021a_unimplemented.patch + '96fe1b15b55611727b0ae76409b89c44ae21a1c10002507ca8e3c06c2b134f4e', + ], + # deliberately not testing in parallel, as that results in (additional) failing tests; + # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, + # see https://github.com/google/jax/issues/7323 and + # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; + # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; + # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + "JAX_ENABLE_X64=true pytest tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 56c82000e55abe221d682e354553f5dbd0ccab04 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 23 Mar 2022 18:45:32 +0100 Subject: [PATCH 3318/9987] adding easyconfigs: VTK-9.1.0-foss-2021b.eb --- .../easyconfigs/v/VTK/VTK-9.1.0-foss-2021b.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.1.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.1.0-foss-2021b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.1.0-foss-2021b.eb new file mode 100644 index 00000000000..0d8e0e801df --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.1.0-foss-2021b.eb @@ -0,0 +1,86 @@ +## +# Authors:: +# * Fotis Georgatos +# * Robert Mijakovic +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '9.1.0' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + '8fed42f4f8f1eb8083107b68eaa9ad71da07110161a3116ad807f43e5ca5ce96', # VTK-9.1.0.tar.gz + 'b9442cf1c30e1e44502e6dc36d3c6c2dc3d3f7d03306ee1d10737e9abadaa85d', # VTKData-9.1.0.tar.gz + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('XZ', '5.2.5'), + ('libGLU', '9.0.2'), + ('X11', '20210802'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + +moduleclass = 'vis' From 6a1a5bd8a9dcf2dd6b781fca274862bdd6cd1101 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 23 Mar 2022 18:46:11 +0100 Subject: [PATCH 3319/9987] adding easyconfigs: NiBabel-3.2.2-foss-2021b.eb --- .../n/NiBabel/NiBabel-3.2.2-foss-2021b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.2-foss-2021b.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.2-foss-2021b.eb new file mode 100644 index 00000000000..f94c485969a --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-3.2.2-foss-2021b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '3.2.2' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Pillow', '8.3.2'), + ('pydicom', '2.2.2'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['b0dcc174b30405ce9e8fec1eab3cbbb20f5c5e4920976c08b22e050b7c124f94'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' From 0a89be3b1abba01ac709680bdd2345a179d4b823 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 23 Mar 2022 18:47:16 +0100 Subject: [PATCH 3320/9987] add pydicom dep --- .../p/pydicom/pydicom-2.2.2-GCCcore-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-2.2.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.2.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ca86fd03b78 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.2.2-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '2.2.2' + +homepage = 'https://pydicom.github.io/' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d827669486414b6b6688ecf4d220065e754fabc1b0d016329fced2da4192555d'] + +builddependencies = [ + ('binutils', '2.37'), +] +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 7f43d64ce6f920438e0ac85a6778838821cfc2c7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 23 Mar 2022 18:47:57 +0100 Subject: [PATCH 3321/9987] adding easyconfigs: MNE-Python-0.24.1-foss-2021a.eb --- .../MNE-Python-0.24.1-foss-2021a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/MNE-Python/MNE-Python-0.24.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MNE-Python/MNE-Python-0.24.1-foss-2021a.eb b/easybuild/easyconfigs/m/MNE-Python/MNE-Python-0.24.1-foss-2021a.eb new file mode 100644 index 00000000000..d16e5256624 --- /dev/null +++ b/easybuild/easyconfigs/m/MNE-Python/MNE-Python-0.24.1-foss-2021a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'MNE-Python' +version = '0.24.1' + +homepage = 'https://mne.tools/stable/index.html' +description = """ +MNE-Python software is an open-source Python package for exploring, +visualizing, and analyzing human neurophysiological data such as MEG, EEG, +sEEG, ECoG, and more. It includes modules for data input/output, preprocessing, +visualization, source estimation, time-frequency analysis, connectivity +analysis, machine learning, and statistics.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('tqdm', '4.61.2'), + ('scikit-learn', '0.24.2'), + ('numba', '0.53.1'), + ('NiBabel', '3.2.1'), + ('h5py', '3.2.1'), + ('imageio', '2.10.5'), + ('VTK', '9.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pooch', '0.5.2', { + 'checksums': ['3d1d815b6b7d0af851d6eb28e6a91d7c99e0c46a528389b37131c73661200908'], + }), + ('python-picard', '0.7', { + 'modulename': 'picard', + 'checksums': ['8061a1f0c4660c805b7617f2f0bd0284c6e6e84ac3ec782081c67b27cfd185a7'], + }), + ('dipy', '1.4.1', { + 'checksums': ['b4bf830feae751f3f985d54cb71031fc35cea612838320f1f74246692b8a3cc0'], + }), + ('scooby', '0.5.12', { + 'checksums': ['874828e38834c1ccb2236a7491e0739675086608c6588abf132cdd0049458192'], + }), + ('pyvista', '0.33.3', { + 'checksums': ['ad690d892185de64695d2ec4b793afa94f3a2b401d8054aa49c363983da67d08'], + }), + ('wrapt', '1.13.3', { + 'checksums': ['1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185'], + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('mffpy', '0.7.1', { + 'checksums': ['83ab48ac12d133a1e06c1f4faaa604a6042370dee26e62f3f3e462bb272b3f16'], + }), + ('h5io', '0.1.7', { + 'checksums': ['be2684e678a28a5d59140de838f0165f095af865e48b8e498a279a3c2b89303e'], + }), + (name, version, { + 'modulename': 'mne', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/mne-tools/mne-python/archive/'], + 'checksums': ['d2283cbfc926eb0c395d8c14180f4699a697017d3e58026be24f2eb7d385fdb7'], + }), +] + +moduleclass = 'math' From 7e610f983075e7068a832389349e36649a761ff9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 23 Mar 2022 18:54:58 +0100 Subject: [PATCH 3322/9987] adding easyconfigs: skorch-0.11.0-foss-2021a-PyTorch-1.10.2.eb --- ...skorch-0.11.0-foss-2021a-PyTorch-1.10.2.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.2.eb diff --git a/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.2.eb b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.2.eb new file mode 100644 index 00000000000..135de7412d7 --- /dev/null +++ b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.2.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'skorch' +version = '0.11.0' +local_pt_version = '1.10.2' +versionsuffix = '-PyTorch-%s' % local_pt_version + +homepage = 'https://skorch.readthedocs.io/' +description = """ +A scikit-learn compatible neural network library that wraps PyTorch.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b35cb4e50045742f0ffcfad33044af691d5d36b50212573753a804483a947ca9'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-learn', '0.24.2'), + ('tqdm', '4.61.2'), + ('PyTorch', local_pt_version), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From 0344124193d7ac1ec39cfb624679b1e3bbba830d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 23 Mar 2022 21:01:00 +0100 Subject: [PATCH 3323/9987] fix PyTorch version --- ...rch-1.10.2.eb => skorch-0.11.0-foss-2021a-PyTorch-1.10.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/skorch/{skorch-0.11.0-foss-2021a-PyTorch-1.10.2.eb => skorch-0.11.0-foss-2021a-PyTorch-1.10.0.eb} (96%) diff --git a/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.2.eb b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0.eb similarity index 96% rename from easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.2.eb rename to easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0.eb index 135de7412d7..094b47c3f67 100644 --- a/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.2.eb +++ b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'skorch' version = '0.11.0' -local_pt_version = '1.10.2' +local_pt_version = '1.10.0' versionsuffix = '-PyTorch-%s' % local_pt_version homepage = 'https://skorch.readthedocs.io/' From c7451238ce0049b68d456daedca3bbe01df3e016 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Mar 2022 21:40:59 +0100 Subject: [PATCH 3324/9987] add Sys::Info, HTML::Template, Log::Report extensions to Perl v5.34.0 --- .../p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 48668be4e1e..5567f17c103 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1764,6 +1764,46 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], }), + ('Sys::Info::Base', '0.7807', { + 'source_tmpl': 'Sys-Info-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['132362b0046e8dc4f12e1560903623a88a8871d09bf1c29d93d48d3f4a582acb'], + }), + ('Sys::Info', '0.7811', { + 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'], + }), + ('HTML::Template', '2.97', { + 'source_tmpl': 'HTML-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR/'], + 'checksums': ['6547af61f3aa85793f8616190938d677d7995fb3b720c16258040bc935e2129f'], + }), + ('MIME::Charset', '1.012.2', { + 'source_tmpl': 'MIME-Charset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI/'], + 'checksums': ['878c779c0256c591666bd06c0cde4c0d7820eeeb98fd1183082aee9a1e7b1d13'], + }), + ('Unicode::LineBreak', '2019.001', { + 'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI/'], + 'checksums': ['486762e4cacddcc77b13989f979a029f84630b8175e7fef17989e157d4b6318a'], + }), + ('String::Print', '0.94', { + 'source_tmpl': 'String-Print-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'], + }), + ('Log::Report', '1.33', { + 'source_tmpl': 'Log-Report-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['49624da338fd7d57288fa22a47241476fb5ce2f6008181f786c7830fe5af01ff'], + }), + ('Log::Report::Optional', '1.07', { + 'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], + }), ] moduleclass = 'lang' From d920e9a80aa99be10bc7caa434c99d044fccf8a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Mar 2022 21:45:39 +0100 Subject: [PATCH 3325/9987] adding easyconfigs: XML-Compile-1.63-GCCcore-11.2.0.eb --- .../XML-Compile-1.63-GCCcore-11.2.0.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9da98746f42 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-11.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'Bundle' + +name = 'XML-Compile' +version = '1.63' + +homepage = 'https://metacpan.org/pod/XML::Compile' +description = "Perl module for compilation based XML processing" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('binutils', '2.37'), +] + +dependencies = [ + ('Perl', '5.34.0'), + ('XML-LibXML', '2.0207'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('XML::LibXML::Simple', '1.01', { + 'source_tmpl': 'XML-LibXML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['cd98c8104b70d7672bfa26b4513b78adf2b4b9220e586aa8beb1a508500365a6'], + }), + ('XML::Compile', version, { + 'source_tmpl': 'XML-Compile-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['4b0871ef4a70bff37266d531bebcd1d065b109e8f5c5e996f87189a9f92d595f'], + }), + ('XML::Compile::Cache', '1.06', { + 'source_tmpl': 'XML-Compile-Cache-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['591b136bd92842c81a5176082503f47df6d5cc4d8e0d78953ef1557f747038a0'], + }), + ('XML::Compile::SOAP', '3.27', { + 'source_tmpl': 'XML-Compile-SOAP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['d656632fdc58665cbe62ede9c35d1f5a871917a79eba11033afd2041152866a8'], + }), + ('XML::Compile::WSDL11', '3.08', { + 'source_tmpl': 'XML-Compile-WSDL11-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['dd687ccf5083fe98fce1dd18540e1d0175042437a986e33eec105eca248f8d42'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/auto/XML/Compile'], +} + +moduleclass = 'data' From 752d6454b6437d018cc0c59b1224c59690538985 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Mar 2022 22:00:04 +0100 Subject: [PATCH 3326/9987] add missing dependencies, fix configure options, extend sanity check, extend $PATH/$PERL5LIB/$PYTHONPATH, and switch to gompi/2021b toolchain rather than GCC/11.2.0 to enable MPI support for MEME v5.4.1 --- ...> MEME-5.4.1-gompi-2021b-Python-2.7.18.eb} | 30 +++++++++++++++---- 1 file changed, 25 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/MEME/{MEME-5.4.1-GCC-11.2.0.eb => MEME-5.4.1-gompi-2021b-Python-2.7.18.eb} (55%) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb similarity index 55% rename from easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-11.2.0.eb rename to easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb index 8c34acb0838..369b5cf382b 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb @@ -6,6 +6,7 @@ easyblock = 'ConfigureMake' name = 'MEME' version = '5.4.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://meme-suite.org/meme/index.html' description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or @@ -14,7 +15,7 @@ description = """The MEME Suite allows you to: * discover motifs using MEME, DRE motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.""" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://%(namelower)s-suite.org/%(namelower)s/%(namelower)s-software/%(version)s'] sources = [SOURCELOWER_TAR_GZ] @@ -25,15 +26,34 @@ dependencies = [ ('libxslt', '1.1.34'), ('zlib', '1.2.11'), ('Perl', '5.34.0'), - ('Python', '3.9.6') + ('Python', '2.7.18'), + ('Ghostscript', '9.54.0'), + ('XML-Compile', '1.63'), ] -configopts = '--enable-build-libxml2 --enable-build-libxslt ' -configopts += '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python ' +# config.log should indicate that all required/optional dependencies were found (see scripts/dependencies.pl) +configopts += " && grep 'All required and optional Perl modules were found' config.log" + +fix_perl_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] +fix_python_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] sanity_check_paths = { - 'files': ['bin/dreme', 'bin/meme', 'bin/dreme', 'bin/meme-chip'], + 'files': ['bin/dreme', 'bin/meme', 'bin/dreme', 'bin/meme-chip', 'libexec/meme-%(version)s/meme2meme'], 'dirs': ['lib'], } +sanity_check_commands = [ + "meme -h 2>&1 | grep 'Usage:'", + "meme2meme --help", + "perl -e 'require MemeSAX'", + "python -c 'import sequence'", +] + +modextrapaths = { + 'PATH': ['libexec/meme-%(version)s'], + 'PERL5LIB': ['lib/meme-%(version)s/perl'], + 'PYTHONPATH': ['lib/meme-%(version)s/python'], +} + moduleclass = 'bio' From 05e75e54ecb4ba24163c27c5b3115ccbad1344fb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 24 Mar 2022 00:49:46 +0200 Subject: [PATCH 3327/9987] fix dependency on PyTorch of ont-remora v0.1.2 --- .../o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb index 5fbd92dcb77..c7f14efe011 100644 --- a/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('ONNX-Runtime', '1.10.0', versionsuffix), - ('PyTorch', '1.10.2'), + ('PyTorch', '1.10.0', versionsuffix), ('scikit-learn', '0.24.2'), ('tqdm', '4.61.2'), ] diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a.eb index 74134fae25d..8e69f9bc1f8 100644 --- a/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a.eb +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a.eb @@ -15,7 +15,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('ONNX-Runtime', '1.10.0'), - ('PyTorch', '1.10.2'), + ('PyTorch', '1.10.0'), ('scikit-learn', '0.24.2'), ('tqdm', '4.61.2'), ] From 159d63458e484fb11b7299fd471075de8ff2598b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 24 Mar 2022 08:16:41 +0100 Subject: [PATCH 3328/9987] remove source_urls --- .../s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0.eb b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0.eb index 094b47c3f67..6bee48b7e93 100644 --- a/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0.eb +++ b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0.eb @@ -11,7 +11,6 @@ A scikit-learn compatible neural network library that wraps PyTorch.""" toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['b35cb4e50045742f0ffcfad33044af691d5d36b50212573753a804483a947ca9'] From b9319dd1f6aaa3a3da548ef70a1d7d353671ab8a Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 24 Mar 2022 09:56:53 +0100 Subject: [PATCH 3329/9987] add WGCNA extension to R-bundle-BioConductor v3.14 --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index 5776a16610b..49646aed92c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1093,6 +1093,9 @@ exts_list = [ ('EnsDb.Hsapiens.v79', '2.99.0', { 'checksums': ['eff1ae8d7f4ed5c6bed335de63a758be593750fb0b3483c01cf50402688d244d'], }), + ('WGCNA', '1.70-3', { + 'checksums': ['b9843b839728183af6b746f239e9519d438b294613362b556002acdb8522cbd4'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From cc7ff2fd6f796c52c6b2646474376dc391d75603 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 24 Mar 2022 11:25:14 +0000 Subject: [PATCH 3330/9987] adding easyconfigs: AmberTools-21-intel-2021b.eb --- .../a/AmberTools/AmberTools-21-intel-2021b.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb new file mode 100644 index 00000000000..2ccde888920 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb @@ -0,0 +1,58 @@ +easyblock = 'EB_Amber' + +name = 'AmberTools' +version = '21' + +homepage = 'https://ambermd.org/' +description = """AmberTools consists of several independently developed packages that work well by themselves, + and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, + with either explicit water or generalized Born solvent models.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True} + +# download requires registration, see http://ambermd.org/AmberTools17-get.html +local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium' +source_urls = ['https://ambermd.org/cgi-bin/AmberTools21-get.pl'] +sources = [{ + 'download_filename': local_download_credentials, + 'filename': SOURCE_TAR_BZ2, +}] +patches = [ + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', +] +checksums = [ + 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools-21.tar.bz2 + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', +] + +builddependencies = [ + ('Bison', '3.7.6'), + ('pkg-config', '0.29.2'), + ('CMake', '3.22.1'), + ('flex', '2.6.4'), + ('make', '4.3'), +] +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('FFTW', '3.3.10'), +] + +# pysander should link with icc and not gcc +prebuildopts = """sed -i 's/import sys/import sys; os.environ["LDSHARED"] = "icc -shared "/g' """ +prebuildopts += "%(builddir)s/AmberTools/src/pysander/setup.py && " + +# Tests use pmemd which is not part of AmberTools +runtest = False + +moduleclass = 'chem' From 7106dc0c846bbfa541af58aab435101de11e2379 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Mar 2022 15:13:17 +0100 Subject: [PATCH 3331/9987] fix sanity check paths for XML-Compile Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../x/XML-Compile/XML-Compile-1.63-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-11.2.0.eb index 9da98746f42..0f42d9742d0 100644 --- a/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/XML-Compile/XML-Compile-1.63-GCCcore-11.2.0.eb @@ -55,7 +55,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/auto/XML/Compile'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/XML/Compile'], } moduleclass = 'data' From 1ec6c95f8daf48b50b48b8a795a516e99db2ce52 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 24 Mar 2022 14:41:59 +0000 Subject: [PATCH 3332/9987] Add postinstallcmds to copy scripts directory to installdir --- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 6 +++++- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb | 6 +++++- .../v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb | 6 +++++- easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb | 6 +++++- 4 files changed, 20 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 734f106ab15..2c9468819fc 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -49,9 +49,13 @@ preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|fileve preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = {'PATH': ['scripts']} + sanity_check_paths = { 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], - 'dirs': [], + 'dirs': ['bin', 'lib', 'scripts'], } sanity_check_commands = ["vcfremap"] diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb index 5217cd5b157..59fce4f5bf9 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb @@ -49,9 +49,13 @@ preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|fileve preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = {'PATH': ['scripts']} + sanity_check_paths = { 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], - 'dirs': [], + 'dirs': ['bin', 'lib', 'scripts'], } sanity_check_commands = ["vcfremap"] diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb index 96720191f53..5321ac63d4e 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb @@ -50,9 +50,13 @@ preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|fileve preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = {'PATH': ['scripts']} + sanity_check_paths = { 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], - 'dirs': [], + 'dirs': ['bin', 'lib', 'scripts'], } sanity_check_commands = ["vcfremap"] diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb index 6d9fe6caf6d..445849a2c3b 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb @@ -49,9 +49,13 @@ preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|fileve preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = {'PATH': ['scripts']} + sanity_check_paths = { 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], - 'dirs': [], + 'dirs': ['bin', 'lib', 'scripts'], } sanity_check_commands = ["vcfremap"] From a9bdd107e4cbeb44e75e7db1990269375e7f8622 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 24 Mar 2022 16:08:52 +0100 Subject: [PATCH 3333/9987] adding easyconfigs: BLIS-3.1-GCCcore-11.2.0-amd.eb --- .../b/BLIS/BLIS-3.1-GCCcore-11.2.0-amd.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-3.1-GCCcore-11.2.0-amd.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.1-GCCcore-11.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.1-GCCcore-11.2.0-amd.eb new file mode 100644 index 00000000000..70fc18ddbcf --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.1-GCCcore-11.2.0-amd.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '3.1' +versionsuffix = '-amd' + +homepage = 'https://developer.amd.com/amd-cpu-libraries/blas-library/' +description = """AMD's fork of BLIS. BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/amd/blis/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch', +] +checksums = [ + '2891948925b9db99eec02a1917d9887a7bee9ad2afc5421c9ba58602a620f2bf', # 3.1.tar.gz + # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch + '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', +] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), + ('Perl', '5.34.0'), +] + +# Build Serial and multithreaded library +configopts = ['--enable-cblas --enable-shared CC="$CC" auto', + '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto'] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT, + 'lib/libblis-mt.a', 'lib/libblis-mt.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' From 4303be193be986105846a188bad5aa9a23e00b32 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 24 Mar 2022 22:10:42 +0200 Subject: [PATCH 3334/9987] adding easyconfigs: PyFrag-2019-20220216-intel-2020b-ASA.eb and patches: PyFrag-2019_fix_flaky_input_fetch.patch --- .../PyFrag-2019-20220216-intel-2020b-ASA.eb | 52 ++++++ .../PyFrag-2019_fix_flaky_input_fetch.patch | 172 ++++++++++++++++++ 2 files changed, 224 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb create mode 100644 easybuild/easyconfigs/p/PyFrag/PyFrag-2019_fix_flaky_input_fetch.patch diff --git a/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb b/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb new file mode 100644 index 00000000000..0a8957eac46 --- /dev/null +++ b/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb @@ -0,0 +1,52 @@ +easyblock = 'Tarball' + +name = 'PyFrag' +version = '2019-20220216' +versionsuffix = '-ASA' +_commit = '5618d5518a8f4a1fc22805feac57b6e6717a08dc' + +homepage = 'https://pyfragdocument.readthedocs.io/en/latest/includeme.html' +description = """ +PyFrag 2019 resolves three main challenges associated with the automatized computational exploration of reaction +mechanisms: 1) the management of multiple parallel calculations to automatically find a reaction path; 2) the monitoring +of the entire computational process along with the extraction and plotting of relevant information from large amounts of +data; and 3) the analysis and presentation of these data in a clear and informative way. + +This module provides the Activation Strain Analysis (ASA) Module of PyFrag 2019 +""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +github_account = 'sunxb05' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%s.tar.gz' % _commit] +patches = ['PyFrag-2019_fix_flaky_input_fetch.patch'] +checksums = [ + # 5618d5518a8f4a1fc22805feac57b6e6717a08dc.tar.gz + 'b987a94c21ddc828167209be3439f13d4f284c56aeb672f8f0bf4c8ae8b25e67', + 'f93f5496caa75fe8886f03605f82b8520842c6b99abbaf4ad830f78b616bfe48', # PyFrag-2019_fix_flaky_input_fetch.patch +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('dill', '0.3.3'), +] + +start_dir = 'host' + +# for PBS based schedulers: +# postinstallcmds = ["sed -i 's/sbatch/qsub/' %(installdir)s/bin/adf.sh"] + +sanity_check_paths = { + 'files': ['bin/pyfrag'], + 'dirs': ['argueparce', 'result', 'standalone'], +} + +sanity_check_commands = ['pyfrag -h | grep "^Usage:"'] + +modextrapaths = { + 'HOSTPYFRAG': '', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyFrag/PyFrag-2019_fix_flaky_input_fetch.patch b/easybuild/easyconfigs/p/PyFrag/PyFrag-2019_fix_flaky_input_fetch.patch new file mode 100644 index 00000000000..a2fd86dcbbd --- /dev/null +++ b/easybuild/easyconfigs/p/PyFrag/PyFrag-2019_fix_flaky_input_fetch.patch @@ -0,0 +1,172 @@ +Avoid false matches by requiring that input keywords are a full line. +Use sed pattern matching to remove arbitrary limit to 200 lines +see issue https://github.com/sunxb05/PyFrag/issues/1 +author: Alex Domingo (Vrije Universiteit Brussel) +diff --git a/host/argueparce/argueparce.sh b/host/argueparce/argueparce.sh +index 9bcc197..afdf06c 100644 +--- a/host/argueparce/argueparce.sh ++++ b/host/argueparce/argueparce.sh +@@ -113,20 +113,20 @@ rm geometry.txt + input=$* + SCRIPTPATH="$( cd "$(dirname "$1")" ; pwd -P )" + +-grep -A 200 'JOBSUB' $input | grep -B 200 'JOBSUB END' | grep -v 'JOBSUB' | grep -v 'JOBSUB END' > jobsub.txt +-grep -A 200 'ADF' $input | grep -B 200 'ADF END' | grep -v 'ADF' | grep -v 'ADF END' > adf.txt +-grep -A 200 'PyFrag' $input | grep -B 200 'PyFrag END' | grep -v 'PyFrag' | grep -v 'PyFrag END' > pyfrag.txt +-grep -A 200 'Geometrycoor' $input | grep -B 200 'Geometrycoor END' | grep -v 'Geometrycoor' | grep -v 'Geometrycoor END' > coor.xyz +-grep -A 200 'R1 EXTRA' $input | grep -B 200 'R1 EXTRA END' | grep -v 'R1 EXTRA' | grep -v 'R1 EXTRA END' > R1_EXTRA.txt +-grep -A 200 'R2 EXTRA' $input | grep -B 200 'R2 EXTRA END' | grep -v 'R2 EXTRA' | grep -v 'R2 EXTRA END' > R2_EXTRA.txt +-grep -A 200 'RC EXTRA' $input | grep -B 200 'RC EXTRA END' | grep -v 'RC EXTRA' | grep -v 'RC EXTRA END' > RC_EXTRA.txt +-grep -A 200 'TS EXTRA' $input | grep -B 200 'TS EXTRA END' | grep -v 'TS EXTRA' | grep -v 'TS EXTRA END' > TS_EXTRA.txt +-grep -A 200 'P EXTRA' $input | grep -B 200 'P EXTRA END' | grep -v 'P EXTRA' | grep -v 'P EXTRA END' > P_EXTRA.txt +-grep -A 200 'IR EXTRA' $input | grep -B 200 'IR EXTRA END' | grep -v 'IR EXTRA' | grep -v 'IR EXTRA END' > IRC_EXTRA.txt +-grep -A 200 'IR_1 EXTRA' $input | grep -B 200 'IR_1 EXTRA END' | grep -v 'IR_1 EXTRA' | grep -v 'IR_1 EXTRA END' > IRC_1_EXTRA.txt +-grep -A 200 'fragment1 EXTRA' $input | grep -B 200 'fragment1 EXTRA END' | grep -v 'fragment1 EXTRA' | grep -v 'fragment1 EXTRA END' > fragment1_EXTRA.txt +-grep -A 200 'fragment2 EXTRA' $input | grep -B 200 'fragment2 EXTRA END' | grep -v 'fragment2 EXTRA' | grep -v 'fragment2 EXTRA END' > fragment2_EXTRA.txt +-grep -A 200 'complex EXTRA' $input | grep -B 200 'complex EXTRA END' | grep -v 'complex EXTRA' | grep -v 'complex EXTRA END' > complex_EXTRA.txt ++sed -n '/^JOBSUB$/,/^JOBSUB END$/{//!p;}' $input > jobsub.txt ++sed -n '/^ADF$/,/^ADF END$/{//!p;}' $input > adf.txt ++sed -n '/^PyFrag$/,/^PyFrag END$/{//!p;}' $input > pyfrag.txt ++sed -n '/^Geometrycoor$/,/^Geometrycoor END$/{//!p;}' $input > coor.xyz ++sed -n '/^R1 EXTRA$/,/^R1 EXTRA END$/{//!p;}' $input > R1_EXTRA.txt ++sed -n '/^R2 EXTRA$/,/^R2 EXTRA END$/{//!p;}' $input > R2_EXTRA.txt ++sed -n '/^RC EXTRA$/,/^RC EXTRA END$/{//!p;}' $input > RC_EXTRA.txt ++sed -n '/^TS EXTRA$/,/^TS EXTRA END$/{//!p;}' $input > TS_EXTRA.txt ++sed -n '/^P EXTRA$/,/^P EXTRA END$/{//!p;}' $input > P_EXTRA.txt ++sed -n '/^IR EXTRA$/,/^IR EXTRA END$/{//!p;}' $input > IRC_EXTRA.txt ++sed -n '/^IR_1 EXTRA$/,/^IR_1 EXTRA END$/{//!p;}' $input > IRC_1_EXTRA.txt ++sed -n '/^fragment1 EXTRA$/,/^fragment1 EXTRA END$/{//!p;}' $input > fragment1_EXTRA.txt ++sed -n '/^fragment2 EXTRA$/,/^fragment2 EXTRA END$/{//!p;}' $input > fragment2_EXTRA.txt ++sed -n '/^complex EXTRA$/,/^complex EXTRA END$/{//!p;}' $input > complex_EXTRA.txt + + + submit="$QMWORKS/bin/python3 $HOSTPYFRAG/job.py \\" +diff --git a/host/standalone/adf_new/pyfragparce.sh b/host/standalone/adf_new/pyfragparce.sh +index 182cef2..6cf5edb 100644 +--- a/host/standalone/adf_new/pyfragparce.sh ++++ b/host/standalone/adf_new/pyfragparce.sh +@@ -74,12 +74,12 @@ fi + input=$* + SCRIPTPATH="$( cd "$(dirname "$1")" ; pwd -P )" + +-grep -A 200 'JOBSUB' $input | grep -B 200 'JOBSUB END' | grep -v 'JOBSUB' | grep -v 'JOBSUB END' > jobsub.txt +-grep -A 200 'ADF' $input | grep -B 200 'ADF END' | grep -v 'ADF' | grep -v 'ADF END' > adf.txt +-grep -A 200 'PyFrag' $input | grep -B 200 'PyFrag END' | grep -v 'PyFrag' | grep -v 'PyFrag END' > pyfrag.txt +-grep -A 200 'fragment1 EXTRA' $input | grep -B 200 'fragment1 EXTRA END' | grep -v 'fragment1 EXTRA' | grep -v 'fragment1 EXTRA END' > fragment1_EXTRA.txt +-grep -A 200 'fragment2 EXTRA' $input | grep -B 200 'fragment2 EXTRA END' | grep -v 'fragment2 EXTRA' | grep -v 'fragment2 EXTRA END' > fragment2_EXTRA.txt +-grep -A 200 'complex EXTRA' $input | grep -B 200 'complex EXTRA END' | grep -v 'complex EXTRA' | grep -v 'complex EXTRA END' > complex_EXTRA.txt ++sed -n '/^JOBSUB$/,/^JOBSUB END$/{//!p;}' $input > jobsub.txt ++sed -n '/^ADF$/,/^ADF END$/{//!p;}' $input > adf.txt ++sed -n '/^PyFrag$/,/^PyFrag END$/{//!p;}' $input > pyfrag.txt ++sed -n '/^fragment1 EXTRA$/,/^fragment1 EXTRA END$/{//!p;}' $input > fragment1_EXTRA.txt ++sed -n '/^fragment2 EXTRA$/,/^fragment2 EXTRA END$/{//!p;}' $input > fragment2_EXTRA.txt ++sed -n '/^complex EXTRA$/,/^complex EXTRA END$/{//!p;}' $input > complex_EXTRA.txt + + + submit="amspython \$HOSTPYFRAG/standalone/adf_new/PyFrag.py \\" +diff --git a/host/standalone/adf_newopen/pyfragparce.sh b/host/standalone/adf_newopen/pyfragparce.sh +index d3216fa..95d562e 100644 +--- a/host/standalone/adf_newopen/pyfragparce.sh ++++ b/host/standalone/adf_newopen/pyfragparce.sh +@@ -61,12 +61,12 @@ done + input=$* + SCRIPTPATH="$( cd "$(dirname "$1")" ; pwd -P )" + +-grep -A 200 'JOBSUB' $input | grep -B 200 'JOBSUB END' | grep -v 'JOBSUB' | grep -v 'JOBSUB END' > jobsub.txt +-grep -A 200 'ADF' $input | grep -B 200 'ADF END' | grep -v 'ADF' | grep -v 'ADF END' > adf.txt +-grep -A 200 'PyFrag' $input | grep -B 200 'PyFrag END' | grep -v 'PyFrag' | grep -v 'PyFrag END' > pyfrag.txt +-grep -A 200 'fragment1 EXTRA' $input | grep -B 200 'fragment1 EXTRA END' | grep -v 'fragment1 EXTRA' | grep -v 'fragment1 EXTRA END' > fragment1_EXTRA.txt +-grep -A 200 'fragment2 EXTRA' $input | grep -B 200 'fragment2 EXTRA END' | grep -v 'fragment2 EXTRA' | grep -v 'fragment2 EXTRA END' > fragment2_EXTRA.txt +-grep -A 200 'complex EXTRA' $input | grep -B 200 'complex EXTRA END' | grep -v 'complex EXTRA' | grep -v 'complex EXTRA END' > complex_EXTRA.txt ++sed -n '/^JOBSUB$/,/^JOBSUB END$/{//!p;}' $input > jobsub.txt ++sed -n '/^ADF$/,/^ADF END$/{//!p;}' $input > adf.txt ++sed -n '/^PyFrag$/,/^PyFrag END$/{//!p;}' $input > pyfrag.txt ++sed -n '/^fragment1 EXTRA$/,/^fragment1 EXTRA END$/{//!p;}' $input > fragment1_EXTRA.txt ++sed -n '/^fragment2 EXTRA$/,/^fragment2 EXTRA END$/{//!p;}' $input > fragment2_EXTRA.txt ++sed -n '/^complex EXTRA$/,/^complex EXTRA END$/{//!p;}' $input > complex_EXTRA.txt + + + submit="python3 \$HOSTPYFRAG/standalone/adf_newopen/PyFrag.py \\" +diff --git a/host/standalone/adf_old/pyfragparce.sh b/host/standalone/adf_old/pyfragparce.sh +index 506ec3e..0edbe4d 100644 +--- a/host/standalone/adf_old/pyfragparce.sh ++++ b/host/standalone/adf_old/pyfragparce.sh +@@ -61,13 +61,12 @@ done + input=$* + SCRIPTPATH="$( cd "$(dirname "$1")" ; pwd -P )" + +-grep -A 200 'JOBSUB' $input | grep -B 200 'JOBSUB END' | grep -v 'JOBSUB' | grep -v 'JOBSUB END' > jobsub.txt +-grep -A 200 'ADF' $input | grep -B 200 'ADF END' | grep -v 'ADF' | grep -v 'ADF END' > adf.txt +-grep -A 200 'PyFrag' $input | grep -B 200 'PyFrag END' | grep -v 'PyFrag' | grep -v 'PyFrag END' > pyfrag.txt +-grep -A 200 'fragment1 EXTRA' $input | grep -B 200 'fragment1 EXTRA END' | grep -v 'fragment1 EXTRA' | grep -v 'fragment1 EXTRA END' > fragment1_EXTRA.txt +-grep -A 200 'fragment2 EXTRA' $input | grep -B 200 'fragment2 EXTRA END' | grep -v 'fragment2 EXTRA' | grep -v 'fragment2 EXTRA END' > fragment2_EXTRA.txt +-grep -A 200 'complex EXTRA' $input | grep -B 200 'complex EXTRA END' | grep -v 'complex EXTRA' | grep -v 'complex EXTRA END' > complex_EXTRA.txt +- ++sed -n '/^JOBSUB$/,/^JOBSUB END$/{//!p;}' $input > jobsub.txt ++sed -n '/^ADF$/,/^ADF END$/{//!p;}' $input > adf.txt ++sed -n '/^PyFrag$/,/^PyFrag END$/{//!p;}' $input > pyfrag.txt ++sed -n '/^fragment1 EXTRA$/,/^fragment1 EXTRA END$/{//!p;}' $input > fragment1_EXTRA.txt ++sed -n '/^fragment2 EXTRA$/,/^fragment2 EXTRA END$/{//!p;}' $input > fragment2_EXTRA.txt ++sed -n '/^complex EXTRA$/,/^complex EXTRA END$/{//!p;}' $input > complex_EXTRA.txt + + submit="python3 \$HOSTPYFRAG/standalone/adf_old/PyFrag.py \\" + subadfinputfile="--adfinputfile "$SCRIPTPATH/"adfinputfile \\" +diff --git a/host/standalone/adf_open/pyfragparce.sh b/host/standalone/adf_open/pyfragparce.sh +index 8fe3ead..edc3c3a 100644 +--- a/host/standalone/adf_open/pyfragparce.sh ++++ b/host/standalone/adf_open/pyfragparce.sh +@@ -98,15 +98,15 @@ done + input=$* + SCRIPTPATH="$( cd "$(dirname "$1")" ; pwd -P )" + +-grep -A 200 'JOBSUB' $input | grep -B 200 'JOBSUB END' | grep -v 'JOBSUB' | grep -v 'JOBSUB END' > jobsub.txt +-grep -A 200 'ADF' $input | grep -B 200 'ADF END' | grep -v 'ADF' | grep -v 'ADF END' > adf.txt +-grep -A 200 'PyFrag' $input | grep -B 200 'PyFrag END' | grep -v 'PyFrag' | grep -v 'PyFrag END' > pyfrag.txt +-grep -A 200 'fragment1 EXTRA' $input | grep -B 200 'fragment1 EXTRA END' | grep -v 'fragment1 EXTRA' | grep -v 'fragment1 EXTRA END' > fragment1_EXTRA.txt +-grep -A 200 'fragment2 EXTRA' $input | grep -B 200 'fragment2 EXTRA END' | grep -v 'fragment2 EXTRA' | grep -v 'fragment2 EXTRA END' > fragment2_EXTRA.txt +-grep -A 200 'complex EXTRA' $input | grep -B 200 'complex EXTRA END' | grep -v 'complex EXTRA' | grep -v 'complex EXTRA END' > complex_EXTRA.txt +-grep -A 200 'fragment1 open EXTRA' $input | grep -B 200 'fragment1 open EXTRA END' | grep -v 'fragment1 open EXTRA' | grep -v 'fragment1 open EXTRA END' > fragment1_open_EXTRA.txt +-grep -A 200 'fragment2 open EXTRA' $input | grep -B 200 'fragment2 open EXTRA END' | grep -v 'fragment2 open EXTRA' | grep -v 'fragment2 open EXTRA END' > fragment2_open_EXTRA.txt +-grep -A 200 'complex open EXTRA' $input | grep -B 200 'complex open EXTRA END' | grep -v 'complex open EXTRA' | grep -v 'complex open EXTRA END' > complex_open_EXTRA.txt ++sed -n '/^JOBSUB$/,/^JOBSUB END$/{//!p;}' $input > jobsub.txt ++sed -n '/^ADF$/,/^ADF END$/{//!p;}' $input > adf.txt ++sed -n '/^PyFrag$/,/^PyFrag END$/{//!p;}' $input > pyfrag.txt ++sed -n '/^fragment1 EXTRA$/,/^fragment1 EXTRA END$/{//!p;}' $input > fragment1_EXTRA.txt ++sed -n '/^fragment2 EXTRA$/,/^fragment2 EXTRA END$/{//!p;}' $input > fragment2_EXTRA.txt ++sed -n '/^complex EXTRA$/,/^complex EXTRA END$/{//!p;}' $input > complex_EXTRA.txt ++sed -n '/^fragment1 open EXTRA$/,/^fragment1 open EXTRA END$/{//!p;}' $input > fragment1_open_EXTRA.txt ++sed -n '/^fragment2 open EXTRA$/,/^fragment2 open EXTRA END$/{//!p;}' $input > fragment2_open_EXTRA.txt ++sed -n '/^complex open EXTRA$/,/^complex open EXTRA END$/{//!p;}' $input > complex_open_EXTRA.txt + + submit="python3 \$HOSTPYFRAG/standalone/adf_open/PyFrag.py \\" + subadfinputfile="--adfinputfile "$SCRIPTPATH/"adfinputfile \\" +diff --git a/host/standalone/adf_openorb/pyfragparce.sh b/host/standalone/adf_openorb/pyfragparce.sh +index b3ba2aa..49e2adb 100644 +--- a/host/standalone/adf_openorb/pyfragparce.sh ++++ b/host/standalone/adf_openorb/pyfragparce.sh +@@ -12,7 +12,7 @@ done < "$pyfrag" + input=$* + SCRIPTPATH="$( cd "$(dirname "$1")" ; pwd -P )" + +-grep -A 200 'PyFrag' $input | grep -B 200 'PyFrag END' | grep -v 'PyFrag' | grep -v 'PyFrag END' > pyfrag.txt ++sed -n '/^PyFrag$/,/^PyFrag END$/{//!p;}' $input > pyfrag.txt + + submit="python3 \$HOSTPYFRAG/standalone/adf_openorb/PyFrag.py \\" + +diff --git a/host/standalone/adf_single/pyfragparce.sh b/host/standalone/adf_single/pyfragparce.sh +index c1444b3..6c3bc66 100644 +--- a/host/standalone/adf_single/pyfragparce.sh ++++ b/host/standalone/adf_single/pyfragparce.sh +@@ -61,9 +61,9 @@ done + input=$* + SCRIPTPATH="$( cd "$(dirname "$1")" ; pwd -P )" + +-grep -A 200 'JOBSUB' $input | grep -B 200 'JOBSUB END' | grep -v 'JOBSUB' | grep -v 'JOBSUB END' > jobsub.txt +-grep -A 200 'ADF' $input | grep -B 200 'ADF END' | grep -v 'ADF' | grep -v 'ADF END' > adf.txt +-grep -A 200 'PyFrag' $input | grep -B 200 'PyFrag END' | grep -v 'PyFrag' | grep -v 'PyFrag END' > pyfrag.txt ++sed -n '/^JOBSUB$/,/^JOBSUB END$/{//!p;}' $input > jobsub.txt ++sed -n '/^ADF$/,/^ADF END$/{//!p;}' $input > adf.txt ++sed -n '/^PyFrag$/,/^PyFrag END$/{//!p;}' $input > pyfrag.txt + + submit="python3 \$HOSTPYFRAG/standalone/adf_single/PyFrag.py \\" + subadfinputfile="--adfinputfile "$SCRIPTPATH/"adfinputfile \\" From 62f723c92c89f7b0cedbda0f03d23fdbf9f36d3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Mar 2022 21:17:23 +0100 Subject: [PATCH 3335/9987] adding easyconfigs: MUSCLE-3.8.31-GCCcore-11.2.0.eb --- .../m/MUSCLE/MUSCLE-3.8.31-GCCcore-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5e25be1d014 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '3.8.31' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] +patches = ['MUSCLE-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + '7486ac0eee30ac3de9ee06020fe8573cf1de8e21ce5f315c3232ec226191a60d', # MUSCLE-3.8.31_fix-mk-hardcoding.patch +] + +builddependencies = [ + ('binutils', '2.37'), +] + +files_to_copy = [ + (["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/muscle"], + 'dirs': [], +} + +sanity_check_commands = ["muscle -version"] + +moduleclass = 'bio' From 8ea2833d5ee247f652a839257188e253675074ae Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 25 Mar 2022 00:35:49 +0200 Subject: [PATCH 3336/9987] fix checksum of PyFrag-2019_fix_flaky_input_fetch.patch --- .../p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb b/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb index 0a8957eac46..a9df7f318e8 100644 --- a/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb +++ b/easybuild/easyconfigs/p/PyFrag/PyFrag-2019-20220216-intel-2020b-ASA.eb @@ -24,7 +24,7 @@ patches = ['PyFrag-2019_fix_flaky_input_fetch.patch'] checksums = [ # 5618d5518a8f4a1fc22805feac57b6e6717a08dc.tar.gz 'b987a94c21ddc828167209be3439f13d4f284c56aeb672f8f0bf4c8ae8b25e67', - 'f93f5496caa75fe8886f03605f82b8520842c6b99abbaf4ad830f78b616bfe48', # PyFrag-2019_fix_flaky_input_fetch.patch + 'bb47a31f14329f5ccb7b58e03ce4bde133739acccc76e65ca0e1d69a8ac3694e', # PyFrag-2019_fix_flaky_input_fetch.patch ] dependencies = [ From d4b924d060be87cb5942ad7f19a596a44ad60b07 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 25 Mar 2022 09:27:54 +0100 Subject: [PATCH 3337/9987] set python3 root dir --- easybuild/easyconfigs/v/VTK/VTK-9.1.0-foss-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.1.0-foss-2021b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.1.0-foss-2021b.eb index 0d8e0e801df..4f1fa372e75 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.1.0-foss-2021b.eb @@ -49,6 +49,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " # Python configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " # Other configopts += "-DVTK_USE_MPI=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" From 70f7aa304821af2e70af6fd966f0b1e71849e260 Mon Sep 17 00:00:00 2001 From: sagon Date: Fri, 25 Mar 2022 13:58:38 +0200 Subject: [PATCH 3338/9987] adding easyconfigs: xtb-6.4.1-foss-2021b.eb --- .../easyconfigs/x/xtb/xtb-6.4.1-foss-2021b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.4.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.4.1-foss-2021b.eb b/easybuild/easyconfigs/x/xtb/xtb-6.4.1-foss-2021b.eb new file mode 100644 index 00000000000..79c3b897d01 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.4.1-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'xtb' +version = '6.4.1' + +homepage = 'https://xtb-docs.readthedocs.io' +description = """ xtb - An extended tight-binding semi-empirical program package. """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['cd7b6ec9b7963012ce71220a70773641f0d9e06e0691750a25b83e823510d1d7'] + +github_account = 'grimme-lab' +builddependencies = [ + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), +] + +configopts = "-Dla_backend='custom' " +configopts += "-Dcustom_libraries='flexiblas' " +configopts += "--optimization=2 " +configopts += "--buildtype release " +configopts += "--warnlevel 0 " +configopts += "-Dpython=false" + +runtest = 'meson' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' # Ensure test don't timeout + +sanity_check_paths = { + 'files': ['bin/xtb', 'include/xtb/xtb.h'] + ['lib/libxtb.%s' % e for e in ('a', SHLIB_EXT)], + 'dirs': ['share'], +} + +modextravars = { + 'XTBHOME': '%(installdir)s', + 'XTBPATH': '%(installdir)s', +} + +moduleclass = 'chem' From 3738083220ed67f1a71bad953fa13271e35db4ad Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 25 Mar 2022 17:09:09 +0100 Subject: [PATCH 3339/9987] Added required changes --- .../p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb | 10 ++++-- .../pyEGA3/pyega3-4.0.0-fixRequirements.patch | 31 ------------------- 2 files changed, 7 insertions(+), 34 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pyEGA3/pyega3-4.0.0-fixRequirements.patch diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb index 719c07934e0..334f40c6ca3 100644 --- a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb @@ -18,7 +18,7 @@ dependencies = [ use_pip = True exts_list = [ - ('humanize', version, { + ('humanize', '4.0.0', { 'checksums': ['ee1f872fdfc7d2ef4a28d4f80ddde9f96d36955b5d6b0dac4bdeb99502bddb00'], }), ('htsget', '0.2.5', { @@ -28,8 +28,8 @@ exts_list = [ 'checksums': ['aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e'], }), (name, version, { - 'patches': ['pyega3-4.0.0-fixRequirements.patch'], 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'preinstallopts': "sed -i 's/==/>=/g' setup.py && ", 'checksums': [ '4a1582da6b3c018e69c9d6023cd0344372e7c3d6be19c8f3f75a5123b53de065', # pyega3-4.0.0.tar.gz '9bf620a327b6743070ed85f3058d9e2d2fb1cf84b6775e499717d735c3c050da', # pyega3-4.0.0-fixRequirements.patch @@ -37,11 +37,15 @@ exts_list = [ }), ] + + sanity_pip_check = True sanity_check_paths = { 'files': ['bin/pyega3'], - 'dirs': [] + 'dirs': ['lib/python%(pyshortver)s/site-packages'] } +sanity_check_commands = ["pyega3 -h"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyEGA3/pyega3-4.0.0-fixRequirements.patch b/easybuild/easyconfigs/p/pyEGA3/pyega3-4.0.0-fixRequirements.patch deleted file mode 100644 index 5136aa3e2af..00000000000 --- a/easybuild/easyconfigs/p/pyEGA3/pyega3-4.0.0-fixRequirements.patch +++ /dev/null @@ -1,31 +0,0 @@ -pyEGA3 has strict version requirements, but included tests run even when -using newer versions. -Author: Orient Kružík (INUITS) -diff -ruN pyega3-4.0.0_orig/pyega3.egg-info/requires.txt pyega3-4.0.0/pyega3.egg-info/requires.txt ---- pyega3-4.0.0_orig/pyega3.egg-info/requires.txt 2021-12-09 14:09:53.000000000 +0100 -+++ pyega3-4.0.0/pyega3.egg-info/requires.txt 2022-03-18 16:17:16.080009959 +0100 -@@ -1,5 +1,5 @@ --requests==2.26.0 --tqdm==4.19.6 --htsget==0.2.5 --psutil==5.6.6 --urllib3==1.26.7 -+requests>=2.26.0 -+tqdm>=4.19.6 -+htsget>=0.2.5 -+psutil>=5.6.6 -+urllib3>=1.26.7 -diff -ruN pyega3-4.0.0_orig/setup.py pyega3-4.0.0/setup.py ---- pyega3-4.0.0_orig/setup.py 2021-12-08 23:16:24.000000000 +0100 -+++ pyega3-4.0.0/setup.py 2022-03-18 16:24:03.075866555 +0100 -@@ -33,8 +33,8 @@ - author="EGA team", - author_email="ega-helpdesk@ebi.ac.uk", - python_requires=">=3.6", -- install_requires=["requests==2.26.0", "tqdm==4.19.6", "htsget==0.2.5", "psutil==5.6.6", "urllib3==1.26.7"], -- tests_require=["pytest~=6.2.5", "coverage==4.5.1", "responses~=0.16.0", "pyfakefs~=4.5.3"], -+ install_requires=["requests>=2.26.0", "tqdm>=4.19.6", "htsget>=0.2.5", "psutil>=5.6.6", "urllib3>=1.26.7"], -+ tests_require=["pytest~=6.2.5", "coverage>=4.5.1", "responses~=0.16.0", "pyfakefs~=4.5.3"], - keywords=["EGA", "archive"], - license="Apache License, Version 2.0", - url="https://github.com/EGA-archive/ega-download-client", From 922c40d0a6cf1aa444c154b1effb449b68551a2c Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 25 Mar 2022 19:29:17 +0100 Subject: [PATCH 3340/9987] Removed empty lines --- easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb index 334f40c6ca3..d35e3548352 100644 --- a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb @@ -37,8 +37,6 @@ exts_list = [ }), ] - - sanity_pip_check = True sanity_check_paths = { From 7007ccec95846d40eb8d6311159f1d52f09c96be Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 25 Mar 2022 20:29:00 +0100 Subject: [PATCH 3341/9987] Removed redundant checksum --- .../easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb index d35e3548352..9a860fd20ee 100644 --- a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb @@ -18,7 +18,7 @@ dependencies = [ use_pip = True exts_list = [ - ('humanize', '4.0.0', { + ('humanize', version, { 'checksums': ['ee1f872fdfc7d2ef4a28d4f80ddde9f96d36955b5d6b0dac4bdeb99502bddb00'], }), ('htsget', '0.2.5', { @@ -28,12 +28,9 @@ exts_list = [ 'checksums': ['aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e'], }), (name, version, { - 'sources': ['%(namelower)s-%(version)s.tar.gz'], 'preinstallopts': "sed -i 's/==/>=/g' setup.py && ", - 'checksums': [ - '4a1582da6b3c018e69c9d6023cd0344372e7c3d6be19c8f3f75a5123b53de065', # pyega3-4.0.0.tar.gz - '9bf620a327b6743070ed85f3058d9e2d2fb1cf84b6775e499717d735c3c050da', # pyega3-4.0.0-fixRequirements.patch - ], + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['4a1582da6b3c018e69c9d6023cd0344372e7c3d6be19c8f3f75a5123b53de065'], }), ] From 58ab9f9d8d467c589f284f294f51d7a5cb6d4ceb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Mar 2022 09:29:50 +0100 Subject: [PATCH 3342/9987] add Sys::Info::Driver::Unknown extension to Perl v5.34.0 --- easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 5567f17c103..3d828aefb87 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1804,6 +1804,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], }), + ('Sys::Info::Driver::Unknown', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), ] moduleclass = 'lang' From 8f3afe69446ffdbd86c95a3d0e7565f28cb20055 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Mar 2022 09:30:56 +0100 Subject: [PATCH 3343/9987] enable running of tests for MEME with gompi/2021b --- .../easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb index 369b5cf382b..bf4ba05527b 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb @@ -35,6 +35,8 @@ configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/b # config.log should indicate that all required/optional dependencies were found (see scripts/dependencies.pl) configopts += " && grep 'All required and optional Perl modules were found' config.log" +runtest = 'test' + fix_perl_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] fix_python_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] From 352d8a2e85f1a86baf767c2bb7c4a16ee3129a77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Mar 2022 08:42:45 +0200 Subject: [PATCH 3344/9987] adding easyconfigs: RevBayes-1.1.1-GCC-11.2.0.eb --- .../r/RevBayes/RevBayes-1.1.1-GCC-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..3512d9cbffc --- /dev/null +++ b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.1.1-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +# easybuild easyconfig +# +# John Dey +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +easyblock = 'CmdCp' + +name = 'RevBayes' +version = '1.1.1' + +homepage = 'https://revbayes.github.io/' + +description = """RevBayes provides an interactive environment for statistical computation in + phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in + evolutionary biology, particularly phylogenetics.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/revbayes/revbayes/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['d61293fceac817d8203ed1e828661d76c73fa16bf04458a50a37057e99fd40c0'] + +builddependencies = [('CMake', '3.22.1')] + +dependencies = [ + ('Boost', '1.77.0'), +] + +start_dir = 'projects/cmake' +local_cmd = './build.sh -DCMAKE_CXX_FLAGS="-pthread" -DBoost_NO_BOOST_CMAKE=ON' +cmds_map = [('', local_cmd)] + +files_to_copy = [(['projects/cmake/rb'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/rb'], + 'dirs': [], +} + +moduleclass = 'bio' From e4db0bf72d943c08f63ca246916095fe730bf65d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Mar 2022 08:49:33 +0200 Subject: [PATCH 3345/9987] also add Sys::Info::Driver::Linux extension for Perl v5.34.0 --- easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 3d828aefb87..750578c043a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1809,6 +1809,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], }), + ('Sys::Info::Driver::Linux', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), ] moduleclass = 'lang' From cc218e22ed5666b3d359619f2eff1e7ba93a90b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Mar 2022 11:07:24 +0200 Subject: [PATCH 3346/9987] also include Unix::Processors extension to Perl v5.34.0 Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 750578c043a..63d38816c14 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1814,6 +1814,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER/'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), ] moduleclass = 'lang' From ef39a71c065efd5f0613d130d1342875c2a7efc4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Mar 2022 13:37:42 +0200 Subject: [PATCH 3347/9987] adding easyconfigs: ecCodes-2.24.2-gompi-2021b.eb --- .../e/ecCodes/ecCodes-2.24.2-gompi-2021b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-gompi-2021b.eb diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-gompi-2021b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-gompi-2021b.eb new file mode 100644 index 00000000000..851fe34ed55 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.24.2-gompi-2021b.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.24.2' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': False} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['c60ad0fd89e11918ace0d84c01489f21222b11d6cad3ff7495856a0add610403'] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [ + ('netCDF', '4.8.1'), + ('JasPer', '2.0.33'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF " +configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " +configopts += "-DENABLE_ECCODES_THREADS=ON" # multi-threading with pthreads + +local_exes = ['%s_%s' % (a, b) + for a in ['bufr', 'grib', 'gts', 'metar'] + for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] +local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + + ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 32265afa43a3558989270ae2cf9f048e07a32d61 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Mar 2022 14:54:04 +0200 Subject: [PATCH 3348/9987] fix GBprocesS easyconfig by switching to source tarball created using git_config (#15048) * fix GBprocesS easyconfig by switching to source tarball created using git_config * clarify why git_config is needed for GBprocesS --- .../GBprocesS-2.3-intel-2020a-Python-3.8.2.eb | 27 ++++++++++--------- 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb index f0eb2e141fb..93638db31a3 100644 --- a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb @@ -1,6 +1,7 @@ easyblock = 'PythonPackage' name = 'GBprocesS' +local_commit = '82e21929' version = '2.3' versionsuffix = '-Python-%(pyver)s' @@ -14,9 +15,18 @@ used.""" toolchain = {'name': 'intel', 'version': '2020a'} -source_urls = ['https://gitlab.com/dschaumont/GBprocesS/-/archive/%(version)s/'] -sources = ['GBprocesS-%(version)s.tar.gz'] -checksums = ['374fa7bc096e0cbc83746f505bea134117debed99b7510cb4123878aeaea9456'] +# need to use git_config rather than just downloading source tarball, +# because .git subdirectory is required by setuptools-scm to determine version +sources = [{ + 'filename': 'GBprocesS-%%(version)s-%s.tar.gz' % local_commit, + 'git_config': { + 'url': 'https://gitlab.com/dschaumont', + 'repo_name': name, + 'commit': local_commit, + 'keep_git_dir': True, + }, +}] +checksums = [None] dependencies = [ ('Python', '3.8.2'), @@ -29,17 +39,8 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -# The package uses setuptools-scm, so we avoid using the "version" part of it. -pretestopts = ( - "sed -i 's/" - "__version__ = get_distribution(__name__).version/" - "__version__ = \"%(version)s\"/g' gbprocess/__init__.py && " - "sed -i \"s|use_scm_version={'write_to': 'gbprocess/version.py'}|version='%(version)s'|g\" setup.py && " -) - -runtest = 'python -m unittest discover -v -s ./test -p test_*.py' - sanity_check_commands = [ + "cd %(builddir)s/GBprocesS && python -m unittest discover -v -s ./test -p test_*.py", "touch %(builddir)s/17146FL-13-01-01_S97_L002_R1_001.fastq", "touch %(builddir)s/17146FL-13-01-01_S97_L002_R2_001.fastq", # Trivial configuration file to use when running gbprocess sanity check From f0b4a6c90cef3775023015e9abd9c9628a84dc16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Mar 2022 15:12:36 +0200 Subject: [PATCH 3349/9987] adding easyconfigs: VirtualGL-3.0-GCC-11.2.0.eb, pocl-1.8-GCC-11.2.0.eb and patches: pocl-1.8_fix-header-install.patch --- .../easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb | 44 +++++++++++++++++++ .../p/pocl/pocl-1.8_fix-header-install.patch | 24 ++++++++++ .../v/VirtualGL/VirtualGL-3.0-GCC-11.2.0.eb | 44 +++++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.8_fix-header-install.patch create mode 100644 easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb new file mode 100644 index 00000000000..8dff6865a13 --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '1.8' + +homepage = 'https://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['pocl-%(version)s_fix-header-install.patch'] +checksums = [ + '0f63377ae1826e16e90038fc8e7f65029be4ff6f9b059f6907174b5c0d1f8ab2', # v1.8.tar.gz + '97dc45437ae7464bda9f13088720482804b8a19a4e71067196daa86af487222d', # pocl-1.8_fix-header-install.patch +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Clang', '12.0.1'), + ('hwloc', '2.5.0'), + ('libtool', '2.4.6'), + ('libxml2', '2.9.10'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8_fix-header-install.patch b/easybuild/easyconfigs/p/pocl/pocl-1.8_fix-header-install.patch new file mode 100644 index 00000000000..aa74658080d --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8_fix-header-install.patch @@ -0,0 +1,24 @@ +see https://github.com/pocl/pocl/issues/1000 + https://github.com/pocl/pocl/pull/1001 + +From f5a841706edd5b201274337660528d75797031bc Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Andr=C3=A9=20Gem=C3=BCnd?= + +Date: Thu, 11 Nov 2021 09:38:24 +0100 +Subject: [PATCH] Add missing cl_ext_pocl.h to install. + +--- + include/CL/CMakeLists.txt | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/include/CL/CMakeLists.txt b/include/CL/CMakeLists.txt +index 63e6b1ba4..eb4f4773d 100644 +--- a/include/CL/CMakeLists.txt ++++ b/include/CL/CMakeLists.txt +@@ -35,6 +35,7 @@ if(INSTALL_OPENCL_HEADERS) + cl_ext.h + cl_egl.h + cl_ext_intel.h ++ cl_ext_pocl.h + cl_gl.h + cl_gl_ext.h + cl_half.h diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.0-GCC-11.2.0.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..7a40a510856 --- /dev/null +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.0-GCC-11.2.0.eb @@ -0,0 +1,44 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# updated by Valentin Plugaru 2019-09-26 + +easyblock = 'CMakeMake' + +name = 'VirtualGL' +version = '3.0' + +homepage = 'https://virtualgl.org/' +description = """VirtualGL is an open source toolkit that gives any Linux or +Unix remote display software the ability to run OpenGL applications with full +hardware acceleration.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d6e00a8d0596cafa67955d6211e0dab6c8aa8239bd718f7eca6eb0b032711f9b'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37'), +] + +dependencies = [ + ('libjpeg-turbo', '2.0.6'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('pocl', '1.8'), +] + +local_binaries = [ + 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', + 'vglclient', 'vglconfig', 'vglconnect', 'vglgenkey', 'vgllogin', 'vglrun', + 'vglserver_config' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib64', 'share', 'include'], +} + +moduleclass = 'vis' From c301161168e23fe9ed5f674df4903491ecbdfc2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Mar 2022 15:46:59 +0200 Subject: [PATCH 3350/9987] adding easyconfigs: SlamDunk-0.4.3-foss-2021b.eb --- .../s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb new file mode 100644 index 00000000000..8bcc3df3072 --- /dev/null +++ b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'SlamDunk' +version = '0.4.3' + +homepage = 'https://t-neumann.github.io/slamdunk' +description = """SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible +SLAMseq data analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8475d4cadad3defda6b11de405fc59de917a6e57468f709a1e28b8a0627f2ff5'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('pybedtools', '0.8.2'), + ('Pysam', '0.17.0'), + ('Biopython', '1.79'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/slamdunk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["slamdunk --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 83072ff812b3394caa592b4a79f4f238e058ce32 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Mar 2022 15:52:33 +0200 Subject: [PATCH 3351/9987] adding easyconfigs: CmdStanR-0.5.0-foss-2021b-R-4.1.2.eb --- .../CmdStanR-0.5.0-foss-2021b-R-4.1.2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.0-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.0-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.0-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..521b4389c86 --- /dev/null +++ b/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.0-foss-2021b-R-4.1.2.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'CmdStanR' +version = '0.5.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://mc-stan.org/cmdstanr' +description = "CmdStanR is a lightweight interface to Stan for R users" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/stan-dev/cmdstanr/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['073847e839d00ba63b3fa24398e7e684d8c3f0797c7ccba7022a2caef6f04305'] + +dependencies = [ + ('R', '4.1.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From 216dc6c4ca9ddc94eb203c42084a6f0c62ef371a Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 28 Mar 2022 17:59:15 +0200 Subject: [PATCH 3352/9987] Fixed bugs + added requested changes --- .../s/SCGid/SCGid-0.9b0-foss-2021b.eb | 31 ++++++++----------- 1 file changed, 13 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index a62b9b2aaaa..d27c3a46083 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -11,20 +11,17 @@ description = 'A consensus approach to contig filtering and genome prediction fr toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ["https://github.com/amsesk/SCGid/archive"] -sources = ['%s.tar.gz' % local_commit] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] patches = [ "SCGid-0.9-fixPrintToPython3.patch", "SCGid-0.9b0-initEdit.patch" ] checksums = [ - # be106e4cd888fd913a527ea821e510e0afb100be.tar.gz - '1f625e8f87b4d5e4ec9831ebe48763676679d6d6c41b05ef0bb59e6a7f839153', + '1f625e8f87b4d5e4ec9831ebe48763676679d6d6c41b05ef0bb59e6a7f839153', # SCGid-0.9b0.tar.gz 'ee251b71ed3eed097b05751a3cea302d954000e1a8112e6e3f297e67c84996f7', # SCGid-0.9-fixPrintToPython3.patch '7ae6759deffbb4f4c07943fd9aa44739e5b3d0e9ef724cee3e1dc03b71ad4735', # SCGid-0.9b0-initEdit.patch ] -local_clams_commit = "e326c34307803b9ea8ffc975ddd9bd05643af931" - dependencies = [ ('Python', '3.9.6'), ('R', '4.1.2'), @@ -43,26 +40,21 @@ download_dep_fail = False exts_defaultclass = "Tarball" -postinstallcmds = [ - 'ln -s %%(installdir)s/ClaMS-CLI-fork-%s/ClaMS-CLI.jar %%(installdir)s/ClaMS-CLI.jar' % local_clams_commit, -] - options = {'modulename': False} +local_clams_commit = "e326c34307803b9ea8ffc975ddd9bd05643af931" + exts_list = [ ('ClaMS-CLI', '31012020', { 'source_urls': ['https://github.com/amsesk/ClaMS-CLI-fork/archive'], - 'sources': [{ - 'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', - 'filename': 'ClaMS-CLI-%(version)s.tar.gz' - }], + 'sources': [{'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', 'filename': 'ClaMS-CLI-%(version)s.tar.gz'}], 'checksums': ['743397fc8308e363f127bd7e5165ac9d769c10305f6e33d9e408db8f343170db'], }), ('ESOM', '1.1', { 'download_instructions': """ - You need to manually provide Databionics ESOM. Please, follow these steps: - (1): Go to https://sourceforge.net/projects/databionic-esom/files/databionic-esom/1.1/ and - download "esom-1.1-installer.jar" + You need to manually provide Databionics ESOM. Please, follow these steps: + (1): Go to https://sourceforge.net/projects/databionic-esom/files/databionic-esom/%(version)s/ and + download "esom-%(version)s-installer.jar" (2): Run the file and follow through the installation process (ensure you have Java installed to run the file) (3): Open terminal in the folder where you have installed ESOM and create Tarball of @@ -71,10 +63,13 @@ exts_list = [ (5): Re-run the build. """, 'source_tmpl': 'esom.tar.gz', - 'checksums': ['0a20649cbeb0d41fbda23137e9d21e306a3d6a642b895204a16b1128fad1c88f'], }), ] +postinstallcmds = [ + 'ln -s %%(installdir)s/ClaMS-CLI-fork-%s/ClaMS-CLI.jar %%(installdir)s/ClaMS-CLI.jar' % local_clams_commit, +] + sanity_check_commands = ["scgid --help"] -moduleclass = 'bio' +moduleclass = 'bio' \ No newline at end of file From 174dbc098a3a959afe1fba5a8db60c79dfb819a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Mar 2022 18:00:48 +0200 Subject: [PATCH 3353/9987] allow oversubscription of MPI ranks to cores when running MEME test suite --- .../easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb index bf4ba05527b..a0127e5697c 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b-Python-2.7.18.eb @@ -35,6 +35,7 @@ configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/b # config.log should indicate that all required/optional dependencies were found (see scripts/dependencies.pl) configopts += " && grep 'All required and optional Perl modules were found' config.log" +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " runtest = 'test' fix_perl_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] From 94c172b6c69f6cd737b1e7876686782e22cb4fe8 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 28 Mar 2022 18:35:59 +0200 Subject: [PATCH 3354/9987] Fixed style errors --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index d27c3a46083..c048e951afd 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -47,7 +47,10 @@ local_clams_commit = "e326c34307803b9ea8ffc975ddd9bd05643af931" exts_list = [ ('ClaMS-CLI', '31012020', { 'source_urls': ['https://github.com/amsesk/ClaMS-CLI-fork/archive'], - 'sources': [{'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', 'filename': 'ClaMS-CLI-%(version)s.tar.gz'}], + 'sources': [{ + 'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', + 'filename': 'ClaMS-CLI-%(version)s.tar.gz' + }], 'checksums': ['743397fc8308e363f127bd7e5165ac9d769c10305f6e33d9e408db8f343170db'], }), ('ESOM', '1.1', { @@ -72,4 +75,4 @@ postinstallcmds = [ sanity_check_commands = ["scgid --help"] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 95b17872c7a805fcf96659f542a98024e721082e Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 28 Mar 2022 19:06:35 +0200 Subject: [PATCH 3355/9987] Checksums fix --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index c048e951afd..36dedcf3d9d 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -48,7 +48,7 @@ exts_list = [ ('ClaMS-CLI', '31012020', { 'source_urls': ['https://github.com/amsesk/ClaMS-CLI-fork/archive'], 'sources': [{ - 'download_filename': 'e326c34307803b9ea8ffc975ddd9bd05643af931.tar.gz', + 'download_filename': '%s.tar.gz' % local_clams_commit, 'filename': 'ClaMS-CLI-%(version)s.tar.gz' }], 'checksums': ['743397fc8308e363f127bd7e5165ac9d769c10305f6e33d9e408db8f343170db'], From 0d923369bca09a023a8029217c7b687bf192e453 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Mon, 28 Mar 2022 19:35:52 +0200 Subject: [PATCH 3356/9987] ESOM checksum set to None --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index 36dedcf3d9d..9287e8372b4 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -66,6 +66,7 @@ exts_list = [ (5): Re-run the build. """, 'source_tmpl': 'esom.tar.gz', + 'checksums': None, }), ] From 0ffcde77060d09112dbd74594672c9bf9889f0e2 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Mon, 28 Mar 2022 19:58:34 +0200 Subject: [PATCH 3357/9987] forgot brackets --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index 9287e8372b4..9b6b22296fb 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -66,7 +66,7 @@ exts_list = [ (5): Re-run the build. """, 'source_tmpl': 'esom.tar.gz', - 'checksums': None, + 'checksums': [None], }), ] From a27d66d3c3b5b888ef85da502f48fff09ebe7aff Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Mon, 28 Mar 2022 20:56:05 +0200 Subject: [PATCH 3358/9987] Added required change --- easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb index 9a860fd20ee..afab7243636 100644 --- a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-4.0.0-GCCcore-11.2.0.eb @@ -18,7 +18,7 @@ dependencies = [ use_pip = True exts_list = [ - ('humanize', version, { + ('humanize', '4.0.0', { 'checksums': ['ee1f872fdfc7d2ef4a28d4f80ddde9f96d36955b5d6b0dac4bdeb99502bddb00'], }), ('htsget', '0.2.5', { From 83fa9380973dff2e78e3913a56289ee1aef35799 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 28 Mar 2022 17:58:22 +0200 Subject: [PATCH 3359/9987] update copyright lines for 2022 --- setup.py | 2 +- test/__init__.py | 2 +- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/styletests.py | 2 +- test/easyconfigs/suite.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/setup.py b/setup.py index 8717395d06d..db67c26c4c4 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ ## -# Copyright 2012-2021 Ghent University +# Copyright 2012-2022 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/__init__.py b/test/__init__.py index 1681f47ed8d..461a6de8085 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -1,5 +1,5 @@ ## -# Copyright 2009-2021 Ghent University +# Copyright 2009-2022 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 10e2be577ed..36ca8a5747c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1,5 +1,5 @@ ## -# Copyright 2013-2021 Ghent University +# Copyright 2013-2022 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index 91f39820898..0cbaca89661 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -1,5 +1,5 @@ ## -# Copyright 2016-2021 Ghent University +# Copyright 2016-2022 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 3d204108c36..eae8bd6dbe3 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -1,6 +1,6 @@ #!/usr/bin/python ## -# Copyright 2012-2021 Ghent University +# Copyright 2012-2022 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), From 8bcc6d54dd860736fcc15ecf7af7672f2e114bce Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 29 Mar 2022 11:59:40 +0100 Subject: [PATCH 3360/9987] Remove extraneous bin, lib directory sanity checks --- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb | 2 +- .../easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 2c9468819fc..80eb7725177 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -55,7 +55,7 @@ modextrapaths = {'PATH': ['scripts']} sanity_check_paths = { 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], - 'dirs': ['bin', 'lib', 'scripts'], + 'dirs': ['scripts'], } sanity_check_commands = ["vcfremap"] diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb index 59fce4f5bf9..17a30c67e16 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb @@ -55,7 +55,7 @@ modextrapaths = {'PATH': ['scripts']} sanity_check_paths = { 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], - 'dirs': ['bin', 'lib', 'scripts'], + 'dirs': ['scripts'], } sanity_check_commands = ["vcfremap"] diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb index 5321ac63d4e..ab1ac8f45ac 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb @@ -56,7 +56,7 @@ modextrapaths = {'PATH': ['scripts']} sanity_check_paths = { 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], - 'dirs': ['bin', 'lib', 'scripts'], + 'dirs': ['scripts'], } sanity_check_commands = ["vcfremap"] diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb index 445849a2c3b..225e8763fb3 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb @@ -55,7 +55,7 @@ modextrapaths = {'PATH': ['scripts']} sanity_check_paths = { 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], - 'dirs': ['bin', 'lib', 'scripts'], + 'dirs': ['scripts'], } sanity_check_commands = ["vcfremap"] From 5e5131d43a2e36fe46061fb4500e8793001361a2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 29 Mar 2022 15:42:40 +0100 Subject: [PATCH 3361/9987] Fix linking of vcflib shared library --- .../easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 5 ++++- .../easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb | 5 ++++- .../v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb | 5 ++++- .../v/vcflib/vcflib-1.0.2_fix-shared-linking.patch | 13 +++++++++++++ .../easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb | 5 ++++- .../v/vcflib/vcflib-1.0.3_fix-shared-linking.patch | 13 +++++++++++++ 6 files changed, 42 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.2_fix-shared-linking.patch create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.3_fix-shared-linking.patch diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 734f106ab15..2692dd43c02 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -14,7 +14,10 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['vcflib-1.0.2_use-external-deps.patch'] +patches = [ + 'vcflib-1.0.2_use-external-deps.patch', + 'vcflib-1.0.2_fix-shared-linking.patch', +] checksums = [ 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb index 5217cd5b157..3cfa00db653 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb @@ -14,7 +14,10 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['vcflib-1.0.2_use-external-deps.patch'] +patches = [ + 'vcflib-1.0.2_use-external-deps.patch', + 'vcflib-1.0.2_fix-shared-linking.patch', +] checksums = [ 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb index 96720191f53..e0f719935f4 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb @@ -15,7 +15,10 @@ toolchain = {'name': 'GCC', 'version': '9.3.0'} source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['vcflib-1.0.2_use-external-deps.patch'] +patches = [ + 'vcflib-1.0.2_use-external-deps.patch', + 'vcflib-1.0.2_fix-shared-linking.patch', +] checksums = [ 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2_fix-shared-linking.patch b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2_fix-shared-linking.patch new file mode 100644 index 00000000000..401204872b9 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2_fix-shared-linking.patch @@ -0,0 +1,13 @@ +Author: Jasper Grimm +Ensure that shared library correctly links dependencies +diff -Nru vcflib-1.0.2/CMakeLists.txt vcflib-1.0.2_p2/CMakeLists.txt +--- vcflib-1.0.2/CMakeLists.txt 2022-03-29 15:31:28.000000000 +0100 ++++ vcflib-1.0.2_p2/CMakeLists.txt 2022-03-29 15:36:28.000000000 +0100 +@@ -197,6 +197,7 @@ + set_target_properties(vcflib_static PROPERTIES OUTPUT_NAME vcflib) + add_library(vcflib SHARED ${SOURCES}) + set_target_properties(vcflib PROPERTIES VERSION ${BUILD_NUMBER} SOVERSION 1) ++target_link_libraries(vcflib tabixpp fastahack sw fsom filevercmp ${LDFLAGS} ${LIBS}) + + # ---- Build htslib + # diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb index 6d9fe6caf6d..ed87a80bc6c 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb @@ -14,7 +14,10 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_use-external-deps.patch'] +patches = [ + '%(name)s-%(version)s_use-external-deps.patch', + 'vcflib-1.0.3_fix-shared-linking.patch', +] checksums = [ '5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c', # v1.0.3.tar.gz '89f99efb35eb3a5fdc5a7fdeb96c204b1af481194bcd788c939c600a985fa8a4', # vcflib-1.0.3_use-external-deps.patch diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3_fix-shared-linking.patch b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3_fix-shared-linking.patch new file mode 100644 index 00000000000..305f5ae0c55 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3_fix-shared-linking.patch @@ -0,0 +1,13 @@ +Author: Jasper Grimm +Ensure that shared library correctly links dependencies +diff -Nru vcflib-1.0.3/CMakeLists.txt vcflib-1.0.3_p2/CMakeLists.txt +--- vcflib-1.0.3/CMakeLists.txt 2022-03-29 15:31:38.000000000 +0100 ++++ vcflib-1.0.3_p2/CMakeLists.txt 2022-03-29 15:36:41.000000000 +0100 +@@ -244,6 +244,7 @@ + set_target_properties(vcflib_static PROPERTIES OUTPUT_NAME vcflib) + add_library(vcflib SHARED ${SOURCES}) + set_target_properties(vcflib PROPERTIES VERSION ${BUILD_NUMBER} SOVERSION 1) ++target_link_libraries(vcflib tabixpp fastahack sw fsom filevercmp ${LDFLAGS} ${LIBS}) + + # ---- Build htslib + # From a972bdb12e6ee6c0ab538488de638532442ca955 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 29 Mar 2022 15:44:28 +0100 Subject: [PATCH 3362/9987] Checksums --- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 1 + easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb | 1 + .../easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb | 1 + easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 2692dd43c02..2047f76e3da 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -21,6 +21,7 @@ patches = [ checksums = [ 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch + '3904fb7ad5d144bf1b6500c985c84c15a5e4ba5299763628de7965cb4efa97f7', # vcflib-1.0.2_fix-shared-linking.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb index 3cfa00db653..5140350d939 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb @@ -21,6 +21,7 @@ patches = [ checksums = [ 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch + '3904fb7ad5d144bf1b6500c985c84c15a5e4ba5299763628de7965cb4efa97f7', # vcflib-1.0.2_fix-shared-linking.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb index e0f719935f4..64abf6f7f93 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb @@ -22,6 +22,7 @@ patches = [ checksums = [ 'a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910', # v1.0.2.tar.gz '8f505c13b258b510b29768d1eaca5c77bc01cb083eec7866bc961a9b647f16d6', # vcflib-1.0.2_use-external-deps.patch + '3904fb7ad5d144bf1b6500c985c84c15a5e4ba5299763628de7965cb4efa97f7', # vcflib-1.0.2_fix-shared-linking.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb index ed87a80bc6c..32121045321 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb @@ -21,6 +21,7 @@ patches = [ checksums = [ '5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c', # v1.0.3.tar.gz '89f99efb35eb3a5fdc5a7fdeb96c204b1af481194bcd788c939c600a985fa8a4', # vcflib-1.0.3_use-external-deps.patch + '2584e33e447c07a66eefc46263161873498910e19035f9beed1600cbd05fd4b0', # vcflib-1.0.3_fix-shared-linking.patch ] builddependencies = [ From b453cb85f1160dfc7d707f59ea0eabb7fe912ad8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2022 09:45:39 +0200 Subject: [PATCH 3363/9987] fix failing sanity check for PRINSEQ --- .../p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb | 3 +++ .../p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb | 3 +++ .../p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb index 108e4aa5d1e..e9f5f8cd9e1 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb @@ -27,6 +27,9 @@ dependencies = [ exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") +# prevent that sanity check requires PRINSEQ itself to be available as a Perl module +options = {'modulename': False} + exts_list = [ ('ExtUtils::Depends', '0.405', { 'source_tmpl': 'ExtUtils-Depends-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb index c2fccb2c6a2..d0822cc92c4 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2020b-Perl-5.32.0.eb @@ -24,6 +24,9 @@ dependencies = [ exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") +# prevent that sanity check requires PRINSEQ itself to be available as a Perl module +options = {'modulename': False} + exts_list = [ ('ExtUtils::Depends', '0.8001', { 'source_tmpl': 'ExtUtils-Depends-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb index 814735de515..18db1b85712 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2021b-Perl-5.34.0.eb @@ -24,6 +24,9 @@ dependencies = [ exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") +# prevent that sanity check requires PRINSEQ itself to be available as a Perl module +options = {'modulename': False} + exts_list = [ ('ExtUtils::Depends', '0.8001', { 'source_tmpl': 'ExtUtils-Depends-%(version)s.tar.gz', From 4fe6020b58a0c5bb86a7cc49a11910f83f6af077 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 30 Mar 2022 10:04:03 +0100 Subject: [PATCH 3364/9987] fix install with setuptools>=61 --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index db67c26c4c4..359806893d7 100644 --- a/setup.py +++ b/setup.py @@ -101,6 +101,7 @@ def get_data_files(): "Programming Language :: Python :: 3.9", "Topic :: Software Development :: Build Tools", ], + packages=[], platforms="Linux", requires=[ "easybuild_framework(>=%s.0)" % MAJ_VER, From e86945c9af57d3fa8938d1454fb01adb9a4b1721 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2022 11:06:24 +0200 Subject: [PATCH 3365/9987] adding easyconfigs: vsc-mympirun-5.2.11.eb --- .../v/vsc-mympirun/vsc-mympirun-5.2.11.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.11.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.11.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.11.eb new file mode 100644 index 00000000000..adcd535ddf7 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.11.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'vsc-mympirun' +version = '5.2.11' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """mympirun is a tool to make it easier for users of HPC clusters to +run MPI programs with good performance.""" + +# we build this to work with every python version +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +use_pip = False + +exts_list = [ + ('setuptools', '41.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6afa61b391dcd16cb8890ec9f66cc4015a8a31a6e1c2b4e0c464514be1a3d722'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('pbr', '5.8.1', { + 'checksums': ['66bc5a34912f408bb3925bf21231cb6f59206267b7f63f3503ef865c1a292e25'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '4.0.3', { + 'checksums': ['7d3fbbde18228f4ff2f1f119a45cdffa458b4c0dee32eb4d2bb2f82554bac7bc'], + }), + ('IPy', '1.01', { + 'modulename': 'IPy', + 'checksums': ['edeca741dea2d54aca568fa23740288c3fe86c0f3ea700344571e9ef14a7cc1a'], + }), + ('vsc-install', '0.17.22', { + 'modulename': 'vsc.install', + 'checksums': ['bd5cc33f3ef67f86aa7827b12b24d66fe5b17995075c1fed3cdc8440155378d3'], + }), + ('vsc-base', '3.4.3', { + 'modulename': 'vsc.utils', + 'checksums': ['11d21d8795c17423febc500d4ba0d987c9e0b2cadb6ded75df34ea4dd77305b4'], + }), + (name, version, { + 'modulename': 'vsc', + 'checksums': ['cadd3371faaebc62c67cfb5487c1dbad1e942cbb523336d07089a39fce775a88'], + }), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mypmirun', 'bin/mympisanity', 'bin/mytasks'], + 'dirs': ['bin/fake'], +} +sanity_check_commands = ["mympirun --help"] + +# can't enable 'pip check' since pip may not be installed in OS +sanity_pip_check = False + +moduleclass = 'tools' From eaac84832f1915f373da03ca730e9e786842ab54 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 30 Mar 2022 15:29:28 +0200 Subject: [PATCH 3366/9987] changes as suggested --- easybuild/easyconfigs/x/xtb/xtb-6.4.1-foss-2021b.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.4.1-foss-2021b.eb b/easybuild/easyconfigs/x/xtb/xtb-6.4.1-foss-2021b.eb index 79c3b897d01..6df7e85ba2d 100644 --- a/easybuild/easyconfigs/x/xtb/xtb-6.4.1-foss-2021b.eb +++ b/easybuild/easyconfigs/x/xtb/xtb-6.4.1-foss-2021b.eb @@ -20,10 +20,7 @@ builddependencies = [ configopts = "-Dla_backend='custom' " configopts += "-Dcustom_libraries='flexiblas' " -configopts += "--optimization=2 " configopts += "--buildtype release " -configopts += "--warnlevel 0 " -configopts += "-Dpython=false" runtest = 'meson' testopts = 'test -C %(builddir)s/easybuild_obj -t 60' # Ensure test don't timeout @@ -33,6 +30,8 @@ sanity_check_paths = { 'dirs': ['share'], } +sanity_check_commands = ["xtb --help"] + modextravars = { 'XTBHOME': '%(installdir)s', 'XTBPATH': '%(installdir)s', From b6bea401de775c442f1b1819bec7308457534e0e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 30 Mar 2022 16:19:39 +0200 Subject: [PATCH 3367/9987] prepare release notes for EasyBuild v4.5.4 + bump version to 4.5.4 --- RELEASE_NOTES | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 56 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 31b393b1762..f7a7e375a2a 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,64 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 14,282 easyconfig files, for 2,647 different software packages, +The latest version of easybuild-easyconfig provides 14,479 easyconfig files, for 2,680 different software packages, incl. 36 different (compiler) toolchains. +v4.5.4 (March 31st 2022) +------------------------ + +update/bugfix release +- added example easyconfig files for 29 new software packages: + - Abseil (#15102), AMS (#1997), ArchR (#15119), CMAverse (#14963), CmdStanR (#15198), CONN (#963), Devito (#15009), GraphMap (#10299), gRPC (#14728), Hydra (#15025), jupyter-server-proxy (#14844), M1QN3 (#15002), MAGeCK (#15082), matplotlib-inline (#15084), MEGAN (#15064), MNE-Python (#15174), ONNX (#15158), ONNX-Runtime (#15158), ont-remora (#15162), Optuna (#15021), patch (#15035), porefoam (#15067), presto (#15119), PyFrag (#15184), skorch (#15175), SlamDunk (#15197), SPM (#15050), STRique (#14980), XML-Compile (#15177) +- added additional easyconfigs for various supported software packages, including: + - ABAQUS 2021, Abseil 20210324.2, AlphaFold 2.1.2, AmberTools 21, AMS 2020.102, ArchR 1.0.1, archspec 0.1.3, ArviZ 0.11.4, AUGUSTUS 3.4.0, Bambi 0.7.1, Bandage 0.9.0, Bio-DB-HTS 3.01, BioPerl 1.7.8, BLIS 3.1, bokeh 2.2.3, boto3 1.20.13, BUSCO 4.0.6, canu 2.2, CapnProto 0.9.1, c-ares 1.18.1, CCL 1.12.1, CharLS 2.3.4, Clang-Python-bindings 13.0.1, CMAverse 20220112, CmdStanR 0.5.0, CONN 21a, dask 2021.2.0, DB_File 1.857, dcm2niix 1.0.20211006, deepTools 3.5.1, Devito 4.6.1, DFTB+ 21.1, dftd3 lib, DIRAC 22.0, ecCodes 2.24.2, ELPA 2021.11.001, ETE 3.1.2, FLASH 2.2.00, FlexiBLAS 3.1.3, FLUENT 2021R2.eb, GATK 4.2.5.0, GEOS 3.8.0, GetOrganelle 1.7.5.3, graphite2 1.3.14, GraphMap 0.5.2, gRPC 1.44.0, Hydra 1.1.1, IgBLAST 1.18.0, imageio 2.10.5, Infernal 1.1.4, IntelClusterChecker 2021.5.0.eb, intervaltree-python 3.1.0, ITSx 1.1.3, JAGS 4.3.0, Julia 1.7.2, Jupyter-server-proxy 3.2.1, kallisto 0.48.0, KMC 3.2.1, libevent 2.1.12.eb, libobjcryst 2021.1.2, libpspio 0.2.4, libtree 3.0.3.eb, Lighter 1.1.2, likwid 5.2.0, loompy 3.0.7, lpsolve 5.5.2.11, M1QN3 3.3, MAGeCK 0.5.9.4, Mash 2.3, matplotlib 3.5.1, MCR R2021b, MCR R2022a, MDAnalysis 1.1.1, MDAnalysis 2.0.0, MDTraj 1.9.7, medaka 1.5.0, MEGAN 6.22.0, MEME 5.4.1, meshalyzer 20200308, MNE-Python 0.24.1, MRtrix 3.0.3, MUSCLE 3.8.31, netcdf4-python 1.5.7, networkx 2.5, NFFT 3.5.2, NiBabel 3.2.2, NLTK 3.6.7, NLTK 3.7, numba 0.54.1, numexpr 2.8.1, ONNX 1.11.0, ont-fast5-api 4.0.0, ont-fast5-api 4.0.2, ont-remora 0.1.2, OpenAI-Gym 0.21.0, OpenBLAS 0.3.20, Optuna 2.10.0, ORCA 5.0.3, parallel-fastq-dump 0.6.6, patch 2.7.6, PIPITS 2.8, PLINK 2.00a2.3, pocl 1.8, porefoam 2021, presto 1.0.0, pycocotools 2.0.4, pydicom 2.2.2, pyEGA3 4.0.0, PyFrag 2019, PyMC3 3.11.1, pyobjcryst 2.2.1, PyQt5 5.15.4, pyradiomics 3.0.1, pyspoa 0.0.8, PyWavelets 1.1.1, RE2 2022, RevBayes 1.1.1, samclip 0.4.0, SAMtools 1.15, SBCL 2.2.1, scikit-image 0.18.1, SeqAn 2.4.0, shovill 1.1.0, Siesta 4.1.5, SKESA 2.4.0, skorch 0.11.0, SlamDunk 0.4.3, SOCI 4.0.3, SPM 12.5_r7771, spoa 4.0.7, Stacks 2.53, STRique 0.4.2, sympy 1.9, TensorFlow 2.4.4, TensorFlow 2.5.3, texlive 20210324, Theano 1.1.2, tmux 3.2a, Velvet 1.2.10, VirtualGL 3.0, vsc-mympirun 5.2.9, vsc-mympirun 5.2.10, VSEARCH 2.21.1, VTK 9.1.0, VTune 2022.2.0, WhatsHap 1.1, XGBoost 1.5.0, XML-Compile 1.63 +- minor enhancements, including: + - update description for Devito (#15009) + - add Flask-Session to Flask v1.1.4 and Flask v2.0.2 (#15027) + - add check to verify that patch files touched in PRs have a description in place (#15061) + - add hash R library as extension to R v4.1.2 easyconfig (#15098) + - add rMATS_P cli tools (#15113) + - add nabor + harmony extensions to R v4.1.2 easyconfig (#15117) + - add chromVAR extension to easyconfig for Bioconductor v3.14 (#15118) + - add apcluster, DataCombine, docstring, gdalUtils, openair, mstate, SNFtool, and deps to R v4.1.2 ec (#15141) + - add EnsDb.Hsapiens.v79 extension to R-bundle-Bioconductor v3.14 (#15154) + - add Sys::Info, HTML::Template, Log::Report extensions to Perl v5.34.0 (#15176) + - add WGCNA extension to R-bundle-BioConductor v3.14 (#15178) + - add Sys::Info::Driver::Unknown + Sys::Info::Driver::Linux + Unix::Processors extensions to Perl v5.34.0 (#15190) + - enable running of tests for MEME with gompi/2021b (#15191) +- various bug fixes, including: + - add missing xxd build dependency for recent PLUMED versions (2.6.2, 2.7.x) (#14847) + - downgrade dependency on nodejs + use jupyter-server-proxy in jupyter-matlab-proxy and configurable-http-proxy easyconfigs using GCCcore/10.3.0 toolchain (#14942) + - add additional valid checksum for norm 1.0-9.5 extension in R 4.1.0 and 4.1.2 easyconfigs (#14987) + - avoid pollution in the tmp directory when running the AlphaFold tests (#14989) + - add additional valid checksum for optmatch 0.9-15 in extension in R 4.1.2 (#14993) + - use typing-extensions from Python v3.9.6 easyconfig in ArviZ and PyMC3 (#15003) + - disable building of documentation for DBus 1.13.18 (#15010) + - consistently enable usempi toolchain option in OSU-Micro-Benchmarks easyconfigs (#15039) + - fix source URL for LAPACK 3.9.1 easyconfig using GCC/10.2.0 (#15047) + - fix GBprocesS easyconfig by switching to source tarball created using git_config (#15048) + - add patches for mauveAligner to fix build on RHEL8 (#15049) + - fix installation of RDKit by using -DBoost_NO_BOOST_CMAKE=ON (#15051) + - add patch to fix linking error for imread extension in scikit-image easyconfigs using intel toolchain (#15054) + - avoid excessively long shebang in Autoconf/Automake Perl scripts + promote Perl to runtime dependency + fix Perl shebang for intltool (#15055) + - fix python shebang in cutadapt script for cutadapt 1.18 w/ GCCcore/8.3.0 (#15059) + - don't use v2.1.0rc1 release candidate of gmpy2, stick to proper release v2.1.2 (#15060) + - add M4 as build dependency for CCL-1.12 (#15075) + - configure libffi 3.4.2 with --disable-exec-static-tramp to prevent segfaults (#15086) + - set XLA_PYTHON_CLIENT_ALLOCATOR=platform for running tests in jax CUDA easyconfigs (#15097) + - remove disable flag for RTTI in snappy v1.1.9 (#15099) + - fix grconvert build for Grace/5.1.25 with foss/2021a by adding libtirpc dependency + related patch (#15121) + - consistently use system toolchain in EasyBuild easyconfigs (#15126) + - clean up PSolver and futile easyconfigs and add dynamic libs (#15148) + - enhance vcflib easyconfigs to also install scripts (#15181) + - allow oversubscription of MPI ranks to cores when running MEME test suite (#15199) + - add patch to fix shared linking in vcflib (#15203) + - fix failing sanity check for PRINSEQ (#15205) +- other changes: + - use EasyBuild hwloc in likwid and move to GCC/intel-compiler level due to Fortran modules (#15149) + + v4.5.3 (February 11th 2022) --------------------------- diff --git a/setup.py b/setup.py index db67c26c4c4..bd88e033cc5 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.4.dev0' +VERSION = '4.5.4' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 330dffc3f243bd1143f566b8f58ab83f99f934a6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 30 Mar 2022 17:15:44 +0100 Subject: [PATCH 3368/9987] use x.py to bootstrap rust --- easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb index 603a5387f6c..e22a5e39fc8 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb @@ -34,6 +34,10 @@ configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " # since Rust is a build dependency for cryptography that is included with Python configopts += "--set=llvm.ninja=false " +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +build_cmd = "./x.py build" +install_cmd = "./x.py install" + # avoid failure when home directory is an NFS mount, # see https://github.com/rust-lang/cargo/issues/6652 prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " From 444e8a529006d3ff1c1612411066cf805995de95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Mar 2022 20:53:18 +0200 Subject: [PATCH 3369/9987] minor tweak release notes for v4.5.4 --- RELEASE_NOTES | 47 ++++++++++++++++++++++++++--------------------- 1 file changed, 26 insertions(+), 21 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index f7a7e375a2a..be851b779c6 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 14,479 easyconfig files, for 2,680 different software packages, +The latest version of easybuild-easyconfig provides 14,449 easyconfig files, for 2,667 different software packages, incl. 36 different (compiler) toolchains. @@ -12,33 +12,37 @@ v4.5.4 (March 31st 2022) update/bugfix release - added example easyconfig files for 29 new software packages: - - Abseil (#15102), AMS (#1997), ArchR (#15119), CMAverse (#14963), CmdStanR (#15198), CONN (#963), Devito (#15009), GraphMap (#10299), gRPC (#14728), Hydra (#15025), jupyter-server-proxy (#14844), M1QN3 (#15002), MAGeCK (#15082), matplotlib-inline (#15084), MEGAN (#15064), MNE-Python (#15174), ONNX (#15158), ONNX-Runtime (#15158), ont-remora (#15162), Optuna (#15021), patch (#15035), porefoam (#15067), presto (#15119), PyFrag (#15184), skorch (#15175), SlamDunk (#15197), SPM (#15050), STRique (#14980), XML-Compile (#15177) + - Abseil (#15102), AMS (#13155), ArchR (#15119), CMAverse (#14963), CmdStanR (#15198), CONN (#15052), + Devito (#14984, #15009), GraphMap (#10299), gRPC (#14728), Hydra (#15025), jupyter-server-proxy (#14844), + M1QN3 (#15002), MAGeCK (#15082), matplotlib-inline (#15084), MEGAN (#15064), MNE-Python (#15174), + ONNX (#15158), ONNX-Runtime (#15158), ont-remora (#15162), Optuna (#15021), patch (#15035), + porefoam (#15067), presto (#15119), PyFrag (#15184), skorch (#15175), SlamDunk (#15197), SPM (#15050), + STRique (#14980), XML-Compile (#15177) - added additional easyconfigs for various supported software packages, including: - - ABAQUS 2021, Abseil 20210324.2, AlphaFold 2.1.2, AmberTools 21, AMS 2020.102, ArchR 1.0.1, archspec 0.1.3, ArviZ 0.11.4, AUGUSTUS 3.4.0, Bambi 0.7.1, Bandage 0.9.0, Bio-DB-HTS 3.01, BioPerl 1.7.8, BLIS 3.1, bokeh 2.2.3, boto3 1.20.13, BUSCO 4.0.6, canu 2.2, CapnProto 0.9.1, c-ares 1.18.1, CCL 1.12.1, CharLS 2.3.4, Clang-Python-bindings 13.0.1, CMAverse 20220112, CmdStanR 0.5.0, CONN 21a, dask 2021.2.0, DB_File 1.857, dcm2niix 1.0.20211006, deepTools 3.5.1, Devito 4.6.1, DFTB+ 21.1, dftd3 lib, DIRAC 22.0, ecCodes 2.24.2, ELPA 2021.11.001, ETE 3.1.2, FLASH 2.2.00, FlexiBLAS 3.1.3, FLUENT 2021R2.eb, GATK 4.2.5.0, GEOS 3.8.0, GetOrganelle 1.7.5.3, graphite2 1.3.14, GraphMap 0.5.2, gRPC 1.44.0, Hydra 1.1.1, IgBLAST 1.18.0, imageio 2.10.5, Infernal 1.1.4, IntelClusterChecker 2021.5.0.eb, intervaltree-python 3.1.0, ITSx 1.1.3, JAGS 4.3.0, Julia 1.7.2, Jupyter-server-proxy 3.2.1, kallisto 0.48.0, KMC 3.2.1, libevent 2.1.12.eb, libobjcryst 2021.1.2, libpspio 0.2.4, libtree 3.0.3.eb, Lighter 1.1.2, likwid 5.2.0, loompy 3.0.7, lpsolve 5.5.2.11, M1QN3 3.3, MAGeCK 0.5.9.4, Mash 2.3, matplotlib 3.5.1, MCR R2021b, MCR R2022a, MDAnalysis 1.1.1, MDAnalysis 2.0.0, MDTraj 1.9.7, medaka 1.5.0, MEGAN 6.22.0, MEME 5.4.1, meshalyzer 20200308, MNE-Python 0.24.1, MRtrix 3.0.3, MUSCLE 3.8.31, netcdf4-python 1.5.7, networkx 2.5, NFFT 3.5.2, NiBabel 3.2.2, NLTK 3.6.7, NLTK 3.7, numba 0.54.1, numexpr 2.8.1, ONNX 1.11.0, ont-fast5-api 4.0.0, ont-fast5-api 4.0.2, ont-remora 0.1.2, OpenAI-Gym 0.21.0, OpenBLAS 0.3.20, Optuna 2.10.0, ORCA 5.0.3, parallel-fastq-dump 0.6.6, patch 2.7.6, PIPITS 2.8, PLINK 2.00a2.3, pocl 1.8, porefoam 2021, presto 1.0.0, pycocotools 2.0.4, pydicom 2.2.2, pyEGA3 4.0.0, PyFrag 2019, PyMC3 3.11.1, pyobjcryst 2.2.1, PyQt5 5.15.4, pyradiomics 3.0.1, pyspoa 0.0.8, PyWavelets 1.1.1, RE2 2022, RevBayes 1.1.1, samclip 0.4.0, SAMtools 1.15, SBCL 2.2.1, scikit-image 0.18.1, SeqAn 2.4.0, shovill 1.1.0, Siesta 4.1.5, SKESA 2.4.0, skorch 0.11.0, SlamDunk 0.4.3, SOCI 4.0.3, SPM 12.5_r7771, spoa 4.0.7, Stacks 2.53, STRique 0.4.2, sympy 1.9, TensorFlow 2.4.4, TensorFlow 2.5.3, texlive 20210324, Theano 1.1.2, tmux 3.2a, Velvet 1.2.10, VirtualGL 3.0, vsc-mympirun 5.2.9, vsc-mympirun 5.2.10, VSEARCH 2.21.1, VTK 9.1.0, VTune 2022.2.0, WhatsHap 1.1, XGBoost 1.5.0, XML-Compile 1.63 + - ABAQUS 2021, AlphaFold 2.1.2, AmberTools 21, archspec 0.1.3, Bandage 0.9.0, BLIS 3.1, c-ares 1.18.1, + CCL 1.12.1, CharLS 2.3.4, Clang-Python-bindings 13.0.1, dcm2niix 1.0.20211006, DFTB+ 21.1, DIRAC 22.0, + ELPA 2021.11.001, FlexiBLAS 3.1.3, FLUENT 2021R2, GATK 4.2.5.0, GetOrganelle 1.7.5.3, IgBLAST 1.18.0, + IntelClusterChecker 2021.5.0, intervaltree-python 3.1.0, ITSx 1.1.3, Julia 1.7.2, kallisto 0.48.0, + KMC 3.2.1, libobjcryst 2021.1.2, libtree 3.0.3, loompy 3.0.7, matplotlib 3.5.1, MCR R2022a, + MDAnalysis 1.1.1+ 2.0.0, MDTraj 1.9.7, medaka 1.5.0, meshalyzer 20200308, MRtrix 3.0.3, NiBabel 3.2.2, + NLTK 3.7, numexpr 2.8.1, ont-fast5-api 4.0.2, OpenAI-Gym 0.21.0, OpenBLAS 0.3.20, ORCA 5.0.3, + parallel-fastq-dump 0.6.6, PIPITS 2.8, pocl 1.8, pycocotools 2.0.4, pyEGA3 4.0.0, pyobjcryst 2.2.1, + RE2 2022-02-01, SAMtools 1.15, SBCL 2.2.1, shovill 1.1.0, SKESA 2.4.0, SOCI 4.0.3, sympy 1.9, TensorFlow 2.5.3, + VirtualGL 3.0, vsc-mympirun 5.2.10, VSEARCH 2.21.1, VTK 9.1.0, VTune 2022.2.0, XGBoost 1.5.0 - minor enhancements, including: - - update description for Devito (#15009) - add Flask-Session to Flask v1.1.4 and Flask v2.0.2 (#15027) - add check to verify that patch files touched in PRs have a description in place (#15061) - - add hash R library as extension to R v4.1.2 easyconfig (#15098) - - add rMATS_P cli tools (#15113) - - add nabor + harmony extensions to R v4.1.2 easyconfig (#15117) - - add chromVAR extension to easyconfig for Bioconductor v3.14 (#15118) - - add apcluster, DataCombine, docstring, gdalUtils, openair, mstate, SNFtool, and deps to R v4.1.2 ec (#15141) - - add EnsDb.Hsapiens.v79 extension to R-bundle-Bioconductor v3.14 (#15154) - - add Sys::Info, HTML::Template, Log::Report extensions to Perl v5.34.0 (#15176) - - add WGCNA extension to R-bundle-BioConductor v3.14 (#15178) - - add Sys::Info::Driver::Unknown + Sys::Info::Driver::Linux + Unix::Processors extensions to Perl v5.34.0 (#15190) - - enable running of tests for MEME with gompi/2021b (#15191) + - add extensions to R v4.1.2 easyconfig: hash (#15098), nabor + harmony (#15117), apluster, DataCombine, docstring, gdalUtils, openair, mstate, SNFtool, and deps (#15141) + - also install rMATS_P commands in rMATS-turbo easyconfig (#15113) + - add extensions to Bioconductor v3.14 easyconfig: chromVAR (#15118), EnsDb.Hsapiens.v79 (#15154), WGCNA (#15178) + - add extensions to Perl v5.34.0 easyconfigs: Sys::Info, HTML::Template, Log::Report (#15176), Sys::Info::Driver::Unknown, Sys::Info::Driver::Linux, Unix::Processors (#15190) + - enable running of tests for MEME with gompi/2021b (#15191, #15199) - various bug fixes, including: - add missing xxd build dependency for recent PLUMED versions (2.6.2, 2.7.x) (#14847) - downgrade dependency on nodejs + use jupyter-server-proxy in jupyter-matlab-proxy and configurable-http-proxy easyconfigs using GCCcore/10.3.0 toolchain (#14942) - - add additional valid checksum for norm 1.0-9.5 extension in R 4.1.0 and 4.1.2 easyconfigs (#14987) + - add additional valid checksum for extensions in R 4.1.0 and 4.1.2 easyconfigs: norm (#14987), optmatch (#14993) - avoid pollution in the tmp directory when running the AlphaFold tests (#14989) - - add additional valid checksum for optmatch 0.9-15 in extension in R 4.1.2 (#14993) - - use typing-extensions from Python v3.9.6 easyconfig in ArviZ and PyMC3 (#15003) - - disable building of documentation for DBus 1.13.18 (#15010) - consistently enable usempi toolchain option in OSU-Micro-Benchmarks easyconfigs (#15039) - - fix source URL for LAPACK 3.9.1 easyconfig using GCC/10.2.0 (#15047) - fix GBprocesS easyconfig by switching to source tarball created using git_config (#15048) - add patches for mauveAligner to fix build on RHEL8 (#15049) - fix installation of RDKit by using -DBoost_NO_BOOST_CMAKE=ON (#15051) @@ -51,13 +55,14 @@ update/bugfix release - set XLA_PYTHON_CLIENT_ALLOCATOR=platform for running tests in jax CUDA easyconfigs (#15097) - remove disable flag for RTTI in snappy v1.1.9 (#15099) - fix grconvert build for Grace/5.1.25 with foss/2021a by adding libtirpc dependency + related patch (#15121) - - consistently use system toolchain in EasyBuild easyconfigs (#15126) - clean up PSolver and futile easyconfigs and add dynamic libs (#15148) - enhance vcflib easyconfigs to also install scripts (#15181) - - allow oversubscription of MPI ranks to cores when running MEME test suite (#15199) - add patch to fix shared linking in vcflib (#15203) - fix failing sanity check for PRINSEQ (#15205) - other changes: + - use typing-extensions from Python v3.9.6 easyconfig in ArviZ and PyMC3 (#15003) + - disable building of documentation for DBus 1.13.18 (#15010) + - consistently use system toolchain in EasyBuild easyconfigs (#15126) - use EasyBuild hwloc in likwid and move to GCC/intel-compiler level due to Fortran modules (#15149) From 5ae9e32f8ec9ce356437eef7feb8cbc3c3d77c59 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 31 Mar 2022 09:20:51 +0200 Subject: [PATCH 3370/9987] adding easyconfigs: eggnog-mapper-2.1.7-foss-2021b.eb --- .../eggnog-mapper-2.1.7-foss-2021b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.7-foss-2021b.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.7-foss-2021b.eb new file mode 100644 index 00000000000..49b9697d45e --- /dev/null +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.7-foss-2021b.eb @@ -0,0 +1,56 @@ +# Eggnog DB installation instructions: +# 1. 'export EGGNOG_DATA_DIR=//eggnog-mapper-data' +# 2. run 'download_eggnog_data.py' +# 3. Check the expected DB version with 'emapper.py --version' + +easyblock = 'PythonPackage' + +name = 'eggnog-mapper' +version = '2.1.7' + +homepage = 'https://github.com/eggnogdb/eggnog-mapper' +description = """EggNOG-mapper is a tool for fast functional annotation of novel +sequences. It uses precomputed orthologous groups and phylogenies from the +eggNOG database (http://eggnog5.embl.de) to transfer functional information from +fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation +of novel genomes, transcriptomes or even metagenomic gene catalogs.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'eggnogdb' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['47654d7f596bb85431a00947479ae11c39f07833cf9465f02490c96a84ccf082'] + +dependencies = [ + ('Python', '3.9.6'), + ('Biopython', '1.79'), + ('HMMER', '3.3.2'), + ('DIAMOND', '2.0.13'), + ('prodigal', '2.6.3'), + ('wget', '1.21.2'), + ('MMseqs2', '13-45111'), + ('XlsxWriter', '3.0.2'), +] + +# strip out (too) strict version requirements for dependencies +preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/create_dbs.py', 'bin/download_eggnog_data.py', 'bin/emapper.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'download_eggnog_data.py --help', + 'create_dbs.py --help', + 'emapper.py --version | grep %(version)s', +] + +options = {'modulename': 'eggnogmapper'} + +moduleclass = 'bio' From dbdcecb28e5d7458dfa4106c2b6abb96d41e093b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2022 11:08:57 +0200 Subject: [PATCH 3371/9987] bump version to 4.5.5dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index bd88e033cc5..00aeb1d85ac 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.4' +VERSION = '4.5.5.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 8f4ed72cecc35e4b767dde75225102d955077907 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 31 Mar 2022 10:37:18 +0100 Subject: [PATCH 3372/9987] expand x.py comments --- easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb index e22a5e39fc8..bff75ea768e 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb @@ -35,6 +35,8 @@ configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " configopts += "--set=llvm.ninja=false " # Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s`) build_cmd = "./x.py build" install_cmd = "./x.py install" From 892bed268c24af8fedb70141fee55ba8a1a3fdd2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2022 11:45:08 +0200 Subject: [PATCH 3373/9987] adding easyconfigs: EasyBuild-4.5.4.eb --- .../e/EasyBuild/EasyBuild-4.5.4.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.4.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.4.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.4.eb new file mode 100644 index 00000000000..3efe84aba68 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.4.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.5.4' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/53/11/cf7d2baffc06b84a60cf7c08c6d2792af438ce189cd8a7494591e5b6ca23/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/01/89/bda8e81643d1718f6ac4cf08a5f1172c126a10e52159521f2b18ca9da08c/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/42/bc/c7b69d44a221fde05ae0d6f093a088f67f2f6138e868e9102a209c3036aa/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '3181c66b25c0bc8691fb91406ad58bca650eee792835f64a19276ebfb7e8f8b4', # easybuild-framework-4.5.4.tar.gz + 'e1c50ee4f5efb3425995153547bc56110d6c63c8d6f4fb40a5a48e5d5a455721', # easybuild-easyblocks-4.5.4.tar.gz + 'bfc0de9edf518210e05e7fababfee7a63510673facf0cf3a81f1eb22e03c8895', # easybuild-easyconfigs-4.5.4.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From e54ebd9b7e5adb34785fc13dc5358f6ecb56bbac Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 31 Mar 2022 10:57:04 +0100 Subject: [PATCH 3374/9987] add -j parallel flag to install_cmd --- easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb index bff75ea768e..9f045c62c02 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb @@ -36,9 +36,9 @@ configopts += "--set=llvm.ninja=false " # Use ./x.py to bootstrap so that options like -j N are correctly passed through # see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy -# (ConfigureMake already adds `-j %(parallel)s`) +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) build_cmd = "./x.py build" -install_cmd = "./x.py install" +install_cmd = "./x.py install -j %(parallel)s" # avoid failure when home directory is an NFS mount, # see https://github.com/rust-lang/cargo/issues/6652 From a3ba91d19da72db95c59491bcd308a99575f7a9a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 31 Mar 2022 11:47:12 +0100 Subject: [PATCH 3375/9987] add R dependency and move to foss --- ...CC-11.2.0.eb => vcflib-1.0.3-foss-2021b-R-4.1.2.eb} | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/v/vcflib/{vcflib-1.0.3-GCC-11.2.0.eb => vcflib-1.0.3-foss-2021b-R-4.1.2.eb} (88%) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021b-R-4.1.2.eb similarity index 88% rename from easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb rename to easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021b-R-4.1.2.eb index 5b4a3808b96..79f3286bc5c 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021b-R-4.1.2.eb @@ -4,24 +4,21 @@ easyblock = 'CMakeMake' name = 'vcflib' version = '1.0.3' +versionsuffix = '-R-%(rver)s' homepage = 'https://github.com/vcflib/vcflib' description = """vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals.""" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'foss', 'version': '2021b'} source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s_use-external-deps.patch', - 'vcflib-1.0.3_fix-shared-linking.patch', -] +patches = ['%(name)s-%(version)s_use-external-deps.patch'] checksums = [ '5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c', # v1.0.3.tar.gz '89f99efb35eb3a5fdc5a7fdeb96c204b1af481194bcd788c939c600a985fa8a4', # vcflib-1.0.3_use-external-deps.patch - '2584e33e447c07a66eefc46263161873498910e19035f9beed1600cbd05fd4b0', # vcflib-1.0.3_fix-shared-linking.patch ] builddependencies = [ @@ -33,6 +30,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.6'), ('Perl', '5.34.0'), + ('R', '4.1.2'), ('XZ', '5.2.5'), ('zlib', '1.2.11'), ('bzip2', '1.0.8'), From f5bc6aa70d6c39ef7255c45b07d579a86d48cc2f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 31 Mar 2022 11:50:45 +0100 Subject: [PATCH 3376/9987] Reinstate shared linking patch --- .../easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021b-R-4.1.2.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021b-R-4.1.2.eb index 79f3286bc5c..7cf7ac98744 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021b-R-4.1.2.eb @@ -15,10 +15,14 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_use-external-deps.patch'] +patches = [ + '%(name)s-%(version)s_use-external-deps.patch', + 'vcflib-1.0.3_fix-shared-linking.patch', +] checksums = [ '5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c', # v1.0.3.tar.gz '89f99efb35eb3a5fdc5a7fdeb96c204b1af481194bcd788c939c600a985fa8a4', # vcflib-1.0.3_use-external-deps.patch + '2584e33e447c07a66eefc46263161873498910e19035f9beed1600cbd05fd4b0', # vcflib-1.0.3_fix-shared-linking.patch ] builddependencies = [ From 63ece50415e464a73ab90cbd153ca6a471b179d6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 31 Mar 2022 11:53:39 +0100 Subject: [PATCH 3377/9987] adding easyconfigs: SeqLib-1.2.0-GCC-11.2.0.eb, fermi-lite-20190320-GCCcore-11.2.0.eb --- .../fermi-lite-20190320-GCCcore-11.2.0.eb | 46 +++++++++++++++++ .../s/SeqLib/SeqLib-1.2.0-GCC-11.2.0.eb | 49 +++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..42f7409c5e6 --- /dev/null +++ b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-11.2.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'fermi-lite' +version = '20190320' +local_commit = 'b499514' + +homepage = 'https://github.com/lh3/fermi-lite' +description = """Standalone C library for assembling Illumina short reads in small regions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = [ + '%(name)s-20190320_avoid-bwa-namespace-conflict.patch', + '%(name)s-20190320_build-shared-lib.patch', +] +checksums = [ + 'ea1230e298b8e7193a996b5aceeff7fea44ef00852b0b87d4fcb504bdca0e712', # b499514.tar.gz + # fermi-lite-20190320_avoid-bwa-namespace-conflict.patch + '27600733f1cea8b1d1503b1a67b9d41526e907c1b6321313ff51194e166c1842', + '43398559fbb3910d6d3d1a41af3fb16bf8f26bd7cc34176dfc9a068a551c3f50', # fermi-lite-20190320_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('zlib', '1.2.11')] + +prebuildopts = 'CFLAGS="$CFLAGS -fcommon"' + +files_to_copy = [ + (['fml-asm'], 'bin'), + (['*.a', '*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/fml'), + 'test', +] + +sanity_check_paths = { + 'files': ['bin/fml-asm', 'lib/libfml.a', 'lib/libfml.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..f2c21abaf40 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-11.2.0.eb @@ -0,0 +1,49 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'SeqLib' +version = '1.2.0' + +homepage = 'https://github.com/walaj/SeqLib' +description = """C++ interface to HTSlib, BWA-MEM and Fermi.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'walaj' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version_major_minor)s.0_avoid-bwa-fml-namespace-conflict.patch', + '%(name)s-%(version_major_minor)s.0_use-external-deps.patch', +] +checksums = [ + '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz + # SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch + '9be9229bcf34db8e4bd1fd49614bb55d84c12df263ca7174980f7f4b1bd63da9', + '8a90edf72f95a52c61e4aed62a9a951bbd56f7c668dec326f2d3836f76b0f71d', # SeqLib-1.2.0_use-external-deps.patch +] + +builddependencies = [('Autotools', '20210726')] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), + ('JsonCpp', '1.9.4'), + ('BWA', '0.7.17'), + ('HTSlib', '1.14'), + ('fermi-lite', '20190320'), + ('SSW', '1.1'), + ('PCRE', '8.45'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/seqtools', 'lib/libseqlib.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["seqtools"] + +moduleclass = 'bio' From a8f7c9475c5589dcc5bb51048f9fc31c04e52d8c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 31 Mar 2022 11:56:04 +0100 Subject: [PATCH 3378/9987] adding easyconfigs: freebayes-1.3.6-foss-2021b-R-4.1.2.eb and patches: freebayes-1.3.6_find-external-libs.patch, freebayes-1.3.6_install-libs-headers.patch --- .../freebayes-1.3.6-foss-2021b-R-4.1.2.eb | 54 +++++++++++ .../freebayes-1.3.6_find-external-libs.patch | 48 ++++++++++ ...freebayes-1.3.6_install-libs-headers.patch | 95 +++++++++++++++++++ 3 files changed, 197 insertions(+) create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021b-R-4.1.2.eb create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.6_find-external-libs.patch create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.6_install-libs-headers.patch diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..0751b860c54 --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021b-R-4.1.2.eb @@ -0,0 +1,54 @@ +easyblock = 'MesonNinja' + +name = 'freebayes' +version = '1.3.6' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/freebayes/freebayes' +description = "Bayesian haplotype-based genetic polymorphism discovery and genotyping." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-1.3.6_find-external-libs.patch', + '%(name)s-1.3.5_fix-includes.patch', + '%(name)s-1.3.6_install-libs-headers.patch', +] +checksums = [ + 'd668c0b433cc0f11498ace10e48d72a7f0f40ca23b391b72e975ffafd1c13044', # v1.3.6.tar.gz + '4836a9ceaa9044e6e66b3ca0387b058a5e0505ddeaa62c428b526b5e234aff3b', # freebayes-1.3.6_find-external-libs.patch + '4c6c74b30bf3b2f04b8a50bbdef26e74f6e2412f3efbd81512226e557c2a53d1', # freebayes-1.3.5_fix-includes.patch + '5ba006ca6956905bbd81107a17e02287c515890ee25884c444ebf5b95da1caae', # freebayes-1.3.6_install-libs-headers.patch +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('R', '4.1.2'), + ('parallel', '20210722'), + ('libffi', '3.4.2'), + ('VCFtools', '0.1.16'), + ('vcflib', '1.0.3', versionsuffix), + ('SeqLib', '1.2.0'), +] + +configopts = "--buildtype release" + +sanity_check_paths = { + 'files': ['bin/freebayes', 'bin/bamleftalign', 'scripts/freebayes-parallel'], + 'dirs': [], +} + +sanity_check_commands = ["freebayes --help"] + +modextrapaths = {'PATH': ['scripts']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6_find-external-libs.patch b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6_find-external-libs.patch new file mode 100644 index 00000000000..492aee5f283 --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6_find-external-libs.patch @@ -0,0 +1,48 @@ +Author: Jasper Grimm (UoY) +Switch to cc.find_library to search for libraries in LD_LIBRARY_PATH +Add dependencies on fastahack, smithwaterman +diff -Nru freebayes-1.3.6.orig/meson.build freebayes-1.3.6_p1/meson.build +--- freebayes-1.3.6.orig/meson.build 2022-01-21 09:38:32.000000000 +0000 ++++ freebayes-1.3.6_p1/meson.build 2022-03-29 12:46:15.000000000 +0100 +@@ -32,8 +32,10 @@ + if get_option('prefer_system_deps') + htslib_dep = dependency('htslib', static: static_build, required: false) + tabixpp_dep = cc.find_library('tabixpp', static: static_build, required: false) +- vcflib_dep = dependency('libvcflib', static: static_build, required: false) +- seqlib_dep = dependency('libseqlib', static: static_build, required: false) ++ vcflib_dep = cc.find_library('libvcflib', static: static_build, required: false) ++ seqlib_dep = cc.find_library('libseqlib', static: static_build, required: false) ++ fastahack_dep = cc.find_library('libfastahack', required : false) ++ sw_dep = cc.find_library('libsw', required : false) + else + # uses the local git submodules + htslib_dep = dependency('', required : false) +@@ -221,7 +223,7 @@ + include_directories : incdir, + cpp_args : extra_cpp_args, + dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep, +- vcflib_dep, seqlib_dep], ++ vcflib_dep, seqlib_dep, fastahack_dep, sw_dep], + install : false, + ) + +@@ -237,7 +239,8 @@ + cpp_args : extra_cpp_args, + link_args: link_arguments, + dependencies: [zlib_dep, lzma_dep, thread_dep, +- htslib_dep, tabixpp_dep, vcflib_dep, seqlib_dep], ++ htslib_dep, tabixpp_dep, vcflib_dep, seqlib_dep, ++ fastahack_dep, sw_dep], + link_with : freebayes_lib, + install: true + ) +@@ -248,7 +251,8 @@ + cpp_args : extra_cpp_args, + link_args: link_arguments, + dependencies: [zlib_dep, lzma_dep, thread_dep, +- htslib_dep, vcflib_dep, seqlib_dep], ++ htslib_dep, vcflib_dep, seqlib_dep, ++ fastahack_dep, sw_dep], + link_with : freebayes_lib, + install: true + ) diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6_install-libs-headers.patch b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6_install-libs-headers.patch new file mode 100644 index 00000000000..a6e399a64db --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6_install-libs-headers.patch @@ -0,0 +1,95 @@ +Created by Jasper Grimm (UoY) +Install header files and scripts +Rename static lib to freebayes, and set install to True +Add target to build shared library +diff -Nru freebayes-1.3.6_p2/meson.build freebayes-1.3.6_p3/meson.build +--- freebayes-1.3.6_p2/meson.build 2022-03-29 12:59:54.000000000 +0100 ++++ freebayes-1.3.6_p3/meson.build 2022-03-29 14:18:24.000000000 +0100 +@@ -203,6 +203,37 @@ + freebayes_src = files('src/freebayes.cpp') + bamleftalign_src = files('src/bamleftalign.cpp') + ++# FreeBayes headers ++freebayes_headers = files( ++ 'src/Allele.h', ++ 'src/AlleleParser.h', ++ 'src/BedReader.h', ++ 'src/Bias.h', ++ 'src/CNV.h', ++ 'src/Contamination.h', ++ 'src/DataLikelihood.h', ++ 'src/Dirichlet.h', ++ 'src/Ewens.h', ++ 'src/FBFasta.h', ++ 'src/Genotype.h', ++ 'src/IndelAllele.h', ++ 'src/LeftAlign.h', ++ 'src/Logging.h', ++ 'src/Marginals.h', ++ 'src/Multinomial.h', ++ 'src/NonCall.h', ++ 'src/Parameters.h', ++ 'src/Product.h', ++ 'src/Result.h', ++ 'src/ResultData.h', ++ 'src/Sample.h', ++ 'src/SegfaultHandler.h', ++ 'src/Sum.h', ++ 'src/TryCatch.h', ++ 'src/Utility.h', ++ 'src/version_git.h', ++ ) ++ + # Include paths + incdir = include_directories( + 'src', +@@ -218,15 +249,29 @@ + ) + + freebayes_lib = static_library( +- 'freebayes_common', ++ 'freebayes', + freebayes_common_src, + include_directories : incdir, + cpp_args : extra_cpp_args, + dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep, + vcflib_dep, seqlib_dep, fastahack_dep, sw_dep], +- install : false, ++ install : true, + ) + ++freebayes_slib = shared_library( ++ 'freebayes', ++ freebayes_common_src, ++ include_directories : incdir, ++ cpp_args : extra_cpp_args, ++ dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep, ++ vcflib_dep, seqlib_dep, fastahack_dep, sw_dep], ++ install : true, ++ ) ++ ++install_headers(freebayes_headers, subdir : 'freebayes') ++ ++install_subdir('scripts', install_dir : '') ++ + if static_build + link_arguments = '-static' + else +@@ -241,7 +286,7 @@ + dependencies: [zlib_dep, lzma_dep, thread_dep, + htslib_dep, tabixpp_dep, vcflib_dep, seqlib_dep, + fastahack_dep, sw_dep], +- link_with : freebayes_lib, ++ link_with : freebayes_slib, + install: true + ) + +@@ -253,7 +298,7 @@ + dependencies: [zlib_dep, lzma_dep, thread_dep, + htslib_dep, vcflib_dep, seqlib_dep, + fastahack_dep, sw_dep], +- link_with : freebayes_lib, ++ link_with : freebayes_slib, + install: true + ) + From 3f4092a9c6a7f2d5eb71a6404ffb84e85af47bb4 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 31 Mar 2022 11:58:56 +0100 Subject: [PATCH 3379/9987] adding easyconfigs: vt-0.57721-GCC-11.2.0.eb, TCLAP-1.2.5-GCCcore-11.2.0.eb, LIBSVM-3.25-GCCcore-11.2.0.eb --- .../l/LIBSVM/LIBSVM-3.25-GCCcore-11.2.0.eb | 38 +++++++++++ .../t/TCLAP/TCLAP-1.2.5-GCCcore-11.2.0.eb | 32 ++++++++++ .../easyconfigs/v/vt/vt-0.57721-GCC-11.2.0.eb | 63 +++++++++++++++++++ 3 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.5-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/v/vt/vt-0.57721-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..958b5331c8a --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM' +version = '3.25' + +homepage = 'https://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression + (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'cjlin1' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%s.tar.gz' % version.replace('.', '')] +patches = ['LIBSVM-3.23_shared_lib.patch'] +checksums = [ + '1f587ec0df6fd422dfe50f942f8836ac179b0723b768fe9d2fabdfd1601a0963', # v325.tar.gz + 'c0ede89365949644f5d7f11382a3f176fd76317c7f5ae5769226ff7c3a801fe6', # LIBSVM-3.23_shared_lib.patch +] + +dependencies = [('binutils', '2.37')] + +local_bins = ['svm-%s' % x for x in ['predict', 'scale', 'train']] + +files_to_copy = [ + (local_bins, 'bin'), + (['svm.o'], 'lib'), + (['libsvm*'], 'lib'), + (['svm.h'], 'include/libsvm'), + 'tools' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + ['lib/libsvm.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e5b0687af1f --- /dev/null +++ b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.5-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'TCLAP' +version = '1.2.5' + +homepage = 'http://tclap.sourceforge.net/' +description = """TCLAP is a small, flexible library that provides a simple interface for defining and accessing +command line arguments. It was intially inspired by the user friendly CLAP libary.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb649f76dae35e8d0dcba4b52acfd4e062d787e6a81b43f7a4b01275153165a6'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "autoreconf -i -f && " + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/tclap/CmdLine.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-11.2.0.eb b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-11.2.0.eb new file mode 100644 index 00000000000..233554e931d --- /dev/null +++ b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-11.2.0.eb @@ -0,0 +1,63 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) + +easyblock = 'MakeCp' + +name = 'vt' +version = '0.57721' + +homepage = 'https://genome.sph.umich.edu/wiki/Vt' +description = """A tool set for short variant discovery in genetic sequence data.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'atks' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-0.57721_use-external-libs.patch', + '%(name)s-0.57721_fix-Rmath-includes.patch', + '%(name)s-0.57721_avoid-implicit-conversion.patch', + '%(name)s-0.57721_fail-on-test-error.patch', + '%(name)s-0.57721_update_htsutils.patch', +] +checksums = [ + '8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17', # 0.57721.tar.gz + '5a31713ae7c5febf850eec294dbba45b6b240d832cb94bdfe9ee695fd13e45bb', # vt-0.57721_use-external-libs.patch + '663525f5180a66d8817f271a69de1884576e2414d46b7ba93029d78f71d5b14c', # vt-0.57721_fix-Rmath-includes.patch + '56d874d5c7d488761f25afb4ee3717c88dfd959ed76efb75a8531b8428d30ccd', # vt-0.57721_avoid-implicit-conversion.patch + '4146282eb6ec852485f5a16e647da9c3b210450ceb5519b9b4a98bc52124469a', # vt-0.57721_fail-on-test-error.patch + '1c170b7ba2a4d392830f64392075ff75bbbc29137fe9f2922aeb7345e2ab6298', # vt-0.57721_update_htsutils.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('TCLAP', '1.2.5'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.78.0'), + ('PCRE', '8.45'), + ('PCRE2', '10.37'), + ('libdeflate', '1.8'), + ('libRmath', '4.1.2'), + ('LIBSVM', '3.25'), + ('HTSlib', '1.14'), +] + +runtest = 'test' + +files_to_copy = [ + (['vt'], 'bin'), + (['*.h'], 'include/vt'), + 'test', 'README.md', 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/vt'], + 'dirs': [], +} + +moduleclass = 'bio' From 62e65bfaf4b3040bd082d25a97f7aa57bbcff704 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 31 Mar 2022 12:01:16 +0100 Subject: [PATCH 3380/9987] adding easyconfigs: snippy-4.6.0-foss-2021b-R-4.1.2.eb, any2fasta-0.4.2-GCCcore-11.2.0.eb, Check-0.15.2-GCCcore-11.2.0.eb, snp-sites-2.5.1-GCCcore-11.2.0.eb, wgsim-20111017-GCC-11.2.0.eb --- .../any2fasta-0.4.2-GCCcore-11.2.0.eb | 35 ++++++++++++++ .../c/Check/Check-0.15.2-GCCcore-11.2.0.eb | 37 +++++++++++++++ .../snippy/snippy-4.6.0-foss-2021b-R-4.1.2.eb | 47 +++++++++++++++++++ .../snp-sites-2.5.1-GCCcore-11.2.0.eb | 37 +++++++++++++++ .../w/wgsim/wgsim-20111017-GCC-11.2.0.eb | 33 +++++++++++++ 5 files changed, 189 insertions(+) create mode 100644 easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/snippy/snippy-4.6.0-foss-2021b-R-4.1.2.eb create mode 100644 easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..86bf9d1770e --- /dev/null +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# Updated by: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'any2fasta' +version = '0.4.2' + +homepage = 'https://github.com/tseemann/any2fasta' +description = "Convert various sequence formats to FASTA" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +# https://github.com/tseemann/any2fasta +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] + +dependencies = [('Perl', '5.34.0')] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['any2fasta'], + 'dirs': [], +} + +sanity_check_commands = [ + 'any2fasta -h', + 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9e27b941bc5 --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Check' +version = '0.15.2' + +homepage = 'https://libcheck.github.io/check/' +description = """ +Check is a unit testing framework for C. It features a simple interface for +defining unit tests, putting little in the way of the developer. Tests are +run in a separate address space, so both assertion failures and code errors +that cause segmentation faults or other signals can be caught. Test results +are reportable in the following: Subunit, TAP, XML, and a generic logging +format.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'libcheck' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['998d355294bb94072f40584272cf4424571c396c631620ce463f6ea97aa67d2e'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-build-docs" + +sanity_check_paths = { + 'files': ['bin/checkmk', 'lib/libcheck.a', 'lib/libcheck.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..c9b055c0b96 --- /dev/null +++ b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-foss-2021b-R-4.1.2.eb @@ -0,0 +1,47 @@ +easyblock = 'Tarball' + +name = 'snippy' +version = '4.6.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/tseemann/snippy' +description = "Rapid haploid variant calling and core genome alignment" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/tseemann/snippy/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7264e3819e249387effd3eba170ff49404b1cf7347dfa25944866f5aeb6b11c3'] + +dependencies = [ + ('R', '4.1.2'), + ('Perl', '5.34.0'), + ('BioPerl', '1.7.8'), + ('BWA', '0.7.17'), + ('BCFtools', '1.14'), + ('BEDTools', '2.30.0'), + ('SAMtools', '1.14'), + ('parallel', '20210722'), + ('minimap2', '2.22'), + ('vt', '0.57721'), + ('samclip', '0.4.0'), + ('seqtk', '1.3'), + ('snp-sites', '2.5.1'), + ('snpEff', '5.0e', '-Java-11'), + ('any2fasta', '0.4.2'), + ('wgsim', '20111017'), + ('freebayes', '1.3.6', versionsuffix) +] + +sanity_check_paths = { + 'files': ['bin/snippy', 'perl5/Snippy/Version.pm'], + 'dirs': ['etc', 'test'], +} + +sanity_check_commands = [ + "snippy --version", + "snippy --check", + "snippy --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..fa59a1e9405 --- /dev/null +++ b/easybuild/easyconfigs/s/snp-sites/snp-sites-2.5.1-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'snp-sites' +version = '2.5.1' + +homepage = 'https://sanger-pathogens.github.io/snp-sites/' +description = """Finds SNP sites from a multi-FASTA alignment file.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'sanger-pathogens' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['913f79302e5d3127aea382756abc9ffeb05e26ce00022f43a6ea16a55cdd7a7e'] + +builddependencies = [ + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), + ('binutils', '2.37'), + ('Check', '0.15.2'), +] + +dependencies = [('zlib', '1.2.11')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/snp-sites'], + 'dirs': [], +} +sanity_check_commands = ["snp-sites -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-11.2.0.eb b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-11.2.0.eb new file mode 100644 index 00000000000..daa306f958e --- /dev/null +++ b/easybuild/easyconfigs/w/wgsim/wgsim-20111017-GCC-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'wgsim' +version = '20111017' +local_commit = 'a12da3375ff3b51a5594d4b6fa35591173ecc229' + +homepage = 'https://github.com/lh3/wgsim/' +description = "Wgsim is a small tool for simulating sequence reads from a reference genome." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_ZIP}] +checksums = ['1180fdd1d66691da5634e8c98b78c4742d0faf10042f35c2d17d26844d550f1c'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Perl', '5.34.0'), +] + +cmds_map = [('.*', "$CC $CFLAGS -o %(name)s %(name)s.c $LDFLAGS -lz -lm")] + +files_to_copy = [(['wgsim', 'wgsim_eval.pl'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/wgsim', 'bin/wgsim_eval.pl'], + 'dirs': [], +} + +sanity_check_commands = ["wgsim -h 2>&1 | grep 'Program: wgsim (short read simulator)'"] + +moduleclass = 'bio' From 3624d106a9c7cea0d57246c0ba2dcc3c6ecea571 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 31 Mar 2022 12:02:49 +0100 Subject: [PATCH 3381/9987] add SSW 1.1 w/ GCCcore 11.2.0 --- .../s/SSW/SSW-1.1-GCCcore-11.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1b8376d76c8 --- /dev/null +++ b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-11.2.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'SSW' +version = '1.1' + +homepage = 'https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library' +description = """SSW is a fast implementation of the Smith-Waterman algorithm, which uses the + Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the + instruction level. SSW library provides an API that can be flexibly used by programs written in + C, C++ and other languages. We also provide a software that can do protein and genome alignment + directly. Current version of our implementation is ~50 times faster than an ordinary + Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path + (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and + location heuristically. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1_build-cpp-lib.patch'] +checksums = [ + 'cdbc20740daeb188ed39413ea5ff9ae4cf72c4d7ccff1d2de2cac0446d64d99f', # v1.1.tar.gz + 'fe0d1f536ecd526dda8879b2f41b62c3c82b39d236f023ee735c1c18d584f06a', # SSW-1.1_build-cpp-lib.patch +] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('zlib', '1.2.11')] + +start_dir = 'src' + +buildopts = 'default' + +files_to_copy = [ + (['ssw_test'], 'bin'), + (['*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/ssw'), +] + +sanity_check_paths = { + 'files': ['bin/ssw_test', 'lib/libssw.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 52167c5178419c51f5e28645c02032cc71b1a5c0 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 31 Mar 2022 12:25:24 +0100 Subject: [PATCH 3382/9987] adding easyconfigs: snpEff-5.0e-GCCcore-11.2.0-Java-11.eb --- .../snpEff-5.0e-GCCcore-11.2.0-Java-11.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb new file mode 100644 index 00000000000..a7a8a7334f4 --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.0e' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d'] + +dependencies = [ + # ignore website claim that Java 12+ is required, nothing is compiled for + # anything newer than Java 11 + ('Java', '11', '', True), + ('Python', '3.9.6'), + ('Perl', '5.34.0'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From 9500af024c902247c5709a1b85adc5817c9c768f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2022 15:26:03 +0200 Subject: [PATCH 3383/9987] adding easyconfigs: FastANI-1.33-GCC-11.2.0.eb --- .../f/FastANI/FastANI-1.33-GCC-11.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-11.2.0.eb new file mode 100644 index 00000000000..55b00814caf --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-11.2.0.eb @@ -0,0 +1,45 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'ConfigureMake' + +name = 'FastANI' +version = '1.33' + +homepage = "https://github.com/ParBLiSS/FastANI" +description = """FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean + nucleotide identity of orthologous gene pairs shared between two microbial + genomes. FastANI supports pairwise comparison of both complete and draft + genome assemblies.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] +sources = ['v%(version)s.zip'] +patches = ['FastANI-1.2-memcpy.patch'] +checksums = [ + 'fb392ffa3c7942091a06de05c56c8e250523723c39da65ae8f245e65e440a74b', # v1.33.zip + 'eebcf0b64c31ee360ca79136f644157064ac69747ed13cff70f5c9932c6bb0d5', # FastANI-1.2-memcpy.patch +] + +builddependencies = [('Autotools', '20210726')] + +dependencies = [ + ('GSL', '2.7'), + ('zlib', '1.2.11'), +] + +preconfigopts = 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/fastANI'], + 'dirs': [] +} + +sanity_check_commands = ["fastANI --help"] + +moduleclass = 'bio' From 5d6d2e70d45aae1c258186f379e1efd1638ae5ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2022 15:35:52 +0200 Subject: [PATCH 3384/9987] adding easyconfigs: EMBOSS-6.6.0-foss-2021b.eb, libharu-2.3.0-foss-2021b.eb --- .../e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb | 58 +++++++++++++++++++ .../l/libharu/libharu-2.3.0-foss-2021b.eb | 44 ++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb new file mode 100644 index 00000000000..9471b613f8d --- /dev/null +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb @@ -0,0 +1,58 @@ +# authors: Kenneth Hoste (Ghent University) +# George Tsouloupas +# Fotis Georgatos +# +# This work implements a part of the HPCBIOS project and is a component +# of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute +# foss-2021a modified by: +# Sebastien Moretti +# SIB Swiss Institute of Bioinformatics +easyblock = 'ConfigureMake' + +name = 'EMBOSS' +version = '6.6.0' + +homepage = 'http://emboss.sourceforge.net/' +description = """EMBOSS is 'The European Molecular Biology Open Software Suite' +. EMBOSS is a free Open Source software analysis package specially developed + for the needs of the molecular biology (e.g. EMBnet) user community.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [ + 'ftp://emboss.open-bio.org/pub/EMBOSS/', + 'ftp://emboss.open-bio.org/pub/EMBOSS/old/%(version_major_minor)s.0', +] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_disable-embossupdate.patch'] +checksums = [ + '7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e', # EMBOSS-6.6.0.tar.gz + '7e0a7deffd76f60093be9c5253605f2d6d2e3b0c2d3c9365035cc6bda43eb46c', # EMBOSS-6.6.0_disable-embossupdate.patch +] + +builddependencies = [('CMake', '3.22.1')] + +dependencies = [ + ('X11', '20210802'), + ('libharu', '2.3.0'), + ('Java', '11', '', True), +] + +configopts = " --with-hpdf=$EBROOTLIBHARU " + +# jemboss.jar does not build in a parallel build +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['seqret', 'aligncopy', 'profit', 'prophet']] + + ['lib/lib%s.a' % x for x in ['acd', 'ajax', 'ajaxdb', 'ajaxg', 'eexpat', 'ensembl', + 'epcre', 'eplplot', 'ezlib', 'nucleus']] + + ['share/EMBOSS/jemboss/lib/jemboss.jar'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021b.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021b.eb new file mode 100644 index 00000000000..a6a8089cd10 --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2021b.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Modified for foss-2016b by: +# Adam Huffman +# The Francis Crick Institute +# +# Modified for foss-2020b by: +# Sebastien Moretti +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'http://libharu.org/' +description = """libHaru is a free, cross platform, open source library for generating PDF files.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/libharu/libharu/archive/'] +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] + +builddependencies = [('CMake', '3.22.1')] + +dependencies = [('libpng', '1.6.37')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': ['if', 'include', 'lib'] +} + +moduleclass = 'lib' From 96f058bddff1d5aa7d3edec4279f0091303d83b6 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 31 Mar 2022 17:04:33 +0200 Subject: [PATCH 3385/9987] Added requested changes --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index 9b6b22296fb..c9cfbe68368 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -61,12 +61,11 @@ exts_list = [ (2): Run the file and follow through the installation process (ensure you have Java installed to run the file) (3): Open terminal in the folder where you have installed ESOM and create Tarball of - its contents (tar -czvf esom.tar.gz *) - (4): Paste the file created (esom.tar.gz) into the same folder where your easyconfig is + its contents (tar -czvf esom-%(version)s.tar.gz *) + (4): Paste the file created (esom-%(version)s.tar.gz) into the same folder where your easyconfig is (5): Re-run the build. """, - 'source_tmpl': 'esom.tar.gz', - 'checksums': [None], + 'source_tmpl': 'esom-%(version)s.tar.gz', }), ] From 72407bccc323f2b1cc28799aee478f63433470aa Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 31 Mar 2022 17:51:58 +0200 Subject: [PATCH 3386/9987] ESOM checksum fix --- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index c9cfbe68368..f9e54ef7979 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -66,6 +66,7 @@ exts_list = [ (5): Re-run the build. """, 'source_tmpl': 'esom-%(version)s.tar.gz', + 'checksums': [None] }), ] From 18a0ef924709688d47a8388c296dd7c81caddf59 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2022 19:51:01 +0200 Subject: [PATCH 3387/9987] adding easyconfigs: barrnap-0.9-gompi-2021b.eb --- .../b/barrnap/barrnap-0.9-gompi-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2021b.eb diff --git a/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2021b.eb b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2021b.eb new file mode 100644 index 00000000000..6be62031149 --- /dev/null +++ b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'barrnap' +version = '0.9' + +homepage = 'https://github.com/tseemann/barrnap' +description = "Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes." + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://github.com/tseemann/barrnap/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['36c27cd4350531d98b3b2fb7d294a2d35c15b7365771476456d7873ba33cce15'] + +dependencies = [ + ('Perl', '5.34.0'), + ('HMMER', '3.3.2'), + ('BEDTools', '2.30.0'), +] + +sanity_check_paths = { + 'files': ['bin/barrnap'], + 'dirs': [], +} + +sanity_check_commands = ["barrnap --help"] + +moduleclass = 'bio' From 2c50632b4d1ffe973ac6b1f6ce77c82621d4730a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Mar 2022 19:58:29 +0200 Subject: [PATCH 3388/9987] adding easyconfigs: BDBag-1.6.3-intel-2021b.eb --- .../b/BDBag/BDBag-1.6.3-intel-2021b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/BDBag/BDBag-1.6.3-intel-2021b.eb diff --git a/easybuild/easyconfigs/b/BDBag/BDBag-1.6.3-intel-2021b.eb b/easybuild/easyconfigs/b/BDBag/BDBag-1.6.3-intel-2021b.eb new file mode 100644 index 00000000000..a8545e1bfcb --- /dev/null +++ b/easybuild/easyconfigs/b/BDBag/BDBag-1.6.3-intel-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'BDBag' +version = '1.6.3' + +homepage = 'https://github.com/fair-research/bdbag' +description = """The bdbag utilities are a collection of software programs for +working with BagIt packages that conform to the Bagit and Bagit/RO profiles.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True + +exts_list = [ + ('setuptools_scm', '5.0.2', { + 'checksums': ['83a0cedd3449e3946307811a4c7b9d89c4b5fd464a2fb5eeccd0a5bb158ae5c8'], + }), + ('tzlocal', '2.1', { + 'checksums': ['643c97c5294aedc737780a49d9df30889321cbe1204eac2c2ec6134035a92e44'], + }), + ('bagit', '1.8.1', { + 'checksums': ['37df1330d2e8640c8dee8ab6d0073ac701f0614d25f5252f9e05263409cee60c'], + }), + ('bagit_profile', '1.3.1', { + 'checksums': ['57798cdcf98b32a413edb29382d85f4f8c44d3204940d7e12d84998521a98c3f'], + }), + ('bdbag', version, { + 'checksums': ['1ad2e4956045cb3d43a6276391ad919e42a90a2443727dbc5b1ac6eeb6d6e3c9'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 07adbcdc3de920c0fa890b40c123098ee02889c6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 1 Apr 2022 12:13:14 +0100 Subject: [PATCH 3389/9987] also use x.py to build/install other recent Rust easyconfigs --- easybuild/easyconfigs/r/Rust/Rust-1.35.0-GCCcore-8.2.0.eb | 6 ++++++ easybuild/easyconfigs/r/Rust/Rust-1.37.0-GCCcore-8.3.0.eb | 6 ++++++ easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb | 6 ++++++ easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb | 6 ++++++ easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb | 6 ++++++ easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 6 ++++++ easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb | 6 ++++++ 7 files changed, 42 insertions(+) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.35.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.35.0-GCCcore-8.2.0.eb index 4ec08e99cfb..201655d76d0 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.35.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.35.0-GCCcore-8.2.0.eb @@ -20,6 +20,12 @@ builddependencies = [ configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + sanity_check_paths = { 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.37.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.37.0-GCCcore-8.3.0.eb index 9a3fe998abe..1b974a5ae88 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.37.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.37.0-GCCcore-8.3.0.eb @@ -20,6 +20,12 @@ builddependencies = [ configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + sanity_check_paths = { 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb index 18a3fc7c04f..1ebc625e84e 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb @@ -20,6 +20,12 @@ builddependencies = [ configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + sanity_check_paths = { 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb index 11b48f9f188..8f1530b3e20 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb @@ -20,6 +20,12 @@ builddependencies = [ configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + sanity_check_paths = { 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb index af22457939e..a24b66528c6 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb @@ -20,6 +20,12 @@ builddependencies = [ configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + sanity_check_paths = { 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index d9802f22e00..eaec7699da4 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -34,6 +34,12 @@ configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " # since Rust is a build dependency for cryptography that is included with Python configopts += "--set=llvm.ninja=false " +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + # avoid failure when home directory is an NFS mount, # see https://github.com/rust-lang/cargo/issues/6652 prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb index ee8b6cb18e5..2a008d86759 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb @@ -34,6 +34,12 @@ configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " # since Rust is a build dependency for cryptography that is included with Python configopts += "--set=llvm.ninja=false " +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + # avoid failure when home directory is an NFS mount, # see https://github.com/rust-lang/cargo/issues/6652 prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " From a8c90ef923e45cca27772d81f62315b669968da9 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 1 Apr 2022 14:34:49 +0100 Subject: [PATCH 3390/9987] adding easyconfigs: fmt-8.1.1-GCCcore-11.2.0.eb --- .../f/fmt/fmt-8.1.1-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-8.1.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-8.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-8.1.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9f7e0454d33 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-8.1.1-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '8.1.1' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['23778bad8edba12d76e4075da06db591f3b0e3c6c04928ced4a7282ca3400e5d'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37') +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' From c463dab795a6f847dce38331e3959f8695a92584 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 1 Apr 2022 14:38:32 +0100 Subject: [PATCH 3391/9987] OpenSSL included instead of relying on OS one --- easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb b/easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb index 4ccea17fa08..3a6f02f699e 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb @@ -14,10 +14,10 @@ source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['597c61358e6a92ecbfad42a9b5321ddd801fc7e7eca08441307c9138382d4f77'] -builddependencies = [('ncurses', '6.2')] - -# Use OS dependencies in order to ensure that CMake can build software that depends on them -osdependencies = [OS_PKG_OPENSSL_DEV] +builddependencies = [ + ('ncurses', '6.2'), + ('OpenSSL', '1.1'), +] configopts = "-- " configopts += "-DCURSES_CURSES_LIBRARY=$EBROOTNCURSES/lib/libcurses.a " From 85748b7c52911fcc73425c4ee8489587355b3826 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 1 Apr 2022 15:31:05 +0100 Subject: [PATCH 3392/9987] adding easyconfigs: crossguide-0.2.2-GCCcore-11.2.0.eb and patches: libuuid.patch --- .../crossguide-0.2.2-GCCcore-11.2.0.eb | 44 +++++++++++++++++++ .../easyconfigs/c/crossguide/libuuid.patch | 19 ++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/c/crossguide/libuuid.patch diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1a98cc2b22f --- /dev/null +++ b/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +# Contribution from Imperial College London, UK +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMakeCp' + +name = 'crossguide' +version = '0.2.2' + +homepage = 'https://github.com/graeme-hill/crossguid' +description = """ +CrossGuid is a minimal, cross platform, C++ GUID library. +It uses the best native GUID/UUID generator on the given platform and has a +generic class for parsing, stringifying, and comparing IDs. +The guid generation technique is determined by your platform:""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/graeme-hill/crossguid/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = ['libuuid.patch'] + +checksums = [ + '48321928473c682b0cdc7e17bbd3390f79f4b98ab22fef3b81a852dda81fd195', # v0.2.2.tar.gz + '6c59e785528fd24ed50304125c07193b9152d81dbc44b52fb2638729265f1bad', # libuuid.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] + +files_to_copy = [ + (['libxg.a'], 'lib'), + (['xgtest'], 'bin'), +] + +sanity_check_paths = { + 'files': [('lib/libxg.a')], + 'dirs': [], +} + +sanity_check_commands = [('xgtest')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/crossguide/libuuid.patch b/easybuild/easyconfigs/c/crossguide/libuuid.patch new file mode 100644 index 00000000000..c5d89a081a8 --- /dev/null +++ b/easybuild/easyconfigs/c/crossguide/libuuid.patch @@ -0,0 +1,19 @@ +Updates the older Libuuid to LibUUID so CMake does not complain +Author: J. Sassmannshausen +diff --git a/crossguid-0.2.2.orig/CMakeLists.txt b/crossguid-0.2.2/CMakeLists.txt +index 761dbc6..22fcee5 100644 +--- a/crossguid-0.2.2.orig/CMakeLists.txt ++++ b/crossguid-0.2.2/CMakeLists.txt +@@ -27,7 +27,7 @@ elseif(APPLE) + elseif(ANDROID) + target_compile_definitions(xg PRIVATE GUID_ANDROID) + else() +- find_package(Libuuid REQUIRED) ++ find_package(LibUUID REQUIRED) + if (NOT LIBUUID_FOUND) + message(FATAL_ERROR + "You might need to run 'sudo apt-get install uuid-dev' or similar") +diff --git a/crossguid-0.2.2.orig/cmake/FindLibuuid.cmake b/crossguid-0.2.2/cmake/FindLibUUID.cmake +similarity index 100% +rename from crossguid-0.2.2.orig/cmake/FindLibuuid.cmake +rename to crossguid-0.2.2/cmake/FindLibUUID.cmake From 5523dbe7a854c40d1fc82c152dd4da7014f28dde Mon Sep 17 00:00:00 2001 From: Carsten Bauer Date: Fri, 1 Apr 2022 17:33:54 +0200 Subject: [PATCH 3393/9987] add Julia 1.6.6 easyconfig --- .../j/Julia/Julia-1.6.6-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb new file mode 100644 index 00000000000..1ceea6444d5 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.6.6' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['c25ff71a4242207ab2681a0fcc5df50014e9d99f814e77cacbc5027e20514945'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From f3dc5fefe592358acd8044ec06e94e4ed4a9dba6 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 1 Apr 2022 16:55:07 +0100 Subject: [PATCH 3394/9987] Shared libs build included, surpluse build-directory directive removed --- easybuild/easyconfigs/f/fmt/fmt-8.1.1-GCCcore-11.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/fmt/fmt-8.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-8.1.1-GCCcore-11.2.0.eb index 9f7e0454d33..23b7cc2ad3e 100644 --- a/easybuild/easyconfigs/f/fmt/fmt-8.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/fmt/fmt-8.1.1-GCCcore-11.2.0.eb @@ -7,7 +7,6 @@ homepage = 'http://fmtlib.net/' description = "fmt (formerly cppformat) is an open-source formatting library." toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -toolchainopts = {'pic': True} source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] sources = ['fmt-%(version)s.zip'] @@ -18,10 +17,11 @@ builddependencies = [ ('binutils', '2.37') ] -separate_build_dir = True +# build static and shared libraries +configopts = ["-DCMAKE_POSTITION_INDEPENDENT_CODE=TRUE", "-DBUILD_SHARED_LIBS=TRUE"] sanity_check_paths = { - 'files': ['lib/libfmt.a'], + 'files': ['lib/libfmt.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': ['include/fmt', 'lib/cmake'], } From 044d3a227b888f9999c7d6c36f00f9862d55f819 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 1 Apr 2022 19:19:32 +0100 Subject: [PATCH 3395/9987] Updated to latest commit as name of lib has changed, patch updated accordingly and renamed --- .../crossguide-0.2.2-GCCcore-11.2.0.eb | 4 +- .../crossguide-20190529-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ .../{libuuid.patch => libuuid-0.2.2.patch} | 0 .../c/crossguide/libuuid-20190529.patch | 19 ++++++++ 4 files changed, 66 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb rename easybuild/easyconfigs/c/crossguide/{libuuid.patch => libuuid-0.2.2.patch} (100%) create mode 100644 easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb index 1a98cc2b22f..70337557908 100644 --- a/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb @@ -17,11 +17,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/graeme-hill/crossguid/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] -patches = ['libuuid.patch'] +patches = ['libuuid-0.2.2.patch'] checksums = [ '48321928473c682b0cdc7e17bbd3390f79f4b98ab22fef3b81a852dda81fd195', # v0.2.2.tar.gz - '6c59e785528fd24ed50304125c07193b9152d81dbc44b52fb2638729265f1bad', # libuuid.patch + '6c59e785528fd24ed50304125c07193b9152d81dbc44b52fb2638729265f1bad', # libuuid-0.2.2.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5481d2e825e --- /dev/null +++ b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +# Contribution from Imperial College London, UK +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMakeCp' + +name = 'crossguide' +local_commit = 'ca1bf4b' +version = '20190529' + +homepage = 'https://github.com/graeme-hill/crossguid' +description = """ +CrossGuid is a minimal, cross platform, C++ GUID library. +It uses the best native GUID/UUID generator on the given platform and has a +generic class for parsing, stringifying, and comparing IDs. +The guid generation technique is determined by your platform:""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/graeme-hill/crossguid/archive/%s' % local_commit] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = ['libuuid-20190529.patch'] + +checksums = [ + '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguide-20190529.tar.gz + '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # libuuid-20190529.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] + +files_to_copy = [ + (['libcrossguid.a'], 'lib'), + (['crossguid-test'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libcrossguid.a', 'bin/crossguid-test'], + 'dirs': [''], +} + +sanity_check_commands = [('crossguid-test')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/crossguide/libuuid.patch b/easybuild/easyconfigs/c/crossguide/libuuid-0.2.2.patch similarity index 100% rename from easybuild/easyconfigs/c/crossguide/libuuid.patch rename to easybuild/easyconfigs/c/crossguide/libuuid-0.2.2.patch diff --git a/easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch b/easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch new file mode 100644 index 00000000000..d75df709152 --- /dev/null +++ b/easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch @@ -0,0 +1,19 @@ +Updates the older Libuuid to LibUUID so CMake does not complain +Author: J. Sassmannshausen +diff --git a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/CMakeLists.txt b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/CMakeLists.txt +index 76b5a62..03291c5 100644 +--- a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/CMakeLists.txt ++++ b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/CMakeLists.txt +@@ -30,7 +30,7 @@ elseif(ANDROID) + # GUID_ANDROID is used in the headers, so make PUBLIC + target_compile_definitions(crossguid PUBLIC GUID_ANDROID) + else() +- find_package(Libuuid REQUIRED) ++ find_package(LibUUID REQUIRED) + if (NOT LIBUUID_FOUND) + message(FATAL_ERROR + "You might need to run 'sudo apt-get install uuid-dev' or similar") +diff --git a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/cmake/FindLibuuid.cmake b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/cmake/FindLibUUID.cmake +similarity index 100% +rename from crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/cmake/FindLibuuid.cmake +rename to crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/cmake/FindLibUUID.cmake From 2bf1f79f62ec57b2d74b76b8cc09ee1b292356cf Mon Sep 17 00:00:00 2001 From: sassy Date: Sat, 2 Apr 2022 11:57:20 +0100 Subject: [PATCH 3396/9987] Trailing whitespaces removed --- .../easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb | 2 +- .../c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb index 70337557908..e962cbe341b 100644 --- a/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb @@ -21,7 +21,7 @@ patches = ['libuuid-0.2.2.patch'] checksums = [ '48321928473c682b0cdc7e17bbd3390f79f4b98ab22fef3b81a852dda81fd195', # v0.2.2.tar.gz - '6c59e785528fd24ed50304125c07193b9152d81dbc44b52fb2638729265f1bad', # libuuid-0.2.2.patch + '6c59e785528fd24ed50304125c07193b9152d81dbc44b52fb2638729265f1bad', # libuuid-0.2.2.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb index 5481d2e825e..7445c960e9c 100644 --- a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb @@ -22,7 +22,7 @@ patches = ['libuuid-20190529.patch'] checksums = [ '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguide-20190529.tar.gz - '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # libuuid-20190529.patch + '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # libuuid-20190529.patch ] builddependencies = [ From 85cc9dc789dd94b49c27ffeb184e40facc4a9709 Mon Sep 17 00:00:00 2001 From: sassy Date: Sat, 2 Apr 2022 18:13:41 +0100 Subject: [PATCH 3397/9987] adding easyconfigs: indicators-2.2-GCCcore-11.2.0.eb --- .../indicators-2.2-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/i/indicators/indicators-2.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/i/indicators/indicators-2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/indicators/indicators-2.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9b76a995eb8 --- /dev/null +++ b/easybuild/easyconfigs/i/indicators/indicators-2.2-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +# Contribution from Imperial College London/UK +# uploaded: J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'indicators' +version = '2.2' + +homepage = 'https://github.com/p-ranav/indicators' +description = """ +- Thread-safe progress bars and spinners +- Header-only library. Grab a copy of include/indicators. +- Single-header version in single_include/indicators. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/p-ranav/indicators/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b768f1b7ca64a413503f72d5460cc617c1458c17fb7a8c0ee503d753e1f20d03'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37') +] + +# build demo and sample program +configopts = ["-DINDICATORS_SAMPLES=ON -DINDICATORS_DEMO=ON -DINDICATORS_BUILD_TESTS=ON"] + +install_cmd = "make install && " +install_cmd += "mkdir %(installdir)s/bin/ && " +install_cmd += "cp demo/demo %(installdir)s/bin/ && " +install_cmd += "cp samples/*bar* samples/dynamic* %(installdir)s/bin/ && " +install_cmd += "cp samples/progress_spinner samples/time_meter samples/max_progress %(installdir)s/bin/" + +sanity_check_paths = { + 'files': ['bin/demo', 'bin/time_meter'], + 'dirs': ['include', 'lib'], +} + +sanity_check_commands = [('demo')] + +moduleclass = 'tools' From 2db6ecaf487286b6f79231d8062a0d6bdfe018fd Mon Sep 17 00:00:00 2001 From: sassy Date: Sat, 2 Apr 2022 20:10:47 +0100 Subject: [PATCH 3398/9987] adding easyconfigs: rapidcsv-8.62-GCCcore-11.2.0.eb --- .../rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d3bd423b610 --- /dev/null +++ b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +# Contribution from Imperial College London/UK +# uploaded: J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'rapidcsv' +version = '8.62' + +homepage = 'https://github.com/d99kris/rapidcsv' +description = """ +Rapidcsv is a C++ header-only library for CSV parsing. +While the name admittedly was inspired by the rapidjson project, +the objectives are not the same. The goal of rapidcsv is to be +an easy-to-use CSV library enabling rapid development. +For optimal performance (be it CPU or memory usage) a CSV parser +implemented for the specific use-case is likely to be more performant. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/d99kris/rapidcsv/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a7efda6324420f2b69d3448672a9553dc91520632409661f9f83ac0425faa31d'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37') +] + +sanity_check_paths = { + 'files': ['include/rapidcsv.h'], + 'dirs': [''], +} + +moduleclass = 'tools' From 60c2e2ab17dd3162c39805f0c9cb134c71ed033b Mon Sep 17 00:00:00 2001 From: sassy Date: Sat, 2 Apr 2022 20:45:28 +0100 Subject: [PATCH 3399/9987] Updated to get full installation, including include and lib folder, and test --- .../crossguide-20190529-GCCcore-11.2.0.eb | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb index 7445c960e9c..4e727a305b1 100644 --- a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb @@ -1,7 +1,7 @@ # Contribution from Imperial College London, UK # uploaded by J. Sassmannshausen -easyblock = 'CMakeMakeCp' +easyblock = 'CMakeMake' name = 'crossguide' local_commit = 'ca1bf4b' @@ -30,14 +30,17 @@ builddependencies = [ ('CMake', '3.22.1'), ] -files_to_copy = [ - (['libcrossguid.a'], 'lib'), - (['crossguid-test'], 'bin'), -] +# build demo +configopts = ["-DCROSSGUID_TESTS=ON"] + +# we want to have the crossguid-test +install_cmd = "make install && " +install_cmd += "mkdir %(installdir)s/bin/ && " +install_cmd += "cp crossguid-test %(installdir)s/bin/ " sanity_check_paths = { 'files': ['lib/libcrossguid.a', 'bin/crossguid-test'], - 'dirs': [''], + 'dirs': ['include'], } sanity_check_commands = [('crossguid-test')] From 6950b9d90fba2c4dabf75707b0444b0881940868 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 4 Apr 2022 10:09:19 +0900 Subject: [PATCH 3400/9987] adding easyconfigs: Bader-1.04-intel-2020b.eb --- .../b/Bader/Bader-1.04-intel-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb b/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb new file mode 100644 index 00000000000..c9f4722d7d7 --- /dev/null +++ b/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'Bader' +version = '1.04' + +homepage = 'http://theory.cm.utexas.edu/henkelman/code/bader/' +description = "A fast algorithm for doing Bader's analysis on a charge density grid." + +toolchain = {'name': 'intel', 'version': '2020b'} + +source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] +sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f20a0a021157d911bea06666911763b737c4ff38b39e793b8560f940fe391b8e'] + +prebuildopts = 'sed -i "s|FFLAGS = -O2||" makefile.lnx_ifort && sed -i "s/LINK = -static/LINK = -static-intel/g" makefile.lnx_ifort && ' +buildopts = '-f makefile.lnx_ifort' +parallel = 1 + +files_to_copy = [(['bader'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bader'], + 'dirs': [], +} + +moduleclass = 'chem' From b7d45a6da5778c83eeabcd3bbe1d995a9182f78c Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 4 Apr 2022 10:19:48 +0900 Subject: [PATCH 3401/9987] adding easyconfigs: EigenExa-2.11-intel-2020b.eb --- .../e/EigenExa/EigenExa-2.11-intel-2020b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb diff --git a/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb b/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb new file mode 100644 index 00000000000..9f693334211 --- /dev/null +++ b/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'EigenExa' +version = '2.11' + +homepage = 'https://www.r-ccs.riken.jp/labs/lpnctrt/projects/eigenexa/' +description = """EigenExa, a part of KMATHLIB, is a high performance eigen-solver.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://www.r-ccs.riken.jp/labs/lpnctrt/projects/eigenexa/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['87dee8ac13f410a007e82df2688fa7f143883229dac729fd20836f4a28fac43d'] + +preconfigopts = './cleanup && ./bootstrap && ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libEigenExa.a'], + 'dirs': [] +} + +moduleclass = 'math' From b0720908d71c4a09a076faa0d69f3588b9311643 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 4 Apr 2022 10:21:34 +0900 Subject: [PATCH 3402/9987] adding easyconfigs: ELPA-2021.05.002-intel-2020b.eb and patches: ELPA-2021.05.002_fix_hardcoded_perl_path.patch --- .../e/ELPA/ELPA-2021.05.002-intel-2020b.eb | 39 +++++++++++++++++++ ...-2021.05.002_fix_hardcoded_perl_path.patch | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002_fix_hardcoded_perl_path.patch diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb new file mode 100644 index 00000000000..bd153664f95 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2021.05.002' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s_bugfix/'] +sources = ['elpa-%(version)s_bugfix.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + 'deabc48de5b9e4b2f073d749d335c8f354a7ce4245b643a23b7951cd6c90224b', # elpa-2021.05.002_bugfix.tar.gz + # ELPA-2021.05.002_fix_hardcoded_perl_path.patch + '69d2a7dcb61a7a699dd469a134a693e74c72b157dc72b3eba7a5dc12eb29893d', +] + +builddependencies = [ + ('Autotools', '20200321'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.8.6'), + ('Perl', '5.32.0'), +] + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002_fix_hardcoded_perl_path.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002_fix_hardcoded_perl_path.patch new file mode 100644 index 00000000000..da534f423e9 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002_fix_hardcoded_perl_path.patch @@ -0,0 +1,39 @@ +Fix hardcoded paths to perl. +We depend on EasyBuild Perl. + +Åke Sandgren, 20210824 +diff -ru elpa-new_release_2021.05.002_bugfix.orig/fdep/fortran_dependencies.pl elpa-new_release_2021.05.002_bugfix/fdep/fortran_dependencies.pl +--- elpa-new_release_2021.05.002_bugfix.orig/fdep/fortran_dependencies.pl 2021-06-07 11:35:08.000000000 +0200 ++++ elpa-new_release_2021.05.002_bugfix/fdep/fortran_dependencies.pl 2021-08-24 18:15:00.133701035 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Copyright 2015 Lorenz Hüdepohl + # +diff -ru elpa-new_release_2021.05.002_bugfix.orig/test_project_1stage/fdep/fortran_dependencies.pl elpa-new_release_2021.05.002_bugfix/test_project_1stage/fdep/fortran_dependencies.pl +--- elpa-new_release_2021.05.002_bugfix.orig/test_project_1stage/fdep/fortran_dependencies.pl 2021-06-07 11:35:08.000000000 +0200 ++++ elpa-new_release_2021.05.002_bugfix/test_project_1stage/fdep/fortran_dependencies.pl 2021-08-24 18:15:33.421492236 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +diff -ru elpa-new_release_2021.05.002_bugfix.orig/test_project_2stage/fdep/fortran_dependencies.pl elpa-new_release_2021.05.002_bugfix/test_project_2stage/fdep/fortran_dependencies.pl +--- elpa-new_release_2021.05.002_bugfix.orig/test_project_2stage/fdep/fortran_dependencies.pl 2021-06-07 11:35:08.000000000 +0200 ++++ elpa-new_release_2021.05.002_bugfix/test_project_2stage/fdep/fortran_dependencies.pl 2021-08-24 18:15:36.101475423 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +diff -ru elpa-new_release_2021.05.002_bugfix.orig/test_project_C/fdep/fortran_dependencies.pl elpa-new_release_2021.05.002_bugfix/test_project_C/fdep/fortran_dependencies.pl +--- elpa-new_release_2021.05.002_bugfix.orig/test_project_C/fdep/fortran_dependencies.pl 2021-06-07 11:35:08.000000000 +0200 ++++ elpa-new_release_2021.05.002_bugfix/test_project_C/fdep/fortran_dependencies.pl 2021-08-24 18:15:38.653459416 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; From b15c3ae03f42b91a812a1cf6a55992273f74fadb Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 4 Apr 2022 10:23:40 +0900 Subject: [PATCH 3403/9987] adding easyconfigs: i7z-0.27.2-GCCcore-11.2.0.eb and patches: i7z-0.27.2_fix_gcc-10.patch --- .../i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb | 50 +++++++++++++++++++ .../i/i7z/i7z-0.27.2_fix_gcc-10.patch | 12 +++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/i/i7z/i7z-0.27.2_fix_gcc-10.patch diff --git a/easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b4f4dcdf06e --- /dev/null +++ b/easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'MakeCp' + +name = 'i7z' +version = '0.27.2' + +homepage = 'https://github.com/ajaiantilal/i7z' +description = """A better i7 (and now i3, i5) reporting tool for Linux +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [{ + 'filename': 'i7z-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/ajaiantilal', + 'repo_name': 'i7z', + 'commit': '5023138', + 'recursive': True, + 'keep_git_dir': True, + }, +}] +patches = [ + ('i7z-%(version)s_fix_gcc-10.patch'), +] +checksums = [ + 'ef895fa04c42cb926c3fd07a1274e16a8606c1ef836a37865bb620e725b317c5', # i7z-0.27.2.tar.gz + 'e6422302070b450c61ba4fd35e01eb4b1c112dd6c89250363ab94a62e5092e68', # i7z-0.27.2_fix_gcc-10.patch +] + +builddependencies = [ + ('binutils', '2.37') +] + +dependencies = [ + ('ncurses', '6.2'), +] + +files_to_copy = [( + [ + 'i7z', + 'i7z_32bit', + 'i7z_64bit' + ], 'bin')] + +sanity_check_paths = { + 'files': ['bin/i7z', 'bin/i7z_32bit', 'bin/i7z_64bit'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/i7z/i7z-0.27.2_fix_gcc-10.patch b/easybuild/easyconfigs/i/i7z/i7z-0.27.2_fix_gcc-10.patch new file mode 100644 index 00000000000..de0f773a434 --- /dev/null +++ b/easybuild/easyconfigs/i/i7z/i7z-0.27.2_fix_gcc-10.patch @@ -0,0 +1,12 @@ +diff -ru i7z.orig/Makefile i7z/Makefile +--- i7z.orig/Makefile 2022-04-01 19:33:00.000000000 +0900 ++++ i7z/Makefile 2022-04-01 19:33:23.000000000 +0900 +@@ -8,7 +8,7 @@ + #here + CFLAGS_FOR_AVOIDING_SEG_FAULT = -fno-schedule-insns2 -fno-schedule-insns -fno-inline-small-functions -fno-caller-saves + CFLAGS ?= -O3 +-CFLAGS += $(CFLAGS_FOR_AVOIDING_SEG_FAULT) -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DBUILD_MAIN -Wimplicit-function-declaration ++CFLAGS += $(CFLAGS_FOR_AVOIDING_SEG_FAULT) -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -DBUILD_MAIN -Wimplicit-function-declaration -fcommon + + LBITS := $(shell getconf LONG_BIT) + ifeq ($(LBITS),64) From a029ece0ac04dd76a3162c18b5f6919e1f3a45db Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 4 Apr 2022 10:53:23 +0900 Subject: [PATCH 3404/9987] adding easyconfigs: NTPoly-2.7.1-intel-2020b.eb --- .../n/NTPoly/NTPoly-2.7.1-intel-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb new file mode 100644 index 00000000000..218a4c9aa75 --- /dev/null +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'NTPoly' +version = '2.7.1' + +homepage = 'https://github.com/william-dawson/NTPoly' +description = """is a massively parallel library for computing the functions of sparse, symmetric matrices based on +polynomial expansions. For sufficiently sparse matrices, most of the matrix functions +in NTPoly can be computed in linear time.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': False, 'usempi': True} + +source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c15d9f51ac054b4ef0565ce5c4c8589c10bdbab4dc3442ebd109691e2bbfc7e2'] + +builddependencies = [('CMake', '3.18.4')] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/%s.mod' % x for x in ['datatypesmodule', 'densitymatrixsolversmodule']] + + ['lib64/libNTPoly.%s' % SHLIB_EXT, 'lib/libNTPoly.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' \ No newline at end of file From c08dbe237e9c3b20463b0d831d2a98f7699eb987 Mon Sep 17 00:00:00 2001 From: Daniel Hedman Date: Mon, 4 Apr 2022 21:06:23 +0900 Subject: [PATCH 3405/9987] Update NTPoly-2.7.1-intel-2020b.eb Add newline to end of file --- easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb index 218a4c9aa75..09ce90d7416 100644 --- a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.7.1-intel-2020b.eb @@ -25,4 +25,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'math' \ No newline at end of file +moduleclass = 'math' From 3a6e0eada4aa33b53eb5e990fdf6acb5552d0701 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 5 Apr 2022 16:44:48 +0100 Subject: [PATCH 3406/9987] adding easyconfigs: MUMPS-5.4.1-intel-2021b-metis.eb, SCOTCH-6.1.2-iimpi-2021b.eb, Hypre-2.24.0-intel-2021b.eb --- .../h/Hypre/Hypre-2.24.0-intel-2021b.eb | 18 ++++++++++ .../m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb | 35 +++++++++++++++++++ .../s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb | 20 +++++++++++ 3 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.24.0-intel-2021b.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.24.0-intel-2021b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.24.0-intel-2021b.eb new file mode 100644 index 00000000000..9bb18b55b78 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.24.0-intel-2021b.eb @@ -0,0 +1,18 @@ +name = 'Hypre' +version = '2.24.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f480e61fc25bf533fc201fdf79ec440be79bb8117650627d1f25151e8be2fdb5'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb new file mode 100644 index 00000000000..3971d5baaa7 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb @@ -0,0 +1,35 @@ +name = 'MUMPS' +version = '5.4.1' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-5.4.0_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-5.4.0_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + '93034a1a9fe0876307136dcde7e98e9086e199de76f1c47da822e7d4de987fa8', # MUMPS_5.4.1.tar.gz + '4c0558690998c12ca959c03856054a75e22f519583a65bd550393c1f81a0b170', # MUMPS-5.4.0_shared-pord.patch + 'd51c2df0de7d7b88d864ceba2d0eea46c755c24c7124003481aced106901109d', # MUMPS-5.4.0_shared-mumps.patch +] + +dependencies = [ + ('SCOTCH', '6.1.2'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb new file mode 100644 index 00000000000..baf59e8b1e0 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb @@ -0,0 +1,20 @@ +name = 'SCOTCH' +version = '6.1.2' + +homepage = 'https://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/%(namelower)s/%(namelower)s/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['9c2c75c75f716914a2bd1c15dffac0e29a2f8069b2df1ad2b6207c984b699450'] + +dependencies = [ + ('zlib', '1.2.11'), +] + + +moduleclass = 'math' From 6fcf12b00a567f30dac188527e5a1b05ac04d0c8 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 5 Apr 2022 17:48:41 +0100 Subject: [PATCH 3407/9987] Moved OpenSSL to dependency where it should have been in the first place --- easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb b/easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb index 3a6f02f699e..8bb971500ae 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.18.4.eb @@ -16,6 +16,9 @@ checksums = ['597c61358e6a92ecbfad42a9b5321ddd801fc7e7eca08441307c9138382d4f77'] builddependencies = [ ('ncurses', '6.2'), +] + +dependencies = [ ('OpenSSL', '1.1'), ] From 621bab27310f2a6fdb49ca74a9edf07596fba0a6 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 5 Apr 2022 19:16:24 +0200 Subject: [PATCH 3408/9987] adding easyconfigs: arosics-1.7.6-foss-2021a.eb --- .../a/arosics/arosics-1.7.6-foss-2021a.eb | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb b/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb new file mode 100644 index 00000000000..f49acc42348 --- /dev/null +++ b/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb @@ -0,0 +1,80 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'arosics' +version = '1.7.6' + +homepage = 'https://github.com/GFZ/arosics' +description = """AROSICS is a python package to perform automatic subpixel co-registration +of two satellite image datasets based on an image matching approach working in the frequency +domain, combined with a multistage workflow for effective detection of false-positives.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('GEOS', '3.9.1'), + ('GDAL', '3.3.0'), + ('Pillow', '8.2.0'), + ('matplotlib', '3.4.2'), + ('scikit-image', '0.18.3'), + ('Fiona', '1.8.20'), + ('Cartopy', '0.20.0'), + ('pyproj', '3.1.0'), + ('dill', '0.3.4'), + ('networkx', '2.6.3'), + ('plotly.pi', '5.1.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('fonttools', '4.29.1', { + 'modulename': 'fontTools', + 'source_tmpl': SOURCE_ZIP, + 'checksums': ['2b18a172120e32128a80efee04cff487d5d140fe7d817deb648b2eee023a40e4'], + }), + ('PyKrige', '1.6.1', { + 'checksums': ['7432287306d13820ed0f0ec2f52c12fa462e18015abbf8fa627beab989ccaff6'], + }), + ('pyFFTW', '0.12.0', { + 'source_tmpl': SOURCE_TAR_GZ, + 'checksums': ['60988e823ca75808a26fd79d88dbae1de3699e72a293f812aa4534f8a0a58cb0'], + }), + ('spectral', '0.22.4', { + 'checksums': ['b208ffd1042e32fd2276a35e098e3df26a5f6ff1310b829e97d222c66645a9af'], + }), + ('py-tools-ds', '0.20.1', { + 'source_tmpl': 'py_tools_ds-%(version)s.tar.gz', + 'checksums': ['c745a3e540c2b75dbffc1783df4307707b0b9f80cc7f30de4f1138983f62d899'], + }), + ('geopandas', '0.10.2', { + 'checksums': ['efbf47e70732e25c3727222019c92b39b2e0a66ebe4fe379fbe1aa43a2a871db'], + }), + ('geojson', '2.5.0', { + 'checksums': ['6e4bb7ace4226a45d9c8c8b1348b3fc43540658359f93c3f7e03efa9f15f658a'], + }), + ('geoarray', '0.15.7', { + 'source_tmpl': SOURCE_TAR_GZ, + 'checksums': ['65678c49332ff471d1c95a26734ee67086fb02490d437647e9de67571022532f'], + }), + ('branca', '0.4.2', { + 'checksums': ['c111453617b17ab2bda60a4cd71787d6f2b59c85cdf71ab160a737606ac66c31'], + }), + ('folium', '0.12.1.post1', { + 'checksums': ['e91e57d8298f3ccf4cce3c5e065bea6eb17033e3c5432b8a22214009c266b2ab'], + }), + ('cmocean', '2.0', { + 'checksums': ['13eea3c8994d8e303e32a2db0b3e686f6edfb41cb21e7b0e663c2b17eea9b03a'], + }), + (name, version, { + 'source_tmpl': SOURCE_TAR_GZ, + 'checksums': ['03f4f952cca5d9d709da1a3c2130ddb3fbb1d21b83998593569638a4b1c7aaa9'], + }), +] + +moduleclass = 'devel' From d388a18a2bdfd96cc11d10dd63c1bb65d1a0092a Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 5 Apr 2022 19:47:34 +0200 Subject: [PATCH 3409/9987] Fixes typos --- easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb b/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb index f49acc42348..4eac1d90e5b 100644 --- a/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb +++ b/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb @@ -26,7 +26,7 @@ dependencies = [ ('pyproj', '3.1.0'), ('dill', '0.3.4'), ('networkx', '2.6.3'), - ('plotly.pi', '5.1.0'), + ('plotly.py', '5.1.0'), ] use_pip = True @@ -59,7 +59,7 @@ exts_list = [ 'checksums': ['6e4bb7ace4226a45d9c8c8b1348b3fc43540658359f93c3f7e03efa9f15f658a'], }), ('geoarray', '0.15.7', { - 'source_tmpl': SOURCE_TAR_GZ, + 'source_tmpl': SOURCE_TAR_GZ, 'checksums': ['65678c49332ff471d1c95a26734ee67086fb02490d437647e9de67571022532f'], }), ('branca', '0.4.2', { From cda0994d2546cb9ec12f9f64f3aa711f75caf1fe Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Tue, 5 Apr 2022 22:09:06 +0200 Subject: [PATCH 3410/9987] Downgrades networkx --- easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb b/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb index 4eac1d90e5b..64dbf3bd32f 100644 --- a/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb +++ b/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb @@ -25,7 +25,7 @@ dependencies = [ ('Cartopy', '0.20.0'), ('pyproj', '3.1.0'), ('dill', '0.3.4'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ('plotly.py', '5.1.0'), ] From 66a0b4617914eaefb1b934042210aa147ba36124 Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Tue, 5 Apr 2022 22:54:38 +0200 Subject: [PATCH 3411/9987] adding easyconfigs: Clang-9.0.1-GCCcore-9.3.0.eb --- .../c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..121f2982213 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb @@ -0,0 +1,69 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '9.0.1' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'clang-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', +] +patches = ['libcxx-%(version)s-ppc64le.patch'] +checksums = [ + '00a1ee1f389f81e9979f3a640a01c431b3021de0d42278f6508391a2f0b81c9a', # llvm-9.0.1.src.tar.xz + '5778512b2e065c204010f88777d44b95250671103e434f9dc7363ab2e3804253', # clang-9.0.1.src.tar.xz + 'c2bfab95c9986318318363d7f371a85a95e333bc0b34fbfa52edbd3f5e3a9077', # compiler-rt-9.0.1.src.tar.xz + '9a4ac69df923230d13eb6cd0d03f605499f6a854b1dc96a9b72c4eb075040fcf', # polly-9.0.1.src.tar.xz + '5c94060f846f965698574d9ce22975c0e9f04c9b14088c3af5f03870af75cace', # openmp-9.0.1.src.tar.xz + '86262bad3e2fd784ba8c5e2158d7aa36f12b85f2515e95bc81d65d75bb9b0c82', # lld-9.0.1.src.tar.xz + '0981ff11b862f4f179a13576ab0a2f5530f46bd3b6b4a90f568ccc6a62914b34', # libcxx-9.0.1.src.tar.xz + 'e8f978aa4cfae2d7a0b4d89275637078557cca74b35c31b7283d4786948a8aac', # libcxxabi-9.0.1.src.tar.xz + '6a39230b9e2b2c61fb5f67ac752d256437ccc56a6a517d7b6d53417d198fdb1f', # libcxx-9.0.1-ppc64le.patch +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.34'), + ('GMP', '6.2.0'), +] + +builddependencies = [ + ('CMake', '3.16.4'), + ('Python', '2.7.18'), + ('libxml2', '2.9.10'), +] + +assertions = True +usepolly = True +build_lld = True +libcxx = True +enable_rtti = True + +skip_all_tests = True + +moduleclass = 'compiler' From ba9c5e5029ce42663cd94c4df3d16b1b837aaabd Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 6 Apr 2022 12:21:38 +0100 Subject: [PATCH 3412/9987] Both shared and static libs build added lesson learned from PR 15226 --- .../c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb index 4e727a305b1..44cb53ad27e 100644 --- a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb @@ -15,6 +15,7 @@ generic class for parsing, stringifying, and comparing IDs. The guid generation technique is determined by your platform:""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} source_urls = ['https://github.com/graeme-hill/crossguid/archive/%s' % local_commit] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] @@ -31,12 +32,13 @@ builddependencies = [ ] # build demo -configopts = ["-DCROSSGUID_TESTS=ON"] +# build static and shared libraries +configopts = ["-DCROSSGUID_TESTS=ON", "-DBUILD_SHARED_LIBS=TRUE"] # we want to have the crossguid-test install_cmd = "make install && " -install_cmd += "mkdir %(installdir)s/bin/ && " -install_cmd += "cp crossguid-test %(installdir)s/bin/ " +install_cmd += "mkdir -p %(installdir)s/bin/ && " +install_cmd += "cp -f crossguid-test %(installdir)s/bin/ " sanity_check_paths = { 'files': ['lib/libcrossguid.a', 'bin/crossguid-test'], From 3bf6b21fd6c774163c69cb56fc0819d3516862fb Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 7 Apr 2022 13:43:44 +0100 Subject: [PATCH 3413/9987] Add Python2 (-bare) build dependency to old Rust versions --- easybuild/easyconfigs/r/Rust/Rust-1.35.0-GCCcore-8.2.0.eb | 1 + easybuild/easyconfigs/r/Rust/Rust-1.37.0-GCCcore-8.3.0.eb | 1 + easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb | 1 + easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb | 1 + easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb | 1 + easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb | 1 + 6 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.35.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.35.0-GCCcore-8.2.0.eb index 201655d76d0..112c2d67ac9 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.35.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.35.0-GCCcore-8.2.0.eb @@ -16,6 +16,7 @@ checksums = ['5a4d637a716bac18d085f44dd87ef48b32195f71b967d872d80280b38cff712d'] builddependencies = [ ('binutils', '2.31.1'), ('CMake', '3.13.3'), + ('Python', '2.7.15', '-bare'), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.37.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.37.0-GCCcore-8.3.0.eb index 1b974a5ae88..b576b38b56e 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.37.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.37.0-GCCcore-8.3.0.eb @@ -16,6 +16,7 @@ checksums = ['120e7020d065499cc6b28759ff04153bfdc2ac9b5adeb252331a4eb87cbe38c3'] builddependencies = [ ('binutils', '2.32'), ('CMake', '3.15.3'), + ('Python', '2.7.16', '-bare'), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb index 6f7bdda2b6b..a690c1ccad7 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb @@ -16,6 +16,7 @@ checksums = ['d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475'] builddependencies = [ ('binutils', '2.30'), ('CMake', '3.12.1'), + ('Python', '2.7.15', '-bare'), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb index 1ebc625e84e..c386da91ae0 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.2.0.eb @@ -16,6 +16,7 @@ checksums = ['d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475'] builddependencies = [ ('binutils', '2.31.1'), ('CMake', '3.13.3'), + ('Python', '2.7.15', '-bare'), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb index 8f1530b3e20..641cc7103f5 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb @@ -16,6 +16,7 @@ checksums = ['d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475'] builddependencies = [ ('binutils', '2.32'), ('CMake', '3.15.3'), + ('Python', '2.7.16', '-bare'), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb index a24b66528c6..821af75b032 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-9.3.0.eb @@ -16,6 +16,7 @@ checksums = ['d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475'] builddependencies = [ ('binutils', '2.34'), ('CMake', '3.16.4'), + ('Python', '2.7.18', '-bare'), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" From afda16ba2b26721454c31b42bd686346ab8094bd Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 7 Apr 2022 14:04:29 +0100 Subject: [PATCH 3414/9987] adding easyconfigs: Python-2.7.15-GCCcore-8.2.0-bare.eb, Python-2.7.16-GCCcore-8.3.0-bare.eb, Python-2.7.18-GCCcore-9.3.0-bare.eb --- .../Python-2.7.15-GCCcore-8.2.0-bare.eb | 34 +++++++++++++++++++ .../Python-2.7.16-GCCcore-8.3.0-bare.eb | 34 +++++++++++++++++++ .../Python-2.7.18-GCCcore-9.3.0-bare.eb | 34 +++++++++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0-bare.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-9.3.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0-bare.eb new file mode 100644 index 00000000000..8734a5abdcd --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0-bare.eb @@ -0,0 +1,34 @@ +name = 'Python' +version = '2.7.15' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['18617d1f15a380a919d517630a9cd85ce17ea602f9bbdc58ddc672df4b0239db'] + +# python needs bzip2 to build the bz2 package + +dependencies = [ + ('binutils', '2.31.1'), # required for pip install that involves compilation + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.1'), + ('SQLite', '3.27.2'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +install_pip = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0-bare.eb new file mode 100644 index 00000000000..3dbf567056b --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0-bare.eb @@ -0,0 +1,34 @@ +name = 'Python' +version = '2.7.16' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['01da813a3600876f03f46db11cc5c408175e99f03af2ba942ef324389a83bad5'] + +# python needs bzip2 to build the bz2 package + +dependencies = [ + ('binutils', '2.32'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.1'), + ('SQLite', '3.29.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +install_pip = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-9.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-9.3.0-bare.eb new file mode 100644 index 00000000000..41c95013bf7 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-9.3.0-bare.eb @@ -0,0 +1,34 @@ +name = 'Python' +version = '2.7.18' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +# python needs bzip2 to build the bz2 package + +dependencies = [ + ('binutils', '2.34'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('SQLite', '3.31.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +install_pip = True + +moduleclass = 'lang' From 93112d62cc9efc56214486a4ebb12c0e2e626104 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 7 Apr 2022 19:29:19 +0200 Subject: [PATCH 3415/9987] Added patch for increasing test tolerances to make them pass with GPUs that support TensorFloat32 datatypes --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 + ...1.11.0_increase_test_tolerances_TF32.patch | 106 ++++++++++++++++++ 2 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_test_tolerances_TF32.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index aad36ceabba..5803d355a79 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -28,6 +28,7 @@ patches = [ 'PyTorch-1.11.0_skip_failing_ops_tests.patch', 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', 'PyTorch-1.11.0_fix_sharded_imports.patch', + 'PyTorch-1.11.0_increase_test_tolerances_TF32.patch' ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -44,6 +45,7 @@ checksums = [ '8f4a27303f8cba2ea90702e494365bf4a3e1c5ade9ed1311b63ad4289793e1af', # PyTorch-1.11.0_skip_failing_ops_tests.patch '10d1f0db8254f7564500fe97f134c3b4fa89156839b5f771a9396d80a0a1ada4', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch + 'a14b511370cf20cadff311ce1c29bf5de3693b46c8927624971122939155c2e9', # PyTorch-1.11.0_increase_test_tolerances_TF32.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_test_tolerances_TF32.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_test_tolerances_TF32.patch new file mode 100644 index 00000000000..7f72e33a7ac --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_test_tolerances_TF32.patch @@ -0,0 +1,106 @@ +# Author: Caspar van Leeuwen, SURF +# Fixes failing tests due to use of TensorFloat32 +# Setting NVIDIA_TF32_OVERRIDE=0 makes these tests pass, proving that TensorFloat32 is the issue +# We increase tolerances for the asserts to make these tests pass +diff -Nru pytorch_orig/test/distributed/_shard/sharded_tensor/ops/test_linear.py pytorch/test/distributed/_shard/sharded_tensor/ops/test_linear.py +--- pytorch_orig/test/distributed/_shard/sharded_tensor/ops/test_linear.py 2022-04-07 18:31:13.069599000 +0200 ++++ pytorch/test/distributed/_shard/sharded_tensor/ops/test_linear.py 2022-04-07 18:32:32.877406000 +0200 +@@ -77,7 +77,7 @@ + local_output = local_linear(inp) + + # Verify +- self.assertEqual(local_output, sharded_output) ++ self.assertEqual(local_output, sharded_output, rtol=0.02, atol=1e-03) + + # Validate for torch.nn.functional.linear version. + local_output = torch.nn.functional.linear( +@@ -91,7 +91,7 @@ + # for reshard. We need to squeeze the # of dimensions manually. + if inp.dim() == 1: + sharded_output = sharded_output.squeeze(reshard_spec.dim) +- self.assertEqual(local_output, sharded_output) ++ self.assertEqual(local_output, sharded_output, rtol=0.02, atol=1e-03) + + # Compute loss and run backward pass. + local_output.sum().backward() +@@ -114,7 +114,7 @@ + + # Test backward gradient calculation. + self.assertEqual(sharded_linear.bias.grad, local_bias_grad) +- self.assertEqual(sharded_weight.grad, local_grad_narrowed) ++ self.assertEqual(sharded_weight.grad, local_grad_narrowed, rtol=0.01, atol=1e-03) + + # Test optimizer. + previous = local_linear.weight.clone().detach() +@@ -135,7 +135,7 @@ + ) + self.assertEqual(sharded_weight.size(), local_weight_narrowed.size()) + self.assertNotEqual(previous_sharded_weight, sharded_weight) +- self.assertEqual(sharded_weight, local_weight_narrowed) ++ self.assertEqual(sharded_weight, local_weight_narrowed, rtol=0.01, atol=1e-04) + self.assertNotEqual(previous_sharded_bias, sharded_linear.bias) + self.assertEqual(sharded_linear.bias, local_linear.bias) + +diff -Nru pytorch_orig/test/distributed/_shard/sharded_tensor/test_megatron_prototype.py pytorch/test/distributed/_shard/sharded_tensor/test_megatron_prototype.py +--- pytorch_orig/test/distributed/_shard/sharded_tensor/test_megatron_prototype.py 2022-04-07 18:31:13.091710000 +0200 ++++ pytorch/test/distributed/_shard/sharded_tensor/test_megatron_prototype.py 2022-04-07 18:41:03.744644000 +0200 +@@ -113,7 +113,7 @@ + local_output = local_megatron_lm(inp) + + # Verify +- self.assertEqual(local_output, sharded_output) ++ self.assertEqual(local_output, sharded_output, rtol=0.01, atol=1e-03) + + # Compute loss and run backward pass. + local_output.sum().backward() +@@ -161,9 +161,9 @@ + ) + + # Test backward gradient calculation. +- self.assertEqual(sharded_weight_fc1.grad, local_grad_narrowed_fc1) +- self.assertEqual(sharded_weight_fc2.grad, local_grad_narrowed_fc2) +- self.assertEqual(bias_grad_fc1, local_bias_grad_fc1) ++ self.assertEqual(sharded_weight_fc1.grad, local_grad_narrowed_fc1, rtol=0.01, atol=2e-03) ++ self.assertEqual(sharded_weight_fc2.grad, local_grad_narrowed_fc2, rtol=0.01, atol=1e-03) ++ self.assertEqual(bias_grad_fc1, local_bias_grad_fc1, rtol=0.01, atol=2e-02) + self.assertEqual(bias_grad_fc2, local_bias_grad_fc2) + + # Test optimizer. +@@ -171,7 +171,7 @@ + local_bias_fc1, local_bias_fc2 = _get_bias(local_megatron_lm) + self.assertEqual(bias_fc1, local_bias_fc1) + self.assertEqual(bias_fc2, local_bias_fc2) +- self.assertEqual(bias_fc1.grad, local_bias_fc1.grad) ++ self.assertEqual(bias_fc1.grad, local_bias_fc1.grad, rtol=0.01, atol=2e-02) + self.assertEqual(bias_fc2.grad, local_bias_fc2.grad) + previous_sharded_weight_fc1 = sharded_weight_fc1.clone() + previous_sharded_weight_fc2 = sharded_weight_fc2.clone() +@@ -197,13 +197,13 @@ + self.assertEqual(sharded_weight_fc2.size(), local_weight_fc2_narrowed.size()) + self.assertNotEqual(previous_sharded_weight_fc1, sharded_weight_fc1) + self.assertNotEqual(previous_sharded_weight_fc2, sharded_weight_fc2) +- self.assertEqual(sharded_weight_fc1, local_weight_fc1_narrowed) +- self.assertEqual(sharded_weight_fc2, local_weight_fc2_narrowed) ++ self.assertEqual(sharded_weight_fc1, local_weight_fc1_narrowed, rtol=0.01, atol=1e-03) ++ self.assertEqual(sharded_weight_fc2, local_weight_fc2_narrowed, rtol=0.01, atol=1e-03) + + # Test bias value after optimizer. + local_bias_fc1, local_bias_fc2 = _get_bias(local_megatron_lm) + self.assertNotEqual(previous_bias_fc1, bias_fc1) +- self.assertEqual(bias_fc1, local_bias_fc1) ++ self.assertEqual(bias_fc1, local_bias_fc1, rtol=0.01, atol=1e-03) + self.assertNotEqual(previous_bias_fc2, bias_fc2) + self.assertEqual(bias_fc2, local_bias_fc2) + +diff -Nru pytorch_orig/test/test_stateless.py pytorch/test/test_stateless.py +--- pytorch_orig/test/test_stateless.py 2022-04-07 18:31:13.029968000 +0200 ++++ pytorch/test/test_stateless.py 2022-04-07 18:43:46.723968000 +0200 +@@ -42,7 +42,7 @@ + # existing params in module. So here we expect the result to be the + # same as the input if the weight swapping went well. + res = _stateless.functional_call(module, parameters, x) +- self.assertEqual(x, res) ++ self.assertEqual(x, res, rtol=1e-04, atol=1e-04) + # check that the weight remain unmodified + cur_weight = to_check.l1.weight + cur_buffer = to_check.buffer From eb9c457e958362932beddc3364ab38f191685403 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 7 Apr 2022 20:00:42 +0200 Subject: [PATCH 3416/9987] Fixed too long line --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 5803d355a79..ca4a0f952fe 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -45,7 +45,8 @@ checksums = [ '8f4a27303f8cba2ea90702e494365bf4a3e1c5ade9ed1311b63ad4289793e1af', # PyTorch-1.11.0_skip_failing_ops_tests.patch '10d1f0db8254f7564500fe97f134c3b4fa89156839b5f771a9396d80a0a1ada4', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch - 'a14b511370cf20cadff311ce1c29bf5de3693b46c8927624971122939155c2e9', # PyTorch-1.11.0_increase_test_tolerances_TF32.patch + # PyTorch-1.11.0_increase_test_tolerances_TF32.patch + 'a14b511370cf20cadff311ce1c29bf5de3693b46c8927624971122939155c2e9', ] osdependencies = [OS_PKG_IBVERBS_DEV] From 3ac497fa66923dac90c4730dc7680df1109806a8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 8 Apr 2022 12:06:41 +0100 Subject: [PATCH 3417/9987] adding easyconfigs: SAMtools-1.15.1-GCC-11.2.0.eb --- .../s/SAMtools/SAMtools-1.15.1-GCC-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.15.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.15.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.15.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..80e29d5b26c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.15.1-GCC-11.2.0.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +# +# Updated to 1.14 and gcc-11.2.0 +# J. Sassmannshausen / GSTT + +name = 'SAMtools' +version = '1.15.1' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['708c525ac76b0532b25f14aadea34a4d11df667bc19bf0a74dae617d80526c6e'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.78.0'), +] + +moduleclass = 'bio' From 9a34221a104952d01c04767a6379f208dca1b029 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 8 Apr 2022 14:49:20 +0200 Subject: [PATCH 3418/9987] adding easyconfigs: StringTie-2.2.1-GCC-11.2.0.eb and patches: StringTie-2.2.1_fix-linking.patch --- .../s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb | 45 +++++++++++++++++++ .../StringTie-2.2.1_fix-linking.patch | 24 ++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-2.2.1_fix-linking.patch diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..1e34435bf96 --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '2.2.1' + +homepage = 'https://ccb.jhu.edu/software/stringtie/' +description = 'StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts' + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ["%(name)s-%(version)s_fix-linking.patch"] +checksums = [ + 'ce4eec532bbbe39af462be844afa6395ab38fa3418ef5fc2431e2d6194129527', # stringtie-2.2.1.tar.gz + 'b82dae4790ea9472fe9fe0578b6659afd8006640c5ea488661a4e222103bab6a', # StringTie-2.2.1_fix-linking.patch +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libdeflate', '1.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), +] + +# the test script downloads some test data from the internet +buildopts = 'release && ./run_tests.sh' + +files_to_copy = [ + (['%(namelower)s', 'prepDE.py'], 'bin'), + 'README.md', + 'LICENSE' +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1_fix-linking.patch b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1_fix-linking.patch new file mode 100644 index 00000000000..8ddd214ac0a --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1_fix-linking.patch @@ -0,0 +1,24 @@ +StringTie searches for static libraries in the source directory but they are provided as a dependency +author: Paul Jähne +--- Makefile.orig 2022-01-26 21:29:54.000000000 +0100 ++++ Makefile 2022-04-08 14:33:11.520174065 +0200 +@@ -1,10 +1,5 @@ + #-- for now these MUST point to the included "samtools-0.x.x" and "gclib" sub-directories + HTSLIB := ./htslib +-#-- +-LIBDEFLATE := ${HTSLIB}/xlibs/lib/libdeflate.a +-LIBBZ2 := ${HTSLIB}/xlibs/lib/libbz2.a +-LIBLZMA := ${HTSLIB}/xlibs/lib/liblzma.a +- + GDIR := ./gclib + #-- + +@@ -31,7 +26,7 @@ + + # LDFLAGS += -L${BAM} + +-LIBS := ${HTSLIB}/libhts.a ${LIBBZ2} ${LIBLZMA} ${LIBDEFLATE} -lz -lm ++LIBS := ${HTSLIB}/libhts.a -lbz2 -llzma -ldeflate -lz -lm + + ifneq (,$(filter %nothreads %prof %profile, $(MAKECMDGOALS))) + NOTHREADS=1 From 66f42cf0393079f74283a571b8ddfd4ee3eca5f2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 8 Apr 2022 17:02:49 +0100 Subject: [PATCH 3419/9987] adding easyconfigs: ARGoS-3.0.0-beta59-GCC-11.2.0.eb, FreeImage-3.18.0-GCCcore-11.2.0.eb --- .../a/ARGoS/ARGoS-3.0.0-beta59-GCC-11.2.0.eb | 40 +++++++++++++++++++ .../FreeImage-3.18.0-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta59-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta59-GCC-11.2.0.eb b/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta59-GCC-11.2.0.eb new file mode 100644 index 00000000000..86bf6af90cd --- /dev/null +++ b/easybuild/easyconfigs/a/ARGoS/ARGoS-3.0.0-beta59-GCC-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'ARGoS' +version = '3.0.0-beta59' + +homepage = 'http://www.argos-sim.info' +description = """A parallel, multi-engine simulator for heterogeneous swarm robotics""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/ilpincy/argos3/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['99007ef5eb10bbe4b8f88dcf0600c62c4cc0a5844e85ec0a3c3499b4637ee8b5'] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [ + ('Lua', '5.4.3'), + ('FreeImage', '3.18.0'), + ('Qt5', '5.15.2'), + ('freeglut', '3.2.1'), + ('motif', '2.3.8'), +] + +start_dir = 'src' + +# documentation requires Doxygen, Graphviz, asciidoc +configopts = '-DARGOS_DOCUMENTATION=OFF -DARGOS_INSTALL_LDSOCONF=OFF -DARGOS_BUILD_NATIVE=ON' + +sanity_check_paths = { + 'files': ['include/argos3/core/config.h', 'lib/argos3/libargos3core_simulator.%s' % SHLIB_EXT], + 'dirs': ['share/argos3'] +} + +sanity_check_commands = ["argos3 --help", "argos3 --version"] + +# ARGoS libaries reside in the argos3 subdirectory +modextrapaths = {'LD_LIBRARY_PATH': 'lib/argos3'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..228efbf8f11 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'FreeImage' +version = '3.18.0' + +homepage = 'http://freeimage.sourceforge.net' +description = """FreeImage is an Open Source library project for developers who would like to support popular graphics +image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to +use, fast, multithreading safe.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'cstd': 'c++14'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s3180.zip'] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip + '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # %(name)s-%(version)s-fix-makefile.patch +] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('zlib', '1.2.11')] + +skipsteps = ['configure'] + +buildopts = ['', '-f Makefile.fip'] + +installopts = [ + "INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib", + "-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib", +] + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'include/FreeImagePlus.h', 'lib/libfreeimage.a', 'lib/libfreeimage.so', 'lib/libfreeimageplus.a', 'lib/libfreeimageplus.so'], + 'dirs': [], +} + +moduleclass = 'vis' From dc8cc4f2e6d52932942f61401a3c60d7eef3eb54 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 8 Apr 2022 17:33:01 +0100 Subject: [PATCH 3420/9987] sanity checks --- .../f/FreeImage/FreeImage-3.18.0-GCCcore-11.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.2.0.eb index 228efbf8f11..63540c629e0 100644 --- a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.2.0.eb @@ -32,8 +32,11 @@ installopts = [ "-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib", ] +_incs = ['include/FreeImage%s.h' % x for x in ['', 'Plus']] +_libs = ['lib/libfreeimage%s.%s' % (x, y) for x in ['', 'plus'] for y in ['a', SHLIB_EXT]] + sanity_check_paths = { - 'files': ['include/%(name)s.h', 'include/FreeImagePlus.h', 'lib/libfreeimage.a', 'lib/libfreeimage.so', 'lib/libfreeimageplus.a', 'lib/libfreeimageplus.so'], + 'files': _incs + _libs, 'dirs': [], } From a69bed9389fba99bbc8bdbfba3b8f7b4c2a8853d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Sat, 9 Apr 2022 16:29:38 +0200 Subject: [PATCH 3421/9987] Use external HTSlib Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb index 1e34435bf96..49a7c125c1e 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb @@ -26,6 +26,7 @@ dependencies = [ ('libdeflate', '1.8'), ('XZ', '5.2.5'), ('zlib', '1.2.11'), + ('HTSlib', '1.14'), ] # the test script downloads some test data from the internet From 5e52146d00f27d209315d04200320b8ea253c04d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Sat, 9 Apr 2022 16:30:17 +0200 Subject: [PATCH 3422/9987] Don't use patch Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb index 49a7c125c1e..f63ddbf7da4 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb @@ -15,11 +15,7 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s'] sources = [SOURCELOWER_TAR_GZ] -patches = ["%(name)s-%(version)s_fix-linking.patch"] -checksums = [ - 'ce4eec532bbbe39af462be844afa6395ab38fa3418ef5fc2431e2d6194129527', # stringtie-2.2.1.tar.gz - 'b82dae4790ea9472fe9fe0578b6659afd8006640c5ea488661a4e222103bab6a', # StringTie-2.2.1_fix-linking.patch -] +checksums = ['ce4eec532bbbe39af462be844afa6395ab38fa3418ef5fc2431e2d6194129527'] dependencies = [ ('bzip2', '1.0.8'), From d7bf494fdf2314ddf4561978059f5a15dd5aa1c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Sat, 9 Apr 2022 16:31:05 +0200 Subject: [PATCH 3423/9987] Override environment variables to use external dependencies Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb index f63ddbf7da4..02568a7ede4 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb @@ -25,8 +25,11 @@ dependencies = [ ('HTSlib', '1.14'), ] +buildopts = 'HTSLIB="$EBROOTHTSLIB/lib" LIBS="-lhts -lbz2 -llzma -ldeflate -lz $LIBS"' + # the test script downloads some test data from the internet -buildopts = 'release && ./run_tests.sh' +runtest = 'test' +testopts = buildopts files_to_copy = [ (['%(namelower)s', 'prepDE.py'], 'bin'), From 4fc3353fabf96ef09d348dc7d35e32bcb71337dc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Sat, 9 Apr 2022 16:31:39 +0200 Subject: [PATCH 3424/9987] Delete StringTie-2.2.1_fix-linking.patch --- .../StringTie-2.2.1_fix-linking.patch | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-2.2.1_fix-linking.patch diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1_fix-linking.patch b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1_fix-linking.patch deleted file mode 100644 index 8ddd214ac0a..00000000000 --- a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1_fix-linking.patch +++ /dev/null @@ -1,24 +0,0 @@ -StringTie searches for static libraries in the source directory but they are provided as a dependency -author: Paul Jähne ---- Makefile.orig 2022-01-26 21:29:54.000000000 +0100 -+++ Makefile 2022-04-08 14:33:11.520174065 +0200 -@@ -1,10 +1,5 @@ - #-- for now these MUST point to the included "samtools-0.x.x" and "gclib" sub-directories - HTSLIB := ./htslib --#-- --LIBDEFLATE := ${HTSLIB}/xlibs/lib/libdeflate.a --LIBBZ2 := ${HTSLIB}/xlibs/lib/libbz2.a --LIBLZMA := ${HTSLIB}/xlibs/lib/liblzma.a -- - GDIR := ./gclib - #-- - -@@ -31,7 +26,7 @@ - - # LDFLAGS += -L${BAM} - --LIBS := ${HTSLIB}/libhts.a ${LIBBZ2} ${LIBLZMA} ${LIBDEFLATE} -lz -lm -+LIBS := ${HTSLIB}/libhts.a -lbz2 -llzma -ldeflate -lz -lm - - ifneq (,$(filter %nothreads %prof %profile, $(MAKECMDGOALS))) - NOTHREADS=1 From cec04bb1d4b7d0b701b7a872cab8455d56c5d26a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 11 Apr 2022 10:17:52 +0200 Subject: [PATCH 3425/9987] Readd release to buildopts --- .../easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb index 02568a7ede4..4af4f7d3da7 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb @@ -25,11 +25,12 @@ dependencies = [ ('HTSlib', '1.14'), ] -buildopts = 'HTSLIB="$EBROOTHTSLIB/lib" LIBS="-lhts -lbz2 -llzma -ldeflate -lz $LIBS"' +local_libs = 'HTSLIB="$EBROOTHTSLIB/lib" LIBS="-lhts -lbz2 -llzma -ldeflate -lz $LIBS"' +buildopts = 'release ' + local_libs # the test script downloads some test data from the internet runtest = 'test' -testopts = buildopts +testopts = local_libs files_to_copy = [ (['%(namelower)s', 'prepDE.py'], 'bin'), From 7a95f84d764217e4f9c85e06e2d43097e3093186 Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Tue, 12 Apr 2022 01:28:40 +0200 Subject: [PATCH 3426/9987] adding easyconfigs: Stata-17-GCCcore-10.2.0.eb --- .../s/Stata/Stata-17-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..effc6281940 --- /dev/null +++ b/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +name = 'Stata' +version = '17' + +homepage = 'https://www.stata.com/' +description = """Stata is a complete, integrated statistical software package that provides +everything you need for data analysis, data management, and graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# requires license to access source files +sources = ['Stata%(version)sLinux64.tar.gz'] +checksums = ['e7bea3d827db2957e5ea67bf3d6747a56f656bb08f40b148ed726ab700cd8ce3'] + +download_instructions = """ +See also https://www.stata.com/support/faqs/unix/install-download-on-linux/ + +You can download the gzipped tar file 'Stata%(version)sLinux64.tar.gz' from: + https://download.stata.com/download/ +and place it under your favorite Easybuild sourcepath, typically under + /s/Stata/ + +After the build, you **must** generate the licence file 'stata.lic' in your +software install path using the `stinit` script: + module load math/Stata + cd $EBROOTSTATA + ./stinit +""" + +dependencies = [ + ('libpng', '1.6.37') +] + +sanity_check_paths = { + 'files': [ + 'stata', # Non-graphical standard Stata/IC + 'stata-se', # Non-graphical Stata/SE designed for large databases + 'xstata', # Graphical standard Stata/IC + 'xstata-se' # Graphical Stata/SE designed for large databases + ], + 'dirs': [ + 'utilities', + 'ado' + ] +} + +moduleclass = 'math' From 84233ef74b722b7c92b365c9d3f8f035edcd6de1 Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Tue, 12 Apr 2022 01:49:08 +0200 Subject: [PATCH 3427/9987] [PR #15264] Fix AssertionError: binutils or GCC is a build dep --- easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb index effc6281940..c15b66f86f6 100644 --- a/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb @@ -26,6 +26,11 @@ software install path using the `stinit` script: ./stinit """ + +builddependencies = [ + ('binutils', '2.35'), +] + dependencies = [ ('libpng', '1.6.37') ] From 9ec4d7e1c3ba2d22ba038357db161482ad21d86e Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Tue, 12 Apr 2022 01:51:42 +0200 Subject: [PATCH 3428/9987] Update easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb index 121f2982213..35d01b09eee 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb @@ -50,6 +50,7 @@ dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too ('binutils', '2.34'), ('GMP', '6.2.0'), + ('ncurses', '6.2'), ] builddependencies = [ From fcdab456d584206cfe5009e9e167dc4b636c8e92 Mon Sep 17 00:00:00 2001 From: Sebastien Varrette Date: Tue, 12 Apr 2022 01:51:58 +0200 Subject: [PATCH 3429/9987] Update easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb index 35d01b09eee..434dfe35415 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb @@ -56,6 +56,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.16.4'), ('Python', '2.7.18'), + ('Perl', '5.30.2'), ('libxml2', '2.9.10'), ] From 170f60bf266ed2c2ed40f9a9545992ec5ba8498c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 12 Apr 2022 08:06:58 +0200 Subject: [PATCH 3430/9987] adding easyconfigs: Cufflinks-20190706-GCC-11.2.0.eb, Boost-1.75.0-GCC-11.2.0.eb --- .../b/Boost/Boost-1.75.0-GCC-11.2.0.eb | 27 +++++++++++++ .../Cufflinks-20190706-GCC-11.2.0.eb | 38 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..053aaaf0ac9 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-11.2.0.eb @@ -0,0 +1,27 @@ +name = 'Boost' +version = '1.75.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['aeb26f80e80945e82ee93e5939baebdca47b9dee80a07d3144be1e1a6a66dd6a'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('ICU', '69.1'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb new file mode 100644 index 00000000000..403c88a5dca --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +name = 'Cufflinks' +version = '20190706' +local_commit = 'dc3b0cb' + +homepage = 'http://cole-trapnell-lab.github.io/%(namelower)s/' +description = "Transcript assembly, differential expression, and differential regulation for RNA-Seq" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'cole-trapnell-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['444c632083a473fe4fd99ff189cef5bbd95daee0912e8eefe79534bf225fbcb6'] + +builddependencies = [ + ('Eigen', '3.3.9'), + ('Autotools', '20210726'), + ('SAMtools', '1.14'), +] + +dependencies = [ + ('Boost', '1.75.0'), + ('zlib', '1.2.11'), + ('HTSlib', '1.14'), +] + +preconfigopts = 'autoreconf -i && export LIBS="${LIBS} -lhts" && export CFLAGS="$CFLAGS -fcommon" && ' +configopts = '--with-boost=${EBROOTBOOST} --with-bam=${EBROOTSAMTOOLS}' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +moduleclass = 'bio' From d7339e34904baafb108857b73b38ca3e080368b9 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Apr 2022 10:23:24 +0100 Subject: [PATCH 3431/9987] adding easyconfigs: XGrafix-2.41-GCCcore-9.3.0.eb --- .../x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..0ed0e6ce16f --- /dev/null +++ b/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb @@ -0,0 +1,43 @@ +# Contribution from Imperial College London, UK +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'XGrafix' +version = '2.41' + +homepage = 'https://ptsg.egr.msu.edu/' +description = """A graphics library and controller for physics simulation programs. +3-d surface plots, scatter plots, 2-d line plots.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://ptsg.egr.msu.edu/pub/codes'] +sources = ['%(namelower)s.tar.gz'] +checksums = ['20daa8f47cb83888e933bb2f451bc8d2b376946b2e7b1ce2252b6e3da0c3b583'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('X11', '20200222'), + ('Tcl', '8.6.10'), + ('Tk', '8.6.10'), + ('ImageMagick', '7.0.10-1'), + ('Bison', '3.5.3'), +] + +# We need to specify where things are, unfortunately. +configopts = '--enable-fulloptimize --with-xpm=$EBROOTX11/lib ' +configopts += '--with-tclconfig=$EBROOTTCL/lib --with-tkconfig=$EBROOTTK/lib' + +sanity_check_paths = { + 'files': ['bin/ps6to1', 'bin/xgmovie', 'bin/xgmreduce', 'bin/xtest'] + + ['lib/libXGC.a', 'lib/libXGCmini.a', 'lib/libXGF.a'], + 'dirs': ['include'], +} + +sanity_check_commands = ["xtest -h"] + +moduleclass = 'vis' From 3f99e88d0c273c6d63af40f1fe2c36bee4f3a968 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Apr 2022 14:44:52 +0100 Subject: [PATCH 3432/9987] adding easyconfigs: XOOPIC-20210302-foss-2020a.eb --- .../x/XOOPIC/XOOPIC-20210302-foss-2020a.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb diff --git a/easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb b/easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb new file mode 100644 index 00000000000..fb76d17ceb8 --- /dev/null +++ b/easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb @@ -0,0 +1,55 @@ +# Contribution from Imperial College London, UK +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'XOOPIC' +version = '20210302' +local_commit = '3fa6670' + +homepage = 'https://github.com/rinku-mishra/xoopic' +description = """XOOPIC is a two-dimensional 3-velocity particle-in-cell simulator. +It can handle electrostatic and electromagnetic models, has a large variety of +boundary conditions, supports multiple gasses and gas chemistry, and is easily +reconfigurable via an input file.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/rinku-mishra/xoopic/archive/%s' % local_commit] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['e81a2b7a527b905fd58afd080f45690963079b0a0493a55929d2a0ef1246d4e3'] + +builddependencies = [ + ('binutils', '2.34'), + ('M4', '1.4.18'), + ('Bison', '3.5.3'), +] + +dependencies = [ + ('X11', '20200222'), + ('Tcl', '8.6.10'), + ('Tk', '8.6.10'), + ('ImageMagick', '7.0.10-1'), + ('XGrafix', '2.41'), + ('HDF5', '1.12.0'), + ('FFTW', '3.3.8'), +] + +# We need to specify where things are, unfortunately. +configopts = '--enable-MPI --enable-fulloptimize --with-xpm=$EBROOTX11/lib ' +configopts += '--with-tclconfig=$EBROOTTCL/lib --with-tkconfig=$EBROOTTK/lib ' +configopts += '--with-XGRAFIX-lib=$EBROOTXGRAFIX/lib --with-XGRAFIX-include=$EBROOTXGRAFIX/include ' +configopts += '--with-X11-include=$EBROOTX11/include --with-X11_LIBDIR=$EBROOTX11/lib ' +configopts += '--with-hdf5-incdir=$EBROOTHDF5/include ' +# This does not seem to be used, so for now we leave it out: +# configopts += '--with-dfftw-incdir=$EBROOTFFTW/include --with-dfftw-libdir=$EBROOTFFTW/lib ' + +sanity_check_paths = { + 'files': ['bin/xoopic'] + + ['lib/libadvisor.a', 'lib/libotools.a', 'lib/libphysics.a', 'lib/libxg.a'], + 'dirs': ['include'], +} + +sanity_check_commands = ["xoopic -h"] + +moduleclass = 'phys' From 2adbd722195a59e24e12fe9befec1c7e14050ae3 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Apr 2022 15:01:27 +0100 Subject: [PATCH 3433/9987] Moved Bison to builddependency, M4 added as well. --- easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb index 0ed0e6ce16f..73ebce3e175 100644 --- a/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb @@ -18,6 +18,8 @@ checksums = ['20daa8f47cb83888e933bb2f451bc8d2b376946b2e7b1ce2252b6e3da0c3b583'] builddependencies = [ ('binutils', '2.34'), + ('Bison', '3.5.3'), + ('M4', '1.4.18'), ] dependencies = [ @@ -25,7 +27,6 @@ dependencies = [ ('Tcl', '8.6.10'), ('Tk', '8.6.10'), ('ImageMagick', '7.0.10-1'), - ('Bison', '3.5.3'), ] # We need to specify where things are, unfortunately. From 5881b837c0631aabc97d456ba168c900278110bb Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Apr 2022 16:04:19 +0100 Subject: [PATCH 3434/9987] Binutils removed as foss toolchain used --- easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb b/easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb index fb76d17ceb8..1ce39e094d4 100644 --- a/easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb +++ b/easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb @@ -20,7 +20,6 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ checksums = ['e81a2b7a527b905fd58afd080f45690963079b0a0493a55929d2a0ef1246d4e3'] builddependencies = [ - ('binutils', '2.34'), ('M4', '1.4.18'), ('Bison', '3.5.3'), ] From cf76586098131ba3ab52d49abe33e064288994a3 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Apr 2022 16:24:52 +0100 Subject: [PATCH 3435/9987] Fortran and PGN added --- easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb index 73ebce3e175..b5e4e004589 100644 --- a/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb @@ -27,11 +27,13 @@ dependencies = [ ('Tcl', '8.6.10'), ('Tk', '8.6.10'), ('ImageMagick', '7.0.10-1'), + ('libpng', '1.6.37'), ] # We need to specify where things are, unfortunately. configopts = '--enable-fulloptimize --with-xpm=$EBROOTX11/lib ' -configopts += '--with-tclconfig=$EBROOTTCL/lib --with-tkconfig=$EBROOTTK/lib' +configopts += '--with-tclconfig=$EBROOTTCL/lib --with-tkconfig=$EBROOTTK/lib ' +configopts += '--enable-fortran LIBPNG_PATH=$EBROOTLIBPNG/lib ' sanity_check_paths = { 'files': ['bin/ps6to1', 'bin/xgmovie', 'bin/xgmreduce', 'bin/xtest'] + From bd3e8b08738fb831317afee7d427bbb3fdc91431 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Apr 2022 17:27:58 +0100 Subject: [PATCH 3436/9987] X11 added --- easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb index b5e4e004589..0f45289211b 100644 --- a/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XGrafix/XGrafix-2.41-GCCcore-9.3.0.eb @@ -33,6 +33,7 @@ dependencies = [ # We need to specify where things are, unfortunately. configopts = '--enable-fulloptimize --with-xpm=$EBROOTX11/lib ' configopts += '--with-tclconfig=$EBROOTTCL/lib --with-tkconfig=$EBROOTTK/lib ' +configopts += '--with-X11-include=$EBROOTX11/include --with-X11_LIBDIR=$EBROOTX11/lib ' configopts += '--enable-fortran LIBPNG_PATH=$EBROOTLIBPNG/lib ' sanity_check_paths = { From b4e0d4e81e57e129779c36700b29d4645b9852f5 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 12 Apr 2022 18:34:08 +0200 Subject: [PATCH 3437/9987] Updated patch for TF32 test tolerances to also cover the test_jit_fuser_te test --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 +- ...1.11.0_increase_test_tolerances_TF32.patch | 39 ++++++++++++++++++- 2 files changed, 39 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index ca4a0f952fe..cbd10b689f3 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -46,7 +46,7 @@ checksums = [ '10d1f0db8254f7564500fe97f134c3b4fa89156839b5f771a9396d80a0a1ada4', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch # PyTorch-1.11.0_increase_test_tolerances_TF32.patch - 'a14b511370cf20cadff311ce1c29bf5de3693b46c8927624971122939155c2e9', + '26e179a4f6f57e49209092612ae5f5cd8c03fd2ca84566ba0244eabefc3736ba', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_test_tolerances_TF32.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_test_tolerances_TF32.patch index 7f72e33a7ac..38a6d0eee38 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_test_tolerances_TF32.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_test_tolerances_TF32.patch @@ -103,4 +103,41 @@ diff -Nru pytorch_orig/test/test_stateless.py pytorch/test/test_stateless.py + self.assertEqual(x, res, rtol=1e-04, atol=1e-04) # check that the weight remain unmodified cur_weight = to_check.l1.weight - cur_buffer = to_check.buffer + uur_buffer = to_check.buffer +c PyTorch-1.11.0_increase_test_tolerances_TF32.patch +rig/test/test_jit_fuser_te.py pytorch/test/test_jit_fuser_te.py +--- pytorch_orig/test/test_jit_fuser_te.py 2022-04-07 18:31:13.046680000 +0200 ++++ pytorch/test/test_jit_fuser_te.py 2022-04-12 18:21:00.355114000 +0200 +@@ -956,7 +956,7 @@ + def test_lstm_traced(self): + for device in self.devices: + inputs = get_lstm_inputs(device) +- ge = self.checkTrace(LSTMCellF, inputs) ++ ge = self.checkTrace(LSTMCellF, inputs, atol=1e-4, rtol=1e-5) + graph = ge.graph_for(*inputs) + fusion_groups = self.findFusionGroups(graph) + # TODO: chunk +diff -Nru pytorch_orig/torch/testing/_internal/jit_utils.py pytorch/torch/testing/_internal/jit_utils.py +--- pytorch_orig/torch/testing/_internal/jit_utils.py 2022-04-07 18:28:54.339477000 +0200 ++++ pytorch/torch/testing/_internal/jit_utils.py 2022-04-12 18:19:59.614272000 +0200 +@@ -525,7 +525,7 @@ + def checkTrace(self, func, reference_tensors, input_tensors=None, + drop=None, allow_unused=False, verbose=False, + inputs_require_grads=True, check_tolerance=1e-5, export_import=True, +- _force_outplace=False): ++ _force_outplace=False, rtol=None, atol=None): + + # TODO: check gradients for parameters, not just inputs + def allSum(vs): +@@ -618,7 +618,10 @@ + + self.assertEqual(outputs, outputs_ge) + if inputs_require_grads: +- self.assertEqual(grads, grads_ge) ++ if atol is not None and rtol is not None: ++ self.assertEqual(grads, grads_ge, atol=atol, rtol=rtol) ++ else: ++ self.assertEqual(grads, grads_ge) + for g2, g2_ge in zip(grads2, grads2_ge): + if g2 is None and g2_ge is None: + continue From 309d6caadd5382da0fa30aa43da72a1fe2d8a6c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 13 Apr 2022 09:17:45 +0200 Subject: [PATCH 3438/9987] Script prepDE.py3 needs Python --- .../easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb index 4af4f7d3da7..abf4cac8ebf 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0.eb @@ -23,6 +23,7 @@ dependencies = [ ('XZ', '5.2.5'), ('zlib', '1.2.11'), ('HTSlib', '1.14'), + ('Python', '3.9.6'), ] local_libs = 'HTSLIB="$EBROOTHTSLIB/lib" LIBS="-lhts -lbz2 -llzma -ldeflate -lz $LIBS"' @@ -33,7 +34,7 @@ runtest = 'test' testopts = local_libs files_to_copy = [ - (['%(namelower)s', 'prepDE.py'], 'bin'), + (['%(namelower)s', 'prepDE.py3'], 'bin'), 'README.md', 'LICENSE' ] @@ -43,4 +44,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['%(namelower)s --help', 'prepDE.py3 --help'] + moduleclass = 'bio' From 95408244393bd2c49a1dd0eda467a63a70b12ce0 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 13 Apr 2022 13:05:47 +0200 Subject: [PATCH 3439/9987] already accepted via PR https://github.com/easybuilders/easybuild-easyconfigs/pull/15071 --- .../i/Infernal/Infernal-1.1.4-foss-2020b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2020b.eb diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2020b.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2020b.eb new file mode 100644 index 00000000000..968e466b4e5 --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2020b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# Updated:: Denis Kristak (INUITS) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.4" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' From ba74f4ecd1821df436521f88f30e98e7eb28a8c9 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 13 Apr 2022 14:28:46 +0200 Subject: [PATCH 3440/9987] adding easyconfigs: MIRA-5.0rc2-foss-2020b.eb --- .../m/MIRA/MIRA-5.0rc2-foss-2020b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb new file mode 100644 index 00000000000..eacfc93d087 --- /dev/null +++ b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'MIRA' +version = '5.0rc2' + +homepage = 'https://sourceforge.net/p/mira-assembler/wiki/Home/' +description = """MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), + IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads).""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = ['mira-V5rc2.tar.bz2'] +source_urls = ['https://github.com/bachev/mira/releases/download/V5rc2/'] +checksums = ['4255aa9c4f09ec686b1c717bffe2dd124d3ef9b87f00e74d1bcd51b8599b8e44'] + +preconfigopts = 'export CFLAGS="$CFLAGS -fpermissive" && ' +preconfigopts += 'export CXXFLAGS="$CXXFLAGS -fpermissive" && ' + +configopts = '--with-boost=$EBROOTBOOST --with-expat=$EBROOTEXPAT --with-zlib=$EBROOTZLIB ' +configopts += '--with-tcmalloc-dir=$EBROOTGPERFTOOLS/lib ' + +builddependencies = [ + ('flex', '2.6.4'), +] +dependencies = [ + ('Boost', '1.74.0'), + ('zlib', '1.2.11'), + ('expat', '2.2.9'), +] + +sanity_check_paths = { + 'files': ["bin/mira"], + 'dirs': ["bin"], +} + +moduleclass = 'bio' From bd22247c7fd7c0bb37af9b5ef3cb8f07113d095a Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Thu, 14 Apr 2022 01:43:50 +0200 Subject: [PATCH 3441/9987] adding easyconfigs: coverage-5.5-GCCcore-10.3.0.eb --- .../c/coverage/coverage-5.5-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..dcb38a14b2e --- /dev/null +++ b/easybuild/easyconfigs/c/coverage/coverage-5.5-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'coverage' +version = '5.5' + +homepage = 'https://coverage.readthedocs.io' +description = """ Coverage.py is a tool for measuring code coverage of Python programs. + It monitors your program, noting which parts of the code have been executed, + then analyzes the source to identify code that could have been executed but was not. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ebe78fe9a0e874362175b02371bdfbee64d8edc42a044253ddf4ee7d3c15212c'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'tools' From e1e7a8fd4053c5ba529b896e567398c0195f5596 Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Thu, 14 Apr 2022 01:46:39 +0200 Subject: [PATCH 3442/9987] adding easyconfigs: pygmo-2.18.0-foss-2021a.eb, pagmo-2.18.0-foss-2021a.eb --- .../p/pagmo/pagmo-2.18.0-foss-2021a.eb | 36 +++++++++++++ .../p/pygmo/pygmo-2.18.0-foss-2021a.eb | 51 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021a.eb b/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021a.eb new file mode 100644 index 00000000000..050cf82b216 --- /dev/null +++ b/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021a.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'pagmo' +version = '2.18.0' + +homepage = 'https://esa.github.io/pagmo2' +description = "pagmo is a C++ scientific library for massively parallel optimization." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/esa/pagmo2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1b95b036f75e6fa0b21082ab228dbd63cd18ca10d9622ac53629245e0f95c35c'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Boost', '1.76.0'), + ('tbb', '2020.3'), + ('Eigen', '3.3.9'), + ('NLopt', '2.7.0'), +] + +configopts = "-DPAGMO_WITH_EIGEN3=ON -DPAGMO_WITH_NLOPT=ON -DPAGMO_BUILD_TESTS=ON" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libpagmo.%s' % SHLIB_EXT], + 'dirs': ['include/pagmo', 'lib/cmake/pagmo'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb new file mode 100644 index 00000000000..1cdd3f18d22 --- /dev/null +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakePythonPackage' + +name = 'pygmo' +version = '2.18.0' + +homepage = 'https://esa.github.io/pygmo2' +description = "pygmo is a scientific Python library for massively parallel optimization." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/esa/pygmo2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['54d4fa99e4bff539fca67dfcdc909499fd3f1a3186f7c7fc8200f19512954166'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('pybind11', '2.6.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Boost', '1.76.0'), + ('pagmo', '2.18.0'), + ('matplotlib', '3.4.2'), + ('networkx', '2.6.3'), +] + +runtest = False + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('dill', '0.3.4', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 6f045c89c74fff5ff9245ac1290af5b30d59e856 Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Thu, 14 Apr 2022 01:49:21 +0200 Subject: [PATCH 3443/9987] adding easyconfigs: geopandas-0.10.2-foss-2021a.eb --- .../geopandas/geopandas-0.10.2-foss-2021a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb new file mode 100644 index 00000000000..c3c1b10749e --- /dev/null +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'geopandas' +version = '0.10.2' + +homepage = 'https://github.com/geopandas/geopandas' +description = """GeoPandas is a project to add support for geographic data to pandas objects. +It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series +and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and +perform geometric operations.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Shapely', '1.8a1'), + ('Fiona', '1.8.20'), + ('matplotlib', '3.4.2'), + ('networkx', '2.6.3'), + ('scikit-learn', '0.24.2'), + ('pyproj', '3.1.0'), +] + +use_pip = True + +exts_list = [ + ('descartes', '1.1.0', { + 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Deprecated', '1.2.10', { + 'checksums': ['525ba66fb5f90b07169fdd48b6373c18f1ee12728ca277ca44567a367d9d7f74'], + }), + ('mapclassify', '2.3.0', { + 'checksums': ['bfe1ec96afe7f866560d25f9f00e5c4dae97d5b69dfe758dbe02c4993261365b'], + }), + (name, version, { + 'checksums': ['e28a729e44ac53c1891b54b1aca60e3bc0bb9e88ad0f2be8e301a03b9510f6e2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 3aec85635e54acdf063aba55a54b86f403c8b887 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 14 Apr 2022 08:13:15 +0200 Subject: [PATCH 3444/9987] Update easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb works for us Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb index eacfc93d087..ec820ab8c20 100644 --- a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb @@ -26,6 +26,7 @@ dependencies = [ ('Boost', '1.74.0'), ('zlib', '1.2.11'), ('expat', '2.2.9'), + ('gperftools', '2.9.1'), ] sanity_check_paths = { From 8f6b1cd779fff2880f66b3215d7c46e7ac7add2f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Apr 2022 10:05:23 +0200 Subject: [PATCH 3445/9987] adding easyconfigs: Arb-2.22.1-GCC-11.2.0.eb, FLINT-2.8.4-GCC-11.2.0.eb --- .../a/Arb/Arb-2.22.1-GCC-11.2.0.eb | 35 +++++++++++++++++++ .../f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb | 34 ++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..f729c96081d --- /dev/null +++ b/easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Arb' +version = '2.22.1' + +homepage = 'https://arblib.org/' + +description = """Arb is a C library for arbitrary-precision interval arithmetic. + It has full support for both real and complex numbers. The library is thread-safe, + portable, and extensively tested.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'fredrik-johansson' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['1ef85518eee04885e8a90196498bc75e4e2410621d4184f2bc01d46b7080a243'] + +dependencies = [ + ('FLINT', '2.8.4'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), +] + +configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb new file mode 100644 index 00000000000..8b3d55e165d --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'FLINT' +version = '2.8.4' + +homepage = 'https://www.flintlib.org/' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.flintlib.org'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['61df92ea8c8e9dc692d46c71d7f50aaa09a33d4ba08d02a1784730a445e5e4be'] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), +] + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'math' From 42128c9b91186d81e6de0aed1a766a3811641c4e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Apr 2022 10:20:10 +0200 Subject: [PATCH 3446/9987] adding easyconfigs: bioawk-1.0-GCC-11.2.0.eb --- .../b/bioawk/bioawk-1.0-GCC-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/bioawk/bioawk-1.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/bioawk/bioawk-1.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/bioawk/bioawk-1.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..e3605a03418 --- /dev/null +++ b/easybuild/easyconfigs/b/bioawk/bioawk-1.0-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'bioawk' +version = '1.0' + +homepage = 'https://github.com/lh3/bioawk' +description = """ Bioawk is an extension to Brian Kernighan's awk, + adding the support of several common biological data formats, + including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. """ + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5cbef3f39b085daba45510ff450afcf943cfdfdd483a546c8a509d3075ff51b5'] + +builddependencies = [('Bison', '3.7.6')] +dependencies = [('zlib', '1.2.11')] + +parallel = 1 + +files_to_copy = [([name], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 6db5c923082b6d1a784548e16ac2904f1ddc0085 Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Thu, 14 Apr 2022 16:34:19 +0800 Subject: [PATCH 3447/9987] make configure step at the installdir --- .../RepeatMasker-4.1.2-p1-foss-2020b.eb | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb index 9d3c0d87244..7b7bd2f8ef3 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb @@ -36,9 +36,16 @@ dependencies = [ local_default_search_engine = 'RMBlast' -preinstall_cmd = './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' -preinstall_cmd += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' -preinstall_cmd += '-default_search_engine %s' % local_default_search_engine.lower() +#preinstall_cmd = './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +#preinstall_cmd += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +#preinstall_cmd += '-default_search_engine %s' % local_default_search_engine.lower() + +local_config_command = 'cd %(installdir)s &&' +local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() + +postinstallcmds = [ local_config_command, ] fix_perl_shebang_for = ['RepeatMasker'] From 50f91699377f4f649f483d0b28a22ea26d4c2533 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Apr 2022 11:08:02 +0200 Subject: [PATCH 3448/9987] adding easyconfigs: crb-blast-0.6.9-gompi-2021b.eb --- .../crb-blast/crb-blast-0.6.9-gompi-2021b.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021b.eb diff --git a/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021b.eb b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021b.eb new file mode 100644 index 00000000000..75bf3cf868b --- /dev/null +++ b/easybuild/easyconfigs/c/crb-blast/crb-blast-0.6.9-gompi-2021b.eb @@ -0,0 +1,63 @@ +easyblock = 'Bundle' + +name = 'crb-blast' +version = '0.6.9' + +homepage = 'https://github.com/cboursnell/crb-blast' +description = """Conditional Reciprocal Best BLAST - high confidence ortholog assignment. + CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. + This is particularly useful in genome and transcriptome annotation.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +dependencies = [ + ('Ruby', '3.0.1'), + ('BLAST+', '2.12.0'), +] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# this is a bundle of Ruby gems +exts_defaultclass = 'RubyGem' + +exts_list = [ + ('facade', '1.2.1', { + 'checksums': ['0764de5519088227675a2a67da23322500c3c507b89486d91296e031d87d036e'], + }), + ('pathname2', '1.8.4', { + 'checksums': ['1711264f3f7c1b380f96e1f0383b135d9703488f7b1acf66346a176efc257b7a'], + }), + ('fixwhich', '1.0.2', { + 'checksums': ['c6a8f796a7eb60ffbc29f0d2af85461761a36c2864d25e445ff18bfbd1657078'], + }), + ('bindeps', '1.2.1', { + 'checksums': ['3c11d75aa722bed67246852bb430a182361a128910d384b664b91f3e65bc34b5'], + }), + ('threach', '0.2.0', { + 'checksums': ['432cbf3569bf9b09e26f93d0959fd6fb911c71e790e8a4cc4d1110e139a2ffca'], + }), + ('bio', '1.5.2', { + 'checksums': ['68a453cdb87e5c8d7ad4b2ad5e76e81822193be0623f53cf53356ca95b55a6b4'], + }), + ('trollop', '2.9.10', { + 'checksums': ['ceca2d91f349163d6ee3e792d356d4ded7472e6da31ac6dcc5956d1b03607bf7'], + }), + (name, version, { + 'checksums': ['69c346e7d83efe9b9a383a39b57e7cce186a82b7074f275b14906f8f05678e3e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bioruby', 'bin/br_biofetch.rb', 'bin/br_bioflat.rb', 'bin/br_biogetseq.rb', + 'bin/br_pmfetch.rb', 'bin/%(name)s'], + 'dirs': ['gems'], +} + +sanity_check_commands = ["%(name)s --help"] + +modextrapaths = {'GEM_PATH': ['']} + +moduleclass = 'bio' From 705476ecb40ccccac84ce53bc1c561572b2e8cea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Apr 2022 11:57:10 +0200 Subject: [PATCH 3449/9987] adding easyconfigs: ViennaRNA-2.5.0-foss-2021b.eb --- .../v/ViennaRNA/ViennaRNA-2.5.0-foss-2021b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.5.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.5.0-foss-2021b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.5.0-foss-2021b.eb new file mode 100644 index 00000000000..5a48408d321 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.5.0-foss-2021b.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'ViennaRNA' +version = '2.5.0' + +homepage = 'https://www.tbi.univie.ac.at/RNA/' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b85544650ee316743173ec9b30497cc4c559f1bfb8f66d16c563f780afd8c0c5'] + +builddependencies = [ + ('Autotools', '20210726'), + ('flex', '2.6.4'), + ('pkg-config', '0.29.2'), + ('Bison', '3.7.6'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('GSL', '2.7'), + ('libgd', '2.3.3'), + ('X11', '20210802'), +] + +configopts = "--with-cluster --with-kinwalker --with-python3" +# Uncomment this if you compile on pre SSE4.1 CPU +# configopts += "--enable-sse " + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/', 'lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 7744248013f1c25dd286ef0435674a68d608d5e8 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 14 Apr 2022 12:04:36 +0200 Subject: [PATCH 3450/9987] remove trailing whitespace --- easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb index ec820ab8c20..69c6533045d 100644 --- a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb @@ -20,7 +20,7 @@ configopts = '--with-boost=$EBROOTBOOST --with-expat=$EBROOTEXPAT --with-zlib=$E configopts += '--with-tcmalloc-dir=$EBROOTGPERFTOOLS/lib ' builddependencies = [ - ('flex', '2.6.4'), + ('flex', '2.6.4'), ] dependencies = [ ('Boost', '1.74.0'), From fdd180b55d435f6f229e53511515fa2162d3fdc5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Apr 2022 12:52:16 +0200 Subject: [PATCH 3451/9987] adding easyconfigs: Kraken2-2.1.2-gompi-2021b.eb --- .../k/Kraken2/Kraken2-2.1.2-gompi-2021b.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021b.eb diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021b.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021b.eb new file mode 100644 index 00000000000..7e70470c5f2 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2021b.eb @@ -0,0 +1,62 @@ +easyblock = 'PackedBinary' + +name = 'Kraken2' +version = '2.1.2' + +homepage = 'https://github.com/DerrickWood/kraken2/wiki' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# part is compiled with $CXX, the rest is in Perl +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-2.1.1_fix_installation_for_easybuild.patch', + '%(name)s-%(version)s_fix_ncbi_https_server.patch', +] +checksums = [ + 'e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3', # v2.1.2.tar.gz + # Kraken2-2.1.1_fix_installation_for_easybuild.patch + '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11', + '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116', # Kraken2-2.1.2_fix_ncbi_https_server.patch +] + +dependencies = [ + ('Perl', '5.34.0'), + ('BLAST+', '2.12.0'), + ('wget', '1.21.2'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken2.sh %(installdir)s/bin' + +# Kraken2 databases can be downloaded from https://benlangmead.github.io/aws-indexes/k2 +# or built as described in https://github.com/DerrickWood/kraken2/wiki/Manual#kraken-2-databases +# The following commands will build and install the standard databases (100GB) in local_db_path +# local_db_path = '%(installdir)s/db' +# postinstallcmds = [ +# 'mkdir %s' % local_db_path, +# 'cd %%(installdir)s/bin && ./kraken2-build --standard --threads %%(parallel)s --db %s' % local_db_path, +# ] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + '16S_gg_installation.sh', '16S_rdp_installation.sh', '16S_silva_installation.sh', 'add_to_library.sh', + 'build_db', 'build_gg_taxonomy.pl', 'build_kraken2_db.sh', 'build_rdp_taxonomy.pl', 'build_silva_taxonomy.pl', + 'classify', 'clean_db.sh', 'cp_into_tempfile.pl', 'download_genomic_library.sh', 'download_taxonomy.sh', + 'dump_table', 'estimate_capacity', 'kraken2', 'kraken2-build', 'kraken2-inspect', 'kraken2lib.pm', + 'lookup_accession_numbers.pl', 'make_seqid2taxid_map.pl', 'mask_low_complexity.sh', 'rsync_from_ncbi.pl', + 'scan_fasta_file.pl']], + 'dirs': [], +} + +moduleclass = 'bio' From 555158b8e136227ef2b4a3df8e3d66459b243909 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Apr 2022 13:21:26 +0200 Subject: [PATCH 3452/9987] adding easyconfigs: QUAST-5.0.2-foss-2021b.eb --- .../q/QUAST/QUAST-5.0.2-foss-2021b.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb new file mode 100644 index 00000000000..eedf3ea7c27 --- /dev/null +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'QUAST' +version = '5.0.2' + +homepage = 'https://github.com/ablab/quast' +description = """QUAST evaluates genome assemblies by computing various metrics. +It works both with and without reference genomes. The tool accepts multiple +assemblies, thus is suitable for comparison.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + + +dependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('matplotlib', '3.4.3'), + ('Java', '11', '', True), + ('Boost', '1.77.0'), +] + +use_pip = True + +github_account = 'ablab' +exts_list = [ + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + (name, version, { + 'install_target': 'install_full', + 'modulename': '%(namelower)s_libs', + 'patches': ['%(name)s-%(version)s_fix-Python-3.8.patch'], + 'source_tmpl': '%(namelower)s_%(version)s.tar.gz', + 'source_urls': [GITHUB_LOWER_SOURCE], + 'checksums': [ + '9f30c03e0bfd261492fe6b72fb07645bdee5b29d741f75fc75857b6fa095d91d', # quast_5.0.2.tar.gz + '8ae7ebf45e5368ebc058fc208822a23d32ce1052bd53fd8c3aaa4ad14d3c95aa', # QUAST-5.0.2_fix-Python-3.8.patch + ], + }), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s %(namelower)s.py %(namelower)s"] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "wget quast.sourceforge.net/test_data.tar.gz && " + "tar xzf test_data.tar.gz && " + "%(namelower)s.py --test && " + "rm -rf ./test_data.tar.gz ./test_data", + "%(namelower)s -h", +] + +sanity_pip_check = True + +moduleclass = 'bio' From d5cbfbaa38dbe0cec3dcd1f163875c8bef411118 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Apr 2022 13:53:53 +0200 Subject: [PATCH 3453/9987] adding easyconfigs: segemehl-0.3.4-GCC-11.2.0.eb --- .../s/segemehl/segemehl-0.3.4-GCC-11.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-11.2.0.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-11.2.0.eb new file mode 100644 index 00000000000..d97799dd2d0 --- /dev/null +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'segemehl' +version = '0.3.4' + +homepage = 'https://www.bioinf.uni-leipzig.de/Software/segemehl/' +description = """segemehl is a software to map short sequencer reads to reference genomes. + Unlike other methods, segemehl is able to detect not only mismatches but also insertions + and deletions. Furthermore, segemehl is not limited to a specific read length and is able + to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads + gziped queries to save both disk and memory space and allows bisulfite sequencing mapping + and split read mapping.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://www.bioinf.uni-leipzig.de/Software/%(name)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('HTSlib', '1.14'), + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +buildopts = 'all' + +files_to_copy = [(["haarz.x", "%(name)s.x"], "bin")] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["haarz.x", "%(name)s.x"]], + 'dirs': [] +} + +moduleclass = 'bio' From 097a8bf07857f2a2da1d7a577685c7284e00c9b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Apr 2022 13:57:03 +0200 Subject: [PATCH 3454/9987] adding easyconfigs: SpaceRanger-1.3.1-GCC-11.2.0.eb --- .../SpaceRanger-1.3.1-GCC-11.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-1.3.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-1.3.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-1.3.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..4c9edaacc3b --- /dev/null +++ b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-1.3.1-GCC-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'SpaceRanger' +version = '1.3.1' + +homepage = 'https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger' +description = """ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output +and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, +perform clustering and gene expression analysis, and place spots in spatial context on the slide image. """ + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +# download sources from homepage, registration required +# https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest +sources = [SOURCELOWER_TAR_GZ] +checksums = ['70f4adbd95967938abbf7aa705228c9b550f07e585ddf3951902c43f1114493d'] + +dependencies = [ + ('bcl2fastq2', '2.20.0'), +] + +allow_prepend_abs_path = True +# prepend reference databases GRCh38 and mm10 to PATH +# modextrapaths = {'PATH': '/path/to/databases/%(namelower)s-%(version)s'} + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['external', 'lib', 'mro'], +} + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From 7bbff35fc64cf8a3b00629d0dd6eb4dfb9cd9567 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 14 Apr 2022 16:42:54 +0200 Subject: [PATCH 3455/9987] Excluded test model dump since it succeeds interactively --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index cbd10b689f3..8ef45e4a894 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -95,6 +95,8 @@ excluded_tests = { 'test_optim', # Test from this suite timeout often. The process group backend is deprecated anyway # 'distributed/rpc/test_process_group_agent', + # This test fails constently when run as part of the test suite, but succeeds when run interactively + 'test_model_dump', ] } From bf83671bf99f4e9defbd56d0cb8c83f67a23799c Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Fri, 15 Apr 2022 10:49:46 +0200 Subject: [PATCH 3456/9987] pygmo-2.18.0: use a more common version for dep networkx --- easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb index 1cdd3f18d22..3c79bf9f50e 100644 --- a/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb @@ -23,7 +23,7 @@ dependencies = [ ('Boost', '1.76.0'), ('pagmo', '2.18.0'), ('matplotlib', '3.4.2'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ] runtest = False From 75d7111813b15930332a6b2f04a84367dffda0be Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Fri, 15 Apr 2022 12:14:53 +0200 Subject: [PATCH 3457/9987] Fix checksum --- .../easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb index c3c1b10749e..060177991e3 100644 --- a/easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb @@ -38,7 +38,7 @@ exts_list = [ 'checksums': ['bfe1ec96afe7f866560d25f9f00e5c4dae97d5b69dfe758dbe02c4993261365b'], }), (name, version, { - 'checksums': ['e28a729e44ac53c1891b54b1aca60e3bc0bb9e88ad0f2be8e301a03b9510f6e2'], + 'checksums': ['efbf47e70732e25c3727222019c92b39b2e0a66ebe4fe379fbe1aa43a2a871db'], }), ] From a42afb6b1bf3a2fe8e6d5ed2c8749bcefd183436 Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Fri, 15 Apr 2022 12:41:10 +0200 Subject: [PATCH 3458/9987] geopandas-0.10.2: use a more common version for dep networkx --- .../easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb index 060177991e3..65cc54a2dc7 100644 --- a/easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.10.2-foss-2021a.eb @@ -17,7 +17,7 @@ dependencies = [ ('Shapely', '1.8a1'), ('Fiona', '1.8.20'), ('matplotlib', '3.4.2'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ('scikit-learn', '0.24.2'), ('pyproj', '3.1.0'), ] From b6eb3b8ffe4cd97402e21fee85feed5e76888dd8 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 15 Apr 2022 11:42:15 -0700 Subject: [PATCH 3459/9987] update LAPACK --- .../l/LAPACK/LAPACK-3.10.1-GCC-11.2.0.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAPACK/LAPACK-3.10.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.10.1-GCC-11.2.0.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.10.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..3496ab88eb2 --- /dev/null +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.10.1-GCC-11.2.0.eb @@ -0,0 +1,16 @@ +name = 'LAPACK' +version = '3.10.1' + +homepage = 'https://www.netlib.org/lapack/' +description = """LAPACK is written in Fortran90 and provides routines for solving systems of + simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue + problems, and singular value problems.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Reference-LAPACK/lapack/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cd005cd021f144d7d5f7f33c943942db9f03a28d110d6a3b80d718a295f7f714'] + +moduleclass = 'numlib' From ea3d520c2fa61245d0affe6f8d572ff50b6619f1 Mon Sep 17 00:00:00 2001 From: Daniel Hedman Date: Sat, 16 Apr 2022 14:50:37 +0900 Subject: [PATCH 3460/9987] Update easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb b/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb index c9f4722d7d7..3b51e4a3eb0 100644 --- a/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb +++ b/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb @@ -6,7 +6,7 @@ version = '1.04' homepage = 'http://theory.cm.utexas.edu/henkelman/code/bader/' description = "A fast algorithm for doing Bader's analysis on a charge density grid." -toolchain = {'name': 'intel', 'version': '2020b'} +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] From 56a8147472a953d33414a1a5cb022d185f24803a Mon Sep 17 00:00:00 2001 From: Daniel Hedman Date: Sat, 16 Apr 2022 14:51:05 +0900 Subject: [PATCH 3461/9987] Update easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb b/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb index 3b51e4a3eb0..d932a6a8ff8 100644 --- a/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb +++ b/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb @@ -12,8 +12,7 @@ source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(ver sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] checksums = ['f20a0a021157d911bea06666911763b737c4ff38b39e793b8560f940fe391b8e'] -prebuildopts = 'sed -i "s|FFLAGS = -O2||" makefile.lnx_ifort && sed -i "s/LINK = -static/LINK = -static-intel/g" makefile.lnx_ifort && ' -buildopts = '-f makefile.lnx_ifort' +buildopts = '-f makefile.lnx_ifort FFLAGS="$FFLAGS" LINK="-static-intel"' parallel = 1 files_to_copy = [(['bader'], 'bin')] From 34594e017fec8ce71d940a66d15efba71f9f1e34 Mon Sep 17 00:00:00 2001 From: easybuild Date: Sat, 16 Apr 2022 14:59:08 +0900 Subject: [PATCH 3462/9987] Updated based on jfgrimm comments --- .../b/Bader/Bader-1.04-iccifort-2020.4.304.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..ef4cb6bb247 --- /dev/null +++ b/easybuild/easyconfigs/b/Bader/Bader-1.04-iccifort-2020.4.304.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'Bader' +version = '1.04' + +homepage = 'http://theory.cm.utexas.edu/henkelman/code/bader/' +description = "A fast algorithm for doing Bader's analysis on a charge density grid." + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] +sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f20a0a021157d911bea06666911763b737c4ff38b39e793b8560f940fe391b8e'] + +buildopts = '-f makefile.lnx_ifort FFLAGS="$FFLAGS" LINK="-static-intel"' +parallel = 1 + +files_to_copy = [(['bader'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bader'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s -h"] + +moduleclass = 'chem' From 420811127745c5d137e2ad65b1dd560c4e2337b1 Mon Sep 17 00:00:00 2001 From: Daniel Hedman Date: Sat, 16 Apr 2022 15:00:27 +0900 Subject: [PATCH 3463/9987] Delete Bader-1.04-intel-2020b.eb --- .../b/Bader/Bader-1.04-intel-2020b.eb | 25 ------------------- 1 file changed, 25 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb b/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb deleted file mode 100644 index d932a6a8ff8..00000000000 --- a/easybuild/easyconfigs/b/Bader/Bader-1.04-intel-2020b.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'MakeCp' - -name = 'Bader' -version = '1.04' - -homepage = 'http://theory.cm.utexas.edu/henkelman/code/bader/' -description = "A fast algorithm for doing Bader's analysis on a charge density grid." - -toolchain = {'name': 'iccifort', 'version': '2020.4.304'} - -source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] -sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['f20a0a021157d911bea06666911763b737c4ff38b39e793b8560f940fe391b8e'] - -buildopts = '-f makefile.lnx_ifort FFLAGS="$FFLAGS" LINK="-static-intel"' -parallel = 1 - -files_to_copy = [(['bader'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/bader'], - 'dirs': [], -} - -moduleclass = 'chem' From 358896aa3e9fdb509ad2041374811ce1a581447f Mon Sep 17 00:00:00 2001 From: easybuild Date: Sat, 16 Apr 2022 15:09:59 +0900 Subject: [PATCH 3464/9987] Updated based on jfgrimm comments --- .../easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb b/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb index 9f693334211..c9a3c391abe 100644 --- a/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb +++ b/easybuild/easyconfigs/e/EigenExa/EigenExa-2.11-intel-2020b.eb @@ -13,12 +13,16 @@ source_urls = ['https://www.r-ccs.riken.jp/labs/lpnctrt/projects/eigenexa/'] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['87dee8ac13f410a007e82df2688fa7f143883229dac729fd20836f4a28fac43d'] +builddependencies = [ + ('Autotools', '20200321') +] + preconfigopts = './cleanup && ./bootstrap && ' parallel = 1 sanity_check_paths = { - 'files': ['lib/libEigenExa.a'], + 'files': ['lib/libEigenExa.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': [] } From 33c9e4b436dd5c866901dbbb9037a3310a693982 Mon Sep 17 00:00:00 2001 From: Daniel Hedman Date: Sat, 16 Apr 2022 15:12:53 +0900 Subject: [PATCH 3465/9987] Update easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb index b4f4dcdf06e..bcbb867714c 100644 --- a/easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb @@ -1,7 +1,8 @@ easyblock = 'MakeCp' name = 'i7z' -version = '0.27.2' +version = '20131012' +local_commit = '5023138' homepage = 'https://github.com/ajaiantilal/i7z' description = """A better i7 (and now i3, i5) reporting tool for Linux @@ -9,16 +10,8 @@ description = """A better i7 (and now i3, i5) reporting tool for Linux toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -sources = [{ - 'filename': 'i7z-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/ajaiantilal', - 'repo_name': 'i7z', - 'commit': '5023138', - 'recursive': True, - 'keep_git_dir': True, - }, -}] +source_urls = ['https://github.com/ajaiantilal/i7z'] +sources = ['%s.tar.gz' % local_commit] patches = [ ('i7z-%(version)s_fix_gcc-10.patch'), ] From c17bb9797e81e26340e3f34bfdfdda0b093ab389 Mon Sep 17 00:00:00 2001 From: easybuild Date: Sat, 16 Apr 2022 15:24:03 +0900 Subject: [PATCH 3466/9987] Updated based on jfgrimm comments --- .../i/i7z/i7z-0.27.2_fix_gcc-10.patch | 4 ++ .../i/i7z/i7z-20131012-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/i/i7z/i7z-20131012-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/i/i7z/i7z-0.27.2_fix_gcc-10.patch b/easybuild/easyconfigs/i/i7z/i7z-0.27.2_fix_gcc-10.patch index de0f773a434..3c65993d11d 100644 --- a/easybuild/easyconfigs/i/i7z/i7z-0.27.2_fix_gcc-10.patch +++ b/easybuild/easyconfigs/i/i7z/i7z-0.27.2_fix_gcc-10.patch @@ -1,3 +1,7 @@ +# Add -fcommon to the CFLAGS +# see https://bugs.gentoo.org/706690 +# +# Daniel Hedman, 20220416 diff -ru i7z.orig/Makefile i7z/Makefile --- i7z.orig/Makefile 2022-04-01 19:33:00.000000000 +0900 +++ i7z/Makefile 2022-04-01 19:33:23.000000000 +0900 diff --git a/easybuild/easyconfigs/i/i7z/i7z-20131012-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/i7z/i7z-20131012-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ecea05b620c --- /dev/null +++ b/easybuild/easyconfigs/i/i7z/i7z-20131012-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'i7z' +version = '20131012' +local_commit = '5023138' + +homepage = 'https://github.com/ajaiantilal/i7z' +description = """A better i7 (and now i3, i5) reporting tool for Linux +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/ajaiantilal/i7z/archive'] +sources = ['%s.tar.gz' % local_commit] +patches = [ + ('i7z-0.27.2_fix_gcc-10.patch'), +] +checksums = [ + 'e127bddf850e7febd39cef2d2b13dca5fe19cc2a1bb1099d72b683be5d8bd1c0', # 5023138.tar.gz + 'e45dbcd5845e9a4480c8a287b47572bc3b93f69d71ae4dc7ab5157b2aa04826e', # i7z-0.27.2_fix_gcc-10.patch +] + +builddependencies = [ + ('binutils', '2.37') +] + +dependencies = [ + ('ncurses', '6.2'), +] + +files_to_copy = [( + [ + 'i7z', + 'i7z_32bit', + 'i7z_64bit' + ], 'bin')] + +sanity_check_paths = { + 'files': ['bin/i7z', 'bin/i7z_32bit', 'bin/i7z_64bit'], + 'dirs': [] +} + +moduleclass = 'tools' \ No newline at end of file From 2de7fba4e1dce347c098bd1356cce89e1d2a1e0c Mon Sep 17 00:00:00 2001 From: Daniel Hedman Date: Sat, 16 Apr 2022 15:24:44 +0900 Subject: [PATCH 3467/9987] Delete i7z-0.27.2-GCCcore-11.2.0.eb --- .../i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb | 43 ------------------- 1 file changed, 43 deletions(-) delete mode 100644 easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb deleted file mode 100644 index bcbb867714c..00000000000 --- a/easybuild/easyconfigs/i/i7z/i7z-0.27.2-GCCcore-11.2.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'MakeCp' - -name = 'i7z' -version = '20131012' -local_commit = '5023138' - -homepage = 'https://github.com/ajaiantilal/i7z' -description = """A better i7 (and now i3, i5) reporting tool for Linux -""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -source_urls = ['https://github.com/ajaiantilal/i7z'] -sources = ['%s.tar.gz' % local_commit] -patches = [ - ('i7z-%(version)s_fix_gcc-10.patch'), -] -checksums = [ - 'ef895fa04c42cb926c3fd07a1274e16a8606c1ef836a37865bb620e725b317c5', # i7z-0.27.2.tar.gz - 'e6422302070b450c61ba4fd35e01eb4b1c112dd6c89250363ab94a62e5092e68', # i7z-0.27.2_fix_gcc-10.patch -] - -builddependencies = [ - ('binutils', '2.37') -] - -dependencies = [ - ('ncurses', '6.2'), -] - -files_to_copy = [( - [ - 'i7z', - 'i7z_32bit', - 'i7z_64bit' - ], 'bin')] - -sanity_check_paths = { - 'files': ['bin/i7z', 'bin/i7z_32bit', 'bin/i7z_64bit'], - 'dirs': [] -} - -moduleclass = 'tools' From 014eb2a5db7580512e635e677bb54e35011fbedb Mon Sep 17 00:00:00 2001 From: Daniel Hedman Date: Sat, 16 Apr 2022 15:25:17 +0900 Subject: [PATCH 3468/9987] Update i7z-20131012-GCCcore-11.2.0.eb --- easybuild/easyconfigs/i/i7z/i7z-20131012-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/i7z/i7z-20131012-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/i7z/i7z-20131012-GCCcore-11.2.0.eb index ecea05b620c..f3652d8c8da 100644 --- a/easybuild/easyconfigs/i/i7z/i7z-20131012-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/i7z/i7z-20131012-GCCcore-11.2.0.eb @@ -40,4 +40,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' From f9779d21c71710313db30d4f7ce355c470ce3907 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Sun, 17 Apr 2022 17:01:03 +0200 Subject: [PATCH 3469/9987] adding easyconfigs: Grace-5.1.25-foss-2021b.eb --- .../g/Grace/Grace-5.1.25-foss-2021b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021b.eb diff --git a/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021b.eb b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021b.eb new file mode 100644 index 00000000000..7a3b2949619 --- /dev/null +++ b/easybuild/easyconfigs/g/Grace/Grace-5.1.25-foss-2021b.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Grace' +version = '5.1.25' + +homepage = 'https://plasma-gate.weizmann.ac.il/Grace/' +description = """Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['Grace-5.1.25-tirpc-dependency.patch'] +checksums = [ + '751ab9917ed0f6232073c193aba74046037e185d73b77bab0f5af3e3ff1da2ac', # grace-5.1.25.tar.gz + '093af4ddf344300aa31561c97e2765ed3fab609b70a5d199ac64a60dbd9e0c34', # Grace-5.1.25-tirpc-dependency.patch +] + +dependencies = [ + ('motif', '2.3.8'), + ('zlib', '1.2.11'), + ('netCDF', '4.8.1'), + ('libtirpc', '1.3.2'), +] + +runtest = 'tests' + +postinstallcmds = ['mv %(installdir)s/grace/* %(installdir)s && rmdir %(installdir)s/grace'] + +sanity_check_paths = { + 'files': ['lib/libgrace_np.a', 'bin/convcal', 'bin/fdf2fit', 'bin/grconvert', 'bin/xmgrace'], + 'dirs': ['include', 'fonts', 'templates'], +} + +modextravars = { + 'GRACE_HOME': '%(installdir)s', +} + +moduleclass = 'vis' From 6c29623452b6ddd56a70449cde4bf10d1c1fd990 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Sun, 17 Apr 2022 22:54:07 +0200 Subject: [PATCH 3470/9987] adding easyconfigs: OpenSceneGraph-3.6.5-foss-2021b.eb, librsvg-2.52.8-GCCcore-11.2.0.eb, DCMTK-3.6.6-GCCcore-11.2.0.eb --- .../d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb | 40 +++++++++++++++ .../librsvg/librsvg-2.52.8-GCCcore-11.2.0.eb | 40 +++++++++++++++ .../OpenSceneGraph-3.6.5-foss-2021b.eb | 51 +++++++++++++++++++ 3 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/librsvg/librsvg-2.52.8-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021b.eb diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..24b265749d0 --- /dev/null +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'DCMTK' +version = '3.6.6' + +homepage = 'https://dicom.offis.de/dcmtk' +description = """DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. +It includes software for examining, constructing and converting DICOM image files, handling offline media, sending +and receiving images over a network connection, as well as demonstrative image storage and worklist servers.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dicom.offis.de/download/dcmtk/dcmtk%s/' % version.replace('.', '')] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['6859c62b290ee55677093cccfd6029c04186d91cf99c7642ae43627387f3458e'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1') +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.3.0'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.10'), + ('libiconv', '1.16'), +] + +sanity_check_paths = { + 'files': ['bin/dcmdump', 'bin/dcmj2pnm'], + 'dirs': ['lib'], +} + +sanity_check_commands = ['%s_tests | grep " 0 failed"' % x for x in [ + 'dcmdata', 'dcmect', 'dcmfg', 'dcmiod', 'dcmnet', 'dcmrt', 'dcmseg', 'dcmsr', 'dcmtls', 'ofstd']] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.52.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.52.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f9c6d6ffbc5 --- /dev/null +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.52.8-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'librsvg' +version = '2.52.8' + +homepage = 'https://wiki.gnome.org/Projects/LibRsvg' +description = "Librsvg is a library to render SVG files using cairo." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['bade8eda74f2d7efb414e9bae53004806e1fa7dc05f04cad59b74eb1a5756962'] + +builddependencies = [ + ('binutils', '2.37'), + ('Rust', '1.54.0'), +] + +dependencies = [ + ('cairo', '1.16.0'), + ('freetype', '2.11.0'), + ('Gdk-Pixbuf', '2.42.6'), + ('HarfBuzz', '2.8.2'), + ('Pango', '1.48.8'), + ('GObject-Introspection', '1.68.0'), +] + +# don't GdkPixbuf loader (which gets added to the Gdk-Pixbuf installation directory) +configopts = "--disable-pixbuf-loader" + +sanity_check_paths = { + 'files': ['bin/rsvg-convert', 'lib/librsvg-%(version_major)s.a', 'lib/librsvg-%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/librsvg-%(version_major)s.0.pc'], + 'dirs': ['include/librsvg-%(version_major)s.0/librsvg', 'share'], +} + +sanity_check_commands = ["rsvg-convert --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021b.eb b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021b.eb new file mode 100644 index 00000000000..4f464558d0e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2021b.eb @@ -0,0 +1,51 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jiri Furst +### + +easyblock = 'CMakeMake' + +name = 'OpenSceneGraph' +version = '3.6.5' + +homepage = 'http://www.openscenegraph.org/' +description = """The OpenSceneGraph is an open source high performance 3D graphics toolkit, +used by application developers in fields such as visual simulation, games, virtual reality, +scientific visualization and modelling. Written entirely in Standard C++ and OpenGL it runs +on all Windows platforms, OSX, GNU/Linux, IRIX, Solaris, HP-Ux, AIX and FreeBSD operating +systems. The OpenSceneGraph is now well established as the world leading scene graph +technology, used widely in the vis-sim, space, scientific, oil-gas, games and virtual +reality industries.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [GITHUB_SOURCE] +sources = ['OpenSceneGraph-%(version)s.tar.gz'] +checksums = ['aea196550f02974d6d09291c5d83b51ca6a03b3767e234a8c0e21322927d1e12'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('GDAL', '3.3.2'), + ('DCMTK', '3.6.6'), + ('OpenEXR', '3.1.1'), + ('SDL2', '2.0.20'), + ('poppler', '22.01.0'), + ('librsvg', '2.52.8'), + ('giflib', '5.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['osgarchive', 'osgconv', 'osgfilecache', 'osgversion', 'osgviewer', 'present3D']], + 'dirs': ['lib'], +} + +sanity_check_commands = ['osgversion'] + +moduleclass = 'vis' From b55583c6bb623b887de94ff46e0b2ed6c258f58c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 18 Apr 2022 11:56:11 +0100 Subject: [PATCH 3471/9987] add hwloc dependency to tbb --- easybuild/easyconfigs/t/tbb/tbb-2021.4.0-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.4.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.4.0-GCCcore-11.2.0.eb index 1db10a3f74d..1fa7d8fd183 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-2021.4.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.4.0-GCCcore-11.2.0.eb @@ -18,6 +18,8 @@ builddependencies = [ ('CMake', '3.21.1'), ] +dependencies = [('hwloc', '2.5.0')] + sanity_check_paths = { 'files': ['lib/libtbb.%s' % SHLIB_EXT, 'lib/libtbbmalloc.%s' % SHLIB_EXT], 'dirs': ['lib', 'include', 'share'], From cd220db5de4735f9dd3aeea4db5b5e46c0e5515e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 19 Apr 2022 08:27:22 +0200 Subject: [PATCH 3472/9987] adding easyconfigs: RSeQC-4.0.0-foss-2021b.eb, bx-python-0.8.13-foss-2021b.eb --- .../bx-python/bx-python-0.8.13-foss-2021b.eb | 34 +++++++++++++ .../r/RSeQC/RSeQC-4.0.0-foss-2021b.eb | 51 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/b/bx-python/bx-python-0.8.13-foss-2021b.eb create mode 100644 easybuild/easyconfigs/r/RSeQC/RSeQC-4.0.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.13-foss-2021b.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.13-foss-2021b.eb new file mode 100644 index 00000000000..70cc43c9f9a --- /dev/null +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.13-foss-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'bx-python' +version = '0.8.13' + +homepage = 'https://github.com/bxlab/bx-python' +description = """The bx-python project is a Python library and associated set of scripts to allow for rapid + implementation of genome scale analyses.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('LZO', '2.10'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True + +exts_list = [ + ('python-lzo', '1.14', { + 'modulename': 'lzo', + 'preinstallopts': "export PREFIX=$EBROOTLZO && ", + 'checksums': ['83cbd8ecaae284735250e31d6c0ecc18ac08763fab2a8c910dc5a6910db6250c'], + }), + (name, version, { + 'modulename': 'bx', + 'checksums': ['5989170d13367e9f811014803bafdbcc893024d63e98b66f734511e4f9e90c7d'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-4.0.0-foss-2021b.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-4.0.0-foss-2021b.eb new file mode 100644 index 00000000000..d75ee7d4c6c --- /dev/null +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-4.0.0-foss-2021b.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'RSeQC' +version = '4.0.0' + +homepage = 'http://rseqc.sourceforge.net/' +description = """RSeQC provides a number of useful modules that can + comprehensively evaluate high throughput sequence data especially RNA-seq + data. Some basic modules quickly inspect sequence quality, nucleotide + composition bias, PCR bias and GC bias, while RNA-seq specific modules + evaluate sequencing saturation, mapped reads distribution, coverage + uniformity, strand specificity, transcript level RNA integrity etc.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5b44932bad669c6d9190c5c111d181e868fb40077ed20c16c0881f67fbcc669b'] + +dependencies = [ + ('Python', '3.9.6'), + ('Pysam', '0.17.0'), + ('bx-python', '0.8.13'), + ('pyBigWig', '0.3.18'), +] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +options = {'modulename': 'qcmodule'} + +sanity_check_paths = { + 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', 'bin/split_paired_bam.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + 'bam_stat.py --help', + 'overlay_bigwig.py --help', + 'split_bam.py --help', +] + +sanity_pip_check = True + +moduleclass = 'bio' From 258e74739d5ad3c7922958e1ae29ed549a70cccd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 19 Apr 2022 11:28:04 +0200 Subject: [PATCH 3473/9987] adding easyconfigs: ncdu-1.16-GCC-11.2.0.eb --- .../n/ncdu/ncdu-1.16-GCC-11.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdu/ncdu-1.16-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.16-GCC-11.2.0.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.16-GCC-11.2.0.eb new file mode 100644 index 00000000000..69cc9a48230 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.16-GCC-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ncdu' +version = '1.16' + +homepage = 'https://dev.yorhel.nl/ncdu' +description = """Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a + remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular + desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like + environment with ncurses installed.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://dev.yorhel.nl/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2b915752a183fae014b5e5b1f0a135b4b408de7488c716e325217c2513980fd4'] + +dependencies = [('ncurses', '6.2')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' From a76760a7e01749410f65daa74129e815867df1f8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 19 Apr 2022 11:51:43 +0200 Subject: [PATCH 3474/9987] adding easyconfigs: LocARNA-1.9.2.3-foss-2021b.eb --- .../l/LocARNA/LocARNA-1.9.2.3-foss-2021b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.3-foss-2021b.eb b/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.3-foss-2021b.eb new file mode 100644 index 00000000000..3ddcdbe1f71 --- /dev/null +++ b/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.3-foss-2021b.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'LocARNA' +version = '1.9.2.3' + +homepage = 'http://www.bioinf.uni-freiburg.de/Software/%(name)s/' +description = """LocARNA is a collection of alignment tools for the structural analysis of RNA. + Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for + your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for + analyzing sets of related RNAs without known common structure.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/s-will/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b28633ad2044e3a87173e255563100c223592d8b089789b77ee7011922c1565e'] + +dependencies = [('ViennaRNA', '2.5.0')] + +configopts = '--with-vrna=$EBROOTVIENNARNA' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [('%(namelower)s -h')] + +moduleclass = 'bio' From 4c20116dbb0fed213fff9c18be347fdf59c13ecd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 19 Apr 2022 12:42:49 +0200 Subject: [PATCH 3475/9987] Don't use template in homepage --- easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.3-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.3-foss-2021b.eb b/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.3-foss-2021b.eb index 3ddcdbe1f71..e4301751af4 100644 --- a/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.3-foss-2021b.eb +++ b/easybuild/easyconfigs/l/LocARNA/LocARNA-1.9.2.3-foss-2021b.eb @@ -5,7 +5,7 @@ easyblock = 'ConfigureMake' name = 'LocARNA' version = '1.9.2.3' -homepage = 'http://www.bioinf.uni-freiburg.de/Software/%(name)s/' +homepage = 'http://www.bioinf.uni-freiburg.de/Software/LocARNA/' description = """LocARNA is a collection of alignment tools for the structural analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for From 1e1ecdce00742550c40a47f8085ce42c326a4b9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2022 15:10:07 +0200 Subject: [PATCH 3476/9987] adding easyconfigs: TRF-4.09.1-GCCcore-11.2.0.eb --- .../t/TRF/TRF-4.09.1-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0d761a6a2e3 --- /dev/null +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'TRF' +version = '4.09.1' + +homepage = 'https://tandem.bu.edu/trf/trf.html' +description = """Tandem Repeats Finder: a program to analyze DNA sequences.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'Benson-Genomics-Lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/trf'], + 'dirs': [], +} + +sanity_check_commands = ["trf -v"] + +moduleclass = 'bio' From 29f95b5009d807c5a5386a322847fce25763e2e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2022 16:43:21 +0200 Subject: [PATCH 3477/9987] adding easyconfigs: VarScan-2.4.4-Java-11.eb --- .../v/VarScan/VarScan-2.4.4-Java-11.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/v/VarScan/VarScan-2.4.4-Java-11.eb diff --git a/easybuild/easyconfigs/v/VarScan/VarScan-2.4.4-Java-11.eb b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.4-Java-11.eb new file mode 100644 index 00000000000..093fff5f3b7 --- /dev/null +++ b/easybuild/easyconfigs/v/VarScan/VarScan-2.4.4-Java-11.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Adam Huffman, based on initial work by Jordi Blasco +# The Francis Crick Institute + +easyblock = 'JAR' + +name = 'VarScan' +version = '2.4.4' +versionsuffix = '-Java-%(javaver)s' + +github_account = "dkoboldt" +homepage = 'https://github.com/%(github_account)s/%(namelower)s' +description = """Variant calling and somatic mutation/CNV detection for next-generation sequencing data""" + +toolchain = SYSTEM + +sources = ['%(name)s.v%(version)s.jar'] +source_urls = ['https://github.com/%(github_account)s/%(namelower)s/raw/master'] +checksums = ['fb23b72ab676fb5a89bd02091c2b6c9aff210b96bee04d9dee6aef4d8b72814d'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +sanity_check_commands = ["java -jar $EBROOTVARSCAN/VarScan.v%(version)s.jar filter --help"] + +modloadmsg = "To execute VarScan run: java -jar $EBROOTVARSCAN/%(name)s.v%(version)s.jar" + +moduleclass = 'bio' From 39419d3888ef21349f5909515179d049a7509836 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2022 16:44:35 +0200 Subject: [PATCH 3478/9987] adding easyconfigs: NextGenMap-0.5.5-GCC-11.2.0.eb --- .../NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb b/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb new file mode 100644 index 00000000000..0a2f01375e9 --- /dev/null +++ b/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'NextGenMap' +version = '0.5.5' + +homepage = 'http://cibiv.github.io/%(name)s/' +description = """NextGenMap is a flexible highly sensitive short read mapping tool that + handles much higher mismatch rates than comparable algorithms while still outperforming + them in terms of runtime.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [' https://github.com/Cibiv/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c205e6cb312d2f495106435f10fb446e6fb073dd1474f4f74ab5980ba9803661'] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('BamTools', '2.5.2'), + ('zlib', '1.2.11'), +] + +skipsteps = ['install'] + +preconfigopts = "sed -i '/add_subdirectory.*\(bamtools\|zlib\).*/d' ../NextGenMap-%(version)s/CMakeLists.txt && " +preconfigopts += "sed -i 's/BamTools-static/bamtools/g' ../NextGenMap-%(version)s/{src,utils}/CMakeLists.txt && " +preconfigopts += "sed -i 's/zlibstatic/z/g' ../NextGenMap-%(version)s/{src,utils}/CMakeLists.txt && " + +buildopts = ' && cp -r ../%(name)s-%(version)s/bin/ngm-%(version)s/. %(installdir)s/bin/' + +# avoid hard overwriting of $LD_LIBRARY_PATH in ngm wrapper script +postinstallcmds = [r"sed -i 's/\(LD_LIBRARY_PATH=[^ ]*\)\"/\1:$LD_LIBRARY_PATH\"/g' %(installdir)s/bin/ngm"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ngm', 'ngm-core', 'ngm-log', 'ngm-utils', 'oclTool']], + 'dirs': ['bin/opencl'] +} + +sanity_check_commands = [ + "ngm --help 2>&1 | grep 'Usage:[ ]*ngm'", +] + +moduleclass = 'bio' From 43f9b0d9f6426b1ac740ecc2433ccb83e8cf4592 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Apr 2022 16:47:19 +0200 Subject: [PATCH 3479/9987] add missing dependencies for SlamDunk (fixes #15208) --- easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb index 8bcc3df3072..63485234dcb 100644 --- a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb @@ -18,6 +18,10 @@ dependencies = [ ('pybedtools', '0.8.2'), ('Pysam', '0.17.0'), ('Biopython', '1.79'), + ('SAMtools', '1.14'), + ('VarScan', '2.4.4', '-Java-11', True), + ('R', '4.1.2'), + ('NextGenMap', '0.5.5'), ] download_dep_fail = True From 0e657b261d291affae8d7fd6a80e55787efec88e Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 19 Apr 2022 18:06:50 +0200 Subject: [PATCH 3480/9987] Increase timeout in c10d_gloo tests --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 4 +++- ...Torch-1.11.0_increase_c10d_gloo_timeout.patch | 16 ++++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_c10d_gloo_timeout.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 8ef45e4a894..2f864983579 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -28,7 +28,8 @@ patches = [ 'PyTorch-1.11.0_skip_failing_ops_tests.patch', 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', 'PyTorch-1.11.0_fix_sharded_imports.patch', - 'PyTorch-1.11.0_increase_test_tolerances_TF32.patch' + 'PyTorch-1.11.0_increase_test_tolerances_TF32.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -47,6 +48,7 @@ checksums = [ '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch # PyTorch-1.11.0_increase_test_tolerances_TF32.patch '26e179a4f6f57e49209092612ae5f5cd8c03fd2ca84566ba0244eabefc3736ba', + '5ab458b0b7305493fda762644bd7243598d0c2a112e7e4c64716f96ef1fa5c42', # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_c10d_gloo_timeout.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_c10d_gloo_timeout.patch new file mode 100644 index 00000000000..96afd0c43e5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_c10d_gloo_timeout.patch @@ -0,0 +1,16 @@ +# Author: Caspar van Leeuwen +# Institute: SURF +# Increase timeout for c10d gloo process group operations since test_allreduce_coalesced_basics +# was failing with a timeout (see https://github.com/easybuilders/easybuild-easyconfigs/pull/15137) +diff -Nru pytorch/test/distributed/test_c10d_gloo.py pytorch_orig/test/distributed/test_c10d_gloo.py +--- pytorch/test/distributed/test_c10d_gloo.py 2022-04-19 15:27:48.540163735 +0200 ++++ pytorch_orig/test/distributed/test_c10d_gloo.py 2022-04-07 18:31:13.110755000 +0200 +@@ -216,7 +216,7 @@ + + def opts(self, threads=2): + opts = c10d.ProcessGroupGloo._Options() +- opts._timeout = 50.0 ++ opts._timeout = 5.0 + opts._devices = [create_device(interface=LOOPBACK)] + opts._threads = threads + return opts From 1a40278c1b7a41112040452a0cd13500e24d3608 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 19 Apr 2022 18:26:06 +0200 Subject: [PATCH 3481/9987] Fixed too long line --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 2f864983579..6413eec54e9 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -48,7 +48,8 @@ checksums = [ '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch # PyTorch-1.11.0_increase_test_tolerances_TF32.patch '26e179a4f6f57e49209092612ae5f5cd8c03fd2ca84566ba0244eabefc3736ba', - '5ab458b0b7305493fda762644bd7243598d0c2a112e7e4c64716f96ef1fa5c42', # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '5ab458b0b7305493fda762644bd7243598d0c2a112e7e4c64716f96ef1fa5c42', ] osdependencies = [OS_PKG_IBVERBS_DEV] From 2613d079f407170cac63338ed0b77c55990f929d Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 19 Apr 2022 20:15:07 +0200 Subject: [PATCH 3482/9987] adding easyconfigs: Albumentations-1.1.0-foss-2021b.eb --- .../Albumentations-1.1.0-foss-2021b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb new file mode 100644 index 00000000000..a9e22d209a5 --- /dev/null +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Albumentations' +version = '1.1.0' + +homepage = 'https://albumentations.ai' +description = "Albumentations is a Python library for fast and flexible image augmentations" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('CMake', '3.21.1'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('PyYAML', '5.4.1'), + ('scikit-image', '0.19.1'), + ('scikit-learn', '1.0.1'), + ('scikit-build', '0.11.1'), + #('OpenCV', '4.5.5', '-contrib'), +] + +use_pip = True + +exts_list = [ + ('opencv-contrib-python-headless', '4.5.5.64', { + 'modulename': 'cv2', + }), # temporary ext, testing only + ('qudida', '0.0.4', { + 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], + }), + ('albumentations', version, { + 'checksums': ['60b067b3093908bcc52adb2aa5d44f57ebdbb8ab57a47b0b42f3dc1d3b1ce824'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From 0832fac33ebcfd9b86933c88733327c4e3f0f679 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 19 Apr 2022 20:23:14 +0200 Subject: [PATCH 3483/9987] Added missing checksum --- .../a/Albumentations/Albumentations-1.1.0-foss-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb index a9e22d209a5..5efc30a2b30 100644 --- a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb @@ -16,7 +16,6 @@ dependencies = [ ('scikit-image', '0.19.1'), ('scikit-learn', '1.0.1'), ('scikit-build', '0.11.1'), - #('OpenCV', '4.5.5', '-contrib'), ] use_pip = True @@ -24,7 +23,8 @@ use_pip = True exts_list = [ ('opencv-contrib-python-headless', '4.5.5.64', { 'modulename': 'cv2', - }), # temporary ext, testing only + 'checksums': ['3ee8a5c9278543ffd0edc19db0b78ce9c7be8e2f20d2cb46e812c67e60bd8a88'], + }), ('qudida', '0.0.4', { 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], }), From 8d2ba87e253521ee45b13fa2763e14d0e8b2dfd8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 20 Apr 2022 09:22:40 +0200 Subject: [PATCH 3484/9987] Change Java version to 11 --- ....2.0-Java-16.eb => RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-11.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/r/RNA-SeQC/{RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb => RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-11.eb} (97%) diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-11.eb similarity index 97% rename from easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb rename to easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-11.eb index 91da70816d5..40c6ad78d8a 100644 --- a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-16.eb +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-11.eb @@ -24,7 +24,7 @@ builddependencies = [('binutils', '2.37')] dependencies = [ ('BWA', '0.7.17'), - ('Java', '16', '', True), + ('Java', '11', '', True), ] modloadmsg = "To execute RNA-SeQC run: java -jar $EBROOTRNAMINSEQC/%(name)s_v%(version)s.jar" From 0638e0084260e411595652cb96ca18c30479a1ee Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 20 Apr 2022 09:55:32 +0200 Subject: [PATCH 3485/9987] Patch was invalid, since I mixed up the original and patched dirs when creating the patch. Should be fixed now. --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../p/PyTorch/PyTorch-1.11.0_increase_c10d_gloo_timeout.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 6413eec54e9..f0844c88ea2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -49,7 +49,7 @@ checksums = [ # PyTorch-1.11.0_increase_test_tolerances_TF32.patch '26e179a4f6f57e49209092612ae5f5cd8c03fd2ca84566ba0244eabefc3736ba', # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch - '5ab458b0b7305493fda762644bd7243598d0c2a112e7e4c64716f96ef1fa5c42', + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_c10d_gloo_timeout.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_c10d_gloo_timeout.patch index 96afd0c43e5..15d6be2f463 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_c10d_gloo_timeout.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase_c10d_gloo_timeout.patch @@ -9,8 +9,8 @@ diff -Nru pytorch/test/distributed/test_c10d_gloo.py pytorch_orig/test/distribut def opts(self, threads=2): opts = c10d.ProcessGroupGloo._Options() -- opts._timeout = 50.0 -+ opts._timeout = 5.0 +- opts._timeout = 5.0 ++ opts._timeout = 50.0 opts._devices = [create_device(interface=LOOPBACK)] opts._threads = threads return opts From 8404b6f51ac9aa9027c7e46fcef716668daf3b3a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 20 Apr 2022 09:36:35 +0100 Subject: [PATCH 3486/9987] adding easyconfigs: SeqKit-2.2.0.eb --- .../easyconfigs/s/SeqKit/SeqKit-2.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeqKit/SeqKit-2.2.0.eb diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-2.2.0.eb b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.2.0.eb new file mode 100644 index 00000000000..92a42cbd16c --- /dev/null +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'GoPackage' + +name = 'SeqKit' +version = '2.2.0' + +homepage = 'https://bioinf.shenwei.me/seqkit/' +description = """SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/shenwei356/seqkit/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6e7e292532d78d54ac7aecb934f992c85d04b2dcb2d7a1141808bada0f5b13ba'] + +builddependencies = [ + ('Go', '1.17.6'), +] + +installopts = './%(namelower)s' + +sanity_check_commands = [ + "seqkit version", + "seqkit genautocomplete" +] + +moduleclass = 'bio' From 1fd25bcca8b645c2cad1df03c7d242da985d1a66 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 20 Apr 2022 10:13:45 +0100 Subject: [PATCH 3487/9987] util-linux added to deal with libuuid requirements --- .../c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb | 4 ++++ .../c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb index e962cbe341b..5cc5419fa3e 100644 --- a/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb @@ -29,6 +29,10 @@ builddependencies = [ ('CMake', '3.22.1'), ] +dependencies = [ + ('util-linux', '2.37'), +] + files_to_copy = [ (['libxg.a'], 'lib'), (['xgtest'], 'bin'), diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb index 44cb53ad27e..b468e316ad3 100644 --- a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb @@ -31,6 +31,10 @@ builddependencies = [ ('CMake', '3.22.1'), ] +dependencies = [ + ('util-linux', '2.37'), +] + # build demo # build static and shared libraries configopts = ["-DCROSSGUID_TESTS=ON", "-DBUILD_SHARED_LIBS=TRUE"] From 362ebbc87ac1cf06c6370f48be291719dc3466ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 20 Apr 2022 11:13:55 +0200 Subject: [PATCH 3488/9987] adding easyconfigs: HTSeq-0.11.3-foss-2021b.eb --- .../h/HTSeq/HTSeq-0.11.3-foss-2021b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2021b.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2021b.eb new file mode 100644 index 00000000000..a43094253e1 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.3-foss-2021b.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonPackage' + +name = 'HTSeq' +version = '0.11.3' + +homepage = 'https://github.com/simon-anders/htseq' +description = """HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] + +checksums = ['abd13b48021340fea783a9dff110534c19a306b54182501e1aa7b324d458b080'] + +builddependencies = [('SWIG', '4.0.2')] + +dependencies = [ + ('Python', '3.9.6'), + ('Pysam', '0.17.0'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'], +} + +sanity_check_commands = ['%(namelower)s-count --help'] + +sanity_pip_check = True + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' From c80214f32a8a8b06925f8c1c957ae87e23e9dcb1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 20 Apr 2022 11:34:06 +0200 Subject: [PATCH 3489/9987] adding easyconfigs: fumi_tools-0.18.2-GCC-11.2.0.eb --- .../fumi_tools-0.18.2-GCC-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-11.2.0.eb b/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..50353828879 --- /dev/null +++ b/easybuild/easyconfigs/f/fumi_tools/fumi_tools-0.18.2-GCC-11.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'fumi_tools' +version = '0.18.2' + +homepage = 'https://ccb-gitlab.cs.uni-saarland.de/tobias/fumi_tools' +description = """This tool is intended to deduplicate UMIs from single-end and paired-end + sequencing data. Reads are considered identical when their UMIs have the same sequence, + they have the same length and map at the same position.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://ccb-gitlab.cs.uni-saarland.de/tobias/%(name)s/uploads/bff8865d9eeaaa27849dd580aa2a9dd1/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3570890e232f4a1862541c08d5755f11a12cf8972e2ee7461adc270ba4a220f1'] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [ + ('Python', '3.9.6'), + ('pigz', '2.6'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ["%(name)s -h"] + +moduleclass = 'bio' From 7190f928c58311a334b4498714bee1cb05fa114b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 20 Apr 2022 11:55:50 +0200 Subject: [PATCH 3490/9987] adding easyconfigs: FASTX-Toolkit-0.0.14-GCC-11.2.0.eb --- .../FASTX-Toolkit-0.0.14-GCC-11.2.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.2.0.eb new file mode 100644 index 00000000000..5c21344e607 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.2.0.eb @@ -0,0 +1,63 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'Bundle' + +name = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +default_easyblock = 'ConfigureMake' + +components = [ + ('libgtextutils', '0.7', { + 'source_urls': ['https://github.com/agordon/libgtextutils/releases/download/%(version)s/'], + 'sources': [SOURCE_TAR_GZ], + 'patches': ['libgtextutils-%(version)s_fix-bool.patch'], + 'checksums': [ + '792e0ea3c96ffe3ad65617a104b7dc50684932bc96d2adab501c952fd65c3e4a', # libgtextutils-0.7.tar.gz + 'bb16a4fd86c2eb12215d8780b09f0898771a73e53889a015e2351f2d737c9a00', # libgtextutils-0.7_fix-bool.patch + ], + 'start_dir': 'libgtextutils-%(version)s', + }), + (name, version, { + 'source_urls': ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'], + 'sources': ['fastx_toolkit-%(version)s.tar.bz2'], + 'checksums': ['9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806'], + 'start_dir': 'fastx_toolkit-%(version)s', + 'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ", + 'configopts': 'CXXFLAGS="$CXXFLAGS -Wno-implicit-fallthrough"', + }), +] + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']] + + ['lib/libgtextutils.%s' % SHLIB_EXT, 'lib/libgtextutils.a'], + 'dirs': [] +} + +moduleclass = 'bio' From 4225b6433ad0a687d5a594a0c9b58bff23d75e0f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 20 Apr 2022 11:58:10 +0200 Subject: [PATCH 3491/9987] adding easyconfigs: fastq-tools-0.8.3-GCC-11.2.0.eb --- .../fastq-tools-0.8.3-GCC-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastq-tools/fastq-tools-0.8.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/f/fastq-tools/fastq-tools-0.8.3-GCC-11.2.0.eb b/easybuild/easyconfigs/f/fastq-tools/fastq-tools-0.8.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..636f79669bf --- /dev/null +++ b/easybuild/easyconfigs/f/fastq-tools/fastq-tools-0.8.3-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'fastq-tools' +version = '0.8.3' + +homepage = 'https://homes.cs.washington.edu/~dcjones/fastq-tools/' +description = """This package provides a number of small and efficient programs to perform + common tasks with high throughput sequencing data in the FASTQ format. All of the programs + work with typical FASTQ files as well as gzipped FASTQ files.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'dcjones' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = ['0cd7436e81129090e707f69695682df80623b06448d95df483e572c61ddf538e'] + +builddependencies = [('Autotools', '20210726')] + +dependencies = [ + ('PCRE', '8.45'), + ('zlib', '1.2.11'), +] + +# unsetting LIBS is needed because configure script can't handle it properly if it is already defined +preconfigopts = './autogen.sh && unset LIBS && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['fastq-grep', 'fastq-kmers', 'fastq-match', 'fastq-qscale', + 'fastq-qual', 'fastq-qualadj', 'fastq-sample', 'fastq-sort', + 'fastq-uniq']], + 'dirs': ['share/man/man1'], +} + +moduleclass = 'bio' From c2cf348c1f163aa0f40e5daf06fe2767cb5ae846 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 20 Apr 2022 14:15:33 +0200 Subject: [PATCH 3492/9987] adding easyconfigs: GCCcore-11.2.1.eb, GCC-11.2.1.eb, Bison-3.8.2-GCCcore-11.2.1.eb, binutils-2.38-GCCcore-11.2.1.eb, binutils-2.38.eb, flex-2.6.4-GCCcore-11.2.1.eb, help2man-1.49.2-GCCcore-11.2.1.eb, M4-1.4.19-GCCcore-11.2.1.eb, zlib-1.2.12-GCCcore-11.2.1.eb, zlib-1.2.12.eb and patches: zlib-1.2.12_fix-CC-logic-in-configure.patch --- .../b/Bison/Bison-3.8.2-GCCcore-11.2.1.eb | 28 ++++++++ .../binutils/binutils-2.38-GCCcore-11.2.1.eb | 31 +++++++++ .../easyconfigs/b/binutils/binutils-2.38.eb | 26 +++++++ .../f/flex/flex-2.6.4-GCCcore-11.2.1.eb | 34 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-11.2.1.eb | 22 ++++++ .../easyconfigs/g/GCCcore/GCCcore-11.2.1.eb | 68 +++++++++++++++++++ .../help2man-1.49.2-GCCcore-11.2.1.eb | 25 +++++++ .../m/M4/M4-1.4.19-GCCcore-11.2.1.eb | 29 ++++++++ .../z/zlib/zlib-1.2.12-GCCcore-11.2.1.eb | 30 ++++++++ easybuild/easyconfigs/z/zlib/zlib-1.2.12.eb | 36 ++++++++++ ...lib-1.2.12_fix-CC-logic-in-configure.patch | 43 ++++++++++++ 11 files changed, 372 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.2.1.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.2.1.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.38.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.1.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-11.2.1.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.1.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.2.1.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.1.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.2.1.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.12.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.12_fix-CC-logic-in-configure.patch diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.2.1.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.2.1.eb new file mode 100644 index 00000000000..8793b6c7bf8 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.2.1.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.1'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.38', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.2.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.2.1.eb new file mode 100644 index 00000000000..15bdd454cef --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.2.1.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.38' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '11.2.1'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b3f1dc5b17e75328f19bd88250bee2ef9f91fc8cbb7bd48bdb31390338636052'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.12'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.38.eb b/easybuild/easyconfigs/b/binutils/binutils-2.38.eb new file mode 100644 index 00000000000..19ac8f19011 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.38.eb @@ -0,0 +1,26 @@ +name = 'binutils' +version = '2.38' + +homepage = 'https://directory.fsf.org/project/binutils/' + +description = "binutils: GNU binary utilities" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b3f1dc5b17e75328f19bd88250bee2ef9f91fc8cbb7bd48bdb31390338636052'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.12'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.1.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.1.eb new file mode 100644 index 00000000000..a73f7805490 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.1.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.2'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.38', '', True), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-11.2.1.eb b/easybuild/easyconfigs/g/GCC/GCC-11.2.1.eb new file mode 100644 index 00000000000..8d84fc48162 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-11.2.1.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '11.2.1' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', '2.38', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.1.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.1.eb new file mode 100644 index 00000000000..f0b9a6f1ff8 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.1.eb @@ -0,0 +1,68 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '11.2.1' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + { + 'source_urls': ['https://gcc.gnu.org/pub/gcc/snapshots/11.3.0-RC-20220414/'], + 'filename': 'gcc-11.3.0-RC-20220414.tar.gz', + }, + # 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.1.0.tar.bz2', + 'mpc-1.2.1.tar.gz', + 'isl-0.24.tar.bz2', + 'newlib-4.1.0.tar.gz', + {'download_filename': 'd0524fb.tar.gz', 'filename': 'nvptx-tools-20210115.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', +] +checksums = [ + '85ab76df03ab566cd7f3471d3b37349163d0cf7ab12e8754290d9db6d2dab82f', # gcc-11.3.0-RC-20220414.tar.gz + 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 + 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 + '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz + 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 + 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz + '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch + '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.38'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.2.1.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.2.1.eb new file mode 100644 index 00000000000..847e0a72a99 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.2.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.2' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.1'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.38', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.1.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.1.eb new file mode 100644 index 00000000000..b49d3847843 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.1'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.38', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.2.1.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.2.1.eb new file mode 100644 index 00000000000..c7a6a244bee --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.2.1.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.12' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = [ + '91844808532e5ce316b3c010929493c0244f3d37593afd6de04f71821d5136d9', # zlib-1.2.12.tar.gz + 'f35eb05334a4f8d7b40b6c5610a6369f654863b5fa1a19c2507888f918025238', # zlib-1.2.12_fix-CC-logic-in-configure.patch +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.38', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12.eb new file mode 100644 index 00000000000..75f1815ef62 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.12' + +homepage = 'https://www.zlib.net/' + +description = """ + zlib is designed to be a free, general-purpose, legally unencumbered -- that + is, not covered by any patents -- lossless data-compression library for use + on virtually any computer hardware and operating system. +""" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = [ + '91844808532e5ce316b3c010929493c0244f3d37593afd6de04f71821d5136d9', # zlib-1.2.12.tar.gz + 'f35eb05334a4f8d7b40b6c5610a6369f654863b5fa1a19c2507888f918025238', # zlib-1.2.12_fix-CC-logic-in-configure.patch +] + +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid +# compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', + 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12_fix-CC-logic-in-configure.patch b/easybuild/easyconfigs/z/zlib/zlib-1.2.12_fix-CC-logic-in-configure.patch new file mode 100644 index 00000000000..f34c40445de --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12_fix-CC-logic-in-configure.patch @@ -0,0 +1,43 @@ +From 80d086357a55b94a13e43756cf3e131f25eef0e4 Mon Sep 17 00:00:00 2001 +From: Sam James +Date: Mon, 28 Mar 2022 08:40:45 +0100 +Subject: [PATCH] Fix CC logic in configure + +In https://github.com/madler/zlib/commit/e9a52aa129efe3834383e415580716a7c4027f8d, +the logic was changed to try check harder for GCC, but it dropped +the default setting of cc=${CC}. It was throwing away any pre-set CC value as +a result. + +The rest of the script then cascades down a bad path because it's convinced +it's not GCC or a GCC-like compiler. + +This led to e.g. misdetection of inability to build shared libs +for say, multilib cases (w/ CC being one thing from the environment being used +for one test (e.g. x86_64-unknown-linux-gnu-gcc -m32 and then 'cc' used for +shared libs (but missing "-m32"!)). Obviously just one example of how +the old logic could break. + +This restores the old default of 'CC' if nothing overrides it later +in configure. + +Bug: https://bugs.gentoo.org/836308 +Signed-off-by: Sam James +--- + configure | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/configure b/configure +index 52ff4a04e..3fa3e8618 100755 +--- a/configure ++++ b/configure +@@ -174,7 +174,10 @@ if test -z "$CC"; then + else + cc=${CROSS_PREFIX}cc + fi ++else ++ cc=${CC} + fi ++ + cflags=${CFLAGS-"-O3"} + # to force the asm version use: CFLAGS="-O3 -DASMV" ./configure + case "$cc" in From 677217959b41f123e09e78a968ff2d06fcc97643 Mon Sep 17 00:00:00 2001 From: Will Furnass Date: Wed, 20 Apr 2022 19:12:38 +0100 Subject: [PATCH 3493/9987] pkg-config-0.29.2 easyconfig: "find /usr" should not descend into other filesystems --- easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb index 18c253b8f94..6281f5a2f9d 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2.eb @@ -23,7 +23,7 @@ checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] tar_config_opts = True # add pkgconfig directories in the system to list of default search paths -preconfigopts = 'EB_SYS_PC_PATH=":$(find /usr -type d -name "pkgconfig" -printf %p: 2>/dev/null)";' +preconfigopts = 'EB_SYS_PC_PATH=":$(find /usr -xdev -type d -name "pkgconfig" -printf %p: 2>/dev/null)";' configopts = '--with-pc-path="%(installdir)s/lib/pkgconfig:%(installdir)s/share/pkgconfig${EB_SYS_PC_PATH%:}"' configopts += " --with-internal-glib" From 2543e90ee3a98842588286a8c53e499b6ab7e1e6 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 20 Apr 2022 21:08:07 +0200 Subject: [PATCH 3494/9987] Added OpenSSL to DCMTK package --- easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb index 24b265749d0..f7c16f218ab 100644 --- a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ] dependencies = [ + ('OpenSSL', '1.1', '', True), ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.6'), ('LibTIFF', '4.3.0'), From dbeda30127c4ee7ae97821044409e1b76161c2fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Apr 2022 12:25:33 +0200 Subject: [PATCH 3495/9987] tweak download instructions for ESOM 1.1 source file --- .../s/SCGid/SCGid-0.9b0-foss-2021b.eb | 24 ++++++++++--------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index f9e54ef7979..dbefc98c9f4 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -44,6 +44,18 @@ options = {'modulename': False} local_clams_commit = "e326c34307803b9ea8ffc975ddd9bd05643af931" +local_esom_download_instructions = """You need to manually provide the Databionics ESOM 'source' file. +Please follow these steps: +(1): Download the installer for ESOM version %(version)s from + https://sourceforge.net/projects/databionic-esom/files/databionic-esom/%(version)s/esom-%(version)s-installer.jar +(2): Run the installer, and follow through the installation process using the GUI: + java -jar esom-%(version)s-installer.jar +(3): Go to the installation directory where you installed ESOM %(version)s, and create a tarball: + tar cvzf esom-%(version)s.tar.gz * +(4): Move esom-%(version)s.tar.gz to the directory with the SCGid source files (in the EasyBuild sourcepath). +(5): Re-run EasyBuild to install this SCGid easyconfig file. +""" + exts_list = [ ('ClaMS-CLI', '31012020', { 'source_urls': ['https://github.com/amsesk/ClaMS-CLI-fork/archive'], @@ -54,17 +66,7 @@ exts_list = [ 'checksums': ['743397fc8308e363f127bd7e5165ac9d769c10305f6e33d9e408db8f343170db'], }), ('ESOM', '1.1', { - 'download_instructions': """ - You need to manually provide Databionics ESOM. Please, follow these steps: - (1): Go to https://sourceforge.net/projects/databionic-esom/files/databionic-esom/%(version)s/ and - download "esom-%(version)s-installer.jar" - (2): Run the file and follow through the installation process (ensure you have Java - installed to run the file) - (3): Open terminal in the folder where you have installed ESOM and create Tarball of - its contents (tar -czvf esom-%(version)s.tar.gz *) - (4): Paste the file created (esom-%(version)s.tar.gz) into the same folder where your easyconfig is - (5): Re-run the build. - """, + 'download_instructions': local_esom_download_instructions, 'source_tmpl': 'esom-%(version)s.tar.gz', 'checksums': [None] }), From 3c94146284a9b6a7f171089de2474defd36300ad Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 21 Apr 2022 11:48:16 +0100 Subject: [PATCH 3496/9987] adding easyconfigs: GTDB-Tk-2.0.0-foss-2021a.eb --- .../g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb new file mode 100644 index 00000000000..d265ec2ef75 --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'GTDB-Tk' +version = '2.0.0' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/g/gtdbtk'] +sources = ['gtdbtk-%(version)s.tar.gz'] +checksums = ['53496443d6fcca675c3f3078d76cef25c2040e894fd403b74397980578ddb815'] + +dependencies = [ + ('Python', '3.9.5'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.4.2'), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', True), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.61.2'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 4cf6ae51bfe1a7cd2d4881834933480cfee7ed28 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 21 Apr 2022 13:00:40 +0200 Subject: [PATCH 3497/9987] update to use final GCC 11.3.0 release --- ....2-GCCcore-11.2.1.eb => Bison-3.8.2-GCCcore-11.3.0.eb} | 2 +- ...-GCCcore-11.2.1.eb => binutils-2.38-GCCcore-11.3.0.eb} | 2 +- ...6.4-GCCcore-11.2.1.eb => flex-2.6.4-GCCcore-11.3.0.eb} | 2 +- .../easyconfigs/g/GCC/{GCC-11.2.1.eb => GCC-11.3.0.eb} | 2 +- .../g/GCCcore/{GCCcore-11.2.1.eb => GCCcore-11.3.0.eb} | 8 ++------ ...CCcore-11.2.1.eb => help2man-1.49.2-GCCcore-11.3.0.eb} | 2 +- ...4.19-GCCcore-11.2.1.eb => M4-1.4.19-GCCcore-11.3.0.eb} | 2 +- ...12-GCCcore-11.2.1.eb => zlib-1.2.12-GCCcore-11.3.0.eb} | 2 +- 8 files changed, 9 insertions(+), 13 deletions(-) rename easybuild/easyconfigs/b/Bison/{Bison-3.8.2-GCCcore-11.2.1.eb => Bison-3.8.2-GCCcore-11.3.0.eb} (93%) rename easybuild/easyconfigs/b/binutils/{binutils-2.38-GCCcore-11.2.1.eb => binutils-2.38-GCCcore-11.3.0.eb} (94%) rename easybuild/easyconfigs/f/flex/{flex-2.6.4-GCCcore-11.2.1.eb => flex-2.6.4-GCCcore-11.3.0.eb} (94%) rename easybuild/easyconfigs/g/GCC/{GCC-11.2.1.eb => GCC-11.3.0.eb} (97%) rename easybuild/easyconfigs/g/GCCcore/{GCCcore-11.2.1.eb => GCCcore-11.3.0.eb} (92%) rename easybuild/easyconfigs/h/help2man/{help2man-1.49.2-GCCcore-11.2.1.eb => help2man-1.49.2-GCCcore-11.3.0.eb} (91%) rename easybuild/easyconfigs/m/M4/{M4-1.4.19-GCCcore-11.2.1.eb => M4-1.4.19-GCCcore-11.3.0.eb} (94%) rename easybuild/easyconfigs/z/zlib/{zlib-1.2.12-GCCcore-11.2.1.eb => zlib-1.2.12-GCCcore-11.3.0.eb} (95%) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.2.1.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb similarity index 93% rename from easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.2.1.eb rename to easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb index 8793b6c7bf8..4ec9c1c877b 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.2.1.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb @@ -7,7 +7,7 @@ homepage = 'https://www.gnu.org/software/bison' description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" -toolchain = {'name': 'GCCcore', 'version': '11.2.1'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.2.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.3.0.eb similarity index 94% rename from easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.2.1.eb rename to easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.3.0.eb index 15bdd454cef..da7b3d38de5 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.2.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.3.0.eb @@ -4,7 +4,7 @@ version = '2.38' homepage = 'https://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'GCCcore', 'version': '11.2.1'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.1.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb similarity index 94% rename from easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.1.eb rename to easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb index a73f7805490..c0e17568f86 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.1.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb @@ -9,7 +9,7 @@ description = """ in text. """ -toolchain = {'name': 'GCCcore', 'version': '11.2.1'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] diff --git a/easybuild/easyconfigs/g/GCC/GCC-11.2.1.eb b/easybuild/easyconfigs/g/GCC/GCC-11.3.0.eb similarity index 97% rename from easybuild/easyconfigs/g/GCC/GCC-11.2.1.eb rename to easybuild/easyconfigs/g/GCC/GCC-11.3.0.eb index 8d84fc48162..57896063fac 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-11.2.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-11.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'GCC' -version = '11.2.1' +version = '11.3.0' homepage = 'https://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.1.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb similarity index 92% rename from easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.1.eb rename to easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb index f0b9a6f1ff8..608faf7241b 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.1.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'EB_GCC' name = 'GCCcore' -version = '11.2.1' +version = '11.3.0' homepage = 'https://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, @@ -21,11 +21,7 @@ source_urls = [ 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools ] sources = [ - { - 'source_urls': ['https://gcc.gnu.org/pub/gcc/snapshots/11.3.0-RC-20220414/'], - 'filename': 'gcc-11.3.0-RC-20220414.tar.gz', - }, - # 'gcc-%(version)s.tar.gz', + 'gcc-%(version)s.tar.gz', 'gmp-6.2.1.tar.bz2', 'mpfr-4.1.0.tar.bz2', 'mpc-1.2.1.tar.gz', diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.2.1.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.3.0.eb similarity index 91% rename from easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.2.1.eb rename to easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.3.0.eb index 847e0a72a99..26957da215e 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.2.1.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.3.0.eb @@ -6,7 +6,7 @@ version = '1.49.2' homepage = 'https://www.gnu.org/software/help2man/' description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" -toolchain = {'name': 'GCCcore', 'version': '11.2.1'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_XZ] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.1.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb similarity index 94% rename from easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.1.eb rename to easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb index b49d3847843..dfdd4df8d10 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.1.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb @@ -8,7 +8,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" -toolchain = {'name': 'GCCcore', 'version': '11.2.1'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.2.1.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb similarity index 95% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.2.1.eb rename to easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb index c7a6a244bee..31726b4af9d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.2.1.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb @@ -8,7 +8,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.""" -toolchain = {'name': 'GCCcore', 'version': '11.2.1'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} source_urls = ['https://zlib.net/fossils'] From da6caee47fbd83103f8c19f5fc38f9d6926f92ea Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 21 Apr 2022 12:02:51 +0100 Subject: [PATCH 3498/9987] add Mash as a dependency --- easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb index d265ec2ef75..3d85efa5db7 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb @@ -25,6 +25,7 @@ dependencies = [ ('pplacer', '1.1.alpha19', '', True), ('FastANI', '1.33'), ('FastTree', '2.1.11'), + ('Mash', '2.3'), ('tqdm', '4.61.2'), ] From 5f4a3cb99f3a8bb95a20f1f7ee191b6b47b9d261 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 20 Apr 2022 15:50:00 +0000 Subject: [PATCH 3499/9987] Remove pkg-config use from SeqLib configure patch There was a syntax error in the autoconf macro, which causes an error if pkg-config is available, and if not available simply causes configure to issue a warning and ignore it. Since the result is not used anyway, we can remove it. --- .../easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb | 2 +- .../easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-9.3.0.eb | 2 +- .../s/SeqLib/SeqLib-1.2.0_use-external-deps.patch | 9 --------- 4 files changed, 3 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb index 507c2fec11f..83b25b66487 100644 --- a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.2.0.eb @@ -21,7 +21,7 @@ checksums = [ '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz # SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch '9be9229bcf34db8e4bd1fd49614bb55d84c12df263ca7174980f7f4b1bd63da9', - '8a90edf72f95a52c61e4aed62a9a951bbd56f7c668dec326f2d3836f76b0f71d', # SeqLib-1.2.0_use-external-deps.patch + '413f0ad8e0963d8922205d31e0c361cfa98a10f93e7d3e0506e0bed539ec70eb', # SeqLib-1.2.0_use-external-deps.patch ] builddependencies = [('Autotools', '20200321')] diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-11.2.0.eb index f2c21abaf40..abbdd256e07 100644 --- a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-11.2.0.eb @@ -21,7 +21,7 @@ checksums = [ '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz # SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch '9be9229bcf34db8e4bd1fd49614bb55d84c12df263ca7174980f7f4b1bd63da9', - '8a90edf72f95a52c61e4aed62a9a951bbd56f7c668dec326f2d3836f76b0f71d', # SeqLib-1.2.0_use-external-deps.patch + '413f0ad8e0963d8922205d31e0c361cfa98a10f93e7d3e0506e0bed539ec70eb', # SeqLib-1.2.0_use-external-deps.patch ] builddependencies = [('Autotools', '20210726')] diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-9.3.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-9.3.0.eb index d8960aa8fe7..f437ba0bbb1 100644 --- a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-9.3.0.eb @@ -21,7 +21,7 @@ checksums = [ '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz # SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch '9be9229bcf34db8e4bd1fd49614bb55d84c12df263ca7174980f7f4b1bd63da9', - '8a90edf72f95a52c61e4aed62a9a951bbd56f7c668dec326f2d3836f76b0f71d', # SeqLib-1.2.0_use-external-deps.patch + '413f0ad8e0963d8922205d31e0c361cfa98a10f93e7d3e0506e0bed539ec70eb', # SeqLib-1.2.0_use-external-deps.patch ] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0_use-external-deps.patch b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0_use-external-deps.patch index 39b81d77a54..14958c2c5b7 100644 --- a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0_use-external-deps.patch +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0_use-external-deps.patch @@ -47,15 +47,6 @@ diff -Nru SeqLib-1.2.0/configure.ac SeqLib-1.2.0b/configure.ac # Check for headers AC_LANG([C++]) -@@ -32,6 +38,8 @@ - fail_on_warning="-Werror" - fi - -+PKG_CHECK_MODULES[[hts], [htslib]] -+ - # Set compiler flags. - AC_SUBST(AM_CXXFLAGS, "-g $fail_on_warning -std=c++11 -Wno-unknown-pragmas") - AC_SUBST(CXXFLAGS, "$CXXFLAGS") diff -Nru SeqLib-1.2.0/Makefile.am SeqLib-1.2.0b/Makefile.am --- SeqLib-1.2.0/Makefile.am 2021-05-10 16:49:50.000000000 +0100 +++ SeqLib-1.2.0b/Makefile.am 2021-05-12 17:22:39.000000000 +0100 From fa497800148289dacd58cff22e52247d9cf9a98b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 21 Apr 2022 14:07:22 +0200 Subject: [PATCH 3500/9987] update checksum --- easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb index 608faf7241b..c526d81322b 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb @@ -35,7 +35,7 @@ patches = [ 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', ] checksums = [ - '85ab76df03ab566cd7f3471d3b37349163d0cf7ab12e8754290d9db6d2dab82f', # gcc-11.3.0-RC-20220414.tar.gz + '98438e6cc7294298b474cf0da7655d9a8c8b796421bb0210531c294a950374ed', # gcc-11.3.0.tar.gz 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz From 8df9226129eebca62a790840e83274aa0df65de3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Apr 2022 16:44:56 +0200 Subject: [PATCH 3501/9987] {bio}[intel/2021b] GTDB-Tk v2.0.0, HMMER v3.3.2, FastANI v1.33, FastTree v2.1.11 w/ Python 3.9.6 --- .../FastANI-1.33-intel-compilers-2021.4.0.eb | 45 +++++++++++ .../FastTree-2.1.11-GCCcore-11.2.0.eb | 37 +++++++++ .../g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb | 43 ++++++++++ .../h/HMMER/HMMER-3.3.2-iimpi-2021b.eb | 78 +++++++++++++++++++ 4 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.33-intel-compilers-2021.4.0.eb create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.33-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..eee713c573b --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-intel-compilers-2021.4.0.eb @@ -0,0 +1,45 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'ConfigureMake' + +name = 'FastANI' +version = '1.33' + +homepage = "https://github.com/ParBLiSS/FastANI" +description = """FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean + nucleotide identity of orthologous gene pairs shared between two microbial + genomes. FastANI supports pairwise comparison of both complete and draft + genome assemblies.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] +sources = ['v%(version)s.zip'] +patches = ['FastANI-1.2-memcpy.patch'] +checksums = [ + 'fb392ffa3c7942091a06de05c56c8e250523723c39da65ae8f245e65e440a74b', # v1.33.zip + 'eebcf0b64c31ee360ca79136f644157064ac69747ed13cff70f5c9932c6bb0d5', # FastANI-1.2-memcpy.patch +] + +builddependencies = [('Autotools', '20210726')] + +dependencies = [ + ('GSL', '2.7'), + ('zlib', '1.2.11'), +] + +preconfigopts = 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/fastANI'], + 'dirs': [] +} + +sanity_check_commands = ["fastANI --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..51f3e343ef9 --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.37')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb new file mode 100644 index 00000000000..d02b7ea9c9c --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb @@ -0,0 +1,43 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'GTDB-Tk' +version = '2.0.0' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'intel', 'version': '2021b'} + +source_urls = ['https://pypi.io/packages/source/g/gtdbtk'] +sources = ['gtdbtk-%(version)s.tar.gz'] +checksums = ['53496443d6fcca675c3f3078d76cef25c2040e894fd403b74397980578ddb815'] + +dependencies = [ + ('Python', '3.9.6'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.4.3'), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', True), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('tqdm', '4.62.3'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2021b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2021b.eb new file mode 100644 index 00000000000..769e545364a --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-iimpi-2021b.eb @@ -0,0 +1,78 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69', # hmmer-3.3.2.tar.gz + '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d', # HMMER-3.3.2_fix_perl.patch +] + +builddependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0', '-minimal'), +] + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From 997f8688dd5968d83b876bd0fab9d9c11d2c407c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Apr 2022 18:10:55 +0200 Subject: [PATCH 3502/9987] add missing Mash dependency for GTDB-Tk 2.0.0 --- .../g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb | 1 + .../Mash/Mash-2.3-intel-compilers-2021.4.0.eb | 48 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mash/Mash-2.3-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb index d02b7ea9c9c..f1bc9b730fe 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb @@ -26,6 +26,7 @@ dependencies = [ ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.62.3'), + ('Mash', '2.3'), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..e11560a4409 --- /dev/null +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-intel-compilers-2021.4.0.eb @@ -0,0 +1,48 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v2.2 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'Mash' +version = '2.3' + +homepage = 'http://mash.readthedocs.org' +description = "Fast genome and metagenome distance estimation using MinHash" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/marbl/Mash/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Mash-2.2_fix-hardcoding.patch', + 'Mash-2.1_disable-memcpy-wrap.patch', + 'Mash-2.3_fix-GCC-11.patch', +] +checksums = [ + 'f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1', # v2.3.tar.gz + '0c7315af727a06f408ab3ca69da0860fc671aa870b448a41a509b1e6d7027db5', # Mash-2.2_fix-hardcoding.patch + '40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch + '47a55459d4e8c57949648e0f33f3ffc3529563db0efe60f495fdec046f48d94e', # Mash-2.3_fix-GCC-11.patch +] + +builddependencies = [('Autotools', '20210726')] +dependencies = [ + ('CapnProto', '0.9.1'), + ('GSL', '2.7'), + ('zlib', '1.2.11'), +] + +preconfigopts = "./bootstrap.sh && " +configopts = "--with-capnp=$EBROOTCAPNPROTO --with-gsl=$EBROOTGSL" + +sanity_check_paths = { + 'files': ['bin/mash', 'lib/libmash.a'], + 'dirs': ['include/mash'], +} + +sanity_check_commands = ['mash --version'] + +moduleclass = 'bio' From a2d5095030c2cc58d9111e85395ba90a64fcc377 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 21 Apr 2022 18:20:09 +0200 Subject: [PATCH 3503/9987] update nvptx to latest and GCC infrastructure mirror --- easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb index c526d81322b..ba49ac08fc3 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb @@ -15,7 +15,7 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies 'http://isl.gforge.inria.fr/', # original HTTP source for ISL 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools @@ -27,7 +27,7 @@ sources = [ 'mpc-1.2.1.tar.gz', 'isl-0.24.tar.bz2', 'newlib-4.1.0.tar.gz', - {'download_filename': 'd0524fb.tar.gz', 'filename': 'nvptx-tools-20210115.tar.gz'}, + {'download_filename': '7292758.tar.gz', 'filename': 'nvptx-tools-20220412.tar.gz'}, ] patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', @@ -41,7 +41,7 @@ checksums = [ '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz + '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080', # nvptx-tools-20220412.tar.gz '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch From e2d3ee81d582f718dd86de717711310f2a0e5463 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 21 Apr 2022 18:20:30 +0200 Subject: [PATCH 3504/9987] GCC: binutils is build with with system toolchain --- easybuild/easyconfigs/g/GCC/GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCC/GCC-11.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-11.3.0.eb index 57896063fac..ee32dbadf52 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-11.3.0.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM dependencies = [ ('GCCcore', version), - # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) ('binutils', '2.38', '', ('GCCcore', version)), ] From ed992984a756545bc333d054b0c27a2c013e3490 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 21 Apr 2022 18:22:58 +0200 Subject: [PATCH 3505/9987] add 2nd source URL for GCC --- easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb index ba49ac08fc3..a911f6cd513 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb @@ -11,6 +11,7 @@ toolchain = SYSTEM source_urls = [ 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC From 02e20534cbceca541cf41b9d0dbe05ef5e444002 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 21 Apr 2022 18:58:46 +0100 Subject: [PATCH 3506/9987] adding easyconfigs: YAXT-0.9.2.1-gompi-2021b.eb --- .../y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb new file mode 100644 index 00000000000..518cded4b86 --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb @@ -0,0 +1,35 @@ +# Updated to new URL and version 0.9.2.1 +# Note: the original tarball does not contain cksum.c and cksum.h +# so this local commit is being used +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.9.2.1' +local_commit = 'd48b290d' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.dkrz.de/dkrz-sw/yaxt/-/archive/%s' % local_commit] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['aa73057270e72aa0ab6f9d2fe2af03b80bd8b3411062ed2eadbbacbfc9f28021'] + +builddependencies = [ + ('Autotools', '20210726'), + ('M4', '1.4.19'), +] + +preconfigopts = 'autoreconf -i && ' +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' From c490d3500491b67d33e4f98e92b299742ae8cf8a Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 21 Apr 2022 20:59:17 +0200 Subject: [PATCH 3507/9987] Added requested changes --- .../a/Albumentations/Albumentations-1.1.0-foss-2021b.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb index 5efc30a2b30..be943b58d77 100644 --- a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb @@ -9,22 +9,19 @@ description = "Albumentations is a Python library for fast and flexible image au toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ - ('CMake', '3.21.1'), ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), ('PyYAML', '5.4.1'), ('scikit-image', '0.19.1'), ('scikit-learn', '1.0.1'), - ('scikit-build', '0.11.1'), + ('OpenCV', '4.5.5', '-contrib'), ] +preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && " + use_pip = True exts_list = [ - ('opencv-contrib-python-headless', '4.5.5.64', { - 'modulename': 'cv2', - 'checksums': ['3ee8a5c9278543ffd0edc19db0b78ce9c7be8e2f20d2cb46e812c67e60bd8a88'], - }), ('qudida', '0.0.4', { 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], }), From c2256e3ed1b91e0a2b384283ba22b05eecc7f7d3 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 21 Apr 2022 21:25:00 +0200 Subject: [PATCH 3508/9987] update source URL for isl in GCCcore --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-5.5.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-6.5.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-7.3.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-7.4.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-8.4.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb | 3 ++- 25 files changed, 50 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb index 757b0cd9eb8..23a101c3f9f 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index d4408b29aa0..d6d21047a9c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb index e34ef9c9972..a3826b1579c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index b6a3f957cab..0bdb99e8555 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb index 4946587aea8..3453620e9f0 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index d253c513a44..6e19891fcb4 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -17,7 +17,8 @@ source_urls = [ 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb index 8a57a97c052..21fac24fad2 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -17,7 +17,8 @@ source_urls = [ 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.5.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.5.0.eb index 926ce1fdeff..4d483888f09 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.5.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index e3852c98e80..6e725dfd473 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -16,9 +16,10 @@ source_urls = [ 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies 'http://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror 'https://ftp.gnu.org/gnu/gcc/gcc-%(version)s/', # Alternative GCC + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index 8a83c3b247d..e26311dea34 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -17,7 +17,8 @@ source_urls = [ 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb index dcc70c8436a..c9b568e3b7b 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.3.0.eb @@ -17,7 +17,8 @@ source_urls = [ 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb index 67069b60574..62cb3dac487 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.4.0.eb @@ -21,7 +21,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP (no HTTPS) mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL (https:// does not work here!) ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.5.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.5.0.eb index 53a05acc638..c11963512d7 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.5.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.5.0.eb @@ -22,7 +22,8 @@ source_urls = [ 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb index a4b046b22c5..e32ec68aca6 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb @@ -17,7 +17,8 @@ source_urls = [ 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb index b23891e03ef..6aa77192675 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.2.0.eb @@ -17,7 +17,8 @@ source_urls = [ 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.3.0.eb index d678689f563..237e121fc05 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.3.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.4.0.eb index 31499195016..e277b2e5c54 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.4.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'http://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'http://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb index c4d39070f95..13a5c03ec2f 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.1.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP (no HTTPS) mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL (https:// does not work here!) ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb index 9ade6ff683a..141cc3d6fae 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP (no HTTPS) mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL (https:// does not work here!) ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb index 37a04c23347..d61a2fae367 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.3.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.4.0.eb index b8fc3a2b366..5f2b82a3257 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-8.4.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb index 1c7ebccd0c2..549a8c7d14f 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.1.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb index 09a142d9b3b..fbb4d77d076 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.2.0.eb @@ -17,7 +17,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] sources = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb index 6b1c47aa3c3..b47467b1233 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb index c02024d4638..17c3c74be73 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.4.0.eb @@ -15,7 +15,8 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies - 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools From 87c3cb5491d52d246293284abcabc854c95f9ecf Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 21 Apr 2022 22:16:02 +0200 Subject: [PATCH 3509/9987] Added all requested changes (imgaug is added as an extension) --- .../a/Albumentations/Albumentations-1.1.0-foss-2021b.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb index be943b58d77..ee48f7fbb6f 100644 --- a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb @@ -25,6 +25,13 @@ exts_list = [ ('qudida', '0.0.4', { 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], }), + ('Shapely', '1.8.1', { + 'checksums': ['0956a3aced40c31a957a52aa1935467334926844a6776b469acb0760a5e6aba8'], + }), + ('imgaug', '0.4.0', { + 'preinstallopts': """sed -i 's|"opencv-python-headless",||g' setup.py && """, + 'checksums': ['46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7'], + }), ('albumentations', version, { 'checksums': ['60b067b3093908bcc52adb2aa5d44f57ebdbb8ab57a47b0b42f3dc1d3b1ce824'], }), From fcd0d900103ba806bb7b4e383de266a4e3d95022 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Axel=20Ros=C3=A9n?= Date: Fri, 22 Apr 2022 13:24:43 +0200 Subject: [PATCH 3510/9987] adding easyconfigs: texlive-20220321-GCC-11.2.0.eb --- .../t/texlive/texlive-20220321-GCC-11.2.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb new file mode 100644 index 00000000000..d249ac772bf --- /dev/null +++ b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb @@ -0,0 +1,63 @@ +# Based off the 2017 version by John Dey jfdey@fredhutch.org +# https://github.com/easybuilders/easybuild-easyconfigs/pull/5085 +easyblock = 'Tarball' + +name = 'texlive' +version = '20220321' + +homepage = 'https://tug.org' +description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript + text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a + PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to + be a representation of the final typeset output, and so can be easily edited and manipulated.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [ + 'ftp://tug.org/texlive/historic/2022/', + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2022/', +] +sources = [ + { + 'download_filename': 'install-tl-unx.tar.gz', + 'filename': 'install-tl-unx-%(version)s.tar.gz', + } +] +checksums = ['e67edec49df6b7c4a987a7d5a9b31bcf41258220f9ac841c7a836080cd334fb5'] + +dependencies = [ + ('X11', '20210802'), + ('libpng', '1.6.37'), + ('libGLU', '9.0.2'), + ('Perl', '5.34.0'), + ('HarfBuzz', '2.8.2'), + ('poppler', '22.01.0'), + ('cairo', '1.16.0'), + ('fontconfig', '2.13.94'), + ('zlib', '1.2.11'), + ('graphite2', '1.3.14'), +] + +postinstallcmds = [ + 'echo "TEXDIR %(installdir)s/" > %(installdir)s/texlive.profile && ' + 'echo "TEXMFLOCAL %(installdir)s/texmf-local" >> %(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' + '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' +] + +modextrapaths = { + 'PATH': 'bin/%(arch)s-linux', + 'INFOPATH': 'texmf-dist/doc/info', + 'MANPATH': 'texmf-dist/doc/man', +} +modextravars = { + 'TEXMFHOME': '%(installdir)s/texmf-dist' +} + +sanity_check_paths = { + 'files': ['bin/%(arch)s-linux/tex', 'bin/%(arch)s-linux/latex'], + 'dirs': ['bin/%(arch)s-linux', 'texmf-dist'], +} + +moduleclass = 'devel' From d88470ee5211c6d2f487cbac9b095b1182bdf357 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 22 Apr 2022 13:42:43 +0200 Subject: [PATCH 3511/9987] perl scripts in HH-suite need HHLIB set to the installation dir. --- .../easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb | 4 ++++ .../easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021a.eb | 4 ++++ .../easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb | 4 ++++ 3 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb index 231c60d49b8..3eae6fe8e46 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2020b.eb @@ -63,4 +63,8 @@ modextrapaths = { 'PERL5LIB': 'scripts', } +modextravars = { + 'HHLIB': '%(installdir)s', +} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021a.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021a.eb index c9dcd2ac6eb..8838f04e411 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021a.eb @@ -63,4 +63,8 @@ modextrapaths = { 'PERL5LIB': 'scripts', } +modextravars = { + 'HHLIB': '%(installdir)s', +} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb index e3d70a3e26a..5e469b0e3d1 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompic-2020b.eb @@ -63,4 +63,8 @@ modextrapaths = { 'PERL5LIB': 'scripts', } +modextravars = { + 'HHLIB': '%(installdir)s', +} + moduleclass = 'bio' From 0b48e536326ae1315e3bafd52b303dd02143965b Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 22 Apr 2022 12:47:55 +0100 Subject: [PATCH 3512/9987] Updated URL to correct repository, left the old URL as well, removed autoreconf as configure is provided in that tarball --- .../y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb | 16 +++++----------- 1 file changed, 5 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb index 518cded4b86..66bd1ebce80 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb @@ -1,13 +1,10 @@ # Updated to new URL and version 0.9.2.1 -# Note: the original tarball does not contain cksum.c and cksum.h -# so this local commit is being used # J. Sassmannshausen (Imperial College London/UK) easyblock = 'ConfigureMake' name = 'YAXT' version = '0.9.2.1' -local_commit = 'd48b290d' homepage = 'https://www.dkrz.de/redmine/projects/yaxt' description = "Yet Another eXchange Tool" @@ -15,16 +12,13 @@ description = "Yet Another eXchange Tool" toolchain = {'name': 'gompi', 'version': '2021b'} toolchainopts = {'usempi': True} -source_urls = ['https://gitlab.dkrz.de/dkrz-sw/yaxt/-/archive/%s' % local_commit] -sources = ['%(namelower)s-v%(version)s.tar.gz'] -checksums = ['aa73057270e72aa0ab6f9d2fe2af03b80bd8b3411062ed2eadbbacbfc9f28021'] - -builddependencies = [ - ('Autotools', '20210726'), - ('M4', '1.4.19'), +source_urls = [ + ('https://swprojects.dkrz.de/redmine/attachments/download/515/'), + ('https://www.dkrz.de/redmine/attachments/download/515/'), ] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cada1ecc479eaf088b8c95d9ae80122842843dd6af0a660ab6191fcb0da20a1e'] -preconfigopts = 'autoreconf -i && ' configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' sanity_check_paths = { From 6f8bea7b76c7d017ff457740e3ec3df635d18fb3 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 22 Apr 2022 12:49:54 +0100 Subject: [PATCH 3513/9987] URL updated to fallback as original URL for source code is broken right now --- easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb | 5 ++++- easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb | 5 ++++- easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb index 9d9730518a3..4b96a924b44 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb @@ -9,7 +9,10 @@ description = "Yet Another eXchange Tool" toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = ['https://www.dkrz.de/redmine/attachments/download/498/'] +source_urls = [ + ('https://swprojects.dkrz.de/redmine/attachments/download/498/'), + ('https://www.dkrz.de/redmine/attachments/download/498/'), +] sources = [SOURCELOWER_TAR_GZ] checksums = ['d3673e88c1cba3b77e0821393b94b5952d8ed7dc494305c8cf93e7ebec19483c'] diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb index 58474ef9a1a..4a627fa4564 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb @@ -9,7 +9,10 @@ description = "Yet Another eXchange Tool" toolchain = {'name': 'gompi', 'version': '2021a'} toolchainopts = {'usempi': True} -source_urls = ['https://www.dkrz.de/redmine/attachments/download/506/'] +source_urls = [ + ('https://swprojects.dkrz.de/redmine/attachments/download/506/'), + ('https://www.dkrz.de/redmine/attachments/download/506/'), +] sources = [SOURCELOWER_TAR_GZ] checksums = ['c87ec59e29b3e4965ce2f8e614bd7f1597012b89af0fda4242f2eef06460794c'] diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb index 4c68128c3c2..eb4dc9cd3c0 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb @@ -9,7 +9,10 @@ description = "Yet Another eXchange Tool" toolchain = {'name': 'iimpi', 'version': '2021b'} toolchainopts = {'usempi': True} -source_urls = ['https://www.dkrz.de/redmine/attachments/download/513/'] +source_urls = [ + ('https://swprojects.dkrz.de/redmine/attachments/download/513/'), + ('https://www.dkrz.de/redmine/attachments/download/513/'), +] sources = [SOURCELOWER_TAR_GZ] checksums = ['b6714e42483486d76db146732bac74bc500096c15c9efa411ece3e00172fc360'] From 0a3ee2004d267b0ae61b4a3d7f786e20a745c37d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2022 14:07:59 +0200 Subject: [PATCH 3514/9987] adding easyconfigs: TreeMix-1.13-GCC-11.2.0.eb --- .../t/TreeMix/TreeMix-1.13-GCC-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-11.2.0.eb b/easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-11.2.0.eb new file mode 100644 index 00000000000..7ec826dfcbd --- /dev/null +++ b/easybuild/easyconfigs/t/TreeMix/TreeMix-1.13-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'TreeMix' +version = '1.13' + +homepage = 'http://bitbucket.org/nygcresearch/treemix' +description = """TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a + set of populations.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://bitbucket.org/nygcresearch/treemix/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fe544f2daa13fd06b20c1a81aac728963ea5b66b75908916ca87ccd7f4cfa3d9'] + +dependencies = [ + ('GSL', '2.7'), + ('Boost', '1.77.0'), +] + +sanity_check_paths = { + 'files': ['bin/treemix'], + 'dirs': [], +} + +sanity_check_commands = ["treemix -h | grep 'TreeMix v. %(version)s'"] + +moduleclass = 'bio' From dae700bd757933ab71ae126d8ede74913444dde1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 22 Apr 2022 17:44:49 +0200 Subject: [PATCH 3515/9987] adding easyconfigs: SPOTPY-1.5.14-intel-2021b.eb --- .../s/SPOTPY/SPOTPY-1.5.14-intel-2021b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPOTPY/SPOTPY-1.5.14-intel-2021b.eb diff --git a/easybuild/easyconfigs/s/SPOTPY/SPOTPY-1.5.14-intel-2021b.eb b/easybuild/easyconfigs/s/SPOTPY/SPOTPY-1.5.14-intel-2021b.eb new file mode 100644 index 00000000000..66db6ca0aeb --- /dev/null +++ b/easybuild/easyconfigs/s/SPOTPY/SPOTPY-1.5.14-intel-2021b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SPOTPY' +version = '1.5.14' + +homepage = 'https://spotpy.readthedocs.io' +description = """SPOTPY is a Python framework that enables the use of Computational optimization techniques for +calibration, uncertainty and sensitivity analysis techniques of almost every (environmental-) model.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b59175fb50807b442b0d98ced7ae403778cc1cb4c2694039478fe32ea57d85c5'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' From 3c5f64e29d88cff6c0a0a6bc0678b4ced76802fd Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 22 Apr 2022 20:59:20 +0200 Subject: [PATCH 3516/9987] Made Albumentations use updated pre-existing easyconfig of imgaug --- .../Albumentations-1.1.0-foss-2021b.eb | 8 +---- .../i/imgaug/imgaug-0.4.0-foss-2021b.eb | 34 +++++++++++++++++++ .../Shapely/Shapely-1.8.1.post1-GCC-11.2.0.eb | 24 +++++++++++++ 3 files changed, 59 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-1.8.1.post1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb index ee48f7fbb6f..9070f94f1bf 100644 --- a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021b.eb @@ -15,6 +15,7 @@ dependencies = [ ('scikit-image', '0.19.1'), ('scikit-learn', '1.0.1'), ('OpenCV', '4.5.5', '-contrib'), + ('imgaug', '0.4.0'), ] preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && " @@ -25,13 +26,6 @@ exts_list = [ ('qudida', '0.0.4', { 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], }), - ('Shapely', '1.8.1', { - 'checksums': ['0956a3aced40c31a957a52aa1935467334926844a6776b469acb0760a5e6aba8'], - }), - ('imgaug', '0.4.0', { - 'preinstallopts': """sed -i 's|"opencv-python-headless",||g' setup.py && """, - 'checksums': ['46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7'], - }), ('albumentations', version, { 'checksums': ['60b067b3093908bcc52adb2aa5d44f57ebdbb8ab57a47b0b42f3dc1d3b1ce824'], }), diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b.eb new file mode 100644 index 00000000000..a90a2300914 --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b.eb @@ -0,0 +1,34 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.0' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('Pillow', '8.3.2'), + ('matplotlib', '3.4.3'), + ('scikit-image', '0.19.1'), + ('OpenCV', '4.5.5', '-contrib'), + ('Shapely', '1.8.1.post1'), + ('imageio', '2.13.5'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['imgaug-0.4.0_openvc_requirement.patch'] +checksums = [ + '46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7', # imgaug-0.4.0.tar.gz + '2ff0b66ba38fdcf5f267a3d0ad1dc2710fee3c2f8cd3d086c56ea538a2a9ffc8', # imgaug-0.4.0_openvc_requirement.patch +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8.1.post1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8.1.post1-GCC-11.2.0.eb new file mode 100644 index 00000000000..9bdd9805f11 --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8.1.post1-GCC-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '1.8.1.post1' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['93ff06ff05fbe2be843b93c7b1ad8292e56e665ba01b4708f75ae8a757972e9f'] + +dependencies = [ + ('Python', '3.9.6'), + ('GEOS', '3.9.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From 11d88eb5013acdf7a3ff937da03c35ca6af543d9 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Sat, 23 Apr 2022 17:29:49 +0200 Subject: [PATCH 3517/9987] adding easyconfigs: ToFu-1.5.0-intel-2020b-Python-3.8.6.eb, ToFu-1.5.0-foss-2020b-Python-3.8.6.eb --- .../ToFu-1.5.0-foss-2020b-Python-3.8.6.eb | 46 +++++++++++++++++++ .../ToFu-1.5.0-intel-2020b-Python-3.8.6.eb | 46 +++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b-Python-3.8.6.eb create mode 100644 easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..228c3c0c72a --- /dev/null +++ b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'ToFu' +version = '1.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ToFuProject/tofu' +description = """Tomography for Fusion.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +exts_list = [ + ('docutils', '0.18', { + 'checksums': ['c1d5dab2b11d16397406a282e53953fe495a46d69ae329f55aa98a5c4e3c5fbb'], + }), + ('Polygon3', '3.0.9.1', { + 'modulename': 'Polygon', + 'checksums': ['2ddf8d06975f728d5b40786136c82e5b9d38a846bce236b7e6587bbd6a5e9b49'], + }), + ('zope.interface', '5.4.0', { + 'checksums': ['5dba5f530fec3f0988d83b78cc591b58c0b6eb8431a85edd1569a0539a8a5a0e'], + }), + ('DateTime', '4.3', { + 'modulename': 'DateTime', + 'checksums': ['5cef605bab8259ff61281762cdf3290e459fbf0b4719951d5fab967d5f2ea0ea'], + }), + ('tofu', version, { + 'checksums': ['3ef4df7750b3e2d445f73f6e58cc3e3cbaeeda064246c86348b020c7f151f790'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import tofu.geom'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..5df09bdc775 --- /dev/null +++ b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b-Python-3.8.6.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'ToFu' +version = '1.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ToFuProject/tofu' +description = """Tomography for Fusion.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +exts_list = [ + ('docutils', '0.18', { + 'checksums': ['c1d5dab2b11d16397406a282e53953fe495a46d69ae329f55aa98a5c4e3c5fbb'], + }), + ('Polygon3', '3.0.9.1', { + 'modulename': 'Polygon', + 'checksums': ['2ddf8d06975f728d5b40786136c82e5b9d38a846bce236b7e6587bbd6a5e9b49'], + }), + ('zope.interface', '5.4.0', { + 'checksums': ['5dba5f530fec3f0988d83b78cc591b58c0b6eb8431a85edd1569a0539a8a5a0e'], + }), + ('DateTime', '4.3', { + 'modulename': 'DateTime', + 'checksums': ['5cef605bab8259ff61281762cdf3290e459fbf0b4719951d5fab967d5f2ea0ea'], + }), + ('tofu', version, { + 'checksums': ['3ef4df7750b3e2d445f73f6e58cc3e3cbaeeda064246c86348b020c7f151f790'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import tofu.geom'"] + +moduleclass = 'tools' From dc98f39e9592267ca1b4e5752c5b40310c6a2598 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Sat, 23 Apr 2022 18:55:01 +0200 Subject: [PATCH 3518/9987] Add missing makedepend --- .../makedepend-1.0.6-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..3295f02cc8a --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.6' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['845f6708fc850bf53f5b1d0fb4352c4feab3949f140b26f71b22faba354c3365'] + +builddependencies = [ + ('binutils', '2.35'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' From 28af5d588b1f251dc21db2b8c1fefa61239ff35b Mon Sep 17 00:00:00 2001 From: kosl Date: Sat, 23 Apr 2022 19:11:01 +0200 Subject: [PATCH 3519/9987] Update and rename ToFu-1.5.0-foss-2020b-Python-3.8.6.eb to ToFu-1.5.0-foss-2020b.eb --- ...1.5.0-foss-2020b-Python-3.8.6.eb => ToFu-1.5.0-foss-2020b.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/t/ToFu/{ToFu-1.5.0-foss-2020b-Python-3.8.6.eb => ToFu-1.5.0-foss-2020b.eb} (97%) diff --git a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb similarity index 97% rename from easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b-Python-3.8.6.eb rename to easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb index 228c3c0c72a..fdcf696edd7 100644 --- a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b-Python-3.8.6.eb +++ b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-foss-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonBundle' name = 'ToFu' version = '1.5.0' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/ToFuProject/tofu' description = """Tomography for Fusion.""" From 22ba74e6a53926d62deca6e6f3ac6746b24018de Mon Sep 17 00:00:00 2001 From: kosl Date: Sat, 23 Apr 2022 19:11:57 +0200 Subject: [PATCH 3520/9987] Update and rename ToFu-1.5.0-intel-2020b-Python-3.8.6.eb to ToFu-1.5.0-intel-2020b.eb --- ...5.0-intel-2020b-Python-3.8.6.eb => ToFu-1.5.0-intel-2020b.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/t/ToFu/{ToFu-1.5.0-intel-2020b-Python-3.8.6.eb => ToFu-1.5.0-intel-2020b.eb} (97%) diff --git a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb similarity index 97% rename from easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b-Python-3.8.6.eb rename to easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb index 5df09bdc775..1f32acaf35f 100644 --- a/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b-Python-3.8.6.eb +++ b/easybuild/easyconfigs/t/ToFu/ToFu-1.5.0-intel-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'PythonBundle' name = 'ToFu' version = '1.5.0' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/ToFuProject/tofu' description = """Tomography for Fusion.""" From 221965cb4873d5cf35addc62e80a020d33d0f09b Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Sat, 23 Apr 2022 19:30:53 +0200 Subject: [PATCH 3521/9987] Add missing g2clib and g2lib --- .../g/g2clib/g2clib-1.6.3-foss-2020b.eb | 24 +++++++++++++ .../g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-foss-2020b.eb create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-foss-2020b.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-foss-2020b.eb new file mode 100644 index 00000000000..f98c2dd2d50 --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-foss-2020b.eb @@ -0,0 +1,24 @@ +name = 'g2clib' +version = '1.6.3' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['83e4f2061b3d4a8bd431ba860dda8c5cf103b25f42d265b7b724b9acafad177c'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('JasPer', '2.0.24'), + ('libpng', '1.6.37'), +] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..eeb1ed2cd3c --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +name = 'g2lib' +version = '3.2.0' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = [ + '%(name)s-%(version)s_compilation.patch', + # '%(name)s-%(version)s_makefile.patch', + # '%(name)s-%(version)s-kind.patch', + # '%(name)s-1.4.0-with-JasPer-2.x.patch', +] +checksums = [ + '9d3866de32e13e80798bfb08dbbea9223f32cec3fce3c57b6838e76f27d5a1d3', # g2lib-3.2.0.tar + 'f85286a1c0dec16e4a9f0abb4517218e4c652080775e34a1806e3687e1277dbb', # g2lib-3.2.0_compilation.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('JasPer', '2.0.24'), + ('libpng', '1.6.37'), +] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 ' +buildopts += '-D__64BIT__" FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -I." FC=$FC CC=$CC' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' From 710e33ab58e6d3d25224507d6d128ccd53989236 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Sat, 23 Apr 2022 22:28:08 +0200 Subject: [PATCH 3522/9987] Add missing g2lib patch --- .../g/g2lib/g2lib-3.2.0_compilation.patch | 1145 +++++++++++++++++ 1 file changed, 1145 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_compilation.patch diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_compilation.patch b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_compilation.patch new file mode 100644 index 00000000000..dc37f945132 --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_compilation.patch @@ -0,0 +1,1145 @@ +diff -Nru g2lib-3.2.0-orig/addfield.f g2lib-3.2.0/addfield.f +--- g2lib-3.2.0-orig/addfield.f 2020-12-16 18:58:40.000000000 +0100 ++++ g2lib-3.2.0/addfield.f 2021-03-18 19:11:48.240496708 +0100 +@@ -264,7 +264,7 @@ + ! + if ( numcoord .ne. 0 ) then + call mkieee(coordlist,coordieee,numcoord) +- call g2_sbytesc(cgrib,coordieee,iofst,32,0,numcoord) ++ call g2_sbytesc(cgrib,int(coordieee),iofst,32,0,numcoord) + iofst=iofst+(32*numcoord) + endif + ! +@@ -311,12 +311,12 @@ + if (nsize .lt. minsize) nsize=minsize + allocate(cpack(nsize),stat=istat) + if (idrsnum.eq.0) then ! Simple Packing +- call simpack(pfld,ndpts,idrstmpl,cpack,lcpack) ++ call simpack(pfld(1),ndpts,idrstmpl,cpack,lcpack) + elseif (idrsnum.eq.2.or.idrsnum.eq.3) then ! Complex Packing + call cmplxpack(pfld,ndpts,idrsnum,idrstmpl,cpack,lcpack) + elseif (idrsnum.eq.50) then ! Sperical Harmonic Simple Packing + call simpack(pfld(2),ndpts-1,idrstmpl,cpack,lcpack) +- call mkieee(real(pfld(1)),re00,1) ! ensure RE(0,0) value is IEEE format ++ call mkieee([real(pfld(1))],[re00(1)],1) ! ensure RE(0,0) value is IEEE format + !call g2_gbytec(re00,idrstmpl(5),0,32) + ire00=transfer(re00,ire00) + idrstmpl(5)=ire00 +diff -Nru g2lib-3.2.0-orig/getfield.f g2lib-3.2.0/getfield.f +--- g2lib-3.2.0-orig/getfield.f 2020-12-16 18:58:40.000000000 +0100 ++++ g2lib-3.2.0/getfield.f 2021-03-18 19:26:45.559344377 +0100 +@@ -295,7 +295,7 @@ + call simunpack(cgrib(ipos+5),lensec-6,idrstmpl,ndpts-1, + & fld(2)) + ieee=idrstmpl(5) +- call rdieee(ieee,fld(1),1) ++ call rdieee(real([ieee]),[fld(1)],1) + have7=.true. + elseif (idrsnum.eq.40 .OR. idrsnum.eq.40000) then + call jpcunpack(cgrib(ipos+5),lensec-5,idrstmpl,ndpts,fld) +@@ -625,7 +625,7 @@ + ! + if ( numcoord .ne. 0 ) then + allocate (coordieee(numcoord)) +- call g2_gbytesc(cgrib,coordieee,iofst,32,0,numcoord) ++ call g2_gbytesc(cgrib,int(coordieee),iofst,32,0,numcoord) + call rdieee(coordieee,coordlist,numcoord) + deallocate (coordieee) + iofst=iofst+(32*numcoord) +diff -Nru g2lib-3.2.0-orig/getfield.f~ g2lib-3.2.0/getfield.f~ +--- g2lib-3.2.0-orig/getfield.f~ 1970-01-01 01:00:00.000000000 +0100 ++++ g2lib-3.2.0/getfield.f~ 2021-03-18 19:20:40.734837860 +0100 +@@ -0,0 +1,829 @@ ++ subroutine getfield(cgrib,lcgrib,ifldnum,igds,igdstmpl,igdslen, ++ & ideflist,idefnum,ipdsnum,ipdstmpl,ipdslen, ++ & coordlist,numcoord,ndpts,idrsnum,idrstmpl, ++ & idrslen,ibmap,bmap,fld,ierr) ++!$$$ SUBPROGRAM DOCUMENTATION BLOCK ++! . . . . ++! SUBPROGRAM: getfield ++! PRGMMR: Gilbert ORG: W/NP11 DATE: 2000-05-26 ++! ++! ABSTRACT: This subroutine returns the Grid Definition, Product Definition, ++! Bit-map ( if applicable ), and the unpacked data for a given data ++! field. Since there can be multiple data fields packed into a GRIB2 ++! message, the calling routine indicates which field is being requested ++! with the ifldnum argument. ++! ++! PROGRAM HISTORY LOG: ++! 2000-05-26 Gilbert ++! ++! USAGE: CALL getfield(cgrib,lcgrib,ifldnum,igds,igdstmpl,igdslen, ++! & ideflist,idefnum,ipdsnum,ipdstmpl,ipdslen, ++! & coordlist,numcoord,ndpts,idrsnum,idrstmpl, ++! & idrslen,ibmap,bmap,fld,ierr) ++! INPUT ARGUMENT LIST: ++! cgrib - Character array that contains the GRIB2 message ++! lcgrib - Length (in bytes) of GRIB message array cgrib. ++! ifldnum - Specifies which field in the GRIB2 message to return. ++! ++! OUTPUT ARGUMENT LIST: ++! igds - Contains information read from the appropriate GRIB Grid ++! Definition Section 3 for the field being returned. ++! Must be dimensioned >= 5. ++! igds(1)=Source of grid definition (see Code Table 3.0) ++! igds(2)=Number of grid points in the defined grid. ++! igds(3)=Number of octets needed for each ++! additional grid points definition. ++! Used to define number of ++! points in each row ( or column ) for ++! non-regular grids. ++! = 0, if using regular grid. ++! igds(4)=Interpretation of list for optional points ++! definition. (Code Table 3.11) ++! igds(5)=Grid Definition Template Number (Code Table 3.1) ++! igdstmpl - Contains the data values for the specified Grid Definition ++! Template ( NN=igds(5) ). Each element of this integer ++! array contains an entry (in the order specified) of Grid ++! Defintion Template 3.NN ++! A safe dimension for this array can be obtained in advance ++! from maxvals(2), which is returned from subroutine gribinfo. ++! igdslen - Number of elements in igdstmpl(). i.e. number of entries ++! in Grid Defintion Template 3.NN ( NN=igds(5) ). ++! ideflist - (Used if igds(3) .ne. 0) This array contains the ++! number of grid points contained in each row ( or column ). ++! (part of Section 3) ++! A safe dimension for this array can be obtained in advance ++! from maxvals(3), which is returned from subroutine gribinfo. ++! idefnum - (Used if igds(3) .ne. 0) The number of entries ++! in array ideflist. i.e. number of rows ( or columns ) ++! for which optional grid points are defined. ++! ipdsnum - Product Definition Template Number ( see Code Table 4.0) ++! ipdstmpl - Contains the data values for the specified Product Definition ++! Template ( N=ipdsnum ). Each element of this integer ++! array contains an entry (in the order specified) of Product ++! Defintion Template 4.N ++! A safe dimension for this array can be obtained in advance ++! from maxvals(4), which is returned from subroutine gribinfo. ++! ipdslen - Number of elements in ipdstmpl(). i.e. number of entries ++! in Product Defintion Template 4.N ( N=ipdsnum ). ++! coordlist- Array containg floating point values intended to document ++! the vertical discretisation associated to model data ++! on hybrid coordinate vertical levels. (part of Section 4) ++! The dimension of this array can be obtained in advance ++! from maxvals(5), which is returned from subroutine gribinfo. ++! numcoord - number of values in array coordlist. ++! ndpts - Number of data points unpacked and returned. ++! idrsnum - Data Representation Template Number ( see Code Table 5.0) ++! idrstmpl - Contains the data values for the specified Data Representation ++! Template ( N=idrsnum ). Each element of this integer ++! array contains an entry (in the order specified) of Product ++! Defintion Template 5.N ++! A safe dimension for this array can be obtained in advance ++! from maxvals(6), which is returned from subroutine gribinfo. ++! idrslen - Number of elements in idrstmpl(). i.e. number of entries ++! in Data Representation Template 5.N ( N=idrsnum ). ++! ibmap - Bitmap indicator ( see Code Table 6.0 ) ++! 0 = bitmap applies and is included in Section 6. ++! 1-253 = Predefined bitmap applies ++! 254 = Previously defined bitmap applies to this field ++! 255 = Bit map does not apply to this product. ++! bmap() - Logical*1 array containing decoded bitmap. ( if ibmap=0 ) ++! The dimension of this array can be obtained in advance ++! from maxvals(7), which is returned from subroutine gribinfo. ++! fld() - Array of ndpts unpacked data points. ++! A safe dimension for this array can be obtained in advance ++! from maxvals(7), which is returned from subroutine gribinfo. ++! ierr - Error return code. ++! 0 = no error ++! 1 = Beginning characters "GRIB" not found. ++! 2 = GRIB message is not Edition 2. ++! 3 = The data field request number was not positive. ++! 4 = End string "7777" found, but not where expected. ++! 6 = GRIB message did not contain the requested number of ++! data fields. ++! 7 = End string "7777" not found at end of message. ++! 9 = Data Representation Template 5.NN not yet implemented. ++! 10 = Error unpacking Section 3. ++! 11 = Error unpacking Section 4. ++! 12 = Error unpacking Section 5. ++! 13 = Error unpacking Section 6. ++! 14 = Error unpacking Section 7. ++! ++! REMARKS: Note that subroutine gribinfo can be used to first determine ++! how many data fields exist in a given GRIB message. ++! ++! ATTRIBUTES: ++! LANGUAGE: Fortran 90 ++! MACHINE: IBM SP ++! ++!$$$ ++ ++ character(len=1),intent(in) :: cgrib(lcgrib) ++ integer,intent(in) :: lcgrib,ifldnum ++ integer,intent(out) :: igds(*),igdstmpl(*),ideflist(*) ++ integer,intent(out) :: ipdsnum,ipdstmpl(*) ++ integer,intent(out) :: idrsnum,idrstmpl(*) ++ integer,intent(out) :: ndpts,ibmap,idefnum,numcoord ++ integer,intent(out) :: ierr ++ logical*1,intent(out) :: bmap(*) ++ real,intent(out) :: fld(*),coordlist(*) ++ ++ character(len=4),parameter :: grib='GRIB',c7777='7777' ++ character(len=4) :: ctemp ++ integer:: listsec0(2) ++ integer iofst,ibeg,istart ++ integer(4) :: ieee ++ logical have3,have4,have5,have6,have7 ++ ++ have3=.false. ++ have4=.false. ++ have5=.false. ++ have6=.false. ++ have7=.false. ++ ierr=0 ++ numfld=0 ++! ++! Check for valid request number ++! ++ if (ifldnum.le.0) then ++ print *,'getfield: Request for field number must be positive.' ++ ierr=3 ++ return ++ endif ++! ++! Check for beginning of GRIB message in the first 100 bytes ++! ++ istart=0 ++ do j=1,100 ++ ctemp=cgrib(j)//cgrib(j+1)//cgrib(j+2)//cgrib(j+3) ++ if (ctemp.eq.grib ) then ++ istart=j ++ exit ++ endif ++ enddo ++ if (istart.eq.0) then ++ print *,'getfield: Beginning characters GRIB not found.' ++ ierr=1 ++ return ++ endif ++! ++! Unpack Section 0 - Indicator Section ++! ++ iofst=8*(istart+5) ++ call g2_gbytec(cgrib,listsec0(1),iofst,8) ! Discipline ++ iofst=iofst+8 ++ call g2_gbytec(cgrib,listsec0(2),iofst,8) ! GRIB edition number ++ iofst=iofst+8 ++ iofst=iofst+32 ++ call g2_gbytec(cgrib,lengrib,iofst,32) ! Length of GRIB message ++ iofst=iofst+32 ++ lensec0=16 ++ ipos=istart+lensec0 ++! ++! Currently handles only GRIB Edition 2. ++! ++ if (listsec0(2).ne.2) then ++ print *,'getfield: can only decode GRIB edition 2.' ++ ierr=2 ++ return ++ endif ++! ++! Loop through the remaining sections keeping track of the ++! length of each. Also keep the latest Grid Definition Section info. ++! Unpack the requested field number. ++! ++ do ++ ! Check to see if we are at end of GRIB message ++ ctemp=cgrib(ipos)//cgrib(ipos+1)//cgrib(ipos+2)//cgrib(ipos+3) ++ if (ctemp.eq.c7777 ) then ++ ipos=ipos+4 ++ ! If end of GRIB message not where expected, issue error ++ if (ipos.ne.(istart+lengrib)) then ++ print *,'getfield: "7777" found, but not where expected.' ++ ierr=4 ++ return ++ endif ++ exit ++ endif ++ ! Get length of Section and Section number ++ iofst=(ipos-1)*8 ++ call g2_gbytec(cgrib,lensec,iofst,32) ! Get Length of Section ++ iofst=iofst+32 ++ call g2_gbytec(cgrib,isecnum,iofst,8) ! Get Section number ++ iofst=iofst+8 ++ !print *,' lensec= ',lensec,' secnum= ',isecnum ++ ! ++ ! If found Section 3, unpack the GDS info using the ++ ! appropriate template. Save in case this is the latest ++ ! grid before the requested field. ++ ! ++ if (isecnum.eq.3) then ++ iofst=iofst-40 ! reset offset to beginning of section ++ call unpack3(cgrib,lcgrib,iofst,igds,igdstmpl,igdslen, ++ & ideflist,idefnum,jerr) ++ if (jerr.eq.0) then ++ have3=.true. ++ else ++ ierr=10 ++ return ++ endif ++ endif ++ ! ++ ! If found Section 4, check to see if this field is the ++ ! one requested. ++ ! ++ if (isecnum.eq.4) then ++ numfld=numfld+1 ++ if (numfld.eq.ifldnum) then ++ iofst=iofst-40 ! reset offset to beginning of section ++ call unpack4(cgrib,lcgrib,iofst,ipdsnum,ipdstmpl,ipdslen, ++ & coordlist,numcoord,jerr) ++ if (jerr.eq.0) then ++ have4=.true. ++ else ++ ierr=11 ++ return ++ endif ++ endif ++ endif ++ ! ++ ! If found Section 5, check to see if this field is the ++ ! one requested. ++ ! ++ if ((isecnum.eq.5).and.(numfld.eq.ifldnum)) then ++ iofst=iofst-40 ! reset offset to beginning of section ++ call unpack5(cgrib,lcgrib,iofst,ndpts,idrsnum,idrstmpl, ++ & idrslen,jerr) ++ if (jerr.eq.0) then ++ have5=.true. ++ else ++ ierr=12 ++ return ++ endif ++ endif ++ ! ++ ! If found Section 6, Unpack bitmap. ++ ! Save in case this is the latest ++ ! bitmap before the requested field. ++ ! ++ if (isecnum.eq.6) then ++ iofst=iofst-40 ! reset offset to beginning of section ++ call unpack6(cgrib,lcgrib,iofst,igds(2),ibmap,bmap,jerr) ++ if (jerr.eq.0) then ++ have6=.true. ++ else ++ ierr=13 ++ return ++ endif ++ endif ++ ! ++ ! If found Section 7, check to see if this field is the ++ ! one requested. ++ ! ++ if ((isecnum.eq.7).and.(numfld.eq.ifldnum)) then ++ if (idrsnum.eq.0) then ++ call simunpack(cgrib(ipos+5),lensec-6,idrstmpl,ndpts,fld) ++ have7=.true. ++ elseif (idrsnum.eq.2.or.idrsnum.eq.3) then ++ call comunpack(cgrib(ipos+5),lensec-6,lensec,idrsnum, ++ & idrstmpl,ndpts,fld,ier) ++ if ( ier .ne. 0 ) then ++ ierr=14 ++ return ++ endif ++ have7=.true. ++ elseif (idrsnum.eq.50) then ++ call simunpack(cgrib(ipos+5),lensec-6,idrstmpl,ndpts-1, ++ & fld(2)) ++ ieee=idrstmpl(5) ++ call rdieee([ieee],[fld(1)],1) ++ have7=.true. ++ elseif (idrsnum.eq.40 .OR. idrsnum.eq.40000) then ++ call jpcunpack(cgrib(ipos+5),lensec-5,idrstmpl,ndpts,fld) ++ have7=.true. ++ elseif (idrsnum.eq.41 .OR. idrsnum.eq.40010) then ++ call pngunpack(cgrib(ipos+5),lensec-5,idrstmpl,ndpts,fld) ++ have7=.true. ++ else ++ print *,'getfield: Data Representation Template ',idrsnum, ++ & ' not yet implemented.' ++ ierr=9 ++ return ++ endif ++ endif ++ ! ++ ! Check to see if we read pass the end of the GRIB ++ ! message and missed the terminator string '7777'. ++ ! ++ ipos=ipos+lensec ! Update beginning of section pointer ++ if (ipos.gt.(istart+lengrib)) then ++ print *,'getfield: "7777" not found at end of GRIB message.' ++ ierr=7 ++ return ++ endif ++ ++ if (have3.and.have4.and.have5.and.have6.and.have7) return ++ ++ enddo ++ ++! ++! If exited from above loop, the end of the GRIB message was reached ++! before the requested field was found. ++! ++ print *,'getfield: GRIB message contained ',numlocal, ++ & ' different fields.' ++ print *,'getfield: The request was for the ',ifldnum, ++ & ' field.' ++ ierr=6 ++ ++ return ++ end ++ ++ ++ subroutine unpack3(cgrib,lcgrib,iofst,igds,igdstmpl, ++ & mapgridlen,ideflist,idefnum,ierr) ++!$$$ SUBPROGRAM DOCUMENTATION BLOCK ++! . . . . ++! SUBPROGRAM: unpack3 ++! PRGMMR: Gilbert ORG: W/NP11 DATE: 2000-05-26 ++! ++! ABSTRACT: This subroutine unpacks Section 3 (Grid Definition Section) ++! starting at octet 6 of that Section. ++! ++! PROGRAM HISTORY LOG: ++! 2000-05-26 Gilbert ++! ++! USAGE: CALL unpack3(cgrib,lcgrib,lensec,iofst,igds,igdstmpl, ++! & mapgridlen,ideflist,idefnum,ierr) ++! INPUT ARGUMENT LIST: ++! cgrib - Character array that contains the GRIB2 message ++! lcgrib - Length (in bytes) of GRIB message array cgrib. ++! iofst - Bit offset of the beginning of Section 3. ++! ++! OUTPUT ARGUMENT LIST: ++! iofst - Bit offset at the end of Section 3, returned. ++! igds - Contains information read from the appropriate GRIB Grid ++! Definition Section 3 for the field being returned. ++! Must be dimensioned >= 5. ++! igds(1)=Source of grid definition (see Code Table 3.0) ++! igds(2)=Number of grid points in the defined grid. ++! igds(3)=Number of octets needed for each ++! additional grid points definition. ++! Used to define number of ++! points in each row ( or column ) for ++! non-regular grids. ++! = 0, if using regular grid. ++! igds(4)=Interpretation of list for optional points ++! definition. (Code Table 3.11) ++! igds(5)=Grid Definition Template Number (Code Table 3.1) ++! igdstmpl - Contains the data values for the specified Grid Definition ++! Template ( NN=igds(5) ). Each element of this integer ++! array contains an entry (in the order specified) of Grid ++! Defintion Template 3.NN ++! mapgridlen- Number of elements in igdstmpl(). i.e. number of entries ++! in Grid Defintion Template 3.NN ( NN=igds(5) ). ++! ideflist - (Used if igds(3) .ne. 0) This array contains the ++! number of grid points contained in each row ( or column ). ++! (part of Section 3) ++! idefnum - (Used if igds(3) .ne. 0) The number of entries ++! in array ideflist. i.e. number of rows ( or columns ) ++! for which optional grid points are defined. ++! ierr - Error return code. ++! 0 = no error ++! 5 = "GRIB" message contains an undefined Grid Definition ++! Template. ++! ++! REMARKS: Uses Fortran 90 module gridtemplates. ++! ++! ATTRIBUTES: ++! LANGUAGE: Fortran 90 ++! MACHINE: IBM SP ++! ++!$$$ ++ ++ use gridtemplates ++ ++ character(len=1),intent(in) :: cgrib(lcgrib) ++ integer,intent(in) :: lcgrib ++ integer,intent(inout) :: iofst ++ integer,intent(out) :: igds(*),igdstmpl(*),ideflist(*) ++ integer,intent(out) :: ierr,idefnum ++ ++ integer,allocatable :: mapgrid(:) ++ integer :: mapgridlen,ibyttem ++ logical needext ++ ++ ierr=0 ++ ++ call g2_gbytec(cgrib,lensec,iofst,32) ! Get Length of Section ++ iofst=iofst+32 ++ iofst=iofst+8 ! skip section number ++ ++ call g2_gbytec(cgrib,igds(1),iofst,8) ! Get source of Grid def. ++ iofst=iofst+8 ++ call g2_gbytec(cgrib,igds(2),iofst,32) ! Get number of grid pts. ++ iofst=iofst+32 ++ call g2_gbytec(cgrib,igds(3),iofst,8) ! Get num octets for opt. list ++ iofst=iofst+8 ++ call g2_gbytec(cgrib,igds(4),iofst,8) ! Get interpret. for opt. list ++ iofst=iofst+8 ++ call g2_gbytec(cgrib,igds(5),iofst,16) ! Get Grid Def Template num. ++ iofst=iofst+16 ++ if (igds(1).eq.0) then ++! if (igds(1).eq.0.OR.igds(1).eq.255) then ! FOR ECMWF TEST ONLY ++ allocate(mapgrid(lensec)) ++ ! Get Grid Definition Template ++ call getgridtemplate(igds(5),mapgridlen,mapgrid,needext, ++ & iret) ++ if (iret.ne.0) then ++ ierr=5 ++ return ++ endif ++ else ++! igdstmpl=-1 ++ mapgridlen=0 ++ needext=.false. ++ endif ++ ! ++ ! Unpack each value into array igdstmpl from the ++ ! the appropriate number of octets, which are specified in ++ ! corresponding entries in array mapgrid. ++ ! ++ ibyttem=0 ++ do i=1,mapgridlen ++ nbits=iabs(mapgrid(i))*8 ++ if ( mapgrid(i).ge.0 ) then ++ call g2_gbytec(cgrib,igdstmpl(i),iofst,nbits) ++ else ++ call g2_gbytec(cgrib,isign,iofst,1) ++ call g2_gbytec(cgrib,igdstmpl(i),iofst+1,nbits-1) ++ if (isign.eq.1) igdstmpl(i)=-igdstmpl(i) ++ endif ++ iofst=iofst+nbits ++ ibyttem=ibyttem+iabs(mapgrid(i)) ++ enddo ++ ! ++ ! Check to see if the Grid Definition Template needs to be ++ ! extended. ++ ! The number of values in a specific template may vary ++ ! depending on data specified in the "static" part of the ++ ! template. ++ ! ++ if ( needext ) then ++ call extgridtemplate(igds(5),igdstmpl,newmapgridlen,mapgrid) ++ ! Unpack the rest of the Grid Definition Template ++ do i=mapgridlen+1,newmapgridlen ++ nbits=iabs(mapgrid(i))*8 ++ if ( mapgrid(i).ge.0 ) then ++ call g2_gbytec(cgrib,igdstmpl(i),iofst,nbits) ++ else ++ call g2_gbytec(cgrib,isign,iofst,1) ++ call g2_gbytec(cgrib,igdstmpl(i),iofst+1,nbits-1) ++ if (isign.eq.1) igdstmpl(i)=-igdstmpl(i) ++ endif ++ iofst=iofst+nbits ++ ibyttem=ibyttem+iabs(mapgrid(i)) ++ enddo ++ mapgridlen=newmapgridlen ++ endif ++ ! ++ ! Unpack optional list of numbers defining number of points ++ ! in each row or column, if included. This is used for non regular ++ ! grids. ++ ! ++ if ( igds(3).ne.0 ) then ++ nbits=igds(3)*8 ++ idefnum=(lensec-14-ibyttem)/igds(3) ++ call g2_gbytesc(cgrib,ideflist,iofst,nbits,0,idefnum) ++ iofst=iofst+(nbits*idefnum) ++ else ++ idefnum=0 ++ endif ++ if( allocated(mapgrid) ) deallocate(mapgrid) ++ return ! End of Section 3 processing ++ end ++ ++ ++ subroutine unpack4(cgrib,lcgrib,iofst,ipdsnum,ipdstmpl,mappdslen, ++ & coordlist,numcoord,ierr) ++!$$$ SUBPROGRAM DOCUMENTATION BLOCK ++! . . . . ++! SUBPROGRAM: unpack4 ++! PRGMMR: Gilbert ORG: W/NP11 DATE: 2000-05-26 ++! ++! ABSTRACT: This subroutine unpacks Section 4 (Product Definition Section) ++! starting at octet 6 of that Section. ++! ++! PROGRAM HISTORY LOG: ++! 2000-05-26 Gilbert ++! ++! USAGE: CALL unpack4(cgrib,lcgrib,iofst,ipdsnum,ipdstmpl,mappdslen, ++! & coordlist,numcoord,ierr) ++! INPUT ARGUMENT LIST: ++! cgrib - Character array that contains the GRIB2 message ++! lcgrib - Length (in bytes) of GRIB message array cgrib. ++! iofst - Bit offset of the beginning of Section 4. ++! ++! OUTPUT ARGUMENT LIST: ++! iofst - Bit offset of the end of Section 4, returned. ++! ipdsnum - Product Definition Template Number ( see Code Table 4.0) ++! ipdstmpl - Contains the data values for the specified Product Definition ++! Template ( N=ipdsnum ). Each element of this integer ++! array contains an entry (in the order specified) of Product ++! Defintion Template 4.N ++! mappdslen- Number of elements in ipdstmpl(). i.e. number of entries ++! in Product Defintion Template 4.N ( N=ipdsnum ). ++! coordlist- Array containg floating point values intended to document ++! the vertical discretisation associated to model data ++! on hybrid coordinate vertical levels. (part of Section 4) ++! numcoord - number of values in array coordlist. ++! ierr - Error return code. ++! 0 = no error ++! 5 = "GRIB" message contains an undefined Product Definition ++! Template. ++! ++! REMARKS: Uses Fortran 90 module pdstemplates. ++! ++! ATTRIBUTES: ++! LANGUAGE: Fortran 90 ++! MACHINE: IBM SP ++! ++!$$$ ++ ++ use pdstemplates ++ ++ character(len=1),intent(in) :: cgrib(lcgrib) ++ integer,intent(in) :: lcgrib ++ integer,intent(inout) :: iofst ++ real,intent(out) :: coordlist(*) ++ integer,intent(out) :: ipdsnum,ipdstmpl(*) ++ integer,intent(out) :: ierr,numcoord ++ ++ real(4),allocatable :: coordieee(:) ++ integer,allocatable :: mappds(:) ++ integer :: mappdslen ++ logical needext ++ ++ ierr=0 ++ ++ call g2_gbytec(cgrib,lensec,iofst,32) ! Get Length of Section ++ iofst=iofst+32 ++ iofst=iofst+8 ! skip section number ++ allocate(mappds(lensec)) ++ ++ call g2_gbytec(cgrib,numcoord,iofst,16) ! Get num of coordinate values ++ iofst=iofst+16 ++ call g2_gbytec(cgrib,ipdsnum,iofst,16) ! Get Prod. Def Template num. ++ iofst=iofst+16 ++ ! Get Product Definition Template ++ call getpdstemplate(ipdsnum,mappdslen,mappds,needext,iret) ++ if (iret.ne.0) then ++ ierr=5 ++ return ++ endif ++ ! ++ ! Unpack each value into array ipdstmpl from the ++ ! the appropriate number of octets, which are specified in ++ ! corresponding entries in array mappds. ++ ! ++ do i=1,mappdslen ++ nbits=iabs(mappds(i))*8 ++ if ( mappds(i).ge.0 ) then ++ call g2_gbytec(cgrib,ipdstmpl(i),iofst,nbits) ++ else ++ call g2_gbytec(cgrib,isign,iofst,1) ++ call g2_gbytec(cgrib,ipdstmpl(i),iofst+1,nbits-1) ++ if (isign.eq.1) ipdstmpl(i)=-ipdstmpl(i) ++ endif ++ iofst=iofst+nbits ++ enddo ++ ! ++ ! Check to see if the Product Definition Template needs to be ++ ! extended. ++ ! The number of values in a specific template may vary ++ ! depending on data specified in the "static" part of the ++ ! template. ++ ! ++ if ( needext ) then ++ call extpdstemplate(ipdsnum,ipdstmpl,newmappdslen,mappds) ++ ! Unpack the rest of the Product Definition Template ++ do i=mappdslen+1,newmappdslen ++ nbits=iabs(mappds(i))*8 ++ if ( mappds(i).ge.0 ) then ++ call g2_gbytec(cgrib,ipdstmpl(i),iofst,nbits) ++ else ++ call g2_gbytec(cgrib,isign,iofst,1) ++ call g2_gbytec(cgrib,ipdstmpl(i),iofst+1,nbits-1) ++ if (isign.eq.1) ipdstmpl(i)=-ipdstmpl(i) ++ endif ++ iofst=iofst+nbits ++ enddo ++ mappdslen=newmappdslen ++ endif ++ ! ++ ! Get Optional list of vertical coordinate values ++ ! after the Product Definition Template, if necessary. ++ ! ++ if ( numcoord .ne. 0 ) then ++ allocate (coordieee(numcoord)) ++ call g2_gbytesc(cgrib,coordieee,iofst,32,0,numcoord) ++ call rdieee(coordieee,int(coordlist),numcoord) ++ deallocate (coordieee) ++ iofst=iofst+(32*numcoord) ++ endif ++ if( allocated(mappds) ) deallocate(mappds) ++ return ! End of Section 4 processing ++ end ++ ++ ++ subroutine unpack5(cgrib,lcgrib,iofst,ndpts,idrsnum,idrstmpl, ++ & mapdrslen,ierr) ++!$$$ SUBPROGRAM DOCUMENTATION BLOCK ++! . . . . ++! SUBPROGRAM: unpack5 ++! PRGMMR: Gilbert ORG: W/NP11 DATE: 2000-05-26 ++! ++! ABSTRACT: This subroutine unpacks Section 5 (Data Representation Section) ++! starting at octet 6 of that Section. ++! ++! PROGRAM HISTORY LOG: ++! 2000-05-26 Gilbert ++! ++! USAGE: CALL unpack5(cgrib,lcgrib,iofst,ndpts,idrsnum,idrstmpl, ++! mapdrslen,ierr) ++! INPUT ARGUMENT LIST: ++! cgrib - Character array that contains the GRIB2 message ++! lcgrib - Length (in bytes) of GRIB message array cgrib. ++! iofst - Bit offset of the beginning of Section 5. ++! ++! OUTPUT ARGUMENT LIST: ++! iofst - Bit offset at the end of Section 5, returned. ++! ndpts - Number of data points unpacked and returned. ++! idrsnum - Data Representation Template Number ( see Code Table 5.0) ++! idrstmpl - Contains the data values for the specified Data Representation ++! Template ( N=idrsnum ). Each element of this integer ++! array contains an entry (in the order specified) of Data ++! Representation Template 5.N ++! mapdrslen- Number of elements in idrstmpl(). i.e. number of entries ++! in Data Representation Template 5.N ( N=idrsnum ). ++! ierr - Error return code. ++! 0 = no error ++! 7 = "GRIB" message contains an undefined Data ++! Representation Template. ++! ++! REMARKS: None ++! ++! ATTRIBUTES: ++! LANGUAGE: Fortran 90 ++! MACHINE: IBM SP ++! ++!$$$ ++ ++ use drstemplates ++ ++ character(len=1),intent(in) :: cgrib(lcgrib) ++ integer,intent(in) :: lcgrib ++ integer,intent(inout) :: iofst ++ integer,intent(out) :: ndpts,idrsnum,idrstmpl(*) ++ integer,intent(out) :: ierr ++ ++C integer,allocatable :: mapdrs(:) ++ integer,allocatable :: mapdrs(:) ++ integer :: mapdrslen ++ logical needext ++ ++ ierr=0 ++ ++ call g2_gbytec(cgrib,lensec,iofst,32) ! Get Length of Section ++ iofst=iofst+32 ++ iofst=iofst+8 ! skip section number ++ allocate(mapdrs(lensec)) ++ ++ call g2_gbytec(cgrib,ndpts,iofst,32) ! Get num of data points ++ iofst=iofst+32 ++ call g2_gbytec(cgrib,idrsnum,iofst,16) ! Get Data Rep Template Num. ++ iofst=iofst+16 ++ ! Gen Data Representation Template ++ call getdrstemplate(idrsnum,mapdrslen,mapdrs,needext,iret) ++ if (iret.ne.0) then ++ ierr=7 ++ return ++ endif ++ ! ++ ! Unpack each value into array ipdstmpl from the ++ ! the appropriate number of octets, which are specified in ++ ! corresponding entries in array mappds. ++ ! ++ do i=1,mapdrslen ++ nbits=iabs(mapdrs(i))*8 ++ if ( mapdrs(i).ge.0 ) then ++ call g2_gbytec(cgrib,idrstmpl(i),iofst,nbits) ++ else ++ call g2_gbytec(cgrib,isign,iofst,1) ++ call g2_gbytec(cgrib,idrstmpl(i),iofst+1,nbits-1) ++ if (isign.eq.1) idrstmpl(i)=-idrstmpl(i) ++ endif ++ iofst=iofst+nbits ++ enddo ++ ! ++ ! Check to see if the Data Representation Template needs to be ++ ! extended. ++ ! The number of values in a specific template may vary ++ ! depending on data specified in the "static" part of the ++ ! template. ++ ! ++ if ( needext ) then ++ call extdrstemplate(idrsnum,idrstmpl,newmapdrslen,mapdrs) ++ ! Unpack the rest of the Data Representation Template ++ do i=mapdrslen+1,newmapdrslen ++ nbits=iabs(mapdrs(i))*8 ++ if ( mapdrs(i).ge.0 ) then ++ call g2_gbytec(cgrib,idrstmpl(i),iofst,nbits) ++ else ++ call g2_gbytec(cgrib,isign,iofst,1) ++ call g2_gbytec(cgrib,idrstmpl(i),iofst+1,nbits-1) ++ if (isign.eq.1) idrstmpl(i)=-idrstmpl(i) ++ endif ++ iofst=iofst+nbits ++ enddo ++ mapdrslen=newmapdrslen ++ endif ++ if( allocated(mapdrs) ) deallocate(mapdrs) ++ return ! End of Section 5 processing ++ end ++ ++ ++ subroutine unpack6(cgrib,lcgrib,iofst,ngpts,ibmap,bmap,ierr) ++!$$$ SUBPROGRAM DOCUMENTATION BLOCK ++! . . . . ++! SUBPROGRAM: unpack6 ++! PRGMMR: Gilbert ORG: W/NP11 DATE: 2000-05-26 ++! ++! ABSTRACT: This subroutine unpacks Section 6 (Bit-Map Section) ++! starting at octet 6 of that Section. ++! ++! PROGRAM HISTORY LOG: ++! 2000-05-26 Gilbert ++! ++! USAGE: CALL unpack6(cgrib,lcgrib,iofst,ngpts,ibmap,bmap,ierr) ++! INPUT ARGUMENT LIST: ++! cgrib - Character array that contains the GRIB2 message ++! lcgrib - Length (in bytes) of GRIB message array cgrib. ++! iofst - Bit offset of the beginning of Section 6. ++! ngpts - Number of grid points specified in the bit-map ++! ++! OUTPUT ARGUMENT LIST: ++! iofst - Bit offset at the end of Section 6, returned. ++! ibmap - Bitmap indicator ( see Code Table 6.0 ) ++! 0 = bitmap applies and is included in Section 6. ++! 1-253 = Predefined bitmap applies ++! 254 = Previously defined bitmap applies to this field ++! 255 = Bit map does not apply to this product. ++! bmap() - Logical*1 array containing decoded bitmap. ( if ibmap=0 ) ++! ierr - Error return code. ++! 0 = no error ++! 4 = Unrecognized pre-defined bit-map. ++! ++! REMARKS: None ++! ++! ATTRIBUTES: ++! LANGUAGE: Fortran 90 ++! MACHINE: IBM SP ++! ++!$$$ ++ ++ character(len=1),intent(in) :: cgrib(lcgrib) ++ integer,intent(in) :: lcgrib,ngpts ++ integer,intent(inout) :: iofst ++ integer,intent(out) :: ibmap ++ integer,intent(out) :: ierr ++ logical*1,intent(out) :: bmap(ngpts) ++ ++ integer :: intbmap(ngpts) ++ ++ ierr=0 ++ ++ iofst=iofst+32 ! skip Length of Section ++ iofst=iofst+8 ! skip section number ++ ++ call g2_gbytec(cgrib,ibmap,iofst,8) ! Get bit-map indicator ++ iofst=iofst+8 ++ ++ if (ibmap.eq.0) then ! Unpack bitmap ++ call g2_gbytesc(cgrib,intbmap,iofst,1,0,ngpts) ++ iofst=iofst+ngpts ++ do j=1,ngpts ++ bmap(j)=.true. ++ if (intbmap(j).eq.0) bmap(j)=.false. ++ enddo ++ elseif (ibmap.eq.254) then ! Use previous bitmap ++ return ++ elseif (ibmap.eq.255) then ! No bitmap in message ++ bmap(1:ngpts)=.true. ++ else ++ print *,'unpack6: Predefined bitmap ',ibmap,' not recognized.' ++ ierr=4 ++ endif ++ ++ return ! End of Section 6 processing ++ end ++ +diff -Nru g2lib-3.2.0-orig/gf_unpack7.f g2lib-3.2.0/gf_unpack7.f +--- g2lib-3.2.0-orig/gf_unpack7.f 2020-12-16 18:58:40.000000000 +0100 ++++ g2lib-3.2.0/gf_unpack7.f 2021-03-18 19:28:41.716536103 +0100 +@@ -89,7 +89,7 @@ + endif + elseif (idrsnum.eq.50) then ! Spectral simple + call simunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts-1, +- & fld(2)) ++ & fld(2:ndpts)) + ieee=idrstmpl(5) + call rdieee(ieee,fld(1),1) + elseif (idrsnum.eq.51) then ! Spectral complex +diff -Nru g2lib-3.2.0-orig/gf_unpack7.f~ g2lib-3.2.0/gf_unpack7.f~ +--- g2lib-3.2.0-orig/gf_unpack7.f~ 1970-01-01 01:00:00.000000000 +0100 ++++ g2lib-3.2.0/gf_unpack7.f~ 2020-12-16 18:58:40.000000000 +0100 +@@ -0,0 +1,125 @@ ++ ++ ++ subroutine gf_unpack7(cgrib,lcgrib,iofst,igdsnum,igdstmpl, ++ & idrsnum,idrstmpl,ndpts,fld,ierr) ++!$$$ SUBPROGRAM DOCUMENTATION BLOCK ++! . . . . ++! SUBPROGRAM: gf_unpack7 ++! PRGMMR: Gilbert ORG: W/NP11 DATE: 2002-01-24 ++! ++! ABSTRACT: This subroutine unpacks GRIB2 Section 7 (Data Section). ++! ++! PROGRAM HISTORY LOG: ++! 2002-01-24 Gilbert ++! 2002-12-17 Gilbert - Added support for new templates using ++! PNG and JPEG2000 algorithms/templates. ++! 2004-12-29 Gilbert - Added check on comunpack return code. ++! ++! USAGE: CALL gf_unpack7(cgrib,lcgrib,iofst,igdsnum,igdstmpl, ++! & idrsnum,idrstmpl,ndpts,fld,ierr) ++! INPUT ARGUMENT LIST: ++! cgrib - Character array that contains the GRIB2 message ++! lcgrib - Length (in bytes) of GRIB message array cgrib. ++! iofst - Bit offset of the beginning of Section 7. ++! igdsnum - Grid Definition Template Number ( see Code Table 3.0) ++! (Only required to unpack DRT 5.51) ++! igdstmpl - Pointer to an integer array containing the data values for ++! the specified Grid Definition ++! Template ( N=igdsnum ). Each element of this integer ++! array contains an entry (in the order specified) of Grid ++! Definition Template 3.N ++! (Only required to unpack DRT 5.51) ++! idrsnum - Data Representation Template Number ( see Code Table 5.0) ++! idrstmpl - Pointer to an integer array containing the data values for ++! the specified Data Representation ++! Template ( N=idrsnum ). Each element of this integer ++! array contains an entry (in the order specified) of Data ++! Representation Template 5.N ++! ndpts - Number of data points unpacked and returned. ++! ++! OUTPUT ARGUMENT LIST: ++! iofst - Bit offset at the end of Section 7, returned. ++! fld() - Pointer to a real array containing the unpacked data field. ++! ierr - Error return code. ++! 0 = no error ++! 4 = Unrecognized Data Representation Template ++! 5 = One of GDT 3.50 through 3.53 required to unpack DRT 5.51 ++! 6 = memory allocation error ++! 7 = corrupt section 7. ++! ++! REMARKS: None ++! ++! ATTRIBUTES: ++! LANGUAGE: Fortran 90 ++! MACHINE: IBM SP ++! ++!$$$ ++ ++ character(len=1),intent(in) :: cgrib(lcgrib) ++ integer,intent(in) :: lcgrib,ndpts,igdsnum,idrsnum ++ integer,intent(inout) :: iofst ++ integer,pointer,dimension(:) :: igdstmpl,idrstmpl ++ integer,intent(out) :: ierr ++ real,pointer,dimension(:) :: fld ++ ++ ++ ierr=0 ++ nullify(fld) ++ ++ call g2_gbytec(cgrib,lensec,iofst,32) ! Get Length of Section ++ iofst=iofst+32 ++ iofst=iofst+8 ! skip section number ++ ++ ipos=(iofst/8)+1 ++ istat=0 ++ allocate(fld(ndpts),stat=istat) ++ if (istat.ne.0) then ++ ierr=6 ++ return ++ endif ++ ++ if (idrsnum.eq.0) then ++ call simunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts,fld) ++ elseif (idrsnum.eq.2.or.idrsnum.eq.3) then ++ call comunpack(cgrib(ipos),lensec-5,lensec,idrsnum,idrstmpl, ++ & ndpts,fld,ier) ++ if ( ier .NE. 0 ) then ++ ierr=7 ++ return ++ endif ++ elseif (idrsnum.eq.50) then ! Spectral simple ++ call simunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts-1, ++ & fld(2)) ++ ieee=idrstmpl(5) ++ call rdieee(ieee,fld(1),1) ++ elseif (idrsnum.eq.51) then ! Spectral complex ++ if (igdsnum.ge.50.AND.igdsnum.le.53) then ++ call specunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts, ++ & igdstmpl(1),igdstmpl(2),igdstmpl(3),fld) ++ else ++ print *,'gf_unpack7: Cannot use GDT 3.',igdsnum, ++ & ' to unpack Data Section 5.51.' ++ ierr=5 ++ nullify(fld) ++ return ++ endif ++ ++ elseif (idrsnum.eq.40 .OR. idrsnum.eq.40000) then ++ call jpcunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts,fld) ++ ++ ++ elseif (idrsnum.eq.41 .OR. idrsnum.eq.40010) then ++ call pngunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts,fld) ++ ++ else ++ print *,'gf_unpack7: Data Representation Template ',idrsnum, ++ & ' not yet implemented.' ++ ierr=4 ++ nullify(fld) ++ return ++ endif ++ ++ iofst=iofst+(8*lensec) ++ ++ return ! End of Section 7 processing ++ end +diff -Nru g2lib-3.2.0-orig/specunpack.f g2lib-3.2.0/specunpack.f +--- g2lib-3.2.0-orig/specunpack.f 2020-12-16 18:58:41.000000000 +0100 ++++ g2lib-3.2.0/specunpack.f 2021-03-18 19:30:01.480741435 +0100 +@@ -45,7 +45,7 @@ + real,allocatable :: pscale(:) + + ieee = idrstmpl(1) +- call rdieee(ieee,ref,1) ++ call rdieee(char(ieee),ref,1) + bscale = 2.0**real(idrstmpl(2)) + dscale = 10.0**real(-idrstmpl(3)) + nbits = idrstmpl(4) +diff -Nru g2lib-3.2.0-orig/specunpack.f~ g2lib-3.2.0/specunpack.f~ +--- g2lib-3.2.0-orig/specunpack.f~ 1970-01-01 01:00:00.000000000 +0100 ++++ g2lib-3.2.0/specunpack.f~ 2020-12-16 18:58:41.000000000 +0100 +@@ -0,0 +1,107 @@ ++ subroutine specunpack(cpack,len,idrstmpl,ndpts,JJ,KK,MM,fld) ++!$$$ SUBPROGRAM DOCUMENTATION BLOCK ++! . . . . ++! SUBPROGRAM: specunpack ++! PRGMMR: Gilbert ORG: W/NP11 DATE: 2002-12-19 ++! ++! ABSTRACT: This subroutine unpacks a spectral data field that was packed ++! using the complex packing algorithm for spherical harmonic data as ++! defined in the GRIB2 documention, ++! using info from the GRIB2 Data Representation Template 5.51. ++! ++! PROGRAM HISTORY LOG: ++! 2002-12-19 Gilbert ++! ++! USAGE: CALL specunpack(cpack,len,idrstmpl,ndpts,JJ,KK,MM,fld) ++! INPUT ARGUMENT LIST: ++! cpack - The packed data field (character*1 array) ++! len - length of packed field cpack(). ++! idrstmpl - Contains the array of values for Data Representation ++! Template 5.51 ++! ndpts - The number of data values to unpack ++! JJ - J - pentagonal resolution parameter ++! KK - K - pentagonal resolution parameter ++! MM - M - pentagonal resolution parameter ++! ++! OUTPUT ARGUMENT LIST: ++! fld() - Contains the unpacked data values ++! ++! REMARKS: None ++! ++! ATTRIBUTES: ++! LANGUAGE: XL Fortran 90 ++! MACHINE: IBM SP ++! ++!$$$ ++ ++ character(len=1),intent(in) :: cpack(len) ++ integer,intent(in) :: ndpts,len,JJ,KK,MM ++ integer,intent(in) :: idrstmpl(*) ++ real,intent(out) :: fld(ndpts) ++ ++ integer :: ifld(ndpts),Ts ++ integer(4) :: ieee ++ real :: ref,bscale,dscale,unpk(ndpts) ++ real,allocatable :: pscale(:) ++ ++ ieee = idrstmpl(1) ++ call rdieee(ieee,ref,1) ++ bscale = 2.0**real(idrstmpl(2)) ++ dscale = 10.0**real(-idrstmpl(3)) ++ nbits = idrstmpl(4) ++ Js=idrstmpl(6) ++ Ks=idrstmpl(7) ++ Ms=idrstmpl(8) ++ Ts=idrstmpl(9) ++ ++ if (idrstmpl(10).eq.1) then ! unpacked floats are 32-bit IEEE ++ !call g2_gbytesc(cpack,ifld,0,32,0,Ts) ++ call rdieee(cpack,unpk,Ts) ! read IEEE unpacked floats ++ iofst=32*Ts ++ call g2_gbytesc(cpack,ifld,iofst,nbits,0,ndpts-Ts) ! unpack scaled data ++! ++! Calculate Laplacian scaling factors for each possible wave number. ++! ++ allocate(pscale(JJ+MM)) ++ tscale=real(idrstmpl(5))*1E-6 ++ do n=Js,JJ+MM ++ pscale(n)=real(n*(n+1))**(-tscale) ++ enddo ++! ++! Assemble spectral coeffs back to original order. ++! ++ inc=1 ++ incu=1 ++ incp=1 ++ do m=0,MM ++ Nm=JJ ! triangular or trapezoidal ++ if ( KK .eq. JJ+MM ) Nm=JJ+m ! rhombodial ++ Ns=Js ! triangular or trapezoidal ++ if ( Ks .eq. Js+Ms ) Ns=Js+m ! rhombodial ++ do n=m,Nm ++ if (n.le.Ns .AND. m.le.Ms) then ! grab unpacked value ++ fld(inc)=unpk(incu) ! real part ++ fld(inc+1)=unpk(incu+1) ! imaginary part ++ inc=inc+2 ++ incu=incu+2 ++ else ! Calc coeff from packed value ++ fld(inc)=((real(ifld(incp))*bscale)+ref)* ++ & dscale*pscale(n) ! real part ++ fld(inc+1)=((real(ifld(incp+1))*bscale)+ref)* ++ & dscale*pscale(n) ! imaginary part ++ inc=inc+2 ++ incp=incp+2 ++ endif ++ enddo ++ enddo ++ ++ deallocate(pscale) ++ ++ else ++ print *,'specunpack: Cannot handle 64 or 128-bit floats.' ++ fld=0.0 ++ return ++ endif ++ ++ return ++ end From 58a178b2bd3f34f1527f0db0636fa166e2994cab Mon Sep 17 00:00:00 2001 From: kosl Date: Sun, 24 Apr 2022 01:11:04 +0200 Subject: [PATCH 3523/9987] Delete makedepend-1.0.6-GCCcore-10.2.0.eb --- .../makedepend-1.0.6-GCCcore-10.2.0.eb | 26 ------------------- 1 file changed, 26 deletions(-) delete mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb deleted file mode 100644 index 3295f02cc8a..00000000000 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'makedepend' -version = '1.0.6' - -homepage = 'https://linux.die.net/man/1/makedepend' -description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = [XORG_UTIL_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['845f6708fc850bf53f5b1d0fb4352c4feab3949f140b26f71b22faba354c3365'] - -builddependencies = [ - ('binutils', '2.35'), - ('xproto', '7.0.31'), - ('xorg-macros', '1.19.2'), -] - -sanity_check_paths = { - 'files': ['bin/makedepend'], - 'dirs': [], -} - -moduleclass = 'devel' From d478dc3203396b5ab43b79a77d9598d29c793fae Mon Sep 17 00:00:00 2001 From: kosl Date: Sun, 24 Apr 2022 01:12:10 +0200 Subject: [PATCH 3524/9987] Delete g2clib-1.6.3-foss-2020b.eb --- .../g/g2clib/g2clib-1.6.3-foss-2020b.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-foss-2020b.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-foss-2020b.eb deleted file mode 100644 index f98c2dd2d50..00000000000 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-foss-2020b.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'g2clib' -version = '1.6.3' - -homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder ('C' version).""" - -toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'pic': True} - -source_urls = [homepage] -sources = ['%(name)s-%(version)s.tar'] -checksums = ['83e4f2061b3d4a8bd431ba860dda8c5cf103b25f42d265b7b724b9acafad177c'] - -builddependencies = [('binutils', '2.35')] - -dependencies = [ - ('JasPer', '2.0.24'), - ('libpng', '1.6.37'), -] - -# parallel build tends to fail -parallel = 1 - -moduleclass = 'data' From ce0545025095db944addac94e0adcad3954cacd9 Mon Sep 17 00:00:00 2001 From: kosl Date: Sun, 24 Apr 2022 01:12:45 +0200 Subject: [PATCH 3525/9987] Delete g2lib-3.2.0-GCCcore-10.2.0.eb --- .../g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb deleted file mode 100644 index eeb1ed2cd3c..00000000000 --- a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -name = 'g2lib' -version = '3.2.0' - -homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' -description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -source_urls = [homepage] -sources = ['%(name)s-%(version)s.tar'] -patches = [ - '%(name)s-%(version)s_compilation.patch', - # '%(name)s-%(version)s_makefile.patch', - # '%(name)s-%(version)s-kind.patch', - # '%(name)s-1.4.0-with-JasPer-2.x.patch', -] -checksums = [ - '9d3866de32e13e80798bfb08dbbea9223f32cec3fce3c57b6838e76f27d5a1d3', # g2lib-3.2.0.tar - 'f85286a1c0dec16e4a9f0abb4517218e4c652080775e34a1806e3687e1277dbb', # g2lib-3.2.0_compilation.patch -] - -builddependencies = [('binutils', '2.35')] - -dependencies = [ - ('JasPer', '2.0.24'), - ('libpng', '1.6.37'), -] - -buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 ' -buildopts += '-D__64BIT__" FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -I." FC=$FC CC=$CC' - -# parallel build tends to fail -parallel = 1 - -moduleclass = 'data' From cc40a82de8101a9cba1fcb49128cbe6aabff05ed Mon Sep 17 00:00:00 2001 From: kosl Date: Sun, 24 Apr 2022 01:13:59 +0200 Subject: [PATCH 3526/9987] Delete g2lib-3.2.0_compilation.patch --- .../g/g2lib/g2lib-3.2.0_compilation.patch | 1145 ----------------- 1 file changed, 1145 deletions(-) delete mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_compilation.patch diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_compilation.patch b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_compilation.patch deleted file mode 100644 index dc37f945132..00000000000 --- a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0_compilation.patch +++ /dev/null @@ -1,1145 +0,0 @@ -diff -Nru g2lib-3.2.0-orig/addfield.f g2lib-3.2.0/addfield.f ---- g2lib-3.2.0-orig/addfield.f 2020-12-16 18:58:40.000000000 +0100 -+++ g2lib-3.2.0/addfield.f 2021-03-18 19:11:48.240496708 +0100 -@@ -264,7 +264,7 @@ - ! - if ( numcoord .ne. 0 ) then - call mkieee(coordlist,coordieee,numcoord) -- call g2_sbytesc(cgrib,coordieee,iofst,32,0,numcoord) -+ call g2_sbytesc(cgrib,int(coordieee),iofst,32,0,numcoord) - iofst=iofst+(32*numcoord) - endif - ! -@@ -311,12 +311,12 @@ - if (nsize .lt. minsize) nsize=minsize - allocate(cpack(nsize),stat=istat) - if (idrsnum.eq.0) then ! Simple Packing -- call simpack(pfld,ndpts,idrstmpl,cpack,lcpack) -+ call simpack(pfld(1),ndpts,idrstmpl,cpack,lcpack) - elseif (idrsnum.eq.2.or.idrsnum.eq.3) then ! Complex Packing - call cmplxpack(pfld,ndpts,idrsnum,idrstmpl,cpack,lcpack) - elseif (idrsnum.eq.50) then ! Sperical Harmonic Simple Packing - call simpack(pfld(2),ndpts-1,idrstmpl,cpack,lcpack) -- call mkieee(real(pfld(1)),re00,1) ! ensure RE(0,0) value is IEEE format -+ call mkieee([real(pfld(1))],[re00(1)],1) ! ensure RE(0,0) value is IEEE format - !call g2_gbytec(re00,idrstmpl(5),0,32) - ire00=transfer(re00,ire00) - idrstmpl(5)=ire00 -diff -Nru g2lib-3.2.0-orig/getfield.f g2lib-3.2.0/getfield.f ---- g2lib-3.2.0-orig/getfield.f 2020-12-16 18:58:40.000000000 +0100 -+++ g2lib-3.2.0/getfield.f 2021-03-18 19:26:45.559344377 +0100 -@@ -295,7 +295,7 @@ - call simunpack(cgrib(ipos+5),lensec-6,idrstmpl,ndpts-1, - & fld(2)) - ieee=idrstmpl(5) -- call rdieee(ieee,fld(1),1) -+ call rdieee(real([ieee]),[fld(1)],1) - have7=.true. - elseif (idrsnum.eq.40 .OR. idrsnum.eq.40000) then - call jpcunpack(cgrib(ipos+5),lensec-5,idrstmpl,ndpts,fld) -@@ -625,7 +625,7 @@ - ! - if ( numcoord .ne. 0 ) then - allocate (coordieee(numcoord)) -- call g2_gbytesc(cgrib,coordieee,iofst,32,0,numcoord) -+ call g2_gbytesc(cgrib,int(coordieee),iofst,32,0,numcoord) - call rdieee(coordieee,coordlist,numcoord) - deallocate (coordieee) - iofst=iofst+(32*numcoord) -diff -Nru g2lib-3.2.0-orig/getfield.f~ g2lib-3.2.0/getfield.f~ ---- g2lib-3.2.0-orig/getfield.f~ 1970-01-01 01:00:00.000000000 +0100 -+++ g2lib-3.2.0/getfield.f~ 2021-03-18 19:20:40.734837860 +0100 -@@ -0,0 +1,829 @@ -+ subroutine getfield(cgrib,lcgrib,ifldnum,igds,igdstmpl,igdslen, -+ & ideflist,idefnum,ipdsnum,ipdstmpl,ipdslen, -+ & coordlist,numcoord,ndpts,idrsnum,idrstmpl, -+ & idrslen,ibmap,bmap,fld,ierr) -+!$$$ SUBPROGRAM DOCUMENTATION BLOCK -+! . . . . -+! SUBPROGRAM: getfield -+! PRGMMR: Gilbert ORG: W/NP11 DATE: 2000-05-26 -+! -+! ABSTRACT: This subroutine returns the Grid Definition, Product Definition, -+! Bit-map ( if applicable ), and the unpacked data for a given data -+! field. Since there can be multiple data fields packed into a GRIB2 -+! message, the calling routine indicates which field is being requested -+! with the ifldnum argument. -+! -+! PROGRAM HISTORY LOG: -+! 2000-05-26 Gilbert -+! -+! USAGE: CALL getfield(cgrib,lcgrib,ifldnum,igds,igdstmpl,igdslen, -+! & ideflist,idefnum,ipdsnum,ipdstmpl,ipdslen, -+! & coordlist,numcoord,ndpts,idrsnum,idrstmpl, -+! & idrslen,ibmap,bmap,fld,ierr) -+! INPUT ARGUMENT LIST: -+! cgrib - Character array that contains the GRIB2 message -+! lcgrib - Length (in bytes) of GRIB message array cgrib. -+! ifldnum - Specifies which field in the GRIB2 message to return. -+! -+! OUTPUT ARGUMENT LIST: -+! igds - Contains information read from the appropriate GRIB Grid -+! Definition Section 3 for the field being returned. -+! Must be dimensioned >= 5. -+! igds(1)=Source of grid definition (see Code Table 3.0) -+! igds(2)=Number of grid points in the defined grid. -+! igds(3)=Number of octets needed for each -+! additional grid points definition. -+! Used to define number of -+! points in each row ( or column ) for -+! non-regular grids. -+! = 0, if using regular grid. -+! igds(4)=Interpretation of list for optional points -+! definition. (Code Table 3.11) -+! igds(5)=Grid Definition Template Number (Code Table 3.1) -+! igdstmpl - Contains the data values for the specified Grid Definition -+! Template ( NN=igds(5) ). Each element of this integer -+! array contains an entry (in the order specified) of Grid -+! Defintion Template 3.NN -+! A safe dimension for this array can be obtained in advance -+! from maxvals(2), which is returned from subroutine gribinfo. -+! igdslen - Number of elements in igdstmpl(). i.e. number of entries -+! in Grid Defintion Template 3.NN ( NN=igds(5) ). -+! ideflist - (Used if igds(3) .ne. 0) This array contains the -+! number of grid points contained in each row ( or column ). -+! (part of Section 3) -+! A safe dimension for this array can be obtained in advance -+! from maxvals(3), which is returned from subroutine gribinfo. -+! idefnum - (Used if igds(3) .ne. 0) The number of entries -+! in array ideflist. i.e. number of rows ( or columns ) -+! for which optional grid points are defined. -+! ipdsnum - Product Definition Template Number ( see Code Table 4.0) -+! ipdstmpl - Contains the data values for the specified Product Definition -+! Template ( N=ipdsnum ). Each element of this integer -+! array contains an entry (in the order specified) of Product -+! Defintion Template 4.N -+! A safe dimension for this array can be obtained in advance -+! from maxvals(4), which is returned from subroutine gribinfo. -+! ipdslen - Number of elements in ipdstmpl(). i.e. number of entries -+! in Product Defintion Template 4.N ( N=ipdsnum ). -+! coordlist- Array containg floating point values intended to document -+! the vertical discretisation associated to model data -+! on hybrid coordinate vertical levels. (part of Section 4) -+! The dimension of this array can be obtained in advance -+! from maxvals(5), which is returned from subroutine gribinfo. -+! numcoord - number of values in array coordlist. -+! ndpts - Number of data points unpacked and returned. -+! idrsnum - Data Representation Template Number ( see Code Table 5.0) -+! idrstmpl - Contains the data values for the specified Data Representation -+! Template ( N=idrsnum ). Each element of this integer -+! array contains an entry (in the order specified) of Product -+! Defintion Template 5.N -+! A safe dimension for this array can be obtained in advance -+! from maxvals(6), which is returned from subroutine gribinfo. -+! idrslen - Number of elements in idrstmpl(). i.e. number of entries -+! in Data Representation Template 5.N ( N=idrsnum ). -+! ibmap - Bitmap indicator ( see Code Table 6.0 ) -+! 0 = bitmap applies and is included in Section 6. -+! 1-253 = Predefined bitmap applies -+! 254 = Previously defined bitmap applies to this field -+! 255 = Bit map does not apply to this product. -+! bmap() - Logical*1 array containing decoded bitmap. ( if ibmap=0 ) -+! The dimension of this array can be obtained in advance -+! from maxvals(7), which is returned from subroutine gribinfo. -+! fld() - Array of ndpts unpacked data points. -+! A safe dimension for this array can be obtained in advance -+! from maxvals(7), which is returned from subroutine gribinfo. -+! ierr - Error return code. -+! 0 = no error -+! 1 = Beginning characters "GRIB" not found. -+! 2 = GRIB message is not Edition 2. -+! 3 = The data field request number was not positive. -+! 4 = End string "7777" found, but not where expected. -+! 6 = GRIB message did not contain the requested number of -+! data fields. -+! 7 = End string "7777" not found at end of message. -+! 9 = Data Representation Template 5.NN not yet implemented. -+! 10 = Error unpacking Section 3. -+! 11 = Error unpacking Section 4. -+! 12 = Error unpacking Section 5. -+! 13 = Error unpacking Section 6. -+! 14 = Error unpacking Section 7. -+! -+! REMARKS: Note that subroutine gribinfo can be used to first determine -+! how many data fields exist in a given GRIB message. -+! -+! ATTRIBUTES: -+! LANGUAGE: Fortran 90 -+! MACHINE: IBM SP -+! -+!$$$ -+ -+ character(len=1),intent(in) :: cgrib(lcgrib) -+ integer,intent(in) :: lcgrib,ifldnum -+ integer,intent(out) :: igds(*),igdstmpl(*),ideflist(*) -+ integer,intent(out) :: ipdsnum,ipdstmpl(*) -+ integer,intent(out) :: idrsnum,idrstmpl(*) -+ integer,intent(out) :: ndpts,ibmap,idefnum,numcoord -+ integer,intent(out) :: ierr -+ logical*1,intent(out) :: bmap(*) -+ real,intent(out) :: fld(*),coordlist(*) -+ -+ character(len=4),parameter :: grib='GRIB',c7777='7777' -+ character(len=4) :: ctemp -+ integer:: listsec0(2) -+ integer iofst,ibeg,istart -+ integer(4) :: ieee -+ logical have3,have4,have5,have6,have7 -+ -+ have3=.false. -+ have4=.false. -+ have5=.false. -+ have6=.false. -+ have7=.false. -+ ierr=0 -+ numfld=0 -+! -+! Check for valid request number -+! -+ if (ifldnum.le.0) then -+ print *,'getfield: Request for field number must be positive.' -+ ierr=3 -+ return -+ endif -+! -+! Check for beginning of GRIB message in the first 100 bytes -+! -+ istart=0 -+ do j=1,100 -+ ctemp=cgrib(j)//cgrib(j+1)//cgrib(j+2)//cgrib(j+3) -+ if (ctemp.eq.grib ) then -+ istart=j -+ exit -+ endif -+ enddo -+ if (istart.eq.0) then -+ print *,'getfield: Beginning characters GRIB not found.' -+ ierr=1 -+ return -+ endif -+! -+! Unpack Section 0 - Indicator Section -+! -+ iofst=8*(istart+5) -+ call g2_gbytec(cgrib,listsec0(1),iofst,8) ! Discipline -+ iofst=iofst+8 -+ call g2_gbytec(cgrib,listsec0(2),iofst,8) ! GRIB edition number -+ iofst=iofst+8 -+ iofst=iofst+32 -+ call g2_gbytec(cgrib,lengrib,iofst,32) ! Length of GRIB message -+ iofst=iofst+32 -+ lensec0=16 -+ ipos=istart+lensec0 -+! -+! Currently handles only GRIB Edition 2. -+! -+ if (listsec0(2).ne.2) then -+ print *,'getfield: can only decode GRIB edition 2.' -+ ierr=2 -+ return -+ endif -+! -+! Loop through the remaining sections keeping track of the -+! length of each. Also keep the latest Grid Definition Section info. -+! Unpack the requested field number. -+! -+ do -+ ! Check to see if we are at end of GRIB message -+ ctemp=cgrib(ipos)//cgrib(ipos+1)//cgrib(ipos+2)//cgrib(ipos+3) -+ if (ctemp.eq.c7777 ) then -+ ipos=ipos+4 -+ ! If end of GRIB message not where expected, issue error -+ if (ipos.ne.(istart+lengrib)) then -+ print *,'getfield: "7777" found, but not where expected.' -+ ierr=4 -+ return -+ endif -+ exit -+ endif -+ ! Get length of Section and Section number -+ iofst=(ipos-1)*8 -+ call g2_gbytec(cgrib,lensec,iofst,32) ! Get Length of Section -+ iofst=iofst+32 -+ call g2_gbytec(cgrib,isecnum,iofst,8) ! Get Section number -+ iofst=iofst+8 -+ !print *,' lensec= ',lensec,' secnum= ',isecnum -+ ! -+ ! If found Section 3, unpack the GDS info using the -+ ! appropriate template. Save in case this is the latest -+ ! grid before the requested field. -+ ! -+ if (isecnum.eq.3) then -+ iofst=iofst-40 ! reset offset to beginning of section -+ call unpack3(cgrib,lcgrib,iofst,igds,igdstmpl,igdslen, -+ & ideflist,idefnum,jerr) -+ if (jerr.eq.0) then -+ have3=.true. -+ else -+ ierr=10 -+ return -+ endif -+ endif -+ ! -+ ! If found Section 4, check to see if this field is the -+ ! one requested. -+ ! -+ if (isecnum.eq.4) then -+ numfld=numfld+1 -+ if (numfld.eq.ifldnum) then -+ iofst=iofst-40 ! reset offset to beginning of section -+ call unpack4(cgrib,lcgrib,iofst,ipdsnum,ipdstmpl,ipdslen, -+ & coordlist,numcoord,jerr) -+ if (jerr.eq.0) then -+ have4=.true. -+ else -+ ierr=11 -+ return -+ endif -+ endif -+ endif -+ ! -+ ! If found Section 5, check to see if this field is the -+ ! one requested. -+ ! -+ if ((isecnum.eq.5).and.(numfld.eq.ifldnum)) then -+ iofst=iofst-40 ! reset offset to beginning of section -+ call unpack5(cgrib,lcgrib,iofst,ndpts,idrsnum,idrstmpl, -+ & idrslen,jerr) -+ if (jerr.eq.0) then -+ have5=.true. -+ else -+ ierr=12 -+ return -+ endif -+ endif -+ ! -+ ! If found Section 6, Unpack bitmap. -+ ! Save in case this is the latest -+ ! bitmap before the requested field. -+ ! -+ if (isecnum.eq.6) then -+ iofst=iofst-40 ! reset offset to beginning of section -+ call unpack6(cgrib,lcgrib,iofst,igds(2),ibmap,bmap,jerr) -+ if (jerr.eq.0) then -+ have6=.true. -+ else -+ ierr=13 -+ return -+ endif -+ endif -+ ! -+ ! If found Section 7, check to see if this field is the -+ ! one requested. -+ ! -+ if ((isecnum.eq.7).and.(numfld.eq.ifldnum)) then -+ if (idrsnum.eq.0) then -+ call simunpack(cgrib(ipos+5),lensec-6,idrstmpl,ndpts,fld) -+ have7=.true. -+ elseif (idrsnum.eq.2.or.idrsnum.eq.3) then -+ call comunpack(cgrib(ipos+5),lensec-6,lensec,idrsnum, -+ & idrstmpl,ndpts,fld,ier) -+ if ( ier .ne. 0 ) then -+ ierr=14 -+ return -+ endif -+ have7=.true. -+ elseif (idrsnum.eq.50) then -+ call simunpack(cgrib(ipos+5),lensec-6,idrstmpl,ndpts-1, -+ & fld(2)) -+ ieee=idrstmpl(5) -+ call rdieee([ieee],[fld(1)],1) -+ have7=.true. -+ elseif (idrsnum.eq.40 .OR. idrsnum.eq.40000) then -+ call jpcunpack(cgrib(ipos+5),lensec-5,idrstmpl,ndpts,fld) -+ have7=.true. -+ elseif (idrsnum.eq.41 .OR. idrsnum.eq.40010) then -+ call pngunpack(cgrib(ipos+5),lensec-5,idrstmpl,ndpts,fld) -+ have7=.true. -+ else -+ print *,'getfield: Data Representation Template ',idrsnum, -+ & ' not yet implemented.' -+ ierr=9 -+ return -+ endif -+ endif -+ ! -+ ! Check to see if we read pass the end of the GRIB -+ ! message and missed the terminator string '7777'. -+ ! -+ ipos=ipos+lensec ! Update beginning of section pointer -+ if (ipos.gt.(istart+lengrib)) then -+ print *,'getfield: "7777" not found at end of GRIB message.' -+ ierr=7 -+ return -+ endif -+ -+ if (have3.and.have4.and.have5.and.have6.and.have7) return -+ -+ enddo -+ -+! -+! If exited from above loop, the end of the GRIB message was reached -+! before the requested field was found. -+! -+ print *,'getfield: GRIB message contained ',numlocal, -+ & ' different fields.' -+ print *,'getfield: The request was for the ',ifldnum, -+ & ' field.' -+ ierr=6 -+ -+ return -+ end -+ -+ -+ subroutine unpack3(cgrib,lcgrib,iofst,igds,igdstmpl, -+ & mapgridlen,ideflist,idefnum,ierr) -+!$$$ SUBPROGRAM DOCUMENTATION BLOCK -+! . . . . -+! SUBPROGRAM: unpack3 -+! PRGMMR: Gilbert ORG: W/NP11 DATE: 2000-05-26 -+! -+! ABSTRACT: This subroutine unpacks Section 3 (Grid Definition Section) -+! starting at octet 6 of that Section. -+! -+! PROGRAM HISTORY LOG: -+! 2000-05-26 Gilbert -+! -+! USAGE: CALL unpack3(cgrib,lcgrib,lensec,iofst,igds,igdstmpl, -+! & mapgridlen,ideflist,idefnum,ierr) -+! INPUT ARGUMENT LIST: -+! cgrib - Character array that contains the GRIB2 message -+! lcgrib - Length (in bytes) of GRIB message array cgrib. -+! iofst - Bit offset of the beginning of Section 3. -+! -+! OUTPUT ARGUMENT LIST: -+! iofst - Bit offset at the end of Section 3, returned. -+! igds - Contains information read from the appropriate GRIB Grid -+! Definition Section 3 for the field being returned. -+! Must be dimensioned >= 5. -+! igds(1)=Source of grid definition (see Code Table 3.0) -+! igds(2)=Number of grid points in the defined grid. -+! igds(3)=Number of octets needed for each -+! additional grid points definition. -+! Used to define number of -+! points in each row ( or column ) for -+! non-regular grids. -+! = 0, if using regular grid. -+! igds(4)=Interpretation of list for optional points -+! definition. (Code Table 3.11) -+! igds(5)=Grid Definition Template Number (Code Table 3.1) -+! igdstmpl - Contains the data values for the specified Grid Definition -+! Template ( NN=igds(5) ). Each element of this integer -+! array contains an entry (in the order specified) of Grid -+! Defintion Template 3.NN -+! mapgridlen- Number of elements in igdstmpl(). i.e. number of entries -+! in Grid Defintion Template 3.NN ( NN=igds(5) ). -+! ideflist - (Used if igds(3) .ne. 0) This array contains the -+! number of grid points contained in each row ( or column ). -+! (part of Section 3) -+! idefnum - (Used if igds(3) .ne. 0) The number of entries -+! in array ideflist. i.e. number of rows ( or columns ) -+! for which optional grid points are defined. -+! ierr - Error return code. -+! 0 = no error -+! 5 = "GRIB" message contains an undefined Grid Definition -+! Template. -+! -+! REMARKS: Uses Fortran 90 module gridtemplates. -+! -+! ATTRIBUTES: -+! LANGUAGE: Fortran 90 -+! MACHINE: IBM SP -+! -+!$$$ -+ -+ use gridtemplates -+ -+ character(len=1),intent(in) :: cgrib(lcgrib) -+ integer,intent(in) :: lcgrib -+ integer,intent(inout) :: iofst -+ integer,intent(out) :: igds(*),igdstmpl(*),ideflist(*) -+ integer,intent(out) :: ierr,idefnum -+ -+ integer,allocatable :: mapgrid(:) -+ integer :: mapgridlen,ibyttem -+ logical needext -+ -+ ierr=0 -+ -+ call g2_gbytec(cgrib,lensec,iofst,32) ! Get Length of Section -+ iofst=iofst+32 -+ iofst=iofst+8 ! skip section number -+ -+ call g2_gbytec(cgrib,igds(1),iofst,8) ! Get source of Grid def. -+ iofst=iofst+8 -+ call g2_gbytec(cgrib,igds(2),iofst,32) ! Get number of grid pts. -+ iofst=iofst+32 -+ call g2_gbytec(cgrib,igds(3),iofst,8) ! Get num octets for opt. list -+ iofst=iofst+8 -+ call g2_gbytec(cgrib,igds(4),iofst,8) ! Get interpret. for opt. list -+ iofst=iofst+8 -+ call g2_gbytec(cgrib,igds(5),iofst,16) ! Get Grid Def Template num. -+ iofst=iofst+16 -+ if (igds(1).eq.0) then -+! if (igds(1).eq.0.OR.igds(1).eq.255) then ! FOR ECMWF TEST ONLY -+ allocate(mapgrid(lensec)) -+ ! Get Grid Definition Template -+ call getgridtemplate(igds(5),mapgridlen,mapgrid,needext, -+ & iret) -+ if (iret.ne.0) then -+ ierr=5 -+ return -+ endif -+ else -+! igdstmpl=-1 -+ mapgridlen=0 -+ needext=.false. -+ endif -+ ! -+ ! Unpack each value into array igdstmpl from the -+ ! the appropriate number of octets, which are specified in -+ ! corresponding entries in array mapgrid. -+ ! -+ ibyttem=0 -+ do i=1,mapgridlen -+ nbits=iabs(mapgrid(i))*8 -+ if ( mapgrid(i).ge.0 ) then -+ call g2_gbytec(cgrib,igdstmpl(i),iofst,nbits) -+ else -+ call g2_gbytec(cgrib,isign,iofst,1) -+ call g2_gbytec(cgrib,igdstmpl(i),iofst+1,nbits-1) -+ if (isign.eq.1) igdstmpl(i)=-igdstmpl(i) -+ endif -+ iofst=iofst+nbits -+ ibyttem=ibyttem+iabs(mapgrid(i)) -+ enddo -+ ! -+ ! Check to see if the Grid Definition Template needs to be -+ ! extended. -+ ! The number of values in a specific template may vary -+ ! depending on data specified in the "static" part of the -+ ! template. -+ ! -+ if ( needext ) then -+ call extgridtemplate(igds(5),igdstmpl,newmapgridlen,mapgrid) -+ ! Unpack the rest of the Grid Definition Template -+ do i=mapgridlen+1,newmapgridlen -+ nbits=iabs(mapgrid(i))*8 -+ if ( mapgrid(i).ge.0 ) then -+ call g2_gbytec(cgrib,igdstmpl(i),iofst,nbits) -+ else -+ call g2_gbytec(cgrib,isign,iofst,1) -+ call g2_gbytec(cgrib,igdstmpl(i),iofst+1,nbits-1) -+ if (isign.eq.1) igdstmpl(i)=-igdstmpl(i) -+ endif -+ iofst=iofst+nbits -+ ibyttem=ibyttem+iabs(mapgrid(i)) -+ enddo -+ mapgridlen=newmapgridlen -+ endif -+ ! -+ ! Unpack optional list of numbers defining number of points -+ ! in each row or column, if included. This is used for non regular -+ ! grids. -+ ! -+ if ( igds(3).ne.0 ) then -+ nbits=igds(3)*8 -+ idefnum=(lensec-14-ibyttem)/igds(3) -+ call g2_gbytesc(cgrib,ideflist,iofst,nbits,0,idefnum) -+ iofst=iofst+(nbits*idefnum) -+ else -+ idefnum=0 -+ endif -+ if( allocated(mapgrid) ) deallocate(mapgrid) -+ return ! End of Section 3 processing -+ end -+ -+ -+ subroutine unpack4(cgrib,lcgrib,iofst,ipdsnum,ipdstmpl,mappdslen, -+ & coordlist,numcoord,ierr) -+!$$$ SUBPROGRAM DOCUMENTATION BLOCK -+! . . . . -+! SUBPROGRAM: unpack4 -+! PRGMMR: Gilbert ORG: W/NP11 DATE: 2000-05-26 -+! -+! ABSTRACT: This subroutine unpacks Section 4 (Product Definition Section) -+! starting at octet 6 of that Section. -+! -+! PROGRAM HISTORY LOG: -+! 2000-05-26 Gilbert -+! -+! USAGE: CALL unpack4(cgrib,lcgrib,iofst,ipdsnum,ipdstmpl,mappdslen, -+! & coordlist,numcoord,ierr) -+! INPUT ARGUMENT LIST: -+! cgrib - Character array that contains the GRIB2 message -+! lcgrib - Length (in bytes) of GRIB message array cgrib. -+! iofst - Bit offset of the beginning of Section 4. -+! -+! OUTPUT ARGUMENT LIST: -+! iofst - Bit offset of the end of Section 4, returned. -+! ipdsnum - Product Definition Template Number ( see Code Table 4.0) -+! ipdstmpl - Contains the data values for the specified Product Definition -+! Template ( N=ipdsnum ). Each element of this integer -+! array contains an entry (in the order specified) of Product -+! Defintion Template 4.N -+! mappdslen- Number of elements in ipdstmpl(). i.e. number of entries -+! in Product Defintion Template 4.N ( N=ipdsnum ). -+! coordlist- Array containg floating point values intended to document -+! the vertical discretisation associated to model data -+! on hybrid coordinate vertical levels. (part of Section 4) -+! numcoord - number of values in array coordlist. -+! ierr - Error return code. -+! 0 = no error -+! 5 = "GRIB" message contains an undefined Product Definition -+! Template. -+! -+! REMARKS: Uses Fortran 90 module pdstemplates. -+! -+! ATTRIBUTES: -+! LANGUAGE: Fortran 90 -+! MACHINE: IBM SP -+! -+!$$$ -+ -+ use pdstemplates -+ -+ character(len=1),intent(in) :: cgrib(lcgrib) -+ integer,intent(in) :: lcgrib -+ integer,intent(inout) :: iofst -+ real,intent(out) :: coordlist(*) -+ integer,intent(out) :: ipdsnum,ipdstmpl(*) -+ integer,intent(out) :: ierr,numcoord -+ -+ real(4),allocatable :: coordieee(:) -+ integer,allocatable :: mappds(:) -+ integer :: mappdslen -+ logical needext -+ -+ ierr=0 -+ -+ call g2_gbytec(cgrib,lensec,iofst,32) ! Get Length of Section -+ iofst=iofst+32 -+ iofst=iofst+8 ! skip section number -+ allocate(mappds(lensec)) -+ -+ call g2_gbytec(cgrib,numcoord,iofst,16) ! Get num of coordinate values -+ iofst=iofst+16 -+ call g2_gbytec(cgrib,ipdsnum,iofst,16) ! Get Prod. Def Template num. -+ iofst=iofst+16 -+ ! Get Product Definition Template -+ call getpdstemplate(ipdsnum,mappdslen,mappds,needext,iret) -+ if (iret.ne.0) then -+ ierr=5 -+ return -+ endif -+ ! -+ ! Unpack each value into array ipdstmpl from the -+ ! the appropriate number of octets, which are specified in -+ ! corresponding entries in array mappds. -+ ! -+ do i=1,mappdslen -+ nbits=iabs(mappds(i))*8 -+ if ( mappds(i).ge.0 ) then -+ call g2_gbytec(cgrib,ipdstmpl(i),iofst,nbits) -+ else -+ call g2_gbytec(cgrib,isign,iofst,1) -+ call g2_gbytec(cgrib,ipdstmpl(i),iofst+1,nbits-1) -+ if (isign.eq.1) ipdstmpl(i)=-ipdstmpl(i) -+ endif -+ iofst=iofst+nbits -+ enddo -+ ! -+ ! Check to see if the Product Definition Template needs to be -+ ! extended. -+ ! The number of values in a specific template may vary -+ ! depending on data specified in the "static" part of the -+ ! template. -+ ! -+ if ( needext ) then -+ call extpdstemplate(ipdsnum,ipdstmpl,newmappdslen,mappds) -+ ! Unpack the rest of the Product Definition Template -+ do i=mappdslen+1,newmappdslen -+ nbits=iabs(mappds(i))*8 -+ if ( mappds(i).ge.0 ) then -+ call g2_gbytec(cgrib,ipdstmpl(i),iofst,nbits) -+ else -+ call g2_gbytec(cgrib,isign,iofst,1) -+ call g2_gbytec(cgrib,ipdstmpl(i),iofst+1,nbits-1) -+ if (isign.eq.1) ipdstmpl(i)=-ipdstmpl(i) -+ endif -+ iofst=iofst+nbits -+ enddo -+ mappdslen=newmappdslen -+ endif -+ ! -+ ! Get Optional list of vertical coordinate values -+ ! after the Product Definition Template, if necessary. -+ ! -+ if ( numcoord .ne. 0 ) then -+ allocate (coordieee(numcoord)) -+ call g2_gbytesc(cgrib,coordieee,iofst,32,0,numcoord) -+ call rdieee(coordieee,int(coordlist),numcoord) -+ deallocate (coordieee) -+ iofst=iofst+(32*numcoord) -+ endif -+ if( allocated(mappds) ) deallocate(mappds) -+ return ! End of Section 4 processing -+ end -+ -+ -+ subroutine unpack5(cgrib,lcgrib,iofst,ndpts,idrsnum,idrstmpl, -+ & mapdrslen,ierr) -+!$$$ SUBPROGRAM DOCUMENTATION BLOCK -+! . . . . -+! SUBPROGRAM: unpack5 -+! PRGMMR: Gilbert ORG: W/NP11 DATE: 2000-05-26 -+! -+! ABSTRACT: This subroutine unpacks Section 5 (Data Representation Section) -+! starting at octet 6 of that Section. -+! -+! PROGRAM HISTORY LOG: -+! 2000-05-26 Gilbert -+! -+! USAGE: CALL unpack5(cgrib,lcgrib,iofst,ndpts,idrsnum,idrstmpl, -+! mapdrslen,ierr) -+! INPUT ARGUMENT LIST: -+! cgrib - Character array that contains the GRIB2 message -+! lcgrib - Length (in bytes) of GRIB message array cgrib. -+! iofst - Bit offset of the beginning of Section 5. -+! -+! OUTPUT ARGUMENT LIST: -+! iofst - Bit offset at the end of Section 5, returned. -+! ndpts - Number of data points unpacked and returned. -+! idrsnum - Data Representation Template Number ( see Code Table 5.0) -+! idrstmpl - Contains the data values for the specified Data Representation -+! Template ( N=idrsnum ). Each element of this integer -+! array contains an entry (in the order specified) of Data -+! Representation Template 5.N -+! mapdrslen- Number of elements in idrstmpl(). i.e. number of entries -+! in Data Representation Template 5.N ( N=idrsnum ). -+! ierr - Error return code. -+! 0 = no error -+! 7 = "GRIB" message contains an undefined Data -+! Representation Template. -+! -+! REMARKS: None -+! -+! ATTRIBUTES: -+! LANGUAGE: Fortran 90 -+! MACHINE: IBM SP -+! -+!$$$ -+ -+ use drstemplates -+ -+ character(len=1),intent(in) :: cgrib(lcgrib) -+ integer,intent(in) :: lcgrib -+ integer,intent(inout) :: iofst -+ integer,intent(out) :: ndpts,idrsnum,idrstmpl(*) -+ integer,intent(out) :: ierr -+ -+C integer,allocatable :: mapdrs(:) -+ integer,allocatable :: mapdrs(:) -+ integer :: mapdrslen -+ logical needext -+ -+ ierr=0 -+ -+ call g2_gbytec(cgrib,lensec,iofst,32) ! Get Length of Section -+ iofst=iofst+32 -+ iofst=iofst+8 ! skip section number -+ allocate(mapdrs(lensec)) -+ -+ call g2_gbytec(cgrib,ndpts,iofst,32) ! Get num of data points -+ iofst=iofst+32 -+ call g2_gbytec(cgrib,idrsnum,iofst,16) ! Get Data Rep Template Num. -+ iofst=iofst+16 -+ ! Gen Data Representation Template -+ call getdrstemplate(idrsnum,mapdrslen,mapdrs,needext,iret) -+ if (iret.ne.0) then -+ ierr=7 -+ return -+ endif -+ ! -+ ! Unpack each value into array ipdstmpl from the -+ ! the appropriate number of octets, which are specified in -+ ! corresponding entries in array mappds. -+ ! -+ do i=1,mapdrslen -+ nbits=iabs(mapdrs(i))*8 -+ if ( mapdrs(i).ge.0 ) then -+ call g2_gbytec(cgrib,idrstmpl(i),iofst,nbits) -+ else -+ call g2_gbytec(cgrib,isign,iofst,1) -+ call g2_gbytec(cgrib,idrstmpl(i),iofst+1,nbits-1) -+ if (isign.eq.1) idrstmpl(i)=-idrstmpl(i) -+ endif -+ iofst=iofst+nbits -+ enddo -+ ! -+ ! Check to see if the Data Representation Template needs to be -+ ! extended. -+ ! The number of values in a specific template may vary -+ ! depending on data specified in the "static" part of the -+ ! template. -+ ! -+ if ( needext ) then -+ call extdrstemplate(idrsnum,idrstmpl,newmapdrslen,mapdrs) -+ ! Unpack the rest of the Data Representation Template -+ do i=mapdrslen+1,newmapdrslen -+ nbits=iabs(mapdrs(i))*8 -+ if ( mapdrs(i).ge.0 ) then -+ call g2_gbytec(cgrib,idrstmpl(i),iofst,nbits) -+ else -+ call g2_gbytec(cgrib,isign,iofst,1) -+ call g2_gbytec(cgrib,idrstmpl(i),iofst+1,nbits-1) -+ if (isign.eq.1) idrstmpl(i)=-idrstmpl(i) -+ endif -+ iofst=iofst+nbits -+ enddo -+ mapdrslen=newmapdrslen -+ endif -+ if( allocated(mapdrs) ) deallocate(mapdrs) -+ return ! End of Section 5 processing -+ end -+ -+ -+ subroutine unpack6(cgrib,lcgrib,iofst,ngpts,ibmap,bmap,ierr) -+!$$$ SUBPROGRAM DOCUMENTATION BLOCK -+! . . . . -+! SUBPROGRAM: unpack6 -+! PRGMMR: Gilbert ORG: W/NP11 DATE: 2000-05-26 -+! -+! ABSTRACT: This subroutine unpacks Section 6 (Bit-Map Section) -+! starting at octet 6 of that Section. -+! -+! PROGRAM HISTORY LOG: -+! 2000-05-26 Gilbert -+! -+! USAGE: CALL unpack6(cgrib,lcgrib,iofst,ngpts,ibmap,bmap,ierr) -+! INPUT ARGUMENT LIST: -+! cgrib - Character array that contains the GRIB2 message -+! lcgrib - Length (in bytes) of GRIB message array cgrib. -+! iofst - Bit offset of the beginning of Section 6. -+! ngpts - Number of grid points specified in the bit-map -+! -+! OUTPUT ARGUMENT LIST: -+! iofst - Bit offset at the end of Section 6, returned. -+! ibmap - Bitmap indicator ( see Code Table 6.0 ) -+! 0 = bitmap applies and is included in Section 6. -+! 1-253 = Predefined bitmap applies -+! 254 = Previously defined bitmap applies to this field -+! 255 = Bit map does not apply to this product. -+! bmap() - Logical*1 array containing decoded bitmap. ( if ibmap=0 ) -+! ierr - Error return code. -+! 0 = no error -+! 4 = Unrecognized pre-defined bit-map. -+! -+! REMARKS: None -+! -+! ATTRIBUTES: -+! LANGUAGE: Fortran 90 -+! MACHINE: IBM SP -+! -+!$$$ -+ -+ character(len=1),intent(in) :: cgrib(lcgrib) -+ integer,intent(in) :: lcgrib,ngpts -+ integer,intent(inout) :: iofst -+ integer,intent(out) :: ibmap -+ integer,intent(out) :: ierr -+ logical*1,intent(out) :: bmap(ngpts) -+ -+ integer :: intbmap(ngpts) -+ -+ ierr=0 -+ -+ iofst=iofst+32 ! skip Length of Section -+ iofst=iofst+8 ! skip section number -+ -+ call g2_gbytec(cgrib,ibmap,iofst,8) ! Get bit-map indicator -+ iofst=iofst+8 -+ -+ if (ibmap.eq.0) then ! Unpack bitmap -+ call g2_gbytesc(cgrib,intbmap,iofst,1,0,ngpts) -+ iofst=iofst+ngpts -+ do j=1,ngpts -+ bmap(j)=.true. -+ if (intbmap(j).eq.0) bmap(j)=.false. -+ enddo -+ elseif (ibmap.eq.254) then ! Use previous bitmap -+ return -+ elseif (ibmap.eq.255) then ! No bitmap in message -+ bmap(1:ngpts)=.true. -+ else -+ print *,'unpack6: Predefined bitmap ',ibmap,' not recognized.' -+ ierr=4 -+ endif -+ -+ return ! End of Section 6 processing -+ end -+ -diff -Nru g2lib-3.2.0-orig/gf_unpack7.f g2lib-3.2.0/gf_unpack7.f ---- g2lib-3.2.0-orig/gf_unpack7.f 2020-12-16 18:58:40.000000000 +0100 -+++ g2lib-3.2.0/gf_unpack7.f 2021-03-18 19:28:41.716536103 +0100 -@@ -89,7 +89,7 @@ - endif - elseif (idrsnum.eq.50) then ! Spectral simple - call simunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts-1, -- & fld(2)) -+ & fld(2:ndpts)) - ieee=idrstmpl(5) - call rdieee(ieee,fld(1),1) - elseif (idrsnum.eq.51) then ! Spectral complex -diff -Nru g2lib-3.2.0-orig/gf_unpack7.f~ g2lib-3.2.0/gf_unpack7.f~ ---- g2lib-3.2.0-orig/gf_unpack7.f~ 1970-01-01 01:00:00.000000000 +0100 -+++ g2lib-3.2.0/gf_unpack7.f~ 2020-12-16 18:58:40.000000000 +0100 -@@ -0,0 +1,125 @@ -+ -+ -+ subroutine gf_unpack7(cgrib,lcgrib,iofst,igdsnum,igdstmpl, -+ & idrsnum,idrstmpl,ndpts,fld,ierr) -+!$$$ SUBPROGRAM DOCUMENTATION BLOCK -+! . . . . -+! SUBPROGRAM: gf_unpack7 -+! PRGMMR: Gilbert ORG: W/NP11 DATE: 2002-01-24 -+! -+! ABSTRACT: This subroutine unpacks GRIB2 Section 7 (Data Section). -+! -+! PROGRAM HISTORY LOG: -+! 2002-01-24 Gilbert -+! 2002-12-17 Gilbert - Added support for new templates using -+! PNG and JPEG2000 algorithms/templates. -+! 2004-12-29 Gilbert - Added check on comunpack return code. -+! -+! USAGE: CALL gf_unpack7(cgrib,lcgrib,iofst,igdsnum,igdstmpl, -+! & idrsnum,idrstmpl,ndpts,fld,ierr) -+! INPUT ARGUMENT LIST: -+! cgrib - Character array that contains the GRIB2 message -+! lcgrib - Length (in bytes) of GRIB message array cgrib. -+! iofst - Bit offset of the beginning of Section 7. -+! igdsnum - Grid Definition Template Number ( see Code Table 3.0) -+! (Only required to unpack DRT 5.51) -+! igdstmpl - Pointer to an integer array containing the data values for -+! the specified Grid Definition -+! Template ( N=igdsnum ). Each element of this integer -+! array contains an entry (in the order specified) of Grid -+! Definition Template 3.N -+! (Only required to unpack DRT 5.51) -+! idrsnum - Data Representation Template Number ( see Code Table 5.0) -+! idrstmpl - Pointer to an integer array containing the data values for -+! the specified Data Representation -+! Template ( N=idrsnum ). Each element of this integer -+! array contains an entry (in the order specified) of Data -+! Representation Template 5.N -+! ndpts - Number of data points unpacked and returned. -+! -+! OUTPUT ARGUMENT LIST: -+! iofst - Bit offset at the end of Section 7, returned. -+! fld() - Pointer to a real array containing the unpacked data field. -+! ierr - Error return code. -+! 0 = no error -+! 4 = Unrecognized Data Representation Template -+! 5 = One of GDT 3.50 through 3.53 required to unpack DRT 5.51 -+! 6 = memory allocation error -+! 7 = corrupt section 7. -+! -+! REMARKS: None -+! -+! ATTRIBUTES: -+! LANGUAGE: Fortran 90 -+! MACHINE: IBM SP -+! -+!$$$ -+ -+ character(len=1),intent(in) :: cgrib(lcgrib) -+ integer,intent(in) :: lcgrib,ndpts,igdsnum,idrsnum -+ integer,intent(inout) :: iofst -+ integer,pointer,dimension(:) :: igdstmpl,idrstmpl -+ integer,intent(out) :: ierr -+ real,pointer,dimension(:) :: fld -+ -+ -+ ierr=0 -+ nullify(fld) -+ -+ call g2_gbytec(cgrib,lensec,iofst,32) ! Get Length of Section -+ iofst=iofst+32 -+ iofst=iofst+8 ! skip section number -+ -+ ipos=(iofst/8)+1 -+ istat=0 -+ allocate(fld(ndpts),stat=istat) -+ if (istat.ne.0) then -+ ierr=6 -+ return -+ endif -+ -+ if (idrsnum.eq.0) then -+ call simunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts,fld) -+ elseif (idrsnum.eq.2.or.idrsnum.eq.3) then -+ call comunpack(cgrib(ipos),lensec-5,lensec,idrsnum,idrstmpl, -+ & ndpts,fld,ier) -+ if ( ier .NE. 0 ) then -+ ierr=7 -+ return -+ endif -+ elseif (idrsnum.eq.50) then ! Spectral simple -+ call simunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts-1, -+ & fld(2)) -+ ieee=idrstmpl(5) -+ call rdieee(ieee,fld(1),1) -+ elseif (idrsnum.eq.51) then ! Spectral complex -+ if (igdsnum.ge.50.AND.igdsnum.le.53) then -+ call specunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts, -+ & igdstmpl(1),igdstmpl(2),igdstmpl(3),fld) -+ else -+ print *,'gf_unpack7: Cannot use GDT 3.',igdsnum, -+ & ' to unpack Data Section 5.51.' -+ ierr=5 -+ nullify(fld) -+ return -+ endif -+ -+ elseif (idrsnum.eq.40 .OR. idrsnum.eq.40000) then -+ call jpcunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts,fld) -+ -+ -+ elseif (idrsnum.eq.41 .OR. idrsnum.eq.40010) then -+ call pngunpack(cgrib(ipos),lensec-5,idrstmpl,ndpts,fld) -+ -+ else -+ print *,'gf_unpack7: Data Representation Template ',idrsnum, -+ & ' not yet implemented.' -+ ierr=4 -+ nullify(fld) -+ return -+ endif -+ -+ iofst=iofst+(8*lensec) -+ -+ return ! End of Section 7 processing -+ end -diff -Nru g2lib-3.2.0-orig/specunpack.f g2lib-3.2.0/specunpack.f ---- g2lib-3.2.0-orig/specunpack.f 2020-12-16 18:58:41.000000000 +0100 -+++ g2lib-3.2.0/specunpack.f 2021-03-18 19:30:01.480741435 +0100 -@@ -45,7 +45,7 @@ - real,allocatable :: pscale(:) - - ieee = idrstmpl(1) -- call rdieee(ieee,ref,1) -+ call rdieee(char(ieee),ref,1) - bscale = 2.0**real(idrstmpl(2)) - dscale = 10.0**real(-idrstmpl(3)) - nbits = idrstmpl(4) -diff -Nru g2lib-3.2.0-orig/specunpack.f~ g2lib-3.2.0/specunpack.f~ ---- g2lib-3.2.0-orig/specunpack.f~ 1970-01-01 01:00:00.000000000 +0100 -+++ g2lib-3.2.0/specunpack.f~ 2020-12-16 18:58:41.000000000 +0100 -@@ -0,0 +1,107 @@ -+ subroutine specunpack(cpack,len,idrstmpl,ndpts,JJ,KK,MM,fld) -+!$$$ SUBPROGRAM DOCUMENTATION BLOCK -+! . . . . -+! SUBPROGRAM: specunpack -+! PRGMMR: Gilbert ORG: W/NP11 DATE: 2002-12-19 -+! -+! ABSTRACT: This subroutine unpacks a spectral data field that was packed -+! using the complex packing algorithm for spherical harmonic data as -+! defined in the GRIB2 documention, -+! using info from the GRIB2 Data Representation Template 5.51. -+! -+! PROGRAM HISTORY LOG: -+! 2002-12-19 Gilbert -+! -+! USAGE: CALL specunpack(cpack,len,idrstmpl,ndpts,JJ,KK,MM,fld) -+! INPUT ARGUMENT LIST: -+! cpack - The packed data field (character*1 array) -+! len - length of packed field cpack(). -+! idrstmpl - Contains the array of values for Data Representation -+! Template 5.51 -+! ndpts - The number of data values to unpack -+! JJ - J - pentagonal resolution parameter -+! KK - K - pentagonal resolution parameter -+! MM - M - pentagonal resolution parameter -+! -+! OUTPUT ARGUMENT LIST: -+! fld() - Contains the unpacked data values -+! -+! REMARKS: None -+! -+! ATTRIBUTES: -+! LANGUAGE: XL Fortran 90 -+! MACHINE: IBM SP -+! -+!$$$ -+ -+ character(len=1),intent(in) :: cpack(len) -+ integer,intent(in) :: ndpts,len,JJ,KK,MM -+ integer,intent(in) :: idrstmpl(*) -+ real,intent(out) :: fld(ndpts) -+ -+ integer :: ifld(ndpts),Ts -+ integer(4) :: ieee -+ real :: ref,bscale,dscale,unpk(ndpts) -+ real,allocatable :: pscale(:) -+ -+ ieee = idrstmpl(1) -+ call rdieee(ieee,ref,1) -+ bscale = 2.0**real(idrstmpl(2)) -+ dscale = 10.0**real(-idrstmpl(3)) -+ nbits = idrstmpl(4) -+ Js=idrstmpl(6) -+ Ks=idrstmpl(7) -+ Ms=idrstmpl(8) -+ Ts=idrstmpl(9) -+ -+ if (idrstmpl(10).eq.1) then ! unpacked floats are 32-bit IEEE -+ !call g2_gbytesc(cpack,ifld,0,32,0,Ts) -+ call rdieee(cpack,unpk,Ts) ! read IEEE unpacked floats -+ iofst=32*Ts -+ call g2_gbytesc(cpack,ifld,iofst,nbits,0,ndpts-Ts) ! unpack scaled data -+! -+! Calculate Laplacian scaling factors for each possible wave number. -+! -+ allocate(pscale(JJ+MM)) -+ tscale=real(idrstmpl(5))*1E-6 -+ do n=Js,JJ+MM -+ pscale(n)=real(n*(n+1))**(-tscale) -+ enddo -+! -+! Assemble spectral coeffs back to original order. -+! -+ inc=1 -+ incu=1 -+ incp=1 -+ do m=0,MM -+ Nm=JJ ! triangular or trapezoidal -+ if ( KK .eq. JJ+MM ) Nm=JJ+m ! rhombodial -+ Ns=Js ! triangular or trapezoidal -+ if ( Ks .eq. Js+Ms ) Ns=Js+m ! rhombodial -+ do n=m,Nm -+ if (n.le.Ns .AND. m.le.Ms) then ! grab unpacked value -+ fld(inc)=unpk(incu) ! real part -+ fld(inc+1)=unpk(incu+1) ! imaginary part -+ inc=inc+2 -+ incu=incu+2 -+ else ! Calc coeff from packed value -+ fld(inc)=((real(ifld(incp))*bscale)+ref)* -+ & dscale*pscale(n) ! real part -+ fld(inc+1)=((real(ifld(incp+1))*bscale)+ref)* -+ & dscale*pscale(n) ! imaginary part -+ inc=inc+2 -+ incp=incp+2 -+ endif -+ enddo -+ enddo -+ -+ deallocate(pscale) -+ -+ else -+ print *,'specunpack: Cannot handle 64 or 128-bit floats.' -+ fld=0.0 -+ return -+ endif -+ -+ return -+ end From 85bbc564baa5e7fcabd64fb1771a10d03ee0c0ce Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Sun, 24 Apr 2022 02:06:44 +0200 Subject: [PATCH 3527/9987] adding easyconfigs: OpenMPI-4.1.2-GCC-10.2.0.eb --- .../o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb new file mode 100644 index 00000000000..b9c33a4d327 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb @@ -0,0 +1,37 @@ +name = 'OpenMPI' +version = '4.1.2' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9b78c7cf7fc32131c5cf43dd2ab9740149d9d87cadb2e2189f02685749a6b527'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), + ('libevent', '2.1.12'), + ('UCX', '1.9.0'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), +] + +# replace -march=skylake-avx512 option with equivalent -m* flags, +# to avoid problems when building on systems which don't support AVX-512; +# cfr. https://github.com/open-mpi/ompi/issues/8306 +preconfigopts = "sed -i 's/-march=skylake-avx512/-mavx512f -mavx512bw -mavx512vl -mavx512dq/g' configure && " + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts = '--with-slurm --with-pmi=/usr --with-pmi-libdir=/usr/lib64' + +moduleclass = 'mpi' From 18120dc2cbb5f0eea0ec53836bd5052579580eef Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 25 Apr 2022 10:29:35 +0200 Subject: [PATCH 3528/9987] remove unneeded parentheses --- easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb | 4 ++-- easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb | 4 ++-- easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb index 4b96a924b44..7febddd76e8 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.0-gompi-2020b.eb @@ -10,8 +10,8 @@ toolchain = {'name': 'gompi', 'version': '2020b'} toolchainopts = {'usempi': True} source_urls = [ - ('https://swprojects.dkrz.de/redmine/attachments/download/498/'), - ('https://www.dkrz.de/redmine/attachments/download/498/'), + 'https://swprojects.dkrz.de/redmine/attachments/download/498/', + 'https://www.dkrz.de/redmine/attachments/download/498/', ] sources = [SOURCELOWER_TAR_GZ] checksums = ['d3673e88c1cba3b77e0821393b94b5952d8ed7dc494305c8cf93e7ebec19483c'] diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb index 4a627fa4564..13ebe254170 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.1-gompi-2021a.eb @@ -10,8 +10,8 @@ toolchain = {'name': 'gompi', 'version': '2021a'} toolchainopts = {'usempi': True} source_urls = [ - ('https://swprojects.dkrz.de/redmine/attachments/download/506/'), - ('https://www.dkrz.de/redmine/attachments/download/506/'), + 'https://swprojects.dkrz.de/redmine/attachments/download/506/', + 'https://www.dkrz.de/redmine/attachments/download/506/', ] sources = [SOURCELOWER_TAR_GZ] checksums = ['c87ec59e29b3e4965ce2f8e614bd7f1597012b89af0fda4242f2eef06460794c'] diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb index eb4dc9cd3c0..fa28ecc4c0d 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2-iimpi-2021b.eb @@ -10,8 +10,8 @@ toolchain = {'name': 'iimpi', 'version': '2021b'} toolchainopts = {'usempi': True} source_urls = [ - ('https://swprojects.dkrz.de/redmine/attachments/download/513/'), - ('https://www.dkrz.de/redmine/attachments/download/513/'), + 'https://swprojects.dkrz.de/redmine/attachments/download/513/', + 'https://www.dkrz.de/redmine/attachments/download/513/', ] sources = [SOURCELOWER_TAR_GZ] checksums = ['b6714e42483486d76db146732bac74bc500096c15c9efa411ece3e00172fc360'] From 33a5976c9390fdae248f8a9e5e69bae23395548c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 09:42:51 +0100 Subject: [PATCH 3529/9987] adding easyconfigs: Fastaq-3.17.0-GCC-10.3.0.eb, SAMtools-0.1.19-GCC-10.3.0.eb --- .../f/Fastaq/Fastaq-3.17.0-GCC-10.3.0.eb | 30 +++++++++++++++++++ .../s/SAMtools/SAMtools-0.1.19-GCC-10.3.0.eb | 24 +++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fastaq/Fastaq-3.17.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/Fastaq/Fastaq-3.17.0-GCC-10.3.0.eb b/easybuild/easyconfigs/f/Fastaq/Fastaq-3.17.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..a826d27d2a3 --- /dev/null +++ b/easybuild/easyconfigs/f/Fastaq/Fastaq-3.17.0-GCC-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Fastaq' +version = '3.17.0' + +homepage = 'https://github.com/sanger-pathogens/Fastaq' +description = "Python3 scripts to manipulate FASTA and FASTQ files." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'sanger-pathogens' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-docker3.tar.gz'] +checksums = ['f65235f5d89f4621cf8e15676448e17d85620c05096cb6413134c4e29717ff5f'] + +dependencies = [ + ('Python', '3.9.5'), + ('SAMtools', '0.1.19'), + ('gzip', '1.10'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_commands = ['fastaq version'] + +options = {'modulename': 'pyfastaq'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-GCC-10.3.0.eb new file mode 100644 index 00000000000..d70838d8cfe --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-GCC-10.3.0.eb @@ -0,0 +1,24 @@ +name = 'SAMtools' +version = '0.1.19' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] +checksums = [ + 'd080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4', # samtools-0.1.19.tar.bz2 + '15334ff773d29dc38df64ec888f3724d7382cf34b013bfc3c868f7593d98b3ff', # SAMtools-0.1.19_Makefile-ncurses.patch +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' From a9038936936a2c085da3029fd6f356e2e4177777 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 10:42:46 +0100 Subject: [PATCH 3530/9987] adding easyconfigs: Roary-3.13.0-foss-2021a.eb, Kraken-1.1.1-GCCcore-10.3.0.eb, MCL-14.137-GCCcore-10.3.0.eb --- .../k/Kraken/Kraken-1.1.1-GCCcore-10.3.0.eb | 50 +++++++++++++++++++ .../m/MCL/MCL-14.137-GCCcore-10.3.0.eb | 41 +++++++++++++++ .../r/Roary/Roary-3.13.0-foss-2021a.eb | 48 ++++++++++++++++++ 3 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/r/Roary/Roary-3.13.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8972c7fe9c5 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-10.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PackedBinary' + +name = 'Kraken' +version = '1.1.1' + +homepage = 'https://ccb.jhu.edu/software/%(namelower)s/' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# Part is compiled with CXX, the rest is in Perl +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'openmp': True} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1_CXX-CXXFLAGS.patch'] +checksums = [ + '73e48f40418f92b8cf036ca1da727ca3941da9b78d4c285b81ba3267326ac4ee', # v1.1.1.tar.gz + '84c017d6a80ccaac1e23561c83cac90bcc3d62baa8d31657a7dafbc2c3f29726', # Kraken-1.1.1_CXX-CXXFLAGS.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Perl', '5.32.1'), + ('wget', '1.21.1'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_%(namelower)s.sh %(installdir)s' + +sanity_check_paths = { + 'files': ['add_to_library.sh', 'build_kraken_db.sh', 'check_for_jellyfish.sh', 'classify', 'clean_db.sh', + 'cp_into_tempfile.pl', 'db_shrink', 'db_sort', 'download_genomic_library.sh', + 'download_taxonomy.sh', 'kraken', 'kraken-build', 'kraken-filter', 'krakenlib.pm', + 'kraken-mpa-report', 'kraken-report', 'kraken-translate', 'make_seqid_to_taxid_map', + 'read_merger.pl', 'report_gi_numbers.pl', 'set_lcas', 'shrink_db.sh', + 'standard_installation.sh', 'upgrade_db.sh', 'verify_gi_numbers.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f6b8f025b67 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-10.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '14.137' + +homepage = 'https://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://micans.org/%(namelower)s/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +patches = ['%(name)s-%(version)s_fixperl.patch'] +checksums = [ + 'b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497', # mcl-14-137.tar.gz + '46988a287b2ee400a54fa485176d043b2a2d6589b6257cc6cf9c21689ea3842d', # MCL-14.137_fixperl.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Perl', '5.32.1'), +] + +preconfigopts = 'export CFLAGS="$CFLAGS -fcommon" && ' +configopts = '--enable-blast ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['clm', 'clmformat', 'clxdo', 'mcl', 'mclblastline', 'mclcm', 'mclpipeline', 'mcx', + 'mcxarray', 'mcxassemble', 'mcxdeblast', 'mcxdump', 'mcxi', 'mcxload', 'mcxmap', + 'mcxrand', 'mcxsubs']], + 'dirs': ['share'] +} + +sanity_check_commands = ["mcl --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Roary/Roary-3.13.0-foss-2021a.eb b/easybuild/easyconfigs/r/Roary/Roary-3.13.0-foss-2021a.eb new file mode 100644 index 00000000000..df89d796e47 --- /dev/null +++ b/easybuild/easyconfigs/r/Roary/Roary-3.13.0-foss-2021a.eb @@ -0,0 +1,48 @@ +easyblock = 'Tarball' + +name = 'Roary' +version = '3.13.0' + +homepage = 'https://github.com/sanger-pathogens/Roary' +description = "Rapid large-scale prokaryote pan genome analysis" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/sanger-pathogens/Roary/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Roary-3.13.0_fix-CD-HIT-regexp.patch'] +checksums = [ + '375f83c8750b0f4dea5b676471e73e94f3710bc3a327ec88b59f25eae1c3a1e8', # v3.13.0.tar.gz + '28b4176ebf20c7bc6f38fdf1cf7e71cae8bd823297543f93fbc28a0c1c3cf791', # Roary-3.13.0_fix-CD-HIT-regexp.patch +] + +dependencies = [ + ('Perl', '5.32.1'), + ('CD-HIT', '4.8.1'), + ('BLAST+', '2.11.0'), + ('MCL', '14.137'), + ('BEDTools', '2.30.0'), + ('PRANK', '170427'), + ('parallel', '20210622'), + ('FastTree', '2.1.11'), + ('Kraken', '1.1.1'), + ('BioPerl', '1.7.8'), + ('R', '4.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/roary', 'lib/Bio/Roary.pm'], + 'dirs': ['lib/Bio/Roary'], +} + +modextrapaths = {'PERL5LIB': 'lib'} + +sanity_check_commands = [ + "perldoc -lm Bio::Roary", + "roary -a", + # make sure all (optional) dependencies are found + # grep exits with '1' if no matches are found, hence we need to test the exit code ($?) + "roary -a 2>&1 | grep 'not found'; test $? -eq 1", +] + +moduleclass = 'bio' From 99c487735e62ceec71b088f80fcbd4ec8fcedcc6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 12:51:21 +0100 Subject: [PATCH 3531/9987] adding easyconfigs: Scoary-1.6.16-foss-2021a.eb, ETE-3.1.2-foss-2021a.eb --- .../easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb | 34 +++++++++++++++++ .../s/Scoary/Scoary-1.6.16-foss-2021a.eb | 38 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb new file mode 100644 index 00000000000..05d4d90ee50 --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.2' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +checksums = ['4fc987b8c529889d6608fab1101f1455cb5cbd42722788de6aea9c7d0a8e59e9'] + +dependencies = [ + ('lxml', '4.6.3'), + ('Python', '3.9.5'), + ('PyQt5', '5.15.4'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb new file mode 100644 index 00000000000..412551c4fc9 --- /dev/null +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Scoary' +version = '1.6.16' + +homepage = 'https://github.com/AdmiralenOla/Scoary' +description = "Microbial pan-GWAS using the output from Roary" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Tkinter', '%(pyver)s'), + ('ETE', '3.1.2'), +] + +exts_list = [ + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + (name, version, { + 'source_tmpl': 'scoary-%(version)s.tar.gz', + 'checksums': ['f433343422c5805a70a20f7fe83851490ae3cdf07745c65680de5feea40a6dca'], + 'modulename': False, + }), +] + + +sanity_check_paths = { + 'files': ['bin/scoary', 'bin/scoary_GUI', 'bin/vcf2scoary'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 98daa962d3a328fac36f19fc4478ef4217d8e0ef Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 13:15:02 +0100 Subject: [PATCH 3532/9987] adding easyconfigs: pastml-1.9.34-foss-2021a.eb --- .../p/pastml/pastml-1.9.34-foss-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/pastml/pastml-1.9.34-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pastml/pastml-1.9.34-foss-2021a.eb b/easybuild/easyconfigs/p/pastml/pastml-1.9.34-foss-2021a.eb new file mode 100644 index 00000000000..017de129f45 --- /dev/null +++ b/easybuild/easyconfigs/p/pastml/pastml-1.9.34-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'pastml' +version = '1.9.34' + +homepage = 'https://pastml.pasteur.fr/' +description = "Ancestor character reconstruction and visualisation for rooted phylogenetic trees" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Biopython', '1.79'), + ('SciPy-bundle', '2021.05'), + ('ETE', '3.1.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('itolapi', '4.1.0', { + 'checksums': ['e52c6ce86ccf8ab6702b8b110543a0d9f8d4eec1f13d5c278e2d1c25e3f7c7f2'], + }), + (name, version, { + 'source_urls': ['https://github.com/evolbioinfo/pastml/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['3ac606b5db79dc311110aa9a19a344ca28797275f174218b095e7874140f70da'], + }), +] + +sanity_check_commands = ['pastml --version'] + +moduleclass = 'bio' From 57a9e0110a0becccbcb0eb7f5541a39f1307b450 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 15:10:54 +0100 Subject: [PATCH 3533/9987] Add missing sanity_pip_check --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index 412551c4fc9..d3a039e9601 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -29,10 +29,11 @@ exts_list = [ }), ] - sanity_check_paths = { 'files': ['bin/scoary', 'bin/scoary_GUI', 'bin/vcf2scoary'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'bio' From 7759425f0ef22774b4967c87825dd87a3bbff6ad Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 15:32:06 +0100 Subject: [PATCH 3534/9987] Add other missing pip boilerplate --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index d3a039e9601..58b68198536 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -18,6 +18,9 @@ dependencies = [ ('ETE', '3.1.2'), ] +download_dep_fail = True +use_pip = True + exts_list = [ ('argparse', '1.4.0', { 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], From 2741fae7c06171aeba482a3cbd2419f679d3bd53 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 15:57:46 +0100 Subject: [PATCH 3535/9987] download_dep_fail not required... --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index 58b68198536..6e3329bd511 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -18,7 +18,6 @@ dependencies = [ ('ETE', '3.1.2'), ] -download_dep_fail = True use_pip = True exts_list = [ From 73f80973b500415c39a3106265baa06ba8788edf Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 21:51:01 +0100 Subject: [PATCH 3536/9987] {bio}[GCC/10.3.0] panito v0.0.1 (#15314) * adding easyconfigs: panito-0.0.1-GCC-10.3.0.eb * remove empty line Co-authored-by: Samuel Moors --- .../p/panito/panito-0.0.1-GCC-10.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/panito/panito-0.0.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/p/panito/panito-0.0.1-GCC-10.3.0.eb b/easybuild/easyconfigs/p/panito/panito-0.0.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..f29a5f36e99 --- /dev/null +++ b/easybuild/easyconfigs/p/panito/panito-0.0.1-GCC-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'panito' +version = '0.0.1' + +homepage = 'https://github.com/sanger-pathogens/panito' +description = """Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'sanger-pathogens' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a97047ab12cb73c90a2b5fe73034f5497a3de2c31459f30d6e9ae90db0fe6f0f'] + +builddependencies = [ + ('Autotools', '20210128'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "autoreconf -i -f && " + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/panito', 'lib/libpanito.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['panito -h'] + +moduleclass = 'bio' From 887d33e03ea93707adf846a058c07379a8f11532 Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 26 Apr 2022 08:46:45 +0200 Subject: [PATCH 3537/9987] adding easyconfigs: Pillow-9.1.0-GCCcore-10.3.0.eb --- .../p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..cf7bb373ec2 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '9.1.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f401ed2bbb155e1ade150ccc63db1a4f6c1909d3d378f7d1235a44e90d75fb97'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.2.0'), + ('freetype', '2.10.4') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From ddca2bd030c76885423bef0ad89e9ea7fa9c4a99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 26 Apr 2022 09:20:42 +0200 Subject: [PATCH 3538/9987] adding easyconfigs: IGV-2.12.3-Java-11.eb --- .../easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb new file mode 100644 index 00000000000..0005d342b59 --- /dev/null +++ b/easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'Tarball' + +name = 'IGV' +version = '2.12.3' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/software/igv/' +description = """This package contains command line utilities for + preprocessing, computing feature count density (coverage), sorting, and + indexing data files.""" + +toolchain = SYSTEM + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s'] +sources = ['%(name)s_%(version)s.zip'] +checksums = ['c87a109deb35994e1b28dee80b5acfd623ec3257f031fcd9cfce008cd32a4cf2'] + +dependencies = [('Java', '11', '', True)] + +sanity_check_paths = { + 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 65c706ec0f3080de33881c02bf4350786111c284 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 26 Apr 2022 09:36:07 +0200 Subject: [PATCH 3539/9987] adding easyconfigs: MultiQC-1.12-foss-2021b.eb --- .../m/MultiQC/MultiQC-1.12-foss-2021b.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb new file mode 100644 index 00000000000..17d9cfe8762 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb @@ -0,0 +1,73 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.12' + +homepage = 'https://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single report. + + MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), + ('PyYAML', '5.4.1'), + ('networkx', '2.6.3'), +] + +use_pip = True +download_dep_fail = True + +exts_list = [ + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('Markdown', '3.2.1', { + 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], + }), + ('lzstring', '1.0.4', { + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('rich', '10.16.0', { + 'checksums': ['06a1355131feda5eba4511dd749e9187ac0fb42209e189845d81e94505fc268e'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('multiqc', version, { + 'checksums': ['c62a8d24e3d1cebb42b615ac48201ecf4f2f863772f8f9fa59e466753d4af531'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 4be9ad102e859227f77951f0048bcfc33bd9ccfa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 26 Apr 2022 09:51:31 +0200 Subject: [PATCH 3540/9987] Remove download_dep_fail --- easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb index 17d9cfe8762..d8d6e704a8d 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb @@ -29,7 +29,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True exts_list = [ ('colormath', '3.0.0', { From 2d3180acc3dc829b2389c04ef109bc06fb528c57 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 26 Apr 2022 08:57:15 +0100 Subject: [PATCH 3541/9987] adding easyconfigs: OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb --- ...-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100755 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb new file mode 100755 index 00000000000..45ef99c6337 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.9' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('NCCL', '2.10.3', versionsuffix), + ('UCX-CUDA', '1.10.0', versionsuffix), +] + +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA --enable-ncclomb --with-nccl=$EBROOTNCCL' + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] + [ + 'libexec/osu-micro-benchmarks/nccl/%s' % x for x in ['collective', 'pt2pt'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From bb7f2d74265fa86665385f76885644043ee57c92 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 26 Apr 2022 11:22:10 +0200 Subject: [PATCH 3542/9987] adding easyconfigs: Arriba-2.2.1-GCC-11.2.0.eb --- .../a/Arriba/Arriba-2.2.1-GCC-11.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arriba/Arriba-2.2.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Arriba/Arriba-2.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/Arriba/Arriba-2.2.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..f66e167b344 --- /dev/null +++ b/easybuild/easyconfigs/a/Arriba/Arriba-2.2.1-GCC-11.2.0.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'Arriba' +version = '2.2.1' + +homepage = 'https://github.com/suhrig/arriba' +description = """Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. + It was developed for the use in a clinical research setting. Therefore, short runtimes and high + sensitivity were important design criteria.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/suhrig/%(namelower)s/releases/download/v%(version)s'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] +checksums = ['9cc14675a65c147b4261372b038d2e4dab1f43ffa1ceadd456c16a49b842f090'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('HTSlib', '1.14'), + ('libdeflate', '1.8'), + ('STAR', '2.7.9a'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +# make target with dynamically linked libraries is called bioconda, default is a statically linked binary +build_cmd_targets = 'bioconda' +# otherwise it fails to find sam.h +buildopts = 'CPATH=${EBROOTHTSLIB}/include/htslib:CPATH' + +postinstallcmds = ['mkdir %(installdir)s/database'] +files_to_copy = ['%(namelower)s', 'documentation', 'download_references.sh', 'draw_fusions.R', 'LICENSE', + 'README.md', 'run_%(namelower)s.sh'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [('%(namelower)s', '-h')] + +moduleclass = 'bio' From 99c6b56200c82f6cb542122a1c594cdc2eca8b0f Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 26 Apr 2022 13:31:51 +0200 Subject: [PATCH 3543/9987] adding easyconfigs: Jorg-1.0.0-foss-2020b.eb --- .../j/Jorg/Jorg-1.0.0-foss-2020b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb new file mode 100644 index 00000000000..61e8f3b6c77 --- /dev/null +++ b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb @@ -0,0 +1,38 @@ +# Author: Ben Langenberg ben.langenberg@ufz.de +# Helmholtz-Centre for Environmental Research +# Leipzig - Germany + +easyblock = 'PackedBinary' + +name = 'Jorg' +version = '1.0.0' + +homepage = 'https://github.com/lmlui/Jorg' +description = "A MAG Circularization Method By Lauren Lui, Torben Nielsen, and Adam Arkin" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/Helmholtz-UFZ', + 'repo_name': 'Jorg', + 'tag': 'v1.0.0', + }, +}] + +checksums = ['bd91baf986df0ba346f2a0fe7d1da47e28fe7411731ca94ac5f0e3c9b936c1ae'] + +prepend_to_path = ['.'] + +dependencies = [ + ('MIRA', '5.0rc2'), + ('seqtk', '1.3'), +] + +sanity_check_paths = { + 'files': ['jorg'], + 'dirs': [], +} + +moduleclass = 'bio' From bc1c4ad8db21ab42a8df4524165caa08ab40c30b Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 26 Apr 2022 13:59:01 +0200 Subject: [PATCH 3544/9987] remove trailing whitespace --- easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb index 61e8f3b6c77..d818d7e0918 100644 --- a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb @@ -31,7 +31,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['jorg'], + 'files': ['jorg'], 'dirs': [], } From f57978ee7d9368b136373bb9beb4866fafa9fc3b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 26 Apr 2022 14:55:12 +0200 Subject: [PATCH 3545/9987] add missing BLIS for FlexiBLAS-3.0.4-GCC-10.3.0 --- .../easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb index 627ddf691a1..47fcb322dc7 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-10.3.0.eb @@ -14,14 +14,17 @@ toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': builddependencies = [ ('CMake', '3.20.1'), ('Python', '3.9.5'), # required for running the tests + ('BLIS', '0.8.1'), ] -# note: first listed library will be used as default by FlexiBLAS, -# unless otherwise specified via easyconfig parameter flexiblas_default dependencies = [ ('OpenBLAS', '0.3.15'), ] +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +local_backends = ['OpenBLAS', 'BLIS'] + default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} sanity_check_all_components = True @@ -31,6 +34,7 @@ components = [ 'source_urls': ['https://csc.mpi-magdeburg.mpg.de/mpcsc/software/flexiblas/'], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['50a88f2e88994dda91b2a2621850afd9654b3b84820e737e335687a46751be5c'], + 'backends': local_backends, }), ('LAPACK', '3.10.0', { 'easyblock': 'CMakeMake', From 102df5da19357c61fa5511c5ed250d12069c3d49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2022 17:23:19 +0200 Subject: [PATCH 3546/9987] adding easyconfigs: NCO-5.0.6-intel-2019b.eb --- .../n/NCO/NCO-5.0.6-intel-2019b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb b/easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb new file mode 100644 index 00000000000..88a458a274d --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.0.6' + +homepage = "https://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d4c74e0268af94bdddcb0c77189830992f61c04147c23669b66470f1a8595d60'] + +builddependencies = [ + ('Bison', '3.3.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.26'), + ('expat', '2.2.7'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.6'), + ('GSL', '2.6'), + ('netCDF', '4.7.1'), + ('ESMF', '8.0.0'), # ncremap needs ESMF_RegridWeightGen +] + +configopts = "--enable-nco_cplusplus" + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] + +moduleclass = 'tools' From ad365668b352e3a654a68a6f09d5a382c188ebea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2022 17:26:56 +0200 Subject: [PATCH 3547/9987] adding easyconfigs: FreeBarcodes-3.0.a5-foss-2021b.eb --- .../FreeBarcodes-3.0.a5-foss-2021b.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeBarcodes/FreeBarcodes-3.0.a5-foss-2021b.eb diff --git a/easybuild/easyconfigs/f/FreeBarcodes/FreeBarcodes-3.0.a5-foss-2021b.eb b/easybuild/easyconfigs/f/FreeBarcodes/FreeBarcodes-3.0.a5-foss-2021b.eb new file mode 100644 index 00000000000..805353e127c --- /dev/null +++ b/easybuild/easyconfigs/f/FreeBarcodes/FreeBarcodes-3.0.a5-foss-2021b.eb @@ -0,0 +1,68 @@ +easyblock = 'PythonBundle' + +name = 'FreeBarcodes' +local_freebayes_commit = 'a684c11' +# see freebarcodes/__init__.py for version +version = '3.0.a5' + +homepage = 'https://github.com/hawkjo/freebarcodes' +description = "A package for the generation and decoding of FREE divergence error-correcting DNA barcodes" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), + ('Biopython', '1.79'), +] + +use_pip = True + +exts_list = [ + ('dill', '0.3.4', { + 'sources': ['dill-%(version)s.zip'], + 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], + }), + ('multiprocess', '0.70.12.2', { + 'sources': ['multiprocess-%(version)s.zip'], + 'checksums': ['206bb9b97b73f87fec1ed15a19f8762950256aa84225450abc7150d02855a083'], + }), + ('pox', '0.3.0', { + 'sources': ['pox-%(version)s.zip'], + 'checksums': ['cb968350b186466bb4905a21084587ec3aa6fd7aa0ef55d416ee0d523e2abe31'], + }), + ('ppft', '1.6.6.4', { + 'sources': ['ppft-%(version)s.zip'], + 'checksums': ['473442cc6731856990bd25bd6b454bb98720007de4523a73c560bdd0060463d2'], + }), + ('pathos', '0.2.8', { + 'sources': ['pathos-%(version)s.zip'], + 'checksums': ['1f0f27a90f7ab66c423ba796529000fde9360d17b2d8e50097641ff405fc6f15'], + }), + (name, version, { + 'sources': [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/hawkjo/', + 'repo_name': 'freebarcodes', + 'commit': 'a684c11', + }, + }], + 'checksums': [None], + }), +] + +sanity_check_paths = { + 'files': ['bin/freebarcodes'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "freebarcodes --help", + "cd %(builddir)s && freebarcodes generate 8 1 && ls -l barcodes8-1.txt", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 9bf6efbcc06d04555283e9ad93ce705d880528e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Apr 2022 19:21:35 +0200 Subject: [PATCH 3548/9987] build NCO 5.0.6 with intel/2019b using -O1 to work around Intel compiler crash --- easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb b/easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb index 88a458a274d..9fc25a873aa 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb @@ -7,6 +7,8 @@ homepage = "https://nco.sourceforge.net" description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" toolchain = {'name': 'intel', 'version': '2019b'} +# compile with -O1 to work around Intel compiler crash (Segmentation violation signal raised) +toolchainopts = {'lowopt': True} source_urls = ['https://github.com/nco/nco/archive/'] sources = ['%(version)s.tar.gz'] From 4d4e68e38ad88b3c458dace2b1268a45cb3240d8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 27 Apr 2022 08:23:18 +0200 Subject: [PATCH 3549/9987] adding easyconfigs: bam-readcount-0.8.0-GCC-11.2.0.eb --- .../bam-readcount-0.8.0-GCC-11.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..35df085ea66 --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-GCC-11.2.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'CMakeMake' + +name = 'bam-readcount' +version = '0.8.0' + +homepage = 'https://github.com/genome/bam-readcount' +description = """Count DNA sequence reads in BAM files""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'genome' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4f4dd558e3c6bfb24d6a57ec441568f7524be6639b24f13ea6f2bb350c7ea65f'] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('ncurses', '6.2'), +] + +# bam-readcount uses git to insert the version during configuration with CMake +# but in the release archives there is no git information +# local_commit is the git commit hash of the release +local_commit = 'dea4199' +local_versionfile = '%(builddir)s/%(name)s*/version/version.h.in' +preconfigopts = "sed -i -e 's/@FULL_VERSION@/%%(version)s/' %s && " % local_versionfile +preconfigopts += "sed -i -e 's/@COMMIT_HASH@/%s/' %s && " % (local_commit, local_versionfile) + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/%(name)s"], + 'dirs': [] +} + +sanity_check_commands = [ + # --help exists with exit code 1, so use grep to check for expected pattern in help output + "%(name)s --help 2>&1 | grep 'Example: bam-readcount -f'", + "%(name)s --version | grep 'version: %(version)s '", +] + +moduleclass = 'bio' From 9dfd0056d06088d9ee5aa63ee5a1bec134f568fd Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 27 Apr 2022 13:58:07 +0100 Subject: [PATCH 3550/9987] adding easyconfigs: FoX-4.1.2-GCC-11.2.0.eb --- .../easyconfigs/f/FoX/FoX-4.1.2-GCC-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/FoX/FoX-4.1.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/f/FoX/FoX-4.1.2-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FoX/FoX-4.1.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..26d2888084a --- /dev/null +++ b/easybuild/easyconfigs/f/FoX/FoX-4.1.2-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'FoX' +version = '4.1.2' + +homepage = 'http://homepages.see.leeds.ac.uk/~earawa/FoX/' +description = """FoX is an XML library written in Fortran 95. +It allows software developers to read, write and modify XML documents from Fortran applications without the +complications of dealing with multi-language development.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['http://homepages.see.leeds.ac.uk/~earawa/FoX/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3b749138229e7808d0009a97e2ac47815ad5278df6879a9cc64351a7921ba06f'] + +sanity_check_paths = { + 'files': ['lib/libFoX_%s.a' % x for x in ['common', 'dom', 'fsys', 'sax', 'utils', 'wcml', 'wkml', 'wxml']], + 'dirs': ['finclude', 'lib', 'bin'] +} + +modextrapaths = { + 'CPATH': ['finclude'], +} + +moduleclass = 'lib' From 566d5e67ba329115dd09e6f2314f19ed578af580 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 27 Apr 2022 14:02:08 +0100 Subject: [PATCH 3551/9987] adding easyconfigs: SUMO-1.12.0-foss-2021b.eb --- .../s/SUMO/SUMO-1.12.0-foss-2021b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb new file mode 100644 index 00000000000..1b0f2968117 --- /dev/null +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb @@ -0,0 +1,54 @@ +easyblock = 'CMakeMake' + +name = 'SUMO' +version = '1.12.0' + +homepage = 'https://sumo.dlr.de/' +description = """ +"Simulation of Urban MObility" (SUMO) is an open source, highly portable, microscopic and continuous traffic simulation +package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a +large set of tools for scenario creation. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/eclipse/sumo/archive/'] +sources = ['v%s.tar.gz' % version.replace('.', '_')] +checksums = ['049f5f50d1d27352d868cbb4b2a4b59bc0a913ef792b619c1adf1a289b3e48a7'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Xerces-C++', '3.2.3'), + ('GL2PS', '1.4.2'), + ('GDAL', '3.3.2'), + ('PROJ', '8.1.0'), + ('FoX', '4.1.2'), +] + +separate_build_dir = True + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'SUMO_HOME': 'share/sumo', +} + +local_bins = ['activitygen', 'dfrouter', 'duarouter', 'emissionsDrivingCycle', 'emissionsMap', 'jtrrouter', + 'marouter', 'netconvert', 'netgenerate', 'od2trips', 'polyconvert', 'sumo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + + ['lib/python%%(pyshortver)s/site-packages/libsumo/_libsumo.%s' % SHLIB_EXT], + 'dirs': ['bin', 'lib', 'share'], +} + +sanity_check_commands = [ + 'sumo --help', + "python -c 'import libsumo'", +] + +moduleclass = 'data' From 51f0522cd8a48dccb8237b4fdc14cb23a991d5c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2022 16:30:01 +0200 Subject: [PATCH 3552/9987] adding easyconfigs: breseq-0.36.1-foss-2021b.eb --- .../b/breseq/breseq-0.36.1-foss-2021b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/breseq/breseq-0.36.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/breseq/breseq-0.36.1-foss-2021b.eb b/easybuild/easyconfigs/b/breseq/breseq-0.36.1-foss-2021b.eb new file mode 100644 index 00000000000..4b2be16516f --- /dev/null +++ b/easybuild/easyconfigs/b/breseq/breseq-0.36.1-foss-2021b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'breseq' +version = '0.36.1' + +homepage = 'https://barricklab.org/breseq' +description = "breseq is a computational pipeline for the analysis of short-read re-sequencing data" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/barricklab/breseq/releases/download/v%(version)s/'] +sources = ['breseq-%(version)s.Source.tar.gz'] +checksums = ['d8904de452366237f9727fe4b025578de158da808cd41de9de042f2ba9233562'] + +dependencies = [ + ('R', '4.1.2'), + ('Bowtie2', '2.4.4'), + ('zlib', '1.2.11'), + ('ncurses', '6.2'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/breseq', 'bin/gdtools'], + 'dirs': [], +} + +# breseq --help exists with non-zero exit code, so use grep +sanity_check_commands = ["breseq --help | grep 'Usage: breseq'"] + +moduleclass = 'bio' From 9ae057f1bd943c5cb880c43ec6115f71ae4469a7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 27 Apr 2022 16:50:48 +0200 Subject: [PATCH 3553/9987] Change to "an HTML" Both "a" and "an" seem to be possible with HTML, but here "an" sounds better. Co-authored-by: Adam Huffman --- easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb index d8d6e704a8d..c0ea630b6fc 100644 --- a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.12-foss-2021b.eb @@ -16,7 +16,7 @@ version = '1.12' homepage = 'https://multiqc.info' description = """Aggregate results from bioinformatics analyses across many samples into a single report. - MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general + MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.""" toolchain = {'name': 'foss', 'version': '2021b'} From 386dd02531bac56459f33c0987bb5f7019135ada Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2022 16:57:18 +0200 Subject: [PATCH 3554/9987] add fallback URL for downloading isl source tarball to easyconfig for GCCcore v11.3.0 --- easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb index a911f6cd513..d877ec7eace 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb @@ -17,7 +17,7 @@ source_urls = [ 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'https://libisl.sourceforge.io/', # fallback URL for isl 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools ] From b1c85510f092cea0568c036108a76d7ef3d61449 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Apr 2022 17:08:04 +0200 Subject: [PATCH 3555/9987] update old GCCcore easyconfigs to use SHA256 checksums --- .../easyconfigs/g/GCCcore/GCCcore-5.3.0.eb | 18 ++++++------- .../easyconfigs/g/GCCcore/GCCcore-5.4.0.eb | 18 ++++++------- .../easyconfigs/g/GCCcore/GCCcore-6.1.0.eb | 26 +++++++++---------- .../easyconfigs/g/GCCcore/GCCcore-6.2.0.eb | 26 +++++++++---------- .../easyconfigs/g/GCCcore/GCCcore-7.1.0.eb | 25 +++++++++--------- 5 files changed, 54 insertions(+), 59 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb index 6e19891fcb4..5b31a2f935b 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.3.0.eb @@ -21,7 +21,6 @@ source_urls = [ 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] - sources = [ 'gcc-%(version)s.tar.bz2', 'gmp-6.1.0.tar.bz2', @@ -29,22 +28,21 @@ sources = [ 'mpc-1.0.3.tar.gz', 'isl-0.15.tar.bz2', ] - patches = [('mpfr-%s-allpatches-20151029.patch' % local_mpfr_version, '../mpfr-%s' % local_mpfr_version)] +checksums = [ + 'b84f5592e9218b73dbae612b5253035a7b34a9a1f7688d2e1bfaaf7267d5c4db', # gcc-5.3.0.tar.bz2 + '498449a994efeba527885c10405993427995d3f86b8768d8cdf8d9dd7c6b73e8', # gmp-6.1.0.tar.bz2 + 'b87feae279e6da95a0b45eabdb04f3a35422dab0d30113d58a7803c0d73a79dc', # mpfr-3.1.3.tar.gz + '617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3', # mpc-1.0.3.tar.gz + '8ceebbf4d9a81afa2b4449113cee4b7cb14a687d7a549a963deb5e2a41458b6b', # isl-0.15.tar.bz2 + 'ccbe4044c12db40d9f85ae5fd2ed443a3b19b95c86ebef05c82f41509cf6d1b4', # mpfr-3.1.3-allpatches-20151029.patch +] builddependencies = [ ('binutils', '2.26'), ('M4', '1.4.17'), ] -checksums = [ - 'c9616fd448f980259c31de613e575719', # gcc-5.3.0.tar.bz2 - '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 - '7b650781f0a7c4a62e9bc8bdaaa0018b', # mpfr-3.1.3.tar.gz - 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz - '8428efbbc6f6e2810ce5c1ba73ecf98c', # isl-0.15.tar.bz2 - '6476b450c3db177b2250f3549362380e', # mpfr-3.1.3-allpatches-20151029.patch -] languages = ['c', 'c++', 'fortran'] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb index 21fac24fad2..2d1a6ef5883 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -21,7 +21,6 @@ source_urls = [ 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] - sources = [ 'gcc-%(version)s.tar.bz2', 'gmp-6.1.0.tar.bz2', @@ -29,22 +28,21 @@ sources = [ 'mpc-1.0.3.tar.gz', 'isl-0.15.tar.bz2', ] - patches = [('mpfr-%s-allpatches-20160601.patch' % local_mpfr_version, '../mpfr-%s' % local_mpfr_version)] +checksums = [ + '608df76dec2d34de6558249d8af4cbee21eceddbcb580d666f7a5a583ca3303a', # gcc-5.4.0.tar.bz2 + '498449a994efeba527885c10405993427995d3f86b8768d8cdf8d9dd7c6b73e8', # gmp-6.1.0.tar.bz2 + '0d4de7e1476f79d24c38d5bc04a06fcc9a1bb9cf35fd654ceada29af03ad1844', # mpfr-3.1.4.tar.gz + '617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3', # mpc-1.0.3.tar.gz + '8ceebbf4d9a81afa2b4449113cee4b7cb14a687d7a549a963deb5e2a41458b6b', # isl-0.15.tar.bz2 + '73816930b9d1324127e41096f0c82ba9a1e82502c3c8e7ed82915d9cbb1a1e40', # mpfr-3.1.4-allpatches-20160601.patch +] builddependencies = [ ('binutils', '2.26'), ('M4', '1.4.17'), ] -checksums = [ - '4c626ac2a83ef30dfb9260e6f59c2b30', # gcc-5.4.0.tar.bz2 - '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 - '482ab3c120ffc959f631b4ba9ec59a46', # mpfr-3.1.4.tar.gz - 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz - '8428efbbc6f6e2810ce5c1ba73ecf98c', # isl-0.15.tar.bz2 - '22164533561142b70fda09af4e775acc', # mpfr-3.1.4-allpatches-20150603.patch -] languages = ['c', 'c++', 'fortran'] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb index 6e725dfd473..4c776b97184 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.1.0.eb @@ -22,7 +22,6 @@ source_urls = [ 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] - sources = [ 'gcc-%(version)s.tar.bz2', 'gmp-6.1.1.tar.bz2', @@ -30,24 +29,25 @@ sources = [ 'mpc-1.0.3.tar.gz', 'isl-0.16.1.tar.bz2', ] - -builddependencies = [ - ('M4', '1.4.17'), - ('binutils', '2.27'), -] - patches = [ ('mpfr-%s-allpatches-20160804.patch' % local_mpfr_version, '../mpfr-%s' % local_mpfr_version), ('%s-%s_fix-find-isl.patch' % (name, version)), 'GCCcore-6.x-fix-ubsan.patch', ] - checksums = [ - '8fb6cb98b8459f5863328380fbf06bd1', # gcc-6.1.0.tar.bz2 - '4c175f86e11eb32d8bf9872ca3a8e11d', # gmp-6.1.1.tar.bz2 - 'b8a2f6b0e68bef46e53da2ac439e1cf4', # mpfr-3.1.4.tar.gz - 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz - 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 + '09c4c85cabebb971b1de732a0219609f93fc0af5f86f6e437fd8d7f832f1a351', # gcc-6.1.0.tar.bz2 + 'a8109865f2893f1373b0a8ed5ff7429de8db696fc451b1036bd7bdf95bbeffd6', # gmp-6.1.1.tar.bz2 + 'd3103a80cdad2407ed581f3618c4bed04e0c92d1cf771a65ead662cc397f7775', # mpfr-3.1.4.tar.bz2 + '617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3', # mpc-1.0.3.tar.gz + '412538bb65c799ac98e17e8cfcdacbb257a57362acfaaff254b0fcae970126d2', # isl-0.16.1.tar.bz2 + '919e0de301f557fc3be8db7652d611adcd339b450994b990b47f6c49d9fac181', # mpfr-3.1.4-allpatches-20160804.patch + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.1.0_fix-find-isl.patch + 'a021bdc9da72438475168639d71dcbd8953becef8230eabd46bc5719519c164e', # GCCcore-6.x-fix-ubsan.patch +] + +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', '2.27'), ] languages = ['c', 'c++', 'fortran'] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb index e26311dea34..2df660db490 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -21,7 +21,6 @@ source_urls = [ 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] - sources = [ 'gcc-%(version)s.tar.bz2', 'gmp-6.1.1.tar.bz2', @@ -29,24 +28,25 @@ sources = [ 'mpc-1.0.3.tar.gz', 'isl-0.16.1.tar.bz2', ] - -builddependencies = [ - ('M4', '1.4.17'), - ('binutils', '2.27'), -] - patches = [ ('mpfr-%s-allpatches-20160804.patch' % local_mpfr_version, '../mpfr-%s' % local_mpfr_version), '%(name)s-%(version)s-fix-find-isl.patch', 'GCCcore-6.x-fix-ubsan.patch', ] - checksums = [ - '9768625159663b300ae4de2f4745fcc4', # gcc-6.2.0.tar.bz2 - '4c175f86e11eb32d8bf9872ca3a8e11d', # gmp-6.1.1.tar.bz2 - 'b8a2f6b0e68bef46e53da2ac439e1cf4', # mpfr-3.1.4.tar.gz - 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz - 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 + '9944589fc722d3e66308c0ce5257788ebd7872982a718aa2516123940671b7c5', # gcc-6.2.0.tar.bz2 + 'a8109865f2893f1373b0a8ed5ff7429de8db696fc451b1036bd7bdf95bbeffd6', # gmp-6.1.1.tar.bz2 + 'd3103a80cdad2407ed581f3618c4bed04e0c92d1cf771a65ead662cc397f7775', # mpfr-3.1.4.tar.bz2 + '617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3', # mpc-1.0.3.tar.gz + '412538bb65c799ac98e17e8cfcdacbb257a57362acfaaff254b0fcae970126d2', # isl-0.16.1.tar.bz2 + '919e0de301f557fc3be8db7652d611adcd339b450994b990b47f6c49d9fac181', # mpfr-3.1.4-allpatches-20160804.patch + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch + 'a021bdc9da72438475168639d71dcbd8953becef8230eabd46bc5719519c164e', # GCCcore-6.x-fix-ubsan.patch +] + +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', '2.27'), ] languages = ['c', 'c++', 'fortran'] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb index e32ec68aca6..bf8045247a3 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-7.1.0.eb @@ -21,7 +21,6 @@ source_urls = [ 'https://libisl.sourceforge.io/', # fallback URL for isl 'http://isl.gforge.inria.fr/', # original HTTP source for ISL ] - sources = [ 'gcc-%(version)s.tar.bz2', 'gmp-6.1.2.tar.bz2', @@ -29,23 +28,23 @@ sources = [ 'mpc-1.0.3.tar.gz', 'isl-0.16.1.tar.bz2', ] - -builddependencies = [ - ('M4', '1.4.18'), - ('binutils', '2.28'), -] - patches = [ ('mpfr-%s-allpatches-20161219.patch' % local_mpfr_version, '../mpfr-%s' % local_mpfr_version), 'GCCcore-6.2.0-fix-find-isl.patch', ] - checksums = [ - '6bf56a2bca9dac9dbbf8e8d1036964a8', # gcc-7.1.0.tar.bz2 - '8ddbb26dc3bd4e2302984debba1406a5', # gmp-6.1.2.tar.bz2 - 'b1d23a55588e3b2a13e3be66bc69fd8d', # mpfr-3.1.5.tar.gz - 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz - 'ac1f25a0677912952718a51f5bc20f32', # isl-0.16.1.tar.bz2 + '8a8136c235f64c6fef69cac0d73a46a1a09bb250776a050aec8f9fc880bebc17', # gcc-7.1.0.tar.bz2 + '5275bb04f4863a13516b2f39392ac5e272f5e1bb8057b18aec1c9b79d73d8fb2', # gmp-6.1.2.tar.bz2 + 'ca498c1c7a74dd37a576f353312d1e68d490978de4395fa28f1cbd46a364e658', # mpfr-3.1.5.tar.bz2 + '617decc6ea09889fb08ede330917a00b16809b8db88c29c31bfbb49cbf88ecc3', # mpc-1.0.3.tar.gz + '412538bb65c799ac98e17e8cfcdacbb257a57362acfaaff254b0fcae970126d2', # isl-0.16.1.tar.bz2 + '223001d1ef6e9a2c8275eb66c07670d2ea378a0b0082c60857ecc273d0ee44b7', # mpfr-3.1.5-allpatches-20161219.patch + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch +] + +builddependencies = [ + ('M4', '1.4.18'), + ('binutils', '2.28'), ] languages = ['c', 'c++', 'fortran'] From 8f3cf5880af7c9b8d2cb4df12158045b270816f9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 27 Apr 2022 17:39:19 +0100 Subject: [PATCH 3556/9987] adding easyconfigs: Rust-1.56.0-GCCcore-11.2.0.eb and patches: Rust-1.56_sysroot-fix-interpreter.patch --- .../r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb | 58 +++++++++++++++++++ .../Rust-1.56_sysroot-fix-interpreter.patch | 31 ++++++++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.56_sysroot-fix-interpreter.patch diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..58777add4e0 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.56.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.56_sysroot-fix-interpreter.patch'] +checksums = [ + 'cd0fd72d698deb3001c18e0f4bf8261d8f86420097eef94ca3a1fe047f2df43f', # rustc-1.56.0-src.tar.gz + 'b2e55ae31d8972c71116fbf3626d421ce270c24c76c1aa2b1d7d2be24576d717', # Rust-1.56_sysroot-fix-interpreter.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Python', '3.9.6', '-bare'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.56_sysroot-fix-interpreter.patch b/easybuild/easyconfigs/r/Rust/Rust-1.56_sysroot-fix-interpreter.patch new file mode 100644 index 00000000000..8c7cd835d04 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.56_sysroot-fix-interpreter.patch @@ -0,0 +1,31 @@ +Use patchelf to fix interpreter of binaries that are used during Rust bootstrap procedure +when EasyBuild is configured to build in an alternate sysroot + +This fixes problems like due to a clash with the interpreter from the host, and a more recent libc.so.6 that's picked up +from the alternate sysroot: +error: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (required by /tmp/easybuild/build/Rust/1.52.1/GCCcore-10.3.0/rustc-1.52.1-src/build/bootstrap/debug/deps/libproc_macro_error_attr-fbfef320d848b049.so) + +author: Kenneth Hoste (HPC-UGent) +ported for 1.56.0 by: Adam Huffman (BDI, University of Oxford) + +--- rustc-1.56.0-src/src/bootstrap/bootstrap.py.orig 2022-04-27 17:29:10.541273561 +0100 ++++ rustc-1.56.0-src/src/bootstrap/bootstrap.py 2022-04-27 17:30:32.959859017 +0100 +@@ -582,6 +582,18 @@ + if ostype != "Linux": + return + ++ sysroot = os.getenv("EASYBUILD_SYSROOT") ++ if sysroot and not fname.endswith(".so"): ++ # determine patch to interpreter in host via output produced by 'file -b /bin/bash' ++ readelf_out = subprocess.check_output(['readelf', '-l', '/bin/bash']).decode('ascii', 'ignore').strip() ++ regex = re.compile('.*program interpreter: ([^\]]+)', re.M) ++ res = regex.search(readelf_out) ++ interpreter_path = os.path.join(sysroot, res.group(1).lstrip('/')) ++ if not os.path.exists(interpreter_path): ++ raise Exception("Derived path to interpreter does not exist: %s" % interpreter_path) ++ cmd = ["patchelf", "--set-interpreter", interpreter_path, fname] ++ run(cmd, verbose=True) ++ + # Use `/etc/os-release` instead of `/etc/NIXOS`. + # The latter one does not exist on NixOS when using tmpfs as root. + try: From 972fbefe0e7928216a0a3b524255963d946e8687 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 27 Apr 2022 13:54:42 -0700 Subject: [PATCH 3557/9987] {langg}[foss/2021b] R 4.2.0 --- .../easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 3234 +++++++++++++++++ 1 file changed, 3234 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb new file mode 100644 index 00000000000..0742b309ce7 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -0,0 +1,3234 @@ +name = 'R' +version = '4.2.0' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-4.1.0_identify-flexiblas-in-configure.patch'] +checksums = [ + '38eab7719b7ad095388f06aa090c5a2b202791945de60d3e2bb0eab1f5097488', # R-4.2.0.tar.gz + '2c6720e2e144ae4fe00842daab0ebba72241080603e0ff1a6ca758738041b257', # R-4.1.0_identify-flexiblas-in-configure.patch +] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.13'), +] +dependencies = [ + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('cairo', '1.16.0'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('SQLite', '3.36'), + ('PCRE2', '10.37'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.6'), # for plottting in R + ('LibTIFF', '4.3.0'), + ('Java', '11', '', True), + ('Tk', '8.6.11'), # for tcltk + ('cURL', '7.78.0'), # for RCurl + ('libxml2', '2.9.10'), # for XML + ('GMP', '6.2.1'), # for igraph + ('NLopt', '2.7.0'), # for nloptr + ('FFTW', '3.3.10'), # for fftw + ('libsndfile', '1.0.31'), # for seewave + ('ICU', '69.1'), # for rJava & gdsfmt + ('HDF5', '1.12.1'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.1.0-4'), # for animation + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '14.17.6'), # for V8 (required by rstan) + ('GDAL', '3.3.2'), # for sf + ('MPFR', '4.1.0'), # for Rmpfr + ('libgit2', '1.1.1'), + ('OpenSSL', '1.1', '', True), +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 1st November 2021 +exts_list = [ + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('Rmpi', '0.6-9.2', { + 'checksums': ['358ac1af97402e676f209261a231f36a35e60f0301edf8ca53dac11af3c3bd1a'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.6-0', { + 'checksums': ['4516d48c9618e3f395db873e886f5deb3b66b32ebe10d4c26c1420ac848acbbf'], + }), + ('Rcpp', '1.0.8.3', { + 'checksums': ['9da5b84cdaf56e972b41e669d496b1ece2e91bcd435505c68b9f2bd98375f8bf'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-4', { + 'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'], + }), + ('geometry', '0.4.6', { + 'checksums': ['910465a8c8043faca73bcc7c81c9249b9938677ee6649468003b438a6503f5d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-3', { + 'checksums': ['f394e2c93233e8ad1c104562ea9349855dc8e303131f559cd59834f9aa3e41bd'], + }), + ('ff', '4.0.5', { + 'checksums': ['9aba9e271144ec224063ddba0d791e2fcdb9c912d48fdc49e204fce628355037'], + }), + ('bnlearn', '4.7.1', { + 'checksums': ['243930daa7f71c63fe1aa6717e5d55a116a597b83e08745cbcbe9a418d7c1509'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.17', { + 'checksums': ['3452601adbead9be4820794e3af2666f710fdf9b801186df565b80b43629c5dd'], + }), + ('formatR', '1.12', { + 'checksums': ['8b52efbf43cbef25d837bb99a793a590c0958b753052c032b52304724e808c8b'], + }), + ('gtools', '3.9.2', { + 'checksums': ['03b1898bf581f6d12fa90e23ff700cfa7c834ac10c6654bdac42d7ec943fa953'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.2', { + 'checksums': ['177d6059fc645d3d8883806d2dea1c5dfc68efdada9aadde8a96b6d57acf35b8'], + }), + ('xfun', '0.30', { + 'checksums': ['ebf81cf302e051f0361dc4c8b519d99e20a353b4b29cee13e768663ff562c0ee'], + }), + ('highr', '0.9', { + 'checksums': ['beff11390d936c90fdcc00e7ed0eb72220f3de403a51b56659e3d3e0b6d8ed4d'], + }), + ('infotheo', '1.2.0.1', { + 'checksums': ['c0fb8ec97ad3a49f231c4c993b5eee70c6a61c8c30dc4a46197867e4763a29d4'], + }), + ('lars', '1.3', { + 'checksums': ['c69e6a8da6a3344c0915dd1fd4c78fec5cdf50c62cf6297476e9bb7dc10b549d'], + }), + ('lazy', '1.2-17', { + 'checksums': ['27bf1216ac6220712fe7e86c0a288b7d7118f9088989f67e0a86b3d0f99c3370'], + }), + ('kernlab', '0.9-30', { + 'checksums': ['48fc3a839ae57e8ab6ec26a34093ca3306391e7b271bef6e69812e2b4859ee81'], + }), + ('mime', '0.12', { + 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-3', { + 'checksums': 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('xopen', '1.0.0', { + 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], + }), + ('sessioninfo', '1.2.2', { + 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], + }), + ('rcmdcheck', '1.4.0', { + 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], + }), + ('remotes', '2.4.2', { + 'checksums': ['f2ef875f24a485bf4f55a8c830f87cdd5db868f9a8cdb624dc452d0bf66ba516'], + }), + ('clisymbols', '1.2.0', { + 'checksums': ['0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.1', { + 'checksums': ['b14aaf4e910a9d2d6c65c93e645f0b0159c00898e669f917f83c03dfedb1dfea'], + }), + ('gh', '1.3.0', { + 'checksums': ['a44039054e8ca56496f2d9c7a10cdadf4a7383bc91086e768ba7e7f1fbcaed1c'], + }), + ('credentials', '1.3.2', { + 'checksums': 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('distillery', '1.2-1', { + 'checksums': ['4b88f0b34e472b9134ad403fb32283424f1883a5943e52c55f1fe05995efb5fa'], + }), + ('extRemes', '2.1-1', { + 'checksums': ['5a1927bb21f178ec5a3e3f862d792e690e45c16c88190e64e83aa1fb9e3ffa02'], + }), + ('tkrplot', '0.0-26', { + 'checksums': ['dd66264c2553f6927aff297c6b1c3b61867d6c63aec080f40a1e9d53cfc9d120'], + }), + ('misc3d', '0.9-1', { + 'checksums': ['a07bbb0de153e806cd79675ed478d2d9221cff825654f59a71a9cf61f4293d65'], + }), + ('multicool', '0.1-12', { + 'checksums': ['487d28d9c3c606be0cf56e2d8f8b0d79fb71949c68886ea9251fbb1c01664a36'], + }), + ('plot3D', '1.4', { + 'checksums': ['d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0'], + }), + ('plot3Drgl', '1.0.2', { + 'checksums': ['aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496'], + }), + ('OceanView', '1.0.6', { + 'checksums': ['2c5165975d6c49fdc83a892cb0406584928dd44000c9774fffc00fbd2fec86f3'], + }), + ('ks', '1.13.5', { + 'checksums': 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+ }), + ('servr', '0.24', { + 'checksums': ['d94e1d31802ce6bbab7a5838ff94cbca8cd998237d834ff25fedf7514f41a087'], + }), + ('rgexf', '0.16.2', { + 'checksums': ['6ee052b0de99d0c7492366b991d345a51b3d0cc890d10a68b8670e1bd4fc8201'], + }), + ('sem', '3.1-15', { + 'checksums': ['ad023b00e6e8eb20d107039caf1008c4b05104c7c69709e59c66fbddbf381316'], + }), + ('statnet.common', '4.5.0', { + 'checksums': ['3cdb23db86f3080462f15e29bcf3e941590bc17ea719993b301199b22d6f882f'], + }), + ('network', '1.17.1', { + 'checksums': ['fc3c3a0014f8895a11c33994c9b44c6ef6cc49c7d026cd41ae6bba5ef63005a7'], + }), + ('rle', '0.9.2', { + 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], + }), + ('sna', '2.6', { + 'checksums': ['3a016550d9f424a0613c3f5b0b680dbd3a1f20a343173d39a96034340ad9202a'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.5', { + 'checksums': 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+ ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-8', { + 'checksums': ['f3c72310f40773b3839a9506c3cb781d044e09b94f2f38d332bb24e5f9960f5a'], + }), + ('here', '1.0.1', { + 'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'], + }), + ('RcppTOML', '0.1.7', { + 'checksums': ['2f09f00cbee6c6eeff5d5f0195c10de0155496de15fbe8189c18627ee3090541'], + }), + ('reticulate', '1.24', { + 'checksums': ['b918c5204916601f757ad0fc629b2ae1eabab7cdf7f6aa2e219d26e506d916cc'], + }), + ('hdf5r', '1.3.5', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['87b75173ab226a9fbaa5b28289349f3c56b638629560a172994b8f9323c1622f'], + }), + ('DTRreg', '1.7', { + 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], + }), + ('pulsar', '0.3.7', { + 'checksums': ['78c9f7e3b2bf8a8d16a81d6ee43bb05b0c360219be473d920c8c8ccb2aba4e3d'], + }), + ('bayesm', '3.1-4', { + 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + }), + ('gsl', '2.1-7.1', { + 'checksums': ['ee98d1382d37ffa77538a90ccdbf44affbf1710a9e66b8ada73fa72e67921985'], + }), + ('energy', '1.7-10', { + 'checksums': ['543de4875c46cc90e711e71c45b082d962fbb5158a094f9f10d37d3f57e1bea7'], + }), + ('compositions', '2.0-4', { + 'checksums': ['7b9c7a3bf654fb02d9eb1b4a7566469b2f5232f3b2c1b324c02239fd31060faf'], + }), + ('clustree', '0.4.4', { + 'checksums': ['7a6100f88c9a6e8d10b253ee227ecf1dc4e84e418eb8da64cd801d2a158b956f'], + }), + ('plotly', '4.10.0', { + 'checksums': ['bd995c654dbc8c09a84adaba8def99766919e3894caf18b551bb26b2f591389a'], + }), + ('tweedie', '2.3.3', { + 'checksums': ['a032cad512dac37a8619e6f66cb513eb82a88a5a2ffbe91e92c2d44d1756d0d9'], + }), + ('RcppGSL', '0.3.11', { + 'checksums': ['f094ea26c99b04d9e203986a1f2003f02472ceca0e2ef1c3beefd3ae80aeada8'], + }), + ('mvabund', '4.2.1', { + 'checksums': ['ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.3.1', { + 'checksums': ['cd3f72b84f0c722e9c0b21c2b2de7683ec742345d7f8e62f67c8c93342c1a5c6'], + }), + ('grpreg', '3.4.0', { + 'checksums': ['fd57d20baf63d2cc5821998bca5c3fdcbe46c933c9553caa492911b12654d6ad'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('lpSolveAPI', '5.5.2.0-17.7', { + 'checksums': ['9ebc8e45ad73eb51e0b25049598a5bc758370cf89508e2328cf4bd93d68d55bb'], + }), + ('ergm', '4.1.2', { + 'checksums': ['1abc6ef53376a4132530c376ce477ae7a2590e95fe8feb011c0da9cfb4d49ba0'], + }), + ('networkDynamic', '0.11.1', { + 'checksums': ['7bbbc4fa3fedf188ca28e1e442be039866cf05ce51efb33fda5023b19dc2737f'], + }), + ('tergm', '4.0.2', { + 'checksums': ['5ab1d61166c90f90c77edd12544b5946e01a933cc3e7ca609cae72075b742a64'], + }), + ('ergm.count', '4.0.2', { + 'checksums': ['316ed3cbe4b472eec79e8a5fd4183ce953070f6d98056d87423bd6d9ac155bd1'], + }), + ('tsna', '0.3.5', { + 'checksums': ['4ee2f773d573f0f4bd93131156fdccf01d7f1a3f725eff3e885021098c6bff65'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.6-3', { + 'checksums': ['cb14ba20690b31fd813b05565484c866425f072a5ad99a5cbf1da63588958db3'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.1', { + 'checksums': ['14f67ce96dd8f1cb457614271b0b4376dd6fd3073a2e727a17c0964be67272cb'], + }), + ('asnipe', '1.1.16', { + 'checksums': ['be50f9fdef0f4bf9676b9c3c2906d0431afc678af55cf48b1119f9fc0adac44f'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.36.0.4', { + 'checksums': ['d33078a4db7a56d890d04a4677f28aeea84939c8fd8df1a8073ffed44af42014'], + }), + ('mlegp', '3.1.9', { + 'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.5', { + 'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.6', { + 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.10', { + 'checksums': ['59266ffdf702ab1ecca7cbcf0538afe38d1a15abea66056734b62c0c15609c7c'], + }), + ('GUTS', '1.2.3', { + 'checksums': ['40061ec1677def40b410b5ef90d01e0bcb0095abed1545513a33a01d4444adc2'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.3.0', { + 'checksums': ['1e9399d6b16079e6cdc43fa33742d6b7e6e2b6bb2ba470bfe9d30d55b7be4cb0'], + }), + ('circular', '0.4-94.1', { + 'checksums': ['82c653230e186e1e2612fa6181253a6484801119cafc2db957e9fa4f3d730a37'], + }), + ('cobs', '1.3-4', { + 'checksums': ['a1c7b77e4ca097349884fd1c0d863d74f9092766131094d603f34d33ab2e3c42'], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.8-10', { + 'checksums': ['af63a28a4958dbe82597586494d0277272842bb3869db70c547d0896f1345d2c'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0.2', { + 'checksums': ['4772c352e8d3d9b5a0b7480c0e0962de4f5060fb7bf3fcb8ee4fa1cb10f93fd4'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.19', { + 'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'], + }), + ('BMA', '3.18.17', { + 'checksums': ['6d8c514fa179f8a48c2105b551a8a08e28ea4375d06150a4b8ab4ccda577daf5'], + }), + ('BCEE', '1.3.0', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-60', { + 'checksums': ['6d21ddfd0d621ed3bac861890c600884b6ed5ff7d2a36c9778b892636dbbef2a'], + }), + ('bdsmatrix', '1.3-4', { + 'checksums': ['251e21f433a016ec85e478811ea3ad34c572eb26137447f48d1bbf3cc8bb06ea'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.21', { + 'checksums': ['0771f82034aa6a77af67f3572c900987b7e6b578d04d707c6e06689d021a2ff8'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.6', { + 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], + }), + ('sampling', '2.9', { + 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '4.3', { + 'checksums': ['f755808fcb618582acb862729b20e267d9c2214f22e6e7a0c8d29073d8faa7b8'], + }), + ('bbmle', '1.0.24', { + 'checksums': ['01edc00479fabf7491e47ff59bc4adbe6f0d4c23d22e76d1d49c4c1b6b4693ad'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.51.2', { + 'checksums': ['c116f979ed891ec55f3e1e7b9a92436b5ec9430c1170439a501ecb7e2a33ef4d'], + }), + ('tictoc', '1.0.1', { + 'checksums': ['a09a1535c417ddf6637bbbda5fca6edab6c7f7b252a64e57e99d4d0748712705'], + }), + ('ISOcodes', '2022.01.10', { + 'checksums': ['b25ddec624b46f5630c29267bdf4a749cfb9d001ef029fb9ca84dafe56b1c73f'], + }), + ('stopwords', '2.3', { + 'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0.1', { + 'checksums': ['1fedbb913bc13c790d2fabfe4edda0a987db3a078bea8c0ca9b777d20af08662'], + }), + ('topicmodels', '0.2-12', { + 'checksums': ['afd83a4381bf39e470446ebefd41ed03f314be400c1b2f702a4b1060eb8fd1b4'], + }), + ('tidytext', '0.3.2', { + 'checksums': ['6fe0ada78ee2cdf77c16e519a29b9baff61d8e23ab56aa0a9adc1b2a99a6472b'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.3.1', { + 'checksums': ['6f5a89f5ce0e90cbed1695b81259326c976e7a8f538157e223ee5f63b54412b8'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-13', { + 'checksums': ['7186d23e561818f3e1f01376a4fb2af9ccee775ce5afc1e3175f3b07a81db515'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.5.1', { + 'checksums': ['866a2f54a4e8726cc3062e27daa8a073e6ac4aeb6719af7845284f7a668745f1'], + }), 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('ismev', '1.42', { + 'checksums': ['0d57fbeca83bd478e84fcff795967d51d8448c629abe7adc6c4c18c7fb8bf1a5'], + }), + ('GJRM', '0.2-6', { + 'checksums': ['f8abe1900a83892a9ee96bc62cdb1a42fabf8ba66eed60e44f59bd203b5f6779'], + }), + ('penfa', '0.1.1', { + 'checksums': ['a22a8ac3d4a040c77e50ddc92328c1989eae536d79fe56013e9372ba27c114e5'], + }), + ('rngWELL', '0.10-7', { + 'checksums': ['0c00c54e69d7d552cfa08d766e4854c01c6c1c8e2c558f387760b91a55ef2d38'], + }), + ('randtoolbox', '1.31.1', { + 'checksums': ['30992e8156782542e9a2bffb75eb2e35f6d302a8c22cb7c3ed9004f0f0973bad'], + }), + ('kde1d', '1.0.4', { + 'checksums': ['124eb2e427e08fd24ca37e0baa697736601785d6c6fb1c97c2ebcc5146bb4556'], + }), + ('RcppThread', '2.1.3', { + 'checksums': ['127e3d333dd412334d89d633e92f40135f65d68c91b7945fa63ce0e35abcf946'], + }), + ('wdm', '0.2.3', { + 'checksums': ['5f0184f6f0f9e9b8c47fb571e4d34dff309644a50afe5f18e42b9c37f52c593b'], + }), + ('rvinecopulib', '0.6.1.1.3', { + 'checksums': ['212189441b4cd2383e485c2aa410837456ba70357834f443c9275e4775b8bf22'], + }), + ('PearsonDS', '1.2.2', { + 'checksums': ['443a0619b824332ba5e50733a2aaf2913230925a64960a9f589ae368bcba3dc8'], + }), + ('covsim', '0.2.1', { + 'checksums': ['57ca810c6950ab295078b745eb87fdd7f195e15082777eed9f1059b6302f13bf'], + }), + ('semTools', '0.5-5', { + 'checksums': ['ddf883753c5964eae8313d7e8a4703be52e649f10d3bc1d12ede6d1707b1fab6'], + }), + ('GPArotation', '2022.4-1', { + 'checksums': ['231e7edcdcc091fbecfb4f2e88d1a4344967cf7ea58074b385a4b8b48d9da224'], + }), + ('dcurver', '0.9.2', { + 'checksums': ['cc6c55090d3607910515981ea0c7221e40e7a29e0da0c5a5f42c3847012290ec'], + }), + ('mirt', '1.36.1', { + 'checksums': ['5215a0f4eb5949a3985a84a7d4776d4dd7471973a980c1d158ce82b3bde185bb'], + }), + ('rpf', '1.0.11', { + 'checksums': ['e1fd670ae7c3e947db08ce50d6b16ce1b3b8f63a9016b03baba760aee78921fb'], + }), + ('OpenMx', '2.20.6', { + 'checksums': ['65c50ce09f9c006b41b7311ec05eba3ae77926d84fb44e3905905208404826ed'], + }), + ('matlab', '1.0.2', { + 'checksums': ['a23dec736c51ae1864c1a53caac556a2f98e8020138a3b121badb0f5b7984154'], + }), + ('FactorCopula', '0.8', { + 'checksums': ['d95b0ccd1b0eebcf27a90286e9392f662b878a669c693fbbb4145798045134ff'], + }), + ('rpact', '3.2.3', { + 'checksums': ['3a6a6840e23209ec2e7634d4b85e232b44b21b520f0f5f369c7bfc0d2deed77e'], + }), + ('ldbounds', '2.0.0', { + 'checksums': ['d4279d5f9952643f9051cf37eeb8441fff7ac050a49ef6363a9f5cbc8287a26a'], + }), + ('catlearn', '0.9.1', { + 'checksums': ['c6c492f5cc6a9ec6fdbd3721dd64a4bb2e146152d64eeeab4db3d0575bd2f650'], + }), +] + +moduleclass = 'lang' From d494530a035a89f6590bb0f8c99be311ee5a1acb Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Thu, 28 Apr 2022 06:57:29 +0200 Subject: [PATCH 3558/9987] Remove unneeded preconfig opts --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb index b9c33a4d327..5148de10aa7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb @@ -23,15 +23,11 @@ dependencies = [ ('PMIx', '3.1.5'), ] -# replace -march=skylake-avx512 option with equivalent -m* flags, -# to avoid problems when building on systems which don't support AVX-512; -# cfr. https://github.com/open-mpi/ompi/issues/8306 -preconfigopts = "sed -i 's/-march=skylake-avx512/-mavx512f -mavx512bw -mavx512vl -mavx512dq/g' configure && " # disable MPI1 compatibility for now, see what breaks... # configopts = '--enable-mpi1-compatibility ' -# to enable SLURM integration (site-specific) +# to enable SLURM integration use e.g. --try-amend="configopts=--with-slurm" # configopts = '--with-slurm --with-pmi=/usr --with-pmi-libdir=/usr/lib64' moduleclass = 'mpi' From 2e2735477bd2212c756567c26c45d9170fb7e18e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 28 Apr 2022 08:09:04 +0200 Subject: [PATCH 3559/9987] adding easyconfigs: Nextflow-22.04.0.eb --- .../n/Nextflow/Nextflow-22.04.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb new file mode 100644 index 00000000000..14616b6305d --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CmdCp' + +name = 'Nextflow' +version = '22.04.0' + +homepage = 'https://www.nextflow.io' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4547a82228d1ad8615dd9916cd47a64a397405058579c0557cd11540633713ad'] + +# specify dependency on Java/11 "wrapper", rather than a specific Java version +dependencies = [('Java', '11', '', True)] + +skipsteps = ['configure', 'build'] + +_exe_files = ['%(namelower)s', 'gradlew'] + +files_to_copy = [ + (_exe_files, '%(installdir)s/bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' From f0e53a7b22d405dd06119454b5e1454b4a657ac3 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea Date: Thu, 28 Apr 2022 08:52:23 +0200 Subject: [PATCH 3560/9987] adding easyconfigs: CellRanger-ATAC-2.1.0.eb --- .../CellRanger-ATAC/CellRanger-ATAC-2.1.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.1.0.eb diff --git a/easybuild/easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.1.0.eb b/easybuild/easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.1.0.eb new file mode 100644 index 00000000000..e36d6f03c90 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.1.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Victor E. Goitea +# Email: victorg@bmb.sdu.dk + +easyblock = 'Tarball' + +name = 'CellRanger-ATAC' +version = '2.1.0' + +homepage = "https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac" +description = """Cell Ranger ATAC is a set of analysis pipelines that process +Chromium Single Cell ATAC data.""" + +toolchain = SYSTEM + +# Download manually from https://support.10xgenomics.com/single-cell-atac/software/downloads/latest +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3f44ba66ae789c2ab03f9c380a6718ca'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ['bin/cellranger-atac', 'cellranger-atac'], + 'dirs': ['bin/atac', 'lib'], +} + +sanity_check_commands = ["cellranger-atac testrun --id=tiny"] + +moduleclass = 'bio' \ No newline at end of file From d75df257bc2fc1b3c53a0b90b5b392201d37afb0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 28 Apr 2022 10:02:54 +0200 Subject: [PATCH 3561/9987] Prokka needs parallel --- easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb | 1 + easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb | 1 + easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb | 1 + easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb index eb877d4f4ae..16863a48b95 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb @@ -23,6 +23,7 @@ dependencies = [ ('BioPerl', '1.7.2', '-Perl-5.28.1'), ('BLAST+', '2.9.0'), ('Java', '11', '', True), + ('parallel', '20190622'), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb index dc0d383a4bd..38df8d57d1e 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb @@ -23,6 +23,7 @@ dependencies = [ ('BioPerl', '1.7.2'), ('BLAST+', '2.9.0'), ('Java', '11', '', True), + ('parallel', '20190622'), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb index 0ba029a4f1a..6b0f94eac8d 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb @@ -24,6 +24,7 @@ dependencies = [ ('BLAST+', '2.11.0'), ('Java', '11', '', True), ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20210322'), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb index edb51666011..d111dde510a 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb @@ -24,6 +24,7 @@ dependencies = [ ('BLAST+', '2.11.0'), ('Java', '11', '', True), ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20210622'), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', From d8ce817b1d5e31fd6638a796f378ce26ed38fe17 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2022 10:07:35 +0200 Subject: [PATCH 3562/9987] tweak MrBayes v3.2.7a easyconfig to align it better with existing MrBayes 3.2.7 easyconfigs --- .../m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb index 77812adf58f..250ee134598 100644 --- a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7a-iimpi-2019a.eb @@ -1,9 +1,11 @@ easyblock = 'ConfigureMake' + name = 'MrBayes' version = '3.2.7a' homepage = 'https://nbisweden.github.io/MrBayes/' -description = "MrBayes is a program for the Bayesian estimation of phylogeny." +description = """MrBayes is a program for Bayesian inference and model choice across + a wide range of phylogenetic and evolutionary models.""" toolchain = {'name': 'iimpi', 'version': '2019a'} toolchainopts = {'usempi': True} @@ -15,15 +17,17 @@ checksums = ['3eed2e3b1d9e46f265b6067a502a89732b6f430585d258b886e008e846ecc5c6'] builddependencies = [('pkg-config', '0.29.2')] dependencies = [ - ('beagle-lib', '3.1.2'), ('libreadline', '8.0'), + ('beagle-lib', '3.1.2'), ] -configopts = '--with-beagle --with-mpi' +configopts = "--with-mpi --with-readline --with-beagle=$EBROOTBEAGLEMINLIB " sanity_check_paths = { 'files': ['bin/mb'], - 'dirs': [] + 'dirs': ['share'] } +sanity_check_commands = ["mb -help"] + moduleclass = 'bio' From 976a7284eca81fb75080233f2a8d1db77a8cc541 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 28 Apr 2022 10:22:15 +0200 Subject: [PATCH 3563/9987] parallel 20190622->20190922 --- easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb index 38df8d57d1e..3f1da2c2203 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb @@ -23,7 +23,7 @@ dependencies = [ ('BioPerl', '1.7.2'), ('BLAST+', '2.9.0'), ('Java', '11', '', True), - ('parallel', '20190622'), + ('parallel', '20190922'), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', From ac096c486377bc7547f361b3a5539b01e540e20d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 28 Apr 2022 10:51:46 +0100 Subject: [PATCH 3564/9987] adding easyconfigs: Spark-3.2.1-foss-2021b.eb --- .../s/Spark/Spark-3.2.1-foss-2021b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb new file mode 100644 index 00000000000..7ae8baa1987 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb @@ -0,0 +1,54 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'Tarball' + +name = 'Spark' +version = '3.2.1' + +homepage = 'https://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [ + 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', + 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' +] +sources = ['%(namelower)s-%(version)s-bin-hadoop3.2.tgz'] +checksums = ['224e058cb0c6fb68b39896427a3ccd11ae2246e9bf465b5e29e4fb192d39a59c'] + +dependencies = [ + ('Python', '3.9.6'), + ('Java', '11', '', True), + # ('Hadoop', '2.10.0', '-native'), + ('Arrow', '6.0.0'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('py4j', '0.10.9.5', { + 'checksums': ['276a4a3c5a2154df1860ef3303a927460e02e97b047dc0a47c1c3fb8cce34db6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyspark', 'bin/spark-shell'], + 'dirs': ['python'] +} + +sanity_check_commands = [ + "pyspark -h", + "python -c 'import pyspark'", +] + +modextrapaths = {'PYTHONPATH': ['python', 'lib/python%(pyshortver)s/site-packages']} + +modextravars = {'SPARK_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 7d559f26d5448eca9f75236c9b2a040b838f45e3 Mon Sep 17 00:00:00 2001 From: nicholascheng94 Date: Thu, 28 Apr 2022 18:31:51 +0800 Subject: [PATCH 3565/9987] adding easyconfigs: libedit-20210910-GCCcore-8.3.0.eb --- .../libedit/libedit-20210910-GCCcore-8.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..b1de36ad1e5 --- /dev/null +++ b/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-8.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libedit' +version = '20210910' + +homepage = 'https://thrysoee.dk/editline/' +description = """ +This BSD-style licensed command line editor library provides generic line editing, +history, and tokenization functions, similar to those found in GNU Readline. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://thrysoee.dk/editline/'] +sources = ['%(namelower)s-%(version)s-3.1.tar.gz'] +checksums = ['6792a6a992050762edcca28ff3318cdb7de37dccf7bc30db59fcd7017eed13c5'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [('ncurses', '6.1')] + +sanity_check_paths = { + 'files': ['include/editline/readline.h', 'lib/libedit.%s' % SHLIB_EXT, 'lib/libedit.a'], + 'dirs': [] +} + +moduleclass = 'lib' From 33a930a3dbfc5ebf3cf451d717c6aed11ecc97cc Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 28 Apr 2022 13:42:58 +0200 Subject: [PATCH 3566/9987] adding easyconfigs: Spack-0.17.2.eb --- easybuild/easyconfigs/s/Spack/Spack-0.17.2.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spack/Spack-0.17.2.eb diff --git a/easybuild/easyconfigs/s/Spack/Spack-0.17.2.eb b/easybuild/easyconfigs/s/Spack/Spack-0.17.2.eb new file mode 100644 index 00000000000..43e2cb3a954 --- /dev/null +++ b/easybuild/easyconfigs/s/Spack/Spack-0.17.2.eb @@ -0,0 +1,32 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Tarball' + +name = 'Spack' +version = '0.17.2' + +homepage = 'https://spack.io/' +description = """Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific + software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, + and all of these builds can coexist on the same machine.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/spack/spack/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3c3c0eccc5c0a1fa89223cbdfd48c71c5be8b4645f5fa4e921426062a9b32d51'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ['bin/spack'], + 'dirs': ['etc/spack/defaults', 'lib/spack', 'share/spack', 'var/spack'], +} + +sanity_check_commands = [ + "spack list", + "spack versions gcc", +] + +moduleclass = 'devel' From 6fbe7d67951d22e21557ef0428d4aa25a39c4413 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 28 Apr 2022 14:11:42 +0200 Subject: [PATCH 3567/9987] adding easyconfigs: MCR-R2022a.1.eb --- easybuild/easyconfigs/m/MCR/MCR-R2022a.1.eb | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2022a.1.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2022a.1.eb b/easybuild/easyconfigs/m/MCR/MCR-R2022a.1.eb new file mode 100644 index 00000000000..f95338fe127 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2022a.1.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'MCR' +version = 'R2022a' # runtime version 9.12 +local_update = '1' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['4b3aab62005e68b18627e53143a6c4fae475fe3f6b7efadc7386aacda27b4248'] + +moduleclass = 'math' From 71ad9dd209a9cdd8cc49b2a673a791f78ba696d5 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 28 Apr 2022 14:35:52 +0200 Subject: [PATCH 3568/9987] adding easyconfigs: Go-1.18.1.eb --- easybuild/easyconfigs/g/Go/Go-1.18.1.eb | 33 +++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.18.1.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.18.1.eb b/easybuild/easyconfigs/g/Go/Go-1.18.1.eb new file mode 100644 index 00000000000..6cb96858b66 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.18.1.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Tarball' + +name = 'Go' +version = '1.18.1' + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] + +local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} +sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] +checksums = [{ + 'go%(version)s.linux-amd64.tar.gz': 'b3b815f47ababac13810fc6021eb73d65478e0b2db4b09d348eefad9581a2334', + 'go%(version)s.linux-arm64.tar.gz': '56a91851c97fb4697077abbca38860f735c32b38993ff79b088dac46e4735633', +}] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +sanity_check_commands = ["go help"] + +modextravars = {'GOROOT': '%(installdir)s'} + +moduleclass = 'compiler' From b13d88598c67a82612e7ebfafbcb24e8e902c055 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 28 Apr 2022 15:04:21 +0200 Subject: [PATCH 3569/9987] adding easyconfigs: Blender-3.1.2-linux-x64.eb --- .../b/Blender/Blender-3.1.2-linux-x64.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blender/Blender-3.1.2-linux-x64.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.1.2-linux-x64.eb b/easybuild/easyconfigs/b/Blender/Blender-3.1.2-linux-x64.eb new file mode 100644 index 00000000000..83ec0cd1fd3 --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-3.1.2-linux-x64.eb @@ -0,0 +1,36 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PackedBinary' + +name = 'Blender' +version = '3.1.2' +versionsuffix = '-linux-x64' + +homepage = 'https://www.blender.org' +description = """ +Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline, +modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video +editing and game creation. +""" + +toolchain = SYSTEM + +source_urls = ['http://ftp.nluug.nl/pub/graphics/%(namelower)s/release/%(name)s%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s-linux-x64.tar.xz'] +checksums = ['c1d345b25c6f83708b2681d354d70a3e6023c04bb73cc7943366c0c19e542958'] + +dependencies = [ + ('CUDA', '11.4.1'), +] + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': ['%(version_major_minor)s'], +} + +modaliases = { + 'blender': 'blender -- --cycles-device CUDA', +} + +moduleclass = 'vis' From 585f133800310b4d21723c246819e4b9500b9688 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 28 Apr 2022 15:10:02 +0200 Subject: [PATCH 3570/9987] adding easyconfigs: ReFrame-3.11.0.eb --- .../easyconfigs/r/ReFrame/ReFrame-3.11.0.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.0.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.0.eb new file mode 100644 index 00000000000..4fa02b9488a --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.0.eb @@ -0,0 +1,68 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.11.0' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + ('wheel', '0.37.0', { + 'checksums': ['e2ef7239991699e3355d54f8e968a21bb940a1dbf34a4d226741e64462516fad'], + }), + ('setuptools', '57.4.0', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['6bac238ffdf24e8806c61440e755192470352850f3419a52f26ffe0a1a64f465'], + }), + ('reframe', version, { + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], + 'checksums': ['3ddfef5482f0c304286a6c8f1ad0b3d75c4c61d0b9f9f8429b6157c189f2bb64'], + }), +] + +postinstallcmds = [ + "cp -r tutorials %(installdir)s", + "cp -r hpctestlib %(installdir)s", + "mkdir -p %(installdir)s/share && cp -r share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['lib', 'tutorials', 'external'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 4d74777f7989c269fe5daea8bada3474f75c38a2 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 28 Apr 2022 13:25:49 +0000 Subject: [PATCH 3571/9987] adding easyconfigs: Perl-5.34.1-GCCcore-11.3.0.eb, expat-2.4.8-GCCcore-11.3.0.eb, ncurses-6.3-GCCcore-11.3.0.eb, libreadline-8.1-GCCcore-11.3.0.eb, groff-1.22.4-GCCcore-11.3.0.eb, DB-18.1.40-GCCcore-11.3.0.eb --- .../d/DB/DB-18.1.40-GCCcore-11.3.0.eb | 33 + .../e/expat/expat-2.4.8-GCCcore-11.3.0.eb | 33 + .../g/groff/groff-1.22.4-GCCcore-11.3.0.eb | 27 + .../libreadline-8.1-GCCcore-11.3.0.eb | 41 + .../n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb | 47 + .../p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 1929 +++++++++++++++++ 6 files changed, 2110 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..21b56c74451 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('OpenSSL', '1.1', '', True)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fa885a3e7a8 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.4.8' + +homepage = 'https://libexpat.github.io' + +description = """ + Expat is an XML parser library written in C. It is a stream-oriented parser + in which an application registers handlers for things the parser might find + in the XML document (like start tags) +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_TAR_BZ2] +checksums = ['a247a7f6bbb21cf2ca81ea4cbb916bfb9717ca523631675f99b3d4a5678dcd16'] + +builddependencies = [('binutils', '2.38')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0cea653ddcc --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.22.4' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] + +builddependencies = [ + ('binutils', '2.38'), +] + +configopts = '--with-doc=no' + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2842a77b597 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.1' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['f8ceb4ee131e3232226a17f51b164afc46cd0b9e6cef344be87c65962cb82b02'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('ncurses', '6.3'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f59b0aedd9a --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.3' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] + +builddependencies = [('binutils', '2.38')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +configopts = [ + # default build + local_common_configopts, + # the UTF-8 enabled version (ncursesw) + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + +local_libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..dd9eb953748 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -0,0 +1,1929 @@ +name = 'Perl' +version = '5.34.1' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = ['perl-%(version)s.tar.gz'] +checksums = ['357951a491b0ba1ce3611263922feec78ccd581dddc24a446b033e25acf242a1'] + +builddependencies = [ + ('binutils', '2.38'), + ('groff', '1.22.4'), +] + +dependencies = [ + ('zlib', '1.2.12'), # for Net::SSLeay + ('expat', '2.4.8'), # for XML::Parser + ('ncurses', '6.3'), # for Term::ReadLine::Gnu + ('libreadline', '8.1'), # for Term::ReadLine::Gnu + ('DB', '18.1.40'), # for DB_File + ('OpenSSL', '1.1', '', True), # required for Net::SSLeay +] + +# !! order of extensions is important !! +# extensions updated on Apr 28th 2022 +exts_list = [ + ('Config::General', '2.65', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['4d6d5754be3a9f30906836f0cc10e554c8832e14e7a1341efb15b05d706fc58f'], + }), + ('File::Listing', '6.15', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['46c4fb9f9eb9635805e26b7ea55b54455e47302758a10ed2a0b92f392713770c'], + }), + ('ExtUtils::InstallPaths', '0.012', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], + }), + ('Test::Harness', '3.44', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7eb591ea6b499ece6745ff3e80e60cee669f0037f9ccbc4e4511425f593e5297'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Test::Fatal', '0.016', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7283d430f2ba2030b8cd979ae3039d3f1b2ec3dde1a11ca6ae09f992a66f788f'], + }), + ('Test::Warnings', '0.031', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['1e542909fef305e45563e9878ea1c3b0c7cef1b28bb7ae07eba2e1efabec477b'], + }), + ('File::ShareDir', '1.118', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], + }), + ('File::ShareDir::Install', '0.13', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['45befdf0d95cbefe7c25a1daf293d85f780d6d2576146546e6828aad26e580f9'], + }), + ('IPC::System::Simple', '1.30', { + 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN/'], + 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], + }), + ('Importer', '0.026', { + 'source_tmpl': 'Importer-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], + }), + ('Term::Table', '0.016', { + 'source_tmpl': 'Term-Table-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], + }), + ('Scope::Guard', '0.21', { + 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE/'], + 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], + }), + ('Sub::Info', '0.002', { + 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], + }), + ('Test2::Require::Module', '0.000145', { + 'source_tmpl': 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['15b8537d40fb3e6dae64b2e7e983c47a99b2c20816a180bb9c868b787a12ab5b'], + }), + ('Text::ParseWords', '3.31', { + 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['2ae555ba084d75b2b8feeeb8d1a00911276815ada86bccb1452236964d5a2fc7'], + }), + ('Encode', '3.17', { + 'source_tmpl': 'Encode-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], + 'checksums': ['b44cbf7dd60ec6128ec575dd348484975086522611bc7580cfd305a095faa6d2'], + }), + ('constant', '1.33', { + 'source_tmpl': 'constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], + }), + ('Data::Dumper', '2.183', { + 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': 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['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], + }), + ('AutoLoader', '5.74', { + 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], + }), + ('URI::Escape', '5.10', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['16325d5e308c7b7ab623d1bf944e1354c5f2245afcfadb8eed1e2cae9a0bd0b5'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], + 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], + }), + ('MCE::Mutex', '1.878', { + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], + 'checksums': ['bb5713197cc5ab91302aec746b5cc7204bf84556c30d6af67ce34a6fd38444ad'], + }), + ('Text::CSV_XS', '1.47', { + 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['4bbaffbdfb68505ef3326dc748e63ebe0db31157b78ca8dfcb8c3cd1d1313262'], + }), + ('DBD::CSV', '0.59', { + 'source_tmpl': 'DBD-CSV-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['2a5fadd1d50c18ea023560d39c2cc660ae2a65fa99d9b8244edca7d2dcce9dc0'], + }), + ('Array::Transpose', '0.06', { + 'source_tmpl': 'Array-Transpose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'], + 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], + }), + ('Config::Simple', '4.58', { + 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], + 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], + }), + ('Business::ISBN', '3.007', { + 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['50cc4686dd21c9537b49a231d71711e814ebd2f19aa4ca331baf92ff2de5ce19'], + }), + ('Business::ISBN::Data', '20210112.006', { + 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['98c2cfb266b5fdd016989abaa471d9dd4c1d593c508a6f01f66d184d5fee8bae'], + }), + ('common::sense', '3.75', { + 'source_tmpl': 'common-sense-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], + }), + ('IO::Compress::Bzip2', '2.106', { + 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['cb9a26ec7d86afb3081b6369620f1f67eaa45b7c41c4eb800e1da5e700a3e3f5'], + }), + ('JSON::XS', '4.03', { + 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], + }), + ('List::MoreUtils::XS', '0.430', { + 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], + }), + ('Authen::NTLM', '1.09', { + 'source_tmpl': 'NTLM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'], + 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('XML::SAX::Expat', '0.51', { + 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN'], + 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], + }), + ('Inline', '0.86', { + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], + }), + ('Sys::Info::Base', '0.7807', { + 'source_tmpl': 'Sys-Info-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['132362b0046e8dc4f12e1560903623a88a8871d09bf1c29d93d48d3f4a582acb'], + }), + ('Sys::Info', '0.7811', { + 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'], + }), + ('HTML::Template', '2.97', { + 'source_tmpl': 'HTML-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR/'], + 'checksums': ['6547af61f3aa85793f8616190938d677d7995fb3b720c16258040bc935e2129f'], + }), + ('MIME::Charset', '1.012.2', { + 'source_tmpl': 'MIME-Charset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI/'], + 'checksums': ['878c779c0256c591666bd06c0cde4c0d7820eeeb98fd1183082aee9a1e7b1d13'], + }), + ('Unicode::LineBreak', '2019.001', { + 'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI/'], + 'checksums': ['486762e4cacddcc77b13989f979a029f84630b8175e7fef17989e157d4b6318a'], + }), + ('String::Print', '0.94', { + 'source_tmpl': 'String-Print-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'], + }), + ('Log::Report', '1.33', { + 'source_tmpl': 'Log-Report-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['49624da338fd7d57288fa22a47241476fb5ce2f6008181f786c7830fe5af01ff'], + }), + ('Log::Report::Optional', '1.07', { + 'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], + }), + ('Sys::Info::Driver::Unknown', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Sys::Info::Driver::Linux', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER/'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), +] + +moduleclass = 'lang' From 01a8d341bab665cf7e98e597494e43508f0b1ec1 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 28 Apr 2022 17:02:16 +0200 Subject: [PATCH 3572/9987] Updates moduleclass --- easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb b/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb index 64dbf3bd32f..17573ab46e9 100644 --- a/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb +++ b/easybuild/easyconfigs/a/arosics/arosics-1.7.6-foss-2021a.eb @@ -77,4 +77,4 @@ exts_list = [ }), ] -moduleclass = 'devel' +moduleclass = 'geo' From 4b92adceb5101ac55ccd15357f4d6b0f13d28a2c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2022 17:09:30 +0200 Subject: [PATCH 3573/9987] adding easyconfigs: parallel-fastq-dump-0.6.7-gompi-2020b.eb --- .../parallel-fastq-dump-0.6.7-gompi-2020b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb new file mode 100644 index 00000000000..c74bb75c503 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2020b.eb @@ -0,0 +1,43 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'parallel-fastq-dump' +version = '0.6.7' + +homepage = 'https://github.com/rvalieris/parallel-fastq-dump' +description = "parallel fastq-dump wrapper" +docurls = ["https://github.com/rvalieris/parallel-fastq-dump"] + +toolchain = {'name': 'gompi', 'version': '2020b'} + +# https://github.com/rvalieris/parallel-fastq-dump/archive/ +github_account = 'rvalieris' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['cb33ea0ed0b1123c100aee7b9ea60a3fc3fc81a3a46be5237c85ba56380617de'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('SRA-Toolkit', '2.10.9'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + "files": ["bin/parallel-fastq-dump"], + "dirs": ["lib/python%(pyshortver)s/site-packages"], +} + +# This package doesn't produce importable module, only executable script. +options = {'modulename': False} + +sanity_check_commands = ["parallel-fastq-dump --version"] + +sanity_pip_check = True + +moduleclass = "bio" From 37f4a80f0c7501a6e35f01c366b8ac76e4d503dc Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 28 Apr 2022 17:15:48 +0200 Subject: [PATCH 3574/9987] adding easyconfigs: AMD-uProf-3.5.671.eb --- .../a/AMD-uProf/AMD-uProf-3.5.671.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.5.671.eb diff --git a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.5.671.eb b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.5.671.eb new file mode 100644 index 00000000000..13e22242029 --- /dev/null +++ b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-3.5.671.eb @@ -0,0 +1,34 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Binary' + +name = 'AMD-uProf' +version = '3.5.671' + +homepage = 'https://developer.amd.com/amd-uprof/' +description = """AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD + operating systems. It allows developers to better understand the runtime performance of their application and + to identify ways to improve its performance.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.amd.com/wordpress/media/files/'] +sources = ['AMDuProf_Linux_x64_%(version)s.tar.bz2'] +checksums = ['a73066305228658a14af5ecd6cf45a1aa47ae94f7e9d14db31f43013d3ef1a43'] + +extract_sources = True + +sanity_check_paths = { + 'files': ['include/AMDTPowerProfileApi.h', 'lib/x64/libAMDProfileController.a', + 'bin/libAMDThreadProfileAPI.%s' % SHLIB_EXT, 'bin/AMDuProf'], + 'dirs': ['Examples'] +} + +sanity_check_commands = ['AMDuProfCLI info --system'] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'bin' +} + +moduleclass = 'perf' From c744b86a039ecab56fedd45c93d8d212ffe9bec6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2022 18:14:47 +0200 Subject: [PATCH 3575/9987] adding easyconfigs: xESMF-0.3.0-foss-2020a-Python-3.8.2.eb, ESMPy-8.0.1-foss-2020a-Python-3.8.2.eb --- .../ESMPy-8.0.1-foss-2020a-Python-3.8.2.eb | 35 +++++++++++++++++++ .../xESMF-0.3.0-foss-2020a-Python-3.8.2.eb | 27 ++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..6ba46627ddf --- /dev/null +++ b/easybuild/easyconfigs/e/ESMPy/ESMPy-8.0.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'ESMPy' +version = '8.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://earthsystemmodeling.org/esmpy' +description = "Earth System Modeling Framework (ESMF) Python Interface" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['ESMF_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['9172fb73f3fe95c8188d889ee72fdadb4f978b1d969e1d8e401e8d106def1d84'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), # for numpy, mpi4py + ('ESMF', version), +] + +start_dir = 'src/addon/ESMPy' + +download_dep_fail = True + +# ESMPy's setup.py script doesn't support using "pip install" +use_pip = False + +buildopts = "--ESMFMKFILE=$EBROOTESMF/lib/esmf.mk" + +options = {'modulename': 'ESMF'} + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..6629bc3cca2 --- /dev/null +++ b/easybuild/easyconfigs/x/xESMF/xESMF-0.3.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'xESMF' +version = '0.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://xesmf.readthedocs.io' +description = "xESMF: Universal Regridder for Geospatial Data" + +toolchain = {'name': 'foss', 'version': '2020a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['66b6deb37f43749df06819fc2003bbd394207617cf7d8fd9dafe655d7af7b94c'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), # for numpy, scipy + ('ESMPy', '8.0.1', versionsuffix), + ('xarray', '0.16.1', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'geo' From 28c5a5537373e4d86bef02839969540518ac7585 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 28 Apr 2022 19:12:00 +0200 Subject: [PATCH 3576/9987] remove unneeded parentheses --- easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb index 66bd1ebce80..b02bf69c435 100644 --- a/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.9.2.1-gompi-2021b.eb @@ -13,8 +13,8 @@ toolchain = {'name': 'gompi', 'version': '2021b'} toolchainopts = {'usempi': True} source_urls = [ - ('https://swprojects.dkrz.de/redmine/attachments/download/515/'), - ('https://www.dkrz.de/redmine/attachments/download/515/'), + 'https://swprojects.dkrz.de/redmine/attachments/download/515/', + 'https://www.dkrz.de/redmine/attachments/download/515/', ] sources = [SOURCELOWER_TAR_GZ] checksums = ['cada1ecc479eaf088b8c95d9ae80122842843dd6af0a660ab6191fcb0da20a1e'] From 808bc8828551a7c9ff458faf7fa01a7b7f462ab2 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 28 Apr 2022 21:29:04 +0000 Subject: [PATCH 3577/9987] Update libreadline to 8.1.2 --- ...-GCCcore-11.3.0.eb => libreadline-8.1.2-GCCcore-11.3.0.eb} | 4 ++-- easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/l/libreadline/{libreadline-8.1-GCCcore-11.3.0.eb => libreadline-8.1.2-GCCcore-11.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-11.3.0.eb similarity index 92% rename from easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-11.3.0.eb index 2842a77b597..b0ba642f9d9 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-11.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libreadline' -version = '8.1' +version = '8.1.2' homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' description = """ @@ -18,7 +18,7 @@ toolchainopts = {'pic': True} source_urls = ['https://ftp.gnu.org/gnu/readline'] sources = ['readline-%(version)s.tar.gz'] -checksums = ['f8ceb4ee131e3232226a17f51b164afc46cd0b9e6cef344be87c65962cb82b02'] +checksums = ['7589a2381a8419e68654a47623ce7dfcb756815c8fee726b98f90bf668af7bc6'] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index dd9eb953748..f27c0c429ee 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ dependencies = [ ('zlib', '1.2.12'), # for Net::SSLeay ('expat', '2.4.8'), # for XML::Parser ('ncurses', '6.3'), # for Term::ReadLine::Gnu - ('libreadline', '8.1'), # for Term::ReadLine::Gnu + ('libreadline', '8.1.2'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File ('OpenSSL', '1.1', '', True), # required for Net::SSLeay ] From addea3483c4385edb17824a28967f3f6ce1fe3f2 Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Fri, 29 Apr 2022 11:50:08 +0800 Subject: [PATCH 3578/9987] {bio}[GCC/11.2.0] GMAP-GSNAP-2021-21-17 --- .../GMAP-GSNAP-2021-21-17-GCC-11.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-21-17-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-21-17-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-21-17-GCC-11.2.0.eb new file mode 100644 index 00000000000..8ec3299dc96 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-21-17-GCC-11.2.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2021-21-17' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9e8368bc997d79292f84a3553bc1a09c1d5ea5337d252dadc0f6ed85b4bb6dae'] + +# with these deps you can use standard compressed files +# details in http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length +# details in http://research-pub.gene.com/gmap/src/README +# configopts = 'MAX_STACK_READLENGTH=300' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +moduleclass = 'bio' From 62323b6c225730873265390db2b30bb879c5ea8a Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Fri, 29 Apr 2022 12:02:00 +0800 Subject: [PATCH 3579/9987] {bio}[foss/2021a] rnaQUAST v2.2.2 w/ Python 3.9.6 --- .../rnaQUAST-2.2.2-foss-2021a-Python-3.9.6.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021a-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021a-Python-3.9.6.eb b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021a-Python-3.9.6.eb new file mode 100644 index 00000000000..3fcf714957f --- /dev/null +++ b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021a-Python-3.9.6.eb @@ -0,0 +1,68 @@ +easyblock = 'Tarball' + +name = 'rnaQUAST' +version = '2.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://cab.spbu.ru/software/rnaquast/' +description = """rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. +In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality +assessment using third-party software.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/ablab/rnaquast/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['117dff9d9c382ba74b7b0ff24bc7b95b9ca6aa701ebf8afd22943aa54e382334'] + +dependencies = [ + ('Python', '3.9.6'), + ('GMAP-GSNAP', '2020-12-17'), + ('Biopython', '1.79', versionsuffix), + ('matplotlib', '3.4.3', versionsuffix), + ('BLAST+', '2.12.0'), +] + +postinstallcmds = [ + 'chmod -x %(installdir)s/VERSION' +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('joblib', '1.0.0', { + 'checksums': ['7ad866067ac1fdec27d51c8678ea760601b70e32ff1881d4dc8e1171f2b64b24'], + }), + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + ('argh', '0.26.2', { + 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], + }), + ('argcomplete', '1.12.2', { + 'checksums': ['de0e1282330940d52ea92a80fea2e4b9e0da1932aaa570f84d268939d1897b04'], + }), + ('pyfaidx', '0.5.9.2', { + 'checksums': ['73e740eaa45c097a09e543450f88d5ed06c0ece4b6936dad7e71077f67797b74'], + }), + ('gffutils', '0.10.1', { + 'checksums': ['a8fc39006d7aa353147238160640e2210b168f7849cb99896be3fc9441e351cb'], + }), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_paths = { + 'files': ['rnaQUAST.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'bio' From a2eed1ce27374f696d58f68bc7c052c28a185549 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 29 Apr 2022 07:30:23 +0200 Subject: [PATCH 3580/9987] adding easyconfigs: MEME-5.4.1-gompi-2021b.eb --- .../m/MEME/MEME-5.4.1-gompi-2021b.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb new file mode 100644 index 00000000000..1f203df24af --- /dev/null +++ b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb @@ -0,0 +1,62 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'MEME' +version = '5.4.1' + +homepage = 'https://meme-suite.org/meme/index.html' +description = """The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or + GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using + MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate + motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment + using SpaMo or CentriMo.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://%(namelower)s-suite.org/%(namelower)s/%(namelower)s-software/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c07fb8afafa60fc5e84ca24493c82fa6f4bd1df1a2622102edbf86a1c30fd11f'] + +dependencies = [ + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.11'), + ('Perl', '5.34.0'), + ('Python', '3.9.6'), + ('Ghostscript', '9.54.0'), + ('XML-Compile', '1.63'), +] + +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python ' +configopts += '--with-gs=${EBROOTGHOSTSCRIPT}/bin/gs ' +# config.log should indicate that all required/optional dependencies were found (see scripts/dependencies.pl) +configopts += " && grep 'All required and optional Perl modules were found' config.log" + +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " +runtest = 'test' + +fix_perl_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] +fix_python_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] + +sanity_check_paths = { + 'files': ['bin/meme', 'bin/dreme', 'bin/meme-chip', 'libexec/meme-%(version)s/meme2meme'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "meme -h 2>&1 | grep 'Usage:'", + "meme2meme --help", + "perl -e 'require MemeSAX'", + "python -c 'import sequence'", +] + +modextrapaths = { + 'PATH': ['libexec/meme-%(version)s'], + 'PERL5LIB': ['lib/meme-%(version)s/perl'], + 'PYTHONPATH': ['lib/meme-%(version)s/python'], +} + +moduleclass = 'bio' From 6ab7734bef47e4fc1072eb22094f9def0fc3589b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 29 Apr 2022 07:59:41 +0200 Subject: [PATCH 3581/9987] Fix module name for Python 3 --- easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb index 1f203df24af..4314a148799 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb @@ -50,7 +50,7 @@ sanity_check_commands = [ "meme -h 2>&1 | grep 'Usage:'", "meme2meme --help", "perl -e 'require MemeSAX'", - "python -c 'import sequence'", + "python -c 'import sequence_py3'", ] modextrapaths = { From e3fabf6acda0b58d35d47dd46200b4c75f6fdcfc Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Fri, 29 Apr 2022 14:11:24 +0800 Subject: [PATCH 3582/9987] {bio}[GCC/11.2.0] ntCard-1.2.1 --- .../n/ntCard/ntCard-1.2.1-GCC-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/n/ntCard/ntCard-1.2.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/n/ntCard/ntCard-1.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/n/ntCard/ntCard-1.2.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..dab98882b89 --- /dev/null +++ b/easybuild/easyconfigs/n/ntCard/ntCard-1.2.1-GCC-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ntCard' +version = '1.2.1' + +homepage = 'https://www.bcgsc.ca/resources/software/ntcard' +description = "ntCard is a streaming algorithm for estimating the frequencies of k-mers in genomics datasets." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/bcgsc/%(name)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2d635dec6e293780a5ae2b7bb422ff5cc825a03270b507f5061cbf0f09ee7076'] + +builddependencies = [ + ('Autotools', '20210726'), +] + +# ignore "type qualifiers ignored on cast result type" warning being treated as error due to -Werror +preconfigopts = 'export CXXFLAGS="$CXXFLAGS -Wno-ignored-qualifiers" && ' + +sanity_check_paths = { + 'files': ['bin/ntcard', 'bin/nthll'], + 'dirs': ['share/doc/ntcard'], +} + +sanity_check_commands = [ + "ntcard --help", + "nthll --help", +] + +moduleclass = 'bio' From a445e34480351185e08b7e118729e00fb64f70e3 Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Fri, 29 Apr 2022 14:16:19 +0800 Subject: [PATCH 3583/9987] {bio}[GCC/11.2.0] RNA-Bloom-1.4.3 --- .../r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..02ac929561f --- /dev/null +++ b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'RNA-Bloom' +version = '1.4.3' + +homepage = 'https://github.com/bcgsc/RNA-Bloom' +description = "RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/bcgsc/%(name)s/releases/download/v%(version)s'] +sources = ['rnabloom_v%(version)s.tar.gz'] +checksums = ['819274d674fe350ae3a1e1136618d52a8abb941280f604c6777ea4540b299a38'] + +dependencies = [ + ('Java', '1.8', '', True), + ('minimap2', '2.24'), + ('Racon', '1.5.0'), + ('ntCard', '1.2.1'), +] + +sanity_check_paths = { + 'files': ['LICENSE', 'README.md', 'rnabloom', 'RNA-Bloom.jar'], + 'dirs': [], +} + +sanity_check_commands = ["rnabloom --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From dbe0792adbd4f222de66dfd86ae5502214b276c0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 29 Apr 2022 11:02:44 +0200 Subject: [PATCH 3584/9987] add missing tbl2asn dependency for prokka 1.14.5 --- .../p/prokka/prokka-1.14.5-gompi-2019a.eb | 1 + .../p/prokka/prokka-1.14.5-gompi-2019b.eb | 1 + .../p/prokka/prokka-1.14.5-gompi-2020b.eb | 1 + .../p/prokka/prokka-1.14.5-gompi-2021a.eb | 1 + .../t/tbl2asn/tbl2asn-20220427-linux64.eb | 40 +++++++++++++++++++ 5 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb index 16863a48b95..97e2f412b2c 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb @@ -24,6 +24,7 @@ dependencies = [ ('BLAST+', '2.9.0'), ('Java', '11', '', True), ('parallel', '20190622'), + ('tbl2asn', '20220427', '-linux64', True), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb index 3f1da2c2203..b0cb7c51077 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb @@ -24,6 +24,7 @@ dependencies = [ ('BLAST+', '2.9.0'), ('Java', '11', '', True), ('parallel', '20190922'), + ('tbl2asn', '20220427', '-linux64', True), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb index 6b0f94eac8d..8f30af1ba54 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb @@ -25,6 +25,7 @@ dependencies = [ ('Java', '11', '', True), ('Bio-SearchIO-hmmer', '1.7.3'), ('parallel', '20210322'), + ('tbl2asn', '20220427', '-linux64', True), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb index d111dde510a..ebd872de355 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb @@ -25,6 +25,7 @@ dependencies = [ ('Java', '11', '', True), ('Bio-SearchIO-hmmer', '1.7.3'), ('parallel', '20210622'), + ('tbl2asn', '20220427', '-linux64', True), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb new file mode 100644 index 00000000000..3c66c131ad8 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CmdCp' + +name = 'tbl2asn' +version = '20220427' +versionsuffix = '-linux64' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = SYSTEM + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but most of the (gunzipped) versions have different sha256 +# checksums. +source_urls = ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])] +sources = [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:], + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}] +checksums = ['c76481700e196ebd98a83f4174e0146569db9d6fe5753ac18691e9836d5c6a75'] + +cmds_map = [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")] + +files_to_copy = [ + (['tbl2asn'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn'], + 'dirs': [], +} + +postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] + +moduleclass = 'bio' From 1ec539a6ab76729fcc3a2b842a0a8ce2a94b941c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 29 Apr 2022 11:05:20 +0200 Subject: [PATCH 3585/9987] add missing tbl2asn dependency for prokka 1.14.5 v2 --- easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb index 3c66c131ad8..8cb78e848ca 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb @@ -16,7 +16,7 @@ description = """Tbl2asn is a command-line program that automates the creation o toolchain = SYSTEM # It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, -# reporiting the same verion (tbl2asn --help -> 25.8) but most of the (gunzipped) versions have different sha256 +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 # checksums. source_urls = ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % (version[:4] + '-' + version[4:6] + '-' + version[6:])] From e8803ab6737fb175c234747af4e33dbf3a8bf024 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Apr 2022 18:12:49 +0200 Subject: [PATCH 3586/9987] {cae}[foss/2021b] GATE v9.2, Geant4 v11.0.1 --- .../easyconfigs/g/GATE/GATE-9.2-foss-2021b.eb | 31 ++ .../g/GATE/GATE-9.2_fix-Geant4-11.0.patch | 380 ++++++++++++++++++ .../g/Geant4/Geant4-11.0.1-GCC-11.2.0.eb | 26 ++ 3 files changed, 437 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATE/GATE-9.2-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GATE/GATE-9.2_fix-Geant4-11.0.patch create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-11.0.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GATE/GATE-9.2-foss-2021b.eb b/easybuild/easyconfigs/g/GATE/GATE-9.2-foss-2021b.eb new file mode 100644 index 00000000000..c211c0ef874 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-9.2-foss-2021b.eb @@ -0,0 +1,31 @@ +name = 'GATE' +version = '9.2' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/OpenGATE/Gate/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['GATE-9.2_fix-Geant4-11.0.patch'] +checksums = [ + '6fad86002dacae9d1f76ed0c455847d5d8960f667570292066b211a8b83247ee', # v9.2.tar.gz + '093a88718ff23edf332ac5a29b2810e77df40d63dd70e3b36f55195e4bb9e0b7', # GATE-9.2_fix-Geant4-11.0.patch +] + +builddependencies = [('CMake', '3.22.1')] +dependencies = [ + ('Geant4', '11.0.1'), + ('CLHEP', '2.4.5.1'), + ('ROOT', '6.24.06'), +] + +preinstallopts = "sed -i 's|/usr/local/bin|%(installdir)s/bin|g' Makefile &&" + +# enable extra capabilities (Davis requires Geant4 10.04 or newer) +configopts = "-DGATE_USE_OPTICAL=1 -DGATE_USE_DAVIS=1" + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GATE/GATE-9.2_fix-Geant4-11.0.patch b/easybuild/easyconfigs/g/GATE/GATE-9.2_fix-Geant4-11.0.patch new file mode 100644 index 00000000000..bfc4d3840a4 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-9.2_fix-Geant4-11.0.patch @@ -0,0 +1,380 @@ +see https://github.com/OpenGATE/Gate/pull/507 + https://github.com/OpenGATE/Gate/pull/508 + +From 1a4e09504359feb06ae68b331b7c54fb080e008d Mon Sep 17 00:00:00 2001 +From: Christian Pommranz +Date: Mon, 4 Apr 2022 21:53:37 +0200 +Subject: [PATCH] Fix gjs compilation against Geant4 v11.0 + +closes #507 +--- + cluster_tools/jobsplitter/gjs.cc | 2 +- + .../jobsplitter/src/GateMacfileParser.cc | 125 +++++++++--------- + .../jobsplitter/src/GateToPlatform.cc | 4 +- + 3 files changed, 66 insertions(+), 65 deletions(-) + +diff --git a/cluster_tools/jobsplitter/gjs.cc b/cluster_tools/jobsplitter/gjs.cc +index 6f786a958..5f6be6a43 100644 +--- a/cluster_tools/jobsplitter/gjs.cc ++++ b/cluster_tools/jobsplitter/gjs.cc +@@ -140,7 +140,7 @@ int main(int argc,char** argv) + if (size>4 && indicator==0) + { + G4String ss(argv[nextArg]); +- if (ss.contains(".mac")) ++ if (G4StrUtil::contains(ss, ".mac")) + { + indicator=1; + macfile=argv[nextArg]; +diff --git a/cluster_tools/jobsplitter/src/GateMacfileParser.cc b/cluster_tools/jobsplitter/src/GateMacfileParser.cc +index e01c97d74..bc45838f8 100644 +--- a/cluster_tools/jobsplitter/src/GateMacfileParser.cc ++++ b/cluster_tools/jobsplitter/src/GateMacfileParser.cc +@@ -122,7 +122,7 @@ G4int GateMacfileParser::GenerateResolvedMacros(G4String directory) + void GateMacfileParser::CleanAbort(ofstream& output, ofstream& splitfile) + { + //erase created files and the directory before error exit +- if( outputDir.contains(".Gate/") ) ++ if( G4StrUtil::contains(outputDir, ".Gate/")) + { //just in case to avoid a catastrophe + if (output) output.close(); + if (splitfile) splitfile.close(); +@@ -226,7 +226,7 @@ void GateMacfileParser::InsertAliases() + nAliases = (G4int)(listOfAliases.size()); + for (G4int i=1;i>lambda; + lambda=log(2.0)/lambda; + macline=""; + } +- else if (macline.contains("/gate/application/setTimeStop")) ++ else if (G4StrUtil::contains(macline, "/gate/application/setTimeStop")) + { + // We first check if we already encountered the addSlice command + if (addSlice!=-1.) +@@ -366,13 +366,13 @@ void GateMacfileParser::DealWithTimeCommands(ofstream& output,G4int splitNumber, + CleanAbort(output,splitfile); + exit(1); + } +- G4String temp=timeStop_str(position-1); +- if (!strcmp(temp,".")) timeStop_str=timeStop_str+"0"; ++ char temp=timeStop_str[position-1]; ++ if (temp != '.') timeStop_str=timeStop_str+"0"; + stringstream timeStop_ss(timeStop_str); + timeStop_ss>>timeStop; + splitfile<<"Stop time is: "<>timeStart; + splitfile<<"Start time is: "<>timeSlice; + splitfile<<"Timeslice is: "<>newAddSlice; +@@ -471,7 +471,7 @@ void GateMacfileParser::DealWithTimeCommands(ofstream& output,G4int splitNumber, + splitfile<<"New add slice: "<0) + { + subString=macline.substr(size,macline.length()); + macline=subString; +- } ++ } + + //remove intermediate spaces >1 + subString=macline; +- while (macline.contains(" ")) ++ while (G4StrUtil::contains(macline, " ")) + { + position=macline.find(" "); + subString=macline.substr(position+1,macline.length()); +@@ -1049,7 +1050,7 @@ const G4String GateMacfileParser::ExtractFileName(G4String key) + + bool GateMacfileParser::TreatOutputStream(G4String key, G4String def, G4String& origFile, char* SplitNumberAsString) + { +- if (!macline.contains(key)) return false; // nothing to do ++ if (!G4StrUtil::contains(macline, key)) return false; // nothing to do + origFile = ExtractFileName(key); // token after key + // look for possible unresolved aliases and replace them with default name + if( Braced(origFile) ) +diff --git a/cluster_tools/jobsplitter/src/GateToPlatform.cc b/cluster_tools/jobsplitter/src/GateToPlatform.cc +index 5b789b1e0..15462d6c9 100644 +--- a/cluster_tools/jobsplitter/src/GateToPlatform.cc ++++ b/cluster_tools/jobsplitter/src/GateToPlatform.cc +@@ -330,10 +330,10 @@ int GateToPlatform::GenerateCondorSubmitfile() + { + scriptFile.getline(buffer,256); + scriptline=buffer; +- if (scriptline.contains("#GJS PART => DO NOT REMOVE")!=0) noCopy=1; ++ if (G4StrUtil::contains(scriptline, "#GJS PART => DO NOT REMOVE")!=0) noCopy=1; + if (noCopy==0) + { +- if (scriptline.contains("Executable")!=0 && scriptline.contains("$GC_EXEC")!=0) ++ if (G4StrUtil::contains(scriptline, "Executable")!=0 && G4StrUtil::contains(scriptline, "$GC_EXEC")!=0) + submitFile<<"Executable = "< Date: Fri, 29 Apr 2022 10:46:28 +0000 Subject: [PATCH 3587/9987] adding easyconfigs: Autotools-20220317-GCCcore-11.3.0.eb, Autoconf-2.71-GCCcore-11.3.0.eb, Automake-1.16.5-GCCcore-11.3.0.eb, libtool-2.4.7-GCCcore-11.3.0.eb --- .../Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb | 48 +++++++++++++++++++ .../Automake-1.16.5-GCCcore-11.3.0.eb | 39 +++++++++++++++ .../Autotools-20220317-GCCcore-11.3.0.eb | 24 ++++++++++ .../l/libtool/libtool-2.4.7-GCCcore-11.3.0.eb | 32 +++++++++++++ 4 files changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..84cfa189e05 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-11.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.71' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('M4', '1.4.19'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.34.1'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +sanity_check_commands = [ + "autoconf --help", + "autom4te --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..dfde2665a12 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.5' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Autoconf', '2.71'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.34.1'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ['bin/aclocal', 'bin/automake'], + 'dirs': [] +} + +sanity_check_commands = [ + "aclocal --help", + "automake --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9a9fec6ec60 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20220317' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +dependencies = [ + ('Autoconf', '2.71'), # 20210128 + ('Automake', '1.16.5'), # 20211003 + ('libtool', '2.4.7'), # 20220317 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3a912298b17 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.7' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' From adbc55754add461b6e6c2f419bba2ec7a9c5aaea Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 29 Apr 2022 11:48:32 +0100 Subject: [PATCH 3588/9987] adding easyconfigs: Boost-1.79.0-GCC-11.2.0.eb --- .../b/Boost/Boost-1.79.0-GCC-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..1574a8a3dc2 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.2.0.eb @@ -0,0 +1,32 @@ +## +# Authors:: Denis Kristak +# +# Updated to 1.79.0: J. Sassmannshausen (Imperial College London, UK) + +name = 'Boost' +version = '1.79.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('ICU', '69.1'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' From 97a01dc24b774c446c774fb5c6f4a100dd0409b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2022 14:08:11 +0200 Subject: [PATCH 3589/9987] adding easyconfigs: purge_dups-1.2.5-foss-2021b.eb --- .../purge_dups/purge_dups-1.2.5-foss-2021b.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb new file mode 100644 index 00000000000..14d325e7688 --- /dev/null +++ b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'purge_dups' +version = '1.2.5' + +homepage = 'https://github.com/dfguan/purge_dups' +description = "purge haplotigs and overlaps in an assembly based on read depth" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), + ('minimap2', '2.24'), + ('zlib', '1.2.11'), +] + +use_pip = True + +default_easyblock = 'MakeCp' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], +} + +components = [ + (name, version, { + 'source_urls': ['https://github.com/dfguan/purge_dups/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['7879a8ecc26e5de1eaaf4b4633cb240ed2802d648068b193652477317a3e2645'], + 'start_dir': 'purge_dups-%(version)s', + 'prebuildopts': "cd src && ", + 'buildopts': 'CC="$CC" CFLAGS="$CFLAGS"', + 'files_to_copy': ['bin', 'scripts'], + }), + ('KMC', '20190629', { + 'source_urls': ['https://github.com/dfguan/KMC/archive/'], + 'sources': [{'download_filename': 'c05a5f9.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['7251941f4b1913bfdd68759d9292b419d95fe7c63815056e15ecb097a12a0bc4'], + 'prebuildopts': 'cd KMC-* && sed -i "s/-O3/$CFLAGS/g" makefile && ', + 'buildopts': 'CC="$CXX"', + 'files_to_copy': ['KMC-*/bin', 'KMC-*/spectra.py'], + }), +] + +exts_list = [ + ('runner', '20191220', { + 'sources': [{ + 'git_config': { + 'url': 'https://github.com/dfguan/', + 'repo_name': 'runner', + 'commit': '73a4d11', + }, + 'filename': 'runner-%(version)s.tar.gz', + }], + 'checksums': [None], + 'preinstallopts': "sed -i 's/0.0.0/%(version)s/g' setup.py && " + }), +] + +sanity_check_paths = { + 'files': ['bin/purge_dups'], + 'dirs': ['scripts'], +} + +sanity_check_commands = [ + "purge_dups -h 2>&1 | grep 'Program: purge_dups'", + "run_purge_dups.py -h", + "hist_plot.py -h", +] + +sanity_pip_check = True + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From 9df8bbcea378ebc0dd1482c05accb541505d26e2 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 29 Apr 2022 14:44:59 +0200 Subject: [PATCH 3590/9987] Disabled tests that are known to fail, see https://github.com/pytorch/pytorch/issues/76107 --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 3 + ...disable_failing_jit_cuda_fuser_tests.patch | 63 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index f0844c88ea2..c0edea843ed 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -30,6 +30,7 @@ patches = [ 'PyTorch-1.11.0_fix_sharded_imports.patch', 'PyTorch-1.11.0_increase_test_tolerances_TF32.patch', 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', ] checksums = [ None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' @@ -50,6 +51,8 @@ checksums = [ '26e179a4f6f57e49209092612ae5f5cd8c03fd2ca84566ba0244eabefc3736ba', # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch + 'c5e1bb0854c6a7724315e25c49f61abccf1d36c271f899bf2520f594bb1ab054', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch new file mode 100644 index 00000000000..0b8202d4611 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch @@ -0,0 +1,63 @@ +# Author: Caspar van Leeuwen +# Company: SURF +# We've seen that these tests fail for version 1.11.0, see https://github.com/pytorch/pytorch/issues/76107 +# These failures probably point to underlying issues, but the PR that fixes them touches a ton of files +# It's near-impossible to cherry pick that, without causing other issues. Moreover, +# PyTorch devs have pointed out that nvfuser is not enabled by default in 1.11.0, so chances of anyone +# hitting these issues are very small +# We simply disable the tests and accept that in v 1.11.0 in PyTorch, this functionality is broken. +diff -Nru pytorch_orig/test/test_jit_cuda_fuser.py pytorch/test/test_jit_cuda_fuser.py +--- pytorch_orig/test/test_jit_cuda_fuser.py 2022-04-29 14:03:49.399226000 +0200 ++++ pytorch/test/test_jit_cuda_fuser.py 2022-04-29 14:05:54.067297000 +0200 +@@ -1301,11 +1308,17 @@ + norm_shape = [input_shape[idx] for idx in range(dims - offset, dims)] + self._native_layer_norm_helper(input_shape, norm_shape, torch.float16, "cuda", 5e-3) + + @unittest.skipIf(not RUN_CUDA, "requires CUDA") + @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + @unittest.skipIf(not TEST_BF16, "device does not support BFloat16") ++ # Disable test, since it fails and nnfuser wasn't enabled by default in 1.11 ++ # Thus, even if this points to an underlying issue, it should be extremely rare that ++ # anyone hits it. ++ # See https://github.com/pytorch/pytorch/issues/76107 ++ # and https://github.com/easybuilders/easybuild-easyconfigs/pull/15137 ++ unittest.skip("Skipping test that is known to fail, see PT #76107") + def test_native_layer_norm_bfloat(self): + dims = 4 + rnds = 3 +@@ -2817,10 +2830,16 @@ + ref_module.bn.running_var, + e0)) + + @unittest.skipIf(not RUN_CUDA, "requires CUDA") + @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") ++ # Disable test, since it fails and nnfuser wasn't enabled by default in 1.11 ++ # Thus, even if this points to an underlying issue, it should be extremely rare that ++ # anyone hits it. ++ # See https://github.com/pytorch/pytorch/issues/76107 ++ # and https://github.com/easybuilders/easybuild-easyconfigs/pull/15137 ++ unittest.skip("Skipping test that is known to fail, see PT #76107") + def test_batch_norm_half(self): + with torch.backends.cudnn.flags(enabled=True): + setups = [ +@@ -2832,10 +2851,16 @@ + training, track_running_stats = training_and_track + self._test_batch_norm_impl_index_helper(4, 8, 5, affine, track_running_stats, training, torch.half) + + @unittest.skipIf(not RUN_CUDA, "requires CUDA") + @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") ++ # Disable test, since it fails and nnfuser wasn't enabled by default in 1.11 ++ # Thus, even if this points to an underlying issue, it should be extremely rare that ++ # anyone hits it. ++ # See https://github.com/pytorch/pytorch/issues/76107 ++ # and https://github.com/easybuilders/easybuild-easyconfigs/pull/15137 ++ unittest.skip("Skipping test that is known to fail, see PT #76107") + def test_batch_norm_impl_index_correctness(self): + with torch.backends.cudnn.flags(enabled=True): + batch = [2, 7, 16] From 166c066eeb92fd59f98928a6dccbc7e564c226ac Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 29 Apr 2022 15:02:16 +0200 Subject: [PATCH 3591/9987] Fixed patch as it wasn't being applied properly --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 +- ...disable_failing_jit_cuda_fuser_tests.patch | 23 ++++--------------- 2 files changed, 6 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index c0edea843ed..53dc59f0a0a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -52,7 +52,7 @@ checksums = [ # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch - 'c5e1bb0854c6a7724315e25c49f61abccf1d36c271f899bf2520f594bb1ab054', + '4882cb6db394152fa996ac32718d1c31f1a361e3eeef5b471a3a50f51a9b3ee1', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch index 0b8202d4611..55c4093db85 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch @@ -2,19 +2,14 @@ # Company: SURF # We've seen that these tests fail for version 1.11.0, see https://github.com/pytorch/pytorch/issues/76107 # These failures probably point to underlying issues, but the PR that fixes them touches a ton of files -# It's near-impossible to cherry pick that, without causing other issues. Moreover, +# It's near-impossible to cherry pick that, without causing other issues. Moreover, # PyTorch devs have pointed out that nvfuser is not enabled by default in 1.11.0, so chances of anyone # hitting these issues are very small # We simply disable the tests and accept that in v 1.11.0 in PyTorch, this functionality is broken. diff -Nru pytorch_orig/test/test_jit_cuda_fuser.py pytorch/test/test_jit_cuda_fuser.py ---- pytorch_orig/test/test_jit_cuda_fuser.py 2022-04-29 14:03:49.399226000 +0200 +--- pytorch_orig/test/test_jit_cuda_fuser.py 2022-04-29 14:54:30.771378000 +0200 +++ pytorch/test/test_jit_cuda_fuser.py 2022-04-29 14:05:54.067297000 +0200 -@@ -1301,11 +1308,17 @@ - norm_shape = [input_shape[idx] for idx in range(dims - offset, dims)] - self._native_layer_norm_helper(input_shape, norm_shape, torch.float16, "cuda", 5e-3) - - @unittest.skipIf(not RUN_CUDA, "requires CUDA") - @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") +@@ -1313,6 +1313,12 @@ @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, "Requires fusion optimization pass to be effective") @unittest.skipIf(not TEST_BF16, "device does not support BFloat16") @@ -27,11 +22,7 @@ diff -Nru pytorch_orig/test/test_jit_cuda_fuser.py pytorch/test/test_jit_cuda_fu def test_native_layer_norm_bfloat(self): dims = 4 rnds = 3 -@@ -2817,10 +2830,16 @@ - ref_module.bn.running_var, - e0)) - - @unittest.skipIf(not RUN_CUDA, "requires CUDA") +@@ -2828,6 +2834,12 @@ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, "Requires fusion optimization pass to be effective") @@ -44,11 +35,7 @@ diff -Nru pytorch_orig/test/test_jit_cuda_fuser.py pytorch/test/test_jit_cuda_fu def test_batch_norm_half(self): with torch.backends.cudnn.flags(enabled=True): setups = [ -@@ -2832,10 +2851,16 @@ - training, track_running_stats = training_and_track - self._test_batch_norm_impl_index_helper(4, 8, 5, affine, track_running_stats, training, torch.half) - - @unittest.skipIf(not RUN_CUDA, "requires CUDA") +@@ -2843,6 +2855,12 @@ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, "Requires fusion optimization pass to be effective") From 21873589442f191f1fdc49100a9f2becb57690d6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 29 Apr 2022 14:46:24 +0100 Subject: [PATCH 3592/9987] adding easyconfigs: bzip2-1.0.8-GCCcore-11.3.0.eb, cURL-7.83.0-GCCcore-11.3.0.eb, libarchive-3.6.1-GCCcore-11.3.0.eb, pkg-config-0.29.2-GCCcore-11.3.0.eb, XZ-5.2.5-GCCcore-11.3.0.eb, CMake-3.23.1-GCCcore-11.3.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-11.3.0.eb | 27 ++++++++++++ .../c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb | 30 +++++++++++++ .../c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ .../libarchive-3.6.1-GCCcore-11.3.0.eb | 33 ++++++++++++++ .../pkg-config-0.29.2-GCCcore-11.3.0.eb | 34 +++++++++++++++ .../x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb | 41 ++++++++++++++++++ 6 files changed, 208 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..39f1645a365 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.38'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d6c0f58b8ae --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.23.1' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['33fd10a8ec687a4d0d5b42473f10459bb92b3ae7def2b745dc10b192760869f3'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('cURL', '7.83.0'), + ('libarchive', '3.6.1'), + ('OpenSSL', '1.1', '', True), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4a4ad41cdfe --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.83.0' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0e64302a33d2fb79e0fc4e674260a22941e92ee2f11b894bf94d32b8f5531af'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', True), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bb86f508a75 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.6.1' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c676146577d989189940f1959d9e3980d28513d74eedfbc6b7f15ea45fe54ee2'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('XZ', '5.2.5'), + ('OpenSSL', '1.1', '', True), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a55b2586ff3 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [('binutils', '2.38')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e604951b507 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.5' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['XZ-5.2.2_compat-libs.patch'] +checksums = [ + '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 + '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch +] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.21', '', True), + ('binutils', '2.38'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' From dbbca7b0d60297aafe1f947009ea5329d7d352ae Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 29 Apr 2022 15:40:48 +0100 Subject: [PATCH 3593/9987] adding easyconfigs: OpenSSL-1.1.1n-GCCcore-11.3.0.eb --- .../OpenSSL/OpenSSL-1.1.1n-GCCcore-11.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1n-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1n-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1n-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bd3715f6733 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1n-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +name = 'OpenSSL' +version = '1.1.1n' + +homepage = 'https://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.openssl.org/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['40dceb51a4f6a5275bde0e6bf20ef4b91bfc32ed57c0552e2e8e15463372b17a'] + +dependencies = [('zlib', '1.2.12')] + +builddependencies = [ + ('Perl', '5.34.1'), + ('binutils', '2.38'), +] + +runtest = 'test' + +moduleclass = 'system' From c3aff2480c0e0064d8e238428aa78657b8d908bf Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 29 Apr 2022 16:30:12 +0100 Subject: [PATCH 3594/9987] adding easyconfigs: pkgconf-1.8.0-GCCcore-11.3.0.eb --- .../p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2acde1a41bd --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '1.8.0' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d7b6fdb522d81c11f5a0e0a0629a9f5480809ec90e595058674c1517822dfb8c'] + +builddependencies = [('binutils', '2.38')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' From 2bd0869064002c49176ba3b345fde5939891d175 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 29 Apr 2022 16:35:51 +0100 Subject: [PATCH 3595/9987] adding easyconfigs: UnZip-6.0-GCCcore-11.3.0.eb, Tcl-8.6.12-GCCcore-11.3.0.eb, SQLite-3.38.3-GCCcore-11.3.0.eb, libreadline-8.1-GCCcore-11.3.0.eb, libffi-3.4.2-GCCcore-11.3.0.eb --- .../l/libffi/libffi-3.4.2-GCCcore-11.3.0.eb | 29 +++++++++++ .../libreadline-8.1-GCCcore-11.3.0.eb | 41 +++++++++++++++ .../s/SQLite/SQLite-3.38.3-GCCcore-11.3.0.eb | 40 ++++++++++++++ .../t/Tcl/Tcl-8.6.12-GCCcore-11.3.0.eb | 41 +++++++++++++++ .../u/UnZip/UnZip-6.0-GCCcore-11.3.0.eb | 52 +++++++++++++++++++ 5 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.38.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8f406d5d7c9 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.2-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.2' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v3.4.2/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['540fb721619a6aba3bdeef7d940d8e9e0e6d2c193595bc243241b77ff9e93620'] + +builddependencies = [ + ('binutils', '2.38'), +] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2842a77b597 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.1' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['f8ceb4ee131e3232226a17f51b164afc46cd0b9e6cef344be87c65962cb82b02'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('ncurses', '6.3'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.38.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.38.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..45edabdef72 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.38.3-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.38.3' +local_filename_version = '3380300' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2022/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['61f2dd93a2e38c33468b7125967c3218bf9f4dd8365def6025e314f905dc942e'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('libreadline', '8.1'), + ('Tcl', '8.6.12'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a45cf5082e2 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.12' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['26c995dd0f167e48b11961d891ee555f680c175f7173ff8cb829f4ebcde4c1a6'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..16a87c4c8fd --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-11.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' +buildopts += 'LF2="$LDFLAGS" ' +# Note: CF is multiple lines +buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' +buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' +buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From 36aaaae674fd547760349ed03da93eaaa13fc06c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 29 Apr 2022 16:42:41 +0100 Subject: [PATCH 3596/9987] adding easyconfigs: Python-3.10.4-GCCcore-11.3.0-bare.eb --- .../Python-3.10.4-GCCcore-11.3.0-bare.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb new file mode 100644 index 00000000000..29484d0d038 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb @@ -0,0 +1,35 @@ +name = 'Python' +version = '3.10.4' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['f3bcc65b1d5f1dc78675c746c98fcee823c038168fc629c5935b044d0911ad28'] + +builddependencies = [ + ('UnZip', '6.0'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('binutils', '2.38'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.1'), + ('ncurses', '6.3'), + ('SQLite', '3.38.3'), + ('XZ', '5.2.5'), + ('libffi', '3.4.2'), + ('OpenSSL', '1.1', '', True), +] + +install_pip = True + +moduleclass = 'lang' From 8c31f88671c81322cf674018508ed607f0c3c4a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2022 17:55:05 +0200 Subject: [PATCH 3597/9987] stick to minimap 2.22 as dependency for purge_deps with foss/2021b --- .../easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb index 14d325e7688..28d039185f1 100644 --- a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb +++ b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Python', '3.9.6'), ('matplotlib', '3.4.3'), - ('minimap2', '2.24'), + ('minimap2', '2.22'), ('zlib', '1.2.11'), ] From 649d84d2747a227f242741da414c3e7d2e377993 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 29 Apr 2022 17:29:45 +0100 Subject: [PATCH 3598/9987] adding easyconfigs: Rust-1.60.0-GCCcore-11.3.0.eb --- .../r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..24e0975288d --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.60.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +#patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] +checksums = [ + '20ca826d1cf674daf8e22c4f8c4b9743af07973211c839b85839742314c838b7', # rustc-1.60.0-src.tar.gz +# 'e3db7005585eb807ecb69929818740f00417cac247b1065a9d43a7f16cf05e0b', # Rust-1.52.1_sysroot-fix-interpreter.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Python', '3.10.4', '-bare'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' From dd20324f1379fd12c9936ed1a98d85bc757d50f1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 29 Apr 2022 17:33:54 +0100 Subject: [PATCH 3599/9987] adding easyconfigs: git-2.36.0-GCCcore-11.3.0-nodocs.eb --- .../g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb diff --git a/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb new file mode 100644 index 00000000000..b4bb0d64474 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb @@ -0,0 +1,47 @@ +## +# Author: Robert Mijakovic +## +# updated to 2.33.1 +# J. Sassmannshausen / GSTT + +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.36.0' +versionsuffix = '-nodocs' + +homepage = 'https://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['59dbc158dce293798570166fe7acfe225514f2868bc2d6e25c1a5a00c4ac0888'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('expat', '2.4.8'), + ('gettext', '0.21'), + ('Perl', '5.34.1'), + ('OpenSSL', '1.1', '', True), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['libexec/git-core', 'share'], +} + +moduleclass = 'tools' From b68dc4ce248d70bc33b9e1694ff135b99d20c101 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 29 Apr 2022 17:34:45 +0100 Subject: [PATCH 3600/9987] add expat, gettext, libxml2 --- .../g/gettext/gettext-0.21-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ .../libxml2/libxml2-2.9.13-GCCcore-11.3.0.eb | 27 ++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.13-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9b5bf58331c --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c77d0da3102aec9c07f43671e60611ebff89a996ef159497ce8e59d075786b12'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('libxml2', '2.9.13'), + ('ncurses', '6.3'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.13-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.13-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..67afe86777d --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.13-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.9.13' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['276130602d12fe484ecc03447ee5e759d0465558fbc9d6bd144e3745306ebf0e'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.12'), +] + +moduleclass = 'lib' From 3f9ec557547d975d5b9b5311924f14091aa99881 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2022 19:41:33 +0200 Subject: [PATCH 3601/9987] add Hmsc extension to R v4.1.2 easyconfig --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index ce4464bb9aa..0fd0db995ad 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3304,6 +3304,12 @@ exts_list = [ ('SNFtool', '2.3.1', { 'checksums': ['982fe7c57f52c0c272b8cb5863dc5d50623b368e24ff6e27fc8b17acc0101f16'], }), + ('BayesLogit', '2.1', { + 'checksums': ['3a423f68339ed1bf25e21be53b1fd68452ed7807b17c36239fba759dc6fc6b70'], + }), + ('Hmsc', '3.0-11', { + 'checksums': ['318e95ea88a15939dac33691886a9ce0c54765b25a3f4ef483d168bfc699098a'], + }), ] moduleclass = 'lang' From affc6fb54b5a596d73734c1f2a689a342948e4e6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 29 Apr 2022 19:18:17 +0100 Subject: [PATCH 3602/9987] adding easyconfigs: GMP-6.2.1-GCCcore-11.3.0.eb --- .../g/GMP/GMP-6.2.1-GCCcore-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..33d857b7858 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.2.1' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +# copy libgmp.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' From 6605f3494f7789e2a1e655ff7a87b539b9345c72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2022 21:19:27 +0200 Subject: [PATCH 3603/9987] adding easyconfigs: libheif-1.12.0-GCC-11.2.0.eb, libde265-1.0.8-GCC-11.2.0.eb --- .../l/libde265/libde265-1.0.8-GCC-11.2.0.eb | 27 +++++++++++++++++++ .../l/libheif/libheif-1.12.0-GCC-11.2.0.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb new file mode 100644 index 00000000000..38d6c4a7d6e --- /dev/null +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'libde265' +version = '1.0.8' + +homepage = 'https://github.com/strukturag/libde265' +description = "libde265 is an open source implementation of the h.265 video codec" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['24c791dd334fa521762320ff54f0febfd3c09fc978880a8c5fbc40a88f21d905'] + +builddependencies = [('CMake', '3.22.1')] + +sanity_check_paths = { + 'files': ['bin/dec265', 'bin/enc265', 'lib/liblibde265.%s' % SHLIB_EXT], + 'dirs': ['include/libde265', 'lib/cmake/libde265'], +} + +sanity_check_commands = [ + "dec265 --help", + "enc265 --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..d2cd1762518 --- /dev/null +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libheif' +version = '1.12.0' + +homepage = 'https://github.com/strukturag/libheif' +description = "libheif is an HEIF and AVIF file format decoder and encoder" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] + +dependencies = [ + ('libde265', '1.0.8'), + ('x265', '3.5'), +] + +sanity_check_paths = { + 'files': ['bin/heif-info', 'lib/libheif.a', 'lib/libheif.%s' % SHLIB_EXT, 'lib/pkgconfig/libheif.pc'], + 'dirs': ['include/libheif', 'share'], +} + +sanity_check_commands = ["heif-info --help"] + +moduleclass = 'tools' From 2e7cc20f9eb5f2ffcf5ab3ae52a1ada1c4ad0107 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Apr 2022 21:53:01 +0200 Subject: [PATCH 3604/9987] fix C++ linker errors for KMC component in purge_dups easyconfig by not replacing -O3 in makefile with $CFLAGS, to avoid introducing -march=native compiler option --- .../p/purge_dups/purge_dups-1.2.5-foss-2021b.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb index 28d039185f1..9fa557852e3 100644 --- a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb +++ b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb @@ -37,9 +37,9 @@ components = [ 'source_urls': ['https://github.com/dfguan/KMC/archive/'], 'sources': [{'download_filename': 'c05a5f9.tar.gz', 'filename': SOURCE_TAR_GZ}], 'checksums': ['7251941f4b1913bfdd68759d9292b419d95fe7c63815056e15ecb097a12a0bc4'], - 'prebuildopts': 'cd KMC-* && sed -i "s/-O3/$CFLAGS/g" makefile && ', + 'prebuildopts': 'cd KMC-* && ', 'buildopts': 'CC="$CXX"', - 'files_to_copy': ['KMC-*/bin', 'KMC-*/spectra.py'], + 'files_to_copy': [(['KMC-*/bin/*kmc*'], 'bin'), 'KMC-*/spectra.py'], }), ] @@ -59,12 +59,13 @@ exts_list = [ ] sanity_check_paths = { - 'files': ['bin/purge_dups'], + 'files': ['bin/kmc', 'bin/purge_dups'], 'dirs': ['scripts'], } sanity_check_commands = [ "purge_dups -h 2>&1 | grep 'Program: purge_dups'", + "kmc --help", "run_purge_dups.py -h", "hist_plot.py -h", ] From 06119fe0bffdfd9ca01c5624b883899d757e0545 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 29 Apr 2022 22:10:07 +0200 Subject: [PATCH 3605/9987] Forget the at in the decorator... --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 +- ...yTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 53dc59f0a0a..0bfccff040f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -52,7 +52,7 @@ checksums = [ # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch - '4882cb6db394152fa996ac32718d1c31f1a361e3eeef5b471a3a50f51a9b3ee1', + 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch index 55c4093db85..c589c52b504 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch @@ -18,7 +18,7 @@ diff -Nru pytorch_orig/test/test_jit_cuda_fuser.py pytorch/test/test_jit_cuda_fu + # anyone hits it. + # See https://github.com/pytorch/pytorch/issues/76107 + # and https://github.com/easybuilders/easybuild-easyconfigs/pull/15137 -+ unittest.skip("Skipping test that is known to fail, see PT #76107") ++ @unittest.skip("Skipping test that is known to fail, see PT #76107") def test_native_layer_norm_bfloat(self): dims = 4 rnds = 3 @@ -31,7 +31,7 @@ diff -Nru pytorch_orig/test/test_jit_cuda_fuser.py pytorch/test/test_jit_cuda_fu + # anyone hits it. + # See https://github.com/pytorch/pytorch/issues/76107 + # and https://github.com/easybuilders/easybuild-easyconfigs/pull/15137 -+ unittest.skip("Skipping test that is known to fail, see PT #76107") ++ @unittest.skip("Skipping test that is known to fail, see PT #76107") def test_batch_norm_half(self): with torch.backends.cudnn.flags(enabled=True): setups = [ @@ -44,7 +44,7 @@ diff -Nru pytorch_orig/test/test_jit_cuda_fuser.py pytorch/test/test_jit_cuda_fu + # anyone hits it. + # See https://github.com/pytorch/pytorch/issues/76107 + # and https://github.com/easybuilders/easybuild-easyconfigs/pull/15137 -+ unittest.skip("Skipping test that is known to fail, see PT #76107") ++ @unittest.skip("Skipping test that is known to fail, see PT #76107") def test_batch_norm_impl_index_correctness(self): with torch.backends.cudnn.flags(enabled=True): batch = [2, 7, 16] From 11371abd06f45a52edc53f5358e9430a6c59ab40 Mon Sep 17 00:00:00 2001 From: sassy Date: Sat, 30 Apr 2022 00:22:17 +0100 Subject: [PATCH 3606/9987] adding easyconfigs: hector-2.5.0-GCC-11.2.0.eb --- .../h/hector/hector-2.5.0-GCC-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/h/hector/hector-2.5.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/h/hector/hector-2.5.0-GCC-11.2.0.eb b/easybuild/easyconfigs/h/hector/hector-2.5.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..7483c75940d --- /dev/null +++ b/easybuild/easyconfigs/h/hector/hector-2.5.0-GCC-11.2.0.eb @@ -0,0 +1,40 @@ +# Contribution from Imperial College London, UK +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'hector' +version = '2.5.0' + +homepage = 'https://github.com/JGCRI/hector' +description = """This is the repository for Hector, an open source, object-oriented, +simple global climate carbon-cycle model. It runs essentially instantaneously while +still representing the most critical global scale earth system processes, and is +one of a class of models heavily used for for emulating complex climate models +and uncertainty analyses.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/JGCRI/hector/archive'] +sources = [{'download_filename': 'rcmip-tier1.tar.gz', 'filename': 'v%(version)s.tar.gz'}] +checksums = ['457fec10f0c59e65b1b00c5d6c9aa66b38cd94c0c5a89444d059bebeb3fba3c9'] + +dependencies = [ + ('Boost', '1.79.0'), +] + +buildopts = 'hector' + +files_to_copy = [ + (['src/hector'], 'bin'), + (['src/libhector.a'], 'lib'), + 'R', 'man', 'LICENSE.md', 'README.md', 'DESCRIPTION', 'scripts', 'data-raw', 'inst', +] + +sanity_check_paths = { + 'files': ['bin/hector'], + 'dirs': [], +} + +moduleclass = 'tools' From 3db546c02da508fe40af57698a8ee2e7b7f035e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2022 10:48:24 +0200 Subject: [PATCH 3607/9987] remove easyconfig for pkg-config with GCCcore/11.3.0, since we intend to use pkgconf instead --- .../pkg-config-0.29.2-GCCcore-11.3.0.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb deleted file mode 100644 index a55b2586ff3..00000000000 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'pkg-config' -version = '0.29.2' - -homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' - -description = """ - pkg-config is a helper tool used when compiling applications and libraries. - It helps you insert the correct compiler options on the command line so an - application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` - for instance, rather than hard-coding values on where to find glib (or other - libraries). -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://pkg-config.freedesktop.org/releases/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] - -builddependencies = [('binutils', '2.38')] - -# don't use PAX, it might break. -tar_config_opts = True - -configopts = " --with-internal-glib" - -sanity_check_paths = { - 'files': ['bin/pkg-config'], - 'dirs': [], -} - -moduleclass = 'devel' From ce4143c727da5cf412ecfbaa1afd0e7ea5965dd2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2022 14:25:57 +0200 Subject: [PATCH 3608/9987] use libreadline 8.1.2 as dependency for SQLite with GCCcore/11.3.0 --- .../libreadline-8.1-GCCcore-11.3.0.eb | 41 ------------------- .../s/SQLite/SQLite-3.38.3-GCCcore-11.3.0.eb | 2 +- 2 files changed, 1 insertion(+), 42 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb deleted file mode 100644 index 2842a77b597..00000000000 --- a/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libreadline' -version = '8.1' - -homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' -description = """ - The GNU Readline library provides a set of functions for use by applications - that allow users to edit command lines as they are typed in. Both Emacs and - vi editing modes are available. The Readline library includes additional - functions to maintain a list of previously-entered command lines, to recall - and perhaps reedit those lines, and perform csh-like history expansion on - previous commands. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://ftp.gnu.org/gnu/readline'] -sources = ['readline-%(version)s.tar.gz'] -checksums = ['f8ceb4ee131e3232226a17f51b164afc46cd0b9e6cef344be87c65962cb82b02'] - -builddependencies = [ - ('binutils', '2.38'), -] -dependencies = [ - ('ncurses', '6.3'), -] - -# for the termcap symbols, use EB ncurses -buildopts = "SHLIB_LIBS='-lncurses'" - -sanity_check_paths = { - 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + - ['include/readline/%s' % x - for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', - 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.38.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.38.3-GCCcore-11.3.0.eb index 45edabdef72..85d8bce8610 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.38.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.38.3-GCCcore-11.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('binutils', '2.38'), ] dependencies = [ - ('libreadline', '8.1'), + ('libreadline', '8.1.2'), ('Tcl', '8.6.12'), ] From 92e06439e81058eec0f83f96125b8a98b7260197 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2022 14:46:44 +0200 Subject: [PATCH 3609/9987] use libreadline 8.1.2 as dependency for (bare) Python with GCCcore/11.3.0 --- .../easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb index 29484d0d038..c1e834e461b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb @@ -22,7 +22,7 @@ dependencies = [ ('binutils', '2.38'), ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib ('zlib', '1.2.12'), - ('libreadline', '8.1'), + ('libreadline', '8.1.2'), ('ncurses', '6.3'), ('SQLite', '3.38.3'), ('XZ', '5.2.5'), From 9c2aadde74968abae6a55a65cf47bdd5550331fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Apr 2022 16:56:13 +0200 Subject: [PATCH 3610/9987] remove commented out patch from easyconfig for Rust 1.60.0 --- easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb index 24e0975288d..bb13c946b9a 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb @@ -11,11 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -#patches = ['Rust-1.52.1_sysroot-fix-interpreter.patch'] -checksums = [ - '20ca826d1cf674daf8e22c4f8c4b9743af07973211c839b85839742314c838b7', # rustc-1.60.0-src.tar.gz -# 'e3db7005585eb807ecb69929818740f00417cac247b1065a9d43a7f16cf05e0b', # Rust-1.52.1_sysroot-fix-interpreter.patch -] +checksums = ['20ca826d1cf674daf8e22c4f8c4b9743af07973211c839b85839742314c838b7'] builddependencies = [ ('binutils', '2.38'), From f6ab53650260d5c6f3b0137e2e246e52695ab981 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 1 May 2022 10:28:53 +0200 Subject: [PATCH 3611/9987] no need to specify default_component_specs in purge_dups easyconfig since each component has 'sources' specified --- .../easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb index 9fa557852e3..c2a1fcd985d 100644 --- a/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb +++ b/easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.5-foss-2021b.eb @@ -19,10 +19,6 @@ use_pip = True default_easyblock = 'MakeCp' -default_component_specs = { - 'sources': [SOURCE_TAR_GZ], -} - components = [ (name, version, { 'source_urls': ['https://github.com/dfguan/purge_dups/archive/refs/tags/'], From f95826737070fe3fba73a327c8f25d3820d609ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 1 May 2022 11:24:40 +0200 Subject: [PATCH 3612/9987] adding easyconfigs: OpenBLAS-0.3.20-GCC-11.3.0.eb, FlexiBLAS-3.1.3-GCC-11.3.0.eb, BLIS-0.9.0-GCC-11.3.0.eb --- .../b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb | 33 +++++++++++ .../f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.3.0.eb | 58 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 28 +++++++++ 3 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..bb3f72c370a --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.9.0' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308'] + +builddependencies = [ + ('Python', '3.10.4', '-bare'), + ('Perl', '5.34.1'), +] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..32e84a14485 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'FlexiBLAS' +version = '3.1.3' + +homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' +description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation +used by a program without recompiling or relinking it.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" +toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} + +builddependencies = [ + ('CMake', '3.23.1'), + ('Python', '3.10.4', '-bare'), # required for running the tests + ('BLIS', '0.9.0'), +] + +dependencies = [ + ('OpenBLAS', '0.3.20'), +] + +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +local_backends = ['OpenBLAS', 'BLIS'] + +# imkl supplies its backend via the imkl module, not as a dependency +if ARCH == 'x86_64': + local_backends.append('imkl') + +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['aac6175660e8475ce478b88673eee330671f8aecc0cb852a25833e23e29a0620'], + 'backends': local_backends, + }), + ('LAPACK', '3.10.0', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['328c1bea493a32cac5257d84157dc686cc3ab0b004e2bea22044e0a59f6f8a19'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb new file mode 100644 index 00000000000..f941cf9f1d4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -0,0 +1,28 @@ +name = 'OpenBLAS' +version = '0.3.20' + +homepage = 'http://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), +] +checksums = [ + '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz +] + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From c29931e86c19c69fb688718836335784327a8a31 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 1 May 2022 11:29:58 +0200 Subject: [PATCH 3613/9987] adding easyconfigs: hwloc-2.7.1-GCCcore-11.3.0.eb, numactl-2.0.14-GCCcore-11.3.0.eb, libpciaccess-0.16-GCCcore-11.3.0.eb, xorg-macros-1.19.3-GCCcore-11.3.0.eb --- .../h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb | 45 +++++++++++++++++++ .../libpciaccess-0.16-GCCcore-11.3.0.eb | 26 +++++++++++ .../numactl/numactl-2.0.14-GCCcore-11.3.0.eb | 34 ++++++++++++++ .../xorg-macros-1.19.3-GCCcore-11.3.0.eb | 27 +++++++++++ 4 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.14-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6b7a745c08c --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.7.1' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4cb0a781ed980b03ad8c48beb57407aa67c4b908e45722954b9730379bc7f6d5'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('numactl', '2.0.14'), + ('libxml2', '2.9.13'), + ('libpciaccess', '0.16'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1f03c09bfad --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.16' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['84413553994aef0070cf420050aa5c0a51b1956b404920e21b81e96db6a61a27'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('xorg-macros', '1.19.3'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.14-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.14-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f0a3761f374 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.14-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.14' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1ee27abd07ff6ba140aaf9bc6379b37825e54496e01d6f7343330cf1a4487035'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5858842fac2 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.3' + +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['8205d210a580da0938f5ce4392a96b60cf1d9a5f792eaa1474fa4c1977aef4d0'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From c14d482d62cc860572d61f8757441b5234248538 Mon Sep 17 00:00:00 2001 From: Michele Martone Date: Sun, 1 May 2022 17:41:21 +0200 Subject: [PATCH 3614/9987] librsb: add v1.3.0.1 (#15401) --- .../l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb new file mode 100644 index 00000000000..52dbf8d89fc --- /dev/null +++ b/easybuild/easyconfigs/l/librsb/librsb-1.3.0.1-GCC-10.2.0.eb @@ -0,0 +1,33 @@ +## +# Author: Michele Martone +## +easyblock = 'ConfigureMake' + +name = 'librsb' +version = '1.3.0.1' + +homepage = 'https://sourceforge.net/projects/librsb/' +description = """A shared memory parallel sparse matrix computations library for the Recursive Sparse Blocks format""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3fc024a410f94aca2a7139ae79f4d713b11fa83304293630c363786874c17db4'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('zlib', '1.2.11') +] + +configopts = '--enable-openmp --enable-fortran-module-install' + +sanity_check_paths = { + 'files': ['bin/rsbench', 'lib/librsb.a', 'lib/librsb.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 06701ada2b22a8d5518dd4f04c543110e6672663 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 2 May 2022 10:21:12 +0200 Subject: [PATCH 3615/9987] Use mpirun for sanity check Co-authored-by: Sam Moors --- easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb index 4314a148799..773730e3fe6 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb @@ -47,7 +47,7 @@ sanity_check_paths = { } sanity_check_commands = [ - "meme -h 2>&1 | grep 'Usage:'", + "mpirun meme -h 2>&1 | grep 'Usage:'", "meme2meme --help", "perl -e 'require MemeSAX'", "python -c 'import sequence_py3'", From d5fae7154abfb755b2facb56ba713b3ee4130f6c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 2 May 2022 11:39:41 +0200 Subject: [PATCH 3616/9987] Add comment on failing test in Ubuntu 20.04 --- easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb index 773730e3fe6..9a0f963d4d6 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-gompi-2021b.eb @@ -36,6 +36,7 @@ configopts += '--with-gs=${EBROOTGHOSTSCRIPT}/bin/gs ' configopts += " && grep 'All required and optional Perl modules were found' config.log" pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " +# test xstreme4 fails on Ubuntu 20.04, see: https://groups.google.com/g/meme-suite/c/GlfpGwApz1Y runtest = 'test' fix_perl_shebang_for = ['bin/*', 'libexec/meme-%(version)s/*'] From 1e62f5cebafea25b91ddbb21127ad74facf05702 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 2 May 2022 10:51:49 +0100 Subject: [PATCH 3617/9987] adding easyconfigs: Python-3.10.4-GCCcore-11.3.0.eb and patches: Python-3.10-bist-1.3.6-compatibility.patch --- ...Python-3.10-bist-1.3.6-compatibility.patch | 182 +++++++ .../p/Python/Python-3.10.4-GCCcore-11.3.0.eb | 480 ++++++++++++++++++ 2 files changed, 662 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.10-bist-1.3.6-compatibility.patch create mode 100644 easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.10-bist-1.3.6-compatibility.patch b/easybuild/easyconfigs/p/Python/Python-3.10-bist-1.3.6-compatibility.patch new file mode 100644 index 00000000000..a19979e4909 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.10-bist-1.3.6-compatibility.patch @@ -0,0 +1,182 @@ +From 4b88010f208080173d0976d271d4c3100bfbef17 Mon Sep 17 00:00:00 2001 +From: Steve Langasek +Date: Thu, 18 Nov 2021 13:42:17 -0400 +Subject: [PATCH 1/2] Python 3.10 support: use Py_SET_REFCNT() + +Py_REFCNT() is no longer an lvalue; use Py_SET_REFCNT() instead. +--- + blist/_blist.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/blist/_blist.c b/blist/_blist.c +index f7fcb60..cacd6f2 100644 +--- a/blist/_blist.c ++++ b/blist/_blist.c +@@ -6589,7 +6589,7 @@ py_blist_sort(PyBListRoot *self, PyObject *args, PyObject *kwds) + memcpy(&saved.BLIST_FIRST_FIELD, &self->BLIST_FIRST_FIELD, + sizeof(*self) - offsetof(PyBListRoot, BLIST_FIRST_FIELD)); + Py_TYPE(&saved) = &PyRootBList_Type; +- Py_REFCNT(&saved) = 1; ++ Py_SET_REFCNT(&saved, 1); + + if (extra_list != NULL) { + self->children = extra_list; + +From fddb7837e2094560789a09790360feb75f06ed86 Mon Sep 17 00:00:00 2001 +From: Steve Langasek +Date: Thu, 18 Nov 2021 13:42:42 -0400 +Subject: [PATCH 2/2] Python 3.10 support: use collections.abc.MutableSet + +collections.MutableSet is obsolete, replaced by +collections.abc.MutableSet. +--- + blist/__init__.py | 2 +- + blist/_btuple.py | 2 +- + blist/_sorteddict.py | 8 ++++---- + blist/_sortedlist.py | 24 ++++++++++++------------ + blist/test/sortedlist_tests.py | 4 ++-- + 5 files changed, 20 insertions(+), 20 deletions(-) + +diff --git a/blist/__init__.py b/blist/__init__.py +index 931aaac..38c01a9 100644 +--- a/blist/__init__.py ++++ b/blist/__init__.py +@@ -1,6 +1,6 @@ + __version__ = '1.3.6' + from blist._blist import * +-import collections ++import collections.abc as collections + if hasattr(collections, 'MutableSet'): # Only supported in Python 2.6+ + from blist._sortedlist import sortedlist, sortedset, weaksortedlist, weaksortedset + from blist._sorteddict import sorteddict +diff --git a/blist/_btuple.py b/blist/_btuple.py +index 1e409cd..3a17972 100644 +--- a/blist/_btuple.py ++++ b/blist/_btuple.py +@@ -1,7 +1,7 @@ + from blist._blist import blist + from ctypes import c_int + import collections +-class btuple(collections.Sequence): ++class btuple(collections.abc.Sequence): + def __init__(self, seq=None): + if isinstance(seq, btuple): + self._blist = seq._blist +diff --git a/blist/_sorteddict.py b/blist/_sorteddict.py +index fcdf7e4..daa132c 100644 +--- a/blist/_sorteddict.py ++++ b/blist/_sorteddict.py +@@ -6,7 +6,7 @@ class missingdict(dict): + def __missing__(self, key): + return self._missing(key) + +-class KeysView(collections.KeysView, collections.Sequence): ++class KeysView(collections.abc.KeysView, collections.abc.Sequence): + def __getitem__(self, index): + return self._mapping._sortedkeys[index] + def __reversed__(self): +@@ -23,7 +23,7 @@ def bisect_right(self, key): + return self._mapping._sortedkeys.bisect_right(key) + bisect = bisect_right + +-class ItemsView(collections.ItemsView, collections.Sequence): ++class ItemsView(collections.abc.ItemsView, collections.abc.Sequence): + def __getitem__(self, index): + if isinstance(index, slice): + keys = self._mapping._sortedkeys[index] +@@ -46,7 +46,7 @@ def _from_iterable(self, it): + else: + return sortedset(it, key=lambda item: keyfunc(item[0])) + +-class ValuesView(collections.ValuesView, collections.Sequence): ++class ValuesView(collections.abc.ValuesView, collections.abc.Sequence): + def __getitem__(self, index): + if isinstance(index, slice): + keys = self._mapping._sortedkeys[index] +@@ -54,7 +54,7 @@ def __getitem__(self, index): + key = self._mapping._sortedkeys[index] + return self._mapping[key] + +-class sorteddict(collections.MutableMapping): ++class sorteddict(collections.abc.MutableMapping): + def __init__(self, *args, **kw): + if hasattr(self, '__missing__'): + self._map = missingdict() +diff --git a/blist/_sortedlist.py b/blist/_sortedlist.py +index b34f69e..7b8a2f3 100644 +--- a/blist/_sortedlist.py ++++ b/blist/_sortedlist.py +@@ -25,7 +25,7 @@ def __exit__(self, exc_type, exc_val, exc_tb): + del self.local.repr_count[self.ob_id] + return False + +-class _sortedbase(collections.Sequence): ++class _sortedbase(collections.abc.Sequence): + def __init__(self, iterable=(), key=None): + self._key = key + if key is not None and not hasattr(key, '__call__'): +@@ -428,23 +428,23 @@ def __iter__(self): + + def safe_cmp(f): + def g(self, other): +- if not isinstance(other, collections.Set): ++ if not isinstance(other, collections.abc.Set): + raise TypeError("can only compare to a set") + return f(self, other) + return g + +-class _setmixin2(collections.MutableSet): +- "methods that override or supplement the collections.MutableSet methods" ++class _setmixin2(collections.abc.MutableSet): ++ "methods that override or supplement the collections.abc.MutableSet methods" + +- __ror__ = collections.MutableSet.__or__ +- __rand__ = collections.MutableSet.__and__ +- __rxor__ = collections.MutableSet.__xor__ ++ __ror__ = collections.abc.MutableSet.__or__ ++ __rand__ = collections.abc.MutableSet.__and__ ++ __rxor__ = collections.abc.MutableSet.__xor__ + + if sys.version_info[0] < 3: # pragma: no cover +- __lt__ = safe_cmp(collections.MutableSet.__lt__) +- __gt__ = safe_cmp(collections.MutableSet.__gt__) +- __le__ = safe_cmp(collections.MutableSet.__le__) +- __ge__ = safe_cmp(collections.MutableSet.__ge__) ++ __lt__ = safe_cmp(collections.abc.MutableSet.__lt__) ++ __gt__ = safe_cmp(collections.abc.MutableSet.__gt__) ++ __le__ = safe_cmp(collections.abc.MutableSet.__le__) ++ __ge__ = safe_cmp(collections.abc.MutableSet.__ge__) + + def __ior__(self, it): + if self is it: +@@ -476,7 +476,7 @@ def __rsub__(self, other): + return self._from_iterable(other) - self + + def _make_set(self, iterable): +- if isinstance(iterable, collections.Set): ++ if isinstance(iterable, collections.abc.Set): + return iterable + return self._from_iterable(iterable) + +diff --git a/blist/test/sortedlist_tests.py b/blist/test/sortedlist_tests.py +index 1cff8b9..ad392e9 100644 +--- a/blist/test/sortedlist_tests.py ++++ b/blist/test/sortedlist_tests.py +@@ -29,7 +29,7 @@ def test_empty_repr(self): + repr(self.type2test())) + + def validate_comparison(self, instance): +- if sys.version_info[0] < 3 and isinstance(instance, collections.Set): ++ if sys.version_info[0] < 3 and isinstance(instance, collections.abc.Set): + ops = ['ne', 'or', 'and', 'xor', 'sub'] + else: + ops = ['lt', 'gt', 'le', 'ge', 'ne', 'or', 'and', 'xor', 'sub'] +@@ -185,7 +185,7 @@ def __cmp__(self, other): # pragma: no cover + def test_order(self): + stuff = [self.build_item(random.randrange(1000000)) + for i in range(1000)] +- if issubclass(self.type2test, collections.Set): ++ if issubclass(self.type2test, collections.abc.Set): + stuff = set(stuff) + sorted_stuff = list(sorted(stuff)) + u = self.type2test diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6c4e89319b9 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb @@ -0,0 +1,480 @@ +name = 'Python' +version = '3.10.4' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['f3bcc65b1d5f1dc78675c746c98fcee823c038168fc629c5935b044d0911ad28'] + +builddependencies = [ + ('UnZip', '6.0'), + ('Rust', '1.60.0'), # required for setuptools-rust, which is needed for cryptography + ('pkgconf', '1.8.0'), + ('git', '2.36.0', '-nodocs'), # required for pbr +] + +dependencies = [ + ('binutils', '2.38'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), + ('SQLite', '3.38.3'), + ('XZ', '5.2.5'), + ('GMP', '6.2.1'), # required for pycrypto + ('libffi', '3.4.2'), + ('OpenSSL', '1.1', '', True), +] + +install_pip = True + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 06 August 2021 +exts_list = [ + ('wheel', '0.37.1', { + 'checksums': ['e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4'], + }), + ('setuptools', '62.1.0', { + 'checksums': ['47c7b0c0f8fc10eec4cf1e71c6fdadf8decaa74ffa087e68cd1c20db7ad6a592'], + }), + ('pip', '22.0.4', { + 'checksums': ['b3a9de2c6ef801e9247d1527a4b16f92f2cc141cd1489f3fffaf6a9e96729764'], + }), + ('blist', '1.3.6', { + 'patches': [ + 'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch', + 'Python-3.10-bist-1.3.6-compatibility.patch', + ], + 'checksums': [ + '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3', # blist-1.3.6.tar.gz + # Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch + '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0', + # Python-3.10-bist-1.3.6-compatibility.patch + '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741', + ], + }), + ('pbr', '5.8.1', { + 'checksums': ['66bc5a34912f408bb3925bf21231cb6f59206267b7f63f3503ef865c1a292e25'], + }), + ('Cython', '0.29.28', { + 'checksums': ['d6fac2342802c30e51426828fe084ff4deb1b3387367cf98976bb2e64b6f8e45'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('flit-core', '3.7.1', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': ['14955af340c43035dbfa96b5ee47407e377ee337f69e70f73064940d27d0a44f'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('setuptools_scm', '6.4.2', { + 'checksums': ['6833ac65c6ed9711a4d5d2266f8024cfa07c533a0e55f4c12f6eff280a5a9e30'], + }), + ('python-dateutil', '2.8.2', { + 'modulename': 'dateutil', + 'checksums': ['0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], + 'checksums': [ + 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz + # pycrypto-2.6.1_remove-usr-include.patch + '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e', + ], + }), + ('ecdsa', '0.17.0', { + 'checksums': ['b9f500bb439e4153d0330610f5d26baaf18d17b8ced1bc54410d189385ea68aa'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.5.1', { + 'checksums': ['13ae38502be632115abf8a24cbe5f4da52e3b5231990aff31123c805306ccb9c'], + }), + ('idna', '3.3', { + 'checksums': ['9d643ff0a55b762d5cdb124b8eaa99c66322e2157b69160bc32796e824360e6d'], + }), + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + ('cffi', '1.15.0', { + 'checksums': ['920f0d66a896c2d99f0adbb391f990a84091179542c205fa53ce5787aff87954'], + }), + ('semantic_version', '2.9.0', { + 'checksums': ['abf54873553e5e07a6fd4d5f653b781f5ae41297a493666b59dcf214006a12b2'], + }), + ('typing_extensions', '4.2.0', { + 'checksums': ['f1c24655a0da0d1b67f07e17a5e6b2a105894e6824b92096378bb3668ef02376'], + }), + ('setuptools-rust', '1.3.0', { + 'checksums': ['958c5bf4ab6483d59dab888538121871cc5006354a42fb0fbd50acf03caad1de'], + }), + ('cryptography', '37.0.1', { + # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, + # see https://github.com/rust-lang/cargo/issues/6652 + 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", + 'checksums': ['d610d0ee14dd9109006215c7c0de15eee91230b70a9bce2263461cf7c3720b83'], + }), + ('pyasn1', '0.4.8', { + 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], + }), + ('PyNaCl', '1.5.0', { + 'modulename': 'nacl', + 'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'], + }), + ('bcrypt', '3.2.0', { + 'checksums': ['5b93c1726e50a93a033c36e5ca7fdcd29a5c7395af50a6892f5d9e7c6cfbfb29'], + }), + ('paramiko', '2.10.4', { + 'checksums': ['3d2e650b6812ce6d160abff701d6ef4434ec97934b13e95cf1ad3da70ffb5c58'], + }), + ('pyparsing', '3.0.8', { + 'checksums': ['7bf433498c016c4314268d95df76c81b842a4cb2b276fa3312cfb1e1d85f6954'], + }), + ('netifaces', '0.11.0', { + 'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'], + }), + ('netaddr', '0.8.0', { + 'checksums': ['d6cc57c7a07b1d9d2e917aa8b36ae8ce61c35ba3fcd1b83ca31c5a0ee2b5a243'], + }), + ('mock', '4.0.3', { + 'checksums': ['7d3fbbde18228f4ff2f1f119a45cdffa458b4c0dee32eb4d2bb2f82554bac7bc'], + }), + ('pytz', '2022.1', { + 'checksums': ['1e760e2fe6a8163bc0b3d9a19c4f84342afa0a2affebfaa84b01b978a02ecaa7'], + }), + ('bitstring', '3.1.9', { + 'checksums': ['a5848a3f63111785224dca8bb4c0a75b62ecdef56a042c8d6be74b16f7e860e7'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.4', { + 'source_tmpl': 'distlib-%(version)s.zip', + 'checksums': ['e4b58818180336dc9c529bfb9a0b58728ffc09ad92027a3f30b7cd91e3458579'], + }), + ('filelock', '3.6.0', { + 'checksums': ['9cd540a9352e432c7246a48fe4e8712b10acb1df2ad1f30e8c070b82ae1fed85'], + }), + ('zipp', '3.8.0', { + 'checksums': ['56bf8aadb83c24db6c4b577e13de374ccfb67da2078beba1d037c17980bf43ad'], + }), + ('importlib_metadata', '4.11.3', { + 'checksums': ['ea4c597ebf37142f827b8f39299579e31685c31d3a438b59f469406afd0f2539'], + }), + ('backports.entry_points_selectable', '1.1.1', { + 'checksums': ['914b21a479fde881635f7af5adc7f6e38d6b274be32269070c53b698c60d5386'], + }), + ('pathspec', '0.9.0', { + 'checksums': ['e564499435a2673d586f6b2130bb5b95f04a3ba06f81b8f895b651a3c76aabb1'], + }), + ('pluggy', '1.0.0', { + 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], + }), + ('packaging', '20.9', { + 'checksums': ['5b327ac1320dc863dca72f4514ecc086f31186744b84a230374cc1fd776feae5'], + }), + ('editables', '0.3', { + 'checksums': ['167524e377358ed1f1374e61c268f0d7a4bf7dbd046c656f7b410cde16161b1a'], + }), + # platformdirs >= 2.5 requires hatchling and that requires packaging>=21.3 + # however poetry requires packaging<21.0,>=20.4, so stick to an older platformdirs to avoid needing hatching + ('platformdirs', '2.4.1', { + 'checksums': ['440633ddfebcc36264232365d7840a970e75e1018d15b4327d11f91909045fda'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.7.post1', { + 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], + }), + ('importlib_resources', '5.7.1', { + 'checksums': ['b6062987dfc51f0fcb809187cffbd60f35df7acb4589091f154214af6d0d49d3'], + }), + ('virtualenv', '20.14.1', { + 'checksums': ['ef589a79795589aada0c1c5b319486797c03b67ac3984c48c669c0e4f50df3a5'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '1.1.0', { + 'checksums': ['4158fcecd13733f8be669be0683b96ebdbbd38d23559f54dca7205aea1bf1e35'], + }), + ('chardet', '4.0.0', { + 'checksums': ['0d6f53a15db4120f2b08c94f11e7d93d2c911ee118b6b30a04ec3ee8310179fa'], + }), + ('certifi', '2021.10.8', { + 'checksums': ['78884e7c1d4b00ce3cea67b44566851c4343c120abd683433ce934a68ea58872'], + }), + ('urllib3', '1.26.9', { + 'checksums': ['aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e'], + }), + ('charset-normalizer', '2.0.12', { + 'checksums': ['2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597'], + }), + ('requests', '2.27.1', { + 'checksums': ['68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61'], + }), + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('py_expression_eval', '0.3.14', { + 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + ('ujson', '5.2.0', { + 'checksums': ['163191b88842d874e081707d35de2e205e0e396e70fd068d1038879bca8b17ad'], + }), + ('atomicwrites', '1.4.0', { + 'checksums': ['ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a'], + }), + ('py', '1.11.0', { + 'checksums': ['51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719'], + }), + ('more-itertools', '8.12.0', { + 'checksums': ['7dc6ad46f05f545f900dd59e8dfb4e84a4827b97b3cfecb175ea0c7d247f6064'], + }), + ('attrs', '21.4.0', { + 'modulename': 'attr', + 'checksums': ['626ba8234211db98e869df76230a137c4c40a12d72445c45d5f5b716f076e2fd'], + }), + ('backports.functools_lru_cache', '1.6.4', { + 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], + }), + ('wcwidth', '0.2.5', { + 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], + }), + ('iniconfig', '1.1.1', { + 'checksums': ['bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32'], + }), + ('colorama', '0.4.4', { + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + ('pytest', '7.1.2', { + 'checksums': ['a06a0425453864a270bc45e71f783330a7428defb4230fb5e6a731fde06ecd45'], + }), + ('MarkupSafe', '2.1.1', { + 'checksums': ['7f91197cc9e48f989d12e4e6fbc46495c446636dfc81b9ccf50bb0ec74b91d4b'], + }), + ('Jinja2', '3.1.2', { + 'checksums': ['31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852'], + }), + ('sphinxcontrib-serializinghtml', '1.1.5', { + 'modulename': 'sphinxcontrib.serializinghtml', + 'checksums': ['aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952'], + }), + ('sphinxcontrib-websupport', '1.2.4', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['4edf0223a0685a7c485ae5a156b6f529ba1ee481a1417817935b20bde1956232'], + }), + ('Pygments', '2.12.0', { + 'checksums': ['5eb116118f9612ff1ee89ac96437bb6b49e8f04d8a13b514ba26f620208e26eb'], + }), + ('imagesize', '1.3.0', { + 'checksums': ['cd1750d452385ca327479d45b64d9c7729ecf0b3969a58148298c77092261f9d'], + }), + ('docutils', '0.17.1', { + 'checksums': ['686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125'], + }), + ('snowballstemmer', '2.2.0', { + 'checksums': ['09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1'], + }), + ('alabaster', '0.7.12', { + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('sphinxcontrib-applehelp', '1.0.2', { + 'modulename': 'sphinxcontrib.applehelp', + 'checksums': ['a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58'], + }), + ('sphinxcontrib-devhelp', '1.0.2', { + 'modulename': 'sphinxcontrib.devhelp', + 'checksums': ['ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4'], + }), + ('sphinxcontrib-htmlhelp', '2.0.0', { + 'modulename': 'sphinxcontrib.htmlhelp', + 'checksums': ['f5f8bb2d0d629f398bf47d0d69c07bc13b65f75a81ad9e2f71a63d4b7a2f6db2'], + }), + ('sphinxcontrib-jsmath', '1.0.1', { + 'modulename': 'sphinxcontrib.jsmath', + 'checksums': ['a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8'], + }), + ('sphinxcontrib-qthelp', '1.0.3', { + 'modulename': 'sphinxcontrib.qthelp', + 'checksums': ['4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72'], + }), + ('Babel', '2.10.1', { + 'checksums': ['98aeaca086133efb3e1e2aad0396987490c8425929ddbcfe0550184fdc54cd13'], + }), + # Sphinx 4.5.0 has requirement docutils<0.18,>=0.14 + ('Sphinx', '4.5.0', { + 'checksums': ['7bf8ca9637a4ee15af412d1a1d9689fec70523a68ca9bb9127c2f3eeb344e2e6'], + }), + ('sphinx-bootstrap-theme', '0.8.1', { + 'checksums': ['683e3b735448dadd0149f76edecf95ff4bd9157787e9e77e0d048ca6f1d680df'], + }), + ('click', '8.1.3', { + 'checksums': ['7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e'], + }), + ('psutil', '5.9.0', { + 'checksums': ['869842dbd66bb80c3217158e629d6fceaecc3a3166d3d1faee515b05dd26ca25'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('zipfile36', '0.1.3', { + 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], + }), + ('tomli_w', '1.0.0', { + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), + ('flit', '3.7.1', { + 'checksums': ['3c9bd9c140515bfe62dd938c6610d10d6efb9e35cc647fc614fe5fb3a5036682'], + }), + ('regex', '2022.4.24', { + 'checksums': ['92183e9180c392371079262879c6532ccf55f808e6900df5d9f03c9ca8807255'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('pylev', '1.4.0', { + 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], + }), + ('pastel', '0.2.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], + }), + ('crashtest', '0.3.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], + }), + ('clikit', '0.6.2', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], + }), + ('jeepney', '0.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], + }), + ('SecretStorage', '3.3.2', { + 'checksums': ['0a8eb9645b320881c222e827c26f4cfcf55363e8b374a021981ef886657a912f'], + }), + ('keyring', '23.5.0', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['9012508e141a80bd1c0b6778d5c610dd9f8c464d75ac6774248500503f972fb9'], + }), + ('keyrings.alt', '4.1.0', { + 'modulename': False, + 'checksums': ['52ccb61d6f16c10f32f30d38cceef7811ed48e086d73e3bae86f0854352c4ab2'], + }), + ('tomlkit', '0.10.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['905cf92c2111ef80d355708f47ac24ad1b6fc2adc5107455940088c9bbecaedb'], + }), + ('shellingham', '1.4.0', { + 'checksums': ['4855c2458d6904829bd34c299f11fdeed7cfefbf8a2c522e4caea6cd76b3171e'], + }), + ('requests-toolbelt', '0.9.1', { + 'checksums': ['968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0'], + }), + ('pyrsistent', '0.18.1', { + 'checksums': ['d4d61f8b993a7255ba714df3aca52700f8125289f84f704cf80916517c46eb96'], + }), + ('pkginfo', '1.8.2', { + 'checksums': ['542e0d0b6750e2e21c20179803e40ab50598d8066d51097a0e382cba9eb02bff'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('jsonschema', '4.4.0', { + 'checksums': ['636694eb41b3535ed608fe04129f26542b59ed99808b4f688aa32dcf55317a83'], + }), + ('simplejson', '3.17.6', { + 'checksums': ['cf98038d2abf63a1ada5730e91e84c642ba6c225b0198c3684151b1f80c5f8a6'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('cleo', '0.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.3', { + 'checksums': ['51fdc7fb93615286428ee7758cecc2f374d5ff363bdd884c7ea622a7a327a81e'], + }), + ('CacheControl', '0.12.11', { + 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.0.8', { + 'modulename': 'poetry.core', + 'checksums': ['951fc7c1f8d710a94cb49019ee3742125039fc659675912ea614ac2aa405b118'], + }), + ('glob2', '0.7', { + 'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'], + }), + # poetry 1.1.13 has requirement packaging<21.0,>=20.4 + ('poetry', '1.1.13', { + 'checksums': ['b905ed610085f568aa61574e0e09260c02bff9eae12ff672af39e9f399357ac4'], + }), + ('fsspec', '2022.3.0', { + 'checksums': ['fd582cc4aa0db5968bad9317cae513450eddd08b2193c4428d9349265a995523'], + }), + ('threadpoolctl', '3.1.0', { + 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), +] + +moduleclass = 'lang' From 151b1841d13c7efe31a8c5426609c08475c8054c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 2 May 2022 10:56:20 +0100 Subject: [PATCH 3618/9987] package version date --- easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb index 6c4e89319b9..875008dfc1d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb @@ -42,7 +42,7 @@ exts_default_options = { } # order is important! -# package versions updated 06 August 2021 +# package versions updated 1 May 2022 exts_list = [ ('wheel', '0.37.1', { 'checksums': ['e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4'], From c101060d8aafea47dc4616d08df31bc3a083f89a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 2 May 2022 10:57:53 +0100 Subject: [PATCH 3619/9987] put comments in correct places --- .../easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb index 875008dfc1d..efea69a151b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb @@ -197,6 +197,7 @@ exts_list = [ ('pluggy', '1.0.0', { 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], }), + # poetry 1.1.13 has requirement packaging<21.0,>=20.4 ('packaging', '20.9', { 'checksums': ['5b327ac1320dc863dca72f4514ecc086f31186744b84a230374cc1fd776feae5'], }), @@ -301,6 +302,7 @@ exts_list = [ ('imagesize', '1.3.0', { 'checksums': ['cd1750d452385ca327479d45b64d9c7729ecf0b3969a58148298c77092261f9d'], }), + # Sphinx 4.5.0 has requirement docutils<0.18,>=0.14 ('docutils', '0.17.1', { 'checksums': ['686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125'], }), @@ -333,7 +335,6 @@ exts_list = [ ('Babel', '2.10.1', { 'checksums': ['98aeaca086133efb3e1e2aad0396987490c8425929ddbcfe0550184fdc54cd13'], }), - # Sphinx 4.5.0 has requirement docutils<0.18,>=0.14 ('Sphinx', '4.5.0', { 'checksums': ['7bf8ca9637a4ee15af412d1a1d9689fec70523a68ca9bb9127c2f3eeb344e2e6'], }), @@ -461,7 +462,6 @@ exts_list = [ ('glob2', '0.7', { 'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'], }), - # poetry 1.1.13 has requirement packaging<21.0,>=20.4 ('poetry', '1.1.13', { 'checksums': ['b905ed610085f568aa61574e0e09260c02bff9eae12ff672af39e9f399357ac4'], }), From a67544b50e233daba9673dd1e76c8336393e5b5c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 2 May 2022 10:58:54 +0100 Subject: [PATCH 3620/9987] improve comment --- easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb index efea69a151b..76c7e75a1dd 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb @@ -205,7 +205,7 @@ exts_list = [ 'checksums': ['167524e377358ed1f1374e61c268f0d7a4bf7dbd046c656f7b410cde16161b1a'], }), # platformdirs >= 2.5 requires hatchling and that requires packaging>=21.3 - # however poetry requires packaging<21.0,>=20.4, so stick to an older platformdirs to avoid needing hatching + # however poetry 1.1.13 requires packaging<21.0,>=20.4, so use an older platformdirs to avoid needing hatchling ('platformdirs', '2.4.1', { 'checksums': ['440633ddfebcc36264232365d7840a970e75e1018d15b4327d11f91909045fda'], }), From 62aae3f484409c2bb0870935413354527233db13 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 2 May 2022 11:29:16 +0100 Subject: [PATCH 3621/9987] Apply suggestions from code review Co-authored-by: SebastianAchilles --- .../easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb index 76c7e75a1dd..6978ff1ec4f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb @@ -148,8 +148,8 @@ exts_list = [ 'modulename': 'nacl', 'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'], }), - ('bcrypt', '3.2.0', { - 'checksums': ['5b93c1726e50a93a033c36e5ca7fdcd29a5c7395af50a6892f5d9e7c6cfbfb29'], + ('bcrypt', '3.2.2', { + 'checksums': ['433c410c2177057705da2a9f2cd01dd157493b2a7ac14c8593a16b3dab6b6bfb'], }), ('paramiko', '2.10.4', { 'checksums': ['3d2e650b6812ce6d160abff701d6ef4434ec97934b13e95cf1ad3da70ffb5c58'], @@ -440,7 +440,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '0.8.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': 'SOURCE_WHL', 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], }), ('cachy', '0.3.0', { From 64d9aa46d0e3f3216e6b50e4a62b44e0f11c138e Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 2 May 2022 11:32:24 +0100 Subject: [PATCH 3622/9987] remove ' --- easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb index 6978ff1ec4f..0d94ec7e686 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb @@ -440,7 +440,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '0.8.1', { - 'source_tmpl': 'SOURCE_WHL', + 'source_tmpl': SOURCE_WHL, 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], }), ('cachy', '0.3.0', { From a33cabcde472ed00357bd6d37133853a094ee615 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2022 13:35:39 +0200 Subject: [PATCH 3623/9987] add DNABarcodes to R-bundle-Bioconductor 3.14 easyconfig --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index 49646aed92c..b7133459ca4 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1096,6 +1096,9 @@ exts_list = [ ('WGCNA', '1.70-3', { 'checksums': ['b9843b839728183af6b746f239e9519d438b294613362b556002acdb8522cbd4'], }), + ('DNABarcodes', '1.24.0', { + 'checksums': ['af73c60288596fad26e077a0d02c9db71f955997d6551a83b7b2a29051faca1f'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 2109981dcf0f97a7a9bad06a05d6a895a17a799e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 May 2022 14:08:29 +0200 Subject: [PATCH 3624/9987] add exception to check for dependency variants for GATE 9.2 with foss/2021b --- test/easyconfigs/easyconfigs.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 36ca8a5747c..fd82b2a03f4 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -468,6 +468,9 @@ def check_dep_vars(self, gen, dep, dep_vars): # EMAN2 2.3 requires Boost(.Python) 1.64.0 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], + # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x + 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], + 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], # VMTK 1.4.x requires ITK 4.13.x From 5f8f02529b32c95ebfc10f039e4c7ffc24416a59 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 2 May 2022 13:40:18 +0000 Subject: [PATCH 3625/9987] adding easyconfigs: FFTW.serial-3.3.10-GCC-11.3.0.eb --- .../FFTW.serial-3.3.10-GCC-11.3.0.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.serial/FFTW.serial-3.3.10-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FFTW.serial/FFTW.serial-3.3.10-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FFTW.serial/FFTW.serial-3.3.10-GCC-11.3.0.eb new file mode 100644 index 00000000000..c5871c38697 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.serial/FFTW.serial-3.3.10-GCC-11.3.0.eb @@ -0,0 +1,18 @@ +easyblock = 'EB_FFTW' +name = 'FFTW.serial' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +runtest = 'check' + +moduleclass = 'numlib' From b246c3c7406db00bcb7ddcfa984ad5d081d5a5fe Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 2 May 2022 15:59:01 +0200 Subject: [PATCH 3626/9987] adding easyconfigs: tmap-20220502-GCC-11.2.0.eb, OGDF-dogwood-202202-GCC-11.2.0.eb and patches: tmap-20220502_add_install.patch, OGDF-dogwood-202202_fix_lib_install_dir.patch --- .../o/OGDF/OGDF-dogwood-202202-GCC-11.2.0.eb | 37 ++++++++++++++++ ...F-dogwood-202202_fix_lib_install_dir.patch | 35 +++++++++++++++ .../t/tmap/tmap-20220502-GCC-11.2.0.eb | 43 +++++++++++++++++++ .../t/tmap/tmap-20220502_add_install.patch | 14 ++++++ 4 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202_fix_lib_install_dir.patch create mode 100644 easybuild/easyconfigs/t/tmap/tmap-20220502-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/t/tmap/tmap-20220502_add_install.patch diff --git a/easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202-GCC-11.2.0.eb new file mode 100644 index 00000000000..afd6fc5aef3 --- /dev/null +++ b/easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202-GCC-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'OGDF' +version = 'dogwood-202202' + +homepage = 'https://ogdf.uos.de/' +description = """OGDF is a self-contained C++ library for graph +algorithms, in particular for (but not restricted to) automatic graph +drawing. It offers sophisticated algorithms and data structures to use +within your own applications or scientific projects.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/ogdf/ogdf/archive'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'OGDF-dogwood-202202_fix_lib_install_dir.patch', +] +checksums = [ + '308cc2749c6a63520f7979bac86a04066dfea2fb9d3a5e89831318db404bfbf5', # dogwood-202202.tar.gz + 'f6c2fab1d01ee82346241d24341475c85ecf9e942659823a54185bb83a717879', # OGDF-dogwood-202202_fix_lib_install_dir.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Doxygen', '1.9.1'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['include/ogdf/basic/List.h'], + 'dirs': ['share/doc/libogdf/examples'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202_fix_lib_install_dir.patch b/easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202_fix_lib_install_dir.patch new file mode 100644 index 00000000000..1d677ca9bee --- /dev/null +++ b/easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202_fix_lib_install_dir.patch @@ -0,0 +1,35 @@ +Don't use CMAKE_LIBRARY_ARCHITECTURE. + +Åke Sandgren, 2022-05-02 +diff -ru ogdf-dogwood-202202.orig/cmake/coin.cmake ogdf-dogwood-202202/cmake/coin.cmake +--- ogdf-dogwood-202202.orig/cmake/coin.cmake 2022-02-02 22:09:01.000000000 +0100 ++++ ogdf-dogwood-202202/cmake/coin.cmake 2022-05-02 14:22:06.017468966 +0200 +@@ -55,10 +55,10 @@ + endif() + + # installation +-set(COIN_INSTALL_LIBRARY_DIR "lib/${CMAKE_LIBRARY_ARCHITECTURE}" CACHE PATH "Installation path of COIN library") ++set(COIN_INSTALL_LIBRARY_DIR "lib" CACHE PATH "Installation path of COIN library") + set(COIN_INSTALL_BIN_DIR "bin" CACHE PATH "Installation path of COIN runtime targets") + set(COIN_INSTALL_INCLUDE_DIR "include" CACHE PATH "Installation path of COIN header files (creates subdirectory)") +-set(COIN_INSTALL_CMAKE_DIR "lib/${CMAKE_LIBRARY_ARCHITECTURE}/cmake/OGDF/" CACHE PATH "Installation path of COIN files for CMake") ++set(COIN_INSTALL_CMAKE_DIR "lib/cmake/OGDF/" CACHE PATH "Installation path of COIN files for CMake") + mark_as_advanced(COIN_INSTALL_LIBRARY_DIR COIN_INSTALL_BIN_DIR COIN_INSTALL_INCLUDE_DIR COIN_INSTALL_CMAKE_DIR) + install(TARGETS COIN + EXPORT CoinTargets +diff -ru ogdf-dogwood-202202.orig/cmake/ogdf.cmake ogdf-dogwood-202202/cmake/ogdf.cmake +--- ogdf-dogwood-202202.orig/cmake/ogdf.cmake 2022-02-02 22:09:01.000000000 +0100 ++++ ogdf-dogwood-202202/cmake/ogdf.cmake 2022-05-02 14:22:16.929387664 +0200 +@@ -193,10 +193,10 @@ + endif() + + # installation +-set(OGDF_INSTALL_LIBRARY_DIR "lib/${CMAKE_LIBRARY_ARCHITECTURE}" CACHE PATH "Installation path of OGDF library") ++set(OGDF_INSTALL_LIBRARY_DIR "lib" CACHE PATH "Installation path of OGDF library") + set(OGDF_INSTALL_BIN_DIR "bin" CACHE PATH "Installation path of OGDF runtime targets") + set(OGDF_INSTALL_INCLUDE_DIR "include" CACHE PATH "Installation path of OGDF header files (creates subdirectory)") +-set(OGDF_INSTALL_CMAKE_DIR "lib/${CMAKE_LIBRARY_ARCHITECTURE}/cmake/OGDF/" CACHE PATH "Installation path of OGDF files for CMake") ++set(OGDF_INSTALL_CMAKE_DIR "lib/cmake/OGDF/" CACHE PATH "Installation path of OGDF files for CMake") + mark_as_advanced(OGDF_INSTALL_LIBRARY_DIR OGDF_INSTALL_BIN_DIR OGDF_INSTALL_INCLUDE_DIR OGDF_INSTALL_CMAKE_DIR) + configure_file(cmake/ogdf-config.cmake "${PROJECT_BINARY_DIR}/ogdf-config.cmake" @ONLY) + install(TARGETS OGDF diff --git a/easybuild/easyconfigs/t/tmap/tmap-20220502-GCC-11.2.0.eb b/easybuild/easyconfigs/t/tmap/tmap-20220502-GCC-11.2.0.eb new file mode 100644 index 00000000000..23f0eeefe31 --- /dev/null +++ b/easybuild/easyconfigs/t/tmap/tmap-20220502-GCC-11.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakePythonPackage' + +name = 'tmap' +version = '20220502' + +homepage = 'https://tmap.gdb.tools' +description = """tmap is a very fast visualization library for large, +high-dimensional data sets. Currently, tmap is available for Python. +tmaps graph layouts are based on the OGDF library.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = [ + { + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/reymond-group', + 'repo_name': '%(name)s', + 'commit': 'c66ff2dadd7118447fc198a5b78aa3a46d4dde69', + }, + }, +] +patches = [ + 'tmap-20220502_add_install.patch', +] +checksums = [ + None, # tmap-20220502.tar.gz + '055f69b36ca3b4c41f1d979193eb6a0471416cf018853511db2ffe7594f35eca', # tmap-20220502_add_install.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('pybind11', '2.7.1'), + ('OGDF', 'dogwood-202202'), +] + +start_dir = 'tmap' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tmap/tmap-20220502_add_install.patch b/easybuild/easyconfigs/t/tmap/tmap-20220502_add_install.patch new file mode 100644 index 00000000000..ae6f6113b12 --- /dev/null +++ b/easybuild/easyconfigs/t/tmap/tmap-20220502_add_install.patch @@ -0,0 +1,14 @@ +Add install target. + +Åke Sandgren, 2022-05-02 +diff --git a/tmap/CMakeLists.txt b/tmap/CMakeLists.txt +index 24ff444..e3ec61f 100644 +--- a/tmap/CMakeLists.txt ++++ b/tmap/CMakeLists.txt +@@ -57,3 +57,6 @@ endif(MSVC) + + target_link_libraries(tmap PRIVATE Threads::Threads) + target_link_libraries(tmap PRIVATE ${OpenMP_CXX_FLAGS}) ++ ++include(GNUInstallDirs) ++install(TARGETS tmap LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages") From 8ae2674b5af67a635be79492439307cf2cadf939 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 2 May 2022 17:43:07 +0200 Subject: [PATCH 3627/9987] Added descriptions to patches --- .../PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 4 ++-- .../PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch | 11 +++++++++++ .../PyTorch-1.11.0_skip_failing_ops_tests.patch | 9 +++++++++ 3 files changed, 22 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 0bfccff040f..7754197d9f6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -44,8 +44,8 @@ checksums = [ 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_cmake_rpath.patch # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', - '8f4a27303f8cba2ea90702e494365bf4a3e1c5ade9ed1311b63ad4289793e1af', # PyTorch-1.11.0_skip_failing_ops_tests.patch - '10d1f0db8254f7564500fe97f134c3b4fa89156839b5f771a9396d80a0a1ada4', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch + '8eaca92d64fcadb0552d28e9c7ea5c4bc669d2fe33004e45a3519ce8d0d136a2', # PyTorch-1.11.0_skip_failing_ops_tests.patch + '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch # PyTorch-1.11.0_increase_test_tolerances_TF32.patch '26e179a4f6f57e49209092612ae5f5cd8c03fd2ca84566ba0244eabefc3736ba', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch index 4c698d6bff2..4368fb8f660 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch @@ -1,3 +1,14 @@ +# Author: Caspar van Leeuwen +# Company: SURF +# The CudaFuser test suite checks CUDA capabilities, even if 'RUN_CUDA' is false. +# That makes the test fail on non-GPU nodes. +# In this patch, I wrapped the logic in 'if RUN_CUDA' blocks in order to make sure +# no CUDA calls are made when RUN_CUDA=false +# Furthermore, I swapped all occurences of @unittest.skipIf(not RUN_CUDA, ...) and @unittest.skipIf(is_pre_volta()) +# The latter check is a more specific 'skip' condition: you should only check if a GPU is pre-volta, +# if there are CUDA devices present to begin with. Again, doing this in the wrong order would incur CUDA calls +# on non-CUDA nodes. +# Note that this has been fixed in master, so we probably don't need this patch beyond PT 1.11 diff -Nru pytorch-1.11.0-rc3.orig/test/test_jit_cuda_fuser.py pytorch-1.11.0-rc3/test/test_jit_cuda_fuser.py --- pytorch-1.11.0-rc3.orig/test/test_jit_cuda_fuser.py 2022-02-24 18:06:55.180421593 +0100 +++ pytorch-1.11.0-rc3/test/test_jit_cuda_fuser.py 2022-02-25 13:30:47.112845480 +0100 diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_skip_failing_ops_tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_skip_failing_ops_tests.patch index 3be9d13dc28..25bac0b7e1b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_skip_failing_ops_tests.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_skip_failing_ops_tests.patch @@ -1,3 +1,12 @@ +# Author: Caspar van Leeuwen +# Company: SURF +# Test 'test_fn_grad_linalg_det_singular_cpu_complex128' and test_variant_consistency_jit_contiguous_cpu_float32 fail +# See https://github.com/pytorch/pytorch/issues/67767 and https://github.com/pytorch/pytorch/issues/67838 +# For the first one, devs recommended to switch it off while they revisit the code. +# For the second: the test works interactively when run with +# python -m unittest test_ops.TestJitCPU.test_variant_consistency_jit_contiguous_cpu_float32 -v +# This shows there is no fundamental problem with the installation, +# but something in the environment when run as 'python run_test.py' makes it fail. diff -Nru pytorch-1.11.0-rc3.orig/torch/testing/_internal/common_methods_invocations.py pytorch-1.11.0-rc3/torch/testing/_internal/common_methods_invocations.py --- pytorch-1.11.0-rc3.orig/torch/testing/_internal/common_methods_invocations.py 2022-02-24 18:07:16.430276050 +0100 +++ pytorch-1.11.0-rc3/torch/testing/_internal/common_methods_invocations.py 2022-02-24 19:38:11.610293957 +0100 From 1210e13684a89f56f842e75afa04d193b2314a2c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 May 2022 10:00:13 +0200 Subject: [PATCH 3628/9987] add missing dependencies for libheif (libpng, libjpeg-turbo) + switch to configuring build with CMake to libde265 dependency is picked up --- .../l/libheif/libheif-1.12.0-GCC-11.2.0.eb | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb index d2cd1762518..e42235b1b9b 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'libheif' version = '1.12.0' @@ -12,14 +12,26 @@ source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(versi sources = [SOURCE_TAR_GZ] checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] +builddependencies = [ + ('CMake', '3.22.1'), +] + dependencies = [ + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), ('libde265', '1.0.8'), ('x265', '3.5'), ] +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + sanity_check_paths = { 'files': ['bin/heif-info', 'lib/libheif.a', 'lib/libheif.%s' % SHLIB_EXT, 'lib/pkgconfig/libheif.pc'], - 'dirs': ['include/libheif', 'share'], + 'dirs': ['include/libheif'], } sanity_check_commands = ["heif-info --help"] From 44b6a759f90f5afc136d3c78b8ee70e90eedc87d Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 3 May 2022 10:23:06 +0100 Subject: [PATCH 3629/9987] Module class changed from tools to geo --- easybuild/easyconfigs/h/hector/hector-2.5.0-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hector/hector-2.5.0-GCC-11.2.0.eb b/easybuild/easyconfigs/h/hector/hector-2.5.0-GCC-11.2.0.eb index 7483c75940d..dc312cac53a 100644 --- a/easybuild/easyconfigs/h/hector/hector-2.5.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/h/hector/hector-2.5.0-GCC-11.2.0.eb @@ -37,4 +37,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'geo' From 2494de1cea267c87bf4e967b47bdb039698dd0a0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 3 May 2022 11:21:34 +0100 Subject: [PATCH 3630/9987] use redist source_urls for cuDNN > 7.5 --- .../easyconfigs/c/cuDNN/cuDNN-7.5.0.56-CUDA-10.0.130.eb | 6 ++++-- .../easyconfigs/c/cuDNN/cuDNN-7.6.2.24-CUDA-10.1.243.eb | 6 ++++-- .../easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb | 7 ++++--- .../easyconfigs/c/cuDNN/cuDNN-7.6.4.38-gcccuda-2019a.eb | 6 ++++-- .../easyconfigs/c/cuDNN/cuDNN-7.6.4.38-gcccuda-2019b.eb | 6 ++++-- 5 files changed, 20 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.5.0.56-CUDA-10.0.130.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.5.0.56-CUDA-10.0.130.eb index 6c683a45119..6a64dfa0b18 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.5.0.56-CUDA-10.0.130.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.5.0.56-CUDA-10.0.130.eb @@ -19,8 +19,10 @@ description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-ac toolchain = SYSTEM -# Nvidia developer registration required. -# Download link: https://developer.nvidia.com/rdp/cudnn-download +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % local_cuda_version_major_minor] checksums = ['701097882cb745d4683bb7ff6c33b8a35c7c81be31bac78f05bad130e7e0b781'] diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.2.24-CUDA-10.1.243.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.2.24-CUDA-10.1.243.eb index fc8f7094184..c43cc00f79e 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.2.24-CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.2.24-CUDA-10.1.243.eb @@ -19,8 +19,10 @@ description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-ac toolchain = SYSTEM -# Nvidia developer registration required. -# Download link: https://developer.nvidia.com/rdp/cudnn-download +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % local_cuda_version_major_minor] checksums = ['afbfd6a61e774beb3851742452c007de4f65f8ec0592d583bc6806f8d386cd1f'] diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb index eaeeaa1312e..13e777d8ffe 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-CUDA-10.0.130.eb @@ -19,9 +19,10 @@ description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-ac toolchain = SYSTEM -# Nvidia developer registration required. -# Download link: https://developer.nvidia.com/rdp/cudnn-download -# Download as cudnn-10.0-linux-x64-v7.6.4.38.tgz +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % local_cuda_version_major_minor] checksums = ['417bb5daf51377037eb2f5c87649000ca1b9cec0acb16cfe07cb1d3e9a961dbf'] diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-gcccuda-2019a.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-gcccuda-2019a.eb index 9a64bced11c..fc46a1bb656 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-gcccuda-2019a.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-gcccuda-2019a.eb @@ -18,8 +18,10 @@ a GPU-accelerated library of primitives for deep neural networks.""" # gcccuda 2019a uses CUDA 10.1 toolchain = {'name': 'gcccuda', 'version': '2019a'} -# Nvidia developer registration required. -# Download link: https://developer.nvidia.com/rdp/cudnn-download +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] sources = ['%(namelower)s-10.1-linux-%(cudnnarch)s-v%(version)s.tgz'] checksums = [ { diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-gcccuda-2019b.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-gcccuda-2019b.eb index 81baae2264b..ef2a412c095 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.6.4.38-gcccuda-2019b.eb @@ -8,8 +8,10 @@ a GPU-accelerated library of primitives for deep neural networks.""" # gcccuda 2019b uses CUDA 10.1 toolchain = {'name': 'gcccuda', 'version': '2019b'} -# Nvidia developer registration required. -# Download link: https://developer.nvidia.com/rdp/cudnn-download +# By downloading, you accept the cuDNN Software License Agreement +# (https://docs.nvidia.com/deeplearning/sdk/cudnn-sla/index.html) +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%s/' % '.'.join(version.split('.')[:3])] sources = ['%(namelower)s-10.1-linux-%(cudnnarch)s-v%(version)s.tgz'] checksums = [ { From 7f56286994c2af98bfee5513b9a15fb9e9d2955a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 3 May 2022 11:40:06 +0100 Subject: [PATCH 3631/9987] Add download_instructions to Java 1.8 > 200 --- easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb | 7 +++++-- easybuild/easyconfigs/j/Java/Java-1.8.0_212.eb | 7 +++++-- easybuild/easyconfigs/j/Java/Java-1.8.0_221.eb | 7 +++++-- easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb | 7 +++++-- easybuild/easyconfigs/j/Java/Java-1.8.0_241.eb | 6 ++++-- easybuild/easyconfigs/j/Java/Java-1.8.0_271.eb | 7 +++++-- easybuild/easyconfigs/j/Java/Java-1.8.0_281.eb | 7 +++++-- easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb | 7 +++++-- 8 files changed, 39 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb index 6219a3794e8..b5f365164e3 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_202.eb @@ -10,11 +10,14 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM -# download the tar.gz directly from -# http://www.oracle.com/technetwork/java/javase/downloads/index.html (local_vp, local_vs) = version.split('_') local_altver = '%su%s' % (local_vp.split('.')[1], local_vs) sources = ['jdk-%s-linux-x64.tar.gz' % local_altver] checksums = ['9a5c32411a6a06e22b69c495b7975034409fa1652d03aeb8eb5b6f59fd4594e0'] +download_instructions = """ +1. Visit https://www.oracle.com/java/technologies/javase/javase8-archive-downloads.html +2. Download %s +""" % sources[0] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_212.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_212.eb index 2f7ac0a4e4c..854577beceb 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_212.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_212.eb @@ -7,11 +7,14 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM -# download the tar.gz directly from -# http://www.oracle.com/technetwork/java/javase/downloads/index.html (local_vp, local_vs) = version.split('_') local_altver = '%su%s' % (local_vp.split('.')[1], local_vs) sources = ['jdk-%s-linux-x64.tar.gz' % local_altver] checksums = ['3160c50aa8d8e081c8c7fe0f859ea452922eca5d2ae8f8ef22011ae87e6fedfb'] +download_instructions = """ +1. Visit https://www.oracle.com/java/technologies/javase/javase8u211-later-archive-downloads.html +2. Download %s +""" % sources[0] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_221.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_221.eb index 7c7c4130442..bdc62964d0a 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_221.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_221.eb @@ -7,11 +7,14 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM -# download the tar.gz directly from -# http://www.oracle.com/technetwork/java/javase/downloads/index.html (local_vp, local_vs) = version.split('_') local_altver = '%su%s' % (local_vp.split('.')[1], local_vs) sources = ['jdk-%s-linux-x64.tar.gz' % local_altver] checksums = ['bac52b7f120a03c4c0815ca8fc77c02a8f3db2ded121ffad7449525f377e2479'] +download_instructions = """ +1. Visit https://www.oracle.com/java/technologies/javase/javase8u211-later-archive-downloads.html +2. Download %s +""" % sources[0] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb index 80106409f15..f178687591c 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_231.eb @@ -7,11 +7,14 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM -# download the tar.gz directly from -# http://www.oracle.com/technetwork/java/javase/downloads/index.html (local_vp, local_vs) = version.split('_') local_altver = '%su%s' % (local_vp.split('.')[1], local_vs) sources = ['jdk-%s-linux-x64.tar.gz' % local_altver] checksums = ['a011584a2c9378bf70c6903ef5fbf101b30b08937441dc2ec67932fb3620b2cf'] +download_instructions = """ +1. Visit https://www.oracle.com/java/technologies/javase/javase8u211-later-archive-downloads.html +2. Download %s +""" % sources[0] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_241.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_241.eb index 53ed1bd56d9..6a672c170ca 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_241.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_241.eb @@ -7,12 +7,14 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM -# download the tar.gz directly from -# http://www.oracle.com/technetwork/java/javase/downloads/index.html (local_vp, local_vs) = version.split('_') local_altver = '%su%s' % (local_vp.split('.')[1], local_vs) sources = ['jdk-%s-linux-x64.tar.gz' % local_altver] checksums = ['419d32677855f676076a25aed58e79432969142bbd778ff8eb57cb618c69e8cb'] +download_instructions = """ +1. Visit https://www.oracle.com/java/technologies/javase/javase8u211-later-archive-downloads.html +2. Download %s +""" % sources[0] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_271.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_271.eb index 3d0757252d3..d9c98062344 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_271.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_271.eb @@ -7,11 +7,14 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM -# download the tar.gz directly from -# http://www.oracle.com/technetwork/java/javase/downloads/index.html (local_vp, local_vs) = version.split('_') local_altver = '%su%s' % (local_vp.split('.')[1], local_vs) sources = ['jdk-%s-linux-x64.tar.gz' % local_altver] checksums = ['eba7926a683bb65c6f4e1c502ce624346c42b00fb5531deba296f2560b452c78'] +download_instructions = """ +1. Visit https://www.oracle.com/java/technologies/javase/javase8u211-later-archive-downloads.html +2. Download %s +""" % sources[0] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_281.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_281.eb index 178694d4363..8c09d548a07 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_281.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_281.eb @@ -7,11 +7,14 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM -# download the tar.gz directly from -# http://www.oracle.com/technetwork/java/javase/downloads/index.html (local_vp, local_vs) = version.split('_') local_altver = '%su%s' % (local_vp.split('.')[1], local_vs) sources = ['jdk-%s-linux-x64.tar.gz' % local_altver] checksums = ['85e8c7da7248c7450fb105567a78841d0973597850776c24a527feb02ef3e586'] +download_instructions = """ +1. Visit https://www.oracle.com/java/technologies/javase/javase8u211-later-archive-downloads.html +2. Download %s +""" % sources[0] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb index 47bc761cc52..79002ebe0ea 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_311.eb @@ -7,11 +7,14 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM -# download the tar.gz directly from -# http://www.oracle.com/technetwork/java/javase/downloads/index.html (local_vp, local_vs) = version.split('_') local_altver = '%su%s' % (local_vp.split('.')[1], local_vs) sources = ['jdk-%s-linux-x64.tar.gz' % local_altver] checksums = ['759823389014292e84742a226b0e8fbaa08efa32adc6e6435a690c5576df3bb4'] +download_instructions = """ +1. Visit https://www.oracle.com/java/technologies/javase/javase8u211-later-archive-downloads.html +2. Download %s +""" % sources[0] + moduleclass = 'lang' From 6cbc43e1fda455b35e6f169554f8c410ffa340e3 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 3 May 2022 12:40:17 +0100 Subject: [PATCH 3632/9987] adding easyconfigs: Z3-4.8.16-GCCcore-11.3.0.eb, zstd-1.5.2-GCCcore-11.3.0.eb, gzip-1.12-GCCcore-11.3.0.eb, lz4-1.9.3-GCCcore-11.3.0.eb, elfutils-0.187-GCCcore-11.3.0.eb --- .../elfutils/elfutils-0.187-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ .../g/gzip/gzip-1.12-GCCcore-11.3.0.eb | 24 +++++++++++ .../l/lz4/lz4-1.9.3-GCCcore-11.3.0.eb | 30 ++++++++++++++ .../z/Z3/Z3-4.8.16-GCCcore-11.3.0.eb | 33 +++++++++++++++ .../z/zstd/zstd-1.5.2-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ 5 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/e/elfutils/elfutils-0.187-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.8.16-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.187-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.187-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e3284824d10 --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.187-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.187' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['e70b0dfbe610f90c4d1fe0d71af142a4e25c3c4ef9ebab8d2d72b65159d454c8'] + +builddependencies = [ + ('M4', '1.4.19'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('binutils', '2.38'), + ('bzip2', '1.0.8'), + ('libarchive', '3.6.1'), + ('XZ', '5.2.5'), + ('zstd', '1.5.2'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c20eb7e5ffe --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.12' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e115c68f16b --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.3-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.3' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['030644df4611007ff7dc962d981f390361e6c97a34e5cbc393ddfbe019ffe2c1'] + +builddependencies = [('binutils', '2.38')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.16-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.16-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5c7df4d4378 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.8.16-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Z3' +version = '4.8.16' + +homepage = 'https://github.com/Z3Prover/z3' +description = """ + Z3 is a theorem prover from Microsoft Research. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/Z3Prover/z3/archive/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['75f95e09f3f35fef746e571d5ec88a4efba27f1bc8f1a0ef1117167486ec3dc6'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = '-DZ3_USE_LIB_GMP=ON -DZ3_LINK_TIME_OPTIMIZATION=ON ' + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..643abebdfdb --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.5.2' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f7de13462f7a82c29ab865820149e778cbfe01087b3a55b5332707abf9db4a6e'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('gzip', '1.12'), + ('XZ', '5.2.5'), + ('lz4', '1.9.3'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From 4c6651a6a81780d841fe9cc4c45d9fc4656d757e Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Tue, 3 May 2022 20:46:55 +0800 Subject: [PATCH 3633/9987] rnaQUAST with corrected foss ersion --- ...ython-3.9.6.eb => rnaQUAST-2.2.2-foss-2021b.eb} | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/r/rnaQUAST/{rnaQUAST-2.2.2-foss-2021a-Python-3.9.6.eb => rnaQUAST-2.2.2-foss-2021b.eb} (83%) diff --git a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021a-Python-3.9.6.eb b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb similarity index 83% rename from easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021a-Python-3.9.6.eb rename to easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb index 3fcf714957f..957dd9b932a 100644 --- a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021a-Python-3.9.6.eb +++ b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb @@ -9,17 +9,17 @@ description = """rnaQUAST is a tool for evaluating RNA-Seq assemblies using refe In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.""" -toolchain = {'name': 'foss', 'version': '2021a'} +toolchain = {'name': 'foss', 'version': '2021b'} -source_urls = ['https://github.com/ablab/rnaquast/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['117dff9d9c382ba74b7b0ff24bc7b95b9ca6aa701ebf8afd22943aa54e382334'] +source_urls = ['https://github.com/ablab/rnaquast/releases/download/v.%(version)s/'] +sources = ['rnaQUAST-%(version)s.tar.gz'] +checksums = ['941aeb9a296aa0135f8973c0cffa76e05d7451cc698f0f56c23c5627ae163c8f'] dependencies = [ ('Python', '3.9.6'), - ('GMAP-GSNAP', '2020-12-17'), - ('Biopython', '1.79', versionsuffix), - ('matplotlib', '3.4.3', versionsuffix), + ('GMAP-GSNAP', '2021-21-17'), + ('Biopython', '1.79'), + ('matplotlib', '3.4.3'), ('BLAST+', '2.12.0'), ] From ec67d76210d3810d01a08af5d2e72c4f5b995d26 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 3 May 2022 14:52:25 +0200 Subject: [PATCH 3634/9987] don't use git_config Co-authored-by: Sam Moors --- .../easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb index d818d7e0918..bfc34d6f38d 100644 --- a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb @@ -12,14 +12,10 @@ description = "A MAG Circularization Method By Lauren Lui, Torben Nielsen, and A toolchain = {'name': 'foss', 'version': '2020b'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/Helmholtz-UFZ', - 'repo_name': 'Jorg', - 'tag': 'v1.0.0', - }, -}] +github_account = 'Helmholtz-UFZ' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['74b1c455ba57ab240921966255ca059840b97c47efcd16e9e66b9b6a8a136ee2'] checksums = ['bd91baf986df0ba346f2a0fe7d1da47e28fe7411731ca94ac5f0e3c9b936c1ae'] From e1a69b1c9c308150061823834aa080b3dd4804c3 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 3 May 2022 14:52:56 +0200 Subject: [PATCH 3635/9987] not needed anymore Co-authored-by: Sam Moors --- easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb index bfc34d6f38d..c79655da73d 100644 --- a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb @@ -17,7 +17,6 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['74b1c455ba57ab240921966255ca059840b97c47efcd16e9e66b9b6a8a136ee2'] -checksums = ['bd91baf986df0ba346f2a0fe7d1da47e28fe7411731ca94ac5f0e3c9b936c1ae'] prepend_to_path = ['.'] From e0e4055f6843b4ac0171086c07e5459729384dca Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 3 May 2022 14:55:07 +0200 Subject: [PATCH 3636/9987] adding easyconfigs: popt-1.16-GCC-10.2.0.eb --- .../p/popt/popt-1.16-GCC-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb new file mode 100644 index 00000000000..5d58b1b1a3c --- /dev/null +++ b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'popt' +version = "1.16" + +homepage = "http://freecode.com/projects/popt" +description = """Popt is a C library for parsing command line parameters.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://src.fedoraproject.org/repo/pkgs/popt/popt-1.16.tar.gz/3743beefa3dd6247a73f8f7a32c14c33/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['e728ed296fe9f069a0e005003c3d6b2dde3d9cad453422a10d6558616d304cc8'] + +toolchainopts = {'optarch': False} +sanity_check_paths = { + 'files': ['include/popt.h', + ('lib/libpopt.a', 'lib64/libpopt.a'), + ('lib/libpopt.%s' % SHLIB_EXT, 'lib64/libpopt.%s' % SHLIB_EXT)], + 'dirs': [], +} + +maxparallel = 1 + +moduleclass = 'lib' From 80cd28be5a7148f036286faac5a7f18978243ef0 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 3 May 2022 14:53:56 +0100 Subject: [PATCH 3637/9987] add patch to fix build on systems with an older glibc --- .../g/gzip/gzip-1.12-GCCcore-11.3.0.eb | 7 ++++- ....12_fix-gnulib-strndup-redeclaration.patch | 27 +++++++++++++++++++ 2 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.12_fix-gnulib-strndup-redeclaration.patch diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-11.3.0.eb index c20eb7e5ffe..d5a319eea58 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-11.3.0.eb @@ -10,7 +10,12 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085'] +patches = ['gzip-1.12_fix-gnulib-strndup-redeclaration.patch'] +checksums = [ + '5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085', # gzip-1.12.tar.gz + # gzip-1.12_fix-gnulib-strndup-redeclaration.patch + '9c67e3e88848f7ff1f19f29d87f286bac1cc8f027f7eea9bcaf53883b95032e4', +] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.12_fix-gnulib-strndup-redeclaration.patch b/easybuild/easyconfigs/g/gzip/gzip-1.12_fix-gnulib-strndup-redeclaration.patch new file mode 100644 index 00000000000..f8cbf883a92 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.12_fix-gnulib-strndup-redeclaration.patch @@ -0,0 +1,27 @@ +Patch taken from: +https://lists.gnu.org/archive/html/bug-gnulib/2022-04/msg00080.html +2022-04-30 Bruno Haible +---------------------------------------------- +diff --git a/lib/string.in.h b/lib/string.in.h +index b6840fa912..33160b2525 100644 +--- a/lib/string.in.h ++++ b/lib/string.in.h +@@ -583,7 +583,7 @@ _GL_FUNCDECL_RPL (strndup, char *, + _GL_ATTRIBUTE_MALLOC _GL_ATTRIBUTE_DEALLOC_FREE); + _GL_CXXALIAS_RPL (strndup, char *, (char const *__s, size_t __n)); + # else +-# if !@HAVE_DECL_STRNDUP@ || __GNUC__ >= 11 ++# if !@HAVE_DECL_STRNDUP@ || (__GNUC__ >= 11 && !defined strndup) + _GL_FUNCDECL_SYS (strndup, char *, + (char const *__s, size_t __n) + _GL_ARG_NONNULL ((1)) +@@ -593,7 +593,7 @@ _GL_CXXALIAS_SYS (strndup, char *, (char const *__s, size_t __n)); + # endif + _GL_CXXALIASWARN (strndup); + #else +-# if __GNUC__ >= 11 ++# if __GNUC__ >= 11 && !defined strndup + /* For -Wmismatched-dealloc: Associate strndup with free or rpl_free. */ + _GL_FUNCDECL_SYS (strndup, char *, + (char const *__s, size_t __n) + From 362b4ff895042b27c2ea77e4267fc30b48d25247 Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Wed, 4 May 2022 00:43:18 +0800 Subject: [PATCH 3638/9987] rnaQUAST with corrected foss version & versionsuffix removed --- easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb index 957dd9b932a..06463e95584 100644 --- a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb @@ -2,7 +2,6 @@ easyblock = 'Tarball' name = 'rnaQUAST' version = '2.2.2' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://cab.spbu.ru/software/rnaquast/' description = """rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. From 70be67196dbba23e9721ef3229a3ac3ce637fc8d Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Wed, 4 May 2022 09:15:57 +0800 Subject: [PATCH 3639/9987] Jellyfish-2.3.0-GCC-11.2.0 --- .../j/Jellyfish/Jellyfish-2.3.0-GCC-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-11.2.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..0d6ce04a273 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-11.2.0.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.3.0' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e195b7cf7ba42a90e5e112c0ed27894cd7ac864476dc5fb45ab169f5b930ea5a'] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, +# they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' From f2839d7210ab29ba885c3f94e2a6b8c23c6a1469 Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Wed, 4 May 2022 09:26:05 +0800 Subject: [PATCH 3640/9987] added Salmon-1.4.0-GCC-11.2.0.eb --- .../s/Salmon/Salmon-1.4.0-GCC-11.2.0.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-1.4.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.4.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.4.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..9b648f228b4 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.4.0-GCC-11.2.0.eb @@ -0,0 +1,61 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GLPv2 +# +# Notes:: +## +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# Thanks to people like Simon Brandord, Mikael Oehmann and Kenneth Hoste +# for their help with the ICE + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '1.4.0' + +homepage = 'https://github.com/COMBINE-lab/salmon' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'COMBINE-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6d3e25387450710f0aa779a1e9aaa9b4dec842324ff8551d66962d7c7606e71d'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('pkg-config', '0.29.2'), + ('jemalloc', '5.2.1'), +] + +dependencies = [ + ('Boost', '1.77.0'), + ('tbb', '2020.3'), +] + +# Disable link-time optimizations (-flto) because it triggers a segfault/internal compiler error (ICE) with GCC 9.3.0 +# This problem might be solved with a newer version of either GCC or Salmon. +configopts = '-DJEMALLOC_ROOT=$EBROOTJEMALLOC -DNO_IPO=1' + +# need to unset the $LD_PRELOAD set be jemalloc to avoid hanging 'make test' +# since jemalloc is statically linked in Salmon (and hence only a build dep), +# this only affects the tests +pretestopts = "unset LD_PRELOAD && " +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'] + ['lib/lib%s.a' % x for x in ['graphdump', 'ntcard', 'salmon_core', 'twopaco']], + 'dirs': [], +} + +sanity_check_commands = ["salmon --help"] + +moduleclass = 'bio' From 042145da74bedbfdfd26866be0af6a9f2708d10e Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 4 May 2022 06:39:31 +0100 Subject: [PATCH 3641/9987] restore comments, restore recently added packages, add alt checksum for rda, remove AnalyzeFMRI --- .../easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 107 +++++++++++++++++- 1 file changed, 101 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 0742b309ce7..5570854d16a 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -78,8 +78,11 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on 1st November 2021 +# packages updated on 27th April 2022 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets', @@ -2313,6 +2316,7 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz @@ -2821,9 +2825,13 @@ exts_list = [ 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], }), ('gWidgets2tcltk', '1.0-8', { - 'modulename': False, - 'preinstallopts': "xvfb-run ", 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, }), ('mgsub', '1.7.3', { 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], @@ -2939,9 +2947,6 @@ exts_list = [ ('fmri', '1.9.6', { 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], }), - ('AnalyzeFMRI', '1.1-24', { - 'checksums': ['0d2acfe9ce8f25eb5cc9e6ef1db3ea8e232a31d46a95e50914489b1997e17062'], - }), ('linkcomm', '1.0-14', { 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], }), @@ -3229,6 +3234,96 @@ exts_list = [ ('catlearn', '0.9.1', { 'checksums': ['c6c492f5cc6a9ec6fdbd3721dd64a4bb2e146152d64eeeab4db3d0575bd2f650'], }), + ('MetaUtility', '2.1.2', { + 'checksums': ['e38c21588c239aa8926e64d916aa0f3b04108c2992f0e801095e4c7920b9ad5d'], + }), + ('EValue', '4.1.3', { + 'checksums': ['52a8d4df8ddc80eddf7c2f6684ed6f0fd71f3bd1bfc096ed07cfe875a367e446'], + }), + ('dagitty', '0.3-1', { + 'checksums': ['7d44b5d259ec3fef776a7e3fcb21d1c379f930d6ae9ae5fbfff54494ad78e8a8'], + }), + ('ggdag', '0.2.4', { + 'checksums': ['372ec4ef0ded9637304a19b50bce908e84a034e54dbd2a52a061bb747b2b08a0'], + }), + ('simex', '1.8', { + 'checksums': ['80c7841196b9377a9367eb6960ad80ca0bf8de511b8b18a0031bfbe7bde289a0'], + }), + ('hash', '2.2.6.2', { + 'checksums': ['75a3a64014d2a99f08d12594d14fdade136f278abcf6252119cc20558ed14c9f'], + }), + ('nabor', '0.5.0', { + 'checksums': ['47938dcc987279281c13abfd667660bf1b3b76af116136a27eb066ee1a4b43da'], + }), + ('harmony', '0.1.0', { + 'checksums': ['e0598c220ae90d1334e47c9958ccccf7defbe6ac530159bc69424923894f724a'], + }), + ('apcluster', '1.4.9', { + 'checksums': ['3aac75e3e640eb89c1337d6f2e72a85d226b9c9483e43e0c76f9d424e758cb72'], + }), + ('DataCombine', '0.2.21', { + 'checksums': ['352b235612e2cf8234b3ab5f9aa6f7a394b006b98d24e315940ccc65c4218b47'], + }), + ('docstring', '1.0.0', { + 'checksums': ['14528bc85bbb299fb8fe1a7116034f8df49ae0c26fb299376185b5d56176e5a7'], + }), + ('gdalUtils', '2.0.3.2', { + 'checksums': ['4c6faabee2db8a87b7ea0f8e67e9fce3c5db7f4be353d7d86ea559507cbb2a4f'], + }), + ('openair', '2.9-1', { + 'checksums': ['4ec840cc9abf75dde3ce5d679e79030d858b18f0c57ad9d68a685b0ee970430c'], + }), + ('pdp', '0.7.0', { + 'checksums': ['28d69eb63b92bdf8e974b3222e1e9565000d7f15a3bd90854a8e0446b0fa9a71'], + }), + ('date', '1.2-39', { + 'checksums': ['b5b1935638b73373809c009f94b77f993cd301744488d9bdf71ef79c82099757'], + }), + ('cmprsk', '2.2-11', { + 'checksums': ['844027cb2c162cf7ef97034d01237ad7b81aa192fe302250d22d2c5528110e14'], + }), + ('mets', '1.2.9', { + 'checksums': ['5faccc064e715c44234def40f4f560e90f2dbd34c915a8687b48103b39814ab5'], + }), + ('Publish', '2020.12.23', { + 'checksums': ['a7a98fc52801bee30b9c8cb423e4e0082ea42d05134f7d3324ac3e95242cfbe2'], + }), + ('riskRegression', '2022.03.22', { + 'checksums': ['4e1a66a45be73ae07bbc537192d3132e1cfc67ad24bc4b281b5cffa44282a047'], + }), + ('pec', '2022.03.06', { + 'checksums': ['d55e1d9b5786537ed127f3c470e8e139a9745969dea9a495afe13743a89883ec'], + }), + ('pammtools', '0.5.8', { + 'checksums': ['37197edd0984f8bf0e0a39a4ac1cfce897050dbb7f610553c349118fceb3ca93'], + }), + ('relsurv', '2.2-7', { + 'checksums': ['82c84bbe0a3eb9b391cbb885b3f3e7114adda5243aa83f974922d2edca918317'], + }), + ('mstate', '0.3.2', { + 'checksums': ['3c473dff6854e31cdbdaf79f8fe7eaf97119b01a581874a894b283555afe8d14'], + }), + ('microbenchmark', '1.4.9', { + 'checksums': ['443d2caf370ef33e4ac2773176ad9eb86f8790f43b430968ef9647699dbbffd2'], + }), + ('prettyGraphs', '2.1.6', { + 'checksums': ['fece08924fc7ed05ec419afa14a2216a2bb23d9da5ed3fc61472d6e45be7577a'], + }), + ('ExPosition', '2.8.23', { + 'checksums': ['0510bc51b1c8c883ff3652a5ed56242f91c2b7b7cf3100755436bffa1e002475'], + }), + ('alluvial', '0.1-2', { + 'checksums': ['77b6dc4651b33b03aaaf1e09a35f9c3536e5fddac2eda34f5a34e0ae33cf2e0d'], + }), + ('SNFtool', '2.3.1', { + 'checksums': ['982fe7c57f52c0c272b8cb5863dc5d50623b368e24ff6e27fc8b17acc0101f16'], + }), + ('BayesLogit', '2.1', { + 'checksums': ['3a423f68339ed1bf25e21be53b1fd68452ed7807b17c36239fba759dc6fc6b70'], + }), + ('Hmsc', '3.0-11', { + 'checksums': ['318e95ea88a15939dac33691886a9ce0c54765b25a3f4ef483d168bfc699098a'], + }), ] moduleclass = 'lang' From d2b63b60b0dc4b00fe5a70ec1a084ea37e20f09a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 4 May 2022 06:48:55 +0100 Subject: [PATCH 3642/9987] adding easyconfigs: jax-0.3.9-foss-2021a-CUDA-11.3.1.eb --- .../j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb | 125 ++++++++++++++++++ 1 file changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..d60c503d380 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,125 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.9' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('pytest-xdist', '2.3.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.32.0', '-nodocs'), +] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', versionsuffix, True), + ('NCCL', '2.10.3', versionsuffix), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.0'), +] + +# running the tests with lots of cores results in test failures because not enough threads can be started, +# and running with a single core also results in systematic test failures +# 4 cores seems to work best +parallel = 4 + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = 'e011187e26dbeed80dede66eb48729d184e3bb1d' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '0.15.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], + }), + ('jaxlib', '0.3.7', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + 'jaxlib-0.1.70_add-bazel-args-to-shutdown.patch', + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.3.7.tar.gz + '60a1ec2f32e28eda90998440c3a3f71dd55abd3e5b033849255ab157c4765632', + # tensorflow-e011187e26dbeed80dede66eb48729d184e3bb1d.tar.gz + 'ef5a001226c37f59eca9c9bf0506b962cf220906bcc8f24df4d1ed6011a593e9', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': ['jax-0.2.19_fix-update-of-cache-access-time.patch'], + 'checksums': [ + '45c526496d525fd04c0c9c705971f4cfa31e6a9f7d25e55a4e3bdcb3a4bbe6ce', # jax-v0.3.9.tar.gz + # jax-0.2.19_fix-update-of-cache-access-time.patch + 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + ], + # deliberately not testing in parallel, as that results in (additional) failing tests; + # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, + # see https://github.com/google/jax/issues/7323 and + # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; + # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; + # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + "JAX_ENABLE_X64=true pytest -vv tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 285c7b0db9aef630b7607c0185c97c135cdab2b5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 4 May 2022 06:59:32 +0100 Subject: [PATCH 3643/9987] remove parallel=4 - sequential testing is controlled elsewhere and this kust slows the build --- .../easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb index d60c503d380..d1a8e445d5a 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb @@ -30,11 +30,6 @@ dependencies = [ ('typing-extensions', '3.10.0.0'), ] -# running the tests with lots of cores results in test failures because not enough threads can be started, -# and running with a single core also results in systematic test failures -# 4 cores seems to work best -parallel = 4 - # downloading TensorFlow tarball to avoid that Bazel downloads it during the build # note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE local_tf_commit = 'e011187e26dbeed80dede66eb48729d184e3bb1d' From e25b2fb41c6cd4d1ab1209f18ae353a76a340048 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 4 May 2022 07:07:00 +0100 Subject: [PATCH 3644/9987] add alt checksums for rda --- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 5570854d16a..7b2370d9201 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -2436,7 +2436,8 @@ exts_list = [ 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.9', { 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], From 39e653abee9f8939394063e50cc3f45b5d6e8f67 Mon Sep 17 00:00:00 2001 From: nicholascheng94 Date: Wed, 4 May 2022 14:26:24 +0800 Subject: [PATCH 3645/9987] use GCCcore/11.2.0 instead of GCCcore/8.3.0 --- ...-GCCcore-8.3.0.eb => libedit-20210910-GCCcore-11.2.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/l/libedit/{libedit-20210910-GCCcore-8.3.0.eb => libedit-20210910-GCCcore-11.2.0.eb} (82%) diff --git a/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-11.2.0.eb similarity index 82% rename from easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-8.3.0.eb rename to easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-11.2.0.eb index b1de36ad1e5..b118a9ce3ad 100644 --- a/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-11.2.0.eb @@ -9,15 +9,15 @@ This BSD-style licensed command line editor library provides generic line editin history, and tokenization functions, similar to those found in GNU Readline. """ -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://thrysoee.dk/editline/'] sources = ['%(namelower)s-%(version)s-3.1.tar.gz'] checksums = ['6792a6a992050762edcca28ff3318cdb7de37dccf7bc30db59fcd7017eed13c5'] -builddependencies = [('binutils', '2.32')] +builddependencies = [('binutils', '2.37')] -dependencies = [('ncurses', '6.1')] +dependencies = [('ncurses', '6.2')] sanity_check_paths = { 'files': ['include/editline/readline.h', 'lib/libedit.%s' % SHLIB_EXT, 'lib/libedit.a'], From e2e2139cbf332a4e2bf6613f75cf0fad9b12685e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 4 May 2022 09:13:50 +0100 Subject: [PATCH 3646/9987] adding easyconfigs: jax-0.3.9-foss-2021a.eb --- .../easyconfigs/j/jax/jax-0.3.9-foss-2021a.eb | 111 ++++++++++++++++++ 1 file changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a.eb new file mode 100644 index 00000000000..2d005f8d575 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a.eb @@ -0,0 +1,111 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.9' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('pytest-xdist', '2.3.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.32.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.0'), +] + +# running the tests with lots of cores results in test failures because not enough threads can be started, +# and running with a single core also results in systematic test failures +# 4 cores seems to work best +parallel = 4 + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = 'e011187e26dbeed80dede66eb48729d184e3bb1d' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '0.15.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], + }), + ('jaxlib', '0.3.7', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + 'jaxlib-0.1.70_add-bazel-args-to-shutdown.patch', + ], + 'checksums': [ + # jaxlib-v0.3.7.tar.gz + '60a1ec2f32e28eda90998440c3a3f71dd55abd3e5b033849255ab157c4765632', + # tensorflow-e011187e26dbeed80dede66eb48729d184e3bb1d.tar.gz + 'ef5a001226c37f59eca9c9bf0506b962cf220906bcc8f24df4d1ed6011a593e9', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': ['jax-0.2.19_fix-update-of-cache-access-time.patch'], + 'checksums': [ + '45c526496d525fd04c0c9c705971f4cfa31e6a9f7d25e55a4e3bdcb3a4bbe6ce', # jax-v0.3.9.tar.gz + # jax-0.2.19_fix-update-of-cache-access-time.patch + 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + ], + 'runtest': "pytest -n %(parallel)s tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 76d0dd4f792a4e8f87383d48a4d707529b2cb53c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 May 2022 11:00:13 +0200 Subject: [PATCH 3647/9987] adding easyconfigs: ABAQUS-2022.eb --- easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb new file mode 100644 index 00000000000..6ce57875272 --- /dev/null +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb @@ -0,0 +1,27 @@ +name = 'ABAQUS' +version = '2022' + +homepage = 'https://www.simulia.com/products/abaqus_fea.html' +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" + +toolchain = SYSTEM + +sources = [ + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-5.tar', +] +checksums = [ + '9025c9bc2d0345c13d96e88c1c422b1979a14bf7ba281bd32dfe093c1446945d', # 2022.AM_SIM_Abaqus_Extend.AllOS.1-5.tar + '14c23b3fdfddb723d84a02eb27edc25162e1d27e8fdce053193f72d28ff0a12c', # 2022.AM_SIM_Abaqus_Extend.AllOS.2-5.tar + '561d54d688ea2f2dcf329701e20502642aecf5526eb56db3a586cbcadfbf20fb', # 2022.AM_SIM_Abaqus_Extend.AllOS.3-5.tar + 'c085066ae2df68c9c61ea345808042ddb205c642d649f1ec3b7db4aaffb3d544', # 2022.AM_SIM_Abaqus_Extend.AllOS.4-5.tar + 'bfbc2c1a402881308f68f054e1e376fe153053b4287018ddbc80e76710f6969f', # 2022.AM_SIM_Abaqus_Extend.AllOS.5-5.tar +] + +dependencies = [('Java', '11')] + +moduleclass = 'cae' From 7ca21f520e8ecc7ff59c992de39aed842e34ea8f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 13:06:34 +0100 Subject: [PATCH 3648/9987] adding easyconfigs: libevent-2.1.12-GCCcore-11.3.0.eb, libfabric-1.15.0-GCCcore-11.3.0.eb, PMIx-4.1.2-GCCcore-11.3.0.eb, UCX-1.12.1-GCCcore-11.3.0.eb, OpenMPI-4.1.4rc1-GCC-11.3.0.eb --- .../libevent-2.1.12-GCCcore-11.3.0.eb | 38 ++++++++++++ .../libfabric-1.15.0-GCCcore-11.3.0.eb | 62 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb | 32 ++++++++++ .../p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb | 48 ++++++++++++++ .../u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb | 54 ++++++++++++++++ 5 files changed, 234 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..09681e8d363 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', True), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9138e8f74cd --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.15.0' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +# The psm3 provider (enabled by default) requires an AVX capable system to run +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'ofiwg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.12.1_disable-psm3-avx-config.patch'] +checksums = [ + '6eb54599dd986acbe72329538b70849fd098ec405f28f7aaaef765be3efebb3d', # v1.15.0.tar.gz + # libfabric-1.12.1_disable-psm3-avx-config.patch + '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', +] + +# Avoid using release tarball since this is incomplete +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('numactl', '2.0.14'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# Regenerate build files +preconfigopts = "autoreconf -if &&" + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) +configopts += "--disable-usnic " + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb new file mode 100644 index 00000000000..6fbf3602b0b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb @@ -0,0 +1,32 @@ +name = 'OpenMPI' +version = '4.1.4rc1' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['46169edd9cf8366608684e5c6a342650b2393d46c9f9a380add8e09f1f8001de'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('hwloc', '2.7.1'), + ('libevent', '2.1.12'), + ('UCX', '1.12.1'), + ('libfabric', '1.15.0'), + ('PMIx', '4.1.2'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fa43b710c05 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '4.1.2' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['670d3a02b39fb2126fe8084174cf03c484e027b5921b5c98a851108134e2597a'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.2.12'), + ('hwloc', '2.7.1'), + ('libfabric', '1.15.0'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --with-ofi=$EBROOTLIBFBARIC' +configopts += ' --enable-pmix-binaries' +configopts += ' --disable-man-pages' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4e90405b0cc --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.12.1' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.10.0-dynamic_modules.patch', + 'UCX-1.11.2-missing_header.patch', +] +checksums = [ + '40b447c8e7da94a253f2828001b2d76021eb4ad39647107d433d62d61e18ae8e', # ucx-1.12.1.tar.gz + '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch + 'fa9052a33da5c8e94bc7df0e5fe6ce3baf613310842ae1ab9ed4ef2d49666c01', # UCX-1.11.2-missing_header.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.12'), + ('numactl', '2.0.14'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From cb0f47ccb19e6fe24cefc77e0261b4ce339767a5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 13:09:06 +0100 Subject: [PATCH 3649/9987] adding easyconfigs: fastp-0.23.2-GCC-11.3.0.eb, ISA-L-2.30.0-GCCcore-11.3.0.eb, libdeflate-1.10-GCCcore-11.3.0.eb, NASM-2.15.05-GCCcore-11.3.0.eb --- .../f/fastp/fastp-0.23.2-GCC-11.3.0.eb | 39 ++++++++++++++++ .../i/ISA-L/ISA-L-2.30.0-GCCcore-11.3.0.eb | 46 +++++++++++++++++++ .../libdeflate-1.10-GCCcore-11.3.0.eb | 40 ++++++++++++++++ .../n/NASM/NASM-2.15.05-GCCcore-11.3.0.eb | 25 ++++++++++ 4 files changed, 150 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.10-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.3.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..fb6a98ab824 --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.23.2' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +# https://github.com/OpenGene/fastp +github_account = 'OpenGene' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['185bd58732e57474fa08aae90e154fbc05f3e437ee2b434386dd2266d60d8ef6'] + +dependencies = [ + ('zlib', '1.2.12'), + ('libdeflate', '1.10'), + ('ISA-L', '2.30.0'), +] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/fastp'], + 'dirs': [], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c547fdfabd7 --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.30.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['bcf592c04fdfa19e723d2adf53d3e0f4efd5b956bb618fed54a1108d76a6eb56'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [('NASM', '2.15.05')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +local_bins = ['bin/igzip'] +local_includes = ['include/%(namelower)s.h'] +local_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test', 'types']] +local_libs = ['lib/libisal.%s' % k for k in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': local_bins + local_includes + local_libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.10-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f1ba77b1e67 --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.10-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to 1.8 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'ConfigureMake' + +name = 'libdeflate' +version = '1.10' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5c1f75c285cd87202226f4de49985dcb75732f527eefba2b3ddd70a8865f2533'] + +builddependencies = [('binutils', '2.38')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0b067430c98 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.15.05' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['3c4b8339e5ab54b1bcb2316101f8985a5da50a3f9e504d43fa6f35668bee2fd0'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' From 61a47a8353072969b3c418094dab4e3be11fcd15 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 14:58:03 +0100 Subject: [PATCH 3650/9987] adding easyconfigs: libpng-1.6.37-GCCcore-11.3.0.eb, libjpeg-turbo-2.1.3-GCCcore-11.3.0.eb, giflib-5.2.1-GCCcore-11.3.0.eb --- .../g/giflib/giflib-5.2.1-GCCcore-11.3.0.eb | 28 +++++++++++++ .../libjpeg-turbo-2.1.3-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ .../l/libpng/libpng-1.6.37-GCCcore-11.3.0.eb | 31 ++++++++++++++ 3 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0d33033c2a6 --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.1' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e88b1b5987f --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.3-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.1.3' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['467b310903832b033fe56cd37720d1b73a6a3bd0171dbf6ff0b620385f4f76d0'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +dependencies = [ + ('NASM', '2.15.05'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f7c2cbef5cd --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.37' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['daeb2620d829575513e35fecc83f0d3791a620b9b93d800b763542ece9390fb4'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('zlib', '1.2.12')] + +local_majminver = '%(version_major)s%(version_minor)s' + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' From e0f85f47503a74563a216b2ab590b7c5e281c2bb Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 15:10:39 +0100 Subject: [PATCH 3651/9987] adding easyconfigs: Meson-0.62.1-GCCcore-11.3.0.eb, Ninja-1.10.2-GCCcore-11.3.0.eb --- .../m/Meson/Meson-0.62.1-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ .../n/Ninja/Ninja-1.10.2-GCCcore-11.3.0.eb | 31 +++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.62.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.62.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Meson/Meson-0.62.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d08a6c8dd95 --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.62.1-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.62.1' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7634ec32955d3f897d623b88e9d2988451035f43d73c17a29caf767387baedb7'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Ninja', '1.10.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0118718b1e5 --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.2-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.10.2' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ce35865411f0490368a8fc383f29071de6690cbadc27704734978221f25e2bed'] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +sanity_check_commands = ["ninja --version"] + +moduleclass = 'tools' From 5829e2aab3cb88a82574c63fa2a028d30ebfe9af Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 15:12:00 +0100 Subject: [PATCH 3652/9987] fix Meson checksum --- easybuild/easyconfigs/m/Meson/Meson-0.62.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.62.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Meson/Meson-0.62.1-GCCcore-11.3.0.eb index d08a6c8dd95..ee6c972568e 100644 --- a/easybuild/easyconfigs/m/Meson/Meson-0.62.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/Meson/Meson-0.62.1-GCCcore-11.3.0.eb @@ -9,7 +9,7 @@ description = "Meson is a cross-platform build system designed to be both as fas toolchain = {'name': 'GCCcore', 'version': '11.3.0'} sources = [SOURCELOWER_TAR_GZ] -checksums = ['7634ec32955d3f897d623b88e9d2988451035f43d73c17a29caf767387baedb7'] +checksums = ['a0f5caa1e70da12d5e63aa6a9504273759b891af36c8d87de381a4ed1380e845'] builddependencies = [ ('binutils', '2.38'), From 14e194cd6180cb392c9b3caceb3926f5e7d9a066 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 15:22:12 +0100 Subject: [PATCH 3653/9987] adding easyconfigs: Brotli-1.0.9-GCCcore-11.3.0.eb, fontconfig-2.13.96-GCCcore-11.3.0.eb, freetype-2.12.1-GCCcore-11.3.0.eb, gperf-3.1-GCCcore-11.3.0.eb, intltool-0.51.0-GCCcore-11.3.0.eb, util-linux-2.38-GCCcore-11.3.0.eb --- .../b/Brotli/Brotli-1.0.9-GCCcore-11.3.0.eb | 36 ++++++++++++++++ .../fontconfig-2.13.96-GCCcore-11.3.0.eb | 40 +++++++++++++++++ .../freetype-2.12.1-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ .../g/gperf/gperf-3.1-GCCcore-11.3.0.eb | 31 +++++++++++++ .../intltool-0.51.0-GCCcore-11.3.0.eb | 37 ++++++++++++++++ .../util-linux-2.38-GCCcore-11.3.0.eb | 41 ++++++++++++++++++ 6 files changed, 228 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.96-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.38-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..47746d232c4 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Brotli' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brotli-%(version)s_pc_link_flags.patch'] +checksums = [ + 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz + '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'dirs': [], +} + +sanity_check_commands = ["brotli --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.96-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.96-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..13ff0f0bb18 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.96-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.13.96' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['dbabc038d41cfc3f14da1b173ae103ba7cc678efb17e091b9e801c6286b3f684'] + +builddependencies = [ + ('binutils', '2.38'), + ('gperf', '3.1'), + ('pkgconf', '1.8.0'), + ('Python', '3.10.4', '-bare'), +] + +dependencies = [ + ('expat', '2.4.8'), + ('freetype', '2.12.1'), + ('util-linux', '2.38'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5a647e0de88 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +name = 'freetype' +version = '2.12.1' + +homepage = 'https://www.freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + GNU_SAVANNAH_SOURCE, + SOURCEFORGE_SOURCE, +] +sources = [SOURCE_TAR_GZ] +checksums = ['efe71fd4b8246f1b0b1b9bfca13cfff1c9ad85930340c27df469733bbb620938'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('Brotli', '1.0.9'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +sanity_check_commands = ["freetype-config --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ebe8489c322 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'https://www.gnu.org/software/gperf/' +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.38'), +] + + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8e4d0c83cd7 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Perl', '5.34.1'), +] + +fix_perl_shebang_for = ['bin/intltool-*'] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +sanity_check_commands = ["intltool-merge --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.38-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.38-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5155dfeff30 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.38-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.38' + +homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c31d4e54f30b56b0f7ec8b342658c07de81378f2c067941c2b886da356f8ad42'] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' From 02b7acdde6c9f52fb266f599edc59e9db6c19c7d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 15:53:57 +0100 Subject: [PATCH 3654/9987] adding easyconfigs: X11-20220504-GCCcore-11.3.0.eb --- .../x/X11/X11-20220504-GCCcore-11.3.0.eb | 210 ++++++++++++++++++ 1 file changed, 210 insertions(+) create mode 100644 easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..256aa479186 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb @@ -0,0 +1,210 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20220504' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('Bison', '3.8.2'), + ('gettext', '0.21'), + ('pkgconf', '1.8.0'), + ('intltool', '0.51.0'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.13.96'), + ('freetype', '2.12.1'), + ('zlib', '1.2.12'), + ('xorg-macros', '1.19.3'), + ('libpciaccess', '0.16'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libpthread-stubs', '0.4', { # 2017-03-14 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('xorgproto', '2022.1', { # 2022-04-21 + 'checksums': ['2a399e77d98fe53e9056726a1934b62cbaa6c41d7b1f41a354911b0925363343'], + }), + ('libXau', '1.0.9', { # 2019-02-10 + 'checksums': ['1f123d8304b082ad63a9e89376400a3b1d4c29e67e3ea07b3f659cccca690eea'], + }), + ('libXdmcp', '1.1.3', { # 2019-03-16 + 'checksums': ['2ef9653d32e09d1bf1b837d0e0311024979653fe755ad3aaada8db1aa6ea180c'], + }), + ('xcb-proto', '1.15', { # 2022-05-03 + 'checksums': ['0e434af76af722ef9b2dc21066da1cd11e5dd85fc1996d66228d090f9ae9b217'], + }), + ('libxcb', '1.15', { # 2022-05-03 + 'checksums': ['1cb65df8543a69ec0555ac696123ee386321dfac1964a3da39976c9a05ad724d'], + }), + ('xtrans', '1.4.0', { # 2019-03-16 + 'checksums': ['48ed850ce772fef1b44ca23639b0a57e38884045ed2cbb18ab137ef33ec713f9'], + }), + ('libxkbcommon', '1.4.0', { # 2022-02-04 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['106cec5263f9100a7e79b5f7220f889bc78e7d7ffc55d2b6fdb1efefb8024031'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.8', { # 2022-04-29 + 'checksums': ['68e0a30c4248b9f41492891a4b49672c3b0c59e84c4868144f03eef01ebc5eea'], + }), + ('libXext', '1.3.4', { # 2019-03-16 + 'checksums': ['8ef0789f282826661ff40a8eef22430378516ac580167da35cc948be9041aac1'], + }), + ('libFS', '1.0.8', { # 2019-03-10 + 'checksums': ['e3da723257f4f4c0c629aec402e0a36fbec66a9418f70d24a159cb0470ec83d2'], + }), + ('libICE', '1.0.10', { # 2019-07-14 + 'checksums': ['1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d'], + }), + ('libSM', '1.2.3', { # 2018-10-10 + 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], + }), + ('libXScrnSaver', '1.2.3', { # 2018-07-05 + 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], + }), + ('libXt', '1.2.1', { # 2021-01-24 + 'checksums': ['6da1bfa9dd0ed87430a5ce95b129485086394df308998ebe34d98e378e3dfb33'], + }), + ('libXmu', '1.1.3', { # 2019-03-16 + 'checksums': ['5bd9d4ed1ceaac9ea023d86bf1c1632cd3b172dce4a193a72a94e1d9df87a62e'], + }), + ('libXpm', '3.5.13', { # 2019-12-13 + 'checksums': ['e3dfb0fb8c1f127432f2a498c7856b37ce78a61e8da73f1aab165a73dd97ad00'], + }), + ('libXaw', '1.0.14', { # 2021-03-27 + 'checksums': ['59cfed2712cc80bbfe62dd1aacf24f58d74a76dd08329a922077b134a8d8048f'], + }), + ('libXfixes', '6.0.0', { # 2021-05-11 + 'checksums': ['82045da5625350838390c9440598b90d69c882c324ca92f73af9f0e992cb57c7'], + }), + ('libXcomposite', '0.4.5', { # 2019-03-11 + 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], + }), + ('libXrender', '0.9.10', { # 2016-10-04 + 'checksums': ['770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf'], + }), + ('libXcursor', '1.2.1', { # 2022-04-03 + 'checksums': ['77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'], + }), + ('libXdamage', '1.1.5', { # 2019-03-11 + 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], + }), + ('libfontenc', '1.1.4', { # 2019-02-20 + 'checksums': ['895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.5', { # 2021-08-02 + 'checksums': ['d7544aa35ea67a87840ff0b1bd15130b102e473de3611b7d78604ba635fd6d94'], + }), + ('libXft', '2.3.4', { # 2021-08-02 + 'checksums': ['1eca71bec9cb483165ce1ab94f5cd3036269f5268651df6a2d99c4a7ab644d79'], + }), + ('libXi', '1.8', { # 2021-09-15 + 'checksums': ['c80fd200a1190e4406bb4cc6958839d9651638cb47fa546a595d4bebcd3b9e2d'], + }), + ('libXinerama', '1.1.4', { # 2018-07-05 + 'checksums': ['64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18'], + }), + ('libXrandr', '1.5.2', { # 2019-03-16 + 'checksums': ['3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e'], + }), + ('libXres', '1.2.1', { # 2021-03-31 + 'checksums': ['918fb33c3897b389a1fbb51571c5c04c6b297058df286d8b48faa5af85e88bcc'], + }), + ('libXtst', '1.2.3', { # 2016-10-04 + 'checksums': ['a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2'], + }), + ('libXv', '1.0.11', { # 2016-10-04 + 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], + }), + ('libXvMC', '1.0.13', { # 2022-03-22 + 'checksums': ['e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'], + }), + ('libXxf86dga', '1.1.5', { # 2019-03-16 + 'checksums': ['715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69'], + }), + ('libXxf86vm', '1.1.4', { # 2015-02-24 + 'checksums': ['5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99'], + }), + ('libdmx', '1.1.4', { # 2018-05-14 + 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], + }), + ('libxkbfile', '1.1.0', { # 2019-03-16 + 'checksums': ['2a92adda3992aa7cbad758ef0b8dfeaedebb49338b772c64ddf369d78c1c51d3'], + }), + ('libxshmfence', '1.3', { # 2018-02-26 + 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], + }), + ('xcb-util', '0.4.0', { # 2014-10-15 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.0', { # 2014-10-15 + 'checksums': ['cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42'], + }), + ('xcb-util-keysyms', '0.4.0', { # 2014-10-01 + 'checksums': ['0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96'], + }), + ('xcb-util-renderutil', '0.3.9', { # 2014-06-13 + 'checksums': ['55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5'], + }), + ('xcb-util-wm', '0.4.1', { # 2014-02-19 + 'checksums': ['038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334'], + }), + ('xcb-util-cursor', '0.1.3', { # 2016-05-12 + 'checksums': ['a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8'], + }), + ('xkeyboard-config', '2.35.1', { # 2022-02-08 + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['18ce50ff0c74ae6093062bce1aeab3d363913ea35162fe271f8a0ce399de85cc'], + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.3', { # 2015-02-21 + 'checksums': ['f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c'], + }), + ('xbitmaps', '1.1.2', { # 2018-03-10 + 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' From a7c2d8bd7f7f00e64b504d41e10955da647281f5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 16:04:18 +0100 Subject: [PATCH 3655/9987] bump fontconfig to 1.14.0 --- .../fontconfig-2.14.0-GCCcore-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4a1e98c2679 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.0-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.14.0' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['dbabc038d41cfc3f14da1b173ae103ba7cc678efb17e091b9e801c6286b3f684'] + +builddependencies = [ + ('binutils', '2.38'), + ('gperf', '3.1'), + ('pkgconf', '1.8.0'), + ('Python', '3.10.4', '-bare'), +] + +dependencies = [ + ('expat', '2.4.8'), + ('freetype', '2.12.1'), + ('util-linux', '2.38'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' From b5977f46c9557ba6c257f447af66b7e5956cafc8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 16:05:22 +0100 Subject: [PATCH 3656/9987] bump fontconfig to 1.14.0 --- easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb index 256aa479186..3f08bca2780 100644 --- a/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb @@ -30,7 +30,7 @@ builddependencies = [ dependencies = [ ('bzip2', '1.0.8'), - ('fontconfig', '2.13.96'), + ('fontconfig', '2.14.0'), ('freetype', '2.12.1'), ('zlib', '1.2.12'), ('xorg-macros', '1.19.3'), From 51efc355e21245f1e507a7382876a4d9a309f97c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 16:15:37 +0100 Subject: [PATCH 3657/9987] correct fontconfig checksum --- .../f/fontconfig/fontconfig-2.14.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.0-GCCcore-11.3.0.eb index 4a1e98c2679..6cee0a74ce9 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.0-GCCcore-11.3.0.eb @@ -15,7 +15,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] sources = [SOURCE_TAR_GZ] -checksums = ['dbabc038d41cfc3f14da1b173ae103ba7cc678efb17e091b9e801c6286b3f684'] +checksums = ['b8f607d556e8257da2f3616b4d704be30fd73bd71e367355ca78963f9a7f0434'] builddependencies = [ ('binutils', '2.38'), From 65e5189af073852fb9c963a4d98dcab8f278a371 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 16:25:32 +0100 Subject: [PATCH 3658/9987] adding easyconfigs: libdrm-2.4.110-GCCcore-11.3.0.eb, libglvnd-1.4.0-GCCcore-11.3.0.eb, libunwind-1.6.2-GCCcore-11.3.0.eb, Mako-1.2.0-GCCcore-11.3.0.eb --- .../l/libdrm/libdrm-2.4.110-GCCcore-11.3.0.eb | 32 ++++++++++++++++++ .../libglvnd/libglvnd-1.4.0-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ .../libunwind-1.6.2-GCCcore-11.3.0.eb | 32 ++++++++++++++++++ .../m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb | 29 ++++++++++++++++ 4 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.110-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libglvnd/libglvnd-1.4.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.110-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.110-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e9c1d0bb274 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.110-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'libdrm' +version = '2.4.110' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['eecee4c4b47ed6d6ce1a9be3d6d92102548ea35e442282216d47d05293cf9737'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] +dependencies = [('X11', '20220504')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '-Dman-pages=false' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.4.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e880f8d7de7 --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'libglvnd' +version = '1.4.0' + +homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] +sources = ['libglvnd-v%(version)s.tar.gz'] +checksums = ['33b8b993adf47a21bc1c46bcf970927edeb9884390d5b09b1aed051d600c0b2f'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [('X11', '20220504')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..67e4afd8e05 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.6.2' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4a6aec666991fb45d0889c44aede8ad6eb108071c3554fcdff671f9c94794976'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('XZ', '5.2.5'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd -fno-common" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b3e830b7063 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.2.0' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9a7c7e922b87db3686210cf49d5d767033a41d4010b284e747682c92bddd8b39'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ["mako-render --help"] + +moduleclass = 'devel' From 0d1feba4563a441038e31381b18c3c2a0327bf24 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 16:44:17 +0100 Subject: [PATCH 3659/9987] switch to meson for xkeyboard-config --- easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb index 3f08bca2780..d417d954c4b 100644 --- a/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb @@ -185,8 +185,10 @@ components = [ 'checksums': ['a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8'], }), ('xkeyboard-config', '2.35.1', { # 2022-02-08 + 'easyblock': 'MesonNinja', 'sources': [SOURCE_TAR_XZ], 'checksums': ['18ce50ff0c74ae6093062bce1aeab3d363913ea35162fe271f8a0ce399de85cc'], + 'preconfigopts': '', }), ('printproto', '1.0.5', { # 2011-01-06 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], From 2782371eff1eb5f5b3e3e99d711e93be7815c539 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 4 May 2022 16:50:11 +0100 Subject: [PATCH 3660/9987] Delete fontconfig-2.13.96-GCCcore-11.3.0.eb --- .../fontconfig-2.13.96-GCCcore-11.3.0.eb | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.96-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.96-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.96-GCCcore-11.3.0.eb deleted file mode 100644 index 13ff0f0bb18..00000000000 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.96-GCCcore-11.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'fontconfig' -version = '2.13.96' - -homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' - -description = """ - Fontconfig is a library designed to provide system-wide font configuration, - customization and application access. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] -sources = [SOURCE_TAR_GZ] -checksums = ['dbabc038d41cfc3f14da1b173ae103ba7cc678efb17e091b9e801c6286b3f684'] - -builddependencies = [ - ('binutils', '2.38'), - ('gperf', '3.1'), - ('pkgconf', '1.8.0'), - ('Python', '3.10.4', '-bare'), -] - -dependencies = [ - ('expat', '2.4.8'), - ('freetype', '2.12.1'), - ('util-linux', '2.38'), -] - -configopts = '--disable-docs ' - -sanity_check_paths = { - 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], - 'dirs': [] -} - -moduleclass = 'vis' From 71ae45da77f6d72aff3f3905ab54bdcd772000e9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 17:41:07 +0100 Subject: [PATCH 3661/9987] adding easyconfigs: LLVM-14.0.3-GCCcore-11.3.0.eb --- .../l/LLVM/LLVM-14.0.3-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6f5e81f54ef --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +name = 'LLVM' +version = '14.0.3' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'cstd': 'gnu++11', 'pic': True} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = ['llvm-%(version)s.src.tar.xz'] +checksums = ['1e09e8c26e1b67bc94a128b62e9b9c24b70c697a2436a479c9e5eedc4ae29654'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Python', '3.10.4'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), +] + +build_shared_libs = True + +#start_dir = '%(namelower)s-%(version)s.src' + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' From 1f180a4fc65daf1b0cd8fd6403aedd1ca736c774 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 17:45:28 +0100 Subject: [PATCH 3662/9987] linting --- easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-11.3.0.eb index 6f5e81f54ef..5f275e0f1aa 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-11.3.0.eb @@ -30,8 +30,6 @@ dependencies = [ build_shared_libs = True -#start_dir = '%(namelower)s-%(version)s.src' - sanity_check_paths = { 'files': ['bin/llvm-ar', 'bin/FileCheck'], 'dirs': ['include/llvm', 'include/llvm-c'], From 6af24bf9248bfc9bf2765b944be4a80cd9af73a3 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 17:50:54 +0100 Subject: [PATCH 3663/9987] adding easyconfigs: Mesa-22.0.2-GCCcore-11.3.0.eb --- .../m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..707ebd09a2e --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,69 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers are enabled based on system architecture: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# Default renderer is llvmpipe. SWR can be enabled by setting the environment +# variable GALLIUM_DRIVER=swr + +name = 'Mesa' +version = '22.0.2' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['df4fa560dcce6680133067cd15b0505fc424ca703244ce9ab247c74d2fab6885'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '1.8.0'), + ('Mako', '1.2.0'), + ('libxml2', '2.9.13'), + ('expat', '2.4.8'), + ('gettext', '0.21'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('zstd', '1.5.2'), + ('libdrm', '2.4.110'), + ('libglvnd', '1.4.0'), + ('libunwind', '1.6.2'), + ('LLVM', '14.0.3'), + ('X11', '20220504'), +] + +configopts = "-Dplatforms=x11 -Dosmesa=true -Ddri-drivers='' -Dvulkan-drivers='' " +configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast,swr -Dswr-arches=avx,avx2,skx,knl" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +# Tells libglvnd where to find EGL libraries +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} + +moduleclass = 'vis' From 6aef1aeb341d2f47735c213d140d391c1ab7eebb Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 17:54:27 +0100 Subject: [PATCH 3664/9987] Add Mako --- .../m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b3e830b7063 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.2.0' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9a7c7e922b87db3686210cf49d5d767033a41d4010b284e747682c92bddd8b39'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ["mako-render --help"] + +moduleclass = 'devel' From 22825a4a7b67721f2fa87a38204503caddf211ed Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 4 May 2022 17:56:00 +0100 Subject: [PATCH 3665/9987] remove duplicate Mako (already in #15432) --- .../m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb deleted file mode 100644 index b3e830b7063..00000000000 --- a/easybuild/easyconfigs/m/Mako/Mako-1.2.0-GCCcore-11.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Mako' -version = '1.2.0' - -homepage = 'https://www.makotemplates.org' -description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['9a7c7e922b87db3686210cf49d5d767033a41d4010b284e747682c92bddd8b39'] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -builddependencies = [('binutils', '2.38')] - -dependencies = [('Python', '3.10.4')] - -sanity_check_paths = { - 'files': ['bin/mako-render'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -sanity_check_commands = ["mako-render --help"] - -moduleclass = 'devel' From 78c8152278d14c2df9a376de9d9d685e9b3eba69 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 May 2022 21:38:04 +0200 Subject: [PATCH 3666/9987] adding easyconfigs: AMPtk-1.5.4-foss-2021b.eb, biom-format-2.1.12-foss-2021b.eb, edlib-1.3.9-GCC-11.2.0.eb --- .../a/AMPtk/AMPtk-1.5.4-foss-2021b.eb | 55 +++++++++++++++++++ .../biom-format-2.1.12-foss-2021b.eb | 47 ++++++++++++++++ .../e/edlib/edlib-1.3.9-GCC-11.2.0.eb | 22 ++++++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMPtk/AMPtk-1.5.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.12-foss-2021b.eb create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/AMPtk/AMPtk-1.5.4-foss-2021b.eb b/easybuild/easyconfigs/a/AMPtk/AMPtk-1.5.4-foss-2021b.eb new file mode 100644 index 00000000000..3f44453c9d7 --- /dev/null +++ b/easybuild/easyconfigs/a/AMPtk/AMPtk-1.5.4-foss-2021b.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'AMPtk' +version = '1.5.4' + +homepage = 'https://amptk.readthedocs.io' +description = """AMPtk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be +used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial +16S, and insect COI amplicons.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('h5py', '3.6.0'), + ('biom-format', '2.1.12'), + ('Seaborn', '0.11.2'), + ('Biopython', '1.79'), + ('edlib', '1.3.9'), +] + +use_pip = True + +exts_list = [ + ('distro', '1.7.0', { + 'checksums': ['151aeccf60c216402932b52e40ee477a939f8d58898927378a02abbe852c1c39'], + }), + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + ('pyfastx', '0.8.4', { + 'checksums': ['20cee9faff140f973c59fbe98121eac2d67acf3eb7fef5fdf69a8b4942b4468c'], + }), + ('amptk', version, { + 'checksums': ['f6ddedccb56f39624bd825c504f15823c4ff1d5d0539ebe746405696c77ce69d'], + }), +] + +fix_python_shebang_for = ['bin/amptk', 'bin/*.py'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/amptk', 'bin/amptk_synthetic_mock.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "amptk | grep '^Usage:'", + "amptk_synthetic_mock.py --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.12-foss-2021b.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.12-foss-2021b.eb new file mode 100644 index 00000000000..20a05a5301d --- /dev/null +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.12-foss-2021b.eb @@ -0,0 +1,47 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Revised BSD +# +# Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b +## + +easyblock = 'PythonPackage' + +name = 'biom-format' +version = '2.1.12' + +homepage = 'https://biom-format.org' +description = """ +The BIOM file format (canonically pronounced biome) is designed to be + a general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth Microbiome + Project and is a Genomics Standards Consortium supported project. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4460e803b2abfcabe76d5d8fec0f3f7e76a8cd0e09bf22bb38dea9fca224ac2'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/biom'], + 'dirs': ['lib'], +} + +options = {'modulename': 'biom'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-11.2.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-11.2.0.eb new file mode 100644 index 00000000000..7bf9d797877 --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-11.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'edlib' +version = '1.3.9' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766'] + +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' From c81dc3e254cb03b62a35d637442f287f1ab8969b Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 4 May 2022 21:49:34 +0100 Subject: [PATCH 3667/9987] Update easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-11.3.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-11.3.0.eb index 67e4afd8e05..58fadfb14b7 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('XZ', '5.2.5'), ] -preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd -fno-common" && ' +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fno-common" && ' sanity_check_paths = { 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], From 6ca9a90271e4e17e6ce96ed59faec7940d037612 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 5 May 2022 11:32:40 +0100 Subject: [PATCH 3668/9987] update example configopts to remove mention of deprecated swr --- easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb index 707ebd09a2e..c123b7dda47 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb @@ -56,7 +56,7 @@ configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" # Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host # If you need a different configuration, it possible to override those values by setting your own configopts -# configopts += " -Dgallium-drivers=swrast,swr -Dswr-arches=avx,avx2,skx,knl" +# configopts += " -Dgallium-drivers=swrast" # symlink indirect to mesa GLX, similar to Debian, see # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 From 92dbe107e62acf355ec1403a15859d4caabed0d4 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 5 May 2022 11:49:57 +0100 Subject: [PATCH 3669/9987] adding easyconfigs: freeglut-3.2.2-GCCcore-11.3.0.eb, libGLU-9.0.2-GCCcore-11.3.0.eb --- .../freeglut/freeglut-3.2.2-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ .../l/libGLU/libGLU-9.0.2-GCCcore-11.3.0.eb | 27 +++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.2.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9c123bace89 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.2-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.2.2' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c5944a082df0bba96b5756dddb1f75d0cd72ce27b5395c6c1dde85c2ff297a50'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('X11', '20220504'), + ('Mesa', '22.0.2'), + ('libGLU', '9.0.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.%s" ' % SHLIB_EXT +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9f0bf07710d --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.2' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.gz'] +checksums = ['24effdfb952453cc00e275e1c82ca9787506aba0282145fff054498e60e19a65'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Mesa', '22.0.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 28b1f0208926e9fc5cfdf8686f915472d290e412 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 5 May 2022 12:16:28 +0100 Subject: [PATCH 3670/9987] adding easyconfigs: PCRE2-10.40-GCCcore-11.3.0.eb, PCRE-8.45-GCCcore-11.3.0.eb --- .../p/PCRE/PCRE-8.45-GCCcore-11.3.0.eb | 45 +++++++++++++++++++ .../p/PCRE2/PCRE2-10.40-GCCcore-11.3.0.eb | 28 ++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1dc03c972d3 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.45' + +homepage = 'https://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.pcre.org/pub/pcre/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4e6ce03e0336e8b4a3d6c2b70b1c5e18590a5673a98186da90d4f33c23defc09'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +configopts = """\ + --enable-utf\ + --enable-unicode-properties\ + --enable-pcre16\ + --enable-pcre32\ +""" + +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1d9ce29ade6 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.40' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ded42661cab30ada2e72ebff9e725e745b4b16ce831993635136f2ef86177724'] + +builddependencies = [('binutils', '2.38')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' From a26bc737258a7e4cf06a14c6f30159b146fd7758 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 May 2022 13:19:17 +0200 Subject: [PATCH 3671/9987] add MonteCarlo and RhpcBLASctl extensions to R v4.1.2 + v4.2.0 easyconfigs --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 0fd0db995ad..82227665190 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3310,6 +3310,12 @@ exts_list = [ ('Hmsc', '3.0-11', { 'checksums': ['318e95ea88a15939dac33691886a9ce0c54765b25a3f4ef483d168bfc699098a'], }), + ('MonteCarlo', '1.0.6', { + 'checksums': ['f21aecfba957bbea9576b09f75b1f7c7621637a04532a8fed2c6bb8ffc1a98cb'], + }), + ('RhpcBLASctl', '0.21-247.1', { + 'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 7b2370d9201..5035a318f69 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -3325,6 +3325,12 @@ exts_list = [ ('Hmsc', '3.0-11', { 'checksums': ['318e95ea88a15939dac33691886a9ce0c54765b25a3f4ef483d168bfc699098a'], }), + ('MonteCarlo', '1.0.6', { + 'checksums': ['f21aecfba957bbea9576b09f75b1f7c7621637a04532a8fed2c6bb8ffc1a98cb'], + }), + ('RhpcBLASctl', '0.21-247.1', { + 'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'], + }), ] moduleclass = 'lang' From d203385578cb32c56c974905d85b5d0c45e0d69d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 5 May 2022 12:30:46 +0100 Subject: [PATCH 3672/9987] adding easyconfigs: cairo-1.17.4-GCCcore-11.3.0.eb, GObject-Introspection-1.72.0-GCCcore-11.3.0.eb, GLib-2.72.1-GCCcore-11.3.0.eb, pixman-0.40.0-GCCcore-11.3.0.eb --- .../c/cairo/cairo-1.17.4-GCCcore-11.3.0.eb | 49 +++++++++++++++++ .../g/GLib/GLib-2.72.1-GCCcore-11.3.0.eb | 52 +++++++++++++++++++ ...ect-Introspection-1.72.0-GCCcore-11.3.0.eb | 44 ++++++++++++++++ .../p/pixman/pixman-0.40.0-GCCcore-11.3.0.eb | 28 ++++++++++ 4 files changed, 173 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.72.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.72.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6d0f9f552ef --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.17.4' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'https://cairographics.org/releases/', + 'https://cairographics.org/snapshots/' +] +sources = [SOURCE_TAR_XZ] +checksums = ['74b24c1ed436bbe87499179a3b27c43f4143b8676d8ad237a6fa787401959705'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('pixman', '0.40.0'), + ('expat', '2.4.8'), + ('GLib', '2.72.1'), + ('X11', '20220504'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.72.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.72.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..88ad2f12f66 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.72.1-GCCcore-11.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.72.1' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c07e57147b254cef92ce80a0378dc0c02a4358e7de4702e9f403069781095fe2'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.10.4', '-bare'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('libffi', '3.4.2'), + ('gettext', '0.21'), + ('libxml2', '2.9.13'), + ('PCRE', '8.45'), + ('util-linux', '2.38'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.72.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.72.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0ef33f9c6c0 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.72.0-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.72.0' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['02fe8e590861d88f83060dd39cda5ccaa60b2da1d21d0f95499301b186beaabc'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('cairo', '1.17.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('GLib', '2.72.1'), + ('libffi', '3.4.2'), + ('util-linux', '2.38'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..893f6803884 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.40.0' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6d200dec3740d9ec4ec8d1180e25779c00bc749f94278c8b9021f5534db223fc'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 50c37896e9f0083f3e9a2444bb3a0c25e6281ab6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 5 May 2022 12:43:52 +0100 Subject: [PATCH 3673/9987] adding easyconfigs: ATK-2.38.0-GCCcore-11.3.0.eb, at-spi2-atk-2.38.0-GCCcore-11.3.0.eb, at-spi2-core-2.44.1-GCCcore-11.3.0.eb, DBus-1.14.0-GCCcore-11.3.0.eb --- .../a/ATK/ATK-2.38.0-GCCcore-11.3.0.eb | 39 ++++++++++++++++ .../at-spi2-atk-2.38.0-GCCcore-11.3.0.eb | 37 ++++++++++++++++ .../at-spi2-core-2.44.1-GCCcore-11.3.0.eb | 39 ++++++++++++++++ .../d/DBus/DBus-1.14.0-GCCcore-11.3.0.eb | 44 +++++++++++++++++++ 4 files changed, 159 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.14.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3c2987a1b4a --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.38.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), + ('GObject-Introspection', '1.72.0'), +] + +dependencies = [ + ('GLib', '2.72.1'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..07a150a7fb1 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('GLib', '2.72.1'), + ('DBus', '1.14.0'), + ('at-spi2-core', '2.44.1'), + ('libxml2', '2.9.13'), + ('ATK', '2.38.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2d3b037b75a --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.44.1' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['4beb23270ba6cf7caf20b597354d75194d89afb69d2efcf15f4271688ba6f746'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('GObject-Introspection', '1.72.0'), + ('gettext', '0.21'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('GLib', '2.72.1'), + ('DBus', '1.14.0'), + ('X11', '20220504'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.14.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.14.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..272fc875d0d --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.14.0-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.14.0' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ccd7cce37596e0a19558fd6648d1272ab43f011d80c8635aea8fd0bad58aebd4'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('expat', '2.4.8'), +] + +configopts = '--with-systemdsystemunitdir=no ' +# disable documentation +configopts += '--disable-xml-docs --disable-doxygen-docs --disable-ducktype-docs' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' From 57e0c60ef2925ec2b53643c393d394d6bdb5976f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 5 May 2022 12:53:53 +0100 Subject: [PATCH 3674/9987] adding easyconfigs: Pango-1.50.7-GCCcore-11.3.0.eb, FriBidi-1.0.12-GCCcore-11.3.0.eb, ICU-71.1-GCCcore-11.3.0.eb, HarfBuzz-4.2.1-GCCcore-11.3.0.eb --- .../FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb | 32 +++++++++++++++ .../HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb | 38 +++++++++++++++++ .../i/ICU/ICU-71.1-GCCcore-11.3.0.eb | 29 +++++++++++++ .../p/Pango/Pango-1.50.7-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ 4 files changed, 140 insertions(+) create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/i/ICU/ICU-71.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.50.7-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..65c4eb01b1c --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.12' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0cd233f97fc8c67bb3ac27ce8440def5d3ffacf516765b91c2cc654498293495'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +configopts = '--disable-docs' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..af1f8d0d274 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '4.2.1' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['99fcd30e2f4c66d05af3d61ad4cdba2abc2a51ecabb7eb6dc222520a892b50b0'] + +builddependencies = [ + ('binutils', '2.38'), + ('GObject-Introspection', '1.72.0'), + ('pkgconf', '1.8.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('GLib', '2.72.1'), + ('ICU', '71.1'), + ('cairo', '1.17.4'), + ('freetype', '2.12.1'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ICU/ICU-71.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-71.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b9651a1c3ec --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-71.1-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '71.1' + +homepage = 'https://icu.unicode.org' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['67a7e6e51f61faf1306b6935333e13b2c48abd8da6d2f46ce6adca24b1e21ebf'] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4', '-bare'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.50.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.50.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3286d679983 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.50.7-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.50.7' + +homepage = 'https://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0477f369a3d4c695df7299a6989dc004756a7f4de27eecac405c6790b7e3ad33'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('GObject-Introspection', '1.72.0'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('X11', '20220504'), + ('GLib', '2.72.1'), + ('cairo', '1.17.4'), + ('HarfBuzz', '4.2.1'), + ('FriBidi', '1.0.12'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 2b6346f86143e9dab85b2cf6443e53bcc17e5feb Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 5 May 2022 14:58:14 +0200 Subject: [PATCH 3675/9987] adding easyconfigs: pydot-1.4.2-GCCcore-10.3.0.eb, detectron2-0.6-foss-2021a.eb --- .../d/detectron2/detectron2-0.6-foss-2021a.eb | 101 ++++++++++++++++++ .../p/pydot/pydot-1.4.2-GCCcore-10.3.0.eb | 25 +++++ 2 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb b/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb new file mode 100644 index 00000000000..d455039e0b3 --- /dev/null +++ b/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb @@ -0,0 +1,101 @@ +easyblock = "PythonBundle" + +name = "detectron2" +version = "0.6" + +homepage = "https://github.com/facebookresearch/detectron2" +description = "Detectron2 is a platform for object detection, segmentation and other visual recognition tasks." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyTorch', '1.10.0', '-CUDA-11.3.1'), + ('torchvision', '0.11.1', '-CUDA-11.3.1'), + ('Hydra', '1.1.1'), + ('tqdm', '4.61.2'), + ('YACS', '0.1.8'), + ('matplotlib', '3.4.2'), + ('pycocotools', '2.0.4'), + ('pydot', '1.4.2'), + ('tensorboard', '2.8.0'), + ('OpenCV', '4.5.3', '-CUDA-11.3.1-contrib'), +] + +exts_list = [ + ('packaging', '21.3', { + 'checksums': ['dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb'], + }), + ('poetry-core', '1.0.8', { + 'modulename': 'poetry.core', + 'checksums': ['951fc7c1f8d710a94cb49019ee3742125039fc659675912ea614ac2aa405b118'], + }), + ('poetry', '1.1.13', { + 'preinstallopts': 'sed -i "s|20.4|21.3|g" pyproject.toml &&', + 'checksums': ['b905ed610085f568aa61574e0e09260c02bff9eae12ff672af39e9f399357ac4'], + }), + ('pytest', '7.1.2', { + 'checksums': ['a06a0425453864a270bc45e71f783330a7428defb4230fb5e6a731fde06ecd45'], + }), + ('pluggy', '1.0.0', { + 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], + }), + ('CacheControl', '0.12.11', { + 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], + }), + ('mypy-extensions', '0.4.3', { + 'source_tmpl': 'mypy_extensions-%(version)s.tar.gz', + 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], + }), + ('pathspec', '0.9.0', { + 'checksums': ['e564499435a2673d586f6b2130bb5b95f04a3ba06f81b8f895b651a3c76aabb1'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('editables', '0.3', { + 'checksums': ['167524e377358ed1f1374e61c268f0d7a4bf7dbd046c656f7b410cde16161b1a'], + }), + ('hatchling', '0.23.0', { + 'checksums': ['c4c5beeffe575e312519ec355a3c82af4491238c1ac4eff6feac3bd471aa5282'], + }), + ('setuptools-scm', '6.4.2', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6833ac65c6ed9711a4d5d2266f8024cfa07c533a0e55f4c12f6eff280a5a9e30'], + }), + ('hatch-vcs', '0.2.0', { + 'source_tmpl': 'hatch_vcs-%(version)s.tar.gz', + 'checksums': ['9913d733b34eec9bb0345d0626ca32165a4ad2de15d1ce643c36d09ca908abff'], + }), + ('platformdirs', '2.5.2', { + 'checksums': ['58c8abb07dcb441e6ee4b11d8df0ac856038f944ab98b7be6b27b2a3c7feef19'], + }), + ('black', '21.4b2', { + 'checksums': ['fc9bcf3b482b05c1f35f6a882c079dc01b9c7795827532f4cc43c0ec88067bbc'], + }), + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('fvcore', '0.1.5.post20220414', { + 'checksums': ['3b95983a799047661422c01671da2fa4749f60fa947e2b0ad0520f1ebc11be43'], + }), + ('portalocker', '2.4.0', { + 'checksums': ['a648ad761b8ea27370cb5915350122cd807b820d2193ed5c9cc28f163df637f4'], + }), + ('iopath', '0.1.9', { + 'source_tmpl': '%(namelower)s-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['9058ac24f0328decdf8dbe209b33074b8702a3c4d9ba2f7801d46cb61a880b6e'], + }), + (name, version, { + 'source_urls': ['https://github.com/facebookresearch/detectron2/archive/refs/tags/'], + 'sources': 'v%(version)s.tar.gz', + 'checksums': ['9757fed05fa32acc2116ea038185f08409d5e854573e70f41909a358b70d1004'], + }), +] + +use_pip = True +sanity_pip_check = True \ No newline at end of file diff --git a/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c4587a7bc28 --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pydot' +version = '1.4.2' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['248081a39bcb56784deb018977e428605c1c758f10897a339fce1dd728ff007d'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('Graphviz', '2.47.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 5bf80bf51d9551490e9b803caae2921295798edc Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 5 May 2022 15:09:22 +0200 Subject: [PATCH 3676/9987] adding easyconfigs: gcloud-382.0.0.eb --- .../easyconfigs/g/gcloud/gcloud-382.0.0.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb diff --git a/easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb b/easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb new file mode 100644 index 00000000000..70fe8445e8e --- /dev/null +++ b/easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb @@ -0,0 +1,17 @@ +easyblock = 'Tarball' + +name = "gcloud" +version = "382.0.0" + +homepage = "https://cloud.google.com/sdk" +description = "Libraries and tools for interacting with Google Cloud products and services." + +toolchain = SYSTEM + +source_urls = ["https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/"] +sources = ["google-cloud-sdk-%(version)s-linux-x86_64.tar.gz"] +checksums = ['335e5a2b4099505372914acfccbb978cf9d4efd8047bda59f910c26daefd554e'] + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +moduleclass = "tools" From febc4340410e74f578d3b2a42229288ce488f8e1 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 5 May 2022 15:14:02 +0200 Subject: [PATCH 3677/9987] Fixed style errors --- .../easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb b/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb index d455039e0b3..6769ff382b4 100644 --- a/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb @@ -98,4 +98,6 @@ exts_list = [ ] use_pip = True -sanity_pip_check = True \ No newline at end of file +sanity_pip_check = True + +moduleclass = 'vis' From 9901b7edbb6344bee5af83592569d0b06649bf91 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 5 May 2022 15:19:06 +0200 Subject: [PATCH 3678/9987] Added versionsuffix --- ...ss-2021a.eb => detectron2-0.6-foss-2021a-CUDA-11.3.1.eb} | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/d/detectron2/{detectron2-0.6-foss-2021a.eb => detectron2-0.6-foss-2021a-CUDA-11.3.1.eb} (96%) diff --git a/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb b/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb similarity index 96% rename from easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb rename to easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb index 6769ff382b4..5840b58014e 100644 --- a/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb @@ -2,6 +2,7 @@ easyblock = "PythonBundle" name = "detectron2" version = "0.6" +versionsuffix = "-CUDA-%(cudaver)s" homepage = "https://github.com/facebookresearch/detectron2" description = "Detectron2 is a platform for object detection, segmentation and other visual recognition tasks." @@ -10,8 +11,9 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), - ('PyTorch', '1.10.0', '-CUDA-11.3.1'), - ('torchvision', '0.11.1', '-CUDA-11.3.1'), + ('CUDA', '11.3.1', '', True), + ('PyTorch', '1.10.0', versionsuffix), + ('torchvision', '0.11.1', versionsuffix), ('Hydra', '1.1.1'), ('tqdm', '4.61.2'), ('YACS', '0.1.8'), From c7ba6ad9be5c07dac5bd70944a60ca9599b4d285 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 5 May 2022 14:25:06 +0100 Subject: [PATCH 3679/9987] adding easyconfigs: R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb, arrow-R-6.0.0.2-foss-2021b-R-4.2.0.eb and patches: RProtoBufLib-2.8.0_fix-protobuf-build.patch --- .../arrow-R-6.0.0.2-foss-2021b-R-4.2.0.eb | 34 + ...le-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 1102 +++++++++++++++++ ...ProtoBufLib-2.8.0_fix-protobuf-build.patch | 41 + 3 files changed, 1177 insertions(+) create mode 100644 easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021b-R-4.2.0.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/RProtoBufLib-2.8.0_fix-protobuf-build.patch diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021b-R-4.2.0.eb new file mode 100644 index 00000000000..fdaeda6b276 --- /dev/null +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-6.0.0.2-foss-2021b-R-4.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'arrow-R' +version = '6.0.0.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/arrow' +description = "R interface to the Apache Arrow C++ library" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['arrow_%(version)s.tar.gz'] +checksums = ['76808692851eca33ff7ea9532b143db4698689081ce2f8cfe53c3e9e0aee1184'] + +dependencies = [ + ('R', '4.2.0'), + ('Arrow', '6.0.0'), +] + +preinstallopts = "export LIBARROW_BINARY=true && " + +sanity_check_paths = { + 'files': [], + 'dirs': ['arrow'], +} + +options = {'modulename': 'arrow'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb new file mode 100644 index 00000000000..15af98e6e4b --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -0,0 +1,1102 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.15' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [ + ('R', '4.2.0'), + ('Boost', '1.77.0'), # for mzR + ('GSL', '2.7'), # for flowClust + ('HDF5', '1.12.1'), # for rhdf5 + ('arrow-R', '6.0.0.2', versionsuffix), # required by RcisTarget +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", 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['22a7e1e1067a435e890d76cc9caaca806d2bcbffb7973207f1a646e0eff96085'], + }), + ('shinyFiles', '0.9.1', { + 'checksums': ['05694630ed5ae6ac15307ffcb211c83097fee0f38ca59340a7e68cac62730d39'], + }), + ('samr', '3.0', { + 'checksums': ['25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506'], + }), + ('DEGseq', '1.50.0', { + 'checksums': ['2e84bf5351579f092df72afba90bab08a70c536e56400a05ae6d80ba1cec5ede'], + }), + ('hgu133plus2.db', '3.13.0', { + 'checksums': ['ddde58e777a8341536a664c7d4be874a2f395f8aaa019c1f738462a8ce74cc44'], + }), + ('illuminaio', '0.38.0', { + 'checksums': ['c240646e8cfe38456c7e223da4edaf8e4526678d887b896247fa129ed42960f6'], + }), + ('BiocIO', '1.6.0', { + 'checksums': ['b7f901ca3e6fa06171f839c088c8769a462533a3cf5b83eb7dabe64fb811489a'], + }), + ('restfulr', '0.0.13', { + 'checksums': ['7b59f5887aaf02f46a80617f4d1e0ffd4e11e4840e9e2fbd486a9a9c7f2d64b6'], + }), + ('rtracklayer', '1.56.0', { + 'checksums': ['cd215e2e7c0c5ab27c037869289598a25b300537d7ee8181dc6ce6dcc3543ab5'], + }), + ('filelock', '1.0.2', { + 'checksums': ['ac2915950789b16c43a625a2b8dab6ba423588db4a7d0daa75b74518b82b1403'], + }), + ('BiocFileCache', '2.4.0', { + 'checksums': ['5cefe2e72648c0003ac74937b390ebda7258b09eed575b84de1cb5dc23adabad'], + }), + ('biomaRt', '2.52.0', { + 'checksums': ['af23f7f9fe0fe9f7a38ea56d49671d62076ec7f8b1039054428cdeecad9ac37a'], + }), + ('GenomicFeatures', '1.48.0', { + 'checksums': ['b86587355c00661257bf89e3c05a4a0da1e372c82f7b6f4263f01c44cdee4586'], + }), + ('bumphunter', '1.38.0', { + 'checksums': ['bc73783c84765a82f182ea17eb2cdaeea7631ed728eb7dd8aa5163c892be224d'], + }), + ('multtest', '2.52.0', { + 'checksums': ['02f5d868a59d849e7c9d528d7242843af2791312d36e5a5f9770f3307965fc0c'], + }), + ('scrime', '1.3.5', { + 'checksums': ['5d97d3e57d8eb30709340fe572746029fd139456d7a955421c4e3aa75d825578'], + }), + ('siggenes', '1.70.0', { + 'checksums': ['f4b454231928de76e85cd5582e69467de9c503b2e72610fa973b5cc444c5b22a'], + }), + ('DynDoc', '1.74.0', { + 'checksums': ['b1bfc7f8a519c4bd36a36bd22b16015900e3210ad3d8931be323d9401b6d117b'], + }), + ('NOISeq', '2.40.0', { + 'checksums': ['47cc6c13a1904f31f1b7ab206e438321208b6614d646ada72445900d6953062a'], + }), + ('Rgraphviz', '2.40.0', { + 'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'], + 'checksums': [ + '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4', # Rgraphviz_2.40.0.tar.gz + # Rgraphviz-2.28.0_fno-tree-vectorize.patch + '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9', + ], + }), + ('RNASeqPower', '1.36.0', { + 'checksums': ['8d9ffdf045b56a69f2109503a733ab9bd55801a42ac6e52b4d7983f1e6ec692f'], + }), + ('annotate', '1.74.0', { + 'checksums': ['4fc0553435855aa7dbf352a26b86e39936d4510ae03816f708e7091e6f6bdb74'], + }), + ('GSEABase', '1.58.0', { + 'checksums': ['0f9d54c3be70854e349e150fcfd28585c67a1eacae5a2c204acd89349e7f1be2'], + }), + ('genefilter', '1.78.0', { + 'checksums': ['58913b670b29109a7226320e1f99d795931991db1939ea3fa25143492d55e3d2'], + }), + ('Category', '2.62.0', { + 'checksums': ['0def183b2707c0a1c2341ba104bfc6cc59df31dd2a92c0fffacfb4e6d8005a1e'], + }), + ('GOstats', '2.62.0', { + 'checksums': ['35cbed07bac0e1c67ea9d469d335d91de8b5c229c810568f472f2b1777f23488'], + }), + ('BSgenome', '1.64.0', { + 'checksums': ['ace392a9db183effb8a55c1f74719ef00dee5ea2da2af6f383af77e354cdf89d'], + }), + ('VariantAnnotation', '1.42.0', { + 'checksums': ['3fae05179d419e49bd5e0e45425eb13b22a1d6f341a8544e0c973a956937aa6d'], + }), + ('interactiveDisplayBase', '1.34.0', { + 'checksums': ['af2d2e7d806a349bf87b0eb969da661c160ce1ff0747375b5708320059e9bc39'], + }), + ('BiocVersion', '3.15.2', { + 'checksums': ['d67d6ecbdc89c9a69bc05a950edde3658411407c67804680981843a2beb74467'], + }), + ('AnnotationHub', '3.4.0', { + 'checksums': ['bacb8e2c4f14168087aa5c463902f3f910acf27d224c4ad2ee69eb3c485fb50d'], + }), + ('AnnotationFilter', '1.20.0', { + 'checksums': ['8d2ab20f253890fd7a560bf16be9e9cdd9d130e66232da6c9f56646f1abb5420'], + }), + ('ProtGenerics', '1.28.0', { + 'checksums': ['05e06c4ed777360f6e027568ff6e3ae6e5de97e07ce52454b87f3584897c0c12'], + }), + ('ensembldb', '2.20.1', { + 'checksums': ['9fc77f065b629d3a4e9d11420f12d44ae15b12814c33337e4f76bb67c9d179a0'], + }), + ('biovizBase', '1.44.0', { + 'checksums': ['cd7f83e8170d22ef45a3a832475edffcc131707aa882a2d046f410bafd71dfb9'], + }), + ('OrganismDbi', '1.38.0', { + 'checksums': ['d9b3e40d252a8d15c50c9444e147b10d3a6474c0d4852092d36957d27c5474f6'], + }), + ('ggbio', '1.44.0', { + 'checksums': ['4734df49744bdc64c01720999565919620c52407c5de0782fb3625b50ed075d3'], + }), + ('geneplotter', '1.74.0', { + 'checksums': ['4cc610c37d6c5fa2eeb6d61c52fa1cb322658216035c99dcb654e5967f05438c'], + }), + ('DESeq2', '1.36.0', { + 'checksums': ['2737cdbb39d393262af22c37aa7e8db72375ff04fb6aeeb849cf098b2558bb1a'], + }), + ('ReportingTools', '2.36.0', { + 'checksums': ['104e5363b8756259028b1aba15d3f3adce99fce8488e09e19b5d06e83e6e0c65'], + }), + ('Glimma', '2.6.0', { + 'checksums': ['df6f7fd11e6c0913a8527d367624dd2ad21feedd2feff0a68262c19d805727cc'], + }), + ('affycoretools', '1.68.0', { + 'checksums': ['9d93de8b27d5b8621643e3f5a3c3bca11fffb30bd8f1c70bb2d848780c7e3993'], + }), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', { + 'checksums': ['063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9'], + }), + ('Homo.sapiens', '1.3.1', { + 'checksums': ['014809fc6ef6410be8dc1094c9cb083719f20d999065ae4bf388855be0913b94'], + }), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.3', { + 'checksums': ['5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a'], + }), + ('AgiMicroRna', '2.46.0', { + 'checksums': ['aa8b1482bae0a7a71f19191a9c0dba1411ac025ca93e47bf3c7bc1eb5f422c4a'], + }), + ('geneLenDataBase', '1.32.0', { + 'checksums': ['5f691667b53acb1769509540bdbdbf7001e5be4973b97a88f5567f8d47ab995c'], + }), + ('goseq', '1.48.0', { + 'checksums': ['88b45cf35e363e3c9b2edd6619d62be902ad97f40c835dfce9e2ee89e1e719f0'], + }), + ('KEGGgraph', '1.56.0', { + 'checksums': ['bdd9104ca0296d8f26d6719a2d9fdfaf9ed553b9b2f6d851c8103d760101f896'], + }), + ('GEOquery', '2.64.0', { + 'checksums': ['3f1a750ac1a7262ad6ac1d4ca69197e4fd64d53e9408f7b2e0be982fee994158'], + }), + ('rARPACK', '0.11-0', { + 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], + }), + ('mixOmics', '6.20.0', { + 'checksums': ['871f11604dd4e1923fc107a4c3df083ff41b8feb7332f765940bc8ec0e178c3b'], + }), + ('Rhdf5lib', '1.18.0', { + 'checksums': ['d253cfc669a2f67db4f0f817e57480178cfe088e380ab8e9cb53052e3bbd8960'], + }), + ('rhdf5filters', '1.8.0', { + 'checksums': ['7ad7b5ae372c1a700976768e37ad227475c675bc15333d8cac317c6cd106efc6'], + }), + ('rhdf5', '2.40.0', { + 'checksums': ['ce4585ddf67848e3b34c531e02df7ee712874127dd54eaa21ce8a2652b489701'], + }), + ('HDF5Array', '1.24.0', { + 'checksums': ['84fbce555988d3883e9c55e1441ba7bac5f97397a1a48c28af93a532c8913b69'], + }), + ('sparseMatrixStats', '1.8.0', { + 'checksums': ['a28fe0592793913b2c9c553bb15c71f741992ce88d27544475eb977bbc9a225c'], + }), + ('DelayedMatrixStats', '1.18.0', { + 'checksums': ['5b637538070ee949bad499390d140c0e8eac0d3f19655de71f5c64c092d99ce2'], + }), + ('minfi', '1.42.0', { + 'checksums': ['06e7596df31e8c01cd990f7f0dde3ef5e001cf58531ecb110f609658f8f9a508'], + }), + ('FDb.InfiniumMethylation.hg19', '2.2.0', { + 'checksums': ['605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f'], + }), + ('methylumi', '2.42.0', { + 'checksums': ['9c4bb87b4f581ebe142ca1bd42434f07248250da793ef4490bd2d152b08d934e'], + }), + ('lumi', '2.48.0', { + 'checksums': ['2d7964151fc7eab8cd4bea18b17f2d3c60f233a5302bbf46d5d5fb200ba5f51b'], + }), + ('widgetTools', '1.74.0', { + 'checksums': ['cd2027038e0cb97a63dd0e7d01d5c3425c3a722c24c80d6f5dd1a84f60d18183'], + }), + ('tkWidgets', '1.74.0', { + 'checksums': ['60124d00b1b0839b6a25befcaa76433ec9c4b867b0457219592335f43561f12c'], + }), + ('Mfuzz', '2.56.0', { + 'checksums': ['04426eed6a20834f793024370cc9120e54be586f7ab417227c0c8b3bf87de567'], + }), + ('admisc', '0.27', { + 'checksums': ['23d46a081714431b6674281b3442ee4f8c3e7050f73b6f9dd38db23b36cc0e1e'], + }), + ('venn', '1.10', { + 'checksums': ['65422a158cdc8581182d3d326e448e43ecc3764501a5dab1ccac1234b4f961e4'], + }), + ('maSigPro', '1.68.0', { + 'checksums': ['2f81ff0150c613c3ebdd2eead744cbf4e5d5c68683be2213eba6b3d1254687d0'], + }), + ('SPIA', '2.48.0', { + 'checksums': ['fc246d7db41f6c34e6ca4d4f8fc63c20e79a171168e9e96283c8bf3e0ce9d5e8'], + }), + ('Gviz', '1.40.0', { + 'checksums': ['dd7e4b6ce5e896145721f1ecb7a2c7484380516285eb22d128eeafae292dd1e6'], + }), + ('cummeRbund', '2.38.0', { + 'checksums': ['185478a9e3ed1b8c8bc9e475a8cf42720ef1ca79078c1cc19dfe9b4162b58adc'], + }), + ('GenomicFiles', '1.32.0', { + 'checksums': ['6ea4efaf63ba8b3c6fe79f0c457115188dc358b25abb34b7c5d89924cee7f761'], + }), + ('derfinderHelper', '1.30.0', { + 'checksums': ['e5527df3b13f13cbfee97af8f60019df8ef2394e0d7911b4640556b74a5fff64'], + }), + ('derfinder', '1.30.0', { + 'checksums': ['3b9f4aea71f556219d262b216dcd5d7d38f5b0d4c09de9b466baa269c477d9ff'], + }), + ('polyester', '1.32.0', { + 'checksums': ['fe7cee66c8bb7bd1eab3a26852c34742524478b2b762bc5806a07b83df5345d0'], + }), + ('Rsubread', '2.10.0', { + 'checksums': ['fc6cbbde18d63c0aa4b3edb14554c23a8d37a545667a39973f4daaef111fa8b9'], + }), + ('pcaMethods', '1.88.0', { + 'checksums': ['2b41f13657f86c404851bc8164f748b755fb42f174b8fb4fa3ff80e30fd50781'], + }), + ('marray', '1.74.0', { + 'checksums': ['11d56753452ad1d9fd1829849dfcfe0de7b09b7a1d7619b8a75e8f3f15f88e2b'], + }), + ('CGHbase', '1.56.0', { + 'checksums': ['9971d4f559ad99604a43c664993360e3b42e5298afb9f5c4f6b63c9281f11ee1'], + }), + ('Wrench', '1.14.0', { + 'checksums': ['8afd0fa42accbd4058cf62a1edba2659047c49b911612d7441928753892ea6ff'], + }), + ('lpsymphony', '1.24.0', { + 'checksums': ['6f8c96972863d3c1ed8f55b937ceaf4e43832d59350d0231e2dfafa23502874d'], + }), + ('IHW', '1.24.0', { + 'checksums': ['aeea5a941d44a9b6c45e2bd7af5bcc40816b6565941282be09b09fdfcaf14ebf'], + }), + ('metagenomeSeq', '1.38.0', { + 'checksums': ['02cc936885c5835fb1a942face09618a4221d11e3c5f0741da00ff471a45106d'], + }), + ('gdsfmt', '1.32.0', { + 'checksums': ['000ff7bdfc325b8f37159d3bd3219fec95d2f92972ac2461e1de30f776f4bcb1'], + }), + ('SNPRelate', '1.30.0', { + 'checksums': ['4944f046e3068c0e018c8f8a4345657f349ec3071d89b1d8d8c6d94e3e8b75c9'], + }), + ('biomformat', '1.24.0', { + 'checksums': ['3669661b489e5bb1b1e230cf6989e2c2d759714b62f4dab2a5f559d86f94988b'], + }), + ('phyloseq', '1.40.0', { + 'checksums': ['5378322e1c0b71a3d7d5703cc8c14df1c7844753ebb89d5825872b1f3fd99e41'], + }), + ('NADA', '1.6-1.1', { + 'checksums': ['670ff6595ba074ed0a930b7a09624d5ef20616379a20e768c1a7b37332aee44a'], + }), + ('zCompositions', '1.4.0-1', { + 'checksums': ['33ee11f635cb87cc9c0617e1cfc91f1ac41c6cfe2b70fc441e226015939230e7'], + }), + ('RcppZiggurat', '0.1.6', { + 'checksums': ['9c78255ca476c945c05a564d1e4da363de714d890e0e27f3b252fd73c50eed71'], + }), + ('Rfast', '2.0.6', { + 'checksums': ['34694b5c67ce8fcbdc90aac2ac80a74d4b66515f383e6301aea7c020009ebe7f'], + }), + ('ALDEx2', '1.28.0', { + 'checksums': ['68f4ddea3d672ed128ec8c48b252042abdfc1a535f9043949f2ce60de48da0b7'], + }), + ('dada2', '1.24.0', { + 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], + 'checksums': [ + '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b', # dada2_1.24.0.tar.gz + # dada2-1.16.0-remove-sse-on-aarch64.patch + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + ], + }), + ('LEA', '3.8.0', { + 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], + 'checksums': [ + 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774', # LEA_3.8.0.tar.gz + # LEA-3.0.0_support_aarch64_and_ppc64le.patch + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', + ], + }), + ('tximport', '1.24.0', { + 'checksums': ['1db129f369b37e5ebaefa85b724b1e640fa50c8317f009834ae7f37d0552d9b2'], + }), + ('SingleCellExperiment', '1.18.0', { + 'checksums': ['f76ccbb90d2cf14edca37f34815b3242e25eb18dd749eedd97f15b47f7c22a68'], + }), + ('beachmat', '2.12.0', { + 'checksums': ['0c292f7368fb6a7d0809f332a02576d6c6cdf3b86ae22fa493ae062ce5de8639'], + }), + ('RcppAnnoy', '0.0.19', { + 'checksums': ['89b209900516f3096b53c90937081fb8965c605c867aa465f1b3b68092b7688a'], + }), + ('RcppHNSW', '0.3.0', { + 'checksums': ['a0eb4eea65e28ba31e8306a1856f7e617a192bd448b148f88abe99181cbde007'], + }), + ('BiocNeighbors', '1.14.0', { + 'checksums': ['bda4dfa69b93b21a4d6949e2ebaa4265d467b253130e7192c271f7cbea8783a8'], + }), + ('rsvd', '1.0.5', { + 'checksums': ['e40686b869acd4f71fdb1e8e7a6c64cd6792fc9d52a78f9e559a7176ab84e21e'], + }), + ('ScaledMatrix', '1.4.0', { + 'checksums': ['949533de2730ae04794dc386e08e08f46a95471e1f32272fbcf01cbb6a31c05c'], + }), + ('BiocSingular', '1.12.0', { + 'checksums': ['7dd45d85c0c8248406caab4accb74b483d0066443e443b51bc5049602df32aeb'], + }), + ('scuttle', '1.6.0', { + 'checksums': ['42921bd382e8760f2c2ff9069192dcc90f81efc159829b33bb7a5d8e98795bd0'], + }), + ('RcppML', '0.3.7', { + 'checksums': ['325c6515085527eb9123cc5e87e028547065771ed4d623048f41886ae28908c6'], + }), + ('scater', '1.24.0', { + 'checksums': ['3c9718fd782a69159d4361f497fea417478682f200274b09b6c5d7c3dfcb1137'], + }), + ('sitmo', '2.0.2', { + 'checksums': ['448ef8d56e36783354011845daf33f1efb83ea3b9685eea75eaf5134e24fa8c2'], + }), + ('dqrng', '0.3.0', { + 'checksums': ['4beeabfe245ce7196b07369f2a7d277cb08869ad8b45a22c6354c4cc70a39abb'], + }), + ('bluster', '1.6.0', { + 'checksums': ['681356e8ff7f8be93115a733f18b8a66a4ae8e841d59908d831ab67a983789bc'], + }), + ('metapod', '1.4.0', { + 'checksums': ['ebe8d6ce014448fe43b21cb5525339be95457931246a104ec6983caa1060e9a5'], + }), + ('scran', '1.24.0', { + 'checksums': ['1c997e6c653e74bc99a4b249ead5490e47523553adcf5f6f31aa8454066de775'], + }), + ('SC3', '1.24.0', { + 'checksums': ['e253051097403d8c5cadad27193cfc35e402efe943ed3132c4ce95fc53073d9d'], + }), + ('ComplexHeatmap', '2.12.0', { + 'checksums': ['c5e8e76184e7bf91b1b1ee36d48dd0b03ff08d019c567038cb37213ae94e6495'], + }), + ('GENIE3', '1.18.0', { + 'checksums': ['54ccf0e155f8160b5903a9bbfa77d05be32a9a65e472f7906a392dfbedb57b40'], + }), + ('dupRadar', '1.26.0', { + 'checksums': ['12b901d6d0cb6e74234a6d136593e06ba8be3ca05d0a92089d64367b9c6dc622'], + }), + ('DNAcopy', '1.70.0', { + 'checksums': ['8cc7c37dd99dc90d0543ae24e7662aa10a52788a6b54fdaccb04d165d1257081'], + }), + ('sva', '3.44.0', { + 'checksums': ['441d2096740bd7acceedd5704b104c077adf0226821f49b584405160732a424d'], + }), + ('ballgown', '2.28.0', { + 'checksums': ['089c8fcc1650fd4872ac5eaeb3dfbfd498d8cb977f46264bd4b54f5dbd1b1851'], + }), + ('DropletUtils', '1.16.0', { + 'checksums': ['9cb38acd4097f448dd39ead182f6cf36a9b83e124245e7e21d4681d323f408ff'], + }), + ('DeconRNASeq', '1.38.0', { + 'checksums': ['661e11800fc7ce9706e735b18e0a16e0176a9a6b133a102944a5f6ac119a5583'], + }), + ('GSVA', '1.44.0', { + 'checksums': ['8fb2759b927aa9b544d16c46737c549d77f06fbf4783984c8a9306850463b706'], + }), + ('PureCN', '2.2.0', { + 'checksums': ['db490d56e6f69c15e3d9967a1e9eecf2647bf029b60b6e032d0a6a297a52a6e5'], + }), + ('globaltest', '5.50.0', { + 'checksums': ['452736d1d75be95b5781888eaf0d0fc0809e9539bb0f74882f111c9a6a4fb055'], + }), + ('GlobalAncova', '4.14.0', { + 'checksums': ['641b24765da7bdbc5fa76c9a3edd19e37274c1e99dc4714e432e3a06e8048507'], + }), + ('vsn', '3.64.0', { + 'checksums': ['0ebf308a53caf996c5cb93685cddef071bb68975df25770a0dc7f4b765db47c9'], + }), + ('mzID', '1.34.0', { + 'checksums': ['c1245fd0cb5cd23601794520b9786e37f63887532d8f7a3449a4d9a4bcc72ae0'], + }), + ('mzR', '2.30.0', { + 'checksums': ['ba318b62d3a5d1297f25360eca1e29f926e7679351cf129ec36b0ab2e0000ab7'], + }), + ('MsCoreUtils', '1.8.0', { + 'checksums': ['f0f7d14b2d8560043a06dcad0c957d4c2070922cc7caa7ea54a81fe1d90ffd1c'], + }), + ('MSnbase', '2.22.0', { + 'checksums': ['a38f0232b8aa8b1713cf5f9071447a3a00c1866f0d82b49f61c672c1c604f6f7'], + }), + ('MassSpecWavelet', '1.62.0', { + 'checksums': ['69b44651c7b7862523617d8f9b4700652af01b5485e0e574fd011e377cfb313d'], + }), + ('MsFeatures', '1.4.0', { + 'checksums': ['037b64dada359ed60c4c5ad474c20560251ba13e827c24c9ba250c4c30c33184'], + }), + ('xcms', '3.18.0', { + 'checksums': ['b58763f7c1520c7b02702cc371a2a0df3419a5deae3d223cc24552248e685f5c'], + }), + ('CAMERA', '1.52.0', { + 'checksums': ['257b25b53fe9e73b6b6d1a366ca0a9160d307527eecd2fbf47c1a1872a88e84b'], + }), + ('fgsea', '1.22.0', { + 'checksums': ['ef56433dfff96c1ab20737d6af954c1c6f5158fb74654ce875849aa8def3d646'], + }), + ('GWASExactHW', '1.01', { + 'checksums': ['e850ed40fbf14b02eb3798603cfb111fe3718bb69d74c0ff4cb6f679209a15a7'], + }), + ('quantsmooth', '1.62.0', { + 'checksums': ['3a2bf8786a52c3709c2b5baf006f77365acd806cc2383005b24d471a43a8ea08'], + }), + ('GWASTools', '1.42.0', { + 'checksums': ['9fc08c28ece2f22ba9b834645f0c2e6bc0105a869f08338012c717a9ae620f58'], + }), + ('SeqArray', '1.36.0', { + 'checksums': ['3e03fd8dfea39b7482d3d76870d41eb93653afbb5b8f3ce2d42611c82af7d58c'], + }), + ('SeqVarTools', '1.34.0', { + 'checksums': ['6a2c3275c4adc0d6fab912b5d00747456fd80c2c8063172ac6de250cde5c2abe'], + }), + ('GENESIS', '2.26.0', { + 'checksums': ['2c517d2e008cd2d4fbb5b19c7ed0e58b33b5fb3a8fa7aec108dd6f9aa4e9c3e2'], + }), + ('MLInterfaces', '1.76.0', { + 'checksums': ['453f7b0aa2a91f5e3815b9ae37fe3e0dff1dfa19a3840f089bee46d9670a2d9d'], + }), + ('pRoloc', '1.36.0', { + 'checksums': ['ffba6a8083ffd1153c6880f3e5f6522a96f5f1c578d29f68f9691bc059b7df86'], + }), + ('pRolocdata', '1.34.0', { + 'checksums': ['10030fafa36d8ab321e98341b471e4f08072974797074bf69d2faa54bddd33ac'], + }), + ('fresh', '0.2.0', { + 'checksums': ['a92db254ae88e8371efac44efe2cf1f5be7cce62291fdf994ebd68c14dad079d'], + }), + ('waiter', '0.2.5', { + 'checksums': ['9ac25e979db9242598bd0492ff862360009b51ce672184ec9f4eeb2232164979'], + }), + ('shinydashboardPlus', '2.0.3', { + 'checksums': ['49a88cfa396f880ff4faf558bb038763084287c932e27b0c9251f4d676584d83'], + }), + ('shinyhelper', '0.3.2', { + 'checksums': ['f7ed62543ab4d05a34b69a9183517a09e93e1b2da85b113282de0f9982db90b0'], + }), + ('shinyWidgets', '0.6.4', { + 'checksums': ['52a3553c41bba75665c2c4f69996653987f894bc4780d282b7c0b00f488cf7c8'], + }), + ('pRolocGUI', '2.6.0', { + 'checksums': ['b097d2c35429c5612b789af3438f9a83926659ffc0e019ef7b32d017fcb48848'], + }), + ('EBImage', '4.38.0', { + 'checksums': ['510381699581592915aa5e73271f99b8ca73fe2a92fb96b86a699ac157219ded'], + }), + ('GenomicScores', '2.8.0', { + 'checksums': ['319d3548cea4d9d5dcd7aa7d479c585f5ee85c60dace9c1c098cb6840299097f'], + }), + ('BSgenome.Mmusculus.UCSC.mm10', '1.4.3', { + 'checksums': ['dcf602bf9fadf1ef4ce70e0c0fc92b6435467df5affe7d0872d88a93b99ff9ee'], + }), + ('TxDb.Mmusculus.UCSC.mm10.knownGene', '3.10.0', { + 'checksums': ['696281749d01737c94894564d62093433045bc007a4528cc3d94f205edb54977'], + }), + ('regioneR', '1.28.0', { + 'checksums': ['6ea89b61959317a16a16a16f589df0996eb55123814a7674fab18720b6889087'], + }), + ('InteractionSet', '1.24.0', { + 'checksums': ['a56a76d729d30824b533e01692f0badfce6abe708b568870d4a86e5944af5162'], + }), + ('ChIPpeakAnno', '3.30.0', { + 'checksums': ['6e3669676cf13cc9d98c6b6eff396cd9396e8696bb1442ad63d0b43fa41906b2'], + }), + ('seqLogo', '1.62.0', { + 'checksums': ['b9f3c5038c8ca343f25a938ccd87a90ef1ee99be4bca474dab4c9d50d11063d2'], + }), + ('rGADEM', '2.44.0', { + 'checksums': ['e4d928382ff48651860057cbf66e30c9670c4ee97322d761b2c00e063e6f7d04'], + }), + ('MotifDb', '1.38.0', { + 'checksums': ['7165a40692d2c906cfbe6513e5e2759ff6efd3e00547d5e288b16d0f28f8ceb3'], + }), + ('poweRlaw', '0.70.6', { + 'checksums': ['efc091449c5c6494c1c13c85a8eb95625d1c55ffffebe86c7ea16e4abbafa191'], + }), + ('CNEr', '1.32.0', { + 'checksums': ['780a43bba1307625b1bf395c20a22002b7338ea3796f2e20eef95ab45dc9fb17'], + }), + ('DirichletMultinomial', '1.38.0', { + 'checksums': ['bdae3433f4fcf27f8aae91f7ee5f14c4b6f6263d7ba89d4bcd9502f4b1808096'], + }), + ('TFMPvalue', '0.0.8', { + 'checksums': ['6d052529f7b59d0384edc097f724f70468013777b6adf4c63e61a359029d3841'], + }), + ('TFBSTools', '1.34.0', { + 'checksums': ['3c899efd9c44cb9398ecff7a6fb40fa8fd2dc9b4deaf8fd3684e9ece440ed250'], + }), + ('motifStack', '1.40.0', { + 'checksums': ['1fe01cd6ae2e700f35d21c937976cbf48a331626c086e4cc5e9f41364e875134'], + }), + ('ATACseqQC', '1.20.2', { + 'checksums': ['17cf6c17610c287a187010f30b880ae57e5e9f9ef42b3d018fec01c92ab0474a'], + }), + ('ResidualMatrix', '1.6.0', { + 'checksums': ['445b280e890d70303200a48599211c25841c03b564928cdf15924ba0f61b59de'], + }), + ('batchelor', '1.12.0', { + 'checksums': ['17dad6caaffa9e663577999ab514a8a143b5019ae58ba253d4487e47c3b7cc56'], + }), + ('gsmoothr', '0.1.7', { + 'checksums': ['b75ffd2a4a0f357762e02e46e355b45cc90ea637830f0a1b01f216bb4541e903'], + }), + ('Ringo', '1.60.0', { + 'checksums': ['ec7e0b3897400f8137b33d01d3f8c0842991c1ac273ea17ea9518617eeefd5fe'], + }), + ('R.devices', '2.17.0', { + 'checksums': ['c2d4b12949e0faab414c9f7575e39ee9dbf50ea12d858143df529f15ea365fb6'], + }), + ('R.filesets', '2.14.0', { + 'checksums': ['707dd7c099aeadbecebbd2ba57e6400405aa44487c641f3729ce06c4c642bb23'], + }), + ('aroma.light', '3.26.0', { + 'checksums': ['da6fd263bcf8a66b8b6f09bc16a1360fc5c92c4c415794d22b4038bd79da8088'], + }), + ('PSCBS', '0.66.0', { + 'checksums': ['58805636e55e0fd3f57bd4a0e296a8bb3d57a7bdd0fdd5868a73ddc83d173a93'], + }), + ('aroma.core', '3.2.2', { + 'checksums': ['35e0312e403a1894da036afac12d1d727c937e666d7eb400bfe4018b21244855'], + }), + ('R.huge', '0.9.0', { + 'checksums': ['f12d113a965603cfdbbb46e1a57331d267916235555b22f2bbc06caa302ae58e'], + }), + ('aroma.apd', '0.6.0', { + 'checksums': ['87513774baeed8e1d43f819e615c85278aef748ebc842f1ee50686c3392e37d1'], + }), + ('aroma.affymetrix', '3.2.0', { + 'checksums': ['d279cf13cf6ed8369cfdf6682ace12924379bad578003453449aa1ccec31b0a7'], + }), + ('Repitools', '1.42.0', { + 'checksums': ['48a60c930cae9343b0820c88e274c6c5c473fc73075ef966ff272a3e70f35ac9'], + }), + ('BSgenome.Hsapiens.UCSC.hg38', '1.4.4', { + 'checksums': ['024e3571b70f8e07bd50c4dd4d2dc05288497bf5409a9ac4ef12db94b081b50f'], + }), + ('MEDIPS', '1.48.0', { + 'checksums': ['a025c9f0c5846ecd9e16ba3945c6522080272789c46ebaffb1cb422c8f12afe3'], + }), + ('RProtoBufLib', '2.8.0', { + 'patches': ['RProtoBufLib-2.8.0_fix-protobuf-build.patch'], + 'checksums': [ + 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7', # RProtoBufLib_2.8.0.tar.gz + # RProtoBufLib-2.8.0_fix-protobuf-build.patch + '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64', + ], + }), + ('cytolib', '2.8.0', { + 'checksums': ['cf4b6d2f32610c14c967ac791ea762e187776ace978c6135a2453116b51865a1'], + }), + ('flowCore', '2.8.0', { + 'checksums': ['19ce4ffbf70bd3b5a68b045f0c4a21f85c0586ff0817be22d01b44c2b289cc9e'], + }), + ('mutoss', '0.1-12', { + 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], + }), + ('qqconf', '1.2.3', { + 'checksums': ['9b5b6042ea8e52e6e049807c0b5e3bfd534b624bd257be769de69cf505fece62'], + }), + ('metap', '1.8', { + 'checksums': ['ee9501a8de8a4c47af1632e6053e42ef53fc4b8bdf0f2759edc4d3eefaf5552b'], + }), + ('uwot', '0.1.11', { + 'checksums': ['4fcf90f1369a2a1f01db9e05a2365b155b2ada8e51e1f7f3ba5122d86affd41b'], + }), + ('scattermore', '0.8', { + 'checksums': ['dbdd73d8261cb063464bb29d5c17733b7e87bc50a19948bc80439e19f2a9f8e5'], + }), + ('SeuratObject', '4.1.0', { + 'checksums': ['9ca406cb3bd95c588e1a81c5383e3173a446cc0667142b139ca32685b4b20a05'], + }), + ('Seurat', '4.1.1', { + 'checksums': ['201aa96919b32378fc4cb67557188214c1242dcbae50cadd7d12c86666af8ace'], + }), + ('ALL', '1.38.0', { + 'checksums': ['1fdce1f158f0c8c68ab9c86e0464ec9e70a8a3470d6a3da7abfc88d10b012010'], + }), + ('ConsensusClusterPlus', '1.60.0', { + 'checksums': ['f7809db4eef81367be8b92b327e64dfd373e689893f0a99dd238e54a7a644180'], + }), + ('flowViz', '1.60.0', { + 'checksums': ['0efd9db768ea51a4137b0991fe6f83a6f25413d23d4275d1aa069b9d997dbe9c'], + }), + ('ncdfFlow', '2.42.0', { + 'checksums': ['9528ac9f6f87a0e749126d7e73a83695775a38c968cc0b4ad03e34f67c466aa1'], + }), + ('aws.signature', '0.6.0', { + 'checksums': ['f7fe4f686979be21e5a8ba7ae11f0fade4f5aaf4e98063b5349ee0962dbb9496'], + }), + ('aws.s3', '0.3.21', { + 'checksums': ['bd21054ab63555d294e7465dcb6c86f107db52ba841aeac5bdf4d00af0674c8c'], + }), + ('flowWorkspace', '4.8.0', { + 'checksums': ['5a6305edbe8da4651bfa8d4d866411b097833d12ad55687a91a133244c8a3e66'], + }), + ('ash', '1.0-15', { + 'checksums': ['8b0a7bc39dd0ce2172f09edc5b5e029347d041a4d508bbff3f3fd6f69450c2ab'], + }), + ('hdrcde', '3.4', { + 'checksums': ['4341c6a021da46dcae3b1ef6d580e84dcf625c2b2139f537d0c26ec90899149b'], + }), + ('rainbow', '3.6', { + 'checksums': ['63d1246f88a498f3db0321b46a552163631b288a25b24400935db41326636e87'], + }), + ('fds', '1.8', { + 'checksums': ['203a5e7671e542dcb83d4c75d0f4012aaebc32d54f94657afaf9e71e99dd0489'], + }), + ('fda', '6.0.3', { + 'checksums': ['205814b9812664e8201221f99e0e8391aa49dba2ae287dc404c57c0c492477d3'], + }), + ('flowStats', '4.8.0', { + 'checksums': ['9243df5cb48531a08137d9789f5e7a797c4cf60102ccb14fb397560195486cc9'], + }), + ('flowClust', '3.34.0', { + 'installopts': "--configure-args='--with-gsl=${EBROOTGSL} --enable-bundled-gsl=false'", + 'checksums': ['93aeb50d3fd5c3fa3c9951496e639e0bf17cff8d13cb0bed1749418574aabb14'], + }), + ('openCyto', '2.8.0', { + 'checksums': ['3ee8bc6bdd7273fe41d6ca7167dd1666f5f2ad9ee5b3e53c97e038095476e5db'], + }), + ('ggcyto', '1.24.0', { + 'checksums': ['a90c69fb3a6c6290f05af1aa6feb478718d8d43d2a8193fff4f51c75dbf6cc6b'], + }), + ('CytoML', '2.8.0', { + 'checksums': ['399f4daacc8b69adc47f9a804041af443d28b5f2ea5f094d2aa805e87653e76e'], + }), + ('colorRamps', '2.3.1', { + 'checksums': ['61f1290824380ae2fe4649f296649e0a155b73ced41479686150400f8a9c568a'], + }), + ('ggnewscale', '0.4.7', { + 'checksums': ['6b12ac9947fd3161941b2bb85c00a18d5fc794ad8b1e22a6f37f63ac8d3f0a81'], + }), + ('ggpointdensity', '0.1.0', { + 'checksums': ['3ea646cf183c8bf7869b122a4ee972b53709056ff443ea71551b823524092a31'], + }), + ('FlowSOM', '2.4.0', { + 'checksums': ['8518c515dfefcf9ba970a6e99815cc2af9809b1d5bb6aa300b28d55a74d3542d'], + }), + ('HMMcopy', '1.38.0', { + 'checksums': ['7d30c261c3c9299c0dcd1f31488a5adb8191ad13b4267aaea0db77ddb920eb42'], + }), + ('diffcyt', '1.16.0', { + 'checksums': ['abe58173f953fd273e93dbc851e0735357fce9f4c4aa1e2a3d8f88573ff5da57'], + }), + ('blme', '1.0-5', { + 'checksums': ['679a4f19d34a584c2390ffab37810a31f6834b913fceaa2409d297ccdf912310'], + }), + ('RhpcBLASctl', '0.21-247.1', { + 'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'], + }), + ('variancePartition', '1.26.0', { + 'checksums': ['9b9fe9790c06ecb7c945685b8956e20d9f5b772745c3f471f6fd818528ee6172'], + }), + ('muscat', '1.10.0', { + 'checksums': ['b967cc258a3e993bb1e09db295b2cb804ca22069b1e961c7831bc6ff1efc1319'], + }), + ('IlluminaHumanMethylation450kmanifest', '0.4.0', { + 'checksums': ['41b2e54bac3feafc7646fe40bce3aa2b92c10871b0a13657c5736517792fa763'], + }), + ('IlluminaHumanMethylationEPICmanifest', '0.3.0', { + 'checksums': ['e39a69d98486cec981e97c56f45bbe47d2ccb5bbb66a1b16fa0685575493902a'], + }), + ('IlluminaHumanMethylation450kanno.ilmn12.hg19', '0.6.1', { + 'checksums': ['3627d75a6303f4d307fa6daf0c5afd57649c60a268b3d4be7e8ac8edc4b1e288'], + }), + ('IlluminaHumanMethylationEPICanno.ilm10b2.hg19', '0.6.0', { + 'checksums': ['4decdbc78a6a8d02bf8aecb0d6e1d81134ae9dbc2375add52574f07829e8cd69'], + }), + ('IlluminaHumanMethylationEPICanno.ilm10b4.hg19', '0.6.0', { + 'checksums': ['2c8128126b63e7fa805a5f3b02449367dca9c3be3eb5f6300acc718826590719'], + }), + ('conumee', '1.30.0', { + 'checksums': ['c80828acdc1855186d6c85cd15c84871a344e2060a43cdf974ad4ffdf736efdf'], + }), + ('BSgenome.Cfamiliaris.UCSC.canFam3', '1.4.0', { + 'checksums': ['99c55b6f7808822a3dae6679e60ecfb88a2b618159484bc35303c000bd4820c7'], + }), + ('ExperimentHub', '2.4.0', { + 'checksums': ['74d2b33433436f0c01e1a5c42538044d130439d84df07be60f5f859a37521686'], + }), + ('SingleR', '1.10.0', { + 'checksums': ['beb04226eb673fc592df7dcf7bd4e5301aaebb1af1a090221dbb0bfebc617e61'], + }), + ('FlowSorted.Blood.EPIC', '2.0.0', { + 'checksums': ['44323f350cec601eb73c3235571b02b18e4f0e9633c9f8ab88377fe9f28a17f3'], + }), + ('FlowSorted.CordBloodCombined.450k', '1.12.0', { + 'checksums': ['9b12170568c3ba8c7f71c339d9c43d020e0c36c21f59851fcef98c78cf0bc0dd'], + }), + ('DRIMSeq', '1.24.0', { + 'checksums': ['94a4fd7143ff3015ebb830445de6517394cb9fb976b5f201f76a10190722f0b6'], + }), + ('stageR', '1.18.0', { + 'checksums': ['3e7141d1b02c44b124a3b6d981b1cdf0389c1af1b1b00c758e4659420d8c435b'], + }), + ('isva', '1.9', { + 'checksums': ['9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17'], + }), + ('org.Mm.eg.db', '3.15.0', { + 'checksums': ['c658df080feb03fedfcbb5f772f3683ff7272b2de3deee055292005b3093d78a'], + }), + ('org.Rn.eg.db', '3.15.0', { + 'checksums': ['e09eb3e6a7d8c73ba3de018d8e9715b353ad5f5dfd8a488d67e016d115dea47b'], + }), + ('ROC', '1.72.0', { + 'checksums': ['62077c63539636fbf21ad5630aafe369d789c8355050a3a56df82f214103d879'], + }), + ('wateRmelon', '2.2.0', { + 'checksums': ['fb92984b6eafe8bc56849e1520961749dec7285e195c5e8754ccedbc94f3b829'], + }), + ('GLAD', '2.60.0', { + 'checksums': ['bf00850efc7a19f61cf3ca825a48f7206e8339e036ce465a7ddc1f6059645509'], + }), + ('missMethyl', '1.30.0', { + 'checksums': ['81fa1e991bc3dbd5c2ec8fbdf2a55ab935f0c231f8bc71666855f7bc8c22d146'], + }), + ('MethylSeekR', '1.36.0', { + 'checksums': ['5fa7880d1967570fa5ea2c2526fe47c6323eba7377cf0cf774fb26e21bd13590'], + }), + ('affxparser', '1.68.1', { + 'checksums': ['9a462b6dc5c3592b32cdc06afc4cc3d50bdb0f419c9156c9f7ed1faff913a99b'], + }), + ('ccdata', '1.22.0', { + 'checksums': ['cc5057a0cdd38adc36fa3642df5d5fa40c4f94029840b8e38b57e0f307cb8fbe'], + }), + ('lsa', '0.73.2', { + 'checksums': ['cb0017bbda9b0eb1d05b451e0f557d02f789f65b2f8bf005606b63a3708e63a8'], + }), + ('ccmap', '1.22.0', { + 'checksums': ['c7cbf2e562b392ec795aebd9bd52313866cfd10add80af012399064bc1143c0f'], + }), + ('oligo', '1.60.0', { + 'checksums': ['7e97ad2b355b31679175634c7a8c1cb120334e1c8808dc75412b55a7b249f278'], + }), + ('SMVar', '1.3.4', { + 'checksums': ['aaea3ef7da6cee1bb86fef166df766229c8b7cac9fcf5bc28da7adff5e2c01d6'], + }), + ('metaMA', '3.1.3', { + 'checksums': ['3a0c0351b83419984095cb2c1d77d222d1cdb7158dd8c80fc384bf175ab9358e'], + }), + ('randomcoloR', '1.1.0.1', { + 'checksums': ['cbae51a47a92b2cc3d5ab48877818404429fb73fc795430ec622a8dff20f1067'], + }), + ('shinyBS', '0.61.1', { + 'checksums': ['0aed72473060531d0e782ba62092493002137df6b251af9e2294e2a40a32a140'], + }), + ('shinypanel', '0.1.5', { + 'checksums': ['3264a5a75a306881e6a1622413298d7f3cda3dc78f54446171925774bab97a00'], + }), + ('crossmeta', '1.22.0', { + 'checksums': ['aeafe570de4b38366911fd748a970c987d0f1a628bdaefd25a6bfdb6ccf7b40e'], + }), + ('snpStats', '1.46.0', { + 'checksums': ['42911ba76e4b38f4d3a01d5de81e59d10462d79f5cc642a62c26d9c3b02dab28'], + }), + ('mixsqp', '0.3-43', { + 'checksums': ['58042d832803462ca03197a9dbd49d022378756de8996682b89e6bc009d02ce2'], + }), + ('susieR', '0.11.92', { + 'checksums': ['6bac024fbaba792531a0f2e3904051dfda8cabd850d87b6b33ee2daa77209cf2'], + }), + ('coloc', '5.1.0', { + 'checksums': ['9a2f65cef45d0626513e7b9b4e10b499a7f737f55ee18110201da1f4d156aceb'], + }), + ('SCANVIS', '1.10.0', { + 'checksums': ['276c44e0c9db797442423f0851a22c8695f547eaa603c3b4ed72587f5ffdd38c'], + }), + ('EnsDb.Hsapiens.v86', '2.99.0', { + 'checksums': ['552c07bcc2a1420089d4330deafaeb5303e03d0fa75c96b78075dfd67eeee7be'], + }), + ('agricolae', '1.3-5', { + 'checksums': ['83822535608b5307ca7d0067dbcf1ea3b7f2b1be17a52a55b72cc9f3c6bdec5d'], + }), + ('bookdown', '0.26', { + 'checksums': ['c6207288cb72ea7c555cbad449c61278e94b742cac1f610879fb3f2d60b2b185'], + }), + ('BiocStyle', '2.24.0', { + 'checksums': ['459527c4b14b003f9446f13ec7518b76032a4bc612c398420f38ad00c48a91db'], + }), + ('estimability', '1.3', { + 'checksums': ['a33179c5fbd6a1a623d90cb6f1743148f92c09429fac466867f3ea70946a2e32'], + }), + ('emmeans', '1.7.3', { + 'checksums': ['c646a62772171f9a6f4810673e61bb6e0a7fb60b6310cc55a91377f7878d6b4d'], + }), + ('ggdendro', '0.1.23', { + 'checksums': ['3a33e988c4fe12eec540876ad8ba09bda998773b2d2a90e043ebae4a69fa8eb8'], + }), + ('pmp', '1.8.0', { + 'checksums': ['692aad74ef842f485969ac2b22dc7d79645cb52f5e9f653fd999eeae375b6e89'], + }), + ('MultiDataSet', '1.24.0', { + 'checksums': ['ce62949e80a88d2e901878a8fc23671751563fa764ba7783ac2406f8a734da65'], + }), + ('ropls', '1.28.0', { + 'checksums': ['c765e47ab30457defa89614695ba5f693e90ed613a5af117152ddb29ab182fc5'], + }), + ('ontologyIndex', '2.7', { + 'checksums': ['33f4918cafb983635f9f831553daf15e10103dc375475e170f104a8eaf0e7048'], + }), + ('rols', '2.24.0', { + 'checksums': ['8229167008f254b6b4c9f3793b94e50ea9ab88b5ebca3b385b7e65049d3d8e16'], + }), + ('struct', '1.8.0', { + 'checksums': ['4080796019da2faed837b098731402a66fda365cfa6e88539ae0822ace168d0d'], + }), + ('ggthemes', '4.2.4', { + 'checksums': ['7b35168cf5b68f6f52dd533a1b345ec87e09d1a85ca68e8dc5377cdf95718567'], + }), + ('structToolbox', '1.8.0', { + 'checksums': ['b29d3000686b4cc73364c30b4b01cb097901cc9036db2648569f78b9f052b104'], + }), + ('EnsDb.Hsapiens.v75', '2.99.0', { + 'checksums': ['2c59f95959f344b2a3eaa65a00086b01a420823e30b0810fc81e49b08dcba64b'], + }), + ('ggseqlogo', '0.1', { + 'checksums': ['c14f145a982597f32264b37a5f2645206a0bee30dd2584a25cb8e3dc2f9b068f'], + }), + ('sparsesvd', '0.2', { + 'checksums': ['1a1f54d6b0dca6ae83e3f729a1895c91c58bfe55427dacc50ddb0d2c5d32a9f6'], + }), + ('docopt', '0.7.1', { + 'checksums': ['9f473887e4607e9b21fd4ab02e802858d0ac2ca6dad9e357a9d884a47fe4b0ff'], + }), + ('qlcMatrix', '0.9.7', { + 'checksums': ['1ef5e0350cfbdb07fca761fc7251584d39d3da2958ea813498b467e4f7661347'], + }), + ('Signac', '1.6.0', { + 'checksums': ['dfb465c18c23ca9d870ca148127bd73d3d840241807ec7c366432eab4bb000ba'], + }), + ('motifmatchr', '1.18.0', { + 'checksums': ['e8a07d39783a8a69c3a69803f5804326265377af6c03654bfe434cde2b0056eb'], + }), + ('extraDistr', '1.9.1', { + 'checksums': ['9990348c4dbc611684fcb58ab8db7e856dfde1c9c86ffb7705f4b3dff6b2d7bf'], + }), + ('PRROC', '1.3.1', { + 'checksums': ['479118ce47c527bc97fb58d531a31cabc094d9843d62f16922009dc62e8248d4'], + }), + ('TSP', '1.2-0', { + 'checksums': ['2a7eee07197d01e3637fbb35beefbcd5211759a20974880d07abb3294e025308'], + }), + ('qap', '0.1-1', { + 'checksums': ['60bd564bb0e6325de44351af33870177d84b1c00ded142a2efb12a16a20d4d34'], + }), + ('seriation', '1.3.5', { + 'checksums': ['f905e02f7cdb8a28c89c1d2578b1bfe62914d14110587fa2a905957771059236'], + }), + ('egg', '0.4.5', { + 'checksums': ['15c8ba7cf2676eb0460de7e5dfbc89fc3175ac22a8869cfd44d66d156fd6c7bb'], + }), + ('heatmaply', '1.3.0', { + 'checksums': ['0a5d269c4837dd66fbfa6b87fd648bdef222f1ad6f33df3f695d5164d6f71ef1'], + }), + ('OUTRIDER', '1.14.0', { + 'checksums': ['d1e57f34c7052db751a639029a47959b9baf9d2988795173ced69c06041cf72a'], + }), + ('FRASER', '1.8.0', { + 'checksums': ['a9f5f8070926a8575cbf61ca4a4c5198ad56fcb4f27f10d820789e18a1d47e61'], + }), + ('JASPAR2020', '0.99.10', { + 'checksums': ['b9b92d141a317ebb32a14708229f6b82522ceeb5f1b88360d93b0a7cfe30375b'], + }), + ('AUCell', '1.18.0', { + 'checksums': ['ffb545fc19b2fae164cc195f812cf062024175c3d0de502b4e5e5237b62db085'], + }), + ('RcisTarget', '1.16.0', { + 'checksums': ['35124ea89250e397cc8ee591c09af1203c85a70ee8517df61812cb6cde94d69d'], + }), + ('NMF', '0.24.0', { + 'checksums': ['481811d35b3bbc07e9a60e2f853b05ef26581b43be9c6c4bab81151b8dcadd93'], + }), + ('densEstBayes', '1.0-2.1', { + 'checksums': ['4b7066e18902ee2a0ea084513b237b5fb8e43fe3102354c2fb216d5a8c7df5df'], + }), + ('reldist', '1.7-0', { + 'checksums': ['51ba13e16fdf8d0c4ea497f2b28369f5d966a0b5d4fce917a9df993cb8690444'], + }), + ('M3Drop', '1.22.0', { + 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], + }), + ('ExomeDepth', '1.1.15', { + 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], + }), + ('bsseq', '1.32.0', { + 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], + }), + ('DSS', '2.44.0', { + 'checksums': ['561a87d9ca20c7607a2c6816ead719d16da4c0f19dd94d9e69543499e058858a'], + }), + ('pathview', '1.36.0', { + 'checksums': ['b861a0bf041ea83a0edd6f3bfe3aa73cd1879e48373ad117752c08774098e290'], + }), + ('chromVAR', '1.18.0', { + 'checksums': ['d514d3a0da41b71daabe7c273ec38fd52577caf46a0427000096ee49eadc1a6e'], + }), + ('EnsDb.Hsapiens.v79', '2.99.0', { + 'checksums': ['eff1ae8d7f4ed5c6bed335de63a758be593750fb0b3483c01cf50402688d244d'], + }), + ('WGCNA', '1.71', { + 'checksums': ['21f5349e888ea76241912600ee5c35a0d2fd50180568b9b08b2b597f099bf708'], + }), + ('DNABarcodes', '1.26.0', { + 'checksums': ['867590e663f88db8f757b275f28cd5c75dc6e14eff1d91d7c83d43c9eea65858'], + }), + ('MultiAssayExperiment', '1.22.0', { + 'checksums': ['0127ce0a68624c313874a177ea58d00046b3d2fdcd3efc79b0ddc59da828d7f2'], + }), + ('CAGEr', '2.2.0', { + 'checksums': ['1cd64f6b045a5e246ae92cd709234c806edfcc25463819df0bd32fe4f4b2fd0d'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/RProtoBufLib-2.8.0_fix-protobuf-build.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/RProtoBufLib-2.8.0_fix-protobuf-build.patch new file mode 100644 index 00000000000..bd942739fc2 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/RProtoBufLib-2.8.0_fix-protobuf-build.patch @@ -0,0 +1,41 @@ +Replace the protobuf map files so that the required symbols are extern "C++" +Fix from https://github.com/protocolbuffers/protobuf/issues/5144#issuecomment-688723405 + +Add extra path to includes. + +Patch by Simon Branford (University of Birmingham) +--- RProtoBufLib/configure.orig 2021-06-05 10:58:25.972255000 +0100 ++++ RProtoBufLib/configure 2021-06-05 11:08:16.635526105 +0100 +@@ -2867,6 +2867,23 @@ + gzip -dc ${PBTGZNAME} | tar -xf - + fi; + ++mapfiles="libprotoc.map libprotobuf-lite.map libprotobuf.map" ++for mapfile in ${mapfiles}; do ++ cat << EOF > protobuf-3.8.0/src/${mapfile} ++{ ++ global: ++ extern "C++" { ++ *google*; ++ }; ++ scc_info_*; ++ descriptor_table_*; ++ ++ local: ++ *; ++}; ++EOF ++done ++ + #run this bootstrap script to update all the gnu auto build files (e.g. automake symlinked fils (e.g. ./compile), alocal.m4,etc... ) + cd ${BASEPBNAME} + #./autogen.sh +--- RProtoBufLib/src/Makevars.in.orig 2021-06-05 11:58:07.587850000 +0100 ++++ RProtoBufLib/src/Makevars.in 2021-06-05 11:58:57.608744000 +0100 +@@ -1,5 +1,5 @@ + CXX_STD = CXX11 +-PKG_CPPFLAGS =-I../inst/include/ -I@PBBUILD@/include/ ++PKG_CPPFLAGS =-I../inst/include/ -I@PBBUILD@/include/ -I@PBBUILD@/src + #expose headers in installed package include folder + USER_INCLUDE = ${R_PACKAGE_DIR}/include + USER_LIB_DIR = ${R_PACKAGE_DIR}/lib${R_ARCH}/ From 0152f219d491ff1b09fe7af8fea7afffde85c07a Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 5 May 2022 15:33:58 +0200 Subject: [PATCH 3680/9987] Added sanity check paths --- easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb b/easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb index 70fe8445e8e..0660d58e047 100644 --- a/easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb +++ b/easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb @@ -14,4 +14,9 @@ checksums = ['335e5a2b4099505372914acfccbb978cf9d4efd8047bda59f910c26daefd554e'] allow_system_deps = [('Python', SYS_PYTHON_VERSION)] +sanity_check_paths = { + 'files': ["bin/gcloud"], + 'dirs': [] +} + moduleclass = "tools" From 8537192f6a13129815e9be607027e7ef1beb1ee6 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 5 May 2022 17:01:26 +0200 Subject: [PATCH 3681/9987] Forgot brackets around sources value --- .../d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb index 5840b58014e..a0a28824b8b 100644 --- a/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb @@ -94,7 +94,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://github.com/facebookresearch/detectron2/archive/refs/tags/'], - 'sources': 'v%(version)s.tar.gz', + 'sources': ['v%(version)s.tar.gz'], 'checksums': ['9757fed05fa32acc2116ea038185f08409d5e854573e70f41909a358b70d1004'], }), ] From 7de4091ca5671759506bd456a54fb251bbce0a55 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 5 May 2022 16:35:25 +0100 Subject: [PATCH 3682/9987] use full python as build dependency Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/g/GLib/GLib-2.72.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.72.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.72.1-GCCcore-11.3.0.eb index 88ad2f12f66..e6aea6b5a56 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.72.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.72.1-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ # Packages that use GLib should either have an explicit # (build)dependency on Python or it will use the system version # EasyBuild itself uses. - ('Python', '3.10.4', '-bare'), + ('Python', '3.10.4'), ('Meson', '0.62.1'), ('Ninja', '1.10.2'), ('binutils', '2.38'), From d51fd4bc4ea3531adebc09928f2db45c514a8a5d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 5 May 2022 16:39:56 +0100 Subject: [PATCH 3683/9987] adding easyconfigs: GTK3-3.24.33-GCCcore-11.3.0.eb, Gdk-Pixbuf-2.42.8-GCCcore-11.3.0.eb, libepoxy-1.5.10-GCCcore-11.3.0.eb --- .../g/GTK3/GTK3-3.24.33-GCCcore-11.3.0.eb | 76 +++++++++++++++++++ .../Gdk-Pixbuf-2.42.8-GCCcore-11.3.0.eb | 46 +++++++++++ .../libepoxy-1.5.10-GCCcore-11.3.0.eb | 37 +++++++++ 3 files changed, 159 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.33-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.33-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.33-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ec127c882ec --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.33-GCCcore-11.3.0.eb @@ -0,0 +1,76 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.33' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('GObject-Introspection', '1.72.0'), + ('gettext', '0.21'), + ('pkgconf', '1.8.0'), + ('cairo', '1.17.4'), + ('Perl', '5.34.1'), +] +dependencies = [ + ('ATK', '2.38.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.8'), + ('Pango', '1.50.7'), + ('libepoxy', '1.5.10'), + ('X11', '20220504'), + ('FriBidi', '1.0.12'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'checksums': ['588b06522e25d1579e989b6f9d8a1bdbf2fe13cde01a04e904ff346a225e7801'], + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '42.0', { + 'preconfigopts': 'autoreconf -f -i && ', + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '5e85b5adc8dee666900fcaf271ba717f7dcb9d0a03d96dae08f9cbd27e18b1e0', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c730b3e3f19 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.8-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.8' + +homepage = 'https://docs.gtk.org/gdk-pixbuf/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['84acea3acb2411b29134b32015a5b1aaa62844b19c4b1ef8b8971c6b0759f4c6'] + +builddependencies = [ + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('GObject-Introspection', '1.72.0'), +] + +dependencies = [ + ('GLib', '2.72.1'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('X11', '20220504'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..049ac4ccfdf --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.10' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a7ced37f4102b745ac86d6a70a9da399cc139ff168ba6b8002b4d8d43c900c15'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('X11', '20220504'), + ('Mesa', '22.0.2'), +] + +configopts = '-Degl=yes --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' From 8f27878d1310e42eee12398aae473e5290edd88a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 5 May 2022 16:41:49 +0100 Subject: [PATCH 3684/9987] adding easyconfigs: GSL-2.7-GCC-11.3.0.eb, Wayland-1.20.0-GCCcore-11.3.0.eb, PyCairo-1.21.0-GCCcore-11.3.0.eb, PyGObject-3.42.1-GCCcore-11.3.0.eb, Graphene-1.10.8-GCCcore-11.3.0.eb, GStreamer-1.20.2-GCC-11.3.0.eb, GST-plugins-bad-1.19.2-GCC-11.3.0.eb, GST-plugins-base-1.20.2-GCC-11.3.0.eb --- .../easyconfigs/g/GSL/GSL-2.7-GCC-11.3.0.eb | 25 ++++++++ .../GST-plugins-bad-1.19.2-GCC-11.3.0.eb | 44 ++++++++++++++ .../GST-plugins-base-1.20.2-GCC-11.3.0.eb | 43 ++++++++++++++ .../GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb | 43 ++++++++++++++ .../Graphene-1.10.8-GCCcore-11.3.0.eb | 31 ++++++++++ .../PyCairo/PyCairo-1.21.0-GCCcore-11.3.0.eb | 44 ++++++++++++++ .../PyGObject-3.42.1-GCCcore-11.3.0.eb | 38 ++++++++++++ .../Wayland/Wayland-1.20.0-GCCcore-11.3.0.eb | 58 +++++++++++++++++++ 8 files changed, 326 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.20.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.21.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyGObject/PyGObject-3.42.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-11.3.0.eb new file mode 100644 index 00000000000..1b9e6e11d40 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.7' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..e386b419c8f --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-bad' +version = '1.19.2' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-bad'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['5382f98a9af2c92e5c0ca4fcb3911025cafd9f89b3142b206eb7b92b812e0979'] + +builddependencies = [ + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('GObject-Introspection', '1.72.0'), + ('gettext', '0.21'), + ('pkgconf', '1.8.0'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('GLib', '2.72.1'), + ('GStreamer', '1.20.2'), + ('Gdk-Pixbuf', '2.42.8'), + ('X11', '20220504'), + ('Mesa', '22.0.2'), + ('Graphene', '1.10.8'), + ('GST-plugins-base', '1.20.2'), +] + +sanity_check_paths = { + 'files': ['bin/gst-transcoder-1.0', 'bin/playout'] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['adaptivedemux', 'badaudio', 'codecs', 'player']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.20.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.20.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..e7ae27d7a27 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.20.2-GCC-11.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-base' +version = '1.20.2' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ab0656f2ad4d38292a803e0cb4ca090943a9b43c8063f650b4d3e3606c317f17'] + +builddependencies = [ + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('GObject-Introspection', '1.72.0'), + ('gettext', '0.21'), + ('pkgconf', '1.8.0'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('GLib', '2.72.1'), + ('GStreamer', '1.20.2'), + ('Gdk-Pixbuf', '2.42.8'), + ('X11', '20220504'), + ('Mesa', '22.0.2'), + ('Graphene', '1.10.8'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..df69820328f --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GStreamer' +version = '1.20.2' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['df24e8792691a02dfe003b3833a51f1dbc6c3331ae625d143b17da939ceb5e0a'] + +builddependencies = [ + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.72.0'), + ('gettext', '0.21'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('zlib', '1.2.12'), + ('GMP', '6.2.1'), + ('GSL', '2.7'), + ('GLib', '2.72.1'), + ('libunwind', '1.6.2'), + ('elfutils', '0.187'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d5f5e9c6df7 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MesonNinja' + +name = 'Graphene' +version = '1.10.8' + +homepage = 'https://ebassi.github.io/graphene/' +description = "Graphene is a thin layer of types for graphic libraries" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'ebassi' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['922dc109d2dc5dc56617a29bd716c79dd84db31721a8493a13a5f79109a4a4ed'] + +builddependencies = [ + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), + ('GObject-Introspection', '1.72.0'), +] +dependencies = [('GLib', '2.72.1')] + +configopts = "-Dgobject_types=true -Dintrospection=enabled" + +sanity_check_paths = { + 'files': ['lib/libgraphene-1.0.%s' % SHLIB_EXT, 'share/gir-1.0/Graphene-1.0.gir'], + 'dirs': ['include/graphene-1.0', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.21.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.21.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c571c3e0f0b --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.21.0-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'PyCairo' +version = '1.21.0' + +homepage = 'https://pycairo.readthedocs.io/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['251907f18a552df938aa3386657ff4b5a4937dde70e11aa042bc297957f4b74b'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('cairo', '1.17.4'), +] + +# PyGTK needs PyCairo installed by pip +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# remove pyproject.toml, which causes trouble (header files and .pc file are not installed) +preinstallopts = "rm pyproject.toml && " + +# Don't build a wheel or the pkg-cfg file won't be installed +installopts = '--no-binary=%(namelower)s' + +sanity_check_paths = { + 'files': ['%s/py3cairo.%s' % (p, e) for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')]], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +options = {'modulename': 'cairo'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.42.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.42.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ddcb0e1c9bf --- /dev/null +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.42.1-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'PyGObject' +version = '3.42.1' + +homepage = 'https://pygobject.readthedocs.io/' +description = """PyGObject is a Python package which provides bindings for GObject based +libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['80d6a3ad1630e9d1edf31b9e9fad9a894c57e18545a3c95ef0044ac4042b8620'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('GLib', '2.72.1'), + ('GObject-Introspection', '1.72.0'), + ('PyCairo', '1.21.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['include/pygobject-%(version_major)s.0/pygobject.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'gi'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..79fa7f3ccfd --- /dev/null +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.3.0.eb @@ -0,0 +1,58 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Bundle' + +name = 'Wayland' +version = '1.20.0' + +homepage = 'https://wayland.freedesktop.org/' +description = """ +Wayland is a project to define a protocol for a compositor to talk to + its clients as well as a library implementation of the protocol. The + compositor can be a standalone display server running on Linux kernel + modesetting and evdev input devices, an X application, or a wayland + client itself. The clients can be traditional applications, X servers + (rootless or fullscreen) or other display servers. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('CMake', '3.23.1'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('libffi', '3.4.2'), + ('expat', '2.4.8'), + ('libxml2', '2.9.13'), +] + +default_easyblock = 'MesonNinja' +default_component_specs = { + 'source_urls': ['https://wayland.freedesktop.org/releases'], + 'sources': [SOURCE_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('wayland', version, { + 'checksums': ['b8a034154c7059772e0fdbd27dbfcda6c732df29cae56a82274f6ec5d7cd8725'], + 'configopts': "-Ddocumentation=false", + }), + ('wayland-protocols', '1.25', { + 'checksums': ['f1ff0f7199d0a0da337217dd8c99979967808dc37731a1e759e822b75b571460'], + 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH " + }), +] + +_libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']] +sanity_check_paths = { + 'files': ['bin/wayland-scanner'] + _libs, + 'dirs': ['lib'], +} + +sanity_check_commands = ["wayland-scanner --help", "wayland-scanner --version"] + +moduleclass = 'vis' From 04827631c06ee2f86200f9cc54d6d0bc748224c4 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 5 May 2022 16:43:07 +0100 Subject: [PATCH 3685/9987] adding easyconfigs: GTK4-4.6.3-GCC-11.3.0.eb --- .../g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb | 82 +++++++++++++++++++ 1 file changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..34f9b46c075 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb @@ -0,0 +1,82 @@ +easyblock = 'Bundle' + +name = 'GTK4' +version = '4.6.3' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('GObject-Introspection', '1.72.0'), + ('gettext', '0.21'), + ('pkgconf', '1.8.0'), + ('cairo', '1.17.4'), + ('Perl', '5.34.1'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] +dependencies = [ + ('ATK', '2.38.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.8'), + ('Pango', '1.50.7'), + ('libepoxy', '1.5.10'), + ('X11', '20220504'), + ('FriBidi', '1.0.12'), + ('GST-plugins-bad', '1.19.2'), + ('Wayland', '1.20.0'), + ('PyGObject', '3.42.1'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK', version, { + 'easyblock': 'MesonNinja', + 'source_urls': [FTPGNOME_SOURCE], + 'configopts': "-Dintrospection=enabled -Dgtk_doc=false", + 'checksums': ['a57acd0e4482981700fdf86596c7413cb61ef47f75e4747fda809e8231b8d96c'], + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '42.0', { + 'preconfigopts': 'autoreconf -f -i && ', + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '5e85b5adc8dee666900fcaf271ba717f7dcb9d0a03d96dae08f9cbd27e18b1e0', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk4-demo', 'gtk4-demo-application', 'gtk4-icon-browser', 'gtk4-widget-factory', + 'gtk4-builder-tool', 'gtk4-launch', 'gtk4-query-settings', + 'gtk4-update-icon-cache', 'gtk4-widget-factory']] + + ['lib/libgtk-4.%s' % SHLIB_EXT], + 'dirs': ['include/%s-%%(version_major)s.0/%s' % ('gtk', x) for x in ['gdk', 'gsk', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + + +moduleclass = 'vis' From cba376787d4084343ab1ee11ed03ae4b0d924bd2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 5 May 2022 16:51:59 +0100 Subject: [PATCH 3686/9987] add adwaita patch for GTK4 --- ...con-theme-3.34.3_disable-svg-conversion.patch | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK4/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch diff --git a/easybuild/easyconfigs/g/GTK4/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch b/easybuild/easyconfigs/g/GTK4/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch new file mode 100644 index 00000000000..bf0b97f9489 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK4/adwaita-icon-theme-3.34.3_disable-svg-conversion.patch @@ -0,0 +1,16 @@ +As we don't have SVG support we disable the search for the converter. + +Author: Alexander Grund (TU Dresden) + +diff -aur a/configure.ac b/configure.ac +--- a/configure.ac 2021-07-16 15:16:15.774630738 +0200 ++++ b/configure.ac 2021-07-16 15:15:10.138814059 +0200 +@@ -49,7 +49,7 @@ + AM_CONDITIONAL(ALLOW_RENDERING, test "x$allow_rendering" = "xyes") + + symbolic_encode_sizes="16x16 24x24 32x32 48x48 64x64 96x96" +-AC_PATH_PROG([GTK_ENCODE_SYMBOLIC_SVG], [gtk-encode-symbolic-svg], [false]) ++GTK_ENCODE_SYMBOLIC_SVG="false" + if test "x$GTK_ENCODE_SYMBOLIC_SVG" = "xfalse"; then + symbolic_encode_sizes="" + fi From 810736ae063b2d050ac1dbb327d8d520d6537786 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 5 May 2022 18:22:13 +0200 Subject: [PATCH 3687/9987] adding easyconfigs: ModelTest-NG-0.1.7-gompi-2021b.eb --- .../ModelTest-NG-0.1.7-gompi-2021b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb diff --git a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb new file mode 100644 index 00000000000..916793b4e8a --- /dev/null +++ b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMakeCp' + +name = 'ModelTest-NG' +version = '0.1.7' + +homepage = 'https://github.com/ddarriba/modeltest' +description = """ +ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. +ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces. +""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'recursive': True, + 'url': 'https://github.com/ddarriba', + 'repo_name': 'modeltest', + 'tag': 'v%(version)s', + } +}] + +builddependencies = [('CMake', '3.22.1')] + +dependencies = { + ('flex', '2.6.4'), + ('Bison', '3.8.2', '', True) +} + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ["bin/modeltest-ng"], + 'dirs': [] +} + +sanity_check_commands = [ + "modeltest-ng --help", + "modeltest-ng -i %(builddir)s/*/example-data/dna/tiny.fas -t ml" +] + +moduleclass = 'bio' From 42a689934134091efaac060383447368cbb10ff5 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 5 May 2022 18:41:59 +0200 Subject: [PATCH 3688/9987] Fixed checksum problem --- .../easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb index 916793b4e8a..cf0f71ea2bc 100644 --- a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb @@ -20,6 +20,7 @@ sources = [{ 'tag': 'v%(version)s', } }] +checksums = [None] builddependencies = [('CMake', '3.22.1')] From 28bab8d2332a7b3dd90ce97bf5f4f784808e9f97 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 May 2022 09:06:02 +0200 Subject: [PATCH 3689/9987] adding easyconfigs: intel-compilers-2022.0.2.eb --- .../intel-compilers-2022.0.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb new file mode 100644 index 00000000000..b54023cfe84 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.0.2.eb @@ -0,0 +1,31 @@ +name = 'intel-compilers' +version = '2022.0.2' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18478/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.84_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18481/'], + 'filename': 'l_fortran-compiler_p_%(version)s.83_offline.sh', + }, +] +checksums = [ + 'ade5bbd203e7226ca096d7bf758dce07857252ec54e83908cac3849e6897b8f3', # l_dpcpp-cpp-compiler_p_2022.0.2.84_offline.sh + '78532b4118fc3d7afd44e679fc8e7aed1e84efec0d892908d9368e0c7c6b190c', # l_fortran-compiler_p_2022.0.2.83_offline.sh +] + +local_gccver = '11.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.38', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' From 1be7a032af41e574822bff8e1465dd20d6852ceb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 May 2022 09:30:22 +0200 Subject: [PATCH 3690/9987] add patch to make AmberTools v21 CMake files aware of FlexiBLAS + remove Python versionsuffix (no longer used for recent toolchains with Pyhton 3) --- ...n-3.9.5.eb => AmberTools-21-foss-2021a.eb} | 12 +-- .../AmberTools-21_CMake-FlexiBLAS.patch | 91 +++++++++++++++++++ 2 files changed, 95 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/a/AmberTools/{AmberTools-21-foss-2021a-Python-3.9.5.eb => AmberTools-21-foss-2021a.eb} (84%) create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_CMake-FlexiBLAS.patch diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb similarity index 84% rename from easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb rename to easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb index 1f399df67c0..c9d49f9a458 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb @@ -2,7 +2,6 @@ easyblock = 'EB_Amber' name = 'AmberTools' version = '21' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://ambermd.org/' description = """AmberTools consists of several independently developed packages that work well by themselves, @@ -13,20 +12,17 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': True} sources = [SOURCE_TAR_BZ2] - patches = [ 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-21_CMake-FlexiBLAS.patch', ] - -# Use included BLAS as FlexiBlas is not linked properly -# configopts = " -DBLA_VENDOR=FlexiBLAS" -configopts = " -DBLA_VENDOR=Generic" - checksums = [ 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools-21.tar.bz2 - '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_CMake-FlexiBLAS.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_CMake-FlexiBLAS.patch new file mode 100644 index 00000000000..669c7e3d305 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_CMake-FlexiBLAS.patch @@ -0,0 +1,91 @@ +make CMake scripts that picks BLAS/LAPACK library aware of FlexiBLAS +author: Kenneth Hoste (HPC-UGent) +--- cmake/patched-cmake-modules/FindBLASFixed.cmake.orig 2022-05-04 18:53:42.410384491 +0200 ++++ cmake/patched-cmake-modules/FindBLASFixed.cmake 2022-05-04 18:54:39.034612008 +0200 +@@ -36,7 +36,7 @@ + # BLA_F95 if set on tries to find the f95 interfaces for BLAS/LAPACK + # + # ######### ## List of vendors (BLA_VENDOR) valid in this module # +-# Goto,OpenBLAS,ATLAS PhiPACK,CXML,DXML,SunPerf,SCSL,SGIMATH,IBMESSL, ++# Goto,OpenBLAS,FlexiBLAS ATLAS PhiPACK,CXML,DXML,SunPerf,SCSL,SGIMATH,IBMESSL, + # ACML,ACML_MP,ACML_GPU,Apple, NAS, Generic + + include(CMakePushCheckState) +@@ -49,8 +49,8 @@ + set(BLA_VENDOR_DEFAULT "All") + endif () + +-set(BLA_VENDOR ${BLA_VENDOR_DEFAULT} CACHE STRING "BLAS vendor to use for BLAS and Lapack. Valid values: All, Goto, OpenBLAS, ATLAS, PhiPACK, CXML, DXML, SunPerf, SCSL, SGIMATH, IBMESSL, ACML, ACML_MP, ACML_GPU, Apple, NAS, Generic") +-validate_configuration_enum(BLA_VENDOR All Goto OpenBLAS ATLAS PhiPACK CXML DXML SunPerf SCSL SGIMATH IBMESSL ACML ACML_MP ACML_GPU Apple NAS Generic) ++set(BLA_VENDOR ${BLA_VENDOR_DEFAULT} CACHE STRING "BLAS vendor to use for BLAS and Lapack. Valid values: All, Goto, OpenBLAS, FlexiBLAS, ATLAS, PhiPACK, CXML, DXML, SunPerf, SCSL, SGIMATH, IBMESSL, ACML, ACML_MP, ACML_GPU, Apple, NAS, Generic") ++validate_configuration_enum(BLA_VENDOR All Goto OpenBLAS FlexiBLAS ATLAS PhiPACK CXML DXML SunPerf SCSL SGIMATH IBMESSL ACML ACML_MP ACML_GPU Apple NAS Generic) + + if(DEFINED BLAS_FIND_QUIETLY) + set(CMAKE_REQUIRED_QUIET ${BLAS_FIND_QUIETLY}) +@@ -159,6 +159,20 @@ + endif() + endif () + ++if (BLA_VENDOR STREQUAL "FlexiBLAS" OR BLA_VENDOR STREQUAL "All") ++ if(NOT BLAS_LIBRARIES) ++ # FlexiBLAS (https://github.com/mpimd-csc/flexiblas) ++ check_fortran_libraries( ++ BLAS_LIBRARIES ++ BLAS ++ sgemm ++ "" ++ "flexiblas" ++ "" ++ ) ++ endif() ++endif () ++ + if (BLA_VENDOR STREQUAL "OpenBLAS" OR BLA_VENDOR STREQUAL "All") + if(NOT BLAS_LIBRARIES) + # OpenBLAS (http://www.openblas.net) +@@ -524,4 +538,4 @@ + endif() + + cmake_pop_check_state() +-set(CMAKE_FIND_LIBRARY_SUFFIXES ${_blas_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES}) +\ No newline at end of file ++set(CMAKE_FIND_LIBRARY_SUFFIXES ${_blas_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES}) +--- cmake/patched-cmake-modules/FindLAPACKFixed.cmake.orig 2022-05-04 18:56:14.315407989 +0200 ++++ cmake/patched-cmake-modules/FindLAPACKFixed.cmake 2022-05-04 18:56:39.930772703 +0200 +@@ -36,7 +36,7 @@ + # BLA_F95 if set on tries to find the f95 interfaces for BLAS/LAPACK + # + # ## List of vendors (BLA_VENDOR) valid in this module: +-# OpenBLAS, ACML,Apple, NAS, Generic ++# OpenBLAS, FlexiBLAS, ACML,Apple, NAS, Generic + + set(_lapack_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES ${CMAKE_FIND_LIBRARY_SUFFIXES}) + +@@ -173,6 +173,20 @@ + endif() + endif () + ++ if(BLA_VENDOR STREQUAL "FlexiBLAS" OR BLA_VENDOR STREQUAL "All") ++ if(NOT LAPACK_LIBRARIES) ++ check_lapack_libraries( ++ LAPACK_LIBRARIES ++ LAPACK ++ cheev ++ "" ++ "flexiblas" ++ "${BLAS_LIBRARIES}" ++ "" ++ ) ++ endif() ++ endif() ++ + if(BLA_VENDOR STREQUAL "OpenBLAS" OR BLA_VENDOR STREQUAL "All") + if(NOT LAPACK_LIBRARIES) + check_lapack_libraries( +@@ -289,4 +303,4 @@ + endif() + + cmake_pop_check_state() +-set(CMAKE_FIND_LIBRARY_SUFFIXES ${_lapack_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES}) +\ No newline at end of file ++set(CMAKE_FIND_LIBRARY_SUFFIXES ${_lapack_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES}) From 71ef05975037ad6d176fb7f3672c8242ab5daf3c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 May 2022 09:49:29 +0200 Subject: [PATCH 3691/9987] adding easyconfigs: UCX-1.12.1-GCCcore-11.3.0.eb --- .../u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4e90405b0cc --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.12.1' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.10.0-dynamic_modules.patch', + 'UCX-1.11.2-missing_header.patch', +] +checksums = [ + '40b447c8e7da94a253f2828001b2d76021eb4ad39647107d433d62d61e18ae8e', # ucx-1.12.1.tar.gz + '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch + 'fa9052a33da5c8e94bc7df0e5fe6ce3baf613310842ae1ab9ed4ef2d49666c01', # UCX-1.11.2-missing_header.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.12'), + ('numactl', '2.0.14'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From 840030aef37b7914cd6b3fa359970c2be8bd2335 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 May 2022 10:08:57 +0200 Subject: [PATCH 3692/9987] adding easyconfigs: impi-2021.5.1-intel-compilers-2022.0.2.eb --- .../impi-2021.5.1-intel-compilers-2022.0.2.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.5.1-intel-compilers-2022.0.2.eb diff --git a/easybuild/easyconfigs/i/impi/impi-2021.5.1-intel-compilers-2022.0.2.eb b/easybuild/easyconfigs/i/impi/impi-2021.5.1-intel-compilers-2022.0.2.eb new file mode 100644 index 00000000000..f175c69a408 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.5.1-intel-compilers-2022.0.2.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.5.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2022.0.2'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/18471/'] +sources = ['l_mpi_oneapi_p_%(version)s.515_offline.sh'] +checksums = ['b992573959e39752e503e691564a0d876b099547c38b322d5775c5b06ec07a7f'] + +dependencies = [('UCX', '1.12.1')] + +moduleclass = 'mpi' From e73b94ffb5d5444b917600182c732f0f0ff6c947 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 May 2022 09:57:15 +0200 Subject: [PATCH 3693/9987] adding easyconfigs: ABAQUS-2022-hotfix-2214.eb --- .../a/ABAQUS/ABAQUS-2022-hotfix-2214.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb new file mode 100644 index 00000000000..76e2b9c6712 --- /dev/null +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb @@ -0,0 +1,39 @@ +name = 'ABAQUS' +version = '2022' +local_hotfix = '2214' +versionsuffix = '-hotfix-%s' % local_hotfix + +homepage = 'https://www.simulia.com/products/abaqus_fea.html' +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" + +toolchain = SYSTEM + +sources = [ + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-5.tar', + # hotfixes + '%%(version)s.FP.CFA.%s.Part_SIMULIA_EstPrd.Linux64.tar' % local_hotfix, + '%%(version)s.FP.CFA.%s.Part_SIMULIA_FlexNet.Linux64.tar' % local_hotfix, + '%%(version)s.FP.CFA.%s.Part_SIMULIA_Readme.AllOS.tar' % local_hotfix, +] +checksums = [ + '9025c9bc2d0345c13d96e88c1c422b1979a14bf7ba281bd32dfe093c1446945d', # 2022.AM_SIM_Abaqus_Extend.AllOS.1-5.tar + '14c23b3fdfddb723d84a02eb27edc25162e1d27e8fdce053193f72d28ff0a12c', # 2022.AM_SIM_Abaqus_Extend.AllOS.2-5.tar + '561d54d688ea2f2dcf329701e20502642aecf5526eb56db3a586cbcadfbf20fb', # 2022.AM_SIM_Abaqus_Extend.AllOS.3-5.tar + 'c085066ae2df68c9c61ea345808042ddb205c642d649f1ec3b7db4aaffb3d544', # 2022.AM_SIM_Abaqus_Extend.AllOS.4-5.tar + 'bfbc2c1a402881308f68f054e1e376fe153053b4287018ddbc80e76710f6969f', # 2022.AM_SIM_Abaqus_Extend.AllOS.5-5.tar + # 2022.FP.CFA.2214.Part_SIMULIA_EstPrd.Linux64.tar + 'da954ac2e24e8e19a527a67d9436ecec4d67cb655cd84b302a15db2b082918c3', + # 2022.FP.CFA.2214.Part_SIMULIA_FlexNet.Linux64.tar + '2d135459211754c7004c8142da7aae5ee2b94d578ef5bb9472de7532a9db0614', + # 2022.FP.CFA.2214.Part_SIMULIA_Readme.AllOS.tar + '88b5c0b182e2dc3e09c14f89be338993cf7edcfeb2f388f405022c63f5512029', +] + +dependencies = [('Java', '11')] + +moduleclass = 'cae' From 547a160ad882439218ee2a4cc90b376fd91b1002 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 6 May 2022 09:52:05 +0100 Subject: [PATCH 3694/9987] adding easyconfigs: libevent-2.1.12-GCCcore-11.3.0.eb, libfabric-1.15.0-GCCcore-11.3.0.eb, PMIx-4.1.2-GCCcore-11.3.0.eb --- .../libevent-2.1.12-GCCcore-11.3.0.eb | 38 +++++++++++ .../libfabric-1.15.0-GCCcore-11.3.0.eb | 65 +++++++++++++++++++ .../p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb | 48 ++++++++++++++ 3 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..09681e8d363 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', True), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a15a4635217 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.15.0' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +# The psm3 provider (enabled by default) requires an AVX capable system to run +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +# 1.15.0 release tarball is missing prov/psm3/VERSION, see: +# https://github.com/ofiwg/libfabric/issues/7735 +# https://github.com/ofiwg/libfabric/issues/7042 +# and build files need to be regenerated to fix aclocal missing error +github_account = 'ofiwg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.12.1_disable-psm3-avx-config.patch'] +checksums = [ + '6eb54599dd986acbe72329538b70849fd098ec405f28f7aaaef765be3efebb3d', # v1.15.0.tar.gz + # libfabric-1.12.1_disable-psm3-avx-config.patch + '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', +] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('numactl', '2.0.14'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# Regenerate build files +preconfigopts = "autoreconf -if &&" + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) +configopts += "--disable-usnic " + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fa43b710c05 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '4.1.2' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['670d3a02b39fb2126fe8084174cf03c484e027b5921b5c98a851108134e2597a'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.2.12'), + ('hwloc', '2.7.1'), + ('libfabric', '1.15.0'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --with-ofi=$EBROOTLIBFBARIC' +configopts += ' --enable-pmix-binaries' +configopts += ' --disable-man-pages' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' From 6ad39154291a80f70baa08acb3cdba167dd378b1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 6 May 2022 09:55:14 +0100 Subject: [PATCH 3695/9987] split libfabric, libevent, UCX, PMIx into other PRs --- .../libevent-2.1.12-GCCcore-11.3.0.eb | 38 ------------ .../libfabric-1.15.0-GCCcore-11.3.0.eb | 62 ------------------- .../p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb | 48 -------------- .../u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb | 54 ---------------- 4 files changed, 202 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb deleted file mode 100644 index 09681e8d363..00000000000 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libevent' -version = '2.1.12' - -homepage = 'https://libevent.org/' - -description = """ - The libevent API provides a mechanism to execute a callback function when - a specific event occurs on a file descriptor or after a timeout has been - reached. Furthermore, libevent also support callbacks due to signals or - regular timeouts. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] -sources = ['%(name)s-%(version)s-stable.tar.gz'] -checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] - -builddependencies = [ - ('binutils', '2.38'), - ('pkgconf', '1.8.0'), -] - -dependencies = [ - ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), -] - -sanity_check_paths = { - 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', - 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], - 'dirs': [], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb deleted file mode 100644 index 9138e8f74cd..00000000000 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb +++ /dev/null @@ -1,62 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libfabric' -version = '1.15.0' - -homepage = 'https://ofiwg.github.io/libfabric/' -description = """ -Libfabric is a core component of OFI. It is the library that defines and exports -the user-space API of OFI, and is typically the only software that applications -deal with directly. It works in conjunction with provider libraries, which are -often integrated directly into libfabric. -""" - -# The psm3 provider (enabled by default) requires an AVX capable system to run -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -github_account = 'ofiwg' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-1.12.1_disable-psm3-avx-config.patch'] -checksums = [ - '6eb54599dd986acbe72329538b70849fd098ec405f28f7aaaef765be3efebb3d', # v1.15.0.tar.gz - # libfabric-1.12.1_disable-psm3-avx-config.patch - '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', -] - -# Avoid using release tarball since this is incomplete -builddependencies = [ - ('binutils', '2.38'), - ('pkgconf', '1.8.0'), - ('Autotools', '20220317'), -] - -dependencies = [ - ('numactl', '2.0.14'), -] - -osdependencies = [OS_PKG_IBVERBS_DEV] - -# Regenerate build files -preconfigopts = "autoreconf -if &&" - -# Disable deprecated "sockets" provider -configopts = "--disable-sockets " - -# Disable usNIC provider by default as this requires specific osdependencies -# If you want to enable this provider you need to uncomment the following line: -# osdependencies.append(('libnl3-devel', 'libnl3-dev')) -configopts += "--disable-usnic " - -buildopts = "V=1" - -sanity_check_paths = { - 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + - ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], - 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] -} - -sanity_check_commands = ['fi_info'] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb deleted file mode 100644 index fa43b710c05..00000000000 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PMIx' -version = '4.1.2' - -homepage = 'https://pmix.org/' -description = """Process Management for Exascale Environments -PMI Exascale (PMIx) represents an attempt to -provide an extended version of the PMI standard specifically designed -to support clusters up to and including exascale sizes. The overall -objective of the project is not to branch the existing pseudo-standard -definitions - in fact, PMIx fully supports both of the existing PMI-1 -and PMI-2 APIs - but rather to (a) augment and extend those APIs to -eliminate some current restrictions that impact scalability, and (b) -provide a reference implementation of the PMI-server that demonstrates -the desired level of scalability. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['670d3a02b39fb2126fe8084174cf03c484e027b5921b5c98a851108134e2597a'] - -builddependencies = [('binutils', '2.38')] - -dependencies = [ - ('libevent', '2.1.12'), - ('zlib', '1.2.12'), - ('hwloc', '2.7.1'), - ('libfabric', '1.15.0'), -] - -configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' -configopts += ' --with-hwloc=$EBROOTHWLOC' -configopts += ' --with-ofi=$EBROOTLIBFBARIC' -configopts += ' --enable-pmix-binaries' -configopts += ' --disable-man-pages' - -buildopts = 'V=1' - -sanity_check_paths = { - 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], - 'dirs': ['etc', 'include', 'lib', 'share'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb deleted file mode 100644 index 4e90405b0cc..00000000000 --- a/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb +++ /dev/null @@ -1,54 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'UCX' -version = '1.12.1' - -homepage = 'https://www.openucx.org/' -description = """Unified Communication X -An open-source production grade communication framework for data centric -and high-performance applications -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.gz'] -patches = [ - 'UCX-1.10.0-dynamic_modules.patch', - 'UCX-1.11.2-missing_header.patch', -] -checksums = [ - '40b447c8e7da94a253f2828001b2d76021eb4ad39647107d433d62d61e18ae8e', # ucx-1.12.1.tar.gz - '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch - 'fa9052a33da5c8e94bc7df0e5fe6ce3baf613310842ae1ab9ed4ef2d49666c01', # UCX-1.11.2-missing_header.patch -] - -builddependencies = [ - ('binutils', '2.38'), - ('Autotools', '20220317'), - ('pkgconf', '1.8.0'), -] - -osdependencies = [OS_PKG_IBVERBS_DEV] - -dependencies = [ - ('zlib', '1.2.12'), - ('numactl', '2.0.14'), -] - -configure_cmd = "contrib/configure-release" - -configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' -configopts += '--without-java --disable-doxygen-doc ' - -buildopts = 'V=1' - -sanity_check_paths = { - 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], - 'dirs': ['include', 'lib', 'share'] -} - -sanity_check_commands = ["ucx_info -d"] - -moduleclass = 'lib' From 4e52c90bc5c3cbb93654499aa459c5b4a816acbb Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 6 May 2022 11:04:41 +0100 Subject: [PATCH 3696/9987] bump Mesa to 22.0.3; update renderer comments --- .../m/Mesa/Mesa-22.0.3-GCCcore-11.3.0.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-22.0.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-22.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-22.0.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..997ab7b2951 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-22.0.3-GCCcore-11.3.0.eb @@ -0,0 +1,69 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers enabled (swr deprecated as of v22): +# - llvmpipe: uses LLVM for JIT code generation (multi-threaded) +# - softpipe: a reference Gallium driver +# Default renderer is llvmpipe. To use softpipe, set the environment +# variable GALLIUM_DRIVER=softpipe + +name = 'Mesa' +version = '22.0.3' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9f2b30f5276a9abaf71aafc6979685e2636189de1a87aea2c9e69744a6d0ebb9'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '1.8.0'), + ('Mako', '1.2.0'), + ('libxml2', '2.9.13'), + ('expat', '2.4.8'), + ('gettext', '0.21'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('zstd', '1.5.2'), + ('libdrm', '2.4.110'), + ('libglvnd', '1.4.0'), + ('libunwind', '1.6.2'), + ('LLVM', '14.0.3'), + ('X11', '20220504'), +] + +configopts = "-Dplatforms=x11 -Dosmesa=true -Ddri-drivers='' -Dvulkan-drivers='' " +configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +# Tells libglvnd where to find EGL libraries +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} + +moduleclass = 'vis' From 5ec0614619cd571e2008887df65a3cef6d9fb503 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 May 2022 12:04:46 +0200 Subject: [PATCH 3697/9987] explicitely disable Go building in UCX 1.12.1 Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb index 4e90405b0cc..0d77ff7687a 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb @@ -40,7 +40,7 @@ dependencies = [ configure_cmd = "contrib/configure-release" configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' -configopts += '--without-java --disable-doxygen-doc ' +configopts += '--without-java --without-go --disable-doxygen-doc ' buildopts = 'V=1' From d76c8509680e6593b183c47486bda4ece2219f87 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 May 2022 12:05:46 +0200 Subject: [PATCH 3698/9987] adding easyconfigs: slow5tools-0.4.0-gompi-2021b.eb --- .../slow5tools-0.4.0-gompi-2021b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/slow5tools/slow5tools-0.4.0-gompi-2021b.eb diff --git a/easybuild/easyconfigs/s/slow5tools/slow5tools-0.4.0-gompi-2021b.eb b/easybuild/easyconfigs/s/slow5tools/slow5tools-0.4.0-gompi-2021b.eb new file mode 100644 index 00000000000..8cbf8e70d8f --- /dev/null +++ b/easybuild/easyconfigs/s/slow5tools/slow5tools-0.4.0-gompi-2021b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'slow5tools' +version = '0.4.0' + +homepage = 'https://hasindu2008.github.io/slow5tools' +description = """slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing + and manipulating data in SLOW5 format.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://github.com/hasindu2008/slow5tools/releases/download/v0.4.0/'] +sources = ['slow5tools-v%(version)s-release.tar.gz'] +checksums = ['d6cf216754781363068a729b08411b85ce97c910c04a2a1d85730a861c163c43'] + +dependencies = [ + ('HDF5', '1.12.1'), + ('zlib', '1.2.11'), + ('zstd', '1.5.0'), +] + +buildopts = 'zstd=1' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/slow5tools'], + 'dirs': [], +} + +sanity_check_commands = ["slow5tools --help"] + +moduleclass = 'data' From 2cc78d7316a3e9bc0824be9e6e2916838735ae86 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 6 May 2022 11:10:04 +0100 Subject: [PATCH 3699/9987] bump Mesa to 22.0.3 --- .../easyconfigs/f/freeglut/freeglut-3.2.2-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.2-GCCcore-11.3.0.eb index 9c123bace89..819686d9ba8 100644 --- a/easybuild/easyconfigs/f/freeglut/freeglut-3.2.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.2.2-GCCcore-11.3.0.eb @@ -19,7 +19,7 @@ builddependencies = [ dependencies = [ ('X11', '20220504'), - ('Mesa', '22.0.2'), + ('Mesa', '22.0.3'), ('libGLU', '9.0.2'), ] diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.3.0.eb index 9f0bf07710d..063587f7e10 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-11.3.0.eb @@ -16,7 +16,7 @@ checksums = ['24effdfb952453cc00e275e1c82ca9787506aba0282145fff054498e60e19a65'] builddependencies = [('binutils', '2.38')] dependencies = [ - ('Mesa', '22.0.2'), + ('Mesa', '22.0.3'), ] sanity_check_paths = { From 3ee285e2902f733c96b97457e29486a18377c485 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 6 May 2022 11:12:16 +0100 Subject: [PATCH 3700/9987] bump Mesa to 22.0.3 --- .../easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-11.3.0.eb index 049ac4ccfdf..33c6130fa0a 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('X11', '20220504'), - ('Mesa', '22.0.2'), + ('Mesa', '22.0.3'), ] configopts = '-Degl=yes --libdir %(installdir)s/lib ' From 8676c58647f0e3c5051215ade120375b86e5d9e4 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 6 May 2022 11:13:13 +0100 Subject: [PATCH 3701/9987] bump Mesa to 22.0.3 --- .../g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb | 2 +- .../g/GST-plugins-base/GST-plugins-base-1.20.2-GCC-11.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb index e386b419c8f..8032e9e1652 100644 --- a/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('GStreamer', '1.20.2'), ('Gdk-Pixbuf', '2.42.8'), ('X11', '20220504'), - ('Mesa', '22.0.2'), + ('Mesa', '22.0.3'), ('Graphene', '1.10.8'), ('GST-plugins-base', '1.20.2'), ] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.20.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.20.2-GCC-11.3.0.eb index e7ae27d7a27..11969bcfc0a 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.20.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.20.2-GCC-11.3.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('GStreamer', '1.20.2'), ('Gdk-Pixbuf', '2.42.8'), ('X11', '20220504'), - ('Mesa', '22.0.2'), + ('Mesa', '22.0.3'), ('Graphene', '1.10.8'), ] From e6ae61e3d49ac543b3b71dcf80f9b11b2071ef98 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 6 May 2022 11:30:17 +0100 Subject: [PATCH 3702/9987] Delete Mesa-22.0.2-GCCcore-11.3.0.eb --- .../m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb | 69 ------------------- 1 file changed, 69 deletions(-) delete mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb deleted file mode 100644 index c123b7dda47..00000000000 --- a/easybuild/easyconfigs/m/Mesa/Mesa-22.0.2-GCCcore-11.3.0.eb +++ /dev/null @@ -1,69 +0,0 @@ -# This is a Mesa using software rendering via Gallium-DRI and libglvnd -# - libglvnd can dynamically choose between system-installed NVidia -# libGLX/libEGL or the software renderers provided by this Mesa -# - EGL is available -# -# Software renderers are enabled based on system architecture: -# - llvmpipe: the high-performance Gallium LLVM driver -# - swr: Intel's OpenSWR -# Default renderer is llvmpipe. SWR can be enabled by setting the environment -# variable GALLIUM_DRIVER=swr - -name = 'Mesa' -version = '22.0.2' - -homepage = 'https://www.mesa3d.org/' -description = """Mesa is an open-source implementation of the OpenGL specification - - a system for rendering interactive 3D graphics.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = [ - 'https://mesa.freedesktop.org/archive/', - 'https://mesa.freedesktop.org/archive/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', -] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['df4fa560dcce6680133067cd15b0505fc424ca703244ce9ab247c74d2fab6885'] - -builddependencies = [ - ('binutils', '2.38'), - ('Meson', '0.62.1'), - ('Ninja', '1.10.2'), - ('flex', '2.6.4'), - ('Bison', '3.8.2'), - ('pkgconf', '1.8.0'), - ('Mako', '1.2.0'), - ('libxml2', '2.9.13'), - ('expat', '2.4.8'), - ('gettext', '0.21'), -] - -dependencies = [ - ('zlib', '1.2.12'), - ('zstd', '1.5.2'), - ('libdrm', '2.4.110'), - ('libglvnd', '1.4.0'), - ('libunwind', '1.6.2'), - ('LLVM', '14.0.3'), - ('X11', '20220504'), -] - -configopts = "-Dplatforms=x11 -Dosmesa=true -Ddri-drivers='' -Dvulkan-drivers='' " -configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" - -# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host -# If you need a different configuration, it possible to override those values by setting your own configopts -# configopts += " -Dgallium-drivers=swrast" - -# symlink indirect to mesa GLX, similar to Debian, see -# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 -# This helps in certain X forwarding situations (e.g. XQuartz) -postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] - -# Tells libglvnd where to find EGL libraries -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} - -moduleclass = 'vis' From 076fd4cb96f1c072046ce50b99e5372b302cd0bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 May 2022 13:39:36 +0200 Subject: [PATCH 3703/9987] adding easyconfigs: MACS2-2.2.7.1-foss-2021b.eb --- .../m/MACS2/MACS2-2.2.7.1-foss-2021b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021b.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021b.eb new file mode 100644 index 00000000000..8e2adf6572b --- /dev/null +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonPackage' + +name = 'MACS2' +version = '2.2.7.1' + +homepage = 'https://github.com/taoliu/MACS' +description = "Model Based Analysis for ChIP-Seq data" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ad2ca69bdd02a8942a68aae23133289b5c16ba382bcbe20c39fabf3948929de5'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/macs2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('%(namelower)s --version')] + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' From 5983128b51f152c2195e2f23e3c69688f97f7ae9 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 6 May 2022 22:45:38 +0100 Subject: [PATCH 3704/9987] adding easyconfigs: Octave-7.1.0-foss-2021b.eb --- .../o/Octave/Octave-7.1.0-foss-2021b.eb | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb new file mode 100644 index 00000000000..03d83437388 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb @@ -0,0 +1,78 @@ +name = 'Octave' +version = '7.1.0' + +homepage = 'https://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d4a9d81f3f67b4a6e07cb7a80dcb10ad5e9176fcc30762c70a81580a64b8b0b6'] + +builddependencies = [ + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('Autotools', '20210726'), + ('gperf', '3.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210802'), + ('PCRE', '8.45'), + ('ncurses', '6.2'), + ('libreadline', '8.1'), + ('arpack-ng', '3.8.0'), + ('cURL', '7.78.0'), + ('FLTK', '1.3.7'), + ('fontconfig', '2.13.94'), + ('freetype', '2.11.0'), + ('GLPK', '5.0'), + ('GL2PS', '1.4.2'), + ('gnuplot', '5.4.2'), + ('Java', '17', '', True), + ('zlib', '1.2.11'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('Qhull', '2020.2'), + ('Qt5', '5.15.2'), + ('HDF5', '1.12.1'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('texinfo', '6.8'), + ('libsndfile', '1.0.31'), + ('GraphicsMagick', '1.3.36'), +] + +configopts = '--disable-docs ' +# correct for both GCC and Intel compilers +configopts += '--enable-fortran-calling-convention=gfortran' + +local_pkg_url = 'https://downloads.sourceforge.net/' +local_pkg_url += 'project/octave/Octave%20Forge%20Packages/Individual%20Package%20Releases/' +exts_default_options = {'source_urls': [local_pkg_url]} + +exts_list = [ + ('control', '3.4.0', { + 'checksums': ['6ec6a06e13ad288afad8631cc41f7247e47096fa1e8d04240d4ed01efbe4a77a'], + }), + ('general', '2.1.2', { + 'checksums': ['a30cd1a79743c62528dae46ebd4a83f848ae46a1c1dac3eaabc36662d42294cf'], + }), + ('io', '2.6.4', { + 'checksums': ['a74a400bbd19227f6c07c585892de879cd7ae52d820da1f69f1a3e3e89452f5a'], + }), + ('signal', '1.4.2', { + 'checksums': ['62a4e06117dcc43c36169905f8255d015481ca982aeae9013b0d9df3e48e7062'], + }), + ('statistics', '1.4.3', { + 'checksums': ['9801b8b4feb26c58407c136a9379aba1e6a10713829701bb3959d9473a67fa05'], + }), + ('struct', '1.0.17', { + 'checksums': ['0137bbb5df650f29104f6243502f3a2302aaaa5e42ea9f02d8a3943aaf668433'], + }), +] + +moduleclass = 'math' From e36c56decf630b9fab7cb622c3cf6f292662943f Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 6 May 2022 22:47:31 +0100 Subject: [PATCH 3705/9987] adding easyconfigs: qrupdate-1.1.2-GCCcore-11.2.0.eb --- .../qrupdate/qrupdate-1.1.2-GCCcore-11.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..412f083ea7b --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'https://sourceforge.net/projects/qrupdate/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_makeconf.patch'] +checksums = [ + 'e2a1c711dc8ebc418e21195833814cb2f84b878b90a2774365f0166402308e08', # qrupdate-1.1.2.tar.gz + '4aa0e61a18bd14c76048f7b2f1f52875f7bac4bc3426ce9a37dfdb5b2b0d2379', # qrupdate-1.1.2_makeconf.patch +] + +builddependencies = [ + ('binutils', '2.37'), +] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' From e0f709a58f277382dc5884ad44e64c84d7c23d9d Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 6 May 2022 22:49:14 +0100 Subject: [PATCH 3706/9987] adding easyconfigs: texinfo-6.8-GCCcore-11.2.0.eb --- .../t/texinfo/texinfo-6.8-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/t/texinfo/texinfo-6.8-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-6.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-6.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c5b14ad74b1 --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-6.8-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'texinfo' +version = '6.8' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """Texinfo is the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['8eb753ed28bca21f8f56c1a180362aed789229bd62fff58bf8368e9beb59fec4'] + +builddependencies = [('binutils', '2.37')] + +osdependencies = ['texlive'] + +preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " + +# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency +modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" + +sanity_check_paths = { + 'files': [ + 'texmf/tex/texinfo/texinfo.tex', + 'bin/install-info', 'bin/makeinfo', 'bin/pdftexi2dvi', 'bin/pod2texi', 'bin/texi2pdf' + ], + 'dirs': ['bin', 'share', 'texmf'], +} + +moduleclass = 'devel' From 3217bd80b50e334b934888c1dc1b37b6a32e8b57 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 8 May 2022 09:18:19 +0100 Subject: [PATCH 3707/9987] alphabetical order for old_dep_versions --- test/easyconfigs/easyconfigs.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 36ca8a5747c..cb45f72025d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -511,6 +511,11 @@ def check_dep_vars(self, gen, dep, dep_vars): r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), ], + # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, + # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; + # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 + 'Pysam': [('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', + 'NGSpeciesID-0.1.1.1-'])], # OPERA requires SAMtools 0.x 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], @@ -518,6 +523,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], # Shasta requires spoa 3.x 'spoa': [(r'3\.4\.0', [r'Shasta-0\.8\.0-'])], + # UShER requires tbb-2020.3 as newer versions will not build + 'tbb': [('2020.3', ['UShER-0.5.0-'])], 'TensorFlow': [ # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), # artic-ncov2019 requires medaka @@ -540,13 +547,6 @@ def check_dep_vars(self, gen, dep, dep_vars): # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 # (for 2021b, UCX was updated to v1.11.2) 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], - # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, - # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; - # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 - 'Pysam': [('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', - 'NGSpeciesID-0.1.1.1-'])], - # UShER requires tbb-2020.3 as newer versions will not build - 'tbb': [('2020.3', ['UShER-0.5.0-'])], } if dep in old_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): From a5dbf14e9eb8aa915ac0be9cc2f9a3622fe9b0ca Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 8 May 2022 10:02:11 +0100 Subject: [PATCH 3708/9987] add arrow-R exception, as it is tied to R and R-bundle-Bioconductor --- test/easyconfigs/easyconfigs.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 36ca8a5747c..7047658f690 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -453,6 +453,12 @@ def check_dep_vars(self, gen, dep, dep_vars): if len(dep_vars) == 1: break + # arrow-R is dep for R-bundle-Bioconductor, but will be tied to a specific R and R-bundle-Bioconductor + if dep == 'arrow-R' and len(dep_vars) > 1: + dep_ver = version_regex.search(key).group('version') + if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: + dep_vars.pop(key) + # filter out variants that are specific to a particular version of CUDA cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] if len(dep_vars) >= len(cuda_dep_vars) and len(dep_vars) > 1: From 336980232359e630eb6ac7943eabba444c65be68 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 8 May 2022 10:03:55 +0100 Subject: [PATCH 3709/9987] remove accidentally added whitespace --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 7047658f690..6b79a5610cf 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -458,7 +458,7 @@ def check_dep_vars(self, gen, dep, dep_vars): dep_ver = version_regex.search(key).group('version') if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: dep_vars.pop(key) - + # filter out variants that are specific to a particular version of CUDA cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] if len(dep_vars) >= len(cuda_dep_vars) and len(dep_vars) > 1: From d36ef53d46094d63dab6cb2f2de694dee5c4bd53 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 8 May 2022 10:25:34 +0100 Subject: [PATCH 3710/9987] different test exception method --- test/easyconfigs/easyconfigs.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 6b79a5610cf..1292dac9a45 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -453,12 +453,6 @@ def check_dep_vars(self, gen, dep, dep_vars): if len(dep_vars) == 1: break - # arrow-R is dep for R-bundle-Bioconductor, but will be tied to a specific R and R-bundle-Bioconductor - if dep == 'arrow-R' and len(dep_vars) > 1: - dep_ver = version_regex.search(key).group('version') - if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: - dep_vars.pop(key) - # filter out variants that are specific to a particular version of CUDA cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] if len(dep_vars) >= len(cuda_dep_vars) and len(dep_vars) > 1: @@ -471,6 +465,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # some software packages require a specific (older/newer) version of a particular dependency old_dep_versions = { + # arrow-R 6.0.0.2 is used for two R/R-bundle-Bioconductor sets (4.1.2/3.14 and 4.2.0/3.15) + 'arrow-R': [('6.0.0.2', [r'R-bundle-Bioconductor-'])], # EMAN2 2.3 requires Boost(.Python) 1.64.0 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], From 1f8df81e32ae052b4f7ece6a63fa9dbb4eade23e Mon Sep 17 00:00:00 2001 From: Zdenek Date: Sun, 8 May 2022 14:44:15 +0200 Subject: [PATCH 3711/9987] Adding PyOpenCL for foss/2021b --- .../PyOpenCL/PyOpenCL-2021.2.13-foss-2021b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.2.13-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.2.13-foss-2021b.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.2.13-foss-2021b.eb new file mode 100644 index 00000000000..c0193438da7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.2.13-foss-2021b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2021.2.13' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('pocl', '1.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2021.2.9', { + 'checksums': ['db6cf83c9ba0a165d545029e2301621486d1e9ef295684072e5cd75316a13755'], + }), + ('pyopencl', version, { + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + 'checksums': ['8b969c3a9d4153adc6b0915301ffdf626a3784b869a964645de100ae60de7b06'], + }), +] + +moduleclass = 'vis' From 9bc3baa722ed883a78fb732cb7f709efaeb85606 Mon Sep 17 00:00:00 2001 From: Zdenek Date: Sun, 8 May 2022 14:49:37 +0200 Subject: [PATCH 3712/9987] Adding PyOpenGL for GCCcore/11.2.0 --- .../PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a78dbcfa2f2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'PyOpenGL' +version = '3.1.6' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8ea6c8773927eda7405bffc6f5bb93be81569a7b05c8cac50cd94e969dce5e27'] + +builddependencies = [ + ('binutils', '2.37'), + ('bzip2', '1.0.8'), +] + +dependencies = [ + ('Mesa', '21.1.7'), + ('Python', '3.9.6'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'OpenGL'} + +moduleclass = 'vis' From 8ca04a5498ad94f7b03a0b72caf854be36292984 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 9 May 2022 08:54:51 +0200 Subject: [PATCH 3713/9987] exclude //tensorflow/core/ir/importexport/tests/roundtrip/ tests --- .../t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 260739bbbdb..2c715b9a427 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -207,6 +207,8 @@ exts_list = [ '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + # All tests in this directory fail with segfault (TensorFlow Graph IR) + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + From 86edb410df8e18c2f7d3acf03bdfaa66d0746ee0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 9 May 2022 10:41:21 +0200 Subject: [PATCH 3714/9987] adding easyconfigs: GCC-12.1.0.eb, GCCcore-12.1.0.eb, Bison-3.8.2-GCCcore-12.1.0.eb, binutils-2.38-GCCcore-12.1.0.eb, flex-2.6.4-GCCcore-12.1.0.eb, help2man-1.49.2-GCCcore-12.1.0.eb, M4-1.4.19-GCCcore-12.1.0.eb, zlib-1.2.12-GCCcore-12.1.0.eb --- .../b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb | 28 +++++++++ .../binutils/binutils-2.38-GCCcore-12.1.0.eb | 31 +++++++++ .../f/flex/flex-2.6.4-GCCcore-12.1.0.eb | 34 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-12.1.0.eb | 22 +++++++ .../easyconfigs/g/GCCcore/GCCcore-12.1.0.eb | 63 +++++++++++++++++++ .../help2man-1.49.2-GCCcore-12.1.0.eb | 25 ++++++++ .../m/M4/M4-1.4.19-GCCcore-12.1.0.eb | 29 +++++++++ .../z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb | 30 +++++++++ 8 files changed, 262 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-12.1.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..88bd7102234 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.38', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..fdfefe7c042 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.38' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b3f1dc5b17e75328f19bd88250bee2ef9f91fc8cbb7bd48bdb31390338636052'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.12'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..b515d9c39a5 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.2'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.38', '', True), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-12.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-12.1.0.eb new file mode 100644 index 00000000000..d9d69140de7 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-12.1.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '12.1.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.38', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb new file mode 100644 index 00000000000..0ef3db46d4d --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb @@ -0,0 +1,63 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '12.1.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.1.0.tar.bz2', + 'mpc-1.2.1.tar.gz', + 'isl-0.24.tar.bz2', + 'newlib-4.1.0.tar.gz', + {'download_filename': '7292758.tar.gz', 'filename': 'nvptx-tools-20220412.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + 'e88a004a14697bbbaba311f38a938c716d9a652fd151aaaa4cf1b5b99b90e2de', # gcc-12.1.0.tar.gz + 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 + 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 + '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz + 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 + 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz + '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080', # nvptx-tools-20220412.tar.gz + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch + '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.38'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..b76db7f347c --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.2' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.38', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..b0d85861200 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.38', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..7cd1927d036 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.12' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = [ + '91844808532e5ce316b3c010929493c0244f3d37593afd6de04f71821d5136d9', # zlib-1.2.12.tar.gz + 'f35eb05334a4f8d7b40b6c5610a6369f654863b5fa1a19c2507888f918025238', # zlib-1.2.12_fix-CC-logic-in-configure.patch +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.38', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 8f529fda592d02e4cfc543af892cb04c208f5542 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 9 May 2022 12:31:57 +0200 Subject: [PATCH 3715/9987] {tools}[iimpi/2021b] worker 1.6.13 --- .../w/worker/worker-1.6.13-iimpi-2021b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2021b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2021b.eb new file mode 100644 index 00000000000..6b8ba29c9a8 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2021b.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.13' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +local_tcname = 'iimpi' +local_tcver = '2021b' +toolchain = {'name': local_tcname, 'version': local_tcver} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b42b8566d82048c706427913c8f7edcd9f5892d61f190ce1f49e428113b7e1bc'] + +dependencies = [ + ('Perl', '5.34.0') +] + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = %s/g" %%(installdir)s/conf/worker.conf' % (local_tcname), + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', + "echo PERL=\\'`which perl`\\' > %(installdir)s/conf/worker_perl.sh", +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['wcat', 'wconvert', 'wload', 'worker', 'wreduce', 'wresume', 'wsub', + 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt'], +} + +sanity_check_commands = ["wsub -help"] + +moduleclass = 'tools' From 68eb1474912ee3934182f843483a17a387afb273 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 9 May 2022 16:16:15 +0200 Subject: [PATCH 3716/9987] adding easyconfigs: num2words-0.5.10-foss-2021a.eb --- .../num2words/num2words-0.5.10-foss-2021a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb new file mode 100644 index 00000000000..6e0d24301fe --- /dev/null +++ b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb @@ -0,0 +1,30 @@ +easyblock = "PythonBundle" + +name = 'num2words' +version = '0.5.10' + +homepage = "https://github.com/savoirfairelinux/num2words" +description = "Modules to convert numbers to words. 42 --> forty-two" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + (name, version, { + 'modulename': False, + 'source_urls': ['https://github.com/savoirfairelinux/num2words/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['ff107ecc0b6709bedf31fdb9e2ca45d29d3fd34b9eb6a0b89a862f337ac5ff00'], + }), +] + +moduleclass = "tools" \ No newline at end of file From 7e286f17cc54e6b844741f12a285355cd00fcd18 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 9 May 2022 16:25:17 +0200 Subject: [PATCH 3717/9987] Added check command --- .../easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb index 6e0d24301fe..70396b1554c 100644 --- a/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb +++ b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb @@ -27,4 +27,6 @@ exts_list = [ }), ] +sanity_check_commands = ["num2words 42"] + moduleclass = "tools" \ No newline at end of file From e29d123d5f400ac876c6bc22f035a275d263ddf8 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 9 May 2022 16:54:28 +0200 Subject: [PATCH 3718/9987] Added newline to the end of file --- .../easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb index 70396b1554c..caab837fee5 100644 --- a/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb +++ b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb @@ -29,4 +29,4 @@ exts_list = [ sanity_check_commands = ["num2words 42"] -moduleclass = "tools" \ No newline at end of file +moduleclass = "tools" From e60bc42f4547e771af6a0f399a6105bcd8c548fd Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 9 May 2022 16:55:19 +0200 Subject: [PATCH 3719/9987] adding easyconfigs: redis-py-4.3.1-foss-2021a.eb --- .../r/redis-py/redis-py-4.3.1-foss-2021a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/r/redis-py/redis-py-4.3.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-4.3.1-foss-2021a.eb b/easybuild/easyconfigs/r/redis-py/redis-py-4.3.1-foss-2021a.eb new file mode 100644 index 00000000000..64dde617242 --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-4.3.1-foss-2021a.eb @@ -0,0 +1,37 @@ +easyblock = "PythonBundle" + +name = "redis-py" +version = "4.3.1" + +homepage = "https://github.com/redis/redis-py" +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('typing-extensions', '3.10.0.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('async-timeout', '4.0.2', { + 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['adb409e9d457394b4eeeac075dd500f132717b66247befe387a85f76d93cf1b4'], + }), +] + +moduleclass = "data" From 14642d81e2d7459c6c8a8567df6cfa4b4eb59f1f Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Mon, 9 May 2022 18:31:57 +0200 Subject: [PATCH 3720/9987] fixup checksums: pagmo-2.18.0-foss-2021a.eb pygmo-2.18.0-foss-2021a.eb --- easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021a.eb | 2 +- easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021a.eb b/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021a.eb index 050cf82b216..4f3c77ebe3a 100644 --- a/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021a.eb @@ -11,7 +11,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/esa/pagmo2/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['1b95b036f75e6fa0b21082ab228dbd63cd18ca10d9622ac53629245e0f95c35c'] +checksums = ['5ad40bf3aa91857a808d6b632d9e1020341a33f1a4115d7a2b78b78fd063ae31'] builddependencies = [ ('CMake', '3.20.1'), diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb index 3c79bf9f50e..f484449a7e2 100644 --- a/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/esa/pygmo2/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] -checksums = ['54d4fa99e4bff539fca67dfcdc909499fd3f1a3186f7c7fc8200f19512954166'] +checksums = ['9f081cc973297894af09f713f889870ac452bfb32b471f9f7ba08a5e0bb9a125'] builddependencies = [ ('CMake', '3.20.1'), From 9e4921578b194aa1b377692d0ba85f66c5495bae Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 9 May 2022 22:12:38 +0200 Subject: [PATCH 3721/9987] adding easyconfigs: line_profiler-3.5.1-foss-2021b.eb --- .../line_profiler-3.5.1-foss-2021b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/line_profiler/line_profiler-3.5.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/l/line_profiler/line_profiler-3.5.1-foss-2021b.eb b/easybuild/easyconfigs/l/line_profiler/line_profiler-3.5.1-foss-2021b.eb new file mode 100644 index 00000000000..1e22501836a --- /dev/null +++ b/easybuild/easyconfigs/l/line_profiler/line_profiler-3.5.1-foss-2021b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'line_profiler' +version = '3.5.1' + +homepage = 'https://github.com/pyutils/line_profiler' +description = """line_profiler is a module for doing line-by-line profiling +of functions. kernprof is a convenient script for running either +line_profiler or the Python standard library's cProfile or profile modules, +depending on what is available.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'pyutils' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['bc9ad7e88112e882b16e3698040c7f9449fe72e4f15f957d2bd5e486484ff75e'] + +builddependencies = [ + ('scikit-build', '0.11.1'), + ('CMake', '3.21.1'), + ('Ninja', '1.10.2'), +] +dependencies = [ + ('Python', '3.9.6'), + ('IPython', '7.26.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/kernprof'], + 'dirs': [], +} + +sanity_check_commands = ['kernprof --help'] + +moduleclass = 'devel' From 15483bd1fece5f16287509388575c0ac34415910 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 9 May 2022 22:18:04 +0200 Subject: [PATCH 3722/9987] adding easyconfigs: XPLOR-NIH-3.4-Linux_x86_64.eb --- .../x/XPLOR-NIH/XPLOR-NIH-3.4-Linux_x86_64.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/x/XPLOR-NIH/XPLOR-NIH-3.4-Linux_x86_64.eb diff --git a/easybuild/easyconfigs/x/XPLOR-NIH/XPLOR-NIH-3.4-Linux_x86_64.eb b/easybuild/easyconfigs/x/XPLOR-NIH/XPLOR-NIH-3.4-Linux_x86_64.eb new file mode 100644 index 00000000000..1f792f4b29e --- /dev/null +++ b/easybuild/easyconfigs/x/XPLOR-NIH/XPLOR-NIH-3.4-Linux_x86_64.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'XPLOR-NIH' +version = '3.4' +versionsuffix = '-Linux_x86_64' + +homepage = 'https://nmr.cit.nih.gov/xplor-nih/' +description = """A System for X-ray Crystallography and NMR""" + +toolchain = SYSTEM + +_extract_cmd = "tar --strip-components 1 -xzf %s" + +source_urls = ['https://bit.niddk.nih.gov/xplor-nih/packages'] +sources = [ + {'filename': '%%(namelower)s-%%(version)s%s.tar.gz' % versionsuffix, 'extract_cmd': _extract_cmd}, + {'filename': '%(namelower)s-%(version)s-db.tar.gz', 'extract_cmd': _extract_cmd}, +] +checksums = [ + '9aa3360c8e4b6f1e28d0911dfc894938d7dc4a90bab1a970d68b8505d878c8e3', # xplor-nih-3.4-Linux_x86_64.tar.gz + '9ce7bf22f40855c8089cd28856961b3a513c771ed56902374e95690ed4f5b69c', # xplor-nih-3.4-db.tar.gz +] + +buildininstalldir = True +skipsteps = ['install'] +postinstallcmds = ['./configure'] + +sanity_check_paths = { + 'files': ['bin/xplor'], + 'dirs': [], +} + +sanity_check_commands = ['xplor -help'] + +moduleclass = 'bio' From 544dc3a6be80090cf181f54a3b79c7bf83281b76 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 9 May 2022 22:21:52 +0200 Subject: [PATCH 3723/9987] adding easyconfigs: inferCNV-1.10.1-foss-2021b-R-4.1.2.eb, rjags-4-12-foss-2021b-R-4.1.2.eb --- .../inferCNV-1.10.1-foss-2021b-R-4.1.2.eb | 53 +++++++++++++++++++ .../r/rjags/rjags-4-12-foss-2021b-R-4.1.2.eb | 29 ++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.10.1-foss-2021b-R-4.1.2.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-12-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.10.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.10.1-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..6bd180c0b08 --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.10.1-foss-2021b-R-4.1.2.eb @@ -0,0 +1,53 @@ +easyblock = 'Bundle' + +name = 'inferCNV' +version = '1.10.1' +versionsuffix = '-R-%(rver)s' +local_biocver = '3.14' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('R', '4.1.2'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-12', '-R-%(rver)s'), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_biocver, + 'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_biocver, + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_list = [ + ('phyclust', '0.1-30', { + 'checksums': ['f7645bfaecfe7a19d213a7d5c42c750f0ccbdd85549dae6e8ba9d2ba4bc2c93b'], + }), + ('infercnv', version, { + 'checksums': ['60235405e928cc16e5d3c1238f2149a3acdf3340ede24f1ca38d70f455fcb3c2'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-12-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/rjags/rjags-4-12-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..de29888de5a --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-12-foss-2021b-R-4.1.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-12' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['b91f34c3f9ebf78fa44bd661346fbb6f28a01693a7203ac133c98392dd273e10'] + +dependencies = [ + ('R', '4.1.2'), + ('JAGS', '4.3.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' From 6f08057be217f24bcc930a0befb46c063120b7b4 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 9 May 2022 22:24:50 +0200 Subject: [PATCH 3724/9987] adding easyconfigs: parameterized-0.8.1-GCCcore-10.3.0.eb --- .../parameterized-0.8.1-GCCcore-10.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/parameterized/parameterized-0.8.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/parameterized/parameterized-0.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/parameterized/parameterized-0.8.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f53d34f3fb2 --- /dev/null +++ b/easybuild/easyconfigs/p/parameterized/parameterized-0.8.1-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'parameterized' +version = '0.8.1' + +homepage = 'https://github.com/wolever/parameterized' +description = """ Parameterized testing with any Python test framework """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['41bbff37d6186430f77f900d777e5bb6a24928a1c46fb1de692f8b52b8833b5c'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From ec3f5823c32fb035ad40166ddc473159f4ea9c10 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 10 May 2022 09:39:12 +0200 Subject: [PATCH 3725/9987] remove source_urls --- .../p/parameterized/parameterized-0.8.1-GCCcore-10.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/parameterized/parameterized-0.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/parameterized/parameterized-0.8.1-GCCcore-10.3.0.eb index f53d34f3fb2..b8228743136 100644 --- a/easybuild/easyconfigs/p/parameterized/parameterized-0.8.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/parameterized/parameterized-0.8.1-GCCcore-10.3.0.eb @@ -8,7 +8,6 @@ description = """ Parameterized testing with any Python test framework """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['41bbff37d6186430f77f900d777e5bb6a24928a1c46fb1de692f8b52b8833b5c'] From 41864a08196abe455e3a9d909a7b1285d53152b2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 10 May 2022 12:34:37 +0100 Subject: [PATCH 3726/9987] add easyconfig for LibTIFF --- .../l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a35ee9ee659 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.3.0' + +homepage = 'https://libtiff.maptools.org/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.osgeo.org/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['0e46e5acb087ce7d1ac53cf4f56a09b221537fc86dfc5daaad1c2e89e1b37ac8'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.3'), + ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('zstd', '1.5.2'), + ('libdeflate', '1.10'), +] + +configopts = "--enable-ld-version-script " +configopts += '--disable-webp' + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' From 8acd135a043a3193b2e276b3d4cb0b83c5af643b Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 10 May 2022 12:55:30 +0100 Subject: [PATCH 3727/9987] add easyconfig for jbigkit --- .../j/jbigkit/jbigkit-2.1-GCCcore-11.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0bbedae22a8 --- /dev/null +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'jbigkit' +version = '2.1' + +homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' + +description = """JBIG-KIT is a software implementation of the JBIG1 data + compression standard (ITU-T T.82), which was designed for bi-level image + data, such as scanned documents.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_libpath.patch', + '%(name)s-%(version)s_shlib.patch', +] +checksums = [ + 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932', # jbigkit-2.1.tar.gz + '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce', # jbigkit-2.1_libpath.patch + '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696', # jbigkit-2.1_shlib.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +files_to_copy = [ + (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), + (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libjbig85.a', 'lib/libjbig.a', + 'bin/pbmtojbg', 'bin/jbgtopbm', + 'include/jbig.h', 'include/jbig_ar.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' From fd0cdb7856f07d0df1163411863d06fb23c36af9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 May 2022 15:27:14 +0200 Subject: [PATCH 3728/9987] adding easyconfigs: intel-compilers-2022.1.0.eb --- .../intel-compilers-2022.1.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb new file mode 100644 index 00000000000..f25617230ac --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.1.0.eb @@ -0,0 +1,32 @@ +name = 'intel-compilers' +version = '2022.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18717/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.137_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18703/'], + 'filename': 'l_fortran-compiler_p_%(version)s.134_offline.sh', + }, +] +checksums = [ + # l_dpcpp-cpp-compiler_p_2022.1.0.137_offline.sh + '1027819581ba820470f351abfc2b2658ff2684ed8da9ed0e722a45774a2541d6', + '583082abe54a657eb933ea4ba3e988eef892985316be13f3e23e18a3c9515020', # l_fortran-compiler_p_2022.1.0.134_offline.sh +] + +local_gccver = '11.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.38', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' From 186e1f40de881ab9fd3a4eccf74bc6f796141447 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 May 2022 15:27:52 +0200 Subject: [PATCH 3729/9987] update to impi 2021.6.0 on top of intel-compilers v2022.1.0 --- ....2.eb => impi-2021.6.0-intel-compilers-2022.1.0.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/i/impi/{impi-2021.5.1-intel-compilers-2022.0.2.eb => impi-2021.6.0-intel-compilers-2022.1.0.eb} (61%) diff --git a/easybuild/easyconfigs/i/impi/impi-2021.5.1-intel-compilers-2022.0.2.eb b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb similarity index 61% rename from easybuild/easyconfigs/i/impi/impi-2021.5.1-intel-compilers-2022.0.2.eb rename to easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb index f175c69a408..b1d328caa62 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.5.1-intel-compilers-2022.0.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.6.0-intel-compilers-2022.1.0.eb @@ -1,15 +1,15 @@ name = 'impi' -version = '2021.5.1' +version = '2021.6.0' homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' description = "Intel MPI Library, compatible with MPICH ABI" -toolchain = {'name': 'intel-compilers', 'version': '2022.0.2'} +toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/18471/'] -sources = ['l_mpi_oneapi_p_%(version)s.515_offline.sh'] -checksums = ['b992573959e39752e503e691564a0d876b099547c38b322d5775c5b06ec07a7f'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18714/'] +sources = ['l_mpi_oneapi_p_%(version)s.602_offline.sh'] +checksums = ['e85db63788c434d43c1378e5e2bf7927a75d11aee8e6b78ee0d933da920977a6'] dependencies = [('UCX', '1.12.1')] From 765a403ed7bb4085bd2f0b8ca794074c2d79d931 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 10 May 2022 16:25:56 +0100 Subject: [PATCH 3730/9987] adding easyconfigs: imkl-2022.1.0.eb --- easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb new file mode 100644 index 00000000000..c34d533cf35 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2022.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +sources = ['l_onemkl_p_%(version)s.223_offline.sh'] +checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' From 4aff00483057ca7caa0671a5bfea49d35d892b9d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 10 May 2022 16:40:21 +0100 Subject: [PATCH 3731/9987] adding easyconfigs: iimpi-2022.05.eb, imkl-FFTW-2022.1.0-iimpi-2022.05.eb --- easybuild/easyconfigs/i/iimpi/iimpi-2022.05.eb | 18 ++++++++++++++++++ .../imkl-FFTW-2022.1.0-iimpi-2022.05.eb | 11 +++++++++++ 2 files changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022.05.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022.05.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022.05.eb new file mode 100644 index 00000000000..e5a33925a5e --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022.05.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022.05' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.1.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.6.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb new file mode 100644 index 00000000000..1d2d73b038e --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022.05'} + +dependencies = [('imkl', version, '', True)] + +moduleclass = 'numlib' From 212e95c2f00d997d10ba564be185b34826e2b36b Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 10 May 2022 16:44:51 +0100 Subject: [PATCH 3732/9987] add intel-2022.05 --- .../easyconfigs/i/intel/intel-2022.05.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/i/intel/intel-2022.05.eb diff --git a/easybuild/easyconfigs/i/intel/intel-2022.05.eb b/easybuild/easyconfigs/i/intel/intel-2022.05.eb new file mode 100644 index 00000000000..b78b8a46bb5 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022.05.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022.05' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.1.0' +local_gccver = '11.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.38', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.6.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', True), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From 60bfb0c3968f83f13e7fe662c5f493c688398b1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 May 2022 19:23:51 +0200 Subject: [PATCH 3733/9987] add Gdk-Pixbuf dependency for libheif Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb index e42235b1b9b..cf871e99182 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb @@ -21,6 +21,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.6'), ('libde265', '1.0.8'), ('x265', '3.5'), + ('Gdk-Pixbuf', '2.42.6'), ] # build both static and shared libraries From 40858d38e264c63b94214a14b1a956739c3caadf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 May 2022 21:44:08 +0200 Subject: [PATCH 3734/9987] {lib,vis}[foss/2021a] Albumentations v1.1.0, imgaug v0.4.0 w/ Python 3.9.5 + CUDA 11.3.1 --- ...mentations-1.1.0-foss-2021a-CUDA-11.3.1.eb | 37 +++++++++++++++++++ .../imgaug-0.4.0-foss-2021a-CUDA-11.3.1.eb | 35 ++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..88479d0582a --- /dev/null +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.1.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'Albumentations' +version = '1.1.0' +versionsuffix = '-CUDA-11.3.1' + +homepage = 'https://albumentations.ai' +description = "Albumentations is a Python library for fast and flexible image augmentations" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('scikit-image', '0.18.3'), + ('scikit-learn', '0.24.2'), + ('OpenCV', '4.5.3', versionsuffix + '-contrib'), + ('imgaug', '0.4.0', versionsuffix), +] + +preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && " + +use_pip = True + +exts_list = [ + ('qudida', '0.0.4', { + 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], + }), + ('albumentations', version, { + 'checksums': ['60b067b3093908bcc52adb2aa5d44f57ebdbb8ab57a47b0b42f3dc1d3b1ce824'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..0fafc26240c --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,35 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.0' +versionsuffix = '-CUDA-11.3.1' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Pillow', '8.2.0'), + ('matplotlib', '3.4.2'), + ('scikit-image', '0.18.3'), + ('OpenCV', '4.5.3', versionsuffix + '-contrib'), + ('Shapely', '1.8a1'), + ('imageio', '2.10.5'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['imgaug-0.4.0_openvc_requirement.patch'] +checksums = [ + '46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7', # imgaug-0.4.0.tar.gz + '2ff0b66ba38fdcf5f267a3d0ad1dc2710fee3c2f8cd3d086c56ea538a2a9ffc8', # imgaug-0.4.0_openvc_requirement.patch +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' From 80675880642e8f2736dfc8d872bb63d958ce0c3d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 11 May 2022 11:19:44 +0100 Subject: [PATCH 3735/9987] bump GST-plugins-bad to 1.20.2 to match other GST-plugins/GStreamer versions --- ...9.2-GCC-11.3.0.eb => GST-plugins-bad-1.20.2-GCC-11.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/GST-plugins-bad/{GST-plugins-bad-1.19.2-GCC-11.3.0.eb => GST-plugins-bad-1.20.2-GCC-11.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.20.2-GCC-11.3.0.eb similarity index 92% rename from easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb rename to easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.20.2-GCC-11.3.0.eb index 8032e9e1652..eddb9cebdb8 100644 --- a/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.19.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.20.2-GCC-11.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'MesonNinja' name = 'GST-plugins-bad' -version = '1.19.2' +version = '1.20.2' homepage = 'https://gstreamer.freedesktop.org/' description = """GStreamer is a library for constructing graphs of media-handling @@ -13,7 +13,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-bad'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['5382f98a9af2c92e5c0ca4fcb3911025cafd9f89b3142b206eb7b92b812e0979'] +checksums = ['4adc4c05f41051f8136b80cda99b0d049a34e777832f9fea7c5a70347658745b'] builddependencies = [ ('Meson', '0.62.1'), From 9c8d18295adad7ce71009e52f6faef3bec0aeef1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 11 May 2022 11:24:02 +0100 Subject: [PATCH 3736/9987] Add binutils builddep to Graphene, update GST-plugins-bad version in GTK4 --- .../g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb | 2 +- .../Graphene-1.10.8-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 2 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb index 34f9b46c075..7a08399299e 100644 --- a/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb @@ -32,7 +32,7 @@ dependencies = [ ('libepoxy', '1.5.10'), ('X11', '20220504'), ('FriBidi', '1.0.12'), - ('GST-plugins-bad', '1.19.2'), + ('GST-plugins-bad', '1.20.2'), ('Wayland', '1.20.0'), ('PyGObject', '3.42.1'), ] diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5fa19ae02fb --- /dev/null +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'Graphene' +version = '1.10.8' + +homepage = 'https://ebassi.github.io/graphene/' +description = "Graphene is a thin layer of types for graphic libraries" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'ebassi' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['922dc109d2dc5dc56617a29bd716c79dd84db31721a8493a13a5f79109a4a4ed'] + +builddependencies = [ + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), + ('GObject-Introspection', '1.72.0'), + ('binutils', '2.38'), +] +dependencies = [('GLib', '2.72.1')] + +configopts = "-Dgobject_types=true -Dintrospection=enabled" + +sanity_check_paths = { + 'files': ['lib/libgraphene-1.0.%s' % SHLIB_EXT, 'share/gir-1.0/Graphene-1.0.gir'], + 'dirs': ['include/graphene-1.0', 'lib/pkgconfig'], +} + +moduleclass = 'lib' From bf40a4a709cba4528fb5ce4a90787a61cad19592 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 11 May 2022 11:26:23 +0100 Subject: [PATCH 3737/9987] remove Graphene --- .../Graphene-1.10.8-GCCcore-11.3.0.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb deleted file mode 100644 index 5fa19ae02fb..00000000000 --- a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'Graphene' -version = '1.10.8' - -homepage = 'https://ebassi.github.io/graphene/' -description = "Graphene is a thin layer of types for graphic libraries" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -github_account = 'ebassi' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['922dc109d2dc5dc56617a29bd716c79dd84db31721a8493a13a5f79109a4a4ed'] - -builddependencies = [ - ('Meson', '0.62.1'), - ('Ninja', '1.10.2'), - ('pkgconf', '1.8.0'), - ('GObject-Introspection', '1.72.0'), - ('binutils', '2.38'), -] -dependencies = [('GLib', '2.72.1')] - -configopts = "-Dgobject_types=true -Dintrospection=enabled" - -sanity_check_paths = { - 'files': ['lib/libgraphene-1.0.%s' % SHLIB_EXT, 'share/gir-1.0/Graphene-1.0.gir'], - 'dirs': ['include/graphene-1.0', 'lib/pkgconfig'], -} - -moduleclass = 'lib' From abc6a978ea9c9c064092a53b05daaee0c9fdf6d5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 11 May 2022 11:27:52 +0100 Subject: [PATCH 3738/9987] add binutils builddep to Graphene --- .../easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb index d5f5e9c6df7..5fa19ae02fb 100644 --- a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-11.3.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ('Ninja', '1.10.2'), ('pkgconf', '1.8.0'), ('GObject-Introspection', '1.72.0'), + ('binutils', '2.38'), ] dependencies = [('GLib', '2.72.1')] From 047fd38b76f6cde7c75b438ec0c73e0766cbdcd0 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 11 May 2022 11:50:10 +0100 Subject: [PATCH 3739/9987] add binutils to Wayland --- easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.3.0.eb index 79fa7f3ccfd..88958af9b50 100644 --- a/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.3.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), ('pkgconf', '1.8.0'), + ('binutils', '2.38'), ] dependencies = [ From 5bba0d608d7d7c5d47403a1c5a97257a09ba413c Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 11 May 2022 11:00:29 +0000 Subject: [PATCH 3740/9987] Rename FFTW.serial to FFTW --- .../FFTW-3.3.10-GCC-11.3.0.eb} | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/f/{FFTW.serial/FFTW.serial-3.3.10-GCC-11.3.0.eb => FFTW/FFTW-3.3.10-GCC-11.3.0.eb} (85%) diff --git a/easybuild/easyconfigs/f/FFTW.serial/FFTW.serial-3.3.10-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-11.3.0.eb similarity index 85% rename from easybuild/easyconfigs/f/FFTW.serial/FFTW.serial-3.3.10-GCC-11.3.0.eb rename to easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-11.3.0.eb index c5871c38697..99e7044835e 100644 --- a/easybuild/easyconfigs/f/FFTW.serial/FFTW.serial-3.3.10-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-11.3.0.eb @@ -1,5 +1,4 @@ -easyblock = 'EB_FFTW' -name = 'FFTW.serial' +name = 'FFTW' version = '3.3.10' homepage = 'https://www.fftw.org' @@ -10,7 +9,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} toolchainopts = {'pic': True} source_urls = [homepage] -sources = ['fftw-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] runtest = 'check' From 89aff63c4ba0adb9547c24d78eda34eac5b655e5 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 11 May 2022 13:31:01 +0100 Subject: [PATCH 3741/9987] update homepage URL Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb index 7a08399299e..546034ed404 100644 --- a/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'Bundle' name = 'GTK4' version = '4.6.3' -homepage = 'https://developer.gnome.org/gtk3/stable/' +homepage = 'https://docs.gtk.org/gtk4/' description = """GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct From fd64ebe7032faaffdf1a33c78b3962b5d085ea01 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 11 May 2022 13:42:23 +0100 Subject: [PATCH 3742/9987] bump GTK4 to 4.7.0 --- .../{GTK4-4.6.3-GCC-11.3.0.eb => GTK4-4.7.0-GCC-11.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/GTK4/{GTK4-4.6.3-GCC-11.3.0.eb => GTK4-4.7.0-GCC-11.3.0.eb} (96%) diff --git a/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GTK4/GTK4-4.7.0-GCC-11.3.0.eb similarity index 96% rename from easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb rename to easybuild/easyconfigs/g/GTK4/GTK4-4.7.0-GCC-11.3.0.eb index 546034ed404..4af9c6eb1dd 100644 --- a/easybuild/easyconfigs/g/GTK4/GTK4-4.6.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GTK4/GTK4-4.7.0-GCC-11.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'GTK4' -version = '4.6.3' +version = '4.7.0' homepage = 'https://docs.gtk.org/gtk4/' description = """GTK+ is the primary library used to construct user interfaces in GNOME. It @@ -49,7 +49,7 @@ components = [ 'easyblock': 'MesonNinja', 'source_urls': [FTPGNOME_SOURCE], 'configopts': "-Dintrospection=enabled -Dgtk_doc=false", - 'checksums': ['a57acd0e4482981700fdf86596c7413cb61ef47f75e4747fda809e8231b8d96c'], + 'checksums': ['913fcd9d065efb348723e18c3b9113e23b92072e927ebd2f61d32745c8228b94'], }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], From be60f8341b874970c78302a245e0f0de2b2980fc Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 11 May 2022 15:11:30 +0100 Subject: [PATCH 3743/9987] gtk4-update-icon-cache --- easybuild/easyconfigs/g/GTK4/GTK4-4.7.0-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GTK4/GTK4-4.7.0-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GTK4/GTK4-4.7.0-GCC-11.3.0.eb index 4af9c6eb1dd..0e6a712b8f0 100644 --- a/easybuild/easyconfigs/g/GTK4/GTK4-4.7.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GTK4/GTK4-4.7.0-GCC-11.3.0.eb @@ -67,7 +67,7 @@ components = [ }), ] -postinstallcmds = ['gtk-update-icon-cache'] +postinstallcmds = ['gtk4-update-icon-cache'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['gtk4-demo', 'gtk4-demo-application', 'gtk4-icon-browser', 'gtk4-widget-factory', From acb84afe74d4ba8c9ab66c62c5ee9917c8f81a8a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 11 May 2022 19:53:50 +0200 Subject: [PATCH 3744/9987] remove obsolate I_MPI_WAIT_MODE --- .../w/worker/worker-1.6.13-iimpi-2021b.eb | 6 ++++- .../w/worker/worker-1.6.13_fixintel.patch | 22 +++++++++++++++++++ 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.13_fixintel.patch diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2021b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2021b.eb index 6b8ba29c9a8..123299fc45c 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2021b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2021b.eb @@ -15,7 +15,11 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['b42b8566d82048c706427913c8f7edcd9f5892d61f190ce1f49e428113b7e1bc'] +patches = ['%(name)s-%(version)s_fixintel.patch'] +checksums = [ + 'b42b8566d82048c706427913c8f7edcd9f5892d61f190ce1f49e428113b7e1bc', # 1.6.13.tar.gz + 'c28bbc837ec5d6fb3390df668b06e0b5169ca31dede907336a2b0637c4a81504', # worker-1.6.13_fixintel.patch +] dependencies = [ ('Perl', '5.34.0') diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.13_fixintel.patch b/easybuild/easyconfigs/w/worker/worker-1.6.13_fixintel.patch new file mode 100644 index 00000000000..6c4e1db83f8 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.13_fixintel.patch @@ -0,0 +1,22 @@ +# Intel MPI > ~2019.5 does not have I_MPI_WAIT_MODE +From b8355b9b6d5e9b77a9a3c50858d95f43b2bc5575 Mon Sep 17 00:00:00 2001 +From: Geert Jan Bex +Date: Thu, 13 Jan 2022 17:28:15 +0100 +Subject: [PATCH] Remove I_MPI_WAIT_MODE since support was dropped + +--- + src/tt/worker.pbs.tt | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/src/tt/worker.pbs.tt b/src/tt/worker.pbs.tt +index 4eefb9f..2e21b3f 100644 +--- a/src/tt/worker.pbs.tt ++++ b/src/tt/worker.pbs.tt +@@ -83,7 +83,6 @@ n_proc=$(cat ${PBS_NODEFILE} | wc -l) + export KMP_AFFINITY=compact + [%END%] + +-export I_MPI_WAIT_MODE=enable + # compute log option + WORKER_LOG_FILE="-l [%logfile%]" + From f29b634460fb985ad63739174b3738d8152c80a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2022 20:47:06 +0200 Subject: [PATCH 3745/9987] adding easyconfigs: DBD-mysql-4.050-GCC-11.2.0.eb --- .../d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb new file mode 100644 index 00000000000..e510e497a7c --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.050' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['4f48541ff15a0a7405f76adc10f81627c33996fbf56c95c26c094444c0928d78'] + +dependencies = [ + ('Perl', '5.34.0'), + ('MariaDB', '10.6.4'), + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1k'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql.pm' % ARCH], + 'dirs': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql' % ARCH], +} + +moduleclass = 'data' From 6442d95a6cdb9843e49ea38314d1157a82f1cdaf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 May 2022 21:07:41 +0200 Subject: [PATCH 3746/9987] fix OpenSSL dependency for DBD-mysql with GCC/11.2.0 --- .../easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb index e510e497a7c..5f7fbe14d4a 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb @@ -16,13 +16,9 @@ dependencies = [ ('Perl', '5.34.0'), ('MariaDB', '10.6.4'), ('zlib', '1.2.11'), - # OS dependency should be preferred if the os version is more recent then this version - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.1k'), + ('OpenSSL', '1.1', '', True), ] -osdependencies = [OS_PKG_OPENSSL_DEV] - options = {'modulename': 'DBD::mysql'} sanity_check_paths = { From 3841acb6bca762a9e3a34d051e8ccbb632e4a586 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 May 2022 09:07:14 +0200 Subject: [PATCH 3747/9987] adding easyconfigs: cryoDRGN-0.3.4-foss-2021a-CUDA-11.3.1.eb --- .../cryoDRGN-0.3.4-foss-2021a-CUDA-11.3.1.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.4-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.4-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.4-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..b7104343785 --- /dev/null +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.4-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'cryoDRGN' +version = '0.3.4' +versionsuffix = '-CUDA-11.3.1' + +homepage = 'https://cb.csail.mit.edu/cb/cryodrgn/' +description = """cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous + reconstruction. + CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In + particular, the method models a continuous distribution over 3D structures by using a neural + network based representation for the volume. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('IPython', '7.25.0'), + ('JupyterLab', '3.0.16'), + ('PyTorch', '1.10.0', versionsuffix), + ('numba', '0.53.1'), + ('plotly.py', '5.1.0'), + ('scikit-learn', '0.24.2'), + ('matplotlib', '3.4.2'), + ('Seaborn', '0.11.2'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('colorlover', '0.3.0', { + 'checksums': ['b8fb7246ab46e1f5e6715649453c1762e245a515de5ff2d2b4aab7a6e67fa4e2'], + }), + ('cufflinks', '0.17.3', { + 'checksums': ['48c1b3406dc030004121966489eebc5518cea70fd4e3f16379b491328501a644'], + }), + ('pynndescent', '0.5.6', { + 'checksums': ['61fb31885baac469d67933e2c7c935b6edebb06ee498e2f0f9dfc97c59d3725c'], + }), + ('umap-learn', '0.5.3', { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), + ('cryodrgn', version, { + 'postinstallcmds': [ + 'cp utils/* analysis_scripts/* %(installdir)s/bin', + 'chmod +x %(installdir)s/bin/*.py', + ], + 'source_urls': ['https://github.com/zhonge/cryodrgn/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['5be9709a2bd19a4ab7c80acd82eef5bfbcdf02b4dd8dcb61113636fa5d44d0c5'], + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +local_scripts = [ + 'add_psize', 'filter_mrcs', 'filter_pkl', 'filter_star', 'flip_hand', 'fsc', 'invert_contrast', 'kmeans', + 'phase_flip', 'plotfsc', 'plot_loss', 'plot_z1', 'plot_z2', 'plot_z_pca', 'run_umap', 'translate_stack', 'tsne', + 'view_header', 'view_stack', 'write_starfile' +] + +sanity_check_paths = { + 'files': ['bin/%s.py' % x for x in local_scripts], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s --help'] +sanity_check_commands += ['%s.py -h' % x for x in local_scripts] + +sanity_pip_check = True + +moduleclass = 'chem' From 76c7687c9c046adfcc0ea2451aaf270dd1032469 Mon Sep 17 00:00:00 2001 From: Robert Mijakovic Date: Thu, 12 May 2022 11:09:55 +0200 Subject: [PATCH 3748/9987] adding easyconfigs: CUDA-11.7.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-11.7.0.eb | 26 +++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.7.0.eb new file mode 100644 index 00000000000..d2192a64746 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.7.0.eb @@ -0,0 +1,26 @@ +name = 'CUDA' +version = '11.7.0' +local_nv_version = '515.43.04' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '087fdfcbba1f79543b1f78e43a8dfdac5f6db242d042dde820e16dc185892f26', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '74a507ac54067c258e6b7c9063c98d411116ecc5c5397b1f6e6a999e86dff08a', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'e777839a618ca9a3d5ad42ded43a1b6392af2321a7327635a4afcc986876a21b', + } +] + +moduleclass = 'system' From d1b381ca3504fcab5a9062df127a5d861c24605f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 12 May 2022 12:23:12 +0200 Subject: [PATCH 3749/9987] adding easyconfigs: PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb --- ...rch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..abd315e1aba --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Ignite' +version = '0.4.9' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch-ignite.ai/' +description = """ +Ignite is a high-level library to help with training and evaluating neural +networks in PyTorch flexibly and transparently.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('PyTorch', '1.10.0', versionsuffix), +] + +exts_list = [ + ('pytorch-lightning', version, { + 'modulename': 'ignite', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pytorch/ignite/archive'], + 'checksums': ['eb9711012c6052e076beec5c47de55a3f861a0fae760c4de684e7971acf38964'], + }), +] + +use_pip = True + +sanity_pip_check = True + +moduleclass = 'lib' From aa77205f58114767a24bf990632e275d95396dec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 12 May 2022 13:02:22 +0200 Subject: [PATCH 3750/9987] Grammatical correction in description Co-authored-by: Adam Huffman --- easybuild/easyconfigs/a/Arriba/Arriba-2.2.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arriba/Arriba-2.2.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/Arriba/Arriba-2.2.1-GCC-11.2.0.eb index f66e167b344..38e5191f62b 100644 --- a/easybuild/easyconfigs/a/Arriba/Arriba-2.2.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/Arriba/Arriba-2.2.1-GCC-11.2.0.eb @@ -7,7 +7,7 @@ version = '2.2.1' homepage = 'https://github.com/suhrig/arriba' description = """Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. - It was developed for the use in a clinical research setting. Therefore, short runtimes and high + It was developed for use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} From bab058712228df4070989796b6c2d389b9e6abae Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 12 May 2022 14:32:44 +0200 Subject: [PATCH 3751/9987] Update easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb index c79655da73d..e5f409bd309 100644 --- a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb @@ -16,8 +16,6 @@ github_account = 'Helmholtz-UFZ' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['74b1c455ba57ab240921966255ca059840b97c47efcd16e9e66b9b6a8a136ee2'] - - prepend_to_path = ['.'] dependencies = [ From edc4744e097fbca877146005adb4fb9e914d0038 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 12 May 2022 14:38:33 +0200 Subject: [PATCH 3752/9987] Update Jorg-1.0.0-foss-2020b.eb add check command as suggested by @smoors --- easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb index e5f409bd309..f66c45f5bd5 100644 --- a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['jorg --help'] + moduleclass = 'bio' From 4eb377c22876edb9a1d61bddd688c89bd1a1d233 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 12 May 2022 14:08:34 +0100 Subject: [PATCH 3753/9987] adding easyconfigs: CellRanger-ARC-2.0.1.eb --- .../c/CellRanger-ARC/CellRanger-ARC-2.0.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellRanger-ARC/CellRanger-ARC-2.0.1.eb diff --git a/easybuild/easyconfigs/c/CellRanger-ARC/CellRanger-ARC-2.0.1.eb b/easybuild/easyconfigs/c/CellRanger-ARC/CellRanger-ARC-2.0.1.eb new file mode 100644 index 00000000000..2e3038da2cf --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger-ARC/CellRanger-ARC-2.0.1.eb @@ -0,0 +1,33 @@ +# The STAR binary included in this version has been vectorized with AVX +# hence it is not recommended for systems that do not support it. + +easyblock = 'Tarball' + +name = 'CellRanger-ARC' +version = '2.0.1' + +homepage = 'https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/' +homepage += 'what-is-cell-ranger-arc' +description = """Cell Ranger ARC is a set of analysis pipelines that process + Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a + variety of analyses pertaining to gene expression, chromatin accessibility and + their linkage. Furthermore, since the ATAC and gene expression measurements are on + the very same cell, we are able to perform analyses that link chromatin + accessibility and gene expression.""" + +toolchain = SYSTEM + +# Download manually from https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/downloads/latest +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00f69dc4b7efa8a76944683d9f766b0cf21947975d8fe742c3b572b771c62d33'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ["bin/cellranger-arc"], + 'dirs': ["bin/rna", "bin/tenkit"], +} + +sanity_check_commands = ['cellranger-arc -h'] + +moduleclass = 'bio' From 025fee32245b9bceb50ab84b5e76e00a1fbb7f7c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 12 May 2022 15:26:00 +0100 Subject: [PATCH 3754/9987] adding easyconfigs: astropy-5.0.4-foss-2021a.eb --- .../a/astropy/astropy-5.0.4-foss-2021a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-5.0.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-5.0.4-foss-2021a.eb b/easybuild/easyconfigs/a/astropy/astropy-5.0.4-foss-2021a.eb new file mode 100644 index 00000000000..05d4b25942e --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-5.0.4-foss-2021a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '5.0.4' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '2.0.0.1', { + 'modulename': 'erfa', + 'checksums': ['2fd4637ffe2c1e6ede7482c13f583ba7c73119d78bef90175448ce506a0ede30'], + }), + ('extension-helpers', '1.0.0', { + 'checksums': ['ca1bfac67c79cf4a7a0c09286ce2a24eec31bf17715818d0726318dd0e5050e6'], + }), + (name, version, { + 'checksums': ['001184f1a9c3f526a363883ce28efb9cbf076df3d151ca3e131509a248f0dfb9'], + }), +] + +moduleclass = 'astro' From 84015ced48a626ede20647e44535b9178de1585b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 May 2022 16:58:39 +0200 Subject: [PATCH 3755/9987] Disable vectorize on OpenFOAM v2112 foss/2021b --- .../easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb index 324e545e4b5..179e3ca08cc 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb @@ -8,7 +8,11 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'cstd': 'c++11'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {'cstd': 'c++11', 'vectorize': False} + source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] From 61310c4e9d3d333959531d9240c26b4dbbadd2a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 May 2022 16:59:42 +0200 Subject: [PATCH 3756/9987] Fix style --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb index 179e3ca08cc..3f2bdc72802 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2021b.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'foss', 'version': '2021b'} # With no test suite, sticking to known working toolchain options until proven otherwise. toolchainopts = {'cstd': 'c++11', 'vectorize': False} - source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] patches = [ From a3b00fc504f5b6ba9b2ba0142f3e5727d4ac680f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 12 May 2022 17:42:55 +0100 Subject: [PATCH 3757/9987] Typo fix --- easybuild/easyconfigs/t/tmap/tmap-20220502-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tmap/tmap-20220502-GCC-11.2.0.eb b/easybuild/easyconfigs/t/tmap/tmap-20220502-GCC-11.2.0.eb index 23f0eeefe31..10c73ff2d3a 100644 --- a/easybuild/easyconfigs/t/tmap/tmap-20220502-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/t/tmap/tmap-20220502-GCC-11.2.0.eb @@ -6,7 +6,7 @@ version = '20220502' homepage = 'https://tmap.gdb.tools' description = """tmap is a very fast visualization library for large, high-dimensional data sets. Currently, tmap is available for Python. -tmaps graph layouts are based on the OGDF library.""" +tmap's graph layouts are based on the OGDF library.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} From 4df73503d591108b3990db83429fdbfbccc35d7f Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 12 May 2022 18:07:35 +0100 Subject: [PATCH 3758/9987] adding easyconfigs: pgplot-5.2.2-GCCcore-11.2.0.eb, pgplot-5.2.2-GCCcore-10.3.0.eb --- .../p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb | 51 +++++++++++++++++++ .../p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb | 51 +++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..9aeb3466d7d --- /dev/null +++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb @@ -0,0 +1,51 @@ +# Contribution from Imperial College London (UK) +# Uploaded by J. Sassmannshausen + +easyblock = 'CmdCp' + +name = 'pgplot' +version = '5.2.2' + +homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/' +description = """The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, +device-independent graphics package for making simple scientific graphs. It is intended +for making graphical images of publication quality with minimum effort on the part of +the user. For most applications, the program can be device-independent, and the output +can be directed to the appropriate device at run time.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/'] +sources = ['%%(name)s%s.tar.gz' % version.replace('.', '')] +patches = ['pgplot-compiler.patch'] + +checksums = [ + 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4', # pgplot522.tar.gz + 'ce098908b69f0a20f4f5e8efdab3779d9674f4ca6f0d4af7861bb0f541384ace', # pgplot-compiler.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +cmds_map = [('.*', './makemake . linux g77_gcc && make ')] + +files_to_copy = [ + (['pgdemo*'], 'bin'), + (['libpgplot.a', 'libpgplot.so'], 'lib'), + (['grfont.dat'], 'share'), +] + +sanity_check_paths = { + 'files': ['lib/libpgplot.a'], + 'dirs': [] +} + +modextravars = {'PGPLOT_FONT': '%(installdir)s/share/grfont.dat'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c9d8a6d0a5a --- /dev/null +++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb @@ -0,0 +1,51 @@ +# Contribution from Imperial College London (UK) +# Uploaded by J. Sassmannshausen + +easyblock = 'CmdCp' + +name = 'pgplot' +version = '5.2.2' + +homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/' +description = """The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, +device-independent graphics package for making simple scientific graphs. It is intended +for making graphical images of publication quality with minimum effort on the part of +the user. For most applications, the program can be device-independent, and the output +can be directed to the appropriate device at run time.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/'] +sources = ['%%(name)s%s.tar.gz' % version.replace('.', '')] +patches = ['pgplot-compiler.patch'] + +checksums = [ + 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4', # pgplot522.tar.gz + 'ce098908b69f0a20f4f5e8efdab3779d9674f4ca6f0d4af7861bb0f541384ace', # pgplot-compiler.patch +] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +cmds_map = [('.*', './makemake . linux g77_gcc && make ')] + +files_to_copy = [ + (['pgdemo*'], 'bin'), + (['libpgplot.a', 'libpgplot.so'], 'lib'), + (['grfont.dat'], 'share'), +] + +sanity_check_paths = { + 'files': ['lib/libpgplot.a'], + 'dirs': [] +} + +modextravars = {'PGPLOT_FONT': '%(installdir)s/share/grfont.dat'} + +moduleclass = 'vis' From a5b97aa7954721ba7800524901c8dcd08264baa6 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 12 May 2022 21:56:28 +0100 Subject: [PATCH 3759/9987] missing patchfile added, also building cpgplot stuff now --- .../p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb | 9 +- .../p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb | 9 +- .../p/pgplot/pgplot-compiler.patch | 265 ++++++++++++++++++ 3 files changed, 275 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb index 9aeb3466d7d..0c13be9dffb 100644 --- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb @@ -21,7 +21,7 @@ patches = ['pgplot-compiler.patch'] checksums = [ 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4', # pgplot522.tar.gz - 'ce098908b69f0a20f4f5e8efdab3779d9674f4ca6f0d4af7861bb0f541384ace', # pgplot-compiler.patch + '6166acd642c581e3f5631f6e03a1e27ac7cc3d5ed484380833bbc4aab1595278', # pgplot-compiler.patch ] builddependencies = [ @@ -33,16 +33,17 @@ dependencies = [ ('zlib', '1.2.11'), ] -cmds_map = [('.*', './makemake . linux g77_gcc && make ')] +cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')] files_to_copy = [ (['pgdemo*'], 'bin'), - (['libpgplot.a', 'libpgplot.so'], 'lib'), + (['libpgplot.a', 'libpgplot.so', 'libcpgplot.a', 'libcpgplot.so'], 'lib'), (['grfont.dat'], 'share'), + (['cpgplot.h'], 'include'), ] sanity_check_paths = { - 'files': ['lib/libpgplot.a'], + 'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb index c9d8a6d0a5a..3bb4f5e1e18 100644 --- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb @@ -21,7 +21,7 @@ patches = ['pgplot-compiler.patch'] checksums = [ 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4', # pgplot522.tar.gz - 'ce098908b69f0a20f4f5e8efdab3779d9674f4ca6f0d4af7861bb0f541384ace', # pgplot-compiler.patch + '6166acd642c581e3f5631f6e03a1e27ac7cc3d5ed484380833bbc4aab1595278', # pgplot-compiler.patch ] builddependencies = [ @@ -33,16 +33,17 @@ dependencies = [ ('zlib', '1.2.11'), ] -cmds_map = [('.*', './makemake . linux g77_gcc && make ')] +cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')] files_to_copy = [ (['pgdemo*'], 'bin'), - (['libpgplot.a', 'libpgplot.so'], 'lib'), + (['libpgplot.a', 'libpgplot.so', 'libcpgplot.a', 'libcpgplot.so'], 'lib'), (['grfont.dat'], 'share'), + (['cpgplot.h'], 'include'), ] sanity_check_paths = { - 'files': ['lib/libpgplot.a'], + 'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch b/easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch new file mode 100644 index 00000000000..58b62e780c4 --- /dev/null +++ b/easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch @@ -0,0 +1,265 @@ +Patch to make sure that gfortran can be used, also includes EasyBuild specific environment variables +Some of it is based on the Debian patches +Author: J. Sassmannshausen (ICL/UK) +diff --git a/pgplot.orig/drivers/pndriv.c b/pgplot/drivers/pndriv.c +index 2b2f87d..63fa246 100644 +--- a/pgplot.orig/drivers/pndriv.c ++++ b/pgplot/drivers/pndriv.c +@@ -222,7 +222,7 @@ static void write_image_file(DeviceData *dev) { + return; + } + +- if (setjmp(png_ptr->jmpbuf)) { /* not really sure what I'm doing here... */ ++ if (setjmp(png_jmpbuf(png_ptr))) { /* not really sure what I'm doing here... */ + fprintf(stderr,"%s: error in libpng while writing file %s, plotting disabled\n", png_ident, filename); + png_destroy_write_struct(&png_ptr,&info_ptr); + dev->error = true; +diff --git a/pgplot.orig/drivers.list b/pgplot/drivers.list +index 11108bb..b6ff758 100644 +--- a/pgplot.orig/drivers.list ++++ b/pgplot/drivers.list +@@ -3,48 +3,50 @@ + ! To configure PGPLOT, ensure that drivers you do not want are + ! commented out (place ! in column 1). N.B. Many device-drivers are + ! available on selected operating systems only. ++! Modified by Gopal Narayanan for debian Jul 6, 2001 + !------------------------------------------------------------------------------ + ! File Code Description Restrictions + ! BCDRIV 0 /BCANON Canon Laser printer (bitmap version), landscape + ! CADRIV 0 /CANON Canon Laser printer, LBP-8/A2, landscape + ! CCDRIV 0 /CCP DEC LJ250 Color Companion printer +-! CGDRIV 1 /CGM CGM metafile, indexed colour selection C +-! CGDRIV 2 /CGMD CGM metafile, direct colour selection C ++ CGDRIV 1 /CGM CGM metafile, indexed colour selection C ++ CGDRIV 2 /CGMD CGM metafile, direct colour selection C + ! CWDRIV 0 /CW6320 Gould/Bryans Colourwriter 6320 pen plotter Std F77 + ! EPDRIV 0 /EPSON Epson FX100 dot matrix printer + ! EXDRIV 1 /EXCL Talaris/EXCL printers, landscape + ! EXDRIV 2 /EXCL Talaris/EXCL printers, portrait + ! GCDRIV 0 /GENICOM Genicom 4410 dot-matrix printer, landscape + ! Caution: use of GIDRIV may require a license from Unisys: +-! GIDRIV 1 /GIF GIF-format file, landscape +-! GIDRIV 2 /VGIF GIF-format file, portrait +-! GLDRIV 1 /HPGL Hewlett-Packard HP-GL plotters, landscape Std F77 +-! GLDRIV 2 /VHPGL Hewlett-Packard HP-GL plotters, portrait Std F77 ++! Since Unisys patent has expired allowing now. ++ GIDRIV 1 /GIF GIF-format file, landscape ++ GIDRIV 2 /VGIF GIF-format file, portrait ++ GLDRIV 1 /HPGL Hewlett-Packard HP-GL plotters, landscape Std F77 ++ GLDRIV 2 /VHPGL Hewlett-Packard HP-GL plotters, portrait Std F77 + ! GODRIV 0 /GOC GOC Sigma T5670 terminal VMS + ! GVDRIV 0 /GVENICOM Genicom 4410 dot-matrix printer, portrait +-! HGDRIV 0 /HPGL2 Hewlett-Packard graphics language ++ HGDRIV 0 /HPGL2 Hewlett-Packard graphics language + ! HIDRIV 0 /HIDMP Houston Instruments HIDMP pen plotter + ! HJDRIV 0 /HJ Hewlett-Packard Desk/Laserjet printer +-! HPDRIV 0 /HP7221 Hewlett-Packard HP7221 pen plotter Std F77 ++ HPDRIV 0 /HP7221 Hewlett-Packard HP7221 pen plotter Std F77 + ! LADRIV 0 /LA50 Dec LA50 and other sixel printers + ! LJDRIV 0 /LJ Hewlett-Packard LaserJet printers VMS + ! LSDRIV 1 /LIPS2 Canon LaserShot printer (landscape) + ! LSDRIV 2 /VLIPS2 Canon LaserShot printer (portrait) + ! LNDRIV 0 /LN03 Dec LN03-PLUS Laser printer (landscape) VMS + ! LVDRIV 0 /LVN03 Dec LN03-PLUS Laser printer (portrait) VMS +-! LXDRIV 0 /LATEX LaTeX picture environment ++ LXDRIV 0 /LATEX LaTeX picture environment + ! MFDRIV 0 /FILE PGPLOT graphics metafile + ! NEDRIV 0 /NEXT Computers running NeXTstep operating system + NUDRIV 0 /NULL Null device (no output) Std F77 +-! PGDRIV 0 /PGMF PGPLOT metafile (new format, experimental) Std F77 +-! PNDRIV 1 /PNG Portable Network Graphics file C +-! PNDRIV 2 /TPNG Portable Network Graphics file - transparent background C ++ PGDRIV 0 /PGMF PGPLOT metafile (new format, experimental) Std F77 ++ PNDRIV 1 /PNG Portable Network Graphics file C ++ PNDRIV 2 /TPNG Portable Network Graphics file - transparent background C + ! PPDRIV 1 /PPM Portable Pixel Map file, landscape + ! PPDRIV 2 /VPPM Portable PIxel Map file, portrait +-! PSDRIV 1 /PS PostScript printers, monochrome, landscape Std F77 +-! PSDRIV 2 /VPS Postscript printers, monochrome, portrait Std F77 +-! PSDRIV 3 /CPS PostScript printers, color, landscape Std F77 +-! PSDRIV 4 /VCPS PostScript printers, color, portrait Std F77 ++ PSDRIV 1 /PS PostScript printers, monochrome, landscape Std F77 ++ PSDRIV 2 /VPS Postscript printers, monochrome, portrait Std F77 ++ PSDRIV 3 /CPS PostScript printers, color, landscape Std F77 ++ PSDRIV 4 /VCPS PostScript printers, color, portrait Std F77 + ! PXDRIV 0 /PRINTRONI Printronix P300 or P600 dot-matrix printer + ! QMDRIV 1 /QMS QUIC devices (QMS and Talaris), landscape Std F77 + ! QMDRIV 2 /VQMS QUIC devices (QMS and Talaris), portrait Std F77 +diff --git a/pgplot.orig/makemake b/pgplot/makemake +index e48455e..93b9985 100755 +--- a/pgplot.orig/makemake ++++ b/pgplot/makemake +@@ -658,6 +658,8 @@ CPGPLOT_LIB=$CPGPLOT_LIB + # + SHARED_LIB=$SHARED_LIB + SHARED_LD=$SHARED_LD ++SHARED_LD_PGPLOT_OPTS=$SHARED_LD_PGPLOT_OPTS ++SHARED_LD_CPGPLOT_OPTS=$SHARED_LD_CPGPLOT_OPTS + # + # The libraries that the shared PGPLOT library depends upon. + # This is for systems that allow one to specify what libraries +@@ -667,6 +669,7 @@ SHARED_LD=$SHARED_LD + # libraries when they link their executables. + # + SHARED_LIB_LIBS=$SHARED_LIB_LIBS ++SHARED_LIB_CPGPLOT_LIBS=$SHARED_LIB_CPGPLOT_LIBS + # + # Ranlib command if required + # +@@ -806,7 +809,8 @@ grexec.o: grexec.f + # libraries. + #----------------------------------------------------------------------- + +-lib : libpgplot.a $(SHARED_LIB) ++#lib : libpgplot.a $(SHARED_LIB) ++lib : libpgplot.a + + libpgplot.a : $(PG_ROUTINES) $(PG_NON_STANDARD) $(GR_ROUTINES) \ + $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) +@@ -816,6 +820,16 @@ libpgplot.a : $(PG_ROUTINES) $(PG_NON_STANDARD) $(GR_ROUTINES) \ + $(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq` + $(RANLIB) libpgplot.a + ++#shared: $(PG_ROUTINES) $(PG_NON_STANDARD) $(GR_ROUTINES) \ ++# $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) ++# $(SHARED_LD) ++ ++shared: $(PG_ROUTINES) $(PG_NON_STANDARD) \ ++ $(GR_ROUTINES) $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) ++ $(SHARED_LD) $(SHARED_LD_PGPLOT_OPTS) `ls $(PG_ROUTINES) \ ++ $(PG_NON_STANDARD) $(GR_ROUTINES) $(DISPATCH_ROUTINE) \ ++ $(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq` $(SHARED_LIB_LIBS) ++ + EOD + + # Emit the shared library dependency if requested. +@@ -824,7 +838,7 @@ if test -n "$SHARED_LIB" -a -n "$SHARED_LD"; then + cat >> makefile << \EOD + $(SHARED_LIB): $(PG_ROUTINES) $(PG_NON_STANDARD) \ + $(GR_ROUTINES) $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) +- $(SHARED_LD) `ls $(PG_ROUTINES) \ ++ $(SHARED_LD) $(SHARED_LD_PGPLOT_OPTS) `ls $(PG_ROUTINES) \ + $(PG_NON_STANDARD) $(GR_ROUTINES) $(DISPATCH_ROUTINE) \ + $(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq` $(SHARED_LIB_LIBS) + EOD +@@ -1019,13 +1033,14 @@ EOD + + cat >> makefile << \EOD + ++DEB_HOST_MULTIARCH=$(shell dpkg-architecture -qDEB_HOST_MULTIARCH) ++ + # Miscellaneous include files required by drivers + + griv00.o : $(DRVDIR)/gadef.h $(DRVDIR)/gmdef.h $(DRVDIR)/gphdef.h + grivas.o : $(DRVDIR)/gadef.h + grtv00.o : $(DRVDIR)/imdef.h + pgxwin.o : $(DRVDIR)/pgxwin.h +-pndriv.o : ./png.h ./pngconf.h ./zlib.h ./zconf.h + + x2driv.o figdisp_comm.o: $(DRVDIR)/commands.h + +@@ -1039,6 +1054,8 @@ cpg: libcpgplot.a cpgplot.h cpgdemo + @echo 'will be needed.' + @echo ' ' + ++cpg-shared: libcpgplot.so ++ + pgbind: $(SRC)/cpg/pgbind.c + $(CCOMPL) $(CFLAGC) $(SRC)/cpg/pgbind.c -o pgbind + +@@ -1050,6 +1067,13 @@ libcpgplot.a cpgplot.h: $(PG_SOURCE) pgbind + $(RANLIB) libcpgplot.a + rm -f cpg*.o + ++libcpgplot.so: $(PG_SOURCE) pgbind ++ ./pgbind $(PGBIND_FLAGS) -w $(PG_SOURCE) ++ $(CCOMPL) -c $(CFLAGC) cpg*.c ++ rm -f cpg*.c ++ $(SHARED_LD) $(SHARED_LD_CPGPLOT_OPTS) cpg*.o $(SHARED_LIB_CPGPLOT_LIBS) ++ rm -f cpg*.o ++ + cpgdemo: cpgplot.h $(SRC)/cpg/cpgdemo.c libcpgplot.a + $(CCOMPL) $(CFLAGD) -c -I. $(SRC)/cpg/cpgdemo.c + $(FCOMPL) -o cpgdemo cpgdemo.o $(CPGPLOT_LIB) $(LIBS) +diff --git a/pgplot.orig/sys_linux/g77_gcc.conf b/pgplot/sys_linux/g77_gcc.conf +index d6b73e6..b3905b0 100644 +--- a/pgplot.orig/sys_linux/g77_gcc.conf ++++ b/pgplot/sys_linux/g77_gcc.conf +@@ -1,11 +1,11 @@ +-# The GNU g77 FORTRAN compiler and Gnu gcc C compiler on an elf-system. ++# The GNU gfortran FORTRAN compiler and Gnu gcc C compiler on an elf-system. + #----------------------------------------------------------------------- + + # Optional: Needed by XWDRIV (/xwindow and /xserve) and + # X2DRIV (/xdisp and /figdisp). + # The arguments needed by the C compiler to locate X-window include files. + +- XINCL="-I/usr/X11R6/include" ++ XINCL="-I${EBROOTLIBPNG}/include -I${BROOTZLIB}/include" + + # Optional: Needed by XMDRIV (/xmotif). + # The arguments needed by the C compiler to locate Motif, Xt and +@@ -34,13 +34,13 @@ + # Mandatory. + # The FORTRAN compiler to use. + +- FCOMPL="g77" ++ FCOMPL="gfortran" + + # Mandatory. + # The FORTRAN compiler flags to use when compiling the pgplot library. + # (NB. makemake prepends -c to $FFLAGC where needed) + +- FFLAGC="-u -Wall -fPIC -O" ++ FFLAGC="-u -Wall -fPIC -O3 -std=legacy " + + # Mandatory. + # The FORTRAN compiler flags to use when compiling fortran demo programs. +@@ -57,12 +57,12 @@ + # Mandatory. + # The C compiler flags to use when compiling the pgplot library. + +- CFLAGC="-Wall -fPIC -DPG_PPU -O" ++ CFLAGC="-Wall -fPIC -DPG_PPU -O3" + + # Mandatory. + # The C compiler flags to use when compiling C demo programs. + +- CFLAGD="-Wall -O" ++ CFLAGD="-Wall -O3" + + # Optional: Only needed if the cpgplot library is to be compiled. + # The flags to use when running pgbind to create the C pgplot wrapper +@@ -74,7 +74,7 @@ + # The library-specification flags to use when linking normal pgplot + # demo programs. + +- LIBS="-L/usr/X11R6/lib -lX11" ++ LIBS="-L${EBROOTLIBPNG}/lib -lpng" + + # Optional: Needed by XMDRIV (/xmotif). + # The library-specification flags to use when linking motif +@@ -108,7 +108,11 @@ + # Optional: Needed if SHARED_LIB is set. + # How to create a shared library from a trailing list of object files. + +- SHARED_LD="gcc -shared -o $SHARED_LIB" ++ SHARED_LD_PGPLOT_OPTS="-o $SHARED_LIB -Wl,-soname,libpgplot.so.\$(VM)" ++ ++ SHARED_LD_CPGPLOT_OPTS="-o libcpgplot.so -Wl,-soname,libcpgplot.so.\$(VM)" ++ ++ SHARED_LD="gfortran -shared" + + # Optional: + # On systems such as Solaris 2.x, that allow specification of the +@@ -117,7 +121,9 @@ + # library-specification flags used to specify these libraries to + # $SHARED_LD + +- SHARED_LIB_LIBS="" ++ SHARED_LIB_LIBS="-L/usr/X11R6/lib -lX11 -lpng -lc -lgfortran" ++ ++ SHARED_LIB_CPGPLOT_LIBS="-L. -lpgplot" + + # Optional: + # Compiler name used on Next systems to compile objective-C files. From 30e8a89eee923bac081f83d47272d4c54f84ed69 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 12 May 2022 22:56:04 +0100 Subject: [PATCH 3760/9987] missing X11 added, shared libs removed as there is a problem --- .../easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb | 5 +++-- .../easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb index 0c13be9dffb..b95eada0090 100644 --- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb @@ -31,13 +31,14 @@ builddependencies = [ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), + ('X11', '20210518'), ] -cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')] +cmds_map = [('.*', './makemake . linux g77_gcc && make && make cpg')] files_to_copy = [ (['pgdemo*'], 'bin'), - (['libpgplot.a', 'libpgplot.so', 'libcpgplot.a', 'libcpgplot.so'], 'lib'), + (['libpgplot.a', 'libcpgplot.a'], 'lib'), (['grfont.dat'], 'share'), (['cpgplot.h'], 'include'), ] diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb index 3bb4f5e1e18..fcfae8351cd 100644 --- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb @@ -31,13 +31,14 @@ builddependencies = [ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), + ('X11', '20210802'), ] -cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')] +cmds_map = [('.*', './makemake . linux g77_gcc && make && make cpg')] files_to_copy = [ (['pgdemo*'], 'bin'), - (['libpgplot.a', 'libpgplot.so', 'libcpgplot.a', 'libcpgplot.so'], 'lib'), + (['libpgplot.a', 'libcpgplot.a'], 'lib'), (['grfont.dat'], 'share'), (['cpgplot.h'], 'include'), ] From 9687ec6af2b338ed3cb07d3693dd624a53036776 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 12 May 2022 23:31:47 +0100 Subject: [PATCH 3761/9987] adding easyconfigs: wcslib-7.11-GCC-11.2.0.eb --- .../w/wcslib/wcslib-7.11-GCC-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb b/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb new file mode 100644 index 00000000000..7a4add2a792 --- /dev/null +++ b/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb @@ -0,0 +1,43 @@ +# Contribution from Imperial College London (UK) +# Uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'wcslib' +version = '7.11' + +homepage = 'https://www.atnf.csiro.au/people/mcalabre/WCS/' +description = """The FITS "World Coordinate System" (WCS) standard defines keywords +and usage that provide for the description of astronomical coordinate systems in a +FITS image header.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.atnf.csiro.au/pub/software/wcslib/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['46befbfdf50cd4953896676a7d570094dc7661e2ae9677b092e7fb13cee3da5f'] + +builddependencies = [ + ('binutils', '2.37'), + ('M4', '1.4.19'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('CFITSIO', '3.49'), + ('pgplot', '5.2.2'), + ('X11', '20210802'), +] + +configure_cmd = './configure --with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include ' +configure_cmd += '--with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include ' + +sanity_check_paths = { + 'files': ['bin/wcsgrid', 'bin/wcsware', 'lib/libpgsbox-7.11.a', 'lib/libpgsbox.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +runtest = 'wcsgrid --help' + +moduleclass = 'geo' From 5fe98e0e97aa50eba0c9f769a1eea55be615f722 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 12 May 2022 23:49:06 +0100 Subject: [PATCH 3762/9987] sanity-check-command removed as it does not work as intended --- easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb b/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb index 7a4add2a792..8025066e463 100644 --- a/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb @@ -38,6 +38,4 @@ sanity_check_paths = { 'dirs': ['include'], } -runtest = 'wcsgrid --help' - moduleclass = 'geo' From 2546ce2bf9a10653a565f3d7ba2f1eda78c52fbe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 13 May 2022 01:49:21 +0200 Subject: [PATCH 3763/9987] adding easyconfigs: Schrodinger-2022-2.eb --- .../s/Schrodinger/Schrodinger-2022-2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-2.eb diff --git a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-2.eb b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-2.eb new file mode 100644 index 00000000000..6dff90c04f5 --- /dev/null +++ b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-2.eb @@ -0,0 +1,31 @@ +easyblock = 'PackedBinary' + +name = 'Schrodinger' +version = '2022-2' + +homepage = 'https://www.schrodinger.com/' +description = """ Schrodinger aims to provide integrated software solutions and services + that truly meet its customers needs. We want to empower researchers around the world to + achieve their goals of improving human health and quality of life through advanced computational + techniques that transform the way chemists design compounds and materials. """ + +toolchain = SYSTEM + +# Download from schrodinger.com +sources = ['%(name)s_Suites_%(version)s_Linux-x86_64.tar'] +checksums = ['98aafc0939fcbfdb7e2290ff3a20847fe3a6dc0c8af27a7bb3242d5f322ab52a'] + +install_cmd = 'cd %(builddir)s/%(name)s_Suites_%(version)s_Linux-x86_64 && ' +install_cmd += './INSTALL -d . -s %(installdir)s -k /usr/tmp -t %(installdir)s/thirdparty -b *' + +sanity_check_paths = { + 'files': ['desmond', 'maestro'], + 'dirs': [], +} + +modextravars = { + 'SCHROD_LICENSE_FILE': '$HOME/.schrodinger_license', + 'SCHRODINGER': '%(installdir)s', +} + +moduleclass = 'bio' From aefd100bc4d382c06fdbca138a82938c9ca2661f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 13 May 2022 09:12:04 +0200 Subject: [PATCH 3764/9987] fix interleave_test --- .../t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 2c715b9a427..7a84c1259e7 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -178,6 +178,7 @@ exts_list = [ 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', 'TensorFlow-2.7.1_fix_protobuf_error_message.patch', 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.7.1_fix_cpu_count.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -234,6 +235,8 @@ exts_list = [ '301ce21845987dc7868624880c0d85e60aa5491c5a0bae0f6ebc8db5727960a5', # TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', + # TensorFlow-2.7.1_fix_cpu_count.patch + '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698', ], }), ] From ea9c17d55b8252a939faaed5f725fdbba06f0956 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 13 May 2022 10:10:48 +0200 Subject: [PATCH 3765/9987] fix interleave_test --- .../TensorFlow-2.7.1_fix_cpu_count.patch | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix_cpu_count.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix_cpu_count.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix_cpu_count.patch new file mode 100644 index 00000000000..504c67136f5 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix_cpu_count.patch @@ -0,0 +1,25 @@ +Use len(os.sched_getaffinity(0)), which returns the number cores available to the job, +rather than multiprocessing.cpu_count(), which returns the total number of cores in the node, +and which causes the interleave_test to fail for less than 8 cores +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur tensorflow-2.7.1.orig/tensorflow/python/data/kernel_tests/interleave_test.py tensorflow-2.7.1/tensorflow/python/data/kernel_tests/interleave_test.py +--- tensorflow-2.7.1.orig/tensorflow/python/data/kernel_tests/interleave_test.py 2022-01-30 16:27:47.000000000 +0100 ++++ tensorflow-2.7.1/tensorflow/python/data/kernel_tests/interleave_test.py 2022-05-12 10:35:46.155364224 +0200 +@@ -59,13 +59,14 @@ + # interleaved. + open_iterators = [] + if cycle_length is None: ++ cpu_count = len(os.sched_getaffinity(0)) + # The logic here needs to match interleave C++ kernels. + if num_parallel_calls is None: +- cycle_length = multiprocessing.cpu_count() ++ cycle_length = cpu_count + elif num_parallel_calls == dataset_ops.AUTOTUNE: +- cycle_length = (multiprocessing.cpu_count() + 2) // 3 ++ cycle_length = (cpu_count + 2) // 3 + else: +- cycle_length = min(num_parallel_calls, multiprocessing.cpu_count()) ++ cycle_length = min(num_parallel_calls, cpu_count) + + for i in range(cycle_length): + if all_iterators: From 2391e5f18f155dfdc94200199b3cbdbbeff82123 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 13 May 2022 11:49:54 +0100 Subject: [PATCH 3766/9987] adding easyconfigs: casacore-3.4.0-foss-2021b.eb --- .../c/casacore/casacore-3.4.0-foss-2021b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb new file mode 100644 index 00000000000..8b35c61878f --- /dev/null +++ b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb @@ -0,0 +1,43 @@ +# Contribution from Imperial College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'casacore' +version = '3.4.0' + +homepage = 'https://github.com/casacore/casacore' +description = "A suite of C++ libraries for radio astronomy data processing." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/casacore/casacore/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '31f02ad2e26f29bab4a47a2a69e049d7bc511084a0b8263360e6157356f92ae1', # v3.4.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), +] + +dependencies = [ + ('CFITSIO', '3.49'), + ('wcslib', '7.11'), + ('HDF5', '1.12.1'), + ('SciPy-bundle', '2021.10'), + ('Boost.Python', '1.77.0'), + ('ncurses', '6.2'), +] + +configopts = ' -DBUILD_PYTHON3=ON -DBUILD_PYTHON=OFF -Wno-dev ' + +sanity_check_paths = { + 'files': [('lib/libcasa_casa.%s', 'lib/libcasa_mirlib.%s' % SHLIB_EXT, 'lib64/libcasa_ms.%s' % SHLIB_EXT)], + 'dirs': ['include/casacore'], +} + +moduleclass = 'lib' From f313241916b6feedd6ff849d155c7af6bb17f584 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 13 May 2022 14:33:15 +0200 Subject: [PATCH 3767/9987] Create Anaconda3-2022.05.eb --- .../a/Anaconda3/Anaconda3-2022.05.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.05.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.05.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.05.eb new file mode 100644 index 00000000000..94da2a52d26 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.05.eb @@ -0,0 +1,29 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, +# 2019.10, 2020.2, 2020.11, 2022.05 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2022.05' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +sources = ['%(name)s-%(version)s-Linux-%(arch)s.sh'] + +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': 'a7c0afe862f6ea19a596801fc138bde0463abcbce1b753e8d5c474b506a2db2d', + '%(name)s-%(version)s-Linux-ppc64le.sh': 'a50bf5bd26b5c5a2c24028c1aff6da2fa4d4586ca43ae3acdf7ffb9b50d7f282', + } +] + +moduleclass = 'lang' From 06a9b1b6e3b6ff0e7b9606207a836934e900ab7f Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 13 May 2022 19:07:42 +0200 Subject: [PATCH 3768/9987] Added sanity check command --- easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb b/easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb index 0660d58e047..888df763d0b 100644 --- a/easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb +++ b/easybuild/easyconfigs/g/gcloud/gcloud-382.0.0.eb @@ -19,4 +19,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = ["gcloud version"] + moduleclass = "tools" From 1ffa5b8d47834a6282ebd99d3766bb13f16d3380 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Mon, 16 May 2022 10:24:35 +0200 Subject: [PATCH 3769/9987] adding easyconfigs: OpenMM-7.7.0-foss-2021a.eb --- .../o/OpenMM/OpenMM-7.7.0-foss-2021a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb new file mode 100644 index 00000000000..5f7e08ce1ce --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb @@ -0,0 +1,69 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.7.0' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] +checksums = [ + '51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25', # 7.7.0.tar.gz + '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('CUDA', '11.2.1', '', True), + ('SWIG', '4.0.2'), +] + +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +#pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" +# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m openmm.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 209d9f7fcc66f29bcda3e08b9fd3e1c65f2ee2c7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 16 May 2022 12:47:09 +0200 Subject: [PATCH 3770/9987] fix extension name --- .../PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb index abd315e1aba..5d1e8bb87bc 100644 --- a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb @@ -18,7 +18,7 @@ dependencies = [ ] exts_list = [ - ('pytorch-lightning', version, { + ('pytorch-ignite', version, { 'modulename': 'ignite', 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/pytorch/ignite/archive'], From 10a73a8c96914d292cc0f15f2d6f3db89d1ae5e2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 May 2022 12:14:52 +0100 Subject: [PATCH 3771/9987] bump libfabric to 1.15.1 --- ....eb => libfabric-1.15.1-GCCcore-11.3.0.eb} | 15 +++------ .../o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb | 32 +++++++++++++++++++ .../p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb | 2 +- 3 files changed, 38 insertions(+), 11 deletions(-) rename easybuild/easyconfigs/l/libfabric/{libfabric-1.15.0-GCCcore-11.3.0.eb => libfabric-1.15.1-GCCcore-11.3.0.eb} (78%) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb similarity index 78% rename from easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb index a15a4635217..aa43321ea8d 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libfabric' -version = '1.15.0' +version = '1.15.1' homepage = 'https://ofiwg.github.io/libfabric/' description = """ @@ -15,16 +15,11 @@ often integrated directly into libfabric. toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -# 1.15.0 release tarball is missing prov/psm3/VERSION, see: -# https://github.com/ofiwg/libfabric/issues/7735 -# https://github.com/ofiwg/libfabric/issues/7042 -# and build files need to be regenerated to fix aclocal missing error -github_account = 'ofiwg' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/ofiwg/libfabric/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] patches = ['%(name)s-1.12.1_disable-psm3-avx-config.patch'] checksums = [ - '6eb54599dd986acbe72329538b70849fd098ec405f28f7aaaef765be3efebb3d', # v1.15.0.tar.gz + 'cafa3005a9dc86064de179b0af4798ad30b46b2f862fe0268db03d13943e10cd', # libfabric-1.15.1.tar.bz2 # libfabric-1.12.1_disable-psm3-avx-config.patch '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', ] @@ -41,7 +36,7 @@ dependencies = [ osdependencies = [OS_PKG_IBVERBS_DEV] -# Regenerate build files +# Regenerate build files to pick up psm3-axv-config patch preconfigopts = "autoreconf -if &&" # Disable deprecated "sockets" provider diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb new file mode 100644 index 00000000000..390744e2e43 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb @@ -0,0 +1,32 @@ +name = 'OpenMPI' +version = '4.1.4rc1' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['46169edd9cf8366608684e5c6a342650b2393d46c9f9a380add8e09f1f8001de'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('hwloc', '2.7.1'), + ('libevent', '2.1.12'), + ('UCX', '1.12.1'), + ('libfabric', '1.15.1'), + ('PMIx', '4.1.2'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb index fa43b710c05..64180caade0 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('libevent', '2.1.12'), ('zlib', '1.2.12'), ('hwloc', '2.7.1'), - ('libfabric', '1.15.0'), + ('libfabric', '1.15.1'), ] configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' From 84a056e025672816c9afdb381eb72f1eaa37b0b6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 May 2022 13:05:59 +0100 Subject: [PATCH 3772/9987] use autogen.sh instead of directly running autoreconf --- .../easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb index aa43321ea8d..21992b21bf9 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb @@ -37,7 +37,7 @@ dependencies = [ osdependencies = [OS_PKG_IBVERBS_DEV] # Regenerate build files to pick up psm3-axv-config patch -preconfigopts = "autoreconf -if &&" +preconfigopts = "./autogen.sh &&" # Disable deprecated "sockets" provider configopts = "--disable-sockets " From 3f3a7f39211c87da18c1cc4f12fb277257a34db9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 May 2022 13:37:38 +0100 Subject: [PATCH 3773/9987] add patch to disable OPX for unsupported architectures --- .../libfabric-1.15.1-GCCcore-11.3.0.eb | 7 ++- ...ic-1.15.1_disable-OPX-if-unsupported.patch | 55 +++++++++++++++++++ 2 files changed, 61 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.15.1_disable-OPX-if-unsupported.patch diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb index 21992b21bf9..f2d512f14d0 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1-GCCcore-11.3.0.eb @@ -17,11 +17,16 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/ofiwg/libfabric/releases/download/v%(version)s'] sources = [SOURCE_TAR_BZ2] -patches = ['%(name)s-1.12.1_disable-psm3-avx-config.patch'] +patches = [ + '%(name)s-1.12.1_disable-psm3-avx-config.patch', + '%(name)s-1.15.1_disable-OPX-if-unsupported.patch', +] checksums = [ 'cafa3005a9dc86064de179b0af4798ad30b46b2f862fe0268db03d13943e10cd', # libfabric-1.15.1.tar.bz2 # libfabric-1.12.1_disable-psm3-avx-config.patch '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a', + # libfabric-1.15.1_disable-OPX-if-unsupported.patch + 'a1af5b985209acf447760f98f852c0c5359b1731fa23b1b893d8cc816a441850', ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1_disable-OPX-if-unsupported.patch b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1_disable-OPX-if-unsupported.patch new file mode 100644 index 00000000000..c177e1de66d --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.15.1_disable-OPX-if-unsupported.patch @@ -0,0 +1,55 @@ +Based on https://github.com/ofiwg/libfabric/pull/7583 by mwheinz +Updated for release version 1.15.1 by Jasper Grimm +---------------------------------------------------------------- +diff -Nru libfabric-1.15.1.orig/prov/opx/configure.m4 b/prov/opx/configure.m4 +--- libfabric-1.15.1.orig/prov/opx/configure.m4 2022-05-16 13:14:58.000000000 +0100 ++++ b/prov/opx/configure.m4 2022-05-16 13:25:28.000000000 +0100 +@@ -44,7 +44,13 @@ + opx_happy=0 + opx_direct=0 + +- AS_IF([test x"$enable_opx" != x"no"],[ ++ ++ dnl OPX hardware is not supported for MacOS or FreeBSD, ++ dnl and is not supported for non-x86 processors. ++ AS_IF([test "x$macos" = "x1"],[opx_happy=0], ++ [test "x$freebsd" = "x1"],[opx_happy=0], ++ [test x$host_cpu != xx86_64],[opx_happy=0], ++ [test x"$enable_opx" != x"no"],[ + + AC_MSG_CHECKING([for opx provider]) + +@@ -91,6 +97,7 @@ + AC_SUBST(opx_reliability, [$OPX_RELIABILITY]) + AC_DEFINE_UNQUOTED(OPX_RELIABILITY, [$OPX_RELIABILITY], [fabric direct reliability]) + ++ opx_happy=1 + FI_CHECK_PACKAGE([opx_uuid], + [uuid/uuid.h], + [uuid], +@@ -98,14 +105,19 @@ + [], + [], + [], +- [opx_happy=1], ++ [], ++ [opx_happy=0]) ++ FI_CHECK_PACKAGE([opx_numa], ++ [numa.h], ++ [numa], ++ [numa_node_of_cpu], ++ [], ++ [], ++ [], ++ [], + [opx_happy=0]) + +- dnl OPX hardware is not available for MacOS or FreeBSD. +- AS_IF([test "x$macos" = "x1"],[opx_happy=0],[]) +- AS_IF([test "x$freebsd" = "x1"],[opx_happy=0],[]) +- +- AC_CHECK_DECL([HAVE_ATOMICS], ++ AC_CHECK_DECL([HAVE_ATOMICS], + [], + [cc_version=`$CC --version | head -n1` + AC_MSG_WARN(["$cc_version" doesn't support native atomics. Disabling OPX provider.]) From 30aae942236c77d6a5394cd468f866e888d2d213 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 16 May 2022 15:40:53 +0200 Subject: [PATCH 3774/9987] Added Redis dependency --- easybuild/easyconfigs/r/redis-py/redis-py-4.3.1-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-4.3.1-foss-2021a.eb b/easybuild/easyconfigs/r/redis-py/redis-py-4.3.1-foss-2021a.eb index 64dde617242..2f495d612cc 100644 --- a/easybuild/easyconfigs/r/redis-py/redis-py-4.3.1-foss-2021a.eb +++ b/easybuild/easyconfigs/r/redis-py/redis-py-4.3.1-foss-2021a.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), ('typing-extensions', '3.10.0.0'), + ('Redis', '6.2.6'), ] use_pip = True From 8ae1a5b30510763dc8884f20ee7f142125251ff9 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 16 May 2022 15:59:57 +0200 Subject: [PATCH 3775/9987] adding easyconfigs: smooth-topk-1.0-20210817-foss-2021a.eb --- .../smooth-topk-1.0-20210817-foss-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb new file mode 100644 index 00000000000..738922df6f1 --- /dev/null +++ b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb @@ -0,0 +1,40 @@ +easyblock = "PythonBundle" + +name = "smooth-topk" +version = "1.0-20210817" +local_commit = "12c1645f187e2fa0c05f47bf1fe48864d4bd2707" + +homepage = "https://github.com/oval-group/smooth-topk" +description = "Smooth Loss Functions for Deep Top-k Classification" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('tqdm', '4.61.2'), + ('PyTorch', '1.10.0'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('logger', '1.4', { + 'checksums': ['4ecac57133c6376fa215f0fe6b4dc4d60e4d1ad8be005cab4e8a702df682f8b3'], + }), + ('torchvision', '0.2.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['b4aadc07407c37542b94e38f710cfee6e53bb8e8633418094d476c5e417cbc80'], + }), + (name, version, { + 'modulename': 'topk', + 'source_urls': ['https://github.com/oval-group/smooth-topk/archive/'], + 'sources': ['%s.tar.gz' % local_commit], + 'checksums': ['ccba089b155c196bb43ab522b5ae00a58d332d856c2ec83b9635cab5eae62be5'], + }), +] From 842cbf1e041be888419207165ae2b966da1f83e8 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 16 May 2022 15:38:54 +0100 Subject: [PATCH 3776/9987] shared libs created, EC linted, name changed to upper-cases --- .../PGPLOT-5.2.2-GCCcore-10.3.0.eb} | 18 ++++++++++++------ .../PGPLOT-5.2.2-GCCcore-11.2.0.eb} | 18 ++++++++++++------ .../pgplot-compiler-pgplot522.patch} | 4 ++-- 3 files changed, 26 insertions(+), 14 deletions(-) rename easybuild/easyconfigs/p/{pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb => PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb} (66%) rename easybuild/easyconfigs/p/{pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb => PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb} (66%) rename easybuild/easyconfigs/p/{pgplot/pgplot-compiler.patch => PGPLOT/pgplot-compiler-pgplot522.patch} (98%) diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb similarity index 66% rename from easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb index b95eada0090..505de914edf 100644 --- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CmdCp' -name = 'pgplot' +name = 'PGPLOT' version = '5.2.2' homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/' @@ -16,12 +16,12 @@ can be directed to the appropriate device at run time.""" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/'] -sources = ['%%(name)s%s.tar.gz' % version.replace('.', '')] -patches = ['pgplot-compiler.patch'] +sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')] +patches = ['pgplot-compiler-pgplot522.patch'] checksums = [ 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4', # pgplot522.tar.gz - '6166acd642c581e3f5631f6e03a1e27ac7cc3d5ed484380833bbc4aab1595278', # pgplot-compiler.patch + 'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec', # pgplot-compiler-pgplot522.patch ] builddependencies = [ @@ -34,15 +34,21 @@ dependencies = [ ('X11', '20210518'), ] -cmds_map = [('.*', './makemake . linux g77_gcc && make && make cpg')] +cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')] files_to_copy = [ (['pgdemo*'], 'bin'), - (['libpgplot.a', 'libcpgplot.a'], 'lib'), + (['libpgplot.*', 'libcpgplot.*'], 'lib'), (['grfont.dat'], 'share'), (['cpgplot.h'], 'include'), ] +postinstallcmds = [ + # create symlinks + "cd %(installdir)s/lib && ln -s libcpgplot.so.5.2.2 libcpgplot.so.5 ; ln -s libcpgplot.so.5.2.2 libcpgplot.so && " + " ln -s libpgplot.so.5.2.2 libpgplot.so.5 ; ln -s libpgplot.so.5.2.2 libpgplot.so" +] + sanity_check_paths = { 'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'], 'dirs': [] diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb similarity index 66% rename from easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb index fcfae8351cd..8bf72fe23f5 100644 --- a/easybuild/easyconfigs/p/pgplot/pgplot-5.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CmdCp' -name = 'pgplot' +name = 'PGPLOT' version = '5.2.2' homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/' @@ -16,12 +16,12 @@ can be directed to the appropriate device at run time.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/'] -sources = ['%%(name)s%s.tar.gz' % version.replace('.', '')] -patches = ['pgplot-compiler.patch'] +sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')] +patches = ['pgplot-compiler-pgplot522.patch'] checksums = [ 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4', # pgplot522.tar.gz - '6166acd642c581e3f5631f6e03a1e27ac7cc3d5ed484380833bbc4aab1595278', # pgplot-compiler.patch + 'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec', # pgplot-compiler-pgplot522.patch ] builddependencies = [ @@ -34,15 +34,21 @@ dependencies = [ ('X11', '20210802'), ] -cmds_map = [('.*', './makemake . linux g77_gcc && make && make cpg')] +cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')] files_to_copy = [ (['pgdemo*'], 'bin'), - (['libpgplot.a', 'libcpgplot.a'], 'lib'), + (['libpgplot.*', 'libcpgplot.*'], 'lib'), (['grfont.dat'], 'share'), (['cpgplot.h'], 'include'), ] +postinstallcmds = [ + # create symlinks + "cd %(installdir)s/lib && ln -s libcpgplot.so.5.2.2 libcpgplot.so.5 ; ln -s libcpgplot.so.5.2.2 libcpgplot.so && " + " ln -s libpgplot.so.5.2.2 libpgplot.so.5 ; ln -s libpgplot.so.5.2.2 libpgplot.so" +] + sanity_check_paths = { 'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'], 'dirs': [] diff --git a/easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch b/easybuild/easyconfigs/p/PGPLOT/pgplot-compiler-pgplot522.patch similarity index 98% rename from easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch rename to easybuild/easyconfigs/p/PGPLOT/pgplot-compiler-pgplot522.patch index 58b62e780c4..d8073c05f6f 100644 --- a/easybuild/easyconfigs/p/pgplot/pgplot-compiler.patch +++ b/easybuild/easyconfigs/p/PGPLOT/pgplot-compiler-pgplot522.patch @@ -244,9 +244,9 @@ index d6b73e6..b3905b0 100644 # How to create a shared library from a trailing list of object files. - SHARED_LD="gcc -shared -o $SHARED_LIB" -+ SHARED_LD_PGPLOT_OPTS="-o $SHARED_LIB -Wl,-soname,libpgplot.so.\$(VM)" ++ SHARED_LD_PGPLOT_OPTS="-o $SHARED_LIB.5.2.2 -Wl,-soname,libpgplot.so.5.2.2" + -+ SHARED_LD_CPGPLOT_OPTS="-o libcpgplot.so -Wl,-soname,libcpgplot.so.\$(VM)" ++ SHARED_LD_CPGPLOT_OPTS="-o libcpgplot.so.5.2.2 -Wl,-soname,libcpgplot.so.5.2.2" + + SHARED_LD="gfortran -shared" From a92b0043c1075f8b5605a8b7ae7721db363cb115 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Mon, 16 May 2022 16:45:11 +0200 Subject: [PATCH 3777/9987] Update cuda version --- easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb index 5f7e08ce1ce..6221e22818b 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb @@ -34,7 +34,7 @@ separate_build_dir = True dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), - ('CUDA', '11.2.1', '', True), + ('CUDA', '11.3.1', '', True), ('SWIG', '4.0.2'), ] From be28de92db8d3365ed68913525c8f0312d279159 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 16 May 2022 16:08:28 +0100 Subject: [PATCH 3778/9987] PGPLOT name updated, configopts used instead of configure_cmd, name changed to upper case and source-name updated --- .../WCSLIB-7.11-GCC-11.2.0.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/w/{wcslib/wcslib-7.11-GCC-11.2.0.eb => WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb} (76%) diff --git a/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb similarity index 76% rename from easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb rename to easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb index 8025066e463..782f085864d 100644 --- a/easybuild/easyconfigs/w/wcslib/wcslib-7.11-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' -name = 'wcslib' +name = 'WCSLIB' version = '7.11' homepage = 'https://www.atnf.csiro.au/people/mcalabre/WCS/' @@ -15,7 +15,7 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} toolchainopts = {'pic': True} source_urls = ['ftp://ftp.atnf.csiro.au/pub/software/wcslib/'] -sources = ['%(name)s-%(version)s.tar.bz2'] +sources = [SOURCELOWER_TAR_BZ2] checksums = ['46befbfdf50cd4953896676a7d570094dc7661e2ae9677b092e7fb13cee3da5f'] builddependencies = [ @@ -26,12 +26,12 @@ builddependencies = [ dependencies = [ ('CFITSIO', '3.49'), - ('pgplot', '5.2.2'), + ('PGPLOT', '5.2.2'), ('X11', '20210802'), ] -configure_cmd = './configure --with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include ' -configure_cmd += '--with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include ' +configopts = '--with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include ' +configopts += '--with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include ' sanity_check_paths = { 'files': ['bin/wcsgrid', 'bin/wcsware', 'lib/libpgsbox-7.11.a', 'lib/libpgsbox.%s' % SHLIB_EXT], From 34716dd9ab1db7ddc7c4cba2a1b63661d2e95eaa Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 16 May 2022 16:32:25 +0100 Subject: [PATCH 3779/9987] wcslib changed to WCSLIB --- easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb index 8b35c61878f..a2ee8e062e5 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb @@ -26,7 +26,7 @@ builddependencies = [ dependencies = [ ('CFITSIO', '3.49'), - ('wcslib', '7.11'), + ('WCSLIB', '7.11'), ('HDF5', '1.12.1'), ('SciPy-bundle', '2021.10'), ('Boost.Python', '1.77.0'), From d62cddeb56279acd1711cd5eb9072d60435fd54e Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Mon, 16 May 2022 22:43:12 +0200 Subject: [PATCH 3780/9987] Update CellRanger-ATAC-2.1.0.eb --- .../easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.1.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.1.0.eb b/easybuild/easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.1.0.eb index e36d6f03c90..1df5c99a7da 100644 --- a/easybuild/easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.1.0.eb +++ b/easybuild/easyconfigs/c/CellRanger-ATAC/CellRanger-ATAC-2.1.0.eb @@ -15,7 +15,7 @@ toolchain = SYSTEM # Download manually from https://support.10xgenomics.com/single-cell-atac/software/downloads/latest sources = [SOURCELOWER_TAR_GZ] -checksums = ['3f44ba66ae789c2ab03f9c380a6718ca'] +checksums = ['0278f1cf7a27ec9cef6b39d674f0b0633d1f0989d3582e7a64c431c029a484c4'] keepsymlinks = True @@ -26,4 +26,4 @@ sanity_check_paths = { sanity_check_commands = ["cellranger-atac testrun --id=tiny"] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 5493d3d87bd39e25e91f91ded70fe918e425c875 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 16 May 2022 17:40:08 -0700 Subject: [PATCH 3781/9987] Google Cloud Utils --- .../g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb | 116 ++++++++++++++++++ 1 file changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..33aa81c24e0 --- /dev/null +++ b/easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb @@ -0,0 +1,116 @@ + +# easybuild easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Center - Seattle Washington - US +# +easyblock = 'PythonBundle' + +name = 'gsutil' +version = '5.10' + +homepage = 'https://cloud.google.com/storage/docs/gsutil' +description = """gsutil is a Python application that lets you access Cloud Storage from the command line.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('Rust', '1.54.0'), # required for setuptools-rust, which is needed for cryptography +] + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('typing-extensions', '4.2.0', { + 'source_tmpl': 'typing_extensions-4.2.0.tar.gz', + 'checksums': ['f1c24655a0da0d1b67f07e17a5e6b2a105894e6824b92096378bb3668ef02376'], + }), + ('importlib-metadata', '4.11.3', { + 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', + 'checksums': ['ea4c597ebf37142f827b8f39299579e31685c31d3a438b59f469406afd0f2539'], + }), + ('argcomplete', '2.0.0', { + 'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'], + }), + ('crcmod', '1.7', { + 'checksums': ['dc7051a0db5f2bd48665a990d3ec1cc305a466a77358ca4492826f41f283601e'], + }), + ('monotonic', '1.6', { + 'checksums': ['3a55207bcfed53ddd5c5bae174524062935efed17792e9de2ad0205ce9ad63f7'], + }), + ('fasteners', '0.17.3', { + 'checksums': ['a9a42a208573d4074c77d041447336cf4e3c1389a256fd3e113ef59cf29b7980'], + }), + ('rsa', '4.7.2', { + 'checksums': ['9d689e6ca1b3038bc82bf8d23e944b6b6037bc02301a574935b2dd946e0353b9'], + }), + ('gcs-oauth2-boto-plugin', '3.0', { + 'modulename': 'gcs_oauth2_boto_plugin', + 'checksums': ['f4120b08b7f8d32904674c98f07d4caf4083a58343c0c0fa0016e0f0254dfe31'], + }), + ('httplib2', '0.20.4', { + 'checksums': ['58a98e45b4b1a48273073f905d2961666ecf0fbac4250ea5b47aef259eb5c585'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('oauth2client', '4.1.3', { + 'checksums': ['d486741e451287f69568a4d26d70d9acd73a2bbfa275746c535b4209891cccc6'], + }), + ('google-apitools', '0.5.32', { + 'modulename': 'apitools', + 'checksums': ['c3763e52289f61e21c41d5531e20fbda9cc8484a088b8686fd460770db8bad13'], + }), + ('pyu2f', '0.1.5', { + 'checksums': ['a3caa3a11842fc7d5746376f37195e6af5f17c0a15737538bb1cebf656fb306b'], + }), + ('cachetools', '5.1.0', { + 'checksums': ['8b3b8fa53f564762e5b221e9896798951e7f915513abf2ba072ce0f07f3f5a98'], + }), + ('google-auth', '2.6.6', { + 'modulename': 'google.auth', + 'checksums': ['1ba4938e032b73deb51e59c4656a00e0939cf0b1112575099f136babb4563312'], + }), + ('google-reauth', '0.1.1', { + 'modulename': 'google_reauth', + 'checksums': ['f9f6852a55c2c5453d581cd01f3d1278e86147c03d008409800390a834235892'], + }), + ('cffi', '1.15.0', { + 'checksums': ['920f0d66a896c2d99f0adbb391f990a84091179542c205fa53ce5787aff87954'], + }), + ('cryptography', '37.0.2', { + 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", + 'checksums': ['f224ad253cc9cea7568f49077007d2263efa57396a2f2f78114066fd54b5c68e'], + }), + ('pyOpenSSL', '22.0.0', { + 'modulename': 'OpenSSL', + 'checksums': ['660b1b1425aac4a1bea1d94168a85d99f0b3144c869dd4390d27629d0087f1bf'], + }), + ('retry_decorator', '1.1.1', { + 'checksums': ['e1e8ad02e518fe11073f2ea7d80b6b8be19daa27a60a1838aff7c731ddcf2ebe'], + }), + ('SocksiPy-branch', '1.01', { + 'modulename': 'socks', + 'checksums': ['17a95060e28c3b9038a9b8c1865c54f8c1c5bef15d561bf777c9bbf3c80e8406'], + }), + ('boto', '2.49.0', { + 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], + }), + (name, version, { + 'modulename': 'gslib', + 'checksums': ['21a02310b425072d3bd580c675b1af48bb30c0f4d1b7b2427893cf70b216387e'], + }), +] + +sanity_check_commands = ['gsutil help'] + +moduleclass = 'tools' From 25779b3b86afd212bbb1da13990930563f2cba22 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 17 May 2022 11:06:50 +0200 Subject: [PATCH 3782/9987] adding easyconfigs: neptune-client-0.16.2-foss-2021a.eb --- .../neptune-client-0.16.2-foss-2021a.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2021a.eb b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2021a.eb new file mode 100644 index 00000000000..a46592bd95a --- /dev/null +++ b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2021a.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'neptune-client' +version = '0.16.2' + +homepage = 'https://docs.neptune.ai' +description = """ +Neptune is an experiment tracking hub that brings organization and collaboration to your data science team. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('GitPython', '3.1.18'), + ('Pillow-SIMD', '8.2.0'), + ('PyYAML', '5.4.1'), + ('typing-extensions', '3.10.0.0'), + ('boto3', '1.20.13'), +] + +use_pip = True + +exts_list = [ + ('monotonic', '1.6', { + 'checksums': ['3a55207bcfed53ddd5c5bae174524062935efed17792e9de2ad0205ce9ad63f7'], + }), + ('swagger-spec-validator', '2.7.4', { + 'checksums': ['2aee5e1fc0503be9f8299378b10c92169572781573c6de3315e831fd0559ba73'], + }), + ('jsonref', '0.2', { + 'checksums': ['f3c45b121cf6257eafabdc3a8008763aed1cd7da06dbabc59a9e4d2a5e4e6697'], + }), + ('bravado-core', '5.17.0', { + 'checksums': ['b3b06ae86d3c80de5694340e55df7c9097857ff965b76642979e2a961f332abf'], + }), + ('bravado', '11.0.3', { + 'checksums': ['1bb6ef75d84140c851fffe6420baaee5037d840070cfe11d60913be6ab8e0530'], + }), + ('PyJWT', '2.3.0', { + 'modulename': 'jwt', + 'checksums': ['b888b4d56f06f6dcd777210c334e69c737be74755d3e5e9ee3fe67dc18a0ee41'], + }), + ('blinker', '1.4', { + 'checksums': ['471aee25f3992bd325afa3772f1063dbdbbca947a041b8b89466dc00d606f8b6'], + }), + ('oauthlib', '3.1.1', { + 'checksums': ['8f0215fcc533dd8dd1bee6f4c412d4f0cd7297307d43ac61666389e3bc3198a3'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('websocket-client', '0.59.0', { + 'modulename': 'websocket', + 'checksums': ['d376bd60eace9d437ab6d7ee16f4ab4e821c9dae591e1b783c58ebd8aaf80c5c'], + }), + (name, version, { + 'modulename': 'neptune', + 'checksums': ['7e5e0261f3ce486f45e3272c5b5e3d563f0765a921bcda159b002e70175a553b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 4741ca68dcb1af72fd4729179fd724d69af6a5dc Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 17 May 2022 16:34:05 +0100 Subject: [PATCH 3783/9987] adding easyconfigs: MUMPS-5.5.0-foss-2021a-metis.eb and patches: MUMPS-5.5.0_shared-mumps.patch, MUMPS-5.5.0_shared-pord.patch --- .../m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb | 35 +++++++++++ .../m/MUMPS/MUMPS-5.5.0_shared-mumps.patch | 62 +++++++++++++++++++ .../m/MUMPS/MUMPS-5.5.0_shared-pord.patch | 44 +++++++++++++ 3 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0_shared-mumps.patch create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0_shared-pord.patch diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb new file mode 100644 index 00000000000..1b9876029cc --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb @@ -0,0 +1,35 @@ +name = 'MUMPS' +version = '5.5.0' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + 'e54d17c5e42a36c40607a03279e0704d239d71d38503aab68ef3bfe0a9a79c13', # MUMPS_5.5.0.tar.gz + 'a21b5c84125dceaf015a54d6d1dea61cb0c93b24130ba5a7d5a2cdf83de5f197', # MUMPS-5.5.0_shared-pord.patch + '7c597d2696dbe48c0a964e332af7e86b2c98daf643ba588d6bd5f2f4864ad015', # MUMPS-5.5.0_shared-mumps.patch +] + +dependencies = [ + ('SCOTCH', '6.1.0'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0_shared-mumps.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0_shared-mumps.patch new file mode 100644 index 00000000000..922d9ceb5d1 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0_shared-mumps.patch @@ -0,0 +1,62 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared.patch +Author: micketeer@gmail.com +Updatd to version 5.5.0: J. Sassmannshausen/ICL (UK) +diff --git a/MUMPS_5.5.0.orig/src/Makefile b/MUMPS_5.5.0/src/Makefile +index 771aebd..1f2d93a 100644 +--- a/MUMPS_5.5.0.orig/src/Makefile ++++ b/MUMPS_5.5.0/src/Makefile +@@ -15,18 +15,23 @@ all: $(incdir)/mumps_int_def.h libcommon s d c z + + libcommon: $(incdir)/mumps_int_def.h + $(MAKE) $(libdir)/libmumps_common$(PLAT)$(LIBEXT) ++ $(MAKE) $(libdir)/libmumps_common$(PLAT).so + + s: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT).so + + d: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT).so + + c: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT).so + + z: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT).so + + + # Rules for shared libraries +@@ -222,6 +227,14 @@ $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT_SHARED): $(OBJS_MOD) $(OBJS_OTHER) + $(FC) $(OPTL) -shared $(OBJS_MOD) $(OBJS_OTHER) -L$(libdir) $(LORDERINGS) $(LIBS) $(LIBOTHERS) -lmumps_common$(PLAT) -o $@ $(RPATH_OPT) + + ++$(libdir)/libmumps_common$(PLAT).so: $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) ++ $(FC) -shared $^ -Wl,-soname,libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) $(LORDERINGS) -lpthread $(MUMPS_LIBF77) $(MPIFLIB) $(MPICLIB) $(METISLIB) -o $(libdir)/libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libmumps_common$(PLAT)-$(SONAME_VERSION).so $@ ++ ++$(libdir)/lib$(ARITH)mumps$(PLAT).so: $(OBJS_MOD) $(OBJS_OTHER) ++ $(FC) -shared $^ -Wl,-soname,lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) -lmumps_common$(PLAT) -lpthread $(MUMPS_LIBF77) $(LORDERINGS) $(MPIFLIB) $(METISLIB) $(SCALAP) -o $(libdir)/lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $@ ++ + # Dependencies between modules: + # i) arithmetic-dependent modules: + $(ARITH)ana_aux.o: $(ARITH)mumps_struc_def.o \ +@@ -435,12 +448,14 @@ $(OBJS_OTHER):$(OBJS_COMMON_MOD) $(OBJS_MOD) + .SUFFIXES: .c .F .o + .F.o: + $(FC) $(OPTF) $(FPIC) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -c $*.F $(OUTF)$*.o ++ $(FC) $(OPTF) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -fPIC -c $*.F $(OUTF)$*.o + .c.o: + $(CC) $(OPTC) $(FPIC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -c $*.c $(OUTC)$*.o ++ $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -fPIC -c $*.c $(OUTC)$*.o + + $(ARITH)mumps_c.o: mumps_c.c + $(CC) $(OPTC) $(FPIC) -I../include $(INCS) $(CDEFS) -DMUMPS_ARITH=MUMPS_ARITH_$(ARITH) \ +- $(IORDERINGSC) $(ORDERINGSC) -c mumps_c.c $(OUTC)$@ ++ $(IORDERINGSC) $(ORDERINGSC) -fPIC -c mumps_c.c $(OUTC)$@ + + clean: + $(RM) *.o *.mod $(incdir)/mumps_int_def.h diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0_shared-pord.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0_shared-pord.patch new file mode 100644 index 00000000000..c23f1c49387 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0_shared-pord.patch @@ -0,0 +1,44 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared.patch +Author: micketeer@gmail.com +Updatd to version 5.5.0: J. Sassmannshausen/ICL (UK) +diff --git a/MUMPS_5.5.0.orig/Makefile b/MUMPS_5.5.0/Makefile +index 59d74d7..0ed4414 100644 +--- a/MUMPS_5.5.0.orig/Makefile ++++ b/MUMPS_5.5.0/Makefile +@@ -65,7 +65,7 @@ Makefile.inc: + + include Makefile.inc + +-prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) ++prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT).so + + prerequisitesshared: Makefile.inc $(LIBSEQNEEDED)sharedlibseq $(libdir)/libpord$(PLAT)$(LIBEXT_SHARED) + +@@ -106,6 +106,12 @@ $(libdir)/libpord$(PLAT)$(LIBEXT_SHARED): + + + ++$(libdir)/libpord$(PLAT).so: ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cd $(LPORDDIR); make CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" ARFUNCT= RANLIB="$(RANLIB)" libpord$(PLAT).so; fi; ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cp -a $(LPORDDIR)/libpord*.so lib/; fi; ++ + clean: + (cd src; $(MAKE) clean) + (cd examples; $(MAKE) clean) +diff --git a/MUMPS_5.5.0.orig/PORD/lib/Makefile b/MUMPS_5.5.0/PORD/lib/Makefile +index 8228f52..2650549 100644 +--- a/MUMPS_5.5.0.orig/PORD/lib/Makefile ++++ b/MUMPS_5.5.0/PORD/lib/Makefile +@@ -31,6 +31,10 @@ libpord$(PLAT)$(LIBEXT):$(OBJS) + libpord$(PLAT)$(LIBEXT_SHARED):$(OBJS) + $(CC) -shared $(OBJS) -o libpord.so + ++libpord$(PLAT).so: $(OBJS) ++ $(CC) -shared $(OBJS) -Wl,-soname,libpord$(PLAT)-$(SONAME_VERSION).so -o libpord$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libpord$(PLAT)-$(SONAME_VERSION).so $@ ++ + clean: + rm -f *.o + From 222e96ced99ba2c1c7a55c08c4320998f01b78ef Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 18 May 2022 09:51:29 +0200 Subject: [PATCH 3784/9987] update Arrow to use EB versions of some dependencies and enable all compression codecs --- .../a/Arrow/Arrow-6.0.0-foss-2021b.eb | 11 ++++++- .../RapidJSON-1.1.0-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 2 files changed, 40 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb index e0529cef302..aca66d53dc2 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb @@ -26,13 +26,22 @@ dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), # for numpy ('Boost', '1.77.0'), + ('lz4', '1.9.3'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.0'), + ('snappy', '1.1.9'), + ('RapidJSON', '1.1.0'), + ('RE2', '2022-02-01'), + ('utf8proc', '2.6.1'), ] start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c6e3e4da6fb --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +version = '1.1.0' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-compiler-errors.patch'] +checksums = [ + 'bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e', # v1.1.0.tar.gz + # %(name)s-%(version_major_minor)s.0_fix-compiler-errors.patch + '2e40ef6c46bf355feac16cd84faad5b7aca0ad54273117b85534b1b781f411c7', +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' From b3e7444ca7fe3d23b1532803e6f235c3bfb9efc4 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 18 May 2022 10:58:38 +0100 Subject: [PATCH 3785/9987] adding easyconfigs: muParser-2.3.3-GCCcore-10.3.0.eb --- .../muParser/muParser-2.3.3-GCCcore-10.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/muParser/muParser-2.3.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.3.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.3.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ec3d168b366 --- /dev/null +++ b/easybuild/easyconfigs/m/muParser/muParser-2.3.3-GCCcore-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'muParser' +version = '2.3.3' + +homepage = 'https://beltoforion.de/article.php?a=muparser' + +description = """ + muParser is an extensible high performance math expression parser library + written in C++. It works by transforming a mathematical expression into + bytecode and precalculating constant parts of the expression. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/beltoforion/muparser/archive/'] +sources = ['v%(version)s-1.tar.gz'] +checksums = [ + '91d26d8274ae9cd9c776ee58250aeddc6b574f369eafd03b25045b858a2b8177', # v2.3.3-1.tar.gz +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +configopts = "-DENABLE_SAMPLES=OFF -DBUILD_SHARED_LIBS=ON" + +sanity_check_paths = { + 'files': ['include/muParser.h', 'lib/libmuparser.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' From ce79d418a7b1683af9024b71704a163fa3760567 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 18 May 2022 11:04:04 +0100 Subject: [PATCH 3786/9987] adding easyconfigs: Mmg-5.6.0-gompi-2021a.eb --- .../m/Mmg/Mmg-5.6.0-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb new file mode 100644 index 00000000000..5f1a28b4c64 --- /dev/null +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Mmg' +version = '5.6.0' + +homepage = 'https://www.mmgtools.org/' +description = """ +Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: +the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional +triangulation and generation of a triangulation from a set of points or from given boundary edges +the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation +and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization +of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, +libmmgs and libmmg3d libraries.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://github.com/MmgTools/mmg/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bbf9163d65bc6e0f81dd3acc5a51e4a8c47a7fdae849abc26277e01154fe2437'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +dependencies = [('SCOTCH', '6.1.0')] + +separate_build_dir = True + +configopts = '-DUSE_SCOTCH=ON ' +configopts += '-DLIBMMG2D_SHARED=ON -DLIBMMG3D_SHARED=ON -DLIBMMGS_SHARED=ON -DLIBMMG_SHARED=ON ' + +sanity_check_paths = { + 'files': ['bin/%s_O3' % x for x in ['mmg2d', 'mmg3d', 'mmgs']] + + ['lib/lib%s.%s' % (x, y) for x in ['mmg2d', 'mmg3d', 'mmgs', 'mmg'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include/mmg/%s' % x for x in ['mmg2d', 'mmg3d', 'mmgs']] +} + +moduleclass = 'math' From 1a65e2f3ac275027918ecea788d8b65646258e9f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 19 May 2022 08:01:29 +0200 Subject: [PATCH 3787/9987] update Arrow for 2021a to use EB versions of some dependencies and enable all compression codecs --- .../a/Arrow/Arrow-6.0.0-foss-2021a.eb | 11 ++++++- .../a/Arrow/Arrow-6.0.1-foss-2021a.eb | 11 ++++++- .../r/RE2/RE2-2022-02-01-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 3 files changed, 53 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/r/RE2/RE2-2022-02-01-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb index 5915b674495..da7afc30a3a 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb @@ -26,13 +26,22 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), # for numpy ('Boost', '1.76.0'), + ('lz4', '1.9.3'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('zstd', '1.4.9'), + ('snappy', '1.1.8'), + ('RapidJSON', '1.1.0'), + ('RE2', '2022-02-01'), + ('utf8proc', '2.6.1'), ] start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb index 026891935f0..ae4130379ec 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb @@ -26,13 +26,22 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('Boost', '1.76.0'), + ('lz4', '1.9.3'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('zstd', '1.4.9'), + ('snappy', '1.1.8'), + ('RapidJSON', '1.1.0'), + ('RE2', '2022-02-01'), + ('utf8proc', '2.6.1'), ] start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON" +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " diff --git a/easybuild/easyconfigs/r/RE2/RE2-2022-02-01-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2022-02-01-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..90c87d7d9d8 --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2022-02-01-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = "CMakeMake" + +name = 'RE2' +version = '2022-02-01' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['9c1e6acfd0fed71f40b025a7a1dabaf3ee2ebb74d64ced1f9ee1b0b01d22fd27'] + +builddependencies = { + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +} + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' From 463fd39113e3a2e877b897433c383a687ae1ee26 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 19 May 2022 10:27:55 +0100 Subject: [PATCH 3788/9987] adding easyconfigs: SuperLU-5.3.0-foss-2021a.eb --- .../s/SuperLU/SuperLU-5.3.0-foss-2021a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2021a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2021a.eb new file mode 100644 index 00000000000..5ef56c45a08 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2021a.eb @@ -0,0 +1,19 @@ +name = 'SuperLU' +version = '5.3.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] + +builddependencies = [('CMake', '3.20.1')] + +moduleclass = 'numlib' From 46fcf3bfd942fa987e263370220991a5265efd6f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 19 May 2022 11:22:00 +0100 Subject: [PATCH 3789/9987] adding easyconfigs: hypothesis-6.46.7-GCCcore-11.3.0.eb --- .../hypothesis-6.46.7-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-6.46.7-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.46.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.46.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6d6e33e62dc --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.46.7-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '6.46.7' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['967009fa561b3a3f8363a73d71923357271c37dc7fa27b30c2d21a1b6092b240'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 09d78023d1ba5967ab330ee20eddfe28caa90727 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 19 May 2022 11:28:18 +0100 Subject: [PATCH 3790/9987] adding easyconfigs: Eigen-3.4.0-GCCcore-11.3.0.eb, pybind11-2.9.2-GCCcore-11.3.0.eb --- .../e/Eigen/Eigen-3.4.0-GCCcore-11.3.0.eb | 21 +++++++++++++++++ .../pybind11/pybind11-2.9.2-GCCcore-11.3.0.eb | 23 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.9.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..45b94168ed0 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.4.0' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.38'), # to make CMake compiler health check pass on old systems + ('CMake', '3.23.1'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.9.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.9.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fb9fa22bd4a --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.9.2-GCCcore-11.3.0.eb @@ -0,0 +1,23 @@ +name = 'pybind11' +version = '2.9.2' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6bd528c4dbe2276635dc787b6b1f2e5316cf6b49ee3e150264e455a0d68d19c1'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Eigen', '3.4.0'), +] +dependencies = [('Python', '3.10.4')] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +moduleclass = 'lib' From 2af7d5533896986e5dae5104f338b558cffa67db Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 19 May 2022 11:53:41 +0100 Subject: [PATCH 3791/9987] adding easyconfigs: SciPy-bundle-2022.05-intel-2022.05.eb --- .../SciPy-bundle-2022.05-intel-2022.05.eb | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb new file mode 100644 index 00000000000..ef55cdd75cc --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2022.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intel', 'version': '2022.05'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.46.7'), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('pybind11', '2.9.2'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.22.3', { + 'patches': [ + 'numpy-1.18.2-mkl.patch', + 'numpy-1.20.3_disable_fortran_callback_test.patch', + ], + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': [ + 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18', # numpy-1.22.3.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + # numpy-1.20.3_disable_fortran_callback_test.patch + '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.11.0', { + 'checksums': ['0b2cba712e09f7630879dff69f268460bfe34a6d6000451b47d598558a92a875'], + }), + ('scipy', '1.8.1', { + # compilation with Pythran enabled fails when using Intel compilers, + # see https://github.com/scipy/scipy/issues/14935 + 'prebuildopts': "export SCIPY_USE_PYTHRAN=0 && ", + 'preinstallopts': "export SCIPY_USE_PYTHRAN=0 && ", + 'checksums': ['9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33'], + }), + ('mpi4py', '3.1.3', { + 'checksums': ['f1e9fae1079f43eafdd9f817cdb3fd30d709edc093b5d5dada57a461b2db3008'], + }), + ('numexpr', '2.8.1', { + 'checksums': ['cd779aa44dd986c4ef10163519239602b027be06a527946656207acf1f58113b'], + }), + ('Bottleneck', '1.3.4', { + 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], + }), + ('pandas', '1.4.2', { + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 9bf55502b495dd9397578916e00c27ca6c72ca5f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 19 May 2022 14:18:33 +0100 Subject: [PATCH 3792/9987] add numpy override patch for version 1.22.3 --- .../SciPy-bundle-2022.05-intel-2022.05.eb | 3 +++ ...mpy-1.22.3_disable-broken-override-test.patch | 16 ++++++++++++++++ 2 files changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.22.3_disable-broken-override-test.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb index ef55cdd75cc..0c362eac31e 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb @@ -27,6 +27,7 @@ exts_list = [ 'patches': [ 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.22.3_disable-broken-override-test.patch', ], 'sources': ['%(name)s-%(version)s.zip'], 'checksums': [ @@ -34,6 +35,8 @@ exts_list = [ 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + # numpy-1.22.3_disable-broken-override-test.patch + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', ], }), ('ply', '3.11', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.22.3_disable-broken-override-test.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.22.3_disable-broken-override-test.patch new file mode 100644 index 00000000000..07d36217216 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.22.3_disable-broken-override-test.patch @@ -0,0 +1,16 @@ +skip broken test, see https://github.com/numpy/numpy/issues/16769 +author: Kenneth Hoste (HPC-UGent) +updated for version 1.22.3 by Jasper Grimm (UoY) +----------------------------------------------------------------- +diff -Nru numpy-1.22.3.orig/numpy/distutils/tests/test_system_info.py numpy-1.22.3/numpy/distutils/tests/test_system_info.py +--- numpy-1.22.3.orig/numpy/distutils/tests/test_system_info.py 2022-05-19 13:52:55.000000000 +0100 ++++ numpy-1.22.3/numpy/distutils/tests/test_system_info.py 2022-05-19 13:54:24.000000000 +0100 +@@ -258,7 +258,7 @@ + + @pytest.mark.xfail(HAS_MKL, reason=("`[DEFAULT]` override doesn't work if " + "numpy is built with MKL support")) +- def test_overrides(self): ++ def ignored_test_overrides(self): + previousDir = os.getcwd() + cfg = os.path.join(self._dir1, 'site.cfg') + shutil.copy(self._sitecfg, cfg) From cf01601f21afd59ab2b75668baa80e4faaf17dad Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 19 May 2022 15:08:02 +0100 Subject: [PATCH 3793/9987] Test added --- easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2021a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2021a.eb index 5ef56c45a08..aeb5519f77e 100644 --- a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2021a.eb @@ -16,4 +16,6 @@ checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] builddependencies = [('CMake', '3.20.1')] +runtest = " test" + moduleclass = 'numlib' From 5af75068a4ff3ef4c603b3ec31c8845938e99520 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 19 May 2022 15:17:14 +0100 Subject: [PATCH 3794/9987] add OpenMPI internal cuda patch --- ....1.3_build_with_internal_cuda_header.patch | 87 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb | 13 ++- 2 files changed, 97 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.3_build_with_internal_cuda_header.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.3_build_with_internal_cuda_header.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.3_build_with_internal_cuda_header.patch new file mode 100644 index 00000000000..c6fd915f4f6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.3_build_with_internal_cuda_header.patch @@ -0,0 +1,87 @@ +--- openmpi-4.1.3.orig/config/opal_check_cuda.m4 2022-03-31 16:04:13.000000000 +0000 ++++ openmpi-4.1.3/config/opal_check_cuda.m4 2022-05-04 17:37:57.576260311 +0000 +@@ -45,6 +45,12 @@ + # macro as that would error out after not finding it in the first directory. + # Note that anywhere CUDA aware code is in the Open MPI repository requires + # us to make use of AC_REQUIRE to ensure this check has been done. ++opal_check_cuda_internal="" ++AS_IF([test "$with_cuda" = "internal"], ++ [AC_MSG_RESULT([internal support requested]) ++ with_cuda="${OPAL_TOP_SRCDIR}/opal/mca/common/cuda/cuda" ++ opal_check_cuda_internal=" (internal)" ++ ]) + AS_IF([test "$with_cuda" = "no" || test "x$with_cuda" = "x"], + [opal_check_cuda_happy="no" + AC_MSG_RESULT([not set (--with-cuda=$with_cuda)])], +@@ -124,7 +130,7 @@ + CUDA_SUPPORT=0 + fi + +-OPAL_SUMMARY_ADD([[Miscellaneous]],[[CUDA support]],[opal_cuda], [$opal_check_cuda_happy]) ++OPAL_SUMMARY_ADD([[Miscellaneous]],[[CUDA support]],[opal_cuda], [$opal_check_cuda_happy$opal_check_cuda_internal]) + + AM_CONDITIONAL([OPAL_cuda_support], [test "x$CUDA_SUPPORT" = "x1"]) + AC_DEFINE_UNQUOTED([OPAL_CUDA_SUPPORT],$CUDA_SUPPORT, +--- openmpi-4.1.3.orig/opal/mca/common/cuda/cuda/cuda.h 1970-01-01 00:00:00.000000000 +0000 ++++ openmpi-4.1.3/opal/mca/common/cuda/cuda/cuda.h 2022-05-04 18:52:14.991300184 +0000 +@@ -0,0 +1,60 @@ ++/* This header provides minimal parts of the CUDA Driver API, without having to ++ rely on the proprietary CUDA toolkit. ++ ++ References (to avoid copying from NVidia's proprietary cuda.h): ++ https://github.com/gcc-mirror/gcc/blob/master/include/cuda/cuda.h ++ https://github.com/Theano/libgpuarray/blob/master/src/loaders/libcuda.h ++ https://github.com/CPFL/gdev/blob/master/cuda/driver/cuda.h ++ https://github.com/CudaWrangler/cuew/blob/master/include/cuew.h ++*/ ++ ++#define CUDA_VERSION 8000 ++ ++typedef void *CUcontext; ++typedef int CUdevice; ++#if defined(__LP64__) || defined(_WIN64) ++typedef unsigned long long CUdeviceptr; ++#else ++typedef unsigned CUdeviceptr; ++#endif ++typedef void *CUevent; ++typedef void *CUstream; ++ ++typedef enum { ++ CUDA_SUCCESS = 0, ++ CUDA_ERROR_NOT_INITIALIZED = 3, ++ CUDA_ERROR_DEINITIALIZED = 4, ++ CUDA_ERROR_ALREADY_MAPPED = 208, ++ CUDA_ERROR_NOT_READY = 600, ++} CUresult; ++ ++enum { ++ CU_EVENT_DISABLE_TIMING = 0x2, ++ CU_EVENT_INTERPROCESS = 0x4, ++}; ++ ++enum { ++ CU_IPC_MEM_LAZY_ENABLE_PEER_ACCESS = 0x1, ++}; ++ ++typedef enum { ++ CU_POINTER_ATTRIBUTE_CONTEXT = 1, ++ CU_POINTER_ATTRIBUTE_MEMORY_TYPE = 2, ++ CU_POINTER_ATTRIBUTE_SYNC_MEMOPS = 6, ++ CU_POINTER_ATTRIBUTE_BUFFER_ID = 7, ++ CU_POINTER_ATTRIBUTE_IS_MANAGED = 8, ++} CUpointer_attribute; ++ ++typedef enum { ++ CU_MEMORYTYPE_HOST = 0x01, ++} CUmemorytype; ++ ++typedef struct CUipcEventHandle CUipcEventHandle; ++ ++#define CU_IPC_HANDLE_SIZE 64 ++typedef struct CUipcMemHandle_st { ++ char reserved[CU_IPC_HANDLE_SIZE]; ++} CUipcMemHandle; ++ ++CUresult cuPointerGetAttributes (unsigned int numAttributes, ++ CUpointer_attribute *attributes, void **data, CUdeviceptr ptr); diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb index 6fbf3602b0b..acb038b725e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb @@ -8,7 +8,12 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['46169edd9cf8366608684e5c6a342650b2393d46c9f9a380add8e09f1f8001de'] +patches = ['OpenMPI-4.1.3_build_with_internal_cuda_header.patch'] +checksums = [ + '46169edd9cf8366608684e5c6a342650b2393d46c9f9a380add8e09f1f8001de', # openmpi-4.1.4rc1.tar.bz2 + # OpenMPI-4.1.3_build_with_internal_cuda_header.patch + '53bff4fcc92350128b17c29d7288391f87f082f45645c631916b90d2fa5b5116', +] builddependencies = [ ('pkgconf', '1.8.0'), @@ -19,12 +24,14 @@ dependencies = [ ('hwloc', '2.7.1'), ('libevent', '2.1.12'), ('UCX', '1.12.1'), - ('libfabric', '1.15.0'), + ('libfabric', '1.15.1'), ('PMIx', '4.1.2'), ] +configopts = '--with-cuda=internal ' + # disable MPI1 compatibility for now, see what breaks... -# configopts = '--enable-mpi1-compatibility ' +# configopts += '--enable-mpi1-compatibility ' # to enable SLURM integration (site-specific) # configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' From 1967eff77c291de2360ba3621aee50f958199e4c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 19 May 2022 16:23:40 +0100 Subject: [PATCH 3795/9987] add deap patch for setuptools>58 --- .../SciPy-bundle-2022.05-intel-2022.05.eb | 6 ++++- .../s/SciPy-bundle/deap-1.3.1_no_2to3.patch | 23 +++++++++++++++++++ 2 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/deap-1.3.1_no_2to3.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb index 0c362eac31e..d6fbee5059b 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb @@ -75,7 +75,11 @@ exts_list = [ 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], }), ('deap', '1.3.1', { - 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + 'patches': ['deap-1.3.1_no_2to3.patch'], + 'checksums': [ + '11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f', # deap-1.3.1.tar.gz + '3fa9fac74b0750ac6667371ce0634c797d62d270c76eee9c258b55f4a5a5e689', # deap-1.3.1_no_2to3.patch + ], }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/deap-1.3.1_no_2to3.patch b/easybuild/easyconfigs/s/SciPy-bundle/deap-1.3.1_no_2to3.patch new file mode 100644 index 00000000000..c319c8f89db --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/deap-1.3.1_no_2to3.patch @@ -0,0 +1,23 @@ +From: Stefano Rivera +Date: Sun, 21 Nov 2021 08:50:34 -0400 +Subject: Drop use_2to3, setuptools 58 no longer supports it + +Bug-Upstream: https://github.com/DEAP/deap/issues/595 +Bug-Debian: https://bugs.debian.org/997609 +Forwarded: not-needed +--- + setup.py | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/setup.py b/setup.py +index e68c052..01ad00b 100644 +--- a/setup.py ++++ b/setup.py +@@ -87,7 +87,6 @@ def run_setup(build_ext): + ext_modules=extra_modules, + cmdclass={"build_ext": ve_build_ext}, + install_requires=['numpy'], +- use_2to3=True + ) + + try: From 5926355123211ccf83c184f4f3a7f403174b4a5e Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 19 May 2022 22:03:30 +0200 Subject: [PATCH 3796/9987] exiting help with exit 0 just patched our jorg fork to handle --help with exit 0 --- easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb index f66c45f5bd5..11b8affb4e2 100644 --- a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb +++ b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb @@ -5,7 +5,7 @@ easyblock = 'PackedBinary' name = 'Jorg' -version = '1.0.0' +version = '1.0.1' homepage = 'https://github.com/lmlui/Jorg' description = "A MAG Circularization Method By Lauren Lui, Torben Nielsen, and Adam Arkin" From 998d05644e323fc3707a8e349d8179595e9c2a7c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 20 May 2022 14:54:56 +0100 Subject: [PATCH 3797/9987] adding easyconfigs: Bazel-4.2.2-GCCcore-11.2.0.eb and patches: Bazel-4.2.2_ftbs-gcc11-2.patch, Bazel-4.2.2_ftbs-gcc11-3.patch, Bazel-4.2.2_ftbs-gcc11-4.patch, Bazel-4.2.2_remove-illegal-reflective.patch --- .../b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb | 43 ++++++++++++++++++ .../b/Bazel/Bazel-4.2.2_ftbs-gcc11-2.patch | 31 +++++++++++++ .../b/Bazel/Bazel-4.2.2_ftbs-gcc11-3.patch | 38 ++++++++++++++++ .../b/Bazel/Bazel-4.2.2_ftbs-gcc11-4.patch | 45 +++++++++++++++++++ ...azel-4.2.2_remove-illegal-reflective.patch | 36 +++++++++++++++ 5 files changed, 193 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-2.patch create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-3.patch create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-4.patch create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_remove-illegal-reflective.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..5935f0d8b4f --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +name = 'Bazel' +version = '4.2.2' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = [ + 'Bazel-3.7.1_fix-protobuf-env.patch', + 'Bazel-3.7.2_fix-GCC-11.patch', + 'Bazel-3.7.2_fix-Java-15.patch', + 'Bazel-4.2.2_ftbs-gcc11-2.patch', + 'Bazel-4.2.2_ftbs-gcc11-3.patch', + 'Bazel-4.2.2_ftbs-gcc11-4.patch', + 'Bazel-4.2.2_remove-illegal-reflective.patch', +] +checksums = [ + '9981d0d53a356c4e87962847750a97c9e8054e460854748006c80f0d7e2b2d33', # bazel-4.2.2-dist.zip + '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', # Bazel-3.7.1_fix-protobuf-env.patch + '7fd5846f2ed1f27af9528a900f284f95ad982f3e7d486264c3bdee890a9c22fb', # Bazel-3.7.2_fix-GCC-11.patch + '28f394f561824abf562556877483bc443dfd3ee0c7cba48a56e22670258669e7', # Bazel-3.7.2_fix-Java-15.patch + '5eb644b5363ba25ccb1f090bbb399f56028bfbcb42f0510d272df9a94836c751', # Bazel-4.2.2_ftbs-gcc11-2.patch + '663f4c1145b53518500a205f644d06cd2b70cdf5a630c9ab77d8a363fb07e8e6', # Bazel-4.2.2_ftbs-gcc11-3.patch + '46b89a5952c3cadcb9a15b41049e338e6150d123da82b08f90ae2795ece0b85d', # Bazel-4.2.2_ftbs-gcc11-4.patch + 'cebaeb45bf71eb29a31bf3b9455055a8e3a03306c992ee0398148b37e8f7e25a', # Bazel-4.2.2_remove-illegal-reflective.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), + ('Zip', '3.0'), +] + +dependencies = [('Java', '11', '', True)] + +runtest = True +testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-2.patch b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-2.patch new file mode 100644 index 00000000000..42e9073296b --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-2.patch @@ -0,0 +1,31 @@ +From a129aeb333d83a4466ac2c996b84a113405acb4d Mon Sep 17 00:00:00 2001 +From: philwo +Date: Mon, 14 Jun 2021 09:10:07 -0700 +Subject: [PATCH] Fix #13575: FTBFS with GCC 11 on ARMv8 + +This supposedly fixes the compiler error reported by the user: + +`error: 'numeric_limits' is not a member of 'std'` + +Thanks to samcom12 for the report and suggested fix. + +RELNOTES: None. +PiperOrigin-RevId: 379291338 +--- + third_party/ijar/zlib_client.h | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/third_party/ijar/zlib_client.h b/third_party/ijar/zlib_client.h +index c4b051e0100c..0a917ff0a99a 100644 +--- a/third_party/ijar/zlib_client.h ++++ b/third_party/ijar/zlib_client.h +@@ -16,7 +16,9 @@ + #define THIRD_PARTY_IJAR_ZLIB_CLIENT_H_ + + #include ++ + #include ++#include + + #include "third_party/ijar/common.h" + diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-3.patch b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-3.patch new file mode 100644 index 00000000000..667110479bc --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-3.patch @@ -0,0 +1,38 @@ +From 9761509f9ccc3892f42425b904adf1ef10bcb1f4 Mon Sep 17 00:00:00 2001 +From: David Ostrovsky +Date: Wed, 16 Jun 2021 07:55:57 -0700 +Subject: [PATCH] Fix building on gcc 11 + +Fixes #12702. + +Without this include the build is failing with: + + third_party/ijar/mapped_file_unix.cc: In constructor 'devtools_ijar::MappedOutputFile::MappedOutputFile(const char*, size_t)': + third_party/ijar/mapped_file_unix.cc:115:21: error: 'numeric_limits' is not a member of 'std' + 115 | std::numeric_limits::max()); + | ^~~~~~~~~~~~~~ + +Closes #13537. + +PiperOrigin-RevId: 379719635 +--- + third_party/ijar/mapped_file_unix.cc | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/third_party/ijar/mapped_file_unix.cc b/third_party/ijar/mapped_file_unix.cc +index 6e3a90871844..65179e3290ec 100644 +--- a/third_party/ijar/mapped_file_unix.cc ++++ b/third_party/ijar/mapped_file_unix.cc +@@ -15,10 +15,11 @@ + #include + #include + #include +-#include + #include ++#include + + #include ++#include + + #include "third_party/ijar/mapped_file.h" + diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-4.patch b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-4.patch new file mode 100644 index 00000000000..8a493f032ef --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_ftbs-gcc11-4.patch @@ -0,0 +1,45 @@ +Taken from the alpine upstream patches: +https://gitlab.alpinelinux.org/alpine/aports/-/merge_requests/29084/diffs#7eb1858ad36525c0b9eefa137dd00e045b0b2e5b +--- a/third_party/grpc/grpc_1.33.1.patch ++++ b/third_party/grpc/grpc_1.33.1.patch +@@ -58,6 +58,14 @@ index 09fcad95a2..9b737e5deb 100644 + ) + + native.bind( ++@@ -245,6 +245,7 @@ def grpc_deps(): ++ "https://storage.googleapis.com/grpc-bazel-mirror/github.com/abseil/abseil-cpp/archive/df3ea785d8c30a9503321a3d35ee7d35808f190d.tar.gz", ++ "https://github.com/abseil/abseil-cpp/archive/df3ea785d8c30a9503321a3d35ee7d35808f190d.tar.gz", ++ ], +++ patches = ["@com_github_grpc_grpc//:third_party/abseil-cpp/absl.patch"], ++ ) ++ ++ if "bazel_toolchains" not in native.existing_rules(): + diff --git a/bazel/grpc_extra_deps.bzl b/bazel/grpc_extra_deps.bzl + index 4c1dfad2e8..f63c54ddef 100644 + --- a/bazel/grpc_extra_deps.bzl +@@ -120,3 +128,25 @@ index c047f0c515..7c24fbc617 100644 + ":windows": "@com_github_grpc_grpc//third_party/cares:config_windows/ares_config.h", + ":android": "@com_github_grpc_grpc//third_party/cares:config_android/ares_config.h", + "//conditions:default": "@com_github_grpc_grpc//third_party/cares:config_linux/ares_config.h", ++ ++--- /dev/null +++++ b/third_party/abseil-cpp/absl.patch ++@@ -0,0 +1,18 @@ +++0e2c62da1dcaf6529abab952bdcc96c6de2d9506 by Abseil Team : +++ +++Add missing include +++ +++PiperOrigin-RevId: 339054753 +++ +++-- +++ +++--- absl/synchronization/internal/graphcycles.cc ++++++ absl/synchronization/internal/graphcycles.cc +++@@ -37,6 +37,7 @@ +++ +++ #include +++ #include ++++#include +++ #include "absl/base/internal/hide_ptr.h" +++ #include "absl/base/internal/raw_logging.h" +++ #include "absl/base/internal/spinlock.h" diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_remove-illegal-reflective.patch b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_remove-illegal-reflective.patch new file mode 100644 index 00000000000..9cd850cbac0 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2_remove-illegal-reflective.patch @@ -0,0 +1,36 @@ +Taken from the alpine upstream patches: +https://gitlab.alpinelinux.org/alpine/aports/-/merge_requests/29084/diffs#7eb1858ad36525c0b9eefa137dd00e045b0b2e5b +--- a/src/main/cpp/blaze.cc ++++ b/src/main/cpp/blaze.cc +@@ -360,13 +360,10 @@ static vector GetServerExeArgs(const blaze_util::Path &jvm_path, + result.push_back("-XX:HeapDumpPath=" + + startup_options.output_base.AsJvmArgument()); + +- // TODO(b/109998449): only assume JDK >= 9 for embedded JDKs +- if (!startup_options.GetEmbeddedJavabase().IsEmpty()) { +- // quiet warnings from com.google.protobuf.UnsafeUtil, +- // see: https://github.com/google/protobuf/issues/3781 +- result.push_back("--add-opens=java.base/java.nio=ALL-UNNAMED"); +- result.push_back("--add-opens=java.base/java.lang=ALL-UNNAMED"); +- } ++ // quiet warnings from com.google.protobuf.UnsafeUtil, ++ // see: https://github.com/google/protobuf/issues/3781 ++ result.push_back("--add-opens=java.base/java.nio=ALL-UNNAMED"); ++ result.push_back("--add-opens=java.base/java.lang=ALL-UNNAMED"); + + vector user_options = startup_options.host_jvm_args; + +--- a/src/main/java/com/google/devtools/build/lib/unsafe/StringUnsafe.java ++++ b/src/main/java/com/google/devtools/build/lib/unsafe/StringUnsafe.java +@@ -72,10 +72,7 @@ public class StringUnsafe { + + Arrays.toString(String.class.getDeclaredFields()), + e); + } +- this.constructor.setAccessible(true); +- valueField.setAccessible(true); + valueOffset = UnsafeProvider.getInstance().objectFieldOffset(valueField); +- coderField.setAccessible(true); + coderOffset = UnsafeProvider.getInstance().objectFieldOffset(coderField); + } + + From ced35216dc405120022401dc7f05bf38a863b172 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 20 May 2022 14:59:49 +0100 Subject: [PATCH 3798/9987] checksums --- easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb index 5935f0d8b4f..0a321f837b9 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb @@ -25,8 +25,8 @@ checksums = [ '28f394f561824abf562556877483bc443dfd3ee0c7cba48a56e22670258669e7', # Bazel-3.7.2_fix-Java-15.patch '5eb644b5363ba25ccb1f090bbb399f56028bfbcb42f0510d272df9a94836c751', # Bazel-4.2.2_ftbs-gcc11-2.patch '663f4c1145b53518500a205f644d06cd2b70cdf5a630c9ab77d8a363fb07e8e6', # Bazel-4.2.2_ftbs-gcc11-3.patch - '46b89a5952c3cadcb9a15b41049e338e6150d123da82b08f90ae2795ece0b85d', # Bazel-4.2.2_ftbs-gcc11-4.patch - 'cebaeb45bf71eb29a31bf3b9455055a8e3a03306c992ee0398148b37e8f7e25a', # Bazel-4.2.2_remove-illegal-reflective.patch + '480c8668d1a95535a673d38bcb42138cfc12a2363707b964b55980f9cefe34a5', # Bazel-4.2.2_ftbs-gcc11-4.patch + 'b0a0df8dc038d1befaa811eb96a554812821f06014f9ad11f86b685fd267edf3', # Bazel-4.2.2_remove-illegal-reflective.patch ] builddependencies = [ From b6920bb0ca97e7faa96e1a10ff3df9780fb6bcbf Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Fri, 20 May 2022 21:10:27 +0200 Subject: [PATCH 3799/9987] Add comment for the changes to the pretestopts, fix comment spacing --- .../OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..88ef97aa375 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,69 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.7.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] +checksums = [ + '51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25', # 7.7.0.tar.gz + '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('CUDA', '11.3.1', '', True), + ('SWIG', '.4.0.2'), +] + +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m openmm.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 8a6fecb0035d4f0b7e3e3fb3a97c7a69a4b491f1 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Fri, 20 May 2022 21:41:56 +0200 Subject: [PATCH 3800/9987] Incorrectly made SWIG module hidden --- .../easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb index 88ef97aa375..d52bab5ca43 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb @@ -36,7 +36,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('CUDA', '11.3.1', '', True), - ('SWIG', '.4.0.2'), + ('SWIG', '4.0.2'), ] # Flags for CUDA-enabled build From 129118a1a029c855850f7d5627148217986af809 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 20 May 2022 15:33:28 -0700 Subject: [PATCH 3801/9987] add binutils --- easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb index 33aa81c24e0..f259a7e854e 100644 --- a/easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb @@ -16,6 +16,7 @@ description = """gsutil is a Python application that lets you access Cloud Stora toolchain = {'name': 'GCCcore', 'version': '11.2.0'} builddependencies = [ + ('buildutils', '2.37'), ('Rust', '1.54.0'), # required for setuptools-rust, which is needed for cryptography ] From 8c0cb82a3e7eea58b56dc3d6936d4ff448045803 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Sat, 21 May 2022 10:37:41 +0200 Subject: [PATCH 3802/9987] Rename easyconfig with incorrect suffix --- .../OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb | 69 ------------------- 1 file changed, 69 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb deleted file mode 100644 index d52bab5ca43..00000000000 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb +++ /dev/null @@ -1,69 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# Update to 7.5.1 -# J. Sassmannshausen / GSTT - -easyblock = 'CMakeMake' - -name = 'OpenMM' -version = '7.7.0' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://openmm.org' -description = "OpenMM is a toolkit for molecular simulation." - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'opt': True} - -source_urls = ['https://github.com/openmm/openmm/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] -checksums = [ - '51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25', # 7.7.0.tar.gz - '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch -] - -builddependencies = [ - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), -] - -separate_build_dir = True - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('CUDA', '11.3.1', '', True), - ('SWIG', '4.0.2'), -] - -# Flags for CUDA-enabled build -configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" - -# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 -pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" -local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" -runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern - -preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' -preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' - -# required to install the python API -installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' - -sanity_check_paths = { - 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], - 'dirs': [] -} - -sanity_check_commands = ["python -m openmm.testInstallation"] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - -moduleclass = 'bio' From 894d7acc7af2c6ebdb59456349823465825fee27 Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Sat, 21 May 2022 20:44:22 +0200 Subject: [PATCH 3803/9987] Re submit the fix for the lint --- .../OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..d52bab5ca43 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,69 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.7.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] +checksums = [ + '51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25', # 7.7.0.tar.gz + '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('CUDA', '11.3.1', '', True), + ('SWIG', '4.0.2'), +] + +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m openmm.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 2660f544186fc8734bfe994670e60bde6816a84c Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Sat, 21 May 2022 22:35:26 +0000 Subject: [PATCH 3804/9987] adding easyconfigs: UCC-1.0.0-GCCcore-11.3.0.eb --- .../u/UCC/UCC-1.0.0-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCC/UCC-1.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..203e678f587 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC/UCC-1.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'UCC' +version = '1.0.0' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + 'd3b4aa7004bf339d35952a1699a6e408064ba578bdc93861f5f07527ad0a5e8c', # v1.0.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCX', '1.12.1'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/ucc_info'], + 'dirs': ['include', 'lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +moduleclass = 'lib' From f723f3799653c5bc56dab64ec2f02f06cd3d6123 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Sun, 22 May 2022 00:49:02 +0000 Subject: [PATCH 3805/9987] OpenMPI 4.1.1: patch and build --with-cuda=internal Allow building Open MPI with --with-cuda=internal, by providing an internal minimal cuda.h header file. This eliminate the CUDA (build)dependency; as long as the runtime CUDA version is 8.0+, libcuda.so will be dlopen'ed and used successfully. --- .../o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb | 9 ++ .../o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 9 ++ ....1.1_build_with_internal_cuda_header.patch | 93 +++++++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb index 57c38134baa..84c6f236bbb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb @@ -15,6 +15,7 @@ patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.1.1_build_with_internal_cuda_header.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -24,10 +25,14 @@ checksums = [ '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', + # OpenMPI-4.1.1_build_with_internal_cuda_header.patch + '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', ] builddependencies = [ ('pkg-config', '0.29.2'), + ('Perl', '5.32.1'), + ('Autotools', '20210128'), ] dependencies = [ @@ -39,6 +44,10 @@ dependencies = [ ('PMIx', '3.2.3'), ] +preconfigopts = './autogen.pl --force && ' + +configopts = '--with-cuda=internal ' + # disable MPI1 compatibility for now, see what breaks... # configopts = '--enable-mpi1-compatibility ' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index 593e8e3be27..7dea8ac1c65 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -14,6 +14,7 @@ patches = [ 'OpenMPI-4.1.1_opal-pmix-package-rank.patch', 'OpenMPI-4.1.1_pmix3x-protection.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.1.1_build_with_internal_cuda_header.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -25,10 +26,14 @@ checksums = [ '384ef9f1fa803b0d71dae2ec0748d0f20295992437532afedf21478bda164ff8', # OpenMPI-4.1.1_pmix3x-protection.patch # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', + # OpenMPI-4.1.1_build_with_internal_cuda_header.patch + '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', ] builddependencies = [ ('pkg-config', '0.29.2'), + ('Perl', '5.34.0'), + ('Autotools', '20210726'), ] dependencies = [ @@ -40,6 +45,10 @@ dependencies = [ ('PMIx', '4.1.0'), ] +preconfigopts = './autogen.pl --force && ' + +configopts = '--with-cuda=internal ' + # disable MPI1 compatibility for now, see what breaks... # configopts = '--enable-mpi1-compatibility ' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch new file mode 100644 index 00000000000..9c5945b7de2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch @@ -0,0 +1,93 @@ +Allow building Open MPI with --with-cuda=internal, by providing an +internal minimal cuda.h header file. This eliminate the CUDA +(build)dependency; as long as the runtime CUDA version is 8.0+, +libcuda.so will be dlopen'ed and used successfully. + +Author: Bart Oldeman +--- openmpi-4.1.3.orig/config/opal_check_cuda.m4 2022-03-31 16:04:13.000000000 +0000 ++++ openmpi-4.1.3/config/opal_check_cuda.m4 2022-05-04 17:37:57.576260311 +0000 +@@ -45,6 +45,12 @@ + # macro as that would error out after not finding it in the first directory. + # Note that anywhere CUDA aware code is in the Open MPI repository requires + # us to make use of AC_REQUIRE to ensure this check has been done. ++opal_check_cuda_internal="" ++AS_IF([test "$with_cuda" = "internal"], ++ [AC_MSG_RESULT([internal support requested]) ++ with_cuda="${OPAL_TOP_SRCDIR}/opal/mca/common/cuda/cuda" ++ opal_check_cuda_internal=" (internal)" ++ ]) + AS_IF([test "$with_cuda" = "no" || test "x$with_cuda" = "x"], + [opal_check_cuda_happy="no" + AC_MSG_RESULT([not set (--with-cuda=$with_cuda)])], +@@ -124,7 +130,7 @@ + CUDA_SUPPORT=0 + fi + +-OPAL_SUMMARY_ADD([[Miscellaneous]],[[CUDA support]],[opal_cuda], [$opal_check_cuda_happy]) ++OPAL_SUMMARY_ADD([[Miscellaneous]],[[CUDA support]],[opal_cuda], [$opal_check_cuda_happy$opal_check_cuda_internal]) + + AM_CONDITIONAL([OPAL_cuda_support], [test "x$CUDA_SUPPORT" = "x1"]) + AC_DEFINE_UNQUOTED([OPAL_CUDA_SUPPORT],$CUDA_SUPPORT, +--- openmpi-4.1.3.orig/opal/mca/common/cuda/cuda/cuda.h 1970-01-01 00:00:00.000000000 +0000 ++++ openmpi-4.1.3/opal/mca/common/cuda/cuda/cuda.h 2022-05-04 18:52:14.991300184 +0000 +@@ -0,0 +1,60 @@ ++/* This header provides minimal parts of the CUDA Driver API, without having to ++ rely on the proprietary CUDA toolkit. ++ ++ References (to avoid copying from NVidia's proprietary cuda.h): ++ https://github.com/gcc-mirror/gcc/blob/master/include/cuda/cuda.h ++ https://github.com/Theano/libgpuarray/blob/master/src/loaders/libcuda.h ++ https://github.com/CPFL/gdev/blob/master/cuda/driver/cuda.h ++ https://github.com/CudaWrangler/cuew/blob/master/include/cuew.h ++*/ ++ ++#define CUDA_VERSION 8000 ++ ++typedef void *CUcontext; ++typedef int CUdevice; ++#if defined(__LP64__) || defined(_WIN64) ++typedef unsigned long long CUdeviceptr; ++#else ++typedef unsigned CUdeviceptr; ++#endif ++typedef void *CUevent; ++typedef void *CUstream; ++ ++typedef enum { ++ CUDA_SUCCESS = 0, ++ CUDA_ERROR_NOT_INITIALIZED = 3, ++ CUDA_ERROR_DEINITIALIZED = 4, ++ CUDA_ERROR_ALREADY_MAPPED = 208, ++ CUDA_ERROR_NOT_READY = 600, ++} CUresult; ++ ++enum { ++ CU_EVENT_DISABLE_TIMING = 0x2, ++ CU_EVENT_INTERPROCESS = 0x4, ++}; ++ ++enum { ++ CU_IPC_MEM_LAZY_ENABLE_PEER_ACCESS = 0x1, ++}; ++ ++typedef enum { ++ CU_POINTER_ATTRIBUTE_CONTEXT = 1, ++ CU_POINTER_ATTRIBUTE_MEMORY_TYPE = 2, ++ CU_POINTER_ATTRIBUTE_SYNC_MEMOPS = 6, ++ CU_POINTER_ATTRIBUTE_BUFFER_ID = 7, ++ CU_POINTER_ATTRIBUTE_IS_MANAGED = 8, ++} CUpointer_attribute; ++ ++typedef enum { ++ CU_MEMORYTYPE_HOST = 0x01, ++} CUmemorytype; ++ ++typedef struct CUipcEventHandle CUipcEventHandle; ++ ++#define CU_IPC_HANDLE_SIZE 64 ++typedef struct CUipcMemHandle_st { ++ char reserved[CU_IPC_HANDLE_SIZE]; ++} CUipcMemHandle; ++ ++CUresult cuPointerGetAttributes (unsigned int numAttributes, ++ CUpointer_attribute *attributes, void **data, CUdeviceptr ptr); From 088d3a03850a73440729e0eaeea767a77b9e0d79 Mon Sep 17 00:00:00 2001 From: casparl Date: Sun, 22 May 2022 10:29:45 +0200 Subject: [PATCH 3806/9987] Replaced buildutils with binutils to fix typo --- easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb index f259a7e854e..70185fe515c 100644 --- a/easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/gsutil/gsutil-5.10-GCCcore-11.2.0.eb @@ -16,7 +16,7 @@ description = """gsutil is a Python application that lets you access Cloud Stora toolchain = {'name': 'GCCcore', 'version': '11.2.0'} builddependencies = [ - ('buildutils', '2.37'), + ('binutils', '2.37'), ('Rust', '1.54.0'), # required for setuptools-rust, which is needed for cryptography ] From 176ac0a58b1cdc89cb742977e9c960a5871ce196 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 22 May 2022 11:13:04 +0100 Subject: [PATCH 3807/9987] Add local::lib and Module::Path to Perl 5.34.1 (2022a) --- .../easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index f27c0c429ee..7354490d5e4 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -1924,6 +1924,16 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER/'], 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), ] moduleclass = 'lang' From f804d20305771baccac5578c30a3b3980fe38b6c Mon Sep 17 00:00:00 2001 From: Inaki Mtz Ilarduya Date: Mon, 23 May 2022 08:59:52 +0200 Subject: [PATCH 3808/9987] Restore the good EasyConfig as I deleted the wrong one by mistake... --- .../o/OpenMM/OpenMM-7.7.0-foss-2021a.eb | 69 ------------------- 1 file changed, 69 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb deleted file mode 100644 index 6221e22818b..00000000000 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb +++ /dev/null @@ -1,69 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# Update to 7.5.1 -# J. Sassmannshausen / GSTT - -easyblock = 'CMakeMake' - -name = 'OpenMM' -version = '7.7.0' - -homepage = 'https://openmm.org' -description = "OpenMM is a toolkit for molecular simulation." - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'opt': True} - -source_urls = ['https://github.com/openmm/openmm/archive/'] -sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-7.5.0_fix_path_to_nvcc.patch'] -checksums = [ - '51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25', # 7.7.0.tar.gz - '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c', # OpenMM-7.5.0_fix_path_to_nvcc.patch -] - -builddependencies = [ - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), -] - -separate_build_dir = True - -dependencies = [ - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('CUDA', '11.3.1', '', True), - ('SWIG', '4.0.2'), -] - -# Flags for CUDA-enabled build -configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" - -#pretestopts = "export OPENMM_CUDA_COMPILER=nvcc && CTEST_OUTPUT_ON_FAILURE=1" -# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 -pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" -local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" -runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern - -preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' -preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' - -# required to install the python API -installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' - -sanity_check_paths = { - 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], - 'dirs': [] -} - -sanity_check_commands = ["python -m openmm.testInstallation"] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - -moduleclass = 'bio' From c52b08233c973a1fd5325a3fd21e371083d71f6a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 23 May 2022 11:13:02 +0100 Subject: [PATCH 3809/9987] update patch, (pre-)configopts to match #15528 --- ...enMPI-4.1.1_build_with_internal_cuda_header.patch} | 6 ++++++ .../o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb | 11 ++++++++--- 2 files changed, 14 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-4.1.3_build_with_internal_cuda_header.patch => OpenMPI-4.1.1_build_with_internal_cuda_header.patch} (91%) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.3_build_with_internal_cuda_header.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch similarity index 91% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.3_build_with_internal_cuda_header.patch rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch index c6fd915f4f6..9c5945b7de2 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.3_build_with_internal_cuda_header.patch +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch @@ -1,3 +1,9 @@ +Allow building Open MPI with --with-cuda=internal, by providing an +internal minimal cuda.h header file. This eliminate the CUDA +(build)dependency; as long as the runtime CUDA version is 8.0+, +libcuda.so will be dlopen'ed and used successfully. + +Author: Bart Oldeman --- openmpi-4.1.3.orig/config/opal_check_cuda.m4 2022-03-31 16:04:13.000000000 +0000 +++ openmpi-4.1.3/config/opal_check_cuda.m4 2022-05-04 17:37:57.576260311 +0000 @@ -45,6 +45,12 @@ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb index acb038b725e..341343fcc47 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb @@ -8,15 +8,17 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['OpenMPI-4.1.3_build_with_internal_cuda_header.patch'] +patches = ['OpenMPI-4.1.1_build_with_internal_cuda_header.patch'] checksums = [ '46169edd9cf8366608684e5c6a342650b2393d46c9f9a380add8e09f1f8001de', # openmpi-4.1.4rc1.tar.bz2 - # OpenMPI-4.1.3_build_with_internal_cuda_header.patch - '53bff4fcc92350128b17c29d7288391f87f082f45645c631916b90d2fa5b5116', + # OpenMPI-4.1.1_build_with_internal_cuda_header.patch + '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', ] builddependencies = [ ('pkgconf', '1.8.0'), + ('Perl', '5.34.1'), + ('Autotools', '20220317'), ] dependencies = [ @@ -26,8 +28,11 @@ dependencies = [ ('UCX', '1.12.1'), ('libfabric', '1.15.1'), ('PMIx', '4.1.2'), + ('UCC', '1.0.0'), ] +preconfigopts = './autogen.pl --force && ' + configopts = '--with-cuda=internal ' # disable MPI1 compatibility for now, see what breaks... From 02f9fa369409bdc6f475a950f1e9ec1969b5b2a1 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 23 May 2022 13:09:51 +0200 Subject: [PATCH 3810/9987] Added requested changes --- .../n/num2words/num2words-0.5.10-foss-2021a.eb | 18 +++++------------- 1 file changed, 5 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb index caab837fee5..28610259880 100644 --- a/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb +++ b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb @@ -1,4 +1,4 @@ -easyblock = "PythonBundle" +easyblock = "PythonPackage" name = 'num2words' version = '0.5.10' @@ -8,6 +8,10 @@ description = "Modules to convert numbers to words. 42 --> forty-two" toolchain = {'name': 'foss', 'version': '2021a'} +source_urls = ['https://github.com/savoirfairelinux/num2words/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ff107ecc0b6709bedf31fdb9e2ca45d29d3fd34b9eb6a0b89a862f337ac5ff00'] + dependencies = [ ('Python', '3.9.5'), ] @@ -15,18 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -exts_list = [ - ('docopt', '0.6.2', { - 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], - }), - (name, version, { - 'modulename': False, - 'source_urls': ['https://github.com/savoirfairelinux/num2words/archive/refs/tags/'], - 'sources': ['v%(version)s.tar.gz'], - 'checksums': ['ff107ecc0b6709bedf31fdb9e2ca45d29d3fd34b9eb6a0b89a862f337ac5ff00'], - }), -] - sanity_check_commands = ["num2words 42"] moduleclass = "tools" From 7cb308cb626b6b053fdb74fa6d4dbfc8a9754daf Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 23 May 2022 13:33:42 +0200 Subject: [PATCH 3811/9987] Added requested changes --- .../s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb index 738922df6f1..784b2db7173 100644 --- a/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb +++ b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb @@ -14,23 +14,16 @@ dependencies = [ ('tqdm', '4.61.2'), ('PyTorch', '1.10.0'), ('SciPy-bundle', '2021.05'), + ('torchvision', '0.11.3'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('future', '0.18.2', { - 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], - }), ('logger', '1.4', { 'checksums': ['4ecac57133c6376fa215f0fe6b4dc4d60e4d1ad8be005cab4e8a702df682f8b3'], }), - ('torchvision', '0.2.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['b4aadc07407c37542b94e38f710cfee6e53bb8e8633418094d476c5e417cbc80'], - }), (name, version, { 'modulename': 'topk', 'source_urls': ['https://github.com/oval-group/smooth-topk/archive/'], From bbcde27f1bef93720120c1787841e44b09ad6c0f Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 23 May 2022 13:36:07 +0200 Subject: [PATCH 3812/9987] Added download_dep_fail --- easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb index 28610259880..2d2be56286a 100644 --- a/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb +++ b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb @@ -18,6 +18,7 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True sanity_check_commands = ["num2words 42"] From 717112f5016847fe430c37aea0b39bc58367ea29 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 23 May 2022 14:33:08 +0200 Subject: [PATCH 3813/9987] adding easyconfigs: CellTypist-1.0.0-foss-2021b.eb, openpyxl-3.0.9-GCCcore-11.2.0.eb --- .../CellTypist/CellTypist-1.0.0-foss-2021b.eb | 28 ++++++++++++++++ .../openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb new file mode 100644 index 00000000000..6a298747054 --- /dev/null +++ b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = "CellTypist" +version = "1.0.0" + +homepage = "https://www.celltypist.org/" +description = "A tool for semi-automatic cell type annotation" + +source_urls = ["https://github.com/Teichlab/celltypist/archive/refs/tags/"] +sources = ["%(version)s.tar.gz"] + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('scikit-learn', '1.0.1'), + ('openpyxl', '3.0.9'), + ('scanpy', '1.8.2'), + ('leidenalg', '0.8.8'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_commands = ["celltypist --help"] + +moduleclass = 'bio' \ No newline at end of file diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..41f92cc59e6 --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.0.9' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('lxml', '4.6.3'), + ('Pillow', '8.3.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('et_xmlfile', '1.1.0', { + 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + }), +] + +moduleclass = 'data' From 57e8228bda383b73fffe1493a6bc695fd747e404 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Mon, 23 May 2022 13:52:27 +0100 Subject: [PATCH 3814/9987] remove OpenMPI from this PR (use #15426) --- .../o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb deleted file mode 100644 index 390744e2e43..00000000000 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'OpenMPI' -version = '4.1.4rc1' - -homepage = 'https://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-3 implementation.""" - -toolchain = {'name': 'GCC', 'version': '11.3.0'} - -source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['46169edd9cf8366608684e5c6a342650b2393d46c9f9a380add8e09f1f8001de'] - -builddependencies = [ - ('pkgconf', '1.8.0'), -] - -dependencies = [ - ('zlib', '1.2.12'), - ('hwloc', '2.7.1'), - ('libevent', '2.1.12'), - ('UCX', '1.12.1'), - ('libfabric', '1.15.1'), - ('PMIx', '4.1.2'), -] - -# disable MPI1 compatibility for now, see what breaks... -# configopts = '--enable-mpi1-compatibility ' - -# to enable SLURM integration (site-specific) -# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' - -moduleclass = 'mpi' From 314279e39e273995abaee6881454346ef13f1dfd Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 23 May 2022 14:57:16 +0200 Subject: [PATCH 3815/9987] Added checksums + added new line to end of file --- .../easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb | 1 + .../easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb index 6a298747054..7ada1382934 100644 --- a/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb @@ -8,6 +8,7 @@ description = "A tool for semi-automatic cell type annotation" source_urls = ["https://github.com/Teichlab/celltypist/archive/refs/tags/"] sources = ["%(version)s.tar.gz"] +checksums = ['dd020902acdb13d2f138ac20ffb6ae28fd6f2d7b758ac6ab05bd4b9030d43e8e'] toolchain = {'name': 'foss', 'version': '2021b'} diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb index 41f92cc59e6..15296c110da 100644 --- a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb @@ -27,6 +27,7 @@ exts_list = [ 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], }), (name, version, { + 'checksums': ['40f568b9829bf9e446acfffce30250ac1fa39035124d55fc024025c41481c90f'], }), ] From 6cd72e3878d03949c088dc6c6e79cfc45744dd6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 May 2022 15:58:23 +0200 Subject: [PATCH 3816/9987] adding easyconfigs: ruamel.yaml-0.17.21-GCCcore-11.2.0.eb --- .../ruamel.yaml-0.17.21-GCCcore-11.2.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..62cdda5df2a --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.17.21' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.clib', '0.2.6', { + 'checksums': ['4ff604ce439abb20794f05613c374759ce10e3595d1867764dd1ae675b85acbd'], + 'modulename': False, + }), + (name, version, { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('configobj', '5.0.6', { + 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], + }), + ('ruamel.yaml.base', '0.3.0', { + 'checksums': ['bee661f95a842c3e90f83560f3a87ad3f9548ed4874af98f36b32aaf8a27462a'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.5.10', { + 'checksums': ['043c149c5517cfd0c7d02bd934224e1c9b0053a05e292a14f1b1a7f15bf0a943'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' From 1e501954a9e51828ed5d180922333a9ace97e661 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 23 May 2022 16:07:41 +0200 Subject: [PATCH 3817/9987] Forgot to save new line --- .../easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb index 7ada1382934..24f0500b7d8 100644 --- a/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb @@ -26,4 +26,4 @@ download_dep_fail = True sanity_check_commands = ["celltypist --help"] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 00bf2a9de213f3b98c8c2311ca3ae846eea8b3a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 May 2022 17:27:07 +0200 Subject: [PATCH 3818/9987] {bio}[GCC/11.2.0] mosdepth v0.3.3, Nim v1.6.6 --- .../m/mosdepth/mosdepth-0.3.3-GCC-11.2.0.eb | 48 +++++++++++++++++++ .../n/Nim/Nim-1.6.6-GCCcore-11.2.0.eb | 17 +++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.3-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/n/Nim/Nim-1.6.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.3-GCC-11.2.0.eb b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..6637f1b8cb1 --- /dev/null +++ b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.3-GCC-11.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'Binary' + +name = 'mosdepth' +version = '0.3.3' +local_hts_nim_ver = '0.3.22' + +homepage = 'https://github.com/brentp/mosdepth' +description = "Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = [ + { + 'source_urls': ['https://github.com/brentp/hts-nim/archive/'], + 'download_filename': 'v%s.tar.gz' % local_hts_nim_ver, + 'filename': 'hts-nim-%s.tar.gz' % local_hts_nim_ver, + }, + { + 'source_urls': ['https://github.com/brentp/mosdepth/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, +] +checksums = [ + '0d2f13b122a59923dc32e479118012396925c2332ec6b260de1d99137f04866c', # hts-nim-0.3.22.tar.gz + '71edbefef8e3a43ddf41f79e24f4a11eb208e6fc0957e4431294a5e9517a3c14', # mosdepth-0.3.3.tar.gz +] + +dependencies = [ + ('Nim', '1.6.6'), + ('HTSlib', '1.14'), + ('PCRE', '8.45'), +] + +extract_sources = True + +install_cmd = "cd %(builddir)s/hts-nim-*/ && nimble install --nimbleDir:%(installdir)s --verbose -y && " +install_cmd += "cd ../mosdepth-*/ && sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " +install_cmd += "nimble install --nimbleDir:%(installdir)s --verbose -y" + +sanity_check_paths = { + 'files': ['bin/mosdepth'], + 'dirs': ['pkgs/hts-%s' % local_hts_nim_ver, 'pkgs/mosdepth-%(version)s'], +} + +sanity_check_commands = ["mosdepth --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/Nim/Nim-1.6.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/Nim/Nim-1.6.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..487417de63d --- /dev/null +++ b/easybuild/easyconfigs/n/Nim/Nim-1.6.6-GCCcore-11.2.0.eb @@ -0,0 +1,17 @@ +name = 'Nim' +version = '1.6.6' + +homepage = 'https://nim-lang.org/' +description = "Nim is a systems and applications programming language." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://nim-lang.org/download/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['67b111ce6f3861503b9fcc1cae59fc34d0122566d3ecfef3a064a2174121a452'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('libreadline', '8.1')] + +moduleclass = 'lang' From c8a05a6cc23647f03b89a898f794f147583521f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 May 2022 17:28:38 +0200 Subject: [PATCH 3819/9987] stick to GCCcore/10.3.0 toolchain for num2words + fix minor style issues --- ....eb => num2words-0.5.10-GCCcore-10.3.0.eb} | 20 ++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/n/num2words/{num2words-0.5.10-foss-2021a.eb => num2words-0.5.10-GCCcore-10.3.0.eb} (65%) diff --git a/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-GCCcore-10.3.0.eb similarity index 65% rename from easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb rename to easybuild/easyconfigs/n/num2words/num2words-0.5.10-GCCcore-10.3.0.eb index 2d2be56286a..8f90ac679f5 100644 --- a/easybuild/easyconfigs/n/num2words/num2words-0.5.10-foss-2021a.eb +++ b/easybuild/easyconfigs/n/num2words/num2words-0.5.10-GCCcore-10.3.0.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' name = 'num2words' version = '0.5.10' @@ -6,20 +6,30 @@ version = '0.5.10' homepage = "https://github.com/savoirfairelinux/num2words" description = "Modules to convert numbers to words. 42 --> forty-two" -toolchain = {'name': 'foss', 'version': '2021a'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/savoirfairelinux/num2words/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['ff107ecc0b6709bedf31fdb9e2ca45d29d3fd34b9eb6a0b89a862f337ac5ff00'] +builddependencies = [ + ('binutils', '2.36.1'), +] + dependencies = [ ('Python', '3.9.5'), ] -use_pip = True -sanity_pip_check = True download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/num2words'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} sanity_check_commands = ["num2words 42"] -moduleclass = "tools" +sanity_pip_check = True + +moduleclass = 'tools' From 2c1dc28d097d162436b283a4936ab322faeec815 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 May 2022 11:23:11 +0200 Subject: [PATCH 3820/9987] adding easyconfigs: MUSCLE-3.8.1551-GCC-10.2.0.eb --- .../m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb new file mode 100644 index 00000000000..75cf15432a6 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = "3.8.1551" + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.drive5.com/muscle/'] +sources = ['%(namelower)s_src_%(version)s.tar.gz'] +checksums = ['c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e'] + +# use correct compiler flags + +# don't use -static when linking, since that implies requiring glibc-static to be installed +buildopts = 'CFLAGS="$CXXFLAGS" LDLIBS="-lm"' + +files_to_copy = [(["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/%(namelower)s"], + 'dirs': [], +} + +moduleclass = 'bio' From aea1ee6b71de067aee01dc68b052650dc517713c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 May 2022 11:24:22 +0200 Subject: [PATCH 3821/9987] add chkptstanr extension to R v4.2.0 --- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 5035a318f69..621dfe94ff8 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -3331,6 +3331,9 @@ exts_list = [ ('RhpcBLASctl', '0.21-247.1', { 'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'], }), + ('chkptstanr', '0.1.1', { + 'checksums': ['433b29d597d7ea6c21ed652782a7bf2d766f9223a3b7bfed235c8fe7fffd175c'], + }), ] moduleclass = 'lang' From 3e8ec3df744c8c8bd801f990fc9c2d5088370fc9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 May 2022 11:24:38 +0200 Subject: [PATCH 3822/9987] adding easyconfigs: RAxML-NG-1.1.0-GCC-11.2.0.eb --- .../r/RAxML-NG/RAxML-NG-1.1.0-GCC-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.1.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.1.0-GCC-11.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.1.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..53e8033612e --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.1.0-GCC-11.2.0.eb @@ -0,0 +1,43 @@ +# EasyBuild easyconfig +# +# Contributed from Fred Hutchinson Cancer Research Center, Seattle WA, US +# John Dey jfdey@fredhutch.org +# +easyblock = 'CMakeMake' + +name = 'RAxML-NG' +version = '1.1.0' + +homepage = 'https://github.com/amkozlov/raxml-ng' +description = """RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) + optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree + Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/amkozlov', + 'repo_name': '%(namelower)s', + 'tag': '%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 0ce7041d3f53ae5dec7a065147eabe70a2d74934 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 May 2022 11:25:47 +0200 Subject: [PATCH 3823/9987] adding easyconfigs: numba-0.54.1-foss-2021b-CUDA-11.4.1.eb --- .../numba-0.54.1-foss-2021b-CUDA-11.4.1.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..f3783e2fc9e --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.54.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('LLVM', '12.0.1'), + ('CUDA', '11.4.1', '', True), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + +exts_list = [ + ('llvmlite', '0.37.0', { + 'patches': ['llvmlite-0.37.0_fix-LLVM-12.patch'], + 'preinstallopts': local_llvmlite_preinstallopts, + 'checksums': [ + '6392b870cd018ec0c645d6bbb918d6aa0eeca8c62674baaee30862d6b6865b15', # llvmlite-0.37.0.tar.gz + 'bcdc530cfd087e8a9f68a73a80fe73f12c7b2adfdb51ded70cd2f4c404846298', # llvmlite-0.37.0_fix-LLVM-12.patch + ], + }), + (name, version, { + 'patches': ['numba-0.54.1_fix-numpy-1.21.patch'], + 'checksums': [ + 'f9dfc803c864edcc2381219b800abf366793400aea55e26d4d5b7d953e14f43f', # numba-0.54.1.tar.gz + 'f038e7adf0cd60f6bdde219b326aad4224fef46515799578ebbbdffa73224199', # numba-0.54.1_fix-numpy-1.21.patch + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -m llvmlite.tests", + "numba --help", +] + +moduleclass = 'lang' From 3c553387ac9193a79cd2027e55500d80b0f85cb9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 May 2022 16:55:46 +0200 Subject: [PATCH 3824/9987] rename source tarball for smooth-topk after download + also set moduleclass --- .../smooth-topk-1.0-20210817-foss-2021a.eb | 22 ++++++++++++------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb index 784b2db7173..e1854dc6989 100644 --- a/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb +++ b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a.eb @@ -1,10 +1,10 @@ -easyblock = "PythonBundle" +easyblock = 'PythonBundle' -name = "smooth-topk" -version = "1.0-20210817" -local_commit = "12c1645f187e2fa0c05f47bf1fe48864d4bd2707" +name = 'smooth-topk' +version = '1.0-20210817' +local_commit = '12c1645' -homepage = "https://github.com/oval-group/smooth-topk" +homepage = 'https://github.com/oval-group/smooth-topk' description = "Smooth Loss Functions for Deep Top-k Classification" toolchain = {'name': 'foss', 'version': '2021a'} @@ -18,16 +18,22 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True exts_list = [ ('logger', '1.4', { 'checksums': ['4ecac57133c6376fa215f0fe6b4dc4d60e4d1ad8be005cab4e8a702df682f8b3'], }), (name, version, { - 'modulename': 'topk', 'source_urls': ['https://github.com/oval-group/smooth-topk/archive/'], - 'sources': ['%s.tar.gz' % local_commit], + 'sources': [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, + }], 'checksums': ['ccba089b155c196bb43ab522b5ae00a58d332d856c2ec83b9635cab5eae62be5'], + 'modulename': 'topk', }), ] + +sanity_pip_check = True + +moduleclass = 'lib' From b8d87bcc7e8438b2235acf4573fe08bad65b4415 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 May 2022 17:00:00 +0200 Subject: [PATCH 3825/9987] {cae}[intel/2021a] OpenFOAM v9, ParaView v5.9.1, CGAL v4.14.3, SCOTCH v6.1.0 --- .../c/CGAL/CGAL-4.14.3-iimpi-2021a.eb | 37 ++++++++++++ .../o/OpenFOAM/OpenFOAM-9-intel-2021a.eb | 37 ++++++++++++ .../ParaView-5.9.1-intel-2021a-mpi.eb | 60 +++++++++++++++++++ .../s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb | 19 ++++++ 4 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-intel-2021a.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-intel-2021a-mpi.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb new file mode 100644 index 00000000000..5c3fd5e8577 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb @@ -0,0 +1,37 @@ +name = 'CGAL' +version = '4.14.3' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['5bafe7abe8435beca17a1082062d363368ec1e3f0d6581bb0da8b010fb389fe4'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Eigen', '3.3.9'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.9.5'), + ('Boost', '1.76.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('Mesa', '21.1.1'), + ('libGLU', '9.0.1'), + ('Qt5', '5.15.2'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-intel-2021a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-intel-2021a.eb new file mode 100644 index 00000000000..bcf1776f980 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-intel-2021a.eb @@ -0,0 +1,37 @@ +name = 'OpenFOAM' +version = '9' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-%(version)s-cleanup.patch'] +checksums = [ + '0c48fb56e2fbb4dd534112811364d3b2dc12106e670a6486b361e4f864b435ee', # version-9.tar.gz + '4b638891f32badde1a5b1b364bc3bd5e0eda180b9d9a8afdf797d5818b8b494e', # OpenFOAM-9-cleanup.patch +] + +builddependencies = [ + ('Bison', '3.7.6'), + ('CMake', '3.20.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.1'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('CGAL', '4.14.3'), + ('ParaView', '5.9.1', '-mpi'), + ('gnuplot', '5.4.2'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-intel-2021a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-intel-2021a-mpi.eb new file mode 100644 index 00000000000..acf68e2e8ce --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-intel-2021a-mpi.eb @@ -0,0 +1,60 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.9.1' +versionsuffix = '-mpi' + +homepage = "https://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +checksums = ['efbcba00ba38c23d0ada1bde7144a8745caa308d9e1f94a4a71d8af63732266f'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('XZ', '5.2.5'), + ('HDF5', '1.10.7'), + ('netCDF', '4.8.0'), + ('libGLU', '9.0.1'), + ('X11', '20210518'), + ('Mesa', '21.1.1'), + ('Qt5', '5.15.2'), + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.2'), + ('Szip', '2.1.1'), +] + +builddependencies = [('CMake', '3.20.1')] + +separate_build_dir = True + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': ['lib64/python%(pyshortver)s/site-packages', 'lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb new file mode 100644 index 00000000000..7baa08f4825 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb @@ -0,0 +1,19 @@ +name = 'SCOTCH' +version = '6.1.0' + +homepage = 'https://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' From 77d3ec06bce92afd7ab53d4dc7916b8dbaf75bc1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 May 2022 19:38:31 +0200 Subject: [PATCH 3826/9987] don't enable separate_build_dir in RAxML-NG easyconfig since it's already enabled by default Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.1.0-GCC-11.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.1.0-GCC-11.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.1.0-GCC-11.2.0.eb index 53e8033612e..e6003772f6c 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.1.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.1.0-GCC-11.2.0.eb @@ -33,8 +33,6 @@ builddependencies = [ ('flex', '2.6.4'), ] -separate_build_dir = True - sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': [], From b708a2318f4c2e3ce4923a8bfd9c584a3ca9714f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 May 2022 20:08:34 +0200 Subject: [PATCH 3827/9987] adding easyconfigs: smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb --- ...opk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ecbc8b58ffd --- /dev/null +++ b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'smooth-topk' +version = '1.0-20210817' +local_commit = '12c1645' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/oval-group/smooth-topk' +description = "Smooth Loss Functions for Deep Top-k Classification" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('tqdm', '4.61.2'), + ('PyTorch', '1.10.0', versionsuffix), + ('SciPy-bundle', '2021.05'), + ('torchvision', '0.11.1', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('logger', '1.4', { + 'checksums': ['4ecac57133c6376fa215f0fe6b4dc4d60e4d1ad8be005cab4e8a702df682f8b3'], + }), + (name, version, { + 'source_urls': ['https://github.com/oval-group/smooth-topk/archive/'], + 'sources': [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, + }], + 'checksums': ['ccba089b155c196bb43ab522b5ae00a58d332d856c2ec83b9635cab5eae62be5'], + 'modulename': 'topk', + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From aea4bdaa77110c41cbb73f09a16d134a32cfb71b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 25 May 2022 09:35:55 +0200 Subject: [PATCH 3828/9987] adding easyconfigs: OpenStackClient-5.8.0-GCCcore-11.2.0.eb --- .../OpenStackClient-5.8.0-GCCcore-11.2.0.eb | 133 ++++++++++++++++++ 1 file changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e590dd730ca --- /dev/null +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-5.8.0-GCCcore-11.2.0.eb @@ -0,0 +1,133 @@ +easyblock = 'PythonBundle' + +name = 'OpenStackClient' +version = '5.8.0' + +homepage = 'https://docs.openstack.org/python-openstackclient/latest/' +description = """OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the +command set for Compute, Identity, Image, Network, Object Store and Block +Storage APIs together in a single shell with a uniform command structure.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +dependencies = [ + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), + ('typing-extensions', '3.10.0.2'), +] +builddependencies = [('binutils', '2.37')] + +exts_default_options = { + 'use_pip': True, +} +exts_list = [ + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('importlib_metadata', '4.11.4', { + 'checksums': ['5d26852efe48c0a32b0509ffbc583fda1a2266545a78d104a6f4aff3db17d700'], + }), + ('cmd2', '2.4.1', { + 'checksums': ['f3b0467daca18fca0dc7838de7726a72ab64127a018a377a86a6ed8ebfdbb25f'], + }), + ('charset-normalizer', '2.0.12', { + 'checksums': ['2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597'], + }), + ('jsonpointer', '2.3', { + 'checksums': ['97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a'], + }), + ('prettytable', '3.3.0', { + 'checksums': ['118eb54fd2794049b810893653b20952349df6d3bc1764e7facd8a18064fa9b0'], + }), + ('autopage', '0.5.0', { + 'checksums': ['5305b43cc0798170d7124e5a2feecf969e45f4a0baf75cb351138114eaf76b83'], + }), + ('stevedore', '3.5.0', { + 'checksums': ['f40253887d8712eaa2bb0ea3830374416736dc8ec0e22f5a65092c1174c44335'], + }), + ('cliff', '3.10.1', { + 'checksums': ['045aee3f3c64471965d7ad507ce8474a4e2f20815fbb5405a770f8596a2a00a0'], + }), + ('dogpile.cache', '1.1.5', { + 'checksums': ['0f01bdc329329a8289af9705ff40fadb1f82a28c336f3174e12142b70d31c756'], + }), + ('iso8601', '1.0.2', { + 'checksums': ['27f503220e6845d9db954fb212b95b0362d8b7e6c1b2326a87061c3de93594b1'], + }), + ('jmespath', '1.0.0', { + 'checksums': ['a490e280edd1f57d6de88636992d05b71e97d69a26a19f058ecf7d304474bf5e'], + }), + ('jsonpatch', '1.32', { + 'checksums': ['b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2'], + }), + ('os-service-types', '1.7.0', { + 'checksums': ['31800299a82239363995b91f1ebf9106ac7758542a1e4ef6dc737a5932878c6c'], + }), + ('keystoneauth1', '4.6.0', { + 'checksums': ['066f1addd89114cd6a1b9cb3555c8eaa7d013673ee1034bdfe506068804a9e05'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + ('requestsexceptions', '1.4.0', { + 'checksums': ['b095cbc77618f066d459a02b137b020c37da9f46d9b057704019c9f77dba3065'], + }), + ('openstacksdk', '0.99.0', { + 'modulename': 'openstack', + 'checksums': ['3f73c3cc28089e93b342eb7f348b285f5a65ffe505898be15db250c75bb855eb'], + }), + ('oslo.i18n', '5.1.0', { + 'modulename': 'oslo_i18n', + 'checksums': ['6bf111a6357d5449640852de4640eae4159b5562bbba4c90febb0034abc095d0'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('debtcollector', '2.5.0', { + 'checksums': ['dc9d1ad3f745c43f4bbedbca30f9ffe8905a8c028c9926e61077847d5ea257ab'], + }), + ('oslo.utils', '4.13.0', { + 'modulename': 'oslo_utils', + 'checksums': ['45ba8aaa5ed056a8e8e46059ef93d5c2d7b9c99bc7480e361cf5783e47f28fba'], + }), + ('osc-lib', '2.6.0', { + 'checksums': ['854eabb14ad3480f4cdc63a55944e0ce2d9cc4ce2683cdfddadcd149821e67ab'], + }), + ('oslo.serialization', '4.3.0', { + 'modulename': 'oslo_serialization', + 'checksums': ['3aa472f434aee8bbcc0725312b7f409aa1fa54bbc134904124cf49b0e86b9115'], + }), + ('rfc3986', '2.0.0', { + 'checksums': ['97aacf9dbd4bfd829baad6e6309fa6573aaf1be3f6fa735c8ab05e46cecb261c'], + }), + ('oslo.config', '8.8.0', { + 'modulename': 'oslo_config', + 'checksums': ['96933d3011dae15608a11616bfb00d947e22da3cb09b6ff37ddd7576abd4764c'], + }), + ('python-novaclient', '18.0.0', { + 'modulename': 'novaclient', + 'checksums': ['e9eb2a9bdba464d820c100775c3c2f6493088df66af13dfb9325cc6b865c8d23'], + }), + ('python-keystoneclient', '4.5.0', { + 'modulename': 'keystoneclient', + 'checksums': ['6d7f05c692e7db2692778284c779ae6cea8b2159914b4417a5fa0bfea1e29cdc'], + }), + ('python-cinderclient', '8.3.0', { + 'modulename': 'cinderclient', + 'checksums': ['e00103875029dc85cbb59131d00ccc8534f692956acde32b5a3cc5af4c24580b'], + }), + ('python-openstackclient', version, { + 'modulename': 'openstackclient', + 'checksums': ['334852df8897b95f0581ec12ee287de8c7a9289a208a18f0a8b38777019fd986'], + }), +] + +sanity_pip_check = True +enhance_sanity_check = True +sanity_check_commands = ['openstack -h'] + +sanity_check_paths = { + 'files': ['bin/openstack'], + 'dirs': ["bin", 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' From 72d1403b37c0504a6f4ef3ce1dd0a004d0b933dd Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 25 May 2022 10:35:53 +0100 Subject: [PATCH 3829/9987] adding easyconfigs: Bazel-5.1.1-GCCcore-11.3.0.eb, Zip-3.0-GCCcore-11.3.0.eb --- .../b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb | 33 +++++++++++++++ .../z/Zip/Zip-3.0-GCCcore-11.3.0.eb | 40 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..666c940a93c --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +name = 'Bazel' +version = '5.1.1' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = [ + 'Bazel-3.7.1_fix-protobuf-env.patch', + 'Bazel-3.7.2_fix-GCC-11.patch', +] +checksums = [ + '7f5d3bc1d344692b2400f3765fd4b5c0b636eb4e7a8a7b17923095c7b56a4f78', # bazel-5.1.1-dist.zip + '8706ecc99b658e0a96c38dc2c23e44da35059b85f308602aac76a6d6680376e7', # Bazel-3.7.1_fix-protobuf-env.patch + '7fd5846f2ed1f27af9528a900f284f95ad982f3e7d486264c3bdee890a9c22fb', # Bazel-3.7.2_fix-GCC-11.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4'), + ('Zip', '3.0'), +] + +dependencies = [('Java', '13', '', True)] + +runtest = True +testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e1a45c110cb --- /dev/null +++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Zip' +version = '3.0' + +homepage = 'http://www.info-zip.org/Zip.html' +description = """Zip is a compression and file packaging/archive utility. +Although highly compatible both with PKWARE's PKZIP and PKUNZIP +utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives +have been portability and other-than-MSDOS functionality""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' +buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' +buildopts += 'generic_gcc' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["zip --version"] + +moduleclass = 'tools' From a93cf12d2b00afdc318503a255a72a44f696d7fe Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 25 May 2022 12:24:23 +0000 Subject: [PATCH 3830/9987] Change _ to - for more consistent patch naming --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb | 4 ++-- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 4 ++-- ...ch => OpenMPI-4.1.1_build-with-internal-cuda-header.patch} | 0 3 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/o/OpenMPI/{OpenMPI-4.1.1_build_with_internal_cuda_header.patch => OpenMPI-4.1.1_build-with-internal-cuda-header.patch} (100%) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb index 84c6f236bbb..eff9374a0b9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb @@ -15,7 +15,7 @@ patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', - 'OpenMPI-4.1.1_build_with_internal_cuda_header.patch', + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -25,7 +25,7 @@ checksums = [ '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', - # OpenMPI-4.1.1_build_with_internal_cuda_header.patch + # OpenMPI-4.1.1_build-with-internal-cuda-header.patch '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index 7dea8ac1c65..f1771a747a4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -14,7 +14,7 @@ patches = [ 'OpenMPI-4.1.1_opal-pmix-package-rank.patch', 'OpenMPI-4.1.1_pmix3x-protection.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', - 'OpenMPI-4.1.1_build_with_internal_cuda_header.patch', + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -26,7 +26,7 @@ checksums = [ '384ef9f1fa803b0d71dae2ec0748d0f20295992437532afedf21478bda164ff8', # OpenMPI-4.1.1_pmix3x-protection.patch # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', - # OpenMPI-4.1.1_build_with_internal_cuda_header.patch + # OpenMPI-4.1.1_build-with-internal-cuda-header.patch '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build-with-internal-cuda-header.patch similarity index 100% rename from easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch rename to easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build-with-internal-cuda-header.patch From b5ed84f6fdbe3a16ccaa5f9674fa73d38bb42b91 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 25 May 2022 12:38:04 +0000 Subject: [PATCH 3831/9987] Add patch removing most Open MPI runtime overhead when CUDA is enabled. The overhead was there even if no GPU is available. --- .../o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb | 3 + .../o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 3 + ...4.1.1_opal-datatype-cuda-performance.patch | 456 ++++++++++++++++++ 3 files changed, 462 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_opal-datatype-cuda-performance.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb index eff9374a0b9..73c3bf883db 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb @@ -16,6 +16,7 @@ patches = [ 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -27,6 +28,8 @@ checksums = [ 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', # OpenMPI-4.1.1_build-with-internal-cuda-header.patch '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', + # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index f1771a747a4..3addfaee232 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -15,6 +15,7 @@ patches = [ 'OpenMPI-4.1.1_pmix3x-protection.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', ] checksums = [ 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 @@ -28,6 +29,8 @@ checksums = [ 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', # OpenMPI-4.1.1_build-with-internal-cuda-header.patch '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', + # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_opal-datatype-cuda-performance.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_opal-datatype-cuda-performance.patch new file mode 100644 index 00000000000..8c1a1f8ec35 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_opal-datatype-cuda-performance.patch @@ -0,0 +1,456 @@ +If Open MPI is built with support for CUDA there's a small +(up to 10%) performance penalty for small messages due to overhead +in the datatype memory copy functionality. + +This eliminates most of this overhead as follows: +1. Seperate compilation of CUDA code paths in pack/unpack routines + instead of runtime checks in inner loops, similar to the existing + checksum functionality. +2. Expose opal_cuda_enabled variable so it can be checked directly + in opal_datatype_copy_content_same_ddt() instead of calling a + function. +3. Eliminate cbmemcpy function pointer as it always points to + opal_cuda_memcpy(), and a direct call is cheaper. + +Signed off by Bart Oldeman + +diff --git a/opal/datatype/Makefile.am b/opal/datatype/Makefile.am +index daaaa8e4b0..ef2da1cd81 100644 +--- a/opal/datatype/Makefile.am ++++ b/opal/datatype/Makefile.am +@@ -44,6 +44,11 @@ noinst_LTLIBRARIES = \ + # these sources will be compiled with the special -D + libdatatype_reliable_la_SOURCES = opal_datatype_pack.c opal_datatype_unpack.c + libdatatype_reliable_la_CFLAGS = -DCHECKSUM $(AM_CFLAGS) ++if OPAL_cuda_support ++libdatatype_gpu_la_SOURCES = opal_datatype_pack.c opal_datatype_unpack.c ++libdatatype_gpu_la_CFLAGS = -DOPAL_DATATYPE_PACK_UNPACK_GPU $(AM_CFLAGS) ++noinst_LTLIBRARIES += libdatatype_gpu.la ++endif + + # these sources will be compiled with the normal CFLAGS only + libdatatype_la_SOURCES = \ +@@ -69,6 +74,9 @@ libdatatype_la_SOURCES = \ + opal_datatype_unpack.c + + libdatatype_la_LIBADD = libdatatype_reliable.la ++if OPAL_cuda_support ++libdatatype_la_LIBADD += libdatatype_gpu.la ++endif + + # Conditionally install the header files + if WANT_INSTALL_HEADERS +diff --git a/opal/datatype/opal_convertor.c b/opal/datatype/opal_convertor.c +index 3931d99d17..33aebe2612 100644 +--- a/opal/datatype/opal_convertor.c ++++ b/opal/datatype/opal_convertor.c +@@ -40,8 +40,6 @@ + #include "opal/datatype/opal_convertor_internal.h" + #if OPAL_CUDA_SUPPORT + #include "opal/datatype/opal_datatype_cuda.h" +-#define MEMCPY_CUDA( DST, SRC, BLENGTH, CONVERTOR ) \ +- CONVERTOR->cbmemcpy( (DST), (SRC), (BLENGTH), (CONVERTOR) ) + #endif + + static void opal_convertor_construct( opal_convertor_t* convertor ) +@@ -51,9 +49,6 @@ static void opal_convertor_construct( opal_convertor_t* convertor ) + convertor->partial_length = 0; + convertor->remoteArch = opal_local_arch; + convertor->flags = OPAL_DATATYPE_FLAG_NO_GAPS | CONVERTOR_COMPLETED; +-#if OPAL_CUDA_SUPPORT +- convertor->cbmemcpy = &opal_cuda_memcpy; +-#endif + } + + +@@ -241,11 +236,7 @@ int32_t opal_convertor_pack( opal_convertor_t* pConv, + if( OPAL_LIKELY(NULL == iov[i].iov_base) ) + iov[i].iov_base = (IOVBASE_TYPE *) base_pointer; + else +-#if OPAL_CUDA_SUPPORT +- MEMCPY_CUDA( iov[i].iov_base, base_pointer, iov[i].iov_len, pConv ); +-#else + MEMCPY( iov[i].iov_base, base_pointer, iov[i].iov_len ); +-#endif + pending_length -= iov[i].iov_len; + base_pointer += iov[i].iov_len; + } +@@ -258,11 +249,7 @@ complete_contiguous_data_pack: + if( OPAL_LIKELY(NULL == iov[i].iov_base) ) + iov[i].iov_base = (IOVBASE_TYPE *) base_pointer; + else +-#if OPAL_CUDA_SUPPORT +- MEMCPY_CUDA( iov[i].iov_base, base_pointer, iov[i].iov_len, pConv ); +-#else + MEMCPY( iov[i].iov_base, base_pointer, iov[i].iov_len ); +-#endif + pConv->bConverted = pConv->local_size; + *out_size = i + 1; + pConv->flags |= CONVERTOR_COMPLETED; +@@ -296,11 +283,7 @@ int32_t opal_convertor_unpack( opal_convertor_t* pConv, + if( iov[i].iov_len >= pending_length ) { + goto complete_contiguous_data_unpack; + } +-#if OPAL_CUDA_SUPPORT +- MEMCPY_CUDA( base_pointer, iov[i].iov_base, iov[i].iov_len, pConv ); +-#else + MEMCPY( base_pointer, iov[i].iov_base, iov[i].iov_len ); +-#endif + pending_length -= iov[i].iov_len; + base_pointer += iov[i].iov_len; + } +@@ -310,11 +293,7 @@ int32_t opal_convertor_unpack( opal_convertor_t* pConv, + + complete_contiguous_data_unpack: + iov[i].iov_len = pending_length; +-#if OPAL_CUDA_SUPPORT +- MEMCPY_CUDA( base_pointer, iov[i].iov_base, iov[i].iov_len, pConv ); +-#else + MEMCPY( base_pointer, iov[i].iov_base, iov[i].iov_len ); +-#endif + pConv->bConverted = pConv->local_size; + *out_size = i + 1; + pConv->flags |= CONVERTOR_COMPLETED; +@@ -530,7 +509,7 @@ size_t opal_convertor_compute_remote_size( opal_convertor_t* pConvertor ) + \ + convertor->remote_size = convertor->local_size; \ + if( OPAL_LIKELY(convertor->remoteArch == opal_local_arch) ) { \ +- if( !(convertor->flags & CONVERTOR_WITH_CHECKSUM) && \ ++ if( !(convertor->flags & (CONVERTOR_WITH_CHECKSUM | CONVERTOR_CUDA)) && \ + ((convertor->flags & OPAL_DATATYPE_FLAG_NO_GAPS) || \ + ((convertor->flags & OPAL_DATATYPE_FLAG_CONTIGUOUS) && (1 == count))) ) { \ + return OPAL_SUCCESS; \ +@@ -541,8 +520,8 @@ size_t opal_convertor_compute_remote_size( opal_convertor_t* pConvertor ) + opal_convertor_compute_remote_size( convertor ); \ + assert( NULL != convertor->use_desc->desc ); \ + /* For predefined datatypes (contiguous) do nothing more */ \ +- /* if checksum is enabled then always continue */ \ +- if( ((convertor->flags & (CONVERTOR_WITH_CHECKSUM | OPAL_DATATYPE_FLAG_NO_GAPS)) \ ++ /* if checksum or cuda is enabled then always continue */ \ ++ if( ((convertor->flags & (CONVERTOR_WITH_CHECKSUM | CONVERTOR_CUDA | OPAL_DATATYPE_FLAG_NO_GAPS)) \ + == OPAL_DATATYPE_FLAG_NO_GAPS) && \ + ((convertor->flags & (CONVERTOR_SEND | CONVERTOR_HOMOGENEOUS)) == \ + (CONVERTOR_SEND | CONVERTOR_HOMOGENEOUS)) ) { \ +@@ -592,7 +571,19 @@ int32_t opal_convertor_prepare_for_recv( opal_convertor_t* convertor, + } + } + } else +-#endif /* defined(CHECKSUM) */ ++#elif OPAL_CUDA_SUPPORT ++ if (OPAL_UNLIKELY(convertor->flags & CONVERTOR_CUDA)) { ++ if (OPAL_UNLIKELY(!(convertor->flags & CONVERTOR_HOMOGENEOUS))) { ++ convertor->fAdvance = opal_unpack_general_gpu; ++ } else { ++ if (convertor->pDesc->flags & OPAL_DATATYPE_FLAG_CONTIGUOUS) { ++ convertor->fAdvance = opal_unpack_homogeneous_contig_gpu; ++ } else { ++ convertor->fAdvance = opal_generic_simple_unpack_gpu; ++ } ++ } ++ } else ++#endif /* defined(CHECKSUM) || OPAL_CUDA_SUPPORT */ + if( OPAL_UNLIKELY(!(convertor->flags & CONVERTOR_HOMOGENEOUS)) ) { + convertor->fAdvance = opal_unpack_general; + } else { +@@ -636,7 +627,25 @@ int32_t opal_convertor_prepare_for_send( opal_convertor_t* convertor, + } + } + } else +-#endif /* defined(CHECKSUM) */ ++#elif OPAL_CUDA_SUPPORT ++ if (OPAL_UNLIKELY(convertor->flags & CONVERTOR_CUDA)) { ++ if (CONVERTOR_SEND_CONVERSION ++ == (convertor->flags & (CONVERTOR_SEND_CONVERSION | CONVERTOR_HOMOGENEOUS))) { ++ convertor->fAdvance = opal_pack_general_gpu; ++ } else { ++ if (datatype->flags & OPAL_DATATYPE_FLAG_CONTIGUOUS) { ++ if (((datatype->ub - datatype->lb) == (ptrdiff_t) datatype->size) ++ || (1 >= convertor->count)) { ++ convertor->fAdvance = opal_pack_homogeneous_contig_gpu; ++ } else { ++ convertor->fAdvance = opal_pack_homogeneous_contig_with_gaps_gpu; ++ } ++ } else { ++ convertor->fAdvance = opal_generic_simple_pack_gpu; ++ } ++ } ++ } else ++#endif /* defined(CHECKSUM) || OPAL_CUDA_SUPPORT */ + if( CONVERTOR_SEND_CONVERSION == (convertor->flags & (CONVERTOR_SEND_CONVERSION|CONVERTOR_HOMOGENEOUS)) ) { + convertor->fAdvance = opal_pack_general; + } else { +@@ -694,9 +703,6 @@ int opal_convertor_clone( const opal_convertor_t* source, + destination->bConverted = source->bConverted; + destination->stack_pos = source->stack_pos; + } +-#if OPAL_CUDA_SUPPORT +- destination->cbmemcpy = source->cbmemcpy; +-#endif + return OPAL_SUCCESS; + } + +diff --git a/opal/datatype/opal_convertor.h b/opal/datatype/opal_convertor.h +index b24d94c37b..53b6f0d526 100644 +--- a/opal/datatype/opal_convertor.h ++++ b/opal/datatype/opal_convertor.h +@@ -118,7 +118,6 @@ struct opal_convertor_t { + dt_stack_t static_stack[DT_STATIC_STACK_SIZE]; /**< local stack for small datatypes */ + + #if OPAL_CUDA_SUPPORT +- memcpy_fct_t cbmemcpy; /**< memcpy or cuMemcpy */ + void * stream; /**< CUstream for async copy */ + #endif + }; +diff --git a/opal/datatype/opal_datatype_copy.c b/opal/datatype/opal_datatype_copy.c +index c70bdd24df..d7c10af3dc 100644 +--- a/opal/datatype/opal_datatype_copy.c ++++ b/opal/datatype/opal_datatype_copy.c +@@ -86,14 +86,6 @@ static size_t opal_datatype_memop_block_size = 128 * 1024; + #define MEM_OP opal_cuda_memmove + #include "opal_datatype_copy.h" + +-#define SET_CUDA_COPY_FCT(cuda_device_bufs, fct, copy_function) \ +- do { \ +- if (true == cuda_device_bufs) { \ +- fct = copy_function; \ +- } \ +- } while(0) +-#else +-#define SET_CUDA_COPY_FCT(cuda_device_bufs, fct, copy_function) + #endif + + int32_t opal_datatype_copy_content_same_ddt( const opal_datatype_t* datatype, int32_t count, +@@ -102,10 +94,6 @@ int32_t opal_datatype_copy_content_same_ddt( const opal_datatype_t* datatype, in + ptrdiff_t extent; + int32_t (*fct)( const opal_datatype_t*, int32_t, char*, char*); + +-#if OPAL_CUDA_SUPPORT +- bool cuda_device_bufs = opal_cuda_check_bufs(destination_base, source_base); +-#endif +- + DO_DEBUG( opal_output( 0, "opal_datatype_copy_content_same_ddt( %p, %d, dst %p, src %p )\n", + (void*)datatype, count, (void*)destination_base, (void*)source_base ); ); + +@@ -122,20 +110,25 @@ int32_t opal_datatype_copy_content_same_ddt( const opal_datatype_t* datatype, in + extent = (datatype->true_ub - datatype->true_lb) + (count - 1) * (datatype->ub - datatype->lb); + + fct = non_overlap_copy_content_same_ddt; +- SET_CUDA_COPY_FCT(cuda_device_bufs, fct, non_overlap_cuda_copy_content_same_ddt); + if( destination_base < source_base ) { + if( (destination_base + extent) > source_base ) { + /* memmove */ + fct = overlap_copy_content_same_ddt; +- SET_CUDA_COPY_FCT(cuda_device_bufs, fct, overlap_cuda_copy_content_same_ddt); + } + } else { + if( (source_base + extent) > destination_base ) { + /* memmove */ + fct = overlap_copy_content_same_ddt; +- SET_CUDA_COPY_FCT(cuda_device_bufs, fct, overlap_cuda_copy_content_same_ddt); + } + } ++ ++#if OPAL_CUDA_SUPPORT ++ if (OPAL_UNLIKELY(opal_cuda_enabled) && opal_cuda_check_bufs(destination_base, source_base)) { ++ fct = (fct == non_overlap_copy_content_same_ddt ? ++ non_overlap_cuda_copy_content_same_ddt : overlap_cuda_copy_content_same_ddt); ++ } ++#endif ++ + return fct( datatype, count, destination_base, source_base ); + } + +diff --git a/opal/datatype/opal_datatype_cuda.c b/opal/datatype/opal_datatype_cuda.c +index 7869f17e90..f3b3cef8da 100644 +--- a/opal/datatype/opal_datatype_cuda.c ++++ b/opal/datatype/opal_datatype_cuda.c +@@ -20,7 +20,7 @@ + + static bool initialized = false; + int opal_cuda_verbose = 0; +-static int opal_cuda_enabled = 0; /* Starts out disabled */ ++int opal_cuda_enabled = 1; /* Starts out enabled */ + static int opal_cuda_output = 0; + static void opal_cuda_support_init(void); + static int (*common_cuda_initialization_function)(opal_common_cuda_function_table_t *) = NULL; +@@ -48,10 +48,6 @@ void mca_cuda_convertor_init(opal_convertor_t* convertor, const void *pUserBuf) + opal_cuda_support_init(); + } + +- /* This is needed to handle case where convertor is not fully initialized +- * like when trying to do a sendi with convertor on the statck */ +- convertor->cbmemcpy = (memcpy_fct_t)&opal_cuda_memcpy; +- + /* If not enabled, then nothing else to do */ + if (!opal_cuda_enabled) { + return; +@@ -192,6 +188,7 @@ static void opal_cuda_support_init(void) + + /* Callback into the common cuda initialization routine. This is only + * set if some work had been done already in the common cuda code.*/ ++ opal_cuda_enabled = 0; + if (NULL != common_cuda_initialization_function) { + if (0 == common_cuda_initialization_function(&ftable)) { + opal_cuda_enabled = 1; +diff --git a/opal/datatype/opal_datatype_cuda.h b/opal/datatype/opal_datatype_cuda.h +index 2789320520..d512e24550 100644 +--- a/opal/datatype/opal_datatype_cuda.h ++++ b/opal/datatype/opal_datatype_cuda.h +@@ -30,4 +30,6 @@ void* opal_cuda_memmove(void * dest, void * src, size_t size); + void opal_cuda_add_initialization_function(int (*fptr)(opal_common_cuda_function_table_t *)); + void opal_cuda_set_copy_function_async(opal_convertor_t* convertor, void *stream); + ++extern int opal_cuda_enabled; ++ + #endif +diff --git a/opal/datatype/opal_datatype_pack.c b/opal/datatype/opal_datatype_pack.c +index b4e03a9bea..f42e292e0b 100644 +--- a/opal/datatype/opal_datatype_pack.c ++++ b/opal/datatype/opal_datatype_pack.c +@@ -45,6 +45,11 @@ + #define opal_pack_homogeneous_contig_with_gaps_function opal_pack_homogeneous_contig_with_gaps_checksum + #define opal_generic_simple_pack_function opal_generic_simple_pack_checksum + #define opal_pack_general_function opal_pack_general_checksum ++#elif defined(OPAL_DATATYPE_PACK_UNPACK_GPU) ++#define opal_pack_homogeneous_contig_function opal_pack_homogeneous_contig_gpu ++#define opal_pack_homogeneous_contig_with_gaps_function opal_pack_homogeneous_contig_with_gaps_gpu ++#define opal_generic_simple_pack_function opal_generic_simple_pack_gpu ++#define opal_pack_general_function opal_pack_general_gpu + #else + #define opal_pack_homogeneous_contig_function opal_pack_homogeneous_contig + #define opal_pack_homogeneous_contig_with_gaps_function opal_pack_homogeneous_contig_with_gaps +diff --git a/opal/datatype/opal_datatype_pack.h b/opal/datatype/opal_datatype_pack.h +index 2a2e79180d..7fbf0c88e2 100644 +--- a/opal/datatype/opal_datatype_pack.h ++++ b/opal/datatype/opal_datatype_pack.h +@@ -19,11 +19,12 @@ + + #include "opal_config.h" + +-#if !defined(CHECKSUM) && OPAL_CUDA_SUPPORT ++#if defined(OPAL_DATATYPE_PACK_UNPACK_GPU) + /* Make use of existing macro to do CUDA style memcpy */ ++#include "opal_datatype_cuda.h" + #undef MEMCPY_CSUM + #define MEMCPY_CSUM( DST, SRC, BLENGTH, CONVERTOR ) \ +- CONVERTOR->cbmemcpy( (DST), (SRC), (BLENGTH), (CONVERTOR) ) ++ opal_cuda_memcpy( (DST), (SRC), (BLENGTH), (CONVERTOR) ) + #endif + + /** +diff --git a/opal/datatype/opal_datatype_prototypes.h b/opal/datatype/opal_datatype_prototypes.h +index 668397112b..111f74f2a4 100644 +--- a/opal/datatype/opal_datatype_prototypes.h ++++ b/opal/datatype/opal_datatype_prototypes.h +@@ -39,6 +39,16 @@ OPAL_DECLSPEC int32_t + opal_unpack_general_checksum( opal_convertor_t* pConvertor, + struct iovec* iov, uint32_t* out_size, + size_t* max_data ); ++#if OPAL_CUDA_SUPPORT ++OPAL_DECLSPEC int32_t ++opal_pack_general_gpu( opal_convertor_t* pConvertor, ++ struct iovec* iov, uint32_t* out_size, ++ size_t* max_data ); ++OPAL_DECLSPEC int32_t ++opal_unpack_general_gpu( opal_convertor_t* pConvertor, ++ struct iovec* iov, uint32_t* out_size, ++ size_t* max_data ); ++#endif + + /* + * Now the internal functions +@@ -83,6 +93,28 @@ int32_t + opal_generic_simple_unpack_checksum( opal_convertor_t* pConvertor, + struct iovec* iov, uint32_t* out_size, + size_t* max_data ); ++#if OPAL_CUDA_SUPPORT ++int32_t ++opal_pack_homogeneous_contig_gpu( opal_convertor_t* pConv, ++ struct iovec* iov, uint32_t* out_size, ++ size_t* max_data ); ++int32_t ++opal_pack_homogeneous_contig_with_gaps_gpu( opal_convertor_t* pConv, ++ struct iovec* iov, uint32_t* out_size, ++ size_t* max_data ); ++int32_t ++opal_generic_simple_pack_gpu( opal_convertor_t* pConvertor, ++ struct iovec* iov, uint32_t* out_size, ++ size_t* max_data ); ++int32_t ++opal_unpack_homogeneous_contig_gpu( opal_convertor_t* pConv, ++ struct iovec* iov, uint32_t* out_size, ++ size_t* max_data ); ++int32_t ++opal_generic_simple_unpack_gpu( opal_convertor_t* pConvertor, ++ struct iovec* iov, uint32_t* out_size, ++ size_t* max_data ); ++#endif + + END_C_DECLS + +diff --git a/opal/datatype/opal_datatype_unpack.c b/opal/datatype/opal_datatype_unpack.c +index 26a5810dc0..668b6624aa 100644 +--- a/opal/datatype/opal_datatype_unpack.c ++++ b/opal/datatype/opal_datatype_unpack.c +@@ -46,6 +46,10 @@ + #define opal_unpack_general_function opal_unpack_general_checksum + #define opal_unpack_homogeneous_contig_function opal_unpack_homogeneous_contig_checksum + #define opal_generic_simple_unpack_function opal_generic_simple_unpack_checksum ++#elif defined(OPAL_DATATYPE_PACK_UNPACK_GPU) ++#define opal_unpack_general_function opal_unpack_general_gpu ++#define opal_unpack_homogeneous_contig_function opal_unpack_homogeneous_contig_gpu ++#define opal_generic_simple_unpack_function opal_generic_simple_unpack_gpu + #else + #define opal_unpack_general_function opal_unpack_general + #define opal_unpack_homogeneous_contig_function opal_unpack_homogeneous_contig +@@ -204,10 +208,10 @@ opal_unpack_partial_predefined(opal_convertor_t *pConvertor, const dt_elem_desc_ + MEMCPY( temporary + start_position, partial_data, length ); + + /* Save the original content of the user memory */ +-#if OPAL_CUDA_SUPPORT ++#if defined(OPAL_DATATYPE_PACK_UNPACK_GPU) + /* In the case where the data is being unpacked from device memory, need to + * use the special host to device memory copy. */ +- pConvertor->cbmemcpy(saved_data, user_data, data_length, pConvertor ); ++ opal_cuda_memcpy(saved_data, user_data, data_length, pConvertor ); + #else + MEMCPY( saved_data, user_data, data_length ); + #endif +@@ -222,15 +226,15 @@ opal_unpack_partial_predefined(opal_convertor_t *pConvertor, const dt_elem_desc_ + + /* Rebuild the data by pulling back the unmodified bytes from the original + * content in the user memory. */ +-#if OPAL_CUDA_SUPPORT ++#if defined(OPAL_DATATYPE_PACK_UNPACK_GPU) + /* Need to copy the modified user_data again so we can see which + * bytes need to be converted back to their original values. */ + { + char resaved_data[16]; +- pConvertor->cbmemcpy(resaved_data, user_data, data_length, pConvertor ); ++ opal_cuda_memcpy(resaved_data, user_data, data_length, pConvertor ); + for(size_t i = 0; i < data_length; i++ ) { + if( unused_byte == resaved_data[i] ) +- pConvertor->cbmemcpy(&user_data[i], &saved_data[i], 1, pConvertor); ++ opal_cuda_memcpy(&user_data[i], &saved_data[i], 1, pConvertor); + } + } + #else +diff --git a/opal/datatype/opal_datatype_unpack.h b/opal/datatype/opal_datatype_unpack.h +index 33db837882..4159a475fc 100644 +--- a/opal/datatype/opal_datatype_unpack.h ++++ b/opal/datatype/opal_datatype_unpack.h +@@ -19,11 +19,12 @@ + + #include "opal_config.h" + +-#if !defined(CHECKSUM) && OPAL_CUDA_SUPPORT ++#if defined(OPAL_DATATYPE_PACK_UNPACK_GPU) + /* Make use of existing macro to do CUDA style memcpy */ ++#include "opal_datatype_cuda.h" + #undef MEMCPY_CSUM + #define MEMCPY_CSUM( DST, SRC, BLENGTH, CONVERTOR ) \ +- CONVERTOR->cbmemcpy( (DST), (SRC), (BLENGTH), (CONVERTOR) ) ++ opal_cuda_memcpy( (DST), (SRC), (BLENGTH), (CONVERTOR) ) + #endif + + /** From 63d81d0058aff107ca63add5985a3533cac5885b Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 25 May 2022 14:39:36 +0000 Subject: [PATCH 3832/9987] Added comment about configopts (@micket) --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb | 1 + easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb index 73c3bf883db..9d2b5068d87 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb @@ -49,6 +49,7 @@ dependencies = [ preconfigopts = './autogen.pl --force && ' +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. configopts = '--with-cuda=internal ' # disable MPI1 compatibility for now, see what breaks... diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index 3addfaee232..24a5ae59bc0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -50,6 +50,7 @@ dependencies = [ preconfigopts = './autogen.pl --force && ' +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. configopts = '--with-cuda=internal ' # disable MPI1 compatibility for now, see what breaks... From f0408566532cc65b72de3b17ec2140d545cb00d6 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 25 May 2022 11:04:13 -0700 Subject: [PATCH 3833/9987] spektral 1.1.0 --- .../spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..b76774997e1 --- /dev/null +++ b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,38 @@ +# easybuild easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Center - Seattle Washington - US +# +easyblock = 'PythonPackage' + +name = 'spektral' +version = '1.1.0' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + +homepage = 'https://github.com/danielegrattarola/spektral' +description = """Spektral is a Python library for graph deep learning. The main goal of this + project is to provide a simple but flexible framework for creating graph neural networks (GNNs).""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3b73549f213f0d36a0bf67595aa3c4d84efb8e0e40d71aeaa1d78ea896245222'] + +dependencies = [ + ('Python', '3.9.6'), + ('lxml', '4.6.3'), + ('SciPy-bundle', '2021.10'), + ('networkx', '2.6.3'), + ('tqdm', '4.62.3'), + ('scikit-learn', '1.0.1'), + ('CUDA', '11.4.1', '', True), + ('TensorFlow', '2.7.1', '-CUDA-%(cudaver)s'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 942d4bf4089090eba430bdc905b888c228aaa52a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 27 May 2022 00:57:50 +0200 Subject: [PATCH 3834/9987] adding easyconfigs: buildenv-default-foss-2021b.eb, buildenv-default-foss-2021b-CUDA-11.4.1.eb --- ...buildenv-default-foss-2021b-CUDA-11.4.1.eb | 19 +++++++++++++++++++ .../b/buildenv/buildenv-default-foss-2021b.eb | 13 +++++++++++++ 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..2aa49ff982a --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,19 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('CUDA', '11.4.1', '', True), + ('UCX-CUDA', '1.11.2', versionsuffix), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b.eb new file mode 100644 index 00000000000..47d30ab8b66 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +moduleclass = 'devel' From 080edcd7bb0f7e0f0df0a2c09faf25806bcad538 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 27 May 2022 10:09:20 +0100 Subject: [PATCH 3835/9987] bump to 4.1.4 release, and update patches to include CUDA performance patch --- ....1.1_build_with_internal_cuda_header.patch | 93 ------------------- .../o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb | 50 ++++++++++ 2 files changed, 50 insertions(+), 93 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch deleted file mode 100644 index 9c5945b7de2..00000000000 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build_with_internal_cuda_header.patch +++ /dev/null @@ -1,93 +0,0 @@ -Allow building Open MPI with --with-cuda=internal, by providing an -internal minimal cuda.h header file. This eliminate the CUDA -(build)dependency; as long as the runtime CUDA version is 8.0+, -libcuda.so will be dlopen'ed and used successfully. - -Author: Bart Oldeman ---- openmpi-4.1.3.orig/config/opal_check_cuda.m4 2022-03-31 16:04:13.000000000 +0000 -+++ openmpi-4.1.3/config/opal_check_cuda.m4 2022-05-04 17:37:57.576260311 +0000 -@@ -45,6 +45,12 @@ - # macro as that would error out after not finding it in the first directory. - # Note that anywhere CUDA aware code is in the Open MPI repository requires - # us to make use of AC_REQUIRE to ensure this check has been done. -+opal_check_cuda_internal="" -+AS_IF([test "$with_cuda" = "internal"], -+ [AC_MSG_RESULT([internal support requested]) -+ with_cuda="${OPAL_TOP_SRCDIR}/opal/mca/common/cuda/cuda" -+ opal_check_cuda_internal=" (internal)" -+ ]) - AS_IF([test "$with_cuda" = "no" || test "x$with_cuda" = "x"], - [opal_check_cuda_happy="no" - AC_MSG_RESULT([not set (--with-cuda=$with_cuda)])], -@@ -124,7 +130,7 @@ - CUDA_SUPPORT=0 - fi - --OPAL_SUMMARY_ADD([[Miscellaneous]],[[CUDA support]],[opal_cuda], [$opal_check_cuda_happy]) -+OPAL_SUMMARY_ADD([[Miscellaneous]],[[CUDA support]],[opal_cuda], [$opal_check_cuda_happy$opal_check_cuda_internal]) - - AM_CONDITIONAL([OPAL_cuda_support], [test "x$CUDA_SUPPORT" = "x1"]) - AC_DEFINE_UNQUOTED([OPAL_CUDA_SUPPORT],$CUDA_SUPPORT, ---- openmpi-4.1.3.orig/opal/mca/common/cuda/cuda/cuda.h 1970-01-01 00:00:00.000000000 +0000 -+++ openmpi-4.1.3/opal/mca/common/cuda/cuda/cuda.h 2022-05-04 18:52:14.991300184 +0000 -@@ -0,0 +1,60 @@ -+/* This header provides minimal parts of the CUDA Driver API, without having to -+ rely on the proprietary CUDA toolkit. -+ -+ References (to avoid copying from NVidia's proprietary cuda.h): -+ https://github.com/gcc-mirror/gcc/blob/master/include/cuda/cuda.h -+ https://github.com/Theano/libgpuarray/blob/master/src/loaders/libcuda.h -+ https://github.com/CPFL/gdev/blob/master/cuda/driver/cuda.h -+ https://github.com/CudaWrangler/cuew/blob/master/include/cuew.h -+*/ -+ -+#define CUDA_VERSION 8000 -+ -+typedef void *CUcontext; -+typedef int CUdevice; -+#if defined(__LP64__) || defined(_WIN64) -+typedef unsigned long long CUdeviceptr; -+#else -+typedef unsigned CUdeviceptr; -+#endif -+typedef void *CUevent; -+typedef void *CUstream; -+ -+typedef enum { -+ CUDA_SUCCESS = 0, -+ CUDA_ERROR_NOT_INITIALIZED = 3, -+ CUDA_ERROR_DEINITIALIZED = 4, -+ CUDA_ERROR_ALREADY_MAPPED = 208, -+ CUDA_ERROR_NOT_READY = 600, -+} CUresult; -+ -+enum { -+ CU_EVENT_DISABLE_TIMING = 0x2, -+ CU_EVENT_INTERPROCESS = 0x4, -+}; -+ -+enum { -+ CU_IPC_MEM_LAZY_ENABLE_PEER_ACCESS = 0x1, -+}; -+ -+typedef enum { -+ CU_POINTER_ATTRIBUTE_CONTEXT = 1, -+ CU_POINTER_ATTRIBUTE_MEMORY_TYPE = 2, -+ CU_POINTER_ATTRIBUTE_SYNC_MEMOPS = 6, -+ CU_POINTER_ATTRIBUTE_BUFFER_ID = 7, -+ CU_POINTER_ATTRIBUTE_IS_MANAGED = 8, -+} CUpointer_attribute; -+ -+typedef enum { -+ CU_MEMORYTYPE_HOST = 0x01, -+} CUmemorytype; -+ -+typedef struct CUipcEventHandle CUipcEventHandle; -+ -+#define CU_IPC_HANDLE_SIZE 64 -+typedef struct CUipcMemHandle_st { -+ char reserved[CU_IPC_HANDLE_SIZE]; -+} CUipcMemHandle; -+ -+CUresult cuPointerGetAttributes (unsigned int numAttributes, -+ CUpointer_attribute *attributes, void **data, CUdeviceptr ptr); diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb new file mode 100644 index 00000000000..d9a823c33d8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb @@ -0,0 +1,50 @@ +name = 'OpenMPI' +version = '4.1.4' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', +] +checksums = [ + '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d', # openmpi-4.1.4.tar.bz2 + # OpenMPI-4.1.1_build-with-internal-cuda-header.patch + '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', + # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', +] + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('Perl', '5.34.1'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('hwloc', '2.7.1'), + ('libevent', '2.1.12'), + ('UCX', '1.12.1'), + ('libfabric', '1.15.1'), + ('PMIx', '4.1.2'), + ('UCC', '1.0.0'), +] + +preconfigopts = './autogen.pl --force && ' + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' + +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From 35869caa593ae4a1637c9173b8bbd321f066dbe5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 27 May 2022 10:11:11 +0100 Subject: [PATCH 3836/9987] remove OpenMPI release candidate --- .../o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb deleted file mode 100644 index 341343fcc47..00000000000 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4rc1-GCC-11.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -name = 'OpenMPI' -version = '4.1.4rc1' - -homepage = 'https://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-3 implementation.""" - -toolchain = {'name': 'GCC', 'version': '11.3.0'} - -source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -sources = [SOURCELOWER_TAR_BZ2] -patches = ['OpenMPI-4.1.1_build_with_internal_cuda_header.patch'] -checksums = [ - '46169edd9cf8366608684e5c6a342650b2393d46c9f9a380add8e09f1f8001de', # openmpi-4.1.4rc1.tar.bz2 - # OpenMPI-4.1.1_build_with_internal_cuda_header.patch - '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', -] - -builddependencies = [ - ('pkgconf', '1.8.0'), - ('Perl', '5.34.1'), - ('Autotools', '20220317'), -] - -dependencies = [ - ('zlib', '1.2.12'), - ('hwloc', '2.7.1'), - ('libevent', '2.1.12'), - ('UCX', '1.12.1'), - ('libfabric', '1.15.1'), - ('PMIx', '4.1.2'), - ('UCC', '1.0.0'), -] - -preconfigopts = './autogen.pl --force && ' - -configopts = '--with-cuda=internal ' - -# disable MPI1 compatibility for now, see what breaks... -# configopts += '--enable-mpi1-compatibility ' - -# to enable SLURM integration (site-specific) -# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' - -moduleclass = 'mpi' From 64ed028069cd011e7b578c4270ebab04ca890682 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 May 2022 14:51:44 +0200 Subject: [PATCH 3837/9987] {toolchain} gompi/2022.05 (+ OSU-Micro-Benchmarks v5.9) --- .../easyconfigs/g/gompi/gompi-2022.05.eb | 20 ++++++++++++++ .../OSU-Micro-Benchmarks-5.9-gompi-2022.05.eb | 26 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2022.05.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022.05.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2022.05.eb b/easybuild/easyconfigs/g/gompi/gompi-2022.05.eb new file mode 100644 index 00000000000..5c575de6aa1 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2022.05.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2022.05' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '11.3.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022.05.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022.05.eb new file mode 100644 index 00000000000..266863179ee --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022.05.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.9' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2022.05'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 8be7ac4ee285e41a2c1aa837d85ec3884929b77f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 27 May 2022 15:26:24 +0100 Subject: [PATCH 3838/9987] adding easyconfigs: json-c-0.16-GCCcore-11.3.0.eb --- .../j/json-c/json-c-0.16-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..de8e08d45c8 --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.16' +local_suff = '-20220414' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['3ecaeedffd99a60b1262819f9e60d7d983844073abc74e495cb822b251904185'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' From 4a2c3c0399d54e5b54733858940ef2f160ea8187 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 27 May 2022 18:29:40 +0200 Subject: [PATCH 3839/9987] adding easyconfigs: magma-2.6.2-foss-2021b-CUDA-11.4.1.eb --- .../magma-2.6.2-foss-2021b-CUDA-11.4.1.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..63a86722411 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,42 @@ +easyblock = "CMakeMake" + +name = 'magma' +version = '2.6.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/magma/downloads/'] +sources = [SOURCE_TAR_GZ] +patches = ['magma-2.6.1_allow-all-sms.patch'] +checksums = [ + '75b554dab00903e2d10b972c913e50e7f88cbc62f3ae432b5a086c7e4eda0a71', # magma-2.6.2.tar.gz + 'b89285bac007b68e88e3b5ddbb7f94dbc8a9d77590e58c352e477574d8dca738', # magma-2.6.1_allow-all-sms.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('CUDAcore', '11.4.1', '', True), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] +# make sure both static and shared libs are built +configopts = [ + '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') +] + +sanity_check_paths = { + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' From 52c767b155b288de6cc207b01ce92c86d8caa4d1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 27 May 2022 19:26:15 +0200 Subject: [PATCH 3840/9987] adding easyconfigs: GCC-9.5.0.eb, GCCcore-9.5.0.eb, Bison-3.8.2-GCCcore-9.5.0.eb, binutils-2.38-GCCcore-9.5.0.eb, flex-2.6.4-GCCcore-9.5.0.eb, help2man-1.49.2-GCCcore-9.5.0.eb, M4-1.4.19-GCCcore-9.5.0.eb, zlib-1.2.12-GCCcore-9.5.0.eb --- .../b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb | 28 ++++++++ .../b/binutils/binutils-2.38-GCCcore-9.5.0.eb | 31 +++++++++ .../f/flex/flex-2.6.4-GCCcore-9.5.0.eb | 34 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-9.5.0.eb | 22 +++++++ .../easyconfigs/g/GCCcore/GCCcore-9.5.0.eb | 66 +++++++++++++++++++ .../help2man/help2man-1.49.2-GCCcore-9.5.0.eb | 25 +++++++ .../m/M4/M4-1.4.19-GCCcore-9.5.0.eb | 29 ++++++++ .../z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb | 30 +++++++++ 8 files changed, 265 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-9.5.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-9.5.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb new file mode 100644 index 00000000000..56c2cc38d82 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '9.5.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.38', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb new file mode 100644 index 00000000000..9e8ca91c080 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.38' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '9.5.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b3f1dc5b17e75328f19bd88250bee2ef9f91fc8cbb7bd48bdb31390338636052'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.12'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb new file mode 100644 index 00000000000..56f3743d5ab --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.5.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.2'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.38', '', True), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-9.5.0.eb b/easybuild/easyconfigs/g/GCC/GCC-9.5.0.eb new file mode 100644 index 00000000000..79a95b0cf0b --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-9.5.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '9.5.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.38', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-9.5.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.5.0.eb new file mode 100644 index 00000000000..17ce889ff68 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-9.5.0.eb @@ -0,0 +1,66 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '9.5.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.1.0.tar.bz2', + 'mpc-1.2.1.tar.gz', + 'isl-0.24.tar.bz2', + 'newlib-4.1.0.tar.gz', + {'download_filename': '7292758.tar.gz', 'filename': 'nvptx-tools-20220412.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', +] +checksums = [ + '15b34072105272a3eb37f6927409f7ce9aa0dd1498efebc35f851d6e6f029a4d', # gcc-9.5.0.tar.gz + 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 + 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 + '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz + 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 + 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz + '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080', # nvptx-tools-20220412.tar.gz + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch + '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.38'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb new file mode 100644 index 00000000000..19d7895e8f1 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.2' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '9.5.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.38', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb new file mode 100644 index 00000000000..95d679a09cf --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '9.5.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.38', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb new file mode 100644 index 00000000000..67c423db857 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.12' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '9.5.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = [ + '91844808532e5ce316b3c010929493c0244f3d37593afd6de04f71821d5136d9', # zlib-1.2.12.tar.gz + 'f35eb05334a4f8d7b40b6c5610a6369f654863b5fa1a19c2507888f918025238', # zlib-1.2.12_fix-CC-logic-in-configure.patch +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.38', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 5fb0e004b924979a534e4c089c6b76681de2088f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 27 May 2022 21:09:00 +0200 Subject: [PATCH 3841/9987] Fix CUDAcore -> CUDA --- .../easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb index 63a86722411..da5c2d7e1a5 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb @@ -24,7 +24,7 @@ builddependencies = [ ] dependencies = [ - ('CUDAcore', '11.4.1', '', True), + ('CUDA', '11.4.1', '', True), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) From e4ebe15bd36b797dbde30f692c7c2947bad9e925 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Sun, 29 May 2022 18:13:02 +0000 Subject: [PATCH 3842/9987] adding easyconfigs: HPL-2.3-foss-2022.05.eb, foss-2022.05.eb, FFTW.MPI-3.3.10-gompi-2022.05.eb, ScaLAPACK-2.2.0-gompi-2022.05-fb.eb and patches: ScaLAPACK-2.2.0_fix-GCC-10.patch --- .../FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.05.eb | 37 +++++++++++ easybuild/easyconfigs/f/foss/foss-2022.05.eb | 28 ++++++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2022.05.eb | 21 ++++++ .../ScaLAPACK-2.2.0-gompi-2022.05-fb.eb | 43 ++++++++++++ .../ScaLAPACK-2.2.0_fix-GCC-10.patch | 65 +++++++++++++++++++ 5 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.05.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2022.05.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.05.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0_fix-GCC-10.patch diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.05.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.05.eb new file mode 100644 index 00000000000..54f03c24575 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.05.eb @@ -0,0 +1,37 @@ +easyblock = 'EB_FFTW' +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022.05'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +with_openmp = False +with_threads = False +with_quad_prec = False + +postinstallcmds = [ + 'rm %(installdir)s/lib/libfftw3.* %(installdir)s/lib/libfftw3[lf].*', + 'rm -rf %(installdir)s/lib/pkgconfig %(installdir)s/lib/cmake', + 'rm -rf %(installdir)s/bin %(installdir)s/share', +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s_mpi.a' % (x) for x in ['', 'f', 'l']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2022.05.eb b/easybuild/easyconfigs/f/foss/foss-2022.05.eb new file mode 100644 index 00000000000..b80dc255154 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2022.05.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2022.05' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '11.3.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.1.3', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.05.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.05.eb new file mode 100644 index 00000000000..a4a3eaef701 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.05.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2022.05'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb new file mode 100644 index 00000000000..b029b592277 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb @@ -0,0 +1,43 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2022.05'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('FlexiBLAS', '3.1.3'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0_fix-GCC-10.patch b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0_fix-GCC-10.patch new file mode 100644 index 00000000000..575462ae08e --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0_fix-GCC-10.patch @@ -0,0 +1,65 @@ +From a0f76fc0c1c16646875b454b7d6f8d9d17726b5a Mon Sep 17 00:00:00 2001 +From: "Jose E. Roman" +Date: Wed, 2 Mar 2022 10:42:17 +0100 +Subject: [PATCH] Fix rank mismatch error in gfortran-10 + +--- + SRC/pdtrord.f | 4 ++-- + SRC/pstrord.f | 4 ++-- + SRC/pstrsen.f | 8 ++++---- + 3 files changed, 8 insertions(+), 8 deletions(-) + +diff --git a/SRC/pdtrord.f b/SRC/pdtrord.f +index 6206ff4..63e9457 100644 +--- a/SRC/pdtrord.f ++++ b/SRC/pdtrord.f +@@ -487,10 +487,10 @@ SUBROUTINE PDTRORD( COMPQ, SELECT, PARA, N, T, IT, JT, + MMAX( 1 ) = M + MMIN( 1 ) = M + IF( NPROCS.GT.1 ) +- $ CALL IGAMX2D( ICTXT, 'All', TOP, 1, 1, MMAX, 1, -1, ++ $ CALL IGAMX2D( ICTXT, 'All', TOP, 1, 1, MMAX( 1 ), 1, -1, + $ -1, -1, -1, -1 ) + IF( NPROCS.GT.1 ) +- $ CALL IGAMN2D( ICTXT, 'All', TOP, 1, 1, MMIN, 1, -1, ++ $ CALL IGAMN2D( ICTXT, 'All', TOP, 1, 1, MMIN( 1 ), 1, -1, + $ -1, -1, -1, -1 ) + IF( MMAX( 1 ).GT.MMIN( 1 ) ) THEN + M = MMAX( 1 ) +diff --git a/SRC/pstrord.f b/SRC/pstrord.f +index 4bd7785..6960914 100644 +--- a/SRC/pstrord.f ++++ b/SRC/pstrord.f +@@ -487,10 +487,10 @@ SUBROUTINE PSTRORD( COMPQ, SELECT, PARA, N, T, IT, JT, + MMAX( 1 ) = M + MMIN( 1 ) = M + IF( NPROCS.GT.1 ) +- $ CALL IGAMX2D( ICTXT, 'All', TOP, 1, 1, MMAX, 1, -1, ++ $ CALL IGAMX2D( ICTXT, 'All', TOP, 1, 1, MMAX( 1 ), 1, -1, + $ -1, -1, -1, -1 ) + IF( NPROCS.GT.1 ) +- $ CALL IGAMN2D( ICTXT, 'All', TOP, 1, 1, MMIN, 1, -1, ++ $ CALL IGAMN2D( ICTXT, 'All', TOP, 1, 1, MMIN( 1 ), 1, -1, + $ -1, -1, -1, -1 ) + IF( MMAX( 1 ).GT.MMIN( 1 ) ) THEN + M = MMAX( 1 ) +diff --git a/SRC/pstrsen.f b/SRC/pstrsen.f +index 83dfd56..7f6d4ee 100644 +--- a/SRC/pstrsen.f ++++ b/SRC/pstrsen.f +@@ -526,11 +526,11 @@ SUBROUTINE PSTRSEN( JOB, COMPQ, SELECT, PARA, N, T, IT, JT, + MMAX( 1 ) = M + MMIN( 1 ) = M + IF( NPROCS.GT.1 ) +- $ CALL IGAMX2D( ICTXT, 'All', TOP, 1, 1, MMAX, 1, -1, +- $ -1, -1, -1, -1 ) ++ $ CALL IGAMX2D( ICTXT, 'All', TOP, 1, 1, MMAX( 1 ), 1, -1, ++ $ -1, -1, -1, -1 ) + IF( NPROCS.GT.1 ) +- $ CALL IGAMN2D( ICTXT, 'All', TOP, 1, 1, MMIN, 1, -1, +- $ -1, -1, -1, -1 ) ++ $ CALL IGAMN2D( ICTXT, 'All', TOP, 1, 1, MMIN( 1 ), 1, -1, ++ $ -1, -1, -1, -1 ) + IF( MMAX( 1 ).GT.MMIN( 1 ) ) THEN + M = MMAX( 1 ) + IF( NPROCS.GT.1 ) From d01fc4988711cd1cfe9ba3e6f2345602795bdee7 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 30 May 2022 01:48:22 +0000 Subject: [PATCH 3843/9987] Use special easyblock for FFTW.MPI --- .../FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.05.eb | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.05.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.05.eb index 54f03c24575..ff23461db85 100644 --- a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.05.eb +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.05.eb @@ -1,4 +1,3 @@ -easyblock = 'EB_FFTW' name = 'FFTW.MPI' version = '3.3.10' @@ -15,23 +14,6 @@ checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] dependencies = [('FFTW', '3.3.10')] -with_openmp = False -with_threads = False -with_quad_prec = False - -postinstallcmds = [ - 'rm %(installdir)s/lib/libfftw3.* %(installdir)s/lib/libfftw3[lf].*', - 'rm -rf %(installdir)s/lib/pkgconfig %(installdir)s/lib/cmake', - 'rm -rf %(installdir)s/bin %(installdir)s/share', -] - runtest = 'check' -sanity_check_paths = { - 'files': ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', - '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + - ['lib/libfftw3%s_mpi.a' % (x) for x in ['', 'f', 'l']], - 'dirs': [], -} - moduleclass = 'numlib' From 498228b75e3ca52e06736ef8148f877e7b8552e8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 30 May 2022 11:35:14 +0100 Subject: [PATCH 3844/9987] adding easyconfigs: SciPy-bundle-2022.05-foss-2022.05.eb --- .../SciPy-bundle-2022.05-foss-2022.05.eb | 88 +++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb new file mode 100644 index 00000000000..72c168899cd --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb @@ -0,0 +1,88 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2022.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'foss', 'version': '2022.05'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.46.7'), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('pybind11', '2.9.2'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.22.3', { + 'patches': [ + 'numpy-1.18.2-mkl.patch', + 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.22.3_disable-broken-override-test.patch', + ], + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': [ + 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18', # numpy-1.22.3.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + # numpy-1.20.3_disable_fortran_callback_test.patch + '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + # numpy-1.22.3_disable-broken-override-test.patch + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.11.0', { + 'checksums': ['0b2cba712e09f7630879dff69f268460bfe34a6d6000451b47d598558a92a875'], + }), + ('scipy', '1.8.1', { + # compilation with Pythran enabled fails when using Intel compilers, + # see https://github.com/scipy/scipy/issues/14935 + 'prebuildopts': "export SCIPY_USE_PYTHRAN=0 && ", + 'preinstallopts': "export SCIPY_USE_PYTHRAN=0 && ", + 'checksums': ['9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33'], + }), + ('mpi4py', '3.1.3', { + 'checksums': ['f1e9fae1079f43eafdd9f817cdb3fd30d709edc093b5d5dada57a461b2db3008'], + }), + ('numexpr', '2.8.1', { + 'checksums': ['cd779aa44dd986c4ef10163519239602b027be06a527946656207acf1f58113b'], + }), + ('Bottleneck', '1.3.4', { + 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], + }), + ('pandas', '1.4.2', { + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'patches': ['deap-1.3.1_no_2to3.patch'], + 'checksums': [ + '11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f', # deap-1.3.1.tar.gz + '3fa9fac74b0750ac6667371ce0634c797d62d270c76eee9c258b55f4a5a5e689', # deap-1.3.1_no_2to3.patch + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 1adbf530c4a4ac59ee6a2c1d0dbc5468bdb97b12 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 30 May 2022 11:42:32 +0100 Subject: [PATCH 3845/9987] patches --- .../s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb index 72c168899cd..b91dbcd6c46 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb @@ -25,14 +25,12 @@ use_pip = True exts_list = [ ('numpy', '1.22.3', { 'patches': [ - 'numpy-1.18.2-mkl.patch', 'numpy-1.20.3_disable_fortran_callback_test.patch', 'numpy-1.22.3_disable-broken-override-test.patch', ], 'sources': ['%(name)s-%(version)s.zip'], 'checksums': [ 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18', # numpy-1.22.3.zip - 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch # numpy-1.20.3_disable_fortran_callback_test.patch '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', # numpy-1.22.3_disable-broken-override-test.patch From 49b36a690e8948b224a4588e68385c1c3a6f2cdf Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 30 May 2022 12:34:41 +0000 Subject: [PATCH 3846/9987] PMIx 4.1.2: remove unused libfabric dep --- easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb index 64180caade0..01fd1c35c00 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb @@ -29,12 +29,10 @@ dependencies = [ ('libevent', '2.1.12'), ('zlib', '1.2.12'), ('hwloc', '2.7.1'), - ('libfabric', '1.15.1'), ] configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' configopts += ' --with-hwloc=$EBROOTHWLOC' -configopts += ' --with-ofi=$EBROOTLIBFBARIC' configopts += ' --enable-pmix-binaries' configopts += ' --disable-man-pages' From 9d0ed05d54c536f31dd43520939e68483bad4e0b Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 30 May 2022 13:21:55 +0000 Subject: [PATCH 3847/9987] Remove obsolete --disable-man-pages --- easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb index 01fd1c35c00..bd61d4a2560 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb @@ -34,7 +34,6 @@ dependencies = [ configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' configopts += ' --with-hwloc=$EBROOTHWLOC' configopts += ' --enable-pmix-binaries' -configopts += ' --disable-man-pages' buildopts = 'V=1' From e21c2b152a8009b5fc70d89477483d20c22d9bcb Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Tue, 31 May 2022 09:35:34 +0800 Subject: [PATCH 3848/9987] fix support for OpenMPI v3.1.3 to external PMIx v3.1 --- .../OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb | 3 + ...3_fix-support-for-external-PMIx-v3.1.patch | 70 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3_fix-support-for-external-PMIx-v3.1.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb index 25a12b9495f..dce3d8fbc8d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb @@ -11,12 +11,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', 'OpenMPI-3.1_fix-ib-query.patch', + 'OpenMPI-3.1.3_fix-support-for-external-PMIx-v3.1.patch', ] checksums = [ '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch + # OpenMPI-3.1.3_fix-support-for-external-PMIx-v3.1.patch + '94846bee50b43b220fd6fead576c4be2cbc8baaa423ce7346d7d193fda523357', ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3_fix-support-for-external-PMIx-v3.1.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3_fix-support-for-external-PMIx-v3.1.patch new file mode 100644 index 00000000000..6a35523ffd3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3_fix-support-for-external-PMIx-v3.1.patch @@ -0,0 +1,70 @@ +From 640f7812c96af286010a87a63ef8e76d1127cc85 Mon Sep 17 00:00:00 2001 +From: Gilles Gouaillardet +Date: Tue, 8 Jan 2019 10:09:10 +0900 +Subject: [PATCH] pmix/ext2x: fix support for external PMIx v3.1 + +The PMIX_MODEX and PMIX_INFO_ARRAY macros were removed from the PMIx 3.1 standard. +Open MPI does not really need them (they are only used to be reported as not supported), +so smply #ifdef protect them to support an external PMIx v3.1 + +external PMIx v3 is supported via the pmix/ext2x component, and it has worked so far +until PMIx v3.1 removed some macros, the change to support external PMIx v3.1 is minimal, +so we do not need to bother creating a new pmix/ext3x component. + +The change only need to be done in ext2x/ext2x.c. +But since this file is automatically generated from pmix2x/pmix2x.c, we have to update +the latter file. + +Refs. open-mpi/ompi#6247 + +Signed-off-by: Gilles Gouaillardet + +(back-ported from commit open-mpi/ompi@950ba16aa16576582eb71941ec45996239c10a46) +--- + opal/mca/pmix/pmix2x/pmix2x.c | 8 ++++++-- + 1 file changed, 6 insertions(+), 2 deletions(-) + +diff --git a/opal/mca/pmix/pmix2x/pmix2x.c b/opal/mca/pmix/pmix2x/pmix2x.c +index a00a6e6328..3abcd29326 100644 +--- a/opal/mca/pmix/pmix2x/pmix2x.c ++++ b/opal/mca/pmix/pmix2x/pmix2x.c +@@ -1,8 +1,8 @@ + /* -*- Mode: C; c-basic-offset:4 ; indent-tabs-mode:nil -*- */ + /* + * Copyright (c) 2014-2018 Intel, Inc. All rights reserved. +- * Copyright (c) 2014-2017 Research Organization for Information Science +- * and Technology (RIST). All rights reserved. ++ * Copyright (c) 2014-2019 Research Organization for Information Science ++ * and Technology (RIST). All rights reserved. + * Copyright (c) 2014-2015 Mellanox Technologies, Inc. + * All rights reserved. + * Copyright (c) 2016 Cisco Systems, Inc. All rights reserved. +@@ -1001,10 +1001,12 @@ int pmix2x_value_unload(opal_value_t *kv, + OPAL_ERROR_LOG(OPAL_ERR_NOT_SUPPORTED); + rc = OPAL_ERR_NOT_SUPPORTED; + break; ++#ifdef PMIX_MODEX + case PMIX_MODEX: + OPAL_ERROR_LOG(OPAL_ERR_NOT_SUPPORTED); + rc = OPAL_ERR_NOT_SUPPORTED; + break; ++#endif /* PMIX_MODEX */ + case PMIX_PERSIST: + kv->type = OPAL_PERSIST; + kv->data.uint8 = pmix2x_convert_persist(v->data.persist); +@@ -1111,10 +1113,12 @@ int pmix2x_value_unload(opal_value_t *kv, + OPAL_ERROR_LOG(OPAL_ERR_NOT_SUPPORTED); + rc = OPAL_ERR_NOT_SUPPORTED; + break; ++#ifdef PMIX_INFO_ARRAY + case PMIX_INFO_ARRAY: + OPAL_ERROR_LOG(OPAL_ERR_NOT_SUPPORTED); + rc = OPAL_ERR_NOT_SUPPORTED; + break; ++#endif /* PMIX_INFO_ARRAY */ + + default: + /* silence warnings */ +-- +2.25.1 + From 55c38ac4fec3270571a0a8ae0ab6ec81e140429a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 May 2022 11:16:18 +0200 Subject: [PATCH 3849/9987] adding easyconfigs: MrBayes-3.2.6-gompi-2020b.eb --- .../m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb new file mode 100644 index 00000000000..417331a216f --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.6-gompi-2020b.eb @@ -0,0 +1,26 @@ +name = 'MrBayes' +version = '3.2.6' + +homepage = "https://nbisweden.github.io/MrBayes/" +description = """MrBayes is a program for Bayesian inference and model choice across + a wide range of phylogenetic and evolutionary models.""" + +toolchain = {'name': 'gompi', 'version': '2020b'} +# add -fcommon as workaround for 'multiple definition' linking errors; +# see also https://www.gnu.org/software/gcc/gcc-10/porting_to.html +toolchainopts = {'usempi': True, 'extra_cflags': '-fcommon'} + +source_urls = ['https://github.com/NBISweden/MrBayes/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f8fea43b5cb5e24a203a2bb233bfe9f6e7f77af48332f8df20085467cc61496d'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('libreadline', '8.0'), + ('beagle-lib', '3.1.2'), +] + +moduleclass = 'bio' From c192d52f13d0d6b32350e3f908c420f7097ed757 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 31 May 2022 11:26:29 +0200 Subject: [PATCH 3850/9987] change bundled pftoolsV3 to version 3.2.11 --- .../InterProScan-5.52-86.0-GCCcore-10.3.0.eb | 12 ++--- ...InterProScan-5.52_proscan_noaffinity.patch | 24 --------- .../l/libharu/libharu-2.3.0-GCCcore-10.3.0.eb | 50 +++++++++++++++++ .../pftoolsV3-3.2.11-GCCcore-10.3.0.eb | 54 +++++++++++++++++++ 4 files changed, 110 insertions(+), 30 deletions(-) delete mode 100644 easybuild/easyconfigs/i/InterProScan/InterProScan-5.52_proscan_noaffinity.patch create mode 100644 easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb index dca22cac5f6..5fb6314ec88 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb @@ -15,20 +15,20 @@ source_urls = [ 'ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/data', ] sources = ['%(namelower)s-%(version)s-64-bit.tar.gz'] -patches = ['InterProScan-5.52_proscan_noaffinity.patch'] -checksums = [ - '50a03c47fb16c669c265e99ba05c4a8558b82047f713c9945f362d3d4be6069a', # interproscan-5.52-86.0-64-bit.tar.gz - 'ee73b11cf4b9187f784055445f9db5623a9affe33ba41aa755143ea4594bf011', # InterProScan-5.52_proscan_noaffinity.patch -] +checksums = ['50a03c47fb16c669c265e99ba05c4a8558b82047f713c9945f362d3d4be6069a'] dependencies = [ ('Java', '11', '', True), ('Perl', '5.32.1'), ('libgd', '2.3.1'), ('Python', '3.9.5'), + ('pftoolsV3', '3.2.11'), ] -postinstallcmds = ["cd %(installdir)s && python initial_setup.py"] +postinstallcmds = [ + "cd %(installdir)s && python initial_setup.py", + "rm -v %(installdir)s/bin/prosite/*V3", +] sanity_check_paths = { 'files': ['interproscan-%(version_major)s.jar', 'interproscan.sh', 'interproscan.properties'], diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52_proscan_noaffinity.patch b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52_proscan_noaffinity.patch deleted file mode 100644 index 7d604e8246a..00000000000 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52_proscan_noaffinity.patch +++ /dev/null @@ -1,24 +0,0 @@ -# Do not use affinity (as it already should be set by the queue system) with proscan utils -# July 15th 2021 by B. Hajgato (UGent) ---- interproscan-5.52-86.0/bin/prosite/ps_scan.pl.org 2021-06-02 16:33:37.000000000 +0200 -+++ interproscan-5.52-86.0/bin/prosite/ps_scan.pl 2021-07-15 16:00:51.589475628 +0200 -@@ -1730,7 +1730,7 @@ - if ($level_arg eq 0) { # yes default scan l=0 is internally run at -1 (so that postprocessing could consider weak matches) - $level_arg = -1; - } -- @pre_command = $use_pfscan_v3 ? "$PFSCAN --matrix-only -o4 -L$level_arg $PROSITE" : "$PFSCAN -flxz -v -C$level_arg"; -+ @pre_command = $use_pfscan_v3 ? "$PFSCAN --no-affinity --matrix-only -o4 -L$level_arg $PROSITE" : "$PFSCAN -flxz -v -C$level_arg"; - @post_command = $use_pfscan_v3 ? "" : $PROSITE; - } - my $out; ---- interproscan-5.52-86.0/bin/prosite/runprosite.py.org 2021-06-02 16:33:37.000000000 +0200 -+++ interproscan-5.52-86.0/bin/prosite/runprosite.py 2021-07-15 16:00:25.908539401 +0200 -@@ -43,7 +43,7 @@ - binary_command = arg_list[4] - binary_switches = arg_list[5:] - -- pfsearch_cmd_switches = ' '.join(binary_switches) -+ pfsearch_cmd_switches = ' '.join(['--no-affinity'] + binary_switches) - #print pfsearch_cmd - - #print (binary_switches) diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ad1a8e66715 --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-10.3.0.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , +# Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Modified for foss-2016b by: +# Adam Huffman +# The Francis Crick Institute +# +# Updated: Pavel Grochal (INUITS) +# + +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'https://github.com/libharu/libharu/' +description = """libHaru is a free, cross platform, open source library for +generating PDF files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +# 'https://github.com/libharu/libharu/archive/' +source_urls = [GITHUB_SOURCE] +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1') +] + +dependencies = [('libpng', '1.6.37')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': ['if', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..bad448850b7 --- /dev/null +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb @@ -0,0 +1,54 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## +easyblock = 'CMakeMake' + +name = 'pftoolsV3' +version = '3.2.11' + +homepage = 'https://github.com/sib-swiss/pftools3' +description = """A suite of tools to build and search generalized profiles (protein and DNA).""" +software_license = 'LicenseGPLv2' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/'] +checksums = ['b45381584c57bc7c3ac6544f8654752095a5c04fd8242ab270b1d8cdce40d94a'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('make', '4.3'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Perl', '5.32.1'), + ('PCRE', '8.44'), + ('libharu', '2.3.0'), + ('zlib', '1.2.11'), + ('libgd', '2.3.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), +] + +configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX:PATH=%(installdir)s -DCMAKE_BUILD_TYPE=Release ' +configure_cmd += '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON ' +configure_cmd += '-DUSE_AFFINITY=OFF ' # Disable affinity for some old architectures +configure_cmd += '../pftools3-%(version)s' + +runtest = 'test' + +sanity_check_paths = { + 'files': [ + 'bin/ptof', 'bin/htop', 'bin/6ft', 'bin/2ft', 'bin/pfdump', 'bin/pfscan', 'bin/pfsearch', + 'bin/pfscanV3', 'bin/pfsearchV3', + ], + 'dirs': ['share/doc', 'share/man'], +} + +moduleclass = 'bio' From cd4a43e6faf8463b3e3a234c2577daf2447bb33a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 31 May 2022 11:41:40 +0200 Subject: [PATCH 3851/9987] add binutils as a builddep --- .../easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb index bad448850b7..561e758d9b6 100644 --- a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb @@ -21,6 +21,7 @@ source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/'] checksums = ['b45381584c57bc7c3ac6544f8654752095a5c04fd8242ab270b1d8cdce40d94a'] builddependencies = [ + ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('make', '4.3'), ('pkg-config', '0.29.2'), From 8fe66c13987077c301beab670d238bac0b8e03d9 Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Tue, 31 May 2022 12:46:52 +0200 Subject: [PATCH 3852/9987] adding easyconfigs: Jellyfish-2.3.0-GCC-10.3.0.eb --- .../j/Jellyfish/Jellyfish-2.3.0-GCC-10.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.3.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..aaefa9c251e --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-10.3.0.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.3.0' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e195b7cf7ba42a90e5e112c0ed27894cd7ac864476dc5fb45ab169f5b930ea5a'] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, +# they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' From 63e6c8dd9ac36134437ac3758c202a4b058bbea9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 31 May 2022 13:22:14 +0200 Subject: [PATCH 3853/9987] location of pftools is hard-coded --- .../i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb index 5fb6314ec88..5dca5d22577 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb @@ -28,6 +28,8 @@ dependencies = [ postinstallcmds = [ "cd %(installdir)s && python initial_setup.py", "rm -v %(installdir)s/bin/prosite/*V3", + "ln -s $EBROOTPFTOOLSV3/bin/pfscanV3 %(installdir)s/bin/prosite/pfscanV3", + "ln -s $EBROOTPFTOOLSV3/bin/pfsearchV3 %(installdir)s/bin/prosite/pfsearchV3", ] sanity_check_paths = { From fe5f2b33a0d51ba27087d27649064dfa00829cd0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 31 May 2022 14:00:26 +0200 Subject: [PATCH 3854/9987] add https fallback, and add sanity check command for pftools --- .../i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb | 2 +- .../p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb index 5dca5d22577..0e448e11898 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} # from my location, the ftp download is 30x faster than http/https source_urls = [ 'ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/%(version)s/', - 'ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/data', + 'https://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/%(version)s/', ] sources = ['%(namelower)s-%(version)s-64-bit.tar.gz'] checksums = ['50a03c47fb16c669c265e99ba05c4a8558b82047f713c9945f362d3d4be6069a'] diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb index 561e758d9b6..7d307b8bedb 100644 --- a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.11-GCCcore-10.3.0.eb @@ -52,4 +52,9 @@ sanity_check_paths = { 'dirs': ['share/doc', 'share/man'], } +sanity_check_commands = [ + 'pfsearchV3 --help', + 'pfscanV3 --help', +] + moduleclass = 'bio' From 06a13a808b0aec555dedaa55943730b1e1d7b919 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 31 May 2022 14:16:12 +0200 Subject: [PATCH 3855/9987] tcsh: add softlink for csh --- easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.2.0.eb | 4 +++- easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb | 4 +++- easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-9.3.0.eb | 4 +++- easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb | 4 +++- easybuild/easyconfigs/t/tcsh/tcsh-6.22.04-GCCcore-10.3.0.eb | 4 +++- 5 files changed, 15 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.2.0.eb index 0a18f40c2bb..7aa3bc8924e 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.2.0.eb @@ -35,8 +35,10 @@ builddependencies = [('binutils', '2.31.1')] dependencies = [('ncurses', '6.1')] +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + sanity_check_paths = { - 'files': ["bin/tcsh"], + 'files': ["bin/tcsh", "bin/csh"], 'dirs': [] } diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb index 5703fe5fafb..4e746222f4a 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-8.3.0.eb @@ -35,8 +35,10 @@ builddependencies = [('binutils', '2.32')] dependencies = [('ncurses', '6.1')] +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + sanity_check_paths = { - 'files': ["bin/tcsh"], + 'files': ["bin/tcsh", "bin/csh"], 'dirs': [] } diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-9.3.0.eb index 6c460841c0a..73e0100cebf 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.02-GCCcore-9.3.0.eb @@ -35,8 +35,10 @@ builddependencies = [('binutils', '2.34')] dependencies = [('ncurses', '6.2')] +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + sanity_check_paths = { - 'files': ["bin/tcsh"], + 'files': ["bin/tcsh", "bin/csh"], 'dirs': [] } diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb index 46a56b3bba5..b317cef4987 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.03-GCCcore-10.2.0.eb @@ -35,8 +35,10 @@ builddependencies = [('binutils', '2.35')] dependencies = [('ncurses', '6.2')] +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + sanity_check_paths = { - 'files': ["bin/tcsh"], + 'files': ["bin/tcsh", "bin/csh"], 'dirs': [] } diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.04-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.04-GCCcore-10.3.0.eb index 06843271545..8d927d3b7c3 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.22.04-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.22.04-GCCcore-10.3.0.eb @@ -35,8 +35,10 @@ builddependencies = [('binutils', '2.36.1')] dependencies = [('ncurses', '6.2')] +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + sanity_check_paths = { - 'files': ["bin/tcsh"], + 'files': ["bin/tcsh", "bin/csh"], 'dirs': [] } From 43abf57d1b342c685220b3fb3afeef117f6bd5dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 May 2022 10:54:24 +0200 Subject: [PATCH 3856/9987] fix trivial style issues in CellTypist + openpyxl easyconfigs --- .../CellTypist/CellTypist-1.0.0-foss-2021b.eb | 22 ++++++++++++------- .../openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb | 3 ++- 2 files changed, 16 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb index 24f0500b7d8..3945fd8a06a 100644 --- a/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.0.0-foss-2021b.eb @@ -1,13 +1,13 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = "CellTypist" -version = "1.0.0" +name = 'CellTypist' +version = '1.0.0' -homepage = "https://www.celltypist.org/" +homepage = 'https://www.celltypist.org/' description = "A tool for semi-automatic cell type annotation" -source_urls = ["https://github.com/Teichlab/celltypist/archive/refs/tags/"] -sources = ["%(version)s.tar.gz"] +source_urls = ['https://github.com/Teichlab/celltypist/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] checksums = ['dd020902acdb13d2f138ac20ffb6ae28fd6f2d7b758ac6ab05bd4b9030d43e8e'] toolchain = {'name': 'foss', 'version': '2021b'} @@ -20,10 +20,16 @@ dependencies = [ ('leidenalg', '0.8.8'), ] -use_pip = True -sanity_pip_check = True download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/celltypist'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} sanity_check_commands = ["celltypist --help"] +sanity_pip_check = True + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb index 15296c110da..7ca4970a7c9 100644 --- a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.9-GCCcore-11.2.0.eb @@ -17,7 +17,6 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True exts_list = [ ('et_xmlfile', '1.1.0', { @@ -31,4 +30,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'data' From 1f2984b778ce3b7df6e4e04c51575ccebc0c475a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 31 May 2022 14:32:17 +0200 Subject: [PATCH 3857/9987] add tcsh-6.24.01 for GCCcore/11.2.0 --- .../t/tcsh/tcsh-6.24.01-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..36da7b42991 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.24.01' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5659a1b973b1f947e36238cb17a00210ac4cff3b496f8f851acd77172ab91d7e'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('ncurses', '6.2')] + +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + +sanity_check_paths = { + 'files': ["bin/tcsh", "bin/csh"], + 'dirs': [] +} + +moduleclass = 'tools' From dae77c56352ecaea18ff716ac88a816d36677261 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 31 May 2022 14:19:53 +0100 Subject: [PATCH 3858/9987] adding easyconfigs: Boost-1.79.0-GCC-11.3.0.eb --- .../b/Boost/Boost-1.79.0-GCC-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..b412f13fe87 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +## +# Authors:: Denis Kristak +## +name = 'Boost' +version = '1.79.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('XZ', '5.2.5'), + ('ICU', '71.1'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' From 28b05185f459da85b76f13de727f5f88b17297d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 May 2022 15:26:08 +0200 Subject: [PATCH 3859/9987] add chkptstanr + MLmetrics extensions to R v4.1.2 easyconfig --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 82227665190..fb101f6257d 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3316,6 +3316,12 @@ exts_list = [ ('RhpcBLASctl', '0.21-247.1', { 'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'], }), + ('chkptstanr', '0.1.1', { + 'checksums': ['433b29d597d7ea6c21ed652782a7bf2d766f9223a3b7bfed235c8fe7fffd175c'], + }), + ('MLmetrics', '1.1.1', { + 'checksums': ['777f1b76b16837387b830e2b65304ede234b9299d17efd09c7fd403356122118'], + }), ] moduleclass = 'lang' From 20782ef35c5ee807ba552404cf60cc608cdf5771 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 May 2022 16:22:35 +0200 Subject: [PATCH 3860/9987] adding easyconfigs: scPred-1.9.2-foss-2021b-R-4.1.2.eb --- .../scPred/scPred-1.9.2-foss-2021b-R-4.1.2.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/scPred/scPred-1.9.2-foss-2021b-R-4.1.2.eb diff --git a/easybuild/easyconfigs/s/scPred/scPred-1.9.2-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/s/scPred/scPred-1.9.2-foss-2021b-R-4.1.2.eb new file mode 100644 index 00000000000..fdafa4dbe96 --- /dev/null +++ b/easybuild/easyconfigs/s/scPred/scPred-1.9.2-foss-2021b-R-4.1.2.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'scPred' +version = '1.9.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/powellgenomicslab/scPred' +description = "scPred package for cell type prediction from scRNA-seq data " + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/powellgenomicslab/scPred/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4c92b4a0d4a94fbaf578cc547f05a3874a7a96fdb5c29f21c8c7d853d4b5e845'] + +dependencies = [ + ('R', '4.1.2'), + ('R-bundle-Bioconductor', '3.14', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +options = {'modulename': name} + +moduleclass = 'bio' From 12969dc7b342bda0e4fbe55b7fc3d5041e88a1ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 May 2022 16:24:54 +0200 Subject: [PATCH 3861/9987] also add renv extension to R v4.1.2 easyconfig --- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index fb101f6257d..39614e50c0d 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3322,6 +3322,9 @@ exts_list = [ ('MLmetrics', '1.1.1', { 'checksums': ['777f1b76b16837387b830e2b65304ede234b9299d17efd09c7fd403356122118'], }), + ('renv', '0.15.5', { + 'checksums': ['b4f1a9a7daa82f0c3123ebd4eeba06e98d5485215518e5292b25bc56741d582e'], + }), ] moduleclass = 'lang' From abb65e9ddd75ce770ada0ee52acab5d8a4e3d228 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 May 2022 16:33:55 +0200 Subject: [PATCH 3862/9987] also add MLmetrics + renv extensions to R v4.2.0 easyconfig --- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 621dfe94ff8..f632984704c 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -3334,6 +3334,12 @@ exts_list = [ ('chkptstanr', '0.1.1', { 'checksums': ['433b29d597d7ea6c21ed652782a7bf2d766f9223a3b7bfed235c8fe7fffd175c'], }), + ('MLmetrics', '1.1.1', { + 'checksums': ['777f1b76b16837387b830e2b65304ede234b9299d17efd09c7fd403356122118'], + }), + ('renv', '0.15.5', { + 'checksums': ['b4f1a9a7daa82f0c3123ebd4eeba06e98d5485215518e5292b25bc56741d582e'], + }), ] moduleclass = 'lang' From 37a44e1c88ceefb05c961b7821f06291bce2b187 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 31 May 2022 18:18:56 +0200 Subject: [PATCH 3863/9987] adding easyconfigs: EvidentialGene-2022.01.14-gompi-2021b.eb, Exonerate-2.4.0-GCC-11.2.0.eb --- .../EvidentialGene-2022.01.14-gompi-2021b.eb | 38 ++++++++++++++++ .../e/Exonerate/Exonerate-2.4.0-GCC-11.2.0.eb | 43 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2022.01.14-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2022.01.14-gompi-2021b.eb b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2022.01.14-gompi-2021b.eb new file mode 100644 index 00000000000..e424ebe3f5e --- /dev/null +++ b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2022.01.14-gompi-2021b.eb @@ -0,0 +1,38 @@ +easyblock = "PackedBinary" + +name = "EvidentialGene" +version = '2022.01.14' +local_month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec'] +local_dlver = version.split('.')[0][-2:] + local_month[int(version.split('.')[1])] + version.split('.')[2] + +homepage = 'http://arthropods.eugenes.org/EvidentialGene/' +description = """EvidentialGene is a genome informatics project for + "Evidence Directed Gene Construction for Eukaryotes", + for constructing high quality, accurate gene sets for + animals and plants (any eukaryotes), being developed by + Don Gilbert at Indiana University, gilbertd at indiana edu.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = [ + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/', + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/', +] +sources = ['evigene%s.tar' % local_dlver] +checksums = ['d464240affb6d293f20dab440abe89381e580154502e777c020c0060c8947ba3'] + +dependencies = [ + ('Perl', '5.34.0'), + ('Exonerate', '2.4.0'), + ('CD-HIT', '4.8.1'), + ('BLAST+', '2.12.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts/'], +} + +modextravars = {'evigene': '%(installdir)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.2.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..dc295ab4445 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.2.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +# also https://github.com/nathanweeks/exonerate +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/%(namelower)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('GLib', '2.69.1'), +] + +# parallel build fails +parallel = 1 + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/fastaclip', 'bin/fastaoverlap'], + 'dirs': ['share'], +} + +moduleclass = 'bio' From 59d4509a020b8611b950ab998c8171d42a8a7cfd Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 31 May 2022 18:21:14 +0200 Subject: [PATCH 3864/9987] adding easyconfigs: cuDNN-8.4.0.27-CUDA-11.6.0.eb --- .../c/cuDNN/cuDNN-8.4.0.27-CUDA-11.6.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.0.27-CUDA-11.6.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.0.27-CUDA-11.6.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.0.27-CUDA-11.6.0.eb new file mode 100644 index 00000000000..0e9a2fe6ebd --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.0.27-CUDA-11.6.0.eb @@ -0,0 +1,42 @@ +name = 'cuDNN' +version = '8.4.0.27' +local_cuda_version = '11.6.0' +local_cuda_version_majmin = '.'.join(local_cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# cuDNN sources used to be available without login from https://developer.download.nvidia.com/compute/redist/cudnn/ +# However, at this time, cuDNN 8.4 sources can only be download manually from +# https://developer.nvidia.com/rdp/cudnn-download after login +local_cudnn_cuda_version = '%%(version)s_cuda{maj_min}'.format(maj_min=local_cuda_version_majmin) +local_tarball_tmpl = '-'.join(['%%(namelower)s', 'linux', '%s', local_cudnn_cuda_version, 'archive.tar.xz']) +sources = [local_tarball_tmpl % '%(cudnnarch)s'] +checksums = [ + { + local_tarball_tmpl % 'x86_64': + 'd19bdafd9800c79d29e6f6fffa9f9e2c10d1132d6c2ff10b1593e057e74dd050', + local_tarball_tmpl % 'ppc64le': + '7ef72353331cf42b357f53cb4a4971fb07e2f0b2ae66e03d54933df52de411c8', + local_tarball_tmpl % 'sbsa': + '3972ab37b6f0271274931f69c5675c3b61d16f8f5a2dedd422a5efd7b0f358e5', + } +] + +dependencies = [('CUDA', local_cuda_version)] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From 966d37bc885c60178160d95266c656dcd0b0d870 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 31 May 2022 18:21:37 +0200 Subject: [PATCH 3865/9987] allow external tools to be located elsewhere for ETE --- .../easyconfigs/e/ETE/ETE-3.1.2-foss-2021b.eb | 6 +++++- .../e/ETE/ETE-3.1.2-foss-2021b_fix_binpath.patch | 14 ++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b_fix_binpath.patch diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b.eb index c7eca019813..bce595d0c24 100644 --- a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b.eb @@ -10,7 +10,11 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://pypi.python.org/packages/source/e/ete3'] sources = ['ete3-%(version)s.tar.gz'] -checksums = ['4fc987b8c529889d6608fab1101f1455cb5cbd42722788de6aea9c7d0a8e59e9'] +patches = ['ETE-3.1.2-foss-2021b_fix_binpath.patch'] +checksums = [ + '4fc987b8c529889d6608fab1101f1455cb5cbd42722788de6aea9c7d0a8e59e9', # ete3-3.1.2.tar.gz + 'f71d1135e87e1035736f67b92ebcfebd2ae4d57e48f45e25c1a6144c60f11fbd', # ETE-3.1.2-foss-2021b_fix_binpath.patch +] dependencies = [ ('lxml', '4.6.3'), diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b_fix_binpath.patch b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b_fix_binpath.patch new file mode 100644 index 00000000000..95d425871ed --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021b_fix_binpath.patch @@ -0,0 +1,14 @@ +Add support for using external binaries that are in the PATH +Author: Samuel Moors (VUB) +diff -ur ete3-3.1.2.orig/ete3/evol/evoltree.py ete3-3.1.2/ete3/evol/evoltree.py +--- ete3-3.1.2.orig/ete3/evol/evoltree.py 2020-08-30 09:08:26.000000000 +0200 ++++ ete3-3.1.2/ete3/evol/evoltree.py 2022-05-30 17:38:35.529290893 +0200 +@@ -248,6 +248,8 @@ + hlddir = os.getcwd() + os.chdir(fullpath) + bin_ = os.path.join(self.execpath, model_obj.properties['exec']) ++ if not os.path.exists(bin_): ++ bin_ = which(model_obj.properties['exec']) + try: + proc = Popen([bin_, 'tmp.ctl'], stdout=PIPE, stdin=PIPE) + except OSError: From e27a1348a723a05df95a3ec421a8434ebfa4da49 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 31 May 2022 18:48:05 +0200 Subject: [PATCH 3866/9987] Fix gmsh 4.9.0 lib and python bindings --- easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a.eb index dbc13d8c38f..72064658427 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.9.0-foss-2021a.eb @@ -16,6 +16,7 @@ checksums = ['b8ef133c9b66ffe12df1747e72d4acf19f1eb1e9cd95eb0f577cbc4081d9bea3'] builddependencies = [ ('CMake', '3.20.1'), ('SWIG', '4.0.2'), + ('Eigen', '3.3.9'), ] dependencies = [ @@ -28,12 +29,12 @@ dependencies = [ separate_build_dir = True -configopts = '-DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' +configopts = '-DENABLE_BUILD_SHARED=ON -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1' -modextrapaths = {'PYTHONPATH': ['lib64']} +modextrapaths = {'PYTHONPATH': ['lib']} sanity_check_paths = { - 'files': ['bin/gmsh', 'bin/onelab.py'], + 'files': ['bin/gmsh', 'bin/onelab.py', 'lib/gmsh.py', 'lib/libgmsh.%s' % SHLIB_EXT], 'dirs': [], } From 21b1779c845c69b0df832ffecdff883396d4235f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 31 May 2022 22:27:38 +0200 Subject: [PATCH 3867/9987] adding easyconfigs: PyAMG-4.2.3-foss-2021a.eb --- .../p/PyAMG/PyAMG-4.2.3-foss-2021a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyAMG/PyAMG-4.2.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-4.2.3-foss-2021a.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.2.3-foss-2021a.eb new file mode 100644 index 00000000000..7eddd0bdbd3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-4.2.3-foss-2021a.eb @@ -0,0 +1,25 @@ +easyblock = "PythonPackage" + +name = 'PyAMG' +version = '4.2.3' + +homepage = 'https://pyamg.github.io' +description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['37ad3c1dcaff2435c2ab7c8ec36942af0726c563d35059bcd18eb07473f7182e'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +options = {'modulename': 'pyamg'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' From 3708a8fe909d8d8adb4ae32f829c9a74ab2dbd93 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Jun 2022 09:21:35 +0200 Subject: [PATCH 3868/9987] adding easyconfigs: PLINK-2.00a3.1-GCC-11.2.0.eb --- .../p/PLINK/PLINK-2.00a3.1-GCC-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.1-GCC-11.2.0.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..3432a43eee3 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.1-GCC-11.2.0.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'PLINK' +version = '2.00a3.1' + +homepage = 'https://www.cog-genomics.org/plink/2.0/' +description = 'Whole-genome association analysis toolset' + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/chrchang/plink-ng/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d48ab87f7e82788a0610c1a8809f9dc9f612d3f021e4866fe00f817d57857969'] + +dependencies = [ + ('FlexiBLAS', '3.0.4'), + ('libdeflate', '1.8'), + ('zstd', '1.5.0'), +] + +start_dir = '2.0' + +# ignore suggested Makefile in build_dynamic, the dev Makefile is better +buildopts = 'BLASFLAGS="-lflexiblas" BLASFLAGS64="-lflexiblas"' +buildopts += ' LDFLAGS="$LIBS -ldeflate -lz -lzstd" ZLIB="" CSRC="include/SFMT.c"' +buildopts += ' BASEFLAGS="$OPTFLAGS -DZSTD_MULTITHREAD"' + +files_to_copy = ['bin', (['include/*.h'], 'include'), 'ReadMe.md'] + +sanity_check_paths = { + 'files': ['bin/plink2', 'bin/pgen_compress'], + 'dirs': ['include'], +} + +sanity_check_commands = ["plink2 --help"] + +moduleclass = 'bio' From c58e9e4bc0ec840b8bed5378df5468005b6d2e27 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 1 Jun 2022 11:01:26 +0200 Subject: [PATCH 3869/9987] Updated with source URL so it can be downloaded again --- .../easyconfigs/c/cuDNN/cuDNN-8.4.0.27-CUDA-11.6.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.0.27-CUDA-11.6.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.0.27-CUDA-11.6.0.eb index 0e9a2fe6ebd..5c7fe910c68 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.0.27-CUDA-11.6.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.0.27-CUDA-11.6.0.eb @@ -10,9 +10,10 @@ a GPU-accelerated library of primitives for deep neural networks.""" toolchain = SYSTEM -# cuDNN sources used to be available without login from https://developer.download.nvidia.com/compute/redist/cudnn/ -# However, at this time, cuDNN 8.4 sources can only be download manually from -# https://developer.nvidia.com/rdp/cudnn-download after login +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/%s/' % + ('.'.join(version.split('.')[:3]), local_cuda_version_majmin) +] local_cudnn_cuda_version = '%%(version)s_cuda{maj_min}'.format(maj_min=local_cuda_version_majmin) local_tarball_tmpl = '-'.join(['%%(namelower)s', 'linux', '%s', local_cudnn_cuda_version, 'archive.tar.xz']) sources = [local_tarball_tmpl % '%(cudnnarch)s'] From 3b725532acc94bd6876c2c3d25d268c28c688ee1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 1 Jun 2022 13:05:01 +0100 Subject: [PATCH 3870/9987] adding easyconfigs: Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb, Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb --- ...Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb | 77 +++++++++++++++++++ ...Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb | 77 +++++++++++++++++++ 2 files changed, 154 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..07a9f5ffa7f --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -0,0 +1,77 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '12.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'clang-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', + 'clang-tools-extra-%(version)s.src.tar.xz', + 'libunwind-%(version)s.src.tar.xz', +] +checksums = [ + '7d9a8405f557cefc5a21bf5672af73903b64749d9bc3a50322239f56f34ffddf', # llvm-12.0.1.src.tar.xz + '6e912133bcf56e9cfe6a346fa7e5c52c2cde3e4e48b7a6cc6fcc7c75047da45f', # clang-12.0.1.src.tar.xz + 'b4c8d5f2a802332987c1c0a95b5afb35b1a66a96fe44add4e4ed4792c4cba0a4', # compiler-rt-12.0.1.src.tar.xz + '2254e25312708a567b1ab00716362db379d265e47a97a94ed74211d57a4cd5f9', # polly-12.0.1.src.tar.xz + '60fe79440eaa9ebf583a6ea7f81501310388c02754dbe7dc210776014d06b091', # openmp-12.0.1.src.tar.xz + '690b3f6a76310e13a783a142f87500ade9cafe003e088b678364487ed873e361', # lld-12.0.1.src.tar.xz + 'a42089cd358f661823c490741f8be98701d983a7ee5152c8649075da681a9d15', # libcxx-12.0.1.src.tar.xz + '88efe8e391767a1e8f42b509879abe766c9f44b1781ad1900975ae6b516b91d0', # libcxxabi-12.0.1.src.tar.xz + '65659efdf97dbed70ae0caee989936b731f249dddc46f1cb4225b2f49b232ae5', # clang-tools-extra-12.0.1.src.tar.xz + '0bea6089518395ca65cf58b0a450716c5c99ce1f041079d3aa42d280ace15ca4', # libunwind-12.0.1.src.tar.xz +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.36.1'), + ('hwloc', '2.4.1'), + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), + ('GMP', '6.2.1'), + ('Z3', '4.8.11'), + ('CUDA', '11.3.1', '', True), +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Python', '3.9.5'), + ('Perl', '5.32.1'), + ('elfutils', '0.185'), +] + +assertions = True +usepolly = True +build_lld = True +libcxx = True +enable_rtti = True +build_extra_clang_tools = True + +skip_all_tests = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb new file mode 100644 index 00000000000..5ee0395dbb9 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -0,0 +1,77 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '13.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'clang-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', + 'clang-tools-extra-%(version)s.src.tar.xz', + 'libunwind-%(version)s.src.tar.xz', +] +checksums = [ + 'ec6b80d82c384acad2dc192903a6cf2cdbaffb889b84bfb98da9d71e630fc834', # llvm-13.0.1.src.tar.xz + '787a9e2d99f5c8720aa1773e4be009461cd30d3bd40fdd24591e473467c917c9', # clang-13.0.1.src.tar.xz + '7b33955031f9a9c5d63077dedb0f99d77e4e7c996266952c1cec55626dca5dfc', # compiler-rt-13.0.1.src.tar.xz + 'f4003e03da57b53bf206faadd0cf53f7b198c38498c605dec45743db23c10ad0', # polly-13.0.1.src.tar.xz + '6b79261371616c31fea18cd3ee1797c79ee38bcaf8417676d4fa366a24c96b4f', # openmp-13.0.1.src.tar.xz + '666af745e8bf7b680533b4d18b7a31dc7cab575b1e6e4d261922bbafd9644cfb', # lld-13.0.1.src.tar.xz + '2f446acc00bb7cfb4e866c2fa46d1b6dbf4e7d2ab62e3c3d84e56f7b9e28110f', # libcxx-13.0.1.src.tar.xz + 'db5fa6093c786051e8b1c85527240924eceb6c95eeff0a2bbc57be8422b3cef1', # libcxxabi-13.0.1.src.tar.xz + 'cc2bc8598848513fa2257a270083e986fd61048347eccf1d801926ea709392d0', # clang-tools-extra-13.0.1.src.tar.xz + 'e206dbf1bbe058a113bffe189386ded99a160b2443ee1e2cd41ff810f78551ba', # libunwind-13.0.1.src.tar.xz +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.37'), + ('hwloc', '2.5.0'), + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), + ('GMP', '6.2.1'), + ('Z3', '4.8.12'), + ('CUDA', '11.4.1', '', True), +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('elfutils', '0.185'), +] + +assertions = True +usepolly = True +build_lld = True +libcxx = True +enable_rtti = True +build_extra_clang_tools = True + +skip_all_tests = True + +moduleclass = 'compiler' From fecc543e20400056c7d0a1195072a17373f2d262 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Jun 2022 18:44:34 +0200 Subject: [PATCH 3871/9987] {bio}[gompi/2021b] IQ-TREE v2.2.1, LSD2 v2.3 --- .../i/IQ-TREE/IQ-TREE-2.2.1-gompi-2021b.eb | 52 +++++++++++++++++++ .../i/IQ-TREE/IQ-TREE-2.2.1_fix-mpi.patch | 13 +++++ .../l/LSD2/LSD2-2.3-GCCcore-11.2.0.eb | 38 ++++++++++++++ 3 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1_fix-mpi.patch create mode 100644 easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1-gompi-2021b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1-gompi-2021b.eb new file mode 100644 index 00000000000..94fa02f1ac2 --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1-gompi-2021b.eb @@ -0,0 +1,52 @@ +# Updated to v2.1.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.2.1' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'IQ-TREE-2.1.2_use_EB_LSD2.patch', + 'IQ-TREE-2.2.1_fix-mpi.patch', +] +checksums = [ + '25d799201cb4a2c5484d4e53f2a58b2c25a1c5435e6316f87d2e7ae3605ee9bb', # v2.2.1.tar.gz + 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816', # IQ-TREE-2.1.2_use_EB_LSD2.patch + '9ead6808efd11d4c01dd265cca6094cffd6377746d3b2fc84b43d2faeee0777c', # IQ-TREE-2.2.1_fix-mpi.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Eigen', '3.3.9'), +] +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.77.0'), + ('LSD2', '2.3'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = ["iqtree2 --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1_fix-mpi.patch b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1_fix-mpi.patch new file mode 100644 index 00000000000..9a6aee528b3 --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1_fix-mpi.patch @@ -0,0 +1,13 @@ +fix MPI compilation issues by not requiring that CLANG_UNDER_VS preprocessor symbol is defined to include mpi.h +author: Kenneth Hoste (HPC-UGent) +--- iqtree2-2.2.1/pll/genericParallelization.h.orig 2022-06-01 18:11:42.563407234 +0200 ++++ iqtree2-2.2.1/pll/genericParallelization.h 2022-06-01 18:10:02.554264000 +0200 +@@ -63,7 +63,7 @@ + /******************/ + /* MPI SPECIFIC */ + /******************/ +-#if defined(_FINE_GRAIN_MPI) || (defined(_IQTREE_MPI) && defined(CLANG_UNDER_VS)) ++#if defined(_FINE_GRAIN_MPI) || defined(_IQTREE_MPI) + #include + #ifdef DEBUG_MPI_EACH_SEND + #define DEBUG_PRINT(text, elem) printf(text, elem) diff --git a/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c9bd84d8797 --- /dev/null +++ b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +# Updated to v2.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'LSD2' +version = '2.3' + +homepage = 'https://github.com/tothuhien/lsd2' +description = "Least-squares methods to estimate rates and dates from phylogenies" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'tothuhien' + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v.%(version)s.tar.gz'] +patches = ['%(name)s-1.9.7_fix_cmake_to_build_lib_and_binary.patch'] +checksums = [ + 'c7819be1204ebf77e3660bba91dbd8629ba9437216814f276a11b9156dbb0649', # v.2.3.tar.gz + # LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch + '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6', +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From eda96a810bca4a3c58ecdee421ede137550b77af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Jun 2022 20:54:25 +0200 Subject: [PATCH 3872/9987] adding easyconfigs: Rust-1.60.0-GCCcore-10.3.0.eb and patches: Rust-1.60_sysroot-fix-interpreter.patch --- .../r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb | 58 +++++++++++++++++++ .../Rust-1.60_sysroot-fix-interpreter.patch | 30 ++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.60_sysroot-fix-interpreter.patch diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..5eab0202819 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.60.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.60_sysroot-fix-interpreter.patch'] +checksums = [ + '20ca826d1cf674daf8e22c4f8c4b9743af07973211c839b85839742314c838b7', # rustc-1.60.0-src.tar.gz + 'b59ed4c2591fc9098277299be21dd6752654f6f193d8652b7d21cb0fa0dd8716', # Rust-1.60_sysroot-fix-interpreter.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('Python', '3.9.5', '-bare'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.60_sysroot-fix-interpreter.patch b/easybuild/easyconfigs/r/Rust/Rust-1.60_sysroot-fix-interpreter.patch new file mode 100644 index 00000000000..3ebb15674f4 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.60_sysroot-fix-interpreter.patch @@ -0,0 +1,30 @@ +Use patchelf to fix interpreter of binaries that are used during Rust bootstrap procedure +when EasyBuild is configured to build in an alternate sysroot + +This fixes problems like due to a clash with the interpreter from the host, and a more recent libc.so.6 that's picked up +from the alternate sysroot: +error: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (required by /tmp/easybuild/build/Rust/1.52.1/GCCcore-10.3.0/rustc-1.52.1-src/build/bootstrap/debug/deps/libproc_macro_error_attr-fbfef320d848b049.so) + +author: Kenneth Hoste (HPC-UGent) + +--- rustc-1.60.0-src/src/bootstrap/bootstrap.py.orig 2022-06-01 16:35:37.111817747 +0200 ++++ rustc-1.60.0-src/src/bootstrap/bootstrap.py 2022-06-01 16:40:27.769571474 +0200 +@@ -671,6 +671,18 @@ + if ostype != "Linux": + return + ++ sysroot = os.getenv("EASYBUILD_SYSROOT") ++ if sysroot and not fname.endswith(".so"): ++ # determine patch to interpreter in host via output produced by 'file -b /bin/bash' ++ readelf_out = subprocess.check_output(['readelf', '-l', '/bin/bash']).decode('ascii', 'ignore').strip() ++ regex = re.compile('.*program interpreter: ([^\]]+)', re.M) ++ res = regex.search(readelf_out) ++ interpreter_path = os.path.join(sysroot, res.group(1).lstrip('/')) ++ if not os.path.exists(interpreter_path): ++ raise Exception("Derived path to interpreter does not exist: %s" % interpreter_path) ++ cmd = ["patchelf", "--set-interpreter", interpreter_path, fname] ++ run(cmd, verbose=True) ++ + # If the user has asked binaries to be patched for Nix, then + # don't check for NixOS or `/lib`, just continue to the patching. + if self.get_toml('patch-binaries-for-nix', 'build') != 'true': From 1e99ae552d5767f214ff9f96d87db5f006380c4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Jun 2022 20:56:19 +0200 Subject: [PATCH 3873/9987] adding easyconfigs: tokenizers-0.12.1-GCCcore-10.3.0.eb --- .../tokenizers-0.12.1-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ea5fce7f67c --- /dev/null +++ b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'tokenizers' +version = '0.12.1' + +homepage = 'https://github.com/huggingface/tokenizers' +description = "Fast State-of-the-Art Tokenizers optimized for Research and Production" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['070746f86efa6c873db341e55cf17bb5e7bdd5450330ca8eca542f5c3dab2c66'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Rust', '1.60.0'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From dcaf15510d7ee82f3c88ca50ae669cb88a1a1be1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Jun 2022 21:01:56 +0200 Subject: [PATCH 3874/9987] {lib}[foss/2021a] flair-NLP v0.11.3, gensim v4.2.0, Hyperopt v0.2.7, SentencePiece v0.1.96 w/ Python 3.9.5 --- .../flair-NLP/flair-NLP-0.11.3-foss-2021a.eb | 95 +++++++++++++++++++ .../g/gensim/gensim-4.2.0-foss-2021a.eb | 30 ++++++ .../h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb | 35 +++++++ .../SentencePiece-0.1.96-GCC-10.3.0.eb | 65 +++++++++++++ 4 files changed, 225 insertions(+) create mode 100644 easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb new file mode 100644 index 00000000000..dd85efe2e48 --- /dev/null +++ b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb @@ -0,0 +1,95 @@ +easyblock = 'PythonBundle' + +name = 'flair-NLP' +version = '0.11.3' + +homepage = 'https://github.com/flairNLP/flair' +description = "A very simple framework for state-of-the-art NLP" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyTorch', '1.10.0'), + ('tqdm', '4.61.2'), + ('matplotlib', '3.4.2'), + ('scikit-learn', '0.24.2'), + ('lxml', '4.6.3'), + ('gensim', '4.2.0'), + ('Hyperopt', '0.2.7'), + ('BeautifulSoup', '4.10.0'), + ('SentencePiece', '0.1.96'), + ('tokenizers', '0.12.1'), +] + +use_pip = True + +exts_list = [ + ('bpemb', '0.3.3', { + 'checksums': ['ad86ba9b1623ecc3be6fcc5ba4408e23a30e118b7e1d683d292f4be788798ffe'], + }), + ('conllu', '4.4.2', { + 'checksums': ['d5ba2f9ebf5c9af86d560e11681a172f6cd8a934967baa6839ba9a0648919c10'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('ftfy', '6.1.1', { + 'checksums': ['bfc2019f84fcd851419152320a6375604a0f1459c281b5b199b2cd0d2e727f8f'], + }), + ('gdown', '4.4.0', { + 'checksums': ['18fc3a4da4a2273deb7aa29c7486be4df3919d904158ad6a6a3e25c8115470d7'], + }), + ('huggingface_hub', '0.7.0', { + 'checksums': ['8154dc2fad84b32a4bca18372a647d9381ed8550a80b11050758357b8fcea639'], + }), + ('Janome', '0.4.2', { + 'checksums': ['14c31bbfc11724da299b4b71a06bccb3af9a105e7c912bc38a22132d8991ec97'], + }), + ('overrides', '3.1.0', { + 'checksums': ['30f761124579e59884b018758c4d7794914ef02a6c038621123fec49ea7599c6'], + }), + ('importlib_metadata', '3.10.1', { + 'checksums': ['c9356b657de65c53744046fa8f7358afe0714a1af7d570c00c3835c2d724a7c1'], + }), + ('konoha', '4.6.5', { + 'checksums': ['c83023e3bda68aa910bfc115c6ab72d10b2b9478093253b4e17a20b0acf6bb7f'], + }), + ('langdetect', '1.0.9', { + 'checksums': ['cbc1fef89f8d062739774bd51eda3da3274006b3661d199c2655f6b3f6d605a0'], + }), + ('mpld3', '0.5.8', { + 'checksums': ['1a167dbef836dd7c66d8aa71c06a32d50bffa18725f304d93cb74fdb3545043b'], + }), + ('pptree', '3.1', { + 'checksums': ['4dd0ba2f58000cbd29d68a5b64bac29bcb5a663642f79404877c0059668a69f6'], + }), + ('segtok', '1.5.11', { + 'checksums': ['8ab2dd44245bcbfec25b575dc4618473bbdf2af8c2649698cd5a370f42f3db23'], + }), + ('sqlitedict', '2.0.0', { + 'checksums': ['23a370416f4e1e962daa293382f3a8dbc4127e6a0abc06a5d4e58e6902f05d17'], + }), + ('transformers', '4.19.2', { + 'checksums': ['e19a4ff07458eda143c738e5259caf48449fcf078a63d6b1bd1aa806543440a3'], + }), + ('Wikipedia-API', '0.5.4', { + 'checksums': ['5173d4db641cdb78d96f2b052df2232bcdc00cf32a424c43402958a40f783992'], + 'modulename': 'wikipediaapi', + }), + ('flair', version, { + # can't use PyPI source tarball, because requirements.txt is missing; + # see also https://github.com/flairNLP/flair/issues/2759 + 'source_urls': ['https://github.com/flairNLP/flair/archive/refs/tags'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c780320d6d85075e25638a7157a16409f46bc9496db31fbbaa92aeac448f1cf9'], + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb b/easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb new file mode 100644 index 00000000000..2270b2977d2 --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'gensim' +version = '4.2.0' + +homepage = 'https://radimrehurek.com/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy, pandas +] + +use_pip = True + +exts_list = [ + ('smart_open', '6.0.0', { + 'checksums': ['d60106b96f0bcaedf5f1cd46ff5524a1c3d02d5653425618bb0fa66e158d22b0'], + }), + (name, version, { + 'checksums': ['995ebd2970a31d47c100aaac10212f47e2bf12e2b06536d38883c951ff34eef1'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb new file mode 100644 index 00000000000..9cc986b48f5 --- /dev/null +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Hyperopt' +version = '0.2.7' + +homepage = 'http://hyperopt.github.io/hyperopt/' +description = """hyperopt is a Python library for optimizing over awkward search spaces with real-valued, + discrete, and conditional dimensions.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('networkx', '2.5.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('py4j', '0.10.9.5', { + 'checksums': ['276a4a3c5a2154df1860ef3303a927460e02e97b047dc0a47c1c3fb8cce34db6'], + }), + ('hyperopt', version, { + 'checksums': ['1bf89ae58050bbd32c7307199046117feee245c2fd9ab6255c7308522b7ca149'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb new file mode 100644 index 00000000000..c4db4aa9a4d --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.1.96' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('gperftools', '2.9.1'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5198f31c3bb25e685e9e68355a3bf67a1db23c9e8bdccc33dc015f496a44df7a'], +} + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'separate_build_dir': True, + 'start_dir': '%(namelower)s-%(version)s', + }), + ('sentencepiece', version, { + 'easyblock': 'PythonPackage', + 'start_dir': '%(namelower)s-%(version)s/python', + 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/'] + +sanity_check_paths = { + 'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] + + ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] + + ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'], +} + +sanity_check_commands = [ + 'spm_train --help', + "python -c 'import sentencepiece'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'lib' From ad07f33a77b3905b533f2d72cbdae2c68fa84626 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 1 Jun 2022 23:56:34 +0000 Subject: [PATCH 3875/9987] Open MPI: elimininate benign libcuda warning --with-cuda=internal If libcuda.so is not found then Open MPI will warn, but this is a common situation if the base Open MPI tries to find libcuda.so even on nodes without GPUs. Therefore disable this warning by default if we use --with-cuda=internal in configure. --- .../o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb | 2 +- .../o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 2 +- ....1.1_build-with-internal-cuda-header.patch | 36 ++++++++++++++++--- .../o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb | 2 +- 4 files changed, 35 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb index 9d2b5068d87..5314ed77d40 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb @@ -27,7 +27,7 @@ checksums = [ # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', # OpenMPI-4.1.1_build-with-internal-cuda-header.patch - '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83', # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index 24a5ae59bc0..762189ad19d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -28,7 +28,7 @@ checksums = [ # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', # OpenMPI-4.1.1_build-with-internal-cuda-header.patch - '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83', # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build-with-internal-cuda-header.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build-with-internal-cuda-header.patch index 9c5945b7de2..9baec9a9129 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build-with-internal-cuda-header.patch +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1_build-with-internal-cuda-header.patch @@ -1,25 +1,29 @@ Allow building Open MPI with --with-cuda=internal, by providing an -internal minimal cuda.h header file. This eliminate the CUDA +internal minimal cuda.h header file. This eliminates the CUDA (build)dependency; as long as the runtime CUDA version is 8.0+, libcuda.so will be dlopen'ed and used successfully. +This then also sets the default value of opal_warn_on_missing_libcuda to false +as missing libcuda is then a common situation. Author: Bart Oldeman --- openmpi-4.1.3.orig/config/opal_check_cuda.m4 2022-03-31 16:04:13.000000000 +0000 -+++ openmpi-4.1.3/config/opal_check_cuda.m4 2022-05-04 17:37:57.576260311 +0000 -@@ -45,6 +45,12 @@ ++++ openmpi-4.1.3/config/opal_check_cuda.m4 2022-06-01 23:30:09.255003842 +0000 +@@ -45,6 +45,14 @@ # macro as that would error out after not finding it in the first directory. # Note that anywhere CUDA aware code is in the Open MPI repository requires # us to make use of AC_REQUIRE to ensure this check has been done. +opal_check_cuda_internal="" ++OPAL_WARN_ON_MISSING_LIBCUDA_DEFAULT=1 +AS_IF([test "$with_cuda" = "internal"], + [AC_MSG_RESULT([internal support requested]) + with_cuda="${OPAL_TOP_SRCDIR}/opal/mca/common/cuda/cuda" + opal_check_cuda_internal=" (internal)" ++ OPAL_WARN_ON_MISSING_LIBCUDA_DEFAULT=0 + ]) AS_IF([test "$with_cuda" = "no" || test "x$with_cuda" = "x"], [opal_check_cuda_happy="no" AC_MSG_RESULT([not set (--with-cuda=$with_cuda)])], -@@ -124,7 +130,7 @@ +@@ -124,7 +132,7 @@ CUDA_SUPPORT=0 fi @@ -28,6 +32,30 @@ Author: Bart Oldeman AM_CONDITIONAL([OPAL_cuda_support], [test "x$CUDA_SUPPORT" = "x1"]) AC_DEFINE_UNQUOTED([OPAL_CUDA_SUPPORT],$CUDA_SUPPORT, +@@ -144,6 +152,9 @@ + AC_DEFINE_UNQUOTED([OPAL_CUDA_GDR_SUPPORT],$CUDA_VERSION_60_OR_GREATER, + [Whether we have CUDA GDR support available]) + ++AM_CONDITIONAL([OPAL_warn_on_missing_libcuda_default], [test "x$OPAL_WARN_ON_MISSING_LIBCUDA_DEFAULT" = "x1"]) ++AC_DEFINE_UNQUOTED([OPAL_WARN_ON_MISSING_LIBCUDA_DEFAULT],$OPAL_WARN_ON_MISSING_LIBCUDA_DEFAULT, ++ [Whether to warn by default if libcuda is not available]) + ]) + + dnl +--- openmpi-4.1.3.orig/opal/runtime/opal_params.c 2022-03-31 16:04:13.000000000 +0000 ++++ openmpi-4.1.3/opal/runtime/opal_params.c 2022-06-01 23:23:11.127963103 +0000 +@@ -246,7 +246,11 @@ + return ret; + } + ++#if OPAL_WARN_ON_MISSING_LIBCUDA_DEFAULT == 1 + opal_warn_on_missing_libcuda = true; ++#else ++ opal_warn_on_missing_libcuda = false; ++#endif + ret = mca_base_var_register ("opal", "opal", NULL, "warn_on_missing_libcuda", + "Whether to print a message when CUDA support is enabled but libcuda is not found", + MCA_BASE_VAR_TYPE_BOOL, NULL, 0, MCA_BASE_VAR_FLAG_SETTABLE, --- openmpi-4.1.3.orig/opal/mca/common/cuda/cuda/cuda.h 1970-01-01 00:00:00.000000000 +0000 +++ openmpi-4.1.3/opal/mca/common/cuda/cuda/cuda.h 2022-05-04 18:52:14.991300184 +0000 @@ -0,0 +1,60 @@ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb index d9a823c33d8..d01bc8b847f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb @@ -15,7 +15,7 @@ patches = [ checksums = [ '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d', # openmpi-4.1.4.tar.bz2 # OpenMPI-4.1.1_build-with-internal-cuda-header.patch - '1ceb82b19f62da2525357debaae694d7751b6352adae7ffa55c71e19a4d7101c', + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83', # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', ] From 4cddc8300106bd3246a4f1d66eca9f3a2f099a8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Jun 2022 11:24:57 +0200 Subject: [PATCH 3876/9987] update fallback version for OpenSSL 1.1 wrapper to v1.1.1o --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb index 336394a94e0..8f021218766 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb @@ -27,11 +27,11 @@ builddependencies = [('pkg-config', '0.29.2')] # component list, which will be build and installed as usual. components = [ - (name, '1.1.1k', { + (name, '1.1.1o', { 'easyblock': 'EB_OpenSSL', 'source_urls': ['https://www.openssl.org/source/'], 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['892a0875b9872acd04a9fde79b1f943075d5ea162415de3047c327df33fbaee5'], + 'checksums': ['9384a2b0570dd80358841464677115df785edb941c71211f75076d72fe6b438f'], 'start_dir': '%(namelower)s-%(version)s', }), ] From 73a0f7c6d717d9ff9abd2e00e46784e941eb5d69 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 2 Jun 2022 16:26:26 +0200 Subject: [PATCH 3877/9987] fix perl shebangs --- .../e/EvidentialGene/EvidentialGene-2022.01.14-gompi-2021b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2022.01.14-gompi-2021b.eb b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2022.01.14-gompi-2021b.eb index e424ebe3f5e..f52d81c3f13 100644 --- a/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2022.01.14-gompi-2021b.eb +++ b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2022.01.14-gompi-2021b.eb @@ -28,6 +28,8 @@ dependencies = [ ('BLAST+', '2.12.0'), ] +fix_perl_shebang_for = ['scripts/*.pl', 'scripts/*/*.pl', 'scripts/*/*/*.pl'] + sanity_check_paths = { 'files': [], 'dirs': ['scripts/'], From ae33f4e4df548a84fc5b37da5f4389a00ba7ce53 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 2 Jun 2022 21:02:59 +0100 Subject: [PATCH 3878/9987] add sysroot patch --- easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb index bb13c946b9a..ecaf7753a89 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -checksums = ['20ca826d1cf674daf8e22c4f8c4b9743af07973211c839b85839742314c838b7'] +patches = ['Rust-1.60_sysroot-fix-interpreter.patch'] +checksums = [ + '20ca826d1cf674daf8e22c4f8c4b9743af07973211c839b85839742314c838b7', # rustc-1.60.0-src.tar.gz + 'b59ed4c2591fc9098277299be21dd6752654f6f193d8652b7d21cb0fa0dd8716', # Rust-1.60_sysroot-fix-interpreter.patch +] builddependencies = [ ('binutils', '2.38'), From ab40be9acc9dee59c4e1df2c0e729c5d3cc7b339 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 3 Jun 2022 08:27:12 +0100 Subject: [PATCH 3879/9987] fix use of close_range in GLib 2.68.2 --- .../g/GLib/GLib-2.68.2-GCCcore-10.3.0.eb | 6 +++- .../GLib-2.68.2_fix-close_range-use.patch | 29 +++++++++++++++++++ 2 files changed, 34 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.68.2_fix-close_range-use.patch diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.68.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.68.2-GCCcore-10.3.0.eb index 14e8b9b0979..4846b0e2477 100644 --- a/easybuild/easyconfigs/g/GLib/GLib-2.68.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GLib/GLib-2.68.2-GCCcore-10.3.0.eb @@ -11,7 +11,11 @@ toolchainopts = {'pic': True} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['ecc7798a9cc034eabdfd7f246e6dd461cdbf1175fcc2e9867cc7da7b7309e0fb'] +patches = ['%(name)s-%(version)s_fix-close_range-use.patch'] +checksums = [ + 'ecc7798a9cc034eabdfd7f246e6dd461cdbf1175fcc2e9867cc7da7b7309e0fb', # glib-2.68.2.tar.xz + 'a13278694107a795a8f55c78703eeebc841f774400e1ebaf5c8c3047c82a239d', # GLib-2.68.2_fix-close_range-use.patch +] builddependencies = [ # Python is required for building against GLib, at least when diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.68.2_fix-close_range-use.patch b/easybuild/easyconfigs/g/GLib/GLib-2.68.2_fix-close_range-use.patch new file mode 100644 index 00000000000..d14bcc671e0 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.68.2_fix-close_range-use.patch @@ -0,0 +1,29 @@ +From 6e59d21b273f026e82adc56fecbec67d1ffa72a4 Mon Sep 17 00:00:00 2001 +From: Khem Raj +Date: Thu, 8 Jul 2021 17:26:43 -0700 +Subject: [PATCH] correctly use 3 parameters for close_range + +libc implementation has 3 parameter e.g. +https://www.freebsd.org/cgi/man.cgi?query=close_range&sektion=2&format=html + +Signed-off-by: Khem Raj +--- + glib/gspawn.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/glib/gspawn.c b/glib/gspawn.c +index 95f5b868eb..a15fb1ca13 100644 +--- a/glib/gspawn.c ++++ b/glib/gspawn.c +@@ -1494,7 +1494,7 @@ safe_closefrom (int lowfd) + * + * Handle ENOSYS in case it’s supported in libc but not the kernel; if so, + * fall back to safe_fdwalk(). */ +- if (close_range (lowfd, G_MAXUINT) != 0 && errno == ENOSYS) ++ if (close_range (lowfd, G_MAXUINT, 0) != 0 && errno == ENOSYS) + #endif /* HAVE_CLOSE_RANGE */ + (void) safe_fdwalk (close_func, GINT_TO_POINTER (lowfd)); + #endif +-- +GitLab + From 3286fa853267c6f3fde9a065a60f8e48625006d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jun 2022 09:34:52 +0200 Subject: [PATCH 3880/9987] add additional sanity check commands for IQ-TREE v2.2.1 --- .../easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1-gompi-2021b.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1-gompi-2021b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1-gompi-2021b.eb index 94fa02f1ac2..d87d337950e 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1-gompi-2021b.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.1-gompi-2021b.eb @@ -47,6 +47,11 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["iqtree2 --help"] +sanity_check_commands = [ + "iqtree2 --help", + "mkdir -p $TMPDIR/{test-omp,test-mpi}", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy", + "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy", +] moduleclass = 'bio' From 47ed57116fac9f1ef556803d9ce2e6d392e69ee8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jun 2022 09:36:52 +0200 Subject: [PATCH 3881/9987] fix download of thrift 0.12.0 for Arrow 0.16.0 --- .../a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb | 4 ++++ .../a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb index 77e68e14b2e..8dcb89cd8dc 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb @@ -35,6 +35,10 @@ start_dir = 'cpp' # see https://arrow.apache.org/docs/python/development.html configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=on -DCMAKE_INSTALL_LIBDIR=lib" +# fix download of thrift 0.12.0, which is now archived +prebuildopts = "sed -i 's@dlcdn.apache.org@archive.apache.org/dist/@g' " +prebuildopts += "thrift_ep-prefix/src/thrift_ep-stamp/download-thrift_ep.cmake && " + # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb index fa3efdcbe4b..bd28ccba5c3 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb @@ -40,6 +40,10 @@ start_dir = 'cpp' configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" +# fix download of thrift 0.12.0, which is now archived +prebuildopts = "sed -i 's@dlcdn.apache.org@archive.apache.org/dist/@g' " +prebuildopts += "thrift_ep-prefix/src/thrift_ep-stamp/download-thrift_ep.cmake && " + # also install Python bindings local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " From 4812d0713494d49f987ad7869535899d6978e772 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jun 2022 09:53:37 +0200 Subject: [PATCH 3882/9987] use minimal makeinfo (+ Perl) as build dep for groff with GCCcore/8.3.0 --- .../g/groff/groff-1.22.4-GCCcore-8.3.0.eb | 2 +- .../makeinfo-6.7-GCCcore-8.3.0-minimal.eb | 35 +++++++++++++++++++ .../Perl/Perl-5.30.0-GCCcore-8.3.0-minimal.eb | 27 ++++++++++++++ 3 files changed, 63 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-8.3.0-minimal.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0-minimal.eb diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-8.3.0.eb index be1a78b6ad3..dbb280e82ab 100644 --- a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-8.3.0.eb @@ -15,7 +15,7 @@ checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] builddependencies = [ ('binutils', '2.32'), - ('makeinfo', '6.7'), + ('makeinfo', '6.7', '-minimal'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-8.3.0-minimal.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-8.3.0-minimal.eb new file mode 100644 index 00000000000..fe565c44e7e --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-8.3.0-minimal.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '6.7' +versionsuffix = '-minimal' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project. + +This is a minimal build with very basic functionality. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] + +builddependencies = [ + ('binutils', '2.32'), +] +dependencies = [ + ('Perl', '5.30.0', '-minimal'), +] + +configopts = '--disable-perl-xs --disable-perl-api-texi-build --disable-pod-simple-texinfo-tests ' + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0-minimal.eb new file mode 100644 index 00000000000..9fd3846f781 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0-minimal.eb @@ -0,0 +1,27 @@ +name = 'Perl' +version = '5.30.0' +versionsuffix = '-minimal' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +This is a minimal build without any modules. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['851213c754d98ccff042caa40ba7a796b2cee88c5325f121be5cbb61bbf975f2'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('zlib', '1.2.11'), + +] + +moduleclass = 'lang' From 35af04304da1ef765821913c068edcecff23f98a Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 3 Jun 2022 11:27:15 +0200 Subject: [PATCH 3883/9987] adding easyconfigs: cuDNN-8.4.1.50-CUDA-11.6.0.eb --- .../c/cuDNN/cuDNN-8.4.1.50-CUDA-11.6.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.6.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.6.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.6.0.eb new file mode 100644 index 00000000000..d7f4c0e10db --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.6.0.eb @@ -0,0 +1,43 @@ +name = 'cuDNN' +version = '8.4.1.50' +local_cuda_version = '11.6.0' +local_cuda_version_majmin = '.'.join(local_cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % local_cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/%s/' % + ('.'.join(version.split('.')[:3]), local_cuda_version_majmin) +] +local_cudnn_cuda_version = '%%(version)s_cuda{maj_min}'.format(maj_min=local_cuda_version_majmin) +local_tarball_tmpl = '-'.join(['%%(namelower)s', 'linux', '%s', local_cudnn_cuda_version, 'archive.tar.xz']) +sources = [local_tarball_tmpl % '%(cudnnarch)s'] +checksums = [ + { + local_tarball_tmpl % 'x86_64': + 'ec96d2376d81fca42bdd3d4c3d705a99b29a065bab57f920561c763e29c67d01', + local_tarball_tmpl % 'ppc64le': + '8b806cbfdc81352bf76716d1e53b42537665d110c6ffc068be910505c10e1b98', + local_tarball_tmpl % 'sbsa': + '0b1b9fac5b78974e2fdaaa74843db18f636ce8f3d999d62ff2a615b9978fc360', + } +] + +dependencies = [('CUDA', local_cuda_version)] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From 1c77d57b80f2dd401f6d1c64ba4f0c2bd08203d8 Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Fri, 3 Jun 2022 11:55:08 +0200 Subject: [PATCH 3884/9987] adding easyconfigs: NGS-2.10.9-GCCcore-10.3.0.eb --- .../n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f07787644a5 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'NGS' +version = '2.10.9' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups +produced from Next Generation Sequencing.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('Perl', '5.32.1'), +] + +dependencies = [('Java', '11', '', True)] + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://github.com/ncbi/ngs/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['1372695af5ac2599c9dad0b8cdce857c95c7827ff831a6709343276a29438b1e'], +} + +components = [ + ('NGS-SDK', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), + ('NGS-Java', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), +] + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' From 59e00f07236b665ec1bbc13cbae473a95873799a Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Fri, 3 Jun 2022 11:58:27 +0200 Subject: [PATCH 3885/9987] adding easyconfigs: Sambamba-0.8.2-GCC-10.3.0.eb --- .../s/Sambamba/Sambamba-0.8.2-GCC-10.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.2-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.2-GCC-10.3.0.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..e7b7e48bac1 --- /dev/null +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-0.8.2-GCC-10.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'Sambamba' +version = '0.8.2' + +homepage = 'https://lomereiter.github.io/sambamba/' +description = """Sambamba is a high performance modern robust and fast tool + (and library), written in the D programming language, for working with SAM + and BAM files. Current functionality is an important subset of samtools + functionality, including view, index, sort, markdup, and depth.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/biod/sambamba/archive/'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/biod', + 'repo_name': 'sambamba', + 'commit': 'f898046', + 'recursive': True, + } +}] +checksums = [None] + +builddependencies = [ + ('LDC', '1.26.0'), + ('Python', '3.9.5'), + ('lz4', '1.9.3'), +] + +files_to_copy = [(['bin/sambamba-%(version)s'], 'bin')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s sambamba-%(version)s sambamba"] + +sanity_check_paths = { + 'files': ['bin/sambamba'], + 'dirs': [], +} + +sanity_check_commands = ["sambamba 2>&1 | grep '^sambamba %(version)s'"] + +moduleclass = 'bio' From 8149f20d5e99f817bb7589f379d126f973cf9782 Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Fri, 3 Jun 2022 12:36:56 +0200 Subject: [PATCH 3886/9987] adding easyconfigs: hifiasm-0.15.2-GCCcore-10.3.0.eb --- .../hifiasm/hifiasm-0.15.2-GCCcore-10.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/h/hifiasm/hifiasm-0.15.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/h/hifiasm/hifiasm-0.15.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.15.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..8232fbde83d --- /dev/null +++ b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.15.2-GCCcore-10.3.0.eb @@ -0,0 +1,36 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'hifiasm' +version = '0.15.2' + +homepage = 'https://github.com/chhylp123/hifiasm' +description = """Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'chhylp123' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e49e38341d6c943902cebc8b0e517e20a6e919659f3dab2bcc24c062524a72da'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="$CC" CXX="$CXX" CPPFLAGS="$CPPFLAGS"' + +files_to_copy = [ + ([name], 'bin'), + (['*.h'], 'include/hifiasm'), + 'LICENSE', 'README.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} +sanity_check_commands = ["%(name)s -h"] + +moduleclass = 'bio' From 528a96edd54306734b2b5ff307dff48f0066e7f6 Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Fri, 3 Jun 2022 13:27:55 +0200 Subject: [PATCH 3887/9987] adding easyconfigs: samblaster-0.1.26-GCC-10.3.0.eb --- .../samblaster-0.1.26-GCC-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.3.0.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.3.0.eb new file mode 100644 index 00000000000..16804ba93b3 --- /dev/null +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-10.3.0.eb @@ -0,0 +1,37 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org fizwit@github.com +easyblock = 'MakeCp' + +name = 'samblaster' +version = '0.1.26' + +description = """samblaster is a fast and flexible program for marking + duplicates in read-id grouped1 paired-end SAM files.""" + +homepage = 'https://github.com/GregoryFaust/samblaster' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/GregoryFaust/samblaster/archive/'] +sources = [{ + 'download_filename': 'v.%(version)s.zip', + 'filename': SOURCE_ZIP +}] +checksums = ['79ff6f8306482e73e04678424bf14b840d80561660bb59deac1b75ada2f330cf'] + +files_to_copy = [ + (["samblaster"], "bin/"), + 'README.md', + 'SAMBLASTER_Supplemental.pdf', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/samblaster', 'README.md'], + 'dirs': [] +} + +sanity_check_commands = ["samblaster --help"] + +moduleclass = 'bio' From 3ab50ebfd572a2bd087131560c025f90736f2826 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 3 Jun 2022 11:44:51 +0000 Subject: [PATCH 3888/9987] {numlib}[GCC/11.3.0] FlexiBLAS v3.1.3 -> v3.2.0 --- ...-3.1.3-GCC-11.3.0.eb => FlexiBLAS-3.2.0-GCC-11.3.0.eb} | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/f/FlexiBLAS/{FlexiBLAS-3.1.3-GCC-11.3.0.eb => FlexiBLAS-3.2.0-GCC-11.3.0.eb} (89%) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-GCC-11.3.0.eb similarity index 89% rename from easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.3.0.eb rename to easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-GCC-11.3.0.eb index 32e84a14485..3485cb581bd 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.1.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-GCC-11.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'FlexiBLAS' -version = '3.1.3' +version = '3.2.0' homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation @@ -37,14 +37,14 @@ components = [ (name, version, { 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['aac6175660e8475ce478b88673eee330671f8aecc0cb852a25833e23e29a0620'], + 'checksums': ['a3f4d66a30b6fa6473e492de86d34abc5f9d4e69d4d91ba23618388e8df05904'], 'backends': local_backends, }), - ('LAPACK', '3.10.0', { + ('LAPACK', '3.10.1', { 'easyblock': 'CMakeMake', 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], 'sources': ['v%(version)s.tar.gz'], - 'checksums': ['328c1bea493a32cac5257d84157dc686cc3ab0b004e2bea22044e0a59f6f8a19'], + 'checksums': ['cd005cd021f144d7d5f7f33c943942db9f03a28d110d6a3b80d718a295f7f714'], 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), From 6542dc941b2914a96ac0187e88b7316b9f522a91 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 3 Jun 2022 11:55:01 +0000 Subject: [PATCH 3889/9987] Bump FlexiBLAS to 3.2.0 --- easybuild/easyconfigs/f/foss/foss-2022.05.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/foss/foss-2022.05.eb b/easybuild/easyconfigs/f/foss/foss-2022.05.eb index b80dc255154..c6ded56db6a 100644 --- a/easybuild/easyconfigs/f/foss/foss-2022.05.eb +++ b/easybuild/easyconfigs/f/foss/foss-2022.05.eb @@ -19,7 +19,7 @@ local_comp_mpi_tc = ('gompi', version) dependencies = [ ('GCC', local_gccver), ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), - ('FlexiBLAS', '3.1.3', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.2.0', '', ('GCC', local_gccver)), ('FFTW', '3.3.10', '', ('GCC', local_gccver)), ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), From 844191f88c25653f4db35eeaff4eb6a50d422724 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jun 2022 14:07:07 +0200 Subject: [PATCH 3890/9987] adding easyconfigs: NetPyNE-1.0.2.1-foss-2021b.eb, NEURON-7.8.2-foss-2021b.eb --- .../n/NEURON/NEURON-7.8.2-foss-2021b.eb | 23 +++++++++ .../n/NetPyNE/NetPyNE-1.0.2.1-foss-2021b.eb | 48 +++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/n/NEURON/NEURON-7.8.2-foss-2021b.eb create mode 100644 easybuild/easyconfigs/n/NetPyNE/NetPyNE-1.0.2.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/n/NEURON/NEURON-7.8.2-foss-2021b.eb b/easybuild/easyconfigs/n/NEURON/NEURON-7.8.2-foss-2021b.eb new file mode 100644 index 00000000000..217413654ce --- /dev/null +++ b/easybuild/easyconfigs/n/NEURON/NEURON-7.8.2-foss-2021b.eb @@ -0,0 +1,23 @@ +name = 'NEURON' +version = '7.8.2' + +homepage = 'https://www.neuron.yale.edu/neuron' +description = """Empirically-based simulations of neurons and networks of neurons.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/neuronsimulator/nrn/releases/download/%(version)s/'] +sources = ['full-src-package-%(version)s.tar.gz'] +checksums = ['7ab615b36370220d5048214463414bc54245489c14c79899d86e7bb6d3549edf'] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('libreadline', '8.1'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NetPyNE/NetPyNE-1.0.2.1-foss-2021b.eb b/easybuild/easyconfigs/n/NetPyNE/NetPyNE-1.0.2.1-foss-2021b.eb new file mode 100644 index 00000000000..7a729a891c0 --- /dev/null +++ b/easybuild/easyconfigs/n/NetPyNE/NetPyNE-1.0.2.1-foss-2021b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'NetPyNE' +version = '1.0.2.1' + +homepage = 'http://www.netpyne.org' +description = """NetPyNE is an open-source Python package to facilitate the development, parallel simulation, analysis, +and optimization of biological neuronal networks using the NEURON simulator.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('bokeh', '2.4.2'), + ('NEURON', '7.8.2'), +] + +use_pip = True + +exts_list = [ + ('MEAutility', '1.5.1', { + 'checksums': ['de12cc9c1772d3321e941af78e6bfb36cdcb5702a7b1272a852cc95f413bbfcb'], + 'modulename': 'MEAutility', + }), + ('LFPykit', '0.4', { + 'checksums': ['ce92f5a987535ee72a76644bac90393eaa669d952f493dc388f3deb1c36f474d'], + }), + ('matplotlib-scalebar', '0.8.1', { + 'checksums': ['14887af1093579c5e6afae51a0a1ecc3f715cdbc5c4d7ef59cdeec76ee6bb15d'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('schema', '0.7.5', { + 'checksums': ['f06717112c61895cabc4707752b88716e8420a8819d71404501e114f91043197'], + }), + ('netpyne', version, { + 'source_urls': ['https://github.com/suny-downstate-medical-center/netpyne/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['f33f783730d237149980101d57f893012cba3ee61c4a2f5bc350922d0a21f05a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 756a1ed66300b49831c1f8bd3663850183fb73b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jun 2022 14:53:09 +0200 Subject: [PATCH 3891/9987] add missing flex + Bison build dependencies for NEURON 7.8.2 --- easybuild/easyconfigs/n/NEURON/NEURON-7.8.2-foss-2021b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NEURON/NEURON-7.8.2-foss-2021b.eb b/easybuild/easyconfigs/n/NEURON/NEURON-7.8.2-foss-2021b.eb index 217413654ce..d904d4d2188 100644 --- a/easybuild/easyconfigs/n/NEURON/NEURON-7.8.2-foss-2021b.eb +++ b/easybuild/easyconfigs/n/NEURON/NEURON-7.8.2-foss-2021b.eb @@ -12,6 +12,8 @@ checksums = ['7ab615b36370220d5048214463414bc54245489c14c79899d86e7bb6d3549edf'] builddependencies = [ ('CMake', '3.22.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), ] dependencies = [ From 41662e6c1b4f46abb5d143083ad598cadf1d6cf6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jun 2022 16:20:33 +0200 Subject: [PATCH 3892/9987] in-place update for cryoDRGN to v0.3.5 with foss/2021a to fix compatibility issue with PyTorch v1.10 --- ...A-11.3.1.eb => cryoDRGN-0.3.5-foss-2021a-CUDA-11.3.1.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/c/cryoDRGN/{cryoDRGN-0.3.4-foss-2021a-CUDA-11.3.1.eb => cryoDRGN-0.3.5-foss-2021a-CUDA-11.3.1.eb} (93%) diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.4-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.5-foss-2021a-CUDA-11.3.1.eb similarity index 93% rename from easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.4-foss-2021a-CUDA-11.3.1.eb rename to easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.5-foss-2021a-CUDA-11.3.1.eb index b7104343785..893db52f7bb 100644 --- a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.4-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-0.3.5-foss-2021a-CUDA-11.3.1.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'cryoDRGN' -version = '0.3.4' +version = '0.3.5' versionsuffix = '-CUDA-11.3.1' homepage = 'https://cb.csail.mit.edu/cb/cryodrgn/' @@ -51,7 +51,7 @@ exts_list = [ ], 'source_urls': ['https://github.com/zhonge/cryodrgn/archive'], 'sources': ['%(version)s.tar.gz'], - 'checksums': ['5be9709a2bd19a4ab7c80acd82eef5bfbcdf02b4dd8dcb61113636fa5d44d0c5'], + 'checksums': ['93f0c939376154bcd5c677406251a6aff794e5d62299a01cdecae1c4947d38e4'], }), ] @@ -60,7 +60,7 @@ fix_python_shebang_for = ['bin/*.py'] local_scripts = [ 'add_psize', 'filter_mrcs', 'filter_pkl', 'filter_star', 'flip_hand', 'fsc', 'invert_contrast', 'kmeans', 'phase_flip', 'plotfsc', 'plot_loss', 'plot_z1', 'plot_z2', 'plot_z_pca', 'run_umap', 'translate_stack', 'tsne', - 'view_header', 'view_stack', 'write_starfile' + 'view_header', 'view_stack', ] sanity_check_paths = { From dd0bb086b04f2b45683bbdcc4987593197b87475 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jun 2022 20:35:19 +0200 Subject: [PATCH 3893/9987] adding easyconfigs: cryoDRGN-1.0.0-beta-foss-2021a-CUDA-11.3.1.eb --- ...oDRGN-1.0.0-beta-foss-2021a-CUDA-11.3.1.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-1.0.0-beta-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-1.0.0-beta-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-1.0.0-beta-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ecd4a3500a5 --- /dev/null +++ b/easybuild/easyconfigs/c/cryoDRGN/cryoDRGN-1.0.0-beta-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'cryoDRGN' +version = '1.0.0-beta' +versionsuffix = '-CUDA-11.3.1' + +homepage = 'https://cb.csail.mit.edu/cb/cryodrgn/' +description = """cryoDRGN: Deep Reconstructing Generative Networks for cryo-EM heterogeneous + reconstruction. + CryoDRGN is a neural network based algorithm for heterogeneous cryo-EM reconstruction. In + particular, the method models a continuous distribution over 3D structures by using a neural + network based representation for the volume. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('IPython', '7.25.0'), + ('JupyterLab', '3.0.16'), + ('PyTorch', '1.10.0', versionsuffix), + ('numba', '0.53.1'), + ('plotly.py', '5.1.0'), + ('scikit-learn', '0.24.2'), + ('matplotlib', '3.4.2'), + ('Seaborn', '0.11.2'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('colorlover', '0.3.0', { + 'checksums': ['b8fb7246ab46e1f5e6715649453c1762e245a515de5ff2d2b4aab7a6e67fa4e2'], + }), + ('cufflinks', '0.17.3', { + 'checksums': ['48c1b3406dc030004121966489eebc5518cea70fd4e3f16379b491328501a644'], + }), + ('pynndescent', '0.5.6', { + 'checksums': ['61fb31885baac469d67933e2c7c935b6edebb06ee498e2f0f9dfc97c59d3725c'], + }), + ('umap-learn', '0.5.3', { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), + ('cryodrgn', version, { + 'postinstallcmds': [ + 'cp utils/* analysis_scripts/* %(installdir)s/bin', + 'chmod +x %(installdir)s/bin/*.py', + ], + 'source_urls': ['https://github.com/zhonge/cryodrgn/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['8e671289bf839ff65433c6758b9ad14d4d7ca419cf3852587b01d850691c57d2'], + }), +] + +fix_python_shebang_for = ['bin/*.py'] + +local_scripts = [ + 'add_psize', 'filter_mrcs', 'filter_pkl', 'filter_star', 'flip_hand', 'fsc', 'invert_contrast', 'kmeans', + 'phase_flip', 'plotfsc', 'plot_loss', 'plot_z1', 'plot_z2', 'plot_z_pca', 'run_umap', 'translate_stack', 'tsne', + 'view_header', 'view_stack', +] + +sanity_check_paths = { + 'files': ['bin/%s.py' % x for x in local_scripts], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s --help'] +sanity_check_commands += ['%s.py -h' % x for x in local_scripts] + +sanity_pip_check = True + +moduleclass = 'chem' From a8ba288f3cbe8f590458ff691db99e9a7de97f1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jun 2022 20:38:17 +0200 Subject: [PATCH 3894/9987] {lib}[foss/2021a] flair-NLP v0.11.3 w/ Python 3.9.5 + CUDA 11.3.1 --- ...flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..1ad8d95623e --- /dev/null +++ b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,97 @@ +easyblock = 'PythonBundle' + +name = 'flair-NLP' +version = '0.11.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/flairNLP/flair' +description = "A very simple framework for state-of-the-art NLP" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('PyTorch', '1.10.0', versionsuffix), + ('tqdm', '4.61.2'), + ('matplotlib', '3.4.2'), + ('scikit-learn', '0.24.2'), + ('lxml', '4.6.3'), + ('gensim', '4.2.0'), + ('Hyperopt', '0.2.7'), + ('BeautifulSoup', '4.10.0'), + ('SentencePiece', '0.1.96'), + ('tokenizers', '0.12.1'), +] + +use_pip = True + +exts_list = [ + ('bpemb', '0.3.3', { + 'checksums': ['ad86ba9b1623ecc3be6fcc5ba4408e23a30e118b7e1d683d292f4be788798ffe'], + }), + ('conllu', '4.4.2', { + 'checksums': ['d5ba2f9ebf5c9af86d560e11681a172f6cd8a934967baa6839ba9a0648919c10'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('ftfy', '6.1.1', { + 'checksums': ['bfc2019f84fcd851419152320a6375604a0f1459c281b5b199b2cd0d2e727f8f'], + }), + ('gdown', '4.4.0', { + 'checksums': ['18fc3a4da4a2273deb7aa29c7486be4df3919d904158ad6a6a3e25c8115470d7'], + }), + ('huggingface_hub', '0.7.0', { + 'checksums': ['8154dc2fad84b32a4bca18372a647d9381ed8550a80b11050758357b8fcea639'], + }), + ('Janome', '0.4.2', { + 'checksums': ['14c31bbfc11724da299b4b71a06bccb3af9a105e7c912bc38a22132d8991ec97'], + }), + ('overrides', '3.1.0', { + 'checksums': ['30f761124579e59884b018758c4d7794914ef02a6c038621123fec49ea7599c6'], + }), + ('importlib_metadata', '3.10.1', { + 'checksums': ['c9356b657de65c53744046fa8f7358afe0714a1af7d570c00c3835c2d724a7c1'], + }), + ('konoha', '4.6.5', { + 'checksums': ['c83023e3bda68aa910bfc115c6ab72d10b2b9478093253b4e17a20b0acf6bb7f'], + }), + ('langdetect', '1.0.9', { + 'checksums': ['cbc1fef89f8d062739774bd51eda3da3274006b3661d199c2655f6b3f6d605a0'], + }), + ('mpld3', '0.5.8', { + 'checksums': ['1a167dbef836dd7c66d8aa71c06a32d50bffa18725f304d93cb74fdb3545043b'], + }), + ('pptree', '3.1', { + 'checksums': ['4dd0ba2f58000cbd29d68a5b64bac29bcb5a663642f79404877c0059668a69f6'], + }), + ('segtok', '1.5.11', { + 'checksums': ['8ab2dd44245bcbfec25b575dc4618473bbdf2af8c2649698cd5a370f42f3db23'], + }), + ('sqlitedict', '2.0.0', { + 'checksums': ['23a370416f4e1e962daa293382f3a8dbc4127e6a0abc06a5d4e58e6902f05d17'], + }), + ('transformers', '4.19.2', { + 'checksums': ['e19a4ff07458eda143c738e5259caf48449fcf078a63d6b1bd1aa806543440a3'], + }), + ('Wikipedia-API', '0.5.4', { + 'checksums': ['5173d4db641cdb78d96f2b052df2232bcdc00cf32a424c43402958a40f783992'], + 'modulename': 'wikipediaapi', + }), + ('flair', version, { + # can't use PyPI source tarball, because requirements.txt is missing; + # see also https://github.com/flairNLP/flair/issues/2759 + 'source_urls': ['https://github.com/flairNLP/flair/archive/refs/tags'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c780320d6d85075e25638a7157a16409f46bc9496db31fbbaa92aeac448f1cf9'], + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 748df63c0515009ef6575e961175fe3d0b1d9f35 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jun 2022 21:52:46 +0200 Subject: [PATCH 3895/9987] adding easyconfigs: uncertainty-calibration-0.0.9-foss-2021b.eb --- ...ncertainty-calibration-0.0.9-foss-2021b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/u/uncertainty-calibration/uncertainty-calibration-0.0.9-foss-2021b.eb diff --git a/easybuild/easyconfigs/u/uncertainty-calibration/uncertainty-calibration-0.0.9-foss-2021b.eb b/easybuild/easyconfigs/u/uncertainty-calibration/uncertainty-calibration-0.0.9-foss-2021b.eb new file mode 100644 index 00000000000..d9e514cc0d6 --- /dev/null +++ b/easybuild/easyconfigs/u/uncertainty-calibration/uncertainty-calibration-0.0.9-foss-2021b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'uncertainty-calibration' +version = '0.0.9' + +homepage = 'https://github.com/p-lambda/verified_calibration' +description = """Python library to measure the calibration error of models, including confidence intervals computed by +Bootstrap resampling, and code to recalibrate models.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('scikit-learn', '1.0.1'), +] + +use_pip = True + +exts_list = [ + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), + ('parameterized', '0.8.1', { + 'checksums': ['41bbff37d6186430f77f900d777e5bb6a24928a1c46fb1de692f8b52b8833b5c'], + }), + (name, version, { + 'checksums': ['4b56be7cb74fa1224222a8eb12d8a896902857f02a63a43206e5c5ea0ac1af1f'], + 'modulename': 'calibration', + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From d17f297793bab20d4f510b7e88257451d772864b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Jun 2022 10:21:09 +0100 Subject: [PATCH 3896/9987] install sklearn meta-package with scikit-learn --- .../scikit-learn-1.0.1-foss-2021b.eb | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb index 98d8ed31026..d3f7980867c 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-foss-2021b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'scikit-learn' version = '1.0.1' @@ -11,18 +11,22 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2021b'} -sources = [SOURCE_TAR_GZ] -checksums = ['ac2ca9dbb754d61cfe1c83ba8483498ef951d29b93ec09d6f002847f210a99da'] - dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10') ] use_pip = True -download_dep_fail = True sanity_pip_check = True -options = {'modulename': 'sklearn'} +exts_list = [ + (name, version, { + 'checksums': ['ac2ca9dbb754d61cfe1c83ba8483498ef951d29b93ec09d6f002847f210a99da'], + 'modulename': 'sklearn', + }), + ('sklearn', '0.0', { # also install the meta-package, as other packages check for this + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }) +] moduleclass = 'data' From 69a9577a630027c3dba779fe35c092a8fafde1c8 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Jun 2022 12:51:41 +0100 Subject: [PATCH 3897/9987] remove unused WITH_BLAS and WITH_LAPACK options for CGAL 5 --- easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb index c03d9e13b12..875af6f2dc4 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb @@ -32,7 +32,6 @@ configopts = "-DCGAL_HEADER_ONLY=OFF " configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT -configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " -configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON -DWITH_GMPXX=ON" moduleclass = 'numlib' From 68b3864e492fca6181c99c65c3994079e6c72774 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Jun 2022 14:30:23 +0200 Subject: [PATCH 3898/9987] also bump to FlexiBLAS 3.2.0 in easyconfig for ScaLAPACK 2.2.0 with gompi/2022.05 --- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb index b029b592277..6b905fb9221 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb @@ -22,7 +22,7 @@ builddependencies = [ ] dependencies = [ - ('FlexiBLAS', '3.1.3'), + ('FlexiBLAS', '3.2.0'), ] # Config Opts based on AOCL User Guide: From 6414269ee5925f731d9351fb46da8bdd151fe2a5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Jun 2022 18:01:54 +0200 Subject: [PATCH 3899/9987] remove commented out lines + fix minor style issues in easyconfig for RepeatMaster v4.1.2-p1 --- .../r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb index 7b7bd2f8ef3..f342fbdcfe0 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.2-p1-foss-2020b.eb @@ -36,16 +36,12 @@ dependencies = [ local_default_search_engine = 'RMBlast' -#preinstall_cmd = './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' -#preinstall_cmd += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' -#preinstall_cmd += '-default_search_engine %s' % local_default_search_engine.lower() - local_config_command = 'cd %(installdir)s &&' local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() -postinstallcmds = [ local_config_command, ] +postinstallcmds = [local_config_command] fix_perl_shebang_for = ['RepeatMasker'] From 9f8700ebb138d4256887793af7a4fd143bc7dbca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Jun 2022 18:30:48 +0200 Subject: [PATCH 3900/9987] switch from pkg-config to pkgconf as build dependency for OpenSSL wrapper easyconfigs --- .../easyconfigs/o/OpenSSL/OpenSSL-1.0.eb | 2 +- .../easyconfigs/o/OpenSSL/OpenSSL-1.1.eb | 2 +- .../easyconfigs/p/pkgconf/pkgconf-1.8.0.eb | 29 +++++++++++++++++++ 3 files changed, 31 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb index 89b0fa362da..e7a9bf5ac96 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} osdependencies = ['perl'] -builddependencies = [('pkg-config', '0.29.2')] +builddependencies = [('pkgconf', '1.8.0')] # This easyconfig will wrap the OpenSSL installation in the host system. # If the system provides the required binary, header files, and libraries for this diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb index 8f021218766..d5f4151e2f2 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb @@ -14,7 +14,7 @@ toolchainopts = {'pic': True} osdependencies = ['perl'] -builddependencies = [('pkg-config', '0.29.2')] +builddependencies = [('pkgconf', '1.8.0')] # This easyconfig will wrap the OpenSSL installation in the host system. # If the system provides the required binary, header files, and libraries for diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb new file mode 100644 index 00000000000..9e00a4dcfd4 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '1.8.0' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = SYSTEM + +source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d7b6fdb522d81c11f5a0e0a0629a9f5480809ec90e595058674c1517822dfb8c'] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' From 13b45ac95b3b2f2ec41fbac17f96351bb7bd3c17 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 Jun 2022 09:43:28 +0200 Subject: [PATCH 3901/9987] make sure that pkgconf built with system toolchain picks up on .pc files in default OS search paths --- easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb index 9e00a4dcfd4..8dfe1dd56e7 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb @@ -14,6 +14,10 @@ source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d7b6fdb522d81c11f5a0e0a0629a9f5480809ec90e595058674c1517822dfb8c'] +# add pkgconfig directories in the system to list of default search paths +preconfigopts = 'EB_SYS_PC_PATH=":$(find /usr -xdev -type d -name "pkgconfig" -printf %p: 2>/dev/null)";' +configopts = '--with-pkg-config-dir="%(installdir)s/lib/pkgconfig:%(installdir)s/share/pkgconfig${EB_SYS_PC_PATH%:}"' + postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] sanity_check_paths = { From 7995bc8801bece7cddc1ac85863e19be6dc7909b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 5 Jun 2022 08:45:36 +0100 Subject: [PATCH 3902/9987] add Bison and flex build dependencies to SCOTCH 6.1.x --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb | 5 +++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb | 5 +++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb | 5 +++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb | 5 +++++ easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb | 5 +++++ 5 files changed, 25 insertions(+) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb index 08a103b4d30..82ed7faf684 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb @@ -12,6 +12,11 @@ source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] +builddependencies = [ + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + dependencies = [ ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb index 19d7a5bdb04..ff933dd4d5c 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb @@ -15,6 +15,11 @@ source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] +builddependencies = [ + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + dependencies = [ ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb index 6e94531d821..01d6e5e9fa2 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2020b.eb @@ -12,6 +12,11 @@ source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] +builddependencies = [ + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + dependencies = [ ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb index 88bf9265ec8..08afa4bdeb2 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb @@ -15,6 +15,11 @@ source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['9c2c75c75f716914a2bd1c15dffac0e29a2f8069b2df1ad2b6207c984b699450'] +builddependencies = [ + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + dependencies = [ ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb index baf59e8b1e0..9f69f5ceddf 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb @@ -12,6 +12,11 @@ source_urls = ['https://gitlab.inria.fr/%(namelower)s/%(namelower)s/-/archive/v% sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['9c2c75c75f716914a2bd1c15dffac0e29a2f8069b2df1ad2b6207c984b699450'] +builddependencies = [ + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + dependencies = [ ('zlib', '1.2.11'), ] From bcd5b96c215c290b53458bf9853bc2cf7e441a73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 Jun 2022 14:38:53 +0200 Subject: [PATCH 3903/9987] add alternative checksums for class, nnet, spatial extensions in R v4.2.0 easyconfig --- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index f632984704c..46759989620 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -539,7 +539,8 @@ exts_list = [ 'checksums': ['eff3a92756ca34cdc1661fa36d2bf7fc8e9f4132d2f1ef9ed0105c83594618bf'], }), ('class', '7.3-20', { - 'checksums': ['e65b046bc72b312ff0c5dc7feba4fa3e9bc63387274d44911493782b85f65483'], + 'checksums': [('e65b046bc72b312ff0c5dc7feba4fa3e9bc63387274d44911493782b85f65483', + '93956d7b66ece2261e8846a1703e28a838c2621e366016f792ad48741f230205')], }), ('proxy', '0.4-26', { 'checksums': ['676bad821343974e0297a0566c4bf0cf0ea890104906a745b87d3b5989c81a4d'], @@ -548,7 +549,8 @@ exts_list = [ 'checksums': ['9bf9a15e7ce0b9b1a57ce3048d29cbea7f2a5bb2e91271b1b6aaafe07c852226'], }), ('nnet', '7.3-17', { - 'checksums': ['ee750bb8164aa058edf93823af987ab2c7ec64128dce2abeaae1b7d3661e9a67'], + 'checksums': [('ee750bb8164aa058edf93823af987ab2c7ec64128dce2abeaae1b7d3661e9a67', + 'd86871d54e4a331cd5e00da28a2f42a56d8976084578ed2fcdb3a7ad25d4dfaa')], }), ('minqa', '1.2.4', { 'checksums': ['cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c'], @@ -845,7 +847,8 @@ exts_list = [ 'checksums': ['a81710357de2dcdaf00d9fa30a29cde0dd83616edc358452fd6105ea88f34218'], }), ('spatial', '7.3-15', { - 'checksums': ['e5613be94d6f5c1f54813dadc96e4a86b3417dea28106cc90cb24dfd6c3c8cef'], + 'checksums': [('e5613be94d6f5c1f54813dadc96e4a86b3417dea28106cc90cb24dfd6c3c8cef', + 'de1dafbccfde599ae24c5a78dbbc2df746d17f4c97d7b1c282a03ddff2f23ecf')], }), ('VGAM', '1.1-6', { 'checksums': ['446a61bac5dd4794e05d20c2f3901eec54afac52c6e23ce2787c5575170dd417'], From 392ab2d3ab2c6c3b3e8bf83146bb006082769094 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 5 Jun 2022 18:26:01 +0200 Subject: [PATCH 3904/9987] adding easyconfigs: mold-1.2.1-GCCcore-11.3.0.eb --- .../m/mold/mold-1.2.1-GCCcore-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fe82f3d27ad --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'mold' +version = '1.2.1' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['41868663ff18afee3fa35e5e3fdf3d9575eb2e4ff49967b8f42f479c61c1ec34'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', True), +] + +skipsteps = ['configure'] + +# PREFIX must be specified when building, to ensure that the mold binary looks for mold-wrapper.so in the right place +buildopts = "PREFIX=%(installdir)s" +installopts = buildopts + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' From 492a9351d7167c80a1a588340bd0dd8c4c67ab81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 6 Jun 2022 03:31:02 +0200 Subject: [PATCH 3905/9987] adding easyconfigs: Mmg-5.6.0-gompi-2021b.eb --- .../m/Mmg/Mmg-5.6.0-gompi-2021b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb new file mode 100644 index 00000000000..2a6288ecfa1 --- /dev/null +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Mmg' +version = '5.6.0' + +homepage = 'https://www.mmgtools.org/' +description = """ +Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: +the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation +and generation of a triangulation from a set of points or from given boundary edges +the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation +and isovalue discretization +the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh +and implicit domain meshing +the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries +""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://github.com/MmgTools/mmg/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bbf9163d65bc6e0f81dd3acc5a51e4a8c47a7fdae849abc26277e01154fe2437'] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [('SCOTCH', '6.1.2')] + +configopts = '-DUSE_SCOTCH=ON -DBUILD_TESTING=ON ' +configopts += '-DLIBMMG2D_SHARED=ON -DLIBMMG3D_SHARED=ON -DLIBMMGS_SHARED=ON -DLIBMMG_SHARED=ON ' + +pretestopts = 'export CTEST_PARALLEL_LEVEL=%(parallel)s &&' +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%s_O3' % x for x in ['mmg2d', 'mmg3d', 'mmgs']] + + ['lib/lib%s.%s' % (x, y) for x in ['mmg2d', 'mmg3d', 'mmgs', 'mmg'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include/mmg/%s' % x for x in ['mmg2d', 'mmg3d', 'mmgs']] +} + +moduleclass = 'math' From 8fbdf2047457b600cc1612917efe2974caf44f94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 6 Jun 2022 10:30:54 +0200 Subject: [PATCH 3906/9987] add missing dependencies + switch to non-static build for Arriba v2.1.0 --- easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb | 7 +++++++ easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb | 7 +++++++ 2 files changed, 14 insertions(+) diff --git a/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb index 2eea4c45f18..05191b206cf 100644 --- a/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.2.0.eb @@ -20,11 +20,18 @@ checksums = ['21c46121e00cf84ad471b2b22fca722d37e55bbdf9e7118978dc250754a264bb'] dependencies = [ ('bzip2', '1.0.8'), + ('HTSlib', '1.11'), + ('libdeflate', '1.7'), ('STAR', '2.7.7a'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), ] +# make target with dynamically linked libraries is called bioconda, default is a statically linked binary +build_cmd_targets = 'bioconda' +# otherwise it fails to find sam.h +buildopts = 'CPATH=${EBROOTHTSLIB}/include/htslib:CPATH' + postinstallcmds = ['mkdir %(installdir)s/database'] files_to_copy = ['%(namelower)s', 'documentation', 'download_references.sh', 'draw_fusions.R', 'LICENSE', 'README.md', 'run_%(namelower)s.sh'] diff --git a/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb index c775fc48a12..3c4c567c48b 100644 --- a/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/a/Arriba/Arriba-2.1.0-GCC-10.3.0.eb @@ -20,11 +20,18 @@ checksums = ['21c46121e00cf84ad471b2b22fca722d37e55bbdf9e7118978dc250754a264bb'] dependencies = [ ('bzip2', '1.0.8'), + ('HTSlib', '1.12'), + ('libdeflate', '1.8'), ('STAR', '2.7.9a'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), ] +# make target with dynamically linked libraries is called bioconda, default is a statically linked binary +build_cmd_targets = 'bioconda' +# otherwise it fails to find sam.h +buildopts = 'CPATH=${EBROOTHTSLIB}/include/htslib:CPATH' + postinstallcmds = ['mkdir %(installdir)s/database'] files_to_copy = ['%(namelower)s', 'documentation', 'download_references.sh', 'draw_fusions.R', 'LICENSE', 'README.md', 'run_%(namelower)s.sh'] From 42476b417a0d7ccaa7d7b823a2a190bf66beed16 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 6 Jun 2022 15:09:25 +0100 Subject: [PATCH 3907/9987] OpenMPI and DATA_DIR added. The latter is deliberately empty so users can define that at runtime --- .../easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb index a2ee8e062e5..8c95efa1c75 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb @@ -7,7 +7,10 @@ name = 'casacore' version = '3.4.0' homepage = 'https://github.com/casacore/casacore' -description = "A suite of C++ libraries for radio astronomy data processing." +description = """A suite of C++ libraries for radio astronomy data processing. +The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime. +Thus user's can update them. +""" toolchain = {'name': 'foss', 'version': '2021b'} @@ -33,7 +36,8 @@ dependencies = [ ('ncurses', '6.2'), ] -configopts = ' -DBUILD_PYTHON3=ON -DBUILD_PYTHON=OFF -Wno-dev ' +configopts = ' -DBUILD_PYTHON3=ON -DBUILD_PYTHON=OFF -Wno-dev -DDATA_DIR=%(installdir)s/data ' +configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON ' sanity_check_paths = { 'files': [('lib/libcasa_casa.%s', 'lib/libcasa_mirlib.%s' % SHLIB_EXT, 'lib64/libcasa_ms.%s' % SHLIB_EXT)], From f0b997208b28c7506b77647e2686b124e863c708 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 6 Jun 2022 17:00:06 +0100 Subject: [PATCH 3908/9987] adding easyconfigs: BLT-20181223-GCCcore-11.2.0.eb --- .../b/BLT/BLT-20181223-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2f5e4bb3ac0 --- /dev/null +++ b/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'ConfigureMake' + +name = 'BLT' +version = '20181223' +_commit = 'b8cdc6c2cd8edba06ad53a5d56e961d35b07af28' + +homepage = 'http://blt.sourceforge.net/' +description = """BLT is an extension to the Tk toolkit, adding new widgets, + geometry managers, and miscellaneous commands.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://sourceforge.net/code-snapshots/git/b/bl/blt/src.git'] +sources = ['blt-src-%s.zip' % _commit] +checksums = ['2c3e24dd985c187d3c76d37444580e1fd540116be6371ccd3fceda92a8d6cfd0'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Tcl', '8.6.11'), + ('Tk', '8.6.11'), + ('libjpeg-turbo', '2.0.6'), + ('X11', '20210802'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('zlib', '1.2.11'), + ('freetype', '2.11.0'), + ('expat', '2.4.1'), + ('SQLite', '3.36'), + ('OpenSSL', '1.1', '', True), +] + +configopts = '--with-tcl=$EBROOTTCL --with-tk=$EBROOTTK --enable-shared' + +_sover = '30' +_bins = ['bin/blt%s%s' % (x, _sover) for x in ['sh', 'wish']] +_libs = ['lib/libBlt%s%s.%s' % (x, _sover, SHLIB_EXT) for x in ['', 'Tcl', 'Tk']] + +sanity_check_paths = { + 'files': _bins + _libs, + 'dirs': ['include'], +} + +moduleclass = 'vis' From 50b6cad5ebdf1471466591fafde023ceb5097a67 Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Tue, 7 Jun 2022 11:49:08 +0200 Subject: [PATCH 3909/9987] Change NGS-2.10.9-GCCcore-10.3.0.eb into NGS-2.11.2-GCCcore-10.3.0.eb --- .../n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e47fab87109 --- /dev/null +++ b/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'NGS' +version = '2.11.2' + +homepage = 'https://github.com/ncbi/ngs' +description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups +produced from Next Generation Sequencing.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('Perl', '5.32.1'), +] + +dependencies = [('Java', '11', '', True)] + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://github.com/ncbi/ngs/archive'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['7555ab7c2f04bd81160859f6c85c65376dc7f7b891804fad9e7636a7788e39c2'], +} + +components = [ + ('NGS-SDK', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), + ('NGS-Java', version, { + 'start_dir': 'ngs-%(version)s/%(namelower)s', + 'configopts': '--build-prefix=%(builddir)s', # change default build directory + }), +] + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' From f958fcbfab698b2a5464a34ea79bb898a90f1d10 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 7 Jun 2022 11:17:33 +0100 Subject: [PATCH 3910/9987] adding easyconfigs: Groovy-4.0.3-Java-11.eb --- .../g/Groovy/Groovy-4.0.3-Java-11.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/Groovy/Groovy-4.0.3-Java-11.eb diff --git a/easybuild/easyconfigs/g/Groovy/Groovy-4.0.3-Java-11.eb b/easybuild/easyconfigs/g/Groovy/Groovy-4.0.3-Java-11.eb new file mode 100644 index 00000000000..9f4f17f0f07 --- /dev/null +++ b/easybuild/easyconfigs/g/Groovy/Groovy-4.0.3-Java-11.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'Groovy' +version = '4.0.3' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://groovy-lang.org' +description = """Groovy is a powerful, optionally typed and dynamic language, with static-typing and static +compilation capabilities, for the Java platform aimed at improving developer productivity thanks to a concise, +familiar and easy to learn syntax.""" + +toolchain = SYSTEM + +source_urls = ['https://groovy.jfrog.io/artifactory/dist-release-local/groovy-zips/'] +sources = ['apache-groovy-sdk-%(version)s.zip'] +checksums = ['7c2e0df8d4c2b4695cb127bcef31e40223671215866fcf23da6fdccbb5ff93c5'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['bin/groovy', 'bin/grape'], + 'dirs': [], +} + +sanity_check_commands = ["groovy --help"] + +moduleclass = 'devel' From e78abde2d20a8cc51c3c38205561fca29a4be1c7 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 7 Jun 2022 12:30:12 +0200 Subject: [PATCH 3911/9987] prepare release notes for EasyBuild v4.5.5 + bump version to 4.5.5 --- RELEASE_NOTES | 115 +++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 115 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index be851b779c6..d42c6ede033 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,123 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 14,449 easyconfig files, for 2,667 different software packages, +The latest version of easybuild-easyconfig provides 14,853 easyconfig files, for 2,711 different software packages, incl. 36 different (compiler) toolchains. +v4.5.5 (June 7th 2022) +---------------------- + +update/bugfix release +- added example easyconfig files for 35 new software packages: + - Albumentations (#15302), AMPtk (#15435), arosics (#15249), CellTypist (#15530), detectron2 (#15442), + EigenExa (#15234), Fastaq (#15332), FFTW.MPI (#15561), FreeBarcodes (#15350), gcloud (#15443), + GST-plugins-bad gsutil (#15507), GTK4 (#15447), hector (#15397), i7z (#15236), libde265 (#15395), + libheif (#15395), ModelTest-NG (#15448), num2words (#15473), OGDF (#15407), panito parameterized (#15481), + purge_dups (#15385), redis-py (#15475), ruamel.yaml (#15531), SCGid (#15065), scPred (#15575), + slow5tools (#15457), smooth-topk (#15506), SPOTPY (#15326), tmap (#4601), UCC (#4291), Wayland (#11107), + XGrafix (#15268), XPLOR-NIH (#15479) +- added additional easyconfigs for various supported software packages, including: + - ABAQUS 2022, Albumentations 1.1.0, AMD uProf 3.5.671, AMPtk 1.5.4, Anaconda3 2022.05, any2fasta 0.4.2, Arb 2.22.1, + ARGoS 3.0.0, arosics 1.7.6, Arriba 2.2.1, arrow-R 6.0.0.2, astropy 5.0.4, ATK 2.38.0, at-spi2-atk 2.38.0, + at-spi2-core 2.44.1, Autoconf 2.71, Automake 1.16.5, Autotools 20220317, Bader 1.04, bam-readcount 0.8.0, + barrnap 0.9, Bazel 4.2.2, Bazel 5.1.1, BDBag 1.6.3, beagle-lib 3.1.2, binutils 2.38, bioawk 1.0, + biom-format 2.1.12, Bison 3.8.2, Blender 3.1.2, BLIS 0.9.0, BLIS 3.0.1, Boost 1.75.0, Boost 1.79.0, breseq 0.36.1, + Brotli 1.0.9, buildenv default, bx-python 0.8.13, bzip2 1.0.8, cairo 1.17.4, CellRanger-ARC 2.0.1, + CellTypist 1.0.0, Check 0.15.2, Clang 9.0.1, Clang 12.0.1, Clang 13.0.1, CMake 3.23.1, coverage 5.5, + crb-blast 0.6.9, cryoDRGN 0.3.5, cryoDRGN 1.0.0, CUDA 11.7.0, cuDNN 8.2.2.26, cuDNN 8.4.0.27, cuDNN 8.4.1.50, + Cufflinks 20190706, cURL 7.83.0, DB 18.1.40, DBD-mysql 4.050, DBus 1.14.0, DCMTK 3.6.6, detectron2 0.6, + EasyBuild 4.5.4, edlib 1.3.9, eggnog-mapper 2.1.7, Eigen 3.4.0, EigenExa 2.11, elfutils 0.187, ELPA 2021.05.002, + EMBOSS 6.6.0, ESMPy 8.0.1, EvidentialGene 2022.01.14, Exonerate 2.4.0, expat 2.4.8, FastANI 1.33, FastANI 1.33, + Fastaq 3.17.0, fastp 0.23.2, fastq-tools 0.8.3, FastTree 2.1.11, FASTX-Toolkit 0.0.14, fermi-lite 20190320, + FFTW 3.3.10, FFTW.MPI 3.3.10, flex 2.6.4, FlexiBLAS 3.2.0, FLINT 2.8.4, fontconfig 2.14.0, foss 2022.05, FoX 4.1.2, + FreeBarcodes 3.0.a5, freebayes 1.3.6, freeglut 3.2.2, FreeImage 3.18.0, freetype 2.12.1, FriBidi 1.0.12, + fumi_tools 0.18.2, GCC 9.5.0, GCC 11.3.0, GCC 12.1.0, GCCcore 9.5.0, GCCcore 11.3.0, GCCcore 12.1.0, + gcloud 382.0.0, Gdk-Pixbuf 2.42.8, geopandas 0.10.2, gettext 0.21, giflib 5.2.1, git 2.36.0, GLib 2.72.1, + GMAP-GSNAP 2021-21-17, GMP 6.2.1, Go 1.18.1, GObject-Introspection 1.72.0, gompi 2022.05, gperf 3.1, Grace 5.1.25, + Graphene 1.10.8, groff 1.22.4, GSL 2.7, GST-plugins-bad 1.20.2, GST-plugins-base 1.20.2, GStreamer 1.20.2, + gsutil 5.10, GTDB-Tk 2.0.0, GTK3 3.24.33, GTK4 4.7.0, gzip 1.12, HarfBuzz 4.2.1, hector 2.5.0, help2man 1.49.2, + HMMER 3.3.2, HPL 2.3, HTSeq 0.11.3, hwloc 2.7.1, hypothesis 6.46.7, Hypre 2.24.0, i7z 20131012, ICU 71.1, + IGV 2.12.3, iimpi 2022.05, IMB 2021.3, imgaug 0.4.0, imkl 2022.1.0, imkl FFTW 2022.1.0, impi 2021.6.0, + inferCNV 1.10.1, intel 2022.05, intel-compilers 2022.1.0, InterProScan 5.52, intltool 0.51.0, IQ-TREE 2.2.1, + ISA-L 2.30.0, jax 0.3.9, jbigkit 2.1, Jellyfish 2.3.0, json-c 0.16, Julia 1.6.6, Kraken 1.1.1, Kraken2 2.1.2, + LAPACK 3.10.1, libarchive 3.6.1, libde265 1.0.8, libdeflate 1.10, libdrm 2.4.110, libedit 20210910, + libepoxy 1.5.10, libevent 2.1.12, libfabric 1.15.1, libffi 3.4.2, libGLU 9.0.2, libglvnd 1.4.0, libharu 2.3.0, + libharu 2.3.0, libheif 1.12.0, libjpeg-turbo 2.1.3, libpciaccess 0.16, libpng 1.6.37, libreadline 8.1.2, + librsb 1.3.0.1, librsvg 2.52.8, LIBSVM 3.25, LibTIFF 4.3.0, libtool 2.4.7, libunwind 1.6.2, libvdwxc 0.4.0, + libvdwxc 0.4.0, libxml2 2.9.13, LLVM 14.0.3, LocARNA 1.9.2.3, LSD2 2.3, lz4 1.9.3, M4 1.4.19, MACS2 2.2.7.1, + magma 2.6.2, makeinfo 6.7, Mako 1.2.0, Mash 2.3, Mathematica 13.0.0, MCL 14.137, MCR R2021b.1, MCR R2022a.1, + MEME 5.4.1, Mesa 22.0.3, Meson 0.62.1, MIRA 5.0rc2, Mmg 5.6.0, ModelTest-NG 0.1.7, mold 1.2.1, mosdepth 0.3.3, + MrBayes 3.2.6, MrBayes 3.2.7a, MultiQC 1.12, MUMPS 5.4.1, MUMPS 5.5.0, muParser 2.3.3, MUSCLE 3.8.1551, + NASM 2.15.05, ncdu 1.16, ncurses 6.3, neptune-client 0.16.2, Nextflow 22.04.0, NextGenMap 0.5.5, Nim 1.6.6, + Ninja 1.10.2, ntCard 1.2.1, NTPoly 2.7.1, num2words 0.5.10, numactl 2.0.14, numba 0.54.1, OGDF dogwood-202202, + OpenBLAS 0.3.20, OpenMPI 4.1.4, openpyxl 3.0.9, OpenSceneGraph 3.6.5, OpenSSL 1.1.1n, OpenStackClient 5.8.0, + OSU-Micro-Benchmarks 5.9, pagmo 2.18.0, Pango 1.50.7, panito 0.0.1, parallel-fastq-dump 0.6.7, parameterized 0.8.1, + PCRE2 10.40, PCRE 8.45, Perl 5.30.0, Perl 5.34.1, pftoolsV3 3.2.11, Pillow 9.1.0, pixman 0.40.0, pkgconf 1.8.0, + pkgconf 1.8.0, PLINK 2.00a3.1, PMIx 4.1.2, purge_dups 1.2.5, PyAMG 4.2.3, pybind11 2.9.2, PyCairo 1.21.0, + pydot 1.4.2, pygmo 2.18.0, PyGObject 3.42.1, Python 2.7.15, Python 2.7.16, Python 2.7.18, Python 3.10.4, + QUAST 5.0.2, R 4.2.0, RapidJSON 1.1.0, RAxML-NG 1.1.0, R-bundle-Bioconductor 3.15, RE2 2022, redis-py 4.3.1, + ReFrame 3.11.0, rjags 4, RNA-Bloom 1.4.3, rnaQUAST 2.2.2, Roary 3.13.0, RSeQC 4.0.0, ruamel.yaml 0.17.21, + Rust 1.56.0, Rust 1.60.0, Salmon 1.4.0, Sambamba 0.8.2, samblaster 0.1.26, SAMtools 0.1.19, SAMtools 1.15.1, + ScaLAPACK 2.2.0, SCGid 0.9b0, SciPy-bundle 2022.05, SCOTCH 6.1.2, scPred 1.9.2, segemehl 0.3.4, SeqKit 2.2.0, + SeqLib 1.2.0, Shapely 1.8.1.post1, slow5tools 0.4.0, smooth-topk 1.0-20210817, snippy 4.6.0, snpEff 5.0e, + snp-sites 2.5.1, SpaceRanger 1.3.1, Spack 0.17.2, Spark 3.2.1, SPOTPY 1.5.14, SQLite 3.38.3, SSW 1.1, + StringTie 2.2.1, SUMO 1.12.0, SuperLU 5.3.0, tbl2asn 20220427, Tcl 8.6.12, TCLAP 1.2.5, tcsh 6.24.01, + texlive 20220321, tmap 20220502, ToFu 1.5.0, TreeMix 1.13, TRF 4.09.1, UCC 1.0.0, UCX 1.12.1, UnZip 6.0, + util-linux 2.38, VarScan 2.4.4, VEP 105, ViennaRNA 2.5.0, vsc-mympirun 5.2.11, vt 0.57721, Wayland 1.20.0, + wgsim 20111017, worker 1.6.13, X11 20220504, xESMF 0.3.0, XGrafix 2.41, xorg-macros 1.19.3, XPLOR-NIH 3.4, + XZ 5.2.5, YAXT 0.9.2.1, Z3 4.8.16, Zip 3.0, zlib 1.2.12, zstd 1.5.2 +- minor enhancements, including: + - use OpenSSL wrapper dependency for CMake 3.18.4 with system toolchain (#15227) + - also build BLIS backend for FlexiBLAS v3.0.4 with GCC/10.3.0 (#15347) + - add Hmsc extension to R v4.1.2 easyconfig (#15393) + - add DNABarcodes to R-bundle-Bioconductor 3.14 easyconfig (#15405) + - use redist source_urls for cuDNN > 7.5 (#15411) + - Add download_instructions to Java 1.8 > 200 (#15412) + - add MonteCarlo and RhpcBLASctl extensions to R v4.1.2 + v4.2.0 easyconfigs (#15438) + - update Arrow to use EB versions of some dependencies and enable all compression codecs (#15512) + - Add local::lib and Module::Path to Perl 5.34.1 easyconfig (#15529) + - add chkptstanr extension to R v4.2.0 (#15540) + - {tools}[GCCcore/11.2.0] tcsh v6.24.01 + add csh -> tcsh symlink in recent tcsh easyconfigs (#15571) + - add chkptstanr + MLmetrics + renv extensions to R v4.1.2 + v4.2.0 easyconfigs (#15573) + - allow external tools to be located elsewhere for ETE (#15578) + - add additional sanity check commands for IQ-TREE v2.2.1 (#15596) +- various bug fixes, including: + - fix source URL for freetype 2.6.5 with foss/2016b (#14204) + - fix installation with setuptools>=61 by explicitly declaring there are no Python packages (#15206) + - use x.py to boostrap Rust so that build options are properly passed through (#15211) + - fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15615) + - add hwloc dependency to easyconfig for tbb v2021.4.0 (#15294) + - remove pkg-config use from SeqLib configure patch (avoids problem due to faulty autoconf macro) (#15316) + - update source URL for isl in GCCcore easyconfigs (#15320) + - update source URLs for YAXT 0.9.x to fix download (#15323) + - define $HHLIB as path to HH-suite installation directory, required by Perl scripts (#15324) + - add missing parallel dependency for prokka 1.14.5 (#15360) + - add missing tbl2asn dependency for prokka 1.14.5 (#15381) + - add missing dependencies for libheif (libpng, libjpeg-turbo) + switch to configuring build with CMake so libde265 dependency is picked up (#15408) + - disable use of -ftree-vectorize for OpenFOAM v2112 with foss/2021b (#15495) + - add patch for OpenMPI 4.1.1 to support building using --with-cuda=internal (#15528) + - remove unused libfabric dependency from easyconfig for PMIx v4.1.2 (#15564) + - {mpi}[GCC/8.2.0] OpenMPI v3.1.3 fix support for external PMIx v3.1 (#15566) + - also build shared library + fix $PYTHONPATH for gmsh 4.9.0 (#15579) + - eliminate benign libcuda warning when OpenMPI is configured with --with-cuda=internal (#15589) + - add sysroot patch to Rust 1.60.0 (GCCcore/11.3.0) (#15593) + - add patch for GLib 2.68.2 to fix use of close_range (#15594) + - fix download of thrift 0.12.0 for Arrow 0.16.0 (#15597) + - fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15615) + - make sure that pkgconf built with system toolchain picks up on .pc files in default OS search paths (#15617) + - add Bison and flex build dependencies to SCOTCH 6.1.x (#15618) + - add alternative checksums for class, nnet, spatial extensions in R v4.2.0 easyconfig (#15619) + - add missing dependencies + switch to non-static build for Arriba v2.1.0 (#15623) +- other changes: + - add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to foss/2021b toochain (#15216) + - tweak find command used in preconfigopts in easyconfig for pkg-config v0.29.2 with system toolchain to avoid descending into other filesystems (#15313) + - update fallback version for OpenSSL 1.1 wrapper to v1.1.1o (#15592) + - in-place update for cryoDRGN to v0.3.5 with foss/2021a to fix compatibility issue with PyTorch v1.10 (#15609) + - install sklearn meta-package with scikit-learn v1.0.1 (#15613) + - switch from pkg-config to pkgconf as build dependency for OpenSSL wrapper easyconfigs (#15616) + + v4.5.4 (March 31st 2022) ------------------------ diff --git a/setup.py b/setup.py index 291cb774717..8ba26931878 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.5.dev0' +VERSION = '4.5.5' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From df12413ca91cbc7e938a0391a6a12c1349dffa9a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 7 Jun 2022 14:57:37 +0100 Subject: [PATCH 3912/9987] add lib directory to TCLLIBPATH --- easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb index 2f5e4bb3ac0..3d71f64de88 100644 --- a/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb @@ -42,4 +42,6 @@ sanity_check_paths = { 'dirs': ['include'], } +modextrapaths = {'TCLLIBPATH': 'lib'} + moduleclass = 'vis' From 0e3477ac8e6f6d3001b46d9b1b80b7cf156a5f60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jun 2022 17:07:42 +0200 Subject: [PATCH 3913/9987] adding easyconfigs: rioxarray-0.11.1-foss-2021b.eb, rasterio-1.2.10-foss-2021b.eb, pyproj-3.3.1-GCCcore-11.2.0.eb --- .../p/pyproj/pyproj-3.3.1-GCCcore-11.2.0.eb | 37 +++++++++++ .../r/rasterio/rasterio-1.2.10-foss-2021b.eb | 64 +++++++++++++++++++ .../rioxarray/rioxarray-0.11.1-foss-2021b.eb | 27 ++++++++ 3 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/rasterio/rasterio-1.2.10-foss-2021b.eb create mode 100644 easybuild/easyconfigs/r/rioxarray/rioxarray-0.11.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c426db6dc89 --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.3.1' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b3d8e14d91cc95fb3dbc03a9d0588ac58326803eefa5bbb0978d109de3304fbe'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('PROJ', '8.1.0'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/rasterio/rasterio-1.2.10-foss-2021b.eb b/easybuild/easyconfigs/r/rasterio/rasterio-1.2.10-foss-2021b.eb new file mode 100644 index 00000000000..2c552ddbca2 --- /dev/null +++ b/easybuild/easyconfigs/r/rasterio/rasterio-1.2.10-foss-2021b.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'rasterio' +version = '1.2.10' + +homepage = 'https://github.com/mapbox/rasterio' +description = "Rasterio reads and writes geospatial raster data." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy + ('matplotlib', '3.4.3'), + ('GDAL', '3.3.2'), +] + +use_pip = True + +exts_list = [ + ('affine', '2.3.1', { + 'checksums': ['d676de66157ad6af99ffd94e0f54e89dfc35b0fb7252ead2ed0ad2dca431bdd0'], + }), + ('jmespath', '1.0.0', { + 'checksums': ['a490e280edd1f57d6de88636992d05b71e97d69a26a19f058ecf7d304474bf5e'], + }), + ('botocore', '1.27.3', { + 'checksums': ['7be5962b956b5770799ba87b0bd2173230068d269982bdf8d16fabaa79483912'], + }), + ('s3transfer', '0.6.0', { + 'checksums': ['2ed07d3866f523cc561bf4a00fc5535827981b117dd7876f036b0c1aca42c947'], + }), + ('boto3', '1.24.3', { + 'checksums': ['7625c5ed92bb7a953e03d2541bcbfcb66c3495f8d7b9421e47b4e2c280dc9162'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('snuggs', '1.4.7', { + 'checksums': ['501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b'], + }), + (name, version, { + 'checksums': ['6062456047ba6494fe18bd0da98a383b6fad5306b16cd52a22e76c59172a2b5f'], + }), +] + +fix_python_shebang_for = ['bin/jp.py', 'bin/rio'] + +sanity_check_paths = { + 'files': ['bin/rio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "jp.py --help", + "rio --help", +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rioxarray/rioxarray-0.11.1-foss-2021b.eb b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.11.1-foss-2021b.eb new file mode 100644 index 00000000000..7b5a3c11a9c --- /dev/null +++ b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.11.1-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'rioxarray' +version = '0.11.1' + +homepage = 'https://github.com/corteva/rioxarray' +description = "geospatial xarray extension powered by rasterio" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('rasterio', '1.2.10'), + ('pyproj', '3.3.1'), + ('xarray', '0.20.1'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['9932db0498d13bd1a2643b0eaa657d3d1558118396af0dd1ea86dae6f91e0ff4'] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'geo' From 75b46a40a55ff45d3b4561bfcfb8e8f25f20b006 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 7 Jun 2022 17:49:13 +0200 Subject: [PATCH 3914/9987] adding easyconfigs: MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb --- ...Estimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb new file mode 100644 index 00000000000..0e578acd269 --- /dev/null +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'MultilevelEstimators' +version = '0.1.0' +local_julia_ver = '1.7.2' +versionsuffix = "-Julia-%s" % local_julia_ver + +homepage = 'https://github.com/PieterjanRobbe/MultilevelEstimators.jl' +description = "The Julia module for Multilevel Monte Carlo methods" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), + ('Julia', local_julia_ver, '-linux-%s' % ARCH, True), +] + +postinstallcmds = [ + "cd %(installdir)s && mkdir pkgs", + """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && + julia -e 'using Pkg;Pkg.add(url="%s")' """ % homepage +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["pkgs"] +} + +modextrapaths = {'JULIA_DEPOT_PATH': 'pkgs'} + +moduleclass = 'lib' From 2267e838b2bc71a0c9d92bda543a126e15af4aa8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jun 2022 19:56:41 +0200 Subject: [PATCH 3915/9987] minor tweaks for release notes for v4.5.5 --- RELEASE_NOTES | 127 +++++++++++++++++++------------------------------- 1 file changed, 47 insertions(+), 80 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index d42c6ede033..86fb42734de 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,121 +3,88 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 14,853 easyconfig files, for 2,711 different software packages, +The latest version of easybuild-easyconfig provides 14,816 easyconfig files, for 2,711 different software packages, incl. 36 different (compiler) toolchains. -v4.5.5 (June 7th 2022) +v4.5.5 (June 8th 2022) ---------------------- update/bugfix release +- add candidates for 2022a common toolchains: foss/2022.05 (#15561), intel/2022.05 (#15485) - added example easyconfig files for 35 new software packages: - Albumentations (#15302), AMPtk (#15435), arosics (#15249), CellTypist (#15530), detectron2 (#15442), EigenExa (#15234), Fastaq (#15332), FFTW.MPI (#15561), FreeBarcodes (#15350), gcloud (#15443), - GST-plugins-bad gsutil (#15507), GTK4 (#15447), hector (#15397), i7z (#15236), libde265 (#15395), - libheif (#15395), ModelTest-NG (#15448), num2words (#15473), OGDF (#15407), panito parameterized (#15481), - purge_dups (#15385), redis-py (#15475), ruamel.yaml (#15531), SCGid (#15065), scPred (#15575), - slow5tools (#15457), smooth-topk (#15506), SPOTPY (#15326), tmap (#4601), UCC (#4291), Wayland (#11107), - XGrafix (#15268), XPLOR-NIH (#15479) + GST-plugins-bad (#15446), gsutil (#15507), GTK4 (#15447), hector (#15397), i7z (#15236), libde265 (#15395), + libheif (#15395), ModelTest-NG (#15448), num2words (#15473), OGDF (#15407), panito (#15314), + parameterized (#15481), purge_dups (#15385), redis-py (#15475), ruamel.yaml (#15531), SCGid (#15065), + scPred (#15575), slow5tools (#15457), smooth-topk (#15506), SPOTPY (#15326), tmap (#4601), UCC (#4291), + Wayland (#11107), XGrafix (#15268), XPLOR-NIH (#15479) - added additional easyconfigs for various supported software packages, including: - - ABAQUS 2022, Albumentations 1.1.0, AMD uProf 3.5.671, AMPtk 1.5.4, Anaconda3 2022.05, any2fasta 0.4.2, Arb 2.22.1, - ARGoS 3.0.0, arosics 1.7.6, Arriba 2.2.1, arrow-R 6.0.0.2, astropy 5.0.4, ATK 2.38.0, at-spi2-atk 2.38.0, - at-spi2-core 2.44.1, Autoconf 2.71, Automake 1.16.5, Autotools 20220317, Bader 1.04, bam-readcount 0.8.0, - barrnap 0.9, Bazel 4.2.2, Bazel 5.1.1, BDBag 1.6.3, beagle-lib 3.1.2, binutils 2.38, bioawk 1.0, - biom-format 2.1.12, Bison 3.8.2, Blender 3.1.2, BLIS 0.9.0, BLIS 3.0.1, Boost 1.75.0, Boost 1.79.0, breseq 0.36.1, - Brotli 1.0.9, buildenv default, bx-python 0.8.13, bzip2 1.0.8, cairo 1.17.4, CellRanger-ARC 2.0.1, - CellTypist 1.0.0, Check 0.15.2, Clang 9.0.1, Clang 12.0.1, Clang 13.0.1, CMake 3.23.1, coverage 5.5, - crb-blast 0.6.9, cryoDRGN 0.3.5, cryoDRGN 1.0.0, CUDA 11.7.0, cuDNN 8.2.2.26, cuDNN 8.4.0.27, cuDNN 8.4.1.50, - Cufflinks 20190706, cURL 7.83.0, DB 18.1.40, DBD-mysql 4.050, DBus 1.14.0, DCMTK 3.6.6, detectron2 0.6, - EasyBuild 4.5.4, edlib 1.3.9, eggnog-mapper 2.1.7, Eigen 3.4.0, EigenExa 2.11, elfutils 0.187, ELPA 2021.05.002, - EMBOSS 6.6.0, ESMPy 8.0.1, EvidentialGene 2022.01.14, Exonerate 2.4.0, expat 2.4.8, FastANI 1.33, FastANI 1.33, - Fastaq 3.17.0, fastp 0.23.2, fastq-tools 0.8.3, FastTree 2.1.11, FASTX-Toolkit 0.0.14, fermi-lite 20190320, - FFTW 3.3.10, FFTW.MPI 3.3.10, flex 2.6.4, FlexiBLAS 3.2.0, FLINT 2.8.4, fontconfig 2.14.0, foss 2022.05, FoX 4.1.2, - FreeBarcodes 3.0.a5, freebayes 1.3.6, freeglut 3.2.2, FreeImage 3.18.0, freetype 2.12.1, FriBidi 1.0.12, - fumi_tools 0.18.2, GCC 9.5.0, GCC 11.3.0, GCC 12.1.0, GCCcore 9.5.0, GCCcore 11.3.0, GCCcore 12.1.0, - gcloud 382.0.0, Gdk-Pixbuf 2.42.8, geopandas 0.10.2, gettext 0.21, giflib 5.2.1, git 2.36.0, GLib 2.72.1, - GMAP-GSNAP 2021-21-17, GMP 6.2.1, Go 1.18.1, GObject-Introspection 1.72.0, gompi 2022.05, gperf 3.1, Grace 5.1.25, - Graphene 1.10.8, groff 1.22.4, GSL 2.7, GST-plugins-bad 1.20.2, GST-plugins-base 1.20.2, GStreamer 1.20.2, - gsutil 5.10, GTDB-Tk 2.0.0, GTK3 3.24.33, GTK4 4.7.0, gzip 1.12, HarfBuzz 4.2.1, hector 2.5.0, help2man 1.49.2, - HMMER 3.3.2, HPL 2.3, HTSeq 0.11.3, hwloc 2.7.1, hypothesis 6.46.7, Hypre 2.24.0, i7z 20131012, ICU 71.1, - IGV 2.12.3, iimpi 2022.05, IMB 2021.3, imgaug 0.4.0, imkl 2022.1.0, imkl FFTW 2022.1.0, impi 2021.6.0, - inferCNV 1.10.1, intel 2022.05, intel-compilers 2022.1.0, InterProScan 5.52, intltool 0.51.0, IQ-TREE 2.2.1, - ISA-L 2.30.0, jax 0.3.9, jbigkit 2.1, Jellyfish 2.3.0, json-c 0.16, Julia 1.6.6, Kraken 1.1.1, Kraken2 2.1.2, - LAPACK 3.10.1, libarchive 3.6.1, libde265 1.0.8, libdeflate 1.10, libdrm 2.4.110, libedit 20210910, - libepoxy 1.5.10, libevent 2.1.12, libfabric 1.15.1, libffi 3.4.2, libGLU 9.0.2, libglvnd 1.4.0, libharu 2.3.0, - libharu 2.3.0, libheif 1.12.0, libjpeg-turbo 2.1.3, libpciaccess 0.16, libpng 1.6.37, libreadline 8.1.2, - librsb 1.3.0.1, librsvg 2.52.8, LIBSVM 3.25, LibTIFF 4.3.0, libtool 2.4.7, libunwind 1.6.2, libvdwxc 0.4.0, - libvdwxc 0.4.0, libxml2 2.9.13, LLVM 14.0.3, LocARNA 1.9.2.3, LSD2 2.3, lz4 1.9.3, M4 1.4.19, MACS2 2.2.7.1, - magma 2.6.2, makeinfo 6.7, Mako 1.2.0, Mash 2.3, Mathematica 13.0.0, MCL 14.137, MCR R2021b.1, MCR R2022a.1, - MEME 5.4.1, Mesa 22.0.3, Meson 0.62.1, MIRA 5.0rc2, Mmg 5.6.0, ModelTest-NG 0.1.7, mold 1.2.1, mosdepth 0.3.3, - MrBayes 3.2.6, MrBayes 3.2.7a, MultiQC 1.12, MUMPS 5.4.1, MUMPS 5.5.0, muParser 2.3.3, MUSCLE 3.8.1551, - NASM 2.15.05, ncdu 1.16, ncurses 6.3, neptune-client 0.16.2, Nextflow 22.04.0, NextGenMap 0.5.5, Nim 1.6.6, - Ninja 1.10.2, ntCard 1.2.1, NTPoly 2.7.1, num2words 0.5.10, numactl 2.0.14, numba 0.54.1, OGDF dogwood-202202, - OpenBLAS 0.3.20, OpenMPI 4.1.4, openpyxl 3.0.9, OpenSceneGraph 3.6.5, OpenSSL 1.1.1n, OpenStackClient 5.8.0, - OSU-Micro-Benchmarks 5.9, pagmo 2.18.0, Pango 1.50.7, panito 0.0.1, parallel-fastq-dump 0.6.7, parameterized 0.8.1, - PCRE2 10.40, PCRE 8.45, Perl 5.30.0, Perl 5.34.1, pftoolsV3 3.2.11, Pillow 9.1.0, pixman 0.40.0, pkgconf 1.8.0, - pkgconf 1.8.0, PLINK 2.00a3.1, PMIx 4.1.2, purge_dups 1.2.5, PyAMG 4.2.3, pybind11 2.9.2, PyCairo 1.21.0, - pydot 1.4.2, pygmo 2.18.0, PyGObject 3.42.1, Python 2.7.15, Python 2.7.16, Python 2.7.18, Python 3.10.4, - QUAST 5.0.2, R 4.2.0, RapidJSON 1.1.0, RAxML-NG 1.1.0, R-bundle-Bioconductor 3.15, RE2 2022, redis-py 4.3.1, - ReFrame 3.11.0, rjags 4, RNA-Bloom 1.4.3, rnaQUAST 2.2.2, Roary 3.13.0, RSeQC 4.0.0, ruamel.yaml 0.17.21, - Rust 1.56.0, Rust 1.60.0, Salmon 1.4.0, Sambamba 0.8.2, samblaster 0.1.26, SAMtools 0.1.19, SAMtools 1.15.1, - ScaLAPACK 2.2.0, SCGid 0.9b0, SciPy-bundle 2022.05, SCOTCH 6.1.2, scPred 1.9.2, segemehl 0.3.4, SeqKit 2.2.0, - SeqLib 1.2.0, Shapely 1.8.1.post1, slow5tools 0.4.0, smooth-topk 1.0-20210817, snippy 4.6.0, snpEff 5.0e, - snp-sites 2.5.1, SpaceRanger 1.3.1, Spack 0.17.2, Spark 3.2.1, SPOTPY 1.5.14, SQLite 3.38.3, SSW 1.1, - StringTie 2.2.1, SUMO 1.12.0, SuperLU 5.3.0, tbl2asn 20220427, Tcl 8.6.12, TCLAP 1.2.5, tcsh 6.24.01, - texlive 20220321, tmap 20220502, ToFu 1.5.0, TreeMix 1.13, TRF 4.09.1, UCC 1.0.0, UCX 1.12.1, UnZip 6.0, - util-linux 2.38, VarScan 2.4.4, VEP 105, ViennaRNA 2.5.0, vsc-mympirun 5.2.11, vt 0.57721, Wayland 1.20.0, - wgsim 20111017, worker 1.6.13, X11 20220504, xESMF 0.3.0, XGrafix 2.41, xorg-macros 1.19.3, XPLOR-NIH 3.4, - XZ 5.2.5, YAXT 0.9.2.1, Z3 4.8.16, Zip 3.0, zlib 1.2.12, zstd 1.5.2 + - ABAQUS 2022, Arb 2.22.1, ARGoS 3.0.0, Arriba 2.2.1, astropy 5.0.4, ATK 2.38.0, Autotools 20220317, + Bader 1.04, Bazel 4.2.2 + 5.1.1, BDBag 1.6.3, binutils 2.38, biom-format 2.1.12, BLIS 0.9.0, Boost 1.79.0, + breseq 0.36.1, bx-python 0.8.13, cairo 1.17.4, CellRanger-ARC 2.0.1, CMake 3.23.1, cryoDRGN 1.0.0, + CUDA 11.7.0, cuDNN 8.4.1.50, cURL 7.83.0, DBus 1.14.0, eggnog-mapper 2.1.7, elfutils 0.187, + EvidentialGene 2022.01.14, expat 2.4.8, FlexiBLAS 3.2.0, FLINT 2.8.4, fontconfig 2.14.0, freebayes 1.3.6, + freeglut 3.2.2, freetype 2.12.1, FriBidi 1.0.12, GCC 9.5.0 + 11.3.0 + GCC 12.1.0, Gdk-Pixbuf 2.42.8, + geopandas 0.10.2, git 2.36.0, GLib 2.72.1, GMAP-GSNAP 2021-21-17, Go 1.18.1, GObject-Introspection 1.72.0, + Graphene 1.10.8, GST-plugins-base 1.20.2, GStreamer 1.20.2, GTDB-Tk 2.0.0, GTK3 3.24.33, gzip 1.12, + HarfBuzz 4.2.1, help2man 1.49.2, hwloc 2.7.1, hypothesis 6.46.7, Hypre 2.24.0, ICU 71.1, IGV 2.12.3, + IMB 2021.3, inferCNV 1.10.1, InterProScan 5.52, IQ-TREE 2.2.1, jax 0.3.9, json-c 0.16, LAPACK 3.10.1, + libarchive 3.6.1, libdeflate 1.10, libdrm 2.4.110, libedit 20210910, libepoxy 1.5.10, libfabric 1.15.1, + libglvnd 1.4.0, libjpeg-turbo 2.1.3, libreadline 8.1.2, librsb 1.3.0.1, librsvg 2.52.8, libtool 2.4.7, + libunwind 1.6.2, libxml2 2.9.13, LLVM 14.0.3, LocARNA 1.9.2.3, MACS2 2.2.7.1, magma 2.6.2, Mako 1.2.0, + Mathematica 13.0.0, MCL 14.137, MCR R2022a.1, Mesa 22.0.3, Meson 0.62.1, MIRA 5.0rc2, Mmg 5.6.0, mold 1.2.1, + mosdepth 0.3.3, MrBayes 3.2.7a, MultiQC 1.12, MUMPS 5.5.0, muParser 2.3.3, ncurses 6.3, neptune-client 0.16.2, + Nextflow 22.04.0, Nim 1.6.6, NTPoly 2.7.1, OpenMPI 4.1.4, openpyxl 3.0.9, OpenSSL 1.1.1n, OpenStackClient 5.8.0, + OSU-Micro-Benchmarks 5.9, pagmo 2.18.0, Pango 1.50.7, parallel-fastq-dump 0.6.7, PCRE2 10.40, Perl 5.34.1, + Pillow 9.1.0, PLINK 2.00a3.1, PMIx 4.1.2, PyAMG 4.2.3, pybind11 2.9.2, PyCairo 1.21.0, pygmo 2.18.0, + PyGObject 3.42.1, Python 3.10.4, R 4.2.0, RAxML-NG 1.1.0, R-bundle-Bioconductor 3.15, ReFrame 3.11.0, + RNA-Bloom 1.4.3, rnaQUAST 2.2.2, Rust 1.60.0, Sambamba 0.8.2, SAMtools 1.15.1, ScaLAPACK 2.2.0, + SciPy-bundle 2022.05, SeqKit 2.2.0, Shapely 1.8.1.post1, SpaceRanger 1.3.1, Spack 0.17.2, Spark 3.2.1, + SQLite 3.38.3, StringTie 2.2.1, SUMO 1.12.0, SuperLU 5.3.0, tbl2asn 20220427, Tcl 8.6.12, TCLAP 1.2.5, + tcsh 6.24.01, texlive 20220321, ToFu 1.5.0, UCX 1.12.1, util-linux 2.38, VEP 105, ViennaRNA 2.5.0, + vsc-mympirun 5.2.11, worker 1.6.13, X11 2022050, YAXT 0.9.2.1, Z3 4.8.16, Zip 3.0, zlib 1.2.12, zstd 1.5.2 - minor enhancements, including: - use OpenSSL wrapper dependency for CMake 3.18.4 with system toolchain (#15227) - also build BLIS backend for FlexiBLAS v3.0.4 with GCC/10.3.0 (#15347) - - add Hmsc extension to R v4.1.2 easyconfig (#15393) - - add DNABarcodes to R-bundle-Bioconductor 3.14 easyconfig (#15405) + - add extensions to R v4.1.2 + v4.2.0 easyconfigs: + - Hmsc (#15393), MonteCarlo + RhpcBLASctl (#15438), chkptstanr (#15540), chkptstanr + MLmetrics + renv (#15573) + - add extensions to R-bundle-Bioconductor 3.14 easyconfig: DNABarcodes (#15405) - use redist source_urls for cuDNN > 7.5 (#15411) - - Add download_instructions to Java 1.8 > 200 (#15412) - - add MonteCarlo and RhpcBLASctl extensions to R v4.1.2 + v4.2.0 easyconfigs (#15438) + - add download_instructions to Java 1.8 > 200 (#15412) - update Arrow to use EB versions of some dependencies and enable all compression codecs (#15512) - - Add local::lib and Module::Path to Perl 5.34.1 easyconfig (#15529) - - add chkptstanr extension to R v4.2.0 (#15540) - - {tools}[GCCcore/11.2.0] tcsh v6.24.01 + add csh -> tcsh symlink in recent tcsh easyconfigs (#15571) - - add chkptstanr + MLmetrics + renv extensions to R v4.1.2 + v4.2.0 easyconfigs (#15573) + - add csh -> tcsh symlink in recent tcsh easyconfigs (#15571) - allow external tools to be located elsewhere for ETE (#15578) - add additional sanity check commands for IQ-TREE v2.2.1 (#15596) - various bug fixes, including: - fix source URL for freetype 2.6.5 with foss/2016b (#14204) - - fix installation with setuptools>=61 by explicitly declaring there are no Python packages (#15206) + - fix installation of easybuild-easyconfigs with setuptools>=61 by explicitly declaring there are no Python packages (#15206) - use x.py to boostrap Rust so that build options are properly passed through (#15211) - - fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15615) - - add hwloc dependency to easyconfig for tbb v2021.4.0 (#15294) + - fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15615, #15615) + - add hwloc dependency to tbb v2021.4.0 (#15294) + - tweak find command used in preconfigopts in easyconfig for pkg-config v0.29.2 with system toolchain to avoid descending into other filesystems (#15313) - remove pkg-config use from SeqLib configure patch (avoids problem due to faulty autoconf macro) (#15316) - update source URL for isl in GCCcore easyconfigs (#15320) - update source URLs for YAXT 0.9.x to fix download (#15323) - define $HHLIB as path to HH-suite installation directory, required by Perl scripts (#15324) - - add missing parallel dependency for prokka 1.14.5 (#15360) - - add missing tbl2asn dependency for prokka 1.14.5 (#15381) - - add missing dependencies for libheif (libpng, libjpeg-turbo) + switch to configuring build with CMake so libde265 dependency is picked up (#15408) + - add missing parallel and tbl2asn dependencies for prokka 1.14.5 (#15360, #15381) + - add missing dependencies for libheif (libpng, libjpeg-turbo) (#15408) + - switch to configuring build of libheif with CMake so libde265 dependency is picked up (#15408) - disable use of -ftree-vectorize for OpenFOAM v2112 with foss/2021b (#15495) - - add patch for OpenMPI 4.1.1 to support building using --with-cuda=internal (#15528) - - remove unused libfabric dependency from easyconfig for PMIx v4.1.2 (#15564) - - {mpi}[GCC/8.2.0] OpenMPI v3.1.3 fix support for external PMIx v3.1 (#15566) + - add patch for OpenMPI 4.1.1 to support building using --with-cuda=internal (#15528, #15589) + - add patch to fix support for external PMIx v3.1 in OpenMPI v3.1.3 (#15566) - also build shared library + fix $PYTHONPATH for gmsh 4.9.0 (#15579) - - eliminate benign libcuda warning when OpenMPI is configured with --with-cuda=internal (#15589) - - add sysroot patch to Rust 1.60.0 (GCCcore/11.3.0) (#15593) - add patch for GLib 2.68.2 to fix use of close_range (#15594) - fix download of thrift 0.12.0 for Arrow 0.16.0 (#15597) - - fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15615) - - make sure that pkgconf built with system toolchain picks up on .pc files in default OS search paths (#15617) - add Bison and flex build dependencies to SCOTCH 6.1.x (#15618) - add alternative checksums for class, nnet, spatial extensions in R v4.2.0 easyconfig (#15619) - add missing dependencies + switch to non-static build for Arriba v2.1.0 (#15623) - other changes: - add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to foss/2021b toochain (#15216) - - tweak find command used in preconfigopts in easyconfig for pkg-config v0.29.2 with system toolchain to avoid descending into other filesystems (#15313) - update fallback version for OpenSSL 1.1 wrapper to v1.1.1o (#15592) - - in-place update for cryoDRGN to v0.3.5 with foss/2021a to fix compatibility issue with PyTorch v1.10 (#15609) - install sklearn meta-package with scikit-learn v1.0.1 (#15613) - - switch from pkg-config to pkgconf as build dependency for OpenSSL wrapper easyconfigs (#15616) + - switch from pkg-config to pkgconf as build dependency for OpenSSL wrapper easyconfigs (#15616, #15617) v4.5.4 (March 31st 2022) From aba9caf80dcdd8bfcc2bb6d25f334511171bba99 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Jun 2022 19:56:41 +0200 Subject: [PATCH 3916/9987] minor tweaks for release notes for v4.5.5 --- RELEASE_NOTES | 129 +++++++++++++++++++------------------------------- 1 file changed, 48 insertions(+), 81 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index d42c6ede033..099d8cb66ce 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,121 +3,88 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 14,853 easyconfig files, for 2,711 different software packages, +The latest version of easybuild-easyconfig provides 14,816 easyconfig files, for 2,711 different software packages, incl. 36 different (compiler) toolchains. -v4.5.5 (June 7th 2022) +v4.5.5 (June 8th 2022) ---------------------- update/bugfix release +- add candidates for 2022a common toolchains: foss/2022.05 (#15561), intel/2022.05 (#15485) - added example easyconfig files for 35 new software packages: - Albumentations (#15302), AMPtk (#15435), arosics (#15249), CellTypist (#15530), detectron2 (#15442), EigenExa (#15234), Fastaq (#15332), FFTW.MPI (#15561), FreeBarcodes (#15350), gcloud (#15443), - GST-plugins-bad gsutil (#15507), GTK4 (#15447), hector (#15397), i7z (#15236), libde265 (#15395), - libheif (#15395), ModelTest-NG (#15448), num2words (#15473), OGDF (#15407), panito parameterized (#15481), - purge_dups (#15385), redis-py (#15475), ruamel.yaml (#15531), SCGid (#15065), scPred (#15575), - slow5tools (#15457), smooth-topk (#15506), SPOTPY (#15326), tmap (#4601), UCC (#4291), Wayland (#11107), - XGrafix (#15268), XPLOR-NIH (#15479) + GST-plugins-bad (#15446), gsutil (#15507), GTK4 (#15447), hector (#15397), i7z (#15236), libde265 (#15395), + libheif (#15395), ModelTest-NG (#15448), num2words (#15473), OGDF (#15407), panito (#15314), + parameterized (#15481), purge_dups (#15385), redis-py (#15475), ruamel.yaml (#15531), SCGid (#15065), + scPred (#15575), slow5tools (#15457), smooth-topk (#15506), SPOTPY (#15326), tmap (#4601), UCC (#4291), + Wayland (#11107), XGrafix (#15268), XPLOR-NIH (#15479) - added additional easyconfigs for various supported software packages, including: - - ABAQUS 2022, Albumentations 1.1.0, AMD uProf 3.5.671, AMPtk 1.5.4, Anaconda3 2022.05, any2fasta 0.4.2, Arb 2.22.1, - ARGoS 3.0.0, arosics 1.7.6, Arriba 2.2.1, arrow-R 6.0.0.2, astropy 5.0.4, ATK 2.38.0, at-spi2-atk 2.38.0, - at-spi2-core 2.44.1, Autoconf 2.71, Automake 1.16.5, Autotools 20220317, Bader 1.04, bam-readcount 0.8.0, - barrnap 0.9, Bazel 4.2.2, Bazel 5.1.1, BDBag 1.6.3, beagle-lib 3.1.2, binutils 2.38, bioawk 1.0, - biom-format 2.1.12, Bison 3.8.2, Blender 3.1.2, BLIS 0.9.0, BLIS 3.0.1, Boost 1.75.0, Boost 1.79.0, breseq 0.36.1, - Brotli 1.0.9, buildenv default, bx-python 0.8.13, bzip2 1.0.8, cairo 1.17.4, CellRanger-ARC 2.0.1, - CellTypist 1.0.0, Check 0.15.2, Clang 9.0.1, Clang 12.0.1, Clang 13.0.1, CMake 3.23.1, coverage 5.5, - crb-blast 0.6.9, cryoDRGN 0.3.5, cryoDRGN 1.0.0, CUDA 11.7.0, cuDNN 8.2.2.26, cuDNN 8.4.0.27, cuDNN 8.4.1.50, - Cufflinks 20190706, cURL 7.83.0, DB 18.1.40, DBD-mysql 4.050, DBus 1.14.0, DCMTK 3.6.6, detectron2 0.6, - EasyBuild 4.5.4, edlib 1.3.9, eggnog-mapper 2.1.7, Eigen 3.4.0, EigenExa 2.11, elfutils 0.187, ELPA 2021.05.002, - EMBOSS 6.6.0, ESMPy 8.0.1, EvidentialGene 2022.01.14, Exonerate 2.4.0, expat 2.4.8, FastANI 1.33, FastANI 1.33, - Fastaq 3.17.0, fastp 0.23.2, fastq-tools 0.8.3, FastTree 2.1.11, FASTX-Toolkit 0.0.14, fermi-lite 20190320, - FFTW 3.3.10, FFTW.MPI 3.3.10, flex 2.6.4, FlexiBLAS 3.2.0, FLINT 2.8.4, fontconfig 2.14.0, foss 2022.05, FoX 4.1.2, - FreeBarcodes 3.0.a5, freebayes 1.3.6, freeglut 3.2.2, FreeImage 3.18.0, freetype 2.12.1, FriBidi 1.0.12, - fumi_tools 0.18.2, GCC 9.5.0, GCC 11.3.0, GCC 12.1.0, GCCcore 9.5.0, GCCcore 11.3.0, GCCcore 12.1.0, - gcloud 382.0.0, Gdk-Pixbuf 2.42.8, geopandas 0.10.2, gettext 0.21, giflib 5.2.1, git 2.36.0, GLib 2.72.1, - GMAP-GSNAP 2021-21-17, GMP 6.2.1, Go 1.18.1, GObject-Introspection 1.72.0, gompi 2022.05, gperf 3.1, Grace 5.1.25, - Graphene 1.10.8, groff 1.22.4, GSL 2.7, GST-plugins-bad 1.20.2, GST-plugins-base 1.20.2, GStreamer 1.20.2, - gsutil 5.10, GTDB-Tk 2.0.0, GTK3 3.24.33, GTK4 4.7.0, gzip 1.12, HarfBuzz 4.2.1, hector 2.5.0, help2man 1.49.2, - HMMER 3.3.2, HPL 2.3, HTSeq 0.11.3, hwloc 2.7.1, hypothesis 6.46.7, Hypre 2.24.0, i7z 20131012, ICU 71.1, - IGV 2.12.3, iimpi 2022.05, IMB 2021.3, imgaug 0.4.0, imkl 2022.1.0, imkl FFTW 2022.1.0, impi 2021.6.0, - inferCNV 1.10.1, intel 2022.05, intel-compilers 2022.1.0, InterProScan 5.52, intltool 0.51.0, IQ-TREE 2.2.1, - ISA-L 2.30.0, jax 0.3.9, jbigkit 2.1, Jellyfish 2.3.0, json-c 0.16, Julia 1.6.6, Kraken 1.1.1, Kraken2 2.1.2, - LAPACK 3.10.1, libarchive 3.6.1, libde265 1.0.8, libdeflate 1.10, libdrm 2.4.110, libedit 20210910, - libepoxy 1.5.10, libevent 2.1.12, libfabric 1.15.1, libffi 3.4.2, libGLU 9.0.2, libglvnd 1.4.0, libharu 2.3.0, - libharu 2.3.0, libheif 1.12.0, libjpeg-turbo 2.1.3, libpciaccess 0.16, libpng 1.6.37, libreadline 8.1.2, - librsb 1.3.0.1, librsvg 2.52.8, LIBSVM 3.25, LibTIFF 4.3.0, libtool 2.4.7, libunwind 1.6.2, libvdwxc 0.4.0, - libvdwxc 0.4.0, libxml2 2.9.13, LLVM 14.0.3, LocARNA 1.9.2.3, LSD2 2.3, lz4 1.9.3, M4 1.4.19, MACS2 2.2.7.1, - magma 2.6.2, makeinfo 6.7, Mako 1.2.0, Mash 2.3, Mathematica 13.0.0, MCL 14.137, MCR R2021b.1, MCR R2022a.1, - MEME 5.4.1, Mesa 22.0.3, Meson 0.62.1, MIRA 5.0rc2, Mmg 5.6.0, ModelTest-NG 0.1.7, mold 1.2.1, mosdepth 0.3.3, - MrBayes 3.2.6, MrBayes 3.2.7a, MultiQC 1.12, MUMPS 5.4.1, MUMPS 5.5.0, muParser 2.3.3, MUSCLE 3.8.1551, - NASM 2.15.05, ncdu 1.16, ncurses 6.3, neptune-client 0.16.2, Nextflow 22.04.0, NextGenMap 0.5.5, Nim 1.6.6, - Ninja 1.10.2, ntCard 1.2.1, NTPoly 2.7.1, num2words 0.5.10, numactl 2.0.14, numba 0.54.1, OGDF dogwood-202202, - OpenBLAS 0.3.20, OpenMPI 4.1.4, openpyxl 3.0.9, OpenSceneGraph 3.6.5, OpenSSL 1.1.1n, OpenStackClient 5.8.0, - OSU-Micro-Benchmarks 5.9, pagmo 2.18.0, Pango 1.50.7, panito 0.0.1, parallel-fastq-dump 0.6.7, parameterized 0.8.1, - PCRE2 10.40, PCRE 8.45, Perl 5.30.0, Perl 5.34.1, pftoolsV3 3.2.11, Pillow 9.1.0, pixman 0.40.0, pkgconf 1.8.0, - pkgconf 1.8.0, PLINK 2.00a3.1, PMIx 4.1.2, purge_dups 1.2.5, PyAMG 4.2.3, pybind11 2.9.2, PyCairo 1.21.0, - pydot 1.4.2, pygmo 2.18.0, PyGObject 3.42.1, Python 2.7.15, Python 2.7.16, Python 2.7.18, Python 3.10.4, - QUAST 5.0.2, R 4.2.0, RapidJSON 1.1.0, RAxML-NG 1.1.0, R-bundle-Bioconductor 3.15, RE2 2022, redis-py 4.3.1, - ReFrame 3.11.0, rjags 4, RNA-Bloom 1.4.3, rnaQUAST 2.2.2, Roary 3.13.0, RSeQC 4.0.0, ruamel.yaml 0.17.21, - Rust 1.56.0, Rust 1.60.0, Salmon 1.4.0, Sambamba 0.8.2, samblaster 0.1.26, SAMtools 0.1.19, SAMtools 1.15.1, - ScaLAPACK 2.2.0, SCGid 0.9b0, SciPy-bundle 2022.05, SCOTCH 6.1.2, scPred 1.9.2, segemehl 0.3.4, SeqKit 2.2.0, - SeqLib 1.2.0, Shapely 1.8.1.post1, slow5tools 0.4.0, smooth-topk 1.0-20210817, snippy 4.6.0, snpEff 5.0e, - snp-sites 2.5.1, SpaceRanger 1.3.1, Spack 0.17.2, Spark 3.2.1, SPOTPY 1.5.14, SQLite 3.38.3, SSW 1.1, - StringTie 2.2.1, SUMO 1.12.0, SuperLU 5.3.0, tbl2asn 20220427, Tcl 8.6.12, TCLAP 1.2.5, tcsh 6.24.01, - texlive 20220321, tmap 20220502, ToFu 1.5.0, TreeMix 1.13, TRF 4.09.1, UCC 1.0.0, UCX 1.12.1, UnZip 6.0, - util-linux 2.38, VarScan 2.4.4, VEP 105, ViennaRNA 2.5.0, vsc-mympirun 5.2.11, vt 0.57721, Wayland 1.20.0, - wgsim 20111017, worker 1.6.13, X11 20220504, xESMF 0.3.0, XGrafix 2.41, xorg-macros 1.19.3, XPLOR-NIH 3.4, - XZ 5.2.5, YAXT 0.9.2.1, Z3 4.8.16, Zip 3.0, zlib 1.2.12, zstd 1.5.2 + - ABAQUS 2022, Arb 2.22.1, ARGoS 3.0.0, Arriba 2.2.1, astropy 5.0.4, ATK 2.38.0, Autotools 20220317, + Bader 1.04, Bazel 4.2.2 + 5.1.1, BDBag 1.6.3, binutils 2.38, biom-format 2.1.12, BLIS 0.9.0, Boost 1.79.0, + breseq 0.36.1, bx-python 0.8.13, cairo 1.17.4, CellRanger-ARC 2.0.1, CMake 3.23.1, cryoDRGN 1.0.0, + CUDA 11.7.0, cuDNN 8.4.1.50, cURL 7.83.0, DBus 1.14.0, eggnog-mapper 2.1.7, elfutils 0.187, + EvidentialGene 2022.01.14, expat 2.4.8, FlexiBLAS 3.2.0, FLINT 2.8.4, fontconfig 2.14.0, freebayes 1.3.6, + freeglut 3.2.2, freetype 2.12.1, FriBidi 1.0.12, GCC 9.5.0 + 11.3.0 + GCC 12.1.0, Gdk-Pixbuf 2.42.8, + geopandas 0.10.2, git 2.36.0, GLib 2.72.1, GMAP-GSNAP 2021-21-17, Go 1.18.1, GObject-Introspection 1.72.0, + Graphene 1.10.8, GST-plugins-base 1.20.2, GStreamer 1.20.2, GTDB-Tk 2.0.0, GTK3 3.24.33, gzip 1.12, + HarfBuzz 4.2.1, help2man 1.49.2, hwloc 2.7.1, hypothesis 6.46.7, Hypre 2.24.0, ICU 71.1, IGV 2.12.3, + IMB 2021.3, inferCNV 1.10.1, InterProScan 5.52, IQ-TREE 2.2.1, jax 0.3.9, json-c 0.16, LAPACK 3.10.1, + libarchive 3.6.1, libdeflate 1.10, libdrm 2.4.110, libedit 20210910, libepoxy 1.5.10, libfabric 1.15.1, + libglvnd 1.4.0, libjpeg-turbo 2.1.3, libreadline 8.1.2, librsb 1.3.0.1, librsvg 2.52.8, libtool 2.4.7, + libunwind 1.6.2, libxml2 2.9.13, LLVM 14.0.3, LocARNA 1.9.2.3, MACS2 2.2.7.1, magma 2.6.2, Mako 1.2.0, + Mathematica 13.0.0, MCL 14.137, MCR R2022a.1, Mesa 22.0.3, Meson 0.62.1, MIRA 5.0rc2, Mmg 5.6.0, mold 1.2.1, + mosdepth 0.3.3, MrBayes 3.2.7a, MultiQC 1.12, MUMPS 5.5.0, muParser 2.3.3, ncurses 6.3, neptune-client 0.16.2, + Nextflow 22.04.0, Nim 1.6.6, NTPoly 2.7.1, OpenMPI 4.1.4, openpyxl 3.0.9, OpenSSL 1.1.1n, OpenStackClient 5.8.0, + OSU-Micro-Benchmarks 5.9, pagmo 2.18.0, Pango 1.50.7, parallel-fastq-dump 0.6.7, PCRE2 10.40, Perl 5.34.1, + Pillow 9.1.0, PLINK 2.00a3.1, PMIx 4.1.2, PyAMG 4.2.3, pybind11 2.9.2, PyCairo 1.21.0, pygmo 2.18.0, + PyGObject 3.42.1, Python 3.10.4, R 4.2.0, RAxML-NG 1.1.0, R-bundle-Bioconductor 3.15, ReFrame 3.11.0, + RNA-Bloom 1.4.3, rnaQUAST 2.2.2, Rust 1.60.0, Sambamba 0.8.2, SAMtools 1.15.1, ScaLAPACK 2.2.0, + SciPy-bundle 2022.05, SeqKit 2.2.0, Shapely 1.8.1.post1, SpaceRanger 1.3.1, Spack 0.17.2, Spark 3.2.1, + SQLite 3.38.3, StringTie 2.2.1, SUMO 1.12.0, SuperLU 5.3.0, tbl2asn 20220427, Tcl 8.6.12, TCLAP 1.2.5, + tcsh 6.24.01, texlive 20220321, ToFu 1.5.0, UCX 1.12.1, util-linux 2.38, VEP 105, ViennaRNA 2.5.0, + vsc-mympirun 5.2.11, worker 1.6.13, X11 2022050, YAXT 0.9.2.1, Z3 4.8.16, Zip 3.0, zlib 1.2.12, zstd 1.5.2 - minor enhancements, including: - use OpenSSL wrapper dependency for CMake 3.18.4 with system toolchain (#15227) - also build BLIS backend for FlexiBLAS v3.0.4 with GCC/10.3.0 (#15347) - - add Hmsc extension to R v4.1.2 easyconfig (#15393) - - add DNABarcodes to R-bundle-Bioconductor 3.14 easyconfig (#15405) + - add extensions to R v4.1.2 + v4.2.0 easyconfigs: + - Hmsc (#15393), MonteCarlo + RhpcBLASctl (#15438), chkptstanr (#15540), chkptstanr + MLmetrics + renv (#15573) + - add extensions to R-bundle-Bioconductor 3.14 easyconfig: DNABarcodes (#15405) - use redist source_urls for cuDNN > 7.5 (#15411) - - Add download_instructions to Java 1.8 > 200 (#15412) - - add MonteCarlo and RhpcBLASctl extensions to R v4.1.2 + v4.2.0 easyconfigs (#15438) - - update Arrow to use EB versions of some dependencies and enable all compression codecs (#15512) - - Add local::lib and Module::Path to Perl 5.34.1 easyconfig (#15529) - - add chkptstanr extension to R v4.2.0 (#15540) - - {tools}[GCCcore/11.2.0] tcsh v6.24.01 + add csh -> tcsh symlink in recent tcsh easyconfigs (#15571) - - add chkptstanr + MLmetrics + renv extensions to R v4.1.2 + v4.2.0 easyconfigs (#15573) + - add download_instructions to Java 1.8 > 200 (#15412) + - update Arrow to use EasyBuild-provided versions of some dependencies and enable all compression codecs (#15512) + - add csh -> tcsh symlink in recent tcsh easyconfigs (#15571) - allow external tools to be located elsewhere for ETE (#15578) - add additional sanity check commands for IQ-TREE v2.2.1 (#15596) - various bug fixes, including: - fix source URL for freetype 2.6.5 with foss/2016b (#14204) - - fix installation with setuptools>=61 by explicitly declaring there are no Python packages (#15206) + - fix installation of easybuild-easyconfigs with setuptools>=61 by explicitly declaring there are no Python packages (#15206) - use x.py to boostrap Rust so that build options are properly passed through (#15211) - - fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15615) - - add hwloc dependency to easyconfig for tbb v2021.4.0 (#15294) + - fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15615, #15615) + - add hwloc dependency to tbb v2021.4.0 (#15294) + - tweak find command used in preconfigopts in easyconfig for pkg-config v0.29.2 with system toolchain to avoid descending into other filesystems (#15313) - remove pkg-config use from SeqLib configure patch (avoids problem due to faulty autoconf macro) (#15316) - update source URL for isl in GCCcore easyconfigs (#15320) - update source URLs for YAXT 0.9.x to fix download (#15323) - define $HHLIB as path to HH-suite installation directory, required by Perl scripts (#15324) - - add missing parallel dependency for prokka 1.14.5 (#15360) - - add missing tbl2asn dependency for prokka 1.14.5 (#15381) - - add missing dependencies for libheif (libpng, libjpeg-turbo) + switch to configuring build with CMake so libde265 dependency is picked up (#15408) + - add missing parallel and tbl2asn dependencies for prokka 1.14.5 (#15360, #15381) + - add missing dependencies for libheif (libpng, libjpeg-turbo) (#15408) + - switch to configuring build of libheif with CMake so libde265 dependency is picked up (#15408) - disable use of -ftree-vectorize for OpenFOAM v2112 with foss/2021b (#15495) - - add patch for OpenMPI 4.1.1 to support building using --with-cuda=internal (#15528) - - remove unused libfabric dependency from easyconfig for PMIx v4.1.2 (#15564) - - {mpi}[GCC/8.2.0] OpenMPI v3.1.3 fix support for external PMIx v3.1 (#15566) + - add patch for OpenMPI 4.1.1 to support building using --with-cuda=internal (#15528, #15589) + - add patch to fix support for external PMIx v3.1 in OpenMPI v3.1.3 (#15566) - also build shared library + fix $PYTHONPATH for gmsh 4.9.0 (#15579) - - eliminate benign libcuda warning when OpenMPI is configured with --with-cuda=internal (#15589) - - add sysroot patch to Rust 1.60.0 (GCCcore/11.3.0) (#15593) - add patch for GLib 2.68.2 to fix use of close_range (#15594) - fix download of thrift 0.12.0 for Arrow 0.16.0 (#15597) - - fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15615) - - make sure that pkgconf built with system toolchain picks up on .pc files in default OS search paths (#15617) - add Bison and flex build dependencies to SCOTCH 6.1.x (#15618) - add alternative checksums for class, nnet, spatial extensions in R v4.2.0 easyconfig (#15619) - add missing dependencies + switch to non-static build for Arriba v2.1.0 (#15623) - other changes: - add R dependency to vcflib 1.0.3, and move from GCC/11.2.0 to foss/2021b toochain (#15216) - - tweak find command used in preconfigopts in easyconfig for pkg-config v0.29.2 with system toolchain to avoid descending into other filesystems (#15313) - update fallback version for OpenSSL 1.1 wrapper to v1.1.1o (#15592) - - in-place update for cryoDRGN to v0.3.5 with foss/2021a to fix compatibility issue with PyTorch v1.10 (#15609) - install sklearn meta-package with scikit-learn v1.0.1 (#15613) - - switch from pkg-config to pkgconf as build dependency for OpenSSL wrapper easyconfigs (#15616) + - switch from pkg-config to pkgconf as build dependency for OpenSSL wrapper easyconfigs (#15616, #15617) v4.5.4 (March 31st 2022) From fd21fd2caa58f12bfebb710a88f5d2118ad8c158 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 7 Jun 2022 20:40:03 +0200 Subject: [PATCH 3917/9987] Removed trailing whitespace --- .../MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index 0e578acd269..ca021785912 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -17,7 +17,7 @@ dependencies = [ postinstallcmds = [ "cd %(installdir)s && mkdir pkgs", - """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && + """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && julia -e 'using Pkg;Pkg.add(url="%s")' """ % homepage ] From eed91dcbdef23c287db671bbdd9e46beb8ab6058 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 7 Jun 2022 21:39:47 +0200 Subject: [PATCH 3918/9987] minor tweaks for release notes for v4.5.5 --- RELEASE_NOTES | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 86fb42734de..15d3ae55113 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -18,7 +18,7 @@ update/bugfix release GST-plugins-bad (#15446), gsutil (#15507), GTK4 (#15447), hector (#15397), i7z (#15236), libde265 (#15395), libheif (#15395), ModelTest-NG (#15448), num2words (#15473), OGDF (#15407), panito (#15314), parameterized (#15481), purge_dups (#15385), redis-py (#15475), ruamel.yaml (#15531), SCGid (#15065), - scPred (#15575), slow5tools (#15457), smooth-topk (#15506), SPOTPY (#15326), tmap (#4601), UCC (#4291), + scPred (#15575), slow5tools (#15457), smooth-topk (#15506), SPOTPY (#15326), tmap (#14601), UCC (#14291), Wayland (#11107), XGrafix (#15268), XPLOR-NIH (#15479) - added additional easyconfigs for various supported software packages, including: - ABAQUS 2022, Arb 2.22.1, ARGoS 3.0.0, Arriba 2.2.1, astropy 5.0.4, ATK 2.38.0, Autotools 20220317, @@ -61,7 +61,7 @@ update/bugfix release - fix source URL for freetype 2.6.5 with foss/2016b (#14204) - fix installation of easybuild-easyconfigs with setuptools>=61 by explicitly declaring there are no Python packages (#15206) - use x.py to boostrap Rust so that build options are properly passed through (#15211) - - fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15615, #15615) + - fix RepeatMasker-4.1.2-p1 easyconfig by moving the database configure command to postinstallcmds (#15280, #15615) - add hwloc dependency to tbb v2021.4.0 (#15294) - tweak find command used in preconfigopts in easyconfig for pkg-config v0.29.2 with system toolchain to avoid descending into other filesystems (#15313) - remove pkg-config use from SeqLib configure patch (avoids problem due to faulty autoconf macro) (#15316) From 17f9a2d0afd710ce2549dc06b23f7300bc5ff892 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jun 2022 08:17:36 +0200 Subject: [PATCH 3919/9987] bump version to 4.5.6dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 8ba26931878..4e3fe1de9d5 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.5' +VERSION = '4.5.6.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From bba03a170a80c4d9ae5a35fb2b729abc4384f8e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Jun 2022 08:40:42 +0200 Subject: [PATCH 3920/9987] adding easyconfigs: EasyBuild-4.5.5.eb --- .../e/EasyBuild/EasyBuild-4.5.5.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.5.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.5.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.5.eb new file mode 100644 index 00000000000..7023fee945c --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.5.5.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.5.5' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/14/f0/cc156a5f886d076fe7f0fef23a267710744608ce623aa85aee8f2cf65d2c/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/b1/c9/99a8888a3ecf544ec6091ff31daa7e39412323e4d13ad423a719d5dd3f67/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/47/96/34a70ba9ebc2b65046f4a5955f681b975dfa31131af9cd87e4ccbc05b0c7/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '9e45c18ab0105da68f5ccba1404515cba3bea4ba6a9fbecbe258addbf623a958', # easybuild-framework-4.5.5.tar.gz + 'aa59432efe389c3d2cfbae61c4083a40d7b9652ebd75bd03da7a8fdb8a139b53', # easybuild-easyblocks-4.5.5.tar.gz + 'ebb85680bc42653ec1816bfcd2e6c6433825191ce5c56ed152cbff5a0e4d7634', # easybuild-easyconfigs-4.5.5.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From c9010afe403b39e2c6126dcb55110d5b5a55ed44 Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Wed, 8 Jun 2022 10:21:32 +0200 Subject: [PATCH 3921/9987] build fails with Rust 1.52.1 (E0658), works with newer Rust --- .../easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb index d982362bf61..db9e0c95129 100644 --- a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb @@ -14,7 +14,7 @@ checksums = ['b51d32e8aee3b9ace08c54397fddb590209571f47f4051077bcb22b98ca3a5ed'] builddependencies = [ ('binutils', '2.36.1'), - ('Rust', '1.52.1'), + ('Rust', '1.60.0'), ('CMake', '3.20.1'), ] From 34ef02187b30406c7881b1d3b4ff5052ed20062b Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Wed, 8 Jun 2022 10:29:59 +0200 Subject: [PATCH 3922/9987] Remove new version as 2.10.9 is needed to build SRA 2.10.9 --- .../n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb deleted file mode 100644 index e47fab87109..00000000000 --- a/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-10.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'Bundle' - -name = 'NGS' -version = '2.11.2' - -homepage = 'https://github.com/ncbi/ngs' -description = """NGS is a new, domain-specific API for accessing reads, alignments and pileups -produced from Next Generation Sequencing.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -builddependencies = [ - ('binutils', '2.36.1'), - ('Perl', '5.32.1'), -] - -dependencies = [('Java', '11', '', True)] - -default_easyblock = 'ConfigureMake' -default_component_specs = { - 'source_urls': ['https://github.com/ncbi/ngs/archive'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'checksums': ['7555ab7c2f04bd81160859f6c85c65376dc7f7b891804fad9e7636a7788e39c2'], -} - -components = [ - ('NGS-SDK', version, { - 'start_dir': 'ngs-%(version)s/%(namelower)s', - 'configopts': '--build-prefix=%(builddir)s', # change default build directory - }), - ('NGS-Java', version, { - 'start_dir': 'ngs-%(version)s/%(namelower)s', - 'configopts': '--build-prefix=%(builddir)s', # change default build directory - }), -] - -sanity_check_paths = { - 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), - ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], - 'dirs': ['include/ngs', 'share'], -} - -modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} - -moduleclass = 'bio' From e335ee75348578ff1f130cee5381076a3f39a117 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 8 Jun 2022 10:48:20 +0200 Subject: [PATCH 3923/9987] adding easyconfigs: sklearn-pandas-2.2.0-foss-2021b.eb --- .../sklearn-pandas-2.2.0-foss-2021b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/sklearn-pandas/sklearn-pandas-2.2.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/sklearn-pandas/sklearn-pandas-2.2.0-foss-2021b.eb b/easybuild/easyconfigs/s/sklearn-pandas/sklearn-pandas-2.2.0-foss-2021b.eb new file mode 100644 index 00000000000..a41c6b4114f --- /dev/null +++ b/easybuild/easyconfigs/s/sklearn-pandas/sklearn-pandas-2.2.0-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'sklearn-pandas' +version = '2.2.0' + +homepage = 'https://github.com/scikit-learn-contrib/sklearn-pandas' +description = """ +This module provides a bridge between Scikit-Learn's machine learning methods +and pandas-style Data Frames. In particular, it provides a way to map DataFrame +columns to transformations, which are later recombined into features.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['bf908ea0e384e132da04355c7db67bd4f8efe145f0c9cd9f14726ce899d27542'] + +dependencies = [ + ('Python', '3.9.6'), + ('scikit-learn', '1.0.1'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'tools' From e738096b76e5a56680b49618321bf9ecc3ed4c2e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 8 Jun 2022 10:51:18 +0200 Subject: [PATCH 3924/9987] adding easyconfigs: category_encoders-2.4.1-foss-2021b.eb --- .../category_encoders-2.4.1-foss-2021b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/category_encoders/category_encoders-2.4.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/category_encoders/category_encoders-2.4.1-foss-2021b.eb b/easybuild/easyconfigs/c/category_encoders/category_encoders-2.4.1-foss-2021b.eb new file mode 100644 index 00000000000..3c65be36c55 --- /dev/null +++ b/easybuild/easyconfigs/c/category_encoders/category_encoders-2.4.1-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'category_encoders' +version = '2.4.1' + +homepage = 'https://github.com/scikit-learn-contrib/category_encoders' +description = """ +A set of scikit-learn-style transformers for encoding categorical variables +into numeric by means of different techniques.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['6e927c9681c68598980d2debed348c7ed39173c616ffe46936ac62c35086cbb4'] + +dependencies = [ + ('Python', '3.9.6'), + ('scikit-learn', '1.0.1'), + ('statsmodels', '0.13.1'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'tools' From 9fcd08dcaa3974ef653497d662c6edd4222c24f1 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 8 Jun 2022 11:47:04 +0100 Subject: [PATCH 3925/9987] adding easyconfigs: PLUMED-2.8.0-foss-2021b.eb --- .../p/PLUMED/PLUMED-2.8.0-foss-2021b.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb new file mode 100644 index 00000000000..675fa899a60 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb @@ -0,0 +1,60 @@ +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.8.0' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['24b243c531fa83752be5e54f5f0b677164855da539bc2b2c5b00dcc9f192aa82'] + +builddependencies = [ + ('xxd', '8.2.4220'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.7'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From 1f7836eafd923aaac108e16a73e2b9090b7fc20c Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Wed, 8 Jun 2022 13:35:20 +0200 Subject: [PATCH 3926/9987] adding easyconfigs: TCLAP-1.2.5-GCCcore-10.3.0.eb --- .../t/TCLAP/TCLAP-1.2.5-GCCcore-10.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.5-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.5-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..9928a1e286a --- /dev/null +++ b/easybuild/easyconfigs/t/TCLAP/TCLAP-1.2.5-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'TCLAP' +version = '1.2.5' + +homepage = 'http://tclap.sourceforge.net/' +description = """TCLAP is a small, flexible library that provides a simple interface for defining and accessing +command line arguments. It was intially inspired by the user friendly CLAP libary.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb649f76dae35e8d0dcba4b52acfd4e062d787e6a81b43f7a4b01275153165a6'] + +builddependencies = [ + ('Autotools', '20210128'), + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "autoreconf -i -f && " + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/tclap/CmdLine.h'], + 'dirs': [], +} + +moduleclass = 'lib' From 0877b5e2604644b9450d9ca86f2d2e8257145a49 Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Wed, 8 Jun 2022 13:50:54 +0200 Subject: [PATCH 3927/9987] adding easyconfigs: libRmath-4.2.0-GCCcore-10.3.0.eb --- .../libRmath/libRmath-4.2.0-GCCcore-10.3.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/l/libRmath/libRmath-4.2.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libRmath/libRmath-4.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..cf6e8b6cc4f --- /dev/null +++ b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# Updated: Denis Kristak (INUITS) +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'libRmath' +version = '4.2.0' + +homepage = 'https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library' +description = """The routines supporting the distribution and special functions in R and a few others are declared + in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = ['R-%(version)s.tar.gz'] +checksums = ['38eab7719b7ad095388f06aa090c5a2b202791945de60d3e2bb0eab1f5097488'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('cURL', '7.76.0'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('PCRE2', '10.36'), +] + +parallel = 1 + +start_dir = 'src/nmath/standalone' + +preconfigopts = 'cd %(builddir)s/R-%(version)s && ' +configopts = '--with-readline=no --with-recommended-packages=no --with-x=no' + +postinstallcmds = ["cp -r %(builddir)s/R-%(version)s/src/include/R_ext %(installdir)s/include/"] + +runtest = 'check' + +sanity_check_paths = { + 'files': ["lib/libRmath.%s" % SHLIB_EXT, "lib/libRmath.a", + "lib/pkgconfig/libRmath.pc", + "include/Rmath.h"], + 'dirs': [] +} + +moduleclass = 'lib' From 04324136b382139302a18bf1bf831818875a1186 Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Wed, 8 Jun 2022 15:02:07 +0200 Subject: [PATCH 3928/9987] adding easyconfigs: LIBSVM-3.25-GCCcore-10.3.0.eb --- .../l/LIBSVM/LIBSVM-3.25-GCCcore-10.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4847897c51d --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.25-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM' +version = '3.25' + +homepage = 'https://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression + (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'cjlin1' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%s.tar.gz' % version.replace('.', '')] +patches = ['LIBSVM-3.23_shared_lib.patch'] +checksums = [ + '1f587ec0df6fd422dfe50f942f8836ac179b0723b768fe9d2fabdfd1601a0963', # v325.tar.gz + 'c0ede89365949644f5d7f11382a3f176fd76317c7f5ae5769226ff7c3a801fe6', # LIBSVM-3.23_shared_lib.patch +] + +dependencies = [('binutils', '2.36.1')] + +local_bins = ['svm-%s' % x for x in ['predict', 'scale', 'train']] + +files_to_copy = [ + (local_bins, 'bin'), + (['svm.o'], 'lib'), + (['libsvm*'], 'lib'), + (['svm.h'], 'include/libsvm'), + 'tools' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + ['lib/libsvm.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 58aec6bee28c5a74b14e091383aef0f613eb743e Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Wed, 8 Jun 2022 15:09:11 +0200 Subject: [PATCH 3929/9987] adding easyconfigs: vt-0.57721-GCC-10.3.0.eb --- .../easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb new file mode 100644 index 00000000000..fe97517832c --- /dev/null +++ b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb @@ -0,0 +1,72 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) + +easyblock = 'MakeCp' + +name = 'vt' +version = '0.57721' + +homepage = 'https://genome.sph.umich.edu/wiki/Vt' +description = """A tool set for short variant discovery in genetic sequence data.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'atks' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-0.57721_use-external-libs.patch', + '%(name)s-0.57721_fix-Rmath-includes.patch', + '%(name)s-0.57721_avoid-implicit-conversion.patch', + '%(name)s-0.57721_fail-on-test-error.patch', + '%(name)s-0.57721_update_htsutils.patch', +] +checksums = [ + '8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17', # 0.57721.tar.gz + '5a31713ae7c5febf850eec294dbba45b6b240d832cb94bdfe9ee695fd13e45bb', # vt-0.57721_use-external-libs.patch + '663525f5180a66d8817f271a69de1884576e2414d46b7ba93029d78f71d5b14c', # vt-0.57721_fix-Rmath-includes.patch + '56d874d5c7d488761f25afb4ee3717c88dfd959ed76efb75a8531b8428d30ccd', # vt-0.57721_avoid-implicit-conversion.patch + '4146282eb6ec852485f5a16e647da9c3b210450ceb5519b9b4a98bc52124469a', # vt-0.57721_fail-on-test-error.patch + '1c170b7ba2a4d392830f64392075ff75bbbc29137fe9f2922aeb7345e2ab6298', # vt-0.57721_update_htsutils.patch +] + +# checksums = [ +# '8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17', # 0.57721.tar.gz +# '5a31713ae7c5febf850eec294dbba45b6b240d832cb94bdfe9ee695fd13e45bb', # vt-0.57721_use-external-libs.patch +# '663525f5180a66d8817f271a69de1884576e2414d46b7ba93029d78f71d5b14c', # vt-0.57721_fix-Rmath-includes.patch +# '56d874d5c7d488761f25afb4ee3717c88dfd959ed76efb75a8531b8428d30ccd', # vt-0.57721_avoid-implicit-conversion.patch +# 'ba2cfc24a88a4291b2da634db49e18199c379eb95d3b3acac59556bc68c292df', # vt-0.57721_update-faidx.patch +# '4146282eb6ec852485f5a16e647da9c3b210450ceb5519b9b4a98bc52124469a', # vt-0.57721_fail-on-test-error.patch +# ] + +builddependencies = [ + ('binutils', '2.36.1'), + ('TCLAP', '1.2.5'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.76.0'), + ('PCRE', '8.44'), + ('PCRE2', '10.36'), + ('libdeflate', '1.7'), + ('libRmath', '4.2.0'), + ('LIBSVM', '3.25'), + ('HTSlib', '1.12'), +] + +runtest = 'test' + +files_to_copy = [ + (['vt'], 'bin'), + (['*.h'], 'include/vt'), + 'test', 'README.md', 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/vt'], + 'dirs': [], +} + +moduleclass = 'bio' From 2dffcdbe2f1ee0d37533366e69e1e933bf6b7567 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 8 Jun 2022 15:37:41 +0200 Subject: [PATCH 3930/9987] match patched jorg version renamed easyconfig in order to match patched Jorg 1.0.1 version --- .../j/Jorg/{Jorg-1.0.0-foss-2020b.eb => Jorg-1.0.1-foss-2020b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/j/Jorg/{Jorg-1.0.0-foss-2020b.eb => Jorg-1.0.1-foss-2020b.eb} (100%) diff --git a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb similarity index 100% rename from easybuild/easyconfigs/j/Jorg/Jorg-1.0.0-foss-2020b.eb rename to easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb From 1d550cf99c8ee54db4c5d030b2b1588436f5d0b1 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 8 Jun 2022 15:16:25 +0100 Subject: [PATCH 3931/9987] PLUMED version 2.8.0 added for GROMACS-2021.5 --- .../GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb | 19 +++- .../GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb | 99 +++++++++++++++++++ 2 files changed, 114 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb index cf94349e8a3..662a10d5c55 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb @@ -9,13 +9,15 @@ # * Kenneth Hoste # * Adam Huffman # * Ake Sandgren -# * J. Sassmannshausen # * Dugan Witherick # * Christoph Siegert +# * J. Sassmannshausen # License:: MIT/GPL name = 'GROMACS' version = '2021.5' +_plumedver = '2.8.0' +versionsuffix = '-PLUMED-%s' % _plumedver versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://www.gromacs.org' @@ -24,10 +26,11 @@ GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. -This is a GPU enabled build, containing both MPI and threadMPI builds. +This is a GPU enabled build, containing both MPI and threadMPI builds +for both single and double precision. -It also contains the gmxapi extension for the single precision MPI build. -""" +It also contains the gmxapi extension for the single precision MPI build +next to PLUMED.""" toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'openmp': True, 'usempi': True} @@ -42,6 +45,7 @@ patches = [ 'GROMACS-2019_increase_test_timeout_for_GPU.patch', 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', 'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021.3_skip_test_for_plumed.patch', ] checksums = [ 'eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6', # gromacs-2021.5.tar.gz @@ -53,21 +57,28 @@ checksums = [ 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', # GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch '7d39da0b431fbc9e94e857552246eb0ec892f26b13e519b3706785cc5e01a563', + # GROMACS-2021.3_skip_test_for_plumed.patch + 'c06d0a8c3e75b232224f46bc3b70e135c4c02ec4151712970f5edd85d890f018', ] builddependencies = [ ('CMake', '3.22.1'), ('scikit-build', '0.11.1'), + ('Doxygen', '1.9.1'), ] dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), ('networkx', '2.6.3'), + ('PLUMED', _plumedver), ('CUDA', '11.4.1', '', True), ('UCX-CUDA', '1.11.2', versionsuffix), ] +# PLUMED-2.8.0 does not officially support GROMACS-2021.5, but seems to work fine +ignore_plumed_version_check = True + exts_defaultclass = 'PythonPackage' exts_default_options = { diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb new file mode 100644 index 00000000000..f9233c3c161 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb @@ -0,0 +1,99 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * Dugan Witherick +# * Christoph Siegert +# * J. Sassmannshausen +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021.5' +_plumedver = '2.8.0' +versionsuffix = '-PLUMED-%s' % _plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI builds +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build +next to PLUMED.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021.3_skip_test_for_plumed.patch', +] +checksums = [ + 'eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6', # gromacs-2021.5.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch + '7d39da0b431fbc9e94e857552246eb0ec892f26b13e519b3706785cc5e01a563', + # GROMACS-2021.3_skip_test_for_plumed.patch + 'c06d0a8c3e75b232224f46bc3b70e135c4c02ec4151712970f5edd85d890f018', +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('scikit-build', '0.11.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('networkx', '2.6.3'), + ('PLUMED', _plumedver), +] + +# PLUMED-2.7.3 does not officially support GROMACS-2021.5, but seems to work fine +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.2.1', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['e24d507585e1a7808a5ee3ed04da5d6577f2a8961bbeafa7068528e00aa6b20d'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 68a6ad8827e899dd5e48ae3d0585a5bf6bc71ac9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 8 Jun 2022 15:59:25 +0100 Subject: [PATCH 3932/9987] adding easyconfigs: SpectrA-1.0.1-GCC-11.2.0.eb --- .../s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..1757c6c746b --- /dev/null +++ b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb @@ -0,0 +1,32 @@ +# EasyBuild easyconfig +# +# Fred Hutchinson Cancer Research Center - Seattle - Washington - US +# https://www.fredhutch.org +# John Dey +# +easyblock = 'CMakeMake' + +name = 'SpectrA' +version = '1.0.1' + +homepage = 'https://spectralib.org/' +description = """Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ + library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/yixuan/spectra/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['919e3fbc8c539a321fd5a0766966922b7637cc52eb50a969241a997c733789f3'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Eigen', '3.4.0'), +] + +sanity_check_paths = { + 'files': ['include/Spectra/SymEigsSolver.h'], + 'dirs': ['include/Spectra/LinAlg', 'share/spectra/cmake'], +} + +moduleclass = 'math' From 69ddead0f49bbbb74f5559930464192689345ac2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 8 Jun 2022 16:01:19 +0100 Subject: [PATCH 3933/9987] adding easyconfigs: GCTA-1.94.0beta-foss-2021b.eb and patches: GCTA-1.94.0beta_allow-BLAS-selection.patch, GCTA-1.94.0beta_lapack-compatibility.patch --- .../g/GCTA/GCTA-1.94.0beta-foss-2021b.eb | 69 ++++++ ...GCTA-1.94.0beta_allow-BLAS-selection.patch | 218 ++++++++++++++++++ ...GCTA-1.94.0beta_lapack-compatibility.patch | 157 +++++++++++++ 3 files changed, 444 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta_allow-BLAS-selection.patch create mode 100644 easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta_lapack-compatibility.patch diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb new file mode 100644 index 00000000000..2fcbfe3bc14 --- /dev/null +++ b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb @@ -0,0 +1,69 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CMakeMakeCp' + +name = 'GCTA' +version = '1.94.0beta' +_plink_commit = '3744540' + +homepage = 'https://yanglab.westlake.edu.cn/software/gcta/' +description = """ +GCTA (Genome-wide Complex Trait Analysis) is a software package, which was + initially developed to estimate the proportion of phenotypic variance explained + by all genome-wide SNPs for a complex trait but has been extensively extended + for many other analyses of data from genome-wide association studies (GWASs). +""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [ + { + 'source_urls': ['https://github.com/jianyangqt/gcta/archive'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/zhilizheng/plink-ng/archive'], + 'download_filename': '%s.tar.gz' % _plink_commit, + 'filename': 'plink-ng-%s.tar.gz' % _plink_commit, + 'extract_cmd': "tar xzvf %%s --strip-components 1 -C gcta-%s/submods/plink-ng" % version, + }, +] +patches = [ + 'GCTA-1.94.0beta_allow-BLAS-selection.patch', + 'GCTA-1.94.0beta_lapack-compatibility.patch', +] +checksums = [ + '9220a6c40f31e3b1ce3d25f7eee3d8c62403bee8d6ed624bd8b61891badcb14f', # GCTA-1.94.0beta.tar.gz + 'a7c70c237d49d64fc1668ced373036c09b41d7c61d0b8b24b47e2fb76474455d', # plink-ng-3744540.tar.gz + '320a5d82d12cf453f1396b228723ac18dc98e32bc459394dd4d712fc16b24747', # GCTA-1.94.0beta_allow-BLAS-selection.patch + '643282a2e2c02fc683431b673a4623a498129870431481d33d33e19a509026ce', # GCTA-1.94.0beta_lapack-compatibility.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), + # Eigen and SpectrA are header-only C++ libraries + ('Eigen', '3.4.0'), + ('SpectrA', '1.0.1'), +] + +dependencies = [ + ('Boost', '1.75.0'), + ('SQLite', '3.36'), + ('zstd', '1.5.0'), + ('GSL', '2.7'), + ('FlexiBLAS', '3.0.4'), +] + +preconfigopts = 'EIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include SPECTRA_LIB=$EBROOTSPECTRA/include' +preconfigopts += ' BOOST_LIB=$EBROOTBOOST/include ' + +files_to_copy = [(['gcta64'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/gcta64'], + 'dirs': [], +} + +sanity_check_commands = ["gcta64 | grep -e 'Analysis started'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta_allow-BLAS-selection.patch b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta_allow-BLAS-selection.patch new file mode 100644 index 00000000000..ce7441656cf --- /dev/null +++ b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta_allow-BLAS-selection.patch @@ -0,0 +1,218 @@ +Author: Jasper Grimm +Description: Allow selection of BLAS, instead of automatically enabling MKL or + OpenBLAS depending on system architecture. +------------------------------------------------------------------------------- +diff -Nru gcta-1.94.0beta.orig/CMakeLists.txt gcta-1.94.0beta/CMakeLists.txt +--- gcta-1.94.0beta.orig/CMakeLists.txt 2022-06-08 14:30:39.000000000 +0100 ++++ gcta-1.94.0beta/CMakeLists.txt 2022-06-08 14:35:08.000000000 +0100 +@@ -63,15 +63,9 @@ + + + message(STATUS "ARCHITECTURE:${CMAKE_LIBRARY_ARCHITECTURE}") +-if(CMAKE_LIBRARY_ARCHITECTURE STREQUAL "aarch64") +- SET(OPENBLAS "$ENV{OPENBLAS}") +- IF(NOT OPENBLAS) +- MESSAGE(FATAL_ERROR "Specify environment variable OPENBLAS to the location of OPENBLAS package") +- ENDIF() +- INCLUDE_DIRECTORIES("${OPENBLAS}/include") +- +- find_library(lib_openblas NAMES openblas PATHS "${OPENBLAS}" "${OPENBLAS}/lib") +- set(BLAS_LIB ${lib_openblas}) ++if(NOT USE_MKL) ++ INCLUDE_DIRECTORIES("$ENV{BLAS_INC_DIR}") ++ set(BLAS_LIB "$ENV{LIBBLAS}") + + if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native -pthread") +diff -Nru gcta-1.94.0beta.orig/include/cpu_f77blas.h gcta-1.94.0beta/include/cpu_f77blas.h +--- gcta-1.94.0beta.orig/include/cpu_f77blas.h 2022-06-08 14:30:39.000000000 +0100 ++++ gcta-1.94.0beta/include/cpu_f77blas.h 2022-06-08 14:35:08.000000000 +0100 +@@ -37,7 +37,7 @@ + #define GCTA_CPU_ARM 0 + #endif + +-#if GCTA_CPU_x86 ++#if USE_MKL + #ifndef EIGEN_USE_MKL_ALL + #define EIGEN_USE_MKL_ALL + #endif +diff -Nru gcta-1.94.0beta.orig/include/cpu.h gcta-1.94.0beta/include/cpu.h +--- gcta-1.94.0beta.orig/include/cpu.h 2022-06-08 14:30:39.000000000 +0100 ++++ gcta-1.94.0beta/include/cpu.h 2022-06-08 14:35:08.000000000 +0100 +@@ -37,7 +37,7 @@ + #define GCTA_CPU_ARM 0 + #endif + +-#if GCTA_CPU_x86 ++#if USE_MKL + #ifndef EIGEN_USE_MKL_ALL + #define EIGEN_USE_MKL_ALL + #endif +diff -Nru gcta-1.94.0beta.orig/include/Matrix.hpp gcta-1.94.0beta/include/Matrix.hpp +--- gcta-1.94.0beta.orig/include/Matrix.hpp 2022-06-08 14:30:39.000000000 +0100 ++++ gcta-1.94.0beta/include/Matrix.hpp 2022-06-08 14:35:08.000000000 +0100 +@@ -29,7 +29,7 @@ + int info, cols = (int)A.cols(); + char uplo = 'L'; + LOGGER.ts("LLT"); +-#if GCTA_CPU_x86 ++#if USE_MKL + dpotrf(&uplo, &cols, vi, &cols, &info); + #else + dpotrf_(&uplo, &cols, vi, &cols, &info); +@@ -38,7 +38,7 @@ + if(info == 0){ + logdet = A.diagonal().array().square().log().sum(); + //LOGGER.ts("LLT_INV"); +-#if GCTA_CPU_x86 ++#if USE_MKL + dpotri(&uplo, &cols, vi, &cols, &info); + #else + dpotri_(&uplo, &cols, vi, &cols, &info); +diff -Nru gcta-1.94.0beta.orig/main/mkl.cpp gcta-1.94.0beta/main/mkl.cpp +--- gcta-1.94.0beta.orig/main/mkl.cpp 2022-06-08 14:30:39.000000000 +0100 ++++ gcta-1.94.0beta/main/mkl.cpp 2022-06-08 14:35:07.000000000 +0100 +@@ -362,7 +362,7 @@ + // MKL's Cholesky decomposition + int info = 0, int_n = (int) n; + char uplo = 'L'; +-#if GCTA_CPU_x86 ++#if USE_MKL + dpotrf(&uplo, &int_n, Vi_mkl, &int_n, &info); + #else + dpotrf_(&uplo, &int_n, Vi_mkl, &int_n, &info); +@@ -383,7 +383,7 @@ + + //LOGGER << "start inverse" << endl; + // Calcualte V inverse +-#if GCTA_CPU_x86 ++#if USE_MKL + dpotri(&uplo, &int_n, Vi_mkl, &int_n, &info); + #else + dpotri_(&uplo, &int_n, Vi_mkl, &int_n, &info); +@@ -428,7 +428,7 @@ + int LWORK = N*N; + double *WORK = new double[n * n]; + int INFO; +-#if GCTA_CPU_x86 ++#if USE_MKL + dgetrf(&N, &N, Vi_mkl, &N, IPIV, &INFO); + #else + dgetrf_(&N, &N, Vi_mkl, &N, IPIV, &INFO); +@@ -447,7 +447,7 @@ + } + + // Calcualte V inverse +-#if GCTA_CPU_x86 ++#if USE_MKL + dgetri(&N, Vi_mkl, &N, IPIV, WORK, &LWORK, &INFO); + #else + dgetri_(&N, Vi_mkl, &N, IPIV, WORK, &LWORK, &INFO); +@@ -490,7 +490,7 @@ + int LWORK = N*N; + double *WORK = new double[n * n]; + int INFO; +-#if GCTA_CPU_x86 ++#if USE_MKL + dgetrf(&N, &N, Vi_mkl, &N, IPIV, &INFO); + #else + dgetrf_(&N, &N, Vi_mkl, &N, IPIV, &INFO); +@@ -511,7 +511,7 @@ + } + + // Calcualte V inverse +-#if GCTA_CPU_x86 ++#if USE_MKL + dgetri(&N, Vi_mkl, &N, IPIV, WORK, &LWORK, &INFO); + #else + dgetri_(&N, Vi_mkl, &N, IPIV, WORK, &LWORK, &INFO); +diff -Nru gcta-1.94.0beta.orig/src/FastFAM.cpp gcta-1.94.0beta/src/FastFAM.cpp +--- gcta-1.94.0beta.orig/src/FastFAM.cpp 2022-06-08 14:30:39.000000000 +0100 ++++ gcta-1.94.0beta/src/FastFAM.cpp 2022-06-08 14:35:08.000000000 +0100 +@@ -22,7 +22,7 @@ + #include + #include + +-#if GCTA_CPU_x86 ++#if USE_MKL + #include + #endif + +@@ -1137,7 +1137,7 @@ + const double b1 = 0; + const double b2 = 1.0; + const int incr = 1; +-#if GCTA_CPU_x86 ++#if USE_MKL + dgemv(&nT, &num_covar, &numi_indi, &a1, H.data(), &num_covar, y.data(), &incr, &b1, Hy, &incr); + dgemv(&nT, &numi_indi, &num_covar, &a2, covar.data(), &numi_indi, Hy, &incr, &b2, y.data(), &incr); + #else +diff -Nru gcta-1.94.0beta.orig/src/GRM.cpp gcta-1.94.0beta/src/GRM.cpp +--- gcta-1.94.0beta.orig/src/GRM.cpp 2022-06-08 14:30:39.000000000 +0100 ++++ gcta-1.94.0beta/src/GRM.cpp 2022-06-08 14:35:08.000000000 +0100 +@@ -972,20 +972,20 @@ + static char uplo='L'; + // A * At + if(part_keep_indices.first == 0){ +-#if GCTA_CPU_x86 ++#if USE_MKL + dsyrk(&uplo, ¬rans, &n, &curNumValidMarkers, &alpha, stdGeno, &n_sample, &beta, grm, &m); + #else + dsyrk_(&uplo, ¬rans, &n, &curNumValidMarkers, &alpha, stdGeno, &n_sample, &beta, grm, &m); + #endif + }else{ + //dgemm(¬rans, &trans, &m, &n, &num_marker, &alpha, stdGeno + part_keep_indices.first, &n_sample, stdGeno, &n_sample, &beta, grm, &m); +-#if GCTA_CPU_x86 ++#if USE_MKL + dgemm(¬rans, &trans, &m, &s_n, &curNumValidMarkers, &alpha, stdGeno + part_keep_indices.first, &n_sample, stdGeno, &n_sample, &beta, grm, &m); + #else + dgemm_(¬rans, &trans, &m, &s_n, &curNumValidMarkers, &alpha, stdGeno + part_keep_indices.first, &n_sample, stdGeno, &n_sample, &beta, grm, &m); + #endif + double * grm_start = grm + ((uint64_t)s_n) * m; +-#if GCTA_CPU_x86 ++#if USE_MKL + dsyrk(&uplo, ¬rans, &m, &curNumValidMarkers, &alpha, stdGeno + part_keep_indices.first, &n_sample, &beta, grm_start, &m); + #else + dsyrk_(&uplo, ¬rans, &m, &curNumValidMarkers, &alpha, stdGeno + part_keep_indices.first, &n_sample, &beta, grm_start, &m); +diff -Nru gcta-1.94.0beta.orig/src/LD.cpp gcta-1.94.0beta/src/LD.cpp +--- gcta-1.94.0beta.orig/src/LD.cpp 2022-06-08 14:30:39.000000000 +0100 ++++ gcta-1.94.0beta/src/LD.cpp 2022-06-08 14:35:08.000000000 +0100 +@@ -62,7 +62,7 @@ + double alpha = 1.0 / (nr - 1); + double *ptr1 = geno_buffer[cacl_index_buffer].get(); + double *res1 = new double[nc1 * nc1]; +-#if GCTA_CPU_x86 ++#if USE_MKL + dsyrk(&uplo, &trans, &nc1, &nr, &alpha, ptr1, &nr, &zero, res1, &nc1); + #else + dsyrk_(&uplo, &trans, &nc1, &nr, &alpha, ptr1, &nr, &zero, res1, &nc1); +@@ -76,7 +76,7 @@ + nc2 = cur_buffer_offset[!cacl_index_buffer] / nr; + double *ptr2 = geno_buffer[!cacl_index_buffer].get(); + res2 = new double[nc2 * nc1]; +-#if GCTA_CPU_x86 ++#if USE_MKL + dgemm(&trans, ¬rans, &nc2, &nc1, &nr, &alpha, ptr2, &nr, ptr1, &nr, &zero, res2, &nc2); + #else + dgemm_(&trans, ¬rans, &nc2, &nc1, &nr, &alpha, ptr2, &nr, ptr1, &nr, &zero, res2, &nc2); +diff -Nru gcta-1.94.0beta.orig/src/StatLib.cpp gcta-1.94.0beta/src/StatLib.cpp +--- gcta-1.94.0beta.orig/src/StatLib.cpp 2022-06-08 14:30:39.000000000 +0100 ++++ gcta-1.94.0beta/src/StatLib.cpp 2022-06-08 14:35:08.000000000 +0100 +@@ -89,7 +89,7 @@ + int info = 0; + int lda = n; + int lwork = n; +-#if GCTA_CPU_x86 ++#if USE_MKL + dgeqrf(&n, &n, X, &lda, tau, work, &lwork, &info); + #else + dgeqrf_(&n, &n, X, &lda, tau, work, &lwork, &info); +@@ -113,7 +113,7 @@ + + char side = 'L'; + char t = 'N'; +-#if GCTA_CPU_x86 ++#if USE_MKL + dormqr(&side, &t, &n, &n, &n, X, &lda, tau, c, + &lda, work, &lwork, &info); + #else diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta_lapack-compatibility.patch b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta_lapack-compatibility.patch new file mode 100644 index 00000000000..21590ee46f3 --- /dev/null +++ b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta_lapack-compatibility.patch @@ -0,0 +1,157 @@ +Author: Jasper Grimm +Description: Update function names to be compatible with recent LAPACK +------------------------------------------------------------------------------- +diff -Nru gcta-1.94.0beta_p1/include/Matrix.hpp gcta-1.94.0beta_p2/include/Matrix.hpp +--- gcta-1.94.0beta_p1/include/Matrix.hpp 2022-06-08 14:48:52.000000000 +0100 ++++ gcta-1.94.0beta_p2/include/Matrix.hpp 2022-06-08 14:49:55.000000000 +0100 +@@ -32,7 +32,7 @@ + #if USE_MKL + dpotrf(&uplo, &cols, vi, &cols, &info); + #else +- dpotrf_(&uplo, &cols, vi, &cols, &info); ++ LAPACK_dpotrf(&uplo, &cols, vi, &cols, &info); + #endif + //LOGGER << " LLT time: " << LOGGER.tp("LLT") << std::endl; + if(info == 0){ +@@ -41,7 +41,7 @@ + #if USE_MKL + dpotri(&uplo, &cols, vi, &cols, &info); + #else +- dpotri_(&uplo, &cols, vi, &cols, &info); ++ LAPACK_dpotri(&uplo, &cols, vi, &cols, &info); + #endif + //LOGGER << " LLT inverse time: " << LOGGER.tp("LLT_INV") << std::endl; + if(info == 0){ +diff -Nru gcta-1.94.0beta_p1/main/mkl.cpp gcta-1.94.0beta_p2/main/mkl.cpp +--- gcta-1.94.0beta_p1/main/mkl.cpp 2022-06-08 14:48:52.000000000 +0100 ++++ gcta-1.94.0beta_p2/main/mkl.cpp 2022-06-08 14:49:54.000000000 +0100 +@@ -365,7 +365,7 @@ + #if USE_MKL + dpotrf(&uplo, &int_n, Vi_mkl, &int_n, &info); + #else +- dpotrf_(&uplo, &int_n, Vi_mkl, &int_n, &info); ++ LAPACK_dpotrf(&uplo, &int_n, Vi_mkl, &int_n, &info); + #endif + //LOGGER << "Finished decompose" << endl; + //spotrf( &uplo, &n, Vi_mkl, &n, &info ); +@@ -386,7 +386,7 @@ + #if USE_MKL + dpotri(&uplo, &int_n, Vi_mkl, &int_n, &info); + #else +- dpotri_(&uplo, &int_n, Vi_mkl, &int_n, &info); ++ LAPACK_dpotri(&uplo, &int_n, Vi_mkl, &int_n, &info); + #endif + //LOGGER << "Inverse finished" << endl; + //spotri( &uplo, &n, Vi_mkl, &n, &info ); +diff -Nru gcta-1.94.0beta_p1/src/StatLib.cpp gcta-1.94.0beta_p2/src/StatLib.cpp +--- gcta-1.94.0beta_p1/src/StatLib.cpp 2022-06-08 14:48:52.000000000 +0100 ++++ gcta-1.94.0beta_p2/src/StatLib.cpp 2022-06-08 14:49:55.000000000 +0100 +@@ -117,7 +117,7 @@ + dormqr(&side, &t, &n, &n, &n, X, &lda, tau, c, + &lda, work, &lwork, &info); + #else +- dormqr_(&side, &t, &n, &n, &n, X, &lda, tau, c, ++ LAPACK_dormqr(&side, &t, &n, &n, &n, X, &lda, tau, c, + &lda, work, &lwork, &info); + #endif + if(info != 0){ +diff -Nru gcta-1.94.0beta_p1/submods/plink-ng/1.9/plink_matrix.c gcta-1.94.0beta_p2/submods/plink-ng/1.9/plink_matrix.c +--- gcta-1.94.0beta_p1/submods/plink-ng/1.9/plink_matrix.c 2022-06-08 14:45:46.000000000 +0100 ++++ gcta-1.94.0beta_p2/submods/plink-ng/1.9/plink_matrix.c 2022-06-08 14:49:47.000000000 +0100 +@@ -288,7 +288,7 @@ + } + #else // !NOLAPACK + int32_t invert_matrix(__CLPK_integer dim, double* matrix, MATRIX_INVERT_BUF1_TYPE* int_1d_buf, double* dbl_2d_buf) { +- // dgetrf_/dgetri_ is more efficient than dpotrf_/dpotri_ on OS X. ++ // dgetrf_/dgetri_ is more efficient than LAPACK_dpotrf/LAPACK_dpotri on OS X. + __CLPK_integer lwork = dim * dim; + __CLPK_integer info; + dgetrf_(&dim, &dim, matrix, &dim, int_1d_buf, &info); +diff -Nru gcta-1.94.0beta_p1/submods/plink-ng/2.0/plink2_matrix.cc gcta-1.94.0beta_p2/submods/plink-ng/2.0/plink2_matrix.cc +--- gcta-1.94.0beta_p1/submods/plink-ng/2.0/plink2_matrix.cc 2022-06-08 14:45:48.000000000 +0100 ++++ gcta-1.94.0beta_p2/submods/plink-ng/2.0/plink2_matrix.cc 2022-06-08 14:49:51.000000000 +0100 +@@ -110,7 +110,7 @@ + __CLPK_integer* lwork, __CLPK_integer* iwork, + __CLPK_integer* liwork, __CLPK_integer* info); + +- int dpotrf_(char* uplo, __CLPK_integer* n, __CLPK_doublereal* a, ++ int LAPACK_dpotrf(char* uplo, __CLPK_integer* n, __CLPK_doublereal* a, + __CLPK_integer* lda, __CLPK_integer* info); + + +@@ -118,7 +118,7 @@ + __CLPK_doublereal* a, __CLPK_integer* lda, __CLPK_doublereal* b, + __CLPK_integer* ldb, __CLPK_integer* info); + +- int dpotri_(char* uplo, __CLPK_integer* n, __CLPK_doublereal* a, ++ int LAPACK_dpotri(char* uplo, __CLPK_integer* n, __CLPK_doublereal* a, + __CLPK_integer* lda, __CLPK_integer* info); + + # ifndef USE_CBLAS_XGEMM +@@ -569,11 +569,11 @@ + BoolErr InvertSymmdefMatrix(__CLPK_integer dim, double* matrix, __maybe_unused MatrixInvertBuf1* int_1d_buf, __maybe_unused double* dbl_2d_buf) { + char uplo = 'U'; + __CLPK_integer info; +- dpotrf_(&uplo, &dim, matrix, &dim, &info); ++ LAPACK_dpotrf(&uplo, &dim, matrix, &dim, &info); + if (info) { + return 1; + } +- dpotri_(&uplo, &dim, matrix, &dim, &info); ++ LAPACK_dpotri(&uplo, &dim, matrix, &dim, &info); + assert(info == 0); + return 0; + } +@@ -583,7 +583,7 @@ + char uplo = 'U'; + double norm = dlansy_(&cc, &uplo, &dim, matrix, &dim, dbl_2d_buf); + __CLPK_integer info; +- dpotrf_(&uplo, &dim, matrix, &dim, &info); ++ LAPACK_dpotrf(&uplo, &dim, matrix, &dim, &info); + if (info > 0) { + return 1; + } +@@ -592,7 +592,7 @@ + if (rcond < kMatrixSingularRcond) { + return 1; + } +- dpotri_(&uplo, &dim, matrix, &dim, &info); ++ LAPACK_dpotri(&uplo, &dim, matrix, &dim, &info); + return 0; + } + +@@ -639,7 +639,7 @@ + char uplo = 'U'; + double norm = dlansy_(&cc, &uplo, &dim, half_inverted, &dim, dbl_2d_buf); + __CLPK_integer info; +- dpotrf_(&uplo, &dim, half_inverted, &dim, &info); ++ LAPACK_dpotrf(&uplo, &dim, half_inverted, &dim, &info); + if (info > 0) { + return 1; + } +@@ -667,7 +667,7 @@ + void InvertSymmdefFmatrixSecondHalf(__CLPK_integer dim, uint32_t stride, double* half_inverted, float* inverted_result, __maybe_unused MatrixInvertBuf1* int_1d_buf, __maybe_unused double* dbl_2d_buf) { + char uplo = 'U'; + __CLPK_integer info; +- dpotri_(&uplo, &dim, half_inverted, &dim, &info); ++ LAPACK_dpotri(&uplo, &dim, half_inverted, &dim, &info); + const double* read_row = half_inverted; + float* write_row = inverted_result; + for (uint32_t row_idx = 0; row_idx != S_CAST(uint32_t, dim); ++row_idx) { +@@ -1348,14 +1348,14 @@ + char uplo = 'U'; + __CLPK_integer tmp_n = predictor_ct; + __CLPK_integer info; +- dpotrf_(&uplo, &tmp_n, xtx_inv, &tmp_n, &info); ++ LAPACK_dpotrf(&uplo, &tmp_n, xtx_inv, &tmp_n, &info); + if (info) { + return 1; + } + memcpy(fitted_coefs_phenomaj, xt_y_phenomaj, predictor_ct * pheno_ct * sizeof(double)); + dpotrs_(&uplo, &tmp_n, &pheno_ct, xtx_inv, &tmp_n, fitted_coefs_phenomaj, &tmp_n, &info); + assert(!info); +- dpotri_(&uplo, &tmp_n, xtx_inv, &tmp_n, &info); ++ LAPACK_dpotri(&uplo, &tmp_n, xtx_inv, &tmp_n, &info); + return (info != 0); + } + #endif // !NOLAPACK From a375372eeb67d79a08ccb12133933e412c7d8f20 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 8 Jun 2022 16:12:20 +0100 Subject: [PATCH 3934/9987] GROMACS-2021.3-foss-2021a-PLUMED-2.7.2 added --- .../GROMACS-2021.3-foss-2021a-PLUMED-2.7.2.eb | 96 +++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-PLUMED-2.7.2.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-PLUMED-2.7.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-PLUMED-2.7.2.eb new file mode 100644 index 00000000000..2eede738232 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-PLUMED-2.7.2.eb @@ -0,0 +1,96 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021.3' +_plumedver = '2.7.2' +versionsuffix = '-PLUMED-%s' % _plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI builds +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build +next to PLUMED.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021.3_skip_test_for_plumed.patch', +] +checksums = [ + 'e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6', # gromacs-2021.3.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch + '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', + # GROMACS-2021.3_skip_test_for_plumed.patch + 'c06d0a8c3e75b232224f46bc3b70e135c4c02ec4151712970f5edd85d890f018', +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('networkx', '2.5.1'), + ('PLUMED', _plumedver), +] +# PLUMED-2.7.2 does not officially support GROMACS-2021.3, but seems to work fine +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 68acf815efcfdfcaabe84df3fc316c1bb1d1a046 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 8 Jun 2022 16:24:58 +0100 Subject: [PATCH 3935/9987] switch Eigen to runtime dependency --- .../easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb index 1757c6c746b..6ba9ed258a5 100644 --- a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb @@ -19,10 +19,9 @@ source_urls = ['https://github.com/yixuan/spectra/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] checksums = ['919e3fbc8c539a321fd5a0766966922b7637cc52eb50a969241a997c733789f3'] -builddependencies = [ - ('CMake', '3.21.1'), - ('Eigen', '3.4.0'), -] +builddependencies = [('CMake', '3.21.1')] + +dependencies = [('Eigen', '3.4.0')] sanity_check_paths = { 'files': ['include/Spectra/SymEigsSolver.h'], From 50eb1309c751b7975cd63c7a40f766981760e90a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 8 Jun 2022 16:29:33 +0100 Subject: [PATCH 3936/9987] drop to GCC level --- .../g/GCTA/GCTA-1.94.0beta-GCC-11.2.0.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-GCC-11.2.0.eb new file mode 100644 index 00000000000..542e042e221 --- /dev/null +++ b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-GCC-11.2.0.eb @@ -0,0 +1,69 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CMakeMakeCp' + +name = 'GCTA' +version = '1.94.0beta' +_plink_commit = '3744540' + +homepage = 'https://yanglab.westlake.edu.cn/software/gcta/' +description = """ +GCTA (Genome-wide Complex Trait Analysis) is a software package, which was + initially developed to estimate the proportion of phenotypic variance explained + by all genome-wide SNPs for a complex trait but has been extensively extended + for many other analyses of data from genome-wide association studies (GWASs). +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = [ + { + 'source_urls': ['https://github.com/jianyangqt/gcta/archive'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/zhilizheng/plink-ng/archive'], + 'download_filename': '%s.tar.gz' % _plink_commit, + 'filename': 'plink-ng-%s.tar.gz' % _plink_commit, + 'extract_cmd': "tar xzvf %%s --strip-components 1 -C gcta-%s/submods/plink-ng" % version, + }, +] +patches = [ + 'GCTA-1.94.0beta_allow-BLAS-selection.patch', + 'GCTA-1.94.0beta_lapack-compatibility.patch', +] +checksums = [ + '9220a6c40f31e3b1ce3d25f7eee3d8c62403bee8d6ed624bd8b61891badcb14f', # GCTA-1.94.0beta.tar.gz + 'a7c70c237d49d64fc1668ced373036c09b41d7c61d0b8b24b47e2fb76474455d', # plink-ng-3744540.tar.gz + '320a5d82d12cf453f1396b228723ac18dc98e32bc459394dd4d712fc16b24747', # GCTA-1.94.0beta_allow-BLAS-selection.patch + '643282a2e2c02fc683431b673a4623a498129870431481d33d33e19a509026ce', # GCTA-1.94.0beta_lapack-compatibility.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), + # Eigen and SpectrA are header-only C++ libraries + ('Eigen', '3.4.0'), + ('SpectrA', '1.0.1'), +] + +dependencies = [ + ('Boost', '1.75.0'), + ('SQLite', '3.36'), + ('zstd', '1.5.0'), + ('GSL', '2.7'), + ('FlexiBLAS', '3.0.4'), +] + +preconfigopts = 'EIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include SPECTRA_LIB=$EBROOTSPECTRA/include' +preconfigopts += ' BOOST_LIB=$EBROOTBOOST/include ' + +files_to_copy = [(['gcta64'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/gcta64'], + 'dirs': [], +} + +sanity_check_commands = ["gcta64 | grep -e 'Analysis started'"] + +moduleclass = 'bio' From 68b6764cd1b47cf4a920f45117427d2c42a5e7a6 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 8 Jun 2022 16:37:56 +0100 Subject: [PATCH 3937/9987] Versionsuffix for CUDA version added --- ...1.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb | 102 ++++++++++++++++++ 1 file changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb new file mode 100644 index 00000000000..f5e901bf2ae --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb @@ -0,0 +1,102 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * Dugan Witherick +# * Christoph Siegert +# * J. Sassmannshausen +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021.5' +_plumedver = '2.8.0' +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = _cuda_suffix + '-PLUMED-%s' % _plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI builds +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build +next to PLUMED.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021.3_skip_test_for_plumed.patch', +] +checksums = [ + 'eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6', # gromacs-2021.5.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch + '7d39da0b431fbc9e94e857552246eb0ec892f26b13e519b3706785cc5e01a563', + # GROMACS-2021.3_skip_test_for_plumed.patch + 'c06d0a8c3e75b232224f46bc3b70e135c4c02ec4151712970f5edd85d890f018', +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('scikit-build', '0.11.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('networkx', '2.6.3'), + ('PLUMED', _plumedver), + ('CUDA', '11.4.1', '', True), + ('UCX-CUDA', '1.11.2', versionsuffix), +] + +# PLUMED-2.8.0 does not officially support GROMACS-2021.5, but seems to work fine +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.2.1', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['e24d507585e1a7808a5ee3ed04da5d6577f2a8961bbeafa7068528e00aa6b20d'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 2b1be9538a4a5892a8abbde967b615634ddff3f2 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 8 Jun 2022 17:31:17 +0100 Subject: [PATCH 3938/9987] Delete GCTA-1.94.0beta-foss-2021b.eb --- .../g/GCTA/GCTA-1.94.0beta-foss-2021b.eb | 69 ------------------- 1 file changed, 69 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb deleted file mode 100644 index 2fcbfe3bc14..00000000000 --- a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb +++ /dev/null @@ -1,69 +0,0 @@ -# Author: Jasper Grimm (UoY) -easyblock = 'CMakeMakeCp' - -name = 'GCTA' -version = '1.94.0beta' -_plink_commit = '3744540' - -homepage = 'https://yanglab.westlake.edu.cn/software/gcta/' -description = """ -GCTA (Genome-wide Complex Trait Analysis) is a software package, which was - initially developed to estimate the proportion of phenotypic variance explained - by all genome-wide SNPs for a complex trait but has been extensively extended - for many other analyses of data from genome-wide association studies (GWASs). -""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -sources = [ - { - 'source_urls': ['https://github.com/jianyangqt/gcta/archive'], - 'download_filename': 'v%(version)s.tar.gz', - 'filename': SOURCE_TAR_GZ, - }, - { - 'source_urls': ['https://github.com/zhilizheng/plink-ng/archive'], - 'download_filename': '%s.tar.gz' % _plink_commit, - 'filename': 'plink-ng-%s.tar.gz' % _plink_commit, - 'extract_cmd': "tar xzvf %%s --strip-components 1 -C gcta-%s/submods/plink-ng" % version, - }, -] -patches = [ - 'GCTA-1.94.0beta_allow-BLAS-selection.patch', - 'GCTA-1.94.0beta_lapack-compatibility.patch', -] -checksums = [ - '9220a6c40f31e3b1ce3d25f7eee3d8c62403bee8d6ed624bd8b61891badcb14f', # GCTA-1.94.0beta.tar.gz - 'a7c70c237d49d64fc1668ced373036c09b41d7c61d0b8b24b47e2fb76474455d', # plink-ng-3744540.tar.gz - '320a5d82d12cf453f1396b228723ac18dc98e32bc459394dd4d712fc16b24747', # GCTA-1.94.0beta_allow-BLAS-selection.patch - '643282a2e2c02fc683431b673a4623a498129870431481d33d33e19a509026ce', # GCTA-1.94.0beta_lapack-compatibility.patch -] - -builddependencies = [ - ('CMake', '3.21.1'), - # Eigen and SpectrA are header-only C++ libraries - ('Eigen', '3.4.0'), - ('SpectrA', '1.0.1'), -] - -dependencies = [ - ('Boost', '1.75.0'), - ('SQLite', '3.36'), - ('zstd', '1.5.0'), - ('GSL', '2.7'), - ('FlexiBLAS', '3.0.4'), -] - -preconfigopts = 'EIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include SPECTRA_LIB=$EBROOTSPECTRA/include' -preconfigopts += ' BOOST_LIB=$EBROOTBOOST/include ' - -files_to_copy = [(['gcta64'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/gcta64'], - 'dirs': [], -} - -sanity_check_commands = ["gcta64 | grep -e 'Analysis started'"] - -moduleclass = 'bio' From 3f4d272daf3c6c9e6569afd89e12caa266b8a9a4 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 8 Jun 2022 20:23:06 +0100 Subject: [PATCH 3939/9987] UCX_CUDA versionsuffix replaced with _cuda_suffix --- ...1.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb | 2 +- .../GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb | 102 ------------------ 2 files changed, 1 insertion(+), 103 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb index f5e901bf2ae..83341fe491d 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb @@ -73,7 +73,7 @@ dependencies = [ ('networkx', '2.6.3'), ('PLUMED', _plumedver), ('CUDA', '11.4.1', '', True), - ('UCX-CUDA', '1.11.2', versionsuffix), + ('UCX-CUDA', '1.11.2', _cuda_suffix), ] # PLUMED-2.8.0 does not officially support GROMACS-2021.5, but seems to work fine diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb deleted file mode 100644 index 662a10d5c55..00000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb +++ /dev/null @@ -1,102 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, -# Ghent University / The Francis Crick Institute -# Authors:: -# * Wiktor Jurkowski -# * Fotis Georgatos -# * George Tsouloupas -# * Kenneth Hoste -# * Adam Huffman -# * Ake Sandgren -# * Dugan Witherick -# * Christoph Siegert -# * J. Sassmannshausen -# License:: MIT/GPL - -name = 'GROMACS' -version = '2021.5' -_plumedver = '2.8.0' -versionsuffix = '-PLUMED-%s' % _plumedver -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://www.gromacs.org' -description = """ -GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the -Newtonian equations of motion for systems with hundreds to millions of -particles. - -This is a GPU enabled build, containing both MPI and threadMPI builds -for both single and double precision. - -It also contains the gmxapi extension for the single precision MPI build -next to PLUMED.""" - -toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = [ - 'https://ftp.gromacs.org/pub/gromacs/', - 'ftp://ftp.gromacs.org/pub/gromacs/', -] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', - 'GROMACS-2019_increase_test_timeout_for_GPU.patch', - 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', - 'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch', - 'GROMACS-2021.3_skip_test_for_plumed.patch', -] -checksums = [ - 'eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6', # gromacs-2021.5.tar.gz - # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch - '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', - # GROMACS-2019_increase_test_timeout_for_GPU.patch - '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', - # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch - 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', - # GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch - '7d39da0b431fbc9e94e857552246eb0ec892f26b13e519b3706785cc5e01a563', - # GROMACS-2021.3_skip_test_for_plumed.patch - 'c06d0a8c3e75b232224f46bc3b70e135c4c02ec4151712970f5edd85d890f018', -] - -builddependencies = [ - ('CMake', '3.22.1'), - ('scikit-build', '0.11.1'), - ('Doxygen', '1.9.1'), -] - -dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('networkx', '2.6.3'), - ('PLUMED', _plumedver), - ('CUDA', '11.4.1', '', True), - ('UCX-CUDA', '1.11.2', versionsuffix), -] - -# PLUMED-2.8.0 does not officially support GROMACS-2021.5, but seems to work fine -ignore_plumed_version_check = True - -exts_defaultclass = 'PythonPackage' - -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'use_pip': True, - 'download_dep_fail': True, - 'sanity_pip_check': True, -} - -exts_list = [ - ('gmxapi', '0.2.2.1', { - 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", - 'checksums': ['e24d507585e1a7808a5ee3ed04da5d6577f2a8961bbeafa7068528e00aa6b20d'], - }), -] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', -} - -moduleclass = 'bio' From f01e0c1eddc730f5a40e0ed4ae623ae298568f5a Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 9 Jun 2022 10:51:10 +0200 Subject: [PATCH 3940/9987] adding easyconfigs: InterProScan-5.55-88.0-foss-2021a.eb --- .../InterProScan-5.55-88.0-foss-2021a.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb new file mode 100644 index 00000000000..e59108c1dbd --- /dev/null +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb @@ -0,0 +1,61 @@ +easyblock = 'Binary' + +name = 'InterProScan' +version = '5.55-88.0' + +homepage = 'https://www.ebi.ac.uk/interpro/' +# also https://github.com/ebi-pf-team/interproscan +description = """InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines + different protein signature recognition methods into one resource [code only: libraries and external binaries + but no data].""" +# software_license = 'LicenseApachev2' + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/%(version)s/alt/', +] +sources = [ + '%(namelower)s-core-%(version)s.tar.gz', +] +checksums = [ + '661e62d6070f2507978ac8879e897e29df0478cbb387ba3c72ca36de52b1af02', # interproscan-core-5.55-88.0.tar.gz +] + +dependencies = [ + ('Java', '11', '', True), + ('Perl', '5.32.1'), + ('libgd', '2.3.1'), + ('Python', '3.9.5'), +] +# NOTE some analyses done by InterProScan require extra tools not included in the interproscan +# distribution because of license issues. +# Those tools are SignalP, TMHMM and Phobius. +# To allow InterProScan to use them you have to copy or symlink their executable in the +# corresponding %(installdir)s/bin/TOOL/VERSION/ folder. + +extract_sources = False + +# NOTE The data can be added manually afterwards with for example a symlink called *data* +# in %(installdir)s/ +# But simpler to use the InterProScan_data-*.eb file. The regular InterProScan data package +# does not contain the lookup_service data way too large! +install_cmd = 'tar xfz %(namelower)s-core-%(version)s.tar.gz && ' +install_cmd += 'cd %(namelower)s-%(version)s/ && ' +install_cmd += 'find . -type d -name bin32 | xargs rm -Rf && ' +install_cmd += 'rm -f test* && rm -Rf src/ && ' +install_cmd += 'chmod -x *.jar && ' +install_cmd += 'cp -r * %(installdir)s/ && cd .. && ' +install_cmd += 'rm -Rf %(namelower)s-%(version)s/' + +sanity_check_paths = { + 'files': ['interproscan-%(version_major)s.jar', 'interproscan.sh', 'interproscan.properties'], + 'dirs': ['bin', 'lib'], +} + +sanity_check_commands = ["interproscan.sh 2>&1 | grep 'Welcome to InterProScan-%(version)s'"] + +# also include top install directory in $PATH, to make interproscan.sh available +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 272d5f51935b254b99c6411b1a00e922299d55d0 Mon Sep 17 00:00:00 2001 From: Pierre Berthier Date: Thu, 9 Jun 2022 11:14:08 +0200 Subject: [PATCH 3941/9987] Update vt-0.57721-GCC-10.3.0.eb: removed superfluous commented out checksums --- easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb index fe97517832c..e3ae717ce00 100644 --- a/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb @@ -30,15 +30,6 @@ checksums = [ '1c170b7ba2a4d392830f64392075ff75bbbc29137fe9f2922aeb7345e2ab6298', # vt-0.57721_update_htsutils.patch ] -# checksums = [ -# '8f06d464ec5458539cfa30f81a034f47fe7f801146fe8ca80c14a3816b704e17', # 0.57721.tar.gz -# '5a31713ae7c5febf850eec294dbba45b6b240d832cb94bdfe9ee695fd13e45bb', # vt-0.57721_use-external-libs.patch -# '663525f5180a66d8817f271a69de1884576e2414d46b7ba93029d78f71d5b14c', # vt-0.57721_fix-Rmath-includes.patch -# '56d874d5c7d488761f25afb4ee3717c88dfd959ed76efb75a8531b8428d30ccd', # vt-0.57721_avoid-implicit-conversion.patch -# 'ba2cfc24a88a4291b2da634db49e18199c379eb95d3b3acac59556bc68c292df', # vt-0.57721_update-faidx.patch -# '4146282eb6ec852485f5a16e647da9c3b210450ceb5519b9b4a98bc52124469a', # vt-0.57721_fail-on-test-error.patch -# ] - builddependencies = [ ('binutils', '2.36.1'), ('TCLAP', '1.2.5'), From 6a02cf0d4574a808fedb8c99febb9ae9cc1e1119 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 9 Jun 2022 10:29:09 +0100 Subject: [PATCH 3942/9987] switch back to foss so BLAS env vars are defined --- ...A-1.94.0beta-GCC-11.2.0.eb => GCTA-1.94.0beta-foss-2021b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/g/GCTA/{GCTA-1.94.0beta-GCC-11.2.0.eb => GCTA-1.94.0beta-foss-2021b.eb} (97%) diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb similarity index 97% rename from easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-GCC-11.2.0.eb rename to easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb index 542e042e221..2fcbfe3bc14 100644 --- a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb @@ -13,7 +13,7 @@ GCTA (Genome-wide Complex Trait Analysis) is a software package, which was for many other analyses of data from genome-wide association studies (GWASs). """ -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'foss', 'version': '2021b'} sources = [ { From 020ecd2837e2258dd59cd802430395758cb0799c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 9 Jun 2022 10:32:37 +0100 Subject: [PATCH 3943/9987] drop from GCC to GCCcore --- ...ctrA-1.0.1-GCC-11.2.0.eb => SpectrA-1.0.1-GCCcore-11.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/SpectrA/{SpectrA-1.0.1-GCC-11.2.0.eb => SpectrA-1.0.1-GCCcore-11.2.0.eb} (94%) diff --git a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.2.0.eb similarity index 94% rename from easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb rename to easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.2.0.eb index 6ba9ed258a5..eab878fd91c 100644 --- a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.2.0.eb @@ -13,7 +13,7 @@ homepage = 'https://spectralib.org/' description = """Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.""" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/yixuan/spectra/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] From 199322cefef511c01f16a2607a6dd9ee2881acf0 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 9 Jun 2022 10:57:42 +0100 Subject: [PATCH 3944/9987] boost version --- easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb index 2fcbfe3bc14..4da0008b1b0 100644 --- a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-foss-2021b.eb @@ -47,7 +47,7 @@ builddependencies = [ ] dependencies = [ - ('Boost', '1.75.0'), + ('Boost', '1.77.0'), ('SQLite', '3.36'), ('zstd', '1.5.0'), ('GSL', '2.7'), From 1b7f71d2bf011f60842bce53cc17d1efc2c09aee Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 9 Jun 2022 11:15:33 +0100 Subject: [PATCH 3945/9987] add binutils builddepency --- .../easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.2.0.eb index eab878fd91c..afeaeacd9ed 100644 --- a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.2.0.eb @@ -19,7 +19,10 @@ source_urls = ['https://github.com/yixuan/spectra/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] checksums = ['919e3fbc8c539a321fd5a0766966922b7637cc52eb50a969241a997c733789f3'] -builddependencies = [('CMake', '3.21.1')] +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] dependencies = [('Eigen', '3.4.0')] From d07cbf9bc11760c7a5d80cc53fe309e2b5967dde Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 9 Jun 2022 12:41:07 +0100 Subject: [PATCH 3946/9987] adding easyconfigs: gfbf-2022.05.eb --- easybuild/easyconfigs/g/gfbf/gfbf-2022.05.eb | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2022.05.eb diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2022.05.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2022.05.eb new file mode 100644 index 00000000000..9c6c99c2e49 --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2022.05.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2022.05' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '11.3.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.2.0', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' From 7e88c53aa62580e2eb9423b9a4d699ba6da88930 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 9 Jun 2022 12:49:07 +0100 Subject: [PATCH 3947/9987] adding easyconfigs: GCTA-1.94.0beta-gfbf-2022.05.eb, SpectrA-1.0.1-GCCcore-11.3.0.eb --- .../g/GCTA/GCTA-1.94.0beta-gfbf-2022.05.eb | 68 +++++++++++++++++++ .../s/SpectrA/SpectrA-1.0.1-GCCcore-11.3.0.eb | 34 ++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022.05.eb create mode 100644 easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022.05.eb b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022.05.eb new file mode 100644 index 00000000000..8ea2cc2a1e2 --- /dev/null +++ b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022.05.eb @@ -0,0 +1,68 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CMakeMakeCp' + +name = 'GCTA' +version = '1.94.0beta' +_plink_commit = '3744540' + +homepage = 'https://yanglab.westlake.edu.cn/software/gcta/' +description = """ +GCTA (Genome-wide Complex Trait Analysis) is a software package, which was + initially developed to estimate the proportion of phenotypic variance explained + by all genome-wide SNPs for a complex trait but has been extensively extended + for many other analyses of data from genome-wide association studies (GWASs). +""" + +toolchain = {'name': 'gfbf', 'version': '2022.05'} + +sources = [ + { + 'source_urls': ['https://github.com/jianyangqt/gcta/archive'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/zhilizheng/plink-ng/archive'], + 'download_filename': '%s.tar.gz' % _plink_commit, + 'filename': 'plink-ng-%s.tar.gz' % _plink_commit, + 'extract_cmd': "tar xzvf %%s --strip-components 1 -C gcta-%s/submods/plink-ng" % version, + }, +] +patches = [ + 'GCTA-1.94.0beta_allow-BLAS-selection.patch', + 'GCTA-1.94.0beta_lapack-compatibility.patch', +] +checksums = [ + '9220a6c40f31e3b1ce3d25f7eee3d8c62403bee8d6ed624bd8b61891badcb14f', # GCTA-1.94.0beta.tar.gz + 'a7c70c237d49d64fc1668ced373036c09b41d7c61d0b8b24b47e2fb76474455d', # plink-ng-3744540.tar.gz + '320a5d82d12cf453f1396b228723ac18dc98e32bc459394dd4d712fc16b24747', # GCTA-1.94.0beta_allow-BLAS-selection.patch + '643282a2e2c02fc683431b673a4623a498129870431481d33d33e19a509026ce', # GCTA-1.94.0beta_lapack-compatibility.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), + # Eigen and SpectrA are header-only C++ libraries + ('Eigen', '3.4.0'), + ('SpectrA', '1.0.1'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('SQLite', '3.38.3'), + ('zstd', '1.5.2'), + ('GSL', '2.7'), +] + +preconfigopts = 'EIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include SPECTRA_LIB=$EBROOTSPECTRA/include' +preconfigopts += ' BOOST_LIB=$EBROOTBOOST/include ' + +files_to_copy = [(['gcta64'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/gcta64'], + 'dirs': [], +} + +sanity_check_commands = ["gcta64 | grep -e 'Analysis started'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3e7a193c7c3 --- /dev/null +++ b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# +# Fred Hutchinson Cancer Research Center - Seattle - Washington - US +# https://www.fredhutch.org +# John Dey +# +easyblock = 'CMakeMake' + +name = 'SpectrA' +version = '1.0.1' + +homepage = 'https://spectralib.org/' +description = """Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ + library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/yixuan/spectra/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['919e3fbc8c539a321fd5a0766966922b7637cc52eb50a969241a997c733789f3'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +dependencies = [('Eigen', '3.4.0')] + +sanity_check_paths = { + 'files': ['include/Spectra/SymEigsSolver.h'], + 'dirs': ['include/Spectra/LinAlg', 'share/spectra/cmake'], +} + +moduleclass = 'math' From 2b623474a3df0c11c17e20da116d85c978ef7e18 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Jun 2022 14:45:30 +0200 Subject: [PATCH 3948/9987] remove sklearn extension from uncertainty-calibration easyconfig, now provided by scikit-learn dependency itself --- .../uncertainty-calibration-0.0.9-foss-2021b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/u/uncertainty-calibration/uncertainty-calibration-0.0.9-foss-2021b.eb b/easybuild/easyconfigs/u/uncertainty-calibration/uncertainty-calibration-0.0.9-foss-2021b.eb index d9e514cc0d6..d3824b588e8 100644 --- a/easybuild/easyconfigs/u/uncertainty-calibration/uncertainty-calibration-0.0.9-foss-2021b.eb +++ b/easybuild/easyconfigs/u/uncertainty-calibration/uncertainty-calibration-0.0.9-foss-2021b.eb @@ -18,9 +18,6 @@ dependencies = [ use_pip = True exts_list = [ - ('sklearn', '0.0', { - 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], - }), ('parameterized', '0.8.1', { 'checksums': ['41bbff37d6186430f77f900d777e5bb6a24928a1c46fb1de692f8b52b8833b5c'], }), From bb25d9c069dae8e477fd4fa01eefab70293f3dcd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Jun 2022 15:29:56 +0200 Subject: [PATCH 3949/9987] adding easyconfigs: scikit-learn-1.0.1-intel-2021b.eb --- .../scikit-learn-1.0.1-intel-2021b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-intel-2021b.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-intel-2021b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-intel-2021b.eb new file mode 100644 index 00000000000..7e9d3d14695 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.1-intel-2021b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.0.1' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10') +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['ac2ca9dbb754d61cfe1c83ba8483498ef951d29b93ec09d6f002847f210a99da'], + 'modulename': 'sklearn', + }), + ('sklearn', '0.0', { # also install the meta-package, as other packages check for this + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }) +] + +moduleclass = 'data' From 471c21ffe686c47c082fd7126ae8f8f9577c002e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Jun 2022 20:08:53 +0200 Subject: [PATCH 3950/9987] avoid that pygmo v2.18.0 installs stuff in Python installation directory (fixes #15631) + add custom sanity check paths to pygmo easyconfigs --- easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb | 5 +++++ easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb | 8 ++++++++ 2 files changed, 13 insertions(+) diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb index 9b5c672dad3..8e5e9cc5010 100644 --- a/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.16.1-foss-2020b.eb @@ -46,6 +46,11 @@ exts_list = [ }), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pygmo'], +} + sanity_pip_check = True moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb index f484449a7e2..ef02c9437a7 100644 --- a/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021a.eb @@ -26,6 +26,9 @@ dependencies = [ ('networkx', '2.5.1'), ] +# make sure that all files are installed in the correct location (-DCMAKE_INSTALL_PREFIX is not enough)... +configopts = "-DPYGMO_INSTALL_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" + runtest = False exts_defaultclass = 'PythonPackage' @@ -46,6 +49,11 @@ exts_list = [ }), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pygmo'], +} + sanity_pip_check = True moduleclass = 'lib' From dc466a706cb66869ab66bc1b9a1c647e09920ad2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jun 2022 10:46:56 +0200 Subject: [PATCH 3951/9987] use system toolchain in STAR-CCM+ easyconfig --- easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-13.04.011.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-13.04.011.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-13.04.011.eb index d8bd830cd11..916287a5174 100644 --- a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-13.04.011.eb +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-13.04.011.eb @@ -5,7 +5,7 @@ homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' description = """STAR-CCM+ is a complete multidisciplinary platform for the simulation of products and designs operating under real-world conditions.""" -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM sources = ['STAR-CCM+%(version)s_01_linux-x86_64-r8.tar.gz'] checksums = ['aa1e41a2dbfc939612b2c2f1aa121558ff5213067757705722d01c1ee2de0b65'] From 09913835aeafbc157684ef6d521a2a18805e577e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jun 2022 11:35:33 +0200 Subject: [PATCH 3952/9987] adding easyconfigs: cuDNN-8.4.1.50-CUDA-11.7.0.eb --- .../c/cuDNN/cuDNN-8.4.1.50-CUDA-11.7.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.7.0.eb new file mode 100644 index 00000000000..26b8bc8e5c3 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.7.0.eb @@ -0,0 +1,39 @@ +name = 'cuDNN' +version = '8.4.1.50' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN 8.4.1 is not specific to CUDA 11.6, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%(version)s/local_installers/11.6/'] +local_cudnn_cuda_version = '%(version)s_cuda11.6' +sources = ['%(namelower)s-linux-%(cudnnarch)s-%(version)s_cuda11.6-archive.tar.xz'] +checksums = [ + { + '%(namelower)s-linux-x86_64-%(version)s_cuda11.6-archive.tar.xz': + 'ec96d2376d81fca42bdd3d4c3d705a99b29a065bab57f920561c763e29c67d01', + '%(namelower)s-linux-ppc64le-%(version)s_cuda11.6-archive.tar.xz': + '8b806cbfdc81352bf76716d1e53b42537665d110c6ffc068be910505c10e1b98', + '%(namelower)s-linux-sbsa-%(version)s_cuda11.6-archive.tar.xz': + '0b1b9fac5b78974e2fdaaa74843db18f636ce8f3d999d62ff2a615b9978fc360', + } +] + +dependencies = [('CUDA', '11.7.0')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From b4f0f9536ea9466fbdbf192fa814f4b39a341394 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 10 Jun 2022 11:34:06 +0100 Subject: [PATCH 3953/9987] Removing GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb and replace with correct GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb --- .../GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb | 99 ------------------- 1 file changed, 99 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb deleted file mode 100644 index f9233c3c161..00000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb +++ /dev/null @@ -1,99 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, -# Ghent University / The Francis Crick Institute -# Authors:: -# * Wiktor Jurkowski -# * Fotis Georgatos -# * George Tsouloupas -# * Kenneth Hoste -# * Adam Huffman -# * Ake Sandgren -# * Dugan Witherick -# * Christoph Siegert -# * J. Sassmannshausen -# License:: MIT/GPL - -name = 'GROMACS' -version = '2021.5' -_plumedver = '2.8.0' -versionsuffix = '-PLUMED-%s' % _plumedver - -homepage = 'https://www.gromacs.org' -description = """ -GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the -Newtonian equations of motion for systems with hundreds to millions of -particles. - -This is a CPU only build, containing both MPI and threadMPI builds -for both single and double precision. - -It also contains the gmxapi extension for the single precision MPI build -next to PLUMED.""" - -toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = [ - 'https://ftp.gromacs.org/pub/gromacs/', - 'ftp://ftp.gromacs.org/pub/gromacs/', -] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', - 'GROMACS-2019_increase_test_timeout_for_GPU.patch', - 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', - 'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch', - 'GROMACS-2021.3_skip_test_for_plumed.patch', -] -checksums = [ - 'eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6', # gromacs-2021.5.tar.gz - # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch - '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', - # GROMACS-2019_increase_test_timeout_for_GPU.patch - '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', - # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch - 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', - # GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch - '7d39da0b431fbc9e94e857552246eb0ec892f26b13e519b3706785cc5e01a563', - # GROMACS-2021.3_skip_test_for_plumed.patch - 'c06d0a8c3e75b232224f46bc3b70e135c4c02ec4151712970f5edd85d890f018', -] - -builddependencies = [ - ('CMake', '3.22.1'), - ('scikit-build', '0.11.1'), - ('Doxygen', '1.9.1'), -] - -dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('networkx', '2.6.3'), - ('PLUMED', _plumedver), -] - -# PLUMED-2.7.3 does not officially support GROMACS-2021.5, but seems to work fine -ignore_plumed_version_check = True - -exts_defaultclass = 'PythonPackage' - -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'use_pip': True, - 'download_dep_fail': True, - 'sanity_pip_check': True, -} - -exts_list = [ - ('gmxapi', '0.2.2.1', { - 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", - 'checksums': ['e24d507585e1a7808a5ee3ed04da5d6577f2a8961bbeafa7068528e00aa6b20d'], - }), -] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', -} - -moduleclass = 'bio' From 8632d9d477acf6aeaeda430a3d08818db4872134 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 10 Jun 2022 11:42:48 +0100 Subject: [PATCH 3954/9987] Correct GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb added --- .../GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb | 99 +++++++++++++++++++ 1 file changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb new file mode 100644 index 00000000000..f9233c3c161 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-PLUMED-2.8.0.eb @@ -0,0 +1,99 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * Dugan Witherick +# * Christoph Siegert +# * J. Sassmannshausen +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021.5' +_plumedver = '2.8.0' +versionsuffix = '-PLUMED-%s' % _plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI builds +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build +next to PLUMED.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021.3_skip_test_for_plumed.patch', +] +checksums = [ + 'eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6', # gromacs-2021.5.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch + '7d39da0b431fbc9e94e857552246eb0ec892f26b13e519b3706785cc5e01a563', + # GROMACS-2021.3_skip_test_for_plumed.patch + 'c06d0a8c3e75b232224f46bc3b70e135c4c02ec4151712970f5edd85d890f018', +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('scikit-build', '0.11.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('networkx', '2.6.3'), + ('PLUMED', _plumedver), +] + +# PLUMED-2.7.3 does not officially support GROMACS-2021.5, but seems to work fine +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.2.1', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['e24d507585e1a7808a5ee3ed04da5d6577f2a8961bbeafa7068528e00aa6b20d'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 3c81c78f4b64bfcc158e70533be5de5e7859af16 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jun 2022 14:20:26 +0200 Subject: [PATCH 3955/9987] fix source URLs in easyconfig for cuDNN 8.4.1.50 with CUDA 11.7.0 --- easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.7.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.7.0.eb index 26b8bc8e5c3..9915457ce82 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.7.0.eb @@ -10,8 +10,10 @@ toolchain = SYSTEM # note: cuDNN 8.4.1 is not specific to CUDA 11.6, # see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions -source_urls = ['https://developer.download.nvidia.com/compute/redist/cudnn/v%(version)s/local_installers/11.6/'] -local_cudnn_cuda_version = '%(version)s_cuda11.6' +local_short_ver = '.'.join(version.split('.')[:3]) +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/11.6/' % local_short_ver, +] sources = ['%(namelower)s-linux-%(cudnnarch)s-%(version)s_cuda11.6-archive.tar.xz'] checksums = [ { From 651124e3ca19165fe3ab68ff9d88bbbf242923d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jun 2022 15:27:40 +0200 Subject: [PATCH 3956/9987] avoid sed command to specify $CC + symlink bin/G-PhoCS + add sanity check commands for G-PhoCS --- ...S-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 29d461af0fd..c9bb146c289 100644 --- a/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/G-PhoCS/G-PhoCS-1.2.3-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -19,13 +19,21 @@ checksums = ['e3854591f68b2111d5095f64221007456ae7a601bf760a21bd00ca5c21273776'] parallel = 1 -prebuildopts = 'sed -i "/^CC=.*/d" Makefile && ' +buildopts = 'CC="$CC"' -files_to_copy = [(['bin/readTrace', 'bin/G-PhoCS-1-2-3'], 'bin')] +local_dash_ver = '-'.join(version.split('.')) +files_to_copy = [(['bin/readTrace', 'bin/G-PhoCS-%s' % local_dash_ver], 'bin')] + +postinstallcmds = ["cd %%(installdir)s/bin && ln -s G-PhoCS-%s G-PhoCS" % local_dash_ver] sanity_check_paths = { - 'files': ['bin/readTrace', 'bin/G-PhoCS-1-2-3'], + 'files': ['bin/G-PhoCS', 'bin/readTrace'], 'dirs': [], } +sanity_check_commands = [ + "G-PhoCS --help | grep 'G-Phocs ver %(version)s'", + "readTrace --help", +] + moduleclass = 'bio' From 0f55a510d099549f15bc0c6d3f10d4c2a281d06f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jun 2022 21:39:52 +0200 Subject: [PATCH 3957/9987] {tools}[foss/2021b] Ray-project v1.13.0, redis-py v4.3.3 w/ Python 3.9.6 --- .../Ray-project-1.13.0-foss-2021b.eb | 54 +++++++++++++++++++ .../r/redis-py/redis-py-4.3.3-foss-2021b.eb | 38 +++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ray-project/Ray-project-1.13.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/r/redis-py/redis-py-4.3.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-1.13.0-foss-2021b.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.13.0-foss-2021b.eb new file mode 100644 index 00000000000..d11cdc2b662 --- /dev/null +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.13.0-foss-2021b.eb @@ -0,0 +1,54 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'Ray-project' +version = '1.13.0' + +homepage = "https://docs.ray.io/en/latest/" +description = "Ray is a fast and simple framework for building and running distributed applications." + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('protobuf-python', '3.17.3'), + ('PyYAML', '5.4.1'), + ('redis-py', '4.3.3'), +] + +use_pip = True + +exts_list = [ + ('grpcio', '1.43.0', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], + }), + ('aiosignal', '1.2.0', { + 'checksums': ['78ed67db6c7b7ced4f98e495e572106d5c432a93e1ddd1bf475e1dc05f5b7df2'], + }), + ('frozenlist', '1.3.0', { + 'checksums': ['ce6f2ba0edb7b0c1d8976565298ad2deba6f8064d2bebb6ffce2ca896eb35b0b'], + }), + ('Ray', version, { + 'source_tmpl': '%(namelower)s-%(version)s-cp39-cp39-manylinux2014_x86_64.whl', + 'checksums': ['ba0829d495dec0bc90a72169f93e4cb004962a37df4d9b0df23004ebefb6d221'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ray'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'ray --help' +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-4.3.3-foss-2021b.eb b/easybuild/easyconfigs/r/redis-py/redis-py-4.3.3-foss-2021b.eb new file mode 100644 index 00000000000..003261a26c7 --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-4.3.3-foss-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'redis-py' +version = '4.3.3' + +homepage = 'https://github.com/redis/redis-py' +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('typing-extensions', '3.10.0.2'), + ('Redis', '6.2.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('async-timeout', '4.0.2', { + 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['8ca81c58dac19fb3c8efa14a95b8652da1c712bca5bc221f61b0d98a5c881fbb'], + }), +] + +moduleclass = "data" From ceb214f08a128bba07ce3378ef56461c0c9eb5ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Jun 2022 22:22:08 +0200 Subject: [PATCH 3958/9987] make binutils a build-only dependency for WildMagic 5.17 --- .../easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb index 0032bcf724f..bfe2c59c4b8 100644 --- a/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/w/WildMagic/WildMagic-5.17-GCCcore-10.3.0.eb @@ -12,8 +12,11 @@ source_urls = ['https://www.geometrictools.com/Downloads/'] sources = ['WildMagic5p17.zip'] checksums = ['b2caf7aa0c5309eb40965ed26439388dc1c93eb632312b40573f83e4746a9ecf'] -dependencies = [ +builddependencies = [ ('binutils', '2.36.1'), +] + +dependencies = [ ('freeglut', '3.2.1'), ] From f8f55ccf4907cd2afc90cb3ad63bec4c5daaab28 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 11 Jun 2022 11:12:10 +0100 Subject: [PATCH 3959/9987] adding easyconfigs: RNA-SeQC-2.4.2-foss-2021a.eb and patches: RNA-SeQC-2.4.2_Makefile.patch, RNA-SeQC-2.4.2_rle_auxtab-gcc-10.patch --- .../r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb | 68 +++++++++++++++++++ .../r/RNA-SeQC/RNA-SeQC-2.4.2_Makefile.patch | 23 +++++++ .../RNA-SeQC-2.4.2_rle_auxtab-gcc-10.patch | 30 ++++++++ 3 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2_Makefile.patch create mode 100644 easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2_rle_auxtab-gcc-10.patch diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb new file mode 100644 index 00000000000..4322f628948 --- /dev/null +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb @@ -0,0 +1,68 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'RNA-SeQC' +version = '2.4.2' +versionsuffix = '' + +homepage = "https://github.com/getzlab/rnaseqc" +description = """Fast, efficient RNA-Seq metrics for quality control and process optimization""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'extra_cflags': '-fpermissive'} + +dependencies = [ + ('bx-python', '0.8.11'), + ('bzip2', '1.0.8'), + ('IPython', '7.25.0'), + ('matplotlib', '3.4.2'), + ('pyBigWig', '0.3.18'), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Seaborn', '0.11.2'), + ('Boost', '1.76.0'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pycryptodomex', '3.9.8', { + 'modulename': 'Cryptodome', + 'checksums': ['48cc2cfc251f04a6142badeb666d1ff49ca6fdfc303fd72579f62b768aaa52b9'], + }), + ('rsa', '4.6', { + 'checksums': ['109ea5a66744dd859bf16fe904b8d8b627adafb9408753161e766a92e7d681fa'], + }), + ('agutil', '4.1.1', { + 'preinstallopts': "sed -i 's/package\.req/package.requirement/g' setup.py &&", + 'checksums': ['e58ed53ae209007328311603bd6e05e8cd2c509204b5e542c87f971a2530fb0d'], + }), + ('qtl', '0.1.8', { + 'checksums': ['8fdb99cda1ceff578a233db6c15a944fa57b43a2826af41c292e36848906117b'], + }), + ('rnaseqc', '0.0.3', { + # Build RNA-SeQC in the preinstall opts for the assocaited Python package + # RNA-SeQC bundles SeqLib, with HTSlib and BWA. These are old versions so we cannot use deps here + # rnaseqc version is from python/rnaseqc/__init__.py in the RNA-SeQC source code + 'patches': [ + 'RNA-SeQC-2.4.2_Makefile.patch', + 'RNA-SeQC-2.4.2_rle_auxtab-gcc-10.patch', + ], + 'source_tmpl': 'rnaseqc.v2.4.2.full_source.tar.gz', + 'source_urls': ['https://github.com/getzlab/rnaseqc/releases/download/v2.4.2'], + 'checksums': [ + 'b214151408696430aead56921b255e2b09efe5f6087a68446deae399227a1303', # rnaseqc.v2.4.2.full_source.tar.gz + '05b537eeef398646f51552c1dd26333e268b9b9eb3af2148681cb40ea0a5e4ba', # RNA-SeQC-2.4.2_Makefile.patch + # RNA-SeQC-2.4.2_rle_auxtab-gcc-10.patch + 'efb9ab63932bf25f3589de1e8f0c17bc1ef5ae928ba73e55d430b8a9761209cb', + ], + 'preinstallopts': "make && mkdir -p %(installdir)s/bin && cp rnaseqc %(installdir)s/bin/. && cd python &&", + }), +] + +sanity_check_commands = ["rnaseqc --version"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2_Makefile.patch b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2_Makefile.patch new file mode 100644 index 00000000000..0a7844d6a71 --- /dev/null +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2_Makefile.patch @@ -0,0 +1,23 @@ +Add the Boost include and library paths; add -fpermissive to fix a compile failure +Patch by Simon Branford (University of Birmingham) +--- Makefile.orig 2022-06-01 14:25:59.350419000 +0100 ++++ Makefile 2022-06-10 10:02:39.517207931 +0100 +@@ -1,7 +1,7 @@ + #Set inclusion paths here (if boost, bamtools, or args are installed outside your path) +-INCLUDE_DIRS=-ISeqLib -ISeqLib/htslib/ ++INCLUDE_DIRS=-ISeqLib -ISeqLib/htslib/ -I${EBROOTBOOST}/include + #Set library paths here (if boost or bamtools are installed outside your path) +-LIBRARY_PATHS= ++LIBRARY_PATHS=-L${EBROOTBOOST}/lib + #Set to 0 if you encounter linker errors regarding strings from the bamtools library + ABI=1 + #Provide full paths here to .a archives for libraries which should be statically linked +@@ -11,7 +11,7 @@ + + CC=g++ + STDLIB=-std=c++14 +-CFLAGS=-Wall $(STDLIB) -D_GLIBCXX_USE_CXX11_ABI=$(ABI) -O3 ++CFLAGS=-Wall $(STDLIB) -D_GLIBCXX_USE_CXX11_ABI=$(ABI) -O3 -fpermissive + SOURCES=BED.cpp Expression.cpp GTF.cpp RNASeQC.cpp Metrics.cpp Fasta.cpp BamReader.cpp + SRCDIR=src + OBJECTS=$(SOURCES:.cpp=.o) diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2_rle_auxtab-gcc-10.patch b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2_rle_auxtab-gcc-10.patch new file mode 100644 index 00000000000..387913e3e06 --- /dev/null +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2_rle_auxtab-gcc-10.patch @@ -0,0 +1,30 @@ +Based off the BWA patch in https://github.com/lh3/bwa/pull/267 +Patch by Simon Branford (University of Birmingham) +diff --git a/SeqLib/bwa/rle.h b/SeqLib/bwa/rle.h +index 0d594846..4f8946dc 100644 +--- a/SeqLib/bwa/rle.h ++++ b/SeqLib/bwa/rle.h +@@ -30,7 +30,7 @@ extern "C" { + *** 43+3 codec *** + ******************/ + +-const uint8_t rle_auxtab[8]; ++extern const uint8_t rle_auxtab[8]; + + #define RLE_MIN_SPACE 18 + #define rle_nptr(block) ((uint16_t*)(block)) + +diff --git a/SeqLib/fermi-lite/rle.h b/SeqLib/fermi-lite/rle.h +index 0d594846..4f8946dc 100644 +--- a/SeqLib/fermi-lite/rle.h ++++ b/SeqLib/fermi-lite/rle.h +@@ -30,7 +30,7 @@ extern "C" { + *** 43+3 codec *** + ******************/ + +-const uint8_t rle_auxtab[8]; ++extern const uint8_t rle_auxtab[8]; + + #define RLE_MIN_SPACE 18 + #define rle_nptr(block) ((uint16_t*)(block)) + From 6cc5d900803d6731fbd6ea7e96e4f14ac0ccebbd Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 12 Jun 2022 14:27:47 +0100 Subject: [PATCH 3960/9987] adding easyconfigs: nettle-3.8-GCCcore-11.3.0.eb, Xvfb-21.1.3-GCCcore-11.3.0.eb --- .../n/nettle/nettle-3.8-GCCcore-11.3.0.eb | 38 ++++++ .../x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb | 111 ++++++++++++++++++ 2 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f7c9790fb40 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.8-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.8' + +homepage = 'https://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['7576c68481c198f644b08c160d1a4850ba9449e308069455b5213319f234e8e6'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = '--disable-openssl ' # openssl is just used for the nettle-openssl example and requires openssl 1.1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..06a745157eb --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '21.1.3' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Python', '3.10.4', '-bare'), +] + +dependencies = [ + ('X11', '20220504'), + ('pixman', '0.40.0'), + ('libdrm', '2.4.110'), + ('Mesa', '22.0.3'), + ('nettle', '3.8'), + ('libunwind', '1.6.2'), + ('XZ', '5.2.5'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.2', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['4a5af55e670713024639a7f7d10826d905d86faf574cd77e0f5aef2d00e70168'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.3.2', { + 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], + }), + ('font-misc-misc', '1.1.2', { + 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], + 'preconfigopts': local_font_misc_preconfigopts, + }), + ('xkbcomp', '1.4.5', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['e88a4d86b9925ea1e8685dd5ea29c815abafb8ddf19bf5f1a1e0650839252c23'], + }), + ('xkeyboard-config', '2.36', { + 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['1f1bb1292a161d520a3485d378609277d108cd07cde0327c16811ff54c3e1595'], + 'configopts': '--with-xkb-rules-symlink=xorg', + }), + ('xauth', '1.1', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['e9fce796c8c5c9368594b9e8bbba237fb54b6615f5fd60e8d0a5b3c52a92c5ef'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual/xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + 'c52403a66935092da86a18052ffdcb93a2762a146901f63c1261744a708b12e2', # xorg-server-21.1.3.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' From d8ad74511219c7e5daf91339a7dccd676203a4f8 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 12 Jun 2022 14:28:20 +0100 Subject: [PATCH 3961/9987] adding easyconfigs: NLopt-2.7.1-GCCcore-11.3.0.eb --- .../n/NLopt/NLopt-2.7.1-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e9b6611e060 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.7.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['db88232fa5cef0ff6e39943fc63ab6074208831dc0031cf1545f6ecd31ae2a1a'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' From e1e5e7c6333dbf47b42482f923af78c3b943e797 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 12 Jun 2022 14:28:41 +0100 Subject: [PATCH 3962/9987] adding easyconfigs: UDUNITS-2.2.28-GCCcore-11.3.0.eb --- .../UDUNITS/UDUNITS-2.2.28-GCCcore-11.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e07aab5a73a --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.28' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/%(version)s/', + 'https://sources.easybuild.io/u/UDUNITS/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['590baec83161a3fd62c00efa66f6113cec8a7c461e3f61a5182167e0cc5d579e'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('expat', '2.4.8')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From eac5757e1b0841760b1eb9c40ede6f5a95bb7cb5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 12 Jun 2022 15:40:30 +0100 Subject: [PATCH 3963/9987] add libxslt ec; add libxcvt to Xvfb ec; xkeyboard-config and libxcvt are MesonNinja builds; add extra build deps --- .../libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ .../x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb | 16 +++++++-- 2 files changed, 48 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..49e57192bf3 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.34' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('zlib', '1.2.12'), + ('libxml2', '2.9.13'), +] + +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb index 06a745157eb..35ddaebf9e8 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb @@ -12,7 +12,12 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} builddependencies = [ ('binutils', '2.38'), ('pkgconf', '1.8.0'), - ('Python', '3.10.4', '-bare'), + ('Python', '3.10.4'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('libxslt', '1.1.34'), + ('gettext', '0.21'), + ('Bison', '3.8.2'), ] dependencies = [ @@ -72,15 +77,22 @@ components = [ 'checksums': ['e88a4d86b9925ea1e8685dd5ea29c815abafb8ddf19bf5f1a1e0650839252c23'], }), ('xkeyboard-config', '2.36', { + 'easyblock': 'MesonNinja', 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], 'sources': [SOURCE_TAR_XZ], 'checksums': ['1f1bb1292a161d520a3485d378609277d108cd07cde0327c16811ff54c3e1595'], - 'configopts': '--with-xkb-rules-symlink=xorg', + 'configopts': '-Dxorg-rules-symlinks=true', }), ('xauth', '1.1', { 'source_urls': ['https://www.x.org/releases/individual/app/'], 'checksums': ['e9fce796c8c5c9368594b9e8bbba237fb54b6615f5fd60e8d0a5b3c52a92c5ef'], }), + ('libxcvt', '0.1.1', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/lib/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['27ebce180d355f94c1992930bedb40a36f6d7312ee50bf7f0acbcd22f33e8c29'], + }), (name, version, { 'source_urls': ['https://www.x.org/releases/individual/xserver/'], 'sources': ['xorg-server-%(version)s.tar.gz'], From 4af6c820ae5c37bae0ce9a8b0b214d566d2f9360 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 12 Jun 2022 16:39:31 +0100 Subject: [PATCH 3964/9987] adding easyconfigs: GLPK-5.0-GCCcore-11.3.0.eb --- .../g/GLPK/GLPK-5.0-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..685f4c6618f --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '5.0' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a1013eebb50f728fc601bdd833b0b2870333c3b3e5a816eeba921d95bec6f15'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('GMP', '6.2.1')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' From 6e4b94090cbd1f3ba9bbfc3d4da390cee297f460 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 12 Jun 2022 16:40:55 +0100 Subject: [PATCH 3965/9987] adding easyconfigs: MPFR-4.1.0-GCCcore-11.3.0.eb --- .../m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7d929a2fd1b --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '4.1.0' + +homepage = 'https://www.mpfr.org' + +description = """ + The MPFR library is a C library for multiple-precision floating-point + computations with correct rounding. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +runtest = 'check' + +# copy libmpfr.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a src/.libs/libmpfr.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' From 7596a555f50781d5847be324fd40bb5bf95e3917 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 12 Jun 2022 16:42:48 +0100 Subject: [PATCH 3966/9987] adding easyconfigs: libgit2-1.4.3-GCCcore-11.3.0.eb --- .../l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c1884e0bb10 --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.4.3' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'libgit2' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f48b961e463a9e4e7e7e58b21a0fb5a9b2a1d24d9ba4d15870a0c9b8ad965163'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('PCRE', '8.45'), + ('OpenSSL', '1.1', '', True), +] + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], + 'dirs': [] +} + +moduleclass = 'devel' From e0e0dbe06236a2f94981e0aca57e395c19550de7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 12 Jun 2022 17:05:20 +0100 Subject: [PATCH 3967/9987] adding easyconfigs: ImageMagick-7.1.0-37-GCCcore-11.3.0.eb, LittleCMS-2.13.1-GCCcore-11.3.0.eb, JasPer-2.0.33-GCCcore-11.3.0.eb, Ghostscript-9.56.1-GCCcore-11.3.0.eb --- .../Ghostscript-9.56.1-GCCcore-11.3.0.eb | 58 +++++++++++++++++++ .../ImageMagick-7.1.0-37-GCCcore-11.3.0.eb | 40 +++++++++++++ .../j/JasPer/JasPer-2.0.33-GCCcore-11.3.0.eb | 36 ++++++++++++ .../LittleCMS-2.13.1-GCCcore-11.3.0.eb | 26 +++++++++ 4 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.56.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.33-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.13.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.56.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.56.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..51219d52026 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.56.1-GCCcore-11.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.56.1' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1598b9a38659cce8448d42a73054b2f9cbfcc40a9b97eeec5f22d4d6cd1de8e6'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('libjpeg-turbo', '2.1.3'), + ('expat', '2.4.8'), + ('GLib', '2.72.1'), + ('cairo', '1.17.4'), + ('LibTIFF', '4.3.0'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +# Avoid race condition in build if too much parallelism is used +maxparallel = 4 + +postinstallcmds = [ + # build and install shared libs + "make so && make soinstall", + # install header files + "mkdir -p %(installdir)s/include/ghostscript", + "install -v -m644 base/*.h %(installdir)s/include/ghostscript", + "install -v -m644 psi/*.h %(installdir)s/include/ghostscript", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/ghostscript', 'include/ghostscript', 'share/man'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9127abd64dc --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.1.0-37' + +homepage = 'https://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/ImageMagick/ImageMagick/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a54888a1a46dbb808705a3e6c6b5ecb93ee30189a8ae6ea0f02300a0ab0d0996'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20220504'), + ('Ghostscript', '9.56.1'), + ('JasPer', '2.0.33'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('LittleCMS', '2.13.1'), +] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', + 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.33-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.33-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ff6ab7548cf --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.33-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.33' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['38b8f74565ee9e7fec44657e69adb5c9b2a966ca5947ced5717cde18a7d2eca6'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.13.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.13.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fd89cefd7af --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.13.1-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.13.1' + +homepage = 'https://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%s/' % '.'.join(version.split('.')[:2])] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['d473e796e7b27c5af01bd6d1552d42b45b43457e7182ce9903f38bb748203b88'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('libjpeg-turbo', '2.1.3')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' From 3e2721b027ef87e8f40b7e2ab1e67902fe276329 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 12 Jun 2022 18:22:27 +0100 Subject: [PATCH 3968/9987] adding easyconfigs: nodejs-16.15.1-GCCcore-11.3.0.eb --- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3fe69b1af4c --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '16.15.1' # LTS on 2022-06-12 +local_libversion = '93' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['308aee7149c4092a53c87c28ef49e23a8d1606119e79ae68333062e2a1f94208'] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4', '-bare'), +] + +configopts = [ + '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library + '--shared --with-intl=none', # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +postinstallcmds = [ + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'dirs': ['lib/node_modules', 'include/node'] +} + +moduleclass = 'lang' From c3fc3e8ea38b16c2d315e723e870b72f08255d1a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 13 Jun 2022 11:52:19 +0100 Subject: [PATCH 3969/9987] adding easyconfigs: ont-fast5-api-4.0.2-foss-2021b.eb, parasail-2.5-GCC-11.2.0.eb, pyfaidx-0.7.0-GCCcore-11.2.0.eb, pyspoa-0.0.8-GCC-11.2.0.eb, spoa-4.0.7-GCC-11.2.0.eb, python-parasail-1.2.4-foss-2021b.eb, WhatsHap-1.4-foss-2021b.eb --- .../ont-fast5-api-4.0.2-foss-2021b.eb | 43 +++++++++++++++ .../p/parasail/parasail-2.5-GCC-11.2.0.eb | 27 ++++++++++ .../p/pyfaidx/pyfaidx-0.7.0-GCCcore-11.2.0.eb | 30 +++++++++++ .../p/pyspoa/pyspoa-0.0.8-GCC-11.2.0.eb | 52 +++++++++++++++++++ .../python-parasail-1.2.4-foss-2021b.eb | 32 ++++++++++++ .../s/spoa/spoa-4.0.7-GCC-11.2.0.eb | 29 +++++++++++ .../w/WhatsHap/WhatsHap-1.4-foss-2021b.eb | 48 +++++++++++++++++ 7 files changed, 261 insertions(+) create mode 100644 easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.2-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/parasail/parasail-2.5-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.2-foss-2021b.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.2-foss-2021b.eb new file mode 100644 index 00000000000..3c150b21b73 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.0.2-foss-2021b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '4.0.2' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + (name, version, { + 'checksums': ['452920ee9976e43cfa0abdee57ce918908050a8be590e5901a3ec1404e135fd6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/compress_fast5', 'bin/fast5_subset', 'bin/multi_to_single_fast5', 'bin/single_to_multi_fast5'], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.5-GCC-11.2.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.5-GCC-11.2.0.eb new file mode 100644 index 00000000000..3c6c53d248d --- /dev/null +++ b/easybuild/easyconfigs/p/parasail/parasail-2.5-GCC-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'parasail' +version = '2.5' + +homepage = 'https://github.com/jeffdaily/parasail' +description = """parasail is a SIMD C (C99) library containing implementations + of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global + pairwise sequence alignment algorithms. """ + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +# https://github.com/jeffdaily/parasail +github_account = 'jeffdaily' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['68ff83c8378f5d9aa8c4618096757e2c5d5c506ce818dcdbb364247d562997b0'] + +builddependencies = [('CMake', '3.21.1')] + +sanity_check_paths = { + 'files': ['bin/parasail_aligner', 'bin/parasail_stats', + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a2af09931ca --- /dev/null +++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.0-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pyfaidx' +version = '0.7.0' + +homepage = 'https://pypi.python.org/pypi/pyfaidx' +description = "pyfaidx: efficient pythonic random access to fasta subsequences" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9ad5cc9381f0de9c43d4bdec0faf106b828cdfb6f8150ec71cab2ca7c8bee770'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/faidx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["faidx --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-11.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-11.2.0.eb new file mode 100644 index 00000000000..c2b2e7caac2 --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.8-GCC-11.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonPackage' + +name = 'pyspoa' +version = '0.0.8' + +homepage = 'https://github.com/nanoporetech/pyspoa' +description = "Python bindings to spoa." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = [ + { + 'source_urls': ['https://github.com/nanoporetech/pyspoa/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'pyspoa-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/USCiLab/cereal/archive/'], + 'download_filename': '3e4d1b8.tar.gz', + 'filename': 'cereal-20200423.tar.gz', + }, +] +patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] +checksums = [ + 'a1e630ef30a42d8e8c076d914261d0d34060631d64694569d52c1a2be5deada7', # pyspoa-0.0.8.tar.gz + '284cd14c1e60b36c966bcc8ce650d0b798b8a836d6c379e021e0da0dbe6ddf38', # cereal-20200423.tar.gz + 'a98c82ae8346b48952b171675f9df7ab1c95ea5421afcf5bcd778c01c5ee5a52', # pyspoa-0.0.8_use-spoa-dep.patch +] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [ + ('Python', '3.9.6'), + ('pybind11', '2.7.1'), + ('spoa', '4.0.7'), +] + +download_dep_fail = True + +preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " +# strip out cmake requirements, since we provide that as proper dependency +preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " + +use_pip = True + +options = {'modulename': 'spoa'} + +sanity_pip_check = True + +sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021b.eb new file mode 100644 index 00000000000..1b586fbe7f0 --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.2.4-foss-2021b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.2.4' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['8e6e0762924a461bb437cbb71122765c6912dace880e338bd19c7f9d12efead2'] + +builddependencies = [ + ('parasail', '2.5'), +] +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-11.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-11.2.0.eb new file mode 100644 index 00000000000..66a17f4eb5b --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '4.0.7' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] +sources = ['spoa-v%(version)s.tar.gz'] +checksums = ['f7a8cd039e4aabea1481e123387fedaa8f87e55418a3649408a615f5c6b1b9a4'] + +builddependencies = [('CMake', '3.21.1')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a', 'lib/pkgconfig/spoa-1.pc'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb new file mode 100644 index 00000000000..8db496eb42a --- /dev/null +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'WhatsHap' +version = '1.4' + +homepage = 'https://whatshap.readthedocs.io' +description = """WhatsHap is a software for phasing genomic variants using DNA +sequencing reads, also called read-based phasing or haplotype assembly. It is +especially suitable for long reads, but works also well with short reads.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('Pysam', '0.18.0'), + ('networkx', '2.6.3'), + ('SciPy-bundle', '2021.10'), + ('Biopython', '1.79'), + ('Yasm', '1.3.0'), + ('pyfaidx', '0.7.0'), + ('python-isal', '0.11.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '1.5.0', { + 'checksums': ['822b926afd39b6904e5d2fdee6e0944d342023f2a42339103c1507b0da48c693'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['4172fc3b8b46344e1d5b07029a1599fb4f53f7d87abbe3a38996e362acdd024f'], + }), +] + +sanity_check_paths = { + 'files': ['bin/whatshap'], + 'dirs': [], +} + +sanity_check_commands = [ + 'whatshap --help', +] + +moduleclass = 'bio' From d5175fc31ba7e3ad50cc85515f8ce4d0b0349ad3 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 13 Jun 2022 12:05:28 +0100 Subject: [PATCH 3970/9987] drop Pysam to 0.17.0 to make CI happy --- easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb index 8db496eb42a..cc905b450c7 100644 --- a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Python', '3.9.6'), - ('Pysam', '0.18.0'), + ('Pysam', '0.17.0'), ('networkx', '2.6.3'), ('SciPy-bundle', '2021.10'), ('Biopython', '1.79'), From 7a1698e74f3e9f01a123976f0461a76a8d70b633 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 13 Jun 2022 12:19:33 +0100 Subject: [PATCH 3971/9987] revert to Pysam 0.18.0 which is required for WhatsHap 1.4 --- easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb index cc905b450c7..8db496eb42a 100644 --- a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.4-foss-2021b.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Python', '3.9.6'), - ('Pysam', '0.17.0'), + ('Pysam', '0.18.0'), ('networkx', '2.6.3'), ('SciPy-bundle', '2021.10'), ('Biopython', '1.79'), From 49f72fb6b7cad81176a875af63f21bcc2060efcc Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 13 Jun 2022 12:28:31 +0100 Subject: [PATCH 3972/9987] add CI exception for Pysam 0.18.0 for WhatsApp 1.4 (foss/2021b) --- test/easyconfigs/easyconfigs.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index b9e8b1d8cad..286be60d2aa 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -516,8 +516,12 @@ def check_dep_vars(self, gen, dep, dep_vars): # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 - 'Pysam': [('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', - 'NGSpeciesID-0.1.1.1-'])], + # WhatsApp 1.4 requires Pysam >= 0.18.0 + 'Pysam': [ + ('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', + 'NGSpeciesID-0.1.1.1-']), + ('0.18.0;', ['WhatsApp-1.4-']), + ], # OPERA requires SAMtools 0.x 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], From b60a21415f6f65fdf758477fc93ecabd3f462790 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 13 Jun 2022 12:55:11 +0100 Subject: [PATCH 3973/9987] fix stupid typo in WhatsHap test exception --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 286be60d2aa..a28bc577446 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -516,11 +516,11 @@ def check_dep_vars(self, gen, dep, dep_vars): # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 - # WhatsApp 1.4 requires Pysam >= 0.18.0 + # WhatsHap 1.4 requires Pysam >= 0.18.0 'Pysam': [ ('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', 'NGSpeciesID-0.1.1.1-']), - ('0.18.0;', ['WhatsApp-1.4-']), + ('0.18.0;', ['WhatsHap-1.4-']), ], # OPERA requires SAMtools 0.x 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', From 967e8b0d36a6c21c5ca05821fe5a69a1f8548ce2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 13 Jun 2022 13:03:28 +0100 Subject: [PATCH 3974/9987] strip trailing whitespace --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a28bc577446..e8fae843422 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -518,7 +518,7 @@ def check_dep_vars(self, gen, dep, dep_vars): # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 # WhatsHap 1.4 requires Pysam >= 0.18.0 'Pysam': [ - ('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', + ('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', 'NGSpeciesID-0.1.1.1-']), ('0.18.0;', ['WhatsHap-1.4-']), ], From 797f35825f1c2881e9f91f79211d69b7fc934500 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 13 Jun 2022 15:03:48 +0200 Subject: [PATCH 3975/9987] adding easyconfigs: ReFrame-3.11.1.eb --- .../easyconfigs/r/ReFrame/ReFrame-3.11.1.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb new file mode 100644 index 00000000000..ddc3893ef62 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb @@ -0,0 +1,67 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.11.1' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + ('wheel', '0.37.1', { + 'checksums': ['e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4'], + }), + ('setuptools', '58.5.3', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['dae6b934a965c8a59d6d230d3867ec408bb95e73bd538ff77e71fedf1eaca729'], + }), + ('reframe', version, { + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], + 'checksums': ['7f591cd8f4fbb2c6255cc8ea02e3814393355a8931ac883e9f57490fde699b63'], + }), +] + +postinstallcmds = [ + "cp -a hpctestlib tools tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'hpctestlib', 'lib', 'tools', 'tutorials'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From f0dcf5c3dc4767d9ecbbdec190e278c0050f9259 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 13 Jun 2022 14:11:08 +0100 Subject: [PATCH 3976/9987] adding easyconfigs: TensorFlow-2.7.1-foss-2021b.eb --- .../TensorFlow/TensorFlow-2.7.1-foss-2021b.eb | 240 ++++++++++++++++++ 1 file changed, 240 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb new file mode 100644 index 00000000000..1169e8334d2 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb @@ -0,0 +1,240 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.7.1' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('protobuf', '3.17.3'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.33.1', '-nodocs'), + ('pybind11', '2.7.1'), + ('UnZip', '6.0'), + ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed +] +dependencies = [ + ('Python', '3.9.6'), + ('h5py', '3.6.0'), + ('cURL', '7.78.0'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.5.0'), + ('ICU', '69.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.29'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.36'), + ('protobuf-python', '3.17.3'), + ('flatbuffers-python', '2.0'), + ('libpng', '1.6.37'), + ('snappy', '1.1.9'), + ('zlib', '1.2.11'), + ('networkx', '2.6.3'), # required for pythran +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + # gast deps beniget and pythran require different version from Scipy-bundle + ('beniget', '0.3.0', { + 'checksums': ['062c893be9cdf87c3144fb15041cce4d81c67107c1591952cd45fdce789a0ff1'], + }), + ('pythran', '0.9.11', { + 'checksums': ['a317f91e2aade9f6550dc3bf40b5caeb45b7e012daf27e2b3e4ad928edb01667'], + }), + ('wrapt', '1.13.3', { + 'checksums': ['1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-io-gcs-filesystem', '0.24.0', { + 'source_tmpl': 'tensorflow_io_gcs_filesystem-0.24.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl', + 'checksums': ['cbc71b3925508bf796644a0083a6f9284f71404654f53092bece701383a69520'], + }), + ('tensorflow_estimator', '2.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['325b5a224864379242b7b76c6987ca544239be82579d33e68ec7c2bda57abc9d'], + }), + ('Werkzeug', '2.0.3', { + 'checksums': ['b863f8ff057c522164b6067c9e28b041161b4be5ba4d0daceeaa50a163822d3c'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('Markdown', '3.3.6', { + 'checksums': ['76df8ae32294ec39dcf89340382882dfa12975f87f45c3ed1ecdb1e8cefc7006'], + }), + ('grpcio', '1.43.0', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], + }), + ('oauthlib', '3.2.0', { + 'checksums': ['23a8208d75b902797ea29fd31fa80a15ed9dc2c6c16fe73f5d346f83f6fa27a2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('rsa', '4.8', { + 'checksums': ['5c6bd9dc7a543b7fe4304a631f8a8a3b674e2bbfc49c2ae96200cdbe55df6b17'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('cachetools', '5.0.0', { + 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], + }), + ('google-auth', '2.6.0', { + 'modulename': 'google.auth', + 'checksums': ['ad160fc1ea8f19e331a16a14a79f3d643d813a69534ba9611d2c80dc10439dad'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('tensorboard', '2.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['65a338e4424e9079f2604923bdbe301792adce2ace1be68da6b3ddf005170def'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('libclang', '13.0.0', { + 'modulename': 'clang', + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-manylinux1_x86_64.whl', + 'checksums': ['9c1e623340ccafe3a10a2abbc90f59593ff29f0c854f4ddb65b6220d9d998fb4'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('keras', '2.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['0c33ae1f728064ca0d35dfba999e9c316f03623bf5688c82fb83cc74a80ea248'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard_plugin_profile', '2.5.0', { + 'checksums': ['f832698d87a773b9a017fc4dd5cf598a1ff942ccfbf3392c83fe12c949ab9f52'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('dill', '0.3.4', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.5.0', { + 'checksums': ['e13b148008adeb2793cf8b55bcd20fdcec4f763f2d3bf3c45f5e5e5d1df7d228'], + }), + ('absl-py', '0.13.0', { + 'modulename': 'absl', + 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.7.1_fix_protobuf_error_message.patch', + 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.7.1_fix_cpu_count.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' + '-benchmark-test,-v1only'), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + # All tests in this directory fail with segfault (TensorFlow Graph IR) + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + 'checksums': [ + 'abebe2cf5ca379e18071693ca5f45b88ade941b16258a21cc1f12d77d5387a21', # v2.7.1.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', + # TensorFlow-2.5.0_disable-avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + # TensorFlow-2.5.0_fix-crash-on-shutdown.patch + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', + # TensorFlow-2.7.1_fix_protobuf_error_message.patch + '301ce21845987dc7868624880c0d85e60aa5491c5a0bae0f6ebc8db5727960a5', + # TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch + 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', + # TensorFlow-2.7.1_fix_cpu_count.patch + '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698', + ], + }), +] + +moduleclass = 'lib' From f90d790469fb74a8837e157b77ffd00b75941229 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 13 Jun 2022 14:12:16 +0100 Subject: [PATCH 3977/9987] adding easyconfigs: medaka-1.6.0-foss-2021b.eb, intervaltree-python-3.1.0-GCCcore-11.2.0.eb --- ...ntervaltree-python-3.1.0-GCCcore-11.2.0.eb | 30 +++++++++ .../m/medaka/medaka-1.6.0-foss-2021b.eb | 61 +++++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..69c4a126501 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'intervaltree-python' +_modname = 'intervaltree' +version = '3.1.0' + +homepage = 'https://github.com/chaimleib/intervaltree' +description = """A mutable, self-balancing interval tree. Queries may be by + point, by range overlap, or by range containment. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/i/%s' % _modname] +sources = ['%s-%s.tar.gz' % (_modname, version)] +checksums = ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': _modname} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb new file mode 100644 index 00000000000..c168c465e07 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb @@ -0,0 +1,61 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.6.0' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20210726')] + +_minimap_ver = '2.24' +dependencies = [ + ('Python', '3.9.6'), # includes cffi + # TensorFlow ~=2.7.0 required by medaka 1.6.0, see requirements.txt + ('TensorFlow', '2.7.1'), + ('Pysam', '0.18.0'), + ('SAMtools', '1.14'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.14'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.0.8'), + ('python-parasail', '1.2.4'), + ('ont-fast5-api', '4.0.2'), + ('WhatsHap', '1.4'), + ('intervaltree-python', '3.1.0'), +] + +use_pip = True + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + }), + (name, version, { + 'checksums': ['a8389f90cba77095061c4ff22c7cce8d73908e2451fa1d07b94c2f8ce4152628'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["medaka --help"] + +moduleclass = 'bio' From b6ba9a750e41e913f641b34445de47d448f6ee9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jun 2022 16:40:31 +0200 Subject: [PATCH 3978/9987] adding easyconfigs: netCDF-4.8.1-gompi-2022.05.eb, HDF5-1.13.1-gompi-2022.05.eb --- .../d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb | 31 ++++++++++++++++ .../h/HDF5/HDF5-1.13.1-gompi-2022.05.eb | 21 +++++++++++ .../libiconv/libiconv-1.17-GCCcore-11.3.0.eb | 23 ++++++++++++ .../n/netCDF/netCDF-4.8.1-gompi-2022.05.eb | 37 +++++++++++++++++++ .../s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb | 29 +++++++++++++++ 5 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022.05.eb create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2022.05.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b6669466085 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +name = 'Doxygen' +version = '1.9.4' + +homepage = 'https://www.doxygen.org' +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['a15e9cd8c0d02b7888bc8356eac200222ecff1defd32f3fe05257d81227b1f37'] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('libiconv', '1.17'), +] + +configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022.05.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022.05.eb new file mode 100644 index 00000000000..f83dfdef664 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022.05.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.13.1' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022.05'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2e42721e294 --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-11.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.17' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8f74213b56238c85a50a5329f77e06198771e70dd9a739779f4c02f65d971313'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2022.05.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2022.05.eb new file mode 100644 index 00000000000..a860ace46c2 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2022.05.eb @@ -0,0 +1,37 @@ +name = 'netCDF' +version = '4.8.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2022.05'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bc018cc30d5da402622bf76462480664c6668b55eb16ba205a0dfb8647161dd0'] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('HDF5', '1.13.1'), + ('cURL', '7.83.0'), + ('Szip', '2.1.1'), +] + +# HDF5 version detection is missed in netCDF 4.8.1 when HDF5_C_LIBRARY, HDF5_INCLUDE_DIR, and HDF5_HL_LIBRARY are set +local_hdf5_version_fix = '-DHDF5_VERSION=$EBVERSIONHDF5' + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF %s " % local_hdf5_version_fix, + "-DBUILD_SHARED_LIBS=ON %s " % local_hdf5_version_fix, +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3dc0b200849 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' From 96bdcbe572b5945c61baef2c28978d71941f9bb0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 13 Jun 2022 18:19:07 +0200 Subject: [PATCH 3979/9987] adding easyconfigs: GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb --- .../GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb | 91 +++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..cf94349e8a3 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,91 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2021.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI builds. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', + 'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch', +] +checksums = [ + 'eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6', # gromacs-2021.5.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch + 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', + # GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch + '7d39da0b431fbc9e94e857552246eb0ec892f26b13e519b3706785cc5e01a563', +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('scikit-build', '0.11.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('networkx', '2.6.3'), + ('CUDA', '11.4.1', '', True), + ('UCX-CUDA', '1.11.2', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.2.2.1', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['e24d507585e1a7808a5ee3ed04da5d6577f2a8961bbeafa7068528e00aa6b20d'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From d0e8259755b1065a0020bfaafdec9907f4269a04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Jun 2022 19:51:28 +0200 Subject: [PATCH 3980/9987] [gompi/2022.05] in-place update to netCDF v4.9.0 --- ...F-4.8.1-gompi-2022.05.eb => netCDF-4.9.0-gompi-2022.05.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/n/netCDF/{netCDF-4.8.1-gompi-2022.05.eb => netCDF-4.9.0-gompi-2022.05.eb} (91%) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2022.05.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb similarity index 91% rename from easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2022.05.eb rename to easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb index a860ace46c2..543bf7b703b 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.8.1-gompi-2022.05.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb @@ -1,5 +1,5 @@ name = 'netCDF' -version = '4.8.1' +version = '4.9.0' homepage = 'https://www.unidata.ucar.edu/software/netcdf/' description = """NetCDF (network Common Data Form) is a set of software libraries @@ -11,7 +11,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['bc018cc30d5da402622bf76462480664c6668b55eb16ba205a0dfb8647161dd0'] +checksums = ['9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6'] builddependencies = [ ('Autotools', '20220317'), From 05d621300a1ee82d317b672a879a61745a00e519 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Jun 2022 19:30:11 +0100 Subject: [PATCH 3981/9987] adding easyconfigs: PROJ-9.0.0-GCCcore-11.3.0.eb, nlohmann_json-3.10.5-GCCcore-11.3.0.eb, googletest-1.11.0-GCCcore-11.3.0.eb --- .../googletest-1.11.0-GCCcore-11.3.0.eb | 28 +++++++++++ .../nlohmann_json-3.10.5-GCCcore-11.3.0.eb | 24 +++++++++ .../p/PROJ/PROJ-9.0.0-GCCcore-11.3.0.eb | 49 +++++++++++++++++++ 3 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.11.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-9.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.11.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.11.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..03e441dbae3 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.11.0-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.11.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['b4870bf121ff7795ba20d20bcdd8627b8e088f2d1dab299a031c1034eddc93d5'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e0e75f7dbd3 --- /dev/null +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.5-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'nlohmann_json' +version = '3.10.5' + +homepage = 'https://github.com/nlohmann/json' +description = """JSON for Modern C++""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['include/nlohmann/json.hpp'], + 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-9.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-9.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ab0f6a5bdbb --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-9.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'CMakeMake' + +name = 'PROJ' +version = '9.0.0' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0620aa01b812de00b54d6c23e7c5cc843ae2cd129b24fabe411800302172b989'] + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('googletest', '1.11.0'), +] + +dependencies = [ + ('SQLite', '3.38.3'), + ('LibTIFF', '4.3.0'), + ('cURL', '7.83.0'), + ('XZ', '5.2.5'), + ('nlohmann_json', '3.10.5'), +] + +# build twice, once for static, once for shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 8c463ae5be1afe92ef01d2b765266b42212cce77 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Jun 2022 19:31:37 +0100 Subject: [PATCH 3982/9987] adding easyconfigs: libtirpc-1.3.2-GCCcore-11.3.0.eb --- .../libtirpc/libtirpc-1.3.2-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0560374219a --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.2-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.2' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['e24eb88b8ce7db3b7ca6eb80115dd1284abc5ec32a8deccfed2224fc2532b9fd'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.38') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' From 76f46fdb5dd7f72c87106e55611585687e2bbd86 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Jun 2022 19:32:08 +0100 Subject: [PATCH 3983/9987] adding easyconfigs: GEOS-3.9.3-GCC-11.3.0.eb --- .../g/GEOS/GEOS-3.9.3-GCC-11.3.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.9.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.9.3-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..e56974f0eb9 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.3-GCC-11.3.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.9.3' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f8b2314e311456f7a449144efb5e3188c2a28774752bc50fc882a3cd5c89ee35'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' From 14af64434b5f0027a1463c82e08b8f7ecbe2e3bc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Jun 2022 19:42:35 +0100 Subject: [PATCH 3984/9987] checksums --- .../n/nlohmann_json/nlohmann_json-3.10.5-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.5-GCCcore-11.3.0.eb index e0e75f7dbd3..7a6ed0fb350 100644 --- a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.10.5-GCCcore-11.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] +checksums = ['5daca6ca216495edf89d167f808d1d03c4a4d929cef7da5e10f135ae1540c7e4'] builddependencies = [ ('binutils', '2.38'), From 543ab5480e16f7f285c2db93b28271de0ba20aa5 Mon Sep 17 00:00:00 2001 From: Carsten Bauer Date: Mon, 13 Jun 2022 20:51:17 +0200 Subject: [PATCH 3985/9987] add / update Julia 1.7.3 --- .../j/Julia/Julia-1.7.3-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb new file mode 100644 index 00000000000..84b7a95dba2 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.7.3' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['9b2f4fa12d92b4dcc5d11dc66fb118c47681a76d3df8da064cc97573f2f5c739'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From 7ad95e8dca158f6415d159926ef3269e4334a16a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Jun 2022 20:37:57 +0100 Subject: [PATCH 3986/9987] adding easyconfigs: FLAC-1.3.4-GCCcore-11.3.0.eb, libogg-1.3.5-GCCcore-11.3.0.eb, libsndfile-1.1.0-GCCcore-11.3.0.eb, libvorbis-1.3.7-GCCcore-11.3.0.eb --- .../f/FLAC/FLAC-1.3.4-GCCcore-11.3.0.eb | 30 +++++++++++++++++ .../l/libogg/libogg-1.3.5-GCCcore-11.3.0.eb | 25 ++++++++++++++ .../libsndfile-1.1.0-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ .../libvorbis-1.3.7-GCCcore-11.3.0.eb | 30 +++++++++++++++++ 4 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.3.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d623911e08f --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.3.4-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.3.4' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['8ff0607e75a322dd7cd6ec48f4f225471404ae2730d0ea945127b1355155e737'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +sanity_check_commands = ["flac --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a669900c9a9 --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.5' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705'] + +builddependencies = [('binutils', '2.38')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7f15c42362e --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsndfile' +version = '1.1.0' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/libsndfile/libsndfile/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['0f98e101c0f7c850a71225fb5feaf33b106227b3d331333ddc9bacee190bcf41'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('FLAC', '1.3.4'), + ('libvorbis', '1.3.7'), +] + +configopts = '--enable-octave=no' + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d16d0768626 --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' From 7de4a504ecd4b3a67b9b58ce5fac7c7014d5d684 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Jun 2022 21:00:12 +0100 Subject: [PATCH 3987/9987] add LAME and libopus to libsndfile and switch to CMake --- .../l/LAME/LAME-3.100-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ .../l/libopus/libopus-1.3.1-GCCcore-11.3.0.eb | 32 +++++++++++++++++ .../libsndfile-1.1.0-GCCcore-11.3.0.eb | 6 ++-- 3 files changed, 72 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f067051ffe7 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +dependencies = [('ncurses', '6.3')] + +preconfigopts = "autoconf && " + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bc92ce3ee71 --- /dev/null +++ b/easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libopus' +version = '1.3.1' + +homepage = 'https://www.opus-codec.org/' +description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive + speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is + standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s + SILK codec and Xiph.Org’s CELT codec.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://archive.mozilla.org/pub/opus/'] +sources = ['opus-%(version)s.tar.gz'] +checksums = ['65b58e1e25b2a114157014736a3d9dfeaad8d41be1c8179866f144a2fb44ff9d'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [] #('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT], + 'dirs': ['include/opus'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb index 7f15c42362e..98d1fa3ef07 100644 --- a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'libsndfile' version = '1.1.0' @@ -21,9 +21,11 @@ builddependencies = [ dependencies = [ ('FLAC', '1.3.4'), ('libvorbis', '1.3.7'), + ('libopus', '1.3.1'), + ('LAME', '3.100'), ] -configopts = '--enable-octave=no' +configopts = ['', '-DBUILD_SHARED_LIBS=ON'] sanity_check_paths = { 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT], From 7888b73c06479010effd05c3822788e2ccc95038 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Jun 2022 21:05:23 +0100 Subject: [PATCH 3988/9987] add CMake dep to libsndfile --- .../easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb index 98d1fa3ef07..abf301e8aed 100644 --- a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.1.0-GCCcore-11.3.0.eb @@ -16,6 +16,7 @@ checksums = ['0f98e101c0f7c850a71225fb5feaf33b106227b3d331333ddc9bacee190bcf41'] builddependencies = [ ('binutils', '2.38'), ('pkgconf', '1.8.0'), + ('CMake', '3.23.1'), ] dependencies = [ From b1a7befe0ee483d9d54651b3747ce76f2bda828b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Jun 2022 21:10:04 +0100 Subject: [PATCH 3989/9987] adding easyconfigs: libreadline-8.1-GCCcore-11.3.0.eb --- .../libreadline-8.1-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2842a77b597 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.1-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.1' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['f8ceb4ee131e3232226a17f51b164afc46cd0b9e6cef344be87c65962cb82b02'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('ncurses', '6.3'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' From 063d38cc330ee58501ad5bad1e0c64d95fb8e607 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Jun 2022 21:11:04 +0100 Subject: [PATCH 3990/9987] adding easyconfigs: Tk-8.6.12-GCCcore-11.3.0.eb --- .../t/Tk/Tk-8.6.12-GCCcore-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.12-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.12-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..423e5e23147 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.12-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.12' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] +checksums = [ + '12395c1f3fcb6bed2938689f797ea3cdf41ed5cb6c4766eec8ac949560310630', # tk8.6.12-src.tar.gz + '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d', # Tk-8.6.4_different-prefix-with-tcl.patch +] + +builddependencies = [('binutils', '2.38')] +dependencies = [ + ('Tcl', version), + ('X11', '20220504'), + ('zlib', '1.2.12'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' From f6aea71d647d8eeae49595464ee6c02b67923f95 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 13 Jun 2022 21:19:22 +0100 Subject: [PATCH 3991/9987] remove mistake line --- easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-11.3.0.eb index bc92ce3ee71..d1024546ca0 100644 --- a/easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('pkgconf', '1.8.0'), ] -dependencies = [] #('libogg', '1.3.5')] +dependencies = [] configopts = '--enable-static --enable-shared' From 4f002c7fc27f1e292a97ed7572f3505a828a12ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 13 Jun 2022 22:28:09 +0200 Subject: [PATCH 3992/9987] adding easyconfigs: pfind-20220604-gompi-2021b.eb and patches: pfind-20220604_fix_help.patch --- .../p/pfind/pfind-20220604-gompi-2021b.eb | 38 +++++++++++++++++++ .../p/pfind/pfind-20220604_fix_help.patch | 21 ++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/pfind/pfind-20220604-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/p/pfind/pfind-20220604_fix_help.patch diff --git a/easybuild/easyconfigs/p/pfind/pfind-20220604-gompi-2021b.eb b/easybuild/easyconfigs/p/pfind/pfind-20220604-gompi-2021b.eb new file mode 100644 index 00000000000..0640184e224 --- /dev/null +++ b/easybuild/easyconfigs/p/pfind/pfind-20220604-gompi-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'Binary' + +name = 'pfind' +version = '20220604' +local_commit = 'd97bcb9' + +homepage = 'https://github.com/VI4IO/pfind' +description = 'Drop-in replacement for find, implemented for using parallel access and MPI.' + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://github.com/VI4IO/pfind/archive'] +sources = [local_commit + '.tar.gz'] +patches = ['pfind-%(version)s_fix_help.patch'] +checksums = [ + '2c60b1a87abc2d72c3b1a54aeb3a27c47dbd1de76a27a54373538cb527894beb', # d97bcb9.tar.gz + '5fbce1b13625511cc8be3a811e5bd4c47fc4ace9001da1831ee26b7dfaaa912d', # pfind-20220604_fix_help.patch +] + +dependencies = [ + ('lz4', '1.9.3'), +] + +extract_sources = True +staged_install = True + +# Less work to write the build command than to try to patch the build scripts +install_cmd = 'mkdir %(installdir)s/bin && ' +install_cmd += '$MPICC -o %(installdir)s/bin/pfind src/*.c $CFLAGS -DLZ4 -llz4' + +sanity_check_paths = { + 'files': ['bin/pfind'], + 'dirs': [], +} + +sanity_check_commands = ['pfind --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pfind/pfind-20220604_fix_help.patch b/easybuild/easyconfigs/p/pfind/pfind-20220604_fix_help.patch new file mode 100644 index 00000000000..68e934e5c27 --- /dev/null +++ b/easybuild/easyconfigs/p/pfind/pfind-20220604_fix_help.patch @@ -0,0 +1,21 @@ +MPI init is required before the help menu is allowed to find the process rank. +Ref. https://github.com/VI4IO/pfind/issues/17 +Author: micketeer@gmail.com +--- src/pfind-main.c.orig 2022-06-13 22:07:24.979936591 +0200 ++++ src/pfind-main.c 2022-06-13 22:06:50.856611055 +0200 +@@ -31,6 +31,7 @@ + } + + int main(int argc, char ** argv){ ++ MPI_Init(&argc, &argv); + // output help with --help to enable running without mpiexec + for(int i=0; i < argc; i++){ + if (strcmp(argv[i], "--help") == 0){ +@@ -41,7 +42,6 @@ + } + } + +- MPI_Init(&argc, &argv); + + pfind_options_t * options = pfind_parse_args(argc, argv, 0, MPI_COMM_WORLD); + From 89c08e2cf421e830f503f74ff6a062b7515b9d4c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 13 Jun 2022 23:05:24 +0200 Subject: [PATCH 3993/9987] Update version --- .../p/pfind/pfind-20220604_fix_help.patch | 21 ------------------- ...2021b.eb => pfind-20220613-gompi-2021b.eb} | 10 +++------ 2 files changed, 3 insertions(+), 28 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pfind/pfind-20220604_fix_help.patch rename easybuild/easyconfigs/p/pfind/{pfind-20220604-gompi-2021b.eb => pfind-20220613-gompi-2021b.eb} (71%) diff --git a/easybuild/easyconfigs/p/pfind/pfind-20220604_fix_help.patch b/easybuild/easyconfigs/p/pfind/pfind-20220604_fix_help.patch deleted file mode 100644 index 68e934e5c27..00000000000 --- a/easybuild/easyconfigs/p/pfind/pfind-20220604_fix_help.patch +++ /dev/null @@ -1,21 +0,0 @@ -MPI init is required before the help menu is allowed to find the process rank. -Ref. https://github.com/VI4IO/pfind/issues/17 -Author: micketeer@gmail.com ---- src/pfind-main.c.orig 2022-06-13 22:07:24.979936591 +0200 -+++ src/pfind-main.c 2022-06-13 22:06:50.856611055 +0200 -@@ -31,6 +31,7 @@ - } - - int main(int argc, char ** argv){ -+ MPI_Init(&argc, &argv); - // output help with --help to enable running without mpiexec - for(int i=0; i < argc; i++){ - if (strcmp(argv[i], "--help") == 0){ -@@ -41,7 +42,6 @@ - } - } - -- MPI_Init(&argc, &argv); - - pfind_options_t * options = pfind_parse_args(argc, argv, 0, MPI_COMM_WORLD); - diff --git a/easybuild/easyconfigs/p/pfind/pfind-20220604-gompi-2021b.eb b/easybuild/easyconfigs/p/pfind/pfind-20220613-gompi-2021b.eb similarity index 71% rename from easybuild/easyconfigs/p/pfind/pfind-20220604-gompi-2021b.eb rename to easybuild/easyconfigs/p/pfind/pfind-20220613-gompi-2021b.eb index 0640184e224..3b0d9e86681 100644 --- a/easybuild/easyconfigs/p/pfind/pfind-20220604-gompi-2021b.eb +++ b/easybuild/easyconfigs/p/pfind/pfind-20220613-gompi-2021b.eb @@ -1,8 +1,8 @@ easyblock = 'Binary' name = 'pfind' -version = '20220604' -local_commit = 'd97bcb9' +version = '20220613' +local_commit = 'bef6b4c' homepage = 'https://github.com/VI4IO/pfind' description = 'Drop-in replacement for find, implemented for using parallel access and MPI.' @@ -11,11 +11,7 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://github.com/VI4IO/pfind/archive'] sources = [local_commit + '.tar.gz'] -patches = ['pfind-%(version)s_fix_help.patch'] -checksums = [ - '2c60b1a87abc2d72c3b1a54aeb3a27c47dbd1de76a27a54373538cb527894beb', # d97bcb9.tar.gz - '5fbce1b13625511cc8be3a811e5bd4c47fc4ace9001da1831ee26b7dfaaa912d', # pfind-20220604_fix_help.patch -] +checksums = ['237b06ec5d0ee881fc52d9b72e366172abf0876734a511eafabd5d380a2cc683'] dependencies = [ ('lz4', '1.9.3'), From 003181f537119c5ef454da44706953eba51d902d Mon Sep 17 00:00:00 2001 From: Ben Moran Date: Tue, 14 Jun 2022 15:29:27 +1100 Subject: [PATCH 3994/9987] adding easyconfigs: samplot-1.3.0-foss-2021b-Python-3.9.6.eb --- .../samplot-1.3.0-foss-2021b-Python-3.9.6.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b-Python-3.9.6.eb new file mode 100644 index 00000000000..d431e3d3e5b --- /dev/null +++ b/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b-Python-3.9.6.eb @@ -0,0 +1,48 @@ +# This easyconfig was written by the HPC team at Agriculture Victoria Research +# http://agriculture.vic.gov.au/agriculture/innovation-and-research +# +# Author: Ben Moran +easyblock = 'PythonBundle' + +name = 'samplot' +version = '1.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/ryanlayer/samplot' +description = """ + Plot structural variant signals from many BAMs and CRAMs. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'ryanlayer' + +dependencies = [ + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), + ('Pysam', '0.17.0'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('wget', '3.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['35e630eca2aa50ce998b9b1a127bb26b30dfee573702782aa982f875e3f16061'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': [GITHUB_SOURCE], + 'checksums': ['c004ee228ec238b919e644218bcf671b072dd4c7b6c6564a8a8b6912168fc00e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/samplot'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 0780a3eaa6ae2cd9ba44d71d404c9f23a7195119 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 14 Jun 2022 09:52:58 +0100 Subject: [PATCH 3995/9987] adding easyconfigs: HDF-4.2.15-GCCcore-11.3.0.eb --- .../h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..682e5e20b6c --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-11.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.15' + +homepage = 'https://www.hdfgroup.org/products/hdf4/' + +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['HDF-4.2.15_fix-aarch64.patch'] +checksums = [ + 'dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459', # hdf-4.2.15.tar.gz + '1b4341e309cccefc6ea4310c8f8b08cc3dfe1fa9609b7fa7aee80e4dac598473', # HDF-4.2.15_fix-aarch64.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '2.1.3'), + ('Szip', '2.1.1'), + ('zlib', '1.2.12'), + ('libtirpc', '1.3.2'), +] + +preconfigopts = "LIBS='-ltirpc' " +local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' +local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' +configopts = [ + # -fallow-argument-mismatch is required to compile with GCC 10.x + local_common_configopts + 'FFLAGS="$FFLAGS -fallow-argument-mismatch"', + # Cannot build shared libraries and Fortran... + # https://trac.osgeo.org/gdal/wiki/HDF#IncompatibilitywithNetCDFLibraries + # netcdf must be disabled to allow HDF to be used by GDAL + local_common_configopts + "--enable-shared --disable-fortran --disable-netcdf", +] + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', + 'lib/libmfhdf.%s' % SHLIB_EXT], + 'dirs': ['include/hdf'], +} + +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + +moduleclass = 'data' From 027c86815689cd4e59ece16b23fc42f8d49c1620 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 14 Jun 2022 09:53:21 +0100 Subject: [PATCH 3996/9987] adding easyconfigs: libgeotiff-1.7.1-GCCcore-11.3.0.eb --- .../libgeotiff-1.7.1-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..424658def7b --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.7.1' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['05ab1347aaa471fc97347d8d4269ff0c00f30fa666d956baba37948ec87e55d6'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('PROJ', '9.0.0'), + ('libjpeg-turbo', '2.1.3'), + ('zlib', '1.2.12'), + ('SQLite', '3.38.3'), + ('LibTIFF', '4.3.0'), + ('cURL', '7.83.0'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From d0a2215676847c0d1ed65fd76d94f900e57b9c62 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 14 Jun 2022 10:14:40 +0100 Subject: [PATCH 3997/9987] bump to latest version (3.10.3) --- ....9.3-GCC-11.3.0.eb => GEOS-3.10.3-GCC-11.3.0.eb} | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/g/GEOS/{GEOS-3.9.3-GCC-11.3.0.eb => GEOS-3.10.3-GCC-11.3.0.eb} (59%) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.9.3-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.10.3-GCC-11.3.0.eb similarity index 59% rename from easybuild/easyconfigs/g/GEOS/GEOS-3.9.3-GCC-11.3.0.eb rename to easybuild/easyconfigs/g/GEOS/GEOS-3.10.3-GCC-11.3.0.eb index e56974f0eb9..c78a111c17d 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.9.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.10.3-GCC-11.3.0.eb @@ -1,7 +1,7 @@ -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'GEOS' -version = '3.9.3' +version = '3.10.3' homepage = 'https://trac.osgeo.org/geos' description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" @@ -10,10 +10,15 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://download.osgeo.org/geos/'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['f8b2314e311456f7a449144efb5e3188c2a28774752bc50fc882a3cd5c89ee35'] +checksums = ['3c141b07d61958a758345d5f54e3c735834b2f4303edb9f67fb26914f0d44770'] + +builddependencies = [('CMake', '3.23.1')] + +# Build static and shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] sanity_check_paths = { - 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos_c.h'], 'dirs': [], } From 8d0f930d1efd9c0320ed525c243edde0ca91db5c Mon Sep 17 00:00:00 2001 From: Ben Moran Date: Tue, 14 Jun 2022 21:02:24 +1100 Subject: [PATCH 3998/9987] implement required changes --- .../s/samplot/samplot-1.3.0-foss-2021b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b.eb b/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b.eb new file mode 100644 index 00000000000..282f035ae1b --- /dev/null +++ b/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b.eb @@ -0,0 +1,47 @@ +# This easyconfig was written by the HPC team at Agriculture Victoria Research +# http://agriculture.vic.gov.au/agriculture/innovation-and-research +# +# Author: Ben Moran +easyblock = 'PythonBundle' + +name = 'samplot' +version = '1.3.0' + +homepage = 'https://github.com/ryanlayer/samplot' +description = """ + Plot structural variant signals from many BAMs and CRAMs. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'ryanlayer' + +dependencies = [ + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), + ('Pysam', '0.17.0'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('wget', '3.2', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['35e630eca2aa50ce998b9b1a127bb26b30dfee573702782aa982f875e3f16061'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': [GITHUB_SOURCE], + 'checksums': ['c004ee228ec238b919e644218bcf671b072dd4c7b6c6564a8a8b6912168fc00e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/samplot'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 46cd612a8978bb2dff92ef8fc71ee2fd93f2a57e Mon Sep 17 00:00:00 2001 From: Ben Moran Date: Tue, 14 Jun 2022 21:29:51 +1000 Subject: [PATCH 3999/9987] remove badly named easyconfig --- .../samplot-1.3.0-foss-2021b-Python-3.9.6.eb | 48 ------------------- 1 file changed, 48 deletions(-) delete mode 100644 easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b-Python-3.9.6.eb deleted file mode 100644 index d431e3d3e5b..00000000000 --- a/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b-Python-3.9.6.eb +++ /dev/null @@ -1,48 +0,0 @@ -# This easyconfig was written by the HPC team at Agriculture Victoria Research -# http://agriculture.vic.gov.au/agriculture/innovation-and-research -# -# Author: Ben Moran -easyblock = 'PythonBundle' - -name = 'samplot' -version = '1.3.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/ryanlayer/samplot' -description = """ - Plot structural variant signals from many BAMs and CRAMs. -""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -github_account = 'ryanlayer' - -dependencies = [ - ('Python', '3.9.6'), - ('matplotlib', '3.4.3'), - ('Pysam', '0.17.0'), -] - -download_dep_fail = True -use_pip = True - -exts_list = [ - ('wget', '3.2', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['35e630eca2aa50ce998b9b1a127bb26b30dfee573702782aa982f875e3f16061'], - }), - (name, version, { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': [GITHUB_SOURCE], - 'checksums': ['c004ee228ec238b919e644218bcf671b072dd4c7b6c6564a8a8b6912168fc00e'], - }), -] - -sanity_check_paths = { - 'files': ['bin/samplot'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -sanity_pip_check = True - -moduleclass = 'bio' From 0a6b07f4d906d03a26cc50a29dce05244dcf1306 Mon Sep 17 00:00:00 2001 From: Ben Moran Date: Tue, 14 Jun 2022 21:30:22 +1000 Subject: [PATCH 4000/9987] remove 'download_dep_fail' --- easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b.eb b/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b.eb index 282f035ae1b..29f17027c05 100644 --- a/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/samplot/samplot-1.3.0-foss-2021b.eb @@ -22,7 +22,6 @@ dependencies = [ ('Pysam', '0.17.0'), ] -download_dep_fail = True use_pip = True exts_list = [ From c9b83e1db6b63b5fbaa1f295fef692c63dc27251 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 14 Jun 2022 13:59:49 +0100 Subject: [PATCH 4001/9987] New qe-gipaw 7 and remove no longer needed patch --- .../QuantumESPRESSO-7.0-foss-2021b.eb | 5 +- ...PRESSO-7.0-gipaw-string-preprocessor.patch | 393 ------------------ .../QuantumESPRESSO-7.0-intel-2021b.eb | 2 +- 3 files changed, 2 insertions(+), 398 deletions(-) delete mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb index af38331564a..a0a1ebea9ea 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-foss-2021b.eb @@ -21,13 +21,10 @@ sources = [ 'qe-gipaw-%(version)s.tar.gz', {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, ] -patches = ['QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch'] checksums = [ '268ec506f88c56ba4e9b691c1e81e33a6ad7949f857f1c6c32197f9c2af2a957', # qe-%(version)s-ReleasePack.tgz - '3055bd56c7e28a4013a06b7ae98d12b1569b0cc790a141d6a9cd8da9c2be3ce7', # qe-gipaw-%(version)s.tar.gz + '0f26055495c5d757ccd388ff3e8fd1ad036a798d3017f6ea0bcd0ea84b8a5bce', # qe-gipaw-%(version)s.tar.gz '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz - # QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch - '8c5026e0b6463f6690238d3aedffe18c7e8b2bfeb52be1454f934a43a2f91fd6', ] dependencies = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch deleted file mode 100644 index 57577470e7c..00000000000 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-gipaw-string-preprocessor.patch +++ /dev/null @@ -1,393 +0,0 @@ -Replace unsupported macros with expanded code - -The preprocessor in foss doesn't handle macros with stringification using # -which occurs GIPAW's xml_routines. - -Author: Lars Viklund (HPC2N, Umea University) - -diff -ru qe-gipaw-7.0.orig/src/xml_routines.f90 qe-gipaw-7.0/src/xml_routines.f90 ---- qe-gipaw-7.0.orig/src/xml_routines.f90 2022-01-13 13:48:03.000000000 +0000 -+++ qe-gipaw-7.0/src/xml_routines.f90 2022-01-24 09:56:30.414934470 +0000 -@@ -93,25 +93,25 @@ - timestamp = 'This run was terminated on: ' // ctime // ' ' // cdate(1:2) // ' '//cdate(3:5) // ' '// cdate (6:9) - - CHECK_IONODE -- _NE(general_info) -- _NE(xml_format) -- _ATTR(NAME, fmt_name) -- _ATTR(VERSION, fmt_version) -+ call XML_NewElement(xmlf, "general_info") -+ call XML_NewElement(xmlf, "xml_format") -+ call XML_AddAttribute(xmlf, "NAME", (fmt_name)) -+ call XML_AddAttribute(xmlf, "VERSION", (fmt_version)) - _ADDV(fmt_name//'_'//fmt_version) -- _EE(xml_format) -- _NE(creator) -- _ATTR(NAME, 'GIPAW') -- _ATTR(VERSION, gipaw_git_revision) -+ call XML_EndElement(xmlf, "xml_format") -+ call XML_NewElement(xmlf, "creator") -+ call XML_AddAttribute(xmlf, "NAME", ('GIPAW')) -+ call XML_AddAttribute(xmlf, "VERSION", (gipaw_git_revision)) - _ADDV('XML file generated by GIPAW') -- _EE(creator) -- _NE(created) -- _ATTR(DATE, cdate) -- _ATTR(TIME, ctime) -+ call XML_EndElement(xmlf, "creator") -+ call XML_NewElement(xmlf, "created") -+ call XML_AddAttribute(xmlf, "DATE", (cdate)) -+ call XML_AddAttribute(xmlf, "TIME", (ctime)) - _ADDS(timestamp) -- _EE(created) -- _NE(job) -- _EE(job) -- _EE(general_info) -+ call XML_EndElement(xmlf, "created") -+ call XML_NewElement(xmlf, "job") -+ call XML_EndElement(xmlf, "job") -+ call XML_EndElement(xmlf, "general_info") - - END SUBROUTINE xml_output_generalinfo - -@@ -131,20 +131,26 @@ - #endif - - CHECK_IONODE -- _NE(parallel_info) -- _NE(nprocs) -+ call XML_NewElement(xmlf, "parallel_info") -+ call XML_NewElement(xmlf, "nprocs") - _ADDV(nproc) -- _EE(nprocs) -- _OUTV(nthreads) -- _NE(ntasks) -+ call XML_EndElement(xmlf, "nprocs") -+ call XML_NewElement(xmlf, "nthreads") -+ call XML_AddCharacters(xmlf, (nthreads)) -+ call XML_EndElement(xmlf, "nthreads") -+ call XML_NewElement(xmlf, "ntasks") - _ADDV(ntask_groups) -- _EE(ntasks) -- _OUTV(nbgrp) -- _OUTV(npool) -- _NE(ndiag) -+ call XML_EndElement(xmlf, "ntasks") -+ call XML_NewElement(xmlf, "nbgrp") -+ call XML_AddCharacters(xmlf, (nbgrp)) -+ call XML_EndElement(xmlf, "nbgrp") -+ call XML_NewElement(xmlf, "npool") -+ call XML_AddCharacters(xmlf, (npool)) -+ call XML_EndElement(xmlf, "npool") -+ call XML_NewElement(xmlf, "ndiag") - _ADDV(nproc_ortho) -- _EE(ndiag) -- _EE(parallel_info) -+ call XML_EndElement(xmlf, "ndiag") -+ call XML_EndElement(xmlf, "parallel_info") - - END SUBROUTINE xml_output_parallelinfo - -@@ -160,42 +166,78 @@ - implicit none - - CHECK_IONODE -- _NE(input) -- _OUTS(job) -- _OUTS(prefix) -- _OUTS(tmp_dir) -- _OUTV(conv_threshold) -- _OUTS(restart_mode) -- _NE(q_gipaw) -+ call XML_NewElement(xmlf, "input") -+ call XML_NewElement(xmlf, "job") -+ call XML_AddCharacters(xmlf, trim((job))) -+ call XML_EndElement(xmlf, "job") -+ call XML_NewElement(xmlf, "prefix") -+ call XML_AddCharacters(xmlf, trim((prefix))) -+ call XML_EndElement(xmlf, "prefix") -+ call XML_NewElement(xmlf, "tmp_dir") -+ call XML_AddCharacters(xmlf, trim((tmp_dir))) -+ call XML_EndElement(xmlf, "tmp_dir") -+ call XML_NewElement(xmlf, "conv_threshold") -+ call XML_AddCharacters(xmlf, (conv_threshold)) -+ call XML_EndElement(xmlf, "conv_threshold") -+ call XML_NewElement(xmlf, "restart_mode") -+ call XML_AddCharacters(xmlf, trim((restart_mode))) -+ call XML_EndElement(xmlf, "restart_mode") -+ call XML_NewElement(xmlf, "q_gipaw") - _ADDV(q_gipaw*tpiba) -- _EE(q_gipaw) -- _OUTS(verbosity) -- _OUTS(filcurr) -- _OUTS(filfield) -- _OUTS(filnics) -- _OUTV(pawproj) -- _OUTV(use_nmr_macroscopic_shape) -- _NE(nmr_macroscopic_shape) -- _ATTR(rank, "2") -- _ATTR(dims, "3 3") -+ call XML_EndElement(xmlf, "q_gipaw") -+ call XML_NewElement(xmlf, "verbosity") -+ call XML_AddCharacters(xmlf, trim((verbosity))) -+ call XML_EndElement(xmlf, "verbosity") -+ call XML_NewElement(xmlf, "filcurr") -+ call XML_AddCharacters(xmlf, trim((filcurr))) -+ call XML_EndElement(xmlf, "filcurr") -+ call XML_NewElement(xmlf, "filfield") -+ call XML_AddCharacters(xmlf, trim((filfield))) -+ call XML_EndElement(xmlf, "filfield") -+ call XML_NewElement(xmlf, "filnics") -+ call XML_AddCharacters(xmlf, trim((filnics))) -+ call XML_EndElement(xmlf, "filnics") -+ call XML_NewElement(xmlf, "pawproj") -+ call XML_AddCharacters(xmlf, (pawproj)) -+ call XML_EndElement(xmlf, "pawproj") -+ call XML_NewElement(xmlf, "use_nmr_macroscopic_shape") -+ call XML_AddCharacters(xmlf, (use_nmr_macroscopic_shape)) -+ call XML_EndElement(xmlf, "use_nmr_macroscopic_shape") -+ call XML_NewElement(xmlf, "nmr_macroscopic_shape") -+ call XML_AddAttribute(xmlf, "rank", ("2")) -+ call XML_AddAttribute(xmlf, "dims", ("3 3")) - _ADDV(nmr_macroscopic_shape) -- _EE(nmr_macroscopic_shape) -- _OUTV(spline_ps) -- _OUTS(diagonalization) -- _NE(q_efg) -- _ATTR(size, nat) -+ call XML_EndElement(xmlf, "nmr_macroscopic_shape") -+ call XML_NewElement(xmlf, "spline_ps") -+ call XML_AddCharacters(xmlf, (spline_ps)) -+ call XML_EndElement(xmlf, "spline_ps") -+ call XML_NewElement(xmlf, "diagonalization") -+ call XML_AddCharacters(xmlf, trim((diagonalization))) -+ call XML_EndElement(xmlf, "diagonalization") -+ call XML_NewElement(xmlf, "q_efg") -+ call XML_AddAttribute(xmlf, "size", (nat)) - _ADDV(q_efg) -- _EE(q_efg) -- _OUTV(max_seconds) -- _OUTV(r_rand) -- _OUTS(hfi_output_unit) -- _NE(hfi_nuclear_g_factor) -- _ATTR(size, nat) -+ call XML_EndElement(xmlf, "q_efg") -+ call XML_NewElement(xmlf, "max_seconds") -+ call XML_AddCharacters(xmlf, (max_seconds)) -+ call XML_EndElement(xmlf, "max_seconds") -+ call XML_NewElement(xmlf, "r_rand") -+ call XML_AddCharacters(xmlf, (r_rand)) -+ call XML_EndElement(xmlf, "r_rand") -+ call XML_NewElement(xmlf, "hfi_output_unit") -+ call XML_AddCharacters(xmlf, trim((hfi_output_unit))) -+ call XML_EndElement(xmlf, "hfi_output_unit") -+ call XML_NewElement(xmlf, "hfi_nuclear_g_factor") -+ call XML_AddAttribute(xmlf, "size", (nat)) - _ADDV(hfi_nuclear_g_factor) -- _EE(hfi_nuclear_g_factor) -- _OUTV(core_relax_method) -- _OUTV(hfi_via_reconstruction_only) -- _EE(input) -+ call XML_EndElement(xmlf, "hfi_nuclear_g_factor") -+ call XML_NewElement(xmlf, "core_relax_method") -+ call XML_AddCharacters(xmlf, (core_relax_method)) -+ call XML_EndElement(xmlf, "core_relax_method") -+ call XML_NewElement(xmlf, "hfi_via_reconstruction_only") -+ call XML_AddCharacters(xmlf, (hfi_via_reconstruction_only)) -+ call XML_EndElement(xmlf, "hfi_via_reconstruction_only") -+ call XML_EndElement(xmlf, "input") - END SUBROUTINE xml_output_namelist - - -@@ -207,17 +249,17 @@ - - CHECK_IONODE - -- _NE(susceptibility_low) -- _ATTR(rank, '2') -- _ATTR(dims, '3 3') -+ call XML_NewElement(xmlf, "susceptibility_low") -+ call XML_AddAttribute(xmlf, "rank", ('2')) -+ call XML_AddAttribute(xmlf, "dims", ('3 3')) - _ADDV(res_suscept1) -- _EE(susceptibility_low) -+ call XML_EndElement(xmlf, "susceptibility_low") - -- _NE(susceptibility_high) -- _ATTR(rank, '2') -- _ATTR(dims, '3 3') -+ call XML_NewElement(xmlf, "susceptibility_high") -+ call XML_AddAttribute(xmlf, "rank", ('2')) -+ call XML_AddAttribute(xmlf, "dims", ('3 3')) - _ADDV(res_suscept2) -- _EE(susceptibility_high) -+ call XML_EndElement(xmlf, "susceptibility_high") - - END SUBROUTINE xml_output_susceptibility - -@@ -231,12 +273,12 @@ - integer, intent(in) :: na - character(*) :: rank, dims, units - -- _ATTR(name, trim(atm(ityp(na)))) -- _ATTR(tau, tau(:,na)) -- _ATTR(index, na) -- _ATTR(rank, rank) -- _ATTR(dims, dims) -- _ATTR(units, units) -+ call XML_AddAttribute(xmlf, "name", (trim(atm(ityp(na))))) -+ call XML_AddAttribute(xmlf, "tau", (tau(:,na))) -+ call XML_AddAttribute(xmlf, "index", (na)) -+ call XML_AddAttribute(xmlf, "rank", (rank)) -+ call XML_AddAttribute(xmlf, "dims", (dims)) -+ call XML_AddAttribute(xmlf, "units", (units)) - - END SUBROUTINE xml_atom_attributes - -@@ -251,65 +293,65 @@ - integer :: na - - CHECK_IONODE -- _NE(output) -+ call XML_NewElement(xmlf, "output") - - !! if (job == 'nmr') then - call xml_output_susceptibility -- _NE(shielding_tensors) -+ call XML_NewElement(xmlf, "shielding_tensors") - do na = 1, nat -- _NE(atom) -+ call XML_NewElement(xmlf, "atom") - call xml_atom_attributes(na, 'ppm', '2', '3 3') - _ADDV(res_nmr_sigma(:,:,na)) -- _EE(atom) -+ call XML_EndElement(xmlf, "atom") - enddo -- _EE(shielding_tensors) -+ call XML_EndElement(xmlf, "shielding_tensors") - !! endif - - !! if (job == 'g_tensor') then - !! call xml_output_susceptibility -- _NE(delta_g) -- _ATTR(rank, '2') -- _ATTR(dims, '3 3') -+ call XML_NewElement(xmlf, "delta_g") -+ call XML_AddAttribute(xmlf, "rank", ('2')) -+ call XML_AddAttribute(xmlf, "dims", ('3 3')) - _ADDV(res_epr_deltag) -- _EE(delta_g) -- _NE(delta_g_paratec) -- _ATTR(rank, '2') -- _ATTR(dims, '3 3') -+ call XML_EndElement(xmlf, "delta_g") -+ call XML_NewElement(xmlf, "delta_g_paratec") -+ call XML_AddAttribute(xmlf, "rank", ('2')) -+ call XML_AddAttribute(xmlf, "dims", ('3 3')) - _ADDV(res_epr_deltag_paratec) -- _EE(delta_g_paratec) -+ call XML_EndElement(xmlf, "delta_g_paratec") - !! endif - - !! if (job == 'efg') then -- _NE(electric_field_gradients) -+ call XML_NewElement(xmlf, "electric_field_gradients") - do na = 1, nat -- _NE(atom) -+ call XML_NewElement(xmlf, "atom") - call xml_atom_attributes(na, 'MHz', '2', '3 3') - _ADDV(res_efg(:,:,na)) -- _EE(atom) -+ call XML_EndElement(xmlf, "atom") - enddo -- _EE(electric_field_gradients) -+ call XML_EndElement(xmlf, "electric_field_gradients") - !! endif - - !! if (job == 'hyperfine') then -- _NE(hyperfine_dipolar) -+ call XML_NewElement(xmlf, "hyperfine_dipolar") - do na = 1, nat -- _NE(atom) -+ call XML_NewElement(xmlf, "atom") - call xml_atom_attributes(na, trim(hfi_output_unit), '2', '3 3') - _ADDV(res_hfi_dip(:,:,na)) -- _EE(atom) -+ call XML_EndElement(xmlf, "atom") - enddo -- _EE(hyperfine_dipolar) -- _NE(hyperfine_fermi_contact) -+ call XML_EndElement(xmlf, "hyperfine_dipolar") -+ call XML_NewElement(xmlf, "hyperfine_fermi_contact") - do na = 1, nat -- _NE(atom) -+ call XML_NewElement(xmlf, "atom") - call xml_atom_attributes(na, trim(hfi_output_unit), '1', '1') - _ADDV(res_hfi_fc(na)) -- _EE(atom) -+ call XML_EndElement(xmlf, "atom") - enddo -- _EE(hyperfine_fermi_contact) -+ call XML_EndElement(xmlf, "hyperfine_fermi_contact") - !! endif - -- _EE(output) -+ call XML_EndElement(xmlf, "output") - - END SUBROUTINE xml_output_results - -@@ -321,7 +363,9 @@ - integer :: exit_status = 0 - - CHECK_IONODE -- _OUTV(exit_status) -+ call XML_NewElement(xmlf, "exit_status") -+ call XML_AddCharacters(xmlf, (exit_status)) -+ call XML_EndElement(xmlf, "exit_status") - - END SUBROUTINE xml_output_status - -@@ -334,10 +378,10 @@ - - CHECK_IONODE - call date_and_tim(cdate, ctime) -- _NE(closed) -- _ATTR(DATE, cdate) -- _ATTR(TIME, ctime) -- _EE(closed) -+ call XML_NewElement(xmlf, "closed") -+ call XML_AddAttribute(xmlf, "DATE", (cdate)) -+ call XML_AddAttribute(xmlf, "TIME", (ctime)) -+ call XML_EndElement(xmlf, "closed") - - END SUBROUTINE xml_output_closed - -@@ -352,17 +396,21 @@ - real(dp) :: wall, cpu - - CHECK_IONODE -- _NE(timing_info) -- _NE(total) -- _ATTR(label, 'GIPAW') -+ call XML_NewElement(xmlf, "timing_info") -+ call XML_NewElement(xmlf, "total") -+ call XML_AddAttribute(xmlf, "label", ('GIPAW')) - cpu = f_tcpu() - wall = f_wall() - !wall = get_clock('GIPAW') -- _OUTV(cpu) -- _OUTV(wall) -- _EE(total) -+ call XML_NewElement(xmlf, "cpu") -+ call XML_AddCharacters(xmlf, (cpu)) -+ call XML_EndElement(xmlf, "cpu") -+ call XML_NewElement(xmlf, "wall") -+ call XML_AddCharacters(xmlf, (wall)) -+ call XML_EndElement(xmlf, "wall") -+ call XML_EndElement(xmlf, "total") - -- _EE(timing_info) -+ call XML_EndElement(xmlf, "timing_info") - - END SUBROUTINE xml_output_timinginfo - diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb index f0c587dbd0e..febc60c8c61 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.0-intel-2021b.eb @@ -23,7 +23,7 @@ sources = [ ] checksums = [ '268ec506f88c56ba4e9b691c1e81e33a6ad7949f857f1c6c32197f9c2af2a957', # qe-%(version)s-ReleasePack.tgz - '3055bd56c7e28a4013a06b7ae98d12b1569b0cc790a141d6a9cd8da9c2be3ce7', # qe-gipaw-%(version)s.tar.gz + '0f26055495c5d757ccd388ff3e8fd1ad036a798d3017f6ea0bcd0ea84b8a5bce', # qe-gipaw-%(version)s.tar.gz '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz ] From 9c4dee262c9e9507610c3c343d02d179c3b83a7c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 14 Jun 2022 15:31:02 +0200 Subject: [PATCH 4002/9987] use wheel for wheel --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb index ddc3893ef62..536b42fd7a6 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb @@ -24,6 +24,7 @@ exts_list = [ 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], }), ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', 'checksums': ['e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4'], }), ('setuptools', '58.5.3', { From adf1216934c67cfb34734491a0891256fbc80831 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 14 Jun 2022 15:34:16 +0200 Subject: [PATCH 4003/9987] fix checksum --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb index 536b42fd7a6..2617252f8fb 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.1.eb @@ -25,7 +25,7 @@ exts_list = [ }), ('wheel', '0.37.1', { 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', - 'checksums': ['e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4'], + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], }), ('setuptools', '58.5.3', { 'source_tmpl': 'setuptools-%(version)s.tar.gz', From 2bc26edf4ef5883f7a3c1a4cd8c721394c37fa39 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jun 2022 18:28:32 +0200 Subject: [PATCH 4004/9987] adding easyconfigs: deal.II-9.3.3-foss-2021a.eb, p4est-2.8-foss-2021a.eb --- .../d/deal.II/deal.II-9.3.3-foss-2021a.eb | 45 +++++++++++++++++ .../p/p4est/p4est-2.8-foss-2021a.eb | 50 +++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/p4est/p4est-2.8-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb b/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb new file mode 100644 index 00000000000..60a54d16d5e --- /dev/null +++ b/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'deal.II' +version = '9.3.3' + +homepage = 'https://www.dealii.org' +description = """deal.II is a C++ program library targeted at the computational solution of + partial differential equations using adaptive finite elements.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/dealii/dealii/releases/download/v%(version)s/'] +sources = ['dealii-%(version)s.tar.gz'] +checksums = ['5dfb59174b341589e92b434398a1b7cc11ad053ce2315cf673f5efc5ba271a29'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Boost', '1.76.0'), + ('GSL', '2.7'), + ('HDF5', '1.10.7'), + ('METIS', '5.1.0'), + ('netCDF', '4.8.0'), + ('p4est', '2.8'), + ('PETSc', '3.15.1'), + ('zlib', '1.2.11'), +] + +configopts = "-DCMAKE_BUILD_TYPE=Release " +configopts += "-DDEAL_II_WITH_LAPACK=ON -DDEAL_II_WITH_MPI=ON " +configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_METIS=ON -DMETIS_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_NETCDF=ON -DNETCDF_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=$EBROOTP4EST" +configopts += "-DDEAL_II_WITH_PETSC=ON -DPETSC_DIR=$EBROOTBOOST" +configopts += "-DDEAL_II_WITH_ZLIB=ON -DZLIB_DIR=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libdeal_II.%s' % SHLIB_EXT], + 'dirs': ['include/deal.II', 'lib/cmake', 'lib/pkgconfig', 'share/deal.II'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/p4est/p4est-2.8-foss-2021a.eb b/easybuild/easyconfigs/p/p4est/p4est-2.8-foss-2021a.eb new file mode 100644 index 00000000000..83f62b1d921 --- /dev/null +++ b/easybuild/easyconfigs/p/p4est/p4est-2.8-foss-2021a.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'p4est' +version = '2.8' + +homepage = 'https://www.p4est.org' +description = """p4est is a C library to manage a collection (a forest) of multiple +connected adaptive quadtrees or octrees in parallel.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://p4est.github.io/release'] +sources = [SOURCE_TAR_GZ] +patches = [ + # 'p4est-2.2_remove_loadsave_tests.patch', + # 'p4est-2.8_automake_version.patch', + # 'sc_test_sort.patch', +] +# checksums = [ +# '6a0586e3abac06c20e31b1018f3a82a564a6a0d9ff6b7f6c772a9e6b0f0cc5e4', # p4est-2.8.tar.gz +# '20cabc7985edbc007fb8190fafc51b873a2c3eb879700ff93432646b563ec642', # p4est-2.2_remove_loadsave_tests.patch +# ] + +builddependencies = [ + ('Autotools', '20210128') +] + +dependencies = [ + ('zlib', '1.2.11'), + ('METIS', '5.1.0') +] + +# preconfigopts = "./bootstrap && " +# preconfigopts = 'autoreconf -f -i && ' +configopts = "--enable-openmp --enable-mpi --with-metis " +configopts += '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' + +configopts += '--disable-shared --enable-static ' + +# commenting out 'make check' - one test fails and if we patched +# runtest = 'check VERBOSE=1' + +sanity_check_paths = { + 'files': ['bin/p4est_simple', 'bin/p4est_step1', 'bin/p4est_step2', 'bin/p4est_step3', 'bin/p4est_step4', + 'lib/libp4est.a', 'lib/libp4est.la'], + 'dirs': [], +} + +moduleclass = 'math' From 48231305f36a9fae2a26815e37b27c969a2dcdc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jun 2022 18:49:27 +0200 Subject: [PATCH 4005/9987] add missing checksum for p4est v2.8 --- easybuild/easyconfigs/p/p4est/p4est-2.8-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/p4est/p4est-2.8-foss-2021a.eb b/easybuild/easyconfigs/p/p4est/p4est-2.8-foss-2021a.eb index 83f62b1d921..b8097204f60 100644 --- a/easybuild/easyconfigs/p/p4est/p4est-2.8-foss-2021a.eb +++ b/easybuild/easyconfigs/p/p4est/p4est-2.8-foss-2021a.eb @@ -17,6 +17,8 @@ patches = [ # 'p4est-2.8_automake_version.patch', # 'sc_test_sort.patch', ] +checksums = ['6a0586e3abac06c20e31b1018f3a82a564a6a0d9ff6b7f6c772a9e6b0f0cc5e4'] + # checksums = [ # '6a0586e3abac06c20e31b1018f3a82a564a6a0d9ff6b7f6c772a9e6b0f0cc5e4', # p4est-2.8.tar.gz # '20cabc7985edbc007fb8190fafc51b873a2c3eb879700ff93432646b563ec642', # p4est-2.2_remove_loadsave_tests.patch From 412c251fe7743f9084efc411a66bc7d05060219a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 14 Jun 2022 19:37:11 +0200 Subject: [PATCH 4006/9987] Rework Mmg-5.6.0 tests, fixes #15662 --- .../m/Mmg/Mmg-5.6.0-gompi-2021b.eb | 12 +- .../m/Mmg/mmg-5.6.0_remove_ci_tests.patch | 149 ++++++++++++++++++ 2 files changed, 158 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/m/Mmg/mmg-5.6.0_remove_ci_tests.patch diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb index 2a6288ecfa1..a27faef39a9 100644 --- a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb @@ -19,16 +19,22 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://github.com/MmgTools/mmg/archive'] sources = ['v%(version)s.tar.gz'] -checksums = ['bbf9163d65bc6e0f81dd3acc5a51e4a8c47a7fdae849abc26277e01154fe2437'] +patches = ['mmg-%(version)s_remove_ci_tests.patch'] +checksums = [ + 'bbf9163d65bc6e0f81dd3acc5a51e4a8c47a7fdae849abc26277e01154fe2437', # v5.6.0.tar.gz + '99de7437fb9d036c786b7f1526da93d4aa1d28e728fe7279f4c9204bbbb9f734', # mmg-5.6.0_remove_ci_tests.patch +] builddependencies = [('CMake', '3.21.1')] dependencies = [('SCOTCH', '6.1.2')] -configopts = '-DUSE_SCOTCH=ON -DBUILD_TESTING=ON ' +# CI tests require downloading of data that might not be available in the future. +# Sticking to tests included in the source with help of patch +configopts = '-DUSE_SCOTCH=ON -DBUILD_TESTING=ON -DONLY_VERY_SHORT_TESTS=ON ' +configopts += '-DTEST_LIBMMG2D=ON -DTEST_LIBMMG3D=ON -DTEST_LIBMMGS=ON ' configopts += '-DLIBMMG2D_SHARED=ON -DLIBMMG3D_SHARED=ON -DLIBMMGS_SHARED=ON -DLIBMMG_SHARED=ON ' -pretestopts = 'export CTEST_PARALLEL_LEVEL=%(parallel)s &&' runtest = 'test' sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/Mmg/mmg-5.6.0_remove_ci_tests.patch b/easybuild/easyconfigs/m/Mmg/mmg-5.6.0_remove_ci_tests.patch new file mode 100644 index 00000000000..da4234aa2fc --- /dev/null +++ b/easybuild/easyconfigs/m/Mmg/mmg-5.6.0_remove_ci_tests.patch @@ -0,0 +1,149 @@ +Remove library CI tests that point to external sources. +These external sources did not have a permanent URL so are unreliable. +Tests can't simply be excluded since CMake will complain about missing sources. + +Author: micketeer@gmail.com +--- cmake/testing/libmmg2d_tests.cmake.orig 2022-06-13 22:54:57.697924494 +0200 ++++ cmake/testing/libmmg2d_tests.cmake 2022-06-13 22:56:27.167776567 +0200 +@@ -36,7 +36,6 @@ + libmmg2d_ls_example0 + libmmg2d_lsOnly + libmmg2d_lsAndMetric +- test_api2d_0 + ) + SET ( MMG2D_LIB_TESTS_MAIN_PATH + ${PROJECT_SOURCE_DIR}/libexamples/mmg2d/adaptation_example0/example0_a/main.c +@@ -47,7 +46,6 @@ + ${PROJECT_SOURCE_DIR}/libexamples/mmg2d/io_multisols_example0/main.c + ${PROJECT_SOURCE_DIR}/libexamples/mmg2d/IsosurfDiscretization_lsOnly/main.c + ${PROJECT_SOURCE_DIR}/libexamples/mmg2d/IsosurfDiscretization_lsAndMetric/main.c +- ${MMG2D_CI_TESTS}/API_tests/2d.c + ) + + IF ( LIBMMG2D_STATIC ) +@@ -69,7 +67,6 @@ + libmmg2d_fortran_io + libmmg2d_fortran_lsOnly + libmmg2d_fortran_lsAndMetric +- test_api2d_fortran_0 + test_io2d_fortran + ) + +@@ -79,7 +76,6 @@ + ${PROJECT_SOURCE_DIR}/libexamples/mmg2d/io_multisols_example0/main.F90 + ${PROJECT_SOURCE_DIR}/libexamples/mmg2d/IsosurfDiscretization_lsOnly/main.F90 + ${PROJECT_SOURCE_DIR}/libexamples/mmg2d/IsosurfDiscretization_lsAndMetric/main.F90 +- ${MMG2D_CI_TESTS}/API_tests/2d.F90 + ${PROJECT_SOURCE_DIR}/cmake/testing/code/mmg2d_io.F90 + ) + +--- cmake/modules/mmg2d.cmake.orig 2022-06-14 18:32:00.431611009 +0200 ++++ cmake/modules/mmg2d.cmake 2022-06-14 18:31:57.852586956 +0200 +@@ -220,10 +220,6 @@ + "${PROJECT_SOURCE_DIR}/libexamples/mmg2d/IsosurfDiscretization_lsOnly/multi-mat-sol.sol" + "${CTEST_OUTPUT_DIR}/libmmg2d_lsAndMetric_multimat.o" + ) +- ADD_TEST(NAME test_api2d_0 COMMAND ${TEST_API2D_EXEC0} +- "${MMG2D_CI_TESTS}/API_tests/2dom.mesh" +- "${CTEST_OUTPUT_DIR}/test_API2d.o" +- ) + + + IF ( CMAKE_Fortran_COMPILER) +@@ -261,18 +257,6 @@ + "${PROJECT_SOURCE_DIR}/libexamples/mmg2d/IsosurfDiscretization_lsOnly/multi-mat-sol.sol" + "${CTEST_OUTPUT_DIR}/libmmg2d_lsAndMetric_multimat.o" + ) +- ADD_TEST(NAME test_api2d_fortran_0 COMMAND ${TEST_API2D_FORTRAN_EXEC0} +- "${MMG2D_CI_TESTS}/API_tests/2dom.mesh" +- "${CTEST_OUTPUT_DIR}/test_API2d.o" +- ) +- ADD_TEST(NAME test_io2d_fortran_scalar COMMAND ${TEST_IO2D_FORTRAN_EXEC} +- "${MMG2D_CI_TESTS}/Hybrid/hybrid.mesh" +- "${CTEST_OUTPUT_DIR}/hybrid-2d-scal.o" 0 +- ) +- ADD_TEST(NAME test_io2d_fortran_array COMMAND ${TEST_IO2D_FORTRAN_EXEC} +- "${MMG2D_CI_TESTS}/Hybrid/hybrid.mesh" +- "${CTEST_OUTPUT_DIR}/hybrid-2d-array.o" 1 +- ) + + ENDIF() + +--- cmake/testing/libmmg3d_tests.cmake.orig 2022-06-14 19:26:45.958431873 +0200 ++++ cmake/testing/libmmg3d_tests.cmake 2022-06-14 19:27:49.551026041 +0200 +@@ -35,9 +35,6 @@ + libmmg3d_example6_io + libmmg3d_lsOnly + libmmg3d_lsAndMetric +- test_api3d_0 +- test_api3d_domain-selection +- test_api3d_vtk2mesh + ) + SET ( MMG3D_LIB_TESTS_MAIN_PATH + ${PROJECT_SOURCE_DIR}/libexamples/mmg3d/adaptation_example0/example0_a/main.c +@@ -48,9 +45,6 @@ + ${PROJECT_SOURCE_DIR}/libexamples/mmg3d/io_multisols_example6/main.c + ${PROJECT_SOURCE_DIR}/libexamples/mmg3d/IsosurfDiscretization_lsOnly/main.c + ${PROJECT_SOURCE_DIR}/libexamples/mmg3d/IsosurfDiscretization_lsAndMetric/main.c +- ${MMG3D_CI_TESTS}/API_tests/3d.c +- ${MMG3D_CI_TESTS}/API_tests/domain-selection.c +- ${MMG3D_CI_TESTS}/API_tests/vtk2mesh.c + ) + + IF ( LIBMMG3D_STATIC ) +@@ -72,7 +66,6 @@ + libmmg3d_fortran_io + libmmg3d_fortran_lsOnly + libmmg3d_fortran_lsAndMetric +- test_api3d_fortran_0 + ) + + SET ( MMG3D_LIB_TESTS_MAIN_PATH ${MMG3D_LIB_TESTS_MAIN_PATH} +@@ -81,7 +74,6 @@ + ${PROJECT_SOURCE_DIR}/libexamples/mmg3d/io_multisols_example6/main.F90 + ${PROJECT_SOURCE_DIR}/libexamples/mmg3d/IsosurfDiscretization_lsOnly/main.F90 + ${PROJECT_SOURCE_DIR}/libexamples/mmg3d/IsosurfDiscretization_lsAndMetric/main.F90 +- ${MMG3D_CI_TESTS}/API_tests/3d.F90 + ) + + ENDIF ( CMAKE_Fortran_COMPILER ) +--- cmake/modules/mmg3d.cmake.orig 2022-06-14 18:30:39.374855012 +0200 ++++ cmake/modules/mmg3d.cmake 2022-06-14 19:22:51.535241582 +0200 +@@ -248,26 +248,6 @@ + "${PROJECT_SOURCE_DIR}/libexamples/mmg3d/IsosurfDiscretization_lsOnly/m.sol" + "${CTEST_OUTPUT_DIR}/libmmg3d_lsAndMetric_multimat.o" + ) +- ADD_TEST(NAME test_api3d_0 COMMAND ${TEST_API3D_EXEC0} +- "${MMG3D_CI_TESTS}/API_tests/2dom.mesh" +- "${CTEST_OUTPUT_DIR}/test_API3d.o" +- ) +- ADD_TEST(NAME test_api3d_domain-selection COMMAND ${TEST_API3D_DOMSEL} +- "${MMG3D_CI_TESTS}/OptLs_plane/plane.mesh" +- "${MMG3D_CI_TESTS}/OptLs_plane/p.sol" +- "${CTEST_OUTPUT_DIR}/test_API3d-domsel-whole.o" +- "${CTEST_OUTPUT_DIR}/test_API3d-domsel-dom2.o" +- ) +- ADD_TEST(NAME test_api3d_vtk2mesh COMMAND ${TEST_API3D_VTK2MESH} +- "${MMG3D_CI_TESTS}/API_tests/cellsAndNode-data.vtk" +- "${CTEST_OUTPUT_DIR}/test_API3d-vtk2mesh.o" +- ) +- +- IF ( NOT VTK_FOUND ) +- SET(expr "VTK library not founded") +- SET_PROPERTY(TEST test_api3d_vtk2mesh +- PROPERTY PASS_REGULAR_EXPRESSION "${expr}") +- ENDIF ( ) + + IF ( CMAKE_Fortran_COMPILER) + SET(LIBMMG3D_EXECFORTRAN_a ${EXECUTABLE_OUTPUT_PATH}/libmmg3d_fortran_a) +@@ -302,10 +282,6 @@ + "${PROJECT_SOURCE_DIR}/libexamples/mmg3d/IsosurfDiscretization_lsOnly/plane.mesh" + "${PROJECT_SOURCE_DIR}/libexamples/mmg3d/IsosurfDiscretization_lsOnly/m.sol" + "${CTEST_OUTPUT_DIR}/libmmg3d_lsAndMetric_multimat.o" ) +- ADD_TEST(NAME test_api3d_fortran_0 COMMAND ${TEST_API3D_FORTRAN_EXEC0} +- "${MMG3D_CI_TESTS}/API_tests/2dom.mesh" +- "${CTEST_OUTPUT_DIR}/test_API3d.o" +- ) + + ENDIF() + From 463e6f6b17745ca34854699f23849621457407dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Jun 2022 21:35:49 +0200 Subject: [PATCH 4007/9987] fix configure options for deal.II v9.3.3 --- .../d/deal.II/deal.II-9.3.3-foss-2021a.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb b/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb index 60a54d16d5e..231e3c4f685 100644 --- a/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb +++ b/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb @@ -28,14 +28,14 @@ dependencies = [ configopts = "-DCMAKE_BUILD_TYPE=Release " configopts += "-DDEAL_II_WITH_LAPACK=ON -DDEAL_II_WITH_MPI=ON " -configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_METIS=ON -DMETIS_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_NETCDF=ON -DNETCDF_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=$EBROOTP4EST" -configopts += "-DDEAL_II_WITH_PETSC=ON -DPETSC_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_ZLIB=ON -DZLIB_DIR=$EBROOTZLIB" +configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST " +configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTGSL " +configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTHDF5 " +configopts += "-DDEAL_II_WITH_METIS=ON -DMETIS_DIR=$EBROOTMETIS " +configopts += "-DDEAL_II_WITH_NETCDF=ON -DNETCDF_DIR=$EBROOTNETCDF " +configopts += "-DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=$EBROOTP4EST " +configopts += "-DDEAL_II_WITH_PETSC=ON -DPETSC_DIR=$EBROOTPETSC " +configopts += "-DDEAL_II_WITH_ZLIB=ON -DZLIB_DIR=$EBROOTZLIB " sanity_check_paths = { 'files': ['lib/libdeal_II.%s' % SHLIB_EXT], From 7201e6fb835075b6ca3e958cb8f5e87988eabe39 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Jun 2022 09:55:54 +0100 Subject: [PATCH 4008/9987] correct configopts in deal.II --- .../d/deal.II/deal.II-9.1.1-intel-2019a.eb | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb index 5cf9458bf12..890ad72614a 100644 --- a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb +++ b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb @@ -26,16 +26,15 @@ dependencies = [ ('zlib', '1.2.11'), ] -configopts = "-DCMAKE_BUILD_TYPE=Release " -configopts += "-DDEAL_II_WITH_LAPACK=ON -DDEAL_II_WITH_MPI=ON " -configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_METIS=ON -DMETIS_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_NETCDF=ON -DNETCDF_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=$EBROOTP4EST" -configopts += "-DDEAL_II_WITH_PETSC=ON -DPETSC_DIR=$EBROOTBOOST" -configopts += "-DDEAL_II_WITH_ZLIB=ON -DZLIB_DIR=$EBROOTZLIB" +configopts = "-DDEAL_II_WITH_LAPACK=ON -DDEAL_II_WITH_MPI=ON " +configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST " +configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTGSL " +configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTHDF5 " +configopts += "-DDEAL_II_WITH_METIS=ON -DMETIS_DIR=$EBROOTMETIS " +configopts += "-DDEAL_II_WITH_NETCDF=ON -DNETCDF_DIR=$EBROOTNETCDF " +configopts += "-DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=$EBROOTP4EST " +configopts += "-DDEAL_II_WITH_PETSC=ON -DPETSC_DIR=$EBROOTPETSC " +configopts += "-DDEAL_II_WITH_ZLIB=ON -DZLIB_DIR=$EBROOTZLIB " sanity_check_paths = { 'files': ['lib/libdeal_II.%s' % SHLIB_EXT], From 9427350d4c0bc8c44c0b3d6981c832a23fbf43e4 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 15 Jun 2022 11:07:23 +0100 Subject: [PATCH 4009/9987] remove netCDF from configopts --- easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb index 890ad72614a..2694ffaf897 100644 --- a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb +++ b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb @@ -31,7 +31,6 @@ configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST " configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTGSL " configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTHDF5 " configopts += "-DDEAL_II_WITH_METIS=ON -DMETIS_DIR=$EBROOTMETIS " -configopts += "-DDEAL_II_WITH_NETCDF=ON -DNETCDF_DIR=$EBROOTNETCDF " configopts += "-DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=$EBROOTP4EST " configopts += "-DDEAL_II_WITH_PETSC=ON -DPETSC_DIR=$EBROOTPETSC " configopts += "-DDEAL_II_WITH_ZLIB=ON -DZLIB_DIR=$EBROOTZLIB " From 5a93e3d3f425ac52ed78fc36e974fc6976bb3b2f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 15 Jun 2022 11:53:07 +0100 Subject: [PATCH 4010/9987] Update easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb --- easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb b/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb index 231e3c4f685..a0ce9cbeb67 100644 --- a/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb +++ b/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb @@ -26,8 +26,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -configopts = "-DCMAKE_BUILD_TYPE=Release " -configopts += "-DDEAL_II_WITH_LAPACK=ON -DDEAL_II_WITH_MPI=ON " +configopts = "-DDEAL_II_WITH_LAPACK=ON -DDEAL_II_WITH_MPI=ON " configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST " configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTGSL " configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTHDF5 " From 0361f5a59306cda00c95aee1bf421bf7d5b5c51f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jun 2022 13:16:02 +0200 Subject: [PATCH 4011/9987] adding easyconfigs: PRISMS-PF-2.2-foss-2021a.eb --- .../p/PRISMS-PF/PRISMS-PF-2.2-foss-2021a.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.2-foss-2021a.eb b/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.2-foss-2021a.eb new file mode 100644 index 00000000000..f759db2d926 --- /dev/null +++ b/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.2-foss-2021a.eb @@ -0,0 +1,72 @@ +easyblock = 'Bundle' + +name = 'PRISMS-PF' +version = '2.2' + +homepage = 'https://prisms-center.github.io/phaseField' +description = """PRISMS-PF is a powerful, massively parallel finite element code for conducting phase field and + other related simulations of microstructural evolution.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Boost', '1.76.0'), + ('GSL', '2.7'), + ('HDF5', '1.10.7'), + ('METIS', '5.1.0'), + ('netCDF', '4.8.0'), + ('p4est', '2.8'), + ('PETSc', '3.15.1'), + ('zlib', '1.2.11'), +] + +local_dealii_configopts = "-DCMAKE_BUILD_TYPE=Release " +local_dealii_configopts += "-DDEAL_II_WITH_LAPACK=ON -DDEAL_II_WITH_MPI=ON " +local_dealii_configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST " +local_dealii_configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTGSL " +local_dealii_configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTHDF5 " +local_dealii_configopts += "-DDEAL_II_WITH_METIS=ON -DMETIS_DIR=$EBROOTMETIS " +local_dealii_configopts += "-DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=$EBROOTP4EST " +local_dealii_configopts += "-DDEAL_II_WITH_PETSC=ON -DPETSC_DIR=$EBROOTPETSC " +local_dealii_configopts += "-DDEAL_II_WITH_ZLIB=ON -DZLIB_DIR=$EBROOTZLIB " + +components = [ + # PRISMS-PF v2.2 is not compatible yet with deal.II v9.3.x, + # so include deal.II v9.2.0 as bundle component (rather than using it as a dependency) + ('deal.II', '9.2.0', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/dealii/dealii/releases/download/v%(version)s/'], + 'sources': ['dealii-%(version)s.tar.gz'], + 'patches': ['deal.II-9.2.0_fix-boost-include.patch'], + 'checksums': [ + 'd05a82fb40f1f1e24407451814b5a6004e39366a44c81208b1ae9d65f3efa43a', # dealii-9.2.0.tar.gz + '3eb1a25123ea2c72835a227a0174c2d0dbb6350793a01375757f06f72e77811a', # deal.II-9.2.0_fix-boost-include.patch + ], + 'start_dir': 'dealii-%(version)s', + 'preconfigopts': 'export LDFLAGS="$LDFLAGS $CFLAGS" && ', + 'configopts': local_dealii_configopts, + }), + (name, version, { + 'easyblock': 'CMakeMakeCp', + 'source_urls': ['https://github.com/prisms-center/phaseField/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['17214a1b04b9e4ae031663831ce20fb30f1db60b0890fe2055d52852798d9ae9'], + 'start_dir': 'phaseField-%(version)s', + 'configopts': "-DCMAKE_PREFIX_PATH=$EBROOTDEALII", + 'buildopts': 'release', + 'files_to_copy': [ + 'applications', + (['include/*'], 'include'), + (['libprisms_pf*.a'], 'lib'), + ], + }), +] + +sanity_check_paths = { + 'files': ['lib/libdeal_II.%s' % SHLIB_EXT, 'lib/libprisms_pf.a', 'lib/libprisms_pf_debug.a'], + 'dirs': ['applications', 'include/deal.II', 'lib/cmake', 'lib/pkgconfig', 'share/deal.II'], +} + +moduleclass = 'phys' From 7c6c30d1f75ba8703e6b711bdda9501f68eb88a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jun 2022 13:31:07 +0200 Subject: [PATCH 4012/9987] drop unused netCDF dependency for deal.II v9.3.3 (netCDF support was removed, see https://github.com/dealii/dealii/pull/10387) --- easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb b/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb index a0ce9cbeb67..8a5a4ae839f 100644 --- a/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb +++ b/easybuild/easyconfigs/d/deal.II/deal.II-9.3.3-foss-2021a.eb @@ -20,7 +20,6 @@ dependencies = [ ('GSL', '2.7'), ('HDF5', '1.10.7'), ('METIS', '5.1.0'), - ('netCDF', '4.8.0'), ('p4est', '2.8'), ('PETSc', '3.15.1'), ('zlib', '1.2.11'), @@ -31,7 +30,6 @@ configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST " configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTGSL " configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTHDF5 " configopts += "-DDEAL_II_WITH_METIS=ON -DMETIS_DIR=$EBROOTMETIS " -configopts += "-DDEAL_II_WITH_NETCDF=ON -DNETCDF_DIR=$EBROOTNETCDF " configopts += "-DDEAL_II_WITH_P4EST=ON -DP4EST_DIR=$EBROOTP4EST " configopts += "-DDEAL_II_WITH_PETSC=ON -DPETSC_DIR=$EBROOTPETSC " configopts += "-DDEAL_II_WITH_ZLIB=ON -DZLIB_DIR=$EBROOTZLIB " From f65dd3909f407acac547be47110a3ceb44acd55f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 15 Jun 2022 13:03:15 +0100 Subject: [PATCH 4013/9987] remove netCDF --- easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb index 2694ffaf897..2b915e9a27c 100644 --- a/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb +++ b/easybuild/easyconfigs/d/deal.II/deal.II-9.1.1-intel-2019a.eb @@ -20,7 +20,6 @@ dependencies = [ ('GSL', '2.5'), ('HDF5', '1.10.5'), ('METIS', '5.1.0'), - ('netCDF', '4.6.2'), ('p4est', '2.2'), ('PETSc', '3.11.1', '-Python-3.7.2'), ('zlib', '1.2.11'), From 2778b658c868295a447db1d9aa5f2cfd483ed4ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jun 2022 14:29:12 +0200 Subject: [PATCH 4014/9987] add patch for deal.II v9.2.0 required by PRISMS-PF v2.2 easyconfig --- .../deal.II-9.2.0_fix-boost-include.patch | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRISMS-PF/deal.II-9.2.0_fix-boost-include.patch diff --git a/easybuild/easyconfigs/p/PRISMS-PF/deal.II-9.2.0_fix-boost-include.patch b/easybuild/easyconfigs/p/PRISMS-PF/deal.II-9.2.0_fix-boost-include.patch new file mode 100644 index 00000000000..e7423007001 --- /dev/null +++ b/easybuild/easyconfigs/p/PRISMS-PF/deal.II-9.2.0_fix-boost-include.patch @@ -0,0 +1,28 @@ +fix for: /software/Boost/1.76.0-GCC-10.3.0/include/boost/geometry/strategies/envelope/services.hpp:32:5: error: static assertion failed: Not implemented for this coordinate system. + 32 | BOOST_GEOMETRY_STATIC_ASSERT_FALSE( + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +cfr. https://github.com/dealii/dealii/pull/11438 + +From 9c1a580139f557433a226da437382b3f4307f7c8 Mon Sep 17 00:00:00 2001 +From: Luca Heltai +Date: Wed, 30 Dec 2020 09:54:02 +0100 +Subject: [PATCH] Fix boost include file. + +--- + source/fe/mapping.cc | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/source/fe/mapping.cc b/source/fe/mapping.cc +index 288a9debcb1e..4ef3ef77149f 100644 +--- a/source/fe/mapping.cc ++++ b/source/fe/mapping.cc +@@ -20,6 +20,8 @@ + + #include + ++#include ++ + DEAL_II_NAMESPACE_OPEN + + From ca35bef4c82e7f88644e30f6759e18d24d1d8038 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jun 2022 14:58:50 +0200 Subject: [PATCH 4015/9987] add missing Python dependency for HPDBSCAN to fix unresolved %(pyshortver)s template --- easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb index f106d8a2279..b96581acb3c 100644 --- a/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb +++ b/easybuild/easyconfigs/h/HPDBSCAN/HPDBSCAN-20210826-foss-2020b.eb @@ -20,6 +20,7 @@ builddependencies = [ dependencies = [ ('HDF5', '1.10.7'), + ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), # for mpi4py ('SWIG', '4.0.2'), ] From b73ea985ad6c30bc22c622b5fe04e2163826840d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 15 Jun 2022 16:01:32 +0200 Subject: [PATCH 4016/9987] adding easyconfigs: MONA-1.4-18-GCC-11.2.0.eb --- .../m/MONA/MONA-1.4-18-GCC-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MONA/MONA-1.4-18-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MONA/MONA-1.4-18-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MONA/MONA-1.4-18-GCC-11.2.0.eb new file mode 100644 index 00000000000..5e144992c6a --- /dev/null +++ b/easybuild/easyconfigs/m/MONA/MONA-1.4-18-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'MONA' +version = '1.4-18' + +homepage = 'https://www.brics.dk/mona/index.html' +description = """ +MONA is a tool that translates formulas to finite-state automata. The formulas +may express search patterns, temporal properties of reactive systems, parse +tree constraints, etc. MONA analyses the automaton resulting from the +compilation and prints out "valid" or a counter-example.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://www.brics.dk/mona/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ece10e1e257dcae48dd898ed3da48f550c6b590f8e5c5a6447d0f384ac040e4c'] + +install_cmd = 'make install-strip' + +sanity_check_paths = { + 'files': ['bin/mona'], + 'dirs': ['include/mona', 'lib', 'share'], +} + +sanity_check_commands = ['mona | grep "Usage: mona"'] + +moduleclass = 'math' From 44e3b5d775e0637da2f5a58ca475b011e1b211c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jun 2022 16:13:48 +0200 Subject: [PATCH 4017/9987] don't use -DCMAKE_BUILD_TYPE=Release since CMakeMake does that by default already --- easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.2-foss-2021a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.2-foss-2021a.eb b/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.2-foss-2021a.eb index f759db2d926..c19bc7c0aa4 100644 --- a/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PRISMS-PF/PRISMS-PF-2.2-foss-2021a.eb @@ -22,8 +22,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -local_dealii_configopts = "-DCMAKE_BUILD_TYPE=Release " -local_dealii_configopts += "-DDEAL_II_WITH_LAPACK=ON -DDEAL_II_WITH_MPI=ON " +local_dealii_configopts = "-DDEAL_II_WITH_LAPACK=ON -DDEAL_II_WITH_MPI=ON " local_dealii_configopts += "-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST " local_dealii_configopts += "-DDEAL_II_WITH_GSL=ON -DGSL_DIR=$EBROOTGSL " local_dealii_configopts += "-DDEAL_II_WITH_HDF5=ON -DHDF5_DIR=$EBROOTHDF5 " From cb7bb113d830b88107672b45583a6650c055c6f6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 15 Jun 2022 16:20:41 +0200 Subject: [PATCH 4018/9987] adding easyconfigs: PnetCDF-1.12.3-gompi-2021b.eb --- .../p/PnetCDF/PnetCDF-1.12.3-gompi-2021b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2021b.eb diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2021b.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2021b.eb new file mode 100644 index 00000000000..83d4cfd6bc0 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2021b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = '1.12.3' + +homepage = 'https://parallel-netcdf.github.io/' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://parallel-netcdf.github.io/Release'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['439e359d09bb93d0e58a6e3f928f39c2eae965b6c97f64e67cd42220d6034f77'] + +builddependencies = [ + ('Autotools', '20210726'), + ('Perl', '5.34.0'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' From 8aafc56f6c59fdb8494a05fa01f8a1a12b0837cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jun 2022 16:41:03 +0200 Subject: [PATCH 4019/9987] adding easyconfigs: ReFrame-3.11.2.eb --- .../easyconfigs/r/ReFrame/ReFrame-3.11.2.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.2.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.2.eb new file mode 100644 index 00000000000..ccc3af8e291 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.11.2.eb @@ -0,0 +1,70 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.11.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + # stick to pip < 22.0, to maintain compatibility with Python 3.6 + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + # stick to setuptools < 59.7.0, to maintain compatibility with Python 3.6 + ('setuptools', '59.6.0', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + }), + ('reframe', version, { + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['d6f36071df316d6a5ef5ce6f0477b3385d9dac5c1b82e54ae6954dc9b68f9440'], + }), +] + +postinstallcmds = [ + "cp -a hpctestlib tools tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'hpctestlib', 'lib', 'tools', 'tutorials'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 937cb1c9608d8db78c7f8001342e9f796f87218b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 15 Jun 2022 16:41:53 +0200 Subject: [PATCH 4020/9987] adding easyconfigs: git-lfs-3.2.0.eb --- .../easyconfigs/g/git-lfs/git-lfs-3.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb new file mode 100644 index 00000000000..172197cedf0 --- /dev/null +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'git-lfs' +version = '3.2.0' + +homepage = 'https://git-lfs.github.com' +description = """Git Large File Storage (LFS) replaces large files such as audio + samples, videos, datasets, and graphics with text pointers inside Git, while + storing the file contents on a remote server like GitHub.com""" + +toolchain = SYSTEM + +github_account = name +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f8e6bbe043b97db8a5c16da7289e149a3fed9f4d4f11cffcc6e517c7870cd9e5'] + +builddependencies = [('Go', '1.17.6')] + +files_to_copy = [(['bin/%(name)s'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/git-lfs'], + 'dirs': [], +} + +sanity_check_commands = [('git-lfs', '--version')] + +# set up Git LFS for the user account +modluafooter = """ +if mode() == "load" then + cmdout = subprocess("git lfs install") + LmodMessage(cmdout) +end""" + +moduleclass = 'tools' From c1e7af567a5b1633d1c9da49db3d779dd923a636 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jun 2022 18:38:27 +0200 Subject: [PATCH 4021/9987] adding easyconfigs: CellRanger-7.0.0.eb --- .../c/CellRanger/CellRanger-7.0.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellRanger/CellRanger-7.0.0.eb diff --git a/easybuild/easyconfigs/c/CellRanger/CellRanger-7.0.0.eb b/easybuild/easyconfigs/c/CellRanger/CellRanger-7.0.0.eb new file mode 100644 index 00000000000..d3770f6b743 --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger/CellRanger-7.0.0.eb @@ -0,0 +1,29 @@ +# The STAR binary included in this version has been vectorized with AVX +# hence it is not recommended for systems that do not support it. + +easyblock = 'Tarball' + +name = 'CellRanger' +version = '7.0.0' + +homepage = 'https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger' +description = """Cell Ranger is a set of analysis pipelines that process Chromium + single-cell RNA-seq output to align reads, generate gene-cell matrices and perform + clustering and gene expression analysis.""" + +toolchain = SYSTEM + +# Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fd0d5b66f9513e6d52d0d4bc7b3d065b877d975280009d1f34d592e4b6d9d84'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ['bin/cellranger'], + 'dirs': ['bin/rna', 'bin/tenkit'], +} + +sanity_check_commands = ['cellranger testrun --id=tiny'] + +moduleclass = 'bio' From a94135c4a4002aa55928cf08ec38282a5b4ac24a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Jun 2022 19:05:11 +0200 Subject: [PATCH 4022/9987] add hypergeo extension to R v4.2.0 --- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 46759989620..3f2e3665256 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -3343,6 +3343,15 @@ exts_list = [ ('renv', '0.15.5', { 'checksums': ['b4f1a9a7daa82f0c3123ebd4eeba06e98d5485215518e5292b25bc56741d582e'], }), + ('elliptic', '1.4-0', { + 'checksums': ['b65729b1a1c7a84a5b1a59bfc893a2d35106853eaadcae31cda5c9ee3c500bb6'], + }), + ('contfrac', '1.1-12', { + 'checksums': ['95bfc5e970513416c080486a1cd8dfd9f8d59fb691b02ef6ccbe0ce1ed61056b'], + }), + ('hypergeo', '1.2-13', { + 'checksums': ['6d5b78353aad1d13091ccbeb340867dad7b9eb00d0e2185286dc7e13848f4d8e'], + }), ] moduleclass = 'lang' From 88d6dd207be494312fd5344dd4ba3b9ae6efb573 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Jun 2022 20:50:01 +0100 Subject: [PATCH 4023/9987] adding easyconfigs: Gibbs2-1.0-GCC-10.3.0.eb --- .../g/Gibbs2/Gibbs2-1.0-GCC-10.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gibbs2/Gibbs2-1.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/g/Gibbs2/Gibbs2-1.0-GCC-10.3.0.eb b/easybuild/easyconfigs/g/Gibbs2/Gibbs2-1.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..61ec9ac3028 --- /dev/null +++ b/easybuild/easyconfigs/g/Gibbs2/Gibbs2-1.0-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Gibbs2' +version = '1.0' + +homepage = 'https://aoterodelaroza.github.io/gibbs2/' +description = """Gibbs2 is a program for the calculation of thermodynamic properties in periodic solids under arbitrary + conditions of temperature and pressure. Gibbs2 uses the results of periodic solid-state quantum-mechanical + calculations, specifically the energy-volume curve and possibly the harmonic phonon frequencies, to compute the + thermodynamic properties of the solid within the framework of the quasiharmonic approximation.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://aoterodelaroza.github.io/assets/gibbs2/versions/'] +sources = [SOURCELOWER_ZIP] +checksums = ['4ded7abcfe0cd4af1e06842face358c800577a7bc6850507d51488da24205f32'] + +builddependencies = [ + ('CMake', '3.20.1'), + # ('numdiff', '5.9.0'), # needed for tests +] + +start_dir = '%(namelower)s-%(version)s' + +# The tests comparison includes the full path to the directory the tests are run in. So they fail. +# configopts = "-DBUILD_TESTING=ON " +# runtest = 'test' + +sanity_check_paths = { + 'files': ["bin/%(namelower)s"], + 'dirs': [] +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' From 600ceadcf9949945aa167870c5759272cf670ee5 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 15 Jun 2022 20:54:08 +0100 Subject: [PATCH 4024/9987] chem, not everything is bio --- easybuild/easyconfigs/g/Gibbs2/Gibbs2-1.0-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gibbs2/Gibbs2-1.0-GCC-10.3.0.eb b/easybuild/easyconfigs/g/Gibbs2/Gibbs2-1.0-GCC-10.3.0.eb index 61ec9ac3028..1c861900a12 100644 --- a/easybuild/easyconfigs/g/Gibbs2/Gibbs2-1.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/Gibbs2/Gibbs2-1.0-GCC-10.3.0.eb @@ -33,4 +33,4 @@ sanity_check_paths = { sanity_check_commands = ["%(namelower)s --help"] -moduleclass = 'bio' +moduleclass = 'chem' From dc02e754060490b06bbbd8e20707a1cf7033ba72 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 16 Jun 2022 08:54:01 +0200 Subject: [PATCH 4025/9987] include flex builddep --- easybuild/easyconfigs/m/MONA/MONA-1.4-18-GCC-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MONA/MONA-1.4-18-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MONA/MONA-1.4-18-GCC-11.2.0.eb index 5e144992c6a..2e3dfd0eeb3 100644 --- a/easybuild/easyconfigs/m/MONA/MONA-1.4-18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MONA/MONA-1.4-18-GCC-11.2.0.eb @@ -16,6 +16,8 @@ source_urls = ['https://www.brics.dk/mona/download/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['ece10e1e257dcae48dd898ed3da48f550c6b590f8e5c5a6447d0f384ac040e4c'] +builddependencies = [('flex', '2.6.4')] + install_cmd = 'make install-strip' sanity_check_paths = { From f19285d233cd65d42f98c1b8497abfdbfc78fced Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 16 Jun 2022 18:42:54 +0200 Subject: [PATCH 4026/9987] adding easyconfigs: fio-3.30-GCCcore-10.3.0.eb --- .../f/fio/fio-3.30-GCCcore-10.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fio/fio-3.30-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/fio/fio-3.30-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/fio/fio-3.30-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..019e1f56d07 --- /dev/null +++ b/easybuild/easyconfigs/f/fio/fio-3.30-GCCcore-10.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'fio' +version = '3.30' + +homepage = 'https://github.com/axboe/fio' + +description = 'Flexible I/O tester' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'axboe' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['305647377527a2827223065582dd8a9269e69866426b341699d55bb4e4d3cc71'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': [], +} + +sanity_check_commands = ['fio -h'] + +moduleclass = 'tools' From c9a77588b2e519f31e4f2abd7888ba4cb2a653db Mon Sep 17 00:00:00 2001 From: John Dey Date: Thu, 16 Jun 2022 10:37:53 -0700 Subject: [PATCH 4027/9987] Update easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb index b76774997e1..32f3f69432e 100644 --- a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb @@ -8,8 +8,7 @@ easyblock = 'PythonPackage' name = 'spektral' version = '1.1.0' -local_cuda_suffix = '-CUDA-%(cudaver)s' -versionsuffix = local_cuda_suffix +versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://github.com/danielegrattarola/spektral' description = """Spektral is a Python library for graph deep learning. The main goal of this From d16bda6e62de21bf6e395f72132a39bf0c8f1d64 Mon Sep 17 00:00:00 2001 From: John Dey Date: Thu, 16 Jun 2022 10:38:00 -0700 Subject: [PATCH 4028/9987] Update easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb index 32f3f69432e..171697664e9 100644 --- a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb @@ -27,7 +27,7 @@ dependencies = [ ('tqdm', '4.62.3'), ('scikit-learn', '1.0.1'), ('CUDA', '11.4.1', '', True), - ('TensorFlow', '2.7.1', '-CUDA-%(cudaver)s'), + ('TensorFlow', '2.7.1', versionsuffix), ] download_dep_fail = True From 431494422ff8f244c58a17fbbb79b6afce1c692d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 17 Jun 2022 16:18:05 +0100 Subject: [PATCH 4029/9987] adding easyconfigs: nvtop-2.0.2-GCCcore-11.3.0.eb --- .../n/nvtop/nvtop-2.0.2-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/n/nvtop/nvtop-2.0.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-2.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-2.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..707aa488e81 --- /dev/null +++ b/easybuild/easyconfigs/n/nvtop/nvtop-2.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'nvtop' +version = '2.0.2' + +homepage = 'https://github.com/Syllo/nvtop' +description = 'htop-like GPU usage monitor' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/Syllo/nvtop/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['7f22bb9f59e36551f5d7640d265b63ec6af1a91a421fa220dd913a5a134e9901'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.23.1'), +] + +# Note: software dlopen's libraries from the OS installed drivers, thus no specific CUDA dependency. +dependencies = [ + ('ncurses', '6.2'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/nvtop'], + 'dirs': [], +} + +sanity_check_commands = ["nvtop --help"] + +moduleclass = 'tools' From ace9718410f24df56b725f70c0cc0faaa16e7452 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 17 Jun 2022 16:24:55 +0100 Subject: [PATCH 4030/9987] correct deps --- easybuild/easyconfigs/n/nvtop/nvtop-2.0.2-GCCcore-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-2.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-2.0.2-GCCcore-11.3.0.eb index 707aa488e81..cb75d8e7684 100644 --- a/easybuild/easyconfigs/n/nvtop/nvtop-2.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nvtop/nvtop-2.0.2-GCCcore-11.3.0.eb @@ -13,13 +13,13 @@ sources = ['%(version)s.tar.gz'] checksums = ['7f22bb9f59e36551f5d7640d265b63ec6af1a91a421fa220dd913a5a134e9901'] builddependencies = [ - ('binutils', '2.36.1'), + ('binutils', '2.38'), ('CMake', '3.23.1'), ] # Note: software dlopen's libraries from the OS installed drivers, thus no specific CUDA dependency. dependencies = [ - ('ncurses', '6.2'), + ('ncurses', '6.3'), ] separate_build_dir = True From f0707192a91ed9a1731247785332d3994aefe6d0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Jun 2022 10:22:16 +0200 Subject: [PATCH 4031/9987] adding easyconfigs: mold-1.3.0-GCCcore-11.3.0.eb --- .../m/mold/mold-1.3.0-GCCcore-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e78902943a2 --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'mold' +version = '1.3.0' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['02132ae717d7f22f8bc7e5c22642ad41541ec4c535fa85f095c60ecc81465a3d'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', True), +] + +skipsteps = ['configure'] + +# PREFIX must be specified when building, to ensure that the mold binary looks for mold-wrapper.so in the right place +buildopts = "PREFIX=%(installdir)s" +installopts = buildopts + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' From 0918e167f7defe16ec0183820b153db3c6c31cc2 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 20 Jun 2022 13:16:26 +0200 Subject: [PATCH 4032/9987] Update Jorg-1.0.1-foss-2020b.eb adjust checksum to version jorg 1.0.1 --- easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb index 11b8affb4e2..582026b28fe 100644 --- a/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/j/Jorg/Jorg-1.0.1-foss-2020b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} github_account = 'Helmholtz-UFZ' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['74b1c455ba57ab240921966255ca059840b97c47efcd16e9e66b9b6a8a136ee2'] +checksums = ['90a63d9dcd32fe7f65946798c98f1551cea20ceab6446e9e5898cbbe6f0be52d'] prepend_to_path = ['.'] dependencies = [ From eea6b67f518909f75e4c7731ab807ae17f7c27fa Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 20 Jun 2022 15:10:29 +0200 Subject: [PATCH 4033/9987] adding easyconfigs: poppler-21.06.1-GCC-10.2.0.eb --- .../p/poppler/poppler-21.06.1-GCC-10.2.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.2.0.eb b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.2.0.eb new file mode 100644 index 00000000000..50d29257193 --- /dev/null +++ b/easybuild/easyconfigs/p/poppler/poppler-21.06.1-GCC-10.2.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'poppler' +version = '21.06.1' + +homepage = 'https://poppler.freedesktop.org' +description = "Poppler is a PDF rendering library" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +builddependencies = [ + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), + ('Python', '3.8.6'), +] + +dependencies = [ + ('freetype', '2.10.3'), + ('fontconfig', '2.13.92'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('NSS', '3.57'), + ('LibTIFF', '4.1.0'), + ('Qt5', '5.14.2'), + ('Boost', '1.74.0'), + ('cairo', '1.16.0'), + ('OpenJPEG', '2.4.0'), + ('zlib', '1.2.11'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['86b09e5a02de40081a3916ef8711c5128eaf4b1fc59d5f87d0ec66f04f595db4'], + 'configopts': "-DENABLE_BOOST=ON", + }), + ('poppler-data', '0.4.10', { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['6e2fcef66ec8c44625f94292ccf8af9f1d918b410d5aa69c274ce67387967b30'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdfinfo', 'lib/libpoppler.%s' % SHLIB_EXT, 'lib/libpoppler-cpp.%s' % SHLIB_EXT, + 'lib/libpoppler-glib.%s' % SHLIB_EXT, 'lib/libpoppler-qt5.%s' % SHLIB_EXT], + 'dirs': ['include/poppler', 'lib/pkgconfig', 'share'], +} + +sanity_check_commands = ["pdfinfo --help"] + +moduleclass = 'lib' From 7a5304e1ad3437f837c9465112c052741efc2a64 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 20 Jun 2022 15:12:21 +0200 Subject: [PATCH 4034/9987] adding easyconfigs: graphite2-1.3.14-GCCcore-10.2.0.eb --- .../graphite2-1.3.14-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0a3fc8da20e --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' From b573353817ff6375da435a49b01b52b4a39da779 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 20 Jun 2022 16:11:57 +0200 Subject: [PATCH 4035/9987] adding easyconfigs: Globus-CLI-3.1.2-GCCcore-10.2.0.eb --- .../Globus-CLI-3.1.2-GCCcore-10.2.0.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..308e879ac99 --- /dev/null +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.2-GCCcore-10.2.0.eb @@ -0,0 +1,57 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'Globus-CLI' +version = '3.1.2' + +homepage = "https://docs.globus.org/cli/" +description = """A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services + from the shell, and is suited to both interactive and simple scripting use cases.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('OpenSSL', '1.1.1h'), + ('Python', '3.8.6'), +] + +builddependencies = [ + ('binutils', '2.35'), + ('OpenSSL', '1.1.1h'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('click', '8.0.3', { + 'checksums': ['410e932b050f5eed773c4cda94de75971c89cdb3155a72a0831139a79e5ecb5b'], + }), + ('configobj', '5.0.6', { + 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], + }), + ('cryptography', '3.3.1', { + 'checksums': ['7e177e4bea2de937a584b13645cab32f25e3d96fc0bc4a4cf99c27dc77682be6'], + }), + ('PyJWT', '2.3.0', { + 'modulename': 'jwt', + 'checksums': ['b888b4d56f06f6dcd777210c334e69c737be74755d3e5e9ee3fe67dc18a0ee41'], + }), + ('globus-sdk', '3.1.0', { + 'checksums': ['22b0f54ea0528f0a6c9906c5f983519482b5f00c2d6f903225a77f52ad22ef28'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + (name, version, { + 'modulename': 'globus_cli', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['b1667efc1bde56b9e6f56d74e7746988c7588f3a88a8264af10c15d5de003c82'], + }), +] + +fix_python_shebang_for = ['bin/globus', 'bin/jp.py', 'bin/pyjwt'] + +sanity_check_commands = ['globus --help'] + +moduleclass = 'data' From a3ad8e8f00478edd69ead5cfc00e804bd97f6232 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 20 Jun 2022 17:05:20 +0200 Subject: [PATCH 4036/9987] Skipping two more tests, as suggested by @Micket --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 7754197d9f6..e4f21197645 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -103,6 +103,9 @@ excluded_tests = { # 'distributed/rpc/test_process_group_agent', # This test fails constently when run as part of the test suite, but succeeds when run interactively 'test_model_dump', + # These tests appear flaky, possibly related to number of GPUs that are used + 'distributed/fsdp/test_fsdp_memory', + 'distributed/fsdp/test_fsdp_overlap', ] } From bf57306a51a943f5ba9ec47843d7fb129e3b769a Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 20 Jun 2022 17:39:30 +0200 Subject: [PATCH 4037/9987] adding easyconfigs: Minipolish-0.1.3-GCC-11.2.0.eb --- .../Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb b/easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..1a2c201654e --- /dev/null +++ b/easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = "Minipolish" +version = "0.1.3" + +homepage = "https://github.com/rrwick/Minipolish" +description = "A tool for Racon polishing of miniasm assemblies" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ["https://github.com/rrwick/Minipolish/archive/refs/tags/"] +sources = ["v%(version)s.tar.gz"] +checksums = ['dad0a477eddce30374ca7ace446c6918493b42d16215725dd6e3fa8e9f50b2a0'] + +dependencies = [ + ('Python', '3.9.6'), + ('edlib', '1.3.9') +] + +use_pip = True +sanity_pip_check = True + +options = {'modulename': False} + +sanity_check_paths = { + 'files': ['bin/minipolish'], + 'dirs': [] +} + +moduleclass = "tools" From bdf28a6d84ea8068c2beff3771b2e56ec12d5538 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Mon, 20 Jun 2022 18:53:49 +0200 Subject: [PATCH 4038/9987] Added download_dep_fail --- .../easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb b/easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb index 1a2c201654e..88e0f2e557b 100644 --- a/easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb @@ -19,6 +19,7 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True options = {'modulename': False} From 3d596e440d6781cb614f5a7fa98752fe0dd03219 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Jun 2022 19:53:55 +0200 Subject: [PATCH 4039/9987] adding easyconfigs: SUNDIALS-6.2.0-intel-2020b.eb, SUNDIALS-6.2.0-foss-2020b.eb --- .../s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb | 38 +++++++++++++++++++ .../s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb | 38 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb new file mode 100644 index 00000000000..794ce9c8257 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '6.2.0' + +homepage = 'https://computing.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['195d5593772fc483f63f08794d79e4bab30c2ec58e6ce4b0fb6bcc0e0c48f31d'] + +# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, +# other for new source tarball downloaded from GitHub + +builddependencies = [('CMake', '3.18.4')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb new file mode 100644 index 00000000000..332c5869a4b --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '6.2.0' + +homepage = 'https://computing.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['195d5593772fc483f63f08794d79e4bab30c2ec58e6ce4b0fb6bcc0e0c48f31d'] + +# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, +# other for new source tarball downloaded from GitHub + +builddependencies = [('CMake', '3.18.4')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' From eb47b0fc73f85623781fbd9d61aa3aead23dbf79 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 20 Jun 2022 17:58:49 +0000 Subject: [PATCH 4040/9987] {compiler}[system/system] Backport GCC 12 -fuse-ld=mold support to GCCcore-11.3.0 --- .../easyconfigs/g/GCCcore/GCCcore-11.3.0.eb | 2 + .../GCCcore/GCCcore-11.3.0_fuse-ld-mold.patch | 126 ++++++++++++++++++ 2 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fuse-ld-mold.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb index d877ec7eace..878c2e4b12a 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb @@ -34,6 +34,7 @@ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCCcore-11.3.0_fuse-ld-mold.patch', ] checksums = [ '98438e6cc7294298b474cf0da7655d9a8c8b796421bb0210531c294a950374ed', # gcc-11.3.0.tar.gz @@ -46,6 +47,7 @@ checksums = [ '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch + 'bba64714f8b84ad58b3b43c0d21b4ffc298274ae699f514ed2934f002146d840', # GCCcore-11.3.0_fuse-ld-mold.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fuse-ld-mold.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fuse-ld-mold.patch new file mode 100644 index 00000000000..72d3a1ace1d --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fuse-ld-mold.patch @@ -0,0 +1,126 @@ +From ad964f7eaef9c03ce68a01cfdd7fde9d56524868 Mon Sep 17 00:00:00 2001 +From: Martin Liska +Date: Tue, 21 Dec 2021 17:43:55 +0100 +Subject: [PATCH] Support ld.mold linker. + +gcc/ChangeLog: + + * collect2.c (main): Add ld.mold. + * common.opt: Add -fuse-ld=mold. + * doc/invoke.texi: Document it. + * gcc.c (driver_handle_option): Handle -fuse-ld=mold. + * opts.c (common_handle_option): Likewise. +--- + gcc/collect2.c | 10 +++++++--- + gcc/common.opt | 4 ++++ + gcc/doc/invoke.texi | 4 ++++ + gcc/gcc.c | 4 ++++ + gcc/opts.c | 1 + + 5 files changed, 20 insertions(+), 3 deletions(-) + +diff --git a/gcc/collect2.c b/gcc/collect2.c +index d47fe3f91959c..b322527847c70 100644 +--- a/gcc/collect2.c ++++ b/gcc/collect2.c +@@ -785,6 +785,7 @@ + USE_GOLD_LD, + USE_BFD_LD, + USE_LLD_LD, ++ USE_MOLD_LD, + USE_LD_MAX + } selected_linker = USE_DEFAULT_LD; + static const char *const ld_suffixes[USE_LD_MAX] = +@@ -793,7 +794,8 @@ + PLUGIN_LD_SUFFIX, + "ld.gold", + "ld.bfd", +- "ld.lld" ++ "ld.lld", ++ "ld.mold" + }; + static const char *const real_ld_suffix = "real-ld"; + static const char *const collect_ld_suffix = "collect-ld"; +@@ -970,6 +972,8 @@ + selected_linker = USE_GOLD_LD; + else if (strcmp (argv[i], "-fuse-ld=lld") == 0) + selected_linker = USE_LLD_LD; ++ else if (strcmp (argv[i], "-fuse-ld=mold") == 0) ++ selected_linker = USE_MOLD_LD; + else if (strncmp (argv[i], "-o", 2) == 0) + { + /* Parse the output filename if it's given so that we can make +@@ -1082,7 +1086,7 @@ + ld_file_name = 0; + #ifdef DEFAULT_LINKER + if (selected_linker == USE_BFD_LD || selected_linker == USE_GOLD_LD || +- selected_linker == USE_LLD_LD) ++ selected_linker == USE_LLD_LD || selected_linker == USE_MOLD_LD) + { + char *linker_name; + # ifdef HOST_EXECUTABLE_SUFFIX +@@ -1317,7 +1321,7 @@ + else if (!use_collect_ld + && strncmp (arg, "-fuse-ld=", 9) == 0) + { +- /* Do not pass -fuse-ld={bfd|gold|lld} to the linker. */ ++ /* Do not pass -fuse-ld={bfd|gold|lld|mold} to the linker. */ + ld1--; + ld2--; + } +diff --git a/gcc/common.opt b/gcc/common.opt +index 2ed818d6057de..dba3fa886f9c6 100644 +--- a/gcc/common.opt ++++ b/gcc/common.opt +@@ -3046,6 +3046,10 @@ fuse-ld=lld + Common Driver Negative(fuse-ld=lld) + Use the lld LLVM linker instead of the default linker. + ++fuse-ld=mold ++Common Driver Negative(fuse-ld=mold) ++Use the Modern linker (MOLD) linker instead of the default linker. ++ + fuse-linker-plugin + Common Undocumented Var(flag_use_linker_plugin) + +diff --git a/gcc/doc/invoke.texi b/gcc/doc/invoke.texi +index e644c63767b88..54fa75ba138ea 100644 +--- a/gcc/doc/invoke.texi ++++ b/gcc/doc/invoke.texi +@@ -16266,6 +16266,10 @@ Use the @command{gold} linker instead of the default linker. + @opindex fuse-ld=lld + Use the LLVM @command{lld} linker instead of the default linker. + ++@item -fuse-ld=mold ++@opindex fuse-ld=mold ++Use the Modern Linker (@command{mold}) instead of the default linker. ++ + @cindex Libraries + @item -l@var{library} + @itemx -l @var{library} +diff --git a/gcc/gcc.c b/gcc/gcc.c +index b75b50b87b2bf..06e18a75b52cc 100644 +--- a/gcc/gcc.c ++++ b/gcc/gcc.c +@@ -4282,6 +4282,10 @@ driver_handle_option (struct gcc_options *opts, + use_ld = ".gold"; + break; + ++ case OPT_fuse_ld_mold: ++ use_ld = ".mold"; ++ break; ++ + case OPT_fcompare_debug_second: + compare_debug_second = 1; + break; +diff --git a/gcc/opts.c b/gcc/opts.c +index e4e47ff77b3d7..f820052307c36 100644 +--- a/gcc/opts.c ++++ b/gcc/opts.c +@@ -3105,6 +3105,7 @@ common_handle_option (struct gcc_options *opts, + case OPT_fuse_ld_bfd: + case OPT_fuse_ld_gold: + case OPT_fuse_ld_lld: ++ case OPT_fuse_ld_mold: + case OPT_fuse_linker_plugin: + /* No-op. Used by the driver and passed to us because it starts with f.*/ + break; From e28876bb9d1a9a560994ec65d5f1e3c00e76f02d Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 21 Jun 2022 02:13:27 +0000 Subject: [PATCH 4041/9987] adding easyconfigs: BLIS-0.9.0-intel-compilers-2022.1.0.eb --- .../BLIS-0.9.0-intel-compilers-2022.1.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-intel-compilers-2022.1.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-intel-compilers-2022.1.0.eb new file mode 100644 index 00000000000..732b183a34d --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-intel-compilers-2022.1.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.9.0' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} +toolchainopts = {'oneapi': True} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308'] + +builddependencies = [ + ('Python', '3.10.4', '-bare'), + ('Perl', '5.34.1'), +] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared --complex-return=intel CC="$CC" auto' + +# Intel expects classic f2c-style calling convention. +pretestopts = 'for cu in c u; do for cz in c z; do ' +pretestopts += 'sed -i "s/\([^ ]*complex\) ${cz}dot${cu}_(/void ${cz}dot${cu}_(\\1 \*, /g;' +pretestopts += 's/\([qz]__1\) = ${cz}dot${cu}_(/${cz}dot${cu}_(\&\\1, /g" blastest/src/${cz}blat1.c; done; done && ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' From cf6953152eeaf3f0ac2aa8c3886cacde84111bd6 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 21 Jun 2022 07:56:58 +0100 Subject: [PATCH 4042/9987] Update easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb Co-authored-by: Adam Huffman --- easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb index 4322f628948..d7d67faaa37 100644 --- a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb @@ -44,7 +44,7 @@ exts_list = [ 'checksums': ['8fdb99cda1ceff578a233db6c15a944fa57b43a2826af41c292e36848906117b'], }), ('rnaseqc', '0.0.3', { - # Build RNA-SeQC in the preinstall opts for the assocaited Python package + # Build RNA-SeQC in the preinstall opts for the associated Python package # RNA-SeQC bundles SeqLib, with HTSlib and BWA. These are old versions so we cannot use deps here # rnaseqc version is from python/rnaseqc/__init__.py in the RNA-SeQC source code 'patches': [ From d515d5fb9eef8b4f22c8b86cf803e226b800fdce Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 21 Jun 2022 07:57:44 +0100 Subject: [PATCH 4043/9987] Remove versionsuffix that should not have been there --- easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb index d7d67faaa37..e2f70437cce 100644 --- a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb @@ -3,7 +3,6 @@ easyblock = 'PythonBundle' name = 'RNA-SeQC' version = '2.4.2' -versionsuffix = '' homepage = "https://github.com/getzlab/rnaseqc" description = """Fast, efficient RNA-Seq metrics for quality control and process optimization""" From 180286112a8aa606cb547cc008e917c06b7f4fad Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 21 Jun 2022 09:04:18 +0200 Subject: [PATCH 4044/9987] adding easyconfigs: InterProScan_data-5.55-88.0-foss-2021a.eb --- .../InterProScan_data-5.55-88.0-foss-2021a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/i/InterProScan_data/InterProScan_data-5.55-88.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/InterProScan_data/InterProScan_data-5.55-88.0-foss-2021a.eb b/easybuild/easyconfigs/i/InterProScan_data/InterProScan_data-5.55-88.0-foss-2021a.eb new file mode 100644 index 00000000000..6caebe55c6b --- /dev/null +++ b/easybuild/easyconfigs/i/InterProScan_data/InterProScan_data-5.55-88.0-foss-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'Binary' + +name = 'InterProScan_data' +version = '5.55-88.0' + +homepage = 'https://www.ebi.ac.uk/interpro/' +# also https://github.com/ebi-pf-team/interproscan +description = """InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines + different protein signature recognition methods into one resource [data only].""" +# software_license = 'LicenseApachev2' + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/%(version)s/alt/', +] +sources = [ + 'interproscan-data-%(version)s.tar.gz', +] +checksums = [ + '2beffa16b367a1884800f0d65c2dcb1e772d7330688e76b8f02f9cc48564f12a', # interproscan-data-5.55-88.0.tar.gz +] + +dependencies = [ + ('InterProScan', '%(version)s'), +] + +extract_sources = False + +# NOTE The regular InterProScan data package does not contain the lookup_service data way too large! +install_cmd = 'tar xfz interproscan-data-%(version)s.tar.gz --directory %(installdir)s/ --strip-components=1 && ' +install_cmd += 'rm -f interproscan-data-%(version)s.tar.gz && ' +install_cmd += 'rm -rf $EBROOTINTERPROSCAN/data && ' +install_cmd += 'ln -s %(installdir)s/data $EBROOTINTERPROSCAN/data' + +# NOTE it finalize the data indexing that needs to be done before/at the first use +postinstallcmds = ["$EBROOTINTERPROSCAN/interproscan.sh"] + +sanity_check_paths = { + 'files': [], + 'dirs': ['data/antifam', 'data/cdd', 'data/gene3d', 'data/hamap', + 'data/panther', 'data/pfam', 'data/phobius', 'data/pirsf', + 'data/pirsr', 'data/prints', 'data/prosite', 'data/sfld', + 'data/smart', 'data/superfamily', 'data/tigrfam', 'data/tmhmm'], +} + +moduleclass = 'bio' From 883aa8a5c0acd8c4a46ba411bc1c2d32e40eb7a6 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 09:58:17 +0200 Subject: [PATCH 4045/9987] adding easyconfigs: BayesTraits-3.0.2-Linux.eb --- .../b/BayesTraits/BayesTraits-3.0.2-Linux.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb new file mode 100644 index 00000000000..7a9fa738f6c --- /dev/null +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'BayesTraits' +version = '3.0.2' +versionsuffix = '-Linux' + +homepage = 'https://github.com/AndrewPMeade/BayesTraits-Public' +description = """ BayesTraits is a computer package for performing analyses of trait + evolution among groups of species for which a phylogeny or sample of phylogenies is + available. This new package incoporates our earlier and separate programes Multistate, + Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt + a finite number of discrete states, or to the analysis of continuously varying traits. + Hypotheses can be tested about models of evolution, about ancestral states and about + correlations among pairs of traits. """ + +toolchain = SYSTEM + +source_urls = ['https://github.com/AndrewPMeade/BayesTraits-Public/blob/main'] +sources = ['%(name)sV%(version)s/%(name)sV%(version)s%(versionsuffix)s.tar.gz'] + +checksums = ['8b4dbd48583f970d3a4e363685940a9c99d412be1b2e96eb682294f751b4fa51'] + +sanity_check_paths = { + 'files': ['BayesTraitsV3', 'Primates.trees', 'Mammal.trees'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 53999f631ea50eb26095714080dfff458aea233c Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 10:58:30 +0200 Subject: [PATCH 4046/9987] adding easyconfigs: ecFlow-5.7.0-GCC-10.2.0.eb --- .../e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..e9de3754b25 --- /dev/null +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = "CMakeMake" + +name = 'ecFlow' +version = '5.7.0' + +homepage = "https://confluence.ecmwf.int/display/ECFLOW/ecflow+home" +description = """ecFlow is a client/server workflow package that enables users to run a large number of programs (with dependencies on each other and on time) in a controlled environment. It provides reasonable tolerance for hardware and software failures, combined with restart capabilities. It is used at ECMWF to run all our operational suites across a range of platforms.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/8650755/'] +sources = ['%(name)s-%(version)s-Source.tar.gz'] +checksums = ['70cbabde5da705239a9e27b1e053dae4bdbee6c604c571a5ff07b47d0a84732f'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Doxygen', '1.8.20'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Boost', '1.74.0'), + ('Boost.Python', '1.74.0'), + ('Qt5', '5.14.2'), + ('OpenSSL', '1.1.1h'), +] + +configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " +prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_commands = ['ecflow_client --help'] + +moduleclass = "vis" From 8a3afbb831d1b4141ccbadeeb24e2e465f278651 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 10:59:41 +0200 Subject: [PATCH 4047/9987] adding easyconfigs: EIGENSOFT-7.2.1-foss-2020b.eb --- .../e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb new file mode 100644 index 00000000000..6199519bcc9 --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 6.1.4 modified by: +# Adam Huffman +# The Francis Crick Institute +# 7.2.1 modified by: +# Tom Strempel +# Helmholtz-Centre for Environmental Research - UFZ + +easyblock = 'MakeCp' + +name = 'EIGENSOFT' +version = '7.2.1' + +homepage = 'https://www.hsph.harvard.edu/alkes-price/software/' +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. +2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal +components analysis to explicitly model ancestry differences between cases and controls along continuous axes of +variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral +populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT +package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/DReichLab/EIG/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_Fix_makefile_openblas.patch'] +checksums = [ + 'f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650', # v7.2.1.tar.gz + 'e49e3754f2326210114fe5a731a77c7ffd240c8a9134eb8e8e1517bfe06c71e1', # EIGENSOFT-7.2.1_Fix_makefile_openblas.patch +] + +dependencies = [ + ('GSL', '2.6'), + ('Perl', '5.32.0'), +] + +start_dir = 'src' + +# Run "make install" after make to copy all binaries to the bin dir +buildopts = ' && make install' + +files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] + +fix_perl_shebang_for = ['bin/*.perl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'dirs': [] +} + +moduleclass = 'bio' From 285f1dbe686e36521b863cac9604f2cbba77e601 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 11:22:59 +0200 Subject: [PATCH 4048/9987] adding easyconfigs: FSON-1.0.5-foss-2020b.eb --- .../f/FSON/FSON-1.0.5-foss-2020b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSON/FSON-1.0.5-foss-2020b.eb diff --git a/easybuild/easyconfigs/f/FSON/FSON-1.0.5-foss-2020b.eb b/easybuild/easyconfigs/f/FSON/FSON-1.0.5-foss-2020b.eb new file mode 100644 index 00000000000..30b8f20b219 --- /dev/null +++ b/easybuild/easyconfigs/f/FSON/FSON-1.0.5-foss-2020b.eb @@ -0,0 +1,27 @@ +easyblock = "CMakeMake" + +name = 'FSON' +version = '1.0.5' + +homepage = "https://github.com/josephalevin/fson" +description = "Fortran 95 JSON Parser" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/josephalevin/fson/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d52f928d59b090eb47ed2bc880ee58d46cd8dd7e554e3df03c7c517d7a6b6012'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['lib64/libFSON.%s' % SHLIB_EXT], + 'dirs': ['include/fson'], +} + +moduleclass = "lib" From cf823cc3ae70e73d905dbdc4dffbec9dbd19541a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 21 Jun 2022 11:30:14 +0100 Subject: [PATCH 4049/9987] adding easyconfigs: SWIPE-2.1.1-GCC-10.3.0.eb --- .../s/SWIPE/SWIPE-2.1.1-GCC-10.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIPE/SWIPE-2.1.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/SWIPE/SWIPE-2.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SWIPE/SWIPE-2.1.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..639ea033e77 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIPE/SWIPE-2.1.1-GCC-10.3.0.eb @@ -0,0 +1,26 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'MakeCp' + +name = 'SWIPE' +version = '2.1.1' + +homepage = "https://github.com/torognes/swipe" +description = """Smith-Waterman database searches with inter-sequence SIMD parallelisation""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'torognes' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cc7cd65ddafd6b9e69975292bee0583bdf64918e8d5c7ddd98ae41a20d3f8b73'] + +# only build swipe and not mpiswipe +buildopts = 'swipe' +files_to_copy = [(['%(namelower)s'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From ef3f58f8d9a43e2e6b7e81df16f7575c45acd947 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Tue, 21 Jun 2022 12:41:53 +0200 Subject: [PATCH 4050/9987] Changed module class --- .../easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb b/easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb index 88e0f2e557b..8f70ccd7391 100644 --- a/easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/Minipolish/Minipolish-0.1.3-GCC-11.2.0.eb @@ -28,4 +28,4 @@ sanity_check_paths = { 'dirs': [] } -moduleclass = "tools" +moduleclass = "bio" From dfc2264881235ba07ac4d83201236e535f82354f Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 13:31:12 +0200 Subject: [PATCH 4051/9987] adding easyconfigs: jq-1.5-GCCcore-10.2.0.eb --- .../easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..139e674e29e --- /dev/null +++ b/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'jq' +version = '1.5' + +homepage = 'https://stedolan.github.io/jq/' +description = """jq is a lightweight and flexible command-line JSON processor.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/stedolan/jq/releases/download/jq-%(version)s'] +sources = ['jq-%(version)s.tar.gz'] +checksums = ['c4d2bfec6436341113419debf479d833692cc5cdab7eb0326b5a4d4fbe9f493c'] + +builddependencies = [ + ('binutils', '2.35'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] + +sanity_check_paths = { + 'files': ['bin/jq'], + 'dirs': [], +} + +moduleclass = 'tools' From 6a065c165110cbad9a1f529a9c96f6598dec0965 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 13:52:20 +0200 Subject: [PATCH 4052/9987] adding easyconfigs: libSBML-5.19.0-GCC-10.2.0.eb --- .../l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb | 82 +++++++++++++++++++ 1 file changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb new file mode 100644 index 00000000000..ea2d22663c1 --- /dev/null +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb @@ -0,0 +1,82 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# Modified by: Toni Harzendorf +# +# Notes:: Patch libsbml-fix_install_libpaths.patch comes from Fedora +# https://src.fedoraproject.org/rpms/libsbml/blob/rawhide/f/libsbml-fix_install_libpaths.patch +## +easyblock = 'CMakeMake' + +name = 'libSBML' +version = '5.19.0' + +# NOTE not in the license list of EB +# software_license = 'LGPLv2+' +software_license_urls = ['http://sbml.org/Software/libSBML/LibSBML_License'] +docurls = [ + 'https://github.com/sbmlteam/libsbml/releases/tag/v%(version)s', + 'http://sbml.org/Software/libSBML', +] + +homepage = 'http://sbml.org/Software/libSBML' +description = """libSBML (Systems Biology Markup Language library) is a free, open-source +programming library to help you read, write, manipulate, translate, and +validate SBML files and data streams. It's not an application itself (though +it does come with example programs), but rather a library you embed in your +own applications.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://downloads.sourceforge.net/project/sbml/libsbml/%(version)s/stable/'] +sources = ['libSBML-%(version)s-core-plus-packages-src.tar.gz'] +patches = [ + 'libsbml-fix_install_libpaths.patch', # Fix some installation library paths (from Fedora) + 'libsbml-fix_perl_auto_case.patch', # Fix the misname for Perl .so binding folder + # (https://sourceforge.net/p/sbml/libsbml/476/) +] +checksums = [ + 'a7f0e18be78ff0e064e4cdb1cd86634d08bc33be5250db4a1878bd81eeb8b547', # libSBML-5.19.0-core-plus-packages-src.tar.gz + '1975b9372be00c5056e1f3408b8829e749adb1edb3345fd109d5c802b5219e45', # libsbml-fix_install_libpaths.patch + '52b3274ce1fdfb329bc53feb67b9862833a1240539eca2f137fcdca00800e34e', # libsbml-fix_perl_auto_case.patch +] + + +builddependencies = [ + ('CMake', '3.18.4'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Perl', '5.32.0'), +] + +# Java jar, Ruby or Octave can also be build here. +# Python libSBML binding better done from https://pypi.org/project/python-libsbml/ +configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX=%(installdir)s -DWITH_JAVA=OFF ' +configure_cmd += '-DWITH_CHECK=ON -DWITH_SWIG=ON -DWITH_PERL=ON -DWITH_PYTHON=OFF ' +configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF ' +configure_cmd += '-DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER,GROUPS,MULTI,DISTRIB}=ON ' +configure_cmd += '../libSBML-%(version)s-Source/' + + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib64/libsbml.so', 'lib64/perl5/vendor_perl/LibSBML.pm'], + 'dirs': ['lib64', 'include', 'share'] +} + +modextrapaths = { + 'PERL5LIB': 'lib64/perl5/vendor_perl/', +} + + +moduleclass = 'bio' From fed847326dfbd78ada1f562add4375294c39d3e2 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 14:05:41 +0200 Subject: [PATCH 4053/9987] adding easyconfigs: Mesquite-2.3.0-GCCcore-10.2.0.eb --- .../Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..5121180a915 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Mesquite' +version = '2.3.0' + +homepage = 'https://software.sandia.gov/mesquite/' + +description = """Mesh-Quality Improvement Library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://software.sandia.gov/mesquite/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4ab4ceadfa596e16c00dbb0e8b830a9112fa1b73291ca07633ec379a39b8bb28'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/msqquality', 'bin/msqshape', 'lib/libmesquite.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' From 9a025c4df95154be0081f21bcda479de3dc6cf0a Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 14:14:12 +0200 Subject: [PATCH 4054/9987] adding easyconfigs: MITObim-1.9.1-foss-2020b.eb --- .../m/MITObim/MITObim-1.9.1-foss-2020b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb b/easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb new file mode 100644 index 00000000000..6711cda43d7 --- /dev/null +++ b/easybuild/easyconfigs/m/MITObim/MITObim-1.9.1-foss-2020b.eb @@ -0,0 +1,34 @@ +easyblock = "CmdCp" + +name = 'MITObim' +version = '1.9.1' + +homepage = "https://github.com/chrishah/MITObim" +description = """The MITObim procedure (mitochondrial baiting and iterative mapping) represents + a highly efficient approach to assembling novel mitochondrial genomes of non-model organisms + directly from total genomic DNA derived NGS reads.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'chrishah' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['8f7d47eb6ea677ca152492a477ee6c7542c0f853e921675b81be509ddd4f75bf'] + +dependencies = [ + ('Perl', '5.32.0'), + ('MIRA', '5.0rc2'), +] + +skipsteps = ['build'] + +files_to_copy = [ + (['MITObim.pl'], 'bin'), +] + +sanity_check_paths = { + 'files': ["bin/MITObim.pl"], + 'dirs': [] +} + +moduleclass = "bio" From 290d646b497d8e70844d7ce1f620093e45dd52e1 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 14:17:09 +0200 Subject: [PATCH 4055/9987] adding easyconfigs: MUST-1.7.1-foss-2020b-Python-3.8.6.eb --- .../MUST-1.7.1-foss-2020b-Python-3.8.6.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..6fd80a401de --- /dev/null +++ b/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,35 @@ +easyblock = "CMakeMake" + +name = 'MUST' +version = '1.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://hpc.rwth-aachen.de/must/" +description = """MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user. + As MPI calls are complex and usage errors common, this functionality is extremely helpful for application developers + that want to develop correct MPI applications. + This includes errors that already manifest – segmentation faults or incorrect results – as well as many errors + that are not visible to the application developer or do not manifest on a certain system or MPI implementation.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://hpc.rwth-aachen.de/must/files/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['de3f6144a433035d24952c1acdf1acac47bcd843b24243bd8c0467a0567b1ed6'] + +builddependencies = [ + ('CMake', '3.18.4') +] + +dependencies = [ + ('Python', '3.8.6'), + ('libxml2', '2.9.10'), + ('Graphviz', '2.47.0', '-Java-11'), +] + +sanity_check_paths = { + 'files': ["bin/mustrun", "bin/wrap.py", "include/mustConfig.h", "lib/libpnmpif.so", "lib/libpnmpi.so"], + 'dirs': ["include/pnmpi", "lib64/pnmpi-modules", "modules", "share", "specifications", "src"], +} + +moduleclass = "perf" From 86928a0349533b81c7f1e781ae1d6fdadc11ae35 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 21 Jun 2022 14:47:18 +0200 Subject: [PATCH 4056/9987] Fix hardcoded mpi command for porefoam --- .../p/porefoam/porefoam-2021-09-21-foss-2020a.eb | 7 ++++++- ...oam-2021-09-21_fix-hardcoded-mpicommand.patch | 16 ++++++++++++++++ 2 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21_fix-hardcoded-mpicommand.patch diff --git a/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb b/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb index 8edfb7a8aad..ca9ea7d9cd0 100644 --- a/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb +++ b/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21-foss-2020a.eb @@ -11,10 +11,15 @@ toolchain = {'name': 'foss', 'version': '2020a'} source_urls = ['https://github.com/ImperialCollegeLondon/porefoam/archive/'] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = ['porefoam-2021-09-21_fix-scotch-linking.patch'] +patches = [ + 'porefoam-2021-09-21_fix-scotch-linking.patch', + 'porefoam-2021-09-21_fix-hardcoded-mpicommand.patch', +] checksums = [ '61b7d23869f5cfadf001def25750576b05f13d3f117ffb409e56996a0de6d696', # porefoam-2021-09-21.tar.gz '86b7e389b62f54bbd3c931ae3dbdc363226e250faa181e7e50ed121da9959a92', # porefoam-2021-09-21_fix-scotch-linking.patch + # porefoam-2021-09-21_fix-hardcoded-mpicommand.patch + '4cfa924c9a5d3ec38cf233312eb325ed625219644468f4b34fba8bc6ceee5ba2', ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21_fix-hardcoded-mpicommand.patch b/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21_fix-hardcoded-mpicommand.patch new file mode 100644 index 00000000000..23c42699def --- /dev/null +++ b/easybuild/easyconfigs/p/porefoam/porefoam-2021-09-21_fix-hardcoded-mpicommand.patch @@ -0,0 +1,16 @@ +# porefome hard-codes mpi command to be "mpirun.openmpi" and also fixes the "-np" switch to set the number of mpi tasks. +# I implemeted here $POREFOAM_MPIRUN_CMD variable to set the mpirun command and the switch to set the number of mpi tasks. +# for example for OpenMPI, use export POREFOAM_MPIRUN_CMD="mpirun -np" before you run porefoem +# June 21st 2022 by B. Hajgato (UGent) +diff -ru porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f.org/src/script/initbash porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f/src/script/initbash +--- porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f.org/src/script/initbash 2021-09-21 19:12:45.000000000 +0200 ++++ porefoam-eb02ba3ede738befe02dc7c587d21f05fd40cb9f/src/script/initbash 2022-06-21 14:24:04.255861222 +0200 +@@ -70,7 +70,7 @@ + else + echo "Running $APP_NAME $@ > $PWD/$LOG_NAME , using $np processes" + # --bind to none ( mpirun -x LD_LIBRARY_PATH -x PATH -x WM_PROJECT_DIR -x WM_PROJECT_INST_DIR -x MPI_BUFFER_SIZE --mca btl_tcp_if_exclude lo --mca btl_tcp_if_exclude eth0:avahi --hostfile machines.txt -np $np $APP_RUN -parallel "$@" < /dev/null > $LOG_NAME 2>&1 ) +- nice mpirun.openmpi -np $np $APP_RUN -parallel "$@" < /dev/null > $LOG_NAME 2>&1 ++ ${POREFOAM_MPIRUN_CMD:- nice mpirun.openmpi -np} $np $APP_RUN -parallel "$@" < /dev/null > $LOG_NAME 2>&1 + [[ $? == 0 ]] || echo "Error: $APP_RUN -parallel $@, exit status: $?, see $(pwd)/$LOG_NAME" >&2 + fi + sleep .1 From fb4eb7416ec4d2fe51d8950e2f3cc55d05b10d86 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 21 Jun 2022 14:54:20 +0200 Subject: [PATCH 4057/9987] adding easyconfigs: OpenFOAM-v2112-foss-2020b.eb --- .../o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb new file mode 100644 index 00000000000..4455c12e406 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb @@ -0,0 +1,44 @@ +## +# Author: Robert Mijakovic +## +name = 'OpenFOAM' +version = 'v2112' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = [ + '3e838731e79db1c288acc27aad8cc8a43d9dac1f24e5773e3b9fa91419a8c3f7', # OpenFOAM-v2112.tgz +] + +dependencies = [ + ('libreadline', '8.0'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('CGAL', '5.2'), + ('ParaView', '5.8.1', '-mpi'), + ('gnuplot', '5.4.1'), +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), +] + +sanity_check_paths = { + 'files': ['%(installdir)s/%(name)s-%(version)s/platforms/linux64GccDPInt32Opt/lib/dummy/libscotchDecomp.so'], + 'dirs': ['%(installdir)s/%(name)s-%(version)s/platforms/linux64GccDPInt32Opt/lib/dummy'], +} + +moduleclass = 'cae' From b3f2d183555d49725c1a95333713c371f6768e3f Mon Sep 17 00:00:00 2001 From: software Date: Tue, 21 Jun 2022 13:36:42 +0000 Subject: [PATCH 4058/9987] adding easyconfigs: Leptonica-1.82.0-GCCcore-10.3.0.eb --- .../Leptonica-1.82.0-GCCcore-10.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/Leptonica/Leptonica-1.82.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.82.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.82.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..35dbc6b8a35 --- /dev/null +++ b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.82.0-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Leptonica' +version = '1.82.0' + +homepage = 'http://www.leptonica.org' +description = """Leptonica is a collection of pedagogically-oriented open source software + that is broadly useful for image processing and image analysis applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/DanBloomberg/leptonica/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['155302ee914668c27b6fe3ca9ff2da63b245f6d62f3061c8f27563774b8ae2d6'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('libpng', '1.6.37'), + ('LibTIFF', '4.2.0'), + ('libjpeg-turbo', '2.0.6'), + ('giflib', '5.2.1'), + ('libwebp', '1.2.0'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/convertformat', 'lib/liblept.%s' % SHLIB_EXT], + 'dirs': ['include/leptonica', 'lib/pkgconfig'] +} + +moduleclass = 'vis' From 30ca86506ca4aef60508bf554d0c54324d6f65e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Jun 2022 17:18:52 +0200 Subject: [PATCH 4059/9987] add rtdists extension for R v4.2.0 --- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 3f2e3665256..bc956988ce7 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -3352,6 +3352,9 @@ exts_list = [ ('hypergeo', '1.2-13', { 'checksums': ['6d5b78353aad1d13091ccbeb340867dad7b9eb00d0e2185286dc7e13848f4d8e'], }), + ('rtdists', '0.11-5', { + 'checksums': ['97cf2ea758aa02b1dfaeef5032c6e50570777552aa771ed9a86df048b7871eed'], + }), ] moduleclass = 'lang' From 98620c39f286c8a701bba98b264d214b0ab7c1e6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 21 Jun 2022 19:19:18 +0100 Subject: [PATCH 4060/9987] relax test tolerance of the single test failing on AMD Rome --- .../j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb | 6 +++++- .../j/jax/jax-0.3.9_relax-test-tolerance.patch | 17 +++++++++++++++++ 2 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.9_relax-test-tolerance.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb index d1a8e445d5a..20d0ce315f7 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb @@ -98,11 +98,15 @@ exts_list = [ (name, version, { 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], - 'patches': ['jax-0.2.19_fix-update-of-cache-access-time.patch'], + 'patches': [ + 'jax-0.2.19_fix-update-of-cache-access-time.patch', + 'jax-0.3.9_relax-test-tolerance.patch', + ], 'checksums': [ '45c526496d525fd04c0c9c705971f4cfa31e6a9f7d25e55a4e3bdcb3a4bbe6ce', # jax-v0.3.9.tar.gz # jax-0.2.19_fix-update-of-cache-access-time.patch 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d', # jax-0.3.9_relax-test-tolerance.patch ], # deliberately not testing in parallel, as that results in (additional) failing tests; # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.9_relax-test-tolerance.patch b/easybuild/easyconfigs/j/jax/jax-0.3.9_relax-test-tolerance.patch new file mode 100644 index 00000000000..89819a2a3de --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.9_relax-test-tolerance.patch @@ -0,0 +1,17 @@ +Relax tolerance for tests/linalg_test.py::ScipyLinalgTest::testLu_shape=float64[50,50] +which failes by a small amount on AMD Rome +Patch by Simon Branford (University of Birmingham) +--- tests/linalg_test.py.orig 2022-06-21 19:05:51.211914000 +0100 ++++ tests/linalg_test.py 2022-06-21 19:10:57.704763179 +0100 +@@ -1031,8 +1031,9 @@ + x, = args_maker() + p, l, u = jsp.linalg.lu(x) + self.assertAllClose(x, np.matmul(p, np.matmul(l, u)), +- rtol={np.float32: 1e-3, np.float64: 1e-12, +- np.complex64: 1e-3, np.complex128: 1e-12}) ++ rtol={np.float32: 1e-3, np.float64: 1e-11, ++ np.complex64: 1e-3, np.complex128: 1e-12}, ++ atol={np.float64: 1e-14}) + self._CompileAndCheck(jsp.linalg.lu, args_maker) + + def testLuOfSingularMatrix(self): From 1c420180c9c9a9b30e268849bce1ea8e9576b0ea Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 21 Jun 2022 19:21:47 +0100 Subject: [PATCH 4061/9987] also add patch to the CPU version --- .../easyconfigs/j/jax/jax-0.3.9-foss-2021a.eb | 115 ++++++++++++++++++ 1 file changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a.eb new file mode 100644 index 00000000000..bf75f491f46 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a.eb @@ -0,0 +1,115 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.9' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('Bazel', '3.7.2'), + ('pytest-xdist', '2.3.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.32.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('flatbuffers-python', '2.0'), + ('typing-extensions', '3.10.0.0'), +] + +# running the tests with lots of cores results in test failures because not enough threads can be started, +# and running with a single core also results in systematic test failures +# 4 cores seems to work best +parallel = 4 + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = 'e011187e26dbeed80dede66eb48729d184e3bb1d' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '0.15.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['72d782fbeafba66ba3e525d46bccac949b9a174dbf66233e50ece09ee688dc81'], + }), + ('jaxlib', '0.3.7', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + 'jaxlib-0.1.70_add-bazel-args-to-shutdown.patch', + ], + 'checksums': [ + # jaxlib-v0.3.7.tar.gz + '60a1ec2f32e28eda90998440c3a3f71dd55abd3e5b033849255ab157c4765632', + # tensorflow-e011187e26dbeed80dede66eb48729d184e3bb1d.tar.gz + 'ef5a001226c37f59eca9c9bf0506b962cf220906bcc8f24df4d1ed6011a593e9', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': [ + 'jax-0.2.19_fix-update-of-cache-access-time.patch', + 'jax-0.3.9_relax-test-tolerance.patch', + ], + 'checksums': [ + '45c526496d525fd04c0c9c705971f4cfa31e6a9f7d25e55a4e3bdcb3a4bbe6ce', # jax-v0.3.9.tar.gz + # jax-0.2.19_fix-update-of-cache-access-time.patch + 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', + '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d', # jax-0.3.9_relax-test-tolerance.patch + ], + 'runtest': "pytest -n %(parallel)s tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 9b43175dae71806e3bf9f460e8147ea848000855 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 22 Jun 2022 08:28:42 +0200 Subject: [PATCH 4062/9987] adding easyconfigs: RapidJSON-1.1.0-GCCcore-10.2.0.eb --- .../RapidJSON-1.1.0-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0fd88903d33 --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +version = '1.1.0' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-compiler-errors.patch'] +checksums = [ + 'bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e', # v1.1.0.tar.gz + # %(name)s-%(version_major_minor)s.0_fix-compiler-errors.patch + '2e40ef6c46bf355feac16cd84faad5b7aca0ad54273117b85534b1b781f411c7', +] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' From 1470f46ef32c6f79b4faf57d4f2f32aa739bcfc9 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 22 Jun 2022 09:17:45 +0200 Subject: [PATCH 4063/9987] Fix indexing exit code --- .../InterProScan_data-5.55-88.0-foss-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/InterProScan_data/InterProScan_data-5.55-88.0-foss-2021a.eb b/easybuild/easyconfigs/i/InterProScan_data/InterProScan_data-5.55-88.0-foss-2021a.eb index 6caebe55c6b..d6622f2f8a5 100644 --- a/easybuild/easyconfigs/i/InterProScan_data/InterProScan_data-5.55-88.0-foss-2021a.eb +++ b/easybuild/easyconfigs/i/InterProScan_data/InterProScan_data-5.55-88.0-foss-2021a.eb @@ -33,8 +33,8 @@ install_cmd += 'rm -f interproscan-data-%(version)s.tar.gz && ' install_cmd += 'rm -rf $EBROOTINTERPROSCAN/data && ' install_cmd += 'ln -s %(installdir)s/data $EBROOTINTERPROSCAN/data' -# NOTE it finalize the data indexing that needs to be done before/at the first use -postinstallcmds = ["$EBROOTINTERPROSCAN/interproscan.sh"] +# NOTE finalize the data indexing that needs to be done before/at the first use +postinstallcmds = ["$EBROOTINTERPROSCAN/interproscan.sh || true"] sanity_check_paths = { 'files': [], From 7523eb1585da0f1504b1dc57687babe37933e38b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Jun 2022 09:32:35 +0200 Subject: [PATCH 4064/9987] add download instructions for CellRanger v7.0.0 Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/c/CellRanger/CellRanger-7.0.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CellRanger/CellRanger-7.0.0.eb b/easybuild/easyconfigs/c/CellRanger/CellRanger-7.0.0.eb index d3770f6b743..0dd53e8c2c8 100644 --- a/easybuild/easyconfigs/c/CellRanger/CellRanger-7.0.0.eb +++ b/easybuild/easyconfigs/c/CellRanger/CellRanger-7.0.0.eb @@ -13,7 +13,9 @@ description = """Cell Ranger is a set of analysis pipelines that process Chromiu toolchain = SYSTEM -# Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest +download_instructions = """ +Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest +""" sources = [SOURCELOWER_TAR_GZ] checksums = ['6fd0d5b66f9513e6d52d0d4bc7b3d065b877d975280009d1f34d592e4b6d9d84'] From 43b396201862b7810bdb88f4819e555d917c62c1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 22 Jun 2022 10:44:35 +0100 Subject: [PATCH 4065/9987] adding easyconfigs: topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb, topaz-0.2.5-foss-2021a.eb --- .../topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb | 41 +++++++++++++++++++ .../t/topaz/topaz-0.2.5-foss-2021a.eb | 39 ++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a.eb diff --git a/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..14ac4f4f602 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'topaz' +version = '0.2.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/tbepler/topaz' +description = """A pipeline for particle detection in cryo-electron microscopy + images using convolutional neural networks trained from positive and unlabeled + examples. Topaz also includes methods for micrograph denoising using deep de- + noising models. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyTorch', '1.10.0', versionsuffix), + ('torchvision', '0.11.1', versionsuffix), + ('scikit-learn', '0.24.2'), + ('CUDA', '11.3.1', '', True), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('topaz-em', version, { + 'checksums': ['002a6eb775598b6c4df0225f3a488bfe6a6da9246e8ca42eb4e7d58f694c25cc'], + 'modulename': name, + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["%(name)s --help", "%(name)s --version"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a.eb b/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a.eb new file mode 100644 index 00000000000..30b6c82cef0 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'topaz' +version = '0.2.5' + +homepage = 'https://github.com/tbepler/topaz' +description = """A pipeline for particle detection in cryo-electron microscopy + images using convolutional neural networks trained from positive and unlabeled + examples. Topaz also includes methods for micrograph denoising using deep de- + noising models. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyTorch', '1.10.0'), + ('torchvision', '0.11.1'), + ('scikit-learn', '0.24.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('topaz-em', version, { + 'checksums': ['002a6eb775598b6c4df0225f3a488bfe6a6da9246e8ca42eb4e7d58f694c25cc'], + 'modulename': name, + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["%(name)s --help", "%(name)s --version"] + +moduleclass = 'chem' From 32883522bd080f9adbe31f1d14a4166549d16daa Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 22 Jun 2022 12:03:46 +0100 Subject: [PATCH 4066/9987] add test exception for torchvision version used in smooth-topk --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index e8fae843422..a2f3511a72b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -550,6 +550,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # medaka 1.5.0 (foss/2021a) depends on TensorFlow >=2.5.2, <2.6.0 ('2.5.3;', ['medaka-1.5.0-']), ], + # smooth-topk uses a newer version of torchvision + 'torchvision': [('0.11.3;', ['smooth-topk-1.0-20210817-'])], # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 # (for 2021b, UCX was updated to v1.11.2) 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], From e01ed4a02f35733e18af7988cbec30a09b3f0399 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 22 Jun 2022 13:14:17 +0200 Subject: [PATCH 4067/9987] adding easyconfigs: Trinity-2.9.1-foss-2020b-Python-3.8.6.eb --- .../Trinity-2.9.1-foss-2020b-Python-3.8.6.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..0375526f35f --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,50 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +checksums = ['98d98bc21cd5dd32b408ed52586d01a15873b49b96de3264d42616bdcfc9d455'] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Java', '11', '', True), + ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Bowtie2', '2.4.2'), + ('HTSlib', '1.12'), + ('Jellyfish', '2.3.0'), + ('kallisto', '0.46.2'), + ('ncurses', '6.2'), + ('Salmon', '1.4.0'), + ('SAMtools', '1.11'), + ('zlib', '1.2.11'), +] + +withsampledata = True + +moduleclass = 'bio' From 08cc268802060f2f3ad266143f053bdcb2174e80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Jun 2022 13:42:29 +0200 Subject: [PATCH 4068/9987] add patch to fix library name for netCDF v4.9.0 + get rid of -DHDF5_VERSION configure option which is no longer needed --- .../n/netCDF/netCDF-4.9.0-gompi-2022.05.eb | 13 ++++++----- .../n/netCDF/netCDF-4.9.0_fix-lib-name.patch | 23 +++++++++++++++++++ 2 files changed, 30 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_fix-lib-name.patch diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb index 543bf7b703b..63a901777cb 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb @@ -11,7 +11,11 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6'] +patches = ['netCDF-%(version)s_fix-lib-name.patch'] +checksums = [ + '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz + 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch +] builddependencies = [ ('Autotools', '20220317'), @@ -25,13 +29,10 @@ dependencies = [ ('Szip', '2.1.1'), ] -# HDF5 version detection is missed in netCDF 4.8.1 when HDF5_C_LIBRARY, HDF5_INCLUDE_DIR, and HDF5_HL_LIBRARY are set -local_hdf5_version_fix = '-DHDF5_VERSION=$EBVERSIONHDF5' - # make sure both static and shared libs are built configopts = [ - "-DBUILD_SHARED_LIBS=OFF %s " % local_hdf5_version_fix, - "-DBUILD_SHARED_LIBS=ON %s " % local_hdf5_version_fix, + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_fix-lib-name.patch b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_fix-lib-name.patch new file mode 100644 index 00000000000..9c671776913 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_fix-lib-name.patch @@ -0,0 +1,23 @@ +From 80a6611cfca98a5979c5ac69cba56a49af8c1e48 Mon Sep 17 00:00:00 2001 +From: Yuriy Chernyshov +Date: Sun, 19 Jun 2022 19:29:20 +0300 +Subject: [PATCH] Fix typo in CMakeLists.txt + +At the time generated dynamic library is named `libnetcdf.so.19}` which looks like a typo. +--- + CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 7bf8641bec..18366d24ad 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -39,7 +39,7 @@ SET(NC_VERSION ${netCDF_VERSION}) + SET(PACKAGE_VERSION ${VERSION}) + + # These values should match those in configure.ac +-SET(netCDF_LIB_VERSION 19}) ++SET(netCDF_LIB_VERSION 19) + SET(netCDF_SO_VERSION 19) + + # Version of the dispatch table. This must match the value in From 8eedc2a55c2e7f33a05675744d2104701a7858e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Jun 2022 14:30:42 +0200 Subject: [PATCH 4069/9987] use jax 0.3.9 as dependency for AlphaFold v2.2.0 --- .../a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb index ebc30d0efc5..2baa109a9a2 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb @@ -28,7 +28,7 @@ dependencies = [ ('HH-suite', '3.3.0'), ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), - ('jax', '0.2.28', versionsuffix), # also provides absl-py + ('jax', '0.3.9', versionsuffix), # also provides absl-py ('UCX-CUDA', '1.10.0', versionsuffix), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), From a33ec531507aa0c6ff22529e2af2627f04a245b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Jun 2022 14:35:31 +0200 Subject: [PATCH 4070/9987] add missing zstd dependency for netCDF v4.9.0 --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb index 63a901777cb..182ce0e5b91 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb @@ -27,6 +27,7 @@ dependencies = [ ('HDF5', '1.13.1'), ('cURL', '7.83.0'), ('Szip', '2.1.1'), + ('zstd', '1.5.2'), ] # make sure both static and shared libs are built From 9ca592cb7be4b2181c21487b432bf9d5bd2ec01e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 22 Jun 2022 15:00:29 +0200 Subject: [PATCH 4071/9987] adding easyconfigs: CESM-deps-2-foss-2021b.eb --- .../c/CESM-deps/CESM-deps-2-foss-2021b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb new file mode 100644 index 00000000000..16b6f109eba --- /dev/null +++ b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'Bundle' + +name = 'CESM-deps' +version = '2' + +homepage = 'https://www.cesm.ucar.edu/models/cesm2/' +description = """CESM is a fully-coupled, community, global climate model that +provides state-of-the-art computer simulations of the Earth's past, present, +and future climate states.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('CMake', '3.22.1'), + ('Python', '3.9.6'), + ('lxml', '4.6.3'), + ('Perl', '5.34.0'), + ('XML-LibXML', '2.0207'), + ('ESMF', '8.2.0'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('netCDF-C++4', '4.3.1'), + ('PnetCDF', '1.12.3'), # optional + ('Subversion', '1.14.1'), + ('git', '2.33.1', '-nodocs'), + ('git-lfs', '3.2.0', '', True), # optional +] + +usage = """Environment to build and run CESM v2 simulations + 1. Download a release of CESM v2: `git clone -b release-cesm2.2.0 https://github.com/ESCOMP/cesm.git cesm-2.2.0` + 2. Add external programs for CESM: `cd cesm-2.2.0; ./manage_externals/checkout_externals` + 3. Create case: `cd cime/scripts && ./create_newcase ...`""" + +moduleclass = 'geo' From 2699a2383bfd4804800c781d15651e1b59f9a97f Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 22 Jun 2022 15:05:19 +0200 Subject: [PATCH 4072/9987] take over suggested changes --- .../f/FSON/FSON-1.0.5-GCC-10.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSON/FSON-1.0.5-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/f/FSON/FSON-1.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/f/FSON/FSON-1.0.5-GCC-10.2.0.eb new file mode 100644 index 00000000000..c81063b3dde --- /dev/null +++ b/easybuild/easyconfigs/f/FSON/FSON-1.0.5-GCC-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = "CMakeMake" + +name = 'FSON' +version = '1.0.5' + +homepage = "https://github.com/josephalevin/fson" +description = "Fortran 95 JSON Parser" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://github.com/josephalevin/fson/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d52f928d59b090eb47ed2bc880ee58d46cd8dd7e554e3df03c7c517d7a6b6012'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['lib64/libFSON.%s' % SHLIB_EXT], + 'dirs': ['include/fson'], +} + +moduleclass = "lib" From 7d3f12de0dce99370b6d13a775f5c17ebea4e1b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Jun 2022 15:07:45 +0200 Subject: [PATCH 4073/9987] bump to AlphaFold v2.2.2 --- ...AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb} | 23 ++++++++----------- 1 file changed, 10 insertions(+), 13 deletions(-) rename easybuild/easyconfigs/a/AlphaFold/{AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb => AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb} (90%) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb similarity index 90% rename from easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb rename to easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb index 2baa109a9a2..5b482dfcfa1 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'AlphaFold' -version = '2.2.0' +version = '2.2.2' versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://deepmind.com/research/case-studies/alphafold' @@ -83,18 +83,15 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', - 'AlphaFold-2.1_fix-alphafold-tests.patch', ], 'checksums': [ - '37c92f31895c1f2cd5d8529176bc27a8d7db7659fff64e0c5f3f99ea35aadfb0', # v2.2.0.tar.gz + 'aa51dc4a1150b92310d20e63e9e4d9279b15b6a1f7e664360f52827f83256cdd', # v2.2.2.tar.gz '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch '6af91706b2a001494ddc0947f89f8b3d3adfcc26177c373824fe8ea1a58c0b48', # AlphaFold-2.1.2_data-dep-paths.patch 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch - # AlphaFold-2.1_fix-alphafold-tests.patch - '1e3f5a7359c46ec27c37043ddc33267e363112c455a5d85f49adb55bb9714588', ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, @@ -112,11 +109,11 @@ exts_list = [ ('toolz', '0.11.2', { 'checksums': ['6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33'], }), - ('chex', '0.1.1', { - 'checksums': ['f319f04568d1a75951f59129973a7852eedab93c4a94f382a65c4d718d9857c1'], + ('chex', '0.1.3', { + 'checksums': ['2cfa6ccd02addd6b113658d03bd5ce8a7b3bd24fa62e746a246073414ea1e103'], }), - ('tabulate', '0.8.9', { - 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + ('tabulate', '0.8.10', { + 'checksums': ['6c57f3f3dd7ac2782770155f3adb2db0b1a269637e42f27599925e64b114f519'], }), ('jmp', '0.0.2', { 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", @@ -128,13 +125,13 @@ exts_list = [ 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['bb038d7b6eae50ad8b59aecaad7b26180261f155c9a789d071133cb2596dc616'], }), - ('dm-tree', '0.1.6', { + ('dm-tree', '0.1.7', { 'modulename': 'tree', - 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + 'checksums': ['30fec8aca5b92823c0e796a2f33b875b4dccd470b57e91e6c542405c5f77fd2a'], }), - ('websocket-client', '1.3.1', { + ('websocket-client', '1.3.3', { 'modulename': 'websocket', - 'checksums': ['6278a75065395418283f887de7c3beafb3aa68dada5cacbe4b214e8d26da499b'], + 'checksums': ['d58c5f284d6a9bf8379dab423259fe8f85b70d5fa5d2916d5791a84594b122b1'], }), ('docker', '5.0.3', { 'checksums': ['d916a26b62970e7c2f554110ed6af04c7ccff8e9f81ad17d0d40c75637e227fb'], From bae368bf1258f5a3a2208a88986634de7317a467 Mon Sep 17 00:00:00 2001 From: James Moore <69149348+jkwmoore@users.noreply.github.com> Date: Wed, 22 Jun 2022 15:00:47 +0100 Subject: [PATCH 4074/9987] Amend to correct set-alias statements. Amends ``$EBROOTMAXQUANT`` to ``%(installdir)s`` as this variable would be undefined (as a TCL variable). --- .../easyconfigs/m/MaxQuant/MaxQuant-2.0.3.0-GCCcore-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.0.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.0.3.0-GCCcore-11.2.0.eb index 66bf848d14f..d38372872cd 100644 --- a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.0.3.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.0.3.0-GCCcore-11.2.0.eb @@ -26,8 +26,8 @@ sanity_check_commands = [ ("mono $EBROOTMAXQUANT/bin/MaxQuantCmd.exe --help 2>&1 | grep -q USAGE", '')] modaliases = { - 'maxquantcmd': 'mono $EBROOTMAXQUANT/bin/%(name)sCmd.exe', - 'maxquantgui': 'mono $EBROOTMAXQUANT/bin/%(name)sGui.exe', + 'maxquantcmd': 'mono %(installdir)s/bin/%(name)sCmd.exe', + 'maxquantgui': 'mono %(installdir)s/bin/%(name)sGui.exe', } modloadmsg = """ From c2204d92f4258a522ba72fe84961e2db5c2ff1f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Jun 2022 16:01:37 +0200 Subject: [PATCH 4075/9987] remove unused jax easyconfig --- .../jax/jax-0.2.28-foss-2021a-CUDA-11.3.1.eb | 129 ------------------ 1 file changed, 129 deletions(-) delete mode 100644 easybuild/easyconfigs/j/jax/jax-0.2.28-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.28-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.2.28-foss-2021a-CUDA-11.3.1.eb deleted file mode 100644 index ccf1ca366a7..00000000000 --- a/easybuild/easyconfigs/j/jax/jax-0.2.28-foss-2021a-CUDA-11.3.1.eb +++ /dev/null @@ -1,129 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'PythonBundle' - -name = 'jax' -version = '0.2.28' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://pypi.python.org/pypi/jax' -description = """Composable transformations of Python+NumPy programs: -differentiate, vectorize, JIT to GPU/TPU, and more""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -builddependencies = [ - ('Bazel', '3.7.2'), - ('pytest-xdist', '2.3.0'), - # git 2.x required to fetch repository 'io_bazel_rules_docker' - ('git', '2.32.0', '-nodocs'), -] - -dependencies = [ - ('CUDA', '11.3.1', '', True), - ('cuDNN', '8.2.1.32', versionsuffix, True), - ('NCCL', '2.10.3', versionsuffix), - ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05'), - ('flatbuffers-python', '2.0'), - ('typing-extensions', '3.10.0.0'), -] - -# running the tests with lots of cores results in test failures because not enough threads can be started, -# and running with a single core also results in systematic test failures -# 4 cores seems to work best -parallel = 4 - -# downloading TensorFlow tarball to avoid that Bazel downloads it during the build -# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE -local_tf_commit = 'e662039f98d2b6a0d8242887d0881bae04e2d590' -local_tf_dir = 'tensorflow-%s' % local_tf_commit -local_tf_builddir = '%(builddir)s/' + local_tf_dir - -# replace remote TensorFlow repository with the local one from EB -local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " -local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir - -use_pip = True - -default_easyblock = 'PythonPackage' -default_component_specs = { - 'sources': [SOURCE_TAR_GZ], - 'source_urls': [PYPI_SOURCE], - 'start_dir': '%(name)s-%(version)s', - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, -} - -components = [ - ('absl-py', '0.13.0', { - 'options': {'modulename': 'absl'}, - 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], - }), - ('jaxlib', '0.1.76', { - 'sources': [ - '%(name)s-v%(version)s.tar.gz', - { - 'download_filename': '%s.tar.gz' % local_tf_commit, - 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, - } - ], - 'source_urls': [ - 'https://github.com/google/jax/archive/', - 'https://github.com/tensorflow/tensorflow/archive/' - ], - 'patches': [ - ('jaxlib_local-tensorflow-repo.sed', '.'), - 'jaxlib-0.1.70_add-bazel-args-to-shutdown.patch', - ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), - ], - 'checksums': [ - # jaxlib-v0.1.76.tar.gz - '6d5e185906dbc8f0f6589c5bc0569ae049bfe6346c271db73d5077f1fda41c7c', - # tensorflow-e662039f98d2b6a0d8242887d0881bae04e2d590.tar.gz - '8d6604640c8092abf640ccfb7222f6f941ee7b409d30292f6261ce3c86e23fab', - # jaxlib_local-tensorflow-repo.sed - 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', - # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch - 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', - # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch - '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', - ], - 'start_dir': 'jax-jaxlib-v%(version)s', - 'prebuildopts': local_jax_prebuildopts, - }), -] - -exts_list = [ - ('opt_einsum', '3.3.0', { - 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], - }), - (name, version, { - 'source_urls': ['https://github.com/google/jax/archive/'], - 'source_tmpl': '%(name)s-v%(version)s.tar.gz', - 'patches': [ - 'jax-0.2.19_fix-update-of-cache-access-time.patch', - 'jax-0.2.24-foss-2021a_unimplemented.patch', - ], - 'checksums': [ - '7c6ffb14c2069d75c0721ec21b35ee253f0f368b84b9ec9459f0870ed902bfa7', # jax-v0.2.28.tar.gz - # jax-0.2.19_fix-update-of-cache-access-time.patch - 'e20562f67d63cc7e3478f7a92940291b2c8e328d605426bbabf89d8c2e1dd806', - # jax-0.2.24-foss-2021a_unimplemented.patch - '96fe1b15b55611727b0ae76409b89c44ae21a1c10002507ca8e3c06c2b134f4e', - ], - # deliberately not testing in parallel, as that results in (additional) failing tests; - # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, - # see https://github.com/google/jax/issues/7323 and - # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; - # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; - # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; - 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " - "JAX_ENABLE_X64=true pytest tests", - }), -] - -sanity_pip_check = True - -moduleclass = 'tools' From 7ddc6958afe6ed7584c329e657dfbe97018a391d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Jun 2022 16:01:56 +0200 Subject: [PATCH 4076/9987] adding easyconfigs: AlphaFold-2.2.2-foss-2021a.eb --- .../a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb | 185 ++++++++++++++++++ 1 file changed, 185 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb new file mode 100644 index 00000000000..46803614756 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb @@ -0,0 +1,185 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.2.2' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + # CMake/Doxygen/SWIG are required for building OpenMM + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('TensorFlow', '2.6.0'), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('jax', '0.3.9'), # also provides absl-py +] +local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " +local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " + +# required to install OpenMM Python API; +# avoid that setup.py partially uninstalls existing OpenMM Python bindings... +local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " +local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + # for simtk + ('OpenMM', '7.5.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/openmm/openmm/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], + 'checksums': [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch + ], + 'start_dir': 'openmm-%(version)s', + 'preinstallopts': local_openmm_preinstallopts, + 'installopts': local_openmm_installopts, + }), + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.1.2_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + 'aa51dc4a1150b92310d20e63e9e4d9279b15b6a1f7e664360f52827f83256cdd', # v2.2.2.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '6af91706b2a001494ddc0947f89f8b3d3adfcc26177c373824fe8ea1a58c0b48', # AlphaFold-2.1.2_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.2', { + 'checksums': ['6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33'], + }), + ('chex', '0.1.3', { + 'checksums': ['2cfa6ccd02addd6b113658d03bd5ce8a7b3bd24fa62e746a246073414ea1e103'], + }), + ('tabulate', '0.8.10', { + 'checksums': ['6c57f3f3dd7ac2782770155f3adb2db0b1a269637e42f27599925e64b114f519'], + }), + ('jmp', '0.0.2', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['fdb5cec0d10aab4116c2770f24b2adf4f503fcfbb96ce8ef583e1879bdbf1b9b'], + }), + ('dm-haiku', '0.0.6', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['bb038d7b6eae50ad8b59aecaad7b26180261f155c9a789d071133cb2596dc616'], + }), + ('dm-tree', '0.1.7', { + 'modulename': 'tree', + 'checksums': ['30fec8aca5b92823c0e796a2f33b875b4dccd470b57e91e6c542405c5f77fd2a'], + }), + ('websocket-client', '1.3.3', { + 'modulename': 'websocket', + 'checksums': ['d58c5f284d6a9bf8379dab423259fe8f85b70d5fa5d2916d5791a84594b122b1'], + }), + ('docker', '5.0.3', { + 'checksums': ['d916a26b62970e7c2f554110ed6af04c7ccff8e9f81ad17d0d40c75637e227fb'], + }), + ('immutabledict', '2.2.1', { + 'checksums': ['1ddb0edf1bb6c70d0197eb90ce1fe2b2d58502334f5fdfde72d7c633d723ec3a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, + 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextrapaths = { + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +modextravars = { + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt +} + +moduleclass = 'bio' From 652906cad04f0644babc8f6561de6111c87d44ca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Jun 2022 16:21:30 +0200 Subject: [PATCH 4077/9987] add exception to easyconfigs test suite for jax 0.3.9 used as dependency for AlphaFold 2.2.2 --- test/easyconfigs/easyconfigs.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index e8fae843422..a79fc338337 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -464,7 +464,8 @@ def check_dep_vars(self, gen, dep, dep_vars): break # some software packages require a specific (older/newer) version of a particular dependency - old_dep_versions = { + alt_dep_versions = { + 'jax': [(r'0\.3\.9', [r'AlphaFold-2\.2\.2-'])], # arrow-R 6.0.0.2 is used for two R/R-bundle-Bioconductor sets (4.1.2/3.14 and 4.2.0/3.15) 'arrow-R': [('6.0.0.2', [r'R-bundle-Bioconductor-'])], # EMAN2 2.3 requires Boost(.Python) 1.64.0 @@ -554,10 +555,10 @@ def check_dep_vars(self, gen, dep, dep_vars): # (for 2021b, UCX was updated to v1.11.2) 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], } - if dep in old_dep_versions and len(dep_vars) > 1: + if dep in alt_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): - for version_pattern, parents in old_dep_versions[dep]: - # filter out known old dependency versions + for version_pattern, parents in alt_dep_versions[dep]: + # filter out known alternative dependency versions if re.search('^version: %s' % version_pattern, key): # only filter if the easyconfig using this dep variants is known if all(any(re.search(p, x) for p in parents) for x in dep_vars[key]): From 97f29bc682c791a7157775147c71fb44409c1d3c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Jun 2022 17:05:13 +0200 Subject: [PATCH 4078/9987] adding easyconfigs: SISSO-3.1-20220324-iimpi-2021b.eb --- .../s/SISSO/SISSO-3.1-20220324-iimpi-2021b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SISSO/SISSO-3.1-20220324-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/s/SISSO/SISSO-3.1-20220324-iimpi-2021b.eb b/easybuild/easyconfigs/s/SISSO/SISSO-3.1-20220324-iimpi-2021b.eb new file mode 100644 index 00000000000..daa47a51e19 --- /dev/null +++ b/easybuild/easyconfigs/s/SISSO/SISSO-3.1-20220324-iimpi-2021b.eb @@ -0,0 +1,29 @@ +easyblock = 'CmdCp' + +name = 'SISSO' +local_commit = '9b6080e' +version = '3.1-20220324' + +homepage = 'https://github.com/rouyang2017/SISSO' +description = """A data-driven method combining symbolic regression and compressed sensing toward accurate & + interpretable models.""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/rouyang2017/SISSO/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['e41ca55d7b66ab52b72059456092428053d4fadc9a69393929c847c49108115b'] + +start_dir = 'src' + +cmds_map = [('.*', "$F90 $FFLAGS var_global.f90 libsisso.f90 DI.f90 FC.f90 SISSO.f90 -o SISSO")] + +files_to_copy = [(['SISSO'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/SISSO'], + 'dirs': [], +} + +moduleclass = 'math' From 164cc13f4911b8da7f706909b1ae4e6252f1a16e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 22 Jun 2022 17:36:21 +0200 Subject: [PATCH 4079/9987] adding easyconfigs: ITK-5.2.1-foss-2021b.eb --- .../easyconfigs/i/ITK/ITK-5.2.1-foss-2021b.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021b.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021b.eb new file mode 100644 index 00000000000..738552724da --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2021b.eb @@ -0,0 +1,59 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.2.1' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6022b2b64624b8bcec3333fe48d5f74ff6ebceb3bdf98258ba7d7fbbc76b99ab'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Bison', '3.7.6'), + ('Eigen', '3.3.9'), +] +dependencies = [ + ('expat', '2.4.1'), + ('HDF5', '1.12.1'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('VTK', '9.1.0'), + ('zlib', '1.2.11'), +] + +local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' +configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], +} + +moduleclass = 'data' From cc3d8c9c260fcf987ba9082576aad10bdd4d0985 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 22 Jun 2022 19:25:48 +0100 Subject: [PATCH 4080/9987] adding easyconfigs: GDAL-3.5.0-foss-2022.05.eb --- .../g/GDAL/GDAL-3.5.0-foss-2022.05.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022.05.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022.05.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022.05.eb new file mode 100644 index 00000000000..b5aeef98264 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022.05.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.5.0' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2022.05'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] +checksums = [ + 'd49121e5348a51659807be4fb866aa840f8dbec4d1acba6d17fdefa72125bfc9', # gdal-3.5.0.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('netCDF', '4.9.0'), + ('expat', '2.4.8'), + ('GEOS', '3.10.3'), + ('SQLite', '3.38.3'), + ('libxml2', '2.9.13'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('JasPer', '2.0.33'), + ('LibTIFF', '4.3.0'), + ('zlib', '1.2.12'), + ('cURL', '7.83.0'), + ('PCRE', '8.45'), + ('PROJ', '9.0.0'), + ('libgeotiff', '1.7.1'), + ('SciPy-bundle', '2022.05'), + ('HDF5', '1.13.1'), + ('HDF', '4.2.15'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import osgeo.gdal'"] + +moduleclass = 'data' From 6dedcf0334dbb7e975f40b85f527a9ce58b90bd6 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 23 Jun 2022 09:45:50 +0200 Subject: [PATCH 4081/9987] adding easyconfigs: SimpleITK-2.1.1.2-foss-2021b.eb and patches: SimpleITK-2.1.1.2_allow-lua54-for-code-generation.patch --- .../SimpleITK/SimpleITK-2.1.1.2-foss-2021b.eb | 51 +++++++++++++++++++ ....1.2_allow-lua54-for-code-generation.patch | 31 +++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2_allow-lua54-for-code-generation.patch diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2021b.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2021b.eb new file mode 100644 index 00000000000..56f8ad1608b --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2021b.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMake' + +name = 'SimpleITK' +version = '2.1.1.2' + +homepage = 'https://www.simpleitk.org' +description = """SimpleITK is a simplified programming interface to the algorithms and data structures of + the Insight Toolkit (ITK).""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://pypi.python.org/packages/source/s/simpleitk/'] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_allow-lua54-for-code-generation.patch'] +checksums = [ + '5c0689b007d449ce0ce17a9ea322152315fb17ed32949005a974d3d9c2f58da3', # SimpleITK-2.1.1.2.tar.gz + # SimpleITK-2.1.1.2_allow-lua54-for-code-generation.patch + 'd1a45b1b64a226b3c22bf83c2f40f7f0e8f0a7d74bea1b2e7f5c5b6ed88b1522', +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('SWIG', '4.0.2'), + ('Lua', '5.4.3'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('ITK', '5.2.1'), + ('scikit-build', '0.11.1'), +] + +start_dir = 'SimpleITK' + +configopts = "-DWRAP_DEFAULT:BOOL=OFF -DWRAP_PYTHON=BOOL:ON " + +postinstallcmds = [ + "cd %(builddir)s/easybuild_obj/Wrapping/Python && " + "pip install --ignore-installed --no-deps --prefix=%(installdir)s . ", +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], + 'dirs': ['include/%(name)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import %(name)s'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2_allow-lua54-for-code-generation.patch b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2_allow-lua54-for-code-generation.patch new file mode 100644 index 00000000000..d29d262f15b --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2_allow-lua54-for-code-generation.patch @@ -0,0 +1,31 @@ +SimpleITK v2.1.1.2 requires Lua 5.3, which is not available in the easybuild foss/2021b toolchain. + +This patch allows the code generation during the configuration step to use Lua 5.4.· +(Lua wrapping has been disabled in the existing SimpleITK easyconfigs, anyway.) + +Author: https://github.com/crubb + +diff -ur SimpleITK-2.1.1.2.orig/SimpleITK/CMake/sitkGenerateFilterSource.cmake SimpleITK-2.1.1.2/SimpleITK/CMake/sitkGenerateFilterSource.cmake +--- SimpleITK-2.1.1.2.orig/SimpleITK/CMake/sitkGenerateFilterSource.cmake 2021-07-23 18:52:45.000000000 +0200 ++++ SimpleITK-2.1.1.2/SimpleITK/CMake/sitkGenerateFilterSource.cmake 2022-06-22 18:10:02.247043199 +0200 +@@ -7,7 +7,7 @@ + get_property( SAVE_LUA_EXECUTABLE_DOCSTRING CACHE LUA_EXECUTABLE PROPERTY HELPSTRING ) + unset(LUA_EXECUTABLE CACHE) + +- find_package( LuaInterp 5.3 REQUIRED ) ++ find_package( LuaInterp 5.4 REQUIRED ) + set( SimpleITK_LUA_EXECUTABLE ${LUA_EXECUTABLE} CACHE PATH "Lua executable used for code generation." ) + + if (DEFINED SAVE_LUA_EXECUTABLE) +@@ -46,9 +46,9 @@ + + if( SITK_LUA_VERSION_RESULT_VARIABLE + OR +- NOT ${SimpleITK_LUA_EXECUTABLE_VERSION} VERSION_GREATER "5.2" ++ NOT ${SimpleITK_LUA_EXECUTABLE_VERSION} VERSION_GREATER "5.3" + OR +- NOT ${SimpleITK_LUA_EXECUTABLE_VERSION} VERSION_LESS "5.4" ) ++ NOT ${SimpleITK_LUA_EXECUTABLE_VERSION} VERSION_LESS "5.5" ) + message(SEND_ERROR "Lua version 5.3 is required for SimpleITK_LUA_EXECUTABLE_VERSION.") + endif() + From 001aa3ef073b1b66ec22b740c8548dd749d34acf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Jun 2022 10:28:43 +0200 Subject: [PATCH 4082/9987] add patch file to fix linking error for netCDF v4.9.0 + run test suite via 'make test' --- .../n/netCDF/netCDF-4.9.0-gompi-2022.05.eb | 11 ++- .../netCDF-4.9.0_fix-linking-errors.patch | 99 +++++++++++++++++++ 2 files changed, 109 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_fix-linking-errors.patch diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb index 182ce0e5b91..a10128b18c4 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb @@ -11,10 +11,14 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['netCDF-%(version)s_fix-lib-name.patch'] +patches = [ + 'netCDF-%(version)s_fix-lib-name.patch', + 'netCDF-%(version)s_fix-linking-errors.patch', +] checksums = [ '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch + '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch ] builddependencies = [ @@ -36,4 +40,9 @@ configopts = [ "-DBUILD_SHARED_LIBS=ON", ] +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_fix-linking-errors.patch b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_fix-linking-errors.patch new file mode 100644 index 00000000000..a4a2ee7f88f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_fix-linking-errors.patch @@ -0,0 +1,99 @@ +fix "multiple definition" linking errors, +see also https://github.com/Unidata/netcdf-c/issues/2419 +author: Kenneth Hoste (HPC-UGent) + Lars Viklund (Umeå University) +--- netcdf-c-4.9.0/include/netcdf_json.h.orig 2022-06-23 08:35:33.345891769 +0200 ++++ netcdf-c-4.9.0/include/netcdf_json.h 2022-06-23 08:37:38.626339409 +0200 +@@ -57,25 +57,25 @@ + #endif + + /* Parse a JSON string */ +-DLLEXPORT int NCJparse(const char* text, unsigned flags, NCjson** jsonp); ++DLLEXPORT static int NCJparse(const char* text, unsigned flags, NCjson** jsonp); + + /* Reclaim a JSON tree */ +-DLLEXPORT extern void NCJreclaim(NCjson* json); ++DLLEXPORT static void NCJreclaim(NCjson* json); + + /* Create a new JSON node of a given sort */ +-DLLEXPORT extern int NCJnew(int sort, NCjson** objectp); ++DLLEXPORT static int NCJnew(int sort, NCjson** objectp); + + /* Create new json object with given string content */ +-DLLEXPORT extern int NCJnewstring(int sort, const char* value, NCjson** jsonp); ++DLLEXPORT static int NCJnewstring(int sort, const char* value, NCjson** jsonp); + + /* Create new json object with given counted string content */ +-DLLEXPORT extern int NCJnewstringn(int sort, size_t len, const char* value, NCjson** jsonp); ++DLLEXPORT static int NCJnewstringn(int sort, size_t len, const char* value, NCjson** jsonp); + + /* Get dict key value by name */ +-DLLEXPORT extern int NCJdictget(const NCjson* dict, const char* key, NCjson** valuep); ++DLLEXPORT static int NCJdictget(const NCjson* dict, const char* key, NCjson** valuep); + + /* Convert one json sort to value of another type; don't use union so we can know when to reclaim sval */ +-DLLEXPORT extern int NCJcvt(const NCjson* value, int outsort, struct NCJconst* output); ++DLLEXPORT static int NCJcvt(const NCjson* value, int outsort, struct NCJconst* output); + + #ifndef NETCDF_JSON_H + +@@ -230,7 +230,7 @@ + + /**************************************************/ + +-int ++static int + NCJparse(const char* text, unsigned flags, NCjson** jsonp) + { + int stat = NCJ_OK; +@@ -579,7 +579,7 @@ + + /**************************************************/ + +-void ++static void + NCJreclaim(NCjson* json) + { + if(json == NULL) return; +@@ -621,7 +621,7 @@ + /**************************************************/ + /* Build Functions */ + +-int ++static int + NCJnew(int sort, NCjson** objectp) + { + int stat = NCJ_OK; +@@ -651,13 +651,13 @@ + return NCJTHROW(stat); + } + +-int ++static int + NCJnewstring(int sort, const char* value, NCjson** jsonp) + { + return NCJTHROW(NCJnewstringn(sort,strlen(value),value,jsonp)); + } + +-int ++static int + NCJnewstringn(int sort, size_t len, const char* value, NCjson** jsonp) + { + int stat = NCJ_OK; +@@ -679,7 +679,7 @@ + return NCJTHROW(stat); + } + +-int ++static int + NCJdictget(const NCjson* dict, const char* key, NCjson** valuep) + { + int i,stat = NCJ_OK; +@@ -755,7 +755,7 @@ + #endif + + /* Convert a JSON value to an equivalent value of a specified sort */ +-int ++static int + NCJcvt(const NCjson* jvalue, int outsort, struct NCJconst* output) + { + int stat = NCJ_OK; From cc18daa1d7255dca7afad53735103566d68cae52 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 23 Jun 2022 14:09:14 +0200 Subject: [PATCH 4083/9987] adding easyconfigs: Transformers-4.20.1-foss-2021a-Python-3.9.5.eb --- ...sformers-4.20.1-foss-2021a-Python-3.9.5.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/t/Transformers/Transformers-4.20.1-foss-2021a-Python-3.9.5.eb diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.20.1-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.20.1-foss-2021a-Python-3.9.5.eb new file mode 100644 index 00000000000..baef0993629 --- /dev/null +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.20.1-foss-2021a-Python-3.9.5.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Transformers' +version = '4.20.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/huggingface/transformers' +description = """ +State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('typing-extensions', '3.10.0.0'), # needed by huggingface-hub + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('regex', '2021.11.10', { + 'checksums': ['f341ee2df0999bfdf7a95e448075effe0db212a59387de1a70690e4acb03d4c6'], + }), + ('sacremoses', '0.0.53', { + 'checksums': ['43715868766c643b35de4b8046cce236bfe59a7fa88b25eaf6ddf02bacf53a7a'], + }), + ('tokenizers', '0.12.1', { + 'source_tmpl': 'tokenizers-%(version)s-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl', + 'checksums': ['619728df2551bdfe6f96ff177f9ded958e7ed9e2af94c8d5ac2834d1eb06d112'], + }), + ('huggingface-hub', '0.8.1', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['75c70797da54b849f06c2cbf7ba2217250ee217230b9f65547d5db3c5bd84bb5'], + }), + ('transformers', version, { + 'checksums': ['65ee4ae9abdeca8fe3a9e351256345e3c4db2a6a68accd5d6a141cfff6192751'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From 04579e635ee6845328e7fd5bd568ecde253b0807 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 23 Jun 2022 14:12:08 +0200 Subject: [PATCH 4084/9987] rename easyconfig to Transformers-4.20.1-foss-2021a.eb --- ...s-2021a-Python-3.9.5.eb => Transformers-4.20.1-foss-2021a.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/t/Transformers/{Transformers-4.20.1-foss-2021a-Python-3.9.5.eb => Transformers-4.20.1-foss-2021a.eb} (97%) diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.20.1-foss-2021a-Python-3.9.5.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.20.1-foss-2021a.eb similarity index 97% rename from easybuild/easyconfigs/t/Transformers/Transformers-4.20.1-foss-2021a-Python-3.9.5.eb rename to easybuild/easyconfigs/t/Transformers/Transformers-4.20.1-foss-2021a.eb index baef0993629..fcc1a9e0a7e 100644 --- a/easybuild/easyconfigs/t/Transformers/Transformers-4.20.1-foss-2021a-Python-3.9.5.eb +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.20.1-foss-2021a.eb @@ -2,7 +2,6 @@ easyblock = 'PythonBundle' name = 'Transformers' version = '4.20.1' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/huggingface/transformers' description = """ From 3f8147af708fd71a3ab954af95bbd2052715e8c9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 23 Jun 2022 14:15:11 +0200 Subject: [PATCH 4085/9987] adding easyconfigs: imbalanced-learn-0.9.0-foss-2021b.eb --- .../imbalanced-learn-0.9.0-foss-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.9.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.9.0-foss-2021b.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.9.0-foss-2021b.eb new file mode 100644 index 00000000000..ba39fe52cf2 --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.9.0-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'imbalanced-learn' +version = '0.9.0' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('scikit-learn', '1.0.1'), +] + +exts_list = [ + (name, version, { + 'modulename': 'imblearn', + 'checksums': ['836a4c137cc3c10310d4f6cd5ec34600ff488d7f8c243a997c3f9b551c91d0b2'], + }), +] + +use_pip = True + +sanity_pip_check = True + +moduleclass = 'tools' From d73489fda85c6f9aac4c7df12c6a15bf8806db42 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 23 Jun 2022 14:39:26 +0100 Subject: [PATCH 4086/9987] adding easyconfigs: xtb-6.5.0-foss-2021b.eb --- .../easyconfigs/x/xtb/xtb-6.5.0-foss-2021b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.5.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.5.0-foss-2021b.eb b/easybuild/easyconfigs/x/xtb/xtb-6.5.0-foss-2021b.eb new file mode 100644 index 00000000000..ff607803c18 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.5.0-foss-2021b.eb @@ -0,0 +1,47 @@ +# Author: Jasper Grimm (UoY) +# Updated to 6.5.0 and moved to foss-toolchain +# Based on xtb-6.4.1-intel-2021a.eb and PR 15187 +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MesonNinja' + +name = 'xtb' +version = '6.5.0' + +homepage = 'https://xtb-docs.readthedocs.io' +description = "Semiempirical Extended Tight-Binding Program Package." + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b39f6e87ce07abcb0884cda5d3370601b6332ad72c8213e87ffa74ae28895fb'] + +builddependencies = [ + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +configopts = "-Dla_backend='custom' " +configopts += "-Dcustom_libraries='flexiblas' " +configopts += "--buildtype release " + +runtest = 'meson' +# Ensure test don't timeout and only use one process: +testopts = 'test -C %(builddir)s/easybuild_obj -t 60 --num-processes=1' + +sanity_check_paths = { + 'files': ['bin/xtb', 'include/xtb.h'] + ['lib/libxtb.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = ["xtb --help"] + +modextrapaths = { + 'XTBHOME': '', + 'XTBPATH': '', +} + +moduleclass = 'chem' From 2a4f20833b8ff66a1da153a6c19c5c523d7c6d14 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 23 Jun 2022 17:28:31 +0100 Subject: [PATCH 4087/9987] adding easyconfigs: Arrow-8.0.0-foss-2022.05.eb, RapidJSON-1.1.0-GCCcore-11.3.0.eb, RE2-2022-06-01-GCCcore-11.3.0.eb, snappy-1.1.9-GCCcore-11.3.0.eb, utf8proc-2.7.0-GCCcore-11.3.0.eb --- .../a/Arrow/Arrow-8.0.0-foss-2022.05.eb | 69 +++++++++++++++++++ .../r/RE2/RE2-2022-06-01-GCCcore-11.3.0.eb | 33 +++++++++ .../RapidJSON-1.1.0-GCCcore-11.3.0.eb | 30 ++++++++ .../s/snappy/snappy-1.1.9-GCCcore-11.3.0.eb | 39 +++++++++++ .../utf8proc/utf8proc-2.7.0-GCCcore-11.3.0.eb | 30 ++++++++ 5 files changed, 201 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb create mode 100644 easybuild/easyconfigs/r/RE2/RE2-2022-06-01-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.7.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb new file mode 100644 index 00000000000..6f01b9c72ba --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb @@ -0,0 +1,69 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '8.0.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'foss', 'version': '2022.05'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Autotools', '20220317'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '1.8.0'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for numpy + ('Boost', '1.79.0'), + ('lz4', '1.9.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.2'), + ('snappy', '1.1.9'), + ('RapidJSON', '1.1.0'), + ('RE2', '2022-06-01'), + ('utf8proc', '2.7.0'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " +configopts += "-DZSTD_ROOT=$EBROOTZSTD " + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/RE2/RE2-2022-06-01-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2022-06-01-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6180050adea --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2022-06-01-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = "CMakeMake" + +name = 'RE2' +version = '2022-06-01' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['f89c61410a072e5cbcf8c27e3a778da7d6fd2f2b5b1445cd4f4508bee946ab0f'] + +builddependencies = { + ('binutils', '2.38'), + ('CMake', '3.23.1'), +} + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3452dfb7caf --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +version = '1.1.0' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-compiler-errors.patch'] +checksums = [ + 'bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e', # v1.1.0.tar.gz + # %(name)s-%(version_major_minor)s.0_fix-compiler-errors.patch + '2e40ef6c46bf355feac16cd84faad5b7aca0ad54273117b85534b1b781f411c7', +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..459be39d9c3 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.9' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_inline-functions.patch', + '%(name)s-%(version)s_use-default-rtti.patch', +] +checksums = [ + '75c1fbb3d618dd3a0483bff0e26d0a92b495bbe5059c8b4f1c962b478b6e06e7', # 1.1.9.tar.gz + 'ad79190b274df5ddabf14eddd2bb0d9a091ee7d44e4afde89febf9a8f783fdce', # snappy-1.1.9_inline-functions.patch + 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d', # snappy-1.1.9_use-default-rtti.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.7.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..be580835593 --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.7.0-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.7.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4bb121e297293c0fd55f08f83afab6d35d48f0af4ecc07523ad8ec99aa2b12a1'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 4bda8a3530b7d6ed6d89d09eb640a06ba3f7fd2b Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 23 Jun 2022 17:42:22 +0100 Subject: [PATCH 4088/9987] adding easyconfigs: GULP-6.1-foss-2021b.eb and patches: GULP-6.1_fftw-blas-linking-gcc-11.patch --- .../easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb | 56 ++++++++++++++++ .../GULP-6.1_fftw-blas-linking-gcc-11.patch | 65 +++++++++++++++++++ 2 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch diff --git a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb new file mode 100644 index 00000000000..548abba02ce --- /dev/null +++ b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb @@ -0,0 +1,56 @@ +# Contribution from Imperial College London / UK +# Based on GULP-6.0-foss-2020b.eb +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'GULP' +version = '6.1' + +homepage = 'https://gulp.curtin.edu.au/gulp/' +description = """GULP is a program for performing a variety of types of simulation on materials + using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs + and grain boundaries), or 3-D (periodic solids)Band Unfolding code for Plane-wave based calculations""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +# download requires registration, https://gulp.curtin.edu.au/gulp/request.cfm?rel=download +sources = [SOURCELOWER_TGZ] +patches = [ + 'GULP-6.1_fftw-blas-linking-gcc-11.patch', +] +checksums = [ + '503dff253f4686c570adfd3ff75a657e29151b4255dec726daa50eda5a7ac3f4', # gulp-6.1.tgz + '156449c96a97ff24f6add83c10fd383f07c43c79420eebe3290387b65b34549b', # gulp-6.1_fftw-blas-linking-gcc-11.patch +] + +start_dir = 'Src' + +# Use external FFTW (-f), enable parallel/MPI build (-m) and set the base compiler (-c). +# Building it this way means both the serial and parallel build are available. +# The serial build can be used like this: +# $ gulp < FILE.gin > OUT.gout +# For the parallel run, just add mpirun: +# $ mpirun -n X gulp < FILE.gin > OUT.gout + +build_cmd = "./mkgulp -f -m -c gfortran" + +files_to_copy = [ + (['gulp'], 'bin'), + (['../Docs', '../Examples', '../Libraries', '../Utils'], ''), +] + +sanity_check_paths = { + 'files': ['bin/gulp'], + 'dirs': ['Docs', 'Examples', 'Libraries', 'Utils'], +} + +modextrapaths = { + 'GULP_LIB': 'Libraries', + 'GULP_DOC': 'Docs', + 'GULP_EXAMPLES': 'Examples', + 'GULP_UTILS': 'Utils', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch b/easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch new file mode 100644 index 00000000000..89f6cc6151d --- /dev/null +++ b/easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch @@ -0,0 +1,65 @@ +Removing hard-coded paths in the mkgulp file, which is creating the makefile +Using the suggested compiler flags for gfortran-10 +author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/gulp-6.1.orig/Src/mkgulp b/gulp-6.1/Src/mkgulp +index 5a6ca20..a1fdb42 100755 +--- a/gulp-6.1.orig/Src/mkgulp ++++ b/gulp-6.1/Src/mkgulp +@@ -196,7 +196,7 @@ fi + # Include file directories + # + #--USER--Start +-echo 'INC=-I.. ' >> makefile ++echo 'INC=-I.. -I'${EBROOTFFTW}/include >> makefile + #--USER--End + # If using Macports then use the following instead + #--USER--Start +@@ -230,7 +230,7 @@ case $compiler in + # On the Mac the following is sufficient when using Macports: + # echo 'MLIBS=-L/opt/local/lib/lapack/ -llapack -lblas ' >> makefile + # If using the accelerate framework then leave blank: +- echo 'MLIBS=' >> makefile ++ echo 'MLIBS=-L'${EBROOTFLEXIBLAS}'/lib -lflexiblas' >> makefile + # Or if optimised maths libraries are not available then: + # echo 'MLIBS=lapack.o blas.o' >> makefile + #--USER--End +@@ -238,7 +238,7 @@ case $compiler in + else + # NB: For gfortran v10 then use these lines + echo 'RUNF90=mpif90 -fallow-argument-mismatch ' >> makefile +- echo 'RUNCC=mpif90 ' >> makefile ++ echo 'RUNCC=mpif90 -fallow-argument-mismatch ' >> makefile + # echo 'RUNF90=mpif90 ' >> makefile + # echo 'RUNCC=mpif90 ' >> makefile + # +@@ -247,14 +247,14 @@ case $compiler in + # On the Mac the following is sufficient when using Macports: + # echo 'MLIBS=-L/opt/local/lib/lapack/ -llapack -lblas ' >> makefile + # If using the accelerate framework then leave blank: +- echo 'MLIBS=' >> makefile ++ echo 'MLIBS=-L'${EBROOTFLEXIBLAS}'/lib -lflexiblas' >> makefile + # Or if optimised maths libraries are not available then: + # echo 'MLIBS=lapack.o blas.o' >> makefile + #--USER--End + # Provide the location and name of Scalapack, Blacs, and Pblas libraries if running in parallel: + #--USER--Start + # For homebrew installation of Scalapack: +- echo 'SLIBS=-L/opt/homebrew/lib -lscalapack ' >> makefile ++ echo 'SLIBS=-L'${EBROOTSCALAPACK}'/lib -lscalapack ' >> makefile + # echo 'SLIBS=-L/opt/local/lib -lscalapack ' >> makefile + #--USER--End + fi +@@ -363,11 +363,11 @@ else + echo 'FDEFS=-DFFTW3 ' >> makefile + if [ "$parallel" = "" ] + #--USER--Start +- echo 'FLIBS=-L/usr/local/lib/ -lfftw3.a' >> makefile ++ echo 'FLIBS=-L'${EBROOTFFTW}'/lib -lfftw3' >> makefile + #--USER--End + then + #--USER--Start +- echo 'FLIBS=-L/usr/local/lib/ -lfftw3 -lfftw3_mpi' >> makefile ++ echo 'FLIBS=-L'${EBROOTFFTW}'/lib -lfftw3 -lfftw3_mpi' >> makefile + # The following is for NCI + # echo 'FLIBS=-mkl -lfftw3x_cdft_openmpi_lp64' + #--USER--End From 022fa2b6d5a1b5fa2fbf5f75f170f0894aeaa2d4 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 23 Jun 2022 18:12:27 +0100 Subject: [PATCH 4089/9987] Restricted to 4 concurrent builds to avoid hickups --- easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb index 548abba02ce..264f38782a5 100644 --- a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb @@ -36,6 +36,10 @@ start_dir = 'Src' build_cmd = "./mkgulp -f -m -c gfortran" +# When building in parallel, it appears that with more than 4 cores it gets confused +maxparallel = 4 + + files_to_copy = [ (['gulp'], 'bin'), (['../Docs', '../Examples', '../Libraries', '../Utils'], ''), From 84d65d23357ed2b87a6f2b33cc8e163e9196dc82 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 24 Jun 2022 08:11:45 +0100 Subject: [PATCH 4090/9987] {foss,intel,gfbf}/2022a --- .../f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022a.eb | 19 ++++ easybuild/easyconfigs/f/foss/foss-2022a.eb | 28 ++++++ .../g/GCTA/GCTA-1.94.0beta-gfbf-2022a.eb | 68 ++++++++++++++ .../g/GDAL/GDAL-3.5.0-foss-2022a.eb | 65 ++++++++++++++ .../h/HDF5/HDF5-1.13.1-gompi-2022a.eb | 21 +++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2022a.eb | 21 +++++ easybuild/easyconfigs/i/iimpi/iimpi-2022a.eb | 18 ++++ .../imkl-FFTW-2022.1.0-iimpi-2022a.eb | 11 +++ easybuild/easyconfigs/i/intel/intel-2022a.eb | 22 +++++ .../n/netCDF/netCDF-4.9.0-gompi-2022a.eb | 48 ++++++++++ .../OSU-Micro-Benchmarks-5.9-gompi-2022a.eb | 26 ++++++ .../ScaLAPACK-2.2.0-gompi-2022a-fb.eb | 43 +++++++++ .../SciPy-bundle-2022.05-foss-2022a.eb | 86 ++++++++++++++++++ .../SciPy-bundle-2022.05-intel-2022a.eb | 88 +++++++++++++++++++ 14 files changed, 564 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022a.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022a.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2022a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022a-fb.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022a.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022a.eb new file mode 100644 index 00000000000..f02489825a9 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022a.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2022a.eb b/easybuild/easyconfigs/f/foss/foss-2022a.eb new file mode 100644 index 00000000000..99d57d2d5fa --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2022a' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '11.3.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.2.0', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022a.eb b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022a.eb new file mode 100644 index 00000000000..6ddc39e6bbb --- /dev/null +++ b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022a.eb @@ -0,0 +1,68 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'CMakeMakeCp' + +name = 'GCTA' +version = '1.94.0beta' +_plink_commit = '3744540' + +homepage = 'https://yanglab.westlake.edu.cn/software/gcta/' +description = """ +GCTA (Genome-wide Complex Trait Analysis) is a software package, which was + initially developed to estimate the proportion of phenotypic variance explained + by all genome-wide SNPs for a complex trait but has been extensively extended + for many other analyses of data from genome-wide association studies (GWASs). +""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/jianyangqt/gcta/archive'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/zhilizheng/plink-ng/archive'], + 'download_filename': '%s.tar.gz' % _plink_commit, + 'filename': 'plink-ng-%s.tar.gz' % _plink_commit, + 'extract_cmd': "tar xzvf %%s --strip-components 1 -C gcta-%s/submods/plink-ng" % version, + }, +] +patches = [ + 'GCTA-1.94.0beta_allow-BLAS-selection.patch', + 'GCTA-1.94.0beta_lapack-compatibility.patch', +] +checksums = [ + '9220a6c40f31e3b1ce3d25f7eee3d8c62403bee8d6ed624bd8b61891badcb14f', # GCTA-1.94.0beta.tar.gz + 'a7c70c237d49d64fc1668ced373036c09b41d7c61d0b8b24b47e2fb76474455d', # plink-ng-3744540.tar.gz + '320a5d82d12cf453f1396b228723ac18dc98e32bc459394dd4d712fc16b24747', # GCTA-1.94.0beta_allow-BLAS-selection.patch + '643282a2e2c02fc683431b673a4623a498129870431481d33d33e19a509026ce', # GCTA-1.94.0beta_lapack-compatibility.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), + # Eigen and SpectrA are header-only C++ libraries + ('Eigen', '3.4.0'), + ('SpectrA', '1.0.1'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('SQLite', '3.38.3'), + ('zstd', '1.5.2'), + ('GSL', '2.7'), +] + +preconfigopts = 'EIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include SPECTRA_LIB=$EBROOTSPECTRA/include' +preconfigopts += ' BOOST_LIB=$EBROOTBOOST/include ' + +files_to_copy = [(['gcta64'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/gcta64'], + 'dirs': [], +} + +sanity_check_commands = ["gcta64 | grep -e 'Analysis started'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb new file mode 100644 index 00000000000..52779e74f85 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '3.5.0' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] +checksums = [ + 'd49121e5348a51659807be4fb866aa840f8dbec4d1acba6d17fdefa72125bfc9', # gdal-3.5.0.tar.xz + '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch +] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('netCDF', '4.9.0'), + ('expat', '2.4.8'), + ('GEOS', '3.10.3'), + ('SQLite', '3.38.3'), + ('libxml2', '2.9.13'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('JasPer', '2.0.33'), + ('LibTIFF', '4.3.0'), + ('zlib', '1.2.12'), + ('cURL', '7.83.0'), + ('PCRE', '8.45'), + ('PROJ', '9.0.0'), + ('libgeotiff', '1.7.1'), + ('SciPy-bundle', '2022.05'), + ('HDF5', '1.13.1'), + ('HDF', '4.2.15'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import osgeo.gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022a.eb new file mode 100644 index 00000000000..069d7bb84d9 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.13.1' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022a.eb new file mode 100644 index 00000000000..094c6181614 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022a.eb new file mode 100644 index 00000000000..346e185e46d --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022a.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022a' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.1.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.6.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb new file mode 100644 index 00000000000..d81a631f10f --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022a'} + +dependencies = [('imkl', version, '', True)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/intel/intel-2022a.eb b/easybuild/easyconfigs/i/intel/intel-2022a.eb new file mode 100644 index 00000000000..b9eb05d6541 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022a.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022a' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.1.0' +local_gccver = '11.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.38', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.6.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', True), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb new file mode 100644 index 00000000000..feefb6d13a7 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb @@ -0,0 +1,48 @@ +name = 'netCDF' +version = '4.9.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-%(version)s_fix-lib-name.patch', + 'netCDF-%(version)s_fix-linking-errors.patch', +] +checksums = [ + '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz + 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch + '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('HDF5', '1.13.1'), + ('cURL', '7.83.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.2'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a.eb new file mode 100644 index 00000000000..6aef7304682 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.9' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022a-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022a-fb.eb new file mode 100644 index 00000000000..5d3f67e7f5f --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022a-fb.eb @@ -0,0 +1,43 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('FlexiBLAS', '3.2.0'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb new file mode 100644 index 00000000000..b93d1166c8a --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb @@ -0,0 +1,86 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2022.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.46.7'), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('pybind11', '2.9.2'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.22.3', { + 'patches': [ + 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.22.3_disable-broken-override-test.patch', + ], + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': [ + 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18', # numpy-1.22.3.zip + # numpy-1.20.3_disable_fortran_callback_test.patch + '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + # numpy-1.22.3_disable-broken-override-test.patch + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.11.0', { + 'checksums': ['0b2cba712e09f7630879dff69f268460bfe34a6d6000451b47d598558a92a875'], + }), + ('scipy', '1.8.1', { + # compilation with Pythran enabled fails when using Intel compilers, + # see https://github.com/scipy/scipy/issues/14935 + 'prebuildopts': "export SCIPY_USE_PYTHRAN=0 && ", + 'preinstallopts': "export SCIPY_USE_PYTHRAN=0 && ", + 'checksums': ['9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33'], + }), + ('mpi4py', '3.1.3', { + 'checksums': ['f1e9fae1079f43eafdd9f817cdb3fd30d709edc093b5d5dada57a461b2db3008'], + }), + ('numexpr', '2.8.1', { + 'checksums': ['cd779aa44dd986c4ef10163519239602b027be06a527946656207acf1f58113b'], + }), + ('Bottleneck', '1.3.4', { + 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], + }), + ('pandas', '1.4.2', { + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'patches': ['deap-1.3.1_no_2to3.patch'], + 'checksums': [ + '11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f', # deap-1.3.1.tar.gz + '3fa9fac74b0750ac6667371ce0634c797d62d270c76eee9c258b55f4a5a5e689', # deap-1.3.1_no_2to3.patch + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb new file mode 100644 index 00000000000..c7dd812dcad --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb @@ -0,0 +1,88 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2022.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.46.7'), + ('UnZip', '6.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('pybind11', '2.9.2'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.22.3', { + 'patches': [ + 'numpy-1.18.2-mkl.patch', + 'numpy-1.20.3_disable_fortran_callback_test.patch', + 'numpy-1.22.3_disable-broken-override-test.patch', + ], + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': [ + 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18', # numpy-1.22.3.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + # numpy-1.20.3_disable_fortran_callback_test.patch + '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + # numpy-1.22.3_disable-broken-override-test.patch + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.11.0', { + 'checksums': ['0b2cba712e09f7630879dff69f268460bfe34a6d6000451b47d598558a92a875'], + }), + ('scipy', '1.8.1', { + # compilation with Pythran enabled fails when using Intel compilers, + # see https://github.com/scipy/scipy/issues/14935 + 'prebuildopts': "export SCIPY_USE_PYTHRAN=0 && ", + 'preinstallopts': "export SCIPY_USE_PYTHRAN=0 && ", + 'checksums': ['9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33'], + }), + ('mpi4py', '3.1.3', { + 'checksums': ['f1e9fae1079f43eafdd9f817cdb3fd30d709edc093b5d5dada57a461b2db3008'], + }), + ('numexpr', '2.8.1', { + 'checksums': ['cd779aa44dd986c4ef10163519239602b027be06a527946656207acf1f58113b'], + }), + ('Bottleneck', '1.3.4', { + 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], + }), + ('pandas', '1.4.2', { + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'patches': ['deap-1.3.1_no_2to3.patch'], + 'checksums': [ + '11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f', # deap-1.3.1.tar.gz + '3fa9fac74b0750ac6667371ce0634c797d62d270c76eee9c258b55f4a5a5e689', # deap-1.3.1_no_2to3.patch + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From a56b1b8daacab797dc5e3f2f8baecd9bc140070c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 24 Jun 2022 08:14:16 +0100 Subject: [PATCH 4091/9987] delete items that have not been in an eb release --- .../g/GCTA/GCTA-1.94.0beta-gfbf-2022.05.eb | 68 ------------------- .../g/GDAL/GDAL-3.5.0-foss-2022.05.eb | 65 ------------------ easybuild/easyconfigs/g/gfbf/gfbf-2022.05.eb | 20 ------ .../h/HDF5/HDF5-1.13.1-gompi-2022.05.eb | 21 ------ .../n/netCDF/netCDF-4.9.0-gompi-2022.05.eb | 48 ------------- 5 files changed, 222 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022.05.eb delete mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022.05.eb delete mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2022.05.eb delete mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022.05.eb delete mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022.05.eb b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022.05.eb deleted file mode 100644 index 8ea2cc2a1e2..00000000000 --- a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.0beta-gfbf-2022.05.eb +++ /dev/null @@ -1,68 +0,0 @@ -# Author: Jasper Grimm (UoY) -easyblock = 'CMakeMakeCp' - -name = 'GCTA' -version = '1.94.0beta' -_plink_commit = '3744540' - -homepage = 'https://yanglab.westlake.edu.cn/software/gcta/' -description = """ -GCTA (Genome-wide Complex Trait Analysis) is a software package, which was - initially developed to estimate the proportion of phenotypic variance explained - by all genome-wide SNPs for a complex trait but has been extensively extended - for many other analyses of data from genome-wide association studies (GWASs). -""" - -toolchain = {'name': 'gfbf', 'version': '2022.05'} - -sources = [ - { - 'source_urls': ['https://github.com/jianyangqt/gcta/archive'], - 'download_filename': 'v%(version)s.tar.gz', - 'filename': SOURCE_TAR_GZ, - }, - { - 'source_urls': ['https://github.com/zhilizheng/plink-ng/archive'], - 'download_filename': '%s.tar.gz' % _plink_commit, - 'filename': 'plink-ng-%s.tar.gz' % _plink_commit, - 'extract_cmd': "tar xzvf %%s --strip-components 1 -C gcta-%s/submods/plink-ng" % version, - }, -] -patches = [ - 'GCTA-1.94.0beta_allow-BLAS-selection.patch', - 'GCTA-1.94.0beta_lapack-compatibility.patch', -] -checksums = [ - '9220a6c40f31e3b1ce3d25f7eee3d8c62403bee8d6ed624bd8b61891badcb14f', # GCTA-1.94.0beta.tar.gz - 'a7c70c237d49d64fc1668ced373036c09b41d7c61d0b8b24b47e2fb76474455d', # plink-ng-3744540.tar.gz - '320a5d82d12cf453f1396b228723ac18dc98e32bc459394dd4d712fc16b24747', # GCTA-1.94.0beta_allow-BLAS-selection.patch - '643282a2e2c02fc683431b673a4623a498129870431481d33d33e19a509026ce', # GCTA-1.94.0beta_lapack-compatibility.patch -] - -builddependencies = [ - ('CMake', '3.23.1'), - # Eigen and SpectrA are header-only C++ libraries - ('Eigen', '3.4.0'), - ('SpectrA', '1.0.1'), -] - -dependencies = [ - ('Boost', '1.79.0'), - ('SQLite', '3.38.3'), - ('zstd', '1.5.2'), - ('GSL', '2.7'), -] - -preconfigopts = 'EIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include SPECTRA_LIB=$EBROOTSPECTRA/include' -preconfigopts += ' BOOST_LIB=$EBROOTBOOST/include ' - -files_to_copy = [(['gcta64'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/gcta64'], - 'dirs': [], -} - -sanity_check_commands = ["gcta64 | grep -e 'Analysis started'"] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022.05.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022.05.eb deleted file mode 100644 index b5aeef98264..00000000000 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022.05.eb +++ /dev/null @@ -1,65 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDAL' -version = '3.5.0' - -homepage = 'https://www.gdal.org' -description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style - Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model - to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for - data translation and processing.""" - -toolchain = {'name': 'foss', 'version': '2022.05'} -toolchainopts = {'usempi': True} - -source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] -sources = [SOURCELOWER_TAR_XZ] -patches = ['GDAL-3.0.0_fix-python-CC-CXX.patch'] -checksums = [ - 'd49121e5348a51659807be4fb866aa840f8dbec4d1acba6d17fdefa72125bfc9', # gdal-3.5.0.tar.xz - '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381', # GDAL-3.0.0_fix-python-CC-CXX.patch -] - -builddependencies = [ - ('pkgconf', '1.8.0'), -] - -dependencies = [ - ('Python', '3.10.4'), - ('netCDF', '4.9.0'), - ('expat', '2.4.8'), - ('GEOS', '3.10.3'), - ('SQLite', '3.38.3'), - ('libxml2', '2.9.13'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.1.3'), - ('JasPer', '2.0.33'), - ('LibTIFF', '4.3.0'), - ('zlib', '1.2.12'), - ('cURL', '7.83.0'), - ('PCRE', '8.45'), - ('PROJ', '9.0.0'), - ('libgeotiff', '1.7.1'), - ('SciPy-bundle', '2022.05'), - ('HDF5', '1.13.1'), - ('HDF', '4.2.15'), -] - -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " -configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' -configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' -configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' -configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' -configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -sanity_check_paths = { - 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] -} - -sanity_check_commands = ["python -c 'import osgeo.gdal'"] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2022.05.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2022.05.eb deleted file mode 100644 index 9c6c99c2e49..00000000000 --- a/easybuild/easyconfigs/g/gfbf/gfbf-2022.05.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'Toolchain' - -name = 'gfbf' -version = '2022.05' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, including - FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" - -toolchain = SYSTEM - -local_gccver = '11.3.0' - -dependencies = [ - ('GCC', local_gccver), - ('FlexiBLAS', '3.2.0', '', ('GCC', local_gccver)), - ('FFTW', '3.3.10', '', ('GCC', local_gccver)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022.05.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022.05.eb deleted file mode 100644 index f83dfdef664..00000000000 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-gompi-2022.05.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'HDF5' -version = '1.13.1' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'gompi', 'version': '2022.05'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] - -dependencies = [ - ('zlib', '1.2.12'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb deleted file mode 100644 index a10128b18c4..00000000000 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022.05.eb +++ /dev/null @@ -1,48 +0,0 @@ -name = 'netCDF' -version = '4.9.0' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompi', 'version': '2022.05'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = [ - 'netCDF-%(version)s_fix-lib-name.patch', - 'netCDF-%(version)s_fix-linking-errors.patch', -] -checksums = [ - '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz - 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch - '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch -] - -builddependencies = [ - ('Autotools', '20220317'), - ('CMake', '3.23.1'), - ('Doxygen', '1.9.4'), -] - -dependencies = [ - ('HDF5', '1.13.1'), - ('cURL', '7.83.0'), - ('Szip', '2.1.1'), - ('zstd', '1.5.2'), -] - -# make sure both static and shared libs are built -configopts = [ - "-DBUILD_SHARED_LIBS=OFF", - "-DBUILD_SHARED_LIBS=ON", -] - -# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests -pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " - -runtest = 'test' - -moduleclass = 'data' From 8f4417674867a42ad76ed657d1a9fc3b46a17f94 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 24 Jun 2022 08:15:53 +0100 Subject: [PATCH 4092/9987] missed the gfbf toolchain ec --- easybuild/easyconfigs/g/gfbf/gfbf-2022a.eb | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2022a.eb diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2022a.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2022a.eb new file mode 100644 index 00000000000..b85e69731d7 --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2022a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2022a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '11.3.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.2.0', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' From 2f87aa12aea82fcba735c428a8d71dbb9eff2bcb Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 24 Jun 2022 09:17:42 +0200 Subject: [PATCH 4093/9987] take over @akesandgren suggestions --- .../o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb | 27 ++++++++++--------- 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb index 4455c12e406..edf177d5994 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb @@ -1,6 +1,8 @@ ## # Author: Robert Mijakovic ## +# Modified by: Ben Langenberg +## name = 'OpenFOAM' version = 'v2112' @@ -11,12 +13,24 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'cstd': 'c++11'} +toolchainopts = {'cstd': 'c++11', 'vectorize': False} source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2012-cleanup.patch', 1), + 'OpenFOAM-v1906-wmake-ompi.patch', +] checksums = [ '3e838731e79db1c288acc27aad8cc8a43d9dac1f24e5773e3b9fa91419a8c3f7', # OpenFOAM-v2112.tgz + 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), ] dependencies = [ @@ -30,15 +44,4 @@ dependencies = [ ('gnuplot', '5.4.1'), ] -builddependencies = [ - ('Bison', '3.7.1'), - ('CMake', '3.18.4'), - ('flex', '2.6.4'), -] - -sanity_check_paths = { - 'files': ['%(installdir)s/%(name)s-%(version)s/platforms/linux64GccDPInt32Opt/lib/dummy/libscotchDecomp.so'], - 'dirs': ['%(installdir)s/%(name)s-%(version)s/platforms/linux64GccDPInt32Opt/lib/dummy'], -} - moduleclass = 'cae' From b0ea8b1df5513441b5e0d79c24429fbc2a1031e2 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 24 Jun 2022 08:33:07 +0100 Subject: [PATCH 4094/9987] forgot gompi --- easybuild/easyconfigs/g/gompi/gompi-2022a.eb | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2022a.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2022a.eb b/easybuild/easyconfigs/g/gompi/gompi-2022a.eb new file mode 100644 index 00000000000..f2ad0f8735d --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2022a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2022a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '11.3.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' From 4cd899f15e9deb8edb5541fc5f45b812b5e00369 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 24 Jun 2022 08:50:08 +0100 Subject: [PATCH 4095/9987] remove FSON foss version --- .../f/FSON/FSON-1.0.5-foss-2020b.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FSON/FSON-1.0.5-foss-2020b.eb diff --git a/easybuild/easyconfigs/f/FSON/FSON-1.0.5-foss-2020b.eb b/easybuild/easyconfigs/f/FSON/FSON-1.0.5-foss-2020b.eb deleted file mode 100644 index 30b8f20b219..00000000000 --- a/easybuild/easyconfigs/f/FSON/FSON-1.0.5-foss-2020b.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = "CMakeMake" - -name = 'FSON' -version = '1.0.5' - -homepage = "https://github.com/josephalevin/fson" -description = "Fortran 95 JSON Parser" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ['https://github.com/josephalevin/fson/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['d52f928d59b090eb47ed2bc880ee58d46cd8dd7e554e3df03c7c517d7a6b6012'] - -builddependencies = [ - ('binutils', '2.35'), - ('CMake', '3.18.4'), -] - -configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] - -sanity_check_paths = { - 'files': ['lib64/libFSON.%s' % SHLIB_EXT], - 'dirs': ['include/fson'], -} - -moduleclass = "lib" From 891504d787ece5b15caf2824a5ee850bbdde0da8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 24 Jun 2022 10:35:48 +0200 Subject: [PATCH 4096/9987] Add a link where to find download files once logged in --- .../easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb index d7523baf6be..adadbfe31a0 100644 --- a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb +++ b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb @@ -31,6 +31,8 @@ docurls = [ toolchain = SYSTEM # Download and license at https://chemaxon.com/products/marvin +# Once logged in download files can be found here: +# https://chemaxon.com/products/marvin/download#download sources = ['marvin_linux_%(version)s.rpm'] checksums = ['3102f30479a365758fd14ca5efcdacfe0624db80a35b146ba9a5d07e948bd8dc'] From 539571a82b51458603a229fcf27cb1d8dadeddf1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 11:09:20 +0200 Subject: [PATCH 4097/9987] {math}[foss/2021b] Clp v1.17.7, CoinUtils v2.11.6, Osi v0.108.7, MUMPS v5.4.1 --- .../c/Clp/Clp-1.17.7-foss-2021b.eb | 61 +++++++++++++++++++ .../CoinUtils/CoinUtils-2.11.6-GCC-11.2.0.eb | 36 +++++++++++ .../m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb | 35 +++++++++++ .../o/Osi/Osi-0.108.7-GCC-11.2.0.eb | 49 +++++++++++++++ 4 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clp/Clp-1.17.7-foss-2021b.eb create mode 100644 easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.6-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb create mode 100644 easybuild/easyconfigs/o/Osi/Osi-0.108.7-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.7-foss-2021b.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.7-foss-2021b.eb new file mode 100644 index 00000000000..ccd520198c3 --- /dev/null +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.7-foss-2021b.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'Clp' +version = '1.17.7' + +homepage = "https://github.com/coin-or/Clp" +description = """Clp (Coin-or linear programming) is an open-source linear programming solver. +It is primarily meant to be used as a callable library, but a basic, +stand-alone executable version is also available.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/Clp/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c4c2c0e014220ce8b6294f3be0f3a595a37bef58a14bf9bac406016e9e73b0f5'] + +builddependencies = [ + ('Autotools', '20210726'), + ('Doxygen', '1.9.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.4.1', '-metis'), + ('CoinUtils', '2.11.6'), + ('Osi', '0.108.7'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# Use BLAS/LAPACK from OpenBLAS +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' + +# Use METIS AND MUMPS from EB +# --with-metis-lib is ignored +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh ' +configopts += '-lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr -lscalapack" ' + +# Disable GLPK because Clp requires headers from its sources +configopts += '--without-glpk ' + +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + +# Use Osi from EB +configopts += '--with-osi-lib="-lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Clp', 'ClpSolver', 'OsiClp']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.6-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.6-GCC-11.2.0.eb new file mode 100644 index 00000000000..c7fb9762bb1 --- /dev/null +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.6-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CoinUtils' +version = '2.11.6' + +homepage = "https://github.com/coin-or/CoinUtils" +description = """CoinUtils (Coin-OR Utilities) is an open-source collection of classes and +functions that are generally useful to more than one COIN-OR project.""" + +source_urls = ['https://github.com/coin-or/CoinUtils/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6ea31d5214f7eb27fa3ffb2bdad7ec96499dd2aaaeb4a7d0abd90ef852fc79ca'] + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +builddependencies = [ + ('Autotools', '20210726'), + ('Doxygen', '1.9.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/libCoinUtils.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb new file mode 100644 index 00000000000..3e031482e5c --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb @@ -0,0 +1,35 @@ +name = 'MUMPS' +version = '5.4.1' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-5.4.0_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-5.4.0_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + '93034a1a9fe0876307136dcde7e98e9086e199de76f1c47da822e7d4de987fa8', # MUMPS_5.4.1.tar.gz + '4c0558690998c12ca959c03856054a75e22f519583a65bd550393c1f81a0b170', # MUMPS-5.4.0_shared-pord.patch + 'd51c2df0de7d7b88d864ceba2d0eea46c755c24c7124003481aced106901109d', # MUMPS-5.4.0_shared-mumps.patch +] + +dependencies = [ + ('SCOTCH', '6.1.2'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.7-GCC-11.2.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.7-GCC-11.2.0.eb new file mode 100644 index 00000000000..3b1c6539336 --- /dev/null +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.7-GCC-11.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'Osi' +version = '0.108.7' + +homepage = "https://github.com/coin-or/Osi" +description = """Osi (Open Solver Interface) provides an abstract base class to a generic linear +programming (LP) solver, along with derived classes for specific solvers. Many +applications may be able to use the Osi to insulate themselves from a specific +LP solver. That is, programs written to the OSI standard may be linked to any +solver with an OSI interface and should produce correct results. The OSI has +been significantly extended compared to its first incarnation. Currently, the +OSI supports linear programming solvers and has rudimentary support for integer +programming.""" + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/coin-or/Osi/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f1bc53a498585f508d3f8d74792440a30a83c8bc934d0c8ecf8cd8bc0e486228'] + +builddependencies = [ + ('Autotools', '20210726'), + ('Doxygen', '1.9.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CoinUtils', '2.11.6'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# Disable GLPK because Osi requires GLPK<=4.48 +configopts = '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + +sanity_check_paths = { + 'files': ['lib/libOsi.%s' % SHLIB_EXT, 'lib/libOsiCommonTests.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" From fd4b8c78a2dbc42649ab7d1f14e4bbdcc9e4dd89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 11:14:22 +0200 Subject: [PATCH 4098/9987] adding easyconfigs: Boost.MPI-1.77.0-gompi-2021b.eb --- .../Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb new file mode 100644 index 00000000000..f0d6e24166d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.77.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['5347464af5b14ac54bb945dc68f1dd7c56f0dad7262816b956138fc53bcc0131'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('ICU', '69.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' From 00ec2cabadf2e7dc79b6d659c0e3a19902837fc5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 11:15:12 +0200 Subject: [PATCH 4099/9987] adding easyconfigs: fmt-7.1.1-GCCcore-11.2.0.eb --- .../f/fmt/fmt-7.1.1-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-7.1.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-7.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-7.1.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6d690690a62 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-7.1.1-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '7.1.1' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['57f8a384285f7e2d8b8da43eb269bb409bad20c440a2153e366be7c799a41cb0'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37') +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' From 4264534fa65657d9a60c7fd9f183ea328194fed6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 11:20:38 +0200 Subject: [PATCH 4100/9987] adding easyconfigs: SISSO++-1.1-foss-2021b.eb --- .../s/SISSO++/SISSO++-1.1-foss-2021b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb new file mode 100644 index 00000000000..53ebb6d4cad --- /dev/null +++ b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'SISSO++' +version = '1.1' + +homepage = 'https://gitlab.com/sissopp_developers/sissopp' +description = "C++ implementation of SISSO with built in Python bindings for an efficient python interface" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/sissopp_developers/sissopp/-/archive/v%(version)s/'] +sources = [{ + 'git_config': { + 'url': 'https://gitlab.com/sissopp_developers/', + 'repo_name': 'sissopp', + 'recursive': True, + 'commit': 'v%(version)s', + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['SISSO++-1.1_cmake-mpi-fix.patch'] +checksums = [ + None, # SISSO++-1.1.tar.gz + '614f13ef34dc1d1b2fe0e9868cdcf576a0dacb336759f5295115131d15e9c35a', +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Boost.Python', '1.77.0'), + ('Boost.MPI', '1.77.0'), + ('Clp', '1.17.7'), + ('NLopt', '2.7.0'), + ('pybind11', '2.7.1'), + ('fmt', '7.1.1'), + ('googletest', '1.11.0'), +] + +preconfigopts = "export BOOST_ROOT=$EBROOTBOOSTMPI && " +configopts = "-DEXTERNAL_BOOST=ON -DBUILD_PYTHON=ON -DPYTHON_INSTDIR=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/sisso++', 'lib/libsisso.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import sissopp'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'math' From 72c10836b64162fb32399acb6c42ee32c4ae7c28 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 12:24:04 +0200 Subject: [PATCH 4101/9987] add patch file for SISSO++ --- .../s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch diff --git a/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch new file mode 100644 index 00000000000..d91c3e3fe6d --- /dev/null +++ b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch @@ -0,0 +1,19 @@ +workaround for $MPI_CXX_LIBRARIES being empty and CMake tripping over that with: +CMake Error at CMakeLists.txt:252 (list): + list GET given empty list +author: Kenneth Hoste (HPC-UGent) +--- sissopp/CMakeLists.txt.orig 2022-06-23 17:17:12.083398990 +0200 ++++ sissopp/CMakeLists.txt 2022-06-23 17:17:26.326311818 +0200 +@@ -248,9 +248,9 @@ + # Check MPI + find_package(MPI REQUIRED) + include_directories(${MPI_CXX_INCLUDE_DIRS}) +-set(MPI_LIBRARIES, ${MPI_CXX_LIBRARIES}) +-list(GET MPI_CXX_LIBRARIES 0 MPI_LIBRARY) +-get_filename_component(MPI_DIR ${MPI_LIBRARY} DIRECTORY) ++#set(MPI_LIBRARIES, ${MPI_CXX_LIBRARIES}) ++#list(GET MPI_CXX_LIBRARIES 0 MPI_LIBRARY) ++#get_filename_component(MPI_DIR ${MPI_LIBRARY} DIRECTORY) + + # Build libnlopt + if(BUILD_PARAMS) From ca232a70979732f178d8d43a4d00dbcec16238fc Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 24 Jun 2022 11:28:42 +0100 Subject: [PATCH 4102/9987] Delete MUMPS-5.4.1_shared-mumps.patch --- .../m/MUMPS/MUMPS-5.4.1_shared-mumps.patch | 62 ------------------- 1 file changed, 62 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-mumps.patch diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-mumps.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-mumps.patch deleted file mode 100644 index edadcc4dc15..00000000000 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-mumps.patch +++ /dev/null @@ -1,62 +0,0 @@ -Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared.patch -Author: micketeer@gmail.com - -diff -ru MUMPS_5.4.0.orig/src/Makefile MUMPS_5.4.0/src/Makefile ---- MUMPS_5.4.0.orig/src/Makefile 2021-08-11 16:22:27.340180216 +0200 -+++ MUMPS_5.4.0/src/Makefile 2021-08-11 16:40:23.930257697 +0200 -@@ -15,18 +15,23 @@ - - libcommon: $(incdir)/mumps_int_def.h - $(MAKE) $(libdir)/libmumps_common$(PLAT)$(LIBEXT) -+ $(MAKE) $(libdir)/libmumps_common$(PLAT).so - - s: $(incdir)/mumps_int_def.h libcommon - $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT)$(LIBEXT) -+ $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT).so - - d: $(incdir)/mumps_int_def.h libcommon - $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT)$(LIBEXT) -+ $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT).so - - c: $(incdir)/mumps_int_def.h libcommon - $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT)$(LIBEXT) -+ $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT).so - - z: $(incdir)/mumps_int_def.h libcommon - $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT)$(LIBEXT) -+ $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT).so - - include $(topdir)/Makefile.inc - -@@ -200,6 +205,14 @@ - $(AR)$@ $? - $(RANLIB) $@ - -+$(libdir)/libmumps_common$(PLAT).so: $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) -+ $(FC) -shared $^ -Wl,-soname,libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) $(LORDERINGS) -lpthread $(MUMPS_LIBF77) $(MPIFLIB) $(MPICLIB) $(METISLIB) -o $(libdir)/libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs -+ ln -fs libmumps_common$(PLAT)-$(SONAME_VERSION).so $@ -+ -+$(libdir)/lib$(ARITH)mumps$(PLAT).so: $(OBJS_MOD) $(OBJS_OTHER) -+ $(FC) -shared $^ -Wl,-soname,lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) -lmumps_common$(PLAT) -lpthread $(MUMPS_LIBF77) $(LORDERINGS) $(MPIFLIB) $(METISLIB) $(SCALAP) -o $(libdir)/lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs -+ ln -fs lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $@ -+ - # Dependencies between modules: - # i) arithmetic-dependent modules: - $(ARITH)ana_aux.o: $(ARITH)mumps_struc_def.o \ -@@ -411,13 +424,13 @@ - - .SUFFIXES: .c .F .o - .F.o: -- $(FC) $(OPTF) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -c $*.F $(OUTF)$*.o -+ $(FC) $(OPTF) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -fPIC -c $*.F $(OUTF)$*.o - .c.o: -- $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -c $*.c $(OUTC)$*.o -+ $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -fPIC -c $*.c $(OUTC)$*.o - - $(ARITH)mumps_c.o: mumps_c.c - $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) -DMUMPS_ARITH=MUMPS_ARITH_$(ARITH) \ -- $(IORDERINGSC) $(ORDERINGSC) -c mumps_c.c $(OUTC)$@ -+ $(IORDERINGSC) $(ORDERINGSC) -fPIC -c mumps_c.c $(OUTC)$@ - - clean: - $(RM) *.o *.mod $(incdir)/mumps_int_def.h build_mumps_int_def From a5c582274f5f695aeba065c4eb746e4276773b68 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 24 Jun 2022 11:28:52 +0100 Subject: [PATCH 4103/9987] Delete MUMPS-5.4.1_shared-pord.patch --- .../m/MUMPS/MUMPS-5.4.1_shared-pord.patch | 51 ------------------- 1 file changed, 51 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-pord.patch diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-pord.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-pord.patch deleted file mode 100644 index 704a8f66e07..00000000000 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1_shared-pord.patch +++ /dev/null @@ -1,51 +0,0 @@ -Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared-pord.patch -Author: micketeer@gmail.com - -diff -ru MUMPS_5.4.0.orig/Makefile MUMPS_5.4.0/Makefile ---- MUMPS_5.4.0.orig/Makefile 2021-08-11 21:41:30.209055262 +0200 -+++ MUMPS_5.4.0/Makefile 2021-08-11 21:41:40.633028157 +0200 -@@ -42,7 +42,7 @@ - - include Makefile.inc - --prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) -+prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT).so - - # dummy MPI library (sequential version) - -@@ -59,6 +59,12 @@ - cp $(LPORDDIR)/libpord$(LIBEXT) $@; \ - fi; - -+$(libdir)/libpord$(PLAT).so: -+ if [ "$(LPORDDIR)" != "" ] ; then \ -+ cd $(LPORDDIR); make CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" ARFUNCT= RANLIB="$(RANLIB)" libpord$(PLAT).so; fi; -+ if [ "$(LPORDDIR)" != "" ] ; then \ -+ cp -a $(LPORDDIR)/libpord*.so lib/; fi; -+ - clean: - (cd src; $(MAKE) clean) - (cd examples; $(MAKE) clean) -diff -ru MUMPS_5.4.0.orig/PORD/lib/Makefile MUMPS_5.4.0/PORD/lib/Makefile ---- MUMPS_5.4.0.orig/PORD/lib/Makefile 2021-08-11 16:22:27.481179848 +0200 -+++ MUMPS_5.4.0/PORD/lib/Makefile 2021-08-11 16:59:17.511334981 +0200 -@@ -9,7 +9,7 @@ - - INCLUDES = -I../include - --COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS) -+COPTIONS = $(INCLUDES) $(CFLAGS) $(OPTFLAGS) -fPIC - - OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \ - multisector.o gelim.o bucket.o tree.o \ -@@ -28,6 +28,10 @@ - $(AR)$@ $(OBJS) - $(RANLIB) $@ - -+libpord$(PLAT).so: $(OBJS) -+ $(CC) -shared $(OBJS) -Wl,-soname,libpord$(PLAT)-$(SONAME_VERSION).so -o libpord$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs -+ ln -fs libpord$(PLAT)-$(SONAME_VERSION).so $@ -+ - clean: - rm -f *.o - From 762e7f67cae60ed4d08bad02a721bf7f61bcf6a4 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 24 Jun 2022 13:49:54 +0200 Subject: [PATCH 4104/9987] remove python version suffix --- .../t/Trinity/Trinity-2.9.1-foss-2020b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb new file mode 100644 index 00000000000..25ad6257c8a --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb @@ -0,0 +1,49 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.9.1' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +checksums = ['98d98bc21cd5dd32b408ed52586d01a15873b49b96de3264d42616bdcfc9d455'] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Java', '11', '', True), + ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Bowtie2', '2.4.2'), + ('HTSlib', '1.12'), + ('Jellyfish', '2.3.0'), + ('kallisto', '0.46.2'), + ('ncurses', '6.2'), + ('Salmon', '1.4.0'), + ('SAMtools', '1.11'), + ('zlib', '1.2.11'), +] + +withsampledata = True + +moduleclass = 'bio' From 8b796db089bc68c281c228674d0f535844959cd0 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 24 Jun 2022 14:08:16 +0200 Subject: [PATCH 4105/9987] use version without suffix --- .../Trinity-2.9.1-foss-2020b-Python-3.8.6.eb | 50 ------------------- 1 file changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb deleted file mode 100644 index 0375526f35f..00000000000 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb +++ /dev/null @@ -1,50 +0,0 @@ -## -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: Custom -# -# Notes:: -## - -name = 'Trinity' -version = '2.9.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://trinityrnaseq.github.io' -description = """Trinity represents a novel method for the efficient and robust de novo reconstruction - of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, - Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" - -toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'optarch': True} - -source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v%(version)s'] -sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] -checksums = ['98d98bc21cd5dd32b408ed52586d01a15873b49b96de3264d42616bdcfc9d455'] - -builddependencies = [ - ('Autotools', '20200321'), - ('CMake', '3.18.4'), -] - -dependencies = [ - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), - ('Perl', '5.32.0'), - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('Bowtie2', '2.4.2'), - ('HTSlib', '1.12'), - ('Jellyfish', '2.3.0'), - ('kallisto', '0.46.2'), - ('ncurses', '6.2'), - ('Salmon', '1.4.0'), - ('SAMtools', '1.11'), - ('zlib', '1.2.11'), -] - -withsampledata = True - -moduleclass = 'bio' From 8d47e77a817b86c084028c1bc0503bce6d8f43dc Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 24 Jun 2022 14:58:51 +0200 Subject: [PATCH 4106/9987] stay with HTSlib 1.11 for foss/2020b --- easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb index 25ad6257c8a..f2e75d38711 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb @@ -35,7 +35,7 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('Bowtie2', '2.4.2'), - ('HTSlib', '1.12'), + ('HTSlib', '1.11'), ('Jellyfish', '2.3.0'), ('kallisto', '0.46.2'), ('ncurses', '6.2'), From cea7816aedfaf75dda95801fd47d547d994a9a82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 16:01:56 +0200 Subject: [PATCH 4107/9987] {lib}[GCCcore/11.3.0] Qt5 v5.15.5 (+ deps) --- .../double-conversion-3.2.0-GCCcore-11.3.0.eb | 38 ++++++++++ .../graphite2-1.3.14-GCCcore-11.3.0.eb | 27 +++++++ .../n/NSPR/NSPR-4.34-GCCcore-11.3.0.eb | 30 ++++++++ .../n/NSS/NSS-3.79-GCCcore-11.3.0.eb | 58 ++++++++++++++ .../Python-2.7.18-GCCcore-11.3.0-bare.eb | 32 ++++++++ .../q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb | 76 +++++++++++++++++++ ...5-5.15.5_fix-qtwebegine-HarfBuzz-3.x.patch | 35 +++++++++ .../r/re2c/re2c-2.2-GCCcore-11.3.0.eb | 27 +++++++ 8 files changed, 323 insertions(+) create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.34-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.5_fix-qtwebegine-HarfBuzz-3.x.patch create mode 100644 easybuild/easyconfigs/r/re2c/re2c-2.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..177cc580c99 --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.2.0' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3dbcdf186ad092a8b71228a5962009b5c96abde9a315257a3452eb988414ea3b'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +separate_build_dir = True + +build_type = 'Release' + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a', + '-DBUILD_SHARED_LIBS=ON' +] + +sanity_check_paths = { + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4b71d740405 --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.34-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.34-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f284259779b --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.34-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.34' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftp.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['beef011cd15d8f40794984d17014366513cec5719bf1a78f5e8a3e3a1cebf99c'] + +builddependencies = [('binutils', '2.38')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +sanity_check_commands = ["nspr-config --version"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3cea93f9ab6 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.79' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', + 'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', +] +checksums = [ + 'ebdf2d6a96613b6fe70ad579e9f983e0e94e0110171cfb2999db633d3394a514', # nss-3.79.tar.gz + '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + # NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch + '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b', +] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('NSPR', '4.34'), + ('zlib', '1.2.12'), +] + +# building in parallel fails +parallel = 1 + +# fix for not being able to find header files +buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], +} + +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb new file mode 100644 index 00000000000..30621d2d5a4 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb @@ -0,0 +1,32 @@ +name = 'Python' +version = '2.7.18' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('binutils', '2.38'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), + ('SQLite', '3.38.3'), + ('OpenSSL', '1.1', '', True), +] + +install_pip = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c12b05d90b1 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb @@ -0,0 +1,76 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.15.5' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] +patches = [ + 'Qt5-5.13.1_fix-avx2.patch', + 'Qt5-5.13.1_fix-qmake-libdir.patch', + 'Qt5-5.14.1_fix-OF-Gentoo.patch', + 'Qt5-5.15.5_fix-qtwebegine-HarfBuzz-3.x.patch', +] +checksums = [ + '5a97827bdf9fd515f43bc7651defaf64fecb7a55e051c79b8f80510d0e990f06', # qt-everywhere-opensource-src-5.15.5.tar.xz + '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch + '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch + '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch + '599cc94535dc276a5d97e002c81907c74ead9dc8d55f35567017fb7a491aaf01', # Qt5-5.15.5_fix-qtwebegine-HarfBuzz-3.x.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + # deps for QtWebEngine + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.10.2'), + # Qt5WebEngine has build dependency on Python 2 + ('Python', '2.7.18', '-bare'), + ('re2c', '2.2'), +] + +dependencies = [ + ('double-conversion', '3.2.0'), + ('GLib', '2.72.1'), + ('PCRE2', '10.40'), + ('libpng', '1.6.37'), + ('HarfBuzz', '4.2.1'), + ('graphite2', '1.3.14'), + # deps for QtWebEngine + ('X11', '20220504'), + ('fontconfig', '2.14.0'), + ('DBus', '1.14.0'), + ('libevent', '2.1.12'), + ('libGLU', '9.0.2'), + ('libjpeg-turbo', '2.1.3'), + ('NSS', '3.79'), + ('snappy', '1.1.9'), + ('JasPer', '2.0.33'), + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', True), + ('ICU', '71.1'), + ('nodejs', '16.15.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +# qtwayland fails to build on (some) Centos 7 systems +configopts = '-skip qtgamepad -skip qtwayland' + +# make sure QtWebEngine component is being built & installed +check_qtwebengine = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5_fix-qtwebegine-HarfBuzz-3.x.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5_fix-qtwebegine-HarfBuzz-3.x.patch new file mode 100644 index 00000000000..1fda2959232 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5_fix-qtwebegine-HarfBuzz-3.x.patch @@ -0,0 +1,35 @@ +fix compatibility with HarfBuzz v3.x or newer: + ../../3rdparty/chromium/components/paint_preview/common/subset_font.cc:74:3: error: hb_subset_input_set_retain_gids was not declared in this scope + ../../3rdparty/chromium/components/paint_preview/common/subset_font.cc:76:35: error: hb_subset was not declared in this scope +see also https://bugs.gentoo.org/817758 +--- qt-everywhere-src-5.15.5/qtwebengine/src/3rdparty/chromium/components/paint_preview/common/subset_font.cc ++++ qt-everywhere-src-5.15.5/qtwebengine/src/3rdparty/chromium/components/paint_preview/common/subset_font.cc +@@ -71,9 +71,9 @@ sk_sp SubsetFont(SkTypeface* typeface, const GlyphUsage& usage) { + hb_set_t* glyphs = + hb_subset_input_glyph_set(input.get()); // Owned by |input|. + usage.ForEach(base::BindRepeating(&AddGlyphs, base::Unretained(glyphs))); +- hb_subset_input_set_retain_gids(input.get(), true); ++ hb_subset_input_set_flags(input.get(), HB_SUBSET_FLAGS_RETAIN_GIDS); + +- HbScoped subset_face(hb_subset(face.get(), input.get())); ++ HbScoped subset_face(hb_subset_or_fail(face.get(), input.get())); + HbScoped subset_blob(hb_face_reference_blob(subset_face.get())); + if (!subset_blob) + return nullptr; +--- qt-everywhere-src-5.15.5/qtwebengine/src/3rdparty/chromium/third_party/skia/src/pdf/SkPDFSubsetFont.cpp ++++ qt-everywhere-src-5.15.5/qtwebengine/src/3rdparty/chromium/third_party/skia/src/pdf/SkPDFSubsetFont.cpp +@@ -71,11 +71,10 @@ static sk_sp subset_harfbuzz(sk_sp fontData, + hb_set_t* glyphs = hb_subset_input_glyph_set(input.get()); + glyphUsage.getSetValues([&glyphs](unsigned gid) { hb_set_add(glyphs, gid);}); + +- hb_subset_input_set_retain_gids(input.get(), true); + // TODO: When possible, check if a font is 'tricky' with FT_IS_TRICKY. + // If it isn't known if a font is 'tricky', retain the hints. +- hb_subset_input_set_drop_hints(input.get(), false); +- HBFace subset(hb_subset(face.get(), input.get())); ++ hb_subset_input_set_flags(input.get(), HB_SUBSET_FLAGS_RETAIN_GIDS | HB_SUBSET_FLAGS_NO_HINTING); ++ HBFace subset(hb_subset_or_fail(face.get(), input.get())); + HBBlob result(hb_face_reference_blob(subset.get())); + return to_data(std::move(result)); + } + diff --git a/easybuild/easyconfigs/r/re2c/re2c-2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/re2c/re2c-2.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..30545460282 --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-2.2-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '2.2' + +homepage = 'https://re2c.org/' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['0fc45e4130a8a555d68e230d1795de0216dfe99096b61b28e67c86dfd7d86bda'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/re2c'], + 'dirs': [], +} + +sanity_check_commands = ["re2c --help"] + +moduleclass = 'tools' From ef9d912d515b36dbc9e06b48c62d198329c590ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 20:17:04 +0200 Subject: [PATCH 4108/9987] {devel}[GCCcore/10.3.0] libxml++ v2.42.1, mm-common v1.0.4, GLibmm v2.66.4, mm-common v1.0.4 --- .../g/GLibmm/GLibmm-2.66.4-GCCcore-10.3.0.eb | 34 ++++++++++++++++++ .../libsigc++-2.10.8-GCCcore-10.3.0.eb | 29 +++++++++++++++ .../l/libxml++/libxml++-2.42.1-GCC-10.3.0.eb | 35 +++++++++++++++++++ .../mm-common-1.0.4-GCCcore-10.3.0.eb | 33 +++++++++++++++++ 4 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLibmm/GLibmm-2.66.4-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml++/libxml++-2.42.1-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/m/mm-common/mm-common-1.0.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GLibmm/GLibmm-2.66.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.66.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c51b5487854 --- /dev/null +++ b/easybuild/easyconfigs/g/GLibmm/GLibmm-2.66.4-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MesonNinja' + +name = 'GLibmm' +version = '2.66.4' + +homepage = 'https://www.gtk.org/' +description = """C++ bindings for Glib""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnome.org/pub/gnome/sources/glibmm/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +checksums = ['199ace5682d81b15a1d565480b4a950682f2db6402c8aa5dd7217d71edff81d5'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('GLib', '2.68.2'), + ('libsigc++', '2.10.8'), +] + +sanity_check_paths = { + 'files': ['lib/libglibmm-2.4.%s' % SHLIB_EXT, 'lib/libgiomm-2.4.%s' % SHLIB_EXT, + 'include/glibmm-2.4/glibmm.h', 'include/giomm-2.4/giomm.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..0c4e7eec7a8 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libsigc++' +version = '2.10.8' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['235a40bec7346c7b82b6a8caae0456353dc06e71f14bc414bcc858af1838719a'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), + ('mm-common', '1.0.4'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libxml++/libxml++-2.42.1-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libxml++/libxml++-2.42.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..149e5c1adfd --- /dev/null +++ b/easybuild/easyconfigs/l/libxml++/libxml++-2.42.1-GCC-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MesonNinja' + +name = 'libxml++' +version = '2.42.1' + +homepage = 'http://libxmlplusplus.sourceforge.net' +description = """libxml++ is a C++ wrapper for the libxml XML parser library.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(name)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9b59059abe5545d28ceb388a55e341095f197bd219c73e6623aeb6d801e00be8'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('mm-common', '1.0.4'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('GLibmm', '2.66.4'), + ('libxml2', '2.9.10'), + ('Boost', '1.76.0'), +] + +sanity_check_paths = { + 'files': ['lib/libxml++-2.6.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/libxml++-2.6/libxml++'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..dfbe081a366 --- /dev/null +++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.4-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'mm-common' +version = '1.0.4' + +homepage = 'https://gitlab.gnome.org/GNOME/mm-common' +description = """The mm-common module provides the build infrastructure and utilities shared among the GNOME C++ binding + libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e954c09b4309a7ef93e13b69260acdc5738c907477eb381b78bb1e414ee6dbd8'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +sanity_check_paths = { + 'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'], + 'dirs': ['share/man/man1'], +} + +sanity_check_commands = ["mm-common-prepare --help"] + +moduleclass = 'devel' From 227101d7b69a88b30a1b2803ff63db70b87e1d23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 20:26:42 +0200 Subject: [PATCH 4109/9987] adding easyconfigs: Qwt-6.2.0-GCCcore-10.3.0.eb --- .../q/Qwt/Qwt-6.2.0-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ae40164274e --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.2.0' + +homepage = 'https://qwt.sourceforge.io/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Qwt-6.2.0_fix-install-prefix.patch'] +checksums = [ + '9194f6513955d0fd7300f67158175064460197abab1a92fa127a67a4b0b71530', # qwt-6.2.0.tar.bz2 + 'ac5c329c0693d565b461cdd3b36c1b96b4d09885e1e0c10929fc7a9021c03bad', # Qwt-6.2.0_fix-install-prefix.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Qt5', '5.15.2'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export QWT_PREFIX=%(installdir)s && ' +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' From 4e3f8db8f374e5a01fd5e9ebf7a3908affe36fe0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 20:32:42 +0200 Subject: [PATCH 4110/9987] add patch for Qwt 6.2.0 --- .../q/Qwt/Qwt-6.2.0_fix-install-prefix.patch | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.2.0_fix-install-prefix.patch diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0_fix-install-prefix.patch b/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0_fix-install-prefix.patch new file mode 100644 index 00000000000..18af690a9be --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0_fix-install-prefix.patch @@ -0,0 +1,18 @@ +Inject correct installation path +Author: Davide Vanzo (Vanderbilt University), ported to Qwt 6.2.0 by Kenneth Hoste (HPC-UGent) + +--- qwt-6.2.0/qwtconfig.pri.orig 2021-07-18 13:19:33.656367878 +0200 ++++ qwt-6.2.0/qwtconfig.pri 2022-06-22 15:27:47.919619835 +0200 +@@ -16,10 +16,10 @@ + # Install paths + ###################################################################### + +-QWT_INSTALL_PREFIX = $$[QT_INSTALL_PREFIX] ++QWT_INSTALL_PREFIX = $$(QWT_PREFIX) + + unix { +- QWT_INSTALL_PREFIX = /usr/local/qwt-$$QWT_VERSION ++ QWT_INSTALL_PREFIX = $$(QWT_PREFIX) + # QWT_INSTALL_PREFIX = /usr/local/qwt-$$QWT_VERSION-qt-$$QT_VERSION + } + From a601c17ce70f9f97fddc7db50560da1ee37dc223 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 20:36:54 +0200 Subject: [PATCH 4111/9987] adding easyconfigs: SISSO-3.0.2-iimpi-2021b.eb --- .../s/SISSO/SISSO-3.0.2-iimpi-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/SISSO/SISSO-3.0.2-iimpi-2021b.eb diff --git a/easybuild/easyconfigs/s/SISSO/SISSO-3.0.2-iimpi-2021b.eb b/easybuild/easyconfigs/s/SISSO/SISSO-3.0.2-iimpi-2021b.eb new file mode 100644 index 00000000000..f1f23682576 --- /dev/null +++ b/easybuild/easyconfigs/s/SISSO/SISSO-3.0.2-iimpi-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'CmdCp' + +name = 'SISSO' +version = '3.0.2' + +homepage = 'https://github.com/rouyang2017/SISSO' +description = """A data-driven method combining symbolic regression and compressed sensing toward accurate & + interpretable models.""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/rouyang2017/SISSO/raw/master/Previous_Versions/'] +sources = ['SISSO.%(version)s.tar'] +checksums = ['faa28172c23bc8906d1ae91ca3a6d17d3427ea14de7c400072d90a0e71f7481e'] + +start_dir = 'src' + +cmds_map = [('.*', "$F90 $FFLAGS var_global.f90 libsisso.f90 DI.f90 FC.f90 SISSO.f90 -o SISSO")] + +files_to_copy = [(['SISSO'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/SISSO'], + 'dirs': [], +} + +moduleclass = 'math' From 01a05a01335d4c946b34dec762a9f8e3d039b377 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 24 Jun 2022 19:36:57 +0100 Subject: [PATCH 4112/9987] adding easyconfigs: R-4.2.1-foss-2022a.eb --- .../easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3359 +++++++++++++++++ 1 file changed, 3359 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb new file mode 100644 index 00000000000..3dc09ab695b --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -0,0 +1,3359 @@ +name = 'R' +version = '4.2.1' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f'] + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('Xvfb', '21.1.3'), +] +dependencies = [ + ('X11', '20220504'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('cairo', '1.17.4'), + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.12'), + ('SQLite', '3.38.3'), + ('PCRE2', '10.40'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.1.3'), # for plottting in R + ('LibTIFF', '4.3.0'), + ('Java', '11', '', True), + ('Tk', '8.6.12'), # for tcltk + ('cURL', '7.83.0'), # for RCurl + ('libxml2', '2.9.13'), # for XML + ('GMP', '6.2.1'), # for igraph + ('NLopt', '2.7.1'), # for nloptr + ('FFTW', '3.3.10'), # for fftw + ('libsndfile', '1.1.0'), # for seewave + ('ICU', '71.1'), # for rJava & gdsfmt + ('HDF5', '1.13.1'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.1.0-37'), # for animation + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '16.15.1'), # for V8 (required by rstan) + ('GDAL', '3.5.0'), # for sf + ('MPFR', '4.1.0'), # for Rmpfr + ('libgit2', '1.4.3'), + ('OpenSSL', '1.1', '', True), +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 23rd June 2022 +exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('Rmpi', '0.6-9.2', { + 'checksums': ['358ac1af97402e676f209261a231f36a35e60f0301edf8ca53dac11af3c3bd1a'], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.6-0', { + 'checksums': ['4516d48c9618e3f395db873e886f5deb3b66b32ebe10d4c26c1420ac848acbbf'], + }), + ('Rcpp', '1.0.8.3', { + 'checksums': ['9da5b84cdaf56e972b41e669d496b1ece2e91bcd435505c68b9f2bd98375f8bf'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.15', { + 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + }), + ('linprog', '0.9-4', { + 'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'], + }), + ('geometry', '0.4.6', { + 'checksums': ['910465a8c8043faca73bcc7c81c9249b9938677ee6649468003b438a6503f5d8'], + }), + ('bit', '4.0.4', { + 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + }), + ('filehash', '2.4-3', { + 'checksums': 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('Rook', '1.1-1', { + 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + }), + ('Cairo', '1.5-15', { + 'checksums': ['bb3ab1ff6431c15eb01a66ddf90695cd9a2af3d5a384753f5180cd0401d2e89d'], + }), + ('RMTstat', '0.3.1', { + 'checksums': ['bb4827d76106f5377044cd2b230208881eb714cae65f512f4b95988d9b162ae4'], + }), + ('Lmoments', '1.3-1', { + 'checksums': ['7c9d489a08f93fa5877e2f233ab9732e0d1b2761596b3f6ac91f2295e41a865d'], + }), + ('distillery', '1.2-1', { + 'checksums': ['4b88f0b34e472b9134ad403fb32283424f1883a5943e52c55f1fe05995efb5fa'], + }), + ('extRemes', '2.1-2', { + 'checksums': ['a7a38dc9a876967d54843872b4355c65e1910c324b0630f91a50009c2f3005a7'], + }), + ('tkrplot', '0.0-26', { + 'checksums': ['dd66264c2553f6927aff297c6b1c3b61867d6c63aec080f40a1e9d53cfc9d120'], + }), + ('misc3d', '0.9-1', { + 'checksums': ['a07bbb0de153e806cd79675ed478d2d9221cff825654f59a71a9cf61f4293d65'], + }), + ('multicool', '0.1-12', { + 'checksums': 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['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + }), + ('gsl', '2.1-7.1', { + 'checksums': ['ee98d1382d37ffa77538a90ccdbf44affbf1710a9e66b8ada73fa72e67921985'], + }), + ('energy', '1.7-10', { + 'checksums': ['543de4875c46cc90e711e71c45b082d962fbb5158a094f9f10d37d3f57e1bea7'], + }), + ('compositions', '2.0-4', { + 'checksums': ['7b9c7a3bf654fb02d9eb1b4a7566469b2f5232f3b2c1b324c02239fd31060faf'], + }), + ('clustree', '0.4.4', { + 'checksums': ['7a6100f88c9a6e8d10b253ee227ecf1dc4e84e418eb8da64cd801d2a158b956f'], + }), + ('tweedie', '2.3.3', { + 'checksums': ['a032cad512dac37a8619e6f66cb513eb82a88a5a2ffbe91e92c2d44d1756d0d9'], + }), + ('RcppGSL', '0.3.11', { + 'checksums': ['f094ea26c99b04d9e203986a1f2003f02472ceca0e2ef1c3beefd3ae80aeada8'], + }), + ('mvabund', '4.2.1', { + 'checksums': ['ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.3.1', { + 'checksums': ['cd3f72b84f0c722e9c0b21c2b2de7683ec742345d7f8e62f67c8c93342c1a5c6'], + }), + ('grpreg', '3.4.0', { + 'checksums': ['fd57d20baf63d2cc5821998bca5c3fdcbe46c933c9553caa492911b12654d6ad'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('lpSolveAPI', '5.5.2.0-17.7', { + 'checksums': ['9ebc8e45ad73eb51e0b25049598a5bc758370cf89508e2328cf4bd93d68d55bb'], + }), + ('ergm', '4.2.2', { + 'checksums': ['ced92b0a32c78c85546d665c32fb3993fe77a3809aa88f43c3eee39e2577f2f0'], + }), + ('networkDynamic', '0.11.2', { + 'checksums': ['beefaf50eb8609528358b75f5814a8f1cdc4d2db8059b99be69919da2bc02beb'], + }), + ('tergm', '4.1.0', { + 'checksums': ['abff35b48b53a182d9424c78c5240bde1259b695c2328861000193bf88044a50'], + }), + ('ergm.count', '4.1.1', { + 'checksums': ['446893614ad8b41aa39c37c2bf45a167f575536bb6778b8ad1fbcddb7b934932'], + }), + ('tsna', '0.3.5', { + 'checksums': ['4ee2f773d573f0f4bd93131156fdccf01d7f1a3f725eff3e885021098c6bff65'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.6-3', { + 'checksums': ['cb14ba20690b31fd813b05565484c866425f072a5ad99a5cbf1da63588958db3'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.1', { + 'checksums': ['14f67ce96dd8f1cb457614271b0b4376dd6fd3073a2e727a17c0964be67272cb'], + }), + ('asnipe', '1.1.16', { + 'checksums': ['be50f9fdef0f4bf9676b9c3c2906d0431afc678af55cf48b1119f9fc0adac44f'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.36.1.2', { + 'checksums': ['d470dc71e637d589bf228e59ddb021ade240d74536323d8ca77ac1fb334d3535'], + }), + ('mlegp', '3.1.9', { + 'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.5', { + 'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.6', { + 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.10', { + 'checksums': ['59266ffdf702ab1ecca7cbcf0538afe38d1a15abea66056734b62c0c15609c7c'], + }), + ('GUTS', '1.2.3', { + 'checksums': ['40061ec1677def40b410b5ef90d01e0bcb0095abed1545513a33a01d4444adc2'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.3.0', { + 'checksums': ['1e9399d6b16079e6cdc43fa33742d6b7e6e2b6bb2ba470bfe9d30d55b7be4cb0'], + }), + ('circular', '0.4-95', { + 'checksums': ['483d3e31e9c7afe59e6bcb98ad17c4f6333d19b6c70f948b168c9ee16e90bce2'], + }), + ('cobs', '1.3-5', { + 'checksums': ['7fae7da8f940975d544120c836e2d3b874f9b0cbab9631851ce986709f51c611'], + }), + ('resample', '0.6', { + 'checksums': ['1b958009b18c92a47971847c782af76952ea4e85d5f1e3e1e70fa35c67b95265'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.8-10', { + 'checksums': ['af63a28a4958dbe82597586494d0277272842bb3869db70c547d0896f1345d2c'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '7.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0.2', { + 'checksums': ['4772c352e8d3d9b5a0b7480c0e0962de4f5060fb7bf3fcb8ee4fa1cb10f93fd4'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.19', { + 'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'], + }), + ('BMA', '3.18.17', { + 'checksums': ['6d8c514fa179f8a48c2105b551a8a08e28ea4375d06150a4b8ab4ccda577daf5'], + }), + ('BCEE', '1.3.0', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-61', { + 'checksums': ['71311b16ce380fd9a8834be95b55b3d1b47e4ee2b8acb35b8d481138c314dc31'], + }), + ('bdsmatrix', '1.3-6', { + 'checksums': ['f9c871d54378408902931792b3dbf8bda863d6aa67af6a0472a6ec1c420760bc'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.21', { + 'checksums': ['0771f82034aa6a77af67f3572c900987b7e6b578d04d707c6e06689d021a2ff8'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.6', { + 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], + }), + ('rda', '1.0.2-2.1', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.9', { + 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '4.3', { + 'checksums': ['f755808fcb618582acb862729b20e267d9c2214f22e6e7a0c8d29073d8faa7b8'], + }), + ('bbmle', '1.0.25', { + 'checksums': ['86a8c69902fbf6caf337f9bc532afe89dc2a59dd24287a2423d781797010b255'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.51.2', { + 'checksums': ['c116f979ed891ec55f3e1e7b9a92436b5ec9430c1170439a501ecb7e2a33ef4d'], + }), + ('tictoc', '1.0.1', { + 'checksums': ['a09a1535c417ddf6637bbbda5fca6edab6c7f7b252a64e57e99d4d0748712705'], + }), + ('ISOcodes', '2022.01.10', { + 'checksums': ['b25ddec624b46f5630c29267bdf4a749cfb9d001ef029fb9ca84dafe56b1c73f'], + }), + ('stopwords', '2.3', { + 'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0.1', { + 'checksums': ['1fedbb913bc13c790d2fabfe4edda0a987db3a078bea8c0ca9b777d20af08662'], + }), + ('topicmodels', '0.2-12', { + 'checksums': ['afd83a4381bf39e470446ebefd41ed03f314be400c1b2f702a4b1060eb8fd1b4'], + }), + ('tidytext', '0.3.3', { + 'checksums': ['753b2bcea6e343ac439869b92e7c11b0aaf98ce5c0373965da6c7d087d57924e'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.3', { + 'checksums': ['6b3910dc48495439cd01828f8999823864a6712f73560ee3e6c903065c67d1e4'], + }), + ('entropy', '1.3.1', { + 'checksums': ['6f5a89f5ce0e90cbed1695b81259326c976e7a8f538157e223ee5f63b54412b8'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-13', { + 'checksums': ['7186d23e561818f3e1f01376a4fb2af9ccee775ce5afc1e3175f3b07a81db515'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.5.1', { + 'checksums': ['866a2f54a4e8726cc3062e27daa8a073e6ac4aeb6719af7845284f7a668745f1'], + }), + ('RcppParallel', '5.1.5', { + 'checksums': ['6396322b3b6d6f7019aac808ceb74707bc5c4ed01677fab408372c2a5508c2ea'], + }), + ('StanHeaders', '2.21.0-7', { + 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], + }), + ('V8', '4.2.0', { + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['6c62fdc974cc30fa975cad4ccb1e3796112fc2490a807f6e3d7878c3a5544743'], + }), + ('rstan', '2.21.5', { + 'checksums': ['86e4fe562d8ddcd0b02336f35a420fa8786dd21de7ca2bebb4ed6e9c252bb9ea'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.2', { + 'checksums': ['a59a3cb3cca89f51d9ee6702cd479fd7db8bc2e25b72f45cb6712da983777ca0'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.3', { + 'checksums': ['ca8545b25590e531512a90a18449a2cbab945f7434a1d60188c41f7d1839a7a9'], + }), + ('corrplot', '0.92', { + 'checksums': ['e8c09f963f9c4837036c439ebfe00fa3a6e462ccbb786d2cf90850ddcd9428bd'], + }), + ('rstatix', '0.7.0', { + 'checksums': ['a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.4.0', { + 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.1.1', { + 'checksums': ['cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481'], + }), + ('leiden', '0.4.2', { + 'checksums': ['cace86748c4aa1720508210658ee2f63f7875be5bac215084001fdc59d22e2bd'], + }), + ('sctransform', '0.3.3', { + 'checksums': ['83af125c40f211e1ddae5098f88766aea1453c02ae98486081f3efadb3620b2b'], + }), + ('packrat', '0.8.0', { + 'checksums': ['3025b9052974bec00fb09299226b80004d48e611e15a65e5a0bc49d3538844ef'], + }), + ('colourpicker', '1.1.1', { + 'checksums': ['a0d09982b048b143e2c3438ccec039dd20d6f892fa0dedc9fdcb0d40de883ce0'], + }), + ('ggExtra', '0.10.0', { + 'checksums': ['dc6855bbb7e81ffa58d6b65b594d22718fa36b7f50b2284386f70fa8ccc6a3e5'], + }), + ('findpython', '1.0.7', { + 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], + }), + ('argparse', '2.1.5', { + 'checksums': ['83e112beb47733849980b286d93ac930f0cbe6ac78fcb94fc9f6b0eea882658d'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.10', { + 'checksums': ['1b655dbab8eed8d0aa3ab2148aac8e0e5bfa190468f5e3c06b001ce88b7f0d3f'], + }), + ('qqman', '0.1.8', { + 'checksums': ['58da8317df8d726d1fde4805919da5d64f880894a423ee20937cafb479b9d8a8'], + }), + ('rstantools', '2.2.0', { + 'checksums': ['cb810baeb90c67668361b666c6862df9917aff6aaec63d2c3a485f28407c4eb7'], + }), + ('distributional', '0.3.0', { + 'checksums': ['fab36c7346617d8f2ca4b3cd0e3c9da93cb2f95fb7f102a3ae88670e694751d6'], + }), + ('posterior', '1.2.2', { + 'checksums': ['d615ed75b43b2927002b79d2982c624a6144c851aac7b81fa14e4ec9cc3d353b'], + }), + ('bayesplot', '1.9.0', { + 'checksums': ['0a81a4b99cf781334e57cfc3c469fad8b932a68204016a3bbca33cab4e2a1e43'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('rsconnect', '0.8.26', { + 'checksums': ['faafabbed803743799b345051f221aef2b4497b421fc98092ca41c05ef6b5fed'], + }), + ('shinystan', '2.6.0', { + 'checksums': ['a084856a2d66d8744f2c72e3e19ca35e600a508ed7ef1f7ebed8c7fc0738d529'], + }), + ('optimx', '2022-4.30', { + 'checksums': ['ebe9887a22296cf4b2db07981aaa1f898bf7c17fb61a4b398c228d4077d0b410'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('projpred', '2.1.2', { + 'checksums': ['a88a651e533c118aad0e8c2c905cfcf688d9c419ed195896036b8f6667b5cfb0'], + }), + ('brms', '2.17.0', { + 'checksums': ['24e5a3a40b81bea558e8f660d0de7fd1a4c2080c7553baac98f34dd2682ece71'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.1', { + 'checksums': ['285335dbe29b6898641e1151ab2f06acf76c6f4d6fbeadd66d151c25d7e38a74'], + }), + ('mcmcse', '1.5-0', { + 'checksums': ['4a820dc22c48efd32b7f9d1e1b897b4b3f165cd64b2ff85ba7029621cf9e7463'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.6.6', { + 'checksums': ['8edb6607c5d91cea5ba32290eeb76c35317383a24d726bde6eca61f9cce96bb9'], + }), + ('drugCombo', '1.2.1', { + 'checksums': ['9a605c655c159604033558d757711e6d83d33dfc286c1280f722d4cb7d130f80'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.2.5', { + 'checksums': ['a54f49f42d30a7a69eb6c3db00d3cd2e1f8e549aec28fa5487fcdd27a37f87fe'], + }), + ('maxlike', '0.1-8', { + 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + }), + ('coxme', '2.2-17', { + 'checksums': ['dd0565f97adb7ff978d1dbd6cb7d6e44edee5e2a31cf6d5d4806a0151d1b1318'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.4', { + 'checksums': ['fd21e5ecf3c1ac00ef1bbe79fab4cdd62789e0c4c45f126f1b64bda667238216'], + }), + ('oai', '0.3.2', { + 'checksums': ['ebfa756e08f6ac0aa61556b1a5bbe611f407bfff8aef1f8d075a24c361678bfd'], + }), + ('wellknown', '0.7.4', { + 'checksums': ['483e6fc43edf09ed583e74ce5ca7e2d7838ef8a32291e06d774c37546eed1a34'], + }), + ('rgbif', '3.7.2', { + 'checksums': ['460f9e80bb3d90618bb80a8b57ac6fed99a22e8919279df47b6d0710b6a89d5f'], + }), + ('rgdal', '1.5-32', { + 'checksums': ['4583a4e187492eb936b59bc6bfeefea687b115bc3ae25172e0ed348b38f473ed'], + }), + ('rgeos', '0.5-9', { + 'checksums': ['ab90cbfe6a3680a9d2eed5e655064a075adc66788e304468969ab7cc2df0e3d4'], + }), + ('mapproj', '1.2.8', { + 'checksums': ['865f108f1ee54cda38571b86cd46063a903824d9b4eabfdf75218023d08a7781'], + }), + ('rbison', '1.0.0', { + 'checksums': ['9957e5f85ce68f5dd0ddc3c4b2b3c9d2f52d6f37587e1022ab8a44863534a83c'], + }), + ('rebird', '1.3.0', { + 'checksums': ['b238d3f246aa0249145894e1f3a90f46902f6615fc2f23b24c99bb5feecc55d3'], + }), + ('rvertnet', '0.8.2', { + 'checksums': ['2de9a3ec33a213c7592b49cca1d510a25aef0625369376d9b1b4e5d0da519226'], + }), + ('ridigbio', '0.3.5', { + 'checksums': ['e5cfb2e4dd8ddd1452a5afcf24fcc260889179d0f52eff4f41835adf99b64614'], + }), + ('spocc', '1.2.0', { + 'checksums': ['4bac45db5e69bfa3bf6cebd1b0c9241214c95561f275cee6d31e00911aa79d84'], + }), + ('spThin', '0.2.0', { + 'checksums': ['2e997afb79a2a990eded34c71afaac83986669cfa9ac51b15ae3f2b558902048'], + }), + ('rangeModelMetadata', '0.1.4', { + 'checksums': ['529d529ca90437db3d1e45118443e27a920422806383c7edaa2102beb43f5f80'], + }), + ('ENMeval', '2.0.3', { + 'checksums': ['4b39173a8d9dc4f36d09509e0177abcf91b7b1b51dc219eebcb007a0fb8c3c41'], + }), + ('plotmo', '3.6.2', { + 'checksums': ['cde33a8ec558b12d8e11d7d0531e73f6678a25ee589b79897d2fc425a3fd353c'], + }), + ('earth', '5.3.1', { + 'checksums': ['0bbe06ba974ceb8ec5de1d59cb53f9487d1828d7130fe2503c48b6cb449c4b03'], + }), + ('mda', '0.5-3', { + 'checksums': ['bda6409c17f385fae97da458cc742334e7b47aab8217a975b7551e2e18d38463'], + }), + ('biomod2', '3.5.1', { + 'checksums': ['30ed33ff980558a59782ec9e35f9c2c710a540718010654363f63878cdc0ac18'], + }), + ('poLCA', '1.6.0.1', { + 'checksums': ['ed8c60a42bff0402c9ba2f9ce1422dd171e711c1a64498c4d96010ddb29f6b16'], + }), + ('PermAlgo', '1.2', { + 'checksums': ['aa2c774d6c6dcfeec882c1936e8723ef49bd36030fb10c17ca60bb9d4a519443'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.13', { + 'checksums': ['90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.3', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-1', { + 'checksums': ['e8abadc5614f132edc3fb9cb1c82ce4dacc1315b727fbd49db7399aee24115ba'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-22', { + 'checksums': ['68fa2bfe274811c91ea7b67da46c4ffe527eb662d75edbec26ffe934ddc7150a'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.7.0', { + 'checksums': ['09a6f0d5b60856c7298371e4a8a085a1db7abf0e71ccb9a2dc9ca24248fb5d81'], + }), + ('outliers', '0.15', { + 'checksums': ['cc31d7f2faefd2c3a27f8ce78c7e67d3b321dcd6690292fad2468125e5e635fb'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-9', { + 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], + }), + ('gWidgets2tcltk', '1.0-8', { + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + }), + ('mgsub', '1.7.3', { + 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], + }), + ('ie2misc', '0.8.8', { + 'checksums': ['c81441af7588c62ab019ef2fbf31f61e0c2e3440a5e131938b1c5946cd2bce1a'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-5', { + 'checksums': ['b68954f53082561f0242682611bf3373e0bf30d8ac2256d82474edc5f992f4dd'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '3.1', { + 'checksums': ['d67f5c71b1209bea655d1e8d7530fa72359e0bcac25312551524501d0287e3cf'], + }), + ('lmom', '2.9', { + 'checksums': ['363e62751a73e0870fd0206206f1743a884a23aeac9b31b9afc71c0a1b51bb90'], + }), + ('gld', '2.6.4', { + 'checksums': ['0db6daee1b6e256d64d292c1f6795c505677331dcf2f97e04e264566ded93323'], + }), + ('DescTools', '0.99.45', { + 'checksums': 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['37197edd0984f8bf0e0a39a4ac1cfce897050dbb7f610553c349118fceb3ca93'], + }), + ('relsurv', '2.2-7', { + 'checksums': ['82c84bbe0a3eb9b391cbb885b3f3e7114adda5243aa83f974922d2edca918317'], + }), + ('mstate', '0.3.2', { + 'checksums': ['3c473dff6854e31cdbdaf79f8fe7eaf97119b01a581874a894b283555afe8d14'], + }), + ('microbenchmark', '1.4.9', { + 'checksums': ['443d2caf370ef33e4ac2773176ad9eb86f8790f43b430968ef9647699dbbffd2'], + }), + ('prettyGraphs', '2.1.6', { + 'checksums': ['fece08924fc7ed05ec419afa14a2216a2bb23d9da5ed3fc61472d6e45be7577a'], + }), + ('ExPosition', '2.8.23', { + 'checksums': ['0510bc51b1c8c883ff3652a5ed56242f91c2b7b7cf3100755436bffa1e002475'], + }), + ('alluvial', '0.1-2', { + 'checksums': ['77b6dc4651b33b03aaaf1e09a35f9c3536e5fddac2eda34f5a34e0ae33cf2e0d'], + }), + ('SNFtool', '2.3.1', { + 'checksums': ['982fe7c57f52c0c272b8cb5863dc5d50623b368e24ff6e27fc8b17acc0101f16'], + }), + ('BayesLogit', '2.1', { + 'checksums': ['3a423f68339ed1bf25e21be53b1fd68452ed7807b17c36239fba759dc6fc6b70'], + }), + ('Hmsc', '3.0-11', { + 'checksums': ['318e95ea88a15939dac33691886a9ce0c54765b25a3f4ef483d168bfc699098a'], + }), + ('MonteCarlo', '1.0.6', { + 'checksums': ['f21aecfba957bbea9576b09f75b1f7c7621637a04532a8fed2c6bb8ffc1a98cb'], + }), + ('RhpcBLASctl', '0.21-247.1', { + 'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'], + }), + ('chkptstanr', '0.1.1', { + 'checksums': ['433b29d597d7ea6c21ed652782a7bf2d766f9223a3b7bfed235c8fe7fffd175c'], + }), + ('MLmetrics', '1.1.1', { + 'checksums': ['777f1b76b16837387b830e2b65304ede234b9299d17efd09c7fd403356122118'], + }), + ('renv', '0.15.5', { + 'checksums': ['b4f1a9a7daa82f0c3123ebd4eeba06e98d5485215518e5292b25bc56741d582e'], + }), + ('elliptic', '1.4-0', { + 'checksums': ['b65729b1a1c7a84a5b1a59bfc893a2d35106853eaadcae31cda5c9ee3c500bb6'], + }), + ('contfrac', '1.1-12', { + 'checksums': ['95bfc5e970513416c080486a1cd8dfd9f8d59fb691b02ef6ccbe0ce1ed61056b'], + }), + ('hypergeo', '1.2-13', { + 'checksums': ['6d5b78353aad1d13091ccbeb340867dad7b9eb00d0e2185286dc7e13848f4d8e'], + }), + ('rtdists', '0.11-5', { + 'checksums': ['97cf2ea758aa02b1dfaeef5032c6e50570777552aa771ed9a86df048b7871eed'], + }), +] + +moduleclass = 'lang' From c2255cfdd3366bac68f71e1f3ab864bb2b982dfc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 20:50:02 +0200 Subject: [PATCH 4113/9987] {bio}[foss/2021a] FSL v6.0.5.1 --- .../f/FSL/FSL-6.0.5.1-foss-2021a.eb | 81 ++++++++++++ .../f/FSL/FSL-6.0.5.1_disable_cuda.patch | 17 +++ .../FSL-6.0.5.1_fix-compat-VTK-9.0.1.patch | 14 ++ .../f/FSL/FSL-6.0.5.1_fix-cprob-include.patch | 123 ++++++++++++++++++ 4 files changed, 235 insertions(+) create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_disable_cuda.patch create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_fix-compat-VTK-9.0.1.patch create mode 100644 easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_fix-cprob-include.patch diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb new file mode 100644 index 00000000000..490c55164b6 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb @@ -0,0 +1,81 @@ +# This build still relies on the following libraries (or part of them) shipped with FSL: +# GDCHART, libprob, libcprob, cprob, newran, newmat +# Attempts to use externally built libraries failed. Worth trying again in the future... +# +# Added fslpy 3.5.3, which provides tools like imcp and imglob + +name = 'FSL' +version = '6.0.5.1' + +homepage = 'https://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://www.fmrib.ox.ac.uk/fsldownloads/'] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] +patches = [ + 'FSL-6.0.4_Makefile_fixes.patch', + 'FSL-6.0.5.1_disable_cuda.patch', + 'FSL-6.0.4_build_fixes.patch', + 'FSL-6.0.2_Build_extras.patch', + 'FSL-6.0.1_Fix_fsl_exec_script.patch', + 'FSL-6.0.5.1_fix-cprob-include.patch', + 'FSL-6.0.5.1_fix-compat-VTK-9.0.1.patch', +] +checksums = [ + 'd8ab2ebc87d3e33ce1097dde18d8a55f62d4a27b45efc4f68adccfb6e8e1425c', # fsl-6.0.5.1-sources.tar.gz + '43217e86e715a149ec27dfad471383e8f142863aa6f3f943ab4db379bc851055', # FSL-6.0.4_Makefile_fixes.patch + 'a1e844507207567b7a1df19b484d66b8b30194e455123b78cfd05e236ed864fb', # FSL-6.0.5.1_disable_cuda.patch + '1bc83cfeffff21a68db47b6929e94634fc8aaf3db8e276e160e3f468f0889000', # FSL-6.0.4_build_fixes.patch + '168157f07818e7dfd04c222916e663e9d21db84b4b86df5b79bab56e3bf8ccf5', # FSL-6.0.2_Build_extras.patch + 'aa155f8576dc5f010757ecf66fc0bf673454b6c6c40346cbb01cbe59236ed6ef', # FSL-6.0.1_Fix_fsl_exec_script.patch + '6c06d92979bf5ef4c24d71fc459a230017398a8124cfa253cbc0556a6cf2d420', # FSL-6.0.5.1_fix-cprob-include.patch + '0bee00eb136d3431fa7332aac7957b1c90bc93c381ecc6379d93e19a933ac4bc', # FSL-6.0.5.1_fix-compat-VTK-9.0.1.patch +] + +dependencies = [ + ('Python', '3.9.5'), + ('Boost', '1.76.0'), + ('libgd', '2.3.1'), + ('libxml2', '2.9.10'), + ('libxml++', '2.42.1'), + ('SQLite', '3.35.4'), + ('libpng', '1.6.37'), + ('Tk', '8.6.11'), + ('NLopt', '2.7.0'), + ('freeglut', '3.2.1'), + ('expat', '2.2.9'), + ('zlib', '1.2.11'), + ('VTK', '9.0.1'), + ('GSL', '2.7'), + ('Qwt', '6.2.0'), + ('h5py', '3.2.1'), +] + +modextrapaths = {'PYTHONPATH': ['fsl/lib/python%(pyshortver)s/site-packages']} + +# The executable files 'imglob' and 'imcp' come from fslpy +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('fslpy', '3.5.3', { + 'installopts': '--prefix=%(installdir)s/fsl', + 'source_urls': ['https://pypi.python.org/packages/source/f/fslpy/'], + 'checksums': ['f80ef8b7b49f475bfb71946619d33c118a7cbbe106c72f7777aaf14d9e261530'], + }), +] + +modextravars = { + 'FSLOUTPUTTYPE': 'NIFTI_GZ', + 'FSLMULTIFILEQUIT': 'TRUE', + 'FSLTCLSH': 'tclsh', + 'FSLWISH': 'wish8.6' +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_disable_cuda.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_disable_cuda.patch new file mode 100644 index 00000000000..6082e083b67 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_disable_cuda.patch @@ -0,0 +1,17 @@ +CUDA must now be disabled explicitly. +Author: Henrik R. Nagel (NTNU), ported to FSL 6.0.5.1 by Kenneth Hoste (HPC-UGent) +--- fsl/config/buildSettings.mk.orig 2022-06-22 19:09:08.833601000 +0200 ++++ fsl/config/buildSettings.mk 2022-06-22 19:13:27.969222000 +0200 +@@ -181,9 +181,9 @@ + #$(info GCC MIN VER $(GCCMIN)) + #$(info GCC PAT VER $(GCCPAT)) + #Project specific variables +-EDDYBUILDPARAMETERS = "cuda=1 CUDAVER=8.0" "cuda=1 CUDAVER=9.1" "cuda=1 CUDAVER=10.2" "cpu=1" +-fdt_MASTERBUILD = COMPILE_GPU = 1 +-ptx2_MASTERBUILD = COMPILE_GPU = 1 ++EDDYBUILDPARAMETERS = "cpu=1" ++fdt_MASTERBUILD = COMPILE_GPU = 0 ++ptx2_MASTERBUILD = COMPILE_GPU = 0 + define newline + + diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_fix-compat-VTK-9.0.1.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_fix-compat-VTK-9.0.1.patch new file mode 100644 index 00000000000..d313d8dfd02 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_fix-compat-VTK-9.0.1.patch @@ -0,0 +1,14 @@ +fix for compiler errors when using VTK v9.0.1 as dependency: + common/shape.cpp:359:61: error: binding reference of type ‘const vtkIdType*&’ {aka ‘const long long int*&’} to ‘vtkIdType*’ {aka ‘long long int*’} discards qualifiers +author: Kenneth Hoste (HPC-UGent) +--- fsl/src/mist/common/shape.cpp.orig 2022-06-24 19:10:57.716622000 +0200 ++++ fsl/src/mist/common/shape.cpp 2022-06-24 19:11:04.593519590 +0200 +@@ -354,7 +354,7 @@ + for (vtkIdType i = 0; i < cells->GetNumberOfIds(); i++) + { + vtkIdType npoints; +- vtkIdType *points; ++ const vtkIdType *points; + + m_polyData->GetCellPoints(cells->GetId(i), npoints, points); + diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_fix-cprob-include.patch b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_fix-cprob-include.patch new file mode 100644 index 00000000000..6cc0e7aea5c --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1_fix-cprob-include.patch @@ -0,0 +1,123 @@ +fix for "cprob/libprob.h: No such file or directory" +author: Kenneth Hoste (HPC-UGent) +diff -ru fsl/src/bint/Makefile fsl.patched/src/bint/Makefile +--- fsl/src/bint/Makefile 2019-01-24 16:13:24.000000000 +0100 ++++ fsl.patched/src/bint/Makefile 2022-06-24 15:34:10.551524000 +0200 +@@ -2,8 +2,8 @@ + + PROJNAME = bint + +-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} +-USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} ++USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_CPROB} -I${INC_ZLIB} ++USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_CPROB} -L${LIB_ZLIB} + + LIBS = -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti -lznz -lprob -lz + +diff -ru fsl/src/eddy/Makefile fsl.patched/src/eddy/Makefile +--- fsl/src/eddy/Makefile 2021-06-15 13:04:56.000000000 +0200 ++++ fsl.patched/src/eddy/Makefile 2022-06-24 15:34:10.567880609 +0200 +@@ -79,7 +79,7 @@ + EXENAME=eddy${TMPNAME_1}${TMPNAME_2} + endif + USRLDFLAGS=-L${LIB_NEWMAT} -Wl,-rpath,/opt/fmrib/fsl/lib -rdynamic +-USRINCFLAGS=-I. -I${INC_NEWMAT} -I${INC_PROB} -I${INC_BOOST} -I${INC_CUDA} -I$(CBF_DIR) -I$(INC_BASISFIELD) ++USRINCFLAGS=-I. -I${INC_NEWMAT} -I${INC_PROB} -I${INC_CPROB} -I${INC_BOOST} -I${INC_CUDA} -I$(CBF_DIR) -I$(INC_BASISFIELD) + + OBJS=eddy.o CPUStackResampler.o BiasFieldEstimatorImpl.o MoveBySuscCF.o PostEddyAlignShellsFunctions.o EddyCommandLineOptions.o ECModels.o KMatrix.o HyParEstimator.o ECScanClasses.o EddyUtils.o EddyHelperClasses.o DiffusionGP.o b0Predictor.o + TESTOBJS=test_s2v_model.o PostEddyAlignShellsFunctions.o EddyCommandLineOptions.o ECModels.o KMatrix.o HyParEstimator.o ECScanClasses.o EddyUtils.o EddyHelperClasses.o DiffusionGP.o b0Predictor.o +diff -ru fsl/src/feat5/Makefile fsl.patched/src/feat5/Makefile +--- fsl/src/feat5/Makefile 2021-04-15 13:34:17.000000000 +0200 ++++ fsl.patched/src/feat5/Makefile 2022-06-24 15:35:08.189816000 +0200 +@@ -2,8 +2,8 @@ + + PROJNAME = feat5 + +-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} +-USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} ++USRINCFLAGS = -I${INC_NEWMAT} -I${INC_CPROB} -I${INC_PROB} -I${INC_ZLIB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} ++USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_CPROB} -L${LIB_PROB} -L${LIB_ZLIB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} + + IOLIBS = -lNewNifti -lznz + LIBS = -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lprob -lnewmat -lutils $(IOLIBS) -lm -lz -lgdc -lgd -lpng +diff -ru fsl/src/filmbabe/Makefile fsl.patched/src/filmbabe/Makefile +--- fsl/src/filmbabe/Makefile 2018-04-23 14:10:04.000000000 +0200 ++++ fsl.patched/src/filmbabe/Makefile 2022-06-24 15:35:08.191008000 +0200 +@@ -2,8 +2,8 @@ + + PROJNAME = filmbabe + +-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} +-USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB} ++USRINCFLAGS = -I${INC_NEWMAT} -I${INC_CPROB} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} ++USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_CPROB} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB} + + LIBS = -lutils -lmiscplot -lmiscpic -lnewimage -lmiscmaths -lnewmat -lNewNifti -lprob -lgdc -lgd -lpng -lznz -lz -lm + +diff -ru fsl/src/libmeshutils/Makefile fsl.patched/src/libmeshutils/Makefile +--- fsl/src/libmeshutils/Makefile 2014-12-16 15:20:18.000000000 +0100 ++++ fsl.patched/src/libmeshutils/Makefile 2022-06-24 15:34:10.552399000 +0200 +@@ -5,8 +5,8 @@ + + LD_LIBRARY_PATH=${FSLDIR}/lib + +-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} +-USRLDFLAGS = -L${LIB_PROB} -L${LIB_NEWMAT} -L${LIB_ZLIB} ++USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_CPROB} -I${INC_BOOST} ++USRLDFLAGS = -L${LIB_PROB} -L${LIB_CPROB} -L${LIB_NEWMAT} -L${LIB_ZLIB} + + BUILT_VTKCONV = $(shell [ -f ../../libfslvtkconv* ]; echo $$?) + +diff -ru fsl/src/libvis/Makefile fsl.patched/src/libvis/Makefile +--- fsl/src/libvis/Makefile 2019-09-20 13:45:59.000000000 +0200 ++++ fsl.patched/src/libvis/Makefile 2022-06-24 15:34:10.550654000 +0200 +@@ -4,8 +4,8 @@ + + PROJNAME = libvis + +-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -I${INC_BOOST} +-USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB} ++USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_CPROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -I${INC_BOOST} ++USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_CPROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB} + + LIBS = -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lfslio -lniftiio -lznz -lnewmat -lprob -lm -lgdc -lgd -lpng -lz + CXXFLAGS += -std=c++98 +--- fsl/src/miscvis/Makefile.orig 2022-06-24 15:42:23.119451000 +0200 ++++ fsl/src/miscvis/Makefile 2022-06-24 15:42:44.790736000 +0200 +@@ -2,8 +2,8 @@ + + PROJNAME = miscvis + +-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} +-USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB} ++USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_CPROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} ++USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_CPROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB} + + LIBS = -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti -lznz -lnewmat -lcprob -lm -lgdc -lgd -lpng -lz + +--- fsl/src/mm/Makefile.orig 2022-06-24 15:43:04.736781000 +0200 ++++ fsl/src/mm/Makefile 2022-06-24 15:43:23.950776000 +0200 +@@ -2,8 +2,8 @@ + + PROJNAME = mm + +-USRINCFLAGS = -I${INC_NEWRAN} -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} +-USRLDFLAGS = -L${LIB_NEWRAN} -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB} ++USRINCFLAGS = -I${INC_NEWRAN} -I${INC_NEWMAT} -I${INC_PROB} -I${INC_CPROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} ++USRLDFLAGS = -L${LIB_NEWRAN} -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_CPROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB} + + LIBS = -lnewimage -lmiscmaths -lutils -lmiscplot -lmiscpic -lNewNifti -lznz -lm -lnewmat -lprob -lgdc -lgd -lpng -lz + +--- fsl/src/possum/Makefile.orig 2022-06-24 15:43:47.443376000 +0200 ++++ fsl/src/possum/Makefile 2022-06-24 15:44:13.001084000 +0200 +@@ -9,8 +9,8 @@ + #with the next line it will not do the table version automatically + #USRCXXFLAGS = -DNOTABLE + +-USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} +-USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB} ++USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_CPROB} -I${INC_ZLIB} ++USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_CPROB} -L${LIB_ZLIB} + + LIBS=-lnewimage -lmiscmaths -lnewmat -lutils -lprob -lNewNifti -lznz -lm -lz + From 1a85c3aaf598884a0fad5be42472f27eb2a354a5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 21:19:40 +0200 Subject: [PATCH 4114/9987] add Doxygen build dependency for libsigc++ v2.10.8 --- .../easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb index 0c4e7eec7a8..8cc57b45af4 100644 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb @@ -16,6 +16,7 @@ checksums = ['235a40bec7346c7b82b6a8caae0456353dc06e71f14bc414bcc858af1838719a'] builddependencies = [ ('binutils', '2.36.1'), ('Autotools', '20210128'), + ('Doxygen', '1.9.1'), ('mm-common', '1.0.4'), ] From c3487524279cbdb73319d88227d632884f17e1b1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 21:58:40 +0200 Subject: [PATCH 4115/9987] add Graphviz + libxslt build dependencies for libsigc++ v2.10.8 --- .../easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb index 8cc57b45af4..95ef05bda6a 100644 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb @@ -17,6 +17,8 @@ builddependencies = [ ('binutils', '2.36.1'), ('Autotools', '20210128'), ('Doxygen', '1.9.1'), + ('Graphviz', '2.47.2'), + ('libxslt', '1.1.34'), ('mm-common', '1.0.4'), ] From 50894ddafc9a46c043f653398b5d684be8d8b053 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 24 Jun 2022 21:24:10 +0100 Subject: [PATCH 4116/9987] download instructions added --- easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb index 264f38782a5..c26d7a70c8c 100644 --- a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb @@ -15,7 +15,6 @@ description = """GULP is a program for performing a variety of types of simulati toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'usempi': True} -# download requires registration, https://gulp.curtin.edu.au/gulp/request.cfm?rel=download sources = [SOURCELOWER_TGZ] patches = [ 'GULP-6.1_fftw-blas-linking-gcc-11.patch', @@ -25,6 +24,10 @@ checksums = [ '156449c96a97ff24f6add83c10fd383f07c43c79420eebe3290387b65b34549b', # gulp-6.1_fftw-blas-linking-gcc-11.patch ] +download_instructions = """Download requires registration, please see +https://gulp.curtin.edu.au/gulp/request.cfm?rel=download +and follow the instructions there""" + start_dir = 'Src' # Use external FFTW (-f), enable parallel/MPI build (-m) and set the base compiler (-c). From 8a19ba1dcc4281070d42cf89c9d193753d15e04a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Jun 2022 20:42:18 +0200 Subject: [PATCH 4117/9987] adding easyconfigs: WPS-3.9.1-foss-2020b-dmpar.eb and patches: WPS-3.9.1_fix-JasPer-2.x.patch, WPS-3.9.1_fix-intmath.patch --- .../w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb | 47 +++++++++++++++++++ .../w/WPS/WPS-3.9.1_fix-JasPer-2.x.patch | 28 +++++++++++ .../w/WPS/WPS-3.9.1_fix-intmath.patch | 23 +++++++++ 3 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.9.1_fix-JasPer-2.x.patch create mode 100644 easybuild/easyconfigs/w/WPS/WPS-3.9.1_fix-intmath.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb new file mode 100644 index 00000000000..9755379bfa3 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb @@ -0,0 +1,47 @@ +name = 'WPS' +version = '3.9.1' +buildtype = 'dmpar' +versionsuffix = '-%s' % buildtype + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True} + +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] +sources = ['%(name)sV%(version)s.TAR.gz'] +patches = [ + 'WPS-3.8.0_netCDF-Fortran_seperate_path.patch', + 'WPS-3.9.1_fix-intmath.patch', + 'WPS-3.9.1_fix-JasPer-2.x.patch', +] +checksums = [ + '48a05cb25d6dcfaf4ba6fc63719b361ae240c79aad8066412646c936eecfcf90', # WPSV3.9.1.TAR.gz + '7ff73248b55eff304bcfd0f7b9e936c4c460dcc351088a15c2c4ac22622b9d41', # WPS-3.8.0_netCDF-Fortran_seperate_path.patch + 'f0c440db2c50cf67b3ee04eff349127d0b5f3b6bed79d136db5e6dcaf11e0e29', # WPS-3.9.1_fix-intmath.patch + '41a82492d230178278da138c5ab530e5084e861147fd98b792392d769ad38091', # WPS-3.9.1_fix-JasPer-2.x.patch +] + +dependencies = [ + ('WRF', '3.9.1.1', versionsuffix), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('JasPer', '2.0.24'), +] + +# required to ensure that netcdf.mod is found +prebuildopts = "sed -i 's@-I\$(NETCDF)/include@-I\$(NETCDF)/include -I\$(NETCDFF)/include@g' configure.wps && " + +# workaround for "Type mismatch between actual argument" compiler errors, +# see also https://www.gnu.org/software/gcc/gcc-10/porting_to.html +prebuildopts += "sed -i 's/ -O / -O -fallow-argument-mismatch /g' configure.wps && " + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.9.1_fix-JasPer-2.x.patch b/easybuild/easyconfigs/w/WPS/WPS-3.9.1_fix-JasPer-2.x.patch new file mode 100644 index 00000000000..e8481d2e906 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.9.1_fix-JasPer-2.x.patch @@ -0,0 +1,28 @@ +fix compatibility with JasPer 2.x + enc_jpeg2000.c:141:10: error: jas_image_t has no member named inmem_ +see also https://github.com/wrf-model/WPS/pull/50 +From e23dbcdb130a2a6306f88e08af3b4c853269a86d Mon Sep 17 00:00:00 2001 +From: Dave Gill +Date: Wed, 6 Dec 2017 21:07:22 -0700 +Subject: [PATCH] image.inmem_=1 causes a compiler error, not fatal to ungrib + +--- + ungrib/src/ngl/g2/enc_jpeg2000.c | 5 ++++- + 1 file changed, 4 insertions(+), 1 deletion(-) + +diff --git a/ungrib/src/ngl/g2/enc_jpeg2000.c b/ungrib/src/ngl/g2/enc_jpeg2000.c +index 7b8528120..2be6c062b 100755 +--- a/ungrib/src/ngl/g2/enc_jpeg2000.c ++++ b/ungrib/src/ngl/g2/enc_jpeg2000.c +@@ -138,7 +138,10 @@ int enc_jpeg2000(unsigned char *cin,g2int *pwidth,g2int *pheight,g2int *pnbits, + image.clrspc_=JAS_CLRSPC_SGRAY; /* grayscale Image */ + image.cmprof_=0; + #endif +- image.inmem_=1; ++ /* ++ * Does not seem to be needed, and throws a compiler error ++ * image.inmem_=1; ++ */ + + cmpt.tlx_=0; + cmpt.tly_=0; diff --git a/easybuild/easyconfigs/w/WPS/WPS-3.9.1_fix-intmath.patch b/easybuild/easyconfigs/w/WPS/WPS-3.9.1_fix-intmath.patch new file mode 100644 index 00000000000..e5cc0ff37fa --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-3.9.1_fix-intmath.patch @@ -0,0 +1,23 @@ +fix compilation of intmath.f with gfortran 10.x + Error: Arguments of iand have different kind type parameters at (1) +see https://github.com/wrf-model/WPS/pull/119 +--- WPS/ungrib/src/ngl/g2/intmath.f.orig 2022-06-24 12:19:49.517587000 +0200 ++++ WPS/ungrib/src/ngl/g2/intmath.f 2022-06-24 12:21:35.498978000 +0200 +@@ -169,7 +169,7 @@ + ilog2_2=0 + i=i_in + if(i<=0) return +- if(iand(i,i-1)/=0) then ++ if(iand(i,i-1_2)/=0) then + !write(0,*) 'iand i-1' + ilog2_2=1 + endif +@@ -204,7 +204,7 @@ + ilog2_1=0 + i=i_in + if(i<=0) return +- if(iand(i,i-1)/=0) then ++ if(iand(i,i-1_1)/=0) then + !write(0,*) 'iand i-1' + ilog2_1=1 + endif From 3d50b12154bd769b636d4ce5cbf76a79fb3ca165 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Jun 2022 21:02:40 +0200 Subject: [PATCH 4118/9987] add exception to test suite for WPS 3.9.1 depending on WRF 3.9.1.1 --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a79fc338337..f7ac92a631b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -554,6 +554,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 # (for 2021b, UCX was updated to v1.11.2) 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], + # WPS 3.9.1 requires WRF 3.9.1.1 + 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], } if dep in alt_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): From b418ff517cc5058b0e570354772ac004e533be1e Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 27 Jun 2022 11:47:38 +0100 Subject: [PATCH 4119/9987] drop minimap2, mappy dependencies to 2.22 add test exception for Pysam dependency version --- easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb | 4 ++-- test/easyconfigs/easyconfigs.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb index c168c465e07..4b426e05a0a 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb @@ -20,7 +20,7 @@ toolchainopts = {'pic': True} builddependencies = [('Autotools', '20210726')] -_minimap_ver = '2.24' +_minimap_ver = '2.22' dependencies = [ ('Python', '3.9.6'), # includes cffi # TensorFlow ~=2.7.0 required by medaka 1.6.0, see requirements.txt @@ -42,7 +42,7 @@ use_pip = True exts_list = [ ('mappy', _minimap_ver, { - 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + 'checksums': ['219c93ab7f8d5d7c26face512a9e738a7306f3376ebfa3017eac70676ba97840'], }), (name, version, { 'checksums': ['a8389f90cba77095061c4ff22c7cce8d73908e2451fa1d07b94c2f8ce4152628'], diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a79fc338337..04dc882f634 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -521,7 +521,7 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Pysam': [ ('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', 'NGSpeciesID-0.1.1.1-']), - ('0.18.0;', ['WhatsHap-1.4-']), + ('0.18.0;', ['WhatsHap-1.4-', 'medaka-1.6.0-']), ], # OPERA requires SAMtools 0.x 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', From 94326f24f6cac0534e49eb906d1a828d7dabd02b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 27 Jun 2022 14:26:17 +0200 Subject: [PATCH 4120/9987] adding easyconfigs: Arriba-2.3.0-GCC-11.2.0.eb --- .../a/Arriba/Arriba-2.3.0-GCC-11.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arriba/Arriba-2.3.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Arriba/Arriba-2.3.0-GCC-11.2.0.eb b/easybuild/easyconfigs/a/Arriba/Arriba-2.3.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..e2efa2c0723 --- /dev/null +++ b/easybuild/easyconfigs/a/Arriba/Arriba-2.3.0-GCC-11.2.0.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'Arriba' +version = '2.3.0' + +homepage = 'https://github.com/suhrig/arriba' +description = """Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. + It was developed for the use in a clinical research setting. Therefore, short runtimes and high + sensitivity were important design criteria.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/suhrig/%(namelower)s/releases/download/v%(version)s'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] +checksums = ['bf7156be297a34fae274b7d2383cd37b90013860c2bfc637ff1b9f3d1f8de666'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('HTSlib', '1.14'), + ('libdeflate', '1.8'), + ('STAR', '2.7.9a'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), +] + +# make target with dynamically linked libraries is called bioconda, default is a statically linked binary +build_cmd_targets = 'bioconda' +# otherwise it fails to find sam.h +buildopts = 'CPATH=${EBROOTHTSLIB}/include/htslib:CPATH' + +postinstallcmds = ['mkdir %(installdir)s/database'] +files_to_copy = ['%(namelower)s', 'documentation', 'download_references.sh', 'draw_fusions.R', 'LICENSE', + 'README.md', 'run_%(namelower)s.sh'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [('%(namelower)s', '-h')] + +moduleclass = 'bio' From f8f0467fbde0144d14657cc4eba0f51934e2268d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 27 Jun 2022 13:59:01 +0100 Subject: [PATCH 4121/9987] adding easyconfigs: IRkernel-1.2-foss-2021b-R-4.2.0.eb --- .../IRkernel-1.2-foss-2021b-R-4.2.0.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021b-R-4.2.0.eb diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021b-R-4.2.0.eb new file mode 100644 index 00000000000..4febd99a1cb --- /dev/null +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021b-R-4.2.0.eb @@ -0,0 +1,68 @@ +easyblock = 'Bundle' + +name = 'IRkernel' +version = '1.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://irkernel.github.io' +description = """The R kernel for the 'Jupyter' environment executes R code + which the front-end (Jupyter Notebook or other front-ends) submits to the + kernel via the network.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('R', '4.2.0'), + ('Python', '3.9.6'), + ('IPython', '7.26.0'), + ('ZeroMQ', '4.3.4'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.rstudio.com/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('repr', '1.1.4', { + 'checksums': ['6f799ca83e0940618dd8c22e62ffdce5ec11ba3366c5306ae58b55b53c097040'], + }), + ('IRdisplay', '1.1', { + 'checksums': ['83eb030ff91f546cb647899f8aa3f5dc9fe163a89a981696447ea49cc98e8d2b'], + }), + ('pbdZMQ', '0.3-7', { + 'checksums': ['df2d2be14b2f57a64d76cdda4c01fd1c3d9aa12221c63524c01c71849df11808'], + }), + (name, version, { + 'checksums': ['5fb4dbdb741d05043120a8be0eb73f054b607d9854f314bd79cfec08d219ff91'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +# IPython notebook looks for the json kernel file in kernels/IRkernel +# We start the kernel with default bitmapType 'cairo'. This is a more sensible default +# for headless nodes. See https://github.com/IRkernel/IRkernel/issues/388 +local_kerneldir = '%(installdir)s/IRkernel' +postinstallcmds = [ + 'mkdir -p %s/kernels/ir' % local_kerneldir, + 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir), + ('sed -i \'s/"IRkernel::main()"/"options(bitmapType=\\x27cairo\\x27); IRkernel::main()"/g\'' + ' %s/kernels/ir/kernel.json') % local_kerneldir +] + +modextravars = {'JUPYTER_PATH': local_kerneldir} + +sanity_check_paths = { + 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], + 'dirs': [name], +} + +moduleclass = 'tools' From 7a5bf6843e4b46463a584b33d9c5abb22e877623 Mon Sep 17 00:00:00 2001 From: software Date: Mon, 27 Jun 2022 13:23:22 +0000 Subject: [PATCH 4122/9987] adding easyconfigs: tesseract-4.1.0-GCCcore-10.3.0.eb --- .../tesseract-4.1.0-GCCcore-10.3.0.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f2343bc2573 --- /dev/null +++ b/easybuild/easyconfigs/t/tesseract/tesseract-4.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,64 @@ +easyblock = 'CMakeMake' + +name = 'tesseract' +version = '4.1.0' + +homepage = 'https://github.com/tesseract-ocr/tesseract' +description = """Tesseract is an optical character recognition engine""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'tesseract-ocr' +source_urls = [GITHUB_SOURCE] +sources = [ + '%(version)s.tar.gz', + { + 'source_urls': ['https://github.com/tesseract-ocr/tessdata/archive/'], + 'download_filename': '4.1.0.tar.gz', + 'filename': 'tessdata-4.1.0.tar.gz', + }, +] +patches = ['tesseract-4.1.0-add-glib-dependency.patch'] +checksums = [ + '5c5ed5f1a76888dc57a83704f24ae02f8319849f5c4cf19d254296978a1a1961', # 4.1.0.tar.gz + '990fffb9b7a9b52dc9a2d053a9ef6852ca2b72bd8dfb22988b0b990a700fd3c7', # tessdata-4.1.0.tar.gz + 'f21ac5ed7d28a07978a6f7230fce2125d98a7264e33ddd3bd648af6da41b6fd1', # tesseract-4.1.0-add-glib-dependency.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2') +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.2.0'), + ('Leptonica', '1.82.0'), + ('libarchive', '3.5.1'), + ('ICU', '69.1'), + ('fontconfig', '2.13.93'), + ('GLib', '2.68.2'), + ('cairo', '1.16.0'), + ('Pango', '1.48.5'), +] + +separate_build_dir = True + +postinstallcmds = [ + 'mkdir %(installdir)s/tessdata', + 'mv %(builddir)s/tessdata-4.1.0/* %(installdir)s/tessdata' +] + +modextrapaths = { + 'TESSDATA_PREFIX': 'tessdata', +} + +sanity_check_paths = { + 'files': ['bin/tesseract', 'lib/libtesseract.%s' % SHLIB_EXT], + 'dirs': ['tessdata', 'include/tesseract'] +} + +moduleclass = 'vis' From 96664c267f66a430255e0b36a27d3e035badf90e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 27 Jun 2022 14:34:20 +0100 Subject: [PATCH 4123/9987] JUPYTER_PATH should be in modextrapaths and there is IRkernel 1.3 available --- ...-R-4.2.0.eb => IRkernel-1.3-foss-2021b-R-4.2.0.eb} | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/i/IRkernel/{IRkernel-1.2-foss-2021b-R-4.2.0.eb => IRkernel-1.3-foss-2021b-R-4.2.0.eb} (91%) diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.3-foss-2021b-R-4.2.0.eb similarity index 91% rename from easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021b-R-4.2.0.eb rename to easybuild/easyconfigs/i/IRkernel/IRkernel-1.3-foss-2021b-R-4.2.0.eb index 4febd99a1cb..3e23b19870d 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.3-foss-2021b-R-4.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'IRkernel' -version = '1.2' +version = '1.3' versionsuffix = '-R-%(rver)s' homepage = 'https://irkernel.github.io' @@ -41,11 +41,14 @@ exts_list = [ 'checksums': ['df2d2be14b2f57a64d76cdda4c01fd1c3d9aa12221c63524c01c71849df11808'], }), (name, version, { - 'checksums': ['5fb4dbdb741d05043120a8be0eb73f054b607d9854f314bd79cfec08d219ff91'], + 'checksums': ['5a7fcbfd978dfb3cca6702a68a21c147551995fc400084ae8382ffcbbdae1903'], }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel # We start the kernel with default bitmapType 'cairo'. This is a more sensible default @@ -58,8 +61,6 @@ postinstallcmds = [ ' %s/kernels/ir/kernel.json') % local_kerneldir ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], From 72ab1ca18f2e461b9468ef42928315b12e00ebf5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 27 Jun 2022 14:38:22 +0100 Subject: [PATCH 4124/9987] set JUPYTER_PATH in modextrapaths for IRkernel 1.x --- .../IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb | 7 ++++--- .../IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb | 7 ++++--- .../IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb | 7 ++++--- .../IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb | 7 ++++--- .../i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb | 7 ++++--- 5 files changed, 20 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb index fe42a2e870a..515926174ff 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb @@ -44,7 +44,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel local_kerneldir = '%(installdir)s/IRkernel' @@ -53,8 +56,6 @@ postinstallcmds = [ 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir) ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb index db893db1a39..68c33b16ff9 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb @@ -45,7 +45,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel # We start the kernel with default bitmapType 'cairo'. This is a more sensible default @@ -58,8 +61,6 @@ postinstallcmds = [ ' %s/kernels/ir/kernel.json') % local_kerneldir ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb index 32f9762476c..c9b0e435d6c 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb @@ -44,7 +44,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel local_kerneldir = '%(installdir)s/IRkernel' @@ -53,8 +56,6 @@ postinstallcmds = [ 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir) ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb index 51142541134..6aba48fcb51 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb @@ -45,7 +45,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel # We start the kernel with default bitmapType 'cairo'. This is a more sensible default @@ -58,8 +61,6 @@ postinstallcmds = [ ' %s/kernels/ir/kernel.json') % local_kerneldir ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb index 4f72aab2b80..33da48260c8 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb @@ -45,7 +45,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel # We start the kernel with default bitmapType 'cairo'. This is a more sensible default @@ -58,8 +61,6 @@ postinstallcmds = [ ' %s/kernels/ir/kernel.json') % local_kerneldir ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], From 29be691c55f4a16ee21d67e7c0c61e479be2b2dd Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 27 Jun 2022 16:28:51 +0100 Subject: [PATCH 4125/9987] adding easyconfigs: flatbuffers-2.0.0-GCCcore-11.3.0.eb, flatbuffers-python-2.0-GCCcore-11.3.0.eb --- .../flatbuffers-python-2.0-GCCcore-11.3.0.eb | 27 +++++++++++++++ .../flatbuffers-2.0.0-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-2.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7913bb7c2be --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-2.0-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'flatbuffers-python' +version = '2.0' + +homepage = 'https://github.com/google/flatbuffers/' +description = """Python Flatbuffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/f/flatbuffers'] +sources = [{'download_filename': 'flatbuffers-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['12158ab0272375eab8db2d663ae97370c33f152b27801fa6024e1d6105fd4dd2'] + +dependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'VERSION=%(version)s ' +options = {'modulename': 'flatbuffers'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..080188887fd --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '2.0.0' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['9ddb9031798f4f8754d00fca2f1a68ecf9d0f83dfac7239af1311e4fd9a565c4'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), + ('Python', '3.10.4'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' From 6bc1d8d5b43f05ffeb1beedb291fbef43e5a5a4d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 27 Jun 2022 16:32:35 +0100 Subject: [PATCH 4126/9987] adding easyconfigs: protobuf-3.19.4-GCCcore-11.3.0.eb, protobuf-python-3.19.4-GCCcore-11.3.0.eb --- .../protobuf-python-3.19.4-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ .../protobuf-3.19.4-GCCcore-11.3.0.eb | 29 +++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.19.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.19.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.19.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.19.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..76dece60b6e --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.19.4-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.19.4' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = [{'download_filename': 'protobuf-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['9df0c10adf3e83015ced42a9a7bd64e13d06c4cf45c340d2c63020ea04499d0a'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('protobuf', version) +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.19.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.19.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7b0be936361 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.19.4-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '3.19.4' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3bd7828aa5af4b13b99c191e8b1e884ebfa9ad371b0ce264605d347f135d2568'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +srcdir = 'cmake' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From 01a78d07e5c3a1ea61c1ad3004a1ca9c982a37b7 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 27 Jun 2022 16:42:30 +0100 Subject: [PATCH 4127/9987] adding easyconfigs: h5py-3.7.0-foss-2022a.eb, pkgconfig-1.5.5-GCCcore-11.3.0-python.eb --- .../h/h5py/h5py-3.7.0-foss-2022a.eb | 34 +++++++++++++++++++ .../pkgconfig-1.5.5-GCCcore-11.3.0-python.eb | 28 +++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.7.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.3.0-python.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.7.0-foss-2022a.eb b/easybuild/easyconfigs/h/h5py/h5py-3.7.0-foss-2022a.eb new file mode 100644 index 00000000000..9d7fd568a45 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.7.0-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.7.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['3fcf37884383c5da64846ab510190720027dca0768def34dd8dcb659dbe5cbf3'] + +builddependencies = [('pkgconfig', '1.5.5', '-python')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('HDF5', '1.13.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.3.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.3.0-python.eb new file mode 100644 index 00000000000..568e0498ef7 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-11.3.0-python.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.5.5' +# The -python versionsuffix is used to avoid confusion between +# pkg-config (the tool) and pkgconfig (the Python wrappers) +versionsuffix = '-python' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('pkgconf', '1.8.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From 3fccfb0cc9d8c449c9f4bb5eabde38a0095d69b8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 27 Jun 2022 16:42:49 +0100 Subject: [PATCH 4128/9987] adding easyconfigs: JsonCpp-1.9.5-GCCcore-11.3.0.eb --- .../j/JsonCpp/JsonCpp-1.9.5-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c1778c26757 --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.5' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['f409856e5920c18d0c2fb85276e24ee607d2a09b5e7d5f0a371368903c275da2'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.so'], + 'dirs': [], +} + +moduleclass = 'lib' From b6dd39c945637ee003496d6adbe5892bdee57027 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 27 Jun 2022 16:45:25 +0100 Subject: [PATCH 4129/9987] adding easyconfigs: LMDB-0.9.29-GCCcore-11.3.0.eb, nsync-1.25.0-GCCcore-11.3.0.eb --- .../l/LMDB/LMDB-0.9.29-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ .../n/nsync/nsync-1.25.0-GCCcore-11.3.0.eb | 26 ++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/nsync/nsync-1.25.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..87af8c0082c --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.29' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['22054926b426c66d8f2bc22071365df6e35f3aacf19ad943bc6167d4cae3bebb'] + +builddependencies = [('binutils', '2.38')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'], 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.25.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.25.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0cb06ad08e7 --- /dev/null +++ b/easybuild/easyconfigs/n/nsync/nsync-1.25.0-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeNinja' + +name = 'nsync' +version = '1.25.0' + +homepage = 'https://github.com/google/nsync' +description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/google/nsync/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['47a6eb2a295be5121a1904a6a775722338a20dc02ee3eec4169ed2c3f203617a'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), +] + +sanity_check_paths = { + 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], + 'dirs': [], +} + +moduleclass = 'devel' From 7c6a0c6ad3e979e8165cc98bf162aad63e763de5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 27 Jun 2022 16:47:45 +0100 Subject: [PATCH 4130/9987] adding easyconfigs: networkx-2.8.4-foss-2022a.eb --- .../n/networkx/networkx-2.8.4-foss-2022a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.8.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.8.4-foss-2022a.eb b/easybuild/easyconfigs/n/networkx/networkx-2.8.4-foss-2022a.eb new file mode 100644 index 00000000000..1fa366be25b --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.8.4-foss-2022a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.8.4' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['5e53f027c0d567cf1f884dbb283224df525644e43afd1145d64c9d88a3584762'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From a105a648301b8ed5d6f9098ce7839ba39b7ef89c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 27 Jun 2022 16:48:34 +0100 Subject: [PATCH 4131/9987] update checksum for nsync --- easybuild/easyconfigs/n/nsync/nsync-1.25.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.25.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.25.0-GCCcore-11.3.0.eb index 0cb06ad08e7..81bcc07cc76 100644 --- a/easybuild/easyconfigs/n/nsync/nsync-1.25.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nsync/nsync-1.25.0-GCCcore-11.3.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/google/nsync/archive/v%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['47a6eb2a295be5121a1904a6a775722338a20dc02ee3eec4169ed2c3f203617a'] +checksums = ['2be9dbfcce417c7abcc2aa6fee351cd4d292518d692577e74a2c6c05b049e442'] builddependencies = [ ('binutils', '2.38'), From 19dcae9129e56447d8b0a41591ce03fa96be3f83 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 27 Jun 2022 16:59:08 +0100 Subject: [PATCH 4132/9987] adding easyconfigs: UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb, NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb, GDRCopy-2.3-GCCcore-11.3.0.eb --- .../g/GDRCopy/GDRCopy-2.3-GCCcore-11.3.0.eb | 52 +++++++++++++++++++ ...NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb | 23 ++++++++ ...-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb | 42 +++++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..43ffd95b310 --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-11.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.3' + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +# This easyconfig only installs the library of GDRCopy. Please keep in mind +# that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] + +local_envopts = "prefix=%(installdir)s" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib %s" % local_envopts +install_cmd = "make lib_install" +installopts = local_envopts + +sanity_check_paths = { + 'files': ['lib/libgdrapi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..026964019f7 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,23 @@ +name = 'NCCL' +version = '2.12.12' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['49b4fbfeebf1f62f6ceb69e72504045d8d1b4e7609e3c2477906f3004c7e2d82'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('UCX-CUDA', '1.12.1', versionsuffix), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..7bf9d3c8710 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,42 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['ucx-%(version)s.tar.gz'] +patches = [ + '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', +] +checksums = [ + '40b447c8e7da94a253f2828001b2d76021eb4ad39647107d433d62d61e18ae8e', # ucx-1.12.1.tar.gz + # UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch + 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3', +] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('UCX', version), + ('CUDA', '11.7.0', '', True), + ('GDRCopy', '2.3'), +] + +moduleclass = 'lib' From ba2c81cf295a70c3726edb6b9bce6213a2721fed Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 28 Jun 2022 15:45:05 +0200 Subject: [PATCH 4133/9987] adding easyconfigs: regionmask-0.9.0-foss-2020a-Python-3.8.2.eb --- ...egionmask-0.9.0-foss-2020a-Python-3.8.2.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..30ba66592cf --- /dev/null +++ b/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'regionmask' +version = '0.9.0' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'https://regionmask.readthedocs.io' +description = """regionmask creates masks of geographical regions. It determines to which +geographic region each grid point belongs.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('geopandas', '0.8.1', versionsuffix), + ('rasterio', '1.1.7', versionsuffix), + ('Shapely', '1.7.1', versionsuffix), + ('xarray', '0.16.1', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('pooch', '1.3.0', { + 'checksums': ['30d448e825904e2d763bbbe418831a788813c32f636b21c8d60ee5f474532898'], + }), + (name, version, { + 'checksums': ['8da1b6359756241867c4e967097810ef86b9dff4e06d11ca648fe1d607e9cf14'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 20e175a44e63f43263be10f323d155ef8a1b685e Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 28 Jun 2022 18:08:27 +0100 Subject: [PATCH 4134/9987] adding easyconfigs: cppy-1.2.1-GCCcore-11.2.0.eb --- .../c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0e3d801d4fa --- /dev/null +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'cppy' +version = '1.2.1' + +homepage = "https://github.com/nucleic/cppy" +description = """A small C++ header library which makes it easier to write +Python extension modules. The primary feature is a PyObject smart pointer +which automatically handles reference counting and provides convenience +methods for performing common object operations.""" + + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), +] + +# we are using PyPi for this: +# source_urls = ['https://github.com/nucleic/cppy/archive/refs/tags/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From 0184464ad802e269e4f363d89ed5bfa53a424e7c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Tue, 28 Jun 2022 21:04:11 +0100 Subject: [PATCH 4135/9987] Update easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb | 23 +++++++++---------- 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb index 0e3d801d4fa..14e7ee67f28 100644 --- a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'cppy' version = '1.2.1' @@ -9,22 +9,21 @@ Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations.""" - toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -builddependencies = [('binutils', '2.37')] +dependencies = [('Python', '3.9.6')] -dependencies = [ - ('Python', '3.9.6'), -] +use_pip = True -# we are using PyPi for this: -# source_urls = ['https://github.com/nucleic/cppy/archive/refs/tags/'] -sources = ['%(name)s-%(version)s.tar.gz'] -checksums = ['83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'] +exts_list = [ + ('setuptools', '62.6.0', { + 'checksums': ['990a4f7861b31532871ab72331e755b5f14efbe52d336ea7f6118144dd478741'], + }), + (name, version, { + 'checksums': ['83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'], + }), +] -download_dep_fail = True sanity_pip_check = True -use_pip = True moduleclass = 'tools' From d9d8eac1c9da9957f4430a9e86f4a594ac07f030 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 29 Jun 2022 14:21:18 +0100 Subject: [PATCH 4136/9987] Updated to foss-2022a as suggested which also solved the problem with setuptools. Thus reverted back to original EC --- ...11.2.0.eb => cppy-1.2.1-GCCcore-11.3.0.eb} | 21 +++++++++---------- 1 file changed, 10 insertions(+), 11 deletions(-) rename easybuild/easyconfigs/c/cppy/{cppy-1.2.1-GCCcore-11.2.0.eb => cppy-1.2.1-GCCcore-11.3.0.eb} (52%) diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.3.0.eb similarity index 52% rename from easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.3.0.eb index 14e7ee67f28..1816a938378 100644 --- a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-11.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'cppy' version = '1.2.1' @@ -9,21 +9,20 @@ Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations.""" -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -dependencies = [('Python', '3.9.6')] +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -use_pip = True +builddependencies = [('binutils', '2.38')] -exts_list = [ - ('setuptools', '62.6.0', { - 'checksums': ['990a4f7861b31532871ab72331e755b5f14efbe52d336ea7f6118144dd478741'], - }), - (name, version, { - 'checksums': ['83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'], - }), +dependencies = [ + ('Python', '3.10.4'), ] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'] + +download_dep_fail = True sanity_pip_check = True +use_pip = True moduleclass = 'tools' From 7ec587e1f60f28b9e5a987ff28bc9619a4f58be3 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 29 Jun 2022 15:08:11 +0100 Subject: [PATCH 4137/9987] adding easyconfigs: Tkinter-3.10.4-GCCcore-11.3.0.eb --- .../Tkinter/Tkinter-3.10.4-GCCcore-11.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..cc05eefb9d4 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.4-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +name = 'Tkinter' +version = '3.10.4' + +homepage = 'https://python.org/' +description = "Tkinter module, built with the Python buildsystem" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['f3bcc65b1d5f1dc78675c746c98fcee823c038168fc629c5935b044d0911ad28'] + +builddependencies = [ + ('binutils', '2.38'), + ('libffi', '3.4.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Tk', '8.6.12'), + ('zlib', '1.2.12'), +] + +moduleclass = 'lang' From a05cc8d469f93c2041ce1f0d812845d9f1584c62 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 29 Jun 2022 20:31:11 +0100 Subject: [PATCH 4138/9987] Update easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-11.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-11.3.0.eb index c1778c26757..76b697e431a 100644 --- a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['include/json/json.h', 'lib/libjsoncpp.so'], + 'files': ['include/json/json.h', 'lib/libjsoncpp.%s' % SHLIB_EXT], 'dirs': [], } From 76420627252afd7a3376f2210e00d4737fcfccbf Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 30 Jun 2022 09:33:44 +0100 Subject: [PATCH 4139/9987] adding easyconfigs: Qhull-2020.2-GCCcore-11.3.0.eb --- .../q/Qhull/Qhull-2020.2-GCCcore-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..da692d927dd --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' From db7ed5dde49a61004bcb0af44060190ef47e7793 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 30 Jun 2022 10:37:50 +0200 Subject: [PATCH 4140/9987] adding easyconfigs: lpsolve-5.5.2.11-GCC-10.3.0.eb --- .../l/lpsolve/lpsolve-5.5.2.11-GCC-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-10.3.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-10.3.0.eb new file mode 100644 index 00000000000..98f6a9defb2 --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.11' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f'] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' From 98fffed3c457f1979f78c5623dca86438cb03139 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 30 Jun 2022 11:53:29 +0100 Subject: [PATCH 4141/9987] adding easyconfigs: ELPA-2021.11.001-foss-2022a.eb, ELPA-2021.11.001-intel-2022a.eb, libxc-5.2.3-GCC-11.3.0.eb, libxc-5.2.3-intel-compilers-2022.1.0.eb, QuantumESPRESSO-7.1-foss-2022a.eb --- .../e/ELPA/ELPA-2021.11.001-foss-2022a.eb | 43 +++++++++++++++++ .../e/ELPA/ELPA-2021.11.001-intel-2022a.eb | 47 +++++++++++++++++++ .../l/libxc/libxc-5.2.3-GCC-11.3.0.eb | 45 ++++++++++++++++++ .../libxc-5.2.3-intel-compilers-2022.1.0.eb | 45 ++++++++++++++++++ .../QuantumESPRESSO-7.1-foss-2022a.eb | 44 +++++++++++++++++ 5 files changed, 224 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2022a.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022a.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2022a.eb new file mode 100644 index 00000000000..16e1636489b --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2022a.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2021.11.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + 'e61048393a5e5f460858a11b216547fa3f434dd620c478cb20a52ebf543260f1', # elpa-new_release_2021.11.001.tar.gz + # ELPA-2021.11.001_fix_hardcoded_perl_path.patch + '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b', +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.4'), + ('Perl', '5.34.1'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022a.eb new file mode 100644 index 00000000000..688418e5474 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022a.eb @@ -0,0 +1,47 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2021.11.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + 'e61048393a5e5f460858a11b216547fa3f434dd620c478cb20a52ebf543260f1', # elpa-new_release_2021.11.001.tar.gz + # ELPA-2021.11.001_fix_hardcoded_perl_path.patch + '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b', +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.4'), + ('Perl', '5.34.1'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' +# If the build is running in a batch job, make sure Intel libmpi does +# not try to use Slurm to run the MPI_THREAD test code that ELPA's +# configure is running without "mpirun". +preconfigopts += 'unset SLURM_JOBID && unset SLURM_NODELIST && unset I_MPI_PMI_LIBRARY && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..e1d6b22c293 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '5.2.3' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['7b7a96d8eeb472c7b8cca7ac38eae27e0a8113ef44dae5359b0eb12592b4bcf2'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Perl', '5.34.1'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb new file mode 100644 index 00000000000..3968f139ee7 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '5.2.3' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['7b7a96d8eeb472c7b8cca7ac38eae27e0a8113ef44dae5359b0eb12592b4bcf2'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Perl', '5.34.1'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb new file mode 100644 index 00000000000..613f138e2a9 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb @@ -0,0 +1,44 @@ +name = 'QuantumESPRESSO' +version = '7.1' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', + 'https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'q-e-qe-%(version)s.tar.gz', + 'qe-gipaw-%(version)s.tar.gz', + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + 'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6', # q-e-qe-7.1.tar.gz + '486b60f38fad7363f81d346adc69de004692f50c9f6be59eee5152a717ca1513', # qe-gipaw-7.1.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.13.1'), + ('ELPA', '2021.11.001'), + ('libxc', '5.2.3'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' From b194a61467c158dbef02b4fabcae66f67ebbd00a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 30 Jun 2022 12:01:21 +0100 Subject: [PATCH 4142/9987] adding easyconfigs: HDF5-1.13.1-iimpi-2022a.eb --- .../h/HDF5/HDF5-1.13.1-iimpi-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-iimpi-2022a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-iimpi-2022a.eb new file mode 100644 index 00000000000..68b63efb0a2 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-iimpi-2022a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.13.1' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From d7c9bec83b6072b786a888f3b54e0beb3a02f9f5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 30 Jun 2022 12:10:40 +0100 Subject: [PATCH 4143/9987] add easyconfig for QE w/ intel toolchain --- .../QuantumESPRESSO-7.1-intel-2022a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb new file mode 100644 index 00000000000..087cd11f71e --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb @@ -0,0 +1,44 @@ +name = 'QuantumESPRESSO' +version = '7.1' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', + 'https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/', + 'https://github.com/wannier-developers/wannier90/archive/' +] +sources = [ + 'q-e-qe-%(version)s.tar.gz', + 'qe-gipaw-%(version)s.tar.gz', + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, +] +checksums = [ + 'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6', # q-e-qe-7.1.tar.gz + '486b60f38fad7363f81d346adc69de004692f50c9f6be59eee5152a717ca1513', # qe-gipaw-7.1.tar.gz + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz +] + +dependencies = [ + ('HDF5', '1.13.1'), + ('ELPA', '2021.11.001'), + ('libxc', '5.2.3'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' From c7163f0c2fbe1ff642784018ef0b1e74a59c9d58 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 30 Jun 2022 12:12:03 +0100 Subject: [PATCH 4144/9987] adding easyconfigs: Perl-5.34.1-GCCcore-11.3.0-minimal.eb --- .../Perl-5.34.1-GCCcore-11.3.0-minimal.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb new file mode 100644 index 00000000000..727f35d6cc4 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb @@ -0,0 +1,26 @@ +name = 'Perl' +version = '5.34.1' +versionsuffix = '-minimal' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +This is a minimal build without any modules. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['357951a491b0ba1ce3611263922feec78ccd581dddc24a446b033e25acf242a1'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +moduleclass = 'lang' From a5ac1f9e0fc40a0c9cc6302a9d3f95bc0136ea57 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 30 Jun 2022 14:05:47 +0200 Subject: [PATCH 4145/9987] adding easyconfigs: AUGUSTUS-3.4.0-foss-2021a.eb --- .../a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021a.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021a.eb new file mode 100644 index 00000000000..989ee23c7a5 --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021a.eb @@ -0,0 +1,64 @@ +# Updated by: Sebastien Moretti (SIB) + +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.4.0' + +homepage = 'https://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" +# software_license = Artistic + +toolchain = {'name': 'foss', 'version': '2021a'} + +# https://github.com/Gaius-Augustus/Augustus/archive +github_account = 'Gaius-Augustus' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['AUGUSTUS-%(version)s_fix-hardcoding.patch'] +checksums = [ + '2c06cf5953da5afdce1478fa10fcd3c280a3b050f1b2367bf3e731d7374d9bb8', # v3.4.0.tar.gz + 'e74023f28ee3e76590f4534d195c313b88b66a92ec779da184d30d056fc8e052', # AUGUSTUS-3.4.0_fix-hardcoding.patch +] + +builddependencies = [ + ('Python', '3.9.5'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.76.0'), + ('GSL', '2.7'), + ('SAMtools', '1.13'), + ('HTSlib', '1.12'), # also provides tabix + ('BCFtools', '1.12'), + ('lpsolve', '5.5.2.11'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('BamTools', '2.5.2'), + ('SQLite', '3.35.4'), +] + +skipsteps = ['configure'] + +# run "make clean" to avoid using binaries included with the source tarball +prebuildopts = "make clean && " + +buildopts = 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" LINK.cc="$CXX" ' +installopts = 'INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch', + 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} +sanity_check_commands = ['augustus --help'] + +modextrapaths = {'PATH': 'scripts'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} + +moduleclass = 'bio' From 18042c5467e8d4ead2e2162853f2123e9bebfccb Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 30 Jun 2022 14:10:07 +0200 Subject: [PATCH 4146/9987] adding easyconfigs: Beast-2.6.7-GCC-10.3.0.eb, beagle-lib-3.1.2-GCC-10.3.0.eb, pocl-1.8-GCC-10.3.0.eb --- .../b/Beast/Beast-2.6.7-GCC-10.3.0.eb | 39 ++++++++++++++++ .../beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb | 35 +++++++++++++++ .../easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb | 44 +++++++++++++++++++ 3 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb new file mode 100644 index 00000000000..09bab325f65 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'Tarball' + +name = 'Beast' +version = '2.6.7' + +homepage = 'http://beast2.org' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%(version)s.Linux.tgz'] +checksums = ['05dcc619c2e10163f2c1089ec66149f6e53ec5a0583cd2cb8ffdccbbdb1d8183'] + +dependencies = [ + # this is not mandatory but beagle-lib is recommended by developers + # beagle-lib will also load the required java dependency + # if you remove this you should add the java dependency + ('beagle-lib', '3.1.2'), +] + +builddependencies = [ + ('Autotools', '20210128'), + ('pkg-config', '0.29.2'), +] + +sanity_check_paths = { + 'files': ['bin/beast'], + 'dirs': [] +} + +sanity_check_commands = ["beast -help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb new file mode 100644 index 00000000000..d665b15fb9b --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'beagle-lib' +version = '3.1.2' + +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] + +builddependencies = [ + ('Autotools', '20210128'), +] + +dependencies = [ + ('Java', '11', '', True), + ('pkg-config', '0.29.2'), + ('pocl', '1.8'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--with-opencl=$EBROOTPOCL --with-cuda=$EBROOTCUDA " + +sanity_check_paths = { + 'files': ['include/libhmsbeagle-1/libhmsbeagle/%s' % x for x in ['beagle.h', 'platform.h']] + + ['lib/libhmsbeagle%s.%s' % (x, SHLIB_EXT) for x in ['-cpu', '-cpu-sse', '-jni', '']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb new file mode 100644 index 00000000000..4075c55b03b --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '1.8' + +homepage = 'https://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['pocl-%(version)s_fix-header-install.patch'] +checksums = [ + '0f63377ae1826e16e90038fc8e7f65029be4ff6f9b059f6907174b5c0d1f8ab2', # v1.8.tar.gz + '97dc45437ae7464bda9f13088720482804b8a19a4e71067196daa86af487222d', # pocl-1.8_fix-header-install.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Clang', '12.0.1'), + ('hwloc', '2.4.1'), + ('libtool', '2.4.6'), + ('libxml2', '2.9.10'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 28176b66e28aa7fd2a3b78a25e1e21df57eceb5f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 30 Jun 2022 15:20:21 +0200 Subject: [PATCH 4147/9987] Keep previous attribution + Add corresponding license entry --- easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021a.eb index 989ee23c7a5..cf9c1125f8b 100644 --- a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021a.eb @@ -1,3 +1,4 @@ +# Updated by: Pavel Grochal (INUITS) # Updated by: Sebastien Moretti (SIB) easyblock = 'ConfigureMake' @@ -7,7 +8,7 @@ version = '3.4.0' homepage = 'https://bioinf.uni-greifswald.de/augustus/' description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" -# software_license = Artistic +# software_license = 'LicenseArtisticv1' toolchain = {'name': 'foss', 'version': '2021a'} From 628df41142d31e32cc161ea7de65cd6648e06908 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 30 Jun 2022 15:46:35 +0100 Subject: [PATCH 4148/9987] fix source unpacking --- .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb | 5 ++++- .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb index 613f138e2a9..59e9cfb2840 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb @@ -17,7 +17,10 @@ source_urls = [ 'https://github.com/wannier-developers/wannier90/archive/' ] sources = [ - 'q-e-qe-%(version)s.tar.gz', + { + 'filename': 'q-e-qe-%(version)s.tar.gz', + 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + }, 'qe-gipaw-%(version)s.tar.gz', {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb index 087cd11f71e..95092eb4639 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb @@ -17,7 +17,10 @@ source_urls = [ 'https://github.com/wannier-developers/wannier90/archive/' ] sources = [ - 'q-e-qe-%(version)s.tar.gz', + { + 'filename': 'q-e-qe-%(version)s.tar.gz', + 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + }, 'qe-gipaw-%(version)s.tar.gz', {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, ] From 71d1af3515c7d5c1032c21a0cdaf86811f9eb7bb Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Thu, 30 Jun 2022 22:09:27 +0200 Subject: [PATCH 4149/9987] adding easyconfigs: mayavi-4.7.4-foss-2021b.eb --- .../m/mayavi/mayavi-4.7.4-foss-2021b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/m/mayavi/mayavi-4.7.4-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/mayavi/mayavi-4.7.4-foss-2021b.eb b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.4-foss-2021b.eb new file mode 100644 index 00000000000..9c4f7bf33c0 --- /dev/null +++ b/easybuild/easyconfigs/m/mayavi/mayavi-4.7.4-foss-2021b.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'mayavi' +version = '4.7.4' + +homepage = 'http://code.enthought.com/projects/mayavi/' +description = """The Mayavi scientific data 3-dimensional visualizer""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('VTK', '9.1.0'), + ('PyQt5', '5.15.4'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('configobj', '5.0.6', { + 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], + }), + ('traits', '6.3.2', { + 'checksums': ['4520ef4a675181f38be4a5bab1b1d5472691597fe2cfe4faf91023e89407e2c6'], + }), + ('pyface', '7.4.1', { + 'checksums': ['52dcf3679ca3e610a3ca7c4b9904a96c691688048db5d7e52af8e5019e47adb6'], + }), + ('traitsui', '7.4.0', { + 'checksums': ['25335affee2342d47e35c25df5e7785d22a533584fe1be0943ccba45dc1ae589'], + }), + ('apptools', '5.1.0', { + 'checksums': ['d093de314f04485a4c108ba3806c514ae3ba39a3210277fef297521634a3a58b'], + }), + ('envisage', '6.0.1', { + 'checksums': ['8864c29aa344f7ac26eeb94788798f2d0cc791dcf95c632da8d79ebc580e114c'], + }), + (name, version, { + 'preinstallopts': "export QT_QPA_PLATFORM=offscreen && ", + 'source_tmpl': 'mayavi-%(version)s.tar.gz', + 'checksums': ['ec50e7ec6afb0f9224ad1863d104a0d1ded6c8deb13e720652007aaca2303332'], + }), +] + +sanity_check_paths = { + 'files': ['bin/mayavi2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' From 97f75b066b0dfb8c8947e96687ef4bbefe3c5320 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 1 Jul 2022 08:14:37 +0100 Subject: [PATCH 4150/9987] adding easyconfigs: jax-0.3.14-foss-2022a-CUDA-11.7.0.eb, pytest-xdist-2.5.0-GCCcore-11.3.0.eb and patches: jax-0.3.14_relax-test-tolerances.patch --- .../jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb | 126 ++++++++++++++++++ .../jax-0.3.14_relax-test-tolerances.patch | 20 +++ .../pytest-xdist-2.5.0-GCCcore-11.3.0.eb | 62 +++++++++ 3 files changed, 208 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.14_relax-test-tolerances.patch create mode 100644 easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..47d57b6a04c --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,126 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.14' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.36.0', '-nodocs'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('cuDNN', '8.4.1.50', versionsuffix, True), + ('NCCL', '2.12.12', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in jaxlib-*/WORKSPACE +local_tf_commit = 'd250676d7776cfbca38e8690b75e1376afecf58d' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.1.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['3aa39f898329c2156ff525dfa69ce709e42d77aab18bf4917719d6f260aa6a08'], + }), + ('jaxlib', '0.3.14', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + 'jaxlib-0.1.70_add-bazel-args-to-shutdown.patch', + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.3.14.tar.gz + '6d6b660cb915b3fbf151dc67a471623e5f83b6a66493b9e438273d290a43b40f', + # tensorflow-d250676d7776cfbca38e8690b75e1376afecf58d.tar.gz + 'a99890443df024e52d9c7b075e9916250c6cc6b778d62c384b7dcd1903d8f4f1', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # jaxlib-0.1.70_add-bazel-args-to-shutdown.patch + 'c0ea6abd7827d3c37bdd60c30c7b0613fc86b91274c6a1a4cf13a3c7f9ce7631', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '0.6.0', { + 'checksums': ['6677241051835d0db11c4947bcad938f57b51ea102290624f892f1e4e51b70e5'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': [ + 'jax-0.3.9_relax-test-tolerance.patch', + 'jax-0.3.14_relax-test-tolerances.patch', + ], + 'checksums': [ + '225624375094d2067bc3af5abe0a73c6b530916edc1422c30a451d3f3e1b5a82', # jax-v0.3.14.tar.gz + '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d', # jax-0.3.9_relax-test-tolerance.patch + # jax-0.3.14_relax-test-tolerances.patch + 'c41061d00e431076a709820f0b3df19b9ef114558dfc2a75a361303c3fc8312e', + ], + # deliberately not testing in parallel, as that results in (additional) failing tests; + # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, + # see https://github.com/google/jax/issues/7323 and + # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; + # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; + # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + "JAX_ENABLE_X64=true pytest -vv tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.14_relax-test-tolerances.patch b/easybuild/easyconfigs/j/jax/jax-0.3.14_relax-test-tolerances.patch new file mode 100644 index 00000000000..f79814fedb1 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.14_relax-test-tolerances.patch @@ -0,0 +1,20 @@ +Relax the tolerance of tests that fail by a small amount +Patch by Simon Branford (University of Birmingham) +--- tests/scipy_optimize_test.py.orig 2022-06-30 18:36:30.056986000 +0100 ++++ tests/scipy_optimize_test.py 2022-06-30 18:36:21.840235000 +0100 +@@ -90,9 +90,14 @@ + ) + return result.x + ++ if func.__name__ == 'eggholder': ++ atol = 4e-5 ++ else: ++ atol = 2e-5 ++ + jax_res = min_op(x0) + scipy_res = scipy.optimize.minimize(func(np), x0, method='BFGS').x +- self.assertAllClose(scipy_res, jax_res, atol=2e-5, check_dtypes=False) ++ self.assertAllClose(scipy_res, jax_res, atol=atol, check_dtypes=False) + + def test_fixes4594(self): + n = 2 diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9d96c47ef05 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-2.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'pytest-xdist' +version = '2.5.0' + +homepage = 'https://github.com/pytest-dev/pytest-xdist' +description = """xdist: pytest distributed testing plugin + +The pytest-xdist plugin extends pytest with some unique test execution modes: + + * test run parallelization: if you have multiple CPUs or hosts you + can use those for a combined test run. This allows to speed up + development or to use special resources of remote machines. + + * --looponfail: run your tests repeatedly in a subprocess. After + each run pytest waits until a file in your project changes and + then re-runs the previously failing tests. This is repeated + until all tests pass after which again a full run is + performed. + + * Multi-Platform coverage: you can specify different Python + interpreters or different platforms and run tests in parallel on + all of them. + +Before running tests remotely, pytest efficiently “rsyncs” your +program source code to the remote place. All test results are reported +back and displayed to your local terminal. You may specify different +Python versions and interpreters.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('apipkg', '1.5', { + 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], + }), + ('execnet', '1.9.0', { + 'checksums': ['8f694f3ba9cc92cab508b152dcfe322153975c29bda272e2fd7f3f00f36e47c5'], + }), + ('pytest-forked', '1.4.0', { + 'checksums': ['8b67587c8f98cbbadfdd804539ed5455b6ed03802203485dd2f53c1422d7440e'], + }), + (name, version, { + 'modulename': 'xdist', + 'checksums': ['4580deca3ff04ddb2ac53eba39d76cb5dd5edeac050cb6fbc768b0dd712b4edf'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 10d28a81e32aec06b7a1325a897c774b800d8512 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 1 Jul 2022 09:55:14 +0200 Subject: [PATCH 4151/9987] adding easyconfigs: gdbm-1.21-GCCcore-10.2.0.eb --- .../g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b28c2fd68d0 --- /dev/null +++ b/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'gdbm' +version = '1.21' + +homepage = "https://www.gnu.org.ua/software/gdbm/gdbm.html" +description = """GNU dbm (or GDBM, for short) is a library of database functions that use extensible hashing + and work similar to the standard UNIX dbm. + These routines are provided to a programmer needing to create and manipulate a hashed database.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/gdbm'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['b0b7dbdefd798de7ddccdd8edf6693a30494f7789777838042991ef107339cc2'] + +builddependencies = [ + ('binutils', '2.35') +] + +dependencies = [ + ('libreadline', '8.0') +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gdbm_dump', 'gdbm_load', 'gdbmtool']] + + ['include/gdbm.h', 'lib/libgdbm.%s' % SHLIB_EXT], + 'dirs': ['share/man'] +} + +moduleclass = "lib" From 6f567c4d362bd963f3809f2191384b3daba829a7 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 1 Jul 2022 09:50:19 +0100 Subject: [PATCH 4152/9987] adding easyconfigs: Pillow-9.1.1-GCCcore-11.3.0.eb --- .../p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..137475682e6 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '9.1.1' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7502539939b53d7565f3d11d87c78e7ec900d3c72945d4ee0e2f250d598309a0'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.12.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From ef6c436b2bdc56b2710e4171c65c6a697472e874 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 1 Jul 2022 10:00:23 +0100 Subject: [PATCH 4153/9987] Switched to pkgconf as suggested --- easybuild/easyconfigs/x/xtb/xtb-6.5.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.5.0-foss-2021b.eb b/easybuild/easyconfigs/x/xtb/xtb-6.5.0-foss-2021b.eb index ff607803c18..69bff689c4e 100644 --- a/easybuild/easyconfigs/x/xtb/xtb-6.5.0-foss-2021b.eb +++ b/easybuild/easyconfigs/x/xtb/xtb-6.5.0-foss-2021b.eb @@ -21,7 +21,7 @@ checksums = ['0b39f6e87ce07abcb0884cda5d3370601b6332ad72c8213e87ffa74ae28895fb'] builddependencies = [ ('Meson', '0.58.2'), ('Ninja', '1.10.2'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ] configopts = "-Dla_backend='custom' " From a1a26486875628fbdfbedaf3b3585aa57e73bebc Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Fri, 1 Jul 2022 12:53:54 +0200 Subject: [PATCH 4154/9987] adding easyconfigs: MUMmer-4.0.0rc1-GCCcore-11.2.0.eb --- .../MUMmer/MUMmer-4.0.0rc1-GCCcore-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..609e244fec2 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'MUMmer' +version = '4.0.0rc1' + +homepage = 'http://mummer.sourceforge.net/' + +description = """ + MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['85006adb2d6539c2f738c3e3bb14b58bb6f62cd6c6ca5ede884a87ae76e07d1d'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', + 'bin/repeat-match', 'bin/show-aligns', 'bin/show-coords', + 'bin/show-tiling', 'bin/show-snps', 'bin/show-diff', 'bin/exact-tandems', + 'bin/mummerplot', 'bin/promer', 'bin/dnadiff', + ], + 'dirs': ['include', 'lib', 'libexec'], +} + +moduleclass = 'bio' From c2b337fed6fa543fb7b29830a583653bd5f4872b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 1 Jul 2022 15:46:43 +0200 Subject: [PATCH 4155/9987] adding easyconfigs: hifiasm-0.16.1-GCCcore-10.3.0.eb --- .../hifiasm/hifiasm-0.16.1-GCCcore-10.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/h/hifiasm/hifiasm-0.16.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/h/hifiasm/hifiasm-0.16.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.16.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..56ac4c7cf62 --- /dev/null +++ b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.16.1-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) +# Update: Sebastien Moretti (SIB) + +easyblock = 'MakeCp' + +name = 'hifiasm' +version = '0.16.1' + +homepage = 'https://github.com/chhylp123/hifiasm' +description = """Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.""" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'chhylp123' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['674b23cf274adfc0f65c2656e9dc24354240d93c397e1d3b88fdd7f673942639'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="$CC" CXX="$CXX" CPPFLAGS="$CPPFLAGS"' + +files_to_copy = [ + ([name], 'bin'), + (['*.h'], 'include/hifiasm'), + 'LICENSE', 'README.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} +sanity_check_commands = ["%(name)s -h"] + +moduleclass = 'bio' From 79099a809f885c3e2f53cbfd736c20f970d3d0c9 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 1 Jul 2022 16:19:40 +0100 Subject: [PATCH 4156/9987] adding easyconfigs: jemalloc-5.3.0-GCCcore-11.3.0.eb --- .../jemalloc/jemalloc-5.3.0-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..217d5554931 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.3.0' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ef6f74fd45e95ee4ef7f9e19ebe5b075ca6b7fbe0140612b2a161abafb7ee179'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' From b969fb609c74dae44735e2bab4da5e8510f2b1a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Jul 2022 12:56:39 +0200 Subject: [PATCH 4157/9987] add geeM extension to R v4.2.0 --- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index bc956988ce7..661ca51251b 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -3355,6 +3355,9 @@ exts_list = [ ('rtdists', '0.11-5', { 'checksums': ['97cf2ea758aa02b1dfaeef5032c6e50570777552aa771ed9a86df048b7871eed'], }), + ('geeM', '0.10.1', { + 'checksums': ['fe76a32981b55835095041e777d1cf2e9ce43edb8d9488db56279f7cb6f43fe5'], + }), ] moduleclass = 'lang' From 798ad2670d6cff9be38f7b759e82cdf3f22102fa Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 4 Jul 2022 16:07:09 +0200 Subject: [PATCH 4158/9987] adding easyconfigs: MaSuRCA-4.0.9-foss-2021a-Perl-5.32.1.eb --- .../MaSuRCA-4.0.9-foss-2021a-Perl-5.32.1.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-4.0.9-foss-2021a-Perl-5.32.1.eb diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-4.0.9-foss-2021a-Perl-5.32.1.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-4.0.9-foss-2021a-Perl-5.32.1.eb new file mode 100644 index 00000000000..ceec62db825 --- /dev/null +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-4.0.9-foss-2021a-Perl-5.32.1.eb @@ -0,0 +1,71 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2017 University of Geneva +# Authors:: Yann Sagon +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'MaSuRCA' +version = '4.0.9' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://www.genome.umd.edu/masurca.html' +software_license = 'LicenseGPLv3' + +description = '''MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph + and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing + only short reads from Illumina sequencing or a mixture of short reads and long reads + (Sanger, 454, Pacbio and Nanopore).''' + +toolchain = {'name': 'foss', 'version': '2021a'} + +# need a temporary url to download it. Do it manually here: +# http://www.genome.umd.edu/masurca_form.html + +source_urls = ['https://github.com/alekseyzimin/masurca/releases/download/v%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['a31c2f786452f207c0b0b20e646b6c85b7357dcfd522b697c1009d902d3ed4cf'] + +builddependencies = [('patchelf', '0.12')] + +dependencies = [ + ('libreadline', '8.1'), + ('Tcl', '8.6.11'), + ('Boost', '1.76.0'), + ('zlib', '1.2.11'), + ('Perl', '5.32.1'), + ('bzip2', '1.0.8'), +] + +buildopts = "install-special" +start_dir = "global-1" + +postinstallcmds = [ + # fix location of 'bin' in install prefix in runCA and runCA-dedupe scripts + # escaping single quotes within single quotes is tricky, so we use $'...' to use ANSI C-like escaping + "sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA", + "sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA-dedupe", + # fix hardcoded path in masurca script, just point back to 'bin' subdirectory instead + "sed -i 's@../CA8/Linux-amd64/bin@../bin@g' %(installdir)s/bin/masurca", + # commands to install built-in version of Flye + "cd ../Flye && make && cp -a ../Flye %(installdir)s", + # fix missing RPATH + "patchelf --force-rpath --set-rpath '$ORIGIN' %(installdir)s/bin/falcon_sense", +] + +sanity_check_paths = { + 'files': ['bin/masurca', 'Flye/bin/flye'], + 'dirs': ['include', 'lib'], +} + +sanity_check_commands = [ + "masurca --help", + "runCA --help", +] + +moduleclass = 'bio' From 952c9170469e8a50f95f33980c28d14ac06f0567 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 4 Jul 2022 16:11:56 +0200 Subject: [PATCH 4159/9987] adding easyconfigs: MetaEuk-4-GCC-10.3.0.eb --- .../m/MetaEuk/MetaEuk-4-GCC-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaEuk/MetaEuk-4-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MetaEuk/MetaEuk-4-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-4-GCC-10.3.0.eb new file mode 100644 index 00000000000..caf30a198fd --- /dev/null +++ b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-4-GCC-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MetaEuk' +version = '4' +local_commit = 'a0f584d' + +homepage = 'https://metaeuk.soedinglab.org' +description = """MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic + metagenomic contigs.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/soedinglab/%(namelower)s/archive'] +sources = ['%%(version)s-%s.tar.gz' % local_commit] +checksums = ['d64eea5244bd1c73a8c229949b2e833ba77e530ea321d5bb1bdea13b759e6efd'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/metaeuk'], + 'dirs': [], +} + +sanity_check_commands = ["metaeuk --help"] + +moduleclass = 'bio' From badf74eb7af2d37f0769faa37e1c87435ff1b7a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 Jul 2022 10:27:50 +0200 Subject: [PATCH 4160/9987] adding easyconfigs: Bracken-2.7-GCCcore-11.2.0.eb --- .../b/Bracken/Bracken-2.7-GCCcore-11.2.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bracken/Bracken-2.7-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Bracken/Bracken-2.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bracken/Bracken-2.7-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7d49a28cded --- /dev/null +++ b/easybuild/easyconfigs/b/Bracken/Bracken-2.7-GCCcore-11.2.0.eb @@ -0,0 +1,55 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'Bracken' +version = '2.7' + +homepage = 'https://ccb.jhu.edu/software/bracken/' +description = """Bracken (Bayesian Reestimation of Abundance with KrakEN) +is a highly accurate statistical method that computes the abundance of +species in DNA sequences from a metagenomics sample. Braken uses the +taxonomy labels assigned by Kraken, a highly accurate metagenomics +classification algorithm, to estimate the number of reads originating +from each species present in a sample. Kraken classifies reads to the +best matching location in the taxonomic tree, but does not estimate +abundances of species. We use the Kraken database itself to derive +probabilities that describe how much sequence from each genome is +identical to other genomes in the database, and combine this information +with the assignments for a particular sample to estimate abundance at +the species level, the genus level, or above. Combined with the Kraken +classifier, Bracken produces accurate species- and genus-level abundance +estimates even when a sample contains two or more near-identical species. + +NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the +default kmer length is different depending on the version of Kraken used. +If you use Kraken 1 defaults, specify 31 as the kmer length. If you use +Kraken 2 defaults, specify 35 as the kmer length.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/jenniferlu717/Bracken/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1795ecd9f9e5582f37549795ba68854780936110a2f6f285c3e626d448cd1532'] + +builddependencies = [('binutils', '2.37')] + +# no need to build in parallel +parallel = 1 + +start_dir = 'src' + +files_to_copy = ['bracken', 'bracken-build', 'src', 'analysis_scripts', 'sample_data'] + +sanity_check_paths = { + 'files': ['bracken', 'bracken-build'], + 'dirs': ['analysis_scripts', 'sample_data', 'src'], +} + +sanity_check_commands = ['bracken --help', 'bracken --version'] + +modextrapaths = {'PATH': '.'} + +moduleclass = 'bio' From 387ad47802fbfa21167d87cf8b90506d20f8e71c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 5 Jul 2022 11:12:03 +0200 Subject: [PATCH 4161/9987] adding easyconfigs: ReFrame-3.12.0.eb --- .../easyconfigs/r/ReFrame/ReFrame-3.12.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb new file mode 100644 index 00000000000..d7a99ed1584 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.12.0' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + ('setuptools', '60.0.3', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['989ab2d3e632ba23358b8d43950bd46babde5bbb1516760dc5f5ccfe7accdd45'], + }), + ('reframe', version, { + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && ./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['425cc546e24edd5b2dbfcdcb61dbbf723ca1a2a2977948e359e893514f5eb10f'], + }), +] + +postinstallcmds = [ + "cp -a hpctestlib tools tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'hpctestlib', 'lib', 'tools', 'tutorials'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 598dcfc56d3f78839a391a4409140174137fa180 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 5 Jul 2022 12:22:42 +0200 Subject: [PATCH 4162/9987] adding easyconfigs: IGMPlot-2.6.9b-GCC-11.2.0.eb --- .../i/IGMPlot/IGMPlot-2.6.9b-GCC-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.6.9b-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.6.9b-GCC-11.2.0.eb b/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.6.9b-GCC-11.2.0.eb new file mode 100644 index 00000000000..dea32d51f80 --- /dev/null +++ b/easybuild/easyconfigs/i/IGMPlot/IGMPlot-2.6.9b-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'IGMPlot' +version = '2.6.9b' + +homepage = 'http://igmplot.univ-reims.fr' +description = """IGMPlot is a free open-source program developed to identify molecular interactions and + prepare data to build 2D and 3D representations of them in the molecular environment.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['http://igmplot.univ-reims.fr/download/'] +sources = ['IGMPLOT-%(version)s.tbz2'] +checksums = ['a7b57ecd03e6b8b1dbaab9231b6d89df9e74b350060b626bd495e1dd41ffe407'] + +start_dir = 'source' + +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS -I src/include" ' + +files_to_copy = [(['source/IGMPLOT'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IGMPLOT'], + 'dirs': [], +} + +sanity_check_commands = ["cd %(builddir)s/IGMPLOT-%(version)s/samples/01_example/test01 && IGMPLOT param.igm"] + +moduleclass = 'chem' From fabb5092f450312eda5da2d2b670e872287cab1b Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 5 Jul 2022 11:22:49 +0100 Subject: [PATCH 4163/9987] add M4 build dependency to QuantumESPRESSO 7.1 Co-authored-by: SebastianAchilles --- .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb | 2 ++ .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb index 59e9cfb2840..0736580b3ec 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb @@ -30,6 +30,8 @@ checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz ] +builddependencies = [('M4', '1.4.19')] + dependencies = [ ('HDF5', '1.13.1'), ('ELPA', '2021.11.001'), diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb index 95092eb4639..cde0d054be4 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb @@ -30,6 +30,8 @@ checksums = [ '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz ] +builddependencies = [('M4', '1.4.19')] + dependencies = [ ('HDF5', '1.13.1'), ('ELPA', '2021.11.001'), From 6430a9f614e6d9d3b5aceea9b23af43053d27941 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 5 Jul 2022 12:38:16 +0200 Subject: [PATCH 4164/9987] adding easyconfigs: Shapely-1.8.2-foss-2021b.eb, Fiona-1.8.21-foss-2021b.eb, geopandas-0.11.0-foss-2021b.eb --- .../f/Fiona/Fiona-1.8.21-foss-2021b.eb | 48 +++++++++++++++++++ .../geopandas/geopandas-0.11.0-foss-2021b.eb | 38 +++++++++++++++ .../s/Shapely/Shapely-1.8.2-foss-2021b.eb | 30 ++++++++++++ 3 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/geopandas/geopandas-0.11.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2021b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2021b.eb new file mode 100644 index 00000000000..5e0371f6538 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2021b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.8.21' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('GDAL', '3.3.2'), + ('Shapely', '1.8.2'), # optional for 'calc' extras +] + +use_pip = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'checksums': ['3a0edca2a7a070db405d71187214a43d2333a57b4097544a3fcc282066a58bfc'], + 'use_pip_extras': 'calc', + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["fio --help"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.11.0-foss-2021b.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.11.0-foss-2021b.eb new file mode 100644 index 00000000000..976a82d9f3d --- /dev/null +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.11.0-foss-2021b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'geopandas' +version = '0.11.0' + +homepage = 'https://github.com/geopandas/geopandas' +description = """GeoPandas is a project to add support for geographic data to pandas objects. +It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series +and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and +perform geometric operations.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Shapely', '1.8.2'), + ('Fiona', '1.8.21'), + ('matplotlib', '3.4.3'), + ('networkx', '2.6.3'), # needed by mapclassify + ('pyproj', '3.3.1'), + ('scikit-learn', '1.0.1'), # needed by mapclassify +] + +use_pip = True + +exts_list = [ + ('mapclassify', '2.4.3', { + 'checksums': ['51b81e1f1ee7f64a4ca1e9f61f01216c364a3f086a48b1be38eb057199cb19bf'], + }), + (name, version, { + 'checksums': ['562fe7dc19a6e0f61532d654c4752f7bf46e0714990c5844fe3de3f9c99cb873'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2021b.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2021b.eb new file mode 100644 index 00000000000..f3498b54092 --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2021b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '1.8.2' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['572af9d5006fd5e3213e37ee548912b0341fb26724d6dc8a4e3950c10197ebb6'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # needed by shapely.vectorized + ('GEOS', '3.9.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'import shapely'", + "python -c 'import shapely.vectorized'", +] + +moduleclass = 'math' From 7b6017a00d8e2f4b685c17a3499cf81899b87711 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 5 Jul 2022 12:39:49 +0200 Subject: [PATCH 4165/9987] adding easyconfigs: makedepend-1.0.6-GCCcore-10.2.0.eb --- .../makedepend-1.0.6-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..3295f02cc8a --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.6-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.6' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['845f6708fc850bf53f5b1d0fb4352c4feab3949f140b26f71b22faba354c3365'] + +builddependencies = [ + ('binutils', '2.35'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' From bba00c116d090547fac7d12c03ed928b32bfb49d Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 5 Jul 2022 12:42:29 +0200 Subject: [PATCH 4166/9987] adding easyconfigs: g2lib-3.2.0-GCCcore-10.2.0.eb --- .../g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9f965a3a424 --- /dev/null +++ b/easybuild/easyconfigs/g/g2lib/g2lib-3.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +name = 'g2lib' +version = '3.2.0' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder and search/indexing routines.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +patches = [ + '%(name)s-%(version)s_makefile.patch', +] +checksums = [ + '9d3866de32e13e80798bfb08dbbea9223f32cec3fce3c57b6838e76f27d5a1d3', # g2lib-3.2.0.tar + 'e434394a6ec8bd68dbd57e3fdb44c47372b07380e362ed955bb038b78dd81812', # g2lib-3.2.0_makefile.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('JasPer', '2.0.24'), + ('libpng', '1.6.37'), +] + +buildopts = 'CFLAGS="$CFLAGS -DLINUXG95 -D__64BIT__" FC=$FC CC=$CC ' +buildopts += 'FFLAGS="$FFLAGS -fno-range-check -fallow-invalid-boz -fallow-argument-mismatch -I."' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' From c7dbb04fb162ff67944a7640ab5f66434c6b269e Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 5 Jul 2022 12:44:12 +0200 Subject: [PATCH 4167/9987] adding easyconfigs: g2clib-1.6.3-GCCcore-10.2.0.eb --- .../g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..1ccb3cd0734 --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.6.3-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +name = 'g2clib' +version = '1.6.3' + +homepage = 'https://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['83e4f2061b3d4a8bd431ba860dda8c5cf103b25f42d265b7b724b9acafad177c'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('JasPer', '2.0.24'), + ('libpng', '1.6.37'), +] + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'data' From 1c5b016b119792d59c930c56359f6e39feabd95a Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 5 Jul 2022 12:46:16 +0200 Subject: [PATCH 4168/9987] adding easyconfigs: NCL-6.6.2-foss-2020b.eb --- .../easyconfigs/n/NCL/NCL-6.6.2-foss-2020b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2020b.eb b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2020b.eb new file mode 100644 index 00000000000..898a5271a13 --- /dev/null +++ b/easybuild/easyconfigs/n/NCL/NCL-6.6.2-foss-2020b.eb @@ -0,0 +1,57 @@ +name = 'NCL' +version = '6.6.2' + +homepage = 'https://www.ncl.ucar.edu' +description = "NCL is an interpreted language designed specifically for scientific data analysis and visualization." + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = { + 'cstd': 'c99', 'openmp': True, 'pic': True, + 'extra_fflags': '-fallow-invalid-boz -fallow-argument-mismatch', +} + +source_urls = ['https://github.com/NCAR/ncl/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'NCL-6.4.0_fix-types.patch', + 'NCL-6.6.2_header_and_operands.patch', + 'NCL-6.6.2_multiple_definitions.patch', +] +checksums = [ + 'cad4ee47fbb744269146e64298f9efa206bc03e7b86671e9729d8986bb4bc30e', # 6.6.2.tar.gz + 'f6dfaf95e5de9045745e122cb44f9c035f81fab92f5892991ddfe93945891c8f', # NCL-6.4.0_fix-types.patch + '5cb62d9a37de8af485b94487692f7e739ca5eb103a6b447e0290a68a6c094808', # NCL-6.6.2_header_and_operands.patch + 'e21503dc46fe6fd360ba7ca4897aa93bf9ec2961bc48634ca46de582710448f7', # NCL-6.6.2_multiple_definitions.patch +] + +builddependencies = [ + ('makedepend', '1.0.6'), + ('Bison', '3.7.1'), + ('flex', '2.6.4'), +] +dependencies = [ + ('cURL', '7.72.0'), + ('JasPer', '2.0.24'), + ('g2lib', '3.2.0'), + ('g2clib', '1.6.3'), + ('HDF', '4.2.15'), + ('HDF5', '1.10.7'), + ('HDF-EOS', '2.20'), + ('HDF-EOS5', '1.16'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('Szip', '2.1.1'), + ('freetype', '2.10.3'), + ('zlib', '1.2.11'), + ('GDAL', '3.2.1'), + ('UDUNITS', '2.2.26'), + ('ESMF', '8.0.1'), + ('bzip2', '1.0.8'), + ('cairo', '1.16.0'), + ('libiconv', '1.16'), + ('GSL', '2.6'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), +] + +moduleclass = 'data' From 235ccb364ab5a7f1fd30858aabe082dd8ed53ee7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 5 Jul 2022 12:47:19 +0200 Subject: [PATCH 4169/9987] adding easyconfigs: regionmask-0.9.0-foss-2021b-Python-3.9.6.eb --- ...egionmask-0.9.0-foss-2021b-Python-3.9.6.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b-Python-3.9.6.eb new file mode 100644 index 00000000000..cb012d8f201 --- /dev/null +++ b/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b-Python-3.9.6.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'regionmask' +version = '0.9.0' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'https://regionmask.readthedocs.io' +description = """regionmask creates masks of geographical regions. It determines to which +geographic region each grid point belongs.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('geopandas', '0.11.0'), + ('rasterio', '1.2.10'), + ('Shapely', '1.8.2'), + ('xarray', '0.20.1'), +] + +use_pip = True + +exts_list = [ + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + (name, version, { + 'checksums': ['8da1b6359756241867c4e967097810ef86b9dff4e06d11ca648fe1d607e9cf14'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 3cb8fec4354873d16578f876acf44995983c1c85 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 5 Jul 2022 12:54:35 +0200 Subject: [PATCH 4170/9987] Fix long line. --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb index d7a99ed1584..99e8c56629b 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb @@ -32,7 +32,9 @@ exts_list = [ 'checksums': ['989ab2d3e632ba23358b8d43950bd46babde5bbb1516760dc5f5ccfe7accdd45'], }), ('reframe', version, { - 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && ./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], 'checksums': ['425cc546e24edd5b2dbfcdcb61dbbf723ca1a2a2977948e359e893514f5eb10f'], From e9bfc0074652b48b1e3ac9718d8b68a5a866f62a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 5 Jul 2022 12:57:48 +0200 Subject: [PATCH 4171/9987] update dependency of imgaug-0.4.0-foss-2021b.eb on Shapely to v1.8.2 --- easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b.eb index a90a2300914..647d4b46efe 100644 --- a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b.eb @@ -16,7 +16,7 @@ dependencies = [ ('matplotlib', '3.4.3'), ('scikit-image', '0.19.1'), ('OpenCV', '4.5.5', '-contrib'), - ('Shapely', '1.8.1.post1'), + ('Shapely', '1.8.2'), ('imageio', '2.13.5'), ] From 120a5bcc3d80ed166508c0814912518a2fd7379e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 5 Jul 2022 15:07:37 +0200 Subject: [PATCH 4172/9987] Update to MetaEuk v5 --- .../{MetaEuk-4-GCC-10.3.0.eb => MetaEuk-5-GCC-10.3.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/m/MetaEuk/{MetaEuk-4-GCC-10.3.0.eb => MetaEuk-5-GCC-10.3.0.eb} (84%) diff --git a/easybuild/easyconfigs/m/MetaEuk/MetaEuk-4-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-5-GCC-10.3.0.eb similarity index 84% rename from easybuild/easyconfigs/m/MetaEuk/MetaEuk-4-GCC-10.3.0.eb rename to easybuild/easyconfigs/m/MetaEuk/MetaEuk-5-GCC-10.3.0.eb index caf30a198fd..81c324e51b9 100644 --- a/easybuild/easyconfigs/m/MetaEuk/MetaEuk-4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-5-GCC-10.3.0.eb @@ -1,8 +1,8 @@ easyblock = 'CMakeMake' name = 'MetaEuk' -version = '4' -local_commit = 'a0f584d' +version = '5' +local_commit = '34c21f2' homepage = 'https://metaeuk.soedinglab.org' description = """MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic @@ -12,7 +12,7 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://github.com/soedinglab/%(namelower)s/archive'] sources = ['%%(version)s-%s.tar.gz' % local_commit] -checksums = ['d64eea5244bd1c73a8c229949b2e833ba77e530ea321d5bb1bdea13b759e6efd'] +checksums = ['560bc174d85c82ee1965b38131a7017f674f341fb73d48e35884fbceda827966'] builddependencies = [('CMake', '3.20.1')] From 8e3b43f8fc93c0b384d1caac07287126ac4ba8c6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 5 Jul 2022 15:21:09 +0200 Subject: [PATCH 4173/9987] remove versionsuffix from regionmask-0.9.0-foss-2021b.eb --- .../regionmask/regionmask-0.9.0-foss-2021b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b.eb b/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b.eb new file mode 100644 index 00000000000..0a3ef2b5475 --- /dev/null +++ b/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'regionmask' +version = '0.9.0' + +homepage = 'https://regionmask.readthedocs.io' +description = """regionmask creates masks of geographical regions. It determines to which +geographic region each grid point belongs.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('geopandas', '0.11.0'), + ('rasterio', '1.2.10'), + ('Shapely', '1.8.2'), + ('xarray', '0.20.1'), +] + +use_pip = True + +exts_list = [ + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + (name, version, { + 'checksums': ['8da1b6359756241867c4e967097810ef86b9dff4e06d11ca648fe1d607e9cf14'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 855c6ebc3cc61a1a41eefe4d59406c769eaf18c8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 5 Jul 2022 15:22:26 +0200 Subject: [PATCH 4174/9987] remove regionmask-0.9.0-foss-2021b-Python-3.9.6.eb --- ...egionmask-0.9.0-foss-2021b-Python-3.9.6.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b-Python-3.9.6.eb deleted file mode 100644 index cb012d8f201..00000000000 --- a/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2021b-Python-3.9.6.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'regionmask' -version = '0.9.0' -versionsuffix = "-Python-%(pyver)s" - -homepage = 'https://regionmask.readthedocs.io' -description = """regionmask creates masks of geographical regions. It determines to which -geographic region each grid point belongs.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('geopandas', '0.11.0'), - ('rasterio', '1.2.10'), - ('Shapely', '1.8.2'), - ('xarray', '0.20.1'), -] - -use_pip = True - -exts_list = [ - ('pooch', '1.6.0', { - 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], - }), - (name, version, { - 'checksums': ['8da1b6359756241867c4e967097810ef86b9dff4e06d11ca648fe1d607e9cf14'], - }), -] - -sanity_pip_check = True - -moduleclass = 'geo' From b210e4af2741b638e81657e9f4b66feb6ddb2136 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 5 Jul 2022 15:59:17 +0100 Subject: [PATCH 4175/9987] add Autotools builddep Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 3dc09ab695b..55526948715 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -14,6 +14,7 @@ checksums = ['4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f'] builddependencies = [ ('pkgconf', '1.8.0'), ('Xvfb', '21.1.3'), + ('Autotools', '20220317'), ] dependencies = [ ('X11', '20220504'), From 96b170e59c60d65e48d6e5a8aefa5e9d1a9a5a69 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 6 Jul 2022 15:36:02 +0100 Subject: [PATCH 4176/9987] add Autootools builddependency to R 4.2.0 --- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 661ca51251b..7bcc0ce4428 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -18,6 +18,7 @@ checksums = [ builddependencies = [ ('pkg-config', '0.29.2'), ('Xvfb', '1.20.13'), + ('Autotools', '20210726'), ] dependencies = [ ('X11', '20210802'), From 8f6c281f96e8b99d02bf2ebf0a4db1f6dfa6b495 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 7 Jul 2022 10:32:13 +0200 Subject: [PATCH 4177/9987] adding easyconfigs: ncview-2.1.8-gompi-2021b.eb --- .../n/ncview/ncview-2.1.8-gompi-2021b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021b.eb diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021b.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021b.eb new file mode 100644 index 00000000000..45dabbb1a7f --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021b.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.8' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e8badc507b9b774801288d1c2d59eb79ab31b004df4858d0674ed0d87dfc91be'] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(which $CC) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('UDUNITS', '2.2.28'), + ('X11', '20210802'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' From e7217f3b4f187d6800b68bd4d930d7d11be8efbc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 7 Jul 2022 13:23:04 +0200 Subject: [PATCH 4178/9987] TensorFlow: Disable flaky GPU test --- .../t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index 18197cfebe6..bb846c638fc 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -217,6 +217,8 @@ exts_list = [ '-//tensorflow/c/eager:c_api_cluster_test_gpu', '-//tensorflow/c/eager:c_api_remote_function_test_gpu', '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Flaky, potentially using to much device space + '-//tensorflow/c/experimental/gradients:custom_gradient_test_gpu', # Fails to open its own test.xml(?) '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 From 3a263b9598e8338e6c8d9384608774437ddad1b8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 7 Jul 2022 13:36:38 +0100 Subject: [PATCH 4179/9987] adding easyconfigs: dotNET-Core-Runtime-5.0.17-GCCcore-10.3.0.eb, MetaMorpheus-0.0.320-GCCcore-10.3.0.eb --- ...tNET-Core-Runtime-5.0.17-GCCcore-10.3.0.eb | 32 +++++++++++++++++++ .../MetaMorpheus-0.0.320-GCCcore-10.3.0.eb | 31 ++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-5.0.17-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-5.0.17-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-5.0.17-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ff2ccba1336 --- /dev/null +++ b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-5.0.17-GCCcore-10.3.0.eb @@ -0,0 +1,32 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Tarball' + +# note: only works on recent OSs, required sufficiently recent glibc (2.14 or newer) +name = 'dotNET-Core-Runtime' +version = '5.0.17' + +homepage = 'https://www.microsoft.com/net/' +description = """.NET is a free, cross-platform, open source developer platform for building many different types + of applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://download.visualstudio.microsoft.com/download/pr/' + + 'e77438f6-865f-45e0-9a52-3e4b04aa609f/024a880ed4bfbfd3b9f222fec0b6aaff'] +sources = ['dotnet-runtime-%(version)s-linux-x64.tar.gz'] +checksums = ['12b44025aabf3d28242c47f84dd14237ad7f496715be55a7c5afd0fb34f66c8b'] + +dependencies = [('libunwind', '1.5.0')] + +sanity_check_paths = { + 'files': ['dotnet'], + 'dirs': ['shared/Microsoft.NETCore.App/%(version)s'], +} + +sanity_check_commands = ["dotnet --info"] + +modextrapaths = {'PATH': ['']} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..9d8cafc2196 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +# Authors: Matt Pickin (UoY) +# Jasper Grimm (UoY) +easyblock = 'Tarball' + +name = 'MetaMorpheus' +version = '0.0.320' + +homepage = 'https://github.com/smith-chem-wisc/MetaMorpheus' +description = """MetaMorpheus is a bottom-up proteomics database search software + with integrated post-translational modification (PTM) discovery capability. + This program combines features of Morpheus and G-PTM-D in a single tool. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/smith-chem-wisc/%(name)s/releases/download/%(version)s'] +sources = ['%(name)s_CommandLine.zip'] + +dependencies = [('dotNET-Core-Runtime', '5.0.17')] + +sanity_check_paths = { + 'files': ['CMD.dll'], + 'dirs': [], +} + +_cmd = "dotnet %(installdir)s/CMD.dll" +sanity_check_commands = ["%s %s" % (_cmd, x) for x in ['--help', '--test -o %(builddir)s/test']] + +modaliases = {'metamorpheus': _cmd} + +moduleclass = 'bio' From df4c21c71e218208488767647188ee4ffa07d9f2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 7 Jul 2022 13:58:36 +0100 Subject: [PATCH 4180/9987] add MetaMorpheus checksum --- .../m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb index 9d8cafc2196..e5dd6066491 100644 --- a/easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/smith-chem-wisc/%(name)s/releases/download/%(version)s'] sources = ['%(name)s_CommandLine.zip'] +checksums = ['9c76babe4e92c8003dd17eb9a3cd80b1c26658dcb175edcc05808cb0e3a7ea37'] dependencies = [('dotNET-Core-Runtime', '5.0.17')] From e00ec763491101088a903d16540de1a5541d3de3 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 7 Jul 2022 14:21:14 +0100 Subject: [PATCH 4181/9987] drop libunwind dep to 1.4.0 to match other ECs --- .../dotNET-Core-Runtime-5.0.17-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-5.0.17-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-5.0.17-GCCcore-10.3.0.eb index ff2ccba1336..9200f0b1ad6 100644 --- a/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-5.0.17-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/dotNET-Core-Runtime/dotNET-Core-Runtime-5.0.17-GCCcore-10.3.0.eb @@ -18,7 +18,7 @@ source_urls = ['https://download.visualstudio.microsoft.com/download/pr/' + sources = ['dotnet-runtime-%(version)s-linux-x64.tar.gz'] checksums = ['12b44025aabf3d28242c47f84dd14237ad7f496715be55a7c5afd0fb34f66c8b'] -dependencies = [('libunwind', '1.5.0')] +dependencies = [('libunwind', '1.4.0')] sanity_check_paths = { 'files': ['dotnet'], From 7c8302c0a27e5125090d30462681f9bb148546cc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 7 Jul 2022 15:35:41 +0200 Subject: [PATCH 4182/9987] use nc-config to determine C compiler of netCDF --- easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021b.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021b.eb index 45dabbb1a7f..e4a7de064e3 100644 --- a/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021b.eb +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2021b.eb @@ -21,7 +21,7 @@ sources = [SOURCE_TAR_GZ] checksums = ['e8badc507b9b774801288d1c2d59eb79ab31b004df4858d0674ed0d87dfc91be'] # specified compiler is hard checked against (full path to) compiler used for netCDF... -preconfigopts = "CC=$(which $CC) " +preconfigopts = "CC=$(nc-config --cc) " configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" From 2d315281d8662f125a98231189edda4c51a26aeb Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 7 Jul 2022 15:53:39 +0200 Subject: [PATCH 4183/9987] Allow for 10 tests to fail using the new EasyBlock https://github.com/easybuilders/easybuild-easyblocks/pull/2742 --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index e4f21197645..5aba12b3957 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -111,6 +111,10 @@ excluded_tests = { runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' +# several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), +# so we allow up to 10 (out of ~90k) tests to fail before treating the installation to be faulty +max_failed_tests = 10 + # The readelf sanity check command can be taken out once the TestRPATH test from # https://github.com/pytorch/pytorch/pull/68912 is accepted, since it is then checked as part of the PyTorch test suite local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT From 6d7282c1f0a5e62536ca62be3259bc3da1508fe3 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 7 Jul 2022 15:10:45 +0100 Subject: [PATCH 4184/9987] ensure MetaMorpeus zip is versioned --- .../m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb index e5dd6066491..842a2f4e945 100644 --- a/easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/MetaMorpheus/MetaMorpheus-0.0.320-GCCcore-10.3.0.eb @@ -14,7 +14,10 @@ description = """MetaMorpheus is a bottom-up proteomics database search software toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/smith-chem-wisc/%(name)s/releases/download/%(version)s'] -sources = ['%(name)s_CommandLine.zip'] +sources = [{ + 'download_filename': '%(name)s_CommandLine.zip', + 'filename': SOURCE_ZIP, +}] checksums = ['9c76babe4e92c8003dd17eb9a3cd80b1c26658dcb175edcc05808cb0e3a7ea37'] dependencies = [('dotNET-Core-Runtime', '5.0.17')] From 5e50cd1566e4b7f1367cfa5170b7ade09cc2d1c1 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 7 Jul 2022 14:43:28 +0200 Subject: [PATCH 4185/9987] Fix BLIS build on PPC --- .../b/BLIS/BLIS-0.8.1-GCC-10.3.0.eb | 3 + .../b/BLIS/BLIS-0.8.1-GCC-11.2.0.eb | 3 + .../b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb | 3 + .../BLIS-0.8.1_enable_ppc_autodetect.patch | 91 +++++++++++++++++++ .../b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb | 8 +- .../BLIS-0.9.0_enable_ppc_autodetect.patch | 91 +++++++++++++++++++ .../b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb | 7 +- .../b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb | 8 ++ .../b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb | 3 + .../b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb | 12 ++- .../b/BLIS/BLIS-3.0.1-GCCcore-10.3.0-amd.eb | 12 ++- .../b/BLIS/BLIS-3.1-GCCcore-11.2.0-amd.eb | 4 +- 12 files changed, 239 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_enable_ppc_autodetect.patch create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_enable_ppc_autodetect.patch diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-10.3.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-10.3.0.eb index d5672a2ca4b..368ad6ddca4 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-10.3.0.eb @@ -12,10 +12,13 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://github.com/flame/blis/archive/'] sources = ['%(version)s.tar.gz'] patches = [ + '%(name)s-%(version)s_enable_ppc_autodetect.patch', '%(name)s-%(version)s_fix_dgemm-fpe-signalling-on-broadwell.patch', ] checksums = [ '729694128719801e82fae7b5f2489ab73e4a467f46271beff09588c9265a697b', # 0.8.1.tar.gz + # BLIS-0.8.1_enable_ppc_autodetect.patch + 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', ] diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-11.2.0.eb index ccc92821863..6ce09ab62c3 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCC-11.2.0.eb @@ -12,10 +12,13 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ['https://github.com/flame/blis/archive/'] sources = ['%(version)s.tar.gz'] patches = [ + '%(name)s-%(version)s_enable_ppc_autodetect.patch', '%(name)s-%(version)s_fix_dgemm-fpe-signalling-on-broadwell.patch', ] checksums = [ '729694128719801e82fae7b5f2489ab73e4a467f46271beff09588c9265a697b', # 0.8.1.tar.gz + # BLIS-0.8.1_enable_ppc_autodetect.patch + 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', ] diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb index 754d814d8a5..3d9aa35b79d 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1-GCCcore-10.3.0.eb @@ -12,10 +12,13 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/flame/blis/archive/'] sources = ['%(version)s.tar.gz'] patches = [ + '%(name)s-%(version)s_enable_ppc_autodetect.patch', '%(name)s-%(version)s_fix_dgemm-fpe-signalling-on-broadwell.patch', ] checksums = [ '729694128719801e82fae7b5f2489ab73e4a467f46271beff09588c9265a697b', # 0.8.1.tar.gz + # BLIS-0.8.1_enable_ppc_autodetect.patch + 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', ] diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_enable_ppc_autodetect.patch b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_enable_ppc_autodetect.patch new file mode 100644 index 00000000000..26e3951ebf9 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.8.1_enable_ppc_autodetect.patch @@ -0,0 +1,91 @@ +Add autodetection for POWER7, POWER9 & POWER10 +See https://github.com/amd/blis/pull/6 + +Author: Alexander Grund (TU Dresden) +diff -aur a/frame/base/bli_cpuid.c b/frame/base/bli_cpuid.c +--- a/frame/base/bli_cpuid.c 2021-03-22 23:42:33.000000000 +0100 ++++ b/frame/base/bli_cpuid.c 2022-07-07 14:05:13.627541000 +0200 +@@ -429,7 +429,7 @@ + return TRUE; + } + +-#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) ++#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) || defined(_ARCH_PPC) + + arch_t bli_cpuid_query_id( void ) + { +@@ -484,9 +484,14 @@ + return BLIS_ARCH_GENERIC; + } + } +- else if ( vendor == VENDOR_UNKNOWN ) ++ else if ( vendor == VENDOR_IBM ) + { +- return BLIS_ARCH_GENERIC; ++ if ( model == MODEL_POWER7) ++ return BLIS_ARCH_POWER7; ++ else if ( model == MODEL_POWER9) ++ return BLIS_ARCH_POWER9; ++ else if ( model == MODEL_POWER10) ++ return BLIS_ARCH_POWER10; + } + + return BLIS_ARCH_GENERIC; +@@ -985,7 +990,7 @@ + } + } + +-#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) ++#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) || defined(_ARCH_PPC) + + #define TEMP_BUFFER_SIZE 200 + +@@ -1007,6 +1012,20 @@ + char feat_str[ TEMP_BUFFER_SIZE ]; + char* r_val; + ++#ifdef _ARCH_PPC ++ r_val = find_string_in( "cpu", proc_str, TEMP_BUFFER_SIZE, pci_str ); ++ if ( r_val == NULL ) return VENDOR_IBM; ++ ++ if ( strstr( proc_str, "POWER7" ) != NULL ) ++ *model = MODEL_POWER7; ++ else if ( strstr( proc_str, "POWER9" ) != NULL ) ++ *model = MODEL_POWER9; ++ else if ( strstr( proc_str, "POWER10" ) != NULL ) ++ *model = MODEL_POWER10; ++ ++ return VENDOR_IBM; ++#endif ++ + //printf( "bli_cpuid_query(): beginning search\n" ); + + // Search /proc/cpuinfo for the 'Processor' entry. +diff -aur a/frame/base/bli_cpuid.h b/frame/base/bli_cpuid.h +--- a/frame/base/bli_cpuid.h 2021-03-22 23:42:33.000000000 +0100 ++++ b/frame/base/bli_cpuid.h 2022-07-07 13:59:51.620586000 +0200 +@@ -158,19 +158,23 @@ + FEATURE_AVX512VL = 0x4000 + }; + +-#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) ++#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) || defined(_ARCH_PPC) + + char* find_string_in( char* target, char* buffer, size_t buf_len, char* filepath ); + + enum + { + VENDOR_ARM = 0, ++ VENDOR_IBM, + VENDOR_UNKNOWN + }; + enum + { + MODEL_ARMV7 = 0, + MODEL_ARMV8, ++ MODEL_POWER7, ++ MODEL_POWER9, ++ MODEL_POWER10, + MODEL_UNKNOWN + }; + enum diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb index bb3f72c370a..6bc1b9f92e8 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb @@ -11,8 +11,12 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/flame/blis/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308'] - +patches = ['%(name)s-%(version)s_enable_ppc_autodetect.patch'] +checksums = [ + '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz + # BLIS-0.9.0_enable_ppc_autodetect.patch + 'f373fb252c0d14036fb631f048091976cceb02abb3e570a97fbaeac2fbb12328', +] builddependencies = [ ('Python', '3.10.4', '-bare'), ('Perl', '5.34.1'), diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_enable_ppc_autodetect.patch b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_enable_ppc_autodetect.patch new file mode 100644 index 00000000000..3c6fca9fbec --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_enable_ppc_autodetect.patch @@ -0,0 +1,91 @@ +Add autodetection for POWER7, POWER9 & POWER10 +See https://github.com/amd/blis/pull/6 + +Author: Alexander Grund (TU Dresden) +diff -ur a/frame/base/bli_cpuid.c b/frame/base/bli_cpuid.c +--- a/frame/base/bli_cpuid.c 2022-04-01 15:12:06.000000000 +0200 ++++ b/frame/base/bli_cpuid.c 2022-07-07 16:15:43.724020000 +0200 +@@ -485,7 +485,7 @@ + return TRUE; + } + +-#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) ++#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) || defined(_ARCH_PPC) + + arch_t bli_cpuid_query_id( void ) + { +@@ -530,9 +530,14 @@ + return BLIS_ARCH_GENERIC; + } + } +- else if ( vendor == VENDOR_UNKNOWN ) ++ else if ( vendor == VENDOR_IBM ) + { +- return BLIS_ARCH_GENERIC; ++ if ( model == MODEL_POWER7) ++ return BLIS_ARCH_POWER7; ++ else if ( model == MODEL_POWER9) ++ return BLIS_ARCH_POWER9; ++ else if ( model == MODEL_POWER10) ++ return BLIS_ARCH_POWER10; + } + + return BLIS_ARCH_GENERIC; +@@ -1203,7 +1208,7 @@ + return VENDOR_ARM; + } + +-#elif defined(__arm__) || defined(_M_ARM) ++#elif defined(__arm__) || defined(_M_ARM) || defined(_ARCH_PPC) + + /* + I can't easily find documentation to do this as for aarch64, though +@@ -1240,6 +1245,20 @@ + char feat_str[ TEMP_BUFFER_SIZE ]; + char* r_val; + ++#ifdef _ARCH_PPC ++ r_val = find_string_in( "cpu", proc_str, TEMP_BUFFER_SIZE, pci_str ); ++ if ( r_val == NULL ) return VENDOR_IBM; ++ ++ if ( strstr( proc_str, "POWER7" ) != NULL ) ++ *model = MODEL_POWER7; ++ else if ( strstr( proc_str, "POWER9" ) != NULL ) ++ *model = MODEL_POWER9; ++ else if ( strstr( proc_str, "POWER10" ) != NULL ) ++ *model = MODEL_POWER10; ++ ++ return VENDOR_IBM; ++#endif ++ + //printf( "bli_cpuid_query(): beginning search\n" ); + + // Search /proc/cpuinfo for the 'Processor' entry. +diff -ur a/frame/base/bli_cpuid.h b/frame/base/bli_cpuid.h +--- a/frame/base/bli_cpuid.h 2022-04-01 15:12:06.000000000 +0200 ++++ b/frame/base/bli_cpuid.h 2022-07-07 16:09:22.617023000 +0200 +@@ -161,19 +161,23 @@ + FEATURE_AVX512VL = 0x4000 + }; + +-#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) ++#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) || defined(_ARCH_PPC) + + char* find_string_in( char* target, char* buffer, size_t buf_len, char* filepath ); + + enum + { + VENDOR_ARM = 0, ++ VENDOR_IBM, + VENDOR_UNKNOWN + }; + enum + { + MODEL_ARMV7 = 0, + MODEL_ARMV8, ++ MODEL_POWER7, ++ MODEL_POWER9, ++ MODEL_POWER10, + MODEL_UNKNOWN + }; + enum diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb index 6b363ab7815..60adbe97e26 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb @@ -12,11 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = ['https://github.com/amd/blis/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['BLIS-2.2-amd_fix-undefined-reference-blist-abort.patch'] +patches = [ + 'BLIS-2.2-amd_fix-undefined-reference-blist-abort.patch', + '%(name)s-0.8.1_enable_ppc_autodetect.patch', +] checksums = [ 'e1feb60ac919cf6d233c43c424f6a8a11eab2c62c2c6e3f2652c15ee9063c0c9', # 2.2.tar.gz # BLIS-2.2-amd_fix-undefined-reference-blist-abort.patch 'e879bd79e4438f7e6905461af1d483d27d14945eb9e75509b22c7584b8ba93c4', + # BLIS-0.8.1_enable_ppc_autodetect.patch + 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb index 0143981fdeb..1c14c4e0bd6 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb @@ -15,8 +15,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/amd/blis/archive/'] sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-0.8.1_enable_ppc_autodetect.patch', + '%(name)s-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch', +] checksums = [ 'ac848c040cd6c3550fe49148dbdf109216cad72d3235763ee7ee8134e1528517', # 3.0.tar.gz + # BLIS-0.8.1_enable_ppc_autodetect.patch + 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', + # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch + '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb index 8b98f370a16..0208b0c8be8 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCC-11.2.0-amd.eb @@ -13,10 +13,13 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ['https://github.com/amd/blis/archive/'] sources = ['%(version)s.tar.gz'] patches = [ + '%(name)s-0.8.1_enable_ppc_autodetect.patch', '%(name)s-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch', ] checksums = [ 'dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e', # 3.0.1.tar.gz + # BLIS-0.8.1_enable_ppc_autodetect.patch + 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', ] diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb index 58742db0fc1..4e65c629936 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.2.0-amd.eb @@ -15,7 +15,17 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/amd/blis/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e'] +patches = [ + '%(name)s-0.8.1_enable_ppc_autodetect.patch', + '%(name)s-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch', +] +checksums = [ + 'dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e', # 3.0.1.tar.gz + # BLIS-0.8.1_enable_ppc_autodetect.patch + 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', + # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch + '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.3.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.3.0-amd.eb index 7a8a7f4e2e7..6705b1177a2 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.3.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0.1-GCCcore-10.3.0-amd.eb @@ -15,7 +15,17 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/amd/blis/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e'] +patches = [ + '%(name)s-0.8.1_enable_ppc_autodetect.patch', + '%(name)s-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch', +] +checksums = [ + 'dff643e6ef946846e91e8f81b75ff8fe21f1f2d227599aecd654d184d9beff3e', # 3.0.1.tar.gz + # BLIS-0.8.1_enable_ppc_autodetect.patch + 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', + # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch + '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', +] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.1-GCCcore-11.2.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.1-GCCcore-11.2.0-amd.eb index 70fc18ddbcf..36484cda2e5 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-3.1-GCCcore-11.2.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.1-GCCcore-11.2.0-amd.eb @@ -13,14 +13,16 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/amd/blis/archive/'] sources = ['%(version)s.tar.gz'] patches = [ + '%(name)s-0.8.1_enable_ppc_autodetect.patch', '%(name)s-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch', ] checksums = [ '2891948925b9db99eec02a1917d9887a7bee9ad2afc5421c9ba58602a620f2bf', # 3.1.tar.gz + # BLIS-0.8.1_enable_ppc_autodetect.patch + 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', ] - builddependencies = [ ('binutils', '2.37'), ('Python', '3.9.6'), From 49fdcf342b92017bfaa15942543b2e6728491d6f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 7 Jul 2022 17:20:34 +0200 Subject: [PATCH 4186/9987] adding easyconfigs: Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb, Megalodon-2.5.0-foss-2021a.eb and patches: Megalodon-2.5.0_fix-samtools-test.patch --- .../Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb | 61 ++++++++++++++++ .../m/Megalodon/Megalodon-2.5.0-foss-2021a.eb | 59 +++++++++++++++ .../Megalodon-2.5.0_fix-samtools-test.patch | 72 +++++++++++++++++++ 3 files changed, 192 insertions(+) create mode 100644 easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0_fix-samtools-test.patch diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..121bec87c85 --- /dev/null +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'Megalodon' +version = '2.5.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/megalodon' +description = """Megalodon is a research command line tool to extract high accuracy modified base and sequence variant +calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference +genome/transriptome.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), + ('ont-fast5-api', '4.0.0'), + ('ont-remora', '1.0.0', versionsuffix), + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.13'), + ('scikit-learn', '0.24.2'), + ('Seaborn', '0.11.2'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('mappy', '2.24', { + 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + }), + ('ont-pyguppy-client-lib', '6.0.6', { + 'modulename': 'pyguppy_client_lib', + 'source_tmpl': 'ont_pyguppy_client_lib-%(version)s-cp39-cp39-manylinux2014_x86_64.whl', + 'checksums': ['ba1f7e7aa02830d1d4760f7871710b1d097a7ab9e5412b127c00474974c271fa'], + }), + ('megalodon', version, { + 'patches': ['Megalodon-2.5.0_fix-samtools-test.patch'], + 'checksums': [ + # megalodon-2.5.0.tar.gz + '60ad1f1191b86d9a1423dcb9c934c7577cf1ce083689337646937be2538953a3', + # Megalodon-2.5.0_fix-samtools-test.patch + 'd90ec766e459a1c657ab8db94a208432845f091550e6bac197ec2d99d7058faa', + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/megalodon'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "megalodon -h", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a.eb new file mode 100644 index 00000000000..6824d5f3590 --- /dev/null +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'Megalodon' +version = '2.5.0' + +homepage = 'https://github.com/nanoporetech/megalodon' +description = """Megalodon is a research command line tool to extract high accuracy modified base and sequence variant +calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference +genome/transriptome.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), + ('ont-fast5-api', '4.0.0'), + ('ont-remora', '1.0.0'), + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.13'), + ('scikit-learn', '0.24.2'), + ('Seaborn', '0.11.2'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('mappy', '2.24', { + 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + }), + ('ont-pyguppy-client-lib', '6.0.6', { + 'modulename': 'pyguppy_client_lib', + 'source_tmpl': 'ont_pyguppy_client_lib-%(version)s-cp39-cp39-manylinux2014_x86_64.whl', + 'checksums': ['ba1f7e7aa02830d1d4760f7871710b1d097a7ab9e5412b127c00474974c271fa'], + }), + ('megalodon', version, { + 'patches': ['Megalodon-2.5.0_fix-samtools-test.patch'], + 'checksums': [ + # megalodon-2.5.0.tar.gz + '60ad1f1191b86d9a1423dcb9c934c7577cf1ce083689337646937be2538953a3', + # Megalodon-2.5.0_fix-samtools-test.patch + 'd90ec766e459a1c657ab8db94a208432845f091550e6bac197ec2d99d7058faa', + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/megalodon'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "megalodon -h", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0_fix-samtools-test.patch b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0_fix-samtools-test.patch new file mode 100644 index 00000000000..1305f51862e --- /dev/null +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0_fix-samtools-test.patch @@ -0,0 +1,72 @@ +Use command `samtools help` to sanity check the installation of SAMtools +PR: https://github.com/nanoporetech/megalodon/pull/302 +author: Alex Domingo (Vrije Universiteit Brussel) +diff --git a/megalodon/mapping.py b/megalodon/mapping.py +index bab93d3..8b9608f 100755 +--- a/megalodon/mapping.py ++++ b/megalodon/mapping.py +@@ -267,44 +267,40 @@ class MapInfo: + + def test_samtools(self): + try: +- test_sort_res = subprocess.run( +- [self.samtools_exec, "sort"], ++ test_help_res = subprocess.run( ++ [self.samtools_exec, "help"], + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) +- test_index_res = subprocess.run( +- [self.samtools_exec, "index"], +- stdout=subprocess.PIPE, +- stderr=subprocess.PIPE, ++ except FileNotFoundError: ++ LOGGER.warning( ++ "Samtools executable not found. Mappings will " ++ + "not be sorted or indexed." + ) +- # Note index returns non-zero exit status +- if test_sort_res.returncode != 0: ++ self.do_sort_mappings = False ++ else: ++ if test_help_res.returncode != 0: + LOGGER.warning( + "Samtools test commands return non-zero exit " + + "status. Mappings will not be sorted or indexed." + ) + LOGGER.debug( + ( +- "MappingTestFail: sort_returncode: {} " +- + "index_returncode: {}\nsort_call_stdout:\n{}\n" +- + "sort_call_stderr:\n{}\nindex_call_stdout:\n{}" +- + "\nindex_call_stderr:\n{}" ++ "MappingTestFail: samtools_returncode: {} " ++ + "\nsamtools_call_stdout:\n{}" ++ + "\nsamtools_call_stderr:\n{}" + ).format( +- test_sort_res.returncode, +- test_index_res.returncode, +- test_sort_res.stdout.decode(), +- test_sort_res.stderr.decode(), +- test_index_res.stdout.decode(), +- test_index_res.stderr.decode(), ++ test_help_res.returncode, ++ test_help_res.stdout.decode(), ++ test_help_res.stderr.decode(), + ) + ) + self.do_sort_mappings = False +- except FileNotFoundError: +- LOGGER.warning( +- "Samtools executable not found. Mappings will " +- + "not be sorted or indexed." +- ) +- self.do_sort_mappings = False ++ else: ++ LOGGER.debug( ++ "Mapping Test Success --- Mappings will be " ++ + "sorted and indexed with samtools" ++ ) + + + def align_read( From aec3d38192799858fc8ab72a8a546fc92d98fac0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 7 Jul 2022 18:21:04 +0100 Subject: [PATCH 4187/9987] relax tolerances for two more tests --- .../jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb | 2 +- .../jax-0.3.14_relax-test-tolerances.patch | 20 +++++++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb index 47d57b6a04c..a4992725207 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb @@ -108,7 +108,7 @@ exts_list = [ '225624375094d2067bc3af5abe0a73c6b530916edc1422c30a451d3f3e1b5a82', # jax-v0.3.14.tar.gz '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d', # jax-0.3.9_relax-test-tolerance.patch # jax-0.3.14_relax-test-tolerances.patch - 'c41061d00e431076a709820f0b3df19b9ef114558dfc2a75a361303c3fc8312e', + '387e98a89ca03ca898a1925d7c2d57d0568f6a72b0cb516469903dddd9424689', ], # deliberately not testing in parallel, as that results in (additional) failing tests; # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.14_relax-test-tolerances.patch b/easybuild/easyconfigs/j/jax/jax-0.3.14_relax-test-tolerances.patch index f79814fedb1..0a4129647a2 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.14_relax-test-tolerances.patch +++ b/easybuild/easyconfigs/j/jax/jax-0.3.14_relax-test-tolerances.patch @@ -18,3 +18,23 @@ Patch by Simon Branford (University of Birmingham) def test_fixes4594(self): n = 2 +--- tests/linalg_test.py.orig 2022-07-07 18:14:10.363577000 +0100 ++++ tests/linalg_test.py 2022-07-07 18:17:21.971203822 +0100 +@@ -286,6 +286,8 @@ + args_maker = lambda: [rng(shape, dtype)] + a, = args_maker() + tol = 1e-4 if dtype in (np.float64, np.complex128) else 1e-1 ++ if dtype == np.complex64: ++ tol = 1 + jtu.check_grads(lambda x: jnp.linalg.eigvals(x), (a,), order=1, + modes=['fwd', 'rev'], rtol=tol, atol=tol) + +@@ -304,7 +306,7 @@ + a, = args_maker() + w1, _ = jnp.linalg.eig(a) + w2 = jnp.linalg.eigvals(a) +- self.assertAllClose(w1, w2, rtol={np.complex128: 1e-14}) ++ self.assertAllClose(w1, w2, rtol={np.complex128: 1e-14, np.complex64: 1e-4}) + + @jtu.skip_on_devices("gpu", "tpu") + def testEigvalsInf(self): From 7f32f12c4a15f621b42953f3b0fc9ca0e4acbca5 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 7 Jul 2022 20:01:29 +0200 Subject: [PATCH 4188/9987] prepare release notes for EasyBuild v4.6.0 + bump version to 4.6.0 --- RELEASE_NOTES | 58 +++++++++++++++++++++++++++++++++++++++++++++++++-- setup.py | 2 +- 2 files changed, 57 insertions(+), 3 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 8fa3b4892b3..b0df378ca66 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,62 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 14,816 easyconfig files, for 2,711 different software packages, -incl. 36 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 15,017 easyconfig files, for 2,735 different software packages, +incl. 37 different (compiler) toolchains. + + +v4.6.0 (July 8th 2022) +---------------------- + +feature release + +- added easyconfigs for foss/2022a, intel/2022a and gfbf/2022a (#15755) common toolchains + - see also https://docs.easybuild.io/en/latest/Common-toolchains.html +- added example easyconfig files for 24 new software packages: + - BLT (#15624), category_encoders (#15638), fio (#10321), FSON (#15721), GCTA (#15649), gfbf (#15653), + Gibbs2 (#15702), G-PhoCS (#7619), InterProScan_data (#15717), Jorg (#15346), libopus (#15682), + Minipolish (#15713), mm-common (#15764), MONA (#15696), NetPyNE (#15606), pfind (#15685), regionmask (#15786), + samplot (#15686), SISSO (#15766), sklearn-pandas (#15637), STAR-CCM+ (#7398), SWIPE (#6795), + uncertainty-calibration (#15612), Virtuoso-opensource (#14102) +- added additional easyconfigs for various supported software packages, including: + - Albumentations 1.1.0, AlphaFold 2.2.2, Arriba 2.3.0, Arrow 8.0.0, BLIS 0.9.0, Bracken 2.7, CellRanger 7.0.0, + Clp 1.17.7, CoinUtils 2.11.6, cppy 1.2.1, cuDNN 8.4.1.50, deal.II 9.3.3, double conversion, Doxygen 1.9.4, + ELPA 2021.11.001, FFTW.MPI 3.3.10, Fiona 1.8.21, FLAC 1.3.4, flatbuffers 2.0.0, flatbuffers-python 2.0, fmt 7.1.1, + FSL 6.0.5.1, g2clib 1.6.3, g2lib 3.2.0, GDAL 3.5.0, gdbm 1.21, GDRCopy 2.3, geopandas 0.11.0, GEOS 3.10.3, + Ghostscript 9.56.1, GLibmm 2.66.4, GLPK 5.0, googletest 1.11.0, graphite2 1.3.14, Groovy 4.0.3, GULP 6.1, + h5py 3.7.0, HDF 4.2.15, HDF5 1.13.1, hifiasm 0.15.2, hifiasm 0.16.1, HPL 2.3, IGMPlot 2.6.9b, ImageMagick 7.1.0, + imgaug 0.4.0, InterProScan 5.55, IRkernel 1.3, ITK 5.2.1, JasPer 2.0.33, jax 0.3.9, jemalloc 5.3.0, JsonCpp 1.9.5, + Julia 1.7.3, LAME 3.100, Leptonica 1.82.0, libgeotiff 1.7.1, libgit2 1.4.3, libiconv 1.17, libogg 1.3.5, + libreadline 8.1, libRmath 4.2.0, libsigc++ 2.10.8, libsndfile 1.1.0, LIBSVM 3.25, libtirpc 1.3.2, libvorbis 1.3.7, + libxc 5.2.3, libxml++ 2.42.1, libxslt 1.1.34, line_profiler 3.5.1, LittleCMS 2.13.1, LMDB 0.9.29, lpsolve 5.5.2.11, + makedepend 1.0.6, MaSuRCA 4.0.9, mayavi 4.7.4, MetaEuk 5, mold 1.3.0, MotionCor2 1.4.4, MPFR 4.1.0, MUMPS 5.4.1, + NCCL 2.12.12, NCL 6.6.2, ncview 2.1.8, netCDF 4.9.0, nettle 3.8, networkx 2.8.4, NEURON 7.8.2, NGS 2.10.9, + nlohmann_json 3.10.5, NLopt 2.7.1, nodejs 16.15.1, NSPR 4.34, NSS 3.79, nsync 1.25.0, nvtop 2.0.2, + ont-fast5-api 4.0.2, Osi 0.108.7, OSU-Micro-Benchmarks 5.9, p4est 2.8, parasail 2.5, Perl 5.34.1, Pillow 9.1.1, + pkgconfig 1.5.5, PLUMED 2.8.0, PnetCDF 1.12.3, poppler 21.06.1, PRISMS PF, PROJ 9.0.0, protobuf 3.19.4, + protobuf-python 3.19.4, pyfaidx 0.7.0, PyOpenGL 3.1.6, pyproj 3.3.1, pyspoa 0.0.8, Python 2.7.18, + python-parasail 1.2.4, Qhull 2020.2, Qt5 5.15.5, QuantumESPRESSO 7.1, Qwt 6.2.0, R 4.2.1, RapidJSON 1.1.0, + rasterio 1.2.10, Ray-project 1.13.0, RE2 2022, re2c 2.2, redis-py 4.3.3, ReFrame 3.11.1, ReFrame 3.11.2, + rioxarray 0.11.1, RNA-SeQC 2.4.2, ScaLAPACK 2.2.0, Schrodinger 2022, scikit-learn 1.0.1, SciPy-bundle 2022.05, + Shapely 1.8.2, Siesta 4.1.5, SimpleITK 2.1.1.2, snappy 1.1.9, SpectrA 1.0.1, spoa 4.0.7, Szip 2.1.1, TCLAP 1.2.5, + TensorFlow 2.7.1, tesseract 4.1.0, Tk 8.6.12, Tkinter 3.10.4, Transformers 4.20.1, UCX-CUDA 1.12.1, UDUNITS 2.2.28, + utf8proc 2.7.0, vt 0.57721, WhatsHap 1.4, WildMagic 5.17, WPS 3.9.1, Xvfb 21.1.3 +- minor enhancements, including: + - add hypergeo extension to R v4.2.0 (#15701 + - add patch for GCCcore 11.3.0 to support using -fuse-ld=mold (#15715) + - add patch for porefoam to fix hardcoded mpirun command and take into account $POREFOAM_MPIRUN_CMD (#15730) + - add rtdists extension for R v4.2.0 (#15734) + - add geeM extension to R v4.2.0 (#15810) +- various bug fixes, including: + - switch to Rust 1.60.0 build dependency for bamtofastq, since build of fails with Rust 1.52.1 (E0658) (#15636) + - avoid that pygmo v2.18.0 installs stuff in Python installation directory + add custom sanity check paths to pygmo easyconfigs (#15657) + - add patch for Mmg v5.6.0 to remove library CI tests that point to external sources (#15691) + - correct configopts in deal.II v9.1.1 easyconfig (#15692) + - add missing Python dependency for HPDBSCAN to fix unresolved %(pyshortver)s template (#15694) +- other changes: + - drop SpectrA 1.0.1 from GCC to GCCcore (#15652) + - in-place update to netCDF v4.9.0 (#15677) + - disable flaky GPU test for TensorFlow 2.6.0 (#15824) v4.5.5 (June 8th 2022) diff --git a/setup.py b/setup.py index 4e3fe1de9d5..b8a0b052239 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.5.6.dev0' +VERSION = '4.6.0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From ba8b56c5e4dc7142250bc754718766e906c24b7d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 7 Jul 2022 19:18:59 +0100 Subject: [PATCH 4189/9987] adding easyconfigs: R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb, arrow-R-8.0.0-foss-2022a-R-4.2.1.eb --- .../arrow-R-8.0.0-foss-2022a-R-4.2.1.eb | 34 + ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 1096 +++++++++++++++++ 2 files changed, 1130 insertions(+) create mode 100644 easybuild/easyconfigs/a/arrow-R/arrow-R-8.0.0-foss-2022a-R-4.2.1.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-8.0.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-8.0.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..df3e4e8a0a2 --- /dev/null +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-8.0.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'arrow-R' +version = '8.0.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/arrow' +description = "R interface to the Apache Arrow C++ library" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['arrow_%(version)s.tar.gz'] +checksums = ['6c9aa08c68b7b39cb7d6b9394c0b94a566c0fe9a85cea61f5ed19e460bdb05ad'] + +dependencies = [ + ('R', '4.2.1'), + ('Arrow', '8.0.0'), +] + +preinstallopts = "export LIBARROW_BINARY=true && " + +sanity_check_paths = { + 'files': [], + 'dirs': ['arrow'], +} + +options = {'modulename': 'arrow'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..9228946a81c --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -0,0 +1,1096 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.15' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [('pkgconf', '1.8.0')] + +dependencies = [ + ('R', '4.2.1'), + ('Boost', '1.79.0'), # for mzR + ('GSL', '2.7'), # for flowClust + ('HDF5', '1.13.1'), # for rhdf5 + ('arrow-R', '8.0.0', versionsuffix), # required by RcisTarget +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on 7th July 2022 +exts_list = [ + ('BiocGenerics', '0.42.0', { + 'checksums': ['0cb6fa74a389693d253a9f61935d335fcfcc1dfe5acbba78b3cc43c1af5d6947'], + }), + ('Biobase', '2.56.0', { + 'checksums': ['7b49f4336b1b9323b02b6819ff3bb8347e47e696ec0802cc4d0758858e9fddd6'], + }), + ('S4Vectors', '0.34.0', { + 'checksums': ['9368ef6636862f02a7cca0022b94975a21a1a4ac434f7b44411c52d83e5c7e48'], + }), + ('IRanges', '2.30.0', { + 'checksums': ['1331cf39cab3d0e2233247bb6e9d439e0e804c2a3336c103cb195fb2802ddd41'], + }), + ('GenomeInfoDbData', '1.2.8', { + 'checksums': ['576750330a011c1eccb47c7154ca1b40ae4cd473fd7973f6c2955237a0729eb4'], + }), + ('GenomeInfoDb', '1.32.2', { + 'checksums': ['b0a7bed8527c89b04f96bcc169366c6b238b45d32fa760177ead6227165f67d8'], + }), + ('zlibbioc', '1.42.0', { + 'checksums': ['fbf78b33def67a1778e97c15c5161c095268c14baf14ab559dcaccd6a34c1e70'], + }), + ('XVector', '0.36.0', { + 'checksums': ['136e5bc29f3d64634eff01794cb7824171df2300721c3ac24ceba5233c5e7ab8'], + }), + ('Biostrings', '2.64.0', { + 'checksums': ['e8c1dfbeb4b00d1dec1234693ab5ed6152fdd93c3afabd84173cd1843e14e5eb'], + }), + ('KEGGREST', '1.36.2', { + 'checksums': ['fc7d4fcad2a08d5b8a7d4cc620a5ad3e2a588e406e4fa8fe5ef902e4111fc0e6'], + }), + ('AnnotationDbi', '1.58.0', { + 'checksums': ['96bf9c24b8401361c2c9d4efbf6f93a790becaba449edc06e5322116e9f19c95'], + }), + ('GenomicRanges', '1.48.0', { + 'checksums': ['d623d25b9eb20d4b48f42f6e30771101503b8e9e1592d76e310273ca54d81921'], + }), + ('BiocParallel', '1.30.3', { + 'checksums': ['22318a3b47b56492445c1f2125a4dcef6dbb40dd94c594863bbd26aa55e543e7'], + }), + ('Rhtslib', '1.28.0', { + 'checksums': ['4e48c8643e5d3429238ee76faa4c68ed8a7028e7f594c109ee75f5e994d17c1e'], + }), + ('Rsamtools', '2.12.0', { + 'checksums': ['20e860c61ef66f8e61f8de7f77c4a244439c8fe39286d080cd580417073894f2'], + }), + ('MatrixGenerics', '1.8.1', { + 'checksums': ['ee8c3c0eab964f505bd570c083e88218bb4d6342adb406f3efd2fbf8afa52bd2'], + }), + ('DelayedArray', '0.22.0', { + 'checksums': ['1ee707dc606f257020c2654b21305045f4da9dc2943e6246a0bd25f5f1302d86'], + }), + ('SummarizedExperiment', '1.26.1', { + 'checksums': ['697c5faf7620dbb336591463bcb027d45a297197ed012a13d0327aaaebc7740b'], + }), + ('GenomicAlignments', '1.32.0', { + 'checksums': ['71354a8f7b07283065bff8280558a15ddfc35a6d225de2d8f7c5214400a3d5c5'], + }), + ('ShortRead', '1.54.0', { + 'checksums': ['18ca2c82688c158cdc952436434d4a608000ec4c02b199a0925c6cb2500a030c'], + }), + ('graph', '1.74.0', { + 'checksums': ['e4d1389e5f148fa6ff55299b29f096bd9cfd5d772691a0298b53a027b9cc10ad'], + }), + ('affyio', '1.66.0', { + 'checksums': ['d7bd8ba9f3a24f6a74c28226765cecc6e917dbf1028cfa04dce6cfbfb1409ca5'], + }), + ('preprocessCore', '1.58.0', { + 'installopts': "--configure-args='--disable-threading'", + 'checksums': ['6e36ad18eae494105b88f5195493b8ac3decf1c588cb4cddf5cf6c0801b817eb'], + }), + ('BiocManager', '1.30.18', { + 'checksums': ['f763126b45614e1b83260da5311923eac50db24002f3c22fa5f667434a5b5c35'], + }), + ('affy', '1.74.0', { + 'checksums': ['87b54c76d72abd9a44041772914451ab426df6d4aac9b1e6e39254d2883f870a'], + }), + ('GO.db', '3.15.0', { + 'checksums': ['bac91d73c57f206fa5bc4a501a2aaf61b365cf411181ce44353370cdbc132d99'], + }), + ('limma', '3.52.2', { + 'checksums': ['c5ccd94d05286cfdbbe7e139281e2a6c41e62b3446e3e1da170e1157f1451755'], + }), + ('RBGL', '1.72.0', { + 'checksums': ['fe301943e9444a43ac14b874bd984931cd9b13f491b70b9ed58928da7742005e'], + }), + ('org.Hs.eg.db', '3.15.0', { + 'checksums': ['1dc9bb6019e0f0a222b9ec84a1c5870cdbca480f45d9ad08e35f77278baa3c5f'], + }), + ('AnnotationForge', '1.38.0', { + 'checksums': ['e8fffd592a364e0154c255964cbfd198b6f6f6b227c83ca4f4efa9d69b722ca3'], + }), + ('annaffy', '1.68.0', { + 'checksums': ['f8d532a12f6d21d7f5c2ef1025a74b75ab9b9ecf0ce66e0c24a310bab89d78b9'], + }), + ('gcrma', '2.68.0', { + 'checksums': ['cd380cfa86dfdddfca88b83a81a23ed03c3ec69a6790618dd24f8025f28b488d'], + }), + ('oligoClasses', '1.58.0', { + 'checksums': ['b3d5a3f276419c27b7e5f1b164713138098101ad67875194e2a5ba401f289dd4'], + }), + ('edgeR', '3.38.1', { + 'checksums': ['3356f4f1349267091db058367f2f74faf78b5a7b42dfc7c1f0af94604e1d23e1'], + }), + ('PFAM.db', '3.15.0', { + 'checksums': ['e7036a5f76779ab6e8a32eb659c54f52426c4824dee02903cffd85bed372720f'], + }), + ('perm', '1.0-0.2', { + 'checksums': ['729294987bb0f367c67c4bf4071464e097ec9a2bbdb2c63f19ebfb907c604aa0'], + }), + ('baySeq', '2.30.0', { + 'checksums': ['52d843b27f8d48b8119ded918fd88b17640c0271d8a07e66165a8ced9b9d1efb'], + }), + ('qvalue', '2.28.0', { + 'checksums': ['dcd72f19ed80eb22b27b04fef42d1472d3246f78b18d2414efd6b24659a97033'], + }), + ('impute', '1.70.0', { + 'checksums': ['22a7e1e1067a435e890d76cc9caaca806d2bcbffb7973207f1a646e0eff96085'], + }), + ('shinyFiles', '0.9.2', { + 'checksums': ['8fbe4b8e1478c5e5efdb8fddcbe210fd2275e61d9ff06efa1672f61dd3268ad0'], + }), + ('samr', '3.0', { + 'checksums': ['25f88ac002c2adce8881a562241bc12d683810a05defb553e8e3d4878f037506'], + }), + ('DEGseq', '1.50.0', { + 'checksums': ['2e84bf5351579f092df72afba90bab08a70c536e56400a05ae6d80ba1cec5ede'], + }), + ('hgu133plus2.db', '3.13.0', { + 'checksums': ['ddde58e777a8341536a664c7d4be874a2f395f8aaa019c1f738462a8ce74cc44'], + }), + ('illuminaio', '0.38.0', { + 'checksums': ['c240646e8cfe38456c7e223da4edaf8e4526678d887b896247fa129ed42960f6'], + }), + ('BiocIO', '1.6.0', { + 'checksums': ['b7f901ca3e6fa06171f839c088c8769a462533a3cf5b83eb7dabe64fb811489a'], + }), + ('restfulr', '0.0.15', { + 'checksums': ['40ff8f1fb2987af2223e1a855bb1680c5ce2143fbce7ebc42f1edb291f80e692'], + }), + ('rtracklayer', '1.56.1', { + 'checksums': ['9acadac5fface3639c779d9116cfaf20708fe200163b1c0e92af8e228c4e1e83'], + }), + ('filelock', '1.0.2', { + 'checksums': ['ac2915950789b16c43a625a2b8dab6ba423588db4a7d0daa75b74518b82b1403'], + }), + ('BiocFileCache', '2.4.0', { + 'checksums': ['5cefe2e72648c0003ac74937b390ebda7258b09eed575b84de1cb5dc23adabad'], + }), + ('biomaRt', '2.52.0', { + 'checksums': ['af23f7f9fe0fe9f7a38ea56d49671d62076ec7f8b1039054428cdeecad9ac37a'], + }), + ('GenomicFeatures', '1.48.3', { + 'checksums': ['815eaac9baf0ded8a5589fd9cf825f49f3ae802cb0769d2e301479a16ab82438'], + }), + ('bumphunter', '1.38.0', { + 'checksums': ['bc73783c84765a82f182ea17eb2cdaeea7631ed728eb7dd8aa5163c892be224d'], + }), + ('multtest', '2.52.0', { + 'checksums': ['02f5d868a59d849e7c9d528d7242843af2791312d36e5a5f9770f3307965fc0c'], + }), + ('scrime', '1.3.5', { + 'checksums': ['5d97d3e57d8eb30709340fe572746029fd139456d7a955421c4e3aa75d825578'], + }), + ('siggenes', '1.70.0', { + 'checksums': ['f4b454231928de76e85cd5582e69467de9c503b2e72610fa973b5cc444c5b22a'], + }), + ('DynDoc', '1.74.0', { + 'checksums': ['b1bfc7f8a519c4bd36a36bd22b16015900e3210ad3d8931be323d9401b6d117b'], + }), + ('NOISeq', '2.40.0', { + 'checksums': ['47cc6c13a1904f31f1b7ab206e438321208b6614d646ada72445900d6953062a'], + }), + ('Rgraphviz', '2.40.0', { + 'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'], + 'checksums': [ + '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4', # Rgraphviz_2.40.0.tar.gz + # Rgraphviz-2.28.0_fno-tree-vectorize.patch + '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9', + ], + }), + ('RNASeqPower', '1.36.0', { + 'checksums': ['8d9ffdf045b56a69f2109503a733ab9bd55801a42ac6e52b4d7983f1e6ec692f'], + }), + ('annotate', '1.74.0', { + 'checksums': ['4fc0553435855aa7dbf352a26b86e39936d4510ae03816f708e7091e6f6bdb74'], + }), + ('GSEABase', '1.58.0', { + 'checksums': ['0f9d54c3be70854e349e150fcfd28585c67a1eacae5a2c204acd89349e7f1be2'], + }), + ('genefilter', '1.78.0', { + 'checksums': ['58913b670b29109a7226320e1f99d795931991db1939ea3fa25143492d55e3d2'], + }), + ('Category', '2.62.0', { + 'checksums': ['0def183b2707c0a1c2341ba104bfc6cc59df31dd2a92c0fffacfb4e6d8005a1e'], + }), + ('GOstats', '2.62.0', { + 'checksums': ['35cbed07bac0e1c67ea9d469d335d91de8b5c229c810568f472f2b1777f23488'], + }), + ('BSgenome', '1.64.0', { + 'checksums': ['ace392a9db183effb8a55c1f74719ef00dee5ea2da2af6f383af77e354cdf89d'], + }), + ('VariantAnnotation', '1.42.1', { + 'checksums': ['e1b5d52ce3f50c480ccda5340cf9f22774b124b9923caf95a0c6af6bfa84a589'], + }), + ('interactiveDisplayBase', '1.34.0', { + 'checksums': ['af2d2e7d806a349bf87b0eb969da661c160ce1ff0747375b5708320059e9bc39'], + }), + ('BiocVersion', '3.15.2', { + 'checksums': ['d67d6ecbdc89c9a69bc05a950edde3658411407c67804680981843a2beb74467'], + }), + ('AnnotationHub', '3.4.0', { + 'checksums': ['bacb8e2c4f14168087aa5c463902f3f910acf27d224c4ad2ee69eb3c485fb50d'], + }), + ('AnnotationFilter', '1.20.0', { + 'checksums': ['8d2ab20f253890fd7a560bf16be9e9cdd9d130e66232da6c9f56646f1abb5420'], + }), + ('ProtGenerics', '1.28.0', { + 'checksums': ['05e06c4ed777360f6e027568ff6e3ae6e5de97e07ce52454b87f3584897c0c12'], + }), + ('ensembldb', '2.20.2', { + 'checksums': ['ac1f2d701e9bf99265c8db18c7be7f30a60af6eaa68e31bff40fb61a590bc28a'], + }), + ('biovizBase', '1.44.0', { + 'checksums': ['cd7f83e8170d22ef45a3a832475edffcc131707aa882a2d046f410bafd71dfb9'], + }), + ('OrganismDbi', '1.38.1', { + 'checksums': ['2998649c56b5f7309dc3853ee9b1b1da05b8393eaea6f1f50d8241d291ecb657'], + }), + ('ggbio', '1.44.1', { + 'checksums': ['6f8ffb3507d81ffbc5f7c2e7d680a8dafc3a05453b02616fa35506cca992d047'], + }), + ('geneplotter', '1.74.0', { + 'checksums': ['4cc610c37d6c5fa2eeb6d61c52fa1cb322658216035c99dcb654e5967f05438c'], + }), + ('DESeq2', '1.36.0', { + 'checksums': ['2737cdbb39d393262af22c37aa7e8db72375ff04fb6aeeb849cf098b2558bb1a'], + }), + ('ReportingTools', '2.36.0', { + 'checksums': ['104e5363b8756259028b1aba15d3f3adce99fce8488e09e19b5d06e83e6e0c65'], + }), + ('Glimma', '2.6.0', { + 'checksums': ['df6f7fd11e6c0913a8527d367624dd2ad21feedd2feff0a68262c19d805727cc'], + }), + ('affycoretools', '1.68.1', { + 'checksums': ['9c0f1ab7e121e6655ce831f70b188ec006ff5fc204f3b8c649af5e593c24a617'], + }), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', { + 'checksums': ['063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9'], + }), + ('Homo.sapiens', '1.3.1', { + 'checksums': ['014809fc6ef6410be8dc1094c9cb083719f20d999065ae4bf388855be0913b94'], + }), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.3', { + 'checksums': ['5bfa65d7836449d9b30c356968497cdfaa98be48c4e329e71e8f8a120f3e9d1a'], + }), + ('AgiMicroRna', '2.46.0', { + 'checksums': ['aa8b1482bae0a7a71f19191a9c0dba1411ac025ca93e47bf3c7bc1eb5f422c4a'], + }), + ('geneLenDataBase', '1.32.0', { + 'checksums': ['5f691667b53acb1769509540bdbdbf7001e5be4973b97a88f5567f8d47ab995c'], + }), + ('goseq', '1.48.0', { + 'checksums': ['88b45cf35e363e3c9b2edd6619d62be902ad97f40c835dfce9e2ee89e1e719f0'], + }), + ('KEGGgraph', '1.56.0', { + 'checksums': ['bdd9104ca0296d8f26d6719a2d9fdfaf9ed553b9b2f6d851c8103d760101f896'], + }), + ('GEOquery', '2.64.2', { + 'checksums': ['3dc51776c33d45371f8913d2593ea0babbbebd1aed018e220e037d0505de73b3'], + }), + ('rARPACK', '0.11-0', { + 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], + }), + ('mixOmics', '6.20.0', { + 'checksums': ['871f11604dd4e1923fc107a4c3df083ff41b8feb7332f765940bc8ec0e178c3b'], + }), + ('Rhdf5lib', '1.18.2', { + 'checksums': ['8f9893a4c8173f5d154e2a0b9f73f0f575ac17481a3bf943f99e88c30e44ebca'], + }), + ('rhdf5filters', '1.8.0', { + 'checksums': ['7ad7b5ae372c1a700976768e37ad227475c675bc15333d8cac317c6cd106efc6'], + }), + ('rhdf5', '2.40.0', { + 'checksums': ['ce4585ddf67848e3b34c531e02df7ee712874127dd54eaa21ce8a2652b489701'], + }), + ('HDF5Array', '1.24.1', { + 'checksums': ['5e35b79abd1115d98dda6551bf61a4adba50f723edfad91322eb6160e67934e4'], + }), + ('sparseMatrixStats', '1.8.0', { + 'checksums': ['a28fe0592793913b2c9c553bb15c71f741992ce88d27544475eb977bbc9a225c'], + }), + ('DelayedMatrixStats', '1.18.0', { + 'checksums': ['5b637538070ee949bad499390d140c0e8eac0d3f19655de71f5c64c092d99ce2'], + }), + ('minfi', '1.42.0', { + 'checksums': ['06e7596df31e8c01cd990f7f0dde3ef5e001cf58531ecb110f609658f8f9a508'], + }), + ('FDb.InfiniumMethylation.hg19', '2.2.0', { + 'checksums': ['605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f'], + }), + ('methylumi', '2.42.0', { + 'checksums': ['9c4bb87b4f581ebe142ca1bd42434f07248250da793ef4490bd2d152b08d934e'], + }), + ('lumi', '2.48.0', { + 'checksums': ['2d7964151fc7eab8cd4bea18b17f2d3c60f233a5302bbf46d5d5fb200ba5f51b'], + }), + ('widgetTools', '1.74.0', { + 'checksums': ['cd2027038e0cb97a63dd0e7d01d5c3425c3a722c24c80d6f5dd1a84f60d18183'], + }), + ('tkWidgets', '1.74.0', { + 'checksums': ['60124d00b1b0839b6a25befcaa76433ec9c4b867b0457219592335f43561f12c'], + }), + ('Mfuzz', '2.56.0', { + 'checksums': ['04426eed6a20834f793024370cc9120e54be586f7ab417227c0c8b3bf87de567'], + }), + ('venn', '1.11', { + 'checksums': ['33d915c7c90078f1e76e803fa3f02ab5b74dd04de7a9700477e51e0235f19314'], + }), + ('maSigPro', '1.68.0', { + 'checksums': ['2f81ff0150c613c3ebdd2eead744cbf4e5d5c68683be2213eba6b3d1254687d0'], + }), + ('SPIA', '2.48.0', { + 'checksums': ['fc246d7db41f6c34e6ca4d4f8fc63c20e79a171168e9e96283c8bf3e0ce9d5e8'], + }), + ('Gviz', '1.40.1', { + 'checksums': ['71af4c24a462438f73f010103ce49f10a2744e8d9839b56fc67805b161d7432b'], + }), + ('cummeRbund', '2.38.0', { + 'checksums': ['185478a9e3ed1b8c8bc9e475a8cf42720ef1ca79078c1cc19dfe9b4162b58adc'], + }), + ('GenomicFiles', '1.32.1', { + 'checksums': ['7fee384a18a2926acf53777ef011cbaefa65c87e975abdf7119d4e239475cc1b'], + }), + ('derfinderHelper', '1.30.0', { + 'checksums': ['e5527df3b13f13cbfee97af8f60019df8ef2394e0d7911b4640556b74a5fff64'], + }), + ('derfinder', '1.30.0', { + 'checksums': ['3b9f4aea71f556219d262b216dcd5d7d38f5b0d4c09de9b466baa269c477d9ff'], + }), + ('polyester', '1.32.0', { + 'checksums': ['fe7cee66c8bb7bd1eab3a26852c34742524478b2b762bc5806a07b83df5345d0'], + }), + ('Rsubread', '2.10.4', { + 'checksums': ['349fe4942612b7192d6de0b31b7e686d4a10e90934c67cf9d1163fb55e11b094'], + }), + ('pcaMethods', '1.88.0', { + 'checksums': ['2b41f13657f86c404851bc8164f748b755fb42f174b8fb4fa3ff80e30fd50781'], + }), + ('marray', '1.74.0', { + 'checksums': ['11d56753452ad1d9fd1829849dfcfe0de7b09b7a1d7619b8a75e8f3f15f88e2b'], + }), + ('CGHbase', '1.56.0', { + 'checksums': ['9971d4f559ad99604a43c664993360e3b42e5298afb9f5c4f6b63c9281f11ee1'], + }), + ('Wrench', '1.14.0', { + 'checksums': ['8afd0fa42accbd4058cf62a1edba2659047c49b911612d7441928753892ea6ff'], + }), + ('lpsymphony', '1.24.0', { + 'checksums': ['6f8c96972863d3c1ed8f55b937ceaf4e43832d59350d0231e2dfafa23502874d'], + }), + ('IHW', '1.24.0', { + 'checksums': ['aeea5a941d44a9b6c45e2bd7af5bcc40816b6565941282be09b09fdfcaf14ebf'], + }), + ('metagenomeSeq', '1.38.0', { + 'checksums': ['02cc936885c5835fb1a942face09618a4221d11e3c5f0741da00ff471a45106d'], + }), + ('gdsfmt', '1.32.0', { + 'checksums': ['000ff7bdfc325b8f37159d3bd3219fec95d2f92972ac2461e1de30f776f4bcb1'], + }), + ('SNPRelate', '1.30.1', { + 'checksums': ['998d11991c8d564932e25e947b164360c9aa9dffa87e533144a42ef00af96cc8'], + }), + ('biomformat', '1.24.0', { + 'checksums': ['3669661b489e5bb1b1e230cf6989e2c2d759714b62f4dab2a5f559d86f94988b'], + }), + ('phyloseq', '1.40.0', { + 'checksums': ['5378322e1c0b71a3d7d5703cc8c14df1c7844753ebb89d5825872b1f3fd99e41'], + }), + ('NADA', '1.6-1.1', { + 'checksums': ['670ff6595ba074ed0a930b7a09624d5ef20616379a20e768c1a7b37332aee44a'], + }), + ('zCompositions', '1.4.0-1', { + 'checksums': ['33ee11f635cb87cc9c0617e1cfc91f1ac41c6cfe2b70fc441e226015939230e7'], + }), + ('RcppZiggurat', '0.1.6', { + 'checksums': ['9c78255ca476c945c05a564d1e4da363de714d890e0e27f3b252fd73c50eed71'], + }), + ('Rfast', '2.0.6', { + 'checksums': ['34694b5c67ce8fcbdc90aac2ac80a74d4b66515f383e6301aea7c020009ebe7f'], + }), + ('ALDEx2', '1.28.1', { + 'checksums': ['492e774d4e72c86511028420eac13ec3cd49a210849c10e9257f51aa45e9f776'], + }), + ('dada2', '1.24.0', { + 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], + 'checksums': [ + '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b', # dada2_1.24.0.tar.gz + # dada2-1.16.0-remove-sse-on-aarch64.patch + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + ], + }), + ('LEA', '3.8.0', { + 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], + 'checksums': [ + 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774', # LEA_3.8.0.tar.gz + # LEA-3.0.0_support_aarch64_and_ppc64le.patch + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', + ], + }), + ('tximport', '1.24.0', { + 'checksums': ['1db129f369b37e5ebaefa85b724b1e640fa50c8317f009834ae7f37d0552d9b2'], + }), + ('SingleCellExperiment', '1.18.0', { + 'checksums': ['f76ccbb90d2cf14edca37f34815b3242e25eb18dd749eedd97f15b47f7c22a68'], + }), + ('beachmat', '2.12.0', { + 'checksums': ['0c292f7368fb6a7d0809f332a02576d6c6cdf3b86ae22fa493ae062ce5de8639'], + }), + ('RcppAnnoy', '0.0.19', { + 'checksums': ['89b209900516f3096b53c90937081fb8965c605c867aa465f1b3b68092b7688a'], + }), + ('RcppHNSW', '0.3.0', { + 'checksums': ['a0eb4eea65e28ba31e8306a1856f7e617a192bd448b148f88abe99181cbde007'], + }), + ('BiocNeighbors', '1.14.0', { + 'checksums': ['bda4dfa69b93b21a4d6949e2ebaa4265d467b253130e7192c271f7cbea8783a8'], + }), + ('rsvd', '1.0.5', { + 'checksums': ['e40686b869acd4f71fdb1e8e7a6c64cd6792fc9d52a78f9e559a7176ab84e21e'], + }), + ('ScaledMatrix', '1.4.0', { + 'checksums': ['949533de2730ae04794dc386e08e08f46a95471e1f32272fbcf01cbb6a31c05c'], + }), + ('BiocSingular', '1.12.0', { + 'checksums': ['7dd45d85c0c8248406caab4accb74b483d0066443e443b51bc5049602df32aeb'], + }), + ('scuttle', '1.6.2', { + 'checksums': ['f64fe1c7478b45d062656cfd2ecad3341abb1b1d9eb0ac0857dd0ce2f8c0d55a'], + }), + ('RcppML', '0.3.7', { + 'checksums': ['325c6515085527eb9123cc5e87e028547065771ed4d623048f41886ae28908c6'], + }), + ('scater', '1.24.0', { + 'checksums': ['3c9718fd782a69159d4361f497fea417478682f200274b09b6c5d7c3dfcb1137'], + }), + ('sitmo', '2.0.2', { + 'checksums': ['448ef8d56e36783354011845daf33f1efb83ea3b9685eea75eaf5134e24fa8c2'], + }), + ('dqrng', '0.3.0', { + 'checksums': ['4beeabfe245ce7196b07369f2a7d277cb08869ad8b45a22c6354c4cc70a39abb'], + }), + ('bluster', '1.6.0', { + 'checksums': ['681356e8ff7f8be93115a733f18b8a66a4ae8e841d59908d831ab67a983789bc'], + }), + ('metapod', '1.4.0', { + 'checksums': ['ebe8d6ce014448fe43b21cb5525339be95457931246a104ec6983caa1060e9a5'], + }), + ('scran', '1.24.0', { + 'checksums': ['1c997e6c653e74bc99a4b249ead5490e47523553adcf5f6f31aa8454066de775'], + }), + ('SC3', '1.24.0', { + 'checksums': ['e253051097403d8c5cadad27193cfc35e402efe943ed3132c4ce95fc53073d9d'], + }), + ('ComplexHeatmap', '2.12.0', { + 'checksums': ['c5e8e76184e7bf91b1b1ee36d48dd0b03ff08d019c567038cb37213ae94e6495'], + }), + ('GENIE3', '1.18.0', { + 'checksums': ['54ccf0e155f8160b5903a9bbfa77d05be32a9a65e472f7906a392dfbedb57b40'], + }), + ('dupRadar', '1.26.1', { + 'checksums': ['b63bd2946ce00e4ce1104c691dea8b8bc7407c9879491ba4e0a8d105ebb3ce51'], + }), + ('DNAcopy', '1.70.0', { + 'checksums': ['8cc7c37dd99dc90d0543ae24e7662aa10a52788a6b54fdaccb04d165d1257081'], + }), + ('sva', '3.44.0', { + 'checksums': ['441d2096740bd7acceedd5704b104c077adf0226821f49b584405160732a424d'], + }), + ('ballgown', '2.28.0', { + 'checksums': ['089c8fcc1650fd4872ac5eaeb3dfbfd498d8cb977f46264bd4b54f5dbd1b1851'], + }), + ('DropletUtils', '1.16.0', { + 'checksums': ['9cb38acd4097f448dd39ead182f6cf36a9b83e124245e7e21d4681d323f408ff'], + }), + ('DeconRNASeq', '1.38.0', { + 'checksums': ['661e11800fc7ce9706e735b18e0a16e0176a9a6b133a102944a5f6ac119a5583'], + }), + ('GSVA', '1.44.2', { + 'checksums': ['580b70cd77d2a38ffda3bba6f78e44f5d27f6ed09b5297a3eed8fd81a1090260'], + }), + ('PureCN', '2.2.0', { + 'checksums': ['db490d56e6f69c15e3d9967a1e9eecf2647bf029b60b6e032d0a6a297a52a6e5'], + }), + ('globaltest', '5.50.0', { + 'checksums': ['452736d1d75be95b5781888eaf0d0fc0809e9539bb0f74882f111c9a6a4fb055'], + }), + ('GlobalAncova', '4.14.0', { + 'checksums': ['641b24765da7bdbc5fa76c9a3edd19e37274c1e99dc4714e432e3a06e8048507'], + }), + ('vsn', '3.64.0', { + 'checksums': ['0ebf308a53caf996c5cb93685cddef071bb68975df25770a0dc7f4b765db47c9'], + }), + ('mzID', '1.34.0', { + 'checksums': ['c1245fd0cb5cd23601794520b9786e37f63887532d8f7a3449a4d9a4bcc72ae0'], + }), + ('mzR', '2.30.0', { + 'checksums': ['ba318b62d3a5d1297f25360eca1e29f926e7679351cf129ec36b0ab2e0000ab7'], + }), + ('MsCoreUtils', '1.8.0', { + 'checksums': ['f0f7d14b2d8560043a06dcad0c957d4c2070922cc7caa7ea54a81fe1d90ffd1c'], + }), + ('MSnbase', '2.22.0', { + 'checksums': ['a38f0232b8aa8b1713cf5f9071447a3a00c1866f0d82b49f61c672c1c604f6f7'], + }), + ('MassSpecWavelet', '1.62.0', { + 'checksums': ['69b44651c7b7862523617d8f9b4700652af01b5485e0e574fd011e377cfb313d'], + }), + ('MsFeatures', '1.4.0', { + 'checksums': ['037b64dada359ed60c4c5ad474c20560251ba13e827c24c9ba250c4c30c33184'], + }), + ('xcms', '3.18.0', { + 'checksums': ['b58763f7c1520c7b02702cc371a2a0df3419a5deae3d223cc24552248e685f5c'], + }), + ('CAMERA', '1.52.0', { + 'checksums': ['257b25b53fe9e73b6b6d1a366ca0a9160d307527eecd2fbf47c1a1872a88e84b'], + }), + ('fgsea', '1.22.0', { + 'checksums': ['ef56433dfff96c1ab20737d6af954c1c6f5158fb74654ce875849aa8def3d646'], + }), + ('GWASExactHW', '1.01', { + 'checksums': ['e850ed40fbf14b02eb3798603cfb111fe3718bb69d74c0ff4cb6f679209a15a7'], + }), + ('quantsmooth', '1.62.0', { + 'checksums': ['3a2bf8786a52c3709c2b5baf006f77365acd806cc2383005b24d471a43a8ea08'], + }), + ('GWASTools', '1.42.0', { + 'checksums': ['9fc08c28ece2f22ba9b834645f0c2e6bc0105a869f08338012c717a9ae620f58'], + }), + ('SeqArray', '1.36.2', { + 'checksums': ['17ca83fdae5175b7f0631f95598602c5f8209ed285899d2b47b13bfae11c9312'], + }), + ('SeqVarTools', '1.34.0', { + 'checksums': ['6a2c3275c4adc0d6fab912b5d00747456fd80c2c8063172ac6de250cde5c2abe'], + }), + ('GENESIS', '2.26.0', { + 'checksums': ['2c517d2e008cd2d4fbb5b19c7ed0e58b33b5fb3a8fa7aec108dd6f9aa4e9c3e2'], + }), + ('MLInterfaces', '1.76.0', { + 'checksums': ['453f7b0aa2a91f5e3815b9ae37fe3e0dff1dfa19a3840f089bee46d9670a2d9d'], + }), + ('pRoloc', '1.36.0', { + 'checksums': ['ffba6a8083ffd1153c6880f3e5f6522a96f5f1c578d29f68f9691bc059b7df86'], + }), + ('pRolocdata', '1.34.0', { + 'checksums': ['10030fafa36d8ab321e98341b471e4f08072974797074bf69d2faa54bddd33ac'], + }), + ('fresh', '0.2.0', { + 'checksums': ['a92db254ae88e8371efac44efe2cf1f5be7cce62291fdf994ebd68c14dad079d'], + }), + ('waiter', '0.2.5', { + 'checksums': ['9ac25e979db9242598bd0492ff862360009b51ce672184ec9f4eeb2232164979'], + }), + ('shinydashboardPlus', '2.0.3', { + 'checksums': ['49a88cfa396f880ff4faf558bb038763084287c932e27b0c9251f4d676584d83'], + }), + ('shinyhelper', '0.3.2', { + 'checksums': ['f7ed62543ab4d05a34b69a9183517a09e93e1b2da85b113282de0f9982db90b0'], + }), + ('shinyWidgets', '0.7.0', { + 'checksums': ['d4cb8ab7a96861a819128f9deeb293e8178f90fcd51f0e84467161ca7cd36711'], + }), + ('pRolocGUI', '2.6.0', { + 'checksums': ['b097d2c35429c5612b789af3438f9a83926659ffc0e019ef7b32d017fcb48848'], + }), + ('EBImage', '4.38.0', { + 'checksums': ['510381699581592915aa5e73271f99b8ca73fe2a92fb96b86a699ac157219ded'], + }), + ('GenomicScores', '2.8.2', { + 'checksums': ['f2a4823ad57d47528044a05ac16b3c84868334f21d95ac0e2e2d58950cef2c8b'], + }), + ('BSgenome.Mmusculus.UCSC.mm10', '1.4.3', { + 'checksums': ['dcf602bf9fadf1ef4ce70e0c0fc92b6435467df5affe7d0872d88a93b99ff9ee'], + }), + ('TxDb.Mmusculus.UCSC.mm10.knownGene', '3.10.0', { + 'checksums': ['696281749d01737c94894564d62093433045bc007a4528cc3d94f205edb54977'], + }), + ('regioneR', '1.28.0', { + 'checksums': ['6ea89b61959317a16a16a16f589df0996eb55123814a7674fab18720b6889087'], + }), + ('InteractionSet', '1.24.0', { + 'checksums': ['a56a76d729d30824b533e01692f0badfce6abe708b568870d4a86e5944af5162'], + }), + ('ChIPpeakAnno', '3.30.1', { + 'checksums': ['1ed141ec6994a7a548e7dcd41de3bfd54352cb7e85b42dab77ecb3de287d4628'], + }), + ('seqLogo', '1.62.0', { + 'checksums': ['b9f3c5038c8ca343f25a938ccd87a90ef1ee99be4bca474dab4c9d50d11063d2'], + }), + ('rGADEM', '2.44.0', { + 'checksums': ['e4d928382ff48651860057cbf66e30c9670c4ee97322d761b2c00e063e6f7d04'], + }), + ('MotifDb', '1.38.0', { + 'checksums': ['7165a40692d2c906cfbe6513e5e2759ff6efd3e00547d5e288b16d0f28f8ceb3'], + }), + ('poweRlaw', '0.70.6', { + 'checksums': ['efc091449c5c6494c1c13c85a8eb95625d1c55ffffebe86c7ea16e4abbafa191'], + }), + ('CNEr', '1.32.0', { + 'checksums': ['780a43bba1307625b1bf395c20a22002b7338ea3796f2e20eef95ab45dc9fb17'], + }), + ('DirichletMultinomial', '1.38.0', { + 'checksums': ['bdae3433f4fcf27f8aae91f7ee5f14c4b6f6263d7ba89d4bcd9502f4b1808096'], + }), + ('TFMPvalue', '0.0.8', { + 'checksums': ['6d052529f7b59d0384edc097f724f70468013777b6adf4c63e61a359029d3841'], + }), + ('TFBSTools', '1.34.0', { + 'checksums': ['3c899efd9c44cb9398ecff7a6fb40fa8fd2dc9b4deaf8fd3684e9ece440ed250'], + }), + ('motifStack', '1.40.0', { + 'checksums': ['1fe01cd6ae2e700f35d21c937976cbf48a331626c086e4cc5e9f41364e875134'], + }), + ('ATACseqQC', '1.20.2', { + 'checksums': ['17cf6c17610c287a187010f30b880ae57e5e9f9ef42b3d018fec01c92ab0474a'], + }), + ('ResidualMatrix', '1.6.0', { + 'checksums': ['445b280e890d70303200a48599211c25841c03b564928cdf15924ba0f61b59de'], + }), + ('batchelor', '1.12.3', { + 'checksums': ['ac4bd7758ddf758ec599873c6ac698721ca11417db7a8b87799daa07371c3d02'], + }), + ('gsmoothr', '0.1.7', { + 'checksums': ['b75ffd2a4a0f357762e02e46e355b45cc90ea637830f0a1b01f216bb4541e903'], + }), + ('Ringo', '1.60.0', { + 'checksums': ['ec7e0b3897400f8137b33d01d3f8c0842991c1ac273ea17ea9518617eeefd5fe'], + }), + ('R.devices', '2.17.1', { + 'checksums': ['3b7e57039311c034ff87ccebef4f16410d59985693c47949ecefa49a166c9c09'], + }), + ('R.filesets', '2.14.0', { + 'checksums': ['707dd7c099aeadbecebbd2ba57e6400405aa44487c641f3729ce06c4c642bb23'], + }), + ('aroma.light', '3.26.0', { + 'checksums': ['da6fd263bcf8a66b8b6f09bc16a1360fc5c92c4c415794d22b4038bd79da8088'], + }), + ('PSCBS', '0.66.0', { + 'checksums': ['58805636e55e0fd3f57bd4a0e296a8bb3d57a7bdd0fdd5868a73ddc83d173a93'], + }), + ('aroma.core', '3.2.2', { + 'checksums': ['35e0312e403a1894da036afac12d1d727c937e666d7eb400bfe4018b21244855'], + }), + ('R.huge', '0.9.0', { + 'checksums': ['f12d113a965603cfdbbb46e1a57331d267916235555b22f2bbc06caa302ae58e'], + }), + ('aroma.apd', '0.6.0', { + 'checksums': ['87513774baeed8e1d43f819e615c85278aef748ebc842f1ee50686c3392e37d1'], + }), + ('aroma.affymetrix', '3.2.0', { + 'checksums': ['d279cf13cf6ed8369cfdf6682ace12924379bad578003453449aa1ccec31b0a7'], + }), + ('Repitools', '1.42.0', { + 'checksums': ['48a60c930cae9343b0820c88e274c6c5c473fc73075ef966ff272a3e70f35ac9'], + }), + ('BSgenome.Hsapiens.UCSC.hg38', '1.4.4', { + 'checksums': ['024e3571b70f8e07bd50c4dd4d2dc05288497bf5409a9ac4ef12db94b081b50f'], + }), + ('MEDIPS', '1.48.0', { + 'checksums': ['a025c9f0c5846ecd9e16ba3945c6522080272789c46ebaffb1cb422c8f12afe3'], + }), + ('RProtoBufLib', '2.8.0', { + 'patches': ['RProtoBufLib-2.8.0_fix-protobuf-build.patch'], + 'checksums': [ + 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7', # RProtoBufLib_2.8.0.tar.gz + # RProtoBufLib-2.8.0_fix-protobuf-build.patch + '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64', + ], + }), + ('cytolib', '2.8.0', { + 'checksums': ['cf4b6d2f32610c14c967ac791ea762e187776ace978c6135a2453116b51865a1'], + }), + ('flowCore', '2.8.0', { + 'checksums': ['19ce4ffbf70bd3b5a68b045f0c4a21f85c0586ff0817be22d01b44c2b289cc9e'], + }), + ('mutoss', '0.1-12', { + 'checksums': ['2889ae3d502157592697124eb86adc14911e2b7fdaa7204743a376b1eeb967fa'], + }), + ('qqconf', '1.2.3', { + 'checksums': ['9b5b6042ea8e52e6e049807c0b5e3bfd534b624bd257be769de69cf505fece62'], + }), + ('metap', '1.8', { + 'checksums': ['ee9501a8de8a4c47af1632e6053e42ef53fc4b8bdf0f2759edc4d3eefaf5552b'], + }), + ('uwot', '0.1.11', { + 'checksums': ['4fcf90f1369a2a1f01db9e05a2365b155b2ada8e51e1f7f3ba5122d86affd41b'], + }), + ('scattermore', '0.8', { + 'checksums': ['dbdd73d8261cb063464bb29d5c17733b7e87bc50a19948bc80439e19f2a9f8e5'], + }), + ('SeuratObject', '4.1.0', { + 'checksums': ['9ca406cb3bd95c588e1a81c5383e3173a446cc0667142b139ca32685b4b20a05'], + }), + ('Seurat', '4.1.1', { + 'checksums': ['201aa96919b32378fc4cb67557188214c1242dcbae50cadd7d12c86666af8ace'], + }), + ('ALL', '1.38.0', { + 'checksums': ['1fdce1f158f0c8c68ab9c86e0464ec9e70a8a3470d6a3da7abfc88d10b012010'], + }), + ('ConsensusClusterPlus', '1.60.0', { + 'checksums': ['f7809db4eef81367be8b92b327e64dfd373e689893f0a99dd238e54a7a644180'], + }), + ('flowViz', '1.60.2', { + 'checksums': ['2531766d40373f44794cb64d8d7ac993e97e1730ae62ac25e7405b6904fb3c23'], + }), + ('ncdfFlow', '2.42.1', { + 'checksums': ['67ef4d897a1a497d6c822bcb924169800773d1bcfb5d5e305cb60971e7eea91c'], + }), + ('aws.signature', '0.6.0', { + 'checksums': ['f7fe4f686979be21e5a8ba7ae11f0fade4f5aaf4e98063b5349ee0962dbb9496'], + }), + ('aws.s3', '0.3.21', { + 'checksums': ['bd21054ab63555d294e7465dcb6c86f107db52ba841aeac5bdf4d00af0674c8c'], + }), + ('flowWorkspace', '4.8.0', { + 'checksums': ['5a6305edbe8da4651bfa8d4d866411b097833d12ad55687a91a133244c8a3e66'], + }), + ('ash', '1.0-15', { + 'checksums': ['8b0a7bc39dd0ce2172f09edc5b5e029347d041a4d508bbff3f3fd6f69450c2ab'], + }), + ('hdrcde', '3.4', { + 'checksums': ['4341c6a021da46dcae3b1ef6d580e84dcf625c2b2139f537d0c26ec90899149b'], + }), + ('rainbow', '3.6', { + 'checksums': ['63d1246f88a498f3db0321b46a552163631b288a25b24400935db41326636e87'], + }), + ('fds', '1.8', { + 'checksums': ['203a5e7671e542dcb83d4c75d0f4012aaebc32d54f94657afaf9e71e99dd0489'], + }), + ('fda', '6.0.5', { + 'checksums': ['14445776fc65284cd6cae98e5b4dd14c2626d96db5f78c0fcc6aabce5419b8f1'], + }), + ('flowStats', '4.8.0', { + 'checksums': ['9243df5cb48531a08137d9789f5e7a797c4cf60102ccb14fb397560195486cc9'], + }), + 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['21f5349e888ea76241912600ee5c35a0d2fd50180568b9b08b2b597f099bf708'], + }), + ('DNABarcodes', '1.26.0', { + 'checksums': ['867590e663f88db8f757b275f28cd5c75dc6e14eff1d91d7c83d43c9eea65858'], + }), + ('CAGEr', '2.2.0', { + 'checksums': ['1cd64f6b045a5e246ae92cd709234c806edfcc25463819df0bd32fe4f4b2fd0d'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' From a4a59919c521336cfb9f294f119af204356fdb8c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 7 Jul 2022 19:44:54 +0100 Subject: [PATCH 4190/9987] add Arrow in 2022a --- .../a/Arrow/Arrow-8.0.0-foss-2022a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb new file mode 100644 index 00000000000..84ee66a73e2 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb @@ -0,0 +1,69 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '8.0.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Autotools', '20220317'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '1.8.0'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for numpy + ('Boost', '1.79.0'), + ('lz4', '1.9.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.2'), + ('snappy', '1.1.9'), + ('RapidJSON', '1.1.0'), + ('RE2', '2022-06-01'), + ('utf8proc', '2.7.0'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " +configopts += "-DZSTD_ROOT=$EBROOTZSTD " + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' From a92f6363b7dea4baa378789a35b4e6c21f071c1d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Jul 2022 21:02:34 +0200 Subject: [PATCH 4191/9987] minor tweaks for release notes for v4.6.0 --- RELEASE_NOTES | 57 +++++++++++++++++++++------------------------------ 1 file changed, 23 insertions(+), 34 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b0df378ca66..3349bc49650 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 15,017 easyconfig files, for 2,735 different software packages, +The latest version of easybuild-easyconfig provides 15,020 easyconfig files, for 2,736 different software packages, incl. 37 different (compiler) toolchains. @@ -12,52 +12,41 @@ v4.6.0 (July 8th 2022) feature release -- added easyconfigs for foss/2022a, intel/2022a and gfbf/2022a (#15755) common toolchains +- added easyconfigs for foss/2022a, intel/2022a common toolchains (#15755) +- add easyconfig for gfbf/2022a toolchain (#15653, #15755) - see also https://docs.easybuild.io/en/latest/Common-toolchains.html - added example easyconfig files for 24 new software packages: - - BLT (#15624), category_encoders (#15638), fio (#10321), FSON (#15721), GCTA (#15649), gfbf (#15653), - Gibbs2 (#15702), G-PhoCS (#7619), InterProScan_data (#15717), Jorg (#15346), libopus (#15682), - Minipolish (#15713), mm-common (#15764), MONA (#15696), NetPyNE (#15606), pfind (#15685), regionmask (#15786), - samplot (#15686), SISSO (#15766), sklearn-pandas (#15637), STAR-CCM+ (#7398), SWIPE (#6795), + - BLT (#15624), category_encoders (#15638), fio (#10321), FSON (#15721), G-PhoCS (#7619), GCTA (#15649), + Gibbs2 (#15702), InterProScan_data (#15717), Jorg (#15346), libopus (#15682), Minipolish (#15713), + mm-common (#15764), MONA (#15696), NetPyNE (#15606), pfind (#15685), regionmask (#15786), samplot (#15686), + SISSO (#15766), sklearn-pandas (#15637), STAR-CCM+ (#7398), SWIPE (#6795), topaz (#15739), uncertainty-calibration (#15612), Virtuoso-opensource (#14102) - added additional easyconfigs for various supported software packages, including: - - Albumentations 1.1.0, AlphaFold 2.2.2, Arriba 2.3.0, Arrow 8.0.0, BLIS 0.9.0, Bracken 2.7, CellRanger 7.0.0, - Clp 1.17.7, CoinUtils 2.11.6, cppy 1.2.1, cuDNN 8.4.1.50, deal.II 9.3.3, double conversion, Doxygen 1.9.4, - ELPA 2021.11.001, FFTW.MPI 3.3.10, Fiona 1.8.21, FLAC 1.3.4, flatbuffers 2.0.0, flatbuffers-python 2.0, fmt 7.1.1, - FSL 6.0.5.1, g2clib 1.6.3, g2lib 3.2.0, GDAL 3.5.0, gdbm 1.21, GDRCopy 2.3, geopandas 0.11.0, GEOS 3.10.3, - Ghostscript 9.56.1, GLibmm 2.66.4, GLPK 5.0, googletest 1.11.0, graphite2 1.3.14, Groovy 4.0.3, GULP 6.1, - h5py 3.7.0, HDF 4.2.15, HDF5 1.13.1, hifiasm 0.15.2, hifiasm 0.16.1, HPL 2.3, IGMPlot 2.6.9b, ImageMagick 7.1.0, - imgaug 0.4.0, InterProScan 5.55, IRkernel 1.3, ITK 5.2.1, JasPer 2.0.33, jax 0.3.9, jemalloc 5.3.0, JsonCpp 1.9.5, - Julia 1.7.3, LAME 3.100, Leptonica 1.82.0, libgeotiff 1.7.1, libgit2 1.4.3, libiconv 1.17, libogg 1.3.5, - libreadline 8.1, libRmath 4.2.0, libsigc++ 2.10.8, libsndfile 1.1.0, LIBSVM 3.25, libtirpc 1.3.2, libvorbis 1.3.7, - libxc 5.2.3, libxml++ 2.42.1, libxslt 1.1.34, line_profiler 3.5.1, LittleCMS 2.13.1, LMDB 0.9.29, lpsolve 5.5.2.11, - makedepend 1.0.6, MaSuRCA 4.0.9, mayavi 4.7.4, MetaEuk 5, mold 1.3.0, MotionCor2 1.4.4, MPFR 4.1.0, MUMPS 5.4.1, - NCCL 2.12.12, NCL 6.6.2, ncview 2.1.8, netCDF 4.9.0, nettle 3.8, networkx 2.8.4, NEURON 7.8.2, NGS 2.10.9, - nlohmann_json 3.10.5, NLopt 2.7.1, nodejs 16.15.1, NSPR 4.34, NSS 3.79, nsync 1.25.0, nvtop 2.0.2, - ont-fast5-api 4.0.2, Osi 0.108.7, OSU-Micro-Benchmarks 5.9, p4est 2.8, parasail 2.5, Perl 5.34.1, Pillow 9.1.1, - pkgconfig 1.5.5, PLUMED 2.8.0, PnetCDF 1.12.3, poppler 21.06.1, PRISMS PF, PROJ 9.0.0, protobuf 3.19.4, - protobuf-python 3.19.4, pyfaidx 0.7.0, PyOpenGL 3.1.6, pyproj 3.3.1, pyspoa 0.0.8, Python 2.7.18, - python-parasail 1.2.4, Qhull 2020.2, Qt5 5.15.5, QuantumESPRESSO 7.1, Qwt 6.2.0, R 4.2.1, RapidJSON 1.1.0, - rasterio 1.2.10, Ray-project 1.13.0, RE2 2022, re2c 2.2, redis-py 4.3.3, ReFrame 3.11.1, ReFrame 3.11.2, - rioxarray 0.11.1, RNA-SeQC 2.4.2, ScaLAPACK 2.2.0, Schrodinger 2022, scikit-learn 1.0.1, SciPy-bundle 2022.05, - Shapely 1.8.2, Siesta 4.1.5, SimpleITK 2.1.1.2, snappy 1.1.9, SpectrA 1.0.1, spoa 4.0.7, Szip 2.1.1, TCLAP 1.2.5, - TensorFlow 2.7.1, tesseract 4.1.0, Tk 8.6.12, Tkinter 3.10.4, Transformers 4.20.1, UCX-CUDA 1.12.1, UDUNITS 2.2.28, - utf8proc 2.7.0, vt 0.57721, WhatsHap 1.4, WildMagic 5.17, WPS 3.9.1, Xvfb 21.1.3 + - AlphaFold 2.2.2, Arriba 2.3.0, Arrow 8.0.0, Bracken 2.7, CellRanger 7.0.0, Clp 1.17.7, CoinUtils 2.11.6, + cppy 1.2.1, deal.II 9.3.3, double-conversion 3.2.0, Doxygen 1.9.4, FLAC 1.3.4, fmt 7.1.1, FSL 6.0.5.1, GDAL 3.5.0, + gdbm 1.21, geopandas 0.11.0, GEOS 3.10.3, Ghostscript 9.56.1, GLibmm 2.66.4, Groovy 4.0.3, GULP 6.1, h5py 3.7.0, + HDF5 1.13.1, hifiasm 0.16.1, IGMPlot 2.6.9b, ImageMagick 7.1.0-37, InterProScan 5.55-88.0, IRkernel 1.3, + jemalloc 5.3.0, JsonCpp 1.9.5, Julia 1.7.3, Leptonica 1.82.0, libgeotiff 1.7.1, libgit2 1.4.3, libiconv 1.17, + libRmath 4.2.0, libsigc++ 2.10.8, libsndfile 1.1.0, libxc 5.2.3, libxml++ 2.42.1, line_profiler 3.5.1, + LittleCMS 2.13.1, MaSuRCA 4.0.9, mayavi 4.7.4, MetaEuk 5, mold 1.3.0, NCCL 2.12.12, netCDF 4.9.0, nettle 3.8, + networkx 2.8.4, NEURON 7.8.2, NLopt 2.7.1, nodejs 16.15.1, NSPR 4.34, NSS 3.79, nsync 1.25.0, nvtop 2.0.2, + Osi 0.108.7, p4est 2.8, parasail 2.5, Pillow 9.1.1, PLUMED 2.8.0, PnetCDF 1.12.3, PRISMS-PF 2.2, PROJ 9.0.0, + protobuf 3.19.4, protobuf-python 3.19.4, pyfaidx 0.7.0, PyOpenGL 3.1.6, pyproj 3.3.1, PyTorch 1.11.0, Qhull 2020.2, + Qt5 5.15.5, QuantumESPRESSO 7.1, Qwt 6.2.0, R 4.2.1, rasterio 1.2.10, Ray-project 1.13.0, RE2 2022-06-01, + redis-py 4.3.3, ReFrame 3.11.2, rioxarray 0.11.1, RNA-SeQC 2.4.2, Schrodinger 2022-2, Shapely 1.8.2, Siesta 4.1.5, + SimpleITK 2.1.1.2, SpectrA 1.0.1, TensorFlow 2.7.1, Tk 8.6.12, Tkinter 3.10.4, Transformers 4.20.1, + UCX-CUDA 1.12.1, utf8proc 2.7.0, WhatsHap 1.4, WPS 3.9.1, Xvfb 21.1.3 - minor enhancements, including: - - add hypergeo extension to R v4.2.0 (#15701 + - add extensions to R v4.2.0: hypergeo (#15701), rtdists (#15734), geeM (#15810) - add patch for GCCcore 11.3.0 to support using -fuse-ld=mold (#15715) - add patch for porefoam to fix hardcoded mpirun command and take into account $POREFOAM_MPIRUN_CMD (#15730) - - add rtdists extension for R v4.2.0 (#15734) - - add geeM extension to R v4.2.0 (#15810) - various bug fixes, including: - - switch to Rust 1.60.0 build dependency for bamtofastq, since build of fails with Rust 1.52.1 (E0658) (#15636) + - switch to Rust 1.60.0 build dependency for bamtofastq, since build of fails with Rust 1.52.1 (#15636) - avoid that pygmo v2.18.0 installs stuff in Python installation directory + add custom sanity check paths to pygmo easyconfigs (#15657) - add patch for Mmg v5.6.0 to remove library CI tests that point to external sources (#15691) - correct configopts in deal.II v9.1.1 easyconfig (#15692) - add missing Python dependency for HPDBSCAN to fix unresolved %(pyshortver)s template (#15694) - other changes: - - drop SpectrA 1.0.1 from GCC to GCCcore (#15652) - - in-place update to netCDF v4.9.0 (#15677) - disable flaky GPU test for TensorFlow 2.6.0 (#15824) From d0a03b75f202b17107befaeb3ca8979e0bf8a494 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Jul 2022 09:26:37 +0200 Subject: [PATCH 4192/9987] bump version to 4.6.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index b8a0b052239..25c95924956 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.6.0' +VERSION = '4.6.1.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From ce2eabce5b45dcfddd34a2ae91c0f956b92eeabc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Jul 2022 09:39:17 +0200 Subject: [PATCH 4193/9987] adding easyconfigs: EasyBuild-4.6.0.eb --- .../e/EasyBuild/EasyBuild-4.6.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.0.eb new file mode 100644 index 00000000000..7fe22124767 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.0.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.6.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/e8/e4/16246c2e65b477eca58a9c3e55a86822d9e1846cd38eef0d316e09f2888e/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/5b/7e/ebb2e41cf8462cb112e31967459fa219755e8746ad2fc1467595bff1dee8/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/b0/e3/99328129438decc5974944c56e7278ddb03fe04b017c2cdf17da6b8e2c38/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '4010e9a0e507328a2b4bc7786c0cba81e63346b1a055fa46e2b6e67453abe30f', # easybuild-framework-4.6.0.tar.gz + 'd0e2104b3265e7f844677edb8659fd29bef4f14fab27502b8afa2b955f165756', # easybuild-easyblocks-4.6.0.tar.gz + '21e1a3681343708ceb3dbf895997de54706ec72fa7c79d17454a44720f298413', # easybuild-easyconfigs-4.6.0.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 3f35a8fbb82a46bafad2af0b30163dcbbf1fca3c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 8 Jul 2022 10:06:53 +0200 Subject: [PATCH 4194/9987] adding easyconfigs: ont-remora-1.0.0-foss-2021a.eb, ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb --- ...ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb | 49 +++++++++++++++++++ .../ont-remora/ont-remora-1.0.0-foss-2021a.eb | 47 ++++++++++++++++++ 2 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..98c30da6dd5 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'ont-remora' +version = '1.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/remora' +description = """Methylation/modified base calling separated from basecalling. Remora primarily +provides an API to call modified bases for basecaller programs such as Bonito. +Remora also provides the tools to prepare datasets, train modified base models +and run simple inference.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('ONNX-Runtime', '1.10.0', versionsuffix), + ('PyTorch', '1.10.2', versionsuffix), + ('scikit-learn', '0.24.2'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('thop', '0.0.31-2005241907', { + 'source_tmpl': 'thop-0.0.31.post2005241907-py3-none-any.whl', + 'checksums': ['86d67af12311b34905949eb91c8c38f92a707de72140c29a94110cc623e21ceb'], + }), + (name, version, { + 'modulename': 'remora', + 'checksums': ['594c7f1d4cc757c0b1d42b1af5203903df10ea11cfc6af3288d60c3df8e37d4a'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/remora'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('remora', '--help'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb new file mode 100644 index 00000000000..c9a9d23f5a0 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ont-remora' +version = '1.0.0' + +homepage = 'https://github.com/nanoporetech/remora' +description = """Methylation/modified base calling separated from basecalling. Remora primarily +provides an API to call modified bases for basecaller programs such as Bonito. +Remora also provides the tools to prepare datasets, train modified base models +and run simple inference.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('ONNX-Runtime', '1.10.0'), + ('PyTorch', '1.10.2'), + ('scikit-learn', '0.24.2'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('thop', '0.0.31-2005241907', { + 'source_tmpl': 'thop-0.0.31.post2005241907-py3-none-any.whl', + 'checksums': ['86d67af12311b34905949eb91c8c38f92a707de72140c29a94110cc623e21ceb'], + }), + (name, version, { + 'modulename': 'remora', + 'checksums': ['594c7f1d4cc757c0b1d42b1af5203903df10ea11cfc6af3288d60c3df8e37d4a'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/remora'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('remora', '--help'), +] + +moduleclass = 'bio' From 9947b5f2be79bf546bff3a66ddeb81872c89a246 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 8 Jul 2022 10:54:15 +0200 Subject: [PATCH 4195/9987] fix dependency on PyTorch in ont-remora v1.0.0 --- .../o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb index 98c30da6dd5..3336e2eb4a7 100644 --- a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('ONNX-Runtime', '1.10.0', versionsuffix), - ('PyTorch', '1.10.2', versionsuffix), + ('PyTorch', '1.10.0', versionsuffix), ('scikit-learn', '0.24.2'), ('tqdm', '4.61.2'), ] diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb index c9a9d23f5a0..e135393f1f5 100644 --- a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a.eb @@ -15,7 +15,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('ONNX-Runtime', '1.10.0'), - ('PyTorch', '1.10.2'), + ('PyTorch', '1.10.0'), ('scikit-learn', '0.24.2'), ('tqdm', '4.61.2'), ] From 2320f3602937abe5afa006543ef4cf81616f5d05 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Jul 2022 11:24:44 +0100 Subject: [PATCH 4196/9987] use pkg-config instead of pkgconf for R-bundle-Bioconductor --- .../pkg-config-0.29.2-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 2 +- 2 files changed, 35 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a55b2586ff3 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [('binutils', '2.38')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 9228946a81c..b7ba755c693 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -10,7 +10,7 @@ description = """Bioconductor provides tools for the analysis and coprehension toolchain = {'name': 'foss', 'version': '2022a'} -builddependencies = [('pkgconf', '1.8.0')] +builddependencies = [('pkg-config', '0.29.2')] dependencies = [ ('R', '4.2.1'), From a7ac8d3b4309fb728234e31a0ea2416298fc8780 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 8 Jul 2022 14:05:03 +0200 Subject: [PATCH 4197/9987] adding easyconfigs: Raven-1.8.1-GCC-11.2.0.eb --- .../r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..a47333637b5 --- /dev/null +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -0,0 +1,46 @@ +easyblock = "CMakeNinja" + +name = "Raven" +version = "1.8.1" + +homepage = "https://github.com/lbcb-sci/raven" +description = "Raven is a de novo genome assembler for long uncorrected reads." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ["https://github.com/lbcb-sci/raven/archive/refs/tags/"] +sources = ["%(version)s.tar.gz"] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Ninja', '1.10.2'), +] + +configopts = ['-DRAVEN_BUILD_EXE=1 -G Ninja '] + +dependencies = [ + ('Python', '3.9.6'), + ('zlib', '1.2.11'), +] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'use_pip': True, + 'download_dep_fail': True, + 'modulename': 'ravenpy', + }) +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': [], + 'dirs': ["/"] +} + +sanity_check_commands = ["pip check"] + +moduleclass = "bio" \ No newline at end of file From 4c1f146463e13af22adba01dcbb4567336291a90 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 8 Jul 2022 14:11:28 +0200 Subject: [PATCH 4198/9987] Fixed sanity_check_paths --- easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index a47333637b5..f50eb573e34 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -37,8 +37,8 @@ exts_list = [ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_paths = { - 'files': [], - 'dirs': ["/"] + 'files': ['bin/raven'], + 'dirs': [] } sanity_check_commands = ["pip check"] From 50a3d6bec53c4cad306b035007eca9bd181a7f69 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 8 Jul 2022 14:37:53 +0200 Subject: [PATCH 4199/9987] Added new line to the end of file --- easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index f50eb573e34..8a170faf9ef 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -43,4 +43,4 @@ sanity_check_paths = { sanity_check_commands = ["pip check"] -moduleclass = "bio" \ No newline at end of file +moduleclass = "bio" From 59e6754e6a1f7cd65f01750fedeb836a7eb3a5d9 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 8 Jul 2022 16:22:18 +0200 Subject: [PATCH 4200/9987] Added checksums --- easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index 8a170faf9ef..0665537f846 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ["https://github.com/lbcb-sci/raven/archive/refs/tags/"] sources = ["%(version)s.tar.gz"] +checksums = ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'] builddependencies = [ ('CMake', '3.22.1'), @@ -26,12 +27,13 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_list = [ (name, version, { + 'download_dep_fail': True, + 'modulename': 'ravenpy', 'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'], 'sources': ['%(version)s.tar.gz'], 'use_pip': True, - 'download_dep_fail': True, - 'modulename': 'ravenpy', - }) + 'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'], + }), ] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 6ea77a900c8c7dd87707277e28d0810a17d66f57 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 8 Jul 2022 18:45:02 +0200 Subject: [PATCH 4201/9987] adding easyconfigs: jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb --- ...ter-resource-usage-0.6.1-GCCcore-10.3.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..c41be955bbb --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-resource-usage' +version = '0.6.1' + +homepage = 'https://github.com/jupyter-server/jupyter-resource-usage' +description = """Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +dependencies = [ + ('Python', '3.9.5'), + ('IPython', '7.25.0'), +] + +use_pip = True +download_dep_fail = True + +exts_list = [ + ('websocket-client', '1.2.1', { + 'modulename': 'websocket', + 'checksums': ['8dfb715d8a992f5712fff8c843adae94e22b22a99b2c5e6b0ec4a1a981cc4e0d'], + }), + ('sniffio', '1.2.0', { + 'checksums': ['c4666eecec1d3f50960c6bdf61ab7bc350648da6c126e3cf6898d8cd4ddcd3de'], + }), + ('anyio', '3.3.4', { + 'checksums': ['67da67b5b21f96b9d3d65daa6ea99f5d5282cb09f50eb4456f8fb51dffefc3ff'], + }), + ('jupyter_server', '1.11.1', { + 'checksums': ['ab7ab1cc38512f15026cbcbb96300fb46ec8b24aa162263d9edd00e0a749b1e8'], + }), + (name, version, { + 'patches': ['jupyter-resource-usage-0.6.1_compatibility.patch'], + 'checksums': [ + '8b766b9dded49e582cc38ebeb7f19af2eae50ccf77730afbe96f4a09def9874b', # jupyter-resource-usage-0.6.1.tar.gz + # jupyter-resource-usage-0.6.1_compatibility.patch + 'b030065413bac04bd40088cd92be98bac3e92d68189d03d338986444af3953f4', + ], + }), +] + +# Add the notebook extension to the search path for jupyter notebooks +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter/', +} + +sanity_check_paths = { + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/jupyter_resource_usage', + 'lib/python%(pyshortver)s/site-packages/jupyter_server' + ], + 'files': ['bin/jupyter-server'], +} + +moduleclass = 'tools' From a230c2325bd772cfeb5d2eae1be32c9e51e1933e Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 8 Jul 2022 19:13:04 +0200 Subject: [PATCH 4202/9987] Added patch to the PR --- ...ter-resource-usage-0.6.1_compatibility.patch | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1_compatibility.patch diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1_compatibility.patch b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1_compatibility.patch new file mode 100644 index 00000000000..af8d04126b3 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1_compatibility.patch @@ -0,0 +1,17 @@ +# Author: Caspar van Leeuwen +# Institute: SURF +# A 'jupyter serverextension enable --py jupyter_resource_usage' would fail, because +# _jupyter_server_extension_paths was not defined, and that's what notebook 6.4.0 +# is looking for when loading extensions. This property got renamed in later versions +# of notebook. We define it here in the __init__ for backward compatibility. +# See https://github.com/jupyter-server/jupyter-resource-usage/issues/91 +diff -Nru jupyter-resource-usage-0.6.1.orig/jupyter_resource_usage/__init__.py jupyter-resource-usage-0.6.1/jupyter_resource_usage/__init__.py +--- jupyter-resource-usage-0.6.1.orig/jupyter_resource_usage/__init__.py 2022-07-08 18:35:27.007610190 +0200 ++++ jupyter-resource-usage-0.6.1/jupyter_resource_usage/__init__.py 2022-07-08 18:35:59.866559304 +0200 +@@ -35,4 +35,6 @@ + ] + + ++# For backward compatibility + load_jupyter_server_extension = load_jupyter_server_extension ++_jupyter_server_extension_paths = _jupyter_server_extension_points From c74a246d6986e6d50f0227760cadc56921f22084 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 8 Jul 2022 19:15:58 +0200 Subject: [PATCH 4203/9987] Added sanity_pip_check = True and stripped download_dep_fail --- .../jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb index c41be955bbb..0c43626e966 100644 --- a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb @@ -14,7 +14,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True exts_list = [ ('websocket-client', '1.2.1', { @@ -53,4 +52,6 @@ sanity_check_paths = { 'files': ['bin/jupyter-server'], } +sanity_pip_check = True + moduleclass = 'tools' From 88bc6d34295266d23c463666879f7d5f2d73f8b3 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 8 Jul 2022 19:25:54 +0200 Subject: [PATCH 4204/9987] Added requests-unixsocket --- .../jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb index 0c43626e966..b40de1f257e 100644 --- a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb @@ -26,6 +26,9 @@ exts_list = [ ('anyio', '3.3.4', { 'checksums': ['67da67b5b21f96b9d3d65daa6ea99f5d5282cb09f50eb4456f8fb51dffefc3ff'], }), + ('requests-unixsocket', '0.3.0', { + 'checksums': ['28304283ea9357d45fff58ad5b11e47708cfbf5806817aa59b2a363228ee971e'], + }), ('jupyter_server', '1.11.1', { 'checksums': ['ab7ab1cc38512f15026cbcbb96300fb46ec8b24aa162263d9edd00e0a749b1e8'], }), From 869b8f3c8daa330e7cd0b9d0957811942a96902b Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 8 Jul 2022 19:33:18 +0200 Subject: [PATCH 4205/9987] Added binutils as build dependency, as the CI seems to suggest --- .../jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb index b40de1f257e..11fb4cfd097 100644 --- a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.1-GCCcore-10.3.0.eb @@ -8,6 +8,10 @@ description = """Jupyter Notebook Extension for monitoring your own Resource Usa toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +builddependencies = [ + ('binutils', '2.36.1'), +] + dependencies = [ ('Python', '3.9.5'), ('IPython', '7.25.0'), From 432a618ab119a31174703400f7f00bfd382b376e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 9 Jul 2022 10:54:25 +0200 Subject: [PATCH 4206/9987] adding easyconfigs: CDO-2.0.5-gompi-2021b.eb --- .../c/CDO/CDO-2.0.5-gompi-2021b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb new file mode 100644 index 00000000000..b24f3a033dc --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.0.5' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'cstd': 'c++14', 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/26823/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('cURL', '7.78.0'), + ('ecCodes', '2.24.2'), + ('FFTW', '3.3.10'), + ('HDF5', '1.12.1'), + ('libxml2', '2.9.10'), + ('netCDF', '4.8.1'), + ('PROJ', '8.1.0'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.37'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["cdo --version"] + +moduleclass = 'data' From 6f1df373d1be8f6f252a1d92ba301a785f7a6d6c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 9 Jul 2022 11:16:11 +0200 Subject: [PATCH 4207/9987] add checksums for CDO v2.0.5 --- easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb index b24f3a033dc..4760913c169 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb @@ -11,6 +11,7 @@ toolchainopts = {'cstd': 'c++14', 'usempi': True} source_urls = ['https://code.mpimet.mpg.de/attachments/download/26823/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['edeebbf1c3b1a1f0c642dae6bc8c7624e0c54babe461064dc5c7daca4a5b0dce'] builddependencies = [ ('pkg-config', '0.29.2'), From 07320f2de8e4956b869c2422c8b9ad33222cb965 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 9 Jul 2022 11:18:00 +0200 Subject: [PATCH 4208/9987] add attributions to CDO-2.0.5-gompi-2021b.eb --- easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb index 4760913c169..5cc675f67e7 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb @@ -1,3 +1,7 @@ +# updated to version 2.0.5, based on the previous 1.9.10 version +# J. Sassmannshausen (Imperical College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) + easyblock = 'ConfigureMake' name = 'CDO' From c342cdbe246233e777c4f28dd325b32abd37af85 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 12 Jul 2022 09:57:10 +0200 Subject: [PATCH 4209/9987] fix typo in attribution of CDO v2.0.5 easyconfig --- easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb index 5cc675f67e7..78745e7806b 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb @@ -1,5 +1,5 @@ # updated to version 2.0.5, based on the previous 1.9.10 version -# J. Sassmannshausen (Imperical College London, UK) +# J. Sassmannshausen (Imperial College London, UK) # Alex Domingo (Vrije Universiteit Brussel, BE) easyblock = 'ConfigureMake' From d4957b460b35204605a7f4b90eeba9c31c6d1efc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B8rgen=20Nordmoen?= Date: Tue, 12 Jul 2022 10:18:19 +0200 Subject: [PATCH 4210/9987] adding easyconfigs: cuTENSOR-1.6.0.3-CUDA-11.3.1.eb --- .../cuTENSOR/cuTENSOR-1.6.0.3-CUDA-11.3.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.0.3-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.0.3-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.0.3-CUDA-11.3.1.eb new file mode 100644 index 00000000000..0de8aeeda56 --- /dev/null +++ b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.0.3-CUDA-11.3.1.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'cuTENSOR' +local_shortver = '1.6.0' +version = local_shortver + '.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cutensor' +description = """The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, + reduction and elementwise operations.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cutensor/redist/libcutensor/linux-x86_64/'] +sources = ['libcutensor-linux-x86_64-%(version)s-archive.tar.xz'] +checksums = ['b07e32a37eee1df7d9330e6d7faf9baf7fffd58007e2544164ea30aec49a5281'] + +local_cudamajver = '11' +dependencies = [('CUDA', local_cudamajver + '.3.1')] + +sanity_check_paths = { + 'files': ['include/cutensor.h', 'include/cutensor/types.h', + 'lib/%s/libcutensor.%s' % (local_cudamajver, SHLIB_EXT), + 'lib/%s/libcutensor_static.a' % local_cudamajver], + 'dirs': [], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib/%s' % local_cudamajver], + 'LIBRARY_PATH': ['lib/%s' % local_cudamajver], +} + +moduleclass = 'lib' From f54019888fe29260d960be75db5a2cd0ef196f16 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 12 Jul 2022 13:13:20 +0200 Subject: [PATCH 4211/9987] {lib}[foss/2021a] scikit-optimize 0.9.0 --- .../pretty-yaml-21.10.1-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ .../scikit-optimize-0.9.0-foss-2021a.eb | 29 +++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-21.10.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.9.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-21.10.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-21.10.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..08a61b6799f --- /dev/null +++ b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-21.10.1-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pretty-yaml' +local_mod = 'pyaml' +version = '21.10.1' + +homepage = 'https://github.com/mk-fg/pretty-yaml' +description = """PyYAML-based python module to produce pretty and readable YAML-serialized data. +This module is for serialization only, see ruamel.yaml module for literate YAML +parsing (keeping track of comments, spacing, line/column numbers of values, etc).""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod] +sources = ['%s-%%(version)s.tar.gz' % local_mod] +checksums = ['c6519fee13bf06e3bb3f20cacdea8eba9140385a7c2546df5dbae4887f768383'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': local_mod} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.9.0-foss-2021a.eb b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.9.0-foss-2021a.eb new file mode 100644 index 00000000000..306d5ba89e8 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.9.0-foss-2021a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'scikit-optimize' +version = '0.9.0' + +homepage = 'https://scikit-optimize.github.io' +description = """Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive + and noisy black-box functions.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['77d8c9e64947fc9f5cc05bbc6aed7b8a9907871ae26fe11997fd67be90f26008'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-learn', '0.24.2'), + ('matplotlib', '3.4.2'), + ('pretty-yaml', '21.10.1'), +] + +options = {'modulename': 'skopt'} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 81692ca6ecee52e530c3b1a4861984ffae66f6af Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 12 Jul 2022 17:00:29 +0200 Subject: [PATCH 4212/9987] Added exts_default_options --- easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index 0665537f846..09bd28b9332 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -25,13 +25,17 @@ dependencies = [ ] exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + exts_list = [ (name, version, { - 'download_dep_fail': True, 'modulename': 'ravenpy', 'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'], 'sources': ['%(version)s.tar.gz'], - 'use_pip': True, 'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'], }), ] From ac94590288cfb7f7d5123a9b6aef4aa76d38873b Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 12 Jul 2022 17:12:02 +0200 Subject: [PATCH 4213/9987] Specified the maximum number of concurrent processes to use when building --- easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index 09bd28b9332..6133c17411e 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -17,6 +17,7 @@ builddependencies = [ ('Ninja', '1.10.2'), ] +preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && " configopts = ['-DRAVEN_BUILD_EXE=1 -G Ninja '] dependencies = [ From 51a6c79cb83fb160464ac0d976dd17bc3975a285 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 12 Jul 2022 17:40:29 +0200 Subject: [PATCH 4214/9987] downgrade SPAdes: Unicycler 0.4.9 isn't working with upper SPAdes version --- .../s/SPAdes/SPAdes-3.13.0-GCC-10.3.0.eb | 46 +++++++++++++++++++ .../Unicycler/Unicycler-0.4.9-gompi-2021a.eb | 2 +- 2 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..a0d2e6b9948 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.0-GCC-10.3.0.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'CMakeMake' + +name = 'SPAdes' +version = '3.13.0' + +homepage = 'https://cab.spbu.ru/software/spades/' +description = "Genome assembler for single-cell and isolates data sets" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['c63442248c4c712603979fa70503c2bff82354f005acda2abc42dd5598427040'] + +builddependencies = [ + ('CMake', '3.20.1'), +] +dependencies = [ + ('Python', '3.9.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('libreadline', '8.1'), +] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', + 'spades-ionhammer', 'spades-kmercount', 'spades.py']], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s.py', '--test')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb index 8a08b0b73e7..5cc941bd5b7 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb @@ -19,7 +19,7 @@ dependencies = [ ('Java', '11', '', True), ('Bowtie2', '2.4.4'), ('SAMtools', '1.13'), - ('SPAdes', '3.15.3'), + ('SPAdes', '3.13.0'), ('Racon', '1.4.21'), ('Pilon', '1.23', '-Java-%(javaver)s', True), ('BLAST+', '2.11.0'), From 5fa18ef8d421f95b229d194544e8b21171fbd612 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 13 Jul 2022 09:23:26 +0200 Subject: [PATCH 4215/9987] Enable HDF5 --- easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021b.eb index c5b823407ea..a44f872bb10 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021b.eb @@ -28,6 +28,7 @@ dependencies = [('HDF5', '1.12.1')] preconfigopts = "cd ../%(name)s-%(version)s/ext/htslib/ && " preconfigopts += "sed -i '/AC_PROG_CC/a AC_CANONICAL_HOST' configure.ac && " preconfigopts += "autoreconf -i && cd - && " +configopts = '-DUSE_HDF5=ON' parallel = 1 From 9016cae093cfe574b19f62ea0c10f9178198d716 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Jul 2022 12:44:24 +0200 Subject: [PATCH 4216/9987] adding easyconfigs: Globus-CLI-3.2.0-GCCcore-10.3.0.eb, Globus-CLI-3.6.0-GCCcore-11.2.0.eb --- .../Globus-CLI-3.2.0-GCCcore-10.3.0.eb | 46 ++++++++++++++++++ .../Globus-CLI-3.6.0-GCCcore-11.2.0.eb | 47 +++++++++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.2.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.6.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..5c173f6d975 --- /dev/null +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'Globus-CLI' +version = '3.2.0' + +homepage = "https://docs.globus.org/cli/" +description = """A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services + from the shell, and is suited to both interactive and simple scripting use cases.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('click', '8.0.4', { + # click in Python v3.9.5 easyconfig is too old for globus-sdk + 'checksums': ['8458d7b1287c5fb128c90e23381cf99dcde74beaf6c7ff6384ce84d6fe090adb'], + }), + ('PyJWT', '2.4.0', { + 'modulename': 'jwt', + 'checksums': ['d42908208c699b3b973cbeb01a969ba6a96c821eefb1c5bfe4c390c01d67abba'], + }), + ('globus-sdk', '3.2.0', { + 'checksums': ['33bc60bf769b2c42eddc2e50c03d3c56ba74660f593a2a207bb46ebd6a8be85a'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + (name, version, { + 'modulename': 'globus_cli', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['860a3245582c79e42168588e5f0478004f29106f74b548ef8d757bb5e8309b96'], + }), +] + +fix_python_shebang_for = ['bin/globus', 'bin/jp.py', 'bin/pyjwt'] + +sanity_check_commands = ['globus --help'] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.6.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.6.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9cf6769c2d8 --- /dev/null +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.6.0-GCCcore-11.2.0.eb @@ -0,0 +1,47 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'Globus-CLI' +version = '3.6.0' + +homepage = "https://docs.globus.org/cli/" +description = """A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services + from the shell, and is suited to both interactive and simple scripting use cases.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('PyJWT', '2.4.0', { + 'modulename': 'jwt', + 'checksums': ['d42908208c699b3b973cbeb01a969ba6a96c821eefb1c5bfe4c390c01d67abba'], + }), + ('typing-extensions', '4.3.0', { + # typing-extensions in Python v3.9.6 easyconfig is too old for globus-sdk + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6'], + }), + ('globus-sdk', '3.9.0', { + 'checksums': ['456f707b25a8c502607134f1d699b5970ef1aa9d17877474db73fc6d87c711e9'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + (name, version, { + 'modulename': 'globus_cli', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['dd1b8d1f384c0010556adc50970ffd1dd2f03ce8d0a5ae315961f32fa0554407'], + }), +] + +fix_python_shebang_for = ['bin/globus', 'bin/jp.py', 'bin/pyjwt'] + +sanity_check_commands = ['globus --help'] + +moduleclass = 'data' From 93912872550ee459b95a4d870afcac619176c33c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Jul 2022 12:48:59 +0200 Subject: [PATCH 4217/9987] downgrade Globus-CLI from v3.1.2 to v3.1.1 in GCCcore/10.2.0 --- ....eb => Globus-CLI-3.1.1-GCCcore-10.2.0.eb} | 21 +++++-------------- 1 file changed, 5 insertions(+), 16 deletions(-) rename easybuild/easyconfigs/g/Globus-CLI/{Globus-CLI-3.1.2-GCCcore-10.2.0.eb => Globus-CLI-3.1.1-GCCcore-10.2.0.eb} (67%) diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb similarity index 67% rename from easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.2-GCCcore-10.2.0.eb rename to easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb index 308e879ac99..30bc7bbffde 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'PythonBundle' name = 'Globus-CLI' -version = '3.1.2' +version = '3.1.1' homepage = "https://docs.globus.org/cli/" description = """A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services @@ -11,13 +11,8 @@ description = """A Command Line Wrapper over the Globus SDK for Python, which pr toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [ - ('OpenSSL', '1.1.1h'), ('Python', '3.8.6'), -] - -builddependencies = [ - ('binutils', '2.35'), - ('OpenSSL', '1.1.1h'), + ('OpenSSL', '1.1', '', True), ] use_pip = True @@ -27,18 +22,12 @@ exts_list = [ ('click', '8.0.3', { 'checksums': ['410e932b050f5eed773c4cda94de75971c89cdb3155a72a0831139a79e5ecb5b'], }), - ('configobj', '5.0.6', { - 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], - }), - ('cryptography', '3.3.1', { - 'checksums': ['7e177e4bea2de937a584b13645cab32f25e3d96fc0bc4a4cf99c27dc77682be6'], - }), ('PyJWT', '2.3.0', { 'modulename': 'jwt', 'checksums': ['b888b4d56f06f6dcd777210c334e69c737be74755d3e5e9ee3fe67dc18a0ee41'], }), - ('globus-sdk', '3.1.0', { - 'checksums': ['22b0f54ea0528f0a6c9906c5f983519482b5f00c2d6f903225a77f52ad22ef28'], + ('globus-sdk', '3.0.3', { + 'checksums': ['f608ce7772dca3c2c8de22b4e89fadae82de7e326f18df3440c99ecac0ae5f55'], }), ('jmespath', '0.10.0', { 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], @@ -46,7 +35,7 @@ exts_list = [ (name, version, { 'modulename': 'globus_cli', 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['b1667efc1bde56b9e6f56d74e7746988c7588f3a88a8264af10c15d5de003c82'], + 'checksums': ['480876fd45f5921369854197a7b6681df1d67831d8c5f503f5d44b8cf39d4e7a'], }), ] From 181d37b5a821eeaff9a3989806816c241ede6cac Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Jul 2022 13:03:05 +0200 Subject: [PATCH 4218/9987] add missing build dependency on binutils to Globus-CLI --- .../g/Globus-CLI/Globus-CLI-3.2.0-GCCcore-10.3.0.eb | 4 ++++ .../g/Globus-CLI/Globus-CLI-3.6.0-GCCcore-11.2.0.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.2.0-GCCcore-10.3.0.eb index 5c173f6d975..45f561b1ab2 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.2.0-GCCcore-10.3.0.eb @@ -10,6 +10,10 @@ description = """A Command Line Wrapper over the Globus SDK for Python, which pr toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +builddependencies = [ + ('binutils', '2.36.1'), +] + dependencies = [ ('Python', '3.9.5'), ] diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.6.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.6.0-GCCcore-11.2.0.eb index 9cf6769c2d8..1ac2753ebc0 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.6.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.6.0-GCCcore-11.2.0.eb @@ -10,6 +10,10 @@ description = """A Command Line Wrapper over the Globus SDK for Python, which pr toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +builddependencies = [ + ('binutils', '2.37'), +] + dependencies = [ ('Python', '3.9.6'), ] From 29d3cb1ef5ad378d795a4e49e44ebd3ffac12f40 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Jul 2022 13:04:13 +0200 Subject: [PATCH 4219/9987] restore build dependency on binutils to Globus-CLI v3.1.1 --- .../g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb index 30bc7bbffde..b8e860947db 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb @@ -10,6 +10,10 @@ description = """A Command Line Wrapper over the Globus SDK for Python, which pr toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [ + ('binutils', '2.35'), +] + dependencies = [ ('Python', '3.8.6'), ('OpenSSL', '1.1', '', True), From a40fbb50e95075037b98fa60d44175368523dc46 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 13 Jul 2022 15:29:37 +0100 Subject: [PATCH 4220/9987] adding easyconfigs: kim-api-2.3.0-GCCcore-11.2.0.eb --- .../k/kim-api/kim-api-2.3.0-GCCcore-11.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..75b74574da8 --- /dev/null +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-11.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'kim-api' +version = '2.3.0' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +KIM is an API and OpenKIM is a collection of interatomic models (potentials) for +atomistic simulations. This is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild only installs the API, the models can be installed with the +package openkim-models, or the user can install them manually by running + kim-api-collections-management install user MODELNAME +or + kim-api-collections-management install user OpenKIM +to install them all. + """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://s3.openkim.org/kim-api/'] +sources = ['%(name)s-%(version)s.txz'] +checksums = ['93673bb8fbc0625791f2ee67915d1672793366d10cabc63e373196862c14f991'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('CMake', '3.22.1'), # Also needed to install models, thus not just a builddependency. +] + +parallel = 1 +separate_build_dir = True +build_type = 'Release' + +modextravars = { + 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' +} + +sanity_check_paths = { + 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'chem' From afc4ce3a208bf9a03d4a30006883cb9e731ec2b1 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 13 Jul 2022 15:37:50 +0100 Subject: [PATCH 4221/9987] adding easyconfigs: molmod-1.4.8-foss-2021b.eb --- .../m/molmod/molmod-1.4.8-foss-2021b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021b.eb new file mode 100644 index 00000000000..ee12c06558e --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = [ + '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8', # molmod-1.4.8.tar.gz +] + +dependencies = [ + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; pytest -ra" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From c3f3b14872e2a107bb3a97225615a15203479c9f Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 13 Jul 2022 19:29:30 +0000 Subject: [PATCH 4222/9987] Add CVE patch, attempt to fix symbol patch for all OSes --- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb | 8 ++++++-- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 8 ++++++-- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb | 8 ++++++-- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb | 8 ++++++-- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb | 8 ++++++-- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb | 8 ++++++-- 6 files changed, 36 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb index e2267db2da0..d39dadea0a5 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb @@ -20,10 +20,14 @@ toolchain = {'name': 'GCCcore', 'version': '10.1.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['XZ-5.2.2_compat-libs.patch'] +patches = [ + 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5-cve-2022-1271.patch', +] checksums = [ '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch + '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch + '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb index 264331a9b0f..e54a2560c6d 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -20,10 +20,14 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['XZ-5.2.2_compat-libs.patch'] +patches = [ + 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5-cve-2022-1271.patch', +] checksums = [ '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch + '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch + '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb index ebb84399388..c02c4e17cc9 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb @@ -13,10 +13,14 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['XZ-5.2.2_compat-libs.patch'] +patches = [ + 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5-cve-2022-1271.patch', +] checksums = [ '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch + '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch + '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb index 0ff1f6a50bc..f6a70e9b211 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb @@ -13,10 +13,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['XZ-5.2.2_compat-libs.patch'] +patches = [ + 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5-cve-2022-1271.patch', +] checksums = [ '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch + '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch + '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb index e604951b507..2ee4825b700 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb @@ -13,10 +13,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['XZ-5.2.2_compat-libs.patch'] +patches = [ + 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5-cve-2022-1271.patch', +] checksums = [ '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch + '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch + '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb index fa1a3854e24..22e7b6ed6ef 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb @@ -10,10 +10,14 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] -patches = ['XZ-5.2.2_compat-libs.patch'] +patches = [ + 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5-cve-2022-1271.patch', +] checksums = [ '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch + '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch + '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch ] builddependencies = [ From bcebb3320ffb63f9804ca8d4d64d1822ec7c9792 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 13 Jul 2022 19:30:30 +0000 Subject: [PATCH 4223/9987] Add the actual patches --- .../x/XZ/XZ-5.2.5_compat-libs.patch | 35 +++++++ .../x/XZ/xz-5.2.5-cve-2022-1271.patch | 94 +++++++++++++++++++ 2 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch create mode 100644 easybuild/easyconfigs/x/XZ/xz-5.2.5-cve-2022-1271.patch diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch b/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch new file mode 100644 index 00000000000..275f9dbe01d --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch @@ -0,0 +1,35 @@ +Based on https://git.centos.org/rpms/xz/blob/c7/f/SOURCES/xz-5.2.2-compat-libs.patch +(which is a CentOS7-only patch) +but includes the XZ_5.2 symbols as the lack of these is causing problems in +other scenarios +(see https://github.com/easybuilders/easybuild-easyconfigs/issues/14991) + +diff -rupN xz-5.2.5/src/liblzma/liblzma.map xz-5.2.5_updated/src/liblzma/liblzma.map +--- xz-5.2.5/src/liblzma/liblzma.map 2020-03-17 14:28:54.000000000 +0000 ++++ xz-5.2.5_updated/src/liblzma/liblzma.map 2022-07-13 18:54:15.280407061 +0000 +@@ -95,14 +95,21 @@ global: + lzma_vli_size; + }; + +-XZ_5.2 { ++XZ_5.1.2alpha { ++global: ++ lzma_stream_encoder_mt; ++ lzma_stream_encoder_mt_memusage; ++} XZ_5.0; ++ ++XZ_5.2.2 { + global: + lzma_block_uncomp_encode; + lzma_cputhreads; + lzma_get_progress; +- lzma_stream_encoder_mt; +- lzma_stream_encoder_mt_memusage; + + local: + *; +-} XZ_5.0; ++} XZ_5.1.2alpha; ++ ++XZ_5.2 { ++} XZ_5.2.2; diff --git a/easybuild/easyconfigs/x/XZ/xz-5.2.5-cve-2022-1271.patch b/easybuild/easyconfigs/x/XZ/xz-5.2.5-cve-2022-1271.patch new file mode 100644 index 00000000000..406ded5903e --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/xz-5.2.5-cve-2022-1271.patch @@ -0,0 +1,94 @@ +From 69d1b3fc29677af8ade8dc15dba83f0589cb63d6 Mon Sep 17 00:00:00 2001 +From: Lasse Collin +Date: Tue, 29 Mar 2022 19:19:12 +0300 +Subject: [PATCH] xzgrep: Fix escaping of malicious filenames (ZDI-CAN-16587). + +Malicious filenames can make xzgrep to write to arbitrary files +or (with a GNU sed extension) lead to arbitrary code execution. + +xzgrep from XZ Utils versions up to and including 5.2.5 are +affected. 5.3.1alpha and 5.3.2alpha are affected as well. +This patch works for all of them. + +This bug was inherited from gzip's zgrep. gzip 1.12 includes +a fix for zgrep. + +The issue with the old sed script is that with multiple newlines, +the N-command will read the second line of input, then the +s-commands will be skipped because it's not the end of the +file yet, then a new sed cycle starts and the pattern space +is printed and emptied. So only the last line or two get escaped. + +One way to fix this would be to read all lines into the pattern +space first. However, the included fix is even simpler: All lines +except the last line get a backslash appended at the end. To ensure +that shell command substitution doesn't eat a possible trailing +newline, a colon is appended to the filename before escaping. +The colon is later used to separate the filename from the grep +output so it is fine to add it here instead of a few lines later. + +The old code also wasn't POSIX compliant as it used \n in the +replacement section of the s-command. Using \ is the +POSIX compatible method. + +LC_ALL=C was added to the two critical sed commands. POSIX sed +manual recommends it when using sed to manipulate pathnames +because in other locales invalid multibyte sequences might +cause issues with some sed implementations. In case of GNU sed, +these particular sed scripts wouldn't have such problems but some +other scripts could have, see: + + info '(sed)Locale Considerations' + +This vulnerability was discovered by: +cleemy desu wayo working with Trend Micro Zero Day Initiative + +Thanks to Jim Meyering and Paul Eggert discussing the different +ways to fix this and for coordinating the patch release schedule +with gzip. +--- + src/scripts/xzgrep.in | 20 ++++++++++++-------- + 1 file changed, 12 insertions(+), 8 deletions(-) + +diff --git a/src/scripts/xzgrep.in b/src/scripts/xzgrep.in +index b180936..e5186ba 100644 +--- a/src/scripts/xzgrep.in ++++ b/src/scripts/xzgrep.in +@@ -180,22 +180,26 @@ for i; do + { test $# -eq 1 || test $no_filename -eq 1; }; then + eval "$grep" + else ++ # Append a colon so that the last character will never be a newline ++ # which would otherwise get lost in shell command substitution. ++ i="$i:" ++ ++ # Escape & \ | and newlines only if such characters are present ++ # (speed optimization). + case $i in + (*' + '* | *'&'* | *'\'* | *'|'*) +- i=$(printf '%s\n' "$i" | +- sed ' +- $!N +- $s/[&\|]/\\&/g +- $s/\n/\\n/g +- ');; ++ i=$(printf '%s\n' "$i" | LC_ALL=C sed 's/[&\|]/\\&/g; $!s/$/\\/');; + esac +- sed_script="s|^|$i:|" ++ ++ # $i already ends with a colon so don't add it here. ++ sed_script="s|^|$i|" + + # Fail if grep or sed fails. + r=$( + exec 4>&1 +- (eval "$grep" 4>&-; echo $? >&4) 3>&- | sed "$sed_script" >&3 4>&- ++ (eval "$grep" 4>&-; echo $? >&4) 3>&- | ++ LC_ALL=C sed "$sed_script" >&3 4>&- + ) || r=2 + exit $r + fi >&3 5>&- +-- +2.35.1 + From 213200088b9adf88937b19111e4648575969c6dd Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 14 Jul 2022 11:57:31 +0200 Subject: [PATCH 4224/9987] adding easyconfigs: bigdft-suite-1.9.1-foss-2021b.eb and patches: bigdft_suite_index_bug.patch --- .../bigdft-suite-1.9.1-foss-2021b.eb | 142 ++++++++++++++++++ .../bigdft-suite/bigdft_suite_index_bug.patch | 19 +++ 2 files changed, 161 insertions(+) create mode 100644 easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch diff --git a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb new file mode 100644 index 00000000000..2ba9facf4b0 --- /dev/null +++ b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb @@ -0,0 +1,142 @@ +easyblock = "Bundle" + +name = "bigdft-suite" +version = "1.9.1" +local_version = "1.9.1" + +homepage = "https://gitlab.com/l_sim/bigdft-suite" +description = """ +BigDFT: electronic structure calculation based on Daubechies wavelets. +bigdft-suite is a set of different packages to run bigdft. +""" + +toolchain = {"name": "foss", "version": "2021b"} +toolchainopts = { + "usempi": True, + "extra_fflags": "-fallow-argument-mismatch", + "extra_fcflags": "-fallow-argument-mismatch", + "extra_f90flags": "-fallow-argument-mismatch -lgain", +} + +default_easyblock = "ConfigureMake" +default_component_specs = { + "source_urls": [ + "https://gitlab.com/l_sim/bigdft-suite/-/archive/%s/" % local_version + ], + "sources": ["bigdft-suite-%s.tar.gz" % local_version], + "start_dir": "bigdft-suite-%s" % local_version, +} + + +local_configopts = """CC=\\"$MPICC\\" FC=\\" $MPIFC \\" \ +--enable-mpi \ +\ +FCFLAGS=\\"$CPPFLAGS -fallow-argument-mismatch -I%(installdir)s/include \ +-I$EBROOTSCALAPACK/include $FCFLAGS -std=legacy \\" \ +\ +FFLAGS=\\"$CPPFLAGS -fallow-argument-mismatch -I%(installdir)s/include \ +-I$EBROOTSCALAPACK/include $FFLAGS -std=legacy \\" \ +\ +F90FLAGS=\\"$CPPFLAGS -fallow-argument-mismatch -I%(installdir)s/include \ +-I$EBROOTSCALAPACK/include $F90FLAGS -std=legacy \\" \ +\ +--with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS \\" \ +--with-yaml-path=\\"$EBROOTLIBYAML\\" """ + + +local_preinstallopts = ( + "export CPATH=%(installdir)s/include/futile:%(installdir)s/include/:$CPATH && " +) +local_preinstallopts += "export LIBRARY_PATH=%(installdir)s/lib:$LIBRARY_PATH && " +local_preinstallopts += ( + "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +) +local_preinstallopts += ( + "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " +) +local_preinstallopts += "export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && " +local_preinstallopts += ( + "export FUTILE_DYNLIB_FLAG=%(installdir)s/lib:$FUTILE_DYNLIB_FLAG && " +) +local_preinstallopts += ( + "export FUTILE_DYNLIB_FLAG=%(installdir)s/lib:$FUTILE_DYNLIB_FLAG && " +) +local_preinstallopts += ( + "export ac_use_libxc=yes && export LIBXC_INCLUDE=$EBROOTLIBXC/include && " +) +local_preinstallopts += "mkdir bigdft_builddir && cd bigdft_builddir && " + +local_preinstallopts += ( + "unset LIBS && python3 ../Installer.py build bigdft -y -v -c %s && " + % local_configopts +) + +local_preinstall = ( + """ + mkdir bigdft_builddir && \ + cd bigdft_builddir && \ + python3 ../Installer.py build bigdft -y -v -c %s && """ + % local_configopts +) + +components = [ + ( + name, + version, + { + # "patches": ["bigdft_remove_dep_lgain.patch"],bigdft_suite_index_bug + "patches": ["bigdft_suite_index_bug.patch"], + "skipsteps": ["configure", "build"], + # "preinstallopts": local_preinstallopts, + "preinstallopts": local_preinstall, + "install_cmd": "rsync -rv %(builddir)s/bigdft-suite-1.9.1/bigdft_builddir/install/ %(installdir)s", + }, + ), +] + +builddependencies = [ + ("CMake", "3.21.1"), +] + +dependencies = [ + ("Autoconf", "2.71"), + ("Python", "3.9.6"), + ("OpenCV", "4.5.5", "-contrib"), + ("XZ", "5.2.5"), +] +modextrapaths = {"PYTHONPATH": ["lib/python%(pyshortver)s/site-packages"]} +modextrapaths = {"PYTHONPATH": ["lib/python%(pyshortver)s/site-packages"]} + +sanity_check_paths = { + "files": [ + "include/futile.mod", + "include/futile.h", + "bin/bigdft", + "bin/bigdftvars.sh", + ] + + [("lib/python3.9/site-packages/BigDFT/Systems.py", "lib64/libbigdft-1.a")], + "dirs": [], +} + +local_test_script = """ +from BigDFT.Systems import System +from BigDFT.Fragments import Fragment +from BigDFT.IO import XYZReader +N2 = System() +with XYZReader("N2") as ifile: + N2["N:0"] = Fragment([next(ifile)]) + N2["N:1"] = Fragment([next(ifile)]) +print(N2.get_posinp()) +""" + +local_cmd = ( + "echo '" + + local_test_script + + "' > " + + "%(installdir)s/bigdft_test.py && python %(installdir)s/bigdft_test.py && rm %(installdir)s/bigdft_test.py " +) + +sanity_check_commands = [(local_cmd)] + + +moduleclass = "phys" diff --git a/easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch b/easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch new file mode 100644 index 00000000000..6fb764780db --- /dev/null +++ b/easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch @@ -0,0 +1,19 @@ +diff -ruN bigdft-suite-1.9.1_orig/futile/flib/f_input_file.f90 bigdft-suite-1.9.1/futile/flib/f_input_file.f90 +--- bigdft-suite-1.9.1_orig/futile/flib/f_input_file.f90 2022-02-22 10:55:06.924505000 +0100 ++++ bigdft-suite-1.9.1/futile/flib/f_input_file.f90 2022-02-22 10:55:57.462690000 +0100 +@@ -172,7 +172,6 @@ + type(dictionary), pointer :: dict + character(len = *), intent(in) :: file, key + +- integer :: i + type(dictionary), pointer :: ref,iter + character(len = max_field_length) :: val, profile_ + double precision, dimension(2) :: rg +@@ -366,6 +365,7 @@ + character(max_field_length), dimension(:), allocatable :: keys + double precision :: var + integer :: dlen, skeys ++ integer :: i + + if (associated(dict%child)) then + if (dict_len(dict) >= 1) then From 245af3b84fb10f639100cdfc3a60a67409cbafd5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Jul 2022 12:14:40 +0200 Subject: [PATCH 4225/9987] adding easyconfigs: miniasm-0.3-20191007-GCCcore-10.3.0.eb, miniasm-0.3-20191007-GCCcore-11.2.0.eb --- .../miniasm-0.3-20191007-GCCcore-10.3.0.eb | 46 +++++++++++++++++++ .../miniasm-0.3-20191007-GCCcore-11.2.0.eb | 46 +++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b2b2261baab --- /dev/null +++ b/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'miniasm' +version = '0.3-20191007' +local_commit = 'ce615d1d6b8678d38f2f9d27c9dccd944436ae75' + +homepage = 'https://github.com/lh3/minimap2' +description = """Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It +takes all-vs-all read self-mappings (typically by minimap) as input and outputs +an assembly graph in the GFA format. Different from mainstream assemblers, +miniasm does not have a consensus step. It simply concatenates pieces of read +sequences to generate the final unitig sequences. Thus the per-base error rate +is similar to the raw input reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['31d62309e8b802d3aebd492c1fed8d2a9197a3243c128345745dccb762457e3d'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" CPPFLAGS="${CPPFLAGS}"' + +files_to_copy = [ + (['%(name)s', 'minidot'], 'bin'), + (['*.h'], 'include'), + (['LICENSE.txt', 'PAF.md', 'README.md'], 'share'), + (['%(name)s.1'], 'share/man/man1'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/minidot'], + 'dirs': ['include', 'share'] +} + +sanity_check_commands = ["miniasm -V"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..03d8f7d2eac --- /dev/null +++ b/easybuild/easyconfigs/m/miniasm/miniasm-0.3-20191007-GCCcore-11.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'miniasm' +version = '0.3-20191007' +local_commit = 'ce615d1d6b8678d38f2f9d27c9dccd944436ae75' + +homepage = 'https://github.com/lh3/minimap2' +description = """Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It +takes all-vs-all read self-mappings (typically by minimap) as input and outputs +an assembly graph in the GFA format. Different from mainstream assemblers, +miniasm does not have a consensus step. It simply concatenates pieces of read +sequences to generate the final unitig sequences. Thus the per-base error rate +is similar to the raw input reads.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['31d62309e8b802d3aebd492c1fed8d2a9197a3243c128345745dccb762457e3d'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" CPPFLAGS="${CPPFLAGS}"' + +files_to_copy = [ + (['%(name)s', 'minidot'], 'bin'), + (['*.h'], 'include'), + (['LICENSE.txt', 'PAF.md', 'README.md'], 'share'), + (['%(name)s.1'], 'share/man/man1'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/minidot'], + 'dirs': ['include', 'share'] +} + +sanity_check_commands = ["miniasm -V"] + +moduleclass = 'bio' From 9ea1cf2cbd77cd055186d44c8d514ee0299d85d2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Jul 2022 12:25:25 +0200 Subject: [PATCH 4226/9987] use build enviroment from EB and add missing dependency on zlib to minimap2 --- .../easyconfigs/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb | 4 ++++ .../easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb | 4 ++++ .../easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb | 4 ++++ .../easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb | 4 ++++ .../easyconfigs/m/minimap2/minimap2-2.22-GCCcore-11.2.0.eb | 4 ++++ .../easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.2.0.eb | 4 ++++ 6 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb index 99066113b93..acf1c417a9b 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.17-GCCcore-9.3.0.eb @@ -26,6 +26,10 @@ checksums = ['b68ac8882d33cc63e9e3246775062aeb159b6990ff7f38099172c3fe6f8a2742'] builddependencies = [('binutils', '2.34')] +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + files_to_copy = [ (['%(name)s'], 'bin'), (['lib%(name)s.a'], 'lib'), diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb index 9f7b208cc9f..d159c3b3967 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.18-GCCcore-10.2.0.eb @@ -26,6 +26,10 @@ checksums = ['7a55101d58ecaec545db51079ad82b214632dc697ee67290b6dc34cc70dbeeb4'] builddependencies = [('binutils', '2.35')] +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + files_to_copy = [ (['%(name)s'], 'bin'), (['lib%(name)s.a'], 'lib'), diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb index 5cff5bf900c..8ba21e5c0fe 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.2.0.eb @@ -26,6 +26,10 @@ checksums = ['f9eff90a7f14f999df93dff6ed4e3428277edbbd6bda6bdb1800e8d57c9135e3'] builddependencies = [('binutils', '2.35')] +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + files_to_copy = [ (['%(name)s'], 'bin'), (['lib%(name)s.a'], 'lib'), diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb index 5fc4e7155b5..03c1e61f914 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.20-GCCcore-10.3.0.eb @@ -28,6 +28,10 @@ checksums = ['f9eff90a7f14f999df93dff6ed4e3428277edbbd6bda6bdb1800e8d57c9135e3'] builddependencies = [('binutils', '2.36.1')] +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + files_to_copy = [ (['%(name)s'], 'bin'), (['lib%(name)s.a'], 'lib'), diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.22-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.22-GCCcore-11.2.0.eb index 81593a1a6e6..3bc73a3ee38 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.22-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.22-GCCcore-11.2.0.eb @@ -28,6 +28,10 @@ checksums = ['c96ecd0a0dbe61eb2da6a7ae06c9fc7249ee63d2ebf1909e07213cb6ec0a4633'] builddependencies = [('binutils', '2.37')] +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + files_to_copy = [ (['%(name)s'], 'bin'), (['lib%(name)s.a'], 'lib'), diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.2.0.eb index aaec55b1014..fc4339d4b56 100644 --- a/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.2.0.eb @@ -28,6 +28,10 @@ checksums = ['9dd4c31ff082182948944bcdad6d328f64f09295d10547d72eba24189880a615'] builddependencies = [('binutils', '2.37')] +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + files_to_copy = [ (['%(name)s'], 'bin'), (['lib%(name)s.a'], 'lib'), From 65829e6e98fc3729f6b8ea384da920769b69d7c7 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 14 Jul 2022 14:26:24 +0200 Subject: [PATCH 4227/9987] fixes for tests --- .../bigdft-suite-1.9.1-foss-2021b.eb | 43 +++---------------- 1 file changed, 5 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb index 2ba9facf4b0..23f3d49f37c 100644 --- a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb @@ -43,35 +43,7 @@ F90FLAGS=\\"$CPPFLAGS -fallow-argument-mismatch -I%(installdir)s/include \ --with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS \\" \ --with-yaml-path=\\"$EBROOTLIBYAML\\" """ - local_preinstallopts = ( - "export CPATH=%(installdir)s/include/futile:%(installdir)s/include/:$CPATH && " -) -local_preinstallopts += "export LIBRARY_PATH=%(installdir)s/lib:$LIBRARY_PATH && " -local_preinstallopts += ( - "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " -) -local_preinstallopts += ( - "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " -) -local_preinstallopts += "export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && " -local_preinstallopts += ( - "export FUTILE_DYNLIB_FLAG=%(installdir)s/lib:$FUTILE_DYNLIB_FLAG && " -) -local_preinstallopts += ( - "export FUTILE_DYNLIB_FLAG=%(installdir)s/lib:$FUTILE_DYNLIB_FLAG && " -) -local_preinstallopts += ( - "export ac_use_libxc=yes && export LIBXC_INCLUDE=$EBROOTLIBXC/include && " -) -local_preinstallopts += "mkdir bigdft_builddir && cd bigdft_builddir && " - -local_preinstallopts += ( - "unset LIBS && python3 ../Installer.py build bigdft -y -v -c %s && " - % local_configopts -) - -local_preinstall = ( """ mkdir bigdft_builddir && \ cd bigdft_builddir && \ @@ -84,11 +56,9 @@ components = [ name, version, { - # "patches": ["bigdft_remove_dep_lgain.patch"],bigdft_suite_index_bug "patches": ["bigdft_suite_index_bug.patch"], "skipsteps": ["configure", "build"], - # "preinstallopts": local_preinstallopts, - "preinstallopts": local_preinstall, + "preinstallopts": local_preinstallopts, "install_cmd": "rsync -rv %(builddir)s/bigdft-suite-1.9.1/bigdft_builddir/install/ %(installdir)s", }, ), @@ -105,7 +75,6 @@ dependencies = [ ("XZ", "5.2.5"), ] modextrapaths = {"PYTHONPATH": ["lib/python%(pyshortver)s/site-packages"]} -modextrapaths = {"PYTHONPATH": ["lib/python%(pyshortver)s/site-packages"]} sanity_check_paths = { "files": [ @@ -113,8 +82,8 @@ sanity_check_paths = { "include/futile.h", "bin/bigdft", "bin/bigdftvars.sh", - ] - + [("lib/python3.9/site-packages/BigDFT/Systems.py", "lib64/libbigdft-1.a")], + "lib/python3.9/site-packages/BigDFT/Systems.py", + "lib64/libbigdft-1.a"], "dirs": [], } @@ -130,10 +99,8 @@ print(N2.get_posinp()) """ local_cmd = ( - "echo '" - + local_test_script - + "' > " - + "%(installdir)s/bigdft_test.py && python %(installdir)s/bigdft_test.py && rm %(installdir)s/bigdft_test.py " + "echo '" + local_test_script + "' > " + "%(installdir)s/bigdft_test.py && " + + "python %(installdir)s/bigdft_test.py && rm %(installdir)s/bigdft_test.py " ) sanity_check_commands = [(local_cmd)] From a68d79ae19578f93e242a8ed1e02cc61b258d35d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Jul 2022 14:45:45 +0200 Subject: [PATCH 4228/9987] adding easyconfigs: CapnProto-0.10.2-GCCcore-11.2.0.eb --- .../CapnProto-0.10.2-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e77dd1efb73 --- /dev/null +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to 0.9.1 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'CapnProto' +version = '0.10.2' + +homepage = 'https://capnproto.org' +description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" +# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." +# (only on Intel Skylake?) +toolchainopts = {'cstd': 'c++17', 'lowopt': True} + +source_urls = ['https://capnproto.org/'] +sources = ['capnproto-c++-%(version)s.tar.gz'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/capnp', 'bin/capnpc', 'bin/capnpc-c++', 'bin/capnpc-capnp'], + 'dirs': ['include/capnp', 'include/kj', 'lib'], +} + +moduleclass = 'bio' From ee60e6561db1f96dbd30b21ab0be99ef90640bee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Jul 2022 14:47:04 +0200 Subject: [PATCH 4229/9987] Explicitly enable HDF5 --- easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb index aa268d4e373..d57bbc1de73 100644 --- a/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.46.2-foss-2020b.eb @@ -25,6 +25,7 @@ builddependencies = [ dependencies = [('HDF5', '1.10.7')] preconfigopts = "cd ../%(name)s-%(version)s/ext/htslib/ && autoreconf && cd - &&" +configopts = '-DUSE_HDF5=ON' parallel = 1 From 7f811b3e75507dd83708d14a272a9107cc61904c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Jul 2022 14:53:36 +0200 Subject: [PATCH 4230/9987] adding easyconfigs: Unicycler-0.5.0-gompi-2021b.eb --- .../Unicycler/Unicycler-0.5.0-gompi-2021b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb new file mode 100644 index 00000000000..d4927e27fab --- /dev/null +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Unicycler' +version = '0.5.0' + +homepage = 'https://github.com/rrwick/Unicycler' +description = """ Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets + where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) + where it runs a miniasm+Racon pipeline. """ + +toolchain = {'name': 'gompi', 'version': '2021b'} + +github_account = 'rrwick' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['84a8709c9f2e624225410af702d779ffb0cb06f7c22c20e1f01b989945e08a47'] + +dependencies = [ + ('Python', '3.9.6'), + ('Java', '11', '', True), + ('Bowtie2', '2.4.4'), + ('SAMtools', '1.14'), + ('SPAdes', '3.15.3'), + ('Racon', '1.5.0'), + ('Pilon', '1.23', '-Java-%(javaver)s', True), + ('BLAST+', '2.12.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' From c3d85c7167e051670c432963fa9d76abfe0171fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 14 Jul 2022 14:56:07 +0200 Subject: [PATCH 4231/9987] adding easyconfigs: RNA-SeQC-2.4.2-foss-2021b.eb --- .../r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021b.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021b.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021b.eb new file mode 100644 index 00000000000..33f4463def8 --- /dev/null +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021b.eb @@ -0,0 +1,67 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'RNA-SeQC' +version = '2.4.2' + +homepage = "https://github.com/getzlab/rnaseqc" +description = """Fast, efficient RNA-Seq metrics for quality control and process optimization""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'extra_cflags': '-fpermissive'} + +dependencies = [ + ('bx-python', '0.8.13'), + ('bzip2', '1.0.8'), + ('IPython', '7.26.0'), + ('matplotlib', '3.4.3'), + ('pyBigWig', '0.3.18'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Seaborn', '0.11.2'), + ('Boost', '1.77.0'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pycryptodomex', '3.9.8', { + 'modulename': 'Cryptodome', + 'checksums': ['48cc2cfc251f04a6142badeb666d1ff49ca6fdfc303fd72579f62b768aaa52b9'], + }), + ('rsa', '4.6', { + 'checksums': ['109ea5a66744dd859bf16fe904b8d8b627adafb9408753161e766a92e7d681fa'], + }), + ('agutil', '4.1.1', { + 'preinstallopts': "sed -i 's/package\.req/package.requirement/g' setup.py &&", + 'checksums': ['e58ed53ae209007328311603bd6e05e8cd2c509204b5e542c87f971a2530fb0d'], + }), + ('qtl', '0.1.8', { + 'checksums': ['8fdb99cda1ceff578a233db6c15a944fa57b43a2826af41c292e36848906117b'], + }), + ('rnaseqc', '0.0.3', { + # Build RNA-SeQC in the preinstall opts for the associated Python package + # RNA-SeQC bundles SeqLib, with HTSlib and BWA. These are old versions so we cannot use deps here + # rnaseqc version is from python/rnaseqc/__init__.py in the RNA-SeQC source code + 'patches': [ + 'RNA-SeQC-2.4.2_Makefile.patch', + 'RNA-SeQC-2.4.2_rle_auxtab-gcc-10.patch', + ], + 'source_tmpl': 'rnaseqc.v2.4.2.full_source.tar.gz', + 'source_urls': ['https://github.com/getzlab/rnaseqc/releases/download/v2.4.2'], + 'checksums': [ + 'b214151408696430aead56921b255e2b09efe5f6087a68446deae399227a1303', # rnaseqc.v2.4.2.full_source.tar.gz + '05b537eeef398646f51552c1dd26333e268b9b9eb3af2148681cb40ea0a5e4ba', # RNA-SeQC-2.4.2_Makefile.patch + # RNA-SeQC-2.4.2_rle_auxtab-gcc-10.patch + 'efb9ab63932bf25f3589de1e8f0c17bc1ef5ae928ba73e55d430b8a9761209cb', + ], + 'preinstallopts': "make && mkdir -p %(installdir)s/bin && cp rnaseqc %(installdir)s/bin/. && cd python &&", + }), +] + +sanity_check_commands = ["rnaseqc --version"] + +moduleclass = 'bio' From 7ba0c14880719a1672bd54e2c3ff20f200143092 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Jul 2022 16:36:27 +0200 Subject: [PATCH 4232/9987] add missing dependencies and execute tests on Trycycler v0.5.2 --- .../t/Trycycler/Trycycler-0.5.2-foss-2021a.eb | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.2-foss-2021a.eb b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.2-foss-2021a.eb index e4fde764933..4337daa5f41 100644 --- a/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.2-foss-2021a.eb +++ b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.2-foss-2021a.eb @@ -15,13 +15,22 @@ checksums = ['6f6007afa6a4f7568d12b48627a09b03d389ae4e7888033433314caadd69d796'] dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), + ('R', '4.1.0'), ('edlib', '1.3.9'), + ('miniasm', '0.3-20191007'), + ('minimap2', '2.20'), + ('Mash', '2.3'), + ('MUSCLE', '3.8.31'), # v3 is preferred, see https://github.com/rrwick/Trycycler/wiki/Software-requirements#muscle ('Pillow', '8.2.0'), ] download_dep_fail = True use_pip = True +runtest = 'pytest' + +sanity_pip_check = True + sanity_check_paths = { 'files': ['bin/trycycler'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], @@ -29,6 +38,4 @@ sanity_check_paths = { sanity_check_commands = ["trycycler --help"] -sanity_pip_check = True - moduleclass = 'bio' From 0c4c067f7ea33e5b9e984649829813a2081b05b1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Jul 2022 16:40:55 +0200 Subject: [PATCH 4233/9987] add missing checksums for CapnProto v0.10.2 --- .../easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb index e77dd1efb73..3bebfc7bc10 100644 --- a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb @@ -19,6 +19,7 @@ toolchainopts = {'cstd': 'c++17', 'lowopt': True} source_urls = ['https://capnproto.org/'] sources = ['capnproto-c++-%(version)s.tar.gz'] +checksums = ['7cd91a244cb330cda5b41f4904f94b61f39ba112835b31fa8c3764cedbed819f'] builddependencies = [('binutils', '2.37')] From 7f2254c488236f656d1d0d3b2dcae4ff56eba7c1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Jul 2022 16:43:11 +0200 Subject: [PATCH 4234/9987] adding easyconfigs: Trycycler-0.5.3-foss-2021b.eb --- .../t/Trycycler/Trycycler-0.5.3-foss-2021b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.3-foss-2021b.eb b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.3-foss-2021b.eb new file mode 100644 index 00000000000..ce700ac9be9 --- /dev/null +++ b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.3-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'Trycycler' +version = '0.5.3' + +homepage = 'https://github.com/rrwick/Trycycler' +description = "Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/rrwick/Trycycler/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9a3a512284a91c8a221e3f4dedbc8acabd8f7b93937ad46402d93eee6c7ee95b'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('R', '4.1.2'), + ('edlib', '1.3.9'), + ('miniasm', '0.3-20191007'), + ('minimap2', '2.24'), + ('Mash', '2.3'), + ('MUSCLE', '3.8.31'), # v3 is preferred, see https://github.com/rrwick/Trycycler/wiki/Software-requirements#muscle + ('Pillow', '8.3.2'), +] + +download_dep_fail = True +use_pip = True + +runtest = 'pytest' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/trycycler'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["trycycler --help"] + +moduleclass = 'bio' From c7e21ba06342563520dadedcd7c05ad1e03a8af5 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Thu, 14 Jul 2022 16:45:54 +0200 Subject: [PATCH 4235/9987] Stripy-2.1.0-foss-2021a --- .../s/stripy/stripy-2.1.0-foss-2021a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/stripy/stripy-2.1.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/stripy/stripy-2.1.0-foss-2021a.eb b/easybuild/easyconfigs/s/stripy/stripy-2.1.0-foss-2021a.eb new file mode 100644 index 00000000000..29fb7e3ef03 --- /dev/null +++ b/easybuild/easyconfigs/s/stripy/stripy-2.1.0-foss-2021a.eb @@ -0,0 +1,36 @@ +easyblock = "PythonBundle" + +name = 'stripy' +version = '2.1.0' + +homepage = 'https://github.com/underworldcode/stripy' +description = """A Python interface to TRIPACK and STRIPACK Fortran code for (constrained) triangulation in Cartesian +coordinates and on a sphere. Stripy is an object-oriented package and includes routines from SRFPACK and SSRFPACK for +interpolation (nearest neighbor, linear and hermite cubic) and to evaluate derivatives (Renka 1996a,b and 1997a,b).""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('imageio', '2.10.5'), + ('Cartopy', '0.20.0'), + ('xarray', '0.19.0'), + ('netcdf4-python', '1.5.7') +] + +use_pip = True + +exts_list = [ + ('litho1pt0', '1.5.0', { + 'checksums': ['5334740cd1fffc6d31ec01a79ce60797352b7bb005a5c1a1bda826dddaf472d2'], + }), + (name, version, { + 'checksums': ['1b60cd6b4a86b07b72491ed871fa95050d5dbb41a40e9a43922b040d38cba033'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 18f2622b1ff1393236358f1fce731f8522822a18 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Jul 2022 17:04:24 +0200 Subject: [PATCH 4236/9987] rename detectron2 to Detectron2 and cleanup unneeded extensions --- .../Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb | 23 ++-- .../d/Detectron2/Detectron2-0.6-foss-2021a.eb | 23 ++-- .../detectron2-0.6-foss-2021a-CUDA-11.3.1.eb | 105 ------------------ 3 files changed, 26 insertions(+), 125 deletions(-) delete mode 100644 easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb index cdd16631b81..3cfdd856379 100644 --- a/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb @@ -24,12 +24,12 @@ dependencies = [ ('CUDA', '11.3.1', '', True), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), + ('PyTorch', '1.10.0', versionsuffix), ('torchvision', '0.11.3', versionsuffix), - ('TensorFlow', '2.6.0', versionsuffix), # provides tensorboard, termcolor + ('tensorboard', '2.8.0'), ('Hydra', '1.1.1'), # provides hydra-core, omegaconf ('matplotlib', '3.4.2'), ('OpenCV', '4.5.3', versionsuffix + '-contrib'), - ('Pillow-SIMD', '8.2.0'), ('pycocotools', '2.0.4'), ('pydot', '1.4.2'), ('tqdm', '4.61.2'), @@ -42,9 +42,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('cloudpickle', '1.6.0', { - 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], - }), ('mypy_extensions', '0.4.3', { 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], }), @@ -54,16 +51,22 @@ exts_list = [ ('black', '21.4b2', { 'checksums': ['fc9bcf3b482b05c1f35f6a882c079dc01b9c7795827532f4cc43c0ec88067bbc'], }), - ('portalocker', '2.3.2', { - 'checksums': ['75cfe02f702737f1726d83e04eedfa0bda2cc5b974b1ceafb8d6b42377efbd5f'], + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('fvcore', '0.1.5.post20220414', { + 'checksums': ['3b95983a799047661422c01671da2fa4749f60fa947e2b0ad0520f1ebc11be43'], + }), + ('portalocker', '2.4.0', { + 'checksums': ['a648ad761b8ea27370cb5915350122cd807b820d2193ed5c9cc28f163df637f4'], }), ('iopath', '0.1.9', { 'source_tmpl': '%(namelower)s-%(version)s-py3-none-any.whl', 'checksums': ['9058ac24f0328decdf8dbe209b33074b8702a3c4d9ba2f7801d46cb61a880b6e'], }), - ('fvcore', '0.1.5.post20211023', { - 'checksums': ['20597a81a5678a3c7f53fa1773ef7fd108ce00ed9da1edd1a1b0092fb1a6d15b'], - }), ('detectron2', version, { 'source_urls': [GITHUB_LOWER_SOURCE], 'sources': ['v%(version)s.tar.gz'], diff --git a/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a.eb b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a.eb index 8d2c0ea3727..ae71ba53b8b 100644 --- a/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a.eb @@ -19,12 +19,12 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), + ('PyTorch', '1.10.0'), ('torchvision', '0.11.3'), - ('TensorFlow', '2.6.0'), # provides tensorboard, termcolor + ('tensorboard', '2.8.0'), ('Hydra', '1.1.1'), # provides hydra-core, omegaconf ('matplotlib', '3.4.2'), ('OpenCV', '4.5.3', '-contrib'), - ('Pillow-SIMD', '8.2.0'), ('pycocotools', '2.0.4'), ('pydot', '1.4.2'), ('tqdm', '4.61.2'), @@ -37,9 +37,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('cloudpickle', '1.6.0', { - 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], - }), ('mypy_extensions', '0.4.3', { 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], }), @@ -49,16 +46,22 @@ exts_list = [ ('black', '21.4b2', { 'checksums': ['fc9bcf3b482b05c1f35f6a882c079dc01b9c7795827532f4cc43c0ec88067bbc'], }), - ('portalocker', '2.3.2', { - 'checksums': ['75cfe02f702737f1726d83e04eedfa0bda2cc5b974b1ceafb8d6b42377efbd5f'], + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('fvcore', '0.1.5.post20220414', { + 'checksums': ['3b95983a799047661422c01671da2fa4749f60fa947e2b0ad0520f1ebc11be43'], + }), + ('portalocker', '2.4.0', { + 'checksums': ['a648ad761b8ea27370cb5915350122cd807b820d2193ed5c9cc28f163df637f4'], }), ('iopath', '0.1.9', { 'source_tmpl': '%(namelower)s-%(version)s-py3-none-any.whl', 'checksums': ['9058ac24f0328decdf8dbe209b33074b8702a3c4d9ba2f7801d46cb61a880b6e'], }), - ('fvcore', '0.1.5.post20211023', { - 'checksums': ['20597a81a5678a3c7f53fa1773ef7fd108ce00ed9da1edd1a1b0092fb1a6d15b'], - }), ('detectron2', version, { 'source_urls': [GITHUB_LOWER_SOURCE], 'sources': ['v%(version)s.tar.gz'], diff --git a/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb deleted file mode 100644 index a0a28824b8b..00000000000 --- a/easybuild/easyconfigs/d/detectron2/detectron2-0.6-foss-2021a-CUDA-11.3.1.eb +++ /dev/null @@ -1,105 +0,0 @@ -easyblock = "PythonBundle" - -name = "detectron2" -version = "0.6" -versionsuffix = "-CUDA-%(cudaver)s" - -homepage = "https://github.com/facebookresearch/detectron2" -description = "Detectron2 is a platform for object detection, segmentation and other visual recognition tasks." - -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), - ('PyTorch', '1.10.0', versionsuffix), - ('torchvision', '0.11.1', versionsuffix), - ('Hydra', '1.1.1'), - ('tqdm', '4.61.2'), - ('YACS', '0.1.8'), - ('matplotlib', '3.4.2'), - ('pycocotools', '2.0.4'), - ('pydot', '1.4.2'), - ('tensorboard', '2.8.0'), - ('OpenCV', '4.5.3', '-CUDA-11.3.1-contrib'), -] - -exts_list = [ - ('packaging', '21.3', { - 'checksums': ['dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb'], - }), - ('poetry-core', '1.0.8', { - 'modulename': 'poetry.core', - 'checksums': ['951fc7c1f8d710a94cb49019ee3742125039fc659675912ea614ac2aa405b118'], - }), - ('poetry', '1.1.13', { - 'preinstallopts': 'sed -i "s|20.4|21.3|g" pyproject.toml &&', - 'checksums': ['b905ed610085f568aa61574e0e09260c02bff9eae12ff672af39e9f399357ac4'], - }), - ('pytest', '7.1.2', { - 'checksums': ['a06a0425453864a270bc45e71f783330a7428defb4230fb5e6a731fde06ecd45'], - }), - ('pluggy', '1.0.0', { - 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], - }), - ('CacheControl', '0.12.11', { - 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], - }), - ('mypy-extensions', '0.4.3', { - 'source_tmpl': 'mypy_extensions-%(version)s.tar.gz', - 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], - }), - ('pathspec', '0.9.0', { - 'checksums': ['e564499435a2673d586f6b2130bb5b95f04a3ba06f81b8f895b651a3c76aabb1'], - }), - ('tomli', '2.0.1', { - 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], - }), - ('editables', '0.3', { - 'checksums': ['167524e377358ed1f1374e61c268f0d7a4bf7dbd046c656f7b410cde16161b1a'], - }), - ('hatchling', '0.23.0', { - 'checksums': ['c4c5beeffe575e312519ec355a3c82af4491238c1ac4eff6feac3bd471aa5282'], - }), - ('setuptools-scm', '6.4.2', { - 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', - 'checksums': ['6833ac65c6ed9711a4d5d2266f8024cfa07c533a0e55f4c12f6eff280a5a9e30'], - }), - ('hatch-vcs', '0.2.0', { - 'source_tmpl': 'hatch_vcs-%(version)s.tar.gz', - 'checksums': ['9913d733b34eec9bb0345d0626ca32165a4ad2de15d1ce643c36d09ca908abff'], - }), - ('platformdirs', '2.5.2', { - 'checksums': ['58c8abb07dcb441e6ee4b11d8df0ac856038f944ab98b7be6b27b2a3c7feef19'], - }), - ('black', '21.4b2', { - 'checksums': ['fc9bcf3b482b05c1f35f6a882c079dc01b9c7795827532f4cc43c0ec88067bbc'], - }), - ('cloudpickle', '2.0.0', { - 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], - }), - ('termcolor', '1.1.0', { - 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], - }), - ('fvcore', '0.1.5.post20220414', { - 'checksums': ['3b95983a799047661422c01671da2fa4749f60fa947e2b0ad0520f1ebc11be43'], - }), - ('portalocker', '2.4.0', { - 'checksums': ['a648ad761b8ea27370cb5915350122cd807b820d2193ed5c9cc28f163df637f4'], - }), - ('iopath', '0.1.9', { - 'source_tmpl': '%(namelower)s-%(version)s-py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['9058ac24f0328decdf8dbe209b33074b8702a3c4d9ba2f7801d46cb61a880b6e'], - }), - (name, version, { - 'source_urls': ['https://github.com/facebookresearch/detectron2/archive/refs/tags/'], - 'sources': ['v%(version)s.tar.gz'], - 'checksums': ['9757fed05fa32acc2116ea038185f08409d5e854573e70f41909a358b70d1004'], - }), -] - -use_pip = True -sanity_pip_check = True - -moduleclass = 'vis' From 8d104f6c93853b5844465762e73b4bae125c30c5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 14 Jul 2022 17:13:32 +0200 Subject: [PATCH 4237/9987] use common dependency on torchvision v0.11.3 in foss/2021a --- easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a.eb b/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a.eb index 30b6c82cef0..a0657518bae 100644 --- a/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a.eb +++ b/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), ('PyTorch', '1.10.0'), - ('torchvision', '0.11.1'), + ('torchvision', '0.11.3'), ('scikit-learn', '0.24.2'), ] From 3233f08e3501101942264269001e20d676301f78 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 15 Jul 2022 10:12:21 +0200 Subject: [PATCH 4238/9987] Add test with sample data --- .../u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb index d4927e27fab..712952beb6f 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb @@ -29,6 +29,16 @@ dependencies = [ download_dep_fail = True use_pip = True +_test_cmd = 'unicycler -t %(parallel)s -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -o outdir' +postinstallcmds = [ + ' '.join([ + "cd %(builddir)s/%(name)s-%(version)s/sample_data &&", + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH", + "PATH=%(installdir)s/bin:$PATH", + _test_cmd, + ]), +] + sanity_pip_check = True moduleclass = 'bio' From e947b2e5e165c3885298e821065263bc14ac7270 Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Fri, 15 Jul 2022 14:24:15 +0200 Subject: [PATCH 4239/9987] easyconfig for phantompeakqualtools --- .../Phantompeakqualtools-1.2.2-foss-2021b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb new file mode 100644 index 00000000000..7064fa3ea24 --- /dev/null +++ b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'Tarball' + +name = 'Phantompeakqualtools' +version = '1.2.2' + +homepage = "https://github.com/kundajelab/phantompeakqualtools" + +description = """ It computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + + +# Download manually from https://github.com/kundajelab/phantompeakqualtools/releases +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b31263b64aefe97bdc4d7fae138f515a7d7a60cd05031d38dd89a10f9ee10cd1'] + +dependencies = [ + ('R', '4.2.0'), + ('SAMtools', '1.15.1'), + ('R-bundle-Bioconductor', '3.15', '-R-4.2.0'), +] + +preinstall_cmd = "rm spp-1.14.tar.gz" + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + # phantompeakqualtools requires spp 1.14 or 1.15.x (1.16 is not supported) + ('spp', '1.15.5', { + 'checksums': ['1c486792ac3feb194c95efe7a8a98eab4331877ba901d774561b8839c958f924'], + }), +] + + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['run_spp.R'], + 'dirs': [], +} + +sanity_check_commands = ['run_spp.R | grep "Usage: Rscript run_spp.R "'] + +moduleclass = 'bio' \ No newline at end of file From 2c88aa6c98434ebd36573366824559485570eb60 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 15 Jul 2022 14:34:53 +0200 Subject: [PATCH 4240/9987] tests --- .../bigdft-suite-1.9.1-foss-2021b.eb | 77 ++++++++----------- .../bigdft-suite/bigdft_suite_index_bug.patch | 2 + 2 files changed, 33 insertions(+), 46 deletions(-) diff --git a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb index 23f3d49f37c..9fa07e0124b 100644 --- a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb @@ -1,8 +1,7 @@ -easyblock = "Bundle" +easyblock = "CmdCp" name = "bigdft-suite" version = "1.9.1" -local_version = "1.9.1" homepage = "https://gitlab.com/l_sim/bigdft-suite" description = """ @@ -15,54 +14,35 @@ toolchainopts = { "usempi": True, "extra_fflags": "-fallow-argument-mismatch", "extra_fcflags": "-fallow-argument-mismatch", - "extra_f90flags": "-fallow-argument-mismatch -lgain", -} - -default_easyblock = "ConfigureMake" -default_component_specs = { - "source_urls": [ - "https://gitlab.com/l_sim/bigdft-suite/-/archive/%s/" % local_version - ], - "sources": ["bigdft-suite-%s.tar.gz" % local_version], - "start_dir": "bigdft-suite-%s" % local_version, + "extra_f90flags": "-fallow-argument-mismatch", } +source_urls = ["https://gitlab.com/l_sim/bigdft-suite/-/archive/%(version)s/"] +sources = ["%(name)s-%(version)s.tar.gz"] +patches = ["bigdft_suite_index_bug.patch"] + +local_configopts = " ".join( + [ + 'CC=\\"$MPICC\\" FC=\\"$MPIFC\\" --enable-mpi', + 'FCFLAGS=\\"$CPPFLAGS $FCFLAGS -std=legacy\\"', + 'FFLAGS=\\"$CPPFLAGS $FFLAGS -std=legacy\\"', + 'F90FLAGS=\\"$CPPFLAGS $F90FLAGS -std=legacy\\"', + '--with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS\\"', + '--with-yaml-path=\\"$EBROOTLIBYAML\\"', + ] +) -local_configopts = """CC=\\"$MPICC\\" FC=\\" $MPIFC \\" \ ---enable-mpi \ -\ -FCFLAGS=\\"$CPPFLAGS -fallow-argument-mismatch -I%(installdir)s/include \ --I$EBROOTSCALAPACK/include $FCFLAGS -std=legacy \\" \ -\ -FFLAGS=\\"$CPPFLAGS -fallow-argument-mismatch -I%(installdir)s/include \ --I$EBROOTSCALAPACK/include $FFLAGS -std=legacy \\" \ -\ -F90FLAGS=\\"$CPPFLAGS -fallow-argument-mismatch -I%(installdir)s/include \ --I$EBROOTSCALAPACK/include $F90FLAGS -std=legacy \\" \ -\ ---with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS \\" \ ---with-yaml-path=\\"$EBROOTLIBYAML\\" """ - -local_preinstallopts = ( +local_comp_cmd = ( """ mkdir bigdft_builddir && \ cd bigdft_builddir && \ - python3 ../Installer.py build bigdft -y -v -c %s && """ + python3 ../Installer.py build bigdft -y -v -c %s """ % local_configopts ) -components = [ - ( - name, - version, - { - "patches": ["bigdft_suite_index_bug.patch"], - "skipsteps": ["configure", "build"], - "preinstallopts": local_preinstallopts, - "install_cmd": "rsync -rv %(builddir)s/bigdft-suite-1.9.1/bigdft_builddir/install/ %(installdir)s", - }, - ), -] +cmds_map = [(".*", local_comp_cmd)] + +files_to_copy = ["bigdft_builddir/install/*"] builddependencies = [ ("CMake", "3.21.1"), @@ -74,6 +54,7 @@ dependencies = [ ("OpenCV", "4.5.5", "-contrib"), ("XZ", "5.2.5"), ] + modextrapaths = {"PYTHONPATH": ["lib/python%(pyshortver)s/site-packages"]} sanity_check_paths = { @@ -83,7 +64,8 @@ sanity_check_paths = { "bin/bigdft", "bin/bigdftvars.sh", "lib/python3.9/site-packages/BigDFT/Systems.py", - "lib64/libbigdft-1.a"], + "lib64/libbigdft-1.a", + ], "dirs": [], } @@ -98,12 +80,15 @@ with XYZReader("N2") as ifile: print(N2.get_posinp()) """ -local_cmd = ( - "echo '" + local_test_script + "' > " + "%(installdir)s/bigdft_test.py && " + - "python %(installdir)s/bigdft_test.py && rm %(installdir)s/bigdft_test.py " +local_sanity_cmd = ( + "echo '" + + local_test_script + + "' > " + + "%(installdir)s/bigdft_test.py && " + + "python %(installdir)s/bigdft_test.py && rm %(installdir)s/bigdft_test.py " ) -sanity_check_commands = [(local_cmd)] +sanity_check_commands = [(local_sanity_cmd)] moduleclass = "phys" diff --git a/easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch b/easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch index 6fb764780db..a9cf85235d6 100644 --- a/easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch +++ b/easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch @@ -1,3 +1,5 @@ +# same effect as patch for futile (futile_index_bug.patch), except due to directory structure, must be regenerated +# Author: Denis Kristak (Inuits) diff -ruN bigdft-suite-1.9.1_orig/futile/flib/f_input_file.f90 bigdft-suite-1.9.1/futile/flib/f_input_file.f90 --- bigdft-suite-1.9.1_orig/futile/flib/f_input_file.f90 2022-02-22 10:55:06.924505000 +0100 +++ bigdft-suite-1.9.1/futile/flib/f_input_file.f90 2022-02-22 10:55:57.462690000 +0100 From db5ce64d7c5136315d612b255bb66c871eb07098 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 15 Jul 2022 15:01:50 +0200 Subject: [PATCH 4241/9987] fix dependency on minimap2 in Trycycler v0.5.3 Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.3-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.3-foss-2021b.eb b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.3-foss-2021b.eb index ce700ac9be9..4ce03f293a2 100644 --- a/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.3-foss-2021b.eb +++ b/easybuild/easyconfigs/t/Trycycler/Trycycler-0.5.3-foss-2021b.eb @@ -18,7 +18,7 @@ dependencies = [ ('R', '4.1.2'), ('edlib', '1.3.9'), ('miniasm', '0.3-20191007'), - ('minimap2', '2.24'), + ('minimap2', '2.22'), ('Mash', '2.3'), ('MUSCLE', '3.8.31'), # v3 is preferred, see https://github.com/rrwick/Trycycler/wiki/Software-requirements#muscle ('Pillow', '8.3.2'), From b6dde32ec885b05b9a3a2a60384b9935afdb5f2b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 15 Jul 2022 15:05:21 +0200 Subject: [PATCH 4242/9987] improve sanity checks in CapnProto v0.10.2 Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb index 3bebfc7bc10..487ff4ad0c9 100644 --- a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb @@ -23,9 +23,13 @@ checksums = ['7cd91a244cb330cda5b41f4904f94b61f39ba112835b31fa8c3764cedbed819f'] builddependencies = [('binutils', '2.37')] +local_bins = ['capnp', 'capnpc', 'capnpc-c++', 'capnpc-capnp'] + sanity_check_paths = { - 'files': ['bin/capnp', 'bin/capnpc', 'bin/capnpc-c++', 'bin/capnpc-capnp'], + 'files': ['bin/%s' % x for x in local_bins], 'dirs': ['include/capnp', 'include/kj', 'lib'], } +sanity_check_commands = ["%s --help" % x for x in local_bins] + moduleclass = 'bio' From 1eaf7ba1ffe351f4758ca45caf34a2af15172961 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 15 Jul 2022 15:07:24 +0200 Subject: [PATCH 4243/9987] move CapnProto v0.10.2 to GCCcore/11.3.0 --- ...2-GCCcore-11.2.0.eb => CapnProto-0.10.2-GCCcore-11.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/CapnProto/{CapnProto-0.10.2-GCCcore-11.2.0.eb => CapnProto-0.10.2-GCCcore-11.3.0.eb} (91%) diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.3.0.eb similarity index 91% rename from easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.3.0.eb index 487ff4ad0c9..c833e53d566 100644 --- a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.3.0.eb @@ -11,7 +11,7 @@ version = '0.10.2' homepage = 'https://capnproto.org' description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} # -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" # lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." # (only on Intel Skylake?) @@ -21,7 +21,7 @@ source_urls = ['https://capnproto.org/'] sources = ['capnproto-c++-%(version)s.tar.gz'] checksums = ['7cd91a244cb330cda5b41f4904f94b61f39ba112835b31fa8c3764cedbed819f'] -builddependencies = [('binutils', '2.37')] +builddependencies = [('binutils', '2.38')] local_bins = ['capnp', 'capnpc', 'capnpc-c++', 'capnpc-capnp'] From 4934ead0191f47325aadff44324c6169de04dbbe Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 15 Jul 2022 16:08:49 +0200 Subject: [PATCH 4244/9987] add postprocessing command to check Unicycler is actually working --- .../u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb index 5cc941bd5b7..2e9b8f68fe0 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb @@ -28,6 +28,16 @@ dependencies = [ download_dep_fail = True use_pip = True +_test_cmd = 'unicycler -t %(parallel)s -1 short_reads_1.fastq.gz -2 short_reads_2.fastq.gz -o outdir' +postinstallcmds = [ + ' '.join([ + "cd %(builddir)s/%(name)s-%(version)s/sample_data &&", + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH", + "PATH=%(installdir)s/bin:$PATH", + _test_cmd, + ]), +] + sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From a7c842a161320fc53e27bb7f837bd5c84d0d166b Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 15 Jul 2022 17:48:31 +0200 Subject: [PATCH 4245/9987] tests --- .../bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb index 9fa07e0124b..9bc91f3f1cf 100644 --- a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb @@ -80,12 +80,14 @@ with XYZReader("N2") as ifile: print(N2.get_posinp()) """ -local_sanity_cmd = ( - "echo '" - + local_test_script - + "' > " - + "%(installdir)s/bigdft_test.py && " - + "python %(installdir)s/bigdft_test.py && rm %(installdir)s/bigdft_test.py " +local_sanity_cmd = " ".join( + [ + "echo '", + local_test_script, + "' > ", + "%(installdir)s/bigdft_test.py && ", + "python %(installdir)s/bigdft_test.py && rm %(installdir)s/bigdft_test.py ", + ] ) sanity_check_commands = [(local_sanity_cmd)] From c104eef5dae2164913e23f239d6e50da8ae477e5 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 15 Jul 2022 18:43:23 +0200 Subject: [PATCH 4246/9987] tests --- .../b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb index 9bc91f3f1cf..37bc3cb15c2 100644 --- a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb @@ -20,6 +20,10 @@ toolchainopts = { source_urls = ["https://gitlab.com/l_sim/bigdft-suite/-/archive/%(version)s/"] sources = ["%(name)s-%(version)s.tar.gz"] patches = ["bigdft_suite_index_bug.patch"] +checksums = [ + '3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41', # bigdft-suite-1.9.1.tar.gz + '81d12edb2319685ede822ca82594ea8278850e52370ced5ea40c88fe17187f8c', # bigdft_suite_index_bug.patch +] local_configopts = " ".join( [ From f12c217fdde72bd19b85389c7d8c1ded27f4ef00 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 15 Jul 2022 18:48:45 +0200 Subject: [PATCH 4247/9987] commentary --- .../b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb index 37bc3cb15c2..74db190099e 100644 --- a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb @@ -1,3 +1,5 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak easyblock = "CmdCp" name = "bigdft-suite" @@ -21,8 +23,8 @@ source_urls = ["https://gitlab.com/l_sim/bigdft-suite/-/archive/%(version)s/"] sources = ["%(name)s-%(version)s.tar.gz"] patches = ["bigdft_suite_index_bug.patch"] checksums = [ - '3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41', # bigdft-suite-1.9.1.tar.gz - '81d12edb2319685ede822ca82594ea8278850e52370ced5ea40c88fe17187f8c', # bigdft_suite_index_bug.patch + "3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41", # bigdft-suite-1.9.1.tar.gz + "81d12edb2319685ede822ca82594ea8278850e52370ced5ea40c88fe17187f8c", # bigdft_suite_index_bug.patch ] local_configopts = " ".join( From f05a609438ad6881e1fbf0d0b45f604dd2ee4367 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Mon, 18 Jul 2022 16:12:54 +0200 Subject: [PATCH 4248/9987] Added sanity check for binary --- easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index 6133c17411e..ff53344aa8a 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -48,6 +48,9 @@ sanity_check_paths = { 'dirs': [] } -sanity_check_commands = ["pip check"] +sanity_check_commands = [ + "pip check", + "raven --help" +] moduleclass = "bio" From 11c548203e2477009d980afabd03be5fb2dfd5e5 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 18 Jul 2022 07:45:46 -0700 Subject: [PATCH 4249/9987] update version --- .../v/ViennaRNA/ViennaRNA-2.5.1-foss-2021b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.5.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.5.1-foss-2021b.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.5.1-foss-2021b.eb new file mode 100644 index 00000000000..44021569e19 --- /dev/null +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.5.1-foss-2021b.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'ViennaRNA' +version = '2.5.1' + +homepage = 'https://www.tbi.univie.ac.at/RNA/' +description = """The Vienna RNA Package consists of a C code library and several +stand-alone programs for the prediction and comparison of RNA secondary structures.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.tbi.univie.ac.at/RNA/download/sourcecode/%(version_major)s_%(version_minor)s_x/'] +sources = [SOURCE_TAR_GZ] +checksums = ['05400437cf15595e10b1a25df6c9c48856f356130f9d1e380fa8866b6d27f457'] + +builddependencies = [ + ('Autotools', '20210726'), + ('flex', '2.6.4'), + ('pkg-config', '0.29.2'), + ('Bison', '3.7.6'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('GSL', '2.7'), + ('libgd', '2.3.3'), + ('X11', '20210802'), +] + +configopts = "--with-cluster --with-kinwalker --with-python3" +# Uncomment this if you compile on pre SSE4.1 CPU +# configopts += "--enable-sse " + +sanity_check_paths = { + 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', + 'inverse', 'plot', 'subopt', 'Lfold', 'cofold', + 'paln', 'duplex', 'alifold', 'plfold', 'up', + 'aliduplex', 'Lalifold', '2Dfold', 'parconv', + 'PKplex', 'plex', 'snoop', 'forester']] + + ['bin/Kinfold'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/', 'lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 3d452e074f02366ad4740c112a614dd026eafff1 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 19 Jul 2022 08:11:31 +0200 Subject: [PATCH 4250/9987] cleanup and upgrade version and toolchain --- .../s/sinto/sinto-0.7.4-foss-2021a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb b/easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb new file mode 100644 index 00000000000..2bade413d0c --- /dev/null +++ b/easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'sinto' + +version = '0.7.4' + +homepage = 'https://timoast.github.io/sinto/index.html' + +description = """Sinto is a toolkit for processing aligned single-cell data. Sinto includes functions to: + + Subset reads from a BAM file by cell barcode + + Create a scATAC-seq fragments file from a BAM file + + Add read tags to a BAM file according to cell barcode information +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a9bee81992939f6240643040551d9c69893ce07d23190e7e3a604eff254d775d'] + +dependencies = [ + ('Python', '3.9.5'), + ('Pysam', '0.16.0.1'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True + +use_pip = True + +sanity_pip_check = True + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'bio' From b684ea7d127a18b4fc28a7098099bb5c7d44a69a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 19 Jul 2022 10:14:28 +0200 Subject: [PATCH 4251/9987] patch for fixing jax0.3.9 nan problem --- .../AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb | 2 ++ .../a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb | 2 ++ .../a/AlphaFold/AlphaFold-2.2.2_jax38_NaN.patch | 16 ++++++++++++++++ 3 files changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2_jax38_NaN.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb index 5b482dfcfa1..6209b784cf4 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb @@ -83,6 +83,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.2.2_jax38_NaN.patch' # acc. to: https://github.com/deepmind/alphafold/issues/513 ], 'checksums': [ 'aa51dc4a1150b92310d20e63e9e4d9279b15b6a1f7e664360f52827f83256cdd', # v2.2.2.tar.gz @@ -92,6 +93,7 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + 'fb00a3c9cb00fe87eef77d48dfd8e44c40ad8b820480c79c5937377da27fea5f', # AlphaFold-2.2.2_jax38_NaN.patch ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb index 46803614756..86c33f118ce 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb @@ -78,6 +78,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.2.2_jax38_NaN.patch' # acc. to: https://github.com/deepmind/alphafold/issues/513 ], 'checksums': [ 'aa51dc4a1150b92310d20e63e9e4d9279b15b6a1f7e664360f52827f83256cdd', # v2.2.2.tar.gz @@ -87,6 +88,7 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + 'fb00a3c9cb00fe87eef77d48dfd8e44c40ad8b820480c79c5937377da27fea5f', # AlphaFold-2.2.2_jax38_NaN.patch ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2_jax38_NaN.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2_jax38_NaN.patch new file mode 100644 index 00000000000..ade1f98f6fe --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2_jax38_NaN.patch @@ -0,0 +1,16 @@ +#Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de +# Resulting pdb files contain NaNs because jax >= 3.8 is used. +# Fix according to https://github.com/deepmind/alphafold/issues/513 and +# https://jax.readthedocs.io/en/latest/changelog.html#jax-0-3-8-april-29-2022 +diff -ru alphafold-2.2.2/alphafold/model/utils.py alphafold-2.2.2_jax38_NaN/alphafold/model/utils.py +--- alphafold-2.2.2/alphafold/model/utils.py 2022-06-13 17:49:22.000000000 +0200 ++++ alphafold-2.2.2_jax38_NaN/alphafold/model/utils.py 2022-07-18 10:17:59.672423061 +0200 +@@ -34,7 +34,7 @@ + + def batched_gather(params, indices, axis=0, batch_dims=0): + """Implements a JAX equivalent of `tf.gather` with `axis` and `batch_dims`.""" +- take_fn = lambda p, i: jnp.take(p, i, axis=axis) ++ take_fn = lambda p, i: jnp.take(p, i, axis=axis, mode="clip") + for _ in range(batch_dims): + take_fn = jax.vmap(take_fn) + return take_fn(params, indices) From 31ef1b936adc922a95b5283da040c9969db5c246 Mon Sep 17 00:00:00 2001 From: Sagon Date: Tue, 19 Jul 2022 10:34:51 +0200 Subject: [PATCH 4252/9987] Delete sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb obsolet version --- .../sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb deleted file mode 100644 index 03810b3b73c..00000000000 --- a/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'sinto' - -version = '0.7.3.1' - -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://timoast.github.io/sinto/index.html' - -description = """Sinto is a toolkit for processing aligned single-cell data. Sinto includes functions to: - - Subset reads from a BAM file by cell barcode - - Create a scATAC-seq fragments file from a BAM file - - Add read tags to a BAM file according to cell barcode information -""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['c4f3c1413a5c5e2d3587654f7bf53669df883e4d77bb64a846bcbc3c74757c53'] - -dependencies = [ - ('Python', '3.8.6'), - ('Pysam', '0.16.0.1'), - ('SciPy-bundle', '2020.11'), -] - -download_dep_fail = True -use_pip = True - -sanity_check_commands = ['%(name)s --version'] - -moduleclass = 'bio' From 652e62f89004b40e014b0d4c997b438cd4599c6c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 19 Jul 2022 11:54:04 +0200 Subject: [PATCH 4253/9987] adding easyconfigs: pagmo-2.18.0-foss-2021b.eb, pygmo-2.18.0-foss-2021b.eb --- .../p/pagmo/pagmo-2.18.0-foss-2021b.eb | 36 +++++++++++ .../p/pygmo/pygmo-2.18.0-foss-2021b.eb | 59 +++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021b.eb b/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021b.eb new file mode 100644 index 00000000000..f85086e034b --- /dev/null +++ b/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2021b.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'pagmo' +version = '2.18.0' + +homepage = 'https://esa.github.io/pagmo2' +description = "pagmo is a C++ scientific library for massively parallel optimization." + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/esa/pagmo2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5ad40bf3aa91857a808d6b632d9e1020341a33f1a4115d7a2b78b78fd063ae31'] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Boost', '1.77.0'), + ('tbb', '2020.3'), + ('Eigen', '3.4.0'), + ('NLopt', '2.7.0'), +] + +configopts = "-DPAGMO_WITH_EIGEN3=ON -DPAGMO_WITH_NLOPT=ON -DPAGMO_BUILD_TESTS=ON" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libpagmo.%s' % SHLIB_EXT], + 'dirs': ['include/pagmo', 'lib/cmake/pagmo'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021b.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021b.eb new file mode 100644 index 00000000000..16518cab2ff --- /dev/null +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2021b.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakePythonPackage' + +name = 'pygmo' +version = '2.18.0' + +homepage = 'https://esa.github.io/pygmo2' +description = "pygmo is a scientific Python library for massively parallel optimization." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/esa/pygmo2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9f081cc973297894af09f713f889870ac452bfb32b471f9f7ba08a5e0bb9a125'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('pybind11', '2.7.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), + ('pagmo', '2.18.0'), + ('matplotlib', '3.4.3'), + ('networkx', '2.6.3'), +] + +# make sure that all files are installed in the correct location (-DCMAKE_INSTALL_PREFIX is not enough)... +configopts = "-DPYGMO_INSTALL_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" + +runtest = False + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('dill', '0.3.4', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['9f9734205146b2b353ab3fec9af0070237b6ddae78452af83d2fca84d739e675'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pygmo'], +} + +sanity_pip_check = True + +moduleclass = 'lib' From 34addc00395fb57177c2efc53f8088790cc27f88 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Tue, 19 Jul 2022 11:08:30 +0000 Subject: [PATCH 4254/9987] adding easyconfigs: LAMMPS-23Jun2022-foss-2021a-kokkos.eb, LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb --- ...LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb | 166 ++++++++++++++++++ .../LAMMPS-23Jun2022-foss-2021a-kokkos.eb | 162 +++++++++++++++++ 2 files changed, 328 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb new file mode 100644 index 00000000000..8340b750c47 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb @@ -0,0 +1,166 @@ +name = 'LAMMPS' +version = '23Jun2022' +versionsuffix = '-CUDA' +versionsuffix += '-kokkos' + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [ + 'stable_%(version)s.tar.gz', +] +checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), + ('archspec', '0.1.2'), +] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('NCCL', '2.10.3', '-CUDA-11.3.1'), + ('Python', '3.9.5'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('netCDF', '4.8.0'), + ('GSL', '2.7'), + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('cURL', '7.76.0'), + ('HDF5', '1.12.1'), + ('tbb', '2020.3'), + ('PCRE', '8.44'), + ('libxml2', '2.9.10'), + ('FFmpeg', '4.3.2'), + ('Voro++', '0.4.6'), + ('kim-api', '2.2.1'), + ('Eigen', '3.3.9'), + ('PLUMED', '2.7.2'), + ('ScaFaCoS', '1.0.1'), + ('SciPy-bundle', '2021.05'), + # VTK package is auto-disabled if this dep is not available + # ('VTK', '9.0.1'), +] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) + +# include the following extra packages into the build +general_packages = [ + 'ASPHERE', + 'ATC', + 'AWPMD', + 'BOCS', + 'BODY', + 'BPM', + 'BROWNIAN', + 'CG-DNA', + 'CG-SDK', + 'CLASS2', + 'COLLOID', + 'COLVARS', + 'COMPRESS', + 'CORESHELL', + 'DIELECTRIC', + 'DIFFRACTION', + 'DIPOLE', + 'DPD-BASIC', + 'DPD-MESO', + 'DPD-REACT', + 'DPD-SMOOTH', + 'DRUDE', + 'EFF', + 'ELECTRODE', + 'EXTRA-COMPUTE', + 'EXTRA-DUMP', + 'EXTRA-FIX', + 'EXTRA-MOLECULE', + 'EXTRA-PAIR', + 'FEP', + 'GRANULAR', + 'H5MD', + 'INTERLAYER', + 'KIM', + 'KSPACE', + 'LATBOLTZ', + 'MANIFOLD', +# 'MACHDYN', # Some issue related to Eigen 3.3.9 when using Kokkos + 'MANYBODY', + 'MC', + 'MEAM', + 'MGPT', + 'MISC', + 'ML-IAP', + 'ML-PACE', + 'ML-RANN', + 'ML-SNAP', + 'MOFFF', + 'MOLECULE', + 'MOLFILE', + 'MPIIO', + 'NETCDF', + 'OPENMP', + 'ORIENT', + 'PERI', + 'PHONON', + 'PLUGIN', + 'PLUMED', + 'POEMS', + 'PTM', + 'PYTHON', + 'QEQ', + 'QTB', + 'REACTION', + 'REAXFF', + 'REPLICA', + 'RIGID', + 'SCAFACOS', + 'SHOCK', + 'SMTBQ', + 'SPH', + 'SPIN', + 'SRD', + 'TALLY', + 'UEF', + 'VORONOI', + 'VTK', + 'YAFF', +] +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + +# hardware-specific option +cuda_compute_capabilities = ['8.0'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb new file mode 100644 index 00000000000..8563ad26181 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb @@ -0,0 +1,162 @@ +name = 'LAMMPS' +version = '23Jun2022' +versionsuffix = '-kokkos' + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [ + 'stable_%(version)s.tar.gz', +] +checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), + ('archspec', '0.1.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('netCDF', '4.8.0'), + ('GSL', '2.7'), + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('cURL', '7.76.0'), + ('HDF5', '1.12.1'), + ('tbb', '2020.3'), + ('PCRE', '8.44'), + ('libxml2', '2.9.10'), + ('FFmpeg', '4.3.2'), + ('Voro++', '0.4.6'), + ('kim-api', '2.2.1'), + ('Eigen', '3.3.9'), + ('PLUMED', '2.7.2'), + ('ScaFaCoS', '1.0.1'), + ('SciPy-bundle', '2021.05'), + # VTK package is auto-disabled if this dep is not available + # ('VTK', '9.0.1'), +] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) + + +# include the following extra packages into the build +general_packages = [ + 'ASPHERE', + 'ATC', + 'AWPMD', + 'BOCS', + 'BODY', + 'BPM', + 'BROWNIAN', + 'CG-DNA', + 'CG-SDK', + 'CLASS2', + 'COLLOID', + 'COLVARS', + 'COMPRESS', + 'CORESHELL', + 'DIELECTRIC', + 'DIFFRACTION', + 'DIPOLE', + 'DPD-BASIC', + 'DPD-MESO', + 'DPD-REACT', + 'DPD-SMOOTH', + 'DRUDE', + 'EFF', + 'ELECTRODE', + 'EXTRA-COMPUTE', + 'EXTRA-DUMP', + 'EXTRA-FIX', + 'EXTRA-MOLECULE', + 'EXTRA-PAIR', + 'FEP', + 'GRANULAR', + 'H5MD', + 'INTERLAYER', + 'KIM', + 'KSPACE', + 'LATBOLTZ', + 'MANIFOLD', + 'MACHDYN', + 'MANYBODY', + 'MC', + 'MEAM', + 'MGPT', + 'MISC', + 'ML-IAP', + 'ML-PACE', + 'ML-RANN', + 'ML-SNAP', + 'MOFFF', + 'MOLECULE', + 'MOLFILE', + 'MPIIO', + 'NETCDF', + 'OPENMP', + 'ORIENT', + 'PERI', + 'PHONON', + 'PLUGIN', + 'PLUMED', + 'POEMS', + 'PTM', + 'PYTHON', + 'QEQ', + 'QTB', + 'REACTION', + 'REAXFF', + 'REPLICA', + 'RIGID', + 'SCAFACOS', + 'SHOCK', + 'SMTBQ', + 'SPH', + 'SPIN', + 'SRD', + 'TALLY', + 'UEF', + 'VORONOI', + 'VTK', + 'YAFF', +] +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + + +moduleclass = 'chem' From 9721c2d164917e07b450b6c987f9a0ad9d00dc95 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Jul 2022 13:10:40 +0200 Subject: [PATCH 4255/9987] Don't include CUDA compute capabilities --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb index 8340b750c47..52a45b7d7f9 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb @@ -161,6 +161,6 @@ general_packages = [ # - QMMM (setup seems complex) # hardware-specific option -cuda_compute_capabilities = ['8.0'] +# cuda_compute_capabilities = ['8.0'] moduleclass = 'chem' From b2fa0c1e050e3cf90264204dea813a34fffb09bd Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 19 Jul 2022 13:27:02 +0200 Subject: [PATCH 4256/9987] Fix style issue --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb index 52a45b7d7f9..e2ee788f76d 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb @@ -109,7 +109,7 @@ general_packages = [ 'KSPACE', 'LATBOLTZ', 'MANIFOLD', -# 'MACHDYN', # Some issue related to Eigen 3.3.9 when using Kokkos + # 'MACHDYN', # Some issue related to Eigen 3.3.9 when using Kokkos 'MANYBODY', 'MC', 'MEAM', From 917c733520e986c0434c06f5c422c5fa19729c6b Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Tue, 19 Jul 2022 12:53:37 +0000 Subject: [PATCH 4257/9987] adding easyconfigs: LAMMPS-23Jun2022-foss-2021b-CUDA-kokkos.eb, LAMMPS-23Jun2022-foss-2021b-kokkos.eb, Voro++-0.4.6-GCCcore-11.2.0.eb --- ...LAMMPS-23Jun2022-foss-2021b-CUDA-kokkos.eb | 163 ++++++++++++++++++ .../LAMMPS-23Jun2022-foss-2021b-kokkos.eb | 160 +++++++++++++++++ .../v/Voro++/Voro++-0.4.6-GCCcore-11.2.0.eb | 40 +++++ 3 files changed, 363 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-CUDA-kokkos.eb create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb create mode 100644 easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-CUDA-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-CUDA-kokkos.eb new file mode 100644 index 00000000000..77c2edf46a6 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-CUDA-kokkos.eb @@ -0,0 +1,163 @@ +name = 'LAMMPS' +version = '23Jun2022' +versionsuffix = '-CUDA-kokkos' + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['stable_%(version)s.tar.gz'] +checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('pkg-config', '0.29.2'), + ('archspec', '0.1.3'), +] +dependencies = [ + ('CUDA', '11.4.1', '', True), + ('NCCL', '2.10.3', '-CUDA-11.4.1'), + ('Python', '3.9.6'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('netCDF', '4.8.1'), + ('GSL', '2.7'), + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('cURL', '7.78.0'), + ('HDF5', '1.12.1'), + ('tbb', '2020.3'), + ('PCRE', '8.45'), + ('libxml2', '2.9.10'), + ('FFmpeg', '4.3.2'), + ('Voro++', '0.4.6'), + ('kim-api', '2.3.0'), + ('Eigen', '3.4.0'), + ('PLUMED', '2.7.3'), + ('ScaFaCoS', '1.0.1'), + ('SciPy-bundle', '2021.10'), + # VTK package is auto-disabled if this dep is not available + ('VTK', '9.1.0'), +] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) + +# include the following extra packages into the build +general_packages = [ + 'ASPHERE', + 'ATC', + 'AWPMD', + 'BOCS', + 'BODY', + 'BPM', + 'BROWNIAN', + 'CG-DNA', + 'CG-SDK', + 'CLASS2', + 'COLLOID', + 'COLVARS', + 'COMPRESS', + 'CORESHELL', + 'DIELECTRIC', + 'DIFFRACTION', + 'DIPOLE', + 'DPD-BASIC', + 'DPD-MESO', + 'DPD-REACT', + 'DPD-SMOOTH', + 'DRUDE', + 'EFF', + 'ELECTRODE', + 'EXTRA-COMPUTE', + 'EXTRA-DUMP', + 'EXTRA-FIX', + 'EXTRA-MOLECULE', + 'EXTRA-PAIR', + 'FEP', + 'GRANULAR', + 'H5MD', + 'INTERLAYER', + 'KIM', + 'KSPACE', + 'LATBOLTZ', + 'MANIFOLD', + 'MACHDYN', + 'MANYBODY', + 'MC', + 'MEAM', + 'MGPT', + 'MISC', + 'ML-IAP', + 'ML-PACE', + 'ML-RANN', + 'ML-SNAP', + 'MOFFF', + 'MOLECULE', + 'MOLFILE', + 'MPIIO', + 'NETCDF', + 'OPENMP', + 'ORIENT', + 'PERI', + 'PHONON', + 'PLUGIN', + 'PLUMED', + 'POEMS', + 'PTM', + 'PYTHON', + 'QEQ', + 'QTB', + 'REACTION', + 'REAXFF', + 'REPLICA', + 'RIGID', + 'SCAFACOS', + 'SHOCK', + 'SMTBQ', + 'SPH', + 'SPIN', + 'SRD', + 'TALLY', + 'UEF', + 'VORONOI', + 'VTK', + 'YAFF', +] + +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + +# hardware-specific option +# cuda_compute_capabilities = ['8.0'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb new file mode 100644 index 00000000000..b0325d03e75 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb @@ -0,0 +1,160 @@ +name = 'LAMMPS' +version = '23Jun2022' +versionsuffix = '-kokkos' + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['stable_%(version)s.tar.gz'] +checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('pkg-config', '0.29.2'), + ('archspec', '0.1.3'), +] +dependencies = [ + ('Python', '3.9.6'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('netCDF', '4.8.1'), + ('GSL', '2.7'), + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('cURL', '7.78.0'), + ('HDF5', '1.12.1'), + ('tbb', '2020.3'), + ('PCRE', '8.45'), + ('libxml2', '2.9.10'), + ('FFmpeg', '4.3.2'), + ('Voro++', '0.4.6'), + ('kim-api', '2.3.0'), + ('Eigen', '3.4.0'), + ('PLUMED', '2.7.3'), + ('ScaFaCoS', '1.0.1'), + ('SciPy-bundle', '2021.10'), + # VTK package is auto-disabled if this dep is not available + ('VTK', '9.1.0'), +] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) + + +# include the following extra packages into the build +general_packages = [ + 'ASPHERE', + 'ATC', + 'AWPMD', + 'BOCS', + 'BODY', + 'BPM', + 'BROWNIAN', + 'CG-DNA', + 'CG-SDK', + 'CLASS2', + 'COLLOID', + 'COLVARS', + 'COMPRESS', + 'CORESHELL', + 'DIELECTRIC', + 'DIFFRACTION', + 'DIPOLE', + 'DPD-BASIC', + 'DPD-MESO', + 'DPD-REACT', + 'DPD-SMOOTH', + 'DRUDE', + 'EFF', + 'ELECTRODE', + 'EXTRA-COMPUTE', + 'EXTRA-DUMP', + 'EXTRA-FIX', + 'EXTRA-MOLECULE', + 'EXTRA-PAIR', + 'FEP', + 'GRANULAR', + 'H5MD', + 'INTERLAYER', + 'KIM', + 'KSPACE', + 'LATBOLTZ', + 'MANIFOLD', + 'MACHDYN', + 'MANYBODY', + 'MC', + 'MEAM', + 'MGPT', + 'MISC', + 'ML-IAP', + 'ML-PACE', + 'ML-RANN', + 'ML-SNAP', + 'MOFFF', + 'MOLECULE', + 'MOLFILE', + 'MPIIO', + 'NETCDF', + 'OPENMP', + 'ORIENT', + 'PERI', + 'PHONON', + 'PLUGIN', + 'PLUMED', + 'POEMS', + 'PTM', + 'PYTHON', + 'QEQ', + 'QTB', + 'REACTION', + 'REAXFF', + 'REPLICA', + 'RIGID', + 'SCAFACOS', + 'SHOCK', + 'SMTBQ', + 'SPH', + 'SPIN', + 'SRD', + 'TALLY', + 'UEF', + 'VORONOI', + 'VTK', + 'YAFF', +] + +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..bf968758c62 --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] + +builddependencies = [('binutils', '2.37')] + + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +moduleclass = 'math' From efb05e9f3a9eb296ac29438ea0463e7531b6f620 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 19 Jul 2022 16:36:36 +0200 Subject: [PATCH 4258/9987] adding easyconfigs: GLM-AED-3.3.0a5-gompi-2021b.eb --- .../g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb diff --git a/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb b/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb new file mode 100644 index 00000000000..21f4c0d71af --- /dev/null +++ b/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb @@ -0,0 +1,48 @@ +easyblock = 'CmdCp' + +name = 'GLM-AED' +version = '3.3.0a5' + +homepage = 'https://github.com/AquaticEcoDynamics/glm-aed' +description = """The General Lake Model (GLM) is a water balance and one-dimensional vertical +stratification hydrodynamic model, which is dynamically coupled with the AED +water quality modelling library. GLM-AED is suitable for simulating conditions +in a wide range of natural and engineered lakes, including shallow (well-mixed) +and deep (stratified) systems. The model has been successfully applied to +systems from the scale of individual ponds and wetlands, to actively operated +reservoirs, upto the scale of the Great Lakes.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://github.com/AquaticEcoDynamics/glm-aed/archive/'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/AquaticEcoDynamics', + 'repo_name': '%(namelower)s', + 'tag': 'v%(version)s', + 'recursive': True, + } +}] +checksums = [None] + +dependencies = [ + ('netCDF-Fortran', '4.5.3'), +] + +start_dir = 'glm-source' + +# Use build environment from EasyBuild +_prebuildcmd = "sed -i 's/FFLAGS=/FFLAGS+=/g' */Makefile && " +cmds_map = [('.*', _prebuildcmd + "./build_glm.sh --gfort")] + +files_to_copy = [(['GLM/glm'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/glm'], + 'dirs': [], +} + +sanity_check_commands = ["glm -h"] + +moduleclass = 'geo' From 4b971cf1ac50483dd82e6a0796417f23a51ed517 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 19 Jul 2022 17:10:04 +0200 Subject: [PATCH 4259/9987] remove unused parameters from GLM-AED v3.3.0a5 Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb b/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb index 21f4c0d71af..6669301238c 100644 --- a/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb +++ b/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb @@ -14,7 +14,6 @@ reservoirs, upto the scale of the Great Lakes.""" toolchain = {'name': 'gompi', 'version': '2021b'} -source_urls = ['https://github.com/AquaticEcoDynamics/glm-aed/archive/'] sources = [{ 'filename': SOURCE_TAR_GZ, 'git_config': { From fd8213610eaf332c7dfb95be32168864ab37f186 Mon Sep 17 00:00:00 2001 From: Bob Date: Wed, 20 Jul 2022 08:30:24 +0200 Subject: [PATCH 4260/9987] adding easyconfigs: GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb --- .../GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb new file mode 100644 index 00000000000..3b8c9ff85d5 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.2.6.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['1125cfc862301d437310506c8774d36c3a90d00d52c7b5d6b59dac7241203628'] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.9.6'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +modloadmsg = "WARNING: GATK v%(version)s support for Java 11 is in beta state. Use at your own risk.\n" + +moduleclass = 'bio' From c47cd1a7546cf761d69da981c37acbd77759c0fb Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 20 Jul 2022 09:25:12 +0200 Subject: [PATCH 4261/9987] Fix versionsuffix --- ...b => LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb} | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/l/LAMMPS/{LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb => LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb} (96%) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb similarity index 96% rename from easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb rename to easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb index e2ee788f76d..b87545a05c6 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-CUDA-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb @@ -1,7 +1,8 @@ name = 'LAMMPS' version = '23Jun2022' -versionsuffix = '-CUDA' -versionsuffix += '-kokkos' +versionsuffix = '-kokkos' +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix += _cuda_suffix homepage = 'https://www.lammps.org' description = """LAMMPS is a classical molecular dynamics code, and an acronym @@ -33,7 +34,7 @@ builddependencies = [ dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('NCCL', '2.10.3', '-CUDA-11.3.1'), + ('NCCL', '2.10.3', _cuda_suffix), ('Python', '3.9.5'), ('libpng', '1.6.37'), ('libjpeg-turbo', '2.0.6'), From 43ede3f999e4100441ff9a949d1296c99aa0035f Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 20 Jul 2022 09:29:58 +0200 Subject: [PATCH 4262/9987] Fix versionsuffix --- ...eb => LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb} | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/l/LAMMPS/{LAMMPS-23Jun2022-foss-2021b-CUDA-kokkos.eb => LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb} (96%) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-CUDA-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb similarity index 96% rename from easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-CUDA-kokkos.eb rename to easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb index 77c2edf46a6..1ed15ce8534 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-CUDA-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb @@ -1,6 +1,8 @@ name = 'LAMMPS' version = '23Jun2022' -versionsuffix = '-CUDA-kokkos' +versionsuffix = '-kokkos' +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix += _cuda_suffix homepage = 'https://www.lammps.org' description = """LAMMPS is a classical molecular dynamics code, and an acronym @@ -29,7 +31,7 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.4.1', '', True), - ('NCCL', '2.10.3', '-CUDA-11.4.1'), + ('NCCL', '2.10.3', _cuda_suffix), ('Python', '3.9.6'), ('libpng', '1.6.37'), ('libjpeg-turbo', '2.0.6'), From dfc30dc5483879e6cd68a3003c9eb12e8365159b Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Wed, 20 Jul 2022 11:07:36 +0200 Subject: [PATCH 4263/9987] Update easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../Phantompeakqualtools-1.2.2-foss-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb index 7064fa3ea24..b043b0b4848 100644 --- a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb @@ -6,8 +6,8 @@ name = 'Phantompeakqualtools' version = '1.2.2' homepage = "https://github.com/kundajelab/phantompeakqualtools" - -description = """ It computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.""" +description = """It computes informative enrichment and quality measures +for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.""" toolchain = {'name': 'foss', 'version': '2021b'} From 6de8e5224ae9686ae16fc269fe6655215f8c4136 Mon Sep 17 00:00:00 2001 From: furst Date: Wed, 20 Jul 2022 12:10:39 +0200 Subject: [PATCH 4264/9987] adding easyconfigs: Dakota-6.16.0-foss-2021b.eb and patches: Dakota-6.16.0-boost177-dllimport.patch --- .../Dakota-6.16.0-boost177-dllimport.patch | 15 +++++ .../d/Dakota/Dakota-6.16.0-foss-2021b.eb | 65 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-boost177-dllimport.patch create mode 100644 easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-boost177-dllimport.patch b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-boost177-dllimport.patch new file mode 100644 index 00000000000..11c029f15a7 --- /dev/null +++ b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-boost177-dllimport.patch @@ -0,0 +1,15 @@ +# Author: Jiri Furst +# Boost dll::import was renamed to dll::import_symbol +# see https://github.com/boostorg/dll/commit/6fed722419caec8ff1049ea0e78afcd75daa6494 + +--- dakota-6.16.0-public-src-cli/src/PluginInterface.cpp.orig 2022-07-20 11:26:50.680437606 +0200 ++++ dakota-6.16.0-public-src-cli/src/PluginInterface.cpp 2022-07-20 11:27:59.736433721 +0200 +@@ -111,7 +111,7 @@ + { + if (pluginInterface) return; + try { +- pluginInterface = boost::dll::import ++ pluginInterface = boost::dll::import_symbol + (pluginPath, + "dakota_interface_plugin" // name of the symbol to import + // TODO: append .dll, .so, .dylib via diff --git a/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb new file mode 100644 index 00000000000..02a4c065c71 --- /dev/null +++ b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb @@ -0,0 +1,65 @@ +# /!\ IMPORTANT: you need at least 8 cores to complete successfully the tests +# Author: Jir Furst +# Based on Dakota 6.15 easyconfig by Sebastien Varrette (Falkor) +easyblock = 'CMakeMake' + +name = 'Dakota' +version = '6.16.0' + +homepage = "https://dakota.sandia.gov/" +description = """ + The Dakota project delivers both state-of-the-art research and robust, usable + software for optimization and UQ. Broadly, the Dakota software's advanced + parametric analyses enable design exploration, model calibration, risk + analysis, and quantification of margins and uncertainty with computational + models. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +# Disable architecture optimization, otherwise the basic tests fail +toolchainopts = {'pic': True, 'usempi': True, 'optarch': False} + +source_urls = ['https://dakota.sandia.gov/sites/default/files/distributions/public/'] +sources = ["%(namelower)s-%(version_major_minor)s.0-public-src-cli.tar.gz"] +patches = ["%(name)s-%(version)s-boost177-dllimport.patch"] +checksums = [ + '49684ade2a937465d85b0fc69c96408be38bc1603ed2e7e8156d93eee3567d2f', # dakota-6.16.0-public-src-cli.tar.gz + 'fdd3181e2e02f5d0a10842d52d81ce4ff6ca81aafa6a50cc696ae51a6d422950', # Dakota-6.16.0-boost177-dllimport.patch +] + +dependencies = [ + ('Boost', '1.77.0'), + ('Perl', '5.34.0'), + ('Python', '3.9.6'), + ('HDF5', '1.12.1'), + ('GSL', '2.7'), +] + +builddependencies = [ + ('CMake', '3.21.1') +] + +separate_build_dir = True +build_shared_libs = True + +# disable GUI +configopts = "-DHAVE_X_GRAPHICS=OFF " +# set other dependencies +configopts += "-DBLAS_LIBS=${EBROOTFLEXIBLAS}/lib/libflexiblas.%s " % SHLIB_EXT +configopts += "-DLAPACK_LIBS=${EBROOTFLEXIBLAS}/lib/libflexiblas.%s " % SHLIB_EXT +configopts += "-DDAKOTA_HAVE_MPI=ON " +configopts += "-DBoost_NO_SYSTEM_PATHS=ON " +configopts += "-DDAKOTA_HAVE_HDF5=ON " +configopts += "-DDAKOTA_HAVE_GSL=ON " + +runtest = ' test ARGS="-L AcceptanceTest -j %(parallel)s" ' + +# Run install step in parallel +installopts = ' -j %(parallel)s ' + +sanity_check_paths = { + 'files': ["bin/dakota"], + 'dirs': [] +} + +moduleclass = 'math' From 0e6d80cb05e9adaccb904eba22182214c42ebb86 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 20 Jul 2022 12:13:46 +0200 Subject: [PATCH 4265/9987] disable build of DEB package in GLM-AED --- .../g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb | 6 ++- .../GLM-AED-3.3.0a5_disable-deb-pkg.patch | 44 +++++++++++++++++++ 2 files changed, 49 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5_disable-deb-pkg.patch diff --git a/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb b/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb index 6669301238c..f77603abc72 100644 --- a/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb +++ b/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5-gompi-2021b.eb @@ -23,7 +23,11 @@ sources = [{ 'recursive': True, } }] -checksums = [None] +patches = ['GLM-AED-3.3.0a5_disable-deb-pkg.patch'] +checksums = [ + None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + 'b5c1a0c0d1c5a47068ad38ec54def75373ea0bb04f6fa43c0d0a0f7f960e26c6', # GLM-AED-3.3.0a5_disable-deb-pkg.patch +] dependencies = [ ('netCDF-Fortran', '4.5.3'), diff --git a/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5_disable-deb-pkg.patch b/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5_disable-deb-pkg.patch new file mode 100644 index 00000000000..3cb63c76e4d --- /dev/null +++ b/easybuild/easyconfigs/g/GLM-AED/GLM-AED-3.3.0a5_disable-deb-pkg.patch @@ -0,0 +1,44 @@ +Disable build of DEB package on Ubuntu systems +author: Alex Domingo (Vrije Universiteit Brussel) +diff --git a/glm-source/build_glm.sh.orig b/glm-source/build_glm.sh +index c0c64a4..255abd4 100755 +--- a/glm-source/build_glm.sh.orig ++++ b/glm-source/build_glm.sh +@@ -216,37 +216,6 @@ ${CURDIR}/vers.sh $VERSION + #${CURDIR}/vers.sh $VERSION + cd ${CURDIR}/.. + +-if [ "$OSTYPE" = "Linux" ] ; then +- if [ $(lsb_release -is) = Ubuntu ] ; then +- if [ ! -d binaries/ubuntu/$(lsb_release -rs) ] ; then +- mkdir -p binaries/ubuntu/$(lsb_release -rs)/ +- fi +- cd ${CURDIR} +- if [ -x glm+ ] ; then +- /bin/cp debian/control-with+ debian/control +- else +- /bin/cp debian/control-no+ debian/control +- fi +- VERSDEB=`head -1 debian/changelog | cut -f2 -d\( | cut -f1 -d-` +- echo debian version $VERSDEB +- if [ "$VERSION" != "$VERSDEB" ] ; then +- echo updating debian version +- dch --newversion ${VERSION}-0 "new version ${VERSION}" +- fi +- VERSRUL=`grep 'version=' debian/rules | cut -f2 -d=` +- if [ "$VERSION" != "$VERSRUL" ] ; then +- sed -i "s/version=$VERSRUL/version=$VERSION/" debian/rules +- fi +- +- fakeroot ${MAKE} -f debian/rules binary || exit 1 +- +- cd .. +- +- mv glm*.deb binaries/ubuntu/$(lsb_release -rs)/ +- else +- echo "No package build for $(lsb_release -is)" +- fi +-fi + if [ "$OSTYPE" = "Darwin" ] ; then + MOSLINE=`grep 'SOFTWARE LICENSE AGREEMENT FOR ' '/System/Library/CoreServices/Setup Assistant.app/Contents/Resources/en.lproj/OSXSoftwareLicense.rtf'` + # pre Lion : MOSNAME=`echo ${MOSLINE} | awk -F 'Mac OS X ' '{print $NF}' | tr -d '\\' | tr ' ' '_'` From af5215c14a9870b6b9c5baa52f480ff307a0b3d7 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Wed, 20 Jul 2022 14:18:20 +0200 Subject: [PATCH 4266/9987] Update easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../Phantompeakqualtools-1.2.2-foss-2021b.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb index b043b0b4848..5da95690eb9 100644 --- a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb @@ -11,9 +11,8 @@ for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.""" toolchain = {'name': 'foss', 'version': '2021b'} - -# Download manually from https://github.com/kundajelab/phantompeakqualtools/releases -sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/kundajelab/%(namelower)s/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] checksums = ['b31263b64aefe97bdc4d7fae138f515a7d7a60cd05031d38dd89a10f9ee10cd1'] dependencies = [ From 3d1d9d8c0711334c0b6706e9204fcda9758b2a43 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Wed, 20 Jul 2022 14:27:54 +0200 Subject: [PATCH 4267/9987] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Thanks @bedroge for all the nice feedback. Co-authored-by: Bob Dröge --- .../Phantompeakqualtools-1.2.2-foss-2021b.eb | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb index 5da95690eb9..1d129abef4f 100644 --- a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb @@ -16,12 +16,12 @@ sources = ['%(version)s.tar.gz'] checksums = ['b31263b64aefe97bdc4d7fae138f515a7d7a60cd05031d38dd89a10f9ee10cd1'] dependencies = [ - ('R', '4.2.0'), - ('SAMtools', '1.15.1'), - ('R-bundle-Bioconductor', '3.15', '-R-4.2.0'), + ('R', '4.1.2'), + ('SAMtools', '1.14'), + ('R-bundle-Bioconductor', '3.14', '-%(rver)s'), ] -preinstall_cmd = "rm spp-1.14.tar.gz" +preinstall_cmd = "rm spp_1.14.tar.gz" exts_defaultclass = 'RPackage' exts_default_options = { @@ -40,7 +40,6 @@ exts_list = [ }), ] - modextrapaths = {'PATH': ''} sanity_check_paths = { @@ -50,4 +49,4 @@ sanity_check_paths = { sanity_check_commands = ['run_spp.R | grep "Usage: Rscript run_spp.R "'] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From b1e268bc27a0b4ee91fe0a5175fa61502c989f75 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Wed, 20 Jul 2022 14:31:48 +0200 Subject: [PATCH 4268/9987] Update Phantompeakqualtools-1.2.2-foss-2021b.eb --- .../Phantompeakqualtools-1.2.2-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb index 1d129abef4f..be1aea63c7a 100644 --- a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb @@ -18,7 +18,7 @@ checksums = ['b31263b64aefe97bdc4d7fae138f515a7d7a60cd05031d38dd89a10f9ee10cd1'] dependencies = [ ('R', '4.1.2'), ('SAMtools', '1.14'), - ('R-bundle-Bioconductor', '3.14', '-%(rver)s'), + ('R-bundle-Bioconductor', '3.14', '-R-%(rver)s'), ] preinstall_cmd = "rm spp_1.14.tar.gz" From 5456a71187c265416f30c1099d83cd7b43dc109c Mon Sep 17 00:00:00 2001 From: furst Date: Wed, 20 Jul 2022 16:32:33 +0200 Subject: [PATCH 4269/9987] Corrected reference to boost commit in the patch --- .../easyconfigs/d/Dakota/Dakota-6.16.0-boost177-dllimport.patch | 2 +- easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-boost177-dllimport.patch b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-boost177-dllimport.patch index 11c029f15a7..db46f2f1604 100644 --- a/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-boost177-dllimport.patch +++ b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-boost177-dllimport.patch @@ -1,6 +1,6 @@ # Author: Jiri Furst # Boost dll::import was renamed to dll::import_symbol -# see https://github.com/boostorg/dll/commit/6fed722419caec8ff1049ea0e78afcd75daa6494 +# see https://github.com/boostorg/dll/commit/6b2e3c7f660199f2bb0d69b667a38ee21cd49626 --- dakota-6.16.0-public-src-cli/src/PluginInterface.cpp.orig 2022-07-20 11:26:50.680437606 +0200 +++ dakota-6.16.0-public-src-cli/src/PluginInterface.cpp 2022-07-20 11:27:59.736433721 +0200 diff --git a/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb index 02a4c065c71..2d38a4be771 100644 --- a/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb +++ b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb @@ -24,7 +24,7 @@ sources = ["%(namelower)s-%(version_major_minor)s.0-public-src-cli.tar.gz"] patches = ["%(name)s-%(version)s-boost177-dllimport.patch"] checksums = [ '49684ade2a937465d85b0fc69c96408be38bc1603ed2e7e8156d93eee3567d2f', # dakota-6.16.0-public-src-cli.tar.gz - 'fdd3181e2e02f5d0a10842d52d81ce4ff6ca81aafa6a50cc696ae51a6d422950', # Dakota-6.16.0-boost177-dllimport.patch + '23aa52a4fe4267ba65368597b2b6c9e6e4bd4a1c8c4f1383055d73602ae9cc2d', # Dakota-6.16.0-boost177-dllimport.patch ] dependencies = [ From 9c9a3d93fa2068b8d521db39ee859eaee3d623ac Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 20 Jul 2022 16:58:34 +0200 Subject: [PATCH 4270/9987] Split out CUDA build of LAMMPS I'll do it in a separate PR --- ...23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb | 167 ------------------ 1 file changed, 167 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb deleted file mode 100644 index b87545a05c6..00000000000 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb +++ /dev/null @@ -1,167 +0,0 @@ -name = 'LAMMPS' -version = '23Jun2022' -versionsuffix = '-kokkos' -_cuda_suffix = '-CUDA-%(cudaver)s' -versionsuffix += _cuda_suffix - -homepage = 'https://www.lammps.org' -description = """LAMMPS is a classical molecular dynamics code, and an acronym -for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has -potentials for solid-state materials (metals, semiconductors) and soft matter -(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be -used to model atoms or, more generically, as a parallel particle simulator at -the atomic, meso, or continuum scale. LAMMPS runs on single processors or in -parallel using message-passing techniques and a spatial-decomposition of the -simulation domain. The code is designed to be easy to modify or extend with new -functionality. -""" - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'openmp': True, 'usempi': True} - -# 'https://github.com/lammps/lammps/archive/' -source_urls = [GITHUB_LOWER_SOURCE] -sources = [ - 'stable_%(version)s.tar.gz', -] -checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] - -builddependencies = [ - ('CMake', '3.20.1'), - ('pkg-config', '0.29.2'), - ('archspec', '0.1.2'), -] - -dependencies = [ - ('CUDA', '11.3.1', '', SYSTEM), - ('NCCL', '2.10.3', _cuda_suffix), - ('Python', '3.9.5'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.6'), - ('netCDF', '4.8.0'), - ('GSL', '2.7'), - ('zlib', '1.2.11'), - ('gzip', '1.10'), - ('cURL', '7.76.0'), - ('HDF5', '1.12.1'), - ('tbb', '2020.3'), - ('PCRE', '8.44'), - ('libxml2', '2.9.10'), - ('FFmpeg', '4.3.2'), - ('Voro++', '0.4.6'), - ('kim-api', '2.2.1'), - ('Eigen', '3.3.9'), - ('PLUMED', '2.7.2'), - ('ScaFaCoS', '1.0.1'), - ('SciPy-bundle', '2021.05'), - # VTK package is auto-disabled if this dep is not available - # ('VTK', '9.0.1'), -] - -# To use additional custom configuration options, use the 'configopts' easyconfig parameter -# See docs and lammps easyblock for more information. -# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options - -# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, -# which is claimed to be faster in pure MPI calculations -# configopts = "-DKokkos_ENABLE_SERIAL=yes " - - -# packages auto-enabled by easyblock -# 'GPU' - if cuda package is present and kokkos is disabled -# 'KOKKOS' - if kokkos is enabled (by default) - -# include the following extra packages into the build -general_packages = [ - 'ASPHERE', - 'ATC', - 'AWPMD', - 'BOCS', - 'BODY', - 'BPM', - 'BROWNIAN', - 'CG-DNA', - 'CG-SDK', - 'CLASS2', - 'COLLOID', - 'COLVARS', - 'COMPRESS', - 'CORESHELL', - 'DIELECTRIC', - 'DIFFRACTION', - 'DIPOLE', - 'DPD-BASIC', - 'DPD-MESO', - 'DPD-REACT', - 'DPD-SMOOTH', - 'DRUDE', - 'EFF', - 'ELECTRODE', - 'EXTRA-COMPUTE', - 'EXTRA-DUMP', - 'EXTRA-FIX', - 'EXTRA-MOLECULE', - 'EXTRA-PAIR', - 'FEP', - 'GRANULAR', - 'H5MD', - 'INTERLAYER', - 'KIM', - 'KSPACE', - 'LATBOLTZ', - 'MANIFOLD', - # 'MACHDYN', # Some issue related to Eigen 3.3.9 when using Kokkos - 'MANYBODY', - 'MC', - 'MEAM', - 'MGPT', - 'MISC', - 'ML-IAP', - 'ML-PACE', - 'ML-RANN', - 'ML-SNAP', - 'MOFFF', - 'MOLECULE', - 'MOLFILE', - 'MPIIO', - 'NETCDF', - 'OPENMP', - 'ORIENT', - 'PERI', - 'PHONON', - 'PLUGIN', - 'PLUMED', - 'POEMS', - 'PTM', - 'PYTHON', - 'QEQ', - 'QTB', - 'REACTION', - 'REAXFF', - 'REPLICA', - 'RIGID', - 'SCAFACOS', - 'SHOCK', - 'SMTBQ', - 'SPH', - 'SPIN', - 'SRD', - 'TALLY', - 'UEF', - 'VORONOI', - 'VTK', - 'YAFF', -] -# Excluded packages due to requiring additional (non-trivial) deps -# - ADIOS -# - LATTE -# - MESONT (requires very large files downloaded during build) -# - ML-HDNNP (requires N2P2) -# - ML-QUIP -# - MSCG -# - QMMM (setup seems complex) - -# hardware-specific option -# cuda_compute_capabilities = ['8.0'] - -moduleclass = 'chem' From 654f0c42fefe1996dfde81e99f919e833ed5a82a Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 20 Jul 2022 16:59:39 +0200 Subject: [PATCH 4271/9987] Split CUDA build into separate PR --- ...23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb | 165 ------------------ 1 file changed, 165 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb deleted file mode 100644 index 1ed15ce8534..00000000000 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb +++ /dev/null @@ -1,165 +0,0 @@ -name = 'LAMMPS' -version = '23Jun2022' -versionsuffix = '-kokkos' -_cuda_suffix = '-CUDA-%(cudaver)s' -versionsuffix += _cuda_suffix - -homepage = 'https://www.lammps.org' -description = """LAMMPS is a classical molecular dynamics code, and an acronym -for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has -potentials for solid-state materials (metals, semiconductors) and soft matter -(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be -used to model atoms or, more generically, as a parallel particle simulator at -the atomic, meso, or continuum scale. LAMMPS runs on single processors or in -parallel using message-passing techniques and a spatial-decomposition of the -simulation domain. The code is designed to be easy to modify or extend with new -functionality. -""" - -toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'openmp': True, 'usempi': True} - -# 'https://github.com/lammps/lammps/archive/' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['stable_%(version)s.tar.gz'] -checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] - -builddependencies = [ - ('CMake', '3.22.1'), - ('pkg-config', '0.29.2'), - ('archspec', '0.1.3'), -] -dependencies = [ - ('CUDA', '11.4.1', '', True), - ('NCCL', '2.10.3', _cuda_suffix), - ('Python', '3.9.6'), - ('libpng', '1.6.37'), - ('libjpeg-turbo', '2.0.6'), - ('netCDF', '4.8.1'), - ('GSL', '2.7'), - ('zlib', '1.2.11'), - ('gzip', '1.10'), - ('cURL', '7.78.0'), - ('HDF5', '1.12.1'), - ('tbb', '2020.3'), - ('PCRE', '8.45'), - ('libxml2', '2.9.10'), - ('FFmpeg', '4.3.2'), - ('Voro++', '0.4.6'), - ('kim-api', '2.3.0'), - ('Eigen', '3.4.0'), - ('PLUMED', '2.7.3'), - ('ScaFaCoS', '1.0.1'), - ('SciPy-bundle', '2021.10'), - # VTK package is auto-disabled if this dep is not available - ('VTK', '9.1.0'), -] - -# To use additional custom configuration options, use the 'configopts' easyconfig parameter -# See docs and lammps easyblock for more information. -# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options - -# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, -# which is claimed to be faster in pure MPI calculations -# configopts = "-DKokkos_ENABLE_SERIAL=yes " - - -# packages auto-enabled by easyblock -# 'GPU' - if cuda package is present and kokkos is disabled -# 'KOKKOS' - if kokkos is enabled (by default) - -# include the following extra packages into the build -general_packages = [ - 'ASPHERE', - 'ATC', - 'AWPMD', - 'BOCS', - 'BODY', - 'BPM', - 'BROWNIAN', - 'CG-DNA', - 'CG-SDK', - 'CLASS2', - 'COLLOID', - 'COLVARS', - 'COMPRESS', - 'CORESHELL', - 'DIELECTRIC', - 'DIFFRACTION', - 'DIPOLE', - 'DPD-BASIC', - 'DPD-MESO', - 'DPD-REACT', - 'DPD-SMOOTH', - 'DRUDE', - 'EFF', - 'ELECTRODE', - 'EXTRA-COMPUTE', - 'EXTRA-DUMP', - 'EXTRA-FIX', - 'EXTRA-MOLECULE', - 'EXTRA-PAIR', - 'FEP', - 'GRANULAR', - 'H5MD', - 'INTERLAYER', - 'KIM', - 'KSPACE', - 'LATBOLTZ', - 'MANIFOLD', - 'MACHDYN', - 'MANYBODY', - 'MC', - 'MEAM', - 'MGPT', - 'MISC', - 'ML-IAP', - 'ML-PACE', - 'ML-RANN', - 'ML-SNAP', - 'MOFFF', - 'MOLECULE', - 'MOLFILE', - 'MPIIO', - 'NETCDF', - 'OPENMP', - 'ORIENT', - 'PERI', - 'PHONON', - 'PLUGIN', - 'PLUMED', - 'POEMS', - 'PTM', - 'PYTHON', - 'QEQ', - 'QTB', - 'REACTION', - 'REAXFF', - 'REPLICA', - 'RIGID', - 'SCAFACOS', - 'SHOCK', - 'SMTBQ', - 'SPH', - 'SPIN', - 'SRD', - 'TALLY', - 'UEF', - 'VORONOI', - 'VTK', - 'YAFF', -] - -# Excluded packages due to requiring additional (non-trivial) deps -# - ADIOS -# - LATTE -# - MESONT (requires very large files downloaded during build) -# - ML-HDNNP (requires N2P2) -# - ML-QUIP -# - MSCG -# - QMMM (setup seems complex) - -# hardware-specific option -# cuda_compute_capabilities = ['8.0'] - -moduleclass = 'chem' From c8347561259f16562dc40c648ffdd7522673b2e1 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 21 Jul 2022 10:40:44 +0200 Subject: [PATCH 4272/9987] Stick to single HDF5 version --- .../easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb index 8563ad26181..527e492d2e8 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb @@ -39,7 +39,7 @@ dependencies = [ ('zlib', '1.2.11'), ('gzip', '1.10'), ('cURL', '7.76.0'), - ('HDF5', '1.12.1'), + ('HDF5', '1.10.7'), ('tbb', '2020.3'), ('PCRE', '8.44'), ('libxml2', '2.9.10'), From 867082dc3957835d2fcf25d561be8057e5956a08 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 21 Jul 2022 12:13:52 +0200 Subject: [PATCH 4273/9987] adding easyconfigs: Advisor-2022.1.0.eb --- .../easyconfigs/a/Advisor/Advisor-2022.1.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb new file mode 100644 index 00000000000..58235ccff90 --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2022.1.0.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'Advisor' +version = '2022.1.0' + +homepage = 'https://software.intel.com/intel-advisor-xe' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18730/'] +sources = ['l_oneapi_advisor_p_%(version)s.171_offline.sh'] +checksums = ['b627dbfefa779b44e7ab40dfa37614e56caa6e245feaed402d51826e6a7cb73b'] + +dontcreateinstalldir = True + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/advisor'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'perf' From 18f2564161033d7bfbf1fcce12f97e6d654a5e6f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Jul 2022 12:56:42 +0200 Subject: [PATCH 4274/9987] OpenBLAS: Fix miscompilation on POWER --- .../o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb | 2 ++ ...S-0.3.15_workaround-gcc-miscompilation.patch | 17 +++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 2 ++ 3 files changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb index ef8207f8887..553433e3e1e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb @@ -17,6 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-%(version)s_icelake-detection.patch', 'OpenBLAS-%(version)s_fix-aarch64.patch', + 'OpenBLAS-%(version)s_workaround-gcc-miscompilation.patch', ] checksums = [ '30a99dec977594b387a17f49904523e6bc8dd88bd247266e83485803759e4bbe', # v0.3.15.tar.gz @@ -24,6 +25,7 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', # OpenBLAS-0.3.15_icelake-detection.patch 'ba7bd45af9fe0516f8c9b1cf047eec7b833996e481bc925d4fb2563865d3db38', # OpenBLAS-0.3.15_fix-aarch64.patch + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch new file mode 100644 index 00000000000..5e6b25003c3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch @@ -0,0 +1,17 @@ +Workaround optimizer bug in GCC on POWER9. +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=100799 + +Author: Alexander Grund (TU Dresden) + +diff --git a/Makefile.power b/Makefile.power +index 946f5523..96b14dca 100644 +--- a/Makefile.power ++++ b/Makefile.power +@@ -35,6 +35,7 @@ endif + ifneq ($(F_COMPILER), PGI) + FCOMMON_OPT += -O2 -frecursive -fno-fast-math + ifeq ($(C_COMPILER), GCC) ++FCOMMON_OPT += -fstack-protector-strong + ifneq ($(GCCVERSIONGT4), 1) + $(warning your compiler is too old to fully support POWER9, getting a newer version of gcc is recommended) + FCOMMON_OPT += -mcpu=power8 -mtune=power8 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index a1b6049921b..e55a7a1f22a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -15,12 +15,14 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch', ] checksums = [ '1632c1e8cca62d8bed064b37747e331a1796fc46f688626337362bf0d16aeadb', # v0.3.18.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] From e8e8166b90490c4f50b411dcb98d45b84f4c276c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Jul 2022 13:20:29 +0200 Subject: [PATCH 4275/9987] Fix formatting --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb | 3 ++- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb index 553433e3e1e..6f209915e17 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb @@ -25,7 +25,8 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', # OpenBLAS-0.3.15_icelake-detection.patch 'ba7bd45af9fe0516f8c9b1cf047eec7b833996e481bc925d4fb2563865d3db38', # OpenBLAS-0.3.15_fix-aarch64.patch - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch + # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index e55a7a1f22a..18fdbab68f8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -22,7 +22,8 @@ checksums = [ '1632c1e8cca62d8bed064b37747e331a1796fc46f688626337362bf0d16aeadb', # v0.3.18.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch + # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] From 65bb048a701982cc8ad687755e7a15b4fe6fe661 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 21 Jul 2022 13:50:45 +0200 Subject: [PATCH 4276/9987] adding easyconfigs: VTune-2022.3.0.eb --- .../easyconfigs/v/VTune/VTune-2022.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb new file mode 100644 index 00000000000..b8a718b77b0 --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2022.3.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +name = 'VTune' +version = '2022.3.0' + +homepage = 'https://software.intel.com/en-us/vtune' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18656/'] +sources = ['l_oneapi_vtune_p_%(version)s.195_offline.sh'] +checksums = ['7921fce7fcc3b82575be22d9c36beec961ba2a9fb5262ba16a04090bcbd2e1a6'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'tools' From 52781f43574b59bb5854d0dba2704f3adf659d66 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 21 Jul 2022 15:10:34 +0200 Subject: [PATCH 4277/9987] adding easyconfigs: STAR-2.7.10a_alpha_220601-GCC-10.3.0.eb --- .../STAR-2.7.10a_alpha_220601-GCC-10.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.10a_alpha_220601-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10a_alpha_220601-GCC-10.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10a_alpha_220601-GCC-10.3.0.eb new file mode 100644 index 00000000000..4cdab2a88f3 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10a_alpha_220601-GCC-10.3.0.eb @@ -0,0 +1,43 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen +# updated by SIB software + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.10a_alpha_220601' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." +# software_license = 'LicenseMIT' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['62b0eb0fd4fc8497a1d9e1a6c3b111b532d6dc0b2576ea14ac3ed63f7b2e41ef'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/STAR', 'bin/STARlong'], + 'dirs': [], +} + +moduleclass = 'bio' From 2a55998e5fbcc1e43f8f1378a3ea17cd5779aeb8 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 21 Jul 2022 15:31:26 +0200 Subject: [PATCH 4278/9987] adding easyconfigs: patchelf-0.15.0-GCCcore-11.3.0.eb --- .../patchelf-0.15.0-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.15.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.15.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.15.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..44c578da855 --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.15.0-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.15.0' + +homepage = 'https://github.com/NixOS/patchelf' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5d1eda9bad4439bb9c0a87fcba198d7c0d372f361e77de41d68d6308062e5000'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +moduleclass = 'tools' From 2b134e387cdd856b4bb7ea59eae9fa929156c195 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Jul 2022 16:06:51 +0200 Subject: [PATCH 4279/9987] BLIS 0.9.0: Fix build/tests on POWER9 --- .../b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb | 7 ++++++- .../BLIS-0.9.0_disable_power9_kernels.patch | 18 ++++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_disable_power9_kernels.patch diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb index 6bc1b9f92e8..a24a015854f 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-11.3.0.eb @@ -11,9 +11,14 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/flame/blis/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_enable_ppc_autodetect.patch'] +patches = [ + '%(name)s-%(version)s_disable_power9_kernels.patch', + '%(name)s-%(version)s_enable_ppc_autodetect.patch', +] checksums = [ '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz + # BLIS-0.9.0_disable_power9_kernels.patch + 'ed7a326bc5c5c21c42faefbec2fd7be609d1c7236981b466475edace39307279', # BLIS-0.9.0_enable_ppc_autodetect.patch 'f373fb252c0d14036fb631f048091976cceb02abb3e570a97fbaeac2fbb12328', ] diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_disable_power9_kernels.patch b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_disable_power9_kernels.patch new file mode 100644 index 00000000000..98daaa8a02e --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_disable_power9_kernels.patch @@ -0,0 +1,18 @@ +There seemingly are bugs in the Power9 kernels. +Workaround this by using the generic kernels on Power9 introduced by +https://github.com/flame/blis/commit/ee9ff988c49f16696679d4c6cd3dcfcac7295be7 +See https://github.com/flame/blis/issues/621 + +diff --git a/build/detect/config/config_detect.c b/build/detect/config/config_detect.c +index 5e29def..5603163 100644 +--- a/build/detect/config/config_detect.c ++++ b/build/detect/config/config_detect.c +@@ -70,6 +70,8 @@ + int main( int argc, char** argv ) + { + arch_t id = bli_cpuid_query_id(); ++ if(id == BLIS_ARCH_POWER9) ++ id = BLIS_ARCH_GENERIC; + char* s = bli_arch_string( id ); + + printf( "%s\n", s ); From 5f16b18fa3afd72f845f159263f3d576638c089e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Robert=20Mijakovi=C4=87?= Date: Thu, 21 Jul 2022 17:03:16 +0200 Subject: [PATCH 4280/9987] adding easyconfigs: AOCC-3.2.0-GCCcore-11.3.0.eb --- .../a/AOCC/AOCC-3.2.0-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-3.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-3.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-3.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e7b4a9c2e01 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-3.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +name = 'AOCC' +version = '3.2.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['8493525b3df77f48ee16f3395a68ad4c42e18233a44b4d9282b25dbb95b113ec'] + +clangversion = '13.0.0' + +dependencies = [ + ('binutils', '2.38'), + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('libxml2', '2.9.13'), +] + +moduleclass = 'compiler' From c12679c242d72cc247593a63f31f8f097fc5fba6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Robert=20Mijakovi=C4=87?= Date: Fri, 22 Jul 2022 14:41:27 +0200 Subject: [PATCH 4281/9987] adding easyconfigs: aria2-1.36.0-GCCcore-11.3.0.eb, c-ares-1.18.1-GCCcore-11.3.0.eb --- .../a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb | 40 +++++++++++++++++++ .../c/c-ares/c-ares-1.18.1-GCCcore-11.3.0.eb | 29 ++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/c-ares/c-ares-1.18.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..591b1cbcd46 --- /dev/null +++ b/easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'aria2' +version = '1.36.0' + +homepage = 'https://aria2.github.io' +description = "aria2 is a lightweight multi-protocol & multi-source command-line download utility." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/aria2/aria2/releases/download/release-%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['b593b2fd382489909c96c62c6e180054c3332b950be3d73e0cb0d21ea8afb3c5'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('CppUnit', '1.15.1'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libxml2', '2.9.13'), + ('SQLite', '3.38.3'), + ('c-ares', '1.18.1'), + ('OpenSSL', '1.1', '', True), +] + +configopts = "--without-gnutls --with-openssl --enable-libaria2 --enable-static" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/aria2c'], + 'dirs': ['share'], +} + +sanity_check_commands = ["aria2c --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/c-ares/c-ares-1.18.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/c-ares/c-ares-1.18.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..aacc900a81e --- /dev/null +++ b/easybuild/easyconfigs/c/c-ares/c-ares-1.18.1-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'c-ares' +version = '1.18.1' + +homepage = 'https://c-ares.org/' +description = "c-ares is a C library for asynchronous DNS requests (including name resolves)" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'c-ares' +source_urls = [GITHUB_SOURCE] +sources = ['%s-%s.tar.gz' % (name.replace('-', ''), version.replace('.', '_'))] +checksums = ['414872549eec4e221b576693fdc9c9bce44ff794d0f1f06f2515b56a7f6ec9c9'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': ['lib/libcares.a', 'lib/libcares.%s' % SHLIB_EXT, 'lib/pkgconfig/libcares.pc'], + 'dirs': ['include', 'share/man'], +} + +moduleclass = 'lib' From d06cd0753d5b6485b41fd971c250f1673d9cccba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Robert=20Mijakovi=C4=87?= Date: Fri, 22 Jul 2022 14:49:43 +0200 Subject: [PATCH 4282/9987] adding easyconfigs: MDAnalysis-2.2.0-foss-2022a.eb, tqdm-4.64.0-GCCcore-11.3.0.eb, Biopython-1.79-foss-2022a.eb --- .../b/Biopython/Biopython-1.79-foss-2022a.eb | 45 +++++++++++++++ .../MDAnalysis/MDAnalysis-2.2.0-foss-2022a.eb | 57 +++++++++++++++++++ .../t/tqdm/tqdm-4.64.0-GCCcore-11.3.0.eb | 25 ++++++++ 3 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2022a.eb create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.2.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/t/tqdm/tqdm-4.64.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2022a.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2022a.eb new file mode 100644 index 00000000000..2633521f6e2 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.79-foss-2022a.eb @@ -0,0 +1,45 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.79' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['edb07eac99d3b8abd7ba56ff4bedec9263f76dfc3c3f450e7d2e2bcdecf8559b'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.2.0-foss-2022a.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.2.0-foss-2022a.eb new file mode 100644 index 00000000000..47b2c19b803 --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.2.0-foss-2022a.eb @@ -0,0 +1,57 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '2.2.0' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('Biopython', '1.79'), + ('networkx', '2.8.4'), + ('tqdm', '4.64.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mrcfile', '1.4.2', { + 'checksums': ['447022f27b7ce4bf57f97010f092a811ce88635479de7f8a86449a0c9cb319fe'], + }), + ('GridDataFormats', '1.0.1', { + 'modulename': 'gridData', + 'checksums': ['ad2c9ab7d672a6d8c426de7d083eee4f3e2b0bd59391675d30683c768ab83cc4'], + }), + ('gsd', '2.5.3', { + 'checksums': ['1593be39eb7a527647a40935a316d594ae20d4c11ff1383c25c8196376314d97'], + }), + ('msgpack', '1.0.4', { + 'checksums': ['f5d869c18f030202eb412f08b28d2afeea553d6613aee89e200d7aca7ef01f5f'], + }), + ('mmtf-python', '1.1.3', { + 'modulename': 'mmtf', + 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('fasteners', '0.17.3', { + 'checksums': ['a9a42a208573d4074c77d041447336cf4e3c1389a256fd3e113ef59cf29b7980'], + }), + (name, version, { + 'modulename': 'MDAnalysis', + 'checksums': ['bf9c9b7a03404e65aad66215d4c2ff8834ab747551eeaee059ff3e599a99d322'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.64.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.64.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e3a61555dec --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.64.0-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.64.0' + +homepage = "https://github.com/tqdm/tqdm" +description = """A fast, extensible progress bar for Python and CLI""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['40be55d30e200777a307a7585aee69e4eabb46b4ec6a4b4a5f2d9f11e7d5408d'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' From 40d1851343bd86586e75eb4fb6642636ce66b88c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Jul 2022 14:52:00 +0200 Subject: [PATCH 4283/9987] Fix PPC autodetect patch for 2.2-3.0 --- .../b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb | 8 +- .../BLIS/BLIS-2.2_enable-ppc-autodetect.patch | 91 +++++++++++++++++++ .../b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb | 6 +- 3 files changed, 98 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-2.2_enable-ppc-autodetect.patch diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb index 60adbe97e26..8018fce99b4 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-2.2-GCCcore-9.3.0-amd.eb @@ -13,15 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = ['https://github.com/amd/blis/archive/'] sources = ['%(version)s.tar.gz'] patches = [ - 'BLIS-2.2-amd_fix-undefined-reference-blist-abort.patch', - '%(name)s-0.8.1_enable_ppc_autodetect.patch', + '%(name)s-%(version)s-amd_fix-undefined-reference-blist-abort.patch', + '%(name)s-%(version)s_enable-ppc-autodetect.patch', ] checksums = [ 'e1feb60ac919cf6d233c43c424f6a8a11eab2c62c2c6e3f2652c15ee9063c0c9', # 2.2.tar.gz # BLIS-2.2-amd_fix-undefined-reference-blist-abort.patch 'e879bd79e4438f7e6905461af1d483d27d14945eb9e75509b22c7584b8ba93c4', - # BLIS-0.8.1_enable_ppc_autodetect.patch - 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', + # BLIS-2.2_enable-ppc-autodetect.patch + '9abf334d0abb6cfdd18bec21c27d114b78a7d97be45883626a547eceea046ccd', ] builddependencies = [ diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-2.2_enable-ppc-autodetect.patch b/easybuild/easyconfigs/b/BLIS/BLIS-2.2_enable-ppc-autodetect.patch new file mode 100644 index 00000000000..e20eb44fa00 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-2.2_enable-ppc-autodetect.patch @@ -0,0 +1,91 @@ +Add autodetection for POWER7 & POWER9 +See https://github.com/amd/blis/pull/6 + +Author: Alexander Grund (TU Dresden) +diff --git a/frame/base/bli_cpuid.c b/frame/base/bli_cpuid.c +index 5858c88a..72ca4479 100644 +--- a/frame/base/bli_cpuid.c ++++ b/frame/base/bli_cpuid.c +@@ -428,7 +428,7 @@ bool_t bli_cpuid_is_bulldozer + return TRUE; + } + +-#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) ++#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) || defined(_ARCH_PPC) + + arch_t bli_cpuid_query_id( void ) + { +@@ -483,9 +483,12 @@ arch_t bli_cpuid_query_id( void ) + return BLIS_ARCH_GENERIC; + } + } +- else if ( vendor == VENDOR_UNKNOWN ) ++ else if ( vendor == VENDOR_IBM ) + { +- return BLIS_ARCH_GENERIC; ++ if ( model == MODEL_POWER7) ++ return BLIS_ARCH_POWER7; ++ else if ( model == MODEL_POWER9) ++ return BLIS_ARCH_POWER9; + } + + return BLIS_ARCH_GENERIC; +@@ -984,7 +987,7 @@ int vpu_count( void ) + } + } + +-#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) ++#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) || defined(_ARCH_PPC) + + #define TEMP_BUFFER_SIZE 200 + +@@ -1006,6 +1009,20 @@ uint32_t bli_cpuid_query + char feat_str[ TEMP_BUFFER_SIZE ]; + char* r_val; + ++#ifdef _ARCH_PPC ++ r_val = find_string_in( "cpu", proc_str, TEMP_BUFFER_SIZE, pci_str ); ++ if ( r_val == NULL ) return VENDOR_IBM; ++ ++ if ( strstr( proc_str, "POWER7" ) != NULL ) ++ *model = MODEL_POWER7; ++ else if ( strstr( proc_str, "POWER9" ) != NULL ) ++ *model = MODEL_POWER9; ++ else if ( strstr( proc_str, "POWER10" ) != NULL ) ++ *model = MODEL_POWER10; ++ ++ return VENDOR_IBM; ++#endif ++ + //printf( "bli_cpuid_query(): beginning search\n" ); + + // Search /proc/cpuinfo for the 'Processor' entry. +diff --git a/frame/base/bli_cpuid.h b/frame/base/bli_cpuid.h +index 9edaf47a..eca76794 100644 +--- a/frame/base/bli_cpuid.h ++++ b/frame/base/bli_cpuid.h +@@ -158,19 +158,23 @@ enum + FEATURE_AVX512VL = 0x4000 + }; + +-#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) ++#elif defined(__aarch64__) || defined(__arm__) || defined(_M_ARM) || defined(_ARCH_PPC) + + char* find_string_in( char* target, char* buffer, size_t buf_len, char* filepath ); + + enum + { + VENDOR_ARM = 0, ++ VENDOR_IBM, + VENDOR_UNKNOWN + }; + enum + { + MODEL_ARMV7 = 0, + MODEL_ARMV8, ++ MODEL_POWER7, ++ MODEL_POWER9, ++ MODEL_POWER10, + MODEL_UNKNOWN + }; + enum diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb b/easybuild/easyconfigs/b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb index 1c14c4e0bd6..3e9b98dbcad 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-3.0-GCCcore-10.3.0-amd.eb @@ -16,15 +16,15 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/amd/blis/archive/'] sources = ['%(version)s.tar.gz'] patches = [ - '%(name)s-0.8.1_enable_ppc_autodetect.patch', '%(name)s-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch', + '%(name)s-2.2_enable-ppc-autodetect.patch', ] checksums = [ 'ac848c040cd6c3550fe49148dbdf109216cad72d3235763ee7ee8134e1528517', # 3.0.tar.gz - # BLIS-0.8.1_enable_ppc_autodetect.patch - 'b8a3d564a8d4f205e70241765ddfd28331c3c12355ef9c44172c9a0cab9f0111', # BLIS-0.8.1_fix_dgemm-fpe-signalling-on-broadwell.patch '345fa39933e9d1442d2eb1e4ed9129df3fe4aefecf4d104e5d4f25b3bca24d0d', + # BLIS-2.2_enable-ppc-autodetect.patch + '9abf334d0abb6cfdd18bec21c27d114b78a7d97be45883626a547eceea046ccd', ] builddependencies = [ From 3f918058be49d288180808407b66afc2b2b38fa5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Robert=20Mijakovi=C4=87?= Date: Fri, 22 Jul 2022 15:05:59 +0200 Subject: [PATCH 4284/9987] Adds CppUnit 1.15.1 --- .../CppUnit/CppUnit-1.15.1-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4fcb8d0cae6 --- /dev/null +++ b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'CppUnit' +version = '1.15.1' + +homepage = 'https://freedesktop.org/wiki/Software/cppunit/' + +description = """ + CppUnit is the C++ port of the famous JUnit framework for unit testing. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://dev-www.libreoffice.org/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['89c5c6665337f56fd2db36bc3805a5619709d51fb136e51937072f63fcc717a7'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['lib/libcppunit.a', 'lib/libcppunit.%s' % SHLIB_EXT, + 'lib/pkgconfig/cppunit.pc'], + 'dirs': ['bin', 'include/cppunit', 'share'], +} + +moduleclass = 'tools' From 40da5cdca8b682bfcd14473fae674cb409677481 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Robert=20Mijakovi=C4=87?= Date: Fri, 22 Jul 2022 15:13:19 +0200 Subject: [PATCH 4285/9987] adds matplotlib --- .../matplotlib/matplotlib-3.5.2-foss-2022a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb new file mode 100644 index 00000000000..ade6e567845 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.5.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('cppy', '1.2.1') +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '9.1.1'), + ('Qhull', '2020.2') +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >setup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.34.0', { + 'modulename': 'fontTools', + 'source_tmpl': SOURCE_ZIP, + 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], + }), + ('Cycler', '0.11.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], + }), + ('kiwisolver', '1.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ab8a15c2750ae8d53e31f77a94f846d0a00772240f1c12817411fa2344351f86'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['48cf850ce14fa18067f2d9e0d646763681948487a8080ec0af2686468b4607a2'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From 49a6ceb09ac2d6c46d0f6c895700d70a02c658cc Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 22 Jul 2022 16:07:33 +0200 Subject: [PATCH 4286/9987] Provide alternative download URL for Voro++ --- .../easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.2.0.eb index bf968758c62..eb847209dbe 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.2.0.eb @@ -16,7 +16,10 @@ to analyze a system of particles.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] From b5832d41583e85ab0fda0c87d0d2e1d97abea9d1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 22 Jul 2022 16:06:47 +0200 Subject: [PATCH 4287/9987] move Stata v17 to SYSTEM toolchain --- .../easyconfigs/n/ncurses/ncurses-5.9.eb | 39 +++++++------- .../s/Stata/Stata-17-GCCcore-10.2.0.eb | 51 ------------------- .../s/Stata/Stata-17-GCCcore-10.3.0.eb | 21 -------- easybuild/easyconfigs/s/Stata/Stata-17.eb | 44 ++++++++++++++++ 4 files changed, 66 insertions(+), 89 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/Stata/Stata-17.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 10662bd7941..25c237795bb 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -26,29 +26,34 @@ checksums = [ # need to use -P preprocessor option for recent GCC versions (cfr. https://gcc.gnu.org/gcc-5/porting_to.html) preconfigopts = "export CPPFLAGS='-P' && " -configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' -] +_config = { + # options to build shared librares and separate libtinfo + 'default': "--with-shared --with-termlib ", + # options to enable UTF-8 + 'utf8': "--enable-ext-colors --enable-widec ", + # options to enable multi-threading + 'mt': "--with-pthread ", +} -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.so.%(version_major)s libtinfo.so.%(version_major)s)", - "(cd %(installdir)s/lib && ln -s libncurses.so.%(version_major_minor)s libtinfo.so.%(version_major_minor)s)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +configopts = [ + # build ncurses: default build overwriting curses (-lcurses) + _config['default'] + '--enable-overwrite', + # build ncursesw: the UTF-8 version + _config['default'] + _config['utf8'] + '--includedir=%(installdir)s/include/ncursesw/', + # build ncursest: the multi-threaded version + _config['default'] + _config['mt'] + '--includedir=%(installdir)s/include/ncursest/', + # build ncursestw: the multi-threaded UTF-8 version + _config['default'] + _config['utf8'] + _config['mt'] + '--includedir=%(installdir)s/include/ncursestw/', ] -local_libs = ["form", "menu", "ncurses", "panel"] +local_libs = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], - 'dirs': ['include', 'include/ncursesw'], + ['lib/lib%s%s%s.a' % (x, y, z) for x in local_libs for y in ['', 'w', 't', 'tw'] for z in ['', '_g']] + + ['lib/lib%s%s.so' % (x, y) for x in local_libs for y in ['', 'w', 't', 'tw']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w', 't', 'tw']], + 'dirs': ['include', 'include/ncursesw', 'include/ncursest', 'include/ncursestw'], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb deleted file mode 100644 index c15b66f86f6..00000000000 --- a/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.2.0.eb +++ /dev/null @@ -1,51 +0,0 @@ -name = 'Stata' -version = '17' - -homepage = 'https://www.stata.com/' -description = """Stata is a complete, integrated statistical software package that provides -everything you need for data analysis, data management, and graphics.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -# requires license to access source files -sources = ['Stata%(version)sLinux64.tar.gz'] -checksums = ['e7bea3d827db2957e5ea67bf3d6747a56f656bb08f40b148ed726ab700cd8ce3'] - -download_instructions = """ -See also https://www.stata.com/support/faqs/unix/install-download-on-linux/ - -You can download the gzipped tar file 'Stata%(version)sLinux64.tar.gz' from: - https://download.stata.com/download/ -and place it under your favorite Easybuild sourcepath, typically under - /s/Stata/ - -After the build, you **must** generate the licence file 'stata.lic' in your -software install path using the `stinit` script: - module load math/Stata - cd $EBROOTSTATA - ./stinit -""" - - -builddependencies = [ - ('binutils', '2.35'), -] - -dependencies = [ - ('libpng', '1.6.37') -] - -sanity_check_paths = { - 'files': [ - 'stata', # Non-graphical standard Stata/IC - 'stata-se', # Non-graphical Stata/SE designed for large databases - 'xstata', # Graphical standard Stata/IC - 'xstata-se' # Graphical Stata/SE designed for large databases - ], - 'dirs': [ - 'utilities', - 'ado' - ] -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb deleted file mode 100644 index 0ef24a2a86e..00000000000 --- a/easybuild/easyconfigs/s/Stata/Stata-17-GCCcore-10.3.0.eb +++ /dev/null @@ -1,21 +0,0 @@ -name = 'Stata' -version = '17' - -homepage = 'https://www.stata.com/' -description = """Stata is a complete, integrated statistical software package that provides everything you need - for data analysis, data management, and graphics.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -# requires license to access source files -sources = ['%(name)s%(version)sLinux64.tar.gz'] -checksums = ['744314cdac7ba7316c82dccebe7c7de8f7fab68841d8fa7de13f8eb4472e6015'] - -dependencies = [ - ('libpng', '1.6.37'), - ('ncurses', '5.9', '', True), -] - -sanity_check_commands = ['stata -h'] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Stata/Stata-17.eb b/easybuild/easyconfigs/s/Stata/Stata-17.eb new file mode 100644 index 00000000000..a5073e16dae --- /dev/null +++ b/easybuild/easyconfigs/s/Stata/Stata-17.eb @@ -0,0 +1,44 @@ +name = 'Stata' +version = '17' + +homepage = 'https://www.stata.com/' +description = """Stata is a complete, integrated statistical software package that provides everything you need + for data analysis, data management, and graphics.""" + +toolchain = SYSTEM + +### Requires license to access source files ### +# See also https://www.stata.com/support/faqs/unix/install-download-on-linux/ +# You can download the source tarball from: https://download.stata.com/download/ +# Once the installation with EB completes, you **must** generate the licence file +# by executing the script "stinit" from the root of the installation directory. + +sources = ['Stata%(version)sLinux64.tar.gz'] +checksums = [ + # the source tarball of Stata seems to change over time without any version change + # so far, these 3 checksum have been reported + ('ac5d49ff27544f801defa27e996d6c6770e94a01ec248bec3021b30ae2b91c45', + '744314cdac7ba7316c82dccebe7c7de8f7fab68841d8fa7de13f8eb4472e6015', + 'e7bea3d827db2957e5ea67bf3d6747a56f656bb08f40b148ed726ab700cd8ce3'), +] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.11'), +] + +# Optional: requirements for xstata +osdependencies = [('xorg', 'xorg-x11', 'xorg-x11-apps', 'xorg-x11-server-Xorg')] +dependencies.append( + ('libpng', '1.5.30'), # default libpng in Centos 7 +) + +# Bindings +modextrapaths = { + 'PYTHONPATH': ['utilities'], + 'CLASSPATH': ['utilities/jar'], +} + +sanity_check_commands = ['stata -h'] + +moduleclass = 'data' From d5daae4dc0c77d741588bad8b5bea8495dc04918 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Fri, 22 Jul 2022 14:19:30 +0000 Subject: [PATCH 4288/9987] Add alternate download URL for Voro++ --- .../easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb | 5 ++++- .../easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.3.0.eb | 5 ++++- easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-6.4.0.eb | 5 ++++- easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb | 5 ++++- easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb | 5 ++++- easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2019b.eb | 5 ++++- easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb | 5 ++++- easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2019b.eb | 5 ++++- 8 files changed, 32 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb index 6eb09719067..b23389e4e99 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.2.0.eb @@ -16,7 +16,10 @@ to analyze a system of particles.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.3.0.eb index cb1a8cb8417..81555d53747 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-10.3.0.eb @@ -16,7 +16,10 @@ to analyze a system of particles.""" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-6.4.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-6.4.0.eb index 9d8d8d4d19c..769428b78d2 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-6.4.0.eb @@ -18,7 +18,10 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb index b3ffe5c5492..10720c28f50 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-9.3.0.eb @@ -14,7 +14,10 @@ to analyze a system of particles.""" toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] builddependencies = [('binutils', '2.34')] diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb index 7020ae2236a..98482913534 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb @@ -14,7 +14,10 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] # Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['2338b824c3b7b25590e18e8df5d68af9'] diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2019b.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2019b.eb index e38391f1ed2..2bad5127b4a 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2019b.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2019b.eb @@ -14,7 +14,10 @@ to analyze a system of particles.""" toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'pic': True} -source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb index d7bac431f70..d4f089e9ee2 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb @@ -14,7 +14,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] # Let's store the checksum in order to be sure it doesn't suddenly change checksums = ['2338b824c3b7b25590e18e8df5d68af9'] diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2019b.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2019b.eb index 2a1b177e02b..874bb558cc6 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2019b.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2019b.eb @@ -13,7 +13,10 @@ to analyze a system of particles.""" toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'pic': True} -source_urls = ['http://math.lbl.gov/voro++/download/dir/'] +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] sources = [SOURCELOWER_TAR_GZ] checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] From f3776bac09854b68686787f98c6594775976d4cb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 22 Jul 2022 16:15:34 +0200 Subject: [PATCH 4289/9987] adding easyconfig: libpng-1.5.30.eb --- .../easyconfigs/l/libpng/libpng-1.5.30.eb | 31 +++++++++++++++++++ .../easyconfigs/n/ncurses/ncurses-5.9.eb | 31 ++++++------------- 2 files changed, 40 insertions(+), 22 deletions(-) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.5.30.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.30.eb b/easybuild/easyconfigs/l/libpng/libpng-1.5.30.eb new file mode 100644 index 00000000000..252ef3d7553 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.5.30.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.5.30' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = SYSTEM + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6c32c7264f040cc6a4b11798c902a16bcd0626c7d7549fa4481264482f129514'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +local_majminver = ''.join(version.split('.')[:2]) + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT), + 'lib/libpng%s.%s.%s' % (local_majminver, SHLIB_EXT, local_majminver)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 25c237795bb..71d76d1c6a4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -26,34 +26,21 @@ checksums = [ # need to use -P preprocessor option for recent GCC versions (cfr. https://gcc.gnu.org/gcc-5/porting_to.html) preconfigopts = "export CPPFLAGS='-P' && " -_config = { - # options to build shared librares and separate libtinfo - 'default': "--with-shared --with-termlib ", - # options to enable UTF-8 - 'utf8': "--enable-ext-colors --enable-widec ", - # options to enable multi-threading - 'mt': "--with-pthread ", -} - configopts = [ - # build ncurses: default build overwriting curses (-lcurses) - _config['default'] + '--enable-overwrite', - # build ncursesw: the UTF-8 version - _config['default'] + _config['utf8'] + '--includedir=%(installdir)s/include/ncursesw/', - # build ncursest: the multi-threaded version - _config['default'] + _config['mt'] + '--includedir=%(installdir)s/include/ncursest/', - # build ncursestw: the multi-threaded UTF-8 version - _config['default'] + _config['utf8'] + _config['mt'] + '--includedir=%(installdir)s/include/ncursestw/', + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] -local_libs = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] +local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s%s.a' % (x, y, z) for x in local_libs for y in ['', 'w', 't', 'tw'] for z in ['', '_g']] + - ['lib/lib%s%s.so' % (x, y) for x in local_libs for y in ['', 'w', 't', 'tw']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w', 't', 'tw']], - 'dirs': ['include', 'include/ncursesw', 'include/ncursest', 'include/ncursestw'], + ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in local_libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], } moduleclass = 'devel' From a0ab455d38b4d6d57f2bd96d5a2d9dc87631249e Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 22 Jul 2022 16:55:32 +0200 Subject: [PATCH 4290/9987] Update Voro++-0.4.6-intel-2016a.eb --- easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb index d4f089e9ee2..9220692cbf9 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb @@ -20,7 +20,7 @@ source_urls = [ ] # Let's store the checksum in order to be sure it doesn't suddenly change -checksums = ['2338b824c3b7b25590e18e8df5d68af9'] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] # No configure skipsteps = ['configure'] From 44b58884644315645525a2610de3f4f91d1ccc86 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Fri, 22 Jul 2022 15:01:31 +0000 Subject: [PATCH 4291/9987] adding easyconfigs: LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb, LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb --- ...23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb | 169 ++++++++++++++++++ ...23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb | 167 +++++++++++++++++ 2 files changed, 336 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb new file mode 100644 index 00000000000..1bb3005cd9f --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb @@ -0,0 +1,169 @@ +name = 'LAMMPS' +version = '23Jun2022' +versionsuffix = '-kokkos' +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix += _cuda_suffix + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [ + 'stable_%(version)s.tar.gz', +] +checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), + ('archspec', '0.1.2'), +] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('UCX-CUDA', '1.10.0', _cuda_suffix), + ('NCCL', '2.10.3', _cuda_suffix), + ('Python', '3.9.5'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('netCDF', '4.8.0'), + ('GSL', '2.7'), + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('cURL', '7.76.0'), + ('HDF5', '1.10.7'), + ('tbb', '2020.3'), + ('PCRE', '8.44'), + ('libxml2', '2.9.10'), + ('FFmpeg', '4.3.2'), + ('Voro++', '0.4.6'), + ('kim-api', '2.2.1'), + ('Eigen', '3.3.9'), + ('PLUMED', '2.7.2'), + ('ScaFaCoS', '1.0.1'), + ('SciPy-bundle', '2021.05'), + # VTK package is auto-disabled if this dep is not available + # ('VTK', '9.0.1'), +] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) + + +# include the following extra packages into the build +general_packages = [ + 'ASPHERE', + 'ATC', + 'AWPMD', + 'BOCS', + 'BODY', + 'BPM', + 'BROWNIAN', + 'CG-DNA', + 'CG-SDK', + 'CLASS2', + 'COLLOID', + 'COLVARS', + 'COMPRESS', + 'CORESHELL', + 'DIELECTRIC', + 'DIFFRACTION', + 'DIPOLE', + 'DPD-BASIC', + 'DPD-MESO', + 'DPD-REACT', + 'DPD-SMOOTH', + 'DRUDE', + 'EFF', + 'ELECTRODE', + 'EXTRA-COMPUTE', + 'EXTRA-DUMP', + 'EXTRA-FIX', + 'EXTRA-MOLECULE', + 'EXTRA-PAIR', + 'FEP', + 'GRANULAR', + 'H5MD', + 'INTERLAYER', + 'KIM', + 'KSPACE', + 'LATBOLTZ', + 'MANIFOLD', + # 'MACHDYN', # Some issue related to Eigen 3.3.9 when using Kokkos + 'MANYBODY', + 'MC', + 'MEAM', + 'MGPT', + 'MISC', + 'ML-IAP', + 'ML-PACE', + 'ML-RANN', + 'ML-SNAP', + 'MOFFF', + 'MOLECULE', + 'MOLFILE', + 'MPIIO', + 'NETCDF', + 'OPENMP', + 'ORIENT', + 'PERI', + 'PHONON', + 'PLUGIN', + 'PLUMED', + 'POEMS', + 'PTM', + 'PYTHON', + 'QEQ', + 'QTB', + 'REACTION', + 'REAXFF', + 'REPLICA', + 'RIGID', + 'SCAFACOS', + 'SHOCK', + 'SMTBQ', + 'SPH', + 'SPIN', + 'SRD', + 'TALLY', + 'UEF', + 'VORONOI', + 'VTK', + 'YAFF', +] +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + +# hardware-specific option +# cuda_compute_capabilities = ['8.0'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb new file mode 100644 index 00000000000..64fdc923e7d --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb @@ -0,0 +1,167 @@ +name = 'LAMMPS' +version = '23Jun2022' +versionsuffix = '-kokkos' +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix += _cuda_suffix + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['stable_%(version)s.tar.gz'] +checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('pkg-config', '0.29.2'), + ('archspec', '0.1.3'), +] +dependencies = [ + ('CUDA', '11.4.1', '', True), + ('UCX-CUDA', '1.11.2', _cuda_suffix), + ('NCCL', '2.10.3', _cuda_suffix), + ('Python', '3.9.6'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('netCDF', '4.8.1'), + ('GSL', '2.7'), + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('cURL', '7.78.0'), + ('HDF5', '1.12.1'), + ('tbb', '2020.3'), + ('PCRE', '8.45'), + ('libxml2', '2.9.10'), + ('FFmpeg', '4.3.2'), + ('Voro++', '0.4.6'), + ('kim-api', '2.3.0'), + ('Eigen', '3.4.0'), + ('PLUMED', '2.7.3'), + ('ScaFaCoS', '1.0.1'), + ('SciPy-bundle', '2021.10'), + # VTK package is auto-disabled if this dep is not available + ('VTK', '9.1.0'), +] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) + + +# include the following extra packages into the build +general_packages = [ + 'ASPHERE', + 'ATC', + 'AWPMD', + 'BOCS', + 'BODY', + 'BPM', + 'BROWNIAN', + 'CG-DNA', + 'CG-SDK', + 'CLASS2', + 'COLLOID', + 'COLVARS', + 'COMPRESS', + 'CORESHELL', + 'DIELECTRIC', + 'DIFFRACTION', + 'DIPOLE', + 'DPD-BASIC', + 'DPD-MESO', + 'DPD-REACT', + 'DPD-SMOOTH', + 'DRUDE', + 'EFF', + 'ELECTRODE', + 'EXTRA-COMPUTE', + 'EXTRA-DUMP', + 'EXTRA-FIX', + 'EXTRA-MOLECULE', + 'EXTRA-PAIR', + 'FEP', + 'GRANULAR', + 'H5MD', + 'INTERLAYER', + 'KIM', + 'KSPACE', + 'LATBOLTZ', + 'MANIFOLD', + 'MACHDYN', + 'MANYBODY', + 'MC', + 'MEAM', + 'MGPT', + 'MISC', + 'ML-IAP', + 'ML-PACE', + 'ML-RANN', + 'ML-SNAP', + 'MOFFF', + 'MOLECULE', + 'MOLFILE', + 'MPIIO', + 'NETCDF', + 'OPENMP', + 'ORIENT', + 'PERI', + 'PHONON', + 'PLUGIN', + 'PLUMED', + 'POEMS', + 'PTM', + 'PYTHON', + 'QEQ', + 'QTB', + 'REACTION', + 'REAXFF', + 'REPLICA', + 'RIGID', + 'SCAFACOS', + 'SHOCK', + 'SMTBQ', + 'SPH', + 'SPIN', + 'SRD', + 'TALLY', + 'UEF', + 'VORONOI', + 'VTK', + 'YAFF', +] + +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + +# hardware-specific option +# cuda_compute_capabilities = ['8.0'] + +moduleclass = 'chem' From 51f2557a5e351cf48d5e73dea7ac7401110b1c9a Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 22 Jul 2022 17:18:19 +0200 Subject: [PATCH 4292/9987] Update Voro++-0.4.6-foss-2016a.eb --- easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb index 98482913534..32879b6ab34 100644 --- a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb @@ -20,7 +20,7 @@ source_urls = [ ] # Let's store the checksum in order to be sure it doesn't suddenly change -checksums = ['2338b824c3b7b25590e18e8df5d68af9'] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] # No configure skipsteps = ['configure'] From f5e6c51043bdeeaf05de66dbc766e946c2a68313 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 22 Jul 2022 17:33:39 +0200 Subject: [PATCH 4293/9987] Update LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb index 64fdc923e7d..bf9851cc73f 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb @@ -30,7 +30,7 @@ builddependencies = [ ('archspec', '0.1.3'), ] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', _cuda_suffix), ('NCCL', '2.10.3', _cuda_suffix), ('Python', '3.9.6'), From 396f263d4c7396bda0da7ebc8f36dc59ad046150 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 22 Jul 2022 17:55:15 +0200 Subject: [PATCH 4294/9987] Update LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb index 1bb3005cd9f..28b49c51cee 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb @@ -33,7 +33,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', SYSTEM), + ('CUDA', '11.3.1', '', True), ('UCX-CUDA', '1.10.0', _cuda_suffix), ('NCCL', '2.10.3', _cuda_suffix), ('Python', '3.9.5'), From 494fc0e98a6533788fb9de22fd12bd9118e2d4f9 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 22 Jul 2022 17:55:32 +0200 Subject: [PATCH 4295/9987] Update LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb index bf9851cc73f..64fdc923e7d 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb @@ -30,7 +30,7 @@ builddependencies = [ ('archspec', '0.1.3'), ] dependencies = [ - ('CUDA', '11.4.1', '', SYSTEM), + ('CUDA', '11.4.1', '', True), ('UCX-CUDA', '1.11.2', _cuda_suffix), ('NCCL', '2.10.3', _cuda_suffix), ('Python', '3.9.6'), From e0ffe5219573ff219ff04be067617b3a390f3267 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 23 Jul 2022 23:57:30 +0200 Subject: [PATCH 4296/9987] add extra symlinks and sanity checks for libtinfo --- .../easyconfigs/n/ncurses/ncurses-5.9.eb | 27 +++++++++++++------ .../easyconfigs/n/ncurses/ncurses-6.0.eb | 24 ++++++++--------- .../easyconfigs/n/ncurses/ncurses-6.1.eb | 22 +++++++-------- .../n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb | 22 +++++++-------- .../n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb | 22 +++++++-------- .../n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb | 22 +++++++-------- .../n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb | 22 +++++++-------- .../easyconfigs/n/ncurses/ncurses-6.2.eb | 22 +++++++-------- 8 files changed, 97 insertions(+), 86 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 71d76d1c6a4..55380094858 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -26,20 +26,31 @@ checksums = [ # need to use -P preprocessor option for recent GCC versions (cfr. https://gcc.gnu.org/gcc-5/porting_to.html) preconfigopts = "export CPPFLAGS='-P' && " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " configopts = [ - # default build - '--with-shared --enable-overwrite', - # the UTF-8 enabled version (ncursesw) - '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + # build ncurses: serial build in default paths with shared libraries + local_common_configopts, + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -local_libs = ["form", "menu", "ncurses", "panel"] +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.so' % (x, y) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index f17cb5fb125..056cfa489fc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -18,11 +18,11 @@ checksums = [ 'f82003be6ce6b87c3dc8a91d97785aab1a76a9e8544c3a3c02283c01dd41aede', # ncurses-6.0_gcc-5.patch ] -local_common_configopts = "--with-shared --enable-overwrite --without-ada " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " configopts = [ - # default build + # build ncurses: serial build in default paths with shared libraries local_common_configopts, - # the UTF-8 enabled version (ncursesw) + # build ncursesw: serial with UTF-8 local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] @@ -30,19 +30,19 @@ configopts = [ # we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" -] +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] -local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb index 9e75f70cd1d..b184d16c7e8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb @@ -16,9 +16,9 @@ checksums = ['aa057eeeb4a14d470101eff4597d5833dcef5965331be3528c08d99cebaa0d17'] local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " configopts = [ - # default build + # build ncurses: serial build in default paths with shared libraries local_common_configopts, - # the UTF-8 enabled version (ncursesw) + # build ncursesw: serial with UTF-8 local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] @@ -26,19 +26,19 @@ configopts = [ # we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" -] +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] -local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb index 5044d91b4c5..1f706304c62 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -22,25 +22,25 @@ builddependencies = [('binutils', '2.35')] local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " configopts = [ - # default build + # build ncurses: serial build in default paths with shared libraries local_common_configopts, - # the UTF-8 enabled version (ncursesw) + # build ncursesw: serial with UTF-8 local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" -] +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] -local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb index 07bfbcd9e14..cfa0268c226 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb @@ -22,25 +22,25 @@ builddependencies = [('binutils', '2.36.1')] local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " configopts = [ - # default build + # build ncurses: serial build in default paths with shared libraries local_common_configopts, - # the UTF-8 enabled version (ncursesw) + # build ncursesw: serial with UTF-8 local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" -] +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] -local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb index 61c14fe5a04..e46eaa1f76f 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb @@ -22,25 +22,25 @@ builddependencies = [('binutils', '2.37')] local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " configopts = [ - # default build + # build ncurses: serial build in default paths with shared libraries local_common_configopts, - # the UTF-8 enabled version (ncursesw) + # build ncursesw: serial with UTF-8 local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" -] +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] -local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb index 18dcd5668cf..19df3d8ddaf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb @@ -22,25 +22,25 @@ builddependencies = [('binutils', '2.34')] local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " configopts = [ - # default build + # build ncurses: serial build in default paths with shared libraries local_common_configopts, - # the UTF-8 enabled version (ncursesw) + # build ncursesw: serial with UTF-8 local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" -] +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] -local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], 'dirs': ['include', 'include/ncursesw'], } diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb index 5df1d2c1038..41416b3aaf2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb @@ -16,9 +16,9 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " configopts = [ - # default build + # build ncurses: serial build in default paths with shared libraries local_common_configopts, - # the UTF-8 enabled version (ncursesw) + # build ncursesw: serial with UTF-8 local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] @@ -26,19 +26,19 @@ configopts = [ # we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" -] +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] -local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], 'dirs': ['include', 'include/ncursesw'], } From adc8b8a52a55cb1c32637e37d70d21a0be4a3bcf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 24 Jul 2022 00:39:19 +0200 Subject: [PATCH 4297/9987] add extra symlinks and sanity checks for libtinfo in ncurses v6.3 --- .../n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb index f59b0aedd9a..b804672db2c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb @@ -22,25 +22,25 @@ builddependencies = [('binutils', '2.38')] local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " configopts = [ - # default build + # build ncurses: serial build in default paths with shared libraries local_common_configopts, - # the UTF-8 enabled version (ncursesw) + # build ncursesw: serial with UTF-8 local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" -] +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] -local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], 'dirs': ['include', 'include/ncursesw'], } From c778ca18c052fc422174fcfe91decf72c23f60e9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 24 Jul 2022 00:40:00 +0200 Subject: [PATCH 4298/9987] adding easyconfig: ncurses-6.3.eb --- .../easyconfigs/n/ncurses/ncurses-6.3.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb new file mode 100644 index 00000000000..934b520cb94 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.3' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts, + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' From ba34a0fb6e58d8aafb4fb2712e3e8feb58ab198d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 24 Jul 2022 00:48:40 +0200 Subject: [PATCH 4299/9987] fix comment formatting in Stata v17 --- easybuild/easyconfigs/s/Stata/Stata-17.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Stata/Stata-17.eb b/easybuild/easyconfigs/s/Stata/Stata-17.eb index a5073e16dae..333ae2fc7bb 100644 --- a/easybuild/easyconfigs/s/Stata/Stata-17.eb +++ b/easybuild/easyconfigs/s/Stata/Stata-17.eb @@ -7,7 +7,7 @@ description = """Stata is a complete, integrated statistical software package th toolchain = SYSTEM -### Requires license to access source files ### +# Requires license to access source files # See also https://www.stata.com/support/faqs/unix/install-download-on-linux/ # You can download the source tarball from: https://download.stata.com/download/ # Once the installation with EB completes, you **must** generate the licence file From 319d4e4383042612ae061078a5c728e931fc9ddb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 24 Jul 2022 01:15:45 +0200 Subject: [PATCH 4300/9987] exclude libncurses++ from libtinfo symlinks --- easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 55380094858..8f2c950f72b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -40,7 +40,7 @@ buildopts = 'CFLAGS="-O2 -fPIC"' # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 056cfa489fc..51cab0973d2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -32,7 +32,7 @@ buildopts = 'CFLAGS="-O2 -fPIC"' # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb index b184d16c7e8..39e4816f441 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb @@ -28,7 +28,7 @@ buildopts = 'CFLAGS="-O2 -fPIC"' # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb index 1f706304c62..d0f89800315 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -30,7 +30,7 @@ configopts = [ # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb index cfa0268c226..da6d4c2d78d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb @@ -30,7 +30,7 @@ configopts = [ # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb index e46eaa1f76f..15191562f91 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb @@ -30,7 +30,7 @@ configopts = [ # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb index 19df3d8ddaf..a5329b525e9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb @@ -30,7 +30,7 @@ configopts = [ # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb index 41416b3aaf2..3a0fb752006 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb @@ -28,7 +28,7 @@ buildopts = 'CFLAGS="-O2 -fPIC"' # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb index b804672db2c..26666e64a97 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb @@ -30,7 +30,7 @@ configopts = [ # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb index 934b520cb94..bf42d2eb8cc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb @@ -31,7 +31,7 @@ buildopts = 'CFLAGS="-O2 -fPIC"' # Symlink libtinfo to libncurses # libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically -postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] _target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw _lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] From f666cec3d36caa76cf6460f31de9e09d3ab7e9d0 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Mon, 25 Jul 2022 09:32:14 +0200 Subject: [PATCH 4301/9987] Remove cuda from beagle-lib configopts --- .../easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb index d665b15fb9b..388390b27a1 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ ] preconfigopts = "./autogen.sh && " -configopts = "--with-opencl=$EBROOTPOCL --with-cuda=$EBROOTCUDA " +configopts = "--with-opencl=$EBROOTPOCL " sanity_check_paths = { 'files': ['include/libhmsbeagle-1/libhmsbeagle/%s' % x for x in ['beagle.h', 'platform.h']] + From 920d48e98913c26dea165cc2532358e387a49e1f Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 25 Jul 2022 09:50:54 +0000 Subject: [PATCH 4302/9987] Fix link issue for 2021a, C++ standard issue for 2021b --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb | 2 +- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb index 28b49c51cee..8e4cf356fc4 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb @@ -45,7 +45,7 @@ dependencies = [ ('gzip', '1.10'), ('cURL', '7.76.0'), ('HDF5', '1.10.7'), - ('tbb', '2020.3'), + # ('tbb', '2020.3'), # Optionally required by Intel package but has a link problem when using nvlink ('PCRE', '8.44'), ('libxml2', '2.9.10'), ('FFmpeg', '4.3.2'), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb index 64fdc923e7d..4705ba3f47f 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb @@ -64,11 +64,12 @@ dependencies = [ # which is claimed to be faster in pure MPI calculations # configopts = "-DKokkos_ENABLE_SERIAL=yes " - # packages auto-enabled by easyblock # 'GPU' - if cuda package is present and kokkos is disabled # 'KOKKOS' - if kokkos is enabled (by default) +# GCC 11/12 defaults to C++17 standard, need to be consistent +configopts = "-DKokkos_CXX_STANDARD=17 " # include the following extra packages into the build general_packages = [ From d8e6d9366cbef28ebfda82bd6693fb33d9da463e Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 25 Jul 2022 12:08:29 +0200 Subject: [PATCH 4303/9987] Fix style issue --- .../LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb index 4705ba3f47f..212a02d80dd 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb @@ -62,14 +62,14 @@ dependencies = [ # OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, # which is claimed to be faster in pure MPI calculations -# configopts = "-DKokkos_ENABLE_SERIAL=yes " +# configopts = "-DKokkos_ENABLE_SERIAL=yes " # packages auto-enabled by easyblock # 'GPU' - if cuda package is present and kokkos is disabled # 'KOKKOS' - if kokkos is enabled (by default) # GCC 11/12 defaults to C++17 standard, need to be consistent -configopts = "-DKokkos_CXX_STANDARD=17 " +configopts = "-DKokkos_CXX_STANDARD=17 " # include the following extra packages into the build general_packages = [ From db7d69ebc1b8c2b7a168f627b4d3f49f6cc5dcbe Mon Sep 17 00:00:00 2001 From: ocaisa Date: Mon, 25 Jul 2022 12:20:46 +0200 Subject: [PATCH 4304/9987] Update LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb index 212a02d80dd..9adbdfe4ad9 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb @@ -42,7 +42,7 @@ dependencies = [ ('gzip', '1.10'), ('cURL', '7.78.0'), ('HDF5', '1.12.1'), - ('tbb', '2020.3'), + # ('tbb', '2020.3'), # Optionally required by Intel package but has a link problem when using nvlink ('PCRE', '8.45'), ('libxml2', '2.9.10'), ('FFmpeg', '4.3.2'), From 05e93adc9c22072e71ac022f97babbbdfd9153d6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Jul 2022 12:40:53 +0200 Subject: [PATCH 4305/9987] adding easyconfigs: GDB-12.1-GCCcore-11.3.0.eb, ISL-0.24-GCCcore-11.3.0.eb, MPC-1.2.1-GCCcore-11.3.0.eb, makeinfo-6.8-GCCcore-11.3.0.eb --- .../g/GDB/GDB-12.1-GCCcore-11.3.0.eb | 44 +++++++++++++++++++ .../i/ISL/ISL-0.24-GCCcore-11.3.0.eb | 23 ++++++++++ .../m/MPC/MPC-1.2.1-GCCcore-11.3.0.eb | 35 +++++++++++++++ .../m/makeinfo/makeinfo-6.8-GCCcore-11.3.0.eb | 25 +++++++++++ 4 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0ff055c409e --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '12.1' + +homepage = 'https://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0e1793bf8f2b54d53f46dea84ccfd446f48f81b297b28c4f7fc017b818d69fed'] + +builddependencies = [ + ('binutils', '2.38'), + ('makeinfo', '6.8'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), + ('expat', '2.4.8'), + ('Python', '3.10.4'), + ('ISL', '0.24'), + ('MPC', '1.2.1'), +] + +preconfigopts = "mkdir obj && cd obj && " +configure_cmd_prefix = '../' +prebuildopts = "cd obj && " +preinstallopts = prebuildopts + +configopts = '--with-system-zlib --with-system-readline --with-expat=$EBROOTEXPAT ' +configopts += '--with-python=$EBROOTPYTHON/bin/python --with-isl=$EBROOTISL --with-mpc=$EBROOTMPC ' +configopts += '--enable-tui --enable-plugins --disable-install-libbfd ' + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0ff69001149 --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.24-GCCcore-11.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.24' + +homepage = 'http://isl.gforge.inria.fr/' +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://isl.gforge.inria.fr/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'] + +builddependencies = [('binutils', '2.38')] +dependencies = [('GMP', '6.2.1')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..db636b0b91e --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.2.1-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.2.1' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0e5c61d4a94 --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.8-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '6.8' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['8eb753ed28bca21f8f56c1a180362aed789229bd62fff58bf8368e9beb59fec4'] + +builddependencies = [('binutils', '2.38')] +dependencies = [('Perl', '5.34.1')] + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' From 1035dd31fb0c1164b9925094483512d839eae380 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Jul 2022 14:03:29 +0200 Subject: [PATCH 4306/9987] Bazel 5.1.1: Use Java 11 --- easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb index 666c940a93c..793f0a2c12f 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ('Zip', '3.0'), ] -dependencies = [('Java', '13', '', True)] +dependencies = [('Java', '11', '', True)] runtest = True testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." From bfa34dedc8c39a165c615aeb9e26b3b8b0fd9018 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 16 Sep 2021 11:36:18 +0200 Subject: [PATCH 4307/9987] Only parse the changed ECs for the PR tests --- test/easyconfigs/easyconfigs.py | 54 +++++++++++++++------------------ 1 file changed, 24 insertions(+), 30 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f112a8a5e70..3889a791b86 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -98,7 +98,7 @@ def skip_if_not_pr_to_non_main_branch(): return lambda func: func -def get_files_from_diff(diff_filter, ext, basename=True): +def get_files_from_diff(diff_filter, ext): """Return the files changed on HEAD relative to the current target branch""" target_branch = get_target_branch() @@ -122,10 +122,7 @@ def get_files_from_diff(diff_filter, ext, basename=True): # determine list of changed files using 'git diff' and merge base determined above cmd = "git diff --name-only --diff-filter=%s %s..HEAD --" % (diff_filter, merge_base) out, _ = run_cmd(cmd, simple=False) - if basename: - files = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith(ext)] - else: - files = [f for f in out.strip().split('\n') if f.endswith(ext)] + files = [os.path.join(top_dir, f) for f in out.strip().split('\n') if f.endswith(ext)] change_dir(cwd) return files @@ -217,8 +214,10 @@ def resolve_all_dependencies(cls): def _get_changed_easyconfigs(self): """Gather all added or modified easyconfigs""" # get list of changed easyconfigs - changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M') - added_ecs_filenames = get_eb_files_from_diff(diff_filter='A') + changed_ecs_files = get_eb_files_from_diff(diff_filter='M') + added_ecs_files = get_eb_files_from_diff(diff_filter='A') + changed_ecs_filenames = [os.path.basename(f) for f in changed_ecs_files] + added_ecs_filenames = [os.path.basename(f) for f in added_ecs_files] if changed_ecs_filenames: print("\nList of changed easyconfig files in this PR:\n\t%s" % '\n\t'.join(changed_ecs_filenames)) if added_ecs_filenames: @@ -228,41 +227,36 @@ def _get_changed_easyconfigs(self): # grab parsed easyconfigs for changed easyconfig files changed_ecs = [] - for ec_fn in changed_ecs_filenames + added_ecs_filenames: - match = None - for ec in self.parsed_easyconfigs: - if os.path.basename(ec['spec']) == ec_fn: - match = ec['ec'] - break + easyconfigs_path = get_paths_for("easyconfigs")[0] + for ec_file in changed_ecs_files + added_ecs_files: + # Search in already parsed ECs first + match = next((ec['ec'] for ec in EasyConfigTest._parsed_easyconfigs if ec['spec'] == ec_file), None) if match: changed_ecs.append(match) + elif ec_file.startswith(easyconfigs_path): + ec = process_easyconfig(ec_file) + # Cache non-archived files + if '__archive__' not in ec_file: + EasyConfigTest._parsed_easyconfigs.extend(ec) + changed_ecs.append(ec[0]['ec']) else: - # if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR... - # so as a last resort, try to find the easyconfig file in __archive__ - easyconfigs_path = get_paths_for("easyconfigs")[0] - specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn)) - if len(specs) == 1: - ec = process_easyconfig(specs[0])[0] - changed_ecs.append(ec['ec']) - else: - raise RuntimeError("Failed to find parsed easyconfig for %s" - " (and could not isolate it in easyconfigs archive either)" % ec_fn) + raise RuntimeError("Failed to find parsed easyconfig for %s" % os.path.basename(ec_file)) EasyConfigTest._changed_ecs = changed_ecs def _get_changed_patches(self): """Gather all added or modified patches""" # get list of changed/added patch files - changed_patches_filenames = get_files_from_diff(diff_filter='M', ext='.patch', basename=False) - added_patches_filenames = get_files_from_diff(diff_filter='A', ext='.patch', basename=False) + changed_patches = get_files_from_diff(diff_filter='M', ext='.patch') + added_patches = get_files_from_diff(diff_filter='A', ext='.patch') - if changed_patches_filenames: - print("\nList of changed patch files in this PR:\n\t%s" % '\n\t'.join(changed_patches_filenames)) - if added_patches_filenames: - print("\nList of added patch files in this PR:\n\t%s" % '\n\t'.join(added_patches_filenames)) + if changed_patches: + print("\nList of changed patch files in this PR:\n\t%s" % '\n\t'.join(changed_patches)) + if added_patches: + print("\nList of added patch files in this PR:\n\t%s" % '\n\t'.join(added_patches)) - EasyConfigTest._changed_patches = changed_patches_filenames + added_patches_filenames + EasyConfigTest._changed_patches = changed_patches + added_patches @property def parsed_easyconfigs(self): From e7a7e58070878a00745e09d1bc3f7ebeff30d351 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 8 Jul 2021 10:26:32 +0200 Subject: [PATCH 4308/9987] Remove superflous -DCMAKE_BUILD_TYPE --- .../a/ANTs/ANTs-2.2.0-foss-2016b-Python-2.7.12.eb | 2 +- .../a/ANTs/ANTs-2.3.0-foss-2017b-Python-2.7.14.eb | 3 +-- .../a/ANTs/ANTs-2.3.0-intel-2017b-Python-2.7.14.eb | 3 +-- .../a/ANTs/ANTs-2.3.1-foss-2018b-Python-3.6.6.eb | 3 +-- .../a/ANTs/ANTs-2.3.2-foss-2019b-Python-3.7.4.eb | 3 +-- easybuild/easyconfigs/a/ANTs/ANTs-2.3.5-foss-2021a.eb | 5 +---- .../b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb | 2 +- .../b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb | 7 ++++--- easybuild/easyconfigs/c/Calib/Calib-0.3.4-GCC-9.3.0.eb | 2 +- .../ConnectomeWorkbench-1.3.2-GCCcore-8.2.0.eb | 2 +- .../ConnectomeWorkbench-1.3.2-foss-2017b.eb | 2 +- .../ConnectomeWorkbench-1.3.2-intel-2017b.eb | 2 +- .../easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb | 3 +-- .../double-conversion-3.1.4-GCCcore-8.2.0.eb | 4 ---- .../double-conversion-3.1.4-GCCcore-8.3.0.eb | 4 ---- .../double-conversion-3.1.5-GCCcore-10.2.0.eb | 4 ---- .../double-conversion-3.1.5-GCCcore-10.3.0.eb | 4 ---- .../double-conversion-3.1.5-GCCcore-11.2.0.eb | 4 ---- .../double-conversion-3.1.5-GCCcore-9.3.0.eb | 4 ---- .../easyconfigs/e/elastix/elastix-4.9.0-foss-2018a.eb | 4 ---- .../f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb | 3 ++- .../f/FLANN/FLANN-1.8.4-intel-2017b-Python-2.7.14.eb | 2 +- .../h/HH-suite/HH-suite-3.0-beta.3-intel-2018a.eb | 4 ---- .../h/HyPo/HyPo-1.0.3-GCC-8.3.0-Python-3.7.4.eb | 3 ++- .../k/Kratos/Kratos-6.0-foss-2018a-Python-3.6.4.eb | 2 +- .../k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb | 2 +- .../easyconfigs/k/kim-api/kim-api-2.1.2-foss-2019a.eb | 2 -- .../easyconfigs/k/kim-api/kim-api-2.1.2-intel-2019a.eb | 3 --- .../easyconfigs/k/kim-api/kim-api-2.1.3-foss-2019b.eb | 3 --- .../easyconfigs/k/kim-api/kim-api-2.1.3-foss-2020a.eb | 2 -- .../easyconfigs/k/kim-api/kim-api-2.1.3-intel-2019b.eb | 3 --- .../easyconfigs/k/kim-api/kim-api-2.1.3-intel-2020a.eb | 2 -- .../easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.2.0.eb | 2 -- .../easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.3.0.eb | 2 -- .../libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb | 1 - .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb | 1 - .../libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb | 2 -- .../l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb | 2 -- easybuild/easyconfigs/m/MRCPP/MRCPP-1.3.6-foss-2020a.eb | 2 -- .../m/MRChem/MRChem-1.0.0-foss-2020a-Python-3.8.2.eb | 2 -- .../easyconfigs/m/MariaDB/MariaDB-10.3.14-foss-2019a.eb | 3 +-- .../easyconfigs/m/MariaDB/MariaDB-10.4.13-gompi-2019b.eb | 3 +-- .../easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb | 3 +-- .../easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb | 3 +-- .../p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb | 3 +-- .../p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb | 2 -- .../PCMSolver/PCMSolver-1.1.4-intel-2016a-Python-2.7.11.eb | 5 +++-- .../p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb | 2 +- .../PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb | 2 +- .../PCMSolver-20160205-intel-2016a-Python-2.7.11.eb | 5 +++-- easybuild/easyconfigs/p/pizzly/pizzly-0.37.3-foss-2018b.eb | 1 - .../q/Qt5Webkit/Qt5Webkit-5.212.0-alpha3-GCCcore-8.2.0.eb | 2 +- .../q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/r/RAxML-NG/RAxML-NG-0.9.0-GCC-8.3.0.eb | 4 ---- .../easyconfigs/r/RAxML-NG/RAxML-NG-0.9.0-gompi-2019b.eb | 4 ---- .../easyconfigs/r/RAxML-NG/RAxML-NG-1.0.1-gompi-2019b.eb | 4 ---- .../easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb | 4 ---- .../s/strelka/strelka-2.9.10-foss-2018b-Python-2.7.15.eb | 2 +- .../s/strelka/strelka-2.9.10-intel-2018b-Python-2.7.15.eb | 2 +- easybuild/easyconfigs/x/XCFun/XCFun-2.1.0-GCCcore-9.3.0.eb | 3 --- .../easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb | 3 --- .../easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.3.0.eb | 3 --- 62 files changed, 40 insertions(+), 137 deletions(-) diff --git a/easybuild/easyconfigs/a/ANTs/ANTs-2.2.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ANTs/ANTs-2.2.0-foss-2016b-Python-2.7.12.eb index 4f2d5cbbc19..b2d2d259758 100644 --- a/easybuild/easyconfigs/a/ANTs/ANTs-2.2.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ANTs/ANTs-2.2.0-foss-2016b-Python-2.7.12.eb @@ -24,7 +24,7 @@ dependencies = [ ('VTK', '6.3.0', versionsuffix), ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DUSE_SYSTEM_ITK=ON ' +configopts = '-DUSE_SYSTEM_ITK=ON ' configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF' configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON -DITK_DIR=$EBROOTITK/lib/cmake/ITK-%s' % local_itkshortver diff --git a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-foss-2017b-Python-2.7.14.eb index d7d2d862a3a..8e30688c8b7 100644 --- a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-foss-2017b-Python-2.7.14.eb @@ -24,8 +24,7 @@ dependencies = [ separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release ' -configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON ' configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF' diff --git a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-intel-2017b-Python-2.7.14.eb index c6b61065738..a8ecce342be 100644 --- a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.0-intel-2017b-Python-2.7.14.eb @@ -24,8 +24,7 @@ dependencies = [ separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release ' -configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON ' configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF' diff --git a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.1-foss-2018b-Python-3.6.6.eb index 201663c8e6b..e5f1a652809 100644 --- a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.1-foss-2018b-Python-3.6.6.eb @@ -28,8 +28,7 @@ dependencies = [ separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release ' -configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON ' configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF' diff --git a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.2-foss-2019b-Python-3.7.4.eb index da82f868f0a..6b49020a633 100644 --- a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.2-foss-2019b-Python-3.7.4.eb @@ -33,8 +33,7 @@ dependencies = [ separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release ' -configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON ' configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF' diff --git a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.5-foss-2021a.eb b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.5-foss-2021a.eb index fe0bc0c4e22..ec2c58de985 100644 --- a/easybuild/easyconfigs/a/ANTs/ANTs-2.3.5-foss-2021a.eb +++ b/easybuild/easyconfigs/a/ANTs/ANTs-2.3.5-foss-2021a.eb @@ -21,10 +21,7 @@ dependencies = [ ('VTK', '9.0.1'), ] -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=Release ' -configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON ' configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF' diff --git a/easybuild/easyconfigs/b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb b/easybuild/easyconfigs/b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb index cca75a1aa04..d7e13667d5a 100644 --- a/easybuild/easyconfigs/b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['1023eb590e2112d5bc213c568a212390fc65ff98732ac8d2ccdda5062e6bc8c6'] builddependencies = [('CMake', '3.16.4')] -configopts = " -DBUILD_STATIC_LIBS=1 -DBUILD_SHARED_LIBS=1 -DCMAKE_BUILD_TYPE=Release " +configopts = " -DBUILD_STATIC_LIBS=1 -DBUILD_SHARED_LIBS=1" sanity_check_paths = { 'files': ['lib/libbufr.a', 'lib/libbufr.so'], diff --git a/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb index 2526494ae82..dc05fe1ecab 100644 --- a/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb +++ b/easybuild/easyconfigs/b/BreakDancer/BreakDancer-1.4.5-intel-2017a.eb @@ -12,13 +12,14 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://github.com/genome/breakdancer/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['BreakDancer-%(version)s_fix-icpc-compilation.patch'] +checksums = [ + '5d74f3a90f5c69026ebb4cf4cb9ccc51ec8dd49ac7a88595a1efabd5a73e92b6', # v1.4.5.tar.gz + '3652cd5fcd02edb8d82a30c4e110ce6a63291608a9e2535525f90636c1840da4', # BreakDancer-1.4.5_fix-icpc-compilation.patch +] dependencies = [('zlib', '1.2.11')] builddependencies = [('CMake', '3.7.2')] -separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=release' - parallel = 1 sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/Calib/Calib-0.3.4-GCC-9.3.0.eb b/easybuild/easyconfigs/c/Calib/Calib-0.3.4-GCC-9.3.0.eb index 3e46af0a6b5..28b8fd81ade 100644 --- a/easybuild/easyconfigs/c/Calib/Calib-0.3.4-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/c/Calib/Calib-0.3.4-GCC-9.3.0.eb @@ -42,7 +42,7 @@ buildopts = 'CXXFLAGS="$CXXFLAGS -pthread -Iclustering/ -lz" && ' # building calib_cons requires SPOA, so build that first buildopts += "mv %(builddir)s/spoa-1.1.3 %(builddir)s/calib-%(version)s/consensus/spoa_v1.1.3 && " buildopts += "mkdir consensus/spoa_v1.1.3/build && cd consensus/spoa_v1.1.3/build && " -buildopts += "cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_VERBOSE_MAKEFILE=ON .. && make && " +buildopts += "cmake -DCMAKE_VERBOSE_MAKEFILE=ON .. && make && " buildopts += "cd - && make -C consensus" files_to_copy = [(['calib', 'consensus/calib_cons'], 'bin')] diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-GCCcore-8.2.0.eb index da15c0b6470..013966d896c 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-GCCcore-8.2.0.eb @@ -30,7 +30,7 @@ dependencies = [ start_dir = 'src' -configopts = '-DCMAKE_BUILD_TYPE=Release -DWORKBENCH_MESA_DIR=${EBROOTMESA} ' +configopts = '-DWORKBENCH_MESA_DIR=${EBROOTMESA} ' configopts += '-DWORKBENCH_USE_QT5=TRUE -Wno-dev ' # It is necessary to deactivate the SIMD optimization in order to build diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-foss-2017b.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-foss-2017b.eb index bb404ae72ba..6ea34df4932 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-foss-2017b.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-foss-2017b.eb @@ -28,7 +28,7 @@ dependencies = [ start_dir = 'src' -configopts = '-DCMAKE_BUILD_TYPE=Release -DWORKBENCH_MESA_DIR=${EBROOTMESA} ' +configopts = '-DWORKBENCH_MESA_DIR=${EBROOTMESA} ' configopts += '-DWORKBENCH_USE_QT5=TRUE -Wno-dev ' # It is necessary to deactivate the SIMD optimization in order to build diff --git a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-intel-2017b.eb b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-intel-2017b.eb index af146369690..c8b593dcf4b 100644 --- a/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-intel-2017b.eb +++ b/easybuild/easyconfigs/c/ConnectomeWorkbench/ConnectomeWorkbench-1.3.2-intel-2017b.eb @@ -28,7 +28,7 @@ dependencies = [ start_dir = 'src' -configopts = '-DCMAKE_BUILD_TYPE=Release -DWORKBENCH_MESA_DIR=${EBROOTMESA} ' +configopts = '-DWORKBENCH_MESA_DIR=${EBROOTMESA} ' configopts += '-DWORKBENCH_USE_QT5=TRUE -Wno-dev ' # It is necessary to deactivate the SIMD optimization in order to build diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb index 0c4d722d921..0653b39665e 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb @@ -46,8 +46,7 @@ builddependencies = [('CMake', '3.9.5')] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' -configopts += '-DENABLE_MPI=ON ' +configopts = '-DENABLE_MPI=ON ' configopts += '-DENABLE_OMP=ON ' # Only enable for BLAS/LAPACK having 8 byte integers (basically MKL) adjust the configopts 'i8' option accordingly configopts += '-DENABLE_64BIT_INTEGERS=ON ' diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.4-GCCcore-8.2.0.eb index 3ac6b74f888..e141a4203de 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.4-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.4-GCCcore-8.2.0.eb @@ -17,10 +17,6 @@ builddependencies = [ ('CMake', '3.13.3'), ] -separate_build_dir = True - -build_type = 'Release' - # Build static lib, static lib with -fPIC and shared lib configopts = [ '', diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.4-GCCcore-8.3.0.eb index 5e4a608dafd..295ca845f6f 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.4-GCCcore-8.3.0.eb @@ -17,10 +17,6 @@ builddependencies = [ ('CMake', '3.15.3'), ] -separate_build_dir = True - -build_type = 'Release' - # Build static lib, static lib with -fPIC and shared lib configopts = [ '', diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb index 23fc1b1e9fb..ba6b262e5e9 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb @@ -17,10 +17,6 @@ builddependencies = [ ('CMake', '3.18.4'), ] -separate_build_dir = True - -build_type = 'Release' - # Build static lib, static lib with -fPIC and shared lib configopts = [ '', diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.3.0.eb index 115873f2963..80a872dea0b 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.3.0.eb @@ -17,10 +17,6 @@ builddependencies = [ ('CMake', '3.20.1'), ] -separate_build_dir = True - -build_type = 'Release' - # Build static lib, static lib with -fPIC and shared lib configopts = [ '', diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-11.2.0.eb index a1ba9120b64..54f1be2f0cd 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-11.2.0.eb @@ -17,10 +17,6 @@ builddependencies = [ ('CMake', '3.21.1'), ] -separate_build_dir = True - -build_type = 'Release' - # Build static lib, static lib with -fPIC and shared lib configopts = [ '', diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-9.3.0.eb index 54a669f1a95..e3b9916c69a 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-9.3.0.eb @@ -17,10 +17,6 @@ builddependencies = [ ('CMake', '3.16.4'), ] -separate_build_dir = True - -build_type = 'Release' - # Build static lib, static lib with -fPIC and shared lib configopts = [ '', diff --git a/easybuild/easyconfigs/e/elastix/elastix-4.9.0-foss-2018a.eb b/easybuild/easyconfigs/e/elastix/elastix-4.9.0-foss-2018a.eb index 11cdeebdd2c..57ae89adca7 100644 --- a/easybuild/easyconfigs/e/elastix/elastix-4.9.0-foss-2018a.eb +++ b/easybuild/easyconfigs/e/elastix/elastix-4.9.0-foss-2018a.eb @@ -19,10 +19,6 @@ dependencies = [ ('ITK', '4.13.0', '-Python-2.7.14'), ] -configopts = '-DCMAKE_BUILD_TYPE=Release ' - -separate_build_dir = True - sanity_check_paths = { 'files': ['bin/elastix', 'bin/transformix'], 'dirs': ['include', 'lib'] diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb index 82bf05536dc..2e3e8f058de 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2016a-Python-2.7.11.eb @@ -12,6 +12,7 @@ toolchainopts = {'openmp': True} source_urls = ['http://www.cs.ubc.ca/research/flann/uploads/FLANN/'] sources = ['flann-%(version)s-src.zip'] +checksums = ['dfbb9321b0d687626a644c70872a2c540b16200e7f4c7bd72f91ae032f445c08'] builddependencies = [('CMake', '3.5.2')] dependencies = [ @@ -20,7 +21,7 @@ dependencies = [ separate_build_dir = True -configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" +configopts = "-DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2017b-Python-2.7.14.eb index 51ef4d7a5b9..cc78e9558be 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-intel-2017b-Python-2.7.14.eb @@ -23,7 +23,7 @@ dependencies = [('Python', '2.7.14')] separate_build_dir = True -configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" +configopts = "-DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.0-beta.3-intel-2018a.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.0-beta.3-intel-2018a.eb index 868b3e1e569..cba105c466c 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.0-beta.3-intel-2018a.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.0-beta.3-intel-2018a.eb @@ -29,10 +29,6 @@ builddependencies = [('CMake', '3.10.2')] preconfigopts = 'cp -a ../ffindex_soedinglab-%s/* ' % local_ffindex_commit preconfigopts += '%(builddir)s/%(namelower)s-%(version)s/lib/ffindex && ' -configopts = '-DCMAKE_BUILD_TYPE=Release -G "Unix Makefiles" ' - -separate_build_dir = True - modextravars = {'HHLIB': '%(installdir)s'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/HyPo/HyPo-1.0.3-GCC-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/HyPo/HyPo-1.0.3-GCC-8.3.0-Python-3.7.4.eb index 5d84f8de4eb..3e9deac9f64 100644 --- a/easybuild/easyconfigs/h/HyPo/HyPo-1.0.3-GCC-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/HyPo/HyPo-1.0.3-GCC-8.3.0-Python-3.7.4.eb @@ -28,7 +28,8 @@ preconfigopts = "rm -r %(builddir)s/hypo*/external/install/htslib/lib && " configopts = "-Doptimise_for_native=ON " # using 'Conda' as build type to make CMake honor the specified location for dependencies -configopts += "-DCMAKE_BUILD_TYPE=Conda -DHTSLIB_INSTALL_DIR=$EBROOTHTSLIB -DSDSLLIB_INSTALL_DIR=$EBROOTSDSL" +build_type = 'Conda' +configopts += "-DHTSLIB_INSTALL_DIR=$EBROOTHTSLIB -DSDSLLIB_INSTALL_DIR=$EBROOTSDSL" sanity_check_paths = { 'files': ['bin/hypo'], diff --git a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-foss-2018a-Python-3.6.4.eb index 1feb856eb57..2084383830f 100644 --- a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-foss-2018a-Python-3.6.4.eb @@ -27,7 +27,7 @@ dependencies = [ separate_build_dir = True # see configure.sh script for default set of configuration options -configopts = "-DCMAKE_BUILD_TYPE=Release -DKRATOS_INSTALL_PREFIX=%(installdir)s " +configopts = "-DKRATOS_INSTALL_PREFIX=%(installdir)s " configopts += "-DBOOST_ROOT=$EBROOTBOOST -DBoost_NO_SYSTEM_PATHS=ON -DBoost_NO_BOOST_CMAKE=ON " configopts += "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python -DINSTALL_EMBEDDED_PYTHON=ON -DINSTALL_PYTHON_FILES=ON " configopts += "-DMESHING_APPLICATION=ON -DEXTERNAL_SOLVERS_APPLICATION=ON -DSTRUCTURAL_MECHANICS_APPLICATION=ON " diff --git a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb index 7df486aa091..70c8492910a 100644 --- a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb @@ -31,7 +31,7 @@ dependencies = [ separate_build_dir = True # see configure.sh script for default set of configuration options -configopts = "-DCMAKE_BUILD_TYPE=Release -DKRATOS_INSTALL_PREFIX=%(installdir)s " +configopts = "-DKRATOS_INSTALL_PREFIX=%(installdir)s " configopts += "-DBOOST_ROOT=$EBROOTBOOST -DBoost_NO_SYSTEM_PATHS=ON -DBoost_NO_BOOST_CMAKE=ON " configopts += "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python -DINSTALL_EMBEDDED_PYTHON=ON -DINSTALL_PYTHON_FILES=ON " configopts += "-DMESHING_APPLICATION=ON -DEXTERNAL_SOLVERS_APPLICATION=ON -DSTRUCTURAL_MECHANICS_APPLICATION=ON " diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.2-foss-2019a.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.2-foss-2019a.eb index ede81d82e98..48fa5205f93 100644 --- a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.2-foss-2019a.eb +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.2-foss-2019a.eb @@ -29,8 +29,6 @@ sources = ['%(name)s-%(version)s.txz'] checksums = ['16c7dd362cf95288b6288e1a76caf8baef652eb2cf8af500a5eb4767ba2fe80c'] parallel = 1 -separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release ' modextravars = { 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.2-intel-2019a.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.2-intel-2019a.eb index add215ba79a..4462a6902a4 100644 --- a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.2-intel-2019a.eb +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.2-intel-2019a.eb @@ -29,9 +29,6 @@ sources = ['%(name)s-%(version)s.txz'] checksums = ['16c7dd362cf95288b6288e1a76caf8baef652eb2cf8af500a5eb4767ba2fe80c'] parallel = 1 -separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release ' - modextravars = { 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' } diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2019b.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2019b.eb index 4ac7ff3989a..d2bbb80d815 100644 --- a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2019b.eb +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2019b.eb @@ -29,9 +29,6 @@ sources = ['%(name)s-%(version)s.txz'] checksums = ['88a5416006c65a2940d82fad49de0885aead05bfa8b59f87d287db5516b9c467'] parallel = 1 -separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release ' - modextravars = { 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' } diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2020a.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2020a.eb index 3fc9c6cb46f..36a0c912cde 100644 --- a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2020a.eb +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-foss-2020a.eb @@ -29,8 +29,6 @@ dependencies = [ ] parallel = 1 -separate_build_dir = True -build_type = 'Release' modextravars = { 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2019b.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2019b.eb index b3f1e459c75..6951314c438 100644 --- a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2019b.eb +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2019b.eb @@ -29,9 +29,6 @@ sources = ['%(name)s-%(version)s.txz'] checksums = ['88a5416006c65a2940d82fad49de0885aead05bfa8b59f87d287db5516b9c467'] parallel = 1 -separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=Release ' - modextravars = { 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' } diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2020a.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2020a.eb index 944a2f80e09..50e1ba1f84c 100644 --- a/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2020a.eb +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.1.3-intel-2020a.eb @@ -29,8 +29,6 @@ dependencies = [ ] parallel = 1 -separate_build_dir = True -build_type = 'Release' modextravars = { 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.2.0.eb index 6c0ae0afd6e..8c5e5691eb1 100644 --- a/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.2.0.eb @@ -31,8 +31,6 @@ dependencies = [ ] parallel = 1 -separate_build_dir = True -build_type = 'Release' modextravars = { 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.3.0.eb index 910fef02a8c..89fd77df997 100644 --- a/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.2.1-GCCcore-10.3.0.eb @@ -31,8 +31,6 @@ dependencies = [ ] parallel = 1 -separate_build_dir = True -build_type = 'Release' modextravars = { 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb index 227d24549a3..ecc93e83772 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2018b-Python-3.6.6.eb @@ -15,7 +15,6 @@ checksums = ['887b6433a30282cb002117da89b05812c770fd9469f93950ff3866ddd02bfc64'] builddependencies = [('CMake', '3.12.1')] -configopts = '-DCMAKE_BUILD_TYPE=Release' dependencies = [ ('Python', '3.6.6'), diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb index d65e2c7c358..f836ce504bd 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019a.eb @@ -22,7 +22,6 @@ dependencies = [ ('NCCL', '2.4.2'), ] -configopts = '-DCMAKE_BUILD_TYPE=Release' exts_defaultclass = 'PythonPackage' exts_default_options = { diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb index 3c578c8cc13..9d6e0f23edb 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2019b-Python-3.7.4.eb @@ -22,8 +22,6 @@ dependencies = [ ('NCCL', '2.4.8'), ] -build_type = 'Release' - exts_defaultclass = 'PythonPackage' exts_default_options = { 'download_dep_fail': True, diff --git a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb index d871b75c78a..2a82e9c481f 100644 --- a/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/l/libgpuarray/libgpuarray-0.7.6-fosscuda-2020b.eb @@ -23,8 +23,6 @@ dependencies = [ ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] -build_type = 'Release' - exts_defaultclass = 'PythonPackage' exts_default_options = { 'download_dep_fail': True, diff --git a/easybuild/easyconfigs/m/MRCPP/MRCPP-1.3.6-foss-2020a.eb b/easybuild/easyconfigs/m/MRCPP/MRCPP-1.3.6-foss-2020a.eb index 453982c6199..4702a4e30f0 100644 --- a/easybuild/easyconfigs/m/MRCPP/MRCPP-1.3.6-foss-2020a.eb +++ b/easybuild/easyconfigs/m/MRCPP/MRCPP-1.3.6-foss-2020a.eb @@ -19,8 +19,6 @@ builddependencies = [ ] configopts = "-DENABLE_MPI=True -DENABLE_OPENMP=True" -separate_build_dir = True -build_type = 'release' runtest = 'test' sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/MRChem/MRChem-1.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MRChem/MRChem-1.0.0-foss-2020a-Python-3.8.2.eb index fa91eb54472..2f9dfbcb7f8 100644 --- a/easybuild/easyconfigs/m/MRChem/MRChem-1.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MRChem/MRChem-1.0.0-foss-2020a-Python-3.8.2.eb @@ -28,8 +28,6 @@ dependencies = [ ] configopts = "-DENABLE_MPI=True -DENABLE_OPENMP=True" -separate_build_dir = True -build_type = 'release' runtest = 'test' sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.3.14-foss-2019a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.3.14-foss-2019a.eb index fa93e55ee62..038db941352 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.3.14-foss-2019a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.3.14-foss-2019a.eb @@ -37,8 +37,7 @@ dependencies = [ separate_build_dir = True -configopts = "-DCMAKE_BUILD_TYPE=Release " -configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) configopts += "-DWITH_PCRE=bundled " # using an external PCRE is broken, see https://bugs.exim.org/show_bug.cgi?id=2173 configopts += "-DWITH_ZLIB=system " diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.4.13-gompi-2019b.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.4.13-gompi-2019b.eb index 92741312fc0..0e511067f4c 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.4.13-gompi-2019b.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.4.13-gompi-2019b.eb @@ -37,8 +37,7 @@ dependencies = [ separate_build_dir = True -configopts = "-DCMAKE_BUILD_TYPE=Release " -configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) configopts += "-DWITH_PCRE=bundled " # using an external PCRE is broken, see https://bugs.exim.org/show_bug.cgi?id=2173 configopts += "-DWITH_ZLIB=system " diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb index db3b9cf4a49..6fe1eb0f6cc 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb @@ -47,8 +47,7 @@ dependencies = [ local_pcre2_path = '%%(builddir)s/pcre2-%s.zip' % local_pcre2_ver preconfigopts = "sed -i 's@http://.*.zip@file://%s@g' ../mariadb-%%(version)s/cmake/pcre.cmake && " % local_pcre2_path -configopts = "-DCMAKE_BUILD_TYPE=Release " -configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) configopts += "-DWITH_PCRE=bundled " # using an external PCRE is broken, see https://bugs.exim.org/show_bug.cgi?id=2173 configopts += "-DWITH_ZLIB=system " diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb index 6473e5c7709..725b0d44831 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb @@ -47,8 +47,7 @@ dependencies = [ local_pcre2_path = '%%(builddir)s/pcre2-%s.zip' % local_pcre2_ver preconfigopts = "sed -i 's@http://.*.zip@file://%s@g' ../mariadb-%%(version)s/cmake/pcre.cmake && " % local_pcre2_path -configopts = "-DCMAKE_BUILD_TYPE=Release " -configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) configopts += "-DWITH_PCRE=bundled " # using an external PCRE is broken, see https://bugs.exim.org/show_bug.cgi?id=2173 configopts += "-DWITH_ZLIB=system " diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb index 2aa07971580..e8c1686fe75 100644 --- a/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PCL/PCL-1.7.2-intel-2016a-Python-2.7.11.eb @@ -13,6 +13,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/PointCloudLibrary/pcl/archive/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['479f84f2c658a6319b78271111251b4c2d6cf07643421b66bbc351d9bed0ae93'] builddependencies = [('CMake', '3.5.2')] dependencies = [ @@ -23,8 +24,6 @@ dependencies = [ ('Qhull', '2015.2'), ] -configopts = '-DCMAKE_BUILD_TYPE=Release ' - sanity_check_paths = { 'files': [], 'dirs': ['bin', 'include/pcl-%(version_major_minor)s/pcl', 'lib', 'share/pcl-%(version_major_minor)s'], diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb index 2455e433618..47629d26e8e 100644 --- a/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb @@ -28,8 +28,6 @@ dependencies = [ ('Qhull', '2015.2'), ] -configopts = '-DCMAKE_BUILD_TYPE=Release ' - sanity_check_paths = { 'files': [], 'dirs': ['bin', 'include/pcl-%(version_major_minor)s/pcl', 'lib', 'share/pcl-%(version_major_minor)s'], diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.1.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.1.4-intel-2016a-Python-2.7.11.eb index cc1a8741b21..f72915ceea0 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.1.4-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.1.4-intel-2016a-Python-2.7.11.eb @@ -10,8 +10,9 @@ description = """An API for the Polarizable Continuum Model.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'cstd': 'c99'} -sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e20d6e984cdb2795351714c2659c71d69fede9ebf159435fc7a0fdf897981ee9'] dependencies = [ ('Python', '2.7.11'), @@ -24,7 +25,7 @@ builddependencies = [ ('Eigen', '3.2.7'), ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN' +configopts = '-DEIGEN3_ROOT=$EBROOTEIGEN' configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS $LIBLAPACK_MT -DEIGEN_USE_MKL_ALL"' separate_build_dir = True diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb index f8ba46b7525..017eaf7df0b 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb @@ -27,7 +27,7 @@ builddependencies = [ ('Eigen', '3.3.7', '', True), ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN' +configopts = '-DEIGEN3_ROOT=$EBROOTEIGEN' separate_build_dir = True diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb index 0274eb69923..1483418bd8d 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb @@ -27,7 +27,7 @@ builddependencies = [ ('Eigen', '3.3.7', '', True), ] -configopts = '-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN' +configopts = '-DEIGEN3_ROOT=$EBROOTEIGEN' separate_build_dir = True diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb index 36dc00869e5..61dd798a80e 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-20160205-intel-2016a-Python-2.7.11.eb @@ -10,8 +10,9 @@ description = """An API for the Polarizable Continuum Model.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'cstd': 'c99'} -sources = ['2473699d6c5db36525160e.tar.gz'] source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] +sources = ['2473699d6c5db36525160e.tar.gz'] +checksums = ['52219902e1cdc7a8f3725f7b72938c7722ecdaf5bfb3ca6fff7917979335eee2'] dependencies = [ ('Python', '2.7.11'), @@ -24,7 +25,7 @@ builddependencies = [ ('Eigen', '3.2.7'), ] -configopts = "-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN " +configopts = "-DEIGEN3_ROOT=$EBROOTEIGEN " configopts += '-DCMAKE_CXX_FLAGS="$LIBLAPACK_MT -DEIGEN_USE_MKL_ALL"' separate_build_dir = True diff --git a/easybuild/easyconfigs/p/pizzly/pizzly-0.37.3-foss-2018b.eb b/easybuild/easyconfigs/p/pizzly/pizzly-0.37.3-foss-2018b.eb index 80427327483..19f28932807 100644 --- a/easybuild/easyconfigs/p/pizzly/pizzly-0.37.3-foss-2018b.eb +++ b/easybuild/easyconfigs/p/pizzly/pizzly-0.37.3-foss-2018b.eb @@ -23,7 +23,6 @@ builddependencies = [('CMake', '3.12.1')] dependencies = [('zlib', '1.2.11')] -configopts = '-DCMAKE_BUILD_TYPE=Release' separate_build_dir = True diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha3-GCCcore-8.2.0.eb index 1de978078f4..9981cd1c560 100644 --- a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha3-GCCcore-8.2.0.eb @@ -39,7 +39,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.2'), ] -configopts = "-G Ninja -DPORT=Qt -DCMAKE_BUILD_TYPE=Release -DUSE_LIBHYPHEN=OFF -DUSE_GSTREAMER=OFF " +configopts = "-DPORT=Qt -DUSE_LIBHYPHEN=OFF -DUSE_GSTREAMER=OFF " sanity_check_paths = { 'files': [ diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb index 0fff752203f..d3095e4a6c1 100644 --- a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-10.2.0.eb @@ -43,7 +43,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.5'), ] -configopts = "-G Ninja -DPORT=Qt -DCMAKE_BUILD_TYPE=Release -DUSE_LIBHYPHEN=OFF -DUSE_GSTREAMER=OFF " +configopts = "-DPORT=Qt -DUSE_LIBHYPHEN=OFF -DUSE_GSTREAMER=OFF " sanity_check_paths = { 'files': [ diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-0.9.0-GCC-8.3.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-0.9.0-GCC-8.3.0.eb index d404a8cd864..6e4afcf7720 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-0.9.0-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-0.9.0-GCC-8.3.0.eb @@ -63,10 +63,6 @@ builddependencies = [ configopts = '-DUSE_MPI=OFF ' configopts += '-DUSE_GMP=ON ' -build_type = 'Release' - -separate_build_dir = True - # too much parallellism makes the build fail with: # No rule to make target 'localdeps/lib/libterraces.a'; # see https://github.com/amkozlov/raxml-ng/issues/108 diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-0.9.0-gompi-2019b.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-0.9.0-gompi-2019b.eb index 983b0a97ec7..dd2cd4fdc19 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-0.9.0-gompi-2019b.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-0.9.0-gompi-2019b.eb @@ -63,10 +63,6 @@ builddependencies = [ configopts = '-DUSE_MPI=ON ' configopts += '-DUSE_GMP=ON ' -build_type = 'Release' - -separate_build_dir = True - # too much parallellism makes the build fail with: # No rule to make target 'localdeps/lib/libterraces.a'; # see https://github.com/amkozlov/raxml-ng/issues/108 diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.1-gompi-2019b.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.1-gompi-2019b.eb index 627946c4e80..4e0ac9e3be5 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.1-gompi-2019b.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.1-gompi-2019b.eb @@ -62,10 +62,6 @@ builddependencies = [ configopts = '-DUSE_MPI=ON ' configopts += '-DUSE_GMP=ON ' -build_type = 'Release' - -separate_build_dir = True - # too much parallellism makes the build fail with: # No rule to make target 'localdeps/lib/libterraces.a'; # see https://github.com/amkozlov/raxml-ng/issues/108 diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb index b18fbb2c5fb..9510c0e8ee0 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.0.2-gompi-2020b.eb @@ -62,10 +62,6 @@ builddependencies = [ configopts = '-DUSE_MPI=ON ' configopts += '-DUSE_GMP=ON ' -build_type = 'Release' - -separate_build_dir = True - # too much parallellism makes the build fail with: # No rule to make target 'localdeps/lib/libterraces.a'; # see https://github.com/amkozlov/raxml-ng/issues/108 diff --git a/easybuild/easyconfigs/s/strelka/strelka-2.9.10-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/strelka/strelka-2.9.10-foss-2018b-Python-2.7.15.eb index b226cfc1474..e980e28cde9 100644 --- a/easybuild/easyconfigs/s/strelka/strelka-2.9.10-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/strelka/strelka-2.9.10-foss-2018b-Python-2.7.15.eb @@ -23,7 +23,7 @@ dependencies = [ ('Python', '2.7.15'), ] -configopts = "-DBOOST_ROOT=$EBROOTBOOST -DCMAKE_BUILD_TYPE=Release" +configopts = "-DBOOST_ROOT=$EBROOTBOOST" separate_build_dir = True diff --git a/easybuild/easyconfigs/s/strelka/strelka-2.9.10-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/strelka/strelka-2.9.10-intel-2018b-Python-2.7.15.eb index 4b623052288..8dc42c17dd0 100644 --- a/easybuild/easyconfigs/s/strelka/strelka-2.9.10-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/strelka/strelka-2.9.10-intel-2018b-Python-2.7.15.eb @@ -25,7 +25,7 @@ dependencies = [ separate_build_dir = True -configopts = "-DBOOST_ROOT=$EBROOTBOOST -DCMAKE_BUILD_TYPE=Release" +configopts = "-DBOOST_ROOT=$EBROOTBOOST" sanity_check_paths = { 'files': ['bin/configureStrelkaGermlineWorkflow.py', 'libexec/strelka%(version_major)s'], diff --git a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.0-GCCcore-9.3.0.eb index 8921a717b36..962ea747cfe 100644 --- a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.0-GCCcore-9.3.0.eb @@ -17,9 +17,6 @@ builddependencies = [ ('CMake', '3.16.4') ] -separate_build_dir = True -build_type = 'release' - modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb index c9423b441d3..b6179c23068 100644 --- a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.2.0.eb @@ -17,9 +17,6 @@ builddependencies = [ ('CMake', '3.18.4') ] -separate_build_dir = True -build_type = 'release' - modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.3.0.eb index b4e94d5e324..250287bce72 100644 --- a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-10.3.0.eb @@ -17,9 +17,6 @@ builddependencies = [ ('CMake', '3.20.1') ] -separate_build_dir = True -build_type = 'release' - modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} sanity_check_paths = { From d896c102954d00038137f926080206318736f7e4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 15 Sep 2021 16:00:35 +0200 Subject: [PATCH 4309/9987] Add missing space in ANTs 2.2.0 EC --- .../easyconfigs/a/ANTs/ANTs-2.2.0-foss-2016b-Python-2.7.12.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ANTs/ANTs-2.2.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ANTs/ANTs-2.2.0-foss-2016b-Python-2.7.12.eb index b2d2d259758..a2581285547 100644 --- a/easybuild/easyconfigs/a/ANTs/ANTs-2.2.0-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/a/ANTs/ANTs-2.2.0-foss-2016b-Python-2.7.12.eb @@ -25,7 +25,7 @@ dependencies = [ ] configopts = '-DUSE_SYSTEM_ITK=ON ' -configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF' +configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON -DITK_DIR=$EBROOTITK/lib/cmake/ITK-%s' % local_itkshortver skipsteps = ['install'] From ebff19df466f9925cfd8f2cdbc8093d063c9904e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 26 Jul 2022 12:56:04 +0200 Subject: [PATCH 4310/9987] fix typo in fastparquet v0.7.2 Co-authored-by: Adam Huffman --- .../easyconfigs/f/fastparquet/fastparquet-0.7.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-0.7.2-foss-2021a.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-0.7.2-foss-2021a.eb index 2d49b22c447..4e5947b7081 100644 --- a/easybuild/easyconfigs/f/fastparquet/fastparquet-0.7.2-foss-2021a.eb +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-0.7.2-foss-2021a.eb @@ -4,7 +4,7 @@ name = 'fastparquet' version = '0.7.2' homepage = "https://fastparquet.readthedocs.io/" -description = """fastparquet is a python implementation of the parquet format, aiming integrate +description = """fastparquet is a python implementation of the parquet format, aiming to integrate into python-based big data work-flows. It is used implicitly by the projects Dask, Pandas and intake-parquet.""" From 8aacbb341bcffb6c4d8ff7e5f6cd8e30ce9706e2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 26 Jul 2022 12:56:29 +0200 Subject: [PATCH 4311/9987] fix typo in fastparquet v0.8.0 Co-authored-by: Adam Huffman --- .../easyconfigs/f/fastparquet/fastparquet-0.8.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-0.8.0-foss-2021b.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-0.8.0-foss-2021b.eb index 682100d629a..baed58072cf 100644 --- a/easybuild/easyconfigs/f/fastparquet/fastparquet-0.8.0-foss-2021b.eb +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-0.8.0-foss-2021b.eb @@ -4,7 +4,7 @@ name = 'fastparquet' version = '0.8.0' homepage = "https://fastparquet.readthedocs.io/" -description = """fastparquet is a python implementation of the parquet format, aiming integrate +description = """fastparquet is a python implementation of the parquet format, aiming to integrate into python-based big data work-flows. It is used implicitly by the projects Dask, Pandas and intake-parquet.""" From 5c9b9ee3a547c02d63c90420eaddaa1e96500061 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 16 Sep 2021 11:36:36 +0200 Subject: [PATCH 4312/9987] Add CI check for CMAKE_BUILD_TYPE --- test/easyconfigs/easyconfigs.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3889a791b86..5780787ba3f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1147,6 +1147,23 @@ def check_https_url(http_url): if failing_checks: self.fail('\n'.join(failing_checks)) + @skip_if_not_pr_to_non_main_branch() + def test_pr_CMAKE_BUILD_TYPE(self): + """Make sure -DCMAKE_BUILD_TYPE is no longer used (replaced by build_type)""" + failing_checks = [] + for ec in self.changed_ecs: + ec_fn = os.path.basename(ec.path) + configopts = ec.get('configopts') + build_type = ec.get('build_type') + + if configopts and '-DCMAKE_BUILD_TYPE' in configopts: + failing_checks.append("Found -DCMAKE_BUILD_TYPE in configopts. Use build_type instead: %s" % ec_fn) + if build_type == 'Release': + failing_checks.append("build_type was set to the default of 'Release'. " + "Ommit this to base it on toolchain_opts.debug: %s" % ec_fn) + if failing_checks: + self.fail('\n'.join(failing_checks)) + @skip_if_not_pr_to_non_main_branch() def test_pr_patch_descr(self): """ From dea17975db4951a08abd292074bbd23e041e9dbb Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Tue, 26 Jul 2022 21:23:13 +0200 Subject: [PATCH 4313/9987] Update easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Thank you @bedroge Co-authored-by: Bob Dröge --- .../Phantompeakqualtools-1.2.2-foss-2021b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb index be1aea63c7a..59ac5c1610a 100644 --- a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb @@ -40,7 +40,10 @@ exts_list = [ }), ] -modextrapaths = {'PATH': ''} +modextrapaths = { + 'PATH': '', + 'R_LIBS_SITE': '', +} sanity_check_paths = { 'files': ['run_spp.R'], From 6bb2fd5a484889ffa379d50476826a8c308eb942 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Tue, 26 Jul 2022 21:47:05 +0200 Subject: [PATCH 4314/9987] Update Phantompeakqualtools-1.2.2-foss-2021b.eb The installation success if we remove the "sanity_check_commands" instance. I checked later and run_spp.R works My guess of why sanity_check_commands fail is because run_spp.R exit with code 1 when it prints usage but maybe I am wrong. The idea of pipe to grep seems it was not enough. Here is an extract of run_spp.R about the exit status I mentioned (print.usage() function is defined earlier and print the help menu): # Check number of arguments minargs = 1; maxargs = 17; if (nargs < minargs | nargs > maxargs) { print.usage() q(save="no",status=1) } Do you know some other way to get around to use some "sanity_check_commands"? --- .../Phantompeakqualtools-1.2.2-foss-2021b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb index 59ac5c1610a..b3a80768f53 100644 --- a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb @@ -50,6 +50,4 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ['run_spp.R | grep "Usage: Rscript run_spp.R "'] - moduleclass = 'bio' From a327f1fb7fa231bd98985fd651a075014dc2ec27 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 27 Jul 2022 14:20:34 +0200 Subject: [PATCH 4315/9987] adding easyconfigs: alevin-fry-0.6.0-GCCcore-10.3.0.eb --- .../alevin-fry-0.6.0-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.6.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.6.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.6.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..19bc9a51461 --- /dev/null +++ b/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.6.0-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'Binary' + +name = 'alevin-fry' +version = '0.6.0' + +homepage = 'https://github.com/COMBINE-lab/alevin-fry' +description = """alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, + currently focused on single-cell transcriptomics and feature barcoding.""" +# software_license = 'LicenseBSD3' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/COMBINE-lab/alevin-fry/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8a368695da8e85826f3d72670c83c44344d5c184a7bccda4ab2dea486eb3e00b'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Rust', '1.60.0'), + ('CMake', '3.20.1'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +extract_sources = True + +install_cmd = "cargo install --root %(installdir)s --path ." + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' From 6ead542eaea72f56b0b7573092db443180966ac4 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 27 Jul 2022 15:15:29 +0100 Subject: [PATCH 4316/9987] adding easyconfigs: BLAST+-2.13.0-gompi-2022a.eb --- .../b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb new file mode 100644 index 00000000000..ac01b7edfc3 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb @@ -0,0 +1,50 @@ +# # +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# # + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.13.0' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['89553714d133daf28c477f83d333794b3c62e4148408c072a1b4620e5ec4feb2'] + +dependencies = [ + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost', '1.79.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('LMDB', '0.9.29'), +] + +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' src/algo/blast/api/Makefile.xblast.lib &&" +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 --with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST --with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG --with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [], +} + +moduleclass = 'bio' From 4c8ea95c73cda9e3165544a9dc0050005b276437 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 27 Jul 2022 15:31:46 +0100 Subject: [PATCH 4317/9987] Update BLAST+-2.13.0-gompi-2022a.eb --- .../b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb index ac01b7edfc3..fcd401581cd 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb @@ -38,9 +38,15 @@ dependencies = [ ('LMDB', '0.9.29'), ] -preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' src/algo/blast/api/Makefile.xblast.lib &&" -configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 --with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST --with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG --with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" - +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" sanity_check_paths = { 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], From 4bad2d22c66991ce4bfc87fedb25f72e553d56c3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 27 Jul 2022 16:39:37 +0200 Subject: [PATCH 4318/9987] adding easyconfigs: MATSim-14.0-GCCcore-11.2.0-Java-11.eb, MATSim-14.0-Java-11.eb --- .../MATSim-14.0-GCCcore-11.2.0-Java-11.eb | 37 +++++++++++++++++++ .../m/MATSim/MATSim-14.0-Java-11.eb | 34 +++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb create mode 100644 easybuild/easyconfigs/m/MATSim/MATSim-14.0-Java-11.eb diff --git a/easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb new file mode 100644 index 00000000000..dd2b476ec76 --- /dev/null +++ b/easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb @@ -0,0 +1,37 @@ +easyblock = 'PackedBinary' + +name = 'MATSim' +version = '14.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.matsim.org/' +description = """MATSim is an open-source framework to implement large-scale agent-based transport simulations.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/matsim-org/matsim-libs/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-release.zip'] +checksums = ['17c7b785678cacd937f5df5b8c80398b73e2e9ceb07cc1ebd175fc94a65ce3c4'] + +dependencies = [ + ('Java', '11', '', True), + ('Mesa', '21.1.7'), + ('X11', '20210802'), +] + +sanity_check_paths = { + 'files': ['%(namelower)s-%(version)s.jar'], + 'dirs': ['libs', 'examples'], +} + +sanity_check_commands = ["java org.matsim.run.ReleaseInfo"] + +modextrapaths = {'CLASSPATH': 'libs/*'} + +modloadmsg = """ +To execute MATSim GUI: java -jar $EBROOTMATSIM/%(namelower)s-%(version)s.jar +To execute MATSim in batch mode: java org.matsim.run.RunMatsim +You might have to adjust the maximum memory of the JVM (-Xmx) +""" + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/m/MATSim/MATSim-14.0-Java-11.eb b/easybuild/easyconfigs/m/MATSim/MATSim-14.0-Java-11.eb new file mode 100644 index 00000000000..11bcf3dbdad --- /dev/null +++ b/easybuild/easyconfigs/m/MATSim/MATSim-14.0-Java-11.eb @@ -0,0 +1,34 @@ +easyblock = 'PackedBinary' + +name = 'MATSim' +version = '14.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.matsim.org/' +description = """MATSim is an open-source framework to implement large-scale agent-based transport simulations.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/matsim-org/matsim-libs/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-release.zip'] +checksums = ['17c7b785678cacd937f5df5b8c80398b73e2e9ceb07cc1ebd175fc94a65ce3c4'] + +dependencies = [ + ('Java', '11'), +] + +sanity_check_paths = { + 'files': ['%(namelower)s-%(version)s.jar'], + 'dirs': ['libs', 'examples'], +} + +sanity_check_commands = ["java org.matsim.run.ReleaseInfo"] + +modextrapaths = {'CLASSPATH': 'libs/*'} + +modloadmsg = """ +To execute MATSim in batch mode: java org.matsim.run.RunMatsim +You might have to adjust the maximum memory of the JVM (-Xmx) +""" + +moduleclass = 'cae' From 9aba41b84f90761eb8ce88576f35057a1d636607 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 27 Jul 2022 16:15:44 +0100 Subject: [PATCH 4319/9987] disabling auto-vectorization no longer needed for AVX512 in 2.13.0 --- easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb index fcd401581cd..fb96f2a9897 100644 --- a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.13.0-gompi-2022a.eb @@ -38,11 +38,6 @@ dependencies = [ ('LMDB', '0.9.29'), ] -# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) -# Compilation fails on src/algo/blast/api/prelim_stage.cpp -local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' -preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake - configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " From 9439d8c7ee25683d6dcc3d2ca1dcf20ee90fa468 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 28 Jul 2022 10:56:27 +0200 Subject: [PATCH 4320/9987] Change version of the toolchain and dependencies --- .../b/BEDTools/BEDTools-2.30.0-GCC-11.3.0.eb | 45 +++++++++++++++++++ .../b/BamTools/BamTools-2.5.2-GCC-11.3.0.eb | 19 ++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..3fe167c952e --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-11.3.0.eb @@ -0,0 +1,45 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.30.0' + +homepage = "https://bedtools.readthedocs.io/" +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8'] + +builddependencies = [('Python', '3.10.4')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +sanity_check_commands = ['bedtools --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..99952934112 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-11.3.0.eb @@ -0,0 +1,19 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +name = 'BamTools' +version = '2.5.2' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8'] + +builddependencies = [('CMake', '3.23.1')] + +moduleclass = 'bio' From ae58cfd81afe62d0c5d201f6fc617271fcc3bf4d Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 28 Jul 2022 11:15:52 +0200 Subject: [PATCH 4321/9987] Update BCFtools and HTSlib --- .../b/BCFtools/BCFtools-1.15.1-GCC-11.3.0.eb | 38 ++++++++++++++++++ .../h/HTSlib/HTSlib-1.15.1-GCC-11.3.0.eb | 39 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.15.1-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.15.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.15.1-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.15.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..2d4f97afdbd --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.15.1-GCC-11.3.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.15.1' + +homepage = 'https://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f21f9564873eb27ccf22d13b91a64acb8fbbfe4f9e4c37933a54b9a95857f2d7'] + +dependencies = [ + ('zlib', '1.2.12'), + ('HTSlib', '1.15.1'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('GSL', '2.7'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['libexec/bcftools'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.15.1-GCC-11.3.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.15.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..bb7636b2af0 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.15.1-GCC-11.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Updated to 1.14 +# J. Sassmannshausen /GSTT + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.15.1' + +homepage = "https://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['8d7f8bf9658226942eeab70af2a22aca618577eaa8fe2ed9416ee306d5351aa1'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.83.0'), +] + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From 19e209bdde59dc301d74ec5dbf7ae98fd7b1d60c Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 28 Jul 2022 11:21:44 +0200 Subject: [PATCH 4322/9987] adding easyconfigs: SAMtools-1.15.1-GCC-11.3.0.eb --- .../s/SAMtools/SAMtools-1.15.1-GCC-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.15.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.15.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.15.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..b935cb8536e --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.15.1-GCC-11.3.0.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +# +# Updated to 1.14 and gcc-11.2.0 +# J. Sassmannshausen / GSTT + +name = 'SAMtools' +version = '1.15.1' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['708c525ac76b0532b25f14aadea34a4d11df667bc19bf0a74dae617d80526c6e'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.83.0'), +] + +moduleclass = 'bio' From 6d60b51ab0eba44f8cc330c8833024f4c0a1891d Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 28 Jul 2022 11:27:56 +0200 Subject: [PATCH 4323/9987] adding easyconfigs: PRSice-2.3.5-GCCcore-11.3.0.eb --- .../p/PRSice/PRSice-2.3.5-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fb98cc63e1a --- /dev/null +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMakeCp' + +name = 'PRSice' +version = '2.3.5' + +homepage = 'https://www.prsice.info/' +description = """PRSice (pronounced 'precise') is a Polygenic Risk +Score software for calculating, applying, evaluating and +plotting the results of polygenic risk scores (PRS) analyses.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/choishingwan/PRSice/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['0a7e649ddebe4e969cd8400c5ad977a7b900be4f5c920a84483cb8930367354d'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), + ('Eigen', '3.4.0'), +] + +files_to_copy = [(['bin/PRSice'], 'bin'), "README.md", "LICENSE"] + +sanity_check_paths = { + 'files': ['bin/PRSice'], + 'dirs': [], +} + +sanity_check_commands = ["PRSice --help"] + +moduleclass = 'bio' From afc827db624c3e277c162dc5b6e31999648cc28e Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 28 Jul 2022 11:37:13 +0200 Subject: [PATCH 4324/9987] adding easyconfigs: Bowtie2-2.4.5-GCC-11.3.0.eb --- .../b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb new file mode 100644 index 00000000000..23f2eb1bda7 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp + +name = 'Bowtie2' +version = '2.4.5' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['d3cbd5f323393b5649aea10325d7c4b77f02035a8b204e5ac18eba95236e076a'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Perl', '5.34.1'), + ('Python', '3.10.4'), +] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] + +moduleclass = 'bio' From a69b9d34bb499bebb958aaf2a6094285b65c22c3 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 28 Jul 2022 14:24:41 +0200 Subject: [PATCH 4325/9987] adding easyconfigs: BBMap-38.96-GCC-10.3.0.eb --- .../b/BBMap/BBMap-38.96-GCC-10.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb new file mode 100644 index 00000000000..d3215416acf --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '38.96' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['18d9c89b02c0ab044b2795a65f6236b2262a494ed83d27e31750437b350ef080'] + +dependencies = [('Java', '11', '', True)] + +prebuildopts = 'cd jni && ' + +local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % local_suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" + +moduleclass = 'bio' From d150184b473b613dab834ae4a08d4889ec199b68 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 28 Jul 2022 15:07:38 +0200 Subject: [PATCH 4326/9987] {tools}[foss/2021a] Ray-project v1.13.0 --- .../Ray-project-1.13.0-foss-2021a.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ray-project/Ray-project-1.13.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-1.13.0-foss-2021a.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.13.0-foss-2021a.eb new file mode 100644 index 00000000000..bcd6321d086 --- /dev/null +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-1.13.0-foss-2021a.eb @@ -0,0 +1,54 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'Ray-project' +version = '1.13.0' + +homepage = "https://docs.ray.io/en/latest/" +description = "Ray is a fast and simple framework for building and running distributed applications." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('protobuf-python', '3.17.3'), + ('PyYAML', '5.4.1'), + ('redis-py', '4.3.1'), +] + +use_pip = True + +exts_list = [ + ('grpcio', '1.43.0', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['735d9a437c262ab039d02defddcb9f8f545d7009ae61c0114e19dda3843febe5'], + }), + ('aiosignal', '1.2.0', { + 'checksums': ['78ed67db6c7b7ced4f98e495e572106d5c432a93e1ddd1bf475e1dc05f5b7df2'], + }), + ('frozenlist', '1.3.0', { + 'checksums': ['ce6f2ba0edb7b0c1d8976565298ad2deba6f8064d2bebb6ffce2ca896eb35b0b'], + }), + ('Ray', version, { + 'source_tmpl': '%(namelower)s-%(version)s-cp39-cp39-manylinux2014_x86_64.whl', + 'checksums': ['ba0829d495dec0bc90a72169f93e4cb004962a37df4d9b0df23004ebefb6d221'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ray'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'ray --help' +] + +sanity_pip_check = True + +moduleclass = 'tools' From fd295ec7d21983404a4246566a15a1d0a0edfcae Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 28 Jul 2022 15:43:12 +0200 Subject: [PATCH 4327/9987] adding easyconfigs: x264-20220620-GCCcore-11.3.0.eb, x265-3.5-GCCcore-11.3.0.eb, Yasm-1.3.0-GCCcore-11.3.0.eb, FFmpeg-5.0.1-GCCcore-11.3.0.eb --- .../f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ .../x/x264/x264-20220620-GCCcore-11.3.0.eb | 33 ++++++++++++++ .../x/x265/x265-3.5-GCCcore-11.3.0.eb | 34 +++++++++++++++ .../y/Yasm/Yasm-1.3.0-GCCcore-11.3.0.eb | 25 +++++++++++ 4 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20220620-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8bb0209eb4e --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '5.0.1' + +homepage = 'https://www.ffmpeg.org/' +description = "A complete, cross-platform solution to record, convert and stream audio and video." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://%(namelower)s.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['28df33d400a1c1c1b20d07a99197809a3b88ef765f5f07dc1ff067fac64c59d6'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] +dependencies = [ + ('NASM', '2.15.05'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('x264', '20220620'), + ('LAME', '3.100'), + ('x265', '3.5'), + ('X11', '20220504'), + ('freetype', '2.12.1'), + ('fontconfig', '2.14.0'), + ('FriBidi', '1.0.12'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x264/x264-20220620-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/x264/x264-20220620-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2b05023e8af --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20220620-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20220620' + +homepage = 'https://www.videolan.org/developers/x264.html' +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/5db6aa6c/'] +sources = [{'download_filename': '%(name)s-5db6aa6c.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['9b5543a5f114f4c6905a2319ea4c2063d6ebd2db209b41642086df3c1f7b6f50'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('NASM', '2.15.05'), +] + +configopts = " --enable-shared --enable-static --disable-bashcompletion" + + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x264_config.h', 'include/%(name)s.h', 'lib/libx264.a', 'lib/libx264.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..281db53772b --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.5' + +homepage = 'https://x265.org/' +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://bitbucket.org/multicoreware/x265_git/downloads/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['e70a3335cacacbba0b3a20ec6fecd6783932288ebc8163ad74bcc9606477cae8'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Yasm', '1.3.0'), +] + +configopts = '-DGIT_ARCHETYPE=1' + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x265_config.h', 'include/%(name)s.h', 'lib/libx265.a', 'lib/libx265.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7c73c4bf3bd --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'https://www.tortall.net/projects/yasm/' +description = "Yasm: Complete rewrite of the NASM assembler with BSD license" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [ + ('binutils', '2.38'), +] + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'lang' From 51afc7abfe83ea9c797767d4fb01cd4493cf2da5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Jul 2022 15:55:46 +0200 Subject: [PATCH 4328/9987] PyTorch 1.9.0: Fix PPC patch --- .../p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 2 +- .../PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 2 +- .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 2 +- ...Torch-1.9.0_fix-vsx-vector-functions.patch | 29 ------------------- 4 files changed, 3 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 34f2218ba3f..bec52561d8b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -46,7 +46,7 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', - '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index a05a60e0fd0..f08d6445a48 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -64,7 +64,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', - '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index 0fc9595a1b1..e075328d5fd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -63,7 +63,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', - '56a46c1690467a7fe7f6b904d152f8a3e2385305c5c29717f66b98b38022bf74', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-vsx-vector-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-vsx-vector-functions.patch index a3c3e0b0b85..3e6225f6aa4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-vsx-vector-functions.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-vsx-vector-functions.patch @@ -160,35 +160,6 @@ index 2a1a87aa72..5bcf818232 100644 } Vec256 C10_ALWAYS_INLINE ceil() const { return {vec_ceil(_vec0), vec_ceil(_vec1)}; -@@ -593,27 +593,7 @@ class Vec256 { - } - - Vec256 C10_ALWAYS_INLINE pow(const Vec256& exp) const { -- auto x = *this; -- auto sign_bit = (*this) & sign_mask; -- // |b| -- auto exp_abs = exp.abs(); -- auto exp_trunc = exp.trunc(); -- Vec256 odd_mask; -- odd_mask._vecb0 = (vec_signed(exp._vec0) & vi_1) != vi_0; -- odd_mask._vecb1 = (vec_signed(exp._vec1) & vi_1) != vi_0; -- // using ln fuction -- auto temp = (abs().log() * exp).exp(); -- -- // is odd or even check from Sleef -- auto is_int = (exp == exp_trunc) | (exp_abs >= vcheck); -- auto is_odd = odd_mask & is_int & (exp_abs < vcheck); -- // if even then then pow result should be absolute -- auto temp_sign = temp | sign_bit; // copy_sign -- auto out = blendv(temp, temp_sign, is_odd); -- // x<0 and y != N, then NAN -- auto out1 = blendv(out, v_nan, ((exp.floor() != exp) & (x < zero))); -- // y = 0 then 1 -- return blendv(out1, one, (exp_abs == zero)); -+ return {Sleef_powf4_u10vsx(_vec0, b._vec0), Sleef_powf4_u10vsx(_vec1, b._vec1)}; - } - - Vec256 fmod(const Vec256& b) const { @@ -653,8 +616,8 @@ class Vec256 { DEFINE_MEMBER_OP(operator-, float, vec_sub) DEFINE_MEMBER_OP(operator*, float, vec_mul) From db42146c6698ca1329c266aeb79e4612e4ffcfad Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 28 Jul 2022 18:21:50 +0200 Subject: [PATCH 4329/9987] adding easyconfigs: libyaml-0.2.5-GCCcore-11.3.0.eb, PyYAML-6.0-GCCcore-11.3.0.eb --- .../l/libyaml/libyaml-0.2.5-GCCcore-11.3.0.eb | 25 +++++++++++++++++ .../p/PyYAML/PyYAML-6.0-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f3386d4eee0 --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.5' + +homepage = 'https://pyyaml.org/wiki/LibYAML' +description = "LibYAML is a YAML parser and emitter written in C." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pyyaml.org/download/%(name)s/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['c642ae9b75fee120b2d96c712538bd2cf283228d2337df2cf2988e3c02678ef4'] + +builddependencies = [ + ('binutils', '2.38'), +] + + +sanity_check_paths = { + 'files': ['include/yaml.h', 'lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0c55d6c41a2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '6.0' + +homepage = 'https://github.com/yaml/pyyaml' +description = "PyYAML is a YAML parser and emitter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('Python', '3.10.4'), + ('libyaml', '0.2.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'yaml'} + +moduleclass = 'lib' From 5ccb86a252382048a49aa99639d4cf8fa5955522 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 28 Jul 2022 18:24:54 +0200 Subject: [PATCH 4330/9987] adding easyconfigs: magma-2.6.2-foss-2022a-CUDA-11.7.0.eb --- .../magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..1e6b82478d4 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'magma' +version = '2.6.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/%(name)s/downloads/'] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version_major_minor)s.1_allow-all-sms.patch'] +checksums = [ + '75b554dab00903e2d10b972c913e50e7f88cbc62f3ae432b5a086c7e4eda0a71', # %(name)s-%(version)s.tar.gz + # %(name)s-%(version_major_minor)s.1_allow-all-sms.patch + 'b89285bac007b68e88e3b5ddbb7f94dbc8a9d77590e58c352e477574d8dca738', +] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), +] + +# make sure both static and shared libs are built +configopts = [ + '-DBUILD_SHARED_LIBS=ON -DGPU_TARGET="%(cuda_sm_space_sep)s" ', + '-DBUILD_SHARED_LIBS=OFF -DGPU_TARGET="%(cuda_sm_space_sep)s" ', +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = [ + '3.5', + '5.0', + '6.0', + '7.0', + '7.5', + '%(cuda_cc_space_sep)s', + '8.6', +] + +sanity_check_paths = { + 'files': ['lib/libmagma.so', 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' From c7591fab37af0505eaac74b61a2bb543ed87838e Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 28 Jul 2022 18:26:10 +0200 Subject: [PATCH 4331/9987] adding easyconfigs: expecttest-0.1.3-GCCcore-11.3.0.eb --- .../expecttest-0.1.3-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..30003e96055 --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.1.3' + +homepage = 'https://github.com/ezyang/expecttest' +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['83057695811d94128aed13ed094a070db90e0a92ea40071f8ee073cbab57149a'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From 57ef1cb4d548bba79d597905435ee8c51c956ae3 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 28 Jul 2022 18:32:37 +0200 Subject: [PATCH 4332/9987] adding easyconfigs: PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb --- .../PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 116 ++++++++++++++++++ 1 file changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..d868b1a890d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,116 @@ +name = 'PyTorch' +version = '1.12.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] + +patches = [ + '%(name)s-1.7.0_avoid-nan-in-test-torch.patch', + '%(name)s-1.7.0_disable-dev-shm-test.patch', + '%(name)s-1.8.1_dont-use-gpu-ccc-in-test.patch', + '%(name)s-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + '%(name)s-1.10.0_fix-test-dataloader-fixed-affinity.patch', + '%(name)s-1.10.0_skip_cmake_rpath.patch', + '%(name)s-1.11.0_increase-distributed-test-timeout.patch', + '%(name)s-1.11.0_skip_failing_ops_tests.patch', + '%(name)s-1.11.0_fix_skip_jit_cuda_fuser.patch', + '%(name)s-1.11.0_fix_sharded_imports.patch', + '%(name)s-1.11.0_increase_test_tolerances_TF32.patch', + '%(name)s-1.11.0_increase_c10d_gloo_timeout.patch', + '%(name)s-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('typing-extensions', '4.3.0'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '5.0.1'), + ('Pillow', '9.1.1'), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', True), + ('magma', '2.6.2', '-CUDA-%(cudaver)s'), + ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = [ + '3.5', + '3.7', + '5.2', + '6.0', + '6.1', + '7.0', + '7.2', + '7.5', + '8.0', + '8.6', +] + +custom_opts = ['USE_CUPTI_SO=1'] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + # 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + # 'distributed/rpc/test_process_group_agent', + # This test fails constently when run as part of the test suite, but succeeds when run interactively + 'test_model_dump', + # These tests appear flaky, possibly related to number of GPUs that are used + 'distributed/fsdp/test_fsdp_memory', + 'distributed/fsdp/test_fsdp_overlap', + ] +} + +runtest = "cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s" + +# several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), +# so we allow up to 10 (out of ~90k) tests to fail before treating the installation to be faulty +max_failed_tests = 10 + +# The readelf sanity check command can be taken out once the TestRPATH test from +# https://github.com/pytorch/pytorch/pull/68912 is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] + +tests = ['%(name)s-check-cpp-extension.py'] + +moduleclass = 'devel' From a8e8b2050770261d6be07609e789b194c7a40ea2 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 29 Jul 2022 10:46:40 +0200 Subject: [PATCH 4333/9987] Make EasyConfig more similar to magma-2.6.2-foss-2021b-CUDA-11.4.1 in terms of syntax/order --- .../magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb index 1e6b82478d4..b15aaf2ae7d 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -27,21 +27,12 @@ dependencies = [ ('CUDA', '11.7.0', '', True), ] +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] + # make sure both static and shared libs are built configopts = [ - '-DBUILD_SHARED_LIBS=ON -DGPU_TARGET="%(cuda_sm_space_sep)s" ', - '-DBUILD_SHARED_LIBS=OFF -DGPU_TARGET="%(cuda_sm_space_sep)s" ', -] - -# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) -cuda_compute_capabilities = [ - '3.5', - '5.0', - '6.0', - '7.0', - '7.5', - '%(cuda_cc_space_sep)s', - '8.6', + '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') ] sanity_check_paths = { From fafbd1633ea43c2a034baf8bf0408b8090cf59c8 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 29 Jul 2022 11:50:40 +0200 Subject: [PATCH 4334/9987] adding easyconfigs: Cartopy-0.20.3-foss-2021b.eb --- .../c/Cartopy/Cartopy-0.20.3-foss-2021b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2021b.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2021b.eb new file mode 100644 index 00000000000..7238ae75ac7 --- /dev/null +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2021b.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Cartopy' +version = '0.20.3' + +homepage = 'https://scitools.org.uk/cartopy/docs/latest/' +description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('Fiona', '1.8.21'), + ('GDAL', '3.3.2'), + ('GEOS', '3.9.1'), + ('matplotlib', '3.4.3'), + ('SciPy-bundle', '2021.10'), + ('Shapely', '1.8.2'), + ('lxml', '4.6.3'), + ('Pillow', '8.3.2'), + ('PROJ', '8.1.0'), + ('PyYAML', '5.4.1'), +] + +use_pip = True +sanity_pip_check = True + +# owslib 0.26.0 requires pyproj < 3.3.0 +exts_list = [ + ('pyproj', '3.2.1', { + 'preinstallopts': "export PROJ_DIR=$EBROOTPROJ && ", + 'checksums': ['4a936093825ff55b24c1fc6cc093541fcf6d0f6d406589ed699e62048ebf3877'], + }), + ('OWSLib', '0.26.0', { + 'checksums': ['8c4cb06338eb6405c2aeced0b6d085682aa61f0f2e528f1c788d68dc50df941b'], + }), + ('pyepsg', '0.4.0', { + 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], + }), + ('pykdtree', '1.3.5', { + 'checksums': ['7342f75e731103e653fc1f6b9fdabc2410cf92b6e7b06160804a75786c9b5747'], + }), + ('pyshp', '2.3.1', { + 'modulename': 'shapefile', + 'checksums': ['4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1'], + }), + (name, version, { + 'checksums': ['0d60fa2e2fbd77c4d1f6b1f9d3b588966147f07c1b179d2d34570ac1e1b49006'], + }), +] + +moduleclass = 'geo' From 1d3c70e8d81e4c6ef1a4fdf40d61c2bdd73000b8 Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 29 Jul 2022 12:07:26 +0200 Subject: [PATCH 4335/9987] adding easyconfigs: p7zip-17.04-GCCcore-11.3.0.eb --- .../p/p7zip/p7zip-17.04-GCCcore-11.3.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..20265bc30b3 --- /dev/null +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '17.04' + +homepage = 'https://github.com/jinfeihan57/p7zip/' +description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of +7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'jinfeihan57' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ea029a2e21d2d6ad0a156f6679bd66836204aa78148a4c5e498fe682e77127ef'] + +builddependencies = [ + ('binutils', '2.38'), +] + +prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" +buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' + +files_to_copy = [ + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.%s' % SHLIB_EXT, 'bin/Codecs'], 'libexec'), # 7z requires 7z.so plugin in same directory +] + +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + "echo '#!/bin/sh\n%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask +] + +sanity_check_paths = { + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.%s' % SHLIB_EXT], + 'dirs': ['libexec/Codecs'], +} + +sanity_check_commands = [ + '7z --help', + '7z x || test $? -gt 0', + "! 7z i | grep -q \"Can't load\" ", +] + +moduleclass = 'tools' From 02cca60f964d600013cf2f129d473674164db981 Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 29 Jul 2022 15:05:41 +0200 Subject: [PATCH 4336/9987] adding easyconfigs: Valgrind-3.19.0-gompi-2022a.eb --- .../v/Valgrind/Valgrind-3.19.0-gompi-2022a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.19.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.19.0-gompi-2022a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.19.0-gompi-2022a.eb new file mode 100644 index 00000000000..b3846caed03 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.19.0-gompi-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.19.0' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'https://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['dd5e34486f1a483ff7be7300cc16b4d6b24690987877c3278d797534d6738f02'] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] +local_archs = ('amd64', 'arm64', 'ppc64le') + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + [['lib/valgrind/libmpiwrap-%s-linux.%s' % (a, SHLIB_EXT) for a in local_archs]], + 'dirs': [] +} + +moduleclass = 'debugger' From f6de77865586c1636ec1fe3da76047e03e90eb96 Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 29 Jul 2022 15:10:48 +0200 Subject: [PATCH 4337/9987] adding easyconfigs: XML-Parser-2.46-GCCcore-11.3.0-Perl-5.34.1.eb --- ...-Parser-2.46-GCCcore-11.3.0-Perl-5.34.1.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-11.3.0-Perl-5.34.1.eb diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-11.3.0-Perl-5.34.1.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-11.3.0-Perl-5.34.1.eb new file mode 100644 index 00000000000..4caf48f0876 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-11.3.0-Perl-5.34.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.46' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://search.cpan.org/~toddr/XML-Parser-2.46/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d331332491c51cccfb4cb94ffc44f9cd73378e618498d4a37df9e043661c515d'] + +builddependencies = [ + ('binutils', '2.38') +] + +dependencies = [ + ('Perl', '5.34.1'), + ('expat', '2.4.8') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML'], +} + +moduleclass = 'data' From 61dd4c6ceb4a6bbeded5d1eecf1d9bd4ce789591 Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 29 Jul 2022 15:35:05 +0200 Subject: [PATCH 4338/9987] adding easyconfigs: itac-2021.6.0.eb --- easybuild/easyconfigs/i/itac/itac-2021.6.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/i/itac/itac-2021.6.0.eb diff --git a/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb new file mode 100644 index 00000000000..22e6230e15b --- /dev/null +++ b/easybuild/easyconfigs/i/itac/itac-2021.6.0.eb @@ -0,0 +1,22 @@ +## +# Author: Robert Mijakovic +## +name = 'itac' +version = '2021.6.0' + +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' +description = """The Intel Trace Collector is a low-overhead tracing library that performs + event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application + activities gathered by the Intel Trace Collector through graphical displays. """ + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18694/'] +sources = ['l_itac_oneapi_p_%(version)s.434_offline.sh'] +checksums = ['1ecc2735da960041b051e377cadb9f6ab2f44e8aa44d0f642529a56a3cbba436'] + +dontcreateinstalldir = True + +preferredmpi = 'impi5' + +moduleclass = 'tools' From d9965efcd296baadcb8ad49a4232bfee329912a5 Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 29 Jul 2022 15:40:33 +0200 Subject: [PATCH 4339/9987] adding easyconfigs: parallel-20220722-GCCcore-11.3.0.eb --- .../parallel-20220722-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20220722-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/parallel/parallel-20220722-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20220722-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..290d6b575fd --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20220722-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20220722' + +homepage = 'https://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['0e4083ac0d850c434598c6dfbf98f3b6dd2cc932a3af9269eb1f9323e43af019'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Perl', '5.34.1')] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +sanity_check_commands = ["parallel --help"] + +moduleclass = 'tools' From 117af7975336209cf8a4b9e36828f6400ac7d8d8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 29 Jul 2022 15:43:55 +0200 Subject: [PATCH 4340/9987] Actually fix the patch --- .../p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 2 +- .../PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 2 +- .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 2 +- ...Torch-1.9.0_fix-vsx-vector-functions.patch | 29 +++++++++++++++++++ 4 files changed, 32 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index bec52561d8b..5931428b705 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -46,7 +46,7 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', - 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index f08d6445a48..b66e3586491 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -64,7 +64,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', - 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index e075328d5fd..0b4f5b7fb31 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -63,7 +63,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', - 'd1f85b2f0f03b500a61b2456d6ec63fccb62f7edc350a820553e2891ec23bf13', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', # PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-vsx-vector-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-vsx-vector-functions.patch index 3e6225f6aa4..d4ba6c36d16 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-vsx-vector-functions.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-vsx-vector-functions.patch @@ -160,6 +160,35 @@ index 2a1a87aa72..5bcf818232 100644 } Vec256 C10_ALWAYS_INLINE ceil() const { return {vec_ceil(_vec0), vec_ceil(_vec1)}; +@@ -593,27 +593,7 @@ class Vec256 { + } + + Vec256 C10_ALWAYS_INLINE pow(const Vec256& exp) const { +- auto x = *this; +- auto sign_bit = (*this) & sign_mask; +- // |b| +- auto exp_abs = exp.abs(); +- auto exp_trunc = exp.trunc(); +- Vec256 odd_mask; +- odd_mask._vecb0 = (vec_signed(exp._vec0) & vi_1) != vi_0; +- odd_mask._vecb1 = (vec_signed(exp._vec1) & vi_1) != vi_0; +- // using ln fuction +- auto temp = (abs().log() * exp).exp(); +- +- // is odd or even check from Sleef +- auto is_int = (exp == exp_trunc) | (exp_abs >= vcheck); +- auto is_odd = odd_mask & is_int & (exp_abs < vcheck); +- // if even then then pow result should be absolute +- auto temp_sign = temp | sign_bit; // copy_sign +- auto out = blendv(temp, temp_sign, is_odd); +- // x<0 and y != N, then NAN +- auto out1 = blendv(out, v_nan, ((exp.floor() != exp) & (x < zero))); +- // y = 0 then 1 +- return blendv(out1, one, (exp_abs == zero)); ++ return {Sleef_powf4_u10vsx(_vec0, exp._vec0), Sleef_powf4_u10vsx(_vec1, exp._vec1)}; + } + + Vec256 fmod(const Vec256& b) const { @@ -653,8 +616,8 @@ class Vec256 { DEFINE_MEMBER_OP(operator-, float, vec_sub) DEFINE_MEMBER_OP(operator*, float, vec_mul) From 6c5b9633f994ba55b594cf0173eb49e43e430468 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 29 Jul 2022 15:56:10 +0200 Subject: [PATCH 4341/9987] Add libdwarf and libelf for 2022a --- .../libdwarf/libdwarf-0.4.1-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ .../l/libelf/libelf-0.8.13-GCCcore-11.3.0.eb | 26 +++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdwarf/libdwarf-0.4.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-0.4.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.4.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3c150818816 --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.4.1-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '0.4.1' + +homepage = 'https://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.prevanders.net'] +sources = [SOURCE_TAR_XZ] +checksums = ['34277b969d30be3cc4c6fbce6926dd3e6f9ea9a27b01951c6753b479aadfd5ef'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('libelf', '0.8.13'), +] + +configopts = "--enable-shared " + +sanity_check_paths = { + 'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +sanity_check_commands = ['dwarfdump --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..40935d6dfe9 --- /dev/null +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libelf' +version = '0.8.13' + +homepage = 'https://sourceware.org/elfutils' +description = """libelf is a free ELF object file access library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://fossies.org/linux/misc/old/'] +sources = [SOURCE_TAR_GZ] +checksums = ['591a9b4ec81c1f2042a97aa60564e0cb79d041c52faa7416acb38bc95bd2c76d'] + +builddependencies = [ + ('binutils', '2.38'), +] + +modextrapaths = {'CPATH': 'include/libelf'} + +sanity_check_paths = { + 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf/libelf.h'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'devel' From ede487e67f70f73ec4a940549b3836bbaa0f77d7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 29 Jul 2022 16:31:04 +0200 Subject: [PATCH 4342/9987] exclude Binary, PackedBinary and JAR from binutils build requirements --- test/easyconfigs/easyconfigs.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f112a8a5e70..829972cf084 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1261,8 +1261,12 @@ def template_easyconfig_test(self, spec): # make sure binutils is included as a (build) dep if toolchain is GCCcore if ec['toolchain']['name'] == 'GCCcore': - # with 'Tarball' easyblock: only unpacking, no building; Eigen is also just a tarball - requires_binutils = ec['easyblock'] not in ['Tarball'] and ec['name'] not in ['ANIcalculator', 'Eigen'] + # easyblocks without a build step + non_build_blocks = ['Binary', 'JAR', 'PackedBinary', 'Tarball'] + # some software packages do not have a build step + non_build_soft = ['ANIcalculator', 'Eigen'] + + requires_binutils = ec['easyblock'] not in non_build_blocks and ec['name'] not in non_build_soft # let's also exclude the very special case where the system GCC is used as GCCcore, and only apply this # exception to the dependencies of binutils (since we should eventually build a new binutils with GCCcore) From 69530a6f4bcecda79146ae16fb95993c35c664ab Mon Sep 17 00:00:00 2001 From: swadmin Date: Fri, 29 Jul 2022 20:04:09 +0200 Subject: [PATCH 4343/9987] adding easyconfigs: LAPACK-3.10.1-GCC-11.3.0.eb --- .../l/LAPACK/LAPACK-3.10.1-GCC-11.3.0.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAPACK/LAPACK-3.10.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.10.1-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.10.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..37ad94e5b2f --- /dev/null +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.10.1-GCC-11.3.0.eb @@ -0,0 +1,16 @@ +name = 'LAPACK' +version = '3.10.1' + +homepage = 'https://www.netlib.org/lapack/' +description = """LAPACK is written in Fortran90 and provides routines for solving systems of + simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue + problems, and singular value problems.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Reference-LAPACK/lapack/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cd005cd021f144d7d5f7f33c943942db9f03a28d110d6a3b80d718a295f7f714'] + +moduleclass = 'numlib' From c17b70a5a6366345f27fc4bb3970b63ffff599cb Mon Sep 17 00:00:00 2001 From: easybuild Date: Sat, 30 Jul 2022 12:34:34 +0800 Subject: [PATCH 4344/9987] Add libffi and elfutils as dependencies --- easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb | 2 ++ easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-11.2.0.eb | 3 ++- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb index a7ec71f94dd..6d6f037e9eb 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-GCCcore-10.2.0.eb @@ -52,6 +52,8 @@ dependencies = [ ('ncurses', '6.2'), ('GMP', '6.2.0'), ('Z3', '4.8.10'), + ('libffi', '3.3'), + ('elfutils', '0.183'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-11.2.0.eb index e95723acdc8..ddef6175415 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-11.2.0.eb @@ -54,13 +54,14 @@ dependencies = [ ('ncurses', '6.2'), ('GMP', '6.2.1'), ('Z3', '4.8.12'), + ('libffi', '3.4.2'), + ('elfutils', '0.185'), ] builddependencies = [ ('CMake', '3.21.1'), ('Python', '3.9.6'), ('Perl', '5.34.0'), - ('elfutils', '0.185'), ] assertions = True From 5444320aa140613a2cddfdb3b0356c6b2bb4e553 Mon Sep 17 00:00:00 2001 From: swadmin Date: Sun, 31 Jul 2022 23:58:58 +0200 Subject: [PATCH 4345/9987] adding easyconfigs: OpenFOAM-v2206-foss-2022a.eb, ParaView-5.10.1-foss-2022a-mpi.eb, CGAL-4.14.3-gompi-2022a.eb, FFmpeg-4.4.2-GCCcore-11.3.0.eb, gnuplot-5.4.4-GCCcore-11.3.0.eb, Lua-5.4.4-GCCcore-11.3.0.eb, libcerf-2.1-GCCcore-11.3.0.eb, libgd-2.3.3-GCCcore-11.3.0.eb, METIS-5.1.0-GCCcore-11.3.0.eb, pkg-config-0.29.2-GCCcore-11.3.0.eb, pkg-config-0.29.2-GCCcore-11.3.0.eb, SCOTCH-7.0.1-gompi-2022a.eb --- .../c/CGAL/CGAL-4.14.3-gompi-2022a.eb | 38 ++++++++++++ .../f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb | 44 ++++++++++++++ .../g/gnuplot/gnuplot-5.4.4-GCCcore-11.3.0.eb | 45 ++++++++++++++ .../l/Lua/Lua-5.4.4-GCCcore-11.3.0.eb | 28 +++++++++ .../l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb | 32 ++++++++++ .../l/libgd/libgd-2.3.3-GCCcore-11.3.0.eb | 37 ++++++++++++ .../m/METIS/METIS-5.1.0-GCCcore-11.3.0.eb | 38 ++++++++++++ .../o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb | 45 ++++++++++++++ .../ParaView-5.10.1-foss-2022a-mpi.eb | 60 +++++++++++++++++++ .../pkg-config-0.29.2-GCCcore-11.3.0.eb | 34 +++++++++++ .../s/SCOTCH/SCOTCH-7.0.1-gompi-2022a.eb | 24 ++++++++ 11 files changed, 425 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.10.1-foss-2022a-mpi.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2022a.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2022a.eb new file mode 100644 index 00000000000..78055d4556d --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2022a.eb @@ -0,0 +1,38 @@ +name = 'CGAL' +version = '4.14.3' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['5bafe7abe8435beca17a1082062d363368ec1e3f0d6581bb0da8b010fb389fe4'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('Python', '3.10.4'), + ('Boost', '1.79.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('Qt5', '5.15.5'), +] + +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' +configopts += '-DOpenGL_GL_PREFERENCE=GLVND ' +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5bcb6802488 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '4.4.2' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ffmpeg.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f98a482520c47507521a907914daa9efbc1384e0591b5afc3da18aa897de2948'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2') +] + +dependencies = [ + ('NASM', '2.15.05'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('x264', '20220620'), + ('LAME', '3.100'), + ('x265', '3.5'), + ('X11', '20220504'), + ('freetype', '2.12.1'), + ('fontconfig', '2.14.0'), + ('FriBidi', '1.0.12'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ca1bcabdf53 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.4-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.4.4' + +homepage = 'http://gnuplot.sourceforge.net' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['372300b7867f5b3538b25fc5d0ac7734af6e3fe0d202b6db926e4369913f0902'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('cairo', '1.17.4'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('libgd', '2.3.3'), + ('Pango', '1.50.7'), + ('libcerf', '2.1'), + ('X11', '20220504'), + ('Qt5', '5.15.5'), + ('Lua', '5.4.4'), +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c530dc1346a --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +name = 'Lua' +version = '5.4.4' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['164c7849653b80ae67bec4b7473b884bf5cc8d2dca05653475ec2ed27b9ebf61'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('libreadline', '8.1.2'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9e8aa712671 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '2.1' + +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['8a1cd8b7fae04b82a95168252129b8c1baca098a285ff8d3f25781dead14b75a'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Perl', '5.34.1'), # required for pod2html +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..edeae044ca8 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.3' + +homepage = 'https://libgd.github.io' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd3f1f0bb016edcc0b2d082e8229c822ad1d02223511997c80461481759b1ed2'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('fontconfig', '2.14.0'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libgd.a', 'lib/libgd.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +sanity_check_commands = ['webpng --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d3593b8ed0e --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +# We use 32bit for indices and 64bit for content +patches = ['%(name)s-%(version)s-use-doubles.patch'] + +checksums = [ + '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2', # source + '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67', # patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb new file mode 100644 index 00000000000..4c58236cb3b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb @@ -0,0 +1,45 @@ +name = 'OpenFOAM' +version = 'v2206' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {'cstd': 'c++11', 'vectorize': False} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2012-cleanup.patch', 1), + 'OpenFOAM-v1906-wmake-ompi.patch', +] +checksums = [ + 'db95eda4afb97ca870733b2d4201ef539099d0778e3f3eca9a075d4f1a0eea46', # OpenFOAM-v2206.tgz + 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.1'), + ('CGAL', '4.14.3'), + ('ParaView', '5.10.1', '-mpi'), + ('gnuplot', '5.4.4'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.10.1-foss-2022a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.10.1-foss-2022a-mpi.eb new file mode 100644 index 00000000000..fe5742c74fe --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.10.1-foss-2022a-mpi.eb @@ -0,0 +1,60 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.10.1' +versionsuffix = '-mpi' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +checksums = [ + '59ca46a929a52d8abec107b72e19447cba3d8e64871b6fbc8e99b0f3b167db46', # ParaView-v5.10.1.tar.gz +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('XZ', '5.2.5'), + ('HDF5', '1.13.1'), + ('netCDF', '4.9.0'), + ('libGLU', '9.0.2'), + ('X11', '20220504'), + ('Mesa', '22.0.3'), + ('Qt5', '5.15.5'), + ('zlib', '1.2.12'), + ('FFmpeg', '4.4.2'), + ('Szip', '2.1.1'), +] + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a55b2586ff3 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [('binutils', '2.38')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a.eb new file mode 100644 index 00000000000..9313e21231d --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a.eb @@ -0,0 +1,24 @@ +name = 'SCOTCH' +version = '7.0.1' + +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['0618e9bc33c02172ea7351600fce4fccd32fe00b3359c4aabb5e415f17c06fed'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +moduleclass = 'math' From bebc443cd8c6131b0bbaf72908e0f15c21494140 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 1 Aug 2022 10:57:31 +0200 Subject: [PATCH 4346/9987] adding easyconfigs: cclib-1.7.2-foss-2021b.eb --- .../c/cclib/cclib-1.7.2-foss-2021b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/cclib/cclib-1.7.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/cclib/cclib-1.7.2-foss-2021b.eb b/easybuild/easyconfigs/c/cclib/cclib-1.7.2-foss-2021b.eb new file mode 100644 index 00000000000..cc730a59c2a --- /dev/null +++ b/easybuild/easyconfigs/c/cclib/cclib-1.7.2-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'cclib' +version = '1.7.2' + +homepage = 'https://cclib.github.io/' + +description = """ + cclib is a Python library that provides parsers for computational chemistry log files. + It also provides a platform to implement algorithms in a package-independent manner. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('periodictable', '1.6.1', { + 'checksums': ['7c501c9f73d77b1fb28cb51e85b28429c2c44a99ce3d1274894564c72d712603'], + }), + (name, version, { + 'checksums': ['bb16b422382f47ead65f92b6cd2d812409436c8306e0c5b049056337a11dfc3a'], + }), +] + +_bins = ['ccframe', 'ccget', 'ccwrite', 'cda'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%s --help' % x for x in _bins] + +moduleclass = 'chem' From 3d2e13800441deb1a5d8dc38c068404746c4ae71 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 1 Aug 2022 11:21:25 +0200 Subject: [PATCH 4347/9987] Add OpenBabel and SWIG --- .../OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb | 56 +++++++++++++++++++ .../s/SWIG/SWIG-4.0.2-GCCcore-11.3.0.eb | 24 ++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb new file mode 100644 index 00000000000..9442aa67aef --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb @@ -0,0 +1,56 @@ +name = 'OpenBabel' +version = '3.1.1' + +homepage = 'https://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +# avoid failing tests on skylake and broadwell CPUs. +# remove option 'optarch' when building on CPUs that don't support AVX2 +# see also: https://github.com/openbabel/openbabel/issues/2138 +toolchainopts = {'pic': True, 'optarch': 'mavx2'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] +patches = [ + # Fix test failure with Python 3 + # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch + 'OpenBabel-3.1.1_fix-distgeom-test.patch' +] +checksums = [ + 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz + '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('SWIG', '4.0.2'), +] +dependencies = [ + ('Python', '3.10.4'), + ('zlib', '1.2.12'), + ('libxml2', '2.9.13'), + ('Eigen', '3.4.0'), + ('RapidJSON', '1.1.0'), + ('cairo', '1.17.4'), # optional: for .png output + ('Boost', '1.79.0'), # optional: for Maestro formats +] + +configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' +# Enable support for OpenMP compilation of forcefield code (optional) +configopts += '-DENABLE_OPENMP=ON ' + +# OpenBabel-3.1.1 creates directories named 3.1.0, which leads to BABEL_LIBDIR and BABEL_DATDIR +# (set in the easyblock) having invalid values. Work around this with some symlinks. +postinstallcmds = [ + 'ln -s %(installdir)s/lib/openbabel/3.1.0 %(installdir)s/lib/openbabel/%(version)s', + 'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s', +] + +pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT +runtest = 'test' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f1a2758986f --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +name = 'SWIG' +version = '4.0.2' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d53be9730d8d58a16bf0cbd1f8ac0c0c3e1090573168bfa151b01eb47fa906fc'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('zlib', '1.2.12'), + ('PCRE', '8.45'), +] + +configopts = '--without-alllang --with-boost=no' + +moduleclass = 'devel' From b1008947c4bc78699209921cbb1901ecd8a5418c Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 1 Aug 2022 11:33:17 +0200 Subject: [PATCH 4348/9987] Add OTF2 and SIONlib --- .../o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb | 50 ++++++++++++++++++ .../SIONlib-1.7.7-GCCcore-11.3.0-tools.eb | 51 +++++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6e982449e9e --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0-GCCcore-11.3.0.eb @@ -0,0 +1,50 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '3.0' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fff0728761556e805b140fd464402ced394a3c622ededdb618025e6cdaa6d8c'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.7', '-tools'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb new file mode 100644 index 00000000000..9d094c2cb89 --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.3.0-tools.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.7' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] + +builddependencies = [ + ('binutils', '2.38'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' From 5042c3bbdd8baca60b832f1b0edc8712c80dcfda Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 1 Aug 2022 12:00:33 +0200 Subject: [PATCH 4349/9987] adding easyconfigs: buildenv-default-foss-2022a.eb, buildenv-default-intel-2021b.eb, buildenv-default-intel-2022a.eb --- .../b/buildenv/buildenv-default-foss-2022a.eb | 13 +++++++++++++ .../b/buildenv/buildenv-default-intel-2021b.eb | 13 +++++++++++++ .../b/buildenv/buildenv-default-intel-2022a.eb | 13 +++++++++++++ 3 files changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2021b.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022a.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a.eb new file mode 100644 index 00000000000..2613e835f8a --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2021b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2021b.eb new file mode 100644 index 00000000000..e31ac49a155 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2021b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2021b'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022a.eb new file mode 100644 index 00000000000..2352adaf9cb --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2022a'} + +moduleclass = 'devel' From 33eb1b02bffcf5d9bd2c907477034477ecc1afcf Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 1 Aug 2022 14:43:27 +0200 Subject: [PATCH 4350/9987] adding easyconfigs: Hypre-2.25.0-foss-2022a.eb --- .../h/Hypre/Hypre-2.25.0-foss-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.25.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.25.0-foss-2022a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.25.0-foss-2022a.eb new file mode 100644 index 00000000000..429ec49389f --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.25.0-foss-2022a.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'Hypre' +version = '2.25.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f9fc8371d91239fca694284dab17175bfda3821d7b7a871fd2e8f9d5930f303c'] + +start_dir = 'src' + +moduleclass = 'numlib' From 07bfd803c614e20cd98bd56026bd2745d79050eb Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 1 Aug 2022 15:04:41 +0200 Subject: [PATCH 4351/9987] Removed some patches for tests, as we don't want to keep maintaining these - lines change with every PT version etc - and we now have the ability to allow for a small number of failed test. Set allowed number of failing tests at 20 (14 fail on my current system). --- .../PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 26 ++++++++++++++----- 1 file changed, 19 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index d868b1a890d..08c753b7af7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -17,7 +17,6 @@ sources = [{ 'recursive': True, }, }] - patches = [ '%(name)s-1.7.0_avoid-nan-in-test-torch.patch', '%(name)s-1.7.0_disable-dev-shm-test.patch', @@ -26,13 +25,26 @@ patches = [ '%(name)s-1.10.0_fix-test-dataloader-fixed-affinity.patch', '%(name)s-1.10.0_skip_cmake_rpath.patch', '%(name)s-1.11.0_increase-distributed-test-timeout.patch', - '%(name)s-1.11.0_skip_failing_ops_tests.patch', - '%(name)s-1.11.0_fix_skip_jit_cuda_fuser.patch', - '%(name)s-1.11.0_fix_sharded_imports.patch', - '%(name)s-1.11.0_increase_test_tolerances_TF32.patch', '%(name)s-1.11.0_increase_c10d_gloo_timeout.patch', '%(name)s-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', ] +checksums = [ + None, # PyTorch-1.12.0.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_cmake_rpath.patch + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch + 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', +] builddependencies = [ ('CMake', '3.23.1'), @@ -101,8 +113,8 @@ excluded_tests = { runtest = "cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s" # several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), -# so we allow up to 10 (out of ~90k) tests to fail before treating the installation to be faulty -max_failed_tests = 10 +# so we allow up to 20 (out of ~90k) tests to fail before treating the installation to be faulty +max_failed_tests = 20 # The readelf sanity check command can be taken out once the TestRPATH test from # https://github.com/pytorch/pytorch/pull/68912 is accepted, since it is then checked as part of the PyTorch test suite From 3835bb496a1e484250eea6533b1bc142db659e64 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 1 Aug 2022 15:08:54 +0200 Subject: [PATCH 4352/9987] Typing-extensions removed as explicit dependency, as 4.2.0 is already part of Python-3.10.4-GCCcore-11.3.0.eb --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index 08c753b7af7..9a48694ea1f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -58,7 +58,6 @@ dependencies = [ ('protobuf-python', '3.19.4'), ('pybind11', '2.9.2'), ('SciPy-bundle', '2022.05'), - ('typing-extensions', '4.3.0'), ('PyYAML', '6.0'), ('MPFR', '4.1.0'), ('GMP', '6.2.1'), From 552966c4ee676cd6319c69e37932453f4be2894b Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 1 Aug 2022 15:17:15 +0200 Subject: [PATCH 4353/9987] Put back the SHLIBEXT template replacement --- easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.3.0.eb index f3386d4eee0..3b7e5265d07 100644 --- a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-11.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ sanity_check_paths = { - 'files': ['include/yaml.h', 'lib/%(name)s.a', 'lib/%(name)s.so'], + 'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT], 'dirs': ['lib/pkgconfig'], } From 1688109b50ca4deb1e989f32f7bcd50910cf382e Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 1 Aug 2022 15:50:51 +0100 Subject: [PATCH 4354/9987] adding easyconfigs: gawk-5.1.1-GCC-11.3.0.eb --- .../g/gawk/gawk-5.1.1-GCC-11.3.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.3.0.eb b/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..a692900e134 --- /dev/null +++ b/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gawk' +version = '5.1.1' + +homepage = 'https://www.gnu.org/software/gawk' +description = """The awk utility interprets a special-purpose programming language that makes it possible to handle +simple data-reformatting jobs with just a few lines of code.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6168d8d1dc8f74bd17d9dc22fa9634c49070f232343b744901da15fb4f06bffd'] + +sanity_check_paths = { + 'files': ['bin/gawk'], + 'dirs': [], +} + +sanity_check_commands = ["gawk --help"] + +moduleclass = 'tools' From bea8ccc74cc347129aa2285d9ac8784c18a7665a Mon Sep 17 00:00:00 2001 From: satishk Date: Mon, 1 Aug 2022 23:17:53 +0200 Subject: [PATCH 4355/9987] adding easyconfigs: libQGLViewer-2.8.0-GCCcore-10.3.0.eb --- .../libQGLViewer-2.8.0-GCCcore-10.3.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..062bd3defd7 --- /dev/null +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb @@ -0,0 +1,21 @@ +name = 'libQGLViewer' +version = '2.8.0' + +homepage = 'http://libqglviewer.com/' +description = "libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://www.libqglviewer.com/src'] +sources = [SOURCE_TAR_GZ] +checksums = ['03d2d3394866cdc419f43713aed827262c714cc4facddea7c3ba1d93dae3c4cc'] + +dependencies = [ + ('libGLU', '9.0.1'), +] + +builddependencies = [('Qt5', '5.15.2')] + +start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' + +moduleclass = 'lib' From b73a81ed37b6fc976b7267b2c1e9c807c661d2d8 Mon Sep 17 00:00:00 2001 From: Satish Kamath Date: Tue, 2 Aug 2022 00:44:52 +0200 Subject: [PATCH 4356/9987] Adding binutils to the build dependencies. --- .../l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb index 062bd3defd7..48a80bd8104 100644 --- a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb @@ -14,7 +14,10 @@ dependencies = [ ('libGLU', '9.0.1'), ] -builddependencies = [('Qt5', '5.15.2')] +builddependencies = [ +('Qt5', '5.15.2'), +('binutils', '2.36.1'), +] start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' From 84b0d0b986efae5575c4006bba899597155a8595 Mon Sep 17 00:00:00 2001 From: Satish Kamath Date: Tue, 2 Aug 2022 01:07:12 +0200 Subject: [PATCH 4357/9987] The builddependencies are indented. --- .../l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb index 48a80bd8104..91badd37039 100644 --- a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb @@ -15,8 +15,8 @@ dependencies = [ ] builddependencies = [ -('Qt5', '5.15.2'), -('binutils', '2.36.1'), + ('Qt5', '5.15.2'), + ('binutils', '2.36.1'), ] start_dir = '%(builddir)s/libQGLViewer-%(version)s/QGLViewer' From bc4b0ba3f343604d7c915dde9a7e63316aabda5f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 2 Aug 2022 09:41:30 +0100 Subject: [PATCH 4358/9987] adding easyconfigs: Lua-5.4.4-GCCcore-11.3.0.eb --- .../l/Lua/Lua-5.4.4-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c530dc1346a --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +name = 'Lua' +version = '5.4.4' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['164c7849653b80ae67bec4b7473b884bf5cc8d2dca05653475ec2ed27b9ebf61'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('libreadline', '8.1.2'), +] + +moduleclass = 'lang' From 010c6cb201a6a07eb4c2435903d7c59a2229e964 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 2 Aug 2022 09:44:22 +0100 Subject: [PATCH 4359/9987] adding easyconfigs: libgd-2.3.3-GCCcore-11.3.0.eb --- .../l/libgd/libgd-2.3.3-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..edeae044ca8 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.3' + +homepage = 'https://libgd.github.io' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd3f1f0bb016edcc0b2d082e8229c822ad1d02223511997c80461481759b1ed2'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('fontconfig', '2.14.0'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libgd.a', 'lib/libgd.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +sanity_check_commands = ['webpng --help'] + +moduleclass = 'lib' From 22383876af21146998a85c6cabf26e0b359a4048 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 2 Aug 2022 09:46:44 +0100 Subject: [PATCH 4360/9987] adding easyconfigs: libcerf-2.1-GCCcore-11.3.0.eb --- .../l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9e8aa712671 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '2.1' + +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['8a1cd8b7fae04b82a95168252129b8c1baca098a285ff8d3f25781dead14b75a'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Perl', '5.34.1'), # required for pod2html +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' From 7eda055fde624009a513b0d694c4cdcf12b30d50 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 2 Aug 2022 09:49:07 +0100 Subject: [PATCH 4361/9987] adding easyconfigs: gnuplot-5.4.4-GCCcore-11.3.0.eb --- .../g/gnuplot/gnuplot-5.4.4-GCCcore-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ca1bcabdf53 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.4-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.4.4' + +homepage = 'http://gnuplot.sourceforge.net' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['372300b7867f5b3538b25fc5d0ac7734af6e3fe0d202b6db926e4369913f0902'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('cairo', '1.17.4'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('libgd', '2.3.3'), + ('Pango', '1.50.7'), + ('libcerf', '2.1'), + ('X11', '20220504'), + ('Qt5', '5.15.5'), + ('Lua', '5.4.4'), +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' From 28aa923ef0eb521a6b9101025b7270e987befbb6 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 2 Aug 2022 12:01:36 +0100 Subject: [PATCH 4362/9987] adding easyconfigs: SWIG-4.0.2-GCCcore-11.3.0.eb --- .../s/SWIG/SWIG-4.0.2-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f1a2758986f --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +name = 'SWIG' +version = '4.0.2' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d53be9730d8d58a16bf0cbd1f8ac0c0c3e1090573168bfa151b01eb47fa906fc'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('zlib', '1.2.12'), + ('PCRE', '8.45'), +] + +configopts = '--without-alllang --with-boost=no' + +moduleclass = 'devel' From e76608bd5c44e5ba0053632ea97119b60dbbd939 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 2 Aug 2022 12:08:20 +0100 Subject: [PATCH 4363/9987] adding easyconfigs: GTS-0.7.6-GCCcore-11.3.0.eb --- .../g/GTS/GTS-0.7.6-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..81da084b988 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. +It is an Open Source Free Software Library intended to provide a set of useful +functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('binutils', '2.38'), +] +dependencies = [ + ('GLib', '2.72.1'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [], +} + +moduleclass = 'vis' From 268d331e0e89d1961e21d3e9625db158a093e2e2 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 2 Aug 2022 12:29:23 +0100 Subject: [PATCH 4364/9987] adding easyconfigs: Graphviz-5.0.0-GCCcore-11.3.0.eb --- .../Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3a6dc3f0712 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,87 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '5.0.0' +local_pyver_major = '3' + +homepage = 'https://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + 'f8cc576694ae93659f453b6b4a4c2f04572a90cfccdca2d4271f2e7c60bb3d60', # graphviz-5.0.0.tar.gz +] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('SWIG', '4.0.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.10.4'), + ('FriBidi', '1.0.12'), + ('Gdk-Pixbuf', '2.42.8'), + ('Ghostscript', '9.56.1'), + ('GTS', '0.7.6'), + ('libgd', '2.3.3'), + ('Pango', '1.50.7'), + ('Perl', '5.34.1'), + ('Qt5', '5.15.5'), + ('Tcl', '8.6.12'), + ('zlib', '1.2.12'), +] + +preconfigopts = './autogen.sh NOCONFIG && ' + +configopts = '--enable-python%s=yes ' % local_pyver_major +configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' +# Use ltdl from libtool in EB +configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' +configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' +# Override the hardcoded paths to Java libraries +configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' +configopts += '--with-javalibdir=$JAVA_HOME/lib' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +postinstallcmds = ['%(installdir)s/bin/dot -c'] # Writes plugin configuration + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acyclic', 'bcomps', 'ccomps', 'cluster', 'diffimg', 'dijkstra', 'dot', + 'dot_builtins', 'dot', 'edgepaint', 'gc', 'gml2gv', 'graphml2gv', 'gv2gml', + 'gvcolor', 'gvedit', 'gvgen', 'gvmap', 'gvmap.sh', 'gvpack', 'gvpr', 'gxl2gv', + 'mm2gv', 'nop', 'prune', 'sccmap', 'tred', 'unflatten', 'vimdot']] + + ['lib/%s.%s' % (x, SHLIB_EXT) for x in ['libcdt', 'libcgraph', 'libgvc', 'libgvpr', 'liblab_gamut', + 'libpathplan', 'libxdot']], + 'dirs': ['include', 'lib/graphviz', 'lib/graphviz/java', 'lib/graphviz/python%s' % local_pyver_major, + 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), + ('python', '-c "import gv"'), +] + +modextrapaths = { + 'CLASSPATH': 'lib/graphviz/java', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'PYTHONPATH': 'lib/graphviz/python%s' % local_pyver_major, + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' From 74090e965e71e979dba128804a61990c7d02d957 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 2 Aug 2022 12:36:31 +0100 Subject: [PATCH 4365/9987] adding easyconfigs: gifsicle-1.93-GCCcore-11.3.0.eb --- .../gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3290d13b65b --- /dev/null +++ b/easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +# Contribution from the Crick Scientific Computing team +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'gifsicle' +version = '1.93' + +github_account = 'kohler' +homepage = 'https://github.com/%(github_account)s/%(namelower)s' +description = """Gifsicle is a command-line tool for creating, editing, +and getting information about GIF images and animations. +Making a GIF animation with gifsicle is easy.""" + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['941c0b1c3ebc748949a0d14363f0fb3c9d2c06ee122b3548315b9233eb956d88'] + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +configure_cmd = "autoreconf -i && ./configure" + +sanity_check_paths = { + 'files': ['bin/gifsicle'], + 'dirs': [] +} + +moduleclass = 'vis' From a8367c5ae50698c54b1abe3c266e0667e1147a14 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 2 Aug 2022 14:18:03 +0200 Subject: [PATCH 4366/9987] Add Score-P and dependencies --- .../c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb | 62 +++++++++++++++++++ .../c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb | 55 ++++++++++++++++ .../CubeWriter-4.7-GCCcore-11.3.0.eb | 53 ++++++++++++++++ .../o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb | 44 +++++++++++++ .../p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb | 37 +++++++++++ .../s/Score-P/Score-P-7.1-gompi-2022a.eb | 59 ++++++++++++++++++ 6 files changed, 310 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..270db629dc6 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb @@ -0,0 +1,62 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeGUI' +version = '4.7' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube graphical report explorer. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['CubeGUI-4.6_qtlibs_symlink_realpath.patch'] +checksums = [ + '103fe00fa9846685746ce56231f64d850764a87737dc0407c9d0a24037590f68', # cubegui-4.7.tar.gz + # '0b382346251b82792393e44103ddb44f9b1665dd3c652670171a0833984e8987', # CubeGUI-4.6_qtlibs_symlink_realpath.patch +] + +preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + ('Autotools', '20220317'), +! ('CubeLib', '4.7'), +] + +dependencies = [ + ('Qt5', '5.15.5'), +] + +configopts = [ + "--with-qt=$EBROOTQT5" +] + +sanity_check_paths = { + 'files': ['bin/cube', 'bin/cubegui-config', + 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], + 'dirs': ['include/cubegui', 'lib/cube-plugins'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bef3ea7d344 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb @@ -0,0 +1,55 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.7' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e44352c80a25a49b0fa0748792ccc9f1be31300a96c32de982b92477a8740938'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + # ('pkg-config', '0.29.2'), + ('pkgconfig', '1.5.5'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..87eb56e48b9 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.7' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['a7c7fca13e6cb252f08d4380223d7c56a8e86a67de147bcc0279ebb849c884a5'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + ('pkgconfig', '1.5.5'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..acc02a8fc51 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.6' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['55972289ce66080bb48622110c3189a36e88a12917635f049b37685b9d3bbcb0'] + +builddependencies = [ + ('binutils', '2.38'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6a7954de21b --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25.1' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +checksums = ['0b6f8a6b8769c181b2ae6cae7298f04b8e3e3d68066f598ed24574e19500bc97'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb new file mode 100644 index 00000000000..773bcc6594b --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb @@ -0,0 +1,59 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '7.1' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['98dea497982001fb82da3429ca55669b2917a0858c71abe2cfe7cd113381f1f7'] + +dependencies = [ + ('CubeLib', '4.7'), + ('CubeWriter', '4.7'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.6'), + ('OTF2', '3.0'), + # Hardware counter support (optional): + ('PAPI', '6.0.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From d86d1d56f84b09fa280ea5d3b2450714ac08dd35 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 2 Aug 2022 14:24:42 +0200 Subject: [PATCH 4367/9987] Cleaning --- easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb | 3 +-- .../easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb index 270db629dc6..91b272b19e3 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb @@ -42,7 +42,7 @@ builddependencies = [ # use same binutils version that was used when building GCCcore ('binutils', '2.38'), ('Autotools', '20220317'), -! ('CubeLib', '4.7'), + ('CubeLib', '4.7'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb index bef3ea7d344..d48598c1cf5 100644 --- a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb @@ -36,8 +36,7 @@ checksums = ['e44352c80a25a49b0fa0748792ccc9f1be31300a96c32de982b92477a8740938'] builddependencies = [ # use same binutils version that was used when building GCCcore ('binutils', '2.38'), - # ('pkg-config', '0.29.2'), - ('pkgconfig', '1.5.5'), + ('pkgconf', '1.8.0'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb index 87eb56e48b9..6649e72f03e 100644 --- a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb @@ -35,7 +35,7 @@ checksums = ['a7c7fca13e6cb252f08d4380223d7c56a8e86a67de147bcc0279ebb849c884a5'] builddependencies = [ # use same binutils version that was used when building GCCcore ('binutils', '2.38'), - ('pkgconfig', '1.5.5'), + ('pkgconf', '1.8.0'), ] dependencies = [ From 07b2db81737166318260f3f2339da5584ba61e2c Mon Sep 17 00:00:00 2001 From: Satish Kamath Date: Tue, 2 Aug 2022 14:53:55 +0200 Subject: [PATCH 4368/9987] Added Qt5 as a dependency since it is required when shared libraries from Qt5 are not RPATHed. --- .../l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb index 91badd37039..9d7bd0007da 100644 --- a/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libQGLViewer/libQGLViewer-2.8.0-GCCcore-10.3.0.eb @@ -11,11 +11,11 @@ sources = [SOURCE_TAR_GZ] checksums = ['03d2d3394866cdc419f43713aed827262c714cc4facddea7c3ba1d93dae3c4cc'] dependencies = [ + ('Qt5', '5.15.2'), ('libGLU', '9.0.1'), ] builddependencies = [ - ('Qt5', '5.15.2'), ('binutils', '2.36.1'), ] From 7c2a64226e9706862782f8ea32e1f71518b38abc Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 2 Aug 2022 14:00:52 +0000 Subject: [PATCH 4369/9987] adding easyconfigs: UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb and patches: UCC-CUDA-1.0.0_link_against_existing_UCC_libs.patch --- ...C-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb | 58 +++++++++++++++++++ ...1.0.0_link_against_existing_UCC_libs.patch | 26 +++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0_link_against_existing_UCC_libs.patch diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..6614a62fef1 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'UCC-CUDA' +version = '1.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. + +This module adds the UCC CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-1.0.0_link_against_existing_UCC_libs.patch', +] +checksums = [ + 'd3b4aa7004bf339d35952a1699a6e408064ba578bdc93861f5f07527ad0a5e8c', # v1.0.0.tar.gz + # UCC-CUDA-1.0.0_link_against_existing_UCC_libs.patch + '9fa11cf6779174f4e9048df5812096e4261e1769d465cc7f34a6354398876856', +] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCC', '1.0.0'), + ('CUDA', '11.7.0', '', True), + ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), +] + +preconfigopts = "./autogen.sh && " + +buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1' +installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install' + +# UCC_COMPONENT_PATH completely overrides $EBROOTUCC/lib/ucc so install symbolic links +# to existing non CUDA related components +postinstallcmds = ['for i in $EBROOTUCC/lib/ucc/*; do ln -s $i %(installdir)s/lib/ucc; done'] + +sanity_check_paths = { + 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +modextravars = {'UCC_COMPONENT_PATH': '%(installdir)s/lib/ucc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0_link_against_existing_UCC_libs.patch b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0_link_against_existing_UCC_libs.patch new file mode 100644 index 00000000000..2f32d7ee417 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0_link_against_existing_UCC_libs.patch @@ -0,0 +1,26 @@ +Make CUDA/NCCL plugins link against the existing ucc libraries. + +Bart Oldeman, 2022-08-02 +diff -ur ucc-1.0.0.orig/src/components/mc/cuda/Makefile.am ucc-1.0.0/src/components/mc/cuda/Makefile.am +--- ucc-1.0.0.orig/src/components/mc/cuda/Makefile.am 2022-04-15 12:43:33.000000000 +0000 ++++ ucc-1.0.0/src/components/mc/cuda/Makefile.am 2022-08-02 12:13:59.332795976 +0000 +@@ -15,7 +15,7 @@ + libucc_mc_cuda_la_CFLAGS = $(BASE_CFLAGS) + libucc_mc_cuda_la_LDFLAGS = -version-info $(SOVERSION) --as-needed $(CUDA_LDFLAGS) + libucc_mc_cuda_la_LIBADD = $(CUDA_LIBS) \ +- $(UCC_TOP_BUILDDIR)/src/libucc.la \ ++ -lucc \ + kernel/libucc_mc_cuda_kernels.la + + include $(top_srcdir)/config/module.am +diff -ur ucc-1.0.0.orig/src/components/tl/nccl/Makefile.am ucc-1.0.0/src/components/tl/nccl/Makefile.am +--- ucc-1.0.0.orig/src/components/tl/nccl/Makefile.am 2022-04-15 12:43:33.000000000 +0000 ++++ ucc-1.0.0/src/components/tl/nccl/Makefile.am 2022-08-02 12:13:59.334795989 +0000 +@@ -21,6 +21,6 @@ + libucc_tl_nccl_la_CPPFLAGS = $(AM_CPPFLAGS) $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) $(NCCL_CPPFLAGS) + libucc_tl_nccl_la_CFLAGS = $(BASE_CFLAGS) + libucc_tl_nccl_la_LDFLAGS = -version-info $(SOVERSION) --as-needed $(CUDA_LDFLAGS) $(NCCL_LDFLAGS) +-libucc_tl_nccl_la_LIBADD = $(CUDA_LIBS) $(NCCL_LIBADD) $(UCC_TOP_BUILDDIR)/src/libucc.la ++libucc_tl_nccl_la_LIBADD = $(CUDA_LIBS) $(NCCL_LIBADD) -lucc + + include $(top_srcdir)/config/module.am From d9ee2e8c5d24989c6738151ac471e549f4031ed2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 2 Aug 2022 16:18:00 +0200 Subject: [PATCH 4370/9987] Speed up OpenMPI 4.1.4 configure --- .../easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb index d01bc8b847f..9e3e26b92da 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb @@ -36,7 +36,15 @@ dependencies = [ ('UCC', '1.0.0'), ] -preconfigopts = './autogen.pl --force && ' +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh; cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) # CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. configopts = '--with-cuda=internal ' From cf1ad05f41f351c90b8304fc94cb7144818391eb Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 2 Aug 2022 16:01:28 +0000 Subject: [PATCH 4371/9987] BLIS with intel compilers: replace sed commands by upstreamed patches --- .../BLIS-0.9.0-intel-compilers-2022.1.0.eb | 18 +- ...blastest-enable-complex-return-intel.patch | 169 ++++++++++++++++++ .../BLIS-0.9.0_ifx-complex-return-intel.patch | 38 ++++ 3 files changed, 218 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_blastest-enable-complex-return-intel.patch create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_ifx-complex-return-intel.patch diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-intel-compilers-2022.1.0.eb index 732b183a34d..e0a1da068c0 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-intel-compilers-2022.1.0.eb @@ -12,19 +12,23 @@ toolchainopts = {'oneapi': True} source_urls = ['https://github.com/flame/blis/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308'] +patches = [ + '%(name)s-%(version)s_blastest-enable-complex-return-intel.patch', + '%(name)s-%(version)s_ifx-complex-return-intel.patch', +] +checksums = [ + '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz + # BLIS-0.9.0_blastest-enable-complex-return-intel.patch + '0f1966b340d1f24cf02070f00f72f232b4cbfcd242ee9ce8c5f09f7220397cb4', + '097a2647b5c66386155cf6a33a2a617b876bd0f9096a2912359eb0897a29d2d5', # BLIS-0.9.0_ifx-complex-return-intel.patch +] builddependencies = [ ('Python', '3.10.4', '-bare'), ('Perl', '5.34.1'), ] -configopts = '--enable-cblas --enable-threading=openmp --enable-shared --complex-return=intel CC="$CC" auto' - -# Intel expects classic f2c-style calling convention. -pretestopts = 'for cu in c u; do for cz in c z; do ' -pretestopts += 'sed -i "s/\([^ ]*complex\) ${cz}dot${cu}_(/void ${cz}dot${cu}_(\\1 \*, /g;' -pretestopts += 's/\([qz]__1\) = ${cz}dot${cu}_(/${cz}dot${cu}_(\&\\1, /g" blastest/src/${cz}blat1.c; done; done && ' +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' runtest = 'check' diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_blastest-enable-complex-return-intel.patch b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_blastest-enable-complex-return-intel.patch new file mode 100644 index 00000000000..488a5e3f17e --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_blastest-enable-complex-return-intel.patch @@ -0,0 +1,169 @@ +From 9b1beec60be31c6ea20b85806d61551497b699e4 Mon Sep 17 00:00:00 2001 +From: bartoldeman +Date: Mon, 11 Jul 2022 20:15:12 -0400 +Subject: [PATCH] Use BLIS_ENABLE_COMPLEX_RETURN_INTEL in blastest files (#636) + +Details: +- Fixed a crash that occurs when either cblat1 or zblat1 are linked + with a build of BLIS that was compiled with '--complex-return=intel'. + This fix involved inserting preprocessor macro guards based on + BLIS_ENABLE_COMPLEX_RETURN_INTEL into blastest/src/cblat1.c and + blastest/src/zblat1.c to correctly handle situations where BLIS is + compiled with Intel/f2c-style calling conventions for complex numbers. +- Updated blastest/src/fortran/run-f2c.sh so that future executions + will insert the aforementioned cpp macro conditional where + appropriate. +--- + blastest/src/cblat1.c | 32 ++++++++++++++++++++++++++++---- + blastest/src/fortran/run-f2c.sh | 20 +++++++++++--------- + blastest/src/zblat1.c | 32 ++++++++++++++++++++++++++++---- + 3 files changed, 67 insertions(+), 17 deletions(-) + +diff --git a/blastest/src/cblat1.c b/blastest/src/cblat1.c +index daccb2f6c..606511662 100644 +--- a/blastest/src/cblat1.c ++++ b/blastest/src/cblat1.c +@@ -475,11 +475,23 @@ static real c_b52 = 0.f; + integer mx, my; + complex cdot[1]; + integer lenx, leny; +- extern /* Complex */ complex cdotc_(integer *, complex *, integer ++ extern /* Complex */ ++#ifdef BLIS_ENABLE_COMPLEX_RETURN_INTEL ++ void cdotc_(complex *, ++#else ++complex cdotc_( ++#endif ++ integer *, complex *, integer + *, complex *, integer *); + extern /* Subroutine */ int ccopy_(integer *, complex *, integer *, + complex *, integer *); +- extern /* Complex */ complex cdotu_(integer *, complex *, integer ++ extern /* Complex */ ++#ifdef BLIS_ENABLE_COMPLEX_RETURN_INTEL ++ void cdotu_(complex *, ++#else ++complex cdotu_( ++#endif ++ integer *, complex *, integer + *, complex *, integer *); + extern /* Subroutine */ int cswap_(integer *, complex *, integer *, + complex *, integer *), ctest_(integer *, complex *, complex *, +@@ -526,14 +538,26 @@ static real c_b52 = 0.f; + } + if (combla_1.icase == 1) { + /* .. CDOTC .. */ +- q__1 = cdotc_(&combla_1.n, cx, &combla_1.incx, cy, & ++ ++#ifdef BLIS_ENABLE_COMPLEX_RETURN_INTEL ++ cdotc_(&q__1, ++#else ++ q__1 = cdotc_( ++#endif ++ &combla_1.n, cx, &combla_1.incx, cy, & + combla_1.incy); + cdot[0].r = q__1.r, cdot[0].i = q__1.i; + ctest_(&c__1, cdot, &ct6[kn + (ki << 2) - 5], &csize1[kn - 1], + sfac); + } else if (combla_1.icase == 2) { + /* .. CDOTU .. */ +- q__1 = cdotu_(&combla_1.n, cx, &combla_1.incx, cy, & ++ ++#ifdef BLIS_ENABLE_COMPLEX_RETURN_INTEL ++ cdotu_(&q__1, ++#else ++ q__1 = cdotu_( ++#endif ++ &combla_1.n, cx, &combla_1.incx, cy, & + combla_1.incy); + cdot[0].r = q__1.r, cdot[0].i = q__1.i; + ctest_(&c__1, cdot, &ct7[kn + (ki << 2) - 5], &csize1[kn - 1], +diff --git a/blastest/src/fortran/run-f2c.sh b/blastest/src/fortran/run-f2c.sh +index fdad4fd34..f0df2f5b8 100755 +--- a/blastest/src/fortran/run-f2c.sh ++++ b/blastest/src/fortran/run-f2c.sh +@@ -50,13 +50,15 @@ recursive-sed.sh -c "s/-4.f };/-4.f }};/g" -p "s*1.c" + + # Convert from brain-dead f2c complex calling conventions to normal + # return-based conventions. +-recursive-sed.sh -c "s/void cdotc_(complex \*, /complex cdotc_(/g" -p "c*1.c" +-recursive-sed.sh -c "s/void cdotu_(complex \*, /complex cdotu_(/g" -p "c*1.c" +-recursive-sed.sh -c "s/cdotc_(&q__1, /q__1 = cdotc_(/g" -p "c*1.c" +-recursive-sed.sh -c "s/cdotu_(&q__1, /q__1 = cdotu_(/g" -p "c*1.c" +- +-recursive-sed.sh -c "s/void zdotc_(doublecomplex \*, /doublecomplex zdotc_(/g" -p "z*1.c" +-recursive-sed.sh -c "s/void zdotu_(doublecomplex \*, /doublecomplex zdotu_(/g" -p "z*1.c" +-recursive-sed.sh -c "s/zdotc_(\&z__1, /z__1 = zdotc_(/g" -p "z*1.c" +-recursive-sed.sh -c "s/zdotu_(\&z__1, /z__1 = zdotu_(/g" -p "z*1.c" ++subst1='\n#ifdef BLIS_ENABLE_COMPLEX_RETURN_INTEL\n&\n#else\n' ++subst2='\n#endif\n' ++recursive-sed.sh -c "s/ void cdotc_(complex \*,/${subst1}complex cdotc_(${subst2}/g" -p "c*1.c" ++recursive-sed.sh -c "s/ void cdotu_(complex \*,/${subst1}complex cdotu_(${subst2}/g" -p "c*1.c" ++recursive-sed.sh -c "s/\(.*\)cdotc_(&q__1,/${subst1}\1q__1 = cdotc_(${subst2}\1/g" -p "c*1.c" ++recursive-sed.sh -c "s/\(.*\)cdotu_(&q__1,/${subst1}\1q__1 = cdotu_(${subst2}\1/g" -p "c*1.c" ++ ++recursive-sed.sh -c "s/ void zdotc_(doublecomplex \*,/${subst1}doublecomplex zdotc_(${subst2}/g" -p "z*1.c" ++recursive-sed.sh -c "s/ void zdotu_(doublecomplex \*,/${subst1}doublecomplex zdotu_(${subst2}/g" -p "z*1.c" ++recursive-sed.sh -c "s/\(.*\)zdotc_(\&z__1,/${subst1}\1z__1 = zdotc_(${subst2}\1/g" -p "z*1.c" ++recursive-sed.sh -c "s/\(.*\)zdotu_(\&z__1,/${subst1}\1z__1 = zdotu_(${subst2}\1/g" -p "z*1.c" + +diff --git a/blastest/src/zblat1.c b/blastest/src/zblat1.c +index c34a57262..b620910be 100644 +--- a/blastest/src/zblat1.c ++++ b/blastest/src/zblat1.c +@@ -459,12 +459,24 @@ static doublereal c_b52 = 0.; + integer lenx, leny; + extern /* Subroutine */ int ctest_(integer *, doublecomplex *, + doublecomplex *, doublecomplex *, doublereal *); +- extern /* Double Complex */ doublecomplex zdotc_(integer *, ++ extern /* Double Complex */ ++#ifdef BLIS_ENABLE_COMPLEX_RETURN_INTEL ++ void zdotc_(doublecomplex *, ++#else ++doublecomplex zdotc_( ++#endif ++ integer *, + doublecomplex *, integer *, doublecomplex *, integer *); + integer ksize; + extern /* Subroutine */ int zcopy_(integer *, doublecomplex *, integer *, + doublecomplex *, integer *); +- extern /* Double Complex */ doublecomplex zdotu_(integer *, ++ extern /* Double Complex */ ++#ifdef BLIS_ENABLE_COMPLEX_RETURN_INTEL ++ void zdotu_(doublecomplex *, ++#else ++doublecomplex zdotu_( ++#endif ++ integer *, + doublecomplex *, integer *, doublecomplex *, integer *); + extern /* Subroutine */ int zswap_(integer *, doublecomplex *, integer *, + doublecomplex *, integer *), zaxpy_(integer *, doublecomplex *, +@@ -508,14 +520,26 @@ static doublereal c_b52 = 0.; + } + if (combla_1.icase == 1) { + /* .. ZDOTC .. */ +- z__1 = zdotc_(&combla_1.n, cx, &combla_1.incx, cy, & ++ ++#ifdef BLIS_ENABLE_COMPLEX_RETURN_INTEL ++ zdotc_(&z__1, ++#else ++ z__1 = zdotc_( ++#endif ++ &combla_1.n, cx, &combla_1.incx, cy, & + combla_1.incy); + cdot[0].r = z__1.r, cdot[0].i = z__1.i; + ctest_(&c__1, cdot, &ct6[kn + (ki << 2) - 5], &csize1[kn - 1], + sfac); + } else if (combla_1.icase == 2) { + /* .. ZDOTU .. */ +- z__1 = zdotu_(&combla_1.n, cx, &combla_1.incx, cy, & ++ ++#ifdef BLIS_ENABLE_COMPLEX_RETURN_INTEL ++ zdotu_(&z__1, ++#else ++ z__1 = zdotu_( ++#endif ++ &combla_1.n, cx, &combla_1.incx, cy, & + combla_1.incy); + cdot[0].r = z__1.r, cdot[0].i = z__1.i; + ctest_(&c__1, cdot, &ct7[kn + (ki << 2) - 5], &csize1[kn - 1], diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_ifx-complex-return-intel.patch b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_ifx-complex-return-intel.patch new file mode 100644 index 00000000000..334b576ee35 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0_ifx-complex-return-intel.patch @@ -0,0 +1,38 @@ +From 98d467891b74021ace7f248cb0856bec734e39b6 Mon Sep 17 00:00:00 2001 +From: bartoldeman +Date: Mon, 11 Jul 2022 19:40:53 -0400 +Subject: [PATCH] Change complex_return='intel' for ifx. (#637) + +Details: +- When checking the version string of the Fortran compiler for the + purposes of determining a default return convention for complex + domain values, grep for "IFORT" instead of "ifort" since that string + is common to both the 'ifx' and 'ifort' binaries provided by Intel: + + $ ifx --version + ifx (IFORT) 2022.1.0 20220316 + Copyright (C) 1985-2022 Intel Corporation. All rights reserved. + + $ ifort --version + ifort (IFORT) 2021.6.0 20220226 + Copyright (C) 1985-2022 Intel Corporation. All rights reserved. +--- + configure | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/configure b/configure +index 5ff877317..a6018edab 100755 +--- a/configure ++++ b/configure +@@ -3688,9 +3688,9 @@ main() + # Query the compiler "vendor" (ie: the compiler's simple name). + # The last part ({ read first rest ; echo $first ; }) is a workaround + # to OS X's egrep only returning the first match. +- fc_vendor=$(echo "${vendor_string}" | egrep -o 'ifort|GNU' | { read first rest ; echo $first ; }) ++ fc_vendor=$(echo "${vendor_string}" | egrep -o 'IFORT|GNU' | { read first rest ; echo $first ; }) + +- if [ "x${fc_vendor}" = "xifort" ]; then ++ if [ "x${fc_vendor}" = "xIFORT" ]; then + complex_return='intel' + elif [ "x${fc_vendor}" = "xGNU" ]; then + complex_return='gnu' From ba53a9f0505d0269e4051d346c7cc46a3e20c615 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 3 Aug 2022 09:26:59 +0200 Subject: [PATCH 4372/9987] Allow use of SYSTEM in dep toolchain for testsuite --- .../LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb | 2 +- .../LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb | 2 +- test/easyconfigs/easyconfigs.py | 6 +++++- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb index 8e4cf356fc4..896102f3284 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb @@ -33,7 +33,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('UCX-CUDA', '1.10.0', _cuda_suffix), ('NCCL', '2.10.3', _cuda_suffix), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb index 9adbdfe4ad9..cb5942ff543 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb @@ -30,7 +30,7 @@ builddependencies = [ ('archspec', '0.1.3'), ] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', _cuda_suffix), ('NCCL', '2.10.3', _cuda_suffix), ('Python', '3.9.6'), diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 829972cf084..6fe83f4c2d4 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1422,7 +1422,11 @@ def template_easyconfig_test(self, spec): # 4th value is toolchain spec if len(dumped_dep) >= 4: if len(orig_dep) >= 4: - self.assertEqual(dumped_dep[3], orig_dep[3]) + # A SYSTEM toolchain is dumped as True + if orig_dep[3] == {'version': 'system', 'name': 'system'}: + self.assertEqual(dumped_dep[3], True) + else: + self.assertEqual(dumped_dep[3], orig_dep[3]) else: # if a subtoolchain is specifed (only) in the dumped easyconfig, # it should *not* be the same as the parent toolchain From afeb66f71edc0e0f2afc0fe8ffde71ce265e54ea Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 3 Aug 2022 11:21:00 +0200 Subject: [PATCH 4373/9987] adding easyconfigs: BUSCO-5.4.2-foss-2021a.eb --- .../b/BUSCO/BUSCO-5.4.2-foss-2021a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.2-foss-2021a.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.2-foss-2021a.eb new file mode 100644 index 00000000000..1360e985e3c --- /dev/null +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.2-foss-2021a.eb @@ -0,0 +1,56 @@ +# Updated by: Pavel Grochal (INUITS) +# Updated by: Sebastien Moretti (SIB) + +easyblock = 'PythonPackage' + +name = 'BUSCO' +version = '5.4.2' + +homepage = 'https://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6fa268097c7fc570f013abd41186e4616a94da4f72ccb006aabe5fd917cb521f'] # busco-5.4.2.tar.bz2 + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for pandas + ('R', '4.1.0'), # for R and ggplot2 + ('Biopython', '1.79'), + ('BLAST+', '2.11.0'), + ('HMMER', '3.3.2'), + ('prodigal', '2.6.3'), + ('AUGUSTUS', '3.4.0'), + ('SEPP', '4.5.0'), + ('MetaEuk', '5'), + ('BBMap', '38.96'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin %(installdir)s/doc', + 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/LICENSE %(installdir)s/doc', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/test_data %(installdir)s', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/config %(installdir)s', +] + +sanity_check_paths = { + 'files': ['bin/busco', 'bin/generate_plot.py'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages/busco'] +} + +sanity_check_commands = [ + "busco --help", + "busco -i %(installdir)s/test_data/bacteria/genome.fna --mode geno --out test_bacteria.out", + "busco -i %(installdir)s/test_data/eukaryota/genome.fna --mode geno --out test_eukaryota.out", +] + +moduleclass = 'bio' From 09c0020e9f40099c7e10c0d965e5e15ad3d11180 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 Aug 2022 10:40:41 +0100 Subject: [PATCH 4374/9987] Missing X11 added --- .../easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb index 3290d13b65b..d184a9ebce1 100644 --- a/easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb @@ -23,7 +23,11 @@ builddependencies = [ ('Autotools', '20220317'), ] -configure_cmd = "autoreconf -i && ./configure" +dependencies = [ + ('X11', '20220504'), +] + +preconfigopts = "autoreconf -i &&" sanity_check_paths = { 'files': ['bin/gifsicle'], From 13190eabfe5b56c660aa5ab769d7fce279bd0a9f Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 Aug 2022 10:44:53 +0100 Subject: [PATCH 4375/9987] Sanity check commands added --- .../easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb index d184a9ebce1..639f0f05b8c 100644 --- a/easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/gifsicle/gifsicle-1.93-GCCcore-11.3.0.eb @@ -34,4 +34,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = [('gifview --help'), ('gifsicle --help')] + moduleclass = 'vis' From 39530f87c28823a50d77656306b7d63de96a0f7f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 3 Aug 2022 12:01:59 +0200 Subject: [PATCH 4376/9987] Fix style issue in preconfigopts Add `cd ..` as its own command like the others --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb index 9e3e26b92da..1594fbc4676 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb @@ -38,7 +38,8 @@ dependencies = [ preconfigopts = ' && '.join([ 'cd config', - 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh; cd ..', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', 'autoconf', 'autoheader', 'aclocal', From c8f66aff1621800a73bd6102ae58f8e04c542fe9 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 Aug 2022 11:05:13 +0100 Subject: [PATCH 4377/9987] adding easyconfigs: libzip-1.9.2-GCCcore-11.3.0.eb --- .../l/libzip/libzip-1.9.2-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libzip/libzip-1.9.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libzip/libzip-1.9.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libzip/libzip-1.9.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..28d6e87b572 --- /dev/null +++ b/easybuild/easyconfigs/l/libzip/libzip-1.9.2-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libzip' +version = '1.9.2' + +homepage = 'https://libzip.org/' +description = "libzip is a C library for reading, creating, and modifying zip archives." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/nih-at/libzip/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7f28eaec7a02ca099ea9dad88fc8023f7f6ddfca54b780040ff7fdb39d9efb3c'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [('zlib', '1.2.12')] + +sanity_check_paths = { + 'files': [ + 'bin/zipcmp', + 'bin/zipmerge', + 'bin/ziptool', + 'lib64/libzip.%s' % SHLIB_EXT, + ], + 'dirs': ['include', 'lib/pkgconfig'], +} + +moduleclass = 'lib' From 1aa2fd8f63aa1179c8aca3e44c9204f65636d960 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 Aug 2022 14:07:43 +0100 Subject: [PATCH 4378/9987] Perl changed to Perl-minimal --- easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb index 9e8aa712671..c3d0238645c 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb @@ -21,7 +21,7 @@ checksums = ['8a1cd8b7fae04b82a95168252129b8c1baca098a285ff8d3f25781dead14b75a'] builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), - ('Perl', '5.34.1'), # required for pod2html + ('Perl', '5.34.1', '-minimal'), # required for pod2html ] sanity_check_paths = { From 6e09e1180386364fa5819105642f7b785768a55f Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 Aug 2022 14:43:26 +0100 Subject: [PATCH 4379/9987] Tests added, following PR #15622 --- .../easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb index 5f1a28b4c64..2339f816add 100644 --- a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb @@ -17,7 +17,13 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://github.com/MmgTools/mmg/archive'] sources = ['v%(version)s.tar.gz'] -checksums = ['bbf9163d65bc6e0f81dd3acc5a51e4a8c47a7fdae849abc26277e01154fe2437'] +patches = ['mmg-%(version)s_remove_ci_tests.patch'] + +checksums = [ + 'bbf9163d65bc6e0f81dd3acc5a51e4a8c47a7fdae849abc26277e01154fe2437', # v5.6.0.tar.gz + '99de7437fb9d036c786b7f1526da93d4aa1d28e728fe7279f4c9204bbbb9f734', # mmg-5.6.0_remove_ci_tests.patch + +] builddependencies = [ ('CMake', '3.20.1'), @@ -28,9 +34,15 @@ dependencies = [('SCOTCH', '6.1.0')] separate_build_dir = True -configopts = '-DUSE_SCOTCH=ON ' +# CI tests require downloading of data that might not be available in the future. +# Sticking to tests included in the source with help of patch +configopts = '-DUSE_SCOTCH=ON -DBUILD_TESTING=ON -DONLY_VERY_SHORT_TESTS=ON ' +configopts += '-DTEST_LIBMMG2D=ON -DTEST_LIBMMG3D=ON -DTEST_LIBMMGS=ON ' configopts += '-DLIBMMG2D_SHARED=ON -DLIBMMG3D_SHARED=ON -DLIBMMGS_SHARED=ON -DLIBMMG_SHARED=ON ' +pretestopts = 'export CTEST_PARALLEL_LEVEL=%(parallel)s &&' +runtest = 'test' + sanity_check_paths = { 'files': ['bin/%s_O3' % x for x in ['mmg2d', 'mmg3d', 'mmgs']] + ['lib/lib%s.%s' % (x, y) for x in ['mmg2d', 'mmg3d', 'mmgs', 'mmg'] for y in ['a', SHLIB_EXT]], From 0125c8e66dca61d894285e99b20ec6bef557eae2 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 Aug 2022 14:51:44 +0100 Subject: [PATCH 4380/9987] binutils removed --- easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb index 2339f816add..80a0bcb4e5e 100644 --- a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb @@ -27,7 +27,6 @@ checksums = [ builddependencies = [ ('CMake', '3.20.1'), - ('binutils', '2.36.1'), ] dependencies = [('SCOTCH', '6.1.0')] From f461780b519772cd9b1812f8153877a37713e463 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 3 Aug 2022 13:53:42 +0000 Subject: [PATCH 4381/9987] Add explicit dependency on UCX-CUDA --- .../u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb index 6614a62fef1..bf163fd4655 100644 --- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -34,6 +34,7 @@ builddependencies = [ dependencies = [ ('UCC', '1.0.0'), ('CUDA', '11.7.0', '', True), + ('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'), ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), ] From c274538476002fe9412bef331761c292e3186fc4 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 Aug 2022 15:40:38 +0100 Subject: [PATCH 4382/9987] Added sanity check for shared libs --- easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb index 505de914edf..e71115ce833 100644 --- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb @@ -50,7 +50,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'], + 'files': ['lib/libpgplot.a', 'lib/libcpgplot.a', 'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb index 8bf72fe23f5..3ffb0eb70e6 100644 --- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb @@ -50,7 +50,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['lib/libpgplot.a', 'lib/libcpgplot.a'], + 'files': ['lib/libpgplot.a', 'lib/libcpgplot.a', 'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT], 'dirs': [] } From 516c4522c919603a9ebb896db02f0cd4847385be Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 3 Aug 2022 18:18:24 +0200 Subject: [PATCH 4383/9987] Add netCDF libraries --- .../netCDF-C++4-4.3.1-gompi-2022a.eb | 25 +++++++++++++ .../netCDF-Fortran-4.6.0-gompi-2022a.eb | 25 +++++++++++++ .../p/PnetCDF/PnetCDF-1.12.3-gompi-2022a.eb | 35 +++++++++++++++++++ 3 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2022a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2022a.eb new file mode 100644 index 00000000000..50ed6850d0a --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.9.0')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb new file mode 100644 index 00000000000..28ae1438dbe --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb @@ -0,0 +1,25 @@ +name = 'netCDF-Fortran' +version = '4.6.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8194aa70e400c0adfc456127c1d97af2c6489207171d13b10cd754a16da8b0ca'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [('netCDF', '4.9.0')] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2022a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2022a.eb new file mode 100644 index 00000000000..44165d52dd2 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = '1.12.3' + +homepage = 'https://parallel-netcdf.github.io/' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://parallel-netcdf.github.io/Release'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['439e359d09bb93d0e58a6e3f928f39c2eae965b6c97f64e67cd42220d6034f77'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Perl', '5.34.1'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' From 99a4a5b5bccb0f0e869f6ecba599a9a215139d38 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 4 Aug 2022 12:05:43 +0200 Subject: [PATCH 4384/9987] adding easyconfigs: Blitz++-1.0.2-GCCcore-10.2.0.eb --- .../b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d6dde31b47c --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'Blitz++' +version = '1.0.2' + +homepage = 'https://github.com/blitzpp/blitz' + +description = """ + Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation + in C++ with a speed comparable to Fortran implementations, while preserving an + object-oriented interface +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [('https://github.com/blitzpp/blitz/archive/')] +sources = ['%(version)s.tar.gz'] +checksums = ['500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'] + +builddependencies = [('CMake', '3.18.4'), ('binutils', '2.35')] + +separate_build_dir = True + +postinstallcmds = ['mkdir %(installdir)s/lib64/blitz'] + +sanity_check_paths = { + 'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT], + 'dirs': ['include/blitz/array', 'include/blitz/meta', + 'include/random', 'lib64/pkgconfig'], +} + +configopts = '--enable-shared' + +moduleclass = 'lib' From fc8be7736bcd4f98e434930b6436815a21cd0593 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Aug 2022 16:04:55 +0200 Subject: [PATCH 4385/9987] fix jax version in filename and description of patch for AlphaFold 2.2.2 --- .../a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb | 4 ++-- .../easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb | 4 ++-- ...2.2.2_jax38_NaN.patch => AlphaFold-2.2.2_jax038_NaN.patch} | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/a/AlphaFold/{AlphaFold-2.2.2_jax38_NaN.patch => AlphaFold-2.2.2_jax038_NaN.patch} (86%) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb index 6209b784cf4..5b4a6edac04 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb @@ -83,7 +83,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', - 'AlphaFold-2.2.2_jax38_NaN.patch' # acc. to: https://github.com/deepmind/alphafold/issues/513 + 'AlphaFold-2.2.2_jax038_NaN.patch', ], 'checksums': [ 'aa51dc4a1150b92310d20e63e9e4d9279b15b6a1f7e664360f52827f83256cdd', # v2.2.2.tar.gz @@ -93,7 +93,7 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch - 'fb00a3c9cb00fe87eef77d48dfd8e44c40ad8b820480c79c5937377da27fea5f', # AlphaFold-2.2.2_jax38_NaN.patch + '0b040ba99208cd9ad79b7d17db5720f7a447a019ac0ca786b3b019a55d1544e0', # AlphaFold-2.2.2_jax038_NaN.patch ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb index 86c33f118ce..a864581a569 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb @@ -78,7 +78,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', - 'AlphaFold-2.2.2_jax38_NaN.patch' # acc. to: https://github.com/deepmind/alphafold/issues/513 + 'AlphaFold-2.2.2_jax038_NaN.patch', ], 'checksums': [ 'aa51dc4a1150b92310d20e63e9e4d9279b15b6a1f7e664360f52827f83256cdd', # v2.2.2.tar.gz @@ -88,7 +88,7 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch - 'fb00a3c9cb00fe87eef77d48dfd8e44c40ad8b820480c79c5937377da27fea5f', # AlphaFold-2.2.2_jax38_NaN.patch + '0b040ba99208cd9ad79b7d17db5720f7a447a019ac0ca786b3b019a55d1544e0', # AlphaFold-2.2.2_jax038_NaN.patch ], 'start_dir': 'alphafold-%(version)s', 'use_pip': True, diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2_jax38_NaN.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2_jax038_NaN.patch similarity index 86% rename from easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2_jax38_NaN.patch rename to easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2_jax038_NaN.patch index ade1f98f6fe..673945afa22 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2_jax38_NaN.patch +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2_jax038_NaN.patch @@ -1,5 +1,5 @@ -#Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de -# Resulting pdb files contain NaNs because jax >= 3.8 is used. +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de +# Resulting pdb files contain NaNs because jax >= 0.3.8 is used. # Fix according to https://github.com/deepmind/alphafold/issues/513 and # https://jax.readthedocs.io/en/latest/changelog.html#jax-0-3-8-april-29-2022 diff -ru alphafold-2.2.2/alphafold/model/utils.py alphafold-2.2.2_jax38_NaN/alphafold/model/utils.py From 8b3d7ab2e735e8aa9543ae9db870b0d2b274934d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Aug 2022 19:02:45 +0200 Subject: [PATCH 4386/9987] adding easyconfigs: Geant4-11.0.2-GCC-11.2.0.eb --- .../g/Geant4/Geant4-11.0.2-GCC-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-11.0.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.0.2-GCC-11.2.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-11.0.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..78635c02ef3 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.0.2-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +name = 'Geant4' +version = '11.0.2' + +homepage = 'https://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'Geant4' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['ddabe8d5cc3bd465c969f375cc43ee537ff33c17dc2943b8a4420cfa83cfcfcc'] + +builddependencies = [('CMake', '3.22.1')] +dependencies = [ + ('expat', '2.4.1'), + # recommended CLHEP version, see https://geant4-data.web.cern.ch/ReleaseNotes/ReleaseNotes.11.0.html + ('CLHEP', '2.4.5.1'), +] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += " -DCLHEP_ROOT_DIR=$EBROOTCLHEP -DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' From 4fe2a103b1881cb6f4e03bdd6f18ee71f4262203 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 5 Aug 2022 15:05:15 +0800 Subject: [PATCH 4387/9987] adding easyconfigs: colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb, einops-0.4.1-GCCcore-10.3.0.eb, OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb, OpenMM-7.5.1-foss-2021a_AlphaFold.eb and patches: OpenMM-7.5.1_AlphaFold.patch --- ...colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb | 55 +++++++++++ .../e/einops/einops-0.4.1-GCCcore-10.3.0.eb | 29 ++++++ .../OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb | 91 +++++++++++++++++++ .../OpenMM-7.5.1-foss-2021a_AlphaFold.eb | 55 +++++++++++ .../o/OpenMM/OpenMM-7.5.1_AlphaFold.patch | 45 +++++++++ 5 files changed, 275 insertions(+) create mode 100644 easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a_AlphaFold.eb create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_AlphaFold.patch diff --git a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ecd12d1162f --- /dev/null +++ b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'colossalai' +version = '0.1.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://colossalai.org/' +description = """Colossal-AI: A Unified Deep Learning System for Big Model Era""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', True), + ('SciPy-bundle', '2021.05'), + ('PyTorch-Lightning', '1.5.9', versionsuffix), + ('torchvision', '0.11.1', versionsuffix), +] + +exts_list = [ + ('cfgv', '3.3.1', { + 'checksums': ['f5a830efb9ce7a445376bb66ec94c638a9787422f96264c98edc6bdeed8ab736'], + }), + ('identify', '2.5.1', { + 'checksums': ['3d11b16f3fe19f52039fb7e39c9c884b21cb1b586988114fbe42671f03de3e82'], + }), + ('nodeenv', '1.6.0', { + 'checksums': ['3ef13ff90291ba2a4a7a4ff9a979b63ffdd00a464dbe04acf0ea6471517a4c2b'], + }), + ('pre_commit', '2.19.0', { + 'checksums': ['4233a1e38621c87d9dda9808c6606d7e7ba0e087cd56d3fe03202a01d2919615'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.4.4', { + 'checksums': ['4c586de507202505346f3e32d1363eb9ed6932f0c2f63184dea88983ff4971e2'], + }), + ('invoke', '1.7.1', { + 'checksums': ['7b6deaf585eee0a848205d0b8c0014b9bf6f287a8eb798818a642dff1df14b19'], + }), + ('fabric', '2.7.1', { + 'checksums': ['76f8fef59cf2061dbd849bbce4fe49bdd820884385004b0ca59136ac3db129e4'], + }), + (name, version, { + 'checksums': ['3a2cdd4dc2d8b4832fa132a0bd1102f86c38f6865d7f119018404069d35984b2'], + }), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..80b81ff50b5 --- /dev/null +++ b/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'einops' +version = '0.4.1' + +homepage = 'https://einops.rocks/' +description = """ +Flexible and powerful tensor operations for readable and reliable code. +Supports numpy, pytorch, tensorflow, jax, and others.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['65ede824fa54ce99ba969c61152f9948eb8cad08d5f0ca97c95e3804bafcce48'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..2dde80a23b1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,91 @@ +easyblock = 'PythonBundle' + +name = 'OpenFold' +version = '1.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/aqlaboratory/openfold' +description = "A faithful PyTorch reproduction of DeepMind's AlphaFold 2" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('CMake', '3.20.1'), # required to build ninja +] + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', True), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('UCX-CUDA', '1.10.0', versionsuffix), + ('cuDNN', '8.2.1.32', versionsuffix, True), + ('NCCL', '2.10.3', versionsuffix), + ('dm-tree', '0.1.6'), + ('einops', '0.4.1'), + ('colossalai', '0.1.8', versionsuffix), + ('scikit-build', '0.11.1'), + ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('ninja', '1.10.2.3', { + 'checksums': ['e1b86ad50d4e681a7dbdff05fc23bb52cb773edb90bc428efba33fa027738408'], + }), + ('hjson', '3.0.2', { + 'checksums': ['2838fd7200e5839ea4516ece953f3a19892c41089f0d933ba3f68e596aacfcd5'], + }), + ('py-cpuinfo', '8.0.0', { + 'modulename': 'cpuinfo', + 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], + }), + ('triton', version, { + 'source_tmpl': '%(name)s-%(version)s-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'checksums': ['37b8d0eb36ed7631a6f9d01bd3183f900ae7dbd9e5e40112468a3568505671dc'], + }), + ('deepspeed', '0.5.9', { + 'checksums': ['7c43d151b51d346a430034e77764097c4af7637217c08503291c48c37ae7d090'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), + ('dllogger', version, { + 'source_urls': ['https://github.com/NVIDIA/dllogger/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['43e5e3c3acf891dfe6151f7d869f3ad2424772fe57fd8dcb0a45bad06de93bf7'], + }), + (name, version, { + 'source_urls': ['https://github.com/aqlaboratory/openfold/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['543cb0d36a6118a60de4b4ec2f4a49ebcc965523e5b31e9ad03425de367384a7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdbfixer'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -c 'import openfold'", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a_AlphaFold.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a_AlphaFold.eb new file mode 100644 index 00000000000..00b1c233032 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a_AlphaFold.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.1' +versionsuffix = '_AlphaFold' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')] +checksums = [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +separate_build_dir = True + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('SWIG', '4.0.2'), +] + +runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_AlphaFold.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_AlphaFold.patch new file mode 100644 index 00000000000..878ffd11b03 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_AlphaFold.patch @@ -0,0 +1,45 @@ +custom patch for OpenMM to use in conjunction with AlphaFold +see https://github.com/deepmind/alphafold/blob/main/docker/openmm.patch + +Index: simtk/openmm/app/topology.py +=================================================================== +--- simtk.orig/openmm/app/topology.py ++++ simtk/openmm/app/topology.py +@@ -356,19 +356,35 @@ + def isCyx(res): + names = [atom.name for atom in res._atoms] + return 'SG' in names and 'HG' not in names ++ # This function is used to prevent multiple di-sulfide bonds from being ++ # assigned to a given atom. This is a DeepMind modification. ++ def isDisulfideBonded(atom): ++ for b in self._bonds: ++ if (atom in b and b[0].name == 'SG' and ++ b[1].name == 'SG'): ++ return True ++ ++ return False + + cyx = [res for res in self.residues() if res.name == 'CYS' and isCyx(res)] + atomNames = [[atom.name for atom in res._atoms] for res in cyx] + for i in range(len(cyx)): + sg1 = cyx[i]._atoms[atomNames[i].index('SG')] + pos1 = positions[sg1.index] ++ candidate_distance, candidate_atom = 0.3*nanometers, None + for j in range(i): + sg2 = cyx[j]._atoms[atomNames[j].index('SG')] + pos2 = positions[sg2.index] + delta = [x-y for (x,y) in zip(pos1, pos2)] + distance = sqrt(delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2]) +- if distance < 0.3*nanometers: +- self.addBond(sg1, sg2) ++ if distance < candidate_distance and not isDisulfideBonded(sg2): ++ candidate_distance = distance ++ candidate_atom = sg2 ++ # Assign bond to closest pair. ++ if candidate_atom: ++ self.addBond(sg1, candidate_atom) ++ ++ + + class Chain(object): + """A Chain object represents a chain within a Topology.""" From 62d2f93dfa68cd11a517a66c4f9d54b787973de3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 5 Aug 2022 15:07:20 +0800 Subject: [PATCH 4388/9987] adding easyconfigs: FastFold-20220729-foss-2021a-CUDA-11.3.1.eb --- ...astFold-20220729-foss-2021a-CUDA-11.3.1.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..a01ad7554fc --- /dev/null +++ b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'FastFold' +version = '20220729' +versionsuffix = '-CUDA-%(cudaver)s' +local_commit = '665e6c97a7d95d3db2df860d104fa3c456c71fe2' + +homepage = 'https://github.com/hpcaitech/FastFold' +description = "Optimizing Protein Structure Prediction Model Training and Inference on GPU Clusters" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', True), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('UCX-CUDA', '1.10.0', versionsuffix), + ('cuDNN', '8.2.1.32', versionsuffix, True), + ('NCCL', '2.10.3', versionsuffix), + ('dm-tree', '0.1.6'), + ('einops', '0.4.1'), + ('colossalai', '0.1.8', versionsuffix), + ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), + (name, version, { + 'preinstallopts': "cp -a benchmark scripts tests %(installdir)s/ && ", + 'source_urls': ['https://github.com/hpcaitech/FastFold/archive/'], + 'sources': [{'download_filename': '665e6c97a7d95d3db2df860d104fa3c456c71fe2.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['79abc27d481f14c9086ee969f55a73645b9669e0608bdb44db22a839765e5739'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdbfixer'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'from fastfold.model.fastnn import Evoformer'", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 35d99db88cd772aaf9a82c3a3bdbf8e5b797950f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 5 Aug 2022 10:21:46 +0200 Subject: [PATCH 4389/9987] Fix checksum test for extensions Extension patches may use templates so use `collect_exts_file_info` to gather the information about extensions and their sources and patches. --- test/easyconfigs/easyconfigs.py | 60 ++++++++++++++++++--------------- 1 file changed, 32 insertions(+), 28 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 829972cf084..2c9f03ef0e3 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1307,7 +1307,6 @@ def template_easyconfig_test(self, spec): src_cnt = len(ec['sources']) patch_checksums = ec['checksums'][src_cnt:] - patch_checksums_cnt = len(patch_checksums) # make sure all patch files are available specdir = os.path.dirname(spec) @@ -1323,7 +1322,7 @@ def template_easyconfig_test(self, spec): self.assertTrue(os.path.isfile(patch_full), msg) # verify checksum for each patch file - if idx < patch_checksums_cnt and (os.path.exists(patch_full) or patch.endswith('.patch')): + if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch.endswith('.patch')): checksum = patch_checksums[idx] error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch, ec_fn, checksum) res = verify_checksum(patch_full, checksum) @@ -1334,35 +1333,40 @@ def template_easyconfig_test(self, spec): error_msg = "'source' step should not be skipped in %s, since that implies not verifying checksums" % ec_fn self.assertFalse(ec['checksums'] and ('source' in ec['skipsteps']), error_msg) - for ext in ec['exts_list']: + for ext in ec.get_ref('exts_list'): if isinstance(ext, (tuple, list)) and len(ext) == 3: - ext_name = ext[0] + self.assertTrue(isinstance(ext[2], dict), + "3rd element of extension spec for %s must be a dictionary" % ext_name) + + # After the sanity check above, use collect_exts_file_info to resolve templates etc. correctly + for ext in app.collect_exts_file_info(fetch_files=False, verify_checksums=False): + try: + ext_options = ext['options'] + except KeyError: + # No options --> Only have a name which is valid, so nothing to check + continue - self.assertTrue(isinstance(ext[2], dict), "3rd element of extension spec is a dictionary") - - # fall back to assuming a single source file for an extension - src_cnt = len(ext[2].get('sources', [])) or 1 - - checksums = ext[2].get('checksums', []) - patch_checksums = checksums[src_cnt:] - - for idx, ext_patch in enumerate(ext[2].get('patches', [])): - if isinstance(ext_patch, (tuple, list)): - ext_patch = ext_patch[0] - - # only check actual patch files, not other files being copied via the patch functionality - ext_patch_full = os.path.join(specdir, ext_patch) - if ext_patch.endswith('.patch'): - msg = "Patch file %s is available for %s" % (ext_patch_full, specfn) - self.assertTrue(os.path.isfile(ext_patch_full), msg) - - # verify checksum for each patch file - if idx < patch_checksums_cnt and (os.path.exists(ext_patch_full) or ext_patch.endswith('.patch')): - checksum = patch_checksums[idx] - error_msg = "Invalid checksum for patch file %s for %s extension in %s: %s" - res = verify_checksum(ext_patch_full, checksum) - self.assertTrue(res, error_msg % (ext_patch, ext_name, ec_fn, checksum)) + checksums = ext_options.get('checksums', []) + src_cnt = len(ext_options.get('sources', [])) or 1 + patch_checksums = checksums[src_cnt:] + + for idx, ext_patch in enumerate(ext.get('patches', [])): + if isinstance(ext_patch, (tuple, list)): + ext_patch = ext_patch[0] + + # only check actual patch files, not other files being copied via the patch functionality + ext_patch_full = os.path.join(specdir, ext_patch['name']) + if ext_patch_full.endswith('.patch'): + msg = "Patch file %s is available for %s" % (ext_patch_full, specfn) + self.assertTrue(os.path.isfile(ext_patch_full), msg) + + # verify checksum for each patch file + if idx < len(patch_checksums) and (os.path.exists(ext_patch_full) or ext_patch.endswith('.patch')): + checksum = patch_checksums[idx] + error_msg = "Invalid checksum for patch %s for %s extension in %s: %s" + res = verify_checksum(ext_patch_full, checksum) + self.assertTrue(res, error_msg % (ext_patch, ext_name, ec_fn, checksum)) # check whether all extra_options defined for used easyblock are defined extra_opts = app.extra_options() From 1744e0ebf117cf9228b934407bfb63bede8a6963 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 4 Aug 2022 18:25:42 +0200 Subject: [PATCH 4390/9987] Numpy: Fix broken test on PPC --- .../SciPy-bundle-2022.05-foss-2022a.eb | 3 ++ ...py-1.22.3_skip-ppc-long-complex-test.patch | 41 +++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.22.3_skip-ppc-long-complex-test.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb index b93d1166c8a..28d43bd947c 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb @@ -27,6 +27,7 @@ exts_list = [ 'patches': [ 'numpy-1.20.3_disable_fortran_callback_test.patch', 'numpy-1.22.3_disable-broken-override-test.patch', + '%(name)s-%(version)s_skip-ppc-long-complex-test.patch', ], 'sources': ['%(name)s-%(version)s.zip'], 'checksums': [ @@ -35,6 +36,8 @@ exts_list = [ '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', # numpy-1.22.3_disable-broken-override-test.patch '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', + # numpy-1.22.3_skip-ppc-long-complex-test.patch + '058c8128b9f7158b4d5bedb2f52ccc7e1362b99c352c3d10335f98a6194c880e', ], }), ('ply', '3.11', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.22.3_skip-ppc-long-complex-test.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.22.3_skip-ppc-long-complex-test.patch new file mode 100644 index 00000000000..7d950c31fc9 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.22.3_skip-ppc-long-complex-test.patch @@ -0,0 +1,41 @@ +Include a PPC detection for the inaccurate trig functions +See https://github.com/numpy/numpy/issues/15763 + +Author: Alexander Grund (TU Dresden) + +diff --git a/numpy/core/tests/test_umath.py b/numpy/core/tests/test_umath.py +index c0b26e75b..ee040fe4b 100644 +--- a/numpy/core/tests/test_umath.py ++++ b/numpy/core/tests/test_umath.py +@@ -37,12 +37,17 @@ def on_powerpc(): + + + def bad_arcsinh(): +- """The blocklisted trig functions are not accurate on aarch64 for ++ """The blocklisted trig functions are not accurate on aarch64/PPC for + complex256. Rather than dig through the actual problem skip the + test. This should be fixed when we can move past glibc2.17 + which is the version in manylinux2014 + """ +- x = 1.78e-10 ++ if platform.machine() == 'aarch64': ++ x = 1.78e-10 ++ elif on_powerpc(): ++ x = 2.16e-10 ++ else: ++ return False + v1 = np.arcsinh(np.float128(x)) + v2 = np.arcsinh(np.complex256(x)).real + # The eps for float128 is 1-e33, so this is way bigger +@@ -3434,9 +3439,9 @@ def check(x, rtol): + x_basic = np.logspace(-2.999, 0, 10, endpoint=False) + + if dtype is np.longcomplex: +- if (platform.machine() == 'aarch64' and bad_arcsinh()): ++ if bad_arcsinh(): + pytest.skip("Trig functions of np.longcomplex values known " +- "to be inaccurate on aarch64 for some compilation " ++ "to be inaccurate on aarch64 and PPC for some compilation " + "configurations.") + # It's not guaranteed that the system-provided arc functions + # are accurate down to a few epsilons. (Eg. on Linux 64-bit) From fca4c21a47464bca1872ef293aa8b4d0f4397e84 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 5 Aug 2022 12:14:11 +0200 Subject: [PATCH 4391/9987] Fix binutils version --- easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb index 6a7954de21b..49e5f3b335f 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb @@ -30,7 +30,7 @@ sources = ['pdtoolkit-%(version)s.tar.gz'] checksums = ['0b6f8a6b8769c181b2ae6cae7298f04b8e3e3d68066f598ed24574e19500bc97'] builddependencies = [ - ('binutils', '2.36.1'), + ('binutils', '2.38'), ] From 6a3dfab78ccb8e07826e1e8e19879c1b4bb1e5be Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 5 Aug 2022 13:26:43 +0200 Subject: [PATCH 4392/9987] Also update newer OpenBLAS ECs --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb | 3 +++ easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 3 +++ easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 3 +++ easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 3 +++ 4 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb index 6feee08faf6..ae8fd51485e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb @@ -15,11 +15,14 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', ] checksums = [ 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f', # v0.3.17.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index b59a24cece2..35e4b615bf8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -15,6 +15,7 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-%(version)s_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch', 'OpenBLAS-%(version)s_fix-segfault-ztrsv.patch', ] @@ -22,6 +23,8 @@ checksums = [ 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f', # v0.3.17.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', # OpenBLAS-0.3.17_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch 'ea76320bc047eff1bf2a2f50c1c19acb4fd6d2b8a5bf81a4dce73145a2a5cfcb', 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index 938962705a6..a6bed05840b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -15,11 +15,14 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', ] checksums = [ '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index f941cf9f1d4..72e27286e56 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -15,11 +15,14 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', ] checksums = [ '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] # extensive testing can be enabled by uncommenting the line below From 873d2184672d32e1f8dffbd319d7216ffe602423 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 5 Aug 2022 14:13:39 +0200 Subject: [PATCH 4393/9987] adding easyconfigs: Schrodinger-2022-3.eb --- .../s/Schrodinger/Schrodinger-2022-3.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-3.eb diff --git a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-3.eb b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-3.eb new file mode 100644 index 00000000000..738c9b63f5f --- /dev/null +++ b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-3.eb @@ -0,0 +1,31 @@ +easyblock = 'PackedBinary' + +name = 'Schrodinger' +version = '2022-3' + +homepage = 'https://www.schrodinger.com/' +description = """ Schrodinger aims to provide integrated software solutions and services + that truly meet its customers needs. We want to empower researchers around the world to + achieve their goals of improving human health and quality of life through advanced computational + techniques that transform the way chemists design compounds and materials. """ + +toolchain = SYSTEM + +# Download from schrodinger.com +sources = ['%(name)s_Suites_%(version)s_Linux-x86_64.tar'] +checksums = ['e607b6b2e1671030a66e7d2ab0fbe22ca5e8414794aaf50a7230c1db4417b762'] + +install_cmd = 'cd %(builddir)s/%(name)s_Suites_%(version)s_Linux-x86_64 && ' +install_cmd += './INSTALL -d . -s %(installdir)s -k /usr/tmp -t %(installdir)s/thirdparty -b *' + +sanity_check_paths = { + 'files': ['desmond', 'maestro'], + 'dirs': [], +} + +modextravars = { + 'SCHROD_LICENSE_FILE': '$HOME/.schrodinger_license', + 'SCHRODINGER': '%(installdir)s', +} + +moduleclass = 'bio' From ccef9b2a721af17a1757ccef1efb5e52456ead9e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 5 Aug 2022 14:35:54 +0200 Subject: [PATCH 4394/9987] Fix some test failures --- .../p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 6 +++++ .../PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 2 ++ .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 6 +++++ .../PyTorch-1.9.0_fix-kineto-crash.patch | 24 +++++++++++++++++++ 4 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-kineto-crash.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 5931428b705..4f48922d68c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -26,6 +26,7 @@ patches = [ 'PyTorch-1.8.1_fix-faulty-asserts-and-skip-test.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', + 'PyTorch-1.9.0_fix-kineto-crash.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', ] @@ -46,6 +47,7 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', + '1ed5e125f7922ea577d43053a6652aedc21cc036157e101c0e3b9aee9029d3b0', # PyTorch-1.9.0_fix-kineto-crash.patch 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', @@ -79,6 +81,10 @@ excluded_tests = { # Bad tests: https://github.com/pytorch/pytorch/issues/60260 'distributed/elastic/utils/distributed_test', 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index b66e3586491..11fe7f4935e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -32,6 +32,7 @@ patches = [ 'PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch', 'PyTorch-1.9.0_fix-testnn-on-A100.patch', 'PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.9.0_fix-kineto-crash.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', @@ -64,6 +65,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', + '1ed5e125f7922ea577d43053a6652aedc21cc036157e101c0e3b9aee9029d3b0', # PyTorch-1.9.0_fix-kineto-crash.patch 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index 0b4f5b7fb31..4aac5785617 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -31,6 +31,7 @@ patches = [ 'PyTorch-1.9.0_fix-min-amount-of-devices-for-test.patch', 'PyTorch-1.9.0_fix-testnn-on-A100.patch', 'PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch', + 'PyTorch-1.9.0_fix-kineto-crash.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', @@ -63,6 +64,7 @@ checksums = [ '8e8b417782e2f3004462c32338e12685e7296d15207f3e3087dcb8015e648f98', # PyTorch-1.9.0_fix-testnn-on-A100.patch # PyTorch-1.9.0_fix-use-after-destruct-in-cudaipctypes.patch '67960bf9140baf004b07e29f7c2b338e7bc4e4e4f2c931768be44f58526e605f', + '1ed5e125f7922ea577d43053a6652aedc21cc036157e101c0e3b9aee9029d3b0', # PyTorch-1.9.0_fix-kineto-crash.patch 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch # PyTorch-1.9.0_increase-test-cuda-tolerance.patch '73de855ab1ed38043c7fb2a983927786b83d7547aefed926f19e554e2214838a', @@ -111,6 +113,10 @@ excluded_tests = { # Bad tests: https://github.com/pytorch/pytorch/issues/60260 'distributed/elastic/utils/distributed_test', 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-kineto-crash.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-kineto-crash.patch new file mode 100644 index 00000000000..928922a5ed5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_fix-kineto-crash.patch @@ -0,0 +1,24 @@ +Fix a crash during application shutdown visible in test_profiler on some machines. +See https://github.com/pytorch/kineto/pull/642 + +Author: Alexander Grund (TU Dresden) + +diff -aur a/third_party/kineto/libkineto/src/EventProfilerController.cpp b/third_party/kineto/libkineto/src/EventProfilerController.cpp +--- a/third_party/kineto/libkineto/src/EventProfilerController.cpp 2022-08-05 13:10:46.175716618 +0200 ++++ b/third_party/kineto/libkineto/src/EventProfilerController.cpp 2022-08-05 13:16:00.654118490 +0200 +@@ -231,9 +231,14 @@ + + // Must be called under lock + void EventProfilerController::start(CUcontext ctx) { +- profilerMap()[ctx] = unique_ptr( ++ // Avoid static initialization order fiasco: ++ // We need the profilerMap and with it all controllers to be destroyed ++ // before everything the controller accesses gets destroyed. ++ // Hence access the profilerMap after initialization of the controller. ++ auto controller = unique_ptr( + new EventProfilerController( + ctx, ConfigLoader::instance(), detail::HeartbeatMonitor::instance())); ++ profilerMap()[ctx] = std::move(controller); + } + + // Must be called under lock From f32a5f5dd3a5e4b5c9d2c0103c01cd2421d3ec75 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 5 Aug 2022 14:44:02 +0200 Subject: [PATCH 4395/9987] add extra configuration files for VSC clusters to CESM-deps --- .../c/CESM-deps/CESM-deps-2-foss-2021b.eb | 24 ++++++++++++++++--- 1 file changed, 21 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb index 16b6f109eba..7622ed76c90 100644 --- a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb @@ -8,6 +8,7 @@ description = """CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.""" +# The following environment is suitable for CESM >= 2.2.0 toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ @@ -20,15 +21,32 @@ dependencies = [ ('netCDF', '4.8.1'), ('netCDF-Fortran', '4.5.3'), ('netCDF-C++4', '4.3.1'), - ('PnetCDF', '1.12.3'), # optional + ('PnetCDF', '1.12.3'), ('Subversion', '1.14.1'), ('git', '2.33.1', '-nodocs'), - ('git-lfs', '3.2.0', '', True), # optional + ('git-lfs', '3.2.0', '', True), ] +components = [ + # install extra configuration tools and files for VSC clusters + ('cesm-config', '1.6.1', { + 'easyblock': 'Tarball', + 'source_urls': ['https://github.com/vub-hpc/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['bd88c32a08439cc0b4395936a2113e83032e43d0c683ffb4dbf651c09d1e9c88'], + 'start_dir': '%(name)s-%(version)s', + }), +] + +sanity_check_paths = { + 'files': ['bin/update-cesm-machines', 'scripts/case.pbs', 'scripts/case.slurm'], + 'dirs': ['machines', 'irods'], +} + usage = """Environment to build and run CESM v2 simulations 1. Download a release of CESM v2: `git clone -b release-cesm2.2.0 https://github.com/ESCOMP/cesm.git cesm-2.2.0` 2. Add external programs for CESM: `cd cesm-2.2.0; ./manage_externals/checkout_externals` - 3. Create case: `cd cime/scripts && ./create_newcase ...`""" + 3. Update config files: `update-cesm-machines cime/config/cesm/machines/ $EBROOTCESMMINDEPS/machines/` + 4. Create case: `cd cime/scripts && ./create_newcase --machine ...`""" moduleclass = 'geo' From 10cd5e823f854e1ad390b5f26cfdea58961b26d4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 5 Aug 2022 15:40:39 +0200 Subject: [PATCH 4396/9987] add module footer in TCL as well for git-lfs --- easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb index 172197cedf0..324690cada5 100644 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb @@ -26,11 +26,15 @@ sanity_check_paths = { sanity_check_commands = [('git-lfs', '--version')] -# set up Git LFS for the user account +# add aliases needed by Git LFS in ~.gitconfig modluafooter = """ if mode() == "load" then cmdout = subprocess("git lfs install") LmodMessage(cmdout) end""" +modtclfooter = """ +if { [ module-info mode load ] } { + exec git lfs install +}""" moduleclass = 'tools' From 9cd691bc54ff9ba6bcd27ca5ff6e011a242d7e8c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 6 Aug 2022 00:44:13 +0800 Subject: [PATCH 4397/9987] remove download_dep_fail --- .../colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb index ecd12d1162f..5a14fa765f1 100644 --- a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb @@ -17,6 +17,9 @@ dependencies = [ ('torchvision', '0.11.1', versionsuffix), ] +use_pip = True +sanity_pip_check = True + exts_list = [ ('cfgv', '3.3.1', { 'checksums': ['f5a830efb9ce7a445376bb66ec94c638a9787422f96264c98edc6bdeed8ab736'], @@ -47,9 +50,4 @@ exts_list = [ }), ] -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - moduleclass = 'ai' From 104fd7e8952572d4526a115f16c33c9494f50f52 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 5 Aug 2022 20:20:25 +0100 Subject: [PATCH 4398/9987] adding easyconfigs: QuickPIC-20210224-gompi-2021b.eb --- .../QuickPIC/QuickPIC-20210224-gompi-2021b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb diff --git a/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb b/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb new file mode 100644 index 00000000000..a0a47f70b8e --- /dev/null +++ b/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb @@ -0,0 +1,45 @@ +# There is unfortunately right now no proper release, thus the +# commit-tag is being used. Does not build in parallel. +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'QuickPIC' +local_commit = '776fcff' +version = '20210224' + +homepage = 'https://github.com/UCLA-Plasma-Simulation-Group/QuickPIC-OpenSource' +description = """ QuickPIC is a 3D parallel (MPI & OpenMP Hybrid) Quasi-Static PIC code, +which is developed based on the framework UPIC. QuickPIC can efficiently simulate plasma +based accelerator problems. This is the UCLA Plasma Simulation Group's official open-source +repository for QuickPIC.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True, 'cstd': 'c99'} + +source_urls = ['https://github.com/UCLA-Plasma-Simulation-Group/QuickPIC-OpenSource/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = ['quickpic-makefile.patch'] + +checksums = [ + '83d3664542ce0a1c1fa055802e214bdba98790ee512f1f2525d0c087d20d88af', # QuickPIC-20210224.tar.gz + '65afe170f89a9eb20ee9d47de147d736a2a25fcc6cc286be3f0b4d08fa17c415', # quickpic-makefile.patch +] + +dependencies = [ + ('HDF5', '1.10.8'), + ('json-fortran', '8.3.0'), +] + +prebuildopts = 'cd source && ' + +parallel = 1 + +files_to_copy = [(['source/qpic.e'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/qpic.e'], + 'dirs': [], +} + +moduleclass = 'phys' From d51d4430bec73c8601cde484093b8bd8bfbe080e Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 5 Aug 2022 20:22:12 +0100 Subject: [PATCH 4399/9987] patchfile added --- .../q/QuickPIC/quickpic-makefile.patch | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch diff --git a/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch b/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch new file mode 100644 index 00000000000..588cbe1c158 --- /dev/null +++ b/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch @@ -0,0 +1,49 @@ +Patch for makefile and make.GF_OPENMPI so HDF5 and json-fortran is being found +instead of hard-coded paths +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/QuickPIC-OpenSource-776fcffaaf9e170fbae80bfe54abc95b1f84dfca.orig/source/make.GF_OPENMPI b/QuickPIC-OpenSource-776fcffaaf9e170fbae80bfe54abc95b1f84dfca/source/make.GF_OPENMPI +index b2f08f0..c1538cf 100644 +--- a/QuickPIC-OpenSource-776fcffaaf9e170fbae80bfe54abc95b1f84dfca.orig/source/make.GF_OPENMPI ++++ b/QuickPIC-OpenSource-776fcffaaf9e170fbae80bfe54abc95b1f84dfca/source/make.GF_OPENMPI +@@ -1,6 +1,6 @@ + # name of the compiler +-JSON_LIB = /usr/local/jsonfortran-gnu-6.3.0/lib/ +-JSON_INC = /usr/local/jsonfortran-gnu-6.3.0/lib/ ++JSON_LIB = ${EBROOTJSONMINFORTRAN}/jsonfortran-gnu-8.3.0/lib ++JSON_INC = ${EBROOTJSONMINFORTRAN}/jsonfortran-gnu-8.3.0/lib + + FC_GF_OPENMPI = mpif90 -c -I$(JSON_INC) -fopenmp + CC_GF_OPENMPI = mpicc -c -O3 -std=c99 +@@ -14,11 +14,11 @@ FORMAT_FIXED_GF_OPENMPI = -ffixed-form + + # hdf5 libraries + +-HDF5_LIB =/usr/local/hdf5/lib +-HDF5_INC =/usr/local/hdf5/include ++HDF5_LIB =${EBROOTHDF5}/include ++HDF5_INC =${EBROOTHDF5}/lib + + HDF_LIBPATH_GF_OPENMPI= -L$(HDF5_LIB) -lhdf5_fortran -lhdf5_hl -lhdf5 -lz +-HDF_INCLUDE_PATH_GF_OPENMPI= -I$(HDF5_INC) -I${HDF5_LIB} -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 ++HDF_INCLUDE_PATH_GF_OPENMPI= -I$(HDF5_INC) -L${HDF5_LIB} -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 + + # other libs + OTHER_LIBS_GF_OPENMPI = -L$(JSON_LIB) -ljsonfortran +diff --git a/QuickPIC-OpenSource-776fcffaaf9e170fbae80bfe54abc95b1f84dfca.orig/source/makefile b/QuickPIC-OpenSource-776fcffaaf9e170fbae80bfe54abc95b1f84dfca/source/makefile +index faf3c77..2deff20 100644 +--- a/QuickPIC-OpenSource-776fcffaaf9e170fbae80bfe54abc95b1f84dfca.orig/source/makefile ++++ b/QuickPIC-OpenSource-776fcffaaf9e170fbae80bfe54abc95b1f84dfca/source/makefile +@@ -42,10 +42,9 @@ OBJS_MAIN = main.o + + OBJS = ${OBJS_BASE} ${OBJS_MAIN} + +-# hdf libraries +-HDF_INCLUDE_PATH = ${HDF_INCLUDE_PATH_${SYS_SFX}} +-HDF_LIBPATH = ${HDF_LIBPATH_${SYS_SFX}} +-HDF_LIBS = ${HDF_LIBPATH} ++HDF_INCLUDE_PATH = -I${EBROOTHDF5}/include ++HDF_LIBPATH = -L${EBROOTHDF5}/lib64 ++HDF_LIBS = -lhdf5_fortran + + # other libs + OTHER_LIBS = ${OTHER_LIBS_${SYS_SFX}} From 1b6fc26b3057b6cd0f7771dad09448d803c03209 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 5 Aug 2022 21:23:47 +0200 Subject: [PATCH 4400/9987] Add WRF and WPS --- .../t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb | 45 +++ .../t/time/time-1.9-GCCcore-11.3.0.eb | 27 ++ .../w/WPS/WPS-4.4-foss-2022a-dmpar.eb | 38 +++ ...WPS-4.4_netCDF-Fortran_separate_path.patch | 91 ++++++ .../w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 51 ++++ ...WRF-4.4_netCDF-Fortran_separate_path.patch | 266 ++++++++++++++++++ 6 files changed, 518 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..27ca241e481 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.24.01' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5659a1b973b1f947e36238cb17a00210ac4cff3b496f8f851acd77172ab91d7e'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('ncurses', '6.3')] + +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + +sanity_check_paths = { + 'files': ["bin/tcsh", "bin/csh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d0b426f3ff8 --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'https://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] + +builddependencies = [('binutils', '2.38')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb new file mode 100644 index 00000000000..f42560bc809 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb @@ -0,0 +1,38 @@ +name = 'WPS' +version = '4.4' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WPS-%(version)s_netCDF-Fortran_separate_path.patch', +] +checksums = [ + 'fe9c8d8a9a4abbf800b30e6cbb378604c6040e4536f5594b8e2dae43e942e2b3', # v4.4.tar.gz + '751bb744bf8e5386b3bcf9c3c92dbd06183acf4007d061a3c10da808387bb0a8', # WPS-4.4_netCDF-Fortran_separate_path.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +builddependencies = [ + ('Perl', '5.34.1'), +] + +dependencies = [ + ('WRF', '4.4', versionsuffix), + ('JasPer', '2.0.33'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..71d67030c7e --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch @@ -0,0 +1,91 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since 2013; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain +# +# updated for WPS v4.1 by Kenneth Hoste (HPC-UGent) +# updated for WPS v4.2 by Åke Sandgren (HPC2N) +# updated for WPS v4.4 by Maxim Masterov (SURF) + +diff -Nru WPS-4.4.orig/arch/Config.pl WPS-4.4/arch/Config.pl +--- WPS-4.4.orig/arch/Config.pl 2022-08-05 20:46:38.790818000 +0200 ++++ WPS-4.4/arch/Config.pl 2022-08-05 20:47:19.544741000 +0200 +@@ -42,6 +42,7 @@ + if(substr( $ARGV[0], 1, 8 ) eq "netcdff=") + { + $sw_netcdff_lib = substr( $ARGV[0], 9); ++ $sw_netcdff_lib =~ s/!/ /g ; + } + if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") + { +diff -Nru WPS-4.4.orig/arch/preamble WPS-4.4/arch/preamble +--- WPS-4.4.orig/arch/preamble 2022-08-05 20:46:38.792313000 +0200 ++++ WPS-4.4/arch/preamble 2022-08-05 20:47:40.331112000 +0200 +@@ -39,7 +39,7 @@ + -I$(WRF_DIR)/external/io_grib1 \ + -I$(WRF_DIR)/external/io_int \ + -I$(WRF_DIR)/inc \ +- -I$(NETCDF)/include ++ -I$(NETCDF)/include -I$(NETCDFF)/include + + WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ + -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ +diff -Nru WPS-4.4.orig/configure WPS-4.4/configure +--- WPS-4.4.orig/configure 2022-08-05 20:46:38.790086000 +0200 ++++ WPS-4.4/configure 2022-08-05 20:48:51.938951000 +0200 +@@ -138,9 +138,14 @@ + echo "Will use NETCDF in dir: $NETCDF" + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available +- NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then +- NETCDFF="-lnetcdff" ++ USENETCDFF=" " ++ # for netCDF 4.2 and greater, the Fortran library is a seperate install ++ if [ -z "$NETCDFF" ] ++ then ++ NETCDFF=$NETCDF ++ fi ++ if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-lnetcdff" + fi + else + echo "Will configure for use without NetCDF" +@@ -239,7 +244,7 @@ + fi + + # Found perl, so proceed with configuration +-perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$NETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir -grib2dir=$grib2dir ++perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$USENETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir + + + #Checking cross-compiling capability for some particular environment +@@ -405,9 +410,9 @@ + end program + EOF + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -lnetcdf $USENETCDFF > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + ./fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then +diff -Nru WPS-4.4.orig/util/src/Makefile WPS-4.4/util/src/Makefile +--- WPS-4.4.orig/util/src/Makefile 2022-08-05 20:46:38.503642000 +0200 ++++ WPS-4.4/util/src/Makefile 2022-08-05 20:52:25.200578000 +0200 +@@ -41,11 +41,11 @@ + write_met_module.o misc_definitions_module.o met_data_module.o + $(SFC) $(LDFLAGS) -o $@ elev_angle.o cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o met_data_module.o \ +- -L$(NETCDF)/lib -I$(NETCDF)/include -lnetcdf ++ -L$(NETCDFF)/lib -I$(NETCDFF)/include -lnetcdff + + elev_angle.o: elev_angle.F cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o +- $(SFC) -c elev_angle.F -I$(NETCDF)/include ++ $(SFC) -c elev_angle.F -I$(NETCDFF)/include + + calc_ecmwf_p.exe: calc_ecmwf_p.o cio.o module_debug.o module_stringutil.o gridinfo_module.o read_met_module.o \ + write_met_module.o module_date_pack.o misc_definitions_module.o met_data_module.o constants_module.o diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb new file mode 100644 index 00000000000..f5772f50f24 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -0,0 +1,51 @@ +name = 'WRF' +version = '4.4' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +# sources = ['v%(version)s.tar.gz'] +sources = [{ + 'filename': 'v4.4.tar.gz', + 'git_config': { + 'url': 'https://github.com/wrf-model', + 'repo_name': 'WRF', + 'tag': 'v4.4', + 'clone_into': 'WRF-4.4', + 'recursive': True, + }, +}] +patches = [ + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', +] +checksums = [ + '92f87fd769867a12dc0bda9778a2ec5319249bc335cbda87043a873d9139088d', # v4.4.tar.gz + '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20220317'), + ('tcsh', '6.24.01'), + ('time', '1.9'), + ('Perl', '5.34.1'), +] + +dependencies = [ + ('JasPer', '2.0.33'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..34e03618a66 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch @@ -0,0 +1,266 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since WRF3.5; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain +# +# updated for WPS v4.4 by Maxim Masterov (SURF) + +diff -Nru WRF-4.4.orig/arch/Config.pl WRF-4.4/arch/Config.pl +--- WRF-4.4.orig/arch/Config.pl 2022-08-05 12:50:41.026673000 +0200 ++++ WRF-4.4/arch/Config.pl 2022-08-05 12:53:16.487608000 +0200 +@@ -11,6 +11,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; # for netCDF 4.2 and greater, Fortran lib might be in a different path + $sw_pnetcdf_path = "" ; + $sw_netcdfpar_path = "" ; + $sw_hdf5_path=""; +@@ -95,6 +96,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -126,6 +131,7 @@ + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { + $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -610,6 +616,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_NETCDFPAR_PATH/$sw_netcdfpar_path/g ; + $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ; +@@ -678,7 +685,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +diff -Nru WRF-4.4.orig/arch/configure.defaults WRF-4.4/arch/configure.defaults +--- WRF-4.4.orig/arch/configure.defaults 2022-08-05 12:50:41.028943000 +0200 ++++ WRF-4.4/arch/configure.defaults 2022-08-05 12:53:38.767002000 +0200 +@@ -1636,6 +1636,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +diff -Nru WRF-4.4.orig/arch/conf_tokens WRF-4.4/arch/conf_tokens +--- WRF-4.4.orig/arch/conf_tokens 2022-08-05 12:50:41.028607000 +0200 ++++ WRF-4.4/arch/conf_tokens 2022-08-05 12:53:57.832914000 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDFF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -Nru WRF-4.4.orig/arch/postamble WRF-4.4/arch/postamble +--- WRF-4.4.orig/arch/postamble 2022-08-05 12:50:41.031770000 +0200 ++++ WRF-4.4/arch/postamble 2022-08-05 12:54:52.759085000 +0200 +@@ -53,6 +53,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/wrftladj \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ ++ -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include \ + -I$(NETCDFPATH)/include \ + CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC + REGISTRY = Registry +@@ -63,6 +64,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + RTTOVPATH = CONFIGURE_RTTOV_PATH +@@ -94,7 +96,7 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + +@@ -105,7 +107,7 @@ + + wrfio_pnf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \ +- make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ ++ make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ + FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_grib_share : +diff -Nru WRF-4.4.orig/configure WRF-4.4/configure +--- WRF-4.4.orig/configure 2022-08-05 12:50:41.453325000 +0200 ++++ WRF-4.4/configure 2022-08-05 12:57:14.821614000 +0200 +@@ -222,9 +222,13 @@ + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then + USENETCDFF="-lnetcdff" + else +- USENETCDFF=" " ++ if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++ else ++ USENETCDFF=" " ++ fi + fi +- if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib/libnetcdf.dll.a" ] ; then ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then + USENETCDF="-lnetcdf" + else + USENETCDF=" " +@@ -566,7 +570,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -648,14 +652,14 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +diff -Nru WRF-4.4.orig/external/io_netcdf/makefile WRF-4.4/external/io_netcdf/makefile +--- WRF-4.4.orig/external/io_netcdf/makefile 2022-08-05 12:50:41.676471000 +0200 ++++ WRF-4.4/external/io_netcdf/makefile 2022-08-05 15:32:21.053573000 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so -o -f $(NETCDFPATH)/lib/libnetcdff.dll.a \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib64/libnetcdff.a -o -f $(NETCDFFPATH)/lib64/libnetcdff.so \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -Nru WRF-4.4.orig/external/io_pnetcdf/Makefile WRF-4.4/external/io_pnetcdf/Makefile +--- WRF-4.4.orig/external/io_pnetcdf/Makefile 2022-08-05 12:50:41.688872000 +0200 ++++ WRF-4.4/external/io_pnetcdf/Makefile 2022-08-05 13:00:28.273185000 +0200 +@@ -9,8 +9,8 @@ + ext_pnc_put_var_td.code \ + ext_pnc_put_var_ti.code \ + transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = -L$(NETCDFPATH)/lib -lpnetcdf ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = -L$(NETCDFFPATH)/lib -lpnetcdf + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -25,15 +25,15 @@ + $(RANLIB) libwrfio_pnf.a + + wrf_io.o: wrf_io.F90 $(CODE) +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f + $(FC) $(FFLAGS) -c wrf_io.f + + module_wrfsi_static.o: module_wrfsi_static.F90 +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f + $(FC) $(FFLAGS) -c module_wrfsi_static.f + + field_routines.o: field_routines.F90 wrf_io.o +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f + $(FC) $(FFLAGS) -c field_routines.f + + superclean: +diff -Nru WRF-4.4.orig/Makefile WRF-4.4/Makefile +--- WRF-4.4.orig/Makefile 2022-08-05 12:50:40.979120000 +0200 ++++ WRF-4.4/Makefile 2022-08-05 13:03:38.672102000 +0200 +@@ -923,7 +923,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \ + FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ +@@ -1070,9 +1070,9 @@ + # rule used by configure to test if this will compile with netcdf4 + nc4_test: + if [ $(USENETCDFPAR) -eq 0 ] ; then \ +- ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ ++ ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ + else \ +- ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ ++ ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ + fi + + # rule used by configure to test if Fortran 2003 IEEE signaling is available From 74f1f9d62dba709eb730a1795029aa3086dd40c8 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 5 Aug 2022 20:24:39 +0100 Subject: [PATCH 4401/9987] adding easyconfigs: json-fortran-8.3.0-GCCcore-11.2.0.eb --- .../json-fortran-8.3.0-GCCcore-11.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..500b78cafc8 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['jsonfortran-gnu-8.3.0/lib/libjsonfortran.a', 'jsonfortran-gnu-8.3.0/lib/libjsonfortran.%s' % SHLIB_EXT], + 'dirs': ['jsonfortran-gnu-8.3.0/cmake'], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': 'jsonfortran-gnu-8.3.0/lib', + 'LIBRARY_PATH': 'jsonfortran-gnu-8.3.0/lib', + 'CMAKE_PREFIX_PATH': 'jsonfortran-gnu-8.3.0/cmake', +} + +moduleclass = 'lib' From 7e71bf72bb51ca47e2c57b9d2e8aab10816ce1a2 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 6 Aug 2022 07:14:06 +0800 Subject: [PATCH 4402/9987] simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM easyconfig --- .../AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb | 35 ++----------------- .../a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb | 35 ++----------------- .../AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb | 35 ++----------------- .../a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb | 35 ++----------------- 4 files changed, 12 insertions(+), 128 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb index d6332594c4b..eb6b1ef8c31 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb @@ -10,12 +10,9 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ - # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), # required for installing dm-tree ('Bazel', '3.7.2'), - ('SWIG', '4.0.2'), + ('CMake', '3.20.1'), ] dependencies = [ @@ -32,34 +29,14 @@ dependencies = [ ('UCX-CUDA', '1.10.0', versionsuffix), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), + ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM ] -local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " -local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " - -# required to install OpenMM Python API; -# avoid that setup.py partially uninstalls existing OpenMM Python bindings... -local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " -local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' components = [ - # for simtk - ('OpenMM', '7.5.1', { - 'easyblock': 'CMakeMake', - 'source_urls': ['https://github.com/openmm/openmm/archive/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], - 'checksums': [ - 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz - '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch - ], - 'start_dir': 'openmm-%(version)s', - 'preinstallopts': local_openmm_preinstallopts, - 'installopts': local_openmm_installopts, - }), (name, version, { 'easyblock': 'PythonPackage', 'source_urls': [ @@ -163,8 +140,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } @@ -177,11 +153,6 @@ sanity_check_commands = [ sanity_pip_check = True -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - # these allow to make predictions on proteins that would typically be too long to fit into GPU memory; # see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py modextravars = { diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb index bb34b753f32..addf0f101a0 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb @@ -9,12 +9,9 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ - # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), # required for installing dm-tree ('Bazel', '3.7.2'), - ('SWIG', '4.0.2'), + ('CMake', '3.20.1'), ] dependencies = [ @@ -27,34 +24,14 @@ dependencies = [ ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), ('jax', '0.2.24'), # also provides absl-py + ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM ] -local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " -local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " - -# required to install OpenMM Python API; -# avoid that setup.py partially uninstalls existing OpenMM Python bindings... -local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " -local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' components = [ - # for simtk - ('OpenMM', '7.5.1', { - 'easyblock': 'CMakeMake', - 'source_urls': ['https://github.com/openmm/openmm/archive/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], - 'checksums': [ - 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz - '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch - ], - 'start_dir': 'openmm-%(version)s', - 'preinstallopts': local_openmm_preinstallopts, - 'installopts': local_openmm_installopts, - }), (name, version, { 'easyblock': 'PythonPackage', 'source_urls': [ @@ -158,8 +135,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } @@ -172,11 +148,6 @@ sanity_check_commands = [ sanity_pip_check = True -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - modextravars = { # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt } diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb index 5b4a6edac04..b3c9ea43636 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb @@ -10,12 +10,9 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ - # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), # required for installing dm-tree ('Bazel', '3.7.2'), - ('SWIG', '4.0.2'), + ('CMake', '3.20.1'), ] dependencies = [ @@ -32,34 +29,14 @@ dependencies = [ ('UCX-CUDA', '1.10.0', versionsuffix), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), + ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM ] -local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " -local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " - -# required to install OpenMM Python API; -# avoid that setup.py partially uninstalls existing OpenMM Python bindings... -local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " -local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' components = [ - # for simtk - ('OpenMM', '7.5.1', { - 'easyblock': 'CMakeMake', - 'source_urls': ['https://github.com/openmm/openmm/archive/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], - 'checksums': [ - 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz - '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch - ], - 'start_dir': 'openmm-%(version)s', - 'preinstallopts': local_openmm_preinstallopts, - 'installopts': local_openmm_installopts, - }), (name, version, { 'easyblock': 'PythonPackage', 'source_urls': [ @@ -166,8 +143,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } @@ -180,11 +156,6 @@ sanity_check_commands = [ sanity_pip_check = True -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - # these allow to make predictions on proteins that would typically be too long to fit into GPU memory; # see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py modextravars = { diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb index a864581a569..8e1e11da53e 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb @@ -9,12 +9,9 @@ description = "AlphaFold can predict protein structures with atomic accuracy eve toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ - # CMake/Doxygen/SWIG are required for building OpenMM - ('CMake', '3.20.1'), - ('Doxygen', '1.9.1'), # required for installing dm-tree ('Bazel', '3.7.2'), - ('SWIG', '4.0.2'), + ('CMake', '3.20.1'), ] dependencies = [ @@ -27,34 +24,14 @@ dependencies = [ ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), ('jax', '0.3.9'), # also provides absl-py + ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM ] -local_openmm_preinstallopts = "export OPENMM_INCLUDE_PATH=%(installdir)s/include && " -local_openmm_preinstallopts += " export OPENMM_LIB_PATH=%(installdir)s/lib && " - -# required to install OpenMM Python API; -# avoid that setup.py partially uninstalls existing OpenMM Python bindings... -local_openmm_installopts = " && cd python && sed -i 's/uninstall()/pass/g' setup.py && " -local_openmm_installopts += "python setup.py build && python setup.py install --prefix=%(installdir)s" # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, # see docker/Dockerfile in AlphaFold repository local_scp_commit = '7102c6' components = [ - # for simtk - ('OpenMM', '7.5.1', { - 'easyblock': 'CMakeMake', - 'source_urls': ['https://github.com/openmm/openmm/archive/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], - 'patches': [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')], - 'checksums': [ - 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', # OpenMM-7.5.1.tar.gz - '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', # OpenMM-7.5.1_AlphaFold.patch - ], - 'start_dir': 'openmm-%(version)s', - 'preinstallopts': local_openmm_preinstallopts, - 'installopts': local_openmm_installopts, - }), (name, version, { 'easyblock': 'PythonPackage', 'source_urls': [ @@ -161,8 +138,7 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'lib/libOpenMM.%s' % SHLIB_EXT, - 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py', 'stereo_chemical_props.txt'], + 'files': ['bin/alphafold', 'bin/pdbfixer', 'stereo_chemical_props.txt'], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } @@ -175,11 +151,6 @@ sanity_check_commands = [ sanity_pip_check = True -modextrapaths = { - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - modextravars = { # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt } From 8f4a1d74672de92db3543c6ae679c0feaa0ac3e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 6 Aug 2022 10:35:30 +0200 Subject: [PATCH 4403/9987] {*}[foss/2022a] GATE v9.2, Geant4 v11.0.2, ROOT v6.26.06, CLHEP v2.4.5.3 (+ deps) --- .../c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb | 50 +++++++++++++++++ .../c/CLHEP/CLHEP-2.4.5.3-GCC-11.3.0.eb | 27 +++++++++ .../easyconfigs/g/GATE/GATE-9.2-foss-2022a.eb | 31 +++++++++++ .../g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb | 34 ++++++++++++ .../g/Geant4/Geant4-11.0.2-GCC-11.3.0.eb | 27 +++++++++ .../r/ROOT/ROOT-6.26.06-foss-2022a.eb | 55 +++++++++++++++++++ 6 files changed, 224 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.5.3-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GATE/GATE-9.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-11.0.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3a3cc7ce5b1 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'CFITSIO' +version = '4.1.0' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-3.48_install_test_data.patch'] +checksums = [ + 'b367c695d2831958e7166921c3b356d5dfa51b1ecee505b97416ba39d1b6c17a', # cfitsio-4.1.0.tar.gz + 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + # curl for HTTPS support + ('cURL', '7.83.0'), + ('zlib', '1.2.12'), +] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +#buildopts = '&& make shared && make testprog' + +configopts = [ + "-DBUILD_SHARED_LIBS=OFF -DTESTS=ON", + "-DBUILD_SHARED_LIBS=ON -DTESTS=ON", +] + +buildopts = " && ./TestProg" + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.5.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..5abbe184435 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.5.3-GCC-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.5.3' + +homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] +sources = [SOURCELOWER_TGZ] +checksums = ['45f63eeb097f02fe67b86a7dadbf10d409b401c28a1a3e172db36252c3097c13'] + +builddependencies = [('CMake', '3.23.1')] + +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GATE/GATE-9.2-foss-2022a.eb b/easybuild/easyconfigs/g/GATE/GATE-9.2-foss-2022a.eb new file mode 100644 index 00000000000..284d0bb64f4 --- /dev/null +++ b/easybuild/easyconfigs/g/GATE/GATE-9.2-foss-2022a.eb @@ -0,0 +1,31 @@ +name = 'GATE' +version = '9.2' + +homepage = 'http://www.opengatecollaboration.org/' +description = """GATE is an advanced opensource software developed by the international OpenGATE collaboration and + dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography + (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/OpenGATE/Gate/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['GATE-9.2_fix-Geant4-11.0.patch'] +checksums = [ + '6fad86002dacae9d1f76ed0c455847d5d8960f667570292066b211a8b83247ee', # v9.2.tar.gz + '093a88718ff23edf332ac5a29b2810e77df40d63dd70e3b36f55195e4bb9e0b7', # GATE-9.2_fix-Geant4-11.0.patch +] + +builddependencies = [('CMake', '3.23.1')] +dependencies = [ + ('Geant4', '11.0.2'), + ('CLHEP', '2.4.5.3'), + ('ROOT', '6.26.06'), +] + +preinstallopts = "sed -i 's|/usr/local/bin|%(installdir)s/bin|g' Makefile &&" + +# enable extra capabilities (Davis requires Geant4 10.04 or newer) +configopts = "-DGATE_USE_OPTICAL=1 -DGATE_USE_DAVIS=1" + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7207dd595c5 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.2' + +homepage = 'https://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] +checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +dependencies = [ + ('X11', '20220504'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('freeglut', '3.2.2'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.0.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-11.0.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..7fe2129d33f --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.0.2-GCC-11.3.0.eb @@ -0,0 +1,27 @@ +name = 'Geant4' +version = '11.0.2' + +homepage = 'https://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'Geant4' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['ddabe8d5cc3bd465c969f375cc43ee537ff33c17dc2943b8a4420cfa83cfcfcc'] + +builddependencies = [('CMake', '3.23.1')] +dependencies = [ + ('expat', '2.4.8'), + # (bugfix update of) recommended CLHEP version, + # see https://geant4-data.web.cern.ch/ReleaseNotes/ReleaseNotes.11.0.html + ('CLHEP', '2.4.5.3'), +] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += " -DCLHEP_ROOT_DIR=$EBROOTCLHEP -DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb new file mode 100644 index 00000000000..60338bda758 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb @@ -0,0 +1,55 @@ +name = 'ROOT' +version = '6.26.06' + +homepage = 'https://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://root.cern.ch/download/'] +sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +checksums = ['b1f73c976a580a5c56c8c8a0152582a1dfc560b4dd80e1b7545237b65e6c89cb'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('GSL', '2.7'), + ('libxml2', '2.9.13'), + ('PCRE', '8.45'), + ('CFITSIO', '4.1.0'), + ('freetype', '2.12.1'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), + ('X11', '20220504'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('GL2PS', '1.4.2'), + ('FFTW', '3.3.10'), + ('SQLite', '3.38.3'), + ('XZ', '5.2.5'), + ('libpng', '1.6.37'), +] + +# NOTE: Ensure that each configopts string begins with a blank +# disable some components +configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" + +# make sure some components are enabled +configopts += " -Dpcre=ON -Dzlib=ON -Dpyroot=ON" +configopts += " -Dunuran=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " + +# Add component-specific settings based on dependencies +configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' + +# Set C++ standard to C++17 for better stability +configopts += ' -DCMAKE_CXX_STANDARD=17' + +configopts += " -Dgallium-drivers=swrast" + +moduleclass = 'data' From 5a640c5470661cd193928da27ba00824689b15f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 6 Aug 2022 11:32:40 +0200 Subject: [PATCH 4404/9987] add sanity check command for OpenFAST --- easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb index 713ddc87bf4..2572502b898 100644 --- a/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/o/OpenFAST/OpenFAST-3.0.0-foss-2021b.eb @@ -26,4 +26,6 @@ sanity_check_paths = { 'dirs': ['include/openfast'], } +sanity_check_commands = ["openfast -h"] + moduleclass = 'cae' From 58fb63a5cc9f9a20da40abab2d8796bf2243a733 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 6 Aug 2022 14:07:34 +0200 Subject: [PATCH 4405/9987] Add comment on libnsl --- easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-3.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-3.eb b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-3.eb index 738c9b63f5f..955e016dc5d 100644 --- a/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-3.eb +++ b/easybuild/easyconfigs/s/Schrodinger/Schrodinger-2022-3.eb @@ -18,6 +18,8 @@ checksums = ['e607b6b2e1671030a66e7d2ab0fbe22ca5e8414794aaf50a7230c1db4417b762'] install_cmd = 'cd %(builddir)s/%(name)s_Suites_%(version)s_Linux-x86_64 && ' install_cmd += './INSTALL -d . -s %(installdir)s -k /usr/tmp -t %(installdir)s/thirdparty -b *' +# Needs libnsl.so, part of glibc on CentOS7 but a separate libnsl package on RHEL8 + sanity_check_paths = { 'files': ['desmond', 'maestro'], 'dirs': [], From 13daa29798f42f9214fa8d74465c8871918bb2b3 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 6 Aug 2022 17:44:32 +0200 Subject: [PATCH 4406/9987] adding easyconfigs: Clang-13.0.1-GCCcore-11.3.0.eb, Z3-4.10.2-GCCcore-11.3.0.eb --- .../c/Clang/Clang-13.0.1-GCCcore-11.3.0.eb | 75 +++++++++++++++++++ .../z/Z3/Z3-4.10.2-GCCcore-11.3.0.eb | 33 ++++++++ 2 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.10.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e61c5f74ce0 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.3.0.eb @@ -0,0 +1,75 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '13.0.1' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'clang-%(version)s.src.tar.xz', + 'compiler-rt-%(version)s.src.tar.xz', + 'polly-%(version)s.src.tar.xz', + 'openmp-%(version)s.src.tar.xz', + # Also include the LLVM linker + 'lld-%(version)s.src.tar.xz', + 'libcxx-%(version)s.src.tar.xz', + 'libcxxabi-%(version)s.src.tar.xz', + 'clang-tools-extra-%(version)s.src.tar.xz', + 'libunwind-%(version)s.src.tar.xz', +] +checksums = [ + 'ec6b80d82c384acad2dc192903a6cf2cdbaffb889b84bfb98da9d71e630fc834', # llvm-13.0.1.src.tar.xz + '787a9e2d99f5c8720aa1773e4be009461cd30d3bd40fdd24591e473467c917c9', # clang-13.0.1.src.tar.xz + '7b33955031f9a9c5d63077dedb0f99d77e4e7c996266952c1cec55626dca5dfc', # compiler-rt-13.0.1.src.tar.xz + 'f4003e03da57b53bf206faadd0cf53f7b198c38498c605dec45743db23c10ad0', # polly-13.0.1.src.tar.xz + '6b79261371616c31fea18cd3ee1797c79ee38bcaf8417676d4fa366a24c96b4f', # openmp-13.0.1.src.tar.xz + '666af745e8bf7b680533b4d18b7a31dc7cab575b1e6e4d261922bbafd9644cfb', # lld-13.0.1.src.tar.xz + '2f446acc00bb7cfb4e866c2fa46d1b6dbf4e7d2ab62e3c3d84e56f7b9e28110f', # libcxx-13.0.1.src.tar.xz + 'db5fa6093c786051e8b1c85527240924eceb6c95eeff0a2bbc57be8422b3cef1', # libcxxabi-13.0.1.src.tar.xz + 'cc2bc8598848513fa2257a270083e986fd61048347eccf1d801926ea709392d0', # clang-tools-extra-13.0.1.src.tar.xz + 'e206dbf1bbe058a113bffe189386ded99a160b2443ee1e2cd41ff810f78551ba', # libunwind-13.0.1.src.tar.xz +] + +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.38'), + ('hwloc', '2.7.1'), + ('libxml2', '2.9.13'), + ('ncurses', '6.3'), + ('GMP', '6.2.1'), + ('Z3', '4.10.2'), +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('elfutils', '0.187'), +] + +assertions = True +usepolly = True +build_lld = True +libcxx = True +enable_rtti = True +build_extra_clang_tools = True + +skip_all_tests = True + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.10.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.10.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..31490776e46 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.10.2-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Z3' +version = '4.10.2' + +homepage = 'https://github.com/Z3Prover/z3' +description = """ + Z3 is a theorem prover from Microsoft Research. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/Z3Prover/z3/archive/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['889fd035b833775c8cd2eb4723eb011bf916a3e9bf08ce66b31c548acee7a321'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = '-DZ3_USE_LIB_GMP=ON -DZ3_LINK_TIME_OPTIMIZATION=ON ' + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From e24daad29fb434d056ef4668c255d751ab50af39 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sun, 7 Aug 2022 02:25:34 +0800 Subject: [PATCH 4407/9987] clarify comments and remove redundant sanity check command --- .../o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb index 2dde80a23b1..209e65a8c5d 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -10,7 +10,8 @@ description = "A faithful PyTorch reproduction of DeepMind's AlphaFold 2" toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ - ('CMake', '3.20.1'), # required to build ninja + # CMake is required to build ninja Python package (included as extension) + ('CMake', '3.20.1'), ] dependencies = [ @@ -29,7 +30,10 @@ dependencies = [ ('einops', '0.4.1'), ('colossalai', '0.1.8', versionsuffix), ('scikit-build', '0.11.1'), - ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM + # OpenFold also requires the AlphaFold modification to OpenMM + # https://github.com/aqlaboratory/openfold/blob/v1.0.0/scripts/install_third_party_dependencies.sh#L20-L24 + # https://github.com/aqlaboratory/openfold/blob/v1.0.0/lib/openmm.patch + ('OpenMM', '7.5.1', '_AlphaFold'), ] use_pip = True @@ -83,7 +87,6 @@ sanity_check_paths = { sanity_check_commands = [ "pdbfixer --help", - "python -c 'import openfold'", ] sanity_pip_check = True From 99d129df26a8fc93a8073c1e1dd6d237b8266702 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sun, 7 Aug 2022 06:52:58 +0800 Subject: [PATCH 4408/9987] change versionsuffix of the OpenMM easyconfig that includes DeepMind's patch to -DeepMind-patch --- .../OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- ...OpenMM-7.5.1-foss-2021a-DeepMind-patch.eb} | 4 +- .../o/OpenMM/OpenMM-7.5.1_DeepMind.patch | 45 +++++++++++++++++++ 3 files changed, 48 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/o/OpenMM/{OpenMM-7.5.1-foss-2021a_AlphaFold.eb => OpenMM-7.5.1-foss-2021a-DeepMind-patch.eb} (93%) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_DeepMind.patch diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb index 209e65a8c5d..f4797eae8eb 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -33,7 +33,7 @@ dependencies = [ # OpenFold also requires the AlphaFold modification to OpenMM # https://github.com/aqlaboratory/openfold/blob/v1.0.0/scripts/install_third_party_dependencies.sh#L20-L24 # https://github.com/aqlaboratory/openfold/blob/v1.0.0/lib/openmm.patch - ('OpenMM', '7.5.1', '_AlphaFold'), + ('OpenMM', '7.5.1', '-DeepMind-patch'), ] use_pip = True diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a_AlphaFold.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-DeepMind-patch.eb similarity index 93% rename from easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a_AlphaFold.eb rename to easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-DeepMind-patch.eb index 00b1c233032..cd9f06a4f42 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a_AlphaFold.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-DeepMind-patch.eb @@ -2,7 +2,7 @@ easyblock = 'CMakeMake' name = 'OpenMM' version = '7.5.1' -versionsuffix = '_AlphaFold' +versionsuffix = '-DeepMind-patch' homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." @@ -12,7 +12,7 @@ toolchainopts = {'opt': True} source_urls = ['https://github.com/openmm/openmm/archive/'] sources = ['%(version)s.tar.gz'] -patches = [('OpenMM-%(version)s_AlphaFold.patch', 'wrappers/python')] +patches = [('OpenMM-%(version)s_DeepMind.patch', 'wrappers/python')] checksums = [ 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_DeepMind.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_DeepMind.patch new file mode 100644 index 00000000000..878ffd11b03 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_DeepMind.patch @@ -0,0 +1,45 @@ +custom patch for OpenMM to use in conjunction with AlphaFold +see https://github.com/deepmind/alphafold/blob/main/docker/openmm.patch + +Index: simtk/openmm/app/topology.py +=================================================================== +--- simtk.orig/openmm/app/topology.py ++++ simtk/openmm/app/topology.py +@@ -356,19 +356,35 @@ + def isCyx(res): + names = [atom.name for atom in res._atoms] + return 'SG' in names and 'HG' not in names ++ # This function is used to prevent multiple di-sulfide bonds from being ++ # assigned to a given atom. This is a DeepMind modification. ++ def isDisulfideBonded(atom): ++ for b in self._bonds: ++ if (atom in b and b[0].name == 'SG' and ++ b[1].name == 'SG'): ++ return True ++ ++ return False + + cyx = [res for res in self.residues() if res.name == 'CYS' and isCyx(res)] + atomNames = [[atom.name for atom in res._atoms] for res in cyx] + for i in range(len(cyx)): + sg1 = cyx[i]._atoms[atomNames[i].index('SG')] + pos1 = positions[sg1.index] ++ candidate_distance, candidate_atom = 0.3*nanometers, None + for j in range(i): + sg2 = cyx[j]._atoms[atomNames[j].index('SG')] + pos2 = positions[sg2.index] + delta = [x-y for (x,y) in zip(pos1, pos2)] + distance = sqrt(delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2]) +- if distance < 0.3*nanometers: +- self.addBond(sg1, sg2) ++ if distance < candidate_distance and not isDisulfideBonded(sg2): ++ candidate_distance = distance ++ candidate_atom = sg2 ++ # Assign bond to closest pair. ++ if candidate_atom: ++ self.addBond(sg1, candidate_atom) ++ ++ + + class Chain(object): + """A Chain object represents a chain within a Topology.""" From 76c6ea95c8967c641e121749c679bd85c25acd4a Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sun, 7 Aug 2022 06:59:46 +0800 Subject: [PATCH 4409/9987] manually remove renamed patch --- .../o/OpenMM/OpenMM-7.5.1_AlphaFold.patch | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_AlphaFold.patch diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_AlphaFold.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_AlphaFold.patch deleted file mode 100644 index 878ffd11b03..00000000000 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_AlphaFold.patch +++ /dev/null @@ -1,45 +0,0 @@ -custom patch for OpenMM to use in conjunction with AlphaFold -see https://github.com/deepmind/alphafold/blob/main/docker/openmm.patch - -Index: simtk/openmm/app/topology.py -=================================================================== ---- simtk.orig/openmm/app/topology.py -+++ simtk/openmm/app/topology.py -@@ -356,19 +356,35 @@ - def isCyx(res): - names = [atom.name for atom in res._atoms] - return 'SG' in names and 'HG' not in names -+ # This function is used to prevent multiple di-sulfide bonds from being -+ # assigned to a given atom. This is a DeepMind modification. -+ def isDisulfideBonded(atom): -+ for b in self._bonds: -+ if (atom in b and b[0].name == 'SG' and -+ b[1].name == 'SG'): -+ return True -+ -+ return False - - cyx = [res for res in self.residues() if res.name == 'CYS' and isCyx(res)] - atomNames = [[atom.name for atom in res._atoms] for res in cyx] - for i in range(len(cyx)): - sg1 = cyx[i]._atoms[atomNames[i].index('SG')] - pos1 = positions[sg1.index] -+ candidate_distance, candidate_atom = 0.3*nanometers, None - for j in range(i): - sg2 = cyx[j]._atoms[atomNames[j].index('SG')] - pos2 = positions[sg2.index] - delta = [x-y for (x,y) in zip(pos1, pos2)] - distance = sqrt(delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2]) -- if distance < 0.3*nanometers: -- self.addBond(sg1, sg2) -+ if distance < candidate_distance and not isDisulfideBonded(sg2): -+ candidate_distance = distance -+ candidate_atom = sg2 -+ # Assign bond to closest pair. -+ if candidate_atom: -+ self.addBond(sg1, candidate_atom) -+ -+ - - class Chain(object): - """A Chain object represents a chain within a Topology.""" From 6fed95e71d29b94a069340149d92504bd56cc22d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 7 Aug 2022 03:03:05 +0200 Subject: [PATCH 4410/9987] fix dependency on FOX Toolkit in SUMO --- .../FOX-Toolkit-1.6.57-GCCcore-11.2.0.eb | 44 ++++++++++++++ .../FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb | 44 ++++++++++++++ .../s/SUMO/SUMO-1.0.0_fix-link-flags.patch | 17 ++++++ .../s/SUMO/SUMO-1.12.0-foss-2021b.eb | 43 ++++++++------ .../s/SUMO/SUMO-1.14.1-foss-2021b.eb | 59 +++++++++++++++++++ .../SUMO-1.7.0-foss-2020a-Python-3.8.2.eb | 40 +++++++------ 6 files changed, 210 insertions(+), 37 deletions(-) create mode 100644 easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/SUMO/SUMO-1.0.0_fix-link-flags.patch create mode 100644 easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b7051f48b64 --- /dev/null +++ b/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'FOX-Toolkit' +version = '1.6.57' + +homepage = 'https://www.fox-toolkit.org/' +description = """FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and +effectively. It offers a wide, and growing, collection of Controls, and +provides state of the art facilities such as drag and drop, selection, as well +as OpenGL widgets for 3D graphical manipulation. FOX also implements icons, +images, and user-convenience features such as status line help, and tooltips.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['ftp://ftp.fox-toolkit.org/pub'] +sources = ['fox-%(version)s.tar.gz'] +checksums = ['65ef15de9e0f3a396dc36d9ea29c158b78fad47f7184780357b929c94d458923'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libGLU', '9.0.2'), + ('X11', '20210802'), +] + +preconfigopts = """sed -i '/^CXXFLAGS=""$/d;/LDFLAGS="-s ${LDFLAGS}"/d' configure.ac && """ +preconfigopts += "autoreconf -f -i && " + +configopts = '--enable-release' + +sanity_check_paths = { + 'files': ['lib/lib%s-%%(version_major_minor)s.%s' % (n, x) for n in ['CHART', 'FOX'] for x in ['a', SHLIB_EXT]] + + ['bin/fox-config'], + 'dirs': ['include'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..8f0547f082c --- /dev/null +++ b/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'FOX-Toolkit' +version = '1.6.57' + +homepage = 'https://www.fox-toolkit.org/' +description = """FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and +effectively. It offers a wide, and growing, collection of Controls, and +provides state of the art facilities such as drag and drop, selection, as well +as OpenGL widgets for 3D graphical manipulation. FOX also implements icons, +images, and user-convenience features such as status line help, and tooltips.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['ftp://ftp.fox-toolkit.org/pub'] +sources = ['fox-%(version)s.tar.gz'] +checksums = ['65ef15de9e0f3a396dc36d9ea29c158b78fad47f7184780357b929c94d458923'] + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libjpeg-turbo', '2.0.4'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('libGLU', '9.0.1'), + ('X11', '20200222'), +] + +preconfigopts = """sed -i '/^CXXFLAGS=""$/d;/LDFLAGS="-s ${LDFLAGS}"/d' configure.ac && """ +preconfigopts += "autoreconf -f -i && " + +configopts = '--enable-release' + +sanity_check_paths = { + 'files': ['lib/lib%s-%%(version_major_minor)s.%s' % (n, x) for n in ['CHART', 'FOX'] for x in ['a', SHLIB_EXT]] + + ['bin/fox-config'], + 'dirs': ['include'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.0.0_fix-link-flags.patch b/easybuild/easyconfigs/s/SUMO/SUMO-1.0.0_fix-link-flags.patch new file mode 100644 index 00000000000..6df89ea692a --- /dev/null +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.0.0_fix-link-flags.patch @@ -0,0 +1,17 @@ +Remove duplicate linker flags from fox-config +author: Alex Domingo (Vrije Universiteit Brussel) +diff --git a/build/cmake_modules/FindFOX.cmake.orig b/build/cmake_modules/FindFOX.cmake +index 6d7b7b4..37f5934 100644 +--- a/build/cmake_modules/FindFOX.cmake.orig ++++ b/build/cmake_modules/FindFOX.cmake +@@ -16,6 +16,10 @@ endif(FOX_CONFIG) + set(FOX_FOUND 0) + # if fox-config was executed successfully, fox was found + if(FOX_LIBRARY AND FOX_CXX_FLAGS) ++ # remove duplicate link flags ++ separate_arguments(FOX_LIBRARY) ++ list(REMOVE_DUPLICATES FOX_LIBRARY) ++ string(REPLACE ";" " " FOX_LIBRARY "${FOX_LIBRARY}") + SET(FOX_FOUND TRUE) + else() + # In Windows system, find the fox directory using as hint the environment variable "FOX_INCLUDE_DIR" diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb index 1b0f2968117..fecda0386ee 100644 --- a/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb @@ -3,47 +3,47 @@ easyblock = 'CMakeMake' name = 'SUMO' version = '1.12.0' -homepage = 'https://sumo.dlr.de/' -description = """ -"Simulation of Urban MObility" (SUMO) is an open source, highly portable, microscopic and continuous traffic simulation -package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a -large set of tools for scenario creation. -""" +homepage = 'https://www.eclipse.org/sumo/' +description = """Simulation of Urban MObility" (SUMO) is an open source, highly portable, +microscopic and continuous traffic simulation package designed to handle large +networks. It allows for intermodal simulation including pedestrians and comes +with a large set of tools for scenario creation.""" toolchain = {'name': 'foss', 'version': '2021b'} -source_urls = ['https://github.com/eclipse/sumo/archive/'] +github_account = 'eclipse' +source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%s.tar.gz' % version.replace('.', '_')] -checksums = ['049f5f50d1d27352d868cbb4b2a4b59bc0a913ef792b619c1adf1a289b3e48a7'] +patches = ['SUMO-1.0.0_fix-link-flags.patch'] +checksums = [ + '049f5f50d1d27352d868cbb4b2a4b59bc0a913ef792b619c1adf1a289b3e48a7', # v1_12_0.tar.gz + 'fe7ef229baeba8a4ea2608f18f531ffbe31da16a274f7383e0d8e30d99e63e87', # SUMO-1.0.0_fix-link-flags.patch +] builddependencies = [ ('CMake', '3.22.1'), ('SWIG', '4.0.2'), + ('Java', '11', '', True), ] dependencies = [ ('Python', '3.9.6'), ('Xerces-C++', '3.2.3'), + ('FOX-Toolkit', '1.6.57'), ('GL2PS', '1.4.2'), ('GDAL', '3.3.2'), ('PROJ', '8.1.0'), - ('FoX', '4.1.2'), ] -separate_build_dir = True - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'SUMO_HOME': 'share/sumo', -} - +local_sumo_home = 'share/sumo' +local_pythonpath = 'lib/python%(pyshortver)s/site-packages' local_bins = ['activitygen', 'dfrouter', 'duarouter', 'emissionsDrivingCycle', 'emissionsMap', 'jtrrouter', - 'marouter', 'netconvert', 'netgenerate', 'od2trips', 'polyconvert', 'sumo'] + 'marouter', 'netconvert', 'netgenerate', 'od2trips', 'polyconvert', 'sumo', 'sumo-gui'] sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bins] + - ['lib/python%%(pyshortver)s/site-packages/libsumo/_libsumo.%s' % SHLIB_EXT], - 'dirs': ['bin', 'lib', 'share'], + ['%s/libsumo/_libsumo.%s' % (local_pythonpath, SHLIB_EXT)], + 'dirs': [local_sumo_home, local_pythonpath], } sanity_check_commands = [ @@ -51,4 +51,9 @@ sanity_check_commands = [ "python -c 'import libsumo'", ] +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'SUMO_HOME': 'share/sumo', +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb new file mode 100644 index 00000000000..17783cb2a67 --- /dev/null +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'SUMO' +version = '1.14.1' + +homepage = 'https://www.eclipse.org/sumo/' +description = """Simulation of Urban MObility" (SUMO) is an open source, highly portable, +microscopic and continuous traffic simulation package designed to handle large +networks. It allows for intermodal simulation including pedestrians and comes +with a large set of tools for scenario creation.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'eclipse' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%s.tar.gz' % version.replace('.', '_')] +patches = ['SUMO-1.0.0_fix-link-flags.patch'] +checksums = [ + '46ee6080902bb9056a1aa6fae72a270d7cfa44642487246760493b4742a2fd24', # v1_14_1.tar.gz + 'fe7ef229baeba8a4ea2608f18f531ffbe31da16a274f7383e0d8e30d99e63e87', # SUMO-1.0.0_fix-link-flags.patch +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('SWIG', '4.0.2'), + ('Java', '11', '', True), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Xerces-C++', '3.2.3'), + ('FOX-Toolkit', '1.6.57'), + ('GL2PS', '1.4.2'), + ('GDAL', '3.3.2'), + ('PROJ', '8.1.0'), +] + +local_sumo_home = 'share/sumo' +local_pythonpath = 'lib/python%(pyshortver)s/site-packages' +local_bins = ['activitygen', 'dfrouter', 'duarouter', 'emissionsDrivingCycle', 'emissionsMap', 'jtrrouter', + 'marouter', 'netconvert', 'netgenerate', 'od2trips', 'polyconvert', 'sumo', 'sumo-gui'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + + ['%s/libsumo/_libsumo.%s' % (local_pythonpath, SHLIB_EXT)], + 'dirs': [local_sumo_home, local_pythonpath], +} + +sanity_check_commands = [ + 'sumo --help', + "python -c 'import libsumo'", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'SUMO_HOME': 'share/sumo', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb index acdae5cac59..30e5d21317c 100644 --- a/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb @@ -4,47 +4,46 @@ name = 'SUMO' version = '1.7.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://sumo.dlr.de/' -description = """ -"Simulation of Urban MObility" (SUMO) is an open source, highly portable, microscopic and continuous traffic simulation -package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a -large set of tools for scenario creation. -""" +homepage = 'https://www.eclipse.org/sumo/' +description = """Simulation of Urban MObility" (SUMO) is an open source, highly portable, +microscopic and continuous traffic simulation package designed to handle large +networks. It allows for intermodal simulation including pedestrians and comes +with a large set of tools for scenario creation.""" toolchain = {'name': 'foss', 'version': '2020a'} source_urls = ['https://github.com/eclipse/sumo/archive/'] sources = ['v%s.tar.gz' % version.replace('.', '_')] -checksums = ['db0868318f2a602475a15ba8b83d30b686e6283b3ff753b9d112217529f2893b'] +patches = ['SUMO-1.0.0_fix-link-flags.patch'] +checksums = [ + 'db0868318f2a602475a15ba8b83d30b686e6283b3ff753b9d112217529f2893b', # v1_7_0.tar.gz + 'fe7ef229baeba8a4ea2608f18f531ffbe31da16a274f7383e0d8e30d99e63e87', # SUMO-1.0.0_fix-link-flags.patch +] builddependencies = [ ('CMake', '3.16.4'), ('SWIG', '4.0.1'), + ('Java', '11', '', True), ] dependencies = [ ('Python', '3.8.2'), ('Xerces-C++', '3.2.3'), + ('FOX-Toolkit', '1.6.57'), ('GL2PS', '1.4.2'), ('GDAL', '3.0.4', versionsuffix), ('PROJ', '7.0.0'), - ('FoX', '4.1.2'), ] -separate_build_dir = True - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'SUMO_HOME': 'share/sumo', -} - +local_sumo_home = 'share/sumo' +local_pythonpath = 'lib/python%(pyshortver)s/site-packages' local_bins = ['activitygen', 'dfrouter', 'duarouter', 'emissionsDrivingCycle', 'emissionsMap', 'jtrrouter', - 'marouter', 'netconvert', 'netgenerate', 'od2trips', 'polyconvert', 'sumo'] + 'marouter', 'netconvert', 'netgenerate', 'od2trips', 'polyconvert', 'sumo', 'sumo-gui'] sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bins] + - ['lib/python%%(pyshortver)s/site-packages/libsumo/_libsumo.%s' % SHLIB_EXT], - 'dirs': ['bin', 'lib', 'share'], + ['%s/libsumo/_libsumo.%s' % (local_pythonpath, SHLIB_EXT)], + 'dirs': [local_sumo_home, local_pythonpath], } sanity_check_commands = [ @@ -52,4 +51,9 @@ sanity_check_commands = [ "python -c 'import libsumo'", ] +modextrapaths = { + 'SUMO_HOME': local_sumo_home, + 'PYTHONPATH': local_pythonpath, +} + moduleclass = 'data' From 054d92d549752655d0ffef46a416fa6ae430a30d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 7 Aug 2022 21:14:02 +0200 Subject: [PATCH 4411/9987] download FOX-Toolkit sources using HTTP --- .../f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-11.2.0.eb | 2 +- .../f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-11.2.0.eb index b7051f48b64..d086f83d7f4 100644 --- a/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-11.2.0.eb @@ -12,7 +12,7 @@ images, and user-convenience features such as status line help, and tooltips.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['ftp://ftp.fox-toolkit.org/pub'] +source_urls = ['http://fox-toolkit.org/ftp'] sources = ['fox-%(version)s.tar.gz'] checksums = ['65ef15de9e0f3a396dc36d9ea29c158b78fad47f7184780357b929c94d458923'] diff --git a/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb index 8f0547f082c..3559c89032e 100644 --- a/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/f/FOX-Toolkit/FOX-Toolkit-1.6.57-GCCcore-9.3.0.eb @@ -12,7 +12,7 @@ images, and user-convenience features such as status line help, and tooltips.""" toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -source_urls = ['ftp://ftp.fox-toolkit.org/pub'] +source_urls = ['http://fox-toolkit.org/ftp'] sources = ['fox-%(version)s.tar.gz'] checksums = ['65ef15de9e0f3a396dc36d9ea29c158b78fad47f7184780357b929c94d458923'] From 241ce2312cf2e3e280939a2483f2435c528d49bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 Aug 2022 10:40:44 +0200 Subject: [PATCH 4412/9987] add missing SciPy-bundle dependency for rMATS-turbo --- .../easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb index 41bc0020a7b..9f2bd8d7260 100644 --- a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.1.1-foss-2020b.eb @@ -13,6 +13,7 @@ builddependencies = [ ] dependencies = [ ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), ('GSL', '2.6'), ('SAMtools', '1.11'), ('STAR', '2.7.6a'), From c179519dcada8cffc2c719f9d78ccff669ae0ed4 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 8 Aug 2022 10:56:54 +0100 Subject: [PATCH 4413/9987] adding easyconfigs: netCDF-Fortran-4.6.0-gompi-2022a.eb --- .../netCDF-Fortran-4.6.0-gompi-2022a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb new file mode 100644 index 00000000000..28ae1438dbe --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb @@ -0,0 +1,25 @@ +name = 'netCDF-Fortran' +version = '4.6.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8194aa70e400c0adfc456127c1d97af2c6489207171d13b10cd754a16da8b0ca'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [('netCDF', '4.9.0')] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' From bffdf61c662d23b80d3bdeedb84c3b435b7c496d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 8 Aug 2022 12:15:32 +0200 Subject: [PATCH 4414/9987] adding easyconfigs: ant-1.10.12-Java-17.eb --- .../easyconfigs/a/ant/ant-1.10.12-Java-17.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.12-Java-17.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.12-Java-17.eb b/easybuild/easyconfigs/a/ant/ant-1.10.12-Java-17.eb new file mode 100644 index 00000000000..9347a656859 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.12-Java-17.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'ant' +version = '1.10.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" + +toolchain = SYSTEM + +source_urls = ['https://archive.apache.org/dist/ant/binaries/'] +sources = ['apache-%(name)s-%(version)s-bin.tar.gz'] +checksums = ['4b3b557279bae4fb80210a5679180fdae3498b44cfd13368e3386e2a21dd853b'] + +dependencies = [('Java', '17')] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 087c29d86733a5510211ee47d8965519004a8e4e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 8 Aug 2022 11:58:48 +0100 Subject: [PATCH 4415/9987] Explicitly get the wannier source from the wannier github --- .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb | 4 ++-- .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb index 0736580b3ec..c97f01ec5e4 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb @@ -14,7 +14,6 @@ toolchainopts = {'usempi': True, 'openmp': True} source_urls = [ 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', 'https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/', - 'https://github.com/wannier-developers/wannier90/archive/' ] sources = [ { @@ -22,7 +21,8 @@ sources = [ 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', }, 'qe-gipaw-%(version)s.tar.gz', - {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, ] checksums = [ 'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6', # q-e-qe-7.1.tar.gz diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb index cde0d054be4..af352696e8e 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb @@ -14,7 +14,6 @@ toolchainopts = {'usempi': True, 'openmp': True} source_urls = [ 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', 'https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/', - 'https://github.com/wannier-developers/wannier90/archive/' ] sources = [ { @@ -22,7 +21,8 @@ sources = [ 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', }, 'qe-gipaw-%(version)s.tar.gz', - {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, ] checksums = [ 'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6', # q-e-qe-7.1.tar.gz From c26b34a4bc557c794045af29564ec5a0aae2b9c7 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 8 Aug 2022 12:00:36 +0100 Subject: [PATCH 4416/9987] Missing bzip2 added as suggested by branfosj --- .../n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb index 28ae1438dbe..062e4b796af 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb @@ -17,7 +17,10 @@ builddependencies = [ ('M4', '1.4.19'), ] -dependencies = [('netCDF', '4.9.0')] +dependencies = [ + ('netCDF', '4.9.0'), + ('bzip2', '1.0.8'), +] # (too) parallel build fails, but single-core build is fairly quick anyway (~1min) parallel = 1 From 9e685fa45406ace0febd5f1bb444a3eaeeb977cc Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 8 Aug 2022 12:35:09 +0100 Subject: [PATCH 4417/9987] Followed the suggestion to use -DUSE_GNU_INSTALL_CONVENTION=TRUE, removed modextrapath --- .../json-fortran-8.3.0-GCCcore-11.2.0.eb | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.2.0.eb index 500b78cafc8..ea4820fb0a6 100644 --- a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.2.0.eb @@ -19,17 +19,15 @@ builddependencies = [ ('CMake', '3.21.1'), ] +configopts = [ + '-DUSE_GNU_INSTALL_CONVENTION=TRUE', +] + runtest = 'check' sanity_check_paths = { - 'files': ['jsonfortran-gnu-8.3.0/lib/libjsonfortran.a', 'jsonfortran-gnu-8.3.0/lib/libjsonfortran.%s' % SHLIB_EXT], - 'dirs': ['jsonfortran-gnu-8.3.0/cmake'], -} - -modextrapaths = { - 'LD_LIBRARY_PATH': 'jsonfortran-gnu-8.3.0/lib', - 'LIBRARY_PATH': 'jsonfortran-gnu-8.3.0/lib', - 'CMAKE_PREFIX_PATH': 'jsonfortran-gnu-8.3.0/cmake', + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'dirs': ['include'], } moduleclass = 'lib' From fb437989bd35af57e8e207926f34f93e17f28f0a Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 8 Aug 2022 12:36:43 +0100 Subject: [PATCH 4418/9987] Updated how json-fortran is being dealt with (PR 15979) --- .../easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb | 2 +- easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb b/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb index a0a47f70b8e..1ff733e3434 100644 --- a/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb +++ b/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb @@ -23,7 +23,7 @@ patches = ['quickpic-makefile.patch'] checksums = [ '83d3664542ce0a1c1fa055802e214bdba98790ee512f1f2525d0c087d20d88af', # QuickPIC-20210224.tar.gz - '65afe170f89a9eb20ee9d47de147d736a2a25fcc6cc286be3f0b4d08fa17c415', # quickpic-makefile.patch + '3d0e8d2d746f5adec3f50ae7df6bf61de1e5ac4ca8f7ae7d3cf15b1eab57d8ec', # quickpic-makefile.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch b/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch index 588cbe1c158..4a834c6cf0f 100644 --- a/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch +++ b/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch @@ -9,8 +9,8 @@ index b2f08f0..c1538cf 100644 # name of the compiler -JSON_LIB = /usr/local/jsonfortran-gnu-6.3.0/lib/ -JSON_INC = /usr/local/jsonfortran-gnu-6.3.0/lib/ -+JSON_LIB = ${EBROOTJSONMINFORTRAN}/jsonfortran-gnu-8.3.0/lib -+JSON_INC = ${EBROOTJSONMINFORTRAN}/jsonfortran-gnu-8.3.0/lib ++JSON_LIB = ${EBROOTJSONMINFORTRAN}/lib ++JSON_INC = ${EBROOTJSONMINFORTRAN}/include FC_GF_OPENMPI = mpif90 -c -I$(JSON_INC) -fopenmp CC_GF_OPENMPI = mpicc -c -O3 -std=c99 From 97410d40fedfd0bcf8bfe105d66cb22a32ac5626 Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 8 Aug 2022 13:48:11 +0200 Subject: [PATCH 4419/9987] adding easyconfigs: VTK-9.2.0.rc2-foss-2022a.eb --- .../v/VTK/VTK-9.2.0.rc2-foss-2022a.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.2.0.rc2-foss-2022a.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.2.0.rc2-foss-2022a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.2.0.rc2-foss-2022a.eb new file mode 100644 index 00000000000..2fd6fa6575a --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.2.0.rc2-foss-2022a.eb @@ -0,0 +1,87 @@ +## +# Authors:: +# * Fotis Georgatos +# * Robert Mijakovic +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '9.2.0.rc2' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + '276f35541a46ef5963ae6667ee60b9cb19c9dc5cb28ae68db71fd8577620b0fc', # VTK-9.2.0.rc2.tar.gz + 'daf6c3ac947b3f1b7b6bfd6dfd17e0beb3df34816c9bab61c4b79294a800a2a3', # VTKData-9.1.0.tar.gz + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('XZ', '5.2.5'), + ('libGLU', '9.0.2'), + ('X11', '20220504'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + +moduleclass = 'vis' From 1d90d23e828f3685c5b0dee2672ccdf8cbf3a23e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 8 Aug 2022 13:56:50 +0200 Subject: [PATCH 4420/9987] adding easyconfigs: Embree-3.13.4.eb --- .../easyconfigs/e/Embree/Embree-3.13.4.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/e/Embree/Embree-3.13.4.eb diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.13.4.eb b/easybuild/easyconfigs/e/Embree/Embree-3.13.4.eb new file mode 100644 index 00000000000..c78954aadaa --- /dev/null +++ b/easybuild/easyconfigs/e/Embree/Embree-3.13.4.eb @@ -0,0 +1,21 @@ +easyblock = 'Tarball' + +name = 'Embree' +version = '3.13.4' + +homepage = 'https://embree.github.io' +description = "High Performance Ray Tracing Kernels" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.x86_64.linux.tar.gz'] +checksums = ['c9a7e9977e170a693117c3521f28152a6e2f2904ab28156a7a8baee339f96c43'] + +sanity_check_paths = { + 'files': ['bin/convert', 'include/embree3/rtcore.h', + 'include/embree3/rtcore_common.h', 'lib64/libembree3.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/embree3', 'lib64/cmake', 'share/man/man3'], +} + +moduleclass = 'vis' From ff9d2f1f6fb14ea00fe8159fe432e31af8f93038 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 8 Aug 2022 14:19:50 +0200 Subject: [PATCH 4421/9987] Fix checksum --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index f5772f50f24..170cb7b35b9 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -27,7 +27,7 @@ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] checksums = [ - '92f87fd769867a12dc0bda9778a2ec5319249bc335cbda87043a873d9139088d', # v4.4.tar.gz + '5332c78f5ea8d1a4475c7cd749e8f22a40b4cc5290bdf0c1c9fb051c8e6e9037', # v4.4.tar.gz '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch ] From 0d01c7e0710c67fc69218961356dde00583a1e64 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 8 Aug 2022 13:38:55 +0100 Subject: [PATCH 4422/9987] restore ploteig in EIGENSOFT 7.2.1 --- .../e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2018b.eb | 10 +- .../e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2019a.eb | 10 +- .../e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2019b.eb | 10 +- .../e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb | 10 +- .../EIGENSOFT/EIGENSOFT-7.2.1-intel-2019a.eb | 10 +- .../EIGENSOFT-7.2.1_restore-ploteig.patch | 234 ++++++++++++++++++ 6 files changed, 269 insertions(+), 15 deletions(-) create mode 100644 easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1_restore-ploteig.patch diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2018b.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2018b.eb index 185743cf6a6..a759779e0b1 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2018b.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2018b.eb @@ -26,10 +26,14 @@ toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/DReichLab/EIG/archive'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_Fix_makefile_openblas.patch'] +patches = [ + '%(name)s-%(version)s_Fix_makefile_openblas.patch', + ('%(name)s-%(version)s_restore-ploteig.patch', 0), +] checksums = [ 'f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650', # v7.2.1.tar.gz 'e49e3754f2326210114fe5a731a77c7ffd240c8a9134eb8e8e1517bfe06c71e1', # EIGENSOFT-7.2.1_Fix_makefile_openblas.patch + '8a7a0273ae4d0d3ec0c9927facd41a1a43b8540725af3bd06e007cd86afaf9e0', # EIGENSOFT-7.2.1_restore-ploteig.patch ] dependencies = [ @@ -44,10 +48,10 @@ buildopts = ' && make install' files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] -fix_perl_shebang_for = ['bin/*.perl'] +fix_perl_shebang_for = ['bin/*.perl', 'bin/ploteig'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL", "ploteig"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2019a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2019a.eb index c6554e9d20e..fc4c22c0c96 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2019a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2019a.eb @@ -23,10 +23,14 @@ toolchain = {'name': 'foss', 'version': '2019a'} source_urls = ['https://github.com/DReichLab/EIG/archive'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_Fix_makefile_openblas.patch'] +patches = [ + '%(name)s-%(version)s_Fix_makefile_openblas.patch', + ('%(name)s-%(version)s_restore-ploteig.patch', 0), +] checksums = [ 'f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650', # v7.2.1.tar.gz 'e49e3754f2326210114fe5a731a77c7ffd240c8a9134eb8e8e1517bfe06c71e1', # EIGENSOFT-7.2.1_Fix_makefile_openblas.patch + '8a7a0273ae4d0d3ec0c9927facd41a1a43b8540725af3bd06e007cd86afaf9e0', # EIGENSOFT-7.2.1_restore-ploteig.patch ] dependencies = [ @@ -41,10 +45,10 @@ buildopts = ' && make install' files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] -fix_perl_shebang_for = ['bin/*.perl'] +fix_perl_shebang_for = ['bin/*.perl', 'bin/ploteig'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL", "ploteig"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2019b.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2019b.eb index 928fcacc43a..c8b8ea7f661 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2019b.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2019b.eb @@ -26,10 +26,14 @@ toolchain = {'name': 'foss', 'version': '2019b'} source_urls = ['https://github.com/DReichLab/EIG/archive'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_Fix_makefile_openblas.patch'] +patches = [ + '%(name)s-%(version)s_Fix_makefile_openblas.patch', + ('%(name)s-%(version)s_restore-ploteig.patch', 0), +] checksums = [ 'f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650', # v7.2.1.tar.gz 'e49e3754f2326210114fe5a731a77c7ffd240c8a9134eb8e8e1517bfe06c71e1', # EIGENSOFT-7.2.1_Fix_makefile_openblas.patch + '8a7a0273ae4d0d3ec0c9927facd41a1a43b8540725af3bd06e007cd86afaf9e0', # EIGENSOFT-7.2.1_restore-ploteig.patch ] dependencies = [ @@ -44,10 +48,10 @@ buildopts = ' && make install' files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] -fix_perl_shebang_for = ['bin/*.perl'] +fix_perl_shebang_for = ['bin/*.perl', 'bin/ploteig'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL", "ploteig"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb index 946ae3d37a6..f120ac870b6 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2021a.eb @@ -26,10 +26,14 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/DReichLab/EIG/archive'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_Fix_makefile_openblas.patch'] +patches = [ + '%(name)s-%(version)s_Fix_makefile_openblas.patch', + ('%(name)s-%(version)s_restore-ploteig.patch', 0), +] checksums = [ 'f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650', # v7.2.1.tar.gz 'e49e3754f2326210114fe5a731a77c7ffd240c8a9134eb8e8e1517bfe06c71e1', # EIGENSOFT-7.2.1_Fix_makefile_openblas.patch + '8a7a0273ae4d0d3ec0c9927facd41a1a43b8540725af3bd06e007cd86afaf9e0', # EIGENSOFT-7.2.1_restore-ploteig.patch ] dependencies = [ @@ -44,10 +48,10 @@ buildopts = 'LDLIBS="-lgsl $LIBBLAS -llapacke $LIBS" && make install' files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] -fix_perl_shebang_for = ['bin/*.perl'] +fix_perl_shebang_for = ['bin/*.perl', 'bin/ploteig'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL", "ploteig"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-intel-2019a.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-intel-2019a.eb index 12dbbc84f75..d1a248f2e08 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-intel-2019a.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-intel-2019a.eb @@ -23,10 +23,14 @@ toolchain = {'name': 'intel', 'version': '2019a'} source_urls = ['https://github.com/DReichLab/EIG/archive'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_Use_mkl.patch'] +patches = [ + '%(name)s-%(version)s_Use_mkl.patch', + ('%(name)s-%(version)s_restore-ploteig.patch', 0), +] checksums = [ 'f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650', # v7.2.1.tar.gz 'e18c91afedec928ebedb05bc13e91baa13973dde60006af88666c40a37248f31', # EIGENSOFT-7.2.1_Use_mkl.patch + '8a7a0273ae4d0d3ec0c9927facd41a1a43b8540725af3bd06e007cd86afaf9e0', # EIGENSOFT-7.2.1_restore-ploteig.patch ] dependencies = [ @@ -41,10 +45,10 @@ buildopts = ' && make install' files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] -fix_perl_shebang_for = ['bin/*.perl'] +fix_perl_shebang_for = ['bin/*.perl', 'bin/ploteig'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL", "ploteig"]], 'dirs': [] } diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1_restore-ploteig.patch b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1_restore-ploteig.patch new file mode 100644 index 00000000000..5a382a99919 --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1_restore-ploteig.patch @@ -0,0 +1,234 @@ +From 7a6036bf36d8d2ed038b83d26112cdde4f383747 Mon Sep 17 00:00:00 2001 +From: Matthew Mah +Date: Mon, 5 Mar 2018 15:14:52 -0500 +Subject: [PATCH] Restore ploteig in bin directory with Nick's version. Fixes + #25. + +--- + bin/ploteig | 217 ++++++++++++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 217 insertions(+) + create mode 100755 bin/ploteig + +diff --git a/bin/ploteig b/bin/ploteig +new file mode 100755 +index 0000000..0871daa +--- /dev/null ++++ bin/ploteig +@@ -0,0 +1,217 @@ ++#!/usr/local/bin/perl -w ++ ++### ploteig -i eigfile -p pops -c a:b [-t title] [-s stem] [-g gstem] [-o outfile] [-x] [-k] [-y] [-z sep] -r colorstring -m xmul -n ymul ++use Getopt::Std ; ++use File::Basename ; ++ ++## pops : separated -x = make postscript and pdf -z use another separator ++## -k keep intermediate files ++## NEW if pops is a file names are read one per line ++## scaling on x, y axes ++ ++getopts('i:o:p:c:s:d:z:t:r:m:n:g:xkyq',\%opts) ; ++$postscmode = $opts{"x"} ; ++$oldkeystyle = $opts{"y"} ; ++$nopoptitle = $opts{"q"} ; ++$kflag = $opts{"k"} ; ++$keepflag = 1 if ($kflag) ; ++$keepflag = 1 unless ($postscmode) ; ++ ++$zsep = ":" ; ++if (defined $opts{"z"}) { ++ $zsep = $opts{"z"} ; ++ $zsep = "\+" if ($zsep eq "+") ; ++} ++ ++if (defined $opts{"r"}) { ++ $colorstr = $opts{"r"} ; ++ setcolor($colorstr) ; ++} ++$xmul = $opts{"m"} ; ++$xmul = 1 unless (defined $xmul) ; ++ ++$ymul = $opts{"n"} ; ++$ymul = 1 unless (defined $ymul) ; ++ ++$title = "" ; ++if (defined $opts{"t"}) { ++ $title = $opts{"t"} ; ++} ++if (defined $opts{"i"}) { ++ $infile = $opts{"i"} ; ++} ++else { ++ usage() ; ++ exit 0 ; ++} ++ ++open (FF, $infile) || die "can't open $infile\n" ; ++@L = () ; ++chomp @L ; ++$nf = 0 ; ++foreach $line (@L) { ++ next if ($line =~ /\#/) ; ++ @Z = split " ", $line ; ++ $x = @Z ; ++ $nf = $x if ($nf < $x) ; ++} ++printf "## number of fields: %d\n", $nf ; ++$popcol = $nf-1 ; ++ ++ ++if (defined $opts{"p"}) { ++ $pops = $opts{"p"} ; ++} ++else { ++ die "p parameter compulsory\n" ; ++} ++ ++$popsname = setpops ($pops) ; ++print "$popsname\n" ; ++ ++$c1 = 1; $c2 =2 ; ++if (defined $opts{"c"}) { ++ $cols = $opts{"c"} ; ++ ($c1, $c2) = split ":", $cols ; ++ die "bad c param: $cols\n" unless (defined $cols) ; ++} ++ ++$stem = "$infile.$c1:$c2" ; ++if (defined $opts{"s"}) { ++ $stem = $opts{"s"} ; ++} ++ ++if (defined $opts{"g"}) { ++ $stem = $gstem = $opts{"g"} ; ++} ++ ++$gstem = "$stem.$popsname" unless (defined $gstem) ; ++$gnfile = "$gstem.xtxt" ; ++ ++if (defined $opts{"o"}) { ++ $gnfile = $opts{"o"} ; ++} ++ ++ ++@T = () ; ## trash ++open (GG, ">$gnfile") || die "can't open $gnfile\n" ; ++print GG "## " unless ($postscmode) ; ++print GG "set terminal postscript color noenhanced\n" ; ++print GG "set title \"$title\" \n" ; ++print GG "set key outside\n" unless ($oldkeystyle) ; ++print GG "set xlabel \"eigenvector $c1\" \n" if ($xmul == 1) ; ++print GG "set xlabel \"eigenvector $c1 (* $xmul) \" \n" if ($xmul != 1) ; ++print GG "set ylabel \"eigenvector $c2\" \n" if ($ymul == 1) ; ++print GG "set ylabel \"eigenvector $c1 (* $ymul) \" \n" if ($ymul != 1) ; ++print GG "plot " ; ++$np = @P ; ++$lastpop = $P[$np-1] ; ++$d1 = $c1+1 ; ++$d2 = $c2+1 ; ++foreach $pop (@P) { ++ $dfile = "$stem:$pop" ; ++ push @T, $dfile ; ++ print GG " \"$dfile\" using (\$$d1)*$xmul:(\$$d2)*$ymul " ; ++ print GG "notitle " if (defined $nopoptitle) ; ++ print GG "title \"$pop\" " unless (defined $nopoptitle) ; ++ if (defined $COL{$pop}) { ++ $color = $COL{$pop} ; ++ print GG "lt rgb \"$color\" " ; ++ } ++ print GG ", \\\n" unless ($pop eq $lastpop) ; ++ open (YY, ">$dfile") || die "can't open $dfile\n" ; ++ foreach $line (@L) { ++ next if ($line =~ /\#/) ; ++ @Z = split " ", $line ; ++ next unless (defined $Z[$popcol]) ; ++ next unless ($Z[$popcol] eq $pop) ; ++ print YY "$line\n" ; ++ } ++ close YY ; ++} ++print GG "\n" ; ++print GG "## " if ($postscmode) ; ++print GG "pause 9999\n" ; ++close GG ; ++ ++if ($postscmode) { ++$psfile = "$stem.ps" ; ++ ++ if ($gnfile =~ /xtxt/) { ++ $psfile = $gnfile ; ++ $psfile =~ s/xtxt/ps/ ; ++ } ++system "gnuplot < $gnfile > $psfile" ; ++system "/home/np29/bin/fixgreen $psfile" ; ++system "ps2pdf $psfile " ; ++} ++unlink (@T) unless $keepflag ; ++ ++sub setcolor { ++ my ($colorst) = @_ ; ++ local ($cp, $pop, $color, @CP, $line) ; ++ if (-r $colorst) { ++ open (C1, $colorst) || die "can't open $colorst\n" ; ++ foreach $line () { ++ chomp $line ; ++ ($pop, $color) = split " ", $line ; ++ next if ($pop =~ /\#/) ; ++ next unless (defined $color) ; ++ print STDERR "setting color for $pop to $color\n" ; ++ $COL{$pop} = $color ; ++ } ++ close C1 ; ++ return ; ++ } ++ ++ @CP = split " ", $colorst ; ++ foreach $cp (@CP) { ++ ($pop, $color) = split ":", $cp ; ++ $COL{$pop} = $color ; ++ } ++} ++ ++sub usage { ++ ++print "ploteig -i eigfile -p pops -c a:b [-t title] [-s stem] [-o outfile] [-x] [-k] -c colorstringh [-m xmul] [-n ymul]\n" ; ++print "-i eigfile input file first col indiv-id last col population\n" ; ++print "## as output by smartpca in outputvecs \n" ; ++print "-c a:b a, b columns to plot. 1:2 would be common and leading 2 eigenvectors\n" ; ++print "-p pops Populations to plot. : delimited. eg -p Bantu:San:French\n" ; ++print "## pops can also be a filename. List populations 1 per line\n" ; ++print "[-s stem] stem will start various output files\n" ; ++print "[-o ofile] ofile will be gnuplot control file. Should have xtxt suffix\n"; ++print "[-x] make ps and pdf files\n" ; ++print "[-k] keep various intermediate files although -x set\n" ; ++print "## necessary if .xtxt file is to be hand edited\n" ; ++print "[-r colorstringpairs or colorstringfile]\n" ; ++print "[-g gstem] make gstem.xtxt gstem.ps gstem.pdf \n" ; ++print "[-y] put key at top right inside box (old mode)\n" ; ++print "[-t] title (legend)\n" ; ++ ++print "The xtxt file is a gnuplot file and can be easily hand edited. Intermediate files ++needed if you want to make your own plot\n" ; ++ ++} ++sub setpops { ++ my ($pops) = @_ ; ++ local (@a, $d, $b, $e) ; ++ ++ if (-e $pops) { ++ open (FF1, $pops) || die "can't open $pops\n" ; ++ @P = () ; ++ foreach $line () { ++ ($a) = split " ", $line ; ++ next unless (defined $a) ; ++ next if ($a =~ /\#/) ; ++ push @P, $a ; ++ } ++ $out = join ":", @P ; ++ print "## pops: $out\n" ; ++ ($b, $d , $e) = fileparse($pops) ; ++ return $b ; ++ } ++ @P = split $zsep, $pops ; ++ return $pops ; ++ ++} From 854cafc23fd4bd821da55210cdd0a0b003b2813e Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 8 Aug 2022 14:00:56 +0100 Subject: [PATCH 4423/9987] adding easyconfigs: Stacks-2.62-foss-2022a.eb --- .../s/Stacks/Stacks-2.62-foss-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-2.62-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.62-foss-2022a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.62-foss-2022a.eb new file mode 100644 index 00000000000..01eb7de7001 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.62-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '2.62' + +homepage = 'https://catchenlab.life.illinois.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, + for the purpose of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['01c814588fd72c13494785af49123a6a2c20495c924ed84965fdd4e0da1ab524'] + +dependencies = [ + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['bin/clone_filter', 'bin/cstacks', 'bin/gstacks', 'bin/kmer_filter', 'bin/phasedstacks', + 'bin/populations', 'bin/process_radtags', 'bin/process_shortreads', 'bin/sstacks', + 'bin/tsv2bam', 'bin/ustacks'], + 'dirs': [], +} + +moduleclass = 'bio' From 93d7d959c409b4f625ba2ff50201f976d6b13959 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 Aug 2022 15:19:05 +0200 Subject: [PATCH 4424/9987] adding easyconfigs: Transformers-4.21.1-foss-2021b.eb --- .../Transformers-4.21.1-foss-2021b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/t/Transformers/Transformers-4.21.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.21.1-foss-2021b.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.21.1-foss-2021b.eb new file mode 100644 index 00000000000..0cc43982c0b --- /dev/null +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.21.1-foss-2021b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'Transformers' +version = '4.21.1' + +homepage = 'https://github.com/huggingface/transformers' +description = """ +State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('PyYAML', '5.4.1'), + ('typing-extensions', '3.10.0.2'), # needed by huggingface-hub + ('tqdm', '4.62.3'), +] + +use_pip = True + +exts_list = [ + ('regex', '2022.7.25', { + 'checksums': ['bd0883e86964cd61360ffc36dbebbc49b928e92a306f886eab02c11dfde5b7aa'], + }), + ('sacremoses', '0.0.53', { + 'checksums': ['43715868766c643b35de4b8046cce236bfe59a7fa88b25eaf6ddf02bacf53a7a'], + }), + ('tokenizers', '0.12.1', { + 'source_tmpl': 'tokenizers-%(version)s-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl', + 'checksums': ['619728df2551bdfe6f96ff177f9ded958e7ed9e2af94c8d5ac2834d1eb06d112'], + }), + ('huggingface-hub', '0.8.1', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['75c70797da54b849f06c2cbf7ba2217250ee217230b9f65547d5db3c5bd84bb5'], + }), + ('transformers', version, { + 'checksums': ['20f895d7304a5c7f5af099f9300b326819df9cf2167cdfb754450facc0e094f6'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From b919902acefb07147402a6fcdb73e86bf69a649e Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 8 Aug 2022 16:10:49 +0200 Subject: [PATCH 4425/9987] Update LAMMPS 23Jun2022 for latest bugfix sources --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb | 4 ++-- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb index 527e492d2e8..97db9f89110 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb @@ -20,9 +20,9 @@ toolchainopts = {'openmp': True, 'usempi': True} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] sources = [ - 'stable_%(version)s.tar.gz', + 'stable_%(version)s_update1.tar.gz', ] -checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] +checksums = ['58e3b2b984f8935bb0db5631e143be2826c45ffd48844f7c394f36624a3e17a2'] builddependencies = [ ('CMake', '3.20.1'), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb index b0325d03e75..d96efa6f439 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb @@ -19,8 +19,8 @@ toolchainopts = {'openmp': True, 'usempi': True} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] -sources = ['stable_%(version)s.tar.gz'] -checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] +sources = ['stable_%(version)s_update1.tar.gz'] +checksums = ['58e3b2b984f8935bb0db5631e143be2826c45ffd48844f7c394f36624a3e17a2'] builddependencies = [ ('CMake', '3.22.1'), From 4f7fb13eb07f173ca0c0dfcc9c720a792ffe49f2 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 8 Aug 2022 16:15:00 +0200 Subject: [PATCH 4426/9987] Update to latest sources --- .../LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb | 4 ++-- .../LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb | 6 ++++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb index 896102f3284..ccd6b3b79e2 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos-CUDA-11.3.1.eb @@ -22,9 +22,9 @@ toolchainopts = {'openmp': True, 'usempi': True} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] sources = [ - 'stable_%(version)s.tar.gz', + 'stable_%(version)s_update1.tar.gz', ] -checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] +checksums = ['58e3b2b984f8935bb0db5631e143be2826c45ffd48844f7c394f36624a3e17a2'] builddependencies = [ ('CMake', '3.20.1'), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb index cb5942ff543..aeba49e36ce 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb @@ -21,8 +21,10 @@ toolchainopts = {'openmp': True, 'usempi': True} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] -sources = ['stable_%(version)s.tar.gz'] -checksums = ['d27ede095c9f00cd13a26f967a723d07cf8f4df65c700ed73573577bc173d5ce'] +sources = [ + 'stable_%(version)s_update1.tar.gz', +] +checksums = ['58e3b2b984f8935bb0db5631e143be2826c45ffd48844f7c394f36624a3e17a2'] builddependencies = [ ('CMake', '3.22.1'), From 2d752ab95491f9f719b67cb4cb72eb44bc5e61cb Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 8 Aug 2022 15:52:46 +0100 Subject: [PATCH 4427/9987] adding easyconfigs: ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb --- .../ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb new file mode 100644 index 00000000000..5c290512f99 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Java', '11', '', True)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +sanity_check_commands = ["antlr --help"] + +moduleclass = 'tools' From 0e1b1f0583615fbac0453f9716a82fb41e1286a5 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 8 Aug 2022 17:14:54 +0200 Subject: [PATCH 4428/9987] Update WRF-4.4-foss-2022a-dmpar.eb --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index 170cb7b35b9..8fdfe98201a 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -27,7 +27,6 @@ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] checksums = [ - '5332c78f5ea8d1a4475c7cd749e8f22a40b4cc5290bdf0c1c9fb051c8e6e9037', # v4.4.tar.gz '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch ] From a936a47145adc3524a1d6f9038cad84e87bae641 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 8 Aug 2022 15:16:51 +0000 Subject: [PATCH 4429/9987] Update Java 11 and 17 --- easybuild/easyconfigs/j/Java/Java-11.0.16.eb | 29 ++++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-11.eb | 12 ++------ easybuild/easyconfigs/j/Java/Java-17.0.4.eb | 29 ++++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-17.eb | 2 +- 4 files changed, 61 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/j/Java/Java-11.0.16.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-17.0.4.eb diff --git a/easybuild/easyconfigs/j/Java/Java-11.0.16.eb b/easybuild/easyconfigs/j/Java/Java-11.0.16.eb new file mode 100644 index 00000000000..731f003e8ab --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-11.0.16.eb @@ -0,0 +1,29 @@ +name = 'Java' +version = '11.0.16' +local_build = '8' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + 'f79506f80c796d8e6a382f00bd8c528a330c5e29581aaf5cb61e1831742d166f', + local_tarball_tmpl % ('aarch64', local_build): + 'bb345cabf3e305ff3ce390918d5f69e5cfbced3d9844e0b0531c2690f9ed06ef', + local_tarball_tmpl % ('ppc64le', local_build): + '40dea12da26443ad731f9348187b65451711659337e83b6409a2bcf0f057cd2a', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-11.eb b/easybuild/easyconfigs/j/Java/Java-11.eb index 9d3c3075a85..640b836dd2c 100644 --- a/easybuild/easyconfigs/j/Java/Java-11.eb +++ b/easybuild/easyconfigs/j/Java/Java-11.eb @@ -1,7 +1,3 @@ -# Contribution from the Crick HPC team -# uploaded by J. Sassmannshausen -# updated to version 202 - easyblock = 'ModuleRC' name = 'Java' @@ -9,14 +5,10 @@ version = '11' homepage = 'https://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy - Java applications on desktops and servers.""" +Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [ - ('Java', {'arch=x86_64': '%(version)s.0.2', - 'arch=AArch64': '%(version)s.0.8-aarch64', - 'arch=POWER': '%(version)s.0.6-ppc64le'}), -] +dependencies = [('Java', '%(version)s.0.4')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.4.eb b/easybuild/easyconfigs/j/Java/Java-17.0.4.eb new file mode 100644 index 00000000000..a321f73ee89 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-17.0.4.eb @@ -0,0 +1,29 @@ +name = 'Java' +version = '17.0.4' +local_build = '8' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + 'c0851d610b03cb51e9b360fef3e9ec2026c62837a143e7786649ba94f38cc0d1', + local_tarball_tmpl % ('aarch64', local_build): + '8c23b0b9c65cfe223a07edb8752026afd1e8ec1682630c2d92db4dd5aa039204', + local_tarball_tmpl % ('ppc64le', local_build): + 'e80a0f6626bd28ea20c43524b3ab10af48b3789317aea5b7019c146fe6268d94', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-17.eb b/easybuild/easyconfigs/j/Java/Java-17.eb index 05f26251775..b5936b5a154 100644 --- a/easybuild/easyconfigs/j/Java/Java-17.eb +++ b/easybuild/easyconfigs/j/Java/Java-17.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.0.2')] +dependencies = [('Java', '%(version)s.0.4')] moduleclass = 'lang' From b8b76806748d8fc9bed0b01d6e9360a486941163 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 8 Aug 2022 17:24:57 +0200 Subject: [PATCH 4430/9987] Update easybuild/easyconfigs/j/Java/Java-11.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/j/Java/Java-11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-11.eb b/easybuild/easyconfigs/j/Java/Java-11.eb index 640b836dd2c..d53c0b9b2f5 100644 --- a/easybuild/easyconfigs/j/Java/Java-11.eb +++ b/easybuild/easyconfigs/j/Java/Java-11.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.0.4')] +dependencies = [('Java', '%(version)s.0.16')] moduleclass = 'lang' From 840c2593870ff11da7dc7d8a2a0fbf34122140fd Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 8 Aug 2022 17:32:37 +0200 Subject: [PATCH 4431/9987] Update WRF-4.4-foss-2022a-dmpar.eb --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index 8fdfe98201a..b59ecf9d60f 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -26,9 +26,11 @@ sources = [{ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] -checksums = [ - '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch -] +# The problem: sources from git clone have different checksum every time +# checksums = [ +# '0d68df19766ad03041126c1531cb115e2d2a69043df96314fd30d897cfca9e4c', # v4.4.tar.gz +# '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch +# ] # csh is used by WRF install scripts builddependencies = [ From a7db65078e497326f319f54bf67960095d4a591e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 8 Aug 2022 17:58:30 +0200 Subject: [PATCH 4432/9987] fix long line --- easybuild/easyconfigs/j/Java/Java-11.0.16.eb | 3 ++- easybuild/easyconfigs/j/Java/Java-17.0.4.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/Java/Java-11.0.16.eb b/easybuild/easyconfigs/j/Java/Java-11.0.16.eb index 731f003e8ab..54edbc4e9f1 100644 --- a/easybuild/easyconfigs/j/Java/Java-11.0.16.eb +++ b/easybuild/easyconfigs/j/Java/Java-11.0.16.eb @@ -12,7 +12,8 @@ local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version # Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions -source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' % local_build] +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] checksums = [ diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.4.eb b/easybuild/easyconfigs/j/Java/Java-17.0.4.eb index a321f73ee89..2fed82fb259 100644 --- a/easybuild/easyconfigs/j/Java/Java-17.0.4.eb +++ b/easybuild/easyconfigs/j/Java/Java-17.0.4.eb @@ -12,7 +12,8 @@ local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version # Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions -source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' % local_build] +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] checksums = [ From 2a8c7eeed6398f53a1b2ed16cd9970c24cafd508 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 8 Aug 2022 22:34:17 +0200 Subject: [PATCH 4433/9987] Update easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb index 3a3cc7ce5b1..21756d0af91 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb @@ -33,7 +33,7 @@ dependencies = [ # make would create just static libcfitsio.a. # Let's create dynamic lib and testprog too. -#buildopts = '&& make shared && make testprog' +# buildopts = '&& make shared && make testprog' configopts = [ "-DBUILD_SHARED_LIBS=OFF -DTESTS=ON", From f3791d09145aea036bfcfe69dd8c36038b9497ce Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Tue, 9 Aug 2022 10:05:55 +0200 Subject: [PATCH 4434/9987] Incorporating sanity_check_commands Thanks @bedroge, your suggestion of using `2>&1` before `grep` did the trick and the installation was successful --- .../Phantompeakqualtools-1.2.2-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb index b3a80768f53..841410ab2b3 100644 --- a/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/p/Phantompeakqualtools/Phantompeakqualtools-1.2.2-foss-2021b.eb @@ -50,4 +50,8 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'run_spp.R 2>&1 | grep "Usage: Rscript run_spp.R "', +] + moduleclass = 'bio' From d769e5165dc1125a70eee0e7fcfcc8bb990ab55b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 9 Aug 2022 12:29:39 +0200 Subject: [PATCH 4435/9987] adding easyconfigs: lxml-4.9.1-GCCcore-11.3.0.eb --- .../l/lxml/lxml-4.9.1-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/lxml/lxml-4.9.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.9.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.9.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b66852ade85 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-4.9.1-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '4.9.1' + +homepage = 'https://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['fe749b052bb7233fe5d072fcb549221a8cb1a16725c47c37e42b0b9cb3ff2c3f'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('libxml2', '2.9.13'), + ('libxslt', '1.1.34'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From a6e7ab092747b48cb412b7b6a9f7f45fe516b7da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 9 Aug 2022 13:06:26 +0200 Subject: [PATCH 4436/9987] Update easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb Co-authored-by: SebastianAchilles --- .../easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb index b15aaf2ae7d..2ed04d457b6 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -36,7 +36,7 @@ configopts = [ ] sanity_check_paths = { - 'files': ['lib/libmagma.so', 'lib/libmagma.a'], + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], 'dirs': ['include'], } From ff5ba6f3f3fcae57568c351e9edf41fac417786f Mon Sep 17 00:00:00 2001 From: alin m elena Date: Tue, 9 Aug 2022 12:55:31 +0100 Subject: [PATCH 4437/9987] [cp2k] add cp2k 9.1 and 2022.1 to foss 2022a --- .../c/CP2K/CP2K-2022.1-foss-2022a.eb | 40 +++++++++++++++++++ .../easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb | 39 ++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb new file mode 100644 index 00000000000..3521d55a090 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb @@ -0,0 +1,40 @@ +## +# Author: Robert Mijakovic +## +name = 'CP2K' +version = '2022.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2c34f1a7972973c62d471cd35856f444f11ab22f2ff930f6ead20f3454fd228b'] + +# https://github.com/cp2k/cp2k/releases/download/v2022.1/cp2k-2022.1.tar.bz2 +dependencies = [ + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '5.2.3'), + ('libxsmm', '1.17'), + ('FFTW', '3.3.10'), + ('PLUMED', '2.8.0'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb new file mode 100644 index 00000000000..b2e72836ed6 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb @@ -0,0 +1,39 @@ +## +# Author: Robert Mijakovic +## +name = 'CP2K' +version = '9.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['fedb4c684a98ad857cd49b69a3ae51a73f85a9c36e9cb63e3b02320c74454ce6'] + +dependencies = [ + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '5.2.3'), + ('libxsmm', '1.17'), + ('FFTW', '3.3.10'), + ('PLUMED', '2.8.0'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' From 68df9d6f35306cc5dd39e278b62e9337dc957ffe Mon Sep 17 00:00:00 2001 From: alin m elena Date: Tue, 9 Aug 2022 13:17:43 +0100 Subject: [PATCH 4438/9987] deps for cp2k 2022a --- .../Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb | 52 ++++++++++++++++ .../l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb | 27 +++++++++ .../p/PLUMED/PLUMED-2.8.0-foss-2022a.eb | 60 +++++++++++++++++++ 3 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb new file mode 100644 index 00000000000..a992dd7921d --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb @@ -0,0 +1,52 @@ +## +# Author: Robert Mijakovic +## +name = 'Libint' +version = '2.6.0' +local_lmax = 6 +# custom configuration, to be used as dependency for CP2K +versionsuffix = '-lmax-%s-cp2k' % local_lmax + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/evaleev/libint/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch', + 'Libint-2.6.0_remove-test-eri.patch', +] +checksums = [ + '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz + # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch + 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', + # Libint-2.6.0_remove-test-eri.patch + 'e47868901250078adeb35b80ab866ba8063ad9756881d1b557cb925334df653b', +] + +builddependencies = [ + ('Autotools', '20220317'), + ('GMP', '6.2.1'), + ('Boost', '1.79.0'), + ('Eigen', '3.4.0'), + ('Python', '3.10.4'), +] + +# configure options as required by CP2K, +# see Jenkinsfile in https://github.com/cp2k/libint-cp2k +local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) +local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) + +libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax +libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am +libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--enable-generic-code --disable-unrolling' + +with_fortran = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb new file mode 100644 index 00000000000..9fbbdba6329 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.17' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb new file mode 100644 index 00000000000..8775e1beada --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb @@ -0,0 +1,60 @@ +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.8.0' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['24b243c531fa83752be5e54f5f0b677164855da539bc2b2c5b00dcc9f192aa82'] + +builddependencies = [ + ('xxd', '8.2.4220'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('GSL', '2.7'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' From 6e65170ef3b3c4ae3a7dec9ae753041effd11fee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 9 Aug 2022 14:23:45 +0200 Subject: [PATCH 4439/9987] Remove unnecessary lines, fix module class --- .../easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb | 7 +------ .../easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb | 7 +------ 2 files changed, 2 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb index 5ef66f2d34d..64d2a0bc9d1 100644 --- a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb +++ b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-foss-2019a.eb @@ -33,10 +33,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -configopts = '-DCMAKE_BUILD_TYPE=Release' - -separate_build_dir = True - runtest = 'test' sanity_check_paths = { @@ -47,5 +43,4 @@ sanity_check_paths = { 'dirs': ['share/doc/crystfel/scripts/'] } - -moduleclass = 'vis' +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb index 4d48b784031..a0ae2b7bb56 100644 --- a/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb +++ b/easybuild/easyconfigs/c/CrystFEL/CrystFEL-0.8.0-intel-2019a.eb @@ -33,10 +33,6 @@ dependencies = [ ('zlib', '1.2.11'), ] -configopts = '-DCMAKE_BUILD_TYPE=Release' - -separate_build_dir = True - runtest = 'test' sanity_check_paths = { @@ -47,5 +43,4 @@ sanity_check_paths = { 'dirs': ['share/doc/crystfel/scripts/'] } - -moduleclass = 'vis' +moduleclass = 'phys' From bdfc8f23c9c1687aacb973777d434dee64dd1de6 Mon Sep 17 00:00:00 2001 From: alin m elena Date: Tue, 9 Aug 2022 13:36:16 +0100 Subject: [PATCH 4440/9987] needed by plumed --- .../x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3aa02fbcfe1 --- /dev/null +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +# Last contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'xxd' +version = '8.2.4220' + +homepage = 'https://www.vim.org' +description = """xxd is part of the VIM package and this will only install xxd, not vim! +xxd converts to/from hexdumps of binary files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/vim/vim/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), +] + +start_dir = 'src/xxd' + +files_to_copy = [ + (['xxd'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/xxd'], + 'dirs': [], +} + +sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"] + +moduleclass = 'tools' From 7d080fa309387da9f03bf3bc426e395660533034 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 9 Aug 2022 15:25:12 +0200 Subject: [PATCH 4441/9987] WIP: CubeGUI --- .../easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb index 91b272b19e3..9dd77a59d31 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb @@ -30,10 +30,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] sources = [SOURCELOWER_TAR_GZ] -# patches = ['CubeGUI-4.6_qtlibs_symlink_realpath.patch'] +patches = [ +# 'CubeGUI-4.6_qtlibs_symlink_realpath.patch', + ('CubeGUI-4.7_missing_compile_file.patch', 1), +] checksums = [ '103fe00fa9846685746ce56231f64d850764a87737dc0407c9d0a24037590f68', # cubegui-4.7.tar.gz - # '0b382346251b82792393e44103ddb44f9b1665dd3c652670171a0833984e8987', # CubeGUI-4.6_qtlibs_symlink_realpath.patch +# '0b382346251b82792393e44103ddb44f9b1665dd3c652670171a0833984e8987', # CubeGUI-4.6_qtlibs_symlink_realpath.patch + 'b451c8570322e5d805573afb4823d689dcad5fbe38b2b286c48b0c41070f115d', # CubeGUI-4.7_missing_compile_file.patch ] preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' From 4731165ef41d13331a11778b5e49e1cfcd5399d0 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 9 Aug 2022 15:25:53 +0200 Subject: [PATCH 4442/9987] Remove netCDF-Fortran --- .../netCDF-Fortran-4.6.0-gompi-2022a.eb | 25 ------------------- 1 file changed, 25 deletions(-) delete mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb deleted file mode 100644 index 28ae1438dbe..00000000000 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022a.eb +++ /dev/null @@ -1,25 +0,0 @@ -name = 'netCDF-Fortran' -version = '4.6.0' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompi', 'version': '2022a'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['8194aa70e400c0adfc456127c1d97af2c6489207171d13b10cd754a16da8b0ca'] - -builddependencies = [ - ('M4', '1.4.19'), -] - -dependencies = [('netCDF', '4.9.0')] - -# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) -parallel = 1 - -moduleclass = 'data' From 47380501e5be0d8a35874c0a233cd15e758d473f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 9 Aug 2022 17:52:03 +0200 Subject: [PATCH 4443/9987] Update easybuild/easyconfigs/h/Hypre/Hypre-2.25.0-foss-2022a.eb --- easybuild/easyconfigs/h/Hypre/Hypre-2.25.0-foss-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.25.0-foss-2022a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.25.0-foss-2022a.eb index 429ec49389f..f61c133f632 100644 --- a/easybuild/easyconfigs/h/Hypre/Hypre-2.25.0-foss-2022a.eb +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.25.0-foss-2022a.eb @@ -1,6 +1,3 @@ -## -# Author: Robert Mijakovic -## name = 'Hypre' version = '2.25.0' From 34f2d2004a2bd823611e529b6ba9bec35f0146c9 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 9 Aug 2022 16:57:44 +0200 Subject: [PATCH 4444/9987] Improved EB file for Blitz++ v1.0.2 for GCCcore/1[01].[23].0 --- .../b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb | 6 ---- .../b/Blitz++/Blitz++-1.0.2-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 2 files changed, 29 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb index d6dde31b47c..b43168655a4 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb @@ -20,16 +20,10 @@ checksums = ['500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'] builddependencies = [('CMake', '3.18.4'), ('binutils', '2.35')] -separate_build_dir = True - -postinstallcmds = ['mkdir %(installdir)s/lib64/blitz'] - sanity_check_paths = { 'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT], 'dirs': ['include/blitz/array', 'include/blitz/meta', 'include/random', 'lib64/pkgconfig'], } -configopts = '--enable-shared' - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e8e388a9902 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'Blitz++' +version = '1.0.2' + +homepage = 'https://github.com/blitzpp/blitz' + +description = """ + Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation + in C++ with a speed comparable to Fortran implementations, while preserving an + object-oriented interface +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [('https://github.com/blitzpp/blitz/archive/')] +sources = ['%(version)s.tar.gz'] +checksums = ['500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'] + +builddependencies = [('CMake', '3.23.1'), ('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT], + 'dirs': ['include/blitz/array', 'include/blitz/meta', + 'include/random', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 712dda550f1138a141d528201057c8177845ccd3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 9 Aug 2022 21:30:36 +0200 Subject: [PATCH 4445/9987] Fix new checksum for plot3Drgl --- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index b897944bd7d..675563ec5bf 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -1650,7 +1650,8 @@ exts_list = [ 'checksums': ['d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0'], }), ('plot3Drgl', '1.0.2', { - 'checksums': ['aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496'], + 'checksums': [('aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496', + '805513029895cf5a81f18ede4123ef2525a236cd555437609229fe720c346e14')], }), ('OceanView', '1.0.5', { 'checksums': ['c16e1bed97f4ede46dc017fdd6bd7575d925b57bd2601317bd3ad2357609f885'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 39614e50c0d..14d1ef08558 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -1683,7 +1683,8 @@ exts_list = [ 'checksums': ['d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0'], }), ('plot3Drgl', '1.0.2', { - 'checksums': ['aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496'], + 'checksums': [('aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496', + '805513029895cf5a81f18ede4123ef2525a236cd555437609229fe720c346e14')], }), ('OceanView', '1.0.6', { 'checksums': ['2c5165975d6c49fdc83a892cb0406584928dd44000c9774fffc00fbd2fec86f3'], diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 7bcc0ce4428..228a2210f44 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -1692,7 +1692,8 @@ exts_list = [ 'checksums': ['d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0'], }), ('plot3Drgl', '1.0.2', { - 'checksums': ['aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496'], + 'checksums': [('aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496', + '805513029895cf5a81f18ede4123ef2525a236cd555437609229fe720c346e14')], }), ('OceanView', '1.0.6', { 'checksums': ['2c5165975d6c49fdc83a892cb0406584928dd44000c9774fffc00fbd2fec86f3'], From da063110b1f9e6a3789a5c3015c35a9b82d8fa4f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 9 Aug 2022 21:40:23 +0200 Subject: [PATCH 4446/9987] Fix CubeGUI --- .../c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb | 6 +- .../CubeGUI-4.7_missing_compile_file.patch | 356 ++++++++++++++++++ 2 files changed, 358 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb index 9dd77a59d31..790b55187fd 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb @@ -31,13 +31,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] sources = [SOURCELOWER_TAR_GZ] patches = [ -# 'CubeGUI-4.6_qtlibs_symlink_realpath.patch', ('CubeGUI-4.7_missing_compile_file.patch', 1), ] checksums = [ '103fe00fa9846685746ce56231f64d850764a87737dc0407c9d0a24037590f68', # cubegui-4.7.tar.gz -# '0b382346251b82792393e44103ddb44f9b1665dd3c652670171a0833984e8987', # CubeGUI-4.6_qtlibs_symlink_realpath.patch - 'b451c8570322e5d805573afb4823d689dcad5fbe38b2b286c48b0c41070f115d', # CubeGUI-4.7_missing_compile_file.patch + '0a3072decf1d4b9f8544331647bb160723733f3579b9d8c64906c45fcf4ce669', # CubeGUI-4.7_missing_compile_file.patch ] preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' @@ -54,7 +52,7 @@ dependencies = [ ] configopts = [ - "--with-qt=$EBROOTQT5" + 'CXX="g++" --with-qt=$EBROOTQT5/bin ', ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch new file mode 100644 index 00000000000..7b08da87205 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch @@ -0,0 +1,356 @@ +# This patch adds the "build-config/compile" file that is missing in v4.7. +# The file is copied "as is" from CubeGUI v4.6. +# +# Author: maxim-masterov (SURF) + +diff -Nru cubegui-4.7.orig/build-config/compile cubegui-4.7/build-config/compile +--- cubegui-4.7.orig/build-config/compile 1970-01-01 01:00:00.000000000 +0100 ++++ cubegui-4.7/build-config/compile 2022-08-09 11:33:06.528166000 +0200 +@@ -0,0 +1,347 @@ ++#! /bin/sh ++# Wrapper for compilers which do not understand '-c -o'. ++ ++scriptversion=2012-10-14.11; # UTC ++ ++# Copyright (C) 1999-2013 Free Software Foundation, Inc. ++# Written by Tom Tromey . ++# ++# This program is free software; you can redistribute it and/or modify ++# it under the terms of the GNU General Public License as published by ++# the Free Software Foundation; either version 2, or (at your option) ++# any later version. ++# ++# This program is distributed in the hope that it will be useful, ++# but WITHOUT ANY WARRANTY; without even the implied warranty of ++# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++# GNU General Public License for more details. ++# ++# You should have received a copy of the GNU General Public License ++# along with this program. If not, see . ++ ++# As a special exception to the GNU General Public License, if you ++# distribute this file as part of a program that contains a ++# configuration script generated by Autoconf, you may include it under ++# the same distribution terms that you use for the rest of that program. ++ ++# This file is maintained in Automake, please report ++# bugs to or send patches to ++# . ++ ++nl=' ++' ++ ++# We need space, tab and new line, in precisely that order. Quoting is ++# there to prevent tools from complaining about whitespace usage. ++IFS=" "" $nl" ++ ++file_conv= ++ ++# func_file_conv build_file lazy ++# Convert a $build file to $host form and store it in $file ++# Currently only supports Windows hosts. If the determined conversion ++# type is listed in (the comma separated) LAZY, no conversion will ++# take place. ++func_file_conv () ++{ ++ file=$1 ++ case $file in ++ / | /[!/]*) # absolute file, and not a UNC file ++ if test -z "$file_conv"; then ++ # lazily determine how to convert abs files ++ case `uname -s` in ++ MINGW*) ++ file_conv=mingw ++ ;; ++ CYGWIN*) ++ file_conv=cygwin ++ ;; ++ *) ++ file_conv=wine ++ ;; ++ esac ++ fi ++ case $file_conv/,$2, in ++ *,$file_conv,*) ++ ;; ++ mingw/*) ++ file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'` ++ ;; ++ cygwin/*) ++ file=`cygpath -m "$file" || echo "$file"` ++ ;; ++ wine/*) ++ file=`winepath -w "$file" || echo "$file"` ++ ;; ++ esac ++ ;; ++ esac ++} ++ ++# func_cl_dashL linkdir ++# Make cl look for libraries in LINKDIR ++func_cl_dashL () ++{ ++ func_file_conv "$1" ++ if test -z "$lib_path"; then ++ lib_path=$file ++ else ++ lib_path="$lib_path;$file" ++ fi ++ linker_opts="$linker_opts -LIBPATH:$file" ++} ++ ++# func_cl_dashl library ++# Do a library search-path lookup for cl ++func_cl_dashl () ++{ ++ lib=$1 ++ found=no ++ save_IFS=$IFS ++ IFS=';' ++ for dir in $lib_path $LIB ++ do ++ IFS=$save_IFS ++ if $shared && test -f "$dir/$lib.dll.lib"; then ++ found=yes ++ lib=$dir/$lib.dll.lib ++ break ++ fi ++ if test -f "$dir/$lib.lib"; then ++ found=yes ++ lib=$dir/$lib.lib ++ break ++ fi ++ if test -f "$dir/lib$lib.a"; then ++ found=yes ++ lib=$dir/lib$lib.a ++ break ++ fi ++ done ++ IFS=$save_IFS ++ ++ if test "$found" != yes; then ++ lib=$lib.lib ++ fi ++} ++ ++# func_cl_wrapper cl arg... ++# Adjust compile command to suit cl ++func_cl_wrapper () ++{ ++ # Assume a capable shell ++ lib_path= ++ shared=: ++ linker_opts= ++ for arg ++ do ++ if test -n "$eat"; then ++ eat= ++ else ++ case $1 in ++ -o) ++ # configure might choose to run compile as 'compile cc -o foo foo.c'. ++ eat=1 ++ case $2 in ++ *.o | *.[oO][bB][jJ]) ++ func_file_conv "$2" ++ set x "$@" -Fo"$file" ++ shift ++ ;; ++ *) ++ func_file_conv "$2" ++ set x "$@" -Fe"$file" ++ shift ++ ;; ++ esac ++ ;; ++ -I) ++ eat=1 ++ func_file_conv "$2" mingw ++ set x "$@" -I"$file" ++ shift ++ ;; ++ -I*) ++ func_file_conv "${1#-I}" mingw ++ set x "$@" -I"$file" ++ shift ++ ;; ++ -l) ++ eat=1 ++ func_cl_dashl "$2" ++ set x "$@" "$lib" ++ shift ++ ;; ++ -l*) ++ func_cl_dashl "${1#-l}" ++ set x "$@" "$lib" ++ shift ++ ;; ++ -L) ++ eat=1 ++ func_cl_dashL "$2" ++ ;; ++ -L*) ++ func_cl_dashL "${1#-L}" ++ ;; ++ -static) ++ shared=false ++ ;; ++ -Wl,*) ++ arg=${1#-Wl,} ++ save_ifs="$IFS"; IFS=',' ++ for flag in $arg; do ++ IFS="$save_ifs" ++ linker_opts="$linker_opts $flag" ++ done ++ IFS="$save_ifs" ++ ;; ++ -Xlinker) ++ eat=1 ++ linker_opts="$linker_opts $2" ++ ;; ++ -*) ++ set x "$@" "$1" ++ shift ++ ;; ++ *.cc | *.CC | *.cxx | *.CXX | *.[cC]++) ++ func_file_conv "$1" ++ set x "$@" -Tp"$file" ++ shift ++ ;; ++ *.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO]) ++ func_file_conv "$1" mingw ++ set x "$@" "$file" ++ shift ++ ;; ++ *) ++ set x "$@" "$1" ++ shift ++ ;; ++ esac ++ fi ++ shift ++ done ++ if test -n "$linker_opts"; then ++ linker_opts="-link$linker_opts" ++ fi ++ exec "$@" $linker_opts ++ exit 1 ++} ++ ++eat= ++ ++case $1 in ++ '') ++ echo "$0: No command. Try '$0 --help' for more information." 1>&2 ++ exit 1; ++ ;; ++ -h | --h*) ++ cat <<\EOF ++Usage: compile [--help] [--version] PROGRAM [ARGS] ++ ++Wrapper for compilers which do not understand '-c -o'. ++Remove '-o dest.o' from ARGS, run PROGRAM with the remaining ++arguments, and rename the output as expected. ++ ++If you are trying to build a whole package this is not the ++right script to run: please start by reading the file 'INSTALL'. ++ ++Report bugs to . ++EOF ++ exit $? ++ ;; ++ -v | --v*) ++ echo "compile $scriptversion" ++ exit $? ++ ;; ++ cl | *[/\\]cl | cl.exe | *[/\\]cl.exe ) ++ func_cl_wrapper "$@" # Doesn't return... ++ ;; ++esac ++ ++ofile= ++cfile= ++ ++for arg ++do ++ if test -n "$eat"; then ++ eat= ++ else ++ case $1 in ++ -o) ++ # configure might choose to run compile as 'compile cc -o foo foo.c'. ++ # So we strip '-o arg' only if arg is an object. ++ eat=1 ++ case $2 in ++ *.o | *.obj) ++ ofile=$2 ++ ;; ++ *) ++ set x "$@" -o "$2" ++ shift ++ ;; ++ esac ++ ;; ++ *.c) ++ cfile=$1 ++ set x "$@" "$1" ++ shift ++ ;; ++ *) ++ set x "$@" "$1" ++ shift ++ ;; ++ esac ++ fi ++ shift ++done ++ ++if test -z "$ofile" || test -z "$cfile"; then ++ # If no '-o' option was seen then we might have been invoked from a ++ # pattern rule where we don't need one. That is ok -- this is a ++ # normal compilation that the losing compiler can handle. If no ++ # '.c' file was seen then we are probably linking. That is also ++ # ok. ++ exec "$@" ++fi ++ ++# Name of file we expect compiler to create. ++cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'` ++ ++# Create the lock directory. ++# Note: use '[/\\:.-]' here to ensure that we don't use the same name ++# that we are using for the .o file. Also, base the name on the expected ++# object file name, since that is what matters with a parallel build. ++lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d ++while true; do ++ if mkdir "$lockdir" >/dev/null 2>&1; then ++ break ++ fi ++ sleep 1 ++done ++# FIXME: race condition here if user kills between mkdir and trap. ++trap "rmdir '$lockdir'; exit 1" 1 2 15 ++ ++# Run the compile. ++"$@" ++ret=$? ++ ++if test -f "$cofile"; then ++ test "$cofile" = "$ofile" || mv "$cofile" "$ofile" ++elif test -f "${cofile}bj"; then ++ test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile" ++fi ++ ++rmdir "$lockdir" ++exit $ret ++ ++# Local Variables: ++# mode: shell-script ++# sh-indentation: 2 ++# eval: (add-hook 'write-file-hooks 'time-stamp) ++# time-stamp-start: "scriptversion=" ++# time-stamp-format: "%:y-%02m-%02d.%02H" ++# time-stamp-time-zone: "UTC" ++# time-stamp-end: "; # UTC" ++# End: From e6b1ccccd867ad20e44ee44fe3b5c8dc26b27e4a Mon Sep 17 00:00:00 2001 From: Maxim Date: Tue, 9 Aug 2022 21:42:02 +0200 Subject: [PATCH 4447/9987] Update easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index b59ecf9d60f..b2412e3eb97 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -27,10 +27,10 @@ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] # The problem: sources from git clone have different checksum every time -# checksums = [ -# '0d68df19766ad03041126c1531cb115e2d2a69043df96314fd30d897cfca9e4c', # v4.4.tar.gz -# '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch -# ] +checksums = [ + None, # v4.4.tar.gz + '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch +] # csh is used by WRF install scripts builddependencies = [ From 4f360552f9facaca8d30c4a44cc6e9cc9eb0f552 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 9 Aug 2022 13:26:02 -0700 Subject: [PATCH 4448/9987] update toolchain --- .../h/HH-suite/HH-suite-3.3.0-gompi-2021b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021b.eb diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021b.eb new file mode 100644 index 00000000000..3beaa3948e1 --- /dev/null +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021b.eb @@ -0,0 +1,66 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Updated to use gompi-2020b toolchain: +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'HH-suite' +version = '3.3.0' + +homepage = 'https://github.com/soedinglab/hh-suite' +description = """The HH-suite is an open-source software package +for sensitive protein sequence searching based on the pairwise +alignment of hidden Markov models (HMMs).""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Perl', '5.34.0'), + ('Python', '3.9.6'), +] + +_binaries = [ + 'hhalign', 'hhalign_mpi', 'hhalign_omp', + 'hhblits', 'hhblits_mpi', 'hhblits_omp', + 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp', + 'hhmake', 'hhfilter', 'hhconsensus', +] + +_scriptfiles = [ + 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', +] + +fix_perl_shebang_for = ['scripts/*pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + ['scripts/%s' % y for y in _scriptfiles], + 'dirs': ['data', 'scripts'] +} + +modextrapaths = { + 'PATH': 'scripts', + 'PERL5LIB': 'scripts', +} + +moduleclass = 'bio' From bf05e8f40a1986f642c88c88b7cd6d7276d8b7e3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 9 Aug 2022 22:48:38 +0200 Subject: [PATCH 4449/9987] Remove trailing space --- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 2 +- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index 675563ec5bf..3bdb84f74b2 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -1650,7 +1650,7 @@ exts_list = [ 'checksums': ['d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0'], }), ('plot3Drgl', '1.0.2', { - 'checksums': [('aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496', + 'checksums': [('aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496', '805513029895cf5a81f18ede4123ef2525a236cd555437609229fe720c346e14')], }), ('OceanView', '1.0.5', { diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 14d1ef08558..9c0872e0343 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -1683,7 +1683,7 @@ exts_list = [ 'checksums': ['d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0'], }), ('plot3Drgl', '1.0.2', { - 'checksums': [('aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496', + 'checksums': [('aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496', '805513029895cf5a81f18ede4123ef2525a236cd555437609229fe720c346e14')], }), ('OceanView', '1.0.6', { diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 228a2210f44..46ee68285da 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -1692,7 +1692,7 @@ exts_list = [ 'checksums': ['d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0'], }), ('plot3Drgl', '1.0.2', { - 'checksums': [('aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496', + 'checksums': [('aa874891446a395f01791d80a5a0f1f9a1c2c41f029de3a8d5af9aa47f46a496', '805513029895cf5a81f18ede4123ef2525a236cd555437609229fe720c346e14')], }), ('OceanView', '1.0.6', { From 4e9c826e6a5776ac5eeb85fea1508a5d843f3f17 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 9 Aug 2022 14:09:13 -0700 Subject: [PATCH 4450/9987] update Kalign --- .../k/Kalign/Kalign-3.3.2-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kalign/Kalign-3.3.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9b5d84c9779 --- /dev/null +++ b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'Kalign' +version = '3.3.2' + +homepage = 'https://github.com/TimoLassmann/kalign' +description = "Kalign is a fast multiple sequence alignment program for biological sequences." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c0b357feda32e16041cf286a4e67626a52bbf78c39e2237b485d54fb38ef319a'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +configure_cmd_prefix = "autoreconf -vfi && " + +sanity_check_paths = { + 'files': ['bin/kchaos', 'bin/kalign'], + 'dirs': [], +} + +sanity_check_commands = ["kalign --help"] + +moduleclass = 'bio' From dbf7314b53344454fd9502cb4256fdb769505da7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 10 Aug 2022 06:53:14 +0800 Subject: [PATCH 4451/9987] remove unnecessary separate_build_dir --- .../o/OpenMM/OpenMM-7.5.1-foss-2021a-DeepMind-patch.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-DeepMind-patch.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-DeepMind-patch.eb index cd9f06a4f42..42a22798b5f 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-DeepMind-patch.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-DeepMind-patch.eb @@ -23,8 +23,6 @@ builddependencies = [ ('Doxygen', '1.9.1'), ] -separate_build_dir = True - dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), From 0821339677f84820e0422b945d2843475b373b97 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Aug 2022 10:29:58 +0200 Subject: [PATCH 4452/9987] adding easyconfigs: Pysam-0.19.1-GCC-11.3.0.eb --- .../p/Pysam/Pysam-0.19.1-GCC-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.19.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.19.1-GCC-11.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.19.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..ba8af04da92 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.19.1-GCC-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.19.1' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c33a51324fc4191bbfb135e93bf0c9b85ac9dad1320fb852a8af47c38626e37a'] + +dependencies = [ + ('Python', '3.10.4'), + ('ncurses', '6.3'), + ('cURL', '7.83.0'), + ('XZ', '5.2.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' From 76764f182fea302289459aabb9d1b363d14f086d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Aug 2022 10:30:11 +0200 Subject: [PATCH 4453/9987] adding easyconfigs: scikit-learn-1.1.2-foss-2022a.eb --- .../scikit-learn-1.1.2-foss-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-foss-2022a.eb new file mode 100644 index 00000000000..f1b408579da --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.1.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'sklearn', + 'checksums': ['7c22d1305b16f08d57751a4ea36071e2215efb4c09cb79183faa4e8e82a3dbf8'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), +] + +moduleclass = 'data' From e965c5b9f8a3d37835f15ddac9871f975e550181 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Aug 2022 10:46:59 +0200 Subject: [PATCH 4454/9987] adding easyconfigs: SMC++-1.15.4-foss-2022a.eb --- .../s/SMC++/SMC++-1.15.4-foss-2022a.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/s/SMC++/SMC++-1.15.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SMC++/SMC++-1.15.4-foss-2022a.eb b/easybuild/easyconfigs/s/SMC++/SMC++-1.15.4-foss-2022a.eb new file mode 100644 index 00000000000..8d45cebda15 --- /dev/null +++ b/easybuild/easyconfigs/s/SMC++/SMC++-1.15.4-foss-2022a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'SMC++' +version = '1.15.4' + +homepage = 'https://github.com/popgenmethods/smcpp' +description = "SMC++ is a program for estimating the size history of populations from whole genome sequence data." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('tqdm', '4.64.0'), + ('Pysam', '0.19.1'), + ('scikit-learn', '1.1.2'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('GSL', '2.7'), +] + +use_pip = True + +exts_list = [ + (name, version, { + # git metadata is required by setup.py, so obtain source tarball via 'git clone' + 'sources': [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/popgenmethods', + 'repo_name': 'smcpp', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, + }], + 'checksums': [None], + 'modulename': 'smcpp', + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/smc++'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "smc++ version", + "smc++ -h", +] + +moduleclass = 'bio' From d48f7d9f3eafeca7f7e54652f00e272fa584c6dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Aug 2022 12:49:27 +0200 Subject: [PATCH 4455/9987] update scikit-learn v1.0.2 easyconfig to be bundle of sckit-learn + sklearn --- .../scikit-learn-1.0.2-foss-2021b.eb | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb index acd09d3ba53..668090f02d8 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.0.2-foss-2021b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'scikit-learn' version = '1.0.2' @@ -11,18 +11,22 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'foss', 'version': '2021b'} -sources = [SOURCE_TAR_GZ] -checksums = ['b5870959a5484b614f26d31ca4c17524b1b0317522199dc985c3b4256e030767'] - dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10') ] use_pip = True -download_dep_fail = True sanity_pip_check = True -options = {'modulename': 'sklearn'} +exts_list = [ + (name, version, { + 'checksums': ['b5870959a5484b614f26d31ca4c17524b1b0317522199dc985c3b4256e030767'], + 'modulename': 'sklearn', + }), + ('sklearn', '0.0', { # also install the meta-package, as other packages check for this + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }) +] moduleclass = 'data' From b997bc7daae48391bccae88796aff3cd3d9bb8b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Aug 2022 17:16:54 +0200 Subject: [PATCH 4456/9987] don't run 'git lfs config' when loading git-lfs module since it updates ~/.gitconfig --- easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb index 324690cada5..35a82d52add 100644 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.2.0.eb @@ -24,17 +24,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = [('git-lfs', '--version')] - -# add aliases needed by Git LFS in ~.gitconfig -modluafooter = """ -if mode() == "load" then - cmdout = subprocess("git lfs install") - LmodMessage(cmdout) -end""" -modtclfooter = """ -if { [ module-info mode load ] } { - exec git lfs install -}""" +sanity_check_commands = ["git-lfs --version"] moduleclass = 'tools' From 8b9e66dada11e3992a54587f730834e291076839 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 10 Aug 2022 18:38:10 +0200 Subject: [PATCH 4457/9987] adding easyconfigs: olaFlow-20210820-foss-2021b.eb --- .../o/olaFlow/olaFlow-20210820-foss-2021b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb diff --git a/easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb b/easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb new file mode 100644 index 00000000000..70b5db53c77 --- /dev/null +++ b/easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'olaFlow' +version = '20210820' +local_commit = 'b3039e055a22ea0b8c7dc9f735f15686976559f6' + +homepage = 'https://olaflow.github.io/' +description = """olaFlow CFD Suite is a free and open source project committed to bringing the latest +advances for the simulation of wave dynamics to the OpenFOAM® and FOAM-extend communities.""" + +sources = [{ + 'source_urls': ['https://github.com/phicau/olaFlow/archive/'], + 'filename': '%s.tar.gz' % local_commit, + 'download_filename': '%(name)s-%(version)s.tar.gz', +}] +checksums = ['126777c2dc5e8fe563251ce9cc8438bd2e90771cc5a9ea2fc47bd4679502c08b'] + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('OpenFOAM', 'v2112') +] + +postinstallcmds = ["source $FOAM_BASH && " + "export FOAM_USER_APPBIN=%(installdir)s/bin && " + "export FOAM_USER_LIBBIN=%(installdir)s/lib && " + "./allMake"] + +sanity_check_paths = { + 'files': ["bin/olaFlow", "lib/libwaveGeneration.so"], + 'dirs': [] +} + +sanity_check_commands = ["olaFlow -help"] + +moduleclass = 'cae' From 1d0d895a6a12d6b6b61ef4a1c5afa5424f0ed28b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 10 Aug 2022 20:30:36 +0200 Subject: [PATCH 4458/9987] FORD/6.1.5, tqdm/4.64.0, BeautifulSoup/4.10.0 and Graphviz/5.0.0 for GCCcore/11.3.0 --- .../BeautifulSoup-4.10.0-GCCcore-11.3.0.eb | 34 +++++++ .../f/FORD/FORD-6.1.15-GCCcore-11.3.0.eb | 57 +++++++++++ .../Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb | 95 +++++++++++++++++++ 3 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/f/FORD/FORD-6.1.15-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6b744088b47 --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.10.0-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.10.0' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38') +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.3.1', { + 'checksums': ['b8d49b1cd4f037c7082a9683dfa1801aa2597fb11c3a1155b7a5b94829b4f1f9'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['c23ad23c521d818955a4151a67d81580319d4bf548d3d49f4223ae041ff98891'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/FORD/FORD-6.1.15-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FORD/FORD-6.1.15-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ed749e791ee --- /dev/null +++ b/easybuild/easyconfigs/f/FORD/FORD-6.1.15-GCCcore-11.3.0.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'FORD' +version = '6.1.15' + +homepage = 'https://github.com/Fortran-FOSS-Programmers/ford/wiki' +description = 'FORD is an automatic documentation generator for modern Fortran programs' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Graphviz', '5.0.0',), + ('BeautifulSoup', '4.10.0'), + ('tqdm', '4.64.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('graphviz', '0.20.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['8c58f14adaa3b947daf26c19bc1e98c4e0702cdc31cf99153e6f06904d492bf8'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('markdown_include', '0.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['a06183b7c7225e73112737acdc6fe0ac0686c39457234eeb5ede23881fed001d'], + }), + ('python-markdown-math', '0.8', { + 'modulename': 'mdx_math', + 'checksums': ['8564212af679fc18d53f38681f16080fcd3d186073f23825c7ce86fadd3e3635'], + }), + ('md-environ', '0.1.0', { + 'checksums': ['fe3c2a255af523d6f522831c699336cd71f9d543714067d93206ed35836f1793'], + }), + ('toposort', '1.7', { + 'checksums': ['ddc2182c42912a440511bd7ff5d3e6a1cabc3accbc674a3258c8c41cbfbb2125'], + }), + (name, version, { + 'checksums': ['d90000f528878738fc55f0f28aa34f36c5cb7f4819d851d10977f8499bf0cae6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ford'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..564c8d5ede5 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,95 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '5.0.0' +local_pyver_major = '3' + +homepage = 'https://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_skip-install-data-hook.patch'] +checksums = [ + 'f8cc576694ae93659f453b6b4a4c2f04572a90cfccdca2d4271f2e7c60bb3d60', # graphviz-5.0.0.tar.gz + '4cafb6eac6f59fa4e90cef6e83c276ad5e4e24b10992b18d4b51c6d28dfe4ca1', # Graphviz-5.0.0_skip-install-data-hook.patch +] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('SWIG', '4.0.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Java', '17', '', True), + ('Python', '3.10.4'), + ('FriBidi', '1.0.12'), + ('Gdk-Pixbuf', '2.42.8'), + ('Ghostscript', '9.56.1'), + ('GTS', '0.7.6'), + ('libgd', '2.3.3'), + ('Pango', '1.50.7'), + ('Perl', '5.34.1'), + ('Qt5', '5.15.5'), + ('Tcl', '8.6.12'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('libjpeg-turbo', '2.1.3'), + ('expat', '2.4.8'), +] + +preconfigopts = './autogen.sh NOCONFIG && ' + +configopts = '--enable-python%s=yes ' % local_pyver_major +configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' +# Use ltdl from libtool in EB +configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' +configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' +# Override the hardcoded paths to Java libraries +configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' +configopts += '--with-javalibdir=$JAVA_HOME/lib' +configopts += '--with-expatincludedir=$EBROOTEXPAT/include --with-expatlibdir=$EBROOTEXPAT/lib' +configopts += '--with-zincludedir=$EBROOTZLIB/include --with-zlibdir=$EBROOTZLIB/lib' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +postinstallcmds = ['%(installdir)s/bin/dot -c'] # Writes plugin configuration + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acyclic', 'bcomps', 'ccomps', 'cluster', 'diffimg', 'dijkstra', 'dot', + 'dot_builtins', 'edgepaint', 'gc', 'gml2gv', 'graphml2gv', 'gv2gml', + 'gvcolor', 'gvedit', 'gvgen', 'gvmap', 'gvmap.sh', 'gvpack', 'gvpr', 'gxl2gv', + 'neato', 'mm2gv', 'nop', 'prune', 'sccmap', 'tred', 'unflatten', + 'vimdot']] + + ['lib/%s.%s' % (x, SHLIB_EXT) for x in ['libcdt', 'libcgraph', 'libgvc', 'libgvpr', 'liblab_gamut', + 'libpathplan', 'libxdot']], + 'dirs': ['include', 'lib/graphviz', 'lib/graphviz/java', 'lib/graphviz/python%s' % local_pyver_major, + 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), + ('python', '-c "import gv"'), +] + +modextrapaths = { + 'CLASSPATH': 'lib/graphviz/java', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'PYTHONPATH': 'lib/graphviz/python%s' % local_pyver_major, + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' From 5684e639378b8782d9a792c29f83732149b52730 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Aug 2022 22:00:39 +0200 Subject: [PATCH 4459/9987] {lib}[GCCcore/10.2.0,GCCcore/10.3.0,GCCcore/11.2.0,GCCcore/11.3.0] scikit-build v0.15.0 w/ Python 3.8.6 + 3.9.5 + 3.9.6 + 3.10.4 --- .../scikit-build-0.15.0-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ .../scikit-build-0.15.0-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ .../scikit-build-0.15.0-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ .../scikit-build-0.15.0-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ 4 files changed, 132 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb create mode 100755 easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.3.0.eb create mode 100755 easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-11.2.0.eb create mode 100755 easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb new file mode 100755 index 00000000000..459369823e8 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.15.0' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('distro', '1.7.0', { + 'checksums': ['151aeccf60c216402932b52e40ee477a939f8d58898927378a02abbe852c1c39'], + }), + (name, version, { + 'checksums': ['e723cd0f3489a042370b9ea988bbb9cfd7725e8b25b20ca1c7981821fcf65fb9'], + 'modulename': 'skbuild', + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.3.0.eb new file mode 100755 index 00000000000..0449d47c021 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.15.0' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('distro', '1.7.0', { + 'checksums': ['151aeccf60c216402932b52e40ee477a939f8d58898927378a02abbe852c1c39'], + }), + (name, version, { + 'checksums': ['e723cd0f3489a042370b9ea988bbb9cfd7725e8b25b20ca1c7981821fcf65fb9'], + 'modulename': 'skbuild', + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-11.2.0.eb new file mode 100755 index 00000000000..ff74dd0f5a7 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.15.0' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('distro', '1.7.0', { + 'checksums': ['151aeccf60c216402932b52e40ee477a939f8d58898927378a02abbe852c1c39'], + }), + (name, version, { + 'checksums': ['e723cd0f3489a042370b9ea988bbb9cfd7725e8b25b20ca1c7981821fcf65fb9'], + 'modulename': 'skbuild', + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-11.3.0.eb new file mode 100755 index 00000000000..ccadbec9f0d --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.15.0-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.15.0' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('distro', '1.7.0', { + 'checksums': ['151aeccf60c216402932b52e40ee477a939f8d58898927378a02abbe852c1c39'], + }), + (name, version, { + 'checksums': ['e723cd0f3489a042370b9ea988bbb9cfd7725e8b25b20ca1c7981821fcf65fb9'], + 'modulename': 'skbuild', + }), +] + +moduleclass = 'lib' From 602a763df69c51453cce6a8312bf0ef36f07f1fb Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 10 Aug 2022 21:35:31 +0100 Subject: [PATCH 4460/9987] Add missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2021 versions --- .../g/GROMACS/GROMACS-2021-fosscuda-2020b.eb | 2 + .../GROMACS/GROMACS-2021.2-fosscuda-2020b.eb | 2 + ...1.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb | 2 + .../GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb | 2 + .../GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb | 2 + .../GROMACS-2021_add-missing-sync.patch | 39 +++++++++++++++++++ 6 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2021_add-missing-sync.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb index 5a529a9533b..706f52ed24b 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021-fosscuda-2020b.eb @@ -40,6 +40,7 @@ patches = [ 'GROMACS-2019_increase_test_timeout_for_GPU.patch', 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021_add-missing-sync.patch', ] checksums = [ 'efa78ab8409b0f5bf0fbca174fb8fbcf012815326b5c71a9d7c385cde9a8f87b', # gromacs-2021.tar.gz @@ -51,6 +52,7 @@ checksums = [ 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', + '52ee257309ff7761c2dd5b26de7dbc63f8ba698082adb88e2843f90e3f9168bf', # GROMACS-2021_add-missing-sync.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb index 13d039f411a..abde5c23639 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.2-fosscuda-2020b.eb @@ -40,6 +40,7 @@ patches = [ 'GROMACS-2019_increase_test_timeout_for_GPU.patch', 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021_add-missing-sync.patch', ] checksums = [ 'd940d865ea91e78318043e71f229ce80d32b0dc578d64ee5aa2b1a4be801aadb', # gromacs-2021.2.tar.gz @@ -51,6 +52,7 @@ checksums = [ 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', + '52ee257309ff7761c2dd5b26de7dbc63f8ba698082adb88e2843f90e3f9168bf', # GROMACS-2021_add-missing-sync.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb index e431ba0f759..aa8b7a249fd 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb @@ -44,6 +44,7 @@ patches = [ 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', 'GROMACS-2021.3_skip_test_for_plumed.patch', + 'GROMACS-2021_add-missing-sync.patch', ] checksums = [ 'e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6', # gromacs-2021.3.tar.gz @@ -56,6 +57,7 @@ checksums = [ # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', 'c06d0a8c3e75b232224f46bc3b70e135c4c02ec4151712970f5edd85d890f018', # GROMACS-2021.3_skip_test_for_plumed.patch + '52ee257309ff7761c2dd5b26de7dbc63f8ba698082adb88e2843f90e3f9168bf', # GROMACS-2021_add-missing-sync.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb index 0b05b269df5..a3519c9ca33 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb @@ -41,6 +41,7 @@ patches = [ 'GROMACS-2019_increase_test_timeout_for_GPU.patch', 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021_add-missing-sync.patch', ] checksums = [ 'e109856ec444768dfbde41f3059e3123abdb8fe56ca33b1a83f31ed4575a1cc6', # gromacs-2021.3.tar.gz @@ -52,6 +53,7 @@ checksums = [ 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', + '52ee257309ff7761c2dd5b26de7dbc63f8ba698082adb88e2843f90e3f9168bf', # GROMACS-2021_add-missing-sync.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb index cf94349e8a3..3226925397d 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb @@ -42,6 +42,7 @@ patches = [ 'GROMACS-2019_increase_test_timeout_for_GPU.patch', 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', 'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-2021_add-missing-sync.patch', ] checksums = [ 'eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6', # gromacs-2021.5.tar.gz @@ -53,6 +54,7 @@ checksums = [ 'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49', # GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch '7d39da0b431fbc9e94e857552246eb0ec892f26b13e519b3706785cc5e01a563', + '52ee257309ff7761c2dd5b26de7dbc63f8ba698082adb88e2843f90e3f9168bf', # GROMACS-2021_add-missing-sync.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021_add-missing-sync.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021_add-missing-sync.patch new file mode 100644 index 00000000000..78b6264feef --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021_add-missing-sync.patch @@ -0,0 +1,39 @@ +Add missing sync in LINCS and SETTLE CUDA kernels +https://gitlab.com/gromacs/gromacs/-/merge_requests/2499 +Patch added to EasyBuild by Simon Branford (University of Birmingham) +diff --git a/src/gromacs/mdlib/lincs_gpu.cu b/src/gromacs/mdlib/lincs_gpu.cu +index 27ad86f17f..4964a3d040 100644 +--- a/src/gromacs/mdlib/lincs_gpu.cu ++++ b/src/gromacs/mdlib/lincs_gpu.cu +@@ -382,11 +382,15 @@ __launch_bounds__(c_maxThreadsPerBlock) __global__ + sm_threadVirial[d * blockDim.x + (threadIdx.x + dividedAt)]; + } + } +- // Syncronize if not within one warp ++ // Synchronize if not within one warp + if (dividedAt > warpSize / 2) + { + __syncthreads(); + } ++ else ++ { ++ __syncwarp(); ++ } + } + // First 6 threads in the block add the results of 6 tensor components to the global memory address. + if (threadIdx.x < 6) +diff --git a/src/gromacs/mdlib/settle_gpu.cu b/src/gromacs/mdlib/settle_gpu.cu +index c02f0d5884..c6ca1e2452 100644 +--- a/src/gromacs/mdlib/settle_gpu.cu ++++ b/src/gromacs/mdlib/settle_gpu.cu +@@ -352,6 +352,10 @@ __launch_bounds__(c_maxThreadsPerBlock) __global__ + { + __syncthreads(); + } ++ else ++ { ++ __syncwarp(); ++ } + } + // First 6 threads in the block add the 6 components of virial to the global memory address + if (tib < 6) From aa4b3ffbb44f56f3fab44cbd730fff3f952be624 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 10 Aug 2022 21:40:34 +0100 Subject: [PATCH 4461/9987] Add missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 versions --- .../g/GROMACS/GROMACS-2020-fosscuda-2019b.eb | 2 + .../GROMACS/GROMACS-2020.3-fosscuda-2019b.eb | 2 + ...MACS-2020.5-fosscuda-2020a-Python-3.8.2.eb | 2 + .../GROMACS-2020_add-missing-sync.patch | 39 +++++++++++++++++++ 4 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2020_add-missing-sync.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020-fosscuda-2019b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020-fosscuda-2019b.eb index c38602c4db9..686ba6389a4 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020-fosscuda-2019b.eb @@ -34,6 +34,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2020_add-missing-sync.patch', ] checksums = [ '477e56142b3dcd9cb61b8f67b24a55760b04d1655e8684f979a75a5eec40ba01', # gromacs-2020.tar.gz @@ -41,6 +42,7 @@ checksums = [ '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', # GROMACS-2019_increase_test_timeout_for_GPU.patch '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + '3c9d7017422a722a960d26ad955d7a0f72a1305a6234bcb53851cc62662b96c9', # GROMACS-2020_add-missing-sync.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.3-fosscuda-2019b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.3-fosscuda-2019b.eb index 0f66c5d02ad..b717b38c5e5 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.3-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.3-fosscuda-2019b.eb @@ -34,6 +34,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', 'GROMACS-2019_increase_test_timeout_for_GPU.patch', + 'GROMACS-2020_add-missing-sync.patch', ] checksums = [ '903183691132db14e55b011305db4b6f4901cc4912d2c56c131edfef18cc92a9', # gromacs-2020.3.tar.gz @@ -41,6 +42,7 @@ checksums = [ '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', # GROMACS-2019_increase_test_timeout_for_GPU.patch '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', + '3c9d7017422a722a960d26ad955d7a0f72a1305a6234bcb53851cc62662b96c9', # GROMACS-2020_add-missing-sync.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.5-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.5-fosscuda-2020a-Python-3.8.2.eb index 0b802e3a1b0..0e0b5ada105 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.5-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.5-fosscuda-2020a-Python-3.8.2.eb @@ -44,6 +44,7 @@ patches = [ 'GROMACS-2020_fix_gmxapi_gmx_allowed_cmd_name.patch', 'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch', 'GROMACS-2020.4_correct_gcc9_check.patch', + 'GROMACS-2020_add-missing-sync.patch', ] checksums = [ '7b6aff647f7c8ee1bf12204d02cef7c55f44402a73195bd5f42cf11850616478', # gromacs-2020.5.tar.gz @@ -58,6 +59,7 @@ checksums = [ # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb', 'fd614b84a48b7702dbb59410f2c6a1604864942caf9594e50c29a73e87023871', # GROMACS-2020.4_correct_gcc9_check.patch + '3c9d7017422a722a960d26ad955d7a0f72a1305a6234bcb53851cc62662b96c9', # GROMACS-2020_add-missing-sync.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020_add-missing-sync.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020_add-missing-sync.patch new file mode 100644 index 00000000000..706888bd2e4 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020_add-missing-sync.patch @@ -0,0 +1,39 @@ +Add missing sync in LINCS and SETTLE CUDA kernels +https://gitlab.com/gromacs/gromacs/-/merge_requests/2499 +Patch added to EasyBuild by Simon Branford (University of Birmingham) +diff --git a/src/gromacs/mdlib/lincs_cuda.cu b/src/gromacs/mdlib/lincs_cuda.cu +index 27ad86f17f..4964a3d040 100644 +--- a/src/gromacs/mdlib/lincs_cuda.cu ++++ b/src/gromacs/mdlib/lincs_cuda.cu +@@ -382,11 +382,15 @@ __launch_bounds__(c_maxThreadsPerBlock) __global__ + sm_threadVirial[d * blockDim.x + (threadIdx.x + dividedAt)]; + } + } +- // Syncronize if not within one warp ++ // Synchronize if not within one warp + if (dividedAt > warpSize / 2) + { + __syncthreads(); + } ++ else ++ { ++ __syncwarp(); ++ } + } + // First 6 threads in the block add the results of 6 tensor components to the global memory address. + if (threadIdx.x < 6) +diff --git a/src/gromacs/mdlib/settle_cuda.cu b/src/gromacs/mdlib/settle_cuda.cu +index c02f0d5884..c6ca1e2452 100644 +--- a/src/gromacs/mdlib/settle_cuda.cu ++++ b/src/gromacs/mdlib/settle_cuda.cu +@@ -352,6 +352,10 @@ __launch_bounds__(c_maxThreadsPerBlock) __global__ + { + __syncthreads(); + } ++ else ++ { ++ __syncwarp(); ++ } + } + // First 6 threads in the block add the 6 components of virial to the global memory address + if (tib < 6) From 90fad42491f0bfef1fb48edb56215a369fd376fc Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 11 Aug 2022 10:20:40 +0200 Subject: [PATCH 4462/9987] adding easyconfigs: Mercurial-6.2-GCCcore-11.3.0.eb --- .../Mercurial/Mercurial-6.2-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mercurial/Mercurial-6.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-6.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..76559a0dc8a --- /dev/null +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.2-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +## +# Author: Robert Mijakovic +## +easyblock = "PythonPackage" + +name = 'Mercurial' +version = '6.2' + +homepage = 'https://www.mercurial-scm.org' +description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects +of any size and offers an easy and intuitive interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.mercurial-scm.org/release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d382b5e3fab8931126013201731416574b35ae85787404bb2a0819f41bb88972'] + +dependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_commands = ["hg --help"] + +moduleclass = 'tools' From c1cbd3d3980430d4668ec103e4e3823fda095b2d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 11 Aug 2022 10:56:14 +0200 Subject: [PATCH 4463/9987] adding easyconfigs: HDF5-1.13.1-GCCcore-11.3.0-serial.eb --- .../HDF5/HDF5-1.13.1-GCCcore-11.3.0-serial.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-GCCcore-11.3.0-serial.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-GCCcore-11.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-GCCcore-11.3.0-serial.eb new file mode 100644 index 00000000000..b73831007eb --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-GCCcore-11.3.0-serial.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.13.1' +versionsuffix = '-serial' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From b2dbaeec7a19cd2dd1673063ad4ba0c6c7e9bf46 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 11 Aug 2022 11:59:10 +0100 Subject: [PATCH 4464/9987] remove unecessary patch in recent JupyterLab --- .../j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb | 7 +------ .../j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb | 7 +------ .../j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb | 7 +------ .../j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb | 7 +------ 4 files changed, 4 insertions(+), 24 deletions(-) mode change 100644 => 100755 easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb mode change 100644 => 100755 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb mode change 100644 => 100755 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb mode change 100644 => 100755 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb old mode 100644 new mode 100755 index ce2bcb29a86..1f63a8e3025 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb @@ -29,13 +29,8 @@ exts_list = [ 'checksums': ['5431d9dde96659364b7cc877693d5d21e7b80cea7ae3959ecc2b87518e5f5d8c'], }), (name, version, { - 'patches': ['%(name)s-1.2.5_set-app-path-for-easybuild.patch'], 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': [ - 'c8377bee30504919c1e79949f9fe35443ab7f5c4be622c95307e8108410c8b8c', # jupyterlab-2.2.8.tar.gz - # JupyterLab-1.2.5_set-app-path-for-easybuild.patch - 'a219b1071f37f848f7e79c6800149c0b2386a2b748be43288bc32af8e7dab668', - ], + 'checksums': ['c8377bee30504919c1e79949f9fe35443ab7f5c4be622c95307e8108410c8b8c'], }), ] diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb old mode 100644 new mode 100755 index 6a8b7a7bec4..adc0ec67695 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb @@ -49,13 +49,8 @@ exts_list = [ 'checksums': ['f300adf6bb0a952bebe9c807a3b2a345d62da39b476b4f69ea0dc6b5f3f6b97d'], }), (name, version, { - 'patches': ['%(name)s-1.2.5_set-app-path-for-easybuild.patch'], 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': [ - '7ad4fbe1f6d38255869410fd151a8b15692a663ca97c0a8146b3f5c40e275c23', # jupyterlab-3.0.16.tar.gz - # JupyterLab-1.2.5_set-app-path-for-easybuild.patch - 'a219b1071f37f848f7e79c6800149c0b2386a2b748be43288bc32af8e7dab668', - ], + 'checksums': ['7ad4fbe1f6d38255869410fd151a8b15692a663ca97c0a8146b3f5c40e275c23'], }), ] diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb old mode 100644 new mode 100755 index 64b0887fb60..97db9ab8ef0 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb @@ -49,13 +49,8 @@ exts_list = [ 'checksums': ['31457ef564febc42043bc539356c804f6f9144f602e2852150bf0820ed6d7e18'], }), (name, version, { - 'patches': ['%(name)s-1.2.5_set-app-path-for-easybuild.patch'], 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': [ - '6d2ada6a333861f33a1b555d3cb7b07aa9d1ab80f07997b3d0c43878a98c1174', # jupyterlab-3.1.6.tar.gz - # JupyterLab-1.2.5_set-app-path-for-easybuild.patch - 'a219b1071f37f848f7e79c6800149c0b2386a2b748be43288bc32af8e7dab668', - ], + 'checksums': ['6d2ada6a333861f33a1b555d3cb7b07aa9d1ab80f07997b3d0c43878a98c1174'], }), ] diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb old mode 100644 new mode 100755 index 44065e7ecf2..c48fd54eda3 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb @@ -49,13 +49,8 @@ exts_list = [ 'checksums': ['3fb84a5813d6d836ceda773fb2d4e9ef3c7944dbc1b45a8d59d98641a80de80a'], }), (name, version, { - 'patches': ['%(name)s-1.2.5_set-app-path-for-easybuild.patch'], 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': [ - '5e4e99868c4f385372686767781408acbb9004b690b198b45597ba869802334b', # jupyterlab-3.2.8.tar.gz - # JupyterLab-1.2.5_set-app-path-for-easybuild.patch - 'a219b1071f37f848f7e79c6800149c0b2386a2b748be43288bc32af8e7dab668', - ], + 'checksums': ['5e4e99868c4f385372686767781408acbb9004b690b198b45597ba869802334b'], }), ] From b0d4db84fce37408b0badc2edc7e566d87666e02 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 11 Aug 2022 14:24:51 +0200 Subject: [PATCH 4465/9987] Change Graphviz-5.0.0-GCCcore-11.3.0.eb to use Java/11 --- .../easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb index 564c8d5ede5..574ffbd5cd3 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb @@ -32,7 +32,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '17', '', True), + ('Java', '11', '', True), ('Python', '3.10.4'), ('FriBidi', '1.0.12'), ('Gdk-Pixbuf', '2.42.8'), From ca102963e6d8d2e87841fe660b48c6b7db8695f4 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 11 Aug 2022 19:19:39 +0200 Subject: [PATCH 4466/9987] adding easyconfigs: ant-1.10.12-Java-11.eb --- .../easyconfigs/a/ant/ant-1.10.12-Java-11.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.12-Java-11.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.12-Java-11.eb b/easybuild/easyconfigs/a/ant/ant-1.10.12-Java-11.eb new file mode 100644 index 00000000000..9e7b8f9f877 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.12-Java-11.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'ant' +version = '1.10.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" + +toolchain = SYSTEM + +source_urls = ['https://archive.apache.org/dist/ant/binaries/'] +sources = ['apache-%(name)s-%(version)s-bin.tar.gz'] +checksums = ['4b3b557279bae4fb80210a5679180fdae3498b44cfd13368e3386e2a21dd853b'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 8fa6b9ec38a2bf611d0fd73ea21b874c91a49700 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 12 Aug 2022 09:44:01 +0200 Subject: [PATCH 4467/9987] Add Graphviz-5.0.0_skip-install-data-hook.patch --- ...raphviz-5.0.0_skip-install-data-hook.patch | 96 +++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0_skip-install-data-hook.patch diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0_skip-install-data-hook.patch b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0_skip-install-data-hook.patch new file mode 100644 index 00000000000..96c30b27410 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0_skip-install-data-hook.patch @@ -0,0 +1,96 @@ +don't create directories and install language bindings in non-owned directories +author: Kenneth Hoste (HPC-UGent) +update version 2.42.2: Alex Domingo (VUB) +update version 5.0.0: Simon Pinches +diff -Nru graphviz-5.0.0-orig/tclpkg/Makefile.am graphviz-5.0.0/tclpkg/Makefile.am +--- graphviz-5.0.0-orig/tclpkg/Makefile.am 2022-07-07 17:40:57.000000000 +0200 ++++ graphviz-5.0.0/tclpkg/Makefile.am 2022-08-09 11:38:18.162458502 +0200 +@@ -33,87 +33,7 @@ + # ./configure --prefix=$HOME/graphviz; make; make install + # without root privileges. + install-data-hook: +-if WITH_LUA +- -mkdir -p $(DESTDIR)$(LUA_INSTALL_DIR); +- if test -w $(DESTDIR)$(LUA_INSTALL_DIR); then \ +- (cd $(DESTDIR)$(LUA_INSTALL_DIR); \ +- cp -f $(DESTDIR)$(pkgluadir)/libgv_lua.so gv.so;) \ +- else \ +- echo "Warning: $(LUA_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of lua binding."; \ +- fi +-endif +-if WITH_PERL +- -mkdir -p $(DESTDIR)$(PERL_INSTALL_DIR); +- if test -w $(DESTDIR)$(PERL_INSTALL_DIR); then \ +- (cd $(DESTDIR)$(PERL_INSTALL_DIR); \ +- cp -f $(DESTDIR)$(pkgperldir)/libgv_perl.so gv.so; \ +- cp -f $(DESTDIR)$(pkgperldir)/gv.pm gv.pm;) \ +- else \ +- echo "Warning: $(PERL_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of perl binding."; \ +- fi +-endif +-if WITH_PHP +- -mkdir -p $(DESTDIR)$(PHP_INSTALL_DIR); +- if test -w $(DESTDIR)$(PHP_INSTALL_DIR); then \ +- (cd $(DESTDIR)$(PHP_INSTALL_DIR); \ +- cp -f $(DESTDIR)$(pkgphpdir)/libgv_php.so gv.so;) \ +- else \ +- echo "Warning: $(PHP_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of php binding."; \ +- fi +- -mkdir -p $(DESTDIR)$(PHP_INSTALL_DATADIR); +- if test -w $(DESTDIR)$(PHP_INSTALL_DATADIR); then \ +- (cd $(DESTDIR)$(PHP_INSTALL_DATADIR); \ +- cp -f $(DESTDIR)$(pkgphpdir)/gv.php gv.php;) \ +- else \ +- echo "Warning: $(PHP_INSTALL_DATADIR) is not writable."; \ +- echo "Skipping system installation of php binding."; \ +- fi +-endif +-if WITH_PYTHON +- -mkdir -p $(DESTDIR)$(PYTHON_INSTALL_DIR); +- if test -w $(DESTDIR)$(PYTHON_INSTALL_DIR); then \ +- (cd $(DESTDIR)$(PYTHON_INSTALL_DIR); \ +- cp -f $(DESTDIR)$(pkgpythondir)/libgv_python.so _gv.so; \ +- cp -f $(DESTDIR)$(pkgpythondir)/gv.py gv.py;) \ +- else \ +- echo "Warning: $(PYTHON_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of python binding."; \ +- fi +-endif +-if WITH_PYTHON3 +- -mkdir -p $(DESTDIR)$(PYTHON3_INSTALL_DIR); +- if test -w $(DESTDIR)$(PYTHON3_INSTALL_DIR); then \ +- (cd $(DESTDIR)$(PYTHON3_INSTALL_DIR); \ +- cp -f $(DESTDIR)$(pkgpython3dir)/libgv_python3.so _gv.so; \ +- cp -f $(DESTDIR)$(pkgpython3dir)/gv.py gv.py;) \ +- else \ +- echo "Warning: $(PYTHON3_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of python3 binding."; \ +- fi +-endif +-if WITH_RUBY +- -mkdir -p $(DESTDIR)$(RUBY_INSTALL_DIR); +- if test -w $(DESTDIR)$(RUBY_INSTALL_DIR); then \ +- (cd $(DESTDIR)$(RUBY_INSTALL_DIR); \ +- cp -f $(DESTDIR)$(pkgrubydir)/libgv_ruby.so gv.so;) \ +- else \ +- echo "Warning: $(RUBY_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of ruby binding."; \ +- fi +-endif +-if WITH_TCL +- -mkdir -p $(DESTDIR)$(TCL_INSTALL_DIR); +- if test -w $(DESTDIR)$(TCL_INSTALL_DIR)/; then \ +- (cd $(DESTDIR)$(TCL_INSTALL_DIR); \ +- cp -rf $(DESTDIR)$(pkgtcldir) $(PACKAGE_NAME);) \ +- else \ +- echo "Warning: $(TCL_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of tcl bindings."; \ +- fi +-endif ++ echo "(installing in non-owned directories has been patched out)" + endif + + # removal of installs into $(xxx_INSTALL_DIR) fail if root From e049494cca2c47be3ca82953c520334c62c7bc51 Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 12 Aug 2022 14:34:56 +0200 Subject: [PATCH 4468/9987] adding easyconfigs: BBMap-38.98-GCC-11.2.0.eb --- .../b/BBMap/BBMap-38.98-GCC-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb new file mode 100644 index 00000000000..e2bd5bd4075 --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '38.98' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['cdc3b8e0530c4a83a728d28da31f0e7ead2bc233d4bf21cd1916572c9b2d0e0e'] + +dependencies = [('Java', '11', '', True)] + +prebuildopts = 'cd jni && ' + +local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % local_suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" + +moduleclass = 'bio' From e2298036582c60fbeb6656fc6bd55fe0ce3d06fe Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Sat, 13 Aug 2022 13:42:07 +0200 Subject: [PATCH 4469/9987] Update easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb --- .../GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb index 83341fe491d..12a2c26d4e1 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb @@ -46,6 +46,7 @@ patches = [ 'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch', 'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch', 'GROMACS-2021.3_skip_test_for_plumed.patch', + 'GROMACS-2021_add-missing-sync.patch', ] checksums = [ 'eba63fe6106812f72711ef7f76447b12dd1ee6c81b3d8d4d0e3098cd9ea009b6', # gromacs-2021.5.tar.gz From 1e5509eda01eecf83058421891ab0b5ae8d7ee36 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Sat, 13 Aug 2022 13:42:14 +0200 Subject: [PATCH 4470/9987] Update easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb --- .../GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb index 12a2c26d4e1..bbe65cdd01e 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb @@ -60,6 +60,7 @@ checksums = [ '7d39da0b431fbc9e94e857552246eb0ec892f26b13e519b3706785cc5e01a563', # GROMACS-2021.3_skip_test_for_plumed.patch 'c06d0a8c3e75b232224f46bc3b70e135c4c02ec4151712970f5edd85d890f018', + '52ee257309ff7761c2dd5b26de7dbc63f8ba698082adb88e2843f90e3f9168bf', # GROMACS-2021_add-missing-sync.patch ] builddependencies = [ From ffd384dde63115304cdb0bc2ddd24d79954b279c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 15 Aug 2022 10:37:41 +0200 Subject: [PATCH 4471/9987] Add comment to descript purpose of preconfigopts --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb index 1594fbc4676..524393cf31b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb @@ -36,6 +36,9 @@ dependencies = [ ('UCC', '1.0.0'), ] +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. preconfigopts = ' && '.join([ 'cd config', 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', From 259f4804fbe015d8797c97379295d4849e87a076 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 15 Aug 2022 12:30:16 +0200 Subject: [PATCH 4472/9987] Include some EC constants in flake8 config Avoids linter warnings in e.g. IDEs when developing ECs. No functional change. --- setup.cfg | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 67 insertions(+) diff --git a/setup.cfg b/setup.cfg index 9b93cac3d31..1209f2f4ea8 100644 --- a/setup.cfg +++ b/setup.cfg @@ -5,6 +5,73 @@ zip_ok = 0 [flake8] max-line-length = 120 +builtins = + # eb --avail-cfgfile-constants + ARCH, + EXTERNAL_MODULE, + HOME, + OS_NAME, + OS_PKG_IBVERBS_DEV, + OS_PKG_OPENSSL_BIN, + OS_PKG_OPENSSL_DEV, + OS_PKG_OPENSSL_LIB, + OS_PKG_PAM_DEV, + OS_TYPE, + OS_VERSION, + SYSTEM, + SYS_PYTHON_VERSION, + # https://docs.easybuild.io/en/latest/version-specific/easyconfig_templates.html + APACHE_SOURCE, + BITBUCKET_SOURCE, + BITBUCKET_DOWNLOADS, + CRAN_SOURCE, + FTPGNOME_SOURCE, + GITHUB_SOURCE, + GITHUB_LOWER_SOURCE, + GNU_SAVANNAH_SOURCE, + GNU_SOURCE, + GOOGLECODE_SOURCE, + LAUNCHPAD_SOURCE, + PYPI_SOURCE, + PYPI_LOWER_SOURCE, + R_SOURCE, + SOURCEFORGE_SOURCE, + XORG_DATA_SOURCE, + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + XORG_UTIL_SOURCE, + XORG_XCB_SOURCE, + SHLIB_EXT, + SOURCE_TAR_GZ, + SOURCELOWER_TAR_GZ, + SOURCE_TAR_XZ, + SOURCELOWER_TAR_XZ, + SOURCE_TAR_BZ2, + SOURCELOWER_TAR_BZ2, + SOURCE_TGZ, + SOURCELOWER_TGZ, + SOURCE_TXZ, + SOURCELOWER_TXZ, + SOURCE_TBZ2, + SOURCELOWER_TBZ2, + SOURCE_TB2, + SOURCELOWER_TB2, + SOURCE_GTGZ, + SOURCELOWER_GTGZ, + SOURCE_ZIP, + SOURCELOWER_ZIP, + SOURCE_TAR, + SOURCELOWER_TAR, + SOURCE_XZ, + SOURCELOWER_XZ, + SOURCE_TAR_Z, + SOURCELOWER_TAR_Z, + SOURCE_WHL, + SOURCELOWER_WHL, + SOURCE_PY2_WHL, + SOURCELOWER_PY2_WHL, + SOURCE_PY3_WHL, + SOURCELOWER_PY3_WHL [sdist] # Don't remove CVS and RCS directories From 9d4e094c1256e1dfa69bcb21fe521aa6fc41488f Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 15 Aug 2022 12:21:43 +0100 Subject: [PATCH 4473/9987] HDF5 lib variable corrected in patchfile, checksum updated of patchfile --- .../easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb | 2 +- easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb b/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb index 1ff733e3434..9b3117a3d99 100644 --- a/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb +++ b/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb @@ -23,7 +23,7 @@ patches = ['quickpic-makefile.patch'] checksums = [ '83d3664542ce0a1c1fa055802e214bdba98790ee512f1f2525d0c087d20d88af', # QuickPIC-20210224.tar.gz - '3d0e8d2d746f5adec3f50ae7df6bf61de1e5ac4ca8f7ae7d3cf15b1eab57d8ec', # quickpic-makefile.patch + 'fd4be47519513ca3add974e5c5964707a7534ef68ad850f775fae3d8e0cdc987', # quickpic-makefile.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch b/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch index 4a834c6cf0f..7163e61dd9b 100644 --- a/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch +++ b/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch @@ -20,8 +20,8 @@ index b2f08f0..c1538cf 100644 -HDF5_LIB =/usr/local/hdf5/lib -HDF5_INC =/usr/local/hdf5/include -+HDF5_LIB =${EBROOTHDF5}/include -+HDF5_INC =${EBROOTHDF5}/lib ++HDF5_LIB =${EBROOTHDF5}/lib ++HDF5_INC =${EBROOTHDF5}/include HDF_LIBPATH_GF_OPENMPI= -L$(HDF5_LIB) -lhdf5_fortran -lhdf5_hl -lhdf5 -lz -HDF_INCLUDE_PATH_GF_OPENMPI= -I$(HDF5_INC) -I${HDF5_LIB} -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 From 948d9a8d27a68e96951b429939fa772013a0847c Mon Sep 17 00:00:00 2001 From: Bob Date: Mon, 15 Aug 2022 13:23:19 +0200 Subject: [PATCH 4474/9987] adding easyconfigs: GetOrganelle-1.7.6.1-foss-2021b.eb --- .../GetOrganelle-1.7.6.1-foss-2021b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.6.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.6.1-foss-2021b.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.6.1-foss-2021b.eb new file mode 100644 index 00000000000..2898fcacaac --- /dev/null +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.6.1-foss-2021b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'GetOrganelle' +version = '1.7.6.1' + +homepage = 'https://github.com/Kinggerm/GetOrganelle' +description = """This toolkit assemblies organelle genome from genomic skimming data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/Kinggerm/GetOrganelle/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['de768619864ca40d7e97e5059db1187c64c53f764c4065731d955c1c53e4ef1d'] + +dependencies = [ + ('Python', '3.9.6'), + ('Bandage', '0.9.0'), + ('SciPy-bundle', '2021.10'), + ('sympy', '1.9'), + ('SPAdes', '3.15.3'), + ('Bowtie2', '2.4.4'), + ('BLAST+', '2.12.0'), + ('Perl', '5.34.0'), + ('matplotlib', '3.4.3') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': False} + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_commands = ["get_organelle_from_reads.py -h"] + +sanity_check_paths = { + 'files': ['bin/check_annotations.py', 'bin/get_organelle_from_reads.py', 'bin/slim_graph.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 657d34cebacc6d3fae34910725796578b602cb15 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 15 Aug 2022 16:08:02 +0200 Subject: [PATCH 4475/9987] Fixed dowload name + fixed sanity check command --- .../easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb b/easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb index 70b5db53c77..03be95afbaa 100644 --- a/easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb +++ b/easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb @@ -8,10 +8,10 @@ homepage = 'https://olaflow.github.io/' description = """olaFlow CFD Suite is a free and open source project committed to bringing the latest advances for the simulation of wave dynamics to the OpenFOAM® and FOAM-extend communities.""" +source_urls = ['https://github.com/phicau/olaFlow/archive/'] sources = [{ - 'source_urls': ['https://github.com/phicau/olaFlow/archive/'], - 'filename': '%s.tar.gz' % local_commit, - 'download_filename': '%(name)s-%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz', + 'download_filename': '%s.tar.gz' % local_commit, }] checksums = ['126777c2dc5e8fe563251ce9cc8438bd2e90771cc5a9ea2fc47bd4679502c08b'] @@ -31,6 +31,6 @@ sanity_check_paths = { 'dirs': [] } -sanity_check_commands = ["olaFlow -help"] +sanity_check_commands = ["source $FOAM_BASH && olaFlow -help"] moduleclass = 'cae' From ddd77368e9c6ac46ae34ebd77853ba806c221522 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 15 Aug 2022 15:50:35 +0100 Subject: [PATCH 4476/9987] HDF5 changed to 1.12.x, required configure flag added --- .../easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb b/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb index 9b3117a3d99..43ec12caea4 100644 --- a/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb +++ b/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb @@ -27,12 +27,16 @@ checksums = [ ] dependencies = [ - ('HDF5', '1.10.8'), + ('HDF5', '1.12.1'), ('json-fortran', '8.3.0'), ] prebuildopts = 'cd source && ' +# See here for documentation +# https://portal.hdfgroup.org/display/HDF5/Migrating+from+HDF5+1.10+to+HDF5+1.12 +configopts = ' --with-default-api-version=v110' + parallel = 1 files_to_copy = [(['source/qpic.e'], 'bin')] From 0e318ad00a06e3439bf29e5c7bc8f982b7a69426 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 15 Aug 2022 17:00:34 +0200 Subject: [PATCH 4477/9987] Skip failing test_optim/test_tensorpipe_agent --- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 8 +++++++- .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 6 +++++- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 8 +++++++- 3 files changed, 19 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 4f48922d68c..68f81ba8ce2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -85,9 +85,15 @@ excluded_tests = { # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html 'distributed/test_distributed_fork', 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', - ] + ], + 'POWER': [ + # Works when run alone, fails when run as part of the suite. So far only observed on PPC + 'distributed/rpc/test_tensorpipe_agent', + ], } runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index 11fe7f4935e..b4662e2722d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -123,7 +123,11 @@ excluded_tests = { 'test_optim', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', - ] + ], + 'POWER': [ + # Works when run alone, fails when run as part of the suite. So far only observed on PPC + 'distributed/rpc/test_tensorpipe_agent', + ], } runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index 4aac5785617..e7070b8d189 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -117,9 +117,15 @@ excluded_tests = { # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html 'distributed/test_distributed_fork', 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', # Test from this suite timeout often. The process group backend is deprecated anyway 'distributed/rpc/test_process_group_agent', - ] + ], + 'POWER': [ + # Works when run alone, fails when run as part of the suite. So far only observed on PPC + 'distributed/rpc/test_tensorpipe_agent', + ], } runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' From b6d1d2ac1cf049799a61a8d37b43a898fe3f5d81 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 15 Aug 2022 17:17:20 +0200 Subject: [PATCH 4478/9987] Exclude failing test in TensorFlow 2.4.1 --- .../TensorFlow/TensorFlow-2.4.1-foss-2020b.eb | 5 +++-- ...rFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb | 5 +++-- .../TensorFlow-2.4.1-fosscuda-2020b.eb | 5 +++-- .../TensorFlow/TensorFlow-2.4.1_add-ldl.patch | 21 +++++++++++++++++++ 4 files changed, 30 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1_add-ldl.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb index 2342aee9b61..b37d88e8be6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-foss-2020b.eb @@ -165,10 +165,10 @@ exts_list = [ 'TensorFlow-2.4.0_fix-eigen-on-power.patch', 'TensorFlow-2.4.0_downgrade-required-versions.patch', 'TensorFlow-2.4.0_add-protobuf-deps.patch', - 'TensorFlow-2.4.0_add-ldl.patch', 'TensorFlow-2.4.0_add-missing-llvm-deps.patch', 'TensorFlow-2.4.0_fix-absl-on-power.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_add-ldl.patch', 'TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', @@ -190,6 +190,7 @@ exts_list = [ '-//tensorflow/c/eager:c_api_distributed_test_gpu', # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test', '-//tensorflow/c/eager:c_api_remote_function_test_gpu', '-//tensorflow/c/eager:c_api_remote_test_gpu', # Invalid alignment: https://github.com/tensorflow/tensorflow/issues/46460 @@ -216,13 +217,13 @@ exts_list = [ 'ac8f53662ad0bb660089c17bb433faf1ce3c2238234a2c3be7d92c8e02c1a8d6', # TensorFlow-2.4.0_add-protobuf-deps.patch '0ae2f4f1f1dc5b85f61edbe8a4a91dcffd5cf7588fa46c6a143455e4bc41a64e', - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch # TensorFlow-2.4.0_add-missing-llvm-deps.patch 'ce8c41e75f9854e547d03de99ae72cf41afa967b20439e864bc4af3dd4f565c7', # TensorFlow-2.4.0_fix-absl-on-power.patch 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', # TensorFlow-2.4.0_dont-use-var-lock.patch 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + 'ab57637e3e64a5ff8345573effed2b229c33579b9ac3c8ceb7e554d236890d4a', # TensorFlow-2.4.1_add-ldl.patch # TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch 'f384cd97e004673ae530b6e5cc826f8fddb46646991f1a228fc07b2aac87ee80', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb index e6fb64444a9..0553100e9ad 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb @@ -154,10 +154,10 @@ exts_list = [ 'TensorFlow-2.4.0_fix-eigen-on-power.patch', 'TensorFlow-2.4.0_downgrade-required-versions.patch', 'TensorFlow-2.4.0_add-protobuf-deps.patch', - 'TensorFlow-2.4.0_add-ldl.patch', 'TensorFlow-2.4.0_add-missing-llvm-deps.patch', 'TensorFlow-2.4.0_fix-absl-on-power.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_add-ldl.patch', 'TensorFlow-2.4.1-fix-alias-violation-in-absl.patch', 'TensorFlow-2.4.1_fix-min-priority-test.patch', 'TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch', @@ -182,6 +182,7 @@ exts_list = [ '-//tensorflow/c/eager:c_api_distributed_test_gpu', # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test', '-//tensorflow/c/eager:c_api_remote_function_test_gpu', '-//tensorflow/c/eager:c_api_remote_test_gpu', # Invalid alignment: https://github.com/tensorflow/tensorflow/issues/46460 @@ -210,12 +211,12 @@ exts_list = [ 'ac8f53662ad0bb660089c17bb433faf1ce3c2238234a2c3be7d92c8e02c1a8d6', # TensorFlow-2.4.0_add-protobuf-deps.patch '0ae2f4f1f1dc5b85f61edbe8a4a91dcffd5cf7588fa46c6a143455e4bc41a64e', - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch # TensorFlow-2.4.0_add-missing-llvm-deps.patch 'ce8c41e75f9854e547d03de99ae72cf41afa967b20439e864bc4af3dd4f565c7', # TensorFlow-2.4.0_fix-absl-on-power.patch 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', # TensorFlow-2.4.0_dont-use-var-lock.patch + 'ab57637e3e64a5ff8345573effed2b229c33579b9ac3c8ceb7e554d236890d4a', # TensorFlow-2.4.1_add-ldl.patch 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', # TensorFlow-2.4.1-fix-alias-violation-in-absl.patch '33744bbf4ccbd5995e5e12336eb571c849ccbbc0e493fee8a3cf03bc7d5a0919', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index ea58071275f..0feb8006d4d 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -166,10 +166,10 @@ exts_list = [ 'TensorFlow-2.4.0_fix-eigen-on-power.patch', 'TensorFlow-2.4.0_downgrade-required-versions.patch', 'TensorFlow-2.4.0_add-protobuf-deps.patch', - 'TensorFlow-2.4.0_add-ldl.patch', 'TensorFlow-2.4.0_add-missing-llvm-deps.patch', 'TensorFlow-2.4.0_fix-absl-on-power.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.4.1_add-ldl.patch', 'TensorFlow-2.4.1_fix-min-priority-test.patch', 'TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch', ], @@ -193,6 +193,7 @@ exts_list = [ '-//tensorflow/c/eager:c_api_distributed_test_gpu', # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test', '-//tensorflow/c/eager:c_api_remote_function_test_gpu', '-//tensorflow/c/eager:c_api_remote_test_gpu', # Invalid alignment: https://github.com/tensorflow/tensorflow/issues/46460 @@ -221,13 +222,13 @@ exts_list = [ 'ac8f53662ad0bb660089c17bb433faf1ce3c2238234a2c3be7d92c8e02c1a8d6', # TensorFlow-2.4.0_add-protobuf-deps.patch '0ae2f4f1f1dc5b85f61edbe8a4a91dcffd5cf7588fa46c6a143455e4bc41a64e', - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch # TensorFlow-2.4.0_add-missing-llvm-deps.patch 'ce8c41e75f9854e547d03de99ae72cf41afa967b20439e864bc4af3dd4f565c7', # TensorFlow-2.4.0_fix-absl-on-power.patch 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', # TensorFlow-2.4.0_dont-use-var-lock.patch 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + 'ab57637e3e64a5ff8345573effed2b229c33579b9ac3c8ceb7e554d236890d4a', # TensorFlow-2.4.1_add-ldl.patch # TensorFlow-2.4.1_fix-min-priority-test.patch '389febce9a0612fd457daf4cb18c02f77fc7311bacae0963602a3198d9f2737f', # TensorFlow-2.4.1_remove-duplicate-gpu-tests.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1_add-ldl.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1_add-ldl.patch new file mode 100644 index 00000000000..2f55ddb6183 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1_add-ldl.patch @@ -0,0 +1,21 @@ +The stacktrace library uses dladdr and friends but doesn't link libdl +See https://github.com/tensorflow/tensorflow/issues/45013 and +https://github.com/tensorflow/tensorflow/pull/56606 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/core/platform/default/BUILD b/tensorflow/core/platform/default/BUILD +index 2f94bce8c5b..3d0d04274e4 100644 +--- a/tensorflow/core/platform/default/BUILD ++++ b/tensorflow/core/platform/default/BUILD +@@ -377,6 +377,10 @@ cc_library( + name = "stacktrace_handler", + srcs = ["stacktrace_handler.cc"], + hdrs = ["//tensorflow/core/platform:stacktrace_handler.h"], ++ linkopts = select({ ++ "//tensorflow:windows": [], ++ "//conditions:default": ["-ldl"], ++ }), + linkstatic = 1, + deps = [ + "//tensorflow/core/platform", From 691b2a6f5311a3f79a6485240583a89ac5605781 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 15 Aug 2022 17:24:03 +0200 Subject: [PATCH 4479/9987] Fix checksum --- .../TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb index 0553100e9ad..f2b7555d0c8 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2019b-Python-3.7.4.eb @@ -216,8 +216,8 @@ exts_list = [ # TensorFlow-2.4.0_fix-absl-on-power.patch 'cd0e1181cfc56c259cb57b7f9590816db5f5cde3fab39b3386c001359ca6e9fa', # TensorFlow-2.4.0_dont-use-var-lock.patch - 'ab57637e3e64a5ff8345573effed2b229c33579b9ac3c8ceb7e554d236890d4a', # TensorFlow-2.4.1_add-ldl.patch 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + 'ab57637e3e64a5ff8345573effed2b229c33579b9ac3c8ceb7e554d236890d4a', # TensorFlow-2.4.1_add-ldl.patch # TensorFlow-2.4.1-fix-alias-violation-in-absl.patch '33744bbf4ccbd5995e5e12336eb571c849ccbbc0e493fee8a3cf03bc7d5a0919', # TensorFlow-2.4.1_fix-min-priority-test.patch From e6dff443e3848535791e3cf0c5c2fcecca58a134 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 16 Aug 2022 09:19:42 +0200 Subject: [PATCH 4480/9987] Restore comments dropped by inject-checksums and lower version of setuptools to retain compat with Py3.6. --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb index 99e8c56629b..34fd85c49e0 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb @@ -19,6 +19,7 @@ req_py_minver = 6 use_pip = True exts_list = [ + # stick to pip < 22.0, to maintain compatibility with Python 3.6 ('pip', '21.3.1', { 'use_pip': False, 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], @@ -27,11 +28,13 @@ exts_list = [ 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], }), - ('setuptools', '60.0.3', { + # stick to setuptools < 59.7.0, to maintain compatibility with Python 3.6 + ('setuptools', '59.6.0', { 'source_tmpl': 'setuptools-%(version)s.tar.gz', - 'checksums': ['989ab2d3e632ba23358b8d43950bd46babde5bbb1516760dc5f5ccfe7accdd45'], + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], }), ('reframe', version, { + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", From 4fb6138728ce1bd92dbb5b9586a9e6e5aeaf860f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 16 Aug 2022 09:42:45 +0200 Subject: [PATCH 4481/9987] adding easyconfigs: libaec-1.0.6-GCCcore-11.2.0.eb, libaec-1.0.6-GCCcore-11.3.0.eb --- .../l/libaec/libaec-1.0.6-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ .../l/libaec/libaec-1.0.6-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2d4b3f1ceb2 --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.0.6' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('binutils', '2.37'), +] + +sanity_check_paths = { + 'files': ['bin/aec', 'include/libaec.h', 'include/szlib.h', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["aec --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..122fabeb939 --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.0.6' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['bin/aec', 'include/libaec.h', 'include/szlib.h', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["aec --help"] + +moduleclass = 'lib' From 93a5db56f7678df95dc46a68f9c8e78a63c83a5b Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 16 Aug 2022 21:56:14 +0100 Subject: [PATCH 4482/9987] adding easyconfigs: GKeyll-20220803-foss-2020a-Python-3.8.2.eb --- ...GKeyll-20220803-foss-2020a-Python-3.8.2.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..51b18de2f7d --- /dev/null +++ b/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,55 @@ +# Author J. Sassmannshause (Imperial College London/UK) + +easyblock = 'Waf' + +name = 'GKeyll' +version = '20220803' +local_commit = '4c3e568' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://gkeyll.readthedocs.io' +description = """Gkeyll v2.0 (pronounced as in the book “The Strange Case of Dr. Jekyll +and Mr. Hyde”) is a computational plasma physics code mostly written in C/C++ and LuaJIT. +Gkeyll contains solvers for gyrokinetic equations, Vlasov-Maxwell equations, and +multi-fluid equations. Gkeyll contains ab-initio and novel implementations of a number +of algorithms, and perhaps is unique in using a JIT compiled typeless dynamic language +for as its main implementation language.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +github_account = 'ammarhakim' +source_urls = ['https://github.com/ammarhakim/gkyl/archive'] +sources = ['%s.tar.gz' % local_commit] + +checksums = [ + '075867b602e3a50c13e72f7f0dc680c3591467ce61debd3c9a11f3e5dced0503', # 4c3e568.tar.gz +] + +dependencies = [ + ('Python', '3.8.2'), + ('ADIOS', '20210804', versionsuffix), + ('Eigen', '3.3.7'), + ('LuaJIT2', 'v2.1-20220411'), +] + +configopts = '--luajit-inc-dir=$EBROOTLUAJIT2/include/luajit-2.1/ ' +configopts += '--extra-link-libs=" hdf5 mxml bz2 lz4 z" ' + +parallel = 4 + +# Seems to be required as else all cores are being used +buildopts = ' -j 4' + +sanity_check_paths = { + 'files': ['bin/gkyl', 'bin/gkyl', 'lib/libcomm.%s' % SHLIB_EXT, + 'lib/libdatastruct.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = [ + 'gkyl -version', + 'ctest_Range -?', +] + +moduleclass = 'phys' From e27deb4ab42a636792474eb0febe675a22725f7c Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 16 Aug 2022 22:03:36 +0100 Subject: [PATCH 4483/9987] adding easyconfigs: ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb, ADIOS-20210804-foss-2020a-Python-3.8.2.eb --- .../ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb | 68 +++++++++++++++++ .../ADIOS-20210804-foss-2020a-Python-3.8.2.eb | 73 +++++++++++++++++++ 2 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..2f77e60a662 --- /dev/null +++ b/easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,68 @@ +# Based on ADIOS-1.13.1-foss-2019a-Python-2.7.15.eb +# Updated to foss-2020a toolchain and switched to ConfigureMake +# Mini-XML updated to latest 2.x. version +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'ADIOS' +version = '1.13.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.olcf.ornl.gov/center-projects/adios/' +description = """The Adaptable IO System (ADIOS) provides a simple, +flexible way for scientists to describe the data in their code that may +need to be written, read, or processed outside of the running +simulation.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +github_account = 'ornladios' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_force_use_of_mpi.patch', + '%(name)s-%(version)s_fix_missing_thread_lib.patch', + '%(name)s-%(version)s_fix_search_for_szip.patch', +] +checksums = [ + 'b1c6949918f5e69f701cabfe5987c0b286793f1057d4690f04747852544e157b', # v1.13.1.tar.gz + '81b9b0a77b23d6137f08900a3ecda4471b806c384cf4ad19c4370fc7ca8d9a82', # ADIOS-1.13.1_force_use_of_mpi.patch + 'a66fab38e5daf40978f9e961d810f9cbf189de8db924a403ae42a01d405f6fdc', # ADIOS-1.13.1_fix_missing_thread_lib.patch + '2e21a5041822c8b57554eb977a3135637c2714d377eee3b0194d377f1458cdab', # ADIOS-1.13.1_fix_search_for_szip.patch +] + +builddependencies = [ + ('Autotools', '20180311'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Szip', '2.1.1'), + ('lz4', '1.9.2'), + ('netCDF', '4.7.4'), + ('Mini-XML', '2.12'), +] + +preconfigopts = ' autoreconf -i && ' +configopts = '--with-zlib=$EBROOTZLIB -with-bzip2=$EBROOTBZIP2 --with-netcdf==$EBROOTNETCDF ' +configopts += '--with-lz4=$EBROOTLZ4 --with-mxml=$EBROOTMINIMINXML --with-phdf5=$EBROOTHDF5 ' + +fix_python_shebang_for = ['bin/gpp.py'] + +runtest = ' check' + +sanity_check_paths = { + 'files': ['bin/adios_list_methods', 'bin/bpappend'], + 'dirs': ['etc/skel/templates', 'lib/python'], +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..71a676dc339 --- /dev/null +++ b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,73 @@ +# Based on ADIOS-1.13.1-foss-2019a-Python-2.7.15.eb +# Updated to foss-2020a toolchain and switched to ConfigureMake +# Latest version from GitHub +# Mini-XML updated to latest 2.x. version +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'ADIOS' +version = '20210804' +local_commit = 'de85222' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.olcf.ornl.gov/center-projects/adios/' +description = """The Adaptable IO System (ADIOS) provides a simple, +flexible way for scientists to describe the data in their code that may +need to be written, read, or processed outside of the running +simulation.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True} + +github_account = 'ornladios' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] + +patches = [ + '%(name)s-1.13.1_force_use_of_mpi.patch', + '%(name)s-1.13.1_fix_missing_thread_lib.patch', + '%(name)s-1.13.1_fix_search_for_szip.patch', +] +checksums = [ + 'c58af40cbdb13843de2c2c157379d069880835c9b932ad05e774910ec23a468f', # v1.13.1.tar.gz + '81b9b0a77b23d6137f08900a3ecda4471b806c384cf4ad19c4370fc7ca8d9a82', # ADIOS-1.13.1_force_use_of_mpi.patch + 'a66fab38e5daf40978f9e961d810f9cbf189de8db924a403ae42a01d405f6fdc', # ADIOS-1.13.1_fix_missing_thread_lib.patch + '2e21a5041822c8b57554eb977a3135637c2714d377eee3b0194d377f1458cdab', # ADIOS-1.13.1_fix_search_for_szip.patch +] + +builddependencies = [ + ('Autotools', '20180311'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Szip', '2.1.1'), + ('lz4', '1.9.2'), + ('netCDF', '4.7.4'), + ('Mini-XML', '2.12'), +] + +preconfigopts = ' autoreconf -i && ' +configopts = '--with-zlib=$EBROOTZLIB -with-bzip2=$EBROOTBZIP2 --with-netcdf==$EBROOTNETCDF ' +configopts += '--with-lz4=$EBROOTLZ4 --with-mxml=$EBROOTMINIMINXML --with-phdf5=$EBROOTHDF5 ' + +fix_python_shebang_for = ['bin/gpp.py'] + +runtest = ' check' + +# options = {'modulename': False} + +sanity_check_paths = { + 'files': ['bin/adios_list_methods', 'bin/bpappend'], + 'dirs': ['etc/skel/templates', 'lib/python'], +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python', +} + +moduleclass = 'phys' From 5333b9c63f52a4b58058eef9aa0b4db73f89ec35 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 16 Aug 2022 22:08:07 +0100 Subject: [PATCH 4484/9987] adding easyconfigs: Mini-XML-2.12-GCCcore-9.3.0.eb, Mini-XML-3.3-GCCcore-11.2.0.eb --- .../m/Mini-XML/Mini-XML-2.12-GCCcore-9.3.0.eb | 23 +++++++++++++++++++ .../m/Mini-XML/Mini-XML-3.3-GCCcore-11.2.0.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mini-XML/Mini-XML-2.12-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/Mini-XML/Mini-XML-2.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/Mini-XML/Mini-XML-2.12-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..9035db82f73 --- /dev/null +++ b/easybuild/easyconfigs/m/Mini-XML/Mini-XML-2.12-GCCcore-9.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Mini-XML' +version = '2.12' + +homepage = 'https://www.msweet.org/mxml' +description = """Mini-XML is a small XML parsing library that you can use to read XML data files or strings in your + application without requiring large non-standard libraries""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/michaelrsweet/mxml/releases/download/v%(version)s/'] +sources = ['mxml-%(version)s.tar.gz'] +checksums = ['6bfb53baa1176e916855bd3b6d592fd5b962c3c259aacdb5670d90c57ce4034f'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['include/mxml.h', 'lib/libmxml.a', 'lib/libmxml.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e973f2a981a --- /dev/null +++ b/easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.3-GCCcore-11.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Mini-XML' +version = '3.3' + +homepage = 'https://www.msweet.org/mxml' +description = """Mini-XML is a small XML parsing library that you can use to read XML data files or strings in your + application without requiring large non-standard libraries""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/michaelrsweet/mxml/releases/download/v%(version)s/'] +sources = ['mxml-%(version)s.tar.gz'] +checksums = ['7cf976366f9e8e4f8cff7d35a59bcf6201c769fce9e58015d64f4b6de1fe3dd8'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['include/mxml.h', 'lib/libmxml.a', 'lib/libmxml.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +moduleclass = 'lib' From b1dac1b8591960841eda698bf071a0ff6c83f5f9 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 16 Aug 2022 22:14:22 +0100 Subject: [PATCH 4485/9987] adding easyconfigs: LuaJIT2-v2.1-20220411-GCC-9.3.0.eb --- .../LuaJIT2-v2.1-20220411-GCC-9.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/LuaJIT2/LuaJIT2-v2.1-20220411-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/l/LuaJIT2/LuaJIT2-v2.1-20220411-GCC-9.3.0.eb b/easybuild/easyconfigs/l/LuaJIT2/LuaJIT2-v2.1-20220411-GCC-9.3.0.eb new file mode 100644 index 00000000000..5adb862878c --- /dev/null +++ b/easybuild/easyconfigs/l/LuaJIT2/LuaJIT2-v2.1-20220411-GCC-9.3.0.eb @@ -0,0 +1,31 @@ +# This is the LuaJIT fork from openresty, not to be mixed up +# with the original LuaJIT version! +# Autor: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = "LuaJIT2" +version = "v2.1-20220411" + +homepage = "https://github.com/openresty/luajit2" +description = """openresty/luajit2 - OpenResty's maintained branch of LuaJIT. +LuaJIT is a Just-In-Time Compiler (JIT) for the Lua +programming language. Lua is a powerful, dynamic and light-weight programming +language. It may be embedded or used as a general-purpose, stand-alone +language. """ + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://github.com/openresty/luajit2/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['d3f2c870f8f88477b01726b32accab30f6e5d57ae59c5ec87374ff73d0794316'] + +skipsteps = ['configure'] +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/luajit"], + 'dirs': [] +} + +moduleclass = "lang" From 79ae0c8289cac36e76a8b917873c9e9a44750274 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 16 Aug 2022 22:18:55 +0100 Subject: [PATCH 4486/9987] Version 3.3 replaced with bugfix 3.3.1 one --- ...3.3-GCCcore-11.2.0.eb => Mini-XML-3.3.1-GCCcore-11.2.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/m/Mini-XML/{Mini-XML-3.3-GCCcore-11.2.0.eb => Mini-XML-3.3.1-GCCcore-11.2.0.eb} (86%) diff --git a/easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.3.1-GCCcore-11.2.0.eb similarity index 86% rename from easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.3-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.3.1-GCCcore-11.2.0.eb index e973f2a981a..594f3ec179d 100644 --- a/easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/Mini-XML/Mini-XML-3.3.1-GCCcore-11.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Mini-XML' -version = '3.3' +version = '3.3.1' homepage = 'https://www.msweet.org/mxml' description = """Mini-XML is a small XML parsing library that you can use to read XML data files or strings in your @@ -11,7 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/michaelrsweet/mxml/releases/download/v%(version)s/'] sources = ['mxml-%(version)s.tar.gz'] -checksums = ['7cf976366f9e8e4f8cff7d35a59bcf6201c769fce9e58015d64f4b6de1fe3dd8'] +checksums = ['0c663ed1fe393b5619f80101798202eea43534abd7c8aff389022fd8c1dacc32'] builddependencies = [('binutils', '2.37')] From 157d368b0788bb594995037d4690ee38a7c1f31c Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 16 Aug 2022 22:57:04 +0100 Subject: [PATCH 4487/9987] ZFP added for ADIOS-20210804, pic=true added for both --- .../a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb | 2 +- .../a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb index 2f77e60a662..34ed5ff5be3 100644 --- a/easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb @@ -16,7 +16,7 @@ need to be written, read, or processed outside of the running simulation.""" toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'pic': True} github_account = 'ornladios' source_urls = [GITHUB_SOURCE] diff --git a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb index 71a676dc339..f8e482c195f 100644 --- a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb @@ -18,7 +18,7 @@ need to be written, read, or processed outside of the running simulation.""" toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'pic': True} github_account = 'ornladios' source_urls = [GITHUB_SOURCE] @@ -49,18 +49,18 @@ dependencies = [ ('lz4', '1.9.2'), ('netCDF', '4.7.4'), ('Mini-XML', '2.12'), + ('zfp', '1.0.0'), ] -preconfigopts = ' autoreconf -i && ' +preconfigopts = ' autoreconf -i && export LIBS="-lgomp" && ' configopts = '--with-zlib=$EBROOTZLIB -with-bzip2=$EBROOTBZIP2 --with-netcdf==$EBROOTNETCDF ' configopts += '--with-lz4=$EBROOTLZ4 --with-mxml=$EBROOTMINIMINXML --with-phdf5=$EBROOTHDF5 ' +configopts += '--with-zfp=$EBROOTZFP ' fix_python_shebang_for = ['bin/gpp.py'] runtest = ' check' -# options = {'modulename': False} - sanity_check_paths = { 'files': ['bin/adios_list_methods', 'bin/bpappend'], 'dirs': ['etc/skel/templates', 'lib/python'], From 59f940942bf23396bc2f3e723547ee825339fa02 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 16 Aug 2022 22:58:07 +0100 Subject: [PATCH 4488/9987] adding easyconfigs: zfp-1.0.0-GCCcore-9.3.0.eb --- .../z/zfp/zfp-1.0.0-GCCcore-9.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..0923191cade --- /dev/null +++ b/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-9.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'MakeCp' + +name = 'zfp' +version = '1.0.0' + +homepage = 'https://github.com/LLNL/zfp' +description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. +zfp provides compressed-array classes that support high throughput read and write random access to individual array +elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications +that read and write large data sets to and from disk.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/zfp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['fe13b03141ee9b571692aed42ff76cf37c9dcda40f9a43a808870dca3558a57c'] + +builddependencies = [ + ('binutils', '2.34'), +] + +prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && " +buildopts = 'ZFP_WITH_OPENMP=1' + +runtest = 'test' + +files_to_copy = ['bin', 'include', 'lib'] + +sanity_check_paths = { + 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], + 'dirs': ['include/zfp'], +} + +sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] + +moduleclass = 'lib' From 2be6b042048fd4beabe8405648945761d213e020 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 16 Aug 2022 23:09:09 +0100 Subject: [PATCH 4489/9987] Name of patchfile changed as suggested --- .../easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb | 4 ++-- ...le.patch => QuickPIC-20210224_fix_paths_in_makefile.patch} | 0 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/q/QuickPIC/{quickpic-makefile.patch => QuickPIC-20210224_fix_paths_in_makefile.patch} (100%) diff --git a/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb b/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb index 43ec12caea4..c7f08ff8d65 100644 --- a/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb +++ b/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224-gompi-2021b.eb @@ -19,11 +19,11 @@ toolchainopts = {'pic': True, 'usempi': True, 'cstd': 'c99'} source_urls = ['https://github.com/UCLA-Plasma-Simulation-Group/QuickPIC-OpenSource/archive'] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = ['quickpic-makefile.patch'] +patches = ['QuickPIC-20210224_fix_paths_in_makefile.patch'] checksums = [ '83d3664542ce0a1c1fa055802e214bdba98790ee512f1f2525d0c087d20d88af', # QuickPIC-20210224.tar.gz - 'fd4be47519513ca3add974e5c5964707a7534ef68ad850f775fae3d8e0cdc987', # quickpic-makefile.patch + 'fd4be47519513ca3add974e5c5964707a7534ef68ad850f775fae3d8e0cdc987', # QuickPIC-20210224_fix_paths_in_makefile.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch b/easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224_fix_paths_in_makefile.patch similarity index 100% rename from easybuild/easyconfigs/q/QuickPIC/quickpic-makefile.patch rename to easybuild/easyconfigs/q/QuickPIC/QuickPIC-20210224_fix_paths_in_makefile.patch From 96598a2ee5a1fae71e8fd06ffc8279ca34f931c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 17 Aug 2022 11:28:03 +0200 Subject: [PATCH 4490/9987] Skip NASA performance test in netCDF --- .../n/netCDF/netCDF-4.9.0-gompi-2022a.eb | 2 ++ .../n/netCDF/netCDF-4.9.0_skip-nasa-test.patch | 17 +++++++++++++++++ 2 files changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-nasa-test.patch diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb index feefb6d13a7..36707a0591d 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb @@ -14,11 +14,13 @@ sources = ['v%(version)s.tar.gz'] patches = [ 'netCDF-%(version)s_fix-lib-name.patch', 'netCDF-%(version)s_fix-linking-errors.patch', + 'netCDF-%(version)s_skip-nasa-test.patch', ] checksums = [ '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a', # netCDF-4.9.0_skip-nasa-test.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-nasa-test.patch b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-nasa-test.patch new file mode 100644 index 00000000000..61bf1ffda4a --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-nasa-test.patch @@ -0,0 +1,17 @@ +The NASA performance test is skipped becuase it is very sentitive to what filesystem is used, causing timeouts. +Author: micketeer@gmail.com +--- nc_test4/run_par_test.sh.in.orig 2022-08-17 11:14:21.827283219 +0200 ++++ nc_test4/run_par_test.sh.in 2022-08-17 11:12:49.547459608 +0200 +@@ -37,9 +37,9 @@ + echo "Testing collective writes with some 0 element writes..." + @MPIEXEC@ -n 4 ./tst_parallel5 + +-echo +-echo "Parallel Performance Test for NASA" +-@MPIEXEC@ -n 4 ./tst_nc4perf ++#echo ++#echo "Parallel Performance Test for NASA" ++#@MPIEXEC@ -n 4 ./tst_nc4perf + + echo + echo "Parallel I/O test for Collective I/O, contributed by HDF Group." From 2b4a6f13caeedaffb5a5d72a44c1b77dcb10d55b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 17 Aug 2022 13:19:08 +0200 Subject: [PATCH 4491/9987] adding easyconfigs: buildenv-default-foss-2022a-CUDA-11.7.0.eb --- ...buildenv-default-foss-2022a-CUDA-11.7.0.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..c1b49d2a91a --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,19 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('UCX-CUDA', '1.12.1', versionsuffix), +] + +moduleclass = 'devel' From 99a74dc5913e2553bf21d7af10737f2d0309ad8c Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 17 Aug 2022 14:20:32 +0100 Subject: [PATCH 4492/9987] Missing zfp gomp libs added, introduced due to the addition of ZFP in Adios --- .../g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb index 51b18de2f7d..97753d6b0fc 100644 --- a/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb @@ -34,7 +34,7 @@ dependencies = [ ] configopts = '--luajit-inc-dir=$EBROOTLUAJIT2/include/luajit-2.1/ ' -configopts += '--extra-link-libs=" hdf5 mxml bz2 lz4 z" ' +configopts += '--extra-link-libs=" hdf5 mxml bz2 lz4 z zfp gomp" ' parallel = 4 From 151db6362df699a18c6bb8442c9c4fdc663f0f07 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 17 Aug 2022 15:20:17 +0100 Subject: [PATCH 4493/9987] adding easyconfigs: Jansson-2.14-GCC-11.2.0.eb --- .../j/Jansson/Jansson-2.14-GCC-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.2.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.2.0.eb new file mode 100644 index 00000000000..f5ec0f5e98f --- /dev/null +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.2.0.eb @@ -0,0 +1,37 @@ +# Contribution from Imperial College Londonb` +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'Jansson' +version = "2.14" + +homepage = 'https://www.digip.org/jansson/' +description = """Jansson is a C library for encoding, decoding and manipulating JSON data. + Its main features and design principles are: + * Simple and intuitive API and data model + * Comprehensive documentation + * No dependencies on other libraries + * Full Unicode support (UTF-8) + * Extensive test suite""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/akheron/jansson/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c739578bf6b764aa0752db9a2fdadcfe921c78f1228c7ec0bb47fa804c55d17b'] + +# The ld.gold linker does not know anything about --default-symver and thus crashes +# So we simnply use the bfd linker +preconfigopts = 'autoreconf -i && CC="$CC -fuse-ld=bfd" ' + +builddependencies = [('Autotools', '20210726')] + +sanity_check_paths = { + 'files': ['lib/libjansson.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +runtest = 'check' + +moduleclass = 'devel' From 1f2d488df9fd48978283d1cd898360d0f74093dd Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 17 Aug 2022 15:34:43 +0100 Subject: [PATCH 4494/9987] Switch to CMake to avoid this issue: https://github.com/akheron/jansson/issues/605, typo corrected --- .../j/Jansson/Jansson-2.14-GCC-11.2.0.eb | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.2.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.2.0.eb index f5ec0f5e98f..e0a04ad918c 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.2.0.eb @@ -1,7 +1,7 @@ -# Contribution from Imperial College Londonb` +# Contribution from Imperial College London # uploaded by J. Sassmannshausen -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'Jansson' version = "2.14" @@ -21,11 +21,14 @@ source_urls = ['https://github.com/akheron/jansson/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['c739578bf6b764aa0752db9a2fdadcfe921c78f1228c7ec0bb47fa804c55d17b'] -# The ld.gold linker does not know anything about --default-symver and thus crashes +# For configure, the ld.gold linker does not know anything about --default-symver and thus crashes # So we simnply use the bfd linker -preconfigopts = 'autoreconf -i && CC="$CC -fuse-ld=bfd" ' +# preconfigopts = 'autoreconf -i && CC="$CC -fuse-ld=bfd" ' +# This is not required with CMake -builddependencies = [('Autotools', '20210726')] +configopts = '-DJANSSON_BUILD_SHARED_LIBS=ON ' + +builddependencies = [('CMake', '3.22.1')] sanity_check_paths = { 'files': ['lib/libjansson.%s' % SHLIB_EXT], From a6d969a07b9668d515f95ae5068db0b55e2c971e Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 17 Aug 2022 15:40:35 +0100 Subject: [PATCH 4495/9987] Version 2.13.1 for GCC-11.2 added --- .../j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..a8a94ef0e0a --- /dev/null +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb @@ -0,0 +1,40 @@ +# Contribution from Imperial College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'Jansson' +version = "2.13.1" + +homepage = 'https://www.digip.org/jansson/' +description = """Jansson is a C library for encoding, decoding and manipulating JSON data. + Its main features and design principles are: + * Simple and intuitive API and data model + * Comprehensive documentation + * No dependencies on other libraries + * Full Unicode support (UTF-8) + * Extensive test suite""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/akheron/jansson/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f22901582138e3203959c9257cf83eba9929ac41d7be4a42557213a22ebcc7a0'] + +# For configure, the ld.gold linker does not know anything about --default-symver and thus crashes +# So we simnply use the bfd linker +# preconfigopts = 'autoreconf -i && CC="$CC -fuse-ld=bfd" ' +# This is not required with CMake + +configopts = '-DJANSSON_BUILD_SHARED_LIBS=ON ' + +builddependencies = [('CMake', '3.22.1')] + +sanity_check_paths = { + 'files': ['lib/libjansson.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +runtest = 'check' + +moduleclass = 'devel' From 1c02a67cc948dd4876b8e4a77729175be65b2422 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 17 Aug 2022 15:43:59 +0100 Subject: [PATCH 4496/9987] version 2.14 pushed to GCC 11.3 --- ...{Jansson-2.14-GCC-11.2.0.eb => Jansson-2.14-GCC-11.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/j/Jansson/{Jansson-2.14-GCC-11.2.0.eb => Jansson-2.14-GCC-11.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.2.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb similarity index 92% rename from easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.2.0.eb rename to easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb index e0a04ad918c..492c8e9f8a6 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb @@ -15,7 +15,7 @@ description = """Jansson is a C library for encoding, decoding and manipulating * Full Unicode support (UTF-8) * Extensive test suite""" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/akheron/jansson/archive/'] sources = ['v%(version)s.tar.gz'] @@ -28,7 +28,7 @@ checksums = ['c739578bf6b764aa0752db9a2fdadcfe921c78f1228c7ec0bb47fa804c55d17b'] configopts = '-DJANSSON_BUILD_SHARED_LIBS=ON ' -builddependencies = [('CMake', '3.22.1')] +builddependencies = [('CMake', '3.23.1')] sanity_check_paths = { 'files': ['lib/libjansson.%s' % SHLIB_EXT], From 5b795076ce25411b19d66c024cf5310bd85a90c1 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 17 Aug 2022 15:51:57 +0100 Subject: [PATCH 4497/9987] adding easyconfigs: CUnit-2.1-3-GCCcore-11.2.0.eb --- .../c/CUnit/CUnit-2.1-3-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c03ee75be97 --- /dev/null +++ b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'CUnit' +version = '2.1-3' + +homepage = 'https://sourceforge.net/projects/cunit/' +description = "Automated testing framework for C." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['f5b29137f845bb08b77ec60584fdb728b4e58f1023e6f249a464efa49a40f214'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +preconfigopts = "autoreconf -i && " + +sanity_check_paths = { + 'files': ['lib/libcunit.a', 'lib/libcunit.%s' % SHLIB_EXT], + 'dirs': ['include/CUnit', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lang' From 57ad98bd308cd53b1929dffe91cc1fc0541a098b Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 17 Aug 2022 18:40:11 +0100 Subject: [PATCH 4498/9987] Name change to LuaJIT2-OpenResty, sanity check command added --- .../LuaJIT2-v2.1-20220411-GCC-9.3.0.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LuaJIT2/LuaJIT2-v2.1-20220411-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/l/LuaJIT2/LuaJIT2-v2.1-20220411-GCC-9.3.0.eb b/easybuild/easyconfigs/l/LuaJIT2/LuaJIT2-v2.1-20220411-GCC-9.3.0.eb deleted file mode 100644 index 5adb862878c..00000000000 --- a/easybuild/easyconfigs/l/LuaJIT2/LuaJIT2-v2.1-20220411-GCC-9.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -# This is the LuaJIT fork from openresty, not to be mixed up -# with the original LuaJIT version! -# Autor: J. Sassmannshausen (Imperial College London/UK) - -easyblock = 'ConfigureMake' - -name = "LuaJIT2" -version = "v2.1-20220411" - -homepage = "https://github.com/openresty/luajit2" -description = """openresty/luajit2 - OpenResty's maintained branch of LuaJIT. -LuaJIT is a Just-In-Time Compiler (JIT) for the Lua -programming language. Lua is a powerful, dynamic and light-weight programming -language. It may be embedded or used as a general-purpose, stand-alone -language. """ - -toolchain = {'name': 'GCC', 'version': '9.3.0'} - -source_urls = ['https://github.com/openresty/luajit2/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['d3f2c870f8f88477b01726b32accab30f6e5d57ae59c5ec87374ff73d0794316'] - -skipsteps = ['configure'] -installopts = 'PREFIX=%(installdir)s' - -sanity_check_paths = { - 'files': ["bin/luajit"], - 'dirs': [] -} - -moduleclass = "lang" From 699ff2bd3758dfbde766ea105a2cdcdb0d0e79d7 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 17 Aug 2022 18:45:33 +0100 Subject: [PATCH 4499/9987] EC File added --- ...uaJIT2-OpenResty-2.1-20220411-GCC-9.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LuaJIT2-OpenResty/LuaJIT2-OpenResty-2.1-20220411-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/l/LuaJIT2-OpenResty/LuaJIT2-OpenResty-2.1-20220411-GCC-9.3.0.eb b/easybuild/easyconfigs/l/LuaJIT2-OpenResty/LuaJIT2-OpenResty-2.1-20220411-GCC-9.3.0.eb new file mode 100644 index 00000000000..e1507faabad --- /dev/null +++ b/easybuild/easyconfigs/l/LuaJIT2-OpenResty/LuaJIT2-OpenResty-2.1-20220411-GCC-9.3.0.eb @@ -0,0 +1,34 @@ +# This is the LuaJIT fork from openresty, not to be mixed up +# with the original LuaJIT version! +# Autor: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = "LuaJIT2-OpenResty" +version = "2.1-20220411" + +homepage = "https://github.com/openresty/luajit2" +description = """openresty/luajit2 - OpenResty's maintained branch of LuaJIT. +LuaJIT is a Just-In-Time Compiler (JIT) for the Lua +programming language. Lua is a powerful, dynamic and light-weight programming +language. It may be embedded or used as a general-purpose, stand-alone +language. """ + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://github.com/openresty/luajit2/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d3f2c870f8f88477b01726b32accab30f6e5d57ae59c5ec87374ff73d0794316'] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_commands = ['luajit -v'] + +sanity_check_paths = { + 'files': ["bin/luajit"], + 'dirs': [] +} + +moduleclass = "lang" From edae4f671762ed34d0b5fd6d56cb72ea27281164 Mon Sep 17 00:00:00 2001 From: anselmicz Date: Wed, 17 Aug 2022 19:48:44 +0200 Subject: [PATCH 4500/9987] updating SoX easyconfig to GCC 11.3.0, including additional support --- .../s/SoX/SoX-14.4.2-GCC-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..441c8f74f44 --- /dev/null +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCC-11.3.0.eb @@ -0,0 +1,34 @@ +# Institution: IT4Innovations National Supercomputing Center, Czech Republic +# Author: Jakub Kropacek +# License: GPLv3 +# Year: 2022 + +easyblock = 'ConfigureMake' + +name = 'SoX' +version = '14.4.2' + +homepage = 'http://sox.sourceforge.net/' +docurls = 'http://sox.sourceforge.net/Docs/Documentation' +description = """Sound eXchange, the Swiss Army knife of audio manipulation""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://sourceforge.net/projects/sox/files/sox/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b45f598643ffbd8e363ff24d61166ccec4836fea6d3888881b8df53e3bb55f6c'] + +dependencies = [ + ('FLAC', '1.3.4'), + ('LAME', '3.100'), + ('libvorbis', '1.3.7'), + ('FFmpeg', '5.0.1'), +] + +sanity_check_paths = { + 'files': ['bin/play', 'bin/rec', 'bin/sox', 'bin/soxi', 'include/sox.h', + 'lib/libsox.la', 'lib/libsox.a', 'lib/pkgconfig/sox.pc', 'lib/libsox.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib', 'lib/pkgconfig', 'share/man'], +} + +moduleclass = 'data' From 08bdfdcd4a7979ace18b09951f45364a95a8f0e7 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 17 Aug 2022 19:21:28 +0100 Subject: [PATCH 4501/9987] Name of luajit dependency changed due to different module name, see PR #16047 --- .../g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb index 97753d6b0fc..8e3a6fb2519 100644 --- a/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb @@ -30,10 +30,10 @@ dependencies = [ ('Python', '3.8.2'), ('ADIOS', '20210804', versionsuffix), ('Eigen', '3.3.7'), - ('LuaJIT2', 'v2.1-20220411'), + ('LuaJIT2-OpenResty', '2.1-20220411'), ] -configopts = '--luajit-inc-dir=$EBROOTLUAJIT2/include/luajit-2.1/ ' +configopts = '--luajit-inc-dir=$EBROOTLUAJIT2MINOPENRESTY/include/luajit-2.1/ ' configopts += '--extra-link-libs=" hdf5 mxml bz2 lz4 z zfp gomp" ' parallel = 4 From 2f88c581af4968d5f0fe4e0c5405ba2b0e3a12c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 18 Aug 2022 10:45:12 +0200 Subject: [PATCH 4502/9987] add pigz as dependency --- easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb | 1 + easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb index f3ffcc20e05..31fce71f997 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.2.0.eb @@ -23,6 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} builddependencies = [('binutils', '2.35')] dependencies = [ + ('pigz', '2.6'), ('Python', '3.8.6'), ('python-isal', '0.11.1'), ] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb index 4477ce27073..49b3dd7c2a9 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.4-GCCcore-10.3.0.eb @@ -23,6 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} builddependencies = [('binutils', '2.36.1')] dependencies = [ + ('pigz', '2.6'), ('Python', '3.9.5'), ('python-isal', '0.11.0'), ] diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb index 7b7603dba94..87a8e6ff5d9 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-3.5-GCCcore-11.2.0.eb @@ -23,6 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} builddependencies = [('binutils', '2.37')] dependencies = [ + ('pigz', '2.6'), ('Python', '3.9.6'), ('python-isal', '0.11.1'), ] From 660a7f06516958a31df78584126e4466e43e618c Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 18 Aug 2022 10:48:23 +0200 Subject: [PATCH 4503/9987] adding easyconfigs: FreeSurfer-7.3.2-centos8_x86_64.eb --- .../FreeSurfer-7.3.2-centos8_x86_64.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos8_x86_64.eb diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos8_x86_64.eb new file mode 100644 index 00000000000..ed3474f3130 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos8_x86_64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.3.2' +versionsuffix = '-centos8_x86_64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + # freesurfer-linux-centos8_x86_64-7.3.2.tar.gz + '1448e64000b02a06aaad81548a4c8f92faf575f8320e67bdcd15a430ad10879b', + '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' From 17475226ca93091fe2bf60272b0a8802be467e32 Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Thu, 18 Aug 2022 10:54:12 +0200 Subject: [PATCH 4504/9987] ADIOS: add sanity check commands --- .../a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb index f8e482c195f..1330ea3c373 100644 --- a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb @@ -66,6 +66,11 @@ sanity_check_paths = { 'dirs': ['etc/skel/templates', 'lib/python'], } +sanity_check_commands = [ + 'adios_list_methods', + 'bpappend -h', +] + modextrapaths = { 'PYTHONPATH': 'lib/python', } From aafb625acaa77d0ab2d4361a55c4a3eb35f4a822 Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 18 Aug 2022 12:49:31 +0100 Subject: [PATCH 4505/9987] Turned tcsh into runtime dependency --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb index b7b2e5f3007..69bd6e602f4 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2020b-mpi.eb @@ -17,11 +17,8 @@ checksums = [ 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch ] -builddependencies = [ - ('tcsh', '6.22.03'), -] - dependencies = [ + ('tcsh', '6.22.03'), ('Tcl', '8.6.10'), ] From 96cb22eea318d1aa49ee4094c2c6c39bc042b7ef Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Thu, 18 Aug 2022 12:50:17 +0100 Subject: [PATCH 4506/9987] Turned tcsh into runtime dependency --- easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb index b938c172e69..bb7d42b87f0 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-fosscuda-2020b.eb @@ -20,12 +20,9 @@ checksums = [ 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch ] -builddependencies = [ - ('tcsh', '6.22.03'), -] - # support for GCC 8+ on POWER dependencies = [ + ('tcsh', '6.22.03'), ('Tcl', '8.6.10'), ] From 87c5f7ad10a5dec5995af5f39eac5852e6bcade9 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 18 Aug 2022 13:55:48 +0200 Subject: [PATCH 4507/9987] adding easyconfigs: Blender-3.2.2-linux-x64.eb --- .../b/Blender/Blender-3.2.2-linux-x64.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blender/Blender-3.2.2-linux-x64.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.2.2-linux-x64.eb b/easybuild/easyconfigs/b/Blender/Blender-3.2.2-linux-x64.eb new file mode 100644 index 00000000000..d1b1e54af9d --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-3.2.2-linux-x64.eb @@ -0,0 +1,36 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PackedBinary' + +name = 'Blender' +version = '3.2.2' +versionsuffix = '-linux-x64' + +homepage = 'https://www.blender.org' +description = """ +Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline, +modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video +editing and game creation. +""" + +toolchain = SYSTEM + +source_urls = ['http://ftp.nluug.nl/pub/graphics/%(namelower)s/release/%(name)s%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s-linux-x64.tar.xz'] +checksums = ['1726560157d90cf2aaaeb6d25ded1783d66bff043814cd95b90fc0af1d9e018b'] + +dependencies = [ + ('CUDA', '11.7.0'), +] + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': ['%(version_major_minor)s'], +} + +modaliases = { + 'blender': 'blender -- --cycles-device CUDA', +} + +moduleclass = 'vis' From bb8536851f88f810d5a922e2eefe06de44f598a1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 9 Aug 2022 14:39:56 +0200 Subject: [PATCH 4508/9987] adding easyconfigs: netCDF-Fortran-4.6.0-iimpi-2022a.eb, netCDF-4.9.0-iimpi-2022a.eb --- .../netCDF-Fortran-4.6.0-iimpi-2022a.eb | 28 +++++++++++ .../n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 48 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb new file mode 100644 index 00000000000..6ccd8e61271 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8194aa70e400c0adfc456127c1d97af2c6489207171d13b10cd754a16da8b0ca'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [ + ('netCDF', '4.9.0'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb new file mode 100644 index 00000000000..b13202347f8 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -0,0 +1,48 @@ +name = 'netCDF' +version = '4.9.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-%(version)s_fix-lib-name.patch', + 'netCDF-%(version)s_fix-linking-errors.patch', +] +checksums = [ + '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz + 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch + '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('HDF5', '1.13.1'), + ('cURL', '7.83.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.2'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' From 1acfc6c5de84bb2bb7e0bc2e47736e54f158cdab Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 18 Aug 2022 18:43:52 +0200 Subject: [PATCH 4509/9987] Add netCDF-4.9.0_skip-nasa-test.patch to netCDF-4.9.0-iimpi-2022a.eb --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index b13202347f8..e8aeb8b93a8 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -14,11 +14,13 @@ sources = ['v%(version)s.tar.gz'] patches = [ 'netCDF-%(version)s_fix-lib-name.patch', 'netCDF-%(version)s_fix-linking-errors.patch', + 'netCDF-%(version)s_skip-nasa-test.patch', ] checksums = [ '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a', # netCDF-4.9.0_skip-nasa-test.patch ] builddependencies = [ From 79e0cc97cdf70b8044d7e8f8aa61f3967e839c18 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 18 Aug 2022 19:26:01 +0200 Subject: [PATCH 4510/9987] Add NWChem and GlobalArrays --- .../GlobalArrays-5.8.1-intel-2022a.eb | 30 +++++++++++++++ .../n/NWChem/NWChem-7.0.2-intel-2022a.eb | 37 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.1-intel-2022a.eb create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.1-intel-2022a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.1-intel-2022a.eb new file mode 100644 index 00000000000..f2b34303ae9 --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.1-intel-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.8.1' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['844639b52444f839854cf9735203a76a9052fd485f2d4eae70d21d03a7ecaade'] + +configopts = ' --with-mpi --enable-i8' +configopts += ' --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' + +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', + 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb new file mode 100644 index 00000000000..e5401556149 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb @@ -0,0 +1,37 @@ +name = 'NWChem' +version = '7.0.2' +local_verdate = '2020-10-12' +local_revision = 'b9985dfa' + +homepage = 'https://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'i8': True} + +source_urls = ['https://github.com/nwchemgit/nwchem/releases/download/v%(version)s-release/'] +sources = ['nwchem-%%(version)s-release.revision-%s-src.%s.tar.bz2' % (local_revision, local_verdate)] +patches = [ + 'NWChem-7.0.2_fix_gnumakefile.patch', +] +checksums = [ + # nwchem-7.0.2-release.revision-b9985dfa-src.2020-10-12.tar.bz2 + 'd9d19d87e70abf43d61b2d34e60c293371af60d14df4a6333bf40ea63f6dc8ce', + '89c634a652d4c8c358f8388ac01ee441659e3c0256c39b6494e2885c91f9aca4', # NWChem-7.0.2_fix_gnumakefile.patch +] + +dependencies = [ + ('GlobalArrays', '5.8.1'), + ('Python', '3.10.4'), +] + +preconfigopts = 'export EXTRA_LIBS=-lutil && ' + +modules = 'all python' + +moduleclass = 'chem' From f33278be0ef217fd3d134653396afa6c8c6864c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 19 Aug 2022 02:24:07 +0200 Subject: [PATCH 4511/9987] Use OpenJDK for Java 8 --- easybuild/easyconfigs/j/Java/Java-1.8.eb | 12 ++------- easybuild/easyconfigs/j/Java/Java-8.eb | 14 ++++++++++ easybuild/easyconfigs/j/Java/Java-8u345.eb | 30 ++++++++++++++++++++++ 3 files changed, 46 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/j/Java/Java-8.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-8u345.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.eb b/easybuild/easyconfigs/j/Java/Java-1.8.eb index ed823a63205..578f332a81b 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.eb @@ -1,7 +1,3 @@ -# Contribution from the Crick HPC team -# uploaded by J. Sassmannshausen -# updated to cope with multiple architectures by A. Edmondson - easyblock = 'ModuleRC' name = 'Java' @@ -9,14 +5,10 @@ version = '1.8' homepage = 'https://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy - Java applications on desktops and servers.""" +Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [ - ('Java', {'arch=x86_64': '%(version)s.0_311', - 'arch=POWER': '%(version)s_191-b26-OpenJDK', - 'arch=AArch64': '%(version)s_265-b01-OpenJDK-aarch64'}), -] +dependencies = [('Java', '%(version_minor)su345')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-8.eb b/easybuild/easyconfigs/j/Java/Java-8.eb new file mode 100644 index 00000000000..9ef99a1c2f3 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-8.eb @@ -0,0 +1,14 @@ +easyblock = 'ModuleRC' + +name = 'Java' +version = '8' + +homepage = 'https://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +dependencies = [('Java', '%(version)su345')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-8u345.eb b/easybuild/easyconfigs/j/Java/Java-8u345.eb new file mode 100644 index 00000000000..28a21e318d4 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-8u345.eb @@ -0,0 +1,30 @@ +name = 'Java' +version = '8u345' +local_build = 'b01' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK8U-jdk_%s_linux_hotspot_%%(version)s%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin8-binaries/releases/download/jdk%%(version)s-%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + 'ed6c9db3719895584fb1fd69fc79c29240977675f26631911c5a1dbce07b7d58', + local_tarball_tmpl % ('aarch64', local_build): + 'c1965fb24dded7d7944e2da36cd902adf3b7b1d327aaa21ea507cff00a5a0090', + local_tarball_tmpl % ('ppc64le', local_build): + 'f2be72678f6c2ad283453d0e21a6cb03144dda356e4edf79f818d99c37feaf34', + } +] + +moduleclass = 'lang' From 420f61de8af6f488e9dde8f6004e64b9d54e2851 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Fri, 19 Aug 2022 10:29:08 +0200 Subject: [PATCH 4512/9987] Update and rename SoX-14.4.2-GCC-11.3.0.eb to SoX-14.4.2-GCCcore-11.3.0.eb Switched from GCC to GCCcore, added binutils to builddependencies --- ...{SoX-14.4.2-GCC-11.3.0.eb => SoX-14.4.2-GCCcore-11.3.0.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/s/SoX/{SoX-14.4.2-GCC-11.3.0.eb => SoX-14.4.2-GCCcore-11.3.0.eb} (90%) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb similarity index 90% rename from easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCC-11.3.0.eb rename to easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb index 441c8f74f44..40dc6df850b 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb @@ -12,12 +12,14 @@ homepage = 'http://sox.sourceforge.net/' docurls = 'http://sox.sourceforge.net/Docs/Documentation' description = """Sound eXchange, the Swiss Army knife of audio manipulation""" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://sourceforge.net/projects/sox/files/sox/%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['b45f598643ffbd8e363ff24d61166ccec4836fea6d3888881b8df53e3bb55f6c'] +builddependencies = [('binutils', '2.38')] + dependencies = [ ('FLAC', '1.3.4'), ('LAME', '3.100'), From d8418629678ffd5860ef6b7e05caef5714b4a96f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 19 Aug 2022 10:57:50 +0200 Subject: [PATCH 4513/9987] Add patch to fix build with python-3.10 --- .../n/NWChem/NWChem-7.0.2-intel-2022a.eb | 2 + .../NWChem-7.0.2_fix_for_python_3_10.patch | 41 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_for_python_3_10.patch diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb index e5401556149..25d9440384b 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb @@ -18,11 +18,13 @@ source_urls = ['https://github.com/nwchemgit/nwchem/releases/download/v%(version sources = ['nwchem-%%(version)s-release.revision-%s-src.%s.tar.bz2' % (local_revision, local_verdate)] patches = [ 'NWChem-7.0.2_fix_gnumakefile.patch', + 'NWChem-7.0.2_fix_for_python_3_10.patch', ] checksums = [ # nwchem-7.0.2-release.revision-b9985dfa-src.2020-10-12.tar.bz2 'd9d19d87e70abf43d61b2d34e60c293371af60d14df4a6333bf40ea63f6dc8ce', '89c634a652d4c8c358f8388ac01ee441659e3c0256c39b6494e2885c91f9aca4', # NWChem-7.0.2_fix_gnumakefile.patch + '2da647217ad72d929f1d495386871a32b7176beb52cbc3dabebbb56abb407e36', # NWChem-7.0.2_fix_for_python_3_10.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_for_python_3_10.patch b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_for_python_3_10.patch new file mode 100644 index 00000000000..e733ea89052 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_for_python_3_10.patch @@ -0,0 +1,41 @@ +# This patch fixes compatibility with Python-3.10. In particular the problem that +# the "graminit.h" header is removed from Python-3.10 together with the "parser" +# module. +# See https://github.com/nwchemgit/nwchem/issues/271 for more info +# +# Author: maxim-masterov (SURF) +# +diff -Nru nwchem-7.0.2.orig/src/config/makefile.h nwchem-7.0.2/src/config/makefile.h +--- nwchem-7.0.2.orig/src/config/makefile.h 2022-08-19 10:47:57.584912000 +0200 ++++ nwchem-7.0.2/src/config/makefile.h 2022-08-19 10:50:18.158831536 +0200 +@@ -2618,12 +2618,12 @@ + GOTPYTHON2 := $(shell command -v python2 2> /dev/null) + GOTPYTHON := $(shell command -v python 2> /dev/null) + ifdef GOTPYTHON3 +- PYTHONVERSION=$(shell python3 -V 2>&1 |cut -c 8-10) ++ PYTHONVERSION=$(shell python3 -c 'import sys; print("{}.{}".format(sys.version_info.major, sys.version_info.minor))') + else ifdef GOTPYTHON2 +- PYTHONVERSION=$(shell python2 -V 2>&1 |cut -c 8-10) ++ PYTHONVERSION=$(shell python2 -c 'import sys; print("{}.{}".format(sys.version_info.major, sys.version_info.minor))') + else ifdef GOTPYTHON + #last try at python2 +- PYTHONVERSION=$(shell python -V 2>&1 |cut -c 8-10) ++ PYTHONVERSION=$(shell python -c 'import sys; print("{}.{}".format(sys.version_info.major, sys.version_info.minor))') + else + errorpython3: + $(info ) +diff -Nru nwchem-7.0.2.orig/src/python/task_python.c nwchem-7.0.2/src/python/task_python.c +--- nwchem-7.0.2.orig/src/python/task_python.c 2022-08-19 10:47:58.966129000 +0200 ++++ nwchem-7.0.2/src/python/task_python.c 2022-08-19 10:51:34.311283000 +0200 +@@ -6,7 +6,11 @@ + #include "ga.h" + + #include ++#if ( PY_MAJOR_VERSION >= 3 && PY_MINOR_VERSION >= 9) ++/* might require new headers and code */ ++#else + #include ++#endif + #include + #include + #include "typesf2c.h" From fe75ad701b04b792a4a0848c89415351f11746c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Fri, 19 Aug 2022 11:23:08 +0200 Subject: [PATCH 4514/9987] Update easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Adding simple sanity check. Co-authored-by: Bob Dröge --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb index 40dc6df850b..eb67b3cb1ce 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb @@ -33,4 +33,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib', 'lib/pkgconfig', 'share/man'], } +sanity_check_commands = ['sox --help'] + moduleclass = 'data' From 3b242246f2f3ec11d498658929249921d374c855 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 19 Aug 2022 10:38:39 +0100 Subject: [PATCH 4515/9987] adding easyconfigs: pugixml-1.12.1-GCCcore-11.2.0.eb --- .../pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b242e8f9927 --- /dev/null +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'pugixml' +version = '1.12.1' + +homepage = 'https://pugixml.org/' +description = """pugixml is a light-weight C++ XML processing library""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/zeux/pugixml/archive/'] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + '1e28ab24b6e04e013d96f45d25e9f2d04c921dc68c613fd010ecaaad3892c14d', # v1.12.1.tar.gz +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1') +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON -DPUGIXML_HEADER_ONLY=True ' + +sanity_check_paths = { + 'files': ['include/pugiconfig.hpp', 'include/pugixml.hpp', 'lib/libpugixml.a', + 'lib/libpugixml.%s' % SHLIB_EXT, 'lib/pkgconfig/pugixml.pc'], + 'dirs': ['lib/cmake/pugixml'], +} + +moduleclass = 'data' From d1adb4ae5a7af17b69a17dd75dd729fe1c56bb06 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 19 Aug 2022 12:18:06 +0200 Subject: [PATCH 4516/9987] Use versioned syms in system level ncurses --- easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb index 39e4816f441..244ea3bdd80 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb @@ -14,7 +14,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['aa057eeeb4a14d470101eff4597d5833dcef5965331be3528c08d99cebaa0d17'] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb index 3a0fb752006..26cb42a20bf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb @@ -14,7 +14,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb index bf42d2eb8cc..3d144c5ab1a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb @@ -17,7 +17,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, From a36972dee47177108f342cd6d048778c462cd946 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 19 Aug 2022 12:21:49 +0200 Subject: [PATCH 4517/9987] fix 6.0 version as well --- easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb index 51cab0973d2..6c66d5c6938 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0.eb @@ -18,7 +18,7 @@ checksums = [ 'f82003be6ce6b87c3dc8a91d97785aab1a76a9e8544c3a3c02283c01dd41aede', # ncurses-6.0_gcc-5.patch ] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, From 87efa70bed6a6b7297f5ea641bbddcd4856f7ec6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Fri, 19 Aug 2022 12:30:09 +0200 Subject: [PATCH 4518/9987] Update easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Use `SOURCEFORGE_SOURCE` instead of full url Co-authored-by: Bob Dröge --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb index eb67b3cb1ce..3216a7a24e7 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb @@ -14,7 +14,7 @@ description = """Sound eXchange, the Swiss Army knife of audio manipulation""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://sourceforge.net/projects/sox/files/sox/%(version)s'] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['b45f598643ffbd8e363ff24d61166ccec4836fea6d3888881b8df53e3bb55f6c'] From 44af1c872bc060b4ab8557d406a740a91a61f72d Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 Aug 2022 13:05:07 +0200 Subject: [PATCH 4519/9987] adding easyconfigs: GCC-12.2.0.eb, GCCcore-12.2.0.eb, binutils-2.39.eb, binutils-2.39-GCCcore-12.2.0.eb, Bison-3.8.2-GCCcore-12.2.0.eb, flex-2.6.4-GCCcore-12.2.0.eb, help2man-1.49.2-GCCcore-12.2.0.eb, M4-1.4.19-GCCcore-12.2.0.eb, zlib-1.2.12-GCCcore-12.2.0.eb --- .../b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb | 28 +++++++++ .../binutils/binutils-2.39-GCCcore-12.2.0.eb | 31 +++++++++ .../easyconfigs/b/binutils/binutils-2.39.eb | 26 ++++++++ .../f/flex/flex-2.6.4-GCCcore-12.2.0.eb | 34 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-12.2.0.eb | 22 +++++++ .../easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 63 +++++++++++++++++++ .../help2man-1.49.2-GCCcore-12.2.0.eb | 25 ++++++++ .../m/M4/M4-1.4.19-GCCcore-12.2.0.eb | 29 +++++++++ .../z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb | 30 +++++++++ 9 files changed, 288 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.39.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4c8dc227e18 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.39', '', True), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..c8ec4f59243 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.39' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d12ea6f239f1ffe3533ea11ad6e224ffcb89eb5d01bbea589e9158780fa11f10'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.12'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.39.eb b/easybuild/easyconfigs/b/binutils/binutils-2.39.eb new file mode 100644 index 00000000000..c2dda2f1464 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.39.eb @@ -0,0 +1,26 @@ +name = 'binutils' +version = '2.39' + +homepage = 'https://directory.fsf.org/project/binutils/' + +description = "binutils: GNU binary utilities" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d12ea6f239f1ffe3533ea11ad6e224ffcb89eb5d01bbea589e9158780fa11f10'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.12'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b953ed29dab --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.2'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.39', '', True), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-12.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-12.2.0.eb new file mode 100644 index 00000000000..81e62378c1d --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-12.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '12.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.39', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb new file mode 100644 index 00000000000..843edfa35ec --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '12.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.1.0.tar.bz2', + 'mpc-1.2.1.tar.gz', + 'isl-0.24.tar.bz2', + 'newlib-4.1.0.tar.gz', + {'download_filename': '472b6e7.tar.gz', 'filename': 'nvptx-tools-20220610.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + 'ac6b317eb4d25444d87cf29c0d141dedc1323a1833ec9995211b13e1a851261c', # gcc-12.2.0.tar.gz + 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 + 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 + '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz + 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 + 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz + '53e7973af841935490b8a7b9e4d1331f775589b54e21f9921f18589183fb9997', # nvptx-tools-20220610.tar.gz + '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch + '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.39'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..712e28926d5 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.2' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.39', '', True), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..568d60035ca --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.39', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a9717ade39b --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.12' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = [ + '91844808532e5ce316b3c010929493c0244f3d37593afd6de04f71821d5136d9', # zlib-1.2.12.tar.gz + 'f35eb05334a4f8d7b40b6c5610a6369f654863b5fa1a19c2507888f918025238', # zlib-1.2.12_fix-CC-logic-in-configure.patch +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.39', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From baa07044c84fa3ceb8e73557215be72ccabdde06 Mon Sep 17 00:00:00 2001 From: Jakub Kropacek Date: Fri, 19 Aug 2022 17:51:12 +0200 Subject: [PATCH 4520/9987] adding easyconfigs: libmad-0.15.1b-GCCcore-11.3.0.eb and patches: libmad-0.15.1b-remove-depreciated-gcc-option.patch --- .../l/libmad/libmad-0.15.1b-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ ....15.1b-remove-depreciated-gcc-option.patch | 29 +++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/l/libmad/libmad-0.15.1b-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libmad/libmad-0.15.1b-remove-depreciated-gcc-option.patch diff --git a/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e5a933378ed --- /dev/null +++ b/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +# Institution: IT4Innovations National Supercomputing Center, Czech Republic +# Author: Jakub Kropacek +# License: GPLv3 +# Year: 2022 + +easyblock = 'ConfigureMake' + +name = 'libmad' +version = '0.15.1b' + +homepage = 'https://www.underbit.com/products/mad/' +description = """MAD is a high-quality MPEG audio decoder.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://sourceforge.net/projects/mad/files/%(name)s/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['libmad-0.15.1b-remove-depreciated-gcc-option.patch'] +checksums = [ + 'bbfac3ed6bfbc2823d3775ebb931087371e142bb0e9bb1bee51a76a6e0078690', # libmad-0.15.1b.tar.gz + # libmad-0.15.1b-remove-depreciated-gcc-option.patch + '8f96a23a22ba66e62f32e20064d01f4c7f6a18ba0aab85d3be9ce63794b2c678', +] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['include/mad.h', 'lib/libmad.a', 'lib/libmad.la', 'lib/libmad.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib', 'lib64'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-remove-depreciated-gcc-option.patch b/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-remove-depreciated-gcc-option.patch new file mode 100644 index 00000000000..287faed3c38 --- /dev/null +++ b/easybuild/easyconfigs/l/libmad/libmad-0.15.1b-remove-depreciated-gcc-option.patch @@ -0,0 +1,29 @@ +# Institution: IT4Innovations National Supercomputing Center, Czech Republic +# Author: Jakub Kropacek +# License: GPLv3 +# Year: 2022 +# +# Option "-fforce-mem" has been removed in GCC 4.3. +# See https://gcc.gnu.org/gcc-4.3/changes.html +diff -Nru libmad-0.15.1b.orig/configure libmad-0.15.1b/configure +--- libmad-0.15.1b.orig/configure 2022-08-19 14:51:49.037627000 +0200 ++++ libmad-0.15.1b/configure 2022-08-19 14:52:05.758321053 +0200 +@@ -19099,7 +19099,6 @@ + case "$optimize" in + -O|"-O "*) + optimize="-O" +- optimize="$optimize -fforce-mem" + optimize="$optimize -fforce-addr" + : #x optimize="$optimize -finline-functions" + : #- optimize="$optimize -fstrength-reduce" +diff -Nru libmad-0.15.1b.orig/configure.ac libmad-0.15.1b/configure.ac +--- libmad-0.15.1b.orig/configure.ac 2022-08-19 14:51:49.051732000 +0200 ++++ libmad-0.15.1b/configure.ac 2022-08-19 14:52:10.953461180 +0200 +@@ -140,7 +140,6 @@ + case "$optimize" in + -O|"-O "*) + optimize="-O" +- optimize="$optimize -fforce-mem" + optimize="$optimize -fforce-addr" + : #x optimize="$optimize -finline-functions" + : #- optimize="$optimize -fstrength-reduce" From 961b93ce50a8a764a5d6f143e6423feb5b8bc0dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2022 10:10:43 +0200 Subject: [PATCH 4521/9987] adding easyconfigs: Satsuma2-2022-03-04-GCC-11.3.0.eb and patches: Satsuma2-2022-03-04_fix-GCC-11.patch --- .../Satsuma2-2022-03-04-GCC-11.3.0.eb | 31 +++++++++++++++++++ .../Satsuma2-2022-03-04_fix-GCC-11.patch | 12 +++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04_fix-GCC-11.patch diff --git a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb new file mode 100644 index 00000000000..bb835d6d34d --- /dev/null +++ b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Satsuma2' +local_commit = '37c5f38' +version = '2022-03-04' + +homepage = 'https://github.com/bioinfologics/satsuma2' +description = """Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequences +providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to +accomodate the billions of base pairs in vertebrate genomes).""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/bioinfologics/satsuma2/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = ['Satsuma2-%(version)s_fix-GCC-11.patch'] +checksums = [ + '75ba38066719c189fba8630326a35afe42421437b55ee9e631973e8be115674c', # Satsuma2-2022-03-04.tar.gz + 'c80755f8942f3a0c9a2598b2a1a6319f508956bc29ccdfdfb9044ec8c50cd691', # Satsuma2-2022-03-04_fix-GCC-11.patch +] + +builddependencies = [('CMake', '3.23.1')] + +sanity_check_paths = { + 'files': ['bin/ChromosomePaint', 'bin/MatchDump', 'bin/SatsumaSynteny2'], + 'dirs': [], +} + +sanity_check_commands = ["SatsumaSynteny2 --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04_fix-GCC-11.patch b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04_fix-GCC-11.patch new file mode 100644 index 00000000000..aefe7fad484 --- /dev/null +++ b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04_fix-GCC-11.patch @@ -0,0 +1,12 @@ +fix for "error: shared_ptr in namespace std does not name a template type" +author: Kenneth Hoste (HPC-UGent) +--- satsuma2-37c5f386819614cd3ce96016b423ddc4df1d86ec/analysis/SatsumaSynteny2.cc.orig 2022-08-22 09:58:49.690714992 +0200 ++++ satsuma2-37c5f386819614cd3ce96016b423ddc4df1d86ec/analysis/SatsumaSynteny2.cc 2022-08-22 09:59:05.103870557 +0200 +@@ -7,6 +7,7 @@ + + #include + #include ++#include + #include "../base/CommandLineParser.h" + #include "SequenceMatch.h" + #include "GridSearch.h" From 20ee65f01f4a16d5d9366b8e5d7aff3bc33ba10d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2022 15:16:46 +0200 Subject: [PATCH 4522/9987] update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) --- .github/workflows/linting.yml | 2 +- .github/workflows/unit_tests.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 9d5354858a1..6346d959773 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -2,7 +2,7 @@ name: Static Analysis on: [push, pull_request] jobs: python-linting: - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 steps: - uses: actions/checkout@v2 diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 02805c08dbc..1a8e16547f5 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -2,7 +2,7 @@ name: easyconfigs unit tests on: [push, pull_request] jobs: test-suite: - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 strategy: matrix: python: [2.7, 3.6] @@ -148,7 +148,7 @@ jobs: eb --prefix /tmp/$USER/$GITHUB_SHA --sourcepath /tmp/sources M4-1.4.18.eb test-sdist: - runs-on: ubuntu-18.04 + runs-on: ubuntu-20.04 strategy: matrix: python: [2.7, 3.6, 3.7] From b95569399b6ef0ed835df16f383f38493d357bf3 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 22 Aug 2022 15:01:16 +0100 Subject: [PATCH 4523/9987] adding easyconfigs: hiredis-1.0.2-GCCcore-11.2.0.eb --- .../h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..be49af696cf --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +# Author J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'hiredis' +version = '1.0.2' + +homepage = 'https://github.com/redis/hiredis' +description = """Hiredis is a minimalistic C client library for the Redis database. + +It is minimalistic because it just adds minimal support for the protocol, +but at the same time it uses a high level printf-alike API in order to +make it much higher level than otherwise suggested by its minimal code base +and the lack of explicit bindings for every Redis command.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/redis/hiredis/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + 'e0ab696e2f07deb4252dda45b703d09854e53b9703c7d52182ce5a22616c3819', # v1.0.2.tar.gz +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), +] + +sanity_check_paths = { + 'files': ['lib/libhiredis.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'tools' From 1162137d86d9987b98fea98b23e949e9c34a12f0 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 22 Aug 2022 15:05:24 +0100 Subject: [PATCH 4524/9987] adding easyconfigs: ccache-4.6.1.eb --- .../easyconfigs/c/ccache/ccache-4.6.1.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb new file mode 100644 index 00000000000..3541b3bdd53 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb @@ -0,0 +1,48 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# Updated to 4.6.1: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.6.1' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['59b28a57c3a45e48d6049001999c9f94cd4d3e9b0196994bed9a6a7437ffa3bc'] + +osdependencies = [('glibc-static', 'libc6-dev')] + +local_gccver = '11.2.0' +builddependencies = [ + ('GCC', local_gccver), + ('CMake', '3.22.1', '', ('GCCcore', local_gccver)), + ('Ninja', '1.10.2', '', ('GCCcore', local_gccver)), + ('zstd', '1.5.0', '', ('GCCcore', local_gccver)), + ('pkg-config', '0.29.2', '', ('GCCcore', local_gccver)) +] + +dependencies = [ + ('hiredis', '1.0.2', '', ('GCCcore', local_gccver)), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS=" -fuse-ld=bfd"' +configopts = '-DENABLE_DOCUMENTATION=OFF -DENABLE_IPO=ON -DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a" ' +# disable hunt for faster linker, since using ld.gold may fail (on CentOS 8, for example) +configopts += '-DUSE_FASTER_LINKER=OFF' + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = ['ccache --help'] + +moduleclass = 'tools' From 8332f8f6fec85aea51e5e12e6b16be9dccee5bbc Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 22 Aug 2022 15:22:12 +0100 Subject: [PATCH 4525/9987] glibc-devel OS dependency added --- easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb index 3541b3bdd53..e9141772cf2 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb @@ -18,7 +18,7 @@ source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/ sources = [SOURCE_TAR_GZ] checksums = ['59b28a57c3a45e48d6049001999c9f94cd4d3e9b0196994bed9a6a7437ffa3bc'] -osdependencies = [('glibc-static', 'libc6-dev')] +osdependencies = [('glibc-static', 'libc6-dev', 'glibc-devel')] local_gccver = '11.2.0' builddependencies = [ From 44adf81c0efedc5d80c31b699675d6367948bd34 Mon Sep 17 00:00:00 2001 From: benjamic Date: Mon, 22 Aug 2022 16:29:37 +0200 Subject: [PATCH 4526/9987] Libint-2.7.2 with new patch --- .../Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb | 49 +++++++++++++++++++ .../Libint-2.7.2_remove-test-permute.patch | 19 +++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.7.2_remove-test-permute.patch diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb new file mode 100644 index 00000000000..0a56b0a8daa --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb @@ -0,0 +1,49 @@ +## +# This easyconfig is based on the easy config written originally by Robert Mijakovic +# Author: Ben Czaja (SURF) +## +name = 'Libint' +version = '2.7.2' +local_lmax = 6 +# custom configuration, to be used as dependency for CP2K +versionsuffix = '-lmax-%s-cp2k' % local_lmax + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/evaleev/libint/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Libint-2.7.2_remove-test-permute.patch', +] +checksums = [ + 'fd0466ce9eb6786b8c5bbe3d510e387ed44b198a163264dfd7e60b337e295fd9', # v2.7.2.tar.gz + 'b019e66a2a3dc7e83ee8a60aa1ae78955a8af4df90ab07b7e57d2ee004ce3677', # Libint-2.7.2_remove-test-permute.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('GMP', '6.2.1'), + ('Boost', '1.79.0'), + ('Eigen', '3.4.0'), + ('Python', '3.10.4'), +] + +# configure options as required by CP2K, +# see Jenkinsfile in https://github.com/cp2k/libint-cp2k +local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) +local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) + +libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax +libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am +libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--enable-generic-code --disable-unrolling' + +with_fortran = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.7.2_remove-test-permute.patch b/easybuild/easyconfigs/l/Libint/Libint-2.7.2_remove-test-permute.patch new file mode 100644 index 00000000000..698f33be731 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.7.2_remove-test-permute.patch @@ -0,0 +1,19 @@ +Disable 2-e 3-c integrals permute correctly (deriv_order=1) unit test +See https://github.com/evaleev/libint/issues/252 +author: Ben Czaja (SURF) +diff -W 152 -Nru libint-2.7.2-orig/tests/unit/test-permute.cc libint-2.7.2/tests/unit/test-permute.cc +--- libint-2.7.2-orig/tests/unit/test-permute.cc 2022-06-20 07:51:55.000000000 +0200 ++++ libint-2.7.2/tests/unit/test-permute.cc 2022-08-17 11:29:30.415136451 +0200 +@@ -539,9 +539,9 @@ + SECTION( "deriv_order=0" ) { + validate3<0>(obs, dfbs, atoms); + } // section +- SECTION( "deriv_order=1" ) { +- validate3<1>(obs, dfbs, atoms); +- } // section ++ // SECTION( "deriv_order=1" ) { ++ // validate3<1>(obs, dfbs, atoms); ++ // } // section + SECTION( "deriv_order=2" ) { + validate3<2>(obs, dfbs, atoms); + } // section \ No newline at end of file From be0cd71d7d4d8e0ed1c4c46fa27270a127c13c9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2022 17:57:28 +0200 Subject: [PATCH 4527/9987] {bio}[foss/2021b] BUSCO v5.4.3, MetaEuk v6 w/ Python 3.9.6 --- .../b/BUSCO/BUSCO-5.4.3-foss-2021b.eb | 56 +++++++++++++++++++ .../m/MetaEuk/MetaEuk-6-GCC-11.2.0.eb | 31 ++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.3-foss-2021b.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.3-foss-2021b.eb new file mode 100644 index 00000000000..9cd3dc82c01 --- /dev/null +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.3-foss-2021b.eb @@ -0,0 +1,56 @@ +# Updated by: Pavel Grochal (INUITS) +# Updated by: Sebastien Moretti (SIB) + +easyblock = 'PythonPackage' + +name = 'BUSCO' +version = '5.4.3' + +homepage = 'https://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['1d2c1a3ff4a847773f2b245b9b91c24ac6cd837b097ea467be07f5a37e460dd1'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for pandas + ('R', '4.1.2'), # for R and ggplot2 + ('Biopython', '1.79'), + ('BLAST+', '2.12.0'), + ('HMMER', '3.3.2'), + ('prodigal', '2.6.3'), + ('AUGUSTUS', '3.4.0'), + ('SEPP', '4.5.1'), + ('MetaEuk', '6'), + ('BBMap', '38.98'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin %(installdir)s/doc', + 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/LICENSE %(installdir)s/doc', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/test_data %(installdir)s', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/config %(installdir)s', +] + +sanity_check_paths = { + 'files': ['bin/busco', 'bin/generate_plot.py'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages/busco'] +} + +sanity_check_commands = [ + "busco --help", + "busco -i %(installdir)s/test_data/bacteria/genome.fna --mode geno --out test_bacteria.out", + "busco -i %(installdir)s/test_data/eukaryota/genome.fna --mode geno --out test_eukaryota.out", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-11.2.0.eb new file mode 100644 index 00000000000..cf853a53080 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MetaEuk' +version = '6' +local_commit = 'a5d39d9' + +homepage = 'https://metaeuk.soedinglab.org' +description = """MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic + metagenomic contigs.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/soedinglab/%(namelower)s/archive'] +sources = ['%%(version)s-%s.tar.gz' % local_commit] +checksums = ['be19c26f5bdb7dcdd7bc48172105afecf19e5a2e5555edb3ba0c4aa0e4aac126'] + +builddependencies = [('CMake', '3.21.1')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/metaeuk'], + 'dirs': [], +} + +sanity_check_commands = ["metaeuk --help"] + +moduleclass = 'bio' From 587d956c03ac086c45e7c1ca2ea3c14f6fdde3dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2022 18:11:35 +0200 Subject: [PATCH 4528/9987] fix typo in description of Satsuma2 Co-authored-by: Adam Huffman --- .../easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb index bb835d6d34d..576218826f6 100644 --- a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb @@ -7,7 +7,7 @@ version = '2022-03-04' homepage = 'https://github.com/bioinfologics/satsuma2' description = """Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to -accomodate the billions of base pairs in vertebrate genomes).""" +accommodate the billions of base pairs in vertebrate genomes).""" toolchain = {'name': 'GCC', 'version': '11.3.0'} From f15be8ded764911e2a82c006e2ef1437f02dea63 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 22 Aug 2022 18:15:50 +0200 Subject: [PATCH 4529/9987] use 20220304 as version of Satsuma2 --- ...-03-04-GCC-11.3.0.eb => Satsuma2-20220304-GCC-11.3.0.eb} | 6 +++--- ..._fix-GCC-11.patch => Satsuma2-20220304_fix-GCC-11.patch} | 0 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/s/Satsuma2/{Satsuma2-2022-03-04-GCC-11.3.0.eb => Satsuma2-20220304-GCC-11.3.0.eb} (90%) rename easybuild/easyconfigs/s/Satsuma2/{Satsuma2-2022-03-04_fix-GCC-11.patch => Satsuma2-20220304_fix-GCC-11.patch} (100%) diff --git a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb similarity index 90% rename from easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb rename to easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb index 576218826f6..e709378f6ea 100644 --- a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304-GCC-11.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'CMakeMake' name = 'Satsuma2' local_commit = '37c5f38' -version = '2022-03-04' +version = '20220304' homepage = 'https://github.com/bioinfologics/satsuma2' description = """Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequences @@ -15,8 +15,8 @@ source_urls = ['https://github.com/bioinfologics/satsuma2/archive/'] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] patches = ['Satsuma2-%(version)s_fix-GCC-11.patch'] checksums = [ - '75ba38066719c189fba8630326a35afe42421437b55ee9e631973e8be115674c', # Satsuma2-2022-03-04.tar.gz - 'c80755f8942f3a0c9a2598b2a1a6319f508956bc29ccdfdfb9044ec8c50cd691', # Satsuma2-2022-03-04_fix-GCC-11.patch + '75ba38066719c189fba8630326a35afe42421437b55ee9e631973e8be115674c', # Satsuma2-20220304.tar.gz + 'c80755f8942f3a0c9a2598b2a1a6319f508956bc29ccdfdfb9044ec8c50cd691', # Satsuma2-20220304_fix-GCC-11.patch ] builddependencies = [('CMake', '3.23.1')] diff --git a/easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04_fix-GCC-11.patch b/easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304_fix-GCC-11.patch similarity index 100% rename from easybuild/easyconfigs/s/Satsuma2/Satsuma2-2022-03-04_fix-GCC-11.patch rename to easybuild/easyconfigs/s/Satsuma2/Satsuma2-20220304_fix-GCC-11.patch From e8e325144e68bd066c09669484d85b010ab8cdad Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 22 Aug 2022 13:49:55 -0700 Subject: [PATCH 4530/9987] resolve outstanding issues, test every binary --- .../h/HH-suite/HH-suite-3.3.0-gompi-2021b.eb | 46 ++++++++++++++----- 1 file changed, 35 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021b.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021b.eb index 3beaa3948e1..9e79945692b 100644 --- a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2021b.eb @@ -20,9 +20,9 @@ name = 'HH-suite' version = '3.3.0' homepage = 'https://github.com/soedinglab/hh-suite' -description = """The HH-suite is an open-source software package -for sensitive protein sequence searching based on the pairwise -alignment of hidden Markov models (HMMs).""" +description = """The HH-suite is an open-source software package + for sensitive protein sequence searching based on the pairwise + alignment of hidden Markov models (HMMs).""" toolchain = {'name': 'gompi', 'version': '2021b'} @@ -39,28 +39,52 @@ dependencies = [ ('Python', '3.9.6'), ] -_binaries = [ - 'hhalign', 'hhalign_mpi', 'hhalign_omp', - 'hhblits', 'hhblits_mpi', 'hhblits_omp', - 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp', - 'hhmake', 'hhfilter', 'hhconsensus', +_binaries_help = [ + 'cstranslate', 'cstranslate_mpi', 'hhalign', 'hhalign_mpi', 'hhalign_omp', 'hhconsensus', + 'hhfilter', 'hhmake' ] -_scriptfiles = [ - 'hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py', +_binaries_h = [ + 'a3m_database_extract', 'a3m_database_filter', 'a3m_database_reduce', 'a3m_extract', 'a3m_reduce', + 'hhblits', 'hhblits_ca3m', 'hhblits_mpi', 'hhblits_omp', 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp' ] +_binaries_version = ['ffindex_build', 'ffindex_from_fasta', 'ffindex_modify'] + +_binaries_v = ['ffindex_from_fasta_with_split'] + +_binaries_helpless = [ + 'ffindex_apply', 'ffindex_apply_mpi', 'ffindex_get', + 'ffindex_order', 'ffindex_reduce', 'ffindex_unpack' +] + +_scriptfiles = ['hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py'] + fix_perl_shebang_for = ['scripts/*pl'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in _binaries] + + 'files': ['bin/%s' % x for x in _binaries_help] + + ['bin/%s' % x for x in _binaries_h] + + ['bin/%s' % x for x in _binaries_version] + + ['bin/%s' % x for x in _binaries_v] + + ['bin/%s' % x for x in _binaries_helpless] + ['scripts/%s' % y for y in _scriptfiles], 'dirs': ['data', 'scripts'] } +sanity_check_commands = ['%s --help' % x for x in _binaries_help] +sanity_check_commands += ['%s -h' % x for x in _binaries_h] +sanity_check_commands += ['%s --version' % x for x in _binaries_version] +sanity_check_commands += ['%s -v' % x for x in _binaries_v] +sanity_check_commands += ['%s 2>&1 | grep USAGE' % x for x in _binaries_helpless] + modextrapaths = { 'PATH': 'scripts', 'PERL5LIB': 'scripts', } +modextravars = { + 'HHLIB': '%(installdir)s', +} + moduleclass = 'bio' From 6f591417ddef24b561da0863bdbe0a9a4b8aa548 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 22 Aug 2022 16:48:40 -0700 Subject: [PATCH 4531/9987] updates --- .../p/Pillow/Pillow-9.1.0-GCCcore-11.2.0.eb | 32 +++++++++++++ .../scikit-bio/scikit-bio-0.5.7-foss-2021b.eb | 47 +++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2d0c6d0f756 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '9.1.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f401ed2bbb155e1ade150ccc63db1a4f6c1909d3d378f7d1235a44e90d75fb97'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.11.0') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021b.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021b.eb new file mode 100644 index 00000000000..dcfe542f498 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scikit-bio' +version = '0.5.7' + +homepage = 'http://scikit-bio.org' +description = """scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms +and educational resources for bioinformatics.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('scikit-learn', '1.0.1'), + ('IPython', '7.26.0'), + ('h5py', '3.6.0'), + ('Pillow', '9.1.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('msgpack', '1.0.1', { + 'checksums': ['7033215267a0e9f60f4a5e4fb2228a932c404f237817caff8dc3115d9e7cd975'], + }), + ('CacheControl', '0.12.11', { + 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], + }), + ('hdmedians', '0.14.2', { + 'checksums': ['b47aecb16771e1ba0736557255d80ae0240b09156bff434321de559b359ac2d6'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + (name, version, { + 'modulename': 'skbio', + 'checksums': ['6343ca0c621e2fcc5d1c042c8be3200664c5325956a83bea751cf1bcc75d1da9'], + }), +] + +moduleclass = 'bio' From d039cf2ac31b568ab1f9b428fcfa174f6e3cf294 Mon Sep 17 00:00:00 2001 From: Abhishek Mukherjee Date: Mon, 22 Aug 2022 22:38:33 -0400 Subject: [PATCH 4532/9987] add new version of Perl(5.36) for GCC 12.1.0 --- .../p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 1939 +++++++++++++++++ 1 file changed, 1939 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..dfcdfe0ee66 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -0,0 +1,1939 @@ +name = 'Perl' +version = '5.36.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = ['perl-%(version)s.tar.gz'] +checksums = ['e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'] + +builddependencies = [ + ('binutils', '2.38'), + ('groff', '1.22.4'), +] + +dependencies = [ + ('zlib', '1.2.12'), # for Net::SSLeay + ('expat', '2.4.8'), # for XML::Parser + ('ncurses', '6.3'), # for Term::ReadLine::Gnu + ('libreadline', '8.1.2'), # for Term::ReadLine::Gnu + ('DB', '18.1.40'), # for DB_File + ('OpenSSL', '1.1', '', True), # required for Net::SSLeay +] + +# !! order of extensions is important !! +# extensions updated on Apr 28th 2022 +exts_list = [ + ('Config::General', '2.65', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['4d6d5754be3a9f30906836f0cc10e554c8832e14e7a1341efb15b05d706fc58f'], + }), + ('File::Listing', '6.15', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['46c4fb9f9eb9635805e26b7ea55b54455e47302758a10ed2a0b92f392713770c'], + }), + ('ExtUtils::InstallPaths', '0.012', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], + }), + ('Test::Harness', '3.44', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7eb591ea6b499ece6745ff3e80e60cee669f0037f9ccbc4e4511425f593e5297'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], + 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'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Test::Fatal', '0.016', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7283d430f2ba2030b8cd979ae3039d3f1b2ec3dde1a11ca6ae09f992a66f788f'], + }), + ('Test::Warnings', '0.031', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['1e542909fef305e45563e9878ea1c3b0c7cef1b28bb7ae07eba2e1efabec477b'], + }), + ('File::ShareDir', '1.118', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], + }), + ('File::ShareDir::Install', '0.13', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['45befdf0d95cbefe7c25a1daf293d85f780d6d2576146546e6828aad26e580f9'], + }), + ('IPC::System::Simple', '1.30', { + 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN/'], + 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], + }), + ('Importer', '0.026', { + 'source_tmpl': 'Importer-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], + }), + ('Term::Table', '0.016', { + 'source_tmpl': 'Term-Table-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], + }), + ('Scope::Guard', '0.21', { + 'source_tmpl': 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['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['16325d5e308c7b7ab623d1bf944e1354c5f2245afcfadb8eed1e2cae9a0bd0b5'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], + 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], + }), + ('MCE::Mutex', '1.878', { + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], + 'checksums': ['bb5713197cc5ab91302aec746b5cc7204bf84556c30d6af67ce34a6fd38444ad'], + }), + ('Text::CSV_XS', '1.47', { + 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['4bbaffbdfb68505ef3326dc748e63ebe0db31157b78ca8dfcb8c3cd1d1313262'], + }), + ('DBD::CSV', '0.59', { + 'source_tmpl': 'DBD-CSV-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['2a5fadd1d50c18ea023560d39c2cc660ae2a65fa99d9b8244edca7d2dcce9dc0'], + }), + ('Array::Transpose', '0.06', { + 'source_tmpl': 'Array-Transpose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'], + 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], + }), + ('Config::Simple', '4.58', { + 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], + 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], + }), + ('Business::ISBN', '3.007', { + 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['50cc4686dd21c9537b49a231d71711e814ebd2f19aa4ca331baf92ff2de5ce19'], + }), + ('Business::ISBN::Data', '20210112.006', { + 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['98c2cfb266b5fdd016989abaa471d9dd4c1d593c508a6f01f66d184d5fee8bae'], + }), + ('common::sense', '3.75', { + 'source_tmpl': 'common-sense-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], + }), + ('IO::Compress::Bzip2', '2.106', { + 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['cb9a26ec7d86afb3081b6369620f1f67eaa45b7c41c4eb800e1da5e700a3e3f5'], + }), + ('JSON::XS', '4.03', { + 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], + }), + ('List::MoreUtils::XS', '0.430', { + 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], + }), + ('Authen::NTLM', '1.09', { + 'source_tmpl': 'NTLM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'], + 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('XML::SAX::Expat', '0.51', { + 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN'], + 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], + }), + ('Inline', '0.86', { + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], + }), + ('Sys::Info::Base', '0.7807', { + 'source_tmpl': 'Sys-Info-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['132362b0046e8dc4f12e1560903623a88a8871d09bf1c29d93d48d3f4a582acb'], + }), + ('Sys::Info', '0.7811', { + 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'], + }), + ('HTML::Template', '2.97', { + 'source_tmpl': 'HTML-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR/'], + 'checksums': ['6547af61f3aa85793f8616190938d677d7995fb3b720c16258040bc935e2129f'], + }), + ('MIME::Charset', '1.012.2', { + 'source_tmpl': 'MIME-Charset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI/'], + 'checksums': ['878c779c0256c591666bd06c0cde4c0d7820eeeb98fd1183082aee9a1e7b1d13'], + }), + ('Unicode::LineBreak', '2019.001', { + 'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI/'], + 'checksums': ['486762e4cacddcc77b13989f979a029f84630b8175e7fef17989e157d4b6318a'], + }), + ('String::Print', '0.94', { + 'source_tmpl': 'String-Print-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'], + }), + ('Log::Report', '1.33', { + 'source_tmpl': 'Log-Report-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['49624da338fd7d57288fa22a47241476fb5ce2f6008181f786c7830fe5af01ff'], + }), + ('Log::Report::Optional', '1.07', { + 'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], + }), + ('Sys::Info::Driver::Unknown', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Sys::Info::Driver::Linux', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER/'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), +] + +moduleclass = 'lang' From d255a35214b7f070944317bf193e7667565143f6 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 23 Aug 2022 09:58:01 +0200 Subject: [PATCH 4533/9987] adding easyconfigs: RheoTool-5.0-foss-2019b.eb --- .../r/RheoTool/RheoTool-5.0-foss-2019b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb diff --git a/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb b/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb new file mode 100644 index 00000000000..2c91848824b --- /dev/null +++ b/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb @@ -0,0 +1,47 @@ +easyblock = "Binary" + +name = "RheoTool" +version = "5.0" + +homepage = "https://github.com/fppimenta/rheoTool" +description = """RheoTool is an open-source toolbox based on OpenFOAM to simulate Generalized Newtonian Fluids (GNF) +and viscoelastic fluids under pressure-driven and/or electrically-driven flows.""" + +toolchain = {"name": "foss", "version": "2019b"} + +source_urls = ["https://github.com/fppimenta/rheoTool/archive/refs/tags/"] +sources = ["v%(version)s.tar.gz"] +checksums = ["2e0899684d6d7f9ddee0d93b39a6ed56262b171bc4e5536914645209b66003ed"] + +dependencies = [ + ("OpenFOAM", "7", "-20200508"), + ("Eigen", "3.3.7", "", True), + ("PETSc", "3.12.4", "-Python-3.7.4"), +] + +extract_sources = True + + +install_cmd = "source $FOAM_BASH && " +install_cmd += "export EIGEN_RHEO=$EBROOTEIGEN && " +install_cmd += "cd of70/src && " + +# variables of target install directory +install_cmd += "export WM_PROJECT_USER_DIR=%(installdir)s && " +install_cmd += "export FOAM_USER_APPBIN=%(installdir)s/bin && " +install_cmd += "export FOAM_USER_LIBBIN=%(installdir)s/lib && " +install_cmd += "export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && " + +install_cmd += "./Allwmake -j %(parallel)s " + +sanity_check_paths = { + "files": ["bin/rheoBDFoam", "lib/libthermoRheoTool.so"], + "dirs": [], +} + +# source $FOAM_BASH must run before using RheoTool, otherwise there will be missing libraries +sanity_check_commands = ["source $FOAM_BASH && rheoBDFoam -help"] + +modloadmsg = 'Please run command "source $FOAM_BASH " before using RheoTool, otherwise there will be missing libraries.' + +moduleclass = "cae" From 5626a6fd306371c1d2b73d81474a1007fe76fff1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 23 Aug 2022 10:51:01 +0200 Subject: [PATCH 4534/9987] adding easyconfigs: EGTtools-0.1.10.dev2-foss-2021b.eb and patches: EGTtools-0.1.10.dev2_fix_include.patch --- .../EGTtools-0.1.10.dev2-foss-2021b.eb | 45 +++++++++++++++++++ .../EGTtools-0.1.10.dev2_fix_include.patch | 13 ++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2-foss-2021b.eb create mode 100644 easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2_fix_include.patch diff --git a/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2-foss-2021b.eb b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2-foss-2021b.eb new file mode 100644 index 00000000000..b721a288373 --- /dev/null +++ b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2-foss-2021b.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'EGTtools' +version = '0.1.10.dev2' + +homepage = 'https://github.com/Socrats/EGTTools' +description = """ +EGTtools provides a centralized repository with analytical and numerical +methods to study/model game theoretical problems under the Evolutionary Game +Theory (EGT) framework.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('CMake', '3.21.1'), + ('Ninja', '1.10.2'), + ('scikit-build', '0.11.1'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('networkx', '2.6.3'), + ('Seaborn', '0.11.2'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'patches': ['%(name)s-%(version)s_fix_include.patch'], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': [ + '0ae38d9945ecd5cb49e8bdd0dcedcd938e3380e5db93fdf74c681ac8abd2317e', # egttools-0.1.10.dev2.tar.gz + # EGTtools-0.1.10.dev2_fix_include.patch + '6237d0ad05d8aca7c9eccc6627f6e91a3511d3a4adbb72c6e881553f088f6c9a', + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2_fix_include.patch b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2_fix_include.patch new file mode 100644 index 00000000000..9dd130a6f83 --- /dev/null +++ b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2_fix_include.patch @@ -0,0 +1,13 @@ +Add missing include to avoid build error: "shared_ptr in namespace std does not name a template type" +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur egttools-0.1.10.dev2.orig/include/egttools/finite_populations/behaviors/NFGStrategies.hpp egttools-0.1.10.dev2/include/egttools/finite_populations/behaviors/NFGStrategies.hpp +--- egttools-0.1.10.dev2.orig/include/egttools/finite_populations/behaviors/NFGStrategies.hpp 2022-08-06 16:35:37.000000000 +0200 ++++ egttools-0.1.10.dev2/include/egttools/finite_populations/behaviors/NFGStrategies.hpp 2022-08-12 17:22:35.065010288 +0200 +@@ -25,6 +25,7 @@ + + #include + #include ++#include + #include + #include + From 00d382d19f7a68eebee0c2a5490fe5c35a2c8f04 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 10:29:26 +0100 Subject: [PATCH 4535/9987] adding easyconfigs: dbus-glib-0.112-GCCcore-11.2.0.eb --- .../dbus-glib-0.112-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2b0e0d55ab9 --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.112' + +homepage = 'https://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] +checksums = ['7d550dccdfcd286e33895501829ed971eeb65c614e73aadb4a08aeef719b143a'] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('Python', '3.9.6', '-bare'), # Python is needed for building against GLib. +] + +dependencies = [ + ('GLib', '2.69.1'), + ('DBus', '1.13.18'), + ('expat', '2.4.1'), +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' From 272c32b0058a9c744041dcd549814ca340280367 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 10:33:12 +0100 Subject: [PATCH 4536/9987] adding easyconfigs: enchant-2-2.3.3-GCCcore-11.2.0.eb --- .../enchant-2-2.3.3-GCCcore-11.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..025a3fe29b1 --- /dev/null +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +# Updated from enchant-1.6.1-intel-2017a.eb +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'enchant-2' +version = '2.3.3' + +homepage = 'https://github.com/AbiWord/enchant' +description = """Enchant aims to provide a simple but comprehensive abstraction for dealing +with different spell checking libraries in a consistent way. A client, such +as a text editor or word processor, need not know anything about a specific +spell-checker, and since all back-ends are plugins, new spell-checkers can +be added without needing any change to the program using Enchant.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/AbiWord/enchant/releases/download/v%(version)s'] +sources = ['enchant-%(version)s.tar.gz'] +checksums = [ + '3da12103f11cf49c3cf2fd2ce3017575c5321a489e5b9bfa81dd91ec413f3891' +] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('M4', '1.4.19'), +] + +preconfigopts = "autoreconf -vfi && " + +dependencies = [ + ('hunspell', '1.7.0'), +] + +buildopts = "LIBTOOL='libtool --tag=CC'" + +sanity_check_paths = { + 'files': ['bin/enchant-2', 'bin/enchant-lsmod-2', + 'lib/libenchant-2.a', 'lib/libenchant-2.%s' % SHLIB_EXT], + 'dirs': ['include/enchant-2', 'lib/enchant-2'], +} + +moduleclass = 'tools' From d74d9289492bbd7460c3614888fe4413a940c45f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 10:35:05 +0100 Subject: [PATCH 4537/9987] adding easyconfigs: hunspell-1.7.0-GCCcore-11.2.0.eb --- .../hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..857561f81b8 --- /dev/null +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'hunspell' +version = '1.7.0' + +homepage = 'http://hunspell.github.io/' +description = """Hunspell is a spell checker and morphological analyzer +library and program designed for languageswith rich morphology and +complex word compounding or character encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/hunspell/hunspell/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bb27b86eb910a8285407cf3ca33b62643a02798cf2eef468c0a74f6c3ee6bc8a'] + +builddependencies = [ + ('Autotools', '20210726'), + ('binutils', '2.37'), + ('M4', '1.4.19'), +] + +preconfigopts = "autoreconf -vfi && " + +sanity_check_paths = { + 'files': ['bin/hunspell', 'lib/libhunspell-%(version_major_minor)s.a', + 'lib/libhunspell-%%(version_major_minor)s.%s' % SHLIB_EXT, 'lib/pkgconfig/hunspell.pc'], + 'dirs': ['include/hunspell'], +} + +moduleclass = 'tools' From 561bc7295b6ed7fd85482b3b6a5f5e0a3d3501e5 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 10:37:55 +0100 Subject: [PATCH 4538/9987] adding easyconfigs: GConf-3.2.6-GCCcore-11.2.0.eb --- .../g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b78028c24b1 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +# The homeage is no longer reachable! +# homepage = 'https://developer.gnome.org/gconf/' +# The project was depricated with the move to Gnome-3 +# Possible alternative, although 6 years old: +homepage = 'https://gitlab.gnome.org/iainl/gconf' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +patches = [ + '%(name)s-%(version)s_call-dbus_g_thread_init.patch', + '%(name)s-%(version)s_fix_wrong_return_value.patch', + '%(name)s-%(version)s_gconf-path-max-hurd.patch', + '%(name)s-%(version)s_readd_gconf_engine_key_is_writable.patch', +] +checksums = [ + '1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c', # GConf-3.2.6.tar.xz + 'ed55bff5bc239115ae27b8520a923ae0d5cab6cb15ca9921a8c23b939306489f', # GConf-3.2.6_call-dbus_g_thread_init.patch + 'f8f7745c3648953098eb56af0f64adc69d8c0b0e78c8db351746a2b4c58e8bb4', # GConf-3.2.6_fix_wrong_return_value.patch + 'ee5524c3cb985088bbe4884531ddc48ba22d2fced2a34865304c77e194a55bde', # GConf-3.2.6_gconf-path-max-hurd.patch + # GConf-3.2.6_readd_gconf_engine_key_is_writable.patch + 'b95dfc2f0474d9162fc686f26cd4d3da5c9b01a9c609dc0a4f2b2bd901d497f3', +] + +builddependencies = [ + ('binutils', '2.37'), + ('GObject-Introspection', '1.68.0'), +] + +dependencies = [ + ('GLib', '2.69.1'), + ('dbus-glib', '0.112'), + ('libxml2', '2.9.10'), + ('GTK3', '3.24.31'), + ('intltool', '0.51.0'), +] + +configopts = '--disable-orbit ' + +local_check_filelist = ['bin/gconf%s' % x for x in ['-merge-tree', 'tool-2']] +local_check_filelist += ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] +local_check_filelist += ['lib/libgconf-2.%s' % x for x in ['a', 'so']] + +sanity_check_paths = { + 'files': local_check_filelist, + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' From 447403daf501f70934e2d375aebc857a93fd78e9 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 10:40:25 +0100 Subject: [PATCH 4539/9987] adding easyconfigs: glib-networking-2.72.1-GCCcore-11.2.0.eb --- .../glib-networking-2.72.1-GCCcore-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f1cc388b36a --- /dev/null +++ b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MesonNinja' + +name = 'glib-networking' +version = '2.72.1' + +homepage = 'https://gitlab.gnome.org/GNOME/glib-networking' +description = "Network extensions for GLib" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/glib-networking/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['675a654ae55d381490c5d76b84e088f684125415fbd2d46f74dfa5522c4a1268'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.69.1'), + ('GnuTLS', '3.7.3'), + ('libidn2', '2.3.2'), +] + +sanity_check_paths = { + 'files': ['lib/gio/modules/libgiognutls.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'GIO_EXTRA_MODULES': 'lib/gio/modules'} + +moduleclass = 'lib' From 103e747c496af95e4a7d92e1e17ef54f8461aa28 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 10:48:52 +0100 Subject: [PATCH 4540/9987] adding easyconfigs: libev-4.33-GCC-11.2.0.eb --- .../l/libev/libev-4.33-GCC-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb new file mode 100644 index 00000000000..30242c7b7e0 --- /dev/null +++ b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb @@ -0,0 +1,37 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'libev' +version = '4.33' + +homepage = 'http://software.schmorp.de/pkg/libev.html' +description = """A full-featured and high-performance (see benchmark) +event loop that is loosely modelled after libevent, but without its +limitations and bugs. It is used in GNU Virtual Private Ethernet, +rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many +other programs.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://dist.schmorp.de/libev'] +sources = ['%(name)s-%(version)s.tar.gz'] + +checksums = [ + '507eb7b8d1015fbec5b935f34ebed15bf346bed04a11ab82b8eee848c4205aea', # libev-4.33.tar.gz +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libev.%s' % SHLIB_EXT], + 'dirs': ['include/', 'share'], +} + +moduleclass = 'lib' From 53dfd97c96b4b5b08ed20199ddfb34eb0237d88a Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 10:51:05 +0100 Subject: [PATCH 4541/9987] adding easyconfigs: libpsl-0.21.1-GCCcore-11.2.0.eb --- .../l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..17dc25fdbc1 --- /dev/null +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libpsl' +version = '0.21.1' + +homepage = 'https://rockdaboot.github.io/libpsl' +description = "C library for the Public Suffix List" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/rockdaboot/libpsl/archive'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ac6ce1e1fbd4d0254c4ddb9d37f1fa99dec83619c1253328155206b896210d4c'] + +builddependencies = [ + ('binutils', '2.37'), + ('libtool', '2.4.6'), + ('Autotools', '20210726'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('libidn2', '2.3.2'), + ('libunistring', '1.0'), +] + +sanity_check_paths = { + 'files': ['bin/psl', 'lib/libpsl.a'], + 'dirs': [] +} + +moduleclass = 'lib' From 845936e6bcea7ee1bcc45d3f89d0f4b6e36f9473 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 11:01:48 +0100 Subject: [PATCH 4542/9987] adding easyconfigs: libwpe-1.13.3-GCCcore-11.2.0.eb --- .../l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..90c0db43eef --- /dev/null +++ b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'libwpe' +version = '1.13.3' + +homepage = 'https://webkit.org/wpe' +description = """WPE is the reference WebKit port for embedded and +low-consumption computer devices. It has been designed from the +ground-up with performance, small footprint, accelerated content +rendering, and simplicity of deployment in mind, bringing the +excellence of the WebKit engine to countless platforms and target devices.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://wpewebkit.org/releases'] +sources = ['%(name)s-%(version)s.tar.xz'] + +checksums = [ + '05f871922f6ca750c5689a38a346c3fba130417d3490dd52362b4fe22f334e96', # libwpe-1.13.3.tar.xz +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('CMake', '3.22.1'), + ('Meson', '0.58.2'), +] + +dependencies = [ + ('glew', '2.2.0', '-egl'), +] + +parallel = 2 + +sanity_check_paths = { + 'files': ['lib/libwpe-1.0.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 361535d2431a52cbef706d6fd0782593f9f5b56a Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 11:03:40 +0100 Subject: [PATCH 4543/9987] adding easyconfigs: Wayland-1.20.0-GCCcore-11.2.0.eb --- .../Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6036be672fc --- /dev/null +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb @@ -0,0 +1,59 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Bundle' + +name = 'Wayland' +version = '1.20.0' + +homepage = 'https://wayland.freedesktop.org/' +description = """ +Wayland is a project to define a protocol for a compositor to talk to + its clients as well as a library implementation of the protocol. The + compositor can be a standalone display server running on Linux kernel + modesetting and evdev input devices, an X application, or a wayland + client itself. The clients can be traditional applications, X servers + (rootless or fullscreen) or other display servers. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('CMake', '3.21.1'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), + ('binutils', '2.37'), +] + +dependencies = [ + ('libffi', '3.4.2'), + ('expat', '2.4.1'), + ('libxml2', '2.9.10'), +] + +default_easyblock = 'MesonNinja' +default_component_specs = { + 'source_urls': ['https://wayland.freedesktop.org/releases'], + 'sources': [SOURCE_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('wayland', version, { + 'checksums': ['b8a034154c7059772e0fdbd27dbfcda6c732df29cae56a82274f6ec5d7cd8725'], + 'configopts': "-Ddocumentation=false", + }), + ('wayland-protocols', '1.25', { + 'checksums': ['f1ff0f7199d0a0da337217dd8c99979967808dc37731a1e759e822b75b571460'], + 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH " + }), +] + +_libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']] +sanity_check_paths = { + 'files': ['bin/wayland-scanner'] + _libs, + 'dirs': ['lib'], +} + +sanity_check_commands = ["wayland-scanner --help", "wayland-scanner --version"] + +moduleclass = 'vis' From 6bc5b2935a0011a55f41c47fbf14de49124c62db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2022 12:13:03 +0200 Subject: [PATCH 4544/9987] add sanity check commands for recent gettext versions (>= 0.20.x) --- .../easyconfigs/g/gettext/gettext-0.20.1-GCCcore-8.3.0.eb | 5 +++++ .../easyconfigs/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb | 5 +++++ easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb | 5 +++++ .../easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb | 5 +++++ .../easyconfigs/g/gettext/gettext-0.21-GCCcore-10.3.0.eb | 5 +++++ .../easyconfigs/g/gettext/gettext-0.21-GCCcore-11.2.0.eb | 5 +++++ .../easyconfigs/g/gettext/gettext-0.21-GCCcore-11.3.0.eb | 5 +++++ easybuild/easyconfigs/g/gettext/gettext-0.21.eb | 5 +++++ 8 files changed, 40 insertions(+) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-8.3.0.eb index a783c28471b..cf0317df5d5 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-8.3.0.eb @@ -29,4 +29,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb index 27b89d2bef1..1ecd5f36852 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.20.1-GCCcore-9.3.0.eb @@ -29,4 +29,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb index 19857c19d59..0967e62738e 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.20.1.eb @@ -31,4 +31,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb index e0d0f8a84f0..1303c6d1923 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb @@ -29,4 +29,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.3.0.eb index 10bb6ad3a5a..c3753a010e5 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.3.0.eb @@ -29,4 +29,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.2.0.eb index 7d329d1be72..8944747f686 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.2.0.eb @@ -29,4 +29,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.3.0.eb index 9b5bf58331c..74724934445 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-11.3.0.eb @@ -29,4 +29,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21.eb index 3faa2c38fab..db1772fc35b 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.21.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21.eb @@ -31,4 +31,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + moduleclass = 'tools' From a0735ae0b1bbaf3fd09c0f8575eacaf3c4042e77 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 11:16:54 +0100 Subject: [PATCH 4545/9987] DPUGIXML_HEADER_ONLY=True removed as requested --- .../easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb index b242e8f9927..ef535d5dfb6 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb @@ -21,7 +21,7 @@ builddependencies = [ ('CMake', '3.22.1') ] -configopts = '-DBUILD_SHARED_LIBS=ON -DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON -DPUGIXML_HEADER_ONLY=True ' +configopts = '-DBUILD_SHARED_LIBS=ON -DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON ' sanity_check_paths = { 'files': ['include/pugiconfig.hpp', 'include/pugixml.hpp', 'lib/libpugixml.a', From f245cb5c529148e665bb7c9d4e292dbda49669e7 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 11:21:20 +0100 Subject: [PATCH 4546/9987] adding easyconfigs: Waylandpp-1.0.0-GCCcore-11.2.0.eb --- .../Waylandpp-1.0.0-GCCcore-11.2.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..327d939ec40 --- /dev/null +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb @@ -0,0 +1,53 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'Waylandpp' +version = '1.0.0' + +homepage = 'https://github.com/NilsBrause/waylandpp' +description = """Wayland is an object oriented display protocol, which +features request and events. Requests can be seen as method calls on +certain objects, whereas events can be seen as signals of an object. +This makes the Wayland protocol a perfect candidate for a C++ binding. + +The goal of this library is to create such a C++ binding for Wayland +using the most modern C++ technology currently available, providing +an easy to use C++ API to Wayland.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/NilsBrause/waylandpp/archive'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + 'b20b45917382c6b87e9380130c9a1a1c563da2f498de5830df12fbce326dd9f5', # 1.0.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('pugixml', '1.12.1'), + ('Wayland', '1.20.0'), +] + +parallel = 2 + +sanity_check_paths = { + 'files': ['bin/wayland-scanner++', 'lib//libwayland-client-extra++.%s' % SHLIB_EXT, + 'lib/libwayland-client++.%s' % SHLIB_EXT, + 'lib/libwayland-client-unstable++.%s' % SHLIB_EXT, + 'lib/libwayland-cursor++.%s' % SHLIB_EXT, + 'lib/libwayland-egl++.%s' % SHLIB_EXT, + 'lib/libwayland-server-extra++.%s' % SHLIB_EXT, + 'lib/libwayland-server++.%s' % SHLIB_EXT, + 'lib/libwayland-server-unstable++.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 86c002427aa49cb0a166b121b4ebe81d0575e781 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 11:34:59 +0100 Subject: [PATCH 4547/9987] adding easyconfigs: wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb --- .../wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e675f510aa1 --- /dev/null +++ b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MesonNinja' + +name = 'wpebackend-fdo' +version = '1.13.1' + +homepage = 'https://wpewebkit.org/' +description = """WPE WebKit allows embedders to create simple and performant +systems based on Web platform technologies. It is a WebKit port designed with +flexibility and hardware acceleration in mind, leveraging common 3D graphics +APIs for best performance.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://wpewebkit.org/releases'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['d61ca47ec52d7cd1d6f869f66d6ea247a53092acfad1a8cbab71836a82d3a0ae'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('pugixml', '1.12.1'), + ('Waylandpp', '1.0.0'), + ('libepoxy', '1.5.8'), + ('glib-networking', '2.72.1'), + ('libwpe', '1.13.3'), +] + +sanity_check_paths = { + 'files': ['lib/libWPEBackend-fdo-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 9884fd1a7933e46b4a0c485d904bd5bb22db1211 Mon Sep 17 00:00:00 2001 From: anselmicz Date: Tue, 23 Aug 2022 12:51:24 +0200 Subject: [PATCH 4548/9987] adding easyconfigs: bwidget-1.9.15-GCCcore-11.3.0.eb, Togl-2.0-GCCcore-11.3.0.eb, XCrySDen-1.6.2-foss-2022a.eb, XCrySDen-1.6.2-intel-2022a.eb and patches: XCrySDen-1.6.2-no-bwidget-tcl-download.patch --- .../bwidget/bwidget-1.9.15-GCCcore-11.3.0.eb | 26 ++++++++++ .../t/Togl/Togl-2.0-GCCcore-11.3.0.eb | 49 +++++++++++++++++++ .../x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb | 42 ++++++++++++++++ .../x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb | 40 +++++++++++++++ ...rySDen-1.6.2-no-bwidget-tcl-download.patch | 16 ++++++ 5 files changed, 173 insertions(+) create mode 100644 easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb create mode 100644 easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-no-bwidget-tcl-download.patch diff --git a/easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..cec51692a1f --- /dev/null +++ b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'bwidget' +version = '1.9.15' + +homepage = 'https://core.tcl-lang.org/bwidget/home' +description = 'The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://downloads.sourceforge.net/project/tcllib/BWidget/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9c4dd648fdfd31de7cb5af44b392a1916f949dd195820684d940edcd8485ac13'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Tk', '8.6.12')] + +modextrapaths = {'TCLLIBPATH': '.'} + +sanity_check_paths = { + 'files': ['button.tcl'], + 'dirs': ['BWman', 'demo', 'images', 'lang', 'tests'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1a55a016951 --- /dev/null +++ b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +# Last contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +easyblock = 'ConfigureMake' + +name = 'Togl' +version = '2.0' + +homepage = 'https://sourceforge.net/projects/togl/' +description = """A Tcl/Tk widget for OpenGL rendering.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://downloads.sourceforge.net/project/%(namelower)s/%(name)s/%(version)s/'] +sources = ['%(name)s%(version)s-src.tar.gz'] +patches = [ + 'Togl-2.0_configure.patch', + 'Togl-2.0_decl.patch', +] +checksums = [ + 'b7d4a90bbad3aca618d505ee99e7fd8fb04c829f63231dda2360f557ba3f7610', # Togl2.0-src.tar.gz + 'da97f36b60cd107444cd92453809135b14dc1e8775146b3ba0731da8002e6f9f', # Togl-2.0_configure.patch + '05db6b3ca5139f60616d074903883a3070fcfb1eb8c965b0938779b4f9a6ec6a', # Togl-2.0_decl.patch +] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Mesa', '22.0.3'), + ('Tk', '8.6.12'), + ('Tcl', '8.6.12'), +] + +preconfigopts = 'export CFLAGS="$CFLAGS -DTOGL_USE_FONTS=0" && ' + +configopts = "--prefix=%(installdir)s --exec-prefix=%(installdir)s " +configopts += "--with-tcl=$EBROOTTCL/lib --with-tk=$EBROOTTK/lib" + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'lib', 'lib/%(name)s%(version)s'], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': 'lib/%(name)s%(version)s', + 'LIBRARY_PATH': 'lib/%(name)s%(version)s', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb new file mode 100644 index 00000000000..14a8346534a --- /dev/null +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb @@ -0,0 +1,42 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +name = 'XCrySDen' +version = '1.6.2' + +homepage = "http://www.xcrysden.org/" +description = """ +XCrySDen is a crystalline and molecular structure visualisation program aiming +at display of isosurfaces and contours, which can be superimposed on +crystalline structures and interactively rotated and manipulated. +""" +docurls = "http://www.xcrysden.org/Documentation.html" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ["http://www.xcrysden.org/download/"] +sources = [SOURCELOWER_TAR_GZ] +patches = ['XCrySDen-1.6.2-no-bwidget-tcl-download.patch'] +checksums = [ + '811736ee598bec1a5b427fd10e4e063a30dd7cadae96a43a50b36ce90a4f503f', # xcrysden-1.6.2.tar.gz + 'e5f79c77116c6faf441d63f62bb3d22c5520163995b28e505d2168424a587bac', # XCrySDen-1.6.2-no-bwidget-tcl-download.patch +] + +dependencies = [ + ('Togl', '2.0'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('bwidget', '1.9.15'), +] + +# gcc fix by Jakob Schiotz, commit 7433b19bd05d1d511ee135a92b3ba845c89814d7 +prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" + +sanity_check_commands = [ + 'xcrysden --help', + # requires DISPLAY + #'xcrysden --xsf $EBROOTXCRYSDEN/share/%(namelower)s-%(version)s/examples/XSF_Files/GaAsH.xsf --print output.png \ + # && rm output.png', +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb new file mode 100644 index 00000000000..0a89de907c9 --- /dev/null +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb @@ -0,0 +1,40 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +name = 'XCrySDen' +version = '1.6.2' + +homepage = "http://www.xcrysden.org/" +docurls = "http://www.xcrysden.org/Documentation.html" +description = """ +XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces +and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. +It also possesses some tools for analysis of properties in reciprocal space such as interactive selection +of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. +""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ["http://www.xcrysden.org/download/"] +sources = [SOURCELOWER_TAR_GZ] +patches = ['XCrySDen-1.6.2-no-bwidget-tcl-download.patch'] +checksums = [ + '811736ee598bec1a5b427fd10e4e063a30dd7cadae96a43a50b36ce90a4f503f', # xcrysden-1.6.2.tar.gz + 'e5f79c77116c6faf441d63f62bb3d22c5520163995b28e505d2168424a587bac', # XCrySDen-1.6.2-no-bwidget-tcl-download.patch +] + +dependencies = [ + ('Togl', '2.0'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('bwidget', '1.9.15'), +] + +sanity_check_commands = [ + 'xcrysden --help', + # requires DISPLAY + #'xcrysden --xsf $EBROOTXCRYSDEN/share/%(namelower)s-%(version)s/examples/XSF_Files/GaAsH.xsf --print output.png \ + # && rm output.png', +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-no-bwidget-tcl-download.patch b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-no-bwidget-tcl-download.patch new file mode 100644 index 00000000000..62f217b05fe --- /dev/null +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-no-bwidget-tcl-download.patch @@ -0,0 +1,16 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 +# +# Do not download and build own BWidget and Tcl; use modules instead. +diff -Nru xcrysden-1.6.2.orig/Makefile xcrysden-1.6.2/Makefile +--- xcrysden-1.6.2.orig/Makefile 2022-08-23 08:23:59.130921000 +0200 ++++ xcrysden-1.6.2/Makefile 2022-08-23 08:39:27.632777181 +0200 +@@ -18,7 +18,7 @@ + + all: tcl tk mesa togl fftw xcrysden + # meschach +-xcrysden: usage bwidget bindir src-C src-F src-Tcl ++xcrysden: usage bindir src-C src-F + + usage: $(TOPDIR)/docs/xcrysden.1 + man $(TOPDIR)/docs/xcrysden.1 | awk 'BEGIN {lprint=0; print "## do not edit changes will be lost (file automatically generated)\n"; } /SYNOPSIS/ { lprint=1; } /SEE ALSO/ { lprint=0; } /a*/ { if (lprint) print; }' > usage From 9441a175961534808f7a18be52a42dfe25a0d861 Mon Sep 17 00:00:00 2001 From: Jakub Kropacek Date: Tue, 23 Aug 2022 13:13:23 +0200 Subject: [PATCH 4549/9987] fix python code style --- easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.3.0.eb | 4 ++-- easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb | 2 +- .../easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.3.0.eb index 1a55a016951..19dd00be65a 100644 --- a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.3.0.eb @@ -42,8 +42,8 @@ sanity_check_paths = { } modextrapaths = { - 'LD_LIBRARY_PATH': 'lib/%(name)s%(version)s', - 'LIBRARY_PATH': 'lib/%(name)s%(version)s', + 'LD_LIBRARY_PATH': 'lib/%(name)s%(version)s', + 'LIBRARY_PATH': 'lib/%(name)s%(version)s', } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb index 14a8346534a..fdd47d28c63 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb @@ -35,7 +35,7 @@ prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&" sanity_check_commands = [ 'xcrysden --help', # requires DISPLAY - #'xcrysden --xsf $EBROOTXCRYSDEN/share/%(namelower)s-%(version)s/examples/XSF_Files/GaAsH.xsf --print output.png \ + # 'xcrysden --xsf $EBROOTXCRYSDEN/share/%(namelower)s-%(version)s/examples/XSF_Files/GaAsH.xsf --print output.png \ # && rm output.png', ] diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb index 0a89de907c9..c9929c6854b 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb @@ -33,7 +33,7 @@ dependencies = [ sanity_check_commands = [ 'xcrysden --help', # requires DISPLAY - #'xcrysden --xsf $EBROOTXCRYSDEN/share/%(namelower)s-%(version)s/examples/XSF_Files/GaAsH.xsf --print output.png \ + # 'xcrysden --xsf $EBROOTXCRYSDEN/share/%(namelower)s-%(version)s/examples/XSF_Files/GaAsH.xsf --print output.png \ # && rm output.png', ] From f94d60dbb9a69b0dfbe1f2bdf2864093209dd3d8 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 12:26:58 +0100 Subject: [PATCH 4550/9987] adding easyconfigs: LibSoup-3.0.7-GCC-11.2.0.eb --- .../l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb new file mode 100644 index 00000000000..33e5fa76118 --- /dev/null +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MesonNinja' + +name = 'LibSoup' +version = '3.0.7' + +homepage = 'https://wiki.gnome.org/Projects/libsoup' +description = """libsoup is an HTTP client/server library for GNOME. It +uses GObjects and the glib main loop, to integrate well with GNOME +applications, and also has a synchronous API, for use in threaded +applications.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'cstd': 'gnu11'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ebdf90cf3599c11acbb6818a9d9e3fc9d2c68e56eb829b93962972683e1bf7c8'] + +builddependencies = [ + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.68.0'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('libxml2', '2.9.10'), + ('SQLite', '3.36'), + ('GLib', '2.69.1'), + ('libpsl', '0.21.1'), + ('cURL', '7.78.0'), + ('GnuTLS', '3.7.3'), + ('nghttp2', '1.48.0'), + ('glib-networking', '2.72.1'), + ('Brotli', '1.0.9'), +] + +# uncomment for checking TLS support +osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['lib/libsoup-3.0.%s' % SHLIB_EXT], + 'dirs': ['include/libsoup-3.0/libsoup/', 'lib/pkgconfig'] +} + +moduleclass = 'lib' From efc2889c43d2e0132eef109693ace58d07470882 Mon Sep 17 00:00:00 2001 From: Jakub Kropacek Date: Tue, 23 Aug 2022 13:29:23 +0200 Subject: [PATCH 4551/9987] unify description --- .../easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb index fdd47d28c63..d9454b6a04c 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb @@ -6,9 +6,10 @@ version = '1.6.2' homepage = "http://www.xcrysden.org/" description = """ -XCrySDen is a crystalline and molecular structure visualisation program aiming -at display of isosurfaces and contours, which can be superimposed on -crystalline structures and interactively rotated and manipulated. +XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces +and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. +It also possesses some tools for analysis of properties in reciprocal space such as interactive selection +of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. """ docurls = "http://www.xcrysden.org/Documentation.html" From e4bbb8c902b303e9030039694adf6b63332460fe Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 12:38:51 +0100 Subject: [PATCH 4552/9987] adding easyconfigs: nghttp2-1.48.0-GCC-11.2.0.eb --- .../n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..4b516f19c4b --- /dev/null +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb @@ -0,0 +1,62 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'nghttp2' +version = '1.48.0' + +homepage = 'https://github.com/nghttp2/nghttp2' +description = """ +This is an implementation of the Hypertext Transfer Protocol version 2 in C. + +The framing layer of HTTP/2 is implemented as a reusable C library. +On top of that, we have implemented an HTTP/2 client, server and proxy. +We have also developed load test and benchmarking tools for HTTP/2. + +An HPACK encoder and decoder are available as a public API.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'nghttp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + '946a8fa490548b67fc6074553cb225279cc6404bae96cf74551f2ad4453be637', # v1.48.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('CMake', '3.22.1'), + ('CUnit', '2.1-3'), + ('Boost', '1.79.0'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), + ('nghttp3', '0.6.0'), + ('Python', '3.9.6'), + ('libxml2', '2.9.10'), + ('Jansson', '2.14'), + ('jemalloc', '5.2.1'), + ('ngtcp2', '0.7.0'), + ('libevent', '2.1.12'), + ('libev', '4.33'), + ('c-ares', '1.18.1'), +] + + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=release ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libnghttp2.%s' % SHLIB_EXT], + 'dirs': ['include/nghttp2', 'share'], +} + +moduleclass = 'lib' From 152f8e510ff1f0ae10b3d3e52f1ae45d82844978 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 12:41:46 +0100 Subject: [PATCH 4553/9987] adding easyconfigs: nghttp3-0.6.0-GCCcore-11.2.0.eb --- .../n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..061f0d2f4c2 --- /dev/null +++ b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'nghttp3' +version = '0.6.0' + +homepage = 'https://github.com/ngtcp2/nghttp3' +description = """ nghttp3 is an implementation of RFC 9114 HTTP/3 +mapping over QUIC and RFC 9204 QPACK in C. +It does not depend on any particular QUIC transport implementation.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'ngtcp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + '3cd5fa107541a2dd11b87a84f251a98fae4c7b67df9d78be7343e4adce540b7f', # v0.6.0.tar.gz +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('pkg-config', '0.29.2'), + ('CUnit', '2.1-3'), +] + +separate_build_dir = True +configopts = '-DCMAKE_BUILD_TYPE=release ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libnghttp3.a', 'lib/libnghttp3.%s' % SHLIB_EXT], + 'dirs': ['include/nghttp3'], +} + +moduleclass = 'lib' From 87781aecc599bad8f4da9473badbf09b914bb907 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 12:44:05 +0100 Subject: [PATCH 4554/9987] adding easyconfigs: ngtcp2-0.7.0-GCCcore-11.2.0.eb --- .../n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..81bcc53c6e2 --- /dev/null +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'ngtcp2' +version = '0.7.0' + +homepage = 'https://github.com/ngtcp2/ngtcp2' +description = """ +'Call it TCP/2. One More Time.' + +ngtcp2 project is an effort to implement RFC9000 QUIC protocol.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'ngtcp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + 'b2015c58e6d249bb71c7f7726a1e5ec5ccc78be7d50d82938358fac14ec98ca9', # v0.6.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('CUnit', '2.1-3'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', True), + ('GnuTLS', '3.7.3'), + ('nghttp3', '0.6.0'), +] + +osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=release -DENABLE_GNUTLS=True' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libngtcp2_static.a', 'lib/libngtcp2.%s' % SHLIB_EXT], + 'dirs': ['share/doc/ngtcp2'], +} + +moduleclass = 'lib' From 58e0d0e5b27b546b7575d963589dd20a19705f01 Mon Sep 17 00:00:00 2001 From: Abhishek Mukherjee Date: Tue, 23 Aug 2022 08:14:29 -0400 Subject: [PATCH 4555/9987] GCCcore 12.1.0 groff-1.22.4 --- .../g/groff/groff-1.22.4-GCCcore-12.1.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.1.0.eb diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.1.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..b7b41cdb5ac --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.1.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.22.4' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] + +builddependencies = [ + ('binutils', '2.38'), +] + +configopts = '--with-doc=no' + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' From 81b1d8c395b5ee5e5a08a59519c1c7d80392b3d0 Mon Sep 17 00:00:00 2001 From: Abhishek Mukherjee Date: Tue, 23 Aug 2022 08:27:12 -0400 Subject: [PATCH 4556/9987] GCCcore12.1.0 expat-2.4.8 --- .../e/expat/expat-2.4.8-GCCcore-12.1.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.1.0.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.1.0.eb b/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..5f2063789b1 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.1.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' +name = 'expat' +version = '2.4.8' + +homepage = 'https://libexpat.github.io' + +description = """ + Expat is an XML parser library written in C. It is a stream-oriented parser + in which an application registers handlers for things the parser might find + in the XML document (like start tags) +""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_TAR_BZ2] +checksums = ['a247a7f6bbb21cf2ca81ea4cbb916bfb9717ca523631675f99b3d4a5678dcd16'] + +builddependencies = [('binutils', '2.38')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From c844e8e85c30dac68b8c012b9842f19da2186001 Mon Sep 17 00:00:00 2001 From: Abhishek Mukherjee Date: Tue, 23 Aug 2022 08:29:17 -0400 Subject: [PATCH 4557/9987] GCCcore12.1.0 ncurses-6.3 --- .../n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..511870df0ab --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.3' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] + +builddependencies = [('binutils', '2.38')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +configopts = [ + # default build + local_common_configopts, + # the UTF-8 enabled version (ncursesw) + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", + "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" +] + +local_libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' From d584ed30bf4c57e87967b08787c016766d2ef27c Mon Sep 17 00:00:00 2001 From: Abhishek Mukherjee Date: Tue, 23 Aug 2022 08:31:59 -0400 Subject: [PATCH 4558/9987] GCCcore12.1.0 libreadline-8.1.2 --- .../libreadline-8.1.2-GCCcore-12.1.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.1.0.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.1.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..2fbe4e7c79b --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.1.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.1.2' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['7589a2381a8419e68654a47623ce7dfcb756815c8fee726b98f90bf668af7bc6'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('ncurses', '6.3'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' From 7574394583394a8d9bf02df27baf548a0a782a31 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2022 14:32:59 +0200 Subject: [PATCH 4559/9987] adding easyconfigs: SPM-12.5_r7771-MATLAB-2021b.eb --- .../s/SPM/SPM-12.5_r7771-MATLAB-2021b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPM/SPM-12.5_r7771-MATLAB-2021b.eb diff --git a/easybuild/easyconfigs/s/SPM/SPM-12.5_r7771-MATLAB-2021b.eb b/easybuild/easyconfigs/s/SPM/SPM-12.5_r7771-MATLAB-2021b.eb new file mode 100644 index 00000000000..21fd484ece9 --- /dev/null +++ b/easybuild/easyconfigs/s/SPM/SPM-12.5_r7771-MATLAB-2021b.eb @@ -0,0 +1,53 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'Tarball' + +name = 'SPM' +version = '12.5_r7771' +_matlab_ver = '2021b' +versionsuffix = '-MATLAB-%s' % _matlab_ver + +homepage = 'https://www.fil.ion.ucl.ac.uk/spm' +description = """SPM (Statistical Parametric Mapping) refers to the construction + and assessment of spatially extended statistical processes used to test hypo- + theses about functional imaging data. These ideas have been instantiated in + software that is called SPM. + The SPM software package has been designed for the analysis of brain imaging + data sequences. The sequences can be a series of images from different cohorts, + or time-series from the same subject. The current release is designed for the + analysis of fMRI, PET, SPECT, EEG and MEG. +""" + +toolchain = SYSTEM + +_spm_maj_ver = version.split('.')[0] +_spm_majmin_ver, _spm_update_ver = version.split('_') + +sources = [ + { + 'source_urls': ['https://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado'], + 'filename': '%%(namelower)s%s.zip' % _spm_majmin_ver, + }, + { + 'source_urls': ['http://www.fil.ion.ucl.ac.uk/spm/download/spm12_updates'], + 'filename': '%%(namelower)s%s_updates_%s.zip' % (_spm_maj_ver, _spm_update_ver), + 'extract_cmd': 'unzip -oqq %%s -d spm%s' % _spm_maj_ver, + }, +] +checksums = [ + '0dc847eb065ccfcefbaefafdc12201dd20a22b9ee9b33a6b1973d07690a21914', # spm12.5.zip + '2b3cbd5f58fe180231d8bdcd0762c8874aee97240de391d876d9f2e33037a293', # spm12_updates_r7771.zip +] + +dependencies = [('MATLAB', _matlab_ver)] + +sanity_check_paths = { + 'files': ['spm.m'], + 'dirs': [], +} + +sanity_check_commands = ['matlab -batch "spm version"'] + +modextrapaths = {'MATLABPATH': ''} + +moduleclass = 'tools' From 39016328c6013a1fdd68ad4a3b5b625a1dfe057d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2022 14:44:47 +0200 Subject: [PATCH 4560/9987] trivial style cleanup in pugixml v1.12.1 easyconfig --- .../easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb index ef535d5dfb6..0c105e447f2 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.2.0.eb @@ -11,10 +11,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/zeux/pugixml/archive/'] sources = ['v%(version)s.tar.gz'] - -checksums = [ - '1e28ab24b6e04e013d96f45d25e9f2d04c921dc68c613fd010ecaaad3892c14d', # v1.12.1.tar.gz -] +checksums = ['1e28ab24b6e04e013d96f45d25e9f2d04c921dc68c613fd010ecaaad3892c14d'] builddependencies = [ ('binutils', '2.37'), From aa09d338fac17834e23a5204494f5eb2f6fb76f7 Mon Sep 17 00:00:00 2001 From: Jakub Kropacek Date: Tue, 23 Aug 2022 14:47:11 +0200 Subject: [PATCH 4561/9987] unify formatting --- easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb index d9454b6a04c..3ceb145d671 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb @@ -5,13 +5,13 @@ name = 'XCrySDen' version = '1.6.2' homepage = "http://www.xcrysden.org/" +docurls = "http://www.xcrysden.org/Documentation.html" description = """ XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. It also possesses some tools for analysis of properties in reciprocal space such as interactive selection of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. """ -docurls = "http://www.xcrysden.org/Documentation.html" toolchain = {'name': 'foss', 'version': '2022a'} From 9a4440c435bbef1c7d3e131986c4802dbf5df16b Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 13:57:20 +0100 Subject: [PATCH 4562/9987] Name of tarball corrected to de85222.tar.gz --- .../a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb index 1330ea3c373..d682c984cca 100644 --- a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb @@ -30,7 +30,7 @@ patches = [ '%(name)s-1.13.1_fix_search_for_szip.patch', ] checksums = [ - 'c58af40cbdb13843de2c2c157379d069880835c9b932ad05e774910ec23a468f', # v1.13.1.tar.gz + 'c58af40cbdb13843de2c2c157379d069880835c9b932ad05e774910ec23a468f', # de85222.tar.gz '81b9b0a77b23d6137f08900a3ecda4471b806c384cf4ad19c4370fc7ca8d9a82', # ADIOS-1.13.1_force_use_of_mpi.patch 'a66fab38e5daf40978f9e961d810f9cbf189de8db924a403ae42a01d405f6fdc', # ADIOS-1.13.1_fix_missing_thread_lib.patch '2e21a5041822c8b57554eb977a3135637c2714d377eee3b0194d377f1458cdab', # ADIOS-1.13.1_fix_search_for_szip.patch From aeb4e5ca9a089754d63e2a7102b2e4f08ed94eeb Mon Sep 17 00:00:00 2001 From: Abhishek Mukherjee Date: Tue, 23 Aug 2022 09:12:15 -0400 Subject: [PATCH 4563/9987] GCCcore12.1.0 DB-18.1.40 --- .../d/DB/DB-18.1.40-GCCcore-12.1.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..d33d1cd6305 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('OpenSSL', '1.1', '', True)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From 31ea876a6bf78f266290056829a840a68090f9c4 Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Tue, 23 Aug 2022 15:18:51 +0200 Subject: [PATCH 4564/9987] ADIOS: Add sanity check commands also to 1.13.1 --- .../a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb index 34ed5ff5be3..6df9ace119f 100644 --- a/easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/ADIOS/ADIOS-1.13.1-foss-2020a-Python-3.8.2.eb @@ -61,6 +61,11 @@ sanity_check_paths = { 'dirs': ['etc/skel/templates', 'lib/python'], } +sanity_check_commands = [ + 'adios_list_methods', + 'bpappend -h', +] + modextrapaths = { 'PYTHONPATH': 'lib/python', } From a8e46f1a47c9e7cfd92b82210aa83a2e3b3f3c79 Mon Sep 17 00:00:00 2001 From: benjamic Date: Tue, 23 Aug 2022 15:21:47 +0200 Subject: [PATCH 4565/9987] Adding test eri patch --- .../Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb | 2 ++ .../l/Libint/Libint-2.7.2_remove-test-eri.patch | 15 +++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.7.2_remove-test-eri.patch diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb index 0a56b0a8daa..a8fc8d88134 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb @@ -19,9 +19,11 @@ source_urls = ['https://github.com/evaleev/libint/archive'] sources = ['v%(version)s.tar.gz'] patches = [ 'Libint-2.7.2_remove-test-permute.patch', + 'Libint-2.7.2_remove-test-eri.patch', ] checksums = [ 'fd0466ce9eb6786b8c5bbe3d510e387ed44b198a163264dfd7e60b337e295fd9', # v2.7.2.tar.gz + '4dd7b2993b6fdebb57e5c14faa9bf46117ae42100c686ace82fe26b7cb0312ab', # Libint-2.7.2_remove-test-eri.patch 'b019e66a2a3dc7e83ee8a60aa1ae78955a8af4df90ab07b7e57d2ee004ce3677', # Libint-2.7.2_remove-test-permute.patch ] diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.7.2_remove-test-eri.patch b/easybuild/easyconfigs/l/Libint/Libint-2.7.2_remove-test-eri.patch new file mode 100644 index 00000000000..8b1ce717603 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.7.2_remove-test-eri.patch @@ -0,0 +1,15 @@ +Disable Fortran ERI tests as those have very strict error tolerances. This patch is updated from Libint-2.6.0_remove-test-eri.patch +See https://github.com/evaleev/libint/issues/188 +author: Ben Czaja (SURF) based on orginal patch from Alex Domingo (Vrije Universiteit Brussel) +diff -W 152 -Nru libint-2.7.2-orig/export/cmake/CMakeLists.txt.export libint-2.7.2/export/cmake/CMakeLists.txt.export +--- libint-2.7.2-orig/export/cmake/CMakeLists.txt.export 2022-06-20 07:51:55.000000000 +0200 ++++ libint-2.7.2/export/cmake/CMakeLists.txt.export 2022-08-16 17:38:22.347117248 +0200 +@@ -443,7 +443,7 @@ + PROPERTIES FIXTURES_REQUIRED LIBINT2_FORTRAN_EXAMPLE_EXEC) + + if (LIBINT_HAS_CXX_API) +- add_executable(fortran_test-libint2 EXCLUDE_FROM_ALL fortran/test.cc fortran/test-eri.cc $) ++ add_executable(fortran_test-libint2 EXCLUDE_FROM_ALL fortran/test.cc $) + target_link_libraries(fortran_test-libint2 libint2_cxx libint_f) + target_include_directories(fortran_test-libint2 PRIVATE $) + add_test(libint2/fortran_test/build "${CMAKE_COMMAND}" --build ${PROJECT_BINARY_DIR} --target fortran_test-libint2) From 98a025d9f0071aca68852cc647825365597ddde2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2022 15:44:53 +0200 Subject: [PATCH 4566/9987] use system toolchain for JavaFX + AptaSUITE, add extra alias for aptasuite CLI command --- .../easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb | 6 +++--- .../easyconfigs/j/JavaFX/JavaFX-11.0.2_linux-x64_bin-sdk.eb | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb b/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb index 84060f3c3eb..b9a71cda462 100644 --- a/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb +++ b/easybuild/easyconfigs/a/AptaSUITE/AptaSUITE-0.9.4-Java-11.eb @@ -13,7 +13,7 @@ homepage = 'https://drivenbyentropy.github.io/' description = """ A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://github.com/drivenbyentropy/aptasuite/releases/download/v%(version)s/'] sources = ['%(namelower)s-%(version)s.zip'] @@ -27,9 +27,9 @@ dependencies = [ postinstallcmds = ["cd %(installdir)s && ln -s aptasuite-%(version)s.jar aptasuite.jar"] modaliases = { + 'aptasuite': 'java -jar ${EBROOTAPTASUITE}/aptasuite.jar', 'aptasuite-gui': 'java -Dprism.order=sw --module-path ${EBROOTJAVAFX}/lib ' + '--add-modules javafx.controls,javafx.fxml -jar ${EBROOTAPTASUITE}/aptasuite.jar', - # split in two lines to make travis happy (line length below 120 characters) } sanity_check_paths = { @@ -38,7 +38,7 @@ sanity_check_paths = { } modloadmsg = """ -To execute on command line run: java -jar ${EBROOTAPTASUITE}/aptasuite.jar +To execute on command line run: aptasuite To launch the graphical interface run: aptasuite-gui """ diff --git a/easybuild/easyconfigs/j/JavaFX/JavaFX-11.0.2_linux-x64_bin-sdk.eb b/easybuild/easyconfigs/j/JavaFX/JavaFX-11.0.2_linux-x64_bin-sdk.eb index b5926bf9dfa..31dd004f828 100644 --- a/easybuild/easyconfigs/j/JavaFX/JavaFX-11.0.2_linux-x64_bin-sdk.eb +++ b/easybuild/easyconfigs/j/JavaFX/JavaFX-11.0.2_linux-x64_bin-sdk.eb @@ -13,7 +13,7 @@ homepage = 'https://openjfx.io/' description = """ OpenJFX is an open source, next generation client application platform for desktop, mobile and embedded systems built on Java """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM source_urls = ['https://download2.gluonhq.com/openjfx/%(version)s/'] sources = ['openjfx-%(version)s%(versionsuffix)s.zip'] From 1077292d28470795781056e1fbec866f70003953 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 15:18:31 +0100 Subject: [PATCH 4567/9987] Sanity check commands added --- .../e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb index 025a3fe29b1..6af0833119a 100644 --- a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb @@ -35,6 +35,11 @@ dependencies = [ buildopts = "LIBTOOL='libtool --tag=CC'" +sanity_check_commands = [ + 'enchant-2 -h', + 'enchant-lsmod-2 -v', +] + sanity_check_paths = { 'files': ['bin/enchant-2', 'bin/enchant-lsmod-2', 'lib/libenchant-2.a', 'lib/libenchant-2.%s' % SHLIB_EXT], From 4e1095f383a4efc36c1cb100ecffe2a62d410339 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 23 Aug 2022 16:19:42 +0200 Subject: [PATCH 4568/9987] Leave out Java 1.8 wrapper, switch to 8.345 version string --- easybuild/easyconfigs/j/Java/Java-1.8.eb | 12 ++++++++++-- .../j/Java/{Java-8u345.eb => Java-8.345.eb} | 8 ++++---- easybuild/easyconfigs/j/Java/Java-8.eb | 2 +- 3 files changed, 15 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/j/Java/{Java-8u345.eb => Java-8.345.eb} (80%) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.eb b/easybuild/easyconfigs/j/Java/Java-1.8.eb index 578f332a81b..ed823a63205 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.eb @@ -1,3 +1,7 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# updated to cope with multiple architectures by A. Edmondson + easyblock = 'ModuleRC' name = 'Java' @@ -5,10 +9,14 @@ version = '1.8' homepage = 'https://java.com/' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy -Java applications on desktops and servers.""" + Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version_minor)su345')] +dependencies = [ + ('Java', {'arch=x86_64': '%(version)s.0_311', + 'arch=POWER': '%(version)s_191-b26-OpenJDK', + 'arch=AArch64': '%(version)s_265-b01-OpenJDK-aarch64'}), +] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-8u345.eb b/easybuild/easyconfigs/j/Java/Java-8.345.eb similarity index 80% rename from easybuild/easyconfigs/j/Java/Java-8u345.eb rename to easybuild/easyconfigs/j/Java/Java-8.345.eb index 28a21e318d4..a13f77db4f2 100644 --- a/easybuild/easyconfigs/j/Java/Java-8u345.eb +++ b/easybuild/easyconfigs/j/Java/Java-8.345.eb @@ -1,5 +1,5 @@ name = 'Java' -version = '8u345' +version = '8.345' local_build = 'b01' homepage = 'http://openjdk.java.net' @@ -8,12 +8,12 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -local_tarball_tmpl = 'OpenJDK8U-jdk_%s_linux_hotspot_%%(version)s%s.tar.gz' +local_tarball_tmpl = 'OpenJDK8U-jdk_%s_linux_hotspot_%%(version_major)su%%(version_minor)s%s.tar.gz' # Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions -source_urls = ['https://github.com/adoptium/temurin8-binaries/releases/download/jdk%%(version)s-%s/' - % local_build] +source_urls = ['https://github.com/adoptium/temurin8-binaries/releases/download/' + 'jdk%%(version_major)su%%(version_minor)s-%s/' % local_build] sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] checksums = [ diff --git a/easybuild/easyconfigs/j/Java/Java-8.eb b/easybuild/easyconfigs/j/Java/Java-8.eb index 9ef99a1c2f3..8c9091f83dd 100644 --- a/easybuild/easyconfigs/j/Java/Java-8.eb +++ b/easybuild/easyconfigs/j/Java/Java-8.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)su345')] +dependencies = [('Java', '%(version)s.345')] moduleclass = 'lang' From 45ee59f684a386cfc80db31f0a6ed4d82e2bc3bf Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 15:21:30 +0100 Subject: [PATCH 4569/9987] Sanity check command added --- .../easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb index 857561f81b8..b37fdbc7121 100644 --- a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb @@ -25,6 +25,10 @@ builddependencies = [ preconfigopts = "autoreconf -vfi && " +sanity_check_commands = [ + 'hunspell -h', +] + sanity_check_paths = { 'files': ['bin/hunspell', 'lib/libhunspell-%(version_major_minor)s.a', 'lib/libhunspell-%%(version_major_minor)s.%s' % SHLIB_EXT, 'lib/pkgconfig/hunspell.pc'], From 479dea890ee4c0ccea53c3e788d3db5d59f7a667 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 15:37:38 +0100 Subject: [PATCH 4570/9987] Toolchain changed to GCCcore-11.2.0 as suggested --- ...che-4.6.1.eb => ccache-4.6.1-GCCcore-11.2.0.eb} | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/c/ccache/{ccache-4.6.1.eb => ccache-4.6.1-GCCcore-11.2.0.eb} (77%) diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb similarity index 77% rename from easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb rename to easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb index e9141772cf2..b3f2927a4f2 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-4.6.1.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb @@ -12,7 +12,7 @@ homepage = 'https://ccache.dev/' description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again""" -toolchain = SYSTEM +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] @@ -20,17 +20,15 @@ checksums = ['59b28a57c3a45e48d6049001999c9f94cd4d3e9b0196994bed9a6a7437ffa3bc'] osdependencies = [('glibc-static', 'libc6-dev', 'glibc-devel')] -local_gccver = '11.2.0' builddependencies = [ - ('GCC', local_gccver), - ('CMake', '3.22.1', '', ('GCCcore', local_gccver)), - ('Ninja', '1.10.2', '', ('GCCcore', local_gccver)), - ('zstd', '1.5.0', '', ('GCCcore', local_gccver)), - ('pkg-config', '0.29.2', '', ('GCCcore', local_gccver)) + ('CMake', '3.22.1'), + ('Ninja', '1.10.2'), + ('zstd', '1.5.0', ), + ('pkg-config', '0.29.2'), ] dependencies = [ - ('hiredis', '1.0.2', '', ('GCCcore', local_gccver)), + ('hiredis', '1.0.2'), ] # use BFD linker rather than default ld.gold (required on CentOS 8) From ab3d18e3f3e720dc00580976279b4838c4e2d61c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 23 Aug 2022 16:44:01 +0200 Subject: [PATCH 4571/9987] Patch pkgconfig file for Blitz++ v1.0.2 --- .../b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb | 6 +++++- .../b/Blitz++/Blitz++-1.0.2-GCCcore-11.3.0.eb | 6 +++++- .../b/Blitz++/blitz-1.0.2_pkgconfig.patch | 14 ++++++++++++++ 3 files changed, 24 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/b/Blitz++/blitz-1.0.2_pkgconfig.patch diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb index b43168655a4..8dfa22d145c 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-10.2.0.eb @@ -16,7 +16,11 @@ toolchainopts = {'pic': True} source_urls = [('https://github.com/blitzpp/blitz/archive/')] sources = ['%(version)s.tar.gz'] -checksums = ['500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'] +patches = ['blitz-%(version)s_pkgconfig.patch'] +checksums = [ + '500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2', # 1.0.2.tar.gz + 'd15fb397e75eb009809ecacdd7f2f154ff05e6586895f3b0511d0b53a6e3b9fe', # blitz-1.0.2_pkgconfig.patch +] builddependencies = [('CMake', '3.18.4'), ('binutils', '2.35')] diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-11.3.0.eb index e8e388a9902..cfd1839eb9d 100644 --- a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-11.3.0.eb @@ -16,7 +16,11 @@ toolchainopts = {'pic': True} source_urls = [('https://github.com/blitzpp/blitz/archive/')] sources = ['%(version)s.tar.gz'] -checksums = ['500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'] +patches = ['blitz-%(version)s_pkgconfig.patch'] +checksums = [ + '500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2', # 1.0.2.tar.gz + 'd15fb397e75eb009809ecacdd7f2f154ff05e6586895f3b0511d0b53a6e3b9fe', # blitz-1.0.2_pkgconfig.patch +] builddependencies = [('CMake', '3.23.1'), ('binutils', '2.38')] diff --git a/easybuild/easyconfigs/b/Blitz++/blitz-1.0.2_pkgconfig.patch b/easybuild/easyconfigs/b/Blitz++/blitz-1.0.2_pkgconfig.patch new file mode 100644 index 00000000000..e379e5eddd4 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/blitz-1.0.2_pkgconfig.patch @@ -0,0 +1,14 @@ +# Correct pkgconfig file +# S.D.Pinches, 2022.08.23 +diff -Nru blitz-1.0.2-orig/cmake/CreatePkgConfig.cmake blitz-1.0.2/cmake/CreatePkgConfig.cmake +--- blitz-1.0.2-orig/cmake/CreatePkgConfig.cmake 2019-10-02 00:50:17.000000000 +0200 ++++ blitz-1.0.2/cmake/CreatePkgConfig.cmake 2022-08-23 16:24:41.509703369 +0200 +@@ -9,7 +9,7 @@ + exec_prefix=\${prefix} + libdir=\${prefix}/@CMAKE_INSTALL_LIBDIR@ + includedir=\${prefix}/@CMAKE_INSTALL_INCLUDEDIR@ +-confdir=\${prefix}/@CMAKE_INSTALL_LIBDIR@/@pkgconfig_package_name@ ++confdir=\${prefix}/lib/cmake + + Name: @pkgconfig_package_name@ + Description: @pkgconfig_package_description@ From 7c2d56af4f44492c0b8541b092ebea919fdf5ec7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 23 Aug 2022 17:42:32 +0200 Subject: [PATCH 4572/9987] adding easyconfigs: GLFW-3.3.8-GCCcore-11.3.0.eb --- .../g/GLFW/GLFW-3.3.8-GCCcore-11.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLFW/GLFW-3.3.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GLFW/GLFW-3.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GLFW/GLFW-3.3.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c8fe2ff276d --- /dev/null +++ b/easybuild/easyconfigs/g/GLFW/GLFW-3.3.8-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'GLFW' +version = '3.3.8' + +homepage = 'https://www.glfw.org' +description = """GLFW is an Open Source, multi-platform library for OpenGL, +OpenGL ES and Vulkan development on the desktop""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f30f42e05f11e5fc62483e513b0488d5bceeab7d9c5da0ffe2252ad81816c713'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('X11', '20220504'), +] + +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +sanity_check_paths = { + 'files': ['include/GLFW/glfw3.h', 'include/GLFW/glfw3native.h', + 'lib/libglfw3.a', 'lib/libglfw.%s' % SHLIB_EXT, 'lib/pkgconfig/glfw3.pc'], + 'dirs': ['include/GLFW', 'lib/cmake/glfw3', 'lib/pkgconfig'], +} + +moduleclass = 'vis' From d5d857285252a61f78f459456a7f43fdc51cc4aa Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Tue, 23 Aug 2022 18:37:49 +0200 Subject: [PATCH 4573/9987] Remove Trailing Whitespace --- .../a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb index d682c984cca..60bc634a417 100644 --- a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb @@ -30,7 +30,7 @@ patches = [ '%(name)s-1.13.1_fix_search_for_szip.patch', ] checksums = [ - 'c58af40cbdb13843de2c2c157379d069880835c9b932ad05e774910ec23a468f', # de85222.tar.gz + 'c58af40cbdb13843de2c2c157379d069880835c9b932ad05e774910ec23a468f', # de85222.tar.gz '81b9b0a77b23d6137f08900a3ecda4471b806c384cf4ad19c4370fc7ca8d9a82', # ADIOS-1.13.1_force_use_of_mpi.patch 'a66fab38e5daf40978f9e961d810f9cbf189de8db924a403ae42a01d405f6fdc', # ADIOS-1.13.1_fix_missing_thread_lib.patch '2e21a5041822c8b57554eb977a3135637c2714d377eee3b0194d377f1458cdab', # ADIOS-1.13.1_fix_search_for_szip.patch From e09e6f8f7755f041487a9a18a1daafac96f1311e Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 17:57:31 +0100 Subject: [PATCH 4574/9987] Whitespace removed --- .../a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb index d682c984cca..60bc634a417 100644 --- a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb @@ -30,7 +30,7 @@ patches = [ '%(name)s-1.13.1_fix_search_for_szip.patch', ] checksums = [ - 'c58af40cbdb13843de2c2c157379d069880835c9b932ad05e774910ec23a468f', # de85222.tar.gz + 'c58af40cbdb13843de2c2c157379d069880835c9b932ad05e774910ec23a468f', # de85222.tar.gz '81b9b0a77b23d6137f08900a3ecda4471b806c384cf4ad19c4370fc7ca8d9a82', # ADIOS-1.13.1_force_use_of_mpi.patch 'a66fab38e5daf40978f9e961d810f9cbf189de8db924a403ae42a01d405f6fdc', # ADIOS-1.13.1_fix_missing_thread_lib.patch '2e21a5041822c8b57554eb977a3135637c2714d377eee3b0194d377f1458cdab', # ADIOS-1.13.1_fix_search_for_szip.patch From bb88dd5d72b3b79eb55818e58a0096960affcfae Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 18:04:18 +0100 Subject: [PATCH 4575/9987] adding easyconfigs: WebKitGTK+-2.37.1-GCC-11.2.0.eb --- .../WebKitGTK+-2.37.1-GCC-11.2.0.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..1ede0f20a54 --- /dev/null +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -0,0 +1,86 @@ +# Updated from WebKitGTK+-2.27.4-GCC-8.3.0.eb with more modules added +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'WebKitGTK+' +version = '2.37.1' + +homepage = 'https://webkitgtk.org/' +description = """WebKitGTK+ is a full-featured port of the WebKit +rendering engine, suitable for projects requiring any kind of web +integration, from hybrid HTML/CSS applications to full-fledged web +browsers. It offers WebKit's full functionality and is useful in a wide +range of systems from desktop computers to embedded systems like phones, +tablets, and televisions.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://webkitgtk.org/releases'] +sources = ['webkitgtk-%(version)s.tar.xz'] +checksums = [ + 'c53326b1751f8c6da3db2f4bfa91c1801755893e287d0e1f6c07344589d4a6a7', # webkitgtk-2.37.1.tar.xz +] + +osdependencies = [ + # Would be better to use the system package due to security reasons + # But we need at least libgcrypt 1.7.0 and Ubuntu 16.04 and RH 7.5 + # are both using a too old version. + # Update: Libcrypt 1.9.3 from EasyBuild added (J.S) + # ('libgcrypt-dev', 'libgcrypt20-dev', 'libgcrypt-devel'), + # libsecret is not actually needed since USE_LIBSECRET option is disabled + # ('libsecret-1-dev', 'libsecret-devel'), +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Python', '3.9.6'), + ('Perl', '5.34.0', '-minimal'), + ('GObject-Introspection', '1.68.0'), + ('pkg-config', '0.29.2'), + ('ccache', '4.6.1', '', True), +] +dependencies = [ + ('GLib', '2.69.1'), + ('gperf', '3.1'), + ('cairo', '1.16.0'), + ('GTK3', '3.24.31'), + ('LibSoup', '3.0.7'), + ('ATK', '2.36.0'), + ('libgcrypt', '1.9.3'), + ('libwebp', '1.2.0'), + ('libxslt', '1.1.34'), + ('libtasn1', '4.18.0'), + ('GStreamer', '1.18.5'), + ('OpenJPEG', '2.4.0'), + ('Ruby', '3.0.1'), + ('GSL', '2.7'), + ('glew', '2.2.0', '-egl'), + ('libwpe', '1.13.3'), + ('pugixml', '1.12.1'), + ('Wayland', '1.20.0'), + ('Waylandpp', '1.0.0'), + ('wpebackend-fdo', '1.13.1'), + ('enchant-2', '2.3.3'), + ('LittleCMS', '2.12'), + ('GST-plugins-base', '1.18.5'), +] + +# The build takes around 2.5 hours on 24 cores on AMD Rome! +# So be patient! + +# Instead of using a patch file, we are disabling problematic builds in the command line. +# At least this way, if something is not needed it can be turned off, without looking into +# a patch file. +configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON -DPORT=GTK -DCMAKE_FIND_USE_PACKAGE_REGISTRY=FALSE " +configopts += "-DENABLE_GAMEPAD=OFF -DUSE_LIBSECRET=OFF -DUSE_LIBHYPHEN=OFF " +configopts += "-DUSE_WOFF2=OFF -DENABLE_JOURNALD_LOG=OFF -DENABLE_BUBBLEWRAP_SANDBOX=OFF " +configopts += "-DENABLE_INTROSPECTION=OFF -DUSE_LIBNOTIFY=OFF " + +sanity_check_paths = { + 'files': ['bin/WebKitWebDriver', 'lib/libwebkit2gtk-4.1.%s' % SHLIB_EXT, + 'lib/libjavascriptcoregtk-4.1.%s' % SHLIB_EXT], + 'dirs': ['include/webkitgtk-4.1/webkit2', 'libexec/webkit2gtk-4.1'], +} + +moduleclass = 'lib' From 9661163ef63f4268dce252b7e5825ce4f92b9926 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2022 19:28:00 +0200 Subject: [PATCH 4576/9987] add missing BCFtools dependency for recent medaka versions (+ run medaka_version_report to catch missing required dependencies) --- easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb | 8 ++++++-- easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb | 8 ++++++-- easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb | 8 ++++++-- 3 files changed, 18 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb index 6619e4a1e9b..a6ccdd55057 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.4.3-foss-2020b.eb @@ -36,6 +36,7 @@ dependencies = [ ('pyspoa', '0.0.8'), ('pyfaidx', '0.5.9.5'), ('python-isal', '0.11.1'), + ('BCFtools', '1.11'), ] use_pip = True @@ -83,10 +84,13 @@ exts_list = [ sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["medaka --help"] +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb index d3f817945e5..75466141935 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.5.0-foss-2021a.eb @@ -35,6 +35,7 @@ dependencies = [ ('ont-fast5-api', '4.0.0'), ('WhatsHap', '1.1'), ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.12'), ] use_pip = True @@ -51,10 +52,13 @@ exts_list = [ sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["medaka --help"] +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb index 4b426e05a0a..f13a44b0e6e 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.6.0-foss-2021b.eb @@ -36,6 +36,7 @@ dependencies = [ ('ont-fast5-api', '4.0.2'), ('WhatsHap', '1.4'), ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.14'), ] use_pip = True @@ -52,10 +53,13 @@ exts_list = [ sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["medaka --help"] +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] moduleclass = 'bio' From 15dce2c38e11541824cf1b64877cc333a59f43b6 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 23 Aug 2022 11:46:06 -0700 Subject: [PATCH 4577/9987] {bio}[foss-2021b]scikit-bio v0.5.7 --- .../p/Pillow/Pillow-9.1.0-GCCcore-11.2.0.eb | 32 ------------------- .../scikit-bio/scikit-bio-0.5.7-foss-2021b.eb | 2 +- 2 files changed, 1 insertion(+), 33 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-11.2.0.eb deleted file mode 100644 index 2d0c6d0f756..00000000000 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-11.2.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pillow' -version = '9.1.0' - -homepage = 'https://pillow.readthedocs.org/' -description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. - PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['f401ed2bbb155e1ade150ccc63db1a4f6c1909d3d378f7d1235a44e90d75fb97'] - -builddependencies = [('binutils', '2.37')] - -dependencies = [ - ('Python', '3.9.6'), - ('libjpeg-turbo', '2.0.6'), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), - ('LibTIFF', '4.3.0'), - ('freetype', '2.11.0') -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -options = {'modulename': 'PIL'} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021b.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021b.eb index dcfe542f498..bd2a4b2590b 100644 --- a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021b.eb +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021b.eb @@ -16,7 +16,7 @@ dependencies = [ ('scikit-learn', '1.0.1'), ('IPython', '7.26.0'), ('h5py', '3.6.0'), - ('Pillow', '9.1.0'), + ('Pillow', '8.3.2'), ] use_pip = True From 7ca6a353a141438667434335ed1d3f5c7c749a31 Mon Sep 17 00:00:00 2001 From: benjamic Date: Tue, 23 Aug 2022 21:13:12 +0200 Subject: [PATCH 4578/9987] Updated order of checksums for patches --- .../easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb index a8fc8d88134..4ab44202876 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb @@ -23,8 +23,8 @@ patches = [ ] checksums = [ 'fd0466ce9eb6786b8c5bbe3d510e387ed44b198a163264dfd7e60b337e295fd9', # v2.7.2.tar.gz - '4dd7b2993b6fdebb57e5c14faa9bf46117ae42100c686ace82fe26b7cb0312ab', # Libint-2.7.2_remove-test-eri.patch 'b019e66a2a3dc7e83ee8a60aa1ae78955a8af4df90ab07b7e57d2ee004ce3677', # Libint-2.7.2_remove-test-permute.patch + '4dd7b2993b6fdebb57e5c14faa9bf46117ae42100c686ace82fe26b7cb0312ab', # Libint-2.7.2_remove-test-eri.patch ] builddependencies = [ From 837039c35be9116f840ea0c0c076606445dc86f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 Aug 2022 21:37:00 +0200 Subject: [PATCH 4579/9987] adding easyconfigs: NGSpeciesID-0.1.2.1-foss-2021b.eb --- .../NGSpeciesID-0.1.2.1-foss-2021b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.2.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.2.1-foss-2021b.eb b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.2.1-foss-2021b.eb new file mode 100644 index 00000000000..85eaf6617e2 --- /dev/null +++ b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.2.1-foss-2021b.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'NGSpeciesID' +version = '0.1.2.1' + +homepage = 'https://github.com/ksahlin/NGSpeciesID' +description = "NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads." + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e7c94b147ceff184ca964a7adbcc0540dac7303136ebc53033245f8e33bd7faa'] + +dependencies = [ + ('Python', '3.9.6'), + ('python-parasail', '1.2.4'), + ('edlib', '1.3.9'), + ('medaka', '1.6.0'), + ('spoa', '4.0.7'), + ('Racon', '1.5.0'), + ('minimap2', '2.22'), +] + +download_dep_fail = True +use_pip = True + +# strip away too strict version requirement for parasail and +preinstallopts = "sed -i 's/parasail==[0-9.]*/parasail/g' setup.py && " + +# no proper namespace for NGSpeciesID +options = {'modulename': 'modules.consensus'} + +sanity_check_paths = { + 'files': ['bin/NGSpeciesID'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NGSpeciesID --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From ece726e32922befb2d8c0df54407d3ce90486dd8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 24 Aug 2022 08:25:44 +0200 Subject: [PATCH 4580/9987] adding easyconfigs: SLiM-4.0-GCC-11.2.0.eb and patches: SLiM-4.0_use_external_zlib_gsl.patch --- .../easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb | 48 ++++++ .../SLiM/SLiM-4.0_use_external_zlib_gsl.patch | 161 ++++++++++++++++++ 2 files changed, 209 insertions(+) create mode 100644 easybuild/easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/SLiM/SLiM-4.0_use_external_zlib_gsl.patch diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..a83b635112e --- /dev/null +++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'SLiM' +version = '4.0' + +homepage = 'https://messerlab.org/slim' +description = """SLiM is an evolutionary simulation framework that combines a powerful engine for population + genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/MesserLab/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_external_zlib_gsl.patch', +] +checksums = [ + 'd53ce9fc4ac00fa1dc3fc046ac21adb461ead46c1a0c54a72537a74873abf894', # v4.0.tar.gz + '7290f24ec9e04edc696aa85e3b4186cfcffa76b3c9b08bdf379ea00eac578755', # SLiM-4.0_use_external_zlib_gsl.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.7'), + ('Mesa', '21.1.7'), + ('libglvnd', '1.3.3'), + ('Qt5', '5.15.2'), +] + +configopts = '-DBUILD_SLIMGUI=ON ' + +sanity_check_paths = { + 'files': ['bin/eidos', 'bin/slim'], + 'dirs': [], +} + +sanity_check_commands = [ + "eidos -usage", + "eidos -testEidos", + "slim -usage", + "slim -testSLiM", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0_use_external_zlib_gsl.patch b/easybuild/easyconfigs/s/SLiM/SLiM-4.0_use_external_zlib_gsl.patch new file mode 100644 index 00000000000..894f69dd4f3 --- /dev/null +++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0_use_external_zlib_gsl.patch @@ -0,0 +1,161 @@ +commit 2ba4892b9327e5d21fdd712e178447d2ecd3665a +Author: Ake Sandgren +Date: Wed Aug 24 08:15:39 2022 +0200 + + Use external Zlib and GSL instead of internal ones. + And use correctly names zlib functions. + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 487c7bcd..0aae03ea 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -157,18 +157,20 @@ endif() + #endif() + + # GSL +-set(TARGET_NAME gsl) +-file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c) +-set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg) +-add_library(${TARGET_NAME} STATIC ${GSL_SOURCES}) +-target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES}) ++# Use external GSL instead ++#set(TARGET_NAME gsl) ++#file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c) ++#set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg) ++#add_library(${TARGET_NAME} STATIC ${GSL_SOURCES}) ++#target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES}) + + # ZLIB +-set(TARGET_NAME eidos_zlib) +-file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c) +-set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib) +-add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES}) +-target_include_directories(${TARGET_NAME} PUBLIC) ++# Use external Zlib instead ++#set(TARGET_NAME eidos_zlib) ++#file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c) ++#set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib) ++#add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES}) ++#target_include_directories(${TARGET_NAME} PUBLIC) + + # KASTORE + set(TARGET_NAME kastore) +@@ -198,7 +200,7 @@ list(APPEND SLIM_SOURCES "${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp" ${PROJECT_SOU + + add_executable(${TARGET_NAME} ${SLIM_SOURCES}) + target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/eidos") +-target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables) ++target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables) + if(WIN32) + set_source_files_properties(${SLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") + set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") +@@ -211,7 +213,7 @@ set(TARGET_NAME eidos) + file(GLOB_RECURSE EIDOS_SOURCES ${PROJECT_SOURCE_DIR}/eidos/*.cpp ${PROJECT_SOURCE_DIR}/eidostool/*.cpp) + add_executable(${TARGET_NAME} ${EIDOS_SOURCES}) + target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/eidos") +-target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables) ++target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables) + if(WIN32) + set_source_files_properties(${EIDOS_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") + set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") +@@ -244,15 +246,15 @@ set_target_properties( ${TARGET_NAME} PROPERTIES LINKER_LANGUAGE CXX) + target_compile_definitions( ${TARGET_NAME} PRIVATE EIDOSGUI=1 SLIMGUI=1) + target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/QtSLiM" "${PROJECT_SOURCE_DIR}/eidos" "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/treerec" "${PROJECT_SOURCE_DIR}/treerec/tskit/kastore") + if(APPLE) +- target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib /usr/lib/libobjc.A.dylib ) ++ target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z /usr/lib/libobjc.A.dylib ) + else() + if(WIN32) + set_source_files_properties(${QTSLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") + set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos SLiMgui PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") + target_include_directories(${TARGET_NAME} BEFORE PUBLIC ${GNU_DIR}) +- target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib gnu ) ++ target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z gnu ) + else() +- target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib ) ++ target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z ) + endif() + endif() + install(TARGETS ${TARGET_NAME} DESTINATION bin) +diff --git a/eidos/eidos_functions.cpp b/eidos/eidos_functions.cpp +index 4f52c763..ac9de199 100644 +--- a/eidos/eidos_functions.cpp ++++ b/eidos/eidos_functions.cpp +@@ -55,11 +55,11 @@ + + #include "string.h" + +-#include "gsl_linalg.h" +-#include "gsl_errno.h" +-#include "gsl_cdf.h" ++#include ++#include ++#include + +-#include "../eidos_zlib/zlib.h" ++#include + + #include "eidos_globals.h" + #if EIDOS_ROBIN_HOOD_HASHING +@@ -11475,7 +11475,7 @@ EidosValue_SP Eidos_ExecuteFunction_writeTempFile(const std::vector + + // for Eidos_calc_sha_256() + #include + + // for _Eidos_FlushZipBuffer() +-#include "../eidos_zlib/zlib.h" ++#include + + // for Eidos_ColorPaletteLookup() + #include "eidos_tinycolormap.h" +@@ -1570,7 +1570,7 @@ bool _Eidos_FlushZipBuffer(const std::string &file_path, const std::string &outs + { + //std::cout << "_Eidos_FlushZipBuffer() called for " << file_path << std::endl; + +- gzFile gzf = z_gzopen(file_path.c_str(), "ab"); ++ gzFile gzf = gzopen(file_path.c_str(), "ab"); + + if (!gzf) + return false; +@@ -1678,7 +1678,7 @@ void Eidos_WriteToFile(const std::string &p_file_path, std::vector ++#include + + #include + #include From f1205fbb828a7b2aa7dffb5d5a60c5a8014ed21c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Aug 2022 10:29:15 +0200 Subject: [PATCH 4581/9987] add exception for indirect Pysam 0.18.0 dependency (via medaka 1.6.0) in NGSpeciesID 0.1.2.1 --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4006a53d37b..ff9c5828c69 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -520,11 +520,11 @@ def check_dep_vars(self, gen, dep, dep_vars): # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 - # WhatsHap 1.4 requires Pysam >= 0.18.0 + # WhatsHap 1.4 + medaka 1.6.0 require Pysam >= 0.18.0 (NGSpeciesID depends on medaka) 'Pysam': [ ('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', 'NGSpeciesID-0.1.1.1-']), - ('0.18.0;', ['WhatsHap-1.4-', 'medaka-1.6.0-']), + ('0.18.0;', ['medaka-1.6.0-', 'NGSpeciesID-0.1.2.1-', 'WhatsHap-1.4-']), ], # OPERA requires SAMtools 0.x 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', From 085f4e943e990a289e1e81fcf0dd7226af4d2adc Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Wed, 24 Aug 2022 11:07:10 +0200 Subject: [PATCH 4582/9987] Update GhostScript --- .../g/GTK2/GTK2-2.24.33-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ .../Ghostscript-9.56.1-GCCcore-11.3.0.eb | 1 + 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7a0e7d915fd --- /dev/null +++ b/easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GTK2' +version = '2.24.33' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/gtk+/%(version_major_minor)s'] +sources = ['gtk+-%(version)s.tar.xz'] +checksums = ['ac2ac757f5942d318a311a54b0c80b5ef295f299c2a73c632f6bfb1ff49cc6da'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('GObject-Introspection', '1.72.0'), +] +dependencies = [ + ('ATK', '2.38.0'), + ('Gdk-Pixbuf', '2.42.8'), + ('Pango', '1.50.7'), +] + +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " + +sanity_check_paths = { + 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-x11-2.0.%s' % SHLIB_EXT], + 'dirs': ['include/gtk-2.0'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.56.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.56.1-GCCcore-11.3.0.eb index 51219d52026..e04d1119352 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.56.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.56.1-GCCcore-11.3.0.eb @@ -30,6 +30,7 @@ dependencies = [ ('GLib', '2.72.1'), ('cairo', '1.17.4'), ('LibTIFF', '4.3.0'), + ('GTK2', '2.24.33'), ] # Do not use local copies of zlib, jpeg, freetype, and png From 1198632476d4ef6f79b184cacdd8e2e69268184e Mon Sep 17 00:00:00 2001 From: benjamic Date: Wed, 24 Aug 2022 11:33:48 +0200 Subject: [PATCH 4583/9987] adding easyconfigs: gperftools-2.10-GCCcore-11.3.0.eb --- .../gperftools-2.10-GCCcore-11.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.10-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.10-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..73c262cf7ed --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.10-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.10' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'gperftools' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b0dcfe3aca1a8355955f4b415ede43530e3bb91953b6ffdd75c45891070fe0f1'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +dependencies = [ + ('libunwind', '1.6.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 219acd09e12ee0fbe3a29f1b74f1cc7d66dfa4dd Mon Sep 17 00:00:00 2001 From: benjamic Date: Wed, 24 Aug 2022 12:05:33 +0200 Subject: [PATCH 4584/9987] adding easyconfigs: PLINK-2.00a3.6-GCC-11.3.0.eb --- .../p/PLINK/PLINK-2.00a3.6-GCC-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.6-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.6-GCC-11.3.0.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.6-GCC-11.3.0.eb new file mode 100644 index 00000000000..d547fba7603 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.6-GCC-11.3.0.eb @@ -0,0 +1,39 @@ +# Author: Ben Czaja (SURF) based on orginal from Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'PLINK' +version = '2.00a3.6' + +homepage = 'https://www.cog-genomics.org/plink/2.0/' +description = 'Whole-genome association analysis toolset' + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/chrchang/plink-ng/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7e650aef534f257c412509bf30afe0dd478fd32069fe8206e258abf35a3cfc6f'] + +dependencies = [ + ('FlexiBLAS', '3.2.0'), + ('libdeflate', '1.10'), + ('zstd', '1.5.2'), +] + +start_dir = '2.0' + +# ignore suggested Makefile in build_dynamic, the dev Makefile is better +buildopts = 'BLASFLAGS="-lflexiblas" BLASFLAGS64="-lflexiblas"' +buildopts += ' LDFLAGS="$LIBS -ldeflate -lz -lzstd" ZLIB="" CSRC="include/SFMT.c"' +buildopts += ' BASEFLAGS="$OPTFLAGS -DZSTD_MULTITHREAD"' + +files_to_copy = ['bin', (['include/*.h'], 'include'), 'ReadMe.md'] + +sanity_check_paths = { + 'files': ['bin/plink2', 'bin/pgen_compress'], + 'dirs': ['include'], +} + +sanity_check_commands = ["plink2 --help"] + +moduleclass = 'bio' From 94c841c061668655a4f4ad9db8b081db55403715 Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 24 Aug 2022 12:24:40 +0200 Subject: [PATCH 4585/9987] adding easyconfigs: tbb-2021.5.0-GCCcore-11.3.0.eb --- .../t/tbb/tbb-2021.5.0-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbb/tbb-2021.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7166912c1c6 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'tbb' +version = '2021.5.0' + +homepage = 'https://github.com/oneapi-src/oneTBB' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e5b57537c741400cf6134b428fc1689a649d7d38d9bb9c1b6d64f092ea28178a'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [('hwloc', '2.7.1')] + +sanity_check_paths = { + 'files': ['lib/libtbb.%s' % SHLIB_EXT, 'lib/libtbbmalloc.%s' % SHLIB_EXT], + 'dirs': ['lib', 'include', 'share'], +} + +moduleclass = 'lib' From 14c72f08b503f2c8829ea5504ae8cc4e7671c4d2 Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 24 Aug 2022 13:12:09 +0200 Subject: [PATCH 4586/9987] Update easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-11.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit good point Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-11.3.0.eb index 7a0e7d915fd..1330c197693 100644 --- a/easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GTK2/GTK2-2.24.33-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'GTK2' version = '2.24.33' -homepage = 'https://developer.gnome.org/gtk+/stable/' +homepage = 'https://www.gtk.org' description = """ The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. """ From f8ce562d6aad114d03736975afdb758cc41e48ef Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 24 Aug 2022 12:28:51 +0100 Subject: [PATCH 4587/9987] adding easyconfigs: muMerge-1.1.0-foss-2022a.eb --- .../m/muMerge/muMerge-1.1.0-foss-2022a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/m/muMerge/muMerge-1.1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/muMerge/muMerge-1.1.0-foss-2022a.eb b/easybuild/easyconfigs/m/muMerge/muMerge-1.1.0-foss-2022a.eb new file mode 100644 index 00000000000..c8507f97777 --- /dev/null +++ b/easybuild/easyconfigs/m/muMerge/muMerge-1.1.0-foss-2022a.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'muMerge' +version = '1.1.0' + +homepage = 'https://github.com/Dowell-Lab/mumerge' +description = """muMerge is a tool for combining bed regions from multiple bed files that overlap.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('SciPy-bundle', '2022.05'), + ('BEDTools', '2.30.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/Dowell-Lab/mumerge/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['f8afd360800567ddb4e7b602ed63ef30d22eb41d7bfbd1dc323295cdc8a98bf3'], + }), +] + +sanity_check_paths = { + 'files': ['bin/mumerge'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "mumerge --help", + "mumerge --version", +] + +moduleclass = 'bio' From d92c616694486b1c411688a56a5281f9e131010d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 24 Aug 2022 15:57:40 +0200 Subject: [PATCH 4588/9987] reviewed & updated EC --- .../b/BigDFT/BigDFT-1.9.1-foss-2021b.eb | 95 +++++++++++++++++++ 1 file changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb new file mode 100644 index 00000000000..8fe0e115fac --- /dev/null +++ b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb @@ -0,0 +1,95 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = "Binary" + +name = "BigDFT" +version = "1.9.1" + +homepage = "https://gitlab.com/l_sim/bigdft-suite" +description = """ +BigDFT: electronic structure calculation based on Daubechies wavelets. +bigdft-suite is a set of different packages to run bigdft. +""" + +toolchain = {"name": "foss", "version": "2021b"} +toolchainopts = { + "usempi": True, + "extra_fflags": "-fallow-argument-mismatch", + "extra_fcflags": "-fallow-argument-mismatch", + "extra_f90flags": "-fallow-argument-mismatch", +} + +source_urls = ["https://gitlab.com/l_sim/bigdft-suite/-/archive/%(version)s/"] +sources = ["bigdft-suite-%(version)s.tar.gz"] +patches = ["bigdft_suite_index_bug.patch"] + +builddependencies = [ + ("CMake", "3.21.1"), +] + +dependencies = [ + ("Autoconf", "2.71"), + ("Python", "3.9.6"), + ("OpenCV", "4.5.5", "-contrib"), + ("XZ", "5.2.5"), +] + +extract_sources = True + +local_configopts = " ".join( + [ + 'CC=\\"$MPICC\\" FC=\\"$MPIFC\\" --enable-mpi', + 'FCFLAGS=\\"$CPPFLAGS $FCFLAGS -std=legacy\\"', + 'FFLAGS=\\"$CPPFLAGS $FFLAGS -std=legacy\\"', + 'F90FLAGS=\\"$CPPFLAGS $F90FLAGS -std=legacy\\"', + '--with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS\\"', + '--with-yaml-path=\\"$EBROOTLIBYAML\\"', + ] +) + +install_cmd = " && ".join( + [ + "mkdir bigdft_builddir", + "cd bigdft_builddir", + "python3 ../Installer.py build bigdft -y -v -c %s" % local_configopts, + "cp -r install/* %(installdir)s", + ] +) + +modextrapaths = {"PYTHONPATH": ["lib/python%(pyshortver)s/site-packages"]} + +sanity_check_paths = { + "files": [ + "include/futile.mod", + "include/futile.h", + "bin/bigdft", + "bin/bigdftvars.sh", + "lib/python3.9/site-packages/BigDFT/Systems.py", + "lib64/libbigdft-1.a", + ], + "dirs": [], +} + +local_test_script = """ +from BigDFT.Systems import System +from BigDFT.Fragments import Fragment +from BigDFT.IO import XYZReader +N2 = System() +with XYZReader("N2") as ifile: + N2["N:0"] = Fragment([next(ifile)]) + N2["N:1"] = Fragment([next(ifile)]) +print(N2.get_posinp()) +""" + +local_sanity_cmd = " && ".join( + [ + "tmpdir=$(mktemp -d)", + "echo '" + local_test_script + "' > " + "$tmpdir/bigdft_test.py", + "python $tmpdir/bigdft_test.py", + "rm -r $tmpdir", + ] +) + +sanity_check_commands = [(local_sanity_cmd)] + +moduleclass = "phys" From 17d76d02f574ec05ef36ae471a376e35a30a95e9 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 24 Aug 2022 14:58:34 +0100 Subject: [PATCH 4589/9987] Delete bigdft-suite-1.9.1-foss-2021b.eb deleting old-name file (switching to BigDFT) --- .../bigdft-suite-1.9.1-foss-2021b.eb | 102 ------------------ 1 file changed, 102 deletions(-) delete mode 100644 easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb deleted file mode 100644 index 74db190099e..00000000000 --- a/easybuild/easyconfigs/b/bigdft-suite/bigdft-suite-1.9.1-foss-2021b.eb +++ /dev/null @@ -1,102 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = "CmdCp" - -name = "bigdft-suite" -version = "1.9.1" - -homepage = "https://gitlab.com/l_sim/bigdft-suite" -description = """ -BigDFT: electronic structure calculation based on Daubechies wavelets. -bigdft-suite is a set of different packages to run bigdft. -""" - -toolchain = {"name": "foss", "version": "2021b"} -toolchainopts = { - "usempi": True, - "extra_fflags": "-fallow-argument-mismatch", - "extra_fcflags": "-fallow-argument-mismatch", - "extra_f90flags": "-fallow-argument-mismatch", -} - -source_urls = ["https://gitlab.com/l_sim/bigdft-suite/-/archive/%(version)s/"] -sources = ["%(name)s-%(version)s.tar.gz"] -patches = ["bigdft_suite_index_bug.patch"] -checksums = [ - "3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41", # bigdft-suite-1.9.1.tar.gz - "81d12edb2319685ede822ca82594ea8278850e52370ced5ea40c88fe17187f8c", # bigdft_suite_index_bug.patch -] - -local_configopts = " ".join( - [ - 'CC=\\"$MPICC\\" FC=\\"$MPIFC\\" --enable-mpi', - 'FCFLAGS=\\"$CPPFLAGS $FCFLAGS -std=legacy\\"', - 'FFLAGS=\\"$CPPFLAGS $FFLAGS -std=legacy\\"', - 'F90FLAGS=\\"$CPPFLAGS $F90FLAGS -std=legacy\\"', - '--with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS\\"', - '--with-yaml-path=\\"$EBROOTLIBYAML\\"', - ] -) - -local_comp_cmd = ( - """ - mkdir bigdft_builddir && \ - cd bigdft_builddir && \ - python3 ../Installer.py build bigdft -y -v -c %s """ - % local_configopts -) - -cmds_map = [(".*", local_comp_cmd)] - -files_to_copy = ["bigdft_builddir/install/*"] - -builddependencies = [ - ("CMake", "3.21.1"), -] - -dependencies = [ - ("Autoconf", "2.71"), - ("Python", "3.9.6"), - ("OpenCV", "4.5.5", "-contrib"), - ("XZ", "5.2.5"), -] - -modextrapaths = {"PYTHONPATH": ["lib/python%(pyshortver)s/site-packages"]} - -sanity_check_paths = { - "files": [ - "include/futile.mod", - "include/futile.h", - "bin/bigdft", - "bin/bigdftvars.sh", - "lib/python3.9/site-packages/BigDFT/Systems.py", - "lib64/libbigdft-1.a", - ], - "dirs": [], -} - -local_test_script = """ -from BigDFT.Systems import System -from BigDFT.Fragments import Fragment -from BigDFT.IO import XYZReader -N2 = System() -with XYZReader("N2") as ifile: - N2["N:0"] = Fragment([next(ifile)]) - N2["N:1"] = Fragment([next(ifile)]) -print(N2.get_posinp()) -""" - -local_sanity_cmd = " ".join( - [ - "echo '", - local_test_script, - "' > ", - "%(installdir)s/bigdft_test.py && ", - "python %(installdir)s/bigdft_test.py && rm %(installdir)s/bigdft_test.py ", - ] -) - -sanity_check_commands = [(local_sanity_cmd)] - - -moduleclass = "phys" From bfe12f0bb6e104e0b78a041a327810f067666cf1 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 24 Aug 2022 15:59:14 +0200 Subject: [PATCH 4590/9987] reviewed & updated EC --- .../b/BigDFT/bigdft_suite_index_bug.patch | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/b/BigDFT/bigdft_suite_index_bug.patch diff --git a/easybuild/easyconfigs/b/BigDFT/bigdft_suite_index_bug.patch b/easybuild/easyconfigs/b/BigDFT/bigdft_suite_index_bug.patch new file mode 100644 index 00000000000..0aa60536adf --- /dev/null +++ b/easybuild/easyconfigs/b/BigDFT/bigdft_suite_index_bug.patch @@ -0,0 +1,22 @@ +# same effect as patch for futile (futile_index_bug.patch), except due to directory structure, must be regenerated +# fix the redefinition of an index variable caught by GCC 11 +# Author: Denis Kristak (Inuits) +diff -ruN bigdft-suite-1.9.1_orig/futile/flib/f_input_file.f90 bigdft-suite-1.9.1/futile/flib/f_input_file.f90 +--- bigdft-suite-1.9.1_orig/futile/flib/f_input_file.f90 2022-02-22 10:55:06.924505000 +0100 ++++ bigdft-suite-1.9.1/futile/flib/f_input_file.f90 2022-02-22 10:55:57.462690000 +0100 +@@ -172,7 +172,6 @@ + type(dictionary), pointer :: dict + character(len = *), intent(in) :: file, key + +- integer :: i + type(dictionary), pointer :: ref,iter + character(len = max_field_length) :: val, profile_ + double precision, dimension(2) :: rg +@@ -366,6 +365,7 @@ + character(max_field_length), dimension(:), allocatable :: keys + double precision :: var + integer :: dlen, skeys ++ integer :: i + + if (associated(dict%child)) then + if (dict_len(dict) >= 1) then From e32ba469bc21255a4b9e9d78a6f9c6587d2be4f4 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 24 Aug 2022 15:01:07 +0100 Subject: [PATCH 4591/9987] Update BigDFT-1.9.1-foss-2021b.eb formatting changes --- .../b/BigDFT/BigDFT-1.9.1-foss-2021b.eb | 46 ++++++++----------- 1 file changed, 20 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb index 8fe0e115fac..2cb95474324 100644 --- a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb @@ -36,25 +36,21 @@ dependencies = [ extract_sources = True -local_configopts = " ".join( - [ - 'CC=\\"$MPICC\\" FC=\\"$MPIFC\\" --enable-mpi', - 'FCFLAGS=\\"$CPPFLAGS $FCFLAGS -std=legacy\\"', - 'FFLAGS=\\"$CPPFLAGS $FFLAGS -std=legacy\\"', - 'F90FLAGS=\\"$CPPFLAGS $F90FLAGS -std=legacy\\"', - '--with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS\\"', - '--with-yaml-path=\\"$EBROOTLIBYAML\\"', - ] -) +local_configopts = " ".join([ + 'CC=\\"$MPICC\\" FC=\\"$MPIFC\\" --enable-mpi', + 'FCFLAGS=\\"$CPPFLAGS $FCFLAGS -std=legacy\\"', + 'FFLAGS=\\"$CPPFLAGS $FFLAGS -std=legacy\\"', + 'F90FLAGS=\\"$CPPFLAGS $F90FLAGS -std=legacy\\"', + '--with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS\\"', + '--with-yaml-path=\\"$EBROOTLIBYAML\\"', + ]) -install_cmd = " && ".join( - [ - "mkdir bigdft_builddir", - "cd bigdft_builddir", - "python3 ../Installer.py build bigdft -y -v -c %s" % local_configopts, - "cp -r install/* %(installdir)s", - ] -) +install_cmd = " && ".join([ + "mkdir bigdft_builddir", + "cd bigdft_builddir", + "python3 ../Installer.py build bigdft -y -v -c %s" % local_configopts, + "cp -r install/* %(installdir)s", +]) modextrapaths = {"PYTHONPATH": ["lib/python%(pyshortver)s/site-packages"]} @@ -81,14 +77,12 @@ with XYZReader("N2") as ifile: print(N2.get_posinp()) """ -local_sanity_cmd = " && ".join( - [ - "tmpdir=$(mktemp -d)", - "echo '" + local_test_script + "' > " + "$tmpdir/bigdft_test.py", - "python $tmpdir/bigdft_test.py", - "rm -r $tmpdir", - ] -) +local_sanity_cmd = " && ".join([ + "tmpdir=$(mktemp -d)", + "echo '" + local_test_script + "' > " + "$tmpdir/bigdft_test.py", + "python $tmpdir/bigdft_test.py", + "rm -r $tmpdir", +]) sanity_check_commands = [(local_sanity_cmd)] From 085c55beee7c0f19faef7b3d97f4924e10ee98f2 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 24 Aug 2022 15:02:42 +0100 Subject: [PATCH 4592/9987] Delete bigdft_suite_index_bug.patch changing name of the file (folder it's in) --- .../bigdft-suite/bigdft_suite_index_bug.patch | 21 ------------------- 1 file changed, 21 deletions(-) delete mode 100644 easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch diff --git a/easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch b/easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch deleted file mode 100644 index a9cf85235d6..00000000000 --- a/easybuild/easyconfigs/b/bigdft-suite/bigdft_suite_index_bug.patch +++ /dev/null @@ -1,21 +0,0 @@ -# same effect as patch for futile (futile_index_bug.patch), except due to directory structure, must be regenerated -# Author: Denis Kristak (Inuits) -diff -ruN bigdft-suite-1.9.1_orig/futile/flib/f_input_file.f90 bigdft-suite-1.9.1/futile/flib/f_input_file.f90 ---- bigdft-suite-1.9.1_orig/futile/flib/f_input_file.f90 2022-02-22 10:55:06.924505000 +0100 -+++ bigdft-suite-1.9.1/futile/flib/f_input_file.f90 2022-02-22 10:55:57.462690000 +0100 -@@ -172,7 +172,6 @@ - type(dictionary), pointer :: dict - character(len = *), intent(in) :: file, key - -- integer :: i - type(dictionary), pointer :: ref,iter - character(len = max_field_length) :: val, profile_ - double precision, dimension(2) :: rg -@@ -366,6 +365,7 @@ - character(max_field_length), dimension(:), allocatable :: keys - double precision :: var - integer :: dlen, skeys -+ integer :: i - - if (associated(dict%child)) then - if (dict_len(dict) >= 1) then From 8577745405730873c4b7c2316f895c806c0e1e3a Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 24 Aug 2022 15:23:51 +0100 Subject: [PATCH 4593/9987] Update BigDFT-1.9.1-foss-2021b.eb adding checksums --- easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb index 2cb95474324..c720cab5130 100644 --- a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb @@ -22,6 +22,10 @@ toolchainopts = { source_urls = ["https://gitlab.com/l_sim/bigdft-suite/-/archive/%(version)s/"] sources = ["bigdft-suite-%(version)s.tar.gz"] patches = ["bigdft_suite_index_bug.patch"] +checksums = [ + '3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41', # bigdft-suite-1.9.1.tar.gz + 'df887c4df1eb3aa4bfe70e52c405525079bcfa54ac26ec5b8f2511fb6204d179', # bigdft_suite_index_bug.patch +] builddependencies = [ ("CMake", "3.21.1"), From 621a78c662211b895110a865e4a9ccb24cb770b8 Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 24 Aug 2022 16:35:39 +0200 Subject: [PATCH 4594/9987] adding easyconfigs: NAMD-2.14-foss-2022a-mpi.eb --- .../n/NAMD/NAMD-2.14-foss-2022a-mpi.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-mpi.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-mpi.eb new file mode 100644 index 00000000000..4001678aadb --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-mpi.eb @@ -0,0 +1,27 @@ +name = 'NAMD' +version = '2.14' +versionsuffix = '-mpi' + +homepage = 'https://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': False, 'pic': True} + +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] +sources = ['NAMD_%(version)s_Source.tar.gz'] +checksums = ['34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235'] + +dependencies = [ + ('Tcl', '8.6.12'), +] + +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + +# Hard to make charm build the mpi version with gcc on POWER, so we don't currently try +charm_arch = 'mpi-linux-x86_64' +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' From 02b60570140c016956b2ebda6c20fac83fc4f4c4 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 24 Aug 2022 15:58:22 +0100 Subject: [PATCH 4595/9987] Update BigDFT-1.9.1-foss-2021b.eb style err --- easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb index c720cab5130..c871bf40a87 100644 --- a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb @@ -47,7 +47,7 @@ local_configopts = " ".join([ 'F90FLAGS=\\"$CPPFLAGS $F90FLAGS -std=legacy\\"', '--with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS\\"', '--with-yaml-path=\\"$EBROOTLIBYAML\\"', - ]) +]) install_cmd = " && ".join([ "mkdir bigdft_builddir", From 96aabade8a3b104d292fafa6869feedeae386937 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 24 Aug 2022 17:12:52 +0200 Subject: [PATCH 4596/9987] adding easyconfigs: MATLAB-Engine-2021a-GCCcore-10.2.0.eb, MATLAB-Engine-2021a-GCCcore-11.2.0.eb --- .../MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 32 +++++++++++++++++++ .../MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..14525297b2f --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = '2021a' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('MATLAB', version, '', True), + ('Python', '3.8.6'), +] + +use_pip = False +download_dep_fail = True + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" + +skipsteps = ['install'] + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +options = {'modulename': 'matlab.engine'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..629c793528c --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = '2021a' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('MATLAB', version, '', True), + ('Python', '3.9.6'), +] + +use_pip = False +download_dep_fail = True + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" + +skipsteps = ['install'] + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +options = {'modulename': 'matlab.engine'} + +moduleclass = 'math' From 3542108d31460a2f890968e31ab8d16eaa14792f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 24 Aug 2022 17:19:53 +0200 Subject: [PATCH 4597/9987] Add ASE --- .../a/ASE/ASE-3.22.1-foss-2022a.eb | 47 ++++++++++++++++ .../f/Flask/Flask-2.2.2-GCCcore-11.3.0.eb | 55 +++++++++++++++++++ .../spglib-python-2.0.0-foss-2022a.eb | 27 +++++++++ 3 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/f/Flask/Flask-2.2.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb new file mode 100644 index 00000000000..98481085f40 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Flask', '2.2.2'), + ('matplotlib', '3.5.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.0.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.8.2', { + 'checksums': ['77f03f4554392558700295e05aed0b1096a20d4a60a4f3ddcde58b0c31c8fca2'], + }), + ('ase', version, { + 'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/Flask/Flask-2.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-2.2.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..644e98a242f --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-2.2.2-GCCcore-11.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '2.2.2' + +homepage = 'https://www.palletsprojects.com/p/flask/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), +] + +builddependencies = [('binutils', '2.38')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('Werkzeug', version, { + 'checksums': ['7ea2d48322cc7c0f8b3a215ed73eabd7b5d75d0b50e31ab006286ccff9e00b8f'], + }), + ('asgiref', '3.5.2', { + 'checksums': ['4a29362a6acebe09bf1d6640db38c1dc3d9217c68e6f9f6204d72667fc19a424'], + }), + (name, version, { + 'checksums': ['642c450d19c4ad482f96729bd2a8f6d32554aa1e231f4f6b4e7e5264b16cca2b'], + }), + ('Flask-Cors', '3.0.10', { + 'checksums': ['b60839393f3b84a0f3746f6cdca56c1ad7426aa738b70d6c61375857823181de'], + }), + ('cachelib', '0.9.0', { + 'checksums': ['38222cc7c1b79a23606de5c2607f4925779e37cdcea1c2ad21b8bae94b5425a5'], + }), + ('Flask-Session', '0.4.0', { + 'checksums': ['c9ed54321fa8c4ca0132ffd3369582759eda7252fb4b3bee480e690d1ba41f46'], + }), +] + +sanity_check_paths = { + 'files': ['bin/flask'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['flask --version'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-foss-2022a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-foss-2022a.eb new file mode 100644 index 00000000000..c1dd837eb0a --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '2.0.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['cbbd5e1d6096577c58b2fa47a5ea4f433a1932e5bc1cd1b691ea387c1b2e9974'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' From 4038b236aafc832399534ee095d4119d5d8d6c00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 24 Aug 2022 17:59:45 +0200 Subject: [PATCH 4598/9987] Add sanity pip check --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 2 ++ .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb index 14525297b2f..3418f6ddc56 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb @@ -27,6 +27,8 @@ skipsteps = ['install'] # Test that connection with MATLAB can be established successfully sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] +sanity_pip_check = True + options = {'modulename': 'matlab.engine'} moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb index 629c793528c..9380e93ff8a 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -27,6 +27,8 @@ skipsteps = ['install'] # Test that connection with MATLAB can be established successfully sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] +sanity_pip_check = True + options = {'modulename': 'matlab.engine'} moduleclass = 'math' From f9aca05904c131b498de16e6df637c3b0da1ce54 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 24 Aug 2022 19:07:26 +0200 Subject: [PATCH 4599/9987] Add Elk --- .../e/Elk/Elk-8.5.02-foss-2022a.eb | 63 +++++++++++++++++++ .../w/Wannier90/Wannier90-3.1.0-foss-2022a.eb | 35 +++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/e/Elk/Elk-8.5.02-foss-2022a.eb create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/Elk/Elk-8.5.02-foss-2022a.eb b/easybuild/easyconfigs/e/Elk/Elk-8.5.02-foss-2022a.eb new file mode 100644 index 00000000000..939ca43c870 --- /dev/null +++ b/easybuild/easyconfigs/e/Elk/Elk-8.5.02-foss-2022a.eb @@ -0,0 +1,63 @@ +easyblock = 'MakeCp' + +name = 'Elk' +version = '8.5.2' + +homepage = 'http://elk.sourceforge.net/' +description = """An all-electron full-potential linearised +augmented-plane wave (FP-LAPW) code with many advanced features. Written +originally at Karl-Franzens-Universität Graz as a milestone of the +EXCITING EU Research and Training Network, the code is designed to be as +simple as possible so that new developments in the field of density +functional theory (DFT) can be added quickly and reliably. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True, 'opt': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TGZ] +checksums = ['2d9d98ddadb8a6e031d32cb0957f41bc53099c286874bd1b38a08164352de7c0'] + +dependencies = [ + ('libxc', '5.2.3'), + ('Wannier90', '3.1.0'), +] + + +# make.inc file is generated interactively by "setup" command, creating it here +prebuildopts = 'echo "F90_OPTS = -std=legacy $FFLAGS" > make.inc && ' +prebuildopts += 'echo "F77_OPTS = -std=legacy $FFLAGS" >> make.inc && ' +prebuildopts += 'echo "LIB_LPK = $LIBLAPACK" >> make.inc && ' +prebuildopts += 'echo "LIB_FFT = $LIBFFT" >> make.inc && ' +prebuildopts += 'echo "LIB_W90 = -lwannier" >> make.inc && ' +prebuildopts += 'echo "LIB_libxc = -lxcf90 -lxc" >> make.inc && ' +prebuildopts += 'echo "SRC_libxc = libxcf90.f90 libxcifc.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_FFT = zfftifc_fftw.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_OBLAS = oblas_stub.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_BLIS = blis_stub.f90" >> make.inc && ' +prebuildopts += 'echo "SRC_MKL = mkl_stub.f90" >> make.inc && ' + +buildopts = 'all' + +runtest = 'test' + +parallel = 1 + +files_to_copy = [( + [ + 'src/elk', 'src/spacegroup/spacegroup', 'src/eos/eos', + 'utilities/elk-bands/elk-bands', 'utilities/elk-optics/elk-optics.py', + 'utilities/wien2k-elk/se.pl' + ], 'bin' +)] + +sanity_check_paths = { + 'files': ['bin/elk', 'bin/spacegroup', 'bin/eos'], + 'dirs': [] +} + +# Elk 8.5.2 reports its version as "8.5.02", so we test only major+minor versions +sanity_check_commands = ["elk | grep '^Elk code version %(version_major)s.%(version_minor)s'"] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2022a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2022a.eb new file mode 100644 index 00000000000..217398eb063 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +# The -fallow-argument-mismatch allows MPI communication calls to be +# called with arrays of different types at different places in the +# code. This otherwise cause an error in GCC 10.X +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' From eeefb982060fd563aabd6ff182f24a122680eaf3 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 24 Aug 2022 10:27:39 -0700 Subject: [PATCH 4600/9987] {bio}[GCCcore/11.2.0] Porechop-0.2.4 w/Python/3.9.6 --- .../Porechop/Porechop-0.2.4-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..3ce7f2cb175 --- /dev/null +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'Porechop' +version = '0.2.4' + +homepage = 'https://github.com/rrwick/Porechop' +description = """Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. + Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, + it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments + to effectively find adapters, even at low sequence identity""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/rrwick/Porechop/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'] + +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From a98ad52edd784d3791f323858958622a29c1f449 Mon Sep 17 00:00:00 2001 From: Bob Date: Thu, 25 Aug 2022 10:29:51 +0200 Subject: [PATCH 4601/9987] adding easyconfigs: Amber-22.0-foss-2021b-AmberTools-22.3.eb and patches: Amber-22_remove_undeclared_redundant_variable.patch, AmberTools-22_fix_cuda_version_check.patch --- .../Amber-22.0-foss-2021b-AmberTools-22.3.eb | 74 +++++++++++++++++++ ...remove_undeclared_redundant_variable.patch | 27 +++++++ ...AmberTools-22_fix_cuda_version_check.patch | 18 +++++ 3 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch create mode 100644 easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb new file mode 100644 index 00000000000..9389944b7fd --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb @@ -0,0 +1,74 @@ +name = 'Amber' +local_amber_ver = 22 +local_ambertools_ver = 22 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (3, 0) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools-%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + 'Amber-22_remove_undeclared_redundant_variable.patch', + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + 'AmberTools-21_CMake-FlexiBLAS.patch', + 'AmberTools-22_fix_cuda_version_check.patch', +] +checksums = [ + '3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16', # Amber22.tar.bz2 + '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools-22.tar.bz2 + # Amber-22_remove_undeclared_redundant_variable.patch + 'f2e21002e00534f14caa00bc5bbf3b1e68acb71aa8dbcfea275d67192e32c15f', + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + '3fc08a2cf61f3eefd094554e60c88b14c9f5071f94e0a0a15c6b55fe321bfc78', # AmberTools-22_fix_cuda_version_check.patch +] + +builddependencies = [ + ('Bison', '3.7.6'), + ('pkg-config', '0.29.2'), + ('CMake', '3.22.1'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # mpi4py required for MMPBSA + ('Perl', '5.34.0'), + ('Boost', '1.77.0'), + ('libreadline', '8.1'), + ('matplotlib', '3.4.3'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.3'), + ('arpack-ng', '3.8.0'), + ('Tkinter', '3.9.6'), + ('X11', '20210802'), + ('CUDA', '11.4.1', '', True), + ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), +] + +# Some CUDA tests differs from expected results +runtest = False + +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch b/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch new file mode 100644 index 00000000000..3bfe94fd93a --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch @@ -0,0 +1,27 @@ +Remove the undeclared (and unused) variable i from the private clause +in an OpenMP pragma, which otherwise results in an error: + + 93 | !$omp parallel do private(ihkl,i,f,angle) + | 1 +Error: Symbol i at (1) has no IMPLICIT type + +Bob Dröge, University of Groningen, 2022-08-18 +--- amber22_src.orig/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:24.807724049 +0200 ++++ amber22_src/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:42.039809811 +0200 +@@ -90,7 +90,7 @@ + call check_precondition(size(frac, 2) == size(scatter_type_index)) + call check_precondition(size(hkl, 2) == size(atomic_scatter_factor, 1)) + +- !$omp parallel do private(ihkl,i,f,angle) ++ !$omp parallel do private(ihkl,f,angle) + do ihkl = 1, size(hkl, 2) + + ! Fhkl = SUM( fj * exp(2 * M_PI * i * (h * xj + k * yj + l * zj)) ), +@@ -127,4 +127,4 @@ + end subroutine calc_f_non_bulk + + +-end module xray_non_bulk_impl_cpu_module +\ No newline at end of file ++end module xray_non_bulk_impl_cpu_module + diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch b/easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch new file mode 100644 index 00000000000..de3b0b115df --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch @@ -0,0 +1,18 @@ +The CUDA_VERSION returned by CMake's FindCUDA module only contains +the major and minor version number, not the patch release. +This makes the check if CUDA_VERSION is less than 11.4.1 broken, +even though only CUDA 11.4.1 supports GCC 11 (11.4.0 does not). +As we know which GCC and CUDA we're using, this patch just compares it to 11.4 anyway. + +Bob Dröge, University of Groningen, 2022-08-18 +--- amber20_src.orig/cmake/CudaConfig.cmake 2022-08-18 08:25:28.236089267 +0200 ++++ amber20_src/cmake/CudaConfig.cmake 2022-08-18 08:24:27.122766862 +0200 +@@ -82,7 +82,7 @@ + # VERSION_EQUAL 10 means 10.0, so use a range for comparing major version. + if ( "${CMAKE_C_COMPILER_ID}" STREQUAL "GNU" AND ( + ( CMAKE_CXX_COMPILER_VERSION VERSION_LESS 12 +- AND CUDA_VERSION VERSION_GREATER_EQUAL 11.4.1 ++ AND CUDA_VERSION VERSION_GREATER_EQUAL 11.4 + AND CUDA_VERSION VERSION_LESS_EQUAL 11.7 ) + OR ( CMAKE_CXX_COMPILER_VERSION VERSION_LESS 11 + AND CUDA_VERSION VERSION_GREATER_EQUAL 11.1 From c17607e3c0aee1fb3401a349ea31253300e37f24 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 25 Aug 2022 10:36:53 +0200 Subject: [PATCH 4602/9987] Add CUDA to versionsuffix and filename --- ....eb => Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/Amber/{Amber-22.0-foss-2021b-AmberTools-22.3.eb => Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb} (96%) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb similarity index 96% rename from easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb rename to easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 9389944b7fd..2630ac53048 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -4,7 +4,7 @@ local_ambertools_ver = 22 # Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php patchlevels = (3, 0) # (AmberTools, Amber) version = '%s.%s' % (local_amber_ver, patchlevels[1]) -versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) +versionsuffix = '-AmberTools-%s.%s-CUDA-%%(cudaver)s' % (local_ambertools_ver, patchlevels[0]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing From d7478421dfff41c63a0af01ee51d96f125e64e66 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Aug 2022 12:01:46 +0200 Subject: [PATCH 4603/9987] remove stripping over parasail version requirement for NGSpeciesID v0.1.2.1, not needed --- .../n/NGSpeciesID/NGSpeciesID-0.1.2.1-foss-2021b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.2.1-foss-2021b.eb b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.2.1-foss-2021b.eb index 85eaf6617e2..ded9e69beb6 100644 --- a/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.2.1-foss-2021b.eb +++ b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.1.2.1-foss-2021b.eb @@ -24,9 +24,6 @@ dependencies = [ download_dep_fail = True use_pip = True -# strip away too strict version requirement for parasail and -preinstallopts = "sed -i 's/parasail==[0-9.]*/parasail/g' setup.py && " - # no proper namespace for NGSpeciesID options = {'modulename': 'modules.consensus'} From d3c3aaf9cb095dda294d28dc44bec5a9581eaf14 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 25 Aug 2022 13:03:25 +0200 Subject: [PATCH 4604/9987] Update --- .../n/NAMD/NAMD-2.14-foss-2022a-mpi.eb | 10 +++++++- .../n/NAMD/NAMD-2.14_fix-LJCorrection.patch | 24 +++++++++++++++++++ .../n/NAMD/NAMD-2.14_fix-constant-pH.patch | 20 ++++++++++++++++ 3 files changed, 53 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14_fix-LJCorrection.patch create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14_fix-constant-pH.patch diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-mpi.eb index 4001678aadb..78c6ee3ba72 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-mpi.eb @@ -11,7 +11,15 @@ toolchainopts = {'usempi': True, 'openmp': False, 'pic': True} source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] sources = ['NAMD_%(version)s_Source.tar.gz'] -checksums = ['34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235'] +patches = [ + 'NAMD-2.14_fix-constant-pH.patch', + 'NAMD-2.14_fix-LJCorrection.patch', +] +checksums = [ + '34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235', # NAMD_2.14_Source.tar.gz + '864c6941b7cf52b78d26f2311236ec717f29399aa71436904930706d5d8b61de', # NAMD-2.14_fix-constant-pH.patch + '7b54cc62c893f00f491d8ff75685c8877d78a9471fa3db6fc70974edba09e70a', # NAMD-2.14_fix-LJCorrection.patch +] dependencies = [ ('Tcl', '8.6.12'), diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14_fix-LJCorrection.patch b/easybuild/easyconfigs/n/NAMD/NAMD-2.14_fix-LJCorrection.patch new file mode 100644 index 00000000000..25a4e59e173 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14_fix-LJCorrection.patch @@ -0,0 +1,24 @@ +# Fix LJ correction for alchemical simulation +# Patch is taken from https://www.ks.uiuc.edu/Research/namd/2.14/bugfixes.html +# Author: maxim-masterov (SURF) +diff -Nru NAMD_2.14_Source.orig/src/Molecule.C NAMD_2.14_Source/src/Molecule.C +--- NAMD_2.14_Source.orig/src/Molecule.C 2022-08-25 12:50:46.282906000 +0200 ++++ NAMD_2.14_Source/src/Molecule.C 2022-08-25 12:54:31.616781099 +0200 +@@ -10159,7 +10159,7 @@ + numLJsites1 = numLJsites2 = numLJsites; + int alch_counter = 0; + for (int i=0; i < numAtoms; ++i) { +- int alchFlagi; ++ int alchFlagi = 0; + if (get_fep_type(i) == 2 || get_fep_type(i) == 4) alchFlagi = -1; + if (get_fep_type(i) == 1 || get_fep_type(i) == 3) alchFlagi = 1; + if (params->get_vdw_pair_params(atoms[i].vdw_type, atoms[i].vdw_type, +@@ -10182,7 +10182,7 @@ + else if (alchFlagi == -1) numLJsites1--; + } + for (int j=i+1; j < numAtoms; ++j) { +- int alchFlagj; ++ int alchFlagj = 0; + if (get_fep_type(j) == 2 || get_fep_type(j) == 4) alchFlagj = -1; + if (get_fep_type(j) == 1 || get_fep_type(j) == 3) alchFlagj = 1; + int alchFlagSum = alchFlagi + alchFlagj; diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14_fix-constant-pH.patch b/easybuild/easyconfigs/n/NAMD/NAMD-2.14_fix-constant-pH.patch new file mode 100644 index 00000000000..331a5e06284 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14_fix-constant-pH.patch @@ -0,0 +1,20 @@ +# Fix constant-pH MD output +# Patch is taken from https://www.ks.uiuc.edu/Research/namd/2.14/bugfixes.html +# Author: maxim-masterov (SURF) +diff -Nru NAMD_2.14_Source.orig/src/ScriptTcl.C NAMD_2.14_Source/src/ScriptTcl.C +--- NAMD_2.14_Source.orig/src/ScriptTcl.C 2022-08-25 12:50:46.325325000 +0200 ++++ NAMD_2.14_Source/src/ScriptTcl.C 2022-08-25 12:51:48.557043174 +0200 +@@ -2085,11 +2085,11 @@ + } + + +-extern "C" void newhandle_msg(void *v, const char *msg) { ++extern "C" void newhandle_msg(void *vdata, void *v, const char *msg) { + CkPrintf("psfgen) %s\n",msg); + } + +-extern "C" void newhandle_msg_ex(void *v, const char *msg, int prepend, int newline) { ++extern "C" void newhandle_msg_ex(void *vdata, void *v, const char *msg, int prepend, int newline) { + CkPrintf("%s%s%s", (prepend ? "psfgen) " : ""), msg, (newline ? "\n" : "")); + } + From c8bbcc4dc3bfbf672adbf34a849a45ea72ae7d56 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 25 Aug 2022 13:14:30 +0200 Subject: [PATCH 4605/9987] Rename file --- .../e/Elk/{Elk-8.5.02-foss-2022a.eb => Elk-8.5.2-foss-2022a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/e/Elk/{Elk-8.5.02-foss-2022a.eb => Elk-8.5.2-foss-2022a.eb} (100%) diff --git a/easybuild/easyconfigs/e/Elk/Elk-8.5.02-foss-2022a.eb b/easybuild/easyconfigs/e/Elk/Elk-8.5.2-foss-2022a.eb similarity index 100% rename from easybuild/easyconfigs/e/Elk/Elk-8.5.02-foss-2022a.eb rename to easybuild/easyconfigs/e/Elk/Elk-8.5.2-foss-2022a.eb From 01809025f6fd943db4b2440f621794f2140c678a Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 25 Aug 2022 14:05:26 +0200 Subject: [PATCH 4606/9987] adding easyconfigs: Emacs-28.1-GCCcore-10.2.0.eb --- .../e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9bfb1e644e7 --- /dev/null +++ b/easybuild/easyconfigs/e/Emacs/Emacs-28.1-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +# +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Robert Mijakovic +# reciPY derived from preexisting reciPy for GCCcore-9.2.0. +# Modder: Ben Langenberg +# +easyblock = 'ConfigureMake' + +name = 'Emacs' +version = '28.1' + +homepage = 'https://www.gnu.org/software/emacs/' +description = """GNU Emacs is an extensible, customizable text editor--and more. + At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming + language with extensions to support text editing.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] +checksums = ['1439bf7f24e5769f35601dbf332e74dfc07634da6b1e9500af67188a92340a28'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.5'), + ('ncurses', '6.2'), + ('LibTIFF', '4.1.0'), + ('X11', '20201008'), + ('GTK+', '3.24.23'), +] + +# If you want to use Emacs plugins you must install the gnutls command line tools +# osdependencies = [('gnutls-utils')] + +configopts = '--with-gif=no --with-tiff=yes --with-x-toolkit=yes --with-xpm=yes --with-gnutls=no ' + +sanity_check_paths = { + 'files': ["bin/emacs", "bin/emacs-%(version)s", "bin/emacsclient", "bin/etags"], + 'dirs': [] +} + +moduleclass = 'tools' From 96b7d8806e0b6c736c4ede8b62354bfc9c997b7f Mon Sep 17 00:00:00 2001 From: benjamic Date: Thu, 25 Aug 2022 14:11:26 +0200 Subject: [PATCH 4607/9987] Added License file --- easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.6-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.6-GCC-11.3.0.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.6-GCC-11.3.0.eb index d547fba7603..7b3c04f52c7 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.6-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.6-GCC-11.3.0.eb @@ -27,7 +27,7 @@ buildopts = 'BLASFLAGS="-lflexiblas" BLASFLAGS64="-lflexiblas"' buildopts += ' LDFLAGS="$LIBS -ldeflate -lz -lzstd" ZLIB="" CSRC="include/SFMT.c"' buildopts += ' BASEFLAGS="$OPTFLAGS -DZSTD_MULTITHREAD"' -files_to_copy = ['bin', (['include/*.h'], 'include'), 'ReadMe.md'] +files_to_copy = ['bin', (['include/*.h'], 'include'), 'ReadMe.md', 'COPYING', 'COPYING.LESSER'] sanity_check_paths = { 'files': ['bin/plink2', 'bin/pgen_compress'], From 634c8a66f6dae7750697c8de8c1c583c3d4ad8a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Aug 2022 14:56:09 +0200 Subject: [PATCH 4608/9987] tweak modloadmsg in RheoTool easyconfig (+ trivial code style tweaks w.r.t. single vs double quotes) --- .../r/RheoTool/RheoTool-5.0-foss-2019b.eb | 31 +++++++++---------- 1 file changed, 15 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb b/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb index 2c91848824b..86bb0bbf1ae 100644 --- a/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb +++ b/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb @@ -1,27 +1,26 @@ -easyblock = "Binary" +easyblock = 'Binary' -name = "RheoTool" -version = "5.0" +name = 'RheoTool' +version = '5.0' -homepage = "https://github.com/fppimenta/rheoTool" +homepage = 'https://github.com/fppimenta/rheoTool' description = """RheoTool is an open-source toolbox based on OpenFOAM to simulate Generalized Newtonian Fluids (GNF) and viscoelastic fluids under pressure-driven and/or electrically-driven flows.""" -toolchain = {"name": "foss", "version": "2019b"} +toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = ["https://github.com/fppimenta/rheoTool/archive/refs/tags/"] -sources = ["v%(version)s.tar.gz"] -checksums = ["2e0899684d6d7f9ddee0d93b39a6ed56262b171bc4e5536914645209b66003ed"] +source_urls = ['https://github.com/fppimenta/rheoTool/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2e0899684d6d7f9ddee0d93b39a6ed56262b171bc4e5536914645209b66003ed'] dependencies = [ - ("OpenFOAM", "7", "-20200508"), - ("Eigen", "3.3.7", "", True), - ("PETSc", "3.12.4", "-Python-3.7.4"), + ('OpenFOAM', '7', '-20200508'), + ('Eigen', '3.3.7', '', True), + ('PETSc', '3.12.4', '-Python-3.7.4'), ] extract_sources = True - install_cmd = "source $FOAM_BASH && " install_cmd += "export EIGEN_RHEO=$EBROOTEIGEN && " install_cmd += "cd of70/src && " @@ -35,13 +34,13 @@ install_cmd += "export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && " install_cmd += "./Allwmake -j %(parallel)s " sanity_check_paths = { - "files": ["bin/rheoBDFoam", "lib/libthermoRheoTool.so"], - "dirs": [], + 'files': ['bin/rheoBDFoam', 'lib/libthermoRheoTool.so'], + 'dirs': [], } # source $FOAM_BASH must run before using RheoTool, otherwise there will be missing libraries sanity_check_commands = ["source $FOAM_BASH && rheoBDFoam -help"] -modloadmsg = 'Please run command "source $FOAM_BASH " before using RheoTool, otherwise there will be missing libraries.' +modloadmsg = "Please run 'source $FOAM_BASH' before using RheoTool." -moduleclass = "cae" +moduleclass = 'cae' From 5985bd270086c3b249d5582ae91ab9a8141b4f4c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Aug 2022 15:16:40 +0200 Subject: [PATCH 4609/9987] add Autotools build dependency for Libint 2.7.2 --- .../l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb index 4ab44202876..316d77e98db 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-11.3.0-lmax-6-cp2k.eb @@ -28,11 +28,12 @@ checksums = [ ] builddependencies = [ - ('CMake', '3.23.1'), + ('Autotools', '20220317'), ('GMP', '6.2.1'), ('Boost', '1.79.0'), ('Eigen', '3.4.0'), ('Python', '3.10.4'), + ('CMake', '3.23.1'), ] # configure options as required by CP2K, From e53cb0e0186459003af075923e64e03c94ce3c0d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Aug 2022 17:52:26 +0200 Subject: [PATCH 4610/9987] make check for toolchain value in dependency spec in easyconfigs test suite aware that dumped easyconfig uses SYSTEM constant --- test/easyconfigs/easyconfigs.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index ff9c5828c69..47aea7dace7 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -42,6 +42,7 @@ from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.easyblocks.generic.pythonpackage import PythonPackage from easybuild.framework.easyblock import EasyBlock +from easybuild.framework.easyconfig.constants import EASYCONFIG_CONSTANTS from easybuild.framework.easyconfig.default import DEFAULT_CONFIG from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for @@ -1429,7 +1430,13 @@ def template_easyconfig_test(self, spec): # 4th value is toolchain spec if len(dumped_dep) >= 4: if len(orig_dep) >= 4: - self.assertEqual(dumped_dep[3], orig_dep[3]) + # if True was used to indicate that dependency should use system toolchain, + # then we need to compare the value for the dumped easyconfig more carefully; + # see also https://github.com/easybuilders/easybuild-framework/pull/4069 + if orig_dep[3] == True: + self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) + else: + self.assertEqual(dumped_dep[3], orig_dep[3]) else: # if a subtoolchain is specifed (only) in the dumped easyconfig, # it should *not* be the same as the parent toolchain From 6bb7a28b0d2f3f12492506be40cb2d0566851b6a Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 25 Aug 2022 14:18:42 -0700 Subject: [PATCH 4611/9987] {math}[foss/2021b] PyStan v3.5.0 --- .../p/PyStan/PyStan-3.5.0-foss-2021b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyStan/PyStan-3.5.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/PyStan/PyStan-3.5.0-foss-2021b.eb b/easybuild/easyconfigs/p/PyStan/PyStan-3.5.0-foss-2021b.eb new file mode 100644 index 00000000000..820ef9e1ad6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyStan/PyStan-3.5.0-foss-2021b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'PyStan' +version = '3.5.0' + +homepage = 'https://github.com/stan-dev/pystan' +description = """Python interface to Stan, a package for Bayesian inference + using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('aiohttp', '3.8.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +exts_list = [ + ('marshmallow', '3.17.1', { + 'checksums': ['48e2d88d4ab431ad5a17c25556d9da529ea6e966876f2a38d274082e270287f0'], + }), + ('webargs', '8.2.0', { + 'checksums': ['99d68940c452e07726485a15fef43f12f8ae6c0c5b391bcba76065d4527fb85d'], + }), + ('httpstan', '4.8.2', { + 'source_tmpl': 'httpstan-4.8.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'checksums': ['94da9bee5e13b5164934a1f0c8986a0b715da37d8a44d0e69167221bb1f334ac'], + }), + ('pysimdjson', '3.2.0', { + 'modulename': 'simdjson', + 'checksums': ['643baa0941752367761dbc091bf552bf4ca196cf67bf41ef89c90c2db2ec1477'], + }), + (name, version, { + 'modulename': 'stan', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['078571d071a5b7c0af59206d4994a0979f4ac4b61f4a720b640c44fe35514929'], + }), +] + +moduleclass = 'math' From ceda73351ab65ff0c30e443a43c5dd75885ffbfa Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 25 Aug 2022 14:32:31 -0700 Subject: [PATCH 4612/9987] add binutils --- .../easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-11.2.0.eb index 3ce7f2cb175..38cc2f58c84 100644 --- a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-11.2.0.eb @@ -20,6 +20,10 @@ source_urls = ['https://github.com/rrwick/Porechop/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'] +builddependencies = [ + ('binutils', '2.37'), +] + dependencies = [ ('Python', '3.9.6'), ] From 5042cb3941b1de6c9f61f84883c1ff505bfb1fcb Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 26 Aug 2022 07:37:00 +0200 Subject: [PATCH 4613/9987] working sanity checks --- .../o/OpenFOAM/OpenFOAM-v2112-cleanup.patch | 150 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb | 10 +- .../OpenFOAM/OpenFOAM-v2112-wmake-ompi.patch | 29 ++++ 3 files changed, 184 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-wmake-ompi.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-cleanup.patch new file mode 100644 index 00000000000..df57e301a60 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-cleanup.patch @@ -0,0 +1,150 @@ +# Replaces OpenFOAM third-party libraries with EASYBUILD variants. +# Uses the OpenFOAM prefs mechanism and the FOAM_CONFIG_ETC variable +# to define the preferred settings without patching the original files +# +# Authors: Mark Olesen +# ------------------------------------------------------------------------- +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2112/etc/prefs.sh 2020-12-14 10:02:26.488430802 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FOAM_CONFIG_ETC="etc/easybuild" ++ ++export WM_MPLIB=EASYBUILDMPI ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2112/etc/easybuild/config.sh/CGAL 2020-12-14 10:10:55.991841204 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++export BOOST_ARCH_PATH="$EBROOTBOOST" ++export CGAL_ARCH_PATH="$EBROOTCGAL" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2112/etc/easybuild/config.sh/FFTW 2020-12-14 10:10:53.735843322 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FFTW_ARCH_PATH="$EBROOTFFTW" ++ ++##EasyBuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2112/etc/easybuild/config.sh/metis 2020-12-11 21:23:28.774934024 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++METIS_VERSION="metis-$EBVERSIONMETIS" ++[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH="$METIS_ROOT" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2112/etc/easybuild/config.sh/readline 2020-12-11 21:23:22.534951043 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export READLINE_ARCH_PATH="$EBROOTLIBREADLINE" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2112/etc/easybuild/config.sh/scotch 2020-12-11 21:23:17.586964539 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export SCOTCH_VERSION="scotch_$EBVERSIONSCOTCH" ++export SCOTCH_ARCH_PATH="$EBROOTSCOTCH" ++[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH="$SCOTCH_ROOT" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2112/etc/easybuild/config.sh/vtk 2020-12-11 21:22:55.463024882 +0100 +@@ -0,0 +1,9 @@ ++##Easybuild## settings -*- sh -*- ++ ++export VTK_DIR="$EBROOTVTK" ++export MESA_ARCH_PATH="$EBROOTMESA" ++ ++# Define paraview-mesa directory as required ++unset ParaView_MESA_DIR ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2112/etc/easybuild/config.sh/paraview 2020-12-14 10:13:53.583674383 +0100 +@@ -0,0 +1,75 @@ ++##Easybuild## settings -*- sh -*- ++# ++# Largely a knockoff of the OpenFOAM etc/config.sh/paraview-system ++# readjusted for easybuild ++# ++# Copyright (C) 2020 OpenCFD Ltd. ++# ++#------------------------------------------------------------------------------ ++# Compiler-specific location for ThirdParty installations ++archDir="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER" ++ ++# Clean path and library path of previous settings ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=LD_LIBRARY_PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++ ++#------------------------------------------------------------------------------ ++ ++##Easybuild## settings ++ ++ParaView_VERSION="$EBVERSIONPARAVIEW" ++export ParaView_DIR="$EBROOTPARAVIEW" ++ ++#------------------------------------------------------------------------------ ++ ++unset PV_PLUGIN_PATH ++ ++# Set API to correspond to VERSION ++# pv_api is . from ParaView_VERSION ++#- ++# Extract API from VERSION ++pv_api=$(echo "$ParaView_VERSION" | \ ++ sed -ne 's/^[^0-9]*\([0-9][0-9]*\.[0-9][0-9]*\).*$/\1/p') ++ ++pv_plugin_dir="$FOAM_LIBBIN/paraview-$pv_api" ++ ++# Set paths if binaries are present ++if [ -r "$ParaView_DIR" ] ++then ++ export PATH="$ParaView_DIR/bin:$PATH" ++ ++ # ParaView libraries ++ # - 5.5 and later: lib/, but could also be lib64/ ++ for libDir in lib64 lib ++ do ++ pvLibDir="$libDir/paraview-$pv_api" ++ if [ -d "$ParaView_DIR/$pvLibDir" ] ++ then ++ export LD_LIBRARY_PATH="$ParaView_DIR/$libDir:$LD_LIBRARY_PATH" ++ break ++ fi ++ done ++ ++ # OpenFOAM plugin directory must be the first in PV_PLUGIN_PATH ++ # and have paraview-major.minor encoded in its name ++ if [ -d "$pv_plugin_dir" ] ++ then ++ export PV_PLUGIN_PATH="$pv_plugin_dir" ++ fi ++fi ++ ++ ++#------------------------------------------------------------------------------ ++ ++unset ParaView_VERSION ++ ++unset archDir libDir ++unset pv_api pv_plugin_dir pvLibDir ++ ++#------------------------------------------------------------------------------ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb index edf177d5994..38e19f85b0b 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb @@ -13,18 +13,18 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'cstd': 'c++11', 'vectorize': False} +toolchainopts = {'cstd': 'c++14', 'vectorize': False} source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] patches = [ - ('OpenFOAM-v2012-cleanup.patch', 1), - 'OpenFOAM-v1906-wmake-ompi.patch', + ('OpenFOAM-v2112-cleanup.patch', 1), + 'OpenFOAM-v2112-wmake-ompi.patch', ] checksums = [ '3e838731e79db1c288acc27aad8cc8a43d9dac1f24e5773e3b9fa91419a8c3f7', # OpenFOAM-v2112.tgz - 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch - '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch + 'e883f628cb393b3ab60317304d7085d0a6ba7b8992feb12c2fab20389af34f1c', # OpenFOAM-v2112-cleanup.patch + '8cc2d9feac07b564abb4a16614f142a7c1aceedc4ad6ee02836e7d4f654410cd', # OpenFOAM-v2112-wmake-ompi.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-wmake-ompi.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-wmake-ompi.patch new file mode 100644 index 00000000000..c7cc5e4a42f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-wmake-ompi.patch @@ -0,0 +1,29 @@ +# - Corrected output of "wmake -show-c" and "wmake -show-c++" with OpenMPI in order to allow compilation of paraFoam +# +# author: Jiri Furst +--- OpenFOAM-v2112/wmake/makefiles/info.orig 2019-11-07 18:12:53.000000000 +0100 ++++ OpenFOAM-v2112/wmake/makefiles/info 2019-11-23 12:52:50.700688579 +0100 +@@ -73,19 +73,19 @@ + + .PHONY: c + c: +- @echo "$(firstword $(cc))" ++ @echo "$(lastword $(cc))" + + .PHONY: cxx + cxx: +- @echo "$(firstword $(CC))" ++ @echo "$(lastword $(CC))" + + .PHONY: cflags + cflags: +- @echo "$(wordlist 2,$(words $(COMPILE_C)), $(COMPILE_C))" ++ @echo "$(wordlist 3,$(words $(COMPILE_C)), $(COMPILE_C))" + + .PHONY: cxxflags + cxxflags: +- @echo "$(wordlist 2,$(words $(COMPILE_CXX)), $(COMPILE_CXX))" ++ @echo "$(wordlist 3,$(words $(COMPILE_CXX)), $(COMPILE_CXX))" + + .PHONY: cflags-arch + cflags-arch: From 54cb4c25ed29632a67e8a2679044ba950ad757cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Aug 2022 08:24:24 +0200 Subject: [PATCH 4614/9987] use alt_location for ambertools patch --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 2630ac53048..6182fcd8066 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -22,7 +22,7 @@ patches = [ 'AmberTools-20_cmake-locate-netcdf.patch', 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_fix_xblas_missing_make_dependency.patch', - 'AmberTools-21_CMake-FlexiBLAS.patch', + {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'} 'AmberTools-22_fix_cuda_version_check.patch', ] checksums = [ From 1dd09cafb532ba6cdc8003433567bb489f8dc180 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Aug 2022 08:50:05 +0200 Subject: [PATCH 4615/9987] add missing comma --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 6182fcd8066..a1dde04b075 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -22,7 +22,7 @@ patches = [ 'AmberTools-20_cmake-locate-netcdf.patch', 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_fix_xblas_missing_make_dependency.patch', - {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'} + {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'}, 'AmberTools-22_fix_cuda_version_check.patch', ] checksums = [ From fb0eb3e86eb670a3bd8abddee9e7897ef20969e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2022 10:50:12 +0200 Subject: [PATCH 4616/9987] fix checksum for Stacks v2.62 (due to silent re-release without version bump) --- easybuild/easyconfigs/s/Stacks/Stacks-2.62-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-2.62-foss-2022a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-2.62-foss-2022a.eb index 01eb7de7001..9f30e27f06f 100644 --- a/easybuild/easyconfigs/s/Stacks/Stacks-2.62-foss-2022a.eb +++ b/easybuild/easyconfigs/s/Stacks/Stacks-2.62-foss-2022a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://catchenlab.life.illinois.edu/stacks/source/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['01c814588fd72c13494785af49123a6a2c20495c924ed84965fdd4e0da1ab524'] +checksums = ['eee85054b0bf0043c03d4766dfebc00682301b8ba1372fc49e08ecad98d3d13b'] dependencies = [ ('zlib', '1.2.12'), From fc3a4443b892cdb3ed6f3f3181a18ea27e22146b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2022 11:51:21 +0200 Subject: [PATCH 4617/9987] adding easyconfigs: Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb --- ...0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb new file mode 100644 index 00000000000..57dc906ad2e --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.25.0' +local_pt_version = '1.10.0' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('CMake', '3.20.1'), + ('flatbuffers', '2.0.0'), +] +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('CUDA', '11.3.1', '', True), + ('NCCL', '2.10.3', local_cuda_suffix), + ('PyTorch', local_pt_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend + +exts_list = [ + ('cloudpickle', '2.1.0', { + 'checksums': ['bb233e876a58491d9590a676f93c7a5473a08f747d5ab9df7f9ce564b3e7938e'], + }), + ('horovod', version, { + 'checksums': ['bc9fed57b67c1b55259671d2439cdbc93aa897ea6e5da459e11e7556972b2355'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["horovodrun --help"] + +moduleclass = 'tools' From 9bac070ab5d02ed6d6e87b454d97f3a749a74cea Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 26 Aug 2022 18:29:31 +0800 Subject: [PATCH 4618/9987] update suffix of OpenMM with DeepMind patch --- .../f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb index a01ad7554fc..38ff91c345f 100644 --- a/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb @@ -25,7 +25,7 @@ dependencies = [ ('dm-tree', '0.1.6'), ('einops', '0.4.1'), ('colossalai', '0.1.8', versionsuffix), - ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM + ('OpenMM', '7.5.1', '-DeepMind-patch'), ] use_pip = True From d376ef012c7e6728bde1564ae87c46919e2e6875 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 26 Aug 2022 18:30:44 +0800 Subject: [PATCH 4619/9987] update suffix of OpenMM with DeepMind patch --- .../a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb | 2 +- .../a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb index eb6b1ef8c31..05ffdaeea4e 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb @@ -29,7 +29,7 @@ dependencies = [ ('UCX-CUDA', '1.10.0', versionsuffix), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), - ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM + ('OpenMM', '7.5.1', '-DeepMind-patch'), ] # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb index addf0f101a0..bb289e74a36 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a.eb @@ -24,7 +24,7 @@ dependencies = [ ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), ('jax', '0.2.24'), # also provides absl-py - ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM + ('OpenMM', '7.5.1', '-DeepMind-patch'), ] # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb index b3c9ea43636..3307a0c7c2b 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb @@ -29,7 +29,7 @@ dependencies = [ ('UCX-CUDA', '1.10.0', versionsuffix), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), - ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM + ('OpenMM', '7.5.1', '-DeepMind-patch'), ] # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb index 8e1e11da53e..749bb12b07b 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a.eb @@ -24,7 +24,7 @@ dependencies = [ ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), ('jax', '0.3.9'), # also provides absl-py - ('OpenMM', '7.5.1', '_AlphaFold'), # patched OpenMM + ('OpenMM', '7.5.1', '-DeepMind-patch'), ] # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, From 7f6b1a6f60cef80c22b80a75df12bf15e6e480b8 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 26 Aug 2022 11:49:32 +0100 Subject: [PATCH 4620/9987] linting MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit use `cond is True` instead of `cond == True` Co-authored-by: Mikael Öhman --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 47aea7dace7..c2c0788b599 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1433,7 +1433,7 @@ def template_easyconfig_test(self, spec): # if True was used to indicate that dependency should use system toolchain, # then we need to compare the value for the dumped easyconfig more carefully; # see also https://github.com/easybuilders/easybuild-framework/pull/4069 - if orig_dep[3] == True: + if orig_dep[3] is True: self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) else: self.assertEqual(dumped_dep[3], orig_dep[3]) From 9c868f5344711bf3621e77d68584f1a9c5422c91 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 26 Aug 2022 13:05:52 +0200 Subject: [PATCH 4621/9987] adding easyconfigs: AmberTools-22.3-foss-2021b.eb and patches: AmberTools-21_fix_DGESVD_workspace_query.patch, AmberTools-21_fix_incorrect_dvout_call.patch, AmberTools-21_fix_incorrect_mexit_calls.patch, AmberTools-21_fix_more_blas_argument_problems.patch, AmberTools-21_fix_multiple_definition.patch, AmberTools-21_fix_potential_use_before_init.patch, AmberTools-21_fix_rism_argument_mismatch.patch, AmberTools-21_fix_xray_fftpack_arg_mismatch.patch, AmberTools-22_fix_missing_error_check_on_test_run.patch, AmberTools-22_fix_test_missing_cuda_dir.patch --- ...rTools-21_fix_DGESVD_workspace_query.patch | 25 +++++ ...berTools-21_fix_incorrect_dvout_call.patch | 29 ++++++ ...erTools-21_fix_incorrect_mexit_calls.patch | 23 +++++ ...s-21_fix_more_blas_argument_problems.patch | 64 +++++++++++++ ...mberTools-21_fix_multiple_definition.patch | 17 ++++ ...ols-21_fix_potential_use_before_init.patch | 15 +++ ...rTools-21_fix_rism_argument_mismatch.patch | 15 +++ ...ols-21_fix_xray_fftpack_arg_mismatch.patch | 17 ++++ .../AmberTools/AmberTools-22.3-foss-2021b.eb | 93 +++++++++++++++++++ ..._fix_missing_error_check_on_test_run.patch | 27 ++++++ ...erTools-22_fix_test_missing_cuda_dir.patch | 14 +++ 11 files changed, 339 insertions(+) create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_DGESVD_workspace_query.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_dvout_call.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_mexit_calls.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_more_blas_argument_problems.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_multiple_definition.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_potential_use_before_init.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_rism_argument_mismatch.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_xray_fftpack_arg_mismatch.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_missing_error_check_on_test_run.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_test_missing_cuda_dir.patch diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_DGESVD_workspace_query.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_DGESVD_workspace_query.patch new file mode 100644 index 00000000000..444eff527ab --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_DGESVD_workspace_query.patch @@ -0,0 +1,25 @@ +Fix DGESVD workspace query + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/sqm/qm2_scf.F90 b/AmberTools/src/sqm/qm2_scf.F90 +index 6185d93dba..93eb7f60e8 100644 +--- a/AmberTools/src/sqm/qm2_scf.F90 ++++ b/AmberTools/src/sqm/qm2_scf.F90 +@@ -2254,7 +2254,7 @@ SUBROUTINE SvdInvert_SymMat(n,a,ainv,thresh) ! THRESH,ERR + _REAL_ :: S(n) + _REAL_ :: U(n,n) + _REAL_ :: VT(n,n) +- _REAL_ :: twork ++ _REAL_ :: twork(1) + _REAL_,ALLOCATABLE :: WORK(:) + INTEGER :: LWORK + +@@ -2269,7 +2269,7 @@ SUBROUTINE SvdInvert_SymMat(n,a,ainv,thresh) ! THRESH,ERR + LWORK = -1 + CALL DGESVD("A","A",n,n, ainv,n, S,U,n, VT,n, twork,LWORK,my_err) + +- LWORK = NINT(twork) ++ LWORK = NINT(twork(1)) + ALLOCATE( WORK(LWORK) ) + WORK = 0.d0 + diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_dvout_call.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_dvout_call.patch new file mode 100644 index 00000000000..dd926c82c9f --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_dvout_call.patch @@ -0,0 +1,29 @@ +Fix incorrect parameter to dvout + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/arpack/dnaitr.f b/AmberTools/src/arpack/dnaitr.f +index 64b008617f..5d3c268a95 100644 +--- a/AmberTools/src/arpack/dnaitr.f ++++ b/AmberTools/src/arpack/dnaitr.f +@@ -373,7 +373,7 @@ c + if (msglvl .gt. 1) then + call ivout (logfil, 1, [j], ndigit, + & '_naitr: generating Arnoldi vector number') +- call dvout (logfil, 1, rnorm, ndigit, ++ call dvout (logfil, 1, [rnorm], ndigit, + & '_naitr: B-norm of the current residual is') + end if + c +diff --git a/AmberTools/src/arpack/dsaitr.f b/AmberTools/src/arpack/dsaitr.f +index f725e23de9..5a29f153e6 100644 +--- a/AmberTools/src/arpack/dsaitr.f ++++ b/AmberTools/src/arpack/dsaitr.f +@@ -366,7 +366,7 @@ c + if (msglvl .gt. 2) then + call ivout (logfil, 1, [j], ndigit, + & '_saitr: generating Arnoldi vector no.') +- call dvout (logfil, 1, rnorm, ndigit, ++ call dvout (logfil, 1, [rnorm], ndigit, + & '_saitr: B-norm of the current residual =') + end if + c diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_mexit_calls.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_mexit_calls.patch new file mode 100644 index 00000000000..617ce26cc7f --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_mexit_calls.patch @@ -0,0 +1,23 @@ +Fix incorrect parameter to mexit + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/sander/fastwt.F90 b/AmberTools/src/sander/fastwt.F90 +index 9863c12e27..f7e2bf1df4 100644 +--- a/AmberTools/src/sander/fastwt.F90 ++++ b/AmberTools/src/sander/fastwt.F90 +@@ -1058,13 +1058,13 @@ subroutine getwds(igraph ,nres ,ipres ,lbres , & + #ifndef API + write(iout,1001) + #endif +- call mexit(1) ++ call mexit(6,1) + end if + else if (abs(roh1-roh2) > small) then + #ifndef API + write(iout,1002) + #endif +- call mexit(1) ++ call mexit(6,1) + else + roh = roh1 + end if diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_more_blas_argument_problems.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_more_blas_argument_problems.patch new file mode 100644 index 00000000000..3298fccaf8e --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_more_blas_argument_problems.patch @@ -0,0 +1,64 @@ +Fix some blas argument problems with newer GCC vewrsions. + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/rism/amber_rism_interface.F90 b/AmberTools/src/rism/amber_rism_interface.F90 +index 7d84de1b7f..2c2a2fa389 100644 +--- a/AmberTools/src/rism/amber_rism_interface.F90 ++++ b/AmberTools/src/rism/amber_rism_interface.F90 +@@ -3159,9 +3159,9 @@ contains + ! Outputting entropy map. + if (len_trim(entropyfile) /= 0 .and. rismprm%entropicDecomp == 1 .and. & + rism3d_canCalc_DT(rism_3d)) then +- call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map, 1, excessChemicalPotential_map, 1) ++ call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map(1,1,1), 1, excessChemicalPotential_map, 1) + call DAXPY(this%grid%totalLocalPointsR*this%solvent%numAtomTypes, -1d0, & +- solvationEnergy_V_map, 1, excessChemicalPotential_V_map, 1) ++ solvationEnergy_V_map(1,1,1,1), 1, excessChemicalPotential_V_map, 1) + call writeThermo(writeVolume,entropyfile, suffix, excessChemicalPotential_map,& + excessChemicalPotential_V_map) + end if +@@ -3200,9 +3200,9 @@ contains + end if + ! Outputting entropy map. + if (len_trim(entropyPCPLUSfile) /= 0) then +- call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map, 1, excessChemicalPotential_map, 1) ++ call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map(1,1,1), 1, excessChemicalPotential_map, 1) + call DAXPY(this%grid%totalLocalPointsR*this%solvent%numAtomTypes, -1d0, & +- solvationEnergy_V_map, 1, excessChemicalPotential_V_map, 1) ++ solvationEnergy_V_map(1,1,1,1), 1, excessChemicalPotential_V_map, 1) + call writeVolume(trim(entropyPCPLUSfile)//suffix, excessChemicalPotential_map, this%grid, & + this%solute, mpirank, mpisize, mpicomm) + end if +@@ -3247,9 +3247,9 @@ contains + end if + ! Outputting entropy map. + if (len_trim(entropyUCfile) /= 0) then +- call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map, 1, excessChemicalPotential_map, 1) ++ call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map(1,1,1), 1, excessChemicalPotential_map, 1) + call DAXPY(this%grid%totalLocalPointsR*this%solvent%numAtomTypes, -1d0, & +- solvationEnergy_V_map, 1, excessChemicalPotential_V_map, 1) ++ solvationEnergy_V_map(1,1,1,1), 1, excessChemicalPotential_V_map, 1) + call writeVolume(trim(entropyUCfile)//suffix, excessChemicalPotential_map, this%grid, & + this%solute, mpirank, mpisize, mpicomm) + end if +@@ -3299,9 +3299,9 @@ contains + ! Outputting entropy map. + if (len_trim(entropyGFfile) /= 0 .and. rismprm%entropicDecomp == 1 .and. & + rism3d_canCalc_DT(rism_3d)) then +- call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map, 1, excessChemicalPotential_map, 1) ++ call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map(1,1,1), 1, excessChemicalPotential_map, 1) + call DAXPY(this%grid%totalLocalPointsR*this%solvent%numAtomTypes, -1d0, & +- solvationEnergy_V_map, 1, excessChemicalPotential_V_map, 1) ++ solvationEnergy_V_map(1,1,1,1), 1, excessChemicalPotential_V_map, 1) + call writeThermo(writeVolume,entropyGFfile, suffix, excessChemicalPotential_map, & + excessChemicalPotential_V_map) + end if +@@ -3415,7 +3415,7 @@ contains + excessChemicalPotential_V_map,1,solventEntropy_V_map,1) + + call DAXPY(this%grid%totalLocalPointsR*this%solvent%numAtomTypes, -1d0, & +- solvationEnergy_V_map, 1, solventEntropy_V_map, 1) ++ solvationEnergy_V_map(1,1,1,1), 1, solventEntropy_V_map, 1) + call writeVolume(trim(entropyfile)//'.mol'//suffix, & + solvententropy_V_map(:, :, :, center_site), this%grid, & + this%solute, mpirank, mpisize, mpicomm) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_multiple_definition.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_multiple_definition.patch new file mode 100644 index 00000000000..b1d06ec5deb --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_multiple_definition.patch @@ -0,0 +1,17 @@ +Fix multiple definition problem. +Not seen by Amber devs so something else might be the real problem. + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/cifparse/cifparse.h b/AmberTools/src/cifparse/cifparse.h +index 3b1f3bca57..4577abf458 100644 +--- a/AmberTools/src/cifparse/cifparse.h ++++ b/AmberTools/src/cifparse/cifparse.h +@@ -102,7 +102,7 @@ int ndb_cif_get_category_id(char*, char*); + + + #ifdef CIF_GLOBAL +- FILE *cifpin; ++ extern FILE *cifpin; + char TempKeyword[MxNameLen+1], TempValue[MAXVALUELENGTH+1]; + NdbCifDatablocksFormat cifFiles; + int lineNo; diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_potential_use_before_init.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_potential_use_before_init.patch new file mode 100644 index 00000000000..d37b0548614 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_potential_use_before_init.patch @@ -0,0 +1,15 @@ +Fix potential use before init. + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/nmr_aux/prepare_input/makeDIST_RST.c b/AmberTools/src/nmr_aux/prepare_input/makeDIST_RST.c +index a455a8bc15..3d6f5baec6 100644 +--- a/AmberTools/src/nmr_aux/prepare_input/makeDIST_RST.c ++++ b/AmberTools/src/nmr_aux/prepare_input/makeDIST_RST.c +@@ -714,6 +714,7 @@ static int read_maplib( FILE *fp ) + printf( "%s: begin;\n", module ); + #endif + nm=0; ++ npseudo=0; + while ( getline ) { + lineno++; + diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_rism_argument_mismatch.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_rism_argument_mismatch.patch new file mode 100644 index 00000000000..277e402242c --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_rism_argument_mismatch.patch @@ -0,0 +1,15 @@ +Fix rism argument mismatch problem with newer GCC versions. + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/rism/CMakeLists.txt b/AmberTools/src/rism/CMakeLists.txt +index d554714923..96a8367693 100644 +--- a/AmberTools/src/rism/CMakeLists.txt ++++ b/AmberTools/src/rism/CMakeLists.txt +@@ -127,6 +127,7 @@ install(TARGETS rism1d rism3d.thermo rism3d.orave DESTINATION ${BINDIR}) + # MPI version + # -------------------------------------------------------------------- + if(MPI) ++ add_compile_options(-fallow-argument-mismatch) + make_mpi_version(rism rism_mpi LANGUAGES Fortran SWAP_SOURCES ${RISM_LIB_SOURCES} TO ${RISM_MPI_SOURCES} INSTALL) + config_module_dirs(rism_mpi ${RISMLIB_MPI_MOD_DIR} ${AMBER_COMMON_MOD_DIR}) + target_link_libraries(rism_mpi fftw_mpi) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_xray_fftpack_arg_mismatch.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_xray_fftpack_arg_mismatch.patch new file mode 100644 index 00000000000..5bfb50d13dd --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_xray_fftpack_arg_mismatch.patch @@ -0,0 +1,17 @@ +Fix xray argument mismatch problem with newer GCC versions. + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/sander/CMakeLists.txt b/AmberTools/src/sander/CMakeLists.txt +index 3bd5e182ac..79ba58cc6f 100644 +--- a/AmberTools/src/sander/CMakeLists.txt ++++ b/AmberTools/src/sander/CMakeLists.txt +@@ -241,6 +241,9 @@ apply_optimization_declarations(${ALL_FORTRAN_SOURCES}) + # reaxff-puremd QMMM extern interface module requires F2003 standard or later + set_source_files_properties(qm2_extern_reaxff_puremd_module.F90 PROPERTIES LANGUAGE Fortran COMPILE_FLAGS -std=f2003) + ++# xray_fftpack has argument mismatch problems ++set_source_files_properties(xray_fftpack.F90 PROPERTIES LANGUAGE Fortran COMPILE_FLAGS -fallow-argument-mismatch) ++ + set_property(SOURCE ${PLUMED_SOURCE} PROPERTY COMPILE_FLAGS ${OPT_CFLAGS_SPC}) + + if(plumed_ENABLED) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb new file mode 100644 index 00000000000..c7abe5a8611 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb @@ -0,0 +1,93 @@ +easyblock = 'EB_Amber' + +name = 'AmberTools' +local_ambertools_ver = 22 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (3, 0) # (AmberTools, Amber) +version = '%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'https://ambermd.org/' +description = """AmberTools consists of several independently developed packages that work well by themselves, + and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, + with either explicit water or generalized Born solvent models.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +# download requires registration +#local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium' +#source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % local_ambertools_ver] +#sources = [{ +# 'download_filename': local_download_credentials, +# 'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, +#}] +sources = ['AmberTools%s.tar.bz2' % local_ambertools_ver] +patches = [ + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + 'AmberTools-21_CMake-FlexiBLAS.patch', + 'AmberTools-21_fix_DGESVD_workspace_query.patch', + 'AmberTools-21_fix_incorrect_dvout_call.patch', + 'AmberTools-21_fix_incorrect_mexit_calls.patch', + 'AmberTools-21_fix_more_blas_argument_problems.patch', + 'AmberTools-21_fix_multiple_definition.patch', + 'AmberTools-21_fix_potential_use_before_init.patch', + 'AmberTools-21_fix_rism_argument_mismatch.patch', + 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', + 'AmberTools-22_fix_test_missing_cuda_dir.patch', + 'AmberTools-22_fix_missing_error_check_on_test_run.patch', +] +checksums = [ + '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools22.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch + # AmberTools-22_fix_missing_error_check_on_test_run.patch + 'a86eee60bd65c16a849469e303cb99dfc207cbadd2ae9e70b9ff580ced785475', +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('pkg-config', '0.29.2'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Perl', '5.34.0'), + ('Boost', '1.77.0'), + ('libreadline', '8.1'), + ('matplotlib', '3.4.3'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.3'), + ('Tkinter', '%(pyver)s'), + ('X11', '20210802'), +] + +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_missing_error_check_on_test_run.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_missing_error_check_on_test_run.patch new file mode 100644 index 00000000000..042fddaadff --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_missing_error_check_on_test_run.patch @@ -0,0 +1,27 @@ +Add missing "|| goto error" for test/pmemdTI/softcore/tishake2vsite/Run.tishake2vsite* + +Åke Sandgren, 2022-08-26 +diff -ru amber22_src.orig/test/pmemdTI/softcore/tishake2vsite/Run.tishake2vsite amber22_src/test/pmemdTI/softcore/tishake2vsite/Run.tishake2vsite +--- amber22_src.orig/test/pmemdTI/softcore/tishake2vsite/Run.tishake2vsite 2022-04-09 03:11:47.000000000 +0200 ++++ amber22_src/test/pmemdTI/softcore/tishake2vsite/Run.tishake2vsite 2022-08-26 09:27:51.875733539 +0200 +@@ -33,7 +33,7 @@ + / + EOF + +-$DO_PARALLEL $TESTsander -O -i mdin.0 -o out.0 -p solvated_prmtop -c solvated_rst -r restrt.0 ++$DO_PARALLEL $TESTsander -O -i mdin.0 -o out.0 -p solvated_prmtop -c solvated_rst -r restrt.0 || goto error + + ../../../dacdif out.0.save out.0 + +diff -ru amber22_src.orig/test/pmemdTI/softcore/tishake2vsite/Run.tishake2vsite_vacuum amber22_src/test/pmemdTI/softcore/tishake2vsite/Run.tishake2vsite_vacuum +--- amber22_src.orig/test/pmemdTI/softcore/tishake2vsite/Run.tishake2vsite_vacuum 2022-04-09 03:11:47.000000000 +0200 ++++ amber22_src/test/pmemdTI/softcore/tishake2vsite/Run.tishake2vsite_vacuum 2022-08-26 09:28:11.971587948 +0200 +@@ -34,7 +34,7 @@ + / + EOF + +-$DO_PARALLEL $TESTsander -O -i mdin.0 -o out2.0 -p prmtop_vacuum -c rst_vacuum -r restrt2.0 ++$DO_PARALLEL $TESTsander -O -i mdin.0 -o out2.0 -p prmtop_vacuum -c rst_vacuum -r restrt2.0 || goto error + + ../../../dacdif out2.0.save out2.0 + diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_test_missing_cuda_dir.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_test_missing_cuda_dir.patch new file mode 100644 index 00000000000..6ebca4c1459 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_test_missing_cuda_dir.patch @@ -0,0 +1,14 @@ +Make sure test_amber_clean.sh dosen't try to cd into a possibly missing directory. + +Åke Sandgren, 2022-08-26 +diff -ru amber22_src.orig/test/test_amber_clean.sh amber22_src/test/test_amber_clean.sh +--- amber22_src.orig/test/test_amber_clean.sh 2021-05-28 16:11:51.000000000 +0200 ++++ amber22_src/test/test_amber_clean.sh 2022-08-26 09:20:58.470586829 +0200 +@@ -1273,4 +1273,6 @@ + echo $delete_list | xargs /bin/rm -f + + # Remove cuda remd test output +-cd cuda/remd && make clean && cd ../.. ++if [ -d "cuda/remd" ]; then ++ cd cuda/remd && make clean && cd ../.. ++fi From 6a656823f7e80d5027eba5d3f4212a3160ea82f6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 26 Aug 2022 13:09:49 +0200 Subject: [PATCH 4622/9987] reinstate auto download for the ambertools source tar file --- .../a/AmberTools/AmberTools-22.3-foss-2021b.eb | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb index c7abe5a8611..a7fbe6089cc 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-22.3-foss-2021b.eb @@ -15,13 +15,12 @@ toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'usempi': True} # download requires registration -#local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium' -#source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % local_ambertools_ver] -#sources = [{ -# 'download_filename': local_download_credentials, -# 'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, -#}] -sources = ['AmberTools%s.tar.bz2' % local_ambertools_ver] +local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium' +source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % local_ambertools_ver] +sources = [{ + 'download_filename': local_download_credentials, + 'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, +}] patches = [ 'AmberTools-20_cmake-locate-netcdf.patch', 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', From 89a87a5aff61fdea133b8b5465320b4f6112096e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Aug 2022 15:38:52 +0200 Subject: [PATCH 4623/9987] adding easyconfigs: RDKit-2022.03.5-foss-2021b.eb --- .../r/RDKit/RDKit-2022.03.5-foss-2021b.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/r/RDKit/RDKit-2022.03.5-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2022.03.5-foss-2021b.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2022.03.5-foss-2021b.eb new file mode 100644 index 00000000000..f551d9ac7c1 --- /dev/null +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2022.03.5-foss-2021b.eb @@ -0,0 +1,77 @@ +easyblock = 'CMakeMake' + +name = 'RDKit' +version = '2022.03.5' + +homepage = 'https://www.rdkit.org' +description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python." + +toolchain = {'name': 'foss', 'version': '2021b'} +# avoid failing tests on skylake CPUs. comment out this line when building on CPUs that don't support AVX2 +# see also: https://github.com/rdkit/rdkit/issues/1674 +toolchainopts = {'optarch': 'mavx2', 'cstd': 'c++11'} + +source_urls = ['https://github.com/rdkit/rdkit/archive/'] +sources = ['Release_%s.tar.gz' % version.replace('.', '_')] +patches = [ + 'RDKit-2021.03.4_skip-broken-test.patch', +] +checksums = [ + '38e6fb9f063b6132310f17e654f2c4350876f9164b0a17b49fe3df7d0555a744', # Release_2022_03_5.tar.gz + '45869e01461b66e42c9305f5e8a65f696417e4777c2da60ef81d1e26e57d1b2e', # RDKit-2021.03.4_skip-broken-test.patch +] + +# Dependencies varies from version to version +# https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source +builddependencies = [ + ('CMake', '3.22.1'), + ('Eigen', '3.4.0'), + ('pkgconf', '1.8.0'), +] +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('SQLite', '3.36'), + ('matplotlib', '3.4.3'), + ('Pillow', '8.3.2'), + ('Boost.Python', '1.77.0'), + ('cairo', '1.16.0'), +] + +separate_build_dir = True + +configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " +configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " +configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " + +# merge source directory into build directory in order to run the tests +buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' +buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' + +# Specify path for libraries so that they are found during the tests when the module is built with --rpath flag. +buildopts += 'export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:${LD_LIBRARY_PATH} && ' + +# 'ctest' allows to pass additional arguments opposed to 'make test' +buildopts += 'ctest --output-on-failure' + +local_libs = ['Alignment', 'Catalogs', 'ChemicalFeatures', 'ChemReactions', 'ChemTransforms', 'coordgen', 'DataStructs', + 'Depictor', 'Descriptors', 'DistGeometry', 'DistGeomHelpers', 'EigenSolvers', 'FileParsers', + 'FilterCatalog', 'Fingerprints', 'FMCS', 'ForceFieldHelpers', 'ForceField', 'FragCatalog', 'GraphMol', + 'hc', 'InfoTheory', 'maeparser', 'MMPA', 'MolAlign', 'MolCatalog', 'MolChemicalFeatures', 'MolDraw2D', + 'MolHash', 'MolInterchange', 'MolStandardize', 'MolTransforms', 'Optimizer', 'PartialCharges', 'RDBoost', + 'RDGeneral', 'RDGeometryLib', 'RDStreams', 'ReducedGraphs', 'RGroupDecomposition', 'RingDecomposerLib', + 'ScaffoldNetwork', 'ShapeHelpers', 'SimDivPickers', 'SLNParse', 'SmilesParse', 'Subgraphs', + 'SubstructLibrary', 'SubstructMatch', 'Trajectory'] + +sanity_check_paths = { + 'files': ['lib/libRDKit%s.%s' % (x, SHLIB_EXT) for x in local_libs], + 'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'], +} + +sanity_check_commands = [ + "python -c 'import rdkit.rdBase'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From 4911ff5baebce0a235328cd3597c1cc8d6f84e93 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 26 Aug 2022 16:45:20 +0200 Subject: [PATCH 4624/9987] Add VCFTools --- .../v/VCFtools/VCFtools-0.1.16-GCC-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.3.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.3.0.eb new file mode 100644 index 00000000000..0af278f65f5 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('HTSlib', '1.15.1'), + ('zlib', '1.2.12'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' From 62a860aeb29b07e803253d7984c9c72087f0bed6 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Aug 2022 17:45:55 +0100 Subject: [PATCH 4625/9987] Moduleclass changed to data --- .../a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb index 60bc634a417..03d791038bf 100644 --- a/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/ADIOS/ADIOS-20210804-foss-2020a-Python-3.8.2.eb @@ -75,4 +75,4 @@ modextrapaths = { 'PYTHONPATH': 'lib/python', } -moduleclass = 'phys' +moduleclass = 'data' From c2b5a03246cddb3bd2cd8150366659202896368e Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Aug 2022 18:07:41 +0100 Subject: [PATCH 4626/9987] Surplus binutils removed --- easybuild/easyconfigs/m/muMerge/muMerge-1.1.0-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/muMerge/muMerge-1.1.0-foss-2022a.eb b/easybuild/easyconfigs/m/muMerge/muMerge-1.1.0-foss-2022a.eb index c8507f97777..c94f9cb9fc2 100644 --- a/easybuild/easyconfigs/m/muMerge/muMerge-1.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/m/muMerge/muMerge-1.1.0-foss-2022a.eb @@ -10,8 +10,6 @@ description = """muMerge is a tool for combining bed regions from multiple bed f toolchain = {'name': 'foss', 'version': '2022a'} -builddependencies = [('binutils', '2.38')] - dependencies = [ ('Python', '3.10.4'), ('matplotlib', '3.5.2'), From 243fdaf94701d212ed6108bfb82794ddfd149fce Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Aug 2022 18:14:37 +0100 Subject: [PATCH 4627/9987] Autotools removed, URL expanded --- easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb index 30242c7b7e0..5249a3a5bdf 100644 --- a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb @@ -15,7 +15,7 @@ other programs.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://dist.schmorp.de/libev'] +source_urls = ['http://dist.schmorp.de/libev/Attic'] sources = ['%(name)s-%(version)s.tar.gz'] checksums = [ @@ -24,9 +24,9 @@ checksums = [ builddependencies = [ ('binutils', '2.37'), - ('Autotools', '20210726'), ] +# No problem to build in parallel but one core is equally fast. parallel = 1 sanity_check_paths = { From 24f102a24350f2ff475a172415f724a1c2659c99 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Aug 2022 18:24:03 +0100 Subject: [PATCH 4628/9987] Python-bare added, surplus build-dependencies removed, sanity check command added --- .../easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb index 17dc25fdbc1..18012521272 100644 --- a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb @@ -14,9 +14,7 @@ checksums = ['ac6ce1e1fbd4d0254c4ddb9d37f1fa99dec83619c1253328155206b896210d4c'] builddependencies = [ ('binutils', '2.37'), - ('libtool', '2.4.6'), - ('Autotools', '20210726'), - ('CMake', '3.22.1'), + ('Python', '3.9.6', '-bare'), ] dependencies = [ @@ -24,6 +22,8 @@ dependencies = [ ('libunistring', '1.0'), ] +sanity_check_commands = [('psl --version')] + sanity_check_paths = { 'files': ['bin/psl', 'lib/libpsl.a'], 'dirs': [] From f92d3ed0857f1a1cdd12347b33bcbcb7540e8e42 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Aug 2022 18:31:22 +0100 Subject: [PATCH 4629/9987] Module class changed to devel --- easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb index a8a94ef0e0a..1f8a7ab39b5 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb @@ -37,4 +37,4 @@ sanity_check_paths = { runtest = 'check' -moduleclass = 'devel' +moduleclass = 'data' diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb index 492c8e9f8a6..8f432120bd6 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb @@ -37,4 +37,4 @@ sanity_check_paths = { runtest = 'check' -moduleclass = 'devel' +moduleclass = 'data' From 01a3860accf8968a6cc0a384947c3a12745ace01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Aug 2022 14:52:04 +0200 Subject: [PATCH 4630/9987] trivial style fixes in BigDFT easyconfig + rename patch to include software version and start with BigDFT- --- .../b/BigDFT/BigDFT-1.9.1-foss-2021b.eb | 91 ++++++++----------- ...patch => BigDFT-1.9.1_fix-index-bug.patch} | 0 2 files changed, 37 insertions(+), 54 deletions(-) rename easybuild/easyconfigs/b/BigDFT/{bigdft_suite_index_bug.patch => BigDFT-1.9.1_fix-index-bug.patch} (100%) diff --git a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb index c871bf40a87..80e61b193c7 100644 --- a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb @@ -1,73 +1,60 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Denis Kristak -easyblock = "Binary" +easyblock = 'Binary' -name = "BigDFT" -version = "1.9.1" +name = 'BigDFT' +version = '1.9.1' -homepage = "https://gitlab.com/l_sim/bigdft-suite" -description = """ -BigDFT: electronic structure calculation based on Daubechies wavelets. -bigdft-suite is a set of different packages to run bigdft. -""" +homepage = 'https://gitlab.com/l_sim/bigdft-suite' +description = """BigDFT: electronic structure calculation based on Daubechies wavelets. +bigdft-suite is a set of different packages to run bigdft.""" -toolchain = {"name": "foss", "version": "2021b"} +toolchain = {'name': 'foss', 'version': '2021b'} +local_extra_flags = '-fallow-argument-mismatch' toolchainopts = { - "usempi": True, - "extra_fflags": "-fallow-argument-mismatch", - "extra_fcflags": "-fallow-argument-mismatch", - "extra_f90flags": "-fallow-argument-mismatch", + 'usempi': True, + 'extra_fflags': local_extra_flags, 'extra_fcflags': local_extra_flags, 'extra_f90flags': local_extra_flags, } -source_urls = ["https://gitlab.com/l_sim/bigdft-suite/-/archive/%(version)s/"] -sources = ["bigdft-suite-%(version)s.tar.gz"] -patches = ["bigdft_suite_index_bug.patch"] +source_urls = ['https://gitlab.com/l_sim/bigdft-suite/-/archive/%(version)s/'] +sources = ['bigdft-suite-%(version)s.tar.gz'] +patches = ['BigDFT-1.9.1_fix-index-bug.patch'] checksums = [ '3c334da26d2a201b572579fc1a7f8caad1cbf971e848a3e10d83bc4dc8c82e41', # bigdft-suite-1.9.1.tar.gz - 'df887c4df1eb3aa4bfe70e52c405525079bcfa54ac26ec5b8f2511fb6204d179', # bigdft_suite_index_bug.patch + 'df887c4df1eb3aa4bfe70e52c405525079bcfa54ac26ec5b8f2511fb6204d179', # BigDFT-1.9.1_fix-index-bug.patch ] builddependencies = [ - ("CMake", "3.21.1"), + ('CMake', '3.21.1'), ] dependencies = [ - ("Autoconf", "2.71"), - ("Python", "3.9.6"), - ("OpenCV", "4.5.5", "-contrib"), - ("XZ", "5.2.5"), + ('Autoconf', '2.71'), + ('Python', '3.9.6'), + ('OpenCV', '4.5.5', '-contrib'), + ('XZ', '5.2.5'), ] extract_sources = True -local_configopts = " ".join([ - 'CC=\\"$MPICC\\" FC=\\"$MPIFC\\" --enable-mpi', - 'FCFLAGS=\\"$CPPFLAGS $FCFLAGS -std=legacy\\"', - 'FFLAGS=\\"$CPPFLAGS $FFLAGS -std=legacy\\"', - 'F90FLAGS=\\"$CPPFLAGS $F90FLAGS -std=legacy\\"', - '--with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS\\"', - '--with-yaml-path=\\"$EBROOTLIBYAML\\"', -]) +local_install_opts = '--enable-mpi --with-yaml-path=\\"$EBROOTLIBYAML\\" ' +local_install_opts += '--with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS\\" ' +local_install_opts += 'CC=\\"$MPICC\\" FC=\\"$MPIFC\\" ' +local_install_opts += 'FCFLAGS=\\"$CPPFLAGS $FCFLAGS -fallow-argument-mismatch -std=legacy\\" ' +local_install_opts += 'FFLAGS=\\"$CPPFLAGS $FFLAGS -fallow-argument-mismatch -std=legacy\\" ' +local_install_opts += 'F90FLAGS=\\"$CPPFLAGS $F90FLAGS -fallow-argument-mismatch -std=legacy\\" ' -install_cmd = " && ".join([ - "mkdir bigdft_builddir", - "cd bigdft_builddir", - "python3 ../Installer.py build bigdft -y -v -c %s" % local_configopts, - "cp -r install/* %(installdir)s", -]) +install_cmd = "mkdir bigdft_builddir && cd bigdft_builddir && " +install_cmd += "python3 ../Installer.py build bigdft -y -v -c %s && " % local_install_opts +install_cmd += "cp -a install/* %(installdir)s" -modextrapaths = {"PYTHONPATH": ["lib/python%(pyshortver)s/site-packages"]} +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} sanity_check_paths = { - "files": [ - "include/futile.mod", - "include/futile.h", - "bin/bigdft", - "bin/bigdftvars.sh", - "lib/python3.9/site-packages/BigDFT/Systems.py", - "lib64/libbigdft-1.a", - ], - "dirs": [], + 'files': ['bin/bigdft', 'bin/bigdftvars.sh', 'include/futile.mod', 'include/futile.h', + 'lib/python%(pyshortver)s/site-packages/BigDFT/Systems.py', + 'lib/libbigdft-1.a'], + 'dirs': [], } local_test_script = """ @@ -81,13 +68,9 @@ with XYZReader("N2") as ifile: print(N2.get_posinp()) """ -local_sanity_cmd = " && ".join([ - "tmpdir=$(mktemp -d)", - "echo '" + local_test_script + "' > " + "$tmpdir/bigdft_test.py", - "python $tmpdir/bigdft_test.py", - "rm -r $tmpdir", -]) +local_sanity_cmd = "tmpdir=$(mktemp -d) && echo '" + local_test_script + "' > " + "$tmpdir/bigdft_test.py && " +local_sanity_cmd += "python $tmpdir/bigdft_test.py && rm -r $tmpdir" -sanity_check_commands = [(local_sanity_cmd)] +sanity_check_commands = [local_sanity_cmd] -moduleclass = "phys" +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BigDFT/bigdft_suite_index_bug.patch b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1_fix-index-bug.patch similarity index 100% rename from easybuild/easyconfigs/b/BigDFT/bigdft_suite_index_bug.patch rename to easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1_fix-index-bug.patch From 8ed0bdc7b69e96bc0cc42fc33cf559c087be7203 Mon Sep 17 00:00:00 2001 From: fizwit Date: Sat, 27 Aug 2022 07:31:23 -0700 Subject: [PATCH 4631/9987] {math}[foss/2020b]PyStan v2.19.1.1 --- .../p/PyStan/PyStan-2.19.1.1-foss-2020b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb new file mode 100644 index 00000000000..67938571cc9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'PyStan' +version = '2.19.1.1' + +homepage = 'https://github.com/stan-dev/pystan' +description = """Python interface to Stan, a package for Bayesian inference + using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fa8bad8dbc0da22bbe6f36af56c9abbfcf10f92df8ce627d59a36bd8d25eb038'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From b07f778a917ff5f910c375997eac681bbd3d5a85 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 Aug 2022 16:32:55 +0200 Subject: [PATCH 4632/9987] adding easyconfigs: pyGenomeTracks-3.7-foss-2021b.eb --- .../pyGenomeTracks-3.7-foss-2021b.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.7-foss-2021b.eb b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.7-foss-2021b.eb new file mode 100644 index 00000000000..f5d7484ca9f --- /dev/null +++ b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.7-foss-2021b.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'pyGenomeTracks' +version = '3.7' + +homepage = 'https://pygenometracks.readthedocs.io' +description = "pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('bx-python', '0.8.13'), + ('pybedtools', '0.8.2'), + ('pyBigWig', '0.3.18'), + ('pyfaidx', '0.7.0'), + ('Pysam', '0.17.0'), + ('tqdm', '4.62.3'), + ('PyTables', '3.6.1'), + ('h5py', '3.6.0'), + ('PyYAML', '5.4.1'), +] + +use_pip = True + +exts_list = [ + ('argcomplete', '2.0.0', { + 'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'], + }), + ('argh', '0.26.2', { + 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], + }), + ('gffutils', '0.11.0', { + 'checksums': ['4593bdf8bda2501b8e0c54cd3366fdaba04b211c86f43c0029e65869d15ec769'], + }), + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('cytoolz', '0.10.1', { + 'checksums': ['82f5bba81d73a5a6b06f2a3553ff9003d865952fcb32e1df192378dd944d8a5c'], + }), + ('dill', '0.3.5.1', { + 'checksums': ['d75e41f3eff1eee599d738e76ba8f4ad98ea229db8b085318aa2b3333a208c86'], + }), + ('multiprocess', '0.70.13', { + 'checksums': ['2e096dd618a84d15aa369a9cf6695815e5539f853dc8fa4f4b9153b11b1d0b32'], + }), + ('pypairix', '0.3.7', { + 'checksums': ['c1b47c05f92b5be628923c60a27344503ddeba5d8f35a3752d646271d38e0525'], + }), + ('cooler', '0.8.11', { + 'checksums': ['367b58efa87647d31acf45e67d852aaee3273845b6e7507ae644d6a86f7526c5'], + }), + ('HiCMatrix', '15', { + 'checksums': ['74e49e7ef2b1ac555333515b8fda67b3ad49ffbdbc92f9e09c31647cbfac00bd'], + }), + (name, version, { + 'checksums': ['600bb836e78a50408d702140ac68248f8442c54201fe07e780e7b6b3e35e62df'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyGenomeTracks'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyGenomeTracks --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 66fdcf9d0d041b23a55096d3e0394062cbefe55d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 28 Aug 2022 16:11:36 +0100 Subject: [PATCH 4633/9987] fix libsanitzer for glibc 2.36 to build GCCcore 11.3.0 --- .../easyconfigs/g/GCCcore/GCCcore-11.3.0.eb | 2 + ...CCcore-11_fix-libsanitzer-glibc-2.36.patch | 41 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-11_fix-libsanitzer-glibc-2.36.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb index 878c2e4b12a..5df5d559914 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCCcore-11.3.0_fuse-ld-mold.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', ] checksums = [ '98438e6cc7294298b474cf0da7655d9a8c8b796421bb0210531c294a950374ed', # gcc-11.3.0.tar.gz @@ -48,6 +49,7 @@ checksums = [ '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch 'bba64714f8b84ad58b3b43c0d21b4ffc298274ae699f514ed2934f002146d840', # GCCcore-11.3.0_fuse-ld-mold.patch + '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60', # GCCcore-11_fix-libsanitzer-glibc-2.36.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11_fix-libsanitzer-glibc-2.36.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-11_fix-libsanitzer-glibc-2.36.patch new file mode 100644 index 00000000000..466910c3970 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11_fix-libsanitzer-glibc-2.36.patch @@ -0,0 +1,41 @@ +From 2701442d0cf6292f6624443c15813d6d1a3562fe Mon Sep 17 00:00:00 2001 +From: Martin Liska +Date: Mon, 11 Jul 2022 22:03:14 +0200 +Subject: [PATCH] libsanitizer: cherry-pick 9cf13067cb5088626ba7 from upstream + +9cf13067cb5088626ba7ee1ec4c42ec59c7995a0 [sanitizer] Remove #include to resolve fsconfig_command/mount_attr conflict with glibc 2.36 +--- + .../sanitizer_platform_limits_posix.cpp | 10 ++++++---- + 1 file changed, 6 insertions(+), 4 deletions(-) + +diff --git a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp +index 8ed3e92d270..97fd07acf9d 100644 +--- a/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp ++++ b/libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp +@@ -73,7 +73,9 @@ + #include + #include + #include ++#if SANITIZER_ANDROID + #include ++#endif + #include + #include + #include +@@ -869,10 +871,10 @@ unsigned struct_ElfW_Phdr_sz = sizeof(Elf_Phdr); + unsigned IOCTL_EVIOCGPROP = IOCTL_NOT_PRESENT; + unsigned IOCTL_EVIOCSKEYCODE_V2 = IOCTL_NOT_PRESENT; + #endif +- unsigned IOCTL_FS_IOC_GETFLAGS = FS_IOC_GETFLAGS; +- unsigned IOCTL_FS_IOC_GETVERSION = FS_IOC_GETVERSION; +- unsigned IOCTL_FS_IOC_SETFLAGS = FS_IOC_SETFLAGS; +- unsigned IOCTL_FS_IOC_SETVERSION = FS_IOC_SETVERSION; ++ unsigned IOCTL_FS_IOC_GETFLAGS = _IOR('f', 1, long); ++ unsigned IOCTL_FS_IOC_GETVERSION = _IOR('v', 1, long); ++ unsigned IOCTL_FS_IOC_SETFLAGS = _IOW('f', 2, long); ++ unsigned IOCTL_FS_IOC_SETVERSION = _IOW('v', 2, long); + unsigned IOCTL_GIO_CMAP = GIO_CMAP; + unsigned IOCTL_GIO_FONT = GIO_FONT; + unsigned IOCTL_GIO_UNIMAP = GIO_UNIMAP; +-- +2.31.1 From 342d60093581f4404b3fccf52e50da66acb0c384 Mon Sep 17 00:00:00 2001 From: am2455 Date: Sun, 28 Aug 2022 21:36:58 -0400 Subject: [PATCH 4634/9987] adding easyconfigs: cURL-7.84.0-GCCcore-12.1.0.eb --- .../c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb new file mode 100644 index 00000000000..fd3ce3f5ac0 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.84.0' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +#checksums = ['c0e64302a33d2fb79e0fc4e674260a22941e92ee2f11b894bf94d32b8f5531af'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', True), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' From aaa0f6b20879bae55add16bbe7064e4cc858d3b8 Mon Sep 17 00:00:00 2001 From: Abhishek Mukherjee Date: Mon, 29 Aug 2022 00:39:38 -0400 Subject: [PATCH 4635/9987] updated extensions --- .../p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 159 +++++++++--------- 1 file changed, 80 insertions(+), 79 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index dfcdfe0ee66..1216443c302 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -103,10 +103,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], }), - ('File::ShareDir::Install', '0.13', { + ('File::ShareDir::Install', '0.14', { 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['45befdf0d95cbefe7c25a1daf293d85f780d6d2576146546e6828aad26e580f9'], + 'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'] }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', @@ -153,15 +153,15 @@ exts_list = [ 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL/'], 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], }), - ('DateTime::Locale', '1.35', { + ('DateTime::Locale', '1.36', { 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['6104a15626331b521746a8ab30c1d978420b3347c235ee52c2e6de5ce2113aac'], + 'checksums': ['90a8243f2b2d4068019c65178600e76e03f5b478cb41d18c8c81cdf0d481f0a4'] }), - ('DateTime::TimeZone', '2.52', { + ('DateTime::TimeZone', '2.53', { 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['8bc5c42082874b0e9c9ef949fa19035ac9b6904ebcda1931aa2d8a13f3950d8f'], + 'checksums': ['4f6e9ff86892a52334bfb8dfa74ebea6adb8afd04fefcba8ae52fc054c4c15b3'] }), ('Test::Requires', '0.11', { 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', @@ -198,10 +198,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], 'checksums': ['63b1f7842cd42d9b538d1e34e0330de5ff1559e4c2737342506418276f646527'], }), - ('Exporter::Tiny', '1.002002', { + ('Exporter::Tiny', '1.004000', { 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], - 'checksums': ['00f0b95716b18157132c6c118ded8ba31392563d19e490433e9a65382e707101'], + 'checksums': ['7f7b3b4fbe923355317243cd434d2319ffbad81c98cf8c8e189a6943b42bfeca'], }), ('Class::Singleton', '1.6', { 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', @@ -283,10 +283,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], }), - ('Test::Simple', '1.302190', { + ('Test::Simple', '1.302191', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], - 'checksums': ['fbb15226f1c605c4466a8c6ba02030083d54333d34fa76c02549cae7014c3a0e'], + 'checksums': ['a82f652bc4f2ef1ddcae99d04fc0f8924a35386066a2ab363aabf8372bc5a7ab'], }), ('Set::Scalar', '1.29', { 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', @@ -408,10 +408,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], 'checksums': ['8816f34e9a38e849a10df756030dccf9fe061a196c11ac3faafd7113c929b964'], }), - ('URI', '5.10', { + ('URI', '5.12', { 'source_tmpl': 'URI-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['16325d5e308c7b7ab623d1bf944e1354c5f2245afcfadb8eed1e2cae9a0bd0b5'], + 'checksums': ['66abe0eaddd76b74801ecd28ec1411605887550fc0a45ef6aa744fdad768d9b3'], }), ('Ima::DBI', '0.35', { 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', @@ -519,10 +519,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['4064f494f5f62587d0ae501ca439105821ee5846c687dc6503233f55300a7c56'], }), - ('Test::Warn', '0.36', { + ('Test::Warn', '0.37', { 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], - 'checksums': ['ecbca346d379cef8d3c0e4ac0c8eb3b2613d737ffaaeae52271c38d7bf3c6cda'], + 'checksums': ['98ca32e7f2f5ea89b8bfb9a0609977f3d153e242e2e51705126cb954f1a06b57'], }), ('MRO::Compat', '0.15', { 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', @@ -559,20 +559,20 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], 'checksums': ['83293737e803b43112830443fb5208ec5208a2e6ea512ed54ef8e4dd2b880827'], }), - ('IPC::Run', '20200505.0', { + ('IPC::Run', '20220807.0', { 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], - 'checksums': ['816ebf217fa0df99c583d73c0acc6ced78ac773787c664c75cbf140bb7e4c901'], + 'checksums': ['277d781dbbc98af18e979c7ef36f222513d7361742c52507c3348b265f6f5e69'], }), ('HTML::Entities::Interpolate', '1.10', { 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], 'checksums': ['f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c'], }), - ('File::Remove', '1.60', { + ('File::Remove', '1.61', { 'source_tmpl': 'File-Remove-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], - 'checksums': ['e86e2a40ffedc6d5697d071503fd6ba14a5f9b8220af3af022110d8e724f8ca6'], + 'checksums': ['fd857f585908fc503461b9e48b3c8594e6535766bc14beb17c90ba58d5dc4975'], }), ('YAML::Tiny', '1.73', { 'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz', @@ -609,10 +609,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], 'checksums': ['18f644fdd4a1fef93ef3f7f67df8e95b593d811899f34bcbbaba4d717222f58f'], }), - ('HTTP::Tiny', '0.080', { + ('HTTP::Tiny', '0.082', { 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], - 'checksums': ['243c6d566aa8f160fa1c6b0b92e5752356136b341ffffdd3ec07b23b745fde15'], + 'checksums': ['54e9e4a559a92cbb90e3f19c8a88ff067ec2f68fbe39bbb694ee70828cd5f4b8'], }), ('Package::DeprecationManager', '0.17', { 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', @@ -779,20 +779,20 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': ['2a48fa779b5297e56156380e8b32637c6c58decb4f4a7f3c7350523e11275f8f'], }), - ('LWP::Simple', '6.55', { + ('LWP::Simple', '6.67', { 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['c1d0d3a44a039b136ebac7336f576e3f5c232347e8221abd69ceb4108e85c920'], + 'checksums': ['96eec40a3fd0aa1bd834117be5eb21c438f73094d861a1a7e5774f0b1226b723'], }), ('Time::Piece::MySQL', '0.06', { 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], 'checksums': ['319601feec17fae344988a5ee91cfc6a0bcfe742af77dba254724c3268b2a60f'], }), - ('Package::Stash::XS', '0.29', { + ('Package::Stash::XS', '0.30', { 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['d3676ba94641e03d6a30e951f09266c4c3ca3f5b58aa7b314a67f28e419878aa'], + 'checksums': ['26bad65c1959c57379b3e139dc776fbec5f702906617ef27cdc293ddf1239231'], }), ('Set::Array', '0.30', { 'source_tmpl': 'Set-Array-%(version)s.tgz', @@ -849,15 +849,15 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], 'checksums': ['d331332491c51cccfb4cb94ffc44f9cd73378e618498d4a37df9e043661c515d'], }), - ('XML::XPath', '1.44', { + ('XML::XPath', '1.48', { 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], - 'checksums': ['1cc9110705165dc09dd09974dd7c0b6709c9351d6b6b1cef5a711055f891dd0f'], + 'checksums': ['7bc75be36b239e5b2e700a9570d2b53b43093d467f2abe6a743f9ff9093790cd'], }), - ('JSON', '4.05', { + ('JSON', '4.09', { 'source_tmpl': 'JSON-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], - 'checksums': ['53839373210bebea0b24fe459d0a8232446b62015c8dc42dc36051da67336bf0'], + 'checksums': ['6780a51f438c0932eec0534fc9cd2b1ad0d64817eda4add8ede5ec77d6d2c991'], }), ('Sub::Exporter', '0.988', { 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', @@ -904,10 +904,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSHERER'], 'checksums': ['44088d6e90712e187b8a5b050ca5b1c70efe2baa32ae123e9bd8f59f29f06e4d'], }), - ('Text::Balanced', '2.04', { + ('Text::Balanced', '2.06', { 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], - 'checksums': ['f49c408b85c80ba762785428a87599bed22dc0fd6bb765c9fa6ddfaa32e4e7e2'], + 'checksums': ['773e0f0f21c0cb2cf664cee6ba28ff70259babcc892f9b650f9cbda00be092ad'], }), ('strictures', '2.000006', { 'source_tmpl': 'strictures-%(version)s.tar.gz', @@ -939,10 +939,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ff786008bf8c022064ececd3b7ed89c76b35e8d1eac6cf472a9f51771c1c9f2c'], }), - ('Text::CSV', '2.01', { + ('Text::CSV', '2.02', { 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], - 'checksums': ['2a90a5eea3f22c40b87932a929621680609ab5f6b874a77c4134c8a04eb8e74b'], + 'checksums': ['84120de3e10489ea8fbbb96411a340c32cafbe5cdff7dd9576b207081baa9d24'], }), ('Test::Output', '1.033', { 'source_tmpl': 'Test-Output-%(version)s.tar.gz', @@ -959,12 +959,13 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['96eafb359339d22bf2a2de421298847a3c40f6a28b6d44005d0965da86a5469d'], }), - ('List::UtilsBy', '0.11', { + ('List::UtilsBy', '0.12', { 'source_tmpl': 'List-UtilsBy-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], - 'checksums': ['faddf43b4bc21db8e4c0e89a26e5f23fe626cde3491ec651b6aa338627f5775a'], - }), - ('List::AllUtils', '0.19', { + 'checksums': ['fff1281fd469fe982b1a58044becfd970f313bff3a26e1c7b2b3f4c0a5ed71e0'], + }), + + ('List::AllUtils', '0.19', { 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['30a8146ab21a7787b8c56d5829cf9a7f2b15276d3b3fca07336ac38d3002ffbc'], @@ -999,10 +1000,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], 'checksums': ['ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad'], }), - ('HTTP::Request', '6.36', { + ('HTTP::Request', '6.37', { 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['576a53b486af87db56261a36099776370c06f0087d179fc8c7bb803b48cddd76'], + 'checksums': ['0e59da0a85e248831327ebfba66796314cb69f1bfeeff7a9da44ad766d07d802'], }), ('XML::Twig', '3.52', { 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', @@ -1171,7 +1172,7 @@ exts_list = [ }), ('File::Slurp', '9999.32', { 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'source_urls': ['https:// cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], 'checksums': ['4c3c21992a9d42be3a79dd74a3c83d27d38057269d65509a2f555ea0fb2bc5b0'], }), ('Package::Stash', '0.40', { @@ -1224,10 +1225,10 @@ exts_list = [ 'source_urls': ['https://www.cpan.org/authors/id/M/MO/MONS/'], 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], }), - ('Text::Template', '1.60', { + ('Text::Template', '1.61', { 'source_tmpl': 'Text-Template-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], - 'checksums': ['d9d57fb3f432b4f100e6ceb06c8363bbaee0ad85d53d728f6ba15a330248501c'], + 'checksums': ['a295ea7d1ef241ae2640c1f7864b628f8e6f99ec14fb1da781b2f5f2168dcf09'], }), ('PadWalker', '2.5', { 'source_tmpl': 'PadWalker-%(version)s.tar.gz', @@ -1249,25 +1250,25 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], 'checksums': ['6312f605172973fa4d017639c217b61b1a8d6c533237ce58d5aacecfa273f0b2'], }), - ('Devel::CheckLib', '1.14', { + ('Devel::CheckLib', '1.16', { 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], - 'checksums': ['f21c5e299ad3ce0fdc0cb0f41378dca85a70e8d6c9a7599f0e56a957200ec294'], + 'checksums': ['869d38c258e646dcef676609f0dd7ca90f085f56cf6fd7001b019a5d5b831fca'], }), - ('SVG', '2.86', { + ('SVG', '2.87', { 'source_tmpl': 'SVG-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], - 'checksums': ['72c6eb6f86bb2c330280f9f3d342bb2673ad5da22d1f44fba3e04cfb5d30a67b'], + 'checksums': ['b3fa58c1c59942b4ebef003da97c3e01e531480ca29e8efbe327ff0589c0bd3c'], }), ('Statistics::Basic', '1.6611', { 'source_tmpl': 'Statistics-Basic-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JETTERO'], 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], }), - ('Log::Log4perl', '1.54', { + ('Log::Log4perl', '1.55', { 'source_tmpl': 'Log-Log4perl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], - 'checksums': ['bbabe42d3b4cdaa3a47666b957be81d55bbd1cbcffcdff2b119586d33602eabe'], + 'checksums': ['c4f3caa1328fdc48595ccd0d1e16c40bd74af2547552370125b4b7e5eae1ff44'], }), ('Math::CDF', '0.1', { 'source_tmpl': 'Math-CDF-%(version)s.tar.gz', @@ -1409,10 +1410,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], 'checksums': ['d7bdee9e138a4f83aa52d0a981625644bda87ff16642dfa845dcb44d9a242b45'], }), - ('Specio', '0.47', { + ('Specio', '0.48', { 'source_tmpl': 'Specio-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['f41307f14444f8777e572f27eeb6a964084399e7e382c47c577827ad8a286a1c'], + 'checksums': ['0c85793580f1274ef08173079131d101f77b22accea7afa8255202f0811682b2'], }), ('Params::ValidationCompiler', '0.30', { 'source_tmpl': 'Params-ValidationCompiler-%(version)s.tar.gz', @@ -1469,20 +1470,20 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], 'checksums': ['6e4e2af42388fa6d2609e0e82417de7cc6be47223f576592c656c73c7524d89d'], }), - ('Role::Identifiable::HasIdent', '0.007', { + ('Role::Identifiable::HasIdent', '0.008', { 'source_tmpl': 'Role-Identifiable-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['561346d1a1a07a45bd851d859a825a7f67925a7a3ba5ba58e0cdad8bb99073ad'], + 'checksums': ['e2b145e97b2526cd2b4fd32c208787f292d3c3bedda5c7ad224fc53c3bf22d71'], }), ('Role::HasMessage', '0.006', { 'source_tmpl': 'Role-HasMessage-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['f6a6dbe0476ff95ee1ffbef825eb18d9b02b0618deba4686e7c63b99d576d4d3'], }), - ('MooseX::OneArgNew', '0.005', { + ('MooseX::OneArgNew', '0.006', { 'source_tmpl': 'MooseX-OneArgNew-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['7e4fcf474ea6c4244f0885f1066729cfdc472fbd7190dd41b4b55bcd67c3103f'], + 'checksums': ['9bd616fb00a03d28509f46b9a541f7eeb26211999d3941f403a2561921406630'], }), ('MooseX::Role::Parameterized', '1.11', { 'source_tmpl': 'MooseX-Role-Parameterized-%(version)s.tar.gz', @@ -1524,10 +1525,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['8ca92ec948974023194197c058e33a98ad00a88561f5bf7fe672329227a910b7'], }), - ('Dist::Zilla', '6.024', { + ('Dist::Zilla', '6.025', { 'source_tmpl': 'Dist-Zilla-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['f063a6839c145a3aafcf0d8d9ec5519601d0c0f61d0174aed424297f65b928a8'], + 'checksums': ['07798e270e5d904d1071e2b421309b732d0be7d682f4d9487945e815012726cc'], }), ('XML::RegExp', '0.04', { 'source_tmpl': 'XML-RegExp-%(version)s.tar.gz', @@ -1599,15 +1600,15 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], 'checksums': ['4a6ac575815c0413b1f58967043cc9f2e166446b73c687f9bc62b5eaed9464a0'], }), - ('List::Util', '1.62', { + ('List::Util', '1.63', { 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], - 'checksums': ['7279c4ec7df0cf2c0acb874abdfe86956f5028d2414974db56edfbed8a4d339f'], + 'checksums': ['cafbdf212f6827dc9a0dd3b57b6ee50e860586d7198228a33262d55c559eb2a9'], }), - ('Module::CoreList', '5.20220420', { + ('Module::CoreList', '5.20220820', { 'source_tmpl': 'Module-CoreList-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], - 'checksums': ['2f587aa37e37381f2cd5de49507f87c461e212e34f81ce74c1880363365a0828'], + 'checksums': ['708effbbf04158b087d34d8acc707f35bdab9dccc61b41d432cb6d995d137f43'], }), ('Module::Metadata', '1.000037', { 'source_tmpl': 'Module-Metadata-%(version)s.tar.gz', @@ -1669,10 +1670,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KH/KHW'], 'checksums': ['65abe3f5363fa4cdc108f5ad9ce5ce91e7a39186a1b297bb7a06fa1b0f45d377'], }), - ('Socket', '2.032', { + ('Socket', '2.036', { 'source_tmpl': 'Socket-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], - 'checksums': ['20ecb6ad469f4a13c5c7a891abfa12a3cecfdeccc7140ad57b05be12815dd517'], + 'checksums': ['1cd8272bccde8098183a60a274b3eda0764cc6984db97f5474b28bebfe2c6b70'], }), ('Time::Local', '1.30', { 'source_tmpl': 'Time-Local-%(version)s.tar.gz', @@ -1699,10 +1700,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABH'], 'checksums': ['122c8900000a9d388aa8e44f911cab6c118fe8497417917a84a8ec183971b449'], }), - ('Test::More', '1.302190', { + ('Test::More', '1.302191', { 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], - 'checksums': ['fbb15226f1c605c4466a8c6ba02030083d54333d34fa76c02549cae7014c3a0e'], + 'checksums': ['a82f652bc4f2ef1ddcae99d04fc0f8924a35386066a2ab363aabf8372bc5a7ab'], }), ('Test::RequiresInternet', '0.05', { 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', @@ -1729,25 +1730,25 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], 'checksums': ['38f58fdef3e28a194c9c8d0dc5d02672faf93c069f40c5bcb1fabeadbbc4d2d1'], }), - ('Net::Domain', '3.13', { + ('Net::Domain', '3.14', { 'source_tmpl': 'libnet-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], - 'checksums': ['5a35fb1f2d4aa291680eb1af38899fab453c22c28e71f7c7bd3747b5a3db348c'], + 'checksums': ['153c8eb8ef0f19cf2c631d5b45d05de98516937f34e261125ef242fba1fe2ea4'], }), - ('Scalar::Util', '1.56', { + ('Scalar::Util', '1.63', { 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], - 'checksums': ['15b8537d40fb3e6dae64b2e7e983c47a99b2c20816a180bb9c868b787a12ab5b'], + 'checksums': ['cafbdf212f6827dc9a0dd3b57b6ee50e860586d7198228a33262d55c559eb2a9'], }), ('Text::ParseWords', '3.31', { 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], 'checksums': ['2ae555ba084d75b2b8feeeb8d1a00911276815ada86bccb1452236964d5a2fc7'], }), - ('Encode', '3.17', { + ('Encode', '3.19', { 'source_tmpl': 'Encode-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], - 'checksums': ['b44cbf7dd60ec6128ec575dd348484975086522611bc7580cfd305a095faa6d2'], + 'checksums': ['9163f848eef69e4d4cc8838397f0861fd9ea7ede001117dbd9694f8d95052ef5'], }), ('constant', '1.33', { 'source_tmpl': 'constant-%(version)s.tar.gz', @@ -1784,25 +1785,25 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], }), - ('URI::Escape', '5.10', { + ('URI::Escape', '5.12', { 'source_tmpl': 'URI-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['16325d5e308c7b7ab623d1bf944e1354c5f2245afcfadb8eed1e2cae9a0bd0b5'], + 'checksums': ['66abe0eaddd76b74801ecd28ec1411605887550fc0a45ef6aa744fdad768d9b3'], }), ('Set::IntervalTree', '0.12', { 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], }), - ('MCE::Mutex', '1.878', { + ('MCE::Mutex', '1.879', { 'source_tmpl': 'MCE-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], - 'checksums': ['bb5713197cc5ab91302aec746b5cc7204bf84556c30d6af67ce34a6fd38444ad'], + 'checksums': ['9c4cf39838b5c113448799af451b3d64b54e0de39d635536d7e85e8bdc5888dc'], }), - ('Text::CSV_XS', '1.47', { + ('Text::CSV_XS', '1.48', { 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], - 'checksums': ['4bbaffbdfb68505ef3326dc748e63ebe0db31157b78ca8dfcb8c3cd1d1313262'], + 'checksums': ['b72a2ed61c63561f6bfc1d5986a09f3ac252bdfda5c1c898b0b677641ce1e8bf'], }), ('DBD::CSV', '0.59', { 'source_tmpl': 'DBD-CSV-%(version)s.tgz', @@ -1834,10 +1835,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], }), - ('IO::Compress::Bzip2', '2.106', { + ('IO::Compress::Bzip2', '2.201', { 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], - 'checksums': ['cb9a26ec7d86afb3081b6369620f1f67eaa45b7c41c4eb800e1da5e700a3e3f5'], + 'checksums': ['f6c55c4e39cfaa3219965dd3b36c9de1edee9a82a10a9cadeb3b74a9ceeeaaad'], }), ('JSON::XS', '4.03', { 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', @@ -1884,10 +1885,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR/'], 'checksums': ['6547af61f3aa85793f8616190938d677d7995fb3b720c16258040bc935e2129f'], }), - ('MIME::Charset', '1.012.2', { + ('MIME::Charset', '1.013', { 'source_tmpl': 'MIME-Charset-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI/'], - 'checksums': ['878c779c0256c591666bd06c0cde4c0d7820eeeb98fd1183082aee9a1e7b1d13'], + 'checksums': ['491c5602eeb2c5c91866fb98fc22deb5e56374909702fbb873f043c770a3b7b8'], }), ('Unicode::LineBreak', '2019.001', { 'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz', From 09f3c688ad30b07830185e0b2f4e281dd1104a85 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Aug 2022 09:31:48 +0200 Subject: [PATCH 4636/9987] adding easyconfigs: attr-2.5.1-GCCcore-11.2.0.eb --- .../a/attr/attr-2.5.1-GCCcore-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a75ad1737e9 --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.5.1' + +homepage = 'https://savannah.nongnu.org/projects/attr' + +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['bae1c6949b258a0d68001367ce0c741cebdacdd3b62965d17e5eb23cd78adaf8'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', + 'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h', + 'include/%(name)s/libattr.h', 'lib/libattr.a', + 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'tools' From b495abc0d2e8fa2ef321e71309753e3404dd931c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Aug 2022 09:59:20 +0200 Subject: [PATCH 4637/9987] add missing depenencies for BigDFT + also run 'bigdft -h' as sanity check command --- easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb index 80e61b193c7..90bf07cd160 100644 --- a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb @@ -33,6 +33,9 @@ dependencies = [ ('Python', '3.9.6'), ('OpenCV', '4.5.5', '-contrib'), ('XZ', '5.2.5'), + ('libarchive', '3.5.1'), + ('bzip2', '1.0.8'), + ('attr', '2.5.1'), ] extract_sources = True @@ -71,6 +74,9 @@ print(N2.get_posinp()) local_sanity_cmd = "tmpdir=$(mktemp -d) && echo '" + local_test_script + "' > " + "$tmpdir/bigdft_test.py && " local_sanity_cmd += "python $tmpdir/bigdft_test.py && rm -r $tmpdir" -sanity_check_commands = [local_sanity_cmd] +sanity_check_commands = [ + "bigdft -h", + local_sanity_cmd, +] moduleclass = 'phys' From fae0e1e3d40dcd314172485dd36bd48d61bcdcad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Aug 2022 10:34:16 +0200 Subject: [PATCH 4638/9987] add Autotools build dependency for BigDFT --- easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb index 90bf07cd160..9df7f1e9b66 100644 --- a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb @@ -26,10 +26,10 @@ checksums = [ builddependencies = [ ('CMake', '3.21.1'), + ('Autotools', '20210726'), ] dependencies = [ - ('Autoconf', '2.71'), ('Python', '3.9.6'), ('OpenCV', '4.5.5', '-contrib'), ('XZ', '5.2.5'), From 4b8cfd4743fcc8b507515c7025e672e27d24f4a1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 29 Aug 2022 11:02:10 +0200 Subject: [PATCH 4639/9987] adding easyconfigs: AmberTools-21.12-foss-2021b.eb and patches: AmberTools-21_fix_DGESVD_workspace_query.patch, AmberTools-21_fix_incorrect_dvout_call.patch, AmberTools-21_fix_incorrect_mexit_calls.patch, AmberTools-21_fix_more_blas_argument_problems.patch, AmberTools-21_fix_multiple_definition.patch, AmberTools-21_fix_potential_use_before_init.patch, AmberTools-21_fix_rism_argument_mismatch.patch, AmberTools-21_fix_xray_fftpack_arg_mismatch.patch, AmberTools-22_fix_test_missing_cuda_dir.patch, AmberTools-21_dont_include_config.h_in_top_Makefile.patch --- .../AmberTools/AmberTools-21.12-foss-2021b.eb | 67 +++++++++++++++++++ ...ont_include_config.h_in_top_Makefile.patch | 18 +++++ ...rTools-21_fix_DGESVD_workspace_query.patch | 25 +++++++ ...berTools-21_fix_incorrect_dvout_call.patch | 29 ++++++++ ...erTools-21_fix_incorrect_mexit_calls.patch | 23 +++++++ ...s-21_fix_more_blas_argument_problems.patch | 64 ++++++++++++++++++ ...mberTools-21_fix_multiple_definition.patch | 17 +++++ ...ols-21_fix_potential_use_before_init.patch | 15 +++++ ...rTools-21_fix_rism_argument_mismatch.patch | 15 +++++ ...ols-21_fix_xray_fftpack_arg_mismatch.patch | 17 +++++ ...erTools-22_fix_test_missing_cuda_dir.patch | 14 ++++ 11 files changed, 304 insertions(+) create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_dont_include_config.h_in_top_Makefile.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_DGESVD_workspace_query.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_dvout_call.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_mexit_calls.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_more_blas_argument_problems.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_multiple_definition.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_potential_use_before_init.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_rism_argument_mismatch.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_xray_fftpack_arg_mismatch.patch create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_test_missing_cuda_dir.patch diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb new file mode 100644 index 00000000000..f9e1fe24c7d --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb @@ -0,0 +1,67 @@ +easyblock = 'EB_Amber' + +name = 'AmberTools' +local_ambertools_ver = 21 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (12, 0) # (AmberTools, Amber) +version = '%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'https://ambermd.org/' +description = """AmberTools consists of several independently developed packages that work well by themselves, + and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, + with either explicit water or generalized Born solvent models.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +# download requires registration, see http://ambermd.org/AmberTools17-get.html +local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium' +source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % local_ambertools_ver] +sources = [{ + 'download_filename': local_download_credentials, + 'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, +}] +patches = [ + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + 'AmberTools-21_CMake-FlexiBLAS.patch', + 'AmberTools-21_fix_DGESVD_workspace_query.patch', + 'AmberTools-21_fix_incorrect_dvout_call.patch', + 'AmberTools-21_fix_incorrect_mexit_calls.patch', + 'AmberTools-21_fix_more_blas_argument_problems.patch', + 'AmberTools-21_fix_multiple_definition.patch', + 'AmberTools-21_fix_potential_use_before_init.patch', + 'AmberTools-21_fix_rism_argument_mismatch.patch', + 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', + 'AmberTools-22_fix_test_missing_cuda_dir.patch', + 'AmberTools-21_dont_include_config.h_in_top_Makefile.patch', +] + +builddependencies = [ + ('Bison', '3.7.6'), + ('pkg-config', '0.29.2'), + ('CMake', '3.21.1'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Perl', '5.34.0'), + ('Boost', '1.77.0'), + ('libreadline', '8.1'), + ('matplotlib', '3.4.3'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.3'), + ('Tkinter', '%(pyver)s'), + ('X11', '20210802'), +] + +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_dont_include_config.h_in_top_Makefile.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_dont_include_config.h_in_top_Makefile.patch new file mode 100644 index 00000000000..2dd5245cfb9 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_dont_include_config.h_in_top_Makefile.patch @@ -0,0 +1,18 @@ +Don't include config.h in top Makefile. +Taken from AmberTools22 + +Åke Sandgren, 2022-08-29 +diff -ru amber20_src.orig/Makefile amber20_src/Makefile +--- amber20_src.orig/Makefile 2021-04-26 15:45:46.000000000 +0200 ++++ amber20_src/Makefile 2022-08-29 09:19:39.921375932 +0200 +@@ -1,7 +1,9 @@ + # Simple top-level Makefile to point users to those hidden below: + + CONFIG_FILE=config.h +-include $(CONFIG_FILE) ++# It was a bad idea to have this dependent on config.h; ++# this starts undoing that dependency. ++#include $(CONFIG_FILE) + + install: ambertools amber + diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_DGESVD_workspace_query.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_DGESVD_workspace_query.patch new file mode 100644 index 00000000000..444eff527ab --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_DGESVD_workspace_query.patch @@ -0,0 +1,25 @@ +Fix DGESVD workspace query + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/sqm/qm2_scf.F90 b/AmberTools/src/sqm/qm2_scf.F90 +index 6185d93dba..93eb7f60e8 100644 +--- a/AmberTools/src/sqm/qm2_scf.F90 ++++ b/AmberTools/src/sqm/qm2_scf.F90 +@@ -2254,7 +2254,7 @@ SUBROUTINE SvdInvert_SymMat(n,a,ainv,thresh) ! THRESH,ERR + _REAL_ :: S(n) + _REAL_ :: U(n,n) + _REAL_ :: VT(n,n) +- _REAL_ :: twork ++ _REAL_ :: twork(1) + _REAL_,ALLOCATABLE :: WORK(:) + INTEGER :: LWORK + +@@ -2269,7 +2269,7 @@ SUBROUTINE SvdInvert_SymMat(n,a,ainv,thresh) ! THRESH,ERR + LWORK = -1 + CALL DGESVD("A","A",n,n, ainv,n, S,U,n, VT,n, twork,LWORK,my_err) + +- LWORK = NINT(twork) ++ LWORK = NINT(twork(1)) + ALLOCATE( WORK(LWORK) ) + WORK = 0.d0 + diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_dvout_call.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_dvout_call.patch new file mode 100644 index 00000000000..dd926c82c9f --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_dvout_call.patch @@ -0,0 +1,29 @@ +Fix incorrect parameter to dvout + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/arpack/dnaitr.f b/AmberTools/src/arpack/dnaitr.f +index 64b008617f..5d3c268a95 100644 +--- a/AmberTools/src/arpack/dnaitr.f ++++ b/AmberTools/src/arpack/dnaitr.f +@@ -373,7 +373,7 @@ c + if (msglvl .gt. 1) then + call ivout (logfil, 1, [j], ndigit, + & '_naitr: generating Arnoldi vector number') +- call dvout (logfil, 1, rnorm, ndigit, ++ call dvout (logfil, 1, [rnorm], ndigit, + & '_naitr: B-norm of the current residual is') + end if + c +diff --git a/AmberTools/src/arpack/dsaitr.f b/AmberTools/src/arpack/dsaitr.f +index f725e23de9..5a29f153e6 100644 +--- a/AmberTools/src/arpack/dsaitr.f ++++ b/AmberTools/src/arpack/dsaitr.f +@@ -366,7 +366,7 @@ c + if (msglvl .gt. 2) then + call ivout (logfil, 1, [j], ndigit, + & '_saitr: generating Arnoldi vector no.') +- call dvout (logfil, 1, rnorm, ndigit, ++ call dvout (logfil, 1, [rnorm], ndigit, + & '_saitr: B-norm of the current residual =') + end if + c diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_mexit_calls.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_mexit_calls.patch new file mode 100644 index 00000000000..617ce26cc7f --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_incorrect_mexit_calls.patch @@ -0,0 +1,23 @@ +Fix incorrect parameter to mexit + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/sander/fastwt.F90 b/AmberTools/src/sander/fastwt.F90 +index 9863c12e27..f7e2bf1df4 100644 +--- a/AmberTools/src/sander/fastwt.F90 ++++ b/AmberTools/src/sander/fastwt.F90 +@@ -1058,13 +1058,13 @@ subroutine getwds(igraph ,nres ,ipres ,lbres , & + #ifndef API + write(iout,1001) + #endif +- call mexit(1) ++ call mexit(6,1) + end if + else if (abs(roh1-roh2) > small) then + #ifndef API + write(iout,1002) + #endif +- call mexit(1) ++ call mexit(6,1) + else + roh = roh1 + end if diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_more_blas_argument_problems.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_more_blas_argument_problems.patch new file mode 100644 index 00000000000..3298fccaf8e --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_more_blas_argument_problems.patch @@ -0,0 +1,64 @@ +Fix some blas argument problems with newer GCC vewrsions. + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/rism/amber_rism_interface.F90 b/AmberTools/src/rism/amber_rism_interface.F90 +index 7d84de1b7f..2c2a2fa389 100644 +--- a/AmberTools/src/rism/amber_rism_interface.F90 ++++ b/AmberTools/src/rism/amber_rism_interface.F90 +@@ -3159,9 +3159,9 @@ contains + ! Outputting entropy map. + if (len_trim(entropyfile) /= 0 .and. rismprm%entropicDecomp == 1 .and. & + rism3d_canCalc_DT(rism_3d)) then +- call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map, 1, excessChemicalPotential_map, 1) ++ call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map(1,1,1), 1, excessChemicalPotential_map, 1) + call DAXPY(this%grid%totalLocalPointsR*this%solvent%numAtomTypes, -1d0, & +- solvationEnergy_V_map, 1, excessChemicalPotential_V_map, 1) ++ solvationEnergy_V_map(1,1,1,1), 1, excessChemicalPotential_V_map, 1) + call writeThermo(writeVolume,entropyfile, suffix, excessChemicalPotential_map,& + excessChemicalPotential_V_map) + end if +@@ -3200,9 +3200,9 @@ contains + end if + ! Outputting entropy map. + if (len_trim(entropyPCPLUSfile) /= 0) then +- call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map, 1, excessChemicalPotential_map, 1) ++ call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map(1,1,1), 1, excessChemicalPotential_map, 1) + call DAXPY(this%grid%totalLocalPointsR*this%solvent%numAtomTypes, -1d0, & +- solvationEnergy_V_map, 1, excessChemicalPotential_V_map, 1) ++ solvationEnergy_V_map(1,1,1,1), 1, excessChemicalPotential_V_map, 1) + call writeVolume(trim(entropyPCPLUSfile)//suffix, excessChemicalPotential_map, this%grid, & + this%solute, mpirank, mpisize, mpicomm) + end if +@@ -3247,9 +3247,9 @@ contains + end if + ! Outputting entropy map. + if (len_trim(entropyUCfile) /= 0) then +- call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map, 1, excessChemicalPotential_map, 1) ++ call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map(1,1,1), 1, excessChemicalPotential_map, 1) + call DAXPY(this%grid%totalLocalPointsR*this%solvent%numAtomTypes, -1d0, & +- solvationEnergy_V_map, 1, excessChemicalPotential_V_map, 1) ++ solvationEnergy_V_map(1,1,1,1), 1, excessChemicalPotential_V_map, 1) + call writeVolume(trim(entropyUCfile)//suffix, excessChemicalPotential_map, this%grid, & + this%solute, mpirank, mpisize, mpicomm) + end if +@@ -3299,9 +3299,9 @@ contains + ! Outputting entropy map. + if (len_trim(entropyGFfile) /= 0 .and. rismprm%entropicDecomp == 1 .and. & + rism3d_canCalc_DT(rism_3d)) then +- call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map, 1, excessChemicalPotential_map, 1) ++ call DAXPY(this%grid%totalLocalPointsR, -1d0, solvationEnergy_map(1,1,1), 1, excessChemicalPotential_map, 1) + call DAXPY(this%grid%totalLocalPointsR*this%solvent%numAtomTypes, -1d0, & +- solvationEnergy_V_map, 1, excessChemicalPotential_V_map, 1) ++ solvationEnergy_V_map(1,1,1,1), 1, excessChemicalPotential_V_map, 1) + call writeThermo(writeVolume,entropyGFfile, suffix, excessChemicalPotential_map, & + excessChemicalPotential_V_map) + end if +@@ -3415,7 +3415,7 @@ contains + excessChemicalPotential_V_map,1,solventEntropy_V_map,1) + + call DAXPY(this%grid%totalLocalPointsR*this%solvent%numAtomTypes, -1d0, & +- solvationEnergy_V_map, 1, solventEntropy_V_map, 1) ++ solvationEnergy_V_map(1,1,1,1), 1, solventEntropy_V_map, 1) + call writeVolume(trim(entropyfile)//'.mol'//suffix, & + solvententropy_V_map(:, :, :, center_site), this%grid, & + this%solute, mpirank, mpisize, mpicomm) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_multiple_definition.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_multiple_definition.patch new file mode 100644 index 00000000000..b1d06ec5deb --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_multiple_definition.patch @@ -0,0 +1,17 @@ +Fix multiple definition problem. +Not seen by Amber devs so something else might be the real problem. + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/cifparse/cifparse.h b/AmberTools/src/cifparse/cifparse.h +index 3b1f3bca57..4577abf458 100644 +--- a/AmberTools/src/cifparse/cifparse.h ++++ b/AmberTools/src/cifparse/cifparse.h +@@ -102,7 +102,7 @@ int ndb_cif_get_category_id(char*, char*); + + + #ifdef CIF_GLOBAL +- FILE *cifpin; ++ extern FILE *cifpin; + char TempKeyword[MxNameLen+1], TempValue[MAXVALUELENGTH+1]; + NdbCifDatablocksFormat cifFiles; + int lineNo; diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_potential_use_before_init.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_potential_use_before_init.patch new file mode 100644 index 00000000000..d37b0548614 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_potential_use_before_init.patch @@ -0,0 +1,15 @@ +Fix potential use before init. + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/nmr_aux/prepare_input/makeDIST_RST.c b/AmberTools/src/nmr_aux/prepare_input/makeDIST_RST.c +index a455a8bc15..3d6f5baec6 100644 +--- a/AmberTools/src/nmr_aux/prepare_input/makeDIST_RST.c ++++ b/AmberTools/src/nmr_aux/prepare_input/makeDIST_RST.c +@@ -714,6 +714,7 @@ static int read_maplib( FILE *fp ) + printf( "%s: begin;\n", module ); + #endif + nm=0; ++ npseudo=0; + while ( getline ) { + lineno++; + diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_rism_argument_mismatch.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_rism_argument_mismatch.patch new file mode 100644 index 00000000000..277e402242c --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_rism_argument_mismatch.patch @@ -0,0 +1,15 @@ +Fix rism argument mismatch problem with newer GCC versions. + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/rism/CMakeLists.txt b/AmberTools/src/rism/CMakeLists.txt +index d554714923..96a8367693 100644 +--- a/AmberTools/src/rism/CMakeLists.txt ++++ b/AmberTools/src/rism/CMakeLists.txt +@@ -127,6 +127,7 @@ install(TARGETS rism1d rism3d.thermo rism3d.orave DESTINATION ${BINDIR}) + # MPI version + # -------------------------------------------------------------------- + if(MPI) ++ add_compile_options(-fallow-argument-mismatch) + make_mpi_version(rism rism_mpi LANGUAGES Fortran SWAP_SOURCES ${RISM_LIB_SOURCES} TO ${RISM_MPI_SOURCES} INSTALL) + config_module_dirs(rism_mpi ${RISMLIB_MPI_MOD_DIR} ${AMBER_COMMON_MOD_DIR}) + target_link_libraries(rism_mpi fftw_mpi) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_xray_fftpack_arg_mismatch.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_xray_fftpack_arg_mismatch.patch new file mode 100644 index 00000000000..5bfb50d13dd --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21_fix_xray_fftpack_arg_mismatch.patch @@ -0,0 +1,17 @@ +Fix xray argument mismatch problem with newer GCC versions. + +Åke Sandgren, 20220623 +diff --git a/AmberTools/src/sander/CMakeLists.txt b/AmberTools/src/sander/CMakeLists.txt +index 3bd5e182ac..79ba58cc6f 100644 +--- a/AmberTools/src/sander/CMakeLists.txt ++++ b/AmberTools/src/sander/CMakeLists.txt +@@ -241,6 +241,9 @@ apply_optimization_declarations(${ALL_FORTRAN_SOURCES}) + # reaxff-puremd QMMM extern interface module requires F2003 standard or later + set_source_files_properties(qm2_extern_reaxff_puremd_module.F90 PROPERTIES LANGUAGE Fortran COMPILE_FLAGS -std=f2003) + ++# xray_fftpack has argument mismatch problems ++set_source_files_properties(xray_fftpack.F90 PROPERTIES LANGUAGE Fortran COMPILE_FLAGS -fallow-argument-mismatch) ++ + set_property(SOURCE ${PLUMED_SOURCE} PROPERTY COMPILE_FLAGS ${OPT_CFLAGS_SPC}) + + if(plumed_ENABLED) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_test_missing_cuda_dir.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_test_missing_cuda_dir.patch new file mode 100644 index 00000000000..6ebca4c1459 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_test_missing_cuda_dir.patch @@ -0,0 +1,14 @@ +Make sure test_amber_clean.sh dosen't try to cd into a possibly missing directory. + +Åke Sandgren, 2022-08-26 +diff -ru amber22_src.orig/test/test_amber_clean.sh amber22_src/test/test_amber_clean.sh +--- amber22_src.orig/test/test_amber_clean.sh 2021-05-28 16:11:51.000000000 +0200 ++++ amber22_src/test/test_amber_clean.sh 2022-08-26 09:20:58.470586829 +0200 +@@ -1273,4 +1273,6 @@ + echo $delete_list | xargs /bin/rm -f + + # Remove cuda remd test output +-cd cuda/remd && make clean && cd ../.. ++if [ -d "cuda/remd" ]; then ++ cd cuda/remd && make clean && cd ../.. ++fi From 4a15829e94c45283e1ad47a6f60702a0e4641450 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 29 Aug 2022 11:04:23 +0200 Subject: [PATCH 4640/9987] Add missing checksums --- .../AmberTools/AmberTools-21.12-foss-2021b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb index f9e1fe24c7d..5d584ac7683 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21.12-foss-2021b.eb @@ -37,6 +37,31 @@ patches = [ 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'AmberTools-21_dont_include_config.h_in_top_Makefile.patch', ] +checksums = [ + 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools21.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch + # AmberTools-21_dont_include_config.h_in_top_Makefile.patch + 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', +] builddependencies = [ ('Bison', '3.7.6'), From 61b87a57069e418f04b40d1bf50190894e42a9ec Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 29 Aug 2022 11:57:59 +0200 Subject: [PATCH 4641/9987] {chem}[gomkl/2021a] Wannier90 3.1.0 --- .../Wannier90/Wannier90-3.1.0-gomkl-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2021a.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2021a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2021a.eb new file mode 100644 index 00000000000..4280cf4b955 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +# The -fallow-argument-mismatch allows MPI communication calls to be +# called with arrays of different types at different places in the +# code. This otherwise cause an error in GCC 10.X +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' From 2453b6818ce928d6302c7ac7a0ad33342ef6c613 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 29 Aug 2022 13:11:17 +0200 Subject: [PATCH 4642/9987] fix top level Makefile for AmberTools 20 --- .../a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb index f3bbb60dad0..6af9be3728e 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb @@ -14,7 +14,7 @@ toolchainopts = {'usempi': True} # download requires registration, see http://ambermd.org/AmberTools17-get.html local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium' -source_urls = ['https://ambermd.org/cgi-bin/AmberTools20-get.pl'] +source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % version] sources = [{ 'download_filename': local_download_credentials, 'filename': SOURCE_TAR_BZ2, @@ -23,6 +23,7 @@ patches = [ 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_cmake-locate-netcdf.patch', 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + 'AmberTools-21_dont_include_config.h_in_top_Makefile.patch', ] checksums = [ 'b1e1f8f277c54e88abc9f590e788bbb2f7a49bcff5e8d8a6eacfaf332a4890f9', # AmberTools-20.tar.bz2 @@ -31,6 +32,8 @@ checksums = [ '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65' + # AmberTools-21_dont_include_config.h_in_top_Makefile.patch + 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', ] builddependencies = [ @@ -54,6 +57,6 @@ prebuildopts = """sed -i 's/import sys/import sys; os.environ["LDSHARED"] = "icc prebuildopts += "%(builddir)s/AmberTools/src/pysander/setup.py && " # Tests use pmemd which is not part of AmberTools -runtest = False +runtest = True moduleclass = 'chem' From e30ae34733c39c7edcd64031c8921b297a7b3a6b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 29 Aug 2022 13:15:50 +0200 Subject: [PATCH 4643/9987] fix top level Makefile for AmberTools 21 --- .../a/AmberTools/AmberTools-21-foss-2021a.eb | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb index c9d49f9a458..6b24915bab3 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb @@ -11,11 +11,18 @@ description = """AmberTools consists of several independently developed packages toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': True} -sources = [SOURCE_TAR_BZ2] +# download requires registration, see http://ambermd.org/AmberTools17-get.html +local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium' +source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % version] +sources = [{ + 'download_filename': local_download_credentials, + 'filename': SOURCE_TAR_BZ2, +}] patches = [ 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_cmake-locate-netcdf.patch', 'AmberTools-21_CMake-FlexiBLAS.patch', + 'AmberTools-21_dont_include_config.h_in_top_Makefile.patch', ] checksums = [ 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools-21.tar.bz2 @@ -23,6 +30,8 @@ checksums = [ '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_dont_include_config.h_in_top_Makefile.patch + 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', ] builddependencies = [ @@ -44,6 +53,6 @@ dependencies = [ ('PnetCDF', '1.12.2'), ] -runtest = False +runtest = True moduleclass = 'chem' From 7143160cd3d13026c7b10ec635d501cbd78e6e23 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 29 Aug 2022 13:16:52 +0200 Subject: [PATCH 4644/9987] fix top level Makefile for AmberTools 21 --- .../easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb index 2ccde888920..f7489ace676 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb @@ -13,7 +13,7 @@ toolchainopts = {'usempi': True} # download requires registration, see http://ambermd.org/AmberTools17-get.html local_download_credentials = '?Name=Easybuild&Institution=Easybuild&City=Internet&State=Other&Country=Belgium' -source_urls = ['https://ambermd.org/cgi-bin/AmberTools21-get.pl'] +source_urls = ['https://ambermd.org/cgi-bin/AmberTools%s-get.pl' % version] sources = [{ 'download_filename': local_download_credentials, 'filename': SOURCE_TAR_BZ2, @@ -22,6 +22,7 @@ patches = [ 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_cmake-locate-netcdf.patch', 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + 'AmberTools-21_dont_include_config.h_in_top_Makefile.patch', ] checksums = [ 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools-21.tar.bz2 @@ -30,6 +31,8 @@ checksums = [ '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + # AmberTools-21_dont_include_config.h_in_top_Makefile.patch + 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', ] builddependencies = [ @@ -52,7 +55,6 @@ dependencies = [ prebuildopts = """sed -i 's/import sys/import sys; os.environ["LDSHARED"] = "icc -shared "/g' """ prebuildopts += "%(builddir)s/AmberTools/src/pysander/setup.py && " -# Tests use pmemd which is not part of AmberTools -runtest = False +runtest = True moduleclass = 'chem' From 74d7f7fe504b01fc7a507db9ce2919c4fea5a842 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 29 Aug 2022 13:30:03 +0200 Subject: [PATCH 4645/9987] Drop HDF5 from 1.13.1 to 1.12.2 --- .../HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb | 26 +++++++++++++++++++ .../h/HDF5/HDF5-1.12.2-gompi-2022a.eb | 21 +++++++++++++++ .../h/HDF5/HDF5-1.12.2-iimpi-2022a.eb | 21 +++++++++++++++ .../h/h5py/h5py-3.7.0-foss-2022a.eb | 2 +- 4 files changed, 69 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb new file mode 100644 index 00000000000..2e0d52cd3c3 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.12.2' +versionsuffix = '-serial' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb new file mode 100644 index 00000000000..1a1d2dbecc0 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.12.2' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb new file mode 100644 index 00000000000..e258fd0f35f --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.12.2' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.7.0-foss-2022a.eb b/easybuild/easyconfigs/h/h5py/h5py-3.7.0-foss-2022a.eb index 9d7fd568a45..d4bf0c2f790 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-3.7.0-foss-2022a.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-3.7.0-foss-2022a.eb @@ -19,7 +19,7 @@ builddependencies = [('pkgconfig', '1.5.5', '-python')] dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ] use_pip = True From d56105dd0a1a1bdc821ddfbde98c43a9f0a58441 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 29 Aug 2022 13:37:55 +0200 Subject: [PATCH 4646/9987] Fix checksum, switch additional deps --- easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb | 2 +- .../easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb | 2 +- easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb | 2 +- easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb | 2 +- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb | 2 +- .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb | 2 +- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb index 52779e74f85..cb1e78203d1 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb @@ -41,7 +41,7 @@ dependencies = [ ('PROJ', '9.0.0'), ('libgeotiff', '1.7.1'), ('SciPy-bundle', '2022.05'), - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('HDF', '4.2.15'), ] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb index 2e0d52cd3c3..11228af032d 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] +checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb index 1a1d2dbecc0..67fcde04744 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb @@ -11,7 +11,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] +checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] dependencies = [ ('zlib', '1.2.12'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb index e258fd0f35f..aefe5af57d0 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb @@ -11,7 +11,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] +checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] dependencies = [ ('zlib', '1.2.12'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb index 36707a0591d..fe451a77f80 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb @@ -30,7 +30,7 @@ builddependencies = [ ] dependencies = [ - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('cURL', '7.83.0'), ('Szip', '2.1.1'), ('zstd', '1.5.2'), diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb index c97f01ec5e4..6c43b84bfc0 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb @@ -33,7 +33,7 @@ checksums = [ builddependencies = [('M4', '1.4.19')] dependencies = [ - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('ELPA', '2021.11.001'), ('libxc', '5.2.3'), ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb index af352696e8e..b39513b3cd8 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb @@ -33,7 +33,7 @@ checksums = [ builddependencies = [('M4', '1.4.19')] dependencies = [ - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('ELPA', '2021.11.001'), ('libxc', '5.2.3'), ] diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 55526948715..1dfdcecb129 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -40,7 +40,7 @@ dependencies = [ ('FFTW', '3.3.10'), # for fftw ('libsndfile', '1.1.0'), # for seewave ('ICU', '71.1'), # for rJava & gdsfmt - ('HDF5', '1.13.1'), # for hdf5r + ('HDF5', '1.12.2'), # for hdf5r ('UDUNITS', '2.2.28'), # for units ('GSL', '2.7'), # for RcppGSL ('ImageMagick', '7.1.0-37'), # for animation From f5c82b0b8a50c4093997e8b7704ffa3df4f13d56 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 29 Aug 2022 13:40:06 +0200 Subject: [PATCH 4647/9987] Add comment in eb files explaining versioning --- .../easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb | 1 + easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb | 1 + easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb index 11228af032d..494b1335329 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb @@ -1,4 +1,5 @@ name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. version = '1.12.2' versionsuffix = '-serial' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb index 67fcde04744..19a00c01481 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2022a.eb @@ -1,4 +1,5 @@ name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. version = '1.12.2' homepage = 'https://portal.hdfgroup.org/display/support' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb index aefe5af57d0..9f8df24dff4 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-iimpi-2022a.eb @@ -1,4 +1,5 @@ name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. version = '1.12.2' homepage = 'https://portal.hdfgroup.org/display/support' From 6d0107319cb427655f4819febddd36a427e423ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 29 Aug 2022 13:57:10 +0200 Subject: [PATCH 4648/9987] Drop dap4 tests for netCDF --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb index fe451a77f80..2d57d9722ac 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb @@ -45,6 +45,7 @@ configopts = [ # some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " -runtest = 'test' +# Excluding dap4 tests which fetch things online +runtest = 'test ARGS="-E dap4"' moduleclass = 'data' From 3339fed38d65f0188b5a635b32c3e0e2e4be1448 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 29 Aug 2022 15:30:09 +0200 Subject: [PATCH 4649/9987] Add Cartopy and dependencies --- .../c/Cartopy/Cartopy-0.20.3-foss-2022a.eb | 50 +++++++++++++++++++ .../f/Fiona/Fiona-1.8.21-foss-2022a.eb | 48 ++++++++++++++++++ .../p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb | 37 ++++++++++++++ .../s/Shapely/Shapely-1.8.2-foss-2022a.eb | 30 +++++++++++ 4 files changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb new file mode 100644 index 00000000000..f8c63257d0f --- /dev/null +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Cartopy' +version = '0.20.3' + +homepage = 'https://scitools.org.uk/cartopy/docs/latest/' +description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Fiona', '1.8.21'), + ('GDAL', '3.5.0'), + ('GEOS', '3.10.3'), + ('matplotlib', '3.5.2'), + ('pyproj', '3.3.1'), + ('SciPy-bundle', '2022.05'), + ('Shapely', '1.8.2'), + ('lxml', '4.9.1'), + ('Pillow', '9.1.1'), + ('PROJ', '9.0.0'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('OWSLib', '0.27.2', { + 'checksums': ['e102aa2444dfe0c8439ab1e1776cc0fa47cea28c09b8a28212c893c6017c179b'], + }), + ('pyepsg', '0.4.0', { + 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], + }), + ('pykdtree', '1.3.5', { + 'checksums': ['7342f75e731103e653fc1f6b9fdabc2410cf92b6e7b06160804a75786c9b5747'], + }), + ('pyshp', '2.3.1', { + 'modulename': 'shapefile', + 'checksums': ['4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1'], + }), + (name, version, { + 'checksums': ['0d60fa2e2fbd77c4d1f6b1f9d3b588966147f07c1b179d2d34570ac1e1b49006'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb new file mode 100644 index 00000000000..a1a8ffdd7e0 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.8.21' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('GDAL', '3.5.0'), + ('Shapely', '1.8.2'), # optional for 'calc' extras +] + +use_pip = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'checksums': ['3a0edca2a7a070db405d71187214a43d2333a57b4097544a3fcc282066a58bfc'], + 'use_pip_extras': 'calc', + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["fio --help"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d70aee5e640 --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.3.1' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b3d8e14d91cc95fb3dbc03a9d0588ac58326803eefa5bbb0978d109de3304fbe'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('PROJ', '9.0.0'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb new file mode 100644 index 00000000000..1a79d23c752 --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '1.8.2' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['572af9d5006fd5e3213e37ee548912b0341fb26724d6dc8a4e3950c10197ebb6'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # needed by shapely.vectorized + ('GEOS', '3.10.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'import shapely'", + "python -c 'import shapely.vectorized'", +] + +moduleclass = 'math' From c23cfa5d4c3f02ba5aed74915a3a2d7a2de16037 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Aug 2022 16:26:44 +0200 Subject: [PATCH 4650/9987] adding easyconfigs: spaln-2.4.12-GCC-10.2.0.eb --- .../s/spaln/spaln-2.4.12-GCC-10.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb new file mode 100644 index 00000000000..364c2101be1 --- /dev/null +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'spaln' +version = '2.4.12' + +homepage = 'https://github.com/ogotoh/spaln' +description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps + and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h; +# see also https://github.com/ogotoh/spaln/issues/56 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/ogotoh/spaln/archive/'] +sources = ['ver%(version)s.tar.gz'] +checksums = ['0c5f842131409686dbaad01778960f53f1ebba8dd83d55b454ec4bf1b6bde2af'] + +dependencies = [('zlib', '1.2.11')] + +start_dir = 'src' + +# we need to make sure not to pass --prefix, otherwise the configure script gets stuck in an infinite loop... +prefix_opt = '--exec_prefix=' + +configopts = "--exec_prefix=%(installdir)s/bin --table_dir=%(installdir)s/table --alndbs_dir=%(installdir)s/seqdb " +configopts += "--use_zlib=1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], + 'dirs': ['seqdb', 'table'], +} + +sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] + +moduleclass = 'bio' From d5b934031f4b44b747e39bbad55b794dc0082373 Mon Sep 17 00:00:00 2001 From: am2455 Date: Mon, 29 Aug 2022 11:05:18 -0400 Subject: [PATCH 4651/9987] added checksum verification --- easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb index fd3ce3f5ac0..69ff9b82788 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.1.0'} source_urls = ['https://curl.haxx.se/download/'] sources = [SOURCELOWER_TAR_GZ] -#checksums = ['c0e64302a33d2fb79e0fc4e674260a22941e92ee2f11b894bf94d32b8f5531af'] +checksums = ['3c6893d38d054d4e378267166858698899e9d87258e8ff1419d020c395384535'] builddependencies = [ ('binutils', '2.38'), From b8afe74f657367ecbd1e98937b1209e16e3a076e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 29 Aug 2022 18:58:01 +0200 Subject: [PATCH 4652/9987] Add sympy and gmpy2 --- .../g/gmpy2/gmpy2-2.1.2-GCC-11.3.0.eb | 25 ++++++++++++ .../s/sympy/sympy-1.10.1-foss-2022a.eb | 40 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..59aba6600bd --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-GCC-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.2' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['da75140bca128ece795895477e53b43773e3748aa90ba6170eae7ca2c74b82d1'] + +dependencies = [ + ('Python', '3.10.4'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb new file mode 100644 index 00000000000..3799a72d02d --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.10.1' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['5939eeffdf9e152172601463626c022a2c27e75cf6278de8d401d50c9d58787b'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('gmpy2', '2.1.2'), +] + +download_dep_fail = True +use_pip = True + +# fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; +# see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 +pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +sanity_check_commands = ["isympy --help"] + +moduleclass = 'math' From 3e44554b0816e839f0a2be46ccc8a58c50fc385c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 29 Aug 2022 19:47:13 +0200 Subject: [PATCH 4653/9987] Drop remote server tests from netCDF 4.9.0 --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb index 36707a0591d..6af7b1b49cf 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb @@ -37,9 +37,10 @@ dependencies = [ ] # make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet configopts = [ - "-DBUILD_SHARED_LIBS=OFF", - "-DBUILD_SHARED_LIBS=ON", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", ] # some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests From 5611a5ea008664b69564eb1034cc56c72380c897 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 29 Aug 2022 20:02:55 +0200 Subject: [PATCH 4654/9987] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Disable DAP remote tests Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index e8aeb8b93a8..7e7c2186c13 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -38,8 +38,8 @@ dependencies = [ # make sure both static and shared libs are built configopts = [ - "-DBUILD_SHARED_LIBS=OFF", - "-DBUILD_SHARED_LIBS=ON", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", ] # some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests From c559eed950aa33e26949e1b6f1aabc3bdce4bf0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 29 Aug 2022 21:09:54 +0200 Subject: [PATCH 4655/9987] {cae}[foss/2019b] CFDEMcoupling v3.8.0, OpenFOAM v5.0-20180606, ParaView v5.4.1 + deps --- .../CFDEMcoupling-3.8.0-foss-2019b.eb | 38 ++++++++ .../CGAL-4.14.1-foss-2019b-Python-2.7.16.eb | 38 ++++++++ .../c/CMake/CMake-3.11.4-GCCcore-8.3.0.eb | 35 +++++++ .../OpenFOAM-5.0-20180606-foss-2019b.eb | 46 +++++++++ .../ParaView/ParaView-5.4.1-foss-2019b-mpi.eb | 59 +++++++++++ .../ParaView-5.4.1_fix-Qt5.11-support.patch | 94 ++++++++++++++++++ .../VTK/VTK-8.2.0-foss-2019b-Python-2.7.16.eb | 97 +++++++++++++++++++ 7 files changed, 407 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2019b.eb create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-5.0-20180606-foss-2019b.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-foss-2019b-mpi.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.4.1_fix-Qt5.11-support.patch create mode 100644 easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019b-Python-2.7.16.eb diff --git a/easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2019b.eb b/easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2019b.eb new file mode 100644 index 00000000000..b5a67158ee5 --- /dev/null +++ b/easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2019b.eb @@ -0,0 +1,38 @@ +name = 'CFDEMcoupling' +version = '3.8.0' + +homepage = 'https://www.cfdem.com/cfdemrcoupling-open-source-cfd-dem-framework' +description = """CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to couple + the DEM engine LIGGGHTS to a CFD framework.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +sources = [ + { + 'source_urls': ['https://github.com/CFDEMproject/CFDEMcoupling-PUBLIC/archive/'], + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/CFDEMproject/LIGGGHTS-PUBLIC/archive/'], + 'download_filename': '%(version)s.tar.gz', + 'filename': 'LIGGGHTS-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/CFDEMproject/LPP/archive/'], + 'download_filename': '633058e.tar.gz', + 'filename': 'LPP-20170223.tar.gz', + }, +] +checksums = [ + '3c90d3178c9667ea84db9507221f65f9efec2aab8d22c51769f8a0c94d813ee4', # CFDEMcoupling-3.8.0.tar.gz + '9cb2e6596f584463ac2f80e3ff7b9588b7e3638c44324635b6329df87b90ab03', # LIGGGHTS-3.8.0.tar.gz + '9b191d89e72fba00bd63b327ee8c79425fb73e4e11aa6c165d464ed8a582627a', # LPP-20170223.tar.gz +] + +dependencies = [ + ('OpenFOAM', '5.0-20180606'), + ('VTK', '8.2.0', '-Python-2.7.16'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..834a3fffca6 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb @@ -0,0 +1,38 @@ +name = 'CGAL' +version = '4.14.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['d4ec2528b88a7c3a07b0b86db96c216822f85b951bf4bc7f9d1f26bf6c369afe'] + +builddependencies = [ + ('CMake', '3.15.3'), + ('Eigen', '3.3.7', '', True), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.16'), + ('Boost', '1.71.0'), + ('MPFR', '4.0.2'), + ('GMP', '6.1.2'), + ('Mesa', '19.1.7'), + ('libGLU', '9.0.1'), + ('Qt5', '5.13.1'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..a2c41a5e43c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.11.4-GCCcore-8.3.0.eb @@ -0,0 +1,35 @@ +name = 'CMake' +version = '3.11.4' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8f864e9f78917de3e1483e256270daabc4a321741592c5b36af028e72bff87f5'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('ncurses', '6.1'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.66.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1d'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-5.0-20180606-foss-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-5.0-20180606-foss-2019b.eb new file mode 100644 index 00000000000..1dedae6b1a1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-5.0-20180606-foss-2019b.eb @@ -0,0 +1,46 @@ +name = 'OpenFOAM' +# bugfix release of OpenFOAM 5.0, see also https://openfoam.org/news/v5-0-patch/ +# https://github.com/OpenFOAM/OpenFOAM-5.x/commit/7f7d351b741bf6406366a043cac98de56d2d44dd +version = '5.0-20180606' +local_commit = '7f7d351' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s.x/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = [ + 'OpenFOAM-5.0-20180108_cleanup.patch', + 'OpenFOAM-5.0-20180108_fix-decomposedBlockData.patch', +] +checksums = [ + '6644cfb3abd230c041232acf32f230be3c6f2f5171a77a1e1e38c0614947b38f', # OpenFOAM-5.0-20180606.tar.gz + 'f5768f5dbc422fc2f4183fd288dc6afb2370115384f3e8b9b0e155c943868989', # OpenFOAM-5.0-20180108_cleanup.patch + # OpenFOAM-5.0-20180108_fix-decomposedBlockData.patch + '62c1585a43503c7550355ec6417fbfd28c22e750f559eaf72785d2bb630a4005', +] + +dependencies = [ + ('libreadline', '8.0'), + ('ncurses', '6.1'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.9'), + ('CGAL', '4.14.1', '-Python-2.7.16'), + ('ParaView', '5.4.1', '-mpi'), + ('gnuplot', '5.2.8'), +] + +builddependencies = [ + ('Bison', '3.3.2'), + ('CMake', '3.15.3'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-foss-2019b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-foss-2019b-mpi.eb new file mode 100644 index 00000000000..73213abe920 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-foss-2019b-mpi.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.4.1' +versionsuffix = '-mpi' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ['ParaView-v%(version)s.tar.gz'] +patches = ['ParaView-5.4.1_fix-Qt5.11-support.patch'] +checksums = [ + '390d0f5dc66bf432e202a39b1f34193af4bf8aad2355338fa5e2778ea07a80e4', # ParaView-v5.4.1.tar.gz + '4041b3c810d8394e8bd0e2ddc9ee1adc773b9adbfd209b7f7dccbdd9a1c1d935', # ParaView-5.4.1_fix-Qt5.11-support.patch +] + +dependencies = [ + ('X11', '20190717'), + ('Mesa', '19.1.7'), + ('libGLU', '9.0.1'), + ('Qt5', '5.13.1'), + ('zlib', '1.2.11'), + ('HDF5', '1.10.5'), + ('Python', '2.7.16'), +] + +# stick to CMake 3.11.x, using a more recent CMake version will cause trouble; +# see https://www.cfd-online.com/Forums/openfoam-installation/213609-v6-problems-installing-parafoam-print.html +builddependencies = [('CMake', '3.11.4')] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON ' +# if you want to build server only Paraview, uncomment the following line: +# configopts += '-DVTK_USE_X=OFF ' + +# Without internet connection turn off testing (uncomment the following line) +configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' + +configopts += ' -DPARAVIEW_QT_VERSION=5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake ' +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1_fix-Qt5.11-support.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1_fix-Qt5.11-support.patch new file mode 100644 index 00000000000..97ecdad2983 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1_fix-Qt5.11-support.patch @@ -0,0 +1,94 @@ +see https://discourse.paraview.org/t/paraview-installation-crashes-at-92-due-to-errors-fehler-originating-from-class-qheaderview/458 +and https://gitlab.kitware.com/paraview/paraview/-/merge_requests/2474 + +fixes backported to ParaView v5.4.1 by Kenneth Hoste (HPC-UGent) + +diff -ru ParaView-v5.4.1.orig/Plugins/SLACTools/pqSLACDataLoadManager.cxx ParaView-v5.4.1/Plugins/SLACTools/pqSLACDataLoadManager.cxx +--- ParaView-v5.4.1.orig/Plugins/SLACTools/pqSLACDataLoadManager.cxx 2017-08-18 15:39:19.000000000 +0200 ++++ ParaView-v5.4.1/Plugins/SLACTools/pqSLACDataLoadManager.cxx 2022-08-29 15:49:56.022696185 +0200 +@@ -33,6 +33,7 @@ + #include "vtkSMProperty.h" + #include "vtkSMSourceProxy.h" + ++#include + #include + #include + +Only in ParaView-v5.4.1/Plugins/SLACTools: pqSLACDataLoadManager.cxx.orig +diff -ru ParaView-v5.4.1.orig/Qt/ApplicationComponents/pqColorMapEditor.cxx ParaView-v5.4.1/Qt/ApplicationComponents/pqColorMapEditor.cxx +--- ParaView-v5.4.1.orig/Qt/ApplicationComponents/pqColorMapEditor.cxx 2017-08-18 15:39:19.000000000 +0200 ++++ ParaView-v5.4.1/Qt/ApplicationComponents/pqColorMapEditor.cxx 2022-08-29 15:49:56.022696185 +0200 +@@ -59,6 +59,7 @@ + #include + #include + #include ++#include + #include + + class pqColorMapEditor::pqInternals +diff -ru ParaView-v5.4.1.orig/Qt/ApplicationComponents/pqDoubleRangeSliderPropertyWidget.cxx ParaView-v5.4.1/Qt/ApplicationComponents/pqDoubleRangeSliderPropertyWidget.cxx +--- ParaView-v5.4.1.orig/Qt/ApplicationComponents/pqDoubleRangeSliderPropertyWidget.cxx 2017-08-18 15:39:19.000000000 +0200 ++++ ParaView-v5.4.1/Qt/ApplicationComponents/pqDoubleRangeSliderPropertyWidget.cxx 2022-08-29 15:49:56.022696185 +0200 +@@ -43,6 +43,7 @@ + #include "vtkSMUncheckedPropertyHelper.h" + + #include ++#include + + class pqDoubleRangeSliderPropertyWidget::pqInternals + { +diff -ru ParaView-v5.4.1.orig/Qt/ApplicationComponents/pqStandardViewFrameActionsImplementation.cxx ParaView-v5.4.1/Qt/ApplicationComponents/pqStandardViewFrameActionsImplementation.cxx +--- ParaView-v5.4.1.orig/Qt/ApplicationComponents/pqStandardViewFrameActionsImplementation.cxx 2017-08-18 15:39:19.000000000 +0200 ++++ ParaView-v5.4.1/Qt/ApplicationComponents/pqStandardViewFrameActionsImplementation.cxx 2022-08-29 15:49:56.022696185 +0200 +@@ -69,6 +69,7 @@ + #include + #include + #include ++#include + + //----------------------------------------------------------------------------- + pqStandardViewFrameActionsImplementation::pqStandardViewFrameActionsImplementation( +diff -ru ParaView-v5.4.1.orig/Qt/ApplicationComponents/pqTimeInspectorWidget.cxx ParaView-v5.4.1/Qt/ApplicationComponents/pqTimeInspectorWidget.cxx +--- ParaView-v5.4.1.orig/Qt/ApplicationComponents/pqTimeInspectorWidget.cxx 2017-08-18 15:39:19.000000000 +0200 ++++ ParaView-v5.4.1/Qt/ApplicationComponents/pqTimeInspectorWidget.cxx 2022-08-29 15:49:56.022696185 +0200 +@@ -49,6 +49,7 @@ + #include "vtkSMPropertyHelper.h" + #include "vtkSMSourceProxy.h" + ++#include + #include + #include + #include +diff -ru ParaView-v5.4.1.orig/Qt/ApplicationComponents/pqViewResolutionPropertyWidget.cxx ParaView-v5.4.1/Qt/ApplicationComponents/pqViewResolutionPropertyWidget.cxx +--- ParaView-v5.4.1.orig/Qt/ApplicationComponents/pqViewResolutionPropertyWidget.cxx 2017-08-18 15:39:19.000000000 +0200 ++++ ParaView-v5.4.1/Qt/ApplicationComponents/pqViewResolutionPropertyWidget.cxx 2022-08-29 15:49:56.022696185 +0200 +@@ -39,6 +39,7 @@ + #include "vtkSMProxy.h" + + #include ++#include + + class pqViewResolutionPropertyWidget::pqInternals + { +diff -ru ParaView-v5.4.1.orig/Qt/Components/pqChangeInputDialog.cxx ParaView-v5.4.1/Qt/Components/pqChangeInputDialog.cxx +--- ParaView-v5.4.1.orig/Qt/Components/pqChangeInputDialog.cxx 2017-08-18 15:39:19.000000000 +0200 ++++ ParaView-v5.4.1/Qt/Components/pqChangeInputDialog.cxx 2022-08-29 15:49:56.022696185 +0200 +@@ -45,6 +45,7 @@ + #include "vtkSMProxy.h" + #include "vtkSmartPointer.h" + ++#include + #include + #include + #include +diff -ru ParaView-v5.4.1.orig/Qt/Components/pqCinemaTrackSelection.cxx ParaView-v5.4.1/Qt/Components/pqCinemaTrackSelection.cxx +--- ParaView-v5.4.1.orig/Qt/Components/pqCinemaTrackSelection.cxx 2017-08-18 15:39:19.000000000 +0200 ++++ ParaView-v5.4.1/Qt/Components/pqCinemaTrackSelection.cxx 2022-08-29 15:49:56.022696185 +0200 +@@ -30,6 +30,7 @@ + + ========================================================================*/ + #include ++#include + + #include "vtkPVArrayInformation.h" + #include "vtkPVDataInformation.h" diff --git a/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..96ef490c839 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-8.2.0-foss-2019b-Python-2.7.16.eb @@ -0,0 +1,97 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '8.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + '34c3dc775261be5e45a8049155f7228b6bd668106c72a3c435d95730d17d57bb', # VTK-8.2.0.tar.gz + 'd1ff312f7a63d90d8b7033a99109801f16a462ae411d648642838aae04bcc21e', # VTKData-8.2.0.tar.gz + '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info +] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('Python', '2.7.16'), + ('SciPy-bundle', '2019.10', '-Python-2.7.16'), + ('XZ', '5.2.4'), + ('HDF5', '1.10.5'), + ('netCDF', '4.7.1'), + ('libGLU', '9.0.1'), + ('X11', '20190717'), +] + +separate_build_dir = True + +# Third party modules +configopts = "-DVTK_USE_SYSTEM_MPI4PY=ON " +configopts += "-DVTK_USE_SYSTEM_LZMA=ON " +configopts += "-DVTK_USE_SYSTEM_HDF5=ON " +configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " +configopts += "-DVTK_USE_SYSTEM_PNG=ON " +# OpenGL +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON " +configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +# Other +configopts += "-DVTK_Group_MPI:BOOL=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/vtk%s-%%(version_major_minor)s' % x for x in + ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] + + ['bin/pvtkpython', 'bin/vtkpython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + ('python', "-c 'import %(namelower)s'"), + ('python', "-c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'"), +] + + +moduleclass = 'vis' From a9af25137f10f6a1524883e9bd4d39dd43227795 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 29 Aug 2022 13:35:45 -0700 Subject: [PATCH 4656/9987] remove download_dep_fail --- easybuild/easyconfigs/p/PyStan/PyStan-3.5.0-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyStan/PyStan-3.5.0-foss-2021b.eb b/easybuild/easyconfigs/p/PyStan/PyStan-3.5.0-foss-2021b.eb index 820ef9e1ad6..b03b97b5db6 100644 --- a/easybuild/easyconfigs/p/PyStan/PyStan-3.5.0-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PyStan/PyStan-3.5.0-foss-2021b.eb @@ -17,7 +17,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('marshmallow', '3.17.1', { From 60848736456277f8a35dcc54ff321779c77443a6 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 29 Aug 2022 14:46:04 -0700 Subject: [PATCH 4657/9987] convert to PythonBundle --- .../p/PyStan/PyStan-2.19.1.1-foss-2020b.eb | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb index 67938571cc9..766b4a7e03f 100644 --- a/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyStan/PyStan-2.19.1.1-foss-2020b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'PyStan' version = '2.19.1.1' @@ -9,16 +9,20 @@ description = """Python interface to Stan, a package for Bayesian inference toolchain = {'name': 'foss', 'version': '2020b'} -sources = [SOURCELOWER_TAR_GZ] -checksums = ['fa8bad8dbc0da22bbe6f36af56c9abbfcf10f92df8ce627d59a36bd8d25eb038'] - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True +exts_list = [ + (name, version, { + 'modulename': '%(namelower)s', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['fa8bad8dbc0da22bbe6f36af56c9abbfcf10f92df8ce627d59a36bd8d25eb038'] + }), +] + moduleclass = 'math' From 68684b417e2162fb7fc07b177608fb4c79dd4f94 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 30 Aug 2022 13:19:14 +0200 Subject: [PATCH 4658/9987] Include fix for netCDF-4.9.0 --- .../easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb index 2d57d9722ac..f79aa51ab54 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb @@ -37,15 +37,15 @@ dependencies = [ ] # make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet configopts = [ - "-DBUILD_SHARED_LIBS=OFF", - "-DBUILD_SHARED_LIBS=ON", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", ] # some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " -# Excluding dap4 tests which fetch things online -runtest = 'test ARGS="-E dap4"' +runtest = 'test' moduleclass = 'data' From 44df340531821fb0e1f87d83d30b0711aefac993 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Aug 2022 13:49:47 +0200 Subject: [PATCH 4659/9987] add missing libyaml dependency for BigDFT --- easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb index 9df7f1e9b66..64317a11c77 100644 --- a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb @@ -36,6 +36,7 @@ dependencies = [ ('libarchive', '3.5.1'), ('bzip2', '1.0.8'), ('attr', '2.5.1'), + ('libyaml', '0.2.5'), ] extract_sources = True From 454b140ffb27392b190c6a7cabad53c5636b2cf3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Aug 2022 13:56:57 +0200 Subject: [PATCH 4660/9987] use Python versionsuffix for ParaView 5.4.1 with foss/2019b + add missing custom sanity_check_paths --- .../o/OpenFOAM/OpenFOAM-5.0-20180606-foss-2019b.eb | 2 +- ...i.eb => ParaView-5.4.1-foss-2019b-Python-2.7.16-mpi.eb} | 7 ++++++- 2 files changed, 7 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/ParaView/{ParaView-5.4.1-foss-2019b-mpi.eb => ParaView-5.4.1-foss-2019b-Python-2.7.16-mpi.eb} (94%) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-5.0-20180606-foss-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-5.0-20180606-foss-2019b.eb index 1dedae6b1a1..a3cc726e3ad 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-5.0-20180606-foss-2019b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-5.0-20180606-foss-2019b.eb @@ -33,7 +33,7 @@ dependencies = [ ('METIS', '5.1.0'), ('SCOTCH', '6.0.9'), ('CGAL', '4.14.1', '-Python-2.7.16'), - ('ParaView', '5.4.1', '-mpi'), + ('ParaView', '5.4.1', '-Python-2.7.16-mpi'), ('gnuplot', '5.2.8'), ] diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-foss-2019b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-foss-2019b-Python-2.7.16-mpi.eb similarity index 94% rename from easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-foss-2019b-mpi.eb rename to easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-foss-2019b-Python-2.7.16-mpi.eb index 73213abe920..39a9b0d5f5e 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-foss-2019b-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.4.1-foss-2019b-Python-2.7.16-mpi.eb @@ -2,7 +2,7 @@ easyblock = 'CMakeMake' name = 'ParaView' version = '5.4.1' -versionsuffix = '-mpi' +versionsuffix = '-Python-%(pyver)s-mpi' homepage = "http://www.paraview.org" description = "ParaView is a scientific parallel visualizer." @@ -56,4 +56,9 @@ configopts += ' -DPARAVIEW_QT_VERSION=5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qma # first serial attempt would fail. prebuildopts = 'make VTKData ;' +sanity_check_paths = { + 'files': ['bin/paraview'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib'], +} + moduleclass = 'vis' From 5c3fad921738eb7d4206362223cff424a632b283 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Aug 2022 13:57:23 +0200 Subject: [PATCH 4661/9987] add exceptions for old OpenFOAM/ParaView used as dependency for CFDEMcoupling --- test/easyconfigs/easyconfigs.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c2c0788b599..e87ea73aa6b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -518,6 +518,14 @@ def check_dep_vars(self, gen, dep, dep_vars): r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), ], + 'OpenFOAM': [ + # CFDEMcoupling requires OpenFOAM 5.x + (r'5\.0-20180606', [r'CFDEMcoupling-3\.8\.0']), + ], + 'ParaView': [ + # OpenFOAM 5.0 requires older ParaView, CFDEMcoupling depends on OpenFOAM 5.0 + (r'5\.4\.1', [r'CFDEMcoupling-3\.8\.0', r'OpenFOAM-5\.0-20180606']), + ], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 From 765cdbbfbe0bf6bea0e0a045042b9f1abbc340b0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 30 Aug 2022 14:12:05 +0200 Subject: [PATCH 4662/9987] add missing comma --- .../a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb index 6af9be3728e..c7813e12832 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-20-intel-2020a-Python-3.8.2.eb @@ -31,7 +31,7 @@ checksums = [ '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_xblas_missing_make_dependency.patch - 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65' + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', # AmberTools-21_dont_include_config.h_in_top_Makefile.patch 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', ] From 6e12cf6ff323415b24ae4e3070f5205ab77f39ec Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 30 Aug 2022 15:14:43 +0200 Subject: [PATCH 4663/9987] adding easyconfigs: MCR-R2022a.5.eb --- easybuild/easyconfigs/m/MCR/MCR-R2022a.5.eb | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2022a.5.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2022a.5.eb b/easybuild/easyconfigs/m/MCR/MCR-R2022a.5.eb new file mode 100644 index 00000000000..9bd0ecded13 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2022a.5.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'MCR' +version = 'R2022a' # runtime version 9.12 +local_update = '5' +versionsuffix = '.%s' % local_update + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%%(version)s_Update_%s_glnxa64.zip' % local_update] +checksums = ['dd5518c233ab1c42839b36730b55232a7b43310e89b0e3f338d8d3defb1a6d62'] + +moduleclass = 'math' From 0e117d3eee6a0859322c995ed035d2688bc5b659 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 30 Aug 2022 15:24:38 +0200 Subject: [PATCH 4664/9987] Add LAMMPS and dependencies --- .../archspec/archspec-0.1.4-GCCcore-11.3.0.eb | 24 +++ .../k/kim-api/kim-api-2.3.0-GCCcore-11.3.0.eb | 46 +++++ .../LAMMPS-23Jun2022-foss-2022a-kokkos.eb | 160 ++++++++++++++++++ .../s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2022a.eb | 43 +++++ .../v/Voro++/Voro++-0.4.6-GCCcore-11.3.0.eb | 43 +++++ 5 files changed, 316 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb create mode 100644 easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..710f53f822e --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.1.4' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b8d5eeb4caf892790ff1aa8ccef442a84187986aeab4da29417c9fe35532d94c'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bc886d05365 --- /dev/null +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'kim-api' +version = '2.3.0' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +KIM is an API and OpenKIM is a collection of interatomic models (potentials) for +atomistic simulations. This is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild only installs the API, the models can be installed with the +package openkim-models, or the user can install them manually by running + kim-api-collections-management install user MODELNAME +or + kim-api-collections-management install user OpenKIM +to install them all. + """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://s3.openkim.org/kim-api/'] +sources = ['%(name)s-%(version)s.txz'] +checksums = ['93673bb8fbc0625791f2ee67915d1672793366d10cabc63e373196862c14f991'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('CMake', '3.23.1'), # Also needed to install models, thus not just a builddependency. +] + +parallel = 1 +separate_build_dir = True +build_type = 'Release' + +modextravars = { + 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' +} + +sanity_check_paths = { + 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb new file mode 100644 index 00000000000..1f99ef0848d --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb @@ -0,0 +1,160 @@ +name = 'LAMMPS' +version = '23Jun2022' +versionsuffix = '-kokkos' + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['stable_%(version)s_update1.tar.gz'] +checksums = ['58e3b2b984f8935bb0db5631e143be2826c45ffd48844f7c394f36624a3e17a2'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), + ('archspec', '0.1.4'), +] +dependencies = [ + ('Python', '3.10.4'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('netCDF', '4.9.0'), + ('GSL', '2.7'), + ('zlib', '1.2.12'), + ('gzip', '1.12'), + ('cURL', '7.83.0'), + ('HDF5', '1.13.1'), + ('tbb', '2021.5.0'), + ('PCRE', '8.45'), + ('libxml2', '2.9.13'), + ('FFmpeg', '4.4.2'), + ('Voro++', '0.4.6'), + ('kim-api', '2.3.0'), + ('Eigen', '3.4.0'), + ('PLUMED', '2.8.0'), + ('ScaFaCoS', '1.0.4'), + ('SciPy-bundle', '2022.05'), + # VTK package is auto-disabled if this dep is not available + ('VTK', '9.2.0.rc2'), +] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) + + +# include the following extra packages into the build +general_packages = [ + 'ASPHERE', + 'ATC', + 'AWPMD', + 'BOCS', + 'BODY', + 'BPM', + 'BROWNIAN', + 'CG-DNA', + 'CG-SDK', + 'CLASS2', + 'COLLOID', + 'COLVARS', + 'COMPRESS', + 'CORESHELL', + 'DIELECTRIC', + 'DIFFRACTION', + 'DIPOLE', + 'DPD-BASIC', + 'DPD-MESO', + 'DPD-REACT', + 'DPD-SMOOTH', + 'DRUDE', + 'EFF', + 'ELECTRODE', + 'EXTRA-COMPUTE', + 'EXTRA-DUMP', + 'EXTRA-FIX', + 'EXTRA-MOLECULE', + 'EXTRA-PAIR', + 'FEP', + 'GRANULAR', + 'H5MD', + 'INTERLAYER', + 'KIM', + 'KSPACE', + 'LATBOLTZ', + 'MANIFOLD', + 'MACHDYN', + 'MANYBODY', + 'MC', + 'MEAM', + 'MGPT', + 'MISC', + 'ML-IAP', + 'ML-PACE', + 'ML-RANN', + 'ML-SNAP', + 'MOFFF', + 'MOLECULE', + 'MOLFILE', + 'MPIIO', + 'NETCDF', + 'OPENMP', + 'ORIENT', + 'PERI', + 'PHONON', + 'PLUGIN', + 'PLUMED', + 'POEMS', + 'PTM', + 'PYTHON', + 'QEQ', + 'QTB', + 'REACTION', + 'REAXFF', + 'REPLICA', + 'RIGID', + 'SCAFACOS', + 'SHOCK', + 'SMTBQ', + 'SPH', + 'SPIN', + 'SRD', + 'TALLY', + 'UEF', + 'VORONOI', + 'VTK', + 'YAFF', +] + +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2022a.eb b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2022a.eb new file mode 100644 index 00000000000..85be515948c --- /dev/null +++ b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'ScaFaCoS' +version = '1.0.4' + +homepage = 'http://www.scafacos.de/' +description = """ScaFaCoS is a library of scalable fast coulomb solvers.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '6634c4202e825e771d1dd75bbe9cac5cee41136c87653fde98fbd634681c1be6', # scafacos-1.0.1.tar.gz +] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('GSL', '2.7'), +] + +preconfigopts = 'unset F77 && ' + +configopts = 'FCFLAGS="-fallow-argument-mismatch $FCFLAGS" ' +configopts += '--enable-shared --enable-static --disable-doc ' +# tell it where to find provided FFTW +configopts += '--without-internal-fftw --with-fftw3-includedir=$EBROOTFFTW/include --with-fftw3-libdir=$EBROOTFFTW/lib ' +# only include the solvers supported for LAMMPS +# (for p2nfft we need an additonal dependency) +configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' + +sanity_check_paths = { + 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..dbf753f975a --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] + +builddependencies = [('binutils', '2.38')] + + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +moduleclass = 'math' From ec1da3bd9fb2125d6323da3e7f2b895e7f0e94c6 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 14:34:32 +0100 Subject: [PATCH 4665/9987] Updated to latest version, affiliation updated --- ...0-GCCcore-11.2.0.eb => hunspell-1.7.1-GCCcore-11.2.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/h/hunspell/{hunspell-1.7.0-GCCcore-11.2.0.eb => hunspell-1.7.1-GCCcore-11.2.0.eb} (86%) diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb similarity index 86% rename from easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb index b37fdbc7121..db6674f606b 100644 --- a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb @@ -1,10 +1,10 @@ -# Contribution from the Crick HPC team +# Contribution from Imperial College London/UK # uploaded by J. Sassmannshausen easyblock = 'ConfigureMake' name = 'hunspell' -version = '1.7.0' +version = '1.7.1' homepage = 'http://hunspell.github.io/' description = """Hunspell is a spell checker and morphological analyzer @@ -15,7 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/hunspell/hunspell/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['bb27b86eb910a8285407cf3ca33b62643a02798cf2eef468c0a74f6c3ee6bc8a'] +checksums = ['6e3557624c608b3e6525b8bd277706db4f5a857c28fdb3cfa8d0d2b67776da8a'] builddependencies = [ ('Autotools', '20210726'), From 096e4416a32c225224fc56494189d908fffe47d4 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 16:07:38 +0100 Subject: [PATCH 4666/9987] adding easyconfigs: x13as-1-1-b59-GCCcore-11.2.0.eb and patches: x13as-1-1-b59_makefile.patch --- .../x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb | 51 +++++++++++++++++++ .../x/x13as/x13as-1-1-b59_makefile.patch | 25 +++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..de01155ab14 --- /dev/null +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb @@ -0,0 +1,51 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'x13as' +version = '1-1-b59' + +homepage = 'https://www.census.gov/data/software/x13as.About_X-13.html' + +description = """ +X-13ARIMA-SEATS is seasonal adjustment software produced, distributed, +and maintained by the Census Bureau. + +Features of X-13ARIMA-SEATS include: + - Extensive time series modeling and model selection capabilities for + linear regression models with ARIMA errors (regARIMA models); + - The capability to generate ARIMA model-based seasonal adjustment + using a version of the SEATS software originally developed by Victor + Gómez and Agustín Maravall at the Bank of Spain, as well as nonparametric + adjustments from the X-11 procedure; + - Diagnostics of the quality and stability of the adjustments + achieved under the options selected; + - The ability to efficiently process many series at once. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [ + 'https://www2.census.gov/software/x-13arima-seats/x13as/unix-linux/program-archives', +] +sources = ['%(name)s_asciisrc-v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + '256ee87f326ef6e0ac33a806812d614a5584c6b9e1f2a67ec06af52f2c3be85d', # x13as_asciisrc-v1-1-b59.tar.gz + '5403011b3781a025887f1c2d17a6ebd55e1eee5c2b65c60b90b1940b3f5c3d83', # x13as-v1-1_makefile.patch +] + +builddependencies = [ + ('binutils', '2.37'), +] + +build_cmd = 'make -f makefile.gf' + +files_to_copy = [(["x13as_ascii"], "bin")] + +sanity_check_paths = { + 'files': ['bin/x13as_ascii'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch new file mode 100644 index 00000000000..b1c29383c33 --- /dev/null +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch @@ -0,0 +1,25 @@ +Patch to build with newer versions of gfortran +see: https://salsa.debian.org/science-team/x13as/-/blob/master/debian/rules#L4 +Author: J. Sassmannshausen, Thomas Hayward-Schneider, Jasper Grimm +diff --git a/x13as_asciisrc-v1-1-b59.orig/makefile.gf b/x13as_asciisrc-v1-1-b59/makefile.gf +index e60896e..5dad49c 100644 +--- a/x13as_asciisrc-v1-1-b59.orig/makefile.gf ++++ b/x13as_asciisrc-v1-1-b59/makefile.gf +@@ -4,7 +4,7 @@ LINKER = gfortran + PROGRAM = x13as_ascii + DEST = . + EXTHDRS = +-FFLAGS = -O2 ++FFLAGS = -O2 -std=legacy + HDRS = + LDFLAGS = -s + LDMAP = +@@ -290,7 +290,7 @@ SRCS = aaamain.f abend.f acf.f acfar.f acfdgn.f \ + testodf.f + + $(PROGRAM): $(OBJS) $(LIBS) +- $(LINKER) -static -o $@ $(OBJS) $(LDMAP) $(LIBS) $(LDFLAGS) ++ $(LINKER) -o $@ $(OBJS) $(LDMAP) $(LIBS) $(LDFLAGS) + + clean:; @rm -f $(OBJS) + From 0552d2660bb20501220b432d9057e89ade74609f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 16:30:32 +0100 Subject: [PATCH 4667/9987] adding easyconfigs: gawk-5.1.1-GCC-11.2.0.eb --- .../g/gawk/gawk-5.1.1-GCC-11.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..26a2216bd7c --- /dev/null +++ b/easybuild/easyconfigs/g/gawk/gawk-5.1.1-GCC-11.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gawk' +version = '5.1.1' + +homepage = 'https://www.gnu.org/software/gawk' +description = """The awk utility interprets a special-purpose programming language that makes it possible to handle +simple data-reformatting jobs with just a few lines of code.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6168d8d1dc8f74bd17d9dc22fa9634c49070f232343b744901da15fb4f06bffd'] + +sanity_check_paths = { + 'files': ['bin/gawk'], + 'dirs': [], +} + +sanity_check_commands = ["gawk --help"] + +moduleclass = 'tools' From 11ff621ba4e3b9bd62a4df551383b86d76d6ceff Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 17:24:26 +0100 Subject: [PATCH 4668/9987] Parallel removed as not needed --- easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb index 5249a3a5bdf..a1a8e171ef6 100644 --- a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.2.0.eb @@ -26,9 +26,6 @@ builddependencies = [ ('binutils', '2.37'), ] -# No problem to build in parallel but one core is equally fast. -parallel = 1 - sanity_check_paths = { 'files': ['lib/libev.%s' % SHLIB_EXT], 'dirs': ['include/', 'share'], From 98b8631cf5f2a49a7906967a13f7cea4b651ced0 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 17:35:43 +0100 Subject: [PATCH 4669/9987] texinfo replaced with makeinfo, pkgconf used instead of pkg-config, optim plugin added as needed by dynare --- .../easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb index 03d83437388..d440fc72013 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb @@ -1,3 +1,6 @@ +# 'optim' plugin added which is required for dynare +# Author: J. Sassmannshausen (Imperial College London/UK) + name = 'Octave' version = '7.1.0' @@ -16,7 +19,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Autotools', '20210726'), ('gperf', '3.1'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ] dependencies = [ @@ -41,7 +44,7 @@ dependencies = [ ('HDF5', '1.12.1'), ('qrupdate', '1.1.2'), ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), - ('texinfo', '6.8'), + ('makeinfo', '6.8'), ('libsndfile', '1.0.31'), ('GraphicsMagick', '1.3.36'), ] @@ -73,6 +76,9 @@ exts_list = [ ('struct', '1.0.17', { 'checksums': ['0137bbb5df650f29104f6243502f3a2302aaaa5e42ea9f02d8a3943aaf668433'], }), + ('optim', '1.6.2', { + 'checksums': ['554a8e18bb7195ae861f5059c14f1a557844265c1addb5bfbf3ab9885524787e'], + }), ] moduleclass = 'math' From 9828c960664e9e72c06504b5f45dd7a744c648ef Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 18:18:38 +0100 Subject: [PATCH 4670/9987] Java version downgraded to 11 --- easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb index d440fc72013..f6c073f2b97 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb @@ -35,7 +35,7 @@ dependencies = [ ('GLPK', '5.0'), ('GL2PS', '1.4.2'), ('gnuplot', '5.4.2'), - ('Java', '17', '', True), + ('Java', '11', '', True), ('zlib', '1.2.11'), ('Mesa', '21.1.7'), ('libGLU', '9.0.2'), From 704b43a24dfcd0d89b94935515922b6784a34e0d Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 18:33:05 +0100 Subject: [PATCH 4671/9987] Name of executable changed to x13as as this seems to be the default --- .../x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb | 6 +++--- .../easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch | 10 +++++++--- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb index de01155ab14..182ad2ee738 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb @@ -32,7 +32,7 @@ sources = ['%(name)s_asciisrc-v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_makefile.patch'] checksums = [ '256ee87f326ef6e0ac33a806812d614a5584c6b9e1f2a67ec06af52f2c3be85d', # x13as_asciisrc-v1-1-b59.tar.gz - '5403011b3781a025887f1c2d17a6ebd55e1eee5c2b65c60b90b1940b3f5c3d83', # x13as-v1-1_makefile.patch + 'cbde094a2396c256e9ac996cd539806bb0274e569d578ad42c4879f0e02c5ef3', # x13as-v1-1_makefile.patch ] builddependencies = [ @@ -41,10 +41,10 @@ builddependencies = [ build_cmd = 'make -f makefile.gf' -files_to_copy = [(["x13as_ascii"], "bin")] +files_to_copy = [(["x13as"], "bin")] sanity_check_paths = { - 'files': ['bin/x13as_ascii'], + 'files': ['bin/x13as'], 'dirs': [], } diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch index b1c29383c33..96ded45a757 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch @@ -2,11 +2,15 @@ Patch to build with newer versions of gfortran see: https://salsa.debian.org/science-team/x13as/-/blob/master/debian/rules#L4 Author: J. Sassmannshausen, Thomas Hayward-Schneider, Jasper Grimm diff --git a/x13as_asciisrc-v1-1-b59.orig/makefile.gf b/x13as_asciisrc-v1-1-b59/makefile.gf -index e60896e..5dad49c 100644 +index e60896e..cb1b38e 100644 --- a/x13as_asciisrc-v1-1-b59.orig/makefile.gf +++ b/x13as_asciisrc-v1-1-b59/makefile.gf -@@ -4,7 +4,7 @@ LINKER = gfortran - PROGRAM = x13as_ascii +@@ -1,10 +1,10 @@ + # MKMF template makefile for protected mode executables. + FC = gfortran + LINKER = gfortran +-PROGRAM = x13as_ascii ++PROGRAM = x13as DEST = . EXTHDRS = -FFLAGS = -O2 From 1618d63e63da710fbb9a63fbc0d5bb68a836137a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 31 Aug 2022 07:54:34 +0200 Subject: [PATCH 4672/9987] adding easyconfigs: Amber-22.0-foss-2021b-AmberTools-22.3.eb --- .../Amber-22.0-foss-2021b-AmberTools-22.3.eb | 96 +++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb new file mode 100644 index 00000000000..07b04661999 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb @@ -0,0 +1,96 @@ +name = 'Amber' +local_amber_ver = 22 +local_ambertools_ver = 22 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (3, 0) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'}, +] +patches = [ + {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_DGESVD_workspace_query.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_dvout_call.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_mexit_calls.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_more_blas_argument_problems.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_multiple_definition.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_potential_use_before_init.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_rism_argument_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_missing_error_check_on_test_run.patch', 'alt_location': 'AmberTools'}, + 'Amber-22_reduce_precision_of_kmmd_test.patch', + 'Amber-22_remove_undeclared_redundant_variable.patch', +] +checksums = [ + '3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16', # Amber22.tar.bz2 + '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools22.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch + # AmberTools-22_fix_missing_error_check_on_test_run.patch + 'a86eee60bd65c16a849469e303cb99dfc207cbadd2ae9e70b9ff580ced785475', + 'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e', # Amber-22_reduce_precision_of_kmmd_test.patch + # Amber-22_remove_undeclared_redundant_variable.patch + 'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb', +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # mpi4py required for MMPBSA + ('Perl', '5.34.0'), + ('Boost', '1.77.0'), + ('libreadline', '8.1'), + ('matplotlib', '3.4.3'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.3'), + ('Tkinter', '3.9.6'), + ('X11', '20210802'), +] + +# All tests are expected to pass or be skipped +runtest = True + +static = False + +moduleclass = 'chem' From 588565ac1d08edc52f067178cca57b2d9da1e853 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 09:57:35 +0200 Subject: [PATCH 4673/9987] Sync with non-CUDA version from PR #16166 --- ...-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 46 +++++++++++++++---- 1 file changed, 36 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index a1dde04b075..03ebe87e522 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -18,30 +18,56 @@ sources = [ 'AmberTools-%s.tar.bz2' % local_ambertools_ver, ] patches = [ - 'Amber-22_remove_undeclared_redundant_variable.patch', - 'AmberTools-20_cmake-locate-netcdf.patch', - 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', - 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'}, {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'}, - 'AmberTools-22_fix_cuda_version_check.patch', + {'name': 'AmberTools-21_fix_DGESVD_workspace_query.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_dvout_call.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_mexit_calls.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_more_blas_argument_problems.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_multiple_definition.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_potential_use_before_init.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_rism_argument_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_missing_error_check_on_test_run.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_cuda_version_check.patch', 'alt_location': 'AmberTools'}, + 'Amber-22_remove_undeclared_redundant_variable.patch', ] checksums = [ '3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16', # Amber22.tar.bz2 - '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools-22.tar.bz2 - # Amber-22_remove_undeclared_redundant_variable.patch - 'f2e21002e00534f14caa00bc5bbf3b1e68acb71aa8dbcfea275d67192e32c15f', + '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools22.tar.bz2 '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch + # AmberTools-22_fix_missing_error_check_on_test_run.patch + 'a86eee60bd65c16a849469e303cb99dfc207cbadd2ae9e70b9ff580ced785475', + 'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e', # Amber-22_reduce_precision_of_kmmd_test.patch '3fc08a2cf61f3eefd094554e60c88b14c9f5071f94e0a0a15c6b55fe321bfc78', # AmberTools-22_fix_cuda_version_check.patch + # Amber-22_remove_undeclared_redundant_variable.patch + 'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb', ] builddependencies = [ ('Bison', '3.7.6'), - ('pkg-config', '0.29.2'), ('CMake', '3.22.1'), ('flex', '2.6.4'), ('make', '4.3'), @@ -67,7 +93,7 @@ dependencies = [ ] # Some CUDA tests differs from expected results -runtest = False +runtest = True static = False From 8320dd1cadbbea86aac4155fd16a930d80ac3ddb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 09:59:11 +0200 Subject: [PATCH 4674/9987] move AmberTools patch to AmberTools directory --- .../AmberTools-22_fix_cuda_version_check.patch | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/{Amber => AmberTools}/AmberTools-22_fix_cuda_version_check.patch (100%) diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_cuda_version_check.patch similarity index 100% rename from easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch rename to easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_cuda_version_check.patch From 82e827952f45379703fedb20e5372191523b3e0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 10:00:26 +0200 Subject: [PATCH 4675/9987] find ambertools source in ambertools dir --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 03ebe87e522..9eba64d3c39 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -16,6 +16,7 @@ toolchainopts = {'usempi': True, 'openmp': True} sources = [ '%%(name)s%s.tar.bz2' % local_amber_ver, 'AmberTools-%s.tar.bz2' % local_ambertools_ver, + {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'}, ] patches = [ {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'}, From 72f24fbf0856fee47c67ded7f7650df252640ba8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 10:03:24 +0200 Subject: [PATCH 4676/9987] remove old ambertools source specification --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 9eba64d3c39..13780bbfe85 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -15,7 +15,6 @@ toolchainopts = {'usempi': True, 'openmp': True} sources = [ '%%(name)s%s.tar.bz2' % local_amber_ver, - 'AmberTools-%s.tar.bz2' % local_ambertools_ver, {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'}, ] patches = [ From f50784be53981ae6ebdc754fefdacec443ab257a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 10:04:11 +0200 Subject: [PATCH 4677/9987] add extra patch --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 13780bbfe85..5c54f0d0606 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -33,6 +33,7 @@ patches = [ {'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'}, {'name': 'AmberTools-22_fix_missing_error_check_on_test_run.patch', 'alt_location': 'AmberTools'}, {'name': 'AmberTools-22_fix_cuda_version_check.patch', 'alt_location': 'AmberTools'}, + 'Amber-22_reduce_precision_of_kmmd_test.patch', 'Amber-22_remove_undeclared_redundant_variable.patch', ] checksums = [ From ed944c10a1e245b48d4b4e00e9cfb5e394912134 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 10:07:21 +0200 Subject: [PATCH 4678/9987] use cmake 3.21.1 --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 5c54f0d0606..83a7a2f9602 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -69,7 +69,7 @@ checksums = [ builddependencies = [ ('Bison', '3.7.6'), - ('CMake', '3.22.1'), + ('CMake', '3.21.1'), ('flex', '2.6.4'), ('make', '4.3'), ] From 685cdf82339b289637e0adaadd603d96e3913c0d Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 31 Aug 2022 09:19:35 +0100 Subject: [PATCH 4679/9987] explain use of pkg-config instead of pkgconf --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index b7ba755c693..016792e499f 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -10,6 +10,8 @@ description = """Bioconductor provides tools for the analysis and coprehension toolchain = {'name': 'foss', 'version': '2022a'} +# lpsymphony fails to build with pkgconf, so stick to pkg-config +# error in: https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286 builddependencies = [('pkg-config', '0.29.2')] dependencies = [ From e92925fb975018d8812e39ecc84ca01b0f7c1c1c Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 31 Aug 2022 09:25:18 +0100 Subject: [PATCH 4680/9987] redirect to pkgconf and explain why this pkg-config is here --- .../p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb index a55b2586ff3..894e8691645 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb @@ -1,3 +1,5 @@ +# pkgconf should be used in preference to pkg-config +# This is included for use only in software that fails to build when using pkgconf easyblock = 'ConfigureMake' name = 'pkg-config' From e58782014fc47e71c1c372582ea466694e941869 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 10:29:25 +0200 Subject: [PATCH 4681/9987] use https --- .../Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 83a7a2f9602..f13532135fb 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -1,12 +1,12 @@ name = 'Amber' local_amber_ver = 22 local_ambertools_ver = 22 -# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php patchlevels = (3, 0) # (AmberTools, Amber) version = '%s.%s' % (local_amber_ver, patchlevels[1]) versionsuffix = '-AmberTools-%s.%s-CUDA-%%(cudaver)s' % (local_ambertools_ver, patchlevels[0]) -homepage = 'http://ambermd.org/amber.html' +homepage = 'https://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.""" From 6bf5830a99f06bf2e98348b17b5d3fdd248b100d Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 31 Aug 2022 10:53:45 +0200 Subject: [PATCH 4682/9987] Change FFmpeg version --- .../easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb index 1f99ef0848d..bc52a152c36 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb @@ -40,7 +40,7 @@ dependencies = [ ('tbb', '2021.5.0'), ('PCRE', '8.45'), ('libxml2', '2.9.13'), - ('FFmpeg', '4.4.2'), + ('FFmpeg', '5.0.1'), ('Voro++', '0.4.6'), ('kim-api', '2.3.0'), ('Eigen', '3.4.0'), From eef360dc8d0f30d27748cef9452087f11dcbaf4a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 31 Aug 2022 11:01:37 +0200 Subject: [PATCH 4683/9987] update urls to use https --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb index 07b04661999..234d491d03b 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb @@ -1,12 +1,12 @@ name = 'Amber' local_amber_ver = 22 local_ambertools_ver = 22 -# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php patchlevels = (3, 0) # (AmberTools, Amber) version = '%s.%s' % (local_amber_ver, patchlevels[1]) versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) -homepage = 'http://ambermd.org/amber.html' +homepage = 'https://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.""" From 4be80fca99362fce0f11d7fd4fd79ba017d1580b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 11:28:42 +0200 Subject: [PATCH 4684/9987] remove optional arpack dep --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index f13532135fb..475f93c1e0c 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -86,7 +86,6 @@ dependencies = [ ('netCDF', '4.8.1'), ('netCDF-Fortran', '4.5.3'), ('PnetCDF', '1.12.3'), - ('arpack-ng', '3.8.0'), ('Tkinter', '3.9.6'), ('X11', '20210802'), ('CUDA', '11.4.1', '', True), From 1687e295d08dd6e763821deb0679384bd557a89c Mon Sep 17 00:00:00 2001 From: easybuild Date: Wed, 31 Aug 2022 11:20:12 +0100 Subject: [PATCH 4685/9987] Removed modextrapaths setting, which resulted in warnings during build that path '' was already added. This parameter is no longer necessary, now that we are using the Binary easyblock, which adds the root of the installation path to PATH by default. --- .../i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb index e59108c1dbd..4c7df3dcf22 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb @@ -55,7 +55,9 @@ sanity_check_paths = { sanity_check_commands = ["interproscan.sh 2>&1 | grep 'Welcome to InterProScan-%(version)s'"] -# also include top install directory in $PATH, to make interproscan.sh available -modextrapaths = {'PATH': ''} +# We want to include the top install directory in PATH, because it contains +# interproscan.sh. Because we're using the Binary easyblock, this directory is +# included in PATH by default (unlike in some previous versions of this +# easyconfig, where we needed to specify 'modextrapaths'.) moduleclass = 'bio' From b377e6281f1a8ac8d34a4e1800cdd8c7c9ff2ea8 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 31 Aug 2022 12:32:31 +0200 Subject: [PATCH 4686/9987] Add MUMPS for 2022 --- .../m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb | 35 +++++++++++ .../m/MUMPS/MUMPS-5.5.1_shared-mumps.patch | 61 +++++++++++++++++++ .../m/MUMPS/MUMPS-5.5.1_shared-pord.patch | 44 +++++++++++++ 3 files changed, 140 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1_shared-mumps.patch create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1_shared-pord.patch diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb new file mode 100644 index 00000000000..d9da01989ea --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb @@ -0,0 +1,35 @@ +name = 'MUMPS' +version = '5.5.1' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + '1abff294fa47ee4cfd50dfd5c595942b72ebfcedce08142a75a99ab35014fa15', # MUMPS_5.5.1.tar.gz + '7990ca13c37aa72daa9e646cc7e6303f3eda01b9c463accea5f0f595fbc13566', # MUMPS-5.5.0_shared-pord.patch + '83c346a16dae059a2f4792ce2f847ca9e8423ef8c6949c3de12960f09383d564', # MUMPS-5.5.0_shared-mumps.patch +] + +dependencies = [ + ('SCOTCH', '7.0.1'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1_shared-mumps.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1_shared-mumps.patch new file mode 100644 index 00000000000..ba51f4a1a28 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1_shared-mumps.patch @@ -0,0 +1,61 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared.patch +Author: micketeer@gmail.com +Updatd to version 5.5.0: J. Sassmannshausen/ICL (UK) +Updatd to version 5.5.1: maxim-masterov (SURF) +diff -Nru MUMPS_5.5.1.orig/src/Makefile MUMPS_5.5.1/src/Makefile +--- MUMPS_5.5.1.orig/src/Makefile 2022-08-31 11:57:42.666642000 +0200 ++++ MUMPS_5.5.1/src/Makefile 2022-08-31 12:02:01.665935000 +0200 +@@ -15,18 +15,23 @@ + + libcommon: $(incdir)/mumps_int_def.h + $(MAKE) $(libdir)/libmumps_common$(PLAT)$(LIBEXT) ++ $(MAKE) $(libdir)/libmumps_common$(PLAT).so + + s: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT).so + + d: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT).so + + c: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT).so + + z: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT).so + + + # Rules for shared libraries +@@ -221,6 +226,13 @@ + $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT_SHARED): $(OBJS_MOD) $(OBJS_OTHER) $(libdir)/libmumps_common$(PLAT)$(LIBEXT_SHARED) + $(FC) $(OPTL) -shared $(OBJS_MOD) $(OBJS_OTHER) -L$(libdir) $(LORDERINGS) $(LIBS) $(LIBOTHERS) -lmumps_common$(PLAT) -o $@ $(RPATH_OPT) + ++$(libdir)/libmumps_common$(PLAT).so: $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) ++ $(FC) -shared $^ -Wl,-soname,libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) $(LORDERINGS) -lpthread $(MUMPS_LIBF77) $(MPIFLIB) $(MPICLIB) $(METISLIB) -o $(libdir)/libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libmumps_common$(PLAT)-$(SONAME_VERSION).so $@ ++ ++$(libdir)/lib$(ARITH)mumps$(PLAT).so: $(OBJS_MOD) $(OBJS_OTHER) ++ $(FC) -shared $^ -Wl,-soname,lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) -lmumps_common$(PLAT) -lpthread $(MUMPS_LIBF77) $(LORDERINGS) $(MPIFLIB) $(METISLIB) $(SCALAP) -o $(libdir)/lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $@ + + # Dependencies between modules: + # i) arithmetic-dependent modules: +@@ -435,12 +447,14 @@ + .SUFFIXES: .c .F .o + .F.o: + $(FC) $(OPTF) $(FPIC) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -c $*.F $(OUTF)$*.o ++ $(FC) $(OPTF) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -fPIC -c $*.F $(OUTF)$*.o + .c.o: + $(CC) $(OPTC) $(FPIC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -c $*.c $(OUTC)$*.o ++ $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -fPIC -c $*.c $(OUTC)$*.o + + $(ARITH)mumps_c.o: mumps_c.c + $(CC) $(OPTC) $(FPIC) -I../include $(INCS) $(CDEFS) -DMUMPS_ARITH=MUMPS_ARITH_$(ARITH) \ +- $(IORDERINGSC) $(ORDERINGSC) -c mumps_c.c $(OUTC)$@ ++ $(IORDERINGSC) $(ORDERINGSC) -fPIC -c mumps_c.c $(OUTC)$@ + + clean: + $(RM) *.o *.mod $(incdir)/mumps_int_def.h diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1_shared-pord.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1_shared-pord.patch new file mode 100644 index 00000000000..37c0d900062 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1_shared-pord.patch @@ -0,0 +1,44 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared.patch +Author: micketeer@gmail.com +Updatd to version 5.5.0: J. Sassmannshausen/ICL (UK) +Updatd to version 5.5.1: maxim-masterov (SURF) +diff -Nru MUMPS_5.5.1.orig/Makefile MUMPS_5.5.1/Makefile +--- MUMPS_5.5.1.orig/Makefile 2022-08-31 11:57:42.628161000 +0200 ++++ MUMPS_5.5.1/Makefile 2022-08-31 12:06:17.800078000 +0200 +@@ -65,7 +65,7 @@ + + include Makefile.inc + +-prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) ++prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT).so + + prerequisitesshared: Makefile.inc $(LIBSEQNEEDED)sharedlibseq $(libdir)/libpord$(PLAT)$(LIBEXT_SHARED) + +@@ -103,8 +103,11 @@ + cp $(LPORDDIR)/libpord$(LIBEXT_SHARED) $@; \ + fi; + +- +- ++$(libdir)/libpord$(PLAT).so: ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cd $(LPORDDIR); make CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" ARFUNCT= RANLIB="$(RANLIB)" libpord$(PLAT).so; fi; ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cp -a $(LPORDDIR)/libpord*.so lib/; fi; + + clean: + (cd src; $(MAKE) clean) +diff -Nru MUMPS_5.5.1.orig/PORD/lib/Makefile MUMPS_5.5.1/PORD/lib/Makefile +--- MUMPS_5.5.1.orig/PORD/lib/Makefile 2022-08-31 11:57:42.938998000 +0200 ++++ MUMPS_5.5.1/PORD/lib/Makefile 2022-08-31 12:06:20.352758000 +0200 +@@ -31,6 +31,10 @@ + libpord$(PLAT)$(LIBEXT_SHARED):$(OBJS) + $(CC) -shared $(OBJS) -o libpord.so + ++libpord$(PLAT).so: $(OBJS) ++ $(CC) -shared $(OBJS) -Wl,-soname,libpord$(PLAT)-$(SONAME_VERSION).so -o libpord$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libpord$(PLAT)-$(SONAME_VERSION).so $@ ++ + clean: + rm -f *.o + From 1f377b1a391f86fc6c678ce8c3db2c11d23db7e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Aug 2022 21:23:05 +0200 Subject: [PATCH 4687/9987] also remove modextrapaths to add top-level install dir to $PATH in easyconfig for InterProScan v5.52-86.0 (+ remove superfluous comment) --- .../i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb | 3 +-- .../i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb | 5 ----- 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb index 0e448e11898..552a8d8df97 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb @@ -37,7 +37,6 @@ sanity_check_paths = { 'dirs': ['bin', 'lib', 'data/panther/15.0'], } -# also include top install directory in $PATH, to make interproscan.sh available -modextrapaths = {'PATH': ''} +sanity_check_commands = ["interproscan.sh 2>&1 | grep 'Welcome to InterProScan-%(version)s'"] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb index 4c7df3dcf22..3107c097d4a 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb @@ -55,9 +55,4 @@ sanity_check_paths = { sanity_check_commands = ["interproscan.sh 2>&1 | grep 'Welcome to InterProScan-%(version)s'"] -# We want to include the top install directory in PATH, because it contains -# interproscan.sh. Because we're using the Binary easyblock, this directory is -# included in PATH by default (unlike in some previous versions of this -# easyconfig, where we needed to specify 'modextrapaths'.) - moduleclass = 'bio' From 0730693852ee2d91bcf908e438d8a7d08637846c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Aug 2022 21:24:26 +0200 Subject: [PATCH 4688/9987] add test to make sure that we don't use an odd minor version of HDF5 as dependency --- test/easyconfigs/easyconfigs.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c2c0788b599..0fb05afe876 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -326,6 +326,25 @@ def test_conflicts(self): self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False), "No conflicts detected") + def test_deps(self): + """Perform checks on dependencies in easyconfig files""" + + fails = [] + + for ec in self.parsed_easyconfigs: + # make sure that no odd versions (like 1.13) of HDF5 are used as a dependency, + # since those are released candidates - only even versions (like 1.12) are stable releases; + # see https://docs.hdfgroup.org/archive/support/HDF5/doc/TechNotes/Version.html + for dep in ec['ec'].dependencies(): + if dep['name'] == 'HDF5': + ver = dep['version'] + if int(ver.split('.')[1]) % 2 == 1: + fail = "Odd minor versions of HDF5 should not be used as a dependency: " + fail += "found HDF5 v%s as dependency in %s" % (ver, os.path.basename(ec['spec'])) + fails.append(fail) + + self.assertFalse(len(fails), '\n'.join(sorted(fails))) + def check_dep_vars(self, gen, dep, dep_vars): """Check whether available variants of a particular dependency are acceptable or not.""" From 32089ec0fe4e5fb10e681b77f394e0b30aa5543a Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 1 Sep 2022 09:44:53 +0200 Subject: [PATCH 4689/9987] Tweak dependencies and settings for Beast and pocl --- easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb | 8 +------- easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb | 2 -- 2 files changed, 1 insertion(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb index 09bab325f65..10b75ac34ee 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb @@ -18,17 +18,11 @@ sources = ['BEAST.v%(version)s.Linux.tgz'] checksums = ['05dcc619c2e10163f2c1089ec66149f6e53ec5a0583cd2cb8ffdccbbdb1d8183'] dependencies = [ + ('Java', '11', '', True), # this is not mandatory but beagle-lib is recommended by developers - # beagle-lib will also load the required java dependency - # if you remove this you should add the java dependency ('beagle-lib', '3.1.2'), ] -builddependencies = [ - ('Autotools', '20210128'), - ('pkg-config', '0.29.2'), -] - sanity_check_paths = { 'files': ['bin/beast'], 'dirs': [] diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb index 4075c55b03b..6caccf9d359 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-10.3.0.eb @@ -29,8 +29,6 @@ dependencies = [ ('libxml2', '2.9.10'), ] -separate_build_dir = True - # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang From 79bae10219fad0ca1dc861f8e099265f9c3f603b Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 1 Sep 2022 10:18:14 +0200 Subject: [PATCH 4690/9987] adding easyconfigs: Inspector-2022.1.0.eb --- .../i/Inspector/Inspector-2022.1.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb new file mode 100644 index 00000000000..a7772259cc8 --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2022.1.0.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'Inspector' +version = '2022.1.0' + +homepage = 'https://software.intel.com/en-us/inspector' +description = """Intel Inspector is a dynamic memory and threading error + checking tool for users developing serial and parallel applications""" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18712/'] +sources = ['l_inspector_oneapi_p_%(version)s.123_offline.sh'] +checksums = ['8551180aa30be3abea11308fb11ea9a296f0e056ab07d9254585448a0b23333e'] + +dontcreateinstalldir = True + +requires_runtime_license = False + +moduleclass = 'tools' From 6e931198bf5edc70a8f67d142064705c37c99356 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 1 Sep 2022 11:27:31 +0200 Subject: [PATCH 4691/9987] Add patches from AT21.12 --- .../a/AmberTools/AmberTools-21-foss-2021a.eb | 34 ++++++++++++++++--- 1 file changed, 30 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb index 6b24915bab3..ddfcb5137b3 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb @@ -19,17 +19,43 @@ sources = [{ 'filename': SOURCE_TAR_BZ2, }] patches = [ - 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'AmberTools-21_CMake-FlexiBLAS.patch', + 'AmberTools-21_fix_DGESVD_workspace_query.patch', + 'AmberTools-21_fix_incorrect_dvout_call.patch', + 'AmberTools-21_fix_incorrect_mexit_calls.patch', + 'AmberTools-21_fix_more_blas_argument_problems.patch', + 'AmberTools-21_fix_multiple_definition.patch', + 'AmberTools-21_fix_potential_use_before_init.patch', + 'AmberTools-21_fix_rism_argument_mismatch.patch', + 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', + 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'AmberTools-21_dont_include_config.h_in_top_Makefile.patch', ] checksums = [ - 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools-21.tar.bz2 + 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools21.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', - '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch # AmberTools-21_dont_include_config.h_in_top_Makefile.patch 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', ] @@ -53,6 +79,6 @@ dependencies = [ ('PnetCDF', '1.12.2'), ] -runtest = True +runtest = False moduleclass = 'chem' From 644f6d3ff7182ac1e81eb4b8be35b1b6c00ef80d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 1 Sep 2022 11:30:14 +0200 Subject: [PATCH 4692/9987] Reactivate testing. --- easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb index ddfcb5137b3..7d0fdd0d4bc 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-foss-2021a.eb @@ -79,6 +79,6 @@ dependencies = [ ('PnetCDF', '1.12.2'), ] -runtest = False +runtest = True moduleclass = 'chem' From 223a52a32c1c2a1b6aae6fd6a1d007f330a8e4e8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 1 Sep 2022 11:32:29 +0200 Subject: [PATCH 4693/9987] Add patches from AT21.12 --- .../a/AmberTools/AmberTools-21-intel-2021b.eb | 31 +++++++++++++++++-- 1 file changed, 28 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb index f7489ace676..b149c772a4a 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-21-intel-2021b.eb @@ -19,18 +19,43 @@ sources = [{ 'filename': SOURCE_TAR_BZ2, }] patches = [ - 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + 'AmberTools-21_CMake-FlexiBLAS.patch', + 'AmberTools-21_fix_DGESVD_workspace_query.patch', + 'AmberTools-21_fix_incorrect_dvout_call.patch', + 'AmberTools-21_fix_incorrect_mexit_calls.patch', + 'AmberTools-21_fix_more_blas_argument_problems.patch', + 'AmberTools-21_fix_multiple_definition.patch', + 'AmberTools-21_fix_potential_use_before_init.patch', + 'AmberTools-21_fix_rism_argument_mismatch.patch', + 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', + 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'AmberTools-21_dont_include_config.h_in_top_Makefile.patch', ] checksums = [ - 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools-21.tar.bz2 + 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools21.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', - '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch # AmberTools-21_dont_include_config.h_in_top_Makefile.patch 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', ] From 4aaed5877b77349fb0be94d4ded97f421f81850d Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 1 Sep 2022 11:52:37 +0200 Subject: [PATCH 4694/9987] Add openMolcas --- .../OpenMolcas-22.06-intel-2022a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb new file mode 100644 index 00000000000..e318c625a36 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'OpenMolcas' +version = '22.06' + +homepage = "https://gitlab.com/Molcas/OpenMolcas" +description = "OpenMolcas is a quantum chemistry software package" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] +sources = ["OpenMolcas-v%(version)s.tar.gz"] +patches = ['OpenMolcas-21.06_mcpdft_deps.patch'] +checksums = [ + '45daca1e6465d59a43479d5509315bca9c19dedbb0a2d4bb4f26f0b443b7670d', # OpenMolcas-v22.06.tar.gz + '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a', # OpenMolcas-21.06_mcpdft_deps.patch +] + +dependencies = [ + ('GlobalArrays', '5.8.1'), + ('HDF5', '1.13.1'), + ('Python', '3.10.4'), +] + +builddependencies = [('CMake', '3.23.1')] + +separate_build_dir = True + +preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' +configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' +configopts += '-DMPI=ON -DOPENMP=ON -DGA=ON ' +configopts += '-DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON' + +modextrapaths = {'PATH': ''} +modextravars = { + 'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', +} + +sanity_check_paths = { + 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, + 'sbin/help_basis', 'pymolcas'], + 'dirs': ['data/', 'basis_library/'], +} + +moduleclass = 'chem' From ec40bbefe87b3252807475f51351dfbcc3732016 Mon Sep 17 00:00:00 2001 From: swadmin Date: Thu, 1 Sep 2022 12:52:29 +0200 Subject: [PATCH 4695/9987] Fix depend versions --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb index 5bcb6802488..4cf10c89fd8 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb @@ -14,7 +14,7 @@ checksums = ['f98a482520c47507521a907914daa9efbc1384e0591b5afc3da18aa897de2948'] builddependencies = [ ('binutils', '2.38'), - ('pkg-config', '0.29.2') + ('pkgconf', '1.8.0') ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb index 9e8aa712671..c3d0238645c 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-2.1-GCCcore-11.3.0.eb @@ -21,7 +21,7 @@ checksums = ['8a1cd8b7fae04b82a95168252129b8c1baca098a285ff8d3f25781dead14b75a'] builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), - ('Perl', '5.34.1'), # required for pod2html + ('Perl', '5.34.1', '-minimal'), # required for pod2html ] sanity_check_paths = { From 55adfaeaf7d8e949ae6e47bf0e0caed18d0c254a Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 1 Sep 2022 13:03:23 +0200 Subject: [PATCH 4696/9987] Downgrade HDF5 --- .../easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb index e318c625a36..77b806ac4f4 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb @@ -19,7 +19,7 @@ checksums = [ dependencies = [ ('GlobalArrays', '5.8.1'), - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('Python', '3.10.4'), ] From 78dfc7768c743f5c727d48b4b5e2c6aa9894089b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 1 Sep 2022 13:40:44 +0200 Subject: [PATCH 4697/9987] Add missing patches. --- ...ber-22_reduce_precision_of_kmmd_test.patch | 29 +++++++++++++++++++ ...remove_undeclared_redundant_variable.patch | 26 +++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-22_reduce_precision_of_kmmd_test.patch create mode 100644 easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-22_reduce_precision_of_kmmd_test.patch b/easybuild/easyconfigs/a/Amber/Amber-22_reduce_precision_of_kmmd_test.patch new file mode 100644 index 00000000000..981f0df3425 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-22_reduce_precision_of_kmmd_test.patch @@ -0,0 +1,29 @@ +Reduce the number of digits checked for kmmd_pmemd/kmmd_pmemd:gb tests. +Partially ok:ed by Amber devs. They will investigate and come back with +more info. + +Åke Sandgren, 2022-08-25 +diff -ru amber22_src.orig/test/kmmd/kmmd_pmemd/Run.kmmd amber22_src/test/kmmd/kmmd_pmemd/Run.kmmd +--- amber22_src.orig/test/kmmd/kmmd_pmemd/Run.kmmd 2022-04-09 03:11:47.000000000 +0200 ++++ amber22_src/test/kmmd/kmmd_pmemd/Run.kmmd 2022-08-25 10:52:13.397649018 +0200 +@@ -64,7 +64,7 @@ + #cp $output $output.save + + ##diff the test and reference +-../../dacdif -t 2 $output.save $output ++../../dacdif -a 0.03 $output.save $output + + /bin/rm -f mdin mdinfo mdcrd mdfrc restrt logfile tidied*txt *.dat + exit(0) +diff -ru amber22_src.orig/test/kmmd/kmmd_pmemd_gb/Run.kmmd amber22_src/test/kmmd/kmmd_pmemd_gb/Run.kmmd +--- amber22_src.orig/test/kmmd/kmmd_pmemd_gb/Run.kmmd 2022-04-09 03:11:47.000000000 +0200 ++++ amber22_src/test/kmmd/kmmd_pmemd_gb/Run.kmmd 2022-08-25 10:52:20.981592091 +0200 +@@ -64,7 +64,7 @@ + #cp $output $output.save + + ##diff the test and reference +-../../dacdif -t 2 $output.save $output ++../../dacdif -a 0.01 $output.save $output + + /bin/rm -f mdin mdinfo mdcrd mdfrc restrt tidied*txt *.dat + exit(0) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch b/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch new file mode 100644 index 00000000000..08658942fb5 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch @@ -0,0 +1,26 @@ +Remove the undeclared (and unused) variable i from the private clause +in an OpenMP pragma, which otherwise results in an error: + + 93 | !$omp parallel do private(ihkl,i,f,angle) + | 1 +Error: Symbol i at (1) has no IMPLICIT type + +Bob Dröge, University of Groningen, 2022-08-18 +--- amber22_src.orig/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:24.807724049 +0200 ++++ amber22_src/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:42.039809811 +0200 +@@ -90,7 +90,7 @@ + call check_precondition(size(frac, 2) == size(scatter_type_index)) + call check_precondition(size(hkl, 2) == size(atomic_scatter_factor, 1)) + +- !$omp parallel do private(ihkl,i,f,angle) ++ !$omp parallel do private(ihkl,f,angle) + do ihkl = 1, size(hkl, 2) + + ! Fhkl = SUM( fj * exp(2 * M_PI * i * (h * xj + k * yj + l * zj)) ), +@@ -127,4 +127,4 @@ + end subroutine calc_f_non_bulk + + +-end module xray_non_bulk_impl_cpu_module +\ No newline at end of file ++end module xray_non_bulk_impl_cpu_module From 6701d0558ea38635c037cc2fae43008bc0eb06e5 Mon Sep 17 00:00:00 2001 From: Maxim Date: Thu, 1 Sep 2022 13:52:42 +0200 Subject: [PATCH 4698/9987] Update LAMMPS-23Jun2022-foss-2022a-kokkos.eb --- .../easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb index bc52a152c36..31d1e6a6b1a 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb @@ -36,7 +36,7 @@ dependencies = [ ('zlib', '1.2.12'), ('gzip', '1.12'), ('cURL', '7.83.0'), - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('tbb', '2021.5.0'), ('PCRE', '8.45'), ('libxml2', '2.9.13'), From 05b400e2a23af859d99418bbc1d23dcfdd34716a Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 1 Sep 2022 15:51:55 +0200 Subject: [PATCH 4699/9987] Add ncview --- .../n/ncview/ncview-2.1.8-gompi-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2022a.eb diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2022a.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2022a.eb new file mode 100644 index 00000000000..bebf2913247 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2022a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.8' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e8badc507b9b774801288d1c2d59eb79ab31b004df4858d0674ed0d87dfc91be'] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(nc-config --cc) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('UDUNITS', '2.2.28'), + ('X11', '20220504'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' From 42804d6b152b0dbc8c504076211e7404929274b8 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 1 Sep 2022 16:18:18 +0200 Subject: [PATCH 4700/9987] adding easyconfigs: Gurobi-9.5.2-GCCcore-11.3.0.eb --- .../g/Gurobi/Gurobi-9.5.2-GCCcore-11.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6cf6ccd4d05 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-9.5.2-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +name = 'Gurobi' +version = '9.5.2' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +patches = ['%(name)s-9.0.1_use-eb-python-gurobi-shell.patch'] +checksums = [ + '95d8ca18b7f86116ba834a27fd6228c5b1708ae67927e7ea0e954c09374a2d0f', # gurobi9.5.0_linux64.tar.gz + 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01', # Gurobi-9.0.1_use-eb-python-gurobi-shell.patch +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license is mandatory for installation +license_file = HOME + '/licenses/%(name)s.lic' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' From e9ccc4f5f246ccedbf3b34d400caa44e1d1583a5 Mon Sep 17 00:00:00 2001 From: swadmin Date: Thu, 1 Sep 2022 16:20:07 +0200 Subject: [PATCH 4701/9987] Downgrade HDF5 1.12.2, as proposed by PR #16153 --- .../easyconfigs/p/ParaView/ParaView-5.10.1-foss-2022a-mpi.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.10.1-foss-2022a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.10.1-foss-2022a-mpi.eb index fe5742c74fe..766c6e809d7 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.10.1-foss-2022a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.10.1-foss-2022a-mpi.eb @@ -26,7 +26,7 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('XZ', '5.2.5'), - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('netCDF', '4.9.0'), ('libGLU', '9.0.2'), ('X11', '20220504'), From 5ec6dc2853dad601aae0ef73345107d030c1e167 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 1 Sep 2022 17:05:29 +0200 Subject: [PATCH 4702/9987] adding easyconfigs: Flye-2.9.1-GCC-11.2.0.eb --- .../f/Flye/Flye-2.9.1-GCC-11.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flye/Flye-2.9.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9.1-GCC-11.2.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..5942fa94383 --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9.1-GCC-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.9.1' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['25a2375cd9ba6b2285f930951ad0fde81628baa97d8709172aa59e931a96678e'] + +dependencies = [('Python', '3.9.6')] + +download_dep_fail = True +use_pip = True + +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' From 81149a15b231acbc277f7e49eaf20921163c9b75 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 2 Sep 2022 10:54:18 +0200 Subject: [PATCH 4703/9987] codestyle and use OpenSSL Wrapper - thx to jfgrimm and boegelbot --- .../easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index e9de3754b25..8e39c2882df 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -1,10 +1,16 @@ +# Written by Tom Strempel +# Modified by Ben Langenberg easyblock = "CMakeMake" name = 'ecFlow' version = '5.7.0' homepage = "https://confluence.ecmwf.int/display/ECFLOW/ecflow+home" -description = """ecFlow is a client/server workflow package that enables users to run a large number of programs (with dependencies on each other and on time) in a controlled environment. It provides reasonable tolerance for hardware and software failures, combined with restart capabilities. It is used at ECMWF to run all our operational suites across a range of platforms.""" +description = """ecFlow is a client/server workflow package that enables users + to run a large number of programs (with dependencies on each other and on time) + in a controlled environment. It provides reasonable tolerance for hardware and + software failures, combined with restart capabilities. + It is used at ECMWF to run all our operational suites across a range of platforms.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} @@ -22,7 +28,7 @@ dependencies = [ ('Boost', '1.74.0'), ('Boost.Python', '1.74.0'), ('Qt5', '5.14.2'), - ('OpenSSL', '1.1.1h'), + ('OpenSSL', '1.1', '', True), ] configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " From 59ce58f9d585cb87af1c836c99b8871d68c5c404 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 2 Sep 2022 12:42:46 +0200 Subject: [PATCH 4704/9987] add sanity_check_paths --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 8e39c2882df..4c712180e7f 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -37,5 +37,9 @@ prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_commands = ['ecflow_client --help'] +sanity_check_paths = { + 'files': ['bin/ecflow_client', 'bin/ecflow_server'] + 'dirs': ['lib/python3.8/site-packages/ecflow', 'share/ecflow/etc'] +} moduleclass = "vis" From 54f5f64576e0beac4cf186336a16b67c1877578c Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 2 Sep 2022 13:06:24 +0200 Subject: [PATCH 4705/9987] Added required changes --- .../o/olaFlow/olaFlow-20210820-foss-2021b.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb b/easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb index 03be95afbaa..2fbd5fd82c1 100644 --- a/easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb +++ b/easybuild/easyconfigs/o/olaFlow/olaFlow-20210820-foss-2021b.eb @@ -1,4 +1,4 @@ -easyblock = 'Tarball' +easyblock = 'Binary' name = 'olaFlow' version = '20210820' @@ -21,13 +21,13 @@ dependencies = [ ('OpenFOAM', 'v2112') ] -postinstallcmds = ["source $FOAM_BASH && " - "export FOAM_USER_APPBIN=%(installdir)s/bin && " - "export FOAM_USER_LIBBIN=%(installdir)s/lib && " - "./allMake"] +extract_sources = True + +install_cmd = "source $FOAM_BASH && export FOAM_USER_APPBIN=%(installdir)s/bin && " +install_cmd += "export FOAM_USER_LIBBIN=%(installdir)s/lib && ls && ./allMake" sanity_check_paths = { - 'files': ["bin/olaFlow", "lib/libwaveGeneration.so"], + 'files': ["bin/olaFlow", "lib/libwaveGeneration.%s" % SHLIB_EXT], 'dirs': [] } From 290a8885ae0c247a329e59176e36dff3a65de3dc Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 2 Sep 2022 13:28:19 +0200 Subject: [PATCH 4706/9987] corrected syntax error --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 4c712180e7f..15338b73d97 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -38,8 +38,8 @@ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_commands = ['ecflow_client --help'] sanity_check_paths = { - 'files': ['bin/ecflow_client', 'bin/ecflow_server'] - 'dirs': ['lib/python3.8/site-packages/ecflow', 'share/ecflow/etc'] + 'files': ['bin/ecflow_client', 'bin/ecflow_server'], + 'dirs': ['lib/python3.8/site-packages/ecflow', 'share/ecflow/etc'], } moduleclass = "vis" From ea8b99205c7cabf54d3e5db9cb13183f3f033526 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 2 Sep 2022 13:56:46 +0200 Subject: [PATCH 4707/9987] no more Python suffix --- ...-1.7.1-foss-2020b-Python-3.8.6.eb => MUST-1.7.1-foss-2020b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/MUST/{MUST-1.7.1-foss-2020b-Python-3.8.6.eb => MUST-1.7.1-foss-2020b.eb} (100%) diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb similarity index 100% rename from easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b-Python-3.8.6.eb rename to easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb From f5bc4fd4ca0aaf1c82d33a813b65244bebde6337 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 2 Sep 2022 16:08:16 +0200 Subject: [PATCH 4708/9987] remove versionsuffix config --- easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb b/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb index 6fd80a401de..b7aef9fc7f7 100644 --- a/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MUST/MUST-1.7.1-foss-2020b.eb @@ -2,7 +2,6 @@ easyblock = "CMakeMake" name = 'MUST' version = '1.7.1' -versionsuffix = '-Python-%(pyver)s' homepage = "https://hpc.rwth-aachen.de/must/" description = """MUST detects usage errors of the Message Passing Interface (MPI) and reports them to the user. From 4a4c348ee4609ddbace5c8234a77c2c71def0fbf Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 2 Sep 2022 16:09:15 +0200 Subject: [PATCH 4709/9987] Add ESMF for 2022a --- .../e/ESMF/ESMF-8.3.0-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb new file mode 100644 index 00000000000..e7645fa6164 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb @@ -0,0 +1,37 @@ +name = 'ESMF' +version = '8.3.0' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + '0ff43ede83d1ac6beabd3d5e2a646f7574174b28a48d1b9f2c318a054ba268fd', # v8.3.0.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +# builddependencies = [('libarchive', '3.6.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('netCDF-C++4', '4.3.1'), + ('libarchive', '3.6.1'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' From 70d346f5af9739b963d7989ffb1d378acfa7d87d Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 2 Sep 2022 16:43:43 +0200 Subject: [PATCH 4710/9987] Update easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb index e7645fa6164..7857718c8b0 100644 --- a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb @@ -16,8 +16,6 @@ checksums = [ '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch ] -# builddependencies = [('libarchive', '3.6.1')] - dependencies = [ ('netCDF', '4.9.0'), ('netCDF-Fortran', '4.6.0'), From 4d9d0cc0826cd10a1d39e97fe6d7b7f476660ba2 Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 2 Sep 2022 16:59:51 +0200 Subject: [PATCH 4711/9987] Update ESMF-8.3.0-foss-2022a.eb --- easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb index 7857718c8b0..215115944a2 100644 --- a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-foss-2022a.eb @@ -16,6 +16,8 @@ checksums = [ '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch ] +builddependencies = [('CMake', '3.23.1')] + dependencies = [ ('netCDF', '4.9.0'), ('netCDF-Fortran', '4.6.0'), From 55e9473be908c560cfdcfc3b6f0f2ad3afa5b8e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Sep 2022 09:22:05 +0200 Subject: [PATCH 4712/9987] adding easyconfigs: atools-1.5.1-GCCcore-11.2.0.eb --- .../a/atools/atools-1.5.1-GCCcore-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b3c29a69c54 --- /dev/null +++ b/easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'atools' +version = '1.5.1' + +homepage = 'https://github.com/gjbex/atools' +description = """Tools to make using job arrays a lot more convenient.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/gjbex/atools/archive'] +sources = [SOURCE_TAR_GZ] +checksums = ['540714c39aa83dd5f1a7367d76f8d6f491336fa5fc00077591a22151ef5d31f4'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +# to enable SLURM integration (site-specific) (options are torque, moab, sge, slurm) +configopts = '--with-batchsystem=slurm' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acreate', 'aenv', 'aload', 'alog', 'arange', 'areduce']], + 'dirs': ['lib/vsc/atools'] +} + +sanity_check_commands = [ + 'acreate -h', + 'aenv -h', + 'aload -h', + 'alog -h', + 'arange -h', + 'areduce -h', +] + +moduleclass = 'tools' From bfe958a2472a63a2cfaf9af7278c24f39dd95143 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 11:42:47 +0100 Subject: [PATCH 4713/9987] adding easyconfigs: SUNDIALS-6.3.0-foss-2022a.eb --- .../s/SUNDIALS/SUNDIALS-6.3.0-foss-2022a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2022a.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2022a.eb new file mode 100644 index 00000000000..efe9f2b54de --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '6.3.0' + +homepage = 'https://computation.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['89a22bea820ff250aa7239f634ab07fa34efe1d2dcfde29cc8d3af11455ba2a7'] + +builddependencies = [('CMake', '3.23.1')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' From eb0f5b6b2334a50556ee4ef2f66a4d0dfe14e16b Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 12:47:27 +0100 Subject: [PATCH 4714/9987] adding easyconfigs: libemf-1.0.13-GCC-11.3.0.eb --- .../l/libemf/libemf-1.0.13-GCC-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libemf/libemf-1.0.13-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libemf/libemf-1.0.13-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libemf/libemf-1.0.13-GCC-11.3.0.eb new file mode 100644 index 00000000000..bda47b3c33b --- /dev/null +++ b/easybuild/easyconfigs/l/libemf/libemf-1.0.13-GCC-11.3.0.eb @@ -0,0 +1,31 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'libemf' +version = '1.0.13' + +homepage = 'https://sourceforge.net/projects/libemf/' +description = "Library implementation of ECMA-234 API for the generation of enhanced metafiles." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://sourceforge.net/projects/%(name)s/files/%(name)s/%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] + +checksums = [ + '74d92c017e8beb41730a8be07c2c6e4ff6547660c84bf91f832d8f325dd0cf82', # libemf-1.0.13.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/printemf', 'lib/libEMF.a', 'lib/libEMF.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 9acd4fec75feb2b80c2c0a1dabc538f21a3953f5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 5 Sep 2022 13:48:22 +0200 Subject: [PATCH 4715/9987] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index 7e7c2186c13..182023f4691 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -30,7 +30,7 @@ builddependencies = [ ] dependencies = [ - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('cURL', '7.83.0'), ('Szip', '2.1.1'), ('zstd', '1.5.2'), From f7c6da9c615dd20942cf5a07b46f0241827a6aa7 Mon Sep 17 00:00:00 2001 From: adam Date: Mon, 5 Sep 2022 13:30:50 +0100 Subject: [PATCH 4716/9987] adding easyconfigs: SAMtools-1.16.1-GCC-11.2.0.eb, SAMtools-1.16.1-GCC-11.3.0.eb --- .../s/SAMtools/SAMtools-1.16.1-GCC-11.2.0.eb | 37 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.16.1-GCC-11.3.0.eb | 37 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.16.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.16.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.16.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.16.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..235090c4882 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.16.1-GCC-11.2.0.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +# +# Updated to 1.14 and gcc-11.2.0 +# J. Sassmannshausen / GSTT + +name = 'SAMtools' +version = '1.16.1' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2fa0a25f78594cf23d07c9d32d5060a14f1c5ee14d7b0af7a8a71abc9fdf1d07'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.78.0'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.16.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.16.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..87c553709eb --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.16.1-GCC-11.3.0.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +# +# Updated to 1.14 and gcc-11.2.0 +# J. Sassmannshausen / GSTT + +name = 'SAMtools' +version = '1.16.1' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2fa0a25f78594cf23d07c9d32d5060a14f1c5ee14d7b0af7a8a71abc9fdf1d07'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.83.0'), +] + +moduleclass = 'bio' From 87cd10d6e6a73b48b5cff42aa48960286ef94036 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 14:41:53 +0100 Subject: [PATCH 4717/9987] Upgraded to 1.21.0, URL for source code upgraded --- ...-GCCcore-11.2.0.eb => Wayland-1.21.0-GCCcore-11.2.0.eb} | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/w/Wayland/{Wayland-1.20.0-GCCcore-11.2.0.eb => Wayland-1.21.0-GCCcore-11.2.0.eb} (82%) diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.2.0.eb similarity index 82% rename from easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.2.0.eb index 6036be672fc..15fd8e5d655 100644 --- a/easybuild/easyconfigs/w/Wayland/Wayland-1.20.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.2.0.eb @@ -1,8 +1,10 @@ # Author: Jasper Grimm (UoY) +# URL of Wayland download changed to GitLab due to changes upstream +# Author: J. Sassmannshausen (Imperial College London/UK) easyblock = 'Bundle' name = 'Wayland' -version = '1.20.0' +version = '1.21.0' homepage = 'https://wayland.freedesktop.org/' description = """ @@ -39,7 +41,8 @@ default_component_specs = { components = [ ('wayland', version, { - 'checksums': ['b8a034154c7059772e0fdbd27dbfcda6c732df29cae56a82274f6ec5d7cd8725'], + 'source_urls': ['https://gitlab.freedesktop.org/wayland/wayland/-/releases/%(version)s/downloads'], + 'checksums': ['6dc64d7fc16837a693a51cfdb2e568db538bfdc9f457d4656285bb9594ef11ac'], 'configopts': "-Ddocumentation=false", }), ('wayland-protocols', '1.25', { From d501882880bfe28e8911e498c7ac37fa247b1a82 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 14:45:45 +0100 Subject: [PATCH 4718/9987] Wayland upgraded to 1.21.0 --- .../easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb index 327d939ec40..ba0e31b6d0c 100644 --- a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb @@ -33,7 +33,7 @@ builddependencies = [ dependencies = [ ('pugixml', '1.12.1'), - ('Wayland', '1.20.0'), + ('Wayland', '1.21.0'), ] parallel = 2 From ea1f630b36744a406b319751d42208a475095e74 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 14:49:23 +0100 Subject: [PATCH 4719/9987] configopts moved as requested --- easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb | 4 ++-- easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb index 1f8a7ab39b5..26a65302e13 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.13.1-GCC-11.2.0.eb @@ -26,10 +26,10 @@ checksums = ['f22901582138e3203959c9257cf83eba9929ac41d7be4a42557213a22ebcc7a0'] # preconfigopts = 'autoreconf -i && CC="$CC -fuse-ld=bfd" ' # This is not required with CMake -configopts = '-DJANSSON_BUILD_SHARED_LIBS=ON ' - builddependencies = [('CMake', '3.22.1')] +configopts = '-DJANSSON_BUILD_SHARED_LIBS=ON ' + sanity_check_paths = { 'files': ['lib/libjansson.%s' % SHLIB_EXT], 'dirs': ['include'], diff --git a/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb index 8f432120bd6..37c841b0d79 100644 --- a/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/j/Jansson/Jansson-2.14-GCC-11.3.0.eb @@ -26,10 +26,10 @@ checksums = ['c739578bf6b764aa0752db9a2fdadcfe921c78f1228c7ec0bb47fa804c55d17b'] # preconfigopts = 'autoreconf -i && CC="$CC -fuse-ld=bfd" ' # This is not required with CMake -configopts = '-DJANSSON_BUILD_SHARED_LIBS=ON ' - builddependencies = [('CMake', '3.23.1')] +configopts = '-DJANSSON_BUILD_SHARED_LIBS=ON ' + sanity_check_paths = { 'files': ['lib/libjansson.%s' % SHLIB_EXT], 'dirs': ['include'], From fb2e4208bdde60fe8c40a2fde9f4427ad75d055d Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 15:07:16 +0100 Subject: [PATCH 4720/9987] pkg-conf updated, CMake removed --- .../g/glib-networking/glib-networking-2.72.1-GCCcore-11.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.2.0.eb index f1cc388b36a..a43faefb8bb 100644 --- a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.2.0.eb @@ -13,11 +13,10 @@ sources = [SOURCE_TAR_GZ] checksums = ['675a654ae55d381490c5d76b84e088f684125415fbd2d46f74dfa5522c4a1268'] builddependencies = [ - ('CMake', '3.22.1'), ('binutils', '2.37'), ('Meson', '0.58.2'), ('Ninja', '1.10.2'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ] dependencies = [ From 11123ccce8cc36b6a193003cd897fa3463d21cd3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Jul 2022 10:37:23 +0200 Subject: [PATCH 4721/9987] TensorFlow: Exclude (flaky) fault_tolerance_test --- .../t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 2 ++ .../easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 7a84c1259e7..2434df0cc60 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -210,6 +210,8 @@ exts_list = [ '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', # All tests in this directory fail with segfault (TensorFlow Graph IR) '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + # Fails on e.g. AMD EPYC and known to be flaky on Mac: https://github.com/tensorflow/tensorflow/issues/56717 + '-//tensorflow/python/data/experimental/kernel_tests/service:fault_tolerance_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb index 1169e8334d2..53a9d683f85 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb @@ -206,6 +206,8 @@ exts_list = [ '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', # All tests in this directory fail with segfault (TensorFlow Graph IR) '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + # Fails on e.g. AMD EPYC and known to be flaky on Mac: https://github.com/tensorflow/tensorflow/issues/56717 + '-//tensorflow/python/data/experimental/kernel_tests/service:fault_tolerance_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + From ea50cabc57803fa6d9a10dee8f4897a6555371b6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Jul 2022 14:27:36 +0200 Subject: [PATCH 4722/9987] Remove tensorflow-io-gcs-filesystem dependency --- ...TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 7 +++---- .../TensorFlow/TensorFlow-2.7.1-foss-2021b.eb | 7 +++---- ...rFlow-2.7.1_remove-io-gcs-dependency.patch | 19 +++++++++++++++++++ 3 files changed, 25 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-io-gcs-dependency.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 2434df0cc60..d5d3eacbe1e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -64,10 +64,6 @@ exts_list = [ ('termcolor', '1.1.0', { 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), - ('tensorflow-io-gcs-filesystem', '0.24.0', { - 'source_tmpl': 'tensorflow_io_gcs_filesystem-0.24.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl', - 'checksums': ['cbc71b3925508bf796644a0083a6f9284f71404654f53092bece701383a69520'], - }), ('tensorflow_estimator', '2.7.0', { 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', 'checksums': ['325b5a224864379242b7b76c6987ca544239be82579d33e68ec7c2bda57abc9d'], @@ -178,6 +174,7 @@ exts_list = [ 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', 'TensorFlow-2.7.1_fix_protobuf_error_message.patch', 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.7.1_remove-io-gcs-dependency.patch', 'TensorFlow-2.7.1_fix_cpu_count.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', @@ -237,6 +234,8 @@ exts_list = [ '301ce21845987dc7868624880c0d85e60aa5491c5a0bae0f6ebc8db5727960a5', # TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', + # TensorFlow-2.7.1_remove-io-gcs-dependency.patch + '01c439749938f9fc23fe8de17592460aa46e201575a3f9465bfb6b39ca50ef20', # TensorFlow-2.7.1_fix_cpu_count.patch '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb index 53a9d683f85..b5376694084 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb @@ -60,10 +60,6 @@ exts_list = [ ('termcolor', '1.1.0', { 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), - ('tensorflow-io-gcs-filesystem', '0.24.0', { - 'source_tmpl': 'tensorflow_io_gcs_filesystem-0.24.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl', - 'checksums': ['cbc71b3925508bf796644a0083a6f9284f71404654f53092bece701383a69520'], - }), ('tensorflow_estimator', '2.7.0', { 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', 'checksums': ['325b5a224864379242b7b76c6987ca544239be82579d33e68ec7c2bda57abc9d'], @@ -174,6 +170,7 @@ exts_list = [ 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', 'TensorFlow-2.7.1_fix_protobuf_error_message.patch', 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.7.1_remove-io-gcs-dependency.patch', 'TensorFlow-2.7.1_fix_cpu_count.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', @@ -233,6 +230,8 @@ exts_list = [ '301ce21845987dc7868624880c0d85e60aa5491c5a0bae0f6ebc8db5727960a5', # TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', + # TensorFlow-2.7.1_remove-io-gcs-dependency.patch + '01c439749938f9fc23fe8de17592460aa46e201575a3f9465bfb6b39ca50ef20', # TensorFlow-2.7.1_fix_cpu_count.patch '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-io-gcs-dependency.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-io-gcs-dependency.patch new file mode 100644 index 00000000000..ddd71bc1607 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-io-gcs-dependency.patch @@ -0,0 +1,19 @@ +This Python package is not available as a binary for all architectures and building it +requires TensorFlow to be installed, i.e. there is a cyclic dependency. +As it is not actually required (but optional) remove it from `REQUIRED_PACKAGES`. +See https://github.com/tensorflow/tensorflow/issues/56636 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index a9ef0ee00b2..bcac1449099 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -106,7 +106,6 @@ REQUIRED_PACKAGES = [ + # Keras release is not backward compatible with old tf release, and we have + # to make the version aligned between TF and Keras. + 'keras >= 2.7.0rc0, < 2.8', +- 'tensorflow-io-gcs-filesystem >= 0.21.0', + ] + + From 0b6c0599f71010c4d4959bc3e23292c51190d8f8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Jul 2022 15:38:20 +0200 Subject: [PATCH 4723/9987] Remove libclang dependency --- ...TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 8 +++---- .../TensorFlow/TensorFlow-2.7.1-foss-2021b.eb | 8 +++---- ...low-2.7.1_remove-libclang-dependency.patch | 22 +++++++++++++++++++ 3 files changed, 28 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-libclang-dependency.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index d5d3eacbe1e..1cd3c17f6d0 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -116,11 +116,6 @@ exts_list = [ ('opt_einsum', '3.3.0', { 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], }), - ('libclang', '13.0.0', { - 'modulename': 'clang', - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-manylinux1_x86_64.whl', - 'checksums': ['9c1e623340ccafe3a10a2abbc90f59593ff29f0c854f4ddb65b6220d9d998fb4'], - }), ('Keras_Preprocessing', '1.1.2', { 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], }), @@ -175,6 +170,7 @@ exts_list = [ 'TensorFlow-2.7.1_fix_protobuf_error_message.patch', 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', 'TensorFlow-2.7.1_remove-io-gcs-dependency.patch', + 'TensorFlow-2.7.1_remove-libclang-dependency.patch', 'TensorFlow-2.7.1_fix_cpu_count.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', @@ -236,6 +232,8 @@ exts_list = [ 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', # TensorFlow-2.7.1_remove-io-gcs-dependency.patch '01c439749938f9fc23fe8de17592460aa46e201575a3f9465bfb6b39ca50ef20', + # TensorFlow-2.7.1_remove-libclang-dependency.patc + 'd202058c0e8a7cdef3157fe12327e23c7291ce2724a15653df0aae3b40c4dadc', # TensorFlow-2.7.1_fix_cpu_count.patch '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb index b5376694084..e54e43b8deb 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb @@ -112,11 +112,6 @@ exts_list = [ ('opt_einsum', '3.3.0', { 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], }), - ('libclang', '13.0.0', { - 'modulename': 'clang', - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-manylinux1_x86_64.whl', - 'checksums': ['9c1e623340ccafe3a10a2abbc90f59593ff29f0c854f4ddb65b6220d9d998fb4'], - }), ('Keras_Preprocessing', '1.1.2', { 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], }), @@ -171,6 +166,7 @@ exts_list = [ 'TensorFlow-2.7.1_fix_protobuf_error_message.patch', 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', 'TensorFlow-2.7.1_remove-io-gcs-dependency.patch', + 'TensorFlow-2.7.1_remove-libclang-dependency.patch', 'TensorFlow-2.7.1_fix_cpu_count.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', @@ -232,6 +228,8 @@ exts_list = [ 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', # TensorFlow-2.7.1_remove-io-gcs-dependency.patch '01c439749938f9fc23fe8de17592460aa46e201575a3f9465bfb6b39ca50ef20', + # TensorFlow-2.7.1_remove-libclang-dependency.patc + 'd202058c0e8a7cdef3157fe12327e23c7291ce2724a15653df0aae3b40c4dadc', # TensorFlow-2.7.1_fix_cpu_count.patch '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-libclang-dependency.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-libclang-dependency.patch new file mode 100644 index 00000000000..18f00da8db5 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_remove-libclang-dependency.patch @@ -0,0 +1,22 @@ +This dependency was introduced in +https://github.com/tensorflow/tensorflow/commit/c211472000ff57bac7fcec9b0465cf73b37bf135 +> This is in preparation to open-source TF's TFRT backend. +> TFRT generates code using libclang python bindings as part of the build. + +Hence it is not currently used and as it is not (easily) available for all architectures +simply remove it. + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index a9ef0ee00b2..6740e2fe3a7 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -82,7 +82,6 @@ REQUIRED_PACKAGES = [ + # Install other dependencies + 'absl-py >= 0.4.0', + 'astunparse >= 1.6.0', +- 'libclang >= 9.0.1', + 'flatbuffers >= 1.12, < 3.0', # capped as jax 0.1.71 needs < 3.0 + 'google_pasta >= 0.1.1', + 'h5py >= 2.9.0', # capped since 3.3.0 lacks py3.6 From fd13d3e28f22cbf43076f8d567e53052cde5af54 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 15:25:13 +0100 Subject: [PATCH 4724/9987] Sanity check commands added, pkg-config replaced with pkgconf --- .../d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb index 2b0e0d55ab9..18c6be8c2e6 100644 --- a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ checksums = ['7d550dccdfcd286e33895501829ed971eeb65c614e73aadb4a08aeef719b143a'] builddependencies = [ ('binutils', '2.37'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ('Python', '3.9.6', '-bare'), # Python is needed for building against GLib. ] @@ -24,6 +24,11 @@ dependencies = [ ('expat', '2.4.1'), ] +sanity_check_commands = [ + 'dbus-binding-tool --version', + 'dbus-binding-tool --help', +] + sanity_check_paths = { 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], 'dirs': ['include', 'share'] From 6d7dec9a74a4efd69c83733baf1ff51d74e802cd Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 15:52:34 +0100 Subject: [PATCH 4725/9987] Surplus configopts removed --- easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb index 061f0d2f4c2..99d8ea62f69 100644 --- a/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb @@ -28,7 +28,6 @@ builddependencies = [ ] separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=release ' runtest = 'check' From 96376e57a4a36fdd4f3654511bd67ac6c04bdba3 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 5 Sep 2022 16:29:39 +0100 Subject: [PATCH 4726/9987] adding easyconfigs: pftoolsV3-3.2.12-GCCcore-11.2.0.eb --- .../pftoolsV3-3.2.12-GCCcore-11.2.0.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0d6af2d1239 --- /dev/null +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb @@ -0,0 +1,70 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## +easyblock = 'CMakeMake' + +name = 'pftoolsV3' +version = '3.2.12' + +homepage = 'https://github.com/sib-swiss/pftools3' +description = """A suite of tools to build and search generalized profiles (protein and DNA).""" +software_license = 'LicenseGPLv2' + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/'] +checksums = ['1de33d6444015942afa690d54a103ad5a3d68f416fad63f247c12fa3f71a550c'] # pftools3-3.2.12.tar.gz + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('make', '4.3'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libgd', '2.3.3'), + ('libharu', '2.3.0', '', ('foss', '2021b')), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('PCRE2', '10.37'), + ('Perl', '5.34.0'), + ('zlib', '1.2.11'), +] + +configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX:PATH=%(installdir)s -DCMAKE_BUILD_TYPE=Release ' +configure_cmd += '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON ' +configure_cmd += '-DUSE_AFFINITY=OFF ' # Disable affinity for some old architectures +configure_cmd += '../pftools3-%(version)s' + +runtest = 'test' + +sanity_check_paths = { + 'files': [ + 'bin/2ft', + 'bin/6ft', + 'bin/htop', + 'bin/pfdump', + 'bin/pfscan', + 'bin/pfscanV3', + 'bin/pfsearch', + 'bin/pfsearchV3', + 'bin/ptof', + ], + 'dirs': [ + 'share/doc', + 'share/man' + ], +} + +sanity_check_commands = [ + 'pfscanV3 --help', + 'pfsearchV3 --help', +] + +moduleclass = 'bio' From 3b7f147beb2a806837d25f8c61743891f81a250c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 5 Sep 2022 17:50:04 +0200 Subject: [PATCH 4727/9987] adding easyconfigs: OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb, OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb --- ...-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb | 37 ++++++++++++++++++ ...-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb | 38 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100755 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb create mode 100755 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb new file mode 100755 index 00000000000..283ed67934d --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.9' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] + +dependencies = [ + ('CUDA', '11.4.1', '', True), + ('NCCL', '2.10.3', versionsuffix), + ('UCX-CUDA', '1.11.0', versionsuffix), +] + +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA --enable-ncclomb --with-nccl=$EBROOTNCCL' + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] + [ + 'libexec/osu-micro-benchmarks/nccl/%s' % x for x in ['collective', 'pt2pt'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb new file mode 100755 index 00000000000..f081748a1b9 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.9' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('NCCL', '2.12.12', versionsuffix), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('UCC-CUDA', '1.0.0', versionsuffix), +] + +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA --enable-ncclomb --with-nccl=$EBROOTNCCL' + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] + [ + 'libexec/osu-micro-benchmarks/nccl/%s' % x for x in ['collective', 'pt2pt'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From b765d5c3fad543b2be84de2fd5e218b681795488 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 5 Sep 2022 18:04:30 +0200 Subject: [PATCH 4728/9987] Fix version of dependency to avoid mixing --- .../OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb index 283ed67934d..65c303f62cb 100755 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb @@ -17,7 +17,7 @@ checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] dependencies = [ ('CUDA', '11.4.1', '', True), ('NCCL', '2.10.3', versionsuffix), - ('UCX-CUDA', '1.11.0', versionsuffix), + ('UCX-CUDA', '1.11.2', versionsuffix), ] configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA --enable-ncclomb --with-nccl=$EBROOTNCCL' From 7920d862bfb31fdd3f6b39aeb259a0212b947ac5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Sep 2022 20:15:26 +0200 Subject: [PATCH 4729/9987] remove easyconfig for pkg-config with GCCcore/11.3.0 (to avoid confusion with pkgconf) --- .../pkg-config-0.29.2-GCCcore-11.3.0.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb deleted file mode 100644 index a55b2586ff3..00000000000 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-11.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'pkg-config' -version = '0.29.2' - -homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' - -description = """ - pkg-config is a helper tool used when compiling applications and libraries. - It helps you insert the correct compiler options on the command line so an - application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` - for instance, rather than hard-coding values on where to find glib (or other - libraries). -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://pkg-config.freedesktop.org/releases/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] - -builddependencies = [('binutils', '2.38')] - -# don't use PAX, it might break. -tar_config_opts = True - -configopts = " --with-internal-glib" - -sanity_check_paths = { - 'files': ['bin/pkg-config'], - 'dirs': [], -} - -moduleclass = 'devel' From 14f1abd76d8d34eeddd40dfa1edd59b69e540a77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Sep 2022 20:22:06 +0200 Subject: [PATCH 4730/9987] add missing binutils build dependency in nghttp3 easyconfig --- easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb index 99d8ea62f69..4ad0ab76d8e 100644 --- a/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb @@ -22,6 +22,7 @@ checksums = [ ] builddependencies = [ + ('binutils', '2.37'), ('CMake', '3.22.1'), ('pkg-config', '0.29.2'), ('CUnit', '2.1-3'), From e14b03f43597c15ccd9ee62585e482edc9fe0ca3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Sep 2022 20:25:22 +0200 Subject: [PATCH 4731/9987] add missing binutils build dependency in ccache easyconfig --- easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb index b3f2927a4f2..355a2da891f 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb @@ -21,6 +21,7 @@ checksums = ['59b28a57c3a45e48d6049001999c9f94cd4d3e9b0196994bed9a6a7437ffa3bc'] osdependencies = [('glibc-static', 'libc6-dev', 'glibc-devel')] builddependencies = [ + ('binutils', '2.37'), ('CMake', '3.22.1'), ('Ninja', '1.10.2'), ('zstd', '1.5.0', ), From a014627bdd1175595d2675b4fbb72e270a77f0e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Sep 2022 20:28:49 +0200 Subject: [PATCH 4732/9987] remove enabling separate_build_dir in nghttp3 easyconfig, since it is already enabled by default --- easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb index 4ad0ab76d8e..3916daaba5e 100644 --- a/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.2.0.eb @@ -28,8 +28,6 @@ builddependencies = [ ('CUnit', '2.1-3'), ] -separate_build_dir = True - runtest = 'check' sanity_check_paths = { From f423c1a2d571c7a7495bc6e4bf691c0031bb0d09 Mon Sep 17 00:00:00 2001 From: Abhishek Mukherjee <65731510+absrocks@users.noreply.github.com> Date: Mon, 5 Sep 2022 15:45:01 -0400 Subject: [PATCH 4733/9987] Update easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 1216443c302..747759ef299 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -1172,7 +1172,7 @@ exts_list = [ }), ('File::Slurp', '9999.32', { 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', - 'source_urls': ['https:// cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], 'checksums': ['4c3c21992a9d42be3a79dd74a3c83d27d38057269d65509a2f555ea0fb2bc5b0'], }), ('Package::Stash', '0.40', { From 196b63523efe2193004cac89ae4aead6e805da8b Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 21:29:21 +0100 Subject: [PATCH 4734/9987] adding easyconfigs: xtrans-1.3.5-GCCcore-11.3.0.eb --- .../x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ebc6c85e148 --- /dev/null +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'xtrans' +version = '1.3.5' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """xtrans includes a number of routines to make X implementations transport-independent; + at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. +""" + +# toolchain = {'name': 'intel', 'version': '2016a'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +checksums = ['b7a577c1b6c75030145e53b4793db9c88f9359ac49e7d771d4385d21b3e5945d'] + +builddependencies = [ + ('xorg-macros', '1.19.3'), + ('libxslt', '1.1.34'), +] + +sanity_check_paths = { + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], + 'dirs': [], +} + +moduleclass = 'devel' From 6f0e2b705c43da2e94395c7bf2db16bc027fed59 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 21:34:38 +0100 Subject: [PATCH 4735/9987] adding easyconfigs: xproto-7.0.31-GCCcore-11.3.0.eb --- .../x/xproto/xproto-7.0.31-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..13e248f42e0 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = 'https://www.freedesktop.org/wiki/Software/xlibs' +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] + +builddependencies = [ + ('binutils', '2.38'), + ('xorg-macros', '1.19.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' From 1e2e12769e5863065b5add0809c71ee742d4455d Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Sep 2022 22:18:48 +0100 Subject: [PATCH 4736/9987] adding easyconfigs: plotutils-2.6-GCC-11.3.0.eb and patches: plotutils-2.6-png.patch --- .../p/plotutils/plotutils-2.6-GCC-11.3.0.eb | 60 +++++++++++++++++++ .../p/plotutils/plotutils-2.6-png.patch | 40 +++++++++++++ 2 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/plotutils/plotutils-2.6-png.patch diff --git a/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb new file mode 100644 index 00000000000..4b23dad22cf --- /dev/null +++ b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb @@ -0,0 +1,60 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'plotutils' +version = '2.6' + +homepage = 'https://www.gnu.org/software/plotutils/' +description = """The GNU plotutils package contains software for both programmers and +technical users. Its centerpiece is libplot, a powerful C/C++ function library for +exporting 2-D vector graphics in many file formats, both vector and bitmap. On the +X Window System, it can also do 2-D vector graphics animations. + +libplot is device-independent, in the sense that its API (application programming interface) +does not depend on the type of graphics file to be exported. A Postscript-like API +is used both for file export and for graphics animations. A libplot programmer needs +to learn only one API: not the details of many graphics file formats.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/plotutils'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-png.patch'] + +checksums = [ + '4f4222820f97ca08c7ea707e4c53e5a3556af4d8f1ab51e0da6ff1627ff433ab', # plotutils-2.6.tar.gz + 'd60997b0608db37d494f60394a468cd5491e200862d8d9af32ba1dbc3c178aaa', # plotutils-2.6-png.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('gawk', '5.1.1'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('X11', '20220504'), + ('libICE', '1.0.9'), +] + +configopts = '--enable-libxmi --enable-ps-fonts-in-pcl --enable-libplotter ' +configopts += '--enable-lj-fonts-in-ps ' + +runtest = 'check' + +local_bin = [ + 'double', 'graph', 'hersheydemo', 'ode', 'pic2plot', 'plot', + 'plotfont', 'spline', 'tek2plot' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin] + + ['lib/libplot.a', 'lib/libplot.%s' % SHLIB_EXT] + + ['lib/libplotter.a', 'lib/libplotter.%s' % SHLIB_EXT] + + ['lib/libxmi.a', 'lib/libxmi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/plotutils/plotutils-2.6-png.patch b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-png.patch new file mode 100644 index 00000000000..abb18420d29 --- /dev/null +++ b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-png.patch @@ -0,0 +1,40 @@ +Patch to ensure png-1.5 and higher can be used, taken from +https://lists.gnu.org/archive/html/bug-plotutils/2011-01/msg00000.html +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/plotutils-2.6.orig/libplot/z_write.c b/plotutils-2.6/libplot/z_write.c +index d76a7cc..173d4a9 100644 +--- a/plotutils-2.6.orig/libplot/z_write.c ++++ b/plotutils-2.6/libplot/z_write.c +@@ -164,7 +164,7 @@ _pl_z_maybe_output_image (S___(Plotter *_plotter)) + } + + /* cleanup after libpng errors (error handler does a longjmp) */ +- if (setjmp (png_ptr->jmpbuf)) ++ if (setjmp (png_jmpbuf (png_ptr))) + { + png_destroy_write_struct (&png_ptr, (png_info **)NULL); + return -1; +@@ -444,7 +444,11 @@ _our_error_fn_stdio (png_struct *png_ptr, const char *data) + #endif + } + ++#if (PNG_LIBPNG_VER < 10500) + longjmp (png_ptr->jmpbuf, 1); ++#else ++ png_longjmp (png_ptr, 1); ++#endif + } + + static void +@@ -515,7 +519,11 @@ _our_error_fn_stream (png_struct *png_ptr, const char *data) + #endif + } + ++#if (PNG_LIBPNG_VER < 10500) + longjmp (png_ptr->jmpbuf, 1); ++#else ++ png_longjmp (png_ptr, 1); ++#endif + } + + static void From a729749b512f121b381c9205b16ad1afccc83f9c Mon Sep 17 00:00:00 2001 From: am2455 Date: Mon, 5 Sep 2022 17:55:17 -0400 Subject: [PATCH 4737/9987] update Perl-5.36.0-GCCcore-12.1.0.eb --- .../p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 25 +++++++++---------- 1 file changed, 12 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 747759ef299..e66b50795a7 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -110,47 +110,47 @@ exts_list = [ }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN/'], + 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN'], 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], }), ('Importer', '0.026', { 'source_tmpl': 'Importer-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], }), ('Term::Table', '0.016', { 'source_tmpl': 'Term-Table-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], }), ('Scope::Guard', '0.21', { 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE/'], + 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE'], 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], }), ('Sub::Info', '0.002', { 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], }), ('Test2::Require::Module', '0.000145', { 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ed44be739c8879fe178d3107b238f2db960d52797db0058de53be5b84600358b'], }), ('Test2::Plugin::NoWarnings', '0.09', { 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY/'], + 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], }), ('Class::Tiny', '1.008', { 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN/'], + 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], }), ('Test::File::ShareDir::Dist', '1.001002', { 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL/'], + 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL'], 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], }), ('DateTime::Locale', '1.36', { @@ -963,9 +963,8 @@ exts_list = [ 'source_tmpl': 'List-UtilsBy-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], 'checksums': ['fff1281fd469fe982b1a58044becfd970f313bff3a26e1c7b2b3f4c0a5ed71e0'], - }), - - ('List::AllUtils', '0.19', { + }), + ('List::AllUtils', '0.19', { 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['30a8146ab21a7787b8c56d5829cf9a7f2b15276d3b3fca07336ac38d3002ffbc'], @@ -1172,7 +1171,7 @@ exts_list = [ }), ('File::Slurp', '9999.32', { 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'source_urls': ['https:// cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], 'checksums': ['4c3c21992a9d42be3a79dd74a3c83d27d38057269d65509a2f555ea0fb2bc5b0'], }), ('Package::Stash', '0.40', { From 12c1f3311a5b597ebc66ff7b529f616d9a9484e9 Mon Sep 17 00:00:00 2001 From: am2455 Date: Mon, 5 Sep 2022 18:14:22 -0400 Subject: [PATCH 4738/9987] update Perl-5.36.0-GCCcore-12.1.0.eb --- easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index e66b50795a7..e7dca1d21be 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -963,7 +963,7 @@ exts_list = [ 'source_tmpl': 'List-UtilsBy-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], 'checksums': ['fff1281fd469fe982b1a58044becfd970f313bff3a26e1c7b2b3f4c0a5ed71e0'], - }), + }), ('List::AllUtils', '0.19', { 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], From 42f0c6d217f05de81039f961f227c38d263628c8 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 6 Sep 2022 09:39:20 +0100 Subject: [PATCH 4739/9987] OS dependencies removed, libev added, toolchain changed to GCC, DCMAKE_BUILD_TYPE=release removed as not needed --- ...-0.7.0-GCCcore-11.2.0.eb => ngtcp2-0.7.0-GCC-11.2.0.eb} | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/n/ngtcp2/{ngtcp2-0.7.0-GCCcore-11.2.0.eb => ngtcp2-0.7.0-GCC-11.2.0.eb} (83%) diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb similarity index 83% rename from easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb index 81bcc53c6e2..6b12dec5b6a 100644 --- a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb @@ -11,7 +11,7 @@ description = """ ngtcp2 project is an effort to implement RFC9000 QUIC protocol.""" -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchain = {'name': 'GCC', 'version': '11.2.0'} toolchainopts = {'pic': True} github_account = 'ngtcp2' @@ -32,13 +32,12 @@ dependencies = [ ('OpenSSL', '1.1', '', True), ('GnuTLS', '3.7.3'), ('nghttp3', '0.6.0'), + ('libev', '4.33'), ] -osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] - separate_build_dir = True -configopts = '-DCMAKE_BUILD_TYPE=release -DENABLE_GNUTLS=True' +configopts = '-DENABLE_GNUTLS=True' runtest = 'check' From 90bc1e79a18e4ee517e79408a291f0c7b6bdfd04 Mon Sep 17 00:00:00 2001 From: anselmicz Date: Tue, 6 Sep 2022 13:19:28 +0200 Subject: [PATCH 4740/9987] adding easyconfigs: fio-3.32-GCCcore-11.3.0.eb --- .../f/fio/fio-3.32-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b06f97130a7 --- /dev/null +++ b/easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'fio' +version = '3.32' + +homepage = 'https://github.com/axboe/fio' + +description = 'Flexible I/O tester' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'axboe' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['409e459840912e68be487dbbda9a7a1b3f6ddf1478e3f456f278f957ce4f7b66'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': [], +} + +sanity_check_commands = ['fio -h'] + +moduleclass = 'tools' From 4a91eb46847c6bc37cb75fb192ed07fc874c47f0 Mon Sep 17 00:00:00 2001 From: anselmicz Date: Tue, 6 Sep 2022 15:13:42 +0200 Subject: [PATCH 4741/9987] adding easyconfigs: nano-6.4.eb --- easybuild/easyconfigs/n/nano/nano-6.4.eb | 30 ++++++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/nano/nano-6.4.eb diff --git a/easybuild/easyconfigs/n/nano/nano-6.4.eb b/easybuild/easyconfigs/n/nano/nano-6.4.eb new file mode 100644 index 00000000000..0fdacab025c --- /dev/null +++ b/easybuild/easyconfigs/n/nano/nano-6.4.eb @@ -0,0 +1,30 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +easyblock = 'ConfigureMake' + +name = 'nano' +version = '6.4' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = SYSTEM + +source_urls = ['https://www.nano-editor.org/dist/v6/'] +sources = [SOURCE_TAR_GZ] +checksums = ['85ebd9b4dba49839821d529bea16ac1acae0c9b9db2157531e40c9dffeb1b656'] + +dependencies = [('ncurses', '6.2')] + +configopts = '--enable-color --enable-extra --enable-multibuffer --enable-nanorc --enable-utf8' + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' From cf101bc2366e038f594b4ab01a64e51677378e08 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Tue, 6 Sep 2022 15:24:33 +0200 Subject: [PATCH 4742/9987] Update fio-3.32-GCCcore-11.3.0.eb --- easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb index b06f97130a7..a6d5afcf82b 100644 --- a/easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ sanity_check_paths = { 'files': ['bin/fio'], - 'dirs': [], + 'dirs': ['bin', 'man', 'share'], } sanity_check_commands = ['fio -h'] From 46585d999ab64a4be918bcef67b1147712977e20 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Sep 2022 15:26:11 +0200 Subject: [PATCH 4743/9987] restore modextrapaths to add top-level install directory to $PATH in InterProScan 5.52-86.0 easyconfig, still required since Tarball easyblock is used --- .../i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb index 552a8d8df97..b3d5765b73d 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb @@ -39,4 +39,7 @@ sanity_check_paths = { sanity_check_commands = ["interproscan.sh 2>&1 | grep 'Welcome to InterProScan-%(version)s'"] +# also include top install directory in $PATH, to make interproscan.sh available +modextrapaths = {'PATH': ''} + moduleclass = 'bio' From 92fbeb97ee861d13eebc2141416646570f7c4137 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Tue, 6 Sep 2022 15:48:32 +0200 Subject: [PATCH 4744/9987] Update fio-3.32-GCCcore-11.3.0.eb --- easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb index a6d5afcf82b..06bbde187fe 100644 --- a/easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/fio/fio-3.32-GCCcore-11.3.0.eb @@ -4,7 +4,7 @@ name = 'fio' version = '3.32' homepage = 'https://github.com/axboe/fio' - +docurls = 'https://fio.readthedocs.io/en/latest/index.html' description = 'Flexible I/O tester' toolchain = {'name': 'GCCcore', 'version': '11.3.0'} From 5508f1bec3f8da72c0986c36d83cb0c93fe43435 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 6 Sep 2022 16:58:12 +0200 Subject: [PATCH 4745/9987] Fix miscomputation in OpenBLAS on POWER --- .../o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 5 +++- ...-0.3.12_add-missing-params-for-power.patch | 23 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb | 13 +++++++---- ...S-0.3.7_add-missing-params-for-power.patch | 23 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb | 11 +++++---- .../o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb | 11 +++++---- 6 files changed, 72 insertions(+), 14 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_add-missing-params-for-power.patch create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_add-missing-params-for-power.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index f3346d9db0a..a0d4dffee1d 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -15,7 +15,8 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), - 'OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-%(version)s_add-missing-params-for-power.patch', '%(name)s-0.3.15_icelake-detection.patch', ] checksums = [ @@ -24,6 +25,8 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch '4b3ab7260975ea2cfd7460731c0201b2c1e374cd83ae90d55b8da3e670633ba0', + # OpenBLAS-0.3.12_add-missing-params-for-power.patch + '4454af07290d1fe33e414023a41bb8999d6ee31887e194daa72bd23d46a0072a', '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', # OpenBLAS-0.3.15_icelake-detection.patch ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_add-missing-params-for-power.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_add-missing-params-for-power.patch new file mode 100644 index 00000000000..3bad4d7bca3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_add-missing-params-for-power.patch @@ -0,0 +1,23 @@ +This fixes inexact calculations on POWER, see https://github.com/xianyi/OpenBLAS/issues/2923 +From https://github.com/xianyi/OpenBLAS/pull/3062 + +Backported by Alexander Grund (TU Dresden) + +--- + param.h | 6 ++++++ + 1 file changed, 6 insertions(+) + +diff --git a/param.h b/param.h +index f3ddde6..35f579b 100644 +--- a/param.h ++++ b/param.h +@@ -2397,6 +2397,9 @@ USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + #define GEMM_DEFAULT_OFFSET_B 65536 + #define GEMM_DEFAULT_ALIGN 0x0ffffUL + ++#define SWITCH_RATIO 16 ++#define GEMM_PREFERED_SIZE 16 ++ + #define SGEMM_DEFAULT_UNROLL_M 16 + #define SGEMM_DEFAULT_UNROLL_N 8 + #define DGEMM_DEFAULT_UNROLL_M 16 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb index 23c7cb7aea5..58fe90fcc5b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb @@ -15,16 +15,19 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), - 'OpenBLAS-0.3.7_fix-build-on-arm-tsv110.patch', - 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', - 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', - 'OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch', - 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', + '%(name)s-%(version)s_add-missing-params-for-power.patch', + '%(name)s-%(version)s_fix-build-on-arm-tsv110.patch', + '%(name)s-%(version)s_fix-missing-sync-on-power.patch', + '%(name)s-%(version)s_reinit-threads-after-fork.patch', + '%(name)s-%(version)s_fix-possible-memory-leak-after-fork.patch', + '%(name)s-0.3.8_fix-dscal-inline-asm.patch', ] checksums = [ 'bde136122cef3dd6efe2de1c6f65c10955bbb0cc01a520c2342f5287c28f9379', # v0.3.7.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.7_add-missing-params-for-power.patch + '969ac4708092a6862cd9a03541c5c0588b191513d15492b022319daed5a1cd89', '5d5ec94002daefe10a839f621bf083c85fbda6c55c5e486f48375a2891f405c5', # OpenBLAS-0.3.7_fix-build-on-arm-tsv110.patch # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_add-missing-params-for-power.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_add-missing-params-for-power.patch new file mode 100644 index 00000000000..cc556272dd6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_add-missing-params-for-power.patch @@ -0,0 +1,23 @@ +This fixes inexact calculations on POWER, see https://github.com/xianyi/OpenBLAS/issues/2923 +From https://github.com/xianyi/OpenBLAS/pull/3062 + +Backported by Alexander Grund (TU Dresden) + +--- + param.h | 6 ++++++ + 1 file changed, 6 insertions(+) + +diff --git a/param.h b/param.h +index 6c5e0f107b..6a790ab615 100644 +--- a/param.h ++++ b/param.h +@@ -2239,6 +2239,9 @@ USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + #define GEMM_DEFAULT_OFFSET_B 65536 + #define GEMM_DEFAULT_ALIGN 0x0ffffUL + ++#define SWITCH_RATIO 16 ++#define GEMM_PREFERED_SIZE 16 ++ + #define SGEMM_DEFAULT_UNROLL_M 16 + #define SGEMM_DEFAULT_UNROLL_N 8 + #define DGEMM_DEFAULT_UNROLL_M 16 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb index 5d292f2abb7..4d8542cb37e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb @@ -15,15 +15,18 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), - 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', - 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', - 'OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch', - 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', + '%(name)s-0.3.7_add-missing-params-for-power.patch', + '%(name)s-0.3.7_fix-missing-sync-on-power.patch', + '%(name)s-0.3.7_reinit-threads-after-fork.patch', + '%(name)s-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-%(version)s_fix-dscal-inline-asm.patch', ] checksums = [ '8f86ade36f0dbed9ac90eb62575137388359d97d8f93093b38abe166ad7ef3a8', # v0.3.8.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.7_add-missing-params-for-power.patch + '969ac4708092a6862cd9a03541c5c0588b191513d15492b022319daed5a1cd89', # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', # OpenBLAS-0.3.7_reinit-threads-after-fork.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb index 1658647c8e2..c390c260b68 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb @@ -15,15 +15,18 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), - 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', - 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', - 'OpenBLAS-0.3.7_fix-possible-memory-leak-after-fork.patch', - 'OpenBLAS-0.3.9_fix-lapack_h.patch', + '%(name)s-0.3.7_add-missing-params-for-power.patch', + '%(name)s-0.3.7_fix-missing-sync-on-power.patch', + '%(name)s-0.3.7_reinit-threads-after-fork.patch', + '%(name)s-0.3.7_fix-possible-memory-leak-after-fork.patch', + '%(name)s-%(version)s_fix-lapack_h.patch', ] checksums = [ '17d4677264dfbc4433e97076220adc79b050e4f8a083ea3f853a53af253bc380', # v0.3.9.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.7_add-missing-params-for-power.patch + '969ac4708092a6862cd9a03541c5c0588b191513d15492b022319daed5a1cd89', # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', # OpenBLAS-0.3.7_reinit-threads-after-fork.patch From 399330a3503ef77cf7c7f2c5d4a80011b5802e77 Mon Sep 17 00:00:00 2001 From: am2455 Date: Tue, 6 Sep 2022 11:40:00 -0400 Subject: [PATCH 4746/9987] update Perl-5.36.0-GCCcore-12.1.0.eb --- easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index e7dca1d21be..2a1efcc2d51 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -1171,7 +1171,7 @@ exts_list = [ }), ('File::Slurp', '9999.32', { 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', - 'source_urls': ['https:// cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], 'checksums': ['4c3c21992a9d42be3a79dd74a3c83d27d38057269d65509a2f555ea0fb2bc5b0'], }), ('Package::Stash', '0.40', { From 794fe30a1bc68952529660a79031d2fe0e9be141 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Tue, 6 Sep 2022 17:18:23 +0100 Subject: [PATCH 4747/9987] Update easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb Erm, yes. Sorry, I did not spot that. :-( Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb index ebc6c85e148..1c2cd18d426 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb @@ -8,7 +8,6 @@ description = """xtrans includes a number of routines to make X implementations at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. """ -# toolchain = {'name': 'intel', 'version': '2016a'} toolchain = {'name': 'GCCcore', 'version': '11.3.0'} sources = [SOURCE_TAR_GZ] From e7e270b0af18e857cd29c3bf1f8e6df29945633f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Tue, 6 Sep 2022 17:19:07 +0100 Subject: [PATCH 4748/9987] Update easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb I am sure one day I remember that! Thanks for spotting it. Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb index 1c2cd18d426..88d3be5c7ec 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-GCCcore-11.3.0.eb @@ -16,6 +16,7 @@ source_urls = [XORG_LIB_SOURCE] checksums = ['b7a577c1b6c75030145e53b4793db9c88f9359ac49e7d771d4385d21b3e5945d'] builddependencies = [ + ('binutils', '2.38'), ('xorg-macros', '1.19.3'), ('libxslt', '1.1.34'), ] From 4ca825aa27c5cf4c1b73efe2b6b02bd318a44d58 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Tue, 6 Sep 2022 20:15:39 +0200 Subject: [PATCH 4749/9987] Update nano-6.4.eb Switched from v6 to v%(version_major)s for future compatibility, removed configopts as they are all enabled by default, see http://git.savannah.gnu.org/cgit/nano.git/tree/src/nano.c#n990 --- easybuild/easyconfigs/n/nano/nano-6.4.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/nano/nano-6.4.eb b/easybuild/easyconfigs/n/nano/nano-6.4.eb index 0fdacab025c..b21cac6032b 100644 --- a/easybuild/easyconfigs/n/nano/nano-6.4.eb +++ b/easybuild/easyconfigs/n/nano/nano-6.4.eb @@ -12,14 +12,12 @@ description = """a simple editor, inspired by Pico""" toolchain = SYSTEM -source_urls = ['https://www.nano-editor.org/dist/v6/'] +source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] sources = [SOURCE_TAR_GZ] checksums = ['85ebd9b4dba49839821d529bea16ac1acae0c9b9db2157531e40c9dffeb1b656'] dependencies = [('ncurses', '6.2')] -configopts = '--enable-color --enable-extra --enable-multibuffer --enable-nanorc --enable-utf8' - sanity_check_paths = { 'files': ['bin/nano'], 'dirs': ['bin', 'share'], From f35ddfe32fe0894d6d4983acfe7892fcf60bf642 Mon Sep 17 00:00:00 2001 From: Carsten Bauer Date: Wed, 7 Sep 2022 09:51:19 +0200 Subject: [PATCH 4750/9987] Create Julia-1.8.0-linux-x86_64.eb --- .../j/Julia/Julia-1.8.0-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb new file mode 100644 index 00000000000..07b8c3a4138 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.8.0' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['e80d732ccb7f79e000d798cb8b656dc3641ab59516d6e4e52e16765017892a00'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From a50c8ce8828c177178f2c4ec98eb454239f90e02 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Wed, 7 Sep 2022 09:40:34 +0100 Subject: [PATCH 4751/9987] Create libharu-2.3.0-GCCcore-11.2.0.eb New build against GCCcore 11.2.0. --- .../l/libharu/libharu-2.3.0-GCCcore-11.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..096b2528e4a --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'http://libharu.org/' +description = """libHaru is a free, cross platform, open source library for generating PDF files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GITHUB_SOURCE] # https://github.com/libharu/libharu/archive/ +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] + +dependencies = [('libpng', '1.6.37')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': [ + 'if', + 'include', + 'lib', + ] +} + +moduleclass = 'lib' From 459899f74c7c2fb0c0cc62915cff3fe1a8470d7e Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Wed, 7 Sep 2022 09:47:32 +0100 Subject: [PATCH 4752/9987] Update pftoolsV3-3.2.12-GCCcore-11.2.0.eb Changed libharu dependency to new version built using GCCcore toolchain. --- .../p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb index 0d6af2d1239..cb6c4a8bce1 100644 --- a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb @@ -1,10 +1,3 @@ -## -# This is a contribution from SIB Swiss Institute of Bioinformatics -# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it -# -# Authors:: Sebastien Moretti -# -## easyblock = 'CMakeMake' name = 'pftoolsV3' @@ -29,7 +22,7 @@ builddependencies = [ dependencies = [ ('libgd', '2.3.3'), - ('libharu', '2.3.0', '', ('foss', '2021b')), + ('libharu', '2.3.0'), ('libjpeg-turbo', '2.0.6'), ('libpng', '1.6.37'), ('PCRE2', '10.37'), From 1dbf21c654ccae652601fd2b67ab191b8bdaa62f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Sep 2022 13:44:53 +0200 Subject: [PATCH 4753/9987] make sure that Python packages like futile are installed in right location BigDFT install script using --with-python-prefix --- easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb index 64317a11c77..cfe636d5d2b 100644 --- a/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/b/BigDFT/BigDFT-1.9.1-foss-2021b.eb @@ -43,6 +43,8 @@ extract_sources = True local_install_opts = '--enable-mpi --with-yaml-path=\\"$EBROOTLIBYAML\\" ' local_install_opts += '--with-ext-linalg=\\"-L$SCALAPACK_LIB_DIR $LIBSCALAPACK -L$LAPACK_LIB_DIR $LIBBLAS\\" ' +# make sure that Python packages like futile are installed to right location by BigDFT install script +local_install_opts += '--with-python_prefix=%(builddir)s/bigdft-suite-%(version)s/bigdft_builddir/install ' local_install_opts += 'CC=\\"$MPICC\\" FC=\\"$MPIFC\\" ' local_install_opts += 'FCFLAGS=\\"$CPPFLAGS $FCFLAGS -fallow-argument-mismatch -std=legacy\\" ' local_install_opts += 'FFLAGS=\\"$CPPFLAGS $FFLAGS -fallow-argument-mismatch -std=legacy\\" ' From b97f6c12dbf1b798b4e014c4e9da56e6daf873e8 Mon Sep 17 00:00:00 2001 From: Jakub Kropacek Date: Wed, 7 Sep 2022 15:09:13 +0200 Subject: [PATCH 4754/9987] switch from system toolchain to GCCcore/11.3.0 --- .../n/nano/nano-6.4-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/nano/nano-6.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nano/nano-6.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nano/nano-6.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9addd89ff5c --- /dev/null +++ b/easybuild/easyconfigs/n/nano/nano-6.4-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +easyblock = 'ConfigureMake' + +name = 'nano' +version = '6.4' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['85ebd9b4dba49839821d529bea16ac1acae0c9b9db2157531e40c9dffeb1b656'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('ncurses', '6.3')] + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' From 1f31ac477d067440fb6cf05363050d1855b8c6f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Wed, 7 Sep 2022 15:13:42 +0200 Subject: [PATCH 4755/9987] Delete nano-6.4.eb --- easybuild/easyconfigs/n/nano/nano-6.4.eb | 28 ------------------------ 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/n/nano/nano-6.4.eb diff --git a/easybuild/easyconfigs/n/nano/nano-6.4.eb b/easybuild/easyconfigs/n/nano/nano-6.4.eb deleted file mode 100644 index b21cac6032b..00000000000 --- a/easybuild/easyconfigs/n/nano/nano-6.4.eb +++ /dev/null @@ -1,28 +0,0 @@ -# Contribution from IT4Innovations National Supercomputing Center, Czech Republic -# Jakub Kropacek, 2022 - -easyblock = 'ConfigureMake' - -name = 'nano' -version = '6.4' - -homepage = 'https://www.nano-editor.org/' -docurls = 'https://www.nano-editor.org/docs.php' -description = """a simple editor, inspired by Pico""" - -toolchain = SYSTEM - -source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['85ebd9b4dba49839821d529bea16ac1acae0c9b9db2157531e40c9dffeb1b656'] - -dependencies = [('ncurses', '6.2')] - -sanity_check_paths = { - 'files': ['bin/nano'], - 'dirs': ['bin', 'share'], -} - -sanity_check_commands = ['nano --version'] - -moduleclass = 'tools' From 5debee7c27b9c4f69777d068f00f6e5a0c19b777 Mon Sep 17 00:00:00 2001 From: Ghepardo <71766441+Ghepardo@users.noreply.github.com> Date: Wed, 7 Sep 2022 15:30:47 +0100 Subject: [PATCH 4756/9987] Update pftoolsV3-3.2.12-GCCcore-11.2.0.eb Made requested amendments - slightly more concisely. --- .../p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb index cb6c4a8bce1..abb076bd8d5 100644 --- a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.2.0.eb @@ -30,10 +30,7 @@ dependencies = [ ('zlib', '1.2.11'), ] -configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX:PATH=%(installdir)s -DCMAKE_BUILD_TYPE=Release ' -configure_cmd += '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON ' -configure_cmd += '-DUSE_AFFINITY=OFF ' # Disable affinity for some old architectures -configure_cmd += '../pftools3-%(version)s' +configopts = '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON -DUSE_AFFINITY=OFF' # Disable affinity for some old architectures runtest = 'test' From 1e1efd0fc0a1874ec469cd861fcfe69694372622 Mon Sep 17 00:00:00 2001 From: am2455 Date: Wed, 7 Sep 2022 12:21:39 -0400 Subject: [PATCH 4757/9987] update ncurses-6.3-GCCcore-12.1.0.eb --- .../n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb index 511870df0ab..32007f86507 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb @@ -28,20 +28,21 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS -postinstallcmds = [ - "(cd %(installdir)s/lib && ln -s libncurses.so libtinfo.so)", - "(cd %(installdir)s/lib && ln -s libncurses.a libtinfo.a)" -] +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] -local_libs = ["form", "menu", "ncurses", "panel"] sanity_check_paths = { 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", "reset", "tabs", "tic", "toe", "tput", "tset"]] + - ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + - ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + - ['lib/libncurses++%s.a' % x for x in ['', 'w']], + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], 'dirs': ['include', 'include/ncursesw'], } + moduleclass = 'devel' From f5867beb0ca7db304316cbe1ea1d724fe202d641 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Sep 2022 18:45:52 +0200 Subject: [PATCH 4758/9987] sync comments + strip empty line in easyconfig for ncurses 6.3 with GCCcore/12.1.0 --- .../easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb index 32007f86507..843c52c75d9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb @@ -22,9 +22,9 @@ builddependencies = [('binutils', '2.38')] local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " configopts = [ - # default build + # build ncurses: serial build in default paths with shared libraries local_common_configopts, - # the UTF-8 enabled version (ncursesw) + # build ncursesw: serial with UTF-8 local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] @@ -44,5 +44,4 @@ sanity_check_paths = { 'dirs': ['include', 'include/ncursesw'], } - moduleclass = 'devel' From 2e91283ebe1b9dbc758cd5383e6821470ca3528d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Sep 2022 10:02:17 +0200 Subject: [PATCH 4759/9987] {lang}[GCCcore/12.2.0] Perl v5.36.0, libreadline v8.1.2, ncurses v6.3, ... --- .../d/DB/DB-18.1.40-GCCcore-12.2.0.eb | 33 + .../e/expat/expat-2.4.8-GCCcore-12.2.0.eb | 30 + .../g/groff/groff-1.22.4-GCCcore-12.2.0.eb | 27 + .../libreadline-8.1.2-GCCcore-12.2.0.eb | 41 + .../n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb | 47 + .../p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 1939 +++++++++++++++++ 6 files changed, 2117 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7bc947e2ae0 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('OpenSSL', '1.1', '', True)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..df978cec524 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' +name = 'expat' +version = '2.4.8' + +homepage = 'https://libexpat.github.io' + +description = """Expat is an XML parser library written in C. It is a stream-oriented parser +in which an application registers handlers for things the parser might find +in the XML document (like start tags).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_TAR_BZ2] +checksums = ['a247a7f6bbb21cf2ca81ea4cbb916bfb9717ca523631675f99b3d4a5678dcd16'] + +builddependencies = [('binutils', '2.39')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e2b37f3dcd4 --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.22.4' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] + +builddependencies = [ + ('binutils', '2.39'), +] + +configopts = '--with-doc=no' + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b164af87b06 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.1.2' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['7589a2381a8419e68654a47623ce7dfcb756815c8fee726b98f90bf668af7bc6'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('ncurses', '6.3'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7fed097a62f --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.3' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] + +builddependencies = [('binutils', '2.39')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts, + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5e960b5fcac --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -0,0 +1,1939 @@ +name = 'Perl' +version = '5.36.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = ['perl-%(version)s.tar.gz'] +checksums = ['e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'] + +builddependencies = [ + ('binutils', '2.39'), + ('groff', '1.22.4'), +] + +dependencies = [ + ('zlib', '1.2.12'), # for Net::SSLeay + ('expat', '2.4.8'), # for XML::Parser + ('ncurses', '6.3'), # for Term::ReadLine::Gnu + ('libreadline', '8.1.2'), # for Term::ReadLine::Gnu + ('DB', '18.1.40'), # for DB_File + ('OpenSSL', '1.1', '', True), # required for Net::SSLeay +] + +# !! order of extensions is important !! +# extensions updated on Apr 28th 2022 +exts_list = [ + ('Config::General', '2.65', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['4d6d5754be3a9f30906836f0cc10e554c8832e14e7a1341efb15b05d706fc58f'], + }), + ('File::Listing', '6.15', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['46c4fb9f9eb9635805e26b7ea55b54455e47302758a10ed2a0b92f392713770c'], + }), + ('ExtUtils::InstallPaths', '0.012', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], + }), + ('Test::Harness', '3.44', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7eb591ea6b499ece6745ff3e80e60cee669f0037f9ccbc4e4511425f593e5297'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7d580ff6ace0cbe555bf36b86dc8ea232581530cbeaaea09bccb57b55797f11c'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Test::Fatal', '0.016', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7283d430f2ba2030b8cd979ae3039d3f1b2ec3dde1a11ca6ae09f992a66f788f'], + }), + ('Test::Warnings', '0.031', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['1e542909fef305e45563e9878ea1c3b0c7cef1b28bb7ae07eba2e1efabec477b'], + }), + ('File::ShareDir', '1.118', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], + }), + ('File::ShareDir::Install', '0.14', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'], + }), + ('IPC::System::Simple', '1.30', { + 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], + }), + ('Importer', '0.026', { + 'source_tmpl': 'Importer-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], + }), + ('Term::Table', '0.016', { + 'source_tmpl': 'Term-Table-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], + }), + ('Scope::Guard', '0.21', { + 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE'], + 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], + }), + ('Sub::Info', '0.002', { + 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], + }), + ('Test2::Require::Module', '0.000145', { + 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['ed44be739c8879fe178d3107b238f2db960d52797db0058de53be5b84600358b'], + }), + ('Test2::Plugin::NoWarnings', '0.09', { + 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], + }), + ('Class::Tiny', '1.008', { + 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], + }), + ('Test::File::ShareDir::Dist', '1.001002', { + 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], + }), + ('DateTime::Locale', '1.36', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['90a8243f2b2d4068019c65178600e76e03f5b478cb41d18c8c81cdf0d481f0a4'], + }), + ('DateTime::TimeZone', '2.53', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['4f6e9ff86892a52334bfb8dfa74ebea6adb8afd04fefcba8ae52fc054c4c15b3'], + }), + ('Test::Requires', '0.11', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': ['4b88de549597eecddf7c3c38a4d0204a16f59ad804577b671896ac04e24e040f'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 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['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['153c8eb8ef0f19cf2c631d5b45d05de98516937f34e261125ef242fba1fe2ea4'], + }), + ('Scalar::Util', '1.63', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['cafbdf212f6827dc9a0dd3b57b6ee50e860586d7198228a33262d55c559eb2a9'], + }), + ('Text::ParseWords', '3.31', { + 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['2ae555ba084d75b2b8feeeb8d1a00911276815ada86bccb1452236964d5a2fc7'], + }), + ('Encode', '3.19', { + 'source_tmpl': 'Encode-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], + 'checksums': ['9163f848eef69e4d4cc8838397f0861fd9ea7ede001117dbd9694f8d95052ef5'], + }), + ('constant', '1.33', { + 'source_tmpl': 'constant-%(version)s.tar.gz', + 'source_urls': 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['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['c8b362b860172a4076acee00438f52b86464f2c500702cfcf7527811ff9a683e'], + }), + ('XSLoader', '0.24', { + 'source_tmpl': 'XSLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'], + 'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], + }), + ('AutoLoader', '5.74', { + 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], + }), + ('URI::Escape', '5.12', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['66abe0eaddd76b74801ecd28ec1411605887550fc0a45ef6aa744fdad768d9b3'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], + 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], + }), + ('MCE::Mutex', '1.879', { + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], + 'checksums': ['9c4cf39838b5c113448799af451b3d64b54e0de39d635536d7e85e8bdc5888dc'], + }), + ('Text::CSV_XS', '1.48', { + 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['b72a2ed61c63561f6bfc1d5986a09f3ac252bdfda5c1c898b0b677641ce1e8bf'], + }), + ('DBD::CSV', '0.59', { + 'source_tmpl': 'DBD-CSV-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['2a5fadd1d50c18ea023560d39c2cc660ae2a65fa99d9b8244edca7d2dcce9dc0'], + }), + ('Array::Transpose', '0.06', { + 'source_tmpl': 'Array-Transpose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'], + 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], + }), + ('Config::Simple', '4.58', { + 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], + 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], + }), + ('Business::ISBN', '3.007', { + 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['50cc4686dd21c9537b49a231d71711e814ebd2f19aa4ca331baf92ff2de5ce19'], + }), + ('Business::ISBN::Data', '20210112.006', { + 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['98c2cfb266b5fdd016989abaa471d9dd4c1d593c508a6f01f66d184d5fee8bae'], + }), + ('common::sense', '3.75', { + 'source_tmpl': 'common-sense-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], + }), + ('IO::Compress::Bzip2', '2.201', { + 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['f6c55c4e39cfaa3219965dd3b36c9de1edee9a82a10a9cadeb3b74a9ceeeaaad'], + }), + ('JSON::XS', '4.03', { + 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], + }), + ('List::MoreUtils::XS', '0.430', { + 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], + }), + ('Authen::NTLM', '1.09', { + 'source_tmpl': 'NTLM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'], + 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('XML::SAX::Expat', '0.51', { + 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN'], + 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], + }), + ('Inline', '0.86', { + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], + }), + ('Sys::Info::Base', '0.7807', { + 'source_tmpl': 'Sys-Info-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['132362b0046e8dc4f12e1560903623a88a8871d09bf1c29d93d48d3f4a582acb'], + }), + ('Sys::Info', '0.7811', { + 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'], + }), + ('HTML::Template', '2.97', { + 'source_tmpl': 'HTML-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR/'], + 'checksums': ['6547af61f3aa85793f8616190938d677d7995fb3b720c16258040bc935e2129f'], + }), + ('MIME::Charset', '1.013.1', { + 'source_tmpl': 'MIME-Charset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI/'], + 'checksums': ['1bb7a6e0c0d251f23d6e60bf84c9adefc5b74eec58475bfee4d39107e60870f0'], + }), + ('Unicode::LineBreak', '2019.001', { + 'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI/'], + 'checksums': ['486762e4cacddcc77b13989f979a029f84630b8175e7fef17989e157d4b6318a'], + }), + ('String::Print', '0.94', { + 'source_tmpl': 'String-Print-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'], + }), + ('Log::Report', '1.33', { + 'source_tmpl': 'Log-Report-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['49624da338fd7d57288fa22a47241476fb5ce2f6008181f786c7830fe5af01ff'], + }), + ('Log::Report::Optional', '1.07', { + 'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV/'], + 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], + }), + ('Sys::Info::Driver::Unknown', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Sys::Info::Driver::Linux', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK/'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER/'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), +] + +moduleclass = 'lang' From 22bf4e74a6fc93817af1ff0af5b237fc2c96c3f7 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 8 Sep 2022 10:14:25 +0100 Subject: [PATCH 4760/9987] adding easyconfigs: MATLAB-2022a.eb, MATLAB-2022a_Update_3.eb --- .../easyconfigs/m/MATLAB/MATLAB-2022a.eb | 26 +++++++++++++++++++ .../m/MATLAB/MATLAB-2022a_Update_3.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2022a.eb create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2022a_Update_3.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2022a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022a.eb new file mode 100644 index 00000000000..0e2c7e7f5aa --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022a.eb @@ -0,0 +1,26 @@ +name = 'MATLAB' +version = '2022a' + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +sources = ['R%(version)s_Linux.iso'] +checksums = ['0d998829fd8b030b83581ca3db414a494a8ad937ad2ed3efefc846a5033fd795'] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server_port = 'XXXXX' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2022a_Update_3.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022a_Update_3.eb new file mode 100644 index 00000000000..4e560cfb59c --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022a_Update_3.eb @@ -0,0 +1,26 @@ +name = 'MATLAB' +version = '2022a_Update_3' + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +sources = ['R%(version)s_Linux.iso'] +checksums = ['7fabee86864e5ac2da4096c2c13dd712b19022ec3fa1c2cc3680df85f3f11e15'] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server_port = 'XXXXX' + +moduleclass = 'math' From 4035fd1b63b5b9711a8994db010bfa29a270a49f Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 8 Sep 2022 12:24:04 +0100 Subject: [PATCH 4761/9987] adding easyconfigs: crossguide-20190529-GCCcore-11.3.0.eb and patches: libuuid-20190529.patch --- .../crossguide-20190529-GCCcore-11.3.0.eb | 54 +++++++++++++++++++ .../c/crossguide/libuuid-20190529.patch | 19 +++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6e0f31e5436 --- /dev/null +++ b/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.3.0.eb @@ -0,0 +1,54 @@ +# Contribution from Imperial College London, UK +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'crossguide' +local_commit = 'ca1bf4b' +version = '20190529' + +homepage = 'https://github.com/graeme-hill/crossguid' +description = """ +CrossGuid is a minimal, cross platform, C++ GUID library. +It uses the best native GUID/UUID generator on the given platform and has a +generic class for parsing, stringifying, and comparing IDs. +The guid generation technique is determined by your platform:""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/graeme-hill/crossguid/archive/%s' % local_commit] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = ['libuuid-20190529.patch'] + +checksums = [ + '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguide-20190529.tar.gz + '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # libuuid-20190529.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('util-linux', '2.38'), +] + +# build demo +# build static and shared libraries +configopts = ["-DCROSSGUID_TESTS=ON", "-DBUILD_SHARED_LIBS=TRUE"] + +# we want to have the crossguid-test +install_cmd = "make install && " +install_cmd += "mkdir -p %(installdir)s/bin/ && " +install_cmd += "cp -f crossguid-test %(installdir)s/bin/ " + +sanity_check_paths = { + 'files': ['lib/libcrossguid.a', 'bin/crossguid-test'], + 'dirs': ['include'], +} + +sanity_check_commands = [('crossguid-test')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch b/easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch new file mode 100644 index 00000000000..d75df709152 --- /dev/null +++ b/easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch @@ -0,0 +1,19 @@ +Updates the older Libuuid to LibUUID so CMake does not complain +Author: J. Sassmannshausen +diff --git a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/CMakeLists.txt b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/CMakeLists.txt +index 76b5a62..03291c5 100644 +--- a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/CMakeLists.txt ++++ b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/CMakeLists.txt +@@ -30,7 +30,7 @@ elseif(ANDROID) + # GUID_ANDROID is used in the headers, so make PUBLIC + target_compile_definitions(crossguid PUBLIC GUID_ANDROID) + else() +- find_package(Libuuid REQUIRED) ++ find_package(LibUUID REQUIRED) + if (NOT LIBUUID_FOUND) + message(FATAL_ERROR + "You might need to run 'sudo apt-get install uuid-dev' or similar") +diff --git a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/cmake/FindLibuuid.cmake b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/cmake/FindLibUUID.cmake +similarity index 100% +rename from crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/cmake/FindLibuuid.cmake +rename to crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/cmake/FindLibUUID.cmake From 4164948e2b20aaf11ca6e467c353fe6525138468 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 8 Sep 2022 12:25:40 +0100 Subject: [PATCH 4762/9987] adding easyconfigs: fmt-9.1.0-GCCcore-11.3.0.eb --- .../f/fmt/fmt-9.1.0-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ee5eb6a8fa8 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '9.1.0' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['cceb4cb9366e18a5742128cb3524ce5f50e88b476f1e54737a47ffdf4df4c996'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38') +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' From 27b2bae7d9176d70bcbfda293a70bd7fce99020a Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 8 Sep 2022 12:27:12 +0100 Subject: [PATCH 4763/9987] adding easyconfigs: indicators-2.2-GCCcore-11.3.0.eb --- .../indicators-2.2-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/i/indicators/indicators-2.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/indicators/indicators-2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/indicators/indicators-2.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ba18df6c7bc --- /dev/null +++ b/easybuild/easyconfigs/i/indicators/indicators-2.2-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +# Contribution from Imperial College London/UK +# uploaded: J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'indicators' +version = '2.2' + +homepage = 'https://github.com/p-ranav/indicators' +description = """ +- Thread-safe progress bars and spinners +- Header-only library. Grab a copy of include/indicators. +- Single-header version in single_include/indicators. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/p-ranav/indicators/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b768f1b7ca64a413503f72d5460cc617c1458c17fb7a8c0ee503d753e1f20d03'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38') +] + +# build demo and sample program +configopts = ["-DINDICATORS_SAMPLES=ON -DINDICATORS_DEMO=ON -DINDICATORS_BUILD_TESTS=ON"] + +install_cmd = "make install && " +install_cmd += "mkdir %(installdir)s/bin/ && " +install_cmd += "cp demo/demo %(installdir)s/bin/ && " +install_cmd += "cp samples/*bar* samples/dynamic* %(installdir)s/bin/ && " +install_cmd += "cp samples/progress_spinner samples/time_meter samples/max_progress %(installdir)s/bin/" + +sanity_check_paths = { + 'files': ['bin/demo', 'bin/time_meter'], + 'dirs': ['include', 'lib'], +} + +sanity_check_commands = [('demo')] + +moduleclass = 'tools' From 2ad8381123bbb6c52df5684bd1181f205258e651 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 8 Sep 2022 12:38:59 +0100 Subject: [PATCH 4764/9987] Update Dakota-6.16.0-foss-2021b.eb adding sanity check command to easyconfig --- .../d/Dakota/Dakota-6.16.0-foss-2021b.eb | 44 +++++++++---------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb index 2d38a4be771..db07b6ad1eb 100644 --- a/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb +++ b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb @@ -1,10 +1,10 @@ # /!\ IMPORTANT: you need at least 8 cores to complete successfully the tests # Author: Jir Furst # Based on Dakota 6.15 easyconfig by Sebastien Varrette (Falkor) -easyblock = 'CMakeMake' +easyblock = "CMakeMake" -name = 'Dakota' -version = '6.16.0' +name = "Dakota" +version = "6.16.0" homepage = "https://dakota.sandia.gov/" description = """ @@ -15,29 +15,27 @@ description = """ models. """ -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {"name": "foss", "version": "2021b"} # Disable architecture optimization, otherwise the basic tests fail -toolchainopts = {'pic': True, 'usempi': True, 'optarch': False} +toolchainopts = {"pic": True, "usempi": True, "optarch": False} -source_urls = ['https://dakota.sandia.gov/sites/default/files/distributions/public/'] +source_urls = ["https://dakota.sandia.gov/sites/default/files/distributions/public/"] sources = ["%(namelower)s-%(version_major_minor)s.0-public-src-cli.tar.gz"] patches = ["%(name)s-%(version)s-boost177-dllimport.patch"] checksums = [ - '49684ade2a937465d85b0fc69c96408be38bc1603ed2e7e8156d93eee3567d2f', # dakota-6.16.0-public-src-cli.tar.gz - '23aa52a4fe4267ba65368597b2b6c9e6e4bd4a1c8c4f1383055d73602ae9cc2d', # Dakota-6.16.0-boost177-dllimport.patch + "49684ade2a937465d85b0fc69c96408be38bc1603ed2e7e8156d93eee3567d2f", # dakota-6.16.0-public-src-cli.tar.gz + "23aa52a4fe4267ba65368597b2b6c9e6e4bd4a1c8c4f1383055d73602ae9cc2d", # Dakota-6.16.0-boost177-dllimport.patch ] dependencies = [ - ('Boost', '1.77.0'), - ('Perl', '5.34.0'), - ('Python', '3.9.6'), - ('HDF5', '1.12.1'), - ('GSL', '2.7'), + ("Boost", "1.77.0"), + ("Perl", "5.34.0"), + ("Python", "3.9.6"), + ("HDF5", "1.12.1"), + ("GSL", "2.7"), ] -builddependencies = [ - ('CMake', '3.21.1') -] +builddependencies = [("CMake", "3.21.1")] separate_build_dir = True build_shared_libs = True @@ -55,11 +53,13 @@ configopts += "-DDAKOTA_HAVE_GSL=ON " runtest = ' test ARGS="-L AcceptanceTest -j %(parallel)s" ' # Run install step in parallel -installopts = ' -j %(parallel)s ' +installopts = " -j %(parallel)s " + +sanity_check_paths = {"files": ["bin/dakota"], "dirs": []} -sanity_check_paths = { - 'files': ["bin/dakota"], - 'dirs': [] -} +sanity_check_commands = [ + "dakota -v", + "dakota -h", +] -moduleclass = 'math' +moduleclass = "math" From 8b654645cae075a7f894876eb0ea4244e33e5d70 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 8 Sep 2022 12:52:44 +0100 Subject: [PATCH 4765/9987] adding easyconfigs: rapidcsv-8.64-GCCcore-11.3.0.eb --- .../rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..113dfcfb507 --- /dev/null +++ b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +# Contribution from Imperial College London/UK +# uploaded: J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'rapidcsv' +version = '8.64' + +homepage = 'https://github.com/d99kris/rapidcsv' +description = """ +Rapidcsv is a C++ header-only library for CSV parsing. +While the name admittedly was inspired by the rapidjson project, +the objectives are not the same. The goal of rapidcsv is to be +an easy-to-use CSV library enabling rapid development. +For optimal performance (be it CPU or memory usage) a CSV parser +implemented for the specific use-case is likely to be more performant. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/d99kris/rapidcsv/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e2ab5231b6e65f1e168dc279bbba2e34afd43c7bc6e2522726b107bcc4e8ebac'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38') +] + +sanity_check_paths = { + 'files': ['include/rapidcsv.h'], + 'dirs': [''], +} + +moduleclass = 'tools' From aee3a3971827e8ea41adf142aa6309e970e7cb81 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 8 Sep 2022 12:57:43 +0100 Subject: [PATCH 4766/9987] adding easyconfigs: healthgps-1.1.3.0-GCCcore-11.3.0.eb and patches: healthgps-20220316-CMake.patch --- .../healthgps-1.1.3.0-GCCcore-11.3.0.eb | 65 +++++++++++++++++++ .../healthgps/healthgps-20220316-CMake.patch | 42 ++++++++++++ 2 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/h/healthgps/healthgps-20220316-CMake.patch diff --git a/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8a31631972f --- /dev/null +++ b/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,65 @@ +# Contribution from Imperial College London, UK +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMakeCp' + +name = 'healthgps' +version = '1.1.3.0' + +homepage = 'https://github.com/imperialCHEPI/healthgps' +description = """ +Health-GPS microsimulation is part of the STOP project, and support researchers +and policy makers in the analysis of the health and economic impacts of alternative +measures to tackle chronic diseases and obesity in children. The model reproduces +the characteristics of a population and simulates key individual event histories +associated with key components of relevant behaviours, such as physical activity, +and diseases such as diabetes or cancer. +To run the test-jobs with HealthGPS.Tests the data-directory, found in your installation +folder, must be in the current path. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/imperialCHEPI/healthgps/archive'] +sources = ['v.%(version)s.tar.gz'] +patches = ['healthgps-20220316-CMake.patch'] + +checksums = [ + '62ff13811ca0ec313aa166bb53bc89516c3135bc78a6fba6711c5a0d8d4c98ec', # healthgps-1.1.3.0.tar.gz + '315e70c12edfe15535dbd54ac99ea66d41df3989a0917b8da7f024fdea2af609', # healthgps-20220316-CMake.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('crossguide', '20190529'), + ('nlohmann_json', '3.10.5'), + ('rapidcsv', '8.64'), + ('fmt', '9.1.0'), + ('googletest', '1.11.0'), + ('cxxopts', '3.0.0', '', True), + ('indicators', '2.2'), +] + +# We need to make sure we find the data-dir, so we just link it. +# This is bash, so we need to do a hack about the source directory. +prebuildopts = 'ln -s ../healthgps*/data data && ' + +files_to_copy = [ + (['src/HealthGPS.Console/HealthGPS.Console', 'src/HealthGPS.Tests/HealthGPS.Tests'], 'bin'), + 'data' +] + + +sanity_check_paths = { + 'files': ['bin/HealthGPS.Console', 'bin/HealthGPS.Tests'], + 'dirs': ['data'], +} + +sanity_check_commands = ['HealthGPS.Tests'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/healthgps/healthgps-20220316-CMake.patch b/easybuild/easyconfigs/h/healthgps/healthgps-20220316-CMake.patch new file mode 100644 index 00000000000..d6c9d394e7e --- /dev/null +++ b/easybuild/easyconfigs/h/healthgps/healthgps-20220316-CMake.patch @@ -0,0 +1,42 @@ +Patch to removed the build dependency to vcpkg as we are using EasyBuild for that +author: J. Sassmannshausen +diff --git a/healthgps.orig/CMakePresets.json b/healthgps/CMakePresets.json +index d29ef60..b3a3132 100644 +--- a/healthgps.orig/CMakePresets.json ++++ b/healthgps/CMakePresets.json +@@ -6,9 +6,9 @@ + "description": "Shared configuration presets", + "hidden": true, + "generator": "Ninja", +- "binaryDir": "${sourceDir}/out/build/${presetName}", ++ "binaryDir": "${sourceDir}/build", + "cacheVariables": { +- "CMAKE_INSTALL_PREFIX": "${sourceDir}/out/install/${presetName}" ++ "CMAKE_INSTALL_PREFIX": "${sourceDir}/build/install/${presetName}" + } + }, + { +@@ -18,15 +18,7 @@ + "inherits": "base", + "cacheVariables": { + "CMAKE_BUILD_TYPE": "Debug", +- "CMAKE_CXX_COMPILER": "g++", +- "CMAKE_TOOLCHAIN_FILE": { +- "value": "$env{VCPKG_ROOT}/scripts/buildsystems/vcpkg.cmake", +- "type": "FILEPATH" +- } +- }, +- "vendor": { +- "microsoft.com/VisualStudioSettings/CMake/1.0": { "hostOS": [ "Linux" ] }, +- "microsoft.com/VisualStudioRemoteSettings/CMake/1.0": { "sourceDir": "$env{HOME}/.vs/$ms{projectDirName}" } ++ "CMAKE_CXX_COMPILER": "g++" + } + }, + { +@@ -108,4 +100,4 @@ + "configurePreset": "x64-debug" + } + ] +-} +\ No newline at end of file ++} From fec5d05b3b12cd2be260119458ed5fd10269ec52 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 8 Sep 2022 15:27:17 +0100 Subject: [PATCH 4767/9987] adding easyconfigs: x13as-1-1-b59-GCCcore-10.2.0.eb --- .../x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b3b916d6405 --- /dev/null +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb @@ -0,0 +1,51 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'x13as' +version = '1-1-b59' + +homepage = 'https://www.census.gov/data/software/x13as.About_X-13.html' + +description = """ +X-13ARIMA-SEATS is seasonal adjustment software produced, distributed, +and maintained by the Census Bureau. + +Features of X-13ARIMA-SEATS include: + - Extensive time series modeling and model selection capabilities for + linear regression models with ARIMA errors (regARIMA models); + - The capability to generate ARIMA model-based seasonal adjustment + using a version of the SEATS software originally developed by Victor + Gómez and Agustín Maravall at the Bank of Spain, as well as nonparametric + adjustments from the X-11 procedure; + - Diagnostics of the quality and stability of the adjustments + achieved under the options selected; + - The ability to efficiently process many series at once. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://www2.census.gov/software/x-13arima-seats/x13as/unix-linux/program-archives', +] +sources = ['%(name)s_asciisrc-v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + '256ee87f326ef6e0ac33a806812d614a5584c6b9e1f2a67ec06af52f2c3be85d', # x13as_asciisrc-v1-1-b59.tar.gz + 'cbde094a2396c256e9ac996cd539806bb0274e569d578ad42c4879f0e02c5ef3', # x13as-v1-1_makefile.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +build_cmd = 'make -f makefile.gf' + +files_to_copy = [(["x13as"], "bin")] + +sanity_check_paths = { + 'files': ['bin/x13as'], + 'dirs': [], +} + +moduleclass = 'tools' From 84e4dfebfed5596f4d75ed040285e958155f81d0 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 8 Sep 2022 15:30:47 +0100 Subject: [PATCH 4768/9987] Patchfile added --- .../x/x13as/x13as-1-1-b59_makefile.patch | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch new file mode 100644 index 00000000000..96ded45a757 --- /dev/null +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59_makefile.patch @@ -0,0 +1,29 @@ +Patch to build with newer versions of gfortran +see: https://salsa.debian.org/science-team/x13as/-/blob/master/debian/rules#L4 +Author: J. Sassmannshausen, Thomas Hayward-Schneider, Jasper Grimm +diff --git a/x13as_asciisrc-v1-1-b59.orig/makefile.gf b/x13as_asciisrc-v1-1-b59/makefile.gf +index e60896e..cb1b38e 100644 +--- a/x13as_asciisrc-v1-1-b59.orig/makefile.gf ++++ b/x13as_asciisrc-v1-1-b59/makefile.gf +@@ -1,10 +1,10 @@ + # MKMF template makefile for protected mode executables. + FC = gfortran + LINKER = gfortran +-PROGRAM = x13as_ascii ++PROGRAM = x13as + DEST = . + EXTHDRS = +-FFLAGS = -O2 ++FFLAGS = -O2 -std=legacy + HDRS = + LDFLAGS = -s + LDMAP = +@@ -290,7 +290,7 @@ SRCS = aaamain.f abend.f acf.f acfar.f acfdgn.f \ + testodf.f + + $(PROGRAM): $(OBJS) $(LIBS) +- $(LINKER) -static -o $@ $(OBJS) $(LDMAP) $(LIBS) $(LDFLAGS) ++ $(LINKER) -o $@ $(OBJS) $(LDMAP) $(LIBS) $(LDFLAGS) + + clean:; @rm -f $(OBJS) + From 430f674f784a9dd3dc3c86ec386a291bea46ee4c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 8 Sep 2022 15:33:45 +0000 Subject: [PATCH 4769/9987] adding easyconfigs: STAR-CCM+-17.02.008.eb, STAR-CCM+-17.02.008-r8.eb, STAR-CCM+-17.04.008.eb --- .../s/STAR-CCM+/STAR-CCM+-17.02.008-r8.eb | 14 ++++++++++++++ .../easyconfigs/s/STAR-CCM+/STAR-CCM+-17.02.008.eb | 13 +++++++++++++ .../easyconfigs/s/STAR-CCM+/STAR-CCM+-17.04.008.eb | 13 +++++++++++++ 3 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.02.008-r8.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.02.008.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.04.008.eb diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.02.008-r8.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.02.008-r8.eb new file mode 100644 index 00000000000..3b0dff61b6b --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.02.008-r8.eb @@ -0,0 +1,14 @@ +name = 'STAR-CCM+' +version = '17.02.008' +versionsuffix = '-r8' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +sources = ['%%(name)s%%(version)s_01_linux-x86_64%s.tar.gz' % versionsuffix] +checksums = ['15a341c7140275498c294f9c573682f57f82110a99f8d59435e8fdc3943ba84c'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.02.008.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.02.008.eb new file mode 100644 index 00000000000..5c454cccf3b --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.02.008.eb @@ -0,0 +1,13 @@ +name = 'STAR-CCM+' +version = '17.02.008' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +sources = ['%(name)s%(version)s_01_linux-x86_64.tar.gz'] +checksums = ['67bbe7215908e01d86f256f1079bb904e6898eb81e59640bcb554bed69c261eb'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.04.008.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.04.008.eb new file mode 100644 index 00000000000..56964b48ab4 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.04.008.eb @@ -0,0 +1,13 @@ +name = 'STAR-CCM+' +version = '17.04.008' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +sources = ['%(name)s%(version)s_01_linux-x86_64.tar.gz'] +checksums = ['c2135f473aeef46808ba4f2b8a242ed2dc15ee9918b77b8cec3ad5cc1c5837e9'] + +moduleclass = 'cae' From a27fd1342b65df388c720a8457335ecedb90cd07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Sep 2022 09:58:55 +0200 Subject: [PATCH 4770/9987] sync Dakota easyconfig with upstream style changes --- .../d/Dakota/Dakota-6.16.0-foss-2021b.eb | 39 +++++++++++-------- 1 file changed, 22 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb index db07b6ad1eb..26d9e284228 100644 --- a/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb +++ b/easybuild/easyconfigs/d/Dakota/Dakota-6.16.0-foss-2021b.eb @@ -1,10 +1,10 @@ # /!\ IMPORTANT: you need at least 8 cores to complete successfully the tests # Author: Jir Furst # Based on Dakota 6.15 easyconfig by Sebastien Varrette (Falkor) -easyblock = "CMakeMake" +easyblock = 'CMakeMake' -name = "Dakota" -version = "6.16.0" +name = 'Dakota' +version = '6.16.0' homepage = "https://dakota.sandia.gov/" description = """ @@ -15,27 +15,29 @@ description = """ models. """ -toolchain = {"name": "foss", "version": "2021b"} +toolchain = {'name': 'foss', 'version': '2021b'} # Disable architecture optimization, otherwise the basic tests fail -toolchainopts = {"pic": True, "usempi": True, "optarch": False} +toolchainopts = {'pic': True, 'usempi': True, 'optarch': False} -source_urls = ["https://dakota.sandia.gov/sites/default/files/distributions/public/"] +source_urls = ['https://dakota.sandia.gov/sites/default/files/distributions/public/'] sources = ["%(namelower)s-%(version_major_minor)s.0-public-src-cli.tar.gz"] patches = ["%(name)s-%(version)s-boost177-dllimport.patch"] checksums = [ - "49684ade2a937465d85b0fc69c96408be38bc1603ed2e7e8156d93eee3567d2f", # dakota-6.16.0-public-src-cli.tar.gz - "23aa52a4fe4267ba65368597b2b6c9e6e4bd4a1c8c4f1383055d73602ae9cc2d", # Dakota-6.16.0-boost177-dllimport.patch + '49684ade2a937465d85b0fc69c96408be38bc1603ed2e7e8156d93eee3567d2f', # dakota-6.16.0-public-src-cli.tar.gz + '23aa52a4fe4267ba65368597b2b6c9e6e4bd4a1c8c4f1383055d73602ae9cc2d', # Dakota-6.16.0-boost177-dllimport.patch ] dependencies = [ - ("Boost", "1.77.0"), - ("Perl", "5.34.0"), - ("Python", "3.9.6"), - ("HDF5", "1.12.1"), - ("GSL", "2.7"), + ('Boost', '1.77.0'), + ('Perl', '5.34.0'), + ('Python', '3.9.6'), + ('HDF5', '1.12.1'), + ('GSL', '2.7'), ] -builddependencies = [("CMake", "3.21.1")] +builddependencies = [ + ('CMake', '3.21.1') +] separate_build_dir = True build_shared_libs = True @@ -53,13 +55,16 @@ configopts += "-DDAKOTA_HAVE_GSL=ON " runtest = ' test ARGS="-L AcceptanceTest -j %(parallel)s" ' # Run install step in parallel -installopts = " -j %(parallel)s " +installopts = ' -j %(parallel)s ' -sanity_check_paths = {"files": ["bin/dakota"], "dirs": []} +sanity_check_paths = { + 'files': ["bin/dakota"], + 'dirs': [] +} sanity_check_commands = [ "dakota -v", "dakota -h", ] -moduleclass = "math" +moduleclass = 'math' From b151919d4aaa19bd3acdaf7b2360f3b1c1b6a3a8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 9 Sep 2022 10:00:34 +0200 Subject: [PATCH 4771/9987] Update easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb --- .../easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb index 03f83bb3c0e..00726da9fca 100644 --- a/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libplinkio/libplinkio-0.9.8-GCCcore-9.3.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'cstd': 'gnu17', 'extra_cflags': '-w'} github_account = "mfranberg" -source_urls = ['https://github.com/%(github_account)s/%(namelower)s/archive/refs/tags'] +source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['de54dd4789b2da9b937a1f445dc6976153211dc35b4376a4cf561ad2ee861075'] From b35bc7bb3f06faef7e010d5001299b88672da9cb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 9 Sep 2022 10:52:54 +0200 Subject: [PATCH 4772/9987] Add r8 variant for 17.04.008 --- .../s/STAR-CCM+/STAR-CCM+-17.04.008-r8.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.04.008-r8.eb diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.04.008-r8.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.04.008-r8.eb new file mode 100644 index 00000000000..996c1eb6f86 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.04.008-r8.eb @@ -0,0 +1,14 @@ +name = 'STAR-CCM+' +version = '17.04.008' +versionsuffix = '-r8' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +sources = ['%%(name)s%%(version)s_01_linux-x86_64%s.tar.gz' % versionsuffix] +checksums = ['d267222a92ffb934983e4639cad13d9a14d15a894eab202715e230c2658b8541'] + +moduleclass = 'cae' From 41856ca8363d12dd5bffc425890d1d4d79f6c080 Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 9 Sep 2022 09:59:53 +0100 Subject: [PATCH 4773/9987] Updated libharu easyconfig as requested --- easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.2.0.eb index 096b2528e4a..29c45f84405 100644 --- a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libharu' version = '2.3.0' -homepage = 'http://libharu.org/' +homepage = 'https://github.com/libharu/libharu/' description = """libHaru is a free, cross platform, open source library for generating PDF files.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} From 6d3ecf3a944076b9644b5993da2e8ed7e660b77e Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 9 Sep 2022 12:09:25 +0200 Subject: [PATCH 4774/9987] adding easyconfigs: VESTA-3.5.8-gtk3.eb --- .../easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb diff --git a/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb b/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb new file mode 100644 index 00000000000..3bba501cdd3 --- /dev/null +++ b/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb @@ -0,0 +1,23 @@ +# Based on https://code.it4i.cz/sccs/easyconfigs-it4i/-/blob/it4i-karolina/v/VESTA/VESTA-3.5.7.eb + +easyblock = 'Binary' + +name = 'VESTA' +version = '3.5.8' +versionsuffix = '-gtk3' + +homepage = "http://www.jp-minerals.org/vesta" +description = """VESTA is a 3D visualization program for structured models, volumetric data such as electron/nuclear densities, and crystal morphologies.""" + +toolchain = SYSTEM + +source_urls = ["http://www.jp-minerals.org/vesta/archives/%(version)s"] +sources = ["%(name)s-gtk3.tar.bz2"] + +extract_sources = True +sanity_check_paths = { + 'files': ['VESTA'], + 'dirs': [], +} + +moduleclass = 'vis' From dc5f84cbe5bf42a6afb577846786000aac0b8f73 Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 9 Sep 2022 12:34:45 +0200 Subject: [PATCH 4775/9987] Add checksums. Style fixes. --- easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb b/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb index 3bba501cdd3..04a2f7c3c56 100644 --- a/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb +++ b/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb @@ -7,17 +7,22 @@ version = '3.5.8' versionsuffix = '-gtk3' homepage = "http://www.jp-minerals.org/vesta" -description = """VESTA is a 3D visualization program for structured models, volumetric data such as electron/nuclear densities, and crystal morphologies.""" +description = """ + VESTA is a 3D visualization program for structured models, + volumetric data such as electron/nuclear densities, + and crystal morphologies. +""" toolchain = SYSTEM source_urls = ["http://www.jp-minerals.org/vesta/archives/%(version)s"] sources = ["%(name)s-gtk3.tar.bz2"] +checksums = ['78bef025c2b31f1d64c9c7e06ad2b139d252b3a686893ee79ac74b3021868df8'] extract_sources = True sanity_check_paths = { - 'files': ['VESTA'], - 'dirs': [], + 'files': ['VESTA'], + 'dirs': [], } moduleclass = 'vis' From 633e2db72c1eb8f5cf538af1d07d6c124a2e2466 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 9 Sep 2022 12:52:24 +0100 Subject: [PATCH 4776/9987] Version for foss-2021b added so it can be added to Ocatve --- .../s/SUNDIALS/SUNDIALS-6.3.0-foss-2021b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2021b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2021b.eb new file mode 100644 index 00000000000..59ea1cd22a1 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2021b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '6.3.0' + +homepage = 'https://computation.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['89a22bea820ff250aa7239f634ab07fa34efe1d2dcfde29cc8d3af11455ba2a7'] + +builddependencies = [('CMake', '3.22.1')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' From 5273f3b39e8ecfbbc23c66385562a37cd9acdf3a Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 9 Sep 2022 14:25:59 +0200 Subject: [PATCH 4777/9987] Update source URL Molekel. --- .../m/Molekel/Molekel-5.4.0-Linux_x86_64.eb | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0-Linux_x86_64.eb b/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0-Linux_x86_64.eb index f69c22f76b8..cee0bcbc267 100644 --- a/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0-Linux_x86_64.eb +++ b/easybuild/easyconfigs/m/Molekel/Molekel-5.4.0-Linux_x86_64.eb @@ -4,16 +4,19 @@ name = "Molekel" version = "5.4.0" versionsuffix = "-Linux_x86_64" -homepage = "http://molekel.cscs.ch/" -description = """Molekel is an open-source multi-platform molecular visualization program.""" +homepage = "http://ugovaretto.github.io/molekel/wiki/pmwiki.php/Main/HomePage.html" +description = """ + Molekel is an open-source multi-platform molecular visualization program. +""" toolchain = SYSTEM -sources = ['molekel_%s_%s.tar.gz' % (version.replace('.', '_'), versionsuffix.lower()[1:])] -source_urls = ['ftp://ftp.cscs.ch/out/molekel/molekel_%(version_major_minor)s'] +sources = ['molekel_%s_%s.tgz' % (version.replace('.', '_'), versionsuffix.lower()[1:])] +source_urls = ["https://github.com/ugovaretto/molekel/releases/download/v%(version_major_minor)s/"] +checksums = ['2a0f58759e7b6053746080813f17fc1df164e9755fcffb7c22470c7371c0de86'] sanity_check_paths = { - 'files': ["bin/Molekel"], + 'files': ['bin/Molekel'], 'dirs': [], } From d5b88d121287db77419e3962188d3781c036d8b1 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 9 Sep 2022 14:43:55 +0100 Subject: [PATCH 4778/9987] SUNDIALS and gawk added, make check enabled --- easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb index f6c073f2b97..8bc5d81d922 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb @@ -20,6 +20,7 @@ builddependencies = [ ('Autotools', '20210726'), ('gperf', '3.1'), ('pkgconf', '1.8.0'), + ('gawk', '5.1.1'), ] dependencies = [ @@ -47,6 +48,7 @@ dependencies = [ ('makeinfo', '6.8'), ('libsndfile', '1.0.31'), ('GraphicsMagick', '1.3.36'), + ('SUNDIALS', '6.3.0'), ] configopts = '--disable-docs ' @@ -81,4 +83,6 @@ exts_list = [ }), ] +runtest = 'check' + moduleclass = 'math' From fee5bf75aa661626ad9adf5d7187a31341795fee Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 9 Sep 2022 16:04:11 +0200 Subject: [PATCH 4779/9987] Switch to Tarball easyblock. Include version in download. --- easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb b/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb index 04a2f7c3c56..84fbb1a1e73 100644 --- a/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb +++ b/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb @@ -1,6 +1,6 @@ # Based on https://code.it4i.cz/sccs/easyconfigs-it4i/-/blob/it4i-karolina/v/VESTA/VESTA-3.5.7.eb -easyblock = 'Binary' +easyblock = 'Tarball' name = 'VESTA' version = '3.5.8' @@ -16,13 +16,17 @@ description = """ toolchain = SYSTEM source_urls = ["http://www.jp-minerals.org/vesta/archives/%(version)s"] -sources = ["%(name)s-gtk3.tar.bz2"] +sources = [{ + 'filename': SOURCE_TAR_BZ2, + 'download_filename': '%(name)s-gtk3.tar.bz2'}] + checksums = ['78bef025c2b31f1d64c9c7e06ad2b139d252b3a686893ee79ac74b3021868df8'] -extract_sources = True sanity_check_paths = { 'files': ['VESTA'], 'dirs': [], } +modextrapaths = {'PATH': ''} + moduleclass = 'vis' From 1870982e4b7f577eaae0e92ae32e6ae595a177ff Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 9 Sep 2022 16:24:16 +0200 Subject: [PATCH 4780/9987] adding easyconfigs: how_are_we_stranded_here-1.0.1-foss-2021b.eb and patches: kallisto-0.44.0-include_limits.patch --- ...w_are_we_stranded_here-1.0.1-foss-2021b.eb | 55 +++++++++++++++++++ .../kallisto-0.44.0-include_limits.patch | 33 +++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/h/how_are_we_stranded_here/kallisto-0.44.0-include_limits.patch diff --git a/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb b/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb new file mode 100644 index 00000000000..31147fb62ff --- /dev/null +++ b/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb @@ -0,0 +1,55 @@ +easyblock = 'Bundle' + +name = 'how_are_we_stranded_here' +version = '1.0.1' + +homepage = 'https://github.com/signalbash/how_are_we_stranded_here' +description = "Python package for testing strandedness of RNA-Seq fastq files" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('Autotools', '20210726'), + ('CMake', '3.22.1'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('RSeQC', '4.0.0'), + ('SciPy-bundle', '2021.10'), + ('HDF5', '1.12.1'), + ('HTSlib', '1.14'), +] + +default_component_specs = { + 'sources': ['v%(version)s.tar.gz'], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('kallisto', '0.44.0', { + 'source_urls': ['https://github.com/pachterlab/kallisto/archive/refs/tags/'], + 'easyblock': 'CMakeMake', + 'patches': ['%(name)s-%(version)s-include_limits.patch'], + 'preconfigopts': "cd ../%(name)s-%(version)s/ext/htslib/ && \ + sed -i '/AC_PROG_CC/a AC_CANONICAL_HOST' configure.ac && \ + autoreconf -i && autoheader && autoconf && cd - && ", + 'checksums': [ + '35a81201a56f4557697e6fe693dc6b701bbbd0a7b2b6e1c6c845ef816d67ca29', # v0.44.0.tag.gz + '4ad7d54f104fe779560107109fd0fc65ffc9af22822765be96816c1424b91da0', # kallisto-0.44.0-include_limits.patch + ], + }), + (name, version, { + 'source_urls': ["https://github.com/signalbash/how_are_we_stranded_here/archive/refs/tags/"], + 'easyblock': 'PythonPackage', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, + 'checksums': ['f66b3f7035d55c4584c4843582c9d94d3fa597cc1dc9ad9f36ffc2d3849a5210'], + }), +] + +parallel = 1 # Build doesn't complete without this + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/how_are_we_stranded_here/kallisto-0.44.0-include_limits.patch b/easybuild/easyconfigs/h/how_are_we_stranded_here/kallisto-0.44.0-include_limits.patch new file mode 100644 index 00000000000..f93f03c6781 --- /dev/null +++ b/easybuild/easyconfigs/h/how_are_we_stranded_here/kallisto-0.44.0-include_limits.patch @@ -0,0 +1,33 @@ +Version 0.44.0 does not include limits library by its own, this fixes it. + +diff -ruN kallisto_orig/src/Inspect.h kallisto/src/Inspect.h +--- kallisto_orig/src/Inspect.h 2022-09-05 15:33:04.350000000 +0200 ++++ kallisto/src/Inspect.h 2022-09-05 15:33:31.070000000 +0200 +@@ -3,6 +3,7 @@ + + #include + #include ++#include + #include "KmerIndex.h" + #include "GeneModel.h" + +diff -ruN kallisto_orig/src/MinCollector.cpp kallisto/src/MinCollector.cpp +--- kallisto_orig/src/MinCollector.cpp 2022-09-05 15:33:04.350000000 +0200 ++++ kallisto/src/MinCollector.cpp 2022-09-05 15:33:53.640000000 +0200 +@@ -1,5 +1,6 @@ + #include "MinCollector.h" + #include ++#include + + // utility functions + +diff -ruN kallisto_orig/src/main.cpp kallisto/src/main.cpp +--- kallisto_orig/src/main.cpp 2022-09-05 15:33:04.350000000 +0200 ++++ kallisto/src/main.cpp 2022-09-05 15:34:20.330000000 +0200 +@@ -7,6 +7,7 @@ + #include + #include + #include ++#include + + #include From 44b82cd59ae5235210436f05c320e7275862a012 Mon Sep 17 00:00:00 2001 From: Guillaume Acke Date: Fri, 9 Sep 2022 16:29:30 +0200 Subject: [PATCH 4781/9987] Update easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb b/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb index 84fbb1a1e73..287e4a46210 100644 --- a/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb +++ b/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb @@ -18,7 +18,8 @@ toolchain = SYSTEM source_urls = ["http://www.jp-minerals.org/vesta/archives/%(version)s"] sources = [{ 'filename': SOURCE_TAR_BZ2, - 'download_filename': '%(name)s-gtk3.tar.bz2'}] + 'download_filename': '%(name)s-gtk3.tar.bz2', +}] checksums = ['78bef025c2b31f1d64c9c7e06ad2b139d252b3a686893ee79ac74b3021868df8'] From 4013e24ecea59ebdf19b7292aaf96d92530af390 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 9 Sep 2022 16:41:32 +0200 Subject: [PATCH 4782/9987] Fixed style errors --- .../how_are_we_stranded_here-1.0.1-foss-2021b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb b/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb index 31147fb62ff..048c4e7ad5f 100644 --- a/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb +++ b/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb @@ -36,8 +36,8 @@ components = [ sed -i '/AC_PROG_CC/a AC_CANONICAL_HOST' configure.ac && \ autoreconf -i && autoheader && autoconf && cd - && ", 'checksums': [ - '35a81201a56f4557697e6fe693dc6b701bbbd0a7b2b6e1c6c845ef816d67ca29', # v0.44.0.tag.gz - '4ad7d54f104fe779560107109fd0fc65ffc9af22822765be96816c1424b91da0', # kallisto-0.44.0-include_limits.patch + '35a81201a56f4557697e6fe693dc6b701bbbd0a7b2b6e1c6c845ef816d67ca29', # v0.44.0.tag.gz + '4ad7d54f104fe779560107109fd0fc65ffc9af22822765be96816c1424b91da0', # kallisto-0.44.0-include_limits.patch ], }), (name, version, { @@ -50,6 +50,6 @@ components = [ }), ] -parallel = 1 # Build doesn't complete without this +parallel = 1 # Build doesn't complete without this moduleclass = 'bio' From 59d80db1854c814ac9fdf7f84dbcd7357ef2db71 Mon Sep 17 00:00:00 2001 From: Guillaume Acke Date: Fri, 9 Sep 2022 16:49:25 +0200 Subject: [PATCH 4783/9987] Update easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb b/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb index 287e4a46210..cd8e34bea7a 100644 --- a/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb +++ b/easybuild/easyconfigs/v/VESTA/VESTA-3.5.8-gtk3.eb @@ -17,8 +17,8 @@ toolchain = SYSTEM source_urls = ["http://www.jp-minerals.org/vesta/archives/%(version)s"] sources = [{ - 'filename': SOURCE_TAR_BZ2, - 'download_filename': '%(name)s-gtk3.tar.bz2', + 'filename': SOURCE_TAR_BZ2, + 'download_filename': '%(name)s-gtk3.tar.bz2', }] checksums = ['78bef025c2b31f1d64c9c7e06ad2b139d252b3a686893ee79ac74b3021868df8'] From 673e0775432ceeb93f7c65480e2e90e0d6085e5e Mon Sep 17 00:00:00 2001 From: Jordi Camps Puchades Date: Fri, 9 Sep 2022 17:15:11 +0200 Subject: [PATCH 4784/9987] adding easyconfigs: miller-6.4.0.eb --- .../easyconfigs/m/miller/miller-6.4.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/miller/miller-6.4.0.eb diff --git a/easybuild/easyconfigs/m/miller/miller-6.4.0.eb b/easybuild/easyconfigs/m/miller/miller-6.4.0.eb new file mode 100644 index 00000000000..12ed20664ce --- /dev/null +++ b/easybuild/easyconfigs/m/miller/miller-6.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'GoPackage' + +name = 'miller' +version = '6.4.0' +modulename = 'github.com/johnkerl/miller/cmd/mlr' + +homepage = 'https://miller.readthedocs.io/' +description = """Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/johnkerl/miller/releases/download/v%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['20a8687a0c5b5fedf4fc3a794ef1cee7e9872e87476e1f24bde8de25799f8c51'] + +builddependencies = [ + ('Go', '1.18.3'), +] + +#installopts = './%(namelower)s' + +sanity_check_commands = [ + "mlr version", +] + +moduleclass = 'tools' From 58566a976698501b7c4ecfe64161f2af2e63e163 Mon Sep 17 00:00:00 2001 From: Jordi Date: Fri, 9 Sep 2022 18:03:59 +0200 Subject: [PATCH 4785/9987] Update easybuild/easyconfigs/m/miller/miller-6.4.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/m/miller/miller-6.4.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/miller/miller-6.4.0.eb b/easybuild/easyconfigs/m/miller/miller-6.4.0.eb index 12ed20664ce..22a909300a1 100644 --- a/easybuild/easyconfigs/m/miller/miller-6.4.0.eb +++ b/easybuild/easyconfigs/m/miller/miller-6.4.0.eb @@ -2,7 +2,6 @@ easyblock = 'GoPackage' name = 'miller' version = '6.4.0' -modulename = 'github.com/johnkerl/miller/cmd/mlr' homepage = 'https://miller.readthedocs.io/' description = """Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON""" From 6328dee673a326344e0fe40a1722fc93f4d3867d Mon Sep 17 00:00:00 2001 From: Jordi Date: Fri, 9 Sep 2022 18:04:06 +0200 Subject: [PATCH 4786/9987] Update easybuild/easyconfigs/m/miller/miller-6.4.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/m/miller/miller-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/miller/miller-6.4.0.eb b/easybuild/easyconfigs/m/miller/miller-6.4.0.eb index 22a909300a1..cc8d1797643 100644 --- a/easybuild/easyconfigs/m/miller/miller-6.4.0.eb +++ b/easybuild/easyconfigs/m/miller/miller-6.4.0.eb @@ -16,7 +16,7 @@ builddependencies = [ ('Go', '1.18.3'), ] -#installopts = './%(namelower)s' +installopts = './cmd/mlr' sanity_check_commands = [ "mlr version", From 4bff5700e85d5e743ac2e1d4214b7a269ed2325b Mon Sep 17 00:00:00 2001 From: Jordi Date: Fri, 9 Sep 2022 18:05:23 +0200 Subject: [PATCH 4787/9987] Update miller-6.4.0.eb Added sanity_check_paths --- easybuild/easyconfigs/m/miller/miller-6.4.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/m/miller/miller-6.4.0.eb b/easybuild/easyconfigs/m/miller/miller-6.4.0.eb index cc8d1797643..ae93edb7daf 100644 --- a/easybuild/easyconfigs/m/miller/miller-6.4.0.eb +++ b/easybuild/easyconfigs/m/miller/miller-6.4.0.eb @@ -22,4 +22,9 @@ sanity_check_commands = [ "mlr version", ] +sanity_check_paths = { + 'files': ['bin/mlr'], + 'dirs': [], +} + moduleclass = 'tools' From cc8d792ba065ce03e25a107855b35809f8577bcd Mon Sep 17 00:00:00 2001 From: Jordi Date: Fri, 9 Sep 2022 18:20:35 +0200 Subject: [PATCH 4788/9987] Fix: proper name capitalization --- .../m/{miller/miller-6.4.0.eb => Miller/Miller-6.4.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/{miller/miller-6.4.0.eb => Miller/Miller-6.4.0.eb} (97%) diff --git a/easybuild/easyconfigs/m/miller/miller-6.4.0.eb b/easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb similarity index 97% rename from easybuild/easyconfigs/m/miller/miller-6.4.0.eb rename to easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb index ae93edb7daf..5d65e1173b4 100644 --- a/easybuild/easyconfigs/m/miller/miller-6.4.0.eb +++ b/easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb @@ -1,6 +1,6 @@ easyblock = 'GoPackage' -name = 'miller' +name = 'Miller' version = '6.4.0' homepage = 'https://miller.readthedocs.io/' From c4ed48538ea2447d08e3203b131d33d650ceb3d1 Mon Sep 17 00:00:00 2001 From: Jordi Date: Fri, 9 Sep 2022 18:31:12 +0200 Subject: [PATCH 4789/9987] Update easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb b/easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb index 5d65e1173b4..e0dbe324d91 100644 --- a/easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb +++ b/easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb @@ -4,7 +4,7 @@ name = 'Miller' version = '6.4.0' homepage = 'https://miller.readthedocs.io/' -description = """Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON""" +description = "Miller is like awk, sed, cut, join, and sort for name-indexed data such as CSV, TSV, and tabular JSON" toolchain = SYSTEM From 56b07e62d28cc1aa13679974dd89724b3be7a3eb Mon Sep 17 00:00:00 2001 From: Jordi Date: Fri, 9 Sep 2022 18:31:49 +0200 Subject: [PATCH 4790/9987] Update Miller-6.4.0.eb --- easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb b/easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb index e0dbe324d91..489fe047327 100644 --- a/easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb +++ b/easybuild/easyconfigs/m/Miller/Miller-6.4.0.eb @@ -9,7 +9,7 @@ description = "Miller is like awk, sed, cut, join, and sort for name-indexed dat toolchain = SYSTEM source_urls = ['https://github.com/johnkerl/miller/releases/download/v%(version)s'] -sources = ['%(name)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['20a8687a0c5b5fedf4fc3a794ef1cee7e9872e87476e1f24bde8de25799f8c51'] builddependencies = [ From 25aed465a9f445809afd2f3e1c109128a5e412dd Mon Sep 17 00:00:00 2001 From: Jordi Camps Puchades Date: Fri, 9 Sep 2022 18:36:25 +0200 Subject: [PATCH 4791/9987] adding easyconfigs: Go-1.18.3.eb --- easybuild/easyconfigs/g/Go/Go-1.18.3.eb | 32 +++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.18.3.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.18.3.eb b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb new file mode 100644 index 00000000000..a0bf953106f --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb @@ -0,0 +1,32 @@ +## +# Author: Robert Mijakovic +## +# Update to 1.18.3 +# Jordi Camps / CNAG +# +easyblock = 'Tarball' + +name = 'Go' +version = "1.18.3" + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] + +local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} +sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] +checksums = [] +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +sanity_check_commands = ["go help"] + +modextravars = {'GOROOT': '%(installdir)s'} + +moduleclass = 'compiler' From 001346c450d0911da6a6e4fd45dbacc9b0e96403 Mon Sep 17 00:00:00 2001 From: Jordi Date: Fri, 9 Sep 2022 18:54:58 +0200 Subject: [PATCH 4792/9987] Update Go-1.18.3.eb Cleanup comments --- easybuild/easyconfigs/g/Go/Go-1.18.3.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/Go/Go-1.18.3.eb b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb index a0bf953106f..f2029a83d21 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.18.3.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb @@ -1,9 +1,6 @@ -## -# Author: Robert Mijakovic -## # Update to 1.18.3 # Jordi Camps / CNAG -# + easyblock = 'Tarball' name = 'Go' From c1eaa6dacdf9c172a1048ca416dfc23471e1116c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Sep 2022 19:27:20 +0200 Subject: [PATCH 4793/9987] add maeparser + CoordgenLibs dependencies to OpenBabel v3.1.1 easyconfig using iimpi/2020a toolchain --- .../CoordgenLibs-3.0.1-iimpi-2020a.eb | 32 ++++++++++++ .../maeparser/maeparser-1.3.0-iimpi-2020a.eb | 26 ++++++++++ ...penBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb | 9 ++-- ...-3.1.1_fix-CoordgenLibs-no-templates.patch | 49 +++++++++++++++++++ 4 files changed, 112 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-iimpi-2020a.eb create mode 100644 easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-iimpi-2020a.eb create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch diff --git a/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-iimpi-2020a.eb b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-iimpi-2020a.eb new file mode 100644 index 00000000000..e08d7e569be --- /dev/null +++ b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-iimpi-2020a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CoordgenLibs' +version = '3.0.1' + +homepage = 'https://github.com/schrodinger/coordgenlibs' +description = "Schrodinger-developed 2D Coordinate Generation" + +toolchain = {'name': 'iimpi', 'version': '2020a'} + +source_urls = ['https://github.com/schrodinger/coordgenlibs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['737fd081bcb8a6913aa00b375be96458fe2821a58209c98e7a7e86a64d73a900'] + +builddependencies = [('CMake', '3.16.4')] + +dependencies = [ + ('Boost', '1.72.0'), + ('maeparser', '1.3.0'), +] + +configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake" + +# work around compiler warning treated as error by stripping out use of -Werror +prebuildopts = "sed -i 's/-Werror//g' CMakeFiles/coordgen.dir/flags.make && " + +sanity_check_paths = { + 'files': ['lib/libcoordgen.%s' % SHLIB_EXT], + 'dirs': ['include/coordgen', 'lib/cmake'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-iimpi-2020a.eb b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-iimpi-2020a.eb new file mode 100644 index 00000000000..c00793c0c3c --- /dev/null +++ b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-iimpi-2020a.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'maeparser' +version = '1.3.0' + +homepage = 'https://github.com/schrodinger/maeparser' +description = "maeparser is a parser for Schrodinger Maestro files." + +toolchain = {'name': 'iimpi', 'version': '2020a'} + +source_urls = ['https://github.com/schrodinger/maeparser/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fa8f9336de1e5d1cabec29a6da04547b1fb040bb32ba511ff30b4a14097c751c'] + +builddependencies = [ + ('CMake', '3.16.4'), +] + +dependencies = [('Boost', '1.72.0')] + +sanity_check_paths = { + 'files': ['lib/libmaeparser.%s' % SHLIB_EXT], + 'dirs': ['include/maeparser', 'lib/cmake'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb index 9a6d9ca1f55..dfdbeab1c4f 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb @@ -18,11 +18,14 @@ patches = [ # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch 'OpenBabel-3.1.1_fix-distgeom-test.patch', 'OpenBabel-3.1.1_fix-testobconv_writers.patch', + 'OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch', ] checksums = [ 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch '6d0b153caadc53141e1578972d632afb82b2fc4abdec6c5f07552b45a20e980c', # OpenBabel-3.1.1_fix-testobconv_writers.patch + # OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch + 'cc0396b38a78ef70c869cd93887210c64d6f4293c016aec9269b5a0230fdb51c', ] builddependencies = [ @@ -37,16 +40,14 @@ dependencies = [ ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output ('Boost', '1.72.0'), # optional: for Maestro formats + ('maeparser', '1.3.0'), + ('CoordgenLibs', '3.0.1'), ] configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' # Enable support for OpenMP compilation of forcefield code (optional) configopts += '-DENABLE_OPENMP=ON ' -# remove use of -Werror to avoid that warnings are treated as errors -# required to work around "integer conversion resulted in a change of sign" error with Intel compiler -prebuildopts = "sed -i 's/-Werror//g' external/coordgen-master/coordgen/CMakeFiles/coordgen.dir/flags.make && " - # OpenBabel-3.1.1 creates directories named 3.1.0, which leads to BABEL_LIBDIR and BABEL_DATDIR # (set in the easyblock) having invalid values. Work around this with some symlinks. postinstallcmds = [ diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch new file mode 100644 index 00000000000..3180da7a0dc --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch @@ -0,0 +1,49 @@ +see also https://github.com/openbabel/openbabel/pull/2297 + +From b6887a8a82162278983a8489e365e61a0372b1b8 Mon Sep 17 00:00:00 2001 +From: Benny Siegert +Date: Wed, 4 Nov 2020 20:31:17 +0100 +Subject: [PATCH] Do not search for coordgen template files. + +The coordgen upstream does not install the template file. It is +also not required at runtime, since its contents are compiled into +the coordgen library itself. + +Fixes #2214 +--- + cmake/modules/Findcoordgen.cmake | 13 +------------ + 1 file changed, 1 insertion(+), 12 deletions(-) + +diff --git a/cmake/modules/Findcoordgen.cmake b/cmake/modules/Findcoordgen.cmake +index ded0a4de7d..9bc5c9557f 100644 +--- a/cmake/modules/Findcoordgen.cmake ++++ b/cmake/modules/Findcoordgen.cmake +@@ -6,7 +6,6 @@ + # + # coordgen_INCLUDE_DIRS - CoordGen's includes directory + # coordgen_LIBRARIES - CoordGen's shared libraries +-# coordgen_TEMPLATE_FILE - CoordGen templates file + # + # + +@@ -28,19 +27,9 @@ find_library(coordgen_LIBRARIES + ) + message(STATUS "coordgen libraries set as '${coordgen_LIBRARIES}'") + +-# Just in case, add parent directory above libraries to templates search hints +-get_filename_component(libs_parent_dir ${coordgen_LIBRARIES} PATH) +-find_file(coordgen_TEMPLATE_FILE +- NAMES templates.mae +- HINTS ${coordgen_DIR} ${libs_parent_dir} +- PATH_SUFFIXES "share" "share/coordgen" +- DOC "templates file for coordgen" +-) +-message(STATUS "coordgen templates file set as '${coordgen_TEMPLATE_FILE}'") +- + find_package_handle_standard_args(coordgen FOUND_VAR coordgen_FOUND + REQUIRED_VARS coordgen_INCLUDE_DIRS +- coordgen_LIBRARIES coordgen_TEMPLATE_FILE) ++ coordgen_LIBRARIES) + + + From 364c9e96b256de4bba68611df3432ccf4f42cc98 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Sep 2022 19:50:57 +0200 Subject: [PATCH 4794/9987] consistently add libffi + elfutils dependencies to recent Clang easyconfigs --- easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb | 3 ++- .../c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb | 3 ++- easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb | 3 ++- .../c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb | 3 ++- easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0.eb | 3 ++- easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.3.0.eb | 3 ++- 6 files changed, 12 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb index 34cb3620042..d5b83b6bd5c 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-11.0.1-gcccuda-2020b.eb @@ -52,13 +52,14 @@ dependencies = [ ('ncurses', '6.2'), ('GMP', '6.2.0'), ('Z3', '4.8.10'), + ('libffi', '3.3'), + ('elfutils', '0.183'), ] builddependencies = [ ('CMake', '3.18.4'), ('Python', '3.8.6'), ('Perl', '5.32.0'), - ('elfutils', '0.183'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb index 07a9f5ffa7f..dead5e2ce6a 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -55,6 +55,8 @@ dependencies = [ ('ncurses', '6.2'), ('GMP', '6.2.1'), ('Z3', '4.8.11'), + ('libffi', '3.3'), + ('elfutils', '0.185'), ('CUDA', '11.3.1', '', True), ] @@ -62,7 +64,6 @@ builddependencies = [ ('CMake', '3.20.1'), ('Python', '3.9.5'), ('Perl', '5.32.1'), - ('elfutils', '0.185'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb index 06e4bde84c9..68bc4567814 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0.eb @@ -54,13 +54,14 @@ dependencies = [ ('ncurses', '6.2'), ('GMP', '6.2.1'), ('Z3', '4.8.11'), + ('libffi', '3.3'), + ('elfutils', '0.185'), ] builddependencies = [ ('CMake', '3.20.1'), ('Python', '3.9.5'), ('Perl', '5.32.1'), - ('elfutils', '0.185'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb index 5ee0395dbb9..42c8ecf704e 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -55,6 +55,8 @@ dependencies = [ ('ncurses', '6.2'), ('GMP', '6.2.1'), ('Z3', '4.8.12'), + ('libffi', '3.4.2'), + ('elfutils', '0.185'), ('CUDA', '11.4.1', '', True), ] @@ -62,7 +64,6 @@ builddependencies = [ ('CMake', '3.21.1'), ('Python', '3.9.6'), ('Perl', '5.34.0'), - ('elfutils', '0.185'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0.eb index 8b5f8271aeb..a2dc6f48037 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0.eb @@ -54,13 +54,14 @@ dependencies = [ ('ncurses', '6.2'), ('GMP', '6.2.1'), ('Z3', '4.8.12'), + ('libffi', '3.4.2'), + ('elfutils', '0.185'), ] builddependencies = [ ('CMake', '3.21.1'), ('Python', '3.9.6'), ('Perl', '5.34.0'), - ('elfutils', '0.185'), ] assertions = True diff --git a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.3.0.eb index e61c5f74ce0..dd166c5e5ad 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.3.0.eb @@ -54,13 +54,14 @@ dependencies = [ ('ncurses', '6.3'), ('GMP', '6.2.1'), ('Z3', '4.10.2'), + ('libffi', '3.4.2'), + ('elfutils', '0.187'), ] builddependencies = [ ('CMake', '3.23.1'), ('Python', '3.10.4'), ('Perl', '5.34.1'), - ('elfutils', '0.187'), ] assertions = True From 8f307e0d09481bea436e4a460a06e11618516ecc Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 9 Sep 2022 19:51:57 +0200 Subject: [PATCH 4795/9987] Added sanity_check_paths --- .../how_are_we_stranded_here-1.0.1-foss-2021b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb b/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb index 048c4e7ad5f..914a67bfd9c 100644 --- a/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb +++ b/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb @@ -52,4 +52,9 @@ components = [ parallel = 1 # Build doesn't complete without this +sanity_check_paths = { + 'files': ["bin/check_strandedness"], + 'dirs': [] +} + moduleclass = 'bio' From aff2cbba385bb8c99a3f16c81c5359ae125c6223 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Sep 2022 21:56:42 +0200 Subject: [PATCH 4796/9987] strip out excess spaces from dependencies in alevin-fry easyconfig --- .../a/alevin-fry/alevin-fry-0.6.0-GCCcore-10.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.6.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.6.0-GCCcore-10.3.0.eb index 19bc9a51461..5e75334e448 100644 --- a/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.6.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/alevin-fry/alevin-fry-0.6.0-GCCcore-10.3.0.eb @@ -16,8 +16,8 @@ checksums = ['8a368695da8e85826f3d72670c83c44344d5c184a7bccda4ab2dea486eb3e00b'] builddependencies = [ ('binutils', '2.36.1'), - ('Rust', '1.60.0'), - ('CMake', '3.20.1'), + ('Rust', '1.60.0'), + ('CMake', '3.20.1'), ] dependencies = [ ('bzip2', '1.0.8'), From a8cc44ac3fc0126318053b1297ac06ecfbb3214d Mon Sep 17 00:00:00 2001 From: guacke Date: Sat, 10 Sep 2022 12:12:41 +0200 Subject: [PATCH 4797/9987] adding easyconfigs: mgltools-1.5.7.eb --- .../easyconfigs/m/mgltools/mgltools-1.5.7.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb diff --git a/easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb b/easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb new file mode 100644 index 00000000000..02d6160cf64 --- /dev/null +++ b/easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb @@ -0,0 +1,35 @@ +easyblock = 'Binary' + +name = "mgltools" +version = "1.5.7" + +homepage = "https://ccsb.scripps.edu/mgltools/" +description = """ + The MGLTools software suite can be used for visualization + and analysis of molecular structures and comprises + the Python Molecular Viewer (PMV, a general purpose molecular viewer), + AutoDockTools (ADT, a set of PMV commands specifically developed to support AutoDock users) + and Vision (a visual programing environment). +""" + +toolchain = SYSTEM + +source_urls = ["https://ccsb.scripps.edu/download/532/"] + +sources = [{ + 'download_filename': 'index.html', + 'filename': SOURCE_TAR_GZ +}] + +checksums = ['3d7aaf852ed9d5ad586326db860aff62d96ed6c0e06bb9535cf7d576e4b615dd'] + +extract_sources = True + +install_cmd = "./install.sh -d %(installdir)s" + +sanity_check_paths = { + 'files': ['bin/pmv', 'bin/adt'], + 'dirs': [], +} + +moduleclass = 'bio' \ No newline at end of file From 0a29999c94737e6e789858940171795016344c5e Mon Sep 17 00:00:00 2001 From: guacke Date: Sat, 10 Sep 2022 12:55:01 +0200 Subject: [PATCH 4798/9987] Add newline at end of file. --- easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb b/easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb index 02d6160cf64..0c2917b25b5 100644 --- a/easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb +++ b/easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb @@ -32,4 +32,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 7a96c1580bffaee6576987194e4b9e61a84a103e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 10 Sep 2022 13:48:08 +0200 Subject: [PATCH 4799/9987] stick to HDF5 v1.12.2 as dependency for R-bundle-Bioconductor with foss/2022a --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 016792e499f..209068efaa5 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -18,7 +18,7 @@ dependencies = [ ('R', '4.2.1'), ('Boost', '1.79.0'), # for mzR ('GSL', '2.7'), # for flowClust - ('HDF5', '1.13.1'), # for rhdf5 + ('HDF5', '1.12.2'), # for rhdf5 ('arrow-R', '8.0.0', versionsuffix), # required by RcisTarget ] From b2b554534280bd19739833fbacfe4df8e34151ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 10 Sep 2022 15:40:42 +0200 Subject: [PATCH 4800/9987] also update $PYTHONPATH for how_are_we_stranded_here + add sanity check command --- .../how_are_we_stranded_here-1.0.1-foss-2021b.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb b/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb index 914a67bfd9c..14feb29031f 100644 --- a/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb +++ b/easybuild/easyconfigs/h/how_are_we_stranded_here/how_are_we_stranded_here-1.0.1-foss-2021b.eb @@ -53,8 +53,12 @@ components = [ parallel = 1 # Build doesn't complete without this sanity_check_paths = { - 'files': ["bin/check_strandedness"], - 'dirs': [] + 'files': ['bin/check_strandedness'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["check_strandedness --help"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'bio' From d2b7b6b67da4f9c9a272d228a5d44b8019a492a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 10 Sep 2022 16:48:27 +0200 Subject: [PATCH 4801/9987] adding easyconfigs: Pyomo-6.4.2-foss-2022a.eb --- .../p/Pyomo/Pyomo-6.4.2-foss-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pyomo/Pyomo-6.4.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.4.2-foss-2022a.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.4.2-foss-2022a.eb new file mode 100644 index 00000000000..f9c607a6ed0 --- /dev/null +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.4.2-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Pyomo' +version = '6.4.2' + +homepage = 'https://www.pyomo.org/' +description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization + capabilities for formulating and analyzing optimization models. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [('Python', '3.10.4')] + +exts_list = [ + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('PyUtilib', '6.0.0', { + 'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'], + 'preinstallopts': """sed -i "s/'nose',//g" setup.py && """, + }), + (name, version, { + 'checksums': ['6f5a867e77bdd6ac2ba0da5d4a251e38543ae05eba5a0c5cf8ab39e7fa8e1ea9'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['pyomo -h'] + +moduleclass = 'math' From dca1259e059b1be0553f7284365c9e010753977b Mon Sep 17 00:00:00 2001 From: guacke Date: Sat, 10 Sep 2022 17:34:32 +0200 Subject: [PATCH 4802/9987] adding easyconfigs: Chimera-1.16-linux_x86_64.eb --- .../c/Chimera/Chimera-1.16-linux_x86_64.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/Chimera/Chimera-1.16-linux_x86_64.eb diff --git a/easybuild/easyconfigs/c/Chimera/Chimera-1.16-linux_x86_64.eb b/easybuild/easyconfigs/c/Chimera/Chimera-1.16-linux_x86_64.eb new file mode 100644 index 00000000000..7e9b63d5336 --- /dev/null +++ b/easybuild/easyconfigs/c/Chimera/Chimera-1.16-linux_x86_64.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +name = "Chimera" +version = "1.16" +versionsuffix = "-linux_x86_64" + +homepage = 'https://www.cgl.ucsf.edu/chimera/' +description = """ UCSF Chimera is a highly extensible program for interactive visualization + and analysis of molecular structures and related data, including density maps, supramolecular + assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. """ + +toolchain = SYSTEM + +# no public download URL. Go to https://www.cgl.ucsf.edu/chimera/download.html +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.bin'] + +# unzip is required to uncompress the provided .bin file +osdependencies = ['unzip'] + +sanity_check_paths = { + 'files': ["bin/chimera"], + 'dirs': [] +} + +moduleclass = 'bio' From a96a9a4212a9e6b2d1fe01210dfa08513820267b Mon Sep 17 00:00:00 2001 From: Jordi Date: Sat, 10 Sep 2022 20:45:24 +0200 Subject: [PATCH 4803/9987] Update Go-1.18.3.eb Added SHA256 checksum --- easybuild/easyconfigs/g/Go/Go-1.18.3.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Go/Go-1.18.3.eb b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb index f2029a83d21..cb532faf480 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.18.3.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb @@ -16,7 +16,8 @@ source_urls = ['https://storage.googleapis.com/golang/'] local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] -checksums = [] +checksums = ['956f8507b302ab0bb747613695cdae10af99bbd39a90cae522b7c0302cc27245'] + sanity_check_paths = { 'files': ['bin/go', 'bin/gofmt'], 'dirs': ['api', 'doc', 'lib', 'pkg'], From e15675bfe6e8b4960ffa3e85151538b5ae6d02e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 10 Sep 2022 22:37:29 +0200 Subject: [PATCH 4804/9987] consistently add maeparser + CoordgenLibs dependencies to OpenBabel v3.1.1 easyconfigs --- .../CoordgenLibs-3.0.1-gompi-2019b.eb | 32 +++++++++++++++++++ .../CoordgenLibs-3.0.1-gompi-2021a.eb | 32 +++++++++++++++++++ .../CoordgenLibs-3.0.1-gompi-2022a.eb | 32 +++++++++++++++++++ .../maeparser/maeparser-1.3.0-gompi-2019b.eb | 26 +++++++++++++++ .../maeparser/maeparser-1.3.0-gompi-2021a.eb | 26 +++++++++++++++ .../maeparser/maeparser-1.3.0-gompi-2022a.eb | 26 +++++++++++++++ ...penBabel-3.1.1-gompi-2019b-Python-3.7.4.eb | 5 ++- .../OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb | 5 ++- .../OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb | 5 ++- 9 files changed, 186 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2019b.eb create mode 100644 easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2019b.eb create mode 100644 easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2019b.eb b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2019b.eb new file mode 100644 index 00000000000..60a7b6fd9ea --- /dev/null +++ b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2019b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CoordgenLibs' +version = '3.0.1' + +homepage = 'https://github.com/schrodinger/coordgenlibs' +description = "Schrodinger-developed 2D Coordinate Generation" + +toolchain = {'name': 'gompi', 'version': '2019b'} + +source_urls = ['https://github.com/schrodinger/coordgenlibs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['737fd081bcb8a6913aa00b375be96458fe2821a58209c98e7a7e86a64d73a900'] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('Boost', '1.71.0'), + ('maeparser', '1.3.0'), +] + +configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake" + +# work around compiler warning treated as error by stripping out use of -Werror +prebuildopts = "sed -i 's/-Werror//g' CMakeFiles/coordgen.dir/flags.make && " + +sanity_check_paths = { + 'files': ['lib/libcoordgen.%s' % SHLIB_EXT], + 'dirs': ['include/coordgen', 'lib/cmake'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2021a.eb b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2021a.eb new file mode 100644 index 00000000000..75ff2d354dc --- /dev/null +++ b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2021a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CoordgenLibs' +version = '3.0.1' + +homepage = 'https://github.com/schrodinger/coordgenlibs' +description = "Schrodinger-developed 2D Coordinate Generation" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://github.com/schrodinger/coordgenlibs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['737fd081bcb8a6913aa00b375be96458fe2821a58209c98e7a7e86a64d73a900'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Boost', '1.76.0'), + ('maeparser', '1.3.0'), +] + +configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake" + +# work around compiler warning treated as error by stripping out use of -Werror +prebuildopts = "sed -i 's/-Werror//g' CMakeFiles/coordgen.dir/flags.make && " + +sanity_check_paths = { + 'files': ['lib/libcoordgen.%s' % SHLIB_EXT], + 'dirs': ['include/coordgen', 'lib/cmake'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2022a.eb b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2022a.eb new file mode 100644 index 00000000000..bab82cf314a --- /dev/null +++ b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.1-gompi-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CoordgenLibs' +version = '3.0.1' + +homepage = 'https://github.com/schrodinger/coordgenlibs' +description = "Schrodinger-developed 2D Coordinate Generation" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/schrodinger/coordgenlibs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['737fd081bcb8a6913aa00b375be96458fe2821a58209c98e7a7e86a64d73a900'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Boost', '1.79.0'), + ('maeparser', '1.3.0'), +] + +configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake" + +# work around compiler warning treated as error by stripping out use of -Werror +prebuildopts = "sed -i 's/-Werror//g' CMakeFiles/coordgen.dir/flags.make && " + +sanity_check_paths = { + 'files': ['lib/libcoordgen.%s' % SHLIB_EXT], + 'dirs': ['include/coordgen', 'lib/cmake'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2019b.eb b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2019b.eb new file mode 100644 index 00000000000..f68ded36ea0 --- /dev/null +++ b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2019b.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'maeparser' +version = '1.3.0' + +homepage = 'https://github.com/schrodinger/maeparser' +description = "maeparser is a parser for Schrodinger Maestro files." + +toolchain = {'name': 'gompi', 'version': '2019b'} + +source_urls = ['https://github.com/schrodinger/maeparser/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fa8f9336de1e5d1cabec29a6da04547b1fb040bb32ba511ff30b4a14097c751c'] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +dependencies = [('Boost', '1.71.0')] + +sanity_check_paths = { + 'files': ['lib/libmaeparser.%s' % SHLIB_EXT], + 'dirs': ['include/maeparser', 'lib/cmake'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2021a.eb b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2021a.eb new file mode 100644 index 00000000000..8f6fd34c7f3 --- /dev/null +++ b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2021a.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'maeparser' +version = '1.3.0' + +homepage = 'https://github.com/schrodinger/maeparser' +description = "maeparser is a parser for Schrodinger Maestro files." + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://github.com/schrodinger/maeparser/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fa8f9336de1e5d1cabec29a6da04547b1fb040bb32ba511ff30b4a14097c751c'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [('Boost', '1.76.0')] + +sanity_check_paths = { + 'files': ['lib/libmaeparser.%s' % SHLIB_EXT], + 'dirs': ['include/maeparser', 'lib/cmake'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2022a.eb b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2022a.eb new file mode 100644 index 00000000000..8ae3df022e8 --- /dev/null +++ b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.0-gompi-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'maeparser' +version = '1.3.0' + +homepage = 'https://github.com/schrodinger/maeparser' +description = "maeparser is a parser for Schrodinger Maestro files." + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/schrodinger/maeparser/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fa8f9336de1e5d1cabec29a6da04547b1fb040bb32ba511ff30b4a14097c751c'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [('Boost', '1.79.0')] + +sanity_check_paths = { + 'files': ['lib/libmaeparser.%s' % SHLIB_EXT], + 'dirs': ['include/maeparser', 'lib/cmake'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb index 9c98a3c4d19..5a3a066ba6d 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb @@ -19,7 +19,8 @@ sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] patches = [ # Fix test failure with Python 3 # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch - 'OpenBabel-3.1.1_fix-distgeom-test.patch' + 'OpenBabel-3.1.1_fix-distgeom-test.patch', + 'OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch', ] checksums = [ 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz @@ -38,6 +39,8 @@ dependencies = [ ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output ('Boost', '1.71.0'), # optional: for Maestro formats + ('maeparser', '1.3.0'), + ('CoordgenLibs', '3.0.1'), ] configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb index e76ffb84b87..8fff753554d 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb @@ -18,7 +18,8 @@ sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] patches = [ # Fix test failure with Python 3 # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch - 'OpenBabel-3.1.1_fix-distgeom-test.patch' + 'OpenBabel-3.1.1_fix-distgeom-test.patch', + 'OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch', ] checksums = [ 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz @@ -37,6 +38,8 @@ dependencies = [ ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output ('Boost', '1.76.0'), # optional: for Maestro formats + ('maeparser', '1.3.0'), + ('CoordgenLibs', '3.0.1'), ] configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb index 9442aa67aef..7497afa5596 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb @@ -18,7 +18,8 @@ sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] patches = [ # Fix test failure with Python 3 # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch - 'OpenBabel-3.1.1_fix-distgeom-test.patch' + 'OpenBabel-3.1.1_fix-distgeom-test.patch', + 'OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch', ] checksums = [ 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz @@ -37,6 +38,8 @@ dependencies = [ ('RapidJSON', '1.1.0'), ('cairo', '1.17.4'), # optional: for .png output ('Boost', '1.79.0'), # optional: for Maestro formats + ('maeparser', '1.3.0'), + ('CoordgenLibs', '3.0.1'), ] configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' From 30ae94da4fd7de97e4a54def6d97c36887dbc233 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 10 Sep 2022 23:15:00 +0200 Subject: [PATCH 4805/9987] add missing checksum for extra patch in OpenBabel v3.1.1 easyconfigs --- .../o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb | 2 ++ .../easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb | 2 ++ .../easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb index 5a3a066ba6d..286b2053ba5 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb @@ -25,6 +25,8 @@ patches = [ checksums = [ 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch + # OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch + 'cc0396b38a78ef70c869cd93887210c64d6f4293c016aec9269b5a0230fdb51c', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb index 8fff753554d..62e0cfda9c0 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb @@ -24,6 +24,8 @@ patches = [ checksums = [ 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch + # OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch + 'cc0396b38a78ef70c869cd93887210c64d6f4293c016aec9269b5a0230fdb51c', ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb index 7497afa5596..f69361b5b44 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb @@ -24,6 +24,8 @@ patches = [ checksums = [ 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02', # openbabel-3-1-1.tar.gz '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd', # OpenBabel-3.1.1_fix-distgeom-test.patch + # OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch + 'cc0396b38a78ef70c869cd93887210c64d6f4293c016aec9269b5a0230fdb51c', ] builddependencies = [ From 6f0a56d0fa9d6c8e041dede86fe20ef619f8e1b2 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sun, 11 Sep 2022 09:33:10 +0800 Subject: [PATCH 4806/9987] prepare release notes for EasyBuild v4.6.1 + bump version to 4.6.1 --- RELEASE_NOTES | 75 +++++++++++++++++++++++++++++++++++++++++++++++++++ setup.py | 2 +- 2 files changed, 76 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 3349bc49650..0aae3e402d8 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -7,6 +7,81 @@ The latest version of easybuild-easyconfig provides 15,020 easyconfig files, for incl. 37 different (compiler) toolchains. +v4.6.1 (September 14th 2022) +---------------------------- + +update/bugfix release + +- added example easyconfig files for 36 new software packages: + - AptaSUITE (#8583), BigDFT (#15860), colossalai (#15971), CrystFEL (#8407), Dakota (#16210), Detectron2 (#15033), + FastFold (#15972), fastparquet (#15020), FOX-Toolkit (#15986), GLM-AED (#15879), hiredis (#16071), + how_are_we_stranded_here (#16227), JavaFX (#8583), json-fortran (#15979), jupyter-resource-usage (#15834), + libev (#16086), libmad (#16067), libplinkio (#13040), LuaJIT2-OpenResty (#16047), MetaMorpheus (#15825), + miniasm (#15858), muMerge (#16115), nano (#16198), nghttp3 (#16097), olaFlow (#16021), OpenFAST (#15983), + OpenFold (#15971), Phantompeakqualtools (#15871), pyGenomeTracks (#16143), QuickPIC (#15978), RheoTool (#16077), + Satsuma2 (#16068), SMC++ (#16017), stripy (#15866), UCC-CUDA (#15956), VESTA (#16217) +- added additional easyconfigs for various supported software packages, including: + - ADIOS 1.13.1, ADIOS 20210804, Advisor 2022.1.0.eb, alevin fry, AmberTools 21, AmberTools 21.12, AmberTools 22.3, ant 1.10.12, ant 1.10.12, ANTLR 2.7.7, AOCC 3.2.0, AptaSUITE 0.9.4, aria2 1.36.0, Arrow 8.0.0, arrow R, ASE 3.22.1, attr 2.5.1, AUGUSTUS 3.4.0, BamTools 2.5.2, BBMap 38.96, BBMap 38.98, BCFtools 1.15.1, BeautifulSoup 4.10.0, BEDTools 2.30.0, BigDFT 1.9.1, binutils 2.39, binutils 2.39.eb, Biopython 1.79, Bison 3.8.2, BLAST+ 2.13.0, Blender 3.2.2, Blitz++ 1.0.2, Blitz++ 1.0.2, Bowtie2 2.4.5, buildenv default, buildenv default, buildenv default, buildenv default, BUSCO 5.4.2, BUSCO 5.4.3, bwidget 1.9.15, CapnProto 0.10.2, c ares, Cartopy 0.20.3, ccache 4.6.1, cclib 1.7.2, CDO 2.0.5, CellRanger ATAC, CESM deps, CGAL 4.14.3, Clang 13.0.1, colossalai 0.1.8, CoordgenLibs 3.0.1, CppUnit 1.15.1, CrystFEL 0.8.0, CrystFEL 0.8.0, CUnit 2.1, cURL 7.84.0, cuTENSOR 1.6.0.3, Dakota 6.16.0, DB 18.1.40, dbus glib, Detectron2 0.6, Detectron2 0.6, dotNET Core, EasyBuild 4.6.0.eb, einops 0.4.1, Elk 8.5.2, ELPA 2021.05.001, Emacs 28.1, Embree 3.13.4.eb, expat 2.4.8, expecttest 0.1.3, FastFold 20220729, fastparquet 0.7.2, fastparquet 0.8.0, FFmpeg 4.4.2, FFmpeg 5.0.1, fio 3.32, Flask 2.2.2, flex 2.6.4, Flye 2.9.1, fmt 9.1.0, FORD 6.1.15, FOX Toolkit, FOX Toolkit, FreeSurfer 7.3.2, GATE 9.2, GATK 4.2.6.1, gawk 5.1.1, GCC 12.2.0.eb, GCCcore 12.2.0.eb, GConf 3.2.6, GDB 12.1, Geant4 11.0.1, Geant4 11.0.2, GetOrganelle 1.7.6.1, gifsicle 1.93, git lfs, GLFW 3.3.8, glib networking, GLM AED, Globus CLI, Globus CLI, Globus CLI, gnuplot 5.4.4, gperftools 2.10, Graphviz 5.0.0, groff 1.22.4, GROMACS 2021.3, GROMACS 2021.5, GROMACS 2021.5, GTK2 2.24.33, GTS 0.7.6, Gurobi 9.5.2, HDF5 1.12.2, HDF5 1.12.2, HDF5 1.12.2, HDF5 1.13.1, help2man 1.49.2, HH suite, hiredis 1.0.2, how_are_we_stranded_here 1.0.1, HTSlib 1.15.1, Hypre 2.25.0, Inspector 2022.1.0.eb, intervaltree python, ISL 0.24, itac 2021.6.0.eb, Jansson 2.13.1, Jansson 2.14, Java 11.0.16.eb, Java 17.0.4.eb, Java 8.345.eb, Java 8.eb, JavaFX 11.0.2_linux, jax 0.3.14, json fortran, jupyter resource, Kalign 3.3.2, kim api, LAMMPS 23Jun2022, LAMMPS 23Jun2022, LAMMPS 23Jun2022, LAMMPS 23Jun2022, LAPACK 3.10.1, libaec 1.0.6, libaec 1.0.6, libcerf 2.1, libdwarf 0.4.1, libelf 0.8.13, libev 4.33, libgd 2.3.3, libharu 2.3.0, Libint 2.7.2, libmad 0.15.1b, libplinkio 0.9.8, libpng 1.5.30.eb, libpsl 0.21.1, libQGLViewer 2.8.0, libreadline 8.1.2, LibSoup 2.74.0, libyaml 0.2.5, libzip 1.9.2, Lua 5.4.4, LuaJIT2 OpenResty, lxml 4.9.1, M4 1.4.19, maeparser 1.3.0, makeinfo 6.8, matplotlib 3.5.2, MATSim 14.0, MATSim 14.0, MDAnalysis 2.2.0, medaka 1.6.0, Megalodon 2.5.0, Megalodon 2.5.0, Mercurial 6.2, MetaEuk 6, MetaMorpheus 0.0.320, METIS 5.1.0, miniasm 0.3, miniasm 0.3, Mini XML, Mini XML, molmod 1.4.8, MPC 1.2.1, muMerge 1.1.0, MUMmer 4.0.0rc1, MUMPS 5.5.1, nano 6.4, ncurses 6.3, ncurses 6.3.eb, ncview 2.1.8, netCDF C++4, netCDF Fortran, nghttp3 0.6.0, NGSpeciesID 0.1.2.1, olaFlow 20210820, ont remora, ont remora, OpenBabel 3.1.1, OpenBabel 3.1.1, OpenFAST 3.0.0, OpenFOAM v2206, OpenFold 1.0.0, OpenMM 7.5.1, OpenMPI 4.1.2, OSU Micro, OSU Micro, OTF2 3.0, p7zip 17.04, pagmo 2.18.0, parallel 20220722, ParaView 5.10.1, patchelf 0.15.0, Perl 5.36.0, pftoolsV3 3.2.12, Phantompeakqualtools 1.2.2, pkg config, PLINK 2.00a3.6, PnetCDF 1.12.3, Porechop 0.2.4, pretty yaml, PRSice 2.3.5, pugixml 1.12.1, pyGenomeTracks 3.7, pygmo 2.18.0, Pyomo 6.4.2, PyOpenCL 2021.2.13, Pysam 0.19.1, PyStan 2.19.1.1, PyStan 3.5.0, pytest xdist, PyYAML 6.0, qrupdate 1.1.2, QuantumESPRESSO 7.0, QuantumESPRESSO 7.0, QuickPIC 20210224, Ray project, Ray project, R bundle, RDKit 2022.03.5, RheoTool 5.0, RNA SeQC, SAMtools 1.15.1, Satsuma2 20220304, Schrodinger 2022, Schrodinger 2022, scikit bio, scikit build, scikit build, scikit build, scikit build, scikit learn, scikit learn, scikit optimize, SCOTCH 7.0.1, SIONlib 1.7.7, SISSO 3.1, SMC++ 1.15.4, SoX 14.4.2, SPAdes 3.13.0, spglib python, SPM 12.5_r7771, Stacks 2.62, STAR 2.7.10a_alpha_220601, Stata 17.eb, stripy 2.1.0, SUMO 1.14.1, SWIG 4.0.2, tbb 2021.5.0, Togl 2.0, torchvision 0.11.3, tqdm 4.64.0, Transformers 4.21.1, Trycycler 0.5.3, UCC CUDA, Unicycler 0.5.0, Valgrind 3.19.0, VCFtools 0.1.16, VESTA 3.5.8, ViennaRNA 2.5.1, Voro++ 0.4.6, VTK 9.2.0.rc2, VTune 2022.3.0.eb, Wannier90 3.1.0, Wannier90 3.1.0, WebKitGTK+ 2.27.4, wxPython 4.1.1, x264 20220620, x265 3.5, XCrySDen 1.6.2, XCrySDen 1.6.2, XML Parser, xtb 6.4.1, Yasm 1.3.0, Z3 4.10.2, zfp 1.0.0, zlib 1.2.12 +- minor enhancements, including: + - add alternate download URL for Voro++ (#15898) + - add extra symlinks and sanity checks for libtinfo in ncurses + synchronize ncurses easyconfigs using system toolchain + add easyconfig for ncurses 5.3 with system toolchain (#15903) + - add sanity check command for OpenFAST (#15983) + - include some easyconfig constants in flake8 configuration file (#16040) + - add pigz dependency for cutadapt v3.4 + v3.5 (#16056) + - add sanity check commands for recent gettext versions (>= 0.20.x) (#16091) + - add sanity check commands for Dakota v6.16.0 (#16210) +- various bug fixes, including: + - use correct Matlab Runtime Compiler (v8.4) for FreeSurfer v7.1.1 (#13375) + - remove superflous -DCMAKE_BUILD_TYPE=Release, use of 'build_type = Release', or enabling separate_build_dir from easyconfigs using CMakeMake easyblock (#13384) + - fix set-alias statements for MaxQuant v2.0.3.0 (#15743) + - add Autotools build dependency to R 4.2.0 w/ foss 2021b (#15822) + - add patch for BLIS to fix auto-detection of POWER (#15826) + - explicitly enable HDF5 from kallisto v0.46.2 onwards (#15843) + - add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all OSs (#15856) + - use build enviroment from EB and add missing dependency on zlib to minimap2 (#15859) + - add missing dependencies and execute tests on Trycycler v0.5.2 (#15864) + - add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9 (#15874) + - work around miscompilation of OpenBLAS on POWER by compiling with -fstack-protector-strong (#15885) + - fix tests on POWER9 for BLIS 0.9.0 + fix auto-detect for POWER10 for BLIS (AMD) v2.0 + v3.0 (#15889) + - exclude Binary, PackedBinary and JAR easyblocks from binutils build requirements (#15932) + - add libffi and elfutils as dependency for Clang v11.0.1 + v12.0.1 (#15935) + - add patch to fix broken test on POWER for numpy in SciPy-bundle 2022.05 (#15968) + - refactor checksum test for extensions to use collect_exts_file_info (#15973) + - fix dependency on FOX Toolkit in SUMO (#15986) + - add missing SciPy-bundle dependency for rMATS-turbo (#15988) + - explictely download wannier90 source tarball from wannier90 GitHub repository in QuantumESPRESSO 7.1 easyconfigs (#15993) + - restore ploteig in EIGENSOFT 7.2.1 (#15996) + - add alternative checksum for plot3Drgl extension in R v4.1.x + v4.2.0 easyconfigs (#16011) + - add patch to fix missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 (#16027) and 2021 (#16026) + - exclude failing test in TensorFlow 2.4.1 (#16042) + - skip NASA performance test in netCDF v4.9.0 (#16050) + - use versioned symbols in ncurses built with system toolchain (by adding --with-versioned-syms configure option) (#16064) + - add patch to fix pkgconfig file for Blitz++ v1.0.2 (#16102) + - add missing BCFtools dependency for recent medaka versions (#16107) + - add GTK2 v2.24.33 as a dependency for Ghostscript v9.56.1 (#16112) + - fix checksum for Stacks v2.62 (due to silent re-release without version bump) (#16134) + - fix libsanitzer for glibc 2.36 to build GCCcore 11.3.0 (#16145) + - fix top level Makefile for AmberTools 20 and enable tests (#16150) + - add missing patches for AmberTools 21 with intel/2021a (#16151) and intel/2021b (#16152) toolchains + enable running tests + - disable remote server tests for netCDF 4.9.0 (#16158) + - remove modextrapaths to add top-level install directory to $PATH for recent InterProScan easyconfigs (now done by default by Binary easyblock) (#16167) + - fix sources + source URL + homepage for Molekel v5.4.0 (#16219) + - consistently add libffi + elfutils dependencies to recent Clang easyconfigs (#16225) + - also update $PYTHONPATH for how_are_we_stranded_here + add sanity check command (#16227) +- other changes: + - downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since v3.15.3 is too new (#15840) + - stick to Java/11 as dependency for Bazel 5.1.1 (which is available for x86_64, aarch64, ppc64le) (#15906) + - speed up OpenMPI 4.1.4 configure by not running "autogen.pl --force", but only running required Autotools commands (#15957) + - replace sed commands by upstreamed patches for BLIS built with intel-compilers toolchain (#15958) + - simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM dependency (#15981) + - update LAMMPS 23Jun2022 easyconfigs to use update1 source tarball (#15999) + - update Java/11 to 11.0.16 and Java/17 to 17.0.4 (#16001) + - remove unecessary patch in recent JupyterLab (#16030) + - update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (#16070) + - make check for toolchain value in dependency spec in easyconfigs test suite aware that dumped easyconfig uses SYSTEM constant (#16126) + - replace HDF5 v1.13.1 with v1.12.1 as dependency, since we shouldn't use odd minor versions of HDF5 which are not stable releases (#16153) + + v4.6.0 (July 8th 2022) ---------------------- diff --git a/setup.py b/setup.py index 25c95924956..e5a633dca74 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.6.1.dev0' +VERSION = '4.6.1' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 0112523f3e377fa9df6d8bb055fe803d92eefa7c Mon Sep 17 00:00:00 2001 From: guacke Date: Sun, 11 Sep 2022 10:10:31 +0200 Subject: [PATCH 4807/9987] Add checksum. --- easybuild/easyconfigs/c/Chimera/Chimera-1.16-linux_x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Chimera/Chimera-1.16-linux_x86_64.eb b/easybuild/easyconfigs/c/Chimera/Chimera-1.16-linux_x86_64.eb index 7e9b63d5336..c50dddc83f8 100644 --- a/easybuild/easyconfigs/c/Chimera/Chimera-1.16-linux_x86_64.eb +++ b/easybuild/easyconfigs/c/Chimera/Chimera-1.16-linux_x86_64.eb @@ -16,6 +16,7 @@ toolchain = SYSTEM # no public download URL. Go to https://www.cgl.ucsf.edu/chimera/download.html sources = ['%(namelower)s-%(version)s%(versionsuffix)s.bin'] +checksums = ['e3a89d1ffd30d7195af6149ea7b3ae23596c4f922424d9c957ded447f8d6883c'] # unzip is required to uncompress the provided .bin file osdependencies = ['unzip'] From ed2613a0a18b09a5a9dd383ff889e06eb33baafd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Sep 2022 11:04:39 +0200 Subject: [PATCH 4808/9987] fix checksum for CUDA 11.4.1 aarch64 installer --- easybuild/easyconfigs/c/CUDA/CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.1.eb index 29d43ce1d79..b9f6fac274d 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.4.1.eb @@ -19,7 +19,7 @@ checksums = [ 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: 'dd92ca04f76ad938da3480e2901c0e52dbff6028ada63c09071ed9e3055dc361', 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: - 'i8efa725a41dfd3c0c0f453c2dd535d149154102bf2b791718859417b4f84f922', + '8efa725a41dfd3c0c0f453c2dd535d149154102bf2b791718859417b4f84f922', } ] From 85b9c4495dd9698abba468335f0716caf5ee95b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Sep 2022 21:53:02 +0200 Subject: [PATCH 4809/9987] add direct Pango dependency in recent ImageMagick easyconfigs (fixes #16236) --- .../i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb | 1 + .../i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb | 1 + .../i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb | 1 + .../i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb | 1 + .../i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb | 1 + .../i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb | 1 + 6 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb index 0d6ab6b1978..b08495a6ea2 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-1-GCCcore-9.3.0.eb @@ -24,6 +24,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.4'), ('LibTIFF', '4.1.0'), ('LittleCMS', '2.9'), + ('Pango', '1.44.7'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb index 980874e68be..f0077dead9e 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.10-35-GCCcore-10.2.0.eb @@ -24,6 +24,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.5'), ('LibTIFF', '4.1.0'), ('LittleCMS', '2.11'), + ('Pango', '1.47.0'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb index f2d23dbd601..d7f3007a2f9 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb @@ -24,6 +24,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.6'), ('LibTIFF', '4.2.0'), ('LittleCMS', '2.12'), + ('Pango', '1.48.5'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb index 86774a66a7a..458934f12f4 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.9-5-GCCcore-8.3.0.eb @@ -24,6 +24,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.3'), ('LibTIFF', '4.0.10'), ('LittleCMS', '2.9'), + ('Pango', '1.44.7'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb index 9127abd64dc..f4a6a273ca9 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb @@ -20,6 +20,7 @@ dependencies = [ ('libjpeg-turbo', '2.1.3'), ('LibTIFF', '4.3.0'), ('LittleCMS', '2.13.1'), + ('Pango', '1.50.7'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb index b1329a25dd6..ff34f39886c 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb @@ -20,6 +20,7 @@ dependencies = [ ('libjpeg-turbo', '2.0.6'), ('LibTIFF', '4.3.0'), ('LittleCMS', '2.12'), + ('Pango', '1.48.8'), ] builddependencies = [ From 59ecc27589afe90924452b66a83ccb054799ec84 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Sep 2022 22:15:25 +0200 Subject: [PATCH 4810/9987] remove incorrect comment for Boost dependency in OpenBabel 3.1.1 easyconfigs --- .../o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb | 2 +- .../easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb | 2 +- .../o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb index 286b2053ba5..6d911749614 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb @@ -40,7 +40,7 @@ dependencies = [ ('Eigen', '3.3.7', '', True), ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output - ('Boost', '1.71.0'), # optional: for Maestro formats + ('Boost', '1.71.0'), ('maeparser', '1.3.0'), ('CoordgenLibs', '3.0.1'), ] diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb index 62e0cfda9c0..82569f0e47d 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2021a.eb @@ -39,7 +39,7 @@ dependencies = [ ('Eigen', '3.3.9'), ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output - ('Boost', '1.76.0'), # optional: for Maestro formats + ('Boost', '1.76.0'), ('maeparser', '1.3.0'), ('CoordgenLibs', '3.0.1'), ] diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb index f69361b5b44..76ae741aa83 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2022a.eb @@ -39,7 +39,7 @@ dependencies = [ ('Eigen', '3.4.0'), ('RapidJSON', '1.1.0'), ('cairo', '1.17.4'), # optional: for .png output - ('Boost', '1.79.0'), # optional: for Maestro formats + ('Boost', '1.79.0'), ('maeparser', '1.3.0'), ('CoordgenLibs', '3.0.1'), ] diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb index dfdbeab1c4f..7dbebd3a06a 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb @@ -39,7 +39,7 @@ dependencies = [ ('Eigen', '3.3.7', '', True), ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output - ('Boost', '1.72.0'), # optional: for Maestro formats + ('Boost', '1.72.0'), ('maeparser', '1.3.0'), ('CoordgenLibs', '3.0.1'), ] From 4b26a205fd8fb8a65f97c19fb5dd9c8487226ae9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Sep 2022 22:18:19 +0200 Subject: [PATCH 4811/9987] fix typo in description in mgltools easyconfig Co-authored-by: Adam Huffman --- easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb b/easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb index 0c2917b25b5..c7c3007a9ea 100644 --- a/easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb +++ b/easybuild/easyconfigs/m/mgltools/mgltools-1.5.7.eb @@ -9,7 +9,7 @@ description = """ and analysis of molecular structures and comprises the Python Molecular Viewer (PMV, a general purpose molecular viewer), AutoDockTools (ADT, a set of PMV commands specifically developed to support AutoDock users) - and Vision (a visual programing environment). + and Vision (a visual programming environment). """ toolchain = SYSTEM From 7bb4e9a8d986f62a89839e3aba013f80d2daadf8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Sep 2022 23:12:39 +0200 Subject: [PATCH 4812/9987] minor tweaks for release notes for v4.6.1 --- RELEASE_NOTES | 67 ++++++++++++++++++++++++++++++++------------------- 1 file changed, 42 insertions(+), 25 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 0aae3e402d8..698ecd7803e 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,48 +3,64 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 15,020 easyconfig files, for 2,736 different software packages, +The latest version of easybuild-easyconfig provides 15,332 easyconfig files, for 2,773 different software packages, incl. 37 different (compiler) toolchains. -v4.6.1 (September 14th 2022) +v4.6.1 (September 12th 2022) ---------------------------- update/bugfix release -- added example easyconfig files for 36 new software packages: - - AptaSUITE (#8583), BigDFT (#15860), colossalai (#15971), CrystFEL (#8407), Dakota (#16210), Detectron2 (#15033), - FastFold (#15972), fastparquet (#15020), FOX-Toolkit (#15986), GLM-AED (#15879), hiredis (#16071), - how_are_we_stranded_here (#16227), JavaFX (#8583), json-fortran (#15979), jupyter-resource-usage (#15834), - libev (#16086), libmad (#16067), libplinkio (#13040), LuaJIT2-OpenResty (#16047), MetaMorpheus (#15825), - miniasm (#15858), muMerge (#16115), nano (#16198), nghttp3 (#16097), olaFlow (#16021), OpenFAST (#15983), - OpenFold (#15971), Phantompeakqualtools (#15871), pyGenomeTracks (#16143), QuickPIC (#15978), RheoTool (#16077), - Satsuma2 (#16068), SMC++ (#16017), stripy (#15866), UCC-CUDA (#15956), VESTA (#16217) +- added example easyconfig files for 37 new software packages: + - AptaSUITE (#8583), BigDFT (#15860), colossalai (#15971), CrystFEL (#8407), Dakota (#15883, #16210), + FastFold (#15972), fastparquet (#15020), FOX-Toolkit (#15986), GLM-AED (#15879), hiredis (#16071), + how_are_we_stranded_here (#16220, #16227), indicators (#16209), JavaFX (#8583), json-fortran (#15979), + jupyter-resource-usage (#15834), libev (#16086), libmad (#16067), libplinkio (#13040), LuaJIT2-OpenResty (#16047), + MetaMorpheus (#15825), mgltools (#16226), miniasm (#15858), muMerge (#16115), nano (#16198), nghttp3 (#16097), + olaFlow (#16021), OpenFAST (#15983, #15983), OpenFold (#15971), Phantompeakqualtools (#15871), + pyGenomeTracks (#16143), QuickPIC (#15978), RheoTool (#16077), Satsuma2 (#16068), SMC++ (#16017), stripy (#15866), + UCC-CUDA (#15956), VESTA (#16217) - added additional easyconfigs for various supported software packages, including: - - ADIOS 1.13.1, ADIOS 20210804, Advisor 2022.1.0.eb, alevin fry, AmberTools 21, AmberTools 21.12, AmberTools 22.3, ant 1.10.12, ant 1.10.12, ANTLR 2.7.7, AOCC 3.2.0, AptaSUITE 0.9.4, aria2 1.36.0, Arrow 8.0.0, arrow R, ASE 3.22.1, attr 2.5.1, AUGUSTUS 3.4.0, BamTools 2.5.2, BBMap 38.96, BBMap 38.98, BCFtools 1.15.1, BeautifulSoup 4.10.0, BEDTools 2.30.0, BigDFT 1.9.1, binutils 2.39, binutils 2.39.eb, Biopython 1.79, Bison 3.8.2, BLAST+ 2.13.0, Blender 3.2.2, Blitz++ 1.0.2, Blitz++ 1.0.2, Bowtie2 2.4.5, buildenv default, buildenv default, buildenv default, buildenv default, BUSCO 5.4.2, BUSCO 5.4.3, bwidget 1.9.15, CapnProto 0.10.2, c ares, Cartopy 0.20.3, ccache 4.6.1, cclib 1.7.2, CDO 2.0.5, CellRanger ATAC, CESM deps, CGAL 4.14.3, Clang 13.0.1, colossalai 0.1.8, CoordgenLibs 3.0.1, CppUnit 1.15.1, CrystFEL 0.8.0, CrystFEL 0.8.0, CUnit 2.1, cURL 7.84.0, cuTENSOR 1.6.0.3, Dakota 6.16.0, DB 18.1.40, dbus glib, Detectron2 0.6, Detectron2 0.6, dotNET Core, EasyBuild 4.6.0.eb, einops 0.4.1, Elk 8.5.2, ELPA 2021.05.001, Emacs 28.1, Embree 3.13.4.eb, expat 2.4.8, expecttest 0.1.3, FastFold 20220729, fastparquet 0.7.2, fastparquet 0.8.0, FFmpeg 4.4.2, FFmpeg 5.0.1, fio 3.32, Flask 2.2.2, flex 2.6.4, Flye 2.9.1, fmt 9.1.0, FORD 6.1.15, FOX Toolkit, FOX Toolkit, FreeSurfer 7.3.2, GATE 9.2, GATK 4.2.6.1, gawk 5.1.1, GCC 12.2.0.eb, GCCcore 12.2.0.eb, GConf 3.2.6, GDB 12.1, Geant4 11.0.1, Geant4 11.0.2, GetOrganelle 1.7.6.1, gifsicle 1.93, git lfs, GLFW 3.3.8, glib networking, GLM AED, Globus CLI, Globus CLI, Globus CLI, gnuplot 5.4.4, gperftools 2.10, Graphviz 5.0.0, groff 1.22.4, GROMACS 2021.3, GROMACS 2021.5, GROMACS 2021.5, GTK2 2.24.33, GTS 0.7.6, Gurobi 9.5.2, HDF5 1.12.2, HDF5 1.12.2, HDF5 1.12.2, HDF5 1.13.1, help2man 1.49.2, HH suite, hiredis 1.0.2, how_are_we_stranded_here 1.0.1, HTSlib 1.15.1, Hypre 2.25.0, Inspector 2022.1.0.eb, intervaltree python, ISL 0.24, itac 2021.6.0.eb, Jansson 2.13.1, Jansson 2.14, Java 11.0.16.eb, Java 17.0.4.eb, Java 8.345.eb, Java 8.eb, JavaFX 11.0.2_linux, jax 0.3.14, json fortran, jupyter resource, Kalign 3.3.2, kim api, LAMMPS 23Jun2022, LAMMPS 23Jun2022, LAMMPS 23Jun2022, LAMMPS 23Jun2022, LAPACK 3.10.1, libaec 1.0.6, libaec 1.0.6, libcerf 2.1, libdwarf 0.4.1, libelf 0.8.13, libev 4.33, libgd 2.3.3, libharu 2.3.0, Libint 2.7.2, libmad 0.15.1b, libplinkio 0.9.8, libpng 1.5.30.eb, libpsl 0.21.1, libQGLViewer 2.8.0, libreadline 8.1.2, LibSoup 2.74.0, libyaml 0.2.5, libzip 1.9.2, Lua 5.4.4, LuaJIT2 OpenResty, lxml 4.9.1, M4 1.4.19, maeparser 1.3.0, makeinfo 6.8, matplotlib 3.5.2, MATSim 14.0, MATSim 14.0, MDAnalysis 2.2.0, medaka 1.6.0, Megalodon 2.5.0, Megalodon 2.5.0, Mercurial 6.2, MetaEuk 6, MetaMorpheus 0.0.320, METIS 5.1.0, miniasm 0.3, miniasm 0.3, Mini XML, Mini XML, molmod 1.4.8, MPC 1.2.1, muMerge 1.1.0, MUMmer 4.0.0rc1, MUMPS 5.5.1, nano 6.4, ncurses 6.3, ncurses 6.3.eb, ncview 2.1.8, netCDF C++4, netCDF Fortran, nghttp3 0.6.0, NGSpeciesID 0.1.2.1, olaFlow 20210820, ont remora, ont remora, OpenBabel 3.1.1, OpenBabel 3.1.1, OpenFAST 3.0.0, OpenFOAM v2206, OpenFold 1.0.0, OpenMM 7.5.1, OpenMPI 4.1.2, OSU Micro, OSU Micro, OTF2 3.0, p7zip 17.04, pagmo 2.18.0, parallel 20220722, ParaView 5.10.1, patchelf 0.15.0, Perl 5.36.0, pftoolsV3 3.2.12, Phantompeakqualtools 1.2.2, pkg config, PLINK 2.00a3.6, PnetCDF 1.12.3, Porechop 0.2.4, pretty yaml, PRSice 2.3.5, pugixml 1.12.1, pyGenomeTracks 3.7, pygmo 2.18.0, Pyomo 6.4.2, PyOpenCL 2021.2.13, Pysam 0.19.1, PyStan 2.19.1.1, PyStan 3.5.0, pytest xdist, PyYAML 6.0, qrupdate 1.1.2, QuantumESPRESSO 7.0, QuantumESPRESSO 7.0, QuickPIC 20210224, Ray project, Ray project, R bundle, RDKit 2022.03.5, RheoTool 5.0, RNA SeQC, SAMtools 1.15.1, Satsuma2 20220304, Schrodinger 2022, Schrodinger 2022, scikit bio, scikit build, scikit build, scikit build, scikit build, scikit learn, scikit learn, scikit optimize, SCOTCH 7.0.1, SIONlib 1.7.7, SISSO 3.1, SMC++ 1.15.4, SoX 14.4.2, SPAdes 3.13.0, spglib python, SPM 12.5_r7771, Stacks 2.62, STAR 2.7.10a_alpha_220601, Stata 17.eb, stripy 2.1.0, SUMO 1.14.1, SWIG 4.0.2, tbb 2021.5.0, Togl 2.0, torchvision 0.11.3, tqdm 4.64.0, Transformers 4.21.1, Trycycler 0.5.3, UCC CUDA, Unicycler 0.5.0, Valgrind 3.19.0, VCFtools 0.1.16, VESTA 3.5.8, ViennaRNA 2.5.1, Voro++ 0.4.6, VTK 9.2.0.rc2, VTune 2022.3.0.eb, Wannier90 3.1.0, Wannier90 3.1.0, WebKitGTK+ 2.27.4, wxPython 4.1.1, x264 20220620, x265 3.5, XCrySDen 1.6.2, XCrySDen 1.6.2, XML Parser, xtb 6.4.1, Yasm 1.3.0, Z3 4.10.2, zfp 1.0.0, zlib 1.2.12 + - alevin-fry 0.6.0, AmberTools 22.3, arrow-R 8.0.0, ASE 3.22.1, BBMap 38.98, BCFtools 1.15.1, binutils 2.39, + BLAST+ 2.13.0, Bowtie2 2.4.5, BUSCO 5.4.3, CapnProto 0.10.2, Cartopy 0.20.3, ccache 4.6.1, cclib 1.7.2, CDO 2.0.5, + CellRanger-ATAC 2.1.0, CoordgenLibs 3.0.1, cURL 7.84.0, cuTENSOR 1.6.0.3, einops 0.4.1, Elk 8.5.2, Emacs 28.1, + Embree 3.13.4, FFmpeg 4.4.2 + 5.0.1, fio 3.32, Flask 2.2.2, Flye 2.9.1, fmt 9.1.0, FORD 6.1.15, FreeSurfer 7.3.2, + GATE 9.2, GATK 4.2.6.1, GCC(core) 12.2.0, GDB 12.1, Geant4 11.0.2, GetOrganelle 1.7.6.1, gifsicle 1.93, GLFW 3.3.8, + glib-networking 2.72.1, Globus-CLI 3.6.0, gnuplot 5.4.4, gperftools 2.10, Graphviz 5.0.0, Gurobi 9.5.2, HDF5 1.12.2, + HTSlib 1.15.1, Hypre 2.25.0, Jansson 2.14, jax 0.3.14, Kalign 3.3.2, kim-api 2.3.0, LAMMPS 23Jun2022, libcerf 2.1, + libdwarf 0.4.1, Libint 2.7.2, libQGLViewer 2.8.0, LibSoup 2.74.0, libzip 1.9.2, Lua 5.4.4, lxml 4.9.1, + maeparser 1.3.0, matplotlib 3.5.2, MATSim 14.0, MDAnalysis 2.2.0, medaka 1.6.0, Megalodon 2.5.0, Mercurial 6.2, + MetaEuk 6, Mini-XML-3.3.1, MUMmer 4.0.0rc1, MUMPS 5.5.1, netCDF-Fortran 4.6.0, NGSpeciesID 0.1.2.1, + ont-remora 1.0.0, OpenFOAM v2206, OTF2 3.0, parallel 20220722, ParaView 5.10.1, patchelf 0.15.0, Perl 5.36.0, + pftoolsV3 3.2.12, PLINK 2.00a3.6, pretty-yaml 21.10.1, PRSice 2.3.5, pugixml 1.12.1, Pyomo 6.4.2, + PyOpenCL 2021.2.13, Pysam 0.19.1, PyStan 3.5.0, PyYAML 6.0, RDKit 2022.03.5, scikit-bio 0.5.7, scikit-build 0.15.0, + scikit-learn 1.1.2, scikit-optimize 0.9.0, SCOTCH 7.0.1, SIONlib 1.7.7, SISSO 3.1, spglib-python 2.0.0, Stacks 2.62, + Stata 17, SUMO 1.14.1, tbb 2021.5.0, tqdm 4.64.0, Transformers 4.21.1, Trycycler 0.5.3, Unicycler 0.5.0, + Valgrind 3.19.0, ViennaRNA 2.5.1, VTune 2022.3.0.eb, wxPython 4.1.1, x264 20220620, Z3 4.10.2, zfp 1.0.0 - minor enhancements, including: - add alternate download URL for Voro++ (#15898) - - add extra symlinks and sanity checks for libtinfo in ncurses + synchronize ncurses easyconfigs using system toolchain + add easyconfig for ncurses 5.3 with system toolchain (#15903) - - add sanity check command for OpenFAST (#15983) + - add extra symlinks and sanity checks for libtinfo in ncurses (#15903) - include some easyconfig constants in flake8 configuration file (#16040) - add pigz dependency for cutadapt v3.4 + v3.5 (#16056) - add sanity check commands for recent gettext versions (>= 0.20.x) (#16091) - - add sanity check commands for Dakota v6.16.0 (#16210) - various bug fixes, including: - use correct Matlab Runtime Compiler (v8.4) for FreeSurfer v7.1.1 (#13375) - - remove superflous -DCMAKE_BUILD_TYPE=Release, use of 'build_type = Release', or enabling separate_build_dir from easyconfigs using CMakeMake easyblock (#13384) - fix set-alias statements for MaxQuant v2.0.3.0 (#15743) - add Autotools build dependency to R 4.2.0 w/ foss 2021b (#15822) - add patch for BLIS to fix auto-detection of POWER (#15826) + - downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since v3.15.3 is too new (#15840) - explicitly enable HDF5 from kallisto v0.46.2 onwards (#15843) - add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all OSs (#15856) - - use build enviroment from EB and add missing dependency on zlib to minimap2 (#15859) + - use build enviroment set by EasyBuild and add missing dependency on zlib to minimap2 (#15859) - add missing dependencies and execute tests on Trycycler v0.5.2 (#15864) - add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9 (#15874) + - exclude (flaky) fault_tolerance_test and fix non-x86 build for TensorFlow 2.7.1 (#15882) - work around miscompilation of OpenBLAS on POWER by compiling with -fstack-protector-strong (#15885) - fix tests on POWER9 for BLIS 0.9.0 + fix auto-detect for POWER10 for BLIS (AMD) v2.0 + v3.0 (#15889) + - add and fix patches for PyTorch 1.9.0 on POWER (#15919) - exclude Binary, PackedBinary and JAR easyblocks from binutils build requirements (#15932) - - add libffi and elfutils as dependency for Clang v11.0.1 + v12.0.1 (#15935) + - consistently add libffi + elfutils dependencies to recent Clang easyconfigs (#15935, #16225) - add patch to fix broken test on POWER for numpy in SciPy-bundle 2022.05 (#15968) - refactor checksum test for extensions to use collect_exts_file_info (#15973) - fix dependency on FOX Toolkit in SUMO (#15986) @@ -54,7 +70,7 @@ update/bugfix release - add alternative checksum for plot3Drgl extension in R v4.1.x + v4.2.0 easyconfigs (#16011) - add patch to fix missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 (#16027) and 2021 (#16026) - exclude failing test in TensorFlow 2.4.1 (#16042) - - skip NASA performance test in netCDF v4.9.0 (#16050) + - skip NASA performance and remote server tests in netCDF v4.9.0 (#16050, #16158) - use versioned symbols in ncurses built with system toolchain (by adding --with-versioned-syms configure option) (#16064) - add patch to fix pkgconfig file for Blitz++ v1.0.2 (#16102) - add missing BCFtools dependency for recent medaka versions (#16107) @@ -62,24 +78,25 @@ update/bugfix release - fix checksum for Stacks v2.62 (due to silent re-release without version bump) (#16134) - fix libsanitzer for glibc 2.36 to build GCCcore 11.3.0 (#16145) - fix top level Makefile for AmberTools 20 and enable tests (#16150) - - add missing patches for AmberTools 21 with intel/2021a (#16151) and intel/2021b (#16152) toolchains + enable running tests - - disable remote server tests for netCDF 4.9.0 (#16158) + - add missing patches + enable running tests for AmberTools 21 with intel/2021a (#16151) and intel/2021b (#16152) + - replace HDF5 v1.13.1 with v1.12.1 as dependency, since we shouldn't use odd minor versions of HDF5 which are not stable releases (#16153) - remove modextrapaths to add top-level install directory to $PATH for recent InterProScan easyconfigs (now done by default by Binary easyblock) (#16167) - fix sources + source URL + homepage for Molekel v5.4.0 (#16219) - - consistently add libffi + elfutils dependencies to recent Clang easyconfigs (#16225) - - also update $PYTHONPATH for how_are_we_stranded_here + add sanity check command (#16227) + - consistently add maeparser + CoordgenLibs dependencies to OpenBabel 3.1.1 easyconfigs (#16231) + - fix checksum for CUDA 11.4.1 aarch64 installer (#16234) + - remove incorrect comment for Boost dependency in OpenBabel 3.1.1 easyconfigs (#16238) + - add direct Pango dependency in recent ImageMagick easyconfigs (#16237) - other changes: - - downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since v3.15.3 is too new (#15840) + - remove superflous -DCMAKE_BUILD_TYPE=Release, use of 'build_type = Release', or enabling separate_build_dir from easyconfigs using CMakeMake easyblock (#13384) + - synchronize ncurses easyconfigs using system toolchain (#15903) - stick to Java/11 as dependency for Bazel 5.1.1 (which is available for x86_64, aarch64, ppc64le) (#15906) - speed up OpenMPI 4.1.4 configure by not running "autogen.pl --force", but only running required Autotools commands (#15957) - replace sed commands by upstreamed patches for BLIS built with intel-compilers toolchain (#15958) - simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM dependency (#15981) - - update LAMMPS 23Jun2022 easyconfigs to use update1 source tarball (#15999) - update Java/11 to 11.0.16 and Java/17 to 17.0.4 (#16001) - remove unecessary patch in recent JupyterLab (#16030) - update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (#16070) - make check for toolchain value in dependency spec in easyconfigs test suite aware that dumped easyconfig uses SYSTEM constant (#16126) - - replace HDF5 v1.13.1 with v1.12.1 as dependency, since we shouldn't use odd minor versions of HDF5 which are not stable releases (#16153) v4.6.0 (July 8th 2022) From 0afca1c2eea5192da643a1cf6b186c8e8f920fff Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 12 Sep 2022 09:14:34 +0800 Subject: [PATCH 4813/9987] adding easyconfigs: EasyBuild-4.6.1.eb --- .../e/EasyBuild/EasyBuild-4.6.1.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.1.eb new file mode 100644 index 00000000000..5edaba5f48e --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.1.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.6.1' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/8f/a8/0a0643997744b98ba58420ac61a4d90a07c7bc55c2e9758c6d6109c830c5/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/44/4e/9c383093e979de7493f9670c1101ab0a259b1e6d3ac975dc8b62d9c78a48/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/a2/23/85ebe66474384de982b949950e62c66fe6bf34dff34317e0a33c96949517/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + 'a085f503be7f01db4711db5c56395eb6867c2688ed652a3c1878fe4d253cf273', # easybuild-framework-4.6.1.tar.gz + 'a2a51c14c916a6561b3a66ca9dbfe09734dcc8450cd69f3196e6cc2541e2cc59', # easybuild-easyblocks-4.6.1.tar.gz + '14eb71e3ebac6c27f5000e450b8d6cf2c83f0a508558d06189314e1051f6be46', # easybuild-easyconfigs-4.6.1.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 635b4d530766f1493000d749fc75f3bf1335a1cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Sep 2022 09:04:42 +0200 Subject: [PATCH 4814/9987] bump version to 4.6.2dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index e5a633dca74..24b137e9759 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.6.1' +VERSION = '4.6.2.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 35bfd8d4f1c1899ace4f6719f5d177952735035b Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Sep 2022 09:34:21 +0100 Subject: [PATCH 4815/9987] Module class changed to data --- .../easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb index 113dfcfb507..3ce9bf655e9 100644 --- a/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb @@ -32,4 +32,4 @@ sanity_check_paths = { 'dirs': [''], } -moduleclass = 'tools' +moduleclass = 'data' From e57b8e27d19ddbd8ecc5f16b2431cec2128ed13c Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Sep 2022 09:35:20 +0100 Subject: [PATCH 4816/9987] Module class changed to data --- .../easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb index d3bd423b610..75368d77747 100644 --- a/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb @@ -32,4 +32,4 @@ sanity_check_paths = { 'dirs': [''], } -moduleclass = 'tools' +moduleclass = 'data' From be219b99b3a6e4c2a8e87508958a1c816196a409 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Sep 2022 09:41:56 +0100 Subject: [PATCH 4817/9987] Name of package corrected --- .../crossguid-20190529-GCCcore-11.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/{crossguide/crossguide-20190529-GCCcore-11.3.0.eb => crossguid/crossguid-20190529-GCCcore-11.3.0.eb} (96%) diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb similarity index 96% rename from easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb index 6e0f31e5436..f9e343734f7 100644 --- a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' -name = 'crossguide' +name = 'crossguid' local_commit = 'ca1bf4b' version = '20190529' @@ -22,7 +22,7 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ patches = ['libuuid-20190529.patch'] checksums = [ - '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguide-20190529.tar.gz + '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguid-20190529.tar.gz '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # libuuid-20190529.patch ] From fb8dceee0c3f57a7668bdad330169ac586efe3c7 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Sep 2022 09:48:27 +0100 Subject: [PATCH 4818/9987] Name of package corrected --- .../crossguid-0.2.2-GCCcore-11.2.0.eb} | 2 +- .../crossguid-20190529-GCCcore-11.2.0.eb} | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/c/{crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb => crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb} (98%) rename easybuild/easyconfigs/c/{crossguide/crossguide-20190529-GCCcore-11.2.0.eb => crossguid/crossguid-20190529-GCCcore-11.2.0.eb} (96%) diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb similarity index 98% rename from easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb index 5cc5419fa3e..3823e69fcd9 100644 --- a/easybuild/easyconfigs/c/crossguide/crossguide-0.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMakeCp' -name = 'crossguide' +name = 'crossguid' version = '0.2.2' homepage = 'https://github.com/graeme-hill/crossguid' diff --git a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb similarity index 96% rename from easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb index b468e316ad3..708cd547629 100644 --- a/easybuild/easyconfigs/c/crossguide/crossguide-20190529-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' -name = 'crossguide' +name = 'crossguid' local_commit = 'ca1bf4b' version = '20190529' @@ -22,7 +22,7 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ patches = ['libuuid-20190529.patch'] checksums = [ - '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguide-20190529.tar.gz + '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguid-20190529.tar.gz '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # libuuid-20190529.patch ] From daa4ff212e99040a55dd13f356a29b97b8a60364 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Sep 2022 09:50:39 +0100 Subject: [PATCH 4819/9987] Name of module crossguid corrected --- .../easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb index 8a31631972f..eb0217ebec9 100644 --- a/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb @@ -36,7 +36,7 @@ builddependencies = [ ] dependencies = [ - ('crossguide', '20190529'), + ('crossguid', '20190529'), ('nlohmann_json', '3.10.5'), ('rapidcsv', '8.64'), ('fmt', '9.1.0'), From 75e4f9aac01d7a520420872fecd0c4eb2dc3afcf Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 12 Sep 2022 10:57:12 +0200 Subject: [PATCH 4820/9987] adding easyconfigs: BioPerl-1.7.8-GCCcore-11.3.0.eb, DB_File-1.858-GCCcore-11.3.0.eb, XML-LibXML-2.0207-GCCcore-11.3.0.eb --- .../b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb | 54 ++++++++++++++++++ .../d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb | 31 ++++++++++ .../XML-LibXML-2.0207-GCCcore-11.3.0.eb | 56 +++++++++++++++++++ 3 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5b7057ffa26 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'Bundle' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Perl', '5.34.1'), + ('XML-LibXML', '2.0207'), + ('DB_File', '1.858'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + ('XML::DOM::XPath', '0.14', { + 'source_tmpl': 'XML-DOM-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': ['0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), + ('BioPerl', version, { + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9ca805bc383 --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.858' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['ceb7a2868bd71f87b31e8b7c38d6f8cc0a31fb0322a377ee448994f094d0a7f6'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fb860328d8f --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0207-GCCcore-11.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0207' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('binutils', '2.38'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('libxml2', '2.9.13'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1011', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'], + }), + ('Alien::Base', '2.68', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['c2436a81b3fe971c75d6a7202557971f09718adddf85c447c0beaabf28f0b11f'], + }), + ('Alien::Libxml2', '0.17', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['73b45244f0b5c36e5332c33569b82a1ab2c33e263f1d00785d2003bcaec68db3'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['903436c9859875bef5593243aae85ced329ad0fb4b57bbf45975e32547c50c15'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' From 4a1f2679da64809757a836e0bae27cc1a33efedc Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Sep 2022 09:58:58 +0100 Subject: [PATCH 4821/9987] Name of module class changed to math --- easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb index b3b916d6405..0687aee7c0e 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb @@ -48,4 +48,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'math' From e46ec84730ad2d59b75aa2106e161db4e15bd443 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Sep 2022 10:03:02 +0100 Subject: [PATCH 4822/9987] Name of module class changed to math --- easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb index 182ad2ee738..4359434e6cf 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb @@ -48,4 +48,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'tools' +moduleclass = 'math' From c939ac06512b432390c45eb98ee35ba32ebfba04 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Sep 2022 16:10:51 +0200 Subject: [PATCH 4823/9987] configure recent pocl versions to -DLLC_HOST_CPU=native to avoid CPU auto-detection --- easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.5-GCC-9.3.0.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb | 4 +++- easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb | 4 +++- 7 files changed, 21 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb index c8b6eda3b49..032f249a058 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-GCC-8.3.0.eb @@ -34,7 +34,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb index 42495666e3e..2939fcf0e31 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.4-gcccuda-2019b.eb @@ -34,7 +34,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so, enable CUDA configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.5-GCC-9.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.5-GCC-9.3.0.eb index 9868608073f..3a67d21dcc9 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.5-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.5-GCC-9.3.0.eb @@ -34,7 +34,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb index 7f2991f31f8..949bd6168a8 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-GCC-10.2.0.eb @@ -30,7 +30,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb index d5d54b8902c..b6ff23250e3 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-gcccuda-2020b.eb @@ -30,7 +30,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so, enable CUDA configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb b/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb index 4dc3a0dc23e..257dcb0f4d9 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.6-iccifort-2020.4.304.eb @@ -30,7 +30,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb index 8dff6865a13..0c7f9416308 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb @@ -34,7 +34,9 @@ separate_build_dir = True # disable attempt to find an ICD loader, always build libOpenCL.so configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " # make sure we use the easybuild Clang -configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON" +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " sanity_check_paths = { 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], From 7c6aac356fa03c85fb293950850e4659d4739e3d Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 12 Sep 2022 21:10:48 +0200 Subject: [PATCH 4824/9987] adding easyconfigs: IPython-8.5.0-GCCcore-11.3.0.eb, libsodium-1.0.18-GCCcore-11.3.0.eb, OpenPGM-5.2.122-GCCcore-11.3.0.eb, ZeroMQ-4.3.4-GCCcore-11.3.0.eb --- .../i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb | 180 ++++++++++++++++++ .../libsodium-1.0.18-GCCcore-11.3.0.eb | 33 ++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb | 45 +++++ .../z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb | 40 ++++ 4 files changed, 298 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4697bcfaf93 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,180 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '8.5.0' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('ZeroMQ', '4.3.4'), + ('lxml', '4.9.1'), + ('BeautifulSoup', '4.10.0'), +] + +use_pip = True + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['097bdf5cd87576fd066179c9f7f208004f7a6864ee1b20f37d346c0bcb099f84'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '3.0.31', { + 'checksums': ['9ada952c9d1787f52ff6d5f3484d0b4df8952787c087edf6a1f7c2cb1ea88148'], + }), + ('traitlets', '5.2.0', { + 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + }), + ('parso', '0.8.3', { + 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], + }), + ('jedi', '0.18.1', { + 'checksums': ['74137626a64a99c8eb6ae5832d99b3bdd7d29a3850fe2aa80a4126b2a7d949ab'], + }), + ('testpath', '0.6.0', { + 'checksums': ['2f1b97e6442c02681ebe01bd84f531028a7caea1af3825000f52345c30285e0f'], + }), + ('Send2Trash', '1.8.0', { + 'checksums': ['d2c24762fd3759860a0aff155e45871447ea58d2be6bdd39b5c8f966a0c99c2d'], + }), + ('bleach', '5.0.1', { + 'checksums': ['0d03255c47eb9bd2f26aa9bb7f2107732e7e8fe195ca2f64709fcf3b0a4a085c'], + }), + ('pandocfilters', '1.5.0', { + 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], + }), + ('pyzmq', '23.2.1', { + 'modulename': 'zmq', + 'checksums': ['2b381aa867ece7d0a82f30a0c7f3d4387b7cf2e0697e33efaa5bed6c5784abcd'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('jupyter_core', '4.10.0', { + 'checksums': ['a6de44b16b7b31d7271130c71a6792c4040f077011961138afed5e5e73181aec'], + }), + ('fastjsonschema', '2.16.1', { + 'checksums': ['d6fa3ffbe719768d70e298b9fb847484e2bdfdb7241ed052b8d57a9294a8c334'], + }), + ('nbformat', '5.4.0', { + 'checksums': ['44ba5ca6acb80c5d5a500f1e5b83ede8cbe364d5a495c4c8cf60aaf1ba656501'], + }), + ('mistune', '0.8.1', { + 'checksums': ['4c0f66924ce28f03b95b210ea57e57bd0b59f479edd91c2fa4fe59331eae4a82'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('nest_asyncio', '1.5.5', { + 'checksums': ['e442291cd942698be619823a17a86a5759eabe1f8613084790de189fe9e16d65'], + }), + ('nbclient', '0.6.3', { + 'checksums': ['b80726fc1fb89a0e8f8be1e77e28d0026b1e8ed90bc143c8a0c7622e4f8cdd9e'], + }), + ('tinycss2', '1.1.1', { + 'checksums': ['b2e44dd8883c360c35dd0d1b5aad0b610e5156c2cb3b33434634e539ead9d8bf'], + }), + ('nbconvert', '6.5.3', { + 'checksums': ['10ed693c4cfd3c63583c87ca5c3a2f6ed874145103595f3824efcc8dfcb7522c'], + }), + ('tornado', '6.2', { + 'checksums': ['9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13'], + }), + ('terminado', '0.13.0', { + 'checksums': ['713531ccb5db7d4f544651f14050da79809030f00d1afa21462088cf32fb143a'], + }), + ('jupyter_client', '7.3.1', { + 'checksums': ['05d4ff6a0ade25138c6bb0fbeac7ddc26b5fe835e7dd816b64b4a45b931bdc0b'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('executing', '1.0.0', { + 'checksums': ['98daefa9d1916a4f0d944880d5aeaf079e05585689bebd9ff9b32e31dd5e1017'], + }), + ('asttokens', '2.0.8', { + 'checksums': ['c61e16246ecfb2cde2958406b4c8ebc043c9e6d73aaa83c941673b35e5d3a76b'], + }), + ('pure_eval', '0.2.2', { + 'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3'], + }), + ('stack_data', '0.5.0', { + 'checksums': ['715c8855fbf5c43587b141e46cc9d9339cc0d1f8d6e0f98ed0d01c6cb974e29f'], + }), + ('ipykernel', '6.13.0', { + 'checksums': ['0e28273e290858393e86e152b104e5506a79c13d25b951ac6eca220051b4be60'], + }), + ('prometheus_client', '0.11.0', { + 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], + }), + ('ipywidgets', '7.6.3', { + 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.0', { + 'checksums': ['b27455d60adc93a7baa2e0b8f386be81b932bb4e3c0116046df9ed230cd3faac'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('jupyterlab_widgets', '3.0.3', { + 'checksums': ['c767181399b4ca8b647befe2d913b1260f51bf9d8ef9b7a14632d4c1a7b536bd'], + }), + ('argon2-cffi', '20.1.0', { + 'modulename': 'argon2', + 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], + }), + ('notebook', '6.4.0', { + 'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + ('matplotlib-inline', '0.1.2', { + 'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'], + }), + ('debugpy', '1.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['84ff51b8b5c847d5421324ca419db1eec813a4dd2bbf19dbbbe132e2ab2b2fc6'], + }), +] + +modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/IPython', + 'share/jupyter' + ], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e62a803500d --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0563e14c45a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + 'OpenPGM-5.2.122-pkgconfig_includes.patch', + 'OpenPGM-5.2.122-python3-compliant.patch' +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0d05aef4ded --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.4' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.38'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = '--with-pic --with-pgm --with-libsodium --disable-Werror' + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From b1cda6332689c9060eebdee5acffddd5ac3ba60f Mon Sep 17 00:00:00 2001 From: guacke Date: Tue, 13 Sep 2022 10:21:27 +0200 Subject: [PATCH 4825/9987] adding easyconfigs: AutoDock-Vina-1.2.3-foss-2021b.eb --- .../AutoDock-Vina-1.2.3-foss-2021b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021b.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021b.eb new file mode 100644 index 00000000000..2a8e3660e44 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021b.eb @@ -0,0 +1,65 @@ +easyblock = 'MakeCp' + +name = 'AutoDock-Vina' +version = '1.2.3' + +homepage = 'https://vina.scripps.edu/' +description = "AutoDock Vina is an open-source program for doing molecular docking." + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'ccsb-scripps' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'] + +builddependencies = [ + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Boost', '1.77.0'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +start_dir = 'build/linux/release' + +buildopts = 'GPP="$CXX" BOOST_INCLUDE="$EBROOTBOOST/include"' + +files_to_copy = [ + (['vina', 'vina_split'], 'bin'), + (['docs', 'example', 'LICENSE', 'README.md'], 'share'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +# fix hardcoded paths in setup.py +_ext_boost_paths = ('$EBROOTBOOST/include', '$EBROOTBOOST/lib') +_ext_fix_paths = 'sed -i "s|= locate_boost()|= \\\"%s\\\", \\\"%s\\\"|" setup.py && ' % _ext_boost_paths +_ext_fix_paths += "sed -i 's|\.\./\.\./src|%%(builddir)s/%%(name)s/%s-%%(version)s/src|g' setup.py && " % name + +exts_list = [ + ('vina', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['22f85b2e770b6acc363429153b9551f56e0a0d88d25f747a40d2f55a263608e0'], + 'start_dir': 'build/python', + 'preinstallopts': _ext_fix_paths, + }), +] + +sanity_check_paths = { + 'files': ['bin/vina', 'bin/vina_split'], + 'dirs': ['share'], +} + +sanity_check_commands = [('vina', '--help')] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' From bf3948c68d80222e7340b9818d05c95686dfe185 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Sep 2022 15:35:35 +0200 Subject: [PATCH 4826/9987] make template_easyconfig_test aware of patches with dicts --- test/easyconfigs/easyconfigs.py | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0fb05afe876..f190f2cba33 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1333,21 +1333,29 @@ def template_easyconfig_test(self, spec): # make sure all patch files are available specdir = os.path.dirname(spec) + basedir = os.path.dirname(os.path.dirname(specdir)) specfn = os.path.basename(spec) for idx, patch in enumerate(ec['patches']): - if isinstance(patch, (tuple, list)): - patch = patch[0] + patch_dir = specdir + if isinstance(patch, str): + patch_name = patch + elif isinstance(patch, (tuple, list)): + patch_name = patch[0] + elif isinstance(patch, dict): + patch_name = patch['name'] + if patch['alt_location']: + patch_dir = os.path.join(basedir, letter_dir_for(patch_name), patch_name) # only check actual patch files, not other files being copied via the patch functionality - patch_full = os.path.join(specdir, patch) - if patch.endswith('.patch'): + patch_full = os.path.join(patch_dir, patch_name) + if patch_name.endswith('.patch'): msg = "Patch file %s is available for %s" % (patch_full, specfn) self.assertTrue(os.path.isfile(patch_full), msg) # verify checksum for each patch file - if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch.endswith('.patch')): + if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch_name.endswith('.patch')): checksum = patch_checksums[idx] - error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch, ec_fn, checksum) + error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch_name, ec_fn, checksum) res = verify_checksum(patch_full, checksum) self.assertTrue(res, error_msg) From f1d1a11248619a3ca73105827971387b2e905ceb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Sep 2022 15:55:10 +0200 Subject: [PATCH 4827/9987] patch_dir for patch in alt_location is in alt_locataion, not patch_name --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f190f2cba33..297025bec2b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1344,7 +1344,7 @@ def template_easyconfig_test(self, spec): elif isinstance(patch, dict): patch_name = patch['name'] if patch['alt_location']: - patch_dir = os.path.join(basedir, letter_dir_for(patch_name), patch_name) + patch_dir = os.path.join(basedir, letter_dir_for(alt_location), alt_location) # only check actual patch files, not other files being copied via the patch functionality patch_full = os.path.join(patch_dir, patch_name) From 03c3c85e9b7b9cb401f6cd24f873a3f5cb1eab7b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Sep 2022 15:59:03 +0200 Subject: [PATCH 4828/9987] Fix typo: alt_location -> patch['alt_location'] --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 297025bec2b..7e40d102230 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1344,7 +1344,7 @@ def template_easyconfig_test(self, spec): elif isinstance(patch, dict): patch_name = patch['name'] if patch['alt_location']: - patch_dir = os.path.join(basedir, letter_dir_for(alt_location), alt_location) + patch_dir = os.path.join(basedir, letter_dir_for(patch['alt_location']), patch['alt_location']) # only check actual patch files, not other files being copied via the patch functionality patch_full = os.path.join(patch_dir, patch_name) From 34cae5483945e9da678188b1ed282ca212e48db2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 14 Sep 2022 16:27:05 +0200 Subject: [PATCH 4829/9987] Update chksum for AmberTools-20_fix_missing_MPI_LIBRARY_error.patch --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb index 234d491d03b..e09a0fe8d70 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb @@ -40,7 +40,7 @@ checksums = [ '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools22.tar.bz2 '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch - '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch From 5912119214d0e7e40830b157e5dac5dd412b7c20 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 14 Sep 2022 21:45:45 +0200 Subject: [PATCH 4830/9987] adding easyconfigs: NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb --- .../NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..89e4a5835bb --- /dev/null +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb @@ -0,0 +1,65 @@ +easyblock = 'ConfigureMake' + +name = 'NVSHMEM' +version = '2.5.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nvshmem' +description = """NVSHMEM is a parallel programming interface based on OpenSHMEM that provides +efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a +global address space for data that spans the memory of multiple GPUs and can be +accessed with fine-grained GPU-initiated operations, CPU-initiated operations, +and operations on CUDA streams. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +# You need to download the source manully from https://developer.nvidia.com/nvshmem-downloads +sources = ['%(namelower)s_src_%(version)s-19.txz'] +checksums = ['dd800b40f1d296e1d3ed2a9885adcfe745c3e57582bc809860e87bd32abcdc60'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('NCCL', '2.12.12', versionsuffix), +] + +skipsteps = ['configure'] + +prebuildopts = 'export NVSHMEM_USE_GDRCOPY=1 && ' +prebuildopts += 'export GDRCOPY_HOME=${EBROOTGDRCOPY} && ' + +prebuildopts += 'export MPI_HOME=${EBROOTOPENMPI} && ' +prebuildopts += 'export NVSHMEM_MPI_SUPPORT=1 && ' +prebuildopts += 'export NVSHMEMTEST_USE_MPI_LAUNCHER=1 && ' + +prebuildopts += 'export NCCL_HOME=${EBROOTNCCL} && ' +prebuildopts += 'export NVSHMEM_USE_NCCL=1 && ' + +prebuildopts += 'export NVSHMEM_BUILDDIR=%(builddir)s && ' +prebuildopts += 'export NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj && ' +prebuildopts += 'export NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj && ' +prebuildopts += 'export NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj && ' +prebuildopts += 'export NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj && ' + +prebuildopts += 'export NVSHMEM_PREFIX=%(installdir)s && ' +prebuildopts += 'export NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples && ' +prebuildopts += 'export NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest && ' +prebuildopts += 'export NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest && ' +prebuildopts += 'export NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test && ' + +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['lib/libnvshmem.a', 'lib/nvshmem_bootstrap_mpi.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +modextravars = {'NVSHMEM_HOME': '%(installdir)s'} + +moduleclass = 'devel' From e17c8a4ad9c8b7189651a207f71e127b9ff42275 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 16 Sep 2022 10:09:49 +0100 Subject: [PATCH 4831/9987] Corrected version of Wayland to 1.21.0 --- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb index 1ede0f20a54..9026c3b2c20 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -58,7 +58,7 @@ dependencies = [ ('glew', '2.2.0', '-egl'), ('libwpe', '1.13.3'), ('pugixml', '1.12.1'), - ('Wayland', '1.20.0'), + ('Wayland', '1.21.0'), ('Waylandpp', '1.0.0'), ('wpebackend-fdo', '1.13.1'), ('enchant-2', '2.3.3'), From a8c0b09f919023448521989f3750615396e6688a Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 16 Sep 2022 10:19:01 +0100 Subject: [PATCH 4832/9987] Missing GLib-2.69.1 added, sanity check command corrected --- .../e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb index 6af0833119a..3f4b2a24826 100644 --- a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb @@ -30,13 +30,14 @@ builddependencies = [ preconfigopts = "autoreconf -vfi && " dependencies = [ - ('hunspell', '1.7.0'), + ('hunspell', '1.7.1'), + ('GLib', '2.69.1'), ] buildopts = "LIBTOOL='libtool --tag=CC'" sanity_check_commands = [ - 'enchant-2 -h', + 'enchant-2 -v', 'enchant-lsmod-2 -v', ] From efde57cb097195438513c94ec4208f548cb9ad8a Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 16 Sep 2022 10:32:35 +0100 Subject: [PATCH 4833/9987] Missing freeglut added --- .../easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb index ba0e31b6d0c..c59f1cf7ccc 100644 --- a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb @@ -34,8 +34,12 @@ builddependencies = [ dependencies = [ ('pugixml', '1.12.1'), ('Wayland', '1.21.0'), + ('freeglut', '3.2.1'), ] +# Required to find EGL +#osdependencies = [('libegl-dev', 'libegl-devel')] + parallel = 2 sanity_check_paths = { From 275e58ef65766731d4ae7ef93d768e916ae9991f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 16 Sep 2022 13:26:20 +0200 Subject: [PATCH 4834/9987] Update chksum for AmberTools-20_fix_missing_MPI_LIBRARY_error.patch --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 475f93c1e0c..9d5139c40a3 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -41,7 +41,7 @@ checksums = [ '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools22.tar.bz2 '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch - '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch From c4c1a9b5ba47224454f3d4eb3502fa2e520eed03 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 16 Sep 2022 16:25:43 +0200 Subject: [PATCH 4835/9987] add download_instructions --- .../n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb index 89e4a5835bb..5e8b6ae2658 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb @@ -14,7 +14,10 @@ and operations on CUDA streams. toolchain = {'name': 'gompi', 'version': '2022a'} -# You need to download the source manully from https://developer.nvidia.com/nvshmem-downloads +download_instructions = """The sources of NVSHMEM can be downloaded at Nvidia's webpage when you have signed up for +their (free) developer program: +https://developer.nvidia.com/nvshmem-downloads""" + sources = ['%(namelower)s_src_%(version)s-19.txz'] checksums = ['dd800b40f1d296e1d3ed2a9885adcfe745c3e57582bc809860e87bd32abcdc60'] From deec58b847dffa1b64da3abb6acd949c32e2bca3 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 16 Sep 2022 16:28:22 +0200 Subject: [PATCH 4836/9987] add download_instructions --- .../n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb index 908356d7fda..ba7dbd9499e 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb @@ -14,7 +14,10 @@ and operations on CUDA streams. toolchain = {'name': 'gompi', 'version': '2021b'} -# You need to download the source manully from https://developer.nvidia.com/nvshmem-downloads +download_instructions = """The sources of NVSHMEM can be downloaded at NVIDIA's webpage when you have signed up for +their (free) developer program: +https://developer.nvidia.com/nvshmem-downloads""" + sources = ['%(namelower)s_src_%(version)s-3.txz'] checksums = ['8b6c0eab321b6352911e470f9e81a777a49e58148ec3728453b9522446dba178'] From dad7ad6a6e4e6df9bdca82c712dbdf1bf8cfea09 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 16 Sep 2022 16:28:48 +0200 Subject: [PATCH 4837/9987] update download_instructions --- .../n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb index 5e8b6ae2658..52e0be373d1 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb @@ -14,7 +14,7 @@ and operations on CUDA streams. toolchain = {'name': 'gompi', 'version': '2022a'} -download_instructions = """The sources of NVSHMEM can be downloaded at Nvidia's webpage when you have signed up for +download_instructions = """The sources of NVSHMEM can be downloaded at NVIDIA's webpage when you have signed up for their (free) developer program: https://developer.nvidia.com/nvshmem-downloads""" From f8283428783661c6f944e8930c2767626e0905a7 Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 16 Sep 2022 17:26:01 +0200 Subject: [PATCH 4838/9987] adding easyconfigs: Avogadro2-1.97.0-linux-x86_64.eb --- .../Avogadro2-1.97.0-linux-x86_64.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb diff --git a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb new file mode 100644 index 00000000000..0e2449a1bdf --- /dev/null +++ b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'Binary' + +name = 'Avogadro2' +version = '1.97.0' +versionsuffix = '-linux-x86_64' + +homepage = 'https://two.avogadro.cc/index.html' +description = """ + Avogadro is an advanced molecule editor and visualizer designed for cross-platform + use in computational chemistry, molecular modeling, bioinformatics, materials science, + and related areas. It offers flexible high quality rendering and + a powerful plugin architecture. +""" + +toolchain = SYSTEM + +sources = [{ + 'source_urls' : ['https://github.com/OpenChemistry/avogadroapp/releases/download/1.97.0'], + 'filename': 'avogadro2', + 'download_filename': 'Avogadro2-x86_64.AppImage' +}] + +checksums = ['cc522dbdaa6e5386cb7101d382c5730f0d1ff71f2e70eb10f7e55f4ca052c89d'] + +sanity_check_paths = { + 'files' : ['avogadro2'], + 'dirs' : [], +} + +moduleclass = 'vis' From e9e653af905a4de4daa8d0e85a4e041133acd0ef Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 16 Sep 2022 18:27:49 +0200 Subject: [PATCH 4839/9987] Style fixes. --- .../Avogadro2-1.97.0-linux-x86_64.eb | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb index 0e2449a1bdf..eacd093cbd5 100644 --- a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb @@ -6,25 +6,24 @@ versionsuffix = '-linux-x86_64' homepage = 'https://two.avogadro.cc/index.html' description = """ - Avogadro is an advanced molecule editor and visualizer designed for cross-platform - use in computational chemistry, molecular modeling, bioinformatics, materials science, - and related areas. It offers flexible high quality rendering and - a powerful plugin architecture. + Avogadro is an advanced molecule editor and visualizer designed for cross-platform + use in computational chemistry, molecular modeling, bioinformatics, materials science, + and related areas. """ toolchain = SYSTEM sources = [{ - 'source_urls' : ['https://github.com/OpenChemistry/avogadroapp/releases/download/1.97.0'], - 'filename': 'avogadro2', - 'download_filename': 'Avogadro2-x86_64.AppImage' + 'source_urls': ['https://github.com/OpenChemistry/avogadroapp/releases/download/1.97.0'], + 'filename': 'avogadro2', + 'download_filename': 'Avogadro2-x86_64.AppImage' }] checksums = ['cc522dbdaa6e5386cb7101d382c5730f0d1ff71f2e70eb10f7e55f4ca052c89d'] sanity_check_paths = { - 'files' : ['avogadro2'], - 'dirs' : [], + 'files': ['avogadro2'], + 'dirs': [], } -moduleclass = 'vis' +moduleclass = 'vis' \ No newline at end of file From d36b8d9745ec9593612d00f6b4004f9dd507741d Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 16 Sep 2022 18:41:34 +0200 Subject: [PATCH 4840/9987] Style fixes. --- .../easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb index eacd093cbd5..0e2597cebb9 100644 --- a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb @@ -26,4 +26,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'vis' \ No newline at end of file +moduleclass = 'vis' From ed3095735a1eaff3e992f9d0c19f0a57da170ace Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Sep 2022 20:27:23 +0200 Subject: [PATCH 4841/9987] Remove AmberTools-20 patch file from Amber, it's now located in AmberTools only. --- ...ols-20_fix_missing_MPI_LIBRARY_error.patch | 21 ------------------- 1 file changed, 21 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch deleted file mode 100644 index 8d96ce176c0..00000000000 --- a/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch +++ /dev/null @@ -1,21 +0,0 @@ -When using "usempi" there will be no MPI_xxx_LIBRARIES set and that causes -import_libraries to error out. We know it is correct so comment out that -FATAL_ERROR. - -Åke Sandgren, 2021-06-16 -diff -ru amber20_src.orig/cmake/LibraryTracking.cmake amber20_src/cmake/LibraryTracking.cmake ---- amber20_src.orig/cmake/LibraryTracking.cmake 2021-04-25 02:51:44.000000000 +0200 -+++ amber20_src/cmake/LibraryTracking.cmake 2021-06-16 13:30:26.568317368 +0200 -@@ -170,9 +170,9 @@ - - cmake_parse_arguments(IMP_LIBS "" "" "LIBRARIES;INCLUDES" ${ARGN}) - -- if("${IMP_LIBS_LIBRARIES}" STREQUAL "") -- message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") -- endif() -+ #if("${IMP_LIBS_LIBRARIES}" STREQUAL "") -+ # message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") -+ #endif() - - if(NOT "${IMP_LIBS_UNPARSED_ARGUMENTS}" STREQUAL "") - message(FATAL_ERROR "Incorrect usage. Extra arguments provided.") From 99b7331dd4785187f3ece14a5f756ef271c7dae2 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Sat, 17 Sep 2022 08:53:30 +0200 Subject: [PATCH 4842/9987] Update easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb | 44 ++++++++++--------- 1 file changed, 23 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb index 52e0be373d1..5c22660ad0b 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb @@ -34,27 +34,29 @@ dependencies = [ skipsteps = ['configure'] -prebuildopts = 'export NVSHMEM_USE_GDRCOPY=1 && ' -prebuildopts += 'export GDRCOPY_HOME=${EBROOTGDRCOPY} && ' - -prebuildopts += 'export MPI_HOME=${EBROOTOPENMPI} && ' -prebuildopts += 'export NVSHMEM_MPI_SUPPORT=1 && ' -prebuildopts += 'export NVSHMEMTEST_USE_MPI_LAUNCHER=1 && ' - -prebuildopts += 'export NCCL_HOME=${EBROOTNCCL} && ' -prebuildopts += 'export NVSHMEM_USE_NCCL=1 && ' - -prebuildopts += 'export NVSHMEM_BUILDDIR=%(builddir)s && ' -prebuildopts += 'export NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj && ' -prebuildopts += 'export NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj && ' -prebuildopts += 'export NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj && ' -prebuildopts += 'export NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj && ' - -prebuildopts += 'export NVSHMEM_PREFIX=%(installdir)s && ' -prebuildopts += 'export NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples && ' -prebuildopts += 'export NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest && ' -prebuildopts += 'export NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest && ' -prebuildopts += 'export NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test && ' +prebuildopts = 'export %s &&' % ' '.join([ + 'NVSHMEM_USE_GDRCOPY=1', + 'GDRCOPY_HOME=${EBROOTGDRCOPY}', + + 'MPI_HOME=${EBROOTOPENMPI}', + 'NVSHMEM_MPI_SUPPORT=1', + 'NVSHMEMTEST_USE_MPI_LAUNCHER=1', + + 'NCCL_HOME=${EBROOTNCCL}', + 'NVSHMEM_USE_NCCL=1', + + 'NVSHMEM_BUILDDIR=%(builddir)s', + 'NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj', + 'NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj', + 'NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj', + 'NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj', + + 'NVSHMEM_PREFIX=%(installdir)s', + 'NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples', + 'NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest', + 'NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest', + 'NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test', +]) preinstallopts = prebuildopts From 8837734e2629fb17cec68918e9720302e2e8e050 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 19 Sep 2022 17:10:09 +0200 Subject: [PATCH 4843/9987] skip flaky test in PyTorch 1.9 --- .../p/PyTorch/PyTorch-1.9.0-foss-2020b.eb | 3 +++ .../PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 3 +++ .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 3 +++ ....0_skip-autograd-thread_shutdown-test.patch | 18 ++++++++++++++++++ 4 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb index 68f81ba8ce2..000f5a2c4f2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-foss-2020b.eb @@ -28,6 +28,7 @@ patches = [ 'PyTorch-1.9.0_avoid-failures-in-test_unary_ufuncs.patch', 'PyTorch-1.9.0_fix-kineto-crash.patch', 'PyTorch-1.9.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch', 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', ] checksums = [ @@ -49,6 +50,8 @@ checksums = [ 'f600e6831f8a03af007845687d1e0f65b2394ca89a9dab5178e2cdc9bd384d43', '1ed5e125f7922ea577d43053a6652aedc21cc036157e101c0e3b9aee9029d3b0', # PyTorch-1.9.0_fix-kineto-crash.patch 'a4733b6b16a0db4ee5f85f2b103abc29bd711cfc5253f8dd8494d2b0c1509516', # PyTorch-1.9.0_fix-vsx-vector-functions.patch + # PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch + '94957de0fd5bcbea37482cb6d0d12b4608dccf50a10da0836e151b414954ccc3', # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index b4662e2722d..12f72390950 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -37,6 +37,7 @@ patches = [ 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch', 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', 'PyTorch-1.9.0_skip-nccl-error-tests.patch', ] @@ -73,6 +74,8 @@ checksums = [ '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch + '94957de0fd5bcbea37482cb6d0d12b4608dccf50a10da0836e151b414954ccc3', # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index e7070b8d189..0982b4f230d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -36,6 +36,7 @@ patches = [ 'PyTorch-1.9.0_increase-test-cuda-tolerance.patch', 'PyTorch-1.9.0_increase-tolerance-for-distributed-tests.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch', 'PyTorch-1.9.0_skip-lstm-serialization-test.patch', 'PyTorch-1.9.0_skip-nccl-error-tests.patch', ] @@ -72,6 +73,8 @@ checksums = [ '725922f0000d51c03f726a34b249db8f53eee7e5c67417774a5113de954f5a5c', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch + '94957de0fd5bcbea37482cb6d0d12b4608dccf50a10da0836e151b414954ccc3', # PyTorch-1.9.0_skip-lstm-serialization-test.patch '0fc14e29bd7530bcc09f4212df3c846072b1313216da86b827e102b85d695f49', '9634fb34fedff4589b9175a4e4c3f278b60d4dcbc7b36b0f19604748d32074f0', # PyTorch-1.9.skip-nccl-error-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch new file mode 100644 index 00000000000..cfb52a911e0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0_skip-autograd-thread_shutdown-test.patch @@ -0,0 +1,18 @@ +This test is flaky due to a race condition. +See https://github.com/pytorch/pytorch/issues/85259 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_autograd.py b/test/test_autograd.py +index 19fe8777d5..bb25e3ef53 100644 +--- a/test/test_autograd.py ++++ b/test/test_autograd.py +@@ -4339,7 +4339,7 @@ class TestAutograd(TestCase): + b.data = a + self.assertTrue(b_id_saved == id(b)) + +- @unittest.skipIf(IS_WINDOWS, "Skipping because doesn't work for windows") ++ @unittest.skip("Skipping due to possible race condition") + def test_thread_shutdown(self): + code = """import torch + from torch.autograd import Function From bfb6b70236547b9cff46f2d8f1b578a2e589f851 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 19 Sep 2022 18:44:44 +0200 Subject: [PATCH 4844/9987] Add UCX-CUDA as dependency --- .../easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb index 2ed04d457b6..a81d983d6e3 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -25,6 +25,7 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.7.0', '', True), + ('UCX-CUDA', '1.12.1', versionsuffix), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) @@ -36,7 +37,7 @@ configopts = [ ] sanity_check_paths = { - 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'files': ['lib/libmagma.so', 'lib/libmagma.a'], 'dirs': ['include'], } From de272ce0ffe470dcf6bc3e695fa31c2216b1246c Mon Sep 17 00:00:00 2001 From: swadmin Date: Mon, 19 Sep 2022 20:02:45 +0200 Subject: [PATCH 4845/9987] adding easyconfigs: OpenFOAM-10-foss-2022a.eb and patches: OpenFOAM-10-ThirdParty.patch --- .../o/OpenFOAM/OpenFOAM-10-ThirdParty.patch | 276 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-10-foss-2022a.eb | 37 +++ 2 files changed, 313 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-ThirdParty.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-ThirdParty.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-ThirdParty.patch new file mode 100644 index 00000000000..4a2dd8f3b77 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-ThirdParty.patch @@ -0,0 +1,276 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Aligned hunks by Leon Kos. Based on patch for OpenFOAM 5.0 and 4.1 by +# Kenneth Hoste (HPC-UGent) and Ward Poelmans + +diff -ru OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2022-09-19 11:34:37.930703275 +0200 +@@ -17,8 +17,8 @@ + fi + + # Ensure CMake gets the correct C/C++ compilers +-[ -n "$WM_CC" ] && export CC="$WM_CC" +-[ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++#[ -n "$WM_CC" ] && export CC="$WM_CC" ++#[ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVblockMesh + wmake $targetType vtkPVFoam +diff -ru OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +--- OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt 2022-09-19 11:34:37.932703249 +0200 +@@ -2,6 +2,8 @@ + + PROJECT(PVReaders) + ++FIND_PACKAGE(MPI REQUIRED) ++ + FIND_PACKAGE(ParaView REQUIRED) + + INCLUDE(GNUInstallDirs) +diff -ru OpenFOAM-10-version-10/etc/bashrc OpenFOAM-10/etc/bashrc +--- OpenFOAM-10-version-10/etc/bashrc 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/bashrc 2022-09-19 11:34:37.934703223 +0200 +@@ -43,8 +43,9 @@ + # Please set to the appropriate path if the default is not correct. + # + [ "$BASH" -o "$ZSH_NAME" ] && \ +-export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++#export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \ ++#export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ru OpenFOAM-10-version-10/etc/config.sh/CGAL OpenFOAM-10/etc/config.sh/CGAL +--- OpenFOAM-10-version-10/etc/config.sh/CGAL 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/CGAL 2022-09-19 11:34:37.935703211 +0200 +@@ -39,22 +39,7 @@ + # + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-#boost_version=boost-1.55.0 +-#boost_version=boost-1.72.0 +- +-cgal_version=cgal-system +-#cgal_version=CGAL-4.10 +-#cgal_version=CGAL-5.0.2 +- +-if [ "$boost_version" != "boost-system" ] +-then +- export BOOST_ARCH_PATH=$WM_THIRD_PARTY_DIR/$boost_version +-fi +- +-if [ "$cgal_version" != "cgal-system" ] +-then +- export CGAL_ARCH_PATH=$WM_THIRD_PARTY_DIR/$cgal_version +-fi ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-10-version-10/etc/config.sh/gperftools OpenFOAM-10/etc/config.sh/gperftools +--- OpenFOAM-10-version-10/etc/config.sh/gperftools 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/gperftools 2022-09-19 11:34:37.937703185 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-10-version-10/etc/config.sh/metis OpenFOAM-10/etc/config.sh/metis +--- OpenFOAM-10-version-10/etc/config.sh/metis 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/metis 2022-09-19 11:34:37.938703172 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-10-version-10/etc/config.sh/mpi OpenFOAM-10/etc/config.sh/mpi +--- OpenFOAM-10-version-10/etc/config.sh/mpi 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/mpi 2022-09-19 11:34:37.939703159 +0200 +@@ -254,6 +254,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib/release + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-10-version-10/etc/config.sh/paraview OpenFOAM-10/etc/config.sh/paraview +--- OpenFOAM-10-version-10/etc/config.sh/paraview 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/paraview 2022-09-19 11:34:37.941703134 +0200 +@@ -41,25 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used. Take the most recent. +-unset CMAKE_HOME CMAKE_ROOT +-for cmake in $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/cmake-* +-do +- if [ -d $cmake ] +- then +- if [ -z $CMAKE_HOME ] || \ +- $WM_PROJECT_DIR/bin/tools/foamVersionCompare $CMAKE_HOME lt $cmake +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- fi +- fi +-done +-if [ -n $CMAKE_HOME ] +-then +- export PATH=$cmake/bin:$PATH +-fi +- + #- ParaView version, automatically determine major version + #export ParaView_VERSION=4.0.1 + #export ParaView_VERSION=4.1.0 +@@ -69,7 +50,8 @@ + #export ParaView_VERSION=5.0.1 + #export ParaView_VERSION=5.4.0 + #export ParaView_VERSION=5.5.0 +-export ParaView_VERSION=5.6.3 ++#export ParaView_VERSION=5.6.3 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + #export ParaView_GL=system +@@ -109,7 +91,8 @@ + export ParaView_VERSION ParaView_MAJOR + + # Set the binary and source directories +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION ++# export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION ++export ParaView_DIR=$EBROOTPARAVIEW + paraviewSrcDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + + # Set paths if binaries or source are present +@@ -129,8 +112,6 @@ + fi + export ParaView_LIB_DIR=$ParaView_DIR/lib$paraviewArch$paraviewLibSubDir + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -142,18 +123,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi +- + # Alias paraview to launch with mesa if necessary + if [ "$ParaView_GL" = mesa ] + then +diff -ru OpenFOAM-10-version-10/etc/config.sh/scotch OpenFOAM-10/etc/config.sh/scotch +--- OpenFOAM-10-version-10/etc/config.sh/scotch 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/scotch 2022-09-19 11:34:37.942703121 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.9 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-10-version-10/etc/config.sh/settings OpenFOAM-10/etc/config.sh/settings +--- OpenFOAM-10-version-10/etc/config.sh/settings 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/settings 2022-09-19 11:34:37.943703108 +0200 +@@ -61,11 +61,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ru OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/Make/options 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/Make/options 2022-09-19 11:34:37.945703082 +0200 +@@ -4,14 +4,7 @@ + $(PFLAGS) $(PINC) \ + -I$(FOAM_SRC)/Pstream/mpi/lnInclude \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ARCH_PATH)/lib \ +- -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \ +- -lptscotch \ +- -lptscotcherrexit \ +- -lscotch \ +- -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2022-09-19 11:34:37.947703057 +0200 +@@ -31,10 +31,11 @@ + #include "SubField.H" + #include "PstreamGlobals.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-10-version-10/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-10/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-10-version-10/src/parallel/decompose/scotchDecomp/Make/options 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/src/parallel/decompose/scotchDecomp/Make/options 2022-09-19 11:34:37.948703044 +0200 +@@ -6,7 +6,6 @@ + EXE_INC = \ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb new file mode 100644 index 00000000000..ac915d6fce3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb @@ -0,0 +1,37 @@ +name = 'OpenFOAM' +version = '10' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-%(version)s-ThirdParty.patch'] +checksums = [ + '59d712ba798ca44b989b6ac50bcb7c534eeccb82bcf961e10ec19fc8d84000cf', # version-10.tar.gz + '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43', # OpenFOAM-10-ThirdParty.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.1'), + ('CGAL', '4.14.3'), + ('ParaView', '5.10.1', '-mpi'), + ('gnuplot', '5.4.4'), +] + +moduleclass = 'cae' From 13a229157d19415bfddfbc22796d08b5675152fb Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 19 Sep 2022 16:52:39 -0700 Subject: [PATCH 4846/9987] {bio}[GCC/11.2.0] AGAT 0.9.2 --- .../a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb new file mode 100644 index 00000000000..97dd5d374f3 --- /dev/null +++ b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb @@ -0,0 +1,57 @@ +# easybuild easyconfig +# +# John Dey Fred Hutchinson Cancer Center +# +easyblock = 'Bundle' + +name = 'AGAT' +version = '0.9.2' + +homepage = 'https://agat.readthedocs.io/en/latest/' +description = """AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations + in any GTF/GFF format.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Perl', '5.34.0'), + ('BioPerl', '1.7.8'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::Share', '0.27', { + 'source_tmpl': 'File-Share-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['d6e8f4b55ebd38e0bb45e44392e3fa27dc1fde16abc5d1ff53e157e19a5755be'], + }), + ('Sort::Naturally', '1.03', { + 'source_tmpl': 'Sort-Naturally-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'], + }), + ('Term::ProgressBar', '2.22', { + 'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['2642ecca5b0b038c14812bcad3a9611ff7911dc59c9104d220797f837a880c49'], + }), + (name, version, { + 'modulename': 'AGAT::Utilities', + 'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['998e32a3cb5e941efd324daf9ee4e0a71d605d06999922f083170b7a9f059899'], + }), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'], +} + +moduleclass = 'bio' From 2e62c073e28d4821a2ef282fd766a4792b397996 Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 20 Sep 2022 11:50:34 +0200 Subject: [PATCH 4847/9987] adding easyconfigs: libcint-5.1.6-foss-2022a.eb --- .../l/libcint/libcint-5.1.6-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcint/libcint-5.1.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/libcint/libcint-5.1.6-foss-2022a.eb b/easybuild/easyconfigs/l/libcint/libcint-5.1.6-foss-2022a.eb new file mode 100644 index 00000000000..6b4b19e2832 --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-5.1.6-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '5.1.6' + +homepage = 'https://github.com/sunqm/libcint' +description = """libcint is an open source library for analytical Gaussian integrals.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/sunqm/libcint/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-4.4.0_remove_pyscftest.patch'] +checksums = [ + 'c111d82140e2e8415775e73f571a16456c9deadd36d58795edd170035b06f8a5', # v5.1.6.tar.gz + '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d', # libcint-4.4.0_remove_pyscftest.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), + # Python with numpy only required for 'make test' + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +separate_build_dir = False # Must use the same directory for tests + +configopts = '-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on' + +buildopts = "VERBOSE=1" + +runtest = 'test ' + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/libcint.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'chem' From 46719281db5b742329591c02af287c5d92a61a3e Mon Sep 17 00:00:00 2001 From: Alex Date: Tue, 20 Sep 2022 12:15:20 +0200 Subject: [PATCH 4848/9987] build: harden linting.yml permissions Signed-off-by: Alex --- .github/workflows/linting.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 6346d959773..b041561e9e4 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,5 +1,7 @@ name: Static Analysis on: [push, pull_request] +permissions: + contents: read # to fetch code (actions/checkout) jobs: python-linting: runs-on: ubuntu-20.04 From a1d8f4898de7d5ece15122a73ff5c06f2f3edf4e Mon Sep 17 00:00:00 2001 From: Alex Date: Tue, 20 Sep 2022 12:16:14 +0200 Subject: [PATCH 4849/9987] build: harden unit_tests.yml permissions Signed-off-by: Alex --- .github/workflows/unit_tests.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 1a8e16547f5..4ce590ffa1f 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -1,5 +1,7 @@ name: easyconfigs unit tests on: [push, pull_request] +permissions: + contents: read # to fetch code (actions/checkout) jobs: test-suite: runs-on: ubuntu-20.04 From 095470f83e7906758f162be7c38941eb201aa5ca Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 20 Sep 2022 12:38:30 +0200 Subject: [PATCH 4850/9987] Add Guile and deps --- .../g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb | 45 +++++++++++++++++++ .../g/gc/gc-8.2.2-GCCcore-11.3.0.eb | 42 +++++++++++++++++ .../libunistring-1.0-GCCcore-11.3.0.eb | 31 +++++++++++++ 3 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0feea67dfc8 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '3.0.8' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f25ae0c26e911af1b5005292d4f56621879f74d6958b30741cf67d8b6feb2016'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +dependencies = [ + ('gc', '8.2.2'), + ('GMP', '6.2.1'), + ('libffi', '3.4.2'), + ('libunistring', '1.0'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0539f756059 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.2.2' +local_libatomic_version = '7.6.14' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a +garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + 'f30107bcb062e0920a790ffffa56d9512348546859364c23a14be264b38836a0', # gc-8.2.2.tar.gz + '390f244d424714735b7050d056567615b3b8f29008a663c262fb548f1802d292', # libatomic_ops-7.6.14.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a6849817c91 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.0' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['5bab55b49f75d77ed26b257997e919b693f29fd4a1bc22e0e6e024c246c72741'] + +builddependencies = [ + ('binutils', '2.38'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' From 4ceccfc979768c33859d99f8a56213811111d634 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 20 Sep 2022 17:45:08 +0200 Subject: [PATCH 4851/9987] Add --with-versioned-syms to ncurses 6.2 and 6.3 --- easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb index 816870478e9..04fddafce58 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-FCC-4.5.0.eb @@ -20,7 +20,7 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] builddependencies = [('binutils', '2.36.1')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # default build local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb index d0f89800315..2ef2ac3431c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] builddependencies = [('binutils', '2.35')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb index da6d4c2d78d..3608131b4d7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-10.3.0.eb @@ -20,7 +20,7 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] builddependencies = [('binutils', '2.36.1')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb index 15191562f91..8c1f8604b30 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-11.2.0.eb @@ -20,7 +20,7 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] builddependencies = [('binutils', '2.37')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb index a5329b525e9..cee6bdc8b98 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2-GCCcore-9.3.0.eb @@ -20,7 +20,7 @@ checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] builddependencies = [('binutils', '2.34')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, From d389fc024851212db53face5674112233eb24785 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 20 Sep 2022 17:47:33 +0200 Subject: [PATCH 4852/9987] Add --with-versioned-syms to 6.3 --- easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb index 26666e64a97..232a2cfedab 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] builddependencies = [('binutils', '2.38')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb index 843c52c75d9..4b9fc292bde 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.1.0.eb @@ -20,7 +20,7 @@ checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] builddependencies = [('binutils', '2.38')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, From 12016618ef7f89ae78b0554263c5a21f3dcc38f1 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 20 Sep 2022 18:24:15 +0200 Subject: [PATCH 4853/9987] ADD CDO --- .../c/CDO/CDO-2.0.6-gompi-2022a.eb | 46 +++++++++++++++++++ .../e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb | 44 ++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb new file mode 100644 index 00000000000..caccb37e498 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.0.6' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'cstd': 'c++17', 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/27276/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef120dea9032b1be80a4cfa201958c3b910107205beb6674195675f1ee8ed402'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('ecCodes', '2.27.0'), + ('FFTW', '3.3.10'), + ('HDF5', '1.12.2'), + ('libxml2', '2.9.13'), + ('netCDF', '4.9.0'), + ('PROJ', '9.0.0'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.38'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb new file mode 100644 index 00000000000..742bdb55b84 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.27.0' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['ede5b3ffd503967a5eac89100e8ead5e16a881b7585d02f033584ed0c4269c99'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('JasPer', '2.0.33'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF " +configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " +configopts += "-DENABLE_ECCODES_THREADS=ON" # multi-threading with pthreads + +local_exes = ['%s_%s' % (a, b) + for a in ['bufr', 'grib', 'gts', 'metar'] + for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] +local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + + ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 84b816b4bf3f165bdd9be22ee2141d4b89f97d23 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 21 Sep 2022 08:14:08 +0200 Subject: [PATCH 4854/9987] adding easyconfigs: Theano-1.0.4-foss-2018b-Python-3.6.6.eb --- .../Theano-1.0.4-foss-2018b-Python-3.6.6.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..92874d5552d --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = "1.0.4" +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] + +dependencies = [('Python', '3.6.6')] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From f8f34d0004023f046b3df614ac7ad921fd8719e5 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 21 Sep 2022 08:48:34 +0200 Subject: [PATCH 4855/9987] improvements from linter --- .../t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb index 92874d5552d..ed46151ae76 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] @@ -18,6 +17,7 @@ dependencies = [('Python', '3.6.6')] use_pip = True download_dep_fail = True +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/theano-cache', 'bin/theano-nose'], From 954022bebd993c28d9c3eecd34b3e3baf57d1295 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Sep 2022 11:43:18 +0200 Subject: [PATCH 4856/9987] adding easyconfigs: TELEMAC-MASCARET-8p3r1-foss-2021b.eb --- .../TELEMAC-MASCARET-8p3r1-foss-2021b.eb | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb new file mode 100644 index 00000000000..bd10f9de826 --- /dev/null +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb @@ -0,0 +1,85 @@ +easyblock = 'Binary' + +name = 'TELEMAC-MASCARET' +version = '8p3r1' + +homepage = 'http://www.opentelemac.org' +description = """TELEMAC-MASCARET is an integrated suite of solvers for use in the field of free-surface flow. Having +been used in the context of many studies throughout the world, it has become one of the major standards in its field.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'extra_fcflags': "-fallow-invalid-boz"} + +source_urls = ['https://gitlab.pam-retd.fr/otm/telemac-mascaret/-/archive/v%(version)s/'] +sources = ['telemac-mascaret-v%(version)s.tar.gz'] +checksums = ['e37ae6b7eefca0e544c6431308e43828d439be08701356814dd1e04ca762fb7d'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # provides numpy, scipy + ('matplotlib', '3.4.3'), + ('HDF5', '1.12.1'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.2'), + ('MUMPS', '5.4.1', '-metis'), +] + +extract_sources = True +unpack_options = '--strip-components=1' + +buildininstalldir = True + +install_cmd = "export HOMETEL=$PWD && " +# add Python scripts to $PATH and $PYTHONPATH +install_cmd += "export PATH=$HOMETEL/scripts/python3/:$PATH && " +install_cmd += "export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH && " +# force python to flush its output +install_cmd += "export PYTHONUNBUFFERED=1 && " + +# export LD_LIBRARY_PATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$LD_LIBRARY_PATH +# export PYTHONPATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$PYTHONPATH + +install_cmd += "cp $HOMETEL/configs/systel.edf.cfg $HOMETEL/configs/systel.easybuild.cfg && " +install_cmd += "sed -i 's/S9.gfortran/easybuild/g' $HOMETEL/configs/systel.easybuild.cfg && " +# strip out use of AED, GOTM, MED (optional dependencies) +install_cmd += "sed -i 's/\(^[a-z]*_aed:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " +install_cmd += "sed -i 's/\(^[a-z]*_gotm:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " +install_cmd += "sed -i 's/\(^[a-z]*_med:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " +# replace -O2 with desired compiler options +install_cmd += 'sed -i "s/-O2/$F90FLAGS/g" $HOMETEL/configs/systel.easybuild.cfg && ' +# fix linker option for BLAS +install_cmd += 'sed -i "s/ -lblas/ $LIBBLAS/g" $HOMETEL/configs/systel.easybuild.cfg && ' +# downgrade Fortran compiler error to warning +install_cmd += "sed -i 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g' $HOMETEL/configs/systel.easybuild.cfg && " +install_cmd += "export SYSTELCFG=$HOMETEL/configs/systel.easybuild.cfg && " +install_cmd += "export USETELCFG=easybuild && " + +install_cmd += "export SCALAPACKHOME=$EBROOTSCALAPACK && " +install_cmd += "export METISHOME=$EBROOTMETIS && " +install_cmd += "export SCOTCHHOME=$EBROOTSCOTCH && " +install_cmd += "export MUMPSHOME=$EBROOTMUMPS && " +install_cmd += "export HDF5HOME=$EBROOTHDF5 && " +install_cmd += "config.py && compile_telemac.py -j %(parallel)s" + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts/python3'], +} + +sanity_check_commands = [ + "tmpdir=$(mktemp -d) && cp -a %(installdir)s/examples/telemac2d/gouttedo $tmpdir/ && " + "cd $tmpdir/gouttedo && telemac2d.py t2d_gouttedo.cas", +] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'builds/easybuild/lib', + 'PATH': 'scripts/python3', + 'PYTHONPATH': 'scripts/python3', +} + +modextravars = { + 'SYSTELCFG': '%(installdir)s/configs/systel.easybuild.cfg', + 'USETELCFG': 'easybuild', +} + +moduleclass = 'geo' From 0b891aeee1dc31e126d9c4cdbfdd66dc644db125 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Sep 2022 11:53:49 +0200 Subject: [PATCH 4857/9987] enhance sanity check for TELEMAC --- .../t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb index bd10f9de826..69b187c36e0 100644 --- a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb @@ -62,7 +62,8 @@ install_cmd += "export HDF5HOME=$EBROOTHDF5 && " install_cmd += "config.py && compile_telemac.py -j %(parallel)s" sanity_check_paths = { - 'files': [], + 'files': ['builds/easybuild/bin/telemac2d', 'builds/easybuild/bin/telemac3d', + 'builds/easybuild/lib/libtelemac2d.%s' % SHLIB_EXT, 'builds/easybuild/lib/libtelemac3d.%s' % SHLIB_EXT], 'dirs': ['scripts/python3'], } From da879364bc7f8c8db0050fca3a8a822ddac6ee0f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Sep 2022 11:55:57 +0200 Subject: [PATCH 4858/9987] enhance sanity check command to make sure that TELEMAC example test case directory is writable --- .../t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb index 69b187c36e0..5b6623b4774 100644 --- a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb @@ -68,7 +68,7 @@ sanity_check_paths = { } sanity_check_commands = [ - "tmpdir=$(mktemp -d) && cp -a %(installdir)s/examples/telemac2d/gouttedo $tmpdir/ && " + "tmpdir=$(mktemp -d) && cp -a %(installdir)s/examples/telemac2d/gouttedo $tmpdir/ && chmod -R u+w $tmpdir && " "cd $tmpdir/gouttedo && telemac2d.py t2d_gouttedo.cas", ] From 70219f9f76ca4815c07aed9a49d983262e928ead Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 21 Sep 2022 11:58:09 +0200 Subject: [PATCH 4859/9987] Add SuiteSparse --- ...iteSparse-5.13.0-foss-2022a-METIS-5.1.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022a-METIS-5.1.0.eb new file mode 100644 index 00000000000..8409675b853 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022a-METIS-5.1.0.eb @@ -0,0 +1,31 @@ +name = 'SuiteSparse' +version = '5.13.0' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['59c6ca2959623f0c69226cf9afb9a018d12a37fab3a8869db5f6d7f83b6b147d'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " +# remove broken symlink +prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && " + +moduleclass = 'numlib' From c65d481876888907a1ea92c95c626eab69a2eec1 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 21 Sep 2022 12:45:06 +0200 Subject: [PATCH 4860/9987] adding easyconfigs: OpenEXR-3.1.5-GCCcore-11.3.0.eb, libwebp-1.2.4-GCCcore-11.3.0.eb, OpenCV-4.6.0-foss-2022a-contrib.eb --- .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 47 ++++++++ .../OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 114 ++++++++++++++++++ .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 40 ++++++ 3 files changed, 201 insertions(+) create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fe7ccf159ab --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.2.4' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +sanity_check_paths = { + 'files': [ + 'include/webp/decode.h', + 'include/webp/demux.h', + 'include/webp/encode.h', + 'include/webp/mux.h', + 'include/webp/mux_types.h', + 'include/webp/types.h', + 'lib/%(name)s.a', + 'lib/libwebpdemux.a', + 'lib/libwebpmux.a', + 'lib/%(name)s.so', + 'lib/libwebpdemux.so', + 'lib/libwebpmux.so' + ], + 'dirs': ['lib/'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb new file mode 100644 index 00000000000..a5dbf2bbda5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -0,0 +1,114 @@ +name = 'OpenCV' +version = '4.6.0' +versionsuffix = '-contrib' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': SOURCELOWER_ZIP + }, + { + 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': '%(namelower)s_contrib-%(version)s.zip' + }, + { + 'source_urls': ['https://raw.githubusercontent.com/%(namelower)s/opencv_3rdparty/a56b6ac6f030c312b2dce17430eef13aed9af274/ippicv'], # noqa: E501 + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', + 'extract_cmd': 'cp %s %(builddir)s' + }, +] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), + ('FFmpeg', '5.0.1'), + ('freetype', '2.12.1'), + ('HarfBuzz', '4.2.1'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.4'), + ('OpenEXR', '3.1.5'), + ('JasPer', '2.0.33'), + ('Java', '17', '', True), + ('ant', '1.10.12', '-Java-%(javaver)s', True), + ('GLib', '2.72.1'), + ('GTK4', '4.7.0'), + ('HDF5', '1.13.1'), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = " ".join([ + "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DFREETYPE_FOUND=ON", + "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", + "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", + "-DHARFBUZZ_FOUND=ON", + "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", + "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", + "-DBUILD_opencv_python2=OFF", + "-DCPU_BASELINE=DETECT", +]) +enhance_sanity_check = True + +sanity_check_paths = { + 'files': [ + 'lib64/libopencv_aruco.so', + 'lib64/libopencv_bgsegm.so', + 'lib64/libopencv_bioinspired.so', + 'lib64/libopencv_ccalib.so', + 'lib64/libopencv_datasets.so', + 'lib64/libopencv_dnn_objdetect.so', + 'lib64/libopencv_dnn_superres.so', + 'lib64/libopencv_dpm.so', + 'lib64/libopencv_face.so', + 'lib64/libopencv_freetype.so', + 'lib64/libopencv_fuzzy.so', + 'lib64/libopencv_hdf.so', + 'lib64/libopencv_hfs.so', + 'lib64/libopencv_img_hash.so', + 'lib64/libopencv_line_descriptor.so', + 'lib64/libopencv_optflow.so', + 'lib64/libopencv_phase_unwrapping.so', + 'lib64/libopencv_plot.so', + 'lib64/libopencv_quality.so', + 'lib64/libopencv_reg.so', + 'lib64/libopencv_rgbd.so', + 'lib64/libopencv_saliency.so', + 'lib64/libopencv_shape.so', + 'lib64/libopencv_stereo.so', + 'lib64/libopencv_structured_light.so', + 'lib64/libopencv_superres.so', + 'lib64/libopencv_surface_matching.so', + 'lib64/libopencv_text.so', + 'lib64/libopencv_tracking.so', + 'lib64/libopencv_videostab.so', + 'lib64/libopencv_xfeatures2d.so', + 'lib64/libopencv_ximgproc.so', + 'lib64/libopencv_xobjdetect.so', + 'lib64/libopencv_xphoto.so' + ], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bc16062bde2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.5' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' + +sanity_check_paths = { + 'files': [ + 'lib/libIex.so', + 'lib/libIlmThread.so', + 'lib/libImath.so', + 'lib/libOpenEXR.so', + 'lib/libOpenEXRUtil.so', + 'bin/exrenvmap', + 'bin/exrheader', + 'bin/exrmakepreview', + 'bin/exrmaketiled', + 'bin/exrmultipart', + 'bin/exrmultiview', + 'bin/exrstdattr' + ], + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' From d9fbc970ce10066118d95b9bd6f80933b2da9d74 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 21 Sep 2022 12:59:37 +0200 Subject: [PATCH 4861/9987] injected checksums, removed OpenCV CPU_BASELINE configopt --- .../easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 1 + .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 6 +++++- .../easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 1 + 3 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb index fe7ccf159ab..6fd104e1260 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['7bf5a8a28cc69bcfa8cb214f2c3095703c6b73ac5fba4d5480c205331d9494df'] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index a5dbf2bbda5..ab2050076ac 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -28,6 +28,11 @@ sources = [ 'extract_cmd': 'cp %s %(builddir)s' }, ] +checksums = [ + '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip + '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] builddependencies = [ ('CMake', '3.23.1'), @@ -67,7 +72,6 @@ configopts = " ".join([ "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", "-DBUILD_opencv_python2=OFF", - "-DCPU_BASELINE=DETECT", ]) enhance_sanity_check = True diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index bc16062bde2..6d2db3b7ccc 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] builddependencies = [ ('binutils', '2.38'), From 16172d66bfc91d25cceade9a48cf45b9fb97c374 Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 21 Sep 2022 13:00:17 +0200 Subject: [PATCH 4862/9987] adding easyconfigs: ncdu-1.17-GCC-11.3.0.eb --- .../n/ncdu/ncdu-1.17-GCC-11.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdu/ncdu-1.17-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.17-GCC-11.3.0.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.17-GCC-11.3.0.eb new file mode 100644 index 00000000000..c3f1012fa69 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.17-GCC-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ncdu' +version = '1.17' + +homepage = 'https://dev.yorhel.nl/ncdu' +description = """Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a + remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular + desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like + environment with ncurses installed.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://dev.yorhel.nl/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['810745a8ed1ab3788c87d3aea4cc1a14edf6ee226f764bcc383e024ba56adbf1'] + +dependencies = [('ncurses', '6.3')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' From 184d5dd288100bc0f5ae347ed62ce6daf4414fd2 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 21 Sep 2022 13:45:09 +0200 Subject: [PATCH 4863/9987] Downgraded OpenCV deps FFMpeg, HDF5, Java --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index ab2050076ac..0d6357a5ca6 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -41,7 +41,7 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('zlib', '1.2.12'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.4.2'), ('freetype', '2.12.1'), ('HarfBuzz', '4.2.1'), ('libjpeg-turbo', '2.1.3'), @@ -50,11 +50,11 @@ dependencies = [ ('libwebp', '1.2.4'), ('OpenEXR', '3.1.5'), ('JasPer', '2.0.33'), - ('Java', '17', '', True), + ('Java', '11', '', True), ('ant', '1.10.12', '-Java-%(javaver)s', True), ('GLib', '2.72.1'), ('GTK4', '4.7.0'), - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ] # XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz From 0d386aa360df7b9cf7f85635fd6c0ca2c1576c06 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 21 Sep 2022 13:49:46 +0200 Subject: [PATCH 4864/9987] Re-pinned OpenCV FFmpeg to v5.0.1 --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 0d6357a5ca6..295bc7ccf2b 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -41,7 +41,7 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('zlib', '1.2.12'), - ('FFmpeg', '4.4.2'), + ('FFmpeg', '5.0.1'), ('freetype', '2.12.1'), ('HarfBuzz', '4.2.1'), ('libjpeg-turbo', '2.1.3'), From eb13f84ac50c1fbebdd31ab64f0d7a92e4742de8 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 21 Sep 2022 12:53:06 +0100 Subject: [PATCH 4865/9987] adding easyconfigs: Automake-1.16.5.eb --- .../easyconfigs/a/Automake/Automake-1.16.5.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb new file mode 100644 index 00000000000..5598e22e1d9 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.5' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] + +dependencies = [ + ('Autoconf', '2.71'), +] + +osdependencies = [ + 'perl-Thread-Queue', +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ['bin/aclocal', 'bin/automake'], + 'dirs': [] +} + +sanity_check_commands = [ + "aclocal --help", + "automake --help", +] + +moduleclass = 'devel' From 10c73ef83017c0123bc87c09c2afe8ad80cda609 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 21 Sep 2022 12:56:25 +0100 Subject: [PATCH 4866/9987] Jansson version corrected --- easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb index 4b516f19c4b..4d87ace9817 100644 --- a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb @@ -39,7 +39,7 @@ dependencies = [ ('nghttp3', '0.6.0'), ('Python', '3.9.6'), ('libxml2', '2.9.10'), - ('Jansson', '2.14'), + ('Jansson', '2.13.1'), ('jemalloc', '5.2.1'), ('ngtcp2', '0.7.0'), ('libevent', '2.1.12'), From 8719c35ac7163f53da9562abcd79b2462f5366ba Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 21 Sep 2022 12:59:08 +0100 Subject: [PATCH 4867/9987] adding easyconfigs: libtool-2.4.7.eb --- .../easyconfigs/l/libtool/libtool-2.4.7.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.7.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.7.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.7.eb new file mode 100644 index 00000000000..493b1c143ee --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.7.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.7' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' From 50f2d3e230b994a3210247845eebb521afcc6021 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 21 Sep 2022 15:11:41 +0200 Subject: [PATCH 4868/9987] Add NCO --- .../l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb | 37 ++++++++++++++++ .../easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb | 44 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..237260a43f7 --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.20.11' + +homepage = 'https://www.opendap.org/software/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 and + DAP4.0. This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415'] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('libxml2', '2.9.13'), + ('libtirpc', '1.3.2'), + ('PCRE', '8.45'), + ('util-linux', '2.38'), +] + +configopts = 'TIRPC_LIBS="-ltirpc"' + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb new file mode 100644 index 00000000000..81047083a23 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.1.0' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6f0ba812e0684881a85ebf3385117761cffbba36ba842889cc96f111157f89c2'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.4.8'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.11'), + ('GSL', '2.7'), + ('netCDF', '4.9.0'), + ('ESMF', '8.3.0'), # ncremap needs ESMF_RegridWeightGen +] + +configopts = "--enable-nco_cplusplus" + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] + +moduleclass = 'tools' From eb337668e75daacdd7eccb209c76e5a148b338b3 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 21 Sep 2022 15:16:54 +0200 Subject: [PATCH 4869/9987] use SHLIB_EXT for shared lib extension in sanity_check_paths --- .../easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb index a81d983d6e3..de1fa80521a 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -37,7 +37,7 @@ configopts = [ ] sanity_check_paths = { - 'files': ['lib/libmagma.so', 'lib/libmagma.a'], + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], 'dirs': ['include'], } From d2be15c7ae2da59b3ef2c0d30c4d12f6501115a9 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 21 Sep 2022 16:34:20 +0100 Subject: [PATCH 4870/9987] adding easyconfigs: DeepLabCut-2.2.0.6-foss-2021a.eb --- .../DeepLabCut-2.2.0.6-foss-2021a.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb new file mode 100644 index 00000000000..e1d4d8dd05a --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -0,0 +1,65 @@ +# Loosely based on PR #7680 +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'DeepLabCut' +version = '2.2.0.6' +local_version = '%(versionsuffix)s-contrib' + +homepage = 'http://www.mousemotorlab.org/deeplabcut' +description = "Markerless tracking of user-defined features with deep learning" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.9.5'), + ('h5py', '3.2.1'), + ('IPython', '7.25.0'), + ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), + ('TensorFlow', '2.6.0'), + ('PyYAML', '5.4.1'), + ('PyTables', '3.6.1'), + ('wxPython', '4.1.1'), + ('OpenCV', '4.5.3', '-contrib'), + ('numba', '0.53.1'), + ('libyaml', '0.2.5'), + ('imgaug', '0.4.0'), + ('tqdm', '4.61.2'), + ('ruamel.yaml', '0.17.21'), + ('PyYAML', '5.4.1'), + ('statsmodels', '0.12.2'), + ('PyTorch', '1.10.0'), +] + +use_pip = True + +exts_list = [ + ('filterpy', '1.4.5', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], + }), + ('pandas', '1.3.3', { + 'checksums': ['272c8cb14aa9793eada6b1ebe81994616e647b5892a370c7135efb2924b701df'], + }), + ('tensorpack', '0.11', { + 'checksums': ['022b610e416e62e3575424cd08e60af27808a5fb6914294615391caf582cbd4f'], + }), + ('tf_slim', '1.1.0', { + 'source_urls': ['https://github.com/google-research/tf-slim/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['964cde4b7728a408dcd5c841ab6b93d95137ab4b60db28b10400f86286bfeb8b'], + }), + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + 'sources': ['msgpack-numpy-0.4.8.tar.gz'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], + }), +] + +moduleclass = 'lib' From f8f562e66cc7066424c34d7daaf1873a27661100 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 21 Sep 2022 16:38:44 +0100 Subject: [PATCH 4871/9987] adding easyconfigs: ruamel.yaml-0.17.21-GCCcore-10.3.0.eb --- .../ruamel.yaml-0.17.21-GCCcore-10.3.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..e7b90307fb9 --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-10.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.17.21' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.clib', '0.2.6', { + 'checksums': ['4ff604ce439abb20794f05613c374759ce10e3595d1867764dd1ae675b85acbd'], + 'modulename': False, + }), + (name, version, { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('configobj', '5.0.6', { + 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], + }), + ('ruamel.yaml.base', '0.3.0', { + 'checksums': ['bee661f95a842c3e90f83560f3a87ad3f9548ed4874af98f36b32aaf8a27462a'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.5.10', { + 'checksums': ['043c149c5517cfd0c7d02bd934224e1c9b0053a05e292a14f1b1a7f15bf0a943'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' From 9be8026ac8f947ee7754d5f365870a64590861cc Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 21 Sep 2022 16:41:39 +0100 Subject: [PATCH 4872/9987] adding easyconfigs: imgaug-0.4.0-foss-2021a.eb --- .../i/imgaug/imgaug-0.4.0-foss-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a.eb new file mode 100644 index 00000000000..b7fac2d92c5 --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021a.eb @@ -0,0 +1,35 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. + +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.0' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Pillow', '8.2.0'), + ('matplotlib', '3.4.2'), + ('scikit-image', '0.18.3'), + ('OpenCV', '4.5.3', '-contrib'), + ('Shapely', '1.8a1'), + ('imageio', '2.10.5'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['imgaug-0.4.0_openvc_requirement.patch'] +checksums = [ + '46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7', # imgaug-0.4.0.tar.gz + '2ff0b66ba38fdcf5f267a3d0ad1dc2710fee3c2f8cd3d086c56ea538a2a9ffc8', # imgaug-0.4.0_openvc_requirement.patch +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' From 2f0c9a08a15784d70cb130b7443805338b2eca1e Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 21 Sep 2022 18:01:35 +0200 Subject: [PATCH 4873/9987] Added exception for FFmpeg versions for Paraview and OpenFOAM --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0fb05afe876..da15318ca58 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -493,6 +493,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], + # ParaView 5.10.x requires FFmpeg 4.x + 'FFmpeg': [(r'4\.4\.', [r'ParaView-5\.10\.', 'OpenFOAM-v2206'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], From ec2c696406bfb08928e199c00ba914e604f20406 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 21 Sep 2022 18:37:05 +0100 Subject: [PATCH 4874/9987] Missing gettext added --- .../easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb index db6674f606b..96a79ee0df8 100644 --- a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.2.0.eb @@ -23,6 +23,10 @@ builddependencies = [ ('M4', '1.4.19'), ] +dependencies = [ + ('gettext', '0.21'), +] + preconfigopts = "autoreconf -vfi && " sanity_check_commands = [ From a248ec88f183f7c09928cb3286da28ab9e646769 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 22 Sep 2022 09:46:31 +0100 Subject: [PATCH 4875/9987] adding easyconfigs: expecttest-0.1.3-GCCcore-11.2.0.eb --- .../expecttest-0.1.3-GCCcore-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8eab7bea399 --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.1.3' + +homepage = 'https://github.com/ezyang/expecttest' +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['83057695811d94128aed13ed094a070db90e0a92ea40071f8ee073cbab57149a'] + +builddependencies = [ + ('binutils', '2.37'), +] +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From b53ad6aea6fd2aac2e4de798ceee7287980b34eb Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 22 Sep 2022 11:12:41 +0200 Subject: [PATCH 4876/9987] adding easyconfigs: netcdf4-python-1.6.1-foss-2022a.eb --- .../netcdf4-python-1.6.1-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb new file mode 100644 index 00000000000..e4909b8b62d --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('netCDF', '4.9.0'), + ('cURL', '7.83.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' From 2e2208b9b3b48639fe927fcb1bd44711cbe05788 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 22 Sep 2022 12:31:20 +0200 Subject: [PATCH 4877/9987] Add TurboVNC --- .../TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 71 +++++++++++++++++++ .../TurboVNC-3.0.1_fix-libX11-libs.patch | 21 ++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1_fix-libX11-libs.patch diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..23252bd15dd --- /dev/null +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -0,0 +1,71 @@ +easyblock = 'CMakeMake' + +name = 'TurboVNC' +version = '3.0.1' + +homepage = 'https://www.turbovnc.org' +description = """TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide + peak performance for 3D and video workloads.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/TurboVNC/turbovnc/archive'] +sources = ['%(version)s.tar.gz'] +patches = ['TurboVNC-%(version)s_fix-libX11-libs.patch'] +checksums = [ + 'f0bd45e4e6f8cb8a52b5ccdef70fbc28ba8776591554c166db113eedc914dd86', # 3.0.1.tar.gz + '11acc18ae10355c7c6816fad0a68ed55fbcb7a04efd30740c619a1d82ecbd4c2', # TurboVNC-3.0.1_fix-libX11-libs.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Java', '11', '', True), + ('X11', '20220504'), + ('pixman', '0.40.0'), + ('libjpeg-turbo', '2.1.3'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('libglvnd', '1.4.0'), + # OS dependency should be preferred if the OS version is more recent then this version, + # it's nice to have an up to date OpenSSL for security reasons + # ('OpenSSL', '1.1'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), + ('pam-devel', 'libpam0g-dev'), +] + +configopts = "-DTVNC_BUILDJAVA=0 -DTVNC_SYSTEMX11=1 " +configopts += "-DX11_X11_LIB=$EBROOTX11/lib/libX11.%s " % SHLIB_EXT +configopts += "-DX11_Xau_LIB=$EBROOTX11/lib/libXau.%s " % SHLIB_EXT +configopts += "-DX11_SM_LIB=$EBROOTX11/lib/libSM.%s " % SHLIB_EXT +configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT +configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libXext.%s " % SHLIB_EXT +configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT +configopts += "-DX11_Pixman_LIB=$EBROOTPIXMAN/lib/libpixman-1.%s.0 " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_egl_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_opengl_LIBRARY=$EBROOTLIBGLVND/lib/libOpenGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glx_LIBRARY=$EBROOTLIBGLVND/lib/libGLX.%s " % SHLIB_EXT + +# if installdir starts with /opt, i.e. /opt/xxx, CMake will set SYSCONFDIR to /etc/opt/xxx instead of /opt/xxx/etc +# https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html +# the solution is to define CMAKE_INSTALL_SYSCONFDIR explicitly +configopts += "-DCMAKE_INSTALL_SYSCONFDIR=%(installdir)s/etc " + +# remove etc/turbovncserver-security.conf, to avoid errors like: +# (EE) Fatal server error: +# (EE) ERROR: .../TurboVNC/2.2.3-GCCcore-8.2.0/etc/turbovncserver-security.conf must be owned by you or by root +postinstallcmds = ["rm -rf %(installdir)s/etc/turbovncserver-security.conf"] + +sanity_check_paths = { + 'files': ['bin/vncserver', 'bin/vncpasswd', 'bin/Xvnc'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1_fix-libX11-libs.patch b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1_fix-libX11-libs.patch new file mode 100644 index 00000000000..877631a18ff --- /dev/null +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1_fix-libX11-libs.patch @@ -0,0 +1,21 @@ +# fix location of libXfont2.so and libfontenc.so +# don't derive location of libpixman-1.so from path to libX11.so +# author: Kenneth Hoste (HPC-UGent) +# +# updated to v3.0.1 by maxim-masterov (SURF) + +diff -Nru turbovnc-3.0.1.orig/unix/Xvnc/CMakeLists.txt turbovnc-3.0.1/unix/Xvnc/CMakeLists.txt +--- turbovnc-3.0.1.orig/unix/Xvnc/CMakeLists.txt 2022-09-22 11:31:39.142872000 +0200 ++++ turbovnc-3.0.1/unix/Xvnc/CMakeLists.txt 2022-09-22 11:33:07.984771000 +0200 +@@ -96,9 +96,8 @@ + if(TVNC_SYSTEMX11) + include_directories(${X11_X11_INCLUDE_PATH} ${X11_Xau_INCLUDE_PATH} + ${X11_Xdmcp_INCLUDE_PATH} ${X11_Xkbfile_INCLUDE_PATH}) +- string(REGEX REPLACE "X11" "Xfont2" X11_Xfont2_LIB ${X11_X11_LIB}) +- string(REGEX REPLACE "X11" "fontenc" X11_Fontenc_LIB ${X11_X11_LIB}) +- string(REGEX REPLACE "X11" "pixman-1" X11_Pixman_LIB ${X11_X11_LIB}) ++ string(REGEX REPLACE "libX11" "libXfont2" X11_Xfont2_LIB ${X11_X11_LIB}) ++ string(REGEX REPLACE "libX11" "libfontenc" X11_Fontenc_LIB ${X11_X11_LIB}) + else() + include_directories(${CMAKE_CURRENT_BINARY_DIR}/X_include) + set(X11_Xau_LIB Xau) From 4a40622848ecd414a86a51fd59842a3d175b8896 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 22 Sep 2022 12:57:12 +0200 Subject: [PATCH 4878/9987] Remove OpenSSL as OS dependency --- .../easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb index 23252bd15dd..9c572a880b6 100644 --- a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -30,13 +30,10 @@ dependencies = [ ('Mesa', '22.0.3'), ('libGLU', '9.0.2'), ('libglvnd', '1.4.0'), - # OS dependency should be preferred if the OS version is more recent then this version, - # it's nice to have an up to date OpenSSL for security reasons - # ('OpenSSL', '1.1'), + ('OpenSSL', '1.1', '', True), ] osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), ('pam-devel', 'libpam0g-dev'), ] From dab8df24e7744ef755ba274f0a4ffaa8d6612272 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 22 Sep 2022 12:59:01 +0200 Subject: [PATCH 4879/9987] Add QIIME2 and deps --- .../m/Miniconda3/Miniconda3-4.12.0.eb | 17 ++++++++++ .../easyconfigs/q/QIIME2/QIIME2-2022.8.eb | 31 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.12.0.eb create mode 100644 easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.12.0.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.12.0.eb new file mode 100644 index 00000000000..5521f6fcca4 --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.12.0.eb @@ -0,0 +1,17 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda3' +version = '4.12.0' + +homepage = 'https://docs.conda.io/en/latest/miniconda.html' +description = """Miniconda is a free minimal installer for conda. It is a small, + bootstrap version of Anaconda that includes only conda, Python, the packages they + depend on, and a small number of other useful packages.""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/miniconda/'] +sources = ['%(name)s-py38_%(version)s-Linux-x86_64.sh'] +checksums = ['3190da6626f86eee8abf1b2fd7a5af492994eb2667357ee4243975cdbb175d7a'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb new file mode 100644 index 00000000000..30c12abc3c2 --- /dev/null +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb @@ -0,0 +1,31 @@ +# EasyBuild recipy for QIIME2 +# Author: Caspar van Leeuwen +# SURFsara - The Netherlands + +easyblock = 'Conda' + +name = 'QIIME2' +version = '2022.8' + +homepage = 'http://qiime2.org/' +description = """QIIME is an open-source bioinformatics pipeline for performing microbiome analysis + from raw DNA sequencing data.""" + +source_urls = ['https://data.qiime2.org/distro/core/'] +sources = ['qiime2-%(version)s-py38-linux-conda.yml'] +checksums = ['454bb219f928c7f4ec0097888db27ab439ba2ef7e4294f38b7033327cb3dafb8'] + +toolchain = SYSTEM + +builddependencies = [('Miniconda3', '4.12.0')] + +environment_file = 'qiime2-%(version)s-py38-linux-conda.yml' + +sanity_check_commands = ['qiime info'] + +sanity_check_paths = { + 'files': ["bin/qiime"], + 'dirs': ["lib", "include"], +} + +moduleclass = 'bio' From c3f9130e7f2cc24e66b88b8b0bafb4710b43df6a Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 22 Sep 2022 13:14:25 +0200 Subject: [PATCH 4880/9987] adding easyconfigs: likwid-5.2.2-GCC-11.3.0.eb --- .../l/likwid/likwid-5.2.2-GCC-11.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.2.2-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.2.2-GCC-11.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.2.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..2febcdf589c --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.2.2-GCC-11.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.2.2' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7dda6af722e04a6c40536fc9f89766ce10f595a8569b29e80563767a6a8f940e'] + +builddependencies = [ + ('Perl', '5.34.1'), +] + +dependencies = [ + ('hwloc', '2.7.1'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCC toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' From 78fcd2dda89e6cac6e6916a94bb4503ee06ea373 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 22 Sep 2022 18:53:02 +0200 Subject: [PATCH 4881/9987] Add wxWidgets and deps --- .../s/SDL2/SDL2-2.0.22-GCCcore-11.3.0.eb | 26 +++++++ .../w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb | 78 +++++++++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.22-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.22-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.22-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..218bf61aeec --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.22-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.22' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['fe7cbf3127882e3fc7259a75a0cb585620272c51745d3852ab9dd87960697f2e'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('X11', '20220504'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..f4c078710de --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb @@ -0,0 +1,78 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.2.1' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +# wxWidgets now contain three submodules: catch, nanosvg and pcre +sources = [{ + 'git_config': { + 'url': 'https://github.com/wxWidgets/', + 'repo_name': 'wxWidgets', + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('gettext', '0.21'), + ('pkgconf', '1.8.0'), + ('Python', '3.10.4'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.3'), + ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.3.0'), + ('expat', '2.4.8'), + ('GTK3', '3.24.33'), + ('X11', '20220504'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('SDL2', '2.0.22'), + ('cairo', '1.17.4'), + ('GST-plugins-base', '1.20.2'), + ('GLib', '2.72.1'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From 31be407cee5520158566119340b2006fc5c10dea Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 22 Sep 2022 21:49:15 +0000 Subject: [PATCH 4882/9987] adding easyconfigs: Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb --- .../Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0973b977079 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '9.2.0' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1c3b4bce334fbb234be506cd3146a93714f9de43032aaf807ff47a20d6b42c95'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.12.1') +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From e519f27f87a3c856f790193512bef68cca5fe5b0 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 22 Sep 2022 21:53:07 +0000 Subject: [PATCH 4883/9987] adding easyconfigs: torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb --- ...rchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..c2820fcd722 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,23 @@ +name = 'torchvision' +version = '0.13.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c32fab734e62c7744dadeb82f7510ff58cc3bca1189d17b16aa99b08afc42249'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('Pillow-SIMD', '9.2.0'), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), +] + +moduleclass = 'vis' From a9dd768833abb2fd849a0401aea1a43b894cc793 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 22 Sep 2022 22:19:20 +0000 Subject: [PATCH 4884/9987] adding easyconfigs: tensorboard-2.10.0-foss-2022a.eb --- .../tensorboard-2.10.0-foss-2022a.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb new file mode 100644 index 00000000000..329c77c8106 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'tensorboard' +version = '2.10.0' + +homepage = 'https://github.com/tensorflow/tensorboard' +description = """TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs +and graphs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('protobuf-python', '3.19.4'), +] + +exts_list = [ + ('absl-py', '1.2.0', { + 'modulename': 'absl', + 'checksums': ['f568809938c49abbda89826223c992b630afd23c638160ad7840cfe347710d97'], + }), + ('cachetools', '5.2.0', { + 'checksums': ['6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('google-auth', '2.11.1', { + 'modulename': 'google.auth', + 'checksums': ['516e6623038b81430dd062a1a25ecd24f173d7c15cdf4e48a9e78bc87e97aeec'], + }), + ('oauthlib', '3.2.1', { + 'checksums': ['1565237372795bf6ee3e5aba5e2a85bd5a65d0e2aa5c628b9a97b7d7a0da3721'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('grpcio', '1.49.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['d4725fc9ec8e8822906ae26bb26f5546891aa7fbc3443de970cc556d43a5c99f'], + }), + ('importlib_metadata', '4.12.0', { + 'checksums': ['637245b8bab2b6502fcbc752cc4b7a6f6243bb02b31c5c26156ad103d3d45670'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('Werkzeug', '2.2.2', { + 'checksums': ['7ea2d48322cc7c0f8b3a215ed73eabd7b5d75d0b50e31ab006286ccff9e00b8f'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['76c91a5e8959cd2208cc32cb17a0cb002badabb66a06ac2af02a7810f49a59e3'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From f92c831a18daa4dd3ec59ba6ee6d040b65134870 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 22 Sep 2022 22:27:53 +0000 Subject: [PATCH 4885/9987] adding easyconfigs: PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb --- ...-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..ff7163f6c19 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.7.7' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('tensorboard', '2.10.0'), + ('typing-extensions', '4.3.0'), +] + + +exts_list = [ + ('fsspec', '2022.8.2', { + 'checksums': ['7f12b90964a98a7e921d27fb36be536ea036b73bf3b724ac0b0bd7b8e39c7c18'], + }), + + ('pyDeprecate', '0.3.2', { + 'modulename': 'deprecate', + 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], + }), + ('torchmetrics', '0.9.3', { + 'checksums': ['4ebfd2466021db26397636966ee1a195d3b340ba5d71bb258e764340dfc2476f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['27c2dd01a18db2415168e3fa3775ccb5a1fa1e2961a50439ad9365507fe9d4ae'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 21cfa6c6e5d8250afe071f4e79c9896736a9f1ec Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 23 Sep 2022 09:15:03 +0200 Subject: [PATCH 4886/9987] adding easyconfigs: GPAW-22.8.0-foss-2021b.eb, GPAW-22.8.0-intel-2021b.eb, ASE-3.22.1-foss-2021b.eb, ASE-3.22.1-intel-2021b.eb, spglib-python-1.16.3-foss-2021b.eb, spglib-python-1.16.3-intel-2021b.eb and patches: GPAW-22.8.0-Remove-MPI-compiler-hack.patch --- .../a/ASE/ASE-3.22.1-foss-2021b.eb | 47 +++++++++++++++++ .../a/ASE/ASE-3.22.1-intel-2021b.eb | 47 +++++++++++++++++ ...GPAW-22.8.0-Remove-MPI-compiler-hack.patch | 35 +++++++++++++ .../g/GPAW/GPAW-22.8.0-foss-2021b.eb | 50 +++++++++++++++++++ .../g/GPAW/GPAW-22.8.0-intel-2021b.eb | 49 ++++++++++++++++++ .../spglib-python-1.16.3-foss-2021b.eb | 27 ++++++++++ .../spglib-python-1.16.3-intel-2021b.eb | 27 ++++++++++ 7 files changed, 282 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2021b.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Remove-MPI-compiler-hack.patch create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-intel-2021b.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2021b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2021b.eb new file mode 100644 index 00000000000..eb2f5708e31 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Flask', '2.0.2'), + ('matplotlib', '3.4.3'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.3'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2021b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2021b.eb new file mode 100644 index 00000000000..d490b91739e --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Flask', '2.0.2'), + ('matplotlib', '3.4.3'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.3'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Remove-MPI-compiler-hack.patch b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Remove-MPI-compiler-hack.patch new file mode 100644 index 00000000000..da9d3311269 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Remove-MPI-compiler-hack.patch @@ -0,0 +1,35 @@ +Author: Jakob Schiøtz +Date: Thu Jan 27 11:55:07 CET 2022 + +This patch removes the part of setup.py responsible for replacing the +normal compiler with an MPI aware compiler, as that is already done +correctly by the EasyBuild system. + +--- setup.old 2022-01-26 14:37:48.522572258 +0100 ++++ setup.py 2022-01-26 14:39:55.973416534 +0100 +@@ -104,25 +104,6 @@ + if platform_id: + os.environ['_PYTHON_HOST_PLATFORM'] = get_platform() + '-' + platform_id + +-if compiler is not None: +- # A hack to change the used compiler and linker: +- try: +- # distutils is deprecated and will be removed in 3.12 +- from distutils.sysconfig import get_config_vars +- except ImportError: +- from sysconfig import get_config_vars +- +- # If CC is set then the following hack will not work +- assert not os.environ.get('CC'), 'Please unset CC' +- +- vars = get_config_vars() +- for key in ['CC', 'LDSHARED']: +- if key in vars: +- value = vars[key].split() +- # first argument is the compiler/linker. Replace with mpicompiler: +- value[0] = compiler +- vars[key] = ' '.join(value) +- + for flag, name in [(noblas, 'GPAW_WITHOUT_BLAS'), + (nolibxc, 'GPAW_WITHOUT_LIBXC'), + (fftw, 'GPAW_WITH_FFTW'), diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb new file mode 100644 index 00000000000..e3d8e921b48 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb @@ -0,0 +1,50 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '22.8.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), + ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), +] +checksums = [ + '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', + '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('ASE', '3.22.1'), + ('libxc', '5.1.6'), + ('PyYAML', '5.4.1'), + ('libvdwxc', '0.4.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb new file mode 100644 index 00000000000..1ca56803196 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb @@ -0,0 +1,49 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '22.8.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), + ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), +] +checksums = [ + '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', + '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('ASE', '3.22.1'), + ('libxc', '5.1.6'), + ('PyYAML', '5.4.1'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-foss-2021b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-foss-2021b.eb new file mode 100644 index 00000000000..d13be3c325e --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.3' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['ff1420967d64c2d4f0d747886116a6836d9b473454cdd73d560dbfe973a8a038'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-intel-2021b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-intel-2021b.eb new file mode 100644 index 00000000000..eaa79870a2b --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.3-intel-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.3' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'intel', 'version': '2021b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['ff1420967d64c2d4f0d747886116a6836d9b473454cdd73d560dbfe973a8a038'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' From bd9e4676ee714e90d78d33be8edd48b97109daee Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 23 Sep 2022 13:26:13 +0200 Subject: [PATCH 4887/9987] Added exception for FFmpeg versions for Paraview and OpenFOAM --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0fb05afe876..da15318ca58 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -493,6 +493,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], + # ParaView 5.10.x requires FFmpeg 4.x + 'FFmpeg': [(r'4\.4\.', [r'ParaView-5\.10\.', 'OpenFOAM-v2206'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], From ad6224a33d7921928d9faa3047427c50c5d495c2 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 23 Sep 2022 13:26:35 +0200 Subject: [PATCH 4888/9987] re-added some nice templates from OpenCV/2021b easyconfig --- .../OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 50 +++++-------------- 1 file changed, 13 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 295bc7ccf2b..dc22d0ca82d 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -2,6 +2,9 @@ name = 'OpenCV' version = '4.6.0' versionsuffix = '-contrib' +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + homepage = 'https://opencv.org/' description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide @@ -23,7 +26,7 @@ sources = [ 'filename': '%(namelower)s_contrib-%(version)s.zip' }, { - 'source_urls': ['https://raw.githubusercontent.com/%(namelower)s/opencv_3rdparty/a56b6ac6f030c312b2dce17430eef13aed9af274/ippicv'], # noqa: E501 + 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', 'extract_cmd': 'cp %s %(builddir)s' }, @@ -73,45 +76,18 @@ configopts = " ".join([ "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", "-DBUILD_opencv_python2=OFF", ]) + enhance_sanity_check = True +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + sanity_check_paths = { - 'files': [ - 'lib64/libopencv_aruco.so', - 'lib64/libopencv_bgsegm.so', - 'lib64/libopencv_bioinspired.so', - 'lib64/libopencv_ccalib.so', - 'lib64/libopencv_datasets.so', - 'lib64/libopencv_dnn_objdetect.so', - 'lib64/libopencv_dnn_superres.so', - 'lib64/libopencv_dpm.so', - 'lib64/libopencv_face.so', - 'lib64/libopencv_freetype.so', - 'lib64/libopencv_fuzzy.so', - 'lib64/libopencv_hdf.so', - 'lib64/libopencv_hfs.so', - 'lib64/libopencv_img_hash.so', - 'lib64/libopencv_line_descriptor.so', - 'lib64/libopencv_optflow.so', - 'lib64/libopencv_phase_unwrapping.so', - 'lib64/libopencv_plot.so', - 'lib64/libopencv_quality.so', - 'lib64/libopencv_reg.so', - 'lib64/libopencv_rgbd.so', - 'lib64/libopencv_saliency.so', - 'lib64/libopencv_shape.so', - 'lib64/libopencv_stereo.so', - 'lib64/libopencv_structured_light.so', - 'lib64/libopencv_superres.so', - 'lib64/libopencv_surface_matching.so', - 'lib64/libopencv_text.so', - 'lib64/libopencv_tracking.so', - 'lib64/libopencv_videostab.so', - 'lib64/libopencv_xfeatures2d.so', - 'lib64/libopencv_ximgproc.so', - 'lib64/libopencv_xobjdetect.so', - 'lib64/libopencv_xphoto.so' - ], + 'files': ['lib64/libopencv_%s.%s' % (l, SHLIB_EXT) for l in local_contrib_libs], 'dirs': [], } From a873082eeb9df75e358a3009eb6e9ea6bdc55946 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 23 Sep 2022 13:44:22 +0200 Subject: [PATCH 4889/9987] re-added templates to OpenEXR, libwebp ec's --- .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 17 ++++------------- .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 19 +++++++------------ 2 files changed, 11 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb index 6fd104e1260..51de3daf755 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -29,20 +29,11 @@ configopts = '--enable-libwebpmux' sanity_check_paths = { 'files': [ - 'include/webp/decode.h', - 'include/webp/demux.h', - 'include/webp/encode.h', - 'include/webp/mux.h', - 'include/webp/mux_types.h', - 'include/webp/types.h', - 'lib/%(name)s.a', - 'lib/libwebpdemux.a', - 'lib/libwebpmux.a', - 'lib/%(name)s.so', - 'lib/libwebpdemux.so', - 'lib/libwebpmux.so' + *['include/webp/%s' % f for f in ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h']], + *['lib/lib%s.a' % l for l in ['webp', 'webpdemux', 'webpmux']], + *['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['webp', 'webpdemux', 'webpmux']], ], - 'dirs': ['lib/'], + 'dirs': ['lib/'] } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index 6d2db3b7ccc..77a049dd6b3 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -20,20 +20,15 @@ builddependencies = [ configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + sanity_check_paths = { 'files': [ - 'lib/libIex.so', - 'lib/libIlmThread.so', - 'lib/libImath.so', - 'lib/libOpenEXR.so', - 'lib/libOpenEXRUtil.so', - 'bin/exrenvmap', - 'bin/exrheader', - 'bin/exrmakepreview', - 'bin/exrmaketiled', - 'bin/exrmultipart', - 'bin/exrmultiview', - 'bin/exrstdattr' + *['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs], + *['bin/exr%s' % bin for bin in local_bins] ], 'dirs': ['include/%(name)s', 'share'], } From 9920070ea2cf9a2f820746237965d0a85e0af165 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 14:10:44 +0200 Subject: [PATCH 4890/9987] add python-irodsclient --- .../python-irodsclient-1.1.4.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb new file mode 100644 index 00000000000..9876e55d90f --- /dev/null +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonBundle' +name = 'python-irodsclient' +version = '1.1.4' +homepage = 'https://github.com/irods/python-irodsclient' +description = "A python API for iRODS" +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +# order is important! +exts_list = [ + ('defusedxml', '0.7.1', {}), + ('prettytable', '3.3.0', {}), + ('python-irodsclient', '1.1.4', {'modulename':'irods'}) +] + +sanity_pip_check = True +moduleclass = 'tools' + From 06cdc6f61197ce2e58ee7e05984ed70d8124c2f4 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 23 Sep 2022 14:17:36 +0200 Subject: [PATCH 4891/9987] adding easyconfigs: matplotlib-3.5.2-intel-2022a.eb --- .../matplotlib-3.5.2-intel-2022a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb new file mode 100644 index 00000000000..2bf90cc74a0 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.5.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('cppy', '1.2.1') +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '9.1.1'), + ('Qhull', '2020.2') +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >setup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.34.0', { + 'modulename': 'fontTools', + 'source_tmpl': SOURCE_ZIP, + 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], + }), + ('Cycler', '0.11.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], + }), + ('kiwisolver', '1.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ab8a15c2750ae8d53e31f77a94f846d0a00772240f1c12817411fa2344351f86'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['48cf850ce14fa18067f2d9e0d646763681948487a8080ec0af2686468b4607a2'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From dafc83c8bc187f651b9c094aed5920cf79bcf34c Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 23 Sep 2022 13:40:15 +0000 Subject: [PATCH 4892/9987] adding easyconfigs: umap-learn-0.5.3-foss-2021a.eb --- .../umap-learn/umap-learn-0.5.3-foss-2021a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb new file mode 100644 index 00000000000..449a1fd265a --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) +# This is a contribution from HPCNow! (http://hpcnow.com) +# Update: Erica Bianco +# License:: GPL-v3.0 +easyblock = "PythonBundle" + +name = 'umap-learn' +version = '0.5.3' + +homepage = 'https://umap-learn.readthedocs.io/en/latest/' +description = """Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique + that can be used for visualisation similarly to t-SNE, but also for general non-linear + dimension reduction.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-learn', '0.24.2'), + ('numba', '0.53.1'), + ('LLVM', '11.1.0'), + ('tqdm', '4.61.1'), +] + +use_pip = True +download_dep_fail = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('pynndescent', '0.5.7', { + 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], + }), + (name, version, { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 80dd609251242b16344fc3a70a2fafb06f161812 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 16:54:25 +0200 Subject: [PATCH 4893/9987] Add python and gcccore version to filename This will be easier to tell versions apart (colleagues asked me to soon make a version with gcccore 10.3.0). I tried to follow the example of other files in the repo. --- ...eb => python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/python-irodsclient/{python-irodsclient-1.1.4.eb => python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb} (100%) diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb similarity index 100% rename from easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4.eb rename to easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb From c9bd54fff8d08483d912fd32ae6f5f9fc4cf88c3 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 16:58:35 +0200 Subject: [PATCH 4894/9987] add checksums --- ...lient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb | 51 +++++++++++-------- 1 file changed, 29 insertions(+), 22 deletions(-) mode change 100644 => 100755 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb old mode 100644 new mode 100755 index 9876e55d90f..f8e17945770 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb @@ -1,22 +1,29 @@ -easyblock = 'PythonBundle' -name = 'python-irodsclient' -version = '1.1.4' -homepage = 'https://github.com/irods/python-irodsclient' -description = "A python API for iRODS" -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -dependencies = [ - ('Python', '3.9.6'), -] - -use_pip = True -# order is important! -exts_list = [ - ('defusedxml', '0.7.1', {}), - ('prettytable', '3.3.0', {}), - ('python-irodsclient', '1.1.4', {'modulename':'irods'}) -] - -sanity_pip_check = True -moduleclass = 'tools' - +easyblock = 'PythonBundle' +name = 'python-irodsclient' +version = '1.1.4' +homepage = 'https://github.com/irods/python-irodsclient' +description = "A python API for iRODS" +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +# order is important! +exts_list = [ + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('prettytable', '3.3.0', { + 'checksums': ['118eb54fd2794049b810893653b20952349df6d3bc1764e7facd8a18064fa9b0'], + }), + (name, version, { + 'modulename': 'irods', + 'checksums': ['f427699739911042dc35a7fbd92f7ba87db9fad3977423c2fa2ab61a0ffebe43'], + }), +] + +sanity_pip_check = True +moduleclass = 'tools' + From dab93d8e3991b7251f6f01d746fa4dc0f3f50389 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 17:01:46 +0200 Subject: [PATCH 4895/9987] Improve style Also switched module type to lib (more appropriate for python library) --- ...thon-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb index f8e17945770..a039002b7e6 100755 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb @@ -1,8 +1,11 @@ easyblock = 'PythonBundle' + name = 'python-irodsclient' version = '1.1.4' + homepage = 'https://github.com/irods/python-irodsclient' description = "A python API for iRODS" + toolchain = {'name': 'GCCcore', 'version': '11.2.0'} dependencies = [ @@ -10,7 +13,8 @@ dependencies = [ ] use_pip = True -# order is important! +sanity_pip_check = True + exts_list = [ ('defusedxml', '0.7.1', { 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], @@ -24,6 +28,5 @@ exts_list = [ }), ] -sanity_pip_check = True -moduleclass = 'tools' +moduleclass = 'lib' From a4620aee58528ac877274c58586475445027a871 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 17:08:51 +0200 Subject: [PATCH 4896/9987] Remove blank line at end of file Apparently style requirement --- .../python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb index a039002b7e6..3286483e5bc 100755 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb @@ -28,5 +28,4 @@ exts_list = [ }), ] -moduleclass = 'lib' - +moduleclass = 'lib' \ No newline at end of file From 930d392f1bea57ad451eb6e498671da53961feee Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Fri, 23 Sep 2022 17:15:27 +0200 Subject: [PATCH 4897/9987] add python version suffix --- .../python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb index 3286483e5bc..5a022f20b13 100755 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb @@ -2,6 +2,7 @@ easyblock = 'PythonBundle' name = 'python-irodsclient' version = '1.1.4' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/irods/python-irodsclient' description = "A python API for iRODS" @@ -28,4 +29,5 @@ exts_list = [ }), ] -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' + From b1bf3645b4d2b35d7aee08b8ec13515b69c39a5d Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 23 Sep 2022 20:16:58 +0200 Subject: [PATCH 4898/9987] adding easyconfigs: FDS-6.7.9-intel-2022a.eb --- .../f/FDS/FDS-6.7.9-intel-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb b/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb new file mode 100644 index 00000000000..ba9526d4281 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.7.9' + +homepage = 'https://pages.nist.gov/fds-smv' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['FDS%(version)s.tar.gz'] +checksums = ['b6889471a56d0ebf07dfc93bbd35600b7c9ea13f194478c9f797cb653624ecd2'] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +buildopts = 'impi_intel_linux_openmp &&' +buildopts += 'cd %(installdir)s/Build && mv fds_impi_intel_linux_openmp fds' + +modextrapaths = {'PATH': 'Build'} + +sanity_check_paths = { +'files': ['Build/fds'], +'dirs': [], +} + +sanity_check_commands = [ + "fds 2>&1 | grep 'MPI Enabled;'", + "fds 2>&1 | grep 'OpenMP Enabled;'", +] + +moduleclass = 'phys' From 9fd620c19fa6392cf59e01e377d5077e3b827e86 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 23 Sep 2022 20:41:22 +0200 Subject: [PATCH 4899/9987] Added requested changes + fixed style errors --- easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb b/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb index ba9526d4281..f26d9139e84 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.7.9-intel-2022a.eb @@ -23,13 +23,13 @@ skipsteps = ['configure', 'install'] buildininstalldir = True buildopts = 'impi_intel_linux_openmp &&' -buildopts += 'cd %(installdir)s/Build && mv fds_impi_intel_linux_openmp fds' +buildopts += 'cd %(installdir)s/Build && ln -s fds_impi_intel_linux_openmp fds' modextrapaths = {'PATH': 'Build'} sanity_check_paths = { -'files': ['Build/fds'], -'dirs': [], + 'files': ['Build/fds'], + 'dirs': [], } sanity_check_commands = [ From bdcf2fa8a7754cc4a57e7b3abf60fbaa39c3cd72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2022 21:08:05 +0200 Subject: [PATCH 4900/9987] {data}[GCC/11.3.0] MariaDB v10.9.3, libaio v0.3.112, LZO v2.10, Judy v1.0.5 --- .../j/Judy/Judy-1.0.5-GCCcore-11.3.0.eb | 34 ++++++++++ .../l/LZO/LZO-2.10-GCCcore-11.3.0.eb | 27 ++++++++ .../l/libaio/libaio-0.3.112-GCCcore-11.3.0.eb | 39 +++++++++++ .../m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb | 65 +++++++++++++++++++ 4 files changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..32dbb74b6cf --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..108c91bc2a7 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.38')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..024258d1792 --- /dev/null +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.112-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.112' +_libversion = '1.0.1' + +homepage = 'https://pagure.io/libaio' +description = "Asynchronous input/output library that uses the kernels native interface." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['4410c033237828c9e1205537df3cc94d4956f39164ef6d17a7813c2c787504c4'] + +builddependencies = [('binutils', '2.38')] + +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + +files_to_copy = [ + (["src/libaio.a", "src/%s" % _soname], "lib"), + (["src/libaio.h"], "include"), +] + +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] + +sanity_check_paths = { + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..0742cb59603 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.9.3' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + '9a1e229972fcccc8270e633f68d3fb824da151dcf4f53da1df8d947aca876bee', # mariadb-10.9.3.tar.gz + '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19', # MariaDB-10.1.13-link-rt-for-jemalloc.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('libaio', '0.3.112'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.3'), # optional + ('XZ', '5.2.5'), # optional + ('jemalloc', '5.3.0'), # optional + ('snappy', '1.1.9'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.9.13'), # needed by Connect XML + ('Boost', '1.79.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.40'), + ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release " +configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_commands = ["mysql --help", "mysqltest --help"] + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' From 8b7eab255b88438a757613242a0c5e766d48799c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2022 21:10:48 +0200 Subject: [PATCH 4901/9987] {bio}[GCC/11.3.0] VEP v107, Archive-Zip v1.68, DBD-mysql v4.050, ... --- .../Archive-Zip-1.68-GCCcore-11.3.0.eb | 32 ++++++++++++++++ .../Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb | 32 ++++++++++++++++ .../Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb | 31 +++++++++++++++ .../d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb | 29 ++++++++++++++ .../easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb | 38 +++++++++++++++++++ 5 files changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ef7187f720d --- /dev/null +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Archive-Zip' +version = '1.68' + +homepage = 'https://metacpan.org/pod/Archive::Zip' +description = "Provide an interface to ZIP archive files." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('UnZip', '6.0'), + ('Zip', '3.0'), +] + +options = {'modulename': 'Archive::Zip'} + +sanity_check_paths = { + 'files': ['bin/crc32'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb new file mode 100644 index 00000000000..68542cd0dae --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Bio-DB-HTS' +version = '3.01' + +homepage = 'https://metacpan.org/release/Bio-DB-HTS' +description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/'] +sources = ['Bio-DB-HTS-%(version)s.tar.gz'] +checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42'] + +builddependencies = [('pkgconf', '1.8.0')] + +dependencies = [ + ('Perl', '5.34.1'), + ('BioPerl', '1.7.8'), + ('HTSlib', '1.15.1'), +] + +preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB" + +options = {'modulename': 'Bio::DB::HTS'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a52e00e9f4b --- /dev/null +++ b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'Compress-Raw-Zlib' +version = '2.202' + +homepage = 'https://metacpan.org/pod/Compress::Raw::Zlib' +description = "Low-Level Interface to zlib or zlib-ng compression library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['96e20946eb457a32d2d7a0050b922e37b5ada41246bcdc824196d3f7c4da91b7'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('zlib', '1.2.12'), +] + +options = {'modulename': 'Compress::Raw::Zlib'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/Compress/Raw/Zlib.pm'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb new file mode 100644 index 00000000000..eb71c16f467 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.050' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['4f48541ff15a0a7405f76adc10f81627c33996fbf56c95c26c094444c0928d78'] + +dependencies = [ + ('Perl', '5.34.1'), + ('MariaDB', '10.9.3'), + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', True), +] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql.pm' % ARCH], + 'dirs': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql' % ARCH], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb b/easybuild/easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb new file mode 100644 index 00000000000..c6e1c1413ca --- /dev/null +++ b/easybuild/easyconfigs/v/VEP/VEP-107-GCC-11.3.0.eb @@ -0,0 +1,38 @@ +name = 'VEP' +version = '107' + +homepage = 'https://www.ensembl.org/info/docs/tools/vep' +description = """Variant Effect Predictor (VEP) determines the effect of your + variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, + transcripts, and protein sequence, as well as regulatory regions. + Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently + used routines in VEP.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4531acfe7a0dc3b1aaf0f9bead043cfb20b6df23a3a922a27a693dc532d0f741'] + +dependencies = [ + ('Perl', '5.34.1'), + ('Archive-Zip', '1.68'), + ('DBD-mysql', '4.050'), + ('BioPerl', '1.7.8'), + ('Bio-DB-HTS', '3.01'), + # VEP requires Compress::Raw::Zlib >= 2.103 + ('Compress-Raw-Zlib', '2.202'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", "") + +exts_list = [ + ('Bio::EnsEMBL::XS', '2.3.2', { + 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], + }), +] + +moduleclass = 'bio' From b398277fcae80f11e705309f0b5d49fb63cf8e5d Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 23 Sep 2022 21:39:25 +0200 Subject: [PATCH 4902/9987] adding easyconfigs: GitPython-3.1.27-GCCcore-11.3.0.eb, buildingspy-4.0.0-foss-2022a.eb --- .../buildingspy-4.0.0-foss-2022a.eb | 48 +++++++++++++++++++ .../GitPython-3.1.27-GCCcore-11.3.0.eb | 33 +++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb new file mode 100644 index 00000000000..52e6907b217 --- /dev/null +++ b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'buildingspy' +version = '4.0.0' + +homepage = 'https://simulationresearch.lbl.gov/modelica/buildingspy' +description = 'Python modules for automating Modelica simulations and for running unit test for the Buildings library' + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('GitPython', '3.1.27'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +exts_list = [ + ('Jinja2', '3.1.2', { + 'checksums': ['31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852'], + }), + ('pytidylib', '0.3.2', { + 'modulename': 'tidylib', + 'checksums': ['22b1c8d75970d8064ff999c2369e98af1d0685417eda4c829a5c9f56764b0af3'], + }), + ('simplejson', '3.16.0', { + 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], + }), + ('six', '1.14.0', { + 'checksums': ['236bdbdce46e6e6a3d61a337c0f8b763ca1e8717c03b369e87a7ec7ce1319c0a'], + }), + ('pyfunnel', '0.3.0', { + 'checksums': ['68256e82ecaa3832741dbf5f9c9a3420fcdb6b0c646406169e6c728ad1d47c6c'], + }), + ('Cerberus', '1.3.4', { + 'checksums': ['d1b21b3954b2498d9a79edf16b3170a3ac1021df88d197dc2ce5928ba519237c'], + }), + (name, version, { + 'checksums': ['78ba40360016850259a3b98fb9a7d1aeceac583a6cc6ae4ef8f684ffbd285f4b'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fd485f5ec39 --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.27' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('git', '2.36.0', '-nodocs'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('smmap', '5.0.0', { + 'checksums': ['c840e62059cd3be204b0c9c9f74be2c09d5648eddd4580d9314c3ecde0b30936'], + }), + ('gitdb', '4.0.9', { + 'checksums': ['bac2fd45c0a1c9cf619e63a90d62bdc63892ef92387424b855792a6cabe789aa'], + }), + (name, version, { + 'modulename': 'git', + }), +] + +moduleclass = 'lib' From 9a705ac2771deced585a414169b299139a75587f Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 23 Sep 2022 21:53:50 +0200 Subject: [PATCH 4903/9987] Added checksum for GitPython --- .../easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb index fd485f5ec39..dfc6291a3e3 100644 --- a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.27-GCCcore-11.3.0.eb @@ -27,6 +27,7 @@ exts_list = [ }), (name, version, { 'modulename': 'git', + 'checksums': ['1c885ce809e8ba2d88a29befeb385fcea06338d3640712b59ca623c220bb5704'], }), ] From 0f74490ab8551514928cee3e88a80de7de3ae6d3 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 23 Sep 2022 22:10:49 +0200 Subject: [PATCH 4904/9987] Removed download_dep_fail from BuildingsPy --- .../easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb index 52e6907b217..782819b71f0 100644 --- a/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb @@ -18,7 +18,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('Jinja2', '3.1.2', { From c18443739a13ec92928a88a4d3d97ea1d17ba908 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2022 22:44:34 +0200 Subject: [PATCH 4905/9987] don't enable separate_build_dir, already done by default by CMakeMake easyblock --- easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb index 6b12dec5b6a..72ff0976e45 100644 --- a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb @@ -35,8 +35,6 @@ dependencies = [ ('libev', '4.33'), ] -separate_build_dir = True - configopts = '-DENABLE_GNUTLS=True' runtest = 'check' From d1372f9c4d5c1a77b2be02d8b4cebf601ff07a67 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2022 22:49:53 +0200 Subject: [PATCH 4906/9987] =?UTF-8?q?=20@boegel=20don't=20enable=20separat?= =?UTF-8?q?e=5Fbuild=5Fdir=20or=20-DCMAKE=5FBUILD=5FTYPE=3DRelease,=20alre?= =?UTF-8?q?ady=20done=20by=20default=20by=20CMakeMake=E2=80=A6?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb index 4d87ace9817..a8a803600e1 100644 --- a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb @@ -47,11 +47,6 @@ dependencies = [ ('c-ares', '1.18.1'), ] - -separate_build_dir = True - -configopts = '-DCMAKE_BUILD_TYPE=release ' - runtest = 'check' sanity_check_paths = { From 75a06833f790027e9d73bb8ed5ac0a936f846261 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Sep 2022 23:25:04 +0200 Subject: [PATCH 4907/9987] remove OS dependency for gnutls, since it's already included as a dependency --- easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb index 33e5fa76118..f30142975fd 100644 --- a/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.7-GCC-11.2.0.eb @@ -37,9 +37,6 @@ dependencies = [ ('Brotli', '1.0.9'), ] -# uncomment for checking TLS support -osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] - sanity_check_paths = { 'files': ['lib/libsoup-3.0.%s' % SHLIB_EXT], 'dirs': ['include/libsoup-3.0/libsoup/', 'lib/pkgconfig'] From e2a27e62d945889dccb6fbbb7e1ad2a3f5f69ffe Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 23 Sep 2022 15:04:00 -0700 Subject: [PATCH 4908/9987] add missing dep: Class::MethodMaker --- easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb index 97dd5d374f3..b9b1b8b9017 100644 --- a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb @@ -34,6 +34,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], 'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'], }), + ('Class::MethodMaker', '2.24', { + 'source_tmpl': 'Class-MethodMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker'], + 'checksums': ['5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328'], + }), ('Term::ProgressBar', '2.22', { 'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], @@ -42,7 +47,7 @@ exts_list = [ (name, version, { 'modulename': 'AGAT::Utilities', 'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['998e32a3cb5e941efd324daf9ee4e0a71d605d06999922f083170b7a9f059899'], }), ] From 141db1f6bd5e4f95c69eef70bacbc6d2c15c8413 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 24 Sep 2022 00:07:26 +0200 Subject: [PATCH 4909/9987] remove commented out lines + hardcoded 'parallel = 2' --- .../w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb index c59f1cf7ccc..26dfe9217da 100644 --- a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.2.0.eb @@ -37,11 +37,6 @@ dependencies = [ ('freeglut', '3.2.1'), ] -# Required to find EGL -#osdependencies = [('libegl-dev', 'libegl-devel')] - -parallel = 2 - sanity_check_paths = { 'files': ['bin/wayland-scanner++', 'lib//libwayland-client-extra++.%s' % SHLIB_EXT, 'lib/libwayland-client++.%s' % SHLIB_EXT, From 5fdb5196322e312af17ee317dfb8acd0771b3b78 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 24 Sep 2022 18:17:22 +0200 Subject: [PATCH 4910/9987] adding easyconfigs: SuperLU-5.3.0-foss-2020b.eb, SuperLU-5.3.0-foss-2022a.eb, SuperLU-5.3.0-intel-2020b.eb, SuperLU-5.3.0-intel-2022a.eb --- .../s/SuperLU/SuperLU-5.3.0-foss-2020b.eb | 21 +++++++++++++++++++ .../s/SuperLU/SuperLU-5.3.0-foss-2022a.eb | 21 +++++++++++++++++++ .../s/SuperLU/SuperLU-5.3.0-intel-2020b.eb | 21 +++++++++++++++++++ .../s/SuperLU/SuperLU-5.3.0-intel-2022a.eb | 21 +++++++++++++++++++ 4 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb create mode 100644 easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb new file mode 100644 index 00000000000..41d145da7ea --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2020b.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '5.3.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] + +builddependencies = [('CMake', '3.18.4')] + +runtest = " test" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2022a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2022a.eb new file mode 100644 index 00000000000..dd4bf92289b --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-foss-2022a.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '5.3.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] + +builddependencies = [('CMake', '3.23.1')] + +runtest = " test" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb new file mode 100644 index 00000000000..2328a049426 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2020b.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '5.3.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] + +builddependencies = [('CMake', '3.18.4')] + +runtest = " test" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2022a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2022a.eb new file mode 100644 index 00000000000..fbc399aa456 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.3.0-intel-2022a.eb @@ -0,0 +1,21 @@ +name = 'SuperLU' +version = '5.3.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the +direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['3e464afa77335de200aeb739074a11e96d9bef6d0b519950cfa6684c4be1f350'] + +builddependencies = [('CMake', '3.23.1')] + +runtest = " test" + +moduleclass = 'numlib' From 6efd1227ad596d32908e8e0e34c776589f1a0af7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 25 Sep 2022 17:26:17 +0200 Subject: [PATCH 4911/9987] use SYSTEM rather than True --- .../easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb index 388390b27a1..dd690af8e5f 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pkg-config', '0.29.2'), ('pocl', '1.8'), ] From 4481295a98162c673193d25a3a0c9e3f1c872719 Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Mon, 26 Sep 2022 09:30:57 +0200 Subject: [PATCH 4912/9987] remove python version suffix --- ...python-irodsclient-1.1.4-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100755 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb new file mode 100755 index 00000000000..a039002b7e6 --- /dev/null +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'python-irodsclient' +version = '1.1.4' + +homepage = 'https://github.com/irods/python-irodsclient' +description = "A python API for iRODS" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('prettytable', '3.3.0', { + 'checksums': ['118eb54fd2794049b810893653b20952349df6d3bc1764e7facd8a18064fa9b0'], + }), + (name, version, { + 'modulename': 'irods', + 'checksums': ['f427699739911042dc35a7fbd92f7ba87db9fad3977423c2fa2ab61a0ffebe43'], + }), +] + +moduleclass = 'lib' + From 7ad8d1262ddbbe424649f5ae520010ed6598347d Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 26 Sep 2022 09:47:19 +0200 Subject: [PATCH 4913/9987] adding easyconfigs: scikit-learn-1.1.2-intel-2022a.eb --- .../scikit-learn-1.1.2-intel-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-intel-2022a.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-intel-2022a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-intel-2022a.eb new file mode 100644 index 00000000000..8150d97c93a --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.1.2-intel-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.1.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'sklearn', + 'checksums': ['7c22d1305b16f08d57751a4ea36071e2215efb4c09cb79183faa4e8e82a3dbf8'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), +] + +moduleclass = 'data' From 2058ab67438c7dda0c45ca4876de53a63fff1ca8 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 26 Sep 2022 09:50:33 +0200 Subject: [PATCH 4914/9987] adding easyconfigs: Wannier90-3.1.0-intel-2022a.eb --- .../Wannier90/Wannier90-3.1.0-intel-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022a.eb new file mode 100644 index 00000000000..ada98a7bdfc --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' From 97b52bacb15c53133e95f2c7a05b8dd6f1eea084 Mon Sep 17 00:00:00 2001 From: robogast Date: Mon, 26 Sep 2022 12:09:26 +0200 Subject: [PATCH 4915/9987] fixed ec for python2.7 syntax --- .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 15 ++++++++++----- .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 8 ++++---- 2 files changed, 14 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb index 51de3daf755..fd1a4dccabd 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -27,12 +27,17 @@ dependencies = [ configopts = '--enable-libwebpmux' +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + sanity_check_paths = { - 'files': [ - *['include/webp/%s' % f for f in ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h']], - *['lib/lib%s.a' % l for l in ['webp', 'webpdemux', 'webpmux']], - *['lib/lib%s.%s' % (l, SHLIB_EXT) for l in ['webp', 'webpdemux', 'webpmux']], - ], + 'files': ( + ['include/webp/%s' % header for header in local_headers] + + ['lib/lib%s.a' % lib for lib in local_libs] + + ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs] + ), 'dirs': ['lib/'] } diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index 77a049dd6b3..fc208f5ca99 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -26,10 +26,10 @@ local_libs, local_bins = [ ] sanity_check_paths = { - 'files': [ - *['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs], - *['bin/exr%s' % bin for bin in local_bins] - ], + 'files': ( + ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs] + + ['bin/exr%s' % bin for bin in local_bins] + ), 'dirs': ['include/%(name)s', 'share'], } From cb65d62214b465837309ff726804537868d3d832 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 26 Sep 2022 12:44:01 +0200 Subject: [PATCH 4916/9987] adding easyconfigs: spglib-python-2.0.0-intel-2022a.eb --- .../spglib-python-2.0.0-intel-2022a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-intel-2022a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-intel-2022a.eb new file mode 100644 index 00000000000..acbc3e85a70 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.0-intel-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '2.0.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['cbbd5e1d6096577c58b2fa47a5ea4f433a1932e5bc1cd1b691ea387c1b2e9974'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' From 228df40dd56d3d589724102d61b216a35384be62 Mon Sep 17 00:00:00 2001 From: robogast Date: Mon, 26 Sep 2022 12:46:24 +0200 Subject: [PATCH 4917/9987] moved temp variables to single letters again --- .../easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 6 +++--- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 2 +- .../easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb index fd1a4dccabd..b78c2f0eccd 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -34,9 +34,9 @@ local_headers, local_libs = ( sanity_check_paths = { 'files': ( - ['include/webp/%s' % header for header in local_headers] - + ['lib/lib%s.a' % lib for lib in local_libs] - + ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs] + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] ), 'dirs': ['lib/'] } diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index dc22d0ca82d..48f3aa8178e 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -87,7 +87,7 @@ local_contrib_libs = [ ] sanity_check_paths = { - 'files': ['lib64/libopencv_%s.%s' % (l, SHLIB_EXT) for l in local_contrib_libs], + 'files': ['lib64/libopencv_%s.%s' % (s, SHLIB_EXT) for s in local_contrib_libs], 'dirs': [], } diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index fc208f5ca99..2f11268c8fd 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -27,8 +27,8 @@ local_libs, local_bins = [ sanity_check_paths = { 'files': ( - ['lib/lib%s.%s' % (lib, SHLIB_EXT) for lib in local_libs] - + ['bin/exr%s' % bin for bin in local_bins] + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] ), 'dirs': ['include/%(name)s', 'share'], } From 8e905ed1097442ec014d9c6bf6e48e5822359958 Mon Sep 17 00:00:00 2001 From: robogast Date: Mon, 26 Sep 2022 13:30:46 +0200 Subject: [PATCH 4918/9987] W503 fix --- .../easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 6 +++--- .../easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb index b78c2f0eccd..0c0b2fbef39 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -34,9 +34,9 @@ local_headers, local_libs = ( sanity_check_paths = { 'files': ( - ['include/webp/%s' % h for h in local_headers] - + ['lib/lib%s.a' % s for s in local_libs] - + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] ), 'dirs': ['lib/'] } diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index 2f11268c8fd..d607a01b64d 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -27,8 +27,8 @@ local_libs, local_bins = [ sanity_check_paths = { 'files': ( - ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] - + ['bin/exr%s' % b for b in local_bins] + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] ), 'dirs': ['include/%(name)s', 'share'], } From 8162d3f8a96280aabc6911aa1cd8521e1109b8ac Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 26 Sep 2022 13:45:19 +0200 Subject: [PATCH 4919/9987] Removed redundant extensions --- .../b/buildingspy/buildingspy-4.0.0-foss-2022a.eb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb index 782819b71f0..31b0718b8fd 100644 --- a/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/b/buildingspy/buildingspy-4.0.0-foss-2022a.eb @@ -20,19 +20,10 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('Jinja2', '3.1.2', { - 'checksums': ['31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852'], - }), ('pytidylib', '0.3.2', { 'modulename': 'tidylib', 'checksums': ['22b1c8d75970d8064ff999c2369e98af1d0685417eda4c829a5c9f56764b0af3'], }), - ('simplejson', '3.16.0', { - 'checksums': ['b1f329139ba647a9548aa05fb95d046b4a677643070dc2afc05fa2e975d09ca5'], - }), - ('six', '1.14.0', { - 'checksums': ['236bdbdce46e6e6a3d61a337c0f8b763ca1e8717c03b369e87a7ec7ce1319c0a'], - }), ('pyfunnel', '0.3.0', { 'checksums': ['68256e82ecaa3832741dbf5f9c9a3420fcdb6b0c646406169e6c728ad1d47c6c'], }), From 981f4dc121a24e5d3028a8dd814dc9396a9c7e7b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 26 Sep 2022 16:44:14 +0200 Subject: [PATCH 4920/9987] Drop Java dep from ABAQUS, new 2223 hotfix --- .../a/ABAQUS/ABAQUS-2022-hotfix-2214.eb | 2 -- .../a/ABAQUS/ABAQUS-2022-hotfix-2223.eb | 34 +++++++++++++++++++ easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb | 2 -- 3 files changed, 34 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2223.eb diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb index 76e2b9c6712..c5076140bfa 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2214.eb @@ -34,6 +34,4 @@ checksums = [ '88b5c0b182e2dc3e09c14f89be338993cf7edcfeb2f388f405022c63f5512029', ] -dependencies = [('Java', '11')] - moduleclass = 'cae' diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2223.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2223.eb new file mode 100644 index 00000000000..84bf03d99d0 --- /dev/null +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022-hotfix-2223.eb @@ -0,0 +1,34 @@ +name = 'ABAQUS' +version = '2022' +local_hotfix = '2223' +versionsuffix = '-hotfix-%s' % local_hotfix + +homepage = 'https://www.simulia.com/products/abaqus_fea.html' +description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit + dynamics FEA.""" + +toolchain = SYSTEM + +sources = [ + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-5.tar', + '%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-5.tar', + # hotfixes + '%%(version)s.FP.CFA.%s.Part_SIMULIA_EstPrd.Linux64.tar' % local_hotfix, + '%%(version)s.FP.CFA.%s.Part_SIMULIA_FlexNet.Linux64.tar' % local_hotfix, +] +checksums = [ + '9025c9bc2d0345c13d96e88c1c422b1979a14bf7ba281bd32dfe093c1446945d', # 2022.AM_SIM_Abaqus_Extend.AllOS.1-5.tar + '14c23b3fdfddb723d84a02eb27edc25162e1d27e8fdce053193f72d28ff0a12c', # 2022.AM_SIM_Abaqus_Extend.AllOS.2-5.tar + '561d54d688ea2f2dcf329701e20502642aecf5526eb56db3a586cbcadfbf20fb', # 2022.AM_SIM_Abaqus_Extend.AllOS.3-5.tar + 'c085066ae2df68c9c61ea345808042ddb205c642d649f1ec3b7db4aaffb3d544', # 2022.AM_SIM_Abaqus_Extend.AllOS.4-5.tar + 'bfbc2c1a402881308f68f054e1e376fe153053b4287018ddbc80e76710f6969f', # 2022.AM_SIM_Abaqus_Extend.AllOS.5-5.tar + # 2022.FP.CFA.2223.Part_SIMULIA_EstPrd.Linux64.tar + 'bb05b07072ded86944eb44908875e6813c6ea18b2e6ab4dc7f8ef1ef368851e2', + # 2022.FP.CFA.2223.Part_SIMULIA_FlexNet.Linux64.tar + '32895726d409af8f7055b0f2bad53d10e7c32e36712e3eda8ff860f02622ee6f', +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb index 6ce57875272..dc2c3525813 100644 --- a/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb +++ b/easybuild/easyconfigs/a/ABAQUS/ABAQUS-2022.eb @@ -22,6 +22,4 @@ checksums = [ 'bfbc2c1a402881308f68f054e1e376fe153053b4287018ddbc80e76710f6969f', # 2022.AM_SIM_Abaqus_Extend.AllOS.5-5.tar ] -dependencies = [('Java', '11')] - moduleclass = 'cae' From c09d5d632246167f20b07780ed9ce5c9cf607e50 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 26 Sep 2022 18:28:28 +0200 Subject: [PATCH 4921/9987] adding easyconfigs: LMfit-1.0.3-foss-2022a.eb, LMfit-1.0.3-intel-2022a.eb --- .../l/LMfit/LMfit-1.0.3-foss-2022a.eb | 33 +++++++++++++++++++ .../l/LMfit/LMfit-1.0.3-intel-2022a.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-intel-2022a.eb diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2022a.eb new file mode 100644 index 00000000000..6b753c7eca3 --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-foss-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.0.3' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = """Lmfit provides a high-level interface to non-linear optimization +and curve fitting problems for Python""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asteval', '0.9.27', { + 'checksums': ['de838c33aed4c9bb25737eadbb7d1edaaf875e2bab505cc079f1a4b35de03e47'], + }), + ('uncertainties', '3.1.7', { + 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['d067c3ea501f035af5d3c079e6e6e35dc3cc1ac7d439429a425b0aeb5a7858a2'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-intel-2022a.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-intel-2022a.eb new file mode 100644 index 00000000000..d68900b073e --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.0.3-intel-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.0.3' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = """Lmfit provides a high-level interface to non-linear optimization +and curve fitting problems for Python""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asteval', '0.9.27', { + 'checksums': ['de838c33aed4c9bb25737eadbb7d1edaaf875e2bab505cc079f1a4b35de03e47'], + }), + ('uncertainties', '3.1.7', { + 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['d067c3ea501f035af5d3c079e6e6e35dc3cc1ac7d439429a425b0aeb5a7858a2'], + }), +] + +moduleclass = 'math' From 16d944dc648b897816e1905885809e733c51ae9c Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 26 Sep 2022 14:00:54 -0700 Subject: [PATCH 4922/9987] one more dep --- easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb index b9b1b8b9017..c541f370006 100644 --- a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb @@ -24,6 +24,11 @@ exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") exts_list = [ + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), ('File::Share', '0.27', { 'source_tmpl': 'File-Share-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], From 17c98f530c96c5c6e3ebed0715acac0fdb9de512 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 26 Sep 2022 14:34:35 -0700 Subject: [PATCH 4923/9987] ncbi-vdb-3.0.0 requires multidep exception for HDF5 --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0fb05afe876..5a2a62e69c1 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -494,8 +494,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], - # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) - 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], + # ncbi-vdb v2.x and v3.0.0 require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) + 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'ncbi-vdb-3\.0\.0', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], # VMTK 1.4.x requires ITK 4.13.x 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) From 7628a715b23afd4eb9fdaa43a0c5f851f2b51ee5 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 26 Sep 2022 15:36:55 -0700 Subject: [PATCH 4924/9987] missing pkg-config --- easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb index 209645c0e7c..456da718458 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb @@ -21,6 +21,7 @@ checksums = ['c7935b7a29e42443f6a35d35cf20ffa7d028c399303f872cd1219598a83656ae'] builddependencies = [ ('Autotools', '20210726'), ('binutils', '2.37'), + ('pkg-config', '0.29.2'), ] dependencies = [ From 9765c203f95b6cc32b17c93247967a707788a56a Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 26 Sep 2022 15:50:18 -0700 Subject: [PATCH 4925/9987] missing pkg-config builddep --- easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb index 17bc1fb9519..2d6a713e053 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb @@ -19,6 +19,7 @@ checksums = ['d8be783efd5cd4ae534cee4132338e3f40f182c3205d23b200094ec85faaaef8'] builddependencies = [('binutils', '2.37')] dependencies = [ + ('pkg-config', '0.29.2'), ('libtasn1', '4.18.0'), ('libffi', '3.4.2'), ] From 530cc4783bde6e5d31de8badea7313f85f3e43e5 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 26 Sep 2022 16:22:34 -0700 Subject: [PATCH 4926/9987] missing build dep pkg-config --- .../easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) mode change 100644 => 100755 easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb old mode 100644 new mode 100755 index 3f4b2a24826..751a1a06f3a --- a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.2.0.eb @@ -25,6 +25,7 @@ builddependencies = [ ('Autotools', '20210726'), ('binutils', '2.37'), ('M4', '1.4.19'), + ('pkg-config', '0.29.2'), ] preconfigopts = "autoreconf -vfi && " From 4ab4314ec1c8b433156adf70e4e2e60135531da8 Mon Sep 17 00:00:00 2001 From: guacke Date: Tue, 27 Sep 2022 10:21:48 +0200 Subject: [PATCH 4927/9987] Bugfix: use version templating. --- .../a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb index 0e2597cebb9..3dd1e871019 100644 --- a/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/a/Avogadro2/Avogadro2-1.97.0-linux-x86_64.eb @@ -14,13 +14,14 @@ description = """ toolchain = SYSTEM sources = [{ - 'source_urls': ['https://github.com/OpenChemistry/avogadroapp/releases/download/1.97.0'], - 'filename': 'avogadro2', - 'download_filename': 'Avogadro2-x86_64.AppImage' + 'source_urls': ['https://github.com/OpenChemistry/avogadroapp/releases/download/%(version)s/'], + 'filename': '%(name)s-%(version)s.bin', + 'download_filename': 'Avogadro2-x86_64.AppImage', }] - checksums = ['cc522dbdaa6e5386cb7101d382c5730f0d1ff71f2e70eb10f7e55f4ca052c89d'] +postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.bin %(installdir)s/avogadro2"] + sanity_check_paths = { 'files': ['avogadro2'], 'dirs': [], From 4770a3875fe686548fda2cc062a10dd207170515 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 27 Sep 2022 09:40:01 +0100 Subject: [PATCH 4928/9987] Entry for ccache corrected so GCCcore will be used --- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb index 9026c3b2c20..5e41bdddcfb 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -38,7 +38,7 @@ builddependencies = [ ('Perl', '5.34.0', '-minimal'), ('GObject-Introspection', '1.68.0'), ('pkg-config', '0.29.2'), - ('ccache', '4.6.1', '', True), + ('ccache', '4.6.1'), ] dependencies = [ ('GLib', '2.69.1'), From a498e98277e9f648b341abe19f483f138604780f Mon Sep 17 00:00:00 2001 From: software Date: Tue, 27 Sep 2022 09:01:31 +0000 Subject: [PATCH 4929/9987] adding easyconfigs: paladin-1.4.6-GCCcore-10.3.0.eb, paladin-1.4.6-GCCcore-11.2.0.eb --- .../p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb | 41 +++++++++++++++++++ .../p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..79ae059d08f --- /dev/null +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb @@ -0,0 +1,41 @@ + +easyblock = 'MakeCp' + +name = 'paladin' +version = '1.4.6' + +homepage = 'https://github.com/ToniWestbrook/paladin' +description = """ +Protein ALignment And Detection INterface + +PALADIN is a protein sequence alignment tool designed for the accurate functional characterization of metagenomes. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ToniWestbrook/paladin/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd23a8907d832cada060e112addb1b3b3751353dda515887c69c1772fd37cc4a'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +# Use EB build flags +buildopts = 'CFLAGS="$CFLAGS"' + +dependencies = [ + ('zlib', '1.2.11'), + ('cURL', '7.76.0'), + ('OpenSSL', '1.1', '', True), +] + +files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] + +sanity_check_paths = { + 'files': ['bin/paladin'], + 'dirs': ['sample_data'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f573e5e725d --- /dev/null +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ + +easyblock = 'MakeCp' + +name = 'paladin' +version = '1.4.6' + +homepage = 'https://github.com/ToniWestbrook/paladin' +description = """ +Protein ALignment And Detection INterface + +PALADIN is a protein sequence alignment tool designed for the accurate functional characterization of metagenomes. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ToniWestbrook/paladin/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd23a8907d832cada060e112addb1b3b3751353dda515887c69c1772fd37cc4a'] + +builddependencies = [ + ('binutils', '2.37'), +] + +# Use EB build flags +buildopts = 'CFLAGS="$CFLAGS"' + +dependencies = [ + ('zlib', '1.2.11'), + ('cURL', '7.78.0'), + ('OpenSSL', '1.1', '', True), +] + +files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] + +sanity_check_paths = { + 'files': ['bin/paladin'], + 'dirs': ['sample_data'], +} + +moduleclass = 'bio' From 3dad2ffddc61bcf245c847efab2c9b0414c0e5b1 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 27 Sep 2022 13:42:11 +0200 Subject: [PATCH 4930/9987] adding easyconfigs: FFTW-3.3.10-iimpi-2022a.eb --- .../f/FFTW/FFTW-3.3.10-iimpi-2022a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022a.eb new file mode 100644 index 00000000000..63d8bd8e1e6 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022a.eb @@ -0,0 +1,27 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# https://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails on AMD systems when configuring with --enable-avx-128-fma, +# because Intel compilers do not support FMA4 instructions +use_fma4 = False + + +runtest = 'check' + +moduleclass = 'numlib' From 00124096c038b6a59f479a3ee4adbb580c69eb8f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 27 Sep 2022 14:07:44 +0200 Subject: [PATCH 4931/9987] adding easyconfigs: PostgreSQL-14.4-GCCcore-11.3.0.eb --- .../PostgreSQL-14.4-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f3972f8c07f --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '14.4' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ebb58a3ac76b910cd7ca103636d19efdc262cab841e9be00705456813d980955'] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Perl', '5.34.1'), + ('Python', '3.10.4'), +] + +dependencies = [ + ('libreadline', '8.1.2'), + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', True), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' From 43718e73d4be1e733b0cff4932896bfc5713e160 Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:22:12 +0200 Subject: [PATCH 4932/9987] change tqdm version in umap-learn recipe Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index 449a1fd265a..7a58535e76e 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -21,7 +21,7 @@ dependencies = [ ('scikit-learn', '0.24.2'), ('numba', '0.53.1'), ('LLVM', '11.1.0'), - ('tqdm', '4.61.1'), + ('tqdm', '4.61.2'), ] use_pip = True From f59935e1db759c1007e09df0fc3444d62eccf0e3 Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:55:37 +0200 Subject: [PATCH 4933/9987] Update easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index 7a58535e76e..52a71470882 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -25,7 +25,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True exts_default_options = {'source_urls': [PYPI_SOURCE]} From 659fdacac8cdb2f1d62e0b13cbb1541ed62d215a Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:55:45 +0200 Subject: [PATCH 4934/9987] Update easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index 52a71470882..366787e8caa 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -40,4 +40,4 @@ exts_list = [ sanity_pip_check = True -moduleclass = 'lib' +moduleclass = 'tools' From e16c6433a7b544d1194e30da7a54a84d5a0e5adf Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:55:51 +0200 Subject: [PATCH 4935/9987] Update easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index 366787e8caa..cc3f7112b03 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -26,8 +26,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('pynndescent', '0.5.7', { 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], From da4055f14050df7a5a90cfc26c8e3929e7aad017 Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:55:59 +0200 Subject: [PATCH 4936/9987] Update easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index cc3f7112b03..8a85ad9aea3 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -8,9 +8,11 @@ name = 'umap-learn' version = '0.5.3' homepage = 'https://umap-learn.readthedocs.io/en/latest/' -description = """Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique - that can be used for visualisation similarly to t-SNE, but also for general non-linear - dimension reduction.""" +description = """ +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique +that can be used for visualisation similarly to t-SNE, but also for general non-linear +dimension reduction. +""" toolchain = {'name': 'foss', 'version': '2021a'} From e680f4518f3beaf137e3698193269e9b675e458c Mon Sep 17 00:00:00 2001 From: kErica <31503643+kErica@users.noreply.github.com> Date: Tue, 27 Sep 2022 14:56:10 +0200 Subject: [PATCH 4937/9987] Update easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb index 8a85ad9aea3..914a9481bfd 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021a.eb @@ -15,8 +15,6 @@ dimension reduction. """ toolchain = {'name': 'foss', 'version': '2021a'} - - dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), From 875a454be18570e744114e1028b30f0ebd31afa6 Mon Sep 17 00:00:00 2001 From: jefscheepers <51341187+jefscheepers@users.noreply.github.com> Date: Tue, 27 Sep 2022 16:42:17 +0200 Subject: [PATCH 4938/9987] Delete python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb --- ...lient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100755 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb deleted file mode 100755 index 5a022f20b13..00000000000 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0-Python-3.9.6.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'python-irodsclient' -version = '1.1.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/irods/python-irodsclient' -description = "A python API for iRODS" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -dependencies = [ - ('Python', '3.9.6'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('defusedxml', '0.7.1', { - 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], - }), - ('prettytable', '3.3.0', { - 'checksums': ['118eb54fd2794049b810893653b20952349df6d3bc1764e7facd8a18064fa9b0'], - }), - (name, version, { - 'modulename': 'irods', - 'checksums': ['f427699739911042dc35a7fbd92f7ba87db9fad3977423c2fa2ab61a0ffebe43'], - }), -] - -moduleclass = 'lib' - From 1218fe448fdb6047c1c2ca877e9591a9c28582ba Mon Sep 17 00:00:00 2001 From: jefscheepers <51341187+jefscheepers@users.noreply.github.com> Date: Tue, 27 Sep 2022 16:57:49 +0200 Subject: [PATCH 4939/9987] Add binutils as builddependency --- .../python-irodsclient-1.1.4-GCCcore-11.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb index a039002b7e6..c68d09039d3 100755 --- a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-11.2.0.eb @@ -8,6 +8,8 @@ description = "A python API for iRODS" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +builddependencies = [('binutils', '2.37')] + dependencies = [ ('Python', '3.9.6'), ] @@ -29,4 +31,3 @@ exts_list = [ ] moduleclass = 'lib' - From 5ba19ccfb4b1d3db8cab2d4b4cebb2dc4d77469d Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 27 Sep 2022 18:18:12 +0200 Subject: [PATCH 4940/9987] Remove importlib_metadata --- .../easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb index 329c77c8106..4cf2f36f1d5 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.10.0-foss-2022a.eb @@ -47,9 +47,6 @@ exts_list = [ 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", 'checksums': ['d4725fc9ec8e8822906ae26bb26f5546891aa7fbc3443de970cc556d43a5c99f'], }), - ('importlib_metadata', '4.12.0', { - 'checksums': ['637245b8bab2b6502fcbc752cc4b7a6f6243bb02b31c5c26156ad103d3d45670'], - }), ('Markdown', '3.4.1', { 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], }), From 66105ebfa3f0c0cdf636caf517e08b6598fd84bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 28 Sep 2022 10:59:09 +0200 Subject: [PATCH 4941/9987] adding easyconfigs: PyCharm-2022.2.2.eb --- .../easyconfigs/p/PyCharm/PyCharm-2022.2.2.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCharm/PyCharm-2022.2.2.eb diff --git a/easybuild/easyconfigs/p/PyCharm/PyCharm-2022.2.2.eb b/easybuild/easyconfigs/p/PyCharm/PyCharm-2022.2.2.eb new file mode 100644 index 00000000000..831033dc25b --- /dev/null +++ b/easybuild/easyconfigs/p/PyCharm/PyCharm-2022.2.2.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = 'PyCharm' +version = "2022.2.2" + +homepage = 'https://www.jetbrains.com/pycharm/' +description = """PyCharm Community Edition: Python IDE for Professional Developers""" + +toolchain = SYSTEM + +source_urls = ['https://download-cf.jetbrains.com/python'] +sources = ['pycharm-community-%(version)s.tar.gz'] +checksums = ['2f361c5f59c685c9f8d1385029ed753eabe5b688a82acef6e83a50f0d2b9d7a8'] + +sanity_check_paths = { + 'files': ["bin/pycharm.sh"], + 'dirs': [], +} + +moduleclass = 'devel' From e0648f8b93c4117e97161c7bc5e5acb902c3b2c8 Mon Sep 17 00:00:00 2001 From: software Date: Wed, 28 Sep 2022 10:24:08 +0000 Subject: [PATCH 4942/9987] Add missing sanity check command --- easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb | 2 ++ easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb index 79ae059d08f..eec314fb855 100644 --- a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb @@ -33,6 +33,8 @@ dependencies = [ files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] +sanity_check_commands = ["paladin version 2>&1 | grep 'Program: PALADIN (Protein Alignment and Detection Interface)'"] + sanity_check_paths = { 'files': ['bin/paladin'], 'dirs': ['sample_data'], diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb index f573e5e725d..22b6836b5ba 100644 --- a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb @@ -33,6 +33,8 @@ dependencies = [ files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] +sanity_check_commands = ["paladin version 2>&1 | grep 'Program: PALADIN (Protein Alignment and Detection Interface)'"] + sanity_check_paths = { 'files': ['bin/paladin'], 'dirs': ['sample_data'], From f81983bf2f8b8c1682c42d237377f34e2392bf31 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 28 Sep 2022 11:27:48 +0100 Subject: [PATCH 4943/9987] Update easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb index 22b6836b5ba..bc0742d120f 100644 --- a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-11.2.0.eb @@ -28,7 +28,7 @@ buildopts = 'CFLAGS="$CFLAGS"' dependencies = [ ('zlib', '1.2.11'), ('cURL', '7.78.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] From a454dc465c7e09dfcdebca6274545ad9b5b2ebd7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 28 Sep 2022 11:27:59 +0100 Subject: [PATCH 4944/9987] Update easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb index eec314fb855..942e8e2ff5d 100644 --- a/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/paladin/paladin-1.4.6-GCCcore-10.3.0.eb @@ -28,7 +28,7 @@ buildopts = 'CFLAGS="$CFLAGS"' dependencies = [ ('zlib', '1.2.11'), ('cURL', '7.76.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] files_to_copy = [(['paladin'], 'bin'), 'run.py', 'sample_data', 'scripts'] From 5bf85e732ec71c1e9ad92dc8da3e5f2866c88b76 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 28 Sep 2022 13:27:06 +0200 Subject: [PATCH 4945/9987] adding easyconfigs: ASAP-2.1-foss-2022a.eb, DCMTK-3.6.7-GCCcore-11.3.0.eb, OpenJPEG-2.5.0-GCCcore-11.3.0.eb, OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb, pugixml-1.12.1-GCCcore-11.3.0.eb and patches: ASAP-2.1-libjpeg.patch, ASAP-2.1-pugixml.patch, ASAP-2.1-cmath.patch --- .../easyconfigs/a/ASAP/ASAP-2.1-cmath.patch | 12 +++ .../easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb | 72 ++++++++++++++ .../easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch | 35 +++++++ .../easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch | 52 ++++++++++ .../d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb | 56 +++++++++++ .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 44 +++++++++ .../OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 94 +++++++++++++++++++ .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 36 +++++++ .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb | 47 ++++++++++ ...enSlide-3.4.1-GCCcore-11.3.0-largefiles.eb | 56 +++++++++++ .../pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 29 ++++++ 11 files changed, 533 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch create mode 100644 easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb create mode 100644 easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch new file mode 100644 index 00000000000..b4ca984d421 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch @@ -0,0 +1,12 @@ +diff --git a/annotation/ImageScopeRepository.cpp b/annotation/ImageScopeRepository.cpp +index 6916a58..c135cb3 100644 +--- a/annotation/ImageScopeRepository.cpp ++++ b/annotation/ImageScopeRepository.cpp +@@ -9,6 +9,7 @@ + #include + #include "pugixml.hpp" + #include ++#include + + ImageScopeRepository::ImageScopeRepository(const std::shared_ptr& list) : + Repository(list), diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb new file mode 100644 index 00000000000..7dd82903d65 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb @@ -0,0 +1,72 @@ +easyblock = 'CMakeMake' + +name = 'ASAP' +version = '2.1' + +homepage = 'https://computationalpathologygroup.github.io/ASAP/' +description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface +for making annotations. It consists of two main components: an IO library for reading and writing +multi-resolution images and a viewer component for visualizing such images.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/computationalpathologygroup/%(name)s/archive'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'ASAP-2.1-libjpeg.patch', + 'ASAP-2.1-pugixml.patch', + 'ASAP-2.1-cmath.patch', +] +checksums = [ + '7ba9f39d09bada808f760c5dc9ac0cda0d221fd1393a0a3f9decfd6b5e913b3c', # ASAP-2.1.tar.gz + 'dbdf26324a7521b4beaa7ec2c0585f0816619cd73b3125efd313eb48c4813a43', # ASAP-2.1-libjpeg.patch + 'f578bb3ec4cbce573d4b9acd695eb55446592f4ac00551656a06f113ba09a9a7', # ASAP-2.1-pugixml.patch + 'e33d83853e0bd51113a886d0793504ce0abfb15fdf88410a19287d46fafd33c4', # ASAP-2.1-cmath.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +dependencies = [ + ('Boost', '1.79.0'), + ('Python', '3.10.4'), + ('OpenCV', '4.6.0', '-contrib'), + ('Qt5', '5.15.5'), + ('LibTIFF', '4.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('JasPer', '2.0.33'), + ('DCMTK', '3.6.7'), + ('SWIG', '4.0.2'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('pugixml', '1.12.1'), + ('zlib', '1.2.12'), +] + +configopts = " ".join([ + "-DOPENSLIDE_INCLUDE_DIR=$EBROOTOPENSLIDE/include/openslide", + "-DPugiXML_INCLUDE_DIR=$EBROOTPUGIXML/include", + "-DDCMTKJPEG_INCLUDE_DIR=$EBROOTDCMTK/include", + "-DWRAP_MULTIRESOLUTIONIMAGEINTERFACE_PYTHON=TRUE", + "-DBUILD_ASAP=TRUE", + "-DBUILD_EXECUTABLES=TRUE", + "-DBUILD_IMAGEPROCESSING=TRUE", + "-DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE", + "-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig" +]) + + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s', + 'bin/multiresolutionimageinterface.py', + 'lib/libmultiresolutionimageinterface.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +sanity_check_commands = ['python -c "import multiresolutionimageinterface"'] + +# ASAP installs its python interface in bin. Ugly, but we'll need to add it to PYTHONPATH +modextrapaths = {'PYTHONPATH': ['bin']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch new file mode 100644 index 00000000000..eeab7c05144 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch @@ -0,0 +1,35 @@ +diff --git a/multiresolutionimageinterface/VSIImage.cpp b/multiresolutionimageinterface/VSIImage.cpp +index 509bb18..1763201 100644 +--- a/multiresolutionimageinterface/VSIImage.cpp ++++ b/multiresolutionimageinterface/VSIImage.cpp +@@ -11,7 +11,7 @@ + // Include DCMTK LIBJPEG for lossy and lossless JPEG compression + extern "C" { + #define boolean ijg_boolean +-#include "dcmtk/dcmjpeg/libijg8/jpeglib8.h" ++#include "jpeglib.h" + #include "jpeg_mem_src.h" + #undef boolean + #undef const +@@ -234,7 +234,7 @@ char* VSIImage::decodeTile(int no, int row, int col) const { + jpeg_source_mgr src_mem; + jpeg_create_decompress(&cinfo); + cinfo.err = jpeg_std_error(&jerr); +- jpeg_mem_src(&cinfo, &src_mem, (void*)buf, size); ++ jpeg_mem_src_asap(&cinfo, &src_mem, (void*)buf, size); + jpeg_read_header(&cinfo, true); + if (_compressionType == 2) { + cinfo.jpeg_color_space = JCS_YCbCr; +diff --git a/multiresolutionimageinterface/jpeg_mem_src.h b/multiresolutionimageinterface/jpeg_mem_src.h +index b9b91e9..13b9040 100644 +--- a/multiresolutionimageinterface/jpeg_mem_src.h ++++ b/multiresolutionimageinterface/jpeg_mem_src.h +@@ -47,7 +47,7 @@ static void mem_skip_input_data( j_decompress_ptr cinfo, long num_bytes ) + } + } + +-static void jpeg_mem_src( j_decompress_ptr cinfo, jpeg_source_mgr * const src, void const * const buffer, long nbytes ) ++static void jpeg_mem_src_asap( j_decompress_ptr cinfo, jpeg_source_mgr * const src, void const * const buffer, long nbytes ) + { + src->init_source = mem_init_source; + src->fill_input_buffer = mem_fill_input_buffer; diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch new file mode 100644 index 00000000000..2b4a652369f --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch @@ -0,0 +1,52 @@ +diff --git a/annotation/CMakeLists.txt b/annotation/CMakeLists.txt +index 114babe..2156cd3 100644 +--- a/annotation/CMakeLists.txt ++++ b/annotation/CMakeLists.txt +@@ -25,10 +25,9 @@ set(ANNOTATION_SOURCE + ) + + add_library(annotation SHARED ${ANNOTATION_SOURCE} ${ANNOTATION_HEADERS}) +-target_compile_definitions(annotation PRIVATE "PUGIXML_HEADER_ONLY") + generate_export_header(annotation) + target_include_directories(annotation PUBLIC $ $ PRIVATE ${DIAGPathology_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR} ${Boost_INCLUDE_DIRS} ${PugiXML_INCLUDE_DIR}) +-target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface) ++target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface ${PUGIXML_LIBRARY}) + set_target_properties(annotation PROPERTIES DEBUG_POSTFIX _d) + + IF(APPLE) +diff --git a/cmakemodules/FindPugiXML.cmake b/cmakemodules/FindPugiXML.cmake +index ccffcc4..9afcfb4 100644 +--- a/cmakemodules/FindPugiXML.cmake ++++ b/cmakemodules/FindPugiXML.cmake +@@ -5,11 +5,12 @@ + # PugiXML_FOUND, If false, do not try to use PugiXML. + + find_path(PugiXML_INCLUDE_DIR pugixml.hpp) ++find_library(PUGIXML_LIBRARY NAMES pugixml) + + # handle the QUIETLY and REQUIRED arguments and set PugiXML_FOUND to TRUE if + # all listed variables are TRUE + include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake) + FIND_PACKAGE_HANDLE_STANDARD_ARGS(PugiXML +- REQUIRED_VARS PugiXML_INCLUDE_DIR) ++ REQUIRED_VARS PUGIXML_LIBRARY PugiXML_INCLUDE_DIR) + +-mark_as_advanced(PugiXML_INCLUDE_DIR) ++mark_as_advanced(PugiXML_INCLUDE_DIR PUGIXML_LIBRARY) +diff --git a/multiresolutionimageinterface/CMakeLists.txt b/multiresolutionimageinterface/CMakeLists.txt +index 132e6ef..8d24176 100644 +--- a/multiresolutionimageinterface/CMakeLists.txt ++++ b/multiresolutionimageinterface/CMakeLists.txt +@@ -87,11 +87,10 @@ endif(BUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT) + + add_library(multiresolutionimageinterface SHARED ${MULTIRESOLUTIONIMAGEINTERFACE_SRCS} ${MULTIRESOLUTIONIMAGEINTERFACE_HS} ${VSI_SOURCE_HS} ${VSI_SOURCE_SRCS}) + target_include_directories(multiresolutionimageinterface PUBLIC $ $ $ $ PRIVATE ${PugiXML_INCLUDE_DIR} ${TIFF_INCLUDE_DIR}) +-target_link_libraries(multiresolutionimageinterface PUBLIC core PRIVATE jpeg2kcodec libtiff) ++target_link_libraries(multiresolutionimageinterface PUBLIC core PRIVATE jpeg2kcodec libtiff ${PUGIXML_LIBRARY}) + IF(NOT WIN32) + target_link_libraries(multiresolutionimageinterface PRIVATE dl) + ENDIF(NOT WIN32) +-target_compile_definitions(multiresolutionimageinterface PRIVATE PUGIXML_HEADER_ONLY) + generate_export_header(multiresolutionimageinterface) + set_target_properties(multiresolutionimageinterface PROPERTIES DEBUG_POSTFIX _d) + diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6bffa6ad7b9 --- /dev/null +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'DCMTK' +version = '3.6.7' + +homepage = 'https://dicom.offis.de/dcmtk' +description = """DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. +It includes software for examining, constructing and converting DICOM image files, handling offline media, sending +and receiving images over a network connection, as well as demonstrative image storage and worklist servers.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +local_stripped_version = version.replace('.', '') + +source_urls = ['https://dicom.offis.de/download/%(namelower)s/dcmtk{}/'.format(local_stripped_version)] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.13'), + ('libiconv', '1.17'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=OFF', + '-DBUILD_SHARED_LIBS=ON' +] + + +sanity_check_paths = { + 'files': ['bin/dcmdump', 'bin/dcmj2pnm'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + 'dcmdata_tests | grep " 0 failed"', + 'dcmect_tests | grep " 0 failed"', + 'dcmfg_tests | grep " 0 failed"', + 'dcmiod_tests | grep " 0 failed"', + 'dcmnet_tests | grep " 0 failed"', + 'dcmrt_tests | grep " 0 failed"', + 'dcmseg_tests | grep " 0 failed"', + 'dcmsr_tests | grep " 0 failed"', + 'dcmtls_tests | grep " 0 failed"', + 'ofstd_tests | grep " 0 failed"', +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0c0b2fbef39 --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.2.4' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7bf5a8a28cc69bcfa8cb214f2c3095703c6b73ac5fba4d5480c205331d9494df'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + +sanity_check_paths = { + 'files': ( + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ), + 'dirs': ['lib/'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb new file mode 100644 index 00000000000..48f3aa8178e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -0,0 +1,94 @@ +name = 'OpenCV' +version = '4.6.0' +versionsuffix = '-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': SOURCELOWER_ZIP + }, + { + 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': '%(namelower)s_contrib-%(version)s.zip' + }, + { + 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', + 'extract_cmd': 'cp %s %(builddir)s' + }, +] +checksums = [ + '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip + '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), + ('FFmpeg', '5.0.1'), + ('freetype', '2.12.1'), + ('HarfBuzz', '4.2.1'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.4'), + ('OpenEXR', '3.1.5'), + ('JasPer', '2.0.33'), + ('Java', '11', '', True), + ('ant', '1.10.12', '-Java-%(javaver)s', True), + ('GLib', '2.72.1'), + ('GTK4', '4.7.0'), + ('HDF5', '1.12.2'), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = " ".join([ + "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DFREETYPE_FOUND=ON", + "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", + "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", + "-DHARFBUZZ_FOUND=ON", + "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", + "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", + "-DBUILD_opencv_python2=OFF", +]) + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (s, SHLIB_EXT) for s in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d607a01b64d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.5' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6c76dae7c5d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchenson Cancer Research Center Seattle WA +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.0' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb new file mode 100644 index 00000000000..b39f32e43c6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide' +version = '3.4.1' +versionsuffix = '-largefiles' + +homepage = 'https://openslide.org/' +description = """OpenSlide is a C library that provides a simple interface to +read whole-slide images (also known as virtual slides).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_large_file_support.patch'] +checksums = [ + # v3.4.1.tar.gz + 'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c', + # %(name)s-%(version_major_minor)s.1_large_file_support.patch + 'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c', +] + +builddependencies = [ + ('Autotools', '20220317'), + ('M4', '1.4.19'), + ('pkg-config', '0.29.2'), + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('OpenJPEG', '2.5.0'), + ('libxml2', '2.9.13'), + ('SQLite', '3.38.3'), + ('cairo', '1.17.4'), + ('Gdk-Pixbuf', '2.42.8'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': [ + 'bin/openslide-quickhash1sum', + 'bin/openslide-show-properties', + 'bin/openslide-write-png', + 'lib/libopenslide.la', + 'lib/libopenslide.%s' % SHLIB_EXT + ], + 'dirs': ['include/openslide'] +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1e32278858c --- /dev/null +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'pugixml' +version = '1.12.1' + +homepage = 'https://pugixml.org/' +description = "pugixml is a light-weight C++ XML processing library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/zeux/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version_major_minor)s.4_pugixml_remove_headeronly.patch'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = "-DBUILD_SHARED_AND_STATIC_LIBS=ON -DPUGIXML_HEADER_ONLY=True " + + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib'], +} + +moduleclass = 'data' From edccc61548f18e5fa1076fc6f39a62627e3150a8 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 28 Sep 2022 13:35:17 +0200 Subject: [PATCH 4946/9987] deleted OpenCV ec and its deps --- .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 44 --------- .../OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 94 ------------------- .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 36 ------- 3 files changed, 174 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb delete mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb deleted file mode 100644 index 0c0b2fbef39..00000000000 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libwebp' -version = '1.2.4' - -homepage = 'https://developers.google.com/speed/webp/' -description = """WebP is a modern image format that provides superior -lossless and lossy compression for images on the web. Using WebP, -webmasters and web developers can create smaller, richer images that -make the web faster.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['7bf5a8a28cc69bcfa8cb214f2c3095703c6b73ac5fba4d5480c205331d9494df'] - -builddependencies = [ - ('binutils', '2.38'), -] -dependencies = [ - ('libjpeg-turbo', '2.1.3'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.3.0'), - ('giflib', '5.2.1'), -] - -configopts = '--enable-libwebpmux' - -local_headers, local_libs = ( - ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], - ['webp', 'webpdemux', 'webpmux'] -) - -sanity_check_paths = { - 'files': ( - ['include/webp/%s' % h for h in local_headers] + - ['lib/lib%s.a' % s for s in local_libs] + - ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] - ), - 'dirs': ['lib/'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb deleted file mode 100644 index 48f3aa8178e..00000000000 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ /dev/null @@ -1,94 +0,0 @@ -name = 'OpenCV' -version = '4.6.0' -versionsuffix = '-contrib' - -# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake -local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' - -homepage = 'https://opencv.org/' -description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision - and machine learning software library. OpenCV was built to provide - a common infrastructure for computer vision applications and to accelerate - the use of machine perception in the commercial products. - Includes extra modules for OpenCV from the contrib repository.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -sources = [ - { - 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], - 'download_filename': '%(version)s.zip', - 'filename': SOURCELOWER_ZIP - }, - { - 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], - 'download_filename': '%(version)s.zip', - 'filename': '%(namelower)s_contrib-%(version)s.zip' - }, - { - 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], - 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', - 'extract_cmd': 'cp %s %(builddir)s' - }, -] -checksums = [ - '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip - '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip - '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz -] - -builddependencies = [ - ('CMake', '3.23.1'), -] -dependencies = [ - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('zlib', '1.2.12'), - ('FFmpeg', '5.0.1'), - ('freetype', '2.12.1'), - ('HarfBuzz', '4.2.1'), - ('libjpeg-turbo', '2.1.3'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.3.0'), - ('libwebp', '1.2.4'), - ('OpenEXR', '3.1.5'), - ('JasPer', '2.0.33'), - ('Java', '11', '', True), - ('ant', '1.10.12', '-Java-%(javaver)s', True), - ('GLib', '2.72.1'), - ('GTK4', '4.7.0'), - ('HDF5', '1.12.2'), -] - -# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz -# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 -configopts = " ".join([ - "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", - "-DFREETYPE_FOUND=ON", - "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", - "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", - "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", - "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", - "-DHARFBUZZ_FOUND=ON", - "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", - "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", - "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", - "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", - "-DBUILD_opencv_python2=OFF", -]) - -enhance_sanity_check = True - -local_contrib_libs = [ - 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', - 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', - 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', - 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' -] - -sanity_check_paths = { - 'files': ['lib64/libopencv_%s.%s' % (s, SHLIB_EXT) for s in local_contrib_libs], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb deleted file mode 100644 index d607a01b64d..00000000000 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenEXR' -version = '3.1.5' - -homepage = 'https://www.openexr.com/' -description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic - for use in computer imaging applications""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] - -builddependencies = [ - ('binutils', '2.38'), - ('CMake', '3.23.1'), -] - -configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' - -local_libs, local_bins = [ - ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil'], - ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] -] - -sanity_check_paths = { - 'files': ( - ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + - ['bin/exr%s' % b for b in local_bins] - ), - 'dirs': ['include/%(name)s', 'share'], -} - -moduleclass = 'vis' From ce611aa982d47c19d0f078bf2a13f8ac80ddeaa7 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 28 Sep 2022 14:41:18 +0200 Subject: [PATCH 4947/9987] removed pugixml header only --- .../p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb index 1e32278858c..1cf51118427 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -9,21 +9,24 @@ description = "pugixml is a light-weight C++ XML processing library" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://github.com/zeux/%(name)s/archive/'] +source_urls = ['https://github.com/zeux/pugixml/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version_major_minor)s.4_pugixml_remove_headeronly.patch'] +checksums = ['1e28ab24b6e04e013d96f45d25e9f2d04c921dc68c613fd010ecaaad3892c14d'] builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), ] -configopts = "-DBUILD_SHARED_AND_STATIC_LIBS=ON -DPUGIXML_HEADER_ONLY=True " - +configopts = " ".join([ + "-DBUILD_SHARED_LIBS=ON", + "-DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON", +]) sanity_check_paths = { - 'files': [], - 'dirs': ['lib'], + 'files': ['include/pugiconfig.hpp', 'include/pugixml.hpp', 'lib/libpugixml.a', + 'lib/libpugixml.%s' % SHLIB_EXT, 'lib/pkgconfig/pugixml.pc'], + 'dirs': ['lib/cmake/pugixml'], } moduleclass = 'data' From dc6b25696beda3085bcbde7a6d7d741162ab7a3d Mon Sep 17 00:00:00 2001 From: Jef Scheepers Date: Wed, 28 Sep 2022 16:02:03 +0200 Subject: [PATCH 4948/9987] add new python-irodsclient easyconfig --- ...python-irodsclient-1.1.4-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100755 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-10.3.0.eb new file mode 100755 index 00000000000..136c97d177d --- /dev/null +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-1.1.4-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'python-irodsclient' +version = '1.1.4' + +homepage = 'https://github.com/irods/python-irodsclient' +description = "A python API for iRODS" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('prettytable', '3.3.0', { + 'checksums': ['118eb54fd2794049b810893653b20952349df6d3bc1764e7facd8a18064fa9b0'], + }), + (name, version, { + 'modulename': 'irods', + 'checksums': ['f427699739911042dc35a7fbd92f7ba87db9fad3977423c2fa2ab61a0ffebe43'], + }), +] + +moduleclass = 'lib' From 5b9ad1f5ecd5dae77dcbc1b351f87b3174e93b9b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 28 Sep 2022 16:30:17 +0200 Subject: [PATCH 4949/9987] adding easyconfigs: netCDF-4.9.0-iimpi-2022a.eb, netcdf4-python-1.6.1-foss-2022a.eb, netcdf4-python-1.6.1-intel-2022a.eb, xarray-2022.6.0-foss-2022a.eb, xarray-2022.6.0-intel-2022a.eb, ArviZ-0.12.1-foss-2022a.eb, ArviZ-0.12.1-intel-2022a.eb --- .../a/ArviZ/ArviZ-0.12.1-foss-2022a.eb | 34 +++++++++++++ .../a/ArviZ/ArviZ-0.12.1-intel-2022a.eb | 34 +++++++++++++ .../n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 50 ++++++++++++++++++ .../netcdf4-python-1.6.1-foss-2022a.eb | 51 +++++++++++++++++++ .../netcdf4-python-1.6.1-intel-2022a.eb | 51 +++++++++++++++++++ .../x/xarray/xarray-2022.6.0-foss-2022a.eb | 25 +++++++++ .../x/xarray/xarray-2022.6.0-intel-2022a.eb | 25 +++++++++ 7 files changed, 270 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb new file mode 100644 index 00000000000..bc9c93cbf77 --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'ArviZ' +version = '0.12.1' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy, scipy, pandas + ('netcdf4-python', '1.6.1'), + ('xarray', '2022.6.0'), + ('matplotlib', '3.5.2'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('xarray-einstats', '0.3.0', { + 'checksums': ['81217c145218479327469f1669f34763b7e149ed6789fd596cc90ff2d772098e'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['57d80eacc51909f18e6ab63c96a6b02227c3b077c5ffa406d5f4dabe03b8f019'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb new file mode 100644 index 00000000000..ac8ac445dc2 --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'ArviZ' +version = '0.12.1' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy, scipy, pandas + ('netcdf4-python', '1.6.1'), + ('xarray', '2022.6.0'), + ('matplotlib', '3.5.2'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('xarray-einstats', '0.3.0', { + 'checksums': ['81217c145218479327469f1669f34763b7e149ed6789fd596cc90ff2d772098e'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['57d80eacc51909f18e6ab63c96a6b02227c3b077c5ffa406d5f4dabe03b8f019'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb new file mode 100644 index 00000000000..182023f4691 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -0,0 +1,50 @@ +name = 'netCDF' +version = '4.9.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-%(version)s_fix-lib-name.patch', + 'netCDF-%(version)s_fix-linking-errors.patch', + 'netCDF-%(version)s_skip-nasa-test.patch', +] +checksums = [ + '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz + 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch + '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a', # netCDF-4.9.0_skip-nasa-test.patch +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('HDF5', '1.12.2'), + ('cURL', '7.83.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.2'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb new file mode 100644 index 00000000000..e4909b8b62d --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('netCDF', '4.9.0'), + ('cURL', '7.83.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb new file mode 100644 index 00000000000..60eb9cd8eef --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('netCDF', '4.9.0'), + ('cURL', '7.83.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + (name, version, { + 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb new file mode 100644 index 00000000000..6b557c9ef71 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '2022.6.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1028d198493f66bb15bd35dcfdd11defd831cbee3af6589fff16f41bddd67e84'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb new file mode 100644 index 00000000000..a0756e083cc --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '2022.6.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1028d198493f66bb15bd35dcfdd11defd831cbee3af6589fff16f41bddd67e84'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From de07c62b780e3c92d11971d7c9473b743f802846 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 28 Sep 2022 16:51:44 +0200 Subject: [PATCH 4950/9987] ArviZ v0.12.1 - Remove download_dep_fail --- easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb | 1 - easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb index bc9c93cbf77..12bc8838f20 100644 --- a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb @@ -16,7 +16,6 @@ dependencies = [ ('matplotlib', '3.5.2'), ] -download_dep_fail = True use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb index ac8ac445dc2..365dbb5575c 100644 --- a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb @@ -16,7 +16,6 @@ dependencies = [ ('matplotlib', '3.5.2'), ] -download_dep_fail = True use_pip = True exts_list = [ From 027a0140f1294c748a86b1b8c4c2da00a4df0bf5 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 28 Sep 2022 13:30:06 -0700 Subject: [PATCH 4951/9987] add sanity_check_commands --- easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb index c541f370006..050b60477d2 100644 --- a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb @@ -64,4 +64,5 @@ sanity_check_paths = { 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'], } +sanity_check_commands = ['agat_convert_bed2gff.pl --help'] moduleclass = 'bio' From 5a9f694e58c90ad77db9fa3e3c3c161f8194ad03 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 28 Sep 2022 13:44:10 -0700 Subject: [PATCH 4952/9987] fix line to long --- test/easyconfigs/easyconfigs.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 5a2a62e69c1..095300b7ae2 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -495,7 +495,10 @@ def check_dep_vars(self, gen, dep, dep_vars): 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x and v3.0.0 require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) - 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'ncbi-vdb-3\.0\.0', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], + 'HDF5': [ + (r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'ncbi-vdb-3\.0\.0', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', + r'shovill-1\.1\.']), + ], # VMTK 1.4.x requires ITK 4.13.x 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) From 72863ee57b6b3bbacd0c63382fbec3d29afe2dc4 Mon Sep 17 00:00:00 2001 From: adam Date: Thu, 29 Sep 2022 10:55:00 +0100 Subject: [PATCH 4953/9987] adding easyconfigs: pairsnp-0.0.7-foss-2021a.eb --- .../p/pairsnp/pairsnp-0.0.7-foss-2021a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/pairsnp/pairsnp-0.0.7-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pairsnp/pairsnp-0.0.7-foss-2021a.eb b/easybuild/easyconfigs/p/pairsnp/pairsnp-0.0.7-foss-2021a.eb new file mode 100644 index 00000000000..faf81064d4d --- /dev/null +++ b/easybuild/easyconfigs/p/pairsnp/pairsnp-0.0.7-foss-2021a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'pairsnp' +version = '0.0.7' + +homepage = 'https://github.com/gtonkinhill/pairsnp' +description = """ + A set of scripts for very quickly obtaining pairwise SNP distance matrices from multiple sequence alignments + using sparse matrix libraries to improve performance. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['591f395c59d91056882f0b349c201b2d708a093d6b6ffd3c2ee34aed8767ee98'] + +sanity_check_commands = ['pairsnp -h'] + +moduleclass = 'bio' From 7d10f04b86bd69104f1c8b2a7f24e7bf00974279 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Thu, 29 Sep 2022 12:39:38 +0200 Subject: [PATCH 4954/9987] Update GPAW to 2022a toolchains and fix incompatibilites between ASE and other packages in said tool chain. --- ....22.1-Compatibility-with-Flask-2-2-2.patch | 26 ++++++++ ...2.1-Compatibility-with-Scipy-2022-05.patch | 66 +++++++++++++++++++ ...ibility-with-pytest-from-Python-3-10.patch | 53 +++++++++++++++ ...2.1-Compatibility-with-pytest-part-2.patch | 25 +++++++ .../a/ASE/ASE-3.22.1-foss-2022a.eb | 18 ++++- .../a/ASE/ASE-3.22.1-intel-2022a.eb | 63 ++++++++++++++++++ .../g/GPAW/GPAW-22.8.0-foss-2022a.eb | 50 ++++++++++++++ .../g/GPAW/GPAW-22.8.0-intel-2022a.eb | 49 ++++++++++++++ .../l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb | 27 ++++++++ 9 files changed, 376 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-part-2.patch create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2022a.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb create mode 100644 easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch new file mode 100644 index 00000000000..003c76ba96d --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch @@ -0,0 +1,26 @@ +From b0ac97556b7f973392fd7610bf39d112093230b3 Mon Sep 17 00:00:00 2001 +From: Jakob Schiotz +Date: Mon, 26 Sep 2022 10:19:45 +0200 +Subject: [PATCH] Fix test suite to work with newer versions of Flask (2.2.2) + +--- + ase/test/db/test_db_web.py | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/ase/test/db/test_db_web.py b/ase/test/db/test_db_web.py +index 8cea28e..73ec70c 100644 +--- a/ase/test/db/test_db_web.py ++++ b/ase/test/db/test_db_web.py +@@ -66,7 +66,8 @@ def test_add_columns(database): + + + def test_favicon(client): +- assert client.get('/favicon.ico').status_code == 308 # redirect ++ # no content or redirect ++ assert client.get('/favicon.ico').status_code in (204, 308) + assert client.get('/favicon.ico/').status_code == 204 # no content + + +-- +1.8.3.1 + diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch new file mode 100644 index 00000000000..7abbd939ea5 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch @@ -0,0 +1,66 @@ +From ead1bd015b52e60cab729081d7c1da2951f1f95c Mon Sep 17 00:00:00 2001 +From: Ask Hjorth Larsen +Date: Sat, 16 Jul 2022 12:48:01 +0200 +Subject: [PATCH] remove test which compares our units to scipy codata. All + the surrounding modules/methods in scipy seem to be deprecated + +--- + ase/test/test_units.py | 39 +-------------------------------------- + 1 file changed, 1 insertion(+), 38 deletions(-) + +diff --git a/ase/test/test_units.py b/ase/test/test_units.py +index b8a1293..fcbe451 100644 +--- a/ase/test/test_units.py ++++ b/ase/test/test_units.py +@@ -2,47 +2,10 @@ + implementation that SciPy brings with it. + """ + +-import numpy as np + import pytest + + import ase.units +-from ase.units import CODATA, create_units +-import scipy.constants.codata +- +- +-# Scipy lacks data for some of the codata versions: +-codata_scipy_versions = set(CODATA) - {'1998', '1986'} +- +- +-@pytest.mark.parametrize('version', sorted(codata_scipy_versions)) +-def test_units(version): +- name_map = {'_c': 'speed of light in vacuum', +- '_mu0': 'mag. const.', +- '_Grav': 'Newtonian constant of gravitation', +- '_hplanck': 'Planck constant', +- '_e': 'elementary charge', +- '_me': 'electron mass', +- '_mp': 'proton mass', +- '_Nav': 'Avogadro constant', +- '_k': 'Boltzmann constant', +- '_amu': 'atomic mass unit-kilogram relationship'} +- +- scipy_CODATA = getattr(scipy.constants.codata, +- f'_physical_constants_{version}', None) +- if version == '2018' and scipy_CODATA is None: +- pytest.skip('No CODATA for 2018 with this scipy') +- +- assert scipy_CODATA is not None +- +- for asename, scipyname in name_map.items(): +- aseval = CODATA[version][asename] +- try: +- scipyval = scipy_CODATA[scipyname][0] +- except KeyError: +- # XXX Can we be more specific? +- continue # 2002 in scipy contains too little data +- +- assert np.isclose(aseval, scipyval), scipyname ++from ase.units import create_units + + + def test_create_units(): +-- +1.8.3.1 + diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch new file mode 100644 index 00000000000..c73f65f4396 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch @@ -0,0 +1,53 @@ +From c0d155a34dd4115c0aa1c16bb218d808ddfcbbeb Mon Sep 17 00:00:00 2001 +From: Ask Hjorth Larsen +Date: Fri, 4 Feb 2022 14:36:13 +0100 +Subject: [PATCH] update warning handling to appease old and new pytest + simultaneously + +--- + ase/test/test_imports.py | 26 ++++++++++++++------------ + 1 file changed, 14 insertions(+), 12 deletions(-) + +diff --git a/ase/test/test_imports.py b/ase/test/test_imports.py +index 5267a06..93c3bfa 100644 +--- a/ase/test/test_imports.py ++++ b/ase/test/test_imports.py +@@ -1,3 +1,4 @@ ++import contextlib + from pathlib import Path + from importlib import import_module + from numpy import VisibleDeprecationWarning +@@ -58,17 +59,18 @@ newpy_only_modules = { + @pytest.mark.filterwarnings('ignore:Moved to') + def test_imports(): + for module in all_modules: +- if module in deprecated_modules: +- warning = (DeprecationWarning, VisibleDeprecationWarning) +- else: +- warning = None ++ with contextlib.ExitStack() as ignored_warnings: ++ if module in deprecated_modules: ++ ignored_warnings.enter_context( ++ pytest.warns((DeprecationWarning, ++ VisibleDeprecationWarning))) + +- try: +- with pytest.warns(warning): ++ try: + import_module(module) +- except SyntaxError: +- if module not in newpy_only_modules: +- raise +- except ImportError as err: +- if err.name not in ignore_imports and 'deprecated' not in str(err): +- raise ++ except SyntaxError: ++ if module not in newpy_only_modules: ++ raise ++ except ImportError as err: ++ ok = err.name in ignore_imports or 'deprecated' in str(err) ++ if not ok: ++ raise +-- +1.8.3.1 + diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-part-2.patch b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-part-2.patch new file mode 100644 index 00000000000..0eb432bf558 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-Compatibility-with-pytest-part-2.patch @@ -0,0 +1,25 @@ +From 74dba1a8cfe4ee79c1436bdcf0195b79e7c5536e Mon Sep 17 00:00:00 2001 +From: Ask Hjorth Larsen +Date: Fri, 4 Feb 2022 14:41:38 +0100 +Subject: [PATCH] update pytest.warns() call to latest pytest + +--- + ase/test/calculator/castep/test_castep_interface.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/ase/test/calculator/castep/test_castep_interface.py b/ase/test/calculator/castep/test_castep_interface.py +index 623836b..08c72c6 100644 +--- a/ase/test/calculator/castep/test_castep_interface.py ++++ b/ase/test/calculator/castep/test_castep_interface.py +@@ -121,7 +121,7 @@ def test_fundamental_params(): + + # Test special parsers + mock_cparam.continuation = 'default' +- with pytest.warns(None): ++ with pytest.warns(UserWarning): + mock_cparam.reuse = 'default' + assert mock_cparam.reuse.value is None + +-- +1.8.3.1 + diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb index 98481085f40..c5a508e2a0d 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022a.eb @@ -29,7 +29,23 @@ exts_list = [ 'checksums': ['77f03f4554392558700295e05aed0b1096a20d4a60a4f3ddcde58b0c31c8fca2'], }), ('ase', version, { - 'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'], + 'patches': [ + 'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch', + 'ASE-3.22.1-Compatibility-with-pytest-part-2.patch', + 'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch', + 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', + ], + 'checksums': [ + '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432', # ase-3.22.1.tar.gz + # ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch + '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac', + # ASE-3.22.1-Compatibility-with-pytest-part-2.patch + '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601', + # ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch + 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8', + # ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch + '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d', + ], }), ('ase-ext', '20.9.0', { 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2022a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2022a.eb new file mode 100644 index 00000000000..6862f915f93 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-intel-2022a.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Flask', '2.2.2'), + ('matplotlib', '3.5.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.0.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.8.2', { + 'checksums': ['77f03f4554392558700295e05aed0b1096a20d4a60a4f3ddcde58b0c31c8fca2'], + }), + ('ase', version, { + 'patches': [ + 'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch', + 'ASE-3.22.1-Compatibility-with-pytest-part-2.patch', + 'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch', + 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', + ], + 'checksums': [ + '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432', # ase-3.22.1.tar.gz + # ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch + '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac', + # ASE-3.22.1-Compatibility-with-pytest-part-2.patch + '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601', + # ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch + 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8', + # ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch + '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d', + ], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb new file mode 100644 index 00000000000..b400a2bd2c3 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb @@ -0,0 +1,50 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '22.8.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), + ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), +] +checksums = [ + '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', + '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ASE', '3.22.1'), + ('libxc', '5.2.3'), + ('libvdwxc', '0.4.0'), + ('PyYAML', '6.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb new file mode 100644 index 00000000000..58087303e00 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb @@ -0,0 +1,49 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '22.8.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), + ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), +] +checksums = [ + '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz + # GPAW-20.1.0-Add-Easybuild-configuration-files.patch + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', + '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ASE', '3.22.1'), + ('libxc', '5.2.3'), + ('PyYAML', '6.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb new file mode 100644 index 00000000000..b1785ef119b --- /dev/null +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +homepage = 'https://libvdwxc.org' +description = """libvdwxc is a general library for evaluating energy and potential for +exchange-correlation (XC) functionals from the vdW-DF family that can be used with various +of density functional theory (DFT) codes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] + +preconfigopts = 'unset CC && unset FC && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', + 'libvdwxc_q0test', 'libvdwxc_q0test2']] + + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] + for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'chem' From c216f1e617e3e1e2921c20b1ba2d38a32362d97b Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 29 Sep 2022 12:11:01 +0100 Subject: [PATCH 4955/9987] adding easyconfigs: TRUST4-1.0.7-GCC-11.3.0.eb --- .../t/TRUST4/TRUST4-1.0.7-GCC-11.3.0.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.7-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.7-GCC-11.3.0.eb b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.7-GCC-11.3.0.eb new file mode 100644 index 00000000000..e0aa3914a2d --- /dev/null +++ b/easybuild/easyconfigs/t/TRUST4/TRUST4-1.0.7-GCC-11.3.0.eb @@ -0,0 +1,71 @@ +easyblock = 'MakeCp' + +name = 'TRUST4' +version = '1.0.7' + +homepage = 'https://github.com/liulab-dfci/TRUST4' +description = """Tcr Receptor Utilities for Solid Tissue (TRUST) is a +computational tool to analyze TCR and BCR sequences using unselected RNA +sequencing data, profiled from solid tissues, including tumors. TRUST4 performs +de novo assembly on V, J, C genes including the hypervariable +complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR +sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to +report the corresponding information. TRUST4 supports both single-end and +paired-end sequencing data with any read length.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'liulab-dfci' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['633cab6ef0fa082012ce6a185e818b5454ef16576e9a165f268d69335b3aef5f'] + +# TRUST4 uses an old API of SAMtools and links agains libbam.a, that has been +# removed in SAMtools 1.14 (https://github.com/liulab-dfci/TRUST4/issues/95). +# For this reason, we use the SAMtools bundled by TRUST4. +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), +] + +# Fix the wrong version in run-trust4 +prebuildopts = 'sed -i "s/v1.0.6/v1.0.7/" run-trust4 && ' + +local_binaries = [ + 'run-trust4', 'trust4', 'bam-extractor', 'fastq-extractor', 'annotator', + 'BuildDatabaseFa.pl', 'BuildImgtAnnot.pl', 'BuildImgtVquestAnnot.pl', + 'FilterAnnotatedAssembly.pl', 'trust-airr.pl', 'trust-barcoderep.pl', + 'trust-simplerep.pl', 'trust-smartseq.pl', +] +local_scripts = [ + 'AddSequenceToCDR3File.pl', 'barcoderep-filter.py', 'GetFullLengthAssembly.pl', + 'trust-barcoderep-to-10X.pl', 'trust-cluster.py', 'trust-stats.py' +] +files_to_copy = [ + (local_binaries, 'bin'), + (['scripts/%s' % x for x in local_scripts], 'bin'), +] + +fix_perl_shebang_for = ['bin/*.pl'] +fix_python_shebang_for = ['bin/*.py'] + +postinstallcmds = ["chmod a+x %(installdir)s/bin/*"] + +sanity_check_paths = { + 'files': ['bin/' + x for x in local_binaries + local_scripts], + 'dirs': [], +} + +sanity_check_commands = [ + "run-trust4 2>&1 | grep 'TRUST4 v%(version)s'", + "BuildDatabaseFa.pl 2>&1 | grep 'usage: perl BuildDatabaseFa.pl'", + "trust-cluster.py 2>&1 | grep 'usage: a.py trust_cdr3.out'", + "cd %(builddir)s/%(name)s-%(version)s && " + "run-trust4 -b example/example.bam -f hg38_bcrtcr.fa --ref human_IMGT+C.fa && " + "test -f example/TRUST_example_report.tsv" +] + +moduleclass = 'bio' From 25a2b32b7906257593ad1239ead671134dfeecae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 29 Sep 2022 12:13:00 +0000 Subject: [PATCH 4956/9987] adding easyconfigs: xprop-1.2.5-GCCcore-11.3.0.eb, FLTK-1.3.8-GCCcore-11.3.0.eb --- .../f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ .../x/xprop/xprop-1.2.5-GCCcore-11.3.0.eb | 32 ++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..899952c376c --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.8' + +homepage = 'https://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-1.3.6_fix-LDFLAGS.patch'] +checksums = [ + '5d2ccb7ad94e595d3d97509c7a931554e059dd970b7b29e6fd84cb70fd5491c6', # fltk-1.3.7-source.tar.gz + 'f8af2414a1ee193a186b0d98d1e3567add0ee003f44ec64dce2ce2dfd6d95ebf', # FLTK-1.3.6_fix-LDFLAGS.patch +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +builddependencies = [ + ('binutils', '2.38'), + ('groff', '1.22.4'), +] + +dependencies = [ + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('xprop', '1.2.5'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2d806a829fc --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.5' + +homepage = "https://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftp.x.org/archive/individual/app/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b7bf6b6be6cf23e7966a153fc84d5901c14f01ee952fbd9d930aa48e2385d670'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('X11', '20220504'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' From bce9138539e26dbf0fee3675888d7d09b28352b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 29 Sep 2022 12:16:38 +0000 Subject: [PATCH 4957/9987] Fix checksum --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb index 899952c376c..602304596e1 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-11.3.0.eb @@ -15,7 +15,7 @@ source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] sources = ['%(namelower)s-%(version)s-source.tar.gz'] patches = ['FLTK-1.3.6_fix-LDFLAGS.patch'] checksums = [ - '5d2ccb7ad94e595d3d97509c7a931554e059dd970b7b29e6fd84cb70fd5491c6', # fltk-1.3.7-source.tar.gz + 'f3c1102b07eb0e7a50538f9fc9037c18387165bc70d4b626e94ab725b9d4d1bf', # fltk-1.3.8-source.tar.gz 'f8af2414a1ee193a186b0d98d1e3567add0ee003f44ec64dce2ce2dfd6d95ebf', # FLTK-1.3.6_fix-LDFLAGS.patch ] From 1f55c6c6bfa6025d6daa1ac4ce6cea53e0aee36e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Sep 2022 14:28:32 +0200 Subject: [PATCH 4958/9987] adding easyconfigs: Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb --- .../Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..9fc1ae2e8bb --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb @@ -0,0 +1,62 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '7.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['98dea497982001fb82da3429ca55669b2917a0858c71abe2cfe7cd113381f1f7'] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('UCX-CUDA', '1.10.0', versionsuffix), + ('CubeLib', '4.6'), + ('CubeWriter', '4.6'), + ('libunwind', '1.4.0'), + ('OPARI2', '2.0.6'), + ('OTF2', '2.3'), + # Hardware counter support (optional): + ('PAPI', '6.0.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 111fe5fa6e1222ce5ffd0bac9578824c0aefaab1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 29 Sep 2022 12:45:06 +0000 Subject: [PATCH 4959/9987] adding easyconfigs: POV-Ray-3.7.0.10-GCC-11.3.0.eb --- .../p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb new file mode 100644 index 00000000000..04c5b90e972 --- /dev/null +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb @@ -0,0 +1,63 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'POV-Ray' +version = '3.7.0.10' + +homepage = 'https://www.povray.org/' +description = """The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program + which generates images from a text-based scene description, and is available for a variety + of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning + three-dimensional graphics. The source code is available for those wanting to do their own ports.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/POV-Ray/povray/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['POV-Ray-3.7.0.7_dont-touch-home.patch'] +checksums = [ + '7bee83d9296b98b7956eb94210cf30aa5c1bbeada8ef6b93bb52228bbc83abff', # v3.7.0.10.tar.gz + '45103afca808e279dcdee80194c65e2a760c76d011d351392a46e817b0b655f7', # POV-Ray-3.7.0.7_dont-touch-home.patch +] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('X11', '20220504'), + ('LibTIFF', '4.3.0'), + ('SDL2', '2.0.22'), +] + +preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " +preconfigopts += " ./prebuild.sh && cd .. && " +configopts = "COMPILED_BY='EasyBuild' " +configopts += "--with-boost=$EBROOTBOOST --with-zlib=$EBROOTZLIB --with-libpng=$EBROOTLIBPNG " +configopts += "--with-libtiff=$EBROOTLIBTIFF --with-libjpeg=$EBROOTLIBJPEGMINTURBO --with-libsdl=$EBROOTSDL2 " +# configopts += " --with-libmkl=DIR " ## upstream needs to fix this, still in BETA + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/povray'], + 'dirs': ['etc/povray/%(version_major_minor)s', 'share'] +} + +moduleclass = 'vis' From de74f8c244d5bd864c589857e93aee80f2293ff5 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 29 Sep 2022 14:47:44 +0200 Subject: [PATCH 4960/9987] adding easyconfigs: Infernal-1.1.4-foss-2021a.eb --- .../i/Infernal/Infernal-1.1.4-foss-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb new file mode 100644 index 00000000000..2f490f5de24 --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: BSD +# Updated:: Denis Kristak (INUITS) +# Updated:: Sebastien Moretti (SIB) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.4" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' From 3e4ecf15507a771836c618b547cd43f42463f47e Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 29 Sep 2022 16:27:34 +0200 Subject: [PATCH 4961/9987] OpenEXR updated: Imath detached, zlib added --- .../i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 6 +++- 2 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b4f0f0223ca --- /dev/null +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Imath' +version = '3.1.5' + +homepage = 'https://imath.readthedocs.io/en/latest/' +description = """ +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +sources = [{ + 'filename': '%(name)s_v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/AcademySoftwareFoundation', + 'repo_name': '%(name)s', + 'tag': 'v%(version)s', + }, +}] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/libImath.%s' % SHLIB_EXT], + 'dirs': ['include/Imath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index d607a01b64d..2e44695eb49 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -17,11 +17,15 @@ builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), ] +dependencies = [ + ('Imath', '3.1.5'), + ('zlib', '1.2.12') +] configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' local_libs, local_bins = [ - ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil'], + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] ] From 459784bb605832a2a69d53c4e2bf809fa8dca508 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 29 Sep 2022 16:32:12 +0200 Subject: [PATCH 4962/9987] OpenEXR updated: removed stray configopt --- easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb index 2e44695eb49..d85c1503e24 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -22,8 +22,6 @@ dependencies = [ ('zlib', '1.2.12') ] -configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' - local_libs, local_bins = [ ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] From 1ae7ca64ec4bf84bc8e8e914c6e91ed48b28b2b0 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 29 Sep 2022 17:15:46 +0200 Subject: [PATCH 4963/9987] Increase the number of allowed test failures, as with https://github.com/easybuilders/easybuild-easyblocks/pull/2794 we'll actually start counting failing tests, instead of failing test suites. Thus, much higher numbers can be expected, since many test suites have multiple failing tests --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index 9a48694ea1f..0840f2a441b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -112,8 +112,8 @@ excluded_tests = { runtest = "cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s" # several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), -# so we allow up to 20 (out of ~90k) tests to fail before treating the installation to be faulty -max_failed_tests = 20 +# so we allow up to 400 (out of ~90k) tests to fail before treating the installation to be faulty +max_failed_tests = 400 # The readelf sanity check command can be taken out once the TestRPATH test from # https://github.com/pytorch/pytorch/pull/68912 is accepted, since it is then checked as part of the PyTorch test suite From 407fb92fc7e89c2d7daf5a42748029410ccb79fc Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 29 Sep 2022 17:17:00 +0200 Subject: [PATCH 4964/9987] Changed moduleclass to 'ai' --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index 0840f2a441b..64343b457dc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -124,4 +124,4 @@ sanity_check_commands = [ tests = ['%(name)s-check-cpp-extension.py'] -moduleclass = 'devel' +moduleclass = 'ai' From 7b72fe8a83006b85204350f18210a0212627a9b7 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 29 Sep 2022 17:25:19 +0200 Subject: [PATCH 4965/9987] DCMTK added hash, pugixml fixed E121 --- .../d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb | 13 +++---------- .../p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 13 +++++++++---- 2 files changed, 12 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb index 6bffa6ad7b9..5d7107ed091 100644 --- a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb @@ -15,6 +15,7 @@ local_stripped_version = version.replace('.', '') source_urls = ['https://dicom.offis.de/download/%(namelower)s/dcmtk{}/'.format(local_stripped_version)] sources = [SOURCELOWER_TAR_GZ] +checksums = ['7c58298e3e8d60232ee6fc8408cfadd14463cc11a3c4ca4c59af5988c7e9710a'] builddependencies = [ ('binutils', '2.38'), @@ -40,17 +41,9 @@ sanity_check_paths = { 'dirs': ['lib'], } +local_test_modules = ['dcmdata', 'dcmect', 'dcmfg', 'dcmiod', 'dcmnet', 'dcmrt', 'dcmseg', 'dcmsr', 'dcmtls', 'ofstd'] sanity_check_commands = [ - 'dcmdata_tests | grep " 0 failed"', - 'dcmect_tests | grep " 0 failed"', - 'dcmfg_tests | grep " 0 failed"', - 'dcmiod_tests | grep " 0 failed"', - 'dcmnet_tests | grep " 0 failed"', - 'dcmrt_tests | grep " 0 failed"', - 'dcmseg_tests | grep " 0 failed"', - 'dcmsr_tests | grep " 0 failed"', - 'dcmtls_tests | grep " 0 failed"', - 'ofstd_tests | grep " 0 failed"', + '%s_tests | grep " 0 failed"' % s for s in local_test_modules ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb index 1cf51118427..c171baaaab1 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -19,13 +19,18 @@ builddependencies = [ ] configopts = " ".join([ - "-DBUILD_SHARED_LIBS=ON", - "-DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON", + "-DBUILD_SHARED_LIBS=ON", + "-DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON", ]) sanity_check_paths = { - 'files': ['include/pugiconfig.hpp', 'include/pugixml.hpp', 'lib/libpugixml.a', - 'lib/libpugixml.%s' % SHLIB_EXT, 'lib/pkgconfig/pugixml.pc'], + 'files': [ + 'include/pugiconfig.hpp', + 'include/pugixml.hpp', + 'lib/libpugixml.a', + 'lib/libpugixml.%s' % SHLIB_EXT, + 'lib/pkgconfig/pugixml.pc' + ], 'dirs': ['lib/cmake/pugixml'], } From 4caeb178a840be213ad37866ffb2c863133c5483 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 29 Sep 2022 18:15:34 +0200 Subject: [PATCH 4966/9987] fix exts_filter --- easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb index 050b60477d2..b269f17cc28 100644 --- a/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/AGAT/AGAT-0.9.2-GCC-11.2.0.eb @@ -21,7 +21,7 @@ dependencies = [ ] exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") +exts_filter = ("perl -e 'require %(ext_name)s'", '') exts_list = [ ('Set::Object', '1.42', { From 107805868dc2a91c8246eeef5b00090a9c3be914 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 29 Sep 2022 18:33:21 -0700 Subject: [PATCH 4967/9987] correct dep pkgconfig for Guile 3.0.7 --- easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb index 456da718458..6e956e7e513 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb @@ -21,7 +21,7 @@ checksums = ['c7935b7a29e42443f6a35d35cf20ffa7d028c399303f872cd1219598a83656ae'] builddependencies = [ ('Autotools', '20210726'), ('binutils', '2.37'), - ('pkg-config', '0.29.2'), + ('pkgconfig', '0.29.2'), ] dependencies = [ From b1882d25d3f73462c6bd2b388cb2ae80c5702522 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Sep 2022 16:07:48 +0200 Subject: [PATCH 4968/9987] adding easyconfigs: ccache-4.6.3.eb, hiredis-1.0.2-GCCcore-11.3.0.eb --- .../easyconfigs/c/ccache/ccache-4.6.3.eb | 54 +++++++ .../h/hiredis/hiredis-1.0.2-GCCcore-11.3.0.eb | 49 ++++++ ...edis-1.0.2_build-also-static-library.patch | 151 ++++++++++++++++++ ...s-1.0.2_use-same-name-for-static-lib.patch | 43 +++++ 4 files changed, 297 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_build-also-static-library.patch create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_use-same-name-for-static-lib.patch diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb new file mode 100644 index 00000000000..68ac0da6cad --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb @@ -0,0 +1,54 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.6.3' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f46ba3706ad80c30d4d5874dee2bf9227a7fcd0ccaac31b51919a3053d84bd05'] + +osdependencies = [('glibc-static', 'libc6-dev')] + +local_gccver = '11.3.0' +builddependencies = [ + ('GCC', local_gccver), + ('CMake', '3.23.1', '', ('GCCcore', local_gccver)), + ('Ninja', '1.10.2', '', ('GCCcore', local_gccver)), + ('hiredis', '1.0.2', '', ('GCCcore', local_gccver)), + ('zstd', '1.5.2', '', ('GCCcore', local_gccver)), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + # Link dependencies and binary statically + '-DCMAKE_EXE_LINKER_FLAGS="-static"', + '-DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a"', + '-DHIREDIS_LIBRARY="$EBROOTHIREDIS/lib/libhiredis.a"', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = [ + 'ccache --help', + # Ensure that the binary does not depend on any shared library + 'ldd $(which ccache) | grep -q "not a dynamic executable"', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3d70862e8f0 --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +# Author: Alexander Grund (TU Dresden) +# Based on EC by J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'hiredis' +version = '1.0.2' + +homepage = 'https://github.com/redis/hiredis' +description = """Hiredis is a minimalistic C client library for the Redis database. + +It is minimalistic because it just adds minimal support for the protocol, +but at the same time it uses a high level printf-alike API in order to +make it much higher level than otherwise suggested by its minimal code base +and the lack of explicit bindings for every Redis command.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'redis' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_build-also-static-library.patch', + '%(name)s-%(version)s_use-same-name-for-static-lib.patch' +] +checksums = [ + 'e0ab696e2f07deb4252dda45b703d09854e53b9703c7d52182ce5a22616c3819', # v1.0.2.tar.gz + # hiredis-1.0.2_build-also-static-library.patch + '224cb6fdbf8488cc6583323f5cde09e98d10fd201ddfd117572594ed98eb642c', + # hiredis-1.0.2_use-same-name-for-static-lib.patch + '7ef1c90331a0ed92e7ae2905827c3c8bb79e19545b0bae3b44a06a11564ec8de', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['lib/libhiredis.a', 'lib/libhiredis.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_build-also-static-library.patch b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_build-also-static-library.patch new file mode 100644 index 00000000000..85f0463b3bf --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_build-also-static-library.patch @@ -0,0 +1,151 @@ +From https://github.com/redis/hiredis/pull/851 + +From 07c3618ffe7912c2ebc589ea45501c687a19cf2c Mon Sep 17 00:00:00 2001 +From: masariello +Date: Wed, 22 Jul 2020 14:23:53 +0100 +Subject: [PATCH 1/2] Add static library target and cpack support + +--- + CMakeLists.txt | 42 +++++++++++++++++++++++++++++++++++++++--- + hiredis.targets | 11 +++++++++++ + 2 files changed, 50 insertions(+), 3 deletions(-) + create mode 100644 hiredis.targets + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 87a4ac614..55c026b8f 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -40,6 +40,7 @@ IF(WIN32) + ENDIF() + + ADD_LIBRARY(hiredis SHARED ${hiredis_sources}) ++ADD_LIBRARY(hiredis_static STATIC ${hiredis_sources}) + + SET_TARGET_PROPERTIES(hiredis + PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE +@@ -48,16 +49,47 @@ IF(WIN32 OR MINGW) + TARGET_LINK_LIBRARIES(hiredis PRIVATE ws2_32) + ENDIF() + +-TARGET_INCLUDE_DIRECTORIES(hiredis PUBLIC $ $) ++TARGET_INCLUDE_DIRECTORIES(hiredis PUBLIC $ $) ++TARGET_INCLUDE_DIRECTORIES(hiredis_static PUBLIC $ $) + + CONFIGURE_FILE(hiredis.pc.in hiredis.pc @ONLY) + +-INSTALL(TARGETS hiredis ++set(CPACK_PACKAGE_VENDOR "Redis") ++set(CPACK_PACKAGE_DESCRIPTION "\ ++Hiredis is a minimalistic C client library for the Redis database. ++ ++It is minimalistic because it just adds minimal support for the protocol, \ ++but at the same time it uses a high level printf-alike API in order to make \ ++it much higher level than otherwise suggested by its minimal code base and the \ ++lack of explicit bindings for every Redis command. ++ ++Apart from supporting sending commands and receiving replies, it comes with a \ ++reply parser that is decoupled from the I/O layer. It is a stream parser designed \ ++for easy reusability, which can for instance be used in higher level language bindings \ ++for efficient reply parsing. ++ ++Hiredis only supports the binary-safe Redis protocol, so you can use it with any Redis \ ++version >= 1.2.0. ++ ++The library comes with multiple APIs. There is the synchronous API, the asynchronous API \ ++and the reply parsing API.") ++set(CPACK_PACKAGE_HOMEPAGE_URL "https://github.com/redis/hiredis") ++set(CPACK_PACKAGE_CONTACT "michael dot grunder at gmail dot com") ++set(CPACK_DEBIAN_PACKAGE_SHLIBDEPS ON) ++set(CPACK_RPM_PACKAGE_AUTOREQPROV ON) ++ ++include(CPack) ++ ++INSTALL(TARGETS hiredis hiredis_static + EXPORT hiredis-targets + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) + ++# For NuGet packages ++INSTALL(FILES hiredis.targets ++ DESTINATION build/native) ++ + INSTALL(FILES hiredis.h read.h sds.h async.h alloc.h + DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/hiredis) + +@@ -98,6 +130,8 @@ IF(ENABLE_SSL) + ssl.c) + ADD_LIBRARY(hiredis_ssl SHARED + ${hiredis_ssl_sources}) ++ ADD_LIBRARY(hiredis_ssl_static STATIC ++ ${hiredis_ssl_sources}) + + IF (APPLE) + SET_PROPERTY(TARGET hiredis_ssl PROPERTY LINK_FLAGS "-Wl,-undefined -Wl,dynamic_lookup") +@@ -109,13 +143,15 @@ IF(ENABLE_SSL) + VERSION "${HIREDIS_SONAME}") + + TARGET_INCLUDE_DIRECTORIES(hiredis_ssl PRIVATE "${OPENSSL_INCLUDE_DIR}") ++ TARGET_INCLUDE_DIRECTORIES(hiredis_ssl_static PRIVATE "${OPENSSL_INCLUDE_DIR}") ++ + TARGET_LINK_LIBRARIES(hiredis_ssl PRIVATE ${OPENSSL_LIBRARIES}) + IF (WIN32 OR MINGW) + TARGET_LINK_LIBRARIES(hiredis_ssl PRIVATE hiredis) + ENDIF() + CONFIGURE_FILE(hiredis_ssl.pc.in hiredis_ssl.pc @ONLY) + +- INSTALL(TARGETS hiredis_ssl ++ INSTALL(TARGETS hiredis_ssl hiredis_ssl_static + EXPORT hiredis_ssl-targets + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} +diff --git a/hiredis.targets b/hiredis.targets +new file mode 100644 +index 000000000..effd8a561 +--- /dev/null ++++ b/hiredis.targets +@@ -0,0 +1,11 @@ ++ ++ ++ ++ ++ $(MSBuildThisFileDirectory)\..\..\include;%(AdditionalIncludeDirectories) ++ ++ ++ $(MSBuildThisFileDirectory)\..\..\lib;%(AdditionalLibraryDirectories) ++ ++ ++ +\ No newline at end of file + +From 1b40ec509628c73ac272c8599a3c923e34800d54 Mon Sep 17 00:00:00 2001 +From: Alessio M +Date: Fri, 4 Sep 2020 09:37:11 +0100 +Subject: [PATCH 2/2] fixed issue with unit test linking on windows with SSL + +--- + CMakeLists.txt | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 4bdee1864..53e9f5871 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -50,7 +50,8 @@ SET_TARGET_PROPERTIES(hiredis + PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE + VERSION "${HIREDIS_SONAME}") + IF(WIN32 OR MINGW) +- TARGET_LINK_LIBRARIES(hiredis PRIVATE ws2_32) ++ TARGET_LINK_LIBRARIES(hiredis PUBLIC ws2_32 crypt32) ++ TARGET_LINK_LIBRARIES(hiredis_static PUBLIC ws2_32 crypt32) + ENDIF() + + TARGET_INCLUDE_DIRECTORIES(hiredis PUBLIC $ $) +@@ -152,6 +153,7 @@ IF(ENABLE_SSL) + TARGET_LINK_LIBRARIES(hiredis_ssl PRIVATE ${OPENSSL_LIBRARIES}) + IF (WIN32 OR MINGW) + TARGET_LINK_LIBRARIES(hiredis_ssl PRIVATE hiredis) ++ TARGET_LINK_LIBRARIES(hiredis_ssl_static PUBLIC hiredis_static) + ENDIF() + CONFIGURE_FILE(hiredis_ssl.pc.in hiredis_ssl.pc @ONLY) + diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_use-same-name-for-static-lib.patch b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_use-same-name-for-static-lib.patch new file mode 100644 index 00000000000..4e6003d989e --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2_use-same-name-for-static-lib.patch @@ -0,0 +1,43 @@ +From https://patch-diff.githubusercontent.com/raw/redis/hiredis/pull/1057 + +From dd4bf97836d07df0a4502b72f9024d0231156711 Mon Sep 17 00:00:00 2001 +From: Orgad Shaneh +Date: Tue, 29 Mar 2022 17:16:19 +0300 +Subject: [PATCH] Use the same name for static and shared libraries + +On all system except MSVC, the targets are different. + +Unix: libhiredis.so, libhiredis.a +MinGW: libhiredis.dll+libhiredis.dll.a, libhiredis.a +MSVC: hiredis.dll+hiredis.lib, hiredis_static.lib +--- + CMakeLists.txt | 9 +++++++++ + 1 file changed, 9 insertions(+) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index fe6720b28..899cd14d0 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -50,6 +50,11 @@ ADD_LIBRARY(hiredis_static STATIC ${hiredis_sources}) + ADD_LIBRARY(hiredis::hiredis ALIAS hiredis) + ADD_LIBRARY(hiredis::hiredis_static ALIAS hiredis_static) + ++IF(NOT MSVC) ++ SET_TARGET_PROPERTIES(hiredis_static ++ PROPERTIES OUTPUT_NAME hiredis) ++ENDIF() ++ + SET_TARGET_PROPERTIES(hiredis + PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE + VERSION "${HIREDIS_SONAME}") +@@ -160,6 +165,10 @@ IF(ENABLE_SSL) + ${hiredis_ssl_sources}) + ADD_LIBRARY(hiredis_ssl_static STATIC + ${hiredis_ssl_sources}) ++ IF(NOT MSVC) ++ SET_TARGET_PROPERTIES(hiredis_ssl_static ++ PROPERTIES OUTPUT_NAME hiredis_ssl) ++ ENDIF() + + IF (APPLE) + SET_PROPERTY(TARGET hiredis_ssl PROPERTY LINK_FLAGS "-Wl,-undefined -Wl,dynamic_lookup") From ea4782886948036ce8d97ed746ff151e80d406df Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Sep 2022 16:44:02 +0200 Subject: [PATCH 4969/9987] Fix PyTorch 1.11 on POWER --- .../PyTorch-1.10.0_fix-XNNPACK-tests.patch | 236 ++++++++++++++++++ .../PyTorch-1.10.0_fix-kineto-crash.patch | 24 ++ ...orch-1.10.0_fix-vsx-vector-functions.patch | 39 +++ ...10.0_skip-nnapi-test-without-qnnpack.patch | 30 +++ .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 69 ++--- ...1.11.0_fix-attention_cpp-compilation.patch | 61 +++++ .../PyTorch-1.11.0_fix-test_utils.patch | 20 ++ ...h-1.11.0_increase-tolerance-test_ops.patch | 22 ++ ...Torch-1.11.0_install-vsx-vec-headers.patch | 30 +++ 9 files changed, 503 insertions(+), 28 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-XNNPACK-tests.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-kineto-crash.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vsx-vector-functions.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-attention_cpp-compilation.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-test_utils.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-tolerance-test_ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-XNNPACK-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-XNNPACK-tests.patch new file mode 100644 index 00000000000..c9a82a56164 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-XNNPACK-tests.patch @@ -0,0 +1,236 @@ +When XNNPACK is disabled tests run into assertion failures. +Fix by using (most of) https://github.com/pytorch/pytorch/pull/72642 + +Author: Digant Desai + +Backported by Alexander Grund (TU Dresden) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 0c11507838..5b74b7f63c 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -275,7 +275,14 @@ option(USE_LITE_INTERPRETER_PROFILER "Enable " ON) + option(USE_VULKAN_FP16_INFERENCE "Vulkan - Use fp16 inference" OFF) + option(USE_VULKAN_RELAXED_PRECISION "Vulkan - Use relaxed precision math in the kernels (mediump)" OFF) + option(USE_VULKAN_SHADERC_RUNTIME "Vulkan - Use runtime shader compilation as opposed to build-time (needs libshaderc)" OFF) +-option(USE_XNNPACK "Use XNNPACK" ON) ++# option USE_XNNPACK: try to enable xnnpack by default. ++set(XNNPACK_MIN_CMAKE_VER 3.12) ++cmake_dependent_option( ++ USE_XNNPACK "Use XNNPACK. Requires cmake >= ${XNNPACK_MIN_CMAKE_VER}." ON ++ "CMAKE_VERSION VERSION_GREATER_EQUAL ${XNNPACK_MIN_CMAKE_VER}" OFF) ++if(NOT USE_XNNPACK AND CMAKE_VERSION VERSION_LESS ${XNNPACK_MIN_CMAKE_VER}) ++ message(WARNING "USE_XNNPACK is set to OFF. XNNPACK requires CMake version ${XNNPACK_MIN_CMAKE_VER} or greater.") ++endif() + option(USE_ZMQ "Use ZMQ" OFF) + option(USE_ZSTD "Use ZSTD" OFF) + # Ensure that an MKLDNN build is the default for x86 CPUs +diff --git a/cmake/Summary.cmake b/cmake/Summary.cmake +index 6d021536c1..7c1ac64539 100644 +--- a/cmake/Summary.cmake ++++ b/cmake/Summary.cmake +@@ -165,6 +165,7 @@ function(caffe2_print_configuration_summary) + message(STATUS " USE_PROF : ${USE_PROF}") + message(STATUS " USE_QNNPACK : ${USE_QNNPACK}") + message(STATUS " USE_PYTORCH_QNNPACK : ${USE_PYTORCH_QNNPACK}") ++ message(STATUS " USE_XNNPACK : ${USE_XNNPACK}") + message(STATUS " USE_REDIS : ${USE_REDIS}") + message(STATUS " USE_ROCKSDB : ${USE_ROCKSDB}") + message(STATUS " USE_ZMQ : ${USE_ZMQ}") +diff --git a/test/jit/test_optimize_for_mobile_preserve_debug_info.py b/test/jit/test_optimize_for_mobile_preserve_debug_info.py +index c08f3b5838..1b93f54c15 100644 +--- a/test/jit/test_optimize_for_mobile_preserve_debug_info.py ++++ b/test/jit/test_optimize_for_mobile_preserve_debug_info.py +@@ -1,8 +1,8 @@ + import torch + import torch._C +-import torch.backends.xnnpack + import torch.nn.functional as F + from torch.testing._internal.jit_utils import JitTestCase ++from torch.testing._internal.common_utils import skipIfNoXNNPACK + + class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + def check_replacement( +@@ -34,6 +34,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + original_source_ranges[replacements[node.kind()]], + ) + ++ @skipIfNoXNNPACK + def test_replace_conv1d_with_conv2d(self): + class TestConv1d(torch.nn.Module): + def __init__(self, weight, bias): +@@ -61,6 +62,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + jit_pass=torch._C._jit_pass_transform_conv1d_to_conv2d, + ) + ++ @skipIfNoXNNPACK + def test_insert_pre_packed_linear_before_inline_and_conv_2d_op(self): + class TestPrepackedLinearBeforeInlineAndConv2dOp(torch.nn.Module): + def __init__( +@@ -137,6 +139,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + jit_pass=torch._C._jit_pass_insert_prepacked_ops, + ) + ++ @skipIfNoXNNPACK + def test_insert_pre_packed_linear_op(self): + self.check_replacement( + model=torch.jit.trace(torch.nn.Linear(5, 4), torch.rand(3, 2, 5)), +@@ -228,6 +231,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + jit_pass=torch._C._jit_pass_fuse_clamp_w_prepacked_linear_conv, + ) + ++ @skipIfNoXNNPACK + def test_fuse_activation_with_pack_ops_linear_conv2d_1(self): + self.run_test_fuse_activation_with_pack_ops_linear_conv2d( + linear_activation=F.hardtanh, +@@ -236,6 +240,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + conv2d_activation_kind="aten::hardtanh_" + ) + ++ @skipIfNoXNNPACK + def test_fuse_activation_with_pack_ops_linear_conv2d_2(self): + self.run_test_fuse_activation_with_pack_ops_linear_conv2d( + linear_activation=F.hardtanh_, +@@ -244,6 +249,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + conv2d_activation_kind="aten::hardtanh" + ) + ++ @skipIfNoXNNPACK + def test_fuse_activation_with_pack_ops_linear_conv2d_3(self): + self.run_test_fuse_activation_with_pack_ops_linear_conv2d( + linear_activation=F.relu, +@@ -252,6 +258,7 @@ class TestOptimizeForMobilePreserveDebugInfo(JitTestCase): + conv2d_activation_kind="aten::relu_" + ) + ++ @skipIfNoXNNPACK + def test_fuse_activation_with_pack_ops_linear_conv2d_4(self): + self.run_test_fuse_activation_with_pack_ops_linear_conv2d( + linear_activation=F.relu_, +diff --git a/test/test_mobile_optimizer.py b/test/test_mobile_optimizer.py +index 19f07e2454..21ae5d3ee9 100644 +--- a/test/test_mobile_optimizer.py ++++ b/test/test_mobile_optimizer.py +@@ -1,9 +1,8 @@ + import unittest + import torch + import torch.nn as nn +-import torch.backends.xnnpack + import torch.utils.bundled_inputs +-from torch.testing._internal.common_utils import TestCase, run_tests ++from torch.testing._internal.common_utils import TestCase, run_tests, skipIfNoXNNPACK + from torch.testing._internal.jit_utils import get_forward, get_forward_graph + from torch.utils.mobile_optimizer import (LintCode, + generate_mobile_module_lints, +@@ -22,9 +21,7 @@ FileCheck = torch._C.FileCheck + + class TestOptimizer(TestCase): + +- @unittest.skipUnless(torch.backends.xnnpack.enabled, +- " XNNPACK must be enabled for these tests." +- " Please build with USE_XNNPACK=1.") ++ @skipIfNoXNNPACK + def test_optimize_for_mobile(self): + batch_size = 2 + input_channels_per_group = 6 +@@ -263,9 +260,7 @@ class TestOptimizer(TestCase): + rtol=1e-2, + atol=1e-3) + +- @unittest.skipUnless(torch.backends.xnnpack.enabled, +- " XNNPACK must be enabled for these tests." +- " Please build with USE_XNNPACK=1.") ++ @skipIfNoXNNPACK + def test_quantized_conv_no_asan_failures(self): + # There were ASAN failures when fold_conv_bn was run on + # already quantized conv modules. Verifying that this does +@@ -359,6 +354,7 @@ class TestOptimizer(TestCase): + bi_module_lint_list = generate_mobile_module_lints(bi_module) + self.assertEqual(len(bi_module_lint_list), 0) + ++ @skipIfNoXNNPACK + def test_preserve_bundled_inputs_methods(self): + class MyBundledInputModule(torch.nn.Module): + def __init__(self): +@@ -413,9 +409,7 @@ class TestOptimizer(TestCase): + incomplete_bi_module_optim = optimize_for_mobile(incomplete_bi_module, preserved_methods=['get_all_bundled_inputs']) + self.assertTrue(hasattr(incomplete_bi_module_optim, 'get_all_bundled_inputs')) + +- @unittest.skipUnless(torch.backends.xnnpack.enabled, +- " XNNPACK must be enabled for these tests." +- " Please build with USE_XNNPACK=1.") ++ @skipIfNoXNNPACK + def test_hoist_conv_packed_params(self): + + if 'qnnpack' not in torch.backends.quantized.supported_engines: +@@ -509,6 +503,7 @@ class TestOptimizer(TestCase): + m_optim_res = m_optim(data) + torch.testing.assert_close(m_res, m_optim_res, rtol=1e-2, atol=1e-3) + ++ @skipIfNoXNNPACK + @unittest.skipUnless(HAS_TORCHVISION, "Needs torchvision") + def test_mobilenet_optimize_for_mobile(self): + m = torchvision.models.mobilenet_v3_small() +diff --git a/test/test_model_dump.py b/test/test_model_dump.py +index 417bb2a91a..e4a9ffa1bd 100644 +--- a/test/test_model_dump.py ++++ b/test/test_model_dump.py +@@ -8,9 +8,10 @@ import urllib + import unittest + + import torch ++import torch.backends.xnnpack + import torch.utils.model_dump + import torch.utils.mobile_optimizer +-from torch.testing._internal.common_utils import TestCase, run_tests, IS_WINDOWS ++from torch.testing._internal.common_utils import TestCase, run_tests, IS_WINDOWS, skipIfNoXNNPACK + from torch.testing._internal.common_quantized import supported_qengines + + +@@ -170,6 +171,7 @@ class TestModelDump(TestCase): + qmodel = self.get_quant_model() + self.do_dump_model(torch.jit.script(qmodel)) + ++ @skipIfNoXNNPACK + @unittest.skipUnless("qnnpack" in supported_qengines, "QNNPACK not available") + def test_optimized_quantized_model(self): + qmodel = self.get_quant_model() +diff --git a/test/test_xnnpack_integration.py b/test/test_xnnpack_integration.py +index a0f8328ec6..a737ed4b8b 100644 +--- a/test/test_xnnpack_integration.py ++++ b/test/test_xnnpack_integration.py +@@ -51,7 +51,6 @@ class TestXNNPACKOps(TestCase): + output_linearprepacked = torch.ops.prepacked.linear_clamp_run(input_data, packed_weight_bias) + torch.testing.assert_close(ref_result, output_linearprepacked, rtol=1e-2, atol=1e-3) + +- + @given(batch_size=st.integers(0, 3), + input_channels_per_group=st.integers(1, 32), + height=st.integers(5, 64), +diff --git a/torch/testing/_internal/common_utils.py b/torch/testing/_internal/common_utils.py +index b4ef79620d..18d8925d6a 100644 +--- a/torch/testing/_internal/common_utils.py ++++ b/torch/testing/_internal/common_utils.py +@@ -56,6 +56,7 @@ from torch._six import string_classes + from torch import Tensor + import torch.backends.cudnn + import torch.backends.mkl ++import torch.backends.xnnpack + from enum import Enum + + torch.backends.disable_global_flags() +@@ -908,6 +909,14 @@ def _test_function(fn, device): + return fn(self, device) + return run_test_function + ++def skipIfNoXNNPACK(fn): ++ @wraps(fn) ++ def wrapper(*args, **kwargs): ++ if not torch.backends.xnnpack.enabled: ++ raise unittest.SkipTest('XNNPACK must be enabled for these tests. Please build with USE_XNNPACK=1.') ++ else: ++ fn(*args, **kwargs) ++ return wrapper + + def skipIfNoLapack(fn): + @wraps(fn) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-kineto-crash.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-kineto-crash.patch new file mode 100644 index 00000000000..7858aa1f8cf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-kineto-crash.patch @@ -0,0 +1,24 @@ +Fix a crash during application shutdown visible in test_profiler on some machines. +See https://github.com/pytorch/kineto/pull/642 + +Author: Alexander Grund (TU Dresden) + +diff -aur a/third_party/kineto/libkineto/src/EventProfilerController.cpp b/third_party/kineto/libkineto/src/EventProfilerController.cpp +--- a/third_party/kineto/libkineto/src/EventProfilerController.cpp 2022-08-05 13:10:46.175716618 +0200 ++++ b/third_party/kineto/libkineto/src/EventProfilerController.cpp 2022-08-05 13:16:00.654118490 +0200 +@@ -233,9 +233,14 @@ EventProfilerController::~EventProfilerController() { + + // Must be called under lock + void EventProfilerController::start(CUcontext ctx, ConfigLoader& configLoader) { +- profilerMap()[ctx] = unique_ptr( ++ // Avoid static initialization order fiasco: ++ // We need the profilerMap and with it all controllers to be destroyed ++ // before everything the controller accesses gets destroyed. ++ // Hence access the profilerMap after initialization of the controller. ++ auto controller = unique_ptr( + new EventProfilerController( + ctx, configLoader, detail::HeartbeatMonitor::instance())); ++ profilerMap()[ctx] = std::move(controller); + } + + // Must be called under lock diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vsx-vector-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vsx-vector-functions.patch new file mode 100644 index 00000000000..7d35ac8d134 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-vsx-vector-functions.patch @@ -0,0 +1,39 @@ +This fixes the remaining bug introduced by the VSX optimized code in https://github.com/pytorch/pytorch/pull/41541 + +See https://github.com/pytorch/pytorch/pull/59382 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +index 2427276bce..2b46e0a662 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +@@ -558,27 +558,7 @@ class Vectorized { + } + + Vectorized C10_ALWAYS_INLINE pow(const Vectorized& exp) const { +- auto x = *this; +- auto sign_bit = (*this) & sign_mask; +- // |b| +- auto exp_abs = exp.abs(); +- auto exp_trunc = exp.trunc(); +- Vectorized odd_mask; +- odd_mask._vecb0 = (vec_signed(exp._vec0) & vi_1) != vi_0; +- odd_mask._vecb1 = (vec_signed(exp._vec1) & vi_1) != vi_0; +- // using ln fuction +- auto temp = (abs().log() * exp).exp(); +- +- // is odd or even check from Sleef +- auto is_int = (exp == exp_trunc) | (exp_abs >= vcheck); +- auto is_odd = odd_mask & is_int & (exp_abs < vcheck); +- // if even then then pow result should be absolute +- auto temp_sign = temp | sign_bit; // copy_sign +- auto out = blendv(temp, temp_sign, is_odd); +- // x<0 and y != N, then NAN +- auto out1 = blendv(out, v_nan, ((exp.floor() != exp) & (x < zero))); +- // y = 0 then 1 +- return blendv(out1, one, (exp_abs == zero)); ++ return {Sleef_powf4_u10vsx(_vec0, exp._vec0), Sleef_powf4_u10vsx(_vec1, exp._vec1)}; + } + + Vectorized fmod(const Vectorized& b) const { diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch new file mode 100644 index 00000000000..ce5acf4a884 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch @@ -0,0 +1,30 @@ +When QNNPACK is not available the test will fail trying to use it. +Skip them conditionally. +See https://github.com/pytorch/pytorch/pull/82882 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_nnapi.py b/test/test_nnapi.py +index f8db7e1a3d..1d4fd52e28 100644 +--- a/test/test_nnapi.py ++++ b/test/test_nnapi.py +@@ -2,8 +2,10 @@ + import os + import ctypes + import torch ++import unittest + from typing import Tuple + from torch.backends._nnapi.prepare import convert_model_to_nnapi ++from torch.testing._internal.common_quantized import supported_qengines + from torch.testing._internal.common_utils import TestCase, run_tests + + +@@ -18,6 +20,8 @@ def nhwc(t): + return t + + ++@unittest.skipUnless('qnnpack' in supported_qengines, ++ "This Pytorch Build has not been built with or does not support QNNPACK") + class TestNNAPI(TestCase): + + def setUp(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 5aba12b3957..75c7d8f133b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -8,51 +8,64 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2021a'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = ['https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', - 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_skip_cmake_rpath.patch', - 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', - 'PyTorch-1.11.0_skip_failing_ops_tests.patch', - 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', + 'PyTorch-1.11.0_fix-attention_cpp-compilation.patch', 'PyTorch-1.11.0_fix_sharded_imports.patch', - 'PyTorch-1.11.0_increase_test_tolerances_TF32.patch', + 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', - 'PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_increase_test_tolerances_TF32.patch', + 'PyTorch-1.11.0_increase-tolerance-test_ops.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.11.0_skip_failing_ops_tests.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + 'dc0c2b8d13c112a2b9ea8757a475b0ce2ca97cd19c50a8b70b8c286676616f1d', # pytorch-v1.11.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch - # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch - 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_cmake_rpath.patch + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch + 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', + # PyTorch-1.11.0_fix-attention_cpp-compilation.patch + '84214fcc7e30cf70659a7c3bd70bf11e73d58fd4f7fff2c233e3225619b0e42c', + '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch + '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', - '8eaca92d64fcadb0552d28e9c7ea5c4bc669d2fe33004e45a3519ce8d0d136a2', # PyTorch-1.11.0_skip_failing_ops_tests.patch - '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch - '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch # PyTorch-1.11.0_increase_test_tolerances_TF32.patch '26e179a4f6f57e49209092612ae5f5cd8c03fd2ca84566ba0244eabefc3736ba', - # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch - '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', - # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch - 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', + # PyTorch-1.11.0_increase-tolerance-test_ops.patch + 'ceec745c68a405bba79efb4dc61c662ca84eb950cd0163c7104330f4bf614cf5', + 'f765093765c07ae488e15b33184709bd1e9c799f6640695be71dca3df02f83c3', # PyTorch-1.11.0_install-vsx-vec-headers.patch + '8eaca92d64fcadb0552d28e9c7ea5c4bc669d2fe33004e45a3519ce8d0d136a2', # PyTorch-1.11.0_skip_failing_ops_tests.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -112,10 +125,10 @@ excluded_tests = { runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' # several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), -# so we allow up to 10 (out of ~90k) tests to fail before treating the installation to be faulty -max_failed_tests = 10 +# so we allow some (out of ~90k) tests to fail before treating the installation to be faulty +max_failed_tests = 1 -# The readelf sanity check command can be taken out once the TestRPATH test from +# The readelf sanity check command can be taken out once the TestRPATH test from # https://github.com/pytorch/pytorch/pull/68912 is accepted, since it is then checked as part of the PyTorch test suite local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT sanity_check_commands = [ diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-attention_cpp-compilation.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-attention_cpp-compilation.patch new file mode 100644 index 00000000000..751e954f75f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-attention_cpp-compilation.patch @@ -0,0 +1,61 @@ +Fix failure to compile attention.cpp on some platforms, e.g. POWER. +I.e. those 3 errors: + +../aten/src/ATen/native/attention.cpp:145:46: error: call to deleted function 'double& at::vec::CPU_CAPABILITY::Vectorized::operator[](int)' + 145 | hmax = std::max(max_input[i], hmax); +[snip] +../aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h:190:11: note: declared here + 190 | double& operator[](int idx) = delete; + +../aten/src/ATen/native/attention.cpp:152:66: error: call to deleted function 'double& at::vec::CPU_CAPABILITY::Vectorized::operator[](int)' + 152 | hsum += std::exp(static_cast(v[i]) - hmax); + +../aten/src/ATen/native/attention.cpp:168:100: error: call to deleted function 'double& at::vec::CPU_CAPABILITY::Vectorized::operator[](int)' + 168 | input_data[t + i] = static_cast(std::exp(static_cast(v[i]) - hmax) * inv_denominator); + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/attention.cpp b/aten/src/ATen/native/attention.cpp +index 188de5e2cd..7f3e8e5af2 100644 +--- a/aten/src/ATen/native/attention.cpp ++++ b/aten/src/ATen/native/attention.cpp +@@ -140,22 +140,18 @@ void masked_softmax_dropout( + max_input = vec::maximum(max_input, v); + } + ++ __at_align__ scalar_t arr_max_input[V]; ++ max_input.store(arr_max_input); + auto hmax = std::numeric_limits::lowest(); + for (auto i = 0; i < V; ++i) { +- hmax = std::max(max_input[i], hmax); ++ hmax = std::max(arr_max_input[i], hmax); + } + accscalar_t hsum = 0; +- for (auto t = 0; t < T; t += V) { +- auto v = Vec::loadu(&input_data[t]); +- // TODO: vectorize in accscalar_t? +- for (auto i = 0; i < V; ++i) { +- hsum += std::exp(static_cast(v[i]) - hmax); +- } ++ for (auto t = 0; t < T; ++t) { ++ hsum += std::exp(static_cast(input_data[t]) - hmax); + } + auto inv_denominator = 1.0 / hsum; +- for (auto t = 0; t < T; t += V) { +- Vec v = Vec::loadu(&input_data[t]); +- ++ for (auto t = 0; t < T; ++t) { + // TODO: vectorize in accscalar_t? + // TODO this faster solution does not work on Android build + /* +@@ -164,9 +160,7 @@ void masked_softmax_dropout( + } + v.store(&input_data[t]); + */ +- for (auto i = 0; i < V; ++i) { +- input_data[t + i] = static_cast(std::exp(static_cast(v[i]) - hmax) * inv_denominator); +- } ++ input_data[t] = static_cast(std::exp(static_cast(input_data[t]) - hmax) * inv_denominator); + } + } + }); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-test_utils.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-test_utils.patch new file mode 100644 index 00000000000..a42166c927c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-test_utils.patch @@ -0,0 +1,20 @@ +The function tested is dependent on the current locale and may fail on non-English systems. +See https://github.com/pytorch/pytorch/pull/85891 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/utils/cpp_extension.py b/torch/utils/cpp_extension.py +index 9c6635f111..d99aae1ca2 100644 +--- a/torch/utils/cpp_extension.py ++++ b/torch/utils/cpp_extension.py +@@ -292,7 +292,9 @@ def check_compiler_ok_for_platform(compiler: str) -> bool: + if any(name in compiler_path for name in _accepted_compilers_for_platform()): + return True + # If compiler wrapper is used try to infer the actual compiler by invoking it with -v flag +- version_string = subprocess.check_output([compiler, '-v'], stderr=subprocess.STDOUT).decode(*SUBPROCESS_DECODE_ARGS) ++ env = os.environ.copy() ++ env['LC_ALL'] = 'C' # Don't localize output ++ version_string = subprocess.check_output([compiler, '-v'], stderr=subprocess.STDOUT, env=env).decode(*SUBPROCESS_DECODE_ARGS) + if IS_LINUX: + # Check for 'gcc' or 'g++' for sccache warpper + pattern = re.compile("^COLLECT_GCC=(.*)$", re.MULTILINE) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-tolerance-test_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-tolerance-test_ops.patch new file mode 100644 index 00000000000..69d58f7a334 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_increase-tolerance-test_ops.patch @@ -0,0 +1,22 @@ +`test_out` may fail due to slightly different values caused by different order of matrizes in SGEMM: + +> Mismatched elements: 1 / 50 (2.0%) +> Greatest absolute difference: 1.430511474609375e-05 at index (4, 5) (up to 1e-05 allowed) +> Greatest relative difference: 4.65393206065873e-06 at index (4, 5) (up to 1.3e-06 allowed) + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_ops.py b/test/test_ops.py +index 291361d53d..2e0597376d 100644 +--- a/test/test_ops.py ++++ b/test/test_ops.py +@@ -418,6 +418,9 @@ class TestCommon(TestCase): + self.skipTest("Skipped! Op has not supported dtypes on this device.") + dtype = torch.float32 if torch.float32 in supported_dtypes else list(supported_dtypes)[0] + ++ if dtype is torch.float32: ++ self.precision, self.rel_tol = (1.5e-05, 1e-05) ++ + # NOTE: only tests on first sample + samples = op.sample_inputs(device, dtype) + sample = first_sample(self, samples) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch new file mode 100644 index 00000000000..a3da950d7d9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch @@ -0,0 +1,30 @@ +Add missing headers to the installation which fixes e.g. test_cpp_extensions_aot_ninja +See https://github.com/pytorch/pytorch/pull/85547 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/CMakeLists.txt b/aten/src/ATen/CMakeLists.txt +index 5710eca27c..0cd15c2ad2 100644 +--- a/aten/src/ATen/CMakeLists.txt ++++ b/aten/src/ATen/CMakeLists.txt +@@ -56,7 +56,7 @@ if(NOT BUILD_CAFFE2 AND NOT BUILD_LITE_INTERPRETER) + EXCLUDE(ATen_CORE_TEST_SRCS "${ATen_CORE_TEST_SRCS}" ${ATen_CORE_EXCLUDED_TEST_SRCS}) + endif() + +-file(GLOB base_h "*.h" "detail/*.h" "cpu/*.h" "cpu/vec/vec512/*.h" "cpu/vec/vec256/*.h" "cpu/vec/*.h" "quantized/*.h") ++file(GLOB base_h "*.h" "detail/*.h" "cpu/*.h" "cpu/vec/vec512/*.h" "cpu/vec/vec256/*.h" "cpu/vec/vec256/vsx/*.h" "cpu/vec/*.h" "quantized/*.h") + file(GLOB base_cpp "*.cpp" "detail/*.cpp" "cpu/*.cpp") + file(GLOB cuda_h "cuda/*.h" "cuda/detail/*.h" "cuda/*.cuh" "cuda/detail/*.cuh") + file(GLOB cuda_cpp "cuda/*.cpp" "cuda/detail/*.cpp") +diff --git a/setup.py b/setup.py +index f1ebab7391..c73b6df665 100644 +--- a/setup.py ++++ b/setup.py +@@ -942,6 +942,7 @@ if __name__ == '__main__': + 'include/ATen/*.h', + 'include/ATen/cpu/*.h', + 'include/ATen/cpu/vec/vec256/*.h', ++ 'include/ATen/cpu/vec/vec256/vsx/*.h', + 'include/ATen/cpu/vec/vec512/*.h', + 'include/ATen/cpu/vec/*.h', + 'include/ATen/core/*.h', From 15c9ee3d42dcab34e47e9eb02c3e24fd4589352f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Sep 2022 17:05:33 +0200 Subject: [PATCH 4970/9987] Add patch for test_fsdp_pure_fp16 --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 ++ .../PyTorch-1.11.0_fix-fsdp-fp16-test.patch | 21 +++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 75c7d8f133b..dfd9742736f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -23,6 +23,7 @@ patches = [ 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', 'PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', 'PyTorch-1.11.0_fix-attention_cpp-compilation.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.0_fix_sharded_imports.patch', 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', 'PyTorch-1.11.0_fix-test_utils.patch', @@ -53,6 +54,7 @@ checksums = [ 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', # PyTorch-1.11.0_fix-attention_cpp-compilation.patch '84214fcc7e30cf70659a7c3bd70bf11e73d58fd4f7fff2c233e3225619b0e42c', + '69546ab7371667370eb52b8e46fee7f39deff493fc12cfdcc6f49dde69848f8d', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch new file mode 100644 index 00000000000..bd860be61f7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch @@ -0,0 +1,21 @@ +The test fails on a node with more than 5 GPUs. +Hence limit the world_size to 5 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/fsdp/test_fsdp_pure_fp16.py b/test/distributed/fsdp/test_fsdp_pure_fp16.py +index eea03bea3d..d3a4bb8257 100644 +--- a/test/distributed/fsdp/test_fsdp_pure_fp16.py ++++ b/test/distributed/fsdp/test_fsdp_pure_fp16.py +@@ -32,6 +32,11 @@ if TEST_WITH_DEV_DBG_ASAN: + + class TestPureFP16(FSDPTest): + ++ @property ++ def world_size(self): ++ # Test fails due to inaccuracies when using more than 5 GPUs ++ return min(5, super().world_size) ++ + @skip_if_lt_x_gpu(2) + @parametrize( + "cpu_offload", From 8a5ffb8dbdcf07d8283f4a77e3886e41e7acd3ae Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 30 Sep 2022 11:32:37 +0200 Subject: [PATCH 4971/9987] adding easyconfigs: htop-3.2.1.eb --- easybuild/easyconfigs/h/htop/htop-3.2.1.eb | 28 ++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/h/htop/htop-3.2.1.eb diff --git a/easybuild/easyconfigs/h/htop/htop-3.2.1.eb b/easybuild/easyconfigs/h/htop/htop-3.2.1.eb new file mode 100644 index 00000000000..c1cdf13a220 --- /dev/null +++ b/easybuild/easyconfigs/h/htop/htop-3.2.1.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'htop' +version = "3.2.1" + +homepage = 'https://htop.dev' + +description = """An interactive process viewer for Unix""" + +toolchain = SYSTEM + +github_account = 'htop-dev' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b5ffac1949a8daaabcffa659c0964360b5008782aae4dfa7702d2323cfb4f438'] + +dependencies = [ + ('ncurses', '6.2'), +] + +preconfigopts = 'LIBS="$LIBS -ltinfo" && ./autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/htop'], + 'dirs': ['share'], +} + +moduleclass = 'tools' From 08d45b3280c471b9881c6661eab445a7abbff9a3 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 30 Sep 2022 12:20:30 +0200 Subject: [PATCH 4972/9987] As discussed in the conf call of https://github.com/easybuilders/easybuild/wiki/Conference-call-notes-20220928 we'll stick to 4.4.2 for 2022a --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index 64343b457dc..cf6a5d92445 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -62,7 +62,7 @@ dependencies = [ ('MPFR', '4.1.0'), ('GMP', '6.2.1'), ('numactl', '2.0.14'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.4.2'), ('Pillow', '9.1.1'), ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', True), ('magma', '2.6.2', '-CUDA-%(cudaver)s'), From 1657192c75113b43f86a1440de39258a09505186 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 30 Sep 2022 13:57:08 +0200 Subject: [PATCH 4973/9987] adding easyconfigs: CWIPI-0.12.0-gompi-2021a.eb --- .../c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb diff --git a/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb b/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb new file mode 100644 index 00000000000..f22001bd4fc --- /dev/null +++ b/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'CWIPI' +version = '0.12.0' + +homepage = 'https://w3.onera.fr/cwipi/' +description = """CWIPI (Coupling With Interpolation Parallel Interface) library helps in +chaining and coupling codes. Provides exchanges of interpolated fields through +a non-compliant geometric interface and allows control of the coupling +algorithm using control parameters. CWIPI takes advantage of the distribution +of the definition of the coupling algorithm in the different codes. +""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://w3.onera.fr/cwipi/sites/w3.onera.fr.cwipi/files/u4'] +sources = [SOURCELOWER_TGZ] +checksums = ['775dedd6afd5e148f008fc19b98ad0879a0091880af682cbed89c4978bef5575'] + +builddependencies = [('CMake', '3.20.1')] + +configopts = "-DCWP_ENABLE_Fortran=ON" + +_cwipi_bin = ['c_linear_coupling', 'c_surf_coupling_P1P0_P0P1', 'c_surf_coupling_P1P1', + 'c_surf_coupling_simple_location', 'c_surf_coupling_vector_exchange', 'c_surf_location_triaP2', + 'c_surf_sequential_coupling', 'c_vol_coupling_P1P1', 'c_vol_coupling_polyhedra_P1P1', + 'fortran_plane_PiQj', 'fortran_surf_P1P1', 'fortran_surf_PiQj'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _cwipi_bin] + + ['lib/libcwp.a', 'lib/libcwp.%s' % SHLIB_EXT, 'lib/libcwpf.a', 'lib/libcwpf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' From b7dab3b09a4204c22c4821d16cdc6972a36bb6ad Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 30 Sep 2022 15:16:37 +0200 Subject: [PATCH 4974/9987] homogenize easyconfigs of Mmg v5.6.0 --- .../easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb | 12 ++++-------- .../easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb | 13 ++++++------- 2 files changed, 10 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb index 80a0bcb4e5e..eb07a34b0a1 100644 --- a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021a.eb @@ -6,11 +6,11 @@ version = '5.6.0' homepage = 'https://www.mmgtools.org/' description = """ Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: -the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional +the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation -and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization -of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, +and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization +of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries.""" toolchain = {'name': 'gompi', 'version': '2021a'} @@ -25,14 +25,10 @@ checksums = [ ] -builddependencies = [ - ('CMake', '3.20.1'), -] +builddependencies = [('CMake', '3.20.1')] dependencies = [('SCOTCH', '6.1.0')] -separate_build_dir = True - # CI tests require downloading of data that might not be available in the future. # Sticking to tests included in the source with help of patch configopts = '-DUSE_SCOTCH=ON -DBUILD_TESTING=ON -DONLY_VERY_SHORT_TESTS=ON ' diff --git a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb index a27faef39a9..517ba6a3440 100644 --- a/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/Mmg/Mmg-5.6.0-gompi-2021b.eb @@ -6,14 +6,12 @@ version = '5.6.0' homepage = 'https://www.mmgtools.org/' description = """ Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: -the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation -and generation of a triangulation from a set of points or from given boundary edges +the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional +triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation -and isovalue discretization -the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh -and implicit domain meshing -the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries -""" +and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization +of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, +libmmgs and libmmg3d libraries.""" toolchain = {'name': 'gompi', 'version': '2021b'} @@ -35,6 +33,7 @@ configopts = '-DUSE_SCOTCH=ON -DBUILD_TESTING=ON -DONLY_VERY_SHORT_TESTS=ON ' configopts += '-DTEST_LIBMMG2D=ON -DTEST_LIBMMG3D=ON -DTEST_LIBMMGS=ON ' configopts += '-DLIBMMG2D_SHARED=ON -DLIBMMG3D_SHARED=ON -DLIBMMGS_SHARED=ON -DLIBMMG_SHARED=ON ' +pretestopts = 'export CTEST_PARALLEL_LEVEL=%(parallel)s &&' runtest = 'test' sanity_check_paths = { From ed7ec796589c4becabfff0d0bf97e08b36067421 Mon Sep 17 00:00:00 2001 From: Christoph Siegert Date: Fri, 30 Sep 2022 16:00:33 +0200 Subject: [PATCH 4975/9987] add patches for ambertools to work with new easyblock --- .../Amber-20.11-foss-2020b-AmberTools-21.3.eb | 38 ++++++++++++++++--- 1 file changed, 33 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb index ee8d80b6270..1f0d542911d 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb @@ -15,21 +15,49 @@ toolchainopts = {'usempi': True, 'openmp': True} sources = [ '%%(name)s%s.tar.bz2' % local_amber_ver, - 'AmberTools%s.tar.bz2' % local_ambertools_ver, + {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'} ] patches = [ - 'AmberTools-20_cmake-locate-netcdf.patch', - 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', - 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_DGESVD_workspace_query.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_dvout_call.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_mexit_calls.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_more_blas_argument_problems.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_multiple_definition.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_potential_use_before_init.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_rism_argument_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_dont_include_config.h_in_top_Makefile.patch', 'alt_location': 'AmberTools'}, ] checksums = [ 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools21.tar.bz2 '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch - '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch + # AmberTools-21_dont_include_config.h_in_top_Makefile.patch + 'b5a20a63904344fc3d1469841f0ea7d5ddaaa01462742bab958c3bba4a9b7ad9', ] builddependencies = [ From 1804e66d1d3462f82a6dbd48465d2c9b66803bcc Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 30 Sep 2022 16:04:38 +0200 Subject: [PATCH 4976/9987] add recipe for torchdata 0.3.0 --- .../t/torchdata-0.3.0-PyTorch-1.11.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb diff --git a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb new file mode 100644 index 00000000000..6f5908e93ce --- /dev/null +++ b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'torchdata' +version = '0.3.0' +local_python_version = '3.9.5' +local_pytorch_version = '1.11.0' +versionsuffix = '-PyTorch-%s' % local_pytorch_version +local_pytorch_versionsuffix = '-foss-2021a-CUDA-11.3.1' + +homepage = 'https://github.com/pytorch/data' +description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', local_python_version), + ('PyTorch', local_pytorch_version, local_pytorch_versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pytorch/data/archive'], + }), +] + +moduleclass = 'lib' From 52a610d9d41431a6bbc928fcc146b61da429c613 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 30 Sep 2022 17:08:42 +0200 Subject: [PATCH 4977/9987] adding easyconfigs: f90wrap-0.2.8-foss-2021a.eb --- .../f/f90wrap/f90wrap-0.2.8-foss-2021a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb diff --git a/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb new file mode 100644 index 00000000000..87eab2439f1 --- /dev/null +++ b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'f90wrap' +version = '0.2.8' + +homepage = 'https://github.com/jameskermode/f90wrap' +description = """f90wrap is a tool to automatically generate Python extension modules which +interface to Fortran code that makes use of derived types. It builds on the +capabilities of the popular f2py utility by generating a simpler Fortran 90 +interface to the original Fortran code which is then suitable for wrapping with +f2py, together with a higher-level Pythonic wrapper that makes the existance of +an additional layer transparent to the final user.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['23524b66ffb71365d93a701065cefb33bc3ba869bed18d0884d08fac05f097f2'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/f2py-f90wrap', 'bin/f90doc', 'bin/f90wrap'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'devel' From a16da39c4d4cb9eadb5a260d904c203abf7f835d Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 30 Sep 2022 19:08:39 +0200 Subject: [PATCH 4978/9987] adding easyconfigs: jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb and patches: jupyter-resource-usage-0.6.2_fix_update_cpu.patch --- ...ter-resource-usage-0.6.2-GCCcore-10.3.0.eb | 69 +++++++++++++++++++ ...-resource-usage-0.6.2_fix_update_cpu.patch | 16 +++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2_fix_update_cpu.patch diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..37c5915ff8e --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-resource-usage' +version = '0.6.2' + +homepage = 'https://github.com/jupyter-server/jupyter-resource-usage' +description = """Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('IPython', '7.25.0'), +] + +use_pip = True + +exts_list = [ + ('websocket-client', '1.4.1', { + 'modulename': 'websocket', + 'checksums': ['f9611eb65c8241a67fb373bef040b3cf8ad377a9f6546a12b620b6511e8ea9ef'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('requests-unixsocket', '0.3.0', { + 'checksums': ['28304283ea9357d45fff58ad5b11e47708cfbf5806817aa59b2a363228ee971e'], + }), + ('jupyter_server', '1.11.1', { + 'checksums': ['ab7ab1cc38512f15026cbcbb96300fb46ec8b24aa162263d9edd00e0a749b1e8'], + }), + (name, version, { + 'patches': [ + 'jupyter-resource-usage-0.6.1_compatibility.patch', + 'jupyter-resource-usage-0.6.2_fix_update_cpu.patch', + ], + 'checksums': [ + '735acfe9516c68d1f50c25f74b236075da2adde49f734b24f6d2578ab9aa8d0c', # jupyter-resource-usage-0.6.2.tar.gz + # jupyter-resource-usage-0.6.1_compatibility.patch + 'b030065413bac04bd40088cd92be98bac3e92d68189d03d338986444af3953f4', + # jupyter-resource-usage-0.6.2_fix_update_cpu.patch + 'e2d2ea15211c90faebb57c1170a105f94fe0fd28055a69969dd53dad9ff7f990', + ], + }), +] + +# Add the notebook extension to the search path for jupyter notebooks +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter/', +} + +sanity_check_paths = { + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/jupyter_resource_usage', + 'lib/python%(pyshortver)s/site-packages/jupyter_server' + ], + 'files': ['bin/jupyter-server'], +} + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2_fix_update_cpu.patch b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2_fix_update_cpu.patch new file mode 100644 index 00000000000..181500591a5 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2_fix_update_cpu.patch @@ -0,0 +1,16 @@ +# Author: Caspar van Leeuwen, SURF +# If the CPU was idle (i.e. cpuPercent=0), the display showing CPU usage wouldn't update, +# because of a faulty logic. This patch fixes that. +# See https://github.com/jupyter-server/jupyter-resource-usage/pull/147 +diff -Nru jupyter-resource-usage-0.6.2.orig/jupyter_resource_usage/static/main.js jupyter-resource-usage-0.6.2/jupyter_resource_usage/static/main.js +--- jupyter-resource-usage-0.6.2.orig/jupyter_resource_usage/static/main.js 2022-09-30 19:02:36.892711996 +0200 ++++ jupyter-resource-usage-0.6.2/jupyter_resource_usage/static/main.js 2022-09-30 19:02:59.994787990 +0200 +@@ -74,7 +74,7 @@ + + // Handle CPU display + var cpuPercent = data['cpu_percent']; +- if (cpuPercent) { ++ if (cpuPercent !== undefined) { + // Remove hide CSS class if the metrics API gives us a CPU percent to display + $('#jupyter-resource-usage-display-cpu').removeClass('jupyter-resource-usage-hide'); + var maxCpu = data['cpu_count']; From 36607a9ddb89c2a619d23a06a46dd7080772513c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 1 Oct 2022 01:46:02 +0200 Subject: [PATCH 4979/9987] remove default source URLs from f90wrap --- easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb index 87eab2439f1..55a22a746dc 100644 --- a/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb +++ b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb @@ -13,7 +13,6 @@ an additional layer transparent to the final user.""" toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['23524b66ffb71365d93a701065cefb33bc3ba869bed18d0884d08fac05f097f2'] From 33b2c8c2b7396932722d01703084bb53d53aa5d6 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 1 Oct 2022 08:48:04 +0200 Subject: [PATCH 4980/9987] use pkgconf rather than pkg-config --- easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb index 6e956e7e513..a5cf58c0819 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.7-GCCcore-11.2.0.eb @@ -21,7 +21,7 @@ checksums = ['c7935b7a29e42443f6a35d35cf20ffa7d028c399303f872cd1219598a83656ae'] builddependencies = [ ('Autotools', '20210726'), ('binutils', '2.37'), - ('pkgconfig', '0.29.2'), + ('pkgconf', '1.8.0'), ] dependencies = [ From 6767e6b2937634ac43833193fe6a1a1ee4275dca Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Sat, 1 Oct 2022 10:49:27 +0200 Subject: [PATCH 4981/9987] Add Julia v1.8.2 --- .../j/Julia/Julia-1.8.2-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb new file mode 100644 index 00000000000..dcca93e7871 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.8.2' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['671cf3a450b63a717e1eedd7f69087e3856f015b2e146cb54928f19a3c05e796'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From 03d8f61650cb93c669251892bc1af1c60aa1f40e Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Sat, 1 Oct 2022 10:51:30 +0200 Subject: [PATCH 4982/9987] Add LTS julia 1.6.7 --- .../j/Julia/Julia-1.6.7-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb new file mode 100644 index 00000000000..65d335bfb8c --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.6.7' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['6c4522d595e4cbcd00157ac458a72f8aec01757053d2073f99daa39e442b2a36'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From d9be0b9a851fddce631ece65c318c3a41cb9d2b1 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sat, 1 Oct 2022 12:38:06 +0200 Subject: [PATCH 4983/9987] Delete easyconfigs.py --- test/easyconfigs/easyconfigs.py | 1512 ------------------------------- 1 file changed, 1512 deletions(-) delete mode 100644 test/easyconfigs/easyconfigs.py diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py deleted file mode 100644 index da15318ca58..00000000000 --- a/test/easyconfigs/easyconfigs.py +++ /dev/null @@ -1,1512 +0,0 @@ -## -# Copyright 2013-2022 Ghent University -# -# This file is part of EasyBuild, -# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), -# with support of Ghent University (http://ugent.be/hpc), -# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), -# Flemish Research Foundation (FWO) (http://www.fwo.be/en) -# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). -# -# https://github.com/easybuilders/easybuild -# -# EasyBuild is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation v2. -# -# EasyBuild is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with EasyBuild. If not, see . -## -""" -Unit tests for easyconfig files. - -@author: Kenneth Hoste (Ghent University) -""" -import glob -import os -import re -import shutil -import sys -import tempfile -from distutils.version import LooseVersion -from unittest import TestCase, TestLoader, main, skip - -import easybuild.main as eb_main -import easybuild.tools.options as eboptions -from easybuild.base import fancylogger -from easybuild.easyblocks.generic.configuremake import ConfigureMake -from easybuild.easyblocks.generic.pythonpackage import PythonPackage -from easybuild.framework.easyblock import EasyBlock -from easybuild.framework.easyconfig.constants import EASYCONFIG_CONSTANTS -from easybuild.framework.easyconfig.default import DEFAULT_CONFIG -from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS -from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for -from easybuild.framework.easyconfig.easyconfig import resolve_template -from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig -from easybuild.framework.easyconfig.tools import check_sha256_checksums, dep_graph, get_paths_for, process_easyconfig -from easybuild.tools import config -from easybuild.tools.build_log import EasyBuildError -from easybuild.tools.config import GENERAL_CLASS, build_option -from easybuild.tools.filetools import change_dir, is_generic_easyblock, read_file, remove_file -from easybuild.tools.filetools import verify_checksum, which, write_file -from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version -from easybuild.tools.modules import modules_tool -from easybuild.tools.py2vs3 import string_type, urlopen -from easybuild.tools.robot import check_conflicts, resolve_dependencies -from easybuild.tools.run import run_cmd -from easybuild.tools.options import set_tmpdir -from easybuild.tools.utilities import nub - - -# indicates whether all the single tests are OK, -# and that bigger tests (building dep graph, testing for conflicts, ...) can be run as well -# other than optimizing for time, this also helps to get around problems like http://bugs.python.org/issue10949 -single_tests_ok = True - - -def is_pr(): - """Return true if run in a pull request CI""" - # $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR - travis_pr_test = re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST', '')) - - # when testing a PR in GitHub Actions, $GITHUB_EVENT_NAME will be set to 'pull_request' - github_pr_test = os.environ.get('GITHUB_EVENT_NAME') == 'pull_request' - return travis_pr_test or github_pr_test - - -def get_target_branch(): - """Return the target branch of a pull request""" - # target branch should be anything other than 'master'; - # usually is 'develop', but could also be a release branch like '3.7.x' - target_branch = os.environ.get('GITHUB_BASE_REF', None) - if not target_branch: - target_branch = os.environ.get('TRAVIS_BRANCH', None) - if not target_branch: - raise RuntimeError("Did not find a target branch") - return target_branch - - -def skip_if_not_pr_to_non_main_branch(): - if not is_pr(): - return skip("Only run for pull requests") - if get_target_branch() == "main": - return skip("Not run for pull requests against main") - return lambda func: func - - -def get_files_from_diff(diff_filter, ext, basename=True): - """Return the files changed on HEAD relative to the current target branch""" - target_branch = get_target_branch() - - # relocate to top-level directory of repository to run 'git diff' command - top_dir = os.path.dirname(os.path.dirname(get_paths_for('easyconfigs')[0])) - cwd = change_dir(top_dir) - - # first determine the 'merge base' between target branch and PR branch - # cfr. https://git-scm.com/docs/git-merge-base - cmd = "git merge-base %s HEAD" % target_branch - out, ec = run_cmd(cmd, simple=False, log_ok=False) - if ec == 0: - merge_base = out.strip() - print("Merge base for %s and HEAD: %s" % (target_branch, merge_base)) - else: - msg = "Failed to determine merge base (ec: %s, output: '%s'), " - msg += "falling back to specifying target branch %s" - print(msg % (ec, out, target_branch)) - merge_base = target_branch - - # determine list of changed files using 'git diff' and merge base determined above - cmd = "git diff --name-only --diff-filter=%s %s..HEAD --" % (diff_filter, merge_base) - out, _ = run_cmd(cmd, simple=False) - if basename: - files = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith(ext)] - else: - files = [f for f in out.strip().split('\n') if f.endswith(ext)] - - change_dir(cwd) - return files - - -def get_eb_files_from_diff(diff_filter): - """Return the easyconfig files changed on HEAD relative to the current target branch""" - return get_files_from_diff(diff_filter, '.eb') - - -class EasyConfigTest(TestCase): - """Baseclass for easyconfig testcases.""" - - @classmethod - def setUpClass(cls): - """Setup environment for all tests. Called once!""" - # make sure that the EasyBuild installation is still known even if we purge an EB module - if os.getenv('EB_SCRIPT_PATH') is None: - eb_path = which('eb') - if eb_path is not None: - os.environ['EB_SCRIPT_PATH'] = eb_path - - # initialize configuration (required for e.g. default modules_tool setting) - eb_go = eboptions.parse_options(args=[]) # Ignore cmdline args as those are meant for the unittest framework - config.init(eb_go.options, eb_go.get_options_by_section('config')) - build_options = { - 'check_osdeps': False, - 'external_modules_metadata': {}, - 'force': True, - 'local_var_naming_check': 'error', - 'optarch': 'test', - 'robot_path': get_paths_for("easyconfigs")[0], - 'silent': True, - 'suffix_modules_path': GENERAL_CLASS, - 'valid_module_classes': config.module_classes(), - 'valid_stops': [x[0] for x in EasyBlock.get_steps()], - } - config.init_build_options(build_options=build_options) - set_tmpdir() - - # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains - cls.TMPDIR = tempfile.mkdtemp() - os.environ['MODULEPATH'] = cls.TMPDIR - write_file(os.path.join(cls.TMPDIR, 'craype-test'), '#%Module\n') - - log = fancylogger.getLogger("EasyConfigTest", fname=False) - - # make sure a logger is present for main - eb_main._log = log - - cls._ordered_specs = None - cls._parsed_easyconfigs = [] - cls._parsed_all_easyconfigs = False - cls._changed_ecs = None # easyconfigs changed in a PR - cls._changed_patches = None # patches changed in a PR - - @classmethod - def tearDownClass(cls): - """Cleanup after running all tests""" - shutil.rmtree(cls.TMPDIR) - - @classmethod - def parse_all_easyconfigs(cls): - """Parse all easyconfigs.""" - if cls._parsed_all_easyconfigs: - return - # all available easyconfig files - easyconfigs_path = get_paths_for("easyconfigs")[0] - specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) - parsed_specs = set(ec['spec'] for ec in cls._parsed_easyconfigs) - for spec in specs: - if spec not in parsed_specs: - cls._parsed_easyconfigs.extend(process_easyconfig(spec)) - cls._parsed_all_easyconfigs = True - - @classmethod - def resolve_all_dependencies(cls): - """Resolve dependencies between easyconfigs""" - # Parse all easyconfigs if not done yet - cls.parse_all_easyconfigs() - # filter out external modules - for ec in cls._parsed_easyconfigs: - for dep in ec['dependencies'][:]: - if dep.get('external_module', False): - ec['dependencies'].remove(dep) - cls._ordered_specs = resolve_dependencies( - cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True) - - def _get_changed_easyconfigs(self): - """Gather all added or modified easyconfigs""" - # get list of changed easyconfigs - changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M') - added_ecs_filenames = get_eb_files_from_diff(diff_filter='A') - if changed_ecs_filenames: - print("\nList of changed easyconfig files in this PR:\n\t%s" % '\n\t'.join(changed_ecs_filenames)) - if added_ecs_filenames: - print("\nList of added easyconfig files in this PR:\n\t%s" % '\n\t'.join(added_ecs_filenames)) - EasyConfigTest._changed_ecs_filenames = changed_ecs_filenames - EasyConfigTest._added_ecs_filenames = added_ecs_filenames - - # grab parsed easyconfigs for changed easyconfig files - changed_ecs = [] - for ec_fn in changed_ecs_filenames + added_ecs_filenames: - match = None - for ec in self.parsed_easyconfigs: - if os.path.basename(ec['spec']) == ec_fn: - match = ec['ec'] - break - - if match: - changed_ecs.append(match) - else: - # if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR... - # so as a last resort, try to find the easyconfig file in __archive__ - easyconfigs_path = get_paths_for("easyconfigs")[0] - specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn)) - if len(specs) == 1: - ec = process_easyconfig(specs[0])[0] - changed_ecs.append(ec['ec']) - else: - raise RuntimeError("Failed to find parsed easyconfig for %s" - " (and could not isolate it in easyconfigs archive either)" % ec_fn) - EasyConfigTest._changed_ecs = changed_ecs - - def _get_changed_patches(self): - """Gather all added or modified patches""" - - # get list of changed/added patch files - changed_patches_filenames = get_files_from_diff(diff_filter='M', ext='.patch', basename=False) - added_patches_filenames = get_files_from_diff(diff_filter='A', ext='.patch', basename=False) - - if changed_patches_filenames: - print("\nList of changed patch files in this PR:\n\t%s" % '\n\t'.join(changed_patches_filenames)) - if added_patches_filenames: - print("\nList of added patch files in this PR:\n\t%s" % '\n\t'.join(added_patches_filenames)) - - EasyConfigTest._changed_patches = changed_patches_filenames + added_patches_filenames - - @property - def parsed_easyconfigs(self): - # parse all easyconfigs if they haven't been already - EasyConfigTest.parse_all_easyconfigs() - return EasyConfigTest._parsed_easyconfigs - - @property - def ordered_specs(self): - # Resolve dependencies if not done - if EasyConfigTest._ordered_specs is None: - EasyConfigTest.resolve_all_dependencies() - return EasyConfigTest._ordered_specs - - @property - def changed_ecs_filenames(self): - if EasyConfigTest._changed_ecs is None: - self._get_changed_easyconfigs() - return EasyConfigTest._changed_ecs_filenames - - @property - def added_ecs_filenames(self): - if EasyConfigTest._changed_ecs is None: - self._get_changed_easyconfigs() - return EasyConfigTest._added_ecs_filenames - - @property - def changed_ecs(self): - if EasyConfigTest._changed_ecs is None: - self._get_changed_easyconfigs() - return EasyConfigTest._changed_ecs - - @property - def changed_patches(self): - if EasyConfigTest._changed_patches is None: - self._get_changed_patches() - return EasyConfigTest._changed_patches - - def test_dep_graph(self): - """Unit test that builds a full dependency graph.""" - # pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6 - if LooseVersion(sys.version) >= LooseVersion('2.6') and single_tests_ok: - # temporary file for dep graph - (hn, fn) = tempfile.mkstemp(suffix='.dot') - os.close(hn) - - dep_graph(fn, self.ordered_specs) - - remove_file(fn) - else: - print("(skipped dep graph test)") - - def test_conflicts(self): - """Check whether any conflicts occur in software dependency graphs.""" - - if not single_tests_ok: - print("(skipped conflicts test)") - return - - self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False), - "No conflicts detected") - - def test_deps(self): - """Perform checks on dependencies in easyconfig files""" - - fails = [] - - for ec in self.parsed_easyconfigs: - # make sure that no odd versions (like 1.13) of HDF5 are used as a dependency, - # since those are released candidates - only even versions (like 1.12) are stable releases; - # see https://docs.hdfgroup.org/archive/support/HDF5/doc/TechNotes/Version.html - for dep in ec['ec'].dependencies(): - if dep['name'] == 'HDF5': - ver = dep['version'] - if int(ver.split('.')[1]) % 2 == 1: - fail = "Odd minor versions of HDF5 should not be used as a dependency: " - fail += "found HDF5 v%s as dependency in %s" % (ver, os.path.basename(ec['spec'])) - fails.append(fail) - - self.assertFalse(len(fails), '\n'.join(sorted(fails))) - - def check_dep_vars(self, gen, dep, dep_vars): - """Check whether available variants of a particular dependency are acceptable or not.""" - - # 'guilty' until proven 'innocent' - res = False - - # filter out wrapped Java versions - # i.e. if the version of one is a prefix of the version of the other one (e.g. 1.8 & 1.8.0_181) - if dep == 'Java': - dep_vars_to_check = sorted(dep_vars.keys()) - - retained_dep_vars = [] - - while dep_vars_to_check: - dep_var = dep_vars_to_check.pop() - dep_var_version = dep_var.split(';')[0] - - # remove dep vars wrapped by current dep var - dep_vars_to_check = [x for x in dep_vars_to_check if not x.startswith(dep_var_version + '.')] - - retained_dep_vars = [x for x in retained_dep_vars if not x.startswith(dep_var_version + '.')] - - retained_dep_vars.append(dep_var) - - for key in list(dep_vars.keys()): - if key not in retained_dep_vars: - del dep_vars[key] - - version_regex = re.compile('^version: (?P[^;]+);') - - # filter out binutils with empty versionsuffix which is used to build toolchain compiler - if dep == 'binutils' and len(dep_vars) > 1: - empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')] - if len(empty_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0]) - - # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools; - # same goes for WRF and WPS; Gurobi and Rgurobi - for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS'), ('Gurobi', 'Rgurobi')]: - if dep == dep_name and len(dep_vars) > 1: - for key in list(dep_vars): - ecs = dep_vars[key] - # filter out dep variants that are only used as dependency for parent with same version - dep_ver = version_regex.search(key).group('version') - if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: - dep_vars.pop(key) - - # multiple versions of Boost is OK as long as they are deps for a matching Boost.Python - if dep == 'Boost' and len(dep_vars) > 1: - for key in list(dep_vars): - ecs = dep_vars[key] - # filter out Boost variants that are only used as dependency for Boost.Python with same version - boost_ver = version_regex.search(key).group('version') - if all(ec.startswith('Boost.Python-%s-' % boost_ver) for ec in ecs): - dep_vars.pop(key) - - # filter out Perl with -minimal versionsuffix which are only used in makeinfo-minimal - if dep == 'Perl': - minimal_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -minimal')] - if len(minimal_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != minimal_vsuff_vars[0]) - - # filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains - if dep in ['FFTW', 'imkl']: - serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] - if len(serial_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) - - # filter out BLIS and libFLAME with -amd versionsuffix - # (AMD forks, used in gobff/*-amd toolchains) - if dep in ['BLIS', 'libFLAME']: - amd_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -amd')] - if len(amd_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != amd_vsuff_vars[0]) - - # filter out ScaLAPACK with -BLIS-* versionsuffix, used in goblf toolchain - if dep == 'ScaLAPACK': - blis_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -BLIS-' in v] - if len(blis_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != blis_vsuff_vars[0]) - - if dep == 'ScaLAPACK': - # filter out ScaLAPACK with -bf versionsuffix, used in gobff toolchain - bf_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bf' in v] - if len(bf_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bf_vsuff_vars[0]) - # filter out ScaLAPACK with -bl versionsuffix, used in goblf toolchain - bl_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bl' in v] - if len(bl_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bl_vsuff_vars[0]) - - # filter out HDF5 with -serial versionsuffix which is used in HDF5 for Python (h5py) - if dep in ['HDF5']: - serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] - if len(serial_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) - - # for some dependencies, we allow exceptions for software that depends on a particular version, - # as long as that's indicated by the versionsuffix - versionsuffix_deps = ['ASE', 'Boost', 'CUDAcore', 'Java', 'Lua', - 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] - if dep in versionsuffix_deps and len(dep_vars) > 1: - - # check for '-CUDA-*' versionsuffix for CUDAcore dependency - if dep == 'CUDAcore': - dep = 'CUDA' - - for key in list(dep_vars): - dep_ver = version_regex.search(key).group('version') - # use version of Java wrapper rather than full Java version - if dep == 'Java': - dep_ver = '.'.join(dep_ver.split('.')[:2]) - # filter out dep version if all easyconfig filenames using it include specific dep version - if all(re.search('-%s-%s' % (dep, dep_ver), v) for v in dep_vars[key]): - dep_vars.pop(key) - # always retain at least one dep variant - if len(dep_vars) == 1: - break - - # filter R dep for a specific version of Python 2.x - if dep == 'R' and len(dep_vars) > 1: - for key in list(dep_vars): - if '; versionsuffix: -Python-2' in key: - dep_vars.pop(key) - # always retain at least one variant - if len(dep_vars) == 1: - break - - # filter out variants that are specific to a particular version of CUDA - cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] - if len(dep_vars) >= len(cuda_dep_vars) and len(dep_vars) > 1: - for key in list(dep_vars): - if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key): - dep_vars.pop(key) - # always retain at least one dep variant - if len(dep_vars) == 1: - break - - # some software packages require a specific (older/newer) version of a particular dependency - alt_dep_versions = { - 'jax': [(r'0\.3\.9', [r'AlphaFold-2\.2\.2-'])], - # arrow-R 6.0.0.2 is used for two R/R-bundle-Bioconductor sets (4.1.2/3.14 and 4.2.0/3.15) - 'arrow-R': [('6.0.0.2', [r'R-bundle-Bioconductor-'])], - # EMAN2 2.3 requires Boost(.Python) 1.64.0 - 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], - 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], - # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x - 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], - # ParaView 5.10.x requires FFmpeg 4.x - 'FFmpeg': [(r'4\.4\.', [r'ParaView-5\.10\.', 'OpenFOAM-v2206'])], - 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], - # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) - 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], - # VMTK 1.4.x requires ITK 4.13.x - 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], - # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) - 'Jellyfish': [(r'1\.', [r'Kraken-1\.', r'Roary-3\.12\.0', r'metaWRAP-1\.2'])], - # Libint 1.1.6 is required by older CP2K versions - 'Libint': [(r'1\.1\.6', [r'CP2K-[3-6]'])], - # libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, horton, PySCF, WIEN2k - # libxc 4.x is required by libGridXC - # (Qiskit depends on PySCF), Elk 7.x requires libxc >= 5 - 'libxc': [ - (r'[23]\.', [r'ABINIT-', r'AtomPAW-', r'CP2K-', r'GPAW-', r'horton-', - r'PySCF-', r'Qiskit-', r'WIEN2k-']), - (r'4\.', [r'libGridXC-']), - (r'5\.', [r'Elk-']), - ], - # some software depends on numba, which typically requires an older LLVM; - # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy - 'LLVM': [ - # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) - (r'8\.', [r'numba-0\.47\.0-', r'librosa-0\.7\.2-', r'BirdNET-20201214-', - r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[346]\.[23]']), - (r'10\.0\.1', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', - r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', - r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), - ], - 'Lua': [ - # SimpleITK 2.1.0 requires Lua 5.3.x, MedPy and nnU-Net depend on SimpleITK - (r'5\.3\.5', [r'nnU-Net-1\.7\.0-', r'MedPy-0\.4\.0-', r'SimpleITK-2\.1\.0-']), - ], - # TensorFlow 2.5+ requires a more recent NCCL than version 2.4.8 used in 2019b generation; - # Horovod depends on TensorFlow, so same exception required there - 'NCCL': [(r'2\.11\.4', [r'TensorFlow-2\.[5-9]\.', r'Horovod-0\.2[2-9]'])], - # rampart requires nodejs > 10, artic-ncov2019 requires rampart - 'nodejs': [('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13'])], - # some software depends on an older numba; - # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy - 'numba': [ - (r'0\.52\.0', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', - r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', - r'umap-learn-0\.4\.6-']), - ], - # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, - # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; - # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 - # WhatsHap 1.4 + medaka 1.6.0 require Pysam >= 0.18.0 (NGSpeciesID depends on medaka) - 'Pysam': [ - ('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', - 'NGSpeciesID-0.1.1.1-']), - ('0.18.0;', ['medaka-1.6.0-', 'NGSpeciesID-0.1.2.1-', 'WhatsHap-1.4-']), - ], - # OPERA requires SAMtools 0.x - 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', - r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], - # NanoPlot, NanoComp use an older version of Seaborn - 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], - # Shasta requires spoa 3.x - 'spoa': [(r'3\.4\.0', [r'Shasta-0\.8\.0-'])], - # UShER requires tbb-2020.3 as newer versions will not build - 'tbb': [('2020.3', ['UShER-0.5.0-'])], - 'TensorFlow': [ - # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), - # artic-ncov2019 requires medaka - ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), - # medaka 1.1.* and 1.2.* requires TensorFlow 2.2.0 - # (while other 2019b easyconfigs use TensorFlow 2.1.0 as dep); - # TensorFlow 2.2.0 is also used as a dep for Horovod 0.19.5; - # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 - ('2.2.0;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'Horovod-0.19.5-', 'decona-0.1.2-', - 'NGSpeciesID-0.1.1.1-']), - # medaka 1.4.3 (foss/2019b) depends on TensorFlow 2.2.2 - ('2.2.2;', ['medaka-1.4.3-']), - # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka - ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), - # AlphaFold 2.1.2 (foss/2020b) depends on TensorFlow 2.5.0 - ('2.5.0;', ['AlphaFold-2.1.2-']), - # medaka 1.5.0 (foss/2021a) depends on TensorFlow >=2.5.2, <2.6.0 - ('2.5.3;', ['medaka-1.5.0-']), - ], - # smooth-topk uses a newer version of torchvision - 'torchvision': [('0.11.3;', ['smooth-topk-1.0-20210817-'])], - # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 - # (for 2021b, UCX was updated to v1.11.2) - 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], - # WPS 3.9.1 requires WRF 3.9.1.1 - 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], - } - if dep in alt_dep_versions and len(dep_vars) > 1: - for key in list(dep_vars): - for version_pattern, parents in alt_dep_versions[dep]: - # filter out known alternative dependency versions - if re.search('^version: %s' % version_pattern, key): - # only filter if the easyconfig using this dep variants is known - if all(any(re.search(p, x) for p in parents) for x in dep_vars[key]): - dep_vars.pop(key) - - # filter out ELSI variants with -PEXSI suffix - if dep == 'ELSI' and len(dep_vars) > 1: - pexsi_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -PEXSI')] - if len(pexsi_vsuff_vars) == 1: - dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != pexsi_vsuff_vars[0]) - - # only single variant is always OK - if len(dep_vars) == 1: - res = True - - elif len(dep_vars) == 2 and dep in ['Python', 'Tkinter']: - # for Python & Tkinter, it's OK to have on 2.x and one 3.x version - v2_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 2.')] - v3_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 3.')] - if len(v2_dep_vars) == 1 and len(v3_dep_vars) == 1: - res = True - - # two variants is OK if one is for Python 2.x and the other is for Python 3.x (based on versionsuffix) - elif len(dep_vars) == 2: - py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] - py3_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-3.' in x] - if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: - res = True - - # for recent generations, there's no versionsuffix anymore for Python 3, - # but we still allow variants depending on Python 2.x + 3.x - is_recent_gen = False - full_toolchain_regex = re.compile(r'^20[1-9][0-9][ab]$') - gcc_toolchain_regex = re.compile(r'^GCC(core)?-[0-9]?[0-9]\.[0-9]$') - if full_toolchain_regex.match(gen): - is_recent_gen = LooseVersion(gen) >= LooseVersion('2020b') - elif gcc_toolchain_regex.match(gen): - genver = gen.split('-', 1)[1] - is_recent_gen = LooseVersion(genver) >= LooseVersion('10.2') - else: - raise EasyBuildError("Unkown type of toolchain generation: %s" % gen) - - if is_recent_gen: - py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] - py3_dep_vars = [x for x in dep_vars.keys() if x.strip().endswith('; versionsuffix:')] - if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: - res = True - - return res - - def test_check_dep_vars(self): - """Test check_dep_vars utility method.""" - - # one single dep version: OK - self.assertTrue(self.check_dep_vars('2019b', 'testdep', { - 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], - })) - self.assertTrue(self.check_dep_vars('2019b', 'testdep', { - 'version: 1.2.3; versionsuffix: -test': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], - })) - - # two or more dep versions (no special case: not OK) - self.assertFalse(self.check_dep_vars('2019b', 'testdep', { - 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], - })) - self.assertFalse(self.check_dep_vars('2019b', 'testdep', { - 'version: 0.0; versionsuffix:': ['foobar-0.0.eb'], - 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], - })) - - # Java is a special case, with wrapped Java versions - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - })) - # two Java wrappers is not OK - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], - })) - # OK to have two or more wrappers if versionsuffix is used to indicate exception - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - })) - # versionsuffix must be there for all easyconfigs to indicate exception - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], - })) - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 12.1.6; versionsuffix:': ['foobar-0.0-Java-12.eb'], - 'version: 12; versionsuffix:': ['foobar-0.0-Java-12.eb'], - })) - - # strange situation: odd number of Java versions - # not OK: two Java wrappers (and no versionsuffix to indicate exception) - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], - })) - # OK because of -Java-11 versionsuffix - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - })) - # not OK: two Java wrappers (and no versionsuffix to indicate exception) - self.assertFalse(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], - })) - # OK because of -Java-11 versionsuffix - self.assertTrue(self.check_dep_vars('2019b', 'Java', { - 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], - })) - - # two different versions of Boost is not OK - self.assertFalse(self.check_dep_vars('2019b', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - - # a different Boost version that is only used as dependency for a matching Boost.Python is fine - self.assertTrue(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - self.assertTrue(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], - 'version: 1.66.0; versionsuffix:': ['Boost.Python-1.66.0-gompi-2019a.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - self.assertFalse(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], - 'version: 1.66.0; versionsuffix:': ['foo-1.2.3.eb'], - 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], - })) - - self.assertTrue(self.check_dep_vars('2018a', 'Boost', { - 'version: 1.63.0; versionsuffix: -Python-2.7.14': ['EMAN2-2.21a-foss-2018a-Python-2.7.14-Boost-1.63.0.eb'], - 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2018a.eb'], - 'version: 1.66.0; versionsuffix:': ['BLAST+-2.7.1-foss-2018a.eb'], - })) - - self.assertTrue(self.check_dep_vars('2019a', 'Boost', { - 'version: 1.64.0; versionsuffix:': [ - 'Boost.Python-1.64.0-gompi-2019a.eb', - 'EMAN2-2.3-foss-2019a-Python-2.7.15.eb', - ], - 'version: 1.70.0; versionsuffix:': [ - 'BLAST+-2.9.0-gompi-2019a.eb', - 'Boost.Python-1.70.0-gompi-2019a.eb', - ], - })) - - # two variants is OK, if they're for Python 2.x and 3.x - self.assertTrue(self.check_dep_vars('2020a', 'Python', { - 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-2.7.18.eb'], - 'version: 3.8.2; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb'], - })) - - self.assertTrue(self.check_dep_vars('2020a', 'SciPy-bundle', { - 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], - 'version: 2020.03; versionsuffix: -Python-3.8.2': ['matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb'], - })) - - # for recent easyconfig generations, there's no versionsuffix anymore for Python 3 - self.assertTrue(self.check_dep_vars('2020b', 'Python', { - 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb'], - 'version: 3.8.6; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b.eb'], - })) - - self.assertTrue(self.check_dep_vars('GCCcore-10.2', 'PyYAML', { - 'version: 5.3.1; versionsuffix:': ['IPython-7.18.1-GCCcore-10.2.0.eb'], - 'version: 5.3.1; versionsuffix: -Python-2.7.18': ['IPython-7.18.1-GCCcore-10.2.0-Python-2.7.18.eb'], - })) - - self.assertTrue(self.check_dep_vars('2020b', 'SciPy-bundle', { - 'version: 2020.11; versionsuffix: -Python-2.7.18': ['matplotlib-3.3.3-foss-2020b-Python-2.7.18.eb'], - 'version: 2020.11; versionsuffix:': ['matplotlib-3.3.3-foss-2020b.eb'], - })) - - # not allowed for older generations (foss/intel 2020a or older, GCC(core) 10.1.0 or older) - self.assertFalse(self.check_dep_vars('2020a', 'SciPy-bundle', { - 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], - 'version: 2020.03; versionsuffix:': ['matplotlib-3.2.1-foss-2020a.eb'], - })) - - def test_dep_versions_per_toolchain_generation(self): - """ - Check whether there's only one dependency version per toolchain generation actively used. - This is enforced to try and limit the chance of running into conflicts when multiple modules built with - the same toolchain are loaded together. - """ - ecs_by_full_mod_name = dict((ec['full_mod_name'], ec) for ec in self.parsed_easyconfigs) - if len(ecs_by_full_mod_name) != len(self.parsed_easyconfigs): - self.fail('Easyconfigs with duplicate full_mod_name found') - - # Cache already determined dependencies - ec_to_deps = dict() - - def get_deps_for(ec): - """Get list of (direct) dependencies for specified easyconfig.""" - ec_mod_name = ec['full_mod_name'] - deps = ec_to_deps.get(ec_mod_name) - if deps is None: - deps = [] - for dep in ec['ec']['dependencies']: - dep_mod_name = dep['full_mod_name'] - deps.append((dep['name'], dep['version'], dep['versionsuffix'], dep_mod_name)) - # Note: Raises KeyError if dep not found - res = ecs_by_full_mod_name[dep_mod_name] - deps.extend(get_deps_for(res)) - ec_to_deps[ec_mod_name] = deps - - return deps - - # some software also follows {a,b} versioning scheme, - # which throws off the pattern matching done below for toolchain versions - false_positives_regex = re.compile('^MATLAB-Engine-20[0-9][0-9][ab]') - - # restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a) - # and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x - for pattern in ['20(1[89]|[2-9][0-9])[ab]', r'GCCcore-([7-9]|[1-9][0-9])\.[0-9]']: - all_deps = {} - regex = re.compile(r'^.*-(?P%s).*\.eb$' % pattern) - - # collect variants for all dependencies of easyconfigs that use a toolchain that matches - for ec in self.ordered_specs: - ec_file = os.path.basename(ec['spec']) - - # take into account software which also follows a {a,b} versioning scheme - ec_file = false_positives_regex.sub('', ec_file) - - res = regex.match(ec_file) - if res: - tc_gen = res.group('tc_gen') - all_deps_tc_gen = all_deps.setdefault(tc_gen, {}) - for dep_name, dep_ver, dep_versuff, dep_mod_name in get_deps_for(ec): - dep_variants = all_deps_tc_gen.setdefault(dep_name, {}) - # a variant is defined by version + versionsuffix - variant = "version: %s; versionsuffix: %s" % (dep_ver, dep_versuff) - # keep track of which easyconfig this is a dependency - dep_variants.setdefault(variant, set()).add(ec_file) - - # check which dependencies have more than 1 variant - multi_dep_vars, multi_dep_vars_msg = [], '' - for tc_gen in sorted(all_deps.keys()): - for dep in sorted(all_deps[tc_gen].keys()): - dep_vars = all_deps[tc_gen][dep] - if not self.check_dep_vars(tc_gen, dep, dep_vars): - multi_dep_vars.append(dep) - multi_dep_vars_msg += "\nfound %s variants of '%s' dependency " % (len(dep_vars), dep) - multi_dep_vars_msg += "in easyconfigs using '%s' toolchain generation\n* " % tc_gen - multi_dep_vars_msg += '\n* '.join("%s as dep for %s" % v for v in sorted(dep_vars.items())) - multi_dep_vars_msg += '\n' - - error_msg = "No multi-variant deps found for '%s' easyconfigs:\n%s" % (regex.pattern, multi_dep_vars_msg) - self.assertFalse(multi_dep_vars, error_msg) - - def test_sanity_check_paths(self): - """Make sure specified sanity check paths adher to the requirements.""" - - for ec in self.parsed_easyconfigs: - ec_scp = ec['ec']['sanity_check_paths'] - if ec_scp != {}: - # if sanity_check_paths is specified (i.e., non-default), it must adher to the requirements - # both 'files' and 'dirs' keys, both with list values and with at least one a non-empty list - error_msg = "sanity_check_paths for %s does not meet requirements: %s" % (ec['spec'], ec_scp) - self.assertEqual(sorted(ec_scp.keys()), ['dirs', 'files'], error_msg) - self.assertTrue(isinstance(ec_scp['dirs'], list), error_msg) - self.assertTrue(isinstance(ec_scp['files'], list), error_msg) - self.assertTrue(ec_scp['dirs'] or ec_scp['files'], error_msg) - - def test_r_libs_site_env_var(self): - """Make sure $R_LIBS_SITE is being updated, rather than $R_LIBS.""" - # cfr. https://github.com/easybuilders/easybuild-easyblocks/pull/2326 - - r_libs_ecs = [] - for ec in self.parsed_easyconfigs: - for key in ('modextrapaths', 'modextravars'): - if 'R_LIBS' in ec['ec'][key]: - r_libs_ecs.append(ec['spec']) - - error_msg = "%d easyconfigs found which set $R_LIBS, should be $R_LIBS_SITE: %s" - self.assertEqual(r_libs_ecs, [], error_msg % (len(r_libs_ecs), ', '.join(r_libs_ecs))) - - def test_easyconfig_locations(self): - """Make sure all easyconfigs files are in the right location.""" - easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[0a-z]/[^/]+$') - topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) - for (dirpath, _, filenames) in os.walk(topdir): - # ignore git/svn dirs & archived easyconfigs - if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: - continue - # check whether list of .eb files is non-empty - easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] - if easyconfig_files: - # check whether path matches required pattern - if not easyconfig_dirs_regex.search(dirpath): - # only exception: TEMPLATE.eb - if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): - self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_sha256_checksums(self): - """Make sure changed easyconfigs have SHA256 checksums in place.""" - - # list of software for which checksums can not be required, - # e.g. because 'source' files need to be constructed manually - whitelist = [ - 'Kent_tools-*', - 'MATLAB-*', - 'OCaml-*', - 'OpenFOAM-Extend-4.1-*', - # sources for old versions of Bioconductor packages are no longer available, - # so not worth adding checksums for at this point - 'R-bundle-Bioconductor-3.[2-5]', - ] - - # the check_sha256_checksums function (again) creates an EasyBlock instance - # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter - # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__; - # therefore, we need to reset 'sources' to an empty list here if Bundle is used... - # likewise for 'patches' and 'checksums' - for ec in self.changed_ecs: - if ec['easyblock'] in ['Bundle', 'PythonBundle', 'EB_OpenSSL_wrapper'] or ec['name'] in ['Clang-AOMP']: - ec['sources'] = [] - ec['patches'] = [] - ec['checksums'] = [] - - # filter out deprecated easyconfigs - retained_changed_ecs = [] - for ec in self.changed_ecs: - if not ec['deprecated']: - retained_changed_ecs.append(ec) - - checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) - self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_python_packages(self): - """Several checks for easyconfigs that install (bundles of) Python packages.""" - - # These packages do not support installation with 'pip' - whitelist_pip = [ - r'ESMPy-.*', - r'MATLAB-Engine-.*', - r'Meld-.*', - r'PyTorch-.*', - ] - - whitelist_pip_check = [ - r'Mako-1.0.4.*Python-2.7.12.*', - # no pip 9.x or newer for configparser easyconfigs using a 2016a or 2016b toolchain - r'configparser-3.5.0.*-2016[ab].*', - # mympirun is installed with system Python, pip may not be installed for system Python - r'vsc-mympirun.*', - ] - - failing_checks = [] - - python_default_urls = PythonPackage.extra_options()['source_urls'][0] - - for ec in self.changed_ecs: - - with ec.disable_templating(): - ec_fn = os.path.basename(ec.path) - easyblock = ec.get('easyblock') - exts_defaultclass = ec.get('exts_defaultclass') - exts_default_options = ec.get('exts_default_options', {}) - - download_dep_fail = ec.get('download_dep_fail') - exts_download_dep_fail = ec.get('exts_download_dep_fail') - use_pip = ec.get('use_pip') - if use_pip is None: - use_pip = exts_default_options.get('use_pip') - - # only easyconfig parameters as they are defined in the easyconfig file, - # does *not* include other easyconfig parameters with their default value! - pure_ec = ec.parser.get_config_dict() - - # download_dep_fail should be set when using PythonPackage - if easyblock == 'PythonPackage': - if download_dep_fail is None: - failing_checks.append("'download_dep_fail' should be set in %s" % ec_fn) - - if pure_ec.get('source_urls') == python_default_urls: - failing_checks.append("'source_urls' should not be defined when using the default value " - "in %s" % ec_fn) - - # use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs) - if easyblock in ['PythonBundle', 'PythonPackage']: - if use_pip is None and not any(re.match(regex, ec_fn) for regex in whitelist_pip): - failing_checks.append("'use_pip' should be set in %s" % ec_fn) - - # download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set - if easyblock == 'PythonBundle': - if download_dep_fail or exts_download_dep_fail: - fail = "'*download_dep_fail' should not be set in %s since PythonBundle easyblock is used" % ec_fn - failing_checks.append(fail) - if pure_ec.get('exts_default_options', {}).get('source_urls') == python_default_urls: - failing_checks.append("'source_urls' should not be defined in exts_default_options when using " - "the default value in %s" % ec_fn) - - elif exts_defaultclass == 'PythonPackage': - # bundle of Python packages should use PythonBundle - if easyblock == 'Bundle': - fail = "'PythonBundle' easyblock should be used for bundle of Python packages in %s" % ec_fn - failing_checks.append(fail) - else: - # both download_dep_fail and use_pip should be set via exts_default_options - # when installing Python packages as extensions - for key in ['download_dep_fail', 'use_pip']: - if exts_default_options.get(key) is None: - failing_checks.append("'%s' should be set in exts_default_options in %s" % (key, ec_fn)) - - # if Python is a dependency, that should be reflected in the versionsuffix - # Tkinter is an exception, since its version always matches the Python version anyway - # Python 3.8.6 and later are also excluded, as we consider python 3 the default python - # Also whitelist some updated versions of Amber - whitelist_python_suffix = [ - 'Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', - 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb', - 'R-keras-2.1.6-foss-2018a-R-3.4.4.eb', - ] - whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix) - has_python_dep = any(LooseVersion(dep['version']) < LooseVersion('3.8.6') - for dep in ec['dependencies'] if dep['name'] == 'Python') - if has_python_dep and ec.name != 'Tkinter' and not whitelisted: - if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): - msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn - # This is only a failure for newly added ECs, not for existing ECS - # As that would probably break many ECs - if ec_fn in self.added_ecs_filenames: - failing_checks.append(msg) - else: - print('\nNote: Failed non-critical check: ' + msg) - else: - has_recent_python3_dep = any(LooseVersion(dep['version']) >= LooseVersion('3.8.6') - for dep in ec['dependencies'] if dep['name'] == 'Python') - if has_recent_python3_dep and re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): - msg = "'-Python-%%(pyver)s' should no longer be included in versionsuffix in %s" % ec_fn - failing_checks.append(msg) - - # require that running of "pip check" during sanity check is enabled via sanity_pip_check - if easyblock in ['PythonBundle', 'PythonPackage']: - sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check') - if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip_check): - failing_checks.append("sanity_pip_check should be enabled in %s" % ec_fn) - - if failing_checks: - self.fail('\n'.join(failing_checks)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_R_packages(self): - """Several checks for easyconfigs that install (bundles of) R packages.""" - failing_checks = [] - - for ec in self.changed_ecs: - ec_fn = os.path.basename(ec.path) - exts_defaultclass = ec.get('exts_defaultclass') - if exts_defaultclass == 'RPackage' or ec.name == 'R': - seen_exts = set() - for ext in ec['exts_list']: - if isinstance(ext, (tuple, list)): - ext_name = ext[0] - else: - ext_name = ext - if ext_name in seen_exts: - failing_checks.append('%s was added multiple times to exts_list in %s' % (ext_name, ec_fn)) - else: - seen_exts.add(ext_name) - self.assertFalse(failing_checks, '\n'.join(failing_checks)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_sanity_check_paths(self): - """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" - - # some generic easyblocks already have a decent customised sanity_check_paths, - # including CMakePythonPackage, GoPackage, PythonBundle & PythonPackage; - # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. - whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'ModuleRC', - 'PythonBundle', 'PythonPackage', 'Toolchain'] - # Bundles of dependencies without files of their own - # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, - # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co - bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm'] - - failing_checks = [] - - for ec in self.changed_ecs: - easyblock = ec.get('easyblock') - if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): - - sanity_check_ok = False - - if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): - sanity_check_ok = True - - # also allow bundles that enable per-component sanity checks - elif easyblock == 'Bundle': - if ec['sanity_check_components'] or ec['sanity_check_all_components']: - sanity_check_ok = True - - if not sanity_check_ok: - ec_fn = os.path.basename(ec.path) - failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) - - self.assertFalse(failing_checks, '\n'.join(failing_checks)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_https(self): - """Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://).""" - - whitelist = [ - 'Kaiju', # invalid certificate at https://kaiju.binf.ku.dk - 'libxml2', # https://xmlsoft.org works, but invalid certificate - 'p4vasp', # https://www.p4vasp.at doesn't work - 'ITSTool', # https://itstool.org/ doesn't work - 'UCX-', # bad certificate for https://www.openucx.org - 'MUMPS', # https://mumps.enseeiht.fr doesn't work - 'PyFR', # https://www.pyfr.org doesn't work - 'PycURL', # bad certificate for https://pycurl.io/ - ] - url_whitelist = [ - # https:// doesn't work, results in index page being downloaded instead - # (see https://github.com/easybuilders/easybuild-easyconfigs/issues/9692) - 'http://isl.gforge.inria.fr', - # https:// leads to File Not Found - 'http://tau.uoregon.edu/', - # https:// has outdated SSL configurations - 'http://faculty.scs.illinois.edu', - ] - # Cache: Mapping of already checked HTTP urls to whether the HTTPS variant works - checked_urls = dict() - - def check_https_url(http_url): - """Check if the https url works""" - http_url = http_url.rstrip('/') # Remove trailing slashes - https_url_works = checked_urls.get(http_url) - if https_url_works is None: - https_url = http_url.replace('http://', 'https://') - try: - https_url_works = bool(urlopen(https_url, timeout=5)) - except Exception: - https_url_works = False - checked_urls[http_url] = https_url_works - - http_regex = re.compile('http://[^"\'\n]+', re.M) - - failing_checks = [] - for ec in self.changed_ecs: - ec_fn = os.path.basename(ec.path) - - # skip whitelisted easyconfigs - if any(ec_fn.startswith(x) for x in whitelist): - continue - - # ignore commented out lines in easyconfig files when checking for http:// URLs - ec_txt = '\n'.join(line for line in ec.rawtxt.split('\n') if not line.startswith('#')) - - for http_url in http_regex.findall(ec_txt): - - # skip whitelisted http:// URLs - if any(http_url.startswith(x) for x in url_whitelist): - continue - - if check_https_url(http_url): - failing_checks.append("Found http:// URL in %s, should be https:// : %s" % (ec_fn, http_url)) - if failing_checks: - self.fail('\n'.join(failing_checks)) - - @skip_if_not_pr_to_non_main_branch() - def test_pr_patch_descr(self): - """ - Check whether all patch files touched in PR have a description on top. - """ - no_descr_patches = [] - for patch in self.changed_patches: - patch_txt = read_file(patch) - if patch_txt.startswith('--- '): - no_descr_patches.append(patch) - - self.assertFalse(no_descr_patches, "No description found in patches: %s" % ', '.join(no_descr_patches)) - - -def template_easyconfig_test(self, spec): - """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" - - # set to False, so it's False in case of this test failing - global single_tests_ok - prev_single_tests_ok = single_tests_ok - single_tests_ok = False - - # parse easyconfig - ecs = process_easyconfig(spec) - if len(ecs) == 1: - ec = ecs[0]['ec'] - - # cache the parsed easyconfig, to avoid that it is parsed again - EasyConfigTest._parsed_easyconfigs.append(ecs[0]) - else: - self.assertTrue(False, "easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) - - # check easyconfig file name - expected_fn = '%s-%s.eb' % (ec['name'], det_full_ec_version(ec)) - msg = "Filename '%s' of parsed easyconfig matches expected filename '%s'" % (spec, expected_fn) - self.assertEqual(os.path.basename(spec), expected_fn, msg) - - name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) - - # make sure easyconfig file is in expected location - expected_subdir = os.path.join('easybuild', 'easyconfigs', letter_dir_for(name), name) - subdir = os.path.join(*spec.split(os.path.sep)[-5:-1]) - fail_msg = "Easyconfig file %s not in expected subdirectory %s" % (spec, expected_subdir) - self.assertEqual(expected_subdir, subdir, fail_msg) - - # sanity check for software name, moduleclass - self.assertEqual(ec['name'], name) - self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) - - # instantiate easyblock with easyconfig file - app_class = get_easyblock_class(easyblock, name=name) - - # check that automagic fallback to ConfigureMake isn't done (deprecated behaviour) - fn = os.path.basename(spec) - error_msg = "%s relies on automagic fallback to ConfigureMake, should use easyblock = 'ConfigureMake' instead" % fn - self.assertTrue(easyblock or app_class is not ConfigureMake, error_msg) - - # dump the easyconfig file; - # this should be done before creating the easyblock instance (done below via app_class), - # because some easyblocks (like PythonBundle) modify easyconfig parameters at initialisation - handle, test_ecfile = tempfile.mkstemp() - os.close(handle) - - ec.dump(test_ecfile) - dumped_ec = EasyConfigParser(test_ecfile).get_config_dict() - os.remove(test_ecfile) - - app = app_class(ec) - - # more sanity checks - self.assertTrue(name, app.name) - self.assertTrue(ec['version'], app.version) - - # make sure that deprecated 'dummy' toolchain is no longer used, should use 'system' toolchain instead - ec_fn = os.path.basename(spec) - error_msg_tmpl = "%s should use 'system' toolchain rather than deprecated 'dummy' toolchain" - self.assertFalse(ec['toolchain']['name'] == 'dummy', error_msg_tmpl % os.path.basename(spec)) - - # make sure that $root is not used, since it is not compatible with module files in Lua syntax - res = re.findall(r'.*\$root.*', ec.rawtxt, re.M) - error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" - self.assertFalse(res, error_msg % res) - - # check for redefined easyconfig parameters, there should be none... - param_def_regex = re.compile(r'^(?P\w+)\s*=', re.M) - keys = param_def_regex.findall(ec.rawtxt) - redefined_keys = [] - for key in sorted(nub(keys)): - cnt = keys.count(key) - if cnt > 1: - redefined_keys.append((key, cnt)) - - redefined_keys_error_msg = "There should be no redefined easyconfig parameters, found %d: " % len(redefined_keys) - redefined_keys_error_msg += ', '.join('%s (%d)' % x for x in redefined_keys) - - self.assertFalse(redefined_keys, redefined_keys_error_msg) - - # make sure old GitHub urls for EasyBuild that include 'hpcugent' are no longer used - old_urls = [ - 'github.com/hpcugent/easybuild', - 'hpcugent.github.com/easybuild', - 'hpcugent.github.io/easybuild', - ] - for old_url in old_urls: - self.assertFalse(old_url in ec.rawtxt, "Old URL '%s' not found in %s" % (old_url, spec)) - - # make sure binutils is included as a (build) dep if toolchain is GCCcore - if ec['toolchain']['name'] == 'GCCcore': - # easyblocks without a build step - non_build_blocks = ['Binary', 'JAR', 'PackedBinary', 'Tarball'] - # some software packages do not have a build step - non_build_soft = ['ANIcalculator', 'Eigen'] - - requires_binutils = ec['easyblock'] not in non_build_blocks and ec['name'] not in non_build_soft - - # let's also exclude the very special case where the system GCC is used as GCCcore, and only apply this - # exception to the dependencies of binutils (since we should eventually build a new binutils with GCCcore) - if ec['toolchain']['version'] == 'system': - binutils_complete_dependencies = ['M4', 'Bison', 'flex', 'help2man', 'zlib', 'binutils'] - requires_binutils &= bool(ec['name'] not in binutils_complete_dependencies) - - # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled) - requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) - - if requires_binutils: - # dependencies() returns both build and runtime dependencies - # in some cases, binutils can also be a runtime dep (e.g. for Clang) - # Also using GCC directly as a build dep is also allowed (it includes the correct binutils) - dep_names = [d['name'] for d in ec.dependencies()] - self.assertTrue('binutils' in dep_names or 'GCC' in dep_names, - "binutils or GCC is a build dep in %s: %s" % (spec, dep_names)) - - # make sure that OpenSSL wrapper is used rather than OS dependency, - # for easyconfigs using a 2021a (sub)toolchain or more recent common toolchain version - osdeps = ec['osdependencies'] - if osdeps: - # check whether any entry in osdependencies related to OpenSSL - openssl_osdep = False - for osdep in osdeps: - if isinstance(osdep, string_type): - osdep = [osdep] - if any('libssl' in x for x in osdep) or any('openssl' in x for x in osdep): - openssl_osdep = True - - if openssl_osdep: - tcname = ec['toolchain']['name'] - tcver = LooseVersion(ec['toolchain']['version']) - - gcc_subtc_2021a = tcname in ('GCCcore', 'GCC') and tcver > LooseVersion('10.3') - if gcc_subtc_2021a or (tcname in ('foss', 'gompi', 'iimpi', 'intel') and tcver >= LooseVersion('2021')): - self.assertFalse(openssl_osdep, "OpenSSL should not be listed as OS dependency in %s" % spec) - - src_cnt = len(ec['sources']) - patch_checksums = ec['checksums'][src_cnt:] - - # make sure all patch files are available - specdir = os.path.dirname(spec) - specfn = os.path.basename(spec) - for idx, patch in enumerate(ec['patches']): - if isinstance(patch, (tuple, list)): - patch = patch[0] - - # only check actual patch files, not other files being copied via the patch functionality - patch_full = os.path.join(specdir, patch) - if patch.endswith('.patch'): - msg = "Patch file %s is available for %s" % (patch_full, specfn) - self.assertTrue(os.path.isfile(patch_full), msg) - - # verify checksum for each patch file - if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch.endswith('.patch')): - checksum = patch_checksums[idx] - error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch, ec_fn, checksum) - res = verify_checksum(patch_full, checksum) - self.assertTrue(res, error_msg) - - # make sure 'source' step is not being skipped, - # since that implies not verifying the checksum - error_msg = "'source' step should not be skipped in %s, since that implies not verifying checksums" % ec_fn - self.assertFalse(ec['checksums'] and ('source' in ec['skipsteps']), error_msg) - - for ext in ec.get_ref('exts_list'): - if isinstance(ext, (tuple, list)) and len(ext) == 3: - ext_name = ext[0] - self.assertTrue(isinstance(ext[2], dict), - "3rd element of extension spec for %s must be a dictionary" % ext_name) - - # After the sanity check above, use collect_exts_file_info to resolve templates etc. correctly - for ext in app.collect_exts_file_info(fetch_files=False, verify_checksums=False): - try: - ext_options = ext['options'] - except KeyError: - # No options --> Only have a name which is valid, so nothing to check - continue - - checksums = ext_options.get('checksums', []) - src_cnt = len(ext_options.get('sources', [])) or 1 - patch_checksums = checksums[src_cnt:] - - for idx, ext_patch in enumerate(ext.get('patches', [])): - if isinstance(ext_patch, (tuple, list)): - ext_patch = ext_patch[0] - - # only check actual patch files, not other files being copied via the patch functionality - ext_patch_full = os.path.join(specdir, ext_patch['name']) - if ext_patch_full.endswith('.patch'): - msg = "Patch file %s is available for %s" % (ext_patch_full, specfn) - self.assertTrue(os.path.isfile(ext_patch_full), msg) - - # verify checksum for each patch file - if idx < len(patch_checksums) and (os.path.exists(ext_patch_full) or ext_patch.endswith('.patch')): - checksum = patch_checksums[idx] - error_msg = "Invalid checksum for patch %s for %s extension in %s: %s" - res = verify_checksum(ext_patch_full, checksum) - self.assertTrue(res, error_msg % (ext_patch, ext_name, ec_fn, checksum)) - - # check whether all extra_options defined for used easyblock are defined - extra_opts = app.extra_options() - for key in extra_opts: - self.assertTrue(key in app.cfg) - - app.close_log() - os.remove(app.logfile) - - # inject dummy values for templates that are only known at a later stage - dummy_template_values = { - 'builddir': '/dummy/builddir', - 'installdir': '/dummy/installdir', - 'parallel': '2', - } - ec.template_values.update(dummy_template_values) - - ec_dict = ec.parser.get_config_dict() - orig_toolchain = ec_dict['toolchain'] - for key in ec_dict: - # skip parameters for which value is equal to default value - orig_val = ec_dict[key] - if key in DEFAULT_CONFIG and orig_val == DEFAULT_CONFIG[key][0]: - continue - if key in extra_opts and orig_val == extra_opts[key][0]: - continue - if key not in DEFAULT_CONFIG and key not in extra_opts: - continue - - orig_val = resolve_template(ec_dict[key], ec.template_values) - dumped_val = resolve_template(dumped_ec[key], ec.template_values) - - # take into account that dumped value for *dependencies may include hard-coded subtoolchains - # if no easyconfig was found for the dependency with the 'parent' toolchain, - # if may get resolved using a subtoolchain, which is then hardcoded in the dumped easyconfig - if key in DEPENDENCY_PARAMETERS: - # number of dependencies should remain the same - self.assertEqual(len(orig_val), len(dumped_val)) - for orig_dep, dumped_dep in zip(orig_val, dumped_val): - # name should always match - self.assertEqual(orig_dep[0], dumped_dep[0]) - - # version should always match, or be a possibility from the version dict - if isinstance(orig_dep[1], dict): - self.assertTrue(dumped_dep[1] in orig_dep[1].values()) - else: - self.assertEqual(orig_dep[1], dumped_dep[1]) - - # 3rd value is versionsuffix; - if len(dumped_dep) >= 3: - # if no versionsuffix was specified in original dep spec, then dumped value should be empty string - if len(orig_dep) >= 3: - self.assertEqual(dumped_dep[2], orig_dep[2]) - else: - self.assertEqual(dumped_dep[2], '') - - # 4th value is toolchain spec - if len(dumped_dep) >= 4: - if len(orig_dep) >= 4: - # if True was used to indicate that dependency should use system toolchain, - # then we need to compare the value for the dumped easyconfig more carefully; - # see also https://github.com/easybuilders/easybuild-framework/pull/4069 - if orig_dep[3] is True: - self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) - else: - self.assertEqual(dumped_dep[3], orig_dep[3]) - else: - # if a subtoolchain is specifed (only) in the dumped easyconfig, - # it should *not* be the same as the parent toolchain - self.assertNotEqual(dumped_dep[3], (orig_toolchain['name'], orig_toolchain['version'])) - - # take into account that for some string-valued easyconfig parameters (configopts & co), - # the easyblock may have injected additional values, which affects the dumped easyconfig file - elif isinstance(orig_val, string_type): - error_msg = "%s value '%s' should start with '%s'" % (key, dumped_val, orig_val) - self.assertTrue(dumped_val.startswith(orig_val), error_msg) - else: - error_msg = "%s value should be equal in original and dumped easyconfig: '%s' vs '%s'" - self.assertEqual(orig_val, dumped_val, error_msg % (key, orig_val, dumped_val)) - - # test passed, so set back to True - single_tests_ok = True and prev_single_tests_ok - - -def suite(loader=None): - """Return all easyblock initialisation tests.""" - def make_inner_test(spec_path): - def innertest(self): - template_easyconfig_test(self, spec_path) - return innertest - - # dynamically generate a separate test for each of the available easyconfigs - # define new inner functions that can be added as class methods to InitTest - easyconfigs_path = get_paths_for('easyconfigs')[0] - cnt = 0 - for (subpath, dirs, specs) in os.walk(easyconfigs_path, topdown=True): - - # ignore archived easyconfigs - if '__archive__' in dirs: - dirs.remove('__archive__') - - for spec in specs: - if spec.endswith('.eb') and spec != 'TEMPLATE.eb': - cnt += 1 - innertest = make_inner_test(os.path.join(subpath, spec)) - innertest.__doc__ = "Test for easyconfig %s" % spec - # double underscore so parsing tests are run first - innertest.__name__ = "test__parse_easyconfig_%s" % spec - setattr(EasyConfigTest, innertest.__name__, innertest) - - print("Found %s easyconfigs..." % cnt) - if not loader: - loader = TestLoader() - return loader.loadTestsFromTestCase(EasyConfigTest) - - -if __name__ == '__main__': - main() From e3096767a8806ccd2bd2b595c934b4e94e699754 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 1 Oct 2022 12:44:25 +0200 Subject: [PATCH 4984/9987] re-add accidentally deleted test/easyconfigs/easyconfigs.py --- test/easyconfigs/easyconfigs.py | 1510 +++++++++++++++++++++++++++++++ 1 file changed, 1510 insertions(+) create mode 100644 test/easyconfigs/easyconfigs.py diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py new file mode 100644 index 00000000000..0fb05afe876 --- /dev/null +++ b/test/easyconfigs/easyconfigs.py @@ -0,0 +1,1510 @@ +## +# Copyright 2013-2022 Ghent University +# +# This file is part of EasyBuild, +# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), +# with support of Ghent University (http://ugent.be/hpc), +# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be), +# Flemish Research Foundation (FWO) (http://www.fwo.be/en) +# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en). +# +# https://github.com/easybuilders/easybuild +# +# EasyBuild is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation v2. +# +# EasyBuild is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with EasyBuild. If not, see . +## +""" +Unit tests for easyconfig files. + +@author: Kenneth Hoste (Ghent University) +""" +import glob +import os +import re +import shutil +import sys +import tempfile +from distutils.version import LooseVersion +from unittest import TestCase, TestLoader, main, skip + +import easybuild.main as eb_main +import easybuild.tools.options as eboptions +from easybuild.base import fancylogger +from easybuild.easyblocks.generic.configuremake import ConfigureMake +from easybuild.easyblocks.generic.pythonpackage import PythonPackage +from easybuild.framework.easyblock import EasyBlock +from easybuild.framework.easyconfig.constants import EASYCONFIG_CONSTANTS +from easybuild.framework.easyconfig.default import DEFAULT_CONFIG +from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS +from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for +from easybuild.framework.easyconfig.easyconfig import resolve_template +from easybuild.framework.easyconfig.parser import EasyConfigParser, fetch_parameters_from_easyconfig +from easybuild.framework.easyconfig.tools import check_sha256_checksums, dep_graph, get_paths_for, process_easyconfig +from easybuild.tools import config +from easybuild.tools.build_log import EasyBuildError +from easybuild.tools.config import GENERAL_CLASS, build_option +from easybuild.tools.filetools import change_dir, is_generic_easyblock, read_file, remove_file +from easybuild.tools.filetools import verify_checksum, which, write_file +from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version +from easybuild.tools.modules import modules_tool +from easybuild.tools.py2vs3 import string_type, urlopen +from easybuild.tools.robot import check_conflicts, resolve_dependencies +from easybuild.tools.run import run_cmd +from easybuild.tools.options import set_tmpdir +from easybuild.tools.utilities import nub + + +# indicates whether all the single tests are OK, +# and that bigger tests (building dep graph, testing for conflicts, ...) can be run as well +# other than optimizing for time, this also helps to get around problems like http://bugs.python.org/issue10949 +single_tests_ok = True + + +def is_pr(): + """Return true if run in a pull request CI""" + # $TRAVIS_PULL_REQUEST should be a PR number, otherwise we're not running tests for a PR + travis_pr_test = re.match('^[0-9]+$', os.environ.get('TRAVIS_PULL_REQUEST', '')) + + # when testing a PR in GitHub Actions, $GITHUB_EVENT_NAME will be set to 'pull_request' + github_pr_test = os.environ.get('GITHUB_EVENT_NAME') == 'pull_request' + return travis_pr_test or github_pr_test + + +def get_target_branch(): + """Return the target branch of a pull request""" + # target branch should be anything other than 'master'; + # usually is 'develop', but could also be a release branch like '3.7.x' + target_branch = os.environ.get('GITHUB_BASE_REF', None) + if not target_branch: + target_branch = os.environ.get('TRAVIS_BRANCH', None) + if not target_branch: + raise RuntimeError("Did not find a target branch") + return target_branch + + +def skip_if_not_pr_to_non_main_branch(): + if not is_pr(): + return skip("Only run for pull requests") + if get_target_branch() == "main": + return skip("Not run for pull requests against main") + return lambda func: func + + +def get_files_from_diff(diff_filter, ext, basename=True): + """Return the files changed on HEAD relative to the current target branch""" + target_branch = get_target_branch() + + # relocate to top-level directory of repository to run 'git diff' command + top_dir = os.path.dirname(os.path.dirname(get_paths_for('easyconfigs')[0])) + cwd = change_dir(top_dir) + + # first determine the 'merge base' between target branch and PR branch + # cfr. https://git-scm.com/docs/git-merge-base + cmd = "git merge-base %s HEAD" % target_branch + out, ec = run_cmd(cmd, simple=False, log_ok=False) + if ec == 0: + merge_base = out.strip() + print("Merge base for %s and HEAD: %s" % (target_branch, merge_base)) + else: + msg = "Failed to determine merge base (ec: %s, output: '%s'), " + msg += "falling back to specifying target branch %s" + print(msg % (ec, out, target_branch)) + merge_base = target_branch + + # determine list of changed files using 'git diff' and merge base determined above + cmd = "git diff --name-only --diff-filter=%s %s..HEAD --" % (diff_filter, merge_base) + out, _ = run_cmd(cmd, simple=False) + if basename: + files = [os.path.basename(f) for f in out.strip().split('\n') if f.endswith(ext)] + else: + files = [f for f in out.strip().split('\n') if f.endswith(ext)] + + change_dir(cwd) + return files + + +def get_eb_files_from_diff(diff_filter): + """Return the easyconfig files changed on HEAD relative to the current target branch""" + return get_files_from_diff(diff_filter, '.eb') + + +class EasyConfigTest(TestCase): + """Baseclass for easyconfig testcases.""" + + @classmethod + def setUpClass(cls): + """Setup environment for all tests. Called once!""" + # make sure that the EasyBuild installation is still known even if we purge an EB module + if os.getenv('EB_SCRIPT_PATH') is None: + eb_path = which('eb') + if eb_path is not None: + os.environ['EB_SCRIPT_PATH'] = eb_path + + # initialize configuration (required for e.g. default modules_tool setting) + eb_go = eboptions.parse_options(args=[]) # Ignore cmdline args as those are meant for the unittest framework + config.init(eb_go.options, eb_go.get_options_by_section('config')) + build_options = { + 'check_osdeps': False, + 'external_modules_metadata': {}, + 'force': True, + 'local_var_naming_check': 'error', + 'optarch': 'test', + 'robot_path': get_paths_for("easyconfigs")[0], + 'silent': True, + 'suffix_modules_path': GENERAL_CLASS, + 'valid_module_classes': config.module_classes(), + 'valid_stops': [x[0] for x in EasyBlock.get_steps()], + } + config.init_build_options(build_options=build_options) + set_tmpdir() + + # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains + cls.TMPDIR = tempfile.mkdtemp() + os.environ['MODULEPATH'] = cls.TMPDIR + write_file(os.path.join(cls.TMPDIR, 'craype-test'), '#%Module\n') + + log = fancylogger.getLogger("EasyConfigTest", fname=False) + + # make sure a logger is present for main + eb_main._log = log + + cls._ordered_specs = None + cls._parsed_easyconfigs = [] + cls._parsed_all_easyconfigs = False + cls._changed_ecs = None # easyconfigs changed in a PR + cls._changed_patches = None # patches changed in a PR + + @classmethod + def tearDownClass(cls): + """Cleanup after running all tests""" + shutil.rmtree(cls.TMPDIR) + + @classmethod + def parse_all_easyconfigs(cls): + """Parse all easyconfigs.""" + if cls._parsed_all_easyconfigs: + return + # all available easyconfig files + easyconfigs_path = get_paths_for("easyconfigs")[0] + specs = glob.glob('%s/*/*/*.eb' % easyconfigs_path) + parsed_specs = set(ec['spec'] for ec in cls._parsed_easyconfigs) + for spec in specs: + if spec not in parsed_specs: + cls._parsed_easyconfigs.extend(process_easyconfig(spec)) + cls._parsed_all_easyconfigs = True + + @classmethod + def resolve_all_dependencies(cls): + """Resolve dependencies between easyconfigs""" + # Parse all easyconfigs if not done yet + cls.parse_all_easyconfigs() + # filter out external modules + for ec in cls._parsed_easyconfigs: + for dep in ec['dependencies'][:]: + if dep.get('external_module', False): + ec['dependencies'].remove(dep) + cls._ordered_specs = resolve_dependencies( + cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True) + + def _get_changed_easyconfigs(self): + """Gather all added or modified easyconfigs""" + # get list of changed easyconfigs + changed_ecs_filenames = get_eb_files_from_diff(diff_filter='M') + added_ecs_filenames = get_eb_files_from_diff(diff_filter='A') + if changed_ecs_filenames: + print("\nList of changed easyconfig files in this PR:\n\t%s" % '\n\t'.join(changed_ecs_filenames)) + if added_ecs_filenames: + print("\nList of added easyconfig files in this PR:\n\t%s" % '\n\t'.join(added_ecs_filenames)) + EasyConfigTest._changed_ecs_filenames = changed_ecs_filenames + EasyConfigTest._added_ecs_filenames = added_ecs_filenames + + # grab parsed easyconfigs for changed easyconfig files + changed_ecs = [] + for ec_fn in changed_ecs_filenames + added_ecs_filenames: + match = None + for ec in self.parsed_easyconfigs: + if os.path.basename(ec['spec']) == ec_fn: + match = ec['ec'] + break + + if match: + changed_ecs.append(match) + else: + # if no easyconfig is found, it's possible some archived easyconfigs were touched in the PR... + # so as a last resort, try to find the easyconfig file in __archive__ + easyconfigs_path = get_paths_for("easyconfigs")[0] + specs = glob.glob('%s/__archive__/*/*/%s' % (easyconfigs_path, ec_fn)) + if len(specs) == 1: + ec = process_easyconfig(specs[0])[0] + changed_ecs.append(ec['ec']) + else: + raise RuntimeError("Failed to find parsed easyconfig for %s" + " (and could not isolate it in easyconfigs archive either)" % ec_fn) + EasyConfigTest._changed_ecs = changed_ecs + + def _get_changed_patches(self): + """Gather all added or modified patches""" + + # get list of changed/added patch files + changed_patches_filenames = get_files_from_diff(diff_filter='M', ext='.patch', basename=False) + added_patches_filenames = get_files_from_diff(diff_filter='A', ext='.patch', basename=False) + + if changed_patches_filenames: + print("\nList of changed patch files in this PR:\n\t%s" % '\n\t'.join(changed_patches_filenames)) + if added_patches_filenames: + print("\nList of added patch files in this PR:\n\t%s" % '\n\t'.join(added_patches_filenames)) + + EasyConfigTest._changed_patches = changed_patches_filenames + added_patches_filenames + + @property + def parsed_easyconfigs(self): + # parse all easyconfigs if they haven't been already + EasyConfigTest.parse_all_easyconfigs() + return EasyConfigTest._parsed_easyconfigs + + @property + def ordered_specs(self): + # Resolve dependencies if not done + if EasyConfigTest._ordered_specs is None: + EasyConfigTest.resolve_all_dependencies() + return EasyConfigTest._ordered_specs + + @property + def changed_ecs_filenames(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._changed_ecs_filenames + + @property + def added_ecs_filenames(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._added_ecs_filenames + + @property + def changed_ecs(self): + if EasyConfigTest._changed_ecs is None: + self._get_changed_easyconfigs() + return EasyConfigTest._changed_ecs + + @property + def changed_patches(self): + if EasyConfigTest._changed_patches is None: + self._get_changed_patches() + return EasyConfigTest._changed_patches + + def test_dep_graph(self): + """Unit test that builds a full dependency graph.""" + # pygraph dependencies required for constructing dependency graph are not available prior to Python 2.6 + if LooseVersion(sys.version) >= LooseVersion('2.6') and single_tests_ok: + # temporary file for dep graph + (hn, fn) = tempfile.mkstemp(suffix='.dot') + os.close(hn) + + dep_graph(fn, self.ordered_specs) + + remove_file(fn) + else: + print("(skipped dep graph test)") + + def test_conflicts(self): + """Check whether any conflicts occur in software dependency graphs.""" + + if not single_tests_ok: + print("(skipped conflicts test)") + return + + self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False), + "No conflicts detected") + + def test_deps(self): + """Perform checks on dependencies in easyconfig files""" + + fails = [] + + for ec in self.parsed_easyconfigs: + # make sure that no odd versions (like 1.13) of HDF5 are used as a dependency, + # since those are released candidates - only even versions (like 1.12) are stable releases; + # see https://docs.hdfgroup.org/archive/support/HDF5/doc/TechNotes/Version.html + for dep in ec['ec'].dependencies(): + if dep['name'] == 'HDF5': + ver = dep['version'] + if int(ver.split('.')[1]) % 2 == 1: + fail = "Odd minor versions of HDF5 should not be used as a dependency: " + fail += "found HDF5 v%s as dependency in %s" % (ver, os.path.basename(ec['spec'])) + fails.append(fail) + + self.assertFalse(len(fails), '\n'.join(sorted(fails))) + + def check_dep_vars(self, gen, dep, dep_vars): + """Check whether available variants of a particular dependency are acceptable or not.""" + + # 'guilty' until proven 'innocent' + res = False + + # filter out wrapped Java versions + # i.e. if the version of one is a prefix of the version of the other one (e.g. 1.8 & 1.8.0_181) + if dep == 'Java': + dep_vars_to_check = sorted(dep_vars.keys()) + + retained_dep_vars = [] + + while dep_vars_to_check: + dep_var = dep_vars_to_check.pop() + dep_var_version = dep_var.split(';')[0] + + # remove dep vars wrapped by current dep var + dep_vars_to_check = [x for x in dep_vars_to_check if not x.startswith(dep_var_version + '.')] + + retained_dep_vars = [x for x in retained_dep_vars if not x.startswith(dep_var_version + '.')] + + retained_dep_vars.append(dep_var) + + for key in list(dep_vars.keys()): + if key not in retained_dep_vars: + del dep_vars[key] + + version_regex = re.compile('^version: (?P[^;]+);') + + # filter out binutils with empty versionsuffix which is used to build toolchain compiler + if dep == 'binutils' and len(dep_vars) > 1: + empty_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: ')] + if len(empty_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0]) + + # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools; + # same goes for WRF and WPS; Gurobi and Rgurobi + for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS'), ('Gurobi', 'Rgurobi')]: + if dep == dep_name and len(dep_vars) > 1: + for key in list(dep_vars): + ecs = dep_vars[key] + # filter out dep variants that are only used as dependency for parent with same version + dep_ver = version_regex.search(key).group('version') + if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: + dep_vars.pop(key) + + # multiple versions of Boost is OK as long as they are deps for a matching Boost.Python + if dep == 'Boost' and len(dep_vars) > 1: + for key in list(dep_vars): + ecs = dep_vars[key] + # filter out Boost variants that are only used as dependency for Boost.Python with same version + boost_ver = version_regex.search(key).group('version') + if all(ec.startswith('Boost.Python-%s-' % boost_ver) for ec in ecs): + dep_vars.pop(key) + + # filter out Perl with -minimal versionsuffix which are only used in makeinfo-minimal + if dep == 'Perl': + minimal_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -minimal')] + if len(minimal_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != minimal_vsuff_vars[0]) + + # filter out FFTW and imkl with -serial versionsuffix which are used in non-MPI subtoolchains + if dep in ['FFTW', 'imkl']: + serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] + if len(serial_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) + + # filter out BLIS and libFLAME with -amd versionsuffix + # (AMD forks, used in gobff/*-amd toolchains) + if dep in ['BLIS', 'libFLAME']: + amd_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -amd')] + if len(amd_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != amd_vsuff_vars[0]) + + # filter out ScaLAPACK with -BLIS-* versionsuffix, used in goblf toolchain + if dep == 'ScaLAPACK': + blis_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -BLIS-' in v] + if len(blis_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != blis_vsuff_vars[0]) + + if dep == 'ScaLAPACK': + # filter out ScaLAPACK with -bf versionsuffix, used in gobff toolchain + bf_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bf' in v] + if len(bf_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bf_vsuff_vars[0]) + # filter out ScaLAPACK with -bl versionsuffix, used in goblf toolchain + bl_vsuff_vars = [v for v in dep_vars.keys() if '; versionsuffix: -bl' in v] + if len(bl_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != bl_vsuff_vars[0]) + + # filter out HDF5 with -serial versionsuffix which is used in HDF5 for Python (h5py) + if dep in ['HDF5']: + serial_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -serial')] + if len(serial_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != serial_vsuff_vars[0]) + + # for some dependencies, we allow exceptions for software that depends on a particular version, + # as long as that's indicated by the versionsuffix + versionsuffix_deps = ['ASE', 'Boost', 'CUDAcore', 'Java', 'Lua', + 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] + if dep in versionsuffix_deps and len(dep_vars) > 1: + + # check for '-CUDA-*' versionsuffix for CUDAcore dependency + if dep == 'CUDAcore': + dep = 'CUDA' + + for key in list(dep_vars): + dep_ver = version_regex.search(key).group('version') + # use version of Java wrapper rather than full Java version + if dep == 'Java': + dep_ver = '.'.join(dep_ver.split('.')[:2]) + # filter out dep version if all easyconfig filenames using it include specific dep version + if all(re.search('-%s-%s' % (dep, dep_ver), v) for v in dep_vars[key]): + dep_vars.pop(key) + # always retain at least one dep variant + if len(dep_vars) == 1: + break + + # filter R dep for a specific version of Python 2.x + if dep == 'R' and len(dep_vars) > 1: + for key in list(dep_vars): + if '; versionsuffix: -Python-2' in key: + dep_vars.pop(key) + # always retain at least one variant + if len(dep_vars) == 1: + break + + # filter out variants that are specific to a particular version of CUDA + cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] + if len(dep_vars) >= len(cuda_dep_vars) and len(dep_vars) > 1: + for key in list(dep_vars): + if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key): + dep_vars.pop(key) + # always retain at least one dep variant + if len(dep_vars) == 1: + break + + # some software packages require a specific (older/newer) version of a particular dependency + alt_dep_versions = { + 'jax': [(r'0\.3\.9', [r'AlphaFold-2\.2\.2-'])], + # arrow-R 6.0.0.2 is used for two R/R-bundle-Bioconductor sets (4.1.2/3.14 and 4.2.0/3.15) + 'arrow-R': [('6.0.0.2', [r'R-bundle-Bioconductor-'])], + # EMAN2 2.3 requires Boost(.Python) 1.64.0 + 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], + 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], + # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x + 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], + 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], + # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) + 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], + # VMTK 1.4.x requires ITK 4.13.x + 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], + # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) + 'Jellyfish': [(r'1\.', [r'Kraken-1\.', r'Roary-3\.12\.0', r'metaWRAP-1\.2'])], + # Libint 1.1.6 is required by older CP2K versions + 'Libint': [(r'1\.1\.6', [r'CP2K-[3-6]'])], + # libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, horton, PySCF, WIEN2k + # libxc 4.x is required by libGridXC + # (Qiskit depends on PySCF), Elk 7.x requires libxc >= 5 + 'libxc': [ + (r'[23]\.', [r'ABINIT-', r'AtomPAW-', r'CP2K-', r'GPAW-', r'horton-', + r'PySCF-', r'Qiskit-', r'WIEN2k-']), + (r'4\.', [r'libGridXC-']), + (r'5\.', [r'Elk-']), + ], + # some software depends on numba, which typically requires an older LLVM; + # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy + 'LLVM': [ + # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) + (r'8\.', [r'numba-0\.47\.0-', r'librosa-0\.7\.2-', r'BirdNET-20201214-', + r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[346]\.[23]']), + (r'10\.0\.1', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', + r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', + r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), + ], + 'Lua': [ + # SimpleITK 2.1.0 requires Lua 5.3.x, MedPy and nnU-Net depend on SimpleITK + (r'5\.3\.5', [r'nnU-Net-1\.7\.0-', r'MedPy-0\.4\.0-', r'SimpleITK-2\.1\.0-']), + ], + # TensorFlow 2.5+ requires a more recent NCCL than version 2.4.8 used in 2019b generation; + # Horovod depends on TensorFlow, so same exception required there + 'NCCL': [(r'2\.11\.4', [r'TensorFlow-2\.[5-9]\.', r'Horovod-0\.2[2-9]'])], + # rampart requires nodejs > 10, artic-ncov2019 requires rampart + 'nodejs': [('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13'])], + # some software depends on an older numba; + # this includes BirdNET, cell2location, cryoDRGN, librosa, PyOD, Python-Geometric, scVelo, scanpy + 'numba': [ + (r'0\.52\.0', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', + r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', + r'umap-learn-0\.4\.6-']), + ], + # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, + # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; + # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 + # WhatsHap 1.4 + medaka 1.6.0 require Pysam >= 0.18.0 (NGSpeciesID depends on medaka) + 'Pysam': [ + ('0.16.0.1;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'medaka-1.4.3-', 'decona-0.1.2-', + 'NGSpeciesID-0.1.1.1-']), + ('0.18.0;', ['medaka-1.6.0-', 'NGSpeciesID-0.1.2.1-', 'WhatsHap-1.4-']), + ], + # OPERA requires SAMtools 0.x + 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', + r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], + # NanoPlot, NanoComp use an older version of Seaborn + 'Seaborn': [(r'0\.10\.1', [r'NanoComp-1\.13\.1-', r'NanoPlot-1\.33\.0-'])], + # Shasta requires spoa 3.x + 'spoa': [(r'3\.4\.0', [r'Shasta-0\.8\.0-'])], + # UShER requires tbb-2020.3 as newer versions will not build + 'tbb': [('2020.3', ['UShER-0.5.0-'])], + 'TensorFlow': [ + # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), + # artic-ncov2019 requires medaka + ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), + # medaka 1.1.* and 1.2.* requires TensorFlow 2.2.0 + # (while other 2019b easyconfigs use TensorFlow 2.1.0 as dep); + # TensorFlow 2.2.0 is also used as a dep for Horovod 0.19.5; + # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 + ('2.2.0;', ['medaka-1.2.[0]-', 'medaka-1.1.[13]-', 'Horovod-0.19.5-', 'decona-0.1.2-', + 'NGSpeciesID-0.1.1.1-']), + # medaka 1.4.3 (foss/2019b) depends on TensorFlow 2.2.2 + ('2.2.2;', ['medaka-1.4.3-']), + # medaka 1.4.3 (foss/2020b) depends on TensorFlow 2.2.3; longread_umi and artic depend on medaka + ('2.2.3;', ['medaka-1.4.3-', 'artic-ncov2019-2021.06.24-', 'longread_umi-0.3.2-']), + # AlphaFold 2.1.2 (foss/2020b) depends on TensorFlow 2.5.0 + ('2.5.0;', ['AlphaFold-2.1.2-']), + # medaka 1.5.0 (foss/2021a) depends on TensorFlow >=2.5.2, <2.6.0 + ('2.5.3;', ['medaka-1.5.0-']), + ], + # smooth-topk uses a newer version of torchvision + 'torchvision': [('0.11.3;', ['smooth-topk-1.0-20210817-'])], + # for the sake of backwards compatibility, keep UCX-CUDA v1.11.0 which depends on UCX v1.11.0 + # (for 2021b, UCX was updated to v1.11.2) + 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], + # WPS 3.9.1 requires WRF 3.9.1.1 + 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], + } + if dep in alt_dep_versions and len(dep_vars) > 1: + for key in list(dep_vars): + for version_pattern, parents in alt_dep_versions[dep]: + # filter out known alternative dependency versions + if re.search('^version: %s' % version_pattern, key): + # only filter if the easyconfig using this dep variants is known + if all(any(re.search(p, x) for p in parents) for x in dep_vars[key]): + dep_vars.pop(key) + + # filter out ELSI variants with -PEXSI suffix + if dep == 'ELSI' and len(dep_vars) > 1: + pexsi_vsuff_vars = [v for v in dep_vars.keys() if v.endswith('versionsuffix: -PEXSI')] + if len(pexsi_vsuff_vars) == 1: + dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != pexsi_vsuff_vars[0]) + + # only single variant is always OK + if len(dep_vars) == 1: + res = True + + elif len(dep_vars) == 2 and dep in ['Python', 'Tkinter']: + # for Python & Tkinter, it's OK to have on 2.x and one 3.x version + v2_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 2.')] + v3_dep_vars = [x for x in dep_vars.keys() if x.startswith('version: 3.')] + if len(v2_dep_vars) == 1 and len(v3_dep_vars) == 1: + res = True + + # two variants is OK if one is for Python 2.x and the other is for Python 3.x (based on versionsuffix) + elif len(dep_vars) == 2: + py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] + py3_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-3.' in x] + if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: + res = True + + # for recent generations, there's no versionsuffix anymore for Python 3, + # but we still allow variants depending on Python 2.x + 3.x + is_recent_gen = False + full_toolchain_regex = re.compile(r'^20[1-9][0-9][ab]$') + gcc_toolchain_regex = re.compile(r'^GCC(core)?-[0-9]?[0-9]\.[0-9]$') + if full_toolchain_regex.match(gen): + is_recent_gen = LooseVersion(gen) >= LooseVersion('2020b') + elif gcc_toolchain_regex.match(gen): + genver = gen.split('-', 1)[1] + is_recent_gen = LooseVersion(genver) >= LooseVersion('10.2') + else: + raise EasyBuildError("Unkown type of toolchain generation: %s" % gen) + + if is_recent_gen: + py2_dep_vars = [x for x in dep_vars.keys() if '; versionsuffix: -Python-2.' in x] + py3_dep_vars = [x for x in dep_vars.keys() if x.strip().endswith('; versionsuffix:')] + if len(py2_dep_vars) == 1 and len(py3_dep_vars) == 1: + res = True + + return res + + def test_check_dep_vars(self): + """Test check_dep_vars utility method.""" + + # one single dep version: OK + self.assertTrue(self.check_dep_vars('2019b', 'testdep', { + 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], + })) + self.assertTrue(self.check_dep_vars('2019b', 'testdep', { + 'version: 1.2.3; versionsuffix: -test': ['foo-1.2.3.eb', 'bar-4.5.6.eb'], + })) + + # two or more dep versions (no special case: not OK) + self.assertFalse(self.check_dep_vars('2019b', 'testdep', { + 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], + })) + self.assertFalse(self.check_dep_vars('2019b', 'testdep', { + 'version: 0.0; versionsuffix:': ['foobar-0.0.eb'], + 'version: 1.2.3; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 4.5.6; versionsuffix:': ['bar-4.5.6.eb'], + })) + + # Java is a special case, with wrapped Java versions + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + })) + # two Java wrappers is not OK + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], + })) + # OK to have two or more wrappers if versionsuffix is used to indicate exception + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + })) + # versionsuffix must be there for all easyconfigs to indicate exception + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb', 'bar-4.5.6.eb'], + })) + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 12.1.6; versionsuffix:': ['foobar-0.0-Java-12.eb'], + 'version: 12; versionsuffix:': ['foobar-0.0-Java-12.eb'], + })) + + # strange situation: odd number of Java versions + # not OK: two Java wrappers (and no versionsuffix to indicate exception) + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], + })) + # OK because of -Java-11 versionsuffix + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8.0_221; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + })) + # not OK: two Java wrappers (and no versionsuffix to indicate exception) + self.assertFalse(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6.eb'], + })) + # OK because of -Java-11 versionsuffix + self.assertTrue(self.check_dep_vars('2019b', 'Java', { + 'version: 1.8; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 11.0.2; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + 'version: 11; versionsuffix:': ['bar-4.5.6-Java-11.eb'], + })) + + # two different versions of Boost is not OK + self.assertFalse(self.check_dep_vars('2019b', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + + # a different Boost version that is only used as dependency for a matching Boost.Python is fine + self.assertTrue(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + self.assertTrue(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], + 'version: 1.66.0; versionsuffix:': ['Boost.Python-1.66.0-gompi-2019a.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + self.assertFalse(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2019a.eb'], + 'version: 1.66.0; versionsuffix:': ['foo-1.2.3.eb'], + 'version: 1.70.0; versionsuffix:': ['foo-2.3.4.eb'], + })) + + self.assertTrue(self.check_dep_vars('2018a', 'Boost', { + 'version: 1.63.0; versionsuffix: -Python-2.7.14': ['EMAN2-2.21a-foss-2018a-Python-2.7.14-Boost-1.63.0.eb'], + 'version: 1.64.0; versionsuffix:': ['Boost.Python-1.64.0-gompi-2018a.eb'], + 'version: 1.66.0; versionsuffix:': ['BLAST+-2.7.1-foss-2018a.eb'], + })) + + self.assertTrue(self.check_dep_vars('2019a', 'Boost', { + 'version: 1.64.0; versionsuffix:': [ + 'Boost.Python-1.64.0-gompi-2019a.eb', + 'EMAN2-2.3-foss-2019a-Python-2.7.15.eb', + ], + 'version: 1.70.0; versionsuffix:': [ + 'BLAST+-2.9.0-gompi-2019a.eb', + 'Boost.Python-1.70.0-gompi-2019a.eb', + ], + })) + + # two variants is OK, if they're for Python 2.x and 3.x + self.assertTrue(self.check_dep_vars('2020a', 'Python', { + 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-2.7.18.eb'], + 'version: 3.8.2; versionsuffix:': ['SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb'], + })) + + self.assertTrue(self.check_dep_vars('2020a', 'SciPy-bundle', { + 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], + 'version: 2020.03; versionsuffix: -Python-3.8.2': ['matplotlib-3.2.1-foss-2020a-Python-3.8.2.eb'], + })) + + # for recent easyconfig generations, there's no versionsuffix anymore for Python 3 + self.assertTrue(self.check_dep_vars('2020b', 'Python', { + 'version: 2.7.18; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b-Python-2.7.18.eb'], + 'version: 3.8.6; versionsuffix:': ['SciPy-bundle-2020.11-foss-2020b.eb'], + })) + + self.assertTrue(self.check_dep_vars('GCCcore-10.2', 'PyYAML', { + 'version: 5.3.1; versionsuffix:': ['IPython-7.18.1-GCCcore-10.2.0.eb'], + 'version: 5.3.1; versionsuffix: -Python-2.7.18': ['IPython-7.18.1-GCCcore-10.2.0-Python-2.7.18.eb'], + })) + + self.assertTrue(self.check_dep_vars('2020b', 'SciPy-bundle', { + 'version: 2020.11; versionsuffix: -Python-2.7.18': ['matplotlib-3.3.3-foss-2020b-Python-2.7.18.eb'], + 'version: 2020.11; versionsuffix:': ['matplotlib-3.3.3-foss-2020b.eb'], + })) + + # not allowed for older generations (foss/intel 2020a or older, GCC(core) 10.1.0 or older) + self.assertFalse(self.check_dep_vars('2020a', 'SciPy-bundle', { + 'version: 2020.03; versionsuffix: -Python-2.7.18': ['matplotlib-3.2.1-foss-2020a-Python-2.7.18.eb'], + 'version: 2020.03; versionsuffix:': ['matplotlib-3.2.1-foss-2020a.eb'], + })) + + def test_dep_versions_per_toolchain_generation(self): + """ + Check whether there's only one dependency version per toolchain generation actively used. + This is enforced to try and limit the chance of running into conflicts when multiple modules built with + the same toolchain are loaded together. + """ + ecs_by_full_mod_name = dict((ec['full_mod_name'], ec) for ec in self.parsed_easyconfigs) + if len(ecs_by_full_mod_name) != len(self.parsed_easyconfigs): + self.fail('Easyconfigs with duplicate full_mod_name found') + + # Cache already determined dependencies + ec_to_deps = dict() + + def get_deps_for(ec): + """Get list of (direct) dependencies for specified easyconfig.""" + ec_mod_name = ec['full_mod_name'] + deps = ec_to_deps.get(ec_mod_name) + if deps is None: + deps = [] + for dep in ec['ec']['dependencies']: + dep_mod_name = dep['full_mod_name'] + deps.append((dep['name'], dep['version'], dep['versionsuffix'], dep_mod_name)) + # Note: Raises KeyError if dep not found + res = ecs_by_full_mod_name[dep_mod_name] + deps.extend(get_deps_for(res)) + ec_to_deps[ec_mod_name] = deps + + return deps + + # some software also follows {a,b} versioning scheme, + # which throws off the pattern matching done below for toolchain versions + false_positives_regex = re.compile('^MATLAB-Engine-20[0-9][0-9][ab]') + + # restrict to checking dependencies of easyconfigs using common toolchains (start with 2018a) + # and GCCcore subtoolchain for common toolchains, starting with GCCcore 7.x + for pattern in ['20(1[89]|[2-9][0-9])[ab]', r'GCCcore-([7-9]|[1-9][0-9])\.[0-9]']: + all_deps = {} + regex = re.compile(r'^.*-(?P%s).*\.eb$' % pattern) + + # collect variants for all dependencies of easyconfigs that use a toolchain that matches + for ec in self.ordered_specs: + ec_file = os.path.basename(ec['spec']) + + # take into account software which also follows a {a,b} versioning scheme + ec_file = false_positives_regex.sub('', ec_file) + + res = regex.match(ec_file) + if res: + tc_gen = res.group('tc_gen') + all_deps_tc_gen = all_deps.setdefault(tc_gen, {}) + for dep_name, dep_ver, dep_versuff, dep_mod_name in get_deps_for(ec): + dep_variants = all_deps_tc_gen.setdefault(dep_name, {}) + # a variant is defined by version + versionsuffix + variant = "version: %s; versionsuffix: %s" % (dep_ver, dep_versuff) + # keep track of which easyconfig this is a dependency + dep_variants.setdefault(variant, set()).add(ec_file) + + # check which dependencies have more than 1 variant + multi_dep_vars, multi_dep_vars_msg = [], '' + for tc_gen in sorted(all_deps.keys()): + for dep in sorted(all_deps[tc_gen].keys()): + dep_vars = all_deps[tc_gen][dep] + if not self.check_dep_vars(tc_gen, dep, dep_vars): + multi_dep_vars.append(dep) + multi_dep_vars_msg += "\nfound %s variants of '%s' dependency " % (len(dep_vars), dep) + multi_dep_vars_msg += "in easyconfigs using '%s' toolchain generation\n* " % tc_gen + multi_dep_vars_msg += '\n* '.join("%s as dep for %s" % v for v in sorted(dep_vars.items())) + multi_dep_vars_msg += '\n' + + error_msg = "No multi-variant deps found for '%s' easyconfigs:\n%s" % (regex.pattern, multi_dep_vars_msg) + self.assertFalse(multi_dep_vars, error_msg) + + def test_sanity_check_paths(self): + """Make sure specified sanity check paths adher to the requirements.""" + + for ec in self.parsed_easyconfigs: + ec_scp = ec['ec']['sanity_check_paths'] + if ec_scp != {}: + # if sanity_check_paths is specified (i.e., non-default), it must adher to the requirements + # both 'files' and 'dirs' keys, both with list values and with at least one a non-empty list + error_msg = "sanity_check_paths for %s does not meet requirements: %s" % (ec['spec'], ec_scp) + self.assertEqual(sorted(ec_scp.keys()), ['dirs', 'files'], error_msg) + self.assertTrue(isinstance(ec_scp['dirs'], list), error_msg) + self.assertTrue(isinstance(ec_scp['files'], list), error_msg) + self.assertTrue(ec_scp['dirs'] or ec_scp['files'], error_msg) + + def test_r_libs_site_env_var(self): + """Make sure $R_LIBS_SITE is being updated, rather than $R_LIBS.""" + # cfr. https://github.com/easybuilders/easybuild-easyblocks/pull/2326 + + r_libs_ecs = [] + for ec in self.parsed_easyconfigs: + for key in ('modextrapaths', 'modextravars'): + if 'R_LIBS' in ec['ec'][key]: + r_libs_ecs.append(ec['spec']) + + error_msg = "%d easyconfigs found which set $R_LIBS, should be $R_LIBS_SITE: %s" + self.assertEqual(r_libs_ecs, [], error_msg % (len(r_libs_ecs), ', '.join(r_libs_ecs))) + + def test_easyconfig_locations(self): + """Make sure all easyconfigs files are in the right location.""" + easyconfig_dirs_regex = re.compile(r'/easybuild/easyconfigs/[0a-z]/[^/]+$') + topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) + for (dirpath, _, filenames) in os.walk(topdir): + # ignore git/svn dirs & archived easyconfigs + if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: + continue + # check whether list of .eb files is non-empty + easyconfig_files = [fn for fn in filenames if fn.endswith('eb')] + if easyconfig_files: + # check whether path matches required pattern + if not easyconfig_dirs_regex.search(dirpath): + # only exception: TEMPLATE.eb + if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): + self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_sha256_checksums(self): + """Make sure changed easyconfigs have SHA256 checksums in place.""" + + # list of software for which checksums can not be required, + # e.g. because 'source' files need to be constructed manually + whitelist = [ + 'Kent_tools-*', + 'MATLAB-*', + 'OCaml-*', + 'OpenFOAM-Extend-4.1-*', + # sources for old versions of Bioconductor packages are no longer available, + # so not worth adding checksums for at this point + 'R-bundle-Bioconductor-3.[2-5]', + ] + + # the check_sha256_checksums function (again) creates an EasyBlock instance + # for easyconfigs using the Bundle easyblock, this is a problem because the 'sources' easyconfig parameter + # is updated in place (sources for components are added to the 'parent' sources) in Bundle's __init__; + # therefore, we need to reset 'sources' to an empty list here if Bundle is used... + # likewise for 'patches' and 'checksums' + for ec in self.changed_ecs: + if ec['easyblock'] in ['Bundle', 'PythonBundle', 'EB_OpenSSL_wrapper'] or ec['name'] in ['Clang-AOMP']: + ec['sources'] = [] + ec['patches'] = [] + ec['checksums'] = [] + + # filter out deprecated easyconfigs + retained_changed_ecs = [] + for ec in self.changed_ecs: + if not ec['deprecated']: + retained_changed_ecs.append(ec) + + checksum_issues = check_sha256_checksums(retained_changed_ecs, whitelist=whitelist) + self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_python_packages(self): + """Several checks for easyconfigs that install (bundles of) Python packages.""" + + # These packages do not support installation with 'pip' + whitelist_pip = [ + r'ESMPy-.*', + r'MATLAB-Engine-.*', + r'Meld-.*', + r'PyTorch-.*', + ] + + whitelist_pip_check = [ + r'Mako-1.0.4.*Python-2.7.12.*', + # no pip 9.x or newer for configparser easyconfigs using a 2016a or 2016b toolchain + r'configparser-3.5.0.*-2016[ab].*', + # mympirun is installed with system Python, pip may not be installed for system Python + r'vsc-mympirun.*', + ] + + failing_checks = [] + + python_default_urls = PythonPackage.extra_options()['source_urls'][0] + + for ec in self.changed_ecs: + + with ec.disable_templating(): + ec_fn = os.path.basename(ec.path) + easyblock = ec.get('easyblock') + exts_defaultclass = ec.get('exts_defaultclass') + exts_default_options = ec.get('exts_default_options', {}) + + download_dep_fail = ec.get('download_dep_fail') + exts_download_dep_fail = ec.get('exts_download_dep_fail') + use_pip = ec.get('use_pip') + if use_pip is None: + use_pip = exts_default_options.get('use_pip') + + # only easyconfig parameters as they are defined in the easyconfig file, + # does *not* include other easyconfig parameters with their default value! + pure_ec = ec.parser.get_config_dict() + + # download_dep_fail should be set when using PythonPackage + if easyblock == 'PythonPackage': + if download_dep_fail is None: + failing_checks.append("'download_dep_fail' should be set in %s" % ec_fn) + + if pure_ec.get('source_urls') == python_default_urls: + failing_checks.append("'source_urls' should not be defined when using the default value " + "in %s" % ec_fn) + + # use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs) + if easyblock in ['PythonBundle', 'PythonPackage']: + if use_pip is None and not any(re.match(regex, ec_fn) for regex in whitelist_pip): + failing_checks.append("'use_pip' should be set in %s" % ec_fn) + + # download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set + if easyblock == 'PythonBundle': + if download_dep_fail or exts_download_dep_fail: + fail = "'*download_dep_fail' should not be set in %s since PythonBundle easyblock is used" % ec_fn + failing_checks.append(fail) + if pure_ec.get('exts_default_options', {}).get('source_urls') == python_default_urls: + failing_checks.append("'source_urls' should not be defined in exts_default_options when using " + "the default value in %s" % ec_fn) + + elif exts_defaultclass == 'PythonPackage': + # bundle of Python packages should use PythonBundle + if easyblock == 'Bundle': + fail = "'PythonBundle' easyblock should be used for bundle of Python packages in %s" % ec_fn + failing_checks.append(fail) + else: + # both download_dep_fail and use_pip should be set via exts_default_options + # when installing Python packages as extensions + for key in ['download_dep_fail', 'use_pip']: + if exts_default_options.get(key) is None: + failing_checks.append("'%s' should be set in exts_default_options in %s" % (key, ec_fn)) + + # if Python is a dependency, that should be reflected in the versionsuffix + # Tkinter is an exception, since its version always matches the Python version anyway + # Python 3.8.6 and later are also excluded, as we consider python 3 the default python + # Also whitelist some updated versions of Amber + whitelist_python_suffix = [ + 'Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', + 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb', + 'R-keras-2.1.6-foss-2018a-R-3.4.4.eb', + ] + whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix) + has_python_dep = any(LooseVersion(dep['version']) < LooseVersion('3.8.6') + for dep in ec['dependencies'] if dep['name'] == 'Python') + if has_python_dep and ec.name != 'Tkinter' and not whitelisted: + if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): + msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn + # This is only a failure for newly added ECs, not for existing ECS + # As that would probably break many ECs + if ec_fn in self.added_ecs_filenames: + failing_checks.append(msg) + else: + print('\nNote: Failed non-critical check: ' + msg) + else: + has_recent_python3_dep = any(LooseVersion(dep['version']) >= LooseVersion('3.8.6') + for dep in ec['dependencies'] if dep['name'] == 'Python') + if has_recent_python3_dep and re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): + msg = "'-Python-%%(pyver)s' should no longer be included in versionsuffix in %s" % ec_fn + failing_checks.append(msg) + + # require that running of "pip check" during sanity check is enabled via sanity_pip_check + if easyblock in ['PythonBundle', 'PythonPackage']: + sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check') + if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip_check): + failing_checks.append("sanity_pip_check should be enabled in %s" % ec_fn) + + if failing_checks: + self.fail('\n'.join(failing_checks)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_R_packages(self): + """Several checks for easyconfigs that install (bundles of) R packages.""" + failing_checks = [] + + for ec in self.changed_ecs: + ec_fn = os.path.basename(ec.path) + exts_defaultclass = ec.get('exts_defaultclass') + if exts_defaultclass == 'RPackage' or ec.name == 'R': + seen_exts = set() + for ext in ec['exts_list']: + if isinstance(ext, (tuple, list)): + ext_name = ext[0] + else: + ext_name = ext + if ext_name in seen_exts: + failing_checks.append('%s was added multiple times to exts_list in %s' % (ext_name, ec_fn)) + else: + seen_exts.add(ext_name) + self.assertFalse(failing_checks, '\n'.join(failing_checks)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_sanity_check_paths(self): + """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" + + # some generic easyblocks already have a decent customised sanity_check_paths, + # including CMakePythonPackage, GoPackage, PythonBundle & PythonPackage; + # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. + whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'ModuleRC', + 'PythonBundle', 'PythonPackage', 'Toolchain'] + # Bundles of dependencies without files of their own + # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, + # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co + bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm'] + + failing_checks = [] + + for ec in self.changed_ecs: + easyblock = ec.get('easyblock') + if is_generic_easyblock(easyblock) and not ec.get('sanity_check_paths'): + + sanity_check_ok = False + + if easyblock in whitelist or (easyblock == 'Bundle' and ec['name'] in bundles_whitelist): + sanity_check_ok = True + + # also allow bundles that enable per-component sanity checks + elif easyblock == 'Bundle': + if ec['sanity_check_components'] or ec['sanity_check_all_components']: + sanity_check_ok = True + + if not sanity_check_ok: + ec_fn = os.path.basename(ec.path) + failing_checks.append("No custom sanity_check_paths found in %s" % ec_fn) + + self.assertFalse(failing_checks, '\n'.join(failing_checks)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_https(self): + """Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://).""" + + whitelist = [ + 'Kaiju', # invalid certificate at https://kaiju.binf.ku.dk + 'libxml2', # https://xmlsoft.org works, but invalid certificate + 'p4vasp', # https://www.p4vasp.at doesn't work + 'ITSTool', # https://itstool.org/ doesn't work + 'UCX-', # bad certificate for https://www.openucx.org + 'MUMPS', # https://mumps.enseeiht.fr doesn't work + 'PyFR', # https://www.pyfr.org doesn't work + 'PycURL', # bad certificate for https://pycurl.io/ + ] + url_whitelist = [ + # https:// doesn't work, results in index page being downloaded instead + # (see https://github.com/easybuilders/easybuild-easyconfigs/issues/9692) + 'http://isl.gforge.inria.fr', + # https:// leads to File Not Found + 'http://tau.uoregon.edu/', + # https:// has outdated SSL configurations + 'http://faculty.scs.illinois.edu', + ] + # Cache: Mapping of already checked HTTP urls to whether the HTTPS variant works + checked_urls = dict() + + def check_https_url(http_url): + """Check if the https url works""" + http_url = http_url.rstrip('/') # Remove trailing slashes + https_url_works = checked_urls.get(http_url) + if https_url_works is None: + https_url = http_url.replace('http://', 'https://') + try: + https_url_works = bool(urlopen(https_url, timeout=5)) + except Exception: + https_url_works = False + checked_urls[http_url] = https_url_works + + http_regex = re.compile('http://[^"\'\n]+', re.M) + + failing_checks = [] + for ec in self.changed_ecs: + ec_fn = os.path.basename(ec.path) + + # skip whitelisted easyconfigs + if any(ec_fn.startswith(x) for x in whitelist): + continue + + # ignore commented out lines in easyconfig files when checking for http:// URLs + ec_txt = '\n'.join(line for line in ec.rawtxt.split('\n') if not line.startswith('#')) + + for http_url in http_regex.findall(ec_txt): + + # skip whitelisted http:// URLs + if any(http_url.startswith(x) for x in url_whitelist): + continue + + if check_https_url(http_url): + failing_checks.append("Found http:// URL in %s, should be https:// : %s" % (ec_fn, http_url)) + if failing_checks: + self.fail('\n'.join(failing_checks)) + + @skip_if_not_pr_to_non_main_branch() + def test_pr_patch_descr(self): + """ + Check whether all patch files touched in PR have a description on top. + """ + no_descr_patches = [] + for patch in self.changed_patches: + patch_txt = read_file(patch) + if patch_txt.startswith('--- '): + no_descr_patches.append(patch) + + self.assertFalse(no_descr_patches, "No description found in patches: %s" % ', '.join(no_descr_patches)) + + +def template_easyconfig_test(self, spec): + """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" + + # set to False, so it's False in case of this test failing + global single_tests_ok + prev_single_tests_ok = single_tests_ok + single_tests_ok = False + + # parse easyconfig + ecs = process_easyconfig(spec) + if len(ecs) == 1: + ec = ecs[0]['ec'] + + # cache the parsed easyconfig, to avoid that it is parsed again + EasyConfigTest._parsed_easyconfigs.append(ecs[0]) + else: + self.assertTrue(False, "easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) + + # check easyconfig file name + expected_fn = '%s-%s.eb' % (ec['name'], det_full_ec_version(ec)) + msg = "Filename '%s' of parsed easyconfig matches expected filename '%s'" % (spec, expected_fn) + self.assertEqual(os.path.basename(spec), expected_fn, msg) + + name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) + + # make sure easyconfig file is in expected location + expected_subdir = os.path.join('easybuild', 'easyconfigs', letter_dir_for(name), name) + subdir = os.path.join(*spec.split(os.path.sep)[-5:-1]) + fail_msg = "Easyconfig file %s not in expected subdirectory %s" % (spec, expected_subdir) + self.assertEqual(expected_subdir, subdir, fail_msg) + + # sanity check for software name, moduleclass + self.assertEqual(ec['name'], name) + self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) + + # instantiate easyblock with easyconfig file + app_class = get_easyblock_class(easyblock, name=name) + + # check that automagic fallback to ConfigureMake isn't done (deprecated behaviour) + fn = os.path.basename(spec) + error_msg = "%s relies on automagic fallback to ConfigureMake, should use easyblock = 'ConfigureMake' instead" % fn + self.assertTrue(easyblock or app_class is not ConfigureMake, error_msg) + + # dump the easyconfig file; + # this should be done before creating the easyblock instance (done below via app_class), + # because some easyblocks (like PythonBundle) modify easyconfig parameters at initialisation + handle, test_ecfile = tempfile.mkstemp() + os.close(handle) + + ec.dump(test_ecfile) + dumped_ec = EasyConfigParser(test_ecfile).get_config_dict() + os.remove(test_ecfile) + + app = app_class(ec) + + # more sanity checks + self.assertTrue(name, app.name) + self.assertTrue(ec['version'], app.version) + + # make sure that deprecated 'dummy' toolchain is no longer used, should use 'system' toolchain instead + ec_fn = os.path.basename(spec) + error_msg_tmpl = "%s should use 'system' toolchain rather than deprecated 'dummy' toolchain" + self.assertFalse(ec['toolchain']['name'] == 'dummy', error_msg_tmpl % os.path.basename(spec)) + + # make sure that $root is not used, since it is not compatible with module files in Lua syntax + res = re.findall(r'.*\$root.*', ec.rawtxt, re.M) + error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" + self.assertFalse(res, error_msg % res) + + # check for redefined easyconfig parameters, there should be none... + param_def_regex = re.compile(r'^(?P\w+)\s*=', re.M) + keys = param_def_regex.findall(ec.rawtxt) + redefined_keys = [] + for key in sorted(nub(keys)): + cnt = keys.count(key) + if cnt > 1: + redefined_keys.append((key, cnt)) + + redefined_keys_error_msg = "There should be no redefined easyconfig parameters, found %d: " % len(redefined_keys) + redefined_keys_error_msg += ', '.join('%s (%d)' % x for x in redefined_keys) + + self.assertFalse(redefined_keys, redefined_keys_error_msg) + + # make sure old GitHub urls for EasyBuild that include 'hpcugent' are no longer used + old_urls = [ + 'github.com/hpcugent/easybuild', + 'hpcugent.github.com/easybuild', + 'hpcugent.github.io/easybuild', + ] + for old_url in old_urls: + self.assertFalse(old_url in ec.rawtxt, "Old URL '%s' not found in %s" % (old_url, spec)) + + # make sure binutils is included as a (build) dep if toolchain is GCCcore + if ec['toolchain']['name'] == 'GCCcore': + # easyblocks without a build step + non_build_blocks = ['Binary', 'JAR', 'PackedBinary', 'Tarball'] + # some software packages do not have a build step + non_build_soft = ['ANIcalculator', 'Eigen'] + + requires_binutils = ec['easyblock'] not in non_build_blocks and ec['name'] not in non_build_soft + + # let's also exclude the very special case where the system GCC is used as GCCcore, and only apply this + # exception to the dependencies of binutils (since we should eventually build a new binutils with GCCcore) + if ec['toolchain']['version'] == 'system': + binutils_complete_dependencies = ['M4', 'Bison', 'flex', 'help2man', 'zlib', 'binutils'] + requires_binutils &= bool(ec['name'] not in binutils_complete_dependencies) + + # if no sources/extensions/components are specified, it's just a bundle (nothing is being compiled) + requires_binutils &= bool(ec['sources'] or ec['exts_list'] or ec.get('components')) + + if requires_binutils: + # dependencies() returns both build and runtime dependencies + # in some cases, binutils can also be a runtime dep (e.g. for Clang) + # Also using GCC directly as a build dep is also allowed (it includes the correct binutils) + dep_names = [d['name'] for d in ec.dependencies()] + self.assertTrue('binutils' in dep_names or 'GCC' in dep_names, + "binutils or GCC is a build dep in %s: %s" % (spec, dep_names)) + + # make sure that OpenSSL wrapper is used rather than OS dependency, + # for easyconfigs using a 2021a (sub)toolchain or more recent common toolchain version + osdeps = ec['osdependencies'] + if osdeps: + # check whether any entry in osdependencies related to OpenSSL + openssl_osdep = False + for osdep in osdeps: + if isinstance(osdep, string_type): + osdep = [osdep] + if any('libssl' in x for x in osdep) or any('openssl' in x for x in osdep): + openssl_osdep = True + + if openssl_osdep: + tcname = ec['toolchain']['name'] + tcver = LooseVersion(ec['toolchain']['version']) + + gcc_subtc_2021a = tcname in ('GCCcore', 'GCC') and tcver > LooseVersion('10.3') + if gcc_subtc_2021a or (tcname in ('foss', 'gompi', 'iimpi', 'intel') and tcver >= LooseVersion('2021')): + self.assertFalse(openssl_osdep, "OpenSSL should not be listed as OS dependency in %s" % spec) + + src_cnt = len(ec['sources']) + patch_checksums = ec['checksums'][src_cnt:] + + # make sure all patch files are available + specdir = os.path.dirname(spec) + specfn = os.path.basename(spec) + for idx, patch in enumerate(ec['patches']): + if isinstance(patch, (tuple, list)): + patch = patch[0] + + # only check actual patch files, not other files being copied via the patch functionality + patch_full = os.path.join(specdir, patch) + if patch.endswith('.patch'): + msg = "Patch file %s is available for %s" % (patch_full, specfn) + self.assertTrue(os.path.isfile(patch_full), msg) + + # verify checksum for each patch file + if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch.endswith('.patch')): + checksum = patch_checksums[idx] + error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch, ec_fn, checksum) + res = verify_checksum(patch_full, checksum) + self.assertTrue(res, error_msg) + + # make sure 'source' step is not being skipped, + # since that implies not verifying the checksum + error_msg = "'source' step should not be skipped in %s, since that implies not verifying checksums" % ec_fn + self.assertFalse(ec['checksums'] and ('source' in ec['skipsteps']), error_msg) + + for ext in ec.get_ref('exts_list'): + if isinstance(ext, (tuple, list)) and len(ext) == 3: + ext_name = ext[0] + self.assertTrue(isinstance(ext[2], dict), + "3rd element of extension spec for %s must be a dictionary" % ext_name) + + # After the sanity check above, use collect_exts_file_info to resolve templates etc. correctly + for ext in app.collect_exts_file_info(fetch_files=False, verify_checksums=False): + try: + ext_options = ext['options'] + except KeyError: + # No options --> Only have a name which is valid, so nothing to check + continue + + checksums = ext_options.get('checksums', []) + src_cnt = len(ext_options.get('sources', [])) or 1 + patch_checksums = checksums[src_cnt:] + + for idx, ext_patch in enumerate(ext.get('patches', [])): + if isinstance(ext_patch, (tuple, list)): + ext_patch = ext_patch[0] + + # only check actual patch files, not other files being copied via the patch functionality + ext_patch_full = os.path.join(specdir, ext_patch['name']) + if ext_patch_full.endswith('.patch'): + msg = "Patch file %s is available for %s" % (ext_patch_full, specfn) + self.assertTrue(os.path.isfile(ext_patch_full), msg) + + # verify checksum for each patch file + if idx < len(patch_checksums) and (os.path.exists(ext_patch_full) or ext_patch.endswith('.patch')): + checksum = patch_checksums[idx] + error_msg = "Invalid checksum for patch %s for %s extension in %s: %s" + res = verify_checksum(ext_patch_full, checksum) + self.assertTrue(res, error_msg % (ext_patch, ext_name, ec_fn, checksum)) + + # check whether all extra_options defined for used easyblock are defined + extra_opts = app.extra_options() + for key in extra_opts: + self.assertTrue(key in app.cfg) + + app.close_log() + os.remove(app.logfile) + + # inject dummy values for templates that are only known at a later stage + dummy_template_values = { + 'builddir': '/dummy/builddir', + 'installdir': '/dummy/installdir', + 'parallel': '2', + } + ec.template_values.update(dummy_template_values) + + ec_dict = ec.parser.get_config_dict() + orig_toolchain = ec_dict['toolchain'] + for key in ec_dict: + # skip parameters for which value is equal to default value + orig_val = ec_dict[key] + if key in DEFAULT_CONFIG and orig_val == DEFAULT_CONFIG[key][0]: + continue + if key in extra_opts and orig_val == extra_opts[key][0]: + continue + if key not in DEFAULT_CONFIG and key not in extra_opts: + continue + + orig_val = resolve_template(ec_dict[key], ec.template_values) + dumped_val = resolve_template(dumped_ec[key], ec.template_values) + + # take into account that dumped value for *dependencies may include hard-coded subtoolchains + # if no easyconfig was found for the dependency with the 'parent' toolchain, + # if may get resolved using a subtoolchain, which is then hardcoded in the dumped easyconfig + if key in DEPENDENCY_PARAMETERS: + # number of dependencies should remain the same + self.assertEqual(len(orig_val), len(dumped_val)) + for orig_dep, dumped_dep in zip(orig_val, dumped_val): + # name should always match + self.assertEqual(orig_dep[0], dumped_dep[0]) + + # version should always match, or be a possibility from the version dict + if isinstance(orig_dep[1], dict): + self.assertTrue(dumped_dep[1] in orig_dep[1].values()) + else: + self.assertEqual(orig_dep[1], dumped_dep[1]) + + # 3rd value is versionsuffix; + if len(dumped_dep) >= 3: + # if no versionsuffix was specified in original dep spec, then dumped value should be empty string + if len(orig_dep) >= 3: + self.assertEqual(dumped_dep[2], orig_dep[2]) + else: + self.assertEqual(dumped_dep[2], '') + + # 4th value is toolchain spec + if len(dumped_dep) >= 4: + if len(orig_dep) >= 4: + # if True was used to indicate that dependency should use system toolchain, + # then we need to compare the value for the dumped easyconfig more carefully; + # see also https://github.com/easybuilders/easybuild-framework/pull/4069 + if orig_dep[3] is True: + self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) + else: + self.assertEqual(dumped_dep[3], orig_dep[3]) + else: + # if a subtoolchain is specifed (only) in the dumped easyconfig, + # it should *not* be the same as the parent toolchain + self.assertNotEqual(dumped_dep[3], (orig_toolchain['name'], orig_toolchain['version'])) + + # take into account that for some string-valued easyconfig parameters (configopts & co), + # the easyblock may have injected additional values, which affects the dumped easyconfig file + elif isinstance(orig_val, string_type): + error_msg = "%s value '%s' should start with '%s'" % (key, dumped_val, orig_val) + self.assertTrue(dumped_val.startswith(orig_val), error_msg) + else: + error_msg = "%s value should be equal in original and dumped easyconfig: '%s' vs '%s'" + self.assertEqual(orig_val, dumped_val, error_msg % (key, orig_val, dumped_val)) + + # test passed, so set back to True + single_tests_ok = True and prev_single_tests_ok + + +def suite(loader=None): + """Return all easyblock initialisation tests.""" + def make_inner_test(spec_path): + def innertest(self): + template_easyconfig_test(self, spec_path) + return innertest + + # dynamically generate a separate test for each of the available easyconfigs + # define new inner functions that can be added as class methods to InitTest + easyconfigs_path = get_paths_for('easyconfigs')[0] + cnt = 0 + for (subpath, dirs, specs) in os.walk(easyconfigs_path, topdown=True): + + # ignore archived easyconfigs + if '__archive__' in dirs: + dirs.remove('__archive__') + + for spec in specs: + if spec.endswith('.eb') and spec != 'TEMPLATE.eb': + cnt += 1 + innertest = make_inner_test(os.path.join(subpath, spec)) + innertest.__doc__ = "Test for easyconfig %s" % spec + # double underscore so parsing tests are run first + innertest.__name__ = "test__parse_easyconfig_%s" % spec + setattr(EasyConfigTest, innertest.__name__, innertest) + + print("Found %s easyconfigs..." % cnt) + if not loader: + loader = TestLoader() + return loader.loadTestsFromTestCase(EasyConfigTest) + + +if __name__ == '__main__': + main() From e18aa2a792eec59ec08c8ecc75084e7a49d72c20 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 3 Oct 2022 09:26:33 +0200 Subject: [PATCH 4985/9987] Revert "Remove AmberTools-20 patch file from Amber, it's now located in AmberTools only." This reverts commit ed3095735a1eaff3e992f9d0c19f0a57da170ace. Must leave this patch in the Amber directory until all older Amber easyconfigs have been changed to use alt_location. --- ...ols-20_fix_missing_MPI_LIBRARY_error.patch | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch new file mode 100644 index 00000000000..8d96ce176c0 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/AmberTools-20_fix_missing_MPI_LIBRARY_error.patch @@ -0,0 +1,21 @@ +When using "usempi" there will be no MPI_xxx_LIBRARIES set and that causes +import_libraries to error out. We know it is correct so comment out that +FATAL_ERROR. + +Åke Sandgren, 2021-06-16 +diff -ru amber20_src.orig/cmake/LibraryTracking.cmake amber20_src/cmake/LibraryTracking.cmake +--- amber20_src.orig/cmake/LibraryTracking.cmake 2021-04-25 02:51:44.000000000 +0200 ++++ amber20_src/cmake/LibraryTracking.cmake 2021-06-16 13:30:26.568317368 +0200 +@@ -170,9 +170,9 @@ + + cmake_parse_arguments(IMP_LIBS "" "" "LIBRARIES;INCLUDES" ${ARGN}) + +- if("${IMP_LIBS_LIBRARIES}" STREQUAL "") +- message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") +- endif() ++ #if("${IMP_LIBS_LIBRARIES}" STREQUAL "") ++ # message(FATAL_ERROR "Incorrect usage. At least one LIBRARY should be provided.") ++ #endif() + + if(NOT "${IMP_LIBS_UNPARSED_ARGUMENTS}" STREQUAL "") + message(FATAL_ERROR "Incorrect usage. Extra arguments provided.") From 5a6407ebe03f4435c7cd6d394b5df896918dc477 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Mon, 3 Oct 2022 11:57:56 +0200 Subject: [PATCH 4986/9987] Update easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb index 6f5908e93ce..4619097f434 100644 --- a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb +++ b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb @@ -2,10 +2,8 @@ easyblock = 'PythonBundle' name = 'torchdata' version = '0.3.0' -local_python_version = '3.9.5' local_pytorch_version = '1.11.0' -versionsuffix = '-PyTorch-%s' % local_pytorch_version -local_pytorch_versionsuffix = '-foss-2021a-CUDA-11.3.1' +versionsuffix = '-PyTorch-%s-CUDA-%(cudaver)s' % local_pytorch_version homepage = 'https://github.com/pytorch/data' description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." From 7721ddef55219ec36719ef0be27de75f46fcf555 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 3 Oct 2022 12:00:10 +0200 Subject: [PATCH 4987/9987] Update LAMMPS-23Jun2022-foss-2022a-kokkos.eb --- .../easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb index 31d1e6a6b1a..94c190d9ed5 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb @@ -40,7 +40,7 @@ dependencies = [ ('tbb', '2021.5.0'), ('PCRE', '8.45'), ('libxml2', '2.9.13'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.4.2'), ('Voro++', '0.4.6'), ('kim-api', '2.3.0'), ('Eigen', '3.4.0'), From e04259dadf79a42c8eb92e006130a636c36a9d7d Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 12:12:26 +0200 Subject: [PATCH 4988/9987] Add back the authors info --- easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb index caccb37e498..1a8eb57f361 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb @@ -1,3 +1,8 @@ +# updated to version 2.0.6, based on the previous 2.0.5 version +# J. Sassmannshausen (Imperial College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) +# Maxim Masterov (SURF, NL) + easyblock = 'ConfigureMake' name = 'CDO' From 37208d40c446fcbf1c2ebfd20b278d2b14b12c06 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 3 Oct 2022 12:13:41 +0200 Subject: [PATCH 4989/9987] Update easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb index 9c572a880b6..62a2ee5fb72 100644 --- a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('X11', '20220504'), ('pixman', '0.40.0'), ('libjpeg-turbo', '2.1.3'), From b6b443d22427f2003ad51dede120246c3576e6a8 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 3 Oct 2022 12:13:57 +0200 Subject: [PATCH 4990/9987] Update easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb index 62a2ee5fb72..1a7ea3b2793 100644 --- a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('Mesa', '22.0.3'), ('libGLU', '9.0.2'), ('libglvnd', '1.4.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] osdependencies = [ From 6db598d1c0501c60521e744950da1343cd4154f4 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 12:29:13 +0200 Subject: [PATCH 4991/9987] Remove duplicate config option --- .../easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb index 9c572a880b6..101ddc3ec47 100644 --- a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -43,7 +43,6 @@ configopts += "-DX11_Xau_LIB=$EBROOTX11/lib/libXau.%s " % SHLIB_EXT configopts += "-DX11_SM_LIB=$EBROOTX11/lib/libSM.%s " % SHLIB_EXT configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libXext.%s " % SHLIB_EXT -configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT configopts += "-DX11_Pixman_LIB=$EBROOTPIXMAN/lib/libpixman-1.%s.0 " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_egl_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s " % SHLIB_EXT From ce120776e83ff72e910fe540daa623fb18724fdd Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 12:46:17 +0200 Subject: [PATCH 4992/9987] Restore sanity check command --- easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb index 1a8eb57f361..8c3b14ced52 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb @@ -48,4 +48,6 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : 2.0.6'"] + moduleclass = 'data' From dafb1e51c4a19b002095a72e5d064316e21e0966 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 3 Oct 2022 13:37:01 +0200 Subject: [PATCH 4993/9987] Update easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb index 8c3b14ced52..2cca13754df 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb @@ -48,6 +48,6 @@ sanity_check_paths = { 'dirs': ['include'], } -sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : 2.0.6'"] +sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : %(version)s'"] moduleclass = 'data' From ec5d169c2af2ecd61ba695a7b70ad28785964213 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 13:54:56 +0200 Subject: [PATCH 4994/9987] Remove duplicate in configopts --- .../easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb index b0e26d19a7b..2301a297350 100644 --- a/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TurboVNC/TurboVNC-3.0.1-GCCcore-11.3.0.eb @@ -42,7 +42,6 @@ configopts += "-DX11_X11_LIB=$EBROOTX11/lib/libX11.%s " % SHLIB_EXT configopts += "-DX11_Xau_LIB=$EBROOTX11/lib/libXau.%s " % SHLIB_EXT configopts += "-DX11_SM_LIB=$EBROOTX11/lib/libSM.%s " % SHLIB_EXT configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libICE.%s " % SHLIB_EXT -configopts += "-DX11_ICE_LIB=$EBROOTX11/lib/libXext.%s " % SHLIB_EXT configopts += "-DX11_Pixman_LIB=$EBROOTPIXMAN/lib/libpixman-1.%s.0 " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DOPENGL_egl_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s " % SHLIB_EXT From 4356dc7b95e3473949f09e4ff7ce4df472f6a203 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Oct 2022 14:02:15 +0200 Subject: [PATCH 4995/9987] adding easyconfigs: bcl-convert-4.0.3-2el7.x86_64.eb --- .../bcl-convert-4.0.3-2el7.x86_64.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb diff --git a/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb new file mode 100644 index 00000000000..e06bf2fdde6 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb @@ -0,0 +1,24 @@ +easyblock = 'Rpm' + +name = 'bcl-convert' +version = '4.0.3-2' +versionsuffix = 'el7.x86_64' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html' +description = """The Illumina BCL Convert v4.0 is a standalone local software app that converts the + Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files.""" + +toolchain = SYSTEM + +source_urls = ['https://webdata.illumina.com/downloads/software/bcl-convert/'] +sources = ['bcl-convert-%(version)s.%(versionsuffix)s.rpm'] +checksums = ['be4f3d1d31cb36618f909cdbc0ed0fe70ef57a645e46b421b6e1a7f90c6c9430'] + +sanity_check_paths = { + 'files': ['usr/bin/bcl-convert'], + 'dirs': [], +} + +sanity_check_commands = ["bcl-convert --help"] + +moduleclass = 'bio' From 62cd95bc3503fb591710a07b60bffa8574639794 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 3 Oct 2022 14:19:21 +0200 Subject: [PATCH 4996/9987] Update easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb index 0feea67dfc8..6a2591a4271 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.8-GCCcore-11.3.0.eb @@ -21,6 +21,7 @@ checksums = ['f25ae0c26e911af1b5005292d4f56621879f74d6958b30741cf67d8b6feb2016'] builddependencies = [ ('Autotools', '20220317'), ('binutils', '2.38'), + ('pkgconf', '1.8.0'), ] dependencies = [ From 22db793612fc2dd55a90e968f595b868fcb94423 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 3 Oct 2022 15:34:46 +0200 Subject: [PATCH 4997/9987] add sanity check commands for f90wrap --- easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb index 55a22a746dc..d4004ab3cc4 100644 --- a/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb +++ b/easybuild/easyconfigs/f/f90wrap/f90wrap-0.2.8-foss-2021a.eb @@ -30,4 +30,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], } +sanity_check_commands = [ + ('f90wrap', '--help'), +] + moduleclass = 'devel' From da7aea23602285dec3a6c89d165c569ea138e78f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 3 Oct 2022 15:39:45 +0200 Subject: [PATCH 4998/9987] CWIPI tools need at least 2 processes to run --- easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb b/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb index f22001bd4fc..cdd531cbacf 100644 --- a/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/c/CWIPI/CWIPI-0.12.0-gompi-2021a.eb @@ -26,6 +26,7 @@ _cwipi_bin = ['c_linear_coupling', 'c_surf_coupling_P1P0_P0P1', 'c_surf_coupling 'c_surf_sequential_coupling', 'c_vol_coupling_P1P1', 'c_vol_coupling_polyhedra_P1P1', 'fortran_plane_PiQj', 'fortran_surf_P1P1', 'fortran_surf_PiQj'] +# Only sanity check installation files as the tools of CWIPI need at least 2 MPI processes to run sanity_check_paths = { 'files': ['bin/%s' % x for x in _cwipi_bin] + ['lib/libcwp.a', 'lib/libcwp.%s' % SHLIB_EXT, 'lib/libcwpf.a', 'lib/libcwpf.%s' % SHLIB_EXT], From b0544535e41fc941a6399e244680c6c0c1ed65cb Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 15:53:32 +0200 Subject: [PATCH 4999/9987] Add libaec as a dependency --- easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb index 742bdb55b84..1f313a6f013 100644 --- a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb @@ -23,6 +23,7 @@ dependencies = [ ('libjpeg-turbo', '2.1.3'), ('libpng', '1.6.37'), ('zlib', '1.2.12'), + ('libaec', '1.0.6'), ] # Python bindings are provided by a separate package 'eccodes-python' From 79a42c0fb12c286248df89dd35515191d7a5b35e Mon Sep 17 00:00:00 2001 From: rocky_build Date: Mon, 3 Oct 2022 14:13:13 -0400 Subject: [PATCH 5000/9987] adding easyconfigs: SRA-Toolkit-3.0.0-centos_linux64.eb --- .../SRA-Toolkit-3.0.0-centos_linux64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-centos_linux64.eb diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-centos_linux64.eb new file mode 100644 index 00000000000..fe5cd26a6c5 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-centos_linux64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# @author: Adam Huffman - The Francis Crick Institute +# Based on work by npklein +# +# updated to version 3.0.0 by +# @author: Graham Derryberry + +easyblock = 'PackedBinary' + +name = 'SRA-Toolkit' +version = '3.0.0' +versionsuffix = '-centos_linux64' + +homepage = 'https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" + +toolchain = SYSTEM + +source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] +sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['89d11fc284e32d38b6639c551df6d658075cd268913f8ba2af65026e4a161dfe'] + +sanity_check_paths = { + 'files': ['bin/abi-load', 'bin/fastq-dump', 'bin/sff-load', 'bin/vdb-dump'], + 'dirs': [] +} + +moduleclass = 'bio' From dc46f4af3c1296788d00a5e4335e661be65dbc2a Mon Sep 17 00:00:00 2001 From: rocky_build Date: Mon, 3 Oct 2022 14:15:37 -0400 Subject: [PATCH 5001/9987] adding easyconfigs: file-5.41-GCCcore-11.3.0.eb --- .../f/file/file-5.41-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f65e804f400 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.41' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['13e532c7b364f7d57e23dfeea3147103150cb90593a57af86c10e4f6e411603f'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From 48ef1a4fa69c9642aa2731cab32b689699f9cb66 Mon Sep 17 00:00:00 2001 From: robogast Date: Tue, 4 Oct 2022 10:50:18 +0200 Subject: [PATCH 5002/9987] Revert "Added exception for FFmpeg versions for Paraview and OpenFOAM" This reverts commit 2f0c9a08a15784d70cb130b7443805338b2eca1e. --- test/easyconfigs/easyconfigs.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index da15318ca58..0fb05afe876 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -493,8 +493,6 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], - # ParaView 5.10.x requires FFmpeg 4.x - 'FFmpeg': [(r'4\.4\.', [r'ParaView-5\.10\.', 'OpenFOAM-v2206'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], From 9063cfbcf942d2e374bbf63f0a4d19ca2e1062da Mon Sep 17 00:00:00 2001 From: robogast Date: Tue, 4 Oct 2022 11:55:15 +0200 Subject: [PATCH 5003/9987] OpenCV FFMpeg back to 4.4.2 --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 48f3aa8178e..25b509d1e9b 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -44,7 +44,7 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('zlib', '1.2.12'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.4.2'), ('freetype', '2.12.1'), ('HarfBuzz', '4.2.1'), ('libjpeg-turbo', '2.1.3'), From bf8be24d19496c1f0fcc0765ea4c78c400748ae2 Mon Sep 17 00:00:00 2001 From: satishk Date: Tue, 4 Oct 2022 12:43:48 +0200 Subject: [PATCH 5004/9987] adding easyconfigs: PETSc-3.17.4-foss-2022a.eb --- .../p/PETSc/PETSc-3.17.4-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb new file mode 100644 index 00000000000..058019a15f9 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb @@ -0,0 +1,51 @@ +## +# Author: Robert Mijakovic +# Author: Jasper Grimm (UoY) +## +name = 'PETSc' +version = '3.17.4' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] +checksums = [ + '99c127486722a3ffd95a268b4ceb0976cbf217926c681a9631bd7246eab8cb2a', # petsc-3.17.4.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.1'), + ('MUMPS', '5.5.1', '-metis'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('Hypre', '2.25.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' From 5fecef6ec8b47119b9a3301e459955413184696a Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 4 Oct 2022 14:28:24 +0200 Subject: [PATCH 5005/9987] Specify CUDA version explicitly --- easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb index 4619097f434..29b133bc3d0 100644 --- a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb +++ b/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb @@ -11,8 +11,9 @@ description = "TorchData is a prototype library of common modular data loading p toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('Python', local_python_version), - ('PyTorch', local_pytorch_version, local_pytorch_versionsuffix), + ('CUDA', '11.3.1', '', True) + ('Python', '3.9.5'), + ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), ] sanity_pip_check = True From 4e9dc088db249774b60b4a26bebeba190e3a0565 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Tue, 4 Oct 2022 14:38:26 +0200 Subject: [PATCH 5006/9987] Update torchdata filename --- .../torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb} | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/t/{torchdata-0.3.0-PyTorch-1.11.0.eb => torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb} (70%) diff --git a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb similarity index 70% rename from easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb rename to easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb index 29b133bc3d0..6f5908e93ce 100644 --- a/easybuild/easyconfigs/t/torchdata-0.3.0-PyTorch-1.11.0.eb +++ b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb @@ -2,8 +2,10 @@ easyblock = 'PythonBundle' name = 'torchdata' version = '0.3.0' +local_python_version = '3.9.5' local_pytorch_version = '1.11.0' -versionsuffix = '-PyTorch-%s-CUDA-%(cudaver)s' % local_pytorch_version +versionsuffix = '-PyTorch-%s' % local_pytorch_version +local_pytorch_versionsuffix = '-foss-2021a-CUDA-11.3.1' homepage = 'https://github.com/pytorch/data' description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." @@ -11,9 +13,8 @@ description = "TorchData is a prototype library of common modular data loading p toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True) - ('Python', '3.9.5'), - ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), + ('Python', local_python_version), + ('PyTorch', local_pytorch_version, local_pytorch_versionsuffix), ] sanity_pip_check = True From 221a748955ba71d2914b3b479846e9a38f054e76 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 4 Oct 2022 15:19:54 +0200 Subject: [PATCH 5007/9987] adding easyconfigs: MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb, Kent_tools-422-GCC-11.2.0-Boost-1.75.0.eb, TopHat-2.1.0-gompi-2021b.eb, Pysam-0.18.0-GCC-11.2.0-Python-2.7.18.eb, pybedtools-0.8.2-GCC-11.2.0-Python-2.7.18.eb, CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb --- ...xplorer2-2.3.8-foss-2021b-Python-2.7.18.eb | 44 +++++++++++++ .../Kent_tools-422-GCC-11.2.0-Boost-1.75.0.eb | 43 ++++++++++++ .../MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb | 66 +++++++++++++++++++ .../Pysam-0.18.0-GCC-11.2.0-Python-2.7.18.eb | 29 ++++++++ ...bedtools-0.8.2-GCC-11.2.0-Python-2.7.18.eb | 26 ++++++++ .../t/TopHat/TopHat-2.1.0-gompi-2021b.eb | 42 ++++++++++++ 6 files changed, 250 insertions(+) create mode 100644 easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0-Boost-1.75.0.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..58a4694ed09 --- /dev/null +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonPackage' + +name = 'CIRCexplorer2' +version = '2.3.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://circexplorer2.readthedocs.io/' +description = "CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset." + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8261ee884f6d895131ce681d5eda6554376e973851a9de4dc50e2b3e242ccc80'] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2021.10', versionsuffix), + # Using version 2.1.0, since there may be problems with newer versions + ('TopHat', '2.1.0'), + ('Cufflinks', '20190706'), + ('BEDTools', '2.30.0'), + ('Kent_tools', '422', '-Boost-1.75.0'), + ('STAR', '2.7.9a'), + ('BWA', '0.7.17'), + ('segemehl', '0.3.4'), + ('Pysam', '0.18.0', versionsuffix), + ('pybedtools', '0.8.2', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'circ2'} + +sanity_check_paths = { + 'files': ['bin/CIRCexplorer2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["CIRCexplorer2 denovo --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0-Boost-1.75.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0-Boost-1.75.0.eb new file mode 100644 index 00000000000..a9c286bf600 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0-Boost-1.75.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'Kent_tools' +version = '422' +versionsuffix = "-Boost-1.75.0" + +homepage = 'https://genome.cse.ucsc.edu/' +description = """Kent utilities: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +source_urls = [ + 'https://hgdownload.cse.ucsc.edu/admin/exe/', + 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', +] +sources = ['userApps.v%(version)s.src.tgz'] +patches = ['%(name)s-%(version)s-openssl.patch'] +checksums = [ + '1edf66ad5f7c8c79586e9f878b5971d7d467c8c5efbeb31c69085d24a6e4671f', # userApps.v422.src.tgz + 'eedd328fc8a8e01806f4de9e8dce5b2a149edf493a17c3758803853e7881f240', # Kent_tools-422-openssl.patch +] + +dependencies = [ + ('MariaDB', '10.6.4', "-Boost-1.75.0"), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('util-linux', '2.37'), + ('OpenSSL', '1.1', '', True), + ('freetype', '2.11.0'), +] + +buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb new file mode 100644 index 00000000000..1eb91a7f0f7 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.6.4' +versionsuffix = "-Boost-1.75.0" + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + '75bf9b147a95d38160d01a73b098d50a1960563b46d16a235971fff64d99643c', # mariadb-10.6.4.tar.gz + '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19', # MariaDB-10.1.13-link-rt-for-jemalloc.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('libaio', '0.3.112'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.3'), # optional + ('XZ', '5.2.5'), # optional + ('jemalloc', '5.2.1'), # optional + ('snappy', '1.1.9'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.9.10'), # needed by Connect XML + ('Boost', '1.75.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.37'), + ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release " +configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_commands = ["mysql --help", "mysqltest --help"] + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..1111d9b3c74 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0-Python-2.7.18.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.18.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['db1ddf41639e4dbb3f94cc9afb14e879bff15690de5b713dec3a81e43f6fa131'] + +dependencies = [ + ('Python', '2.7.18'), + ('ncurses', '6.2'), + ('cURL', '7.78.0'), + ('XZ', '5.2.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..e506572279e --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0-Python-2.7.18.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pybedtools' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://daler.github.io/pybedtools' +description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a184a36099458627e7ef52ea88218f7c00dc9c505b4256ece9ede58b1efa8771'] + +dependencies = [ + ('Python', '2.7.18'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.18.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb new file mode 100644 index 00000000000..122c25025cc --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.0' + +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' +description = "TopHat is a fast splice junction mapper for RNA-Seq reads." + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'cstd': 'gnu++98', 'pic': True} + +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +builddependencies = [('Autoconf', '2.71')] + +dependencies = [ + ('Python', '2.7.18'), + ('SAMtools', '1.16.1'), + ('Boost', '1.75.0'), + ('zlib', '1.2.11'), +] + +local_include_dir = '%(builddir)s/%(namelower)s-%(version)s/src' +preconfigopts = 'sed -i "s|bam/sam.h|htslib/sam.h|g" %s/*.h &&' % local_include_dir +configopts = '--with-boost=$EBROOTBOOST --with-bam=$EBROOTSAMTOOLS' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 3536a93aefcb086a257f7ea569f78fc33e6e3ec1 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 4 Oct 2022 15:20:49 +0200 Subject: [PATCH 5008/9987] adding easyconfigs: StringTie-2.2.1-GCC-11.2.0-Python-2.7.18.eb, CLEAR-20210117-foss-2021b-Python-2.7.18.eb --- ...CLEAR-20210117-foss-2021b-Python-2.7.18.eb | 30 +++++++++++ ...tringTie-2.2.1-GCC-11.2.0-Python-2.7.18.eb | 50 +++++++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..c92c97068f9 --- /dev/null +++ b/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,30 @@ +easyblock = "PythonPackage" + +name = "CLEAR" +version = "20210117" +versionsuffix = "-Python-%(pyver)s" +local_commit = "64bc22d52d99466a044848992fd0d775a983d60c" + +homepage = "https://github.com/YangLab/CLEAR" +description = "Direct comparison of circular and linear RNA expression" + +source_urls = ["https://github.com/YangLab/CLEAR/archive"] +sources = ["%s.tar.gz" % local_commit] + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '2.7.18'), + ('CIRCexplorer2', '2.3.8', versionsuffix), + ('HISAT2', '2.2.1'), + ('StringTie', '2.2.1', versionsuffix), + ('Bowtie', '1.3.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["clear_quant -h"] + +options = {'modulename': False} \ No newline at end of file diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..e5106af9959 --- /dev/null +++ b/easybuild/easyconfigs/s/StringTie/StringTie-2.2.1-GCC-11.2.0-Python-2.7.18.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'StringTie' +version = '2.2.1' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'https://ccb.jhu.edu/software/stringtie/' +description = 'StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts' + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ce4eec532bbbe39af462be844afa6395ab38fa3418ef5fc2431e2d6194129527'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libdeflate', '1.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('HTSlib', '1.14'), + ('Python', '2.7.18'), +] + +local_libs = 'HTSLIB="$EBROOTHTSLIB/lib" LIBS="-lhts -lbz2 -llzma -ldeflate -lz $LIBS"' +buildopts = 'release ' + local_libs + +# the test script downloads some test data from the internet +runtest = 'test' +testopts = local_libs + +files_to_copy = [ + (['%(namelower)s', 'prepDE.py3'], 'bin'), + 'README.md', + 'LICENSE' +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help', 'prepDE.py3 --help'] + +moduleclass = 'bio' From 75141c67a19e2f0bd70618eebdc9f6d7b0e962c8 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 4 Oct 2022 15:38:26 +0200 Subject: [PATCH 5009/9987] Added checksum for TopHat --- easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb index 122c25025cc..2979ac7be83 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb @@ -18,6 +18,7 @@ toolchainopts = {'cstd': 'gnu++98', 'pic': True} source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['e7fa2b170408e785e4fafd0bccf4ecfab5151c480a2438dffa42183cfda71f99'] builddependencies = [('Autoconf', '2.71')] From 114ee8140e7ebe5899eb26e267e6bb7b514373dc Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 4 Oct 2022 16:05:44 +0200 Subject: [PATCH 5010/9987] Added version suffix for TopHat --- ...-gompi-2021b.eb => TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/t/TopHat/{TopHat-2.1.0-gompi-2021b.eb => TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb} (97%) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb similarity index 97% rename from easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb rename to easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb index 2979ac7be83..5916981e8c1 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb @@ -9,6 +9,7 @@ easyblock = 'ConfigureMake' name = 'TopHat' version = '2.1.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' description = "TopHat is a fast splice junction mapper for RNA-Seq reads." From 99e1a8ed4d4cfda5565591fca80a7d96107ebb0d Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 4 Oct 2022 16:23:58 +0200 Subject: [PATCH 5011/9987] Fixed dependency in CIRCexplorer2 --- .../CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb index 58a4694ed09..82872607b68 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '2.7.18'), ('SciPy-bundle', '2021.10', versionsuffix), # Using version 2.1.0, since there may be problems with newer versions - ('TopHat', '2.1.0'), + ('TopHat', '2.1.0', versionsuffix), ('Cufflinks', '20190706'), ('BEDTools', '2.30.0'), ('Kent_tools', '422', '-Boost-1.75.0'), From 6d9ccdf10ecae21a4d75091149ca48a83ef901e9 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Tue, 4 Oct 2022 16:50:26 +0200 Subject: [PATCH 5012/9987] Revert changes that slipped with rename --- ...0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ec87e0cccd0 --- /dev/null +++ b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'torchdata' +version = '0.3.0' +local_pytorch_version = '1.11.0' +versionsuffix = '-PyTorch-' + local_pytorch_version + '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pytorch/data' +description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pytorch/data/archive'], + }), +] + +moduleclass = 'lib' From 6158fc35374138734d455fc8fa35203962a7b9ac Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 4 Oct 2022 16:52:34 +0200 Subject: [PATCH 5013/9987] Delete torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb --- ...rchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb diff --git a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb deleted file mode 100644 index 6f5908e93ce..00000000000 --- a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'torchdata' -version = '0.3.0' -local_python_version = '3.9.5' -local_pytorch_version = '1.11.0' -versionsuffix = '-PyTorch-%s' % local_pytorch_version -local_pytorch_versionsuffix = '-foss-2021a-CUDA-11.3.1' - -homepage = 'https://github.com/pytorch/data' -description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." - -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', local_python_version), - ('PyTorch', local_pytorch_version, local_pytorch_versionsuffix), -] - -sanity_pip_check = True -use_pip = True - -exts_list = [ - (name, version, { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/pytorch/data/archive'], - }), -] - -moduleclass = 'lib' From d201e3509999a437bb6a4dd9f340915c193e2245 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 4 Oct 2022 17:11:42 +0200 Subject: [PATCH 5014/9987] Fixed SAMtools version mismatch --- .../t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb index 5916981e8c1..14084b9267a 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb @@ -25,7 +25,7 @@ builddependencies = [('Autoconf', '2.71')] dependencies = [ ('Python', '2.7.18'), - ('SAMtools', '1.16.1'), + ('SAMtools', '1.14'), ('Boost', '1.75.0'), ('zlib', '1.2.11'), ] From 863242e3a6656471cde1f631be68f190a7e9f83d Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 4 Oct 2022 17:14:03 +0200 Subject: [PATCH 5015/9987] Added newline --- .../c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb index c92c97068f9..9fe20fcc0a3 100644 --- a/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb @@ -27,4 +27,4 @@ sanity_pip_check = True sanity_check_commands = ["clear_quant -h"] -options = {'modulename': False} \ No newline at end of file +options = {'modulename': False} From 288ddd3205bc8191aef50afea11eb77c4831eb9d Mon Sep 17 00:00:00 2001 From: rocky_build Date: Tue, 4 Oct 2022 16:21:45 -0400 Subject: [PATCH 5016/9987] Updated for file version 5.43 as requested --- .../f/file/file-5.43-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1128c37d6ac --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.43' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From d208e43d9c247055273d3f46d3a6aa49c4d1cf23 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 5 Oct 2022 08:53:03 +0200 Subject: [PATCH 5017/9987] adding easyconfigs: AMS-2022.102-iimpi-2021b-intelmpi.eb --- .../AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb diff --git a/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb new file mode 100644 index 00000000000..466df5f61ac --- /dev/null +++ b/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb @@ -0,0 +1,41 @@ +easyblock = 'Tarball' + +name = 'AMS' +version = '2022.102' +versionsuffix = '-intelmpi' + +homepage = 'https://www.scm.com/amsterdam-modeling-suite/' +description = """ +The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for computational chemistry and materials +science, from quantum mechanics to fluid thermodynamics. +""" + +toolchain = {'name': 'iimpi', 'version': '2021b'} + +sources = ['ams%(version)s.pc64_linux.intelmpi.bin.tgz'] +checksums = ['a1791e0ea17426199a8c82668858a509debd3a6b99adc107e452084095d72344'] + +dependencies = [('libGLU', '9.0.2')] + +keepsymlinks = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +# check if license file is installed +# sanity_check_commands = ['dirac check'] + +modextrapaths = { + 'AMSHOME': '', + 'AMSBIN': 'bin', + 'AMSRESOURCES': 'atomicdata', +} + +modloadmsg = """These environment variables need to be defined before using AMS: + * $SCMLICENSE: path to AMS license file + * $SCM_TMPDIR: path to user scratch directory +""" + +moduleclass = 'chem' From 4ceed01f1b3f80c735890e720da178292d253ae0 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 Oct 2022 12:23:52 +0200 Subject: [PATCH 5018/9987] Fix test_model_dump and test_cpp_extensions_aot* --- .../PyTorch-1.10.0_fix-test-model_dump.patch | 36 +++++++++++++++++++ .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 13 +++---- ...Torch-1.11.0_install-vsx-vec-headers.patch | 10 +++++- 3 files changed, 49 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-model_dump.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-model_dump.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-model_dump.patch new file mode 100644 index 00000000000..1891c93e93f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-test-model_dump.patch @@ -0,0 +1,36 @@ +From https://github.com/pytorch/pytorch/pull/84744 + +Author: Alexander Grund (TU Dresden) + +From 4d99f72dcf71bffa7ff4275750cb86d872ac653f Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Fri, 9 Sep 2022 11:10:05 +0200 +Subject: [PATCH] Fix failing test_model_dump due to empty file + +The `torch.jit.save` call on a file object may not actually write the +data to disk due to buffering. The call to `model_dump.main` on that +file will when fail with an error like + +> zipfile.BadZipFile: File is not a zip file + +Inspecting the file confirms that it is either empty (usually) or +incomplete (possible). + +Fix this by flushing the file after saving the model. +--- + test/test_model_dump.py | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/test/test_model_dump.py b/test/test_model_dump.py +index a8add0e2cd923..3c682b6ce6805 100644 +--- a/test/test_model_dump.py ++++ b/test/test_model_dump.py +@@ -131,6 +131,8 @@ def test_main(self): + + with tempfile.NamedTemporaryFile() as tf: + torch.jit.save(torch.jit.script(SimpleModel()), tf) ++ # Actually write contents to disk so we can read it below ++ tf.flush() + + stdout = io.StringIO() + torch.utils.model_dump.main( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index dfd9742736f..2192c824b84 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -17,6 +17,7 @@ patches = [ 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_skip_cmake_rpath.patch', @@ -43,6 +44,8 @@ checksums = [ 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vsx-vector-functions.patch '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', # PyTorch-1.10.0_fix-XNNPACK-tests.patch @@ -66,7 +69,7 @@ checksums = [ '26e179a4f6f57e49209092612ae5f5cd8c03fd2ca84566ba0244eabefc3736ba', # PyTorch-1.11.0_increase-tolerance-test_ops.patch 'ceec745c68a405bba79efb4dc61c662ca84eb950cd0163c7104330f4bf614cf5', - 'f765093765c07ae488e15b33184709bd1e9c799f6640695be71dca3df02f83c3', # PyTorch-1.11.0_install-vsx-vec-headers.patch + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch '8eaca92d64fcadb0552d28e9c7ea5c4bc669d2fe33004e45a3519ce8d0d136a2', # PyTorch-1.11.0_skip_failing_ops_tests.patch ] @@ -108,16 +111,8 @@ excluded_tests = { # Bad tests: https://github.com/pytorch/pytorch/issues/60260 'distributed/elastic/utils/distributed_test', 'distributed/elastic/multiprocessing/api_test', - # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. - # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html - # 'distributed/test_distributed_fork', - 'distributed/test_distributed_spawn', # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 'test_optim', - # Test from this suite timeout often. The process group backend is deprecated anyway - # 'distributed/rpc/test_process_group_agent', - # This test fails constently when run as part of the test suite, but succeeds when run interactively - 'test_model_dump', # These tests appear flaky, possibly related to number of GPUs that are used 'distributed/fsdp/test_fsdp_memory', 'distributed/fsdp/test_fsdp_overlap', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch index a3da950d7d9..628a59ec0a2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_install-vsx-vec-headers.patch @@ -17,7 +17,7 @@ index 5710eca27c..0cd15c2ad2 100644 file(GLOB cuda_h "cuda/*.h" "cuda/detail/*.h" "cuda/*.cuh" "cuda/detail/*.cuh") file(GLOB cuda_cpp "cuda/*.cpp" "cuda/detail/*.cpp") diff --git a/setup.py b/setup.py -index f1ebab7391..c73b6df665 100644 +index f1ebab7391..92de0367ac 100644 --- a/setup.py +++ b/setup.py @@ -942,6 +942,7 @@ if __name__ == '__main__': @@ -28,3 +28,11 @@ index f1ebab7391..c73b6df665 100644 'include/ATen/cpu/vec/vec512/*.h', 'include/ATen/cpu/vec/*.h', 'include/ATen/core/*.h', +@@ -1043,6 +1044,7 @@ if __name__ == '__main__': + 'include/THH/*.cuh', + 'include/THH/*.h*', + 'include/THH/generic/*.h', ++ 'include/sleef.h', + 'share/cmake/ATen/*.cmake', + 'share/cmake/Caffe2/*.cmake', + 'share/cmake/Caffe2/public/*.cmake', From 5419c788c5bac42bb934104a9c716a6f7e1351b3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 Oct 2022 13:04:27 +0200 Subject: [PATCH 5019/9987] Reduce max GPUs to 4 for fsdp test --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch | 9 +++++---- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 2192c824b84..32f4323e49d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -57,7 +57,7 @@ checksums = [ 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', # PyTorch-1.11.0_fix-attention_cpp-compilation.patch '84214fcc7e30cf70659a7c3bd70bf11e73d58fd4f7fff2c233e3225619b0e42c', - '69546ab7371667370eb52b8e46fee7f39deff493fc12cfdcc6f49dde69848f8d', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + 'ca48576014bceb8c6c0d06cbab666be96cb44804e0215f5c025397a75a675bab', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch index bd860be61f7..401d0865d49 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch @@ -1,5 +1,6 @@ -The test fails on a node with more than 5 GPUs. -Hence limit the world_size to 5 +The test fails on a node with more than 5 V100 GPUs or more than 4 A100 GPUs. +Hence limit the world_size to 4 +See https://github.com/pytorch/pytorch/issues/78975 Author: Alexander Grund (TU Dresden) @@ -13,8 +14,8 @@ index eea03bea3d..d3a4bb8257 100644 + @property + def world_size(self): -+ # Test fails due to inaccuracies when using more than 5 GPUs -+ return min(5, super().world_size) ++ # Test fails due to inaccuracies when using more than 4 GPUs ++ return min(4, super().world_size) + @skip_if_lt_x_gpu(2) @parametrize( From 57a9f46f2b343c94660c0f149cb22266b4bd6767 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Oct 2022 14:42:43 +0200 Subject: [PATCH 5020/9987] adding easyconfigs: biogeme-3.2.10-foss-2022a.eb --- .../b/biogeme/biogeme-3.2.10-foss-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/biogeme/biogeme-3.2.10-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/biogeme/biogeme-3.2.10-foss-2022a.eb b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.10-foss-2022a.eb new file mode 100644 index 00000000000..efe335afb48 --- /dev/null +++ b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.10-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'biogeme' +version = '3.2.10' + +homepage = 'https://pypi.python.org/pypi/biogeme' +description = """Biogeme is a open source Python package designed for +the maximum likelihood estimation of parametric models in general, +with a special emphasis on discrete choice models.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('Unidecode', '1.3.6', { + 'checksums': ['fed09cf0be8cf415b391642c2a5addfc72194407caee4f98719e40ec2a72b830'], + }), + (name, version, { + 'checksums': ['60b865e54f4c5ed22eb4a13dc277b72a2fec13e22d243a6f97d05fe7df984d63'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From 7a17935b7e9cade82bbb4f820e87cc62297e897b Mon Sep 17 00:00:00 2001 From: dithwick <46924962+dithwick@users.noreply.github.com> Date: Wed, 5 Oct 2022 14:14:45 +0100 Subject: [PATCH 5021/9987] Update easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb index 5598e22e1d9..2d7a7d90220 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb @@ -18,7 +18,9 @@ dependencies = [ ] osdependencies = [ - 'perl-Thread-Queue', + # Thread::Queue is already available by default in Ubuntu + # providing a package that is automatically installed as workaround + ('perl-Thread-Queue', 'debianutils'), ] preconfigopts = "export PERL='/usr/bin/env perl' && " From d877bb14838740f7a6be1a636077463a8d5f2a34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Oct 2022 17:09:00 +0200 Subject: [PATCH 5022/9987] adding easyconfigs: openpyxl-3.0.10-GCCcore-11.3.0.eb --- .../openpyxl-3.0.10-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bc8a63f9df3 --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.0.10' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('lxml', '4.9.1'), + ('Pillow', '9.1.1'), +] + +use_pip = True + +exts_list = [ + ('et_xmlfile', '1.1.0', { + 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['e47805627aebcf860edb4edf7987b1309c1b3632f3750538ed962bbcc3bd7449'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 9ed5dc61975ade0e7786f7b7faa6b3412cb544e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Oct 2022 20:08:26 +0200 Subject: [PATCH 5023/9987] adding easyconfigs: sympy-1.11.1-foss-2022a.eb --- .../s/sympy/sympy-1.11.1-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb new file mode 100644 index 00000000000..50b43150f3e --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.11.1' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e32380dce63cb7c0108ed525570092fd45168bdae2faa17e528221ef72e88658'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('gmpy2', '2.1.2'), +] + +download_dep_fail = True +use_pip = True + +# fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; +# see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 +#pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +sanity_check_commands = ["isympy --help"] + +moduleclass = 'math' From 32e6ae03357bbfd0ab6922c3efffd6a127e6bfbf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 08:51:58 +0200 Subject: [PATCH 5024/9987] remove commented out pretestopts in sympy 1.11.1 easyconfig --- easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb index 50b43150f3e..9e54ecf5751 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb @@ -23,9 +23,6 @@ dependencies = [ download_dep_fail = True use_pip = True -# fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; -# see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 -#pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ runtest = 'python setup.py test' sanity_pip_check = True From ef9b787f5cecfdaabab19a09274883c21b2755bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 09:32:34 +0200 Subject: [PATCH 5025/9987] fix description in Horovod easyconfig to clarify that it is configured for PyTorch --- .../Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb index 57dc906ad2e..dc0b6545e61 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb @@ -7,7 +7,8 @@ local_cuda_suffix = '-CUDA-%(cudaver)s' versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version homepage = 'https://github.com/uber/horovod' -description = "Horovod is a distributed training framework for TensorFlow." +description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. +This build only have PyTorch enabled.""" toolchain = {'name': 'foss', 'version': '2021a'} From a9652df05c1ab4fb4447a2e772535549df04b842 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 09:59:17 +0200 Subject: [PATCH 5026/9987] adding easyconfigs: OpenMM-7.7.0-foss-2021a.eb --- .../o/OpenMM/OpenMM-7.7.0-foss-2021a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb new file mode 100644 index 00000000000..400ea7aa3b7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a.eb @@ -0,0 +1,57 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.7.0' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('SWIG', '4.0.2'), +] + +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/__init__.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m openmm.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 0bb76f4d3675b03ef7163499aa027dec449ced36 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 6 Oct 2022 10:09:28 +0200 Subject: [PATCH 5027/9987] Added Imath checksum --- easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb index b4f0f0223ca..a85a08e980d 100644 --- a/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb @@ -19,6 +19,7 @@ sources = [{ 'tag': 'v%(version)s', }, }] +checksums = ['5167b1441e4eaeb0f238faaac02c52ecd89940e7c77a3ed0c7356fb8934db570'] builddependencies = [ ('binutils', '2.38'), From 27eabe4cbea5923f42c791790b705589a363b548 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 10:57:40 +0200 Subject: [PATCH 5028/9987] adding easyconfigs: MDTraj-1.9.7-intel-2022a.eb --- .../m/MDTraj/MDTraj-1.9.7-intel-2022a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2022a.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2022a.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2022a.eb new file mode 100644 index 00000000000..d94d68ccbdc --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-intel-2022a.eb @@ -0,0 +1,45 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.7' + +homepage = 'https://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), +] + +use_pip = True +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('pymbar', '3.1', { + # pymbar 3.1 is not available via PyPI, see https://github.com/choderalab/pymbar/issues/475 + 'source_urls': ['https://github.com/choderalab/pymbar/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7a996e5d3fd8143378f9e18662483446a4a2fe7e57917511e96beb6b07fd6232'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('mdtraj', version, { + 'checksums': ['8a3309d2ef6ddb1023dcf48300d5df9b190469b63f69af9d55490bc4799d3757'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' From 632caa0e3ddfdfeebafa7c3d1e5ad84a434c6c70 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 10:57:52 +0200 Subject: [PATCH 5029/9987] adding easyconfigs: OpenMM-7.7.0-foss-2022a.eb --- .../o/OpenMM/OpenMM-7.7.0-foss-2022a.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2022a.eb new file mode 100644 index 00000000000..7dbd4dd5249 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2022a.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.7.0' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['51970779b8dc639ea192e9c61c67f70189aa294575acb915e14be1670a586c25'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SWIG', '4.0.2'), +] + +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 3a1ffc81f8e300d858c00b996f1e473ac8d5828b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 11:14:18 +0200 Subject: [PATCH 5030/9987] adding easyconfigs: MMseqs2-13-45111-gompi-2021a.eb --- .../m/MMseqs2/MMseqs2-13-45111-gompi-2021a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021a.eb diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021a.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021a.eb new file mode 100644 index 00000000000..79c3a69f62c --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-13-45111-gompi-2021a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +version = '13-45111' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['6444bb682ebf5ced54b2eda7a301fa3e933c2a28b7661f96ef5bdab1d53695a2'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [('bzip2', '1.0.8')] + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' From 3becb6b4c1dde38a1adc73727e21fcb23a09a882 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 6 Oct 2022 11:20:33 +0200 Subject: [PATCH 5031/9987] use Intel MPI from EasyBuild toolchain in AMS (#16363) --- .../easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb | 5 +++++ .../easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb index 0e032547e34..0d9ba4e2d49 100644 --- a/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb +++ b/easybuild/easyconfigs/a/AMS/AMS-2020.102-iimpi-2020b-intelmpi.eb @@ -30,6 +30,11 @@ modextrapaths = { 'AMSRESOURCES': 'atomicdata', } +modextravars = { + # use Intel MPI from EasyBuild + 'SCM_USE_LOCAL_IMPI': '1', +} + modloadmsg = """These environment variables need to be defined before using AMS: * $SCMLICENSE: path to AMS license file * $SCM_TMPDIR: path to user scratch directory diff --git a/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb index 466df5f61ac..fade2732728 100644 --- a/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb +++ b/easybuild/easyconfigs/a/AMS/AMS-2022.102-iimpi-2021b-intelmpi.eb @@ -33,6 +33,11 @@ modextrapaths = { 'AMSRESOURCES': 'atomicdata', } +modextravars = { + # use Intel MPI from EasyBuild + 'SCM_USE_LOCAL_IMPI': '1', +} + modloadmsg = """These environment variables need to be defined before using AMS: * $SCMLICENSE: path to AMS license file * $SCM_TMPDIR: path to user scratch directory From 5b9dae8afecda66984041eaccb942c7c594a3fd3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 11:25:50 +0200 Subject: [PATCH 5032/9987] adding easyconfigs: MDTraj-1.9.7-foss-2022a.eb --- .../m/MDTraj/MDTraj-1.9.7-foss-2022a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2022a.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2022a.eb new file mode 100644 index 00000000000..f6dd1f827d5 --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2022a.eb @@ -0,0 +1,45 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.7' + +homepage = 'https://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), +] + +use_pip = True +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('pymbar', '3.1', { + # pymbar 3.1 is not available via PyPI, see https://github.com/choderalab/pymbar/issues/475 + 'source_urls': ['https://github.com/choderalab/pymbar/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7a996e5d3fd8143378f9e18662483446a4a2fe7e57917511e96beb6b07fd6232'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('mdtraj', version, { + 'checksums': ['8a3309d2ef6ddb1023dcf48300d5df9b190469b63f69af9d55490bc4799d3757'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' From 494d36e8566d6d2e70835a73994d4f7bcebe023c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Oct 2022 11:26:31 +0200 Subject: [PATCH 5033/9987] adding easyconfigs: MDTraj-1.9.7-foss-2021a.eb --- .../m/MDTraj/MDTraj-1.9.7-foss-2021a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021a.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021a.eb new file mode 100644 index 00000000000..acc6867ceed --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.7-foss-2021a.eb @@ -0,0 +1,45 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.7' + +homepage = 'https://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('zlib', '1.2.11'), +] + +use_pip = True +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('pymbar', '3.1', { + # pymbar 3.1 is not available via PyPI, see https://github.com/choderalab/pymbar/issues/475 + 'source_urls': ['https://github.com/choderalab/pymbar/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7a996e5d3fd8143378f9e18662483446a4a2fe7e57917511e96beb6b07fd6232'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('mdtraj', version, { + 'checksums': ['8a3309d2ef6ddb1023dcf48300d5df9b190469b63f69af9d55490bc4799d3757'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' From 921406cbde39c082cd922df644fe4c09b7578b21 Mon Sep 17 00:00:00 2001 From: scimerman <80223690+scimerman@users.noreply.github.com> Date: Thu, 6 Oct 2022 14:40:47 +0200 Subject: [PATCH 5034/9987] Create OpenSSL-1.1.1q-GCCcore-10.3.0.eb A latest version of OpenSSL with GCC 10.3.0 --- .../OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..25d87d8dddb --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +name = 'OpenSSL' +version = '1.1.1q' + +homepage = 'https://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.openssl.org/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d7939ce614029cdff0b6c20f0e2e5703158a489a72b2507b8bd51bf8c8fd10ca'] + +dependencies = [('zlib', '1.2.11')] + +builddependencies = [ + ('Perl', '5.32.1'), + ('binutils', '2.36.1'), +] + +runtest = 'test' + +moduleclass = 'system' From 3f672f474e9b751042cba9b859280d1050a66f33 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 6 Oct 2022 09:44:42 -0400 Subject: [PATCH 5035/9987] Drop old 5.41 version --- .../f/file/file-5.41-GCCcore-11.3.0.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb deleted file mode 100644 index f65e804f400..00000000000 --- a/easybuild/easyconfigs/f/file/file-5.41-GCCcore-11.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'file' -version = '5.41' - -homepage = 'https://www.darwinsys.com/file/' -description = """The file command is 'a file type guesser', that is, a command-line tool - that tells you in words what kind of data a file contains.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['ftp://ftp.astron.com/pub/file/'] -sources = [SOURCE_TAR_GZ] -checksums = ['13e532c7b364f7d57e23dfeea3147103150cb90593a57af86c10e4f6e411603f'] - -builddependencies = [ - ('Autotools', '20220317'), - ('binutils', '2.38'), -] - -preconfigopts = "autoreconf -f -i && " - -sanity_check_paths = { - 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], - 'dirs': ['share'] -} - -moduleclass = 'system' From e6c111837b8212654199b0162d1f24821de92c0e Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 6 Oct 2022 15:56:00 +0200 Subject: [PATCH 5036/9987] Added OpenJPEG dep to OpenCV --- .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6c76dae7c5d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchenson Cancer Research Center Seattle WA +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.0' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' From f5cd89f0bfe6fab34a0b2d954e3b0337319d6a04 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 6 Oct 2022 16:07:32 +0200 Subject: [PATCH 5037/9987] Actually added OpenJPEG dep to OpenCV --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 25b509d1e9b..3676ebf7da8 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -48,6 +48,7 @@ dependencies = [ ('freetype', '2.12.1'), ('HarfBuzz', '4.2.1'), ('libjpeg-turbo', '2.1.3'), + ('OpenJPEG', '2.5.0'), ('libpng', '1.6.37'), ('LibTIFF', '4.3.0'), ('libwebp', '1.2.4'), From e85a350aeb28ba6501b4f5674430b996de6120e7 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 6 Oct 2022 16:09:16 +0200 Subject: [PATCH 5038/9987] moved OpenJPEG dep to PR #16276 --- .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb deleted file mode 100644 index 6c76dae7c5d..00000000000 --- a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -# easybuild easyconfig -# -# John Dey jfdey@fredhutch.org -# -# Fred Hutchenson Cancer Research Center Seattle WA -easyblock = 'CMakeMake' - -name = 'OpenJPEG' -version = '2.5.0' - -homepage = 'https://www.openjpeg.org/' -description = """OpenJPEG is an open-source JPEG 2000 codec written in - C language. It has been developed in order to promote the use of JPEG 2000, - a still-image compression standard from the Joint Photographic Experts Group - (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as - a JPEG 2000 Reference Software.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] - -builddependencies = [ - ('binutils', '2.38'), - ('CMake', '3.23.1'), -] -# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. -dependencies = [ - ('zlib', '1.2.12'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.3.0'), -] - -sanity_check_paths = { - 'files': [ - 'bin/opj_compress', - 'bin/opj_decompress', - 'bin/opj_dump', - 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', - 'lib/libopenjp2.%s' % SHLIB_EXT - ], - 'dirs': ['bin', 'include', 'lib'], -} - -moduleclass = 'lib' From 986e4079fd1502bcb7046ab1ff587994c216063c Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 6 Oct 2022 16:15:26 +0200 Subject: [PATCH 5039/9987] Removed OpenJPEG header comment --- .../easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb index 6c76dae7c5d..a3ccd969fc7 100644 --- a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb @@ -1,8 +1,3 @@ -# easybuild easyconfig -# -# John Dey jfdey@fredhutch.org -# -# Fred Hutchenson Cancer Research Center Seattle WA easyblock = 'CMakeMake' name = 'OpenJPEG' From a1e42d736151b3e26075a70aeeca85905aa29661 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 6 Oct 2022 16:36:23 +0200 Subject: [PATCH 5040/9987] Inject checksum --- .../torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb index ec87e0cccd0..9c2141e4169 100644 --- a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -23,6 +23,7 @@ exts_list = [ (name, version, { 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/pytorch/data/archive'], + 'checksums': ['ac36188bf133cf5f1041a28ccb3ee82ba52d4b5d99617be37d64d740acd6cfd4'], }), ] From b92974d8bff1ac48ee3e79a45392479c50b3d07a Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 6 Oct 2022 16:58:34 +0200 Subject: [PATCH 5041/9987] Adapt .eb from torchvision 0.11 --- ...0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..ca3b8eac2e9 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -0,0 +1,24 @@ +name = 'torchvision' +version = '0.12.0' +local_pytorch_version = '1.11.0' +versionsuffix = '-PyTorch-' + local_pytorch_version + '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['99e6d3d304184895ff4f6152e2d2ec1cbec89b3e057d9c940ae0125546b04e91'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('Pillow-SIMD', '8.2.0'), + ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), +] + +moduleclass = 'vis' From eb1691f0f7f4abe3d751888cae1a9e09bb1dc953 Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Thu, 24 Mar 2022 14:46:35 -0400 Subject: [PATCH 5042/9987] Update triqs and application packages to version 3.1.0 --- .../TRIQS-cthyb-3.1.0-foss-2021b.eb | 69 ++++++++++++++++++ .../TRIQS-dft_tools-3.1.0-foss-2021b.eb | 70 +++++++++++++++++++ .../TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb | 70 +++++++++++++++++++ .../t/TRIQS/TRIQS-3.1.0-foss-2021b.eb | 70 +++++++++++++++++++ 4 files changed, 279 insertions(+) create mode 100644 easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb new file mode 100644 index 00000000000..19e698e99bd --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb @@ -0,0 +1,69 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-cthyb' +version = '3.1.0' + +homepage = 'https://triqs.github.io/cthyb/' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + cthyb = continuous-time hybridisation-expansion quantum Monte Carlo + + The TRIQS-based hybridization-expansion solver allows to solve the + generic problem of a quantum impurity embedded in a conduction bath + for an arbitrary local interaction vertex. The “impurity” can be any + set of orbitals, on one or several atoms. +""" + +docurls = ['https://triqs.github.io/cthyb/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/cthyb/releases/download/%(version)s/'] +sources = ['cthyb-%(version)s.tar.gz'] +checksums = ['8d6d2c4d5b3928d062b72fad4ea9df9aae198e39dd9c1fd3cc5dc34a5019acc0'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), + ('Clang', '13.0.1'), + ('Clang-Python-bindings', '13.0.1'), + ('GMP', '6.2.1'), + ('HDF5', '1.10.7'), + ('Mako', '1.1.4'), + ('TRIQS', '3.1.0'), + ('NFFT', '3.5.2') +] + +builddependencies = [ + ('CMake', '3.22.1') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs_cthyb_c.a'], + 'dirs': ['include', 'include/triqs_cthyb', 'lib', + 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = ["python -c 'import triqs_cthyb'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_cthyb', +} +modextravars = { + 'TRIQS_CTHYB_ROOT': '%(installdir)s', + 'TRIQS_CTHYB_VERSION': '%(version)s', +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb new file mode 100644 index 00000000000..abb330f2b46 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb @@ -0,0 +1,70 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-dft_tools' +version = '3.1.0' + +homepage = 'https://triqs.github.io/dft_tools/' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + This TRIQS-based-based application is aimed at ab-initio calculations + for correlated materials, combining realistic DFT band-structure calculation + with the dynamical mean-field theory. Together with the necessary tools to + perform the DMFT self-consistency loop for realistic multi-band problems, + the package provides a full-fledged charge self-consistent interface to the + Wien2K package. In addition, if Wien2k is not available, it provides a generic + interface for one-shot DFT+DMFT calculations, where only the single-particle + Hamiltonian in orbital space has to be provided. +""" + +docurls = ['https://triqs.github.io/dft_tools/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/dft_tools/releases/download/%(version)s/'] +sources = ['dft_tools-%(version)s.tar.gz'] +checksums = ['57b7d0fe5a96c5a42bb684c60ca8e136a33e1385bf6cd7e9d1371fa507dc2ec4'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), + ('Clang', '13.0.1'), + ('Clang-Python-bindings', '13.0.1'), + ('GMP', '6.2.1'), + ('HDF5', '1.10.7'), + ('Mako', '1.1.4'), + ('TRIQS', '3.1.0'), +] + +builddependencies = [ + ('CMake', '3.22.1') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/dmftproj', 'lib/libtriqs_dft_tools_c.a'], + 'dirs': ['include/triqs_dft_tools', 'bin', 'lib', 'share', + 'lib/python%(pyshortver)s/site-packages/triqs_dft_tools'], +} + +sanity_check_commands = ["python -c 'import triqs_dft_tools'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_dft_tools', +} +modextravars = { + 'TRIQS_DFT_TOOLS_ROOT': '%(installdir)s', + 'TRIQS_DFT_TOOLS_VERSION': '%(version)s', +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb new file mode 100644 index 00000000000..d79e17f9ac6 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb @@ -0,0 +1,70 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-tprf' +version = '3.1.0' + +homepage = 'https://triqs.github.io/tprf' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + TPRF is a TRIQS-based two-particle response function tool box that + implements basic operations for higher order response functions such + as inversion, products, the random phase approximation, the bethe + salpeter equation (in the local vertex approximation), etc.. + + The aim is to provide efficient (C++/OpenMP/MPI) implementations of + the basic operations needed to compute the two-particle response in + the different two-particle channels (particle-hole, particle-particle). +""" + +docurls = ['https://triqs.github.io/tprf/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/tprf/releases/download/%(version)s/'] +sources = ['tprf-%(version)s.tar.gz'] +checksums = ['75f6e79d891342951652353ea4d9914074d9947c67cad60844ebaa3f82bd17b5'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), + ('Clang', '13.0.1'), + ('Clang-Python-bindings', '13.0.1'), + ('GMP', '6.2.1'), + ('HDF5', '1.10.7'), + ('Mako', '1.1.4'), + ('TRIQS', '3.1.0'), +] + +builddependencies = [ + ('CMake', '3.22.1') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs_tprf_c.a'], + 'dirs': ['include/triqs_tprf', 'lib', 'share', + 'lib/python%(pyshortver)s/site-packages/triqs_tprf'], +} + +sanity_check_commands = ["python -c 'import triqs_tprf'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_tprf', +} +modextravars = { + 'TRIQS_TPRF_ROOT': '%(installdir)s', + 'TRIQS_TPRF_VERSION': '%(version)s' +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb new file mode 100644 index 00000000000..b4176524bb5 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb @@ -0,0 +1,70 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS' +version = '3.1.0' + +homepage = 'https://triqs.github.io/triqs' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. +""" + +docurls = ['https://triqs.github.io/triqs/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/triqs/releases/download/%(version)s/'] +sources = ['triqs-%(version)s.tar.gz'] +checksums = ['f1f358ec73498bc7ac3ed9665829d8605908f7f7fc876a5c2a01efe37d368f0e'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), + ('Clang', '13.0.1'), + ('Clang-Python-bindings', '13.0.1'), + ('GMP', '6.2.1'), + ('HDF5', '1.10.7'), + ('Mako', '1.1.4') +] + +builddependencies = [ + ('CMake', '3.22.1') +] + +separate_build_dir = True + +# Remove installation directory before building. This fixes problems with +# failing builds in the presence of preexisting installation. +preconfigopts = "rm -rf %(installdir)s && " + +configopts = "" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs.%s' % SHLIB_EXT], + 'dirs': ['include/triqs', 'include/itertools', 'include/mpi', 'include/cpp2py', + 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = [ + "triqs++ --help", + "c++2py --help", + "python -c 'import triqs'" +] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': ['lib/cmake/triqs', 'lib/cmake/cpp2py'] +} +modextravars = { + 'TRIQS_ROOT': '%(installdir)s', + 'TRIQS_VERSION': '%(version)s' +} + +moduleclass = 'phys' From 8b3550f9c227343868da1612c17f8d9b6389ddcb Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Thu, 24 Mar 2022 18:26:34 -0400 Subject: [PATCH 5043/9987] Bump hdf5 version to 1.12.1 --- .../easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb | 2 +- .../t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb | 2 +- .../easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb index 19e698e99bd..73c6a1b8c97 100644 --- a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb @@ -34,7 +34,7 @@ dependencies = [ ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.10.7'), + ('HDF5', '1.12.1'), ('Mako', '1.1.4'), ('TRIQS', '3.1.0'), ('NFFT', '3.5.2') diff --git a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb index abb330f2b46..3f219978bb8 100644 --- a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb @@ -36,7 +36,7 @@ dependencies = [ ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.10.7'), + ('HDF5', '1.12.1'), ('Mako', '1.1.4'), ('TRIQS', '3.1.0'), ] diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb index d79e17f9ac6..c4595b68429 100644 --- a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb @@ -36,7 +36,7 @@ dependencies = [ ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.10.7'), + ('HDF5', '1.12.1'), ('Mako', '1.1.4'), ('TRIQS', '3.1.0'), ] diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb index b4176524bb5..b0b03529c2c 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb @@ -27,7 +27,7 @@ dependencies = [ ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.10.7'), + ('HDF5', '1.12.1'), ('Mako', '1.1.4') ] From 49f9ac7876c2f340fe5c9f815fa2f01d9627be83 Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Fri, 25 Mar 2022 09:49:59 -0400 Subject: [PATCH 5044/9987] Bump python-igraph clang dep to 13.0.1 --- .../p/python-igraph/python-igraph-0.9.8-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb index f16f7fbcc66..d810a435204 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.9.6'), ('igraph', '0.9.5'), ('PyCairo', '1.20.1'), - ('Clang', '12.0.1'), + ('Clang', '13.0.1'), ('libxml2', '2.9.10'), ('zlib', '1.2.11'), ] From 48f056d380db8a5b554a791380326832639a61cf Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Tue, 29 Mar 2022 10:31:13 -0400 Subject: [PATCH 5045/9987] No need to set configopts to empty string --- easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb index b0b03529c2c..71cf1646135 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb @@ -41,8 +41,6 @@ separate_build_dir = True # failing builds in the presence of preexisting installation. preconfigopts = "rm -rf %(installdir)s && " -configopts = "" - runtest = 'test' sanity_check_paths = { From 738be44783df1a0c9822dc767a4a68475b75f15b Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Wed, 29 Jun 2022 11:19:44 -0400 Subject: [PATCH 5046/9987] Update clang version for pocl-1.8 to 13 --- easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb index 0c7f9416308..3ae0aa3485d 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('Clang', '12.0.1'), + ('Clang', '13.0.1'), ('hwloc', '2.5.0'), ('libtool', '2.4.6'), ('libxml2', '2.9.10'), From e2d3b4371cbff53a4a35b70bfcc083be4863f0eb Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Wed, 29 Jun 2022 11:20:56 -0400 Subject: [PATCH 5047/9987] Update triqs to version from 3.1.0 to patch release 3.1.1 --- .../easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb | 2 +- .../t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb | 2 +- .../easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb | 2 +- .../{TRIQS-3.1.0-foss-2021b.eb => TRIQS-3.1.1-foss-2021b.eb} | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/t/TRIQS/{TRIQS-3.1.0-foss-2021b.eb => TRIQS-3.1.1-foss-2021b.eb} (94%) diff --git a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb index 73c6a1b8c97..e81b7e7e49b 100644 --- a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb @@ -36,7 +36,7 @@ dependencies = [ ('GMP', '6.2.1'), ('HDF5', '1.12.1'), ('Mako', '1.1.4'), - ('TRIQS', '3.1.0'), + ('TRIQS', '3.1.1'), ('NFFT', '3.5.2') ] diff --git a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb index 3f219978bb8..dd112010867 100644 --- a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb @@ -38,7 +38,7 @@ dependencies = [ ('GMP', '6.2.1'), ('HDF5', '1.12.1'), ('Mako', '1.1.4'), - ('TRIQS', '3.1.0'), + ('TRIQS', '3.1.1'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb index c4595b68429..b66a8fcd147 100644 --- a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb @@ -38,7 +38,7 @@ dependencies = [ ('GMP', '6.2.1'), ('HDF5', '1.12.1'), ('Mako', '1.1.4'), - ('TRIQS', '3.1.0'), + ('TRIQS', '3.1.1'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb similarity index 94% rename from easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb rename to easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb index 71cf1646135..8800fcb529b 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'TRIQS' -version = '3.1.0' +version = '3.1.1' homepage = 'https://triqs.github.io/triqs' description = """ @@ -18,7 +18,7 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/TRIQS/triqs/releases/download/%(version)s/'] sources = ['triqs-%(version)s.tar.gz'] -checksums = ['f1f358ec73498bc7ac3ed9665829d8605908f7f7fc876a5c2a01efe37d368f0e'] +checksums = ['cf4f6064ea962fc088e0c2833bf7c4e52f4c827ea331bf3c57d1c9303649042b'] dependencies = [ ('Python', '3.9.6'), From 832b8d6905f2c9d27378e839473c560dc06d567b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 6 Oct 2022 18:35:38 +0200 Subject: [PATCH 5048/9987] Update patches to fix remaining failures --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 8 +++++- .../PyTorch-1.11.0_fix-fsdp-fp16-test.patch | 13 ++++++++++ ...1.1_skip-test_init_from_local_shards.patch | 25 +++++++++++++++++++ ...orch-1.11.1_skip-test_sibling_fusion.patch | 17 +++++++++++++ 4 files changed, 62 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_init_from_local_shards.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_sibling_fusion.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 32f4323e49d..8385d91b7f0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -34,6 +34,8 @@ patches = [ 'PyTorch-1.11.0_increase-tolerance-test_ops.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.0_skip_failing_ops_tests.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.11.1_skip-test_sibling_fusion.patch', ] checksums = [ 'dc0c2b8d13c112a2b9ea8757a475b0ce2ca97cd19c50a8b70b8c286676616f1d', # pytorch-v1.11.0.tar.gz @@ -57,7 +59,7 @@ checksums = [ 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', # PyTorch-1.11.0_fix-attention_cpp-compilation.patch '84214fcc7e30cf70659a7c3bd70bf11e73d58fd4f7fff2c233e3225619b0e42c', - 'ca48576014bceb8c6c0d06cbab666be96cb44804e0215f5c025397a75a675bab', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch @@ -71,6 +73,10 @@ checksums = [ 'ceec745c68a405bba79efb4dc61c662ca84eb950cd0163c7104330f4bf614cf5', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch '8eaca92d64fcadb0552d28e9c7ea5c4bc669d2fe33004e45a3519ce8d0d136a2', # PyTorch-1.11.0_skip_failing_ops_tests.patch + # PyTorch-1.11.1_skip-test_init_from_local_shards.patch + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + # PyTorch-1.11.1_skip-test_sibling_fusion.patch + '3d6f6395d98e8e4ad76b0b63c625fddf082cf7f066eb97d4d82401f96dab2555', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch index 401d0865d49..dc9159e5cf9 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fsdp-fp16-test.patch @@ -4,6 +4,19 @@ See https://github.com/pytorch/pytorch/issues/78975 Author: Alexander Grund (TU Dresden) +diff --git a/torch/testing/_internal/common_fsdp.py b/torch/testing/_internal/common_fsdp.py +index ff0fbb69e3..6bf3e71fde 100644 +--- a/torch/testing/_internal/common_fsdp.py ++++ b/torch/testing/_internal/common_fsdp.py +@@ -324,7 +324,7 @@ class FSDPTest(MultiProcessTestCase): + + @property + def world_size(self): +- return torch.cuda.device_count() if torch.cuda.is_available() else 4 ++ return min(4, torch.cuda.device_count()) if torch.cuda.is_available() else 4 + + @property + def init_method(self): diff --git a/test/distributed/fsdp/test_fsdp_pure_fp16.py b/test/distributed/fsdp/test_fsdp_pure_fp16.py index eea03bea3d..d3a4bb8257 100644 --- a/test/distributed/fsdp/test_fsdp_pure_fp16.py diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_init_from_local_shards.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_init_from_local_shards.patch new file mode 100644 index 00000000000..c63d7193b7e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_init_from_local_shards.patch @@ -0,0 +1,25 @@ +The test often times out and seems to be considered flaky by PyTorch: +https://github.com/pytorch/pytorch/issues/78068 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/_shard/sharded_tensor/test_sharded_tensor.py b/test/distributed/_shard/sharded_tensor/test_sharded_tensor.py +index cbad9458ae..72a36e0e9a 100644 +--- a/test/distributed/_shard/sharded_tensor/test_sharded_tensor.py ++++ b/test/distributed/_shard/sharded_tensor/test_sharded_tensor.py +@@ -6,6 +6,7 @@ import io + import itertools + import pickle + import sys ++from unittest import skip + import torch + import torch.distributed as dist + from torch.distributed import rpc +@@ -1817,6 +1818,7 @@ class TestShardedTensorFromLocalShards(ShardedTensorTestBase): + @with_comms + @skip_if_lt_x_gpu(4) + @requires_nccl() ++ @skip("Times out often") + def test_init_from_local_shards(self): + local_shard_metadata = ShardMetadata( + shard_offsets=[(self.rank // 2) * 5, (self.rank % 2) * 5], diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_sibling_fusion.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_sibling_fusion.patch new file mode 100644 index 00000000000..6845706f484 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.1_skip-test_sibling_fusion.patch @@ -0,0 +1,17 @@ +The test fails on pre-volta devices as fusing the at::sum/at::add +is skipped if the device is not of compute capability >= 7 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_jit_cuda_fuser.py b/test/test_jit_cuda_fuser.py +index c03ff0b311..feb6e281f9 100644 +--- a/test/test_jit_cuda_fuser.py ++++ b/test/test_jit_cuda_fuser.py +@@ -3053,6 +3054,7 @@ class TestCudaFuser(JitTestCase): + self.assertGraphContainsExactly(graph, op, 0) + + @unittest.skipIf(not RUN_CUDA, "requires CUDA") ++ @unittest.skipIf(is_pre_volta(), "reduction not supported in pre volta device") + @unittest.skipIf(GRAPH_EXECUTOR != ProfilingMode.PROFILING, + "Requires fusion optimization pass to be effective") + def test_sibling_fusion(self): From 903cb2de9cc708dac83ba7a5cfc85726d10660a9 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 6 Oct 2022 14:51:34 -0400 Subject: [PATCH 5049/9987] adding easyconfigs: ncbi-vdb-3.0.0-gompi-2022a.eb --- .../f/file/file-5.43-GCCcore-11.3.0.eb | 28 +++++++++ .../h/HDF5/HDF5-1.10.8-gompi-2022a.eb | 28 +++++++++ .../n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb | 58 +++++++++++++++++++ 3 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1128c37d6ac --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.43' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2022a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2022a.eb new file mode 100644 index 00000000000..3091b947d74 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2022a.eb @@ -0,0 +1,28 @@ +# Updated to version 1.10.8, needed for HISAT2-2.2.1 +# J. Sassmannshausen + +name = 'HDF5' +version = '1.10.8' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['66ec544b195a4cb9f6ffed034fd82e52429d6112747c2996ab69853f606e546b'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +# needed to build HL-tools: gif2h5 gif2h5 and h5watch +# beware that gif tools are affected by multiple CVEs: CVE-2018-17433, CVE-2018-17436, CVE-2020-10809 +# configopts = "--enable-hltools" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb new file mode 100644 index 00000000000..b02b422d181 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'ncbi-vdb' +version = '3.0.0' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch', + 'ncbi-vdb-cstdlib.patch', +] +checksums = [ + '154317ef265104861fe8d3d2e439939ae98f33b1e28da3c45f32ae8534dbfad7', # ncbi-vdb-3.0.0.tar.gz + 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch + 'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655', # ncbi-vdb-cstdlib.patch +] + +builddependencies = [ + ('Perl', '5.34.1', '-minimal'), + ('Python', '3.10.4', '-bare'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('file', '5.43'), # provides libmagic + ('HDF5', '1.10.8'), # version 1.12.x has changes to API and is not compatible + ('libxml2', '2.9.13'), + ('bzip2', '1.0.8'), +] + +# add addtional libraries needed to statically link HDF5 from EB +preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/'" +preconfigopts += " %(builddir)s/%(namelower)s-%(version)s/setup/konfigure.perl &&" + +configopts = '' +configopts += ' -DHDF5_LIBDIR=$EBROOTHDF5/lib -DXML2_LIBDIR=$EBROOTLIBXML2/lib' +configopts += ' -DHDF5_INCDIR=$EBROOTHDF5/include -DXML2_INCDIR=$EBROOTLIBXML2/include' + + +# replace hardcoded optimization flags with EB settings +prebuildopts = "find %(builddir)s/%(namelower)s-%(version)s/build/ -name \"Makefile*\" " +prebuildopts += "-exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " +preinstallopts = 'EBFLAGS="$CFLAGS" ' + +sanity_check_paths = { + 'files': [('lib/libncbi-%s.%s' % (k, e), 'lib64/libncbi-%s.%s' % (k, e)) + for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' From a8daaba18b9522f284babf79aa7d3d2a3e909856 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 7 Oct 2022 08:34:47 +0200 Subject: [PATCH 5050/9987] Conform to style guide --- .../torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb index 9c2141e4169..b6e1c9385c7 100644 --- a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -6,7 +6,10 @@ local_pytorch_version = '1.11.0' versionsuffix = '-PyTorch-' + local_pytorch_version + '-CUDA-%(cudaver)s' homepage = 'https://github.com/pytorch/data' -description = "TorchData is a prototype library of common modular data loading primitives for easily constructing flexible and performant data pipelines." +description = """ +TorchData is a prototype library of common modular data loading primitives for +easily constructing flexible and performant data pipelines." +""" toolchain = {'name': 'foss', 'version': '2021a'} From 45b9d5f351439197ec11442bda41cfec91a16475 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Oct 2022 16:05:29 +0200 Subject: [PATCH 5051/9987] {tools}[GCCcore/11.3.0] onedrive v2.4.21, LDC v1.30.0 --- .../easyconfigs/l/LDC/LDC-1.24.0-x86_64.eb | 25 +++++++++++ .../l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb | 39 +++++++++++++++++ .../onedrive-2.4.21-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ 3 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/l/LDC/LDC-1.24.0-x86_64.eb create mode 100644 easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/onedrive/onedrive-2.4.21-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.24.0-x86_64.eb b/easybuild/easyconfigs/l/LDC/LDC-1.24.0-x86_64.eb new file mode 100644 index 00000000000..7b726673f51 --- /dev/null +++ b/easybuild/easyconfigs/l/LDC/LDC-1.24.0-x86_64.eb @@ -0,0 +1,25 @@ +easyblock = 'Tarball' + +name = 'LDC' +version = '1.24.0' +versionsuffix = '-x86_64' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = SYSTEM + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s/'] +sources = ['ldc2-%(version)s-linux%(versionsuffix)s.tar.xz'] +checksums = ['868e070fe90b06549f5fb19882a58a920c0052fad29b764eee9f409f08892ba3'] + +unpack_options = '--strip-components=1' + +sanity_check_paths = { + 'files': ['bin/dub', 'bin/ldc2', 'bin/ldmd2', 'lib/libdruntime-ldc.a'], + 'dirs': [], +} + +sanity_check_commands = ["ldc2 --help"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9e9a544e9f6 --- /dev/null +++ b/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeNinja' + +name = 'LDC' +version = '1.30.0' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s'] +sources = ['ldc-%(version)s-src.tar.gz'] +checksums = ['fdbb376f08242d917922a6a22a773980217fafa310046fc5d6459490af23dacd'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), + # building LDC from source requires LDC + ('LDC', '1.24.0', '-%(arch)s', True), +] + +dependencies = [ + ('LLVM', '14.0.3'), +] + +configopts = "-DLLVM_ROOT_DIR=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/ldc2', 'bin/ldmd2'], + 'dirs': ['include/d', 'lib'], +} + +sanity_check_commands = [ + "ldc2 --help", + "ldmd2 --help", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/onedrive/onedrive-2.4.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/onedrive/onedrive-2.4.21-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b75326b187d --- /dev/null +++ b/easybuild/easyconfigs/o/onedrive/onedrive-2.4.21-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'onedrive' +version = '2.4.21' + +homepage = 'https://abraunegg.github.io/' +description = """ +A free Microsoft OneDrive Client which supports OneDrive Personal, OneDrive for Business, +OneDrive for Office365 and SharePoint.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/abraunegg/onedrive/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c9991970cbb108368d16a4e6aefe66f0d61d66791ab3bbc526bff2237b926c51'] + +builddependencies = [ + ('binutils', '2.38'), + ('LDC', '1.30.0'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('SQLite', '3.38.3'), +] + +_compldir = '%(installdir)s/share/tab_completion' +configopts = 'DC="$EBROOTLDC"/bin/ldc2 --with-systemdsystemunitdir=no ' +configopts += '--enable-completions --with-bash-completion-dir=%s ' % _compldir +configopts += '--with-zsh-completion-dir=%s --with-fish-completion-dir=%s ' % (_compldir, _compldir) + +sanity_check_paths = { + 'files': ['bin/onedrive'], + 'dirs': ['etc', 'share'], +} + +sanity_check_commands = ['onedrive -h'] + +# optionally enable tab completion for bash (zsh: '_onedrive', fish: 'onedrive.fish') +modluafooter = 'execute {cmd="source $EBROOTONEDRIVE/share/tab_completion/onedrive",modeA={"load"}}' + +moduleclass = 'tools' From 26bf4b354a1859dfeec24be5d2a968a51088c83b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 7 Oct 2022 15:56:31 +0100 Subject: [PATCH 5052/9987] adding easyconfigs: libconfig-1.7.3-GCCcore-10.3.0.eb --- .../libconfig-1.7.3-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6210df9240e --- /dev/null +++ b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libconfig' +version = '1.7.3' + +homepage = 'https://hyperrealm.github.io/libconfig' +description = "Libconfig is a simple library for processing structured configuration files" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://hyperrealm.github.io/libconfig/dist/'] +sources = [SOURCE_TAR_GZ] +checksums = ['545166d6cac037744381d1e9cc5a5405094e7bfad16a411699bcff40bbb31ee7'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +sanity_check_paths = { + 'files': ['include/libconfig.h', 'include/libconfig.h++', 'lib/libconfig.a', 'lib/libconfig++.a', + 'lib/libconfig.%s' % SHLIB_EXT, 'lib/libconfig++.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' From c2e45e758cdd8b1cde51040b04ed6b3b2f587c0d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 10 Oct 2022 11:48:17 +0200 Subject: [PATCH 5053/9987] Update easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb --- .../torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb index b6e1c9385c7..5995d9c3e6f 100644 --- a/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchdata/torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -14,7 +14,7 @@ easily constructing flexible and performant data pipelines." toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), ] From 6e75480914e06d5e61bbbc851ec60d3bb7bbda52 Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Thu, 6 Oct 2022 12:53:36 -0400 Subject: [PATCH 5054/9987] Move TRIQS packages to 2022a toolchain, add NFFT-3.5.3-foss-2022a -Add easyconfig Clang-Python-bindings-13.0.1-GCCcore-11.3.0 --- ...g-Python-bindings-13.0.1-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ .../n/NFFT/NFFT-3.5.3-foss-2022a.eb | 31 +++++++++++++++++++ .../easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb | 2 +- .../python-igraph-0.9.8-foss-2021b.eb | 2 +- ...21b.eb => TRIQS-cthyb-3.1.0-foss-2022a.eb} | 16 +++++----- ...eb => TRIQS-dft_tools-3.1.0-foss-2022a.eb} | 14 ++++----- ...021b.eb => TRIQS-tprf-3.1.1-foss-2022a.eb} | 18 +++++------ ...oss-2021b.eb => TRIQS-3.1.1-foss-2022a.eb} | 14 ++++----- 8 files changed, 95 insertions(+), 33 deletions(-) create mode 100644 easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb rename easybuild/easyconfigs/t/TRIQS-cthyb/{TRIQS-cthyb-3.1.0-foss-2021b.eb => TRIQS-cthyb-3.1.0-foss-2022a.eb} (88%) rename easybuild/easyconfigs/t/TRIQS-dft_tools/{TRIQS-dft_tools-3.1.0-foss-2021b.eb => TRIQS-dft_tools-3.1.0-foss-2022a.eb} (91%) rename easybuild/easyconfigs/t/TRIQS-tprf/{TRIQS-tprf-3.1.0-foss-2021b.eb => TRIQS-tprf-3.1.1-foss-2022a.eb} (85%) rename easybuild/easyconfigs/t/TRIQS/{TRIQS-3.1.1-foss-2021b.eb => TRIQS-3.1.1-foss-2022a.eb} (89%) diff --git a/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fcbc32b1b75 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-13.0.1-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'Clang-Python-bindings' +version = '13.0.1' + +homepage = 'https://clang.llvm.org' +description = """Python bindings for libclang""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/"] +sources = ['clang-%(version)s.src.tar.xz'] +checksums = ['787a9e2d99f5c8720aa1773e4be009461cd30d3bd40fdd24591e473467c917c9'] + +dependencies = [ + ('Clang', version), + ('Python', '3.10.4') +] + +start_dir = 'bindings/python' + +sanity_check_paths = { + 'files': ['clang/cindex.py'], + 'dirs': ['clang'] +} + +sanity_check_commands = ["python -c 'import clang'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb new file mode 100644 index 00000000000..5787c0ee569 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.5.3' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/NFFT/nfft/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['caf1b3b3e5bf8c33a6bfd7eca811d954efce896605ecfd0144d47d0bebdf4371'] + +dependencies = [('FFTW', '3.3.10')] + +builddependencies = [('Autotools', '20220317')] + +configure_cmd_prefix = './bootstrap.sh ; ' + +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3_threads.a', 'lib/libnfft3.a', + 'lib/libnfft3_threads.%s' % SHLIB_EXT, 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb index 3ae0aa3485d..0c7f9416308 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('Clang', '13.0.1'), + ('Clang', '12.0.1'), ('hwloc', '2.5.0'), ('libtool', '2.4.6'), ('libxml2', '2.9.10'), diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb index d810a435204..f16f7fbcc66 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.9.8-foss-2021b.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.9.6'), ('igraph', '0.9.5'), ('PyCairo', '1.20.1'), - ('Clang', '13.0.1'), + ('Clang', '12.0.1'), ('libxml2', '2.9.10'), ('zlib', '1.2.11'), ] diff --git a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2022a.eb similarity index 88% rename from easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb rename to easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2022a.eb index e81b7e7e49b..84ff74d8ecc 100644 --- a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.1.0-foss-2022a.eb @@ -20,7 +20,7 @@ description = """ docurls = ['https://triqs.github.io/cthyb/%(version_major_minor)s.x/'] software_license = 'LicenseGPLv3' -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/TRIQS/cthyb/releases/download/%(version)s/'] @@ -28,20 +28,20 @@ sources = ['cthyb-%(version)s.tar.gz'] checksums = ['8d6d2c4d5b3928d062b72fad4ea9df9aae198e39dd9c1fd3cc5dc34a5019acc0'] dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('Boost', '1.77.0'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.12.1'), - ('Mako', '1.1.4'), + ('HDF5', '1.12.2'), + ('Mako', '1.2.0'), ('TRIQS', '3.1.1'), - ('NFFT', '3.5.2') + ('NFFT', '3.5.3') ] builddependencies = [ - ('CMake', '3.22.1') + ('CMake', '3.23.1') ] separate_build_dir = True diff --git a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2022a.eb similarity index 91% rename from easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb rename to easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2022a.eb index dd112010867..78221bf72e6 100644 --- a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.1.0-foss-2022a.eb @@ -22,7 +22,7 @@ description = """ docurls = ['https://triqs.github.io/dft_tools/%(version_major_minor)s.x/'] software_license = 'LicenseGPLv3' -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/TRIQS/dft_tools/releases/download/%(version)s/'] @@ -30,19 +30,19 @@ sources = ['dft_tools-%(version)s.tar.gz'] checksums = ['57b7d0fe5a96c5a42bb684c60ca8e136a33e1385bf6cd7e9d1371fa507dc2ec4'] dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('Boost', '1.77.0'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.12.1'), - ('Mako', '1.1.4'), + ('HDF5', '1.12.2'), + ('Mako', '1.2.0'), ('TRIQS', '3.1.1'), ] builddependencies = [ - ('CMake', '3.22.1') + ('CMake', '3.23.1') ] separate_build_dir = True diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.1-foss-2022a.eb similarity index 85% rename from easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb rename to easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.1-foss-2022a.eb index b66a8fcd147..6ba4a624278 100644 --- a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.1.1-foss-2022a.eb @@ -1,7 +1,7 @@ easyblock = 'CMakeMake' name = 'TRIQS-tprf' -version = '3.1.0' +version = '3.1.1' homepage = 'https://triqs.github.io/tprf' description = """ @@ -22,27 +22,27 @@ description = """ docurls = ['https://triqs.github.io/tprf/%(version_major_minor)s.x/'] software_license = 'LicenseGPLv3' -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/TRIQS/tprf/releases/download/%(version)s/'] sources = ['tprf-%(version)s.tar.gz'] -checksums = ['75f6e79d891342951652353ea4d9914074d9947c67cad60844ebaa3f82bd17b5'] +checksums = ['63d4de9cfc3daf0d74db45cfa7445b817fd22a38a8485db3ce9a81febe263b50'] dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('Boost', '1.77.0'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.12.1'), - ('Mako', '1.1.4'), + ('HDF5', '1.12.2'), + ('Mako', '1.2.0'), ('TRIQS', '3.1.1'), ] builddependencies = [ - ('CMake', '3.22.1') + ('CMake', '3.23.1') ] separate_build_dir = True diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2022a.eb similarity index 89% rename from easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb rename to easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2022a.eb index 8800fcb529b..ca1bf2e6a62 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.1.1-foss-2022a.eb @@ -13,7 +13,7 @@ description = """ docurls = ['https://triqs.github.io/triqs/%(version_major_minor)s.x/'] software_license = 'LicenseGPLv3' -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/TRIQS/triqs/releases/download/%(version)s/'] @@ -21,18 +21,18 @@ sources = ['triqs-%(version)s.tar.gz'] checksums = ['cf4f6064ea962fc088e0c2833bf7c4e52f4c827ea331bf3c57d1c9303649042b'] dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('Boost', '1.77.0'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), ('Clang', '13.0.1'), ('Clang-Python-bindings', '13.0.1'), ('GMP', '6.2.1'), - ('HDF5', '1.12.1'), - ('Mako', '1.1.4') + ('HDF5', '1.12.2'), + ('Mako', '1.2.0') ] builddependencies = [ - ('CMake', '3.22.1') + ('CMake', '3.23.1') ] separate_build_dir = True From 737d5eedb5a9cb75def0295a421c141a8bd5cc32 Mon Sep 17 00:00:00 2001 From: Nils Wentzell Date: Mon, 10 Oct 2022 13:02:30 -0400 Subject: [PATCH 5055/9987] Fix sha256 for NFFT 3.5.3 tarball --- easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb index 5787c0ee569..36911997f51 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2022a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://github.com/NFFT/nfft/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['caf1b3b3e5bf8c33a6bfd7eca811d954efce896605ecfd0144d47d0bebdf4371'] +checksums = ['ccef7a8e97e40e5f962df94626ade5adc7db1fb7948e3c75aa70393468e2e8fb'] dependencies = [('FFTW', '3.3.10')] From 5c0b21b325e9ef49307de47d176c926be7c2a327 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 10 Oct 2022 23:40:06 +0000 Subject: [PATCH 5056/9987] adding easyconfigs: ACTC-1.1-GCCcore-11.3.0.eb, VMD-1.9.4a57-foss-2022a.eb and patches: VMD-1.9.4a57_configure.patch --- .../a/ACTC/ACTC-1.1-GCCcore-11.3.0.eb | 35 ++++ .../v/VMD/VMD-1.9.4a57-foss-2022a.eb | 46 +++++ .../v/VMD/VMD-1.9.4a57_configure.patch | 172 ++++++++++++++++++ 3 files changed, 253 insertions(+) create mode 100644 easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb create mode 100644 easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..12bca02e2a6 --- /dev/null +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'ACTC' +version = '1.1' + +homepage = 'https://sourceforge.net/projects/actc' +description = "ACTC converts independent triangles into triangle strips or fans." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3a1303291629b9de6008c3c9d7b020a4b854802408fb3f8222ec492808c8b44d'] + +builddependencies = [('binutils', '2.38')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['tcsample', 'tctest', 'tctest2'], 'bin'), + (['tc.h'], 'include/ac'), + (['libactc.a'], 'lib'), + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README', +] + +sanity_check_paths = { + 'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README'], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/ac'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb new file mode 100644 index 00000000000..c79d12f48f5 --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb @@ -0,0 +1,46 @@ +name = 'VMD' +version = '1.9.4a57' + +homepage = 'https://www.ks.uiuc.edu/Research/vmd' +description = """VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular + systems using 3-D graphics and built-in scripting.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', + 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', + 'https://webclu.bio.wzw.tum.de/stride/' +] +sources = [ + 'vmd-%(version)s.src.tar.gz', + {'filename': 'stride.tar.gz', 'extract_cmd': "tar -C vmd-%(version)s/lib/stride -xf %s"}, +] +patches = [ + ('VMD-1.9.3_plugins.patch'), + ('VMD-1.9.3_surf_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_surf_bad_printfs.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_Makefile.patch', 'vmd-%(version)s'), + ('VMD-1.9.3_stride_MAX_AT_IN_RES.patch', 'vmd-%(version)s'), + ('VMD-%(version)s_configure.patch', 'vmd-%(version)s'), + ('VMD-1.9.4a51_extra_colors.patch', 'vmd-%(version)s'), +] + +dependencies = [ + ('Tcl', '8.6.12'), + ('Tk', '8.6.12'), + ('FLTK', '1.3.8'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Tkinter', '%(pyver)s'), + ('Mesa', '22.0.3'), + ('netCDF', '4.9.0'), + ('FFmpeg', '4.4.2'), + ('ImageMagick', '7.1.0-37'), + ('ACTC', '1.1'), + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('POV-Ray', '3.7.0.10'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch new file mode 100644 index 00000000000..63b8e014f84 --- /dev/null +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch @@ -0,0 +1,172 @@ +--- configure.orig 2022-10-03 21:19:36.313951477 +0000 ++++ configure 2022-10-03 21:44:36.664710705 +0000 +@@ -498,17 +498,17 @@ + + $arch_cc = "cc"; + $arch_ccpp = "CC"; +-$arch_nvcc = "/usr/local/cuda-10.2/bin/nvcc"; ++$arch_nvcc = "nvcc"; + $arch_nvccflags = "-lineinfo --ptxas-options=-v " . +- "-gencode arch=compute_30,code=compute_30 " . +- "-gencode arch=compute_30,code=sm_35 " . +- "-gencode arch=compute_30,code=sm_37 " . + "-gencode arch=compute_50,code=compute_50 " . + "-gencode arch=compute_50,code=sm_50 " . + "-gencode arch=compute_60,code=compute_60 " . + "-gencode arch=compute_60,code=sm_60 " . + "-gencode arch=compute_70,code=compute_70 " . + "-gencode arch=compute_70,code=sm_70 " . ++ "-gencode arch=compute_75,code=sm_75 " . ++ "-gencode arch=compute_80,code=sm_80 " . ++ "-gencode arch=compute_86,code=sm_86 " . + "--ftz=true "; + # "-gencode arch=compute_75,code=sm_75 " . + $arch_gcc = "gcc"; +@@ -634,17 +634,17 @@ + # location of Mesa library and include files; basically does the same + # as OpenGL. This is based on the default instructions from the Mesa + # README; the include files should by default be in /usr/local/include/GL. +-$mesa_dir = "$vmd_library_dir/Mesa"; ++$mesa_dir = "$ENV{'EBROOTMESA'}"; + $mesa_include = "-I$mesa_dir/include"; + $mesa_library = "-L$mesa_dir/lib_$config_arch"; + #$mesa_libs = "-lMesaGL -lMesaGLU"; +-$mesa_libs = "-lMesaGL"; ++$mesa_libs = "-lGL -lGLU"; + $mesa_defines = "-DUSELINEAXES -DVMDMESA -DVMDOPENGL"; + @mesa_cc = (); + @mesa_cu = (); +-@mesa_ccpp = @opengl_ccpp; +-@mesa_h = @opengl_h; +-@mesa_extra = @opengl_extra; ++@mesa_ccpp = (); ++@mesa_h = (); ++@mesa_extra = (); + + + # +@@ -720,10 +720,10 @@ + + ################ FLTK GUI + $fltk_defines = "-DVMDGUI -DVMDFLTK"; +-$fltk_dir = "$vmd_library_dir/fltk"; ++$fltk_dir = "$ENV{'EBROOTFLTK'}"; + $fltk_include = "-I$fltk_dir/include"; + $fltk_library = "-L$fltk_dir/$config_arch"; +-$fltk_libs = "-lfltk -lX11"; ++$fltk_libs = "-lfltk -lX11 -lXfixes -lXcursor -lXinerama"; + #@fltk_cc = ('forms_ui.c'); + @fltk_cu = (); + @fltk_ccpp = ( 'ColorFltkMenu.C', +@@ -783,8 +783,8 @@ + if ($config_tk) { $tcl_include .= " -I$stock_tk_include_dir"; } + $tcl_library = "-L$stock_tcl_library_dir"; + if ($config_tk) { $tcl_library .= " -L$stock_tk_library_dir"; } +-$tcl_libs = "-ltcl8.5"; +-if ($config_tk) { $tcl_libs = "-ltk8.5 -lX11 " . $tcl_libs; } ++$tcl_libs = "-ltcl8.6"; ++if ($config_tk) { $tcl_libs = "-ltk8.6 -lX11 " . $tcl_libs; } + + @tcl_cc = (); + @tcl_cu = (); +@@ -1006,7 +1006,7 @@ + # This option enables the use of CUDA GPU acceleration functions. + ####################### + $cuda_defines = "-DVMDCUDA -DMSMPOT_CUDA"; +-$cuda_dir = "/usr/local/cuda-10.2"; ++$cuda_dir = "$ENV{'CUDA_HOME'}"; + $cuda_include = ""; + $cuda_library = ""; + $cuda_libs = "-Wl,-rpath -Wl,\$\$ORIGIN/ -lcudart_static -lrt"; +@@ -1215,7 +1215,7 @@ + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-5.0.1-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-5.1.0-linux64"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-6.0.0-linux64"; +-$liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-6.5.0-linux64"; ++$liboptix_dir = "$ENV{'EBROOTOPTIX'}"; + # $liboptix_dir = "/usr/local/encap/NVIDIA-OptiX-SDK-7.0.0-linux64"; + + # NCSA Blue Waters +@@ -1370,7 +1370,7 @@ + die "LIBPNG option requires ZLIB!"; + } + $libpng_defines = "-DVMDLIBPNG"; +-$libpng_dir = "/Projects/vmd/vmd/lib/libpng"; ++$libpng_dir = "$ENV{'EBROOTLIBPNG'}"; + $libpng_include = "-I$libpng_dir/include"; + $libpng_library = "-L$libpng_dir/lib_$config_arch"; + $libpng_libs = "-lpng16"; +@@ -1398,7 +1398,7 @@ + # OPTIONAL COMPONENT: Data compresssion library + # This may be commented out if not required. + $zlib_defines = "-DVMDZLIB"; +-$zlib_dir = "/Projects/vmd/vmd/lib/zlib"; ++$zlib_dir = "$ENV{'EBROOTZLIB'}"; + $zlib_include = "-I$zlib_dir/include"; + $zlib_library = "-L$zlib_dir/lib_$config_arch"; + $zlib_libs = "-lz"; +@@ -1589,7 +1589,7 @@ + # primitives. + ####################### + $actc_defines = "-DVMDACTC"; +-$actc_dir = "$vmd_library_dir/actc"; ++$actc_dir = "$ENV{'EBROOTACTC'}"; + $actc_include = "-I$actc_dir/include"; + $actc_library = "-L$actc_dir/lib_$config_arch"; + $actc_libs = "-lactc"; +@@ -1604,7 +1604,7 @@ + # OPTIONAL COMPONENT: NetCDF I/O Library (Used by cdfplugin) + ####################### + $netcdf_defines = ""; +-$netcdf_dir = "$vmd_library_dir/netcdf"; ++$netcdf_dir = "$ENV{'EBROOTNETCDF'}"; + $netcdf_include = "-I$netcdf_dir/include"; + $netcdf_library = "-L$netcdf_dir/lib_$config_arch"; + $netcdf_libs = "-lnetcdf"; +@@ -1662,7 +1662,7 @@ + $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "$conda_root/lib/python3.7/config-3.7m-x86_64-linux-gnu"; + $stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "$conda_root/lib/python3.7/site-packages/numpy/core/include/numpy"; + $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$conda_root/lib/python-3.7/site-packages/numpy/core/include"; +- $python_libs = "-fno-lto -lpython3.7m -lpthread"; ++ $python_libs = "$ENV{'PYTHON_LIBRARIES'}" || "-fno-lto -lpython3.7m -lpthread"; + } else { + # $stock_python_include_dir=$ENV{"PYTHON_INCLUDE_DIR"} || "/usr/local/include"; + # $stock_python_library_dir=$ENV{"PYTHON_LIBRARY_DIR"} || "/usr/local/lib"; +@@ -1673,7 +1673,7 @@ + # $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "/usr/local/lib"; + $stock_numpy_include_dir=$ENV{"NUMPY_INCLUDE_DIR"} || "$vmd_library_dir/numpy/lib_$config_arch/include"; + $stock_numpy_library_dir=$ENV{"NUMPY_LIBRARY_DIR"} || "$vmd_library_dir/python/lib_$config_arch/lib/python2.5/site-packages/numpy/core/include"; +- $python_libs = "-lpython2.5 -lpthread"; ++ $python_libs = "$ENV{'PYTHON_LIBRARIES'}" || "-lpython2.5 -lpthread"; + } + + $python_defines = "-DVMDPYTHON"; +@@ -2593,7 +2593,7 @@ + + if ($config_cuda) { + $arch_nvccflags .= " --machine 64 -O3 $cuda_include"; +- $cuda_library = "-L/usr/local/cuda-10.2/lib64"; ++ $cuda_library = "-L$ENV{'EBROOTCUDA'}/lib64"; + } + + $arch_lex = "flex"; # has problems with vendor lex +@@ -2602,8 +2602,8 @@ + # override code probably date back to RHEL4.x or earlier, and + # they likely serve no useful purpose going forward. + if (!$config_opengl_dispatch) { +- $opengl_dep_libs = "-L/usr/X11R6/lib64 -lGL -lX11"; +- $mesa_libs = "-lMesaGL -L/usr/X11R6/lib64 -lXext -lX11"; ++ $opengl_dep_libs = " -lGL -lX11"; ++ $mesa_libs = "-lGL -lGLU -lXext -lX11"; + } + + # this is to make tcl happy +@@ -3789,7 +3789,7 @@ + + .cu.ptx: + \$(ECHO) "Compiling " \$< " --> " \$*.ptx " ..."; \\ +- \$(NVCC) \$(DEFINES) --use_fast_math $liboptix_include -gencode arch=compute_50,code=compute_50 -ptx \$< $arch_coptout$vmd_arch_dir/\$\@ ++ \$(NVCC) \$(DEFINES) --use_fast_math $liboptix_include -gencode arch=compute_80,code=compute_80 -ptx \$< $arch_coptout$vmd_arch_dir/\$\@ + + .y.o: + From 9bca3ca354b09bbc79e0691125fce4a96102d918 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2022 09:54:53 +0200 Subject: [PATCH 5057/9987] fix execution permissions for bin/ngm* for NextGenMap v0.5.5 --- .../n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb b/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb index 0a2f01375e9..a7e7ef4fe7c 100644 --- a/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb @@ -34,8 +34,12 @@ preconfigopts += "sed -i 's/zlibstatic/z/g' ../NextGenMap-%(version)s/{src,utils buildopts = ' && cp -r ../%(name)s-%(version)s/bin/ngm-%(version)s/. %(installdir)s/bin/' -# avoid hard overwriting of $LD_LIBRARY_PATH in ngm wrapper script -postinstallcmds = [r"sed -i 's/\(LD_LIBRARY_PATH=[^ ]*\)\"/\1:$LD_LIBRARY_PATH\"/g' %(installdir)s/bin/ngm"] +postinstallcmds = [ + # avoid hard overwriting of $LD_LIBRARY_PATH in ngm wrapper script + r"sed -i 's/\(LD_LIBRARY_PATH=[^ ]*\)\"/\1:$LD_LIBRARY_PATH\"/g' %(installdir)s/bin/ngm", + # fix execution permissions for ngm* binaries/scripts + "chmod a+x %(installdir)s/bin/ngm*", +] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['ngm', 'ngm-core', 'ngm-log', 'ngm-utils', 'oclTool']], From a6fe5e929c7e40029a5996954525b9de5c081b8a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 11 Oct 2022 09:56:55 +0100 Subject: [PATCH 5058/9987] deprecate use of True to indicate system-toolchain dependency in favour of the more intuitive SYSTEM template --- test/easyconfigs/easyconfigs.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0fb05afe876..21c4692ec27 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1449,11 +1449,11 @@ def template_easyconfig_test(self, spec): # 4th value is toolchain spec if len(dumped_dep) >= 4: if len(orig_dep) >= 4: - # if True was used to indicate that dependency should use system toolchain, - # then we need to compare the value for the dumped easyconfig more carefully; - # see also https://github.com/easybuilders/easybuild-framework/pull/4069 + # use of `True` is deprecated in favour of the more intuitive `SYSTEM` template if orig_dep[3] is True: - self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) + error_msg = "use of `True` to indicate the system toolchain for dependency " + error_msg += "%s is deprecated, use the `SYSTEM` template instead" % dumped_dep[0] + self.fail(error_msg) else: self.assertEqual(dumped_dep[3], orig_dep[3]) else: From b3f9824e19daf673e9e9fac9740525f34371eb6a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 11 Oct 2022 11:04:26 +0100 Subject: [PATCH 5059/9987] update easyconfigs to use SYSTEM instead of True in dependencies --- .../__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb | 2 +- .../__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb | 2 +- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 2 +- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 2 +- .../b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb | 4 ++-- .../b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb | 2 +- .../b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb | 2 +- .../b/beagle-lib/beagle-lib-20141202-intel-2015a.eb | 2 +- .../b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb | 2 +- .../b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb | 2 +- .../__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb | 2 +- .../d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb | 2 +- .../__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb | 2 +- .../__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb | 2 +- .../__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb | 2 +- .../__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb | 2 +- .../__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb | 2 +- .../__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb | 2 +- .../__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb | 2 +- .../Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 2 +- .../HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb | 4 ++-- .../HPCBIOS_Profilers-20130829-goolf-1.4.10.eb | 6 +++--- .../hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb | 2 +- .../i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb | 2 +- .../i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb | 2 +- ...ModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb | 4 ++-- ...plus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 2 +- .../MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb | 4 ++-- .../__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb | 4 ++-- .../__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb | 2 +- .../__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb | 2 +- .../__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb | 2 +- .../p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 2 +- .../p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb | 2 +- .../p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb | 2 +- .../p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb | 2 +- .../__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb | 2 +- .../__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb | 2 +- .../__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb | 2 +- .../__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb | 2 +- .../__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb | 2 +- .../__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb | 2 +- .../__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb | 2 +- .../__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb | 2 +- .../__archive__/r/R/R-3.1.2-intel-2015a-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb | 2 +- .../__archive__/r/R/R-3.2.0-foss-2015a-bare.eb | 2 +- .../__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- .../__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb | 2 +- .../__archive__/r/R/R-3.2.0-intel-2015a-bare.eb | 2 +- .../__archive__/r/R/R-3.2.1-foss-2015b-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb | 2 +- .../__archive__/r/R/R-3.2.1-intel-2015b-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb | 2 +- .../s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb | 2 +- .../Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb | 2 +- .../Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb | 2 +- .../s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb | 2 +- .../s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb | 2 +- .../__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb | 4 ++-- .../__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb | 4 ++-- .../__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb | 2 +- .../t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb | 2 +- .../t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb | 2 +- .../t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb | 2 +- .../vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- .../vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb | 4 ++-- .../vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb | 4 ++-- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb | 2 +- .../x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb | 2 +- .../x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb | 2 +- .../x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb | 2 +- .../easyconfigs/a/ABRA2/ABRA2-2.22-iccifort-2019.5.281.eb | 4 ++-- easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb | 4 ++-- easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb | 4 ++-- ...AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb | 2 +- .../easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb | 2 +- .../easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.2.0.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-8.3.0-Java-11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb | 2 +- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb | 2 +- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2019a.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2017b-Python-2.7.14.eb | 2 +- easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2018a-Python-3.6.4.eb | 2 +- .../easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/a/ASTRID/ASTRID-2.2.1-gompi-2019a.eb | 2 +- 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.../easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb | 2 +- .../easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb | 2 +- .../a/arcasHLA/arcasHLA-0.2.0-foss-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb | 2 +- .../easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019a.eb | 2 +- .../easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb | 2 +- .../a/arpack-ng/arpack-ng-3.7.0-intel-2019b.eb | 2 +- .../artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb | 6 +++--- .../artic-ncov2019-2021.06.24-foss-2020b.eb | 4 ++-- .../b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb | 2 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.../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.5.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-5.5.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.2.2-GCCcore-7.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.7.6-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb | 2 +- .../easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb | 2 +- .../Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb | 2 +- .../easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb | 2 +- .../b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb | 2 +- .../b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb | 2 +- .../b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb | 2 +- .../b/beagle-lib/beagle-lib-2.1.2-foss-2017a.eb | 2 +- .../b/beagle-lib/beagle-lib-3.0.1-foss-2018a.eb | 2 +- .../b/beagle-lib/beagle-lib-3.0.1-intel-2018a.eb | 2 +- .../beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb | 4 ++-- .../b/beagle-lib/beagle-lib-3.0.2-foss-2018b.eb | 2 +- .../b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb | 2 +- .../b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb | 2 +- .../b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb | 2 +- .../b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb | 2 +- ...agle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 2 +- .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb | 2 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.../b/binutils/binutils-2.36.1-GCCcore-10.3.0.eb | 2 +- .../b/binutils/binutils-2.36.1-GCCcore-11.1.0.eb | 2 +- .../b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb | 2 +- .../b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb | 2 +- .../b/binutils/binutils-2.37-GCCcore-11.2.0.eb | 2 +- .../b/binutils/binutils-2.38-GCCcore-11.3.0.eb | 2 +- .../b/binutils/binutils-2.38-GCCcore-12.1.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb | 2 +- .../b/binutils/binutils-2.39-GCCcore-12.2.0.eb | 2 +- .../b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb | 2 +- .../b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb | 2 +- .../b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb | 2 +- .../b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb | 2 +- .../easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb | 2 +- .../c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb | 2 +- .../c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb | 2 +- .../c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb | 2 +- .../c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb | 2 +- .../c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb | 2 +- .../c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb | 2 +- .../c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb | 2 +- .../CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb | 2 +- .../CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb | 2 +- .../c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb | 2 +- .../c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb | 2 +- .../c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb | 2 +- .../CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb | 4 ++-- .../c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb | 4 ++-- easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb | 2 +- .../easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb | 2 +- easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb | 2 +- .../easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb | 2 +- .../Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 4 ++-- .../c/Cantera/Cantera-2.3.0-foss-2017b-Python-2.7.14.eb | 2 +- .../c/Cantera/Cantera-2.3.0-intel-2017a-Python-2.7.13.eb | 2 +- .../c/Cantera/Cantera-2.3.0-intel-2017b-Python-2.7.14.eb | 2 +- .../c/Cantera/Cantera-2.3.0-intel-2018a-Python-2.7.14.eb | 2 +- .../c/Cantera/Cantera-2.4.0-intel-2018a-Python-2.7.14.eb | 2 +- .../c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb | 2 +- .../c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb | 2 +- .../c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb | 2 +- .../c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb | 2 +- .../c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb | 2 +- .../c/CheckM/CheckM-1.0.18-foss-2019a-Python-2.7.15.eb | 2 +- .../c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb | 2 +- .../c/CheckM/CheckM-1.1.2-foss-2019b-Python-3.7.4.eb | 2 +- .../c/CheckM/CheckM-1.1.2-intel-2019b-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb | 2 +- easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb | 2 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.../easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb | 2 +- easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb | 2 +- .../c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb | 2 +- .../easyconfigs/c/canu/canu-1.8-foss-2017b-Perl-5.26.0.eb | 2 +- .../easyconfigs/c/canu/canu-1.8-foss-2018b-Perl-5.28.0.eb | 2 +- .../c/canu/canu-1.8-intel-2017b-Perl-5.26.0.eb | 2 +- .../easyconfigs/c/canu/canu-1.9-GCCcore-8.3.0-Java-11.eb | 2 +- easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb | 2 +- .../c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb | 2 +- .../easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb | 2 +- easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb | 2 +- .../cell2location-0.05-alpha-fosscuda-2020b.eb | 2 +- .../colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb | 2 +- .../c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb | 2 +- .../easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb | 2 +- .../easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb | 2 +- .../DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb | 2 +- .../DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb | 4 ++-- .../easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb | 4 ++-- .../easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb | 4 ++-- .../d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb | 2 +- .../d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb | 2 +- .../easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb | 2 +- .../DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb | 2 +- .../d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb | 2 +- .../d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb | 2 +- .../e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb | 2 +- .../easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb | 2 +- .../e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb | 2 +- .../EMBOSS-6.6.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 2 +- .../e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb | 2 +- .../easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb | 2 +- .../Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb | 2 +- .../easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb | 2 +- .../f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb | 4 ++-- .../f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb | 4 ++-- .../FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb | 2 +- .../FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb | 2 +- easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-11.eb | 2 +- easybuild/easyconfigs/f/FastQC/FastQC-0.11.9-Java-11.eb | 2 +- .../FastViromeExplorer-20180422-foss-2019b.eb | 2 +- easybuild/easyconfigs/f/Ferret/Ferret-7.3-intel-2017b.eb | 2 +- easybuild/easyconfigs/f/Ferret/Ferret-7.5.0-foss-2019b.eb | 2 +- easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb | 2 +- easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb | 2 +- easybuild/easyconfigs/f/Fiji/Fiji-20201104-1356.eb | 2 +- .../easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb | 2 +- .../easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb | 2 +- .../FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb | 4 ++-- .../FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb | 4 ++-- .../f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb | 2 +- .../f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb | 2 +- .../f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-5.5.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb | 2 +- .../f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb | 2 +- .../fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb | 2 +- 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.../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb | 6 +++--- .../l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb | 2 +- .../easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb | 2 +- .../easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb | 2 +- .../easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb | 2 +- .../l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb | 2 +- .../l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.5-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb | 2 +- .../easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb | 2 +- .../easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb | 2 +- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb | 2 +- .../MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb | 2 +- .../MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb | 2 +- .../MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb | 2 +- .../MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb | 2 +- .../m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb | 2 +- .../m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb | 2 +- .../m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb | 2 +- .../MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb | 2 +- ...Splus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 2 +- .../MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 2 +- .../MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb | 2 +- .../MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb | 2 +- .../m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb | 2 +- .../m/MRtrix/MRtrix-3.0_RC3-intel-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb | 2 +- .../easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb | 2 +- .../m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.9-Java-1.8.eb | 2 +- easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-1.8.eb | 2 +- easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb | 2 +- .../m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb | 2 +- .../m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb | 4 ++-- .../m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb | 2 +- .../m/MotionCor2/MotionCor2-1.2.6-GCCcore-8.2.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.3.2-GCCcore-8.3.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb | 2 +- .../m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb | 2 +- .../MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb | 2 +- .../m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb | 2 +- .../m/magma/magma-2.3.0-foss-2018a-CUDA-9.1.85.eb | 2 +- .../m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb | 2 +- .../m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb | 2 +- .../m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb | 2 +- .../m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb | 2 +- .../m/metaWRAP/metaWRAP-1.2.2-foss-2019a-Python-2.7.15.eb | 4 ++-- .../m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb | 4 ++-- .../m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb | 2 +- .../easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb | 2 +- .../minieigen-0.5.4-intel-2018a-Python-2.7.14.eb | 2 +- easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb | 2 +- .../mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb | 4 ++-- .../mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb | 4 ++-- .../mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb | 4 ++-- .../mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb | 4 ++-- .../easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb | 2 +- .../n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb | 2 +- .../n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb | 2 +- .../n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb | 2 +- .../n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb | 4 ++-- .../n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb | 4 ++-- easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb | 2 +- .../n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-1.8.eb | 2 +- .../easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-11.eb | 2 +- .../easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb | 2 +- .../n/NGS/NGS-2.9.1-foss-2018a-Java-1.8.0_162.eb | 2 +- .../n/NGS/NGS-2.9.1-intel-2018a-Java-1.8.0_162.eb | 2 +- .../easyconfigs/n/NGS/NGS-2.9.3-foss-2018b-Java-1.8.eb | 2 +- .../n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb | 2 +- .../n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-19.07.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-19.12.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-20.01.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-20.10.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-21.03.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb | 2 +- easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb | 2 +- .../nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb | 2 +- .../nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb | 2 +- .../nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb | 2 +- .../nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb | 2 +- .../n/nanopolish/nanopolish-0.9.2-intel-2018a.eb | 2 +- .../easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb | 2 +- .../n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb | 2 +- .../ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb | 4 ++-- .../OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb | 2 +- .../OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb | 2 +- .../OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb | 2 +- .../OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb | 2 +- .../easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.2.1-foss-2018a.eb | 2 +- .../easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 2 +- .../easyconfigs/o/Octave/Octave-4.2.1-intel-2017a-mt.eb | 2 +- .../easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.2.2-foss-2018a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.4.1-foss-2018b.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019b.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb | 2 +- .../OpenBabel-2.4.1-intel-2017b-Python-2.7.14.eb | 2 +- .../OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb | 2 +- .../OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb | 2 +- .../OpenBabel/OpenBabel-2.4.1-intel-2019a-Python-3.7.2.eb | 2 +- .../OpenBabel/OpenBabel-3.0.0-gompi-2019b-Python-3.7.4.eb | 2 +- .../OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb | 2 +- .../OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb | 4 ++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb | 4 ++-- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb | 4 ++-- .../easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb | 4 ++-- .../o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb | 4 ++-- .../OpenCV-3.4.1-foss-2018a-Python-3.6.4-contrib.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-3.6.4.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.5-foss-2018b-Python-2.7.15.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-2.7.15.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-3.7.2.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-2.7.15.eb | 4 ++-- .../o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-3.7.2.eb | 4 ++-- .../o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-2.7.15.eb | 4 ++-- .../o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb | 4 ++-- .../o/OpenCV/OpenCV-4.2.0-foss-2019b-Python-3.7.4.eb | 4 ++-- .../OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb | 4 ++-- .../o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb | 4 ++-- .../o/OpenCV/OpenCV-4.2.0-fosscuda-2019b-Python-3.7.4.eb | 4 ++-- .../o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb | 4 ++-- .../o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb | 4 ++-- .../OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb | 8 ++++---- .../o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb | 4 ++-- .../o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb | 4 ++-- .../o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb | 4 ++-- .../o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/o/OpenMS/OpenMS-2.4.0-foss-2018b.eb | 2 +- .../o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb | 2 +- .../easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb | 2 +- .../o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 2 +- .../ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb | 2 +- .../ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb | 2 +- .../PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb | 2 +- .../PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb | 2 +- .../PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb | 2 +- .../p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb | 2 +- .../p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb | 4 ++-- easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb | 4 ++-- ...Lplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb | 2 +- ...plot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb | 2 +- .../easyconfigs/p/PRSice/PRSice-2.2.12-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb | 2 +- .../p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 2 +- .../easyconfigs/p/PTESFinder/PTESFinder-1-intel-2017b.eb | 2 +- easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 2 +- .../PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb | 2 +- .../p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb | 2 +- .../p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb | 2 +- .../p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb | 2 +- .../p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb | 2 +- .../p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb | 2 +- ...CUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb | 2 +- .../p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb | 2 +- .../PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb | 2 +- .../PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb | 2 +- .../PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb | 2 +- .../p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 4 ++-- .../p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 2 +- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 4 ++-- .../easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb | 2 +- .../PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb | 2 +- .../p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb | 2 +- .../p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb | 2 +- .../p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb | 2 +- .../easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 2 +- .../p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb | 2 +- .../p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb | 2 +- .../easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb | 2 +- .../p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb | 2 +- .../easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb | 2 +- .../p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb | 2 +- .../easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb | 2 +- .../pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb | 2 +- .../pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb | 2 +- ...arallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb | 2 +- ...arallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb | 2 +- easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb | 2 +- .../easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb | 2 +- .../p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb | 2 +- .../p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb | 2 +- .../p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb | 4 ++-- .../easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb | 4 ++-- .../easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb | 4 ++-- .../easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb | 4 ++-- easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 2 +- .../easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb | 2 +- easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb | 2 +- .../p/pybind11/pybind11-2.2.4-foss-2018a-Python-3.6.4.eb | 2 +- .../p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb | 2 +- .../pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb | 2 +- ...python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb | 2 +- .../q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb | 2 +- .../q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb | 2 +- easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb | 2 +- easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb | 2 +- easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb | 2 +- .../q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb | 2 +- .../q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb | 2 +- .../q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb | 2 +- .../easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb | 2 +- .../easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 2 +- .../easyconfigs/r/R/R-3.3.3-intel-2016b-X11-20160819.eb | 2 +- .../easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 2 +- .../easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb | 2 +- .../easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb | 2 +- .../r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb | 2 +- .../easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb | 2 +- .../easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb | 2 +- .../easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb | 2 +- .../easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb | 2 +- .../easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb | 2 +- .../easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 4 ++-- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 4 ++-- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 4 ++-- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 4 ++-- .../r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb | 2 +- .../r/RDKit/RDKit-2019.09.3-foss-2019b-Python-3.7.4.eb | 2 +- .../r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb | 2 +- .../r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb | 2 +- .../r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb | 2 +- .../r/RELION/RELION-2.1-foss-2018a-CUDA-9.1.85.eb | 2 +- .../easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb | 2 +- .../easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb | 2 +- .../RNA-SeQC/RNA-SeQC-1.1.8-foss-2016b-Java-1.8.0_121.eb | 2 +- .../r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2018b-Java-1.8.eb | 2 +- .../r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb | 2 +- .../r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb | 2 +- .../RStudio-Server-1.2.5033-fosscuda-2019b-Java-11.eb | 4 ++-- .../RStudio-Server-1.2.5042-foss-2019b-Java-11.eb | 4 ++-- .../RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb | 4 ++-- .../RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb | 4 ++-- .../RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb | 4 ++-- ...RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb | 2 +- ...ccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb | 2 +- .../RepeatMasker-4.0.8-intel-2018b-Perl-5.28.0-HMMER.eb | 2 +- .../RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb | 2 +- .../easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb | 2 +- .../r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 4 ++-- .../s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb | 6 +++--- .../s/SRPRISM/SRPRISM-3.1.1-GCCcore-8.2.0-Java-11.eb | 2 +- .../easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb | 2 +- .../s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb | 2 +- .../SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb | 2 +- .../s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb | 2 +- .../easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb | 2 +- ...-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb | 2 +- .../s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb | 2 +- .../s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb | 2 +- ...-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb | 2 +- .../s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb | 2 +- .../s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb | 2 +- .../Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb | 2 +- .../s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb | 2 +- .../s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb | 2 +- .../s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb | 2 +- .../easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb | 2 +- .../SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb | 8 ++++---- .../SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb | 8 ++++---- .../s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb | 8 ++++---- .../s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb | 2 +- .../s/Subversion/Subversion-1.10.0-foss-2017b.eb | 2 +- .../s/Subversion/Subversion-1.10.0-intel-2017b.eb | 2 +- ...iteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb | 2 +- .../s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb | 2 +- .../s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb | 4 ++-- .../s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb | 4 ++-- .../easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb | 4 ++-- .../smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb | 2 +- .../snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb | 2 +- .../snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb | 2 +- .../s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb | 2 +- .../s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb | 2 +- .../t/THetA/THetA-0.7-foss-2018b-Python-2.7.15.eb | 4 ++-- .../easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/t/TagDust/TagDust-2.33-GCCcore-8.3.0.eb | 2 +- .../TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb | 4 ++-- .../TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb | 2 +- .../t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb | 2 +- .../t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb | 2 +- .../TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb | 2 +- .../TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 2 +- .../t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb | 2 +- .../easyconfigs/t/Tracer/Tracer-1.7.1-GCCcore-8.2.0.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.5.0-foss-2018b.eb | 2 +- .../Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb | 2 +- .../Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb | 2 +- .../Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb | 2 +- .../Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb | 2 +- .../Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb | 2 +- .../Trim_Galore-0.6.2-GCCcore-8.2.0-Java-11.eb | 4 ++-- .../Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb | 2 +- .../Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb | 2 +- ...rim_Galore-0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4.eb | 4 ++-- .../Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb | 4 ++-- .../Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb | 4 ++-- .../t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb | 4 ++-- .../t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb | 2 +- .../t/Trinity/Trinity-2.10.0-foss-2019b-Python-3.7.4.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017a.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017b.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb | 4 ++-- .../easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb | 4 ++-- .../t/Trinity/Trinity-2.8.5-GCC-8.3.0-Java-11.eb | 2 +- .../Trinity-2.8.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb | 4 ++-- .../t/Trinity/Trinity-2.9.1-foss-2019b-Python-2.7.16.eb | 4 ++-- .../t/Trinity/Trinity-2.9.1-foss-2019b-Python-3.7.4.eb | 4 ++-- .../easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb | 2 +- .../t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb | 2 +- .../torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb | 2 +- .../UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb | 2 +- .../UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb | 2 +- .../UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb | 2 +- .../UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb | 2 +- .../UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb | 2 +- .../u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb | 2 +- .../u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb | 2 +- .../u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb | 2 +- .../Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb | 4 ++-- .../Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb | 4 ++-- .../u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb | 4 ++-- .../u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb | 4 ++-- easybuild/easyconfigs/u/units/units-2.19-GCCcore-8.2.0.eb | 2 +- .../v/VMD/VMD-1.9.4a43-fosscuda-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb | 2 +- .../VirSorter-20160601-foss-2016a-Perl-5.22.1.eb | 4 ++-- .../Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb | 2 +- .../vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb | 4 ++-- easybuild/easyconfigs/w/WCT/WCT-4.6.0-Java-11.eb | 2 +- .../easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb | 4 ++-- easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb | 2 +- .../XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb | 2 +- .../x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb | 2 +- .../x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb | 4 ++-- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb | 2 +- .../x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb | 2 +- .../x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb | 4 ++-- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb | 2 +- .../Xmipp-3.19.04-Apollo-foss-2019a-Python-2.7.15.eb | 2 +- .../Xmipp-3.19.04-Apollo-fosscuda-2019a-Python-2.7.15.eb | 2 +- .../x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb | 2 +- .../x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb | 2 +- .../xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb | 2 +- .../xcb-util-keysyms-0.4.0-intel-2016a.eb | 2 +- .../xcb-util-renderutil-0.3.9-foss-2016a.eb | 2 +- .../xcb-util-renderutil-0.3.9-intel-2016a.eb | 2 +- .../x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb | 2 +- .../x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb | 2 +- .../easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb | 2 +- .../easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb | 2 +- .../x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb | 2 +- .../y/Yade/Yade-2018.02b-intel-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.1.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.5.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb | 2 +- .../z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb | 2 +- .../z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb | 2 +- .../z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb | 2 +- 1300 files changed, 1446 insertions(+), 1446 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb index f40658d1411..539a0958608 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -dependencies = [('Java', '1.7.0_60', '', True)] +dependencies = [('Java', '1.7.0_60', '', SYSTEM)] configopts = "--disable-examples --disable-csharp" diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb index 8ba4070760d..72a027af04f 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -dependencies = [('Java', '1.7.0_60', '', True)] +dependencies = [('Java', '1.7.0_60', '', SYSTEM)] configopts = "--disable-examples --disable-csharp" diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb index 31ae0ccb152..0d8e1343e3d 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb @@ -20,7 +20,7 @@ pythonversion = '2.7.10' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('Java', '1.8.0_60', '', True), + ('Java', '1.8.0_60', '', SYSTEM), ('Python', pythonversion), ] diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb index 00631356607..8b6c127a237 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb @@ -20,7 +20,7 @@ pythonversion = '2.7.10' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('Java', '1.8.0_66', '', True), + ('Java', '1.8.0_66', '', SYSTEM), ('Python', pythonversion), ] diff --git a/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb index 41b26e296f8..c99f5de5a6b 100644 --- a/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb @@ -19,7 +19,7 @@ patches = [ dependencies = [ ('libpng', '1.6.6'), ('LibTIFF', '4.0.3'), - ('Java', '1.7.0_15', '', True), + ('Java', '1.7.0_15', '', SYSTEM), ('lynx', '2.8.7'), ('makedepend', '1.0.4'), ('imake', '1.0.5'), diff --git a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 938cb4bc7e4..174260cddaf 100644 --- a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -14,7 +14,7 @@ sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver, '', True)] +dependencies = [(java, javaver, '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index 83c91ab617b..01cd8fffd9e 100644 --- a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -14,7 +14,7 @@ sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver, '', True)] +dependencies = [(java, javaver, '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb index eb31afb5518..ec0b679c595 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb @@ -13,9 +13,9 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] -dependencies = [('Java', '1.7.0_80', '', True)] +dependencies = [('Java', '1.7.0_80', '', SYSTEM)] -builddependencies = [('Autotools', '20150215', '', True)] +builddependencies = [('Autotools', '20150215', '', SYSTEM)] # parallel build does not work (to test) parallel = 1 diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb index eba16d5a4e3..ac6f731032d 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.7.0_15', '', True)] +dependencies = [('Java', '1.7.0_15', '', SYSTEM)] builddependencies = [('Autotools', '20150215', '', ('GCC', '4.7.2'))] diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb index 6d20b44133f..371db8bef3c 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.7.0_15', '', True)] +dependencies = [('Java', '1.7.0_15', '', SYSTEM)] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb index 0349d94e2ac..939c36e304f 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.8.0_31', '', True)] +dependencies = [('Java', '1.8.0_31', '', SYSTEM)] builddependencies = [('Autotools', '20150215')] preconfigopts = './autogen.sh && ' diff --git a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb index 847f0357417..0cfcc327bdb 100644 --- a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb +++ b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb @@ -30,7 +30,7 @@ dependencies = [ ('Boost', '1.51.0', '-Python-2.7.3'), ('SAMtools', '0.1.18'), ('Perl', '5.16.3', '-bare'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ('libpng', '1.5.13'), ] diff --git a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb index 3354b93931c..0b3d2f04c2b 100644 --- a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb +++ b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb @@ -30,7 +30,7 @@ dependencies = [ ('Boost', '1.51.0', '-Python-2.7.3'), ('SAMtools', '0.1.18'), ('Perl', '5.16.3', '-bare'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ('libpng', '1.5.13'), ] diff --git a/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb b/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb index fc4d0275894..28db135235f 100644 --- a/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['cplex_studio%s.linux-x86-64.bin' % ''.join(version.split('.'))] dependencies = [ - ('Java', '1.8.0_66', '', True), + ('Java', '1.8.0_66', '', SYSTEM), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb index 77e43460d5c..5705d1a9f0d 100644 --- a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -46,7 +46,7 @@ dependencies = [ ('CGAL', '4.0', versionsuffix), ('PETSc', '3.3-p2', versionsuffix), ('SLEPc', '3.3-p1', versionsuffix), - ('MTL4', '4.0.8878', '', True), + ('MTL4', '4.0.8878', '', SYSTEM), ('Trilinos', '10.12.2', versionsuffix), ('Sphinx', '1.1.3', versionsuffix), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb index f6b89c67c7a..851a565e755 100644 --- a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb @@ -42,7 +42,7 @@ dependencies = [ ('CGAL', '4.7', versionsuffix), ('PETSc', '3.6.3', versionsuffix), ('SLEPc', '3.6.2', versionsuffix), - ('MTL4', '4.0.9555', '', True), + ('MTL4', '4.0.9555', '', SYSTEM), ('HDF5', '1.8.15-patch1'), ('Trilinos', '12.4.2', versionsuffix), ('Sphinx', '1.3.3', versionsuffix), diff --git a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb index 573a00a1859..4c53065ba15 100644 --- a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb @@ -23,7 +23,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb index cfcf1c4b41a..c5f9edb822c 100644 --- a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb @@ -23,7 +23,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb b/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb index 3968d910aa4..5bb43ab8b18 100644 --- a/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = ['otp_src_%(version)s.tar.gz'] source_urls = ['http://www.erlang.org/download'] -builddependencies = [('Java', '1.7.0_45', '', True)] +builddependencies = [('Java', '1.7.0_45', '', SYSTEM)] configopts = '--with-javac ' diff --git a/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb index d05befd06c3..b12f25299be 100644 --- a/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb @@ -18,7 +18,7 @@ dependencies = [ ('cURL', '7.27.0'), ('ncurses', '5.9'), ('libreadline', '6.2'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ] parallel = 1 diff --git a/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb index 2f7b37d7ff4..640ab72c71a 100644 --- a/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ] builddependencies = [ - ('GHC', '6.12.3', '', True), + ('GHC', '6.12.3', '', SYSTEM), ('libxslt', '1.1.28'), ] diff --git a/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb index 7a5dd73b3c9..8db9f79f94f 100644 --- a/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] builddependencies = [ - ('Autotools', '20150215', '', True), + ('Autotools', '20150215', '', SYSTEM), ] # enable C++ interface diff --git a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb index 4634a7fb1a9..3caf8585701 100644 --- a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb @@ -26,7 +26,7 @@ dependencies = [ ('Ghostscript', '9.14'), ('GLib', '2.40.0'), ('GTS', '0.7.6'), - ('Java', '1.7.0_60', '', True), + ('Java', '1.7.0_60', '', SYSTEM), ('libpng', '1.6.12'), ('Pango', '1.36.7'), ('Perl', '5.20.0'), diff --git a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb index c9fd0d8f277..f0c9457cf81 100644 --- a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -28,7 +28,7 @@ dependencies = [ ('fontconfig', '2.11.94'), ('Ghostscript', '9.16'), ('GTS', '0.7.6', glibsuff), - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ('libpng', '1.6.17'), ('Pango', '1.37.2'), ('Perl', '5.20.0'), diff --git a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb index 1b8304beca1..936ae21c317 100644 --- a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb @@ -25,8 +25,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ ('GDB', '7.5.1'), - ('TotalView', '8.12.0-0', '-linux-x86-64', True), # provides MemoryScape - ('icc', '2013.5.192', '', True), # provides IDB in ictce/5.3.0 compatible mode + ('TotalView', '8.12.0-0', '-linux-x86-64', SYSTEM), # provides MemoryScape + ('icc', '2013.5.192', '', SYSTEM), # provides IDB in ictce/5.3.0 compatible mode ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb index a39dfd95472..6a56ae85cc2 100644 --- a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb @@ -21,9 +21,9 @@ description = """Common Set of Profilers""" toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ - ('VTune', '2013_update10', '', True), - ('Inspector', '2013_update6', '', True), - ('itac', '8.0.0.011', '', True), + ('VTune', '2013_update10', '', SYSTEM), + ('Inspector', '2013_update6', '', SYSTEM), + ('itac', '8.0.0.011', '', SYSTEM), ('PAPI', '5.0.1'), ('Valgrind', '3.8.1'), ('binutils', '2.22'), # this one provides gprof diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb index 9272f98ff58..fac7767346e 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '2.1.2', '', True), + ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-base', '2.1.2', '', SYSTEM), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb index a096633f0b1..f619e97afdd 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '2.1.2', '', True), + ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-base', '2.1.2', '', SYSTEM), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb index c0a03ce83e5..eb3c96bcc41 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '2.1.2', '', True), + ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-base', '2.1.2', '', SYSTEM), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb index b6761f74452..90c502a0495 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', True), - ('vsc-base', '2.1.2', '', True), + ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-base', '2.1.2', '', SYSTEM), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb index f8c93660f1c..858b4f06340 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', True), + ('setuptools', '1.4.2', '', SYSTEM), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb index bcf97f426c7..e19609bcd3b 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', True), + ('setuptools', '1.4.2', '', SYSTEM), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb index 5a2ff293ea6..050fc9722ee 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', True), + ('setuptools', '1.4.2', '', SYSTEM), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb index b4fa5862100..8cec50e09ab 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', True), + ('setuptools', '1.4.2', '', SYSTEM), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb index 7cd4104ad9f..92eb557b169 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', True), + ('setuptools', '1.4.2', '', SYSTEM), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb index 3f166576635..f0bc1aefaff 100644 --- a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb @@ -13,7 +13,7 @@ source_urls = ['http://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s sources = ['%(namelower)s-%(version)s-64-bit.tar.gz'] dependencies = [ - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ('Perl', '5.20.3'), ('libgd', '2.1.1'), ('Python', '2.7.10'), diff --git a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb index 2388f280096..ec5a5e2789d 100644 --- a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb @@ -23,7 +23,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ('Perl', '5.20.3'), ('libgd', '2.1.1'), ('Python', '2.7.10'), diff --git a/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index dafa45afa95..a7381adc66f 100644 --- a/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -20,7 +20,7 @@ java = 'Java' javaver = '1.7.0_75' versionsuffix = '-%s-%s' % (java, javaver) -builddependencies = [('ant', '1.9.6', '-Java-1.7.0_75', True)] +builddependencies = [('ant', '1.9.6', '-Java-1.7.0_75', SYSTEM)] dependencies = [('MPJ-Express', '0.44', '%(versionsuffix)s')] diff --git a/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb index fe336c46e0c..d334e3cb6ea 100644 --- a/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb @@ -26,7 +26,7 @@ unpack_options = '--strip-components=1' builddependencies = [ ('CMake', '3.4.3'), - ('Autotools', '20150215', '', True), + ('Autotools', '20150215', '', SYSTEM), ] dependencies = [ @@ -34,7 +34,7 @@ dependencies = [ ('zlib', '1.2.8'), ('samblaster', '0.1.24'), ('SAMtools', '1.3.1'), - ('Sambamba', '0.6.6', '', True), + ('Sambamba', '0.6.6', '', SYSTEM), ('gawk', '4.0.2'), ] diff --git a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb index 92964498140..904997dd1d9 100644 --- a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ - ('Java', '1.7.0_79', '', True), + ('Java', '1.7.0_79', '', SYSTEM), ('Python', '2.7.9'), ('HDF5', '1.8.9'), ('libxml2', '2.9.2'), diff --git a/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index e553dd3905a..ac36c94964b 100644 --- a/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (java, javaver) builddependencies = [('CMake', '2.8.12')] dependencies = [ - (java, javaver, '', True), + (java, javaver, '', SYSTEM), ] # compile JNI wrapper library as described in docs diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb index 4231bf81f8c..3a1bccbc96e 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb @@ -31,8 +31,8 @@ dependencies = [ ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - ('Java', '1.7.0_79', '', True), - ('ant', '1.9.3', '-Java-%(javaver)s', True), + ('Java', '1.7.0_79', '', SYSTEM), + ('ant', '1.9.3', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.40.0') ] diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb index bf5ac8dc56d..b495fa3ffb7 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb @@ -31,8 +31,8 @@ dependencies = [ ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - ('Java', '1.7.0_60', '', True), - ('ant', '1.9.3', '-Java-%(javaver)s', True), + ('Java', '1.7.0_60', '', SYSTEM), + ('ant', '1.9.3', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.40.0') ] diff --git a/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb index 8ad72ec52f4..3599c26e381 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ] builddependencies = [ - ('FCM', '2.3.1', '', True), + ('FCM', '2.3.1', '', SYSTEM), ('Perl', '5.16.3'), ] diff --git a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb index ba3147aeda1..41390bba2c2 100644 --- a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ ('make', '3.82'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ('Bash', '4.2'), ('tcsh', '6.18.01'), ('Tcl', '8.5.12'), diff --git a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb index e1d90973574..ea816765bb3 100644 --- a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} dependencies = [ ('make', '3.82'), - ('Java', '1.7.0_10', '', True), + ('Java', '1.7.0_10', '', SYSTEM), ('Bash', '4.2'), ('tcsh', '6.18.01'), ('Tcl', '8.5.12'), diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb index 9948217fd4e..239d653b543 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', True)] +dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb index 4043dd5630c..c658a85d703 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', True)] +dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb index 161ca2d3837..7c33ed3c62f 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', True)] +dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 8b0668a68f1..8391bc11951 100644 --- a/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -19,7 +19,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} dependencies = [ - ('Java', '1.7.0_60', '', True), + ('Java', '1.7.0_60', '', SYSTEM), ('libreadline', '6.3'), ('zlib', '1.2.8'), # OS dependency should be preferred if the os version is more recent then this version, diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index e8adea5cdda..5afdb61e1c4 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -20,7 +20,7 @@ source_urls = [ mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb index 9bf66b57282..0b59ed106c8 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb @@ -20,7 +20,7 @@ mpich_opts = '--enable-static' threaded = True dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb index 8251dde430d..9c841513aa2 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb index c6290e63183..09cc0738ddc 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb index b23784df275..cff665b0ada 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb index 4bb85edabe4..7d9a9a6b9be 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb index b5a30ff434c..70a3f64db0d 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb index 419fa691885..8fcddd02617 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb index 2437804b50b..cd8a6bcddf6 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb index c0064ba6a8c..a85fdf5d8fc 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb index 3b03bc30042..8939ec6a4eb 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb index 7db65a77f3e..edd7812782e 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb index 1c63079ab4a..5aa63fa961d 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb index ea1488b7501..b3be0a49a90 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb index 72798af0c69..bb2cdf29ef3 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb index 7b3d9ff4712..cac8a78c01f 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.9'), # for plotting in R - ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb index 4125b82ac4e..faed73f4aef 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.9'), # for plotting in R - ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb index 0b46e45f459..e9736a0d521 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb @@ -17,7 +17,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plotting in R - ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb index 33df27d4460..8f2c4740b2d 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb @@ -17,7 +17,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plotting in R - ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb index 3462ebf3f2c..f55402b39c8 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plottting in R - ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb index 32f9e3876e9..cfb1fdded86 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb index 8dfe1121a12..6e9bb7dd130 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb index 95f4896bccf..c704735c37c 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb index 20b83d30bca..a2c3729ee62 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb index 2b252579399..c96c15e9389 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('NLopt', '2.4.2'), # for nloptr diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb index 1992cbe8043..db6599ad293 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('NLopt', '2.4.2'), # for nloptr diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb index 83033319bd9..3de945fb60b 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb index 712ca683f37..35f77ae5f85 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb index fc8747efae8..034bec8b1d3 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb index dec3fef7965..9789a570017 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ] diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb index 68941ac7809..282eb2bede6 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb index f4738f44f4b..f37ad6d3f33 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb index eb6d134dc02..77140a3bb18 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb index bf999bcdca7..4b3e1115ed6 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb index ad909a5e62b..25e622f04e6 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb index 28a924627e0..b00f07b4b09 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb index dba91bd2533..986af941152 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.45.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb index b503f4c6397..8bde637585c 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.55.0', versionsuffix), - ('tbb', '4.0.5.339', '', True), + ('tbb', '4.0.5.339', '', SYSTEM), ('Jellyfish', '2.1.3'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb index c80c41e1d54..93274668b83 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', True), + ('tbb', '4.3.6.211', '', SYSTEM), ('Jellyfish', '2.2.3'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb index b4805f08e04..37c7bd731e4 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb @@ -29,7 +29,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', True), + ('tbb', '4.3.6.211', '', SYSTEM), ('Jellyfish', '2.2.4'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb index 878c68876e0..9317f21af8c 100644 --- a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', True), + ('tbb', '4.3.6.211', '', SYSTEM), ('Jellyfish', '2.2.3'), ] builddependencies = [('CMake', '3.2.3')] diff --git a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb index 7699ae06d5a..0f6804b6b3c 100644 --- a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', True), + ('tbb', '4.3.6.211', '', SYSTEM), ('Jellyfish', '2.2.4'), ] builddependencies = [('CMake', '3.2.3')] diff --git a/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb index f895fa63df1..dffa4ab145e 100644 --- a/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -16,7 +16,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.10.1', '-Java-1.7.0_80', True), + ('FastQC', '0.10.1', '-Java-1.7.0_80', SYSTEM), ('cutadapt', '1.5', '-Python-2.7.10'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb index 821333d6ef7..abd5e0edeaa 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb @@ -19,8 +19,8 @@ sources = ['v%(version)s.tar.gz'] patches = ['Trinity-%(version)s_plugins-Makefile.patch'] dependencies = [ - ('Java', '1.7.0_80', '', True), - ('ant', '1.9.6', '-Java-%(javaver)s', True), + ('Java', '1.7.0_80', '', SYSTEM), + ('ant', '1.9.6', '-Java-%(javaver)s', SYSTEM), ('ncurses', '5.9'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb index 014e8ca4110..7fb8a37a67b 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb @@ -19,8 +19,8 @@ sources = ['v%(version)s.tar.gz'] patches = ['Trinity-2.0.4_plugins-Makefile.patch'] dependencies = [ - ('Java', '1.7.0_80', '', True), - ('ant', '1.9.6', '-Java-%(javaver)s', True), + ('Java', '1.7.0_80', '', SYSTEM), + ('ant', '1.9.6', '-Java-%(javaver)s', SYSTEM), ('ncurses', '5.9'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb index 71643e32bd6..063da9c3d98 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - (java, javaver, '', True), + (java, javaver, '', SYSTEM), ('ant', '1.9.6', '-%s-%s' % (java, javaver), True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.6'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb index dcb9ea5cadb..2092bcc77db 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb @@ -24,7 +24,7 @@ java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', True), + (java, javaver, '', SYSTEM), ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb index 7f5d5792225..afb90c64534 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb @@ -25,7 +25,7 @@ java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', True), + (java, javaver, '', SYSTEM), ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb index f6e15e437ab..10bbd992eac 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb @@ -23,7 +23,7 @@ java = 'Java' javaver = '1.7.0_15' dependencies = [ - (java, javaver, '', True), + (java, javaver, '', SYSTEM), ('ant', '1.9.0', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb index dfd259613d8..50efb697da2 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.6' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '', True), - ('vsc-mympirun', version, '', True), + ('vsc-processcontrol', '1.0', '', SYSTEM), + ('vsc-mympirun', version, '', SYSTEM), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb index 1bbd44502a0..8afa94b6137 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), - ('vsc-mympirun', '3.4.2', '', True), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), + ('vsc-mympirun', '3.4.2', '', SYSTEM), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb index 24d1ff604f7..f2a99790fa6 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), - ('vsc-mympirun', '3.4.2', '', True), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), + ('vsc-mympirun', '3.4.2', '', SYSTEM), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb index f5d80fe9e55..99d0531e740 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.4', '', True), + ('gettext', '0.19.4', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb index 4c118e934ff..9c13936bba0 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215', '', ('GCC', '4.7.2')), - ('gettext', '0.18.2', '', True), + ('gettext', '0.18.2', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb index 43117900f60..df2d19b7d0b 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.18.2', '', True), + ('gettext', '0.18.2', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb index 63e623f082d..092e66d8068 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb @@ -20,7 +20,7 @@ pyver = '2.7.9' versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Java', '1.8.0_40', '', True), + ('Java', '1.8.0_40', '', SYSTEM), ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb index 18d8b11833b..3f34c8c15f5 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -12,6 +12,6 @@ sources = ['Xmipp-%(version)s-src.tar.gz'] toolchain = {'name': 'goolf', 'version': '1.4.10'} # note: all other dependencies are taken care of by Xmipp itself -dependencies = [('Java', '1.7.0_80', '', True)] +dependencies = [('Java', '1.7.0_80', '', SYSTEM)] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb index d6d8c64ef43..294af452fee 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb @@ -20,7 +20,7 @@ pyver = '2.7.9' versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Java', '1.8.0_40', '', True), + ('Java', '1.8.0_40', '', SYSTEM), ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.22-iccifort-2019.5.281.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.22-iccifort-2019.5.281.eb index 855e80e9b9d..29a1e735bcb 100644 --- a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.22-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.22-iccifort-2019.5.281.eb @@ -16,10 +16,10 @@ checksums = [ '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch ] -builddependencies = [('Maven', '3.6.3', '', True)] +builddependencies = [('Maven', '3.6.3', '', SYSTEM)] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('BWA', '0.7.17'), ] diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb index f62a0b1e28b..b06c4f9ab4d 100644 --- a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-10.2.0.eb @@ -16,10 +16,10 @@ checksums = [ '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch ] -builddependencies = [('Maven', '3.6.3', '', True)] +builddependencies = [('Maven', '3.6.3', '', SYSTEM)] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('BWA', '0.7.17'), ] diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb index f93ab230e6b..842e9e8cdfe 100644 --- a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb @@ -16,10 +16,10 @@ checksums = [ '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch ] -builddependencies = [('Maven', '3.6.3', '', True)] +builddependencies = [('Maven', '3.6.3', '', SYSTEM)] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('BWA', '0.7.17'), ] diff --git a/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb b/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb index c9a3002ee86..176bd70202f 100644 --- a/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb +++ b/easybuild/easyconfigs/a/AMPHORA2/AMPHORA2-20190730-gompi-2020b-Java-13-pthreads-avx2.eb @@ -21,7 +21,7 @@ checksums = ['2d361fcc2b800c3daaf25692988af6105669cba2ff513aba82f36089beb2839f'] dependencies = [ ('Perl', '5.32.0'), - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('BioPerl', '1.7.8'), ('HMMER', '3.3.2'), ('EMBOSS', '6.6.0', local_javasuffix), diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb index 7f7064ef519..740009f42a3 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb @@ -21,7 +21,7 @@ checksums = [ ] builddependencies = [('binutils', '2.35')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb index e1357bf2785..dca4fd3a96b 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-10.3.0-Java-11.eb @@ -21,7 +21,7 @@ checksums = [ ] builddependencies = [('binutils', '2.36.1')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb index 05e3b23c3c8..10c24b2e952 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.2.0-Java-11.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [('binutils', '2.37')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb index 5c290512f99..034e0e39566 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-11.3.0-Java-11.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [('binutils', '2.38')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb index 8b3f8a98607..89f841e46fa 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-7.3.0.eb @@ -20,7 +20,7 @@ checksums = [ ] builddependencies = [('binutils', '2.30')] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.2.0.eb index 25422d7f57a..d7596e6036d 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ checksums = [ ] builddependencies = [('binutils', '2.31.1')] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.3.0-Java-11.eb index 492d77e6e4f..a3ead0bb703 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-8.3.0-Java-11.eb @@ -21,7 +21,7 @@ checksums = [ ] builddependencies = [('binutils', '2.32')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb index 39ff4c9c5da..25632498de1 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-9.3.0-Java-11.eb @@ -21,7 +21,7 @@ checksums = [ ] builddependencies = [('binutils', '2.34')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb index ddbfe7c0922..654825d9ff3 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_includes.patch'] dependencies = [ - ('Java', '1.8.0_74', '', True), + ('Java', '1.8.0_74', '', SYSTEM), ('Python', '2.7.11'), ] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb index 10ff1403b09..12cc04a02e7 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2017b.eb @@ -19,7 +19,7 @@ checksums = [ 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch ] -dependencies = [('Java', '1.8.0_152', '', True)] +dependencies = [('Java', '1.8.0_152', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb index 3a34a478986..f1981196919 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018a-Python-2.7.14.eb @@ -21,7 +21,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('Python', '2.7.14'), ] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb index 867b9d56beb..7bc12739569 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2018b.eb @@ -19,7 +19,7 @@ checksums = [ 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2019a.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2019a.eb index ba4fd58a573..51bebed49f8 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2019a.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2019a.eb @@ -20,7 +20,7 @@ checksums = [ ] builddependencies = [('binutils', '2.31.1')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb index e00f225a130..123c3e1e968 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_includes.patch'] dependencies = [ - ('Java', '1.8.0_131', '', True), + ('Java', '1.8.0_131', '', SYSTEM), ('Python', '2.7.13'), ] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b-Python-2.7.14.eb index 132b4a836cc..408bb64f951 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b-Python-2.7.14.eb @@ -21,7 +21,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ('Python', '2.7.14'), ] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b.eb index ec6fe2656ce..d0f5a966868 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017b.eb @@ -19,7 +19,7 @@ checksums = [ 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch ] -dependencies = [('Java', '1.8.0_152', '', True)] +dependencies = [('Java', '1.8.0_152', '', SYSTEM)] configopts = '--disable-examples --disable-csharp --disable-python' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018a-Python-3.6.4.eb index e1528a3b461..39bdcb9da81 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2018a-Python-3.6.4.eb @@ -21,7 +21,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('Python', '3.6.4'), ] diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb index 8ccff72840b..4595800f99c 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.0-foss-2021a-CUDA-11.3.1.eb @@ -29,7 +29,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Boost', '1.76.0'), ('Python', '3.9.5'), ('OpenCV', '4.5.3', '-CUDA-%(cudaver)s-contrib'), diff --git a/easybuild/easyconfigs/a/ASTRID/ASTRID-2.2.1-gompi-2019a.eb b/easybuild/easyconfigs/a/ASTRID/ASTRID-2.2.1-gompi-2019a.eb index ea1dba9f73d..4a752357e25 100644 --- a/easybuild/easyconfigs/a/ASTRID/ASTRID-2.2.1-gompi-2019a.eb +++ b/easybuild/easyconfigs/a/ASTRID/ASTRID-2.2.1-gompi-2019a.eb @@ -18,7 +18,7 @@ checksums = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('phylokit', '1.0'), ('Boost', '1.70.0'), ] diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb index 05ffdaeea4e..7911a59e768 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb @@ -17,7 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('PyYAML', '5.4.1'), ('TensorFlow', '2.6.0', versionsuffix), diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb index 3307a0c7c2b..2ab59fb243c 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb @@ -17,7 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('PyYAML', '5.4.1'), ('TensorFlow', '2.6.0', versionsuffix), diff --git a/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb index d3c79474bb6..1f73638a1c1 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb @@ -27,7 +27,7 @@ patches = [ ] dependencies = [ - ('CUDA', '7.5.18', '', True), + ('CUDA', '7.5.18', '', SYSTEM), ('netCDF', '4.4.0'), ('netCDF-Fortran', '4.4.4'), ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb index 4193c584dca..5b391327a36 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb @@ -23,7 +23,7 @@ patches = ['Amber-%(version)s_fix-hardcoding.patch', dependencies = [ - ('CUDA', '7.5.18', '', True), + ('CUDA', '7.5.18', '', SYSTEM), ('netCDF', '4.4.0'), ('netCDF-Fortran', '4.4.4'), ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb index 5a8159af3bb..431f7a09b12 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020a-AmberTools-20.15-Python-3.8.2.eb @@ -42,7 +42,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('libreadline', '8.0'), ('matplotlib', '3.2.1', '-Python-%(pyver)s'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', SYSTEM), ('netCDF-Fortran', '4.5.2'), ('netCDF', '4.7.4'), ('Perl', '5.30.2'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb index fc45e8660c5..638decc861e 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-20.11-fosscuda-2020b-AmberTools-21.3.eb @@ -53,7 +53,7 @@ dependencies = [ ('PnetCDF', '1.12.2'), ('Tkinter', '3.8.6'), ('X11', '20201008'), - ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', True), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s', SYSTEM), ] # Some CUDA tests differs from expected results diff --git a/easybuild/easyconfigs/a/AmrPlusPlus/AmrPlusPlus-2.0-20200114-GCC-8.3.0.eb b/easybuild/easyconfigs/a/AmrPlusPlus/AmrPlusPlus-2.0-20200114-GCC-8.3.0.eb index c2864dc231d..6cdb4f111e7 100644 --- a/easybuild/easyconfigs/a/AmrPlusPlus/AmrPlusPlus-2.0-20200114-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/a/AmrPlusPlus/AmrPlusPlus-2.0-20200114-GCC-8.3.0.eb @@ -32,11 +32,11 @@ sources = [{ checksums = ['04af67517b752e15b5add27f4584f8c11293a0ed1353d3c1dd60c3c6e2dcb329'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('BWA', '0.7.17'), - ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', SYSTEM), ('SAMtools', '1.10'), - ('Nextflow', '19.12.0', '', True), + ('Nextflow', '19.12.0', '', SYSTEM), ] local_exe_files = [ diff --git a/easybuild/easyconfigs/a/ArrayFire/ArrayFire-3.6.4-foss-2018b-CUDA-9.2.88.eb b/easybuild/easyconfigs/a/ArrayFire/ArrayFire-3.6.4-foss-2018b-CUDA-9.2.88.eb index 8549e014005..7efc990a687 100644 --- a/easybuild/easyconfigs/a/ArrayFire/ArrayFire-3.6.4-foss-2018b-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/a/ArrayFire/ArrayFire-3.6.4-foss-2018b-CUDA-9.2.88.eb @@ -29,7 +29,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.67.0'), - ('CUDA', local_cudaver, '', True), + ('CUDA', local_cudaver, '', SYSTEM), ] separate_build_dir = True diff --git a/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb index 90e04c1f06b..7998e273f4c 100644 --- a/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -21,7 +21,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['6557df95eed99323befddcef6b8da8b67eba22476efccd1e69a87ffdf075e5f4'] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] parallel = 1 diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.2.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.2.eb index d2c6124a0ad..fed83b82ecb 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.2.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.3.0.eb index 7d84000783a..029fc124736 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.3.0.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb index b0b5d3dc351..76f7bbb3a51 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.1.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.1.0.eb index 47f11e88e4c..acd3e293abe 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.1.0.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.2.0.eb index 0d4d4fbba39..f8696b70aa8 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.2.0.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb index 56c44c440ee..8c7c17b1767 100644 --- a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-6.3.0.eb @@ -19,7 +19,7 @@ checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb index d469fdb58f5..263e4f8bb5e 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.2.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb index 9d0d0b21a79..a2333fa888f 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.3.0.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb index 3ee3bf9adf7..b62e65b9410 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-5.4.0.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb index 1b4be92da39..c36cbe68b6a 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.1.0.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb index c8c1c5b5d60..d0a1c837755 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.2.0.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb index e447b6af5a2..8ba57370da3 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-6.3.0.eb @@ -31,7 +31,7 @@ checksums = [ dependencies = [('Autoconf', '2.69')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/automake', 'bin/aclocal'], diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb index 1ffd386831a..ed1e72fae99 100644 --- a/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb +++ b/easybuild/easyconfigs/a/ant/ant-1.10.1-Java-1.8.eb @@ -17,7 +17,7 @@ sources = ['apache-%(name)s-%(version)s-src.tar.gz'] checksums = ['68f7ced0aa15d1f9f672f23d67c86deaf728e9576936313cfbff4f7a0e6ce382'] # specify dependency on Java/1.8 "wrapper", rather than a specific Java version -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] builddependencies = [('JUnit', '4.12', versionsuffix)] diff --git a/easybuild/easyconfigs/a/arcasHLA/arcasHLA-0.2.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/arcasHLA/arcasHLA-0.2.0-foss-2019b-Python-3.7.4.eb index bc81df83420..816d044d50f 100644 --- a/easybuild/easyconfigs/a/arcasHLA/arcasHLA-0.2.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/arcasHLA/arcasHLA-0.2.0-foss-2019b-Python-3.7.4.eb @@ -24,7 +24,7 @@ dependencies = [ ('SAMtools', '1.10'), ('pigz', '2.4'), ('git', '2.23.0', '-nodocs'), - ('git-lfs', '2.11.0', '', True), + ('git-lfs', '2.11.0', '', SYSTEM), ] # Download and install the reference database (1.8 GB) diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb index 341a8dd97ca..c0280bde061 100644 --- a/easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/aria2/aria2-1.35.0-GCCcore-10.3.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('libxml2', '2.9.10'), ('SQLite', '3.35.4'), ('c-ares', '1.17.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--without-gnutls --with-openssl --enable-libaria2 --enable-static" diff --git a/easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb index 591b1cbcd46..baafaf4f5e3 100644 --- a/easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/a/aria2/aria2-1.36.0-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('libxml2', '2.9.13'), ('SQLite', '3.38.3'), ('c-ares', '1.18.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--without-gnutls --with-openssl --enable-libaria2 --enable-static" diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019a.eb index b598e539cc1..25065d06f05 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019a.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019a.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('Eigen', '3.3.7', '', True) + ('Eigen', '3.3.7', '', SYSTEM) ] preconfigopts = "sh bootstrap && " diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb index be0c9d7dedd..69babe0c5ea 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-foss-2019b.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('Eigen', '3.3.7', '', True) + ('Eigen', '3.3.7', '', SYSTEM) ] preconfigopts = "sh bootstrap && " diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-intel-2019b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-intel-2019b.eb index e60710e4b02..f262b1d4d67 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-intel-2019b.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.7.0-intel-2019b.eb @@ -24,7 +24,7 @@ builddependencies = [ ] dependencies = [ - ('Eigen', '3.3.7', '', True) + ('Eigen', '3.3.7', '', SYSTEM) ] separate_build_dir = True diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb index 574183e62e3..6a4cd8d698a 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb @@ -20,7 +20,7 @@ dependencies = [ ('Biopython', '1.72', versionsuffix), ('Pysam', '0.15.1', versionsuffix), ('BWA', '0.7.17'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('minimap2', '2.13'), ('SAMtools', '1.9'), ('MUSCLE', '3.8.31'), @@ -33,8 +33,8 @@ dependencies = [ ('python-parasail', '1.1.16', versionsuffix), ('PhyML', '3.3.20190321'), ('nodejs', '12.16.1'), - ('goalign', '0.3.2', '', True), - ('gotree', '0.4.0', '', True), + ('goalign', '0.3.2', '', SYSTEM), + ('gotree', '0.4.0', '', SYSTEM), ('rampart', '1.2.0rc3', versionsuffix), ('libdeflate', '1.5'), ('nanopolish', '0.13.1', versionsuffix), diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb index c4995246973..80e2cc8068d 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2021.06.24-foss-2020b.eb @@ -33,8 +33,8 @@ dependencies = [ ('python-parasail', '1.2.4'), ('PhyML', '3.3.20200621'), ('nodejs', '12.19.0'), - ('goalign', '0.3.2', '', True), - ('gotree', '0.4.0', '', True), + ('goalign', '0.3.2', '', SYSTEM), + ('gotree', '0.4.0', '', SYSTEM), ('rampart', '1.2.0'), ('libdeflate', '1.7'), ('nanopolish', '0.13.3'), diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb index d90fb13229d..3d6512a5f33 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_112', '', True)] +dependencies = [('Java', '1.8.0_112', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-37.93-foss-2018a.eb b/easybuild/easyconfigs/b/BBMap/BBMap-37.93-foss-2018a.eb index eeb78bfbdb9..53aeebfca89 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-37.93-foss-2018a.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-37.93-foss-2018a.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['21be384f8535094b8b4695134b0b132863e6599811b8ea2d311960b7ba88df8f'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-37.93-intel-2018a.eb b/easybuild/easyconfigs/b/BBMap/BBMap-37.93-intel-2018a.eb index 4c2ee3855a4..c5b17a83ed9 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-37.93-intel-2018a.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-37.93-intel-2018a.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['21be384f8535094b8b4695134b0b132863e6599811b8ea2d311960b7ba88df8f'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.26-foss-2018b.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.26-foss-2018b.eb index 350359097a1..f8bdee8c943 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.26-foss-2018b.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.26-foss-2018b.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['e439709d6d294aae5938cb253c8640f8e0dfeb227d5b01ce17c37e9871a458b4'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.50b-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.50b-GCC-8.2.0-2.31.1.eb index 0c565ba0482..1e4f8b426cf 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.50b-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.50b-GCC-8.2.0-2.31.1.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['b3b8eefc2e32d035fb7c1732048dca81e367a7e5e43416c993c88683fc19ade7'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.76-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.76-GCC-8.2.0-2.31.1.eb index a3018663e1c..1356c84ed94 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.76-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.76-GCC-8.2.0-2.31.1.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['4f6e3c6a3b56c8514ddcd9e2bebe0f2c89698b16f3af9f52916f55d2a59f406b'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb index 90bb802ed78..d0cb1b445ca 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.79-GCC-8.3.0.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['72891105b6d3e190b5b1d60fb964077a997cf5d2647c472b213a6dd46e1ca07c'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.87-iccifort-2020.1.217.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.87-iccifort-2020.1.217.eb index 980626868d9..772b81bc312 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.87-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.87-iccifort-2020.1.217.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['22ab642b8af88faf208a56763158da895004c5231df572d3163ce52fbfb63240'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb index 94e6c8540fe..d0f16e3b3bd 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-10.2.0.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-9.3.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-9.3.0.eb index 6d1053ec36a..45b3f610c87 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.90-GCC-9.3.0.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb index d3215416acf..9088c7a0387 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.96-GCC-10.3.0.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['18d9c89b02c0ab044b2795a65f6236b2262a494ed83d27e31750437b350ef080'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb index e2bd5bd4075..d439a3560c1 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.98-GCC-11.2.0.eb @@ -12,7 +12,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['cdc3b8e0530c4a83a728d28da31f0e7ead2bc233d4bf21cd1916572c9b2d0e0e'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb index 3d71f64de88..19c368807ef 100644 --- a/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/BLT/BLT-20181223-GCCcore-11.2.0.eb @@ -28,7 +28,7 @@ dependencies = [ ('freetype', '2.11.0'), ('expat', '2.4.1'), ('SQLite', '3.36'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-tcl=$EBROOTTCL --with-tk=$EBROOTTK --enable-shared' diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.2-intel-2019a.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.2-intel-2019a.eb index 6b33d7c53c6..9f70e27003e 100644 --- a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.2-intel-2019a.eb +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.2-intel-2019a.eb @@ -19,7 +19,7 @@ dependencies = [ ('GeneMark-ET', '4.38'), ('BamTools', '2.5.1'), ('SAMtools', '1.9'), - ('GenomeThreader', '1.7.1', '-Linux_x86_64-64bit', True), + ('GenomeThreader', '1.7.1', '-Linux_x86_64-64bit', SYSTEM), ('spaln', '2.3.3c'), ('Exonerate', '2.4.0'), ('BLAST+', '2.9.0'), diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb index e356a0da97b..33487e8713e 100644 --- a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.5-intel-2019b-Python-3.7.4.eb @@ -20,7 +20,7 @@ dependencies = [ ('GeneMark-ET', '4.57'), ('BamTools', '2.5.1'), ('SAMtools', '1.10'), - ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', True), + ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', SYSTEM), ('spaln', '2.4.03'), ('Exonerate', '2.4.0'), ('BLAST+', '2.9.0'), diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb index 76b9371ed08..d2534be82ac 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.10.0-GCCcore-6.4.0.eb @@ -16,6 +16,6 @@ checksums = [ ] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.11.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.11.0-GCCcore-6.4.0.eb index 5829b4dc01c..ee1d8079476 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.11.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.11.0-GCCcore-6.4.0.eb @@ -12,6 +12,6 @@ sources = ['%(namelower)s-%(version)s-dist.zip'] checksums = ['abfeccc94728cb46be8dbb3507a23ccffbacef9fbda96a977ef4ea8d6ab0d384'] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.11.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.11.1-GCCcore-6.4.0.eb index 7d06a6a61a7..6f59179f3cd 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.11.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.11.1-GCCcore-6.4.0.eb @@ -12,6 +12,6 @@ sources = ['%(namelower)s-%(version)s-dist.zip'] checksums = ['e8d762bcc01566fa50952c8028e95cfbe7545a39b8ceb3a0d0d6df33b25b333f'] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.12.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.12.0-GCCcore-6.4.0.eb index ba628d6babe..2596352a994 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.12.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.12.0-GCCcore-6.4.0.eb @@ -12,6 +12,6 @@ sources = ['%(namelower)s-%(version)s-dist.zip'] checksums = ['3b3e7dc76d145046fdc78db7cac9a82bc8939d3b291e53a7ce85315feb827754'] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-6.4.0.eb index 9553e22d089..8215c28cdfc 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-6.4.0.eb @@ -16,6 +16,6 @@ checksums = [ ] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-7.3.0.eb index d6095508300..95378852161 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.16.0-GCCcore-7.3.0.eb @@ -16,6 +16,6 @@ checksums = [ ] builddependencies = [('binutils', '2.30')] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb index 088dbc8deb5..d7273df067b 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.18.0-GCCcore-7.3.0.eb @@ -21,7 +21,7 @@ builddependencies = [ ('Zip', '3.0'), ] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb index c98144ae9a1..5fd1011783f 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-7.3.0.eb @@ -21,7 +21,7 @@ builddependencies = [ ('Zip', '3.0'), ] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb index 72f11b4ee5b..59d5f18e87f 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.20.0-GCCcore-8.2.0.eb @@ -20,6 +20,6 @@ builddependencies = [ ('Python', '3.7.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb index 5de84907639..74f98e271dd 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.25.2-GCCcore-8.2.0.eb @@ -21,6 +21,6 @@ builddependencies = [ ('Python', '3.7.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb index 62c42905710..9a23b912978 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.2.0.eb @@ -21,6 +21,6 @@ builddependencies = [ ('Python', '3.7.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb index bf9db9bef97..b6becac4ae4 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.26.1-GCCcore-8.3.0.eb @@ -21,6 +21,6 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb index 699ad4853c3..da42845ee5c 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.2.0.eb @@ -26,6 +26,6 @@ builddependencies = [ ('Python', '3.7.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb index 720da63a770..a859c64611e 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-8.3.0.eb @@ -26,6 +26,6 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb index 9544908a761..4a205b4f676 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.29.1-GCCcore-9.3.0-Java-1.8.eb @@ -27,6 +27,6 @@ builddependencies = [ ('Python', '3.8.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-0.7.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.7.0-GCCcore-6.4.0.eb index 386939c6183..279f3636e1b 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-0.7.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.7.0-GCCcore-6.4.0.eb @@ -12,6 +12,6 @@ sources = ['%(namelower)s-%(version)s-dist.zip'] checksums = ['a084a9c5d843e2343bf3f319154a48abe3d35d52feb0ad45dec427a1c4ffc416'] builddependencies = [('binutils', '2.28')] -dependencies = [('Java', '1.8.0_152', '', True)] +dependencies = [('Java', '1.8.0_152', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb index 52fd06b9233..8ed77b68a9b 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-1.1.0-GCCcore-8.3.0.eb @@ -25,6 +25,6 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb index 64cebdfa53f..3c49531cee4 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Python', '3.8.6'), ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb index 106e2146849..1a5d8224c02 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-2.0.0-GCCcore-8.3.0.eb @@ -20,6 +20,6 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.4.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.4.1-GCCcore-8.3.0.eb index fd6d2288410..54da4a210b6 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.4.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.4.1-GCCcore-8.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb index 386bdf9a4c8..6daf4172fef 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Python', '3.8.2'), ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.1-GCCcore-8.3.0.eb index 1088865bda9..2877264df72 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.1-GCCcore-8.3.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('Python', '3.7.4'), ('Zip', '3.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb index 6b259a49b41..f5408193257 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('Python', '3.8.6'), ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb index 32ed844cbb5..aecd7128568 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-10.3.0.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Zip', '3.0'), ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] runtest = True diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb index 8c61b1cbe83..76adb8a37b4 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-11.2.0.eb @@ -29,7 +29,7 @@ builddependencies = [ ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb index c72ee0d0455..ddadf77aa93 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.7.2-GCCcore-8.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ('Zip', '3.0'), ('UnZip', '6.0'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] runtest = True testopts = ' '.join([ diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb index 0a321f837b9..8680e49eb46 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-4.2.2-GCCcore-11.2.0.eb @@ -35,7 +35,7 @@ builddependencies = [ ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb index 793f0a2c12f..2550749a059 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-5.1.1-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ('Zip', '3.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] runtest = True testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb index 8b901156428..ca38ef74542 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb @@ -22,7 +22,7 @@ source_urls = ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(ver sources = ['BEASTv%(version)s.tgz'] dependencies = [ - ('Java', '1.8.0_74', '', True), + ('Java', '1.8.0_74', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb index 10b75ac34ee..8f2c406f424 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.6.7-GCC-10.3.0.eb @@ -18,7 +18,7 @@ sources = ['BEAST.v%(version)s.Linux.tgz'] checksums = ['05dcc619c2e10163f2c1089ec66149f6e53ec5a0583cd2cb8ffdccbbdb1d8183'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # this is not mandatory but beagle-lib is recommended by developers ('beagle-lib', '3.1.2'), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb index 9fe7a6ae5b3..8176cae55eb 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb index ac0a67174d3..0768a39fbc4 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb index ef2c714b609..8a0e1981820 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb index 60fefc39bf5..a06558cc2cb 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.2.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.3.eb index d968d2c56be..79f08754508 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.3.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb index 01ec53eafb9..cd8a216a60e 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb index 0fc748e278b..2703ab53907 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.3.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb index 82200e98744..585c3a2730a 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.5.0.eb index 61b101b4d57..ab8762d3b91 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.5.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb index dab8d891914..0294b6dc75e 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.1.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb index da4efd77c4a..fc56131f50f 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.17'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb index 5a746f36187..5b4b26b3b8a 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.3.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb index cd56e251253..0c3cd239602 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.4.0.eb @@ -24,7 +24,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb index cfb4a2fcbf0..e43482d5649 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.1.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb index 0e32b008b26..ce7fec7fcfa 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.2.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.29', '', True), + ('binutils', '2.29', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb index ec463c45cfa..2de144d05ab 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-7.3.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb index d0e9458243e..6ed65c27da2 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-8.1.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-5.5.0.eb index a9e1ab6bf9f..5209b761d92 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-5.5.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.3.0.eb index 0dfdab7a31f..4043ac56cd3 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.4.0.eb index e7ec0780223..db24b4bf394 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-6.4.0.eb @@ -20,7 +20,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.2.0.eb index b38f9eaef5a..966f9bd8f1e 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.2.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.29', '', True), + ('binutils', '2.29', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb index 957290a803b..eb4866bb158 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-7.3.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.1.0.eb index ec067261a20..65af1da859e 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.1.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.2.0.eb index 56d6cbacbbf..35c51fb65f2 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.5-GCCcore-8.2.0.eb @@ -16,7 +16,7 @@ checksums = ['cd399d2bee33afa712bac4b1f4434e20379e9b4099bce47189e09a7675a2d566'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.2.2-GCCcore-7.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.2.2-GCCcore-7.4.0.eb index 89abd0d346f..fcc092af430 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.2.2-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.2.2-GCCcore-7.4.0.eb @@ -16,7 +16,7 @@ checksums = ['3ffd2201041c6c56064b4bdad4dfb8959751efbefa823775242b4f32aa37786c'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.2.0.eb index e6731677f86..93c8a305b46 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.2.0.eb @@ -16,7 +16,7 @@ checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb index d6c005dfb35..cea2cb041fc 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.3.0.eb @@ -16,7 +16,7 @@ checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb index 2530ede83d4..a9eb850d760 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-8.4.0.eb @@ -16,7 +16,7 @@ checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb index b46a869bd63..0fb633083da 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.1.0.eb @@ -16,7 +16,7 @@ checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.2.0.eb index 5193a9f616f..358a90c1322 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.3.2-GCCcore-9.2.0.eb @@ -16,7 +16,7 @@ checksums = ['0fda1d034185397430eb7b0c9e140fb37e02fbfc53b90252fa5575e382b6dbd1'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb index c20e3f3948d..7924ce69695 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ checksums = ['34e201d963156618a0ea5bc87220f660a1e08403dd3c7c7903d4f38db3f40039'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb index 2da53fce904..f9deb82e85d 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.5.3-GCCcore-9.3.0.eb @@ -16,7 +16,7 @@ checksums = ['34e201d963156618a0ea5bc87220f660a1e08403dd3c7c7903d4f38db3f40039'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb index b30667a9417..adb0912d13d 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.6.1-GCCcore-10.1.0.eb @@ -16,7 +16,7 @@ checksums = ['1120f8bfe2cc13e5e1e3f671dc41b1a535ca5a75a70d5b349c19da9d4389f74d'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb index 55d04ef9b9d..8edc3c84d84 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ checksums = ['1dd952839cf0d5a8178c691eeae40dc48fa50d18dcce648b1ad9ae0195367d13'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-10.3.0.eb index 8c2f1680328..1b290ba82b4 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-10.3.0.eb @@ -16,7 +16,7 @@ checksums = ['69dc0bb46ea8fc307d4ca1e0b61c8c355eb207d0b0c69f4f8462328e74d7b9ea'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.1.0.eb index d5ee76339b3..6add8cb0941 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.1.0.eb @@ -16,7 +16,7 @@ checksums = ['69dc0bb46ea8fc307d4ca1e0b61c8c355eb207d0b0c69f4f8462328e74d7b9ea'] builddependencies = [ ('M4', '1.4.18'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb index c272626ed8f..2f5f0c2547d 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-11.2.0.eb @@ -16,7 +16,7 @@ checksums = ['69dc0bb46ea8fc307d4ca1e0b61c8c355eb207d0b0c69f4f8462328e74d7b9ea'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.37', '', True), + ('binutils', '2.37', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb index 7b61d615084..e5d42bae065 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.6-GCCcore-9.4.0.eb @@ -16,7 +16,7 @@ checksums = ['69dc0bb46ea8fc307d4ca1e0b61c8c355eb207d0b0c69f4f8462328e74d7b9ea'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb index 4ec9c1c877b..51a53e9d6fa 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.3.0.eb @@ -16,7 +16,7 @@ checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb index 88bd7102234..d87bb83ccc5 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.1.0.eb @@ -16,7 +16,7 @@ checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb index 4c8dc227e18..adcb9e42b3c 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.2.0.eb @@ -16,7 +16,7 @@ checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.39', '', True), + ('binutils', '2.39', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb index 56c2cc38d82..82a5c2763df 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-9.5.0.eb @@ -16,7 +16,7 @@ checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb index 8b80ac71ba2..f85a0804f2a 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb @@ -24,7 +24,7 @@ dependencies = [ ('libGLU', '9.0.0'), ('OpenColorIO', '1.1.0'), # for advanced color management ('OpenImageIO', '1.8.16'), # required for cycles render engine - ('CUDA', local_cuda_ver, '', True), + ('CUDA', local_cuda_ver, '', SYSTEM), ] builddependencies = [('CMake', '3.12.1')] diff --git a/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb index b0ee97e8f9e..6210023c8d0 100644 --- a/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://download.bpipe.org/versions/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('Java', '1.8.0_131', '', True)] +dependencies = [('Java', '1.8.0_131', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/bpipe', 'lib/bpipe.jar'], diff --git a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb index 616d4405ec0..19bf7119f78 100644 --- a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb +++ b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('Perl', '5.26.1'), ('HMMER', '3.1b2'), ('MUSCLE', '3.8.31'), - ('Gblocks', '0.91b', '', True), + ('Gblocks', '0.91b', '', SYSTEM), ('RAxML', '8.2.11', '-hybrid-avx2'), ] diff --git a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb index 4f4b3613521..374d15e26a6 100644 --- a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('Perl', '5.28.0'), ('HMMER', '3.2.1'), ('MUSCLE', '3.8.31'), - ('Gblocks', '0.91b', '', True), + ('Gblocks', '0.91b', '', SYSTEM), ('RAxML', '8.2.12', '-hybrid-avx2'), ] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb index 76868b55c45..fa78496309d 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] -dependencies = [('Java', '1.8.0_74', '', True)] +dependencies = [('Java', '1.8.0_74', '', SYSTEM)] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2017a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2017a.eb index 88be4437d43..f69171cc680 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2017a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2017a.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] checksums = ['82ff13f4e7d7bffab6352e4551dfa13afabf82bff54ea5761d1fc1e78341d7de'] -dependencies = [('Java', '1.8.0_144', '', True)] +dependencies = [('Java', '1.8.0_144', '', SYSTEM)] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-foss-2018a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-foss-2018a.eb index 8ea77e9a5bd..ca5de62a8c9 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-foss-2018a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-foss-2018a.eb @@ -13,7 +13,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['d94b3b440ea64c564005f4eadceff8d502129dd22369f6045e40121ca383a6ca'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] builddependencies = [('Autotools', '20170619')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-intel-2018a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-intel-2018a.eb index 11f42e93a75..0b71e37b50f 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-intel-2018a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.1-intel-2018a.eb @@ -13,7 +13,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['d94b3b440ea64c564005f4eadceff8d502129dd22369f6045e40121ca383a6ca'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] builddependencies = [('Autotools', '20170619')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb index 32be3e9381f..8df8f31d4d3 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b-CUDA-9.2.88.eb @@ -15,8 +15,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['59a7081b61ead0a5738e813c6fcfb614d2c5bb49c29b28609de8e2b51bea3ec0'] dependencies = [ - ('Java', '1.8', '', True), - ('CUDA', local_cuda_ver, '', True), + ('Java', '1.8', '', SYSTEM), + ('CUDA', local_cuda_ver, '', SYSTEM), ] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b.eb index d3d114b1a46..571ffcfac1f 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.0.2-foss-2018b.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['59a7081b61ead0a5738e813c6fcfb614d2c5bb49c29b28609de8e2b51bea3ec0'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb index f40b3b1712f..e676c19b2af 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-10.2.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pkg-config', '0.29.2'), ('pocl', '1.6'), ] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb index d300d9d5ff7..d464264930a 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-8.2.0-2.31.1.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb index f0dc7a138e7..f7afb71fa1b 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-GCC-9.3.0.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb index ecacb7868ce..97e7108bf28 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-gcccuda-2019b.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pkg-config', '0.29.2'), ('pocl', '1.4'), ] diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index ce1ff6795f0..67aec4c48d2 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-3.1.2-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['dd872b484a3a9f0bce369465e60ccf4e4c0cd7bd5ce41499415366019f236275'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] builddependencies = [('Autotools', '20180311')] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index 08e10d150ca..dfa2e11582d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 9709696cf5d..7627c686af3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index d6e68008e5b..9be29fca484 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb index 9ec7a3f3f32..0e86573cab6 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index f411442d121..f331b902250 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb index 4eee9df8fa2..e631c72676f 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb index d7c829040f2..ecd95aca019 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb index 2ae6ba18a54..7122f8fed1d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb index 2d41305b4cf..1ff0485bfc7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.5.0.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb index d95c058f0c8..c9f35fe7a36 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb index 215aaf0cb28..847c265d57c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb index 88e16771dff..00cbe46a478 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb index 9346ceba7e7..e56efe34428 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb index 93b20c17e20..0759f7aae9e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.3.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb index 3cdec71af84..43d45b40723 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-6.4.0.eb @@ -15,7 +15,7 @@ builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, # to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb index 7b12c3e7b9b..6cacb8636c8 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.28-GCCcore-7.1.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.3'), ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb index c35f4248bb2..ec297ac8a27 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.29-GCCcore-7.2.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb index 562cf4dc332..9ecaf6bc39b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-7.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb index 51db6bef353..f20a4a66372 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.30-GCCcore-8.1.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb index 3db9b24875c..3d6ec7437bb 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-7.4.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.2.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb index ef31e6f73c4..8876efd1b6c 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.31.1-GCCcore-8.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.0.5'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb index 5e7624cfb62..a1384a814f7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-8.3.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb index 2482db7b76a..7283ba452d4 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.1.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.2.0.eb index c7966387725..beeca4aff16 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.32-GCCcore-9.2.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb index fb99acd8de8..e7807685469 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-10.1.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.6.1'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-9.3.0.eb index f74f0325c09..34dc183b567 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.34-GCCcore-9.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.5.3'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb index c3fb942ee7d..43435891a60 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.35-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.1'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-10.3.0.eb index 8a7c407a6bb..6dd4731d702 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-10.3.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.6'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-11.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-11.1.0.eb index 9d954efae4e..4b6a60c48f3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-11.1.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.6'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb index 5fe10da2880..efcc5a27842 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-8.4.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.3.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb index 9440aa2ae70..cdcea5ab36a 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.36.1-GCCcore-9.4.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.6'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb index 2f25a58407b..e655d705347 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.37-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.6'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.3.0.eb index da7b3d38de5..ddecfa4f7db 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-11.3.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.8.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb index fdfefe7c042..3710a56f322 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-12.1.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.8.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb index 9e8ca91c080..bea25508b1e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.38-GCCcore-9.5.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.8.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb index c8ec4f59243..f105d46cf0e 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.39-GCCcore-12.2.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.8.2'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', True) + ('binutils', version, '', SYSTEM) ] dependencies = [ diff --git a/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb index 138a0a59d7f..86e013bcdfd 100644 --- a/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'cstd': 'c++03'} builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb index 1cba3eeb025..60d41ad83e5 100644 --- a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021a-CUDA-11.3.1.eb @@ -12,7 +12,7 @@ description = """This module sets a group of environment variables for compilers toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb index 2aa49ff982a..b72970646fb 100644 --- a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2021b-CUDA-11.4.1.eb @@ -12,7 +12,7 @@ description = """This module sets a group of environment variables for compilers toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb index c1b49d2a91a..c3cb995d63e 100644 --- a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022a-CUDA-11.7.0.eb @@ -12,7 +12,7 @@ description = """This module sets a group of environment variables for compilers toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('UCX-CUDA', '1.12.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb index d9104ae02c8..aeea4de6789 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-5.4.0.eb @@ -18,6 +18,6 @@ checksums = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb index 333dfab361e..8ff51f5bd3e 100644 --- a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-6.3.0.eb @@ -18,6 +18,6 @@ checksums = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb index 7622ed76c90..6dcf10dda3d 100644 --- a/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CESM-deps/CESM-deps-2-foss-2021b.eb @@ -24,7 +24,7 @@ dependencies = [ ('PnetCDF', '1.12.3'), ('Subversion', '1.14.1'), ('git', '2.33.1', '-nodocs'), - ('git-lfs', '3.2.0', '', True), + ('git-lfs', '3.2.0', '', SYSTEM), ] components = [ diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb index 843dd43347b..a891c0367b1 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.0'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb index c34f9e1cc3a..b4f032df4ee 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.0'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb index 4c9db1623b7..7cceb21f898 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.9.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb index 020c81029d7..55e0812e853 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb index 7e6d5bdcc6f..fa530f73cc2 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.0'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb index f9297a5a469..08ece993edb 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.2'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb index 1c2a60faa0a..4b1ed1907c7 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.2'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb index e8f39c66d57..8f439a24c42 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.11.4'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb index dc1d8abbeca..693040076f8 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.11.4'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb index 27070c69ab0..b0310dabbf2 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb @@ -25,7 +25,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.10.2'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb index 4d717d55089..83445a5c0a6 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb @@ -15,7 +15,7 @@ checksums = ['59464b1eaee892f2223ba570a7642892c999e29524ab102a6efd7c29c94a29f7'] builddependencies = [ ('CMake', '3.13.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb index 7af7769dea5..e2824c61604 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb @@ -15,7 +15,7 @@ checksums = ['59464b1eaee892f2223ba570a7642892c999e29524ab102a6efd7c29c94a29f7'] builddependencies = [ ('CMake', '3.13.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb index 06c6212ddb5..8258003e2a5 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb @@ -15,7 +15,7 @@ checksums = ['d4ec2528b88a7c3a07b0b86db96c216822f85b951bf4bc7f9d1f26bf6c369afe'] builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb index 5872c04d23b..b0045e26225 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb @@ -15,7 +15,7 @@ checksums = ['d4ec2528b88a7c3a07b0b86db96c216822f85b951bf4bc7f9d1f26bf6c369afe'] builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb index 18103c12dc1..217755142f3 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb @@ -14,7 +14,7 @@ dependencies = [ ('TopHat', '2.1.1'), ('Cufflinks', '2.2.1'), ('BEDTools', '2.26.0'), - ('Kent_tools', '20171107', '-linux.x86_64', True), + ('Kent_tools', '20171107', '-linux.x86_64', SYSTEM), ('STAR', '2.5.3a'), ('BWA', '0.7.17'), ('segemehl', '0.2.0'), diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb index edff9ff989f..2362960ae99 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb @@ -18,7 +18,7 @@ dependencies = [ ('TopHat', '2.1.0', versionsuffix), ('Cufflinks', '2.2.1'), ('BEDTools', '2.27.1'), - ('Kent_tools', '20180716', '-linux.x86_64', True), + ('Kent_tools', '20180716', '-linux.x86_64', SYSTEM), ('STAR', '2.6.0c'), ('BWA', '0.7.17'), ('segemehl', '0.2.0'), diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.3.0.eb index 8407f07472a..8c8d1b0745c 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.20.1-GCCcore-10.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('cURL', '7.76.0'), ('libarchive', '3.5.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb index 60e004e5627..e09ed862f94 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.21.1-GCCcore-11.2.0.eb @@ -24,7 +24,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('cURL', '7.78.0'), ('libarchive', '3.5.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb index 7d88407d378..87996bb065a 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.22.1-GCCcore-11.2.0.eb @@ -24,7 +24,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('cURL', '7.78.0'), ('libarchive', '3.5.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb index d6c0f58b8ae..069c6a25c27 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.23.1-GCCcore-11.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('cURL', '7.83.0'), ('libarchive', '3.6.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb index 6b1b02e8197..113d81b7610 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb @@ -22,7 +22,7 @@ dependencies = [ ('scikit-learn', '0.19.1', versionsuffix), ('MEGAHIT', '1.1.3', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', True), + ('picard', '2.18.27', '-Java-1.8', SYSTEM), ('SAMtools', '1.6'), ('Bowtie2', '2.3.4.1'), ('parallel', '20171122'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb index 30bfadb038e..22128baa385 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb @@ -22,7 +22,7 @@ dependencies = [ ('scikit-learn', '0.19.1', versionsuffix), ('MEGAHIT', '1.1.3', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', True), + ('picard', '2.18.27', '-Java-1.8', SYSTEM), ('SAMtools', '1.6'), ('Bowtie2', '2.3.4.1'), ('parallel', '20171122'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb index b8d52d0019d..dc99d2aeb67 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb @@ -23,7 +23,7 @@ dependencies = [ ('scikit-learn', '0.20.2', versionsuffix), ('MEGAHIT', '1.1.4', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', True), + ('picard', '2.18.27', '-Java-1.8', SYSTEM), ('SAMtools', '1.9'), ('Bowtie2', '2.3.4.2'), ('parallel', '20190222'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb index f1334d88a22..df708ac5e1f 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb @@ -27,7 +27,7 @@ dependencies = [ ('scikit-learn', '0.20.3'), ('MEGAHIT', '1.2.8'), ('BEDTools', '2.28.0'), - ('picard', '2.21.1', '-Java-11', True), + ('picard', '2.21.1', '-Java-11', SYSTEM), ('SAMtools', '1.9'), ('Bowtie2', '2.3.5.1'), ('parallel', '20190622'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb index 9c7b23d10c7..e8a5cb71f32 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2020b-Python-2.7.18.eb @@ -25,7 +25,7 @@ dependencies = [ ('GSL', '2.6'), ('MEGAHIT', '1.2.9', versionsuffix), ('parallel', '20210322'), - ('picard', '2.25.0', '-Java-11', True), + ('picard', '2.25.0', '-Java-11', SYSTEM), ('Pysam', '0.16.0.1', versionsuffix), ('SAMtools', '1.11'), ('scikit-learn', '0.20.4', versionsuffix), diff --git a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb index 854f8a57c6c..2bb7d98cdcf 100644 --- a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.10-GCCcore-8.3.0-Python-3.7.4.eb @@ -19,7 +19,7 @@ checksums = ['cd530eb9c6d446bd18b5dc5a3d61070bfad92c3efd6565d2d8e31a2acfb496f7'] builddependencies = [('binutils', '2.32')] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Python', '3.7.4'), ] diff --git a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb index a35951482e9..4ccf2abec92 100644 --- a/easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/CPLEX/CPLEX-12.9-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ multi_deps = {'Python': ['3.7.2', '2.7.15']} builddependencies = [('binutils', '2.31.1')] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb index 4024c882cdb..e815134c6ec 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.1.2-foss-2020b-Python-2.7.18.eb @@ -24,11 +24,11 @@ checksums = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '2.7.18'), ('SciPy-bundle', '2020.11', '-Python-%(pyver)s'), ('matplotlib', '2.2.5', '-Python-%(pyver)s'), - ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', SYSTEM), ('FLASH', '2.2.00'), ('SAMtools', '1.11'), ('Bowtie2', '2.4.2'), diff --git a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb index 10d20ead474..e1a264c229a 100644 --- a/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/c/CRISPResso2/CRISPResso2-2.2.1-foss-2020b.eb @@ -23,11 +23,11 @@ checksums = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('matplotlib', '3.3.3'), - ('Trimmomatic', '0.39', '-Java-%(javashortver)s', True), + ('Trimmomatic', '0.39', '-Java-%(javashortver)s', SYSTEM), ('FLASH', '2.2.00'), ('SAMtools', '1.11'), ('Bowtie2', '2.4.2'), diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb index c193a9b0bcd..23109630c34 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb @@ -10,7 +10,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'GCC', 'version': '9.3.0'} -dependencies = [('CUDAcore', '11.0.2', '', True)] +dependencies = [('CUDAcore', '11.0.2', '', SYSTEM)] altroot = 'CUDAcore' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb index 7f77cc256bf..a2eecc5b703 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb @@ -10,7 +10,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -dependencies = [('CUDAcore', '11.0.2', '', True)] +dependencies = [('CUDAcore', '11.0.2', '', SYSTEM)] altroot = 'CUDAcore' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb index d6d90b81331..02cea32f4a5 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-GCC-10.2.0.eb @@ -10,7 +10,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'GCC', 'version': '10.2.0'} -dependencies = [('CUDAcore', version, '', True)] +dependencies = [('CUDAcore', version, '', SYSTEM)] altroot = 'CUDAcore' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb index c9848f32320..60c8e706731 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.1.1-iccifort-2020.4.304.eb @@ -10,7 +10,7 @@ description = """CUDA (formerly Compute Unified Device Architecture) is a parall toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -dependencies = [('CUDAcore', version, '', True)] +dependencies = [('CUDAcore', version, '', SYSTEM)] altroot = 'CUDAcore' diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index bcf0c9ef120..cf48d75ac7f 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -29,8 +29,8 @@ dependencies = [ ('glog', '0.3.4'), ('gflags', '2.1.2'), ('OpenCV', '3.1.0'), - ('CUDA', local_cudaversion, '', True), - ('cuDNN', '4.0', '', True), + ('CUDA', local_cudaversion, '', SYSTEM), + ('cuDNN', '4.0', '', SYSTEM), ('LMDB', '0.9.18'), ('LevelDB', '1.18'), ('snappy', '1.1.3'), diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2017b-Python-2.7.14.eb index dea47b25389..4b4cf0047b5 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-foss-2017b-Python-2.7.14.eb @@ -31,7 +31,7 @@ dependencies = [ ] builddependencies = [ ('SCons', '3.0.1', versionsuffix), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('googletest', '1.8.0'), ('fmt', '3.0.2'), ] diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017a-Python-2.7.13.eb index 2aca050dae2..a34dff6cd90 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017a-Python-2.7.13.eb @@ -30,7 +30,7 @@ dependencies = [ builddependencies = [ ('SCons', '2.5.1', versionsuffix), ('3to2', '1.1.1', versionsuffix), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('fmt', '3.0.2'), ('googletest', '1.8.0'), ] diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017b-Python-2.7.14.eb index adf2eb1798e..cd969a41467 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2017b-Python-2.7.14.eb @@ -31,7 +31,7 @@ dependencies = [ ] builddependencies = [ ('SCons', '3.0.1', versionsuffix), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('fmt', '3.0.2'), ('googletest', '1.8.0'), ] diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2018a-Python-2.7.14.eb index 49e2af27122..396bc3cc844 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.3.0-intel-2018a-Python-2.7.14.eb @@ -31,7 +31,7 @@ dependencies = [ ] builddependencies = [ ('SCons', '3.0.1', versionsuffix), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('fmt', '3.0.2'), ('googletest', '1.8.0'), ] diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.4.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.4.0-intel-2018a-Python-2.7.14.eb index dd2f84d5e11..64fbb834858 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.4.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.4.0-intel-2018a-Python-2.7.14.eb @@ -21,7 +21,7 @@ dependencies = [ ] builddependencies = [ ('SCons', '3.0.1', versionsuffix), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('fmt', '3.0.2'), ('googletest', '1.8.0'), ] diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb index c6904d99cd1..55855240f3f 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.1b2'), ('matplotlib', '2.1.0', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb index e714707c6e2..5e8e0e8c81c 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.1b2'), ('matplotlib', '2.1.0', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb index a86d3eb6269..f4962c34698 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-foss-2018b-Python-2.7.15.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [ ('Python', '2.7.15'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), ('matplotlib', '2.2.3', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb index 3896c5c1e88..be840290424 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.1b2'), ('matplotlib', '2.1.0', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb index a37f08d8828..d4b79112d0a 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.13-intel-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.1b2'), ('matplotlib', '2.1.0', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2019a-Python-2.7.15.eb index 4514d763794..ff1a1fe08e9 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2019a-Python-2.7.15.eb @@ -22,7 +22,7 @@ checksums = ['0dcf31eab5e340a0fff37d7a5091d46d9269b0708db8f789adcd7cbd2a09a2b7'] # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '2.7.15'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), ('SciPy-bundle', '2019.03'), # numpy diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb index b5127b17c53..3930c1d64ba 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.0.18-foss-2020b-Python-2.7.18.eb @@ -32,7 +32,7 @@ checksums = [ dependencies = [ ('Python', '2.7.18'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), ('SciPy-bundle', '2020.11', versionsuffix), diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-foss-2019b-Python-3.7.4.eb index 5c9942d78bd..76cd653d9bc 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-foss-2019b-Python-3.7.4.eb @@ -34,7 +34,7 @@ checksums = [ # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '3.7.4'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), ('SciPy-bundle', '2019.10', versionsuffix), # numpy diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-intel-2019b-Python-3.7.4.eb index 59a8d8608ce..07591763a36 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.2-intel-2019b-Python-3.7.4.eb @@ -34,7 +34,7 @@ checksums = [ # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '3.7.4'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), ('SciPy-bundle', '2019.10', versionsuffix), # numpy diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb index a7e58e823a7..7fb4d447164 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021a.eb @@ -33,7 +33,7 @@ checksums = [ # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '3.9.5'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), ('SciPy-bundle', '2021.05'), # numpy diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb index c1bc07048f5..9cf5f49131d 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-foss-2021b.eb @@ -34,7 +34,7 @@ checksums = [ # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '3.9.6'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), ('SciPy-bundle', '2021.10'), # numpy diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-intel-2020a-Python-3.8.2.eb index 27fd970b63a..c7dd8d34897 100644 --- a/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.1.3-intel-2020a-Python-3.8.2.eb @@ -34,7 +34,7 @@ checksums = [ # https://github.com/Ecogenomics/CheckM/blob/master/setup.py dependencies = [ ('Python', '3.8.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('prodigal', '2.6.3'), ('HMMER', '3.3.1'), ('SciPy-bundle', '2020.03', versionsuffix), # numpy diff --git a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb index dead5e2ce6a..60ac440d2d1 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-12.0.1-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -57,7 +57,7 @@ dependencies = [ ('Z3', '4.8.11'), ('libffi', '3.3'), ('elfutils', '0.185'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb index 42c8ecf704e..f051e776913 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-13.0.1-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -57,7 +57,7 @@ dependencies = [ ('Z3', '4.8.12'), ('libffi', '3.4.2'), ('elfutils', '0.185'), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb index b4f7a627ae0..ea670d2cb0c 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb @@ -54,7 +54,7 @@ dependencies = [ ('binutils', '2.31.1'), ('ncurses', '6.1'), ('GMP', '6.1.2'), - ('CUDA', local_cudaver, '', True), + ('CUDA', local_cudaver, '', SYSTEM), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb index 7a92cacfd67..dddce517cbc 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-8.5.0-fosscuda-2020b.eb @@ -13,9 +13,9 @@ builddependencies = [('Cython', '0.29.22')] dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), - ('cuTENSOR', '1.2.2.5', '-CUDA-%(cudaver)s', True), + ('cuTENSOR', '1.2.2.5', '-CUDA-%(cudaver)s', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2018b.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2018b.eb index 744472a8a39..c3ad4a5a02a 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2018b.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2018b.eb @@ -24,7 +24,7 @@ checksums = [ ] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('SAMtools', '0.1.20'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-gompi-2019b.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-gompi-2019b.eb index 81654b4596c..5ec63582c06 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-gompi-2019b.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-gompi-2019b.eb @@ -24,7 +24,7 @@ checksums = [ ] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('SAMtools', '0.1.20'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2017b.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2017b.eb index 89252c31854..c322edc64a1 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2017b.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2017b.eb @@ -15,7 +15,7 @@ checksums = [ '9199390a11376ffba0583741752faca277c82ce3ab665a66ba8dc5991c45088f', # Cufflinks-2.2.1_fix-boost-inc.patch ] -builddependencies = [('Eigen', '3.3.4', '', True)] +builddependencies = [('Eigen', '3.3.4', '', SYSTEM)] dependencies = [ ('Boost', '1.65.1'), ('SAMtools', '0.1.20'), diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2018a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2018a.eb index 11a20f70733..94cc688d081 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2018a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-intel-2018a.eb @@ -16,7 +16,7 @@ checksums = [ ] builddependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('SAMtools', '0.1.20'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-gompi-2019a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-gompi-2019a.eb index fb65a457aae..881426fe576 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-gompi-2019a.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-gompi-2019a.eb @@ -16,7 +16,7 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ checksums = ['444c632083a473fe4fd99ff189cef5bbd95daee0912e8eefe79534bf225fbcb6'] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('Autotools', '20180311'), ('SAMtools', '1.9'), ] diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb index a4c5a87e6b9..34bc1da2fd4 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-GCCcore-5.4.0.eb @@ -17,7 +17,7 @@ source_urls = ['http://curl.haxx.se/download/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['ff3e80c1ca6a068428726cd7dd19037a47cc538ce58ef61c59587191039b2ca6'] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb index 09811fccdee..28584d265c3 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb index 8d7f087e2b7..9c8d5222d95 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-10.3.0.eb index 0c3b29d5863..27b19b6d9c6 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.76.0-GCCcore-10.3.0.eb @@ -30,7 +30,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-zlib' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb index e66d05453ca..ad57d96beb2 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.78.0-GCCcore-11.2.0.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-zlib ' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb index 4a4ad41cdfe..2813650a0d3 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.83.0-GCCcore-11.3.0.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-zlib ' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb index 69ff9b82788..7ff88d2ae52 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.84.0-GCCcore-12.1.0.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-zlib ' diff --git a/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb index ff486b7b508..d3b3a9cf790 100755 --- a/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb @@ -25,7 +25,7 @@ start_dir = 'src' files_to_copy = ['Linux-amd64/*'] dependencies = [ - ('Java', '1.8.0_112', '', True), + ('Java', '1.8.0_112', '', SYSTEM), ('Perl', '5.24.0'), ('gnuplot', '5.0.5'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb b/easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb index 5c98cf65e4e..5eb3e8890bb 100644 --- a/easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.8-GCCcore-8.2.0-Perl-5.28.1.eb @@ -16,7 +16,7 @@ checksums = ['30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4'] builddependencies = [('binutils', '2.31.1')] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Perl', '5.28.1'), ('gnuplot', '5.2.6'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-1.8-foss-2017b-Perl-5.26.0.eb b/easybuild/easyconfigs/c/canu/canu-1.8-foss-2017b-Perl-5.26.0.eb index 31877e3e7dd..54dd03ba54b 100644 --- a/easybuild/easyconfigs/c/canu/canu-1.8-foss-2017b-Perl-5.26.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.8-foss-2017b-Perl-5.26.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Perl', '5.26.0'), ('gnuplot', '5.2.2'), ('Boost', '1.65.1'), diff --git a/easybuild/easyconfigs/c/canu/canu-1.8-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/c/canu/canu-1.8-foss-2018b-Perl-5.28.0.eb index 1066c169c5e..114020eb165 100644 --- a/easybuild/easyconfigs/c/canu/canu-1.8-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.8-foss-2018b-Perl-5.28.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Perl', '5.28.0'), ('gnuplot', '5.2.5'), ('Boost', '1.67.0'), diff --git a/easybuild/easyconfigs/c/canu/canu-1.8-intel-2017b-Perl-5.26.0.eb b/easybuild/easyconfigs/c/canu/canu-1.8-intel-2017b-Perl-5.26.0.eb index e74e3dbe8b9..75b1d610731 100644 --- a/easybuild/easyconfigs/c/canu/canu-1.8-intel-2017b-Perl-5.26.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.8-intel-2017b-Perl-5.26.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Perl', '5.26.0'), ('gnuplot', '5.2.2'), ('Boost', '1.65.1'), diff --git a/easybuild/easyconfigs/c/canu/canu-1.9-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/c/canu/canu-1.9-GCCcore-8.3.0-Java-11.eb index a1185d44d41..b9a96798841 100644 --- a/easybuild/easyconfigs/c/canu/canu-1.9-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.9-GCCcore-8.3.0-Java-11.eb @@ -16,7 +16,7 @@ checksums = ['6b086ab6086c050752166500378bc4b3b3543d4c617863e894d296171cee3385'] builddependencies = [('binutils', '2.32')] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.30.0'), ('gnuplot', '5.2.8'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb index 7a7d3c59ec8..1a81cacc467 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.32.0'), ('gnuplot', '5.4.1'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb index 990e0dcabec..8e5ee7b58b9 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.1.1-GCCcore-9.3.0-Java-11.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.30.2'), ('gnuplot', '5.2.8'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb index 42b5f5b32b9..441c3224e45 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0-Java-11.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.32.1'), ('gnuplot', '5.4.2'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb index 688753bfca0..1eff45bbc43 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-10.3.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.32.1'), ('gnuplot', '5.4.2'), ] diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb index 946fb4dd038..4d58483415e 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.34.0'), ('gnuplot', '5.4.2'), ] diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 7d60fb1c61d..8356b39778a 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -18,7 +18,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('SciPy-bundle', '2020.11'), ('leidenalg', '0.8.3'), ('hyperopt', '0.2.5'), diff --git a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb index 5a14fa765f1..c4b1c45f09f 100644 --- a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('PyTorch-Lightning', '1.5.9', versionsuffix), ('torchvision', '0.11.1', versionsuffix), diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb index 8a1c4c6c03a..87813b35bd9 100644 --- a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2021a-CUDA-11.3.1.eb @@ -35,7 +35,7 @@ dependencies = [ ('LibTIFF', '4.2.0'), ('GSL', '2.7'), ('wxWidgets', '3.1.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] configopts = '--enable-openmp ' diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb index eb7933a6c04..3552aab690a 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-FCC-4.5.0.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [('binutils', '2.36.1')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.3.0.eb index 4b461e5efbd..2d38e9742d4 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.3.0.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [('binutils', '2.36.1')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb index 94dd6b092b5..e05ffa92185 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.2.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.37')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb index 21b56c74451..1217b252c49 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.38')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb index d33d1cd6305..0d52a3be447 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.1.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.38')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb index c78178d6997..515c85e1a9c 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.31.1')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb index 0c21b4fc363..1a66d75ceb1 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-8.3.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.32')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb index 5f7fbe14d4a..094f7bc25d2 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.2.0.eb @@ -16,7 +16,7 @@ dependencies = [ ('Perl', '5.34.0'), ('MariaDB', '10.6.4'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] options = {'modulename': 'DBD::mysql'} diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb index eb71c16f467..6d67a433eb4 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-11.3.0.eb @@ -16,7 +16,7 @@ dependencies = [ ('Perl', '5.34.1'), ('MariaDB', '10.9.3'), ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] options = {'modulename': 'DBD::mysql'} diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb index f7c16f218ab..2e64cfeb8f1 100644 --- a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.6-GCCcore-11.2.0.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('zlib', '1.2.11'), ('libjpeg-turbo', '2.0.6'), ('LibTIFF', '4.3.0'), diff --git a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb index 61ccdb3b120..197ea4e94e2 100644 --- a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb @@ -34,7 +34,7 @@ dependencies = [ ('Trilinos', '12.12.1', versionsuffix), ('zlib', '1.2.11'), ('libxml2', '2.9.7'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('PLY', '3.11', versionsuffix), ('VTK', '8.1.0', versionsuffix), ('petsc4py', '3.9.1', versionsuffix), diff --git a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb index 51c770e09cc..067b5659b17 100644 --- a/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb @@ -33,7 +33,7 @@ dependencies = [ ('Trilinos', '12.12.1', versionsuffix), ('zlib', '1.2.11'), ('libxml2', '2.9.9'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('PLY', '3.11', versionsuffix), ('VTK', '8.2.0', versionsuffix), ('petsc4py', '3.12.0', versionsuffix), diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb index 020b8f5f672..e06ee84b7f4 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.0.3-foss-2020b-R-4.0.3.eb @@ -13,7 +13,7 @@ dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), ('tMAE', '1.0.0', '-R-%(rver)s'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('GATK', '4.2.0.0', '-Java-%(javaver)s'), ('Graphviz', '2.47.0', '-Java-%(javaver)s'), ('Python', '3.8.6'), @@ -23,7 +23,7 @@ dependencies = [ ('HTSlib', '1.11'), # for tabix ('SAMtools', '1.11'), ('BCFtools', '1.11'), - ('Pandoc', '2.13', '', True), + ('Pandoc', '2.13', '', SYSTEM), ] # postinstallcmds for pandoc are required to avoid that import fails because pandoc/definitions dir is not installed diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb index 014ae7c311e..8091ae5611b 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.1.0-foss-2020b-R-4.0.3.eb @@ -13,7 +13,7 @@ dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', '-R-%(rver)s'), ('tMAE', '1.0.0', '-R-%(rver)s'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('GATK', '4.2.0.0', '-Java-%(javaver)s'), ('Graphviz', '2.47.0', '-Java-%(javaver)s'), ('Python', '3.8.6'), @@ -23,7 +23,7 @@ dependencies = [ ('HTSlib', '1.11'), # for tabix ('SAMtools', '1.11'), ('BCFtools', '1.11'), - ('Pandoc', '2.13', '', True), + ('Pandoc', '2.13', '', SYSTEM), ] exts_list = [ diff --git a/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb index db1db5f1d92..64d414e98e3 100644 --- a/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/d/DROP/DROP-1.1.1-foss-2021b-R-4.1.2.eb @@ -13,7 +13,7 @@ dependencies = [ ('R', '4.1.2'), ('R-bundle-Bioconductor', '3.14', '-R-%(rver)s'), ('tMAE', '1.0.1', '-R-%(rver)s'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('GATK', '4.2.3.0', '-Java-%(javaver)s'), ('Graphviz', '2.50.0'), ('Python', '3.9.6'), @@ -23,7 +23,7 @@ dependencies = [ ('HTSlib', '1.14'), # for tabix ('SAMtools', '1.14'), ('BCFtools', '1.14'), - ('Pandoc', '2.13', '', True), + ('Pandoc', '2.13', '', SYSTEM), ] exts_list = [ diff --git a/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb index 3cfdd856379..1a94e28f534 100644 --- a/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/Detectron2/Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('PyTorch', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb index 5077e846a5f..43608ef12b5 100644 --- a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb @@ -18,7 +18,7 @@ source_urls = ['https://bitbucket.org/nrg/dicombrowser/downloads/'] sources = ['%(name)s-%(version)s-bin-with-dependencies.jar'] dependencies = [ - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb index 90fd7aad74c..3b4f5c86dc5 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.13-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ checksums = ['af667887bd7a87dc0dbf9ac8d86c96b552dfb8ca9c790ed1cbffaa6131573f6b'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('CMake', '3.7.2'), ('flex', '2.6.3'), ('Bison', '3.0.4'), diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb index 45622c59260..737412283c0 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0-CUDA-11.4.1.eb @@ -30,7 +30,7 @@ checksums = [ srcdir = 'src/source' builddependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('CMake', '3.21.1'), ] diff --git a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb index c9fb8927779..319fbdda612 100644 --- a/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/deepmedic/deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb @@ -10,7 +10,7 @@ description = "Efficient Multi-Scale 3D Convolutional Neural Network for Segment toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('TensorFlow', '2.6.0', versionsuffix), ('SciPy-bundle', '2021.05'), diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb index e62049c61b8..3448b11526f 100644 --- a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb @@ -25,7 +25,7 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('cuDNN', '8.2.1.32', versionsuffix, True), ] diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb index eaf6f22dc12..e32b7fad6ce 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-10.2.0-Java-13.eb @@ -42,7 +42,7 @@ builddependencies = [('CMake', '3.18.4')] dependencies = [ ('X11', '20201008'), ('libharu', '2.3.0'), - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb index a4cabd71a43..df004f43de0 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.2.0-2.31.1.eb @@ -37,7 +37,7 @@ builddependencies = [('CMake', '3.13.3')] dependencies = [ ('X11', '20190311'), ('libharu', '2.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb index e34109b6a96..aee6c64e90f 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-GCC-8.3.0-Java-11.eb @@ -42,7 +42,7 @@ builddependencies = [('CMake', '3.15.3')] dependencies = [ ('X11', '20190717'), ('libharu', '2.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb index 0d6ccf3dc76..08887154a33 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb @@ -29,7 +29,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.3.0'), - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb index 1e20c9bdaa4..ab468ed2c59 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2018b.eb @@ -36,7 +36,7 @@ builddependencies = [('CMake', '3.11.4')] dependencies = [ ('X11', '20180604'), ('libharu', '2.3.0'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb index 2b478b1b9ea..11a7dcee8c2 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021a.eb @@ -39,7 +39,7 @@ builddependencies = [('CMake', '3.20.1')] dependencies = [ ('X11', '20210518'), ('libharu', '2.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb index 9471b613f8d..84ecb49dc1e 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2021b.eb @@ -39,7 +39,7 @@ builddependencies = [('CMake', '3.22.1')] dependencies = [ ('X11', '20210802'), ('libharu', '2.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index 3a560dce5d2..c5ee371b0db 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -37,7 +37,7 @@ builddependencies = [('CMake', '3.13.3')] dependencies = [ ('X11', '20190311'), ('libharu', '2.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb index fc0789ffe30..71a682b454e 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a-X11-20170314.eb @@ -35,7 +35,7 @@ dependencies = [ ('X11', local_x11ver), ('libgd', '2.2.4'), ('libharu', '2.3.0'), - ('Java', '1.8.0_144', '', True), + ('Java', '1.8.0_144', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb index d6fa49965ac..8796b8995a5 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb @@ -29,7 +29,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.3.0'), - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb index 6c9d498a0a4..9da803147ab 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2018b.eb @@ -33,7 +33,7 @@ dependencies = [ ('X11', '20180604'), ('libgd', '2.2.5'), ('libharu', '2.3.0'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb index 328732419a3..8f17e9edb17 100644 --- a/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/e/Embree/Embree-3.4.0-iccifort-2018.1.163-GCC-6.4.0-2.28.eb @@ -21,7 +21,7 @@ checksums = ['22229f19332d4fd08eb3bf60198211bda674f51632b977c9d7fd09531e09dd8d'] builddependencies = [('CMake', '3.11.4')] dependencies = [ - ('ispc', '1.10.0', '', True), + ('ispc', '1.10.0', '', SYSTEM), ('tbb', '2018_U5'), ] diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb index a00b575cac8..4cf6ddc59a4 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-5.4.0.eb @@ -10,7 +10,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori toolchain = {'name': 'GCCcore', 'version': '5.4.0'} toolchainopts = {'pic': True} -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] sources = [SOURCE_TAR_BZ2] diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb index e68f2d8d88a..b897f140c89 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_BZ2] checksums = ['d9e50ff2d19b3538bd2127902a89987474e1a4db8e43a66a4d1a712ab9a504ff'] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb index 20703396833..fdb59680efe 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ - ('NASM', '2.12.02', '', True), + ('NASM', '2.12.02', '', SYSTEM), ('x264', '20170406'), ('X11', '20170129'), # pulls in bzip2 and zlib ] diff --git a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb index 4cb227e1d23..0e1c47bba9b 100644 --- a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb @@ -17,8 +17,8 @@ dependencies = [ ('FSL', '5.0.11', versionsuffix), ('ANTs', '2.3.1', versionsuffix), ('AFNI', '18.3.00', versionsuffix), - ('C3D', '1.0.0', '', True), - ('FreeSurfer', '6.0.1', '-centos6_x86_64', True), + ('C3D', '1.0.0', '', SYSTEM), + ('FreeSurfer', '6.0.1', '-centos6_x86_64', SYSTEM), ('ICA-AROMA', '0.4.4-beta', versionsuffix), ('Seaborn', '0.9.0', versionsuffix), ('PyYAML', '3.13', versionsuffix), diff --git a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb index b12cefc9057..81bb446518f 100644 --- a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.4.1-foss-2018b-Python-3.6.6.eb @@ -17,8 +17,8 @@ dependencies = [ ('FSL', '5.0.11', versionsuffix), ('ANTs', '2.3.1', versionsuffix), ('AFNI', '18.3.00', versionsuffix), - ('C3D', '1.0.0', '', True), - ('FreeSurfer', '6.0.1', '-centos6_x86_64', True), + ('C3D', '1.0.0', '', SYSTEM), + ('FreeSurfer', '6.0.1', '-centos6_x86_64', SYSTEM), ('ICA-AROMA', '0.4.4-beta', versionsuffix), ('Seaborn', '0.9.0', versionsuffix), ('PyYAML', '3.13', versionsuffix), diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb index f96cf15c130..e5ab2e466bf 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.2-foss-2018b-Python-2.7.15-CUDA-9.2.88.eb @@ -60,7 +60,7 @@ dependencies = [ ('VTK', '8.1.1', local_python_suffix), ('GSL', '2.5'), ('Qwt', '6.1.4'), - ('CUDA', local_CUDA_ver, '', True), + ('CUDA', local_CUDA_ver, '', SYSTEM), ] # FSLDIR needs to be defined when running postinstall to get the correct shebang diff --git a/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb index 38ff91c345f..2e329e07f19 100644 --- a/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('PyYAML', '5.4.1'), ('Biopython', '1.79'), diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb index 9251dd40828..daee979d9db 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-1.8.eb @@ -21,7 +21,7 @@ checksums = [ '684701634440864750c9a0b99d81e122a1def78672d436daf5497bff61d9a356', # FastQC_shebang.patch ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] postinstallcmds = ["chmod +x %(installdir)s/fastqc"] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-11.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-11.eb index f075347905b..ef747fd9625 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-11.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.8-Java-11.eb @@ -25,7 +25,7 @@ checksums = [ '684701634440864750c9a0b99d81e122a1def78672d436daf5497bff61d9a356', # FastQC_shebang.patch ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] postinstallcmds = ["chmod +x %(installdir)s/fastqc"] diff --git a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.9-Java-11.eb b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.9-Java-11.eb index bbe1b9f0240..5fa46779ccc 100644 --- a/easybuild/easyconfigs/f/FastQC/FastQC-0.11.9-Java-11.eb +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.11.9-Java-11.eb @@ -25,7 +25,7 @@ checksums = [ '684701634440864750c9a0b99d81e122a1def78672d436daf5497bff61d9a356', # FastQC_shebang.patch ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] postinstallcmds = ["chmod +x %(installdir)s/fastqc"] diff --git a/easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb b/easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb index 0fad82d9d44..e16acdff154 100644 --- a/easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb +++ b/easybuild/easyconfigs/f/FastViromeExplorer/FastViromeExplorer-20180422-foss-2019b.eb @@ -14,7 +14,7 @@ sources = [{'download_filename': 'FastViromeExplorer-%s.tar.gz' % local_commit, checksums = ['3a8e7842e83539cd36f619f1e01761e2c5b87a44a5f51328287b6dd20ef47384'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('kallisto', '0.46.1'), ('SAMtools', '1.10'), ] diff --git a/easybuild/easyconfigs/f/Ferret/Ferret-7.3-intel-2017b.eb b/easybuild/easyconfigs/f/Ferret/Ferret-7.3-intel-2017b.eb index 3c6dcc5750c..afc3e88aa32 100644 --- a/easybuild/easyconfigs/f/Ferret/Ferret-7.3-intel-2017b.eb +++ b/easybuild/easyconfigs/f/Ferret/Ferret-7.3-intel-2017b.eb @@ -22,7 +22,7 @@ dependencies = [ ('cURL', '7.56.0'), ('ncurses', '6.0'), ('libreadline', '7.0'), - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ] parallel = 1 diff --git a/easybuild/easyconfigs/f/Ferret/Ferret-7.5.0-foss-2019b.eb b/easybuild/easyconfigs/f/Ferret/Ferret-7.5.0-foss-2019b.eb index 1b061234a1c..ad0059c286e 100644 --- a/easybuild/easyconfigs/f/Ferret/Ferret-7.5.0-foss-2019b.eb +++ b/easybuild/easyconfigs/f/Ferret/Ferret-7.5.0-foss-2019b.eb @@ -24,7 +24,7 @@ dependencies = [ ('cURL', '7.66.0'), ('ncurses', '6.1'), ('libreadline', '8.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] # /bin/csh is required for installation by bin/make_executable_tar, bin/make_environment_tar diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb b/easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb index b1a1a6b217b..b7dd6766d3f 100644 --- a/easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb +++ b/easybuild/easyconfigs/f/Fiji/Fiji-20170530.eb @@ -14,7 +14,7 @@ source_urls = ['https://downloads.imagej.net/fiji/Life-Line/'] sources = ['%(namelower)s-nojre-%(version)s.zip'] checksums = ['cf9fb45c48b22a7888b479968477f1f7a300a9c833e47244cbe0d1e93890bd20'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] postinstallcmds = [ # Remove binaries for other platforms diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb b/easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb index 3309bd66a45..c4f26af3680 100644 --- a/easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb +++ b/easybuild/easyconfigs/f/Fiji/Fiji-20191119-2057.eb @@ -17,7 +17,7 @@ sources = [{ }] checksums = ['7fad8e8f8676edbcfe7eb979421ab163e8d48bb7950a815f7821cbe58b8bb051'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] postinstallcmds = [ # Remove binaries for other platforms diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-20201104-1356.eb b/easybuild/easyconfigs/f/Fiji/Fiji-20201104-1356.eb index efe07f936b3..aac8b8d8de9 100644 --- a/easybuild/easyconfigs/f/Fiji/Fiji-20201104-1356.eb +++ b/easybuild/easyconfigs/f/Fiji/Fiji-20201104-1356.eb @@ -17,7 +17,7 @@ sources = [{ }] checksums = ['ea60c212f0c123c2e947f0171b3a3ec83c38f0a6bd4c2bf2d5a5c53ba5e464cb'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] postinstallcmds = [ # Remove binaries for other platforms diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb index d84be83b2a1..f779e1cdeac 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4-GCC-11.2.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('BLIS', '0.8.1'), # imkl is commented out, since installing it requires accepting the Intel oneAPI EULA; # note: also commented out the lines below to add imkl to 'backends'! - # ('imkl', {'arch=x86_64': '2021.4.0', 'arch=*': False}, '', True), + # ('imkl', {'arch=x86_64': '2021.4.0', 'arch=*': False}, '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb index e56c85b532c..8467c1d6f61 100644 --- a/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/FreeTDS/FreeTDS-1.3.3-GCCcore-10.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('libreadline', '8.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-openssl' diff --git a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb index 5db5fc0424e..6d3a32e9eac 100644 --- a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.20-foss-2019b-Python-2.7.16.eb @@ -13,7 +13,7 @@ github_account = 'ndaniel' toolchain = {'name': 'foss', 'version': '2019b'} dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '2.7.16'), ('SciPy-bundle', '2019.10', versionsuffix), ('Biopython', '1.75', versionsuffix), @@ -24,7 +24,7 @@ dependencies = [ ('Kent_tools', '401'), # required for liftOver ('SRA-Toolkit', '2.10.4'), ('STAR', '2.7.2b'), - ('picard', '2.21.6', '-Java-11', True), # optional + ('picard', '2.21.6', '-Java-11', SYSTEM), # optional ('Velvet', '1.2.10', '-mt-kmer_191'), # optional ('openpyxl', '2.6.4', versionsuffix), # optional ('parallel', '20190922'), # optional diff --git a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb index 1f85b510834..19f5df4c694 100644 --- a/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/f/FusionCatcher/FusionCatcher-1.30-foss-2019b-Python-2.7.16.eb @@ -13,7 +13,7 @@ github_account = 'ndaniel' toolchain = {'name': 'foss', 'version': '2019b'} dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '2.7.16'), ('SciPy-bundle', '2019.10', versionsuffix), ('Biopython', '1.75', versionsuffix), @@ -24,7 +24,7 @@ dependencies = [ ('Kent_tools', '401'), # required for liftOver ('SRA-Toolkit', '2.10.4'), ('STAR', '2.7.2b'), - ('picard', '2.21.6', '-Java-11', True), # optional + ('picard', '2.21.6', '-Java-11', SYSTEM), # optional ('Velvet', '1.2.10', '-mt-kmer_191'), # optional ('openpyxl', '2.6.4', versionsuffix), # optional ('parallel', '20190922'), # optional diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb index ac2d9ea1647..f93575efa78 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb index 72d2805b5fe..5845a2c4a99 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb index facf8e7f13d..6dfeb43eb04 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb index a28470817bb..77843fba611 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb index 68344b21cb3..db2144c50dd 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb index f579ff8a965..152ebf1d622 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb index bf74b3065c0..fd99cc06be2 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb @@ -14,6 +14,6 @@ checksums = ['71dd1b58158c935027104c830c019e48c73250708af5def45ea256c789318948'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.28', '', True)] +builddependencies = [('binutils', '2.28', '', SYSTEM)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb index b7b82f91973..92ac3157fe7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb index 73279c6d88c..18c962e0803 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index 954dea0d03b..adf1e7911c6 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb index ee9b4ed94d3..171d19af2db 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb index 51d6c9f7b63..1f313caa5a3 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb index 43cfdfac42c..cafaa07872a 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb index fea26879081..50026211e06 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb index e7dd6de964c..b8bb432df65 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb index 28c855c205d..8f9ab00f288 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb index e615af45793..b0c78713c4d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.1.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.6.1'), ('help2man', '1.47.15'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb index d6bae199dd3..f9dd97bb264 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.1'), ('help2man', '1.47.16'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.3.0.eb index cf948060781..9c8be6a9616 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-10.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.6'), ('help2man', '1.48.3'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.1.0.eb index 4ca376c2d43..0b7ca6dcc6a 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.1.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.6'), ('help2man', '1.48.3'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb index bd40de3b73d..78207419ed1 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.6'), ('help2man', '1.48.3'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.37', '', True), + ('binutils', '2.37', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb index c0e17568f86..dcf62626f8b 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.8.2'), ('help2man', '1.49.2'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb index b515d9c39a5..98d514c2d78 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.1.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.8.2'), ('help2man', '1.49.2'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb index b953ed29dab..63776909de0 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.8.2'), ('help2man', '1.49.2'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.39', '', True), + ('binutils', '2.39', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-5.5.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-5.5.0.eb index ffa930b4898..6e2346cb45a 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-5.5.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.5'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb index 20fcbab0a05..9f150f124f7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] # glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb index 17af2c37c99..9879fbf3e84 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-6.4.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb index 85ed2ec7911..e22e1391359 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.29', '', True), + ('binutils', '2.29', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.3.0.eb index 94729110abe..aed4ab61424 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.4.0.eb index ae0550f73c3..179da80d419 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-7.4.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.2.2'), ('help2man', '1.47.8'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb index ac19425d0d4..92b958e6a97 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.1.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.6'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.2.0.eb index 01fb067c997..059e88ff05c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.0.5'), ('help2man', '1.47.7'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb index f5fc0ba9248..11a535f092d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.3.2'), ('help2man', '1.47.8'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb index 36aad7de33d..39338043fd8 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-8.4.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.3.2'), ('help2man', '1.47.8'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb index 256f72bf9e9..b1e5c067383 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.1.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.3.2'), ('help2man', '1.47.10'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.2.0.eb index 6a58f80946f..de9e537294f 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.3.2'), ('help2man', '1.47.10'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.3.0.eb index 5f380c6db6e..f61ebc628c7 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.5.3'), ('help2man', '1.47.12'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb index 7d4dffd6bd2..6cae0620be3 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.4.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.7.6'), ('help2man', '1.48.3'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb index 56f3743d5ab..24974f71c4d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-9.5.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.8.2'), ('help2man', '1.49.2'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb index fc9583cf3bc..8f37cf904d2 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ('pkg-config', '0.29.1'), ] diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb index 0b86b4b9dbd..d9df0e9ca8d 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb index 2ff9e6f9623..4c6ef6f4dd4 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb index 266f40adb09..191eede5cf5 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('zlib', '1.2.8'), ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb index f01c0208b56..c1cfebce521 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb index 2b17c553f92..eb85cf2630c 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -20,7 +20,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb index a9afba8996d..f8625f2b6eb 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0.eb @@ -19,7 +19,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.10.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.10.0-foss-2018b-Python-3.6.6.eb index f77438c3055..08f154e2df5 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.10.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.10.0-foss-2018b-Python-3.6.6.eb @@ -39,7 +39,7 @@ checksums = ['6a149750dfcdb250e07198cf1726d2f0958d2b8f257618b3b585194c4c392283'] dependencies = [ ('Python', '3.6.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.12.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.12.0-foss-2018b-Python-3.6.6.eb index 389c8248e1e..2b2f1c7f916 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.12.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.12.0-foss-2018b-Python-3.6.6.eb @@ -35,7 +35,7 @@ checksums = ['733134303f4961dec589247ff006612b7a94171fab8913c5d44c836aa086865f'] dependencies = [ ('Python', '3.6.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-2.7.14.eb index 4a926a82dd9..5b5158ceae2 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-2.7.14.eb @@ -34,7 +34,7 @@ checksums = ['801bbb181c275cfabc96dc0cb21f3f901634cec11efde9ba9c8b91e2834feef4'] dependencies = [ ('Python', '2.7.14'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-3.6.4.eb index 597a6f976c6..f1cff8ec83e 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.4.0-intel-2018a-Python-3.6.4.eb @@ -34,7 +34,7 @@ checksums = ['801bbb181c275cfabc96dc0cb21f3f901634cec11efde9ba9c8b91e2834feef4'] dependencies = [ ('Python', '3.6.4'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.5.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.5.1-foss-2018a-Python-3.6.4.eb index c6bfdc3bc56..0eb7cbd64a4 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.5.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.5.1-foss-2018a-Python-3.6.4.eb @@ -35,7 +35,7 @@ checksums = ['3847f540beeb02651f0cf8f14bb0c6ed4e837f1ea73bc6d04cbe38d217c1b25f'] dependencies = [ ('Python', '3.6.4'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-2.7.14.eb index e82571bce37..ba6dfc0ee3a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-2.7.14.eb @@ -35,7 +35,7 @@ checksums = ['9dda57e82471e67151a442c4751308b6db4e88db315b2f5ed10a41f0b2acbf7c'] dependencies = [ ('Python', '2.7.14'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-3.6.4.eb index 4570b7031c6..0a969762ea5 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.7.0-intel-2018a-Python-3.6.4.eb @@ -35,7 +35,7 @@ checksums = ['9dda57e82471e67151a442c4751308b6db4e88db315b2f5ed10a41f0b2acbf7c'] dependencies = [ ('Python', '3.6.4'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-2.7.15.eb index 77b1b7f821b..ced47b570c5 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-2.7.15.eb @@ -35,7 +35,7 @@ checksums = ['e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9'] dependencies = [ ('Python', '2.7.15'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-3.6.6.eb index 7e9fea1dd4b..2007bd75f4d 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.0.8.1-foss-2018b-Python-3.6.6.eb @@ -35,7 +35,7 @@ checksums = ['e4bb082d8c8826d4f8bc8c2f83811d0e81e5088b99099d3396d284f82fbf28c9'] dependencies = [ ('Python', '3.6.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb index d559c597928..a883aa385e9 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.0.0-foss-2018b-Python-3.6.6.eb @@ -35,7 +35,7 @@ checksums = ['148aa061328d922a570d0120d88f27e61e5da877f542206f4d77f2d788b7d21d'] dependencies = [ ('Python', '3.6.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.2.0-GCCcore-8.2.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.2.0-GCCcore-8.2.0-Java-1.8.eb index 259b1fc261c..48b0ca81c08 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.2.0-GCCcore-8.2.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.2.0-GCCcore-8.2.0-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['ffc5f9b3d4b35772ee5dac3060b59dc657f30e830745160671d84d732c30dc65'] multi_deps = {'Python': ['3.7.2', '2.7.15']} dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.3.0-GCCcore-8.3.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.3.0-GCCcore-8.3.0-Java-1.8.eb index dd822ef8725..988b75dedf0 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.3.0-GCCcore-8.3.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.3.0-GCCcore-8.3.0-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['56fd4f03b15a8a01eaa4629f62e3ab15e4d4b957c787efd2d5629b2658c3df0a'] multi_deps = {'Python': ['3.7.4', '2.7.16']} dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-1.8.eb index 6e29aeb7a94..59f9839ebb3 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['21ae694cfc8b7447381ad5ce62ed4af22e53a228b12495bdcca7df0c73b09cea'] multi_deps = {'Python': ['3.7.4', '2.7.16']} dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-11.eb index 6f9d693a6ff..105c7c506f8 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.4.1-GCCcore-8.3.0-Java-11.eb @@ -36,7 +36,7 @@ checksums = ['21ae694cfc8b7447381ad5ce62ed4af22e53a228b12495bdcca7df0c73b09cea'] multi_deps = {'Python': ['3.7.4', '2.7.16']} dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-1.8.eb index d0ea17e1743..4296a3c1049 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['6fc152c2cae0cc54c7c4cfdfd865a64f7054a820f7d02ca2549511af1dd9882b'] multi_deps = {'Python': ['3.8.2', '2.7.18']} dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb index 03050c2a5c7..007404e1392 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.5.0-GCCcore-9.3.0-Java-11.eb @@ -36,7 +36,7 @@ checksums = ['6fc152c2cae0cc54c7c4cfdfd865a64f7054a820f7d02ca2549511af1dd9882b'] multi_deps = {'Python': ['3.8.2', '2.7.18']} dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb index 18bc8061965..f93742a9063 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['42e6de5059232df1ad5785c68c39a53dc1b54afe7bb086d0129f4dc95fb182bc'] multi_deps = {'Python': ['3.8.2', '2.7.18']} dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb index 610d9d24aa1..097bd00e48f 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-1.8.eb @@ -34,7 +34,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['dd11cc8e3bc7a23c2c226366428f0908c902765eabbc1c641c736c06b80aaf78'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb index f11ab541250..515f6cea9b1 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.0.0-GCCcore-10.2.0-Java-11.eb @@ -34,7 +34,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['dd11cc8e3bc7a23c2c226366428f0908c902765eabbc1c641c736c06b80aaf78'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb index cd0447168d9..e965471f65a 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.3.0-GCCcore-11.2.0-Java-11.eb @@ -35,7 +35,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['12fbd03142311419a050dba8009d615ee8faceb32b46aad8f4448dafd61e11eb'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.6'), ] diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb index 49709d4a376..d9e3451ed2f 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.5.0-GCCcore-11.2.0-Java-11.eb @@ -35,7 +35,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['203f17868f0a73a8322d2f8bd568b9f7b4bb81e36d37db5b6a142d8050ef049f'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.6'), ] diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb index 3b8c9ff85d5..1d4af9b3398 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-11.2.0-Java-11.eb @@ -35,7 +35,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['1125cfc862301d437310506c8774d36c3a90d00d52c7b5d6b59dac7241203628'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.6'), ] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb index ecc2aa7e0a6..c99c15a13e4 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('CUDAcore', local_cudaversion, '', True), # needed by GDRCopy binaries, which are tools for testing + ('CUDAcore', local_cudaversion, '', SYSTEM), # needed by GDRCopy binaries, which are tools for testing ('Check', '0.15.2'), ] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb index 4e78c65fb6b..accc04a5bde 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('CUDAcore', local_cudaversion, '', True), # needed by GDRCopy binaries, which are tools for testing + ('CUDAcore', local_cudaversion, '', SYSTEM), # needed by GDRCopy binaries, which are tools for testing ('Check', '0.15.2'), ] diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb index 63ed61f6150..864159cc441 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', local_cudaversion, '', SYSTEM), ('Check', '0.15.2'), ] diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb index 8606dd48d2a..66240220c01 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.97-foss-2016b.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['9b22a61f01af27e60d483cb7bca73e397d8ca4719c741349a8551984c6c33976'] builddependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb index 4824b4d661d..149f74bea8f 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.1-foss-2018b.eb @@ -18,7 +18,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['6beeed4a9e727a96fdea9e86e39bbe9cbc9f0540ad3a1053814e95b0863a7e6b'] builddependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb index d489fda525c..06af8a8bbb1 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb @@ -29,7 +29,7 @@ dependencies = [ ('ASE', '3.16.2', versionsuffix), ('libxc', '3.0.1'), ('libvdwxc', '0.3.2'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb index 8e5a3d625fa..fa75dd66180 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('Python', '3.6.6'), ('ASE', '3.16.2', versionsuffix), ('libxc', '3.0.1'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb index 6a5eb1c4ce2..660743db68a 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('ASE', local_aseversion, local_pythonsuffix), ('libxc', '3.0.1'), # Old version to maintain consistency with AtomPAW and ABINIT. ('libvdwxc', '0.3.2'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb index ed31bbedf0e..6c10491a0d2 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb @@ -27,7 +27,7 @@ dependencies = [ ('ASE', '3.18.0', versionsuffix), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb index c06fe0fe7ca..3158794bf1a 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('Python', '3.6.6'), ('ASE', local_aseversion, local_pythonsuffix), ('libxc', '3.0.1'), # Old version to maintain consistency with AtomPAW and ABINIT. - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb index 337d63d58b0..b6da87b17cc 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb @@ -26,7 +26,7 @@ dependencies = [ ('SciPy-bundle', '2019.03'), ('ASE', '3.18.0', versionsuffix), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb index 06c705f51cb..67b6ba7a5f0 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb @@ -32,7 +32,7 @@ dependencies = [ ('ASE', '3.19.0', versionsuffix), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb index fc6b25cdb3d..e2df43f33a3 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb @@ -32,7 +32,7 @@ dependencies = [ ('SciPy-bundle', '2019.10', versionsuffix), ('ASE', '3.19.0', versionsuffix), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb index 31e4e602dc0..3226c8a9aca 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2019b-ASE-3.20.1-Python-3.7.4.eb @@ -34,7 +34,7 @@ dependencies = [ ('ASE', _aseversion, _pythonsuffix), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb index 1b322074614..6758eb60891 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-foss-2020b.eb @@ -29,7 +29,7 @@ dependencies = [ ('ASE', '3.20.1'), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb index 7535f24c1a0..d19ddaf4ded 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2019b-ASE-3.20.1-Python-3.7.4.eb @@ -33,7 +33,7 @@ dependencies = [ ('SciPy-bundle', '2019.10', _pythonsuffix), ('ASE', _aseversion, _pythonsuffix), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb index 861a80e2fd1..0714f4060f1 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.10.0-intel-2020b.eb @@ -29,7 +29,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('ASE', '3.20.1'), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb index 7a2e4989e8a..7c888723000 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-foss-2020b-ASE-3.21.1.eb @@ -29,7 +29,7 @@ dependencies = [ ('ASE', _aseversion), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb index 1f22f89cc83..978ddc9ef57 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.1.0-intel-2020b-ASE-3.21.1.eb @@ -28,7 +28,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('ASE', _aseversion), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb index 582e90ea73b..465fd9c9b07 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2020b-ASE-3.22.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('ASE', _aseversion), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb index 4abf305f2a6..2abce4c3ad2 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-foss-2021a.eb @@ -28,7 +28,7 @@ dependencies = [ ('ASE', '3.22.0'), ('libxc', '5.1.5'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb index bba61ad1209..56885619470 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-21.6.0-intel-2020b-ASE-3.22.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('SciPy-bundle', '2020.11'), ('ASE', _aseversion), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb index e3d8e921b48..cc8928a6e81 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2021b.eb @@ -31,7 +31,7 @@ dependencies = [ ('libxc', '5.1.6'), ('PyYAML', '5.4.1'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb index b400a2bd2c3..a5bf81c6abc 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb @@ -31,7 +31,7 @@ dependencies = [ ('libxc', '5.2.3'), ('libvdwxc', '0.4.0'), ('PyYAML', '6.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb index 1ca56803196..343180bbb51 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2021b.eb @@ -30,7 +30,7 @@ dependencies = [ ('ASE', '3.22.1'), ('libxc', '5.1.6'), ('PyYAML', '5.4.1'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb index 58087303e00..126147e70d5 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb @@ -30,7 +30,7 @@ dependencies = [ ('ASE', '3.22.1'), ('libxc', '5.2.3'), ('PyYAML', '6.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' diff --git a/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb b/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb index 633322c56c4..a8e13772a67 100644 --- a/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb @@ -16,7 +16,7 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ builddependencies = [('sbt', '1.0.2', versionsuffix, True)] dependencies = [ - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ('XGBoost', '20171120', versionsuffix), ('Spark', '2.2.0', '-Hadoop-2.6' + versionsuffix, True), ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb index aa8b7a249fd..60b10be1daf 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1-PLUMED-2.7.2.eb @@ -69,7 +69,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('networkx', '2.5.1'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('PLUMED', _plumedver), ('UCX-CUDA', '1.10.0', _cuda_suffix), ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb index a3519c9ca33..88ab48e3311 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.3-foss-2021a-CUDA-11.3.1.eb @@ -65,7 +65,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('networkx', '2.5.1'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb index bbe65cdd01e..f54123b4866 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0.eb @@ -74,7 +74,7 @@ dependencies = [ ('SciPy-bundle', '2021.10'), ('networkx', '2.6.3'), ('PLUMED', _plumedver), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', _cuda_suffix), ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb index 3226925397d..2ae42d897ca 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2021.5-foss-2021b-CUDA-11.4.1.eb @@ -66,7 +66,7 @@ dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), ('networkx', '2.6.3'), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb index 083ad67f279..b3f086375fe 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2016a.eb @@ -19,7 +19,7 @@ dependencies = [('GStreamer', '0.10.36')] # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb index 74bd62f7515..b77d7997cff 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-foss-2018b.eb @@ -21,7 +21,7 @@ dependencies = [ # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb index 23b2a931e08..7c60f600376 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016a.eb @@ -19,7 +19,7 @@ dependencies = [('GStreamer', '0.10.36')] # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb index 60907564e6e..37624651adc 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2016b.eb @@ -19,7 +19,7 @@ dependencies = [('GStreamer', '0.10.36')] # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb index 858a8095477..d7288a32aba 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-0.10.36-intel-2017a.eb @@ -19,7 +19,7 @@ dependencies = [('GStreamer', '0.10.36')] # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb index 663148178bc..69edf4e5879 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb @@ -18,7 +18,7 @@ checksums = ['7a193e2a66b0d7411160ef2a373184c8aa3cdeaa576fa270be346716220d9606'] dependencies = [('GStreamer', '1.6.4')] builddependencies = [ - ('Bison', '3.0.4', '', True), + ('Bison', '3.0.4', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb index 0c4cb354f0c..178b50575df 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.8.3-foss-2016a.eb @@ -23,7 +23,7 @@ dependencies = [ builddependencies = [ ('Autotools', '20150215'), ('pkg-config', '0.29.1'), - ('Bison', '3.0.4', '', True), + ('Bison', '3.0.4', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb index 31e79963a2f..c3a7851b678 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2016a.eb @@ -23,7 +23,7 @@ dependencies = [ # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb index 941ced47c5b..dd3738d82c9 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-foss-2018b.eb @@ -23,8 +23,8 @@ dependencies = [ # does not work with Bison 3.x builddependencies = [ - ('flex', '2.6.4', '', True), - ('Bison', '2.7', '', True), + ('flex', '2.6.4', '', SYSTEM), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb index 49d0445dfd4..fd95931f5df 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016a.eb @@ -23,7 +23,7 @@ dependencies = [ # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb index df0cc749083..d24fcda642a 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-0.10.36-intel-2016b.eb @@ -23,7 +23,7 @@ dependencies = [ # does not work with Bison 3.x builddependencies = [ - ('Bison', '2.7', '', True), + ('Bison', '2.7', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb index 0fd9f637575..c7044fe5592 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ ] builddependencies = [ - ('Bison', '3.0.4', '', True), + ('Bison', '3.0.4', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb index c6e3c5bf573..f73039f0fbb 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb @@ -15,7 +15,7 @@ dependencies = [ ('matplotlib', '2.2.3', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.1'), ('FastTree', '2.1.10'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb index 96d22c898b8..baa0455e8d4 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb @@ -19,7 +19,7 @@ dependencies = [ ('matplotlib', '2.2.4', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.2'), ('FastTree', '2.1.11'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb index 89a5cfe9651..234c38d3b4a 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb @@ -19,7 +19,7 @@ dependencies = [ ('matplotlib', '2.2.4', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.2'), ('FastTree', '2.1.11'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.0.2-intel-2019b-Python-3.7.4.eb index a3ec2738504..c35fe8da4a6 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.0.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.0.2-intel-2019b-Python-3.7.4.eb @@ -23,7 +23,7 @@ dependencies = [ ('matplotlib', '3.1.1', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.3'), ('FastTree', '2.1.11'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb index 54dc20a75fc..13e7349e42f 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb @@ -23,7 +23,7 @@ dependencies = [ ('matplotlib', '3.2.1', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.3.1'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.31'), ('FastTree', '2.1.11'), ('tqdm', '4.47.0'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb index 0ff0be7b625..5f2ae473469 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.5.0-intel-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.56.2'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb index d0bc5d3e526..d40e1ff699c 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.56.2'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb index 05e89644664..8022a696c23 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-foss-2021a.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.4.2'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.61.2'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb index 2e0232fed40..4d81bd500b9 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.7.0-intel-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.56.2'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb index 3d85efa5db7..741d72ebed0 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-foss-2021a.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.4.2'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('Mash', '2.3'), diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb index f1bc9b730fe..d7ed1a25516 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.0.0-intel-2021b.eb @@ -22,7 +22,7 @@ dependencies = [ ('matplotlib', '3.4.3'), ('prodigal', '2.6.3'), ('HMMER', '3.3.2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('FastANI', '1.33'), ('FastTree', '2.1.11'), ('tqdm', '4.62.3'), diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.2-foss-2020a-Python-3.8.2.eb index 1e00e8c37de..112304a7a38 100644 --- a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.2-foss-2020a-Python-3.8.2.eb @@ -15,7 +15,7 @@ checksums = ['54923ca971d68620aaf036a324b554084b00f7c209b0b3a234f815c82ee6d079'] dependencies = [ ('Python', '3.8.2'), - ('Bandage', '0.8.1', '_Centos', True), + ('Bandage', '0.8.1', '_Centos', SYSTEM), ('SciPy-bundle', '2020.03', versionsuffix), ('sympy', '1.6.2', versionsuffix), ('SPAdes', '3.14.1', versionsuffix), diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb index 095a77b88cf..2eabe89e524 100644 --- a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.4-pre2-foss-2020b.eb @@ -15,7 +15,7 @@ checksums = ['ee3dc807e0fb59c1788717a155238115d7a860191f686ef2c5a5b685aa2a2948'] dependencies = [ ('Python', '3.8.6'), - ('Bandage', '0.8.1', '_Centos', True), + ('Bandage', '0.8.1', '_Centos', SYSTEM), ('SciPy-bundle', '2020.11'), ('sympy', '1.7.1'), ('SPAdes', '3.15.2'), diff --git a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb index b8e860947db..65e2cb11638 100644 --- a/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/Globus-CLI/Globus-CLI-3.1.1-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb index efe696b4984..da1e8ab0a6a 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.12.1-GCCcore-7.3.0.eb @@ -17,7 +17,7 @@ checksums = ['0be127684df4b842a64e58093154f9d15422f1405f1fcff4b2c36ffc6a15818a'] builddependencies = [ ('binutils', '2.30'), # go requires Go to install from source, see https://golang.org/doc/install/source - ('Go', '1.12', '', True), + ('Go', '1.12', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb index ef9c393d1a7..5584942b29c 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb @@ -21,7 +21,7 @@ dependencies = [ ('freetype', '2.6.5'), ('Ghostscript', '9.20'), ('GTS', '0.7.6'), - ('Java', '1.8.0_92', '', True), + ('Java', '1.8.0_92', '', SYSTEM), ('libpng', '1.6.24'), ('Pango', '1.40.3'), ('Perl', '5.24.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb index 50d0e0b4494..2a678bb2b9e 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb @@ -21,7 +21,7 @@ dependencies = [ ('freetype', '2.6.5'), ('Ghostscript', '9.20'), ('GTS', '0.7.6'), - ('Java', '1.8.0_92', '', True), + ('Java', '1.8.0_92', '', SYSTEM), ('libpng', '1.6.24'), ('Pango', '1.40.3'), ('Perl', '5.24.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb index 3393732425c..062902b979a 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b-Python-2.7.15.eb @@ -54,7 +54,7 @@ dependencies = [ ('Gdk-Pixbuf', '2.36.12'), ('Ghostscript', '9.23'), ('GTS', '0.7.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('libgd', '2.2.5'), ('Pango', '1.42.4'), ('Perl', '5.28.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb index dad37c034a9..15a13ec7078 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-foss-2018b.eb @@ -51,7 +51,7 @@ dependencies = [ ('Gdk-Pixbuf', '2.36.12'), ('Ghostscript', '9.23'), ('GTS', '0.7.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('libgd', '2.2.5'), ('Pango', '1.42.4'), ('Perl', '5.28.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb index ae0ee795432..604d4417f17 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.40.1-intel-2018a.eb @@ -41,7 +41,7 @@ dependencies = [ ('freetype', '2.9'), ('Ghostscript', '9.22', '-cairo-1.14.12'), ('GTS', '0.7.6'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('libpng', '1.6.34'), ('Pango', '1.41.1'), ('Perl', '5.26.1'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-GCCcore-8.3.0-Java-11.eb index bc1b89f5f65..7ac2a75670e 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-GCCcore-8.3.0-Java-11.eb @@ -40,7 +40,7 @@ dependencies = [ ('Gdk-Pixbuf', '2.38.2'), ('Ghostscript', '9.50'), ('GTS', '0.7.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('libgd', '2.2.5'), ('Pango', '1.44.7'), ('Perl', '5.30.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb index 1ca2e2d4744..26ac994d037 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b-Python-3.7.4.eb @@ -44,7 +44,7 @@ dependencies = [ ('Gdk-Pixbuf', '2.38.2'), ('Ghostscript', '9.50'), ('GTS', '0.7.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('libgd', '2.2.5'), ('Pango', '1.44.7'), ('Perl', '5.30.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb index def5b531355..bd1974fc84c 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.42.2-foss-2019b.eb @@ -38,7 +38,7 @@ dependencies = [ ('Gdk-Pixbuf', '2.38.2'), ('Ghostscript', '9.50'), ('GTS', '0.7.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('libgd', '2.2.5'), ('Pango', '1.44.7'), ('Perl', '5.30.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11-Python-3.8.2.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11-Python-3.8.2.eb index ac21ce695d2..f19b861f72c 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11-Python-3.8.2.eb @@ -33,7 +33,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.8.2'), ('FriBidi', '1.0.9'), ('Gdk-Pixbuf', '2.40.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11.eb index 5d7b20ee277..e532aad271a 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.44.1-GCCcore-9.3.0-Java-11.eb @@ -32,7 +32,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('FriBidi', '1.0.9'), ('Gdk-Pixbuf', '2.40.0'), ('Ghostscript', '9.52'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb index fe7ec68c3fe..740e71bf496 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.0-GCCcore-10.2.0-Java-11.eb @@ -33,7 +33,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.8.6'), ('FriBidi', '1.0.10'), ('Gdk-Pixbuf', '2.40.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.2-GCCcore-10.3.0.eb index 82bbddffe8d..efaf644fa43 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.47.2-GCCcore-10.3.0.eb @@ -32,7 +32,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.5'), ('FriBidi', '1.0.10'), ('Gdk-Pixbuf', '2.42.6'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb index f2fff0736b3..e96a04c6708 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.50.0-GCCcore-11.2.0.eb @@ -32,7 +32,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.6'), ('FriBidi', '1.0.10'), ('Gdk-Pixbuf', '2.42.6'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb index 574ffbd5cd3..a2f44ff0ff8 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb @@ -32,7 +32,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.10.4'), ('FriBidi', '1.0.12'), ('Gdk-Pixbuf', '2.42.8'), diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb index 4f4fa3e2f0c..35dbf494bc9 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = " --enable-error-on-warning=no" diff --git a/easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb index 7c7a4e106cf..a7c26ea7739 100644 --- a/easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/gRPC/gRPC-1.44.0-GCCcore-11.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('Abseil', '20210324.2'), ('c-ares', '1.18.1'), ('protobuf', '3.17.3'), diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb index 4a9705e7ef7..7bbdba6432e 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-5.4.0.eb @@ -24,7 +24,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb index 691a5661ac0..7acb30d5912 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8.1-GCCcore-6.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' diff --git a/easybuild/easyconfigs/g/gifsicle/gifsicle-1.92-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/gifsicle/gifsicle-1.92-GCCcore-8.2.0.eb index ec28d95cf35..a56f14839cf 100644 --- a/easybuild/easyconfigs/g/gifsicle/gifsicle-1.92-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/gifsicle/gifsicle-1.92-GCCcore-8.2.0.eb @@ -18,7 +18,7 @@ checksums = ['f8a944f47faa9323bcc72c6e2239e0608bf30693894aee61512aba107a4c6b55'] toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] configure_cmd = "./bootstrap.sh && ./configure" diff --git a/easybuild/easyconfigs/g/git/git-2.32.0-GCCcore-10.3.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.32.0-GCCcore-10.3.0-nodocs.eb index 5559af9962b..6a9f8e88f5b 100644 --- a/easybuild/easyconfigs/g/git/git-2.32.0-GCCcore-10.3.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.32.0-GCCcore-10.3.0-nodocs.eb @@ -27,7 +27,7 @@ dependencies = [ ('expat', '2.2.9'), ('gettext', '0.21'), ('Perl', '5.32.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] preconfigopts = 'make configure && ' diff --git a/easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb index ed7c62fbd3b..08aff1076cb 100644 --- a/easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.33.1-GCCcore-11.2.0-nodocs.eb @@ -30,7 +30,7 @@ dependencies = [ ('expat', '2.4.1'), ('gettext', '0.21'), ('Perl', '5.34.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] preconfigopts = 'make configure && ' diff --git a/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb index b4bb0d64474..214a4cc7228 100644 --- a/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb @@ -30,7 +30,7 @@ dependencies = [ ('expat', '2.4.8'), ('gettext', '0.21'), ('Perl', '5.34.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] preconfigopts = 'make configure && ' diff --git a/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb b/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb index 3bd71c3f03d..c209965f2eb 100644 --- a/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb +++ b/easybuild/easyconfigs/g/gubbins/gubbins-2.4.0.eb @@ -30,7 +30,7 @@ channels = ['r', 'conda-forge', 'bioconda'] requirements = '%(namelower)s=%(version)s python=3.6' dependencies = [ - ('Miniconda3', '4.7.10', '', True) + ('Miniconda3', '4.7.10', '', SYSTEM) ] sanity_check_commands = [('gubbins', '-h')] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb index cb15f9404ed..795f421b233 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-10.2.0-native-Java-1.8.eb @@ -29,7 +29,7 @@ checksums = [ builddependencies = [ ('binutils', '2.35'), - ('Maven', '3.6.3', '', True), + ('Maven', '3.6.3', '', SYSTEM), ('protobuf', '2.5.0'), # *must* be this version - https://issues.apache.org/jira/browse/HADOOP-13363 ('CMake', '3.18.4'), ('snappy', '1.1.8'), @@ -39,7 +39,7 @@ builddependencies = [ # https://cwiki.apache.org/confluence/display/HADOOP/Hadoop+Java+Versions dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('libtirpc', '1.3.1'), ] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb index c1fa9fa3cdc..039bc9f1132 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb @@ -29,7 +29,7 @@ checksums = [ builddependencies = [ ('binutils', '2.32'), - ('Maven', '3.6.3', '', True), + ('Maven', '3.6.3', '', SYSTEM), ('protobuf', '2.5.0'), # *must* be this version - https://issues.apache.org/jira/browse/HADOOP-13363 ('CMake', '3.15.3'), ('snappy', '1.1.7'), @@ -39,7 +39,7 @@ builddependencies = [ # https://cwiki.apache.org/confluence/display/HADOOP/Hadoop+Java+Versions dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('libtirpc', '1.2.6'), ] diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb index 1e22b4574c8..22aad2469d9 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.9.2-GCCcore-7.3.0-native.eb @@ -24,7 +24,7 @@ checksums = [ builddependencies = [ ('binutils', '2.30'), - ('Maven', '3.6.0', '', True), + ('Maven', '3.6.0', '', SYSTEM), ('protobuf', '2.5.0'), # *must* be this version ('CMake', '3.12.1'), ('snappy', '1.1.7'), @@ -32,7 +32,7 @@ builddependencies = [ ('bzip2', '1.0.6'), ] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] build_native_libs = True diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb index 4ad47ea0521..6933ece700e 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb @@ -16,7 +16,7 @@ builddependencies = [ ('flatbuffers', '2.0.0'), ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('UCX-CUDA', '1.10.0', local_cuda_suffix), ('NCCL', '2.10.3', local_cuda_suffix), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb index 1a551228e8f..ff4cb82b3f6 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb @@ -18,7 +18,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), ('PyYAML', '5.4.1'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('NCCL', '2.10.3', local_cuda_suffix), ('PyTorch', local_pt_version, local_cuda_suffix), ] diff --git a/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb index 08c0a3b716c..0bb49bddc8e 100644 --- a/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/Hydra/Hydra-1.1.1-GCCcore-10.3.0.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} builddependencies = [ ('binutils', '2.36.1'), - ('Java', '11', '', True), # needed by ANTLR runtime + ('Java', '11', '', SYSTEM), # needed by ANTLR runtime ] dependencies = [ diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb index 2c4fe36c213..594056facd2 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.1.0.eb @@ -14,7 +14,7 @@ checksums = ['f371cbfd63f879065422b58fa6b81e21870cd791ef6e11d4528608204aa4dcfb'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.2.0.eb index b2566498fcf..4aa3a420ef1 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.10-GCCcore-9.2.0.eb @@ -14,7 +14,7 @@ checksums = ['f371cbfd63f879065422b58fa6b81e21870cd791ef6e11d4528608204aa4dcfb'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.12-GCCcore-9.3.0.eb index 10eb7812dcd..77bffeabf8a 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.12-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.12-GCCcore-9.3.0.eb @@ -14,7 +14,7 @@ checksums = ['7d0ba64cf9d16ec97cc11aafb659b55aa7bdec99072ff2aec5fcecf0fbeab160'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb index 2d8893f9c12..113edba6b65 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.15-GCCcore-10.1.0.eb @@ -14,7 +14,7 @@ checksums = ['c25a35b30eceb315361484b0ff1f81c924e8ee5c8881576f1ee762f001dbcd1c'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.34', '', True), + ('binutils', '2.34', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb index 16eb74c38c5..48daa7126a1 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.16-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ checksums = ['3ef8580c5b86e32ca092ce8de43df204f5e6f714b0cd32bc6237e6cd0f34a8f4'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.35', '', True), + ('binutils', '2.35', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb index 0d730043fba..1257db05441 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb index 4931b9f6ce3..3ff4d3ef78f 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb index c354ad33693..c1f8fcc9061 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.4.0.eb @@ -18,7 +18,7 @@ checksums = ['d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb index f487ba55300..402e97d506e 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb index 63e4b751a13..ab49db02c27 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.2.0.eb @@ -14,7 +14,7 @@ checksums = ['d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.29', '', True), + ('binutils', '2.29', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.3.0.eb index 50e6f6e2199..d125e15db98 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.3.0.eb @@ -14,7 +14,7 @@ checksums = ['d4ecf697d13f14dd1a78c5995f06459bff706fd1ce593d1c02d81667c0207753'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.5-GCCcore-5.5.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.5-GCCcore-5.5.0.eb index 54568207731..c429f8c03fd 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.5-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.5-GCCcore-5.5.0.eb @@ -14,7 +14,7 @@ checksums = ['7ca60b2519fdbe97f463fe2df66a6188d18b514bfd44127d985f0234ee2461b1'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.6-GCCcore-8.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.6-GCCcore-8.1.0.eb index a6acf99d4a7..8a4a5572203 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.6-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.6-GCCcore-8.1.0.eb @@ -14,7 +14,7 @@ checksums = ['d91b0295b72a638e4a564f643e4e6d1928779131f628c00f356c13bf336de46f'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.30', '', True), + ('binutils', '2.30', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.7-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.7-GCCcore-8.2.0.eb index 3de5a41822f..81085956428 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.7-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.7-GCCcore-8.2.0.eb @@ -14,7 +14,7 @@ checksums = ['585b8e88ed04bdb426403cf7d9b0c0bb9c7630755b0096c2b018a024b29bec0d'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-7.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-7.4.0.eb index d2c9f0677aa..d71469d2a1a 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-7.4.0.eb @@ -14,7 +14,7 @@ checksums = ['528f6a81ad34cbc76aa7dce5a82f8b3d2078ef065271ab81fda033842018a8dc'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb index 21de8022b13..2c4f4f0dbdb 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.3.0.eb @@ -14,7 +14,7 @@ checksums = ['528f6a81ad34cbc76aa7dce5a82f8b3d2078ef065271ab81fda033842018a8dc'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.4.0.eb index 08d063f0300..6d131fe3331 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.8-GCCcore-8.4.0.eb @@ -14,7 +14,7 @@ checksums = ['528f6a81ad34cbc76aa7dce5a82f8b3d2078ef065271ab81fda033842018a8dc'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.32', '', True), + ('binutils', '2.32', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-10.3.0.eb index 8697c849e41..2253777a680 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-10.3.0.eb @@ -14,7 +14,7 @@ checksums = ['8361ff3c643fbd391064e97e5f54592ca28b880eaffbf566a68e0ad800d1a8ac'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.1.0.eb index c5323938915..7b7405ce180 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.1.0.eb @@ -14,7 +14,7 @@ checksums = ['8361ff3c643fbd391064e97e5f54592ca28b880eaffbf566a68e0ad800d1a8ac'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb index dd03b0d33f5..ea6ea4b507b 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ checksums = ['8361ff3c643fbd391064e97e5f54592ca28b880eaffbf566a68e0ad800d1a8ac'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.37', '', True), + ('binutils', '2.37', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-9.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-9.4.0.eb index a3563b02d50..2e1ff3703b1 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.48.3-GCCcore-9.4.0.eb @@ -14,7 +14,7 @@ checksums = ['8361ff3c643fbd391064e97e5f54592ca28b880eaffbf566a68e0ad800d1a8ac'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.3.0.eb index 26957da215e..d434ddefe0d 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-11.3.0.eb @@ -14,7 +14,7 @@ checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb index b76db7f347c..6c618e880ac 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.1.0.eb @@ -14,7 +14,7 @@ checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb index 712e28926d5..3fa0f481563 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-12.2.0.eb @@ -14,7 +14,7 @@ checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.39', '', True), + ('binutils', '2.39', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb index 19d7895e8f1..dbe1f931596 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.2-GCCcore-9.5.0.eb @@ -14,7 +14,7 @@ checksums = ['9e2e0e213a7e0a36244eed6204d902b6504602a578b6ecd15268b1454deadd36'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.38', '', True), + ('binutils', '2.38', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb index d06d9b20df6..ee5c6c8ec69 100644 --- a/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/h/hipify-clang/hipify-clang-4.2.0-gcccuda-2020b.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('Clang', '11.0.1'), - # ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', True), + # ('cuDNN', '8.0.4.30', '-CUDA-11.1.1', SYSTEM), # ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb index be49af696cf..28463835271 100644 --- a/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.0.2-GCCcore-11.2.0.eb @@ -28,7 +28,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb b/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb index 94664ec45e6..4e2be23df1d 100644 --- a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb +++ b/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb @@ -23,7 +23,7 @@ dependencies = [ ('SciPy-bundle', '2019.10', local_python_versionsuffix), # for numpy, scipy ('networkx', '2.4', local_python_versionsuffix), ('scikit-learn', '0.21.3', local_python_versionsuffix), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Spark', '2.4.5', versionsuffix), ] diff --git a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb b/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb index 4f7660f2938..8a744cd8d26 100644 --- a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb @@ -20,7 +20,7 @@ dependencies = [ ('networkx', '2.5'), ('scikit-learn', '0.23.2'), ('tqdm', '4.56.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Spark', '3.1.1'), ] diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb index 0005d342b59..7e992b8bba5 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.12.3-Java-11.eb @@ -22,7 +22,7 @@ source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_ sources = ['%(name)s_%(version)s.zip'] checksums = ['c87a109deb35994e1b28dee80b5acfd623ec3257f031fcd9cfce008cd32a4cf2'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] sanity_check_paths = { 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb index 175e1547ee9..1716dc4a133 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.5.0-Java-11.eb @@ -22,7 +22,7 @@ source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_ sources = ['%(name)s_%(version)s.zip'] checksums = ['44efdd0500dd6ace8e1c70dad0d758d9ab90492b391d2af4a416f03808fee471'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] sanity_check_paths = { 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.8.0-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.8.0-Java-11.eb index 870e1a93e0d..9369fb4f3ad 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.8.0-Java-11.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.8.0-Java-11.eb @@ -22,7 +22,7 @@ source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_ sources = ['%(name)s_%(version)s.zip'] checksums = ['33f3ac57017907b931f90c35b63b2de2e4f8d2452f0fbb5be39d30288fc9b2c6'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] sanity_check_paths = { 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.9.4-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.9.4-Java-11.eb index 3e9176b8a21..f257993866e 100644 --- a/easybuild/easyconfigs/i/IGV/IGV-2.9.4-Java-11.eb +++ b/easybuild/easyconfigs/i/IGV/IGV-2.9.4-Java-11.eb @@ -22,7 +22,7 @@ source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_ sources = ['%(name)s_%(version)s.zip'] checksums = ['05717ec6d0386a5eafe93c8b1af371c0013355eae74312b78eae5fdd99fc5fc1'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] sanity_check_paths = { 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb index fa2d35b964b..d3a1580f52b 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-foss-2020b.eb @@ -34,7 +34,7 @@ checksums = [ dependencies = [ ('LibTIFF', '4.1.0'), ('Qt5', '5.14.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('HDF5', '1.10.7'), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb index d2bc021cbb9..1f1c6e82c8a 100644 --- a/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb @@ -37,7 +37,7 @@ checksums = [ dependencies = [ ('LibTIFF', '4.1.0'), ('Qt5', '5.14.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('HDF5', '1.10.7'), ('Python', '3.8.6'), ] diff --git a/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb index abf9e6ec074..78711215507 100644 --- a/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/i/INTEGRATE-Neo/INTEGRATE-Neo-1.2.1-foss-2018b-Python-3.6.6.eb @@ -22,7 +22,7 @@ dependencies = [ ('Python', '3.6.6'), ('BWA', '0.7.17'), ('HLAminer', '1.4', '-Perl-5.28.0'), - ('netMHC', '4.0a', '', True), + ('netMHC', '4.0a', '', SYSTEM), ] start_dir = '%(name)s-V-%(version)s' diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb index aec8a7ac610..ad5e295f908 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb @@ -17,7 +17,7 @@ checksums = ['9614092de7a157de82c9cc402b19cc8bfa0cb0ffc93b91817875c2b4bb46a284'] builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [('zlib', '1.2.11')] diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-intel-2019b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-intel-2019b.eb index a27292fd82e..cb0a9baa6c5 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-intel-2019b.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-intel-2019b.eb @@ -16,7 +16,7 @@ checksums = ['9614092de7a157de82c9cc402b19cc8bfa0cb0ffc93b91817875c2b4bb46a284'] builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [('zlib', '1.2.11')] diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.6-intel-2018a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.6-intel-2018a.eb index 66ddae35864..a3b9c543ee0 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.6-intel-2018a.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.6-intel-2018a.eb @@ -16,7 +16,7 @@ checksums = ['31bc44e3a79edb889f3e2ed396d1492b8e38d93437b2ae64deb452867929dc56'] builddependencies = [ ('CMake', '3.10.2'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] dependencies = [('zlib', '1.2.11')] diff --git a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb index 8108fd7121c..4d7e044fc45 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-4.13.1-foss-2019b-Python-3.7.4.eb @@ -24,7 +24,7 @@ checksums = ['b352060d8b7289916a3cb033dfdbcf423423ba474643b79706966e679268e3d7'] builddependencies = [ ('CMake', '3.15.3'), ('Bison', '3.3.2'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb index 62e178a70de..a435dbd1e32 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019a-Python-3.7.2.eb @@ -30,7 +30,7 @@ checksums = ['c6b3c33ecc73104c906e0e1a1bfaa41a09af24bf53a4ec5e5c265d7e82bdf69f'] builddependencies = [ ('CMake', '3.13.3'), ('Bison', '3.0.5'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb index 091109392a2..63a9196709b 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.0.1-foss-2019b-Python-3.7.4.eb @@ -30,7 +30,7 @@ checksums = ['c6b3c33ecc73104c906e0e1a1bfaa41a09af24bf53a4ec5e5c265d7e82bdf69f'] builddependencies = [ ('CMake', '3.15.3'), ('Bison', '3.3.2'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb index 7d9f547d493..ac587d50840 100644 --- a/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb +++ b/easybuild/easyconfigs/i/ImageJ/ImageJ-1.51a.eb @@ -16,7 +16,7 @@ sources = ['ij%(version_major)s%(version_minor)s-src.zip'] checksums = ['1fe77bedd792f095bc51d7b12083319b04124bb82f2dc5eb0552089880cf1a4f'] # specify dependency on Java/1.8 "wrapper", rather than a specific Java version -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] builddependencies = [('ant', '1.10.1', '-Java-%(javaver)s')] diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.26-65.0-intel-2017b.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.26-65.0-intel-2017b.eb index 76b2b69e139..03a9b9f0119 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.26-65.0-intel-2017b.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.26-65.0-intel-2017b.eb @@ -26,7 +26,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ('Perl', '5.26.0'), ('libgd', '2.2.5'), ('Python', '2.7.14'), diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.27-66.0-intel-2017b.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.27-66.0-intel-2017b.eb index 1542ef84a85..bb69e1b65bb 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.27-66.0-intel-2017b.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.27-66.0-intel-2017b.eb @@ -26,7 +26,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ('Perl', '5.26.0'), ('libgd', '2.2.5'), ('Python', '2.7.14'), diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.28-67.0-intel-2018a.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.28-67.0-intel-2018a.eb index c82158bd56c..129c5160aa2 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.28-67.0-intel-2018a.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.28-67.0-intel-2018a.eb @@ -26,7 +26,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('Perl', '5.26.1'), ('libgd', '2.2.5'), ('Python', '2.7.14'), diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb index b3d5765b73d..fdfeaac821f 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.52-86.0-GCCcore-10.3.0.eb @@ -18,7 +18,7 @@ sources = ['%(namelower)s-%(version)s-64-bit.tar.gz'] checksums = ['50a03c47fb16c669c265e99ba05c4a8558b82047f713c9945f362d3d4be6069a'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.32.1'), ('libgd', '2.3.1'), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb index 3107c097d4a..d4535511479 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb @@ -23,7 +23,7 @@ checksums = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Perl', '5.32.1'), ('libgd', '2.3.1'), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb b/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb index 95b0d643515..90f8eac533d 100644 --- a/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb +++ b/easybuild/easyconfigs/i/Iris/Iris-1.0.5-GCC-11.2.0-Java-15.eb @@ -15,7 +15,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['a71718d418fb8b1afacbe2b3a6b91fd50cadc9e12c0b532739b955e455913b0b'] dependencies = [ - ('Java', '15', '', True), + ('Java', '15', '', SYSTEM), ('minimap2', '2.22'), ('HTSlib', '1.14'), ('SAMtools', '1.14'), diff --git a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb index 56433fb0b9c..1cdc59d3ecd 100644 --- a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb @@ -34,7 +34,7 @@ dependencies = [ ('ImageMagick', '6.9.4-8'), ('STAMP', '1.3'), ('Cluster-Buster', '20160106'), - ('Kent_tools', '20130806', '-linux.x86_64', True), + ('Kent_tools', '20130806', '-linux.x86_64', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021b.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021b.eb index 8a42ae8abf5..03a7f2798db 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-gompi-2021b.eb @@ -6,6 +6,6 @@ description = "FFTW interfaces using Intel oneAPI Math Kernel Library" toolchain = {'name': 'gompi', 'version': '2021b'} -dependencies = [('imkl', version, '', True)] +dependencies = [('imkl', version, '', SYSTEM)] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021b.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021b.eb index e1f4249fb2b..e411b2b3923 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021b.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2021.4.0-iimpi-2021b.eb @@ -6,6 +6,6 @@ description = "FFTW interfaces using Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2021b'} -dependencies = [('imkl', version, '', True)] +dependencies = [('imkl', version, '', SYSTEM)] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb index 2eaf7432065..07d65f3a80f 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.0.1-iimpi-2022.00.eb @@ -6,6 +6,6 @@ description = "FFTW interfaces using Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2022.00'} -dependencies = [('imkl', version, '', True)] +dependencies = [('imkl', version, '', SYSTEM)] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb index 1d2d73b038e..203a8e9f0ef 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022.05.eb @@ -6,6 +6,6 @@ description = "FFTW interfaces using Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2022.05'} -dependencies = [('imkl', version, '', True)] +dependencies = [('imkl', version, '', SYSTEM)] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb index d81a631f10f..a18ad2d9d36 100644 --- a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.1.0-iimpi-2022a.eb @@ -6,6 +6,6 @@ description = "FFTW interfaces using Intel oneAPI Math Kernel Library" toolchain = {'name': 'iimpi', 'version': '2022a'} -dependencies = [('imkl', version, '', True)] +dependencies = [('imkl', version, '', SYSTEM)] moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/intel/intel-2021b.eb b/easybuild/easyconfigs/i/intel/intel-2021b.eb index 68916794a30..8d5b83ca141 100644 --- a/easybuild/easyconfigs/i/intel/intel-2021b.eb +++ b/easybuild/easyconfigs/i/intel/intel-2021b.eb @@ -15,7 +15,7 @@ dependencies = [ ('binutils', '2.37', '', ('GCCcore', local_gccver)), ('intel-compilers', local_comp_ver), ('impi', local_comp_ver, '', ('intel-compilers', local_comp_ver)), - ('imkl', local_comp_ver, '', True), + ('imkl', local_comp_ver, '', SYSTEM), ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), ] diff --git a/easybuild/easyconfigs/i/intel/intel-2022.00.eb b/easybuild/easyconfigs/i/intel/intel-2022.00.eb index 756e76c67c6..d4c1c743073 100644 --- a/easybuild/easyconfigs/i/intel/intel-2022.00.eb +++ b/easybuild/easyconfigs/i/intel/intel-2022.00.eb @@ -15,7 +15,7 @@ dependencies = [ ('binutils', '2.37', '', ('GCCcore', local_gccver)), ('intel-compilers', local_comp_ver), ('impi', '2021.5.0', '', ('intel-compilers', local_comp_ver)), - ('imkl', local_comp_ver, '', True), + ('imkl', local_comp_ver, '', SYSTEM), ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), ] diff --git a/easybuild/easyconfigs/i/intel/intel-2022.05.eb b/easybuild/easyconfigs/i/intel/intel-2022.05.eb index b78b8a46bb5..1dd52139097 100644 --- a/easybuild/easyconfigs/i/intel/intel-2022.05.eb +++ b/easybuild/easyconfigs/i/intel/intel-2022.05.eb @@ -15,7 +15,7 @@ dependencies = [ ('binutils', '2.38', '', ('GCCcore', local_gccver)), ('intel-compilers', local_comp_ver), ('impi', '2021.6.0', '', ('intel-compilers', local_comp_ver)), - ('imkl', local_comp_ver, '', True), + ('imkl', local_comp_ver, '', SYSTEM), ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), ] diff --git a/easybuild/easyconfigs/i/intel/intel-2022a.eb b/easybuild/easyconfigs/i/intel/intel-2022a.eb index b9eb05d6541..59f22dc713b 100644 --- a/easybuild/easyconfigs/i/intel/intel-2022a.eb +++ b/easybuild/easyconfigs/i/intel/intel-2022a.eb @@ -15,7 +15,7 @@ dependencies = [ ('binutils', '2.38', '', ('GCCcore', local_gccver)), ('intel-compilers', local_comp_ver), ('impi', '2021.6.0', '', ('intel-compilers', local_comp_ver)), - ('imkl', local_comp_ver, '', True), + ('imkl', local_comp_ver, '', SYSTEM), ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), ] diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb index d773a1008c5..9c828ff708b 100644 --- a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.eb @@ -17,7 +17,7 @@ sources = ['%(namelower)s-%(version)s.jar'] checksums = ['59721f0805e223d84b90677887d9ff567dc534d7c502ca903c0c2b17f05c116a'] # specify dependency on Java/1.8 "wrapper", rather than a specific Java version -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': sources, diff --git a/easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb b/easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb index 811d9481443..781822576b5 100644 --- a/easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb +++ b/easybuild/easyconfigs/j/Jasmine/Jasmine-1.1.4-GCC-11.2.0-Java-15.eb @@ -15,7 +15,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['b52e13964b41f7659368965cd9e0537b151a6b52cf41dc8634ba67b1384113ec'] dependencies = [ - ('Java', '15', '', True), + ('Java', '15', '', SYSTEM), ('Iris', '1.0.5', versionsuffix), ] diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb index 3457f1b8086..97b36ac60d2 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.4.1-GCCcore-10.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('IPython', '7.25.0'), ('Mako', '1.1.4'), ('configurable-http-proxy', '4.4.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb index f138187813d..039ed9bd0d2 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.19-fosscuda-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('flatbuffers-python', '1.12'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb index 770de325d37..d9c4a4c51a4 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb index a4992725207..387bbe5cc6c 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('cuDNN', '8.4.1.50', versionsuffix, True), ('NCCL', '2.12.12', versionsuffix), ('Python', '3.10.4'), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb index 20d0ce315f7..92459f0310c 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb index 6fbb4b351ab..46515f5f9c2 100644 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.1-GCCcore-10.3.0.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), ('JupyterHub', '1.4.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('aiohttp', '3.8.1'), ] diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb index e5ec4e0190e..23a32baffb9 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), ('util-linux', '2.36'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb index 6e386edc292..866d7dadb81 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.11'), ('util-linux', '2.37'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('freetype', '2.11.0'), ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb index 5649a33478f..bb60e5f730f 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb @@ -56,7 +56,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), ('kim-api', '2.1.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('yaff', '1.6.0', local_python_versionsuffix), ('PLUMED', '2.5.3', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index 722f37b89e8..a96f4e1bf04 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -60,7 +60,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), ('kim-api', '2.1.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('yaff', '1.6.0', local_python_versionsuffix), ('PLUMED', '2.5.3', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb index b380301035a..3b651f5bb18 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb @@ -56,7 +56,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), ('kim-api', '2.1.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('yaff', '1.6.0', local_python_versionsuffix), ('PLUMED', '2.5.3', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb index f8494e9734b..f6d6351c64b 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb @@ -63,7 +63,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), ('kim-api', '2.1.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('yaff', '1.6.0', local_python_versionsuffix), ('PLUMED', '2.5.3', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb index 35c2a48a208..23b825e617b 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb @@ -56,7 +56,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('Voro++', '0.4.6'), ('kim-api', '2.1.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('yaff', '1.6.0', local_python_versionsuffix), ('PLUMED', '2.5.3', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb index f509313572d..a022ed94c45 100644 --- a/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LDC/LDC-1.25.1-GCCcore-10.2.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('CMake', '3.18.4'), ('Ninja', '1.10.1'), # building LDC from source required LDC 0.17.x - ('LDC', '0.17.6', '-%(arch)s', True), + ('LDC', '0.17.6', '-%(arch)s', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.26.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.26.0-GCCcore-10.3.0.eb index 01d38679892..55231353b25 100644 --- a/easybuild/easyconfigs/l/LDC/LDC-1.26.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/LDC/LDC-1.26.0-GCCcore-10.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('CMake', '3.20.1'), ('Ninja', '1.10.2'), # building LDC from source required LDC 0.17.x - ('LDC', '0.17.6', '-%(arch)s', True), + ('LDC', '0.17.6', '-%(arch)s', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb index e8d3bf16a0c..ea74d83de75 100644 --- a/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/l/LOHHLA/LOHHLA-2018.11.05-foss-2018b-R-3.5.1.eb @@ -29,7 +29,7 @@ dependencies = [ ('BEDTools', '2.27.1'), ('SAMtools', '1.9'), ('novoalign', '3.09.01', versionsuffix), - ('picard', '2.18.27', '-Java-1.8', True), + ('picard', '2.18.27', '-Java-1.8', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/LiBis/LiBis-20200428-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/l/LiBis/LiBis-20200428-foss-2019b-Python-3.7.4.eb index 1788ec1f1d8..4eadb4441ed 100644 --- a/easybuild/easyconfigs/l/LiBis/LiBis-20200428-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/l/LiBis/LiBis-20200428-foss-2019b-Python-3.7.4.eb @@ -24,7 +24,7 @@ checksums = [ dependencies = [ ('Python', '3.7.4'), - ('FastQC', '0.11.9', '-Java-11', True), + ('FastQC', '0.11.9', '-Java-11', SYSTEM), ('SciPy-bundle', '2019.10', versionsuffix), # pandas ('matplotlib', '3.1.1', versionsuffix), ('cutadapt', '2.7', versionsuffix), diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb index f36862909d7..a9f94d66090 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.4.2-intel-2018a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('Autotools', '20170619'), ('GMP', '6.1.2'), ('Boost', '1.66.0', '-Python-2.7.14'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('Python', '2.7.14'), ] diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.5.0-gompi-2019a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.5.0-gompi-2019a.eb index 7bdd390fc27..ea2d5040ce7 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.5.0-gompi-2019a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.5.0-gompi-2019a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('Autotools', '20180311'), ('GMP', '6.1.2'), ('Boost', '1.70.0'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('Python', '2.7.15'), ] diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.5.0-iimpi-2019a.eb b/easybuild/easyconfigs/l/Libint/Libint-2.5.0-iimpi-2019a.eb index 3983e2d6057..87d30d047ad 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.5.0-iimpi-2019a.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.5.0-iimpi-2019a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('Autotools', '20180311'), ('GMP', '6.1.2'), ('Boost', '1.70.0'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('Python', '2.7.15'), ] diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb index 29c369131f2..f0c3fff870f 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb index 52b296562ea..7fb4df0019e 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb index 5d0e481e2b0..f0d08dd8dd7 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb index ecc53857740..d3c68c53159 100644 --- a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb index 8068f14ea72..9b673d9b132 100644 --- a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb index b9a8c3b204c..2e7d6b7a9f3 100644 --- a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb index bbe2ea95f7e..1eb5c2b11e2 100644 --- a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb index dcc203e11e3..4d51c3577b5 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), ('libpthread-stubs', '0.3'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index ba7aa8aa456..40f48498460 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), ('libpthread-stubs', '0.3'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb index 76dc5940533..9478bc5d4a6 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb index d0b72a86ea2..bcc8bb91b85 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb index 5af14da529b..f215f8541e5 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb index 8117c7c96b3..50f49048f36 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb index b95d581275b..7512c727f34 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb index 1cc411ee297..c06e453df9d 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb index 6589aeeb492..f5d786fdb45 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb index 2f7d28f58a9..e95534157b7 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), ] diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb index 028286d1610..c23a7491a1f 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), ] diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb index 7f990b2124d..787ed0a6b96 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xorg-macros', '1.19.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb index 7e2411fa015..20acc539c5d 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xorg-macros', '1.19.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb index 62c62161692..1f7e10f14bb 100644 --- a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('libpthread-stubs', '0.3'), ('randrproto', '1.5.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb index d6e4b7406dd..66d8e8e7988 100644 --- a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('libpthread-stubs', '0.3'), ('randrproto', '1.5.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index b4c2ef6a53d..f3c947b005a 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb index 2c473580acb..c981feacb52 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb index c7e832fe55b..61d8f22229f 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('kbproto', '1.0.7'), ('xorg-macros', '1.19.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('xextproto', '7.3.0'), ('inputproto', '2.3.1'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb index e12535727a9..4401fe752de 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('kbproto', '1.0.7'), ('xorg-macros', '1.19.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('libpthread-stubs', '0.3'), ('xextproto', '7.3.0'), ('inputproto', '2.3.1'), diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb index 9f8743b3091..df8e63cdd74 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('XZ', '5.2.5'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb index a5bba4c08fc..c0609d8718e 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.5.1-GCCcore-11.2.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('XZ', '5.2.5'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb index bb86f508a75..2f0d0841e1b 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), ('XZ', '5.2.5'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb index fe73b8ae707..8c219ad876e 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb @@ -18,7 +18,7 @@ sources = ['%(name)s-%(version)s-stable.tar.gz'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.3.0.eb index b5cc4b2c7c0..a5d36861e3f 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.3.0.eb @@ -29,7 +29,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb index ce86a4e932c..03d032cf290 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.2.0.eb @@ -26,7 +26,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb index 09681e8d363..d88edcd0b49 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-11.3.0.eb @@ -26,7 +26,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb index 380578da359..1013ed198c1 100644 --- a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ checksums = [ '078bec207fc3d5a0581f2a952d1c014b76a6e84a93a6a089ff9b9fe5b3908cb9', # libffi-3.2.1_fix-include-location.patch ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': [('lib/libffi.%s' % SHLIB_EXT, 'lib64/libffi.%s' % SHLIB_EXT), ('lib/libffi.a', 'lib64/libffi.a')], diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.3.0.eb index 363d1410af2..072c87fca91 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.0-GCCcore-10.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('PCRE', '8.44'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb index 085a5fb9f66..67f2252522d 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.1.1-GCCcore-11.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('PCRE', '8.45'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb index c1884e0bb10..24bafd95d41 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.4.3-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('PCRE', '8.45'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb index c2a203f1b2d..0e6381d00bb 100644 --- a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb @@ -12,7 +12,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb index 8fe50e9968e..33ce05138dc 100644 --- a/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-5.4.0.eb index 160e79719f9..4343922d7ce 100644 --- a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.0-GCCcore-5.4.0.eb @@ -13,7 +13,7 @@ source_urls = ['https://ftpmirror.gnu.org/gnu/libidn'] sources = [SOURCELOWER_TAR_GZ] checksums = ['e1cb1db3d2e249a6a3eb6f0946777c2e892d5c5dc7bd91c74394fc3a01cab8b5'] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/idn2', 'lib/libidn2.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb index 886c796fe1a..0a3c4a9ccac 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('NASM', '2.11.08'), ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = "--with-jpeg8" runtest = "test" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb index c90941e7e9e..5c9da9b3258 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ checksums = ['be46e0d14ccac3800f816ae860d191a1187a40164b7552c44afeee97a9caa0a3'] dependencies = [('zlib', '1.2.8')] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb index f33c3fbc3e1..5679b67d18b 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.11')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb index 49f53a9c0c2..9cb10e36685 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ checksums = ['b6cec903e74e9fdd7b5bbcde0ab2415dd12f2f9e84d9e4d9ddd2ba26a41623b2'] dependencies = [('zlib', '1.2.11')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb index 8c7fd2019e9..156f6db5ca5 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.11')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb index 4e54ffba1c2..21a8965354a 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ checksums = [ '46317932e1af8c5e0916930e545a354f5ce821f34fa1c5b40619b77e50400ffd', # libreadline-6.3-bugfix.patch ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/l/libsamplerate/libsamplerate-0.1.9-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libsamplerate/libsamplerate-0.1.9-GCCcore-8.2.0.eb index 3e47dc3c618..d0959ea0cea 100644 --- a/easybuild/easyconfigs/l/libsamplerate/libsamplerate-0.1.9-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libsamplerate/libsamplerate-0.1.9-GCCcore-8.2.0.eb @@ -15,7 +15,7 @@ checksums = ['0a7eb168e2f21353fb6d84da152e4512126f7dc48ccb0be80578c565413444c1'] builddependencies = [ ('binutils', '2.31.1'), # need to include gompi too to ensure FFTW can be loaded in case hierarchical module naming scheme is used - ('gompi', '2019a', '', True), + ('gompi', '2019a', '', SYSTEM), # FFTW is only required for tests ('FFTW', '3.3.8', '', ('gompi', '2019a')), ] diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb index e8763aba9c4..82f2dfb2315 100644 --- a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb index fdb971d5a6b..5cb32f20da8 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb index 42794e4902b..11b1fbaf2be 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb index e7ade18cd5e..2e615320fc8 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb index 09f8321dfd0..91409103d4c 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb index f8debfbbbad..763a4f1aefd 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb index f22547e6446..fe4f7047b25 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb index a3916dbea56..5e2eece33bb 100644 --- a/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libtree/libtree-2.0.0-GCCcore-10.3.0.eb @@ -21,9 +21,9 @@ checksums = ['099e85d8ba3c3d849ce05b8ba2791dd25cd042a813be947fb321b0676ef71883'] builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), - ('cxxopts', '3.0.0', '', True), - ('ELFIO', '3.9', '', True), - ('termcolor', '2.0.0', '', True), + ('cxxopts', '3.0.0', '', SYSTEM), + ('ELFIO', '3.9', '', SYSTEM), + ('termcolor', '2.0.0', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb index c1f1541e7ad..e97d8ea1348 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_XZ] source_urls = [GNU_SOURCE] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] parallel = 1 diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb index 7a2944d9e46..965a763a8c8 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('pkg-config', '0.29'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb index ab5bcf6b380..3ec05ecfbde 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index c69ddcedb6e..4f81dd3b454 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('pkg-config', '0.29'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb index 2ec01ebf7f2..835f4ff45f3 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb @@ -16,7 +16,7 @@ checksums = ['0bb3cfd46dbd90066bf4d7de3cad73ec1024c7325a4a0cbf5f4a0d4fa91155fb'] builddependencies = [ ('binutils', '2.28'), ('pkg-config', '0.29.2'), - ('xcb-proto', '1.13', '', True), + ('xcb-proto', '1.13', '', SYSTEM), ('xproto', '7.0.31'), ('libpthread-stubs', '0.4'), ('xorg-macros', '1.19.1'), diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb index 54ae8147222..690edb297f9 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb index b3bcbc8fa66..7c8c84e827d 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb index 346410c130c..7cfd54f4e1b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-5.4.0.eb @@ -22,6 +22,6 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb index b71554c4dfa..f5aef73bc13 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb @@ -21,6 +21,6 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.5-GCCcore-6.3.0.eb index 8452f3187e2..42dac0e7a79 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.5-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.5-GCCcore-6.3.0.eb @@ -22,6 +22,6 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb index d33516e092f..6d0bea61d24 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['ba65236116de8326d83378b2bd929879fa185195bc530b9d1aba72107910b6b3'] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb index fe7ed2be661..d198d46a308 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb index 0f3443b3e7f..da1de09fb7b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb index 23ce8933d1c..085515a2705 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb index 7886d1c9ada..4fc80e53b4a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.2.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb index 7b223299334..0a707b51b00 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.3.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb index 45af326f45d..5f4d20ef856 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb index e2473bcff4d..c3716a65a86 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.3.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb index d7aa39079a3..fe316e7657a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb index 8f7d944e2e1..a8faaec3954 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.1.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCCcore -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb index 70f9de4b636..388f76f2753 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb index 9bd978b3ec9..bd7b15d0f99 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.34', '', True)] +builddependencies = [('binutils', '2.34', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb index 50594f87ece..40d8acc91af 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.35', '', True)] +builddependencies = [('binutils', '2.35', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb index e7dee0ddd89..aaa4eda2c91 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb index e63d5912066..c1852324b5b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb index 13063f1b7f6..90f3441ae31 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index 362ecb6b5e5..44174916f39 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ checksums = [ 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb index 7d867eee4d9..bb84008fe0d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb index 19fb0b8badd..42ac0537642 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb index 33da257c441..abedf0b58b2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -24,7 +24,7 @@ checksums = [ # use same binutils version that was used when building GCC toolchain builddependencies = [ - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb index 4f300fc47cf..70675bd26d4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.28', '', True)] +builddependencies = [('binutils', '2.28', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb index f4ec9a042e1..95c1d432cdf 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.29', '', True)] +builddependencies = [('binutils', '2.29', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb index 709134121bf..d435d9cf19f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.30', '', True)] +builddependencies = [('binutils', '2.30', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb index 89a858a24f8..18817b26e32 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb index a92a076f9bc..f268c01aaed 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.30', '', True)] +builddependencies = [('binutils', '2.30', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb index 3f8004316c4..cdf833ca394 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb index 0d5a496fbf0..b21fcafc4f7 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb index c52483a837d..30d2b32da00 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb index 7cb0d843963..aac98bc3c12 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb index 2d1822b6404..c70532aeb1f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb index 5e4d0740ee7..61100b9eb44 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb @@ -19,7 +19,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.34', '', True)] +builddependencies = [('binutils', '2.34', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb index 0f426d46de5..7818364f1ae 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.2.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.37', '', True)] +builddependencies = [('binutils', '2.37', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb index dfdd4df8d10..41a76cb08ba 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb index b0d85861200..7e38a77b438 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.1.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb index 568d60035ca..4061197926d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.2.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.39', '', True)] +builddependencies = [('binutils', '2.39', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb index 6e539babe63..e59b0628b8e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.4.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb index 95d679a09cf..e586ce4a60a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-9.5.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb index 7009268301e..17a1f835e91 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('MATLAB', version, '', True) + ('MATLAB', version, '', SYSTEM) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb index d7fcbc99902..55b0c6ce81f 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('MATLAB', version, '', True) + ('MATLAB', version, '', SYSTEM) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb index fc816ba2323..14e3d088e33 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('MATLAB', version, '', True) + ('MATLAB', version, '', SYSTEM) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb index 0c39c8a729c..76000b4dc4a 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('MATLAB', version, '', True) + ('MATLAB', version, '', SYSTEM) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb index 7ce8669e278..8ac5cb405dc 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} multi_deps = {'Python': ['3.7.4', '2.7.16']} dependencies = [ - ('MATLAB', version, '', True) + ('MATLAB', version, '', SYSTEM) ] use_pip = False diff --git a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb index f41f912592a..13a5f06fec5 100644 --- a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/matsim-org/matsim/releases/download/%(namelow sources = ['%(namelower)s-%(version)s.zip'] dependencies = [ - ('Java', '1.8.0_112', '', True), + ('Java', '1.8.0_112', '', SYSTEM), ('X11', '20160819'), ] diff --git a/easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb index dd2b476ec76..0c14fa80736 100644 --- a/easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/m/MATSim/MATSim-14.0-GCCcore-11.2.0-Java-11.eb @@ -14,7 +14,7 @@ sources = ['%(namelower)s-%(version)s-release.zip'] checksums = ['17c7b785678cacd937f5df5b8c80398b73e2e9ceb07cc1ebd175fc94a65ce3c4'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Mesa', '21.1.7'), ('X11', '20210802'), ] diff --git a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb index 3b6f548fcac..e26b1a04135 100644 --- a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb +++ b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb @@ -24,7 +24,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('MDSplus', version), ] diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index 9b8ad14bb5f..05e8b2e18a0 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ - ('Java', '1.7.0_79', '', True), + ('Java', '1.7.0_79', '', SYSTEM), ('Python', '2.7.11'), ('HDF5', '1.8.16'), ('libxml2', '2.9.3'), diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index d8d121944ac..97b0d2699a0 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -21,7 +21,7 @@ sources = ['mpj-v%s.tar.gz' % (version.replace('.', '_'))] builddependencies = [('CMake', '3.5.2')] dependencies = [ - ('Java', '1.8.0_92', '', True), + ('Java', '1.8.0_92', '', SYSTEM), ] # compile JNI wrapper library as described in docs diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb index 7f066294b57..61d2d07255f 100644 --- a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-2.7.16.eb @@ -15,7 +15,7 @@ sources = ['%s.tar.gz' % local_commit] checksums = ['7140934dc653ee5edf807120a8e9cf23a0bf72f01bbe4dfbe2a15206ce6812db'] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb index 7163dd84d46..186b2b4b72a 100644 --- a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0-rc-20191217-foss-2019b-Python-3.7.4.eb @@ -15,7 +15,7 @@ sources = ['%s.tar.gz' % local_commit] checksums = ['7140934dc653ee5edf807120a8e9cf23a0bf72f01bbe4dfbe2a15206ce6812db'] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb index aa0e747a561..b8433c3a9de 100644 --- a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC2-foss-2017a-Python-2.7.13.eb @@ -14,7 +14,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['88187f3498f4ee215b2a51d16acb7f2e6c33217e72403a7d48c2ec5da6e2218b'] builddependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC3-intel-2018a-Python-2.7.14.eb index fc29aa69abd..aaddadd44e2 100644 --- a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0_RC3-intel-2018a-Python-2.7.14.eb @@ -14,7 +14,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['1eebd96d476772b4f1aaad2d362af575e70fd2de0bede61a658758ffd9793b4d'] builddependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb index 55513948cde..c6e9f493935 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb @@ -34,7 +34,7 @@ dependencies = [ ('Boost', '1.77.0'), # needed by OQGraph ('Judy', '1.0.5'), # needed by OQGraph ('PCRE2', '10.37'), - ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest + ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest ] separate_build_dir = True diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb index 0742cb59603..12a89338f1e 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb @@ -34,7 +34,7 @@ dependencies = [ ('Boost', '1.79.0'), # needed by OQGraph ('Judy', '1.0.5'), # needed by OQGraph ('PCRE2', '10.40'), - ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest + ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest ] separate_build_dir = True diff --git a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb index 121bec87c85..6e267773c52 100644 --- a/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/Megalodon/Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb @@ -12,7 +12,7 @@ genome/transriptome.""" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('h5py', '3.2.1'), diff --git a/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.9-Java-1.8.eb b/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.9-Java-1.8.eb index c1dfbf5a270..ca85b3b0c8f 100644 --- a/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.9-Java-1.8.eb +++ b/easybuild/easyconfigs/m/MiGEC/MiGEC-1.2.9-Java-1.8.eb @@ -19,7 +19,7 @@ source_urls = ['https://github.com/mikessh/migec/releases/download/%(version)s/' sources = ['%(namelower)s-%(version)s.zip'] checksums = ['4a9ace1ab932d06154cdd3eaf6724f55c8dc5c3ce68108b8a4d30ecb0d58ea7e'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['migec', 'migec-%(version)s.jar'], diff --git a/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-1.8.eb b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-1.8.eb index 4287f32cf3f..93646ef7373 100644 --- a/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-1.8.eb +++ b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.13-Java-1.8.eb @@ -19,7 +19,7 @@ source_urls = ['https://github.com/milaboratory/mixcr/releases/download/v%(versi sources = ['%(namelower)s-%(version)s.zip'] checksums = ['f0b32efadf6dae95819cd90cf49978e48797fc9f2685af1fd282a47d3f9fda08'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['mixcr', 'mixcr.jar'], diff --git a/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb index 864fd64611c..b1db223674b 100644 --- a/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb +++ b/easybuild/easyconfigs/m/MiXCR/MiXCR-3.0.3-Java-1.8.eb @@ -19,7 +19,7 @@ source_urls = ['https://github.com/milaboratory/mixcr/releases/download/v%(versi sources = ['%(namelower)s-%(version)s.zip'] checksums = ['a969d815f8e7a8c3ffe082fdfe8f63cadbef7820b9299d648a454fe9480c72af'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['mixcr', 'mixcr.jar'], diff --git a/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb index 4cb42765502..5301799bdd2 100644 --- a/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/m/MinCED/MinCED-0.4.2-GCCcore-8.3.0-Java-11.eb @@ -19,7 +19,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['35b6ee22fe6bdc26a31d0203a7dcc6bd1a19fd6733c60d80ceb44431884af165'] builddependencies = [('binutils', '2.32')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] # minced executable has to be in the same directory as jar files_to_copy = [(['minced', 'minced.jar'], 'bin')] diff --git a/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb index d5bfff12153..e33cd3c0183 100644 --- a/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/MitoZ/MitoZ-2.3-foss-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ checksums = ['13fc5d3c6f41a6eb17498dfb1e69735a2b3f4e62ac7393d3ed71ea9502038841'] dependencies = [ ('Python', '3.6.6'), ('Perl', '5.28.0'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('libgd', '2.2.5'), ('Biopython', '1.72', versionsuffix), ('BioPerl', '1.7.2', '-Perl-%(perlver)s'), @@ -28,7 +28,7 @@ dependencies = [ ('SAMtools', '1.9'), ('Infernal', '1.1.2'), ('ETE', '3.1.1', versionsuffix), - ('tbl2asn', '20200302', '-linux64', True), + ('tbl2asn', '20200302', '-linux64', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb index cf0f71ea2bc..7402e2f2b74 100644 --- a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb @@ -26,7 +26,7 @@ builddependencies = [('CMake', '3.22.1')] dependencies = { ('flex', '2.6.4'), - ('Bison', '3.8.2', '', True) + ('Bison', '3.8.2', '', SYSTEM) } files_to_copy = ['bin'] diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.2.6-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.2.6-GCCcore-8.2.0.eb index eb939d50379..25197a7fbf6 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.2.6-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.2.6-GCCcore-8.2.0.eb @@ -36,7 +36,7 @@ checksums = [ # of MotionCor2 builddependencies = [ ('binutils', '2.31.1'), - ('CUDA', '10.1.105', '', True), + ('CUDA', '10.1.105', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb index dfaa5e0b7fd..3989ce20c54 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.1-GCCcore-8.3.0.eb @@ -36,7 +36,7 @@ checksums = [ # of MotionCor2 builddependencies = [ ('binutils', '2.32'), - ('CUDA', '10.1.243', '', True), + ('CUDA', '10.1.243', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.2-GCCcore-8.3.0.eb index c0a0396d15d..29958aa847c 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.3.2-GCCcore-8.3.0.eb @@ -36,7 +36,7 @@ checksums = [ # of MotionCor2 builddependencies = [ ('binutils', '2.32'), - ('CUDA', '10.1.243', '', True), + ('CUDA', '10.1.243', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb index 4f2bf4aeabb..0bbb8322a60 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.2-GCCcore-10.2.0.eb @@ -34,7 +34,7 @@ checksums = ['5a1b952f46816e396b918b92fcb118376c02be3636371bd6fcef00f315685b8d'] # of MotionCor2 builddependencies = [ ('binutils', '2.35'), - ('CUDAcore', '11.1.1', '', True), + ('CUDAcore', '11.1.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb index ed127443bf8..836b2d4668c 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] # of MotionCor2 builddependencies = [ ('binutils', '2.35'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb index 642b53c9aeb..632abd81b22 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.4.4-GCCcore-10.3.0.eb @@ -32,7 +32,7 @@ checksums = ['128f5cdf83b5023204c10b4801baa13f0a56a950e0bc6e0ed26c7f3aa1df59d7'] # of MotionCor2 builddependencies = [ ('binutils', '2.36.1'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb b/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb index 839d7674129..4fcc2d91235 100644 --- a/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb @@ -23,7 +23,7 @@ checksums = [ dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.0'), - ('netMHCpan', '4.0a', '', True), + ('netMHCpan', '4.0a', '', SYSTEM), ('VEP', '94.0', '-Perl-%(perlver)s'), ('Biopython', '1.72', '-Python-%(pyver)s'), ('psutil', '5.4.7', '-Python-%(pyver)s'), diff --git a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb index 6a07a625057..af248bb974a 100644 --- a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb @@ -27,7 +27,7 @@ dependencies = [ ('matplotlib', '2.2.4', versionsuffix), ('prodigal', '2.6.3'), ('fetchMG', '1.0'), - ('UCLUST', '1.2.22q', '-i86linux64', True), + ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), ('CD-HIT', '4.8.1'), ('tsne', '0.1.8', versionsuffix), ] diff --git a/easybuild/easyconfigs/m/magma/magma-2.3.0-foss-2018a-CUDA-9.1.85.eb b/easybuild/easyconfigs/m/magma/magma-2.3.0-foss-2018a-CUDA-9.1.85.eb index 0791cbd4c8e..36e4ae6c390 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.3.0-foss-2018a-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.3.0-foss-2018a-CUDA-9.1.85.eb @@ -20,7 +20,7 @@ checksums = [ '47e734cf30577b563377c946fb7897da2fd53d050f7e4fe83d8bb11b8d157913', # magma-2.3.0-fix-makefile.patch ] -dependencies = [('CUDA', local_cuda_ver, '', True)] +dependencies = [('CUDA', local_cuda_ver, '', SYSTEM)] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb index 8b6cf89878b..18427a5c0bf 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.1-foss-2021a-CUDA-11.3.1.eb @@ -24,7 +24,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb index da5c2d7e1a5..e1b180e8d15 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.4.1.eb @@ -24,7 +24,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb index de1fa80521a..5c0b53f2a56 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2022a-CUDA-11.7.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('CMake', '3.23.1'), ] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('UCX-CUDA', '1.12.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb index b7d5d70c2df..fb935602693 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [XORG_UTIL_SOURCE] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('xproto', '7.0.31'), ('xorg-macros', '1.19.1'), ] diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb index 0340543f67d..4e25ce407a7 100644 --- a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2-foss-2018b-Python-2.7.15.eb @@ -36,7 +36,7 @@ dependencies = [ ('Seaborn', '0.9.0', versionsuffix), ('BLAST+', '2.7.1'), ('Bowtie2', '2.3.4.2'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('Trim_Galore', '0.6.0', versionsuffix), ('bmtagger', '3.101'), ('taxator-tk', '1.3.3'), diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2.2-foss-2019a-Python-2.7.15.eb index c8c34cc86a5..9e626cd3f73 100644 --- a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.2.2-foss-2019a-Python-2.7.15.eb @@ -21,7 +21,7 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ checksums = ['67e1d86cafc20a8b2713000d18a169a25b4a7dd7c2d4433b51b2e8ad1d4627ff'] builddependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] # see https://github.com/bxlab/metaWRAP/blob/master/installation/dependancies.md @@ -44,7 +44,7 @@ dependencies = [ ('Seaborn', '0.9.0', versionsuffix), ('BLAST+', '2.9.0'), ('Bowtie2', '2.3.5.1'), - ('FastQC', '0.11.8', '-Java-11', True), + ('FastQC', '0.11.8', '-Java-11', SYSTEM), ('Trim_Galore', '0.6.2', '-Java-11'), ('bmtagger', '3.101'), ('taxator-tk', '1.3.3'), diff --git a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb index bb979fb26e2..382b15693e9 100644 --- a/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/metaWRAP/metaWRAP-1.3-foss-2020b-Python-2.7.18.eb @@ -17,7 +17,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['ffdbccf340dc0b1ebd0ad6f222e3bdef1e22bbd6e4e5156bf93500a3a834dd52'] builddependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] # see https://github.com/bxlab/metaWRAP/blob/master/installation/dependancies.md @@ -30,7 +30,7 @@ dependencies = [ ('Bowtie2', '2.4.2'), ('BWA', '0.7.17'), ('CheckM', '1.0.18', versionsuffix), - ('FastQC', '0.11.9', '-Java-11', True), + ('FastQC', '0.11.9', '-Java-11', SYSTEM), ('Kraken', '1.1.1'), ('KronaTools', '2.8'), ('MEGAHIT', '1.2.9', versionsuffix), diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb index 388d152019f..e87d9e19fd7 100644 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb @@ -19,7 +19,7 @@ dependencies = [ ('Bowtie2', '2.3.2'), ('Bowtie', '1.1.2'), ('SAMtools', '1.6'), - ('picard', '2.6.0', '-Java-1.8.0_131', True), + ('picard', '2.6.0', '-Java-1.8.0_131', SYSTEM), ('GSL', '2.3'), ] diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb index c66bd30a717..ffeef5eccb8 100644 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.2.9-foss-2021b.eb @@ -19,7 +19,7 @@ dependencies = [ ('Bowtie2', '2.4.4'), ('Bowtie', '1.3.1'), ('SAMtools', '1.14'), - ('picard', '2.25.1', '-Java-11', True), + ('picard', '2.25.1', '-Java-11', SYSTEM), ('GSL', '2.7'), ('Kent_tools', '422'), ] diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb index 4a532cf4fe8..fd51cdde93e 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb @@ -19,7 +19,7 @@ checksums = [ builddependencies = [('Boost.Python', '1.66.0', versionsuffix)] dependencies = [ - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('Python', '2.7.14'), ] diff --git a/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb index d5203935c90..c7fdb119d30 100644 --- a/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-0.9.6-GCCcore-11.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ dependencies = [ ('xxHash', '0.8.0'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb index 98e1d3c8a65..abcdedea8e6 100644 --- a/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-1.0.0-GCCcore-11.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ dependencies = [ ('xxHash', '0.8.0'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb index fe82f3d27ad..7dbc871c42a 100644 --- a/easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-1.2.1-GCCcore-11.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ] dependencies = [ ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb index e78902943a2..874c4beff87 100644 --- a/easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-1.3.0-GCCcore-11.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ] dependencies = [ ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb index 321116d715d..c76c50c23f9 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.15'), - ('vsc-base', '2.8.3', '', True), - ('vsc-mympirun', '4.1.8', '', True), + ('vsc-base', '2.8.3', '', SYSTEM), + ('vsc-mympirun', '4.1.8', '', SYSTEM), ('matplotlib', '2.2.4', versionsuffix), ('h5py', '2.9.0'), ('mpi4py', '3.0.2', '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb index e26533855e6..194aa344082 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.13'), - ('vsc-base', '2.5.8', '', True), - ('vsc-mympirun', '4.0.2', '', True), + ('vsc-base', '2.5.8', '', SYSTEM), + ('vsc-mympirun', '4.0.2', '', SYSTEM), ('matplotlib', '2.0.2', versionsuffix), ('h5py', '2.7.1', versionsuffix), ('mpi4py', '2.0.0', versionsuffix + '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb index 7c14b8aa091..9c4144e7c47 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.14'), - ('vsc-base', '2.8.1', '', True), - ('vsc-mympirun', '4.1.5', '', True), + ('vsc-base', '2.8.1', '', SYSTEM), + ('vsc-mympirun', '4.1.5', '', SYSTEM), ('matplotlib', '2.1.2', versionsuffix), ('h5py', '2.7.1', versionsuffix), ('mpi4py', '3.0.0', versionsuffix + '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb index 5c72b2d9539..6202bc1f6ce 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.15'), - ('vsc-base', '2.8.3', '', True), - ('vsc-mympirun', '4.1.8', '', True), + ('vsc-base', '2.8.3', '', SYSTEM), + ('vsc-mympirun', '4.1.8', '', SYSTEM), ('matplotlib', '2.2.4', versionsuffix), ('h5py', '2.9.0'), ('mpi4py', '3.0.2', '-timed-pingpong'), diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb index 59d28ad1fac..4cb8911d18f 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['9da3a0291a0bdc06305b7ba194f1e2c2b55ae6f11210b4af43729868149d5445'] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/nasm'], diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb index ce83714e0e1..16e18e8e36e 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -16,7 +16,7 @@ checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] builddependencies = [('binutils', '2.36.1')] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb index 6375266362f..63927a18ac1 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -16,7 +16,7 @@ checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] builddependencies = [('binutils', '2.37')] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb index 026964019f7..2282286a915 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -16,7 +16,7 @@ checksums = ['49b4fbfeebf1f62f6ceb69e72504045d8d1b4e7609e3c2477906f3004c7e2d82'] builddependencies = [('binutils', '2.38')] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('UCX-CUDA', '1.12.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb index cbf8532c70e..81fa9b3dfaa 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -10,8 +10,8 @@ communication primitives that are performance optimized for NVIDIA GPUs.""" toolchain = {'name': 'GCCcore', 'version': local_gcc_ver} -builddependencies = [('GCC', local_gcc_ver, '', True)] -dependencies = [('CUDAcore', local_cuda_version, '', True)] +builddependencies = [('GCC', local_gcc_ver, '', SYSTEM)] +dependencies = [('CUDAcore', local_cuda_version, '', SYSTEM)] github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb index 50bb04e3b90..140a12a4575 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -10,8 +10,8 @@ communication primitives that are performance optimized for NVIDIA GPUs.""" toolchain = {'name': 'GCCcore', 'version': local_gcc_ver} -builddependencies = [('GCC', local_gcc_ver, '', True)] -dependencies = [('CUDAcore', local_cuda_version, '', True)] +builddependencies = [('GCC', local_gcc_ver, '', SYSTEM)] +dependencies = [('CUDAcore', local_cuda_version, '', SYSTEM)] github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb index 5ebb8f01ff7..abba6ab7b5b 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_92', '', True)] +dependencies = [('Java', '1.8.0_92', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb index ed0e37836cc..5375c605408 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_77', '', True)] +dependencies = [('Java', '1.8.0_77', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb index 8b032e04685..e2ec60825f6 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_92', '', True)] +dependencies = [('Java', '1.8.0_92', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb index 85280ff5970..c6bfafd32a6 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-GCCcore-6.4.0.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['803c650a6de5bb38231d9ced7587f3ab788b415cac04b0ef4152546b18713ef2'] -dependencies = [('Java', '1.8.0_192', '', True)] +dependencies = [('Java', '1.8.0_192', '', SYSTEM)] builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb index 8d0219a7422..fc51bb5ca7f 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_121', '', True)] +dependencies = [('Java', '1.8.0_121', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-1.8.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-1.8.eb index bc20255c082..de7c2047d29 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-1.8.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-1.8.eb @@ -20,7 +20,7 @@ checksums = ['4139adff83af213d7880bc80d1c0f5ee9b00c6c4e615d00aa47aaa267e40ed25'] builddependencies = [('binutils', '2.31.1')] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-11.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-11.eb index f32799f658e..c95aef751b3 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-11.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.0-GCCcore-8.2.0-Java-11.eb @@ -20,7 +20,7 @@ checksums = ['4139adff83af213d7880bc80d1c0f5ee9b00c6c4e615d00aa47aaa267e40ed25'] builddependencies = [('binutils', '2.31.1')] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb index bf41fbf66b7..04f599cb3a4 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.4-GCCcore-8.3.0-Java-11.eb @@ -15,7 +15,7 @@ builddependencies = [ ('Perl', '5.30.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] default_easyblock = 'ConfigureMake' default_component_specs = { diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb index 8a3ae837e9e..c6f2f988ec1 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.5-GCCcore-9.3.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('Perl', '5.30.2'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] default_easyblock = 'ConfigureMake' default_component_specs = { diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb index 3ca4af87ce9..3ef383ecc8b 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('Perl', '5.32.0'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] default_easyblock = 'ConfigureMake' default_component_specs = { diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb index f07787644a5..9c8a9ae5026 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.10.9-GCCcore-10.3.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('Perl', '5.32.1'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] default_easyblock = 'ConfigureMake' default_component_specs = { diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb index d410657900f..785c1683f20 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.11.2-GCCcore-11.2.0.eb @@ -14,7 +14,7 @@ builddependencies = [ ('Perl', '5.34.0', '-minimal'), ] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] default_easyblock = 'ConfigureMake' default_component_specs = { diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.9.1-foss-2018a-Java-1.8.0_162.eb b/easybuild/easyconfigs/n/NGS/NGS-2.9.1-foss-2018a-Java-1.8.0_162.eb index 8c00266c360..1255f097104 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.9.1-foss-2018a-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.9.1-foss-2018a-Java-1.8.0_162.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['c24c93bd70ed198a44c6b9dba0d6704edc90f228f832f2fef21fa5342303fc50'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.9.1-intel-2018a-Java-1.8.0_162.eb b/easybuild/easyconfigs/n/NGS/NGS-2.9.1-intel-2018a-Java-1.8.0_162.eb index ec99368e887..6f21a2ce8b4 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.9.1-intel-2018a-Java-1.8.0_162.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.9.1-intel-2018a-Java-1.8.0_162.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['c24c93bd70ed198a44c6b9dba0d6704edc90f228f832f2fef21fa5342303fc50'] -dependencies = [('Java', '1.8.0_162', '', True)] +dependencies = [('Java', '1.8.0_162', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-2.9.3-foss-2018b-Java-1.8.eb b/easybuild/easyconfigs/n/NGS/NGS-2.9.3-foss-2018b-Java-1.8.eb index b65402280d4..37d4558ef19 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-2.9.3-foss-2018b-Java-1.8.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-2.9.3-foss-2018b-Java-1.8.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['d16cdf340f4c66e449cc490a222e54e9074cd15fe0938cb75b951a72985f757d'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb b/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb index 492ce96c1a9..bd388fb7582 100644 --- a/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb +++ b/easybuild/easyconfigs/n/NIMBLE/NIMBLE-0.7.0-foss-2018b-R-3.5.1.eb @@ -17,7 +17,7 @@ source_urls = [ sources = ['%(namelower)s_%(version)s.tar.gz'] checksums = ['661a5bb626164c145ae9c5ba5c3d9c30b0ecc1b83d86eae25d83745324906f7e'] -builddependencies = [('Eigen', '3.3.7', '', True)] +builddependencies = [('Eigen', '3.3.7', '', SYSTEM)] dependencies = [('R', '3.5.1')] diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb index 5c22660ad0b..db905d3342f 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.5.0-gompi-2022a-CUDA-11.7.0.eb @@ -27,7 +27,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('UCX-CUDA', '1.12.1', versionsuffix), ('NCCL', '2.12.12', versionsuffix), ] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb index 4c737da9890..b145b8018a3 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.04.0.eb @@ -17,7 +17,7 @@ sources = ['%(namelower)s-%(version)s-all'] checksums = ['10d96864489a5d6b4de3a730307871ca865e2f1c49a14cd5c4051cae5dca8d8e'] # specify dependency on Java/1.8 "wrapper", rather than a specific Java version -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] install_cmd = "[ -d %(builddir)s/bin ] || mkdir -p %(installdir)s/bin &&" install_cmd += "cp %(builddir)s/nextflow-%(version)s-all %(installdir)s/bin &&" diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.07.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.07.0.eb index 1e97a00e55f..87b4b238692 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.07.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.07.0.eb @@ -17,7 +17,7 @@ sources = ['%(namelower)s-%(version)s-all'] checksums = ['6f7069b43f395c5d902321745d37988fed7ef84d2006ea00be0df19de97c1986'] # specify dependency on Java/1.8 "wrapper", rather than a specific Java version -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] install_cmd = "[ -d %(builddir)s/bin ] || mkdir -p %(installdir)s/bin &&" install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.12.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.12.0.eb index 4cb30cd7747..f7ce8ad37cd 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-19.12.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-19.12.0.eb @@ -24,7 +24,7 @@ sources = ['v%(version)s-edge.tar.gz'] checksums = ['16d38a14aeab636531da6d5d1894898d13a359c5f699eefcfb433fc3340e1b8a'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.01.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.01.0.eb index 012c69b71df..90347313e4c 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.01.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.01.0.eb @@ -25,7 +25,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['011b0b74df612a001bee05c75ee3eb93caff76eb2facd39527a092b86c3373ab'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb index cf8212fe26f..f55c9aac668 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.04.1.eb @@ -25,7 +25,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['ec939568585454cad3ab1a4f6510f0dee707e02ce44324bd43a05e5601d28136'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.10.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.10.0.eb index 01b4e6dcf2f..029737900a7 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-20.10.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-20.10.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['5ebf674c75ff73cd7a090921942fb1234653f50beaac09962022f20fa2ef4fc9'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.03.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.03.0.eb index d7d137ebdf3..4ee8f8aca28 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.03.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.03.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s-edge.tar.gz'] checksums = ['7b10fe1d8cf5dc6aba810e36b28aa360cd186cd583208542422daf1f08089692'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb index 7e99ffb9bd6..42acc235e75 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.08.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s-edge.tar.gz'] checksums = ['ab47af92e6f5c5c08a43b70e60cc3d8720e267a507f21af62ac24805b02a2e8b'] # specify dependency on Java/13 "wrapper", rather than a specific Java version -dependencies = [('Java', '13', '', True)] +dependencies = [('Java', '13', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb index ed4ceee4b28..d610c0c4a0d 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-21.10.6.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['91b108cba321cb5500e2e811c446b04aee152dc2f97cb2cf4ae00eeecd4f332f'] # specify dependency on Java/13 "wrapper", rather than a specific Java version -dependencies = [('Java', '13', '', True)] +dependencies = [('Java', '13', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb index 14616b6305d..1dd727aee12 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.04.0.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['4547a82228d1ad8615dd9916cd47a64a397405058579c0557cd11540633713ad'] # specify dependency on Java/11 "wrapper", rather than a specific Java version -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] skipsteps = ['configure', 'build'] diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb index 801d95801e6..91d4c8cbd71 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-foss-2018b-Python-2.7.15.eb @@ -22,7 +22,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.5', '', True)] +builddependencies = [('Eigen', '3.3.5', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb index 6799dfdb146..98affa6d3c8 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.10.2-intel-2018b-Python-2.7.15.eb @@ -22,7 +22,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.4', '', True)] +builddependencies = [('Eigen', '3.3.4', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb index 8bfbce42b87..ec682cb63db 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb @@ -22,7 +22,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.7', '', True)] +builddependencies = [('Eigen', '3.3.7', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb index 5a800af7bf5..edaace23ac2 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.2-foss-2020a-Python-3.8.2.eb @@ -23,7 +23,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.7', '', True)] +builddependencies = [('Eigen', '3.3.7', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.9.2-intel-2018a.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.9.2-intel-2018a.eb index f7f74b3e462..b6658ad065b 100644 --- a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.9.2-intel-2018a.eb +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.9.2-intel-2018a.eb @@ -21,7 +21,7 @@ checksums = [ 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz ] -builddependencies = [('Eigen', '3.3.4', '', True)] +builddependencies = [('Eigen', '3.3.4', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb index a8a803600e1..52735d76539 100644 --- a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.2.0.eb @@ -35,7 +35,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('nghttp3', '0.6.0'), ('Python', '3.9.6'), ('libxml2', '2.9.10'), diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb index 72ff0976e45..2c658278a18 100644 --- a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.2.0.eb @@ -29,7 +29,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('GnuTLS', '3.7.3'), ('nghttp3', '0.6.0'), ('libev', '4.33'), diff --git a/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb index f3783e2fc9e..60d55c02ccc 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.54.1-foss-2021b-CUDA-11.4.1.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), ('LLVM', '12.0.1'), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb index 02d864af126..a2434cbbc44 100644 --- a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -27,7 +27,7 @@ checksums = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('ONNX', '1.11.0'), ('flatbuffers-python', '2.0'), diff --git a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb index 9c57ffb879e..6e9d0724196 100644 --- a/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OR-Tools/OR-Tools-7.1-foss-2019a-Python-3.7.2.eb @@ -30,9 +30,9 @@ local_gurobiver = '8.1.1' dependencies = [ ('Python', '3.7.2'), ('zlib', '1.2.11'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # Gurobi is optional - ('Gurobi', local_gurobiver, '', True), + ('Gurobi', local_gurobiver, '', SYSTEM), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb index 81a663791de..cd846a70218 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.7.1-gompi-2021a-CUDA-11.3.1.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TGZ] checksums = ['cb5ce4e2e68ed012d9952e96ef880a802058c87a1d840a2093b19bddc7faa165'] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb index 45ef99c6337..bc0b6fe9631 100755 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021a-CUDA-11.3.1.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('UCX-CUDA', '1.10.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb index 65c303f62cb..6122b5221dd 100755 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-CUDA-11.4.1.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('UCX-CUDA', '1.11.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb index f081748a1b9..f1ffbd93b35 100755 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2022a-CUDA-11.7.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('NCCL', '2.12.12', versionsuffix), ('UCX-CUDA', '1.12.1', versionsuffix), ('UCC-CUDA', '1.0.0', versionsuffix), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb index ff686a0a357..5c5cf246ba1 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.58'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.3'), - ('Java', '1.8.0_72', '', True), + ('Java', '1.8.0_72', '', SYSTEM), ('zlib', '1.2.8'), ('Mesa', '11.1.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb index ce3a19f67d0..c2c9f653f54 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.60'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.5'), - ('Java', '1.8.0_112', '', True), + ('Java', '1.8.0_112', '', SYSTEM), ('zlib', '1.2.8'), ('Mesa', '12.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-foss-2018a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-foss-2018a.eb index 433b701f926..bd551db8f61 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-foss-2018a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-foss-2018a.eb @@ -40,7 +40,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.0'), ('gnuplot', '5.2.2'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '17.3.6'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index ea85cfeafc9..20d927dc1fb 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -33,7 +33,7 @@ dependencies = [ ('GLPK', '4.60'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.5'), - ('Java', '1.8.0_121', '', True), + ('Java', '1.8.0_121', '', SYSTEM), ('zlib', '1.2.8'), ('Mesa', '12.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a-mt.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a-mt.eb index f623cd98f9f..2f8f0f23352 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a-mt.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a-mt.eb @@ -37,7 +37,7 @@ dependencies = [ ('GLPK', '4.61'), ('GL2PS', '1.4.0'), ('gnuplot', '5.0.6'), - ('Java', '1.8.0_131', '', True), + ('Java', '1.8.0_131', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '17.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb index 913fdc43d8f..e5240000ae6 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2017a.eb @@ -36,7 +36,7 @@ dependencies = [ ('GLPK', '4.61'), ('GL2PS', '1.4.0'), ('gnuplot', '5.0.6'), - ('Java', '1.8.0_131', '', True), + ('Java', '1.8.0_131', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '17.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.2-foss-2018a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.2-foss-2018a.eb index 9f2386fc73e..3765993042c 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.2-foss-2018a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.2-foss-2018a.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.0'), ('gnuplot', '5.2.2'), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '17.3.6'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.4.1-foss-2018b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.4.1-foss-2018b.eb index 843200f9542..5662e74132d 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.4.1-foss-2018b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.4.1-foss-2018b.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.0'), ('gnuplot', '5.2.5'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '18.1.1'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019a.eb b/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019a.eb index 287bbf1c983..38880eb0332 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019a.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.0'), ('gnuplot', '5.2.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '19.0.1'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019b.eb b/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019b.eb index b37ef2c4129..3a702aad19f 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-5.1.0-foss-2019b.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.0'), ('gnuplot', '5.2.8'), - ('Java', '11.0.2', '', True), + ('Java', '11.0.2', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '19.1.7'), ('libGLU', '9.0.1'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb index 3da5bd86b42..03e6837966e 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-6.2.0-foss-2020b.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.65'), ('GL2PS', '1.4.2'), ('gnuplot', '5.4.1'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '20.2.1'), ('libGLU', '9.0.1'), diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2017b-Python-2.7.14.eb index 143c4e517cd..c100a2239ce 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2017b-Python-2.7.14.eb @@ -29,7 +29,7 @@ dependencies = [ ('Python', '2.7.14'), ('zlib', '1.2.11'), ('libxml2', '2.9.7'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb index 303e55408ce..1aac64ecdbe 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-2.7.15.eb @@ -29,7 +29,7 @@ dependencies = [ ('Python', '2.7.15'), ('zlib', '1.2.11'), ('libxml2', '2.9.8'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb index fe1c852d320..f10768b4b02 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2018b-Python-3.6.6.eb @@ -31,7 +31,7 @@ dependencies = [ ('Python', '3.6.6'), ('zlib', '1.2.11'), ('libxml2', '2.9.8'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2019a-Python-3.7.2.eb index ad1ddc252ce..263cec8636f 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-2.4.1-intel-2019a-Python-3.7.2.eb @@ -30,7 +30,7 @@ dependencies = [ ('Python', '3.7.2'), ('zlib', '1.2.11'), ('libxml2', '2.9.8'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] runtest = 'test' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.0.0-gompi-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.0.0-gompi-2019b-Python-3.7.4.eb index d49bf26cef7..2b022edef2d 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.0.0-gompi-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.0.0-gompi-2019b-Python-3.7.4.eb @@ -26,7 +26,7 @@ dependencies = [ ('Python', '3.7.4'), ('zlib', '1.2.11'), ('libxml2', '2.9.9'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output ('Boost', '1.71.0'), # optional: for Maestro formats diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb index 6d911749614..cf4291bf2cc 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2019b-Python-3.7.4.eb @@ -37,7 +37,7 @@ dependencies = [ ('Python', '3.7.4'), ('zlib', '1.2.11'), ('libxml2', '2.9.9'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output ('Boost', '1.71.0'), diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb index 7dbebd3a06a..77d78162002 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-iimpi-2020a-Python-3.8.2.eb @@ -36,7 +36,7 @@ dependencies = [ ('Python', '3.8.2'), ('zlib', '1.2.11'), ('libxml2', '2.9.10'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('RapidJSON', '1.1.0'), ('cairo', '1.16.0'), # optional: for .png output ('Boost', '1.72.0'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb index 70e5bf517cc..258ec7b63f6 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.12-intel-2016a.eb @@ -31,8 +31,8 @@ dependencies = [ ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), - ('Java', '1.7.0_80', '', True), - ('ant', '1.9.6', '-Java-%(javaver)s', True), + ('Java', '1.7.0_80', '', SYSTEM), + ('ant', '1.9.6', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.48.0'), ('GTK+', '2.24.30'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb index 71a179c34f1..f3e4bca8821 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016a.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), - ('Java', '1.8.0_92', '', True), - ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('Java', '1.8.0_92', '', SYSTEM), + ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.48.0'), ('GTK+', '2.24.30'), ('GStreamer', '1.6.4'), diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb index c983e1fdf0b..c05ad6cd156 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-foss-2016b.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.24'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), - ('Java', '1.8.0_92', '', True), - ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('Java', '1.8.0_92', '', SYSTEM), + ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.49.5'), ('GTK+', '2.24.31'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb index 1ea167eadfc..56882999097 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.21'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), - ('Java', '1.8.0_92', '', True), - ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('Java', '1.8.0_92', '', SYSTEM), + ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.48.0'), ('GTK+', '2.24.30'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb index 554cb1cb273..b5a7c1b3002 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.24'), ('LibTIFF', '4.0.6'), ('JasPer', '1.900.1'), - ('Java', '1.8.0_92', '', True), - ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('Java', '1.8.0_92', '', SYSTEM), + ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.49.5'), ('GTK+', '2.24.31'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb index 204d5064bea..c6c1d65f281 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-2.7.14.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.32'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb index 6727d4e58da..79e2cee0431 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-foss-2017b-Python-3.6.3.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.32'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb index 750d74b0485..74c953d5cba 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-2.7.13.eb @@ -38,8 +38,8 @@ dependencies = [ ('libpng', '1.6.29'), ('LibTIFF', '4.0.8'), ('JasPer', '2.0.12'), - ('Java', '1.8.0_144', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_144', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.31'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb index 6d11e2ff77d..789d6aaf637 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017a-Python-3.6.1.eb @@ -38,8 +38,8 @@ dependencies = [ ('libpng', '1.6.29'), ('LibTIFF', '4.0.8'), ('JasPer', '2.0.12'), - ('Java', '1.8.0_144', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_144', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.31'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb index 293945598e4..8b301fd1a19 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-2.7.14.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.32'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb index 7c0fdad4b14..40f101d42e3 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.3.0-intel-2017b-Python-3.6.3.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.32'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.53.5'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb index 842fafdf34b..b5a104f5992 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-2.7.14.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4-contrib.eb index 74d3fa4a8c9..7df03a1aa93 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4-contrib.eb @@ -42,8 +42,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4.eb index a0370ed6840..ecd2995c966 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-foss-2018a-Python-3.6.4.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb index e017af4d366..87b5199daa2 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-2.7.14.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-3.6.4.eb index e9800cb3a37..91670fc7d49 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.1-intel-2018a-Python-3.6.4.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.5-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.5-foss-2018b-Python-2.7.15.eb index 614a84cbc6b..9766e39c514 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.5-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.5-foss-2018b-Python-2.7.15.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.5', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-2.7.15.eb index 708d99f1e04..f9e7d4e506a 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-2.7.15.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.36'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.60.1'), ('GTK+', '3.24.8'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-3.7.2.eb index c01e9fa3946..5d57f174681 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-foss-2019a-Python-3.7.2.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.36'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.60.1'), ('GTK+', '3.24.8'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-2.7.15.eb index d32d54e08be..8acf1dbbfc3 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-2.7.15.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.36'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.60.1'), ('GTK+', '3.24.8'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-3.7.2.eb index 1e78bb05a9d..727c24fe4ec 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.4.7-fosscuda-2019a-Python-3.7.2.eb @@ -39,8 +39,8 @@ dependencies = [ ('libpng', '1.6.36'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.60.1'), ('GTK+', '3.24.8'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-2.7.15.eb index fbd9e8d0fcf..ae5711df4af 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-2.7.15.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.5', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb index 0aa61fe1e65..23ce3d0dc51 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.0.1-foss-2018b-Python-3.6.6.eb @@ -36,8 +36,8 @@ dependencies = [ ('libpng', '1.6.34'), ('LibTIFF', '4.0.9'), ('JasPer', '2.0.14'), - ('Java', '1.8', '', True), - ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.5', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.54.3'), ('GTK+', '2.24.32'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2019b-Python-3.7.4.eb index 9bc89cf3d0f..d38ec1d62da 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2019b-Python-3.7.4.eb @@ -37,8 +37,8 @@ dependencies = [ ('libpng', '1.6.37'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.62.0'), ('GTK+', '3.24.13'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb index 8d9b3948a85..8870feae56a 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2-contrib.eb @@ -43,8 +43,8 @@ dependencies = [ ('libwebp', '1.1.0'), ('OpenEXR', '2.4.1'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.8', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.64.1'), ('GTK+', '3.24.17'), ('HDF5', '1.10.6'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb index 49b5c8ba29b..bb85b7a793f 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb @@ -39,8 +39,8 @@ dependencies = [ ('libwebp', '1.1.0'), ('OpenEXR', '2.4.1'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.8', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.64.1'), ('GTK+', '3.24.17'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-fosscuda-2019b-Python-3.7.4.eb index 184171377df..7c1b760a1bc 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-fosscuda-2019b-Python-3.7.4.eb @@ -43,8 +43,8 @@ dependencies = [ ('libpng', '1.6.37'), ('LibTIFF', '4.0.10'), ('JasPer', '2.0.14'), - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.62.0'), ('GTK+', '3.24.13'), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb index cf24b5ca039..f866015943d 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-foss-2020b-contrib.eb @@ -45,8 +45,8 @@ dependencies = [ ('libwebp', '1.1.0'), ('OpenEXR', '2.5.5'), ('JasPer', '2.0.24'), - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.66.1'), ('GTK+', '3.24.23'), ('HDF5', '1.10.7'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb index 5fe200231f7..6bd1dad125b 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.1-fosscuda-2020b-contrib.eb @@ -45,8 +45,8 @@ dependencies = [ ('libwebp', '1.1.0'), ('OpenEXR', '2.5.5'), ('JasPer', '2.0.24'), - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.66.1'), ('GTK+', '3.24.23'), ('HDF5', '1.10.7'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb index f9b43027447..9c0af78eb10 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-CUDA-11.3.1-contrib.eb @@ -45,13 +45,13 @@ dependencies = [ ('libwebp', '1.2.0'), ('OpenEXR', '3.0.1'), ('JasPer', '2.0.28'), - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.68.2'), ('GTK3', '3.24.29'), ('HDF5', '1.10.7'), # needed by hdf from contrib - ('CUDA', '11.3.1', '', True), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('CUDA', '11.3.1', '', SYSTEM), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ] # XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb index 9dd6c211740..39fac2609e2 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.3-foss-2021a-contrib.eb @@ -45,8 +45,8 @@ dependencies = [ ('libwebp', '1.2.0'), ('OpenEXR', '3.0.1'), ('JasPer', '2.0.28'), - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.68.2'), ('GTK3', '3.24.29'), ('HDF5', '1.10.7'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb index 5b3d0e27351..86531a76eb5 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-contrib.eb @@ -45,8 +45,8 @@ dependencies = [ ('libwebp', '1.2.0'), ('OpenEXR', '3.1.1'), ('JasPer', '2.0.33'), - ('Java', '11', '', True), - ('ant', '1.10.11', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.69.1'), ('GTK3', '3.24.31'), ('HDF5', '1.12.1'), # needed by hdf from contrib diff --git a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb index b7b2f6058eb..10c57638036 100644 --- a/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFace/OpenFace-2.2.0-foss-2021a-CUDA-11.3.1.eb @@ -26,8 +26,8 @@ builddependencies = [ ('patchelf', '0.12') ] dependencies = [ - ('CUDA', '11.3.1', '', True), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('CUDA', '11.3.1', '', SYSTEM), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('OpenCV', '4.5.3', '-CUDA-%(cudaver)s-contrib'), ('dlib', '19.22', '-CUDA-%(cudaver)s'), ('SDL2', '2.0.14'), diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb index f4797eae8eb..1d5296cc0d5 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -16,7 +16,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('PyYAML', '5.4.1'), ('Biopython', '1.79'), diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb index d52bab5ca43..61a9e74745f 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.7.0-foss-2021a-CUDA-11.3.1.eb @@ -35,7 +35,7 @@ separate_build_dir = True dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SWIG', '4.0.2'), ] diff --git a/easybuild/easyconfigs/o/OpenMS/OpenMS-2.4.0-foss-2018b.eb b/easybuild/easyconfigs/o/OpenMS/OpenMS-2.4.0-foss-2018b.eb index c2c006a21f5..0be7211a54e 100644 --- a/easybuild/easyconfigs/o/OpenMS/OpenMS-2.4.0-foss-2018b.eb +++ b/easybuild/easyconfigs/o/OpenMS/OpenMS-2.4.0-foss-2018b.eb @@ -33,7 +33,7 @@ dependencies = [ ('Xerces-C++', '3.2.0'), ('LIBSVM', '3.23'), ('GLPK', '4.65'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('SQLite', '3.24.0'), ('bzip2', '1.0.6'), ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb index ff54cc30a4b..a5bd30ffa85 100644 --- a/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb +++ b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-2.7-Java-1.8.0_144.eb @@ -15,7 +15,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['16f8c86db061d1c24f1fc64897eb23742e73415a019dd8ea3f39782de833146b'] builddependencies = [ - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Java', '1.8.0_144'), diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb index 29256de39d1..86f569eb1f8 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.openssl.org/source/'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index 904ddedf279..f80a7efa49f 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('Perl', '5.24.0'), ('MCL', '%s.%s' % (local_mcl_majver, local_mcl_minver)), ('BioPerl', '1.7.1', versionsuffix), - ('BLAST', '2.2.26', '-Linux_x86_64', True), + ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), ] start_dir = 'ORTHOMCLV%(version)s' diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb index c7f14efe011..09952eda5e0 100644 --- a/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb @@ -13,7 +13,7 @@ and run simple inference.""" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('ONNX-Runtime', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb index 3336e2eb4a7..3298c090913 100644 --- a/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -13,7 +13,7 @@ and run simple inference.""" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('ONNX-Runtime', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb index 47629d26e8e..710857fb134 100644 --- a/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PCL/PCL-1.8.1-intel-2017b-Python-2.7.14.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [('CMake', '3.9.5')] dependencies = [ ('Boost', '1.65.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('FLANN', '1.8.4', versionsuffix), ('VTK', '8.0.1', versionsuffix), ('Qhull', '2015.2'), diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb index 017eaf7df0b..558337872ed 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-foss-2018b-Python-3.6.6.eb @@ -24,7 +24,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] configopts = '-DEIGEN3_ROOT=$EBROOTEIGEN' diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb index 1483418bd8d..fc5b5e2cff7 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-gompi-2019a-Python-3.7.2.eb @@ -24,7 +24,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.13.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] configopts = '-DEIGEN3_ROOT=$EBROOTEIGEN' diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb index 4862bbfa6aa..ee6f7d3f34e 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb @@ -18,7 +18,7 @@ checksums = ['d1ef6bdc268a2e719b36c85125c3543df7a26e1a738daf4483f4ded0c76f5b60'] builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb index 9dc98305542..484eb213be4 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb index 53475269537..ece457c65a0 100644 --- a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb @@ -18,7 +18,7 @@ source_urls = ['http://cmpg.unibe.ch/software/PGDSpider/'] sources = ['%(name)s_%(version)s.zip'] dependencies = [ - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb index 2167bd9bd68..a62393975f0 100644 --- a/easybuild/easyconfigs/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.7-foss-2020a-Python-3.8.2.eb @@ -18,8 +18,8 @@ dependencies = [ ('FASTX-Toolkit', '0.0.14'), ('ITSx', '1.1.2'), ('HMMER', '3.3.1'), - ('RDP-Classifier', '2.13', '-Java-11', True), - ('SeqKit', '0.13.2', '', True), + ('RDP-Classifier', '2.13', '-Java-11', SYSTEM), + ('SeqKit', '0.13.2', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb index 0d9fdbabdc7..e4b4218920f 100644 --- a/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PIPITS/PIPITS-2.8-foss-2021a.eb @@ -17,8 +17,8 @@ dependencies = [ ('FASTX-Toolkit', '0.0.14'), ('ITSx', '1.1.3'), ('HMMER', '3.3.2'), - ('RDP-Classifier', '2.13', '-Java-11', True), - ('SeqKit', '2.1.0', '', True), + ('RDP-Classifier', '2.13', '-Java-11', SYSTEM), + ('SeqKit', '2.1.0', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb index a77bf58f492..83910094da9 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ('Python', '2.7.11'), ('Perl', '5.22.1'), ('Tcl', '8.6.4'), diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb index fb25f08bf9e..79bce614bbe 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.8'), - ('Java', '1.7.0_80', '', True), + ('Java', '1.7.0_80', '', SYSTEM), ('Python', '2.7.12'), ('Perl', '5.24.0'), ('cairo', '1.14.6'), diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.2.12-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PRSice/PRSice-2.2.12-GCCcore-8.3.0.eb index 4408537b08e..2e22ee69d17 100644 --- a/easybuild/easyconfigs/p/PRSice/PRSice-2.2.12-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.2.12-GCCcore-8.3.0.eb @@ -21,7 +21,7 @@ checksums = ['1e3d43f269ad6c4c703431e3a96084e7c85391e00061684d60a8599d4e158c84'] builddependencies = [ ('CMake', '3.15.3'), ('binutils', '2.32'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] files_to_copy = [(['bin/PRSice'], 'bin'), "README.md", "LICENSE"] diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb index 0d030134301..1a07392a87c 100644 --- a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.1-GCCcore-9.3.0.eb @@ -21,7 +21,7 @@ checksums = ['b4adec078d7101d00390e529c9cb6d935c50d60ae17db6fa044295767d3131a4'] builddependencies = [ ('CMake', '3.16.4'), ('binutils', '2.34'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] files_to_copy = [(['bin/PRSice'], 'bin'), "README.md", "LICENSE"] diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index 99940a8a08d..e0de2012bfd 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -20,7 +20,7 @@ dependencies = [ ('Perl', '5.22.1'), ('libpsortb', '1.0'), ('BioPerl', '1.6.924', '-Perl-5.22.1'), - ('BLAST', '2.2.26', '-Linux_x86_64', True), + ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), ('pftoolsV3', '20160324'), ] diff --git a/easybuild/easyconfigs/p/PTESFinder/PTESFinder-1-intel-2017b.eb b/easybuild/easyconfigs/p/PTESFinder/PTESFinder-1-intel-2017b.eb index c495729322c..1885396ad81 100644 --- a/easybuild/easyconfigs/p/PTESFinder/PTESFinder-1-intel-2017b.eb +++ b/easybuild/easyconfigs/p/PTESFinder/PTESFinder-1-intel-2017b.eb @@ -16,7 +16,7 @@ dependencies = [ ('Bowtie', '1.2.1.1'), ('Bowtie2', '2.3.3.1'), ('BEDTools', '2.26.0'), - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb index 903ad1a1e1c..6b718496c02 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.1'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] exts_default_options = {'buildopts': 'CC="$CC"'} diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb index 947436d0265..c06f75ac1bd 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.1'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] # !! order of extensions is important !! diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 63d38816c14..596de0bad6b 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.1'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] # !! order of extensions is important !! diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index 7354490d5e4..b998f1d93d0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '6.3'), # for Term::ReadLine::Gnu ('libreadline', '8.1.2'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] # !! order of extensions is important !! diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 2a1efcc2d51..1424b9a1a56 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('ncurses', '6.3'), # for Term::ReadLine::Gnu ('libreadline', '8.1.2'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] # !! order of extensions is important !! diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb index 98b660aba06..4b0003f906b 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0-foss-2020a-Python-3.8.2.eb @@ -36,7 +36,7 @@ dependencies = [ ('SEPP', '4.3.10', versionsuffix), ('trimAl', '1.4.1'), ('BLAST+', '2.10.1'), - ('USEARCH', '11.0.667-i86linux32', '', True), + ('USEARCH', '11.0.667-i86linux32', '', SYSTEM), ('DIAMOND', '2.0.4'), ] diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb index 0e70c4e11de..7d564d27db0 100644 --- a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.2-foss-2021a.eb @@ -36,7 +36,7 @@ dependencies = [ ('SEPP', '4.5.0'), ('trimAl', '1.4.1'), ('BLAST+', '2.11.0'), - ('USEARCH', '11.0.667-i86linux32', '', True), + ('USEARCH', '11.0.667-i86linux32', '', SYSTEM), ('DIAMOND', '2.0.11'), ] diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb index bbe63ecc522..eb61569278c 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.3-GCCcore-10.3.0.eb @@ -30,7 +30,7 @@ builddependencies = [ dependencies = [ ('libreadline', '8.1'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-python --with-openssl' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb index 8c788d103e7..5cf9564e87f 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-13.4-GCCcore-11.2.0.eb @@ -30,7 +30,7 @@ builddependencies = [ dependencies = [ ('libreadline', '8.1'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-python --with-openssl' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb index f3972f8c07f..ae344d6e856 100644 --- a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-14.4-GCCcore-11.3.0.eb @@ -30,7 +30,7 @@ builddependencies = [ dependencies = [ ('libreadline', '8.1.2'), ('zlib', '1.2.12'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = '--with-python --with-openssl' diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb index 2899a206f1b..ce30da2a7da 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb @@ -15,7 +15,7 @@ checksums = ['a7dbdac7e2f0c0d2ad98f5f281d5a9d29d6673b3c20210e261b96e9a2d0b6e37'] dependencies = [ ('Python', '2.7.12'), - ('CUDA', '8.0.61', '', True), + ('CUDA', '8.0.61', '', SYSTEM), ('Boost', '1.61.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb index 4d6b28f646a..fcdf4189ca2 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('CUDA', '9.0.176', '', True), + ('CUDA', '9.0.176', '', SYSTEM), ('Boost.Python', '1.65.1', '-Python-%(pyver)s'), ('Mako', '1.0.7', '-Python-%(pyver)s'), ('pytest', '3.8.2', '-Python-%(pyver)s'), diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb index e98942047c3..13947e02b8c 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb @@ -15,7 +15,7 @@ checksums = ['6b5a9384e38c603ee429f8a6bee424532db7b3505027ce22f7e18ad19564b563'] dependencies = [ ('Python', '2.7.14'), - ('CUDA', '9.1.85', '', True), + ('CUDA', '9.1.85', '', SYSTEM), ('Boost.Python', '1.66.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb index a3f849bd92e..1d9ef9ef9e6 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb @@ -15,7 +15,7 @@ checksums = ['7079f7738e83ee79ae26f0827ada29fe55921fec9760201199cc2bfb69446c92'] dependencies = [ ('Python', '3.6.4'), - ('CUDA', '9.1.85', '', True), + ('CUDA', '9.1.85', '', SYSTEM), ('Boost.Python', '1.66.0', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb index 134d0b6c5f4..b2c7e5f1d25 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb @@ -23,7 +23,7 @@ checksums = ['0799e6c3021d6e163ef7250853922fc365c3fb94246c2cb0984381741b83ea98'] dependencies = [ ('Python', '2.7.12'), ('PyCogent', '1.9', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', True), + ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), ] options = {'modulename': '%(namelower)s'} diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb index 3d6d9af5489..d4fd449da32 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb @@ -24,7 +24,7 @@ checksums = ['0799e6c3021d6e163ef7250853922fc365c3fb94246c2cb0984381741b83ea98'] dependencies = [ ('Python', '2.7.15'), ('PyCogent', '1.9', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', True), + ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), ] options = {'modulename': '%(namelower)s'} diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb index 651a588075e..dcf058b6b89 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb @@ -19,7 +19,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.12'), ('PyCogent', '1.5.3', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', True), + ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), ] options = {'modulename': 'pynast'} diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb index e8d997ccd68..cf88ff010b2 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb @@ -10,7 +10,7 @@ description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML resea toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('PyTorch', '1.10.0', versionsuffix), ('tqdm', '4.61.2'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb index 2a45738b149..b6ac75df40b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb @@ -72,7 +72,7 @@ builddependencies = [('CMake', '3.10.2')] dependencies = [ ('Python', '3.6.4'), ('PyYAML', '3.12', '-Python-%(pyver)s'), - ('CUDA', local_cuda_ver, '', True), + ('CUDA', local_cuda_ver, '', SYSTEM), ('magma', '2.3.0', '-CUDA-%s' % local_cuda_ver), ('cuDNN', '7.0.5', '-CUDA-%s' % local_cuda_ver, True), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index cecec914c70..3dedead0354 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -73,7 +73,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions ('Python', '3.9.5'), ('protobuf', '3.17.3'), @@ -87,7 +87,7 @@ dependencies = [ ('numactl', '2.0.14'), ('FFmpeg', '4.3.2'), ('Pillow', '8.2.0'), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.6.1', '-CUDA-%(cudaver)s'), ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), ('expecttest', '0.1.3'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index a7ff2a282f4..938b94c4f93 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -86,7 +86,7 @@ dependencies = [ ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), ('expecttest', '0.1.3'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 5aba12b3957..37b6a8f47f0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -63,7 +63,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions ('Python', '3.9.5'), ('protobuf', '3.17.3'), @@ -77,7 +77,7 @@ dependencies = [ ('numactl', '2.0.14'), ('FFmpeg', '4.3.2'), ('Pillow', '8.2.0'), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.6.1', '-CUDA-%(cudaver)s'), ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), ('expecttest', '0.1.3'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb index 20dd004271e..1e64c9e1b94 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2020b.eb @@ -277,7 +277,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb index 5483fb70434..64428626873 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020a-Python-3.8.2.eb @@ -320,7 +320,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.2.2'), ('Pillow', '7.0.0', versionsuffix), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb index 5b00155d13b..63ff087989b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.7.1-fosscuda-2020b.eb @@ -28,7 +28,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb index a32c54ea29e..90e96f96e04 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.8.1-fosscuda-2020b.eb @@ -97,7 +97,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb index b4662e2722d..bcfc0d48d26 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b-imkl.eb @@ -99,7 +99,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('imkl', '2020.4.304'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb index e7070b8d189..55ca64a6024 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.9.0-fosscuda-2020b.eb @@ -98,7 +98,7 @@ dependencies = [ ('numactl', '2.0.13'), ('FFmpeg', '4.3.1'), ('Pillow', '8.0.1'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.5.4'), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb index 6f6385c7887..5ce78d117e8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.3.0-bare.eb @@ -24,7 +24,7 @@ dependencies = [ ('libreadline', '8.1'), ('ncurses', '6.2'), ('SQLite', '3.35.4'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb index 1975150da07..32a0a66ea27 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0-bare.eb @@ -24,7 +24,7 @@ dependencies = [ ('libreadline', '8.1'), ('ncurses', '6.2'), ('SQLite', '3.36'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb index c9a13925842..40d1364f4e5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('SQLite', '3.36'), ('GMP', '6.2.1'), # required for pycrypto ('libffi', '3.4.2'), # required for cryptography - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb index 30621d2d5a4..f2ad29b3f79 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.3.0-bare.eb @@ -24,7 +24,7 @@ dependencies = [ ('libreadline', '8.1.2'), ('ncurses', '6.3'), ('SQLite', '3.38.3'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb index c1e834e461b..2209fb0498b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0-bare.eb @@ -27,7 +27,7 @@ dependencies = [ ('SQLite', '3.38.3'), ('XZ', '5.2.5'), ('libffi', '3.4.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb index 0d94ec7e686..1cfac838d2c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('XZ', '5.2.5'), ('GMP', '6.2.1'), # required for pycrypto ('libffi', '3.4.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb index d4ac365a6cb..451ff497b6e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0-bare.eb @@ -27,7 +27,7 @@ dependencies = [ ('SQLite', '3.35.4'), ('XZ', '5.2.5'), ('libffi', '3.3'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb index 577405f03b6..f225ea27ce8 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.5-GCCcore-10.3.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('XZ', '5.2.5'), ('GMP', '6.2.1'), # required for pycrypto ('libffi', '3.3'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb index 6ce8d0e64b2..44e990e3147 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0-bare.eb @@ -27,7 +27,7 @@ dependencies = [ ('SQLite', '3.36'), ('XZ', '5.2.5'), ('libffi', '3.4.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb index d729015147b..707d986560a 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.9.6-GCCcore-11.2.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('XZ', '5.2.5'), ('GMP', '6.2.1'), # required for pycrypto ('libffi', '3.4.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] install_pip = True diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb index 0e997ce499e..fa0cc0df4bd 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ dependencies = [ ('libffi', '3.2.1'), ] -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/p11-kit', 'bin/trust'] + diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb index a782c5e9a6a..b84ba84bea4 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.11-foss-2020b.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Biopython', '1.78'), - ('gofasta', '0.0.5', '', True), + ('gofasta', '0.0.5', '', SYSTEM), ('minimap2', '2.18'), ('Pysam', '0.16.0.1'), ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb index 6d54365d3d7..9ed7733f533 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-10-18.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Biopython', '1.79'), - ('gofasta', '0.0.5', '', True), + ('gofasta', '0.0.5', '', SYSTEM), ('minimap2', '2.22'), ('Pysam', '0.17.0'), ('Python', '3.9.6'), diff --git a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb index ebc0440bf2b..7057ca7d244 100644 --- a/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb +++ b/easybuild/easyconfigs/p/pangolin/pangolin-3.1.16-foss-2021b-pangoLEARN-2021-11-25.eb @@ -19,7 +19,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Biopython', '1.79'), - ('gofasta', '0.0.5', '', True), + ('gofasta', '0.0.5', '', SYSTEM), ('minimap2', '2.22'), ('Pysam', '0.17.0'), ('Python', '3.9.6'), diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb index c92a89c0b3d..99145dac6d6 100644 --- a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb @@ -26,7 +26,7 @@ builddependencies = [('binutils', '2.31.1')] dependencies = [ ('Python', '3.7.2'), - ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', True) + ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', SYSTEM) ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb index 234ce1ed45d..b401fc90655 100644 --- a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb @@ -23,7 +23,7 @@ builddependencies = [('binutils', '2.34')] dependencies = [ ('Python', '3.8.2'), - ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', True) + ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', SYSTEM) ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb b/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb index ad1bce59ad9..58561192969 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.18.14-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['4941719941a46c72e72a3b160ff8b8fc7e2af90198004bd727526ce522ae8575'] postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['picard.jar'], diff --git a/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb b/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb index 570181a5407..88b4346cba4 100644 --- a/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb +++ b/easybuild/easyconfigs/p/picard/picard-2.18.17-Java-1.8.eb @@ -36,7 +36,7 @@ checksums = ['f51f64824072f26dc5d0932376929b20e6f66ff478810bcf8145792773f5474f'] postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['picard.jar'], diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb index 185ce92b1dc..6b79129e1de 100644 --- a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb index 0320934f75e..a5ae68a1194 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-5.4.0.eb @@ -17,7 +17,7 @@ checksums = ['beb43c9e064555469bd4390dcfd8030b1536e0aa103f08d7abf7ae8cac0cb001'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] # don't use PAX, it might break. diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb index dadba07804c..876023e3f43 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb @@ -19,7 +19,7 @@ patches = [ builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] # don't use PAX, it might break. diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb index b75a0d85ea9..60acff26e4a 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ source_urls = ['https://pkg-config.freedesktop.org/releases/'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] # don't use PAX, it might break. diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb index 97e2f412b2c..275ef39e9b8 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019a.eb @@ -22,9 +22,9 @@ checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] dependencies = [ ('BioPerl', '1.7.2', '-Perl-5.28.1'), ('BLAST+', '2.9.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('parallel', '20190622'), - ('tbl2asn', '20220427', '-linux64', True), + ('tbl2asn', '20220427', '-linux64', SYSTEM), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb index b0cb7c51077..fba179ce972 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2019b.eb @@ -22,9 +22,9 @@ checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] dependencies = [ ('BioPerl', '1.7.2'), ('BLAST+', '2.9.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('parallel', '20190922'), - ('tbl2asn', '20220427', '-linux64', True), + ('tbl2asn', '20220427', '-linux64', SYSTEM), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb index 8f30af1ba54..d5adf00b384 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2020b.eb @@ -22,10 +22,10 @@ checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] dependencies = [ ('BioPerl', '1.7.8'), ('BLAST+', '2.11.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bio-SearchIO-hmmer', '1.7.3'), ('parallel', '20210322'), - ('tbl2asn', '20220427', '-linux64', True), + ('tbl2asn', '20220427', '-linux64', SYSTEM), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb index ebd872de355..39eb4f8fef4 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021a.eb @@ -22,10 +22,10 @@ checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] dependencies = [ ('BioPerl', '1.7.8'), ('BLAST+', '2.11.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bio-SearchIO-hmmer', '1.7.3'), ('parallel', '20210622'), - ('tbl2asn', '20220427', '-linux64', True), + ('tbl2asn', '20220427', '-linux64', SYSTEM), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index dfba4ffaa84..4af4cb4cfef 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -20,7 +20,7 @@ source_urls = [ mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb index 1bfdad4fb7a..7c6c53dd6bf 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb @@ -20,7 +20,7 @@ mpich_opts = '--enable-static' threaded = True dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb index 93f76f8af09..4937bd9d705 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', True), + ('pscom', '5.0.48-1', '', SYSTEM), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-foss-2018a-Python-3.6.4.eb index 6bd38d27263..24a72d64d3a 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-foss-2018a-Python-3.6.4.eb @@ -16,7 +16,7 @@ checksums = ['b69e83658513215b8d1443544d0549b7d231b9f201f6fc787a2b2218b408181e'] builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('pytest', '3.8.0', versionsuffix), ] dependencies = [('Python', '3.6.4')] diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb index 65b955a13b7..968a6a89f01 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.2.4-intel-2018b-Python-3.6.6.eb @@ -16,7 +16,7 @@ checksums = ['b69e83658513215b8d1443544d0549b7d231b9f201f6fc787a2b2218b408181e'] builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ('pytest', '3.8.2', versionsuffix), ] dependencies = [('Python', '3.6.6')] diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb index 37a8909ca53..fbdf9a41967 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.4.3-GCCcore-8.3.0-Python-3.7.4.eb @@ -19,7 +19,7 @@ checksums = [ builddependencies = [ ('binutils', '2.32'), ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [('Python', '3.7.4')] diff --git a/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb index b3f71b6a46b..eafbd05b096 100644 --- a/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/python-weka-wrapper3/python-weka-wrapper3-0.1.11-foss-2019b-Python-3.7.4.eb @@ -13,7 +13,7 @@ dependencies = [ ('Python', '3.7.4'), ('matplotlib', '3.1.1', versionsuffix), ('Pillow', '6.2.1'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb index 341f884f89e..43f185c60fd 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb @@ -25,7 +25,7 @@ dependencies = [ ('Python', '3.5.2'), ('Perl', '5.24.0'), ('matplotlib', '1.5.3', versionsuffix), - ('Java', '1.8.0_131', '', True), + ('Java', '1.8.0_131', '', SYSTEM), ('Boost', '1.63.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb index f0f4d2c5b81..79f2d229658 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb @@ -23,7 +23,7 @@ dependencies = [ ('Python', '3.6.4'), ('Perl', '5.26.1'), ('matplotlib', '2.1.2', versionsuffix), - ('Java', '1.8.0_162', '', True), + ('Java', '1.8.0_162', '', SYSTEM), ('Boost', '1.66.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb index f3b210b0ca5..da0694b350b 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.0'), ('matplotlib', '2.2.3', versionsuffix), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Boost', '1.67.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb index cef7ad2f682..aee9ee6a397 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.1'), ('matplotlib', '2.2.4', versionsuffix), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.70.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb index 01960475b5e..9e7475ccdd8 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-3.7.2.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '3.7.2'), ('Perl', '5.28.1'), ('matplotlib', '3.0.3', versionsuffix), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.70.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb index 87ae71af604..e0f1cd1e1ce 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020a-Python-3.8.2.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '3.8.2'), ('Perl', '5.30.2'), ('matplotlib', '3.2.1', versionsuffix), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.72.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb index 58f9709a656..81762184ba7 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b-Python-2.7.18.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '2.7.18'), ('Perl', '5.32.0'), ('matplotlib', '2.2.5', versionsuffix), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.74.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb index 53e95a0065d..d0057cb1ac6 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2020b.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.8.6'), ('Perl', '5.32.0'), ('matplotlib', '3.3.3'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.74.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb index 2fa06228d15..435b062ca1e 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.9.5'), ('Perl', '5.32.1'), ('matplotlib', '3.4.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.76.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb index eedf3ea7c27..6a2efd7b120 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2021b.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.9.6'), ('Perl', '5.34.0'), ('matplotlib', '3.4.3'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Boost', '1.77.0'), ] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb index 26cc0e00521..d81dfc2eebd 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb index 5bc3462602c..dc3c3684a36 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb index 0d7bdcbe989..ec6b5ac968f 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb @@ -56,7 +56,7 @@ dependencies = [ ('snappy', '1.1.8'), ('JasPer', '2.0.28'), ('bzip2', '1.0.8'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index 16cca743fc8..ab34684b136 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -61,7 +61,7 @@ dependencies = [ ('snappy', '1.1.9'), ('JasPer', '2.0.33'), ('bzip2', '1.0.8'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('ICU', '69.1'), ] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb index c12b05d90b1..a9d014e9d75 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb @@ -61,7 +61,7 @@ dependencies = [ ('snappy', '1.1.9'), ('JasPer', '2.0.33'), ('bzip2', '1.0.8'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('ICU', '71.1'), ('nodejs', '16.15.1'), ] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb index ea7a0361a22..5138261fdec 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb @@ -23,7 +23,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb index cb2811a839e..cf7f35e5fee 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb @@ -23,7 +23,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb index 316cae4a7e0..4309fafb895 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-foss-2016a.eb @@ -23,7 +23,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb index 6ddda44037e..db20d4633cd 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.7.0-intel-2016a.eb @@ -23,7 +23,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb index 90bf997ca5c..35374dd4af2 100644 --- a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2019a-R-3.6.0.eb @@ -16,7 +16,7 @@ sources = ['qualimap_v%(version)s.zip'] checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('R', '3.6.0'), ('R-bundle-Bioconductor', '3.9', versionsuffix), ] diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb index 4b25f9686c6..70260a39f73 100644 --- a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2020b-R-4.0.3.eb @@ -16,7 +16,7 @@ sources = ['qualimap_v%(version)s.zip'] checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', versionsuffix), ] diff --git a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb index fdbfeb2bd21..ee634ca5d69 100644 --- a/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/q/Qualimap/Qualimap-2.2.1-foss-2021b-R-4.1.2.eb @@ -16,7 +16,7 @@ sources = ['qualimap_v%(version)s.zip'] checksums = ['08f1d66e49c83c76c56c4225c53aee44f41e0592c8bdc84b8c4ecd975700e045'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('R', '4.1.2'), ('R-bundle-Bioconductor', '3.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb index 503529a7dda..856611cdef4 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb index 4606a8754dd..8598fef3f0a 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb index 10bcf7e69ec..acb8163c2da 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb index aa995966ac0..cf10b5462d5 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index f3ec1cac38c..c5c88c181d4 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -23,7 +23,7 @@ dependencies = [ ('libjpeg-turbo', '1.4.2'), # for plottting in R ('LibTIFF', '4.0.6'), # for plotting in R ('cairo', '1.14.6'), # for plotting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', versionsuffix), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 841c073f2b3..4f6c9a71091 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb index 067c596089e..84e20abc2e2 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb index cd605ba827a..32c2e7ab309 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb index ebe33155b56..724a3ceed71 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb index 13ed7e3b872..2f0044cf886 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.24'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2016b-X11-20160819.eb index c9d9b92cc47..c29dcf3fa05 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2016b-X11-20160819.eb @@ -27,7 +27,7 @@ dependencies = [ ('libpng', '1.6.24'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 11f7ae9944f..8436e30f382 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.29'), # for plotting in R ('libjpeg-turbo', '1.5.1'), # for plottting in R ('LibTIFF', '4.0.7'), - ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_121', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.6'), # for tcltk ('Tk', '8.6.6'), # for tcltk ('cURL', '7.53.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index 01b9b412a37..c8fa9e81b36 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.29'), # for plotting in R ('libjpeg-turbo', '1.5.1'), # for plottting in R ('LibTIFF', '4.0.7'), - ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_121', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.6'), # for tcltk ('Tk', '8.6.6'), # for tcltk ('cURL', '7.53.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb index 515080f4f37..e6902b752ee 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb @@ -32,7 +32,7 @@ dependencies = [ ('libpng', '1.6.24'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_141', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_141', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb index 93b5974cfca..25a9ce4249a 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.55.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb index 72a1d8f4d5b..f09e4a993e8 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb @@ -31,7 +31,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.8'), - ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.56.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb index 10a97cc8586..ea2dd212efd 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.8'), - ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.56.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb index 25d65103609..70cf55f16c3 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb index dc9f868dc2b..5422e8e8b16 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb index 83ac3843168..df2f0ef39b8 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb index 7c15c4437a8..0852baef0e8 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.0-iomkl-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb index b13278061d0..3cf0f77bff8 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-Python-2.7.15.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '2.0.0'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Tk', '8.6.8'), # for tcltk ('cURL', '7.60.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb index b6425f1a0f4..75f04ccc800 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb @@ -36,7 +36,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '2.0.0'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Tk', '8.6.8'), # for tcltk ('cURL', '7.60.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb index 72905166d7d..e0d6e243698 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b.eb @@ -28,7 +28,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '2.0.0'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Tk', '8.6.8'), # for tcltk ('cURL', '7.60.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb index 4fad425acdd..85c028d5c76 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-intel-2018b.eb @@ -28,7 +28,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '2.0.0'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Tk', '8.6.8'), # for tcltk ('cURL', '7.60.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb index b3dfeeb1012..4e4d1c99a5f 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-foss-2019a.eb @@ -29,7 +29,7 @@ dependencies = [ ('libpng', '1.6.36'), # for plotting in R ('libjpeg-turbo', '2.0.2'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.63.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb index df2b372cf23..f20ae1ce680 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-fosscuda-2019a.eb @@ -29,7 +29,7 @@ dependencies = [ ('libpng', '1.6.36'), # for plotting in R ('libjpeg-turbo', '2.0.2'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.63.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb b/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb index 190263d2d3c..385c219696e 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.0-intel-2019a.eb @@ -29,7 +29,7 @@ dependencies = [ ('libpng', '1.6.36'), # for plotting in R ('libjpeg-turbo', '2.0.2'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.63.0'), # for RCurl ('libxml2', '2.9.8'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb index 0bc641a52fc..70af7d3e9fd 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-foss-2019b.eb @@ -35,7 +35,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.3'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.66.0'), # for RCurl ('libxml2', '2.9.9'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb index c455fc487cf..99a3664d030 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-fosscuda-2019b.eb @@ -35,7 +35,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.3'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.66.0'), # for RCurl ('libxml2', '2.9.9'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb index cabb0423e80..a3abe2e37ee 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb @@ -33,7 +33,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.3'), # for plottting in R ('LibTIFF', '4.0.10'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.9'), # for tcltk ('cURL', '7.66.0'), # for RCurl ('libxml2', '2.9.9'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb index dc8f3642b9a..ad7708d2b1f 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb @@ -29,7 +29,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.4'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.69.1'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 9afb0e13b61..faa29bd2b3e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -34,7 +34,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.4'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.69.1'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb index 4bd3700f409..e1e620b5669 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-fosscuda-2020a.eb @@ -34,7 +34,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.4'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.69.1'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb index 3226ee0f4bc..782f039b492 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-foss-2020b.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb index d35824d64ba..db5d9c9e47c 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.3-fosscuda-2020b.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb index 26d6cbdb27b..c7d07e5f2ac 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-foss-2020b.eb @@ -36,7 +36,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb index 9c612d32b95..afc6216b0bf 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.4-fosscuda-2020b.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb index febdb0ca5e7..bf2b31d78ee 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-foss-2020b.eb @@ -33,7 +33,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb index d1e5430a104..be10c211dc4 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.5-fosscuda-2020b.eb @@ -33,7 +33,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.5'), # for plottting in R ('LibTIFF', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.10'), # for tcltk ('cURL', '7.72.0'), # for RCurl ('libxml2', '2.9.10'), # for XML diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index 3bdb84f74b2..d7eb4353a4d 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -34,7 +34,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.6'), # for plottting in R ('LibTIFF', '4.2.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.11'), # for tcltk ('cURL', '7.76.0'), # for RCurl ('libxml2', '2.9.10'), # for XML @@ -51,7 +51,7 @@ dependencies = [ ('nodejs', '14.17.0'), # for V8 (required by rstan) ('GDAL', '3.3.0'), # for sf ('libgit2', '1.1.0'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 9c0872e0343..97750491d42 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -34,7 +34,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.6'), # for plottting in R ('LibTIFF', '4.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.11'), # for tcltk ('cURL', '7.78.0'), # for RCurl ('libxml2', '2.9.10'), # for XML @@ -52,7 +52,7 @@ dependencies = [ ('GDAL', '3.3.2'), # for sf ('MPFR', '4.1.0'), # for Rmpfr ('libgit2', '1.1.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 46ee68285da..6175f90d834 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -35,7 +35,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.0.6'), # for plottting in R ('LibTIFF', '4.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.11'), # for tcltk ('cURL', '7.78.0'), # for RCurl ('libxml2', '2.9.10'), # for XML @@ -53,7 +53,7 @@ dependencies = [ ('GDAL', '3.3.2'), # for sf ('MPFR', '4.1.0'), # for Rmpfr ('libgit2', '1.1.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 1dfdcecb129..b97f484e225 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -31,7 +31,7 @@ dependencies = [ ('libpng', '1.6.37'), # for plotting in R ('libjpeg-turbo', '2.1.3'), # for plottting in R ('LibTIFF', '4.3.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Tk', '8.6.12'), # for tcltk ('cURL', '7.83.0'), # for RCurl ('libxml2', '2.9.13'), # for XML @@ -49,7 +49,7 @@ dependencies = [ ('GDAL', '3.5.0'), # for sf ('MPFR', '4.1.0'), # for Rmpfr ('libgit2', '1.4.3'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb index 84be9e4f58f..5cec5783bdc 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2018.09.3-intel-2018b-Python-3.6.6.eb @@ -15,7 +15,7 @@ checksums = ['3be20bade43657c0d74617ab99ca30f872eaaedc314a87f690ac38e5ef590224'] builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2019.09.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2019.09.3-foss-2019b-Python-3.7.4.eb index d7db7604054..eb85dc0a82a 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2019.09.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2019.09.3-foss-2019b-Python-3.7.4.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb index 0f3478b407f..3ddb556d58b 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-foss-2020a-Python-3.8.2.eb @@ -26,7 +26,7 @@ checksums = [ # https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source builddependencies = [ ('CMake', '3.16.4'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb index 9114ab335e8..33bde2b7c1f 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2020.03.3-intel-2020a-Python-3.8.2.eb @@ -26,7 +26,7 @@ checksums = [ # https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source builddependencies = [ ('CMake', '3.16.4'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb index 30280d9b65f..501cd89e3bc 100644 --- a/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2020.09.3-foss-2019b-Python-3.7.4.eb @@ -24,7 +24,7 @@ checksums = [ # https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('pkg-config', '0.29.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2018a-CUDA-9.1.85.eb b/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2018a-CUDA-9.1.85.eb index 747d228757a..c9c0251c232 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2018a-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-2.1-foss-2018a-CUDA-9.1.85.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [('CMake', '3.10.1')] dependencies = [ - ('CUDA', local_cuda_ver, '', True), + ('CUDA', local_cuda_ver, '', SYSTEM), ('X11', '20180131'), ('FLTK', '1.3.4'), ] diff --git a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb index dbd242572b8..babe47dcf73 100644 --- a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.2.3-GCC-8.3.0.eb @@ -13,7 +13,7 @@ sources = ['rnabloom_v%(version)s.tar.gz'] checksums = ['7418761ff99f24f0edc23772cfa517c3d7401eac98642dcb017d48fb35c6ee4a'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('minimap2', '2.17'), ('Racon', '1.4.13'), ('ntCard', '1.2.1'), diff --git a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb index 02ac929561f..86df5571106 100644 --- a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-1.4.3-GCC-11.2.0.eb @@ -13,7 +13,7 @@ sources = ['rnabloom_v%(version)s.tar.gz'] checksums = ['819274d674fe350ae3a1e1136618d52a8abb941280f604c6777ea4540b299a38'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('minimap2', '2.24'), ('Racon', '1.5.0'), ('ntCard', '1.2.1'), diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2016b-Java-1.8.0_121.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2016b-Java-1.8.0_121.eb index 9ff75608237..f6ee37eac64 100644 --- a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2016b-Java-1.8.0_121.eb +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2016b-Java-1.8.0_121.eb @@ -22,7 +22,7 @@ checksums = ['0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793'] dependencies = [ ('BWA', '0.7.16a'), - ('Java', '1.8.0_121', '', True), + ('Java', '1.8.0_121', '', SYSTEM), ] modloadmsg = """To execute RNA-SeQC run: java -jar $EBROOTRNAMINSEQC/%(name)s_v%(version)s.jar\n""" diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2018b-Java-1.8.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2018b-Java-1.8.eb index 75bf91935f7..22e20680911 100644 --- a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2018b-Java-1.8.eb +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-foss-2018b-Java-1.8.eb @@ -22,7 +22,7 @@ checksums = ['0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793'] dependencies = [ ('BWA', '0.7.17'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] modloadmsg = "To execute RNA-SeQC run: java -jar $EBROOTRNAMINSEQC/%(name)s_v%(version)s.jar" diff --git a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb index 7cc11725a88..147016a5526 100644 --- a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.6.6'), ('Pysam', '0.15.1', versionsuffix), ('scikit-learn', '0.20.0', versionsuffix), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb index dc9c93177cf..1a666f6fc94 100644 --- a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.6.6'), ('Pysam', '0.15.1', versionsuffix), ('scikit-learn', '0.20.0', versionsuffix), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5033-fosscuda-2019b-Java-11.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5033-fosscuda-2019b-Java-11.eb index e68f58adf65..0e6ae1282eb 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5033-fosscuda-2019b-Java-11.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5033-fosscuda-2019b-Java-11.eb @@ -29,13 +29,13 @@ checksums = [ builddependencies = [ ('pkg-config', '0.29.2'), ('CMake', '3.15.3'), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Boost', '1.71.0'), ('R', '3.6.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] osdependencies = [ diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5042-foss-2019b-Java-11.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5042-foss-2019b-Java-11.eb index 756445042c1..b91df14e310 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5042-foss-2019b-Java-11.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.2.5042-foss-2019b-Java-11.eb @@ -29,13 +29,13 @@ checksums = [ builddependencies = [ ('pkg-config', '0.29.2'), ('CMake', '3.15.3'), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Boost', '1.71.0'), ('R', '3.6.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] osdependencies = [ diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb index 4c871371f5e..80dfe9052a9 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb @@ -29,13 +29,13 @@ checksums = [ builddependencies = [ ('pkg-config', '0.29.2'), ('CMake', '3.16.4'), - ('ant', '1.10.8', '-Java-%(javaver)s', True), + ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Boost', '1.72.0'), ('R', '4.0.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] osdependencies = [ diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb index 26f4b962160..2ef5e389064 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.3.959-foss-2020a-Java-11-R-4.0.0.eb @@ -25,13 +25,13 @@ checksums = [ builddependencies = [ ('pkg-config', '0.29.2'), ('CMake', '3.16.4'), - ('ant', '1.10.8', '-Java-%(javaver)s', True), + ('ant', '1.10.8', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Boost', '1.72.0'), ('R', '4.0.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] osdependencies = [ diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb index d163c925d0c..db9cd5d65bf 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-1.4.1717-foss-2021a-Java-11-R-4.1.0.eb @@ -21,13 +21,13 @@ checksums = ['3af234180fd7cef451aef40faac2c7b52860f14a322244c1c7aede029814d261'] builddependencies = [ ('pkg-config', '0.29.2'), ('CMake', '3.20.1'), - ('ant', '1.10.11', '-Java-%(javaver)s', True), + ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), ] dependencies = [ ('Boost', '1.76.0'), ('R', '4.1.0'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('SOCI', '4.0.2'), ] diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb index e8ef0ee102f..786360704ba 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb @@ -14,7 +14,7 @@ checksums = ['e294396f49ec236626c47020ce3c893ba08a50bce204e1d51a074978d215b558'] dependencies = [ ('Perl', '5.26.0'), - ('TRF', '4.09', '-linux64', True), + ('TRF', '4.09', '-linux64', SYSTEM), ('HMMER', '3.1b2'), ] diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb index 52f3b80f931..7eafecb7975 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-iccifort-2017.4.196-GCC-6.4.0-2.28-Perl-5.26.0-HMMER.eb @@ -14,7 +14,7 @@ checksums = ['e294396f49ec236626c47020ce3c893ba08a50bce204e1d51a074978d215b558'] dependencies = [ ('Perl', '5.26.0'), - ('TRF', '4.09', '-linux64', True), + ('TRF', '4.09', '-linux64', SYSTEM), ('HMMER', '3.1b2'), ] diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-intel-2018b-Perl-5.28.0-HMMER.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-intel-2018b-Perl-5.28.0-HMMER.eb index 49bf1b790e1..ffb217fc6f4 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-intel-2018b-Perl-5.28.0-HMMER.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.8-intel-2018b-Perl-5.28.0-HMMER.eb @@ -14,7 +14,7 @@ checksums = ['e294396f49ec236626c47020ce3c893ba08a50bce204e1d51a074978d215b558'] dependencies = [ ('Perl', '5.28.0'), - ('TRF', '4.09', '-linux64', True), + ('TRF', '4.09', '-linux64', SYSTEM), ('HMMER', '3.2.1'), ] diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb index bb5f15e74c3..9f6c7bc0b01 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.0.9-p2-gompi-2019b-HMMER.eb @@ -25,7 +25,7 @@ checksums = [ dependencies = [ ('Perl', '5.30.0'), - ('TRF', '4.09', '-linux64', True), + ('TRF', '4.09', '-linux64', SYSTEM), ('HMMER', '3.2.1'), ] diff --git a/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb b/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb index 86bb0bbf1ae..b9117db641e 100644 --- a/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb +++ b/easybuild/easyconfigs/r/RheoTool/RheoTool-5.0-foss-2019b.eb @@ -15,7 +15,7 @@ checksums = ['2e0899684d6d7f9ddee0d93b39a6ed56262b171bc4e5536914645209b66003ed'] dependencies = [ ('OpenFOAM', '7', '-20200508'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('PETSc', '3.12.4', '-Python-3.7.4'), ] diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb index eaec7699da4..7eab5f3ec8d 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb index 2a008d86759..8d66638b61d 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.52.1-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb index 9f045c62c02..3916f14fbd9 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.54.0-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb index 58777add4e0..c70ed36ffd9 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.56.0-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb index 5eab0202819..0b1bb2ee921 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb index ecaf7753a89..0a1bf6c1485 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.60.0-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " diff --git a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb index 6680caa1442..2a055d37ff0 100644 --- a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2021a-CUDA-11.3.1.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'PhoenixDL' dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), # provides numpy ('PyTorch', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index dbefc98c9f4..173bc41c41a 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -27,8 +27,8 @@ dependencies = [ ('R', '4.1.2'), ('BLAST+', '2.12.0'), ('AUGUSTUS', '3.4.0'), - ('Java', '11', '', True), - ('Maven', '3.6.3', '', True), + ('Java', '11', '', SYSTEM), + ('Maven', '3.6.3', '', SYSTEM), ('plotly.py', '5.4.0'), ('ETE', '3.1.2'), ('PyYAML', '5.4.1'), diff --git a/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb index f137d101fa2..e19b28dbb97 100644 --- a/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/s/SECAPR/SECAPR-1.1.15-foss-2019b-Python-2.7.16.eb @@ -17,16 +17,16 @@ dependencies = [ ('ABySS', '2.1.5'), ('Biopython', '1.75', versionsuffix), ('BWA', '0.7.17'), - ('picard', '2.21.6', '-Java-11', True), + ('picard', '2.21.6', '-Java-11', SYSTEM), ('BCFtools', '1.10.2'), ('EMBOSS', '6.6.0', '-Java-11'), - ('FastQC', '0.11.9', '-Java-11', True), + ('FastQC', '0.11.9', '-Java-11', SYSTEM), ('LASTZ', '1.04.03'), ('MAFFT', '7.453', '-with-extensions'), ('MUSCLE', '3.8.1551'), ('SAMtools', '1.10'), ('seqtk', '1.3'), - ('Trimmomatic', '0.39', '-Java-11', True), + ('Trimmomatic', '0.39', '-Java-11', SYSTEM), ('Trinity', '2.9.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.1-GCCcore-8.2.0-Java-11.eb b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.1-GCCcore-8.2.0-Java-11.eb index dcc982d7e1f..ae01366c9ef 100644 --- a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.1-GCCcore-8.2.0-Java-11.eb +++ b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.1-GCCcore-8.2.0-Java-11.eb @@ -20,7 +20,7 @@ checksums = ['11cd754087fc3a8a12362af6140949726d4c32f1097a7c387d116cc1cf7e234e'] builddependencies = [('binutils', '2.31.1')] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('NGS', '2.10.0', '-Java-11'), ('bzip2', '1.0.6'), ] diff --git a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb index 41984431bdc..3aac6838fbf 100644 --- a/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SRPRISM/SRPRISM-3.1.2-GCCcore-10.2.0.eb @@ -15,7 +15,7 @@ checksums = ['93e6864b7ab18be96584950227426102b545db7d6d02762490a43e1610b7eb9b'] builddependencies = [('binutils', '2.35')] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('NGS', '2.10.9'), ('bzip2', '1.0.8'), ] diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb index fecda0386ee..5d5ce7762a7 100644 --- a/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.12.0-foss-2021b.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [ ('CMake', '3.22.1'), ('SWIG', '4.0.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb index 17783cb2a67..fb78dda30bc 100644 --- a/easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.14.1-foss-2021b.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [ ('CMake', '3.22.1'), ('SWIG', '4.0.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb index 30e5d21317c..eb4f55f2430 100644 --- a/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb @@ -23,7 +23,7 @@ checksums = [ builddependencies = [ ('CMake', '3.16.4'), ('SWIG', '4.0.1'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb index d65645b9dd5..d319f5ccfa1 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ dependencies = [ ('APR', '1.7.0'), ('APR-util', '1.6.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb index c6fb0da1ec0..72cdc72b88f 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ dependencies = [ ('APR', '1.7.0'), ('APR-util', '1.6.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" diff --git a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb index 3781b94855a..b6965d55e69 100644 --- a/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Shasta/Shasta-0.8.0-foss-2020b.eb @@ -29,7 +29,7 @@ checksums = [ builddependencies = [ ('CMake', '3.18.4'), - ('Cereal', '1.3.0', '', True), + ('Cereal', '1.3.0', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb index 03165ec8f41..29d9b21e0d8 100644 --- a/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/SimpleElastix/SimpleElastix-1.1.0-foss-2019b-Python-3.7.4.eb @@ -16,7 +16,7 @@ toolchainopts = {'pic': True} builddependencies = [ ('CMake', '3.15.3'), ('Bison', '3.3.2'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ('googletest', '1.10.0'), ] diff --git a/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb index 35d4801c28d..01f18a9bb75 100644 --- a/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb @@ -23,7 +23,7 @@ dependencies = [ ('OrfM', '0.7.1'), ('HMMER', '3.2.1'), ('fxtract', '2.3'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('KronaTools', '2.7.1'), ('DIAMOND', '0.9.24'), ] diff --git a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb index 63485234dcb..996aeca133c 100644 --- a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb @@ -19,7 +19,7 @@ dependencies = [ ('Pysam', '0.17.0'), ('Biopython', '1.79'), ('SAMtools', '1.14'), - ('VarScan', '2.4.4', '-Java-11', True), + ('VarScan', '2.4.4', '-Java-11', SYSTEM), ('R', '4.1.2'), ('NextGenMap', '0.5.5'), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb index 0e81ab6be6c..31aafdd2c90 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb @@ -18,7 +18,7 @@ source_urls = [ checksums = ['86f33f6f4fe545cb848600004144f09b6e8413af47ce02c1203c3ecda075288d'] dependencies = [ - ('Java', '1.8.0_152', '', True), + ('Java', '1.8.0_152', '', SYSTEM), ('Python', '3.6.3'), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb index 073734a3f85..f14e575058a 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-Hadoop-2.7-Java-1.8.eb @@ -17,7 +17,7 @@ source_urls = [ ] checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/spark-shell'], diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb index 23510072e38..d780b9c3b02 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-foss-2018b-Python-2.7.15.eb @@ -19,7 +19,7 @@ checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] dependencies = [ ('Python', '2.7.15'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.9.2', '-native'), ('Arrow', '0.12.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb index 6fa3caf6ede..e643595c370 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Hadoop-2.7-Java-1.8-Python-3.6.6.eb @@ -19,7 +19,7 @@ sources = ['%%(namelower)s-%%(version)s-bin-hadoop%s.tgz' % local_hadoopver] checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Python', '3.6.6'), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb index 387340456d0..f7991b20743 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-2.7.15.eb @@ -19,7 +19,7 @@ checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] dependencies = [ ('Python', '2.7.15'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.9.2', '-native'), ('Arrow', '0.12.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb index cd360504934..7dd10c2a0c7 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.0-intel-2018b-Python-3.6.6.eb @@ -19,7 +19,7 @@ checksums = ['c93c096c8d64062345b26b34c85127a6848cff95a4bb829333a06b83222a5cfa'] dependencies = [ ('Python', '3.6.6'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.9.2', '-native'), ('Arrow', '0.12.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb b/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb index f8644c9fdea..46a739bcb58 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.4.5-intel-2019b-Python-3.7.4-Java-1.8.eb @@ -22,7 +22,7 @@ checksums = ['020be52524e4df366eb974d41a6e18fcb6efcaba9a51632169e917c74267dd81'] dependencies = [ ('Python', '3.7.4'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.10.0', '-native'), ('Arrow', '0.16.0', local_python_versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb index adae6b1c2c7..c7ad27d0aa2 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-foss-2018b-Python-2.7.15.eb @@ -18,7 +18,7 @@ checksums = ['98f6b92e5c476d7abb93cc179c2616aa5dc897da25753bd197e20ef54a28d945'] dependencies = [ ('Python', '2.7.15'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.9.2', '-native'), ('Arrow', '0.12.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb index df8e7e468b1..64cc3061e75 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.0.0-intel-2018b-Python-2.7.15.eb @@ -18,7 +18,7 @@ checksums = ['98f6b92e5c476d7abb93cc179c2616aa5dc897da25753bd197e20ef54a28d945'] dependencies = [ ('Python', '2.7.15'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Hadoop', '2.9.2', '-native'), ('Arrow', '0.12.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb index cecf3035382..fd433043377 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020a-Python-3.8.2.eb @@ -20,7 +20,7 @@ checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] dependencies = [ ('Python', '3.8.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # ('Hadoop', '2.10.0', '-native'), ('Arrow', '0.17.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb index 5cb1ec3c5ee..c5815aa76aa 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-foss-2020b.eb @@ -19,7 +19,7 @@ checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] dependencies = [ ('Python', '3.8.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # ('Hadoop', '2.10.0', '-native'), ('Arrow', '0.17.1'), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb index b4585778e53..e08aae3577c 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.1.1-fosscuda-2020b.eb @@ -19,7 +19,7 @@ checksums = ['4e0846207bf10311de43451bc99309086fce7990aaf54bf3038608b1981afbe7'] dependencies = [ ('Python', '3.8.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # ('Hadoop', '2.10.0', '-native'), ('Arrow', '0.17.1'), ] diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb b/easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb index 7ae8baa1987..f9867229cb9 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.2.1-foss-2021b.eb @@ -19,7 +19,7 @@ checksums = ['224e058cb0c6fb68b39896427a3ccd11ae2246e9bf465b5e29e4fb192d39a59c'] dependencies = [ ('Python', '3.9.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), # ('Hadoop', '2.10.0', '-native'), ('Arrow', '6.0.0'), ] diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb index 99b2e9b26ea..a6aacdefcaf 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-0.4.3-foss-2018b-Python-2.7.15.eb @@ -34,12 +34,12 @@ dependencies = [ ('DIAMOND', '0.9.22'), ('MEGAHIT', '1.1.4', versionsuffix), ('minimap2', '2.13'), - ('Java', '1.8', '', True), - ('RDP-Classifier', '2.12', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('RDP-Classifier', '2.12', '-Java-%(javaver)s', SYSTEM), ('MetaBAT', '2.12.1', versionsuffix), ('MinPath', '1.4', versionsuffix), # depends on GPLK (which provides glpsol) ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), - ('Trimmomatic', '0.38', '-Java-%(javaver)s', True), + ('Trimmomatic', '0.38', '-Java-%(javaver)s', SYSTEM), ('AMOS', '3.1.0'), ('MaxBin', '2.2.6', '-Perl-%(perlver)s'), ('SPAdes', '3.13.0'), @@ -47,7 +47,7 @@ dependencies = [ ('canu', '1.8', '-Perl-%(perlver)s'), ('HMMER', '3.2.1'), ('MUMmer', '4.0.0beta2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ] keepsymlinks = True diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb index bc932b4a6c7..49bda51b080 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.0.0-foss-2018b-Python-2.7.15.eb @@ -33,12 +33,12 @@ dependencies = [ ('DIAMOND', '0.9.22'), ('MEGAHIT', '1.1.4', versionsuffix), ('minimap2', '2.13'), - ('Java', '1.8', '', True), - ('RDP-Classifier', '2.12', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('RDP-Classifier', '2.12', '-Java-%(javaver)s', SYSTEM), ('MetaBAT', '2.12.1', versionsuffix), ('MinPath', '1.4', versionsuffix), # depends on GPLK (which provides glpsol) ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), - ('Trimmomatic', '0.38', '-Java-%(javaver)s', True), + ('Trimmomatic', '0.38', '-Java-%(javaver)s', SYSTEM), ('AMOS', '3.1.0'), ('MaxBin', '2.2.6', '-Perl-%(perlver)s'), ('SPAdes', '3.13.0'), @@ -46,7 +46,7 @@ dependencies = [ ('canu', '1.8', '-Perl-%(perlver)s'), ('HMMER', '3.2.1'), ('MUMmer', '4.0.0beta2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('Short-Pair', '20170125', versionsuffix), ('SAMtools', '1.9'), ('CompareM', '0.0.23', versionsuffix), diff --git a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb index 492c34fe96c..f1a8cec6d8d 100644 --- a/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SqueezeMeta/SqueezeMeta-1.5.0-foss-2021b.eb @@ -30,12 +30,12 @@ dependencies = [ ('DIAMOND', '2.0.13'), ('MEGAHIT', '1.2.9'), ('minimap2', '2.22'), - ('Java', '11', '', True), - ('RDP-Classifier', '2.13', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('RDP-Classifier', '2.13', '-Java-%(javaver)s', SYSTEM), ('MetaBAT', '2.15'), ('MinPath', '1.6'), # depends on GPLK (which provides glpsol) ('PRINSEQ', '0.20.4', '-Perl-%(perlver)s'), - ('Trimmomatic', '0.39', '-Java-%(javaver)s', True), + ('Trimmomatic', '0.39', '-Java-%(javaver)s', SYSTEM), ('AMOS', '3.1.0'), ('MaxBin', '2.2.7'), ('SPAdes', '3.15.3'), @@ -43,7 +43,7 @@ dependencies = [ ('canu', '2.2'), ('HMMER', '3.3.2'), ('MUMmer', '4.0.0beta2'), - ('pplacer', '1.1.alpha19', '', True), + ('pplacer', '1.1.alpha19', '', SYSTEM), ('Short-Pair', '20170125'), ('SAMtools', '1.14'), ('CompareM', '0.1.2'), diff --git a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb index 9721dbb7e51..b360d49ed19 100644 --- a/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/s/StringTie/StringTie-1.3.5-GCCcore-8.2.0.eb @@ -14,7 +14,7 @@ source_urls = ['http://ccb.jhu.edu/software/%(namelower)s/dl/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['f16ec07d4869b7656bc1a9b6eb662fd9404c122d18431c845e93d810840c5db9'] -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-foss-2017b.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-foss-2017b.eb index 309d66a48c7..cd483fdf31e 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-foss-2017b.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-foss-2017b.eb @@ -30,7 +30,7 @@ dependencies = [ ('Python', '2.7.14'), ('Perl', '5.26.1'), ('Ruby', '2.4.2'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('SWIG', '3.0.12', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-intel-2017b.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-intel-2017b.eb index 8d399be6349..ca96dc353d4 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-intel-2017b.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.10.0-intel-2017b.eb @@ -30,7 +30,7 @@ dependencies = [ ('Python', '2.7.14'), ('Perl', '5.26.1'), ('Ruby', '2.5.0'), - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('SWIG', '3.0.12', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb index 2ef23ba8a82..0b9443692f3 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-foss-2021a-METIS-5.1.0-CUDA-11.3.1.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('METIS', local_metis_ver), ('MPFR', '4.1.0'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb index d42e2e93387..b69c7feaf2e 100644 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ checksums = ['a816d95d5662e8279625abdbea7d0e62157d7d1f028020b1075500bf483ed5ef'] configopts = "--with-pic" -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + diff --git a/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb b/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb index 09e6c9dafd7..8fa744e8aee 100644 --- a/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/s/sbt/sbt-1.0.2-Java-1.8.0_152.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/sbt/sbt/releases/download/v%(version)s'] sources = [SOURCE_TGZ] checksums = ['c3f063d8122d87f0d80b25221d76b0a164e9247d35190f31ec360edcb4352ef0'] -dependencies = [('Java', '1.8.0_152', '', True)] +dependencies = [('Java', '1.8.0_152', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/sbt'], diff --git a/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb index 06f3fc97f7e..e45a4e372cc 100644 --- a/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/shar', 'bin/uudecode', 'bin/uuencode', 'bin/unshar'], diff --git a/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb index 86ecd27ae6a..45fe9061553 100644 --- a/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb @@ -23,11 +23,11 @@ dependencies = [ ('SKESA', '2.2'), ('MEGAHIT', '1.1.3', versionsuffix), ('KMC', '3.1.0'), - ('Pilon', '1.22', '-Java-1.8.0_162', True), + ('Pilon', '1.22', '-Java-1.8.0_162', SYSTEM), ('SPAdes', '3.12.0'), ('Lighter', '1.1.1'), ('FLASH', '1.2.11'), - ('Trimmomatic', '0.38', '-Java-1.8.0_162', True), + ('Trimmomatic', '0.38', '-Java-1.8.0_162', SYSTEM), ('Velvet', '1.2.10', '-mt-kmer_191'), ('pigz', '2.4'), ] diff --git a/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb index fed24b4cdcb..b5a0a68a8c9 100644 --- a/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb @@ -23,11 +23,11 @@ dependencies = [ ('SKESA', '2.3.0'), ('MEGAHIT', '1.1.4', versionsuffix), ('KMC', '3.1.0'), - ('Pilon', '1.23', '-Java-1.8', True), + ('Pilon', '1.23', '-Java-1.8', SYSTEM), ('SPAdes', '3.13.0'), ('Lighter', '1.1.2'), ('FLASH', '1.2.11'), - ('Trimmomatic', '0.38', '-Java-1.8', True), + ('Trimmomatic', '0.38', '-Java-1.8', SYSTEM), ('Velvet', '1.2.10', '-mt-kmer_191'), ('pigz', '2.4'), ('samclip', '0.2', '-Perl-5.28.0'), diff --git a/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb b/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb index d71b5e0fb90..dfc9a1c3943 100644 --- a/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb @@ -22,11 +22,11 @@ dependencies = [ ('SKESA', '2.4.0', '_saute.1.3.0_1'), ('MEGAHIT', '1.2.9'), ('KMC', '3.2.1'), - ('Pilon', '1.23', '-Java-11', True), + ('Pilon', '1.23', '-Java-11', SYSTEM), ('SPAdes', '3.15.3'), ('Lighter', '1.1.2'), ('FLASH', '2.2.00'), - ('Trimmomatic', '0.39', '-Java-11', True), + ('Trimmomatic', '0.39', '-Java-11', SYSTEM), ('Velvet', '1.2.10', '-mt-kmer_191'), ('pigz', '2.6'), ('samclip', '0.4.0'), diff --git a/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb index ecbc8b58ffd..9cdb80b108b 100644 --- a/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/s/smooth-topk/smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb @@ -11,7 +11,7 @@ description = "Smooth Loss Functions for Deep Top-k Classification" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('tqdm', '4.61.2'), ('PyTorch', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb index 3d829256a63..aba93468232 100644 --- a/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/snippy/snippy-4.6.0-GCC-9.3.0-Java-13-Python-3.8.2.eb @@ -21,7 +21,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['7264e3819e249387effd3eba170ff49404b1cf7347dfa25944866f5aeb6b11c3'] dependencies = [ - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('Python', '3.8.2'), ('Perl', '5.30.2'), ('BioPerl', '1.7.7'), diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb index f3814608665..e05db5008e7 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0-GCCcore-9.3.0-Java-13-Python-3.8.2.eb @@ -15,7 +15,7 @@ sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] checksums = ['2b177440eb4a2c3bbfc8f50d4adf9e405f3dcfc05a31a55c96f773f07832af34'] dependencies = [ - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('Python', '3.8.2'), ('Perl', '5.30.2'), ] diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb index cfde903143c..2e5679be3cd 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-10.2.0-Java-13.eb @@ -15,7 +15,7 @@ sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] checksums = ['85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d'] dependencies = [ - ('Java', '13', '', True), + ('Java', '13', '', SYSTEM), ('Python', '3.8.6'), ('Perl', '5.32.0'), ] diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb index a7a8a7334f4..3281c84b650 100644 --- a/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.0e-GCCcore-11.2.0-Java-11.eb @@ -17,7 +17,7 @@ checksums = ['85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d'] dependencies = [ # ignore website claim that Java 12+ is required, nothing is compiled for # anything newer than Java 11 - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.9.6'), ('Perl', '5.34.0'), ] diff --git a/easybuild/easyconfigs/t/THetA/THetA-0.7-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/THetA/THetA-0.7-foss-2018b-Python-2.7.15.eb index 003a47f61ba..bd37bacce14 100644 --- a/easybuild/easyconfigs/t/THetA/THetA-0.7-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/THetA/THetA-0.7-foss-2018b-Python-2.7.15.eb @@ -18,8 +18,8 @@ checksums = ['474452fa87a1ca0228137693bfede3200b91e4e166b2216c4bd24f8b270c1dea'] dependencies = [ ('Python', '2.7.15'), ('bnpy', '0.1.6', versionsuffix), - ('ant', '1.10.5', '-Java-1.8', True), # (Optional) needed for preprocessing script - # ('MATLAB', '2018b', '', True), # (Optional) provides interface to Matlab + ('ant', '1.10.5', '-Java-1.8', SYSTEM), # (Optional) needed for preprocessing script + # ('MATLAB', '2018b', '', SYSTEM), # (Optional) provides interface to Matlab ] cmds_map = [('', "ant")] diff --git a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb index 003fb9008b0..fd542467800 100644 --- a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-10.2.0.eb @@ -27,7 +27,7 @@ parallel = 1 builddependencies = [ ('binutils', '2.35'), - ('Pandoc', '2.10', '', True), + ('Pandoc', '2.10', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-8.3.0.eb index 5675584ba3d..cbf5ee21bc6 100644 --- a/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/TagDust/TagDust-2.33-GCCcore-8.3.0.eb @@ -23,7 +23,7 @@ parallel = 1 builddependencies = [ ('binutils', '2.32'), - ('Pandoc', '2.10', '', True), + ('Pandoc', '2.10', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb index 3bf1060dd25..ad59ec63441 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb @@ -17,8 +17,8 @@ local_pymajmin = local_pymaj + local_pymin dependencies = [ ('Python', '%s.%s.2' % (local_pymaj, local_pymin)), ('protobuf-python', '3.3.0', local_pythonsuffix), - ('CUDA', '8.0.44', '', True), - ('cuDNN', '5.1', '-CUDA-8.0.44', True), + ('CUDA', '8.0.44', '', SYSTEM), + ('cuDNN', '5.1', '-CUDA-8.0.44', SYSTEM), ] exts_list = [ diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb index 5cae5dc8c13..54fdbc44964 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2020a-Python-3.8.2.eb @@ -18,7 +18,7 @@ builddependencies = [ ('pybind11', '2.4.3', versionsuffix), ] dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.2'), ('h5py', '2.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb index 0feb8006d4d..110b07df5a5 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.4.1-fosscuda-2020b.eb @@ -19,7 +19,7 @@ builddependencies = [ ('UnZip', '6.0'), ] dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.6'), # Next 2 are for h5py diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index c1662ad3a3b..b4daf67aaa3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -19,7 +19,7 @@ builddependencies = [ ('UnZip', '6.0'), ] dependencies = [ - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), ('Python', '3.8.6'), ('h5py', '3.1.0'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb index 59a083f5333..0ac39221678 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb @@ -19,7 +19,7 @@ builddependencies = [ ('UnZip', '6.0'), ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index bb846c638fc..8c4c862c922 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -19,7 +19,7 @@ builddependencies = [ ('UnZip', '6.0'), ] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('cuDNN', '8.2.1.32', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 1cd3c17f6d0..24cafa17438 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -20,7 +20,7 @@ builddependencies = [ ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed ] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('cuDNN', '8.2.2.26', versionsuffix, True), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.6'), diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb index c7c4aba1c1b..7acce00ef7d 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.1.2-fosscuda-2020b-PyMC.eb @@ -19,7 +19,7 @@ checksums = ['5da6c2242ea72a991c8446d7fe7d35189ea346ef7d024c890397011114bf10fc'] dependencies = [ ('Python', '3.8.6'), ('libgpuarray', '0.7.6'), - ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.0.4.30', '-CUDA-%(cudaver)s', SYSTEM), ('SciPy-bundle', '2020.11'), ] diff --git a/easybuild/easyconfigs/t/Tracer/Tracer-1.7.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/t/Tracer/Tracer-1.7.1-GCCcore-8.2.0.eb index ee85d771a64..0cf3c7d492b 100644 --- a/easybuild/easyconfigs/t/Tracer/Tracer-1.7.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/t/Tracer/Tracer-1.7.1-GCCcore-8.2.0.eb @@ -18,7 +18,7 @@ sources = [{'download_filename': '%(name)s_v%(version)s.tgz', 'filename': SOURCE checksums = ['200d7ffa1e48994b71245994e299847ac2be72d3d5c37d9048418557e1d8c12e'] dependencies = [ - ('Java', '1.8', '', True), + ('Java', '1.8', '', SYSTEM), ('Mesa', '19.0.1'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb index b6070a5118c..5a6e085b08a 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb @@ -21,7 +21,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.11.5', '-Java-1.7.0_80', True), + ('FastQC', '0.11.5', '-Java-1.7.0_80', SYSTEM), ('cutadapt', '1.9.1', '-Python-2.7.12'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb index ed3b6794101..132db8b33b2 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb @@ -21,7 +21,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.11.5', '-Java-1.7.0_80', True), + ('FastQC', '0.11.5', '-Java-1.7.0_80', SYSTEM), ('cutadapt', '1.9.1', '-Python-2.7.12'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb index 934d2bd4129..5dd29ffb263 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-intel-2017a.eb @@ -22,7 +22,7 @@ install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s & install_cmd += "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.11.5', '-Java-1.8.0_144', True), + ('FastQC', '0.11.5', '-Java-1.8.0_144', SYSTEM), ('cutadapt', '1.14', '-Python-2.7.13'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-foss-2018b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-foss-2018b.eb index 751ec831e27..939e4aa653a 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-foss-2018b.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-foss-2018b.eb @@ -15,7 +15,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['9a7966bcfdea5d8c4f14c669904fb44693ac5d9392caa4d49dd11254a0a6753d'] dependencies = [ - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', '-Python-3.6.6'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb index 54a9e8723f4..9fffbfd9a38 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.5.0-intel-2018b-Python-3.6.6.eb @@ -16,7 +16,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['9a7966bcfdea5d8c4f14c669904fb44693ac5d9392caa4d49dd11254a0a6753d'] dependencies = [ - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb index e30697fa9a2..50baaf11de7 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-2.7.15.eb @@ -17,7 +17,7 @@ checksums = ['f374dfa4c94e2ad50c63276dda0f341fd95b29cb1d5a0e2ad56e8b0168b758ec'] dependencies = [ ('Python', '2.7.15'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix), ('Perl', '5.28.0'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb index f03c582405b..d4df9526da5 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.0-foss-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ checksums = ['f374dfa4c94e2ad50c63276dda0f341fd95b29cb1d5a0e2ad56e8b0168b758ec'] dependencies = [ ('Python', '3.6.6'), # multi-core support requires Python 3.x + pigz ('pigz', '2.4'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix), ('Perl', '5.28.0'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb index 96d93d982ce..aabeeaa87aa 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-2.7.15.eb @@ -22,7 +22,7 @@ checksums = ['658578c29d007fe66f9ab49608442be703a6fcf535db06eb82659c7edccb62b0'] dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.0'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix) ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb index 07037434493..7a5caa1e5a3 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.1-foss-2018b-Python-3.6.6.eb @@ -23,7 +23,7 @@ dependencies = [ ('Python', '3.6.6'), # multi-core support requires Python 3.x + pigz ('pigz', '2.4'), ('Perl', '5.28.0'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix) ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-GCCcore-8.2.0-Java-11.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-GCCcore-8.2.0-Java-11.eb index 2cd8ff63867..43cccd80beb 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-GCCcore-8.2.0-Java-11.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-GCCcore-8.2.0-Java-11.eb @@ -28,10 +28,10 @@ multi_deps = {'Python': ['3.7.2', '2.7.15']} builddependencies = [('binutils', '2.31.1')] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pigz', '2.4'), ('Perl', '5.28.1'), - ('FastQC', '0.11.8', '-Java-11', True), + ('FastQC', '0.11.8', '-Java-11', SYSTEM), ('cutadapt', '1.18'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb index cf2e0c9f7dc..a8df5a83fbe 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-2.7.15.eb @@ -22,7 +22,7 @@ checksums = ['c50b841bdc294a6cdc6a27fb7bfbed1973541d20a68a4708584b817c58b3f376'] dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.0'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix) ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb index b4fc90cc570..d6fb92d2cb4 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.2-foss-2018b-Python-3.6.6.eb @@ -23,7 +23,7 @@ dependencies = [ ('Python', '3.6.6'), # multi-core support requires Python 3.x + pigz ('pigz', '2.4'), ('Perl', '5.28.0'), - ('FastQC', '0.11.8', '-Java-1.8', True), + ('FastQC', '0.11.8', '-Java-1.8', SYSTEM), ('cutadapt', '1.18', versionsuffix) ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4.eb index b7d71152b88..e3c7224c9f5 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4.eb @@ -27,10 +27,10 @@ builddependencies = [('binutils', '2.32')] dependencies = [ ('Python', '3.7.4'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pigz', '2.4'), ('Perl', '5.30.0'), - ('FastQC', '0.11.9', '-Java-%(javaver)s', True), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), ('cutadapt', '2.7', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb index add75646761..36e73454652 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCC-10.2.0-Python-2.7.18.eb @@ -25,10 +25,10 @@ builddependencies = [('binutils', '2.35')] dependencies = [ ('Python', '2.7.18'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pigz', '2.6'), ('Perl', '5.32.0'), - ('FastQC', '0.11.9', '-Java-%(javaver)s', True), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), ('cutadapt', '1.18', versionsuffix), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb index e55fe4ccfae..48d1f2c85a2 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb @@ -27,10 +27,10 @@ builddependencies = [('binutils', '2.34')] dependencies = [ ('Python', '3.8.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pigz', '2.4'), ('Perl', '5.30.2'), - ('FastQC', '0.11.9', '-Java-%(javaver)s', True), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), ('cutadapt', '2.10', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb index cf5350b94a4..495deb9a976 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.7-GCCcore-10.3.0.eb @@ -25,11 +25,11 @@ checksums = [ dependencies = [ ('Python', '3.9.5'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('pigz', '2.6'), ('Perl', '5.32.1'), ('cutadapt', '3.4'), - ('FastQC', '0.11.9', '-Java-%(javaver)s', True), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), ] postinstallcmds = [ diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb index da61b4d7b33..80d1c83a61f 100644 --- a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.38-Java-1.8.eb @@ -20,7 +20,7 @@ source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/' sources = [SOURCE_ZIP] checksums = ['d428af42b6c400a2e7ee5e6b4cab490eddc621f949b086bd7dddb698dcf1647c'] -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '1.8', '', SYSTEM)] modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar\n""" diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.10.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.10.0-foss-2019b-Python-3.7.4.eb index 009b1080766..5f6beb23aa6 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.10.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.10.0-foss-2019b-Python-3.7.4.eb @@ -30,8 +30,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('Perl', '5.30.0'), ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb index b4e2affc990..65072fe8b8e 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb @@ -26,8 +26,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_92', '', True), - ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('Java', '1.8.0_92', '', SYSTEM), + ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.8'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb index 98a63c78c78..044419c7ace 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.4.0-foss-2017a.eb @@ -25,8 +25,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_121', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_121', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.1.2'), ('Bowtie2', '2.3.2'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017a.eb index b081019d430..834721f2ac7 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017a.eb @@ -28,8 +28,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_152', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_152', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.1.2'), ('Bowtie2', '2.3.2'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017b.eb index 75a7be3a9af..29331247179 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.5.1-intel-2017b.eb @@ -28,8 +28,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_152', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_152', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.2.2'), ('Bowtie2', '2.3.4'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb index 35b020b401a..5e8309a25ee 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb @@ -27,8 +27,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_162', '', True), - ('ant', '1.10.1', '-Java-%(javaver)s', True), + ('Java', '1.8.0_162', '', SYSTEM), + ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.2.2'), ('Bowtie2', '2.3.4.1'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb index 655df5ae21a..2f8bbf8e3f6 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.4-foss-2018b.eb @@ -19,8 +19,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8', '', True), - ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.5', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.2.2'), ('Bowtie2', '2.3.4.2'), ('ncurses', '6.1'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-GCC-8.3.0-Java-11.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-GCC-8.3.0-Java-11.eb index aaf6957b7ae..8d8703a5561 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-GCC-8.3.0-Java-11.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-GCC-8.3.0-Java-11.eb @@ -26,7 +26,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('ant', '1.10.7', versionsuffix, True), ('Bowtie', '1.2.3'), ('Bowtie2', '2.3.5.1'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb index eeef16155fb..654e032e6c6 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.8.5-iccifort-2019.1.144-GCC-8.2.0-2.31.1.eb @@ -25,8 +25,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8', '', True), - ('ant', '1.10.5', '-Java-%(javaver)s', True), + ('Java', '1.8', '', SYSTEM), + ('ant', '1.10.5', '-Java-%(javaver)s', SYSTEM), ('Bowtie', '1.2.3'), ('Bowtie2', '2.3.5.1'), ('ncurses', '6.1'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-2.7.16.eb index 706bcf94ecb..3ca740f8aab 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-2.7.16.eb @@ -30,8 +30,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('Perl', '5.30.0'), ('Python', '2.7.16'), ('SciPy-bundle', '2019.10', versionsuffix), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-3.7.4.eb index 92750de5d52..923a3cd1f94 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2019b-Python-3.7.4.eb @@ -30,8 +30,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), - ('ant', '1.10.7', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.7', '-Java-%(javaver)s', SYSTEM), ('Perl', '5.30.0'), ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb index 7522e28d255..843aa1c597d 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb @@ -29,7 +29,7 @@ source_urls = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb index fcc5a44425a..5586784fcf2 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb @@ -30,7 +30,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['b89de7064ab54dac454a266cfe5d8bf66940cb5ed048d0c30674ea62e7ecef9d'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.28', '', True)] +builddependencies = [('binutils', '2.28', '', SYSTEM)] dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb index bb013b1619c..0e32b78cf2d 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', True), + ('binutils', '2.25', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb index 14ac4f4f602..6e1e1c39fdf 100644 --- a/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/topaz/topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb @@ -18,7 +18,7 @@ dependencies = [ ('PyTorch', '1.10.0', versionsuffix), ('torchvision', '0.11.1', versionsuffix), ('scikit-learn', '0.24.2'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] use_pip = True diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb index 7e64e72a452..d3755b1e9fc 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.9.5'), ('Pillow-SIMD', '8.2.0'), ('PyTorch', '1.10.0', '-CUDA-%(cudaver)s'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] # Defaults. Can be changed with --cuda-compute-capabilities diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb index 3eb21ffbed3..7c591865f3a 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb @@ -14,7 +14,7 @@ checksums = ['b4c51d27589783e6e6941ecaa67b55f6f41633874ec37f80b64a0c92c3196e0c'] builddependencies = [('CMake', '3.20.1')] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('Pillow-SIMD', '8.2.0'), ('PyTorch', '1.10.0', versionsuffix), diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb index ebf9a1d24b8..41eb21d1767 100644 --- a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-10.3.0.eb @@ -19,7 +19,7 @@ source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] start_dir = 'source' files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb index a509e00b02e..52c4b51c8b1 100644 --- a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-9.3.0.eb @@ -16,7 +16,7 @@ github_account = 'scapella' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] -builddependencies = [('binutils', '2.34', '', True)] +builddependencies = [('binutils', '2.34', '', SYSTEM)] start_dir = 'source' files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb index bf163fd4655..e213c78d3b7 100644 --- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.0.0-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -33,7 +33,7 @@ builddependencies = [ dependencies = [ ('UCC', '1.0.0'), - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'), ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), ] diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb index 67d9cdb0044..70a85299c29 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.10.0-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -35,7 +35,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('UCX', version), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('GDRCopy', '2.2'), ] diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb index 1dad569119f..ce3211904db 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -35,7 +35,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('UCX', version), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('GDRCopy', '2.3'), ] diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb index bc3201ec688..d5f4602d19f 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -35,7 +35,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.11'), ('UCX', version), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('GDRCopy', '2.3'), ] diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb index 7bf9d3c8710..0fb175ca066 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -35,7 +35,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), ('UCX', version), - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('GDRCopy', '2.3'), ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb index cc2d5938c65..bfafd2ff9cd 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -38,7 +38,7 @@ osdependencies = [OS_PKG_IBVERBS_DEV] dependencies = [ ('numactl', '2.0.13'), - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', local_cudaversion, '', SYSTEM), ('GDRCopy', '2.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb index 48c65be2945..4f58f9acc83 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -30,7 +30,7 @@ osdependencies = [OS_PKG_IBVERBS_DEV] dependencies = [ ('numactl', '2.0.13'), - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', local_cudaversion, '', SYSTEM), ('GDRCopy', '2.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb index fd3d6e7b5dc..11fabfc2ea7 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0-CUDA-11.2.1.eb @@ -30,7 +30,7 @@ osdependencies = [OS_PKG_IBVERBS_DEV] dependencies = [ ('numactl', '2.0.13'), - ('CUDAcore', local_cudaversion, '', True), + ('CUDAcore', local_cudaversion, '', SYSTEM), ('GDRCopy', '2.1', versionsuffix), ] diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb index 890acbbf6f4..a83700d58cd 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.7-foss-2019a-Python-3.7.2.eb @@ -17,12 +17,12 @@ checksums = ['a8cf65e46dc2694b0fbd4e9190c73a1f300921457aadfab27a1792b785620d63'] dependencies = [ ('Python', '3.7.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bowtie2', '2.3.5.1'), ('SAMtools', '1.9'), ('SPAdes', '3.13.1'), ('Racon', '1.3.2'), - ('Pilon', '1.23', '-Java-%(javaver)s', True), + ('Pilon', '1.23', '-Java-%(javaver)s', SYSTEM), ('BLAST+', '2.9.0'), ] diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb index 70ef7ebfed1..ae461e506cd 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.8-gompi-2020a-Python-3.8.2.eb @@ -17,12 +17,12 @@ checksums = ['e948871e4de9db5964c9ca6f8f877c3cbe6a46f62052dfab52ffe0f45bbbd203'] dependencies = [ ('Python', '3.8.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bowtie2', '2.4.1'), ('SAMtools', '1.10'), ('SPAdes', '3.14.1', versionsuffix), ('Racon', '1.4.13'), - ('Pilon', '1.23', '-Java-%(javaver)s', True), + ('Pilon', '1.23', '-Java-%(javaver)s', SYSTEM), ('BLAST+', '2.10.1'), ] diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb index 2e9b8f68fe0..1ca53bc8f78 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.4.9-gompi-2021a.eb @@ -16,12 +16,12 @@ checksums = ['84bea8f3e8f99a1e63e5230ffe474a696db8caa67569c3a96ae12906d32a35eb'] dependencies = [ ('Python', '3.9.5'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bowtie2', '2.4.4'), ('SAMtools', '1.13'), ('SPAdes', '3.13.0'), ('Racon', '1.4.21'), - ('Pilon', '1.23', '-Java-%(javaver)s', True), + ('Pilon', '1.23', '-Java-%(javaver)s', SYSTEM), ('BLAST+', '2.11.0'), ] diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb index 712952beb6f..3fc79ebf2db 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb @@ -17,12 +17,12 @@ checksums = ['84a8709c9f2e624225410af702d779ffb0cb06f7c22c20e1f01b989945e08a47'] dependencies = [ ('Python', '3.9.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Bowtie2', '2.4.4'), ('SAMtools', '1.14'), ('SPAdes', '3.15.3'), ('Racon', '1.5.0'), - ('Pilon', '1.23', '-Java-%(javaver)s', True), + ('Pilon', '1.23', '-Java-%(javaver)s', SYSTEM), ('BLAST+', '2.12.0'), ] diff --git a/easybuild/easyconfigs/u/units/units-2.19-GCCcore-8.2.0.eb b/easybuild/easyconfigs/u/units/units-2.19-GCCcore-8.2.0.eb index 72f4c73aa6c..d86c35faedf 100644 --- a/easybuild/easyconfigs/u/units/units-2.19-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/u/units/units-2.19-GCCcore-8.2.0.eb @@ -17,7 +17,7 @@ checksums = ['4262136bdfc152b63ff5a9b93a7d80ce18b5e8bebdcffddc932dda769e306556'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.31.1', '', True), + ('binutils', '2.31.1', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a43-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a43-fosscuda-2019b-Python-3.7.4.eb index 5c2bcb96f52..331d66698e0 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a43-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a43-fosscuda-2019b-Python-3.7.4.eb @@ -54,7 +54,7 @@ dependencies = [ ('FFmpeg', '4.2.1'), ('ImageMagick', '7.0.9-5'), ('ACTC', '1.1'), - ('OptiX', '6.5.0', '', True), + ('OptiX', '6.5.0', '', SYSTEM), ('zlib', '1.2.11'), ('libpng', '1.6.37'), ] diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb index 854dade5cbe..0ad4daad390 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -52,7 +52,7 @@ dependencies = [ ('FFmpeg', '4.3.1'), ('ImageMagick', '7.0.10-35'), ('ACTC', '1.1'), - ('OptiX', '6.5.0', '', True), + ('OptiX', '6.5.0', '', SYSTEM), ('zlib', '1.2.11'), ('libpng', '1.6.37'), ('POV-Ray', '3.7.0.8'), diff --git a/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb index daa2ad6b936..ae2ec85f0ff 100644 --- a/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb @@ -17,9 +17,9 @@ dependencies = [ ('BioPerl', '1.6.924', '-Perl-%(perlver)s'), ('HMMER', '3.1b2'), ('MCL', '14.137'), - ('MetaGeneAnnotator', '20080819', '-x86-64', True), + ('MetaGeneAnnotator', '20080819', '-x86-64', SYSTEM), ('MUSCLE', '3.8.31'), - ('BLAST', '2.2.26', '-Linux_x86_64', True), + ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb b/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb index 6b38503aeb7..01fc5ff1dce 100644 --- a/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/v/Virtuoso-opensource/Virtuoso-opensource-7.2.6.1-GCC-10.3.0.eb @@ -30,7 +30,7 @@ builddependencies = [ ] dependencies = [ - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ('libreadline', '8.1'), ] diff --git a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb index fa730a6cadd..076c0558ad7 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun-scoop/archive/'] dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), - ('vsc-mympirun', '3.4.2', '', True), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), + ('vsc-mympirun', '3.4.2', '', SYSTEM), ('Python', '2.7.12'), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/w/WCT/WCT-4.6.0-Java-11.eb b/easybuild/easyconfigs/w/WCT/WCT-4.6.0-Java-11.eb index a889d75fa0b..0b5db53df8a 100644 --- a/easybuild/easyconfigs/w/WCT/WCT-4.6.0-Java-11.eb +++ b/easybuild/easyconfigs/w/WCT/WCT-4.6.0-Java-11.eb @@ -22,7 +22,7 @@ source_urls = ['https://www.ncdc.noaa.gov/wct/app/dist/'] sources = ['%(namelower)s-%(version)s.zip'] checksums = ['951ba0137582d2cd33e18ec61e1bb63c8f775b4ddf23bb21b4784b7ef5d28aad'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb index c6ac6a93321..f9313fcbc6e 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ('PCRE', '8.44'), ('libidn2', '2.3.0'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date gnutls for security reasons # ('GnuTLS', '3.7.1'), diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb index 3c7a5559b3a..3e0a4fdaa71 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb @@ -26,7 +26,7 @@ dependencies = [ ('PCRE', '8.45'), ('libidn2', '2.3.2'), ('zlib', '1.2.11'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date gnutls for security reasons # ('GnuTLS', '3.7.1'), diff --git a/easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb b/easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb index 57e58e0097f..7732b3063a7 100644 --- a/easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20160819-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ source_urls = [ builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ('Autotools', '20150215'), ('Bison', '3.0.4'), ('gettext', '0.19.8'), diff --git a/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb index f7fe477cb1b..c7c2384daaa 100644 --- a/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20170129-GCCcore-6.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('Autotools', '20150215'), ('Bison', '3.0.4'), ('gettext', '0.19.8.1'), diff --git a/easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb b/easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb index cfe2be0316b..f0f68e4c70a 100644 --- a/easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb +++ b/easybuild/easyconfigs/x/X11/X11-20170129-gimkl-2017a.eb @@ -23,9 +23,9 @@ dependencies = [ ('zlib', '1.2.11'), ] builddependencies = [ - ('Autotools', '20150215', '', True), + ('Autotools', '20150215', '', SYSTEM), ('Bison', '3.0.4'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ('pkg-config', '0.29.1'), ('intltool', '0.51.0', '-Perl-5.24.0') ] diff --git a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb index e36cb012947..4b11b1d6bfa 100644 --- a/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20170314-GCCcore-6.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('Autotools', '20150215'), ('Bison', '3.0.4'), ('gettext', '0.19.8.1'), diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb index 3fb7c1d49dd..71022a19045 100644 --- a/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-20171120-intel-2017b-Java-1.8.0_152.eb @@ -24,7 +24,7 @@ sources = [{ checksums = [None] builddependencies = [('CMake', '3.9.5')] -dependencies = [('Java', '1.8.0_152', '', True)] +dependencies = [('Java', '1.8.0_152', '', SYSTEM)] buildopts = " && cd jvm-packages && mvn install -Dmaven.repo.local=%(builddir)s/m2" diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb index 1c770debd8e..dd1c04c7392 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb @@ -20,7 +20,7 @@ builddependencies = [ ('gettext', '0.19.7'), ('intltool', '0.51.0', '-Perl-5.22.1'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb index ce56b41359e..a565c8676f4 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb @@ -20,7 +20,7 @@ builddependencies = [ ('gettext', '0.19.7'), ('intltool', '0.51.0', '-Perl-5.22.1'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb index 0423282a108..3f6ba215d4d 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb index 6c49a4458b9..ec46a64b897 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb index 001a737c6ef..3082194c6b5 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ('binutils', '2.25'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb index c9e9efec327..c705099c18c 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-5.4.0.eb @@ -17,9 +17,9 @@ checksums = [ ] builddependencies = [ - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.26', '', True), + ('binutils', '2.26', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb index 08aad5d870e..1ba4448757e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb index 8b076ecba44..96249ed4220 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb @@ -18,7 +18,7 @@ versionsuffix = '-gettext-%s' % local_gettext_ver builddependencies = [ ('Autotools', '20150215'), - ('gettext', local_gettext_ver, '', True), + ('gettext', local_gettext_ver, '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb index a0c7f313e03..0c774d43908 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.6', '', True), + ('gettext', '0.19.6', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb index e891d5536ae..64b7587aa4a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb index d8184d70d32..3393bb06e20 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb @@ -18,7 +18,7 @@ versionsuffix = '-gettext-%s' % local_gettext_ver builddependencies = [ ('Autotools', '20150215'), - ('gettext', local_gettext_ver, '', True), + ('gettext', local_gettext_ver, '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb index fdf1453ac4a..243db8e7d90 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.6', '', True), + ('gettext', '0.19.6', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb index 85431b3d6e9..60aeff8c712 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', True), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb index 735c3cbe5ba..8ac99515760 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb @@ -14,9 +14,9 @@ source_urls = ['http://tukaani.org/xz/'] patches = ['XZ-5.2.2_compat-libs.patch'] builddependencies = [ - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb index c02558f16a4..e6e62af6bf5 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.4.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.28'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb index cc9e04a5714..8cc83b07a7f 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb @@ -17,8 +17,8 @@ patches = ['XZ-5.2.2_compat-libs.patch'] # XZ (presumably its executables) depends on gettext, which depends on # xmllib2, which depends (optionally) on XZ builddependencies = [ - ('Autotools', '20150215', '', True), - ('gettext', '0.19.8', '', True), + ('Autotools', '20150215', '', SYSTEM), + ('gettext', '0.19.8', '', SYSTEM), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb index 34d93c09f7b..072decdbb68 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.2.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.29'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb index 4807e850e05..90c2e0ed3e8 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-7.3.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.30'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb index e082fd1cfcb..4447786633d 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.2.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.31.1'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb index cd9e93e00e0..0d03926cd60 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-8.3.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with dummy as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.19.8.1', '', True), + ('gettext', '0.19.8.1', '', SYSTEM), # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.32'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb index 368d09a41f9..1622d47af78 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.4-GCCcore-9.2.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.20.1', '', True), + ('gettext', '0.20.1', '', SYSTEM), ('binutils', '2.32'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb index d39dadea0a5..c7d8e9fe1d7 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb @@ -32,7 +32,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.20.1', '', True), + ('gettext', '0.20.1', '', SYSTEM), ('binutils', '2.34'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb index e54a2560c6d..2ba344e0acb 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.21', '', True), + ('gettext', '0.21', '', SYSTEM), ('binutils', '2.35'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb index c02c4e17cc9..2f9102b6d69 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.21', '', True), + ('gettext', '0.21', '', SYSTEM), ('binutils', '2.36.1'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb index f6a70e9b211..a482f548042 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb @@ -25,7 +25,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.21', '', True), + ('gettext', '0.21', '', SYSTEM), ('binutils', '2.37'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb index 2ee4825b700..c965c1e1efa 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.21', '', True), + ('gettext', '0.21', '', SYSTEM), ('binutils', '2.38'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb index 22e7b6ed6ef..73a74e9e92a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb @@ -22,7 +22,7 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) - ('gettext', '0.20.1', '', True), + ('gettext', '0.20.1', '', SYSTEM), ('binutils', '2.34'), ] diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-foss-2019a-Python-2.7.15.eb index 69c5636677f..4923b4db8d7 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-foss-2019a-Python-2.7.15.eb @@ -76,7 +76,7 @@ builddependencies = [ dependencies = [ ('Python', '2.7.15'), ('SciPy-bundle', '2019.03'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('OpenCV', '3.4.7', versionsuffix), ('SQLite', '3.27.2'), ('HDF5', '1.10.5'), diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-fosscuda-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-fosscuda-2019a-Python-2.7.15.eb index 771ce085a68..2c960877bb0 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-fosscuda-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.19.04-Apollo-fosscuda-2019a-Python-2.7.15.eb @@ -82,7 +82,7 @@ builddependencies = [ dependencies = [ ('Python', '2.7.15'), ('SciPy-bundle', '2019.03'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('OpenCV', '3.4.7', versionsuffix), ('SQLite', '3.27.2'), ('HDF5', '1.10.5'), diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb index 43b7d9e5a54..7551f83a6ff 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb index 599b3a7ea3e..823375c47ae 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb index 6694d3c8d1a..c61c6116cfc 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb index 6d95a13dc49..d6b82b3a951 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb index 20b75e6be45..e7c963b2128 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb index 2470683fb8a..db62de8e619 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb index 1c0793e3c1a..738376cb603 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb index c5509644a13..25da228279f 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb index 42b8d1faf07..8cbd9faeae4 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb index f862af46cb9..1dfef47a2f7 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', True), + ('xcb-proto', '1.11', '', SYSTEM), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb index 5ffb3e6b974..fe9d080b2b4 100755 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.1-GCCcore-6.3.0.eb @@ -24,7 +24,7 @@ checksums = ['0bb70872f45d9973db645123fe9fae9c587d1cc0ad1b3bfa67864c3f99adbd2a'] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('Autotools', '20150215'), ] diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb index 06e2a620f7b..4fdb9b6d636 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [XORG_PROTO_SOURCE] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', True), + ('binutils', '2.27', '', SYSTEM), ('xorg-macros', '1.19.1'), ] diff --git a/easybuild/easyconfigs/y/Yade/Yade-2018.02b-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/y/Yade/Yade-2018.02b-intel-2018a-Python-2.7.14.eb index a81eb292daf..3f708d997cf 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-2018.02b-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-2018.02b-intel-2018a-Python-2.7.14.eb @@ -43,7 +43,7 @@ dependencies = [ builddependencies = [ ('CMake', '3.12.1'), - ('Eigen', '3.3.4', '', True), + ('Eigen', '3.3.4', '', SYSTEM), ] separate_build_dir = True diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb index a7164e8d8fc..169f8988f8e 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.1.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.34', '', True)] +builddependencies = [('binutils', '2.34', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb index c26c13b8e50..5a346a38f11 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.35', '', True)] +builddependencies = [('binutils', '2.35', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.3.0.eb index e6d6bbf5052..982b3609ed3 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-10.3.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.1.0.eb index 38623a5181d..307df551e63 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.1.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.36.1', '', True)] +builddependencies = [('binutils', '2.36.1', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb index a7d80d3c9c2..dfca691dd42 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-11.2.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.37', '', True)] +builddependencies = [('binutils', '2.37', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb index 8409e2aa5cb..5d1b362aa15 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.5.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.5.0.eb index bb5db1a26d2..734b6bda65c 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.5.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb index a15fb20fe64..520d56351d8 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb index acbff073f4e..4cabf0a2d5d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.4.0.eb @@ -20,7 +20,7 @@ checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain builddependencies = [ - ('binutils', '2.28', '', True), + ('binutils', '2.28', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb index bec9454ed8e..5ba01e22f5b 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.28', '', True)] +builddependencies = [('binutils', '2.28', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb index 016a24fff22..ee843d04c0c 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.2.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.29', '', True)] +builddependencies = [('binutils', '2.29', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb index 6576f6849f4..9753d8d119d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.3.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.30', '', True)] +builddependencies = [('binutils', '2.30', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.4.0.eb index b8e35c68d3a..0bb6e2b7da5 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.4.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb index f97c6752989..3741db1cf3b 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.1.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.30', '', True)] +builddependencies = [('binutils', '2.30', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.2.0.eb index ec3c9d04c8e..20709893f33 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.2.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.31.1', '', True)] +builddependencies = [('binutils', '2.31.1', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb index b1c7a447036..b868b235321 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.3.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb index 6c89bf42f36..a090047e74b 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-8.4.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb index 25ecfcd4a9e..6649905e484 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.1.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.2.0.eb index a5107c7bfea..dda890bf849 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.2.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.32', '', True)] +builddependencies = [('binutils', '2.32', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb index bbc278b1c0e..090662b5e71 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.3.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.34', '', True)] +builddependencies = [('binutils', '2.34', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb index 670d5940075..3a0036514da 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-9.4.0.eb @@ -17,7 +17,7 @@ checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] # use same binutils version that was used when building GCC toolchain builddependencies = [ - ('binutils', '2.36.1', '', True), + ('binutils', '2.36.1', '', SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb index 31726b4af9d..0c3148f7ed0 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb index 7cd1927d036..f31b53b8ff3 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.1.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb index a9717ade39b..f7bcf94b72a 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-12.2.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.39', '', True)] +builddependencies = [('binutils', '2.39', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb index 67c423db857..b350c9f3c4f 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12-GCCcore-9.5.0.eb @@ -20,7 +20,7 @@ checksums = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.38', '', True)] +builddependencies = [('binutils', '2.38', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb index 6aa4e52aa9e..8da5a8874c1 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb index 9ab612053c2..1221095c524 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb index 3475aad2a70..53d82c7a9a8 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb index a7b3977bb9a..274d794a4aa 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb index 1353624765d..360c1a11cb8 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb index 1b44bb97802..b5265dc9d78 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', True)] +builddependencies = [('binutils', '2.25', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb index f4a9aac7763..a8a5212f418 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb index b139c1dc9a6..5117fda9bf4 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb @@ -16,7 +16,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['36658cb768a54c1d4dec43c3116c27ed893e88b02ecfcb44f2166f9c0b7f2a0d'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', True)] +builddependencies = [('binutils', '2.26', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb index 47a40a40359..55078920d1d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb index ecd6eff1be1..16c8391ed1e 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', True)] +builddependencies = [('binutils', '2.27', '', SYSTEM)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb index 5c5b309e903..1b7951ca5cc 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', # use same binutils version that was used when building GCC toolchain builddependencies = [ - ('binutils', '2.27', '', True) + ('binutils', '2.27', '', SYSTEM) ] sanity_check_paths = { From 9fc3b9b934a7625bed127ed5c20f0be1009623da Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 11 Oct 2022 11:17:15 +0100 Subject: [PATCH 5060/9987] remove unused import --- test/easyconfigs/easyconfigs.py | 1 - 1 file changed, 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 21c4692ec27..e749c268c42 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -42,7 +42,6 @@ from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.easyblocks.generic.pythonpackage import PythonPackage from easybuild.framework.easyblock import EasyBlock -from easybuild.framework.easyconfig.constants import EASYCONFIG_CONSTANTS from easybuild.framework.easyconfig.default import DEFAULT_CONFIG from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for From 4cb22e752342a1424e6267c1d62b0f355fb7f1cf Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 11 Oct 2022 12:20:06 +0100 Subject: [PATCH 5061/9987] make sure ModelTest-NG list is a list, not dict --- .../m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb index 7402e2f2b74..e07ae257936 100644 --- a/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/ModelTest-NG/ModelTest-NG-0.1.7-gompi-2021b.eb @@ -24,10 +24,10 @@ checksums = [None] builddependencies = [('CMake', '3.22.1')] -dependencies = { +dependencies = [ ('flex', '2.6.4'), ('Bison', '3.8.2', '', SYSTEM) -} +] files_to_copy = ['bin'] From f4ac9aa0777d7710d1938a8566c95c788e1c260f Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 11 Oct 2022 13:47:12 +0100 Subject: [PATCH 5062/9987] undo changes to archived easyconfigs --- .../__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb | 2 +- .../__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb | 2 +- .../easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb | 2 +- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb | 2 +- .../b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb | 2 +- .../b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb | 4 ++-- .../b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb | 2 +- .../b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb | 2 +- .../b/beagle-lib/beagle-lib-20141202-intel-2015a.eb | 2 +- .../b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb | 2 +- .../b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb | 2 +- .../__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb | 2 +- .../d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb | 2 +- .../d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb | 2 +- .../__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb | 2 +- .../__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb | 2 +- .../__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb | 2 +- .../__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb | 2 +- .../__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb | 2 +- .../g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb | 2 +- .../HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb | 4 ++-- .../HPCBIOS_Profilers-20130829-goolf-1.4.10.eb | 6 +++--- .../hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb | 4 ++-- .../hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb | 2 +- .../hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb | 2 +- .../i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb | 2 +- .../i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb | 2 +- .../jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb | 4 ++-- ...DSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb | 2 +- .../MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb | 2 +- .../__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb | 4 ++-- .../__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb | 4 ++-- .../__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb | 2 +- .../__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb | 2 +- .../__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb | 2 +- .../__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb | 2 +- .../p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb | 2 +- .../p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb | 2 +- .../p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb | 2 +- .../p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb | 2 +- .../__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb | 2 +- .../__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb | 2 +- .../__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb | 2 +- .../__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb | 2 +- .../__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb | 2 +- easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb | 2 +- easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb | 2 +- .../__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb | 2 +- easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb | 2 +- .../easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb | 2 +- easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb | 2 +- .../s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb | 2 +- .../s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb | 2 +- .../s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb | 2 +- .../s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb | 2 +- .../s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb | 2 +- .../t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb | 2 +- .../__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb | 4 ++-- .../__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb | 4 ++-- .../__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb | 2 +- .../t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb | 2 +- .../__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb | 2 +- .../t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb | 2 +- .../vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb | 4 ++-- .../vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb | 4 ++-- .../vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb | 4 ++-- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb | 2 +- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb | 2 +- .../easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb | 2 +- .../x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb | 2 +- .../x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb | 2 +- .../x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb | 2 +- 108 files changed, 124 insertions(+), 124 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb index 539a0958608..f40658d1411 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -dependencies = [('Java', '1.7.0_60', '', SYSTEM)] +dependencies = [('Java', '1.7.0_60', '', True)] configopts = "--disable-examples --disable-csharp" diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb index 72a027af04f..8ba4070760d 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['ANTLR-%(version)s_cpp-headers.patch'] -dependencies = [('Java', '1.7.0_60', '', SYSTEM)] +dependencies = [('Java', '1.7.0_60', '', True)] configopts = "--disable-examples --disable-csharp" diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb index 0d8e1343e3d..31ae0ccb152 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015a-Python-2.7.10.eb @@ -20,7 +20,7 @@ pythonversion = '2.7.10' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('Java', '1.8.0_60', '', SYSTEM), + ('Java', '1.8.0_60', '', True), ('Python', pythonversion), ] diff --git a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb index 8b6c127a237..00631356607 100644 --- a/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ANTLR/ANTLR-2.7.7-intel-2015b-Python-2.7.10.eb @@ -20,7 +20,7 @@ pythonversion = '2.7.10' versionsuffix = "-Python-%s" % pythonversion dependencies = [ - ('Java', '1.8.0_66', '', SYSTEM), + ('Java', '1.8.0_66', '', True), ('Python', pythonversion), ] diff --git a/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb index c99f5de5a6b..41b26e296f8 100644 --- a/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5-goolf-1.4.10.eb @@ -19,7 +19,7 @@ patches = [ dependencies = [ ('libpng', '1.6.6'), ('LibTIFF', '4.0.3'), - ('Java', '1.7.0_15', '', SYSTEM), + ('Java', '1.7.0_15', '', True), ('lynx', '2.8.7'), ('makedepend', '1.0.4'), ('imake', '1.0.5'), diff --git a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb index 174260cddaf..938cb4bc7e4 100644 --- a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb +++ b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb @@ -14,7 +14,7 @@ sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_66' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver, '', SYSTEM)] +dependencies = [(java, javaver, '', True)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb index 01cd8fffd9e..83c91ab617b 100644 --- a/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb +++ b/easybuild/easyconfigs/__archive__/b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb @@ -14,7 +14,7 @@ sources = ['%(name)s_%(version)s.tar.gz'] java = 'Java' javaver = '1.8.0_74' versionsuffix = '-%s-%s' % (java, javaver) -dependencies = [(java, javaver, '', SYSTEM)] +dependencies = [(java, javaver, '', True)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb index ec0b679c595..eb31afb5518 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-2.1.2-goolf-1.7.20.eb @@ -13,9 +13,9 @@ toolchain = {'name': 'goolf', 'version': '1.7.20'} source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] -dependencies = [('Java', '1.7.0_80', '', SYSTEM)] +dependencies = [('Java', '1.7.0_80', '', True)] -builddependencies = [('Autotools', '20150215', '', SYSTEM)] +builddependencies = [('Autotools', '20150215', '', True)] # parallel build does not work (to test) parallel = 1 diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb index ac6f731032d..eba16d5a4e3 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goolf-1.4.10.eb @@ -16,7 +16,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.7.0_15', '', SYSTEM)] +dependencies = [('Java', '1.7.0_15', '', True)] builddependencies = [('Autotools', '20150215', '', ('GCC', '4.7.2'))] diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb index 371db8bef3c..6d20b44133f 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-5.3.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.7.0_15', '', SYSTEM)] +dependencies = [('Java', '1.7.0_15', '', True)] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb index 939c36e304f..0349d94e2ac 100644 --- a/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20141202-intel-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2015a'} # svn checkout http://beagle-lib.googlecode.com/svn/trunk/ beagle-lib sources = [SOURCE_TGZ] -dependencies = [('Java', '1.8.0_31', '', SYSTEM)] +dependencies = [('Java', '1.8.0_31', '', True)] builddependencies = [('Autotools', '20150215')] preconfigopts = './autogen.sh && ' diff --git a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb index 0cfcc327bdb..847f0357417 100644 --- a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb +++ b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb @@ -30,7 +30,7 @@ dependencies = [ ('Boost', '1.51.0', '-Python-2.7.3'), ('SAMtools', '0.1.18'), ('Perl', '5.16.3', '-bare'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ('libpng', '1.5.13'), ] diff --git a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb index 0b3d2f04c2b..3354b93931c 100644 --- a/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb +++ b/easybuild/easyconfigs/__archive__/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb @@ -30,7 +30,7 @@ dependencies = [ ('Boost', '1.51.0', '-Python-2.7.3'), ('SAMtools', '0.1.18'), ('Perl', '5.16.3', '-bare'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ('libpng', '1.5.13'), ] diff --git a/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb b/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb index 28db135235f..fc4d0275894 100644 --- a/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/c/CPLEX/CPLEX-12.6.3-foss-2015b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['cplex_studio%s.linux-x86-64.bin' % ''.join(version.split('.'))] dependencies = [ - ('Java', '1.8.0_66', '', SYSTEM), + ('Java', '1.8.0_66', '', True), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb index 5705d1a9f0d..77e43460d5c 100644 --- a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -46,7 +46,7 @@ dependencies = [ ('CGAL', '4.0', versionsuffix), ('PETSc', '3.3-p2', versionsuffix), ('SLEPc', '3.3-p1', versionsuffix), - ('MTL4', '4.0.8878', '', SYSTEM), + ('MTL4', '4.0.8878', '', True), ('Trilinos', '10.12.2', versionsuffix), ('Sphinx', '1.1.3', versionsuffix), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb index 851a565e755..f6b89c67c7a 100644 --- a/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/__archive__/d/DOLFIN/DOLFIN-1.6.0-intel-2015b-Python-2.7.11.eb @@ -42,7 +42,7 @@ dependencies = [ ('CGAL', '4.7', versionsuffix), ('PETSc', '3.6.3', versionsuffix), ('SLEPc', '3.6.2', versionsuffix), - ('MTL4', '4.0.9555', '', SYSTEM), + ('MTL4', '4.0.9555', '', True), ('HDF5', '1.8.15-patch1'), ('Trilinos', '12.4.2', versionsuffix), ('Sphinx', '1.3.3', versionsuffix), diff --git a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb index 4c53065ba15..573a00a1859 100644 --- a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-goolf-1.4.10.eb @@ -23,7 +23,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb index c5f9edb822c..cfcf1c4b41a 100644 --- a/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/e/EMBOSS/EMBOSS-6.5.7-ictce-5.3.0.eb @@ -23,7 +23,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.2.0'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb b/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb index 5bb43ab8b18..3968d910aa4 100644 --- a/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/__archive__/e/ErlangOTP/ErlangOTP-R16B02-GCC-4.7.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.7.2'} sources = ['otp_src_%(version)s.tar.gz'] source_urls = ['http://www.erlang.org/download'] -builddependencies = [('Java', '1.7.0_45', '', SYSTEM)] +builddependencies = [('Java', '1.7.0_45', '', True)] configopts = '--with-javac ' diff --git a/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb index b12f25299be..d05befd06c3 100644 --- a/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/f/Ferret/Ferret-6.72-goolf-1.4.10.eb @@ -18,7 +18,7 @@ dependencies = [ ('cURL', '7.27.0'), ('ncurses', '5.9'), ('libreadline', '6.2'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ] parallel = 1 diff --git a/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb index 640ab72c71a..2f7b37d7ff4 100644 --- a/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/g/GHC/GHC-7.4.2-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ] builddependencies = [ - ('GHC', '6.12.3', '', SYSTEM), + ('GHC', '6.12.3', '', True), ('libxslt', '1.1.28'), ] diff --git a/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb index 8db9f79f94f..7a5dd73b3c9 100644 --- a/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/g/GMP/GMP-6.1.0-goolf-1.7.20.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ftp.gnu.org/gnu/gmp'] builddependencies = [ - ('Autotools', '20150215', '', SYSTEM), + ('Autotools', '20150215', '', True), ] # enable C++ interface diff --git a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb index 3caf8585701..4634a7fb1a9 100644 --- a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2014b.eb @@ -26,7 +26,7 @@ dependencies = [ ('Ghostscript', '9.14'), ('GLib', '2.40.0'), ('GTS', '0.7.6'), - ('Java', '1.7.0_60', '', SYSTEM), + ('Java', '1.7.0_60', '', True), ('libpng', '1.6.12'), ('Pango', '1.36.7'), ('Perl', '5.20.0'), diff --git a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb index f0c9457cf81..c9fd0d8f277 100644 --- a/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -28,7 +28,7 @@ dependencies = [ ('fontconfig', '2.11.94'), ('Ghostscript', '9.16'), ('GTS', '0.7.6', glibsuff), - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ('libpng', '1.6.17'), ('Pango', '1.37.2'), ('Perl', '5.20.0'), diff --git a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb index 936ae21c317..1b8304beca1 100644 --- a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Debuggers/HPCBIOS_Debuggers-20130829-goolf-1.4.10.eb @@ -25,8 +25,8 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ ('GDB', '7.5.1'), - ('TotalView', '8.12.0-0', '-linux-x86-64', SYSTEM), # provides MemoryScape - ('icc', '2013.5.192', '', SYSTEM), # provides IDB in ictce/5.3.0 compatible mode + ('TotalView', '8.12.0-0', '-linux-x86-64', True), # provides MemoryScape + ('icc', '2013.5.192', '', True), # provides IDB in ictce/5.3.0 compatible mode ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb index 6a56ae85cc2..a39dfd95472 100644 --- a/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Profilers/HPCBIOS_Profilers-20130829-goolf-1.4.10.eb @@ -21,9 +21,9 @@ description = """Common Set of Profilers""" toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ - ('VTune', '2013_update10', '', SYSTEM), - ('Inspector', '2013_update6', '', SYSTEM), - ('itac', '8.0.0.011', '', SYSTEM), + ('VTune', '2013_update10', '', True), + ('Inspector', '2013_update6', '', True), + ('itac', '8.0.0.011', '', True), ('PAPI', '5.0.1'), ('Valgrind', '3.8.1'), ('binutils', '2.22'), # this one provides gprof diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb index fac7767346e..9272f98ff58 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', SYSTEM), - ('vsc-base', '2.1.2', '', SYSTEM), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb index f619e97afdd..a096633f0b1 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', SYSTEM), - ('vsc-base', '2.1.2', '', SYSTEM), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb index eb3c96bcc41..c0a03ce83e5 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', SYSTEM), - ('vsc-base', '2.1.2', '', SYSTEM), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb index 90c502a0495..b6761f74452 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb @@ -23,8 +23,8 @@ versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ (python, pythonver), ('pbs_python', '4.6.0', versionsuffix), - ('vsc-mympirun', '3.4.2', '', SYSTEM), - ('vsc-base', '2.1.2', '', SYSTEM), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), ('netifaces', '0.10.4', versionsuffix), ('netaddr', '0.7.14', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb index 858b4f06340..f8c93660f1c 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.0-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', SYSTEM), + ('setuptools', '1.4.2', '', True), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb index e19609bcd3b..bcf97f426c7 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.1-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', SYSTEM), + ('setuptools', '1.4.2', '', True), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb index 050fc9722ee..5a2ff293ea6 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.2-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', SYSTEM), + ('setuptools', '1.4.2', '', True), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb index 8cec50e09ab..b4fa5862100 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.3-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', SYSTEM), + ('setuptools', '1.4.2', '', True), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb index 92eb557b169..7cd4104ad9f 100644 --- a/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/h/hanythingondemand/hanythingondemand-3.0.4-intel-2015b-Python-2.7.10.eb @@ -22,7 +22,7 @@ dependencies = [ (python, pythonver), # provides netaddr, netifaces, mpi4py ('pbs_python', '4.6.0', versionsuffix), ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.4.2'), - ('setuptools', '1.4.2', '', SYSTEM), + ('setuptools', '1.4.2', '', True), ] install_target = 'easy_install' diff --git a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb index f0bc1aefaff..3f166576635 100644 --- a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.16-55.0-intel-2015b.eb @@ -13,7 +13,7 @@ source_urls = ['http://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s sources = ['%(namelower)s-%(version)s-64-bit.tar.gz'] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ('Perl', '5.20.3'), ('libgd', '2.1.1'), ('Python', '2.7.10'), diff --git a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb index ec5a5e2789d..2388f280096 100644 --- a/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/i/InterProScan/InterProScan-5.21-60.0-intel-2015b.eb @@ -23,7 +23,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ('Perl', '5.20.3'), ('libgd', '2.1.1'), ('Python', '2.7.10'), diff --git a/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb index a7381adc66f..dafa45afa95 100644 --- a/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/__archive__/j/jModelTest/jModelTest-2.1.9r20160115-goolf-1.4.10-Java-1.7.0_75.eb @@ -20,7 +20,7 @@ java = 'Java' javaver = '1.7.0_75' versionsuffix = '-%s-%s' % (java, javaver) -builddependencies = [('ant', '1.9.6', '-Java-1.7.0_75', SYSTEM)] +builddependencies = [('ant', '1.9.6', '-Java-1.7.0_75', True)] dependencies = [('MPJ-Express', '0.44', '%(versionsuffix)s')] diff --git a/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb index d334e3cb6ea..fe336c46e0c 100644 --- a/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/l/LUMPY/LUMPY-0.2.13-goolf-1.7.20.eb @@ -26,7 +26,7 @@ unpack_options = '--strip-components=1' builddependencies = [ ('CMake', '3.4.3'), - ('Autotools', '20150215', '', SYSTEM), + ('Autotools', '20150215', '', True), ] dependencies = [ @@ -34,7 +34,7 @@ dependencies = [ ('zlib', '1.2.8'), ('samblaster', '0.1.24'), ('SAMtools', '1.3.1'), - ('Sambamba', '0.6.6', '', SYSTEM), + ('Sambamba', '0.6.6', '', True), ('gawk', '4.0.2'), ] diff --git a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb index 904997dd1d9..92964498140 100644 --- a/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/m/MDSplus/MDSplus-7.0.67-goolf-1.5.16-Java-1.7.0_79-Python-2.7.9.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ - ('Java', '1.7.0_79', '', SYSTEM), + ('Java', '1.7.0_79', '', True), ('Python', '2.7.9'), ('HDF5', '1.8.9'), ('libxml2', '2.9.2'), diff --git a/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index ac36c94964b..e553dd3905a 100644 --- a/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/__archive__/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (java, javaver) builddependencies = [('CMake', '2.8.12')] dependencies = [ - (java, javaver, '', SYSTEM), + (java, javaver, '', True), ] # compile JNI wrapper library as described in docs diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb index 3a1bccbc96e..4231bf81f8c 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb @@ -31,8 +31,8 @@ dependencies = [ ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - ('Java', '1.7.0_79', '', SYSTEM), - ('ant', '1.9.3', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.7.0_79', '', True), + ('ant', '1.9.3', '-Java-%(javaver)s', True), ('GLib', '2.40.0') ] diff --git a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb index b495fa3ffb7..bf5ac8dc56d 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenCV/OpenCV-2.4.9-intel-2014b.eb @@ -31,8 +31,8 @@ dependencies = [ ('libpng', '1.6.12'), ('LibTIFF', '4.0.3'), ('JasPer', '1.900.1'), - ('Java', '1.7.0_60', '', SYSTEM), - ('ant', '1.9.3', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.7.0_60', '', True), + ('ant', '1.9.3', '-Java-%(javaver)s', True), ('GLib', '2.40.0') ] diff --git a/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb index 3599c26e381..8ad72ec52f4 100644 --- a/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/o/OpenIFS/OpenIFS-38r1v01-goolf-1.4.10.eb @@ -16,7 +16,7 @@ dependencies = [ ] builddependencies = [ - ('FCM', '2.3.1', '', SYSTEM), + ('FCM', '2.3.1', '', True), ('Perl', '5.16.3'), ] diff --git a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb index 41390bba2c2..ba3147aeda1 100644 --- a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-goolf-1.4.10.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ ('make', '3.82'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ('Bash', '4.2'), ('tcsh', '6.18.01'), ('Tcl', '8.5.12'), diff --git a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb index ea816765bb3..e1d90973574 100644 --- a/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/PRACE/PRACE-20130605-ictce-5.3.0.eb @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} dependencies = [ ('make', '3.82'), - ('Java', '1.7.0_10', '', SYSTEM), + ('Java', '1.7.0_10', '', True), ('Bash', '4.2'), ('tcsh', '6.18.01'), ('Tcl', '8.5.12'), diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb index 239d653b543..9948217fd4e 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-goolf-1.4.10.eb @@ -7,7 +7,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] +dependencies = [('tbb', '4.0.5.339', '', True)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb index c658a85d703..4043dd5630c 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.3-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] +dependencies = [('tbb', '4.0.5.339', '', True)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb index 7c33ed3c62f..161ca2d3837 100644 --- a/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/p/Pasha/Pasha-1.0.5-ictce-5.3.0.eb @@ -8,7 +8,7 @@ description = "PASHA is a parallel short read assembler for large genomes using toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True, 'opt': True, 'optarch': True} -dependencies = [('tbb', '4.0.5.339', '', SYSTEM)] +dependencies = [('tbb', '4.0.5.339', '', True)] source_urls = ['http://downloads.sourceforge.net/pasha'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb index 8391bc11951..8b0668a68f1 100644 --- a/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -19,7 +19,7 @@ sources = [SOURCELOWER_TAR_GZ] toolchain = {'name': 'intel', 'version': '2014b'} dependencies = [ - ('Java', '1.7.0_60', '', SYSTEM), + ('Java', '1.7.0_60', '', True), ('libreadline', '6.3'), ('zlib', '1.2.8'), # OS dependency should be preferred if the os version is more recent then this version, diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb index 5afdb61e1c4..e8adea5cdda 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.0-1-iccifort-2015.1.133.eb @@ -20,7 +20,7 @@ source_urls = [ mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb index 0b59ed106c8..9bf66b57282 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133-mt.eb @@ -20,7 +20,7 @@ mpich_opts = '--enable-static' threaded = True dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb index 9c841513aa2..8251dde430d 100644 --- a/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb +++ b/easybuild/easyconfigs/__archive__/p/psmpi/psmpi-5.1.5-1-iccifort-2015.1.133.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb index 09cc0738ddc..c6290e63183 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb index cff665b0ada..b23784df275 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb index 7d9a9a6b9be..4bb85edabe4 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb index 70a3f64db0d..b5a30ff434c 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.2-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.5.13'), # for plotting in R - ('Java', '1.7.0_10', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_10', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb index 8fcddd02617..419fa691885 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb index cd8a6bcddf6..2437804b50b 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-2.15.3-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb index a85fdf5d8fc..c0064ba6a8c 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-goolf-1.4.10-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb index 8939ec6a4eb..3b03bc30042 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.1-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.2'), # for plotting in R - ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb index edd7812782e..7db65a77f3e 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-goolf-1.4.10.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb index 5aa63fa961d..1c63079ab4a 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_21', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_21', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb index b3be0a49a90..ea1488b7501 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.3.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb index bb2cdf29ef3..72798af0c69 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.0.2-ictce-5.5.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.6'), # for plotting in R - ('Java', '1.7.0_15', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_15', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb index cac8a78c01f..7b3d9ff4712 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0-bare.eb @@ -14,7 +14,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.9'), # for plotting in R - ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb index faed73f4aef..4125b82ac4e 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.0-ictce-5.5.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('libreadline', '6.2'), ('ncurses', '5.9'), ('libpng', '1.6.9'), # for plotting in R - ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb index e9736a0d521..0b46e45f459 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-bare-mt.eb @@ -17,7 +17,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plotting in R - ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb index 8f2c4740b2d..33df27d4460 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-ictce-6.2.5-default-mt.eb @@ -17,7 +17,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plotting in R - ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb index f55402b39c8..3462ebf3f2c 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.1-intel-2014b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.12'), # for plotting in R ('libjpeg-turbo', '1.3.1'), # for plottting in R - ('Java', '1.7.0_60', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_60', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb index cfb1fdded86..32f9e3876e9 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-foss-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb index 6e9bb7dd130..8dfe1121a12 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-goolf-1.5.14.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb index c704735c37c..95f4896bccf 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb index a2c3729ee62..20b83d30bca 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.2-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb index c96c15e9389..2b252579399 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-foss-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('NLopt', '2.4.2'), # for nloptr diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb index db6599ad293..1992cbe8043 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.1.3-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.8.0_25', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('NLopt', '2.4.2'), # for nloptr diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb index 3de945fb60b..83033319bd9 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-foss-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb index 35f77ae5f85..712ca683f37 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb index 034bec8b1d3..fc8747efae8 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-goolf-1.7.20.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb index 9789a570017..dec3fef7965 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-ictce-7.3.5-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ] diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb index 282eb2bede6..68941ac7809 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.0-intel-2015a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R - ('Java', '1.7.0_80', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb index f37ad6d3f33..f4738f44f4b 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb index 77140a3bb18..eb6d134dc02 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-foss-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb index 4b3e1115ed6..bf999bcdca7 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb index 25e622f04e6..ad909a5e62b 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb index b00f07b4b09..28a924627e0 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.1-intel-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_45', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.43.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb index 986af941152..dba91bd2533 100644 --- a/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/__archive__/r/R/R-3.2.3-foss-2015b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '5.9'), ('libpng', '1.6.17'), # for plotting in R ('libjpeg-turbo', '1.4.1'), # for plottting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.45.0'), # for RCurl diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb index 8bde637585c..b503f4c6397 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.55.0', versionsuffix), - ('tbb', '4.0.5.339', '', SYSTEM), + ('tbb', '4.0.5.339', '', True), ('Jellyfish', '2.1.3'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb index 93274668b83..c80c41e1d54 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -27,7 +27,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', SYSTEM), + ('tbb', '4.3.6.211', '', True), ('Jellyfish', '2.2.3'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb index 37c7bd731e4..b4805f08e04 100644 --- a/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Sailfish/Sailfish-0.8.0-intel-2015b-Python-2.7.10.eb @@ -29,7 +29,7 @@ builddependencies = [ dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', SYSTEM), + ('tbb', '4.3.6.211', '', True), ('Jellyfish', '2.2.4'), ('g2log', '1.0'), ] diff --git a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb index 9317f21af8c..878c68876e0 100644 --- a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.4.2-intel-2015b-Python-2.7.10.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', SYSTEM), + ('tbb', '4.3.6.211', '', True), ('Jellyfish', '2.2.3'), ] builddependencies = [('CMake', '3.2.3')] diff --git a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb index 0f6804b6b3c..7699ae06d5a 100644 --- a/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/s/Salmon/Salmon-0.5.1-intel-2015b-Python-2.7.10.eb @@ -24,7 +24,7 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ ('Boost', '1.59.0', versionsuffix), - ('tbb', '4.3.6.211', '', SYSTEM), + ('tbb', '4.3.6.211', '', True), ('Jellyfish', '2.2.4'), ] builddependencies = [('CMake', '3.2.3')] diff --git a/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb index dffa4ab145e..f895fa63df1 100644 --- a/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -16,7 +16,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.10.1', '-Java-1.7.0_80', SYSTEM), + ('FastQC', '0.10.1', '-Java-1.7.0_80', True), ('cutadapt', '1.5', '-Python-2.7.10'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb index abd5e0edeaa..821333d6ef7 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.4-goolf-1.4.10.eb @@ -19,8 +19,8 @@ sources = ['v%(version)s.tar.gz'] patches = ['Trinity-%(version)s_plugins-Makefile.patch'] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), - ('ant', '1.9.6', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.7.0_80', '', True), + ('ant', '1.9.6', '-Java-%(javaver)s', True), ('ncurses', '5.9'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb index 7fb8a37a67b..014e8ca4110 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.0.6-goolf-1.4.10.eb @@ -19,8 +19,8 @@ sources = ['v%(version)s.tar.gz'] patches = ['Trinity-2.0.4_plugins-Makefile.patch'] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), - ('ant', '1.9.6', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.7.0_80', '', True), + ('ant', '1.9.6', '-Java-%(javaver)s', True), ('ncurses', '5.9'), ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb index 063da9c3d98..71643e32bd6 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2.1.1-intel-2015b.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - (java, javaver, '', SYSTEM), + (java, javaver, '', True), ('ant', '1.9.6', '-%s-%s' % (java, javaver), True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.6'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb index 2092bcc77db..dcb9ea5cadb 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb @@ -24,7 +24,7 @@ java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', SYSTEM), + (java, javaver, '', True), ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb index afb90c64534..7f5d5792225 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2012-10-05-ictce-5.3.0.eb @@ -25,7 +25,7 @@ java = 'Java' javaver = '1.7.0_10' dependencies = [ - (java, javaver, '', SYSTEM), + (java, javaver, '', True), ('ant', '1.8.4', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb index 10bbd992eac..f6e15e437ab 100644 --- a/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/t/Trinity/Trinity-2013-02-25-goolf-1.4.10.eb @@ -23,7 +23,7 @@ java = 'Java' javaver = '1.7.0_15' dependencies = [ - (java, javaver, '', SYSTEM), + (java, javaver, '', True), ('ant', '1.9.0', '-%s-%s' % (java, javaver), True), ('ncurses', '5.9'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb index 50efb697da2..dfd259613d8 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.6' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '', SYSTEM), - ('vsc-mympirun', version, '', SYSTEM), + ('vsc-processcontrol', '1.0', '', True), + ('vsc-mympirun', version, '', True), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb index 8afa94b6137..1bbd44502a0 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-intel-2015b-Python-2.7.10.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), - ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), + ('vsc-mympirun', '3.4.2', '', True), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb index f2a99790fa6..24d1ff604f7 100644 --- a/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2015b-Python-2.7.10.eb @@ -16,8 +16,8 @@ python = 'Python' pyver = '2.7.10' versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), - ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), + ('vsc-mympirun', '3.4.2', '', True), (python, pyver), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb index 99d0531e740..f5d80fe9e55 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-foss-2015a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.4', '', SYSTEM), + ('gettext', '0.19.4', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb index 9c13936bba0..4c118e934ff 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-goolf-1.4.10.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215', '', ('GCC', '4.7.2')), - ('gettext', '0.18.2', '', SYSTEM), + ('gettext', '0.18.2', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb index df2d19b7d0b..43117900f60 100644 --- a/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/x/XZ/XZ-5.2.2-ictce-5.3.0.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.18.2', '', SYSTEM), + ('gettext', '0.18.2', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb index 092e66d8068..63e623f082d 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb @@ -20,7 +20,7 @@ pyver = '2.7.9' versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Java', '1.8.0_40', '', SYSTEM), + ('Java', '1.8.0_40', '', True), ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb index 3f34c8c15f5..18d8b11833b 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -12,6 +12,6 @@ sources = ['Xmipp-%(version)s-src.tar.gz'] toolchain = {'name': 'goolf', 'version': '1.4.10'} # note: all other dependencies are taken care of by Xmipp itself -dependencies = [('Java', '1.7.0_80', '', SYSTEM)] +dependencies = [('Java', '1.7.0_80', '', True)] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb index 294af452fee..d6d8c64ef43 100644 --- a/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/__archive__/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb @@ -20,7 +20,7 @@ pyver = '2.7.9' versionsuffix = '-Python-%s' % pyver dependencies = [ - ('Java', '1.8.0_40', '', SYSTEM), + ('Java', '1.8.0_40', '', True), ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), ('HDF5', '1.8.14'), From 31ea71fd860f2fee1ed1e1fc9adcf48dad29621f Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 11 Oct 2022 14:39:01 +0100 Subject: [PATCH 5063/9987] undo changes from old easyconfigs failing other CI tests --- .../a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb | 2 +- .../a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb | 2 +- .../Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb | 2 +- ...16.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb | 2 +- easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb | 2 +- easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb | 2 +- .../easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb | 2 +- .../b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb | 2 +- .../b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb | 2 +- .../easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb | 2 +- .../CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb | 2 +- .../CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb | 2 +- .../c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb | 2 +- .../c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb | 2 +- .../c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb | 4 ++-- easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb | 2 +- easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb | 2 +- easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb | 2 +- .../f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb | 4 ++-- .../f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb | 2 +- .../fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb | 2 +- .../f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb | 2 +- .../f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb | 2 +- .../g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb | 2 +- .../g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb | 2 +- .../g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb | 2 +- .../g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb | 2 +- .../g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb | 2 +- .../g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb | 2 +- .../easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb | 2 +- .../easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb | 2 +- easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb | 2 +- .../i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb | 2 +- .../easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb | 2 +- .../easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb | 2 +- .../easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb | 2 +- .../easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb | 2 +- .../easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb | 2 +- .../easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb | 2 +- .../easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb | 2 +- .../l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb | 2 +- easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb | 2 +- .../l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb | 2 +- easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb | 2 +- .../easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb | 2 +- .../l/libXinerama/libXinerama-1.1.3-intel-2016a.eb | 2 +- .../easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb | 2 +- .../easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb | 2 +- .../easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb | 2 +- .../easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb | 2 +- .../easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb | 2 +- .../easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb | 2 +- .../l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb | 2 +- easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb | 2 +- .../l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb | 2 +- .../l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb | 2 +- .../easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb | 2 +- .../easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb | 2 +- .../MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb | 2 +- .../MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb | 2 +- .../MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb | 2 +- .../MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb | 2 +- .../m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb | 2 +- .../m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb | 2 +- .../m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb | 2 +- .../m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb | 2 +- .../mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb | 4 ++-- .../mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb | 4 ++-- .../mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb | 4 ++-- .../mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb | 4 ++-- easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb | 2 +- easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb | 2 +- easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb | 2 +- .../easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb | 2 +- .../o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb | 2 +- easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb | 2 +- .../p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb | 2 +- .../p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb | 2 +- .../p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb | 2 +- .../PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb | 2 +- .../p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb | 2 +- .../PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb | 2 +- .../easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb | 2 +- .../parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb | 2 +- easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb | 2 +- .../p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb | 2 +- .../p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb | 2 +- easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb | 2 +- .../q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb | 2 +- .../q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb | 2 +- .../q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb | 2 +- easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb | 2 +- .../easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb | 2 +- easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb | 2 +- easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb | 2 +- .../r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb | 2 +- easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb | 2 +- .../r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb | 2 +- .../r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb | 2 +- .../s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb | 2 +- .../easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb | 2 +- .../TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb | 4 ++-- easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb | 4 ++-- easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb | 4 ++-- easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb | 2 +- .../v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb | 4 ++-- .../vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb | 4 ++-- .../x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb | 2 +- .../x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb | 2 +- .../easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb | 2 +- .../easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb | 4 ++-- .../x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb | 2 +- .../x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb | 2 +- .../x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb | 2 +- .../x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb | 2 +- .../xcb-util-renderutil-0.3.9-foss-2016a.eb | 2 +- .../xcb-util-renderutil-0.3.9-intel-2016a.eb | 2 +- .../easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb | 2 +- .../x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb | 2 +- .../easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb | 2 +- easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb | 2 +- .../easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb | 2 +- 212 files changed, 225 insertions(+), 225 deletions(-) diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb index 654825d9ff3..ddbfe7c0922 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-foss-2016a-Python-2.7.11.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_includes.patch'] dependencies = [ - ('Java', '1.8.0_74', '', SYSTEM), + ('Java', '1.8.0_74', '', True), ('Python', '2.7.11'), ] diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb index 123c3e1e968..e00f225a130 100644 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2017a-Python-2.7.13.eb @@ -18,7 +18,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_includes.patch'] dependencies = [ - ('Java', '1.8.0_131', '', SYSTEM), + ('Java', '1.8.0_131', '', True), ('Python', '2.7.13'), ] diff --git a/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb index 1f73638a1c1..d3c79474bb6 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb @@ -27,7 +27,7 @@ patches = [ ] dependencies = [ - ('CUDA', '7.5.18', '', SYSTEM), + ('CUDA', '7.5.18', '', True), ('netCDF', '4.4.0'), ('netCDF-Fortran', '4.4.4'), ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb index 5b391327a36..4193c584dca 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb @@ -23,7 +23,7 @@ patches = ['Amber-%(version)s_fix-hardcoding.patch', dependencies = [ - ('CUDA', '7.5.18', '', SYSTEM), + ('CUDA', '7.5.18', '', True), ('netCDF', '4.4.0'), ('netCDF-Fortran', '4.4.4'), ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb index ca38ef74542..8b901156428 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-1.8.4.eb @@ -22,7 +22,7 @@ source_urls = ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(ver sources = ['BEASTv%(version)s.tgz'] dependencies = [ - ('Java', '1.8.0_74', '', SYSTEM), + ('Java', '1.8.0_74', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb index 6210023c8d0..b0ee97e8f9e 100644 --- a/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb +++ b/easybuild/easyconfigs/b/Bpipe/Bpipe-0.9.9.2-intel-2017a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://download.bpipe.org/versions/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('Java', '1.8.0_131', '', SYSTEM)] +dependencies = [('Java', '1.8.0_131', '', True)] sanity_check_paths = { 'files': ['bin/bpipe', 'lib/bpipe.jar'], diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb index fa78496309d..76868b55c45 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/'] sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')] -dependencies = [('Java', '1.8.0_74', '', SYSTEM)] +dependencies = [('Java', '1.8.0_74', '', True)] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb index dfa2e11582d..08e10d150ca 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb index 7627c686af3..9709696cf5d 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb index 9be29fca484..d6e68008e5b 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb index 0e86573cab6..9ec7a3f3f32 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.2.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb index f331b902250..f411442d121 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.3.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb index e631c72676f..4eee9df8fa2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb @@ -16,7 +16,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb index ecd95aca019..d7c829040f2 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.3.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked instatically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb index c9f35fe7a36..d95c058f0c8 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb index 847c265d57c..215aaf0cb28 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.1.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb index 00cbe46a478..88e16771dff 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.8'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb index e56efe34428..9346ceba7e7 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ builddependencies = [ # zlib required, but being linked in statically, so not a runtime dep ('zlib', '1.2.11'), # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils - ('binutils', version, '', SYSTEM) + ('binutils', version, '', True) ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb index 86e013bcdfd..138a0a59d7f 100644 --- a/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/b/bnpy/bnpy-0.1.6-foss-2018b-Python-2.7.15.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'cstd': 'c++03'} builddependencies = [ - ('Eigen', '3.3.7', '', SYSTEM), + ('Eigen', '3.3.7', '', True), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb index 217755142f3..18103c12dc1 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.2-intel-2017b-Python-2.7.14.eb @@ -14,7 +14,7 @@ dependencies = [ ('TopHat', '2.1.1'), ('Cufflinks', '2.2.1'), ('BEDTools', '2.26.0'), - ('Kent_tools', '20171107', '-linux.x86_64', SYSTEM), + ('Kent_tools', '20171107', '-linux.x86_64', True), ('STAR', '2.5.3a'), ('BWA', '0.7.17'), ('segemehl', '0.2.0'), diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb index 2362960ae99..edff9ff989f 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.3-intel-2018a-Python-2.7.14.eb @@ -18,7 +18,7 @@ dependencies = [ ('TopHat', '2.1.0', versionsuffix), ('Cufflinks', '2.2.1'), ('BEDTools', '2.27.1'), - ('Kent_tools', '20180716', '-linux.x86_64', SYSTEM), + ('Kent_tools', '20180716', '-linux.x86_64', True), ('STAR', '2.6.0c'), ('BWA', '0.7.17'), ('segemehl', '0.2.0'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb index 113d81b7610..6b1b02e8197 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-2.7.14.eb @@ -22,7 +22,7 @@ dependencies = [ ('scikit-learn', '0.19.1', versionsuffix), ('MEGAHIT', '1.1.3', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', SYSTEM), + ('picard', '2.18.27', '-Java-1.8', True), ('SAMtools', '1.6'), ('Bowtie2', '2.3.4.1'), ('parallel', '20171122'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb index 22128baa385..30bfadb038e 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2017b-Python-3.6.3.eb @@ -22,7 +22,7 @@ dependencies = [ ('scikit-learn', '0.19.1', versionsuffix), ('MEGAHIT', '1.1.3', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', SYSTEM), + ('picard', '2.18.27', '-Java-1.8', True), ('SAMtools', '1.6'), ('Bowtie2', '2.3.4.1'), ('parallel', '20171122'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb index dc99d2aeb67..b8d52d0019d 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.0.0-foss-2018b-Python-2.7.15.eb @@ -23,7 +23,7 @@ dependencies = [ ('scikit-learn', '0.20.2', versionsuffix), ('MEGAHIT', '1.1.4', versionsuffix), ('BEDTools', '2.27.1'), - ('picard', '2.18.27', '-Java-1.8', SYSTEM), + ('picard', '2.18.27', '-Java-1.8', True), ('SAMtools', '1.9'), ('Bowtie2', '2.3.4.2'), ('parallel', '20190222'), diff --git a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb index df708ac5e1f..f1334d88a22 100644 --- a/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CONCOCT/CONCOCT-1.1.0-foss-2019a-Python-2.7.15.eb @@ -27,7 +27,7 @@ dependencies = [ ('scikit-learn', '0.20.3'), ('MEGAHIT', '1.2.8'), ('BEDTools', '2.28.0'), - ('picard', '2.21.1', '-Java-11', SYSTEM), + ('picard', '2.21.1', '-Java-11', True), ('SAMtools', '1.9'), ('Bowtie2', '2.3.5.1'), ('parallel', '20190622'), diff --git a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb index cf48d75ac7f..bcf0c9ef120 100644 --- a/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/Caffe/Caffe-rc3-foss-2016a-CUDA-7.5.18-Python-2.7.11.eb @@ -29,8 +29,8 @@ dependencies = [ ('glog', '0.3.4'), ('gflags', '2.1.2'), ('OpenCV', '3.1.0'), - ('CUDA', local_cudaversion, '', SYSTEM), - ('cuDNN', '4.0', '', SYSTEM), + ('CUDA', local_cudaversion, '', True), + ('cuDNN', '4.0', '', True), ('LMDB', '0.9.18'), ('LevelDB', '1.18'), ('snappy', '1.1.3'), diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb index 28584d265c3..09811fccdee 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.53.1-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb index 9c8d5222d95..8d7f087e2b7 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.54.0-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://curl.haxx.se/download/'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] diff --git a/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb index d3b3a9cf790..ff486b7b508 100755 --- a/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb +++ b/easybuild/easyconfigs/c/canu/canu-1.4-foss-2016b.eb @@ -25,7 +25,7 @@ start_dir = 'src' files_to_copy = ['Linux-amd64/*'] dependencies = [ - ('Java', '1.8.0_112', '', SYSTEM), + ('Java', '1.8.0_112', '', True), ('Perl', '5.24.0'), ('gnuplot', '5.0.5'), ] diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb index 08887154a33..0d6ccf3dc76 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-foss-2016b.eb @@ -29,7 +29,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.3.0'), - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb index 8796b8995a5..d6fa49965ac 100644 --- a/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb +++ b/easybuild/easyconfigs/e/EMBOSS/EMBOSS-6.6.0-intel-2017a.eb @@ -29,7 +29,7 @@ patches = ['EMBOSS_disable-embossupdate.patch'] dependencies = [ ('libharu', '2.3.0'), - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ] configopts = " --with-hpdf=$EBROOTLIBHARU " diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb index fdb59680efe..20703396833 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.2.4-gimkl-2017a.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://ffmpeg.org/releases/'] dependencies = [ - ('NASM', '2.12.02', '', SYSTEM), + ('NASM', '2.12.02', '', True), ('x264', '20170406'), ('X11', '20170129'), # pulls in bzip2 and zlib ] diff --git a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb index 0e1c47bba9b..4cb227e1d23 100644 --- a/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/f/FMRIprep/FMRIprep-1.1.8-foss-2018b-Python-3.6.6.eb @@ -17,8 +17,8 @@ dependencies = [ ('FSL', '5.0.11', versionsuffix), ('ANTs', '2.3.1', versionsuffix), ('AFNI', '18.3.00', versionsuffix), - ('C3D', '1.0.0', '', SYSTEM), - ('FreeSurfer', '6.0.1', '-centos6_x86_64', SYSTEM), + ('C3D', '1.0.0', '', True), + ('FreeSurfer', '6.0.1', '-centos6_x86_64', True), ('ICA-AROMA', '0.4.4-beta', versionsuffix), ('Seaborn', '0.9.0', versionsuffix), ('PyYAML', '3.13', versionsuffix), diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb index 8f37cf904d2..fc9583cf3bc 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.26', '', SYSTEM), + ('binutils', '2.26', '', True), ('pkg-config', '0.29.1'), ] diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb index d9df0e9ca8d..0b86b4b9dbd 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb index 4c6ef6f4dd4..2ff9e6f9623 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-GCCcore-6.3.0.eb @@ -20,7 +20,7 @@ dependencies = [ # use same binutils version that was used when building GCCcore toolchain builddependencies = [ - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb index c1cfebce521..f01c0208b56 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb index eb85cf2630c..2b17c553f92 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.7.1-GCCcore-6.3.0-libpng-1.6.29.eb @@ -20,7 +20,7 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] configopts = '--with-harfbuzz=no' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb index 06af8a8bbb1..d489fda525c 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-foss-2018b-Python-3.6.6.eb @@ -29,7 +29,7 @@ dependencies = [ ('ASE', '3.16.2', versionsuffix), ('libxc', '3.0.1'), ('libvdwxc', '0.3.2'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb index fa75dd66180..8e5a3d625fa 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-1.4.0-intel-2018b-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('Python', '3.6.6'), ('ASE', '3.16.2', versionsuffix), ('libxc', '3.0.1'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb index 660743db68a..6a5eb1c4ce2 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2018b-ASE-3.18.0-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('ASE', local_aseversion, local_pythonsuffix), ('libxc', '3.0.1'), # Old version to maintain consistency with AtomPAW and ABINIT. ('libvdwxc', '0.3.2'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb index 6c10491a0d2..ed31bbedf0e 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-foss-2019a-Python-3.7.2.eb @@ -27,7 +27,7 @@ dependencies = [ ('ASE', '3.18.0', versionsuffix), ('libxc', '4.3.4'), ('libvdwxc', '0.4.0'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb index 3158794bf1a..c06fe0fe7ca 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2018b-ASE-3.18.0-Python-3.6.6.eb @@ -28,7 +28,7 @@ dependencies = [ ('Python', '3.6.6'), ('ASE', local_aseversion, local_pythonsuffix), ('libxc', '3.0.1'), # Old version to maintain consistency with AtomPAW and ABINIT. - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb index b6da87b17cc..337d63d58b0 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-19.8.1-intel-2019a-Python-3.7.2.eb @@ -26,7 +26,7 @@ dependencies = [ ('SciPy-bundle', '2019.03'), ('ASE', '3.18.0', versionsuffix), ('libxc', '4.3.4'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '0.9.20000', '', True), ] buildcmd = 'build --customize=eb_customize.py' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb index f73039f0fbb..c6e3c5bf573 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.2.2-intel-2018b-Python-2.7.15.eb @@ -15,7 +15,7 @@ dependencies = [ ('matplotlib', '2.2.3', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', SYSTEM), + ('pplacer', '1.1.alpha19', '', True), ('FastANI', '1.1'), ('FastTree', '2.1.10'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb index baa0455e8d4..96d22c898b8 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-foss-2019a-Python-2.7.15.eb @@ -19,7 +19,7 @@ dependencies = [ ('matplotlib', '2.2.4', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', SYSTEM), + ('pplacer', '1.1.alpha19', '', True), ('FastANI', '1.2'), ('FastTree', '2.1.11'), ] diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb index 234c38d3b4a..89a5cfe9651 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-0.3.2-intel-2019a-Python-2.7.15.eb @@ -19,7 +19,7 @@ dependencies = [ ('matplotlib', '2.2.4', versionsuffix), ('prodigal', '2.6.3'), ('HMMER', '3.2.1'), - ('pplacer', '1.1.alpha19', '', SYSTEM), + ('pplacer', '1.1.alpha19', '', True), ('FastANI', '1.2'), ('FastTree', '2.1.11'), ] diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb index 5584942b29c..ef9c393d1a7 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-foss-2016b.eb @@ -21,7 +21,7 @@ dependencies = [ ('freetype', '2.6.5'), ('Ghostscript', '9.20'), ('GTS', '0.7.6'), - ('Java', '1.8.0_92', '', SYSTEM), + ('Java', '1.8.0_92', '', True), ('libpng', '1.6.24'), ('Pango', '1.40.3'), ('Perl', '5.24.0'), diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb index 2a678bb2b9e..50d0e0b4494 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2016b.eb @@ -21,7 +21,7 @@ dependencies = [ ('freetype', '2.6.5'), ('Ghostscript', '9.20'), ('GTS', '0.7.6'), - ('Java', '1.8.0_92', '', SYSTEM), + ('Java', '1.8.0_92', '', True), ('libpng', '1.6.24'), ('Pango', '1.40.3'), ('Perl', '5.24.0'), diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb index 35dbf494bc9..4f4fa3e2f0c 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GCCcore-5.4.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('libreadline', '6.3'), ] -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] configopts = " --enable-error-on-warning=no" diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb index 1257db05441..0d730043fba 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-5.4.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', SYSTEM), + ('binutils', '2.26', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb index 3ff4d3ef78f..4931b9f6ce3 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb index 402e97d506e..f487ba55300 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.47.4-GCCcore-7.1.0.eb @@ -13,7 +13,7 @@ sources = [SOURCE_TAR_XZ] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', SYSTEM), + ('binutils', '2.28', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb index 1cdc59d3ecd..56433fb0b9c 100644 --- a/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb @@ -34,7 +34,7 @@ dependencies = [ ('ImageMagick', '6.9.4-8'), ('STAMP', '1.3'), ('Cluster-Buster', '20160106'), - ('Kent_tools', '20130806', '-linux.x86_64', SYSTEM), + ('Kent_tools', '20130806', '-linux.x86_64', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb index f0c3fff870f..29c369131f2 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb index 7fb4df0019e..52b296562ea 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb index f0d08dd8dd7..5d0e481e2b0 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb index d3c68c53159..ecc53857740 100644 --- a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb index 9b673d9b132..8068f14ea72 100644 --- a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb index 2e7d6b7a9f3..b9a8c3b204c 100644 --- a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb index 1eb5c2b11e2..bbe2ea95f7e 100644 --- a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb index 4d51c3577b5..dcc203e11e3 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), ('libpthread-stubs', '0.3'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 40f48498460..ba7aa8aa456 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -15,7 +15,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), ('libpthread-stubs', '0.3'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb index 9478bc5d4a6..76dc5940533 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb index bcc8bb91b85..d0b72a86ea2 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb index f215f8541e5..5af14da529b 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('inputproto', '2.3.1'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb index 50f49048f36..8117c7c96b3 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb index 7512c727f34..b95d581275b 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb index c06e453df9d..1cc411ee297 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb @@ -17,7 +17,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb index f5d786fdb45..6589aeeb492 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb index e95534157b7..2f7d28f58a9 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), ] diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb index c23a7491a1f..028286d1610 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xorg-macros', '1.19.0'), ('fixesproto', '5.0'), ('kbproto', '1.0.7'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), ] diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb index 787ed0a6b96..7f990b2124d 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xorg-macros', '1.19.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb index 20acc539c5d..7e2411fa015 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb @@ -18,7 +18,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('xorg-macros', '1.19.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('libpthread-stubs', '0.3'), ('xtrans', '1.3.5'), diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb index 1f7e10f14bb..62c62161692 100644 --- a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('libpthread-stubs', '0.3'), ('randrproto', '1.5.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb index 66d8e8e7988..d6e4b7406dd 100644 --- a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb @@ -17,7 +17,7 @@ builddependencies = [ ('libpthread-stubs', '0.3'), ('randrproto', '1.5.0'), ('renderproto', '0.11'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index f3c947b005a..b4c2ef6a53d 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb index c981feacb52..2c473580acb 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('renderproto', '0.11'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb index 61d8f22229f..c7e832fe55b 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('kbproto', '1.0.7'), ('xorg-macros', '1.19.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('xextproto', '7.3.0'), ('inputproto', '2.3.1'), diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb index 4401fe752de..e12535727a9 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb @@ -16,7 +16,7 @@ builddependencies = [ ('xproto', '7.0.28'), ('kbproto', '1.0.7'), ('xorg-macros', '1.19.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('libpthread-stubs', '0.3'), ('xextproto', '7.3.0'), ('inputproto', '2.3.1'), diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb index 8c219ad876e..fe73b8ae707 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCCcore-4.9.3.eb @@ -18,7 +18,7 @@ sources = ['%(name)s-%(version)s-stable.tar.gz'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', SYSTEM), + ('binutils', '2.25', '', True), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb index 0e6381d00bb..c2a203f1b2d 100644 --- a/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.15-GCCcore-6.3.0.eb @@ -12,7 +12,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb index 33ce05138dc..8fe50e9968e 100644 --- a/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libidn/libidn-1.32-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] sanity_check_paths = { 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb index 5679b67d18b..f33c3fbc3e1 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.28-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.11')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb index 156f6db5ca5..8c7fd2019e9 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.29-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] dependencies = [('zlib', '1.2.11')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] configopts = "--with-pic" diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb index 82f2dfb2315..e8763aba9c4 100644 --- a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.12-GCCcore-5.4.0.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] sanity_check_paths = { 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb index 5cb32f20da8..fdb971d5a6b 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.2.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb index 11b1fbaf2be..42794e4902b 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.3.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb index 2e615320fc8..e7ade18cd5e 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-5.4.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb index 91409103d4c..09f8321dfd0 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.1.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb index 763a4f1aefd..f8debfbbbad 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.2.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb index fe4f7047b25..f22547e6446 100644 --- a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-6.3.0.eb @@ -16,6 +16,6 @@ checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb index e97d8ea1348..c1f1541e7ad 100644 --- a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-GCCcore-5.4.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} sources = [SOURCELOWER_TAR_XZ] source_urls = [GNU_SOURCE] -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] parallel = 1 diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb index 965a763a8c8..7a2944d9e46 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('pkg-config', '0.29'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb index 3ec05ecfbde..ab5bcf6b380 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-gimkl-2.11.5.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index 4f81dd3b454..c69ddcedb6e 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('pkg-config', '0.29'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb index 690edb297f9..54ae8147222 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb index 7c8c84e827d..b3bcbc8fa66 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb @@ -22,7 +22,7 @@ dependencies = [ builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb index f5aef73bc13..b71554c4dfa 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-6.3.0.eb @@ -21,6 +21,6 @@ dependencies = [ ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb index 6d0bea61d24..d33516e092f 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.30-GCCcore-6.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['ba65236116de8326d83378b2bd929879fa185195bc530b9d1aba72107910b6b3'] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb index 17a1f835e91..7009268301e 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('MATLAB', version, '', SYSTEM) + ('MATLAB', version, '', True) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb index 55b0c6ce81f..d7fcbc99902 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-foss-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('MATLAB', version, '', SYSTEM) + ('MATLAB', version, '', True) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb index 14e3d088e33..fc816ba2323 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-2.7.14.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '2.7.14'), - ('MATLAB', version, '', SYSTEM) + ('MATLAB', version, '', True) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb index 76000b4dc4a..0c39c8a729c 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2018b-intel-2017b-Python-3.6.3.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} dependencies = [ ('Python', '3.6.3'), - ('MATLAB', version, '', SYSTEM) + ('MATLAB', version, '', True) ] # Since this setup.py does not provide a separate --build-base for the install diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb index 8ac5cb405dc..7ce8669e278 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2019b-GCCcore-8.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} multi_deps = {'Python': ['3.7.4', '2.7.16']} dependencies = [ - ('MATLAB', version, '', SYSTEM) + ('MATLAB', version, '', True) ] use_pip = False diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb index fb935602693..b7d5d70c2df 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [XORG_UTIL_SOURCE] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ('xproto', '7.0.31'), ('xorg-macros', '1.19.1'), ] diff --git a/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb index e87d9e19fd7..388d152019f 100644 --- a/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/methylpy/methylpy-1.1.9-foss-2017a-Python-2.7.13.eb @@ -19,7 +19,7 @@ dependencies = [ ('Bowtie2', '2.3.2'), ('Bowtie', '1.1.2'), ('SAMtools', '1.6'), - ('picard', '2.6.0', '-Java-1.8.0_131', SYSTEM), + ('picard', '2.6.0', '-Java-1.8.0_131', True), ('GSL', '2.3'), ] diff --git a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb index fd51cdde93e..4a532cf4fe8 100644 --- a/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.4-intel-2018a-Python-2.7.14.eb @@ -19,7 +19,7 @@ checksums = [ builddependencies = [('Boost.Python', '1.66.0', versionsuffix)] dependencies = [ - ('Eigen', '3.3.4', '', SYSTEM), + ('Eigen', '3.3.4', '', True), ('Python', '2.7.14'), ] diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb index c76c50c23f9..321116d715d 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-foss-2019a-Python-2.7.15.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.15'), - ('vsc-base', '2.8.3', '', SYSTEM), - ('vsc-mympirun', '4.1.8', '', SYSTEM), + ('vsc-base', '2.8.3', '', True), + ('vsc-mympirun', '4.1.8', '', True), ('matplotlib', '2.2.4', versionsuffix), ('h5py', '2.9.0'), ('mpi4py', '3.0.2', '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb index 194aa344082..e26533855e6 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2017a-Python-2.7.13.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.13'), - ('vsc-base', '2.5.8', '', SYSTEM), - ('vsc-mympirun', '4.0.2', '', SYSTEM), + ('vsc-base', '2.5.8', '', True), + ('vsc-mympirun', '4.0.2', '', True), ('matplotlib', '2.0.2', versionsuffix), ('h5py', '2.7.1', versionsuffix), ('mpi4py', '2.0.0', versionsuffix + '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb index 9c4144e7c47..7c14b8aa091 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2018a-Python-2.7.14.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.14'), - ('vsc-base', '2.8.1', '', SYSTEM), - ('vsc-mympirun', '4.1.5', '', SYSTEM), + ('vsc-base', '2.8.1', '', True), + ('vsc-mympirun', '4.1.5', '', True), ('matplotlib', '2.1.2', versionsuffix), ('h5py', '2.7.1', versionsuffix), ('mpi4py', '3.0.0', versionsuffix + '-timed-pingpong'), diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb index 6202bc1f6ce..5c72b2d9539 100644 --- a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.8.0-intel-2019a-Python-2.7.15.eb @@ -14,8 +14,8 @@ checksums = ['ebc056374a071e49cd13c49c4d5274cf4eee6eb68a7c9033ba2929db27b8bfac'] dependencies = [ ('Python', '2.7.15'), - ('vsc-base', '2.8.3', '', SYSTEM), - ('vsc-mympirun', '4.1.8', '', SYSTEM), + ('vsc-base', '2.8.3', '', True), + ('vsc-mympirun', '4.1.8', '', True), ('matplotlib', '2.2.4', versionsuffix), ('h5py', '2.9.0'), ('mpi4py', '3.0.2', '-timed-pingpong'), diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb index abba6ab7b5b..5ebb8f01ff7 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_92', '', SYSTEM)] +dependencies = [('Java', '1.8.0_92', '', True)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb index 5375c605408..ed0e37836cc 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.3-intel-2016a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_77', '', SYSTEM)] +dependencies = [('Java', '1.8.0_77', '', True)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb index e2ec60825f6..8b032e04685 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.2.5-foss-2016b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_92', '', SYSTEM)] +dependencies = [('Java', '1.8.0_92', '', True)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb index fc51bb5ca7f..8d0219a7422 100644 --- a/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb +++ b/easybuild/easyconfigs/n/NGS/NGS-1.3.0-intel-2017a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://github.com/ncbi/ngs/archive/'] sources = ['%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_121', '', SYSTEM)] +dependencies = [('Java', '1.8.0_121', '', True)] # override default of using $HOME/ncbi-outdir configopts = "--build-prefix=%(builddir)s/ncbi-outdir" diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb index 5c5cf246ba1..ff686a0a357 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.0-foss-2016a.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.58'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.3'), - ('Java', '1.8.0_72', '', SYSTEM), + ('Java', '1.8.0_72', '', True), ('zlib', '1.2.8'), ('Mesa', '11.1.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb index c2c9f653f54..ce3a19f67d0 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.0.3-intel-2016b.eb @@ -32,7 +32,7 @@ dependencies = [ ('GLPK', '4.60'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.5'), - ('Java', '1.8.0_112', '', SYSTEM), + ('Java', '1.8.0_112', '', True), ('zlib', '1.2.8'), ('Mesa', '12.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb index 20d927dc1fb..ea85cfeafc9 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-4.2.1-intel-2016b.eb @@ -33,7 +33,7 @@ dependencies = [ ('GLPK', '4.60'), ('GL2PS', '1.3.9'), ('gnuplot', '5.0.5'), - ('Java', '1.8.0_121', '', SYSTEM), + ('Java', '1.8.0_121', '', True), ('zlib', '1.2.8'), ('Mesa', '12.0.2'), ('libGLU', '9.0.0'), diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb index 86f569eb1f8..29256de39d1 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2g-GCCcore-4.9.3.eb @@ -14,7 +14,7 @@ source_urls = ['http://www.openssl.org/source/'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', SYSTEM), + ('binutils', '2.25', '', True), ] dependencies = [('zlib', '1.2.8')] diff --git a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb index f80a7efa49f..904ddedf279 100644 --- a/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/o/OrthoMCL/OrthoMCL-1.4-intel-2016b-Perl-5.24.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('Perl', '5.24.0'), ('MCL', '%s.%s' % (local_mcl_majver, local_mcl_minver)), ('BioPerl', '1.7.1', versionsuffix), - ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), + ('BLAST', '2.2.26', '-Linux_x86_64', True), ] start_dir = 'ORTHOMCLV%(version)s' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb index 484eb213be4..9dc98305542 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.40-GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb index e0de2012bfd..99940a8a08d 100644 --- a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -20,7 +20,7 @@ dependencies = [ ('Perl', '5.22.1'), ('libpsortb', '1.0'), ('BioPerl', '1.6.924', '-Perl-5.22.1'), - ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), + ('BLAST', '2.2.26', '-Linux_x86_64', True), ('pftoolsV3', '20160324'), ] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb index ce30da2a7da..2899a206f1b 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2016.1.2-intel-2016b-Python-2.7.12.eb @@ -15,7 +15,7 @@ checksums = ['a7dbdac7e2f0c0d2ad98f5f281d5a9d29d6673b3c20210e261b96e9a2d0b6e37'] dependencies = [ ('Python', '2.7.12'), - ('CUDA', '8.0.61', '', SYSTEM), + ('CUDA', '8.0.61', '', True), ('Boost', '1.61.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb index 13947e02b8c..e98942047c3 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-intel-2018a-Python-2.7.14.eb @@ -15,7 +15,7 @@ checksums = ['6b5a9384e38c603ee429f8a6bee424532db7b3505027ce22f7e18ad19564b563'] dependencies = [ ('Python', '2.7.14'), - ('CUDA', '9.1.85', '', SYSTEM), + ('CUDA', '9.1.85', '', True), ('Boost.Python', '1.66.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb index 1d9ef9ef9e6..a3f849bd92e 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2018.1-intel-2018a-Python-3.6.4-CUDA-9.1.85.eb @@ -15,7 +15,7 @@ checksums = ['7079f7738e83ee79ae26f0827ada29fe55921fec9760201199cc2bfb69446c92'] dependencies = [ ('Python', '3.6.4'), - ('CUDA', '9.1.85', '', SYSTEM), + ('CUDA', '9.1.85', '', True), ('Boost.Python', '1.66.0', '-Python-%(pyver)s'), ] diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb index b2c7e5f1d25..134d0b6c5f4 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2016b-Python-2.7.12.eb @@ -23,7 +23,7 @@ checksums = ['0799e6c3021d6e163ef7250853922fc365c3fb94246c2cb0984381741b83ea98'] dependencies = [ ('Python', '2.7.12'), ('PyCogent', '1.9', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), + ('UCLUST', '1.2.22q', '-i86linux64', True), ] options = {'modulename': '%(namelower)s'} diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb index d4fd449da32..3d6d9af5489 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-foss-2018b-Python-2.7.15.eb @@ -24,7 +24,7 @@ checksums = ['0799e6c3021d6e163ef7250853922fc365c3fb94246c2cb0984381741b83ea98'] dependencies = [ ('Python', '2.7.15'), ('PyCogent', '1.9', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), + ('UCLUST', '1.2.22q', '-i86linux64', True), ] options = {'modulename': '%(namelower)s'} diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb index dcf058b6b89..651a588075e 100644 --- a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb @@ -19,7 +19,7 @@ sources = ['%(version)s.tar.gz'] dependencies = [ ('Python', '2.7.12'), ('PyCogent', '1.5.3', versionsuffix), - ('UCLUST', '1.2.22q', '-i86linux64', SYSTEM), + ('UCLUST', '1.2.22q', '-i86linux64', True), ] options = {'modulename': 'pynast'} diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb index b6ac75df40b..2a45738b149 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-0.3.1-foss-2018a-Python-3.6.4-CUDA-9.1.85.eb @@ -72,7 +72,7 @@ builddependencies = [('CMake', '3.10.2')] dependencies = [ ('Python', '3.6.4'), ('PyYAML', '3.12', '-Python-%(pyver)s'), - ('CUDA', local_cuda_ver, '', SYSTEM), + ('CUDA', local_cuda_ver, '', True), ('magma', '2.3.0', '-CUDA-%s' % local_cuda_ver), ('cuDNN', '7.0.5', '-CUDA-%s' % local_cuda_ver, True), ] diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb index fa0cc0df4bd..0e997ce499e 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.23.2-GCCcore-5.4.0.eb @@ -20,7 +20,7 @@ dependencies = [ ('libffi', '3.2.1'), ] -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] sanity_check_paths = { 'files': ['bin/p11-kit', 'bin/trust'] + diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb index 99145dac6d6..c92a89c0b3d 100644 --- a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.5-GCCcore-8.2.0-Python-3.7.2.eb @@ -26,7 +26,7 @@ builddependencies = [('binutils', '2.31.1')] dependencies = [ ('Python', '3.7.2'), - ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', SYSTEM) + ('SRA-Toolkit', '2.9.6-1', '-centos_linux64', True) ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb index 6b79129e1de..185ce92b1dc 100644 --- a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pixman/pixman-0.34.0-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = ['http://cairographics.org/releases/'] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb index 876023e3f43..dadba07804c 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-6.3.0.eb @@ -19,7 +19,7 @@ patches = [ builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] # don't use PAX, it might break. diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb index 60acff26e4a..b75a0d85ea9 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ source_urls = ['https://pkg-config.freedesktop.org/releases/'] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] # don't use PAX, it might break. diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb index 4af4cb4cfef..dfba4ffaa84 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.0-1-GCC-4.9.2.eb @@ -20,7 +20,7 @@ source_urls = [ mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb index 7c6c53dd6bf..1bfdad4fb7a 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3-mt.eb @@ -20,7 +20,7 @@ mpich_opts = '--enable-static' threaded = True dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb index 4937bd9d705..93f76f8af09 100644 --- a/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb +++ b/easybuild/easyconfigs/p/psmpi/psmpi-5.1.5-1-GCC-4.9.3.eb @@ -17,7 +17,7 @@ source_urls = ['https://github.com/ParaStation/psmpi2/archive/'] mpich_opts = '--enable-static' dependencies = [ - ('pscom', '5.0.48-1', '', SYSTEM), + ('pscom', '5.0.48-1', '', True), ] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb index 43f185c60fd..341f884f89e 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.0-foss-2016b-Python-3.5.2.eb @@ -25,7 +25,7 @@ dependencies = [ ('Python', '3.5.2'), ('Perl', '5.24.0'), ('matplotlib', '1.5.3', versionsuffix), - ('Java', '1.8.0_131', '', SYSTEM), + ('Java', '1.8.0_131', '', True), ('Boost', '1.63.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb index 79f2d229658..f0f4d2c5b81 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-4.6.3-foss-2018a-Python-3.6.4.eb @@ -23,7 +23,7 @@ dependencies = [ ('Python', '3.6.4'), ('Perl', '5.26.1'), ('matplotlib', '2.1.2', versionsuffix), - ('Java', '1.8.0_162', '', SYSTEM), + ('Java', '1.8.0_162', '', True), ('Boost', '1.66.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb index da0694b350b..f3b210b0ca5 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2018b-Python-2.7.15.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.0'), ('matplotlib', '2.2.3', versionsuffix), - ('Java', '1.8', '', SYSTEM), + ('Java', '1.8', '', True), ('Boost', '1.67.0'), ] diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb index aee9ee6a397..cef7ad2f682 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.0.2-foss-2019a-Python-2.7.15.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '2.7.15'), ('Perl', '5.28.1'), ('matplotlib', '2.2.4', versionsuffix), - ('Java', '11', '', SYSTEM), + ('Java', '11', '', True), ('Boost', '1.70.0'), ] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb index d81dfc2eebd..26cc0e00521 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb index dc3c3684a36..5bc3462602c 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb @@ -24,7 +24,7 @@ builddependencies = [ ('kbproto', '1.0.7'), ('libpthread-stubs', '0.3'), ('pkg-config', '0.29.1'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), ('xorg-macros', '1.19.0'), ('xproto', '7.0.28'), diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb index 856611cdef4..503529a7dda 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb index 8598fef3f0a..4606a8754dd 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb index acb8163c2da..10bcf7e69ec 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb index cf10b5462d5..aa995966ac0 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb @@ -15,7 +15,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ] configopts = "--with-pic --enable-threads --enable-R-shlib" diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index c5c88c181d4..f3ec1cac38c 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -23,7 +23,7 @@ dependencies = [ ('libjpeg-turbo', '1.4.2'), # for plottting in R ('LibTIFF', '4.0.6'), # for plotting in R ('cairo', '1.14.6'), # for plotting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', versionsuffix), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 4f6c9a71091..841c073f2b3 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -14,7 +14,7 @@ dependencies = [ ('ncurses', '6.0'), ('libpng', '1.6.21'), # for plotting in R ('libjpeg-turbo', '1.4.2'), # for plottting in R - ('Java', '1.8.0_72', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.4'), # for tcltk ('Tk', '8.6.4', '-no-X11'), # for tcltk ('cURL', '7.47.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb index 84e20abc2e2..067c596089e 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb index 32c2e7ab309..cd605ba827a 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb index 724a3ceed71..ebe33155b56 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb @@ -20,7 +20,7 @@ dependencies = [ ('libpng', '1.6.23'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb index 2f0044cf886..13ed7e3b872 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-foss-2016b-X11-20160819.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.24'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_92', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb index 8436e30f382..11f7ae9944f 100644 --- a/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.3.3-intel-2017a-X11-20170314.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.29'), # for plotting in R ('libjpeg-turbo', '1.5.1'), # for plottting in R ('LibTIFF', '4.0.7'), - ('Java', '1.8.0_121', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.6'), # for tcltk ('Tk', '8.6.6'), # for tcltk ('cURL', '7.53.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb index c8fa9e81b36..01b9b412a37 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.0-intel-2017a-X11-20170314.eb @@ -26,7 +26,7 @@ dependencies = [ ('libpng', '1.6.29'), # for plotting in R ('libjpeg-turbo', '1.5.1'), # for plottting in R ('LibTIFF', '4.0.7'), - ('Java', '1.8.0_121', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_121', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.6'), # for tcltk ('Tk', '8.6.6'), # for tcltk ('cURL', '7.53.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb b/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb index e6902b752ee..515080f4f37 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.1-foss-2016b-X11-20160819.eb @@ -32,7 +32,7 @@ dependencies = [ ('libpng', '1.6.24'), # for plotting in R ('libjpeg-turbo', '1.5.0'), # for plottting in R ('LibTIFF', '4.0.6'), - ('Java', '1.8.0_141', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_141', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.5'), # for tcltk ('Tk', '8.6.5'), # for tcltk ('cURL', '7.49.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb index 25a9ce4249a..93b5974cfca 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-foss-2017b-X11-20171023.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.55.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb index f09e4a993e8..72a1d8f4d5b 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb @@ -31,7 +31,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.8'), - ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.56.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb index ea2dd212efd..10a97cc8586 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.32'), # for plotting in R ('libjpeg-turbo', '1.5.2'), # for plottting in R ('LibTIFF', '4.0.8'), - ('Java', '1.8.0_152', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk ('cURL', '7.56.1'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb index 70cf55f16c3..25d65103609 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-foss-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb index 5422e8e8b16..dc9f868dc2b 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-intel-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb index df2f0ef39b8..83ac3843168 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.4-iomkl-2018a-X11-20180131.eb @@ -30,7 +30,7 @@ dependencies = [ ('libpng', '1.6.34'), # for plotting in R ('libjpeg-turbo', '1.5.3'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', SYSTEM), # Java bindings are built if Java is found, might as well provide it + ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.8'), # for tcltk ('Tk', '8.6.8'), # for tcltk ('cURL', '7.58.0'), # for RCurl diff --git a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb index 147016a5526..7cc11725a88 100644 --- a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-0.3.0-intel-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.6.6'), ('Pysam', '0.15.1', versionsuffix), ('scikit-learn', '0.20.0', versionsuffix), - ('Java', '1.8', '', SYSTEM), + ('Java', '1.8', '', True), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb index 1a666f6fc94..dc9c93177cf 100644 --- a/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/RNAIndel/RNAIndel-1.0.0-intel-2018b-Python-3.6.6.eb @@ -18,7 +18,7 @@ dependencies = [ ('Python', '3.6.6'), ('Pysam', '0.15.1', versionsuffix), ('scikit-learn', '0.20.0', versionsuffix), - ('Java', '1.8', '', SYSTEM), + ('Java', '1.8', '', True), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb index 01f18a9bb75..35d4801c28d 100644 --- a/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/SingleM/SingleM-0.12.1-intel-2019a-Python-2.7.15.eb @@ -23,7 +23,7 @@ dependencies = [ ('OrfM', '0.7.1'), ('HMMER', '3.2.1'), ('fxtract', '2.3'), - ('pplacer', '1.1.alpha19', '', SYSTEM), + ('pplacer', '1.1.alpha19', '', True), ('KronaTools', '2.7.1'), ('DIAMOND', '0.9.24'), ] diff --git a/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb b/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb index e45a4e372cc..06f3fc97f7e 100644 --- a/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/s/sharutils/sharutils-4.15-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['bin/shar', 'bin/uudecode', 'bin/uuencode', 'bin/unshar'], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb index ad59ec63441..3bf1060dd25 100755 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-1.2.1-foss-2016b-GPU-Python-3.5.2.eb @@ -17,8 +17,8 @@ local_pymajmin = local_pymaj + local_pymin dependencies = [ ('Python', '%s.%s.2' % (local_pymaj, local_pymin)), ('protobuf-python', '3.3.0', local_pythonsuffix), - ('CUDA', '8.0.44', '', SYSTEM), - ('cuDNN', '5.1', '-CUDA-8.0.44', SYSTEM), + ('CUDA', '8.0.44', '', True), + ('cuDNN', '5.1', '-CUDA-8.0.44', True), ] exts_list = [ diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb index 65072fe8b8e..b4e2affc990 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb @@ -26,8 +26,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_92', '', SYSTEM), - ('ant', '1.9.7', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.8.0_92', '', True), + ('ant', '1.9.7', '-Java-%(javaver)s', True), ('Bowtie', '1.1.2'), ('Bowtie2', '2.2.8'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb index 5e8309a25ee..35b020b401a 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.6.6-intel-2018a.eb @@ -27,8 +27,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.8.0_162', '', SYSTEM), - ('ant', '1.10.1', '-Java-%(javaver)s', SYSTEM), + ('Java', '1.8.0_162', '', True), + ('ant', '1.10.1', '-Java-%(javaver)s', True), ('Bowtie', '1.2.2'), ('Bowtie2', '2.3.4.1'), ('ncurses', '6.0'), diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb index 843aa1c597d..7522e28d255 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-5.4.0.eb @@ -29,7 +29,7 @@ source_urls = [ ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb index 0e32b78cf2d..bb013b1619c 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version builddependencies = [ # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.25', '', SYSTEM), + ('binutils', '2.25', '', True), ] dependencies = [ diff --git a/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb index ae2ec85f0ff..daa2ad6b936 100644 --- a/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb @@ -17,9 +17,9 @@ dependencies = [ ('BioPerl', '1.6.924', '-Perl-%(perlver)s'), ('HMMER', '3.1b2'), ('MCL', '14.137'), - ('MetaGeneAnnotator', '20080819', '-x86-64', SYSTEM), + ('MetaGeneAnnotator', '20080819', '-x86-64', True), ('MUSCLE', '3.8.31'), - ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), + ('BLAST', '2.2.26', '-Linux_x86_64', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb index 076c0558ad7..fa730a6cadd 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb @@ -13,8 +13,8 @@ sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/hpcugent/vsc-mympirun-scoop/archive/'] dependencies = [ - ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', SYSTEM), - ('vsc-mympirun', '3.4.2', '', SYSTEM), + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), + ('vsc-mympirun', '3.4.2', '', True), ('Python', '2.7.12'), ('SCOOP', '0.6.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb index dd1c04c7392..1c770debd8e 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb @@ -20,7 +20,7 @@ builddependencies = [ ('gettext', '0.19.7'), ('intltool', '0.51.0', '-Perl-5.22.1'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb index a565c8676f4..ce56b41359e 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb @@ -20,7 +20,7 @@ builddependencies = [ ('gettext', '0.19.7'), ('intltool', '0.51.0', '-Perl-5.22.1'), ('xextproto', '7.3.0'), - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('inputproto', '2.3.1'), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb index 3f6ba215d4d..0423282a108 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-4.9.2.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb index ec46a64b897..6c49a4458b9 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCC-5.4.0-2.26.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb index 3082194c6b5..001a737c6ef 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ('binutils', '2.25'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb index 1ba4448757e..08aad5d870e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016.04.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb index 96249ed4220..8b076ecba44 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb @@ -18,7 +18,7 @@ versionsuffix = '-gettext-%s' % local_gettext_ver builddependencies = [ ('Autotools', '20150215'), - ('gettext', local_gettext_ver, '', SYSTEM), + ('gettext', local_gettext_ver, '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb index 0c774d43908..a0c7f313e03 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.6', '', SYSTEM), + ('gettext', '0.19.6', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb index 64b7587aa4a..e891d5536ae 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb index 3393bb06e20..d8184d70d32 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb @@ -18,7 +18,7 @@ versionsuffix = '-gettext-%s' % local_gettext_ver builddependencies = [ ('Autotools', '20150215'), - ('gettext', local_gettext_ver, '', SYSTEM), + ('gettext', local_gettext_ver, '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb index 243db8e7d90..fdf1453ac4a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.6', '', SYSTEM), + ('gettext', '0.19.6', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb index 60aeff8c712..85431b3d6e9 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb @@ -15,7 +15,7 @@ patches = ['XZ-%(version)s_compat-libs.patch'] builddependencies = [ ('Autotools', '20150215'), - ('gettext', '0.19.8', '', SYSTEM), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb index 8ac99515760..735c3cbe5ba 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-GCCcore-6.3.0.eb @@ -14,9 +14,9 @@ source_urls = ['http://tukaani.org/xz/'] patches = ['XZ-5.2.2_compat-libs.patch'] builddependencies = [ - ('gettext', '0.19.8.1', '', SYSTEM), + ('gettext', '0.19.8.1', '', True), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb index 8cc83b07a7f..cc9e04a5714 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.3-gimkl-2017a.eb @@ -17,8 +17,8 @@ patches = ['XZ-5.2.2_compat-libs.patch'] # XZ (presumably its executables) depends on gettext, which depends on # xmllib2, which depends (optionally) on XZ builddependencies = [ - ('Autotools', '20150215', '', SYSTEM), - ('gettext', '0.19.8', '', SYSTEM), + ('Autotools', '20150215', '', True), + ('gettext', '0.19.8', '', True), ] # may become useful in non-x86 archs diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb index 7551f83a6ff..43b7d9e5a54 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb index 823375c47ae..599b3a7ea3e 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb index c61c6116cfc..6694d3c8d1a 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb index d6b82b3a951..6d95a13dc49 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb index e7c963b2128..20b75e6be45 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb index db62de8e619..2470683fb8a 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb @@ -12,7 +12,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb index 738376cb603..1c0793e3c1a 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb index 25da228279f..c5509644a13 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ('xorg-macros', '1.19.0'), diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb index 8cbd9faeae4..42b8d1faf07 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb index 1dfef47a2f7..f862af46cb9 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb @@ -13,7 +13,7 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ - ('xcb-proto', '1.11', '', SYSTEM), + ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), ] diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb index 4fdb9b6d636..06e2a620f7b 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-6.3.0.eb @@ -13,7 +13,7 @@ source_urls = [XORG_PROTO_SOURCE] builddependencies = [ # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ('xorg-macros', '1.19.1'), ] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb index 5d1b362aa15..8409e2aa5cb 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-5.4.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb index 520d56351d8..a15fb20fe64 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-6.3.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb index 5ba01e22f5b..bec9454ed8e 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11-GCCcore-7.1.0.eb @@ -15,7 +15,7 @@ source_urls = ['http://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.28', '', SYSTEM)] +builddependencies = [('binutils', '2.28', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb index 8da5a8874c1..6aa4e52aa9e 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb index 1221095c524..9ab612053c2 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb index 53d82c7a9a8..3475aad2a70 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb index 274d794a4aa..a7b3977bb9a 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.2.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb index 360c1a11cb8..1353624765d 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb index b5265dc9d78..1b44bb97802 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb index a8a5212f418..f4a9aac7763 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.26', '', SYSTEM)] +builddependencies = [('binutils', '2.26', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb index 55078920d1d..47a40a40359 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.1.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb index 16c8391ed1e..ecd6eff1be1 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] sanity_check_paths = { 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb index 1b7951ca5cc..5c5b309e903 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.3.0.eb @@ -16,7 +16,7 @@ source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', # use same binutils version that was used when building GCC toolchain builddependencies = [ - ('binutils', '2.27', '', SYSTEM) + ('binutils', '2.27', '', True) ] sanity_check_paths = { From 0f0d7886acb607803d6cb8d2d8d59900486ef5e7 Mon Sep 17 00:00:00 2001 From: scimerman <80223690+scimerman@users.noreply.github.com> Date: Tue, 11 Oct 2022 16:03:02 +0200 Subject: [PATCH 5064/9987] Changed to perl minimal --- .../easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb index 25d87d8dddb..1aedc1e69df 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1q-GCCcore-10.3.0.eb @@ -16,7 +16,7 @@ checksums = ['d7939ce614029cdff0b6c20f0e2e5703158a489a72b2507b8bd51bf8c8fd10ca'] dependencies = [('zlib', '1.2.11')] builddependencies = [ - ('Perl', '5.32.1'), + ('Perl', '5.32.1', '-minimal'), ('binutils', '2.36.1'), ] From 7672eda7e0ed7e954e15bc0743ee5394f6b20d1f Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 11 Oct 2022 15:17:10 +0100 Subject: [PATCH 5065/9987] more changes undone from old easyconfigs failing other CI tests --- .../b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb | 2 +- .../d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb | 2 +- .../g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb | 2 +- .../m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb | 2 +- .../MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb | 2 +- .../m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb | 2 +- .../easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb | 2 +- .../PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb | 2 +- .../PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb | 2 +- ...-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb | 2 +- .../easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb | 2 +- .../easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb index 3d6512a5f33..d90fb13229d 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] -dependencies = [('Java', '1.8.0_112', '', SYSTEM)] +dependencies = [('Java', '1.8.0_112', '', True)] prebuildopts = 'cd jni && ' diff --git a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb index 43608ef12b5..5077e846a5f 100644 --- a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb @@ -18,7 +18,7 @@ source_urls = ['https://bitbucket.org/nrg/dicombrowser/downloads/'] sources = ['%(name)s-%(version)s-bin-with-dependencies.jar'] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb b/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb index a8e13772a67..633322c56c4 100644 --- a/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb +++ b/easybuild/easyconfigs/g/GRNBoost/GRNBoost-20171009-intel-2017b-Java-1.8.0_152.eb @@ -16,7 +16,7 @@ sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_ builddependencies = [('sbt', '1.0.2', versionsuffix, True)] dependencies = [ - ('Java', '1.8.0_152', '', SYSTEM), + ('Java', '1.8.0_152', '', True), ('XGBoost', '20171120', versionsuffix), ('Spark', '2.2.0', '-Hadoop-2.6' + versionsuffix, True), ] diff --git a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb index 13a5f06fec5..f41f912592a 100644 --- a/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb +++ b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb @@ -13,7 +13,7 @@ source_urls = ['https://github.com/matsim-org/matsim/releases/download/%(namelow sources = ['%(namelower)s-%(version)s.zip'] dependencies = [ - ('Java', '1.8.0_112', '', SYSTEM), + ('Java', '1.8.0_112', '', True), ('X11', '20160819'), ] diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb index 05e8b2e18a0..9b8ad14bb5f 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] sources = ['stable_release-%s.zip' % version.replace('.', '-')] dependencies = [ - ('Java', '1.7.0_79', '', SYSTEM), + ('Java', '1.7.0_79', '', True), ('Python', '2.7.11'), ('HDF5', '1.8.16'), ('libxml2', '2.9.3'), diff --git a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb index 97b0d2699a0..d8d121944ac 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -21,7 +21,7 @@ sources = ['mpj-v%s.tar.gz' % (version.replace('.', '_'))] builddependencies = [('CMake', '3.5.2')] dependencies = [ - ('Java', '1.8.0_92', '', SYSTEM), + ('Java', '1.8.0_92', '', True), ] # compile JNI wrapper library as described in docs diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb index ece457c65a0..53475269537 100644 --- a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb +++ b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb @@ -18,7 +18,7 @@ source_urls = ['http://cmpg.unibe.ch/software/PGDSpider/'] sources = ['%(name)s_%(version)s.zip'] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb index 83910094da9..a77bf58f492 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-foss-2016a-Java-1.7.0_80-Python-2.7.11.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ('Python', '2.7.11'), ('Perl', '5.22.1'), ('Tcl', '8.6.4'), diff --git a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb index 79bce614bbe..fb25f08bf9e 100644 --- a/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb +++ b/easybuild/easyconfigs/p/PLplot/PLplot-5.11.1-intel-2016b-Java-1.7.0_80-Python-2.7.12.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.8'), - ('Java', '1.7.0_80', '', SYSTEM), + ('Java', '1.7.0_80', '', True), ('Python', '2.7.12'), ('Perl', '5.24.0'), ('cairo', '1.14.6'), diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb index 31aafdd2c90..0e81ab6be6c 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-2.2.0-intel-2017b-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3.eb @@ -18,7 +18,7 @@ source_urls = [ checksums = ['86f33f6f4fe545cb848600004144f09b6e8413af47ce02c1203c3ecda075288d'] dependencies = [ - ('Java', '1.8.0_152', '', SYSTEM), + ('Java', '1.8.0_152', '', True), ('Python', '3.6.3'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb index 5a6e085b08a..b6070a5118c 100644 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.2-foss-2016b.eb @@ -21,7 +21,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.11.5', '-Java-1.7.0_80', SYSTEM), + ('FastQC', '0.11.5', '-Java-1.7.0_80', True), ('cutadapt', '1.9.1', '-Python-2.7.12'), ] diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb index 132db8b33b2..ed3b6794101 100755 --- a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.4.4-foss-2016b.eb @@ -21,7 +21,7 @@ source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s' install_cmd = "cp -a * %(installdir)s && chmod +x %(installdir)s/%(namelower)s" dependencies = [ - ('FastQC', '0.11.5', '-Java-1.7.0_80', SYSTEM), + ('FastQC', '0.11.5', '-Java-1.7.0_80', True), ('cutadapt', '1.9.1', '-Python-2.7.12'), ] From dd57d5e74656e72be224fa5ce3b02ddc8f3eb39e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 11 Oct 2022 16:29:43 +0200 Subject: [PATCH 5066/9987] Increase tolerance in the compression test --- .../netcdf4-python-1.6.1-foss-2022a.eb | 7 ++++++- ...n-1.6.1_relax_tolerance_compression_test.patch | 15 +++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1_relax_tolerance_compression_test.patch diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb index e4909b8b62d..3073dcfd28b 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb @@ -24,13 +24,18 @@ exts_list = [ 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], }), (name, version, { - 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'patches': [ + 'netcdf4-python-1.1.8-avoid-diskless-test.patch', + 'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch', + ], 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], 'checksums': [ 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + # netcdf4-python-1.6.1_relax_tolerance_compression_test.patch + '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166', ], }), ] diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1_relax_tolerance_compression_test.patch b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1_relax_tolerance_compression_test.patch new file mode 100644 index 00000000000..57dda863c8b --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1_relax_tolerance_compression_test.patch @@ -0,0 +1,15 @@ +# Relax tolerance in the compression_szip test to avoid fails on some systems. +# author: maxim-masterov (SURF) +# +diff -Nru netcdf4-python-1.6.1.orig/test/tst_compression_szip.py netcdf4-python-1.6.1/test/tst_compression_szip.py +--- netcdf4-python-1.6.1.orig/test/tst_compression_szip.py 2022-10-11 14:47:31.830359000 +0200 ++++ netcdf4-python-1.6.1/test/tst_compression_szip.py 2022-10-11 14:48:13.300393000 +0200 +@@ -33,7 +33,7 @@ + assert_almost_equal(datarr,f.variables['data'][:]) + assert f.variables['data'].filters() ==\ + {'zlib':False,'szip':False,'zstd':False,'bzip2':False,'blosc':False,'shuffle':False,'complevel':0,'fletcher32':False} +- assert_almost_equal(datarr,f.variables['data_szip'][:]) ++ assert_almost_equal(datarr,f.variables['data_szip'][:], 6) + dtest = {'zlib': False, 'szip': {'coding': 'ec', 'pixels_per_block': 32}, 'zstd': False, 'bzip2': False, 'blosc': False, 'shuffle': False, 'complevel': 0, 'fletcher32': False} + assert f.variables['data_szip'].filters() == dtest + f.close() From 6b0e07573193c0fe87407ed2dcfe5a52e81466f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 11 Oct 2022 16:41:28 +0200 Subject: [PATCH 5067/9987] Fix patch description + checksum --- .../easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb | 11 +++++++++++ .../easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch | 2 ++ 2 files changed, 13 insertions(+) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb index c79d12f48f5..33c06f706b8 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb @@ -25,6 +25,17 @@ patches = [ ('VMD-%(version)s_configure.patch', 'vmd-%(version)s'), ('VMD-1.9.4a51_extra_colors.patch', 'vmd-%(version)s'), ] +checksums = [ + 'de278d0c5d969336d89068e0806fb50aaa0cb0f546ba985d840b279357860679', # vmd-1.9.4a57.src.tar.gz + '51a8bc2988bb184bd08216124f61725225bb1a6f563bdf8cd35154cb5d621c1a', # stride.tar.gz + '85760d6ae838e2b09801e34b36b484532383f7aaf2e8634b3ef808002a92baa3', # VMD-1.9.3_plugins.patch + 'd5cfa88064b7cffbc75accd69707d4e45fda974e8127de9ab606fdad501bd68a', # VMD-1.9.3_surf_Makefile.patch + 'f3c2a8c155e38db8e644cee6a01f6beaea5988e72ac74cde26b71670b151cc34', # VMD-1.9.3_surf_bad_printfs.patch + 'eb194ac0d8c086b73f87b29f7d732687f902431b1cdfa139c090401fefdee51e', # VMD-1.9.3_stride_Makefile.patch + 'eff1ca00cec637a6c8a156b2fb038e078d1835ba0eb15a571ed820bca5a866d9', # VMD-1.9.3_stride_MAX_AT_IN_RES.patch + '231b55bcc2e9e71a0934b2693b56170be4d922a9afe98f39b583617533ef1349', # VMD-1.9.4a57_configure.patch + '253eba282b570eb00e4764f46f77fd5ca898d10360d5707dd50ad1f14615af80', # VMD-1.9.4a51_extra_colors.patch +] dependencies = [ ('Tcl', '8.6.12'), diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch index 63b8e014f84..da64877ec97 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57_configure.patch @@ -1,3 +1,5 @@ +Update hardcoded configurations to be compatible with EB +Author: Last updated micketeer@gmail.com --- configure.orig 2022-10-03 21:19:36.313951477 +0000 +++ configure 2022-10-03 21:44:36.664710705 +0000 @@ -498,17 +498,17 @@ From dcc80e2c754d267162097da3d9a4a742f8e3fb78 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 11 Oct 2022 15:45:21 +0100 Subject: [PATCH 5068/9987] revert old flex easyconfig changes --- .../easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb | 2 +- .../easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb | 2 +- .../easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb | 2 +- easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb | 2 +- 16 files changed, 16 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb index f93575efa78..ac2d9ea1647 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb index 5845a2c4a99..72d2805b5fe 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb index 6dfeb43eb04..facf8e7f13d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb index 77843fba611..a28470817bb 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.2.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb index db2144c50dd..68344b21cb3 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-4.9.3.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.17')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.25', '', SYSTEM)] +builddependencies = [('binutils', '2.25', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb index 152ebf1d622..f579ff8a965 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.3.0.eb @@ -17,6 +17,6 @@ checksums = [ dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.27', '', SYSTEM)] +builddependencies = [('binutils', '2.27', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb index fd99cc06be2..bf74b3065c0 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCCcore-6.4.0.eb @@ -14,6 +14,6 @@ checksums = ['71dd1b58158c935027104c830c019e48c73250708af5def45ea256c789318948'] dependencies = [('M4', '1.4.18')] # use same binutils version that was used when building GCCcore toolchain -builddependencies = [('binutils', '2.28', '', SYSTEM)] +builddependencies = [('binutils', '2.28', '', True)] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb index 92ac3157fe7..b7b82f91973 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.3.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', SYSTEM), + ('binutils', '2.25', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb index 18c962e0803..73279c6d88c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.25', '', SYSTEM), + ('binutils', '2.25', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb index adf1e7911c6..954dea0d03b 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.3.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', SYSTEM), + ('binutils', '2.26', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb index 171d19af2db..ee9b4ed94d3 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', SYSTEM), + ('binutils', '2.26', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb index 1f313caa5a3..51d6c9f7b63 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.1.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb index cafaa07872a..43cfdfac42c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.eb @@ -19,7 +19,7 @@ dependencies = [('M4', '1.4.17')] builddependencies = [ ('Bison', '3.0.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb index 50026211e06..fea26879081 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-5.4.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.26', '', SYSTEM), + ('binutils', '2.26', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb index b8bb432df65..e7dd6de964c 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-6.3.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.27', '', SYSTEM), + ('binutils', '2.27', '', True), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb index 8f9ab00f288..28c855c205d 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.3-GCCcore-7.1.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Bison', '3.0.4'), ('help2man', '1.47.4'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.28', '', SYSTEM), + ('binutils', '2.28', '', True), ] moduleclass = 'lang' From e239ae1a429fdfc7641e2d8142d714fa7ad48dcc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2022 22:50:41 +0200 Subject: [PATCH 5069/9987] add sanity check command for x13as --- easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb index 0687aee7c0e..efe8235a510 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-10.2.0.eb @@ -41,11 +41,13 @@ builddependencies = [ build_cmd = 'make -f makefile.gf' -files_to_copy = [(["x13as"], "bin")] +files_to_copy = [(['x13as'], 'bin')] sanity_check_paths = { 'files': ['bin/x13as'], 'dirs': [], } +sanity_check_commands = ["x13as --help"] + moduleclass = 'math' From 257ee5bd5ac65516629326ba112e76d4bb522780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Oct 2022 23:09:37 +0200 Subject: [PATCH 5070/9987] add sanity check command for x13as --- easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb index 4359434e6cf..92ba2cefb87 100644 --- a/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/x13as/x13as-1-1-b59-GCCcore-11.2.0.eb @@ -41,11 +41,13 @@ builddependencies = [ build_cmd = 'make -f makefile.gf' -files_to_copy = [(["x13as"], "bin")] +files_to_copy = [(['x13as'], 'bin')] sanity_check_paths = { 'files': ['bin/x13as'], 'dirs': [], } +sanity_check_commands = ["x13as --help"] + moduleclass = 'math' From 84d47b9e40f33867fc246bd2e456fb1021ad987d Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 12:03:33 +0100 Subject: [PATCH 5071/9987] exclude older toolchain easyconfigs from SYSTEM template constant check --- test/easyconfigs/easyconfigs.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 766b4bad1eb..2d0e06c6ace 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1424,6 +1424,11 @@ def template_easyconfig_test(self, spec): orig_val = resolve_template(ec_dict[key], ec.template_values) dumped_val = resolve_template(dumped_ec[key], ec.template_values) + # skip SYSTEM template constant check for pre-2019b toolchain generation easyconfigs + # since these fail other CI checks when updated + regex = re.compile('(201\d[ab])|(^[1-8]\.\d+\.\d+)') + skip_system_template_check = regex.match(ec['toolchain']['version']) + # take into account that dumped value for *dependencies may include hard-coded subtoolchains # if no easyconfig was found for the dependency with the 'parent' toolchain, # if may get resolved using a subtoolchain, which is then hardcoded in the dumped easyconfig @@ -1452,9 +1457,9 @@ def template_easyconfig_test(self, spec): if len(dumped_dep) >= 4: if len(orig_dep) >= 4: # use of `True` is deprecated in favour of the more intuitive `SYSTEM` template - if orig_dep[3] is True: + if orig_dep[3] is True and not skip_system_template_check: error_msg = "use of `True` to indicate the system toolchain for dependency " - error_msg += "%s is deprecated, use the `SYSTEM` template instead" % dumped_dep[0] + error_msg += "%s is deprecated, use the `SYSTEM` template constant instead" % dumped_dep[0] self.fail(error_msg) else: self.assertEqual(dumped_dep[3], orig_dep[3]) From a9afaa4b990f1c715823056f0fe8dac89354c446 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 12:11:45 +0100 Subject: [PATCH 5072/9987] linting --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2d0e06c6ace..741effc1729 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1426,7 +1426,7 @@ def template_easyconfig_test(self, spec): # skip SYSTEM template constant check for pre-2019b toolchain generation easyconfigs # since these fail other CI checks when updated - regex = re.compile('(201\d[ab])|(^[1-8]\.\d+\.\d+)') + regex = re.compile(r'(201\d[ab])|(^[1-8]\.\d+\.\d+)') skip_system_template_check = regex.match(ec['toolchain']['version']) # take into account that dumped value for *dependencies may include hard-coded subtoolchains From f99a9299ab2dfc457792ea53e2d84b33985b12e7 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 12:29:27 +0100 Subject: [PATCH 5073/9987] fix logic and re-instate original test for easyconfigs excluded from the SYSTEM template constant check --- test/easyconfigs/easyconfigs.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 741effc1729..b4f60e5a0c8 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -42,6 +42,7 @@ from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.easyblocks.generic.pythonpackage import PythonPackage from easybuild.framework.easyblock import EasyBlock +from easybuild.framework.easyconfig.constants import EASYCONFIG_CONSTANTS from easybuild.framework.easyconfig.default import DEFAULT_CONFIG from easybuild.framework.easyconfig.format.format import DEPENDENCY_PARAMETERS from easybuild.framework.easyconfig.easyconfig import get_easyblock_class, letter_dir_for @@ -1457,10 +1458,13 @@ def template_easyconfig_test(self, spec): if len(dumped_dep) >= 4: if len(orig_dep) >= 4: # use of `True` is deprecated in favour of the more intuitive `SYSTEM` template - if orig_dep[3] is True and not skip_system_template_check: - error_msg = "use of `True` to indicate the system toolchain for dependency " - error_msg += "%s is deprecated, use the `SYSTEM` template constant instead" % dumped_dep[0] - self.fail(error_msg) + if orig_dep[3] is True: + if skip_system_template_check: + self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) + else: + error_msg = "use of `True` to indicate the system toolchain for dependency " + error_msg += "%s is deprecated, use the `SYSTEM` template constant instead" % dumped_dep[0] + self.fail(error_msg) else: self.assertEqual(dumped_dep[3], orig_dep[3]) else: From f441f621127d3a6dc74c5eb29272dd215e8e13b4 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 13:41:32 +0100 Subject: [PATCH 5074/9987] also exempt old toolchains of the form 201X.YZ --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index b4f60e5a0c8..3d18c0cf585 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1425,9 +1425,9 @@ def template_easyconfig_test(self, spec): orig_val = resolve_template(ec_dict[key], ec.template_values) dumped_val = resolve_template(dumped_ec[key], ec.template_values) - # skip SYSTEM template constant check for pre-2019b toolchain generation easyconfigs + # skip SYSTEM template constant check for 2019b and older toolchain generation easyconfigs # since these fail other CI checks when updated - regex = re.compile(r'(201\d[ab])|(^[1-8]\.\d+\.\d+)') + regex = re.compile(r'(201\d([ab]|\.\d+))|(^[1-8]\.\d+\.\d+)') skip_system_template_check = regex.match(ec['toolchain']['version']) # take into account that dumped value for *dependencies may include hard-coded subtoolchains From 9dfd27048cee13c0a6f179123c2924c01ca4d90e Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 13:49:16 +0100 Subject: [PATCH 5075/9987] switch to SYSTEM template constant in the remaining easyconfigs overlooked in #16386 --- .../a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb | 2 +- .../a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb | 2 +- .../f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb | 2 +- .../easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb | 2 +- .../o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 4 ++-- .../t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb | 2 +- .../t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 2 +- ...orchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb | 2 +- 14 files changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb index 7911a59e768..1a85d18683e 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb @@ -27,7 +27,7 @@ dependencies = [ ('Kalign', '3.3.1'), ('jax', '0.2.24', versionsuffix), # also provides absl-py ('UCX-CUDA', '1.10.0', versionsuffix), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('OpenMM', '7.5.1', '-DeepMind-patch'), ] diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb index 2ab59fb243c..b6993861962 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb @@ -27,7 +27,7 @@ dependencies = [ ('Kalign', '3.3.1'), ('jax', '0.3.9', versionsuffix), # also provides absl-py ('UCX-CUDA', '1.10.0', versionsuffix), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('OpenMM', '7.5.1', '-DeepMind-patch'), ] diff --git a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb index 3448b11526f..ff8966f9f92 100644 --- a/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/dlib/dlib-19.22-foss-2021a-CUDA-11.3.1.eb @@ -26,7 +26,7 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb index 2e329e07f19..0149030d604 100644 --- a/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/f/FastFold/FastFold-20220729-foss-2021a-CUDA-11.3.1.eb @@ -20,7 +20,7 @@ dependencies = [ ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), ('UCX-CUDA', '1.10.0', versionsuffix), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('dm-tree', '0.1.6'), ('einops', '0.4.1'), diff --git a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb index d9c4a4c51a4..a50c9db2fc7 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.2.24-foss-2021a-CUDA-11.3.1.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb index 387bbe5cc6c..c7812a8bd25 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.14-foss-2022a-CUDA-11.7.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), - ('cuDNN', '8.4.1.50', versionsuffix, True), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), ('NCCL', '2.12.12', versionsuffix), ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb index 92459f0310c..d77b7c6e666 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.9-foss-2021a-CUDA-11.3.1.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb index 9e9a544e9f6..91983a9e242 100644 --- a/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LDC/LDC-1.30.0-GCCcore-11.3.0.eb @@ -17,7 +17,7 @@ builddependencies = [ ('CMake', '3.23.1'), ('Ninja', '1.10.2'), # building LDC from source requires LDC - ('LDC', '1.24.0', '-%(arch)s', True), + ('LDC', '1.24.0', '-%(arch)s', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb index 1d5296cc0d5..52743c921ac 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -24,7 +24,7 @@ dependencies = [ ('HMMER', '3.3.2'), ('Kalign', '3.3.1'), ('UCX-CUDA', '1.10.0', versionsuffix), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('dm-tree', '0.1.6'), ('einops', '0.4.1'), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index cf6a5d92445..e6bc2880ce8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -51,7 +51,7 @@ builddependencies = [ ('hypothesis', '6.46.7'), ] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions ('Python', '3.10.4'), ('protobuf', '3.19.4'), @@ -64,7 +64,7 @@ dependencies = [ ('numactl', '2.0.14'), ('FFmpeg', '4.4.2'), ('Pillow', '9.1.1'), - ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', True), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), ('magma', '2.6.2', '-CUDA-%(cudaver)s'), ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), ('expecttest', '0.1.3'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb index 0ac39221678..32ddf1501b5 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), ('h5py', '3.2.1'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index 8c4c862c922..21750d02e0a 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', versionsuffix, True), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.5'), ('h5py', '3.2.1'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 24cafa17438..6f8467a3d68 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.4.1', '', SYSTEM), - ('cuDNN', '8.2.2.26', versionsuffix, True), + ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('Python', '3.9.6'), ('h5py', '3.6.0'), diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb index ca3b8eac2e9..041a172edb9 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb @@ -15,7 +15,7 @@ checksums = ['99e6d3d304184895ff4f6152e2d2ec1cbec89b3e057d9c940ae0125546b04e91'] builddependencies = [('CMake', '3.20.1')] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('Pillow-SIMD', '8.2.0'), ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), From 681e7267b08ae0801a557f91db5e01665c4aab9f Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 12 Oct 2022 13:53:37 +0100 Subject: [PATCH 5076/9987] line length --- test/easyconfigs/easyconfigs.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3d18c0cf585..35b3a60886f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1462,8 +1462,10 @@ def template_easyconfig_test(self, spec): if skip_system_template_check: self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) else: - error_msg = "use of `True` to indicate the system toolchain for dependency " - error_msg += "%s is deprecated, use the `SYSTEM` template constant instead" % dumped_dep[0] + error_msg = ( + "use of `True` to indicate the system toolchain for dependency " + "%s is deprecated, use the `SYSTEM` template constant instead" % dumped_dep[0] + ) self.fail(error_msg) else: self.assertEqual(dumped_dep[3], orig_dep[3]) From 1937a12077392134a19cea2b599cfb54d0c864a3 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 12 Oct 2022 14:12:56 +0100 Subject: [PATCH 5077/9987] adding easyconfigs: DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb --- ...epLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..1d6063dbbd9 --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,68 @@ +# Loosely based on PR #7680 +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'DeepLabCut' +version = '2.2.0.6' +versionsuffix = '-CUDA-%(cudaver)s' +local_version = '%(versionsuffix)s-contrib' + +homepage = 'http://www.mousemotorlab.org/deeplabcut' +description = "Markerless tracking of user-defined features with deep learning" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('Python', '3.9.5'), + ('h5py', '3.2.1'), + ('IPython', '7.25.0'), + ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), + ('TensorFlow', '2.6.0', versionsuffix), + ('PyYAML', '5.4.1'), + ('PyTables', '3.6.1'), + ('wxPython', '4.1.1'), + ('OpenCV', '4.5.3', local_version), + ('numba', '0.53.1'), + ('libyaml', '0.2.5'), + ('imgaug', '0.4.0', versionsuffix), + ('tqdm', '4.61.2'), + ('ruamel.yaml', '0.17.21'), + ('PyYAML', '5.4.1'), + ('statsmodels', '0.12.2'), + ('PyTorch', '1.10.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('filterpy', '1.4.5', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], + }), + ('pandas', '1.3.3', { + 'checksums': ['272c8cb14aa9793eada6b1ebe81994616e647b5892a370c7135efb2924b701df'], + }), + ('tensorpack', '0.11', { + 'checksums': ['022b610e416e62e3575424cd08e60af27808a5fb6914294615391caf582cbd4f'], + }), + ('tf_slim', '1.1.0', { + 'source_urls': ['https://github.com/google-research/tf-slim/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['964cde4b7728a408dcd5c841ab6b93d95137ab4b60db28b10400f86286bfeb8b'], + }), + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + 'sources': ['msgpack-numpy-0.4.8.tar.gz'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], + }), +] + +moduleclass = 'lib' From 56f6898350ae23dc0829890e1dc67c6fed6fc371 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 12 Oct 2022 14:46:54 +0100 Subject: [PATCH 5078/9987] adding easyconfigs: imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb --- .../imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..e724dbda37e --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,35 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.0' +versionsuffix = '-CUDA-11.4.1' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('Pillow', '8.3.2'), + ('matplotlib', '3.4.3'), + ('scikit-image', '0.19.1'), + ('OpenCV', '4.5.5', versionsuffix + '-contrib'), + ('Shapely', '1.8.2'), + ('imageio', '2.13.5'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['imgaug-0.4.0_openvc_requirement.patch'] +checksums = [ + '46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7', # imgaug-0.4.0.tar.gz + '2ff0b66ba38fdcf5f267a3d0ad1dc2710fee3c2f8cd3d086c56ea538a2a9ffc8', # imgaug-0.4.0_openvc_requirement.patch +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' From 017727e76347b0711c241238746e57bd8be6e32c Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 12 Oct 2022 14:55:05 +0100 Subject: [PATCH 5079/9987] adding easyconfigs: OpenCV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb --- ...CV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb new file mode 100644 index 00000000000..935c5f8c301 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.5.5-foss-2021b-CUDA-11.4.1-contrib.eb @@ -0,0 +1,86 @@ +name = 'OpenCV' +version = '4.5.5' +versionsuffix = '-CUDA-%(cudaver)s-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [ + {'source_urls': ['https://github.com/opencv/opencv/archive/'], + 'download_filename': '%(version)s.zip', 'filename': SOURCELOWER_ZIP}, + {'source_urls': ['https://github.com/opencv/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', 'filename': '%(namelower)s_contrib-%(version)s.zip'}, + {'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + 'fb16b734db3a28e5119d513bd7c61ef417edf3756165dc6259519bb9d23d04e2', # opencv-4.5.5.zip + 'f53a0e531b2e284d2d1af013f5d96a86dfc1165d71eb47ddc9e7b834cc803091', # opencv_contrib-4.5.5.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.2'), + ('freetype', '2.11.0'), + ('HarfBuzz', '2.8.2'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.0'), + ('OpenEXR', '3.1.1'), + ('JasPer', '2.0.33'), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), + ('GLib', '2.69.1'), + ('GTK3', '3.24.31'), + ('HDF5', '1.12.1'), # needed by hdf from contrib + ('CUDA', '11.4.1', '', SYSTEM), + ('cuDNN', '8.2.2.26', '-CUDA-%(cudaver)s', SYSTEM), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = '-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules ' +configopts += '-DFREETYPE_FOUND=ON ' +configopts += '-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/ ' +configopts += '-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so ' +configopts += '-DFREETYPE_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DHARFBUZZ_FOUND=ON ' +configopts += '-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz ' +configopts += '-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so ' +configopts += '-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON ' +configopts += '-DBUILD_opencv_python2=OFF ' + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' From 9704a24ceae84106f69fde86ed50258f8d719cf6 Mon Sep 17 00:00:00 2001 From: guacke Date: Wed, 12 Oct 2022 16:24:35 +0200 Subject: [PATCH 5080/9987] adding easyconfigs: PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb --- .../PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb new file mode 100644 index 00000000000..b597c4a7e59 --- /dev/null +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonPackage' + +name = 'PyMOL' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/schrodinger/pymol-open-source' +description = """ +PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D +visualization of proteins, small molecules, density, surfaces, and trajectories. +It also includes molecular editing, ray tracing, and movies. Open Source PyMOL +is free to everyone! +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"] +sources = ['v%(version)s.tar.gz'] +checksums = ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('Pmw', '2.0.1', { + 'buildopts': '', + 'installopts': '', + 'modulename': 'Pmw', + 'sources': [{ + 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', + 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], + 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], + 'use_pip': True, + 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], + }), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyQt5', '5.15.1'), + ('glew', '2.1.0'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.10'), + ('freetype', '2.10.3'), + ('GLM', '0.9.9.8'), + ('netCDF', '4.7.4'), + ('Tkinter', '%(pyver)s'), +] + +download_dep_fail = True +use_pip = False + +buildopts = '' +buildopts += '--use-msgpackc=no ' +installopts = buildopts + +modextravars = {'PYMOL_PATH': 'lib/python%(pyshortver)s/site-packages/pymol/pymol_path'} + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/pymol'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'vis' From 924191a138166afc6e0e431646fada1e913e0c2a Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Wed, 12 Oct 2022 17:36:30 +0200 Subject: [PATCH 5081/9987] adding easyconfigs: Delly-1.1.5-GCC-11.3.0.eb --- .../d/Delly/Delly-1.1.5-GCC-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/d/Delly/Delly-1.1.5-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/d/Delly/Delly-1.1.5-GCC-11.3.0.eb b/easybuild/easyconfigs/d/Delly/Delly-1.1.5-GCC-11.3.0.eb new file mode 100644 index 00000000000..fdbd1ffc53e --- /dev/null +++ b/easybuild/easyconfigs/d/Delly/Delly-1.1.5-GCC-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'Delly' +version = '1.1.5' + +homepage = 'https://github.com/dellytools/delly/' +description = """Delly is an integrated structural variant (SV) prediction +method that can discover, genotype and visualize deletions, tandem duplications, +inversions and translocations at single-nucleotide resolution in short-read +massively parallel sequencing data. It uses paired-ends, split-reads and +read-depth to sensitively and accurately delineate genomic rearrangements +throughout the genome.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'dellytools' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['aa5d994d4bd973e519931845c27f53a647d21ea6f649c651c0c2836b2bc7e801'] + +dependencies = [ + ('HTSlib', '1.15.1'), + ('Boost', '1.79.0'), +] + +build_cmd = 'make PARALLEL=1 -B src/delly' + +files_to_copy = [ + (['src/delly'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/delly'], + 'dirs': ['bin'] +} + +sanity_check_commands = ['delly'] + +moduleclass = 'bio' From c85aec299ad057cb912231bdc72c0d5ff7a9eff4 Mon Sep 17 00:00:00 2001 From: guacke Date: Wed, 12 Oct 2022 18:04:17 +0200 Subject: [PATCH 5082/9987] Style fixes. --- .../easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb index b597c4a7e59..ba9045003d0 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb @@ -46,9 +46,6 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ] -download_dep_fail = True -use_pip = False - buildopts = '' buildopts += '--use-msgpackc=no ' installopts = buildopts From 0893308e9988d05dc23a8e9c827639301c0634f5 Mon Sep 17 00:00:00 2001 From: guacke Date: Wed, 12 Oct 2022 18:31:36 +0200 Subject: [PATCH 5083/9987] Style fixes. --- .../p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb index ba9045003d0..227d4407f08 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb @@ -28,10 +28,16 @@ exts_list = [ 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], - 'use_pip': True, 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], }), ] +exts_default_options = { + 'use_pip': True, + 'download_dep_fail': True, +} + +download_dep_fail = True +use_pip = False dependencies = [ ('Python', '3.8.6'), From ddcc55e8ce2893b6a4ed3b0260cfca3b36db3f56 Mon Sep 17 00:00:00 2001 From: guacke Date: Wed, 12 Oct 2022 18:49:19 +0200 Subject: [PATCH 5084/9987] Style fixes. --- .../p/PyMOL/PyMOL-2.5.0-foss-2020b.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb new file mode 100644 index 00000000000..8173740a5a3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonPackage' + +name = 'PyMOL' +version = '2.5.0' + +homepage = 'https://github.com/schrodinger/pymol-open-source' +description = """ +PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D +visualization of proteins, small molecules, density, surfaces, and trajectories. +It also includes molecular editing, ray tracing, and movies. Open Source PyMOL +is free to everyone! +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"] +sources = ['v%(version)s.tar.gz'] +checksums = ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('Pmw', '2.0.1', { + 'buildopts': '', + 'installopts': '', + 'modulename': 'Pmw', + 'sources': [{ + 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', + 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], + 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], + 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], + }), +] +exts_default_options = { + 'use_pip': True, + 'download_dep_fail': True, +} + +download_dep_fail = True +use_pip = False + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('PyQt5', '5.15.1'), + ('glew', '2.1.0'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.10'), + ('freetype', '2.10.3'), + ('GLM', '0.9.9.8'), + ('netCDF', '4.7.4'), + ('Tkinter', '%(pyver)s'), +] + +buildopts = '' +buildopts += '--use-msgpackc=no ' +installopts = buildopts + +modextravars = {'PYMOL_PATH': 'lib/python%(pyshortver)s/site-packages/pymol/pymol_path'} + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/pymol'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'vis' From d24202dc9b38f21d2993ad3c02e3fecbc474d1f2 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 12 Oct 2022 18:54:08 +0200 Subject: [PATCH 5085/9987] fix using system qhull and freetype for matplotlib --- .../easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb index ade6e567845..3a1a017fd44 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2022a.eb @@ -30,7 +30,7 @@ sanity_pip_check = True # avoid that matplotlib downloads and builds its own copies of freetype and qhull _fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " -_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >setup.cfg && " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg && " _include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " From fb26afdc27696923eedf8e713aae6576fbae0014 Mon Sep 17 00:00:00 2001 From: Guillaume Acke Date: Wed, 12 Oct 2022 19:57:37 +0200 Subject: [PATCH 5086/9987] Delete PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb --- .../PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb | 67 ------------------- 1 file changed, 67 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb deleted file mode 100644 index 227d4407f08..00000000000 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b-Python-3.8.6.eb +++ /dev/null @@ -1,67 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyMOL' -version = '2.5.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/schrodinger/pymol-open-source' -description = """ -PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D -visualization of proteins, small molecules, density, surfaces, and trajectories. -It also includes molecular editing, ray tracing, and movies. Open Source PyMOL -is free to everyone! -""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"] -sources = ['v%(version)s.tar.gz'] -checksums = ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'] - -exts_defaultclass = 'PythonPackage' -exts_list = [ - ('Pmw', '2.0.1', { - 'buildopts': '', - 'installopts': '', - 'modulename': 'Pmw', - 'sources': [{ - 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', - 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], - 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], - 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], - }), -] -exts_default_options = { - 'use_pip': True, - 'download_dep_fail': True, -} - -download_dep_fail = True -use_pip = False - -dependencies = [ - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('PyQt5', '5.15.1'), - ('glew', '2.1.0'), - ('libpng', '1.6.37'), - ('libxml2', '2.9.10'), - ('freetype', '2.10.3'), - ('GLM', '0.9.9.8'), - ('netCDF', '4.7.4'), - ('Tkinter', '%(pyver)s'), -] - -buildopts = '' -buildopts += '--use-msgpackc=no ' -installopts = buildopts - -modextravars = {'PYMOL_PATH': 'lib/python%(pyshortver)s/site-packages/pymol/pymol_path'} - -sanity_pip_check = True -sanity_check_paths = { - 'files': ['bin/pymol'], - 'dirs': ['bin', 'lib'], -} - -moduleclass = 'vis' From 7f3973d12d919b1446fb2313ec7d3555ed3cfaeb Mon Sep 17 00:00:00 2001 From: Randy Pittman Date: Wed, 12 Oct 2022 11:16:38 -0700 Subject: [PATCH 5087/9987] Fix GitHub download link in libpsl-0.21.1-GCCcore-11.2.0.eb The existing download link in this doesn't work anymore. This file was added by #16087. --- easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb index 18012521272..66143f4a39a 100644 --- a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.2.0.eb @@ -8,7 +8,7 @@ description = "C library for the Public Suffix List" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['https://github.com/rockdaboot/libpsl/archive'] +source_urls = ['https://github.com/rockdaboot/libpsl/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['ac6ce1e1fbd4d0254c4ddb9d37f1fa99dec83619c1253328155206b896210d4c'] From 6e3a4e67d11c077851405490dd0c98ea28fb482c Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Wed, 12 Oct 2022 20:54:24 +0200 Subject: [PATCH 5088/9987] adding easyconfigs: pocl-1.8-GCC-11.3.0.eb --- .../easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb new file mode 100644 index 00000000000..469e6ffef6f --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '1.8' + +homepage = 'https://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['pocl-%(version)s_fix-header-install.patch'] +checksums = [ + '0f63377ae1826e16e90038fc8e7f65029be4ff6f9b059f6907174b5c0d1f8ab2', # v1.8.tar.gz +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Clang', '13.0.1'), + ('hwloc', '2.7.1'), + ('libtool', '2.4.7'), + ('libxml2', '2.9.13'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From a17ed42e18d40031eaf73d225aacc85c7a8e5fb5 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Wed, 12 Oct 2022 21:20:26 +0200 Subject: [PATCH 5089/9987] Forgot patch checksum --- easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb index 469e6ffef6f..d9dbdf2fa1d 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb @@ -13,6 +13,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['pocl-%(version)s_fix-header-install.patch'] checksums = [ '0f63377ae1826e16e90038fc8e7f65029be4ff6f9b059f6907174b5c0d1f8ab2', # v1.8.tar.gz + '97dc45437ae7464bda9f13088720482804b8a19a4e71067196daa86af487222d', # pocl-1.8_fix-header-install.patch ] builddependencies = [ From fee40ea341c5c36158344b058fe42a18c13b36ec Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 12 Oct 2022 21:15:35 +0100 Subject: [PATCH 5090/9987] pkgconf added as more modern compared to the suggested pkg-config --- easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb index b78028c24b1..8145961cb31 100644 --- a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.2.0.eb @@ -34,6 +34,7 @@ checksums = [ builddependencies = [ ('binutils', '2.37'), ('GObject-Introspection', '1.68.0'), + ('pkgconf', '1.8.0'), ] dependencies = [ From a660197549c9b5db8d05e16b28b17cde0f555faf Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 13 Oct 2022 11:10:37 +0200 Subject: [PATCH 5091/9987] also add the intel twin --- .../easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb index 2bf90cc74a0..34b9ef271bb 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-intel-2022a.eb @@ -30,7 +30,7 @@ sanity_pip_check = True # avoid that matplotlib downloads and builds its own copies of freetype and qhull _fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " -_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >setup.cfg && " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg && " _include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " From d3779ab7745e23d7fa84a8e26923c1bf3ea3fe97 Mon Sep 17 00:00:00 2001 From: Maxim Date: Thu, 13 Oct 2022 13:09:54 +0200 Subject: [PATCH 5092/9987] Update QIIME2-2022.8.eb --- easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb index 30c12abc3c2..ecd06506127 100644 --- a/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb @@ -13,7 +13,7 @@ description = """QIIME is an open-source bioinformatics pipeline for performing source_urls = ['https://data.qiime2.org/distro/core/'] sources = ['qiime2-%(version)s-py38-linux-conda.yml'] -checksums = ['454bb219f928c7f4ec0097888db27ab439ba2ef7e4294f38b7033327cb3dafb8'] +checksums = ['e43bffad08dfd8ab9054f1530e501258525a7b9a3f3079ac04fad701d797c90b'] toolchain = SYSTEM From 8d58eee940e79d90e948e193be979d15c03041ae Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 13 Oct 2022 15:31:32 +0200 Subject: [PATCH 5093/9987] adding easyconfigs: motif-2.3.8-GCCcore-11.3.0.eb, motif-2.3.8-GCCcore-10.2.0.eb --- .../m/motif/motif-2.3.8-GCCcore-10.2.0.eb | 40 ++++++++++++++++++ .../m/motif/motif-2.3.8-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..63dcdcf5ab5 --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.8' + +homepage = 'https://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] + +builddependencies = [ + ('Autotools', '20200321'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('util-linux', '2.36'), +] + +dependencies = [ + ('X11', '20201008'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('libjpeg-turbo', '2.0.5'), + ('bzip2', '1.0.8'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8f4a300dbef --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.8' + +homepage = 'https://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] + +builddependencies = [ + ('Autotools', '20220317'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('binutils', '2.38'), + ('util-linux', '2.38'), +] + +dependencies = [ + ('X11', '20220504'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('libjpeg-turbo', '2.1.3'), + ('bzip2', '1.0.8'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' From aef3eeeb5ce80afff447b2cf6fc788f128f0e1fd Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 13 Oct 2022 16:53:03 +0200 Subject: [PATCH 5094/9987] adding easyconfigs: PyTorch-1.12.0-foss-2022a.eb --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb new file mode 100644 index 00000000000..06f29a6402e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb @@ -0,0 +1,97 @@ +name = 'PyTorch' +version = '1.12.0' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'pytorch', + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +patches = [ + '%(name)s-1.7.0_avoid-nan-in-test-torch.patch', + '%(name)s-1.7.0_disable-dev-shm-test.patch', + '%(name)s-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', + '%(name)s-1.10.0_fix-test-dataloader-fixed-affinity.patch', + '%(name)s-1.10.0_skip_cmake_rpath.patch', + '%(name)s-1.11.0_increase-distributed-test-timeout.patch', + '%(name)s-1.11.0_increase_c10d_gloo_timeout.patch', + '%(name)s-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', +] +checksums = [ + None, # PyTorch-1.12.0.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_cmake_rpath.patch + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch + 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), +] +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.4.2'), + ('Pillow', '9.1.1'), + ('expecttest', '0.1.3'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +excluded_tests = { + '': [ + # Bad tests: https://github.com/pytorch/pytorch/issues/60260 + 'distributed/elastic/utils/distributed_test', + 'distributed/elastic/multiprocessing/api_test', + # These tests fail on A10s at the very least, they time out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + # 'distributed/test_distributed_fork', + 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + 'test_optim', + # Test from this suite timeout often. The process group backend is deprecated anyway + # 'distributed/rpc/test_process_group_agent', + # This test fails constently when run as part of the test suite, but succeeds when run interactively + 'test_model_dump', + # These tests appear flaky, possibly related to number of GPUs that are used + 'distributed/fsdp/test_fsdp_memory', + 'distributed/fsdp/test_fsdp_overlap', + ] +} + +runtest = "cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s" + +# several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), +# so we allow up to 400 (out of ~90k) tests to fail before treating the installation to be faulty +max_failed_tests = 400 + +tests = ['%(name)s-check-cpp-extension.py'] + +moduleclass = 'ai' From fce73ff22f18fc49d84d1a7493d29a9d36eb0324 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 13 Oct 2022 16:40:09 +0100 Subject: [PATCH 5095/9987] True changed to SYSTEM --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 1d6063dbbd9..086b4db0913 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -15,8 +15,8 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True} dependencies = [ - ('CUDA', '11.3.1', '', True), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('CUDA', '11.3.1', '', SYSTEM), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('Python', '3.9.5'), ('h5py', '3.2.1'), ('IPython', '7.25.0'), From 924cb472a1a8a02b373719653540ff9e671c7522 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 13 Oct 2022 17:21:33 +0100 Subject: [PATCH 5096/9987] True replaced with SYSTEM --- .../easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb index eb0217ebec9..30a1fdb6714 100644 --- a/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb @@ -41,7 +41,7 @@ dependencies = [ ('rapidcsv', '8.64'), ('fmt', '9.1.0'), ('googletest', '1.11.0'), - ('cxxopts', '3.0.0', '', True), + ('cxxopts', '3.0.0', '', SYSTEM), ('indicators', '2.2'), ] From 1ba6b33dbd674864db989db72bcaa032a87f39de Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 13 Oct 2022 17:49:45 +0100 Subject: [PATCH 5097/9987] True replaced with SYSTEM --- easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb index 8bc5d81d922..a22e3ec4093 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb @@ -36,7 +36,7 @@ dependencies = [ ('GLPK', '5.0'), ('GL2PS', '1.4.2'), ('gnuplot', '5.4.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '21.1.7'), ('libGLU', '9.0.2'), From 64312589a59a183b433d1b46c54d38575758b8fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 13 Oct 2022 17:47:07 +0000 Subject: [PATCH 5098/9987] use http due to bad ssl cert --- easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb index 33c06f706b8..791a53cb6f9 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a57-foss-2022a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = [ 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', - 'https://webclu.bio.wzw.tum.de/stride/' + 'http://webclu.bio.wzw.tum.de/stride/' # bad SSL cert ] sources = [ 'vmd-%(version)s.src.tar.gz', From 7ab5413e8737afd32254d31a3200c980d3d23e16 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 13 Oct 2022 20:53:48 +0200 Subject: [PATCH 5099/9987] use source tarball --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a.eb | 39 ++++++++----------- 1 file changed, 16 insertions(+), 23 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb index 06f29a6402e..acaa8d0b12a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb @@ -7,15 +7,8 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2022a'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ '%(name)s-1.7.0_avoid-nan-in-test-torch.patch', '%(name)s-1.7.0_disable-dev-shm-test.patch', @@ -27,20 +20,20 @@ patches = [ '%(name)s-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', ] checksums = [ - None, # PyTorch-1.12.0.tar.gz - 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch - '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch - 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', - 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_cmake_rpath.patch - # PyTorch-1.11.0_increase-distributed-test-timeout.patch - '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', - # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch - '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', - # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch - 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', + {'pytorch-v1.12.0.tar.gz': '46eff236370b759c427b03ff535c3597099043e8e467b8f81f9cd4b258a7a321'}, + {'PyTorch-1.7.0_avoid-nan-in-test-torch.patch': 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch': + 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea'}, + {'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch': + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707'}, + {'PyTorch-1.10.0_skip_cmake_rpath.patch': 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448'}, + {'PyTorch-1.11.0_increase-distributed-test-timeout.patch': + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f'}, + {'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch': + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953'}, + {'PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch': + 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51'}, ] builddependencies = [ From 29645050f50cb0c2b2da344b6ca58d08e4808348 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 09:40:05 +0200 Subject: [PATCH 5100/9987] stick to http in source URL for stride.tar.gz in VMD 1.9.4a51 easyconfigs due to problems with SSL certificate --- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb | 2 +- easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb index e2b6645847e..b170a6dc5ff 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-foss-2020b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [ 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', - 'https://webclu.bio.wzw.tum.de/stride/' + 'http://webclu.bio.wzw.tum.de/stride/' ] sources = [ 'vmd-%(version)s.src.tar.gz', diff --git a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb index 0ad4daad390..6a7845eece2 100644 --- a/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/v/VMD/VMD-1.9.4a51-fosscuda-2020b.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} source_urls = [ 'https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.4/files/alpha/', 'https://www.ks.uiuc.edu/Research/vmd/vmd-%(version)s/files/final', - 'https://webclu.bio.wzw.tum.de/stride/' + 'http://webclu.bio.wzw.tum.de/stride/' ] sources = [ 'vmd-%(version)s.src.tar.gz', From 8694579f9d500a5c1489404ef051420086d13f5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 11:31:39 +0200 Subject: [PATCH 5101/9987] enable running of LAPACK tests for recent OpenBLAS easyconfigs + set max. number of failing tests due to numerical errors to 150 --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 6 ++++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 6 ++++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 6 ++++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 6 ++++++ 4 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 35e4b615bf8..d9c5442457e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -5,6 +5,9 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} +# disable use -free-vectorize to work around compiler miscompilation bug, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 +toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -30,6 +33,9 @@ checksums = [ 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 18fdbab68f8..8329f09da38 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -5,6 +5,9 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} +# disable use -free-vectorize to work around compiler miscompilation bug, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 +toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -27,6 +30,9 @@ checksums = [ 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index a6bed05840b..8d3d92504a6 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -5,6 +5,9 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} +# disable use -free-vectorize to work around compiler miscompilation bug, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 +toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -25,6 +28,9 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 72e27286e56..95511e2adc0 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -5,6 +5,9 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.3.0'} +# disable use -free-vectorize to work around compiler miscompilation bug, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 +toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -25,6 +28,9 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' From 20b690f55c211bec8d5d5cdb914d9b8724a8ca59 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 14 Oct 2022 11:43:57 +0100 Subject: [PATCH 5102/9987] detect available cores and remove unneeded deps in Unicycler 0.5.0 --- .../Unicycler/Unicycler-0.5.0-gompi-2021b.eb | 10 ++-- .../Unicycler-0.5.0_available-cpus.patch | 51 +++++++++++++++++++ 2 files changed, 56 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0_available-cpus.patch diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb index 3fc79ebf2db..68544dec87b 100644 --- a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0-gompi-2021b.eb @@ -13,16 +13,16 @@ toolchain = {'name': 'gompi', 'version': '2021b'} github_account = 'rrwick' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['84a8709c9f2e624225410af702d779ffb0cb06f7c22c20e1f01b989945e08a47'] +patches = ['%(name)s-%(version)s_available-cpus.patch'] +checksums = [ + {'v0.5.0.tar.gz': '84a8709c9f2e624225410af702d779ffb0cb06f7c22c20e1f01b989945e08a47'}, + {'Unicycler-0.5.0_available-cpus.patch': '4c99e889826924b375e07f264b8a8a875a094d63127d5b39c3ebfaab267ce235'}, +] dependencies = [ ('Python', '3.9.6'), - ('Java', '11', '', SYSTEM), - ('Bowtie2', '2.4.4'), - ('SAMtools', '1.14'), ('SPAdes', '3.15.3'), ('Racon', '1.5.0'), - ('Pilon', '1.23', '-Java-%(javaver)s', SYSTEM), ('BLAST+', '2.12.0'), ] diff --git a/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0_available-cpus.patch b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0_available-cpus.patch new file mode 100644 index 00000000000..b8b2c8b49f3 --- /dev/null +++ b/easybuild/easyconfigs/u/Unicycler/Unicycler-0.5.0_available-cpus.patch @@ -0,0 +1,51 @@ +Determine the number of cores available to avoid using all that the system has. +Patch by Simon Branford (University of Birmingham) +--- setup.py.orig 2022-10-14 11:09:52.253946000 +0100 ++++ setup.py 2022-10-14 11:18:10.743520156 +0100 +@@ -104,7 +104,11 @@ + # Build Unicycler's C++ code. + make_cmd = ['make'] + try: +- make_cmd += ['-j', str(min(8, multiprocessing.cpu_count()))] ++ num_cpus = len(os.sched_getaffinity(0)) ++ except AttributeError: ++ num_cpus = multiprocessing.cpu_count() ++ try: ++ make_cmd += ['-j', str(min(8, num_cpus))] + except NotImplementedError: + pass + if self.makeargs: +--- unicycler/unicycler.py.orig 2022-10-14 11:09:58.407681000 +0100 ++++ unicycler/unicycler.py 2022-10-14 11:16:43.446404128 +0100 +@@ -627,9 +627,13 @@ + log.log('Unicycler version: v' + __version__) + log.log('Using ' + str(args.threads) + ' thread' + ('' if args.threads == 1 else 's')) + log.log('') +- if args.threads > 2 * multiprocessing.cpu_count(): +- log.log(red('Warning: you have specified a lot more threads than this machine seems to ' +- 'have! Was this intentional?')) ++ try: ++ num_cpus = len(os.sched_getaffinity(0)) ++ except AttributeError: ++ num_cpus = multiprocessing.cpu_count() ++ if args.threads > 2 * num_cpus: ++ log.log(red('Warning: you have specified a lot more threads than available! ' ++ 'Was this intentional?')) + log.log('') + log.log(out_dir_message) + +--- unicycler/misc.py.orig 2022-10-14 11:10:02.942374000 +0100 ++++ unicycler/misc.py 2022-10-14 11:17:30.093646345 +0100 +@@ -793,7 +793,11 @@ + + + def get_default_thread_count(): +- return min(multiprocessing.cpu_count(), settings.MAX_AUTO_THREAD_COUNT) ++ try: ++ num_cpus = len(os.sched_getaffinity(0)) ++ except AttributeError: ++ num_cpus = multiprocessing.cpu_count() ++ return min(num_cpus, settings.MAX_AUTO_THREAD_COUNT) + + + def spades_path_and_version(spades_path): From 83e4d44f949995fb07a9306f84ef1ebb4ef7b994 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 13:52:18 +0200 Subject: [PATCH 5103/9987] make requested changes to spaln 2.4.12 easyconfig --- easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb index 364c2101be1..6012bf6434b 100644 --- a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb @@ -16,7 +16,10 @@ source_urls = ['https://github.com/ogotoh/spaln/archive/'] sources = ['ver%(version)s.tar.gz'] checksums = ['0c5f842131409686dbaad01778960f53f1ebba8dd83d55b454ec4bf1b6bde2af'] -dependencies = [('zlib', '1.2.11')] +dependencies = [ + ('zlib', '1.2.11'), + ('Perl', '5.32.0'), +] start_dir = 'src' @@ -26,6 +29,8 @@ prefix_opt = '--exec_prefix=' configopts = "--exec_prefix=%(installdir)s/bin --table_dir=%(installdir)s/table --alndbs_dir=%(installdir)s/seqdb " configopts += "--use_zlib=1" +fix_perl_shebang_for = ['seqdb/*.pl'] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], 'dirs': ['seqdb', 'table'], @@ -33,4 +38,6 @@ sanity_check_paths = { sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] +modextrapaths = {'PATH': 'seqdb'} + moduleclass = 'bio' From cace0a6cae60891fc7840fc9ea0594220b40a986 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 14 Oct 2022 11:56:45 +0000 Subject: [PATCH 5104/9987] Add OpenEXR to POV-Ray --- .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ .../p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb | 1 + 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e81697b1a73 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.5' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/openexr/openexr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in + ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil']] + + ['bin/exr%s' % x for x in + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr']], + 'dirs': ['include/OpenEXR', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb index 04c5b90e972..de9f5ed3ce8 100644 --- a/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/POV-Ray/POV-Ray-3.7.0.10-GCC-11.3.0.eb @@ -44,6 +44,7 @@ dependencies = [ ('X11', '20220504'), ('LibTIFF', '4.3.0'), ('SDL2', '2.0.22'), + ('OpenEXR', '3.1.5'), ] preconfigopts = "cd unix && sed -i 's/^automake/automake --add-missing; automake/g' prebuild.sh && " From db5244f51d0d4ef4305ae6997c9b6891c7916b5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 13:58:10 +0200 Subject: [PATCH 5105/9987] also update $PERL5LIB to Perl module required by spaln Perl scripts are found --- easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb index 6012bf6434b..1d2162cf617 100644 --- a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-10.2.0.eb @@ -38,6 +38,9 @@ sanity_check_paths = { sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] -modextrapaths = {'PATH': 'seqdb'} +modextrapaths = { + 'PATH': 'seqdb', + 'PERL5LIB': 'seqdb', +} moduleclass = 'bio' From 55822cabf6b4a71d5609ffd9d4132aa5eea6dbd4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 16:20:07 +0200 Subject: [PATCH 5106/9987] {vis}[foss/2021a] Nipype v1.6.0, RDFlib v6.2.0 w/ Python 3.9.5 --- .../n/Nipype/Nipype-1.6.0-foss-2021a.eb | 58 +++++++++++++++++++ .../r/RDFlib/RDFlib-6.2.0-GCCcore-10.3.0.eb | 29 ++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb new file mode 100644 index 00000000000..6eb80b477ea --- /dev/null +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'Nipype' +version = '1.6.0' + +homepage = 'https://nipype.readthedocs.io' +description = """Nipype is a Python project that provides a uniform interface to existing neuroimaging software and + facilitates interaction between these packages within a single workflow.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('lxml', '4.6.3'), + ('networkx', '2.6.3'), + ('pydot', '1.4.2'), + ('NiBabel', '3.2.1'), + ('RDFlib', '6.2.0'), + ('pytest-xdist', '2.3.0'), +] + +use_pip = True + +exts_list = [ + ('traits', '6.4.1', { + 'checksums': ['78bb2ccafd60aff606515aac46de64668a0a81cb5c54c650b9877a841aa9e812'], + }), + ('pydotplus', '2.0.2', { + 'checksums': ['91e85e9ee9b85d2391ead7d635e3d9c7f5f44fd60a60e59b13e2403fa66505c4'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('prov', '2.0.0', { + 'checksums': ['b6438f2195ecb9f6e8279b58971e02bc51814599b5d5383366eef91d867422ee'], + }), + ('ci-info', '0.3.0', { + 'checksums': ['1fd50cbd401f29adffeeb18b0489e232d16ac1a7458ac6bc316deab6ae535fb0'], + }), + ('etelemetry', '0.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['78febd59a22eb53d052d731f10f24139eb2854fd237348fba683dd8616fb4a67'], + }), + ('nipype', version, { + 'checksums': ['bc56ce63f74c9a9a23c6edeaf77631377e8ad2bea928c898cc89527a47f101cf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/nipypecli'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import nipype.interfaces'"] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..17b46ad32a5 --- /dev/null +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-10.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'RDFlib' +version = '6.2.0' + +homepage = 'https://github.com/RDFLib/rdflib' +description = """RDFLib is a Python library for working with RDF, a simple yet powerful language + for representing information.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +use_pip = True + +exts_list = [ + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', version, { + 'checksums': ['62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 0d40c7ea5318cc8a04bafb3c78abceedde953492 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Fri, 14 Oct 2022 16:20:24 +0200 Subject: [PATCH 5107/9987] Added download link to the tarbal instead of clone. Also, updated the checksums accordingly --- .../i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb index a85a08e980d..36142e01453 100644 --- a/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.5-GCCcore-11.3.0.eb @@ -11,15 +11,9 @@ Imath is a C++ and python library of 2D and 3D vector, matrix, and math operatio toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -sources = [{ - 'filename': '%(name)s_v%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/AcademySoftwareFoundation', - 'repo_name': '%(name)s', - 'tag': 'v%(version)s', - }, -}] -checksums = ['5167b1441e4eaeb0f238faaac02c52ecd89940e7c77a3ed0c7356fb8934db570'] +source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1e9c7c94797cf7b7e61908aed1f80a331088cc7d8873318f70376e4aed5f25fb'] builddependencies = [ ('binutils', '2.38'), From abe3ca5503ca8621d355b7068bff41cddfaaffcc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 16:24:29 +0200 Subject: [PATCH 5108/9987] add Python build dependency for OpenBLAS easyconfigs that run LAPACK tests --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 5 +++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 5 +++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 5 +++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 5 +++++ 4 files changed, 20 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index d9c5442457e..756da27b0e7 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -33,6 +33,11 @@ checksums = [ 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] +builddependencies = [ + # required by LAPACK test suite + ('Python', '3.9.6', '-bare'), +] + run_lapack_tests = True max_failing_lapack_tests_num_errors = 150 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 8329f09da38..971d85d6a77 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -30,6 +30,11 @@ checksums = [ 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch ] +builddependencies = [ + # required by LAPACK test suite + ('Python', '3.9.6', '-bare'), +] + run_lapack_tests = True max_failing_lapack_tests_num_errors = 150 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index 8d3d92504a6..b4c9931fbae 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -28,6 +28,11 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] +builddependencies = [ + # required by LAPACK test suite + ('Python', '3.9.6', '-bare'), +] + run_lapack_tests = True max_failing_lapack_tests_num_errors = 150 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 95511e2adc0..a7ebb133ddc 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -28,6 +28,11 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] +builddependencies = [ + # required by LAPACK test suite + ('Python', '3.10.4', '-bare'), +] + run_lapack_tests = True max_failing_lapack_tests_num_errors = 150 From c948ceeb9b7dda1ea626d65a67aa782ea1a50101 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Oct 2022 16:33:57 +0200 Subject: [PATCH 5109/9987] stick to networkx 2.5.1 as dependency for Nipype 1.6.0 with foss/2021a --- easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb index 6eb80b477ea..9315c346305 100644 --- a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), ('lxml', '4.6.3'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ('pydot', '1.4.2'), ('NiBabel', '3.2.1'), ('RDFlib', '6.2.0'), From 05bf8888038857818c3f51f55483d77bbf37939a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 14 Oct 2022 14:36:01 +0000 Subject: [PATCH 5110/9987] Drop openexr easyconfig --- .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb deleted file mode 100644 index e81697b1a73..00000000000 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenEXR' -version = '3.1.5' - -homepage = 'https://www.openexr.com/' -description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic - for use in computer imaging applications""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://github.com/openexr/openexr/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] - -builddependencies = [ - ('binutils', '2.38'), - ('CMake', '3.23.1'), -] - -configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' - -sanity_check_paths = { - 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in - ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil']] + - ['bin/exr%s' % x for x in - ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr']], - 'dirs': ['include/OpenEXR', 'share'], -} - -moduleclass = 'vis' From fd422dd641e726a1398f9ae94a0cd8cca5b84569 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Fri, 14 Oct 2022 16:54:50 +0200 Subject: [PATCH 5111/9987] Replace True by System for the system toolchain --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 3676ebf7da8..4e7764a13b8 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -54,7 +54,7 @@ dependencies = [ ('libwebp', '1.2.4'), ('OpenEXR', '3.1.5'), ('JasPer', '2.0.33'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('ant', '1.10.12', '-Java-%(javaver)s', True), ('GLib', '2.72.1'), ('GTK4', '4.7.0'), From 142a79f971f88cbfc6fd3f72e7f58c786bd17324 Mon Sep 17 00:00:00 2001 From: guacke Date: Fri, 14 Oct 2022 17:00:05 +0200 Subject: [PATCH 5112/9987] Switch to PythonBundle. --- .../p/PyMOL/PyMOL-2.5.0-foss-2020b.eb | 53 ++++++++----------- 1 file changed, 21 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb index 8173740a5a3..642fc01b62c 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'PyMOL' version = '2.5.0' @@ -11,33 +11,6 @@ It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone! """ -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"] -sources = ['v%(version)s.tar.gz'] -checksums = ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'] - -exts_defaultclass = 'PythonPackage' -exts_list = [ - ('Pmw', '2.0.1', { - 'buildopts': '', - 'installopts': '', - 'modulename': 'Pmw', - 'sources': [{ - 'download_filename': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', - 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], - 'filename': 'Pmw-patched-2.0.1-20200210-8bedfc8.zip'}], - 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], - }), -] -exts_default_options = { - 'use_pip': True, - 'download_dep_fail': True, -} - -download_dep_fail = True -use_pip = False - dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), @@ -51,13 +24,29 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ] -buildopts = '' -buildopts += '--use-msgpackc=no ' -installopts = buildopts +toolchain = {'name': 'foss', 'version': '2020b'} + +use_pip = False +sanity_pip_check = True + +exts_list = [ + ('Pmw', '2.0.1', { + 'modulename': 'Pmw', + 'source_tmpl': 'Pmw-patched-%(version)s-20200210-8bedfc8.zip', + 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], + 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], + }), + (name, version, { + 'buildopts': '--use-msgpackc=no', + 'installopts': '--use-msgpackc=no', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ["https://github.com/schrodinger/pymol-open-source/archive/refs/tags/"], + 'checksums': ['aa828bf5719bd9a14510118a93182a6e0cadc03a574ba1e327e1e9780a0e80b3'], + }), +] modextravars = {'PYMOL_PATH': 'lib/python%(pyshortver)s/site-packages/pymol/pymol_path'} -sanity_pip_check = True sanity_check_paths = { 'files': ['bin/pymol'], 'dirs': ['bin', 'lib'], From 8b779b2776025525a295811c7ed013e6cbf0eaa7 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Fri, 14 Oct 2022 17:23:41 +0200 Subject: [PATCH 5113/9987] Now also change True to SYSTEM for ant... --- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 4e7764a13b8..b957c01b7d4 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -55,7 +55,7 @@ dependencies = [ ('OpenEXR', '3.1.5'), ('JasPer', '2.0.33'), ('Java', '11', '', SYSTEM), - ('ant', '1.10.12', '-Java-%(javaver)s', True), + ('ant', '1.10.12', '-Java-%(javaver)s', SYSTEM), ('GLib', '2.72.1'), ('GTK4', '4.7.0'), ('HDF5', '1.12.2'), From 587e56a62c7ba7413c5cc02f0049e070b3e1dd4b Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 14 Oct 2022 17:43:04 +0200 Subject: [PATCH 5114/9987] adding easyconfigs: libunistring-1.0-GCCcore-10.3.0.eb --- .../libunistring-1.0-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..619ae320573 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.0' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['5bab55b49f75d77ed26b257997e919b693f29fd4a1bc22e0e6e024c246c72741'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' From 1905e9aec20e1c34888567d69f3859065bc01edb Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 14 Oct 2022 17:57:04 +0200 Subject: [PATCH 5115/9987] Previous libpsl was missing libunistring dependency. On os-es where this dependency was not provided by the system, the configure for libpsl would fail --- .../easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb index 58d836e0aab..6eef44963b1 100644 --- a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb @@ -19,6 +19,10 @@ builddependencies = [ ('CMake', '3.20.1'), ] +dependencies = [ + ('libunistring', '1.0'), +] + sanity_check_paths = { 'files': ['bin/psl', 'lib/libpsl.a'], 'dirs': [] From c786e68f2819aef06318a81316073cd0f52c9c7d Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 14 Oct 2022 18:37:51 +0200 Subject: [PATCH 5116/9987] There was apparently already a libunistring in this toolchain. Using that version now --- .../l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb | 2 +- .../libunistring-1.0-GCCcore-10.3.0.eb | 31 ------------------- 2 files changed, 1 insertion(+), 32 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb index 6eef44963b1..a7d264de762 100644 --- a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('libunistring', '1.0'), + ('libunistring', '0.9.10'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb deleted file mode 100644 index 619ae320573..00000000000 --- a/easybuild/easyconfigs/l/libunistring/libunistring-1.0-GCCcore-10.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libunistring' -version = '1.0' - -homepage = 'https://www.gnu.org/software/libunistring/' - -description = """This library provides functions for manipulating Unicode strings and for - manipulating C strings according to the Unicode standard.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -toolchainopts = {'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['5bab55b49f75d77ed26b257997e919b693f29fd4a1bc22e0e6e024c246c72741'] - -builddependencies = [ - ('binutils', '2.36.1'), -] - -parallel = 1 - -sanity_check_paths = { - 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + - ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', - 'stdio', 'str', 'types', 'wbrk', 'width']], - 'dirs': ['include/unistring'], -} - -moduleclass = 'lib' From 68eda9133825288f21280833f64260813f18924c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 14 Oct 2022 20:31:04 +0200 Subject: [PATCH 5117/9987] add typing-extensions dep --- ...-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb | 2 -- .../typing-extensions-4.3.0-GCCcore-11.3.0.eb | 22 +++++++++++++++++++ 2 files changed, 22 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb index ff7163f6c19..07edd99a9cf 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb @@ -18,12 +18,10 @@ dependencies = [ ('typing-extensions', '4.3.0'), ] - exts_list = [ ('fsspec', '2022.8.2', { 'checksums': ['7f12b90964a98a7e921d27fb36be536ea036b73bf3b724ac0b0bd7b8e39c7c18'], }), - ('pyDeprecate', '0.3.2', { 'modulename': 'deprecate', 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ada44caf01a --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.3.0' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions – Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From c75621aa2cffa3765b5dd6d737eceb29f12b10fa Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 14 Oct 2022 20:33:47 +0200 Subject: [PATCH 5118/9987] use SYSTEM rather than True --- .../PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb index 07edd99a9cf..5acbc803ac9 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a-CUDA-11.7.0.eb @@ -10,7 +10,7 @@ description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML resea toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('Python', '3.10.4'), ('PyTorch', '1.12.0', versionsuffix), ('tqdm', '4.64.0'), From c5260433af2e7cda65e89a9cbddd33edee5b17f6 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 14 Oct 2022 18:51:35 +0000 Subject: [PATCH 5119/9987] Add backported GCC fix for vectorizer --- .../easyconfigs/g/GCCcore/GCCcore-11.3.0.eb | 2 + .../GCCcore-11.3.0_fix-vectorizer.patch | 137 ++++++++++++++++++ 2 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fix-vectorizer.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb index 5df5d559914..1b248b2368e 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb @@ -36,6 +36,7 @@ patches = [ 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCCcore-11.3.0_fuse-ld-mold.patch', 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', + 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ '98438e6cc7294298b474cf0da7655d9a8c8b796421bb0210531c294a950374ed', # gcc-11.3.0.tar.gz @@ -50,6 +51,7 @@ checksums = [ '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch 'bba64714f8b84ad58b3b43c0d21b4ffc298274ae699f514ed2934f002146d840', # GCCcore-11.3.0_fuse-ld-mold.patch '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60', # GCCcore-11_fix-libsanitzer-glibc-2.36.patch + '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98', # GCCcore-11.3.0_fix-vectorizer.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fix-vectorizer.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fix-vectorizer.patch new file mode 100644 index 00000000000..372397d96fe --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0_fix-vectorizer.patch @@ -0,0 +1,137 @@ +From 9ed4a849afb5b18b462bea311e7eee454c2c9f68 Mon Sep 17 00:00:00 2001 +From: Richard Biener +Date: Fri, 14 Oct 2022 11:14:59 +0200 +Subject: [PATCH] tree-optimization/107254 - check and support live lanes from + permutes + +The following fixes an omission from adding SLP permute nodes which +is live lanes originating from those. We have to check that we +can extract the lane and have to actually code generate them. + + PR tree-optimization/107254 + * tree-vect-slp.cc (vect_slp_analyze_node_operations_1): + For permutes also analyze live lanes. + (vect_schedule_slp_node): For permutes also code generate + live lane extracts. + + * gfortran.dg/vect/pr107254.f90: New testcase. +--- + gcc/testsuite/gfortran.dg/vect/pr107254.f90 | 49 +++++++++++++++++++++ + gcc/tree-vect-slp.cc | 33 +++++++++++--- + 2 files changed, 77 insertions(+), 5 deletions(-) + create mode 100644 gcc/testsuite/gfortran.dg/vect/pr107254.f90 + +diff --git a/gcc/testsuite/gfortran.dg/vect/pr107254.f90 b/gcc/testsuite/gfortran.dg/vect/pr107254.f90 +new file mode 100644 +index 0000000000000..85bcb5f3fa2e3 +--- /dev/null ++++ b/gcc/testsuite/gfortran.dg/vect/pr107254.f90 +@@ -0,0 +1,49 @@ ++! { dg-do run } ++ ++subroutine dlartg( f, g, s, r ) ++ implicit none ++ double precision :: f, g, r, s ++ double precision :: d, p ++ ++ d = sqrt( f*f + g*g ) ++ p = 1.d0 / d ++ if( abs( f ) > 1 ) then ++ s = g*sign( p, f ) ++ r = sign( d, f ) ++ else ++ s = g*sign( p, f ) ++ r = sign( d, f ) ++ end if ++end subroutine ++ ++subroutine dhgeqz( n, h, t ) ++ implicit none ++ integer n ++ double precision h( n, * ), t( n, * ) ++ integer jc ++ double precision c, s, temp, temp2, tempr ++ temp2 = 10d0 ++ call dlartg( 10d0, temp2, s, tempr ) ++ c = 0.9d0 ++ s = 1.d0 ++ do jc = 1, n ++ temp = c*h( 1, jc ) + s*h( 2, jc ) ++ h( 2, jc ) = -s*h( 1, jc ) + c*h( 2, jc ) ++ h( 1, jc ) = temp ++ temp2 = c*t( 1, jc ) + s*t( 2, jc ) ++ t( 2, jc ) = -s*t( 1, jc ) + c*t( 2, jc ) ++ t( 1, jc ) = temp2 ++ enddo ++end subroutine dhgeqz ++ ++program test ++ implicit none ++ double precision h(2,2), t(2,2) ++ h = 0 ++ t(1,1) = 1 ++ t(2,1) = 0 ++ t(1,2) = 0 ++ t(2,2) = 0 ++ call dhgeqz( 2, h, t ) ++ if (t(2,2).ne.0) STOP 1 ++end program test +diff --git a/gcc/tree-vect-slp.c b/gcc/tree-vect-slp.c +index 229f2663ebcc6..af27fd56e0242 100644 +--- a/gcc/tree-vect-slp.c ++++ b/gcc/tree-vect-slp.c +@@ -5930,7 +5930,23 @@ vect_slp_analyze_node_operations_1 (vec_info *vinfo, slp_tree node, + + /* Handle purely internal nodes. */ + if (SLP_TREE_CODE (node) == VEC_PERM_EXPR) +- return vectorizable_slp_permutation (vinfo, NULL, node, cost_vec); ++ { ++ if (!vectorizable_slp_permutation (vinfo, NULL, node, cost_vec)) ++ return false; ++ ++ stmt_vec_info slp_stmt_info; ++ unsigned int i; ++ FOR_EACH_VEC_ELT (SLP_TREE_SCALAR_STMTS (node), i, slp_stmt_info) ++ { ++ if (STMT_VINFO_LIVE_P (slp_stmt_info) ++ && !vectorizable_live_operation (vinfo, ++ slp_stmt_info, NULL, node, ++ node_instance, i, ++ false, cost_vec)) ++ return false; ++ } ++ return true; ++ } + + gcc_assert (STMT_SLP_TYPE (stmt_info) != loop_vect); + +@@ -8897,8 +8913,6 @@ vect_schedule_slp_node (vec_info *vinfo, + } + } + +- bool done_p = false; +- + /* Handle purely internal nodes. */ + if (SLP_TREE_CODE (node) == VEC_PERM_EXPR) + { +@@ -8909,9 +8923,18 @@ vect_schedule_slp_node (vec_info *vinfo, + but open-code it here (partly). */ + bool done = vectorizable_slp_permutation (vinfo, &si, node, NULL); + gcc_assert (done); +- done_p = true; ++ stmt_vec_info slp_stmt_info; ++ unsigned int i; ++ FOR_EACH_VEC_ELT (SLP_TREE_SCALAR_STMTS (node), i, slp_stmt_info) ++ if (STMT_VINFO_LIVE_P (slp_stmt_info)) ++ { ++ done = vectorizable_live_operation (vinfo, ++ slp_stmt_info, &si, node, ++ instance, i, true, NULL); ++ gcc_assert (done); ++ } + } +- if (!done_p) ++ else + vect_transform_stmt (vinfo, stmt_info, &si, node, instance); + } + From fa0336ce6e0cf7e368f4870c6b1eaf84edf9afa0 Mon Sep 17 00:00:00 2001 From: guacke Date: Sat, 15 Oct 2022 13:07:54 +0200 Subject: [PATCH 5120/9987] Fix download link Pmw. --- easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb index 642fc01b62c..c96cc51c180 100644 --- a/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PyMOL/PyMOL-2.5.0-foss-2020b.eb @@ -32,7 +32,7 @@ sanity_pip_check = True exts_list = [ ('Pmw', '2.0.1', { 'modulename': 'Pmw', - 'source_tmpl': 'Pmw-patched-%(version)s-20200210-8bedfc8.zip', + 'source_tmpl': '8bedfc8747e7757c1048bc5e11899d1163717a43.zip', 'source_urls': ['https://github.com/schrodinger/pmw-patched/archive/'], 'checksums': ['db1ab4ee1020023ad814bb24c74f6361fb72e1011871911f7d37bb6ecf6c79ed'], }), From c24f8e557aad37ae971ec4e9152c56dcf1992fef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Oct 2022 13:48:31 +0200 Subject: [PATCH 5121/9987] update to Nipype 1.8.5 --- ...1.6.0-foss-2021a.eb => Nipype-1.8.5-foss-2021a.eb} | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/n/Nipype/{Nipype-1.6.0-foss-2021a.eb => Nipype-1.8.5-foss-2021a.eb} (81%) diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.8.5-foss-2021a.eb similarity index 81% rename from easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb rename to easybuild/easyconfigs/n/Nipype/Nipype-1.8.5-foss-2021a.eb index 9315c346305..fe53e82f565 100644 --- a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.8.5-foss-2021a.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'Nipype' -version = '1.6.0' +version = '1.8.5' homepage = 'https://nipype.readthedocs.io' description = """Nipype is a Python project that provides a uniform interface to existing neuroimaging software and @@ -22,8 +22,8 @@ dependencies = [ use_pip = True exts_list = [ - ('traits', '6.4.1', { - 'checksums': ['78bb2ccafd60aff606515aac46de64668a0a81cb5c54c650b9877a841aa9e812'], + ('traits', '6.3.2', { + 'checksums': ['4520ef4a675181f38be4a5bab1b1d5472691597fe2cfe4faf91023e89407e2c6'], }), ('pydotplus', '2.0.2', { 'checksums': ['91e85e9ee9b85d2391ead7d635e3d9c7f5f44fd60a60e59b13e2403fa66505c4'], @@ -41,8 +41,11 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['78febd59a22eb53d052d731f10f24139eb2854fd237348fba683dd8616fb4a67'], }), + ('looseversion', '1.0.2', { + 'checksums': ['8b9f2e649eb81620c4527ba33ba87505eb69d4bb3f66523b34182a0450c294bc'], + }), ('nipype', version, { - 'checksums': ['bc56ce63f74c9a9a23c6edeaf77631377e8ad2bea928c898cc89527a47f101cf'], + 'checksums': ['e3842743fb660464dd29de73dcfc9ef66d273be10bcc64059ff21cd5ef1e9655'], }), ] From 0f74df6cda92500d3578be036898b75085c43b31 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Oct 2022 15:14:46 +0200 Subject: [PATCH 5122/9987] also apply patch to fix vectorizer bug to GCC 11.1, 11.2, 12.1, 12.2 --- .../easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 1 + .../easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 1 + .../easyconfigs/g/GCCcore/GCCcore-12.1.0.eb | 1 + .../easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 1 + .../GCCcore-12.2.0_fix-vectorizer.patch | 137 ++++++++++++++++++ 5 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-vectorizer.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index 0bdb99e8555..42fb74e6c11 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ 'e7abb1b4cb58aaa67c5eb49d98e89d13363b8e258ac2b5b105c197b441c09f85', # gcc-11.1.0.tar.gz diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb index 3453620e9f0..954772edd58 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -34,6 +34,7 @@ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ 'f0837f1bf8244a5cc23bd96ff6366712a791cfae01df8e25b137698aca26efc1', # gcc-11.2.0.tar.gz diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb index 0ef3db46d4d..b8b94b6b2fc 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb @@ -33,6 +33,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ 'e88a004a14697bbbaba311f38a938c716d9a652fd151aaaa4cf1b5b99b90e2de', # gcc-12.1.0.tar.gz diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb index 843edfa35ec..f898df53dc8 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -33,6 +33,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ 'ac6b317eb4d25444d87cf29c0d141dedc1323a1833ec9995211b13e1a851261c', # gcc-12.2.0.tar.gz diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-vectorizer.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-vectorizer.patch new file mode 100644 index 00000000000..ba4e65259e4 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-vectorizer.patch @@ -0,0 +1,137 @@ +From 9ed4a849afb5b18b462bea311e7eee454c2c9f68 Mon Sep 17 00:00:00 2001 +From: Richard Biener +Date: Fri, 14 Oct 2022 11:14:59 +0200 +Subject: [PATCH] tree-optimization/107254 - check and support live lanes from + permutes + +The following fixes an omission from adding SLP permute nodes which +is live lanes originating from those. We have to check that we +can extract the lane and have to actually code generate them. + + PR tree-optimization/107254 + * tree-vect-slp.cc (vect_slp_analyze_node_operations_1): + For permutes also analyze live lanes. + (vect_schedule_slp_node): For permutes also code generate + live lane extracts. + + * gfortran.dg/vect/pr107254.f90: New testcase. +--- + gcc/testsuite/gfortran.dg/vect/pr107254.f90 | 49 +++++++++++++++++++++ + gcc/tree-vect-slp.cc | 33 +++++++++++--- + 2 files changed, 77 insertions(+), 5 deletions(-) + create mode 100644 gcc/testsuite/gfortran.dg/vect/pr107254.f90 + +diff --git a/gcc/testsuite/gfortran.dg/vect/pr107254.f90 b/gcc/testsuite/gfortran.dg/vect/pr107254.f90 +new file mode 100644 +index 0000000000000..85bcb5f3fa2e3 +--- /dev/null ++++ b/gcc/testsuite/gfortran.dg/vect/pr107254.f90 +@@ -0,0 +1,49 @@ ++! { dg-do run } ++ ++subroutine dlartg( f, g, s, r ) ++ implicit none ++ double precision :: f, g, r, s ++ double precision :: d, p ++ ++ d = sqrt( f*f + g*g ) ++ p = 1.d0 / d ++ if( abs( f ) > 1 ) then ++ s = g*sign( p, f ) ++ r = sign( d, f ) ++ else ++ s = g*sign( p, f ) ++ r = sign( d, f ) ++ end if ++end subroutine ++ ++subroutine dhgeqz( n, h, t ) ++ implicit none ++ integer n ++ double precision h( n, * ), t( n, * ) ++ integer jc ++ double precision c, s, temp, temp2, tempr ++ temp2 = 10d0 ++ call dlartg( 10d0, temp2, s, tempr ) ++ c = 0.9d0 ++ s = 1.d0 ++ do jc = 1, n ++ temp = c*h( 1, jc ) + s*h( 2, jc ) ++ h( 2, jc ) = -s*h( 1, jc ) + c*h( 2, jc ) ++ h( 1, jc ) = temp ++ temp2 = c*t( 1, jc ) + s*t( 2, jc ) ++ t( 2, jc ) = -s*t( 1, jc ) + c*t( 2, jc ) ++ t( 1, jc ) = temp2 ++ enddo ++end subroutine dhgeqz ++ ++program test ++ implicit none ++ double precision h(2,2), t(2,2) ++ h = 0 ++ t(1,1) = 1 ++ t(2,1) = 0 ++ t(1,2) = 0 ++ t(2,2) = 0 ++ call dhgeqz( 2, h, t ) ++ if (t(2,2).ne.0) STOP 1 ++end program test +diff --git a/gcc/tree-vect-slp.cc b/gcc/tree-vect-slp.cc +index 229f2663ebcc6..af27fd56e0242 100644 +--- a/gcc/tree-vect-slp.cc ++++ b/gcc/tree-vect-slp.cc +@@ -5930,7 +5930,23 @@ vect_slp_analyze_node_operations_1 (vec_info *vinfo, slp_tree node, + + /* Handle purely internal nodes. */ + if (SLP_TREE_CODE (node) == VEC_PERM_EXPR) +- return vectorizable_slp_permutation (vinfo, NULL, node, cost_vec); ++ { ++ if (!vectorizable_slp_permutation (vinfo, NULL, node, cost_vec)) ++ return false; ++ ++ stmt_vec_info slp_stmt_info; ++ unsigned int i; ++ FOR_EACH_VEC_ELT (SLP_TREE_SCALAR_STMTS (node), i, slp_stmt_info) ++ { ++ if (STMT_VINFO_LIVE_P (slp_stmt_info) ++ && !vectorizable_live_operation (vinfo, ++ slp_stmt_info, NULL, node, ++ node_instance, i, ++ false, cost_vec)) ++ return false; ++ } ++ return true; ++ } + + gcc_assert (STMT_SLP_TYPE (stmt_info) != loop_vect); + +@@ -8897,8 +8913,6 @@ vect_schedule_slp_node (vec_info *vinfo, + } + } + +- bool done_p = false; +- + /* Handle purely internal nodes. */ + if (SLP_TREE_CODE (node) == VEC_PERM_EXPR) + { +@@ -8909,9 +8923,18 @@ vect_schedule_slp_node (vec_info *vinfo, + but open-code it here (partly). */ + bool done = vectorizable_slp_permutation (vinfo, &si, node, NULL); + gcc_assert (done); +- done_p = true; ++ stmt_vec_info slp_stmt_info; ++ unsigned int i; ++ FOR_EACH_VEC_ELT (SLP_TREE_SCALAR_STMTS (node), i, slp_stmt_info) ++ if (STMT_VINFO_LIVE_P (slp_stmt_info)) ++ { ++ done = vectorizable_live_operation (vinfo, ++ slp_stmt_info, &si, node, ++ instance, i, true, NULL); ++ gcc_assert (done); ++ } + } +- if (!done_p) ++ else + vect_transform_stmt (vinfo, stmt_info, &si, node, instance); + } + From 3464b7f52649d503e0aece1b64504733e5fafdad Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 15 Oct 2022 16:10:29 +0200 Subject: [PATCH 5123/9987] adding easyconfigs: PyTorch-Lightning-1.7.7-foss-2022a.eb --- .../PyTorch-Lightning-1.7.7-foss-2022a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a.eb new file mode 100644 index 00000000000..2ad23369cd6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.7.7-foss-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.7.7' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('tensorboard', '2.10.0'), + ('typing-extensions', '4.3.0'), +] + +exts_list = [ + ('fsspec', '2022.8.2', { + 'checksums': ['7f12b90964a98a7e921d27fb36be536ea036b73bf3b724ac0b0bd7b8e39c7c18'], + }), + ('pyDeprecate', '0.3.2', { + 'modulename': 'deprecate', + 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], + }), + ('torchmetrics', '0.9.3', { + 'checksums': ['4ebfd2466021db26397636966ee1a195d3b340ba5d71bb258e764340dfc2476f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['27c2dd01a18db2415168e3fa3775ccb5a1fa1e2961a50439ad9365507fe9d4ae'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From e30aeac29a712478fdbd0237d18a919f3b09e971 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Oct 2022 16:36:31 +0200 Subject: [PATCH 5124/9987] add checksum for patch to fix vectorizer bug in GCC v11.x + v12.x --- .../easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 24 +++++++++-------- .../easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 22 ++++++++------- .../easyconfigs/g/GCCcore/GCCcore-11.3.0.eb | 27 ++++++++++--------- .../easyconfigs/g/GCCcore/GCCcore-12.1.0.eb | 19 ++++++------- .../easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 19 ++++++------- 5 files changed, 59 insertions(+), 52 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index 42fb74e6c11..a5a30163948 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -38,17 +38,19 @@ patches = [ 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ - 'e7abb1b4cb58aaa67c5eb49d98e89d13363b8e258ac2b5b105c197b441c09f85', # gcc-11.1.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d', # isl-0.23.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-11.1.0.tar.gz': 'e7abb1b4cb58aaa67c5eb49d98e89d13363b8e258ac2b5b105c197b441c09f85'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.23.tar.bz2': 'c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20210115.tar.gz': '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb index 954772edd58..5efade9fb39 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -37,16 +37,18 @@ patches = [ 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ - 'f0837f1bf8244a5cc23bd96ff6366712a791cfae01df8e25b137698aca26efc1', # gcc-11.2.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch + {'gcc-11.2.0.tar.gz': 'f0837f1bf8244a5cc23bd96ff6366712a791cfae01df8e25b137698aca26efc1'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20210115.tar.gz': '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb index 1b248b2368e..479660986dc 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.3.0.eb @@ -39,19 +39,20 @@ patches = [ 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ - '98438e6cc7294298b474cf0da7655d9a8c8b796421bb0210531c294a950374ed', # gcc-11.3.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080', # nvptx-tools-20220412.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'bba64714f8b84ad58b3b43c0d21b4ffc298274ae699f514ed2934f002146d840', # GCCcore-11.3.0_fuse-ld-mold.patch - '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60', # GCCcore-11_fix-libsanitzer-glibc-2.36.patch - '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98', # GCCcore-11.3.0_fix-vectorizer.patch + {'gcc-11.3.0.tar.gz': '98438e6cc7294298b474cf0da7655d9a8c8b796421bb0210531c294a950374ed'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20220412.tar.gz': '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCCcore-11.3.0_fuse-ld-mold.patch': 'bba64714f8b84ad58b3b43c0d21b4ffc298274ae699f514ed2934f002146d840'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, + {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb index b8b94b6b2fc..da98d2ef021 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb @@ -36,15 +36,16 @@ patches = [ 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ - 'e88a004a14697bbbaba311f38a938c716d9a652fd151aaaa4cf1b5b99b90e2de', # gcc-12.1.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080', # nvptx-tools-20220412.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + {'gcc-12.1.0.tar.gz': 'e88a004a14697bbbaba311f38a938c716d9a652fd151aaaa4cf1b5b99b90e2de'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20220412.tar.gz': '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb index f898df53dc8..623abd95ffe 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -36,15 +36,16 @@ patches = [ 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ - 'ac6b317eb4d25444d87cf29c0d141dedc1323a1833ec9995211b13e1a851261c', # gcc-12.2.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0', # isl-0.24.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '53e7973af841935490b8a7b9e4d1331f775589b54e21f9921f18589183fb9997', # nvptx-tools-20220610.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch + {'gcc-12.2.0.tar.gz': 'ac6b317eb4d25444d87cf29c0d141dedc1323a1833ec9995211b13e1a851261c'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20220610.tar.gz': '53e7973af841935490b8a7b9e4d1331f775589b54e21f9921f18589183fb9997'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, ] builddependencies = [ From c94ee34ced3170f45e67f8851519311c1ef58bc5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Oct 2022 17:42:41 +0200 Subject: [PATCH 5125/9987] use SYSTEM template constant to indicate that CUDA dependency of torchvision uses system toolchain --- .../t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb index c2820fcd722..3ab02f0dc56 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a-CUDA-11.7.0.eb @@ -14,7 +14,7 @@ checksums = ['c32fab734e62c7744dadeb82f7510ff58cc3bca1189d17b16aa99b08afc42249'] builddependencies = [('CMake', '3.23.1')] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('Python', '3.10.4'), ('Pillow-SIMD', '9.2.0'), ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), From bf2fc71d7727c27bd735dc3c8d240b2996a91498 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 09:48:18 +0100 Subject: [PATCH 5126/9987] pandas removed as already in SciPy-bundle --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 086b4db0913..26c7449b3c6 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -44,9 +44,6 @@ exts_list = [ 'sources': ['%(name)s-%(version)s.zip'], 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], }), - ('pandas', '1.3.3', { - 'checksums': ['272c8cb14aa9793eada6b1ebe81994616e647b5892a370c7135efb2924b701df'], - }), ('tensorpack', '0.11', { 'checksums': ['022b610e416e62e3575424cd08e60af27808a5fb6914294615391caf582cbd4f'], }), From c282fb2ec3b963795ecbc29b12ecfb2e759a60ab Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Jul 2022 09:15:03 +0200 Subject: [PATCH 5127/9987] Fix PyTorch 1.10.0 build on PPC --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 53 +++++--- .../p/PyTorch/PyTorch-1.10.0-foss-2021a.eb | 47 ++++--- .../PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 53 +++++--- ...ch-1.10.0_add-dummy-bfloat16-for-ppc.patch | 116 ++++++++++++++++++ ...> PyTorch-1.10.0_fix-faulty-asserts.patch} | 21 +--- ...orch-1.10.0_fix-missing-VSX-dispatch.patch | 26 ++++ ...rch-1.10.0_remove-vec-dump-functions.patch | 114 +++++++++++++++++ 7 files changed, 356 insertions(+), 74 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch rename easybuild/easyconfigs/p/PyTorch/{PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch => PyTorch-1.10.0_fix-faulty-asserts.patch} (88%) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index 3dedead0354..fbed1049947 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -8,15 +8,9 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2021a'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', @@ -24,18 +18,25 @@ patches = [ 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', - 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_remove-vec-dump-functions.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', - 'PyTorch-1.10.0_skip_cmake_rpath.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '1970225700d1f9791eb553855ad3c22e7c9fd69cff2765d532506b33e449831e', # pytorch-v1.10.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch @@ -45,24 +46,38 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch + '0c8bf4b284c5c2cb4d175645d44bed674cca5218de741a8ea698cef2884a86da', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', - # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch - '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-faulty-asserts.patch + '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch + '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vnni-detection.patch '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_remove-vec-dump-functions.patch + '5e796c83f74e77aa193fef2720a7a41e3e0eb39df726a6f0a2a1c55d37d8fcc8', + # PyTorch-1.10.0_skip_cmake_rpath.patch + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_failing_ops_tests.patch '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', - # PyTorch-1.10.0_skip_cmake_rpath.patch - 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb index c05632ab43f..27db7713d1d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb @@ -7,32 +7,33 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2021a'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', - 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_remove-vec-dump-functions.patch', 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '1970225700d1f9791eb553855ad3c22e7c9fd69cff2765d532506b33e449831e', # pytorch-v1.10.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch @@ -41,22 +42,36 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch + '0c8bf4b284c5c2cb4d175645d44bed674cca5218de741a8ea698cef2884a86da', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', - # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch - '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-faulty-asserts.patch + '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch + '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vnni-detection.patch '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_remove-vec-dump-functions.patch + '5e796c83f74e77aa193fef2720a7a41e3e0eb39df726a6f0a2a1c55d37d8fcc8', # PyTorch-1.10.0_skip_failing_ops_tests.patch '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 938b94c4f93..450db866c3a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -7,15 +7,9 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', @@ -23,18 +17,25 @@ patches = [ 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', - 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_remove-vec-dump-functions.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', - 'PyTorch-1.10.0_skip_cmake_rpath.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '1970225700d1f9791eb553855ad3c22e7c9fd69cff2765d532506b33e449831e', # pytorch-v1.10.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch @@ -44,24 +45,38 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch + '0c8bf4b284c5c2cb4d175645d44bed674cca5218de741a8ea698cef2884a86da', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', - # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch - '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-faulty-asserts.patch + '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch + '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vnni-detection.patch '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_remove-vec-dump-functions.patch + '5e796c83f74e77aa193fef2720a7a41e3e0eb39df726a6f0a2a1c55d37d8fcc8', + # PyTorch-1.10.0_skip_cmake_rpath.patch + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_failing_ops_tests.patch '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', - # PyTorch-1.10.0_skip_cmake_rpath.patch - 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch new file mode 100644 index 00000000000..8e74d538e62 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch @@ -0,0 +1,116 @@ +Fix missing `vec_scalar_t` on PPC during compilation. + +From https://github.com/pytorch/pytorch/pull/67331 + +From: Nikita Shulga +Date: Wed, 27 Oct 2021 08:04:08 -0700 +Subject: [PATCH] Add dummy bfloat16 VSX implementation + +Just a copy of DEFAULT bfloat16 implementation and revert restriction +introduced by https://github.com/pytorch/pytorch/pull/61630 + +Fixes https://github.com/pytorch/pytorch/issues/66867 and https://github.com/pytorch/pytorch/issues/62016 +--- + aten/src/ATen/cpu/vec/functional.h | 2 - + .../cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h | 54 +++++++++++++++++++ + .../cpu/vec/vec256/vsx/vec256_common_vsx.h | 6 +++ + 3 files changed, 60 insertions(+), 2 deletions(-) + create mode 100644 aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h + +diff --git a/aten/src/ATen/cpu/vec/functional.h b/aten/src/ATen/cpu/vec/functional.h +index 210ae9e9e883..388b3170d5b5 100644 +--- a/aten/src/ATen/cpu/vec/functional.h ++++ b/aten/src/ATen/cpu/vec/functional.h +@@ -1,6 +1,4 @@ + #pragma once + + #include +-#if !defined(__VSX__) || !defined(CPU_CAPABILITY_VSX) + #include +-#endif +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h +new file mode 100644 +index 000000000000..ee8ca997a20e +--- /dev/null ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h +@@ -0,0 +1,54 @@ ++#pragma once ++ ++#include ++#include ++#include ++namespace at { ++namespace vec { ++// See Note [Acceptable use of anonymous namespace in header] ++namespace { ++ ++inline std::tuple, Vectorized> convert_bfloat16_float( ++ const Vectorized& a) { ++ constexpr int64_t K = Vectorized::size(); ++ __at_align__ float arr[K]; ++ __at_align__ BFloat16 arr2[K]; ++ a.store(arr2); ++ convert(arr2, arr, K); ++ return std::make_tuple( ++ Vectorized::loadu(arr), ++ Vectorized::loadu(arr + Vectorized::size())); ++} ++ ++inline Vectorized convert_float_bfloat16( ++ const Vectorized& a, ++ const Vectorized& b) { ++ constexpr int64_t K = Vectorized::size(); ++ __at_align__ float arr[K]; ++ __at_align__ BFloat16 arr2[K]; ++ a.store(arr); ++ b.store(arr + Vectorized::size()); ++ convert(arr, arr2, K); ++ return Vectorized::loadu(arr2); ++} ++ ++void load_fp32_from_bf16(const c10::BFloat16* data, Vectorized& out) { ++ __at_align__ float values[Vectorized::size()]; ++ for (int k = 0; k < Vectorized::size(); ++k) { ++ values[k] = data[k]; ++ } ++ out = Vectorized::loadu(values); ++} ++ ++C10_UNUSED void load_fp32_from_bf16( ++ const c10::BFloat16* data, ++ Vectorized& out1, ++ Vectorized& out2) { ++ load_fp32_from_bf16(data, out1); ++ data += Vectorized::size(); ++ load_fp32_from_bf16(data, out2); ++} ++ ++} // namespace ++} // namespace vec ++} // namespace at +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h +index 3d798a7f6268..b06f6a4bd1b5 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h +@@ -3,6 +3,8 @@ + #include + #include + #include ++ ++// Note: header order is important here + #include + #include + #include +@@ -11,8 +13,12 @@ + #include + #include + #include ++ + #include + #include ++ ++#include ++ + namespace at { + namespace vec { + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts.patch similarity index 88% rename from easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch rename to easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts.patch index eab07090d2a..1ba71564df7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts.patch @@ -1,6 +1,6 @@ From: Alexander Grund Date: Tue, 18 May 2021 15:08:41 +0200 -Subject: [PATCH 1/2] Fix usage of TORCH_INTERNAL_ASSERT with message +Subject: Fix usage of TORCH_INTERNAL_ASSERT with message Using only a string as the argument for TORCH_INTERNAL_ASSERT will never trigger a failure as a string is always a truethy value. @@ -8,11 +8,6 @@ This hides actual bugs and makes users and devs think all worked while it did not. Change to use TORCH_INTERNAL_ASSERT(false, "msg") -Subject: [PATCH 2/2] Add missing skip decorator for -test_preserve_bundled_inputs_methods - -This test uses optimize_for_mobile which requires NNPACK to work - diff --git a/aten/src/ATen/native/BinaryOps.cpp b/aten/src/ATen/native/BinaryOps.cpp index c4edadb03e..e889cd03a8 100644 --- a/aten/src/ATen/native/BinaryOps.cpp @@ -83,20 +78,6 @@ index 6de646acfe..66341c959d 100644 } for (int i = num_output_channels; i < num_output_channels_padded; ++i) { weight_scales_data[i] = 1.f; -diff --git a/test/test_mobile_optimizer.py b/test/test_mobile_optimizer.py -index 11ef019a26..7b5ac1a239 100644 ---- a/test/test_mobile_optimizer.py -+++ b/test/test_mobile_optimizer.py -@@ -269,6 +269,9 @@ class TestOptimizer(TestCase): - bi_module_lint_list = generate_mobile_module_lints(bi_module) - self.assertEqual(len(bi_module_lint_list), 0) - -+ @unittest.skipUnless(torch.backends.xnnpack.enabled, -+ " XNNPACK must be enabled for these tests." -+ " Please build with USE_XNNPACK=1.") - def test_preserve_bundled_inputs_methods(self): - class MyBundledInputModule(torch.nn.Module): - def __init__(self): diff --git a/torch/csrc/jit/api/module.cpp b/torch/csrc/jit/api/module.cpp index 38592b80b9..8f9508321b 100644 --- a/torch/csrc/jit/api/module.cpp diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch new file mode 100644 index 00000000000..dcc0eac4bf0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch @@ -0,0 +1,26 @@ + +Fix for following error on PPC: +> undefined reference to `at::native::DispatchStub, c10::ArrayRef, c10::ArrayRef, void const*, c10::ArrayRef, void*), at::native::fft_fill_with_conjugate_symmetry_stub>::VSX' + +From https://github.com/pytorch/pytorch/pull/68914 + +From: Deepali Chourasia +Date: Thu, 25 Nov 2021 12:29:50 +0000 +Subject: [PATCH] add VSX dispatch for fft_fill_with_conjugate_symmetry_stub + +--- + aten/src/ATen/native/mkl/SpectralOps.cpp | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/aten/src/ATen/native/mkl/SpectralOps.cpp b/aten/src/ATen/native/mkl/SpectralOps.cpp +index 0625110a04ff..2bd05ca19cac 100644 +--- a/aten/src/ATen/native/mkl/SpectralOps.cpp ++++ b/aten/src/ATen/native/mkl/SpectralOps.cpp +@@ -151,6 +151,7 @@ static void _fft_fill_with_conjugate_symmetry_cpu_( + REGISTER_ARCH_DISPATCH(fft_fill_with_conjugate_symmetry_stub, DEFAULT, &_fft_fill_with_conjugate_symmetry_cpu_) + REGISTER_AVX2_DISPATCH(fft_fill_with_conjugate_symmetry_stub, &_fft_fill_with_conjugate_symmetry_cpu_) + REGISTER_AVX512_DISPATCH(fft_fill_with_conjugate_symmetry_stub, &_fft_fill_with_conjugate_symmetry_cpu_) ++REGISTER_VSX_DISPATCH(fft_fill_with_conjugate_symmetry_stub, &_fft_fill_with_conjugate_symmetry_cpu_) + + // _out variants can be shared between PocketFFT and MKL + Tensor& _fft_r2c_mkl_out(const Tensor& self, IntArrayRef dim, int64_t normalization, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch new file mode 100644 index 00000000000..b6e2100a178 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch @@ -0,0 +1,114 @@ +Fix compilation on PPC due to missing include + +From https://patch-diff.githubusercontent.com/raw/pytorch/pytorch/pull/66085 + +From e0fa15d188986e2a68973e3facf9d794f6cfc5df Mon Sep 17 00:00:00 2001 +From: Nikita Shulga +Date: Mon, 4 Oct 2021 09:26:37 -0700 +Subject: [PATCH] Remove unused `dump` method from VSX vec256 methods + +Follow up after https://github.com/pytorch/pytorch/pull/63533 + +Probably fixes https://github.com/pytorch/pytorch/issues/65956 +--- + .../ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h | 5 ----- + .../ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h | 8 -------- + aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h | 3 --- + aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h | 7 ------- + aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h | 9 --------- + 5 files changed, 32 deletions(-) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +index 888f2f0b932b..3a3e0daade09 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +@@ -356,11 +356,6 @@ class Vectorized { + return {vec_sqrt(_vec0), vec_sqrt(_vec1)}; + } + +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << ","; +- std::cout << _vec1[0] << "," << _vec1[1] << std::endl; +- } +- + Vectorized sqrt() const { + return map(std::sqrt); + } +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +index 0aa726b9bfdd..712de24597dc 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +@@ -144,7 +144,6 @@ class Vectorized { + // convert std::complex index mask to V index mask: xy -> xxyy + auto mask_complex = Vectorized( + vec_mergeh(mask._vec0, mask._vec0), vec_mergeh(mask._vec1, mask._vec1)); +- // mask_complex.dump(); + return { + vec_sel(a._vec0, b._vec0, mask_complex._vec0), + vec_sel(a._vec1, b._vec1, mask_complex._vec1), +@@ -409,13 +408,6 @@ class Vectorized { + return {vec_sqrt(_vec0), vec_sqrt(_vec1)}; + } + +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << "," << _vec0[2] << "," +- << _vec0[3] << ","; +- std::cout << _vec1[0] << "," << _vec1[1] << "," << _vec1[2] << "," +- << _vec1[3] << std::endl; +- } +- + Vectorized sqrt() const { + return map(std::sqrt); + } +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +index 29616182fe12..0d5b5cb39384 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +@@ -188,9 +188,6 @@ class Vectorized { + } + const double& operator[](int idx) const = delete; + double& operator[](int idx) = delete; +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << "," << _vec1[0] << "," << _vec1[1] << std::endl; +- } + Vectorized map(double (*const f)(double)) const { + Vectorized ret; + for (int i = 0; i < size()/2; i++) { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +index 2427276bcea2..58d4b057b507 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +@@ -436,13 +436,6 @@ class Vectorized { + return {vec_neg(_vec0), vec_neg(_vec1)}; + } + +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << "," << _vec0[2] << "," +- << _vec0[3] << ","; +- std::cout << _vec1[0] << "," << _vec1[1] << "," << _vec1[2] << "," +- << _vec1[3] << std::endl; +- } +- + Vectorized C10_ALWAYS_INLINE round() const { + return {vec_round(_vec0), vec_round(_vec1)}; + } +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +index c335ace0ced6..2482af6ec232 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +@@ -369,15 +369,6 @@ struct Vectorized { + return {vec0, vec1}; + } + +- void dump() const { +- value_type vals[size()]; +- store((void*)vals); +- for (int i = 0; i < size(); ++i) { +- std::cout << (int)(vals[i]) << " "; +- } +- std::cout << std::endl; +- } +- + DEFINE_MEMBER_OP(operator==, c10::quint8, vec_cmpeq) + DEFINE_MEMBER_OP(operator!=, c10::quint8, vec_cmpne) + DEFINE_MEMBER_OP(operator<, c10::quint8, vec_cmplt) From 642d33b48aae5ea6aef3a5ecebbcafa4e6fc8644 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Sep 2022 16:40:19 +0200 Subject: [PATCH 5128/9987] Fix FP16 quantization (fixes test_quantization) --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 3 ++ .../p/PyTorch/PyTorch-1.10.0-foss-2021a.eb | 3 ++ .../PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 3 ++ ...fix-fp16-quantization-without-fbgemm.patch | 43 +++++++++++++++++++ 4 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index fbed1049947..f16073d8956 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -21,6 +21,7 @@ patches = [ 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -52,6 +53,8 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts.patch '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch + 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb index 27db7713d1d..20e9c720a35 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb @@ -19,6 +19,7 @@ patches = [ 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -48,6 +49,8 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts.patch '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch + 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 450db866c3a..412066dcf6f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -20,6 +20,7 @@ patches = [ 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -51,6 +52,8 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts.patch '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch + 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 00000000000..b62f757853f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,43 @@ +From https://github.com/pytorch/pytorch/pull/84750 + +From d5480f56374e7612d4400e845b05bc3a4507d87c Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Fri, 9 Sep 2022 14:39:49 +0200 +Subject: [PATCH] Fix Use-after-Free in qembeddingbag_byte_prepack_out + +When FBGEMM is not used (either manually disabled or on platforms such +as POWER where it isn't supported at all) the fallback code requests a +`data_ptr` on a `Tensor` object returned by +`to(ScalarType::Float)` in the same line. This object will be destroyed +at the end of the line leading to a dangling pointer. + +On some platforms this manifests in wrong results being returned as the +memory gets overwritten. + +Fix this by binding the temporary object (or initial object) to a const +value reference which extents its lifetime and getting the `data_ptr` +from that. + +Fixes #84748 +--- + .../ATen/native/quantized/cpu/qembeddingbag_prepack.cpp | 7 ++++--- + 1 file changed, 4 insertions(+), 3 deletions(-) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 614e274b54..6c04d0ae12 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -242,9 +242,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row: c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; From c1f6e508906b9a59d2ce250b896d5b46474bd1c9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 22 Sep 2022 11:04:57 +0200 Subject: [PATCH 5129/9987] Add PyTorch-1.10.0_fix-kineto-crash.patch --- .../p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 3 +++ easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb | 3 +++ .../easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index f16073d8956..33304aa7d22 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -22,6 +22,7 @@ patches = [ 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -55,6 +56,8 @@ checksums = [ '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb index 20e9c720a35..208a35c065a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb @@ -20,6 +20,7 @@ patches = [ 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -51,6 +52,8 @@ checksums = [ '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 412066dcf6f..ffbf98f586c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -21,6 +21,7 @@ patches = [ 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -54,6 +55,8 @@ checksums = [ '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch From 28080783312808a6655707e2e179679577067b9a Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 10:22:14 +0100 Subject: [PATCH 5130/9987] Duplicated PyYAML removed --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 26c7449b3c6..b210c0f9419 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -32,7 +32,6 @@ dependencies = [ ('imgaug', '0.4.0', versionsuffix), ('tqdm', '4.61.2'), ('ruamel.yaml', '0.17.21'), - ('PyYAML', '5.4.1'), ('statsmodels', '0.12.2'), ('PyTorch', '1.10.0', versionsuffix), ] From 162a08790eb6dfdeb33d5fafaa1ccadb12e23613 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 10:24:18 +0100 Subject: [PATCH 5131/9987] Duplicated PyYAML and pandas removed --- .../easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb index e1d4d8dd05a..41ace2269ef 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -29,7 +29,6 @@ dependencies = [ ('imgaug', '0.4.0'), ('tqdm', '4.61.2'), ('ruamel.yaml', '0.17.21'), - ('PyYAML', '5.4.1'), ('statsmodels', '0.12.2'), ('PyTorch', '1.10.0'), ] @@ -41,9 +40,6 @@ exts_list = [ 'sources': ['%(name)s-%(version)s.zip'], 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], }), - ('pandas', '1.3.3', { - 'checksums': ['272c8cb14aa9793eada6b1ebe81994616e647b5892a370c7135efb2924b701df'], - }), ('tensorpack', '0.11', { 'checksums': ['022b610e416e62e3575424cd08e60af27808a5fb6914294615391caf582cbd4f'], }), From bb0269a6931a99cf6ae3b1f2bf7cc65a6d7232cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Oct 2022 12:04:16 +0200 Subject: [PATCH 5132/9987] add patch to fix failing LAPACK tests due to -ftree-vectorize + lower max. number of failing LAPACK tests due to numerical errors to 10 + don't disable vectorize toolchain option --- .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 24 +++++------ .../o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 20 ++++----- .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 18 ++++---- .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 18 ++++---- ...nBLAS-0.3.21_fix-order-vectorization.patch | 43 +++++++++++++++++++ 5 files changed, 83 insertions(+), 40 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_fix-order-vectorization.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 756da27b0e7..63c99b77086 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -5,9 +5,6 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} -# disable use -free-vectorize to work around compiler miscompilation bug, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 -toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -21,16 +18,19 @@ patches = [ 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-%(version)s_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch', 'OpenBLAS-%(version)s_fix-segfault-ztrsv.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', ] checksums = [ - 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f', # v0.3.17.tar.gz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', - # OpenBLAS-0.3.17_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch - 'ea76320bc047eff1bf2a2f50c1c19acb4fd6d2b8a5bf81a4dce73145a2a5cfcb', - 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch + {'v0.3.17.tar.gz': 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.17_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch': + 'ea76320bc047eff1bf2a2f50c1c19acb4fd6d2b8a5bf81a4dce73145a2a5cfcb'}, + {'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch': 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, ] builddependencies = [ @@ -39,7 +39,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 150 +max_failing_lapack_tests_num_errors = 10 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 971d85d6a77..3a587ae6e7d 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -5,9 +5,6 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} -# disable use -free-vectorize to work around compiler miscompilation bug, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 -toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -20,14 +17,17 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', ] checksums = [ - '1632c1e8cca62d8bed064b37747e331a1796fc46f688626337362bf0d16aeadb', # v0.3.18.tar.gz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', - 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111', # OpenBLAS-0.3.17_fix-segfault-ztrsv.patch + {'v0.3.18.tar.gz': '1632c1e8cca62d8bed064b37747e331a1796fc46f688626337362bf0d16aeadb'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch': 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, ] builddependencies = [ @@ -36,7 +36,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 150 +max_failing_lapack_tests_num_errors = 10 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index b4c9931fbae..8d3080bf8fd 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -5,9 +5,6 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.2.0'} -# disable use -free-vectorize to work around compiler miscompilation bug, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 -toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -19,13 +16,16 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', ] checksums = [ - '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', + {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, ] builddependencies = [ @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 150 +max_failing_lapack_tests_num_errors = 10 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index a7ebb133ddc..2e1cdaca17e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -5,9 +5,6 @@ homepage = 'http://www.openblas.net/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '11.3.0'} -# disable use -free-vectorize to work around compiler miscompilation bug, -# see https://github.com/easybuilders/easybuild-easyconfigs/issues/16380 -toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble @@ -19,13 +16,16 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', ] checksums = [ - '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', + {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, ] builddependencies = [ @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 150 +max_failing_lapack_tests_num_errors = 10 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_fix-order-vectorization.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_fix-order-vectorization.patch new file mode 100644 index 00000000000..846ffbe1c84 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_fix-order-vectorization.patch @@ -0,0 +1,43 @@ +add parentheses to force a certain order that is compatible with non-FMA instructions; +fixes failing LAPACK tests when -ftree-vectorize is used +author: Bart Oldeman (Digital Research Alliance of Canada) +--- OpenBLAS-0.3.21/lapack-netlib/SRC/clahqr.f.orig 2022-08-07 20:36:26.000000000 +0000 ++++ OpenBLAS-0.3.21/lapack-netlib/SRC/clahqr.f 2022-10-15 02:56:05.646906448 +0000 +@@ -484,7 +484,7 @@ + * in columns K to I2. + * + DO 80 J = K, I2 +- SUM = CONJG( T1 )*H( K, J ) + T2*H( K+1, J ) ++ SUM = CONJG( T1 )*H( K, J ) + ( T2*H( K+1, J ) ) + H( K, J ) = H( K, J ) - SUM + H( K+1, J ) = H( K+1, J ) - SUM*V2 + 80 CONTINUE +@@ -493,7 +493,7 @@ + * matrix in rows I1 to min(K+2,I). + * + DO 90 J = I1, MIN( K+2, I ) +- SUM = T1*H( J, K ) + T2*H( J, K+1 ) ++ SUM = T1*H( J, K ) + ( T2*H( J, K+1 ) ) + H( J, K ) = H( J, K ) - SUM + H( J, K+1 ) = H( J, K+1 ) - SUM*CONJG( V2 ) + 90 CONTINUE +--- OpenBLAS-0.3.21/lapack-netlib/SRC/zlahqr.f.orig 2022-08-07 20:36:26.000000000 +0000 ++++ OpenBLAS-0.3.21/lapack-netlib/SRC/zlahqr.f 2022-10-15 02:11:54.111966029 +0000 +@@ -484,7 +484,7 @@ + * in columns K to I2. + * + DO 80 J = K, I2 +- SUM = DCONJG( T1 )*H( K, J ) + T2*H( K+1, J ) ++ SUM = DCONJG( T1 )*H( K, J ) + ( T2*H( K+1, J ) ) + H( K, J ) = H( K, J ) - SUM + H( K+1, J ) = H( K+1, J ) - SUM*V2 + 80 CONTINUE +@@ -493,7 +493,7 @@ + * matrix in rows I1 to min(K+2,I). + * + DO 90 J = I1, MIN( K+2, I ) +- SUM = T1*H( J, K ) + T2*H( J, K+1 ) ++ SUM = T1*H( J, K ) + ( T2*H( J, K+1 ) ) + H( J, K ) = H( J, K ) - SUM + H( J, K+1 ) = H( J, K+1 ) - SUM*DCONJG( V2 ) + 90 CONTINUE From 5bb40ac4e28cb836ede916e1c4f070bab24211d3 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 11:13:04 +0100 Subject: [PATCH 5133/9987] pip_sanity_check added --- .../easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb index 41ace2269ef..d18669a6863 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -33,6 +33,8 @@ dependencies = [ ('PyTorch', '1.10.0'), ] +download_dep_fail = True +sanity_pip_check = True use_pip = True exts_list = [ From 6506f62a95d89a03b51d048c05931f2eba66fc32 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 11:14:56 +0100 Subject: [PATCH 5134/9987] pip_sanity_check added --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index b210c0f9419..3349b849e4f 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -36,6 +36,8 @@ dependencies = [ ('PyTorch', '1.10.0', versionsuffix), ] +download_dep_fail = True +sanity_pip_check = True use_pip = True exts_list = [ From 3ffe48ee0b3ee63e48116d5270c11f48868ec72f Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 11:42:19 +0100 Subject: [PATCH 5135/9987] download_dep removed as PythonBundle being used --- .../easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb index d18669a6863..e1b28de60f0 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -33,7 +33,6 @@ dependencies = [ ('PyTorch', '1.10.0'), ] -download_dep_fail = True sanity_pip_check = True use_pip = True From 3b822c4244353022b1da082f570d12e30f2b3398 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 11:44:21 +0100 Subject: [PATCH 5136/9987] download_dep removed as PythonBundle being used --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 3349b849e4f..9416f4eee39 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -36,7 +36,6 @@ dependencies = [ ('PyTorch', '1.10.0', versionsuffix), ] -download_dep_fail = True sanity_pip_check = True use_pip = True From 394461632696f6a991511352b7f3ae19d858ebae Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Oct 2022 13:41:19 +0200 Subject: [PATCH 5137/9987] Added ICU dependency --- easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb index a7d264de762..51cd88b1aaa 100644 --- a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-10.3.0.eb @@ -20,6 +20,7 @@ builddependencies = [ ] dependencies = [ + ('ICU', '69.1'), ('libunistring', '0.9.10'), ] From 35cf91b72ca9ff877866ada47660b6383c0dc954 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Mon, 17 Oct 2022 13:54:33 +0200 Subject: [PATCH 5138/9987] adding easyconfigs: TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb --- ...w-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..38e8358f882 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow-Datasets' +version = '4.7.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/datasets' +description = """ +TensorFlow Datasets is a collection of datasets ready to use, with TensorFlow or other Python ML frameworks, such as +Jax. All datasets are exposed as tf.data.Datasets , enabling easy-to-use and high-performance input pipelines. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('tqdm', '4.61.2'), + ('TensorFlow', '2.6.0', '-CUDA-%(cudaver)s'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('promise', '2.3', { + 'checksums': ['dfd18337c523ba4b6a58801c164c1904a9d4d1b1747c7d5dbf45b693a49d93d0'], + }), + ('googleapis-common-protos', '1.56.4', { + 'modulename': 'google', + 'checksums': ['c25873c47279387cfdcbdafa36149887901d36202cb645a0e4f29686bf6e4417'], + }), + ('tensorflow-metadata', '1.10.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_urls': [ + 'https://files.pythonhosted.org/packages/3a/86/' + + '2b3251bb560068f31817d9b678588098e28f396c1f6b88c57cf5d28670af/' + + 'tensorflow_metadata-1.10.0-py3-none-any.whl' + + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3', + ], + 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'download_filename': 'v(%version)s.tar.gz', + 'filename': '%(name)s-v(%version)s.tar.gz', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/datasets/archive'], + 'checksums': ['ed7c3b959d10ba762137e18b93631ab42f4ed0915bc3d9ce98ee66eef9c61418'], + }), +] + +moduleclass = 'lib' From bf17187f91939a0e298c9e4550cd63af4759e062 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 17 Oct 2022 14:03:52 +0200 Subject: [PATCH 5139/9987] Add GITHUB_(LOWER_)RELEASE to known constants --- setup.cfg | 2 ++ 1 file changed, 2 insertions(+) diff --git a/setup.cfg b/setup.cfg index 1209f2f4ea8..c1167840f91 100644 --- a/setup.cfg +++ b/setup.cfg @@ -28,6 +28,8 @@ builtins = FTPGNOME_SOURCE, GITHUB_SOURCE, GITHUB_LOWER_SOURCE, + GITHUB_RELEASE, + GITHUB_LOWER_RELEASE, GNU_SAVANNAH_SOURCE, GNU_SOURCE, GOOGLECODE_SOURCE, From 299c6dc7bfae327daddc8a22dd6158b915da995e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Jul 2022 13:34:21 +0200 Subject: [PATCH 5140/9987] adding easyconfigs: CUDAcompat-11.6.eb, CUDAcompat-11.7.eb --- .../c/CUDAcompat/CUDAcompat-11.6.eb | 38 ++++++++++++++++++ .../c/CUDAcompat/CUDAcompat-11.7.eb | 39 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb create mode 100644 easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb new file mode 100644 index 00000000000..ec72ddcd2eb --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb @@ -0,0 +1,38 @@ +name = 'CUDAcompat' +version = '11.6' +nv_version = '510.73.08' + +# Compatible driver versions: +# 418.40.04+ (CUDA 10.1) +# 450.36.06+ (CUDA 11.0) +# 470.57.02+ (CUDA 11.4) + +homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' +description = """Using the CUDA Forward Compatibility package, + system administrators can run applications built using a newer toolkit + even when an older driver that does not satisfy the minimum required driver version + is installed on the system. + This forward compatibility allows the CUDA deployments in data centers and enterprises + to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. +""" + +toolchain = SYSTEM + +# The full driver runfile installers are downloaded but we will only use a small portion of them +# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) +# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver +# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) + +# accept_eula = True +source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] +sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] +checksums = [{ + 'NVIDIA-Linux-aarch64-%s.run' % nv_version: + '99fbb188e69513c970bb20c530323ea1205a93245fd0316723ad7308dde8d362', + 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: + 'f9b77f8d6a12a499a146ca6ac1b4fba26268956e308f7272753d53f92cd5b830', + 'NVIDIA-Linux-x86_64-%s.run' % nv_version: + 'c854bb2dc3368c0127dc08a85bd902f8558a5149085af13d061c612cf06c2913', +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb new file mode 100644 index 00000000000..4ca891db19f --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb @@ -0,0 +1,39 @@ +name = 'CUDAcompat' +version = '11.7' +nv_version = '515.48.07' + +# Compatible driver versions: +# 450.36.06+ (CUDA 11.0) +# 470.57.02+ (CUDA 11.4) +# 510.39.01+ (CUDA 11.6) + +homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' +description = """Using the CUDA Forward Compatibility package, + system administrators can run applications built using a newer toolkit + even when an older driver that does not satisfy the minimum required driver version + is installed on the system. + This forward compatibility allows the CUDA deployments in data centers and enterprises + to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. +""" + +toolchain = SYSTEM + +# The full driver runfile installers are downloaded but we will only use a small portion of them +# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) +# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver +# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) + +# accept_eula = True + +source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] +sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] +checksums = [{ + 'NVIDIA-Linux-aarch64-%s.run' % nv_version: + 'a4e071055a5f6c110fd49264d76c57a07f3fbd37b8ee2f9eb90c25f51fa59ef5', + 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: + '476466e768ca3cd4e5d01b2467bed61623728e637efbe7f81ac976bb2dd96aa8', + 'NVIDIA-Linux-x86_64-%s.run' % nv_version: + 'e28764cc5b13c32e76370513daeafc05c289b77ee0511552450f1a00e31ae1e3', +}] + +moduleclass = 'system' From f2e6b052039b34bb0d37702552d5a6602face865 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Jul 2022 14:15:21 +0200 Subject: [PATCH 5141/9987] Add alias modules and the compatible driver versions a list --- .../c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb | 45 +++++++++++++++++++ .../c/CUDAcompat/CUDAcompat-11.6.eb | 25 ++--------- .../c/CUDAcompat/CUDAcompat-11.7-515.65.01.eb | 45 +++++++++++++++++++ .../c/CUDAcompat/CUDAcompat-11.7.eb | 26 ++--------- .../easyconfigs/c/CUDAcompat/CUDAcompat-11.eb | 19 ++++++++ 5 files changed, 115 insertions(+), 45 deletions(-) create mode 100644 easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb create mode 100644 easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7-515.65.01.eb create mode 100644 easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.eb diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb new file mode 100644 index 00000000000..7bc5e5a3d2d --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb @@ -0,0 +1,45 @@ +name = 'CUDAcompat' +version = '11.6' +nv_version = '510.85.02' +versionsuffix = "-" + nv_version + +# Minimal driver requirements for each production branch / major version as found on +# https://docs.nvidia.com/deploy/cuda-compatibility/index.html#use-the-right-compat-package +# Compatibility test can be skipped with --skip-test-step/--ignore-test-failure +# but then tests running actual CUDA applications should be used to verify compatibility +compatible_driver_versions = [ + '418.40.04', # (CUDA 10.1) + '450.36.06', # (CUDA 11.0) + '470.57.02', # (CUDA 11.4) +] + +homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' +description = """Using the CUDA Forward Compatibility package, + system administrators can run applications built using a newer toolkit + even when an older driver that does not satisfy the minimum required driver version + is installed on the system. + This forward compatibility allows the CUDA deployments in data centers and enterprises + to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. +""" + +toolchain = SYSTEM + +# The full driver runfile installers are downloaded but we will only use a small portion of them +# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) +# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver +# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) + +# accept_eula = True + +source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] +sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] +checksums = [{ + 'NVIDIA-Linux-aarch64-%s.run' % nv_version: + 'bb5e844a69bc05dade9148438a71f2bb7dea1864278d37864f1a303e437e40c3', + 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: + '46626294cf18ead6eeb53a6614f7b340e66c57ea50f95d4dc670e90b4650c335', + 'NVIDIA-Linux-x86_64-%s.run' % nv_version: + '372427e633f32cff6dd76020e8ed471ef825d38878bd9655308b6efea1051090', +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb index ec72ddcd2eb..f931186e517 100644 --- a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6.eb @@ -1,11 +1,7 @@ +easyblock = 'ModuleRC' + name = 'CUDAcompat' version = '11.6' -nv_version = '510.73.08' - -# Compatible driver versions: -# 418.40.04+ (CUDA 10.1) -# 450.36.06+ (CUDA 11.0) -# 470.57.02+ (CUDA 11.4) homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' description = """Using the CUDA Forward Compatibility package, @@ -18,21 +14,6 @@ description = """Using the CUDA Forward Compatibility package, toolchain = SYSTEM -# The full driver runfile installers are downloaded but we will only use a small portion of them -# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) -# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver -# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) - -# accept_eula = True -source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] -sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] -checksums = [{ - 'NVIDIA-Linux-aarch64-%s.run' % nv_version: - '99fbb188e69513c970bb20c530323ea1205a93245fd0316723ad7308dde8d362', - 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: - 'f9b77f8d6a12a499a146ca6ac1b4fba26268956e308f7272753d53f92cd5b830', - 'NVIDIA-Linux-x86_64-%s.run' % nv_version: - 'c854bb2dc3368c0127dc08a85bd902f8558a5149085af13d061c612cf06c2913', -}] +dependencies = [(name, version, "-510.85.02")] moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7-515.65.01.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7-515.65.01.eb new file mode 100644 index 00000000000..eba7e2ca957 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7-515.65.01.eb @@ -0,0 +1,45 @@ +name = 'CUDAcompat' +version = '11.7' +nv_version = '515.65.01' +versionsuffix = "-" + nv_version + +# Minimal driver requirements for each production branch / major version as found on +# https://docs.nvidia.com/deploy/cuda-compatibility/index.html#use-the-right-compat-package +# Compatibility test can be skipped with --skip-test-step/--ignore-test-failure +# but then tests running actual CUDA applications should be used to verify compatibility +compatible_driver_versions = [ + '450.36.06', # (CUDA 11.0) + '470.57.02', # (CUDA 11.4) + '510.39.01', # (CUDA 11.6) +] + +homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' +description = """Using the CUDA Forward Compatibility package, + system administrators can run applications built using a newer toolkit + even when an older driver that does not satisfy the minimum required driver version + is installed on the system. + This forward compatibility allows the CUDA deployments in data centers and enterprises + to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. +""" + +toolchain = SYSTEM + +# The full driver runfile installers are downloaded but we will only use a small portion of them +# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) +# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver +# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) + +# accept_eula = True + +source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] +sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] +checksums = [{ + 'NVIDIA-Linux-aarch64-%s.run' % nv_version: + '0d2ac6c6ca144c8c7bbf1a62034998463b21f2660a793607d88c031650d93e93', + 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: + 'd217c7539d049ab1b7a889815d14d1655116616e7e9943387a1b190aec816063', + 'NVIDIA-Linux-x86_64-%s.run' % nv_version: + '0492ddc5b5e65aa00cbc762e8d6680205c8d08e103b7131087a15126aee495e9', +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb index 4ca891db19f..c3a7b3b2e0e 100644 --- a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.7.eb @@ -1,11 +1,7 @@ +easyblock = 'ModuleRC' + name = 'CUDAcompat' version = '11.7' -nv_version = '515.48.07' - -# Compatible driver versions: -# 450.36.06+ (CUDA 11.0) -# 470.57.02+ (CUDA 11.4) -# 510.39.01+ (CUDA 11.6) homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' description = """Using the CUDA Forward Compatibility package, @@ -18,22 +14,6 @@ description = """Using the CUDA Forward Compatibility package, toolchain = SYSTEM -# The full driver runfile installers are downloaded but we will only use a small portion of them -# (see https://docs.nvidia.com/deploy/cuda-compatibility/index.html#manually-installing-from-runfile) -# By downloading, you accept the "License For Customer Use of NVIDIA Software for use of the driver -# (https://www.nvidia.com/content/DriverDownload-March2009/licence.php?lang=us) - -# accept_eula = True - -source_urls = ['https://us.download.nvidia.com/tesla/' + nv_version] -sources = ['NVIDIA-Linux-%%(arch)s-%s.run' % nv_version] -checksums = [{ - 'NVIDIA-Linux-aarch64-%s.run' % nv_version: - 'a4e071055a5f6c110fd49264d76c57a07f3fbd37b8ee2f9eb90c25f51fa59ef5', - 'NVIDIA-Linux-ppc64le-%s.run' % nv_version: - '476466e768ca3cd4e5d01b2467bed61623728e637efbe7f81ac976bb2dd96aa8', - 'NVIDIA-Linux-x86_64-%s.run' % nv_version: - 'e28764cc5b13c32e76370513daeafc05c289b77ee0511552450f1a00e31ae1e3', -}] +dependencies = [(name, version, '-515.65.01')] moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.eb new file mode 100644 index 00000000000..17159182bc1 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.eb @@ -0,0 +1,19 @@ +easyblock = 'ModuleRC' + +name = 'CUDAcompat' +version = '11' + +homepage = 'https://docs.nvidia.com/deploy/cuda-compatibility/index.html' +description = """Using the CUDA Forward Compatibility package, + system administrators can run applications built using a newer toolkit + even when an older driver that does not satisfy the minimum required driver version + is installed on the system. + This forward compatibility allows the CUDA deployments in data centers and enterprises + to benefit from the faster release cadence and the latest features and performance of CUDA Toolkit. +""" + +toolchain = SYSTEM + +dependencies = [(name, '11.7')] + +moduleclass = 'system' From 352b6273fb575bb9ec7299b039850a0d5ca2921b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 19 Sep 2022 14:00:57 +0200 Subject: [PATCH 5142/9987] Mark 11.6 as compatible to R440 and R460 As tested by @Flamefire and @ocaisa --- easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb index 7bc5e5a3d2d..721f22cf426 100644 --- a/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb +++ b/easybuild/easyconfigs/c/CUDAcompat/CUDAcompat-11.6-510.85.02.eb @@ -9,7 +9,9 @@ versionsuffix = "-" + nv_version # but then tests running actual CUDA applications should be used to verify compatibility compatible_driver_versions = [ '418.40.04', # (CUDA 10.1) + '440.33.00', # (CUDA 10.2, actually EoL but works) '450.36.06', # (CUDA 11.0) + '460.73.01', # (CUDA 11.2, actually EoL but works) '470.57.02', # (CUDA 11.4) ] From c65bed37af572d6a2bfd13266c2ad88021b33687 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Oct 2022 14:38:32 +0200 Subject: [PATCH 5143/9987] fix checksum for GULP 6.1 (fixes #15984) --- easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb index c26d7a70c8c..4a48ff9555c 100644 --- a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb @@ -20,7 +20,7 @@ patches = [ 'GULP-6.1_fftw-blas-linking-gcc-11.patch', ] checksums = [ - '503dff253f4686c570adfd3ff75a657e29151b4255dec726daa50eda5a7ac3f4', # gulp-6.1.tgz + '1b52fe2928ccf2cea5d2c3466162764d0de6b4d06e86fe292ab37859d6a0e6d6', # gulp-6.1.tgz '156449c96a97ff24f6add83c10fd383f07c43c79420eebe3290387b65b34549b', # gulp-6.1_fftw-blas-linking-gcc-11.patch ] From 4fcf6ec98a14756f8b9b327f178df5b1833edb43 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Mon, 17 Oct 2022 15:42:03 +0200 Subject: [PATCH 5144/9987] Add missing parenthesis --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 38e8358f882..667bb710d9e 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -32,12 +32,12 @@ exts_list = [ }), ('tensorflow-metadata', '1.10.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'source_urls': [ + 'source_urls': [( 'https://files.pythonhosted.org/packages/3a/86/' + '2b3251bb560068f31817d9b678588098e28f396c1f6b88c57cf5d28670af/' + 'tensorflow_metadata-1.10.0-py3-none-any.whl' - + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3', - ], + + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3' + )], 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], }), ('etils', '0.8.0', { From c474ce7cb330ff51fe7aa6c548f5e6e40d570f56 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Oct 2022 18:18:37 +0200 Subject: [PATCH 5145/9987] increase max. number of failing LAPACK tests with numerical error to 100 for recent OpenBLAS easyconfigs, due to eigenvalue test being a bit too strict --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 63c99b77086..545706a97b2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -39,7 +39,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 10 +max_failing_lapack_tests_num_errors = 100 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 3a587ae6e7d..e60362e973a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -36,7 +36,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 10 +max_failing_lapack_tests_num_errors = 100 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index 8d3080bf8fd..1bcda13c08c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 10 +max_failing_lapack_tests_num_errors = 100 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 2e1cdaca17e..29dff20315a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 10 +max_failing_lapack_tests_num_errors = 100 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' From 6abf54083c07e611aecb575a5dbda45e3b456b53 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Oct 2022 18:21:53 +0200 Subject: [PATCH 5146/9987] adding easyconfigs: JupyterHub-3.0.0-GCCcore-11.3.0.eb, configurable-http-proxy-4.5.3-GCCcore-11.3.0.eb --- ...gurable-http-proxy-4.5.3-GCCcore-11.3.0.eb | 33 ++++ .../i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb | 180 ++++++++++++++++++ .../JupyterHub-3.0.0-GCCcore-11.3.0.eb | 114 +++++++++++ .../libsodium-1.0.18-GCCcore-11.3.0.eb | 33 ++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb | 45 +++++ .../z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb | 40 ++++ 6 files changed, 445 insertions(+) create mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7ae94e8d06f --- /dev/null +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.3-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'Binary' + +name = 'configurable-http-proxy' +version = '4.5.3' + +homepage = 'https://github.com/jupyterhub/configurable-http-proxy' +description = """HTTP proxy for node.js including a REST API for updating the routing table. + Developed as a part of the Jupyter Hub multi-user server.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = { + ('binutils', '2.38'), +} + +dependencies = [ + ('nodejs', '16.15.1'), +] + +source_urls = ['https://github.com/jupyterhub/configurable-http-proxy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b3bb67baa097ff670ad4e3c7770ccd5468f4fb56a91d91b735c9b8bdecee935e'] + +install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz' + +sanity_check_paths = { + 'files': ['bin/configurable-http-proxy'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4697bcfaf93 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,180 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '8.5.0' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('ZeroMQ', '4.3.4'), + ('lxml', '4.9.1'), + ('BeautifulSoup', '4.10.0'), +] + +use_pip = True + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['097bdf5cd87576fd066179c9f7f208004f7a6864ee1b20f37d346c0bcb099f84'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '3.0.31', { + 'checksums': ['9ada952c9d1787f52ff6d5f3484d0b4df8952787c087edf6a1f7c2cb1ea88148'], + }), + ('traitlets', '5.2.0', { + 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + }), + ('parso', '0.8.3', { + 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], + }), + ('jedi', '0.18.1', { + 'checksums': ['74137626a64a99c8eb6ae5832d99b3bdd7d29a3850fe2aa80a4126b2a7d949ab'], + }), + ('testpath', '0.6.0', { + 'checksums': ['2f1b97e6442c02681ebe01bd84f531028a7caea1af3825000f52345c30285e0f'], + }), + ('Send2Trash', '1.8.0', { + 'checksums': ['d2c24762fd3759860a0aff155e45871447ea58d2be6bdd39b5c8f966a0c99c2d'], + }), + ('bleach', '5.0.1', { + 'checksums': ['0d03255c47eb9bd2f26aa9bb7f2107732e7e8fe195ca2f64709fcf3b0a4a085c'], + }), + ('pandocfilters', '1.5.0', { + 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], + }), + ('pyzmq', '23.2.1', { + 'modulename': 'zmq', + 'checksums': ['2b381aa867ece7d0a82f30a0c7f3d4387b7cf2e0697e33efaa5bed6c5784abcd'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('jupyter_core', '4.10.0', { + 'checksums': ['a6de44b16b7b31d7271130c71a6792c4040f077011961138afed5e5e73181aec'], + }), + ('fastjsonschema', '2.16.1', { + 'checksums': ['d6fa3ffbe719768d70e298b9fb847484e2bdfdb7241ed052b8d57a9294a8c334'], + }), + ('nbformat', '5.4.0', { + 'checksums': ['44ba5ca6acb80c5d5a500f1e5b83ede8cbe364d5a495c4c8cf60aaf1ba656501'], + }), + ('mistune', '0.8.1', { + 'checksums': ['4c0f66924ce28f03b95b210ea57e57bd0b59f479edd91c2fa4fe59331eae4a82'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('nest_asyncio', '1.5.5', { + 'checksums': ['e442291cd942698be619823a17a86a5759eabe1f8613084790de189fe9e16d65'], + }), + ('nbclient', '0.6.3', { + 'checksums': ['b80726fc1fb89a0e8f8be1e77e28d0026b1e8ed90bc143c8a0c7622e4f8cdd9e'], + }), + ('tinycss2', '1.1.1', { + 'checksums': ['b2e44dd8883c360c35dd0d1b5aad0b610e5156c2cb3b33434634e539ead9d8bf'], + }), + ('nbconvert', '6.5.3', { + 'checksums': ['10ed693c4cfd3c63583c87ca5c3a2f6ed874145103595f3824efcc8dfcb7522c'], + }), + ('tornado', '6.2', { + 'checksums': ['9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13'], + }), + ('terminado', '0.13.0', { + 'checksums': ['713531ccb5db7d4f544651f14050da79809030f00d1afa21462088cf32fb143a'], + }), + ('jupyter_client', '7.3.1', { + 'checksums': ['05d4ff6a0ade25138c6bb0fbeac7ddc26b5fe835e7dd816b64b4a45b931bdc0b'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('executing', '1.0.0', { + 'checksums': ['98daefa9d1916a4f0d944880d5aeaf079e05585689bebd9ff9b32e31dd5e1017'], + }), + ('asttokens', '2.0.8', { + 'checksums': ['c61e16246ecfb2cde2958406b4c8ebc043c9e6d73aaa83c941673b35e5d3a76b'], + }), + ('pure_eval', '0.2.2', { + 'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3'], + }), + ('stack_data', '0.5.0', { + 'checksums': ['715c8855fbf5c43587b141e46cc9d9339cc0d1f8d6e0f98ed0d01c6cb974e29f'], + }), + ('ipykernel', '6.13.0', { + 'checksums': ['0e28273e290858393e86e152b104e5506a79c13d25b951ac6eca220051b4be60'], + }), + ('prometheus_client', '0.11.0', { + 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], + }), + ('ipywidgets', '7.6.3', { + 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.0', { + 'checksums': ['b27455d60adc93a7baa2e0b8f386be81b932bb4e3c0116046df9ed230cd3faac'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('jupyterlab_widgets', '3.0.3', { + 'checksums': ['c767181399b4ca8b647befe2d913b1260f51bf9d8ef9b7a14632d4c1a7b536bd'], + }), + ('argon2-cffi', '20.1.0', { + 'modulename': 'argon2', + 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], + }), + ('notebook', '6.4.0', { + 'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + ('matplotlib-inline', '0.1.2', { + 'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'], + }), + ('debugpy', '1.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['84ff51b8b5c847d5421324ca419db1eec813a4dd2bbf19dbbbe132e2ab2b2fc6'], + }), +] + +modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/IPython', + 'share/jupyter' + ], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a5ba7921650 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,114 @@ +easyblock = 'PythonBundle' + +name = 'JupyterHub' +version = '3.0.0' + +homepage = 'https://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed + for centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = { + ('binutils', '2.38'), +} + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('Mako', '1.2.0'), + ('configurable-http-proxy', '4.5.3'), + ('OpenSSL', '1.1', '', True), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('certipy', '0.1.3', { + 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], + }), + ('pamela', '1.0.0', { + 'checksums': ['65c9389bef7d1bb0b168813b6be21964df32016923aac7515bdf05366acbab6c'], + }), + ('greenlet', '1.1.3.post0', { + 'checksums': ['f5e09dc5c6e1796969fd4b775ea1417d70e49a5df29aaa8e5d10675d9e11872c'], + }), + ('SQLAlchemy', '1.4.42', { + 'checksums': ['177e41914c476ed1e1b77fd05966ea88c094053e17a85303c4ce007f88eff363'], + }), + ('alembic', '1.8.1', { + 'checksums': ['cd0b5e45b14b706426b833f06369b9a6d5ee03f826ec3238723ce8caaf6e5ffa'], + }), + ('oauthlib', '3.2.1', { + 'checksums': ['1565237372795bf6ee3e5aba5e2a85bd5a65d0e2aa5c628b9a97b7d7a0da3721'], + }), + ('pyOpenSSL', '21.0.0', { + 'modulename': 'OpenSSL', + 'checksums': ['5e2d8c5e46d0d865ae933bef5230090bdaf5506281e9eec60fa250ee80600cb3'], + }), + ('python-json-logger', '2.0.4', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['764d762175f99fcc4630bd4853b09632acb60a6224acb27ce08cd70f0b1b81bd'], + }), + ('ruamel.yaml', '0.17.21', { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('ruamel.yaml.clib', '0.2.6', { + 'modulename': False, + 'checksums': ['4ff604ce439abb20794f05613c374759ce10e3595d1867764dd1ae675b85acbd'], + }), + ('jupyter-telemetry', '0.1.0', { + 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', + 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], + }), + ('jupyterhub', version, { + 'checksums': ['05cdfebd800cf3e55566fb5b61110c5f64fed8ca3c56ef0142290baffbc7fb69'], + }), + ('batchspawner', '1.2.0', { + 'checksums': ['b1924bb4f3a3f527a1e312ecdaff3dbc5acfd91e6b13cf074a62cd74340a2e21'], + }), + ('jupyterhub-systemdspawner', '0.16', { + 'modulename': 'systemdspawner', + 'checksums': ['a7aeea1e8cb081a9c4de14475504199bbe249d93ea317da5c09d536b7b11b300'], + }), + ('jupyterhub-simplespawner', '0.1', { + 'modulename': 'simplespawner', + 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], + }), + ('ldap3', '2.9.1', { + 'checksums': ['f3e7fc4718e3f09dda568b57100095e0ce58633bcabbed8667ce3f8fbaa4229f'], + }), + ('jupyterhub-ldapauthenticator', '1.3.2', { + 'modulename': 'ldapauthenticator', + 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], + }), + ('PyJWT', '2.5.0', { + 'modulename': 'jwt', + 'checksums': ['e77ab89480905d86998442ac5788f35333fa85f65047a534adc38edf3c88fc3b'], + }), + ('jupyterhub-jwtauthenticator-v2', '2.0.3', { + 'modulename': 'jwtauthenticator', + 'checksums': ['b94b6dff8246250904c5ee511da3f062680eb657dabe766d75993cbe72747d41'], + }), + ('onetimepass', '1.0.1', { + 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], + }), + ('jupyterhub-nativeauthenticator', '1.1.0', { + 'modulename': 'nativeauthenticator', + 'checksums': ['190e760da620acea25246eb215ff671da7aee8a1603f9cbf3c359a404f009088'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/jupyterhub'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], +} + +sanity_pip_check = True + +sanity_check_commands = ['jupyterhub --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e62a803500d --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0563e14c45a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + 'OpenPGM-5.2.122-pkgconfig_includes.patch', + 'OpenPGM-5.2.122-python3-compliant.patch' +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0d05aef4ded --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.4' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.38'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = '--with-pic --with-pgm --with-libsodium --disable-Werror' + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From 5b708a67446831f9090944788da4265fc31fa751 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 17 Oct 2022 18:22:51 +0200 Subject: [PATCH 5147/9987] Delete IPython-8.5.0-GCCcore-11.3.0.eb --- .../i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb | 180 ------------------ 1 file changed, 180 deletions(-) delete mode 100644 easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb deleted file mode 100644 index 4697bcfaf93..00000000000 --- a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb +++ /dev/null @@ -1,180 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'IPython' -version = '8.5.0' - -homepage = 'https://ipython.org/index.html' -description = """IPython provides a rich architecture for interactive computing with: - Powerful interactive shells (terminal and Qt-based). - A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. - Support for interactive data visualization and use of GUI toolkits. - Flexible, embeddable interpreters to load into your own projects. - Easy to use, high performance tools for parallel computing.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -builddependencies = [('binutils', '2.38')] - -dependencies = [ - ('Python', '3.10.4'), - ('ZeroMQ', '4.3.4'), - ('lxml', '4.9.1'), - ('BeautifulSoup', '4.10.0'), -] - -use_pip = True - -exts_list = [ - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('ipython', version, { - 'modulename': 'IPython', - 'checksums': ['097bdf5cd87576fd066179c9f7f208004f7a6864ee1b20f37d346c0bcb099f84'], - }), - ('pickleshare', '0.7.5', { - 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], - }), - ('prompt_toolkit', '3.0.31', { - 'checksums': ['9ada952c9d1787f52ff6d5f3484d0b4df8952787c087edf6a1f7c2cb1ea88148'], - }), - ('traitlets', '5.2.0', { - 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], - }), - ('parso', '0.8.3', { - 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], - }), - ('jedi', '0.18.1', { - 'checksums': ['74137626a64a99c8eb6ae5832d99b3bdd7d29a3850fe2aa80a4126b2a7d949ab'], - }), - ('testpath', '0.6.0', { - 'checksums': ['2f1b97e6442c02681ebe01bd84f531028a7caea1af3825000f52345c30285e0f'], - }), - ('Send2Trash', '1.8.0', { - 'checksums': ['d2c24762fd3759860a0aff155e45871447ea58d2be6bdd39b5c8f966a0c99c2d'], - }), - ('bleach', '5.0.1', { - 'checksums': ['0d03255c47eb9bd2f26aa9bb7f2107732e7e8fe195ca2f64709fcf3b0a4a085c'], - }), - ('pandocfilters', '1.5.0', { - 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], - }), - ('pyzmq', '23.2.1', { - 'modulename': 'zmq', - 'checksums': ['2b381aa867ece7d0a82f30a0c7f3d4387b7cf2e0697e33efaa5bed6c5784abcd'], - }), - ('entrypoints', '0.4', { - 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], - }), - ('jupyter_core', '4.10.0', { - 'checksums': ['a6de44b16b7b31d7271130c71a6792c4040f077011961138afed5e5e73181aec'], - }), - ('fastjsonschema', '2.16.1', { - 'checksums': ['d6fa3ffbe719768d70e298b9fb847484e2bdfdb7241ed052b8d57a9294a8c334'], - }), - ('nbformat', '5.4.0', { - 'checksums': ['44ba5ca6acb80c5d5a500f1e5b83ede8cbe364d5a495c4c8cf60aaf1ba656501'], - }), - ('mistune', '0.8.1', { - 'checksums': ['4c0f66924ce28f03b95b210ea57e57bd0b59f479edd91c2fa4fe59331eae4a82'], - }), - ('defusedxml', '0.7.1', { - 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], - }), - ('async_generator', '1.10', { - 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], - }), - ('nest_asyncio', '1.5.5', { - 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}), - ('asttokens', '2.0.8', { - 'checksums': ['c61e16246ecfb2cde2958406b4c8ebc043c9e6d73aaa83c941673b35e5d3a76b'], - }), - ('pure_eval', '0.2.2', { - 'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3'], - }), - ('stack_data', '0.5.0', { - 'checksums': ['715c8855fbf5c43587b141e46cc9d9339cc0d1f8d6e0f98ed0d01c6cb974e29f'], - }), - ('ipykernel', '6.13.0', { - 'checksums': ['0e28273e290858393e86e152b104e5506a79c13d25b951ac6eca220051b4be60'], - }), - ('prometheus_client', '0.11.0', { - 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], - }), - ('ipywidgets', '7.6.3', { - 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], - }), - ('deprecation', '2.1.0', { - 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], - }), - ('jupyter_packaging', '0.12.0', { - 'checksums': ['b27455d60adc93a7baa2e0b8f386be81b932bb4e3c0116046df9ed230cd3faac'], - }), - ('jupyterlab_pygments', '0.1.2', { - 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], - }), - ('jupyterlab_widgets', '3.0.3', { - 'checksums': ['c767181399b4ca8b647befe2d913b1260f51bf9d8ef9b7a14632d4c1a7b536bd'], - }), - ('argon2-cffi', '20.1.0', { - 'modulename': 'argon2', - 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], - }), - ('notebook', '6.4.0', { - 'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'], - }), - ('widgetsnbextension', '3.5.1', { - 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], - }), - ('matplotlib-inline', '0.1.2', { - 'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'], - }), - ('debugpy', '1.4.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - 'checksums': ['84ff51b8b5c847d5421324ca419db1eec813a4dd2bbf19dbbbe132e2ab2b2fc6'], - }), -] - -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} - -sanity_check_paths = { - 'files': ['bin/ipython'], - 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/IPython', - 'share/jupyter' - ], -} - -sanity_check_commands = [ - "ipython -h", - "jupyter notebook --help", -] - -sanity_pip_check = True - -moduleclass = 'tools' From fc8b4c6534cb9c0f8dc18a846f08bad5c21819bb Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 17 Oct 2022 18:23:11 +0200 Subject: [PATCH 5148/9987] Delete libsodium-1.0.18-GCCcore-11.3.0.eb --- .../libsodium-1.0.18-GCCcore-11.3.0.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb deleted file mode 100644 index e62a803500d..00000000000 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libsodium' -version = '1.0.18' - -homepage = 'https://doc.libsodium.org/' - -description = """ - Sodium is a modern, easy-to-use software library for encryption, decryption, - signatures, password hashing and more. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - 'https://download.libsodium.org/libsodium/releases/', - 'https://download.libsodium.org/libsodium/releases/old/', - 'https://download.libsodium.org/libsodium/releases/old/unsupported/', -] -sources = [SOURCE_TAR_GZ] -checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] - -builddependencies = [ - ('binutils', '2.38'), -] - -sanity_check_paths = { - 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], - 'dirs': ['include/sodium', 'lib/pkgconfig'], -} - -moduleclass = 'lib' From 00b45a59d0404a7aa3558a2bb9725b838da38313 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 17 Oct 2022 18:23:18 +0200 Subject: [PATCH 5149/9987] Delete OpenPGM-5.2.122-GCCcore-11.3.0.eb --- .../OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb deleted file mode 100644 index 0563e14c45a..00000000000 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OpenPGM' -version = '5.2.122' - -homepage = 'https://code.google.com/p/openpgm/' - -description = """ - OpenPGM is an open source implementation of the Pragmatic General Multicast - (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable - and scalable multicast protocol that enables receivers to detect loss, request - retransmission of lost data, or notify an application of unrecoverable loss. - PGM is a receiver-reliable protocol, which means the receiver is responsible - for ensuring all data is received, absolving the sender of reception - responsibility. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] -sources = ['libpgm-%(version)s.tar.gz'] -patches = [ - 'OpenPGM-5.2.122-pkgconfig_includes.patch', - 'OpenPGM-5.2.122-python3-compliant.patch' -] -checksums = [ - '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz - '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch - 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch -] - -builddependencies = [ - ('binutils', '2.38'), - ('Python', '3.10.4'), -] - -start_dir = 'pgm' - -sanity_check_paths = { - 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], - 'dirs': ['include'], -} - -moduleclass = 'system' From bbbd73eca03bae6390c2badf0370ca9b2a70f98a Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 17 Oct 2022 18:23:27 +0200 Subject: [PATCH 5150/9987] Delete ZeroMQ-4.3.4-GCCcore-11.3.0.eb --- .../z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb deleted file mode 100644 index 0d05aef4ded..00000000000 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ZeroMQ' -version = '4.3.4' - -homepage = 'https://www.zeromq.org/' -description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. - It gives you sockets that carry atomic messages across various transports like in-process, - inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, - pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered - products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous - message-processing tasks. It has a score of language APIs and runs on most operating systems.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] - -builddependencies = [ - ('binutils', '2.38'), - ('pkgconf', '1.8.0'), -] - -dependencies = [ - ('OpenPGM', '5.2.122'), - ('libsodium', '1.0.18'), - ('util-linux', '2.38'), -] - -# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 -# Needto disable warnings as errors. -configopts = '--with-pic --with-pgm --with-libsodium --disable-Werror' - -sanity_check_paths = { - 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], - 'dirs': ['include', 'lib'], -} - -moduleclass = 'devel' From f17b7b818f20e030e72feaf565684a8bf3c84f7c Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Oct 2022 18:59:20 +0200 Subject: [PATCH 5151/9987] Replace True with SYSTEM for system toolchain --- .../i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb | 180 ++++++++++++++++++ .../JupyterHub-3.0.0-GCCcore-11.3.0.eb | 2 +- .../libsodium-1.0.18-GCCcore-11.3.0.eb | 33 ++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb | 45 +++++ .../z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb | 40 ++++ 5 files changed, 299 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4697bcfaf93 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,180 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '8.5.0' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('ZeroMQ', '4.3.4'), + ('lxml', '4.9.1'), + ('BeautifulSoup', '4.10.0'), +] + +use_pip = True + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['097bdf5cd87576fd066179c9f7f208004f7a6864ee1b20f37d346c0bcb099f84'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '3.0.31', { + 'checksums': ['9ada952c9d1787f52ff6d5f3484d0b4df8952787c087edf6a1f7c2cb1ea88148'], + }), + ('traitlets', '5.2.0', { + 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + }), + ('parso', '0.8.3', { + 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], + }), + ('jedi', '0.18.1', { + 'checksums': ['74137626a64a99c8eb6ae5832d99b3bdd7d29a3850fe2aa80a4126b2a7d949ab'], + }), + ('testpath', '0.6.0', { + 'checksums': ['2f1b97e6442c02681ebe01bd84f531028a7caea1af3825000f52345c30285e0f'], + }), + ('Send2Trash', '1.8.0', { + 'checksums': ['d2c24762fd3759860a0aff155e45871447ea58d2be6bdd39b5c8f966a0c99c2d'], + }), + ('bleach', '5.0.1', { + 'checksums': ['0d03255c47eb9bd2f26aa9bb7f2107732e7e8fe195ca2f64709fcf3b0a4a085c'], + }), + ('pandocfilters', '1.5.0', { + 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], + }), + ('pyzmq', '23.2.1', { + 'modulename': 'zmq', + 'checksums': ['2b381aa867ece7d0a82f30a0c7f3d4387b7cf2e0697e33efaa5bed6c5784abcd'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('jupyter_core', '4.10.0', { + 'checksums': ['a6de44b16b7b31d7271130c71a6792c4040f077011961138afed5e5e73181aec'], + }), + ('fastjsonschema', '2.16.1', { + 'checksums': ['d6fa3ffbe719768d70e298b9fb847484e2bdfdb7241ed052b8d57a9294a8c334'], + }), + ('nbformat', '5.4.0', { + 'checksums': ['44ba5ca6acb80c5d5a500f1e5b83ede8cbe364d5a495c4c8cf60aaf1ba656501'], + }), + ('mistune', '0.8.1', { + 'checksums': ['4c0f66924ce28f03b95b210ea57e57bd0b59f479edd91c2fa4fe59331eae4a82'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('nest_asyncio', '1.5.5', { + 'checksums': ['e442291cd942698be619823a17a86a5759eabe1f8613084790de189fe9e16d65'], + }), + ('nbclient', '0.6.3', { + 'checksums': ['b80726fc1fb89a0e8f8be1e77e28d0026b1e8ed90bc143c8a0c7622e4f8cdd9e'], + }), + ('tinycss2', '1.1.1', { + 'checksums': ['b2e44dd8883c360c35dd0d1b5aad0b610e5156c2cb3b33434634e539ead9d8bf'], + }), + ('nbconvert', '6.5.3', { + 'checksums': ['10ed693c4cfd3c63583c87ca5c3a2f6ed874145103595f3824efcc8dfcb7522c'], + }), + ('tornado', '6.2', { + 'checksums': ['9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13'], + }), + ('terminado', '0.13.0', { + 'checksums': ['713531ccb5db7d4f544651f14050da79809030f00d1afa21462088cf32fb143a'], + }), + ('jupyter_client', '7.3.1', { + 'checksums': ['05d4ff6a0ade25138c6bb0fbeac7ddc26b5fe835e7dd816b64b4a45b931bdc0b'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('executing', '1.0.0', { + 'checksums': ['98daefa9d1916a4f0d944880d5aeaf079e05585689bebd9ff9b32e31dd5e1017'], + }), + ('asttokens', '2.0.8', { + 'checksums': ['c61e16246ecfb2cde2958406b4c8ebc043c9e6d73aaa83c941673b35e5d3a76b'], + }), + ('pure_eval', '0.2.2', { + 'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3'], + }), + ('stack_data', '0.5.0', { + 'checksums': ['715c8855fbf5c43587b141e46cc9d9339cc0d1f8d6e0f98ed0d01c6cb974e29f'], + }), + ('ipykernel', '6.13.0', { + 'checksums': ['0e28273e290858393e86e152b104e5506a79c13d25b951ac6eca220051b4be60'], + }), + ('prometheus_client', '0.11.0', { + 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], + }), + ('ipywidgets', '7.6.3', { + 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.0', { + 'checksums': ['b27455d60adc93a7baa2e0b8f386be81b932bb4e3c0116046df9ed230cd3faac'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('jupyterlab_widgets', '3.0.3', { + 'checksums': ['c767181399b4ca8b647befe2d913b1260f51bf9d8ef9b7a14632d4c1a7b536bd'], + }), + ('argon2-cffi', '20.1.0', { + 'modulename': 'argon2', + 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], + }), + ('notebook', '6.4.0', { + 'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + ('matplotlib-inline', '0.1.2', { + 'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'], + }), + ('debugpy', '1.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['84ff51b8b5c847d5421324ca419db1eec813a4dd2bbf19dbbbe132e2ab2b2fc6'], + }), +] + +modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/IPython', + 'share/jupyter' + ], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb index a5ba7921650..6adf35be8ad 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ ('IPython', '8.5.0'), ('Mako', '1.2.0'), ('configurable-http-proxy', '4.5.3'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] sanity_pip_check = True diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e62a803500d --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0563e14c45a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + 'OpenPGM-5.2.122-pkgconfig_includes.patch', + 'OpenPGM-5.2.122-python3-compliant.patch' +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0d05aef4ded --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.4' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.38'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = '--with-pic --with-pgm --with-libsodium --disable-Werror' + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From 225d7439f8e487e6461c3e1e405a2c79f36e4e38 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 17 Oct 2022 18:59:54 +0200 Subject: [PATCH 5152/9987] Delete IPython-8.5.0-GCCcore-11.3.0.eb --- .../i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb | 180 ------------------ 1 file changed, 180 deletions(-) delete mode 100644 easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb deleted file mode 100644 index 4697bcfaf93..00000000000 --- a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb +++ /dev/null @@ -1,180 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'IPython' -version = '8.5.0' - -homepage = 'https://ipython.org/index.html' -description = """IPython provides a rich architecture for interactive computing with: - Powerful interactive shells (terminal and Qt-based). - A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. - Support for interactive data visualization and use of GUI toolkits. - Flexible, embeddable interpreters to load into your own projects. - Easy to use, high performance tools for parallel computing.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -builddependencies = [('binutils', '2.38')] - -dependencies = [ - ('Python', '3.10.4'), - ('ZeroMQ', '4.3.4'), - ('lxml', '4.9.1'), - ('BeautifulSoup', '4.10.0'), -] - -use_pip = True - -exts_list = [ - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('ipython', version, { - 'modulename': 'IPython', - 'checksums': ['097bdf5cd87576fd066179c9f7f208004f7a6864ee1b20f37d346c0bcb099f84'], - }), - ('pickleshare', '0.7.5', { - 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], - }), - ('prompt_toolkit', '3.0.31', { - 'checksums': ['9ada952c9d1787f52ff6d5f3484d0b4df8952787c087edf6a1f7c2cb1ea88148'], - }), - ('traitlets', '5.2.0', { - 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], - }), - ('parso', '0.8.3', { - 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], - }), - ('jedi', '0.18.1', { - 'checksums': ['74137626a64a99c8eb6ae5832d99b3bdd7d29a3850fe2aa80a4126b2a7d949ab'], - }), - ('testpath', '0.6.0', { - 'checksums': ['2f1b97e6442c02681ebe01bd84f531028a7caea1af3825000f52345c30285e0f'], - }), - ('Send2Trash', '1.8.0', { - 'checksums': ['d2c24762fd3759860a0aff155e45871447ea58d2be6bdd39b5c8f966a0c99c2d'], - }), - ('bleach', '5.0.1', { - 'checksums': ['0d03255c47eb9bd2f26aa9bb7f2107732e7e8fe195ca2f64709fcf3b0a4a085c'], - }), - ('pandocfilters', '1.5.0', { - 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], - }), - ('pyzmq', '23.2.1', { - 'modulename': 'zmq', - 'checksums': ['2b381aa867ece7d0a82f30a0c7f3d4387b7cf2e0697e33efaa5bed6c5784abcd'], - }), - ('entrypoints', '0.4', { - 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], - }), - ('jupyter_core', '4.10.0', { - 'checksums': ['a6de44b16b7b31d7271130c71a6792c4040f077011961138afed5e5e73181aec'], - }), - ('fastjsonschema', '2.16.1', { - 'checksums': ['d6fa3ffbe719768d70e298b9fb847484e2bdfdb7241ed052b8d57a9294a8c334'], - }), - ('nbformat', '5.4.0', { - 'checksums': ['44ba5ca6acb80c5d5a500f1e5b83ede8cbe364d5a495c4c8cf60aaf1ba656501'], - }), - ('mistune', '0.8.1', { - 'checksums': ['4c0f66924ce28f03b95b210ea57e57bd0b59f479edd91c2fa4fe59331eae4a82'], - }), - ('defusedxml', '0.7.1', { - 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], - }), - ('async_generator', '1.10', { - 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], - }), - ('nest_asyncio', '1.5.5', { - 'checksums': ['e442291cd942698be619823a17a86a5759eabe1f8613084790de189fe9e16d65'], - }), - ('nbclient', '0.6.3', { - 'checksums': ['b80726fc1fb89a0e8f8be1e77e28d0026b1e8ed90bc143c8a0c7622e4f8cdd9e'], - }), - ('tinycss2', '1.1.1', { - 'checksums': ['b2e44dd8883c360c35dd0d1b5aad0b610e5156c2cb3b33434634e539ead9d8bf'], - }), - ('nbconvert', '6.5.3', { - 'checksums': ['10ed693c4cfd3c63583c87ca5c3a2f6ed874145103595f3824efcc8dfcb7522c'], - }), - ('tornado', '6.2', { - 'checksums': ['9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13'], - }), - ('terminado', '0.13.0', { - 'checksums': ['713531ccb5db7d4f544651f14050da79809030f00d1afa21462088cf32fb143a'], - }), - ('jupyter_client', '7.3.1', { - 'checksums': ['05d4ff6a0ade25138c6bb0fbeac7ddc26b5fe835e7dd816b64b4a45b931bdc0b'], - }), - ('backcall', '0.2.0', { - 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], - }), - ('executing', '1.0.0', { - 'checksums': ['98daefa9d1916a4f0d944880d5aeaf079e05585689bebd9ff9b32e31dd5e1017'], - }), - ('asttokens', '2.0.8', { - 'checksums': ['c61e16246ecfb2cde2958406b4c8ebc043c9e6d73aaa83c941673b35e5d3a76b'], - }), - ('pure_eval', '0.2.2', { - 'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3'], - }), - ('stack_data', '0.5.0', { - 'checksums': ['715c8855fbf5c43587b141e46cc9d9339cc0d1f8d6e0f98ed0d01c6cb974e29f'], - }), - ('ipykernel', '6.13.0', { - 'checksums': ['0e28273e290858393e86e152b104e5506a79c13d25b951ac6eca220051b4be60'], - }), - ('prometheus_client', '0.11.0', { - 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], - }), - ('ipywidgets', '7.6.3', { - 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], - }), - ('deprecation', '2.1.0', { - 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], - }), - ('jupyter_packaging', '0.12.0', { - 'checksums': ['b27455d60adc93a7baa2e0b8f386be81b932bb4e3c0116046df9ed230cd3faac'], - }), - ('jupyterlab_pygments', '0.1.2', { - 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], - }), - ('jupyterlab_widgets', '3.0.3', { - 'checksums': ['c767181399b4ca8b647befe2d913b1260f51bf9d8ef9b7a14632d4c1a7b536bd'], - }), - ('argon2-cffi', '20.1.0', { - 'modulename': 'argon2', - 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], - }), - ('notebook', '6.4.0', { - 'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'], - }), - ('widgetsnbextension', '3.5.1', { - 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], - }), - ('matplotlib-inline', '0.1.2', { - 'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'], - }), - ('debugpy', '1.4.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - 'checksums': ['84ff51b8b5c847d5421324ca419db1eec813a4dd2bbf19dbbbe132e2ab2b2fc6'], - }), -] - -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} - -sanity_check_paths = { - 'files': ['bin/ipython'], - 'dirs': [ - 'lib/python%(pyshortver)s/site-packages/IPython', - 'share/jupyter' - ], -} - -sanity_check_commands = [ - "ipython -h", - "jupyter notebook --help", -] - -sanity_pip_check = True - -moduleclass = 'tools' From b0c9df6d6da3940efbc2c5a9eeac9bd514c9b4a9 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 17 Oct 2022 19:00:03 +0200 Subject: [PATCH 5153/9987] Delete libsodium-1.0.18-GCCcore-11.3.0.eb --- .../libsodium-1.0.18-GCCcore-11.3.0.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb deleted file mode 100644 index e62a803500d..00000000000 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libsodium' -version = '1.0.18' - -homepage = 'https://doc.libsodium.org/' - -description = """ - Sodium is a modern, easy-to-use software library for encryption, decryption, - signatures, password hashing and more. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = [ - 'https://download.libsodium.org/libsodium/releases/', - 'https://download.libsodium.org/libsodium/releases/old/', - 'https://download.libsodium.org/libsodium/releases/old/unsupported/', -] -sources = [SOURCE_TAR_GZ] -checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] - -builddependencies = [ - ('binutils', '2.38'), -] - -sanity_check_paths = { - 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], - 'dirs': ['include/sodium', 'lib/pkgconfig'], -} - -moduleclass = 'lib' From b561425a510605db73ada66ae5e44ccf5980b5e0 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 17 Oct 2022 19:00:10 +0200 Subject: [PATCH 5154/9987] Delete OpenPGM-5.2.122-GCCcore-11.3.0.eb --- .../OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb deleted file mode 100644 index 0563e14c45a..00000000000 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OpenPGM' -version = '5.2.122' - -homepage = 'https://code.google.com/p/openpgm/' - -description = """ - OpenPGM is an open source implementation of the Pragmatic General Multicast - (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable - and scalable multicast protocol that enables receivers to detect loss, request - retransmission of lost data, or notify an application of unrecoverable loss. - PGM is a receiver-reliable protocol, which means the receiver is responsible - for ensuring all data is received, absolving the sender of reception - responsibility. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] -sources = ['libpgm-%(version)s.tar.gz'] -patches = [ - 'OpenPGM-5.2.122-pkgconfig_includes.patch', - 'OpenPGM-5.2.122-python3-compliant.patch' -] -checksums = [ - '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz - '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch - 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch -] - -builddependencies = [ - ('binutils', '2.38'), - ('Python', '3.10.4'), -] - -start_dir = 'pgm' - -sanity_check_paths = { - 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], - 'dirs': ['include'], -} - -moduleclass = 'system' From a03bf7e3a25b0cc42dd9a65e3b1d6f2f24819e30 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 17 Oct 2022 19:00:17 +0200 Subject: [PATCH 5155/9987] Delete ZeroMQ-4.3.4-GCCcore-11.3.0.eb --- .../z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb deleted file mode 100644 index 0d05aef4ded..00000000000 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ZeroMQ' -version = '4.3.4' - -homepage = 'https://www.zeromq.org/' -description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. - It gives you sockets that carry atomic messages across various transports like in-process, - inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, - pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered - products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous - message-processing tasks. It has a score of language APIs and runs on most operating systems.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] - -builddependencies = [ - ('binutils', '2.38'), - ('pkgconf', '1.8.0'), -] - -dependencies = [ - ('OpenPGM', '5.2.122'), - ('libsodium', '1.0.18'), - ('util-linux', '2.38'), -] - -# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 -# Needto disable warnings as errors. -configopts = '--with-pic --with-pgm --with-libsodium --disable-Werror' - -sanity_check_paths = { - 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], - 'dirs': ['include', 'lib'], -} - -moduleclass = 'devel' From 2f5a689abdfa247175985cfd772d13aa18a45838 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Oct 2022 19:27:02 +0200 Subject: [PATCH 5156/9987] Add jupyter-server-proxy to this PR --- .../a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb | 57 ++++++ .../i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb | 180 ++++++++++++++++++ ...pyter-server-proxy-3.2.2-GCCcore-11.3.0.eb | 54 ++++++ .../libsodium-1.0.18-GCCcore-11.3.0.eb | 33 ++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb | 45 +++++ .../z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb | 40 ++++ 6 files changed, 409 insertions(+) create mode 100644 easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2765106fe4f --- /dev/null +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'aiohttp' +version = '3.8.3' + +homepage = 'https://github.com/aio-libs/aiohttp' +description = "Asynchronous HTTP client/server framework for asyncio and Python." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +# aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies +exts_list = [ + ('multidict', '6.0.2', { + 'checksums': ['5ff3bd75f38e4c43f1f470f2df7a4d430b821c4ce22be384e1459cb57d6bb013'], + }), + ('async-timeout', '4.0.2', { + 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], + }), + ('yarl', '1.8.1', { + 'checksums': ['af887845b8c2e060eb5605ff72b6f2dd2aab7a761379373fd89d314f4752abbf'], + }), + ('frozenlist', '1.3.1', { + 'checksums': ['3a735e4211a04ccfa3f4833547acdf5d2f863bfeb01cfd3edaffbc251f15cec8'], + }), + ('aiosignal', '1.2.0', { + 'checksums': ['78ed67db6c7b7ced4f98e495e572106d5c432a93e1ddd1bf475e1dc05f5b7df2'], + }), + (name, version, { + 'checksums': ['3828fb41b7203176b82fe5d699e0d845435f2374750a44b480ea6b930f6be269'], + }), + ('aiohttp-jinja2', '1.5', { + 'checksums': ['7c3ba5eac060b691f4e50534af2d79fca2a75712ebd2b25e6fcb1295859f910b'], + }), + ('hiredis', '2.0.0', { + 'checksums': ['81d6d8e39695f2c37954d1011c0480ef7cf444d4e3ae24bc5e89ee5de360139a'], + }), + ('aioredis', '2.0.1', { + 'checksums': ['eaa51aaf993f2d71f54b70527c440437ba65340588afeb786cd87c55c89cd98e'], + }), + ('aiosignal', '1.2.0', { + 'checksums': ['78ed67db6c7b7ced4f98e495e572106d5c432a93e1ddd1bf475e1dc05f5b7df2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4697bcfaf93 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,180 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '8.5.0' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('ZeroMQ', '4.3.4'), + ('lxml', '4.9.1'), + ('BeautifulSoup', '4.10.0'), +] + +use_pip = True + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['097bdf5cd87576fd066179c9f7f208004f7a6864ee1b20f37d346c0bcb099f84'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '3.0.31', { + 'checksums': ['9ada952c9d1787f52ff6d5f3484d0b4df8952787c087edf6a1f7c2cb1ea88148'], + }), + ('traitlets', '5.2.0', { + 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + }), + ('parso', '0.8.3', { + 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], + }), + ('jedi', '0.18.1', { + 'checksums': ['74137626a64a99c8eb6ae5832d99b3bdd7d29a3850fe2aa80a4126b2a7d949ab'], + }), + ('testpath', '0.6.0', { + 'checksums': ['2f1b97e6442c02681ebe01bd84f531028a7caea1af3825000f52345c30285e0f'], + }), + ('Send2Trash', '1.8.0', { + 'checksums': ['d2c24762fd3759860a0aff155e45871447ea58d2be6bdd39b5c8f966a0c99c2d'], + }), + ('bleach', '5.0.1', { + 'checksums': ['0d03255c47eb9bd2f26aa9bb7f2107732e7e8fe195ca2f64709fcf3b0a4a085c'], + }), + ('pandocfilters', '1.5.0', { + 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], + }), + ('pyzmq', '23.2.1', { + 'modulename': 'zmq', + 'checksums': ['2b381aa867ece7d0a82f30a0c7f3d4387b7cf2e0697e33efaa5bed6c5784abcd'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('jupyter_core', '4.10.0', { + 'checksums': ['a6de44b16b7b31d7271130c71a6792c4040f077011961138afed5e5e73181aec'], + }), + ('fastjsonschema', '2.16.1', { + 'checksums': ['d6fa3ffbe719768d70e298b9fb847484e2bdfdb7241ed052b8d57a9294a8c334'], + }), + ('nbformat', '5.4.0', { + 'checksums': ['44ba5ca6acb80c5d5a500f1e5b83ede8cbe364d5a495c4c8cf60aaf1ba656501'], + }), + ('mistune', '0.8.1', { + 'checksums': ['4c0f66924ce28f03b95b210ea57e57bd0b59f479edd91c2fa4fe59331eae4a82'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('nest_asyncio', '1.5.5', { + 'checksums': ['e442291cd942698be619823a17a86a5759eabe1f8613084790de189fe9e16d65'], + }), + ('nbclient', '0.6.3', { + 'checksums': ['b80726fc1fb89a0e8f8be1e77e28d0026b1e8ed90bc143c8a0c7622e4f8cdd9e'], + }), + ('tinycss2', '1.1.1', { + 'checksums': ['b2e44dd8883c360c35dd0d1b5aad0b610e5156c2cb3b33434634e539ead9d8bf'], + }), + ('nbconvert', '6.5.3', { + 'checksums': ['10ed693c4cfd3c63583c87ca5c3a2f6ed874145103595f3824efcc8dfcb7522c'], + }), + ('tornado', '6.2', { + 'checksums': ['9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13'], + }), + ('terminado', '0.13.0', { + 'checksums': ['713531ccb5db7d4f544651f14050da79809030f00d1afa21462088cf32fb143a'], + }), + ('jupyter_client', '7.3.1', { + 'checksums': ['05d4ff6a0ade25138c6bb0fbeac7ddc26b5fe835e7dd816b64b4a45b931bdc0b'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('executing', '1.0.0', { + 'checksums': ['98daefa9d1916a4f0d944880d5aeaf079e05585689bebd9ff9b32e31dd5e1017'], + }), + ('asttokens', '2.0.8', { + 'checksums': ['c61e16246ecfb2cde2958406b4c8ebc043c9e6d73aaa83c941673b35e5d3a76b'], + }), + ('pure_eval', '0.2.2', { + 'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3'], + }), + ('stack_data', '0.5.0', { + 'checksums': ['715c8855fbf5c43587b141e46cc9d9339cc0d1f8d6e0f98ed0d01c6cb974e29f'], + }), + ('ipykernel', '6.13.0', { + 'checksums': ['0e28273e290858393e86e152b104e5506a79c13d25b951ac6eca220051b4be60'], + }), + ('prometheus_client', '0.11.0', { + 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], + }), + ('ipywidgets', '7.6.3', { + 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.0', { + 'checksums': ['b27455d60adc93a7baa2e0b8f386be81b932bb4e3c0116046df9ed230cd3faac'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('jupyterlab_widgets', '3.0.3', { + 'checksums': ['c767181399b4ca8b647befe2d913b1260f51bf9d8ef9b7a14632d4c1a7b536bd'], + }), + ('argon2-cffi', '20.1.0', { + 'modulename': 'argon2', + 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], + }), + ('notebook', '6.4.0', { + 'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + ('matplotlib-inline', '0.1.2', { + 'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'], + }), + ('debugpy', '1.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['84ff51b8b5c847d5421324ca419db1eec813a4dd2bbf19dbbbe132e2ab2b2fc6'], + }), +] + +modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/IPython', + 'share/jupyter' + ], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a530e4aa23a --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server-proxy' +version = '3.2.2' + +homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' +description = """Jupyter Server Proxy lets you run arbitrary external processes +(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) +alongside your notebook server and provide authenticated web access to them +using a path like /rstudio next to others like /lab. Alongside the python +package that provides the main functionality, the JupyterLab extension +(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window +to get to RStudio for example.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('JupyterHub', '3.0.0'), + ('OpenSSL', '1.1', '', SYSTEM), + ('aiohttp', '3.8.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('websocket-client', '1.4.1', { + 'modulename': 'websocket', + 'checksums': ['f9611eb65c8241a67fb373bef040b3cf8ad377a9f6546a12b620b6511e8ea9ef'], + }), + ('jupyter-server', '1.21.0', { + 'source_tmpl': 'jupyter_server-%(version)s.tar.gz', + 'checksums': ['d0adca19913a3763359be7f0b8c2ea8bfde356f4b8edd8e3149d7d0fbfaa248b'], + }), + ('simpervisor', '0.4', { + 'checksums': ['cec79e13cdbd6edb04a5c98c1ff8d4bd9713e706c069226909a1ef0e89d393c5'], + }), + (name, version, { + 'checksums': ['54690ea9467035d187c930c599e76065017baf16e118e6eebae0d3a008c4d946'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e62a803500d --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0563e14c45a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + 'OpenPGM-5.2.122-pkgconfig_includes.patch', + 'OpenPGM-5.2.122-python3-compliant.patch' +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0d05aef4ded --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.4' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.38'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = '--with-pic --with-pgm --with-libsodium --disable-Werror' + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From 5684611d9b9e14ed541eb0b8bbefb27e93db75bc Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Oct 2022 22:27:56 +0200 Subject: [PATCH 5157/9987] Removed duplicate sanity_pip_check in JupyterHub easyconfig. Add jupyter-resource-usage. --- ...ter-resource-usage-0.6.3-GCCcore-11.3.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4df869c2369 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-resource-usage' +version = '0.6.3' + +homepage = 'https://github.com/jupyter-server/jupyter-resource-usage' +description = """Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), +] + +use_pip = True + +exts_list = [ + ('websocket-client', '1.4.1', { + 'modulename': 'websocket', + 'checksums': ['f9611eb65c8241a67fb373bef040b3cf8ad377a9f6546a12b620b6511e8ea9ef'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('jupyter_server', '1.21.0', { + 'checksums': ['d0adca19913a3763359be7f0b8c2ea8bfde356f4b8edd8e3149d7d0fbfaa248b'], + }), + (name, version, { + 'checksums': ['230faa15c19a8aa0456028c327c9c00759d2ef5713096ee3a0eb82c85be8d9c2'], + }), +] + +# Add the notebook extension to the search path for jupyter notebooks +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter/', +} + +sanity_check_paths = { + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/jupyter_resource_usage', + 'lib/python%(pyshortver)s/site-packages/jupyter_server' + ], + 'files': ['bin/jupyter-server'], +} + +sanity_pip_check = True + +moduleclass = 'tools' From 3f8a3ed2c5682ded3f1e804ea0ccc11534bcc906 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Oct 2022 22:31:10 +0200 Subject: [PATCH 5158/9987] increase max. number of failing LAPACK tests with numerical error a bit more to 150 for recent OpenBLAS easyconfigs --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 545706a97b2..93e65aa9221 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -39,7 +39,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 100 +max_failing_lapack_tests_num_errors = 150 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index e60362e973a..866cd7de515 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -36,7 +36,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 100 +max_failing_lapack_tests_num_errors = 150 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index 1bcda13c08c..c654f92e700 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 100 +max_failing_lapack_tests_num_errors = 150 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 29dff20315a..bb82984319e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -34,7 +34,7 @@ builddependencies = [ ] run_lapack_tests = True -max_failing_lapack_tests_num_errors = 100 +max_failing_lapack_tests_num_errors = 150 # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' From 3b7a55c5c9e335990a119bd650c73045d37d6965 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Oct 2022 22:55:01 +0200 Subject: [PATCH 5159/9987] Create separate jupyter-server bundle, and use that as a common dep between jupyterlmod, jupyter-resource-usage and jupyter-server-proxy --- .../JupyterHub-3.0.0-GCCcore-11.3.0.eb | 1 - ...ter-resource-usage-0.6.3-GCCcore-11.3.0.eb | 14 +------ ...pyter-server-proxy-3.2.2-GCCcore-11.3.0.eb | 15 +------ .../jupyter-server-1.21.0-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ .../jupyterlmod-3.0.0-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ 5 files changed, 86 insertions(+), 28 deletions(-) create mode 100644 easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb index 6adf35be8ad..1406f7d6fa6 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb @@ -21,7 +21,6 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] -sanity_pip_check = True use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb index 4df869c2369..68cf4e31593 100644 --- a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb @@ -15,24 +15,12 @@ builddependencies = [ dependencies = [ ('Python', '3.10.4'), ('IPython', '8.5.0'), + ('jupyter-server', '1.21.0'), ] use_pip = True exts_list = [ - ('websocket-client', '1.4.1', { - 'modulename': 'websocket', - 'checksums': ['f9611eb65c8241a67fb373bef040b3cf8ad377a9f6546a12b620b6511e8ea9ef'], - }), - ('sniffio', '1.3.0', { - 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], - }), - ('anyio', '3.6.1', { - 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], - }), - ('jupyter_server', '1.21.0', { - 'checksums': ['d0adca19913a3763359be7f0b8c2ea8bfde356f4b8edd8e3149d7d0fbfaa248b'], - }), (name, version, { 'checksums': ['230faa15c19a8aa0456028c327c9c00759d2ef5713096ee3a0eb82c85be8d9c2'], }), diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb index a530e4aa23a..648b76a2e90 100644 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb @@ -23,26 +23,13 @@ dependencies = [ ('JupyterHub', '3.0.0'), ('OpenSSL', '1.1', '', SYSTEM), ('aiohttp', '3.8.3'), + ('jupyter-server', '1.21.0'), ] sanity_pip_check = True use_pip = True exts_list = [ - ('sniffio', '1.3.0', { - 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], - }), - ('anyio', '3.6.1', { - 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], - }), - ('websocket-client', '1.4.1', { - 'modulename': 'websocket', - 'checksums': ['f9611eb65c8241a67fb373bef040b3cf8ad377a9f6546a12b620b6511e8ea9ef'], - }), - ('jupyter-server', '1.21.0', { - 'source_tmpl': 'jupyter_server-%(version)s.tar.gz', - 'checksums': ['d0adca19913a3763359be7f0b8c2ea8bfde356f4b8edd8e3149d7d0fbfaa248b'], - }), ('simpervisor', '0.4', { 'checksums': ['cec79e13cdbd6edb04a5c98c1ff8d4bd9713e706c069226909a1ef0e89d393c5'], }), diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f44e22d0b9f --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = '1.21.0' + +homepage = 'https://github.com/jupyter-server/jupyter-server' +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +use_pip = True + +exts_list = [ + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('websocket-client', '1.4.1', { + 'modulename': 'websocket', + 'checksums': ['f9611eb65c8241a67fb373bef040b3cf8ad377a9f6546a12b620b6511e8ea9ef'], + }), + (name, version, { + 'source_tmpl': 'jupyter_server-%(version)s.tar.gz', + 'checksums': ['d0adca19913a3763359be7f0b8c2ea8bfde356f4b8edd8e3149d7d0fbfaa248b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c7917ccd912 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'jupyterlmod' +version = '3.0.0' + +homepage = 'https://pypi.org/project/jupyterlmod/' +description = """Jupyter interactive notebook server extension that allows user to select software modules + to load with Lmod before launching kernels.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +#source_urls = [PYPI_SOURCE] +#sources = [SOURCE_TAR_GZ] +#checksums = ['da769078650766b1fca6ef1e673d15ddd6ce7428001e05cc364cba246a77c3fe'] + +dependencies = [ + ('Python', '3.10.4'), + ('JupyterHub', '3.0.0'), + ('jupyter-server', '1.21.0'), +] + +use_pip = True + +exts_list = [ + ('jupyter_server', '1.21.0'), + (name, version), +] + +# Add the notebook extension to the search path for jupyter notebooks +# +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter/', +} + +sanity_check_paths = { + 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterlmod'], + 'files': [], +} + +sanity_pip_check = True + +moduleclass = 'tools' From e03a46b12ee0f7ea3933b6eb6a523e860432482a Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 17 Oct 2022 23:07:02 +0200 Subject: [PATCH 5160/9987] Forgot to remove the jupyter-server sanity check path from jupyter-resource-usage. Did that now --- .../jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb index 68cf4e31593..3de71514e8c 100644 --- a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.3-GCCcore-11.3.0.eb @@ -34,9 +34,8 @@ modextrapaths = { sanity_check_paths = { 'dirs': [ 'lib/python%(pyshortver)s/site-packages/jupyter_resource_usage', - 'lib/python%(pyshortver)s/site-packages/jupyter_server' ], - 'files': ['bin/jupyter-server'], + 'files': [], } sanity_pip_check = True From 14e91fc4df7d2d9dc7f286b1c514492b8a3b9032 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 18 Oct 2022 09:41:25 +0200 Subject: [PATCH 5161/9987] tfds to pypi version Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 667bb710d9e..60233e3f9ff 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -44,11 +44,8 @@ exts_list = [ 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], }), (name, version, { - 'download_filename': 'v(%version)s.tar.gz', - 'filename': '%(name)s-v(%version)s.tar.gz', - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/datasets/archive'], - 'checksums': ['ed7c3b959d10ba762137e18b93631ab42f4ed0915bc3d9ce98ee66eef9c61418'], + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'checksums': ['590faf3763bc14757906b36c718389eeded533ee8ae4d030ede140db86aca4cd'], }), ] From 367f739096267f6f81fee2e1ab0fac847d124aae Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 18 Oct 2022 09:41:53 +0200 Subject: [PATCH 5162/9987] Update easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 60233e3f9ff..08ec6bcebe1 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -16,7 +16,7 @@ dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('tqdm', '4.61.2'), - ('TensorFlow', '2.6.0', '-CUDA-%(cudaver)s'), + ('TensorFlow', '2.6.0', versionsuffix), ] sanity_pip_check = True From a80dadb4d8639b292ac7ce2c8759b1f7733432c0 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 18 Oct 2022 10:27:03 +0200 Subject: [PATCH 5163/9987] Remove url specification for tf metadata Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 08ec6bcebe1..4242b5cd1ae 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -32,12 +32,6 @@ exts_list = [ }), ('tensorflow-metadata', '1.10.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'source_urls': [( - 'https://files.pythonhosted.org/packages/3a/86/' - + '2b3251bb560068f31817d9b678588098e28f396c1f6b88c57cf5d28670af/' - + 'tensorflow_metadata-1.10.0-py3-none-any.whl' - + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3' - )], 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], }), ('etils', '0.8.0', { From d69075a34a59a510476dd9429101e80c73691c67 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Tue, 18 Oct 2022 10:28:04 +0200 Subject: [PATCH 5164/9987] adding easyconfigs: ruffus-2.8.4-foss-2021b.eb --- .../r/ruffus/ruffus-2.8.4-foss-2021b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb new file mode 100644 index 00000000000..f2046029233 --- /dev/null +++ b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'ruffus' +version = '2.8.4' + +homepage = 'http://www.ruffus.org.uk/' +description = "Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics." + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'] + +dependencies = [ + ('Python', '3.9.6'), + ('Graphviz', '2.50.0'), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'import ruffus'", + "python -c 'import ruffus.graph'", +] + +moduleclass = 'vis' From f3a5278b2a9275e8472964e5b6915046eae67ea4 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 18 Oct 2022 10:36:25 +0200 Subject: [PATCH 5165/9987] Add checksum to jupyterlmod and remove unnecessary comment. Shorten line in jupyter-server. Add binutils to jupyterlmod as builddep. --- .../jupyter-server-1.21.0-GCCcore-11.3.0.eb | 3 ++- .../jupyterlmod-3.0.0-GCCcore-11.3.0.eb | 15 +++++++++------ 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb index f44e22d0b9f..4c395ad4b1c 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb @@ -4,7 +4,8 @@ name = 'jupyter-server' version = '1.21.0' homepage = 'https://github.com/jupyter-server/jupyter-server' -description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila.""" +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) +for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb index c7917ccd912..8ddf17c5047 100644 --- a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb @@ -9,9 +9,9 @@ description = """Jupyter interactive notebook server extension that allows user toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -#source_urls = [PYPI_SOURCE] -#sources = [SOURCE_TAR_GZ] -#checksums = ['da769078650766b1fca6ef1e673d15ddd6ce7428001e05cc364cba246a77c3fe'] +builddependencies = [ + ('binutils', '2.38'), +] dependencies = [ ('Python', '3.10.4'), @@ -22,12 +22,15 @@ dependencies = [ use_pip = True exts_list = [ - ('jupyter_server', '1.21.0'), - (name, version), + ('jupyter_server', '1.21.0', { + 'checksums': ['d0adca19913a3763359be7f0b8c2ea8bfde356f4b8edd8e3149d7d0fbfaa248b'], + }), + (name, version, { + 'checksums': ['da769078650766b1fca6ef1e673d15ddd6ce7428001e05cc364cba246a77c3fe'], + }), ] # Add the notebook extension to the search path for jupyter notebooks -# modextrapaths = { 'JUPYTER_PATH': 'share/jupyter/', } From 4a164a0cac6a93664677ef3ebfbca0f0630eb2a1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 18 Oct 2022 11:33:16 +0100 Subject: [PATCH 5166/9987] update libxml2, libxslt sources to use gnome.org (#16419) --- .../l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb | 9 +++------ .../l/libxml2/libxml2-2.9.10-GCCcore-10.3.0.eb | 9 +++------ .../l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb | 9 +++------ .../l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb | 9 +++------ .../l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb | 9 +++------ .../easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.2.0.eb | 9 +++------ .../easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.3.0.eb | 9 +++------ .../easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-8.2.0.eb | 9 +++------ .../easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb | 9 +++------ .../l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb | 9 +++------ 17 files changed, 51 insertions(+), 102 deletions(-) diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb index 38a25e4b1a7..aeed9cfa941 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.3.0.eb index 8b050c1144f..d8f7f588096 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.3.0.eb @@ -14,12 +14,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb index c0fa3931030..4e4b321a783 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-11.2.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb index 5e7273f67e7..d256f11c658 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.2.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb index 53b484f969b..3669c4c6bca 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-9.3.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['593b7b751dd18c2d6abcd0c4bcb29efc203d0b4373a6df98e3a455ea74ae2813'] builddependencies = [('binutils', '2.34')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.2.0.eb index 8f28af864fe..a9f2c2e2125 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.2.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['dcca21d624bbbe094fcc104e1f15f2eacfb65aecd0e38ed220aeca56b62c81e2'] builddependencies = [('binutils', '2.29')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.3.0.eb index d85ba7444da..417881a12ed 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-7.3.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['dcca21d624bbbe094fcc104e1f15f2eacfb65aecd0e38ed220aeca56b62c81e2'] builddependencies = [('binutils', '2.30')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-8.2.0.eb index 9a02ed10f47..fc27adc85d2 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-8.2.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['dcca21d624bbbe094fcc104e1f15f2eacfb65aecd0e38ed220aeca56b62c81e2'] builddependencies = [('binutils', '2.31.1')] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb index 7f8f41a3902..e427981571a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.9-GCCcore-8.3.0.eb @@ -11,12 +11,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['94fb70890143e3c6549f265cee93ec064c80a84c42ad0f23e85ee1fd6540a871'] +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['58a5c05a2951f8b47656b676ce1017921a29f6b1419c45e3baed0d6435ba03f5'] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb index 9f2ba0ca1be..140e353a598 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['526ecd0abaf4a7789041622c3950c0e7f2c4c8835471515fd77eec684a355460'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b7da90eaa6b0dae9e9a3769e29a757342eef0edb9a7b431424814375414422af'] builddependencies = [('binutils', '2.30')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb index 0df6959430a..07d27c99af2 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['8e36605144409df979cab43d835002f63988f3dc94d5d3537c12796db90e38c8'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['3944d3a74b4ca6b40f59967e2a587abc6994f6935d697d9fa1b8edd722513e90'] builddependencies = [('binutils', '2.31.1')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb index d17aa440dc4..fc7feb6f53a 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb index 121392cf7dc..304d2938dcd 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb index 705654d4093..5cc9afc5c7f 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb index 49e57192bf3..14d3083a7bc 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb index 6097396bc50..edec6edc2cb 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb index f414649f8fe..33d3ef1c1a8 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb @@ -9,12 +9,9 @@ description = """Libxslt is the XSLT C library developed for the GNOME project toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -source_urls = [ - 'http://xmlsoft.org/sources/', - 'http://xmlsoft.org/sources/old/' -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['98b1bd46d6792925ad2dfe9a87452ea2adebf69dcb9919ffd55bf926a7f93f7f'] +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] builddependencies = [('binutils', '2.34')] From 8bc993e53c3199e287655db2cc92b1d773582762 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Oct 2022 12:40:30 +0200 Subject: [PATCH 5167/9987] adding easyconfigs: MIGRATE-N-5.0.4-foss-2021b.eb and patches: migrate-5.0.4_install.patch, migrate-5.0.4_locale.patch --- .../m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb | 41 +++++++++++++++++++ .../m/MIGRATE-N/migrate-5.0.4_install.patch | 14 +++++++ .../m/MIGRATE-N/migrate-5.0.4_locale.patch | 15 +++++++ 3 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb new file mode 100644 index 00000000000..5abedc1fb58 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'MIGRATE-N' +version = '5.0.4' + +homepage = 'https://peterbeerli.com/migrate-html5/index.html' +description = """ +Migrate estimates population parameters, effective population sizes +and migration rates of n populations, using genetic data. It +uses a coalescent theory approach taking into account history of +mutations and uncertainty of the genealogy. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ["https://peterbeerli.com/migrate-html5/download_version4"] +sources = ['migrate-%(version)s.src.tar.gz'] +patches = [ + 'migrate-%(version)s_install.patch', + 'migrate-%(version)s_locale.patch', +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-A4 "CC=$CC" STDCPLUS=-lstdc++' +prebuildopts = 'make mpis && make clean &&' +installopts = "&& make clean && make installmpi" + +parallel = 1 + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['migrate-n', 'migrate-n-mpi']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch new file mode 100644 index 00000000000..ba33af1af0a --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch @@ -0,0 +1,14 @@ +Create parent directories during install +Author: B. Hajgato +Updated: Orient Kružík (INUITS) +--- migrate-5.0.3_orig/src/configure 2021-11-08 22:48:21.000000000 +0100 ++++ migrate-5.0.3/src/configure 2022-05-09 17:15:29.368752420 +0200 +@@ -4104,7 +4104,7 @@ + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then +- ac_cv_path_install="$as_dir$ac_prog$ac_exec_ext -c" ++ ac_cv_path_install="$as_dir$ac_prog$ac_exec_ext -c -D" + break 3 + fi + fi \ No newline at end of file diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch new file mode 100644 index 00000000000..29cd65e5d99 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch @@ -0,0 +1,15 @@ +Don't use the xlocale.h header since it is an OS package and not always provided. +Author: R. van Dijk, 2018-03-07 +Updated by: Orient Kružík (INUITS) +--- migrate-5.0.3_orig/src/src/data.c 2022-04-03 00:11:20.000000000 +0200 ++++ migrate-5.0.3/src/src/data.c 2022-05-09 17:17:46.836503576 +0200 +@@ -53,9 +53,6 @@ + + #include + #include +-#ifndef WIN32 +-#include +-#endif + #include "migration.h" + #include "sighandler.h" + #include "tools.h" \ No newline at end of file From 330da15302a5eeb245d5e9617af746e8740f1c93 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Tue, 18 Oct 2022 13:02:23 +0200 Subject: [PATCH 5168/9987] Fixed style error --- .../easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb index 5abedc1fb58..624706433b6 100644 --- a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb @@ -17,8 +17,8 @@ toolchainopts = {'usempi': True} source_urls = ["https://peterbeerli.com/migrate-html5/download_version4"] sources = ['migrate-%(version)s.src.tar.gz'] patches = [ - 'migrate-%(version)s_install.patch', - 'migrate-%(version)s_locale.patch', + 'migrate-%(version)s_install.patch', + 'migrate-%(version)s_locale.patch', ] dependencies = [ From aa1bea027d51f4571b2e7fa42e690e479c8686d8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 18 Oct 2022 12:05:06 +0100 Subject: [PATCH 5169/9987] add sanity_check_paths to older libxslt easyconfigs --- .../easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb | 5 +++++ .../easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb index 140e353a598..7d24e0af0d1 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.32-GCCcore-7.3.0.eb @@ -20,4 +20,9 @@ dependencies = [ ('libxml2', '2.9.8'), ] +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb index 07d27c99af2..e1b9d08e742 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.33-GCCcore-8.2.0.eb @@ -20,4 +20,9 @@ dependencies = [ ('libxml2', '2.9.8'), ] +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + moduleclass = 'lib' From a8843f563495686c1edd706450e7e8f6e81b5821 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 14:30:20 +0200 Subject: [PATCH 5170/9987] fix patch for latest revision of source tarball of GULP 6.1 --- .../easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb | 4 ++-- .../GULP-6.1_fftw-blas-linking-gcc-11.patch | 23 +++++-------------- 2 files changed, 8 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb index 4a48ff9555c..707e2eb1bb0 100644 --- a/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GULP/GULP-6.1-foss-2021b.eb @@ -20,8 +20,8 @@ patches = [ 'GULP-6.1_fftw-blas-linking-gcc-11.patch', ] checksums = [ - '1b52fe2928ccf2cea5d2c3466162764d0de6b4d06e86fe292ab37859d6a0e6d6', # gulp-6.1.tgz - '156449c96a97ff24f6add83c10fd383f07c43c79420eebe3290387b65b34549b', # gulp-6.1_fftw-blas-linking-gcc-11.patch + {'gulp-6.1.tgz': '1b52fe2928ccf2cea5d2c3466162764d0de6b4d06e86fe292ab37859d6a0e6d6'}, + {'GULP-6.1_fftw-blas-linking-gcc-11.patch': 'd32babd56e859a9378548981a00b876a88b66e392cb532d33193b6e3362f7940'}, ] download_instructions = """Download requires registration, please see diff --git a/easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch b/easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch index 89f6cc6151d..a43f7ed0e14 100644 --- a/easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch +++ b/easybuild/easyconfigs/g/GULP/GULP-6.1_fftw-blas-linking-gcc-11.patch @@ -1,11 +1,9 @@ Removing hard-coded paths in the mkgulp file, which is creating the makefile Using the suggested compiler flags for gfortran-10 author: J. Sassmannshausen (Imperial College London/UK) -diff --git a/gulp-6.1.orig/Src/mkgulp b/gulp-6.1/Src/mkgulp -index 5a6ca20..a1fdb42 100755 ---- a/gulp-6.1.orig/Src/mkgulp -+++ b/gulp-6.1/Src/mkgulp -@@ -196,7 +196,7 @@ fi +--- gulp-6.1.orig/Src/mkgulp.orig 2022-10-14 05:14:21.541000000 +0200 ++++ gulp-6.1/Src/mkgulp 2022-10-18 13:18:12.812436767 +0200 +@@ -196,7 +196,7 @@ # Include file directories # #--USER--Start @@ -14,16 +12,7 @@ index 5a6ca20..a1fdb42 100755 #--USER--End # If using Macports then use the following instead #--USER--Start -@@ -230,7 +230,7 @@ case $compiler in - # On the Mac the following is sufficient when using Macports: - # echo 'MLIBS=-L/opt/local/lib/lapack/ -llapack -lblas ' >> makefile - # If using the accelerate framework then leave blank: -- echo 'MLIBS=' >> makefile -+ echo 'MLIBS=-L'${EBROOTFLEXIBLAS}'/lib -lflexiblas' >> makefile - # Or if optimised maths libraries are not available then: - # echo 'MLIBS=lapack.o blas.o' >> makefile - #--USER--End -@@ -238,7 +238,7 @@ case $compiler in +@@ -242,7 +242,7 @@ else # NB: For gfortran v10 then use these lines echo 'RUNF90=mpif90 -fallow-argument-mismatch ' >> makefile @@ -32,7 +21,7 @@ index 5a6ca20..a1fdb42 100755 # echo 'RUNF90=mpif90 ' >> makefile # echo 'RUNCC=mpif90 ' >> makefile # -@@ -247,14 +247,14 @@ case $compiler in +@@ -251,14 +251,14 @@ # On the Mac the following is sufficient when using Macports: # echo 'MLIBS=-L/opt/local/lib/lapack/ -llapack -lblas ' >> makefile # If using the accelerate framework then leave blank: @@ -49,7 +38,7 @@ index 5a6ca20..a1fdb42 100755 # echo 'SLIBS=-L/opt/local/lib -lscalapack ' >> makefile #--USER--End fi -@@ -363,11 +363,11 @@ else +@@ -371,11 +371,11 @@ echo 'FDEFS=-DFFTW3 ' >> makefile if [ "$parallel" = "" ] #--USER--Start From ad4dc970f99b7f12134b8ce2ddf5ba67e5cafaf0 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Tue, 18 Oct 2022 14:31:37 +0200 Subject: [PATCH 5171/9987] fixed sanity check, multi-line description and moduleclass --- .../easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb index f2046029233..122b155d477 100644 --- a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb @@ -4,7 +4,8 @@ name = 'ruffus' version = '2.8.4' homepage = 'http://www.ruffus.org.uk/' -description = "Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, and widely used in science and bioinformatics." +description = """Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, + and widely used in science and bioinformatics.""" toolchain = {'name': 'foss', 'version': '2021b'} @@ -17,11 +18,7 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True -sanity_check_commands = [ - "python -c 'import ruffus'", - "python -c 'import ruffus.graph'", -] +sanity_check_commands = ["python -c 'import ruffus.graph'"] -moduleclass = 'vis' +moduleclass = 'lib' From 42c98d8ed8c1f8943b455ef704ca5a4bad0bfd48 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 14:43:34 +0200 Subject: [PATCH 5172/9987] add --with-versioned-syms configure option for ncurses 6.3 with GCCcore/12.2 Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb index 7fed097a62f..6e0cca39d81 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3-GCCcore-12.2.0.eb @@ -20,7 +20,7 @@ checksums = ['97fc51ac2b085d4cde31ef4d2c3122c21abc217e9090a43a30fc5ec21684e059'] builddependencies = [('binutils', '2.39')] -local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " configopts = [ # build ncurses: serial build in default paths with shared libraries local_common_configopts, From 40ba6f2468269d23a348c2a5c47624fa1e793550 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 14:49:06 +0200 Subject: [PATCH 5173/9987] update to expat 2.4.9 + libreadline 8.2 as dependencies for Perl 5.36.0 with GCCcore/12.2.0 --- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb | 2 +- ....4.8-GCCcore-12.2.0.eb => expat-2.4.9-GCCcore-12.2.0.eb} | 5 +++-- ...-GCCcore-12.2.0.eb => libreadline-8.2-GCCcore-12.2.0.eb} | 4 ++-- easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 6 +++--- 4 files changed, 9 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/e/expat/{expat-2.4.8-GCCcore-12.2.0.eb => expat-2.4.9-GCCcore-12.2.0.eb} (90%) rename easybuild/easyconfigs/l/libreadline/{libreadline-8.1.2-GCCcore-12.2.0.eb => libreadline-8.2-GCCcore-12.2.0.eb} (92%) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb index 7bc947e2ae0..83b4de99325 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.2.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [('binutils', '2.39')] -dependencies = [('OpenSSL', '1.1', '', True)] +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] sanity_check_paths = { 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', diff --git a/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.4.9-GCCcore-12.2.0.eb similarity index 90% rename from easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/e/expat/expat-2.4.9-GCCcore-12.2.0.eb index df978cec524..2adfd581f7c 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.4.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.4.9-GCCcore-12.2.0.eb @@ -1,6 +1,7 @@ easyblock = 'ConfigureMake' + name = 'expat' -version = '2.4.8' +version = '2.4.9' homepage = 'https://libexpat.github.io' @@ -13,7 +14,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] sources = [SOURCE_TAR_BZ2] -checksums = ['a247a7f6bbb21cf2ca81ea4cbb916bfb9717ca523631675f99b3d4a5678dcd16'] +checksums = ['7f44d1469b110773a94b0d5abeeeffaef79f8bd6406b07e52394bcf48126437a'] builddependencies = [('binutils', '2.39')] diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.2.0.eb similarity index 92% rename from easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.2.0.eb index b164af87b06..569af9fc736 100644 --- a/easybuild/easyconfigs/l/libreadline/libreadline-8.1.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'libreadline' -version = '8.1.2' +version = '8.2' homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' description = """ @@ -18,7 +18,7 @@ toolchainopts = {'pic': True} source_urls = ['https://ftp.gnu.org/gnu/readline'] sources = ['readline-%(version)s.tar.gz'] -checksums = ['7589a2381a8419e68654a47623ce7dfcb756815c8fee726b98f90bf668af7bc6'] +checksums = ['3feb7171f16a84ee82ca18a36d7b9be109a52c04f492a053331d7d1095007c35'] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 5e960b5fcac..168f7b94b45 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -18,11 +18,11 @@ builddependencies = [ dependencies = [ ('zlib', '1.2.12'), # for Net::SSLeay - ('expat', '2.4.8'), # for XML::Parser + ('expat', '2.4.9'), # for XML::Parser ('ncurses', '6.3'), # for Term::ReadLine::Gnu - ('libreadline', '8.1.2'), # for Term::ReadLine::Gnu + ('libreadline', '8.2'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', True), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] # !! order of extensions is important !! From dd6aec8b72adb7a7fea50e3c35bfe7bf165098ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 15:03:25 +0200 Subject: [PATCH 5174/9987] fix comment in Perl 5.36.0 using GCCcore/12.2.0 toolchain w.r.t. when list of extensions was updated --- easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 168f7b94b45..df8c81ece83 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -26,7 +26,7 @@ dependencies = [ ] # !! order of extensions is important !! -# extensions updated on Apr 28th 2022 +# extensions updated on 8 Sept 2022 exts_list = [ ('Config::General', '2.65', { 'source_tmpl': 'Config-General-%(version)s.tar.gz', From f515ed8e185f92018515c7ee74819452f882ba5b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 15:12:30 +0200 Subject: [PATCH 5175/9987] {devel}[GCCcore/12.2.0] Autotools v20220317: Autoconf v2.71, Automake v1.16.5, libtool v2.4.7 --- .../Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb | 48 +++++++++++++++++++ .../Automake-1.16.5-GCCcore-12.2.0.eb | 39 +++++++++++++++ .../Autotools-20220317-GCCcore-12.2.0.eb | 24 ++++++++++ .../l/libtool/libtool-2.4.7-GCCcore-12.2.0.eb | 32 +++++++++++++ 4 files changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4e315d3a24c --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.71' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('M4', '1.4.19'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.36.0'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +sanity_check_commands = [ + "autoconf --help", + "autom4te --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ff89d29e31a --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.5' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Autoconf', '2.71'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.36.0'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ['bin/aclocal', 'bin/automake'], + 'dirs': [] +} + +sanity_check_commands = [ + "aclocal --help", + "automake --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..80a6cff18b1 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20220317' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Autoconf', '2.71'), # 20210128 + ('Automake', '1.16.5'), # 20211003 + ('libtool', '2.4.7'), # 20220317 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..249e1aff8db --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.7' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' From 6dfe21e8c53184fc8f11ee47aee273b7e410ed06 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 18 Oct 2022 15:35:42 +0200 Subject: [PATCH 5176/9987] adding easyconfigs: Mamba-4.14.0-0.eb --- .../easyconfigs/m/Mamba/Mamba-4.14.0-0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb diff --git a/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb new file mode 100644 index 00000000000..65373fbe5fb --- /dev/null +++ b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb @@ -0,0 +1,29 @@ +# author: Caspar van Leeuwen +easyblock = 'EB_Mamba' + +name = 'Mamba' +version = '4.14.0-0' + +homepage = 'https://mamba.readthedocs.io/' +description = """Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux +(ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands. +""" + +toolchain = SYSTEM + +# Note: Using Mambaforge is the recommended way of installing mamba, +# according to https://mamba.readthedocs.io/en/latest/installation.html +local_name = 'Mambaforge' +source_urls = ['https://github.com/conda-forge/miniforge/releases/download/%(version)s'] +sources = ['{local_name}-%(version)s-Linux-%(arch)s.sh'.format(local_name = local_name)] + +checksums = [ + { + '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name = local_name): + 'd47b78b593e3cf5513bafbfa6a51eafcd9f0e164c41c79c790061bb583c82859', + '{local_name}-%(version)s-Linux-ppc64le.sh'.format(local_name = local_name): + '607bbd38aa21af4c79a663f2a183a06cca054efdd8d617c17370522504c7be1e', + } +] + +moduleclass = 'lang' From 03ff8e1ea1283f49e94b700ff91fe0701efbbc15 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 18 Oct 2022 16:38:19 +0200 Subject: [PATCH 5177/9987] Fixed formatting errors --- easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb index 65373fbe5fb..4abc47f1660 100644 --- a/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb +++ b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb @@ -15,13 +15,13 @@ toolchain = SYSTEM # according to https://mamba.readthedocs.io/en/latest/installation.html local_name = 'Mambaforge' source_urls = ['https://github.com/conda-forge/miniforge/releases/download/%(version)s'] -sources = ['{local_name}-%(version)s-Linux-%(arch)s.sh'.format(local_name = local_name)] +sources = ['{local_name}-%(version)s-Linux-%(arch)s.sh'.format(local_name=local_name)] checksums = [ { - '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name = local_name): + '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name=local_name): 'd47b78b593e3cf5513bafbfa6a51eafcd9f0e164c41c79c790061bb583c82859', - '{local_name}-%(version)s-Linux-ppc64le.sh'.format(local_name = local_name): + '{local_name}-%(version)s-Linux-ppc64le.sh'.format(local_name=local_name): '607bbd38aa21af4c79a663f2a183a06cca054efdd8d617c17370522504c7be1e', } ] From 8297a3a702a631ab1cb0ea68b3146df5ae0a718d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 17:41:45 +0200 Subject: [PATCH 5178/9987] adding easyconfigs: pkgconf-1.9.3-GCCcore-12.2.0.eb --- .../p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..bd5895c7aa0 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '1.9.3' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6d73ac21a9410f5cc636acf730f3a5bf46b28d1e18a239c89efc4b2c5548792f'] + +builddependencies = [('binutils', '2.39')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' From a0e4239c307dc7b55269558b3b27a7265af51b19 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 17:45:56 +0200 Subject: [PATCH 5179/9987] {lib}[GCCcore/12.2.0] UCX v1.13.1, numactl v2.0.16 --- .../numactl/numactl-2.0.16-GCCcore-12.2.0.eb | 34 ++++++++++++ .../u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb | 54 +++++++++++++++++++ .../u/UCX/UCX-1.13.1-dynamic_modules.patch | 29 ++++++++++ .../u/UCX/UCX-1.13.1_fix-undeclared-PTR.patch | 27 ++++++++++ 4 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.13.1-dynamic_modules.patch create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.13.1_fix-undeclared-PTR.patch diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d9344685b43 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.16' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a35c3bdb3efab5c65927e0de5703227760b1101f5e27ab741d8f32b3d5f0a44c'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..bdc002c20df --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.13.1' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', + 'UCX-1.13.1_fix-undeclared-PTR.patch', +] +checksums = [ + {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, + {'UCX-1.13.1_fix-undeclared-PTR.patch': 'ef22c29604552ad3223f2a6bac352f30023cc5cf68f786abfdc4ad7c04189a76'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.12'), + ('numactl', '2.0.16'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-dynamic_modules.patch b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-dynamic_modules.patch new file mode 100644 index 00000000000..bf0e5564853 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-dynamic_modules.patch @@ -0,0 +1,29 @@ +# UCX is hardcoded to only load the modules it is compiled with. +# This patch adds an optional EB_UCX_xxx_MODULES that can override this list, allowing new modules to be loaded later. +# Author: micketeer@gmail.com - updated for UCX 1.13.1 by Kenneth Hoste (HPC-UGent) +--- ucx-1.13.1.orig/src/ucs/sys/module.c 2022-09-07 09:16:18.000000000 +0200 ++++ ucx-1.13.1/src/ucs/sys/module.c 2022-10-18 16:29:29.318490689 +0200 +@@ -271,6 +271,8 @@ + char *modules_str; + char *saveptr; + char *module_name; ++ char *env_modules; ++ char buf[64]; + + ucs_module_loader_init_paths(); + +@@ -278,7 +280,13 @@ + ucs_assert(ucs_sys_is_dynamic_lib()); + + ucs_module_debug("loading modules for %s", framework); +- modules_str = ucs_strdup(modules, "modules_list"); ++ ucs_snprintf_safe(buf, sizeof(buf), "EB_UCX_%s_MODULES", framework); ++ env_modules = getenv(buf); ++ if (env_modules != NULL) { ++ modules_str = ucs_strdup(env_modules, "modules_list"); ++ } else { ++ modules_str = ucs_strdup(modules, "modules_list"); ++ } + if (modules_str != NULL) { + saveptr = NULL; + module_name = strtok_r(modules_str, ":", &saveptr); diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.13.1_fix-undeclared-PTR.patch b/easybuild/easyconfigs/u/UCX/UCX-1.13.1_fix-undeclared-PTR.patch new file mode 100644 index 00000000000..4551b62371b --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.13.1_fix-undeclared-PTR.patch @@ -0,0 +1,27 @@ +From 6b6128efd416831cec3a1820f7d1c8e648b79448 Mon Sep 17 00:00:00 2001 +From: Hui Zhou +Date: Sun, 14 Aug 2022 23:29:09 -0500 +Subject: [PATCH] UCS/DEBUG: replace PTR with void * + +The PTR macro is missing on the latest Arch linux. +--- + src/ucs/debug/debug.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/ucs/debug/debug.c b/src/ucs/debug/debug.c +index 4ab9a9b7a2a..c51c99ba2b1 100644 +--- a/src/ucs/debug/debug.c ++++ b/src/ucs/debug/debug.c +@@ -272,10 +272,10 @@ static int load_file(struct backtrace_file *file) + goto err_close; + } + +- symcount = bfd_read_minisymbols(file->abfd, 0, (PTR)&file->syms, &size); ++ symcount = bfd_read_minisymbols(file->abfd, 0, (void *)&file->syms, &size); + if (symcount == 0) { + free(file->syms); +- symcount = bfd_read_minisymbols(file->abfd, 1, (PTR)&file->syms, &size); ++ symcount = bfd_read_minisymbols(file->abfd, 1, (void *)&file->syms, &size); + } + if (symcount < 0) { + goto err_close; From 31b2da0662c986d394ce0ec507675f0ec8aeb150 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 17:52:12 +0200 Subject: [PATCH 5180/9987] {toolchain} intel/2022.09 --- .../h/HPL/HPL-2.3-intel-2022.09.eb | 21 ++++++++++++ .../easyconfigs/i/iimpi/iimpi-2022.09.eb | 18 ++++++++++ .../imkl-FFTW-2022.2.0-iimpi-2022.09.eb | 11 +++++++ easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb | 18 ++++++++++ .../impi-2021.7.0-intel-compilers-2022.2.0.eb | 16 +++++++++ .../intel-compilers-2022.2.0.eb | 33 +++++++++++++++++++ .../easyconfigs/i/intel/intel-2022.09.eb | 22 +++++++++++++ 7 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.09.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022.09.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.0-iimpi-2022.09.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2022.09.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.09.eb new file mode 100644 index 00000000000..fb7197f51a4 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.09.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022.09'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022.09.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022.09.eb new file mode 100644 index 00000000000..f29ac7e5524 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022.09.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022.09' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.2.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.0-iimpi-2022.09.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.0-iimpi-2022.09.eb new file mode 100644 index 00000000000..ed5487ee565 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.0-iimpi-2022.09.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022.09'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb new file mode 100644 index 00000000000..82776023871 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.0.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2022.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18898/'] +sources = ['l_onemkl_p_%(version)s.8748_offline.sh'] +checksums = ['07d7caedd4b9f025c6fd439a0d2c2f279b18ecbbb63cadb864f6c63c1ed942db'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb new file mode 100644 index 00000000000..8f400fabac4 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.0-intel-compilers-2022.2.0.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.7.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.0'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18926/'] +sources = ['l_mpi_oneapi_p_%(version)s.8711_offline.sh'] +checksums = ['4eb1e1487b67b98857bc9b7b37bcac4998e0aa6d1b892b2c87b003bf84fb38e9'] + +dependencies = [('UCX', '1.13.1')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb new file mode 100644 index 00000000000..17262278b13 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.0.eb @@ -0,0 +1,33 @@ +name = 'intel-compilers' +version = '2022.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18849/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.8772_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18909/'], + 'filename': 'l_fortran-compiler_p_%(version)s.8773_offline.sh', + }, +] +checksums = [ + {'l_dpcpp-cpp-compiler_p_2022.2.0.8772_offline.sh': + '8ca97f7ea8abf7876df6e10ce2789ea8cbc310c100ad7bf0b5ffccc4f3c7f2c9'}, + {'l_fortran-compiler_p_2022.2.0.8773_offline.sh': + '4054e4bf5146d55638d21612396a19ea623d22cbb8ac63c0a7150773541e0311'}, +] + +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2022.09.eb b/easybuild/easyconfigs/i/intel/intel-2022.09.eb new file mode 100644 index 00000000000..8e5967bdb58 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022.09.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022.09' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.2.0' +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From e2c9ce8d712e1ea47b837298d4d047b921dbabb3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 18:27:44 +0200 Subject: [PATCH 5181/9987] adding easyconfigs: CDBtools-0.99-GCC-10.2.0.eb --- .../c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb new file mode 100644 index 00000000000..11fc1a9fd9c --- /dev/null +++ b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'CDBtools' +version = '0.99' + +homepage = 'http://compbio.dfci.harvard.edu/tgi' +description = "CDB (Constant DataBase) indexing and retrieval tools for FASTA files" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta'] +sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c'] + +buildopts = 'CC="$CXX" DBGFLAGS="$CXXFLAGS"' + +files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cdbfasta', 'bin/cdbyank'], + 'dirs': [], +} + +sanity_check_commands = [ + "cdbfasta -v", + "cdbyank -v", +] + +moduleclass = 'bio' From ef9535969aa1b9b3bd4e797f0debedcb840f093d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 19:55:27 +0200 Subject: [PATCH 5182/9987] adding easyconfigs: biogeme-3.2.6-foss-2022a.eb --- .../b/biogeme/biogeme-3.2.6-foss-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/biogeme/biogeme-3.2.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/biogeme/biogeme-3.2.6-foss-2022a.eb b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.6-foss-2022a.eb new file mode 100644 index 00000000000..21a1c2ddb5e --- /dev/null +++ b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.6-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'biogeme' +version = '3.2.6' + +homepage = 'https://pypi.python.org/pypi/biogeme' +description = """Biogeme is a open source Python package designed for +the maximum likelihood estimation of parametric models in general, +with a special emphasis on discrete choice models.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('Unidecode', '1.3.6', { + 'checksums': ['fed09cf0be8cf415b391642c2a5addfc72194407caee4f98719e40ec2a72b830'], + }), + (name, version, { + 'checksums': ['ff8d492019e15aecdfe7c72cff3b2616845cdf80bd2f1bde9031d94601f3faf7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From adb81d77b0d1f6606407cdbf5d16c71228326ae8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2022 08:52:14 +0200 Subject: [PATCH 5183/9987] adding easyconfigs: AMAPVox-1.9.4-Java-11.eb --- .../a/AMAPVox/AMAPVox-1.9.4-Java-11.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb diff --git a/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb b/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb new file mode 100644 index 00000000000..af51c0503ca --- /dev/null +++ b/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'AMAPVox' +version = '1.9.4' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://amap-dev.cirad.fr/projects/amapvox' +description = "LiDAR data voxelisation software" + +toolchain = SYSTEM + +source_urls = ['http://amap-dev.cirad.fr/attachments/download/1916/'] +sources = ['AMAPVox-%(version)s.zip'] +checksums = ['6d3e65fbd17a8e3a45962f5d1ce60a58ad0bfd899fa704dc172f2819fc309b74'] + +dependencies = [('Java', '11')] + +postinstallcmds = ["chmod a+x %(installdir)s/AMAPVox.sh"] + +sanity_check_paths = { + 'files': ['AMAPVox.sh', 'AMAPVox-1.9.4.jar'], + 'dirs': ['lib'], +} + +sanity_check_commands = ["AMAPVox.sh -h"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'data' From edf648109147b06ac9c55135c3ec21bb89cb3f25 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2022 08:57:02 +0200 Subject: [PATCH 5184/9987] drop explicit easyblock specification in Mamba easyconfig (derived from name by default) + add checksum for aarch64 installer --- easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb index 4abc47f1660..aad49d0ae6b 100644 --- a/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb +++ b/easybuild/easyconfigs/m/Mamba/Mamba-4.14.0-0.eb @@ -1,6 +1,4 @@ # author: Caspar van Leeuwen -easyblock = 'EB_Mamba' - name = 'Mamba' version = '4.14.0-0' @@ -16,13 +14,14 @@ toolchain = SYSTEM local_name = 'Mambaforge' source_urls = ['https://github.com/conda-forge/miniforge/releases/download/%(version)s'] sources = ['{local_name}-%(version)s-Linux-%(arch)s.sh'.format(local_name=local_name)] - checksums = [ { - '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name=local_name): - 'd47b78b593e3cf5513bafbfa6a51eafcd9f0e164c41c79c790061bb583c82859', + '{local_name}-%(version)s-Linux-aarch64.sh'.format(local_name=local_name): + '37221b8d818951fab125c0bfb6cc6e83dac059f66892d2544a83192828d8e2c4', '{local_name}-%(version)s-Linux-ppc64le.sh'.format(local_name=local_name): '607bbd38aa21af4c79a663f2a183a06cca054efdd8d617c17370522504c7be1e', + '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name=local_name): + 'd47b78b593e3cf5513bafbfa6a51eafcd9f0e164c41c79c790061bb583c82859', } ] From f85a4f85f84eeead0789f46416df0c627c57f132 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2022 08:59:18 +0200 Subject: [PATCH 5185/9987] add AMAPVox extension to R v4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index b97f484e225..49b9a97d1a0 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3355,6 +3355,9 @@ exts_list = [ ('rtdists', '0.11-5', { 'checksums': ['97cf2ea758aa02b1dfaeef5032c6e50570777552aa771ed9a86df048b7871eed'], }), + ('AMAPVox', '0.12.0', { + 'checksums': ['b30fefef8661e27ffe3883665204b623eda2143dbcd3084a1d5810f8ea834c85'], + }), ] moduleclass = 'lang' From de9e295548ff7663079328caae55e70ba02cdd51 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 19 Oct 2022 09:16:31 +0200 Subject: [PATCH 5186/9987] added sanity_pip_check and download_dep_fail --- easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb index 122b155d477..1d9f666570f 100644 --- a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-foss-2021b.eb @@ -17,7 +17,11 @@ dependencies = [ ('Graphviz', '2.50.0'), ] +download_dep_fail = True + use_pip = True +sanity_pip_check = True + sanity_check_commands = ["python -c 'import ruffus.graph'"] From 72425460ca636b8f1f71f2c30319937e95651d2f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 19 Oct 2022 11:34:56 +0200 Subject: [PATCH 5187/9987] adding easyconfigs: jq-1.6-GCCcore-11.2.0.eb, jq-1.6-GCCcore-11.3.0.eb, jq-1.6-GCCcore-12.2.0.eb --- .../easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb | 31 +++++++++++++++++++ .../easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ .../easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 3 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..e02bc430983 --- /dev/null +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'jq' +version = '1.6' + +homepage = 'https://stedolan.github.io/jq/' +description = """jq is a lightweight and flexible command-line JSON processor.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/stedolan/jq/releases/download/jq-%(version)s'] +sources = ['jq-%(version)s.tar.gz'] +checksums = ['5de8c8e29aaa3fb9cc6b47bb27299f271354ebb72514e3accadc7d38b5bbaa72'] + +builddependencies = [ + ('binutils', '2.37'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('Autotools', '20210726'), +] + +preconfigopts = "autoreconf -fi && " + +configopts = '--with-oniguruma=builtin' + +sanity_check_paths = { + 'files': ['bin/jq'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e70d4d8080f --- /dev/null +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'jq' +version = '1.6' + +homepage = 'https://stedolan.github.io/jq/' +description = """jq is a lightweight and flexible command-line JSON processor.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/stedolan/jq/releases/download/jq-%(version)s'] +sources = ['jq-%(version)s.tar.gz'] +checksums = ['5de8c8e29aaa3fb9cc6b47bb27299f271354ebb72514e3accadc7d38b5bbaa72'] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -fi && " + +configopts = '--with-oniguruma=builtin' + +sanity_check_paths = { + 'files': ['bin/jq'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6fd2d201102 --- /dev/null +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'jq' +version = '1.6' + +homepage = 'https://stedolan.github.io/jq/' +description = """jq is a lightweight and flexible command-line JSON processor.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/stedolan/jq/releases/download/jq-%(version)s'] +sources = ['jq-%(version)s.tar.gz'] +checksums = ['5de8c8e29aaa3fb9cc6b47bb27299f271354ebb72514e3accadc7d38b5bbaa72'] + +builddependencies = [ + ('binutils', '2.39'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -fi && " + +configopts = '--with-oniguruma=builtin' + +sanity_check_paths = { + 'files': ['bin/jq'], + 'dirs': [], +} + +moduleclass = 'tools' From 047f5028ebb35ea4a7ee64ce5ebe0ec81ee09873 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2022 13:13:58 +0200 Subject: [PATCH 5188/9987] adding easyconfigs: Nextflow-22.10.0.eb --- .../n/Nextflow/Nextflow-22.10.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.0.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.0.eb new file mode 100644 index 00000000000..70231eabec8 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CmdCp' + +name = 'Nextflow' +version = '22.10.0' + +homepage = 'https://www.nextflow.io' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7eceff3e32bd1bcd09744890501456e0a2b5448916fb25f3e6a8f338a239af8b'] + +# specify dependency on Java/11 "wrapper", rather than a specific Java version +dependencies = [('Java', '11', '', SYSTEM)] + +skipsteps = ['configure', 'build'] + +_exe_files = ['%(namelower)s', 'gradlew'] + +files_to_copy = [ + (_exe_files, '%(installdir)s/bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' From c0c71387faa66ba04eaefc506d0ff61ef80d16ce Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 19 Oct 2022 16:04:05 +0200 Subject: [PATCH 5189/9987] Update easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb index e02bc430983..4f44b8686e1 100644 --- a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.2.0.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['jq --help', 'jq --version'] + moduleclass = 'tools' From 91865347b77ae3dc2b7041bd2c674bb1c8820a09 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 19 Oct 2022 16:04:12 +0200 Subject: [PATCH 5190/9987] Update easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb index e70d4d8080f..06922fad5b8 100644 --- a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-11.3.0.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['jq --help', 'jq --version'] + moduleclass = 'tools' From 3afe1287da9feda33d1c288ff24f9b26269a44b7 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 19 Oct 2022 16:04:18 +0200 Subject: [PATCH 5191/9987] Update easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb index 6fd2d201102..8ffe5702c24 100644 --- a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.2.0.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['jq --help', 'jq --version'] + moduleclass = 'tools' From 0cd66fd8614e50df8389ad31436706564b755021 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 19 Oct 2022 16:39:37 +0200 Subject: [PATCH 5192/9987] adding easyconfigs: python-telegram-bot-20.0a0-GCCcore-10.2.0.eb --- ...thon-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..925a1086d5a --- /dev/null +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -0,0 +1,97 @@ +easyblock = 'PythonBundle' + +name = 'python-telegram-bot' +version = '20.0a0' + +homepage = 'https://python-telegram-bot.org/' +description = """This library provides a pure Python, asynchronous interface for the Telegram Bot API. + It's compatible with Python versions 3.7+.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('APScheduler', '3.9.1', { + 'checksums': ['65e6574b6395498d371d045f2a8a7e4f7d50c6ad21ef7313d15b1c7cf20df1e3'], + }), + ('anyio', '3.6.2', { + 'checksums': ['25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421'], + }), + ('backports.zoneinfo', '0.2.1', { + 'checksums': ['fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2'], + }), + ('cachetools', '5.0.0', { + 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], + }), + ('certifi', '2022.9.24', { + 'checksums': ['0d9c601124e5a6ba9712dbc60d9c53c21e34f5f641fe83002317394311bdce14'], + }), + ('charset-normalizer', '2.1.1', { + 'checksums': ['5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845'], + }), + ('flit_core', '3.7.1', { + 'checksums': ['14955af340c43035dbfa96b5ee47407e377ee337f69e70f73064940d27d0a44f'], + }), + ('h11', '0.12.0', { + 'checksums': ['47222cb6067e4a307d535814917cd98fd0a57b6788ce715755fa2b6c28b56042'], + }), + ('httpcore', '0.14.7', { + 'checksums': ['7503ec1c0f559066e7e39bc4003fd2ce023d01cf51793e3c173b864eb456ead1'], + }), + ('httpx', '0.22.0', { + 'checksums': ['d8e778f76d9bbd46af49e7f062467e3157a5a3d2ae4876a4bbfd8a51ed9c9cb4'], + }), + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('pytz_deprecation_shim', '0.1.0.post0', { + 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], + }), + ('pytz', '2022.4', { + 'checksums': ['48ce799d83b6f8aab2020e369b627446696619e79645419610b9facd909b3174'], + }), + ('requests', '2.28.1', { + 'checksums': ['7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('ruffus', '2.8.4', { + 'checksums': ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'], + }), + ('setuptools', '65.5.0', { + 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('tzdata', '2022.5', { + 'checksums': ['e15b2b3005e2546108af42a0eb4ccab4d9e225e2dfbf4f77aad50c70a4b1f3ab'], + }), + ('tzlocal', '4.2', { + 'checksums': ['ee5842fa3a795f023514ac2d801c4a81d1743bbe642e3940143326b3a00addd7'], + }), + (name, version, { + 'modulename': 'telegram', + 'checksums': ['a182a3d081071f1ea34833bc68ed7d0843c1fe0d6dca1d260a0e2d253b150f71'], + }), +] + +sanity_check_commands = [ + "python -c 'from telegram import Update'", + "python -c 'from telegram.ext import ApplicationBuilder, CommandHandler, ContextTypes'", +] + +moduleclass = 'lib' From af51ab97117abc587762627c3af87e1b4a72b4b7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 19 Oct 2022 16:47:08 +0200 Subject: [PATCH 5193/9987] adding easyconfigs: LIBSVM-3.30-GCCcore-11.3.0.eb and patches: LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch --- .../l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb | 43 ++++++++++ ...0_add_namespace_for_benefit_of_Xmipp.patch | 83 +++++++++++++++++++ 2 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d58a61173b8 --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'LIBSVM' +version = '3.30' + +homepage = 'https://www.csie.ntu.edu.tw/~cjlin/libsvm/' +description = """LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression + (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'cjlin1' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%s.tar.gz' % version.replace('.', '')] +patches = [ + 'LIBSVM-3.23_shared_lib.patch', + 'LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch', +] +checksums = [ + {'v330.tar.gz': 'e4fe41308c87cc210aec73e4f5f0fb4da14234d90e7a131763fbad3788ca2d80'}, + {'LIBSVM-3.23_shared_lib.patch': 'c0ede89365949644f5d7f11382a3f176fd76317c7f5ae5769226ff7c3a801fe6'}, + {'LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch': + 'f51e4d0b6899041799f43a09aad1e3711a93615a8cc453243042ed8357cabb28'}, +] + +dependencies = [('binutils', '2.38')] + +local_bins = ['svm-%s' % x for x in ['predict', 'scale', 'train']] + +files_to_copy = [ + (local_bins, 'bin'), + (['svm.o'], 'lib'), + (['libsvm*'], 'lib'), + (['svm.h'], 'include/libsvm'), + 'tools' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + ['lib/libsvm.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch new file mode 100644 index 00000000000..d79d00d78a0 --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch @@ -0,0 +1,83 @@ +Taken from https://github.com/cossorzano/libsvm which Xmipp uses. + +Also added "using namespace libsvm" to svm-train.c and svm-predict.c + +Åke Sandgren 2022-10-19 + +commit 2a0db2ec1330db8cd45bf5ba7d55d850ce5c8318 +Author: Carlos Oscar Sorzano +Date: Fri Nov 5 13:37:31 2021 +0100 + + Namespace added + +diff --git a/svm.cpp b/svm.cpp +index fa44818..814b1b6 100644 +--- a/svm.cpp ++++ b/svm.cpp +@@ -1,3 +1,7 @@ ++/* This file has been taken from LibSVM 3.25 */ ++/* Authors: Chih-Chung Chang and Chih-Jen Lin, LIBSVM :*/ ++/* Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm */ ++ + #include + #include + #include +@@ -8,6 +12,8 @@ + #include + #include + #include "svm.h" ++using namespace libsvm; ++ + int libsvm_version = LIBSVM_VERSION; + typedef float Qfloat; + typedef signed char schar; +diff --git a/svm.h b/svm.h +index 5dfc1f7..ba47063 100644 +--- a/svm.h ++++ b/svm.h +@@ -1,3 +1,7 @@ ++/* This file has been taken from LibSVM 3.25 */ ++/* Authors: Chih-Chung Chang and Chih-Jen Lin, LIBSVM : */ ++/* Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm */ ++ + #ifndef _LIBSVM_H + #define _LIBSVM_H + +@@ -22,8 +26,10 @@ struct svm_problem + struct svm_node **x; + }; + +-enum { C_SVC, NU_SVC, ONE_CLASS, EPSILON_SVR, NU_SVR }; /* svm_type */ +-enum { LINEAR, POLY, RBF, SIGMOID, PRECOMPUTED }; /* kernel_type */ ++namespace libsvm { ++ enum { C_SVC, NU_SVC, ONE_CLASS, EPSILON_SVR, NU_SVR }; /* svm_type */ ++ enum { LINEAR, POLY, RBF, SIGMOID, PRECOMPUTED }; /* kernel_type */ ++} + + struct svm_parameter + { +diff --git a/svm-train.c b/svm-train.c +index b6ce987..064c29b 100644 +--- a/svm-train.c ++++ b/svm-train.c +@@ -4,6 +4,8 @@ + #include + #include + #include "svm.h" ++using namespace libsvm; ++ + #define Malloc(type,n) (type *)malloc((n)*sizeof(type)) + + void print_null(const char *s) {} +diff --git a/svm-predict.c b/svm-predict.c +index 7a0fa15..328f815 100644 +--- a/svm-predict.c ++++ b/svm-predict.c +@@ -4,6 +4,7 @@ + #include + #include + #include "svm.h" ++using namespace libsvm; + + int print_null(const char *s,...) {return 0;} + From 13b10372e9ce58d1d5abf4cc937c6bd79e7ee0b1 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 19 Oct 2022 16:55:57 +0200 Subject: [PATCH 5194/9987] added binutils as builddependency --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index 925a1086d5a..f98289dd3bc 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -13,6 +13,8 @@ dependencies = [ ('Python', '3.8.6'), ] +builddependencies = [('binutils', '2.35')] + use_pip = True sanity_pip_check = True From 8ace4ccbeb4496bec7f411ee8ac74d4f8700abb2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 19 Oct 2022 20:23:10 +0200 Subject: [PATCH 5195/9987] Apply suggestions from code review don't hardcode version in sanity_check_paths for AMAPVox + use SOURCE_ZIP template in sources Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb b/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb index af51c0503ca..d0d5c54fd5e 100644 --- a/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb +++ b/easybuild/easyconfigs/a/AMAPVox/AMAPVox-1.9.4-Java-11.eb @@ -10,7 +10,7 @@ description = "LiDAR data voxelisation software" toolchain = SYSTEM source_urls = ['http://amap-dev.cirad.fr/attachments/download/1916/'] -sources = ['AMAPVox-%(version)s.zip'] +sources = [SOURCE_ZIP] checksums = ['6d3e65fbd17a8e3a45962f5d1ce60a58ad0bfd899fa704dc172f2819fc309b74'] dependencies = [('Java', '11')] @@ -18,7 +18,7 @@ dependencies = [('Java', '11')] postinstallcmds = ["chmod a+x %(installdir)s/AMAPVox.sh"] sanity_check_paths = { - 'files': ['AMAPVox.sh', 'AMAPVox-1.9.4.jar'], + 'files': ['AMAPVox.sh', 'AMAPVox-%(version)s.jar'], 'dirs': ['lib'], } From dca1c0e2cbc9fcb628ec070b71c6e48f3b0731fa Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 19 Oct 2022 21:34:44 +0200 Subject: [PATCH 5196/9987] adding easyconfigs: archspec-0.1.4-GCCcore-11.3.0.eb --- .../archspec/archspec-0.1.4-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..710f53f822e --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.1.4' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b8d5eeb4caf892790ff1aa8ccef442a84187986aeab4da29417c9fe35532d94c'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +moduleclass = 'tools' From 314650e894a8b06fab1448e9b54fb31a5f600db8 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Thu, 20 Oct 2022 07:06:39 +0200 Subject: [PATCH 5197/9987] removed ruffus as dependency --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index f98289dd3bc..34c1581e97c 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -64,9 +64,6 @@ exts_list = [ ('rfc3986', '1.5.0', { 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], }), - ('ruffus', '2.8.4', { - 'checksums': ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'], - }), ('setuptools', '65.5.0', { 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], }), From 47ac220bd54bdf003b4e7530393d8f3d5203bc98 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Thu, 20 Oct 2022 09:55:25 +0200 Subject: [PATCH 5198/9987] removed unnecessary dependencies --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index 34c1581e97c..dfb7a16b6ba 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -31,9 +31,6 @@ exts_list = [ ('cachetools', '5.0.0', { 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], }), - ('certifi', '2022.9.24', { - 'checksums': ['0d9c601124e5a6ba9712dbc60d9c53c21e34f5f641fe83002317394311bdce14'], - }), ('charset-normalizer', '2.1.1', { 'checksums': ['5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845'], }), @@ -55,21 +52,13 @@ exts_list = [ ('pytz_deprecation_shim', '0.1.0.post0', { 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], }), - ('pytz', '2022.4', { - 'checksums': ['48ce799d83b6f8aab2020e369b627446696619e79645419610b9facd909b3174'], - }), + # to overwrite Python's requests requirement which requires older version of idna ('requests', '2.28.1', { 'checksums': ['7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983'], }), ('rfc3986', '1.5.0', { 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], }), - ('setuptools', '65.5.0', { - 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], - }), - ('six', '1.16.0', { - 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], - }), ('sniffio', '1.3.0', { 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], }), From 37d77d518b1a4dc9e2d40d894900a1198d8c8f54 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 10:35:49 +0200 Subject: [PATCH 5199/9987] adding easyconfigs: pyWannier90-2021-12-07-foss-2021a.eb --- .../pyWannier90-2021-12-07-foss-2021a.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb new file mode 100644 index 00000000000..ec32ef804a9 --- /dev/null +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb @@ -0,0 +1,76 @@ +easyblock = 'MakeCp' + +name = 'pyWannier90' +local_commit = '8354e91' +version = '2021-12-07' + +homepage = 'https://github.com/hungpham2017/pyWannier90' +description = "A Wannier90 Python interface for VASP and PySCF" + +toolchain = {'name': 'foss', 'version': '2021a'} + +local_wannier90_version = '3.1.0' + +sources = [ + { + 'source_urls': ['https://github.com/hungpham2017/pyWannier90/archive/'], + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ + }, + { + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'], + 'download_filename': 'v%s.tar.gz' % local_wannier90_version, + 'filename': 'Wannier90-%s.tar.gz' % local_wannier90_version, + }, +] +checksums = [ + {'pyWannier90-2021-12-07.tar.gz': '27233891fe39e0f45914dfa756b28319ebd4c3b5ec2124f4c9d1d3816fc0887e'}, + {'Wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('pybind11', '2.6.2'), +] + +local_pymaj = '3' +local_pymin = '9' +local_pymajmin = local_pymaj + local_pymin + +dependencies = [ + ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('SciPy-bundle', '2021.05'), + ('PySCF', '1.7.6'), +] + +local_wannier90_make = 'make -j %(parallel)s F90="$F90" FCOPTS="$FFLAGS -fPIC" LDOPTS="$FFLAGS" ' +local_wannier90_make += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK"' + +prebuildopts = "cd %%(builddir)s/wannier90-%s && touch make.inc && " % local_wannier90_version +prebuildopts += "cp %(builddir)s/pyWannier90-*/src/wannier_lib.F90 src/wannier_lib.F90 && " +prebuildopts += local_wannier90_make + " && " +prebuildopts += local_wannier90_make + " lib && " +prebuildopts += "cd %(builddir)s/pyWannier90-*/src && pwd && " + +buildopts = 'CPP="$CXX" LIBS="-L%%(builddir)s/wannier90-%s $LIBLAPACK -lwannier" ' % local_wannier90_version +# with Intel compilers, use libwannier90_intel as make target +# with GCC compilers, use libwannier90_gf as make target +buildopts += "libwannier90_gf && " +buildopts += """sed -i "s@W90LIB = .*@W90LIB = '%(installdir)s'@g" pywannier90.py""" + +files_to_copy = [ + (['src/pywannier90.py', 'src/libwannier90.*.%s' % SHLIB_EXT], 'lib/python%(pyshortver)s/site-packages'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import libwannier90'", + "python -c 'import pywannier90'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From 85dbd36904fe1f0ee5709fdd5df2292c27c42c73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 10:40:38 +0200 Subject: [PATCH 5200/9987] adding easyconfigs: SciPy-bundle-2021.05-gomkl-2021a.eb --- .../SciPy-bundle-2021.05-gomkl-2021a.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb new file mode 100644 index 00000000000..89b95c194e8 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2021.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'gomkl', 'version': '2021a'} +toolchainopts = {'pic': True, 'lowopt': True, 'strict': True} + +builddependencies = [('hypothesis', '6.13.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('pybind11', '2.6.2'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.20.3', { + 'patches': [ + 'numpy-1.18.2-mkl.patch', + 'numpy-1.20.3_disable-broken-override-test.patch', + 'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch', + 'numpy-1.20.3_fix-target-test-ccompiler-opt.patch', + 'numpy-1.20.3_disable_fortran_callback_test.patch', + ], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': [ + 'e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69', # numpy-1.20.3.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + # numpy-1.20.3_disable-broken-override-test.patch + '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', + # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch + '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046', + # numpy-1.20.3_fix-target-test-ccompiler-opt.patch + '3d84e8b7d48387778974a5f6ae342a690ab5989547206b6add9d9667f8d7572a', + # numpy-1.20.3_disable_fortran_callback_test.patch + '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + ], + }), + ('scipy', '1.6.3', { + 'checksums': ['a75b014d3294fce26852a9d04ea27b5671d86736beb34acdfc05859246260707'], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('numexpr', '2.7.3', { + 'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '1.2.4', { + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'checksums': ['649ecab692fade3cbfcf967ff936496b0cfba0af00a55dfaacd82bdda5cb2279'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 84a08d27303526272f93ccb4f227f49bbb08dd68 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 20 Oct 2022 10:59:01 +0200 Subject: [PATCH 5201/9987] Use SYSTEM template instead of True for system-toolchain dependency --- .../r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-11.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-11.eb index 40c6ad78d8a..b2abeb093c0 100644 --- a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-11.eb +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-1.1.8-GCCcore-11.2.0-Java-11.eb @@ -24,7 +24,7 @@ builddependencies = [('binutils', '2.37')] dependencies = [ ('BWA', '0.7.17'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] modloadmsg = "To execute RNA-SeQC run: java -jar $EBROOTRNAMINSEQC/%(name)s_v%(version)s.jar" From 67f9f8c3fdd341ecc78eb28dfe00497a08271dc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 11:14:45 +0200 Subject: [PATCH 5202/9987] {chem}[gomkl/2021a] pyWannier90 v2021-12-07, PySCF v1.7.6, h5py v3.2.1, libcint v4.4.0 w/ Python 3.9.5 --- .../h/h5py/h5py-3.2.1-gomkl-2021a.eb | 34 +++++++++ .../l/libcint/libcint-4.4.0-gomkl-2021a.eb | 39 ++++++++++ .../p/PySCF/PySCF-1.7.6-gomkl-2021a.eb | 45 +++++++++++ .../pyWannier90-2021-12-07-gomkl-2021a.eb | 76 +++++++++++++++++++ 4 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb new file mode 100644 index 00000000000..a21aff6972d --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.2.1' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['89474be911bfcdb34cbf0d98b8ec48b578c27a89fdb1ae4ee7513f1ef8d9249e'] + +builddependencies = [('pkgconfig', '1.5.4', '-python')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('HDF5', '1.10.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb new file mode 100644 index 00000000000..8dc84fd9e8f --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '4.4.0' + +homepage = 'https://github.com/sunqm/libcint' +description = """libcint is an open source library for analytical Gaussian integrals.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +source_urls = ['https://github.com/sunqm/libcint/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_remove_pyscftest.patch'] +checksums = [ + '39a831e9131395e7ac312608981495aed3e44d0511b0700b2a1fb163b32c89c1', # v4.4.0.tar.gz + '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d', # libcint-4.4.0_remove_pyscftest.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + # Python with numpy only required for 'make test' + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +separate_build_dir = False # Must use the same directory for tests + +configopts = '-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on' + +buildopts = "VERBOSE=1" + +runtest = 'test ' + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/libcint.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb new file mode 100644 index 00000000000..cf0c6a26ccc --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMakeCp' + +name = 'PySCF' +version = '1.7.6' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1805819557cf78fb5938a2141a429c74dabb3ba664b60420032584d7a876c2ab'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy, scipy + ('h5py', '3.2.1'), + ('libcint', '4.4.0'), + ('libxc', '5.1.5'), + ('XCFun', '2.1.1'), +] + +start_dir = 'pyscf/lib' + +separate_build_dir = True + +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" + +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +files_to_copy = ['pyscf'] + +sanity_check_paths = { + 'files': ['pyscf/__init__.py'], + 'dirs': ['pyscf/data', 'pyscf/lib'], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb new file mode 100644 index 00000000000..2a045c216cc --- /dev/null +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb @@ -0,0 +1,76 @@ +easyblock = 'MakeCp' + +name = 'pyWannier90' +local_commit = '8354e91' +version = '2021-12-07' + +homepage = 'https://github.com/hungpham2017/pyWannier90' +description = "A Wannier90 Python interface for VASP and PySCF" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +local_wannier90_version = '3.1.0' + +sources = [ + { + 'source_urls': ['https://github.com/hungpham2017/pyWannier90/archive/'], + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ + }, + { + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'], + 'download_filename': 'v%s.tar.gz' % local_wannier90_version, + 'filename': 'Wannier90-%s.tar.gz' % local_wannier90_version, + }, +] +checksums = [ + {'pyWannier90-2021-12-07.tar.gz': '27233891fe39e0f45914dfa756b28319ebd4c3b5ec2124f4c9d1d3816fc0887e'}, + {'Wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('pybind11', '2.6.2'), +] + +local_pymaj = '3' +local_pymin = '9' +local_pymajmin = local_pymaj + local_pymin + +dependencies = [ + ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('SciPy-bundle', '2021.05'), + ('PySCF', '1.7.6'), +] + +local_wannier90_make = 'make -j %(parallel)s F90="$F90" FCOPTS="$FFLAGS -fPIC" LDOPTS="$FFLAGS" ' +local_wannier90_make += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK"' + +prebuildopts = "cd %%(builddir)s/wannier90-%s && touch make.inc && " % local_wannier90_version +prebuildopts += "cp %(builddir)s/pyWannier90-*/src/wannier_lib.F90 src/wannier_lib.F90 && " +prebuildopts += local_wannier90_make + " && " +prebuildopts += local_wannier90_make + " lib && " +prebuildopts += "cd %(builddir)s/pyWannier90-*/src && pwd && " + +buildopts = 'CPP="$CXX" LIBS="-L%%(builddir)s/wannier90-%s $LIBLAPACK -lwannier" ' % local_wannier90_version +# with Intel compilers, use libwannier90_intel as make target +# with GCC compilers, use libwannier90_gf as make target +buildopts += "libwannier90_gf && " +buildopts += """sed -i "s@W90LIB = .*@W90LIB = '%(installdir)s'@g" pywannier90.py""" + +files_to_copy = [ + (['src/pywannier90.py', 'src/libwannier90.*.%s' % SHLIB_EXT], 'lib/python%(pyshortver)s/site-packages'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import libwannier90'", + "python -c 'import pywannier90'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From 3f74f3b08f830eb6b2d472b8194d13eb0a0281e0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 20 Oct 2022 10:17:37 +0100 Subject: [PATCH 5203/9987] add bzip2 and libxml2 as deps to netCDF 4.9.0 --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb index f79aa51ab54..6aad7ec4860 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022a.eb @@ -34,6 +34,8 @@ dependencies = [ ('cURL', '7.83.0'), ('Szip', '2.1.1'), ('zstd', '1.5.2'), + ('bzip2', '1.0.8'), + ('libxml2', '2.9.13'), ] # make sure both static and shared libs are built From 93dfe13c78ed24d585aafb31724d0003b5b7f4c8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Oct 2022 13:12:00 +0200 Subject: [PATCH 5204/9987] adding easyconfigs: Boost.Python-1.79.0-GCC-11.3.0.eb --- .../Boost.Python-1.79.0-GCC-11.3.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..8f02a65562d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.79.0' + +homepage = 'https://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('Boost', version), + ('Python', '3.10.4'), +] + +only_python_bindings = True + +moduleclass = 'lib' From 8370597d0dc21f229d096f02b69becc8b970fa57 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Oct 2022 13:24:00 +0200 Subject: [PATCH 5205/9987] adding easyconfigs: FTGL-2.1.3-rc5-GCCcore-11.3.0.eb --- .../f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5f44a321631 --- /dev/null +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FTGL' +version = '2.1.3-rc5' + +homepage = 'http://ftgl.sourceforge.net/docs/html/' +description = """ FTGL is a free open source library to enable developers to use arbitrary +fonts in their OpenGL (www.opengl.org) applications. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5458d62122454869572d39f8aa85745fc05d5518001bcefa63bd6cbb8d26565b'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('freetype', '2.12.1'), + ('libGLU', '9.0.2'), + ('Mesa', '22.0.3'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/ftgl.pc', 'lib/libftgl.a', 'lib/libftgl.la', 'lib/libftgl.%s' % SHLIB_EXT], + 'dirs': ['include/FTGL', 'share'] +} + +moduleclass = 'lib' From 4c2da2454182b30ea9e3c1a713c2e4add46d69a3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Oct 2022 13:38:57 +0200 Subject: [PATCH 5206/9987] Add missing checksum --- .../easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb index 8f02a65562d..edd662ea181 100644 --- a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.79.0-GCC-11.3.0.eb @@ -12,6 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c'] dependencies = [ ('Boost', version), From 3382c5fb798c3db9f6eb7427be6125dfc17dffff Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Oct 2022 16:42:17 +0200 Subject: [PATCH 5207/9987] use FTGL 2.4.0 instead --- ...e-11.3.0.eb => FTGL-2.4.0-GCCcore-11.3.0.eb} | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/f/FTGL/{FTGL-2.1.3-rc5-GCCcore-11.3.0.eb => FTGL-2.4.0-GCCcore-11.3.0.eb} (65%) diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb similarity index 65% rename from easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb index 5f44a321631..343402f780d 100644 --- a/easybuild/easyconfigs/f/FTGL/FTGL-2.1.3-rc5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb @@ -1,20 +1,23 @@ easyblock = 'ConfigureMake' name = 'FTGL' -version = '2.1.3-rc5' +version = '2.4.0' -homepage = 'http://ftgl.sourceforge.net/docs/html/' +homepage = 'https://github.com/frankheckenbach/ftgl' description = """ FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications. """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['5458d62122454869572d39f8aa85745fc05d5518001bcefa63bd6cbb8d26565b'] +github_account = 'frankheckenbach' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] -builddependencies = [('binutils', '2.38')] +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] dependencies = [ ('freetype', '2.12.1'), @@ -22,6 +25,8 @@ dependencies = [ ('Mesa', '22.0.3'), ] +preconfigopts = './autogen.sh && ' + sanity_check_paths = { 'files': ['lib/pkgconfig/ftgl.pc', 'lib/libftgl.a', 'lib/libftgl.la', 'lib/libftgl.%s' % SHLIB_EXT], 'dirs': ['include/FTGL', 'share'] From 84f4715a19987a7f36e7c8b59f7dc0b37e2407da Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Oct 2022 17:00:56 +0200 Subject: [PATCH 5208/9987] Add missing checksum --- easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb index 343402f780d..87757d797fb 100644 --- a/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FTGL/FTGL-2.4.0-GCCcore-11.3.0.eb @@ -13,6 +13,7 @@ toolchainopts = {'pic': True} github_account = 'frankheckenbach' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] +checksums = ['aa97da1c3442a8fd3941037655df18016d70b5266381c81d81e8b5335f196ea8'] builddependencies = [ ('binutils', '2.38'), From 54770a0d7116397f9b4e09cb94fa36193bccc97f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 17:13:02 +0200 Subject: [PATCH 5209/9987] adding easyconfigs: jax-0.3.23-foss-2022a.eb --- .../j/jax/jax-0.3.23-foss-2022a.eb | 109 ++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb new file mode 100644 index 00000000000..23d90b71f8b --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -0,0 +1,109 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.23' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.36.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in WORKSPACE +local_tf_commit = 'cb946f223b9b3fa04efdbb7a0e6a9dabb22a7057' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.3.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['463c38a08d2e4cef6c498b76ba5bd4858e4c6ef51da1a5a1f27139a022e20248'], + }), + ('jaxlib', '0.3.22', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.3.22.tar.gz + '680a6f5265ba26d5515617a95ae47244005366f879a5c321782fde60f34e6d0d', + # tensorflow-cb946f223b9b3fa04efdbb7a0e6a9dabb22a7057.tar.gz + '9a7a7a87356bdeef5874fae135de380466482b593469035be3609a9cd2c153c4', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'patches': [ + 'jax-0.3.9_relax-test-tolerance.patch', + ], + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': [ + {'jax-v0.3.23.tar.gz': 'fa8c68a82fa2fcf3d272bf239c77e7028bb6077466a53349ce85f6e85ed623db'}, + {'jax-0.3.9_relax-test-tolerance.patch': + '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 44f8c71cb913161c41e8d43cb63f6740291b5145 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 17:44:25 +0200 Subject: [PATCH 5210/9987] {bio}[foss/2021a] scvi-tools v0.16.4, scikit-misc v0.1.4 w/ Python 3.9.5 --- .../scikit-misc-0.1.4-foss-2021a.eb | 25 +++++ .../scvi-tools-0.16.4-foss-2021a.eb | 92 +++++++++++++++++++ 2 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2021a.eb b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2021a.eb new file mode 100644 index 00000000000..d50466cda7d --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2021a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'scikit-misc' +version = '0.1.4' + +homepage = 'https://github.com/has2k1/scikit-misc' +description = "Miscellaneous tools for data analysis and scientific computing" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f7746a0347811063e1ecf9121df94835785003953c38b5ba84f63fc508c22911'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'skmisc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a.eb new file mode 100644 index 00000000000..39b2aa92da3 --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a.eb @@ -0,0 +1,92 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '0.16.4' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('h5py', '3.2.1'), + ('IPython', '7.25.0'), + ('jax', '0.3.9'), + ('openpyxl', '3.0.7'), + ('PyTorch-Lightning', '1.5.9'), + ('scikit-learn', '0.24.2'), + ('dm-tree', '0.1.6'), + ('scanpy', '1.8.1'), + ('scikit-misc', '0.1.4'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + # stick to flax v0.5.2, which does not require tensorstore (which is built with Bazel) or a very recent jax yet... + ('flax', '0.5.2', { + 'checksums': ['5f07775fd4ba1926192ab6eb48c9adbd5658ddaf8585fb0c561741400d5599ff'], + }), + ('multipledispatch', '0.6.0', { + 'checksums': ['a7ab1451fd0bf9b92cab3edbd7b205622fb767aeefb4fb536c2e3de9e0a38bea'], + }), + ('numpyro', '0.10.1', { + 'checksums': ['dfa896f01c8df43ddd41663af2b3e2fc4aea73489e669474e83329b183b29150'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.5', { + 'checksums': ['686858320f8f220c82a6c7eeb54dcdcaa4f3d7f66690dacd13a24baa1ee8299e'], + }), + ('optax', '0.1.3', { + 'checksums': ['159e954405c3ba2072c2add7cec5532be7399bcafab3039acbf608b11844a879'], + }), + ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + }), + ('pyro-ppl', '1.8.0', { + 'modulename': 'pyro', + 'checksums': ['68e4ea30f219227dd88e55de2550d3f8c20a20adbdb67ad1e13b50868bb2ac0c'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '11.1.0', { + 'checksums': ['43e03d8eec12e21beaecc22c828a41c4247356414a12d5879834863d4ad53816'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('mudata', '0.2.0', { + 'checksums': ['6eef13ec2165340cd6d79fe4aabe687e9c53867c818c8dbe1cf0b6be0e5d1e75'], + }), + (name, version, { + 'modulename': 'scvi', + 'checksums': ['95c67870ecfa1d0e0b80027d3239bb47ca6cd3db2f2524985f5d31903b766eeb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 77049b4165359c8246354200de75b6b2ab6024e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 17:51:30 +0200 Subject: [PATCH 5211/9987] {bio}[foss/2021a] scvi-tools v0.16.4 w/ Python 3.9.5 + CUDA 11.3.1 --- ...cvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb | 94 +++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..a5b9c930ebd --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,94 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '0.16.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('h5py', '3.2.1'), + ('IPython', '7.25.0'), + ('jax', '0.3.9', versionsuffix), + ('openpyxl', '3.0.7'), + ('PyTorch-Lightning', '1.5.9', versionsuffix), + ('scikit-learn', '0.24.2'), + ('dm-tree', '0.1.6'), + ('scanpy', '1.8.1'), + ('scikit-misc', '0.1.4'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + # stick to flax v0.5.2, which does not require tensorstore (which is built with Bazel) or a very recent jax yet... + ('flax', '0.5.2', { + 'checksums': ['5f07775fd4ba1926192ab6eb48c9adbd5658ddaf8585fb0c561741400d5599ff'], + }), + ('multipledispatch', '0.6.0', { + 'checksums': ['a7ab1451fd0bf9b92cab3edbd7b205622fb767aeefb4fb536c2e3de9e0a38bea'], + }), + ('numpyro', '0.10.1', { + 'checksums': ['dfa896f01c8df43ddd41663af2b3e2fc4aea73489e669474e83329b183b29150'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.5', { + 'checksums': ['686858320f8f220c82a6c7eeb54dcdcaa4f3d7f66690dacd13a24baa1ee8299e'], + }), + ('optax', '0.1.3', { + 'checksums': ['159e954405c3ba2072c2add7cec5532be7399bcafab3039acbf608b11844a879'], + }), + ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + }), + ('pyro-ppl', '1.8.0', { + 'modulename': 'pyro', + 'checksums': ['68e4ea30f219227dd88e55de2550d3f8c20a20adbdb67ad1e13b50868bb2ac0c'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '11.1.0', { + 'checksums': ['43e03d8eec12e21beaecc22c828a41c4247356414a12d5879834863d4ad53816'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('mudata', '0.2.0', { + 'checksums': ['6eef13ec2165340cd6d79fe4aabe687e9c53867c818c8dbe1cf0b6be0e5d1e75'], + }), + (name, version, { + 'modulename': 'scvi', + 'checksums': ['95c67870ecfa1d0e0b80027d3239bb47ca6cd3db2f2524985f5d31903b766eeb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 934e5be97e2f87044b863f3c682192d40b984c2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 18:14:21 +0200 Subject: [PATCH 5212/9987] adding easyconfigs: Fiji-2.9.0-Java-1.8.eb --- .../easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb new file mode 100644 index 00000000000..c655cd16540 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb @@ -0,0 +1,49 @@ +easyblock = 'PackedBinary' + +name = 'Fiji' +version = '2.9.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://fiji.sc' +description = """Fiji is an image processing package—a 'batteries-included' distribution of + ImageJ, bundling a lot of plugins which facilitate scientific image analysis. +This release is based on ImageJ-2.1.0 and Fiji-2.1.1""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s/'] +sources = ['fiji-%(version)s-nojre.zip'] +checksums = ['970fb80cf2a4fe8bfcecc2cc9a8617b9ab28f19fbe229ea6ae2f7f42674c8a42'] + +dependencies = [('Java', '1.8', '', SYSTEM)] + +postinstallcmds = [ + # Remove binaries for other platforms + 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}', + # Enable any update site (edit existing site with same parameters to enable it) + # Full list at https://imagej.github.io/list-of-update-sites/ + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' + ' https://sites.imagej.net/ImageScience/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' + ' https://sites.imagej.net/Tboudier/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ilastik"' + ' https://sites.imagej.net/Ilastik/', + # Add a new update site + # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' + # ' https://site.url/NewName/', + # Update the installation + '%(installdir)s/ImageJ-linux64 --headless --update update', +] + +sanity_check_paths = { + 'files': ['ImageJ-linux64'], + 'dirs': [], +} + +modloadmsg = """ +Additional plugins can be installed in your $HOME/.plugins folder or requested to user support +Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless` +More information at https://imagej.net/Headless +""" + +moduleclass = 'vis' From aad5dd9d48c61292e060975d9453fa51e3bb820f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 18:35:17 +0200 Subject: [PATCH 5213/9987] allow use of jax 0.3.9 as dependency for scvi-tools --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 45c9bcfa712..2e63f19e967 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -485,7 +485,7 @@ def check_dep_vars(self, gen, dep, dep_vars): # some software packages require a specific (older/newer) version of a particular dependency alt_dep_versions = { - 'jax': [(r'0\.3\.9', [r'AlphaFold-2\.2\.2-'])], + 'jax': [(r'0\.3\.9', [r'AlphaFold-2\.2\.2-foss-2021a', r'scvi-tools-0\.16\.4-foss-2021a'])], # arrow-R 6.0.0.2 is used for two R/R-bundle-Bioconductor sets (4.1.2/3.14 and 4.2.0/3.15) 'arrow-R': [('6.0.0.2', [r'R-bundle-Bioconductor-'])], # EMAN2 2.3 requires Boost(.Python) 1.64.0 From d184b5d302a432d653c4e1709e1d87d6469fa689 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 18:24:45 +0200 Subject: [PATCH 5214/9987] add exception for egl dependency variant of glew --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 518f5594e1d..4eb56e770a7 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -473,6 +473,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], + # egl variant of glew is required by libwpe + 'glew': [('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], From 7b731cbcbd5f437aa69d5bd389e3d7d001f1289e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 19:57:26 +0200 Subject: [PATCH 5215/9987] clean up TELEMAC-MASCARET easyconfig based on suggestions by @jfgrimm --- .../TELEMAC-MASCARET-8p3r1-foss-2021b.eb | 63 ++++++++++--------- 1 file changed, 32 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb index 5b6623b4774..a28af36eaef 100644 --- a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb @@ -29,37 +29,38 @@ unpack_options = '--strip-components=1' buildininstalldir = True -install_cmd = "export HOMETEL=$PWD && " -# add Python scripts to $PATH and $PYTHONPATH -install_cmd += "export PATH=$HOMETEL/scripts/python3/:$PATH && " -install_cmd += "export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH && " -# force python to flush its output -install_cmd += "export PYTHONUNBUFFERED=1 && " - -# export LD_LIBRARY_PATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$LD_LIBRARY_PATH -# export PYTHONPATH=$HOMETEL/builds/$USETELCFG/wrap_api/lib:$PYTHONPATH - -install_cmd += "cp $HOMETEL/configs/systel.edf.cfg $HOMETEL/configs/systel.easybuild.cfg && " -install_cmd += "sed -i 's/S9.gfortran/easybuild/g' $HOMETEL/configs/systel.easybuild.cfg && " -# strip out use of AED, GOTM, MED (optional dependencies) -install_cmd += "sed -i 's/\(^[a-z]*_aed:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " -install_cmd += "sed -i 's/\(^[a-z]*_gotm:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " -install_cmd += "sed -i 's/\(^[a-z]*_med:\).*/\\1/g' $HOMETEL/configs/systel.easybuild.cfg && " -# replace -O2 with desired compiler options -install_cmd += 'sed -i "s/-O2/$F90FLAGS/g" $HOMETEL/configs/systel.easybuild.cfg && ' -# fix linker option for BLAS -install_cmd += 'sed -i "s/ -lblas/ $LIBBLAS/g" $HOMETEL/configs/systel.easybuild.cfg && ' -# downgrade Fortran compiler error to warning -install_cmd += "sed -i 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g' $HOMETEL/configs/systel.easybuild.cfg && " -install_cmd += "export SYSTELCFG=$HOMETEL/configs/systel.easybuild.cfg && " -install_cmd += "export USETELCFG=easybuild && " - -install_cmd += "export SCALAPACKHOME=$EBROOTSCALAPACK && " -install_cmd += "export METISHOME=$EBROOTMETIS && " -install_cmd += "export SCOTCHHOME=$EBROOTSCOTCH && " -install_cmd += "export MUMPSHOME=$EBROOTMUMPS && " -install_cmd += "export HDF5HOME=$EBROOTHDF5 && " -install_cmd += "config.py && compile_telemac.py -j %(parallel)s" +local_tweak_cfg_cmd = ' '.join([ + "sed -i -e 's/S9.gfortran/easybuild/g'", + # strip out use of AED, GOTM, MED (optional dependencies) + "-e 's/\(^[a-z]*_aed:\).*/\\1/g' -e 's/\(^[a-z]*_gotm:\).*/\\1/g' -e 's/\(^[a-z]*_med:\).*/\\1/g'", + # replace -O2 with desired compiler options + '-e "s/-O2/$F90FLAGS/g"', + # fix linker option for BLAS + '-e "s/ -lblas/ $LIBBLAS/g"', + # downgrade Fortran compiler error to warning + "-e 's/^fflags_gfo:/fflags_gfo: -fallow-invalid-boz/g'", + "$HOMETEL/configs/systel.easybuild.cfg", +]) + +install_cmd = ' && '.join([ + "export HOMETEL=$PWD", + # add Python scripts to $PATH and $PYTHONPATH + "export PATH=$HOMETEL/scripts/python3/:$PATH", + "export PYTHONPATH=$HOMETEL/scripts/python3:$PYTHONPATH", + # force python to flush its output + "export PYTHONUNBUFFERED=1", + "cp $HOMETEL/configs/systel.edf.cfg $HOMETEL/configs/systel.easybuild.cfg", + local_tweak_cfg_cmd, + "export SYSTELCFG=$HOMETEL/configs/systel.easybuild.cfg", + "export USETELCFG=easybuild", + "export SCALAPACKHOME=$EBROOTSCALAPACK", + "export METISHOME=$EBROOTMETIS", + "export SCOTCHHOME=$EBROOTSCOTCH", + "export MUMPSHOME=$EBROOTMUMPS", + "export HDF5HOME=$EBROOTHDF5", + "config.py", + "compile_telemac.py -j %(parallel)s", +]) sanity_check_paths = { 'files': ['builds/easybuild/bin/telemac2d', 'builds/easybuild/bin/telemac3d', From 67912caf99d976e37dbc601db97a9d382c2c8fe7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 21 Oct 2022 13:17:34 +0800 Subject: [PATCH 5216/9987] prepare release notes for EasyBuild v4.6.2 + bump version to 4.6.2 --- RELEASE_NOTES | 49 ++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 49 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 698ecd7803e..2abf240dc2b 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,57 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 15,332 easyconfig files, for 2,773 different software packages, +The latest version of easybuild-easyconfig provides 15,535 easyconfig files, for 2,798 different software packages, incl. 37 different (compiler) toolchains. +4.6.2 (October 21st 2022) +------------------------- + +update/bugfix release + +- added example easyconfig files for 25 new software packages: + - AGAT (#16261), AMAPVox (#16438), Avogadro2 (#16257), buildingspy (#16308), CDBtools (#16436), + Compress-Raw-Zlib (#16307), CUDAcompat (#15892), CWIPI (#16342), enchant-2 (#16319), f90wrap (#16346), + Imath (#16276), Mamba (#16432), Miller (#16221), nghttp2 (#16096), ngtcp2 (#16098), NVSHMEM (#16254), + pairsnp (#16331), paladin (#16320), PyMOL (#16394), python-irodsclient (#16328), ruffus (#16428), + TELEMAC-MASCARET (#16274), torchdata (#16344), Waylandpp (#16092), x13as (#16163) +- added additional easyconfigs for various supported software packages, including: + - ABAQUS 2022, ACTC 1.1, AGAT 0.9.2, AMAPVox 1.9.4, Amber 22.0, AMS 2022.102, Archive Zip, ASE 3.22.1, ASE 3.22.1, ASE 3.22.1, atools 1.5.1, Autoconf 2.71, AutoDock Vina, Automake 1.16.5, Automake 1.16.5.eb, Autotools 20220317, Avogadro2 1.97.0, beagle lib, Beast 2.6.7, Bio DB, biogeme 3.2.10, BioPerl 1.7.8, Boost.Python 1.79.0, buildingspy 4.0.0, ccache 4.6.3.eb, CDBtools 0.99, Clang Python, Compress Raw, CUDAcompat 11.6, CUDAcompat 11.6.eb, CUDAcompat 11.7, CUDAcompat 11.7.eb, CUDAcompat 11.eb, CWIPI 0.12.0, DB 18.1.40, DBD mysql, DB_File 1.858, dbus glib, deal.II 9.1.1, Delly 1.1.5, EasyBuild 4.6.1.eb, enchant 2, ESMF 8.3.0, expat 2.4.9, expecttest 0.1.3, f90wrap 0.2.8, FDS 6.7.9, FFTW 3.3.10, file 5.43, FLTK 1.3.8, FTGL 2.4.0, gawk 5.1.1, gc 8.2.2, GConf 3.2.6, GitPython 3.1.27, gmpy2 2.1.2, Go 1.18.3.eb, GPAW 22.8.0, GPAW 22.8.0, GPAW 22.8.0, GPAW 22.8.0, groff 1.22.4, Guile 3.0.8, hiredis 1.0.2, HPL 2.3, htop 3.2.1.eb, hunspell 1.7.1, iimpi 2022.09.eb, Imath 3.1.5, imgaug 0.4.0, imgaug 0.4.0, imkl 2022.2.0.eb, imkl FFTW, impi 2021.7.0, intel 2022.09.eb, intel compilers, IPython 8.5.0, jq 1.6, jq 1.6, jq 1.6, Judy 1.0.5, Julia 1.6.7, Julia 1.8.0, Julia 1.8.2, LDC 1.24.0, LDC 1.30.0, libaio 0.3.112, libcint 5.1.6, libconfig 1.7.3, libreadline 8.2, libsodium 1.0.18, LibSoup 3.0.7, LIBSVM 3.30, libtool 2.4.7, libtool 2.4.7.eb, libunistring 1.0, libvdwxc 0.4.0, libwebp 1.2.4, likwid 5.2.2, LMfit 1.0.3, LMfit 1.0.3, LZO 2.10, magma 2.6.2, Mamba 4.14.0, MariaDB 10.9.3, matplotlib 3.5.2, MDTraj 1.9.7, MDTraj 1.9.7, MDTraj 1.9.7, Miller 6.4.0.eb, Mmg 5.6.0, MMseqs2 13, ncdu 1.17, ncurses 6.3, netcdf4 python, Nextflow 22.10.0.eb, NFFT 3.5.3, nghttp2 1.48.0, ngtcp2 0.7.0, Nipype 1.8.5, numactl 2.0.16, NVSHMEM 2.5.0, onedrive 2.4.21, OpenCV 4.5.5, OpenCV 4.6.0, OpenEXR 3.1.5, OpenJPEG 2.5.0, OpenMM 7.7.0, OpenMM 7.7.0, OpenMM 7.7.0, OpenPGM 5.2.122, OpenSSL 1.1.1q, p4est 2.2, pairsnp 0.0.7, paladin 1.4.6, paladin 1.4.6, Perl 5.36.0, Pillow SIMD, pkgconf 1.9.3, pocl 1.8, pocl 1.8, PostgreSQL 14.4, POV Ray, PRISMS PF, PyCharm 2022.2.2.eb, PyMOL 2.5.0, pyqstem 1.0.3, pyqstem 1.0.3, python irodsclient, python irodsclient, PyTorch 1.12.0, PyTorch 1.12.0, PyTorch Lightning, PyTorch Lightning, RDFlib 6.2.0, ruamel.yaml 0.17.21, ruffus 2.8.4, SAMtools 1.16.1, SAMtools 1.16.1, scikit learn, Score P, SDL2 2.0.22, spaln 2.4.12, spglib python, spglib python, spglib python, SRA Toolkit, SuiteSparse 5.13.0, SUNDIALS 6.3.0, SUNDIALS 6.3.0, SuperLU 5.3.0, SuperLU 5.3.0, SuperLU 5.3.0, SuperLU 5.3.0, sympy 1.10.1, sympy 1.11.1, TELEMAC MASCARET, tensorboard 2.10.0, torchdata 0.3.0, torchvision 0.12.0, torchvision 0.13.1, TRIQS 3.1.1, TRIQS cthyb, TRIQS dft_tools, TRIQS tprf, TRUST4 1.0.7, TurboVNC 3.0.1, typing extensions, UCX 1.13.1, umap learn, VEP 107, VMD 1.9.4a57, Wannier90 3.1.0, Wayland 1.21.0, Waylandpp 1.0.0, wxWidgets 3.2.1, x13as 1, x13as 1, XML LibXML, xprop 1.2.5, xproto 7.0.31, xtrans 1.3.5, ZeroMQ 4.3.4 +- minor enhancements, including: + - configure recent pocl versions to -DLLC_HOST_CPU=native to avoid CPU auto-detection (#16246) + - add multidep exception for ncbi-vdb-3.0.0 which requires HDF5 1.10.x (#16316) + - deprecate use of True in favour of SYSTEM for system-toolchain dependencies in easyconfigs using a recent toolchain version (>2019b) (#16384) + - enable running of LAPACK tests for recent OpenBLAS easyconfigs + add patch to fix failing LAPACK tests due to use of -ftree-vectorize (#16406) + - add GITHUB_(LOWER_)RELEASE to known constants in setup.cfg (#16422) + - add AMAPVox extension to R v4.2.1 (#16439) + - add OpenEXR depenency to POV-Ray 3.7.0.10 (#16408) +- various bug fixes, including: + - add patch for OpenBLAS 0.3.7-0.3.12 to fix miscomputation on POWER (#16199) + - skip flaky test in PyTorch 1.9.0 (#16258) + - add --with-versioned-syms to ncurses 6.2 and 6.3 (#16270) + - add missing pkg-config builddep to Guile (#16317) + - add missing build dep pkg-config to enchant-2 (#16319) + - add patches to fix incompatibilites between ASE and other packages in 2022a toolchain (#16332) + - add patches to fix PyTorch 1.11 on POWER (#16339) + - add patches for Ambertools 21 to Amber 20.11 to work with new easyblock (#16343) + - use Intel MPI from EasyBuild toolchain in AMS (#16363) + - fix execution permissions for bin/ngm* for NextGenMap v0.5.5 (#16383) + - fix using provided qhull and freetype dependencies for matplotlib 3.5.2 by creating mplsetup.cfg rather than setup.cfg (#16396) + - fix GitHub download link in for libpsl 0.21.1 (#16397) + - stick to http in source URL for stride.tar.gz in VMD 1.9.4a51 easyconfigs due to problems with SSL certificate (#16403) + - add patch to detect available cores and remove unneeded deps for Unicycler 0.5.0 (#16407) + - add missing ICU + libunistring dependencies for libpsl 0.21.1 w/ GCCcore/10.3.0 (#16410) + - add patch to GCC 11.x + 12.x to fix vectorizer bug (#16411) + - use SYSTEM template constant to indicate that CUDA dependency of torchvision uses system toolchain (#16418) + - fix checksum for GULP 6.1 (#16423) + - add bzip2 and libxml2 as dependencies for netCDF 4.9.0 (#16450) +- other changes: + - drop Java dep from ABAQUS 2022 (#16314) + - update easyconfigs to use `SYSTEM` template constant instead of `True` in dependencies (#16386) + - update libxml2 + libxslt easyconfigs to use gnome.org source URL (#16429) + + v4.6.1 (September 12th 2022) ---------------------------- diff --git a/setup.py b/setup.py index 24b137e9759..0528da1ca3f 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.6.2.dev0' +VERSION = '4.6.2' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From bee15c936201b7ed0610c4f634dca86d437428e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Oct 2022 09:37:01 +0200 Subject: [PATCH 5217/9987] minor tweaks for release notes for v4.6.2 --- RELEASE_NOTES | 32 +++++++++++++++++++++----------- 1 file changed, 21 insertions(+), 11 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 2abf240dc2b..693825cf873 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -12,18 +12,29 @@ incl. 37 different (compiler) toolchains. update/bugfix release +- add easyconfig for intel/2022.09 toolchain (#16435) - added example easyconfig files for 25 new software packages: - AGAT (#16261), AMAPVox (#16438), Avogadro2 (#16257), buildingspy (#16308), CDBtools (#16436), - Compress-Raw-Zlib (#16307), CUDAcompat (#15892), CWIPI (#16342), enchant-2 (#16319), f90wrap (#16346), + Compress-Raw-Zlib (#16307), CUDAcompat (#15892), CWIPI (#16342), enchant-2 (#16082, #16319), f90wrap (#16346), Imath (#16276), Mamba (#16432), Miller (#16221), nghttp2 (#16096), ngtcp2 (#16098), NVSHMEM (#16254), pairsnp (#16331), paladin (#16320), PyMOL (#16394), python-irodsclient (#16328), ruffus (#16428), TELEMAC-MASCARET (#16274), torchdata (#16344), Waylandpp (#16092), x13as (#16163) - added additional easyconfigs for various supported software packages, including: - - ABAQUS 2022, ACTC 1.1, AGAT 0.9.2, AMAPVox 1.9.4, Amber 22.0, AMS 2022.102, Archive Zip, ASE 3.22.1, ASE 3.22.1, ASE 3.22.1, atools 1.5.1, Autoconf 2.71, AutoDock Vina, Automake 1.16.5, Automake 1.16.5.eb, Autotools 20220317, Avogadro2 1.97.0, beagle lib, Beast 2.6.7, Bio DB, biogeme 3.2.10, BioPerl 1.7.8, Boost.Python 1.79.0, buildingspy 4.0.0, ccache 4.6.3.eb, CDBtools 0.99, Clang Python, Compress Raw, CUDAcompat 11.6, CUDAcompat 11.6.eb, CUDAcompat 11.7, CUDAcompat 11.7.eb, CUDAcompat 11.eb, CWIPI 0.12.0, DB 18.1.40, DBD mysql, DB_File 1.858, dbus glib, deal.II 9.1.1, Delly 1.1.5, EasyBuild 4.6.1.eb, enchant 2, ESMF 8.3.0, expat 2.4.9, expecttest 0.1.3, f90wrap 0.2.8, FDS 6.7.9, FFTW 3.3.10, file 5.43, FLTK 1.3.8, FTGL 2.4.0, gawk 5.1.1, gc 8.2.2, GConf 3.2.6, GitPython 3.1.27, gmpy2 2.1.2, Go 1.18.3.eb, GPAW 22.8.0, GPAW 22.8.0, GPAW 22.8.0, GPAW 22.8.0, groff 1.22.4, Guile 3.0.8, hiredis 1.0.2, HPL 2.3, htop 3.2.1.eb, hunspell 1.7.1, iimpi 2022.09.eb, Imath 3.1.5, imgaug 0.4.0, imgaug 0.4.0, imkl 2022.2.0.eb, imkl FFTW, impi 2021.7.0, intel 2022.09.eb, intel compilers, IPython 8.5.0, jq 1.6, jq 1.6, jq 1.6, Judy 1.0.5, Julia 1.6.7, Julia 1.8.0, Julia 1.8.2, LDC 1.24.0, LDC 1.30.0, libaio 0.3.112, libcint 5.1.6, libconfig 1.7.3, libreadline 8.2, libsodium 1.0.18, LibSoup 3.0.7, LIBSVM 3.30, libtool 2.4.7, libtool 2.4.7.eb, libunistring 1.0, libvdwxc 0.4.0, libwebp 1.2.4, likwid 5.2.2, LMfit 1.0.3, LMfit 1.0.3, LZO 2.10, magma 2.6.2, Mamba 4.14.0, MariaDB 10.9.3, matplotlib 3.5.2, MDTraj 1.9.7, MDTraj 1.9.7, MDTraj 1.9.7, Miller 6.4.0.eb, Mmg 5.6.0, MMseqs2 13, ncdu 1.17, ncurses 6.3, netcdf4 python, Nextflow 22.10.0.eb, NFFT 3.5.3, nghttp2 1.48.0, ngtcp2 0.7.0, Nipype 1.8.5, numactl 2.0.16, NVSHMEM 2.5.0, onedrive 2.4.21, OpenCV 4.5.5, OpenCV 4.6.0, OpenEXR 3.1.5, OpenJPEG 2.5.0, OpenMM 7.7.0, OpenMM 7.7.0, OpenMM 7.7.0, OpenPGM 5.2.122, OpenSSL 1.1.1q, p4est 2.2, pairsnp 0.0.7, paladin 1.4.6, paladin 1.4.6, Perl 5.36.0, Pillow SIMD, pkgconf 1.9.3, pocl 1.8, pocl 1.8, PostgreSQL 14.4, POV Ray, PRISMS PF, PyCharm 2022.2.2.eb, PyMOL 2.5.0, pyqstem 1.0.3, pyqstem 1.0.3, python irodsclient, python irodsclient, PyTorch 1.12.0, PyTorch 1.12.0, PyTorch Lightning, PyTorch Lightning, RDFlib 6.2.0, ruamel.yaml 0.17.21, ruffus 2.8.4, SAMtools 1.16.1, SAMtools 1.16.1, scikit learn, Score P, SDL2 2.0.22, spaln 2.4.12, spglib python, spglib python, spglib python, SRA Toolkit, SuiteSparse 5.13.0, SUNDIALS 6.3.0, SUNDIALS 6.3.0, SuperLU 5.3.0, SuperLU 5.3.0, SuperLU 5.3.0, SuperLU 5.3.0, sympy 1.10.1, sympy 1.11.1, TELEMAC MASCARET, tensorboard 2.10.0, torchdata 0.3.0, torchvision 0.12.0, torchvision 0.13.1, TRIQS 3.1.1, TRIQS cthyb, TRIQS dft_tools, TRIQS tprf, TRUST4 1.0.7, TurboVNC 3.0.1, typing extensions, UCX 1.13.1, umap learn, VEP 107, VMD 1.9.4a57, Wannier90 3.1.0, Wayland 1.21.0, Waylandpp 1.0.0, wxWidgets 3.2.1, x13as 1, x13as 1, XML LibXML, xprop 1.2.5, xproto 7.0.31, xtrans 1.3.5, ZeroMQ 4.3.4 + - Amber 22.0, AMS 2022.102, ASE 3.22.1, atools 1.5.1, Beast 2.6.7, biogeme 3.2.10, Boost.Python 1.79.0, ccache 4.6.3, + dbus-glib 0.112, Delly 1.1.5, ESMF 8.3.0, expat 2.4.9, FDS 6.7.9, file 5.43, FLTK 1.3.8, FTGL 2.4.0, gc 8.2.2, + GitPython 3.1.27, Go 1.18.3, GPAW 22.8.0, Guile 3.0.8, htop 3.2.1, hunspell 1.7.1, IPython 8.5.0, jq 1.6, + Julia 1.8.2, LDC 1.30.0, libcint 5.1.6, libconfig 1.7.3, libreadline 8.2, LibSoup 3.0.7, LIBSVM 3.30, + libwebp 1.2.4, likwid 5.2.2, MariaDB 10.9.3, matplotlib 3.5.2, ncdu 1.17, netcdf4-python 1.6.1, Nextflow 22.10.0, + NFFT 3.5.3, Nipype 1.8.5, numactl 2.0.16, onedrive 2.4.21, OpenCV 4.6.0, OpenEXR 3.1.5, OpenJPEG 2.5.0, + OpenMM 7.7.0, OpenPGM 5.2.122, OpenSSL 1.1.1q, Perl 5.36.0, Pillow-SIMD 9.2.0, pkgconf 1.9.3, PostgreSQL 14.4, + PyCharm 2022.2.2, PyTorch 1.12.0, PyTorch 1.12.0, PyTorch-Lightning 1.7.7, RDFlib 6.2.0, SAMtools 1.16.1, + scikit-learn 1.1.2, Score-P 7.1, SDL2 2.0.22, spaln 2.4.12, spglib-python 2.0.0, SuiteSparse 5.13.0, SUNDIALS 6.3.0, + sympy 1.11.1, tensorboard 2.10.0, torchvision 0.13.1, TRIQS 3.1.1, TRIQS-cthyb 3.1.0, TRIQS-dft_tools 3.1.0, + TRIQS-tprf 3.1.1, TRUST4 1.0.7, TurboVNC 3.0.1, typing-extensions 4.3.0, UCX 1.13.1, umap-learn 0.5.3, VEP 107, + VMD 1.9.4a57, Wayland 1.21.0, wxWidgets 3.2.1, xprop 1.2.5 - minor enhancements, including: - - configure recent pocl versions to -DLLC_HOST_CPU=native to avoid CPU auto-detection (#16246) - - add multidep exception for ncbi-vdb-3.0.0 which requires HDF5 1.10.x (#16316) - - deprecate use of True in favour of SYSTEM for system-toolchain dependencies in easyconfigs using a recent toolchain version (>2019b) (#16384) + - configure recent pocl versions with -DLLC_HOST_CPU=native to avoid CPU auto-detection (#16246) + - add multi-dep exception to easyconfigs test suite for ncbi-vdb-3.0.0 which requires HDF5 1.10.x (#16316) - enable running of LAPACK tests for recent OpenBLAS easyconfigs + add patch to fix failing LAPACK tests due to use of -ftree-vectorize (#16406) - add GITHUB_(LOWER_)RELEASE to known constants in setup.cfg (#16422) - add AMAPVox extension to R v4.2.1 (#16439) @@ -32,25 +43,24 @@ update/bugfix release - add patch for OpenBLAS 0.3.7-0.3.12 to fix miscomputation on POWER (#16199) - skip flaky test in PyTorch 1.9.0 (#16258) - add --with-versioned-syms to ncurses 6.2 and 6.3 (#16270) - - add missing pkg-config builddep to Guile (#16317) - - add missing build dep pkg-config to enchant-2 (#16319) + - add missing pkg-config build dependency to Guile (#16317) - add patches to fix incompatibilites between ASE and other packages in 2022a toolchain (#16332) - add patches to fix PyTorch 1.11 on POWER (#16339) - - add patches for Ambertools 21 to Amber 20.11 to work with new easyblock (#16343) + - add patches for Ambertools 21 to Amber 20.11 to work with updated Amber easyblock (#16343) - use Intel MPI from EasyBuild toolchain in AMS (#16363) - fix execution permissions for bin/ngm* for NextGenMap v0.5.5 (#16383) - - fix using provided qhull and freetype dependencies for matplotlib 3.5.2 by creating mplsetup.cfg rather than setup.cfg (#16396) + - fix using provided Qhull and freetype dependencies for matplotlib 3.5.2 by creating mplsetup.cfg rather than setup.cfg (#16396) - fix GitHub download link in for libpsl 0.21.1 (#16397) - stick to http in source URL for stride.tar.gz in VMD 1.9.4a51 easyconfigs due to problems with SSL certificate (#16403) - add patch to detect available cores and remove unneeded deps for Unicycler 0.5.0 (#16407) - add missing ICU + libunistring dependencies for libpsl 0.21.1 w/ GCCcore/10.3.0 (#16410) - add patch to GCC 11.x + 12.x to fix vectorizer bug (#16411) - - use SYSTEM template constant to indicate that CUDA dependency of torchvision uses system toolchain (#16418) - fix checksum for GULP 6.1 (#16423) - add bzip2 and libxml2 as dependencies for netCDF 4.9.0 (#16450) - other changes: - drop Java dep from ABAQUS 2022 (#16314) - - update easyconfigs to use `SYSTEM` template constant instead of `True` in dependencies (#16386) + - deprecate use of True in favour of SYSTEM for system-toolchain dependencies in easyconfigs using a recent toolchain version (>2019b) (#16384) + - update easyconfigs to use `SYSTEM` template constant instead of `True` in dependencies (#16386, #16418) - update libxml2 + libxslt easyconfigs to use gnome.org source URL (#16429) From 5fbc3d70eb522ff05453c781536f45a371335d16 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 21 Oct 2022 10:54:44 +0200 Subject: [PATCH 5218/9987] adding easyconfigs: Coreutils-9.1-GCCcore-11.3.0.eb, Coreutils-9.1-GCCcore-12.2.0.eb --- .../Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ .../Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c17a9e2fafd --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "9.1" + +homepage = 'https://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text +manipulation utilities of the GNU operating system. These are +the core utilities which are expected to exist on every +operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d180e31a737 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = "Coreutils" +version = "9.1" + +homepage = 'https://www.gnu.org/software/coreutils/' +description = """The GNU Core Utilities are the basic file, shell and text +manipulation utilities of the GNU operating system. These are +the core utilities which are expected to exist on every +operating system. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ['bin/sort', 'bin/echo', 'bin/du', 'bin/date', 'bin/true'], + 'dirs': [] +} + +moduleclass = 'tools' From f11d34b8b40d453c80eaff9bbfdee60c9fd69eb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Oct 2022 10:58:59 +0200 Subject: [PATCH 5219/9987] bump version to 4.6.3dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0528da1ca3f..75d8dacffe3 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.6.2' +VERSION = '4.6.3.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From acd1e0442d09ab4cc9f01210f6f84313776a1260 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 21 Oct 2022 11:48:47 +0200 Subject: [PATCH 5220/9987] adding easyconfigs: torchsampler-0.1.2-foss-2022a.eb, torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb --- ...rchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb | 30 +++++++++++++++++++ .../torchsampler-0.1.2-foss-2022a.eb | 28 +++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..30864489390 --- /dev/null +++ b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'torchsampler' +version = '0.1.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/ufoym/imbalanced-dataset-sampler' +description = """ +A (PyTorch) imbalanced dataset sampler for oversampling low classes and +undersampling high frequent ones.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.0', versionsuffix), + ('torchvision', '0.13.1', versionsuffix), +] + +exts_list = [ + (name, version, { + 'checksums': ['6503acf0ff76888905595006a45c2a2fa017f7a13fffbfcddb3827ef8226ea78'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb new file mode 100644 index 00000000000..3b4a760bfbc --- /dev/null +++ b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'torchsampler' +version = '0.1.2' + +homepage = 'https://github.com/ufoym/imbalanced-dataset-sampler' +description = """ +A (PyTorch) imbalanced dataset sampler for oversampling low classes and +undersampling high frequent ones.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('torchvision', '0.13.1'), +] + +exts_list = [ + (name, version, { + 'checksums': ['6503acf0ff76888905595006a45c2a2fa017f7a13fffbfcddb3827ef8226ea78'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'devel' From d15b1ead95141beae65f0c396f9c9d1a59062081 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Oct 2022 11:20:46 +0100 Subject: [PATCH 5221/9987] Add patch for correctly skipping a test and add matplotlib builddep --- .../easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb | 5 +++++ ...-0.3.23_correctly-skip-from_dlpack-tests.patch | 15 +++++++++++++++ 2 files changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb index 23d90b71f8b..54a86884e76 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -17,6 +17,7 @@ builddependencies = [ ('pytest-xdist', '2.5.0'), # git 2.x required to fetch repository 'io_bazel_rules_docker' ('git', '2.36.0', '-nodocs'), + ('matplotlib', '3.5.2'), # required for tests/lobpcg_test.py ] dependencies = [ @@ -93,6 +94,7 @@ exts_list = [ (name, version, { 'patches': [ 'jax-0.3.9_relax-test-tolerance.patch', + 'jax-0.3.23_correctly-skip-from_dlpack-tests.patch', ], 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], @@ -100,7 +102,10 @@ exts_list = [ {'jax-v0.3.23.tar.gz': 'fa8c68a82fa2fcf3d272bf239c77e7028bb6077466a53349ce85f6e85ed623db'}, {'jax-0.3.9_relax-test-tolerance.patch': '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d'}, + {'jax-0.3.23_correctly-skip-from_dlpack-tests.patch': + 'a69ce7280ca8bb42e671217f00d9147f8c64b4b7ba65dea7f05f2c6de757b279'}, ], + 'runtest': "pytest -n %(parallel)s tests", }), ] diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch b/easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch new file mode 100644 index 00000000000..7354e39c8e3 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch @@ -0,0 +1,15 @@ +np.from_dlpack was not added until numpy 1.23 +Patch based off https://github.com/google/jax/pull/12900 and added by Simon Branford (University of Birmingham) +diff --git a/tests/array_interoperability_test.py b/tests/array_interoperability_test.py +index cc2f3a6c08d..ac04ee637c8 100644 +--- a/tests/array_interoperability_test.py ++++ b/tests/array_interoperability_test.py +@@ -200,7 +200,7 @@ def testNumpyToJax(self, shape, dtype): + "shape": shape, "dtype": dtype} + for shape in all_shapes + for dtype in torch_dtypes)) +- @unittest.skipIf(numpy_version < (1, 22, 0), "Requires numpy 1.22 or newer") ++ @unittest.skipIf(numpy_version < (1, 23, 0), "Requires numpy 1.23 or newer") + @jtu.skip_on_devices("gpu") + def testJaxToNumpy(self, shape, dtype): + rng = jtu.rand_default(self.rng()) From 430735ccd8c455694dcca5aa2f6e18e4756f3d91 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 21 Oct 2022 18:24:29 +0800 Subject: [PATCH 5222/9987] adding easyconfigs: EasyBuild-4.6.2.eb --- .../e/EasyBuild/EasyBuild-4.6.2.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb new file mode 100644 index 00000000000..6168661c256 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.6.2' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/88/7f/67dd44ae3204cba36c66578b14e284ce5210d8217fb383eb24c1691a1bfd/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/fe/52/2609eb0d2b9e9678670c2faec23b14c9c180b4a1d2494fd91c29df2a9a5e/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/5c/6b/1ead89a64a19717e5b0a0c8453458e7186928a36280e9592092ee6d58273/', + +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '136a49ed40b4d7fed1b3d3d47f0f2804cb7744fd886eb9887672e85f7e820499', # easybuild-framework-4.6.2.tar.gz + 'b88059feeb2a97c944f6a71dc88cec683fef650ac081f8563b3f312cf8fe2794', # easybuild-easyblocks-4.6.2.tar.gz + 'b9a305200c8874852cfa3d07d72ed7295481c1b532f7579dcf1212deebcd393b', # easybuild-easyconfigs-4.6.2.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 116bd8f61120841cc0809ad734c9d3c682e8890c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 21 Oct 2022 12:25:38 +0200 Subject: [PATCH 5223/9987] add torchvision dep easyconfig --- .../torchvision-0.13.1-foss-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb new file mode 100644 index 00000000000..26cf963f6da --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb @@ -0,0 +1,21 @@ +name = 'torchvision' +version = '0.13.1' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c32fab734e62c7744dadeb82f7510ff58cc3bca1189d17b16aa99b08afc42249'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('Pillow-SIMD', '9.2.0'), + ('PyTorch', '1.12.0'), +] + +moduleclass = 'vis' From 0335eb886702eb91e125f6513bea4a2f863097aa Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 12:32:28 +0200 Subject: [PATCH 5224/9987] adding easyconfigs: sfftk-0.7.4-foss-2021a.eb --- .../s/sfftk/sfftk-0.7.4-foss-2021a.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb b/easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb new file mode 100644 index 00000000000..b2736681544 --- /dev/null +++ b/easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb @@ -0,0 +1,70 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 +easyblock = 'PythonBundle' + +name = 'sfftk' +version = '0.7.4' + +homepage = 'https://emdb-empiar.github.io/EMDB-SFF/' +description = """ +sfftk is a set of utilities that facilitate creation, conversion and +modification of Electron Microscopy Data Bank - Segmentation File Format +(EMDB-SFF) files. EMDB-SFF is an open, community-driven file format to handle +annotated segmentations and subtomogram averages that facilitates segmentation +file interchange. It is written in Python and provides both a command-line suite +of commands and a Python API.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('mrcfile', '1.3.0'), + ('lxml', '4.6.3'), + ('h5py', '3.2.1'), + ('scikit-image', '0.18.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bitarray', '2.6.0', { + 'checksums': ['56d3f16dd807b1c56732a244ce071c135ee973d3edc9929418c1b24c5439a0fd'], + }), + ('ahds', '0.2.4', { + 'checksums': ['3356115351f7f6089f44c6f6503daa4985f158b7dfb730ef88ab3c6a7f8cc1a6'], + }), + ('styled', '0.2.0', { + 'checksums': ['91ab8022913de87fe1a614d3caeebafe046fd20cdd7d821a61738c1ce86e7276'], + }), + ('numpy-stl', '2.17.1', { + 'modulename': 'stl', + 'checksums': ['36c920192f445dd57f091a63629bdda5a9274d47513a33ac2efad12737394b7a'], + }), + ('python-utils', '3.3.3', { + 'checksums': ['3b1c8b706e40e91280eec5fa72ea730880a166cee99afa5555b863d55664478d'], + }), + ('RandomWords', '0.4.0', { + 'modulename': 'random_words', + 'checksums': ['0bb64dc14f7f5d96597e9a08e185b874a3ea20955a1acce632b87122d66d3d6b'], + }), + ('SimpleParse', '2.2.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['2c1b130017e708a2c87b3a6119b5844f08a0d53b9e4c9d48da5e6c409798e979'], + }), + ('sfftk-rw', '0.7.2', { + 'modulename': 'sfftkrw', + 'source_urls': ['https://github.com/emdb-empiar/sfftk-rw/archive/refs/tags/'], + 'sources': [{'filename': '%(name)s-%(version)s.tar.gz', 'download_filename': 'v%(version)s.tar.gz'}], + 'checksums': ['c858377d987090aa08984e8ae8dd09d5553eabc3bbea5c0ecc9994c06d474500'], + }), + (name, version, { + 'checksums': ['f165d377d4b7d42bc800a08f220169b7baf5e2faafe337beb77ee0754d52e038'], + }), +] + +sanity_check_commands = [ + "sff -h", +] + +moduleclass = 'tools' From 46c3331eb2937e72122b4dac931e73b9132d0f35 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 12:48:45 +0200 Subject: [PATCH 5225/9987] add mrcfile-1.3.0-foss-2021a.eb --- .../m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb new file mode 100644 index 00000000000..4597b91cf82 --- /dev/null +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -0,0 +1,22 @@ +#Thomas Hoffmann, EMBL Heidelberg, 2022/10 +easyblock = 'PythonPackage' +name = 'mrcfile' +version = '1.3.0' +homepage = 'https://github.com/ccpem/mrcfile' +description = """ mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. + +It allows MRC files to be created and opened easily using a very simple API, which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. + +This library aims to allow users and developers to read and write standard-compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions. """ + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +dependencies = [ + ('Python','3.9.5'), + ('SciPy-bundle','2021.05'), + ] + +use_pip=True +moduleclass = 'bio' From bc45390a1d7bad6fe4260be2c3c97b149edca089 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:25:25 +0200 Subject: [PATCH 5226/9987] mrcfile-1.3.0-foss-2021a.eb: fixed style --- .../m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 25 +++++++++++++------ 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb index 4597b91cf82..6222f530615 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -1,22 +1,31 @@ -#Thomas Hoffmann, EMBL Heidelberg, 2022/10 +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 easyblock = 'PythonPackage' name = 'mrcfile' version = '1.3.0' homepage = 'https://github.com/ccpem/mrcfile' -description = """ mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. +description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in +structural biology to store image and volume data. -It allows MRC files to be created and opened easily using a very simple API, which exposes the file’s header and data as numpy arrays. The code runs in Python 2 and 3 and is fully unit-tested. +It allows MRC files to be created and opened easily using a very simple API, +which exposes the file’s header and data as numpy arrays. The code runs in +Python 2 and 3 and is fully unit-tested. -This library aims to allow users and developers to read and write standard-compliant MRC files in Python as easily as possible, and with no dependencies on any compiled libraries except numpy. You can use it interactively to inspect files, correct headers and so on, or in scripts and larger software packages to provide basic MRC file I/O functions. """ +This library aims to allow users and developers to read and write standard- +compliant MRC files in Python as easily as possible, and with no dependencies on +any compiled libraries except numpy. You can use it interactively to inspect +files, correct headers and so on, or in scripts and larger software packages to +provide basic MRC file I/O functions. """ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] + dependencies = [ - ('Python','3.9.5'), - ('SciPy-bundle','2021.05'), - ] + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] -use_pip=True +use_pip = True moduleclass = 'bio' From 9bf9b3af85b2b2e4def1ac14c68105585482e10f Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:31:45 +0200 Subject: [PATCH 5227/9987] adding easyconfigs: napari-0.4.15-foss-2021a.eb --- .../n/napari/napari-0.4.15-foss-2021a.eb | 161 ++++++++++++++++++ 1 file changed, 161 insertions(+) create mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb new file mode 100644 index 00000000000..2eb76e76f3e --- /dev/null +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb @@ -0,0 +1,161 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/06 +easyblock = 'PythonBundle' + +name = 'napari' +version = '0.4.15' + +homepage = 'https://napari.org/' +description = """napari is a fast, interactive, multi-dimensional image viewer for Python. It's +designed for browsing, annotating, and analyzing large multi-dimensional images. +It's built on top of Qt (for the GUI), vispy (for performant GPU-based +rendering), and the scientific Python stack (numpy, scipy).""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyQt5', '5.15.4', '-tools'), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('dask', '2021.9.1'), + ('PyOpenGL', '3.1.5'), + ('imageio', '2.10.5'), # ext + ('tqdm', '4.61.1'), + ('IPython', '7.25.0'), + # ('VisPy', '0.6.6'), + # ('Qtconsole', '5.0.2'), + ('typing-extensions', '3.10.0.0'), + # ('scikit-image', '0.19.1') # ext . + ('networkx', '2.5.1'), # req. for scikit-image ext + ('matplotlib', '3.4.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True +exts_list = [ + ('pytomlpp', '1.0.10', { + 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], + }), + ('freetype_py', '2.3.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-%(version)s.zip'], + 'checksums': ['f9b64ce3272a5c358dcee824800a32d70997fb872a0965a557adca20fce7a5d0'], + }), + ('hsluv', '5.0.3', { + 'checksums': ['2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377'], + }), + ('vispy', '0.10.0', { + 'checksums': ['b76ad6f3eacadbfc4944cfb8211eadb6ea8417a590993ece5aa7caac082cffc2'], + }), + ('qtconsole', '5.3.1', { + 'checksums': ['b73723fac43938b684dcb237a88510dc7721c43a726cea8ade179a2927c0a2f3'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('cachey', '0.2.1', { + 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], + }), + ('docstring-parser', '0.14.1', { + 'sources': 'docstring_parser-%(version)s.tar.gz', + 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], + }), + ('pep517', '0.12.0', { + 'checksums': ['931378d93d11b298cf511dd634cf5ea4cb249a28ef84160b3247ee9afb4e8ab0'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('magicgui', '0.5.1', { + 'checksums': ['dcd05c4c9bbd55bdeb72d41069b2d4304952dabe04c2aac7bdd43f5a4e3a8a94'], + }), + ('napari-console', '0.0.4', { + 'modulename': 'napari_console', + 'checksums': ['ea0e30fbfdd76542adda44be457f1306a65146fe7578f95838e28d62874f4c45'], + }), + ('napari-plugin-engine', '0.2.0', { + 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], + }), + ('napari-svg', '0.1.6', { + 'checksums': ['12fa5c64995fc7179349969a39316355496b463858c3b0815e3b3e7ffcdced34'], + }), + ('Pint', '0.19.2', { + 'checksums': ['e1d4989ff510b378dad64f91711e7bdabe5ca78d75b06a18569ac454678c4baf'], + }), + ('build', '0.8.0', { + 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], + }), + ('psygnal', '0.3.5', { + 'patches': ['http://two.embl.de/psygnal-0.3.5_python3.8.patch'], + 'checksums': [ + '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz + 'c55cc07c646cb66e8c5d2ea227249216dbd1a1a9405acbd330d70105a3fd8890', # psygnal-0.3.5_python3.8.patch + ], + }), + ('pydantic', '1.9.1', { + 'checksums': ['1ed987c3ff29fff7fd8c3ea3a3ea877ad310aae2ef9889a119e22d3f2db0691a'], + }), + ('typer', '0.4.1', { + 'checksums': ['5646aef0d936b2c761a10393f0384ee6b5c7fe0bb3e5cd710b17134ca1d99cff'], + }), + ('npe2', '0.5.0', { + 'checksums': ['3d3d43b99bbd3b189fedd7313589c89642a4af0f14b24b9763eb134ba6a5548c'], + }), + ('numpydoc', '1.4.0', { + 'checksums': ['9494daf1c7612f59905fa09e65c9b8a90bbacb3804d91f7a94e778831e6fcfa5'], + }), + ('QtPy', '2.1.0', { + 'checksums': ['ca8cd4217175186344299ee4c0f7e7adcf362c70852ba35b255a534077025c06'], + }), + ('superqt', '0.3.2', { + 'checksums': ['a37df244a2d6e4387e865cdedabe925798b3352ab9cdc52f60701eb12d907960'], + }), + ('tifffile', '2022.5.4', { + 'checksums': ['b03147a15862b7c1d90d47435197f149bef7a52c25ad67cf1f9b465faa71b8d2'], + }), + ('pandas', '1.3.0', { + 'checksums': ['c554e6c9cf2d5ea1aba5979cc837b3649539ced0e18ece186f055450c86622e2'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('pythran', '0.10.0', { + 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], + }), + ('PyWavelets', '1.2.0', { + 'modulename': 'pywt', + 'checksums': ['6cbd69b047bb4e00873097472133425f5f08a4e6bc8b3f0ae709274d4d5e9a8d'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('scikit-image', '0.19.1', { + 'modulename': 'skimage', + 'checksums': ['48f00ee1e8ec2818ae6a152c72df15f4db7f566e839f5c34e1a0c3c9e5210138'], + }), + (name, version, { + 'checksums': ['0d4cf6067d2112c78a705917aa5e74371463982d80147a898c6b5d2f0b514baa'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = [ + '%(name)s --help', + 'pyrcc5 -version 2>&1 |grep pyrcc5' # make sure PyQt5 module was not built with --no-tools +] + +moduleclass = 'vis' From 8bdd165cf0f944d2c3f96df5da2bd117789ad1b9 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 13:34:21 +0200 Subject: [PATCH 5228/9987] add psygnal-0.3.5_python3.8.patch --- .../n/napari/psygnal-0.3.5_python3.8.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch diff --git a/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch new file mode 100644 index 00000000000..9ef096a19a4 --- /dev/null +++ b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch @@ -0,0 +1,12 @@ +#Thomas Hoffmann, EMLB Heidelberg, structures-it@embl.de +#python > 3.7: prevent comple error future feature annotations is not defined +diff -ru psygnal-0.3.5/psygnal/_evented_model.py psygnal-0.3.5_python3.8/psygnal/_evented_model.py +--- psygnal-0.3.5/psygnal/_evented_model.py 2022-05-26 02:03:19.000000000 +0200 ++++ psygnal-0.3.5_python3.8/psygnal/_evented_model.py 2022-06-23 10:41:46.536586585 +0200 +@@ -1,5 +1,4 @@ +-from __future__ import annotations +- ++import annotations + import operator + import sys + import warnings From 0c145a2e2ae761c89ff06b8ecb15cc7b20d450e4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:46:04 +0200 Subject: [PATCH 5229/9987] add PyQt5-5.15.4-GCCcore-10.3.0-tools.eb --- .../PyQt5-5.15.4-GCCcore-10.3.0-tools.eb | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb new file mode 100644 index 00000000000..12f9c77e512 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb @@ -0,0 +1,104 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.4' +versionsuffix = '-tools' +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.36.1')] +dependencies = [ + ('Python', '3.9.5'), + ('Qt5', '5.15.2'), +] + +default_easyblock = 'PythonPackage' + +local_sipdir = '%(installdir)s/share/sip' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_sipver = '5.5.0' +components = [ + ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + ('PyQt-builder', '1.10.1', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['967b0c7bac0331597e9f8c5b336660f173a9896830b721d6d025e14bde647e17'], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + ('PyQt5_sip', '12.9.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + # run python configure.py in order to set bindir, which is no possible with sip-install: + 'configopts': local_pyqt_configopts, + }), + ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['cedc28f54165f4b8067652145aec7f732a17eadf6736835852868cf76119cc19'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip5 --help", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' From 3f22cdee665855a679086f6f28e6daa97af3798a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:49:45 +0200 Subject: [PATCH 5230/9987] fix mrcfile-1.3.0-foss-2021a.eb --- easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb index 6222f530615..aff2c2636c7 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -18,7 +18,6 @@ provide basic MRC file I/O functions. """ toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] @@ -27,5 +26,8 @@ dependencies = [ ('SciPy-bundle', '2021.05'), ] +download_dep_fail = True +sanity_pip_check = True + use_pip = True moduleclass = 'bio' From 128ef1d53bdeafdb44043b28a1545c2b60b725e6 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 14:15:37 +0200 Subject: [PATCH 5231/9987] fix patch url --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb index 2eb76e76f3e..3f04fc5590d 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb @@ -87,7 +87,7 @@ exts_list = [ 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], }), ('psygnal', '0.3.5', { - 'patches': ['http://two.embl.de/psygnal-0.3.5_python3.8.patch'], + 'patches': ['psygnal-0.3.5_python3.8.patch'], 'checksums': [ '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz 'c55cc07c646cb66e8c5d2ea227249216dbd1a1a9405acbd330d70105a3fd8890', # psygnal-0.3.5_python3.8.patch From a4b320225ccaf553e112b3088604ca69f156aab0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 14:27:20 +0200 Subject: [PATCH 5232/9987] mrcfile-1.3.0-foss-2021a.eb: fix style --- easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb index aff2c2636c7..c6e040ded1b 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -27,7 +27,7 @@ dependencies = [ ] download_dep_fail = True -sanity_pip_check = True +sanity_pip_check = True use_pip = True moduleclass = 'bio' From 81d20f68a5a96294b2d1c0db2b034dec7172278a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Oct 2022 13:37:49 +0100 Subject: [PATCH 5233/9987] relax tolerance of testPoly5 --- .../easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb | 3 +++ .../jax/jax-0.3.23_relax-testPoly5-tolerance.patch | 14 ++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb index 54a86884e76..d5c28009d97 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -95,6 +95,7 @@ exts_list = [ 'patches': [ 'jax-0.3.9_relax-test-tolerance.patch', 'jax-0.3.23_correctly-skip-from_dlpack-tests.patch', + 'jax-0.3.23_relax-testPoly5-tolerance.patch', ], 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], @@ -104,6 +105,8 @@ exts_list = [ '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d'}, {'jax-0.3.23_correctly-skip-from_dlpack-tests.patch': 'a69ce7280ca8bb42e671217f00d9147f8c64b4b7ba65dea7f05f2c6de757b279'}, + {'jax-0.3.23_relax-testPoly5-tolerance.patch': + '47e74771049364e8db9743f8c5f3d0d784e1e4d21595bdd07da94d5b9b42b83d'}, ], 'runtest': "pytest -n %(parallel)s tests", }), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch new file mode 100644 index 00000000000..7df1c1dfe7f --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch @@ -0,0 +1,14 @@ +Relax the tolerance for the testPoly5 test +Patch by Simon Branford (University of Birmingham) +--- tmp/jax-jax-v0.3.23/tests/lax_numpy_test.py 2022-10-12 16:23:43.000000000 +0100 ++++ lax_numpy_test.py 2022-10-21 13:33:59.871417000 +0100 +@@ -1277,6 +1277,9 @@ + if jtu.device_under_test() == "tpu": + tol[np.int32] = tol[np.float32] = 1e-1 + tol = jtu.tolerance(dtype, tol) ++ if rank == 2 and dtype == np.int8 and a_shape == (12,): ++ # relax tolerance (from 1e-3) for testPoly5 ++ tol = 2e-3 + args_maker = lambda: [rng(a_shape * rank, dtype)] + self._CheckAgainstNumpy(np.poly, jnp.poly, args_maker, check_dtypes=False, tol=tol) + self._CompileAndCheck(jnp.poly, args_maker, check_dtypes=True, rtol=tol, atol=tol) From bcf403138bd737fdfabae7cd10805a8efaf3fe83 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Oct 2022 13:43:55 +0100 Subject: [PATCH 5234/9987] correctly generate the patch --- easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb | 2 +- .../j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb index d5c28009d97..769a042f02f 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -106,7 +106,7 @@ exts_list = [ {'jax-0.3.23_correctly-skip-from_dlpack-tests.patch': 'a69ce7280ca8bb42e671217f00d9147f8c64b4b7ba65dea7f05f2c6de757b279'}, {'jax-0.3.23_relax-testPoly5-tolerance.patch': - '47e74771049364e8db9743f8c5f3d0d784e1e4d21595bdd07da94d5b9b42b83d'}, + 'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'}, ], 'runtest': "pytest -n %(parallel)s tests", }), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch index 7df1c1dfe7f..38729edac87 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch @@ -1,7 +1,7 @@ Relax the tolerance for the testPoly5 test Patch by Simon Branford (University of Birmingham) ---- tmp/jax-jax-v0.3.23/tests/lax_numpy_test.py 2022-10-12 16:23:43.000000000 +0100 -+++ lax_numpy_test.py 2022-10-21 13:33:59.871417000 +0100 +--- tests/lax_numpy_test.py 2022-10-12 16:23:43.000000000 +0100 ++++ tests/lax_numpy_test.py 2022-10-21 13:33:59.871417000 +0100 @@ -1277,6 +1277,9 @@ if jtu.device_under_test() == "tpu": tol[np.int32] = tol[np.float32] = 1e-1 From 8360dbde5376958b38cd69763d93758860ec5014 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:09:10 +0200 Subject: [PATCH 5235/9987] build missing tool pyrcc5 --- .../p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb | 23 ++++++++++++++----- 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb index 18614197333..e21ab740946 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb @@ -18,15 +18,26 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' + local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.5.0' @@ -57,10 +68,10 @@ components = [ 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'Binary', + 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', - 'skipsteps': ['configure', 'build'], - 'install_cmd': local_setup_env + local_pyqt5_sip_install, + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts }), ('PyQtWebEngine', version, { 'source_urls': [PYPI_SOURCE], @@ -75,7 +86,7 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From 8cac0b4b373bf6eb09bcc8dcd47de39ff9927d6a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:17:52 +0200 Subject: [PATCH 5236/9987] adding easyconfigs: QtPy-2.2.1-GCCcore-11.2.0.eb --- .../q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..deb1b3231ed --- /dev/null +++ b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'QtPy' +version = '2.2.1' + +homepage = "https://github.com/spyder-ide/qtpy" +description = """QtPy is a small abstraction layer that lets you write applications using a +single API call to either PyQt or PySide. +It provides support for PyQt5, PyQt4, PySide2 and PySide.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7d5231133b772e40b4ee514b6673aca558331e4b88ca038b26c9e16c5c95524f'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('PyQt5', '5.15.4') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 6687320ff6d271c5b89489d0fea56c9493ab4fe6 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:20:19 +0200 Subject: [PATCH 5237/9987] adding easyconfigs: Qtconsole-5.3.2-GCCcore-11.2.0.eb --- .../Qtconsole-5.3.2-GCCcore-11.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..cd750a04be5 --- /dev/null +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Qtconsole' +version = '5.3.2' + +homepage = 'https://jupyter.org/' +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media +output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a +terminal, but provides a number of enhancements only possible in a GUI, such as +inline figures, proper multiline editing with syntax highlighting, graphical +calltips, and more.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8eadf012e83ab018295803c247c6ab7eacd3d5ab1e1d88a0f37fdcfdab9295a3'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('IPython', '7.26.0'), + ('QtPy', '2.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 4e648e638a1d845d6361bbb0c0b628f8f00c9f3c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:24:23 +0200 Subject: [PATCH 5238/9987] bump to foss/2021b --- .../n/napari/napari-0.4.15-foss-2021b.eb | 136 ++++++++++++++++++ .../n/napari/psygnal-0.3.5_python3.8.patch | 2 +- 2 files changed, 137 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb new file mode 100644 index 00000000000..1326a9f443b --- /dev/null +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb @@ -0,0 +1,136 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/10 +easyblock = 'PythonBundle' + +name = 'napari' +version = '0.4.15' + +homepage = 'https://napari.org/' +description = """napari is a fast, interactive, multi-dimensional image viewer for Python. It's +designed for browsing, annotating, and analyzing large multi-dimensional images. +It's built on top of Qt (for the GUI), vispy (for performant GPU-based +rendering), and the scientific Python stack (numpy, scipy).""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('PyQt5', '5.15.4'), + ('SciPy-bundle', '2021.10'), + ('PyYAML', '5.4.1'), + ('dask', '2022.1.0'), + ('PyOpenGL', '3.1.6'), + ('imageio', '2.13.5'), + ('tqdm', '4.62.3'), + ('IPython', '7.26.0'), + ('Qtconsole', '5.3.2'), + ('typing-extensions', '3.10.0.2'), + ('scikit-image', '0.19.1'), + ('matplotlib', '3.4.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True +exts_list = [ + ('pytomlpp', '1.0.10', { + 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], + }), + ('freetype_py', '2.3.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-%(version)s.zip'], + 'checksums': ['f9b64ce3272a5c358dcee824800a32d70997fb872a0965a557adca20fce7a5d0'], + }), + ('hsluv', '5.0.3', { + 'checksums': ['2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377'], + }), + ('vispy', '0.10.0', { + 'checksums': ['b76ad6f3eacadbfc4944cfb8211eadb6ea8417a590993ece5aa7caac082cffc2'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('cachey', '0.2.1', { + 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], + }), + ('docstring-parser', '0.14.1', { + 'sources': 'docstring_parser-%(version)s.tar.gz', + 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], + }), + ('pep517', '0.12.0', { + 'checksums': ['931378d93d11b298cf511dd634cf5ea4cb249a28ef84160b3247ee9afb4e8ab0'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('magicgui', '0.5.1', { + 'checksums': ['dcd05c4c9bbd55bdeb72d41069b2d4304952dabe04c2aac7bdd43f5a4e3a8a94'], + }), + ('napari-console', '0.0.4', { + 'modulename': 'napari_console', + 'checksums': ['ea0e30fbfdd76542adda44be457f1306a65146fe7578f95838e28d62874f4c45'], + }), + ('napari-plugin-engine', '0.2.0', { + 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], + }), + ('napari-svg', '0.1.6', { + 'checksums': ['12fa5c64995fc7179349969a39316355496b463858c3b0815e3b3e7ffcdced34'], + }), + ('Pint', '0.19.2', { + 'checksums': ['e1d4989ff510b378dad64f91711e7bdabe5ca78d75b06a18569ac454678c4baf'], + }), + ('build', '0.8.0', { + 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], + }), + ('psygnal', '0.3.5', { + 'patches': ['psygnal-0.3.5_python3.8.patch'], + 'checksums': [ + '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz + '34c36af20b555c7201da1c4cd26180aa446d9670f55a6e89a27152e4f50e0e29', # psygnal-0.3.5_python3.8.patch + ], + }), + ('pydantic', '1.9.1', { + 'checksums': ['1ed987c3ff29fff7fd8c3ea3a3ea877ad310aae2ef9889a119e22d3f2db0691a'], + }), + ('typer', '0.4.1', { + 'checksums': ['5646aef0d936b2c761a10393f0384ee6b5c7fe0bb3e5cd710b17134ca1d99cff'], + }), + ('npe2', '0.5.0', { + 'checksums': ['3d3d43b99bbd3b189fedd7313589c89642a4af0f14b24b9763eb134ba6a5548c'], + }), + ('numpydoc', '1.4.0', { + 'checksums': ['9494daf1c7612f59905fa09e65c9b8a90bbacb3804d91f7a94e778831e6fcfa5'], + }), + ('superqt', '0.3.2', { + 'checksums': ['a37df244a2d6e4387e865cdedabe925798b3352ab9cdc52f60701eb12d907960'], + }), + ('tifffile', '2022.5.4', { + 'checksums': ['b03147a15862b7c1d90d47435197f149bef7a52c25ad67cf1f9b465faa71b8d2'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('pythran', '0.10.0', { + 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], + }), + (name, version, { + 'checksums': ['0d4cf6067d2112c78a705917aa5e74371463982d80147a898c6b5d2f0b514baa'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = [ + '%(name)s --help', + 'pyrcc5 -version 2>&1 |grep pyrcc5' # make sure PyQt5 module was not built with --no-tools +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch index 9ef096a19a4..b8f4bace8b2 100644 --- a/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch +++ b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch @@ -1,4 +1,4 @@ -#Thomas Hoffmann, EMLB Heidelberg, structures-it@embl.de +#Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 #python > 3.7: prevent comple error future feature annotations is not defined diff -ru psygnal-0.3.5/psygnal/_evented_model.py psygnal-0.3.5_python3.8/psygnal/_evented_model.py --- psygnal-0.3.5/psygnal/_evented_model.py 2022-05-26 02:03:19.000000000 +0200 From 07e39d076f350b7b76461fbcc5d205bc73539b2f Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 17:28:42 +0200 Subject: [PATCH 5239/9987] Delete PyQt5-5.15.4-GCCcore-10.3.0-tools.eb see #16469 --- .../PyQt5-5.15.4-GCCcore-10.3.0-tools.eb | 104 ------------------ 1 file changed, 104 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb deleted file mode 100644 index 12f9c77e512..00000000000 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb +++ /dev/null @@ -1,104 +0,0 @@ -easyblock = 'Bundle' - -name = 'PyQt5' -version = '5.15.4' -versionsuffix = '-tools' -homepage = 'https://www.riverbankcomputing.com/software/pyqt' -description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. -This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -toolchainopts = {'cstd': 'c++11'} - -builddependencies = [('binutils', '2.36.1')] -dependencies = [ - ('Python', '3.9.5'), - ('Qt5', '5.15.2'), -] - -default_easyblock = 'PythonPackage' - -local_sipdir = '%(installdir)s/share/sip' - -local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' - -local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " - -local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " -local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir -local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir -local_pyqtweb_configopts += "--no-stubs --no-dist-info" - -local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir -local_pyqt_configopts += "--no-stubs " -local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " -# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: -local_pyqt_configopts += "--bindir=%(installdir)s/bin " -local_pyqt_configopts += "--sipdir=%s " % local_sipdir - -local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " -local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -local_sipver = '5.5.0' -components = [ - ('SIP', local_sipver, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], - 'start_dir': 'sip-%s' % local_sipver, - 'use_pip': True, - 'options': {'modulename': 'PyQt5.sip'}, - }), - ('PyQt-builder', '1.10.1', { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['967b0c7bac0331597e9f8c5b336660f173a9896830b721d6d025e14bde647e17'], - 'start_dir': 'PyQt-builder-%(version)s', - 'use_pip': True, - }), - ('PyQt5_sip', '12.9.0', { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], - 'start_dir': 'PyQt5_sip-%(version)s', - 'use_pip': True, - }), - (name, version, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'ConfigureMakePythonPackage', - 'start_dir': '%(name)s-%(version)s', - 'preconfigopts': local_setup_env, - # run python configure.py in order to set bindir, which is no possible with sip-install: - 'configopts': local_pyqt_configopts, - }), - ('PyQtWebEngine', version, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['cedc28f54165f4b8067652145aec7f732a17eadf6736835852868cf76119cc19'], - 'easyblock': 'ConfigureMakePythonPackage', - 'start_dir': '%(name)s-%(version)s', - 'preconfigopts': local_setup_env, - 'configopts': local_pyqtweb_configopts, - 'options': {'modulename': 'PyQt5.QtWebEngine'}, - }), -] - -sanity_check_paths = { - 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "python -c 'import PyQt5.QtCore'", - "sip5 --help", -] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'QT_INSTALL_DATA': 'qsci', -} - -moduleclass = 'vis' From 46ba80c925e0af2188ce63c74612d4a3fb718cff Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 17:44:13 +0200 Subject: [PATCH 5240/9987] Delete napari-0.4.15-foss-2021a.eb --- .../n/napari/napari-0.4.15-foss-2021a.eb | 161 ------------------ 1 file changed, 161 deletions(-) delete mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb deleted file mode 100644 index 3f04fc5590d..00000000000 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb +++ /dev/null @@ -1,161 +0,0 @@ -# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/06 -easyblock = 'PythonBundle' - -name = 'napari' -version = '0.4.15' - -homepage = 'https://napari.org/' -description = """napari is a fast, interactive, multi-dimensional image viewer for Python. It's -designed for browsing, annotating, and analyzing large multi-dimensional images. -It's built on top of Qt (for the GUI), vispy (for performant GPU-based -rendering), and the scientific Python stack (numpy, scipy).""" - -toolchain = {'name': 'foss', 'version': '2021a'} - -dependencies = [ - ('Python', '3.9.5'), - ('PyQt5', '5.15.4', '-tools'), - ('SciPy-bundle', '2021.05'), - ('PyYAML', '5.4.1'), - ('dask', '2021.9.1'), - ('PyOpenGL', '3.1.5'), - ('imageio', '2.10.5'), # ext - ('tqdm', '4.61.1'), - ('IPython', '7.25.0'), - # ('VisPy', '0.6.6'), - # ('Qtconsole', '5.0.2'), - ('typing-extensions', '3.10.0.0'), - # ('scikit-image', '0.19.1') # ext . - ('networkx', '2.5.1'), # req. for scikit-image ext - ('matplotlib', '3.4.2'), -] - -use_pip = True -sanity_pip_check = True -download_dep_fail = True -exts_list = [ - ('pytomlpp', '1.0.10', { - 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], - }), - ('freetype_py', '2.3.0', { - 'modulename': 'freetype', - 'sources': ['freetype-py-%(version)s.zip'], - 'checksums': ['f9b64ce3272a5c358dcee824800a32d70997fb872a0965a557adca20fce7a5d0'], - }), - ('hsluv', '5.0.3', { - 'checksums': ['2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377'], - }), - ('vispy', '0.10.0', { - 'checksums': ['b76ad6f3eacadbfc4944cfb8211eadb6ea8417a590993ece5aa7caac082cffc2'], - }), - ('qtconsole', '5.3.1', { - 'checksums': ['b73723fac43938b684dcb237a88510dc7721c43a726cea8ade179a2927c0a2f3'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('cachey', '0.2.1', { - 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], - }), - ('docstring-parser', '0.14.1', { - 'sources': 'docstring_parser-%(version)s.tar.gz', - 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], - }), - ('pep517', '0.12.0', { - 'checksums': ['931378d93d11b298cf511dd634cf5ea4cb249a28ef84160b3247ee9afb4e8ab0'], - }), - ('tomli', '2.0.1', { - 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], - }), - ('magicgui', '0.5.1', { - 'checksums': ['dcd05c4c9bbd55bdeb72d41069b2d4304952dabe04c2aac7bdd43f5a4e3a8a94'], - }), - ('napari-console', '0.0.4', { - 'modulename': 'napari_console', - 'checksums': ['ea0e30fbfdd76542adda44be457f1306a65146fe7578f95838e28d62874f4c45'], - }), - ('napari-plugin-engine', '0.2.0', { - 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], - }), - ('napari-svg', '0.1.6', { - 'checksums': ['12fa5c64995fc7179349969a39316355496b463858c3b0815e3b3e7ffcdced34'], - }), - ('Pint', '0.19.2', { - 'checksums': ['e1d4989ff510b378dad64f91711e7bdabe5ca78d75b06a18569ac454678c4baf'], - }), - ('build', '0.8.0', { - 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], - }), - ('psygnal', '0.3.5', { - 'patches': ['psygnal-0.3.5_python3.8.patch'], - 'checksums': [ - '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz - 'c55cc07c646cb66e8c5d2ea227249216dbd1a1a9405acbd330d70105a3fd8890', # psygnal-0.3.5_python3.8.patch - ], - }), - ('pydantic', '1.9.1', { - 'checksums': ['1ed987c3ff29fff7fd8c3ea3a3ea877ad310aae2ef9889a119e22d3f2db0691a'], - }), - ('typer', '0.4.1', { - 'checksums': ['5646aef0d936b2c761a10393f0384ee6b5c7fe0bb3e5cd710b17134ca1d99cff'], - }), - ('npe2', '0.5.0', { - 'checksums': ['3d3d43b99bbd3b189fedd7313589c89642a4af0f14b24b9763eb134ba6a5548c'], - }), - ('numpydoc', '1.4.0', { - 'checksums': ['9494daf1c7612f59905fa09e65c9b8a90bbacb3804d91f7a94e778831e6fcfa5'], - }), - ('QtPy', '2.1.0', { - 'checksums': ['ca8cd4217175186344299ee4c0f7e7adcf362c70852ba35b255a534077025c06'], - }), - ('superqt', '0.3.2', { - 'checksums': ['a37df244a2d6e4387e865cdedabe925798b3352ab9cdc52f60701eb12d907960'], - }), - ('tifffile', '2022.5.4', { - 'checksums': ['b03147a15862b7c1d90d47435197f149bef7a52c25ad67cf1f9b465faa71b8d2'], - }), - ('pandas', '1.3.0', { - 'checksums': ['c554e6c9cf2d5ea1aba5979cc837b3649539ced0e18ece186f055450c86622e2'], - }), - ('beniget', '0.4.1', { - 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], - }), - ('ply', '3.11', { - 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], - }), - ('gast', '0.5.3', { - 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], - }), - ('pythran', '0.10.0', { - 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], - }), - ('PyWavelets', '1.2.0', { - 'modulename': 'pywt', - 'checksums': ['6cbd69b047bb4e00873097472133425f5f08a4e6bc8b3f0ae709274d4d5e9a8d'], - }), - ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], - }), - ('pooch', '1.5.2', { - 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], - }), - ('scikit-image', '0.19.1', { - 'modulename': 'skimage', - 'checksums': ['48f00ee1e8ec2818ae6a152c72df15f4db7f566e839f5c34e1a0c3c9e5210138'], - }), - (name, version, { - 'checksums': ['0d4cf6067d2112c78a705917aa5e74371463982d80147a898c6b5d2f0b514baa'], - }), -] - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], -} - -sanity_check_commands = [ - '%(name)s --help', - 'pyrcc5 -version 2>&1 |grep pyrcc5' # make sure PyQt5 module was not built with --no-tools -] - -moduleclass = 'vis' From 69161e475b54b98514eb45ccef68b95c1e418b62 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 21 Oct 2022 19:10:57 +0200 Subject: [PATCH 5241/9987] adding easyconfigs: Scalene-1.5.13-GCCcore-11.2.0.eb --- .../Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..838f20f9ff1 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'Scalene' +version = '1.5.13' + +homepage = 'https://github.com/plasma-umass/scalene' +description = """Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things +that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while +delivering far more detailed information.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + ('pynvml', '11.4.1', { + 'checksums': ['b2e4a33b80569d093b513f5804db0c7f40cfc86f15a013ae7a8e99c5e175d5dd'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.6.0', { + 'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['0077d517249cfa6ad0953d85c9656bdaca57b863159bbb78969987d9bdbb539c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/scalene'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["scalene --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From b5fb3cea9f0d353188d0430cb139a6f61641a707 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:46:08 +0100 Subject: [PATCH 5242/9987] adding easyconfigs: HTSeq-2.0.2-foss-2022a.eb --- .../h/HTSeq/HTSeq-2.0.2-foss-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb new file mode 100644 index 00000000000..912a8595037 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb @@ -0,0 +1,42 @@ +# Updated to PythonBundle and latest version from Pypi +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'HTSeq' +version = '2.0.2' + +homepage = 'https://github.com/simon-anders/htseq' +description = """HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [('SWIG', '4.0.2')] + +dependencies = [ + ('Python', '3.10.4'), + ('Pysam', '0.19.1'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['e2c7442d6ff3f97293cfa0da276576f0996eae0a66eb3c2006332ef198f7ea09'], + 'modulename': '%(name)s', + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'], +} + +sanity_check_commands = ['%(namelower)s-count --help'] + +moduleclass = 'bio' From 390bd6fef6998dc0f5701e8617ce384600f55aef Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:50:10 +0100 Subject: [PATCH 5243/9987] adding easyconfigs: psutil-5.9.3-GCCcore-11.3.0.eb --- .../p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c8b8ea559e1 --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '5.9.3' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +download_dep_fail = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['7ccfcdfea4fc4b0a02ca2c31de7fcd186beb9cff8207800e14ab66f79c773af6'], + }), +] + +moduleclass = 'lib' From f9de54bbd6b5cff81931c993c093cf37f0bb15c1 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:52:27 +0100 Subject: [PATCH 5244/9987] adding easyconfigs: pybedtools-0.9.0-GCC-11.3.0.eb --- .../pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..80c02fc63c7 --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'pybedtools' +version = '0.9.0' + +homepage = 'https://daler.github.io/pybedtools' +description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.19.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://daler.github.io/pybedtools/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['9267c92cd764173449d9c31baedac0659b4eccc3d7c05e22ec378f86c0fc30a3'], + }), +] + +moduleclass = 'bio' From 767f5978691fc05f090417bfe2980802277b0345 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:55:27 +0100 Subject: [PATCH 5245/9987] adding easyconfigs: TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb and patches: tfea-1.1.4-README.md.patch --- .../TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb | 67 ++ .../t/TFEA/tfea-1.1.4-README.md.patch | 754 ++++++++++++++++++ 2 files changed, 821 insertions(+) create mode 100644 easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb create mode 100644 easybuild/easyconfigs/t/TFEA/tfea-1.1.4-README.md.patch diff --git a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb new file mode 100644 index 00000000000..94610d8bfd0 --- /dev/null +++ b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb @@ -0,0 +1,67 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'TFEA' +version = '1.1.4' +_mumergever = '1.1.0' +versionsuffix = '-muMerge-%s' % _mumergever + + +homepage = 'https://github.com/Dowell-Lab/TFEA' +description = """Transcription Factor Enrichment Analysis """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.5.1'), + ('SciPy-bundle', '2020.11'), + ('pybedtools', '0.8.2'), + ('psutil', '5.9.3'), + ('SWIG', '4.0.2'), + ('ncurses', '6.2'), + ('cURL', '7.72.0'), + ('XZ', '5.2.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('ujson', '5.5.0', { + 'checksums': ['b25077a971c7da47bd6846a912a747f6963776d90720c88603b1b55d81790780'], + }), + ('pysam', '0.15.2', { + 'checksums': ['d049efd91ed5b1af515aa30280bc9cb46a92ddd15d546c9b21ee68a6ed4055d9'], + }), + ('HTSeq', '2.0.2', { + 'checksums': ['e2c7442d6ff3f97293cfa0da276576f0996eae0a66eb3c2006332ef198f7ea09'], + 'modulename': '%(name)s', + }), + ('mumerge', '1.1.0', { + 'source_urls': ['https://github.com/Dowell-Lab/mumerge/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['f8afd360800567ddb4e7b602ed63ef30d22eb41d7bfbd1dc323295cdc8a98bf3'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'patches': ['tfea-1.1.4-README.md.patch'], + 'checksums': [('fa74d0e4ab11fa7ca125d86b76ee1cb66480374a220ab01d61433d4302cb9b3a'), + ('92e53d05c2422e422e6744d42afdd04ffc267a743f6a39c9c6957be3c6bf3b30')], + 'modulename': 'TFEA' + }), +] + +sanity_check_paths = { + 'files': ['bin/TFEA', 'bin/TFEA-annotate', 'bin/TFEA-simulate'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "TFEA --help", + "TFEA-simulate -h", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TFEA/tfea-1.1.4-README.md.patch b/easybuild/easyconfigs/t/TFEA/tfea-1.1.4-README.md.patch new file mode 100644 index 00000000000..4cf540c4921 --- /dev/null +++ b/easybuild/easyconfigs/t/TFEA/tfea-1.1.4-README.md.patch @@ -0,0 +1,754 @@ +Missing README.md added +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/tfea-1.1.4.orig/setup.py b/tfea-1.1.4/setup.py +index 416aa4e..14d21ff 100644 +--- a/tfea-1.1.4.orig/setup.py ++++ b/tfea-1.1.4/setup.py +@@ -3,7 +3,7 @@ import TFEA + + with open("README.md", "r") as fh: + long_description = fh.read() +- ++ + setuptools.setup( + name="tfea", + version=TFEA.__version__, #Version read from __init__.py +diff --git a/tfea-1.1.4/README.md b/tfea-1.1.4/README.md +new file mode 100644 +index 0000000..5e3975a +--- /dev/null ++++ b/tfea-1.1.4/README.md +@@ -0,0 +1,733 @@ ++

Transcription Factor Enrichment Analysis (TFEA)

++

Table of Contents

++ ++1. Pipeline ++2. Installation and Requirements ++ - TFEA ++ - DESeq ++ - Bedtools ++ - Samtools ++ - MEME Suite ++ - Image Magick ++ - FIJI Modules ++4. Basic Usage ++ - Testing TFEA ++ - Running TFEA ++5. Advanced Usage ++ - Configuration File ++ - Using SBATCH ++ - Pre-Processed Inputs ++ - Secondary Analysis (MD, MDD) ++ - Measuring TF FPKM ++ - Generating Simulated Data ++ - Rerunning TFEA ++ - Help Message ++6. Example Output ++7. Contact Information ++ ++

++ ++

TFEA Pipeline

++ ++![TFEA Pipeline](https://github.com/jdrubin91/TFEA/blob/master/README_images/TFEAPipelinev5.png) ++ ++

++ ++

Installation and Requirements

++ ++

TFEA

++ ++To install, this package and all python3 dependencies: ++ ++``` ++python3 -m pip install tfea ++``` ++ ++This should take no longer than several minutes. ++ ++Once successfully installed, you should be able to run the tfea command from anywhere, try: ++ ++``` ++TFEA --help ++``` ++ ++*Note:* If you plan to run TFEA only on FIJI using the --sbatch flag, then you only need to install DESeq and DESeq2. Otherwise, follow the instructions below for installing all TFEA dependencies. ++ ++

DESeq

++ TFEA uses DESeq or DESeq2 (depending on replicate number) to rank inputted bed files based on fold change significance. If on FIJI, make sure all gcc modules are unloaded before installing DESeq or DESeq2. This can be accomplished with: ++ ++ ``` ++ module unload gcc ++ ``` ++ ++ or ++ ++ ``` ++ module purge ++ ``` ++ ++ To install DESeq and DESeq2 type in your terminal: ++ ++ ``` ++ R ++ ++ > if (!requireNamespace("BiocManager", quietly = TRUE)) ++ > install.packages("BiocManager") ++ ++ > BiocManager::install("DESeq") ++ > BiocManager::install("DESeq2") ++ ``` ++ ++

Bedtools

++ TFEA uses Bedtools to do several genomic computations. Instructions for installing bedtools can be found here: ++ ++ Bedtools Installation ++ ++ If you are on FIJI compute cluster, bedtools is available as a module: ++ ++ ``` ++ module load bedtools/2.25.0 ++ ``` ++ ++

Samtools

++ TFEA uses samtools to index bam files. Samtools download and install instructions can be found here: ++ Samtools Download and Install ++ ++ If you are on FIJI compute cluster, bedtools is available as a module: ++ ++ ``` ++ module load samtools/1.8 ++ ``` ++ ++

MEME Suite

++ TFEA uses the MEME suite to scan sequences from inputted bed files for motif hits using the background atcg distribution form inputted bed file regions. TFEA also uses the MEME suite to generate motif logos for html display. Instructions for downloading and installing the MEME suite can be found here: ++ ++ MEME Download and Installation ++ ++ If you are on FIJI compute cluster, the meme suite is available as a module: ++ ++ ``` ++ module load meme/5.0.3 ++ ``` ++ ++

Image Magick

++ TFEA uses the meme2images script within MEME to produce motif logo figures. This requires Image Magick, which is a common linux utility package sometimes pre-installed on machines. To check if you have Image Magick installed try: ++ ++ ``` ++ identify -version ++ ``` ++ ++ If you do not have Image Magick installed, follow these instructions: ++ ++ Image Magick Download and Installation ++ ++

FIJI Modules

++ Below is a summary of all FIJI modules needed to run TFEA. ++ ++ ``` ++ module load python/3.6.3 ++ module load python/3.6.3/matplotlib/1.5.1 ++ module load python/3.6.3/scipy/0.17.1 ++ module load python/3.6.3/numpy/1.14.1 ++ module load python/3.6.3/htseq/0.9.1 ++ module load python/3.6.3/pybedtools/0.7.10 ++ ++ module load samtools/1.8 ++ module load bedtools/2.25.0 ++ module load meme/5.0.3 ++ ``` ++ ++

++

BasicUsage

++

Testing TFEA

++To make sure TFEA is installed properly, run the following tests: ++ ++*Note:* If you chose to skip installations because you were going to run TFEA using the --sbatch flag, make sure you load the appropriate modules on FIJI or these tests will fail. ++ ++``` ++TFEA --test-install ++TFEA --test-full ++``` ++ ++These should each take no longer than several minutes to run ++ ++If on a compute cluster with slurm the --sbatch flag is compatible with --test-full and is recommended on FIJI. Execute like so: ++ ++``` ++TFEA --test-full --sbatch your_email@address.com ++``` ++ ++

Running TFEA

++Once you've run the above tests successfully, you should be ready to run the full version of TFEA. Below are the minimum required inputs to run the full TFEA pipeline. Test files are provided in './TFEA/test/test_files' within this repository. ++ ++``` ++TFEA --output ./TFEA/test/test_files/test_output \ ++--bed1 ./TFEA/test/test_files/SRR1105736.tfit_bidirs.chr22.bed ./TFEA/test/test_files/SRR1105737.tfit_bidirs.chr22.bed \ ++--bed2 ./TFEA/test/test_files/SRR1105738.tfit_bidirs.chr22.bed ./TFEA/test/test_files/SRR1105739.tfit_bidirs.chr22.bed \ ++--bam1 ./TFEA/test/test_files/SRR1105736.sorted.chr22.subsample.bam ./TFEA/test/test_files/SRR1105737.sorted.chr22.subsample.bam \ ++--bam2 ./TFEA/test/test_files/SRR1105738.sorted.chr22.subsample.bam ./TFEA/test/test_files/SRR1105739.sorted.chr22.subsample.bam \ ++--label1 DMSO --label2 Nutlin \ ++--genomefasta ./TFEA/test/test_files/chr22.fa \ ++--fimo_motifs ./TFEA/test/test_files/test_database.meme ++``` ++ ++

Advanced Usage

++

Configuration File

++TFEA can be run exclusively through the command line using flags. Alternatively, TFEA can be run using a configuration file (.ini) that takes in flags as variables. For example: ++ ++``` ++TFEA --config ./TFEA/test/test_files/test_config.ini ++``` ++ ++This can be helpful to keep track of different TFEA runs and because you can use variables within the config file to clean up your input. For documentation on config files and what you can do with them see Supported INI File Structure and Interpolation of values (ExtendedInterpolation) ++ ++*Notes:* ++ ++1. Section headers (ex: `[OUTPUT]`) don't matter but you need to have at least ONE section header to be a viable .ini file. ++2. Capitalization of variables doesn't matter. ++3. Feel free to specify any additional variables you like (variables are bash-like), TFEA will only parse variables that match a flag input. ++4. If an input is provided both as a flag and in a configuration file, TFEA prioritizes the command line flag input. ++ ++Below is an example of a configuration file (./test_files/test_config.ini): ++ ++ ```bash ++[OUTPUT] ++OUTPUT='./TFEA/test/test_files/test_output/' ++LABEL1='Condition 1' ++LABEL2='Condition 2' ++ ++[DATA] ++TEST_FILES='./TFEA/test/test_files/' ++BED1=[${TEST_FILES}+'SRR1105736.tfit_bidirs.chr22.bed',${TEST_FILES}+'SRR1105737.tfit_bidirs.chr22.bed'] ++BED2=[${TEST_FILES}+'SRR1105738.tfit_bidirs.chr22.bed',${TEST_FILES}+'SRR1105739.tfit_bidirs.chr22.bed'] ++BAM1=[${TEST_FILES}+'SRR1105736.sorted.chr22.subsample.bam', ${TEST_FILES}+'SRR1105737.sorted.chr22.subsample.bam'] ++BAM2=[${TEST_FILES}+'SRR1105738.sorted.chr22.subsample.bam', ${TEST_FILES}+'SRR1105739.sorted.chr22.subsample.bam'] ++ ++[MODULES] ++TEST_FILES='./TFEA/test/test_files/' #You need to re-initialize variables within each [MODULE] ++FIMO_MOTIFS=${TEST_FILES}+'test_database.meme' ++GENOMEFASTA=${TEST_FILES}+'chr22.fa' ++ ++[OPTIONS] ++OUTPUT_TYPE='html' ++PLOTALL=True ++``` ++ ++ ++

Using SBATCH

++Specifying the `--sbatch` flag will submit TFEA to a compute cluster assuming you are logged into one. If the `--sbatch` flag is specified, it MUST be followed by an e-mail address to send job information to. For example: ++ ++ ++``` ++TFEA --config ./TFEA/test/test_files/test_config.ini --sbatch your_email@address.com ++``` ++ ++Additionally, the following flags can be used to change some of the job parameters: ++ ++``` ++ --cpus CPUS Number of processes to run in parallel. Warning: ++ Increasing this value will significantly increase ++ memory footprint. Default: 1 ++ --mem MEM Amount of memory to request forsbatch script. Default: ++ 50gb ++``` ++ ++*Note:* `--cpus` also works without the `--sbatch` flag ++ ++ ++

Using Pre-processed Inputs

++TFEA has several pipeline elements to it that a user may bypass by providing downstream pre-processed files. These files can be generated by TFEA if running the full pipeline and may also be used to speed up reruns of TFEA. Below are the three types of pre-processed inputs, short descriptions, an example of the file, and a usage example with TFEA (in some cases there are other inputs needed to go along with the pre-processed file). If multiple pre-processed inputs specified, TFEA will use the most downstream one. ++ ++

combined_file

++ ++A sorted (by chrom, start, stop) bed file containing regions of interest ++ ++Example (./test_files/test_combined_file.bed) ++``` ++#chrom start stop ++chr22 10683195 10683999 ++chr22 16609343 16609405 ++chr22 16901069 16902599 ++chr22 17036962 17037636 ++chr22 17158022 17160214 ++... ++``` ++ ++Usage with TFEA ++``` ++TFEA --output ./TFEA/test/test_files/test_output \ ++--combined_file ./TFEA/test/test_files/test_combined_file.bed \ ++--bam1 ./TFEA/test/test_files/SRR1105736.sorted.chr22.subsample.bam ./test_files/SRR1105737.sorted.chr22.subsample.bam \ ++--bam2 ./TFEA/test/test_files/SRR1105738.sorted.chr22.subsample.bam ./test_files/SRR1105739.sorted.chr22.subsample.bam \ ++--label1 condition1 --label2 condition2 \ ++--genomefasta ./TFEA/test/test_files/chr22.fa \ ++--fimo_motifs ./TFEA/test/test_files/test_database.meme ++``` ++ ++

ranked_file

++ ++A ranked bed file with regions of interest. ++ ++*Note:* Specifying a ranked_file turns off some plotting functionality ++ ++Example (./test_files/test_ranked_file.bed) ++ ++``` ++#chrom start stop ++chr22 50794870 50797870 ++chr22 21554591 21557591 ++chr22 50304644 50307644 ++chr22 39096295 39099295 ++chr22 31176104 31179104 ++... ++``` ++ ++Usage with TFEA ++ ++``` ++TFEA --output ./TFEA/test/test_files/test_output \ ++--ranked_file ./TFEA/test/test_files/test_ranked_file.bed \ ++--label1 condition1 --label2 condition2 \ ++--genomefasta ./TFEA/test/test_files/chr22.fa \ ++--fimo_motifs ./TFEA/test/test_files/test_database.meme ++``` ++ ++

fasta_file

++ ++A ranked fasta file with regions of interest (sequences must have unique names but these names aren't used for anything). ++ ++*Note:* Specifying a fasta_file turns off some plotting functionality ++ ++Example (./test_files/test_fasta_file.bed) ++ ++``` ++>chr22:50794870-50797870 ++ccgccccacactgacgcagt...ccgcctcagcctcctaaa ++>chr22:21554591-21557591 ++cttggggagagcagaagcca...gtgcagtggtgcaatctt ++>chr22:50304644-50307644 ++CTGAGCACCCCCCACCAGCCA...GGAGACGGGGCCTTTGT ++... ++``` ++ ++Usage with TFEA ++ ++``` ++TFEA --output ./TFEA/test/test_files/test_output \ ++--fasta_file ./TFEA/test/test_files/test_fasta_file.fa \ ++--label1 condition1 --label2 condition2 \ ++--genomefasta ./TFEA/test/test_files/chr22.fa \ ++--fimo_motifs ./TFEA/test/test_files/test_database.meme ++``` ++ ++

Secondary Analysis

++TFEA can also perform MD-Score analysis and differential MD-Score analysis. This can be switched on easily if running the full pipeline: ++ ++``` ++TFEA --output ./TFEA/test/test_files/test_output \ ++--combined_file ./TFEA/test/test_files/test_combined_file.bed \ ++--bam1 ./TFEA/test/test_files/SRR1105736.sorted.chr22.subsample.bam ./TFEA/test/test_files/SRR1105737.sorted.chr22.subsample.bam \ ++--bam2 ./TFEA/test/test_files/SRR1105738.sorted.chr22.subsample.bam ./TFEA/test/test_files/SRR1105739.sorted.chr22.subsample.bam \ ++--label1 condition1 --label2 condition2 \ ++--genomefasta ./TFEA/test/test_files/chr22.fa \ ++--fimo_motifs ./TFEA/test/test_files/test_database.meme \ ++--md --mdd ++``` ++ ++These secondary analyses can also take pre-processed input similar to TFEA. See the 'Secondary Analysis Inputs' section in the help message for more information. ++ ++

Measuring TF FPKM

++TFEA will also measure the FPKM of TF genes within your data if desired. This requires input into the `--motif_annotations` flag which is a bed file with motif names as the 4th column. Example: ++ ++``` ++chr1 3698045 3733079 P73_HUMAN.H11MO.0.A 0 + ++chr1 6579990 6589212 ZBT48_HUMAN.H11MO.0.C 0 + ++chr1 15941868 15948495 ZBT17_HUMAN.H11MO.0.A 0 - ++chr1 23359447 23368005 ZN436_HUMAN.H11MO.0.C 0 - ++``` ++ ++This special bed file can be generated from a .meme database file using a tab-separated 2-column file containing motif names to gene names and a gene annotation file: ++ ++Example of a motif_to_gene.tsv (this was generated on the HOCOMOCO v11 website): ++ ++``` ++Model Transcription factor ++ANDR_HUMAN.H11MO.0.A AR ++AP2A_HUMAN.H11MO.0.A TFAP2A ++AP2C_HUMAN.H11MO.0.A TFAP2C ++ASCL1_HUMAN.H11MO.0.A ASCL1 ++``` ++ ++Example of gene annotations: ++ ++``` ++chr1 11873 14409 DDX11L1;NR_046018;chr1:11873-14409 0 + ++chr1 14361 29370 WASH7P;NR_024540;chr1:14361-29370 0 - ++chr1 17368 17436 MIR6859-1;NR_106918;chr1:17368-17436 0 - ++chr1 17368 17436 MIR6859-4;NR_128720;chr1:17368-17436 0 - ++chr1 17368 17436 MIR6859-3;NR_107063;chr1:17368-17436 0 - ++``` ++ ++The script works by looking for gene names that correspond to each motif within the 4th column of the gene annotation file. It expects the 4th column to be ';' delimited. ++ ++Already generated motif_annotation.bed files (and also intermediate .tsv files) are located within './motif_files/' ++ ++

Generating Simulated Data

++TFEA has a subpackage that is capable of generating simulated data for testing. If you have installed TFEA, it can be invoked with: ++ ++```TFEA-simulate --help``` ++ ++The purpose of this subpackage is to embed motif instances into fasta sequences that can be generated randomly or be from an experimental dataset (e.g. untreated control sample). There are several key flags that control this process (each of these may be a comma-delimited list of values that would indicate multiple instances of motif adding): ++ ++`--distance_mu` : This flag controls where the center of the distribution is located (note: only normal distributions are supported at this point) ++ ++`--distance_sigma` : Controls the standard deviation of the normal distribution ++ ++`--rank_range` : Controls the range of sequences in which to add a motif ++ ++`--motif_number` : Controls the number of motifs to add to your range of sequences ++ ++ ++

Rerunning TFEA

++TFEA can be easily rerun given one or multiple TFEA output folders. This works simply by rerunning the rerun.sh script which contains all command-line flag inputs. TFEA also automatically creates a copy of your configuration file (if used) within the output folder which is then also used when rerunning (so no need to worry about editing the original configuration file). To rerun a single TFEA output folder: ++ ++``` ++TFEA --rerun ./TFEA/test/test_files/test_output ++``` ++ ++The `--rerun` flag also supports patterns containing wildcards to rerun all TFEA output folders that match. For example: ++ ++``` ++TFEA --rerun ./TFEA/test/test_files/test* ++``` ++ ++This works by looking recursively into all folders and subfolders for rerun.sh scripts and then executing `sh rerun.sh`, so use with caution! ++ ++

Help Message

++Below are all the possible flags that can be provided to TFEA with a short description and default values. ++ ++``` ++usage: TFEA [-h] [--output DIR] ++ [--bed1 [FILE1 FILE2 ... FILEN [FILE1 FILE2 ... FILEN ...]]] ++ [--bed2 [FILE1 FILE2 ... FILEN [FILE1 FILE2 ... FILEN ...]]] ++ [--bam1 [BAM1 [BAM1 ...]]] [--bam2 [BAM2 [BAM2 ...]]] ++ [--label1 LABEL1] [--label2 LABEL2] [--config CONFIG] ++ [--sbatch SBATCH] [--test-install] [--test-full] ++ [--combined_file COMBINED_FILE] [--ranked_file RANKED_FILE] ++ [--fasta_file FASTA_FILE] [--md] [--mdd] ++ [--md_bedfile1 MD_BEDFILE1] [--md_bedfile2 MD_BEDFILE2] ++ [--mdd_bedfile1 MDD_BEDFILE1] [--mdd_bedfile2 MDD_BEDFILE2] ++ [--md_fasta1 MD_FASTA1] [--md_fasta2 MD_FASTA2] ++ [--mdd_fasta1 MDD_FASTA1] [--mdd_fasta2 MDD_FASTA2] ++ [--mdd_pval MDD_PVAL] [--mdd_percent MDD_PERCENT] ++ [--combine {intersect/merge,merge all,tfit clean,tfit remove small,False}] ++ [--rank {deseq,fc,False}] [--scanner {fimo,genome hits}] ++ [--enrichment {auc,auc_bgcorrect}] [--debug] ++ [--genomefasta GENOMEFASTA] [--fimo_motifs FIMO_MOTIFS] ++ [--fimo_thresh FIMO_THRESH] [--fimo_background FIMO_BACKGROUND] ++ [--genomehits GENOMEHITS] [--singlemotif SINGLEMOTIF] ++ [--permutations PERMUTATIONS] [--largewindow LARGEWINDOW] ++ [--smallwindow SMALLWINDOW] [--dpi DPI] [--padjcutoff PADJCUTOFF] ++ [--plotall] [--output_type {txt,html}] [--cpus CPUS] [--mem MEM] ++ [--motif_annotations MOTIF_ANNOTATIONS] [--bootstrap BOOTSTRAP] ++ [--basemean_cut BASEMEAN_CUT] [--rerun [RERUN [RERUN ...]]] ++ [--gc GC] ++ ++Transcription Factor Enrichment Analysis (TFEA) ++ ++optional arguments: ++ -h, --help show this help message and exit ++ ++Main Inputs: ++ Inputs required for full pipeline ++ ++ --output DIR, -o DIR Full path to output directory. If it exists, overwrite ++ its contents. ++ --bed1 [FILE1 FILE2 ... FILEN [FILE1 FILE2 ... FILEN ...]] ++ Bed files associated with condition 1 ++ --bed2 [FILE1 FILE2 ... FILEN [FILE1 FILE2 ... FILEN ...]] ++ Bed files associated with condition 2 ++ --bam1 [BAM1 [BAM1 ...]] ++ Sorted bam files associated with condition 1. Must be ++ indexed. ++ --bam2 [BAM2 [BAM2 ...]] ++ Sorted bam files associated with condition 2. Must be ++ indexed. ++ --label1 LABEL1 An informative label for condition 1 ++ --label2 LABEL2 An informative label for condition 2 ++ --config CONFIG, -c CONFIG ++ A configuration file that a user may use instead of ++ specifying flags. Command line flags will overwrite ++ options within the config file. See examples in the ++ config_files folder. ++ --sbatch SBATCH, -s SBATCH ++ Submits an sbatch (slurm) job. If specified, input an ++ e-mail address. ++ --test-install, -ti Checks whether all requirements are installed and ++ command-line runnable. ++ --test-full, -t Performs unit testing on full TFEA pipeline. ++ ++Processed Inputs: ++ Input options for pre-processed data ++ ++ --combined_file COMBINED_FILE ++ A single bed file combining regions of interest. ++ --ranked_file RANKED_FILE ++ A bed file containing each regions rank as the 4th ++ column. ++ --fasta_file FASTA_FILE ++ A fasta file containing sequences to be analyzed, ++ ranked by the user. ++ ++Secondary Analysis Inputs: ++ Input options for performing MD-Score and Differential MD-Score analysis ++ ++ --md Switch that controls whether to perform MD analysis. ++ --mdd Switch that controls whether to perform differential ++ MD analysis. ++ --md_bedfile1 MD_BEDFILE1 ++ A bed file for MD-Score analysis associated with ++ condition 1. ++ --md_bedfile2 MD_BEDFILE2 ++ A bed file for MD-Score analysis associated with ++ condition 2. ++ --mdd_bedfile1 MDD_BEDFILE1 ++ A bed file for Differential MD-Score analysis ++ associated with condition 1. ++ --mdd_bedfile2 MDD_BEDFILE2 ++ A bed file for Differential MD-Score analysis ++ associated with condition 2. ++ --md_fasta1 MD_FASTA1 ++ A fasta file for MD-Score analysis associated with ++ condition 1. ++ --md_fasta2 MD_FASTA2 ++ A fasta file for MD-Score analysis associated with ++ condition 2. ++ --mdd_fasta1 MDD_FASTA1 ++ A fasta file for Differential MD-Score analysis ++ associated with condition 1. ++ --mdd_fasta2 MDD_FASTA2 ++ A fasta file for Differential MD-Score analysis ++ associated with condition 2. ++ --mdd_pval MDD_PVAL P-value cutoff for retaining differential regions. ++ Default: 0.2 ++ --mdd_percent MDD_PERCENT ++ Percentage cutoff for retaining differential regions. ++ Default: False ++ ++Module Switches: ++ Switches for different modules ++ ++ --combine {intersect/merge,merge all,tfit clean,tfit remove small,False} ++ Method for combining input bed files ++ --rank {deseq,fc,False} ++ Method for ranking combined bed file ++ --scanner {fimo,genome hits} ++ Method for scanning fasta files for motifs ++ --enrichment {auc,auc_bgcorrect} ++ Method for calculating enrichment ++ --debug Print memory and CPU usage to stderr ++ ++Scanner Options: ++ Options for performing motif scanning ++ ++ --genomefasta GENOMEFASTA ++ Genomic fasta file ++ --fimo_motifs FIMO_MOTIFS ++ Full path to a .meme formatted motif databse file. ++ Some databases included in motif_databases folder. ++ --fimo_thresh FIMO_THRESH ++ P-value threshold for calling FIMO motif hits. ++ Default: 1e-6 ++ --fimo_background FIMO_BACKGROUND ++ Options for choosing mononucleotide background ++ distribution to use with FIMO. {'largewindow', ++ 'smallwindow', int, file} ++ --genomehits GENOMEHITS ++ A folder containing bed files with pre-calculated ++ motif hits to a genome. For use with 'genome hits' ++ scanner option. ++ --singlemotif SINGLEMOTIF ++ Option to run analysis on a subset of motifs within ++ specified motif database or genome hits. Can be a ++ single motif or a comma-separated list of motifs. ++ ++Enrichment Options: ++ Options for performing enrichment analysis ++ ++ --permutations PERMUTATIONS ++ Number of permutations to perfrom for calculating ++ p-value. Default: 1000 ++ --largewindow LARGEWINDOW ++ The size (bp) of a large window around input regions ++ that captures background. Default: 1500 ++ --smallwindow SMALLWINDOW ++ The size (bp) of a small window arount input regions ++ that captures signal. Default: 150 ++ ++Output Options: ++ Options for the output. ++ ++ --dpi DPI Resolution of output figures. Default: 100 ++ --padjcutoff PADJCUTOFF ++ A p-adjusted cutoff value that determines some ++ plotting output. ++ --plotall Plot graphs for all motifs.Warning: This will make ++ TFEA run much slower andwill result in a large output ++ folder. ++ --output_type {txt,html} ++ Specify output type. Selecting html will increase ++ processing time and memory usage. Default: txt ++ ++Miscellaneous Options: ++ Other options. ++ ++ --cpus CPUS Number of processes to run in parallel. Note: ++ Increasing this value will significantly increase ++ memory footprint. Default: 1 ++ --mem MEM Amount of memory to request forsbatch script. Default: ++ 50gb ++ --motif_annotations MOTIF_ANNOTATIONS ++ A bed file specifying genomic coordinates for genes ++ corresponding to motifs. Motif name must be in the 4th ++ column and match what is in the database. ++ --bootstrap BOOTSTRAP ++ Amount to subsample motifhits to. Set to False to turn ++ off. Default: False ++ --basemean_cut BASEMEAN_CUT ++ Basemean cutoff value for inputted regions. Default: 0 ++ --rerun [RERUN [RERUN ...]] ++ Rerun TFEA in all folders of aspecified directory. ++ Default: False ++ --gc GC Perform GC-correction. Default: True ++``` ++ ++

++ ++

Example Output

++TFEA will output all files and folders into the directory specified by the `--output` flag. The output directory structure is as follows: ++ ++``` ++./TFEA/test/test_output ++│ rerun.sh ++│ test_config.ini ++│ inputs.txt ++│ results.txt ++│ md_results.txt ++│ mdd_results.txt ++│ results.html ++│ ++└───e_and_o ++│ TFEA_test_output.err ++│ TFEA_test_output.out ++│ ++└───plots ++│ logo_rcMOTIF.eps ++│ logo_rcMOTIF.png ++│ logoMOTIF.eps ++│ logoMOTIF.png ++│ MOTIF_enrichment_plot.png ++│ MOTIF_simulation_plot.png ++│ MOTIF.results.html ++│ ++└───temp_files ++ combined_file.mergeall.bed ++ count_file.bed ++ count_file.header.bed ++ DESeq.R ++ DESeq.Rout ++ DESeq.res.txt ++ markov_background.txt ++ ranked_file.bed ++ ranked_file.fa ++``` ++ ++A brief description of the files contained within this output directory are below: ++ ++

rerun.sh

++This bash script can be used at any time to regenerate a TFEA output folder in its entirety, run it using: ++ ++``` ++sh ./TFEA/test/test_output/rerun.sh ++``` ++ ++

test_config.ini

++ ++TFEA copies the config file you are using into the output directoy. This file is then referenced by rerun.sh. ++ ++ ++

inputs.txt

++ ++A .txt file that contains all user-provided inputs into TFEA ++ ++

results.txt

++Contains TFEA results tab-delimited in .txt format. For example: ++ ++``` ++#TF AUC Events p-val p-adj ++P53_HUMAN.H11MO.0.A 0.2795355012578686 5 0.02464223619276762 0.04928447238553524 ++SP2_HUMAN.H11MO.0.A -0.04994116666412335 114 0.027169601555608307 0.054339203111216615 ++``` ++ ++TF = The name of the motif analyzed ++ ++AUC = Area under the curve ++ ++Events = Number of motif hits within smallwindow ++ ++p-val = P-value ++ ++p-adj = adjusted p-value (Bonferroni) ++ ++

md_results.txt and mdd_results.txt

++Contains tab-delimited results for secondary MD-Score (MDS) and Differential MD-Score (MDD) analysis if these flags were specified ++ ++

results.html

++ ++The main results html (if `--output_type 'html'` specified). For example: ++ ++![TFEA Pipeline](https://github.com/jdrubin91/TFEA/blob/master/README_images/ExampleResults.png) ++ ++1. TFEA MA-plot - An MA-like plot with each dot representing a TF motif analyzed (red=significant below specified p-adj cutoff). On the y-axis is the area under the curve (AUC) which is the main TFEA statistic. On the x-axis is the log10 of the number of motif hits within the largewindow input ++ ++2. TFEA Volcano Plot - Similar to the MA-Plot, each dot is a TF motif (red=significant below specified p-adj cutoff). X-axis = area under the curve (AUC). Y-axis = -log10 of the p-adjusted value. Dashed line is the specified p-adjusted cutoff. ++ ++3. DE-Seq MA-plot - An actual MA-plot where each dot represents a region specified by the user. On the x-axis is the log10 of the average expression across conditions and replicates. On the y-axis is the log2 fold change between both conditions. The dots on this plot are colored based on how they are ranked. ++ ++4. Link to inputs.txt file, MD MA-plot and volcano (if `--md` specified), MDD MA-plot and volcano (if `--mdd` specified), and a table of time to perform each module in TFEA and the total time to run TFEA. ++ ++5. A list of TF motifs analyzed that have positive AUC values (headers correspond to the same headers as in results.txt). If red, then this TF motif was significant below the p-adj cutoff. Clickable links will direct to a separate MOTIF.results.html file contained within the plots/ directory in output. ++ ++6. A list of TF motifs analyzed that have negative AUC values (headers correspond to the same headers as in results.txt). If red, then this TF motif was significant below the p-adj cutoff. Clickable links will direct to a separate MOTIF.results.html file contained within the plots/ directory in output. ++ ++

MOTIF.results.html

++ ++Each signficant TF motif (or all motifs if `--plotall` specified) will produce its own MOTIF.results.html file contained within the plots/ directory in the specified output directory. All images are also self-contained within the plots/ folder. For example: ++ ++![TFEA Pipeline](https://github.com/jdrubin91/TFEA/blob/master/README_images/ExampleMotifResults.png) ++ ++1. Results for this specific motif (identical to what's reported in results.html) ++ ++2. Enrichment line plot - The running sum statistic (green) for the specified TF motif. The blue dashed line indicates the random background expectation. The area under the curve (AUC) is calculated as the area between the green and dashed blue line (directional). ++ ++3. Score bar plot - Quantification of the amount added to the running sum statistic at any given point. ++ ++4. Motif hit scatter plot - The actual motif hits for each region centered on the region and bounded by the largewindow input. ++ ++5. Rank metric fill plot - A visual representation of the ranking metric used (log10(DE-Seq p-value) with direction dependent on fold change) ++ ++6. Meta plot - A meta plot of read coverage over regions separated by quartiles. ++ ++7. Heat map - A heatmap of motif hits for each quartile ++ ++8. The forward motif logo ++ ++9. The reverse complement motif logo ++ ++10. Simulation plot - The distribution of simulated AUC values (number of simulations specified with `--permutations` flag). The observed AUC is the red bar. ++ ++

++ ++

Contact Information

++Jonathan.Rubin@colorado.edu ++ From 756cca0dc2ae8128d92391352646f9e80bf1f14b Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:31:04 +0100 Subject: [PATCH 5246/9987] download_dep_fail removed as PythonBundle --- easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb index 912a8595037..241a26b0ee6 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb @@ -22,7 +22,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From fb21f3d920704c4fa21a24cbba474254ecf5e83c Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:33:45 +0100 Subject: [PATCH 5247/9987] download_dep_fail removed, sanity_pip_check added --- easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb index c8b8ea559e1..062ec65ec9a 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb @@ -13,7 +13,7 @@ builddependencies = [('binutils', '2.38')] dependencies = [('Python', '3.10.4')] use_pip = True -download_dep_fail = True +sanity_pip_check = True exts_list = [ (name, version, { From 0b76dbb3ae04ff41c0c8aed5ca4dcc4c1760b917 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:34:55 +0100 Subject: [PATCH 5248/9987] download_dep_fail removed as PythonBundle --- .../easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb index 94610d8bfd0..ef3a56457df 100644 --- a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb +++ b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb @@ -26,7 +26,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From 6986e0ef3950f7ff15acd1a0deb46ccb414f16a3 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:36:39 +0100 Subject: [PATCH 5249/9987] download_dep_fail removed as PythonBundle --- .../easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb index 80c02fc63c7..4b4c5f40023 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb @@ -14,7 +14,6 @@ dependencies = [ ('Pysam', '0.19.1'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From 5954dcafb701f24464d162c15db74a06b7cc8006 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 22 Oct 2022 10:27:25 +0200 Subject: [PATCH 5250/9987] adding easyconfigs: captum-0.5.0-foss-2022a-CUDA-11.7.0.eb, captum-0.5.0-foss-2022a.eb --- .../captum-0.5.0-foss-2022a-CUDA-11.7.0.eb | 33 +++++++++++++++++++ .../c/captum/captum-0.5.0-foss-2022a.eb | 31 +++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..cb2d2bdffbe --- /dev/null +++ b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'captum' +version = '0.5.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://captum.ai/' +description = """ +Captum is a model interpretability and understanding library for PyTorch. +Captum means comprehension in Latin and contains general purpose +implementations of integrated gradients, saliency maps, smoothgrad, vargrad and +others for PyTorch models. It has quick integration for models built with +domain-specific libraries such as torchvision, torchtext, and others.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['84af2c8793d34c440a351793b5ca705b8542745e2dc8bc24afb1d9b86f3bf6ec'], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb new file mode 100644 index 00000000000..7836096aaf7 --- /dev/null +++ b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'captum' +version = '0.5.0' + +homepage = 'https://captum.ai/' +description = """ +Captum is a model interpretability and understanding library for PyTorch. +Captum means comprehension in Latin and contains general purpose +implementations of integrated gradients, saliency maps, smoothgrad, vargrad and +others for PyTorch models. It has quick integration for models built with +domain-specific libraries such as torchvision, torchtext, and others.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['84af2c8793d34c440a351793b5ca705b8542745e2dc8bc24afb1d9b86f3bf6ec'], + }), +] + +moduleclass = 'ai' From ba3741e917188f3b0e2573509f515d35a63282d2 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Sat, 22 Oct 2022 11:09:12 +0200 Subject: [PATCH 5251/9987] Update napari-0.4.15-foss-2021b.eb remove download_dep_fail --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb index 1326a9f443b..914242860a4 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb @@ -30,7 +30,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('pytomlpp', '1.0.10', { 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], From ed4dd1f420b4222632beb2dd1b06aa94272ae6ef Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 24 Oct 2022 10:29:52 +0200 Subject: [PATCH 5252/9987] adding easyconfigs: RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb and patches: RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch, RStudio-Server-2022.07.1+554_fix-libsoci-search.patch, RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch --- ...2022.07.1+554_allow-disabling-quarto.patch | 46 ++++++++ ...ver-2022.07.1+554_fix-libsoci-search.patch | 27 +++++ ...ver-2022.07.1+554_use-XDG_CACHE_HOME.patch | 71 +++++++++++ ...022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb | 111 ++++++++++++++++++ 4 files changed, 255 insertions(+) create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch new file mode 100644 index 00000000000..f57b688b6a5 --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch @@ -0,0 +1,46 @@ +From 9b7ac4b2952a47568d23f6cbfed4a797798ee161 Mon Sep 17 00:00:00 2001 +From: Kevin Ushey +Date: Fri, 19 Aug 2022 10:01:14 -0700 +Subject: [PATCH] make it possible to control QUARTO_ENABLED from command line + +--- + CMakeGlobals.txt | 26 ++++++++++++++------------ + 1 file changed, 14 insertions(+), 12 deletions(-) + +diff --git a/CMakeGlobals.txt b/CMakeGlobals.txt +index 6dfe1017a9a..cbd8e865672 100644 +--- a/CMakeGlobals.txt ++++ b/CMakeGlobals.txt +@@ -244,18 +244,20 @@ if(LINUX AND EXISTS "/etc/centos-release") + endif() + + # quarto support +-if(LINUX AND UNAME_M STREQUAL aarch64) +- # disabled on linux aarch64 +- message(STATUS "quarto does not yet support aarch64 builds of Linux; disabling quarto") +- set(QUARTO_ENABLED FALSE CACHE INTERNAL "") +-elseif(IS_CENTOS7) +- # disable quarto on Centos 7 +- message(STATUS "quarto is not supported on Centos7; disabling quarto") +- set(QUARTO_ENABLED FALSE CACHE INTERNAL "") +-else() +- # enable by default +- set(QUARTO_ENABLED TRUE CACHE INTERNAL "") +- add_definitions(-DQUARTO_ENABLED) ++if(NOT DEFINED QUARTO_ENABLED) ++ if(LINUX AND UNAME_M STREQUAL aarch64) ++ # disabled on linux aarch64 ++ message(STATUS "quarto does not yet support aarch64 builds of Linux; disabling quarto") ++ set(QUARTO_ENABLED FALSE CACHE INTERNAL "") ++ elseif(IS_CENTOS7) ++ # disable quarto on Centos 7 ++ message(STATUS "quarto is not supported on Centos7; disabling quarto") ++ set(QUARTO_ENABLED FALSE CACHE INTERNAL "") ++ else() ++ # enable by default ++ set(QUARTO_ENABLED TRUE CACHE INTERNAL "") ++ add_definitions(-DQUARTO_ENABLED) ++ endif() + endif() + + # install freedesktop integration files if we are installing into /usr diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch new file mode 100644 index 00000000000..25cae4ea6db --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch @@ -0,0 +1,27 @@ +Allow to find system SOCI_* libraries + +Add a second `find_library` call which will find the SOCI libraries in default locations if it hasn't been found already in `SOCI_LIBRARY_DIR` +See https://github.com/rstudio/rstudio/pull/11691 + +Author: Alexander Grund (TU Dresden) + +diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt +index d2be417b40..6a42b4614d 100644 +--- a/src/cpp/CMakeLists.txt ++++ b/src/cpp/CMakeLists.txt +@@ -467,12 +467,12 @@ endif() + # find SOCI libraries + if(UNIX) + set(SOCI_LIBRARY_DIR "${RSTUDIO_TOOLS_SOCI}/build/lib") +- if(NOT APPLE AND RSTUDIO_USE_SYSTEM_SOCI) +- set(SOCI_LIBRARY_DIR "/usr/lib") +- endif() + find_library(SOCI_CORE_LIB NAMES "libsoci_core.a" "soci_core" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) ++ find_library(SOCI_CORE_LIB NAMES "libsoci_core.a" "soci_core") + find_library(SOCI_SQLITE_LIB NAMES "libsoci_sqlite3.a" "soci_sqlite3" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) ++ find_library(SOCI_SQLITE_LIB NAMES "libsoci_sqlite3.a" "soci_sqlite3") + find_library(SOCI_POSTGRESQL_LIB NAMES "libsoci_postgresql.a" "soci_postgresql" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) ++ find_library(SOCI_POSTGRESQL_LIB NAMES "libsoci_postgresql.a" "soci_postgresql") + find_library(DL_LIB "dl") + find_library(SQLITE_LIB "sqlite3") + get_filename_component(SQLITE_LIB "${SQLITE_LIB}" REALPATH) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch new file mode 100644 index 00000000000..9df3a006a82 --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch @@ -0,0 +1,71 @@ +From https://github.com/rstudio/rstudio/pull/11976 + +From c131989e8ecb19733fe274fe7ad8a18d490fdcf9 Mon Sep 17 00:00:00 2001 +From: Jonathan McPherson +Date: Mon, 19 Sep 2022 14:34:18 -0700 +Subject: [PATCH] use XDG_CACHE_HOME for secure cookie key in low privilege + mode + +--- + src/cpp/core/include/core/system/Xdg.hpp | 7 +++++++ + src/cpp/core/system/Xdg.cpp | 15 +++++++++++++++ + src/cpp/server_core/SecureKeyFile.cpp | 2 +- + 3 files changed, 23 insertions(+), 1 deletion(-) + +diff --git a/src/cpp/core/include/core/system/Xdg.hpp b/src/cpp/core/include/core/system/Xdg.hpp +index 71cb2a8d50f..ed848ca2476 100644 +--- a/src/cpp/core/include/core/system/Xdg.hpp ++++ b/src/cpp/core/include/core/system/Xdg.hpp +@@ -66,6 +66,13 @@ FilePath userDataDir(const boost::optional& user = boost::none, + // Returns the user-specific logging directory underneath the userDataDir + FilePath userLogDir(); + ++// Returns the RStudio XDG user cache directory. ++// ++// On Unix-alikes, this is ~/.cache, or XDG_CACHE_HOME. ++// On Windows, this is 'FOLDERID_InternetCache' (typically 'AppData/Local/Microsoft/Windows/Temporary Files') ++FilePath userCacheDir(const boost::optional& user = boost::none, ++ const boost::optional& homeDir = boost::none); ++ + // This function verifies that the userConfigDir() and userDataDir() exist and are owned by the running user. + // + // It should be invoked once. Any issues with these directories will be emitted to the session log. +diff --git a/src/cpp/core/system/Xdg.cpp b/src/cpp/core/system/Xdg.cpp +index 3866f286437..ca1e7923ac5 100644 +--- a/src/cpp/core/system/Xdg.cpp ++++ b/src/cpp/core/system/Xdg.cpp +@@ -218,6 +218,21 @@ FilePath userDataDir( + ); + } + ++FilePath userCacheDir( ++ const boost::optional& user, ++ const boost::optional& homeDir) ++{ ++ return resolveXdgDir("RSTUDIO_CACHE_HOME", ++ "XDG_CACHE_HOME", ++#ifdef _WIN32 ++ FOLDERID_InternetCache, ++#endif ++ "~/.cache", ++ user, ++ homeDir ++ ); ++} ++ + FilePath userLogDir() + { + return userDataDir().completePath("log"); +diff --git a/src/cpp/server_core/SecureKeyFile.cpp b/src/cpp/server_core/SecureKeyFile.cpp +index d3a5e37c1bd..cbc3a91a44c 100644 +--- a/src/cpp/server_core/SecureKeyFile.cpp ++++ b/src/cpp/server_core/SecureKeyFile.cpp +@@ -113,7 +113,7 @@ core::Error readSecureKeyFile(const std::string& filename, + } + else + { +- secureKeyPath = core::FilePath("/tmp/rstudio-server").completePath(filename); ++ secureKeyPath = core::system::xdg::userCacheDir().completePath(filename); + if (secureKeyPath.exists()) + { + LOG_INFO_MESSAGE("Running without privilege; using secure key at " + secureKeyPath.getAbsolutePath()); diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb new file mode 100644 index 00000000000..1f49f98c15c --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb @@ -0,0 +1,111 @@ +easyblock = 'CMakeNinja' + +name = 'RStudio-Server' +version = '2022.07.2+576' +versionsuffix = '-Java-%(javaver)s-R-%(rver)s' +local_git_rev = '7872775ebddc40635780ca1ed238934c3345c5de' + +homepage = 'https://www.rstudio.com/' +description = """This is the RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file "${MYTMP}/db.conf" +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-2022.07.1+554_allow-disabling-quarto.patch', + '%(name)s-2022.07.1+554_fix-libsoci-search.patch', + '%(name)s-2022.07.1+554_use-XDG_CACHE_HOME.patch', +] +checksums = [ + '55705c36a9b826064b4d9aa87b58c40bb9f7cd2f149b16d554e20136306ce301', + # RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch + '165306d976c7b851e1e6a2d1f0c2967984b0cd203006aa834a1a6ff17894cf81', + # RStudio-Server-2022.07.1+554_fix-libsoci-search.patch + '0dafd9fa45d745d350c0c852fe03e3e1e77558d94baae2b5c595d97765002cd5', + # RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch + 'd033a383c8518a85dcdf45baf14d0a9d6283d03a28576a6eb03bbfb3682d2b00', +] + +builddependencies = [ + ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('Java', '11', '', SYSTEM), + ('R', '4.2.1'), + ('SOCI', '4.0.3'), + ('yaml-cpp', '0.7.0'), +] + +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] + +# Required until https://github.com/easybuilders/easybuild-framework/pull/4035 +local_start_dir = "%(builddir)s/rstudio-" + version.replace("+", "-") + +preconfigopts = " && ".join([ + # Install dependencies via scripts. Done in subshell to preserve PWD + "(export RSTUDIO_TOOLS_ROOT='%(builddir)s'", + "cd '%s/dependencies/common'" % local_start_dir, + "./install-cef", + "./install-dictionaries", + "./install-mathjax", + "./install-pandoc", + "./install-packages", + "./install-npm-dependencies)", + "" +]) + +configopts = " ".join([ + "-DRSTUDIO_TOOLS_ROOT='%(builddir)s'", + "-DRSTUDIO_TARGET=Server", + "-DRSTUDIO_USE_SYSTEM_BOOST=ON", + "-DRSTUDIO_USE_SYSTEM_SOCI=ON", + "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON", + "-DQUARTO_ENABLED=OFF", # Not available on all archs, use pandoc fallback + "-DRSTUDIO_GIT_REVISION_HASH=" + local_git_rev +]) + +sanity_check_commands = [ + # RSession requires environment variables R_HOME and R_DOC_DIR + 'R_HOME="$EBROOTR/lib64/R" R_DOC_DIR="$R_HOME/doc" rsession --verify-installation=1', + # RServer requires a db conf (this may also be needed for live use) + # Also create and set a soem dirs so it doesn't try to use $HOME + 'MYTMP=`mktemp -d`' + ' && export RSTUDIO_CONFIG_DIR="$MYTMP"' + ' && export XDG_DATA_HOME="$MYTMP/.data"' + ' && export XDG_CACHE_HOME="$MYTMP/.cache"' + ' && mkdir "$XDG_DATA_HOME" "$XDG_CACHE_HOME"' + ' && export RS_LOG_DIR="$MYTMP/log"' + ' && echo -e "provider=sqlite\\ndirectory=$MYTMP/db" >> "$MYTMP/db.conf"' + ' && rserver ' + ' '.join([ + '--verify-installation=1', + '--server-user="$USER"', + '--database-config-file="$MYTMP/db.conf"', + '--server-data-dir="$MYTMP/sdd"', + '--secure-cookie-key-file="$MYTMP/secure-cookie-key"', + ]), +] + +sanity_check_paths = { + 'files': ['bin/rstudio-server'], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +moduleclass = 'lang' From d46d46113fd3c6840f138d95449051eac2ffa601 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Mon, 24 Oct 2022 12:03:25 +0200 Subject: [PATCH 5253/9987] Typo dependency name "-" -> "_" Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 4242b5cd1ae..f6ed3b365e2 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -30,7 +30,7 @@ exts_list = [ 'modulename': 'google', 'checksums': ['c25873c47279387cfdcbdafa36149887901d36202cb645a0e4f29686bf6e4417'], }), - ('tensorflow-metadata', '1.10.0', { + ('tensorflow_metadata', '1.10.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], }), From 1e50f35c8b4072935096f4275f9e9f7dfae5aa64 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 11:13:29 +0100 Subject: [PATCH 5254/9987] adding easyconfigs: MoviePy-1.0.3-foss-2021a.eb and patches: moviepy-1.0.3-setup.py.patch --- .../m/MoviePy/MoviePy-1.0.3-foss-2021a.eb | 42 +++++++++++++++++++ .../m/MoviePy/moviepy-1.0.3-setup.py.patch | 16 +++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch diff --git a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb new file mode 100644 index 00000000000..a5a67866969 --- /dev/null +++ b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb @@ -0,0 +1,42 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +# Updated to foss 2021a: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'MoviePy' +version = '1.0.3' + +homepage = "https://zulko.github.io/moviepy/" +description = """MoviePy (full documentation) is a Python library for video editing: cutting, concatenations, + title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('FFmpeg', '4.3.2'), + ('Python', '3.9.5'), + ('Pillow', '8.2.0'), + ('SciPy-bundle', '2021.05'), + ('tqdm', '4.61.2'), + ('imageio', '2.10.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('imageio-ffmpeg', '0.4.7', { + 'checksums': ['7a08838f97f363e37ca41821b864fd3fdc99ab1fe2421040c78eb5f56a9e723e'], + }), + ('proglog', '0.1.10', { + 'checksums': ['658c28c9c82e4caeb2f25f488fff9ceace22f8d69b15d0c1c86d64275e4ddab4'], + }), + (name, version, { + 'source_tmpl': 'moviepy-%(version)s.tar.gz', + 'patches': ['moviepy-1.0.3-setup.py.patch'], + 'checksums': [('2884e35d1788077db3ff89e763c5ba7bfddbd7ae9108c9bc809e7ba58fa433f5'), + ('beca82ff8dfbc9cd0b97296f310de3ddfc43e2e49344a32375d4438485c3f3df')], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch b/easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch new file mode 100644 index 00000000000..ce24edbfaea --- /dev/null +++ b/easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch @@ -0,0 +1,16 @@ +Changed the max. version of decorator to <6.0 +https://github.com/Zulko/moviepy/blob/master/setup.py +Author: J. Sassmannshausen +diff --git a/moviepy-1.0.3.orig/setup.py b/moviepy-1.0.3/setup.py +index f8088bb..feb7da7 100644 +--- a/moviepy-1.0.3.orig/setup.py ++++ b/moviepy-1.0.3/setup.py +@@ -62,7 +62,7 @@ exec(open('moviepy/version.py').read()) # loads __version__ + + # Define the requirements for specific execution needs. + requires = [ +- 'decorator>=4.0.2,<5.0', ++ 'decorator>=4.0.2,<6.0', + "imageio>=2.5,<3.0; python_version>='3.4'", + "imageio>=2.0,<2.5; python_version<'3.4'", + "imageio_ffmpeg>=0.2.0; python_version>='3.4'", From a00e25f72c3e369e977d91da33be44b6deb3b8da Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 12:13:47 +0100 Subject: [PATCH 5255/9987] GCCcore-10.2.0 EasyConfig file added --- .../p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9bae7e1c2ba --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '5.9.3' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['7ccfcdfea4fc4b0a02ca2c31de7fcd186beb9cff8207800e14ab66f79c773af6'], + }), +] + +moduleclass = 'lib' From d3643f8f9cd6569726f06ed0ebc3e0e51fac46ad Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 12:24:18 +0100 Subject: [PATCH 5256/9987] MoviePi added, scikit-image downgraded --- .../DeepLabCut-2.2.0.6-foss-2021a.eb | 30 ++++++++++++++++++- 1 file changed, 29 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb index e1b28de60f0..37f47381608 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -1,4 +1,6 @@ # Loosely based on PR #7680 +# Scikit-image is added as an extension to avoid problems with imageio, +# which comes in from MoviePy # J. Sassmannshausen (Imperial College London/UK) easyblock = 'PythonBundle' @@ -18,7 +20,6 @@ dependencies = [ ('h5py', '3.2.1'), ('IPython', '7.25.0'), ('scikit-learn', '0.24.2'), - ('scikit-image', '0.18.3'), ('TensorFlow', '2.6.0'), ('PyYAML', '5.4.1'), ('PyTables', '3.6.1'), @@ -31,6 +32,7 @@ dependencies = [ ('ruamel.yaml', '0.17.21'), ('statsmodels', '0.12.2'), ('PyTorch', '1.10.0'), + ('MoviePy', '1.0.3'), ] sanity_pip_check = True @@ -53,6 +55,32 @@ exts_list = [ 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], 'sources': ['msgpack-numpy-0.4.8.tar.gz'], }), + + # this is for scikit-image + ('PyWavelets', '1.1.1', { + 'modulename': 'pywt', + 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('tifffile', '2021.10.12', { + 'checksums': ['0a78268a2d844af94929512d28b39bd1ea6fe46de4124103840b5fe4e1c555cd'], + }), + ('scikit-image', '0.18.1', { + 'modulename': 'skimage', + 'patches': ['scikit-image-0.18.1_fix-README-cache-perms.patch'], + 'checksums': [ + 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz + # scikit-image-0.18.1_fix-README-cache-perms.patch + '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', + ], + }), + # end of scikit-image + (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], From 09b501df5ed25a2b5a89c9d1e0e6a8603c753e87 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 12:36:28 +0100 Subject: [PATCH 5257/9987] MoviePi added, scikit-image downgraded --- ...epLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 34 +++++++++++++++++-- 1 file changed, 31 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 9416f4eee39..0a0782a73af 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -1,4 +1,6 @@ # Loosely based on PR #7680 +# Scikit-image is added as an extension to avoid problems with imageio, +# which comes in from MoviePy # J. Sassmannshausen (Imperial College London/UK) easyblock = 'PythonBundle' @@ -15,13 +17,12 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True} dependencies = [ - ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), ('Python', '3.9.5'), ('h5py', '3.2.1'), ('IPython', '7.25.0'), ('scikit-learn', '0.24.2'), - ('scikit-image', '0.18.3'), ('TensorFlow', '2.6.0', versionsuffix), ('PyYAML', '5.4.1'), ('PyTables', '3.6.1'), @@ -34,6 +35,7 @@ dependencies = [ ('ruamel.yaml', '0.17.21'), ('statsmodels', '0.12.2'), ('PyTorch', '1.10.0', versionsuffix), + ('MoviePy', '1.0.3'), ] sanity_pip_check = True @@ -56,6 +58,32 @@ exts_list = [ 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], 'sources': ['msgpack-numpy-0.4.8.tar.gz'], }), + + # this is for scikit-image + ('PyWavelets', '1.1.1', { + 'modulename': 'pywt', + 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('tifffile', '2021.10.12', { + 'checksums': ['0a78268a2d844af94929512d28b39bd1ea6fe46de4124103840b5fe4e1c555cd'], + }), + ('scikit-image', '0.18.1', { + 'modulename': 'skimage', + 'patches': ['scikit-image-0.18.1_fix-README-cache-perms.patch'], + 'checksums': [ + 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz + # scikit-image-0.18.1_fix-README-cache-perms.patch + '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', + ], + }), + # end of scikit-image + (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], From 03c6a0b337b37f16a536474ef3f62640e119bd6c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 24 Oct 2022 13:58:39 +0200 Subject: [PATCH 5258/9987] Remove superflous example parameter --- ...RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb index 1f49f98c15c..b63011c23f4 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb @@ -10,12 +10,12 @@ description = """This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: - rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) + rserver --server-daemonize=0 --www-port=8787 If you need a database config one can be created with: MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" and then used with: - rserver ... --database-config-file "${MYTMP}/db.conf" + rserver ... --database-config-file="${MYTMP}/db.conf" """ toolchain = {'name': 'foss', 'version': '2022a'} From 3fcbcc9a601c1fe03a7f05e0b0724dc85d0a8b6e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 24 Oct 2022 14:00:56 +0200 Subject: [PATCH 5259/9987] Add dependencies --- .../s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb | 52 +++++++ .../yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb | 30 ++++ .../yaml-cpp-0.7.0_fix-cmake-export.patch | 143 ++++++++++++++++++ 3 files changed, 225 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..63024d01cc2 --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.3' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('SQLite', '3.38.3'), + ('PostgreSQL', '14.4'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c218e476fb7 --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' +name = 'yaml-cpp' +version = '0.7.0' + +homepage = "https://github.com/jbeder/yaml-cpp" +description = """yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/jbeder/%(name)s/archive/'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-cmake-export.patch'] +checksums = [ + '43e6a9fcb146ad871515f0d0873947e5d497a1c9c60c58cb102a97b47208b7c3', + 'c562a575bbb161af478795e43bfd9073e3f874bea07134a321c1063cd7098c1c', # yaml-cpp-0.7.0_fix-cmake-export.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1') +] + +sanity_check_paths = { + 'files': ['lib/libyaml-cpp.a', 'include/yaml-cpp/yaml.h'], + 'dirs': ['lib', 'include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch new file mode 100644 index 00000000000..45933bb6962 --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch @@ -0,0 +1,143 @@ +Fix installed CMake config files. +From https://patch-diff.githubusercontent.com/raw/jbeder/yaml-cpp/pull/1077 + +From a339bea6bb7bd461a41e874f78b46a5af98277ff Mon Sep 17 00:00:00 2001 +From: Felix +Date: Thu, 30 Dec 2021 12:53:31 +0100 +Subject: [PATCH 1/2] untabify CMakeLists.txt in some places + +This is to align with the other code parts in this file. +--- + CMakeLists.txt | 16 ++++++++-------- + 1 file changed, 8 insertions(+), 8 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index f65efefa..6adbf45a 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -141,30 +141,30 @@ write_basic_package_version_file( + configure_file(yaml-cpp.pc.in yaml-cpp.pc @ONLY) + + if (YAML_CPP_INSTALL) +- install(TARGETS yaml-cpp ++ install(TARGETS yaml-cpp + EXPORT yaml-cpp-targets + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) +- install(DIRECTORY ${PROJECT_SOURCE_DIR}/include/ ++ install(DIRECTORY ${PROJECT_SOURCE_DIR}/include/ + DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} +- FILES_MATCHING PATTERN "*.h") ++ FILES_MATCHING PATTERN "*.h") + install(EXPORT yaml-cpp-targets + DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") +- install(FILES +- "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" +- "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" ++ install(FILES ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" + DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") + install(FILES "${PROJECT_BINARY_DIR}/yaml-cpp.pc" + DESTINATION ${CMAKE_INSTALL_DATADIR}/pkgconfig) + endif() + + if(YAML_CPP_BUILD_TESTS) +- add_subdirectory(test) ++ add_subdirectory(test) + endif() + + if(YAML_CPP_BUILD_TOOLS) +- add_subdirectory(util) ++ add_subdirectory(util) + endif() + + if (YAML_CPP_CLANG_FORMAT_EXE) + +From c1f987850a6282435f499bee76b12e32d7472f12 Mon Sep 17 00:00:00 2001 +From: Felix +Date: Thu, 30 Dec 2021 15:35:54 +0100 +Subject: [PATCH 2/2] fix cmake export + +After configure the file `yaml-cpp-config.cmake.in` the result ends up with +empty variables. (see also the discussion in #774). + +Rework this file and the call to `configure_package_config_file` according the +cmake documentation +(https://cmake.org/cmake/help/v3.22/module/CMakePackageConfigHelpers.html?highlight=configure_package_config#command:configure_package_config_file) +to overcome this issue and allow a simple `find_package` after install. + +As there was some discussion about the place where to install the +`yaml-cpp-config.cmake` file, e.g. #1055, factor out the install location into +an extra variable to make it easier changing this location in the future. +--- + CMakeLists.txt | 17 ++++++++++++----- + yaml-cpp-config.cmake.in | 10 ++++++---- + 2 files changed, 18 insertions(+), 9 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 6adbf45a..e9310792 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -129,10 +129,16 @@ set_target_properties(yaml-cpp PROPERTIES + PROJECT_LABEL "yaml-cpp ${yaml-cpp-label-postfix}" + DEBUG_POSTFIX "${CMAKE_DEBUG_POSTFIX}") + ++# FIXME(felix2012): A more common place for the cmake export would be ++# `CMAKE_INSTALL_LIBDIR`, as e.g. done in ubuntu or in this project for GTest ++set(CONFIG_EXPORT_DIR "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++set(EXPORT_TARGETS yaml-cpp) + configure_package_config_file( + "${PROJECT_SOURCE_DIR}/yaml-cpp-config.cmake.in" + "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" +- INSTALL_DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++ INSTALL_DESTINATION "${CONFIG_EXPORT_DIR}" ++ PATH_VARS CMAKE_INSTALL_INCLUDEDIR CONFIG_EXPORT_DIR) ++unset(EXPORT_TARGETS) + + write_basic_package_version_file( + "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" +@@ -150,14 +156,15 @@ if (YAML_CPP_INSTALL) + DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} + FILES_MATCHING PATTERN "*.h") + install(EXPORT yaml-cpp-targets +- DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++ DESTINATION "${CONFIG_EXPORT_DIR}") + install(FILES +- "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" +- "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" +- DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" ++ DESTINATION "${CONFIG_EXPORT_DIR}") + install(FILES "${PROJECT_BINARY_DIR}/yaml-cpp.pc" + DESTINATION ${CMAKE_INSTALL_DATADIR}/pkgconfig) + endif() ++unset(CONFIG_EXPORT_DIR) + + if(YAML_CPP_BUILD_TESTS) + add_subdirectory(test) +diff --git a/yaml-cpp-config.cmake.in b/yaml-cpp-config.cmake.in +index 7b41e3f3..a7ace3dc 100644 +--- a/yaml-cpp-config.cmake.in ++++ b/yaml-cpp-config.cmake.in +@@ -3,12 +3,14 @@ + # YAML_CPP_INCLUDE_DIR - include directory + # YAML_CPP_LIBRARIES - libraries to link against + +-# Compute paths +-get_filename_component(YAML_CPP_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) +-set(YAML_CPP_INCLUDE_DIR "@CONFIG_INCLUDE_DIRS@") ++@PACKAGE_INIT@ ++ ++set_and_check(YAML_CPP_INCLUDE_DIR "@PACKAGE_CMAKE_INSTALL_INCLUDEDIR@") + + # Our library dependencies (contains definitions for IMPORTED targets) +-include("${YAML_CPP_CMAKE_DIR}/yaml-cpp-targets.cmake") ++include(@PACKAGE_CONFIG_EXPORT_DIR@/yaml-cpp-targets.cmake) + + # These are IMPORTED targets created by yaml-cpp-targets.cmake + set(YAML_CPP_LIBRARIES "@EXPORT_TARGETS@") ++ ++check_required_components(@EXPORT_TARGETS@) From 7211d86c16354a8e7c0e084c94e148ddd2911ffc Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 24 Oct 2022 15:18:55 +0200 Subject: [PATCH 5260/9987] Update napari-0.4.15-foss-2021b.eb typo --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb index 914242860a4..f439e3019c2 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb @@ -1,4 +1,4 @@ -# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/10 +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 easyblock = 'PythonBundle' name = 'napari' From 9102b2e16bb86cd14d65df2ab77d435b79bb83ba Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 14:32:09 +0100 Subject: [PATCH 5261/9987] True reverted to system, scikit-image readded and setup.py patched to newer version of scikit-image --- ...epLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 37 ++++--------------- 1 file changed, 7 insertions(+), 30 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 0a0782a73af..ce1fb1bf8a9 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -1,6 +1,4 @@ # Loosely based on PR #7680 -# Scikit-image is added as an extension to avoid problems with imageio, -# which comes in from MoviePy # J. Sassmannshausen (Imperial College London/UK) easyblock = 'PythonBundle' @@ -17,12 +15,13 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True} dependencies = [ - ('CUDA', '11.3.1', '', True), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('CUDA', '11.3.1', '', SYSTEM), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('Python', '3.9.5'), ('h5py', '3.2.1'), ('IPython', '7.25.0'), ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), ('TensorFlow', '2.6.0', versionsuffix), ('PyYAML', '5.4.1'), ('PyTables', '3.6.1'), @@ -59,34 +58,12 @@ exts_list = [ 'sources': ['msgpack-numpy-0.4.8.tar.gz'], }), - # this is for scikit-image - ('PyWavelets', '1.1.1', { - 'modulename': 'pywt', - 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], - }), - ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], - }), - ('pooch', '1.5.2', { - 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], - }), - ('tifffile', '2021.10.12', { - 'checksums': ['0a78268a2d844af94929512d28b39bd1ea6fe46de4124103840b5fe4e1c555cd'], - }), - ('scikit-image', '0.18.1', { - 'modulename': 'skimage', - 'patches': ['scikit-image-0.18.1_fix-README-cache-perms.patch'], - 'checksums': [ - 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz - # scikit-image-0.18.1_fix-README-cache-perms.patch - '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', - ], - }), - # end of scikit-image - (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], + 'patches': ['deeplabcut-2.2.0.6-setup.py.patch'], + 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84', + # deeplabcut-2.2.0.6-setup.py.patch: + '1dbef23575b105a6b2fa39f28d67bf926701d4c0b4f48bed7a6b179b7e5df2b0'], }), ] From 6edee6bab09760d21ddd8c6e7f6d3fe89767571c Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 14:35:40 +0100 Subject: [PATCH 5262/9987] patchfile added --- .../DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch diff --git a/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch b/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch new file mode 100644 index 00000000000..9bef2d46b0c --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch @@ -0,0 +1,15 @@ +scikit-imiage version bumped to 0.18.3 to use the one in EasyBuild +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/deeplabcut-2.2.0.6.orig/setup.py b/deeplabcut-2.2.0.6/setup.py +index 3bff4f2..2e0926b 100644 +--- a/deeplabcut-2.2.0.6.orig/setup.py ++++ b/deeplabcut-2.2.0.6/setup.py +@@ -33,7 +33,7 @@ setuptools.setup( + "networkx", + "numpy", + "pandas>=1.0.1", +- "scikit-image>=0.17,<=0.18.1", ++ "scikit-image>=0.17,<=0.18.3", + "scikit-learn", + "scipy>=1.4", + "statsmodels>=0.11", From 6bd55cd6ab70a9e9dbac3955a8111719cfbf3ade Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 14:40:56 +0100 Subject: [PATCH 5263/9987] scikit-image readded and setup.py patched to newer version of scikit-image --- .../DeepLabCut-2.2.0.6-foss-2021a.eb | 33 +++---------------- .../deeplabcut-2.2.0.6-setup.py.patch | 15 +++++++++ 2 files changed, 20 insertions(+), 28 deletions(-) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb index 37f47381608..39f304ae009 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a.eb @@ -1,6 +1,4 @@ # Loosely based on PR #7680 -# Scikit-image is added as an extension to avoid problems with imageio, -# which comes in from MoviePy # J. Sassmannshausen (Imperial College London/UK) easyblock = 'PythonBundle' @@ -20,6 +18,7 @@ dependencies = [ ('h5py', '3.2.1'), ('IPython', '7.25.0'), ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), ('TensorFlow', '2.6.0'), ('PyYAML', '5.4.1'), ('PyTables', '3.6.1'), @@ -56,34 +55,12 @@ exts_list = [ 'sources': ['msgpack-numpy-0.4.8.tar.gz'], }), - # this is for scikit-image - ('PyWavelets', '1.1.1', { - 'modulename': 'pywt', - 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], - }), - ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], - }), - ('pooch', '1.5.2', { - 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], - }), - ('tifffile', '2021.10.12', { - 'checksums': ['0a78268a2d844af94929512d28b39bd1ea6fe46de4124103840b5fe4e1c555cd'], - }), - ('scikit-image', '0.18.1', { - 'modulename': 'skimage', - 'patches': ['scikit-image-0.18.1_fix-README-cache-perms.patch'], - 'checksums': [ - 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz - # scikit-image-0.18.1_fix-README-cache-perms.patch - '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', - ], - }), - # end of scikit-image - (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], + 'patches': ['deeplabcut-2.2.0.6-setup.py.patch'], + 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84', + # deeplabcut-2.2.0.6-setup.py.patch: + '1dbef23575b105a6b2fa39f28d67bf926701d4c0b4f48bed7a6b179b7e5df2b0'], }), ] diff --git a/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch b/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch new file mode 100644 index 00000000000..9bef2d46b0c --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch @@ -0,0 +1,15 @@ +scikit-imiage version bumped to 0.18.3 to use the one in EasyBuild +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/deeplabcut-2.2.0.6.orig/setup.py b/deeplabcut-2.2.0.6/setup.py +index 3bff4f2..2e0926b 100644 +--- a/deeplabcut-2.2.0.6.orig/setup.py ++++ b/deeplabcut-2.2.0.6/setup.py +@@ -33,7 +33,7 @@ setuptools.setup( + "networkx", + "numpy", + "pandas>=1.0.1", +- "scikit-image>=0.17,<=0.18.1", ++ "scikit-image>=0.17,<=0.18.3", + "scikit-learn", + "scipy>=1.4", + "statsmodels>=0.11", From 4bf1cbefb5f7888caddb40fa7a3d9f64f168e403 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 24 Oct 2022 16:13:09 +0200 Subject: [PATCH 5264/9987] adding easyconfigs: Seurat-4.2.0-foss-2022a-R-4.2.1.eb --- .../Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..af03c570285 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.2.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} + +exts_list = [ + ('Matrix', '1.5-1', { + 'checksums': ['557dba0358172d67dc63eb5db90841915bb5ce1528f941a8005ae808d635575d'], + }), + ('SeuratObject', '4.1.2', { + 'checksums': ['6a5945f501b573dbe44a15e7d969e63fd5be0c4f8e9d716b71ca29f695236d0d'], + }), + ('sctransform', '0.3.5', { + 'checksums': ['c08e56df05d64ed04ee53eb9e1d4d321da8aff945e36d56db1d5ceb1cd7e6e0b'], + }), + ('uwot', '0.1.14', { + 'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'], + }), + (name, version, { + 'checksums': ['22a3d22a9ba255c4db5b37339b183fdfb91e2d37a8b8d58a9ff45b1bc414ebef'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 9042e641ac937d534e88989b4ff4f67f9c79b9c0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 24 Oct 2022 16:31:52 +0200 Subject: [PATCH 5265/9987] Update PyQt5-5.15.4-GCCcore-11.2.0.eb add sanity check commands for pyuic5, pylupdate5, and pyrcc5 --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb index e21ab740946..97b56cff0b2 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb @@ -93,6 +93,9 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { From bbd4bb4620ef1ee9029a862ee85207370aa1f06b Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 15:58:10 +0100 Subject: [PATCH 5266/9987] download_dep_fail removed sanity_pip_check added --- easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb index 9bae7e1c2ba..6cb55d20405 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] use_pip = True -download_dep_fail = True +sanity_pip_check = True exts_list = [ (name, version, { From 80b2ba06f7d79853259febdd9c292a511f0b7b93 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 16:44:32 +0100 Subject: [PATCH 5267/9987] adding easyconfigs: MoviePy-1.0.3-foss-2021b.eb --- .../m/MoviePy/MoviePy-1.0.3-foss-2021b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb new file mode 100644 index 00000000000..dbe91a2e7ff --- /dev/null +++ b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb @@ -0,0 +1,42 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +# Updated to foss 2021b: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'MoviePy' +version = '1.0.3' + +homepage = "https://zulko.github.io/moviepy/" +description = """MoviePy (full documentation) is a Python library for video editing: cutting, concatenations, + title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('FFmpeg', '4.3.2'), + ('Python', '3.9.6'), + ('Pillow', '8.3.2'), + ('SciPy-bundle', '2021.10'), + ('tqdm', '4.62.3'), + ('imageio', '2.13.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('imageio-ffmpeg', '0.4.7', { + 'checksums': ['7a08838f97f363e37ca41821b864fd3fdc99ab1fe2421040c78eb5f56a9e723e'], + }), + ('proglog', '0.1.10', { + 'checksums': ['658c28c9c82e4caeb2f25f488fff9ceace22f8d69b15d0c1c86d64275e4ddab4'], + }), + (name, version, { + 'source_tmpl': 'moviepy-%(version)s.tar.gz', + 'patches': ['moviepy-1.0.3-setup.py.patch'], + 'checksums': [('2884e35d1788077db3ff89e763c5ba7bfddbd7ae9108c9bc809e7ba58fa433f5'), + ('beca82ff8dfbc9cd0b97296f310de3ddfc43e2e49344a32375d4438485c3f3df')], + }), +] + +moduleclass = 'tools' From 29b3e49e44732deeb4ce465b77061370a363b6f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2022 10:06:01 +0200 Subject: [PATCH 5268/9987] extend acceptance of -egl dependency variant of glew to wpebackend-fdo and WebKitGTK+ --- test/easyconfigs/easyconfigs.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f9a7d053f83..374e82ddb0c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -493,8 +493,12 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], - # egl variant of glew is required by libwpe - 'glew': [('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0'])], + # egl variant of glew is required by libwpe, wpebackend-fdo + WebKitGTK+ depend on libwpe + 'glew': [ + ('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0', + r'wpebackend-fdo-1\.13\.1-GCCcore-11\.2\.0', + r'WebKitGTK\+-2\.37\.1-GCC-11\.2\.0']), + ], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x and v3.0.0 require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [ From 49d6e098fc35372a98d9421f094843235bced23b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 25 Oct 2022 10:59:31 +0200 Subject: [PATCH 5269/9987] binutils --- .../easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb index 838f20f9ff1..5f49d35f2d6 100644 --- a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb @@ -10,6 +10,10 @@ delivering far more detailed information.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +builddependencies = [ + ('binutils', '2.37'), +] + dependencies = [ ('Python', '3.9.6'), ] From 4aa4c45da8ac56279c7ac80143398e9e61fcd963 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 25 Oct 2022 14:27:15 +0200 Subject: [PATCH 5270/9987] Fixed style issues --- .../p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb index c171baaaab1..d507f7f7f30 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -25,11 +25,11 @@ configopts = " ".join([ sanity_check_paths = { 'files': [ - 'include/pugiconfig.hpp', - 'include/pugixml.hpp', - 'lib/libpugixml.a', + 'include/pugiconfig.hpp', + 'include/pugixml.hpp', + 'lib/libpugixml.a', 'lib/libpugixml.%s' % SHLIB_EXT, - 'lib/pkgconfig/pugixml.pc' + 'lib/pkgconfig/pugixml.pc' ], 'dirs': ['lib/cmake/pugixml'], } From d2341f47d675a5576b6774dff5b616606dc485fa Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 25 Oct 2022 15:37:31 +0200 Subject: [PATCH 5271/9987] @jfgrimm added sanity check commands for tools pyuic5, pylupdate5, and pyrcc5; port changes to recent-ish easyconfigs. --- ...PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb | 19 ++++++++++-- .../p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb | 29 ++++++++++++++----- .../p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb | 27 +++++++++++++---- .../p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb | 3 +- 4 files changed, 60 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb index 2122c835fca..400130674cd 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -19,15 +19,24 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.4.0' @@ -76,13 +85,17 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb index b04ed87846e..775d1c1a6e6 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb @@ -19,20 +19,28 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - local_sipver = '5.5.0' - components = [ ('SIP', local_sipver, { 'source_urls': [PYPI_SOURCE], @@ -63,10 +71,10 @@ components = [ 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'Binary', + 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', - 'skipsteps': ['configure', 'build'], - 'install_cmd': local_setup_env + local_pyqt5_sip_install, + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts }), ('PyQtWebEngine', version, { @@ -82,13 +90,18 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip-wheel'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip-wheel --help", + "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb index 54c02ccf191..01de04b0208 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb @@ -18,15 +18,26 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' + local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.5.0' @@ -57,10 +68,10 @@ components = [ 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'Binary', + 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', - 'skipsteps': ['configure', 'build'], - 'install_cmd': local_setup_env + local_pyqt5_sip_install, + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts }), ('PyQtWebEngine', version, { 'source_urls': [PYPI_SOURCE], @@ -75,13 +86,17 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb index 97b56cff0b2..cc175935b12 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb @@ -86,7 +86,8 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From c26186efb83d45bc17bf86faf76942aa68ab3174 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 25 Oct 2022 16:20:32 +0200 Subject: [PATCH 5272/9987] Switched to MakeCp easyblock and applied instructions from README --- .../m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb | 22 +++++++++++++------ 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb index 624706433b6..b27d825a42d 100644 --- a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'MIGRATE-N' version = '5.0.4' @@ -12,7 +12,6 @@ mutations and uncertainty of the genealogy. """ toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'usempi': True} source_urls = ["https://peterbeerli.com/migrate-html5/download_version4"] sources = ['migrate-%(version)s.src.tar.gz'] @@ -20,22 +19,31 @@ patches = [ 'migrate-%(version)s_install.patch', 'migrate-%(version)s_locale.patch', ] +checksums = [ + 'd25ba8ed112b81ee5fdc77759a5886b0f50ece834fd8db445b9c833742c3a1b9', # migrate-5.0.4.src.tar.gz + 'aaba4dbd8d868f80afd9645ae84d5b8c153de85a4f616a8585950593655d6fcf', # migrate-5.0.4_install.patch + '67f2dec0a2fcd432e12747f979a381f7d5e5ad73b885b485c829e50613aba35b', # migrate-5.0.4_locale.patch +] dependencies = [ ('zlib', '1.2.11'), ] -configopts = '--enable-A4 "CC=$CC" STDCPLUS=-lstdc++' -prebuildopts = 'make mpis && make clean &&' -installopts = "&& make clean && make installmpi" - parallel = 1 - start_dir = 'src' +prebuildopts = './configure --prefix=%(installdir)s --enable-A4 "CC=$CC" STDCPLUS=-lstdc++ && ' +buildopts = ' && make mpis CC="$MPICC"' +files_to_copy = [(['migrate-n', 'migrate-n-mpi'], 'bin')] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['migrate-n', 'migrate-n-mpi']], 'dirs': [], } +sanity_check_commands = [ + "echo Q | migrate-n", + "echo Q | mpirun -np 1 migrate-n-mpi", +] + moduleclass = 'bio' From cdc56f3ff989905cf61c0d04acbd2c0533db7171 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2022 17:09:48 +0200 Subject: [PATCH 5273/9987] fix installation of Python 2.7.18 with GCCcore/11.2.0 (fixes #16467) --- easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb index 40d1364f4e5..6cae29ec4ff 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -175,6 +175,7 @@ exts_list = [ }), ('backports.entry_points_selectable', '1.1.0', { 'checksums': ['988468260ec1c196dab6ae1149260e2f5472c9110334e5d51adcb77867361f6a'], + 'preinstallopts': "sed -i 's/^author =.*/version = %(version)s/g' setup.cfg && ", }), ('virtualenv', '20.7.0', { 'checksums': ['97066a978431ec096d163e72771df5357c5c898ffdd587048f45e0aecc228094'], @@ -245,6 +246,7 @@ exts_list = [ }), ('backports.functools_lru_cache', '1.6.4', { 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], + 'preinstallopts': "sed -i 's/^author .*/version = %(version)s/g' setup.cfg && ", }), ('wcwidth', '0.2.5', { 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], @@ -306,6 +308,7 @@ exts_list = [ }), ('singledispatch', '3.7.0', { 'checksums': ['c1a4d5c1da310c3fd8fccfb8d4e1cb7df076148fd5d858a819e37fffe44f3092'], + 'preinstallopts': "sed -i 's/^author .*/version = %(version)s/g' setup.cfg && ", }), ('sortedcontainers', '2.4.0', { 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], From 5e900a1aa53fc1dc8540e063ecda03a05b4d5c8d Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 25 Oct 2022 17:17:07 +0200 Subject: [PATCH 5274/9987] Backport glibc-2.34 SIGSTKSZ patch --- .../easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-10.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-10.3.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-11.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-5.3.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-5.5.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-6.3.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.2.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.3.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.4.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-8.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-8.2.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-8.3.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-8.4.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-9.1.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-9.2.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-9.3.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-system.eb | 7 +- easybuild/easyconfigs/m/M4/M4-1.4.18.eb | 7 +- .../m/M4/M4-1.4.18_glibc_2.34.patch | 106 ++++++++++++++++++ 24 files changed, 257 insertions(+), 23 deletions(-) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb index bc8af908fd7..6daf6b4d3cc 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'FCC', 'version': '4.5.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use binutils from the OS, since M4 is itself a dependency of the easybuilt binutils (via flex and Bison) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb index bd7b15d0f99..c2cdc5682d3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb index 40d8acc91af..eb7a850b087 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb index aaa4eda2c91..691dd0696ef 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb index c1852324b5b..6730f48fb80 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '11.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb index 90f3441ae31..d63b2609039 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '5.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index 44174916f39..9c980305317 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -13,11 +13,17 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] + # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', SYSTEM)] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb index bb84008fe0d..4b63035ae7b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '5.5.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb index 42ac0537642..9a72c72b661 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb index abedf0b58b2..c5d9b7af082 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -16,10 +16,16 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb index 70675bd26d4..d6b25a708e0 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '7.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb index 95c1d432cdf..20fed34dea2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '7.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb index d435d9cf19f..692b6fd6d43 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb index 18817b26e32..e0164f7af7f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '7.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb index f268c01aaed..59a6abb4da2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '8.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb index cdf833ca394..b294b3ad96a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb index b21fcafc4f7..c5bded45603 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb index 30d2b32da00..f8bc2dc62b3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '8.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb index aac98bc3c12..464d943e7b5 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '9.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb index c70532aeb1f..031f28e5ef4 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '9.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb index 61100b9eb44..96842f7085b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb index 72020d96254..03d16d2f2b2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb @@ -15,10 +15,15 @@ toolchainopts = {'optarch': False} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb index 79f53be742f..1c23e05d614 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -17,10 +17,15 @@ toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch b/easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch new file mode 100644 index 00000000000..9935b43323a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch @@ -0,0 +1,106 @@ +c-stack: stop using SIGSTKSZ + +It’s been proposed to stop making SIGSTKSZ an integer constant: +https://sourceware.org/pipermail/libc-alpha/2020-September/118028.html +Also, using SIGSTKSZ in #if did not conform to current POSIX. +Also, avoiding SIGSTKSZ makes the code simpler and easier to grok. +* lib/c-stack.c (SIGSTKSZ): Remove. +(alternate_signal_stack): Now a 64 KiB array, for simplicity. +All uses changed. + +[Retrieved (and backported) from: +https://git.savannah.gnu.org/cgit/gnulib.git/patch/?id=f9e2b20a12a230efa30f1d479563ae07d276a94b] +Signed-off-by: Fabrice Fontaine + +diff -Nura m4-1.4.18.orig/lib/c-stack.c m4-1.4.18/lib/c-stack.c +--- m4-1.4.18.orig/lib/c-stack.c 2021-04-11 19:12:14.086494029 +0200 ++++ m4-1.4.18/lib/c-stack.c 2021-04-11 19:48:46.316862760 +0200 +@@ -50,15 +50,16 @@ + #if ! HAVE_STACK_T && ! defined stack_t + typedef struct sigaltstack stack_t; + #endif +-#ifndef SIGSTKSZ +-# define SIGSTKSZ 16384 +-#elif HAVE_LIBSIGSEGV && SIGSTKSZ < 16384 +-/* libsigsegv 2.6 through 2.8 have a bug where some architectures use +- more than the Linux default of an 8k alternate stack when deciding +- if a fault was caused by stack overflow. */ +-# undef SIGSTKSZ +-# define SIGSTKSZ 16384 +-#endif ++ ++/* Storage for the alternate signal stack. ++ 64 KiB is not too large for Gnulib-using apps, and is large enough ++ for all known platforms. Smaller sizes may run into trouble. ++ For example, libsigsegv 2.6 through 2.8 have a bug where some ++ architectures use more than the Linux default of an 8 KiB alternate ++ stack when deciding if a fault was caused by stack overflow. */ ++static max_align_t alternate_signal_stack[(64 * 1024 ++ + sizeof (max_align_t) - 1) ++ / sizeof (max_align_t)]; + + #include + #include +@@ -128,19 +129,6 @@ + #if (HAVE_SIGALTSTACK && HAVE_DECL_SIGALTSTACK \ + && HAVE_STACK_OVERFLOW_HANDLING) || HAVE_LIBSIGSEGV + +-/* Storage for the alternate signal stack. */ +-static union +-{ +- char buffer[SIGSTKSZ]; +- +- /* These other members are for proper alignment. There's no +- standard way to guarantee stack alignment, but this seems enough +- in practice. */ +- long double ld; +- long l; +- void *p; +-} alternate_signal_stack; +- + static void + null_action (int signo __attribute__ ((unused))) + { +@@ -205,8 +193,8 @@ + + /* Always install the overflow handler. */ + if (stackoverflow_install_handler (overflow_handler, +- alternate_signal_stack.buffer, +- sizeof alternate_signal_stack.buffer)) ++ alternate_signal_stack, ++ sizeof alternate_signal_stack)) + { + errno = ENOTSUP; + return -1; +@@ -279,14 +267,14 @@ + stack_t st; + struct sigaction act; + st.ss_flags = 0; ++ st.ss_sp = alternate_signal_stack; ++ st.ss_size = sizeof alternate_signal_stack; + # if SIGALTSTACK_SS_REVERSED + /* Irix mistakenly treats ss_sp as the upper bound, rather than + lower bound, of the alternate stack. */ +- st.ss_sp = alternate_signal_stack.buffer + SIGSTKSZ - sizeof (void *); +- st.ss_size = sizeof alternate_signal_stack.buffer - sizeof (void *); +-# else +- st.ss_sp = alternate_signal_stack.buffer; +- st.ss_size = sizeof alternate_signal_stack.buffer; ++ st.ss_size -= sizeof (void *); ++ char *ss_sp = st.ss_sp; ++ st.ss_sp = ss_sp + st.ss_size; + # endif + r = sigaltstack (&st, NULL); + if (r != 0) +diff -Nura m4-1.4.18.orig/lib/c-stack.h m4-1.4.18/lib/c-stack.h +--- m4-1.4.18.orig/lib/c-stack.h 2021-04-11 19:12:14.098494042 +0200 ++++ m4-1.4.18/lib/c-stack.h 2021-04-11 19:17:42.138848378 +0200 +@@ -34,7 +34,7 @@ + A null ACTION acts like an action that does nothing. + + ACTION must be async-signal-safe. ACTION together with its callees +- must not require more than SIGSTKSZ bytes of stack space. Also, ++ must not require more than 64 KiB bytes of stack space. Also, + ACTION should not call longjmp, because this implementation does + not guarantee that it is safe to return to the original stack. + From bb3ab265775f54661775dd52f1b834ee4e674399 Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 25 Oct 2022 17:42:52 +0200 Subject: [PATCH 5275/9987] Fix mixed spaces/tabs --- easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18.eb | 4 ++-- 23 files changed, 46 insertions(+), 46 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb index 6daf6b4d3cc..bc86a842bf0 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb index c2cdc5682d3..23e948da86e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb index eb7a850b087..a8d9bfb5194 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb index 691dd0696ef..70575029ae0 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb index 6730f48fb80..63f864a0d85 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb index d63b2609039..43408ff8fac 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index 9c980305317..7c7bb607dc6 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb index 4b63035ae7b..1c0ae73d6d8 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb index 9a72c72b661..9b67783cc40 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb index c5d9b7af082..5bb8c417674 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -18,8 +18,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb index d6b25a708e0..43b5a997994 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb index 20fed34dea2..c6ea670638e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb index 692b6fd6d43..0fd28aca84f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb index e0164f7af7f..3957e4980e2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb index 59a6abb4da2..3ae81595fa9 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb index b294b3ad96a..a646315f4d9 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb index c5bded45603..bba6ee5bb81 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb index f8bc2dc62b3..84ace55818b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb index 464d943e7b5..abe9dbefd21 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb index 031f28e5ef4..2db382b9321 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb index 96842f7085b..e0dffd89a28 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb index 03d16d2f2b2..6df13418cc3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb @@ -16,8 +16,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb index 1c23e05d614..d181fe31631 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -18,8 +18,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ From 8657f4aa2c7c65aa9a4aa66aa3ef599667319c04 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 25 Oct 2022 18:04:47 +0200 Subject: [PATCH 5276/9987] @jfgrimm revert PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb --- ...PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb | 19 +++---------------- 1 file changed, 3 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb index 400130674cd..2122c835fca 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -19,24 +19,15 @@ dependencies = [ default_easyblock = 'PythonPackage' -local_sipdir = '%(installdir)s/share/sip' local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " -local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir -local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " local_pyqtweb_configopts += "--no-stubs --no-dist-info" -local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir -local_pyqt_configopts += "--no-stubs " -local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " -# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: -local_pyqt_configopts += "--bindir=%(installdir)s/bin " -local_pyqt_configopts += "--sipdir=%s " % local_sipdir local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.4.0' @@ -85,17 +76,13 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in [ - 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], + 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", - "pyuic5 --help", - "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", - "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { From 781250e6de3b80c19a25a58abc3e59e0ddb949d0 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 25 Oct 2022 18:50:40 +0100 Subject: [PATCH 5277/9987] Patch added to ensure test-jobs are not failing due to blanks (https://github.com/pybind/pybind11/issues/3680) --- ...04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch | 121 ++++++++++++++++++ .../pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb | 11 +- 2 files changed, 131 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch diff --git a/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch b/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch new file mode 100644 index 00000000000..5d0bcd18dba --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch @@ -0,0 +1,121 @@ +From 1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= +Date: Thu, 3 Feb 2022 18:29:46 +0100 +URL: https://github.com/pybind/pybind11/commit/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch +Subject: [PATCH] test: Strip whitespace when comparing numpy dtypes for 1.22 + compat (#3682) + +* test: Strip whitespace when comparing numpy dtypes for 1.22 compat + +Strip whitespace when comparing numpy dtype str() in order to preserve +test compatibility with both numpy 1.22 and older versions whose output +differ by whitespace. + +Fixes #3680 + +diff --git a/pybind11-2.6.0.orig/tests/test_numpy_dtypes.py b/pybind11-2.6.0/tests/test_numpy_dtypes.py +index f56b776..228ef63 100644 +--- a/pybind11-2.6.0.orig/tests/test_numpy_dtypes.py ++++ b/pybind11-2.6.0/tests/test_numpy_dtypes.py +@@ -33,8 +33,8 @@ def dt_fmt(): + e = "<" if byteorder == "little" else ">" + return ( + "{{'names':['bool_','uint_','float_','ldbl_']," +- " 'formats':['?','" + e + "u4','" + e + "f4','" + e + "f{}']," +- " 'offsets':[0,4,8,{}], 'itemsize':{}}}" ++ "'formats':['?','" + e + "u4','" + e + "f4','" + e + "f{}']," ++ "'offsets':[0,4,8,{}],'itemsize':{}}}" + ) + + +@@ -47,7 +47,7 @@ def simple_dtype_fmt(): + def packed_dtype_fmt(): + from sys import byteorder + +- return "[('bool_', '?'), ('uint_', '{e}u4'), ('float_', '{e}f4'), ('ldbl_', '{e}f{}')]".format( ++ return "[('bool_','?'),('uint_','{e}u4'),('float_','{e}f4'),('ldbl_','{e}f{}')]".format( + np.dtype("longdouble").itemsize, e="<" if byteorder == "little" else ">" + ) + +@@ -72,7 +72,7 @@ def partial_nested_fmt(): + partial_nested_off = 8 + 8 * (ld.alignment > 8) + partial_ld_off = partial_ld_offset() + partial_nested_size = partial_nested_off * 2 + partial_ld_off + ld.itemsize +- return "{{'names':['a'], 'formats':[{}], 'offsets':[{}], 'itemsize':{}}}".format( ++ return "{{'names':['a'],'formats':[{}],'offsets':[{}],'itemsize':{}}}".format( + partial_dtype_fmt(), partial_nested_off, partial_nested_size + ) + +@@ -116,25 +116,25 @@ def test_dtype(simple_dtype): + + e = "<" if byteorder == "little" else ">" + +- assert m.print_dtypes() == [ ++ assert [x.replace(" ", "") for x in m.print_dtypes()] == [ + simple_dtype_fmt(), + packed_dtype_fmt(), +- "[('a', {}), ('b', {})]".format(simple_dtype_fmt(), packed_dtype_fmt()), ++ "[('a',{}),('b',{})]".format(simple_dtype_fmt(), packed_dtype_fmt()), + partial_dtype_fmt(), + partial_nested_fmt(), +- "[('a', 'S3'), ('b', 'S3')]", ++ "[('a','S3'),('b','S3')]", + ( +- "{{'names':['a','b','c','d'], " +- + "'formats':[('S4', (3,)),('" ++ "{{'names':['a','b','c','d']," ++ + "'formats':[('S4',(3,)),('" + + e +- + "i4', (2,)),('u1', (3,)),('" ++ + "i4',(2,)),('u1',(3,)),('" + + e +- + "f4', (4, 2))], " +- + "'offsets':[0,12,20,24], 'itemsize':56}}" ++ + "f4',(4,2))]," ++ + "'offsets':[0,12,20,24],'itemsize':56}}" + ).format(e=e), +- "[('e1', '" + e + "i8'), ('e2', 'u1')]", +- "[('x', 'i1'), ('y', '" + e + "u8')]", +- "[('cflt', '" + e + "c8'), ('cdbl', '" + e + "c16')]", ++ "[('e1','" + e + "i8'),('e2','u1')]", ++ "[('x','i1'),('y','" + e + "u8')]", ++ "[('cflt','" + e + "c8'),('cdbl','" + e + "c16')]", + ] + + d1 = np.dtype( +@@ -228,7 +228,7 @@ def test_recarray(simple_dtype, packed_dtype): + ] + + arr = m.create_rec_partial(3) +- assert str(arr.dtype) == partial_dtype_fmt() ++ assert str(arr.dtype).replace(" ", "") == partial_dtype_fmt() + partial_dtype = arr.dtype + assert "" not in arr.dtype.fields + assert partial_dtype.itemsize > simple_dtype.itemsize +@@ -236,7 +236,7 @@ def test_recarray(simple_dtype, packed_dtype): + assert_equal(arr, elements, packed_dtype) + + arr = m.create_rec_partial_nested(3) +- assert str(arr.dtype) == partial_nested_fmt() ++ assert str(arr.dtype).replace(" ", "") == partial_nested_fmt() + assert "" not in arr.dtype.fields + assert "" not in arr.dtype.fields["a"][0].fields + assert arr.dtype.itemsize > partial_dtype.itemsize +@@ -275,12 +275,12 @@ def test_array_array(): + e = "<" if byteorder == "little" else ">" + + arr = m.create_array_array(3) +- assert str(arr.dtype) == ( +- "{{'names':['a','b','c','d'], " +- + "'formats':[('S4', (3,)),('" ++ assert str(arr.dtype).replace(" ", "") == ( ++ "{{'names':['a','b','c','d']," ++ + "'formats':[('S4',(3,)),('" + + e +- + "i4', (2,)),('u1', (3,)),('{e}f4', (4, 2))], " +- + "'offsets':[0,12,20,24], 'itemsize':56}}" ++ + "i4',(2,)),('u1',(3,)),('{e}f4',(4,2))]," ++ + "'offsets':[0,12,20,24],'itemsize':56}}" + ).format(e=e) + assert m.print_array_array(arr) == [ + "a={{A,B,C,D},{K,L,M,N},{U,V,W,X}},b={0,1}," diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb index 60135a6d7f6..8e9b6e72bfe 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb @@ -1,3 +1,7 @@ +# include patch to fix failing test jobs due to additional white space +# see https://github.com/pybind/pybind11/issues/3680 +# Authors: J. Sassmannshausen / Alexander Grund + name = 'pybind11' version = '2.6.0' @@ -9,7 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/pybind/pybind11/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571'] +patches = ['1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch'] +checksums = [ + '90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571', + # 1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch: + 'f0ff7416d14f9589b5d100ad021e18690cb08cb662df9d0ac21327d04bdb96fc', +] builddependencies = [ ('binutils', '2.35'), From ad17fc07ee1bdc8748cff9da1619b117e3443e44 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2022 21:55:37 +0200 Subject: [PATCH 5278/9987] work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml --- .../easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb index 630fe512e04..7dfe39787ec 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb @@ -37,6 +37,11 @@ exts_default_options = { 'sanity_pip_check': True, } +# workaround for: AttributeError: 'module' object has no attribute '__legacy__' +# see also https://github.com/pypa/pip/issues/6264 +local_fix_pyproject_toml_cmd = """sed -i 's/\(\[build-system\]\)/\\1\\nbuild-backend="setuptools.build_meta"/g' """ +local_fix_pyproject_toml_cmd += "pyproject.toml && " + # order is important! # package versions updated Sept 13th 2019 exts_list = [ @@ -125,6 +130,7 @@ exts_list = [ ('PyNaCl', '1.3.0', { 'modulename': 'nacl', 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), ('bcrypt', '3.1.7', { 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], @@ -209,9 +215,11 @@ exts_list = [ }), ('importlib_metadata', '0.22', { 'checksums': ['652234b6ab8f2506ae58e528b6fbcc668831d3cc758e1bc01ef438d328b68cdb'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), ('pluggy', '0.13.0', { 'checksums': ['fa5fa1622fa6dd5c030e9cad086fa19ef6a0cf6d7a2d12318e10cb49d6d68f34'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), # more-itertools 5.0.0 is the most recent version still supporting Python 2.x ('more-itertools', '5.0.0', { From 36183b5d248d5dfa112a3414b38b6c92c83dccfe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Oct 2022 09:41:15 +0200 Subject: [PATCH 5279/9987] avoid that ~/.ccache is used when building/installing WebKitGTK+ --- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb index 5e41bdddcfb..d944a2691e6 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -77,6 +77,9 @@ configopts += "-DENABLE_GAMEPAD=OFF -DUSE_LIBSECRET=OFF -DUSE_LIBHYPHEN=OFF " configopts += "-DUSE_WOFF2=OFF -DENABLE_JOURNALD_LOG=OFF -DENABLE_BUBBLEWRAP_SANDBOX=OFF " configopts += "-DENABLE_INTROSPECTION=OFF -DUSE_LIBNOTIFY=OFF " +prebuildopts = "export CCACHE_DIR=%(builddir)s/ccache && " +preinstallopts = prebuildopts + sanity_check_paths = { 'files': ['bin/WebKitWebDriver', 'lib/libwebkit2gtk-4.1.%s' % SHLIB_EXT, 'lib/libjavascriptcoregtk-4.1.%s' % SHLIB_EXT], From f02b3d7184ab235372c4de70876b1e83bd5b8818 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 26 Oct 2022 09:42:51 +0100 Subject: [PATCH 5280/9987] remove ExomeDepth from recent R-bundle-Bioconductor --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 3 --- .../R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 3 --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 --- 3 files changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index b7133459ca4..761944fd152 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1075,9 +1075,6 @@ exts_list = [ ('M3Drop', '1.20.0', { 'checksums': ['b82772303c624ff01418e66cefd751a0f6f9d819ea2cf3c9c20a9acd1fc106e5'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.30.0', { 'checksums': ['2dada40e222d4f42510deeb99c24043078420a4d3d214d4cc3409d428cfb60c4'], }), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index 15af98e6e4b..1c4ffc3555e 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -1060,9 +1060,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 209068efaa5..e9595a58dd4 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1059,9 +1059,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), From ace549bec0cd223ae2c0b2885306453f59cb9945 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 26 Oct 2022 11:49:59 +0200 Subject: [PATCH 5281/9987] adding easyconfigs: NiBabel-4.0.2-foss-2022a.eb, pydicom-2.3.0-GCCcore-11.3.0.eb --- .../n/NiBabel/NiBabel-4.0.2-foss-2022a.eb | 46 +++++++++++++++++++ .../p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb | 26 +++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb new file mode 100644 index 00000000000..2691a91e34a --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '4.0.2' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Pillow', '9.1.1'), + ('pydicom', '2.3.0'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['45c49b5349351b45f6c045a91aa02b4f0d367686ff3284632ef95ac65b930786'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a92eebf56b9 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '2.3.0' + +homepage = 'https://pydicom.github.io/' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e50dfa6bc44516816248c750a93b07fa577b867433bd8bf4fd3319a4a19259a5'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 1f1ddd397839cc246317b5cfa9333199ad7068ff Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 26 Oct 2022 12:20:49 +0200 Subject: [PATCH 5282/9987] adding easyconfigs: IJulia-1.23.3-Julia-1.6.7.eb --- .../i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb diff --git a/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb new file mode 100644 index 00000000000..54566147c74 --- /dev/null +++ b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb @@ -0,0 +1,87 @@ +easyblock = 'Bundle' + +name = 'IJulia' +version = '1.23.3' +_julia_ver = '1.6.7' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/JuliaLang/IJulia.jl' +description = "Julia kernel for Jupyter" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), +] + +exts_defaultclass = 'JuliaPackage' +exts_filter = ("julia -e 'using %(ext_name)s'", "") +exts_default_options = { + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], +} + +exts_list = [ + ('Parsers', '2.4.2', { + 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], + 'checksums': ['44036a59b047f704d6b7841e3edf12fe2a53aa797254086fdd0709f0cdebac89'], + }), + ('JSON', '0.21.3', { + 'source_urls': ['https://github.com/JuliaIO/JSON.jl/archive/'], + 'checksums': ['bd02a015da24b03f79d55967b29f5ceaba2477b559242576d74f02623bb1b6b1'], + }), + ('MbedTLS', '1.1.7', { + 'source_urls': ['https://github.com/JuliaLang/MbedTLS.jl/archive/'], + 'checksums': ['3df27a16ea31acf4eaf6cc9f3bd25b81960c10662722ffa22b13cb0e6ac11b12'], + }), + ('VersionParsing', '1.3.0', { + 'source_urls': ['https://github.com/JuliaInterop/VersionParsing.jl/archive/'], + 'checksums': ['f90fe419e1a40ef0eccfaaed1d1b7792d9115a059a82d0c23e3c04c944d0f8ca'], + }), + ('Conda', '1.7.0', { + 'source_urls': ['https://github.com/JuliaPy/Conda.jl/archive/'], + 'checksums': ['2077b1192e1cfa206caf441d9d91b0ca83aa935db89918f1fd69cd25c2415ced'], + }), + ('SoftGlobalScope', '1.1.0', { + 'source_urls': ['https://github.com/stevengj/SoftGlobalScope.jl/archive/'], + 'checksums': ['8d4264386c859403938498cd9ddd5e94e10181deba4a3e71d391b16750e3848b'], + }), + ('Preferences', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['a87c1fc863fcb6240c3f4327776fa01a1f87e0d2df5a0c1850f789ce24469da2'], + }), + ('JLLWrappers', '1.4.1', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], + }), + ('libsodium_jll', '1.0.20+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/libsodium_jll.jl/archive/'], + 'sources': [{'filename': 'libsodium-v%(version)s.tar.gz'}], + 'checksums': ['f7c3a17acc3a478ec10a4a49a0dd04694140f4483644ec9db638706ea9844aba'], + }), + ('ZeroMQ_jll', '4.3.4+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/ZeroMQ_jll.jl/archive/'], + 'sources': [{'filename': 'ZeroMQ-v%(version)s.tar.gz'}], + 'checksums': ['aa98ae3c7e050fc6bdf0b0132bb607dea2f6c062da7870b1ecada9f3c8ea8d72'], + }), + ('ZMQ', '1.2.1', { + 'source_urls': ['https://github.com/JuliaInterop/ZMQ.jl/archive/'], + 'checksums': ['8b42555340d0208e5a36cd5e8f29a3f0d44c13c064382d4b1e5d00c1c4a9dd96'], + }), + (name, version, { + 'source_urls': ['https://github.com/JuliaLang/IJulia.jl/archive/'], + 'checksums': ['1471ed94093efd24bae5e6ff1d3f7fa61901bf8834a737eeae2a9e620f50f07c'], + 'preinstallopts': "mkdir -p %(installdir)s/jupyter && export JUPYTER_DATA_DIR=%(installdir)s/jupyter && ", + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['packages'], +} + +modextrapaths = { + 'JULIA_DEPOT_PATH': '', + 'JUPYTER_PATH': 'jupyter', +} + +moduleclass = 'lib' From 3b68a7b68e8b390f477d58adca126af3e4e24aa8 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 26 Oct 2022 12:18:12 +0100 Subject: [PATCH 5283/9987] Name of patchfile changed --- .../easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb | 4 ++-- ...5.patch => pybind11-2.6.0_fix-test-extra-whitespace.patch} | 0 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/pybind11/{1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch => pybind11-2.6.0_fix-test-extra-whitespace.patch} (100%) diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb index 8e9b6e72bfe..9eddf8c8ef2 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb @@ -13,10 +13,10 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/pybind/pybind11/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch'] +patches = ['pybind11-2.6.0_fix-test-extra-whitespace.patch'] checksums = [ '90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571', - # 1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch: + # pybind11-2.6.0_fix-test-extra-whitespace.patch: 'f0ff7416d14f9589b5d100ad021e18690cb08cb662df9d0ac21327d04bdb96fc', ] diff --git a/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0_fix-test-extra-whitespace.patch similarity index 100% rename from easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch rename to easybuild/easyconfigs/p/pybind11/pybind11-2.6.0_fix-test-extra-whitespace.patch From 4ddd6621d457e813acbaa22d94b5d1e69e3c46b0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 26 Oct 2022 13:51:19 +0200 Subject: [PATCH 5284/9987] adding easyconfigs: dask-2022.10.0-foss-2022a.eb, bokeh-2.4.3-foss-2022a.eb --- .../b/bokeh/bokeh-2.4.3-foss-2022a.eb | 38 ++++++++++ .../d/dask/dask-2022.10.0-foss-2022a.eb | 72 +++++++++++++++++++ 2 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb new file mode 100644 index 00000000000..4f2830449ae --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.4.3' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('Pillow', '9.1.1'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True + +exts_list = [ + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + (name, version, { + 'checksums': ['ef33801161af379665ab7a34684f2209861e3aefd5c803a21fbbb99d94874b03'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb b/easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb new file mode 100644 index 00000000000..ab9413891e9 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2022.10.0' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2022.05'), + ('bokeh', '2.4.3'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('locket', '1.0.0', { + 'checksums': ['5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632'], + }), + ('partd', '1.3.0', { + 'checksums': ['ce91abcdc6178d668bcaa431791a5a917d902341cb193f543fe445d494660485'], + }), + ('fsspec', '2021.7.0', { + 'checksums': ['792ebd3b54de0b30f1ce73f0ba0a8bcc864724f2d9f248cb8d0ece47db0cbde8'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '2.2.0', { + 'checksums': ['d7366c2e2293314112dcf2432108428a67b927b00005619feefc310d12d833f3'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + (name, version, { + 'checksums': ['f277a3b300ecc1d0be232a339f346dff686e0becdb0843c0aaf2ae943d5492d3'], + }), + ('distributed', version, { + 'checksums': ['dcfbc9c528bcd9e4f9686e673956a90172826395ac5b258039e580777d50782f'], + }), + ('dask-mpi', '2022.4.0', { + 'checksums': ['0a04f1d7d35a06cdff506593330d4414ea242c9172498ce191f5742eac499e17'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.8.1', { + 'checksums': ['16fd1b646a073ad3de75dde12a0dfe529b836f21a3bdbcee2a88bef24e9112a7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + +moduleclass = 'data' From 9a1bce2ff7b11da801999840338254fca578060d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 26 Oct 2022 17:32:55 +0200 Subject: [PATCH 5285/9987] adding easyconfigs: ITK-5.2.1-foss-2022a.eb --- .../easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb new file mode 100644 index 00000000000..22f773b4840 --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb @@ -0,0 +1,59 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.2.1' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6022b2b64624b8bcec3333fe48d5f74ff6ebceb3bdf98258ba7d7fbbc76b99ab'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Bison', '3.8.2'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('expat', '2.4.8'), + ('HDF5', '1.12.2'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('VTK', '9.2.0.rc2'), + ('zlib', '1.2.12'), +] + +local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' +configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], +} + +moduleclass = 'data' From 806133fd03c318084c697007ecc50286d54a788c Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 26 Oct 2022 20:38:38 +0100 Subject: [PATCH 5286/9987] adding easyconfigs: TBA-1.0-foss-2020b.eb --- .../easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb new file mode 100644 index 00000000000..d6d7f6ff551 --- /dev/null +++ b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb @@ -0,0 +1,65 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'Tarball' + +name = 'TBA' +version = '1.0' + +homepage = 'https://github.com/jenhantao/tba' +description = """TBA (a Transcription factor Binding Analysis): +TBA is a multi-functional machine learning tool for identifying +transcription factors associated with genomic features""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/jenhantao/tba/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['97acb78e045bbd066d67213c84417f2af7f48fde1f513be22cbb46ad2966ae2c'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), + ('scikit-learn', '0.23.2'), + ('Seaborn', '0.11.1'), + ('matplotlib', '3.5.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('idr', '2.0.3', { + 'source_urls': ['https://github.com/nboley/idr/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['63e3be099b2deadfa8c7ccc3ab83659afe683f6a35bd41b2319c6ad58ca74de6'], + }), + ('joblib', '1.2.0', { + 'checksums': ['e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018'], + }), +] + +postinstallcmds = [ + "mv %(installdir)s/model_training/* %(installdir)s/bin ", + "mv %(installdir)s/default_motifs %(installdir)s/share ", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/train_model_default.sh', 'bin/train_classifier.py', + 'bin/create_features.py', 'bin/idr'], + 'dirs': ['share'], +} + +sanity_check_commands = [ + "idr --version", + "train_classifier.py -h", +] + +moduleclass = 'bio' From 1410906635e24073738aa8d0e83af731e6c5aca3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Wed, 26 Oct 2022 21:40:11 +0100 Subject: [PATCH 5287/9987] Update TBA-1.0-foss-2020b.eb matplotlib demoted to 3.3.3 to avoid conflicts --- easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb index d6d7f6ff551..c3f0e23f2d8 100644 --- a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('Biopython', '1.78'), ('scikit-learn', '0.23.2'), ('Seaborn', '0.11.1'), - ('matplotlib', '3.5.1'), + ('matplotlib', '3.3.3'), ] exts_defaultclass = 'PythonPackage' From 3404ec4b937e3ceb332d2b6ccff5fd61b91041da Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 11:16:17 +0200 Subject: [PATCH 5288/9987] adding easyconfigs: Xmipp-3.22.07-Helios-foss-2022a.eb and patches: Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch, Xmipp-3.22.07-Helios_dont_add_useless_libs.patch, Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch, Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch, Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch, XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch, XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch, XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch, XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch --- .../Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb | 87 +++++++++++++++++++ ...-Helios_correct_order_of_cu_includes.patch | 19 ++++ ...3.22.07-Helios_dont_add_useless_libs.patch | 21 +++++ ...07-Helios_dont_change_EB_build_flags.patch | 41 +++++++++ ...Helios_drop_useless_CXXFLAGS_setting.patch | 18 ++++ ...07-Helios_fix_scons_Environent_calls.patch | 37 ++++++++ ...07-Helios_fix_scons_Environent_calls.patch | 28 ++++++ ...-3.22.07-Helios_use_CXXFLAGS_from_EB.patch | 24 +++++ ...07-Helios_fix_scons_Environent_calls.patch | 28 ++++++ ...-3.22.07-Helios_use_CXXFLAGS_from_EB.patch | 25 ++++++ 10 files changed, 328 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb new file mode 100644 index 00000000000..9174334361e --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb @@ -0,0 +1,87 @@ +name = 'Xmipp' +version = '3.22.07-Helios' + +homepage = 'https://github.com/I2PC/scipion/wiki' +description = """Scipion is an image processing framework to obtain 3D +models of macromolecular complexes using Electron Microscopy (3DEM). It +integrates several software packages and presents an unified interface +for both biologists and developers. Scipion allows to execute workflows +combining different software tools, while taking care of formats and +conversions. Additionally, all steps are tracked and can be reproduced +later on. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/I2PC/xmipp/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(namelower)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippCore/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippCore-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippViz/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippViz-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, +] +patches = [ + '%(name)s-%(version)s_fix_scons_Environent_calls.patch', + '%(name)s-%(version)s_drop_useless_CXXFLAGS_setting.patch', + '%(name)s-%(version)s_correct_order_of_cu_includes.patch', + '%(name)s-%(version)s_dont_add_useless_libs.patch', + '%(name)s-%(version)s_dont_change_EB_build_flags.patch', + ('XmippCore-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippCore'), + ('XmippCore-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippCore'), + ('XmippViz-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippViz'), + ('XmippViz-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippViz'), +] +checksums = [ + {'xmipp-v3.22.07-Helios.tar.gz': 'f62e2729130b63d18e518930dd96a7a5250219e40c155abb78942a0642237ecf'}, + {'xmippCore-v3.22.07-Helios.tar.gz': '58e1143626cf807655a4756b165c21578d6f1b1777b43d363a2845d92d0bab8f'}, + {'xmippViz-v3.22.07-Helios.tar.gz': 'e1ce2cbbd57d3307d38538b29194a0190d633e5e062685387a6baf0329ad05b3'}, + {'Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch': + '5b59babad5a445ec7315a809509704d2d07232d2a5d180bfb78ebc8007bd0c95'}, + {'Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch': + '34ed0cb591e1e2788acd3e58696b1f45ce9210836d14ed1c99de1e574e4824e6'}, + {'Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch': + '2b0b2ddf349003be4112f4dca623586a03235214d6e64d232deb26468b52f0e3'}, + {'Xmipp-3.22.07-Helios_dont_add_useless_libs.patch': + '284b8ec1e514fb84b7680c8b3f59b3d5931b564beb444d3301504e3170e9a49e'}, + {'Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch': + '1514eaa5de35b38b5a10e949edf5c94ba95bbd05e0b9fbf70db2ea98967394e3'}, + {'XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch': + '8dcf0f3648f4b3438374ba629a9efa2e5c08eb25ae76ed420513664d21e2246b'}, + {'XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'd86b0d3ecc339b81c9aa7a33d2b44b428643aa7e2e686529b4bb6b16d36805c2'}, + {'XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch': + '7724fc3953d9c4c308a5755f54229259425fdbad5a909153bd173292434407b9'}, + {'XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'a8bea23c243174fb27a140a34a064a622cc96f0e7231fd31caf20f90c7ba9555'}, +] + +builddependencies = [ + ('SCons', '4.4.0'), + ('CTPL', '0.0.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Java', '11', '', SYSTEM), + ('OpenCV', '4.6.0', '-contrib'), + ('SQLite', '3.38.3'), + ('HDF5', '1.12.2'), + ('LibTIFF', '4.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('LIBSVM', '3.30'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch new file mode 100644 index 00000000000..8b61aa94613 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch @@ -0,0 +1,19 @@ +commit baac03018283296f90c08366e0e092c95d25173b +Author: Ake Sandgren +Date: Tue Oct 18 14:34:34 2022 +0200 + + cuda_gpu_multidim_array.cu is just an include file containing templates. + Needs to be before cuda_gpu_geo_transformer.cu + +diff --git xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp +index f7e5178c..8ccbefd3 100644 +--- xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp ++++ xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp +@@ -31,6 +31,6 @@ + */ + + #include "cuda_gpu_bilib.cu" ++#include "cuda_gpu_multidim_array.cu" + #include "cuda_gpu_geo_transformer.cu" + #include "cuda_gpu_iirconvolve.cu" +-#include "cuda_gpu_multidim_array.cu" diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch new file mode 100644 index 00000000000..a0ad7920a2d --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch @@ -0,0 +1,21 @@ +commit 4c1e2d678c5a33eae2ddb9f0558523d6d697e2b6 +Author: Ake Sandgren +Date: Thu Oct 27 08:04:04 2022 +0200 + + Don't add useless libraries to XmippInterfaceCuda and XmippParallelCuda + +diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct +index e70ea2cd..077541e8 100644 +--- xmipp-3.22.07-Helios/src/xmipp/SConstruct ++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct +@@ -209,9 +209,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + """ + _libs = list(libs) + _libpath = list(libpath)+external_libdirs +- if name == "XmippInterfaceCuda": +- _libs.append("XmippCuda") +- if "Cuda" in name: ++ if name == "XmippCuda": + _libs.append("cudart") + #_libs.append("cuda") + _libs.append("cufft") diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch new file mode 100644 index 00000000000..3c7171f617a --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch @@ -0,0 +1,41 @@ +commit e53881505ae212fa913fc536e60869e9b8e7f73c +Author: Ake Sandgren +Date: Thu Oct 27 09:45:11 2022 +0200 + + Don't change flags from what EasyBuild has decided to use. + +diff --git xmipp-3.22.07-Helios/scripts/config.py xmipp-3.22.07-Helios/scripts/config.py +index 0f58cbe3..b442a035 100644 +--- xmipp-3.22.07-Helios/scripts/config.py ++++ xmipp-3.22.07-Helios/scripts/config.py +@@ -293,7 +293,7 @@ class Config: + self.configDict["CCFLAGS"] += " -std=c99" + if 'g++' in self.get(Config.KEY_CXX): + # optimize for current machine +- self.configDict["CXXFLAGS"] += " -mtune=native -march=native -flto" ++ #self.configDict["CXXFLAGS"] += " -mtune=native -march=native -flto" + if "-std=c99" not in self.configDict["CXXFLAGS"]: + self.configDict["CXXFLAGS"] += " -std=c++17" + if isCIBuild(): +@@ -301,8 +301,8 @@ class Config: + self.configDict["CXXFLAGS"] += " -Werror" + # don't optimize, as it slows down the build + self.configDict["CXXFLAGS"] += " -O0" +- else: +- self.configDict["CXXFLAGS"] += " -O3" ++ #else: ++ # self.configDict["CXXFLAGS"] += " -O3" + if self.is_true("DEBUG"): + self.configDict["CXXFLAGS"] += " -g" + +@@ -315,8 +315,8 @@ class Config: + if self.configDict["LIBDIRFLAGS"] == "": + # /usr/local/lib or /path/to/virtEnv/lib + localLib = "%s/lib" % info['data'] +- self.configDict["LIBDIRFLAGS"] = "-L%s" % localLib +- self.environment.update(LD_LIBRARY_PATH=localLib) ++ #self.configDict["LIBDIRFLAGS"] = "-L%s" % localLib ++ #self.environment.update(LD_LIBRARY_PATH=localLib) + + # extra libs + hdf5InLocalLib = findFileInDirList("libhdf5*", localLib) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch new file mode 100644 index 00000000000..7e4c8618625 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch @@ -0,0 +1,18 @@ +commit f647cd54c8fa2b0894f347cbf7f13aacc0b8c785 +Author: Ake Sandgren +Date: Tue Oct 18 14:30:08 2022 +0200 + + Drop redundant setting of env var CXXFLAGS to what it already is. + +diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct +index c921c3c5..e70ea2cd 100644 +--- xmipp-3.22.07-Helios/src/xmipp/SConstruct ++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct +@@ -148,7 +148,6 @@ env['LINKERFORPROGRAMS'] = os.environ.get('LINKERFORPROGRAMS') + env['CCFLAGS'] = os.environ.get('CCFLAGS', '').split() + cxxFlags = os.environ.get('CXXFLAGS', '') + env['CXXFLAGS'] = cxxFlags.split() +-os.environ['CXXFLAGS'] = cxxFlags # FIXME use only env or os.environ in the rest of the code + env['LINKFLAGS'] = os.environ.get('LINKFLAGS', '').split() + + diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch new file mode 100644 index 00000000000..3eb4c9cf326 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch @@ -0,0 +1,37 @@ +commit 8ff0a1295743fae1eb069fe8242e524f348f5937 +Author: Ake Sandgren +Date: Tue Oct 18 14:28:47 2022 +0200 + + Make sure SCons sees the complete environment from EasyBuild. + +diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct +index 22ea72cf..c921c3c5 100644 +--- xmipp-3.22.07-Helios/src/xmipp/SConstruct ++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct +@@ -236,7 +236,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + # the reason is a compilation error for CUDA, which results in a multiple symbol detection + # when the order is different. This has to be fixed in the future by changing the CUDA + # build system FIXME David Strelak +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['PATH'] = env['ENV']['PATH'] + env2['CXXFLAGS']=list(env['CXXFLAGS']) # list(.) causes a true copy and not just a pointer + env2['LINKFLAGS']=list(env['LINKFLAGS']) +@@ -425,7 +425,7 @@ def addProgram(env, name, src=None, pattern=None, installDir=None, + ldLibraryPathCopy = [env['LIBPATH']] + appendUnique(libPathsCopy, external_libdirs) # This order is important, because if we should use Scipion libs, these will be before the system libs + appendUnique(libPathsCopy, env.get('LIBPATH', '').split(os.pathsep)) +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['LD_LIBRARY_PATH'] = env['ENV'].get('LD_LIBRARY_PATH', '') + env2['ENV']['PATH'] = env['ENV']['PATH'] + +@@ -486,7 +486,7 @@ def compilerConfig(env): + + def libraryTest(env, name, lang='c'): + """Check the existence of a concrete C/C++ library.""" +- env2 = Environment(LIBS=env.get('LIBS','')) ++ env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS','')) + conf = Configure(env2) + conf.CheckLib(name, language=lang) + env2 = conf.Finish() diff --git a/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch new file mode 100644 index 00000000000..06c3697efcb --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch @@ -0,0 +1,28 @@ +commit 901b41d324b351995b9256d7ee6b370276274497 +Author: Ake Sandgren +Date: Tue Oct 18 14:21:03 2022 +0200 + + Make sure SCons sees the complete environment from EasyBuild. + +diff --git xmippCore-3.22.07-Helios/SConstruct xmippCore-3.22.07-Helios/SConstruct +index 1c5fec3..40ed01f 100644 +--- xmippCore-3.22.07-Helios/SConstruct ++++ xmippCore-3.22.07-Helios/SConstruct +@@ -207,7 +207,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + if not sources and env.TargetInBuild(name): + Exit('No sources found for Library: %s. Exiting!!!' % name) + +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['PATH'] = env['ENV']['PATH'] + env2['CXX'] = env['CXX'] + +@@ -363,7 +363,7 @@ def compilerConfig(env): + + def libraryTest(env, name, lang='c'): + """Check the existence of a concrete C/C++ library.""" +- env2 = Environment(LIBS=env.get('LIBS','')) ++ env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS','')) + conf = Configure(env2) + conf.CheckLib(name, language=lang) + env2 = conf.Finish() diff --git a/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch new file mode 100644 index 00000000000..f1ac9fff312 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch @@ -0,0 +1,24 @@ +commit 36ca78858e442f1df23f5cb6b87c877a864eff44 +Author: Ake Sandgren +Date: Tue Oct 18 14:23:16 2022 +0200 + + Only use CXXFLAGS from EasyBuild. + +diff --git xmippCore-3.22.07-Helios/SConstruct xmippCore-3.22.07-Helios/SConstruct +index 40ed01f..277443d 100644 +--- xmippCore-3.22.07-Helios/SConstruct ++++ xmippCore-3.22.07-Helios/SConstruct +@@ -136,13 +136,7 @@ env['CXX'] = os.environ.get('CXX') + env['LINKERFORPROGRAMS'] = os.environ.get('LINKERFORPROGRAMS') + env['CCFLAGS'] = os.environ.get('CCFLAGS', '').split() + cxxFlags = os.environ.get('CXXFLAGS', '') +-if os.environ.get('DEBUG', '0') == 'True': #FIXME, use 1, true, yes... +- cxxFlags += ' -g' +-else: +- if cxxFlags.find("-O")==-1: +- cxxFlags += (" -O3" if 'TRAVIS' not in os.environ else " -O0") #don't optimize on Travis, as it slows down the build + env['CXXFLAGS'] = cxxFlags.split() +-os.environ['CXXFLAGS'] = cxxFlags # FIXME use only env or os.environ in the rest of the code + env['LINKFLAGS'] = os.environ.get('LINKFLAGS', '').split() + + diff --git a/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch new file mode 100644 index 00000000000..1cdd9c3add5 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch @@ -0,0 +1,28 @@ +commit 0e749b55db29360c9804f8c5e07094b7a5bf0597 +Author: Ake Sandgren +Date: Tue Oct 18 14:25:17 2022 +0200 + + Make sure scons sees the complete environment from EasyBuild. + +diff --git xmippViz-3.22.07-Helios/SConstruct xmippViz-3.22.07-Helios/SConstruct +index dc0a809..32c75be 100644 +--- xmippViz-3.22.07-Helios/SConstruct ++++ xmippViz-3.22.07-Helios/SConstruct +@@ -237,7 +237,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + if not sources and env.TargetInBuild(name): + Exit('No sources found for Library: %s. Exiting!!!' % name) + +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['PATH'] = env['ENV']['PATH'] + + mpiArgs = {} +@@ -474,7 +474,7 @@ def compilerConfig(env): + + def libraryTest(env, name, lang='c'): + """Check the existence of a concrete C/C++ library.""" +- env2 = Environment(LIBS=env.get('LIBS', '')) ++ env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS', '')) + conf = Configure(env2) + conf.CheckLib(name, language=lang) + env2 = conf.Finish() diff --git a/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch new file mode 100644 index 00000000000..6d8802ccb21 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch @@ -0,0 +1,25 @@ +commit 3d1e0e6e6da7aa7cc605be2a699f02b6cfbf4ca5 +Author: Ake Sandgren +Date: Tue Oct 18 14:26:22 2022 +0200 + + Only use CXXFLAGS from EasyBuild. + +diff --git xmippViz-3.22.07-Helios/SConstruct xmippViz-3.22.07-Helios/SConstruct +index 32c75be..fecd394 100644 +--- xmippViz-3.22.07-Helios/SConstruct ++++ xmippViz-3.22.07-Helios/SConstruct +@@ -143,14 +143,7 @@ env['CXX'] = os.environ.get('CXX') + env['LINKERFORPROGRAMS'] = os.environ.get('LINKERFORPROGRAMS') + env['CCFLAGS'] = os.environ.get('CCFLAGS', '').split() + cxxFlags = os.environ.get('CXXFLAGS', '') +-if os.environ.get('DEBUG', '0') == 'True': # FIXME, use 1, true, yes... +- cxxFlags += ' -g' +-else: +- if cxxFlags.find("-O") == -1: +- cxxFlags += ( +- " -O3" if 'TRAVIS' not in os.environ else " -O0") # don't optimize on Travis, as it slows down the build + env['CXXFLAGS'] = cxxFlags.split() +-os.environ['CXXFLAGS'] = cxxFlags # FIXME use only env or os.environ in the rest of the code + env['LINKFLAGS'] = os.environ.get('LINKFLAGS', '').split() + + for path in ['JAVA_HOME', 'JAVA_BINDIR']: From 265e2707a3dbc3ef9d9278d71806d80703f5302b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 11:39:09 +0200 Subject: [PATCH 5289/9987] Add missing CTPL dep --- .../c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..360aea103ca --- /dev/null +++ b/easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CmdCp' + +name = 'CTPL' +version = '0.0.2' + +homepage = 'https://github.com/vit-vit/CTPL.git' + +description = "Modern and efficient C++ Thread Pool Library" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'vit-vit' +source_urls = [GITHUB_SOURCE] +sources = ['%(namelower)s_v.%(version)s.tar.gz'] +checksums = ['8c1cec7c570d6d84be1d29283af5039ea27c3e69703bd446d396424bf619816e'] + +dependencies = [ + ('Boost', '1.79.0'), +] + +cmds_map = [('.*', "echo Nothing to build")] + +files_to_copy = [(['ctpl.h', 'ctpl_stl.h'], 'include/CTPL'), 'LICENSE', 'example.cpp'] + +sanity_check_paths = { + 'files': ['include/CTPL/%s' % x for x in ['ctpl.h', 'ctpl_stl.h']], + 'dirs': [] +} + +moduleclass = 'devel' From 191e0c22e05b8d60b8b193c98dc025be20cbf535 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 12:33:45 +0200 Subject: [PATCH 5290/9987] Add missing SCons dep --- .../s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ ...ns-4.4.0_install_man_pages_correctly.patch | 15 ++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8b3bae7755a --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'SCons' +version = '4.4.0' + +homepage = 'https://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': False, + 'patches': ['SCons-4.4.0_install_man_pages_correctly.patch'], + 'checksums': [ + {'SCons-4.4.0.tar.gz': '7703c4e9d2200b4854a31800c1dbd4587e1fa86e75f58795c740bcfa7eca7eaa'}, + {'SCons-4.4.0_install_man_pages_correctly.patch': + '9d216c2ea8e152ae1531593b17adc4042eb88f1d9524d7f3b08ace5137d6d5e7'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/sconsign'], + 'dirs': ['lib/pythoni%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ["scons --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch b/easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch new file mode 100644 index 00000000000..4c482a86c5e --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch @@ -0,0 +1,15 @@ +Install the man pages in the correct directory. + +Åke Sandgren, 2022-10-27 +diff -ru SCons-4.4.0.orig/setup.cfg SCons-4.4.0/setup.cfg +--- SCons-4.4.0.orig/setup.cfg 2022-07-30 23:16:02.000000000 +0200 ++++ SCons-4.4.0/setup.cfg 2022-10-27 11:55:33.457877253 +0200 +@@ -58,7 +58,7 @@ + SCons.Tool.docbook = *.* + + [options.data_files] +-. = scons.1 ++man/man1 = scons.1 + scons-time.1 + sconsign.1 + From 1edcba7fa4d21e5bc98fef154cf4ddf231c4b8ca Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 12:38:52 +0200 Subject: [PATCH 5291/9987] SCons: Fix typo --- easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb index 8b3bae7755a..22668b263b2 100644 --- a/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb @@ -29,7 +29,7 @@ exts_list = [ sanity_check_paths = { 'files': ['bin/scons', 'bin/sconsign'], - 'dirs': ['lib/pythoni%(pyshortver)s/site-packages/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], } sanity_check_commands = ["scons --help"] From 882d3673c93229c62dca34816d4b42936ebd190f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 18:39:34 +0200 Subject: [PATCH 5292/9987] adding easyconfigs: PyQt5-5.15.5-GCCcore-11.3.0.eb --- .../p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb | 102 ++++++++++++++++++ 1 file changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a052b69a2df --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb @@ -0,0 +1,102 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.5' + +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.38')] +dependencies = [ + ('Python', '3.10.4'), + ('Qt5', '5.15.5'), +] + +default_easyblock = 'PythonPackage' + +local_sipdir = '%(installdir)s/share/sip' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_sipver = '5.5.0' +components = [ + ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + ('PyQt-builder', '1.14.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + ('PyQt5_sip', '12.11.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts + }), + ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' From 0b6b8131e2b2f73363367341f60edbf47079e721 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 19:48:44 +0200 Subject: [PATCH 5293/9987] Add missing checksums --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb index a052b69a2df..594f66926cc 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb @@ -45,6 +45,7 @@ components = [ ('SIP', local_sipver, { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], 'start_dir': 'sip-%s' % local_sipver, 'use_pip': True, 'options': {'modulename': 'PyQt5.sip'}, @@ -52,18 +53,21 @@ components = [ ('PyQt-builder', '1.14.0', { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['6755931c6d2f8940553e0334d10c933ce5cc18b64425e94fda1accf4ff774f59'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.11.0', { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['b4710fd85b57edef716cc55fae45bfd5bfac6fc7ba91036f1dcc3f331ca0eb39'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['b411b7a8fa03901c9feb1dcbac7ea1fc3ce20b9ae682762b777cd5398749ca2b'], 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', 'preconfigopts': local_setup_env, @@ -72,6 +76,7 @@ components = [ ('PyQtWebEngine', version, { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['ab47608dccf2b5e4b950d5a3cc704b17711af035024d07a9b71ad29fc103b941'], 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', 'preconfigopts': local_setup_env, From d56c22e819ef39fad047ae05b6f62527f1961c3c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 28 Oct 2022 07:46:55 +0200 Subject: [PATCH 5294/9987] adding easyconfigs: PyOpenGL-3.1.6-GCCcore-11.3.0.eb --- .../PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..202415c4bdc --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenGL' +version = '3.1.6' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + + +builddependencies = [ + ('binutils', '2.38'), + ('bzip2', '1.0.8'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Mesa', '22.0.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'OpenGL', + 'checksums': ['8ea6c8773927eda7405bffc6f5bb93be81569a7b05c8cac50cd94e969dce5e27'], + }), +] + +moduleclass = 'vis' From e3925ab4dfc73f8c851ed9ea864821152998b6c4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 28 Oct 2022 08:45:04 +0100 Subject: [PATCH 5295/9987] fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x --- .../easyconfigs/g/GCCcore/GCCcore-10.1.0.eb | 21 ++++++----- .../easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 36 ++++++++++--------- .../easyconfigs/g/GCCcore/GCCcore-10.3.0.eb | 29 ++++++++------- .../easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 2 ++ .../easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 2 ++ 5 files changed, 52 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb index 23a101c3f9f..5ad49480069 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb @@ -31,17 +31,20 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', ] checksums = [ - '954057239c89d25bc7a62bfbceb58026363ad74f079c63fdba27f95abbf60900', # gcc-10.1.0.tar.gz - 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea', # gmp-6.2.0.tar.bz2 - 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc', # mpfr-4.0.2.tar.bz2 - '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz - '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-10.1.0.tar.gz': '954057239c89d25bc7a62bfbceb58026363ad74f079c63fdba27f95abbf60900'}, + {'gmp-6.2.0.tar.bz2': 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'}, + {'mpfr-4.0.2.tar.bz2': 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc'}, + {'mpc-1.1.0.tar.gz': '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e'}, + {'isl-0.22.1.tar.bz2': '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index d6d21047a9c..880ff3864f6 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -39,24 +39,28 @@ patches = [ 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', ] checksums = [ - '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d', # gcc-10.2.0.tar.gz - 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea', # gmp-6.2.0.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz - '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 - '58dd9e3eaedf519360d92d84205c3deef0b3fc286685d1c562e245914ef72c66', # newlib-3.3.0.tar.gz - 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705', # nvptx-tools-20180301.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch - 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCCcore-10.2.0_fix-has-include-Fortran.patch - '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278', # GCCcore-10.2.0_fix-ice-on-arm.patch - # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch - 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962', - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-10.2.0.tar.gz': '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d'}, + {'gmp-6.2.0.tar.bz2': 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.1.0.tar.gz': '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e'}, + {'isl-0.22.1.tar.bz2': '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd'}, + {'newlib-3.3.0.tar.gz': '58dd9e3eaedf519360d92d84205c3deef0b3fc286685d1c562e245914ef72c66'}, + {'nvptx-tools-20180301.tar.gz': 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.3.0_nvptx_sm_35_default.patch': '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108'}, + {'GCCcore-10.2.0_fix-has-include-Fortran.patch': + 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6'}, + {'GCCcore-10.2.0_fix-ice-on-arm.patch': '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278'}, + {'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch': + 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb index a3826b1579c..7f9079c65c0 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb @@ -37,21 +37,24 @@ patches = [ 'gcc-10.3.0_fix-ice-in-tsubst.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', ] checksums = [ - '8fcf994811ad4e5c7ac908e8cf62af2c1982319e5551f62ae72016064dacdf16', # gcc-10.3.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d', # isl-0.23.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch - '74e6e019458aa2feb36ae3c45f45e164725ca5edd66f4fe9f873c8ee78c35717', # gcc-10.3.0_fix-ice-in-tsubst.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-10.3.0.tar.gz': '8fcf994811ad4e5c7ac908e8cf62af2c1982319e5551f62ae72016064dacdf16'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.23.tar.bz2': 'c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20210115.tar.gz': '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.3.0_nvptx_sm_35_default.patch': '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108'}, + {'gcc-10.3.0_fix-ice-in-tsubst.patch': '74e6e019458aa2feb36ae3c45f45e164725ca5edd66f4fe9f873c8ee78c35717'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index a5a30163948..dde91967953 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ @@ -50,6 +51,7 @@ checksums = [ {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb index 5efade9fb39..9d40637c25c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -34,6 +34,7 @@ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ @@ -48,6 +49,7 @@ checksums = [ {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] From b4320eab9ed3f4b592917353cb6d3ac4e21607ed Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 28 Oct 2022 13:54:11 +0200 Subject: [PATCH 5296/9987] adding easyconfigs: cwltool-3.1.20221018083734-GCCcore-10.3.0.eb --- ...ltool-3.1.20221018083734-GCCcore-10.3.0.eb | 115 ++++++++++++++++++ 1 file changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..cfc690a27ae --- /dev/null +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb @@ -0,0 +1,115 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'cwltool' +version = '3.1.20221018083734' + +homepage = 'https://github.com/common-workflow-language/cwltool' +description = """Common workflow language (CWL) reference implementation.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# The Qt5 dependency of Graphviz (required by pydot) may be long to build and +# requires a lot of disk space and memory! +dependencies = [ + ('Python', '3.9.5'), + ('typing-extensions', '3.10.0.0'), + ('pydot', '1.4.2'), + ('lxml', '4.6.3'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('argcomplete', '2.0.0', { + 'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': 'ruamel.yaml', + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('ruamel.yaml', '0.17.14', { + 'modulename': 'ruamel', + 'checksums': ['4185fcfa9e037fea9ffd0bb6172354a03ec98c21e462355d72e068c74e493512'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', '6.2.0', { + 'checksums': ['62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('schema-salad', '8.3.20221016151607', { + 'modulename': 'schema_salad', + 'checksums': ['c61a517c945cd383445ebecbc085b00766913a3fdd7df9699a0fa4c41728ca1f'], + }), + ('shellescape', '3.8.1', { + 'checksums': ['40b310b30479be771bf3ab28bd8d40753778488bd46ea0969ba0b35038c3ec26'], + }), + ('cwlformat', '2022.2.18', { + 'modulename': 'cwlformat', + 'source_tmpl': 'cwlformat-%(version)s-py3-none-any.whl', + 'checksums': ['d3e2dca192ce10e703ed4eb0bae26539db08d8ddd7c6a6fe9d1406c3f1b53cda'], + }), + ('cwl-upgrader', '1.2.4', { + 'modulename': 'cwlupgrader', + 'checksums': ['b25fc236407343d44cc830ac3f63eed395b8d872fc7e17db92cde583d4a3b2ec'], + }), + ('cwl-utils', '0.20', { + 'modulename': 'cwl_utils', + 'checksums': ['28472aaba50ab4e8380c29f31c27beb63f60a1af1690369ab7bb7e31e71e66d9'], + }), + ('mypy-extensions', '0.4.3', { + 'modulename': 'mypy_extensions', + 'source_tmpl': 'mypy_extensions-%(version)s.tar.gz', + 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], + }), + ('networkx', '2.8.7', { + 'checksums': ['815383fd52ece0a7024b5fd8408cc13a389ea350cd912178b82eed8b96f82cd3'], + }), + ('prov', '1.5.1', { + 'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'], + }), + ('bagit', '1.8.1', { + 'checksums': ['37df1330d2e8640c8dee8ab6d0073ac701f0614d25f5252f9e05263409cee60c'], + }), + ('cwltool', '3.1.20221018083734', { + 'checksums': ['06d08f390ed7577ac66c6eef0c98f915363b5e36c04daa1353e3f2d0c5e19f17'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cwltool'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cwltool --version"] + +moduleclass = 'tools' From 9daea5ff0b20098eb2870fcc0dadc296fbb7d437 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 28 Oct 2022 15:28:51 +0200 Subject: [PATCH 5297/9987] Add missing sanity_pip_check --- .../c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb index cfc690a27ae..1d9ccc685eb 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb @@ -112,4 +112,6 @@ sanity_check_paths = { sanity_check_commands = ["cwltool --version"] +sanity_pip_check = True + moduleclass = 'tools' From 07493ac0283d1ff8b447a97e020d44fdc92f317b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 28 Oct 2022 17:02:56 +0200 Subject: [PATCH 5298/9987] Use ruamel.yaml and networkx from EB --- .../cwltool-3.1.20221018083734-GCCcore-10.3.0.eb | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb index 1d9ccc685eb..b40b9c1e883 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb @@ -34,6 +34,8 @@ dependencies = [ ('typing-extensions', '3.10.0.0'), ('pydot', '1.4.2'), ('lxml', '4.6.3'), + ('ruamel.yaml', '0.17.21'), + ('networkx', '2.6.3', '', ('foss', '2021a')), ] use_pip = True @@ -49,14 +51,6 @@ exts_list = [ ('coloredlogs', '15.0.1', { 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], }), - ('ruamel.yaml.clib', '0.2.7', { - 'modulename': 'ruamel.yaml', - 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], - }), - ('ruamel.yaml', '0.17.14', { - 'modulename': 'ruamel', - 'checksums': ['4185fcfa9e037fea9ffd0bb6172354a03ec98c21e462355d72e068c74e493512'], - }), ('isodate', '0.6.1', { 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], }), @@ -91,9 +85,6 @@ exts_list = [ 'source_tmpl': 'mypy_extensions-%(version)s.tar.gz', 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], }), - ('networkx', '2.8.7', { - 'checksums': ['815383fd52ece0a7024b5fd8408cc13a389ea350cd912178b82eed8b96f82cd3'], - }), ('prov', '1.5.1', { 'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'], }), From 5822cf971248270b67fcdf12b3f057eff278950d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 28 Oct 2022 18:10:36 +0200 Subject: [PATCH 5299/9987] Update napari-0.4.15-foss-2021b.eb fox sources list docstring-parser --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb index f439e3019c2..18337a90cfd 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb @@ -52,7 +52,7 @@ exts_list = [ 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], }), ('docstring-parser', '0.14.1', { - 'sources': 'docstring_parser-%(version)s.tar.gz', + 'sources': ['docstring_parser-%(version)s.tar.gz'], 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], }), ('pep517', '0.12.0', { From 560d52ba93aaf34f7137c70d30baa99999553367 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 18:31:57 +0100 Subject: [PATCH 5300/9987] adding easyconfigs: svist4get-1.3.1-foss-2020b.eb --- .../s/svist4get/svist4get-1.3.1-foss-2020b.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb new file mode 100644 index 00000000000..8ec2b2b0060 --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -0,0 +1,59 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'svist4get' +version = '1.3.1' + +homepage = 'https://github.com/art-egorov/svist4get' +description = """Svist4get is a simple bioinformatics tool for visualization of +genomic signal tracks in user-defined genomic windows, either arbitrary selected +by genomic coordinates or anchored to particular transcripts or genes.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('pybedtools', '0.8.2'), + ('Biopython', '1.78'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('reportlab', '3.6.9', { + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84'], + }), + + ('configs', '3.0.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('Wand', '0.6.10', { + 'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + + (name, version, { + 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/svist4get', 'bin/svist4get_copier'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "svist4get --help", + "svist4get -v", +] + +moduleclass = 'bio' From d12f1b147c7ad739e4603458a4aef74285b2c013 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 18:33:08 +0100 Subject: [PATCH 5301/9987] adding easyconfigs: TOBIAS-0.14.0-foss-2020b.eb --- .../t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb new file mode 100644 index 00000000000..124583e843d --- /dev/null +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb @@ -0,0 +1,83 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'TOBIAS' +version = '0.14.0' + +homepage = 'https://github.com/loosolab/TOBIAS' +description = """TOBIAS is a collection of command-line bioinformatics tools +for performing footprinting analysis on ATAC-seq data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Seaborn', '0.11.1'), + ('pybedtools', '0.8.2'), + ('pyBigWig', '0.3.18'), + ('scikit-learn', '0.23.2'), + ('PyYAML', '5.3.1'), + ('XlsxWriter', '1.4.0'), + ('svist4get', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('adjustText', '0.7.3', { + 'checksums': ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'], + 'modulename': 'adjustText', + }), + ('botocore', '1.28.2', { + 'checksums': ['9890005735652555d1183b44bad729603d26922dc08e261e1e0a35a7bf26ba38'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.6.0', { + 'checksums': ['2ed07d3866f523cc561bf4a00fc5535827981b117dd7876f036b0c1aca42c947'], + }), + ('boto3', '1.25.2', { + 'checksums': ['43a93f8cecd882cccb2815cd76fc07a73b076027ab092a1c7cede89cb9b075f8'], + }), + ('kneed', '0.7.0', { + 'checksums': ['340d67fa183a72b0afae19846dd246a6fb7204e8d54243d8b8d3d9932f887c6e'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('MOODS-python', '1.9.4.1', { + 'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'], + 'modulename': 'MOODS', + }), + ('flit_core', '3.7.1', { + 'checksums': ['14955af340c43035dbfa96b5ee47407e377ee337f69e70f73064940d27d0a44f'], + }), + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('PyPDF2', '2.11.1', { + 'checksums': ['3c7badd512c21711eb1789c2eadbf96279289c0f94452ee54a86473bfbefd732'], + 'modulename': 'PyPDF2', + }), + + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['ac74c35f981d499425147054f82142d22e52858d402d0c63ab7e8481bd156589'], + }), +] + +sanity_check_paths = { + 'files': ['bin/TOBIAS', 'bin/cluster_sites_by_overlap.py', 'bin/moods-dna.py', 'bin/jp.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "TOBIAS --help", +] + +moduleclass = 'bio' From c5c6cdf960b42a6c5df9d32ae61befdf7973b5bf Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 23:37:54 +0100 Subject: [PATCH 5302/9987] reportlab patched so it finds EB fontconfig instead system one --- .../s/svist4get/svist4get-1.3.1-foss-2020b.eb | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index 8ec2b2b0060..c228ca9af49 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -16,17 +16,19 @@ dependencies = [ ('Python', '3.8.6'), ('pybedtools', '0.8.2'), ('Biopython', '1.78'), - ('Pillow', '8.0.1'), + ('Pillow', '9.2.0'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('reportlab', '3.6.9', { - 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84'], + ('reportlab', '3.6.12', { + 'patches': ['reportlab-3.6.12-fontconfig.patch'], + 'checksums': ['b13cebf4e397bba14542bcd023338b6ff2c151a3a12aabca89eecbf972cb361a', + # reportlab-3.6.12-fontconfig.patch: + '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], }), - ('configs', '3.0.3', { 'sources': ['%(name)s-%(version)s.zip'], 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], @@ -40,7 +42,6 @@ exts_list = [ ('statistics', '1.0.3.5', { 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], }), - (name, version, { 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], }), @@ -52,7 +53,7 @@ sanity_check_paths = { } sanity_check_commands = [ - "svist4get --help", + "svist4get --help", "svist4get -v", ] From 479ed72ae7168d43ea554240fc34c381c8c88929 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 23:39:29 +0100 Subject: [PATCH 5303/9987] adding easyconfigs: Pillow-9.2.0-GCCcore-10.2.0.eb --- .../p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..38e7492daf9 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '9.2.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = [ + '75e636fd3e0fb872693f23ccb8a5ff2cd578801251f3a4f6854c6a5d437d3c04', # Pillow-8.0.1.tar.gz +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.1.0'), + ('freetype', '2.10.3') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From af342d68b218ed49e52240d56a5d750c226b883f Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 23:49:12 +0100 Subject: [PATCH 5304/9987] Patchfile added --- .../reportlab-3.6.12-fontconfig.patch | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch diff --git a/easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch b/easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch new file mode 100644 index 00000000000..92e6ce51369 --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch @@ -0,0 +1,25 @@ +Patch to make sure the fontconfig from EasyBuild will be found +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/reportlab-3.6.12.orig/setup.py b/reportlab-3.6.12/setup.py +index 4b380b6..2ccfa93 100644 +--- a/reportlab-3.6.12.orig/setup.py ++++ b/reportlab-3.6.12/setup.py +@@ -277,14 +277,11 @@ class inc_lib_dirs: + # darwin ports installation directories + aDir(L, "/opt/local/lib") + aDir(I, "/opt/local/include") +- aDir(I, "/usr/local/include") +- aDir(L, "/usr/local/lib") +- aDir(I, "/usr/include") +- aDir(L, "/usr/lib") +- aDir(I, "/usr/include/freetype2") + if addrSize==64: +- aDir(L, "/usr/lib/lib64") +- aDir(L, "/usr/lib/x86_64-linux-gnu") ++ freepath = os.getenv("EBROOTFREETYPE") ++ aDir(L, pjoin(freepath, "lib64")) ++ aDir(I, pjoin(freepath, "include/freetype2")) ++ + else: + aDir(L, "/usr/lib/lib32") + prefix = sysconfig.get_config_var("prefix") From 160c1da84942a6311bb12c0a5e0e90835668b57c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 00:38:28 +0100 Subject: [PATCH 5305/9987] Update svist4get-1.3.1-foss-2020b.eb Missing ImageMagick added (picked up OS installation before) --- easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index c228ca9af49..d9b689ae40e 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -17,6 +17,7 @@ dependencies = [ ('pybedtools', '0.8.2'), ('Biopython', '1.78'), ('Pillow', '9.2.0'), + ('ImageMagick', '7.0.10-35'), ] use_pip = True From ca066e8f6222f3c8ab16b502e2d614d92ebf7af2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 00:53:11 +0100 Subject: [PATCH 5306/9987] Update svist4get-1.3.1-foss-2020b.eb Pillow downgraded to 8.0.1, reportlab downgraded to 3.6.9 due to conflicts with TOBIAS --- .../easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index d9b689ae40e..a6339d51f19 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.8.6'), ('pybedtools', '0.8.2'), ('Biopython', '1.78'), - ('Pillow', '9.2.0'), + ('Pillow', '8.0.1'), ('ImageMagick', '7.0.10-35'), ] @@ -24,9 +24,9 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('reportlab', '3.6.12', { + ('reportlab', '3.6.9', { 'patches': ['reportlab-3.6.12-fontconfig.patch'], - 'checksums': ['b13cebf4e397bba14542bcd023338b6ff2c151a3a12aabca89eecbf972cb361a', + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84', # reportlab-3.6.12-fontconfig.patch: '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], }), From d9798882dc8f2681816c6e473b6107257f534715 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 09:12:32 +0100 Subject: [PATCH 5307/9987] Update TOBIAS-0.14.0-foss-2020b.eb Empty line removed --- easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb index 124583e843d..862d4fe55c1 100644 --- a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb @@ -64,7 +64,6 @@ exts_list = [ 'checksums': ['3c7badd512c21711eb1789c2eadbf96279289c0f94452ee54a86473bfbefd732'], 'modulename': 'PyPDF2', }), - (name, version, { 'sources': ['%(namelower)s-%(version)s.tar.gz'], 'checksums': ['ac74c35f981d499425147054f82142d22e52858d402d0c63ab7e8481bd156589'], From 769fde96b1588d61317942682d27a64a0f4a25b1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 29 Oct 2022 12:14:17 +0200 Subject: [PATCH 5308/9987] adding easyconfigs: make-4.3-GCCcore-11.3.0.eb, tmux-3.3a-GCCcore-11.3.0.eb --- .../m/make/make-4.3-GCCcore-11.3.0.eb | 29 +++++++++++++++ .../t/tmux/tmux-3.3a-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..508f420c75e --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.3' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e05fdde47c5f7ca45cb697e973894ff4f5d79e13b750ed57d7b66d8defc78e19'] + +builddependencies = [('binutils', '2.38')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..de3e3e02e01 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.3a' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e4fd347843bd0772c4f48d6dde625b0b109b7a380ff15db21e97c11a4dcdf93f'] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('make', '4.3'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.3'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' From b40096676f0a96b0c47cb55a576e3f489cc73ac3 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 31 Oct 2022 02:29:29 +0000 Subject: [PATCH 5309/9987] Add OpenBLAS patches to disable FMA in [cz]cal and fix crash in zdot --- .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 5 ++ .../o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 5 ++ .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 5 ++ .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 5 ++ .../OpenBLAS-0.3.21_avoid-crash-in-zdot.patch | 19 ++++++ ...AS-0.3.21_disable-fma-in-cscal-zscal.patch | 68 +++++++++++++++++++ 6 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 93e65aa9221..c4b29c67422 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -19,6 +19,8 @@ patches = [ 'OpenBLAS-%(version)s_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch', 'OpenBLAS-%(version)s_fix-segfault-ztrsv.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.17.tar.gz': 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f'}, @@ -31,6 +33,9 @@ checksums = [ {'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch': 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 866cd7de515..762a9558bfb 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -18,6 +18,8 @@ patches = [ 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.18.tar.gz': '1632c1e8cca62d8bed064b37747e331a1796fc46f688626337362bf0d16aeadb'}, @@ -28,6 +30,9 @@ checksums = [ {'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch': 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index c654f92e700..98f44c83e7c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -17,6 +17,8 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, @@ -26,6 +28,9 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index bb82984319e..4496c0bc5b3 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -17,6 +17,8 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, @@ -26,6 +28,9 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch new file mode 100644 index 00000000000..d96341d6de5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch @@ -0,0 +1,19 @@ +Avoid crash with GCC 11's vectorizer involving 256-bit ymm registers. + +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=107451 + +Bart Oldeman + +diff --git a/kernel/x86_64/zdot.c b/kernel/x86_64/zdot.c +index 27397ccf..e1d43be1 100644 +--- a/kernel/x86_64/zdot.c ++++ b/kernel/x86_64/zdot.c +@@ -97,7 +97,7 @@ extern int blas_level1_thread_with_return_value(int mode, BLASLONG m, BLASLONG n + + + +-static void zdot_compute (BLASLONG n, FLOAT *x, BLASLONG inc_x, FLOAT *y, BLASLONG inc_y,OPENBLAS_COMPLEX_FLOAT *result) ++__attribute__((target("prefer-vector-width=128"))) static void zdot_compute (BLASLONG n, FLOAT *x, BLASLONG inc_x, FLOAT *y, BLASLONG inc_y,OPENBLAS_COMPLEX_FLOAT *result) + { + BLASLONG i; + BLASLONG ix,iy; diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch new file mode 100644 index 00000000000..6e2cb2e62e0 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch @@ -0,0 +1,68 @@ +From e7e3aa29482281edba46a27fcd452d7ed630f46a Mon Sep 17 00:00:00 2001 +From: Bart Oldeman +Date: Thu, 27 Oct 2022 17:20:44 -0400 +Subject: [PATCH] x86_64: prevent GCC and Clang from generating FMAs in + cscal/zscal. + +If e.g. -march=haswell is set in CFLAGS, GCC generates FMAs by default, which +is inconsistent with the microkernels, none of which use FMAs. These +inconsistencies cause a few failures in the LAPACK testcases, where +eigenvalue results with/without eigenvectors are compared. + +Moreover using FMAs for multiplication of complex numbers can give surprising +results, see 22aa81f for more information. + +This uses the same syntax as used in 22aa81f for zarch (s390x). +--- + kernel/x86_64/cscal.c | 13 +++++++++++++ + kernel/x86_64/zscal.c | 13 +++++++++++++ + 2 files changed, 26 insertions(+) + +diff --git a/kernel/x86_64/cscal.c b/kernel/x86_64/cscal.c +index dc3f688c69..6ae66d9731 100644 +--- a/kernel/x86_64/cscal.c ++++ b/kernel/x86_64/cscal.c +@@ -25,6 +25,19 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + +diff --git a/kernel/x86_64/zscal.c b/kernel/x86_64/zscal.c +index 3744c98bb7..dfdb4230b6 100644 +--- a/kernel/x86_64/zscal.c ++++ b/kernel/x86_64/zscal.c +@@ -25,6 +25,19 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + From e2abe951628c519b1dc970064b3c36682e02d0ec Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 31 Oct 2022 11:28:16 +0100 Subject: [PATCH 5310/9987] adding easyconfigs: MotionCor2-1.5.0-GCCcore-11.3.0.eb --- .../MotionCor2-1.5.0-GCCcore-11.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6c70f59b67b --- /dev/null +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ake Sandgren +# HPC2N +# Umea University + +name = 'MotionCor2' +version = '1.5.0' + +homepage = 'https://msg.ucsf.edu/' +description = """MotionCor2 correct anisotropic image motion at the +single pixel level across the whole frame, suitable for both single +particle and tomographic images. Iterative, patch-based motion detection +is combined with spatial and temporal constraints and dose weighting. + +Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, +Yifan Cheng and David A. Agard (2016) Anisotropic Correction of +Beam-induced Motion for Improved Single-particle Electron +Cryo-microscopy, Nature Methods, submitted. +BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +# No longer directly downloadable, available from https://msg.ucsf.edu/software +sources = [ + '%(name)s_%(version)s.zip', +] +checksums = ['cdb7b9aceb42d52e2a4c7a5e80270371376aea412d21fa1f1f28d4cc71c81834'] + +# CUDA is a build dependency to make sure it gets installed. +# It's actually a runtime dependency, but that's handled in the wrapper to +# make sure it doesn't conflict with whatever toolchain happens to be loaded. +# Change CUDA version to match the latest one used in this version +# of MotionCor2 +builddependencies = [ + ('binutils', '2.38'), + ('CUDA', '11.6.0', '', SYSTEM), +] + +dependencies = [ + ('LibTIFF', '4.3.0'), +] + +moduleclass = 'bio' From e71962b1ce6e45abbd51a7b7372828216bde1819 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 Oct 2022 11:57:54 +0100 Subject: [PATCH 5311/9987] add LMERConvenienceFunctions extension for R v4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 49b9a97d1a0..e3da8a7d9fa 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3358,6 +3358,12 @@ exts_list = [ ('AMAPVox', '0.12.0', { 'checksums': ['b30fefef8661e27ffe3883665204b623eda2143dbcd3084a1d5810f8ea834c85'], }), + ('LCFdata', '2.0', { + 'checksums': ['b58f4d93b9023dd1ba2db96a59ddfc058397085933d8de4cdb38ee064d5e7bf4'], + }), + ('LMERConvenienceFunctions', '3.0', { + 'checksums': ['eb430de9fbf836173f716960d60afc2de91de7f986471f406c3ca9027142e849'], + }), ] moduleclass = 'lang' From abc4ba47ae726bf6f7b18947f076e352b596221a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85ke=20Sandgren?= Date: Mon, 31 Oct 2022 12:50:33 +0100 Subject: [PATCH 5312/9987] Update easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb index 6c70f59b67b..13e710f1fd7 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb @@ -26,6 +26,7 @@ sources = [ '%(name)s_%(version)s.zip', ] checksums = ['cdb7b9aceb42d52e2a4c7a5e80270371376aea412d21fa1f1f28d4cc71c81834'] +download_instructions = """Visit https://msg.ucsf.edu/software and fill in the form to download %s""" % sources[0] # CUDA is a build dependency to make sure it gets installed. # It's actually a runtime dependency, but that's handled in the wrapper to From 32c0d75f717c18624bb44eceae50c0ba5636bc62 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85ke=20Sandgren?= Date: Mon, 31 Oct 2022 12:50:45 +0100 Subject: [PATCH 5313/9987] Update easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb index 13e710f1fd7..1ce57f532b7 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb @@ -21,7 +21,6 @@ BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -# No longer directly downloadable, available from https://msg.ucsf.edu/software sources = [ '%(name)s_%(version)s.zip', ] From ed75daa514deeb52189905dac31b76e6fcb6ab07 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 31 Oct 2022 13:35:42 +0100 Subject: [PATCH 5314/9987] favor decision in https://github.com/easybuilders/easybuild-easyconfigs/issues/16330 --- easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb index f2e75d38711..fabca76f18f 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb @@ -29,8 +29,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('Perl', '5.32.0'), ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), From 9f7abcccf2da1180d57821caca6da9abbaba35a7 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 31 Oct 2022 13:41:08 +0100 Subject: [PATCH 5315/9987] Update easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb thanks for the hint Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 15338b73d97..96cb3e18281 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -7,10 +7,10 @@ version = '5.7.0' homepage = "https://confluence.ecmwf.int/display/ECFLOW/ecflow+home" description = """ecFlow is a client/server workflow package that enables users - to run a large number of programs (with dependencies on each other and on time) - in a controlled environment. It provides reasonable tolerance for hardware and - software failures, combined with restart capabilities. - It is used at ECMWF to run all our operational suites across a range of platforms.""" + to run a large number of programs (with dependencies on each other and on time) + in a controlled environment. It provides reasonable tolerance for hardware and + software failures, combined with restart capabilities. + It is used at ECMWF to run all our operational suites across a range of platforms.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} From 5dadf89e31d09d3abc481fe865ce9653a9958897 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 31 Oct 2022 13:44:32 +0100 Subject: [PATCH 5316/9987] favor decision in https://github.com/easybuilders/easybuild-easyconfigs/issues/16330 --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 96cb3e18281..fa918e82340 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -28,7 +28,7 @@ dependencies = [ ('Boost', '1.74.0'), ('Boost.Python', '1.74.0'), ('Qt5', '5.14.2'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " From 64400bf1141f3e8e49a6f2b590870a6284356a57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 Oct 2022 15:14:37 +0100 Subject: [PATCH 5317/9987] adding easyconfigs: cdsapi-0.5.1-GCCcore-11.3.0.eb --- .../c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c70d2401d59 --- /dev/null +++ b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'cdsapi' +version = '0.5.1' + +homepage = 'https://pypi.org/project/cdsapi' +description = "Climate Data Store API" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['19f3e92f1996cc1115d0b0281617edeaecf3eefca03fbd384cfbc520d5f0476d'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('tqdm', '4.64.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From bdf19a088b0c99038d13c2911447c4b78f81d8e3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 1 Nov 2022 08:37:25 +0100 Subject: [PATCH 5318/9987] add missing build dependency on Perl for GStreamer. And make sure to not make files suid. --- .../GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb | 9 +++++++- .../g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb | 9 +++++++- .../GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb | 9 +++++++- .../GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb | 9 +++++++- .../GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb | 9 +++++++- .../GStreamer-1.18_fix_bad_suid.patch | 22 +++++++++++++++++++ .../GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb | 9 +++++++- 7 files changed, 70 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb index 3c94c21acae..1e320e100bf 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb @@ -13,9 +13,16 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['0e8e2f7118be437cba879353970cf83c2acced825ecb9275ba05d9186ef07c00'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.16.0.tar.xz': '0e8e2f7118be437cba879353970cf83c2acced825ecb9275ba05d9186ef07c00'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ + ('Perl', '5.28.1'), ('Bison', '3.0.5'), ('flex', '2.6.4'), ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb index 92e0c55eca2..370fa85b4cf 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb @@ -13,9 +13,16 @@ toolchain = {'name': 'GCC', 'version': '8.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['e3f044246783fd685439647373fa13ba14f7ab0b346eadd06437092f8419e94e'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.16.2.tar.xz': 'e3f044246783fd685439647373fa13ba14f7ab0b346eadd06437092f8419e94e'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ + ('Perl', '5.30.0'), ('Bison', '3.3.2'), ('flex', '2.6.4'), ('GObject-Introspection', '1.63.1', '-Python-3.7.4'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb index a4c5be90916..cc7e4f4623c 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.18.4.tar.xz': '9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.55.3'), ('Ninja', '1.10.1'), + ('Perl', '5.32.0'), ('Bison', '3.7.1'), ('flex', '2.6.4'), ('GObject-Introspection', '1.66.1'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb index 2c38b4b9151..11f4d5afc2e 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.18.4.tar.xz': '9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.58.0'), ('Ninja', '1.10.2'), + ('Perl', '5.32.1'), ('Bison', '3.7.6'), ('flex', '2.6.4'), ('GObject-Introspection', '1.68.0'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb index 7d550bd31b6..45f9ea5e5d0 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['55862232a63459bbf56abebde3085ca9aec211b478e891dacea4d6df8cafe80a'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.18.5.tar.xz': '55862232a63459bbf56abebde3085ca9aec211b478e891dacea4d6df8cafe80a'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.58.2'), ('Ninja', '1.10.2'), + ('Perl', '5.34.0'), ('Bison', '3.7.6'), ('flex', '2.6.4'), ('GObject-Introspection', '1.68.0'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch new file mode 100644 index 00000000000..4fff14d8b7a --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch @@ -0,0 +1,22 @@ +Do NOT make files setuid or try to do setcap. +That's a recipe for disaster. + +Åke Sandgren, 20221031 +diff -ru gstreamer-1.20.2.orig/libs/gst/helpers/ptp_helper_post_install.sh gstreamer-1.20.2/libs/gst/helpers/ptp_helper_post_install.sh +--- gstreamer-1.20.2.orig/libs/gst/helpers/ptp_helper_post_install.sh 2022-05-03 00:29:29.000000000 +0200 ++++ gstreamer-1.20.2/libs/gst/helpers/ptp_helper_post_install.sh 2022-10-31 16:39:11.959435316 +0100 +@@ -11,14 +11,10 @@ + setuid-root) + echo "$0: permissions before: " + ls -l "$ptp_helper" +- chown root "$ptp_helper" || true +- chmod u+s "$ptp_helper" || true + echo "$0: permissions after: " + ls -l "$ptp_helper" + ;; + capabilities) +- echo "Calling $setcap cap_net_bind_service,cap_net_admin+ep $ptp_helper" +- $setcap cap_net_bind_service,cap_net_admin+ep "$ptp_helper" || true + ;; + none) + echo "No perms/caps to set for $ptp_helper" diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb index df69820328f..d942105b5f7 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['df24e8792691a02dfe003b3833a51f1dbc6c3331ae625d143b17da939ceb5e0a'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.20.2.tar.xz': 'df24e8792691a02dfe003b3833a51f1dbc6c3331ae625d143b17da939ceb5e0a'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), + ('Perl', '5.34.1'), ('Bison', '3.8.2'), ('flex', '2.6.4'), ('GObject-Introspection', '1.72.0'), From 9914b1c520060e5cea9fdc0621f431d86ae42fbb Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:10:58 +0100 Subject: [PATCH 5319/9987] adding easyconfigs: wandb-0.13.4-GCCcore-11.3.0.eb --- .../w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1fdb7113a4e --- /dev/null +++ b/easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'wandb' +version = '0.13.4' + +homepage = 'https://www.wandb.com/' +description = """ +CLI and Python API for Weights and Biases: a tool for visualizing and tracking +your machine learning experiments.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('GitPython', '3.1.27'), + ('PyYAML', '6.0'), + ('protobuf-python', '3.19.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('yaspin', '2.1.0', { + 'checksums': ['c8d34eca9fda3f4dfbe59f57f3cf0f3641af3eefbf1544fbeb9b3bacf82c580a'], + }), + ('shortuuid', '1.0.9', { + 'checksums': ['459f12fa1acc34ff213b1371467c0325169645a31ed989e268872339af7563d5'], + }), + ('setproctitle', '1.3.2', { + 'checksums': ['b9fb97907c830d260fa0658ed58afd48a86b2b88aac521135c352ff7fd3477fd'], + }), + ('sentry-sdk', '1.8.0', { + 'checksums': ['9c68e82f7b1ad78aee6cdef57c2c0f6781ddd9ffa8848f4503c5a8e02b360eea'], + }), + ('charset-normalizer', '2.0.12', { + 'checksums': ['2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597'], + }), + ('promise', '2.3', { + 'checksums': ['dfd18337c523ba4b6a58801c164c1904a9d4d1b1747c7d5dbf45b693a49d93d0'], + }), + ('pathtools', '0.1.2', { + 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], + }), + ('docker-pycreds', '0.4.0', { + 'modulename': 'dockerpycreds', + 'checksums': ['6ce3270bcaf404cc4c3e27e4b6c70d3521deae82fb508767870fdbf772d584d4'], + }), + (name, version, { + 'checksums': ['51e2672e12cca94680f6bcff0af80822d562e6b7846036050fc5bdd00240ea75'], + }), +] + +sanity_check_paths = { + 'files': ['bin/wandb', 'bin/wb'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ['wandb --help'] + +moduleclass = 'tools' From 20cbc3a794cc30e10944f430a07c2a336a9782d7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:15:17 +0100 Subject: [PATCH 5320/9987] adding easyconfigs: SimpleITK-2.1.1.2-foss-2022a.eb --- .../SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb new file mode 100644 index 00000000000..9a0f8d8c8e2 --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'SimpleITK' +version = '2.1.1.2' + +homepage = 'https://www.simpleitk.org' +description = """SimpleITK is a simplified programming interface to the algorithms and data structures of + the Insight Toolkit (ITK).""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_allow-lua54-for-code-generation.patch'] +checksums = [ + '5c0689b007d449ce0ce17a9ea322152315fb17ed32949005a974d3d9c2f58da3', # SimpleITK-2.1.1.2.tar.gz + # SimpleITK-2.1.1.2_allow-lua54-for-code-generation.patch + 'd1a45b1b64a226b3c22bf83c2f40f7f0e8f0a7d74bea1b2e7f5c5b6ed88b1522', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('SWIG', '4.0.2'), + ('Lua', '5.4.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('ITK', '5.2.1'), + ('scikit-build', '0.15.0'), +] + +start_dir = 'SimpleITK' + +configopts = "-DWRAP_DEFAULT:BOOL=OFF -DWRAP_PYTHON=BOOL:ON " + +postinstallcmds = [ + "cd %(builddir)s/easybuild_obj/Wrapping/Python && " + "pip install --ignore-installed --no-deps --prefix=%(installdir)s . ", +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], + 'dirs': ['include/%(name)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import %(name)s'"] + +moduleclass = 'tools' From c5c539d4f0362b6f0d87358de38fb0948af5030b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:17:03 +0100 Subject: [PATCH 5321/9987] adding easyconfigs: MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb, MONAI-1.0.1-foss-2022a.eb, einops-0.4.1-GCCcore-11.3.0.eb --- .../e/einops/einops-0.4.1-GCCcore-11.3.0.eb | 29 +++++++++++ .../MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb | 50 +++++++++++++++++++ .../m/MONAI/MONAI-1.0.1-foss-2022a.eb | 48 ++++++++++++++++++ 3 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e31c2fbbbba --- /dev/null +++ b/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'einops' +version = '0.4.1' + +homepage = 'https://einops.rocks/' +description = """ +Flexible and powerful tensor operations for readable and reliable code. +Supports numpy, pytorch, tensorflow, jax, and others.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['65ede824fa54ce99ba969c61152f9948eb8cad08d5f0ca97c95e3804bafcce48'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..bd6d8765a06 --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'Project-MONAI' + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('einops', '0.4.1'), + ('ITK', '5.2.1'), + ('NiBabel', '4.0.2'), + ('scikit-image', '0.19.3'), + ('tensorboard', '2.10.0'), + ('torchvision', '0.13.1', versionsuffix), + ('tqdm', '4.64.0'), +] + +exts_list = [ + (name, version, { + 'preinstallopts': 'BUILD_MONAI=1', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'], + }), +] + +use_pip = True + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb new file mode 100644 index 00000000000..0d272341e2c --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.0.1' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'Project-MONAI' + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('einops', '0.4.1'), + ('ITK', '5.2.1'), + ('NiBabel', '4.0.2'), + ('scikit-image', '0.19.3'), + ('tensorboard', '2.10.0'), + ('torchvision', '0.13.1'), + ('tqdm', '4.64.0'), +] + +exts_list = [ + (name, version, { + 'preinstallopts': 'BUILD_MONAI=1', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'], + }), +] + +use_pip = True + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': [''], +} + +moduleclass = 'vis' From 269db8f055bb836dc74be57f242a48c0a75e1f53 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:22:48 +0100 Subject: [PATCH 5322/9987] adding easyconfigs: scikit-image-0.19.3-foss-2022a.eb, imageio-2.22.2-foss-2022a.eb --- .../i/imageio/imageio-2.22.2-foss-2022a.eb | 25 +++++++++++ .../scikit-image-0.19.3-foss-2022a.eb | 43 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb b/easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb new file mode 100644 index 00000000000..a340e81b29e --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.22.2' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['db7010cd10712518819a4187baf61b05988361ea20c23e829918727b27acb977'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Pillow', '9.1.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb new file mode 100644 index 00000000000..2cc7bce06b1 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.19.3' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('Pillow', '9.1.1'), + ('networkx', '2.8.4'), + ('dask', '2022.10.0'), + ('imageio', '2.22.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('PyWavelets', '1.4.1', { + 'modulename': 'pywt', + 'checksums': ['6437af3ddf083118c26d8f97ab43b0724b956c9f958e9ea788659f6a2834ba93'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + ('tifffile', '2022.10.10', { + 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], + }), + (name, version, { + 'modulename': 'skimage', + 'checksums': ['24b5367de1762da6ee126dd8f30cc4e7efda474e0d7d70685433f0e3aa2ec450'], + }), +] + +moduleclass = 'vis' From 6126fd1a5ce64be4d99aa459d9d49d122f29308f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 1 Nov 2022 15:13:22 +0000 Subject: [PATCH 5323/9987] adding easyconfigs: pyro-ppl-1.8.0-foss-2021a-CUDA-11.3.1.eb --- .../pyro-ppl-1.8.0-foss-2021a-CUDA-11.3.1.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..fe9debfd281 --- /dev/null +++ b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INU) +# Updated to 1.8.2, pyro-api as extension added +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'pyro-ppl' +version = '1.8.0' +versionsuffix = '-CUDA-%(cudaver)s' +local_pytorch_version = '1.10.0' + +homepage = 'https://github.com/pyro-ppl/pyro' +description = """Pyro is a flexible, scalable deep probabilistic programming +library built on PyTorch.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('tqdm', '4.61.2'), + ('CUDA', '11.3.1', '', SYSTEM), + ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), +] + +use_pip = True + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('pyro-api', '0.1.2', { + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + 'modulename': 'pyroapi' + }), + (name, version, { + 'checksums': ['68e4ea30f219227dd88e55de2550d3f8c20a20adbdb67ad1e13b50868bb2ac0c'], + 'modulename': 'pyro', + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From beaed9282b95ecc76803630bfad3d7c46d1fce1c Mon Sep 17 00:00:00 2001 From: robogast Date: Tue, 1 Nov 2022 17:07:18 +0100 Subject: [PATCH 5324/9987] added comments to ASAP patch files, updated checksums accordingly --- easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch | 4 ++++ easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb | 6 +++--- easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch | 6 ++++++ easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch | 3 +++ 4 files changed, 16 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch index b4ca984d421..d836a0466d2 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch @@ -1,3 +1,7 @@ +# Author: Robert Jan Schlimbach (SURF) +# ASAP/2.1 forgets a few headers, in this case cmath +# Possibly fixed if https://github.com/computationalpathologygroup/ASAP/pull/241 gets merged + diff --git a/annotation/ImageScopeRepository.cpp b/annotation/ImageScopeRepository.cpp index 6916a58..c135cb3 100644 --- a/annotation/ImageScopeRepository.cpp diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb index 7dd82903d65..1a9c9bccc8b 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb @@ -19,9 +19,9 @@ patches = [ ] checksums = [ '7ba9f39d09bada808f760c5dc9ac0cda0d221fd1393a0a3f9decfd6b5e913b3c', # ASAP-2.1.tar.gz - 'dbdf26324a7521b4beaa7ec2c0585f0816619cd73b3125efd313eb48c4813a43', # ASAP-2.1-libjpeg.patch - 'f578bb3ec4cbce573d4b9acd695eb55446592f4ac00551656a06f113ba09a9a7', # ASAP-2.1-pugixml.patch - 'e33d83853e0bd51113a886d0793504ce0abfb15fdf88410a19287d46fafd33c4', # ASAP-2.1-cmath.patch + '78337d0250c567335f1a356f8761587000170b71a87b3e546b6b9330d3236b0f', # ASAP-2.1-libjpeg.patch + 'ab6104fb19515d0b042944bbe95fa67f55f47ef3bf18a91d337e0ca476c7385d', # ASAP-2.1-pugixml.patch + '15cf6bf2ab65ce37338ea571d80ced59b4e35cf82e434b2ccec7b534778f4a33', # ASAP-2.1-cmath.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch index eeab7c05144..b2030303872 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch @@ -1,3 +1,9 @@ +# Author: Robert Jan Schlimbach (SURF) +# ASAP/2.1 uses DCMKT jpeg sources directly by manually setting a PATH +# see https://github.com/computationalpathologygroup/ASAP/issues/32 +# we simply replace DCMTK jpeg with the default jpeglib header. +# Need to rename jpeg_mem_src to avoid a resulting name conflic. + diff --git a/multiresolutionimageinterface/VSIImage.cpp b/multiresolutionimageinterface/VSIImage.cpp index 509bb18..1763201 100644 --- a/multiresolutionimageinterface/VSIImage.cpp diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch index 2b4a652369f..751d179cb19 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch @@ -1,3 +1,6 @@ +# Author: Robert Jan Schlimbach (SURF) +# Patch to make ASAP/2.1 accept pugixml as non-header-only shared lib + diff --git a/annotation/CMakeLists.txt b/annotation/CMakeLists.txt index 114babe..2156cd3 100644 --- a/annotation/CMakeLists.txt From a0732b63add05a61e1f72e0aa5d57bf2af2c8e94 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 2 Nov 2022 15:53:44 +0100 Subject: [PATCH 5325/9987] adding easyconfigs: ESM-2-2.0.0-foss-2021a.eb --- .../e/ESM-2/ESM-2-2.0.0-foss-2021a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb new file mode 100644 index 00000000000..d33ee519c80 --- /dev/null +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'ESM-2' +version = '2.0.0' + +homepage = 'https://github.com/facebookresearch/esm' +description = """ESM-2 outperforms all tested single-sequence protein language models + across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate + accurate structure predictions end to end directly from the sequence of a protein.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/f/fair-esm'] +sources = ['fair-esm-%(version)s.tar.gz'] +checksums = ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'] + +dependencies = [ + ('Python', '3.9.5'), + ('PyTorch', '1.10.0'), +] + +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'esm'} + +sanity_check_commands = [ + "python -c 'import esm.pretrained'", +] + +moduleclass = 'bio' From d73fe2ec878074d495f94b2e8e7889ecb91cafa5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Nov 2022 00:34:10 +0100 Subject: [PATCH 5326/9987] build nodejs with external OpenSSL and ICU --- .../n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb | 32 +++++++++++++------ .../n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb | 25 ++++++++++----- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 25 ++++++++++----- 3 files changed, 57 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb index deaf600ec19..b75eb3495ef 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.0' # LTS on 2021-06-03 -local_libversion = '83' +_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -14,11 +14,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['http://%(name)s.org/dist/v%(version)s/'] sources = ['node-v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix-argument-list-too-long.patch'] +patches = [ + '%(name)s-%(version)s_fix-argument-list-too-long.patch', + '%(name)s-%(version)s_use_new_icu69_calls.patch', +] checksums = [ '6114e82d3256136dc85a509d835442fbdf2f8430dcd8bfa7c304097344d06fb7', # node-v14.17.0.tar.gz # nodejs-14.17.0_fix-argument-list-too-long.patch 'b0eac4b478a9268c8902ec701f99e1445eeba2a70927bfacdeb5ba243e668550', + # nodejs-14.17.0_use_new_icu69_calls.patch + '24fbc749d225b395184aa9c4c3880665026ced898474d77259c597f6b790e290', ] builddependencies = [ @@ -26,21 +31,30 @@ builddependencies = [ ('Python', '3.9.5'), ] +dependencies = [ + ('ICU', '69.1'), + ('OpenSSL', '1.1', '', True), +] + +# Use ICU and OpenSSL from EasyBuild +_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + _common_configopts, # Static build + '--shared %s' % _common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] +_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb index 569932aa452..e81302ffc40 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.6' # LTS on 2020-08-31 -local_libversion = '83' +_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -21,21 +21,30 @@ builddependencies = [ ('Python', '3.9.6', '-bare'), ] +dependencies = [ + ('ICU', '69.1'), + ('OpenSSL', '1.1', '', True), +] + +# Use ICU and OpenSSL from EasyBuild +_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + _common_configopts, # Static build + '--shared %s' % _common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] +_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index 3fe69b1af4c..73aeb628575 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '16.15.1' # LTS on 2022-06-12 -local_libversion = '93' +_libversion = '93' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -21,21 +21,30 @@ builddependencies = [ ('Python', '3.10.4', '-bare'), ] +dependencies = [ + ('ICU', '71.1'), + ('OpenSSL', '1.1', '', True), +] + +# Use ICU and OpenSSL from EasyBuild +_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + _common_configopts, # Static build + '--shared %s' % _common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] +_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } From 9a403292a75a1d9a16753c4ac9404a04da4446a7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Nov 2022 00:43:07 +0100 Subject: [PATCH 5327/9987] add patch to fix ICU v69 support in nodejs v14 --- .../nodejs-14.17.0_use_new_icu69_calls.patch | 92 +++++++++++++++++++ 1 file changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch new file mode 100644 index 00000000000..9b635d20f3d --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch @@ -0,0 +1,92 @@ +From 035c305ce7761f51328b45f1bd83e26aef267c9d Mon Sep 17 00:00:00 2001 +From: Frank Tang +Date: Thu, 15 Oct 2020 22:44:27 -0700 +Subject: [PATCH] [Intl] call new ListFormatter::createInstance + +The one we currently using is now marked as internal and to be removed +for 68. Migrating to the style which already avaiable in ICU 67-1. + +Bug: v8:11031 +Change-Id: I668382a2e1b8602ddca02bf231c5008a6c92bf2d +Reviewed-on: https://chromium-review.googlesource.com/c/v8/v8/+/2477751 +Reviewed-by: Jakob Kummerow +Commit-Queue: Frank Tang +Cr-Commit-Position: refs/heads/master@{#70638} +--- + +diff --git a/deps/v8/src/objects/js-list-format.cc b/deps/v8/src/objects/js-list-format.cc +index b17d38c..e48a387 100644 +--- a/deps/v8/src/objects/js-list-format.cc ++++ b/deps/v8/src/objects/js-list-format.cc +@@ -29,46 +29,27 @@ + namespace internal { + + namespace { +-const char* kStandard = "standard"; +-const char* kOr = "or"; +-const char* kUnit = "unit"; +-const char* kStandardShort = "standard-short"; +-const char* kOrShort = "or-short"; +-const char* kUnitShort = "unit-short"; +-const char* kStandardNarrow = "standard-narrow"; +-const char* kOrNarrow = "or-narrow"; +-const char* kUnitNarrow = "unit-narrow"; + +-const char* GetIcuStyleString(JSListFormat::Style style, +- JSListFormat::Type type) { ++UListFormatterWidth GetIcuWidth(JSListFormat::Style style) { ++ switch (style) { ++ case JSListFormat::Style::LONG: ++ return ULISTFMT_WIDTH_WIDE; ++ case JSListFormat::Style::SHORT: ++ return ULISTFMT_WIDTH_SHORT; ++ case JSListFormat::Style::NARROW: ++ return ULISTFMT_WIDTH_NARROW; ++ } ++ UNREACHABLE(); ++} ++ ++UListFormatterType GetIcuType(JSListFormat::Type type) { + switch (type) { + case JSListFormat::Type::CONJUNCTION: +- switch (style) { +- case JSListFormat::Style::LONG: +- return kStandard; +- case JSListFormat::Style::SHORT: +- return kStandardShort; +- case JSListFormat::Style::NARROW: +- return kStandardNarrow; +- } ++ return ULISTFMT_TYPE_AND; + case JSListFormat::Type::DISJUNCTION: +- switch (style) { +- case JSListFormat::Style::LONG: +- return kOr; +- case JSListFormat::Style::SHORT: +- return kOrShort; +- case JSListFormat::Style::NARROW: +- return kOrNarrow; +- } ++ return ULISTFMT_TYPE_OR; + case JSListFormat::Type::UNIT: +- switch (style) { +- case JSListFormat::Style::LONG: +- return kUnit; +- case JSListFormat::Style::SHORT: +- return kUnitShort; +- case JSListFormat::Style::NARROW: +- return kUnitNarrow; +- } ++ return ULISTFMT_TYPE_UNITS; + } + UNREACHABLE(); + } +@@ -143,7 +124,7 @@ + icu::Locale icu_locale = r.icu_locale; + UErrorCode status = U_ZERO_ERROR; + icu::ListFormatter* formatter = icu::ListFormatter::createInstance( +- icu_locale, GetIcuStyleString(style_enum, type_enum), status); ++ icu_locale, GetIcuType(type_enum), GetIcuWidth(style_enum), status); + if (U_FAILURE(status) || formatter == nullptr) { + delete formatter; + THROW_NEW_ERROR(isolate, NewRangeError(MessageTemplate::kIcuError), From d2457c0740f4846fa8f8224974ed8a2ab3712e04 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Nov 2022 01:02:47 +0100 Subject: [PATCH 5328/9987] fix dependency on OpenSSL to use SYSTEM template --- easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb index b75eb3495ef..bf1db1aa052 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb @@ -33,7 +33,7 @@ builddependencies = [ dependencies = [ ('ICU', '69.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Use ICU and OpenSSL from EasyBuild diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb index e81302ffc40..a6fe9b552ba 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('ICU', '69.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Use ICU and OpenSSL from EasyBuild diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index 73aeb628575..bcd9c8dded1 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('ICU', '71.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Use ICU and OpenSSL from EasyBuild From 8da47cb621791fe7fce2c92e31742c0306ee1850 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Thu, 3 Nov 2022 08:28:15 +0100 Subject: [PATCH 5329/9987] added download_dep_fail --- easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb index d33ee519c80..e3ea302ffec 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb @@ -20,6 +20,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True options = {'modulename': 'esm'} From 0273721033e985b841678403fb7827b93ba087e9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 3 Nov 2022 08:39:24 +0100 Subject: [PATCH 5330/9987] adding easyconfigs: ctffind-4.1.14-foss-2022a.eb --- .../c/ctffind/ctffind-4.1.14-foss-2022a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb new file mode 100644 index 00000000000..59e562d1e6b --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University +# +# Author: Thomas Hoffmann, EMBL Heidelberg + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('GSL', '2.7',), + ('wxWidgets', '3.2.1'), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From c92ba4b925937d47cbd836691b10c67e665dcd88 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jurij=20Pe=C4=8Dar?= Date: Thu, 3 Nov 2022 11:30:49 +0100 Subject: [PATCH 5331/9987] adding easyconfigs: Nextflow-22.10.1.eb --- .../n/Nextflow/Nextflow-22.10.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb new file mode 100644 index 00000000000..896a6c321e3 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb @@ -0,0 +1,33 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '22.10.1' + +homepage = 'https://www.%(namelower)s.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-all'] +checksums = ['c5edc9fc81d9c6eb4f628505f14f8bb4fe044d4fc7d9ef60654ba0d73abf5a80'] + +dependencies = [('Java', '11', '', True)] + +install_cmd = "[ -d %(builddir)s/bin ] || mkdir -p %(installdir)s/bin &&" +install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" +install_cmd += "cd %(installdir)s/bin && ln -s %(namelower)s-%(version)s-all %(namelower)s &&" +install_cmd += "chmod +x %(installdir)s/bin/%(namelower)s-%(version)s-all" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-%(version)s-all', 'bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' From 88a15c893eb2a0f1767a8255c201dba3c630e450 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 3 Nov 2022 12:07:54 +0100 Subject: [PATCH 5332/9987] adding easyconfigs: DRAGMAP-1.3.0-foss-2021b.eb --- .../d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb new file mode 100644 index 00000000000..23c3faed318 --- /dev/null +++ b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'DRAGMAP' +version = '1.3.0' + +homepage = 'https://github.com/Illumina/DRAGMAP' +description = 'Dragmap is the Dragen mapper/aligner Open Source Software.' + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/Illumina/DRAGMAP/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['baf546c2f53b13e2bce4c937201e38459f3ce2f1069722ca670d8726a4bae224'] + +skipsteps = ['configure'] +prebuildopts = 'sed -i "s|-msse4.2 -mavx2|$CXXFLAGS|g" config.mk &&' +buildopts = 'CC="$CC" CXX="$CXX"' +preinstallopts = 'mkdir %(installdir)s/bin &&' +installopts = 'DESTDIR=%(installdir)s' + +dependencies = { + ('Boost', '1.77.0'), + ('googletest', '1.11.0'), +} + +sanity_check_paths = { + 'files': ['bin/dragen-os'], + 'dirs': [] +} + +sanity_check_commands = ['dragen-os --help'] + +moduleclass = 'bio' From fb6f9fc133fc94006fca6494e9a68f2f99d09e78 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 3 Nov 2022 11:12:18 +0000 Subject: [PATCH 5333/9987] adding easyconfigs: bsddb3-6.2.9-GCCcore-11.3.0.eb --- .../b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8a366485ad0 --- /dev/null +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'bsddb3' +version = '6.2.9' + +homepage = 'https://pypi.org/project/bsddb3/' +description = """bsddb3 is a nearly complete Python binding of the +Oracle/Sleepycat C API for the Database Environment, Database, Cursor, +Log Cursor, Sequence and Transaction objects.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +components = [ + ('DB', '5.3.28', { + 'source_urls': ['https://github.com/berkeleydb/libdb/releases/download/v%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['e0a992d740709892e81f9d93f06daf305cf73fb81b545afe72478043172c3628'], + 'start_dir': '%(namelower)s-%(version)s', + }), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'preinstallopts': "unset LIBS && BERKELEYDB_DIR=%(installdir)s/ ", + 'checksums': ['70d05ec8dc568f42e70fc919a442e0daadc2a905a1cfb7ca77f549d49d6e7801'], + }), +] + +sanity_check_paths = { + 'files': ['bin/db_archive', 'include/db.h', 'lib/libdb.a', + 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'data' From 67d85f9f722bc9647453bb01ba96719498c7a932 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 16:04:49 +0200 Subject: [PATCH 5334/9987] adding easyconfigs: cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb --- .../cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..b741f7e44e0 --- /dev/null +++ b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,58 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 +easyblock = 'PythonBundle' + +name = 'cryoCARE' +version = '0.2.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/juglab/cryoCARE_pip' +description = """This package is a memory efficient implementation of cryoCARE. + +This setup trains a denoising U-Net for tomographic reconstruction according to + the Noise2Noise training paradigm. Therefore the user has to provide two +tomograms of the same sample. The simplest way to achieve this is with direct- +detector movie-frames. + +You can use Warp to generate two reconstructed tomograms based on the even/odd +frames. Alternatively, the movie-frames can be split in two halves (e.g. with +MotionCor2 -SplitSum 1 or with IMOD alignframes -debug 10000) from which two +identical, up to random noise, tomograms can be reconstructed. + +These two (even and odd) tomograms can be used as input to this cryoCARE +implementation.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', True), + ('SciPy-bundle', '2021.05'), + ('TensorFlow', '2.6.0', versionsuffix), + ('mrcfile', '1.3.0'), + ('tqdm', '4.61.2'), + ('matplotlib', '3.4.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tifffile', '2022.10.10', { + 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], + }), + ('csbdeep', '0.7.2', { + 'checksums': ['8a000eb71d04aa753f52ffe81a34c0a30a06ee986d20b9986d76272253e2fd53'], + }), + (name, version, { + 'checksums': ['b66989acb6eadf771de08a46e4860d041113527205eebb2cf5d13ae3dc9cb43b'], + }), +] + +sanity_check_commands = [ + 'cryoCARE_extract_train_data.py --help', + 'cryoCARE_train.py --help', + 'cryoCARE_predict.py --help', +] + +moduleclass = 'vis' From 053b93f8ca8694203aa7c111e8a746696fa43c3d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 16:11:08 +0200 Subject: [PATCH 5335/9987] adding easyconfigs: n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb --- .../n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..7a91bbffaf4 --- /dev/null +++ b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,61 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 +easyblock = 'PythonBundle' + +name = 'n2v' +version = '0.3.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/juglab/cryoCARE_pip' +description = """ +Noise2Void - Learning Denoising from Single Noisy Images +The field of image denoising is currently dominated by discriminative deep +learning methods that are trained on pairs of noisy input and clean target +images. Recently it has been shown that such methods can also be trained without +clean targets. Instead, independent pairs of noisy images can be used, in an +approach known as NOISE2NOISE (N2N). Here, we introduce NOISE2VOID (N2V), a +training scheme that takes this idea one step further. It does not require noisy +image pairs, nor clean target images. Consequently, N2V allows us to train +directly on the body of data to be denoised and can therefore be applied when +other methods cannot. Especially interesting is the application to biomedical +image data, where the acquisition of training targets, clean or noisy, is +frequently not possible. We compare the performance of N2V to approaches that +have either clean target images and/or noisy image pairs available. Intuitively, +N2V cannot be expected to outperform methods that have more information +available during training. Still, we observe that the denoising performance of +NOISE2VOID drops in moderation and compares favorably to training-free denoising +methods.""" +toolchain = {'name': 'foss', 'version': '2021a'} + + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', True), + ('TensorFlow', '2.6.0', versionsuffix), + ('mrcfile', '1.3.0'), + ('tqdm', '4.61.2'), + ('matplotlib', '3.4.2'), + ('ruamel.yaml', '0.17.21'), + ('imagecodecs', '2022.9.26'), + ('JupyterLab', '3.0.16'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tifffile', '2022.10.10', { + 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], + }), + ('csbdeep', '0.7.2', { + 'checksums': ['8a000eb71d04aa753f52ffe81a34c0a30a06ee986d20b9986d76272253e2fd53'], + }), + (name, version, { + 'checksums': ['8662aa5e903e170a1c9769882da241d669b6e7efd8b164b68723c675539ec06f'], + }), +] + +sanity_check_commands = [ + '%s --help' % x for x in ['care_predict', 'trainN2V.py', 'care_predict'] +] + +moduleclass = 'bio' From 606d0f82fb5779f1b553693e80a525a8f776d338 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 3 Nov 2022 15:25:34 +0100 Subject: [PATCH 5336/9987] Update cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb --- .../c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb index b741f7e44e0..81b96e34eb7 100644 --- a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb @@ -26,7 +26,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('TensorFlow', '2.6.0', versionsuffix), ('mrcfile', '1.3.0'), From f5063794a4ff1dab9dda71a411593e0f825abfd9 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 3 Nov 2022 15:27:05 +0100 Subject: [PATCH 5337/9987] Update n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb --- easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb index 7a91bbffaf4..a6c09399b71 100644 --- a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb @@ -29,7 +29,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('TensorFlow', '2.6.0', versionsuffix), ('mrcfile', '1.3.0'), ('tqdm', '4.61.2'), From d81b3437d6dc0a92a91c540fcaab2d9e9c5cb279 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:15:40 +0200 Subject: [PATCH 5338/9987] adding easyconfigs: imagecodecs-2022.9.26-foss-2021a.eb --- .../imagecodecs-2022.9.26-foss-2021a.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb new file mode 100644 index 00000000000..55bf95340ff --- /dev/null +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb @@ -0,0 +1,72 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'PythonBundle' + +name = 'imagecodecs' +version = '2022.9.26' + +homepage = 'https://github.com/cgohlke/imagecodecs' +description = """Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, +compression, and decompression functions for use in the tifffile, czifile, zarr, and other +scientific image input/output modules.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +local_openjpeg_maj_min = '2.4' +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # required for numpy + ('matplotlib', '3.4.2'), + ('Brotli', '1.0.9'), + ('bzip2', '1.0.8'), + ('Blosc', '1.21.0'), + ('Blosc2', '2.0.4'), + ('CFITSIO', '3.49'), + ('CharLS', '2.3.4'), + ('giflib', '5.2.1'), + ('jxrlib', '1.1'), + ('LittleCMS', '2.12'), + ('LERC', '3.0'), + ('libaec', '1.0.6'), + ('libavif', '0.11.1'), + ('libdeflate', '1.8'), + ('libjpeg-turbo', '2.0.6'), + ('libjxl', '0.5'), + ('LibLZF', '3.6'), + ('libpng', '1.6.37'), + ('XZ', '5.2.5'), + ('LibTIFF', '4.2.0'), + ('libwebp', '1.2.0'), + ('lz4', '1.9.3'), + ('OpenJPEG', local_openjpeg_maj_min + '.0'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), + ('zlib-ng', '2.0.6'), + ('Zopfli', '1.0.3'), + ('zfp', '1.0.0'), + ('zstd', '1.4.9'), + ('Brunsli', '0.1'), + ('HDF5', '1.12.1'), + ('h5py', '3.2.1'), + ('libheif', '1.12.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bitshuffle', '0.3.5', { + 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['c3f4461d8013e3d9db0d58defec77b143164652de505a1fba3df088eaa19be2f'], + }), + (name, version, { + 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", + 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.4/:$CPATH && ", + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['04d5757d8fd7819844b0f8d9eed05025dca4962f280d0010b42c7c9c993fe371'], + }), +] + +moduleclass = 'lib' From 5ee258f18cb9d63a4c80caa2564e33f4403711c4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:33:37 +0200 Subject: [PATCH 5339/9987] adding easyconfigs: Blosc2-2.0.4-GCCcore-10.3.0.eb --- .../b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..7736eae4911 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.0.4' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['90c78edcc262759dd16d243141513310624bb4fda3d98ac34dcfb78255e151c1'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 341cb16b6e28ac08e6907fc122a61c5535e5b2af Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:36:30 +0200 Subject: [PATCH 5340/9987] adding easyconfigs: CFITSIO-3.49-GCCcore-10.3.0.eb --- .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..1b080d80935 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.49' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-3.48_install_test_data.patch'] +checksums = [ + '5b65a20d5c53494ec8f638267fca4a629836b7ac8dd0ef0266834eab270ed4b3', # cfitsio-3.49.tar.gz + 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch +] + +# curl for HTTPs support +dependencies = [('cURL', '7.76.0')] + +builddependencies = [('binutils', '2.36.1')] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = '&& make shared && make testprog' + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + ('cd %(installdir)s/share && testprog'), +] + +moduleclass = 'lib' From e34a43b98c10d409280e46bb0ac8151e9bcb5c8c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:39:12 +0200 Subject: [PATCH 5341/9987] adding easyconfigs: jxrlib-1.1-GCCcore-10.3.0.eb --- .../j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6257a6cbb8b --- /dev/null +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +# Update: Thomas Hoffmann (EMBL) +## + +easyblock = 'CMakeMake' + +name = 'jxrlib' +version = '1.1' + +homepage = 'https://github.com/4creators/jxrlib' +description = """Open source implementation of jpegxr""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] +sources = ['%(name)s_%(version)s.orig.tar.gz'] +patches = [('jxrlib-%(version)s_cmake.patch', 1)] +checksums = [ + 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303', # jxrlib_1.1.orig.tar.gz + 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74', # jxrlib-1.1_cmake.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] + +modextrapaths = {'CPATH': 'include/jxrlib'} + +moduleclass = 'lib' From 133d1c682e91c11e2605e369b85a4fd5620a2e93 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:40:26 +0200 Subject: [PATCH 5342/9987] adding easyconfigs: LERC-3.0-GCCcore-10.3.0.eb --- .../l/LERC/LERC-3.0-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b1976a9c3c2 --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'LERC' +version = '3.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/Esri/lerc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8c0148f5c22d823eff7b2c999b0781f8095e49a7d3195f13c68c5541dd5740a1'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +postinstallcmds = [ + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/test.c", +] + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cd %(builddir)s && g++ %(installdir)s/test.c -o lerctest -lLerc && ./lerctest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 8745875102720aad4cfb7057f4d6c948f013bd65 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:41:40 +0200 Subject: [PATCH 5343/9987] adding easyconfigs: libaec-1.0.6-GCCcore-10.3.0.eb --- .../l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..7ed6541d683 --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.0.6' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/aec', 'include/libaec.h', 'include/szlib.h', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["aec --help"] + +moduleclass = 'lib' From 558ec0d37917214b025769dc27d7b9f58d21c91d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:42:44 +0200 Subject: [PATCH 5344/9987] adding easyconfigs: libavif-0.11.1-foss-2021a.eb --- .../l/libavif/libavif-0.11.1-foss-2021a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb new file mode 100644 index 00000000000..2f4ed93c1c9 --- /dev/null +++ b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'libavif' +version = '0.11.1' + +homepage = 'https://github.com/AOMediaCodec/libavif' +description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format, +as described here: https://aomediacodec.github.io/av1-avif/ +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0eb49965562a0e5e5de58389650d434cff32af84c34185b6c9b7b2fccae06d4e'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('NASM', '2.15.05'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('Rust', '1.52.1'), +] + +sanity_check_paths = { + 'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'], + 'dirs': [], +} + +moduleclass = 'tools' From a24bdbaeacba00b74f4fde6ee3551355c153b925 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:46:49 +0200 Subject: [PATCH 5345/9987] adding easyconfigs: LibLZF-3.6-GCCcore-10.3.0.eb --- .../l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..63540846348 --- /dev/null +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'ConfigureMake' + +name = 'LibLZF' +version = '3.6' + +homepage = 'http://oldhome.schmorp.de/marc/liblzf.html' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] +sources = ['liblzf-%(version)s.tar.gz'] +checksums = ['9c5de01f7b9ccae40c3f619d26a7abec9986c06c36d260c179cedd04b89fb46a'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +sanity_check_commands = ['lzf -h'] + +sanity_check_paths = { + 'files': ['bin/lzf', 'lib/liblzf.a'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' From 06597b301e85a56bda66dce126cb5e90bb3a4909 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:47:53 +0200 Subject: [PATCH 5346/9987] adding easyconfigs: zlib-ng-2.0.6-GCCcore-10.3.0.eb --- .../z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..529355b3749 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'zlib-ng' +version = '2.0.6' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8258b75a72303b661a238047cb348203d88d9dddf85d480ed885f375916fcab6'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +configopts = ' -DZLIB_ENABLE_TESTS=True ' + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From 3e4cb429acf96e8bee8dff44e638024f2cd727f0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:49:01 +0200 Subject: [PATCH 5347/9987] adding easyconfigs: Zopfli-1.0.3-GCCcore-10.3.0.eb --- .../z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d08922dc6c9 --- /dev/null +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Zopfli' +version = '1.0.3' + +homepage = 'https://github.com/google/zopfli' +description = """Zopfli Compression Algorithm is a compression library programmed in C to perform +very good, but slow, deflate or zlib compression.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF', +] + +sanity_check_paths = { + 'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["zopfli --help"] + +moduleclass = 'tools' From 1ec9bfdd271c08ac548e4c04e30cc65abc656207 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:50:02 +0200 Subject: [PATCH 5348/9987] adding easyconfigs: zfp-1.0.0-GCCcore-10.3.0.eb --- .../z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..3901a6550a2 --- /dev/null +++ b/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'MakeCp' + +name = 'zfp' +version = '1.0.0' + +homepage = 'https://github.com/LLNL/zfp' +description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. +zfp provides compressed-array classes that support high throughput read and write random access to individual array +elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications +that read and write large data sets to and from disk.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/zfp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['fe13b03141ee9b571692aed42ff76cf37c9dcda40f9a43a808870dca3558a57c'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && " +buildopts = 'ZFP_WITH_OPENMP=1' + +runtest = 'test' + +files_to_copy = ['bin', 'include', 'lib'] + +sanity_check_paths = { + 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], + 'dirs': ['include/zfp'], +} + +sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] + +moduleclass = 'lib' From 9fe9959d6f35c302b56e8636f829179890846879 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:51:37 +0200 Subject: [PATCH 5349/9987] adding easyconfigs: Brunsli-0.1-GCCcore-10.3.0.eb --- .../b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..20cd4b20aef --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '0.12.2'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib*/", + "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' From 21102edbd215c924de05f0e9fde3c45ea1049084 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:52:42 +0200 Subject: [PATCH 5350/9987] adding easyconfigs: libheif-1.12.0-GCC-10.3.0.eb --- .../l/libheif/libheif-1.12.0-GCC-10.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..bb5cb6bf57c --- /dev/null +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'libheif' +version = '1.12.0' + +homepage = 'https://github.com/strukturag/libheif' +description = "libheif is an HEIF and AVIF file format decoder and encoder" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('libde265', '1.0.8'), + ('x265', '3.5'), + ('Gdk-Pixbuf', '2.42.6'), +] + +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +sanity_check_paths = { + 'files': ['bin/heif-info', 'lib/libheif.a', 'lib/libheif.%s' % SHLIB_EXT, 'lib/pkgconfig/libheif.pc'], + 'dirs': ['include/libheif'], +} + +sanity_check_commands = ["heif-info --help"] + +moduleclass = 'tools' From f1d51b596f316a30aad8436d5d0715de30c16f56 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 3 Nov 2022 17:51:18 +0100 Subject: [PATCH 5351/9987] Rename package name --- .../Chemaxon-Marvin-21.14.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/{Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb => Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb} (99%) diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb similarity index 99% rename from easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb rename to easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb index adadbfe31a0..69f794a1422 100644 --- a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb +++ b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb @@ -10,7 +10,7 @@ # Summary and License fields must be present in package: (main package) easyblock = 'Binary' -name = 'Chemaxon_Marvin' +name = 'Chemaxon-Marvin' version = '21.14' homepage = 'https://chemaxon.com/products/marvin' From 1da56a693b2a047860ea239717bb1698d7a6aff3 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 19:11:22 +0200 Subject: [PATCH 5352/9987] adding easyconfigs: libde265-1.0.8-GCC-10.3.0.eb --- .../l/libde265/libde265-1.0.8-GCC-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb new file mode 100644 index 00000000000..647d345e73e --- /dev/null +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'libde265' +version = '1.0.8' + +homepage = 'https://github.com/strukturag/libde265' +description = "libde265 is an open source implementation of the h.265 video codec" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['24c791dd334fa521762320ff54f0febfd3c09fc978880a8c5fbc40a88f21d905'] + +builddependencies = [('CMake', '3.20.1')] + +sanity_check_paths = { + 'files': ['bin/dec265', 'bin/enc265', 'lib/liblibde265.%s' % SHLIB_EXT], + 'dirs': ['include/libde265', 'lib/cmake/libde265'], +} + +sanity_check_commands = [ + "dec265 --help", + "enc265 --help", +] + +moduleclass = 'tools' From afd61fb09cc2d8ed5970973f8b96f842e415f025 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jurij=20Pe=C4=8Dar?= Date: Thu, 3 Nov 2022 20:21:06 +0100 Subject: [PATCH 5353/9987] shortened Java dependency and removed test -d --- easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb index 896a6c321e3..cb17ec4556a 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb @@ -13,9 +13,9 @@ source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/releases/downl sources = ['%(namelower)s-%(version)s-all'] checksums = ['c5edc9fc81d9c6eb4f628505f14f8bb4fe044d4fc7d9ef60654ba0d73abf5a80'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11')] -install_cmd = "[ -d %(builddir)s/bin ] || mkdir -p %(installdir)s/bin &&" +install_cmd = "mkdir -p %(installdir)s/bin &&" install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" install_cmd += "cd %(installdir)s/bin && ln -s %(namelower)s-%(version)s-all %(namelower)s &&" install_cmd += "chmod +x %(installdir)s/bin/%(namelower)s-%(version)s-all" From db3c378611f30e7b425ea94e91f13d8f62b69c6c Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 3 Nov 2022 20:56:45 +0000 Subject: [PATCH 5354/9987] adding easyconfigs: KITE-1.1-gompi-2022a.eb --- .../k/KITE/KITE-1.1-gompi-2022a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb new file mode 100644 index 00000000000..d1f4c2ad3a1 --- /dev/null +++ b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb @@ -0,0 +1,38 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'KITE' +version = '1.1' + +homepage = 'https://github.com/quantum-kite/kite' +description = """KITE is an open-source Python/C++ software suite for efficient real-space tight-binding (TB) +simulations of electronic structure and bulk quantum transport properties of disordered systems scalable to +multi billions of atomic orbitals.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/quantum-kite/kite/archive/'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + 'a480fe46f2220ab6c2d6b9914e0673580121de703523dc22658fe50dc676e47e', # 1.1.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Eigen', '3.4.0'), + ('HDF5', '1.12.2'), +] + +sanity_check_paths = { + 'files': ['bin/KITEx'], + 'dirs': [], +} + +moduleclass = 'chem' From 3efeea3c0dc2ebb94dd4b36bbc782b97b232c8fe Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 4 Nov 2022 10:55:52 +0100 Subject: [PATCH 5355/9987] Move to toolchain foss-2021a + Report issue with cwlformat upstream --- ...ore-10.3.0.eb => cwltool-3.1.20221018083734-foss-2021a.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/cwltool/{cwltool-3.1.20221018083734-GCCcore-10.3.0.eb => cwltool-3.1.20221018083734-foss-2021a.eb} (96%) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb similarity index 96% rename from easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb index b40b9c1e883..15b2225906c 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb @@ -14,7 +14,7 @@ version = '3.1.20221018083734' homepage = 'https://github.com/common-workflow-language/cwltool' description = """Common workflow language (CWL) reference implementation.""" -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ ('binutils', '2.36.1'), @@ -35,7 +35,7 @@ dependencies = [ ('pydot', '1.4.2'), ('lxml', '4.6.3'), ('ruamel.yaml', '0.17.21'), - ('networkx', '2.6.3', '', ('foss', '2021a')), + ('networkx', '2.6.3'), ] use_pip = True From 1d8333aba2e19716d792229dd353060d401c30a6 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 14:44:45 +0100 Subject: [PATCH 5356/9987] adding easyconfigs: CUDA-11.8.0.eb, cuDNN-8.6.0.163-CUDA-11.8.0.eb, NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb, UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb, GDRCopy-2.3-GCCcore-12.2.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb | 17 ++++++ .../c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb | 33 ++++++++++++ .../g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ .../NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb | 24 +++++++++ ...-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb | 42 +++++++++++++++ 5 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb new file mode 100644 index 00000000000..e0ea509fe8b --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb @@ -0,0 +1,17 @@ +name = 'CUDA' +version = '11.8.0' +local_nv_version = '520.61.05' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = ['9223c4af3aebe4a7bbed9abd9b163b03a1b34b855fbc2b4a0d1b706ac09a5a16'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb new file mode 100644 index 00000000000..23f76bb3dca --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb @@ -0,0 +1,33 @@ +name = 'cuDNN' +version = '8.6.0.163' +versionsuffix = '-CUDA-%(cudaver)s' +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN is tied to specific to CUDA versions, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +local_cuda_major = '11' # Is there a way to make this parametric? '%(cudaver)'.split(...) obviously doesn't work... + +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/%%(cudashortver)s/' % local_short_ver # noqa: E501 +] +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = ['bbc396df47294c657edc09c600674d608cb1bfc80b82dcf4547060c21711159e'] + +dependencies = [('CUDA', '11.8.0')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0fb6d9b4864 --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.3' + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib prefix=%(installdir)s" + +installopts = 'prefix=%(installdir)s' + +github_account = 'NVIDIA' +# This easyconfig only installs the library of GDRCopy. Please keep in mind +# that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] +install_cmd = "make lib_install" + +sanity_check_paths = { + 'files': ['lib/libgdrapi.so'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb new file mode 100644 index 00000000000..eaacb222314 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb @@ -0,0 +1,24 @@ +name = 'NCCL' +version = '2.15.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['f4ac3c74d469c9cd718f82e1477759785db9b9f8cc9d9ecc103485805b8394a3'] + +builddependencies = [('binutils', '2.39')] +buildopts = ['NVCC_APPEND_FLAGS="-allow-unsupported-compiler"'] # CUDA 11.8 doesn't officially support GCC 12.2 yet... + +dependencies = [ + ('CUDA', '11.8.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', versionsuffix), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb new file mode 100644 index 00000000000..e2d761a00ca --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb @@ -0,0 +1,42 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.13.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['ucx-%(version)s.tar.gz'] +patches = [ + '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', +] +checksums = [ + {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('UCX', version), + ('CUDA', '11.8.0', '', SYSTEM), + ('GDRCopy', '2.3'), +] + +moduleclass = 'lib' From faf4b17772355e79fa62b0eb7a94c5d5403199ca Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 4 Nov 2022 15:30:30 +0100 Subject: [PATCH 5357/9987] Move to networkx 2.5.1 to satisfy multi-variant deps for networkx in foss-2021a --- .../c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb index 15b2225906c..170d12542ff 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb @@ -35,7 +35,7 @@ dependencies = [ ('pydot', '1.4.2'), ('lxml', '4.6.3'), ('ruamel.yaml', '0.17.21'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ] use_pip = True From ff022b85236ce9d0ed96a0600810d7bcc600b87f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 4 Nov 2022 17:05:23 +0100 Subject: [PATCH 5358/9987] set JUPYTER_CONFIG_PATH in IPython --- .../easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb | 5 ++++- .../easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb | 5 ++++- .../easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb index 0ecf20cc339..a6f424ca75b 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb @@ -142,7 +142,10 @@ exts_list = [ }), ] -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} sanity_check_paths = { 'files': ['bin/ipython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb index b8a2d71f584..ab9abddc1bf 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb @@ -142,7 +142,10 @@ exts_list = [ }), ] -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} sanity_check_paths = { 'files': ['bin/ipython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb index 4697bcfaf93..57bf257cf0c 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb @@ -160,7 +160,10 @@ exts_list = [ }), ] -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} sanity_check_paths = { 'files': ['bin/ipython'], From 620492f519a44217ea0461e28baee7f421e53d64 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 17:14:30 +0100 Subject: [PATCH 5359/9987] removed NCCL, UCX-CUDA, GDCopy --- .../g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb | 52 ------------------- .../NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb | 24 --------- ...-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb | 42 --------------- 3 files changed, 118 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb delete mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb delete mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb deleted file mode 100644 index 0fb6d9b4864..00000000000 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDRCopy' -version = '2.3' - -homepage = 'https://github.com/NVIDIA/gdrcopy' -description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -toolchainopts = {'pic': True} - -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] - -builddependencies = [ - ('binutils', '2.39'), - ('Autotools', '20220317'), - ('pkgconf', '1.9.3'), -] - -prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found -buildopts = "config lib prefix=%(installdir)s" - -installopts = 'prefix=%(installdir)s' - -github_account = 'NVIDIA' -# This easyconfig only installs the library of GDRCopy. Please keep in mind -# that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. - -skipsteps = ['configure'] -install_cmd = "make lib_install" - -sanity_check_paths = { - 'files': ['lib/libgdrapi.so'], - 'dirs': ['include'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb deleted file mode 100644 index eaacb222314..00000000000 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'NCCL' -version = '2.15.5' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://developer.nvidia.com/nccl' -description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective -communication primitives that are performance optimized for NVIDIA GPUs.""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -github_account = 'NVIDIA' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s-1.tar.gz'] -checksums = ['f4ac3c74d469c9cd718f82e1477759785db9b9f8cc9d9ecc103485805b8394a3'] - -builddependencies = [('binutils', '2.39')] -buildopts = ['NVCC_APPEND_FLAGS="-allow-unsupported-compiler"'] # CUDA 11.8 doesn't officially support GCC 12.2 yet... - -dependencies = [ - ('CUDA', '11.8.0', '', SYSTEM), - ('UCX-CUDA', '1.13.1', versionsuffix), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb deleted file mode 100644 index e2d761a00ca..00000000000 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'EB_UCX_Plugins' - -name = 'UCX-CUDA' -version = '1.13.1' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'http://www.openucx.org/' -description = """Unified Communication X -An open-source production grade communication framework for data centric -and high-performance applications - -This module adds the UCX CUDA support. -""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] -patches = [ - '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', -] -checksums = [ - {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, - {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': - 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3'}, -] - -builddependencies = [ - ('binutils', '2.39'), - ('Autotools', '20220317'), - ('pkgconf', '1.9.3'), -] - -dependencies = [ - ('zlib', '1.2.12'), - ('UCX', version), - ('CUDA', '11.8.0', '', SYSTEM), - ('GDRCopy', '2.3'), -] - -moduleclass = 'lib' From 5d266b29427ef54b284728e5910e7452828143bb Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 18:24:15 +0100 Subject: [PATCH 5360/9987] added ppc64le & sbsa checksums --- .../easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb index 23f76bb3dca..bc2f6803e9b 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb @@ -16,7 +16,14 @@ source_urls = [ 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/%%(cudashortver)s/' % local_short_ver # noqa: E501 ] sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] -checksums = ['bbc396df47294c657edc09c600674d608cb1bfc80b82dcf4547060c21711159e'] +checksums = [{ + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'bbc396df47294c657edc09c600674d608cb1bfc80b82dcf4547060c21711159e', + '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'c8a25e7e3df1bb9c4e18a4f24dd5f25cfd4bbe8b7054e34008e53b2be4f58a80', + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'a0202278d3cbd4f3adc3f7816bff6071621cb042b0903698b477acac8928ac06', +}] dependencies = [('CUDA', '11.8.0')] From 1a68db0bf0aba9ac35ef256bdce1d4970dad0c46 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 18:51:21 +0100 Subject: [PATCH 5361/9987] added checksums for CUDA ppc and sbsa --- easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb index e0ea509fe8b..4fc4d6173ce 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb @@ -12,6 +12,13 @@ toolchain = SYSTEM source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] -checksums = ['9223c4af3aebe4a7bbed9abd9b163b03a1b34b855fbc2b4a0d1b706ac09a5a16'] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '9223c4af3aebe4a7bbed9abd9b163b03a1b34b855fbc2b4a0d1b706ac09a5a16', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'f917fb7617033223938543ad3ae923190d99507acc08a399d752a2868e87349d', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'e6e9a8d31163c9776b5e313fd7590877c5684e1ecddee741154f95704d4ed27c' +}] moduleclass = 'system' From 96505b3dd71113eb316457251c6c5fa9d5bab799 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 5 Nov 2022 11:29:41 +0100 Subject: [PATCH 5362/9987] populate JUPYTER_PATH and JUPYTER_CONFIG_PATH in JupyterLab --- .../j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb | 12 +++++++++--- .../j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb | 12 +++++++++--- .../j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb | 12 +++++++++--- 3 files changed, 27 insertions(+), 9 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb mode change 100755 => 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb mode change 100755 => 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb old mode 100755 new mode 100644 index adc0ec67695..83e3efa4e84 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb @@ -48,14 +48,20 @@ exts_list = [ ('jupyterlab_server', '2.6.0', { 'checksums': ['f300adf6bb0a952bebe9c807a3b2a345d62da39b476b4f69ea0dc6b5f3f6b97d'], }), - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + ('jupyterlab', version, { 'checksums': ['7ad4fbe1f6d38255869410fd151a8b15692a663ca97c0a8146b3f5c40e275c23'], }), ] sanity_check_commands = ["jupyter lab --help"] -modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb old mode 100755 new mode 100644 index 97db9ab8ef0..d4ac5f149b9 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb @@ -48,14 +48,20 @@ exts_list = [ ('jupyterlab_server', '2.7.0', { 'checksums': ['31457ef564febc42043bc539356c804f6f9144f602e2852150bf0820ed6d7e18'], }), - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + ('jupyterlab', version, { 'checksums': ['6d2ada6a333861f33a1b555d3cb7b07aa9d1ab80f07997b3d0c43878a98c1174'], }), ] sanity_check_commands = ["jupyter lab --help"] -modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb old mode 100755 new mode 100644 index c48fd54eda3..303ede67642 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb @@ -48,14 +48,20 @@ exts_list = [ ('jupyterlab_server', '2.10.3', { 'checksums': ['3fb84a5813d6d836ceda773fb2d4e9ef3c7944dbc1b45a8d59d98641a80de80a'], }), - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + ('jupyterlab', version, { 'checksums': ['5e4e99868c4f385372686767781408acbb9004b690b198b45597ba869802334b'], }), ] sanity_check_commands = ["jupyter lab --help"] -modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} moduleclass = 'tools' From a8bcc6962a63d55b527445fd11bd1c2fb5676907 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 11:06:14 +0100 Subject: [PATCH 5363/9987] adding easyconfigs: JupyterLab-3.5.0-GCCcore-11.3.0.eb, jupyter-server-1.21.0-GCCcore-11.3.0.eb --- .../JupyterLab-3.5.0-GCCcore-11.3.0.eb | 56 +++++++++++++++++++ .../jupyter-server-1.21.0-GCCcore-11.3.0.eb | 41 ++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb create mode 100755 easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1ce74b3d8a8 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '3.5.0' + +homepage = "https://jupyter.org/" +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('jupyter-server', '1.21.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('json5', '0.9.10', { + 'checksums': ['ad9f048c5b5a4c3802524474ce40a622fae789860a86f10cc4f7e5f9cf9b46ab'], + }), + ('notebook_shim', '0.1.0', { + 'checksums': ['7897e47a36d92248925a2143e3596f19c60597708f7bef50d81fcd31d7263e85'], + }), + ('nbclassic', '0.4.8', { + 'checksums': ['c74d8a500f8e058d46b576a41e5bc640711e1032cf7541dde5f73ea49497e283'], + }), + ('jupyterlab_server', '2.13.0', { + 'checksums': ['2040298a133458aa22f287a877d6bb91ff973f6298d562264f9f7b75e92a5ace'], + }), + ('jupyterlab', version, { + 'checksums': ['e02556c8ea1b386963c4b464e4618aee153c5416b07ab481425c817a033323a2'], + }), +] + +sanity_check_commands = ["jupyter lab --help"] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb new file mode 100755 index 00000000000..b511014596e --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = '1.21.0' + +homepage = "https://jupyter.org/" +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST +endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and +Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + ('jupyter_server', version, { + 'checksums': ['d0adca19913a3763359be7f0b8c2ea8bfde356f4b8edd8e3149d7d0fbfaa248b'], + }), +] + +moduleclass = 'tools' From 43e24efb2dd6a85c81f113e2424d3f69cdfd79a3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 11:12:04 +0100 Subject: [PATCH 5364/9987] adding easyconfigs: jupyterlmod-3.0.0-GCCcore-11.3.0.eb, jupyterlab-lmod-1.0.2-GCCcore-11.3.0.eb --- .../jupyterlab-lmod-1.0.2-GCCcore-11.3.0.eb | 54 +++++++++++++++++++ .../jupyterlmod-3.0.0-GCCcore-11.3.0.eb | 41 ++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/j/jupyterlab-lmod/jupyterlab-lmod-1.0.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyterlab-lmod/jupyterlab-lmod-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyterlab-lmod/jupyterlab-lmod-1.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b52bbae206b --- /dev/null +++ b/easybuild/easyconfigs/j/jupyterlab-lmod/jupyterlab-lmod-1.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'Binary' + +name = 'jupyterlab-lmod' +version = '1.0.2' + +homepage = 'https://github.com/cmd-ntrf/jupyter-lmod' +description = """ JupyterLab extension that allows user to interact with environment modules +before launching kernels. The extension use Lmod's Python interface to accomplish +module related task like loading, unloading, saving collection, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://registry.npmjs.org/jupyterlab-lmod/-'] +sources = [SOURCE_TGZ] +checksums = ['f6db445f14741ef342f3dbc857afea1ea347893adb6bdbef9027c42522cfbf7a'] + +builddependencies = [ + ('binutils', '2.38'), + ('nodejs', '16.15.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('JupyterLab', '3.5.0'), + ('jupyterlmod', '3.0.0'), +] + +# WARNING: this module of jupyterlab-lmod will replace the JupyterLab App directory (JUPYTERLAB_DIR) +# current version of jupyterlab-lmod can only be installed as source extension in JUPYTERLAB_DIR +# this is not an issue with the default installation of JupyterLab in EB as it has no apps/extensions +_jupyterlab_dir = '%(installdir)s/share/jupyter/lab' + +install_cmd = "mkdir -p %s && " % _jupyterlab_dir +install_cmd += "JUPYTERLAB_DIR=%s " % _jupyterlab_dir +install_cmd += "jupyter labextension install %s" % SOURCE_TGZ + +sanity_check_commands = [ + "jupyter labextension check %(name)s", +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["%s/%s" % (_jupyterlab_dir, x) for x in ['extensions', 'schemas', 'staging', 'static', 'themes']], +} + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} +modextravars = { + 'JUPYTERLAB_DIR': _jupyterlab_dir, +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..85768e925c3 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-3.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'jupyterlmod' +version = '3.0.0' + +# This easyconfig only installs the notebook extension of Jupyter Lmod +# not the extension for Jupyter Lab + +homepage = 'https://github.com/cmd-ntrf/jupyter-lmod' +description = """Jupyter interactive notebook server extension that allows user to interact with +environment modules before launching kernels. The extension use Lmod's Python +interface to accomplish module related task like loading, unloading, saving +collection, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('jupyter-server', '1.21.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['da769078650766b1fca6ef1e673d15ddd6ce7428001e05cc364cba246a77c3fe'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'tools' From 735198dcf7b221a270fd93c09ec88076dc6aaddb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 11:13:25 +0100 Subject: [PATCH 5365/9987] adding easyconfigs: Panedr-0.7.0-foss-2021a.eb --- .../p/Panedr/Panedr-0.7.0-foss-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/Panedr/Panedr-0.7.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/Panedr/Panedr-0.7.0-foss-2021a.eb b/easybuild/easyconfigs/p/Panedr/Panedr-0.7.0-foss-2021a.eb new file mode 100644 index 00000000000..1b9dbb3a29d --- /dev/null +++ b/easybuild/easyconfigs/p/Panedr/Panedr-0.7.0-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Panedr' +version = '0.7.0' + +homepage = 'https://github.com/MDAnalysis/panedr' +description = """Panedr uses the Pyedr library to read a Gromacs EDR binary +energy XDR file and returns its contents as a pandas dataframe.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('pyedr', version, { + 'checksums': ['2906fa86950a519ada711520cb18aa3bb49df5d992473f0c7b5359ba226c7ac2'], + # remove references to out-of-tree files + 'preinstallopts': "sed -i '8,10d' setup.cfg && " + }), + ('panedr', version, { + 'checksums': ['ef1f3163cd88ff5d69f9aabc1e5850a47cc5325d8421e57510bfa7cae5956838'], + # remove references to out-of-tree files + 'preinstallopts': "sed -i '8,10d' setup.cfg && " + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 8cbbb761cbf86493124b68bf8606370c00923544 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 11:14:36 +0100 Subject: [PATCH 5366/9987] adding easyconfigs: nglview-3.0.3-foss-2021a.eb, MDAnalysis-2.0.0-foss-2021a.eb --- .../MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb | 45 +++++++++++++++++++ .../n/nglview/nglview-3.0.3-foss-2021a.eb | 44 ++++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb new file mode 100644 index 00000000000..64300f8f2f7 --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '2.0.0' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('Biopython', '1.79'), + ('networkx', '2.5.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('GridDataFormats', '0.6.0', { + 'modulename': 'gridData', + 'checksums': ['f14e00e8b795f8021f6069935e1133352224775c9bd97f395beb2bcd64a19b86'], + }), + ('gsd', '2.5.1', { + 'checksums': ['76bf228b1d8e95e7d6a334e8cc7712c0bd8c256148007f7ce88a489c21996593'], + }), + ('msgpack', '1.0.3', { + 'checksums': ['51fdc7fb93615286428ee7758cecc2f374d5ff363bdd884c7ea622a7a327a81e'], + }), + ('mmtf-python', '1.1.2', { + 'modulename': 'mmtf', + 'checksums': ['a5caa7fcd2c1eaa16638b5b1da2d3276cbd3ed3513f0c2322957912003b6a8df'], + }), + (name, version, { + 'modulename': name, + 'checksums': ['aa3079d1a82305eba58cf567fac8fc231940184ed88f9a4451be8433f4a06d3e'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb new file mode 100644 index 00000000000..f4c5a62bada --- /dev/null +++ b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'nglview' +version = '3.0.3' + +homepage = 'https://github.com/arose/nglview' +description = "IPython widget to interactively view molecular structures and trajectories." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('IPython', '7.25.0'), + ('JupyterLab', '3.2.8'), + ('nodejs', '14.17.0'), + ('MDAnalysis', '2.0.0'), # optional +] + +use_pip = True + +exts_list = [ + ('versioneer', '0.24', { + 'checksums': ['1b8dba9e51e2f0e04c7e8545216eecdea2d63e1bd5569448ee66c549f7e7782f'], + }), + (name, version, { + 'use_pip_extras': 'MDAnalysis', + 'checksums': ['3253c44bd071e4701c288de44997471608487d5191ab3d3b7736c8651335c1af'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/nglview'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'chem' From a2d2c2cfde8ad1f2de5a1feac758a05e809ac1ed Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 12:26:56 +0100 Subject: [PATCH 5367/9987] downgrade dependency of nglview-3.0.3-foss-2021a.eb on JupyterLab to v3.0.16 --- easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb index f4c5a62bada..0d555c1e891 100644 --- a/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb +++ b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb @@ -12,7 +12,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('IPython', '7.25.0'), - ('JupyterLab', '3.2.8'), + ('JupyterLab', '3.0.16'), ('nodejs', '14.17.0'), ('MDAnalysis', '2.0.0'), # optional ] From 439cb7b0e790eca1a8b3be13cce88776e67a3a91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 7 Nov 2022 14:01:02 +0100 Subject: [PATCH 5368/9987] adding easyconfigs: MCU-3366c85-gomkl-2021a.eb, matplotlib-3.4.2-gomkl-2021a.eb, spglib-python-1.16.1-gomkl-2021a.eb --- .../m/MCU/MCU-3366c85-gomkl-2021a.eb | 33 ++++++++++ .../matplotlib-3.4.2-gomkl-2021a.eb | 64 +++++++++++++++++++ .../spglib-python-1.16.1-gomkl-2021a.eb | 27 ++++++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-gomkl-2021a.eb diff --git a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb new file mode 100644 index 00000000000..74d3aa4c388 --- /dev/null +++ b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'MCU' +version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work + +homepage = 'https://hungqpham.com/mcu/' +description = """A package for periodic wavefunction and crystallography analysis. + mcu is designed to support large scale analysis and topological descriptions for periodic wavefunction.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +source_urls = ['https://github.com/hungpham2017/mcu/archive/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['96553924c57ca27d2e4d8668be2c97fc6019c139f91950a798733c5575a8b44a'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('spglib-python', '1.16.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'mcu'} + +sanity_check_commands = [ + "python -c 'from mcu import VASP'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb new file mode 100644 index 00000000000..ca47ecae358 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.4.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('cppy', '1.1.0') +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('libpng', '1.6.37'), + ('freetype', '2.10.4'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.2.0'), + ('Qhull', '2020.2') +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' setup.cfg.template >setup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['950a199911a8d94683a6b10321f9345d5a3a8433ec58b217ace979e18f16e248'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['d8d994cefdff9aaba45166eb3de4f5211adb4accac85cbf97137e98f26ea0219'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-gomkl-2021a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-gomkl-2021a.eb new file mode 100644 index 00000000000..6079d940a72 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-gomkl-2021a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.1' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['9fd2fefbd83993b135877a69c498d8ddcf20a9980562b65b800cfb4cdadad003'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' From 1972ddbd3fce77cd788f6444cade40df3d9d2bd3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 7 Nov 2022 14:16:27 +0100 Subject: [PATCH 5369/9987] style fix --- easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb index 74d3aa4c388..5a722540235 100644 --- a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb +++ b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'MCU' -version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work +version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work homepage = 'https://hungqpham.com/mcu/' description = """A package for periodic wavefunction and crystallography analysis. From 088501e33cb81906978c5b9c7a678b3eaefbe120 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Mon, 7 Nov 2022 14:48:45 +0100 Subject: [PATCH 5370/9987] Moved dependencies to its usual place --- .../easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb index 23c3faed318..e6bb3dd3a74 100644 --- a/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb +++ b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb @@ -12,17 +12,17 @@ source_urls = ['https://github.com/Illumina/DRAGMAP/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] checksums = ['baf546c2f53b13e2bce4c937201e38459f3ce2f1069722ca670d8726a4bae224'] +dependencies = { + ('Boost', '1.77.0'), + ('googletest', '1.11.0'), +} + skipsteps = ['configure'] prebuildopts = 'sed -i "s|-msse4.2 -mavx2|$CXXFLAGS|g" config.mk &&' buildopts = 'CC="$CC" CXX="$CXX"' preinstallopts = 'mkdir %(installdir)s/bin &&' installopts = 'DESTDIR=%(installdir)s' -dependencies = { - ('Boost', '1.77.0'), - ('googletest', '1.11.0'), -} - sanity_check_paths = { 'files': ['bin/dragen-os'], 'dirs': [] From 773580293233ea6b9387985596155d641eaeadef Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 7 Nov 2022 15:55:10 +0100 Subject: [PATCH 5371/9987] Switched to new JuliaPackage easyblock + changed True to SYSTEM as requested --- ...Estimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 79 +++++++++++++++++-- 1 file changed, 71 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index ca021785912..d9bb1bafff0 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Tarball' +easyblock = 'Bundle' name = 'MultilevelEstimators' version = '0.1.0' @@ -12,20 +12,83 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} dependencies = [ ('Python', '3.9.6'), - ('Julia', local_julia_ver, '-linux-%s' % ARCH, True), + ('Julia', local_julia_ver, '-linux-%s' % ARCH, SYSTEM), ] -postinstallcmds = [ - "cd %(installdir)s && mkdir pkgs", - """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && - julia -e 'using Pkg;Pkg.add(url="%s")' """ % homepage +exts_defaultclass = 'JuliaPackage' +exts_filter = ("julia -e 'using %(ext_name)s'", "") +exts_default_options = { + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], +} + +exts_list = [ + ('Preferences', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + }), + ('JLLWrappers', '1.4.1', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + }), + ('OpenSpecFun_jll', '0.5.5+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl/archive/'], + 'sources': ['OpenSpecFun-v%(version)s.tar.gz'], + }), + ('InverseFunctions', '0.1.8', { + 'source_urls': ['https://github.com/JuliaMath/InverseFunctions.jl/archive/'], + }), + ('DocStringExtensions', '0.9.2', { + 'source_urls': ['https://github.com/JuliaDocs/DocStringExtensions.jl/archive/'], + }), + ('IrrationalConstants', '0.1.1', { + 'source_urls': ['https://github.com/JuliaMath/IrrationalConstants.jl/archive/'], + }), + ('Compat', '4.3.0', { + 'source_urls': ['https://github.com/JuliaLang/Compat.jl/archive/'], + }), + ('ChainRulesCore', '1.15.6', { + 'source_urls': ['https://github.com/JuliaDiff/ChainRulesCore.jl/archive/'], + }), + ('ChangesOfVariables', '0.1.4', { + 'source_urls': ['https://github.com/JuliaMath/ChangesOfVariables.jl/archive/'], + }), + ('LogExpFunctions', '0.3.18', { + 'source_urls': ['https://github.com/JuliaStats/LogExpFunctions.jl/archive/'], + }), + ('SpecialFunctions', '1.8.7', { + 'source_urls': ['https://github.com/JuliaMath/SpecialFunctions.jl/archive/'], + }), + ('TranscodingStreams', '0.9.9', { + 'source_urls': ['https://github.com/JuliaIO/TranscodingStreams.jl/archive/'], + }), + ('Reexport', '1.2.2', { + 'source_urls': ['https://github.com/simonster/Reexport.jl/archive/'], + }), + ('OrderedCollections', '1.4.1', { + 'source_urls': ['https://github.com/JuliaCollections/OrderedCollections.jl/archive/'], + }), + ('MacroTools', '0.5.10', { + 'source_urls': ['https://github.com/FluxML/MacroTools.jl/archive/'], + }), + ('Requires', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Requires.jl/archive/'], + }), + ('FileIO', '1.16.0', { + 'source_urls': ['https://github.com/JuliaIO/FileIO.jl/archive/'], + }), + ('JLD2', '0.4.24', { + 'source_urls': ['https://github.com/JuliaIO/JLD2.jl/archive/'], + }), + (name, version, { + 'source_urls': ['https://github.com/PieterjanRobbe/MultilevelEstimators.jl/archive/'], + }), ] sanity_check_paths = { 'files': [], - 'dirs': ["pkgs"] + 'dirs': ['packages'] } -modextrapaths = {'JULIA_DEPOT_PATH': 'pkgs'} +modextrapaths = { + 'JULIA_DEPOT_PATH': '', +} moduleclass = 'lib' From 04340fd1ae7c02dc8d1a01fd471374ba2ee8cced Mon Sep 17 00:00:00 2001 From: eb-test Date: Mon, 7 Nov 2022 16:00:29 +0100 Subject: [PATCH 5372/9987] add new SPOTlight package --- .../R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index 1c4ffc3555e..cb2f31c3821 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -43,7 +43,7 @@ exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_s # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! -# packages updated on 4th May 2022 +# packages updated on 7th Nov 2022 exts_list = [ ('BiocGenerics', '0.42.0', { 'checksums': ['0cb6fa74a389693d253a9f61935d335fcfcc1dfe5acbba78b3cc43c1af5d6947'], @@ -1060,6 +1060,9 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), + ('ExomeDepth', '1.1.15', { + 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], + }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), @@ -1087,6 +1090,9 @@ exts_list = [ ('CAGEr', '2.2.0', { 'checksums': ['1cd64f6b045a5e246ae92cd709234c806edfcc25463819df0bd32fe4f4b2fd0d'], }), + ('SPOTlight', '1.0.0', { + 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 98ae750d79d281d348741e7007089e48573c348f Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 7 Nov 2022 16:01:58 +0100 Subject: [PATCH 5373/9987] Added checksums for all packages --- ...Estimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index d9bb1bafff0..e048be328cf 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -24,61 +24,80 @@ exts_default_options = { exts_list = [ ('Preferences', '1.3.0', { 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['a87c1fc863fcb6240c3f4327776fa01a1f87e0d2df5a0c1850f789ce24469da2'], }), ('JLLWrappers', '1.4.1', { 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], }), ('OpenSpecFun_jll', '0.5.5+0', { 'source_urls': ['https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl/archive/'], 'sources': ['OpenSpecFun-v%(version)s.tar.gz'], + 'checksums': ['6d1df617dd0a80fc0de5bc41a092e51f72782dbfd296c64e151707733cb57b6f'], }), ('InverseFunctions', '0.1.8', { 'source_urls': ['https://github.com/JuliaMath/InverseFunctions.jl/archive/'], + 'checksums': ['6b3e72037c2198268bc5247daeb14eaa5cf2b37f41c7c735b3cd2355bad1584b'], }), ('DocStringExtensions', '0.9.2', { 'source_urls': ['https://github.com/JuliaDocs/DocStringExtensions.jl/archive/'], + 'checksums': ['ff7869968381f17b24b3f471a88dd96b7008e8b8d7a14079d4667d87db0037dd'], }), ('IrrationalConstants', '0.1.1', { 'source_urls': ['https://github.com/JuliaMath/IrrationalConstants.jl/archive/'], + 'checksums': ['2eccfb55449d25d363d96ce116c45b39110d1572248e04e136ec4c37fe84ba96'], }), ('Compat', '4.3.0', { 'source_urls': ['https://github.com/JuliaLang/Compat.jl/archive/'], + 'checksums': ['0d792ec0912a8d3ed30329fc44073e964be3cd314671594dd16f8570c51b2c19'], }), ('ChainRulesCore', '1.15.6', { 'source_urls': ['https://github.com/JuliaDiff/ChainRulesCore.jl/archive/'], + 'checksums': ['79e22fc981fa7c44b3efc2f07903f555c5520dc38d0d3d31b6390980c786cb60'], }), ('ChangesOfVariables', '0.1.4', { 'source_urls': ['https://github.com/JuliaMath/ChangesOfVariables.jl/archive/'], + 'checksums': ['2eb2eb59711d53d284a9cc998e9facf3a1720cfde26eb672676cbe944fa9224a'], }), ('LogExpFunctions', '0.3.18', { 'source_urls': ['https://github.com/JuliaStats/LogExpFunctions.jl/archive/'], + 'checksums': ['f169c5512f79746987858dd19d05d6fdd4017f2b817d9cd8831bde3c3e398a82'], }), ('SpecialFunctions', '1.8.7', { 'source_urls': ['https://github.com/JuliaMath/SpecialFunctions.jl/archive/'], + 'checksums': ['3f2ecec0506fe47cfa5e436ac510e2a82d39f74fceaeb422572cf06d90f2096a'], }), ('TranscodingStreams', '0.9.9', { 'source_urls': ['https://github.com/JuliaIO/TranscodingStreams.jl/archive/'], + 'checksums': ['c341df1b582e6289fd5d5bd682111876b01582792687c0812fd093c085b12e68'], }), ('Reexport', '1.2.2', { 'source_urls': ['https://github.com/simonster/Reexport.jl/archive/'], + 'checksums': ['2566f7776aae9697cbf15765fc32187f46dd51200abc953a0266863ad67132b3'], }), ('OrderedCollections', '1.4.1', { 'source_urls': ['https://github.com/JuliaCollections/OrderedCollections.jl/archive/'], + 'checksums': ['ad6d191a2bf6f0c04abaf795fa93b3db6c3f3fb97498b464fcf7297b3a4bf6b6'], }), ('MacroTools', '0.5.10', { 'source_urls': ['https://github.com/FluxML/MacroTools.jl/archive/'], + 'checksums': ['0c61fe20a40346b0d1c248ff57e047b669ae47ad2d971b2ca7b91efdddff71ac'], }), ('Requires', '1.3.0', { 'source_urls': ['https://github.com/JuliaPackaging/Requires.jl/archive/'], + 'checksums': ['8af4dac29839e796a651b8cb6a325b6f9c7eee5d5620b3e366b64f58325ebeb7'], }), ('FileIO', '1.16.0', { 'source_urls': ['https://github.com/JuliaIO/FileIO.jl/archive/'], + 'checksums': ['c447263eb2fac0bd1c7822b97b64f4274e8eeb52bdd5fdc8dc413342a547759f'], }), ('JLD2', '0.4.24', { 'source_urls': ['https://github.com/JuliaIO/JLD2.jl/archive/'], + 'checksums': ['fdcc4a9af9eaaa9013724deb2649ba00aa987ae5d3753a7af389ab7720bf19a9'], }), (name, version, { 'source_urls': ['https://github.com/PieterjanRobbe/MultilevelEstimators.jl/archive/'], + 'checksums': ['53bd629506cbe2472c9fb061a5a64523478556264e7fc98a3b6503dc1e7ef039'], }), ] From 4906ccbb280b753019ab454bea1fbca708772df4 Mon Sep 17 00:00:00 2001 From: eb-test Date: Mon, 7 Nov 2022 16:07:01 +0100 Subject: [PATCH 5374/9987] add it also to 2022a --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index e9595a58dd4..cac7fb0b26b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -45,7 +45,7 @@ exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_s # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! -# packages updated on 7th July 2022 +# packages updated on 7th Nov 2022 exts_list = [ ('BiocGenerics', '0.42.0', { 'checksums': ['0cb6fa74a389693d253a9f61935d335fcfcc1dfe5acbba78b3cc43c1af5d6947'], @@ -1059,6 +1059,9 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), + ('ExomeDepth', '1.1.15', { + 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], + }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), @@ -1083,6 +1086,9 @@ exts_list = [ ('CAGEr', '2.2.0', { 'checksums': ['1cd64f6b045a5e246ae92cd709234c806edfcc25463819df0bd32fe4f4b2fd0d'], }), + ('SPOTlight', '1.0.0', { + 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 4ac5f57ff988d0e8fbf891c789b2d8f57279e5ef Mon Sep 17 00:00:00 2001 From: eb-test Date: Mon, 7 Nov 2022 16:12:58 +0100 Subject: [PATCH 5375/9987] remove ExomeDepth as is gone due to #16492 --- .../R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 3 --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 --- 2 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index cb2f31c3821..9c7b01b9137 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -1060,9 +1060,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index cac7fb0b26b..db12f43dc2b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1059,9 +1059,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), From e303fcc683a3d7e3052020d25087157fdad982c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Nov 2022 16:17:19 +0100 Subject: [PATCH 5376/9987] define $GTKDOCIZE as 'echo' before generating configure script for recent HarfBuzz versions (fixes #16567) --- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb | 3 ++- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb | 3 ++- .../easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb index 5662fb3cc49..61d5d7f6ffc 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb @@ -30,7 +30,8 @@ dependencies = [ ('freetype', '2.10.4'), ] -preconfigopts = "./autogen.sh && " +# define $GTKDOCIZE to 'echo' as workaround for https://github.com/easybuilders/easybuild-easyconfigs/issues/16567 +preconfigopts = "GTKDOCIZE=echo ./autogen.sh && " configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb index 57ecf2bd16c..2be2036a9b2 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb @@ -27,7 +27,8 @@ dependencies = [ ('freetype', '2.11.0'), ] -preconfigopts = "./autogen.sh && " +# define $GTKDOCIZE to 'echo' as workaround for https://github.com/easybuilders/easybuild-easyconfigs/issues/16567 +preconfigopts = "GTKDOCIZE=echo ./autogen.sh && " configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb index af1f8d0d274..389711e5230 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb @@ -27,7 +27,8 @@ dependencies = [ ('freetype', '2.12.1'), ] -preconfigopts = "./autogen.sh && " +# define $GTKDOCIZE to 'echo' as workaround for https://github.com/easybuilders/easybuild-easyconfigs/issues/16567 +preconfigopts = "GTKDOCIZE=echo ./autogen.sh && " configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " sanity_check_paths = { From 2ce828930e93303842546c5914ddb1458a4c6b7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Nov 2022 16:55:38 +0100 Subject: [PATCH 5377/9987] disable use of -Werror in recent NSS easyconfigs --- easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb | 5 ++++- easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb | 5 ++++- easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb index 1153b4b58a8..cc653fd5135 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb @@ -31,8 +31,11 @@ dependencies = [ # building in parallel fails parallel = 1 +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb index 0ea01ba44d0..55fbfa38a92 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb @@ -34,8 +34,11 @@ dependencies = [ # building in parallel fails parallel = 1 +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb index 3cea93f9ab6..40d16c445eb 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb @@ -32,8 +32,11 @@ dependencies = [ # building in parallel fails parallel = 1 +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) From 589da76b23b7828955ee9c4a8021e71a9b269e5f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 7 Nov 2022 17:50:26 +0100 Subject: [PATCH 5378/9987] adding easyconfigs: InParanoid-5.0.79d8e39-GCC-10.3.0.eb --- .../InParanoid-5.0.79d8e39-GCC-10.3.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb new file mode 100644 index 00000000000..61194783a6d --- /dev/null +++ b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb @@ -0,0 +1,65 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'Tarball' + +name = 'InParanoid' +version = '5.0.79d8e39' + +homepage = 'https://inparanoid.sbc.su.se' +description = """InParanoid: ortholog groups with inparalogs.""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://bitbucket.org/sonnhammergroup/inparanoid/get/'] +sources = ['79d8e39bb243d403ce57b699c1ae104a8a640389.tar.gz'] +checksums = ['efe1a35bbb70608385780c4bf62969a29c46dd8132fbe472034422d23ad4b0c2'] # for commit 79d8e39 + +builddependencies = [('binutils', '2.36.1')] + +# NOTE some dependencies are not listed on the web site such as Java! +dependencies = [ + ('Perl', '5.32.1'), # brings libmoose-perl and libparallel-forkmanager-perl + ('BioPerl', '1.7.8'), + ('Java', '11', '', SYSTEM), + ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), + ('DIAMOND', '2.0.13'), +] + +# NOTE inparanoid.pl uses only local (same directory) paths, so patch it +postinstallcmds = ["rm -rf %(installdir)s/docker/ %(installdir)s/singularity/ && " + "chmod a+rx %(installdir)s/*.pl && " + "chmod -x %(installdir)s/*.jar && " + "perl -i -pe 's|helpfile = \"help\"|helpfile = \"%(installdir)s/help\"|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|seqstat = \"|seqstat = \"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|blastParser = \"|blastParser = \"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|diamondParser = \"|diamondParser = \"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|copy\(\"\./|copy\(\"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|\./\$blastParser|\$blastParser|g' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|#!.*perl|#!/usr/bin/env perl|' %(installdir)s/*.pl"] + +sanity_check_paths = { + 'files': ['inparanoid.pl', 'blast_parser.pl', 'diamondParser.pl'], + 'dirs': ['matrices'], +} + +modextrapaths = { + 'PATH': '', +} + +sanity_check_commands = ["inparanoid.pl -input-dir %(installdir)s/testInput/ && " + "rm -Rf %(installdir)s/output/"] + +moduleclass = 'bio' From e300c9937fb0e36dbf415eaea0a264063fd206a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 8 Nov 2022 09:30:36 +0100 Subject: [PATCH 5379/9987] fixed naming and versioning --- .../mcu-2021-04-06-gomkl-2021a.eb} | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/{MCU/MCU-3366c85-gomkl-2021a.eb => mcu/mcu-2021-04-06-gomkl-2021a.eb} (76%) diff --git a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb similarity index 76% rename from easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb rename to easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb index 5a722540235..5a34c8b03a6 100644 --- a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb +++ b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb @@ -1,7 +1,8 @@ easyblock = 'PythonPackage' -name = 'MCU' -version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work +name = 'mcu' +local_commit = '3366c85' +version = '2021-04-06' # There is a 0.2 release but it's too old and it doesn't work homepage = 'https://hungqpham.com/mcu/' description = """A package for periodic wavefunction and crystallography analysis. @@ -10,7 +11,7 @@ description = """A package for periodic wavefunction and crystallography analysi toolchain = {'name': 'gomkl', 'version': '2021a'} source_urls = ['https://github.com/hungpham2017/mcu/archive/'] -sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] checksums = ['96553924c57ca27d2e4d8668be2c97fc6019c139f91950a798733c5575a8b44a'] dependencies = [ @@ -24,8 +25,6 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -options = {'modulename': 'mcu'} - sanity_check_commands = [ "python -c 'from mcu import VASP'", ] From f184bf0f4a276c02194f833960c6c5b1b42f3bc7 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 09:45:01 +0100 Subject: [PATCH 5380/9987] adding easyconfigs: Godon-20210913-x86_64.eb --- .../g/Godon/Godon-20210913-x86_64.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb diff --git a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb new file mode 100644 index 00000000000..576e9b6362d --- /dev/null +++ b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb @@ -0,0 +1,42 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Compilation with GO looks to use a broken dependency +# +# SO use the pre-compiled binaries! +## + +easyblock = 'Binary' + +name = 'Godon' +version = '20210913' +versionsuffix = '-x86_64' + +software_license = 'LicenseGPLv3' + +homepage = 'https://bitbucket.org/Davydov/godon/' +description = """Godon is codon models software written in Go.""" + +toolchain = SYSTEM + +source_urls = ['https://bitbucket.org/Davydov/godon/downloads'] +sources = ['godon-master-linux-gnu-x86_64'] +checksums = ['159058f7577093548f3ced1540d1ff9fd5f7915cdfcb8f8cd7fb40f5c202fcca'] + + +extract_sources = False + +postinstallcmds = ["mkdir -p %(installdir)s/bin/ && cd %(installdir)s/bin/ && " + "ln -s ../godon-master-linux-gnu-x86_64 godon"] + +sanity_check_paths = { + 'files': ["bin/godon"], + 'dirs': ['bin'], +} + +sanity_check_commands = ["godon --help"] + +moduleclass = 'bio' From 34ffbf8e8618aad39c9188e3097f1e3464e69110 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 10:18:21 +0100 Subject: [PATCH 5381/9987] adding easyconfigs: NanoLyse-1.2.1-foss-2021a.eb --- .../n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb new file mode 100644 index 00000000000..a6b362f5ae5 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb @@ -0,0 +1,56 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'NanoLyse' +version = '1.2.1' + +homepage = 'https://github.com/wdecoster/nanolyse' +description = """Remove reads mapping to the lambda phage genome from a fastq file.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Biopython', '1.79'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('mappy', '2.24', { + 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + }), + ('NanoLyse', '1.2.1', { + 'checksums': ['933ee668da805fc9ec9fa86c9fca81a073438d45b5f64e23cf606c01e715b1d5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/NanoLyse'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoLyse --version"] + +sanity_pip_check = True + +moduleclass = 'bio' From 147604a643395b467b19273f00aeaafa1ef7a1f6 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 11:14:17 +0100 Subject: [PATCH 5382/9987] adding easyconfigs: PyDamage-0.70-foss-2021a.eb --- .../p/PyDamage/PyDamage-0.70-foss-2021a.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb new file mode 100644 index 00000000000..45477aba7e9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb @@ -0,0 +1,65 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'PyDamage' +version = '0.70' + +homepage = 'https://github.com/maxibor/pydamage' +description = """Pydamage, is a Python software to automate the process of +contig damage identification and estimation. After modelling the ancient DNA +damage using the C to T transitions, Pydamage uses a likelihood ratio test +to discriminate between truly ancient, and modern contigs originating from +sample contamination.""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Biopython', '1.79'), + ('Pysam', '0.16.0.1'), + ('statsmodels', '0.12.2'), + ('matplotlib', '3.4.2'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('kneed', '0.7.0', { + 'checksums': ['340d67fa183a72b0afae19846dd246a6fb7204e8d54243d8b8d3d9932f887c6e'], + }), + ('pydamage', '0.70', { + 'checksums': ['1dcd6ebae431f758c9434785c668351f82926847f9eda76413e96b7481138d78'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pydamage'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pydamage --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From ff135866cea1a5bb953de5ccdc4ee508a3a51e05 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 8 Nov 2022 11:46:10 +0100 Subject: [PATCH 5383/9987] Update imagecodecs-2022.9.26-foss-2021a.eb --- .../i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb index 55bf95340ff..2a32ac22f2e 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb @@ -47,7 +47,7 @@ dependencies = [ ('zfp', '1.0.0'), ('zstd', '1.4.9'), ('Brunsli', '0.1'), - ('HDF5', '1.12.1'), + ('HDF5', '1.10.7'), ('h5py', '3.2.1'), ('libheif', '1.12.0'), ] From 91d4154016519c6f550bbf367df983561d14aeca Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 12:02:18 +0100 Subject: [PATCH 5384/9987] adding easyconfigs: CAT-BAT-5.2.3-GCC-10.3.0.eb --- .../c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..20b588f3e11 --- /dev/null +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'Tarball' + +name = 'CAT-BAT' +version = '5.2.3' + +homepage = 'https://github.com/dutilh/CAT' +description = """Tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs).""" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/dutilh/CAT/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['19a8eb28c0ebd3fc5a04b006d305a916dd1af00a32b70d2f30df35f32ca2929b'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('DIAMOND', '2.0.13'), + ('prodigal', '2.6.3'), +] + +postinstallcmds = ["cd %(installdir)s/ && ln -s CAT_pack bin && " + "chmod a+rx %(installdir)s/CAT_pack/*.py && " + "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' " + "%(installdir)s/CAT_pack/check.py"] + +sanity_check_paths = { + 'files': ['CAT_pack/CAT', 'README.md'], + 'dirs': ['CAT_pack'], +} + +modextrapaths = { + 'PATH': '', +} + +sanity_check_commands = ["CAT --help"] + +moduleclass = 'bio' From 3e5ad955853e91bd8fee4cfd83c76779def2febc Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 12:28:40 +0100 Subject: [PATCH 5385/9987] Fix install cmd + Remove empty line + Dont test bin/ dir already tested --- .../easyconfigs/g/Godon/Godon-20210913-x86_64.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb index 576e9b6362d..7014125e51c 100644 --- a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb +++ b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb @@ -23,18 +23,19 @@ description = """Godon is codon models software written in Go.""" toolchain = SYSTEM source_urls = ['https://bitbucket.org/Davydov/godon/downloads'] -sources = ['godon-master-linux-gnu-x86_64'] +sources = [{ + 'download_filename': 'godon-master-linux-gnu-x86_64', + 'filename': 'godon', +}] checksums = ['159058f7577093548f3ced1540d1ff9fd5f7915cdfcb8f8cd7fb40f5c202fcca'] - extract_sources = False -postinstallcmds = ["mkdir -p %(installdir)s/bin/ && cd %(installdir)s/bin/ && " - "ln -s ../godon-master-linux-gnu-x86_64 godon"] +install_cmd = "mkdir -p %(installdir)s/bin/ && mv godon %(installdir)s/bin/" sanity_check_paths = { 'files': ["bin/godon"], - 'dirs': ['bin'], + 'dirs': [], } sanity_check_commands = ["godon --help"] From 6ee549a5cf2a9b1d30e4e8b69786b57a1dc0fad7 Mon Sep 17 00:00:00 2001 From: eb-test Date: Tue, 8 Nov 2022 12:55:52 +0100 Subject: [PATCH 5386/9987] include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0 --- .../easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb index d156b3c22fc..2b39682fdb8 100644 --- a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb @@ -19,15 +19,17 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), ('coverage', '5.5'), - ('tqdm', '4.60.0'), ] use_pip = True exts_list = [ ('pytest-runner', '5.3.0', { - 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], 'modulename': 'ptr', + 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], + }), + ('tqdm', '4.60.0', { + 'checksums': ['ebdebdb95e3477ceea267decfc0784859aa3df3e27e22d23b83e9b272bf157ae'], }), (name, version, { 'checksums': ['590980baaf810c8a02705efd50eb4ace644c360470fc3dc4491d077bbb6b26fc'], From 3f68011737a67fa7a0e1187f937ef408406e2b9e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 14:06:41 +0100 Subject: [PATCH 5387/9987] Remove useless buildrequirements + Add missing minimap2 requirement --- .../n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb index a6b362f5ae5..fe176ac7b26 100644 --- a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb @@ -13,31 +13,26 @@ version = '1.2.1' homepage = 'https://github.com/wdecoster/nanolyse' description = """Remove reads mapping to the lambda phage genome from a fastq file.""" +software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ ('binutils', '2.36.1'), - ('CMake', '3.20.1'), - ('make', '4.3'), - ('Check', '0.15.2'), - ('SWIG', '4.0.2'), - ('expat', '2.2.9'), - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), ] dependencies = [ ('Python', '3.9.5'), ('Biopython', '1.79'), + ('minimap2', '2.20'), ] use_pip = True # Fetch the tar.gz, not the whl files! exts_list = [ - ('mappy', '2.24', { - 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + ('mappy', '2.20', { + 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], }), ('NanoLyse', '1.2.1', { 'checksums': ['933ee668da805fc9ec9fa86c9fca81a073438d45b5f64e23cf606c01e715b1d5'], From ee0deec486b0c0b1b2f976ef15ed3d96e0c4a1c5 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 14:35:16 +0100 Subject: [PATCH 5388/9987] Remove useless buildrequirements --- easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb index fe176ac7b26..b31eb661ab9 100644 --- a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb @@ -17,10 +17,6 @@ software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2021a'} -builddependencies = [ - ('binutils', '2.36.1'), -] - dependencies = [ ('Python', '3.9.5'), ('Biopython', '1.79'), From ce4fe5319f93754c1005cef4e927d338322174c4 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 14:53:39 +0100 Subject: [PATCH 5389/9987] Use postinstall cmd list + Use fix_perl_shebang_for + Test if testInput/ exists + Test outside of the install dir --- .../InParanoid-5.0.79d8e39-GCC-10.3.0.eb | 38 +++++++++---------- 1 file changed, 17 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb index 61194783a6d..5bfa4ca673a 100644 --- a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb @@ -21,8 +21,6 @@ source_urls = ['https://bitbucket.org/sonnhammergroup/inparanoid/get/'] sources = ['79d8e39bb243d403ce57b699c1ae104a8a640389.tar.gz'] checksums = ['efe1a35bbb70608385780c4bf62969a29c46dd8132fbe472034422d23ad4b0c2'] # for commit 79d8e39 -builddependencies = [('binutils', '2.36.1')] - # NOTE some dependencies are not listed on the web site such as Java! dependencies = [ ('Perl', '5.32.1'), # brings libmoose-perl and libparallel-forkmanager-perl @@ -33,33 +31,31 @@ dependencies = [ ] # NOTE inparanoid.pl uses only local (same directory) paths, so patch it -postinstallcmds = ["rm -rf %(installdir)s/docker/ %(installdir)s/singularity/ && " - "chmod a+rx %(installdir)s/*.pl && " - "chmod -x %(installdir)s/*.jar && " - "perl -i -pe 's|helpfile = \"help\"|helpfile = \"%(installdir)s/help\"|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|seqstat = \"|seqstat = \"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|blastParser = \"|blastParser = \"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|diamondParser = \"|diamondParser = \"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|copy\(\"\./|copy\(\"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|\./\$blastParser|\$blastParser|g' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|#!.*perl|#!/usr/bin/env perl|' %(installdir)s/*.pl"] +postinstallcmds = [ + "rm -rf %(installdir)s/docker/ %(installdir)s/singularity/", + "chmod a+rx %(installdir)s/*.pl", + "chmod -x %(installdir)s/*.jar", + "perl -i -pe 's|helpfile = \"help\"|helpfile = \"%(installdir)s/help\"|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|seqstat = \"|seqstat = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|blastParser = \"|blastParser = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|diamondParser = \"|diamondParser = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|copy\(\"\./|copy\(\"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|\./\$blastParser|\$blastParser|g' %(installdir)s/inparanoid.pl", +] + +fix_perl_shebang_for = ['*.pl'] sanity_check_paths = { 'files': ['inparanoid.pl', 'blast_parser.pl', 'diamondParser.pl'], - 'dirs': ['matrices'], + 'dirs': ['matrices', 'testInput'], } modextrapaths = { 'PATH': '', } -sanity_check_commands = ["inparanoid.pl -input-dir %(installdir)s/testInput/ && " - "rm -Rf %(installdir)s/output/"] +sanity_check_commands = [ + "cd %(builddir)s && inparanoid.pl -input-dir %(installdir)s/testInput/", +] moduleclass = 'bio' From 931102f16450a7734781e26800043cb245d7c4f5 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 15:10:45 +0100 Subject: [PATCH 5390/9987] Remove useless builddependencies --- .../p/PyDamage/PyDamage-0.70-foss-2021a.eb | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb index 45477aba7e9..c2ff6ff71da 100644 --- a/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb @@ -21,17 +21,6 @@ software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2021a'} -builddependencies = [ - ('binutils', '2.36.1'), - ('CMake', '3.20.1'), - ('make', '4.3'), - ('Check', '0.15.2'), - ('SWIG', '4.0.2'), - ('expat', '2.2.9'), - ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), -] - dependencies = [ ('Python', '3.9.5'), ('Biopython', '1.79'), From ab1ac7f2f6f502670404cc6a381cc4eb927f508b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 15:22:49 +0100 Subject: [PATCH 5391/9987] Remove useless buildrequirements + Use postinstallcmds list + Remove useless PATH extension --- .../c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb index 20b588f3e11..6707fbe1fc7 100644 --- a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb @@ -21,28 +21,23 @@ source_urls = ['https://github.com/dutilh/CAT/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['19a8eb28c0ebd3fc5a04b006d305a916dd1af00a32b70d2f30df35f32ca2929b'] -builddependencies = [('binutils', '2.36.1')] - dependencies = [ ('Python', '3.9.5'), ('DIAMOND', '2.0.13'), ('prodigal', '2.6.3'), ] -postinstallcmds = ["cd %(installdir)s/ && ln -s CAT_pack bin && " - "chmod a+rx %(installdir)s/CAT_pack/*.py && " - "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' " - "%(installdir)s/CAT_pack/check.py"] +postinstallcmds = [ + "cd %(installdir)s/ && ln -s CAT_pack bin", + "chmod a+rx %(installdir)s/CAT_pack/*.py", + "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' %(installdir)s/CAT_pack/check.py", +] sanity_check_paths = { 'files': ['CAT_pack/CAT', 'README.md'], 'dirs': ['CAT_pack'], } -modextrapaths = { - 'PATH': '', -} - sanity_check_commands = ["CAT --help"] moduleclass = 'bio' From 73e4fa376f981612261e656a0101bc52eccbe3ab Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 15:48:32 +0100 Subject: [PATCH 5392/9987] Use version in binary name --- easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb index 7014125e51c..aa401a18c4f 100644 --- a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb +++ b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb @@ -25,13 +25,14 @@ toolchain = SYSTEM source_urls = ['https://bitbucket.org/Davydov/godon/downloads'] sources = [{ 'download_filename': 'godon-master-linux-gnu-x86_64', - 'filename': 'godon', + 'filename': 'godon-%(version)s-linux-gnu-x86_64', }] checksums = ['159058f7577093548f3ced1540d1ff9fd5f7915cdfcb8f8cd7fb40f5c202fcca'] extract_sources = False -install_cmd = "mkdir -p %(installdir)s/bin/ && mv godon %(installdir)s/bin/" +install_cmd = "mkdir -p %(installdir)s/bin/ && cp -a godon-%(version)s-linux-gnu-x86_64 %(installdir)s/bin/ && " +install_cmd += "cd %(installdir)s/bin && ln -s godon-%(version)s-linux-gnu-x86_64 godon" sanity_check_paths = { 'files': ["bin/godon"], From 629be09f0cbcff3655396ddbf63e1d7b7c77c2a9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 8 Nov 2022 15:47:37 +0000 Subject: [PATCH 5393/9987] Add HiCcompare and dependencies --- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 33 ++++++++++++------- 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index db12f43dc2b..d34e406d5d8 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -222,9 +222,9 @@ exts_list = [ ('Rgraphviz', '2.40.0', { 'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'], 'checksums': [ - '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4', # Rgraphviz_2.40.0.tar.gz - # Rgraphviz-2.28.0_fno-tree-vectorize.patch - '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9', + {'Rgraphviz_2.40.0.tar.gz': '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4'}, + {'Rgraphviz-2.28.0_fno-tree-vectorize.patch': + '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9'}, ], }), ('RNASeqPower', '1.36.0', { @@ -443,17 +443,17 @@ exts_list = [ ('dada2', '1.24.0', { 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], 'checksums': [ - '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b', # dada2_1.24.0.tar.gz - # dada2-1.16.0-remove-sse-on-aarch64.patch - 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + {'dada2_1.24.0.tar.gz': '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b'}, + {'dada2-1.16.0-remove-sse-on-aarch64.patch': + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935'}, ], }), ('LEA', '3.8.0', { 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], 'checksums': [ - 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774', # LEA_3.8.0.tar.gz - # LEA-3.0.0_support_aarch64_and_ppc64le.patch - 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', + {'LEA_3.8.0.tar.gz': 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774'}, + {'LEA-3.0.0_support_aarch64_and_ppc64le.patch': + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881'}, ], }), ('tximport', '1.24.0', { @@ -720,9 +720,9 @@ exts_list = [ ('RProtoBufLib', '2.8.0', { 'patches': ['RProtoBufLib-2.8.0_fix-protobuf-build.patch'], 'checksums': [ - 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7', # RProtoBufLib_2.8.0.tar.gz - # RProtoBufLib-2.8.0_fix-protobuf-build.patch - '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64', + {'RProtoBufLib_2.8.0.tar.gz': 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7'}, + {'RProtoBufLib-2.8.0_fix-protobuf-build.patch': + '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64'}, ], }), ('cytolib', '2.8.0', { @@ -1086,6 +1086,15 @@ exts_list = [ ('SPOTlight', '1.0.0', { 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], }), + ('CGHcall', '2.58.0', { + 'checksums': ['c5e86b9234685462b7330c85b91ca648a801a76c99f3e98cd509ac47ee8afae2'], + }), + ('QDNAseq', '1.32.0', { + 'checksums': ['75bbde9b6cc55cd6a47b9f466358033a180b480def2144abdcc93a2a8e066668'], + }), + ('HiCcompare', '1.18.0', { + 'checksums': ['b9320fa7a9f10832e2ac7ade0245f85ac4c2c26edef2580078888f5e1050ee2d'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 09d88f791a5e9a6659f4ab7a76a4f9b1d8b24d41 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:11:16 +0100 Subject: [PATCH 5394/9987] adding easyconfigs: pullseq-1.0.2-GCCcore-10.3.0.eb --- .../p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..bd94483da59 --- /dev/null +++ b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'pullseq' +version = '1.0.2' + +homepage = 'https://github.com/bcthomas/pullseq' +description = "Utility program for extracting sequences from a fasta/fastq file" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/bcthomas/pullseq/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a295d7e0e2d64ed05d293d795d1716376707e465f2c42ede6454f27db586c85f'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), +] +dependencies = [ + ('PCRE', '8.44'), +] + +preconfigopts = "./bootstrap && " + +buildopts = 'CFLAGS="$CFLAGS -fcommon"' + +sanity_check_paths = { + 'files': ['bin/pullseq', 'bin/seqdiff'], + 'dirs': [], +} + +sanity_check_commands = [ + "pullseq --help 2>&1 | grep 'pullseq - a bioinformatics tool'", + "seqdiff --help 2>&1 | grep 'seqdiff - a bioinformatics tool'", +] + +moduleclass = 'bio' From fe12a8b8778e44b8765d8b97ead5176f1b84e1fc Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:12:16 +0100 Subject: [PATCH 5395/9987] adding easyconfigs: IDBA-UD-1.1.3-GCC-10.3.0.eb --- .../i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..6b69859e259 --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Updated: Pavel Grochal (INUITS) +# License: GPLv2 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in prebuildopts + +# modified by Tom Strempel +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.3' + +homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads +Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. +IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth +contigs are removed iteratively with cutoff threshold from low to high to reduce the errors +in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled +locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD +can iterate k value of de Bruijn graph to a very large value with less gaps and less branches +to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] +sources = ['idba-%(version)s.tar.gz'] +checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] + +prebuildopts = './configure && ' + +# we delete every .o and Makefile file which is left in bin folder +buildopts = ' && rm -fr bin/*.o bin/Makefile*' + +files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] + +pretestopts = "cd test && " +runtest = "check" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' From 2ee8b1f495828d5a226a4dabd775c8ed35a00ab2 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:13:18 +0100 Subject: [PATCH 5396/9987] adding easyconfigs: FragGeneScan-1.31-GCCcore-10.3.0.eb --- .../FragGeneScan-1.31-GCCcore-10.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4870fb3bdfa --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.31' + +homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [("Perl", "5.32.1")] + +fix_perl_shebang_for = ['*.pl'] + +prebuildopts = "make clean && " +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' + +files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FragGeneScan', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +sanity_check_commands = [ + './run_FragGeneScan.pl help', + './run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete' +] + +moduleclass = 'bio' From 79d2a7ababdee961b9316a5c7d938dc14827b96c Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:30:10 +0100 Subject: [PATCH 5397/9987] adding easyconfigs: SSW-1.1-GCCcore-10.3.0.eb --- .../s/SSW/SSW-1.1-GCCcore-10.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f8abd16d82d --- /dev/null +++ b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'SSW' +version = '1.1' + +homepage = 'https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library' +description = """SSW is a fast implementation of the Smith-Waterman algorithm, which uses the + Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the + instruction level. SSW library provides an API that can be flexibly used by programs written in + C, C++ and other languages. We also provide a software that can do protein and genome alignment + directly. Current version of our implementation is ~50 times faster than an ordinary + Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path + (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and + location heuristically. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1_build-cpp-lib.patch'] +checksums = [ + 'cdbc20740daeb188ed39413ea5ff9ae4cf72c4d7ccff1d2de2cac0446d64d99f', # v1.1.tar.gz + 'fe0d1f536ecd526dda8879b2f41b62c3c82b39d236f023ee735c1c18d584f06a', # SSW-1.1_build-cpp-lib.patch +] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('zlib', '1.2.11')] + +start_dir = 'src' + +buildopts = 'default' + +files_to_copy = [ + (['ssw_test'], 'bin'), + (['*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/ssw'), +] + +sanity_check_paths = { + 'files': ['bin/ssw_test', 'lib/libssw.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 50ebf6f6d3dd2e38a69642179c28121ea1c97578 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:33:12 +0100 Subject: [PATCH 5398/9987] adding easyconfigs: fermi-lite-20190320-GCCcore-10.3.0.eb --- .../fermi-lite-20190320-GCCcore-10.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6daf5a68037 --- /dev/null +++ b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'fermi-lite' +version = '20190320' +local_commit = 'b499514' + +homepage = 'https://github.com/lh3/fermi-lite' +description = """Standalone C library for assembling Illumina short reads in small regions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = [ + '%(name)s-20190320_avoid-bwa-namespace-conflict.patch', + '%(name)s-20190320_build-shared-lib.patch', +] +checksums = [ + 'ea1230e298b8e7193a996b5aceeff7fea44ef00852b0b87d4fcb504bdca0e712', # b499514.tar.gz + # fermi-lite-20190320_avoid-bwa-namespace-conflict.patch + '27600733f1cea8b1d1503b1a67b9d41526e907c1b6321313ff51194e166c1842', + '43398559fbb3910d6d3d1a41af3fb16bf8f26bd7cc34176dfc9a068a551c3f50', # fermi-lite-20190320_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('zlib', '1.2.11')] + +prebuildopts = 'CFLAGS="$CFLAGS -fcommon"' + +files_to_copy = [ + (['fml-asm'], 'bin'), + (['*.a', '*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/fml'), + 'test', +] + +sanity_check_paths = { + 'files': ['bin/fml-asm', 'lib/libfml.a', 'lib/libfml.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From 143e7ae01b8298310d9b79667fe7e979aa8d1ef9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 8 Nov 2022 20:55:07 +0100 Subject: [PATCH 5399/9987] adding easyconfigs: CMake-3.24.3-GCCcore-11.3.0.eb --- .../c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d5b6ac8b205 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.24.3' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b53aa10fa82bff84ccdb59065927b72d3bee49f4d86261249fc0984b3b367291'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('cURL', '7.83.0'), + ('libarchive', '3.6.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'devel' From ae07a8f91ee2a5a1c4b720658ec2fc1fcd369551 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Nov 2022 22:32:24 +0100 Subject: [PATCH 5400/9987] {tools}[GCCcore/12.2.0] XZ v5.2.7 --- .../easyconfigs/g/gettext/gettext-0.21.1.eb | 39 +++++++++++++++++++ .../x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb | 37 ++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb new file mode 100644 index 00000000000..9525991ab15 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21.1' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e8c3650e1d8cee875c4f355642382c1df83058bd5a11ee8555c0cf276d646d45'] + +dependencies = [ + ('ncurses', '6.3'), +] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2942a648d38 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.7' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b65f1d0c2708e57716f4dd2216989a73847ac6fdb4168ffceb155767e22b834b'] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.21.1', '', SYSTEM), + ('binutils', '2.39'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' From 5c72c29cf95f639526b7bf4a98a508dc018b365f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:19:27 +0100 Subject: [PATCH 5401/9987] adding easyconfigs: MaxBin-2.2.7-gompi-2021a.eb --- .../m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb new file mode 100644 index 00000000000..338bf18f42b --- /dev/null +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'MaxBin' +version = '2.2.7' + +# https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html doesn't work +homepage = 'https://sourceforge.net/projects/maxbin/' +description = """MaxBin is software for binning assembled metagenomic sequences +based on an Expectation-Maximization algorithm.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Perl', '5.32.1'), + ('Bowtie2', '2.4.4'), + ('FragGeneScan', '1.31'), + ('HMMER', '3.3.2'), + ('IDBA-UD', '1.1.3'), +] + +prebuildopts = "cd src && " + +files_to_copy = ['*'] + +fix_perl_shebang_for = ['run_MaxBin.pl'] + +sanity_check_paths = { + 'files': ['run_MaxBin.pl', 'src/MaxBin'], + 'dirs': [], +} + +modextrapaths = {'PATH': ['', 'src']} + +moduleclass = 'bio' From 54362da083f45edc31479bd1ab614bff278f0250 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:24:51 +0100 Subject: [PATCH 5402/9987] adding easyconfigs: DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb --- .../DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..12a3da12443 --- /dev/null +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Tarball' + +name = 'DAS_Tool' +version = '1.1.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/cmks/DAS_Tool' +description = """DAS Tool is an automated method that integrates the results of a flexible number of binning + algorithms to calculate an optimized, non-redundant set of bins from a single assembly.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] +checksums = [ + '2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a', # 1.1.1.tar.gz + 'dc89e6ab7129d170d24da28720cec0937b4d958b5ae46049373d57dde8b8a27a', # DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch +] + +dependencies = [ + ('R', '4.1.0'), + ('Python', '3.9.5'), + ('Ruby', '3.0.1'), + ('pullseq', '1.0.2'), + ('prodigal', '2.6.3'), + ('BLAST+', '2.11.0'), +] + +exts_defaultclass = 'RPackage' + +exts_list = [ + (name, version, { + 'modulename': 'DASTool', + 'source_tmpl': 'DASTool_%(version)s.tar.gz', + 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], + 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], + }), +] + +postinstallcmds = [ + "cd %(installdir)s; unzip db.zip", + "chmod a+x %(installdir)s/DAS_Tool", +] + +sanity_check_paths = { + 'files': ['DAS_Tool', 'arc.all.faa', 'arc.scg.lookup'], + 'dirs': ['DASTool/R'], +} + +sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] +# Help gets printed correctly, but the error code is 1 + +modextrapaths = { + 'PATH': '', + 'R_LIBS_SITE': '', +} + +moduleclass = 'bio' From e71706e9dd6b6e09e219cffb16ff75435eddb9cc Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:40:14 +0100 Subject: [PATCH 5403/9987] Add comment for the shebang fix + Test bin/CAT symlink --- easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb index 6707fbe1fc7..12d6688ec5a 100644 --- a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb @@ -30,11 +30,12 @@ dependencies = [ postinstallcmds = [ "cd %(installdir)s/ && ln -s CAT_pack bin", "chmod a+rx %(installdir)s/CAT_pack/*.py", + # fix shebang in check.py script ('/env/' should be '/env') "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' %(installdir)s/CAT_pack/check.py", ] sanity_check_paths = { - 'files': ['CAT_pack/CAT', 'README.md'], + 'files': ['CAT_pack/CAT', 'bin/CAT', 'README.md'], 'dirs': ['CAT_pack'], } From ae21dff077b8bc7fa0551fb94f3ad0a726d41495 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:48:00 +0100 Subject: [PATCH 5404/9987] adding easyconfigs: MetaBAT-2.15-gompi-2021a.eb --- .../m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb new file mode 100644 index 00000000000..a94f4f9953a --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'MetaBAT' +version = '2.15' + +homepage = 'https://bitbucket.org/berkeleylab/metabat' +description = "An efficient tool for accurately reconstructing single genomes from complex microbial communities" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), + ('Boost', '1.76.0'), + ('zlib', '1.2.11'), + ('SAMtools', '1.13'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), +] + +fix_perl_shebang_for = ['bin/*.pl'] + +prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " + +sanity_check_paths = { + 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], + 'dirs': [""], +} + +moduleclass = 'bio' From ccc288eca099a7be7cdb8e893ae776dd3007b65e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:53:09 +0100 Subject: [PATCH 5405/9987] adding easyconfigs: MEGAHIT-1.2.9-GCCcore-10.3.0.eb --- .../m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..279dcf61042 --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'MEGAHIT' +version = '1.2.9' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex +metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('bzip2', '1.0.8'), + ('gzip', '1.10'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(namelower)s', + 'bin/%(namelower)s_core', + 'bin/%(namelower)s_core_no_hw_accel', + 'bin/%(namelower)s_core_popcnt', + 'bin/%(namelower)s_toolkit', + ], + 'dirs': [], +} + +sanity_check_commands = [ + "megahit --version", + "megahit --test", +] + +moduleclass = 'bio' From 4b5d1b297e33663fbba1e6ba9d92012874f65491 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 10:02:35 +0100 Subject: [PATCH 5406/9987] Rename file on download + Better version string --- ...9-GCC-10.3.0.eb => InParanoid-5.0-20220607-GCC-10.3.0.eb} | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/i/InParanoid/{InParanoid-5.0.79d8e39-GCC-10.3.0.eb => InParanoid-5.0-20220607-GCC-10.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb similarity index 92% rename from easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb rename to easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb index 5bfa4ca673a..97e0d20fb04 100644 --- a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb @@ -9,7 +9,8 @@ easyblock = 'Tarball' name = 'InParanoid' -version = '5.0.79d8e39' +version = '5.0-20220607' +local_commit = '79d8e39bb243d403ce57b699c1ae104a8a640389' homepage = 'https://inparanoid.sbc.su.se' description = """InParanoid: ortholog groups with inparalogs.""" @@ -18,7 +19,7 @@ software_license = 'LicenseGPLv3' toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://bitbucket.org/sonnhammergroup/inparanoid/get/'] -sources = ['79d8e39bb243d403ce57b699c1ae104a8a640389.tar.gz'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] checksums = ['efe1a35bbb70608385780c4bf62969a29c46dd8132fbe472034422d23ad4b0c2'] # for commit 79d8e39 # NOTE some dependencies are not listed on the web site such as Java! From ddbbb99b4554786f94cdc18bc15a84f28b09c540 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 14:36:38 +0100 Subject: [PATCH 5407/9987] adding easyconfigs: typing-extensions-4.3.0-GCCcore-10.3.0.eb --- .../typing-extensions-4.3.0-GCCcore-10.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..d62b98215f8 --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.3.0' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions - Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From 29b4e32d07b930856f8c5fdac6fe5ca882efbbd1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 9 Nov 2022 15:46:39 +0100 Subject: [PATCH 5408/9987] adding easyconfigs: Seaborn-0.12.1-foss-2022a.eb --- .../s/Seaborn/Seaborn-0.12.1-foss-2022a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb new file mode 100644 index 00000000000..e3f97801473 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.12.1' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb1eb1d51d3097368c187c3ef089c0288ec1fe8aa1c69fb324c68aa1d02df4c1'] + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 601a39e5412437b1ef3c1358501c3fccbdc2b6d1 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 15:48:32 +0100 Subject: [PATCH 5409/9987] adding easyconfigs: freebayes-1.3.6-foss-2021a-R-4.1.0.eb, vcflib-1.0.3-foss-2021a-R-4.1.0.eb, SeqLib-1.2.0-GCC-10.3.0.eb --- .../freebayes-1.3.6-foss-2021a-R-4.1.0.eb | 54 +++++++++++++++ .../s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb | 49 +++++++++++++ .../vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb | 69 +++++++++++++++++++ 3 files changed, 172 insertions(+) create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb create mode 100644 easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..cc4ea323667 --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb @@ -0,0 +1,54 @@ +easyblock = 'MesonNinja' + +name = 'freebayes' +version = '1.3.6' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/freebayes/freebayes' +description = "Bayesian haplotype-based genetic polymorphism discovery and genotyping." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-1.3.6_find-external-libs.patch', + '%(name)s-1.3.5_fix-includes.patch', + '%(name)s-1.3.6_install-libs-headers.patch', +] +checksums = [ + 'd668c0b433cc0f11498ace10e48d72a7f0f40ca23b391b72e975ffafd1c13044', # v1.3.6.tar.gz + '4836a9ceaa9044e6e66b3ca0387b058a5e0505ddeaa62c428b526b5e234aff3b', # freebayes-1.3.6_find-external-libs.patch + '4c6c74b30bf3b2f04b8a50bbdef26e74f6e2412f3efbd81512226e557c2a53d1', # freebayes-1.3.5_fix-includes.patch + '5ba006ca6956905bbd81107a17e02287c515890ee25884c444ebf5b95da1caae', # freebayes-1.3.6_install-libs-headers.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('R', '4.1.0'), + ('parallel', '20210622'), + ('libffi', '3.3'), + ('VCFtools', '0.1.16'), + ('vcflib', '1.0.3', versionsuffix), + ('SeqLib', '1.2.0'), +] + +configopts = "--buildtype release" + +sanity_check_paths = { + 'files': ['bin/freebayes', 'bin/bamleftalign', 'scripts/freebayes-parallel'], + 'dirs': [], +} + +sanity_check_commands = ["freebayes --help"] + +modextrapaths = {'PATH': ['scripts']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..21b5647395b --- /dev/null +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb @@ -0,0 +1,49 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'SeqLib' +version = '1.2.0' + +homepage = 'https://github.com/walaj/SeqLib' +description = """C++ interface to HTSlib, BWA-MEM and Fermi.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'walaj' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version_major_minor)s.0_avoid-bwa-fml-namespace-conflict.patch', + '%(name)s-%(version_major_minor)s.0_use-external-deps.patch', +] +checksums = [ + '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz + # SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch + '9be9229bcf34db8e4bd1fd49614bb55d84c12df263ca7174980f7f4b1bd63da9', + '413f0ad8e0963d8922205d31e0c361cfa98a10f93e7d3e0506e0bed539ec70eb', # SeqLib-1.2.0_use-external-deps.patch +] + +builddependencies = [('Autotools', '20210128')] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), + ('JsonCpp', '1.9.4'), + ('BWA', '0.7.17'), + ('HTSlib', '1.12'), + ('fermi-lite', '20190320'), + ('SSW', '1.1'), + ('PCRE', '8.44'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/seqtools', 'lib/libseqlib.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["seqtools"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..1fd858e08a4 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb @@ -0,0 +1,69 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/vcflib/vcflib' +description = """vcflib provides methods to manipulate and interpret sequence variation as it can be + described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended + to concisely describe reference-indexed genetic variations between individuals.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use-external-deps.patch', + 'vcflib-1.0.3_fix-shared-linking.patch', +] +checksums = [ + '5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c', # v1.0.3.tar.gz + '89f99efb35eb3a5fdc5a7fdeb96c204b1af481194bcd788c939c600a985fa8a4', # vcflib-1.0.3_use-external-deps.patch + '2584e33e447c07a66eefc46263161873498910e19035f9beed1600cbd05fd4b0', # vcflib-1.0.3_fix-shared-linking.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), + ('R', '4.1.0'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.12'), + ('tabixpp', '1.1.0'), + ('intervaltree', '0.1'), + ('fastahack', '1.0.0'), + ('filevercmp', '20191210'), + ('fsom', '20141119'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), +] + +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f -regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" +preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" +preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" +preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" +preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " + +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = {'PATH': ['scripts']} + +sanity_check_paths = { + 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], + 'dirs': ['scripts'], +} + +sanity_check_commands = ["vcfremap"] + +moduleclass = 'bio' From 08832cc28564f07f4ac02d2e0166396122caae1d Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 17:16:19 +0100 Subject: [PATCH 5410/9987] Update to the last version --- ...re-10.3.0.eb => typing-extensions-4.4.0-GCCcore-10.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/t/typing-extensions/{typing-extensions-4.3.0-GCCcore-10.3.0.eb => typing-extensions-4.4.0-GCCcore-10.3.0.eb} (83%) diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.4.0-GCCcore-10.3.0.eb similarity index 83% rename from easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.4.0-GCCcore-10.3.0.eb index d62b98215f8..ea51e13ece0 100644 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.4.0-GCCcore-10.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'typing-extensions' -version = '4.3.0' +version = '4.4.0' homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' description = 'Typing Extensions - Backported and Experimental Type Hints for Python' @@ -9,7 +9,7 @@ description = 'Typing Extensions - Backported and Experimental Type Hints for Py toolchain = {'name': 'GCCcore', 'version': '10.3.0'} sources = ['typing_extensions-%(version)s.tar.gz'] -checksums = ['e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6'] +checksums = ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'] builddependencies = [('binutils', '2.36.1')] From 5781cd9d12fdde97531d3919ed60857da00b9d6f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 17:51:19 +0100 Subject: [PATCH 5411/9987] templating the name, but hardcoding the patch version --- easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb | 4 ++-- .../easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb index 21b5647395b..27a50312ce6 100644 --- a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb @@ -14,8 +14,8 @@ github_account = 'walaj' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] patches = [ - '%(name)s-%(version_major_minor)s.0_avoid-bwa-fml-namespace-conflict.patch', - '%(name)s-%(version_major_minor)s.0_use-external-deps.patch', + '%(name)s-1.2.0_avoid-bwa-fml-namespace-conflict.patch', + '%(name)s-1.2.0_use-external-deps.patch', ] checksums = [ '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb index 1fd858e08a4..9061ba602b3 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb @@ -16,8 +16,8 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] patches = [ - '%(name)s-%(version)s_use-external-deps.patch', - 'vcflib-1.0.3_fix-shared-linking.patch', + '%(name)s-1.0.3_use-external-deps.patch', + '%(name)s-1.0.3_fix-shared-linking.patch', ] checksums = [ '5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c', # v1.0.3.tar.gz From 8c9b31f081ea5134b06804aad059bd2d6508637a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:18:46 +0100 Subject: [PATCH 5412/9987] adding easyconfigs: libxml2-2.10.3-GCCcore-12.2.0.eb --- .../libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..899bcfe4e7f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.10.3' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5d2cc3d78bec3dbe212a9d7fa629ada25a7da928af432c93060ff5c17ee28a9c'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), +] + +moduleclass = 'lib' From c1c8a42c28f4823a37f93e483f0a044e77353494 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:51:53 +0100 Subject: [PATCH 5413/9987] adding easyconfigs: Python-3.10.8-GCCcore-12.2.0-bare.eb, SQLite-3.39.4-GCCcore-12.2.0.eb, Tcl-8.6.12-GCCcore-12.2.0.eb, libffi-3.4.4-GCCcore-12.2.0.eb, bzip2-1.0.8-GCCcore-12.2.0.eb, UnZip-6.0-GCCcore-12.2.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb | 27 ++++++++++ .../l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb | 29 +++++++++++ .../Python-3.10.8-GCCcore-12.2.0-bare.eb | 35 +++++++++++++ .../s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb | 39 ++++++++++++++ .../t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb | 41 +++++++++++++++ .../u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ 6 files changed, 223 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d2ce38e1732 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.39'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f9c248d7fd7 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.4' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d66c56ad259a82cf2a9dfc408b32bf5da52371500b84745f7fb8b645712df676'] + +builddependencies = [ + ('binutils', '2.39'), +] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb new file mode 100644 index 00000000000..39fbf14affe --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb @@ -0,0 +1,35 @@ +name = 'Python' +version = '3.10.8' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a'] + +builddependencies = [ + ('UnZip', '6.0'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('binutils', '2.39'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('SQLite', '3.39.4'), + ('XZ', '5.2.7'), + ('libffi', '3.4.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..cc6b559ef73 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.39.4' +local_filename_version = '3390400' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2022/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['f31d445b48e67e284cf206717cc170ab63cbe4fd7f79a82793b772285e78fdbb'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('libreadline', '8.2'), + ('Tcl', '8.6.12'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d86abbb9d4d --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.12' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['26c995dd0f167e48b11961d891ee555f680c175f7173ff8cb829f4ebcde4c1a6'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2b85900a4d8 --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' +buildopts += 'LF2="$LDFLAGS" ' +# Note: CF is multiple lines +buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' +buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' +buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From 4e58dc480e02a1ef47a382bc40ee872bcbc203e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:53:58 +0100 Subject: [PATCH 5414/9987] adding easyconfigs: cURL-7.86.0-GCCcore-12.2.0.eb --- .../c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4e108bdbc19 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.86.0' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dfdd39ba95e18847965cd3051ea6d22586609d9011d91df7bc5521288987a82'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' From 8df94ddb722ef38af443951adf5ed0f462661a03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:54:12 +0100 Subject: [PATCH 5415/9987] adding easyconfigs: libarchive-3.6.1-GCCcore-12.2.0.eb --- .../libarchive-3.6.1-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8cc05cbcb01 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.6.1' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c676146577d989189940f1959d9e3980d28513d74eedfbc6b7f15ea45fe54ee2'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('XZ', '5.2.7'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' From 4dd41bfb994262fabb743d9e4da47cd4b3ab0881 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:55:24 +0100 Subject: [PATCH 5416/9987] adding easyconfigs: CMake-3.24.3-GCCcore-12.2.0.eb --- .../c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..86db778efcb --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.24.3' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b53aa10fa82bff84ccdb59065927b72d3bee49f4d86261249fc0984b3b367291'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('cURL', '7.86.0'), + ('libarchive', '3.6.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'devel' From b0f5a08b7873d0bcf346dbda7b49417980638983 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:57:44 +0100 Subject: [PATCH 5417/9987] adding easyconfigs: FlexiBLAS-3.2.1-GCC-12.2.0.eb, BLIS-0.9.0-GCC-12.2.0.eb, OpenBLAS-0.3.21-GCC-12.2.0.eb --- .../b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb | 42 ++++++++++++++ .../f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb | 58 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 47 +++++++++++++++ 3 files changed, 147 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..3fdd482cf5a --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.9.0' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_disable_power9_kernels.patch', + '%(name)s-%(version)s_enable_ppc_autodetect.patch', +] +checksums = [ + '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz + # BLIS-0.9.0_disable_power9_kernels.patch + 'ed7a326bc5c5c21c42faefbec2fd7be609d1c7236981b466475edace39307279', + # BLIS-0.9.0_enable_ppc_autodetect.patch + 'f373fb252c0d14036fb631f048091976cceb02abb3e570a97fbaeac2fbb12328', +] +builddependencies = [ + ('Python', '3.10.8', '-bare'), + ('Perl', '5.36.0'), +] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..9a77c6b3a77 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'FlexiBLAS' +version = '3.2.1' + +homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' +description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation +used by a program without recompiling or relinking it.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" +toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} + +builddependencies = [ + ('CMake', '3.24.3'), + ('Python', '3.10.8', '-bare'), # required for running the tests + ('BLIS', '0.9.0'), +] + +dependencies = [ + ('OpenBLAS', '0.3.21'), +] + +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +local_backends = ['OpenBLAS', 'BLIS'] + +# imkl supplies its backend via the imkl module, not as a dependency +if ARCH == 'x86_64': + local_backends.append('imkl') + +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5be7e508e2dbb751b3bf372639d8e82a11f79e9ef6cbf243b64981c24a5703cf'], + 'backends': local_backends, + }), + ('LAPACK', '3.10.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['cd005cd021f144d7d5f7f33c943942db9f03a28d110d6a3b80d718a295f7f714'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb new file mode 100644 index 00000000000..eee3ebc9454 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -0,0 +1,47 @@ +name = 'OpenBLAS' +version = '0.3.21' + +homepage = 'http://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', +] +checksums = [ + {'v0.3.21.tar.gz': 'f36ba3d7a60e7c8bcc54cd9aaa9b1223dd42eaf02c811791c37e8ca707c241ca'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, +] + +builddependencies = [ + # required by LAPACK test suite + ('Python', '3.10.8', '-bare'), +] + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From b23bc8abe61cca25d721e9efdcbd8a0733275e9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:06:22 +0100 Subject: [PATCH 5418/9987] adding easyconfigs: hwloc-2.8.0-GCCcore-12.2.0.eb, libpciaccess-0.17-GCCcore-12.2.0.eb, xorg-macros-1.19.3-GCCcore-12.2.0.eb --- .../h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb | 45 +++++++++++++++++++ .../libpciaccess-0.17-GCCcore-12.2.0.eb | 26 +++++++++++ .../xorg-macros-1.19.3-GCCcore-12.2.0.eb | 27 +++++++++++ 3 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f6483901c2b --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.8.0' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['20b2bd4df436827d8e50f7afeafb6f967259f2fb374ce7330244f8d0ed2dde6f'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('numactl', '2.0.16'), + ('libxml2', '2.10.3'), + ('libpciaccess', '0.17'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0c9005d81c0 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.17' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bf6985a77d2ecb00e2c79da3edfb26b909178ffca3f2e9d14ed0620259ab733b'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('xorg-macros', '1.19.3'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..23dad904c35 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.3' + +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['8205d210a580da0938f5ce4392a96b60cf1d9a5f792eaa1474fa4c1977aef4d0'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From 7fd3bc769e202c71bff87cb387d7223b27583fc8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:34:01 +0100 Subject: [PATCH 5419/9987] adding easyconfigs: OpenMPI-4.1.4-GCC-12.2.0.eb, libevent-2.1.12-GCCcore-12.2.0.eb, libfabric-1.16.1-GCCcore-12.2.0.eb, PMIx-4.2.2-GCCcore-12.2.0.eb, UCC-1.1.0-GCCcore-12.2.0.eb --- .../libevent-2.1.12-GCCcore-12.2.0.eb | 38 ++++++++++++ .../libfabric-1.16.1-GCCcore-12.2.0.eb | 62 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb | 62 +++++++++++++++++++ .../p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb | 45 ++++++++++++++ .../u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb | 37 +++++++++++ 5 files changed, 244 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..99908875d8c --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..97eacfc006e --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.16.1' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +# The psm3 provider (enabled by default) requires an AVX capable system to run +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ofiwg/libfabric/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +patches = [ + '%(name)s-1.12.1_disable-psm3-avx-config.patch', +] +checksums = [ + {'libfabric-1.16.1.tar.bz2': '53f992d33f9afe94b8a4ea3d105504887f4311cf4b68cea99a24a85fcc39193f'}, + {'libfabric-1.12.1_disable-psm3-avx-config.patch': + '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('numactl', '2.0.16'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# Regenerate build files to pick up psm3-axv-config patch +preconfigopts = "./autogen.sh &&" + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) +configopts += "--disable-usnic " + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb new file mode 100644 index 00000000000..09a6bc393d3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb @@ -0,0 +1,62 @@ +name = 'OpenMPI' +version = '4.1.4' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', +] +checksums = [ + '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d', # openmpi-4.1.4.tar.bz2 + # OpenMPI-4.1.1_build-with-internal-cuda-header.patch + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83', + # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', +] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('Perl', '5.36.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('hwloc', '2.8.0'), + ('libevent', '2.1.12'), + ('UCX', '1.13.1'), + ('libfabric', '1.16.1'), + ('PMIx', '4.2.2'), + ('UCC', '1.1.0'), +] + +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' + +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ffe8c9fba65 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '4.2.2' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['935b2f492e4bc409017f1425a83366aa72a7039605ea187c9fac7bb1371cd73c'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.2.12'), + ('hwloc', '2.8.0'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b5ff6ef4e42 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'UCC' +version = '1.1.0' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCX', '1.13.1'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/ucc_info'], + 'dirs': ['include', 'lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +moduleclass = 'lib' From 2fea5fff4cb20690af3a56e49a6441a8c231675e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:36:23 +0100 Subject: [PATCH 5420/9987] adding easyconfigs: gompi-2022.10.eb --- .../easyconfigs/g/gompi/gompi-2022.10.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2022.10.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2022.10.eb b/easybuild/easyconfigs/g/gompi/gompi-2022.10.eb new file mode 100644 index 00000000000..9d5e2752969 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2022.10.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2022.10' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' From b0e358cbfd08891ead6d086aadc81b452d909c49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:37:21 +0100 Subject: [PATCH 5421/9987] adding easyconfigs: FFTW-3.3.10-GCC-12.2.0.eb, FFTW.MPI-3.3.10-gompi-2022.10.eb --- .../FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb | 19 +++++++++++++++++++ .../f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb | 17 +++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb new file mode 100644 index 00000000000..dacac34b6e3 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022.10'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb new file mode 100644 index 00000000000..90dce63b19c --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +runtest = 'check' + +moduleclass = 'numlib' From 443aca94e6dfeb2c4eb16dc0f412566ccb62af31 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:39:30 +0100 Subject: [PATCH 5422/9987] {toolchain} foss/2022.10 --- easybuild/easyconfigs/f/foss/foss-2022.10.eb | 28 ++++++++++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb | 21 +++++++++ .../ScaLAPACK-2.2.0-gompi-2022.10-fb.eb | 43 +++++++++++++++++++ 3 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/f/foss/foss-2022.10.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2022.10.eb b/easybuild/easyconfigs/f/foss/foss-2022.10.eb new file mode 100644 index 00000000000..023dc177384 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2022.10.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2022.10' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.2.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb new file mode 100644 index 00000000000..453f6a14c83 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2022.10'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb new file mode 100644 index 00000000000..5b5a3e57d38 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb @@ -0,0 +1,43 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2022.10'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.2.1'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From c6a622be78d7044e477d203e1a9ddec8af7bf375 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:49:33 +0100 Subject: [PATCH 5423/9987] construct 'buildopts' value in a more transparent way in UnZip easyconfig --- .../u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb index 2b85900a4d8..042b74c404e 100644 --- a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb @@ -33,12 +33,19 @@ dependencies = [ skipsteps = ['configure'] -buildopts = '-f unix/Makefile CC="$CC" D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' -buildopts += 'LF2="$LDFLAGS" ' -# Note: CF is multiple lines -buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' -buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' -buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' +local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT' + '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD', + '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT'] + +buildopts = ' '.join([ + "-f unix/Makefile", + 'CC="$CC"', + 'D_USE_BZ2=-DUSE_BZIP2', + 'L_BZ2=-lbz2', + 'LF2="$LDFLAGS"', + 'CF="%s"' % ' '.join(local_cf), + 'unzips', +]) installopts = '-f unix/Makefile prefix=%(installdir)s ' From 2745967c83fc6c5dd3c06b2c051338d7a9b0f294 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 10 Nov 2022 08:54:23 +0000 Subject: [PATCH 5424/9987] adding easyconfigs: OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb --- .../OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb new file mode 100644 index 00000000000..9326eb7240e --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '6.2' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2022.10'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb9dbc87dcf8ec6785977a61f6fceee8febf1a682488eaab4c58cf50e4fa985f'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From a010106a159d8b9ad639128420ba6861ef42f21f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 09:59:48 +0100 Subject: [PATCH 5425/9987] adding easyconfigs: python-libsbml-5.19.2-foss-2021a.eb --- .../python-libsbml-5.19.2-foss-2021a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb new file mode 100644 index 00000000000..3ff630bebf1 --- /dev/null +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb @@ -0,0 +1,51 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'python-libsbml' +version = '5.19.2' + +homepage = 'https://sbml.org/' +description = """LibSBML Python API.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), +] + +use_pip = True + +# NOTE Use version 5.19.2 because is the last one provided as tarball and not as weird whl +exts_list = [ + (name, version, { + 'modulename': 'libsbml', + 'checksums': ['b11a79a5421abba9f8874ebbc1c479cbdb3c1827697db74b687705632583a0e5'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 2538811517d07628a0d89709afd06376df1898bb Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 10:20:48 +0100 Subject: [PATCH 5426/9987] Add missing sanity_pip_check --- .../p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb index 3ff630bebf1..ebe73922184 100644 --- a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb @@ -48,4 +48,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'bio' From 23b69b499eb00902e17dd2c31bb5e82d0706b1ba Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 10 Nov 2022 10:52:08 +0000 Subject: [PATCH 5427/9987] switch 'www.cpan.org' to 'cpan.metacpan.org' in extension source_urls for recent Perl easyconfigs --- .../p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 42 +++++++++---------- .../p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 42 +++++++++---------- .../p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 42 +++++++++---------- 3 files changed, 63 insertions(+), 63 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index b998f1d93d0..9c3e8483a03 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -110,47 +110,47 @@ exts_list = [ }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN/'], 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], }), ('Importer', '0.026', { 'source_tmpl': 'Importer-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], }), ('Term::Table', '0.016', { 'source_tmpl': 'Term-Table-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], }), ('Scope::Guard', '0.21', { 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE/'], 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], }), ('Sub::Info', '0.002', { 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], }), ('Test2::Require::Module', '0.000145', { 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['ed44be739c8879fe178d3107b238f2db960d52797db0058de53be5b84600358b'], }), ('Test2::Plugin::NoWarnings', '0.09', { 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], }), ('Class::Tiny', '1.008', { 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], }), ('Test::File::ShareDir::Dist', '1.001002', { 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL/'], 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], }), ('DateTime::Locale', '1.35', { @@ -210,12 +210,12 @@ exts_list = [ }), ('CPAN::Meta::Check', '0.014', { 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LE/LEONT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT/'], 'checksums': ['28a0572bfc1c0678d9ce7da48cf521097ada230f96eb3d063fcbae1cfe6a351f'], }), ('Test::Without::Module', '0.20', { 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CO/CORION/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION/'], 'checksums': ['8e9aeb7c32a6c6d0b8a93114db2a8c072721273a9d9a2dd4f9ca86cfd28aa524'], }), ('DateTime', '1.58', { @@ -1051,7 +1051,7 @@ exts_list = [ }), ('Test::Needs', '0.002009', { 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/H/HA/HAARG/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], 'checksums': ['571c21193ad16195df58b06b268798796a391b398c443271721d2cc0fb7c4ac3'], }), ('HTTP::Daemon', '6.14', { @@ -1131,12 +1131,12 @@ exts_list = [ }), ('Module::Runtime::Conflicts', '0.003', { 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], }), ('Test::CleanNamespaces', '0.24', { 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], }), ('Moose', '2.2201', { @@ -1221,7 +1221,7 @@ exts_list = [ }), ('Test::More::UTF8', '0.05', { 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/M/MO/MONS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS/'], 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], }), ('Text::Template', '1.60', { @@ -1231,17 +1231,17 @@ exts_list = [ }), ('PadWalker', '2.5', { 'source_tmpl': 'PadWalker-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RO/ROBIN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], }), ('Devel::Cycle', '1.12', { 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LD/LDS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS/'], 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], }), ('Test::Memory::Cycle', '1.06', { 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/P/PE/PETDANCE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], }), ('PDF::API2', '2.043', { @@ -1301,12 +1301,12 @@ exts_list = [ }), ('Set::Object', '1.42', { 'source_tmpl': 'Set-Object-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RU/RURBAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], }), ('Heap', '0.80', { 'source_tmpl': 'Heap-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JM/JMM/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], }), ('Graph', '0.9725', { @@ -1376,7 +1376,7 @@ exts_list = [ }), ('Variable::Magic', '0.62', { 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/V/VP/VPIT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT/'], 'checksums': ['3f9a18517e33f006a9c2fc4f43f01b54abfe6ff2eae7322424f31069296b615c'], }), ('B::Hooks::EndOfScope', '0.26', { diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 1424b9a1a56..78044193927 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -110,47 +110,47 @@ exts_list = [ }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], }), ('Importer', '0.026', { 'source_tmpl': 'Importer-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], }), ('Term::Table', '0.016', { 'source_tmpl': 'Term-Table-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], }), ('Scope::Guard', '0.21', { 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], }), ('Sub::Info', '0.002', { 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], }), ('Test2::Require::Module', '0.000145', { 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ed44be739c8879fe178d3107b238f2db960d52797db0058de53be5b84600358b'], }), ('Test2::Plugin::NoWarnings', '0.09', { 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], }), ('Class::Tiny', '1.008', { 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], }), ('Test::File::ShareDir::Dist', '1.001002', { 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], }), ('DateTime::Locale', '1.36', { @@ -210,12 +210,12 @@ exts_list = [ }), ('CPAN::Meta::Check', '0.014', { 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LE/LEONT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT/'], 'checksums': ['28a0572bfc1c0678d9ce7da48cf521097ada230f96eb3d063fcbae1cfe6a351f'], }), ('Test::Without::Module', '0.20', { 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CO/CORION/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION/'], 'checksums': ['8e9aeb7c32a6c6d0b8a93114db2a8c072721273a9d9a2dd4f9ca86cfd28aa524'], }), ('DateTime', '1.58', { @@ -1051,7 +1051,7 @@ exts_list = [ }), ('Test::Needs', '0.002009', { 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/H/HA/HAARG/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], 'checksums': ['571c21193ad16195df58b06b268798796a391b398c443271721d2cc0fb7c4ac3'], }), ('HTTP::Daemon', '6.14', { @@ -1131,12 +1131,12 @@ exts_list = [ }), ('Module::Runtime::Conflicts', '0.003', { 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], }), ('Test::CleanNamespaces', '0.24', { 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], }), ('Moose', '2.2201', { @@ -1221,7 +1221,7 @@ exts_list = [ }), ('Test::More::UTF8', '0.05', { 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/M/MO/MONS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS/'], 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], }), ('Text::Template', '1.61', { @@ -1231,17 +1231,17 @@ exts_list = [ }), ('PadWalker', '2.5', { 'source_tmpl': 'PadWalker-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RO/ROBIN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], }), ('Devel::Cycle', '1.12', { 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LD/LDS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS/'], 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], }), ('Test::Memory::Cycle', '1.06', { 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/P/PE/PETDANCE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], }), ('PDF::API2', '2.043', { @@ -1301,12 +1301,12 @@ exts_list = [ }), ('Set::Object', '1.42', { 'source_tmpl': 'Set-Object-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RU/RURBAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], }), ('Heap', '0.80', { 'source_tmpl': 'Heap-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JM/JMM/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], }), ('Graph', '0.9725', { @@ -1376,7 +1376,7 @@ exts_list = [ }), ('Variable::Magic', '0.62', { 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/V/VP/VPIT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT/'], 'checksums': ['3f9a18517e33f006a9c2fc4f43f01b54abfe6ff2eae7322424f31069296b615c'], }), ('B::Hooks::EndOfScope', '0.26', { diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index df8c81ece83..9e66a846bc3 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -110,47 +110,47 @@ exts_list = [ }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], }), ('Importer', '0.026', { 'source_tmpl': 'Importer-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], }), ('Term::Table', '0.016', { 'source_tmpl': 'Term-Table-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], }), ('Scope::Guard', '0.21', { 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], }), ('Sub::Info', '0.002', { 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], }), ('Test2::Require::Module', '0.000145', { 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ed44be739c8879fe178d3107b238f2db960d52797db0058de53be5b84600358b'], }), ('Test2::Plugin::NoWarnings', '0.09', { 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], }), ('Class::Tiny', '1.008', { 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], }), ('Test::File::ShareDir::Dist', '1.001002', { 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], }), ('DateTime::Locale', '1.36', { @@ -210,12 +210,12 @@ exts_list = [ }), ('CPAN::Meta::Check', '0.014', { 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LE/LEONT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT/'], 'checksums': ['28a0572bfc1c0678d9ce7da48cf521097ada230f96eb3d063fcbae1cfe6a351f'], }), ('Test::Without::Module', '0.20', { 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CO/CORION/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION/'], 'checksums': ['8e9aeb7c32a6c6d0b8a93114db2a8c072721273a9d9a2dd4f9ca86cfd28aa524'], }), ('DateTime', '1.58', { @@ -1051,7 +1051,7 @@ exts_list = [ }), ('Test::Needs', '0.002009', { 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/H/HA/HAARG/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], 'checksums': ['571c21193ad16195df58b06b268798796a391b398c443271721d2cc0fb7c4ac3'], }), ('HTTP::Daemon', '6.14', { @@ -1131,12 +1131,12 @@ exts_list = [ }), ('Module::Runtime::Conflicts', '0.003', { 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], }), ('Test::CleanNamespaces', '0.24', { 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], }), ('Moose', '2.2201', { @@ -1221,7 +1221,7 @@ exts_list = [ }), ('Test::More::UTF8', '0.05', { 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/M/MO/MONS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS/'], 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], }), ('Text::Template', '1.61', { @@ -1231,17 +1231,17 @@ exts_list = [ }), ('PadWalker', '2.5', { 'source_tmpl': 'PadWalker-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RO/ROBIN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], }), ('Devel::Cycle', '1.12', { 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LD/LDS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS/'], 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], }), ('Test::Memory::Cycle', '1.06', { 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/P/PE/PETDANCE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], }), ('PDF::API2', '2.043', { @@ -1301,12 +1301,12 @@ exts_list = [ }), ('Set::Object', '1.42', { 'source_tmpl': 'Set-Object-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RU/RURBAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], }), ('Heap', '0.80', { 'source_tmpl': 'Heap-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JM/JMM/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], }), ('Graph', '0.9725', { @@ -1376,7 +1376,7 @@ exts_list = [ }), ('Variable::Magic', '0.62', { 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/V/VP/VPIT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT/'], 'checksums': ['3f9a18517e33f006a9c2fc4f43f01b54abfe6ff2eae7322424f31069296b615c'], }), ('B::Hooks::EndOfScope', '0.26', { From 6b3b897fcfa09c66a861fd71c41e229a2e3c4df5 Mon Sep 17 00:00:00 2001 From: easybuild Date: Thu, 10 Nov 2022 13:09:59 +0000 Subject: [PATCH 5428/9987] adding easyconfigs: Centrifuge-1.0.4-gompi-2021a.eb --- .../Centrifuge-1.0.4-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb diff --git a/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb b/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb new file mode 100644 index 00000000000..d73a84e0a4c --- /dev/null +++ b/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Centrifuge' +version = '1.0.4' + +homepage = 'https://ccb.jhu.edu/software/centrifuge' +description = 'Classifier for metagenomic sequences' + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/DaehwanKimLab/centrifuge/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '929daed0f84739f7636cc1ea2757527e83373f107107ffeb5937a403ba5201bc', # v1.0.4.tar.gz +] + +dependencies = [ + ('NGS', '2.10.9'), + ('ncbi-vdb', '2.10.9'), +] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CXXFLAGS" ' +buildopts += 'USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB' + +installopts = "prefix=%(installdir)s" + +fix_perl_shebang_for = ['bin/centrifuge*.pl'] + +sanity_check_paths = { + 'files': ['bin/centrifuge%s' % x for x in ['', '-build', '-build-bin', '-class', '-download', + '-inspect', '-inspect-bin']], + 'dirs': [], +} + +sanity_check_commands = ["centrifuge --help"] + +moduleclass = 'bio' From 41f160ccd11862234a24aa8308ad16c8f36ecfdf Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 14:57:01 +0100 Subject: [PATCH 5429/9987] Update to version 1.1.3, the last one with the R tarball --- ...021a-R-4.1.0.eb => DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/d/DAS_Tool/{DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb => DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb} (88%) diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb similarity index 88% rename from easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb rename to easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb index 12a3da12443..8889f759be9 100644 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb @@ -1,7 +1,7 @@ easyblock = 'Tarball' name = 'DAS_Tool' -version = '1.1.1' +version = '1.1.3' versionsuffix = '-R-%(rver)s' homepage = 'https://github.com/cmks/DAS_Tool' @@ -14,7 +14,7 @@ source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] sources = ['%(version)s.tar.gz'] patches = ['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] checksums = [ - '2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a', # 1.1.1.tar.gz + 'c2d41a38a7a92d53d412ac3f2b8ab5b9fa64c56021aa5c4dd51fefd7c96b68f4', # 1.1.3.tar.gz 'dc89e6ab7129d170d24da28720cec0937b4d958b5ae46049373d57dde8b8a27a', # DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch ] @@ -34,7 +34,7 @@ exts_list = [ 'modulename': 'DASTool', 'source_tmpl': 'DASTool_%(version)s.tar.gz', 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], - 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], + 'checksums': ['050ba4fa061ceb398a6881652b4b5f14736581a35edd00ef9ae4cea986f38d18'], }), ] From b6783e1df0dcc157bccab2574dd932728a292ba7 Mon Sep 17 00:00:00 2001 From: easybuild Date: Thu, 10 Nov 2022 15:38:01 +0000 Subject: [PATCH 5430/9987] Fix Perl version in gompi-2021a in ncbi-vdb update --- .../n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb new file mode 100644 index 00000000000..aa5ea3306c4 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.10.9' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch'] +checksums = [ + '3707f81412dbf6ce2b29d3e65e364116c86acc534543e5a084cf8a666b81960d', # ncbi-vdb-2.10.9.tar.gz + 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch +] + +builddependencies = [('Perl', '5.32.1')] + +dependencies = [ + ('NGS', '2.10.9'), + ('file', '5.40'), # provides libmagic + ('HDF5', '1.10.7'), + ('libxml2', '2.9.10'), + ('bzip2', '1.0.8'), +] + +# add addtional libraries needed to statically link HDF5 from EB +preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl &&" + +configopts = "--build-prefix=%(builddir)s " # change default build directory +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS/jar/ngs-java.jar " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +# replace hardcoded optimization flags with EB settings +prebuildopts = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " +preinstallopts = 'EBFLAGS="$CFLAGS" ' + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + + [('lib/libncbi-%s.%s' % (l, e), 'lib64/libncbi-%s.%s' % (l, e)) + for l in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' From e443f54e1cfd4976395154afd6ce8e69f18b4476 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 16:44:08 +0100 Subject: [PATCH 5431/9987] Update to last version after fixes on the pypi side --- ...9.2-foss-2021a.eb => python-libsbml-5.19.7-foss-2021a.eb} | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/python-libsbml/{python-libsbml-5.19.2-foss-2021a.eb => python-libsbml-5.19.7-foss-2021a.eb} (83%) diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb similarity index 83% rename from easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb rename to easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb index ebe73922184..4fb837dd9a0 100644 --- a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb @@ -9,7 +9,7 @@ easyblock = 'PythonBundle' name = 'python-libsbml' -version = '5.19.2' +version = '5.19.7' homepage = 'https://sbml.org/' description = """LibSBML Python API.""" @@ -35,11 +35,10 @@ dependencies = [ use_pip = True -# NOTE Use version 5.19.2 because is the last one provided as tarball and not as weird whl exts_list = [ (name, version, { 'modulename': 'libsbml', - 'checksums': ['b11a79a5421abba9f8874ebbc1c479cbdb3c1827697db74b687705632583a0e5'], + 'checksums': ['447b1fde7aceccd11a93dc9f589ffd9319ba854d7b7583f911259a8b0127ab7b'], }), ] From 633254f688e76b47bfdba646d29240aa4541a4f8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 17:01:26 +0100 Subject: [PATCH 5432/9987] adding easyconfigs: Nextflow-pipeline-20221110-foss-2021a-mag.eb --- ...xtflow-pipeline-20221110-foss-2021a-mag.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb diff --git a/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb b/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb new file mode 100644 index 00000000000..d37829af6c2 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'Bundle' + +name = 'Nextflow-pipeline' +version = '20221110' +versionsuffix = '-mag' + +homepage = 'https://nf-co.re/mag' +description = """The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +# NOTE The long reads sequencing part tools will be added later +dependencies = [ + ('Nextflow', '22.10.1', '', SYSTEM), + ('AdapterRemoval', '2.3.2'), + ('BCFtools', '1.12'), + ('Bowtie2', '2.4.4'), + ('BUSCO', '5.4.2'), + ('CAT-BAT', '5.2.3'), + ('Centrifuge', '1.0.4'), + ('DAS_Tool', '1.1.3', '', ('foss', '2021a-R-4.1.0')), + ('fastp', '0.23.2'), + ('FastQC', '0.11.9', '-Java-11', SYSTEM), + ('freebayes', '1.3.6', '', ('foss', '2021a-R-4.1.0')), + ('GTDB-Tk', '2.0.0'), + ('Kraken2', '2.1.2'), + ('KronaTools', '2.8'), + ('MaxBin', '2.2.7'), + ('MEGAHIT', '1.2.9'), + ('MetaBAT', '2.15'), + ('MultiQC', '1.11'), + ('NanoLyse', '1.2.1'), + ('prodigal', '2.6.3'), + ('prokka', '1.14.5'), + ('PyDamage', '0.70'), + ('QUAST', '5.0.2'), + ('SPAdes', '3.15.3'), +] + +moduleclass = 'bio' From d523a904efe69621d9267ed6d2519dd6fd43f5d4 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 18:30:34 +0100 Subject: [PATCH 5433/9987] adding easyconfigs: Filtlong-0.2.1-GCC-10.3.0.eb --- .../f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..8ed16b2cc4c --- /dev/null +++ b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'Filtlong' +version = '0.2.1' + +homepage = 'https://github.com/rrwick/Filtlong' +description = """Filtlong is a tool for filtering long reads by quality. It can take a set + of long reads and produce a smaller, better subset. It uses both read length (longer is better) + and read identity (higher is better) when choosing which reads pass the filter""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/rrwick/Filtlong/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e6f47675e87f98cf2481a60bef5cad38396f1e4db653a5c1673139f37770273a'] + +unpack_options = '--strip-components=1' + +parallel = 1 + +dependencies = [ + ('zlib', '1.2.11'), +] + +files_to_copy = ["*"] + +sanity_check_paths = { + 'files': ['bin/filtlong'], + 'dirs': [] +} + +sanity_check_commands = ["filtlong --help"] + +moduleclass = 'bio' From 820ea192af5b7d8eff4735f91552097e21283438 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 10 Nov 2022 18:34:21 +0100 Subject: [PATCH 5434/9987] Sanity check now checks for the exact folder --- .../MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index e048be328cf..b26dd65738e 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -103,7 +103,7 @@ exts_list = [ sanity_check_paths = { 'files': [], - 'dirs': ['packages'] + 'dirs': ['packages/%(name)s'] } modextrapaths = { From 9e5bd95f46e0e292c61401b1810f5399b5716558 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 18:35:04 +0100 Subject: [PATCH 5435/9987] Add a missing long read part software --- .../Nextflow-pipeline-20221110-foss-2021a-mag.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb b/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb index d37829af6c2..af7cdd8d297 100644 --- a/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb +++ b/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb @@ -17,7 +17,7 @@ description = """The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.""" toolchain = {'name': 'foss', 'version': '2021a'} -# NOTE The long reads sequencing part tools will be added later +# TODO The long reads sequencing part tools will be added later dependencies = [ ('Nextflow', '22.10.1', '', SYSTEM), ('AdapterRemoval', '2.3.2'), @@ -29,6 +29,7 @@ dependencies = [ ('DAS_Tool', '1.1.3', '', ('foss', '2021a-R-4.1.0')), ('fastp', '0.23.2'), ('FastQC', '0.11.9', '-Java-11', SYSTEM), + ('Filtlong', '0.2.1'), ('freebayes', '1.3.6', '', ('foss', '2021a-R-4.1.0')), ('GTDB-Tk', '2.0.0'), ('Kraken2', '2.1.2'), From fae36b681c85e52a93d7bada9ffd39c902a7eb8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Nov 2022 21:06:20 +0100 Subject: [PATCH 5436/9987] strip out sanity_check_paths from python-libsbml easyconfig, PythonBundle checks by non-empty lib/python*/site-packages by default --- .../p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb index 4fb837dd9a0..04cf6dfe9e0 100644 --- a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb @@ -42,11 +42,6 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_pip_check = True moduleclass = 'bio' From 342043332611daa94060ef014943f504a78a909a Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 09:10:51 +0100 Subject: [PATCH 5437/9987] adding easyconfigs: COBRApy-0.26.0-foss-2021a.eb --- .../c/COBRApy/COBRApy-0.26.0-foss-2021a.eb | 98 +++++++++++++++++++ 1 file changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb new file mode 100644 index 00000000000..7cce7c9bf0f --- /dev/null +++ b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb @@ -0,0 +1,98 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'COBRApy' +version = '0.26.0' + +homepage = 'https://opencobra.github.io/cobrapy/' +description = """COBRApy is a package for constraint-based modeling of metabolic networks.""" +software_license = 'LicenseGPLv2' + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('ruamel.yaml', '0.17.21'), + ('SciPy-bundle', '2021.05'), + ('sympy', '1.8'), + ('GLPK', '5.0'), + ('python-libsbml', '5.19.7'), +] + +use_pip = True + +exts_list = [ + ('typing-extensions', '4.4.0', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.6.0', { + 'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('swiglpk', '5.0.8', { + 'checksums': ['9b933d7ba17c619f5d838b6b3216647bcf8a2e22cd67ea89b0f2e2f50f7be0ae'], + }), + ('optlang', '1.6.0', { + 'checksums': ['b503b05e4f434c5c69e4aac90b2dfd3cba9fa8ae24899a9a820017ce1d3d370c'], + }), + ('importlib_resources', '5.10.0', { + 'checksums': ['c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.2', { + 'checksums': ['25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421'], + }), + ('h11', '0.12.0', { + 'checksums': ['47222cb6067e4a307d535814917cd98fd0a57b6788ce715755fa2b6c28b56042'], + }), + ('httpcore', '0.15.0', { + 'checksums': ['18b68ab86a3ccf3e7dc0f43598eaddcf472b602aba29f9aa6ab85fe2ada3980b'], + }), + ('httpx', '0.23.0', { + 'checksums': ['f28eac771ec9eb4866d3fb4ab65abd42d38c424739e80c08d8d20570de60b0ef'], + }), + ('diskcache', '5.4.0', { + 'checksums': ['8879eb8c9b4a2509a5e633d2008634fb2b0b35c2b36192d89655dbde02419644'], + }), + # More recent versions of pipdeptree do not provide the same methods + ('pipdeptree', '1.0.0', { + 'checksums': ['5fe866a38113d28d527033ececc57b8e86df86b7c29edbacb33f41ee50f75b31'], + }), + ('versioneer', '0.28', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['11ffc09427ac99db4ce61bdc85785dae819618d0de28153adfce3085956125a8'], + }), + ('depinfo', '1.7.0', { + 'checksums': ['770c82e02f7f1f58c8ff87f8ad132ef3b5f5acbce586b838fadd0eb25b131340'], + }), + ('cobra', version, { + 'checksums': ['4c19ed3a1af8376479cc276b83fb3ceb3a373c75353f4d9d41995c6fe81e03ad'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 3ffcba6d152aaf9ca2eb43b09d74aadf93ab696e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 09:50:15 +0100 Subject: [PATCH 5438/9987] Update bundle package name + Fix sanity_check_paths --- .../nf-core-mag-20221110-foss-2021a.eb} | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/n/{Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb => nf-core-mag/nf-core-mag-20221110-foss-2021a.eb} (78%) diff --git a/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb similarity index 78% rename from easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb rename to easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb index af7cdd8d297..ef6918ce6df 100644 --- a/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb +++ b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb @@ -8,16 +8,15 @@ easyblock = 'Bundle' -name = 'Nextflow-pipeline' +name = 'nf-core-mag' version = '20221110' -versionsuffix = '-mag' homepage = 'https://nf-co.re/mag' description = """The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.""" toolchain = {'name': 'foss', 'version': '2021a'} -# TODO The long reads sequencing part tools will be added later +# TODO The long reads sequencing part (2) tools will be added later dependencies = [ ('Nextflow', '22.10.1', '', SYSTEM), ('AdapterRemoval', '2.3.2'), @@ -26,11 +25,11 @@ dependencies = [ ('BUSCO', '5.4.2'), ('CAT-BAT', '5.2.3'), ('Centrifuge', '1.0.4'), - ('DAS_Tool', '1.1.3', '', ('foss', '2021a-R-4.1.0')), + ('DAS_Tool', '1.1.3', '-R-4.1.0'), ('fastp', '0.23.2'), ('FastQC', '0.11.9', '-Java-11', SYSTEM), ('Filtlong', '0.2.1'), - ('freebayes', '1.3.6', '', ('foss', '2021a-R-4.1.0')), + ('freebayes', '1.3.6', '-R-4.1.0'), ('GTDB-Tk', '2.0.0'), ('Kraken2', '2.1.2'), ('KronaTools', '2.8'), @@ -46,4 +45,11 @@ dependencies = [ ('SPAdes', '3.15.3'), ] +postinstallcmds = ["echo 'Bundle for the Nextflow pipeline https://nf-co.re/mag' > %(installdir)s/README"] + +sanity_check_paths = { + 'files': ['README'], + 'dirs': [], +} + moduleclass = 'bio' From 677f7d24e4b14f8a0453b0a17402de7d06f78230 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 10:19:56 +0100 Subject: [PATCH 5439/9987] Use SPAdes version already used in the toolchain --- .../n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb index ef6918ce6df..2f394f3514e 100644 --- a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb +++ b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb @@ -42,7 +42,7 @@ dependencies = [ ('prokka', '1.14.5'), ('PyDamage', '0.70'), ('QUAST', '5.0.2'), - ('SPAdes', '3.15.3'), + ('SPAdes', '3.13.0'), ] postinstallcmds = ["echo 'Bundle for the Nextflow pipeline https://nf-co.re/mag' > %(installdir)s/README"] From 1201ed530f22a9375fc7f6a6573afc42bd2b7dc1 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 10:44:25 +0100 Subject: [PATCH 5440/9987] adding easyconfigs: Porechop-0.2.4-GCCcore-10.3.0.eb --- .../Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..06648897819 --- /dev/null +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'Porechop' +version = '0.2.4' + +homepage = 'https://github.com/rrwick/Porechop' +description = """Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. + Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, + it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments + to effectively find adapters, even at low sequence identity""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/rrwick/Porechop/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From 2043a13a426aa1d8fd61052c72c9710e986dfc09 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 11:00:31 +0100 Subject: [PATCH 5441/9987] Add missing binutils --- .../easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb index 06648897819..b637b657763 100644 --- a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb @@ -20,6 +20,10 @@ source_urls = ['https://github.com/rrwick/Porechop/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'] +builddependencies = [ + ('binutils', '2.36.1'), +] + dependencies = [ ('Python', '3.9.5'), ] From 411efa84f07ffcf24aeae0446ead03fd5a66be93 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Fri, 11 Nov 2022 11:27:59 +0100 Subject: [PATCH 5442/9987] adding easyconfigs: Blender-3.3.1.eb --- .../easyconfigs/b/Blender/Blender-3.3.1.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb new file mode 100644 index 00000000000..71c7f00f840 --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb @@ -0,0 +1,38 @@ +# EasyConfig based on the official Blender binaries, which should work +# on any system that has glibc >= 2.17. As the main binary is statically +# linked and includes a Python interpreter no other dependencies should +# be necessary +easyblock = 'PackedBinary' + +name = 'Blender' +version = '3.3.1' +versionsuffix = '' + +homepage = 'https://www.blender.org/' +description = """Blender is the free and open source 3D creation suite. It supports + the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, + compositing and motion tracking, even video editing and game creation.""" + +toolchain = {'name': 'system', 'version': ''} + +sources = ['blender-%(version)s-linux-x64.tar.xz'] +source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender%(version_major_minor)s/'] +patches = [] +checksums = [ + '3089a485dd621785d7a702089aba72d07b8f733a362e901ec1449b9a379546f2' +] + +builddependencies = [] + +dependencies = [] + +sanity_check_paths = { + 'files': ['blender', 'blender-softwaregl'], + 'dirs': ['3.3'] +} + +#modextrapaths = { +# 'PATH' : '', +#} + +moduleclass = 'vis' From df9c497e8bb289ca7677ca4772bb237f6a3d41a5 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Fri, 11 Nov 2022 11:40:43 +0100 Subject: [PATCH 5443/9987] Clean up comments --- easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb | 8 -------- 1 file changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb index 71c7f00f840..fdfe525853e 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb @@ -1,7 +1,3 @@ -# EasyConfig based on the official Blender binaries, which should work -# on any system that has glibc >= 2.17. As the main binary is statically -# linked and includes a Python interpreter no other dependencies should -# be necessary easyblock = 'PackedBinary' name = 'Blender' @@ -31,8 +27,4 @@ sanity_check_paths = { 'dirs': ['3.3'] } -#modextrapaths = { -# 'PATH' : '', -#} - moduleclass = 'vis' From 0506670629eeba206d73315aa85ce65e000d0cd3 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Fri, 11 Nov 2022 12:08:27 +0100 Subject: [PATCH 5444/9987] Add CUDA as depedency --- easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb index fdfe525853e..7669c41af2b 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb @@ -20,7 +20,9 @@ checksums = [ builddependencies = [] -dependencies = [] +dependencies = [ + ('CUDA', '11.7.0') +] sanity_check_paths = { 'files': ['blender', 'blender-softwaregl'], From 94bb82b0263edae500c8a5f18340d6911d15e914 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 11 Nov 2022 16:34:14 +0000 Subject: [PATCH 5445/9987] Adjust disable-fma-in-cscal-zscal.patch for GCC 12 For some reason (GCC bug report pending) -ffp-contract=off is not sufficient for GCC 12, so we also need -mno-fma, implemented via a GCC pragma. --- .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 6 +- ...CC-12.2.0_disable-fma-in-cscal-zscal.patch | 73 +++++++++++++++++++ 2 files changed, 76 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb index eee3ebc9454..b0244cb98ce 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -17,7 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', - 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ @@ -28,8 +28,8 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, - {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': - 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch': + '9784e93567d100960a4c34d86e215bd7aa70bb28b0bc2c6bf1b22c6a05d56003'}, {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch new file mode 100644 index 00000000000..ff665e1300d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch @@ -0,0 +1,73 @@ +From e7e3aa29482281edba46a27fcd452d7ed630f46a Mon Sep 17 00:00:00 2001 +From: Bart Oldeman +Date: Thu, 27 Oct 2022 17:20:44 -0400 +Subject: [PATCH] x86_64: prevent GCC and Clang from generating FMAs in + cscal/zscal. + +If e.g. -march=haswell is set in CFLAGS, GCC generates FMAs by default, which +is inconsistent with the microkernels, none of which use FMAs. These +inconsistencies cause a few failures in the LAPACK testcases, where +eigenvalue results with/without eigenvectors are compared. + +Moreover using FMAs for multiplication of complex numbers can give surprising +results, see 22aa81f for more information. + +This uses the same syntax as used in 22aa81f for zarch (s390x). + +Edit: 2022-11-11: add no-fma target since fp-contract=off isn't sufficient for +GCC 12.2. +--- + kernel/x86_64/cscal.c | 14 +++++++++++++ + kernel/x86_64/zscal.c | 14 +++++++++++++ + 2 files changed, 28 insertions(+) + +diff --git a/kernel/x86_64/cscal.c b/kernel/x86_64/cscal.c +index dc3f688c69..6ae66d9731 100644 +--- a/kernel/x86_64/cscal.c ++++ b/kernel/x86_64/cscal.c +@@ -25,6 +25,20 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#pragma GCC target ("no-fma") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + +diff --git a/kernel/x86_64/zscal.c b/kernel/x86_64/zscal.c +index 3744c98bb7..dfdb4230b6 100644 +--- a/kernel/x86_64/zscal.c ++++ b/kernel/x86_64/zscal.c +@@ -25,6 +25,20 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#pragma GCC target ("no-fma") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + From 984f088a26a28517e2f3979ed8f1328cef4b9d35 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 11 Nov 2022 17:42:25 +0000 Subject: [PATCH 5446/9987] adding easyconfigs: MITgcmutils-0.1.2-foss-2022a.eb --- .../MITgcmutils-0.1.2-foss-2022a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb new file mode 100644 index 00000000000..4459e4473f3 --- /dev/null +++ b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb @@ -0,0 +1,46 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'MITgcmutils' +version = '0.1.2' + +homepage = 'https://mitgcm.org/' +description = """A numerical model designed for study of the atmosphere, ocean, +and climate, MITgcm’s flexible non-hydrostatic formulation enables it to +efficiently simulate fluid phenomena over a wide range of scales; its adjoint +capabilities enable it to be applied to sensitivity questions and to parameter +and state estimation problems. By employing fluid equation isomorphisms, a +single dynamical kernel can be used to simulate flow of both the atmosphere +and ocean. The model is developed to perform efficiently on a wide variety of +computational platforms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['5f15e0ad7a1e2451532facd3e83e8a0a2cea41d5c04df8272c4d31780e28ab2d'], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'modulename': 'MITgcmutils', + }), +] + +sanity_check_paths = { + 'files': ['bin/gluemncbig'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "gluemncbig --help", +] + +moduleclass = 'geo' From 769aeff75110baf1235fe12cb7848ba33ce3057b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 17:30:32 +0100 Subject: [PATCH 5447/9987] avoid that zlib + htslib are downloaded and built during installation of MetaBAT --- .../m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb | 7 ++-- .../MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 7 ++-- .../m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 8 +++-- .../m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb | 7 ++-- .../m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch | 35 +++++++++++++++++++ 5 files changed, 56 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb index 7746c998d4c..a40c2edb844 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'gompi', 'version': '2019a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = [ 'd43d5e91afa8f2d211a913739127884669516bfbed870760597fcee2b513abe2', # v2.14.tar.gz ] @@ -35,9 +36,11 @@ dependencies = [ ('bzip2', '1.0.6'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index 827c80520e1..d8416cf32df 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] builddependencies = [ @@ -29,9 +30,11 @@ dependencies = [ ('bzip2', '1.0.8'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index a94f4f9953a..6ad2548c41f 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] builddependencies = [ @@ -26,11 +27,14 @@ dependencies = [ ('SAMtools', '1.13'), ('XZ', '5.2.5'), ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index 3a2f07771f6..670e4554b36 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] builddependencies = [ @@ -28,9 +29,11 @@ dependencies = [ ('bzip2', '1.0.8'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch new file mode 100644 index 00000000000..9914848cdc0 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch @@ -0,0 +1,35 @@ +avoid downloading and building of zlib and htslib, since they're provided as dependencies by EasyBuild +author: Kenneth Hoste (HPC-UGent) +--- berkeleylab-metabat-0db17a40717d/CMakeLists.txt.orig 2022-11-11 12:11:10.473978638 +0000 ++++ berkeleylab-metabat-0db17a40717d/CMakeLists.txt 2022-11-11 12:12:34.246072148 +0000 +@@ -8,8 +8,8 @@ + message("Installing ${CMAKE_BUILD_TYPE} MetaBAT into ${CMAKE_INSTALL_PREFIX}") + + include(${CMAKE_ROOT}/Modules/ExternalProject.cmake) +-include(cmake/zlib.cmake) +-include(cmake/htslib.cmake) ++set(zlib_LIB ${ZLIB_LIBRARY}) ++set(htslib_LIB ${HTSLIB_LIBRARY}) + + set(CMAKE_CXX_STANDARD 11) + set(CMAKE_CXX_STANDARD_REQUIRED ON) +--- berkeleylab-metabat-0db17a40717d/src/CMakeLists.txt.orig 2022-11-11 12:23:52.313823937 +0000 ++++ berkeleylab-metabat-0db17a40717d/src/CMakeLists.txt 2022-11-11 12:24:18.424465217 +0000 +@@ -36,7 +36,7 @@ + foreach(target ${targets}) + + add_executable(${target} ${target}.cpp) +- add_dependencies(${target} htslib zlib check_git_repository) ++ add_dependencies(${target} check_git_repository) + target_link_libraries(${target} ${zlib_LIB} ${Boost_LIBRARIES} ${EXTRALIBS} ) + + endforeach() +@@ -48,7 +48,7 @@ + set(targets jgi_summarize_bam_contig_depths contigOverlaps) + foreach(target ${targets}) + add_executable(${target} ${target}.cpp) +- add_dependencies(${target} htslib zlib check_git_repository) ++ add_dependencies(${target} check_git_repository) + target_link_libraries(${target} ${htslib_LIB} ${zlib_LIB} ${Boost_LIBRARIES} ) + endforeach() + From 417104a83c72d19e3c91bf1101521ff57d57b4d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 18:10:03 +0100 Subject: [PATCH 5448/9987] add checksum for MetaBAT patch --- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb | 3 ++- .../m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 5 ++++- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 5 ++++- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb | 5 ++++- 4 files changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb index a40c2edb844..d906664f6db 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb @@ -16,7 +16,8 @@ source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = [ - 'd43d5e91afa8f2d211a913739127884669516bfbed870760597fcee2b513abe2', # v2.14.tar.gz + {'v2.14.tar.gz': 'd43d5e91afa8f2d211a913739127884669516bfbed870760597fcee2b513abe2'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, ] multi_deps = {'Python': ['3.7.2', '2.7.15']} diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index d8416cf32df..de525664832 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] -checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] +checksums = [ + {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index 6ad2548c41f..5c65ffd3edd 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] -checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] +checksums = [ + {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, +] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index 670e4554b36..ef62c68ea78 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] -checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] +checksums = [ + {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, +] builddependencies = [ ('binutils', '2.37'), From b6a4a54e13289acabe9a2b2bfc897082a1cfcf8d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 19:44:39 +0100 Subject: [PATCH 5449/9987] remove duplicate zlib dependency in MetaBAT easyconfig --- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index 5c65ffd3edd..a552166e24f 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -30,7 +30,6 @@ dependencies = [ ('SAMtools', '1.13'), ('XZ', '5.2.5'), ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), ] configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' From cfe4dd28c0745b9c39dbb3ad52f6d999df63a780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:39:25 +0100 Subject: [PATCH 5450/9987] adding easyconfigs: Python-2.7.18-GCCcore-12.2.0-bare.eb --- .../Python-2.7.18-GCCcore-12.2.0-bare.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb new file mode 100644 index 00000000000..f8c443163d4 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb @@ -0,0 +1,32 @@ +name = 'Python' +version = '2.7.18' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +builddependencies = [ + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('binutils', '2.39'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('SQLite', '3.39.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +moduleclass = 'lang' From c058550aa3096feff13dad0032c03fafa0353539 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:39:36 +0100 Subject: [PATCH 5451/9987] adding easyconfigs: Ninja-1.11.1-GCCcore-12.2.0.eb --- .../n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e6cefd164e7 --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.11.1' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['31747ae633213f1eda3842686f83c2aa1412e0f5691d1c14dbbcc67fe7400cea'] + +builddependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8', '-bare'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +sanity_check_commands = ["ninja --version"] + +moduleclass = 'tools' From 308e86a4dc784296d2b8ab229053dece648d25bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:41:58 +0100 Subject: [PATCH 5452/9987] adding easyconfigs: GMP-6.2.1-GCCcore-12.2.0.eb --- .../g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8d18902ab40 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.2.1' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +# copy libgmp.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' From d4066666ae8b2a9c03a5be3c9ea6003233b5c06e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:45:21 +0100 Subject: [PATCH 5453/9987] adding easyconfigs: gettext-0.21.1-GCCcore-12.2.0.eb --- .../gettext/gettext-0.21.1-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a7ad515633f --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21.1' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e8c3650e1d8cee875c4f355642382c1df83058bd5a11ee8555c0cf276d646d45'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('libxml2', '2.10.3'), + ('ncurses', '6.3'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' From 5d1c5cfe5d37610f8848161c87e052cf33263eea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:45:33 +0100 Subject: [PATCH 5454/9987] adding easyconfigs: git-2.38.1-GCCcore-12.2.0-nodocs.eb --- .../g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb diff --git a/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb new file mode 100644 index 00000000000..7760dcfd6bd --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb @@ -0,0 +1,47 @@ +## +# Author: Robert Mijakovic +## +# updated to 2.33.1 +# J. Sassmannshausen / GSTT + +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.38.1' +versionsuffix = '-nodocs' + +homepage = 'https://git-scm.com' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91456b031324f7909f35e067dcfb907956d1a5c3d2069cfc5b4549e42089e546'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('cURL', '7.86.0'), + ('expat', '2.4.9'), + ('gettext', '0.21.1'), + ('Perl', '5.36.0'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['libexec/git-core', 'share'], +} + +moduleclass = 'tools' From 6b678b7965f224d22583846ef4afa0f505c71d03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:55:20 +0100 Subject: [PATCH 5455/9987] adding easyconfigs: libpng-1.6.38-GCCcore-12.2.0.eb --- .../l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..c3a6b1c3387 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.38' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e2b5e1b4329650992c041996cf1269681b341191dc07ffed816c555769cceb77'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('zlib', '1.2.12')] + +local_majminver = '%(version_major)s%(version_minor)s' + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' From 9b05a53e14a92631d2f30667058f21e5f866908a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 21:29:25 +0100 Subject: [PATCH 5456/9987] adding easyconfigs: Rust-1.65.0-GCCcore-12.2.0.eb --- .../r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..757f1d6d4bf --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.65.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.60_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.65.0-src.tar.gz': '5828bb67f677eabf8c384020582b0ce7af884e1c84389484f7f8d00dd82c0038'}, + {'Rust-1.60_sysroot-fix-interpreter.patch': 'b59ed4c2591fc9098277299be21dd6752654f6f193d8652b7d21cb0fa0dd8716'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Python', '3.10.8', '-bare'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' From cbb0c9c3e4a057557cc1edc382a421fae6d4e1d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Nov 2022 17:25:15 +0100 Subject: [PATCH 5457/9987] adding easyconfigs: Python-3.10.8-GCCcore-12.2.0.eb --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 510 ++++++++++++++++++ 1 file changed, 510 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f0bca199736 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -0,0 +1,510 @@ +name = 'Python' +version = '3.10.8' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a'] + +builddependencies = [ + ('UnZip', '6.0'), + ('Rust', '1.65.0'), # required for setuptools-rust, which is needed for cryptography + ('pkgconf', '1.9.3'), + ('git', '2.38.1', '-nodocs'), # required for pbr +] + +dependencies = [ + ('binutils', '2.39'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('SQLite', '3.39.4'), + ('XZ', '5.2.7'), + ('GMP', '6.2.1'), # required for pycrypto + ('libffi', '3.4.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 12 Nov 2022 +exts_list = [ + ('wheel', '0.38.4', { + 'checksums': ['965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac'], + }), + ('setuptools', '65.5.1', { + 'checksums': ['e197a19aa8ec9722928f2206f8de752def0e4c9fc6953527360d1c36d94ddb2f'], + }), + ('pip', '22.3.1', { + 'checksums': ['65fd48317359f3af8e593943e6ae1506b66325085ea64b706a998c6e83eeaf38'], + }), + ('blist', '1.3.6', { + 'patches': [ + 'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch', + 'Python-3.10-bist-1.3.6-compatibility.patch', + ], + 'checksums': [ + {'blist-1.3.6.tar.gz': '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'}, + {'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch': + '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0'}, + {'Python-3.10-bist-1.3.6-compatibility.patch': + '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741'}, + ], + }), + ('pbr', '5.11.0', { + 'checksums': ['b97bc6695b2aff02144133c2e7399d5885223d42b7912ffaec2ca3898e673bfe'], + }), + ('Cython', '0.29.32', { + 'checksums': ['8733cf4758b79304f2a4e39ebfac5e92341bce47bcceb26c1254398b2f8c1af7'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('flit-core', '3.8.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': 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+ }), + ('sphinxcontrib-qthelp', '1.0.3', { + 'modulename': 'sphinxcontrib.qthelp', + 'checksums': ['4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72'], + }), + ('Babel', '2.11.0', { + 'checksums': ['5ef4b3226b0180dedded4229651c8b0e1a3a6a2837d45a073272f313e4cf97f6'], + }), + ('Sphinx', '5.3.0', { + 'checksums': ['51026de0a9ff9fc13c05d74913ad66047e104f56a129ff73e174eb5c3ee794b5'], + }), + ('sphinx-bootstrap-theme', '0.8.1', { + 'checksums': ['683e3b735448dadd0149f76edecf95ff4bd9157787e9e77e0d048ca6f1d680df'], + }), + ('click', '8.1.3', { + 'checksums': ['7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e'], + }), + ('psutil', '5.9.4', { + 'checksums': ['3d7f9739eb435d4b1338944abe23f49584bde5395f27487d2ee25ad9a8774a62'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('zipfile36', '0.1.3', { + 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], + }), + ('tomli-w', '1.0.0', { + 'sources': ['tomli_w-%(version)s.tar.gz'], + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), + ('flit', '3.8.0', { + 'checksums': ['d0f2a8f4bd45dc794befbf5839ecc0fd3830d65a57bd52b5997542fac5d5e937'], + }), + ('regex', '2022.10.31', { + 'checksums': ['a3a98921da9a1bf8457aeee6a551948a83601689e5ecdd736894ea9bbec77e83'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('pylev', '1.4.0', { + 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], + }), + ('pastel', '0.2.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], + }), + ('crashtest', '0.3.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], + }), + ('clikit', '0.6.2', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], + }), + ('jeepney', '0.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], + }), + ('SecretStorage', '3.3.3', { + 'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'], + }), + ('keyring', '23.11.0', { + 'modulename': False, + 'checksums': ['ad192263e2cdd5f12875dedc2da13534359a7e760e77f8d04b50968a821c2361'], + }), + ('jaraco.classes', '3.2.3', { + 'checksums': ['89559fa5c1d3c34eff6f631ad80bb21f378dbcbb35dd161fd2c6b93f5be2f98a'], + }), + ('keyrings.alt', '4.2.0', { + 'modulename': False, + 'checksums': ['2ba3d56441ba0637f5f9c096068f67010ac0453f9d0b626de2aa3019353b6431'], + }), + ('tomlkit', '0.11.6', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b'], + }), + ('shellingham', '1.5.0', { + 'checksums': ['72fb7f5c63103ca2cb91b23dee0c71fe8ad6fbfd46418ef17dbe40db51592dad'], + }), + ('requests-toolbelt', '0.9.1', { + 'checksums': ['968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0'], + }), + ('pyrsistent', '0.19.2', { + 'checksums': ['bfa0351be89c9fcbcb8c9879b826f4353be10f58f8a677efab0c017bf7137ec2'], + }), + ('pkginfo', '1.8.3', { + 'checksums': ['a84da4318dd86f870a9447a8c98340aa06216bfc6f2b7bdc4b8766984ae1867c'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('hatch-fancy-pypi-readme', '22.8.0', { + 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], + 'checksums': ['da91282ca09601c18aded8e378daf8b578c70214866f0971156ee9bb9ce6c26a'], + }), + ('jsonschema', '4.17.0', { + 'checksums': ['5bfcf2bca16a087ade17e02b282d34af7ccd749ef76241e7f9bd7c0cb8a9424d'], + }), + ('simplejson', '3.17.6', { + 'checksums': ['cf98038d2abf63a1ada5730e91e84c642ba6c225b0198c3684151b1f80c5f8a6'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('cleo', '1.0.0a5', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff53056589300976e960f75afb792dfbfc9c78dcbb5a448e207a17b643826360'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.4', { + 'checksums': ['f5d869c18f030202eb412f08b28d2afeea553d6613aee89e200d7aca7ef01f5f'], + }), + ('CacheControl', '0.12.11', { + 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.3.2', { + 'modulename': 'poetry.core', + 'checksums': ['0ab006a40cb38d6a38b97264f6835da2f08a96912f2728ce668e9ac6a34f686f'], + }), + ('glob2', '0.7', { + 'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'], + }), + ('dulwich', '0.20.50', { + 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], + }), + ('poetry-plugin-export', '1.2.0', { + 'sources': ['poetry_plugin_export-%(version)s.tar.gz'], + 'checksums': ['9a1dd42765408931d7831738749022651d43a2968b67c988db1b7a567dfe41ef'], + }), + ('poetry', '1.2.2', { + 'checksums': ['6d9ed0b1b826a0a79190f2078d7d78483fa24bf2494f3b170e354eaa5e7b5ea1'], + }), + ('fsspec', '2022.11.0', { + 'checksums': ['259d5fd5c8e756ff2ea72f42e7613c32667dc2049a4ac3d84364a7ca034acb8b'], + }), + ('threadpoolctl', '3.1.0', { + 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), +] + +moduleclass = 'lang' From f67e8904af10fc8f97f28f3099d48e6275948ae1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Nov 2022 17:53:44 +0100 Subject: [PATCH 5458/9987] add patch to fix installation of MetaBAT 2.15 on aarch64 --- .../MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 6 +++- .../m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 6 +++- .../m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb | 6 +++- .../m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch | 31 +++++++++++++++++++ 4 files changed, 46 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index de525664832..0852b759a00 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -11,10 +11,14 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] -patches = ['MetaBAT-2.15_zlib-htslib.patch'] +patches = [ + 'MetaBAT-2.15_zlib-htslib.patch', + 'MetaBAT-2.15_fix-aarch64.patch', +] checksums = [ {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, + {'MetaBAT-2.15_fix-aarch64.patch': '061b43d6c0ac4a9acf3bd7cf3c62efc856661993a61e7d4652ed68aafb7aa7af'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index a552166e24f..dc2afdaad6f 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -10,10 +10,14 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] -patches = ['MetaBAT-2.15_zlib-htslib.patch'] +patches = [ + 'MetaBAT-2.15_zlib-htslib.patch', + 'MetaBAT-2.15_fix-aarch64.patch', +] checksums = [ {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, + {'MetaBAT-2.15_fix-aarch64.patch': '061b43d6c0ac4a9acf3bd7cf3c62efc856661993a61e7d4652ed68aafb7aa7af'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index ef62c68ea78..3ffd2f88277 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -10,10 +10,14 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] -patches = ['MetaBAT-2.15_zlib-htslib.patch'] +patches = [ + 'MetaBAT-2.15_zlib-htslib.patch', + 'MetaBAT-2.15_fix-aarch64.patch', +] checksums = [ {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, + {'MetaBAT-2.15_fix-aarch64.patch': '061b43d6c0ac4a9acf3bd7cf3c62efc856661993a61e7d4652ed68aafb7aa7af'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch new file mode 100644 index 00000000000..b3029a247bf --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch @@ -0,0 +1,31 @@ +fixes "error: impossible constraint in asm" when building on aarch64/amr64 +see https://bitbucket.org/berkeleylab/metabat/issues/151 +From a01eafa174e01f6a46ef71b63daa7695d2c3834e Mon Sep 17 00:00:00 2001 +From: Rob Egan +Date: Mon, 26 Sep 2022 09:19:32 -0700 +Subject: [PATCH] removed unused function using assembly types + +--- + src/metabat2.h | 6 ------ + 1 file changed, 6 deletions(-) + +diff --git a/src/metabat2.h b/src/metabat2.h +index b1cb5d3..7accc1a 100644 +--- a/src/metabat2.h ++++ b/src/metabat2.h +@@ -258,12 +258,6 @@ public: + + void gen_tnf_graph(Graph& g, Similarity cutoff); + +-unsigned long long rdtsc() { +- unsigned int lo, hi; +- __asm__ __volatile__ ("rdtsc" : "=a" (lo), "=d" (hi)); +- return ((unsigned long long) hi << 32) | lo; +-} +- + static void trim_fasta_label(std::string &label) { + size_t pos = label.find_first_of(" \t"); + if (pos != std::string::npos) +-- +2.38.1 + From 74a363dc9bb8126ba79a85f38bbca34ed71d2365 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 14 Nov 2022 09:39:37 +0100 Subject: [PATCH 5459/9987] Fix DIAMOND duplicate choice in the foss-2021a toolchain --- easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb index 12d6688ec5a..5ff808c82d1 100644 --- a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb @@ -23,7 +23,7 @@ checksums = ['19a8eb28c0ebd3fc5a04b006d305a916dd1af00a32b70d2f30df35f32ca2929b'] dependencies = [ ('Python', '3.9.5'), - ('DIAMOND', '2.0.13'), + ('DIAMOND', '2.0.11'), ('prodigal', '2.6.3'), ] From 63eeebd063e2da748b043d0f1db1cac6af62b2af Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 14 Nov 2022 10:52:16 +0000 Subject: [PATCH 5460/9987] Add ROntoTools extension to Bioconductor bundle --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index d34e406d5d8..43c53a70184 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1095,6 +1095,9 @@ exts_list = [ ('HiCcompare', '1.18.0', { 'checksums': ['b9320fa7a9f10832e2ac7ade0245f85ac4c2c26edef2580078888f5e1050ee2d'], }), + ('ROntoTools', '2.24.0', { + 'checksums': ['dec7ec0d6d709fbdb44d595d776fc462420957e5c23c7bd6d2d63f5a44df04dd'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 6f6478bc51b997eef54222864da8107f2698ff48 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 14 Nov 2022 14:01:50 +0000 Subject: [PATCH 5461/9987] adding easyconfigs: xmitgcm-0.5.2-foss-2022a.eb --- .../x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb new file mode 100644 index 00000000000..aeac427c9c5 --- /dev/null +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -0,0 +1,41 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'xmitgcm' +version = '0.5.2' + +homepage = 'https://github.com/MITgcm/xmitgcm' +description = """xmitgcm is a python package for reading MITgcm binary +MDS files into xarray data structures. By storing data in dask arrays, +xmitgcm enables parallel, out-of-core analysis of MITgcm output data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('MITgcmutils', '0.1.2'), + ('dask', '2022.10.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cachetools', '5.2.0', { + 'checksums': ['6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757'], + }), + ('xarray', '2022.9.0', { + 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], + }), + (name, version, { + 'checksums': ['7dda45fdf6182a859f5c441cd5928a7c99d41c8bcea9fccf471b7011791b1131'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From ca10418869f217d7788ffe405fa8add40505dd1b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 14 Nov 2022 15:05:55 +0100 Subject: [PATCH 5462/9987] Add another long read missing tool --- .../n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb index 2f394f3514e..9699267036a 100644 --- a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb +++ b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb @@ -16,7 +16,7 @@ description = """The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.""" toolchain = {'name': 'foss', 'version': '2021a'} -# TODO The long reads sequencing part (2) tools will be added later +# TODO The long reads sequencing part (1 missing) tools will be added later dependencies = [ ('Nextflow', '22.10.1', '', SYSTEM), ('AdapterRemoval', '2.3.2'), @@ -38,6 +38,7 @@ dependencies = [ ('MetaBAT', '2.15'), ('MultiQC', '1.11'), ('NanoLyse', '1.2.1'), + ('Porechop', '0.2.4'), ('prodigal', '2.6.3'), ('prokka', '1.14.5'), ('PyDamage', '0.70'), From e2a48ad045d3f29e3cf5d23f371f553569013015 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 14 Nov 2022 15:16:34 +0100 Subject: [PATCH 5463/9987] Add SWIG as missing requirement --- easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb index 7cce7c9bf0f..54f52a70197 100644 --- a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb @@ -22,6 +22,7 @@ dependencies = [ ('ruamel.yaml', '0.17.21'), ('SciPy-bundle', '2021.05'), ('sympy', '1.8'), + ('SWIG', '4.0.2'), ('GLPK', '5.0'), ('python-libsbml', '5.19.7'), ] From 38ed74ce899c2df641b51fd6718d377cd98d1c68 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 14 Nov 2022 16:25:41 +0100 Subject: [PATCH 5464/9987] adding easyconfigs: GD-2.75-GCCcore-11.3.0.eb, Circos-0.69-9-GCCcore-11.3.0.eb --- .../c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb | 41 +++++++++++++ .../g/GD/GD-2.75-GCCcore-11.3.0.eb | 57 +++++++++++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bdb8092c8c6 --- /dev/null +++ b/easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'Tarball' + +name = 'Circos' +version = '0.69-9' + +homepage = 'http://www.circos.ca/' +description = """Circos is a software package for visualizing data and information. + It visualizes data in a circular layout - this makes Circos ideal for exploring + relationships between objects or positions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://circos.ca/distribution/'] +sources = [SOURCELOWER_TGZ] +checksums = ['34d8d7ebebf3f553d62820f8f4a0a57814b610341f836b4740c46c3057f789d2'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Perl', '5.34.1'), + ('GD', '2.75'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/%(name)s'], +} + +modextrapaths = {'PERL5LIB': 'lib'} + +sanity_check_commands = [('perl', '-e "use Circos"')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d889cb7d1f5 --- /dev/null +++ b/easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb @@ -0,0 +1,57 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester (The Francis Crick Insitute, London, UK) +# Update to v2.71: Alex Domingo (Vrije Universiteit Brussel) +# Update to v2.73: Sebastien Moretti (SIB Swiss Institute of Bioinformatics) +# + +easyblock = 'Bundle' + +name = 'GD' +version = '2.75' + +homepage = 'https://github.com/lstein/Perl-GD' +description = """GD.pm - Interface to Gd Graphics Library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('X11', '20220504'), + ('libgd', '2.3.3'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::PkgConfig', '1.16', { + 'source_tmpl': 'ExtUtils-PkgConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e'], + }), + (name, version, { + 'source_tmpl': 'release_%(version_major)s_%(version_minor)s.tar.gz', + 'source_urls': ['https://github.com/lstein/Perl-GD/archive/'], + 'checksums': ['b82ca67fa67446f16ee7ba8bccee2062644816a83cb2ee4e4de2fa3ee8ab359d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bdf2gdfont.pl', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s'], +} + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +moduleclass = 'bio' From f7403cdf9b53f80c37ad83c1451761ed7dd872d1 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 14 Nov 2022 18:43:51 +0000 Subject: [PATCH 5465/9987] adding easyconfigs: oceanspy-0.2.0-foss-2022a.eb --- .../o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb new file mode 100644 index 00000000000..d73a95fced8 --- /dev/null +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -0,0 +1,40 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'oceanspy' +version = '0.2.0' + +homepage = 'https://github.com/hainegroup/oceanspy' +description = """OceanSpy - A Python package to facilitate ocean model data analysis +and visualization.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('dask', '2022.10.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xarray', '2022.9.0', { + 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], + }), + ('xgcm', '0.8.0', { + 'checksums': ['99e7e2fc9268fb13827f8849dbae279eaaa4960d51872d62bc38293605b0215f'], + }), + + (name, version, { + 'checksums': ['8c684ecdfe03bade171e17f5ae6bedd422e51db6faffed0303e1839051d40614'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 2e3e7bd67c1faf07c838a1d64a13f28d22334417 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2022 20:16:32 +0100 Subject: [PATCH 5466/9987] use new EasyBuild logo in README --- README.rst | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index cb4636846ac..b06cc3cf03a 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,8 @@ -.. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg - -.. image:: https://easybuilders.github.io/easybuild/images/easybuild_logo_small.png +.. image:: https://github.com/easybuilders/easybuild/raw/develop/logo/png/easybuild_logo_2022_horizontal_dark_bg_transparent.png :align: center + :height: 400px + +.. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg `EasyBuild `_ is a software build and installation framework that allows you to manage (scientific) software From 09ce7360d06affcf127854d9b8eab140c80d18c4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 14 Nov 2022 23:50:27 +0100 Subject: [PATCH 5467/9987] use new SYSTEM constant in dependencies of MATLAB-Engine-2021a-GCCcore-10.2.0.eb --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb index 3418f6ddc56..83a3d5d719c 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb @@ -10,7 +10,7 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [ - ('MATLAB', version, '', True), + ('MATLAB', version, '', SYSTEM), ('Python', '3.8.6'), ] From a62c38ef82a9fb81bca8a34f8413b6e13ed3a465 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 14 Nov 2022 23:50:59 +0100 Subject: [PATCH 5468/9987] use new SYSTEM constant in dependencies of MATLAB-Engine-2021a-GCCcore-11.2.0.eb --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb index 9380e93ff8a..e60cc61f004 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -10,7 +10,7 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '11.2.0'} dependencies = [ - ('MATLAB', version, '', True), + ('MATLAB', version, '', SYSTEM), ('Python', '3.9.6'), ] From 98b2773c34a35e4ab8ad8f3472e39ef421ad26f4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 15 Nov 2022 00:32:14 +0100 Subject: [PATCH 5469/9987] enable support in MATLAB-Engine for Python version used in EasyBuild --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb index e60cc61f004..c1558fb7dc9 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -17,9 +17,11 @@ dependencies = [ use_pip = False download_dep_fail = True +# Enable support for this current version of Python +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +prebuildopts += "sed -i 's/^_supported_versions =.*/_supported_versions = ["%(pyshortver)s"]/' setup.py &&" # Since this setup.py does not provide a separate --build-base for the install # step, both build and install must be performed in a single command. -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" skipsteps = ['install'] From 72f2ed94534866e8ff42ee891c4566e1644d08a2 Mon Sep 17 00:00:00 2001 From: adam Date: Tue, 15 Nov 2022 08:52:30 +0000 Subject: [PATCH 5470/9987] Fix modulename and add sanity_check_command --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index 6e3329bd511..5deaefa438c 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -27,7 +27,7 @@ exts_list = [ (name, version, { 'source_tmpl': 'scoary-%(version)s.tar.gz', 'checksums': ['f433343422c5805a70a20f7fe83851490ae3cdf07745c65680de5feea40a6dca'], - 'modulename': False, + 'modulename': 'scoary.methods', }), ] @@ -38,4 +38,6 @@ sanity_check_paths = { sanity_pip_check = True +sanity_check_commands = [('scoary', '--version')] + moduleclass = 'bio' From dbf74553f8ff671f9a520098289c2103b03e979a Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 10:02:33 +0000 Subject: [PATCH 5471/9987] adding easyconfigs: gsw-3.6.16-foss-2022a.eb --- .../g/gsw/gsw-3.6.16-foss-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb new file mode 100644 index 00000000000..aa8438cd21e --- /dev/null +++ b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb @@ -0,0 +1,42 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'gsw' +version = '3.6.16' + +homepage = 'https://github.com/TEOS-10/GSW-python' +description = """This Python implementation of the Thermodynamic Equation of +Seawater 2010 (TEOS-10) is based primarily on numpy ufunc wrappers of the GSW-C +implementation. This library replaces the original python-gsw pure-python +implementation.. The primary reasons for this change are that by building on +the C implementation we reduce code duplication and we gain an immediate update +to the 75-term equation. +Additional benefits include a major increase in speed, a reduction in memory +usage, and the inclusion of more functions. The penalty is that a C +(or MSVC C++ for Windows) compiler is required to build the package from source.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + + (name, version, { + 'checksums': ['d24d820c8b43dbf72206cf5e3b0ed800b05aa85ca40afd39c9abd19849714197'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From e932e0d6366d8b05d06f1bdfd5a5db95a44e2f83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2022 11:15:02 +0100 Subject: [PATCH 5472/9987] clean up version of Python dependency in pyWannier90 easyconfig --- .../p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb index ec32ef804a9..f4d75a875c3 100644 --- a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb @@ -32,12 +32,8 @@ builddependencies = [ ('pybind11', '2.6.2'), ] -local_pymaj = '3' -local_pymin = '9' -local_pymajmin = local_pymaj + local_pymin - dependencies = [ - ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('PySCF', '1.7.6'), ] From e9fde4dae46df5bd922be8ec679aa7ec2cb5731d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 15 Nov 2022 11:46:23 +0100 Subject: [PATCH 5473/9987] Fix matlab version for 2021b --- .../MATLAB-Engine-2021b-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a188c57dcad --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = '2021b' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('MATLAB', version, '', True), + ('Python', '3.9.6'), +] + +use_pip = False +download_dep_fail = True + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" + +skipsteps = ['install'] + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +sanity_pip_check = True + +options = {'modulename': 'matlab.engine'} + +moduleclass = 'math' From 65119867029b4e74a665ec7013ddcaa8f4fb6b61 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 10:50:13 +0000 Subject: [PATCH 5474/9987] adding easyconfigs: pyproj-3.4.0-GCCcore-11.3.0.eb --- .../p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2fecab55426 --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.4.0' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a708445927ace9857f52c3ba67d2915da7b41a8fdcd9b8f99a4c9ed60a75eb33'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('PROJ', '9.0.0'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' From 6481ad003ff37ddc871a31436c89826013f7e268 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 15 Nov 2022 14:01:28 +0100 Subject: [PATCH 5475/9987] adding easyconfigs: Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb, OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb and patches: Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch, Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch --- ...CV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb | 99 +++++++++++++++++++ ...p-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb | 92 +++++++++++++++++ ...issing_cuda_compatibility.cu_include.patch | 55 +++++++++++ ....07-Helios_fix_opencv_cuda_detection.patch | 25 +++++ 4 files changed, 271 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb new file mode 100644 index 00000000000..70276c87526 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb @@ -0,0 +1,99 @@ +name = 'OpenCV' +version = '4.6.0' +versionsuffix = '-CUDA-%(cudaver)s-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'cstd': 'c++14'} + +sources = [ + { + 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': SOURCELOWER_ZIP + }, + { + 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': '%(namelower)s_contrib-%(version)s.zip' + }, + { + 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', + 'extract_cmd': 'cp %s %(builddir)s' + }, +] +checksums = [ + '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip + '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), + ('FFmpeg', '4.4.2'), + ('freetype', '2.12.1'), + ('HarfBuzz', '4.2.1'), + ('libjpeg-turbo', '2.1.3'), + ('OpenJPEG', '2.5.0'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.4'), + ('OpenEXR', '3.1.5'), + ('JasPer', '2.0.33'), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.12', '-Java-%(javaver)s', SYSTEM), + ('GLib', '2.72.1'), + ('GTK4', '4.7.0'), + ('HDF5', '1.12.2'), + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = " ".join([ + "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DFREETYPE_FOUND=ON", + "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", + "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", + "-DHARFBUZZ_FOUND=ON", + "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", + "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", + "-DBUILD_opencv_python2=OFF", + "-DCUDA_NVCC_FLAGS=--std=c++14", +]) + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..4093b1d0ecf --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,92 @@ +name = 'Xmipp' +version = '3.22.07-Helios' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/I2PC/scipion/wiki' +description = """Scipion is an image processing framework to obtain 3D +models of macromolecular complexes using Electron Microscopy (3DEM). It +integrates several software packages and presents an unified interface +for both biologists and developers. Scipion allows to execute workflows +combining different software tools, while taking care of formats and +conversions. Additionally, all steps are tracked and can be reproduced +later on. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/I2PC/xmipp/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(namelower)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippCore/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippCore-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippViz/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippViz-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, +] +patches = [ + '%(name)s-%(version)s_fix_scons_Environent_calls.patch', + '%(name)s-%(version)s_drop_useless_CXXFLAGS_setting.patch', + '%(name)s-%(version)s_correct_order_of_cu_includes.patch', + '%(name)s-%(version)s_dont_add_useless_libs.patch', + '%(name)s-%(version)s_dont_change_EB_build_flags.patch', + '%(name)s-%(version)s_fix_missing_cuda_compatibility.cu_include.patch', + '%(name)s-%(version)s_fix_opencv_cuda_detection.patch', + ('XmippCore-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippCore'), + ('XmippCore-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippCore'), + ('XmippViz-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippViz'), + ('XmippViz-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippViz'), +] +checksums = [ + {'xmipp-v3.22.07-Helios.tar.gz': 'f62e2729130b63d18e518930dd96a7a5250219e40c155abb78942a0642237ecf'}, + {'xmippCore-v3.22.07-Helios.tar.gz': '58e1143626cf807655a4756b165c21578d6f1b1777b43d363a2845d92d0bab8f'}, + {'xmippViz-v3.22.07-Helios.tar.gz': 'e1ce2cbbd57d3307d38538b29194a0190d633e5e062685387a6baf0329ad05b3'}, + {'Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch': + '5b59babad5a445ec7315a809509704d2d07232d2a5d180bfb78ebc8007bd0c95'}, + {'Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch': + '34ed0cb591e1e2788acd3e58696b1f45ce9210836d14ed1c99de1e574e4824e6'}, + {'Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch': + '2b0b2ddf349003be4112f4dca623586a03235214d6e64d232deb26468b52f0e3'}, + {'Xmipp-3.22.07-Helios_dont_add_useless_libs.patch': + '284b8ec1e514fb84b7680c8b3f59b3d5931b564beb444d3301504e3170e9a49e'}, + {'Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch': + '1514eaa5de35b38b5a10e949edf5c94ba95bbd05e0b9fbf70db2ea98967394e3'}, + {'XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch': + '8dcf0f3648f4b3438374ba629a9efa2e5c08eb25ae76ed420513664d21e2246b'}, + {'XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'd86b0d3ecc339b81c9aa7a33d2b44b428643aa7e2e686529b4bb6b16d36805c2'}, + {'XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch': + '7724fc3953d9c4c308a5755f54229259425fdbad5a909153bd173292434407b9'}, + {'XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'a8bea23c243174fb27a140a34a064a622cc96f0e7231fd31caf20f90c7ba9555'}, +] + +builddependencies = [ + ('SCons', '4.4.0'), + ('CTPL', '0.0.2'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Java', '11', '', SYSTEM), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), + ('SQLite', '3.38.3'), + ('HDF5', '1.12.2'), + ('LibTIFF', '4.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('LIBSVM', '3.30'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch new file mode 100644 index 00000000000..52dc98a1212 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch @@ -0,0 +1,55 @@ +Fix support for CUDA arch < 6.0 + +Åke Sandgren, 2022-11-14 +diff --git a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu +index 83189250..f125e47d 100644 +--- a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu ++++ b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu +@@ -28,8 +28,9 @@ + + #include "cuda_compatibility.h" + ++#if defined(__CUDA_ARCH__) + #if __CUDA_ARCH__ < 600 +-__device__ double atomicAdd(double* address, double val) ++static __inline__ __device__ double atomicAdd(double* address, double val) + { + unsigned long long int* address_as_ull = + (unsigned long long int*)address; +@@ -47,6 +48,7 @@ __device__ double atomicAdd(double* address, double val) + return __longlong_as_double(old); + } + #endif ++#endif + + + #endif /* LIBRARIES_RECONSTRUCTION_CUDA_CUDA_COMPATIBILITY_CU_ */ +diff --git a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h +index 3bb44e0f..279ccbcb 100644 +--- a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h ++++ b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h +@@ -27,7 +27,11 @@ + #define LIBRARIES_RECONSTRUCTION_CUDA_CUDA_COMPATIBILITY_H_ + + +-__device__ double atomicAdd(double* address, double val); ++#if defined(__CUDA_ARCH__) ++#if __CUDA_ARCH__ < 600 ++static __inline__ __device__ double atomicAdd(double* address, double val); ++#endif ++#endif + + + #endif /* LIBRARIES_RECONSTRUCTION_CUDA_CUDA_COMPATIBILITY_H_ */ +diff --git a/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu b/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu +index c7dea8fb..9e267336 100644 +--- a/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu ++++ b/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu +@@ -27,6 +27,7 @@ + #define LIBRARIES_RECONSTRUCTION_CUDA_CUDA_CORRELATION_CU_ + + #include "cuda_compatibility.h" ++#include "cuda_compatibility.cu" + + /** + * Function computes sum and sum squared for each 2D signal diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch new file mode 100644 index 00000000000..0575ef6a225 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch @@ -0,0 +1,25 @@ +Fix detection of OpenCV >= 3 + +Åke Sandgren, 2022-11-14 +diff --git a/src/xmipp/SConscript b/src/xmipp/SConscript +index a767fb99..89777947 100644 +--- a/src/xmipp/SConscript ++++ b/src/xmipp/SConscript +@@ -46,7 +46,7 @@ debug = get('DEBUG') + matlab = get('MATLAB') + opencv = env.GetOption('opencv') and get('OPENCV') + opencvsupportscuda = get('OPENCVSUPPORTSCUDA') +-opencv_3 = get('OPENCV3') ++opencv_ver = int(os.environ.get('OPENCV_VERSION', '0')) + starpu = get('STARPU') + + if opencv: +@@ -55,7 +55,7 @@ if opencv: + 'opencv_video', + 'libopencv_calib3d'] + if opencvsupportscuda: +- if opencv_3: ++ if opencv_ver >= 3: + opencvLibs+=['libopencv_cudaoptflow', 'libopencv_cudaarithm'] + else: + opencvLibs+=['libopencv_gpu'] From 5b850bac0acb053edd023b59e930b9216ae39022 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 15 Nov 2022 14:02:35 +0100 Subject: [PATCH 5476/9987] adding easyconfigs: NanoPlot-1.33.0-foss-2021a.eb, nanomath-1.2.1-foss-2021a.eb, nanoget-1.18.1-foss-2021a.eb, pauvre-0.2.3-foss-2021a.eb --- .../n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb | 47 +++++++++++++++++++ .../n/nanoget/nanoget-1.18.1-foss-2021a.eb | 29 ++++++++++++ .../n/nanomath/nanomath-1.2.1-foss-2021a.eb | 33 +++++++++++++ .../p/pauvre/pauvre-0.2.3-foss-2021a.eb | 40 ++++++++++++++++ 4 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb new file mode 100644 index 00000000000..400d3660c4d --- /dev/null +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb @@ -0,0 +1,47 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'NanoPlot' +version = '1.33.0' + +homepage = 'https://github.com/wdecoster/NanoPlot' +description = "Plotting suite for long read sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['caf69a5789625e746814238cb4f0d510ed6768a094566e8f1dcaa77933c4d6fd'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('Pysam', '0.16.0.1'), + ('nanomath', '1.2.1'), + ('nanoget', '1.18.1'), + ('Seaborn', '0.11.2'), + ('plotly.py', '5.1.0'), + ('pauvre', '0.2.3'), + ('statsmodels', '0.12.2'), + ('Arrow', '6.0.0'), # for pyarrow + ('Kaleido', '0.2.1'), +] + +download_dep_fail = True +use_pip = True + +# replace strict Seaborn & pauvre version requirement with minimal version requirements +preinstallopts = "sed -i 's/==0/>=0/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/NanoPlot'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoPlot --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb new file mode 100644 index 00000000000..82b4f0b5841 --- /dev/null +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb @@ -0,0 +1,29 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'nanoget' +version = '1.18.1' + +homepage = 'https://github.com/wdecoster/nanoget' +description = "Functions to extract information from Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e4fa37ab1bccc3287947f5792acad3c96fd1c02cb9c0a1f5d218d26bcdbe1632'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('Pysam', '0.16.0.1'), + ('nanomath', '1.2.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb new file mode 100644 index 00000000000..5d1a69c2f73 --- /dev/null +++ b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'nanomath' +version = '1.2.1' + +homepage = 'https://github.com/wdecoster/nanomath' +description = "A few simple math function for other Oxford Nanopore processing scripts" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True + +exts_list = [ + ('Python-Deprecated', '1.1.0', { + 'modulename': 'deprecated', + 'checksums': ['a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f'], + }), + (name, version, { + 'checksums': ['3c611c3b0a8fa364b8afe87c948f31d5d8009a212c28954382e926f36f90e060'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb b/easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb new file mode 100644 index 00000000000..5bd495d2adb --- /dev/null +++ b/easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb @@ -0,0 +1,40 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'pauvre' +version = '0.2.3' + +homepage = 'https://github.com/conchoecia/pauvre' +description = "Tools for plotting Oxford Nanopore and other long-read data" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ba756bc9025ae7edafd91092d12a57864f018958fd46b548e9eeda7167ee197d'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('scikit-learn', '0.24.2'), + ('matplotlib', '3.4.2'), +] + +download_dep_fail = True +use_pip = True + +# fix incorrect requirement, correct name is 'scikit-learn' +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/pauvre'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pauvre --help"] + +sanity_pip_check = True + +moduleclass = 'math' From d6d8efaeb2b212f224ca7aadbd451f3185d63702 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 13:04:53 +0000 Subject: [PATCH 5477/9987] adding easyconfigs: basemap-1.3.6-foss-2022a.eb --- .../b/basemap/basemap-1.3.6-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb new file mode 100644 index 00000000000..9b019b172c7 --- /dev/null +++ b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb @@ -0,0 +1,51 @@ +# The newer version require also the installation of basemap-data. +# Conveniently, the tarball contains that too, so that is the one +# being used here. +# Based on basemap-1.2.2-foss-2020a-Python-3.8.2.eb +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'basemap' +version = '1.3.6' + +homepage = 'https://matplotlib.org/basemap/' +description = """The matplotlib basemap toolkit is a library for plotting +2D data on maps in Python""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('GEOS', '3.10.3'), + ('Pillow', '9.1.1'), + ('pyproj', '3.4.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyshp', '2.3.1', { + 'modulename': 'shapefile', + 'checksums': ['4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1'], + }), + ('basemap_data', version, { + 'modulename': 'mpl_toolkits.basemap_data', + 'preinstallopts': 'cd packages/%(name)s && GEOS_DIR=$EBROOTGEOS', + 'sources': ['v%(version)s.tar.gz'], + 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], + 'checksums': ['42adbd039b4afbe93ca2fa32cfab456d4fd590cb8ed1c28e4aa94dcb957b58ac'], + }), + (name, version, { + 'modulename': 'mpl_toolkits.basemap', + 'prebuildopts': 'GEOS_DIR=$EBROOTGEOS', + 'preinstallopts': 'cd packages/%(name)s && GEOS_DIR=$EBROOTGEOS', + 'sources': ['v%(version)s.tar.gz'], + 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], + 'checksums': ['42adbd039b4afbe93ca2fa32cfab456d4fd590cb8ed1c28e4aa94dcb957b58ac'], + }), +] + +moduleclass = 'vis' From 92db9c418e97d27131129390c58cfc7b640eb856 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 15 Nov 2022 14:28:06 +0100 Subject: [PATCH 5478/9987] delete easyconfig MATLAB-Engine-2021a-GCCcore-11.2.0.eb --- .../MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb deleted file mode 100644 index c1558fb7dc9..00000000000 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'MATLAB-Engine' -version = '2021a' - -homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' -description = """The MATLAB Engine API for Python provides a package for Python - to call MATLAB as a computational engine.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -dependencies = [ - ('MATLAB', version, '', SYSTEM), - ('Python', '3.9.6'), -] - -use_pip = False -download_dep_fail = True - -# Enable support for this current version of Python -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " -prebuildopts += "sed -i 's/^_supported_versions =.*/_supported_versions = ["%(pyshortver)s"]/' setup.py &&" -# Since this setup.py does not provide a separate --build-base for the install -# step, both build and install must be performed in a single command. -buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" - -skipsteps = ['install'] - -# Test that connection with MATLAB can be established successfully -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] - -sanity_pip_check = True - -options = {'modulename': 'matlab.engine'} - -moduleclass = 'math' From 2f5588ac858d263d70cd36b50c30f9fe558bce4d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2022 14:58:22 +0100 Subject: [PATCH 5479/9987] clean up version of Python dependency in pyWannier90 easyconfig --- .../p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb index 2a045c216cc..3a1d4b39c48 100644 --- a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb @@ -32,12 +32,8 @@ builddependencies = [ ('pybind11', '2.6.2'), ] -local_pymaj = '3' -local_pymin = '9' -local_pymajmin = local_pymaj + local_pymin - dependencies = [ - ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('PySCF', '1.7.6'), ] From 128ac0711acc1726eb87226ec706e199781e4048 Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 15 Nov 2022 15:04:34 +0100 Subject: [PATCH 5480/9987] adding easyconfigs: resolos-0.3.5.eb --- .../easyconfigs/r/resolos/resolos-0.3.5.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb new file mode 100644 index 00000000000..f588b3b926d --- /dev/null +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'resolos' +version = '0.3.5' + +homepage = 'https://gitlab.unige.ch/resolos/resolos' +description = """Resolos is a toolkit written in Python for maintaining reproducible environments for scientific computations. +It's main goal is to enable researchers to easily replicate environments through space (running code on HPC environment) +and time (environment preservation for long term archival). +For installation and detailed usage, check out the documentation.""" + +toolchain = {'name': 'system', 'version': ''} + +# source_urls = [PYPI_SOURCE] +# Link copy from pypi.org | PYPI_SOURCE is not working +sources = ["https://files.pythonhosted.org/packages/15/0b/fa95a349434f77d8afc775dd999152d7612b6baed52083981ac84eaa41e9/resolos-0.3.5.tar.gz"] +checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] + + +use_pip = True +use_pip_for_deps = True +moduleclass = 'data' + +sanity_check_commands = ["r3s info"] +sanity_check_paths = { + 'files': ["bin/r3s"], + 'dirs': [] +} From a55fa6e6769ed3a1a727065e23fe96017df4fda9 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 15 Nov 2022 15:58:30 +0100 Subject: [PATCH 5481/9987] Add the last missing tool of the pipeline + Sync with develop --- .../n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb index 9699267036a..2e45780b042 100644 --- a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb +++ b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb @@ -16,7 +16,6 @@ description = """The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.""" toolchain = {'name': 'foss', 'version': '2021a'} -# TODO The long reads sequencing part (1 missing) tools will be added later dependencies = [ ('Nextflow', '22.10.1', '', SYSTEM), ('AdapterRemoval', '2.3.2'), @@ -38,6 +37,7 @@ dependencies = [ ('MetaBAT', '2.15'), ('MultiQC', '1.11'), ('NanoLyse', '1.2.1'), + ('NanoPlot', '1.33.0'), ('Porechop', '0.2.4'), ('prodigal', '2.6.3'), ('prokka', '1.14.5'), From fb8f6c3b3fed32f72044265daa3bbc02ca00dca6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2022 16:48:12 +0100 Subject: [PATCH 5482/9987] {toolchain} intel/2022.11 --- .../h/HPL/HPL-2.3-intel-2022.11.eb | 21 ++++++++++++ .../easyconfigs/i/iimpi/iimpi-2022.11.eb | 18 ++++++++++ .../imkl-FFTW-2022.2.1-iimpi-2022.11.eb | 11 +++++++ easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb | 18 ++++++++++ .../impi-2021.7.1-intel-compilers-2022.2.1.eb | 16 +++++++++ .../intel-compilers-2022.2.1.eb | 33 +++++++++++++++++++ .../easyconfigs/i/intel/intel-2022.11.eb | 22 +++++++++++++ 7 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2022.11.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb new file mode 100644 index 00000000000..6b5eb683de8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022.11'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb new file mode 100644 index 00000000000..49aa4591617 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022.11' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.1', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb new file mode 100644 index 00000000000..ff00372cf4e --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022.11'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb new file mode 100644 index 00000000000..3daf55958a3 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19038/'] +sources = ['l_onemkl_p_%(version)s.16993_offline.sh'] +checksums = ['eedd4b795720de776b1fc5f542ae0fac37ec235cdb567f7c2ee3182e73e3e59d'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..68aeb9beb63 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.7.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19010/'] +sources = ['l_mpi_oneapi_p_%(version)s.16815_offline.sh'] +checksums = ['90e7804f2367d457cd4cbf7aa29f1c5676287aa9b34f93e7c9a19e4b8583fff7'] + +dependencies = [('UCX', '1.13.1')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..a6ae8170105 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb @@ -0,0 +1,33 @@ +name = 'intel-compilers' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19030/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.16991_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18998/'], + 'filename': 'l_fortran-compiler_p_%(version)s.16992_offline.sh', + }, +] +checksums = [ + {'l_dpcpp-cpp-compiler_p_2022.2.1.16991_offline.sh': + '3f0f02f9812a0cdf01922d2df9348910c6a4cb4f9dfe50fc7477a59bbb1f7173'}, + {'l_fortran-compiler_p_2022.2.1.16992_offline.sh': + '64f1d1efbcdc3ac2182bec18313ca23f800d94f69758db83a1394490d9d4b042'}, +] + +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2022.11.eb b/easybuild/easyconfigs/i/intel/intel-2022.11.eb new file mode 100644 index 00000000000..9dd32ad27d5 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022.11.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022.11' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.1', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From ed16eb8d76b55f3a37df562ae89fd33ff850c127 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 16:38:33 +0000 Subject: [PATCH 5483/9987] adding easyconfigs: zarr-2.13.3-foss-2022a.eb --- .../z/zarr/zarr-2.13.3-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb new file mode 100644 index 00000000000..ff8bb790e8f --- /dev/null +++ b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = "PythonBundle" + +name = 'zarr' +version = '2.13.3' + +homepage = 'https://zarr.readthedocs.io/en/stable/' +description = """Zarr is a Python package providing an implementation of compressed, +chunked, N-dimensional arrays, designed for use in parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('entrypoints', '0.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + ('monotonic', '1.6', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/atdt/monotonic/archive'], + 'checksums': ['9609c249aed584fd714811014870650d08d6f6414402b5a190663c49bf83b221'], + }), + ('numcodecs', '0.10.2', { + 'checksums': ['22838c6b3fd986bd9c724039b88870057f790e22b20e6e1cbbaa0de142dd59c4'], + }), + (name, version, { + 'checksums': ['db24b090616c638f65e33a6bc5d956d642221182961515ccbc28b17fb0d0b48c'], + }), +] + +moduleclass = 'data' From 5a553631d9eab4892c2ef75825406ec479bea08e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 15 Nov 2022 17:41:54 +0100 Subject: [PATCH 5484/9987] Use SWIG as builddependencies --- easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb index 54f52a70197..50daf951ccb 100644 --- a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb @@ -17,12 +17,15 @@ software_license = 'LicenseGPLv2' toolchain = {'name': 'foss', 'version': '2021a'} +builddependencies = [ + ('SWIG', '4.0.2'), +] + dependencies = [ ('Python', '3.9.5'), ('ruamel.yaml', '0.17.21'), ('SciPy-bundle', '2021.05'), ('sympy', '1.8'), - ('SWIG', '4.0.2'), ('GLPK', '5.0'), ('python-libsbml', '5.19.7'), ] From 0c896f78ee96f01b133e49d801b6a68b5c7dec48 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 17:30:09 +0000 Subject: [PATCH 5485/9987] adding easyconfigs: lagrangian-filtering-0.8.3-foss-2022a.eb --- .../lagrangian-filtering-0.8.3-foss-2022a.eb | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb new file mode 100644 index 00000000000..2b248447592 --- /dev/null +++ b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb @@ -0,0 +1,83 @@ +# This installation unfortunately requires the GitHub dance, as the tarball +# is simply not installing. For that reason there is no checksum! +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'lagrangian-filtering' +version = '0.8.3' + +homepage = 'https://github.com/angus-g/lagrangian-filtering' +description = """Temporal filtering of data in a Lagrangian frame of reference.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('dask', '2022.10.2'), + ('h5py', '3.7.0'), + ('SciPy-bundle', '2022.05'), + ('netcdf4-python', '1.6.1'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), + ('zarr', '2.13.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('parcels', '2.4.0', { + 'checksums': ['221ce49b6cb5bb4996aa3c817c0de7f022c952a4d8cb4160ca7df7dd940714b5'], + }), + ('xarray', '2022.9.0', { + 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], + }), + ('pykdtree', '1.3.6', { + 'checksums': ['780b693d0555b857d7aab31e35d4293bf4ebdb9dec7a45ba4bb23b4400f626dc'], + }), + ('sosfilt', '1.2.0', { + 'checksums': ['b3083fd2edf723a6163f00ddc36ec3ca20fbf6112cc68573dad9356544a9d734'], + }), + ('psutil', '5.9.4', { + 'checksums': ['3d7f9739eb435d4b1338944abe23f49584bde5395f27487d2ee25ad9a8774a62'], + }), + ('progressbar2', '4.2.0', { + 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], + 'modulename': 'progressbar', + }), + ('cgen', '2020.1', { + 'checksums': ['4ec99d0c832d9f95f5e51dd18a629ad50df0b5464ce557ef42c6e0cd9478bfcf'], + }), + ('pymbolic', '2022.1', { + 'checksums': ['b52f451dd0b9803e03de3320af3b7ce5723070061c6d231c00216f6da4259012'], + }), + ('pytools', '2022.1.12', { + 'checksums': ['4d62875e9a2ab2a24e393a9a8b799492f1a721bffa840af3807bfd42871dd1f4'], + }), + ('python-utils', '3.4.5', { + 'checksums': ['7e329c427a6d23036cfcc4501638afb31b2ddc8896f25393562833874b8c6e0a'], + }), + + (name, version, { + 'sources': [{ + 'filename': '%(name)s-%(version)s-commit.tar.gz', + 'git_config': { + 'url': 'https://github.com/angus-g/', + 'repo_name': name, + 'commit': 'b942ff3', + 'recursive': True, + 'keep_git_dir': True, + }, + }], + 'checksums': [None], + 'modulename': 'filtering', + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 11f9457cddcb386b1bfd6aaf2e2759386ffb852e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 15 Nov 2022 19:13:34 +0100 Subject: [PATCH 5486/9987] Add missing checksums --- .../x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb index 4093b1d0ecf..fc96f59b860 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb @@ -60,6 +60,10 @@ checksums = [ '284b8ec1e514fb84b7680c8b3f59b3d5931b564beb444d3301504e3170e9a49e'}, {'Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch': '1514eaa5de35b38b5a10e949edf5c94ba95bbd05e0b9fbf70db2ea98967394e3'}, + {'Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch': + 'b478c08a6a260021b4b91e5a8f6d9c5637eafdedcd99fcb672fe356d1744d349'}, + {'Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch': + '9d7c90a8cdeca24dba41a0d2f11f59ab34a438ed34fa7f4850172848505ecbae'}, {'XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch': '8dcf0f3648f4b3438374ba629a9efa2e5c08eb25ae76ed420513664d21e2246b'}, {'XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': From bb635813adaecf716c61c72ac083d73e49f84177 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 02:26:55 +0100 Subject: [PATCH 5487/9987] update MATLAB-Engine v2021a to PyPI package v2021a-9.10.1 --- ...TLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ .../MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 34 ----------------- 2 files changed, 38 insertions(+), 34 deletions(-) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..97c48e8fad3 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'MATLAB-Engine' +_matlab_version = '2021a' +_engine_version = '9.10.1' +version = "%s-%s" % (_matlab_version, _engine_version) + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('MATLAB', _matlab_version, '', SYSTEM), + ('Python', '3.8.6'), +] + +use_pip = True + +exts_list = [ + ('matlabengine', '9.10.1', { + 'modulename': 'matlab.engine', + 'checksums': ['c1610690dbe58ac00e74e8cbb20406208235ede47da7960238e0c2fd3bd496c0'], + }), +] + +sanity_pip_check = True + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +# Systems with old glibc (e.g. CentOS7) need to preload shim library +# modluafooter = """ +# setenv("LD_PRELOAD", pathJoin(os.getenv("EBROOTMATLAB"), "bin", "glnxa64", "glibc-2.17_shim.so")) +# """ + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb deleted file mode 100644 index 83a3d5d719c..00000000000 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'MATLAB-Engine' -version = '2021a' - -homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' -description = """The MATLAB Engine API for Python provides a package for Python - to call MATLAB as a computational engine.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -dependencies = [ - ('MATLAB', version, '', SYSTEM), - ('Python', '3.8.6'), -] - -use_pip = False -download_dep_fail = True - -# Since this setup.py does not provide a separate --build-base for the install -# step, both build and install must be performed in a single command. -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " -buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" - -skipsteps = ['install'] - -# Test that connection with MATLAB can be established successfully -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] - -sanity_pip_check = True - -options = {'modulename': 'matlab.engine'} - -moduleclass = 'math' From abbb3aa220b6ab59d9720d484cb12aa0774d6ec8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 02:28:13 +0100 Subject: [PATCH 5488/9987] update MATLAB-Engine v2021b to PyPI package v2021b-9.11.19 --- ...LAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ .../MATLAB-Engine-2021b-GCCcore-11.2.0.eb | 34 ----------------- 2 files changed, 38 insertions(+), 34 deletions(-) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb delete mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c7c345f46d5 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'MATLAB-Engine' +_matlab_version = '2021b' +_engine_version = '9.11.19' +version = "%s-%s" % (_matlab_version, _engine_version) + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('MATLAB', _matlab_version, '', SYSTEM), + ('Python', '3.9.6'), +] + +use_pip = True + +exts_list = [ + ('matlabengine', '9.11.19', { + 'modulename': 'matlab.engine', + 'checksums': ['9385a13c27daa18f6cbfbe1669237e86692a51f317775a3f40e9e3d8090c679b'], + }), +] + +sanity_pip_check = True + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +# Systems with old glibc (e.g. CentOS7) need to preload shim library +# modluafooter = """ +# setenv("LD_PRELOAD", pathJoin(os.getenv("EBROOTMATLAB"), "bin", "glnxa64", "glibc-2.17_shim.so")) +# """ + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb deleted file mode 100644 index a188c57dcad..00000000000 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'MATLAB-Engine' -version = '2021b' - -homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' -description = """The MATLAB Engine API for Python provides a package for Python - to call MATLAB as a computational engine.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -dependencies = [ - ('MATLAB', version, '', True), - ('Python', '3.9.6'), -] - -use_pip = False -download_dep_fail = True - -# Since this setup.py does not provide a separate --build-base for the install -# step, both build and install must be performed in a single command. -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " -buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" - -skipsteps = ['install'] - -# Test that connection with MATLAB can be established successfully -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] - -sanity_pip_check = True - -options = {'modulename': 'matlab.engine'} - -moduleclass = 'math' From 1b69e4da4ebe89d50fdde47eb3518d14ac80572d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 08:24:15 +0100 Subject: [PATCH 5489/9987] adding easyconfigs: Meson-0.64.0-GCCcore-12.2.0.eb --- .../m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..167a5228187 --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.64.0' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5e27e091c2a35b9049e152a6535045ebbd057253aeb67856de6ecbb7b917bab'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), # includes required 'wheel' package + ('Ninja', '1.11.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["meson --help"] + +moduleclass = 'tools' From 34b52a6d8a9dfb1a127cf9091d6edac8e56994f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 16 Nov 2022 12:32:59 +0000 Subject: [PATCH 5490/9987] adding easyconfigs: ANSYS-2022R2.eb --- easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb diff --git a/easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb b/easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb new file mode 100644 index 00000000000..5c94e25f8af --- /dev/null +++ b/easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb @@ -0,0 +1,30 @@ +name = 'ANSYS' +version = '2022R2' + +homepage = 'https://www.ansys.com' +description = """ANSYS simulation software enables organizations to confidently predict + how their products will operate in the real world. We believe that every product is + a promise of something greater. """ + +toolchain = SYSTEM + +download_instructions = 'Manually obtain (ANSYS%(version)s_LINX64_DiskX.iso) from your ANSYS vendor' +# Custom extract command is used since iso sources contain duplicate file. +sources = [ + {'filename': 'ANSYS%(version)s_LINX64_Disk1.iso', 'extract_cmd': '7z x -aos %s'}, + {'filename': 'ANSYS%(version)s_LINX64_Disk2.iso', 'extract_cmd': '7z x -aos %s'}, + {'filename': 'ANSYS%(version)s_LINX64_Disk3.iso', 'extract_cmd': '7z x -aos %s'}, +] +checksums = [ + {'ANSYS2022R2_LINX64_Disk1.iso': '7c9b2a57dd3b87c1dabcd84c913135c83aaac46bf75fbe3fae8da61c85e78198'}, + {'ANSYS2022R2_LINX64_Disk2.iso': '7962ef251e2edb7e999bfb6a857272597973d7ac4c17c2271cfd891347fd452a'}, + {'ANSYS2022R2_LINX64_Disk3.iso': '58d4b72e90a27fe11aee3cd7db251ecd1f80b2353441e7061543c0fc21c14dac'}, +] + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Specify license_server and license_server_port here, or use EB_ANSYS_LICENSE_SERVER and EB_ANSYS_LICENSE_SERVER_PORT +# license_server = "ansys.lic.example.com" +# license_server_port = "1234:5678" + +moduleclass = 'tools' From d431b26b6874c8baec79d10637f28eef402851e8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 16 Nov 2022 15:40:37 +0100 Subject: [PATCH 5491/9987] adding easyconfigs: IOR-3.3.0-gompi-2022a.eb --- .../i/IOR/IOR-3.3.0-gompi-2022a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb new file mode 100644 index 00000000000..9b3059aa224 --- /dev/null +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Åke Sandgren, HPC2N, Umeå University + +easyblock = 'ConfigureMake' + +name = "IOR" +version = "3.3.0" + +homepage = 'https://github.com/hpc/ior' +description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, + or HDF5 interfaces. """ + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/hpc/ior/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['41fe66f91aead70f7e53246de68dd194e7ade72070faf696f88efffdcf1bf68b'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Perl', '5.34.1'), +] +dependencies = [ + ('HDF5', '1.12.2'), +] + +configopts = '--with-hdf5 ' +buildopts = 'V=1 ' + +sanity_check_paths = { + 'files': ["bin/ior"], + 'dirs': ["share"] +} + +moduleclass = 'tools' From 4b5e30730dc76f670816a72e2c72017ceeab7685 Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Wed, 16 Nov 2022 15:50:27 +0100 Subject: [PATCH 5492/9987] adding easyconfigs: FreeSurfer-7.3.2-centos7_x86_64.eb --- .../FreeSurfer-7.3.2-centos7_x86_64.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb new file mode 100644 index 00000000000..56892c77fd0 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.3.2' +versionsuffix = '-centos7_x86_64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + {'freesurfer-linux-centos7_x86_64-7.3.2.tar.gz': + '58518d3ee5abd2e05109208aed2eef145c4e3b994164df8c4e0033c1343b9e56'}, + {'runtime2014bLinux.tar.gz': '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648'}, +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' From 70debb7b60b88734a6f13e6e6e6e4575bc2ed55e Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 16 Nov 2022 14:59:19 +0000 Subject: [PATCH 5493/9987] adding easyconfigs: cmocean-2.0-foss-2022a.eb --- .../c/cmocean/cmocean-2.0-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb new file mode 100644 index 00000000000..3531eb02047 --- /dev/null +++ b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb @@ -0,0 +1,31 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = "PythonBundle" + +name = 'cmocean' +version = '2.0' + +homepage = 'https://github.com/matplotlib/cmocean' +description = """This package contains colormaps for commonly-used +oceanographic variables. Most of the colormaps started from +matplotlib colormaps, but have now been adjusted using the viscm +tool to be perceptually uniform.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['13eea3c8994d8e303e32a2db0b3e686f6edfb41cb21e7b0e663c2b17eea9b03a'], + }), +] + +moduleclass = 'data' From 1f6acfd410de14901f935a58f00c6ff363dc4529 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 16 Nov 2022 15:05:56 +0000 Subject: [PATCH 5494/9987] Sanity check added --- easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb index 3531eb02047..452ee96673d 100644 --- a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb @@ -28,4 +28,9 @@ exts_list = [ }), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + moduleclass = 'data' From e5deb360201cab927d4603083b499a16f4b871b7 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 16 Nov 2022 15:18:07 +0000 Subject: [PATCH 5495/9987] adding easyconfigs: astropy-5.1.1-foss-2022a.eb --- .../a/astropy/astropy-5.1.1-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb b/easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb new file mode 100644 index 00000000000..1e3d64025d1 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = "PythonBundle" + +name = 'astropy' +version = '5.1.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop a common +core package for Astronomy in Python and foster an ecosystem of interoperable +astronomy packages. + +The Astropy community is committed to supporting diversity and inclusion.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '2.0.0.1', { + 'modulename': 'erfa', + 'checksums': ['2fd4637ffe2c1e6ede7482c13f583ba7c73119d78bef90175448ce506a0ede30'], + }), + ('extension-helpers', '1.0.0', { + 'checksums': ['ca1bfac67c79cf4a7a0c09286ce2a24eec31bf17715818d0726318dd0e5050e6'], + }), + (name, version, { + 'checksums': ['ba4bd696af7090fd399b464c704bf27b5633121e461785edc70432606a94bd81'], + }), +] + +moduleclass = 'astro' From d0033ea45c9888ee61dbca3e9bb5cbb632b5ddc6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:34:47 +0100 Subject: [PATCH 5496/9987] adding easyconfigs: intltool-0.51.0-GCCcore-12.2.0.eb --- .../intltool-0.51.0-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..68c3f09136f --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Perl', '5.36.0'), +] + +fix_perl_shebang_for = ['bin/intltool-*'] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +sanity_check_commands = ["intltool-merge --help"] + +moduleclass = 'devel' From 6ae319ac98043b85b314fcb44757bfce5ef34628 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:36:54 +0100 Subject: [PATCH 5497/9987] adding easyconfigs: freetype-2.12.1-GCCcore-12.2.0.eb, Brotli-1.0.9-GCCcore-12.2.0.eb --- .../b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb | 36 ++++++++++++++++ .../freetype-2.12.1-GCCcore-12.2.0.eb | 43 +++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8056873eb95 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Brotli' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brotli-%(version)s_pc_link_flags.patch'] +checksums = [ + 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz + '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'dirs': [], +} + +sanity_check_commands = ["brotli --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4b7d4298ad1 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +name = 'freetype' +version = '2.12.1' + +homepage = 'https://www.freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + GNU_SAVANNAH_SOURCE, + SOURCEFORGE_SOURCE, +] +sources = [SOURCE_TAR_GZ] +checksums = ['efe71fd4b8246f1b0b1b9bfca13cfff1c9ad85930340c27df469733bbb620938'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), + ('Brotli', '1.0.9'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +sanity_check_commands = ["freetype-config --help"] + +moduleclass = 'vis' From e7441c854d59e7bc4fbe2d10743688559653681b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:37:46 +0100 Subject: [PATCH 5498/9987] adding easyconfigs: fontconfig-2.14.1-GCCcore-12.2.0.eb, util-linux-2.38.1-GCCcore-12.2.0.eb, gperf-3.1-GCCcore-12.2.0.eb --- .../fontconfig-2.14.1-GCCcore-12.2.0.eb | 40 ++++++++++++++++++ .../g/gperf/gperf-3.1-GCCcore-12.2.0.eb | 32 +++++++++++++++ .../util-linux-2.38.1-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ 3 files changed, 113 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6a514ecbd3c --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.14.1' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ae480e9ca34382790312ff062c625ec70df94d6d9a9366e2b2b3d525f7f90387'] + +builddependencies = [ + ('binutils', '2.39'), + ('gperf', '3.1'), + ('pkgconf', '1.9.3'), + ('Python', '3.10.8', '-bare'), +] + +dependencies = [ + ('expat', '2.4.9'), + ('freetype', '2.12.1'), + ('util-linux', '2.38.1'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5f019911975 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'https://www.gnu.org/software/gperf/' +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [], +} + +sanity_check_commands = ["gperf --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ddc2a4e1286 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.38.1' + +homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0820eb8eea90408047e3715424bc6be771417047f683950fecb4bdd2e2cbbc6e'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), +] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' From 4fe7551a558ac201f4797a64a3dd0dbf032eefff Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 16:39:26 +0100 Subject: [PATCH 5499/9987] replace hardcoded versions for matlabengine extensions --- .../MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 2 +- .../MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb index 97c48e8fad3..d559c0538dd 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ use_pip = True exts_list = [ - ('matlabengine', '9.10.1', { + ('matlabengine', _engine_version, { 'modulename': 'matlab.engine', 'checksums': ['c1610690dbe58ac00e74e8cbb20406208235ede47da7960238e0c2fd3bd496c0'], }), diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb index c7c345f46d5..d1457326e93 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ use_pip = True exts_list = [ - ('matlabengine', '9.11.19', { + ('matlabengine', _engine_version, { 'modulename': 'matlab.engine', 'checksums': ['9385a13c27daa18f6cbfbe1669237e86692a51f317775a3f40e9e3d8090c679b'], }), From 36c48a24e97ca94cef58dacbb5f3aa81cbb59a6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:42:05 +0100 Subject: [PATCH 5500/9987] adding easyconfigs: X11-20221110-GCCcore-12.2.0.eb --- .../x/X11/X11-20221110-GCCcore-12.2.0.eb | 213 ++++++++++++++++++ 1 file changed, 213 insertions(+) create mode 100644 easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ea22050d122 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb @@ -0,0 +1,213 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20221110' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('Bison', '3.8.2'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), + ('intltool', '0.51.0'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.14.1'), + ('freetype', '2.12.1'), + ('zlib', '1.2.12'), + ('xorg-macros', '1.19.3'), + ('libpciaccess', '0.17'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libpthread-stubs', '0.4', { # 2017-03-14 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('xorgproto', '2022.2', { # 2022-08-11 + 'checksums': ['da351a403d07a7006d7bdc8dcfc14ddc1b588b38fb81adab9989a8eef605757b'], + }), + ('libXau', '1.0.10', { # 2022-08-26 + 'checksums': ['51a54da42475d4572a0b59979ec107c27dacf6c687c2b7b04e5cf989a7c7e60c'], + }), + ('libXdmcp', '1.1.3', { # 2019-03-16 + 'checksums': ['2ef9653d32e09d1bf1b837d0e0311024979653fe755ad3aaada8db1aa6ea180c'], + }), + ('xcb-proto', '1.15.2', { # 2022-06-17 + 'checksums': ['6b1ed9cd7cf35e37913eeecca37e5b85b14903002942b3e332f321335c27a8eb'], + }), + ('libxcb', '1.15', { # 2022-05-03 + 'checksums': ['1cb65df8543a69ec0555ac696123ee386321dfac1964a3da39976c9a05ad724d'], + }), + ('xtrans', '1.4.0', { # 2019-03-16 + 'checksums': ['48ed850ce772fef1b44ca23639b0a57e38884045ed2cbb18ab137ef33ec713f9'], + }), + ('libxkbcommon', '1.4.1', { # 2022-05-21 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['943c07a1e2198026d8102b17270a1f406e4d3d6bbc4ae105b9e1b82d7d136b39'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.8.2', { # 2022-11-10 + 'checksums': ['f1bc56187bee0f830e1179ac5068ac93b78c51ace94eb27702ffb2efd116587b'], + }), + ('libXext', '1.3.5', { # 2022-10-29 + 'checksums': ['1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'], + }), + ('libFS', '1.0.9', { # 2022-08-26 + 'checksums': ['8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'], + }), + ('libICE', '1.0.10', { # 2019-07-14 + 'checksums': ['1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d'], + }), + ('libSM', '1.2.3', { # 2018-10-10 + 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], + }), + ('libXScrnSaver', '1.2.3', { # 2018-07-05 + 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], + }), + ('libXt', '1.2.1', { # 2021-01-24 + 'checksums': ['6da1bfa9dd0ed87430a5ce95b129485086394df308998ebe34d98e378e3dfb33'], + }), + ('libXmu', '1.1.4', { # 2022-10-17 + 'checksums': ['3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'], + }), + ('libXpm', '3.5.13', { # 2019-12-13 + 'checksums': ['e3dfb0fb8c1f127432f2a498c7856b37ce78a61e8da73f1aab165a73dd97ad00'], + }), + ('libXaw', '1.0.14', { # 2021-03-27 + 'checksums': ['59cfed2712cc80bbfe62dd1aacf24f58d74a76dd08329a922077b134a8d8048f'], + }), + ('libXfixes', '6.0.0', { # 2021-05-11 + 'checksums': ['82045da5625350838390c9440598b90d69c882c324ca92f73af9f0e992cb57c7'], + }), + ('libXcomposite', '0.4.5', { # 2019-03-11 + 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], + }), + ('libXrender', '0.9.11', { # 2022-10-22 + 'checksums': ['6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'], + }), + ('libXcursor', '1.2.1', { # 2022-04-03 + 'checksums': ['77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'], + }), + ('libXdamage', '1.1.5', { # 2019-03-11 + 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], + }), + ('libfontenc', '1.1.6', { # 2022-08-30 + 'checksums': ['c103543a47ce5c0200fb1867f32df5e754a7c3ef575bf1fe72187117eac22a53'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.6', { # 2022-08-26 + 'checksums': ['a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'], + }), + ('libXft', '2.3.6', { # 2022-09-10 + 'checksums': ['b7e59f69e0bbabe9438088775f7e5a7c16a572e58b11f9722519385d38192df5'], + }), + ('libXi', '1.8', { # 2021-09-15 + 'checksums': ['c80fd200a1190e4406bb4cc6958839d9651638cb47fa546a595d4bebcd3b9e2d'], + }), + ('libXinerama', '1.1.5', { # 2022-10-29 + 'checksums': ['2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'], + }), + ('libXrandr', '1.5.2', { # 2019-03-16 + 'checksums': ['3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e'], + }), + ('libXres', '1.2.1', { # 2021-03-31 + 'checksums': ['918fb33c3897b389a1fbb51571c5c04c6b297058df286d8b48faa5af85e88bcc'], + }), + ('libXtst', '1.2.4', { # 2022-09-27 + 'checksums': ['01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'], + }), + ('libXv', '1.0.11', { # 2016-10-04 + 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], + }), + ('libXvMC', '1.0.13', { # 2022-03-22 + 'checksums': ['e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'], + }), + ('libXxf86dga', '1.1.5', { # 2019-03-16 + 'checksums': ['715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69'], + }), + ('libXxf86vm', '1.1.5', { # 2022-09-27 + 'checksums': ['f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'], + }), + ('libdmx', '1.1.4', { # 2018-05-14 + 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], + }), + ('libxkbfile', '1.1.1', { # 2022-10-18 + 'checksums': ['87faee6d4873c5631e8bb53e85134084b862185da682de8617f08ca18d82e216'], + }), + ('libxshmfence', '1.3', { # 2018-02-26 + 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], + }), + ('xcb-util', '0.4.0', { # 2014-10-15 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.1', { # 2022-10-18 + 'checksums': ['0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'], + }), + ('xcb-util-keysyms', '0.4.1', { # 2022-10-19 + 'checksums': ['1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'], + }), + ('xcb-util-renderutil', '0.3.10', { # 2022-10-19 + 'checksums': ['e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'], + }), + ('xcb-util-wm', '0.4.2', { # 2022-10-19 + 'checksums': ['dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'], + }), + ('xcb-util-cursor', '0.1.4', { # 2022-10-18 + 'checksums': ['cc8608ebb695742b6cf84712be29b2b66aa5f6768039528794fca0fa283022bf'], + }), + ('xkeyboard-config', '2.37', { # 2022-10-04 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['eb1383a5ac4b6210d7c7302b9d6fab052abdf51c5d2c9b55f1f779997ba68c6c'], + # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing + 'preconfigopts': '', + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.4', { # 2022-09-12 + 'checksums': ['05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'], + }), + ('xbitmaps', '1.1.2', { # 2018-03-10 + 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' From 6cf1b4bf4a135e5b20243ba4cfe8f8f954cea413 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 16 Nov 2022 16:12:15 +0000 Subject: [PATCH 5501/9987] adding easyconfigs: SpaceRanger-2.0.0-GCC-11.2.0.eb --- .../SpaceRanger-2.0.0-GCC-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..b6aba4be749 --- /dev/null +++ b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'SpaceRanger' +version = '2.0.0' + +homepage = 'https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger' +description = """ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output +and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, +perform clustering and gene expression analysis, and place spots in spatial context on the slide image. """ + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +download_instructions = """ +Download sources from homepage, registration required +https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest +""" + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bdaa784e433c2e3707bed6a868042e954248e97fb4021d7179460a2b3702205c'] + +dependencies = [ + ('bcl2fastq2', '2.20.0'), +] + +allow_prepend_abs_path = True +# prepend reference databases GRCh38 and mm10 to PATH +# modextrapaths = {'PATH': '/path/to/databases/%(namelower)s-%(version)s'} + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['external', 'lib', 'mro'], +} + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From 59a818348d8e797c2b498412f5fede03c16ae7bc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 17:11:14 +0100 Subject: [PATCH 5502/9987] switch IJulia and MultilevelEstimators to JuliaBundle easyblock --- .../i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb | 14 +------------- ...elEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 17 +---------------- 2 files changed, 2 insertions(+), 29 deletions(-) diff --git a/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb index 54566147c74..06667a1bbf8 100644 --- a/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb +++ b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'JuliaBundle' name = 'IJulia' version = '1.23.3' @@ -14,12 +14,6 @@ dependencies = [ ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), ] -exts_defaultclass = 'JuliaPackage' -exts_filter = ("julia -e 'using %(ext_name)s'", "") -exts_default_options = { - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], -} - exts_list = [ ('Parsers', '2.4.2', { 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], @@ -74,13 +68,7 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['packages'], -} - modextrapaths = { - 'JULIA_DEPOT_PATH': '', 'JUPYTER_PATH': 'jupyter', } diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index b26dd65738e..822fe47b647 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'JuliaBundle' name = 'MultilevelEstimators' version = '0.1.0' @@ -15,12 +15,6 @@ dependencies = [ ('Julia', local_julia_ver, '-linux-%s' % ARCH, SYSTEM), ] -exts_defaultclass = 'JuliaPackage' -exts_filter = ("julia -e 'using %(ext_name)s'", "") -exts_default_options = { - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], -} - exts_list = [ ('Preferences', '1.3.0', { 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], @@ -101,13 +95,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['packages/%(name)s'] -} - -modextrapaths = { - 'JULIA_DEPOT_PATH': '', -} - moduleclass = 'lib' From f6b8d3a7a30b02164d0d60654b1412d18a3288b4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 16 Nov 2022 17:44:51 +0100 Subject: [PATCH 5503/9987] IOR: Drop leftover builddep from old easyconfig. --- easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb index 9b3059aa224..4ddd258e440 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb @@ -18,9 +18,9 @@ sources = [SOURCELOWER_TAR_BZ2] checksums = ['41fe66f91aead70f7e53246de68dd194e7ade72070faf696f88efffdcf1bf68b'] builddependencies = [ - ('Autotools', '20220317'), ('Perl', '5.34.1'), ] + dependencies = [ ('HDF5', '1.12.2'), ] From 4849ec35cc212b948195b1f82eb9e4716b3d0c23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 18:31:41 +0100 Subject: [PATCH 5504/9987] add missing pyWannier90 dependency for mcu + enhance sanity check --- easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb index 5a34c8b03a6..c70eb5db0f6 100644 --- a/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb +++ b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb @@ -19,14 +19,17 @@ dependencies = [ ('SciPy-bundle', '2021.05'), ('matplotlib', '3.4.2'), ('spglib-python', '1.16.1'), + ('pyWannier90', '2021-12-07'), ] -use_pip = True download_dep_fail = True -sanity_pip_check = True +use_pip = True sanity_check_commands = [ "python -c 'from mcu import VASP'", + "python -c 'import mcu.wannier90.pywannier90_vasp'", ] +sanity_pip_check = True + moduleclass = 'lib' From 3af237407132078871596275cfe66d571d7246aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 19:27:55 +0100 Subject: [PATCH 5505/9987] adding easyconfigs: snakemake-7.18.2-foss-2021b.eb --- .../snakemake/snakemake-7.18.2-foss-2021b.eb | 96 +++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-7.18.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-7.18.2-foss-2021b.eb b/easybuild/easyconfigs/s/snakemake/snakemake-7.18.2-foss-2021b.eb new file mode 100644 index 00000000000..2dcc4ecc1c5 --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-7.18.2-foss-2021b.eb @@ -0,0 +1,96 @@ +easyblock = 'PythonBundle' + +name = 'snakemake' +version = '7.18.2' + +homepage = 'https://snakemake.readthedocs.io' +description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('GitPython', '3.1.24'), + ('IPython', '7.26.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('ratelimiter', '1.2.0.post0', { + 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], + }), + ('ConfigArgParse', '1.5.3', { + 'checksums': ['1b0b3cbf664ab59dada57123c81eff3d9737e0d11d8cf79e3d6eb10823f1739f'], + }), + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('toposort', '1.7', { + 'checksums': ['ddc2182c42912a440511bd7ff5d3e6a1cabc3accbc674a3258c8c41cbfbb2125'], + }), + ('amply', '0.1.5', { + 'checksums': ['ad717b490b6b7055909faa195e82a4432b706f8f95854050172f42931e478426'], + }), + ('PuLP', '2.7.0', { + 'checksums': ['e73ee6b32d639c9b8cf4b4aded334ba158be5f8313544e056f796ace0a10ae63'], + }), + ('smart_open', '6.2.0', { + 'checksums': ['1b4df5c8365218f3852c507451920ccad606c80b0acb4e67508e50ba9b5d2632'], + }), + ('connection_pool', '0.0.3', { + 'checksums': ['bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc'], + }), + ('stopit', '1.1.2', { + 'checksums': ['f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d'], + }), + ('reretry', '0.11.1', { + 'checksums': ['4ae1840ae9e443822bb70543c485bb9c45d1d009e32bd6809f2a9f2839149f5d'], + }), + ('throttler', '1.2.1', { + 'checksums': ['8b23d3485a96d98484024a850c1887ccc685bead17e86c8a9e4b0335e7d74778'], + # workaround for https://github.com/uburuntu/throttler/issues/3 + 'preinstallopts': "touch readme.md requirements-dev.txt && ", + }), + ('dpath', '2.0.6', { + 'checksums': ['5a1ddae52233fbc8ef81b15fb85073a81126bb43698d3f3a1b6aaf561a46cdc0'], + }), + ('plac', '1.3.5', { + 'checksums': ['38bdd864d0450fb748193aa817b9c458a8f5319fbf97b2261151cfc0a5812090'], + }), + # yte requires PyYAML >= 6.0 + ('PyYAML', '6.0', { + 'checksums': ['68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2'], + 'modulename': 'yaml', + }), + ('yte', '1.5.1', { + 'checksums': ['6d0b315b78af83276d78f5f67c107c84238f772a76d74f4fc77905b46f3731f5'], + }), + (name, version, { + # patch is needed for clusters that do not support copying the full env into the batch job + # 'patches': ['snakemake-%(version)s_fix_jobs.patch'], + 'checksums': [ + '23f52b9a0c86da3b974a3cfc097fa82b41c49dab05543c0d18377c854852f771', # snakemake-7.18.2 + # '916875eaf4869c65b93098e362b8676cf55c6e37067a54b191f34b13e06c37e3', # snakemake-6.6.1_fix_jobs.patch + ], + }), +] + +# SNAKEMAKE_LOAD_MODULE is needed for snakemake-6.6.1_fix_jobs.patch to work +# local_snakemake_load is the command for loading this module (here: default EB module naming scheme) +# local_snakemake_load = 'module load %(module_name)s' +# modextravars = {'SNAKEMAKE_LOAD_MODULE': local_snakemake_load} + +sanity_check_paths = { + 'files': ['bin/snakemake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], +} + +sanity_check_commands = ['snakemake --help'] + +moduleclass = 'tools' From 40bad0fb605e2e69b99a1d12bdc7b59fb63189b6 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 16 Nov 2022 20:45:54 +0000 Subject: [PATCH 5506/9987] remove unused prebuildopts --- easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb index 9b019b172c7..456ebc34788 100644 --- a/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb +++ b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb @@ -40,7 +40,6 @@ exts_list = [ }), (name, version, { 'modulename': 'mpl_toolkits.basemap', - 'prebuildopts': 'GEOS_DIR=$EBROOTGEOS', 'preinstallopts': 'cd packages/%(name)s && GEOS_DIR=$EBROOTGEOS', 'sources': ['v%(version)s.tar.gz'], 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], From a715b34768b61935a0d74e8dc6ec4c96b8313203 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 22:45:24 +0100 Subject: [PATCH 5507/9987] add build dependency on binutils to MATLAB-Engine v2021a-9.10.1 --- .../MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb index d559c0538dd..f9fc548a6ee 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -11,6 +11,8 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] + dependencies = [ ('MATLAB', _matlab_version, '', SYSTEM), ('Python', '3.8.6'), From 5b1cfd90607afa5f3f7a31275d9669f8ad6a7850 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 22:46:05 +0100 Subject: [PATCH 5508/9987] add build dependency on binutils to MATLAB-Engine v2021b-9.11.19 --- .../MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb index d1457326e93..7bbd5629949 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb @@ -11,6 +11,8 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +builddependencies = [('binutils', '2.37')] + dependencies = [ ('MATLAB', _matlab_version, '', SYSTEM), ('Python', '3.9.6'), From 1880305e6208d1c6f1c9fd6736bf455b226ca87d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Nov 2022 09:40:16 +0100 Subject: [PATCH 5509/9987] using SYSTEM rather than True for CUDA dependency in NAMD easyconfig --- .../easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb index ba107970cf1..d89411f76cc 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb @@ -24,7 +24,7 @@ checksums = [ # support for GCC 8+ on POWER dependencies = [ ('Tcl', '8.6.11'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] builddependencies = [ From 09eacbe4fb9de594bcbd0b5587cd50ef6ce85159 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Nov 2022 10:08:16 +0100 Subject: [PATCH 5510/9987] simplify 'sources' spec in NAMD 2.14 easyconfig + remove useless comment --- .../easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb index d89411f76cc..eafa0dbcabf 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': False, 'openmp': False, 'pic': True} source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] -sources = [{'filename': 'NAMD_%(version)s_Source.tar.gz'}] +sources = ['NAMD_%(version)s_Source.tar.gz'] patches = [ "%(name)s-%(version)s_Linux-POWER-cuda.patch", "%(name)s-%(version)s-use_system_mremap_decl.patch" @@ -21,7 +21,6 @@ checksums = [ 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch ] -# support for GCC 8+ on POWER dependencies = [ ('Tcl', '8.6.11'), ('CUDA', '11.3.1', '', SYSTEM), From 9885375556349694732e58132ba0e5411bf98b9a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 17 Nov 2022 11:04:14 +0100 Subject: [PATCH 5511/9987] Add missing cuFFTAdvisor source --- .../x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb index fc96f59b860..f3e9847d3b7 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb @@ -32,6 +32,12 @@ sources = [ 'filename': 'xmippViz-v%(version)s.tar.gz', 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', }, + { + 'source_urls': ['https://github.com/DStrelak/cuFFTAdvisor/archive/'], + 'download_filename': '14523b8ca7e2f5474feae49eb5ac8ca1fa25f5cd.tar.gz', + 'filename': 'cuFFTAdvisor-20191010.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, ] patches = [ '%(name)s-%(version)s_fix_scons_Environent_calls.patch', @@ -50,6 +56,7 @@ checksums = [ {'xmipp-v3.22.07-Helios.tar.gz': 'f62e2729130b63d18e518930dd96a7a5250219e40c155abb78942a0642237ecf'}, {'xmippCore-v3.22.07-Helios.tar.gz': '58e1143626cf807655a4756b165c21578d6f1b1777b43d363a2845d92d0bab8f'}, {'xmippViz-v3.22.07-Helios.tar.gz': 'e1ce2cbbd57d3307d38538b29194a0190d633e5e062685387a6baf0329ad05b3'}, + {'cuFFTAdvisor-20191010.tar.gz': '2d97cc1c9c955fa5bee44eb232d49f25f2c8ad164ea2be754d44c723c613be46'}, {'Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch': '5b59babad5a445ec7315a809509704d2d07232d2a5d180bfb78ebc8007bd0c95'}, {'Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch': From 16045c6c49fc7b7d237e39facdebe7ef016b9b3a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 17 Nov 2022 17:15:22 +0100 Subject: [PATCH 5512/9987] adding easyconfigs: cdo-bindings-1.5.7-foss-2021b.eb --- .../cdo-bindings-1.5.7-foss-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb new file mode 100644 index 00000000000..e387e1c022c --- /dev/null +++ b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'cdo-bindings' +version = '1.5.7' + +homepage = 'https://github.com/Try2Code/cdo-bindings' +description = "Python interface to CDO." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('CDO', '2.0.5'), + ('netcdf4-python', '1.5.8'), + ('xarray', '0.20.1'), # optional +] + +use_pip = True + +exts_list = [ + ('cdo', version, { + 'checksums': ['898c2b0ff97ec494569e5d94302350538efa898d42998bfed76b4f52c6c16f3c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 2a8ed2478b091d20ffb02aa0242b7594ea7d1717 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 17 Nov 2022 23:32:54 +0100 Subject: [PATCH 5513/9987] downgrade dependency on netcdf-python from cdo-bindings v1.5.7 --- .../easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb index e387e1c022c..b3f6ed923ba 100644 --- a/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb +++ b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Python', '3.9.6'), ('CDO', '2.0.5'), - ('netcdf4-python', '1.5.8'), + ('netcdf4-python', '1.5.7'), ('xarray', '0.20.1'), # optional ] From 26c14ad2227b6a8022cff046833b5cf34a1af51d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Nov 2022 00:41:38 +0100 Subject: [PATCH 5514/9987] remove default sanity checks from cmocean v2.0 --- easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb index 452ee96673d..3531eb02047 100644 --- a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb @@ -28,9 +28,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' From 84bf86d4e5b38adca88f3058f5eb06ca77b325b1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Nov 2022 02:07:59 +0100 Subject: [PATCH 5515/9987] remove default sanity checks from gsw v3.6.16 --- easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb index aa8438cd21e..b18c6a53181 100644 --- a/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb +++ b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb @@ -21,22 +21,15 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ] use_pip = True sanity_pip_check = True exts_list = [ - (name, version, { 'checksums': ['d24d820c8b43dbf72206cf5e3b0ed800b05aa85ca40afd39c9abd19849714197'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' From 521a6fedbe179e49bf8ca8a79469997f26676345 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 18 Nov 2022 08:54:49 +0100 Subject: [PATCH 5516/9987] Add missing Authors from previous easyconfigs of IOR. --- easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb index 4ddd258e440..770777c7b5e 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb @@ -1,4 +1,8 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Robert Mijakovic Date: Fri, 18 Nov 2022 10:14:48 +0100 Subject: [PATCH 5517/9987] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index 182023f4691..c97a027b5c3 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -34,6 +34,8 @@ dependencies = [ ('cURL', '7.83.0'), ('Szip', '2.1.1'), ('zstd', '1.5.2'), + ('bzip2', '1.0.8'), + ('libxml2', '2.9.13'), ] # make sure both static and shared libs are built From d15b3d9fa8012cae723a8e32b4634cb0ef15d1ff Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 10:25:32 +0100 Subject: [PATCH 5518/9987] adding easyconfigs: ITSTool-2.0.7-GCCcore-11.3.0.eb --- .../i/ITSTool/ITSTool-2.0.7-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.7-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d456df2601d --- /dev/null +++ b/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.7-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ITSTool' +version = '2.0.7' + +homepage = 'http://itstool.org/' +description = "ITS Tool allows you to translate your XML documents with PO files" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://files.itstool.org/itstool/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6b9a7cd29a12bb95598f5750e8763cee78836a1a207f85b74d8b3275b27e87ca'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('libxml2-python', '2.9.13'), +] + +sanity_check_paths = { + 'files': ['bin/itstool'], + 'dirs': ['share/itstool/its', 'share/man'], +} +sanity_check_commands = ["itstool --help"] + +moduleclass = 'tools' From 88fc4eefb4cb7ea38b7578e57f6e7b7a1e5e7504 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 10:36:52 +0100 Subject: [PATCH 5519/9987] adding easyconfigs: libxml2-python-2.9.13-GCCcore-11.3.0.eb --- .../libxml2-python-2.9.13-GCCcore-11.3.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a63e21ba634 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonPackage' + +name = 'libxml2-python' +version = '2.9.13' + +homepage = 'http://xmlsoft.org/' +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). This is the Python binding.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = ['libxml2-%(version)s.tar.xz'] +patches = [ + 'libxml2-2.9.7_fix-hardcoded-paths.patch', +] +checksums = [ + '276130602d12fe484ecc03447ee5e759d0465558fbc9d6bd144e3745306ebf0e', # libxml2-2.9.13.tar.gz + '3d5651c015fd375d855421983b7d33ffd4af797b7411f46e05cd8c57b210e542', # libxml2-2.9.7_fix-hardcoded-paths.patch +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('XZ', '5.2.5'), + ('Python', '3.10.4'), + ('libxml2', version), + ('libiconv', '1.17'), +] + +start_dir = 'python' + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'libxml2'} + +moduleclass = 'lib' From b6ee6a570e2700a2ad68cb6034c3f0ba18199815 Mon Sep 17 00:00:00 2001 From: garadar Date: Fri, 18 Nov 2022 10:47:29 +0100 Subject: [PATCH 5520/9987] Update easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb index f588b3b926d..efcf60ced34 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'system', 'version': ''} # source_urls = [PYPI_SOURCE] # Link copy from pypi.org | PYPI_SOURCE is not working -sources = ["https://files.pythonhosted.org/packages/15/0b/fa95a349434f77d8afc775dd999152d7612b6baed52083981ac84eaa41e9/resolos-0.3.5.tar.gz"] +sources = [SOURCE_TAR_GZ] checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] From c41940db6347f79adba9bd48a5306c546c47c1a7 Mon Sep 17 00:00:00 2001 From: garadar Date: Fri, 18 Nov 2022 10:54:33 +0100 Subject: [PATCH 5521/9987] Update and rename resolos-0.3.5.eb to resolos-0.3.5-GCCcore-11.3.0.eb --- ...os-0.3.5.eb => resolos-0.3.5-GCCcore-11.3.0.eb} | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/r/resolos/{resolos-0.3.5.eb => resolos-0.3.5-GCCcore-11.3.0.eb} (75%) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb similarity index 75% rename from easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb rename to easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index efcf60ced34..e3cc4db884a 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -4,18 +4,26 @@ name = 'resolos' version = '0.3.5' homepage = 'https://gitlab.unige.ch/resolos/resolos' -description = """Resolos is a toolkit written in Python for maintaining reproducible environments for scientific computations. -It's main goal is to enable researchers to easily replicate environments through space (running code on HPC environment) +description = """Resolos is a toolkit written in Python for maintaining reproducible environments +for scientific computations. +It's main goal is to enable researchers to easily replicate environments through space +(running code on HPC environment) + and time (environment preservation for long term archival). For installation and detailed usage, check out the documentation.""" -toolchain = {'name': 'system', 'version': ''} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} # source_urls = [PYPI_SOURCE] # Link copy from pypi.org | PYPI_SOURCE is not working sources = [SOURCE_TAR_GZ] checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] +dependencies = { + ('Python', '3.10.4'), + ('PyYAML', '6.0'), +} + use_pip = True use_pip_for_deps = True From 35f7c584e93f395a9ec79c219b6e57f9d47e82e1 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Fri, 18 Nov 2022 12:07:04 +0100 Subject: [PATCH 5522/9987] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index c97a027b5c3..8cec66eec5a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -39,6 +39,7 @@ dependencies = [ ] # make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet configopts = [ "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", From 2220ddf00633babcac55f4402fbef3d63b7bf304 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 12:11:56 +0100 Subject: [PATCH 5523/9987] adding easyconfigs: ABINIT-9.6.2-foss-2022a.eb, ABINIT-9.6.2-intel-2022a.eb --- .../a/ABINIT/ABINIT-9.6.2-foss-2022a.eb | 75 +++++++++++++++++++ .../a/ABINIT/ABINIT-9.6.2-intel-2022a.eb | 71 ++++++++++++++++++ 2 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb new file mode 100644 index 00000000000..7f51bbe7c76 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb @@ -0,0 +1,75 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.6.2' + +homepage = 'https://www.abinit.org/' +description = """ +ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of +systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using +pseudopotentials and a planewave or wavelet basis. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b018c2ff24338a5952c5550a7e09d4c7793b62402c7aa4e09273e9a666e674fb'] + +builddependencies = [ + ('Python', '3.10.4'), +] +dependencies = [ + ('libxc', '5.2.3'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('HDF5', '1.12.2'), + ('Wannier90', '3.1.0'), +] + +# Needed due to changes in GCC10. +configopts = 'FCFLAGS="-fallow-argument-mismatch -ffree-line-length-none $FCFLAGS" ' +configopts += 'FFLAGS="-fallow-argument-mismatch $FFLAGS" ' + +# Ensure MPI +configopts += '--with-mpi="yes" ' +# configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# Enable OpenMP +configopts += '--enable-openmp="yes" ' + +# BLAS/Lapack from OpenBLAS +configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="${LIBLAPACK_MT}" ' + +# FFTW +configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# Enable double precision for GW calculations +configopts += '--enable-gw-dpc ' + +# Enable OpenMP +configopts += '--enable-openmp ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb new file mode 100644 index 00000000000..fbf7936af3f --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb @@ -0,0 +1,71 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.6.2' + +homepage = 'https://www.abinit.org/' +description = """ +ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of +systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using +pseudopotentials and a planewave or wavelet basis. +""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b018c2ff24338a5952c5550a7e09d4c7793b62402c7aa4e09273e9a666e674fb'] + +builddependencies = [ + ('Python', '3.10.4'), +] +dependencies = [ + ('libxc', '5.2.3'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('HDF5', '1.12.2'), + ('Wannier90', '3.1.0'), +] + +# Ensure MPI with intel wrappers. +configopts = '--with-mpi="yes" ' +configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# Enable OpenMP +configopts += '--enable-openmp="yes" ' + +# BLAS/Lapack from MKL +configopts += '--with-linalg-flavor=mkl ' + +# FFTW from MKL +configopts += '--with-fft-flavor=dfti ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# Enable double precision for GW calculations +configopts += '--enable-gw-dpc ' + +# Enable OpenMP +configopts += '--enable-openmp ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' From f951ddcf2b93259bc3a8ecf6a169075421186d90 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 13:56:21 +0100 Subject: [PATCH 5524/9987] adding easyconfigs: libyaml-0.2.5-GCCcore-12.2.0.eb, PyYAML-6.0-GCCcore-12.2.0.eb --- .../l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb | 25 +++++++++++++++++ .../p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6085128a05b --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.5' + +homepage = 'https://pyyaml.org/wiki/LibYAML' +description = "LibYAML is a YAML parser and emitter written in C." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://pyyaml.org/download/%(name)s/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['c642ae9b75fee120b2d96c712538bd2cf283228d2337df2cf2988e3c02678ef4'] + +builddependencies = [ + ('binutils', '2.39'), +] + + +sanity_check_paths = { + 'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6f216f2874f --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '6.0' + +homepage = 'https://github.com/yaml/pyyaml' +description = "PyYAML is a YAML parser and emitter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('Python', '3.10.8'), + ('libyaml', '0.2.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'yaml'} + +moduleclass = 'lib' From ab1b91e436a4ea1e46927f12c90737e6d231577c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 14:01:30 +0100 Subject: [PATCH 5525/9987] adding easyconfigs: OpenStackClient-6.0.0-GCCcore-12.2.0.eb --- .../OpenStackClient-6.0.0-GCCcore-12.2.0.eb | 129 ++++++++++++++++++ 1 file changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4b6ae3f06fe --- /dev/null +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,129 @@ +easyblock = 'PythonBundle' + +name = 'OpenStackClient' +version = '6.0.0' + +homepage = 'https://docs.openstack.org/python-openstackclient/latest/' +description = """OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the +command set for Compute, Identity, Image, Network, Object Store and Block +Storage APIs together in a single shell with a uniform command structure.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +dependencies = [ + ('Python', '3.10.8'), + ('PyYAML', '6.0'), +] +builddependencies = [('binutils', '2.39')] + +exts_default_options = { + 'use_pip': True, +} +exts_list = [ + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('importlib_metadata', '5.0.0', { + 'checksums': ['da31db32b304314d044d3c12c79bd59e307889b287ad12ff387b3500835fc2ab'], + }), + ('cmd2', '2.4.2', { + 'checksums': ['073e555c05853b0f6965f3d03329babdf9e38a5f2cea028e61a64cd7eeb74ad5'], + }), + ('jsonpointer', '2.3', { + 'checksums': ['97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a'], + }), + ('prettytable', '3.5.0', { + 'checksums': ['52f682ba4efe29dccb38ff0fe5bac8a23007d0780ff92a8b85af64bc4fc74d72'], + }), + ('autopage', '0.5.1', { + 'checksums': ['01be3ee61bb714e9090fcc5c10f4cf546c396331c620c6ae50a2321b28ed3199'], + }), + ('stevedore', '4.1.1', { + 'checksums': ['7f8aeb6e3f90f96832c301bff21a7eb5eefbe894c88c506483d355565d88cc1a'], + }), + ('cliff', '4.0.0', { + 'checksums': ['3b0d30e7acf50e3c214a39ee3e66aa2f2b5957e2a1de373e17bba8e98c7501a5'], + }), + ('dogpile.cache', '1.1.8', { + 'checksums': ['d844e8bb638cc4f544a4c89a834dfd36fe935400b71a16cbd744ebdfb720fd4e'], + }), + ('iso8601', '1.1.0', { + 'checksums': ['32811e7b81deee2063ea6d2e94f8819a86d1f3811e49d23623a41fa832bef03f'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('jsonpatch', '1.32', { + 'checksums': ['b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2'], + }), + ('os-service-types', '1.7.0', { + 'checksums': ['31800299a82239363995b91f1ebf9106ac7758542a1e4ef6dc737a5932878c6c'], + }), + ('keystoneauth1', '5.0.0', { + 'checksums': ['6ebb5f044c9dfd263087a328d51d479947d1ddc90c09daf4191df7dc71334323'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + ('requestsexceptions', '1.4.0', { + 'checksums': ['b095cbc77618f066d459a02b137b020c37da9f46d9b057704019c9f77dba3065'], + }), + ('openstacksdk', '0.102.0', { + 'modulename': 'openstack', + 'checksums': ['b2a18feba79eac2ac3469c8dafe01d4008c8ac30be3a4c6b53275b4f1c6ba2ad'], + }), + ('oslo.i18n', '5.1.0', { + 'modulename': 'oslo_i18n', + 'checksums': ['6bf111a6357d5449640852de4640eae4159b5562bbba4c90febb0034abc095d0'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('debtcollector', '2.5.0', { + 'checksums': ['dc9d1ad3f745c43f4bbedbca30f9ffe8905a8c028c9926e61077847d5ea257ab'], + }), + ('oslo.utils', '6.1.0', { + 'modulename': 'oslo_utils', + 'checksums': ['76bc0108d50aca972b68fec8298e791b5fbcbeb9a51a27c6986b41b0a6a62eeb'], + }), + ('osc-lib', '2.6.2', { + 'checksums': ['879b6c5a142f3294464748ab14adde0cba0a14a5f704a0d840c9e92144489dba'], + }), + ('oslo.serialization', '5.0.0', { + 'modulename': 'oslo_serialization', + 'checksums': ['2845328d0f47dc8a23fed2a82253e90acff0aa731dbd24f379cf8e50e6cc66ba'], + }), + ('rfc3986', '2.0.0', { + 'checksums': ['97aacf9dbd4bfd829baad6e6309fa6573aaf1be3f6fa735c8ab05e46cecb261c'], + }), + ('oslo.config', '9.0.0', { + 'modulename': 'oslo_config', + 'checksums': ['3b6b63c43cf1e09344ba850bcb11d6f2b9201086fbeb0a97a8950e7eac3f2645'], + }), + ('python-novaclient', '18.2.0', { + 'modulename': 'novaclient', + 'checksums': ['185bbf2cafb5f3d761f272e3e184a700cc7ba5cf7d51619065be7f5c4b5b7cf4'], + }), + ('python-keystoneclient', '5.0.1', { + 'modulename': 'keystoneclient', + 'checksums': ['a8bbf671f56c24aa5a37a225b98f2994b82063d73e3486657eb500a33a406d29'], + }), + ('python-cinderclient', '9.1.0', { + 'modulename': 'cinderclient', + 'checksums': ['f9b30af2e6e6e5a126c2c81f35145c5aee70c20955e6dd409919be4d1b87b343'], + }), + ('python-openstackclient', version, { + 'modulename': 'openstackclient', + 'checksums': ['91c3ac12da4b423c16b3917616f84a23e2961e750fce590d409ecc50ee0431ce'], + }), +] + +sanity_pip_check = True +enhance_sanity_check = True +sanity_check_commands = ['openstack -h'] + +sanity_check_paths = { + 'files': ['bin/openstack'], + 'dirs': ["bin", 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' From 8b2ece0a3dc79b234c63d4b37a3cba1d48ac9ed8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 18 Nov 2022 14:21:04 +0100 Subject: [PATCH 5526/9987] build nodejs with full ICU support, required for matlab-proxy --- .../a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb | 60 +++++++++++++++++++ .../matlab-proxy-0.5.4-GCCcore-11.3.0.eb | 39 ++++++++++++ .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 9 ++- 3 files changed, 106 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a9701a12117 --- /dev/null +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'aiohttp' +version = '3.8.3' + +homepage = 'https://github.com/aio-libs/aiohttp' +description = "Asynchronous HTTP client/server framework for asyncio and Python." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +# aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies +exts_list = [ + ('multidict', '6.0.2', { + 'checksums': ['5ff3bd75f38e4c43f1f470f2df7a4d430b821c4ce22be384e1459cb57d6bb013'], + }), + ('async-timeout', '4.0.2', { + 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], + }), + ('yarl', '1.8.1', { + 'checksums': ['af887845b8c2e060eb5605ff72b6f2dd2aab7a761379373fd89d314f4752abbf'], + }), + ('frozenlist', '1.3.3', { + 'checksums': ['58bcc55721e8a90b88332d6cd441261ebb22342e238296bb330968952fbb3a6a'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + (name, version, { + 'checksums': ['3828fb41b7203176b82fe5d699e0d845435f2374750a44b480ea6b930f6be269'], + }), + ('aiohttp-jinja2', '1.5', { + 'checksums': ['7c3ba5eac060b691f4e50534af2d79fca2a75712ebd2b25e6fcb1295859f910b'], + }), + ('hiredis', '2.0.0', { + 'checksums': ['81d6d8e39695f2c37954d1011c0480ef7cf444d4e3ae24bc5e89ee5de360139a'], + }), + ('aioredis', '2.0.1', { + 'checksums': ['eaa51aaf993f2d71f54b70527c440437ba65340588afeb786cd87c55c89cd98e'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + ('aiohttp-session', '2.12.0', { + 'checksums': ['0ccd11a7c77cb9e5a61f4daacdc9170d561112f9cfaf9e9a2d9867c0587d1950'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ce43706b20b --- /dev/null +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = "PythonBundle" + +name = 'matlab-proxy' +version = '0.5.4' + +homepage = 'https://github.com/mathworks/matlab-proxy' +description = 'MATLAB Integration for Jupyter' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('nodejs', '16.15.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Xvfb', '21.1.3'), + ('aiohttp', '3.8.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['534531135ae341bd86de6c18ce2694b38614deeedf57a57d4cba1d2079eb662e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/matlab-proxy-app'], + 'dirs': ['lib64/python%(pyshortver)s/site-packages'] +} + +modloadmsg = 'matlab-proxy requires MATLAB to be loaded separately (2020b or later)' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index 3fe69b1af4c..00b497b22e5 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -19,11 +19,16 @@ checksums = ['308aee7149c4092a53c87c28ef49e23a8d1606119e79ae68333062e2a1f94208'] builddependencies = [ ('binutils', '2.38'), ('Python', '3.10.4', '-bare'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('ICU', '71.1'), ] configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + '--with-intl=system-icu', + '--shared --with-intl=system-icu', # Build libnode.so in a second run ] # Link libv8 libs to libnode From 4f968721d9f31ad662b58778cf8503c8444e3b3f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 18 Nov 2022 13:45:54 +0000 Subject: [PATCH 5527/9987] use _ instead of - to simplify package downloads and re-add comment for Python 3.10.8 --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 40 +++++++------------ 1 file changed, 15 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index f0bca199736..59243c2b5dc 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -78,8 +78,7 @@ exts_list = [ ('toml', '0.10.2', { 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], }), - ('flit-core', '3.8.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', + ('flit_core', '3.8.0', { 'checksums': ['b305b30c99526df5e63d6022dd2310a0a941a187bd3884f4c8ef0418df6c39f3'], }), ('tomli', '2.0.1', { @@ -88,8 +87,7 @@ exts_list = [ ('packaging', '21.3', { 'checksums': ['dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb'], }), - ('setuptools-scm', '7.0.5', { - 'sources': ['setuptools_scm-%(version)s.tar.gz'], + ('setuptools_scm', '7.0.5', { 'checksums': ['031e13af771d6f892b941adb6ea04545bbf91ebc5ce68c78aaf3fff6e1fb4844'], }), ('python-dateutil', '2.8.2', { @@ -130,18 +128,18 @@ exts_list = [ ('cffi', '1.15.1', { 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], }), - ('semantic-version', '2.10.0', { - 'sources': ['semantic_version-%(version)s.tar.gz'], + ('semantic_version', '2.10.0', { 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], }), - ('typing-extensions', '4.4.0', { - 'sources': ['typing_extensions-%(version)s.tar.gz'], + ('typing_extensions', '4.4.0', { 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], }), ('setuptools-rust', '1.5.2', { 'checksums': ['d8daccb14dc0eae1b6b6eb3ecef79675bd37b4065369f79c35393dd5c55652c7'], }), ('cryptography', '38.0.3', { + # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, + # see https://github.com/rust-lang/cargo/issues/6652 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['bfbe6ee19615b07a98b1d2287d6a6073f734735b49ee45b11324d85efc4d5cbd'], }), @@ -188,8 +186,7 @@ exts_list = [ ('zipp', '3.10.0', { 'checksums': ['7a7262fd930bd3e36c50b9a64897aec3fafff3dfdeec9623ae22b40e93f99bb8'], }), - ('importlib-metadata', '5.0.0', { - 'sources': ['importlib_metadata-%(version)s.tar.gz'], + ('importlib_metadata', '5.0.0', { 'checksums': ['da31db32b304314d044d3c12c79bd59e307889b287ad12ff387b3500835fc2ab'], }), ('backports.entry-points-selectable', '1.2.0', { @@ -208,8 +205,7 @@ exts_list = [ ('hatchling', '1.11.1', { 'checksums': ['9f84361f70cf3a7ab9543b0c3ecc64211ed2ba8a606a71eb6a473c1c9b08e1d0'], }), - ('hatch-vcs', '0.2.0', { - 'sources': ['hatch_vcs-%(version)s.tar.gz'], + ('hatch_vcs', '0.2.0', { 'checksums': ['9913d733b34eec9bb0345d0626ca32165a4ad2de15d1ce643c36d09ca908abff'], }), ('platformdirs', '2.5.3', { @@ -221,8 +217,7 @@ exts_list = [ ('pathlib2', '2.3.7.post1', { 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], }), - ('importlib-resources', '5.10.0', { - 'sources': ['importlib_resources-%(version)s.tar.gz'], + ('importlib_resources', '5.10.0', { 'checksums': ['c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668'], }), ('virtualenv', '20.16.6', { @@ -252,8 +247,7 @@ exts_list = [ ('xlrd', '2.0.1', { 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], }), - ('py-expression-eval', '0.3.14', { - 'sources': ['py_expression_eval-%(version)s.tar.gz'], + ('py_expression_eval', '0.3.14', { 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], }), ('tabulate', '0.9.0', { @@ -275,8 +269,7 @@ exts_list = [ 'modulename': 'attr', 'checksums': ['29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6'], }), - ('backports.functools-lru-cache', '1.6.4', { - 'sources': ['backports.functools_lru_cache-%(version)s.tar.gz'], + ('backports.functools_lru_cache', '1.6.4', { 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], }), ('wcwidth', '0.2.5', { @@ -288,8 +281,7 @@ exts_list = [ ('colorama', '0.4.6', { 'checksums': ['08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44'], }), - ('flit-scm', '1.7.0', { - 'sources': ['flit_scm-%(version)s.tar.gz'], + ('flit_scm', '1.7.0', { 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], }), ('exceptiongroup', '1.0.1', { @@ -377,8 +369,7 @@ exts_list = [ ('zipfile36', '0.1.3', { 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], }), - ('tomli-w', '1.0.0', { - 'sources': ['tomli_w-%(version)s.tar.gz'], + ('tomli_w', '1.0.0', { 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], }), ('flit', '3.8.0', { @@ -446,7 +437,7 @@ exts_list = [ ('pexpect', '4.8.0', { 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], }), - ('hatch-fancy-pypi-readme', '22.8.0', { + ('hatch_fancy_pypi_readme', '22.8.0', { 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], 'checksums': ['da91282ca09601c18aded8e378daf8b578c70214866f0971156ee9bb9ce6c26a'], }), @@ -488,8 +479,7 @@ exts_list = [ ('dulwich', '0.20.50', { 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], }), - ('poetry-plugin-export', '1.2.0', { - 'sources': ['poetry_plugin_export-%(version)s.tar.gz'], + ('poetry_plugin_export', '1.2.0', { 'checksums': ['9a1dd42765408931d7831738749022651d43a2968b67c988db1b7a567dfe41ef'], }), ('poetry', '1.2.2', { From cc7a26bef21b44ae8a6ce40df5f02f6b81e23a13 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 14:47:01 +0100 Subject: [PATCH 5528/9987] update easyconfig OpenStackClient-6.0.0-GCCcore-12.2.0.eb: remove importlib_metadata --- .../o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb index 4b6ae3f06fe..6b695f63279 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb @@ -22,9 +22,6 @@ exts_list = [ ('pyperclip', '1.8.2', { 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], }), - ('importlib_metadata', '5.0.0', { - 'checksums': ['da31db32b304314d044d3c12c79bd59e307889b287ad12ff387b3500835fc2ab'], - }), ('cmd2', '2.4.2', { 'checksums': ['073e555c05853b0f6965f3d03329babdf9e38a5f2cea028e61a64cd7eeb74ad5'], }), From b87080a98c61bf43a3760d02006f9e41f748aba7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 18 Nov 2022 13:54:01 +0000 Subject: [PATCH 5529/9987] use SOURCE_WHL / SOURCE_PY3_WHL --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index 59243c2b5dc..2f5d77e3671 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -385,19 +385,19 @@ exts_list = [ 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], }), ('pastel', '0.2.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], }), ('crashtest', '0.3.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], }), ('clikit', '0.6.2', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], }), ('jeepney', '0.8.0', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], }), ('SecretStorage', '3.3.3', { @@ -415,7 +415,7 @@ exts_list = [ 'checksums': ['2ba3d56441ba0637f5f9c096068f67010ac0453f9d0b626de2aa3019353b6431'], }), ('tomlkit', '0.11.6', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b'], }), ('shellingham', '1.5.0', { @@ -431,14 +431,13 @@ exts_list = [ 'checksums': ['a84da4318dd86f870a9447a8c98340aa06216bfc6f2b7bdc4b8766984ae1867c'], }), ('ptyprocess', '0.7.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], }), ('pexpect', '4.8.0', { 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], }), ('hatch_fancy_pypi_readme', '22.8.0', { - 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], 'checksums': ['da91282ca09601c18aded8e378daf8b578c70214866f0971156ee9bb9ce6c26a'], }), ('jsonschema', '4.17.0', { @@ -454,7 +453,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '1.0.0a5', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['ff53056589300976e960f75afb792dfbfc9c78dcbb5a448e207a17b643826360'], }), ('cachy', '0.3.0', { From 4283912a26d50c111ea52aae0d4ef5c1e1588dcd Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 18 Nov 2022 14:01:09 +0000 Subject: [PATCH 5530/9987] Version bump. New dependencies of latest tensorboard and Lightning --- ...-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..8f4749f4dae --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.8.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('tensorboard', '2.10.0'), + ('typing-extensions', '4.3.0'), +] + +exts_list = [ + ('fsspec', '2022.11.0', { + 'checksums': ['259d5fd5c8e756ff2ea72f42e7613c32667dc2049a4ac3d84364a7ca034acb8b'], + }), + ('pyDeprecate', '0.3.2', { + 'modulename': 'deprecate', + 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], + }), + ('torchmetrics', '0.10.3', { + 'checksums': ['9e6ab66175f2dc13e246c37485b2c27c77931dfe47fc2b81c76217b8efdc1e57'], + }), + ('termcolor', '2.1.0', { + 'checksums': ['b80df54667ce4f48c03fe35df194f052dc27a541ebbf2544e4d6b47b5d6949c4'], + }), + ('fire', '0.4.0', { + 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], + }), + ('lightning-utilities', '0.3.0', { + 'checksums': ['d769ab9b76ebdee3243d1051d509aafee57d7947734ddc22977deef8a6427f2f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['480f3396cd63888c4e5ec2f21c02fe662a2b035d9634e6f31fcf1197a36ebd15'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From a6c6965a67bce61982442492260081e8108ce84a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 18 Nov 2022 15:23:05 +0100 Subject: [PATCH 5531/9987] drop download_dep_fail since it is the default --- .../m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb index ce43706b20b..6628aef3943 100644 --- a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb @@ -19,7 +19,6 @@ dependencies = [ ('aiohttp', '3.8.3'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From 05cdc1aae7e190ede058643b5d7e0a0afb8494c5 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Fri, 18 Nov 2022 14:56:07 +0000 Subject: [PATCH 5532/9987] adding easyconfigs: Cytoscape-3.9.1-Java-11.eb --- .../c/Cytoscape/Cytoscape-3.9.1-Java-11.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb diff --git a/easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb b/easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb new file mode 100644 index 00000000000..3d967783b2c --- /dev/null +++ b/easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb @@ -0,0 +1,36 @@ +easyblock = 'Binary' + +name = 'Cytoscape' +version = '3.9.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://cytoscape.org/' +description = """Cytoscape is an open source software platform for visualizing + complex networks and integrating these with any type of attribute data. + A lot of Apps are available for various kinds of problem domains, + including bioinformatics, social network analysis, and semantic web.""" + +toolchain = SYSTEM + +_underscore_version = version.replace('.', '_') + +# https://github.com/cytoscape/cytoscape/releases/download/3.9.1/Cytoscape_3_9_1_unix.sh +source_urls = ['https://github.com/cytoscape/cytoscape/releases/download/3.9.1/'] +sources = ['%%(name)s_%s_unix.sh' % _underscore_version] + +checksums = ['0b20ac377dc01e6b0f7067104c2e463d8f834e50ee19dc302bb101dfcbc342a1'] + +dependencies = [ + ('Java', '11'), +] + +install_cmd = "./%%(name)s_%s_unix.sh -q -dir %%(installdir)s" % _underscore_version + +sanity_check_paths = { + 'files': ['cytoscape.sh', 'Cytoscape'], + 'dirs': ['framework', 'apps', 'sampleData'], +} + +sanity_check_commands = ["%(namelower)s.sh --help"] + +moduleclass = 'bio' From 09f76145da119c55329d42a55794316010aa2e31 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 18 Nov 2022 18:39:40 +0100 Subject: [PATCH 5533/9987] Update easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb index 63dcdcf5ab5..29f68f317f9 100644 --- a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-10.2.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ('Autotools', '20200321'), ('flex', '2.6.4'), ('Bison', '3.7.1'), + ('binutils', '2.35'), ('util-linux', '2.36'), ] From 0f953f7ac202a170f232cffbe376ce437ad8c8ae Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 19 Nov 2022 16:09:59 +0100 Subject: [PATCH 5534/9987] adding easyconfigs: Siesta-4.1.5-foss-2022a.eb --- .../s/Siesta/Siesta-4.1.5-foss-2022a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2022a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2022a.eb new file mode 100644 index 00000000000..00cced1d88a --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2022a.eb @@ -0,0 +1,26 @@ +name = 'Siesta' +version = '4.1.5' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'precise': True} + +source_urls = ['https://gitlab.com/siesta-project/siesta/-/releases/v%(version)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['518df31aa6213af5e24cc73abb537b2c89a925b487171f5339d743d0c7140b3f'] + +dependencies = [ + ('netCDF-Fortran', '4.6.0'), + ('METIS', '5.1.0'), + ('ELPA', '2021.11.001'), +] + +# transiesta is now siesta --electrode +with_transiesta = False + +runtest = 'check' + +moduleclass = 'phys' From 038dc2a87e80d8958742728a216ad5f26bb87762 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 19 Nov 2022 16:10:21 +0100 Subject: [PATCH 5535/9987] adding easyconfigs: Siesta-4.1.5-intel-2022a.eb --- .../s/Siesta/Siesta-4.1.5-intel-2022a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2022a.eb diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2022a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2022a.eb new file mode 100644 index 00000000000..0b269542103 --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2022a.eb @@ -0,0 +1,26 @@ +name = 'Siesta' +version = '4.1.5' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'precise': True} + +source_urls = ['https://gitlab.com/siesta-project/siesta/-/releases/v%(version)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['518df31aa6213af5e24cc73abb537b2c89a925b487171f5339d743d0c7140b3f'] + +dependencies = [ + ('netCDF-Fortran', '4.6.0'), + ('METIS', '5.1.0'), + ('ELPA', '2021.11.001'), +] + +# transiesta is now siesta --electrode +with_transiesta = False + +runtest = 'check' + +moduleclass = 'phys' From e93413cf51ff51a78519259e7e80f95d061376d8 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:12:23 +0000 Subject: [PATCH 5536/9987] sanity_check_paths added as a check --- easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb index dbe91a2e7ff..0526cbdc186 100644 --- a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb @@ -39,4 +39,9 @@ exts_list = [ }), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + moduleclass = 'tools' From 6cad70bc4ac115d05608737b4ee703af68fafe41 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:20:26 +0000 Subject: [PATCH 5537/9987] Correct sanity-check-command added --- easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb index d1f4c2ad3a1..cfd3b1b4d0f 100644 --- a/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb @@ -35,4 +35,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['KITEx |grep "^Starting program..."'] + moduleclass = 'chem' From e5fad376f9c3ea85eb9cb08d0942e6b13445a32f Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:26:46 +0000 Subject: [PATCH 5538/9987] tqdm removed --- .../easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb index 4459e4473f3..12bc9138bfa 100644 --- a/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb @@ -20,7 +20,6 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('tqdm', '4.64.0'), ] use_pip = True From 1ac26c04bb217380dde675cd83509a22cfd4476a Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:39:12 +0000 Subject: [PATCH 5539/9987] dask version changed to 2022.10.0 --- .../lagrangian-filtering-0.8.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb index 2b248447592..fa2d8f0e962 100644 --- a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb +++ b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), - ('dask', '2022.10.2'), + ('dask', '2022.10.0'), ('h5py', '3.7.0'), ('SciPy-bundle', '2022.05'), ('netcdf4-python', '1.6.1'), From 2cd36bf71be4edfea029b23106457aee2d71b0f4 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:45:23 +0000 Subject: [PATCH 5540/9987] entrypoints added to close PR #16651 --- easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb index ff8bb790e8f..8c6c042e34d 100644 --- a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb +++ b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb @@ -19,6 +19,9 @@ use_pip = True sanity_pip_check = True exts_list = [ + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), ('asciitree', '0.3.3', { 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], }), From bf57a8625d1298cc3d1db2999b240ccfd0f52526 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:52:53 +0000 Subject: [PATCH 5541/9987] dask version changed to 2022.10.0 --- easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb index aeac427c9c5..fbdcdebc32d 100644 --- a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('MITgcmutils', '0.1.2'), - ('dask', '2022.10.2'), + ('dask', '2022.10.0'), ] use_pip = True From 7755da5e2cbe6cd064f3467fb3667de518de4a29 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:57:32 +0000 Subject: [PATCH 5542/9987] dask version changed to 2022.10.0 --- easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb index d73a95fced8..55ff2f1d94f 100644 --- a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), - ('dask', '2022.10.2'), + ('dask', '2022.10.0'), ] use_pip = True From f89845cb8f9044ba73ebdb72acdc296830407741 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 21:10:01 +0000 Subject: [PATCH 5543/9987] adding easyconfigs: xarray-2022.9.0-foss-2022a.eb --- .../x/xarray/xarray-2022.9.0-foss-2022a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb b/easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb new file mode 100644 index 00000000000..5d3d2e2cf28 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'xarray' +version = '2022.9.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], + }), +] + +moduleclass = 'data' From e64a4a41ca05d7f80acbbec5ec5aaf6589e17902 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 21:34:20 +0000 Subject: [PATCH 5544/9987] xarray as dependency added, psutil removed, tag used instead of commit --- .../lagrangian-filtering-0.8.3-foss-2022a.eb | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb index fa2d8f0e962..f057408344e 100644 --- a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb +++ b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb @@ -21,6 +21,7 @@ dependencies = [ ('scikit-learn', '1.1.2'), ('tqdm', '4.64.0'), ('zarr', '2.13.3'), + ('xarray', '2022.9.0'), ] use_pip = True @@ -30,18 +31,12 @@ exts_list = [ ('parcels', '2.4.0', { 'checksums': ['221ce49b6cb5bb4996aa3c817c0de7f022c952a4d8cb4160ca7df7dd940714b5'], }), - ('xarray', '2022.9.0', { - 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], - }), ('pykdtree', '1.3.6', { 'checksums': ['780b693d0555b857d7aab31e35d4293bf4ebdb9dec7a45ba4bb23b4400f626dc'], }), ('sosfilt', '1.2.0', { 'checksums': ['b3083fd2edf723a6163f00ddc36ec3ca20fbf6112cc68573dad9356544a9d734'], }), - ('psutil', '5.9.4', { - 'checksums': ['3d7f9739eb435d4b1338944abe23f49584bde5395f27487d2ee25ad9a8774a62'], - }), ('progressbar2', '4.2.0', { 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], 'modulename': 'progressbar', @@ -65,7 +60,7 @@ exts_list = [ 'git_config': { 'url': 'https://github.com/angus-g/', 'repo_name': name, - 'commit': 'b942ff3', + 'tag': version, 'recursive': True, 'keep_git_dir': True, }, From c738921011e77e1ab6057d34302597d89bc7fd22 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 21:38:43 +0000 Subject: [PATCH 5545/9987] entrypoint dependency removed --- easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb index 8c6c042e34d..b04ea6aea02 100644 --- a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb +++ b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('entrypoints', '0.4'), ] use_pip = True From ad2331ea10c39203802a22ebcb30c78e261f543a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Nov 2022 08:44:45 +0100 Subject: [PATCH 5546/9987] add scDblFinder extension to Bioconductor 3.15 --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 43c53a70184..118a0158da3 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1098,6 +1098,9 @@ exts_list = [ ('ROntoTools', '2.24.0', { 'checksums': ['dec7ec0d6d709fbdb44d595d776fc462420957e5c23c7bd6d2d63f5a44df04dd'], }), + ('scDblFinder', '1.10.0', { + 'checksums': ['c0834495a342c6467d64dc899ba5913354ea5d53037c9be95e639950db6e2478'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From f3facbd38a67d9d047cddd06a6e2e7dee1f62f30 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 21 Nov 2022 10:28:02 +0100 Subject: [PATCH 5547/9987] adding easyconfigs: APR-1.7.0-GCCcore-11.3.0.eb, APR-util-1.6.1-GCCcore-11.3.0.eb --- .../APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ .../a/APR/APR-1.7.0-GCCcore-11.3.0.eb | 22 +++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..52ae17f084c --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.1' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('APR', '1.7.0'), + ('SQLite', '3.38.3'), + ('expat', '2.4.8'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..200453bcb54 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.0' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' From 3e01282dd85ef34dd215ffe5652c3f3accac5523 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 21 Nov 2022 10:28:27 +0100 Subject: [PATCH 5548/9987] adding easyconfigs: Serf-1.3.9-GCCcore-11.3.0.eb --- .../s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..41c4515fadd --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'SCons' +name = 'Serf' +version = '1.3.9' + +homepage = 'https://serf.apache.org/' +description = """The serf library is a high performance C-based HTTP client library + built upon the Apache Portable Runtime (APR) library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Serf-%(version)s_python3_scons.patch'] +checksums = [ + '549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc', # serf-1.3.9.tar.bz2 + 'db401893bfb464ddcf369b543cacb9a165a21f8ff9bf1a819e4b61550bb9d3d0', # Serf-1.3.9_python3_scons.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4'), + ('SCons', '4.4.0'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" + +sanity_check_paths = { + 'files': ['include/serf-1/serf.h'] + + ['lib/libserf-1.%s' % x for x in ['a', 'so']], + 'dirs': [], +} + +moduleclass = 'tools' From 83461873b5433fb047f2b002204843a03f647183 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 21 Nov 2022 10:28:55 +0100 Subject: [PATCH 5549/9987] adding easyconfigs: Subversion-1.14.2-GCCcore-11.3.0.eb --- .../Subversion-1.14.2-GCCcore-11.3.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d7aacc65f36 --- /dev/null +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'Subversion' +version = '1.14.2' + +homepage = 'https://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'https://apache.belnet.be/%(namelower)s', + 'http://www.eu.apache.org/dist/%(namelower)s', + 'http://www.us.apache.org/dist/%(namelower)s', + 'https://archive.apache.org/dist/%(namelower)s', +] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Subversion-1.12.0-no_swig.patch'] +checksums = [ + 'c9130e8d0b75728a66f0e7038fc77052e671830d785b5616aad53b4810d3cc28', # subversion-1.14.2.tar.bz2 + '539ea2118f958d152d78438c81649eb727ff0b2e8491295702ee98e1f922041f', # Subversion-1.12.0-no_swig.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('SQLite', '3.38.3'), + ('zlib', '1.2.12'), + ('lz4', '1.9.3'), + ('utf8proc', '2.8.0'), + ('Serf', '1.3.9'), +] + +preconfigopts = './autogen.sh && ' + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-lz4=$EBROOTLZ4 --with-serf=$EBROOTSERF" + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +moduleclass = 'tools' From 26170fc62bc501a8c74a12e43c8cd5dc94562f4d Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 21 Nov 2022 10:38:26 +0100 Subject: [PATCH 5550/9987] adding easyconfigs: qrupdate-1.1.2-GCCcore-11.3.0.eb --- .../qrupdate/qrupdate-1.1.2-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a0bb33bae79 --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'https://sourceforge.net/projects/qrupdate/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_makeconf.patch'] +checksums = [ + 'e2a1c711dc8ebc418e21195833814cb2f84b878b90a2774365f0166402308e08', # qrupdate-1.1.2.tar.gz + '4aa0e61a18bd14c76048f7b2f1f52875f7bac4bc3426ce9a37dfdb5b2b0d2379', # qrupdate-1.1.2_makeconf.patch +] + +builddependencies = [ + ('binutils', '2.38'), +] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' From a62c303ac31f35f0295906aa9cb10c0650ef38bc Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 21 Nov 2022 10:01:36 +0000 Subject: [PATCH 5551/9987] adding easyconfigs: GnuTLS-3.7.8-GCCcore-11.3.0.eb, alsa-lib-1.2.8-GCCcore-11.3.0.eb, libidn-1.41-GCCcore-11.3.0.eb, libtasn1-4.19.0-GCCcore-11.3.0.eb, p11-kit-0.24.1-GCCcore-11.3.0.eb --- .../alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb | 24 +++++++++++ .../g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ .../l/libidn/libidn-1.41-GCCcore-11.3.0.eb | 22 ++++++++++ .../libtasn1-4.19.0-GCCcore-11.3.0.eb | 25 +++++++++++ .../p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb | 38 +++++++++++++++++ 5 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.41-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtasn1/libtasn1-4.19.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1476c378366 --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.8' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['ftp://ftp.alsa-project.org/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347'] + +dependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c604f1a0fa0 --- /dev/null +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GnuTLS' +version = '3.7.8' + +homepage = 'https://www.gnutls.org' +description = """GnuTLS is a secure communications library implementing the SSL, TLS + and DTLS protocols and technologies around them. It provides a simple + C language application programming interface (API) to access the secure + communications protocols as well as APIs to parse and write X.509, PKCS #12, + OpenPGP and other required structures. It is aimed to be portable + and efficient with focus on security and interoperability.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.gnupg.org/ftp/gcrypt/gnutls/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c58ad39af0670efe6a8aee5e3a8b2331a1200418b64b7c51977fb396d4617114'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('GMP', '6.2.1'), + ('nettle', '3.8'), + ('Guile', '3.0.8'), + ('libtasn1', '4.19.0'), + ('libidn', '1.41'), + ('p11-kit', '0.24.1'), +] + +configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " +configopts += "--with-guile-site-ccache-dir=%(installdir)s/lib/guile/site-ccache " +configopts += "--with-guile-extension-dir=%(installdir)s/lib/guile/extensions" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['certtool', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]], + 'dirs': ['include/gnutls', 'lib/guile'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.41-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.41-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7a37e088e10 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.41-GCCcore-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.41' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['884d706364b81abdd17bee9686d8ff2ae7431c5a14651047c68adf8b31fd8945'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.19.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.19.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..be6a5c351a4 --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.19.0-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.19.0' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and + some other packages. It was written by Fabio Fiorina, and has been shipped as + part of GnuTLS for some time but is now a proper GNU package.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1613f0ac1cf484d6ec0ce3b8c06d56263cc7242f1c23b30d82d23de345a63f7a'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4a07aaf936c --- /dev/null +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'p11-kit' +version = '0.24.1' + +homepage = 'https://p11-glue.freedesktop.org/p11-kit.html' +description = """Provides a way to load and enumerate PKCS#11 modules. + Provides a standard configuration setup for installing + PKCS#11 modules in such a way that they're discoverable. + Also solves problems with coordinating the use of PKCS#11 + by different components or libraries living in the same process.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/p11-glue/p11-kit/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['d8be783efd5cd4ae534cee4132338e3f40f182c3205d23b200094ec85faaaef8'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('libtasn1', '4.19.0'), + ('libffi', '3.4.2'), +] + +preconfigopts = "bashcompdir=%(installdir)s/share/bash-completions " + +configopts = "--without-systemd" + +sanity_check_paths = { + 'files': ['bin/p11-kit', 'bin/trust'] + + ['lib/libp11-kit.%s' % SHLIB_EXT], + 'dirs': ['include/p11-kit-1/p11-kit'], +} + +sanity_check_commands = ["p11-kit --help"] + +moduleclass = 'lib' From 057dca5363ed71ef4b156c4925a39e890644a0b8 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 21 Nov 2022 12:13:20 +0200 Subject: [PATCH 5552/9987] fix source_urls --- .../c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb index c4b1c45f09f..805ff73105f 100644 --- a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb @@ -46,7 +46,9 @@ exts_list = [ 'checksums': ['76f8fef59cf2061dbd849bbce4fe49bdd820884385004b0ca59136ac3db129e4'], }), (name, version, { - 'checksums': ['3a2cdd4dc2d8b4832fa132a0bd1102f86c38f6865d7f119018404069d35984b2'], + 'source_urls': ['https://github.com/hpcaitech/ColossalAI/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e0975cd9a0860a2d00d1f725baaee3652e2f601724968628d8750021ef483320'], }), ] From 5fe59c9f66198ca47bc7f8569596fe8b5681ecda Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 21 Nov 2022 12:14:46 +0200 Subject: [PATCH 5553/9987] fix dllogger checksum --- .../o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb index 52743c921ac..9eec3b5f807 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -71,7 +71,7 @@ exts_list = [ ('dllogger', version, { 'source_urls': ['https://github.com/NVIDIA/dllogger/archive/refs/tags/'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['43e5e3c3acf891dfe6151f7d869f3ad2424772fe57fd8dcb0a45bad06de93bf7'], + 'checksums': ['abae2b2ac73b9e176fa87144bf6c2048ddd3dae8e7002d6d5a270bc7e4da6b4d'], }), (name, version, { 'source_urls': ['https://github.com/aqlaboratory/openfold/archive/refs/tags/'], From d0b9ec13d111bdd95fff4432f3a35e69a4ec984f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Nov 2022 11:47:10 +0100 Subject: [PATCH 5554/9987] adding easyconfigs: RLCard-1.0.9-foss-2022a.eb --- .../r/RLCard/RLCard-1.0.9-foss-2022a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/r/RLCard/RLCard-1.0.9-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/RLCard/RLCard-1.0.9-foss-2022a.eb b/easybuild/easyconfigs/r/RLCard/RLCard-1.0.9-foss-2022a.eb new file mode 100644 index 00000000000..b0c6e795abf --- /dev/null +++ b/easybuild/easyconfigs/r/RLCard/RLCard-1.0.9-foss-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'RLCard' +version = '1.0.9' + +homepage = 'https://www.rlcard.org' +description = "RLCard is a toolkit for Reinforcement Learning (RL) in card games." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # provides numpy + ('PyTorch', '1.12.0'), + ('GitPython', '3.1.27'), + ('matplotlib', '3.5.2'), +] + +use_pip = True + +exts_list = [ + # stick to termcolor 1.x, to avoid hatchling required dependency + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('rlcard', version, { + 'checksums': ['6454d2203220b7acff855cad35c9e24aabadfd664048aee45054a04adc842c75'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 4dfba82a0fc56d09f89ddcdb886d833b907946d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Nov 2022 12:37:06 +0100 Subject: [PATCH 5555/9987] use same patches for netcdf4-python 1.6.1 in foss/intel easyconfigs --- .../n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb index 60eb9cd8eef..d5d6084f968 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb @@ -24,13 +24,18 @@ exts_list = [ 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], }), (name, version, { - 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + 'patches': [ + 'netcdf4-python-1.1.8-avoid-diskless-test.patch', + 'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch', + ], 'source_tmpl': 'netCDF4-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], 'checksums': [ 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + # netcdf4-python-1.6.1_relax_tolerance_compression_test.patch + '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166', ], }), ] From 587568e5cd02e8be3360409615b99cbd377b6387 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 13:09:49 +0100 Subject: [PATCH 5556/9987] adding easyconfigs: ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb --- .../ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..7cde2f7f6bf --- /dev/null +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'ESM-2' +version = '2.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/facebookresearch/esm' +description = """ESM-2 outperforms all tested single-sequence protein language models + across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate + accurate structure predictions end to end directly from the sequence of a protein.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/f/fair-esm'] +sources = ['fair-esm-%(version)s.tar.gz'] +checksums = ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('PyTorch', '1.10.2', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'esm'} + +sanity_check_commands = [ + "python -c 'import esm.pretrained'", +] + +moduleclass = 'bio' From 98ffbdb85b6f9ea656fe77c45bf08dc0448df20a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 21 Nov 2022 13:20:13 +0100 Subject: [PATCH 5557/9987] rename hyperopt to Hyperopt --- .../cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 2 +- .../Hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb} | 4 ++-- .../Hyperopt-0.2.5-fosscuda-2020b.eb} | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/h/{hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb => Hyperopt/Hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb} (97%) rename easybuild/easyconfigs/h/{hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb => Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb} (96%) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 8356b39778a..23a780fa2a1 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -21,7 +21,7 @@ dependencies = [ ('Java', '11', '', SYSTEM), ('SciPy-bundle', '2020.11'), ('leidenalg', '0.8.3'), - ('hyperopt', '0.2.5'), + ('Hyperopt', '0.2.5'), ('CMake', '3.18.4'), ('dill', '0.3.3'), ('IPython', '7.18.1'), diff --git a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb similarity index 97% rename from easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb rename to easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb index 4e2be23df1d..f9b60c91c8e 100644 --- a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' -name = 'hyperopt' +name = 'Hyperopt' version = '0.2.4' local_python_versionsuffix = '-Python-%(pyver)s' local_java_versionsuffix = '-Java-%(javaver)s' @@ -43,7 +43,7 @@ exts_list = [ ('lightgbm', '2.3.1', { 'checksums': ['bd1817be401e74c0d8b049e97ea2f35d2ce155cfa130119ce4195ea207bd6388'], }), - (name, version, { + ('hyperopt', version, { 'use_pip_extras': 'SparkTrials,MongoTrials,ATPE', 'checksums': ['6e72089a42eb70cf84b0567d4552a908adff7cfc5cf6b1c38add41adc775d9c6'], }), diff --git a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb similarity index 96% rename from easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb rename to easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb index 8a744cd8d26..e78c32c2658 100644 --- a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb @@ -2,7 +2,7 @@ easyblock = 'PythonBundle' -name = 'hyperopt' +name = 'Hyperopt' version = '0.2.5' homepage = 'https://github.com/hyperopt/hyperopt' @@ -40,7 +40,7 @@ exts_list = [ ('py4j', '0.10.9.2', { 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], }), - (name, version, { + ('hyperopt', version, { 'use_pip_extras': 'SparkTrials,MongoTrials,ATPE', 'checksums': ['bc6047d50f956ae64eebcb34b1fd40f186a93e214957f20e87af2f10195295cc'], }), From c491dfb6f9bf924c18a92af311a41954d4d34da8 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 13:33:38 +0100 Subject: [PATCH 5558/9987] use correct PyTorch version --- .../easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb index 7cde2f7f6bf..c4eb572620d 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb @@ -18,7 +18,7 @@ checksums = ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), - ('PyTorch', '1.10.2', versionsuffix), + ('PyTorch', '1.10.0', versionsuffix), ] use_pip = True From 0dcbf4e8f71e4b7b28bd9598918cfd8c04c19376 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 13:36:55 +0100 Subject: [PATCH 5559/9987] adding easyconfigs: OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb --- .../OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..5d2f680ca42 --- /dev/null +++ b/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'OmegaFold' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/HeliXonProtein/OmegaFold' +description = """OmegaFold: High-resolution de novo Structure Prediction from Primary Sequence""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), + ('Biopython', '1.79'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'preinstallopts': """sed -i '/^setup(/a \ version="%(version)s",' setup.py && """, + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/HeliXonProtein/OmegaFold/archive/'], + 'checksums': ['ab3b48fe7721539b6943b49cdbafc9799e15b4425a324cc25daf15a24e3f9e37'], + }), +] + +sanity_check_paths = { + 'files': ['bin/omegafold'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/omegafold'], +} + +sanity_check_commands = [ + "omegafold --help", +] + +moduleclass = 'bio' From 92a83bf682fbc93dfc2b4b103440f6aad2ac9ef8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 21 Nov 2022 14:28:42 +0100 Subject: [PATCH 5560/9987] use PythonBundle with resolos v0.3.5 --- .../r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index e3cc4db884a..efe3f01dcbc 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -1,36 +1,36 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'resolos' version = '0.3.5' homepage = 'https://gitlab.unige.ch/resolos/resolos' description = """Resolos is a toolkit written in Python for maintaining reproducible environments -for scientific computations. -It's main goal is to enable researchers to easily replicate environments through space -(running code on HPC environment) - +for scientific computations. It's main goal is to enable researchers to easily +replicate environments through space (running code on HPC environment) and time (environment preservation for long term archival). For installation and detailed usage, check out the documentation.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -# source_urls = [PYPI_SOURCE] -# Link copy from pypi.org | PYPI_SOURCE is not working -sources = [SOURCE_TAR_GZ] -checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] - dependencies = { ('Python', '3.10.4'), ('PyYAML', '6.0'), } - use_pip = True -use_pip_for_deps = True -moduleclass = 'data' + +exts_list = [ + (name, version, { + 'checksums': ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'], + }), +] + +sanity_pip_check = True sanity_check_commands = ["r3s info"] sanity_check_paths = { 'files': ["bin/r3s"], - 'dirs': [] + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } + +moduleclass = 'tools' From 9b5627504dcf2de5ba8caf1976e32804aaf69f30 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 21 Nov 2022 14:56:11 +0100 Subject: [PATCH 5561/9987] use SYSTEM global in flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb --- .../f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb index 1ad8d95623e..7223c3f1260 100644 --- a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb @@ -10,7 +10,7 @@ description = "A very simple framework for state-of-the-art NLP" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('PyTorch', '1.10.0', versionsuffix), ('tqdm', '4.61.2'), From 675a7ec13b0a7b359ce47aa491da28e71d126af1 Mon Sep 17 00:00:00 2001 From: garadar Date: Mon, 21 Nov 2022 15:29:06 +0100 Subject: [PATCH 5562/9987] Update easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index efe3f01dcbc..7aaeaad8e10 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -12,6 +12,8 @@ For installation and detailed usage, check out the documentation.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +builddependencies = [('binutils', '2.38')] + dependencies = { ('Python', '3.10.4'), ('PyYAML', '6.0'), From 97e7e854b4affd0d73ecc8dcb1bc18b8e6393497 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Nov 2022 16:49:51 +0100 Subject: [PATCH 5563/9987] add missing extensions to easyconfig for R-bundle-Bioconductor v3.15 with foss/2021b --- ...bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index 9c7b01b9137..b6ac8e83c45 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -1090,6 +1090,21 @@ exts_list = [ ('SPOTlight', '1.0.0', { 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], }), + ('CGHcall', '2.58.0', { + 'checksums': ['c5e86b9234685462b7330c85b91ca648a801a76c99f3e98cd509ac47ee8afae2'], + }), + ('QDNAseq', '1.32.0', { + 'checksums': ['75bbde9b6cc55cd6a47b9f466358033a180b480def2144abdcc93a2a8e066668'], + }), + ('HiCcompare', '1.18.0', { + 'checksums': ['b9320fa7a9f10832e2ac7ade0245f85ac4c2c26edef2580078888f5e1050ee2d'], + }), + ('ROntoTools', '2.24.0', { + 'checksums': ['dec7ec0d6d709fbdb44d595d776fc462420957e5c23c7bd6d2d63f5a44df04dd'], + }), + ('scDblFinder', '1.10.0', { + 'checksums': ['c0834495a342c6467d64dc899ba5913354ea5d53037c9be95e639950db6e2478'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 3c66bade085902d638af6a6e73852c496697d445 Mon Sep 17 00:00:00 2001 From: garadar Date: Mon, 21 Nov 2022 16:57:17 +0100 Subject: [PATCH 5564/9987] Update easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb Co-authored-by: Alex Domingo --- .../r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index 7aaeaad8e10..4a7708038c7 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -22,6 +22,19 @@ dependencies = { use_pip = True exts_list = [ + ('click-log', '0.4.0', { + 'checksums': ['3970f8570ac54491237bcdb3d8ab5e3eef6c057df29f8c3d1151a51a9c23b975'], + }), + ('conda-pack', '0.6.0', { + 'checksums': ['615f41353fdc8793b0edb55702212273f17e40b43cc2c17493430e9c66d9f0b3'], + }), + ('semver', '2.13.0', { + 'checksums': ['fa0fe2722ee1c3f57eac478820c3a5ae2f624af8264cbdf9000c980ff7f75e3f'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), (name, version, { 'checksums': ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'], }), From 048d1168850897b96d49c05f63752d4bd731dacf Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 21:28:45 +0100 Subject: [PATCH 5565/9987] add comment for missing version --- .../o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb index 5d2f680ca42..0008cde884d 100644 --- a/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb @@ -19,9 +19,10 @@ dependencies = [ use_pip = True sanity_pip_check = True +# add missing version for OmegaFold exts_list = [ (name, version, { - 'preinstallopts': """sed -i '/^setup(/a \ version="%(version)s",' setup.py && """, + 'preinstallopts': """sed -i '/^setup(/a \ version="%(version)s",' setup.py && """, # noqa: W605 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/HeliXonProtein/OmegaFold/archive/'], 'checksums': ['ab3b48fe7721539b6943b49cdbafc9799e15b4425a324cc25daf15a24e3f9e37'], From 010536c00c9d1afb9459a581c594c3c4c278dedf Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 22:00:45 +0100 Subject: [PATCH 5566/9987] update pyproj version for Cartopy 0.20.3 --- easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb index f8c63257d0f..436e9a24ca9 100644 --- a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('GDAL', '3.5.0'), ('GEOS', '3.10.3'), ('matplotlib', '3.5.2'), - ('pyproj', '3.3.1'), + ('pyproj', '3.4.0'), ('SciPy-bundle', '2022.05'), ('Shapely', '1.8.2'), ('lxml', '4.9.1'), From f637208154f00f5670f28f9aa0830ec86b2e6cce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 11:45:57 +0100 Subject: [PATCH 5567/9987] adding easyconfigs: Valgrind-3.20.0-gompi-2022a.eb --- .../v/Valgrind/Valgrind-3.20.0-gompi-2022a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.20.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.20.0-gompi-2022a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.20.0-gompi-2022a.eb new file mode 100644 index 00000000000..45e2a41ecda --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.20.0-gompi-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.20.0' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'https://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['8536c031dbe078d342f121fa881a9ecd205cb5a78e639005ad570011bdb9f3c6'] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] +local_archs = ('amd64', 'arm64', 'ppc64le') + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + [['lib/valgrind/libmpiwrap-%s-linux.%s' % (a, SHLIB_EXT) for a in local_archs]], + 'dirs': [] +} + +moduleclass = 'debugger' From 84856245897c83e988e80b691273deb21e18ad65 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Tue, 22 Nov 2022 10:50:35 +0000 Subject: [PATCH 5568/9987] adding easyconfigs: Clang-15.0.5-GCCcore-11.3.0.eb --- .../c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2e95433ea04 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb @@ -0,0 +1,51 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '15.0.5' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-project-%(version)s.src.tar.xz', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Perl', '5.34.1'), + ('elfutils', '0.187'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.38'), + ('hwloc', '2.7.1'), + ('libxml2', '2.9.13'), + ('ncurses', '6.3'), + ('GMP', '6.2.1'), + ('Z3', '4.10.2'), + ('Python', '3.10.4'), +] + +assertions = True +enable_rtti = True +python_bindings = True +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' From d9d7c82f7c936623f56403625c806f84917962ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 17:23:13 +0100 Subject: [PATCH 5569/9987] stick to older PyQt-builder in easyconfig for PyQt5 5.15.5, so that 'pip check' passes --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb index 594f66926cc..11986d88534 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb @@ -50,10 +50,10 @@ components = [ 'use_pip': True, 'options': {'modulename': 'PyQt5.sip'}, }), - ('PyQt-builder', '1.14.0', { + ('PyQt-builder', '1.11.0', { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], - 'checksums': ['6755931c6d2f8940553e0334d10c933ce5cc18b64425e94fda1accf4ff774f59'], + 'checksums': ['40f6df88c00e6aa9ac9a8bc5688f9fe2a4bd56c06cdb0a0b00ce8955ec34ffe5'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), @@ -97,6 +97,7 @@ sanity_check_commands = [ "pyuic5 --help", "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", + "pip check", ] modextrapaths = { From 0541ccc6695609f2f646ccd0810362055159a4d3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 22 Nov 2022 17:54:54 +0100 Subject: [PATCH 5570/9987] adding easyconfigs: EGTtools-0.1.11-foss-2022a.eb --- .../e/EGTtools/EGTtools-0.1.11-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb new file mode 100644 index 00000000000..88ad1c992f3 --- /dev/null +++ b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'EGTtools' +version = '0.1.11' + +homepage = 'https://github.com/Socrats/EGTTools' +description = """ +EGTtools provides a centralized repository with analytical and numerical +methods to study/model game theoretical problems under the Evolutionary Game +Theory (EGT) framework.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.10.2'), + ('scikit-build', '0.15.0'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('networkx', '2.8.4'), + ('Seaborn', '0.11.2'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['b736bc00f80e11987ca51eaa11f013a29ccca835a05b6eb91b3850c1e5680e8e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From 497ee827e02fd25aae30206316b44b04461a26be Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 22 Nov 2022 17:32:56 +0000 Subject: [PATCH 5571/9987] xarray added as dependency instead of extension --- easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb index fbdcdebc32d..c8a25756118 100644 --- a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -16,6 +16,7 @@ dependencies = [ ('Python', '3.10.4'), ('MITgcmutils', '0.1.2'), ('dask', '2022.10.0'), + ('xarray', '2022.9.0'), ] use_pip = True @@ -25,9 +26,6 @@ exts_list = [ ('cachetools', '5.2.0', { 'checksums': ['6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757'], }), - ('xarray', '2022.9.0', { - 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], - }), (name, version, { 'checksums': ['7dda45fdf6182a859f5c441cd5928a7c99d41c8bcea9fccf471b7011791b1131'], }), From 0d413469b3877fad7783bff87ba2fe9f10a22b67 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 22 Nov 2022 18:24:09 +0000 Subject: [PATCH 5572/9987] xarray added as dependency instead of extension --- .../easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb index 55ff2f1d94f..b81f3b84574 100644 --- a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -14,19 +14,16 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('dask', '2022.10.0'), + ('xarray', '2022.9.0'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('xarray', '2022.9.0', { - 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], - }), ('xgcm', '0.8.0', { 'checksums': ['99e7e2fc9268fb13827f8849dbae279eaaa4960d51872d62bc38293605b0215f'], }), - (name, version, { 'checksums': ['8c684ecdfe03bade171e17f5ae6bedd422e51db6faffed0303e1839051d40614'], }), From 27d802f112e033736cceb2688ef41162e673aae6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 20:20:50 +0100 Subject: [PATCH 5573/9987] avoid using empty string in sanity_check_paths in MONAI easyconfigs --- .../easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb | 2 +- easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb index bd6d8765a06..c4ae75df709 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb @@ -44,7 +44,7 @@ sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'" sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], - 'dirs': [''], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb index 0d272341e2c..0314fc871d4 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb @@ -42,7 +42,7 @@ sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'" sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], - 'dirs': [''], + 'dirs': [], } moduleclass = 'vis' From 704e6881b6a5d53486347b9a14eec021e2c34b54 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 22 Nov 2022 20:39:33 +0100 Subject: [PATCH 5574/9987] fix Seaborn version --- easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb index 88ad1c992f3..b400270aca9 100644 --- a/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb @@ -23,7 +23,7 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('matplotlib', '3.5.2'), ('networkx', '2.8.4'), - ('Seaborn', '0.11.2'), + ('Seaborn', '0.12.1'), ] use_pip = True From e9c43504d842606b3d71eb3abaed14571651d65e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 22:21:59 +0100 Subject: [PATCH 5575/9987] adding easyconfigs: scanpy-1.9.1-foss-2021b.eb --- .../s/scanpy/scanpy-1.9.1-foss-2021b.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb new file mode 100644 index 00000000000..3967f4007cf --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.9.1' + +homepage = 'https://scanpy.readthedocs.io/en/stable/' +description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), + ('networkx', '2.6.3'), + ('numba', '0.54.1'), + ('PyTables', '3.6.1'), + ('statsmodels', '0.13.1'), + ('scikit-learn', '1.0.1'), + ('Seaborn', '0.11.2'), + ('tqdm', '4.62.3'), + ('leidenalg', '0.8.8'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.2.0', { + 'checksums': ['57f85b72c688b09e053cdac302dd5b5b53df5f73ae20b4874fcbffd8bf783d11'], + }), + # anndata 0.7.8 needs xlrd<2.0 + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + ('pynndescent', '0.5.8', { + 'checksums': ['a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b'], + }), + ('umap-learn', '0.5.3', { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.4', { + 'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'], + }), + ('session_info', '1.0.0', { + 'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'], + }), + (name, version, { + 'checksums': ['00c9a83b649da7e0171c91e9a08cff632102faa760614fd05cd4d1dbba4eb541'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "natsort --help", + "scanpy --help", +] + +moduleclass = 'bio' From b8bed9f936c7067b63bc49aa7bca17c574f3cba7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 22:46:18 +0100 Subject: [PATCH 5576/9987] avoid hardcoding OpenJPEG version in preinstallopts in imagecodecs easyconfig --- .../i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb index 2a32ac22f2e..284a8b29cb8 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb @@ -63,7 +63,7 @@ exts_list = [ }), (name, version, { 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", - 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.4/:$CPATH && ", + 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-%s/:$CPATH && " % local_openjpeg_maj_min, 'sources': ['%(name)s-%(version)s.tar.gz'], 'checksums': ['04d5757d8fd7819844b0f8d9eed05025dca4962f280d0010b42c7c9c993fe371'], }), From ef035ef6bf0fdcd102eff3a2810ad4a8dd1e2ba4 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 22 Nov 2022 22:49:21 +0100 Subject: [PATCH 5577/9987] Update Clang-15.0.5-GCCcore-11.3.0.eb --- easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb index 2e95433ea04..06fb908fe9f 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb @@ -23,6 +23,7 @@ source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-% sources = [ 'llvm-project-%(version)s.src.tar.xz', ] +checksums = ['9c4278a6b8884eb7f4ae7dfe3c8e5445019824885e47cfdf1392563c47316fd6'] builddependencies = [ ('CMake', '3.23.1'), From a8cf06cf7f9db89b306bf07aba66a5e5a84425eb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 00:31:32 +0100 Subject: [PATCH 5578/9987] downgrade dependency of oceanspy v0.2.0 on xarray to v2022.6.0 --- easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb index b81f3b84574..ac13454ba89 100644 --- a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('dask', '2022.10.0'), - ('xarray', '2022.9.0'), + ('xarray', '2022.6.0'), ] use_pip = True From 0a9d01452b248f18dda7d527ed5be70e5733c5de Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 00:32:43 +0100 Subject: [PATCH 5579/9987] downgrade dependency of xmitgcm v0.5.2 on xarray to v2022.6.0 --- easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb index c8a25756118..cf4cebe8ec1 100644 --- a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.10.4'), ('MITgcmutils', '0.1.2'), ('dask', '2022.10.0'), - ('xarray', '2022.9.0'), + ('xarray', '2022.6.0'), ] use_pip = True From 2bf335ffc8a813774c7857fc06e8b7f78ea6fb59 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 10:29:00 +0100 Subject: [PATCH 5580/9987] adding easyconfigs: CheMPS2-1.8.12-foss-2022a.eb, PyCheMPS2-1.8.12-foss-2022a.eb --- .../c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb | 31 +++++++++++++++++ .../PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb | 33 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb new file mode 100644 index 00000000000..91535173b68 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.8.12' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('HDF5', '1.12.2') +] + +pretestopts = 'export OMP_NUM_THREADS=1 && ' +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb new file mode 100644 index 00000000000..3226a9c3db3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PyCheMPS2' +version = '1.8.12' + +homepage = 'https://sebwouters.github.io/CheMPS2' +description = """PyCheMPS2 is a python interface to CheMPS2, for compilation without +MPI. CheMPS2 is a scientific library which contains a spin-adapted +implementation of the density matrix renormalization group (DMRG) +for ab initio quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('CheMPS2', version), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/SebWouters/CheMPS2/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'install_src': './%(name)s', + 'modulename': '%(name)s', + }), +] + +sanity_pip_check = True + +moduleclass = 'chem' From c701b35d61ba228e882874f8f511b490a78e1ec1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 10:34:52 +0100 Subject: [PATCH 5581/9987] adding easyconfigs: Block-1.5.3-20210723-foss-2022a.eb and patches: Block-1.5.3_use-eb-environment.patch --- .../Block/Block-1.5.3-20210723-foss-2022a.eb | 50 +++++++++++ .../Block-1.5.3_use-eb-environment.patch | 89 +++++++++++++++++++ 2 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/b/Block/Block-1.5.3-20210723-foss-2022a.eb create mode 100644 easybuild/easyconfigs/b/Block/Block-1.5.3_use-eb-environment.patch diff --git a/easybuild/easyconfigs/b/Block/Block-1.5.3-20210723-foss-2022a.eb b/easybuild/easyconfigs/b/Block/Block-1.5.3-20210723-foss-2022a.eb new file mode 100644 index 00000000000..2d686663504 --- /dev/null +++ b/easybuild/easyconfigs/b/Block/Block-1.5.3-20210723-foss-2022a.eb @@ -0,0 +1,50 @@ +easyblock = 'MakeCp' + +name = 'Block' +version = '1.5.3-20210723' +_commit = 'db27636b762aa5921b90de35ac2c08928e57db43' + +homepage = 'https://sanshar.github.io/Block/' +description = """Block implements the density matrix renormalization group (DMRG) algorithm for +quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'cstd': 'c++11'} + +github_account = 'pyscf' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] +patches = ['Block-1.5.3_use-eb-environment.patch'] +checksums = [ + {'1.5.3-20210723.tar.gz': 'f1d8bd664ccf222bc3d73535ab7ff6faa92f2e22109fb44ca3e7f443e0f8e3f8'}, + {'Block-1.5.3_use-eb-environment.patch': '7c954ac4b12fe99c51290a4c19788dc175a109339fe821a90394af34bc974a76'}, +] + +builddependencies = [ + ('Python', '3.10.4'), +] + +dependencies = [ + ('Boost.MPI', '1.79.0'), +] + +buildopts = [ + # Serial build (block.spin_adapted-serial) + "EXECUTABLE=block.spin_adapted-serial ", + # MPI build (block.spin_adapted) + "USE_MPI=yes ", +] + +files_to_copy = [(['block.spin_adapted*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/block.spin_adapted', 'bin/block.spin_adapted-serial'], + 'dirs': [], +} + +sanity_check_commands = [ + "block.spin_adapted-serial --version", + "%(mpi_cmd_prefix)s block.spin_adapted --version", +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/Block/Block-1.5.3_use-eb-environment.patch b/easybuild/easyconfigs/b/Block/Block-1.5.3_use-eb-environment.patch new file mode 100644 index 00000000000..08abde50219 --- /dev/null +++ b/easybuild/easyconfigs/b/Block/Block-1.5.3_use-eb-environment.patch @@ -0,0 +1,89 @@ +Use build environment defined by EasyBuild +author: Nicholas Cheng (@nicholascheng94) +author: Alex Domingo (Vrije Universiteit Brussel) +--- input.h.orig 2022-11-22 15:28:24.141800278 +0100 ++++ input.h 2022-11-22 15:28:56.761244080 +0100 +@@ -18,7 +18,7 @@ + #include "SpinQuantum.h" + #include "timer.h" + #include "couplingCoeffs.h" +-#include ++#include + #include "IntegralMatrix.h" + + +--- makefile.orig 2022-11-22 16:40:08.227179000 +0100 ++++ makefile 2022-11-22 16:41:34.467330533 +0100 +@@ -6,28 +6,28 @@ + + ######### GENERAL OPTIONS FOR USER ######### + #specify boost include file +-BOOSTINCLUDE = /opt/local/include ++BOOSTINCLUDE = ${EBROOTBOOST}/include + + #specify boost and lapack-blas library locations +-BOOSTLIB = -L/opt/local/lib -lboost_system -lboost_filesystem -lboost_serialization ++BOOSTLIB = -L${EBROOTBOOST}/lib -lboost_system -lboost_filesystem -lboost_serialization + #BOOSTLIB = -lboost_serialization -lboost_system -lboost_filesystem +-LAPACKBLAS = /usr/lib/liblapack.dylib /usr/lib/libblas.dylib ++LAPACKBLAS = ${LIBLAPACK} + + # set if using BOOST version >= 1.56.0 +-USE_BOOST56 = no ++USE_BOOST56 = yes + ifeq ($(USE_BOOST56), yes) + B56 = -DBOOST_1_56_0 + endif + + #use these variable to set if we will use mpi or not + USE_MPI = no + USE_MKL = no + + # change to icpc for Intel +-CXX = icpc +-MPICXX = mpiicpc +-export CXX +-export MPICXX ++#CXX = icpc ++#MPICXX = mpiicpc ++#export CXX ++#export MPICXX + + # use this variable to set if we will use integer size of 8 or not. + # molpro compilation requires I8, since their integers are long +@@ -40,7 +40,7 @@ + # molcas compilation w/ -64 option requires I8 as well + MOLCAS = no + +-OPENMP = no ++OPENMP = yes + + ifeq ($(USE_MKL), yes) + MKLLIB = /opt/intel/compilers_and_libraries/linux/mkl/lib/intel64 +@@ -101,7 +101,7 @@ + OPENMP_FLAGS= -openmp -D_OPENMP + endif + # Intel compiler +- OPT = -DNDEBUG -O3 -funroll-loops -Werror ++ OPT = -DNDEBUG -funroll-loops $(OPTFLAGS) + # OPT = -g -fPIC + ifeq ($(USE_MPI), no) + CXX = icc +@@ -113,7 +113,7 @@ + ifeq ($(OPENMP), yes) + OPENMP_FLAGS= -fopenmp #-D_OPENMP + endif +- OPT = -DNDEBUG -O3 -g -funroll-loops -Werror ++ OPT = -DNDEBUG -g -funroll-loops $(OPTFLAGS) + # OPT = -g -fPIC + endif + +@@ -122,7 +122,7 @@ + OPENMP_FLAGS= -fopenmp #-D_OPENMP + endif + +- OPT = -DNDEBUG -g -Werror ++ OPT = -DNDEBUG -g $(OPTFLAGS) + endif + + ifeq ($(DOPROF),yes) From 52bdfbb11e07ff946c90cb9ed25c209874c27aaa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 10:47:34 +0100 Subject: [PATCH 5582/9987] adding easyconfigs: infercnvpy-0.4.0-foss-2021b.eb --- .../infercnvpy/infercnvpy-0.4.0-foss-2021b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb new file mode 100644 index 00000000000..afaff507ff2 --- /dev/null +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'infercnvpy' +version = '0.4.0' + +homepage = 'https://github.com/icbi-lab/infercnvpy' +description = "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('leidenalg', '0.8.8'), + ('scanpy', '1.9.1'), +] + +use_pip = True + +# avoid hatcling requirement to install infercnvpy +# (since installing it introduces conflicting version requirements with poetry included with Python) +local_preinstallopts = """sed -i 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' pyproject.toml && """ +local_preinstallopts += """sed -i 's/^requires = .*/requires = ["setuptools"]/g' pyproject.toml && """ +local_preinstallopts += """sed -i 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ + +exts_list = [ + ('setuptools', '65.6.0', { + 'checksums': ['d1eebf881c6114e51df1664bc2c9133d022f78d12d5f4f665b9191f084e2862d'], + }), + ('gtfparse', '1.2.1', { + 'checksums': ['559d4d36b0bd5d4494f925cab3c00cd969783ebb6408fa025df92663965834b8'], + }), + ('pyreadr', '0.4.7', { + 'checksums': ['901110d62b4bedaef288f4db81425fb696edc721fe2c34c1083f5fb11050a73c'], + }), + ('tqdm', '4.64.1', { + 'checksums': ['5f4f682a004951c1b450bc753c710e9280c5746ce6ffedee253ddbcbf54cf1e4'], + }), + (name, version, { + 'preinstallopts': """sed -i 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' pyproject.toml && sed -i 's/^requires = .*/requires = ["setuptools"]/g' pyproject.toml && sed -i 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """, + 'checksums': ['00b8d78726db0a70bdb4d887fd503a484873244a60b9f58a0979aa75ba6e48cb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 0ae557bd93cf3e13fe872f03288dfe6c2a560439 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 10:52:35 +0100 Subject: [PATCH 5583/9987] adding easyconfigs: nodejs-18.12.1-GCCcore-12.2.0.eb --- .../n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..46b6a0c4ae4 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '18.12.1' # LTS on 2022-11-22 +local_libversion = '108' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['ba8174dda00d5b90943f37c6a180a1d37c861d91e04a4cb38dc1c0c74981c186'] + +builddependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8', '-bare'), +] + +configopts = [ + '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library + '--shared --with-intl=none', # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +postinstallcmds = [ + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s' % SHLIB_EXT, 'lib/libv8.%s' % SHLIB_EXT], + 'dirs': ['lib/node_modules', 'include/node'] +} + +sanity_check_commands = ["node --help"] + +moduleclass = 'lang' From b8afb95e3a087af571d132b17546419eb84438eb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 11:27:18 +0100 Subject: [PATCH 5584/9987] add missing checksums for CheMPS2 and PyCheMPS2 v1.8.12 --- easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb | 3 +-- .../easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb | 3 ++- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb index 91535173b68..482ab997133 100644 --- a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83'] builddependencies = [('CMake', '3.23.1')] @@ -21,8 +22,6 @@ dependencies = [ pretestopts = 'export OMP_NUM_THREADS=1 && ' runtest = 'test' -separate_build_dir = True - sanity_check_paths = { 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], 'dirs': ['include/chemps2'] diff --git a/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb index 3226a9c3db3..ed3cf0c39be 100644 --- a/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb @@ -21,10 +21,11 @@ use_pip = True exts_list = [ (name, version, { + 'modulename': '%(name)s', 'source_urls': ['https://github.com/SebWouters/CheMPS2/archive/'], 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83'], 'install_src': './%(name)s', - 'modulename': '%(name)s', }), ] From a3c4da77a27192f4369b8e83391b990a75b358b5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 11:31:59 +0100 Subject: [PATCH 5585/9987] adding easyconfigs: Boost.MPI-1.79.0-gompi-2022a.eb --- .../Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb new file mode 100644 index 00000000000..be6c179e528 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.79.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('XZ', '5.2.5'), + ('ICU', '71.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' From 811ef35e395c75580ddfeec617d0cbaac2650231 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 12:40:15 +0100 Subject: [PATCH 5586/9987] prefix custom parameters with local in nodejs --- .../n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb | 18 +++++++++--------- .../n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb | 18 +++++++++--------- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 18 +++++++++--------- 3 files changed, 27 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb index bf1db1aa052..866799bfdea 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.0' # LTS on 2021-06-03 -_libversion = '83' +local_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -37,24 +37,24 @@ dependencies = [ ] # Use ICU and OpenSSL from EasyBuild -_common_configopts = "--with-intl=system-icu --shared-openssl " +local_common_configopts = "--with-intl=system-icu --shared-openssl " configopts = [ - _common_configopts, # Static build - '--shared %s' % _common_configopts, # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode -_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] -_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] -_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) postinstallcmds = [ - "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb index a6fe9b552ba..6be4d509878 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.6' # LTS on 2020-08-31 -_libversion = '83' +local_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -27,24 +27,24 @@ dependencies = [ ] # Use ICU and OpenSSL from EasyBuild -_common_configopts = "--with-intl=system-icu --shared-openssl " +local_common_configopts = "--with-intl=system-icu --shared-openssl " configopts = [ - _common_configopts, # Static build - '--shared %s' % _common_configopts, # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode -_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] -_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] -_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) postinstallcmds = [ - "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index bcd9c8dded1..117331f1af8 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '16.15.1' # LTS on 2022-06-12 -_libversion = '93' +local_libversion = '93' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -27,24 +27,24 @@ dependencies = [ ] # Use ICU and OpenSSL from EasyBuild -_common_configopts = "--with-intl=system-icu --shared-openssl " +local_common_configopts = "--with-intl=system-icu --shared-openssl " configopts = [ - _common_configopts, # Static build - '--shared %s' % _common_configopts, # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode -_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] -_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] -_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) postinstallcmds = [ - "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } From d8364b3d5b9b06d6057c7e9de380ebb80a93ab00 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Wed, 23 Nov 2022 12:55:10 +0100 Subject: [PATCH 5587/9987] adding easyconfigs: GLM-0.9.9.8-GCCcore-11.3.0.eb --- .../g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..22d687ed0f4 --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '0.9.9.8' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'GLM-0.9.9.8_fix_missing_install.patch', +] +checksums = [ + '7d508ab72cb5d43227a3711420f06ff99b0a0cb63ee2f93631b162bfe1fe9592', # 0.9.9.8.tar.gz + '1cc199f9d66679b0b5e9a9fbe20bca0d9b15760fa172ca8759dd15bab35802ca', # GLM-0.9.9.8_fix_missing_install.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' From acff80f03c68708109802872b0db1993a9964020 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 23 Nov 2022 12:05:06 +0000 Subject: [PATCH 5588/9987] adding easyconfigs: libspatialindex-1.9.3-GCCcore-11.3.0.eb --- .../libspatialindex-1.9.3-GCCcore-11.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..445496497a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'libspatialindex' +version = '1.9.3' + +homepage = 'https://libspatialindex.org' +description = """C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/libspatialindex/libspatialindex/releases/download/%(version)s/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['47d8779e32477b330e46b62fb7e62cb812caee5d8e684c35cb635a42a749f3fc'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/libspatialindex.%s' % SHLIB_EXT], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' From 46b4c405d06e84d3fb1e72bed94dc5082e123311 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 14:30:41 +0100 Subject: [PATCH 5589/9987] use proper dependencies for ICU and OpenSSL for nodejs 18.12.1 --- .../i/ICU/ICU-72.1-GCCcore-12.2.0.eb | 29 +++++++++++++++++++ .../n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb | 23 ++++++++++----- 2 files changed, 45 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9b141a4671d --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '72.1' + +homepage = 'https://icu.unicode.org' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['a2d2d38217092a7ed56635e34467f92f976b370e20182ad325edea6681a71d68'] + +builddependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8', '-bare'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb index 46b6a0c4ae4..2ea5d3c974f 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb @@ -21,21 +21,30 @@ builddependencies = [ ('Python', '3.10.8', '-bare'), ] +dependencies = [ + ('ICU', '72.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# Use ICU and OpenSSL from EasyBuild +local_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s' % SHLIB_EXT, 'lib/libv8.%s' % SHLIB_EXT], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } From 6361e43ad12699fc7afaed695b7cc9d8a5c3f780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 15:30:58 +0100 Subject: [PATCH 5590/9987] adding easyconfigs: LLVM-15.0.5-GCCcore-12.2.0.eb --- .../l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..fad97fede29 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb @@ -0,0 +1,46 @@ +name = 'LLVM' +version = '15.0.5' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'cstd': 'gnu++11', 'pic': True} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'cmake-%(version)s.src.tar.xz', +] +checksums = [ + {'llvm-15.0.5.src.tar.xz': '4428688b567ab1c9911aa9e13cb44c9bc1b14431713c14de491e10369f2b0370'}, + {'cmake-15.0.5.src.tar.xz': '61a9757f2fb7dd4c992522732531eb58b2bb031a2ca68848ff1cfda1fc07b7b3'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Python', '3.10.8'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' From 92fc2709508968c682fa2884e44e930f84d28992 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 23 Nov 2022 16:06:11 +0100 Subject: [PATCH 5591/9987] adding easyconfigs: Circuitscape-5.11.2-Julia-1.7.2.eb --- .../Circuitscape-5.11.2-Julia-1.7.2.eb | 322 ++++++++++++++++++ 1 file changed, 322 insertions(+) create mode 100644 easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb new file mode 100644 index 00000000000..4b2dae94cfd --- /dev/null +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb @@ -0,0 +1,322 @@ +easyblock = 'Bundle' + +name = 'Circuitscape' +version = '5.11.2' +_julia_ver = '1.7.2' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/Circuitscape/Circuitscape.jl' +description = "Algorithms from circuit theory to predict connectivity in heterogeneous landscapes" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, True), +] + +exts_defaultclass = 'JuliaPackage' +exts_filter = ("LD_LIBRARY_PATH="" julia -e 'using %(ext_name)s'", "") +exts_default_options = { + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], +} + + +exts_list = [ + ('Preferences', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['a87c1fc863fcb6240c3f4327776fa01a1f87e0d2df5a0c1850f789ce24469da2'], + }), + ('JLLWrappers', '1.4.1', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], + }), + ('CommonSolve', '0.2.3', { + 'source_urls': ['https://github.com/SciML/CommonSolve.jl/archive/'], + }), + ('Reexport', '1.2.2', { + 'source_urls': ['https://github.com/simonster/Reexport.jl/archive/'], + 'checksums': ['2566f7776aae9697cbf15765fc32187f46dd51200abc953a0266863ad67132b3'], + }), + ('AlgebraicMultigrid', '0.5.1', { + 'source_urls': ['https://github.com/JuliaLinearAlgebra/AlgebraicMultigrid.jl/archive/'], + }), + ('CEnum', '0.4.2', { + 'source_urls': ['https://github.com/JuliaInterop/CEnum.jl/archive/'], + }), + ('Requires', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Requires.jl/archive/'], + 'checksums': ['8af4dac29839e796a651b8cb6a325b6f9c7eee5d5620b3e366b64f58325ebeb7'], + }), + ('FixedPointNumbers', '0.8.4', { + 'source_urls': ['https://github.com/JuliaMath/FixedPointNumbers.jl/archive/'], + }), + ('ColorTypes', '0.11.1', { + 'source_urls': ['https://github.com/JuliaGraphics/ColorTypes.jl/archive/'], + }), + ('Adapt', '3.4.0', { + 'source_urls': ['https://github.com/JuliaGPU/Adapt.jl/archive/'], + }), + ('OffsetArrays', '1.12.8', { + 'source_urls': ['https://github.com/JuliaArrays/OffsetArrays.jl/archive/'], + }), + ('DiskArrays', '0.3.7', { + 'source_urls': ['https://github.com/meggart/DiskArrays.jl/archive/'], + }), + ('Extents', '0.1.1', { + 'source_urls': ['https://github.com/rafaqz/Extents.jl/archive/'], + }), + ('JpegTurbo_jll', '2.1.2+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/JpegTurbo_jll.jl/archive/'], + 'sources': ['JpegTurbo-v%(version)s.tar.gz'], + }), + ('LERC_jll', '3.0.0+1', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/LERC_jll.jl/archive/'], + 'sources': ['LERC-v%(version)s.tar.gz'], + }), + ('Zstd_jll', '1.5.2+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/Zstd_jll.jl/archive/'], + 'sources': ['Zstd-v%(version)s.tar.gz'], + }), + ('Libtiff_jll', '4.4.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/Libtiff_jll.jl/archive/'], + 'sources': ['Libtiff-v%(version)s.tar.gz'], + }), + ('SQLite_jll', '3.40.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/SQLite_jll.jl/archive/'], + 'sources': ['SQLite-v%(version)s.tar.gz'], + }), + ('PROJ_jll', '900.100.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/PROJ_jll.jl/archive/'], + 'sources': ['PROJ-v%(version)s.tar.gz'], + }), + ('libgeotiff_jll', '100.700.100+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/libgeotiff_jll.jl/archive/'], + 'sources': ['libgeotiff-v%(version)s.tar.gz'], + }), + ('Kerberos_krb5_jll', '1.19.3+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/Kerberos_krb5_jll.jl/archive/'], + 'sources': ['Kerberos_krb5-v%(version)s.tar.gz'], + }), + ('OpenSSL_jll', '1.1.19+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/OpenSSL_jll.jl/archive/'], + 'sources': ['OpenSSL-v%(version)s.tar.gz'], + }), + ('LibPQ_jll', '14.3.0+1', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/LibPQ_jll.jl/archive/'], + 'sources': ['LibPQ-v%(version)s.tar.gz'], + }), + ('HDF5_jll', '1.12.2+2', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/HDF5_jll.jl/archive/'], + 'sources': ['HDF5-v%(version)s.tar.gz'], + }), + ('libpng_jll', '1.6.38+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/libpng_jll.jl/archive/'], + 'sources': ['libpng-v%(version)s.tar.gz'], + }), + ('LittleCMS_jll', '2.12.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/LittleCMS_jll.jl/archive/'], + 'sources': ['LittleCMS-v%(version)s.tar.gz'], + }), + ('OpenJpeg_jll', '2.4.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/OpenJpeg_jll.jl/archive/'], + 'sources': ['OpenJpeg-v%(version)s.tar.gz'], + }), + ('Libiconv_jll', '1.16.0+8', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/Libiconv_jll.jl/archive/'], + 'sources': ['Libiconv-v%(version)s.tar.gz'], + }), + ('XML2_jll', '2.10.3+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/XML2_jll.jl/archive/'], + 'sources': ['XML2-v%(version)s.tar.gz'], + }), + ('NetCDF_jll', '400.902.5+1', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/NetCDF_jll.jl/archive/'], + 'sources': ['NetCDF-v%(version)s.tar.gz'], + }), + ('GEOS_jll', '3.11.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/GEOS_jll.jl/archive/'], + 'sources': ['GEOS-v%(version)s.tar.gz'], + }), + ('boost_jll', '1.79.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/boost_jll.jl/archive/'], + 'sources': ['boost-v%(version)s.tar.gz'], + }), + ('Thrift_jll', '0.16.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/Thrift_jll.jl/archive/'], + 'sources': ['Thrift-v%(version)s.tar.gz'], + }), + ('Lz4_jll', '1.9.3+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/Lz4_jll.jl/archive/'], + 'sources': ['Lz4-v%(version)s.tar.gz'], + }), + ('Bzip2_jll', '1.0.7+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/Bzip2_jll.jl/archive/'], + 'sources': ['Bzip2-v%(version)s.tar.gz'], + }), + ('LZO_jll', '2.10.1+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/LZO_jll.jl/archive/'], + 'sources': ['LZO-v%(version)s.tar.gz'], + }), + ('snappy_jll', '1.1.9+1', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/snappy_jll.jl/archive/'], + 'sources': ['snappy-v%(version)s.tar.gz'], + }), + ('Arrow_jll', '10.0.0+1', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/Arrow_jll.jl/archive/'], + 'sources': ['Arrow-v%(version)s.tar.gz'], + }), + ('Expat_jll', '2.4.8+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/Expat_jll.jl/archive/'], + 'sources': ['Expat-v%(version)s.tar.gz'], + }), + ('GDAL_jll', '300.500.200+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/GDAL_jll.jl/archive/'], + 'sources': ['GDAL-v%(version)s.tar.gz'], + }), + ('GDAL', '1.4.0', { + 'source_urls': ['https://github.com/JuliaGeo/GDAL.jl/archive/'], + }), + ('GeoFormatTypes', '0.4.1', { + 'source_urls': ['https://github.com/JuliaGeo/GeoFormatTypes.jl/archive/'], + }), + ('RecipesBase', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPlots/RecipesBase.jl/archive/'], + }), + ('GeoInterface', '1.0.1', { + 'source_urls': ['https://github.com/JuliaGeo/GeoInterface.jl/archive/'], + }), + ('Compat', '4.3.0', { + 'source_urls': ['https://github.com/JuliaLang/Compat.jl/archive/'], + 'checksums': ['0d792ec0912a8d3ed30329fc44073e964be3cd314671594dd16f8570c51b2c19'], + }), + ('ChainRulesCore', '1.15.6', { + 'source_urls': ['https://github.com/JuliaDiff/ChainRulesCore.jl/archive/'], + 'checksums': ['79e22fc981fa7c44b3efc2f07903f555c5520dc38d0d3d31b6390980c786cb60'], + }), + ('AbstractFFTs ', '1.2.1', { + 'source_urls': ['https://github.com/JuliaMath/AbstractFFTs.jl/archive/'], + }), + ('SpecialFunctions', '1.8.7', { + 'source_urls': ['https://github.com/JuliaMath/SpecialFunctions.jl/archive/'], + 'checksums': ['3f2ecec0506fe47cfa5e436ac510e2a82d39f74fceaeb422572cf06d90f2096a'], + }), + ('TensorCore', '0.1.1', { + 'source_urls': ['https://github.com/JuliaMath/TensorCore.jl/archive/'], + }), + ('ColorVectorSpace', '0.9.9', { + 'source_urls': ['https://github.com/JuliaGraphics/ColorVectorSpace.jl/archive/'], + }), + ('Colors', '0.12.8', { + 'source_urls': ['https://github.com/JuliaGraphics/Colors.jl/archive/'], + }), + ('NaNMath', '1.0.1', { + 'source_urls': ['https://github.com/JuliaMath/NaNMath.jl/archive/'], + }), + ('Graphics', '1.1.2', { + 'source_urls': ['https://github.com/JuliaGraphics/Graphics.jl/archive/'], + }), + ('MappedArrays', '0.4.1', { + 'source_urls': ['https://github.com/JuliaArrays/MappedArrays.jl/archive/'], + }), + ('MosaicViews', '0.3.3', { + 'source_urls': ['https://github.com/JuliaArrays/MosaicViews.jl/archive/'], + }), + ('PaddedViews', '0.5.11', { + 'source_urls': ['https://github.com/JuliaArrays/PaddedViews.jl/archive/'], + }), + ('StackViews', '0.1.1', { + 'source_urls': ['https://github.com/JuliaArrays/StackViews.jl/archive/'], + }), + ('ImageCore', '0.9.4', { + 'source_urls': ['https://github.com/JuliaImages/ImageCore.jl/archive/'], + }), + ('DataAPI', '1.13.0', { + 'source_urls': ['https://github.com/JuliaData/DataAPI.jl/archive/'], + }), + ('DataValueInterfaces ', '1.0.0', { + 'source_urls': ['https://github.com/queryverse/DataValueInterfaces.jl/archive/'], + }), + ('IteratorInterfaceExtensions ', '1.0.0', { + 'source_urls': ['https://github.com/queryverse/IteratorInterfaceExtensions.jl/archive/'], + }), + ('OrderedCollections', '1.4.1', { + 'source_urls': ['https://github.com/JuliaCollections/OrderedCollections.jl/archive/'], + 'checksums': ['ad6d191a2bf6f0c04abaf795fa93b3db6c3f3fb97498b464fcf7297b3a4bf6b6'], + }), + ('TableTraits ', '1.0.1', { + 'source_urls': ['https://github.com/queryverse/TableTraits.jl/archive/'], + }), + ('Tables ', '1.10.0', { + 'source_urls': ['https://github.com/JuliaData/Tables.jl/archive/'], + }), + ('ArchGDAL', '0.9.3', { + 'source_urls': ['https://github.com/yeesian/ArchGDAL.jl/archive/'], + }), + ('GZip ', '0.5.1', { + 'source_urls': ['https://github.com/JuliaIO/GZip.jl/archive/'], + }), + ('StaticArraysCore ', '1.4.0', { + 'source_urls': ['https://github.com/JuliaArrays/StaticArraysCore.jl/archive/'], + }), + ('StaticArrays ', '1.5.10', { + 'source_urls': ['https://github.com/JuliaArrays/StaticArrays.jl/archive/'], + }), + ('ArnoldiMethod ', '0.2.0', { + 'source_urls': ['https://github.com/JuliaLinearAlgebra/ArnoldiMethod.jl/archive/'], + }), + ('DataStructures ', '0.18.13', { + 'source_urls': ['https://github.com/JuliaCollections/DataStructures.jl/archive/'], + }), + ('TranscodingStreams', '0.9.9', { + 'source_urls': ['https://github.com/JuliaIO/TranscodingStreams.jl/archive/'], + }), + ('CodecZlib', '0.7.0', { + 'source_urls': ['https://github.com/JuliaIO/CodecZlib.jl/archive/'], + }), + ('Inflate', '0.1.2', { + 'source_urls': ['https://github.com/GunnarFarneback/Inflate.jl/archive/'], + }), + ('MacroTools', '0.5.10', { + 'source_urls': ['https://github.com/FluxML/MacroTools.jl/archive/'], + }), + ('SimpleTraits', '0.9.4', { + 'source_urls': ['https://github.com/mauro3/SimpleTraits.jl/archive/'], + }), + ('Graphs ', '1.7.4', { + 'source_urls': ['https://github.com/JuliaGraphs/Graphs.jl/archive/'], + }), + ('IterativeSolvers', '0.9.2', { + 'source_urls': ['https://github.com/JuliaLinearAlgebra/IterativeSolvers.jl/archive/'], + }), + ('IntelOpenMP_jll', '2018.0.3+2', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/IntelOpenMP_jll.jl/archive/'], + 'sources': ['IntelOpenMP-v%(version)s.tar.gz'], + }), + ('MKL_jll', '2022.2.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/MKL_jll.jl/archive/'], + 'sources': ['MKL-v%(version)s.tar.gz'], + }), + ('Pardiso', '0.5.4', { + 'source_urls': ['https://github.com/JuliaSparse/Pardiso.jl/archive/'], + }), + ('LightGraphs', '1.3.5', { + 'source_urls': ['https://github.com/sbromberger/LightGraphs.jl/archive/'], + }), + ('SimpleWeightedGraphs', '1.1.0', { + 'source_urls': ['https://github.com/sbromberger/SimpleWeightedGraphs.jl/archive/'], + }), + (name, version, { + 'source_urls': ['https://github.com/Circuitscape/Circuitscape.jl/archive/'] + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['packages'], +} + +modextrapaths = { + 'JULIA_DEPOT_PATH': '', +} + +moduleclass = 'lib' From 09e832fc190757d9ce10f0e701ca6e9c0b521790 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Dvo=C5=99=C3=A1=C4=8Dek=20Josef?= Date: Wed, 23 Nov 2022 17:26:33 +0100 Subject: [PATCH 5592/9987] adding easyconfigs: libconfig-1.7.3-GCCcore-11.2.0.eb --- .../libconfig-1.7.3-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4cf46abac37 --- /dev/null +++ b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libconfig' +version = '1.7.3' + +homepage = 'https://hyperrealm.github.io/libconfig' +description = "Libconfig is a simple library for processing structured configuration files" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://hyperrealm.github.io/libconfig/dist/'] +sources = [SOURCE_TAR_GZ] +checksums = ['545166d6cac037744381d1e9cc5a5405094e7bfad16a411699bcff40bbb31ee7'] + +builddependencies = [ + ('binutils', '2.37'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +sanity_check_paths = { + 'files': ['include/libconfig.h', 'include/libconfig.h++', 'lib/libconfig.a', 'lib/libconfig++.a', + 'lib/libconfig.%s' % SHLIB_EXT, 'lib/libconfig++.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' From b16f1b5994d5848d15ea4138af0442c5b4269c5f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 23 Nov 2022 18:49:02 +0000 Subject: [PATCH 5593/9987] adding easyconfigs: NVHPC-22.7-CUDA-11.7.0.eb, FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb, OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb, BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb, FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb, ScaLAPACK-2.2.0-nvompi-2022.07.eb, nvofbf-2022.07.eb --- .../BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb | 44 +++++++++++++ .../FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb | 20 ++++++ .../FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 59 +++++++++++++++++ .../n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb | 66 +++++++++++++++++++ .../easyconfigs/n/nvofbf/nvofbf-2022.07.eb | 25 +++++++ .../OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb | 31 +++++++++ .../ScaLAPACK-2.2.0-nvompi-2022.07.eb | 42 ++++++++++++ 7 files changed, 287 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb new file mode 100644 index 00000000000..9928532de5e --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.9.0' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_disable_power9_kernels.patch', + '%(name)s-%(version)s_enable_ppc_autodetect.patch', +] +checksums = [ + '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz + # BLIS-0.9.0_disable_power9_kernels.patch + 'ed7a326bc5c5c21c42faefbec2fd7be609d1c7236981b466475edace39307279', + # BLIS-0.9.0_enable_ppc_autodetect.patch + 'f373fb252c0d14036fb631f048091976cceb02abb3e570a97fbaeac2fbb12328', +] +builddependencies = [ + ('Python', '3.10.4', '-bare'), + ('Perl', '5.34.1'), +] + +preconfigopts = "sed -i 's/LINKER.*/LINKER := nvc/' common.mk &&" +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' +configopts += ' --complex-return=intel CC=gcc CFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno"' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb new file mode 100644 index 00000000000..9a75ff49951 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,20 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +# Does not work with nvc +with_quad_prec = False + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb new file mode 100644 index 00000000000..07c769edc08 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'FlexiBLAS' +version = '3.2.0' + +homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' +description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation +used by a program without recompiling or relinking it.""" + +toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} +local_extra_flags = "-D__ELF__" +toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} + +builddependencies = [ + ('CMake', '3.23.1'), + ('Python', '3.10.4', '-bare'), # required for running the tests + ('BLIS', '0.9.0'), +] + +dependencies = [ + ('OpenBLAS', '0.3.20'), +] + +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +local_backends = ['OpenBLAS', 'BLIS'] + +# imkl supplies its backend via the imkl module, not as a dependency +if ARCH == 'x86_64': + local_backends.append('imkl') + +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['a3f4d66a30b6fa6473e492de86d34abc5f9d4e69d4d91ba23618388e8df05904'], + 'configopts': '-DABI=Intel', + 'backends': local_backends, + }), + ('LAPACK', '3.10.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['cd005cd021f144d7d5f7f33c943942db9f03a28d110d6a3b80d718a295f7f714'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb new file mode 100644 index 00000000000..4922cc417e6 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,66 @@ +name = 'NVHPC' +version = '22.7' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2022_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + '2aae3fbfd2d0d2d09448a36166c42311368f5600c7c346f159c280b412fe924a', + local_tarball_tmpl % 'ppc64le': + '6dd4fd382c22769e4fa9508714119abd7d1df3dc58c69414a14b0b0dbc34564f', + local_tarball_tmpl % 'x86_64': + '3ce1c346f8bc7e50defb41c545c8907fdc012ff60b27eb8985cf3213f19d863a', + } +] + +local_gccver = '11.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.38', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.14', '', ('GCCcore', local_gccver)), + ('CUDA', '11.7.0', '', SYSTEM), +] + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.4.1')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = '7.0' +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = True # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = True # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = True # Add NVHPC's NVIDIA Profilers +# module_add_nccl = True # Add NVHPC's NCCL library +# module_add_nvshmem = True # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb b/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb new file mode 100644 index 00000000000..af891ade799 --- /dev/null +++ b/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb @@ -0,0 +1,25 @@ +easyblock = 'Toolchain' + +name = 'nvofbf' +version = '2022.07' + +homepage = '(none)' +description = """NVHPC based toolchain, including OpenMPI for MPI support, +OpenBLAS (via FlexiBLAS for BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_compiler = ('NVHPC', '22.7-CUDA-11.7.0') + +local_comp_mpi_tc = ('nvompi', version) + +dependencies = [ + local_compiler, + ('OpenMPI', '4.1.4', '', local_compiler), + ('FlexiBLAS', '3.2.0', '', local_compiler), + ('FFTW', '3.3.10', '', local_compiler), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb new file mode 100644 index 00000000000..a05030ce4e3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,31 @@ +name = 'OpenBLAS' +version = '0.3.20' + +homepage = 'http://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', +] +checksums = [ + '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', +] + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb new file mode 100644 index 00000000000..85b567d8d10 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb @@ -0,0 +1,42 @@ +name = 'ScaLAPACK' +version = '2.2.0' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'nvompi', 'version': '2022.07'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('FlexiBLAS', '3.2.0'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From ce2947aead4d9ae74e80445e06f913db4c6168f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:44:22 +0100 Subject: [PATCH 5594/9987] adding easyconfigs: zstd-1.5.2-GCCcore-12.2.0.eb, gzip-1.12-GCCcore-12.2.0.eb, lz4-1.9.4-GCCcore-12.2.0.eb --- .../g/gzip/gzip-1.12-GCCcore-12.2.0.eb | 29 +++++++++++++ .../l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb | 30 ++++++++++++++ .../z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..22956fb64c7 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.12' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['gzip-1.12_fix-gnulib-strndup-redeclaration.patch'] +checksums = [ + '5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085', # gzip-1.12.tar.gz + # gzip-1.12_fix-gnulib-strndup-redeclaration.patch + '9c67e3e88848f7ff1f19f29d87f286bac1cc8f027f7eea9bcaf53883b95032e4', +] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6f3f81b768d --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.4' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b0e3aa07c8c063ddf40b082bdf7e37a1562bda40a0ff5272957f3e987e0e54b'] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7176db3c09e --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.5.2' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f7de13462f7a82c29ab865820149e778cbfe01087b3a55b5332707abf9db4a6e'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('gzip', '1.12'), + ('XZ', '5.2.7'), + ('lz4', '1.9.4'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From 6266613ac52a07184c8d2b51c1fa352fabdcf366 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:46:43 +0100 Subject: [PATCH 5595/9987] {vis}[GCCcore/12.2.0] Mesa v22.2.4, Mako v1.2.4, libglvnd v1.6.0, libdrm v2.4.114, libunwind v1.6.2 --- .../l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb | 32 +++++++++ .../libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb | 33 +++++++++ .../libunwind-1.6.2-GCCcore-12.2.0.eb | 32 +++++++++ .../m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb | 29 ++++++++ .../m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb | 69 +++++++++++++++++++ 5 files changed, 195 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..613ec59df25 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'libdrm' +version = '2.4.114' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['3049cf843a47d12e5eeefbc3be3496d782fa09f42346bf0b7defe3d1e598d026'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] +dependencies = [('X11', '20221110')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '-Dman-pages=false' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b953d44c572 --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'libglvnd' +version = '1.6.0' + +homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] +sources = ['libglvnd-v%(version)s.tar.gz'] +checksums = ['33b8b993adf47a21bc1c46bcf970927edeb9884390d5b09b1aed051d600c0b2f'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] + +dependencies = [('X11', '20221110')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5e849e316cd --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.6.2' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4a6aec666991fb45d0889c44aede8ad6eb108071c3554fcdff671f9c94794976'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('XZ', '5.2.7'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fno-common" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5aaa05828b2 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.2.4' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d60a3903dc3bb01a18ad6a89cdbe2e4eadc69c0bc8ef1e3773ba53d44c3f7a34'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ["mako-render --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f59d911be6a --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb @@ -0,0 +1,69 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers enabled (swr deprecated as of v22): +# - llvmpipe: uses LLVM for JIT code generation (multi-threaded) +# - softpipe: a reference Gallium driver +# Default renderer is llvmpipe. To use softpipe, set the environment +# variable GALLIUM_DRIVER=softpipe + +name = 'Mesa' +version = '22.2.4' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['65d76b53ca5c7b46019e0e8e5b414de45d2fecd3fcd71707f6c3bc7691c9f7ab'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '1.9.3'), + ('Mako', '1.2.4'), + ('libxml2', '2.10.3'), + ('expat', '2.4.9'), + ('gettext', '0.21.1'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('zstd', '1.5.2'), + ('libdrm', '2.4.114'), + ('libglvnd', '1.6.0'), + ('libunwind', '1.6.2'), + ('LLVM', '15.0.5'), + ('X11', '20221110'), +] + +configopts = "-Dplatforms=x11 -Dosmesa=true -Ddri-drivers='' -Dvulkan-drivers='' " +configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +# Tells libglvnd where to find EGL libraries +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} + +moduleclass = 'vis' From 8338bf7b0d8e45eb8a6155dae9792dc14be1f10d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:52:50 +0100 Subject: [PATCH 5596/9987] use 'disabled' to skip installation of man pages for libdrm 2.4.114 --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb index 613ec59df25..40a3653b38d 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [('X11', '20221110')] # installing manpages requires an extra build dependency (docbook xsl) -configopts = '-Dman-pages=false' +configopts = '-Dman-pages=disabled' sanity_check_paths = { 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], From 205429ecc30c39fab6171fe430898c5d73a1a925 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:54:14 +0100 Subject: [PATCH 5597/9987] fix checksum for libglvnd 1.6.0 --- .../easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb index b953d44c572..6e95158d902 100644 --- a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] sources = ['libglvnd-v%(version)s.tar.gz'] -checksums = ['33b8b993adf47a21bc1c46bcf970927edeb9884390d5b09b1aed051d600c0b2f'] +checksums = ['efc756ffd24b24059e1c53677a9d57b4b237b00a01c54a6f1611e1e51661d70c'] builddependencies = [ ('binutils', '2.39'), From 0dc8178599b7c7d388169d5db7797275ba873a9c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:05:33 +0100 Subject: [PATCH 5598/9987] adding easyconfigs: libGLU-9.0.2-GCCcore-12.2.0.eb --- .../l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2a35c328e4b --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.2' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.gz'] +checksums = ['24effdfb952453cc00e275e1c82ca9787506aba0282145fff054498e60e19a65'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Mesa', '22.2.4'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From ea2ea8b366a92933d652ae53987e948b85f64687 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:22:08 +0100 Subject: [PATCH 5599/9987] {lib}[GCCcore/12.2.0] libjpeg-turbo v2.1.4, NASM v2.15.05 --- .../libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb | 42 +++++++++++++++++++ .../n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb | 25 +++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0117bb716bf --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.1.4' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d3ed26a1131a13686dfca4935e520eb7c90ae76fbc45d98bb50a8dc86230342b'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('NASM', '2.15.05'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e4fa39b554e --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.15.05' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['3c4b8339e5ab54b1bcb2316101f8985a5da50a3f9e504d43fa6f35668bee2fd0'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' From 8cdfede4b48a9bd320ece80e54808ae9ed538224 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:24:56 +0100 Subject: [PATCH 5600/9987] adding easyconfigs: double-conversion-3.2.1-GCCcore-12.2.0.eb --- .../double-conversion-3.2.1-GCCcore-12.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d3221353d9f --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.2.1' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e40d236343cad807e83d192265f139481c51fc83a1c49e406ac6ce0a0ba7cd35'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +separate_build_dir = True + +build_type = 'Release' + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a', + '-DBUILD_SHARED_LIBS=ON' +] + +sanity_check_paths = { + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' From d0d8e02b7a4101b871dfe52484c14b546f85384c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:27:06 +0100 Subject: [PATCH 5601/9987] adding easyconfigs: cairo-1.17.4-GCCcore-12.2.0.eb, GLib-2.75.0-GCCcore-12.2.0.eb, pixman-0.42.2-GCCcore-12.2.0.eb, PCRE2-10.40-GCCcore-12.2.0.eb --- .../c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb | 49 +++++++++++++++++ .../g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ .../p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb | 28 ++++++++++ .../p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb | 28 ++++++++++ 4 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a9661b33bce --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.17.4' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + 'https://cairographics.org/releases/', + 'https://cairographics.org/snapshots/' +] +sources = [SOURCE_TAR_XZ] +checksums = ['74b24c1ed436bbe87499179a3b27c43f4143b8676d8ad237a6fa787401959705'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('freetype', '2.12.1'), + ('pixman', '0.42.2'), + ('expat', '2.4.9'), + ('GLib', '2.75.0'), + ('X11', '20221110'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0390a9a2e54 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.75.0' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['6dde8e55cc4a2c83d96797120b08bcffb5f645b2e212164ae22d63c40e0e6360'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.10.8'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('libffi', '3.4.4'), + ('gettext', '0.21.1'), + ('libxml2', '2.10.3'), + ('PCRE2', '10.40'), + ('util-linux', '2.38.1'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7aed3007b9f --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.40' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ded42661cab30ada2e72ebff9e725e745b4b16ce831993635136f2ef86177724'] + +builddependencies = [('binutils', '2.39')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..17b7e5b6432 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.42.2' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ea1480efada2fd948bc75366f7c349e1c96d3297d09a3fe62626e38e234a625e'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From d6999f0e4958a0ce6afed3d64824c0659ea0405a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:41:12 +0100 Subject: [PATCH 5602/9987] adding easyconfigs: NSS-3.85-GCCcore-12.2.0.eb, NSPR-4.35-GCCcore-12.2.0.eb --- .../n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb | 30 +++++++++ .../n/NSS/NSS-3.85-GCCcore-12.2.0.eb | 61 +++++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..1795b557f16 --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.35' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7ea3297ea5969b5d25a5dd8d47f2443cda88e9ee746301f6e1e1426f8a6abc8f'] + +builddependencies = [('binutils', '2.39')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +sanity_check_commands = ["nspr-config --version"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e0d91d152f0 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.85' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', + 'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', +] +checksums = [ + {'nss-3.85.tar.gz': 'afd9d64510b1154debbd6cab3571e9ff64a3373898e03483e4c85cdada13d297'}, + {'NSS-3.39_pkgconfig.patch': '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774'}, + {'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch': + '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'}, +] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('NSPR', '4.35'), + ('zlib', '1.2.12'), +] + +# building in parallel fails +parallel = 1 + +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " +# fix for not being able to find header files +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], +} + +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' From cbf1e6db9570125f7566c5ddb35445cc9c588fd5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:29:04 +0100 Subject: [PATCH 5603/9987] {vis}[GCCcore/12.2.0] HarfBuzz v5.3.1, GObject-Introspection v1.74.0 --- ...ect-Introspection-1.74.0-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ .../HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb | 38 ++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f4d572664a7 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.74.0' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['347b3a719e68ba4c69ff2d57ee2689233ea8c07fc492205e573386779e42d653'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('cairo', '1.17.4'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('GLib', '2.75.0'), + ('libffi', '3.4.4'), + ('util-linux', '2.38.1'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e39adfe0f43 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '5.3.1' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['77c8c903f4539b050a6d3a5be79705c7ccf7b1cb66d68152a651486e261edbd2'] + +builddependencies = [ + ('binutils', '2.39'), + ('GObject-Introspection', '1.74.0'), + ('pkgconf', '1.9.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('GLib', '2.75.0'), + ('ICU', '72.1'), + ('cairo', '1.17.4'), + ('freetype', '2.12.1'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' From dce9c8a5771b6bf09e4c5f6d13cd479151df907c Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Thu, 24 Nov 2022 12:07:53 +0100 Subject: [PATCH 5604/9987] adding easyconfigs: OpenImageIO-2.3.17.0-GCC-11.3.0.eb --- .../OpenImageIO-2.3.17.0-GCC-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..30ccd8238c3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'OpenImageIO' +version = '2.3.17.0' + +homepage = 'https://openimageio.org/' +description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, + and applications.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['22d38347b40659d218fcafcadc9258d3f6eda0be02029b11969361c9a6fa9f5c'] +#patches = ['oiio-tiff.patch'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('git', '2.36.0', '-nodocs'), +] +dependencies = [ + ('Boost', '1.79.0'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('OpenEXR', '3.1.5'), + ('freetype', '2.12.1'), + ('zlib', '1.2.12'), +] + +separate_build_dir = True + +configopts = '-DSTOP_ON_WARNING=OFF -DUSE_PYTHON=OFF' + +sanity_check_paths = { + 'files': ['bin/oiiotool', 'lib/libOpenImageIO.%s' % SHLIB_EXT, 'lib/libOpenImageIO_Util.%s' % SHLIB_EXT], + 'dirs': ['include/OpenImageIO', 'share'], +} + +moduleclass = 'lib' + From 77e4bcb0d05710fdd2ce697b4401a71269815b07 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Thu, 24 Nov 2022 13:35:07 +0100 Subject: [PATCH 5605/9987] Fix style errors --- .../o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb index 30ccd8238c3..9b762b8294b 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['22d38347b40659d218fcafcadc9258d3f6eda0be02029b11969361c9a6fa9f5c'] -#patches = ['oiio-tiff.patch'] builddependencies = [ ('CMake', '3.23.1'), @@ -38,4 +37,3 @@ sanity_check_paths = { } moduleclass = 'lib' - From 312d9f5dde534e928abfd5c6aa93be762bb961eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 24 Nov 2022 14:43:46 +0100 Subject: [PATCH 5606/9987] adding easyconfigs: bamFilters-2022-06-30-GCC-11.3.0.eb, SAMtools-1.13-GCC-11.3.0.eb --- .../bamFilters-2022-06-30-GCC-11.3.0.eb | 37 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.13-GCC-11.3.0.eb | 25 +++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb new file mode 100644 index 00000000000..b9a1c04fdf2 --- /dev/null +++ b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'bamFilters' +local_commit = '93e334e' +version = '2022-06-30' + +homepage = 'https://github.com/institut-de-genomique/bamFilters' +description = """A utility tool to filter alignments from bam files, + using identity percent, low complexity and read coverage.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/institut-de-genomique/bamFilters/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['63a2a57093f0d360ce21775de8bb118e60cbd8856593e02c608f930745e1b463'] + +dependencies = [ + ('HTSlib', '1.15.1'), + ('BamTools', '2.5.2'), + ('SAMtools', '1.13'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), +] +prebuildopts = 'mkdir obj && ' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" SAMTOOLS_LIBDIR="$EBROOTSAMTOOLS/lib" LIBS="$LIBS -lhts -lbam -lz -lbz2 -lcurl -lssl -lcrypto -llzma"' + +files_to_copy = [ + (['bamFilters'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/bamFilters'], + 'dirs': [] +} + +sanity_check_commands = ['bamFilters -h 2>&1 | grep "Usage"'] + diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-11.3.0.eb new file mode 100644 index 00000000000..2f667a4e3e8 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-11.3.0.eb @@ -0,0 +1,25 @@ +name = 'SAMtools' +version = '1.13' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.83.0'), +] + +moduleclass = 'bio' From b7fd2f640c125f4027e313f72178f03ebe931914 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 24 Nov 2022 15:11:31 +0100 Subject: [PATCH 5607/9987] fixed line too long --- .../b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb index b9a1c04fdf2..75f1c57d85f 100644 --- a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb @@ -22,7 +22,8 @@ dependencies = [ ('bzip2', '1.0.8'), ] prebuildopts = 'mkdir obj && ' -buildopts = 'CC="$CC" CFLAGS="$CFLAGS" SAMTOOLS_LIBDIR="$EBROOTSAMTOOLS/lib" LIBS="$LIBS -lhts -lbam -lz -lbz2 -lcurl -lssl -lcrypto -llzma"' +buildopts = '''CC="$CC" CFLAGS="$CFLAGS" SAMTOOLS_LIBDIR="$EBROOTSAMTOOLS/lib" + LIBS="$LIBS -lhts -lbam -lz -lbz2 -lcurl -lssl -lcrypto -llzma"''' files_to_copy = [ (['bamFilters'], 'bin'), @@ -34,4 +35,3 @@ sanity_check_paths = { } sanity_check_commands = ['bamFilters -h 2>&1 | grep "Usage"'] - From cf9f3ee8f3cf666ec75061ab57c2090d11883760 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 24 Nov 2022 15:26:28 +0100 Subject: [PATCH 5608/9987] fixed line too long --- .../b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb index 75f1c57d85f..158a44d6dd8 100644 --- a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb @@ -22,8 +22,8 @@ dependencies = [ ('bzip2', '1.0.8'), ] prebuildopts = 'mkdir obj && ' -buildopts = '''CC="$CC" CFLAGS="$CFLAGS" SAMTOOLS_LIBDIR="$EBROOTSAMTOOLS/lib" - LIBS="$LIBS -lhts -lbam -lz -lbz2 -lcurl -lssl -lcrypto -llzma"''' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" SAMTOOLS_LIBDIR="$EBROOTSAMTOOLS/lib"' +buildopts += ' LIBS="$LIBS -lhts -lbam -lz -lbz2 -lcurl -lssl -lcrypto -llzma"' files_to_copy = [ (['bamFilters'], 'bin'), From 73349af426ba4f81cfac40b3ee0fd56744983ed1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Nov 2022 15:53:21 +0100 Subject: [PATCH 5609/9987] adding easyconfigs: Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb --- .../Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0a9f224eba9 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx-RTD-Theme' +version = '1.1.1' + +homepage = 'https://sphinx-rtd-theme.readthedocs.io' +description = """Sphinx theme was designed to provide a great reader experience + for documentation users on both desktop and mobile devices""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [('Python', '3.8.6')] + +use_pip = True +exts_download_dep_fail = True + +exts_list = [ + ('sphinx_rtd_theme', version, { + 'checksums': ['6146c845f1e1947b3c3dd4432c28998a1693ccc742b4f9ad7c63129f0757c103'], + }), +] + +moduleclass = 'vis' From 40fa15da4cc66bea24d8f9d6b3a64baaa4a01666 Mon Sep 17 00:00:00 2001 From: guacke Date: Thu, 24 Nov 2022 16:53:28 +0100 Subject: [PATCH 5610/9987] adding easyconfigs: HighFive-2.6.2-foss-2021a.eb --- .../h/HighFive/HighFive-2.6.2-foss-2021a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb new file mode 100644 index 00000000000..402ae469606 --- /dev/null +++ b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'HighFive' +version = '2.6.2' + +homepage = 'https://github.com/BlueBrain/HighFive' +description = """HighFive is a modern header-only C++11 friendly interface for libhdf5.""" + +toolchain = {'name': 'foss', 'version' : '2021a'} + +github_account = 'BlueBrain' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ab51b9fbb49e877dd1aa7b53b4b26875f41e4e0b8ee0fc2f1d735e0d1e43d708'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1') +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('Boost', '1.76.0'), + ('Eigen', '3.3.9'), +] + +sanity_check_paths = { + 'files' : ['include/highfive/H5File.hpp'], + 'dirs' : [], +} + +configopts = '-DHIGHFIVE_USE_EIGEN=ON' + +moduleclass = 'lib' \ No newline at end of file From e1ea5df5ee45f8f4336002f90a11c0d8e272f478 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Thu, 24 Nov 2022 16:43:37 +0000 Subject: [PATCH 5611/9987] Make sure VTK finds the specified Python --- easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb | 1 + easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb index b4161f95eaf..c92d21af64b 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -54,6 +54,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " # Python configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Other configopts += "-DVTK_USE_MPI=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb index b6987d9bb81..c2ca95e963f 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb @@ -49,6 +49,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " # Python configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Other configopts += "-DVTK_USE_MPI=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" From 231f4477cadb15978b6cec96c58320589ca7c090 Mon Sep 17 00:00:00 2001 From: guacke Date: Thu, 24 Nov 2022 19:33:53 +0100 Subject: [PATCH 5612/9987] style fixes --- .../easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb index 402ae469606..8fc40328d05 100644 --- a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb @@ -6,7 +6,7 @@ version = '2.6.2' homepage = 'https://github.com/BlueBrain/HighFive' description = """HighFive is a modern header-only C++11 friendly interface for libhdf5.""" -toolchain = {'name': 'foss', 'version' : '2021a'} +toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'BlueBrain' source_urls = [GITHUB_SOURCE] @@ -25,10 +25,10 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/highfive/H5File.hpp'], - 'dirs' : [], + 'files': ['include/highfive/H5File.hpp'], + 'dirs': [], } configopts = '-DHIGHFIVE_USE_EIGEN=ON' -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' From 1218b03af4935fcb966673a092aa13cc8b103f45 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Nov 2022 22:36:31 +0100 Subject: [PATCH 5613/9987] make test_pr_sanity_check_paths aware of JuliaBundle --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 374e82ddb0c..82f50ce177d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1092,9 +1092,9 @@ def test_pr_sanity_check_paths(self): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # some generic easyblocks already have a decent customised sanity_check_paths, - # including CMakePythonPackage, GoPackage, PythonBundle & PythonPackage; + # including CMakePythonPackage, GoPackage, JuliaBundle, PythonBundle & PythonPackage; # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. - whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'ModuleRC', + whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'ModuleRC', 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, From d8dea68a53dfdf34c3962dcf65652e60fa9d0d6b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 25 Nov 2022 09:05:23 +0100 Subject: [PATCH 5614/9987] update Coreutils: add patch for older glibc version --- .../Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb | 6 ++- .../Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb | 6 ++- ...tils-9.1_avoid-syntax-error-on-glibc.patch | 43 +++++++++++++++++++ 3 files changed, 53 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/c/Coreutils/Coreutils-9.1_avoid-syntax-error-on-glibc.patch diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb index c17a9e2fafd..bf09e2c9248 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb @@ -15,7 +15,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'] +patches = ['Coreutils-9.1_avoid-syntax-error-on-glibc.patch'] +checksums = [ + {'coreutils-9.1.tar.xz': '61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'}, + {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, +] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb index d180e31a737..020674819a0 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb @@ -15,7 +15,11 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'] +patches = ['Coreutils-9.1_avoid-syntax-error-on-glibc.patch'] +checksums = [ + {'coreutils-9.1.tar.xz': '61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'}, + {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, +] builddependencies = [('binutils', '2.39')] diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1_avoid-syntax-error-on-glibc.patch b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1_avoid-syntax-error-on-glibc.patch new file mode 100644 index 00000000000..9a0cf753d29 --- /dev/null +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1_avoid-syntax-error-on-glibc.patch @@ -0,0 +1,43 @@ +From 84863a1c4dc8cca8fb0f6f670f67779cdd2d543b Mon Sep 17 00:00:00 2001 +From: Bruno Haible +Date: Sat, 30 Apr 2022 14:09:00 +0200 +Subject: string: Avoid syntax error on glibc systems with GCC 11. + +Reported by Tom Tromey in + +and by Satadru Pramanik in +. + +* lib/string.in.h (strndup): Don't rededeclare strndup if it is defined +as a macro. +--- + ChangeLog | 10 ++++++++++ + lib/string.in.h | 4 ++-- + 2 files changed, 12 insertions(+), 2 deletions(-) + + stdlib: Fix error in C++ mode on glibc systems (regr. 2022-04-13). +diff --git a/lib/string.in.h b/lib/string.in.h +index b6840fa..33160b2 100644 +--- a/lib/string.in.h ++++ b/lib/string.in.h +@@ -583,7 +583,7 @@ _GL_FUNCDECL_RPL (strndup, char *, + _GL_ATTRIBUTE_MALLOC _GL_ATTRIBUTE_DEALLOC_FREE); + _GL_CXXALIAS_RPL (strndup, char *, (char const *__s, size_t __n)); + # else +-# if !@HAVE_DECL_STRNDUP@ || __GNUC__ >= 11 ++# if !@HAVE_DECL_STRNDUP@ || (__GNUC__ >= 11 && !defined strndup) + _GL_FUNCDECL_SYS (strndup, char *, + (char const *__s, size_t __n) + _GL_ARG_NONNULL ((1)) +@@ -593,7 +593,7 @@ _GL_CXXALIAS_SYS (strndup, char *, (char const *__s, size_t __n)); + # endif + _GL_CXXALIASWARN (strndup); + #else +-# if __GNUC__ >= 11 ++# if __GNUC__ >= 11 && !defined strndup + /* For -Wmismatched-dealloc: Associate strndup with free or rpl_free. */ + _GL_FUNCDECL_SYS (strndup, char *, + (char const *__s, size_t __n) +-- +cgit v1.1 + From e34acae5bf6f2fa7a62fd76ea91ff4c4b3fa337c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 25 Nov 2022 09:44:57 +0100 Subject: [PATCH 5615/9987] update Coreutils: fix E501 line too long --- .../easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb | 3 ++- .../easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb index bf09e2c9248..7279f966bb8 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-11.3.0.eb @@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_XZ] patches = ['Coreutils-9.1_avoid-syntax-error-on-glibc.patch'] checksums = [ {'coreutils-9.1.tar.xz': '61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'}, - {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, + {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': + '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, ] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb index 020674819a0..52a1be553ba 100644 --- a/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/c/Coreutils/Coreutils-9.1-GCCcore-12.2.0.eb @@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_XZ] patches = ['Coreutils-9.1_avoid-syntax-error-on-glibc.patch'] checksums = [ {'coreutils-9.1.tar.xz': '61a1f410d78ba7e7f37a5a4f50e6d1320aca33375484a3255eddf17a38580423'}, - {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, + {'Coreutils-9.1_avoid-syntax-error-on-glibc.patch': + '57d081aaef10c65f34798475821e75352e57cc2248384a7f82e0960234a6b9d6'}, ] builddependencies = [('binutils', '2.39')] From 1593e419b60dc6f7f4e58b3c1f0c44f7f6ac6d9b Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 25 Nov 2022 11:01:15 +0100 Subject: [PATCH 5616/9987] Disable RTTI when using flang project --- .../easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb index 06fb908fe9f..f70ecde5774 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb @@ -41,8 +41,13 @@ dependencies = [ ('Python', '3.10.4'), ] +# enabling RTTI makes the flang compiler need to link to libc++ so instead of +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 +# you would need +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++ +enable_rtti = False + assertions = True -enable_rtti = True python_bindings = True skip_all_tests = True From de68939a253670d92cac32fce497f5c800b59c83 Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 25 Nov 2022 11:08:01 +0100 Subject: [PATCH 5617/9987] adding easyconfigs: nano-7.0-GCCcore-11.3.0.eb --- .../n/nano/nano-7.0-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/nano/nano-7.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nano/nano-7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nano/nano-7.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..37267b01fc7 --- /dev/null +++ b/easybuild/easyconfigs/n/nano/nano-7.0-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +easyblock = 'ConfigureMake' + +name = 'nano' +version = '7.0' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['767d595237a4b40b981e2daaeb31de94283d60b1fae03fbd52a67d95c454518a'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('ncurses', '6.3')] + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' From 32b0374e6674f9ddea4de2c3e2ff663ac24e590a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 25 Nov 2022 11:41:45 +0100 Subject: [PATCH 5618/9987] make SAMtools a build dependency --- .../b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb index 158a44d6dd8..82f31b5dfb2 100644 --- a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb @@ -14,10 +14,11 @@ source_urls = ['https://github.com/institut-de-genomique/bamFilters/archive/'] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] checksums = ['63a2a57093f0d360ce21775de8bb118e60cbd8856593e02c608f930745e1b463'] +builddependencies = [('SAMtools', '1.13')] # libbam.a, is provided by SAMtools only up to version 1.13 + dependencies = [ ('HTSlib', '1.15.1'), ('BamTools', '2.5.2'), - ('SAMtools', '1.13'), ('zlib', '1.2.12'), ('bzip2', '1.0.8'), ] From dd920df794a7221b7ef157295397b3a4a28341e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Nov 2022 15:22:08 +0100 Subject: [PATCH 5619/9987] add HGNChelper extension to R 4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index e3da8a7d9fa..3e4080c1ebf 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3364,6 +3364,9 @@ exts_list = [ ('LMERConvenienceFunctions', '3.0', { 'checksums': ['eb430de9fbf836173f716960d60afc2de91de7f986471f406c3ca9027142e849'], }), + ('HGNChelper', '0.8.1', { + 'checksums': ['aa3f0b3a8691ed93d63bec8f36d2954c6fcfd0b8b3efc705379248544c999363'], + }), ] moduleclass = 'lang' From 5644eb72a00df067560a8e4bce84f05f30cbd10e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 25 Nov 2022 15:43:49 +0100 Subject: [PATCH 5620/9987] adding easyconfigs: cuTENSOR-1.6.1.5-CUDA-11.7.0.eb --- .../cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb new file mode 100644 index 00000000000..32caad1f155 --- /dev/null +++ b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'cuTENSOR' +local_shortver = '1.6.1' +version = local_shortver + '.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cutensor' +description = """The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, + reduction and elementwise operations.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cutensor/redist/libcutensor/linux-x86_64/'] +sources = ['libcutensor-linux-x86_64-%(version)s-archive.tar.xz'] +checksums = ['793b425c30ffd423c4f3a2e94acaf4fcb6752264aa73b74695a002dd2fe94b1a'] + +local_cudamajver = '11' +dependencies = [('CUDA', local_cudamajver + '.7.0')] + +sanity_check_paths = { + 'files': ['include/cutensor.h', 'include/cutensor/types.h', + 'lib/%s/libcutensor.%s' % (local_cudamajver, SHLIB_EXT), + 'lib/%s/libcutensor_static.a' % local_cudamajver], + 'dirs': [], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib/%s' % local_cudamajver], + 'LIBRARY_PATH': ['lib/%s' % local_cudamajver], +} + +moduleclass = 'lib' From f6d050dfa43a3633aa45ddf755c4342f2dda6e30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Nov 2022 16:18:25 +0100 Subject: [PATCH 5621/9987] minor cleanup + use proper versionsuffix in Blender 3.3.1 easyconfig --- ...> Blender-3.3.1-linux-x86_64-CUDA-11.7.0.eb} | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/b/Blender/{Blender-3.3.1.eb => Blender-3.3.1-linux-x86_64-CUDA-11.7.0.eb} (73%) diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb b/easybuild/easyconfigs/b/Blender/Blender-3.3.1-linux-x86_64-CUDA-11.7.0.eb similarity index 73% rename from easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb rename to easybuild/easyconfigs/b/Blender/Blender-3.3.1-linux-x86_64-CUDA-11.7.0.eb index 7669c41af2b..096a48791f5 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-3.3.1-linux-x86_64-CUDA-11.7.0.eb @@ -2,23 +2,18 @@ easyblock = 'PackedBinary' name = 'Blender' version = '3.3.1' -versionsuffix = '' +versionsuffix = '-linux-x86_64-CUDA-%(cudaver)s' homepage = 'https://www.blender.org/' description = """Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.""" -toolchain = {'name': 'system', 'version': ''} +toolchain = SYSTEM -sources = ['blender-%(version)s-linux-x64.tar.xz'] source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender%(version_major_minor)s/'] -patches = [] -checksums = [ - '3089a485dd621785d7a702089aba72d07b8f733a362e901ec1449b9a379546f2' -] - -builddependencies = [] +sources = ['blender-%(version)s-linux-x64.tar.xz'] +checksums = ['3089a485dd621785d7a702089aba72d07b8f733a362e901ec1449b9a379546f2'] dependencies = [ ('CUDA', '11.7.0') @@ -26,7 +21,9 @@ dependencies = [ sanity_check_paths = { 'files': ['blender', 'blender-softwaregl'], - 'dirs': ['3.3'] + 'dirs': ['%(version_major_minor)s'], } +sanity_check_commands = ["blender --help"] + moduleclass = 'vis' From ec57679185f46c6c2bee9b441810b158d57791bd Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Fri, 25 Nov 2022 17:10:22 +0000 Subject: [PATCH 5622/9987] adding easyconfigs: Fiji-2.9.0-Java-8.eb --- .../easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb new file mode 100644 index 00000000000..a0253523720 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb @@ -0,0 +1,49 @@ +easyblock = 'PackedBinary' + +name = 'Fiji' +version = '2.9.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://fiji.sc' +description = """Fiji is an image processing package—a 'batteries-included' distribution of + ImageJ, bundling a lot of plugins which facilitate scientific image analysis. +This release is based on ImageJ-2.1.0 and Fiji-2.1.1""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s/'] +sources = ['fiji-%(version)s-nojre.zip'] +checksums = ['970fb80cf2a4fe8bfcecc2cc9a8617b9ab28f19fbe229ea6ae2f7f42674c8a42'] + +dependencies = [('Java', '8', '', SYSTEM)] + +postinstallcmds = [ + # Remove binaries for other platforms + 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}', + # Enable any update site (edit existing site with same parameters to enable it) + # Full list at https://imagej.github.io/list-of-update-sites/ + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' + ' https://sites.imagej.net/ImageScience/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' + ' https://sites.imagej.net/Tboudier/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ilastik"' + ' https://sites.imagej.net/Ilastik/', + # Add a new update site + # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' + # ' https://site.url/NewName/', + # Update the installation + '%(installdir)s/ImageJ-linux64 --headless --update update', +] + +sanity_check_paths = { + 'files': ['ImageJ-linux64'], + 'dirs': [], +} + +modloadmsg = """ +Additional plugins can be installed in your $HOME/.plugins folder or requested to user support +Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless` +More information at https://imagej.net/Headless +""" + +moduleclass = 'vis' From cd5a96ce1bf1ee9120042544d578039f442c7c74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 25 Nov 2022 18:06:20 +0000 Subject: [PATCH 5623/9987] Include missing easyconfigs --- .../FFTW.MPI-3.3.10-nvompi-2022.07.eb | 19 ++++++ .../easyconfigs/n/nvompi/nvompi-2022.07.eb | 19 ++++++ .../OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb | 65 +++++++++++++++++++ 3 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-nvompi-2022.07.eb create mode 100644 easybuild/easyconfigs/n/nvompi/nvompi-2022.07.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-nvompi-2022.07.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-nvompi-2022.07.eb new file mode 100644 index 00000000000..48501672627 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-nvompi-2022.07.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'nvompi', 'version': '2022.07'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/nvompi/nvompi-2022.07.eb b/easybuild/easyconfigs/n/nvompi/nvompi-2022.07.eb new file mode 100644 index 00000000000..1a1647cbfa2 --- /dev/null +++ b/easybuild/easyconfigs/n/nvompi/nvompi-2022.07.eb @@ -0,0 +1,19 @@ +easyblock = 'Toolchain' + +name = 'nvompi' +version = '2022.07' + +homepage = '(none)' +description = 'NVHPC based compiler toolchain, including OpenMPI for MPI support.' + +toolchain = SYSTEM + +local_compiler = ('NVHPC', '22.7-CUDA-11.7.0') + +dependencies = [ + local_compiler, + ('OpenMPI', '4.1.4', '', local_compiler), + ('CUDA', '11.7.0', '', SYSTEM), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb new file mode 100644 index 00000000000..34c4551c73e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,65 @@ +name = 'OpenMPI' +version = '4.1.4' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', +] +checksums = [ + '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d', # openmpi-4.1.4.tar.bz2 + # OpenMPI-4.1.1_build-with-internal-cuda-header.patch + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83', + # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', +] + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('Perl', '5.34.1'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('hwloc', '2.7.1'), + ('libevent', '2.1.12'), + ('UCX', '1.12.1'), + ('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'), + ('libfabric', '1.15.1'), + ('PMIx', '4.1.2'), + ('UCC', '1.0.0'), + ('UCC-CUDA', '1.0.0', '-CUDA-%(cudaver)s'), +] + +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' +configopts += ' CC=pgcc CXX=pgc++ FC=pgfortran' + +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From 579c97a9f3909ffdd2bae39485db94749b454ce6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 25 Nov 2022 18:24:42 +0000 Subject: [PATCH 5624/9987] Fix configopts for BLIS --- .../easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb index 9928532de5e..ec901262836 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -28,8 +28,8 @@ builddependencies = [ ] preconfigopts = "sed -i 's/LINKER.*/LINKER := nvc/' common.mk &&" -configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' -configopts += ' --complex-return=intel CC=gcc CFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno"' +configopts = '--enable-cblas --enable-threading=openmp --enable-shared' +configopts += ' --complex-return=intel CC=gcc CFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno" auto' runtest = 'check' From 876bdb05adbbcc76565a20fa2d19fe24b079919c Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 25 Nov 2022 22:31:59 +0100 Subject: [PATCH 5625/9987] adding easyconfigs: Vim-9.0.0950-GCCcore-11.3.0.eb --- .../v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..cde4ee8d056 --- /dev/null +++ b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +# Last contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +easyblock = 'ConfigureMake' + +name = 'Vim' +version = '9.0.0950' + +homepage = 'http://www.vim.org' +description = """ Vim is an advanced text editor that seeks to provide the power + of the de-facto Unix editor 'Vi', with a more complete feature set. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/vim/vim/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c53542fbec58362c3a5ed60a0fe5aa219ef49cd15d9545311ec0f6d1f03e2fdd'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('PCRE', '8.45') +] + +configopts = '--with-features=huge --enable-python3interp=yes --enable-perlinterp=yes' + +sanity_check_paths = { + 'files': ['bin/vim', 'bin/vimtutor', 'bin/xxd'], + 'dirs': ['bin', 'share'], +} + +moduleclass = 'tools' From 59bcc0d5b70753a1a32b229456caedecfdf6873c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Fri, 25 Nov 2022 22:37:13 +0100 Subject: [PATCH 5626/9987] Update Vim-9.0.0950-GCCcore-11.3.0.eb Add basic sanity check. --- easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb index cde4ee8d056..3ebc9ac6bd5 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': ['bin', 'share'], } +sanity_check_commands = ['vim --version'] + moduleclass = 'tools' From 868d0e04dbfa240714de7e71a0de7d27b156f63b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 17:00:18 +0100 Subject: [PATCH 5627/9987] adding easyconfigs: CPPE-0.3.1-GCC-11.3.0.eb --- .../c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..73a254132a8 --- /dev/null +++ b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'CPPE' +version = '0.3.1' + +homepage = 'https://github.com/maxscheurer/cppe' +description = """CPPE is an open-source, light-weight C++ and Python library for Polarizable +Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE +for ground-state self-consistent field (SCF) calculations and post-SCF methods. +A convenient Python interface is also available.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'maxscheurer' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['38d4230ba3ace78936049c23ad4b1fe9e704fd250ec57cc9733cb3904b62cf7c'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pybind11', '2.9.2'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('cppe', version, { + 'download_dep_fail': True, + 'use_pip': True, + 'checksums': ['b0aef578d6919f8c103d4d4a9fcd3db481bd73c59c157985f52bf62477425d6c'], + }), +] + +sanity_check_paths = { + 'files': ['lib/libcppe.%s' % SHLIB_EXT], + 'dirs': ['include/cppe', 'lib/python%(pyshortver)s/site-packages', 'share/cmake'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From 818c6bc1011f6f78b799ef90ce9a1ddda106c1be Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 17:00:55 +0100 Subject: [PATCH 5628/9987] adding easyconfigs: PyBerny-0.6.3-foss-2022a.eb --- .../p/PyBerny/PyBerny-0.6.3-foss-2022a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.eb b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.eb new file mode 100644 index 00000000000..1d3ffa473d1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.eb @@ -0,0 +1,38 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'PyBerny' +version = '0.6.3' + +homepage = 'https://github.com/jhrmnn/pyberny' +description = """PyBerny is an optimizer of molecular geometries with respect to the total energy, +using nuclear gradient information.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True + +exts_list = [ + ('pyberny', version, { + 'modulename': 'berny', + 'checksums': ['b4bd9d3d2d58261e8f1d91b8204cc563617044d4b9daf6aae8feee31893cb336'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/berny'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["berny -h"] + +moduleclass = 'chem' From 74bba6153408a470a0aa939c6f12d7e49fbacada Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 17:01:47 +0100 Subject: [PATCH 5629/9987] adding easyconfigs: NECI-20220711-foss-2022a.eb --- .../n/NECI/NECI-20220711-foss-2022a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb b/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb new file mode 100644 index 00000000000..71c70f8ab4a --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMakeCp' +name = 'NECI' +version = '20220711' +_commit = 'd7a9e87ed6a4a29479dc25fbf36a7bb556c3f5a3' + +homepage = 'https://github.com/ghb24/NECI_STABLE' +description = """Standalone NECI codebase designed for FCIQMC and other stochastic quantum +chemistry methods.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +sources = [{ + 'git_config': { + 'url': 'https://github.com/ghb24', + 'repo_name': 'NECI_STABLE', + 'recursive': True, + 'commit': _commit, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +dependencies = [ + ('HDF5', '1.12.2'), +] + +# enable support for HDF5 +configopts = "-DENABLE_HDF5=ON" + +test_cmd = 'ctest' +runtest = '-j' + +files_to_copy = ['bin', 'lib', (['modules'], 'include')] + +_binaries = ['dneci', 'kdneci', 'kmneci', 'kneci', 'mneci', 'neci'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/lib%s.a' % x for x in _binaries], + 'dirs': ['include'], +} + +moduleclass = 'chem' From 73f8903ebb2034e6f2c26f66da4c1bcc040f4077 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 17:02:57 +0100 Subject: [PATCH 5630/9987] adding easyconfigs: Dice-20221025-foss-2022a.eb and patches: Dice-20221025_icpt-mkl-to-flexiblas.patch --- .../d/Dice/Dice-20221025-foss-2022a.eb | 50 +++++++++++++++++++ .../Dice-20221025_icpt-mkl-to-flexiblas.patch | 23 +++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dice/Dice-20221025-foss-2022a.eb create mode 100644 easybuild/easyconfigs/d/Dice/Dice-20221025_icpt-mkl-to-flexiblas.patch diff --git a/easybuild/easyconfigs/d/Dice/Dice-20221025-foss-2022a.eb b/easybuild/easyconfigs/d/Dice/Dice-20221025-foss-2022a.eb new file mode 100644 index 00000000000..b4315ca4f5f --- /dev/null +++ b/easybuild/easyconfigs/d/Dice/Dice-20221025-foss-2022a.eb @@ -0,0 +1,50 @@ +easyblock = 'MakeCp' + +name = 'Dice' +version = '20221025' +_commit = 'f14e4249c69ec30b53491297049546f3ef1d8a55' + +homepage = 'https://github.com/sanshar/Dice' +description = """Dice contains code for performing SHCI, VMC, GFMC, DMC, FCIQMC, stochastic MRCI +and SC-NEVPT2, and AFQMC calculations with a focus on ab initio systems.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'cstd': 'c++14'} + +github_account = 'sanshar' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +patches = ['Dice-20221025_icpt-mkl-to-flexiblas.patch'] +checksums = [ + {'Dice-20221025.tar.gz': '56da2c0f4bc3e9a786ae8c3193cb06df5cf20a90af29ee95ad39a10e525db315'}, + {'Dice-20221025_icpt-mkl-to-flexiblas.patch': 'a712913e5b372017be0ea7508479094e96f06c0cfd46d0bfe61d85ef42cd1386'}, +] + +builddependencies = [ + ('Eigen', '3.4.0'), + ('git', '2.36.0', '-nodocs'), +] + +dependencies = [ + ('Boost.MPI', '1.79.0'), + ('HDF5', '1.12.2'), +] + +# Use build environment defined by EB +prebuildopts = "sed -i 's/^FLAGS_BASE =.*/FLAGS_BASE=$(CXXFLAGS) -g -w -I. $(CPPFLAGS)/' Makefile && " +buildopts = 'CXX="$MPICXX" USE_INTEL="no" HAS_AVX2="no" ' # avoid changes to -march +buildopts += 'INCLUDE_MKL="-I${EBROOTOPENBLAS}/include" LIB_MKL="${LIBBLAS}" ' # use OpenBLAS +buildopts += 'GIT_BRANCH="master" GIT_HASH="%s"' % _commit +buildopts += 'BOOST="${EBROOTBOOSTMPI}" ' +buildopts += 'EIGEN="${EBROOTEIGEN}/include" ' +buildopts += 'HDF5="${EBROOTHDF5}" ' + +files_to_copy = ['bin'] + +_binaries = ['Dice', 'DQMC', 'FCIQMC', 'GFMC', 'ICPT', 'VMC', 'ZDice2', 'ZSHCI'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/Dice/Dice-20221025_icpt-mkl-to-flexiblas.patch b/easybuild/easyconfigs/d/Dice/Dice-20221025_icpt-mkl-to-flexiblas.patch new file mode 100644 index 00000000000..8cf99685cd3 --- /dev/null +++ b/easybuild/easyconfigs/d/Dice/Dice-20221025_icpt-mkl-to-flexiblas.patch @@ -0,0 +1,23 @@ +Replace Intel MKL subroutines with FlexiBLAS wrappers +author: Alex Domingo (Vrije Universiteit Brussel) +--- a/executables/ICPT.cpp 2022-10-26 01:45:54.000000000 +0200 ++++ b/executables/ICPT.cpp 2022-11-26 11:23:28.845637000 +0100 +@@ -7,8 +7,7 @@ + #include "BlockContract.h" + #include "CxDefs.h" + #include "icpt.h" +-#include "mkl.h" +-#include "mkl_cblas.h" ++#include "flexiblas_api.h" + using ct::TArray; + using ct::FMemoryStack; + using boost::format; +@@ -25,7 +24,7 @@ + // - something to split up tensors (H) and combine them (RDM) + // regarding universal indices + +- mkl_set_num_threads(numthrds); ++ flexiblas_set_num_threads(numthrds); + + FJobContext + Job; From e5ba592dd6c81aeaf2eb06682e9b47a8a27be15f Mon Sep 17 00:00:00 2001 From: anselmicz Date: Sat, 26 Nov 2022 19:03:35 +0100 Subject: [PATCH 5631/9987] adding easyconfigs: HyperQueue-0.13.0.eb --- .../h/HyperQueue/HyperQueue-0.13.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb diff --git a/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb new file mode 100644 index 00000000000..59158297e6f --- /dev/null +++ b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb @@ -0,0 +1,28 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +easyblock = 'PackedBinary' + +name = 'HyperQueue' +version = '0.13.0' + +homepage = 'https://it4innovations.github.io/hyperqueue/' +description = """HyperQueue lets you build a computation plan consisting of a large amount of tasks +and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs +and distributes them to fully utilize allocated notes. +You thus do not have to manually aggregate your tasks into SLURM/PBS jobs.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/It4innovations/hyperqueue/releases/download/v%(version)s/'] +sources = ['hq-v%(version)s-linux-x64.tar.gz'] +checksums = ['4c3dac11cc01ef2a0c222099e484fd1b23ac52d8db234855ec1f0685543b4e0d'] + +sanity_check_paths = { + 'files': ['hq'], + 'dirs': [], +} + +sanity_check_commands = ['hq --version'] + +moduleclass = 'tools' From b431022f8bb856e4a5142ea711977216caf90423 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 19:04:46 +0100 Subject: [PATCH 5632/9987] move default extension parameters to exts_default_options in CPPE v0.3.1 --- easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb index 73a254132a8..b2a546120a1 100644 --- a/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb @@ -26,10 +26,13 @@ dependencies = [ ] exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} exts_list = [ ('cppe', version, { - 'download_dep_fail': True, - 'use_pip': True, + 'source_urls': [PYPI_SOURCE], 'checksums': ['b0aef578d6919f8c103d4d4a9fcd3db481bd73c59c157985f52bf62477425d6c'], }), ] From d02193954ad5c855ba4ece63e873cf42a3a9e553 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Sat, 26 Nov 2022 19:13:47 +0100 Subject: [PATCH 5633/9987] Update HyperQueue-0.13.0.eb fix typo --- easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb index 59158297e6f..bcb5f1b6be5 100644 --- a/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb +++ b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb @@ -9,7 +9,7 @@ version = '0.13.0' homepage = 'https://it4innovations.github.io/hyperqueue/' description = """HyperQueue lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs -and distributes them to fully utilize allocated notes. +and distributes them to fully utilize allocated nodes. You thus do not have to manually aggregate your tasks into SLURM/PBS jobs.""" toolchain = SYSTEM From eabbbddc00ce7c196dc78f324cb843e9eb23a792 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 27 Nov 2022 01:06:48 +0100 Subject: [PATCH 5634/9987] Drop BLIS --- .../BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb | 44 ------------------- .../FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 3 +- 2 files changed, 1 insertion(+), 46 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb deleted file mode 100644 index ec901262836..00000000000 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'BLIS' -version = '0.9.0' - -homepage = 'https://github.com/flame/blis/' -description = """BLIS is a portable software framework for instantiating high-performance -BLAS-like dense linear algebra libraries.""" - -toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} - -source_urls = ['https://github.com/flame/blis/archive/'] -sources = ['%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s_disable_power9_kernels.patch', - '%(name)s-%(version)s_enable_ppc_autodetect.patch', -] -checksums = [ - '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz - # BLIS-0.9.0_disable_power9_kernels.patch - 'ed7a326bc5c5c21c42faefbec2fd7be609d1c7236981b466475edace39307279', - # BLIS-0.9.0_enable_ppc_autodetect.patch - 'f373fb252c0d14036fb631f048091976cceb02abb3e570a97fbaeac2fbb12328', -] -builddependencies = [ - ('Python', '3.10.4', '-bare'), - ('Perl', '5.34.1'), -] - -preconfigopts = "sed -i 's/LINKER.*/LINKER := nvc/' common.mk &&" -configopts = '--enable-cblas --enable-threading=openmp --enable-shared' -configopts += ' --complex-return=intel CC=gcc CFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno" auto' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['include/blis/cblas.h', 'include/blis/blis.h', - 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], - 'dirs': [], -} - -modextrapaths = {'CPATH': 'include/blis'} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb index 07c769edc08..36c0727160b 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -14,7 +14,6 @@ toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': builddependencies = [ ('CMake', '3.23.1'), ('Python', '3.10.4', '-bare'), # required for running the tests - ('BLIS', '0.9.0'), ] dependencies = [ @@ -23,7 +22,7 @@ dependencies = [ # note: first listed backend will be used as default by FlexiBLAS, # unless otherwise specified via easyconfig parameter flexiblas_default -local_backends = ['OpenBLAS', 'BLIS'] +local_backends = ['OpenBLAS'] # imkl supplies its backend via the imkl module, not as a dependency if ARCH == 'x86_64': From fc26d3c11c5baeae5915e91165fb90fc8c79da53 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 20 Oct 2022 16:54:02 +0200 Subject: [PATCH 5635/9987] adding easyconfigs: PyTorch-1.12.1-foss-2021a.eb, PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 129 ++++++++ .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 115 +++++++ ...2.1_fix-TestCudaFuser.test_unary_ops.patch | 26 ++ ...PyTorch-1.12.1_fix-TestTorch.test_to.patch | 21 ++ ...ch-1.12.1_fix-cuda-gcc-version-check.patch | 79 +++++ ...x-use-after-free-in-tensorpipe-agent.patch | 24 ++ .../PyTorch-1.12.1_fix-vsx-loadu.patch | 109 ++++++ .../PyTorch-1.12.1_fix-vsx-vector-funcs.patch | 310 ++++++++++++++++++ ...2.1_increase-test-adadelta-tolerance.patch | 22 ++ ...h-1.12.1_increase-tolerance-test_ops.patch | 27 ++ .../PyTorch-1.12.1_no-cuda-stubs-rpath.patch | 159 +++++++++ ...skip-ao-sparsity-test-without-fbgemm.patch | 26 ++ ...yTorch-1.12.1_skip-failing-grad-test.patch | 51 +++ 13 files changed, 1098 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..564c7ada0c8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,129 @@ +name = 'PyTorch' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), + ('hypothesis', '6.13.1'), +] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.5'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.6.2'), + ('SciPy-bundle', '2021.05'), + ('typing-extensions', '3.10.0.0'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.2.0'), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), + ('magma', '2.6.1', '-CUDA-%(cudaver)s'), + ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# The readelf sanity check command can be taken out once the TestRPATH test from +# https://github.com/pytorch/pytorch/pull/87593 is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb new file mode 100644 index 00000000000..cd38c8b8e9c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -0,0 +1,115 @@ +name = 'PyTorch' +version = '1.12.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), + ('hypothesis', '6.13.1'), +] + +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.5'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.6.2'), + ('SciPy-bundle', '2021.05'), + ('typing-extensions', '3.10.0.0'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.2.0'), + ('expecttest', '0.1.3'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch new file mode 100644 index 00000000000..28a8238fb30 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch @@ -0,0 +1,26 @@ +Fix test failure with a commit contained in https://github.com/pytorch/pytorch/pull/78244 + +From fade8da55e60a118c5595378896d34b862b2fcc3 Mon Sep 17 00:00:00 2001 +From: "S. Song" <41357537+shmsong@users.noreply.github.com> +Date: Mon, 23 May 2022 16:41:01 -0700 +Subject: [PATCH] patch python test for bfloat16 (#1724) + +* patch python test +--- + test/test_jit_cuda_fuser.py | 5 +++-- + 1 file changed, 3 insertions(+), 2 deletions(-) + +diff --git a/test/test_jit_cuda_fuser.py b/test/test_jit_cuda_fuser.py +index 48dd8a4659f1..324a758ff713 100644 +--- a/test/test_jit_cuda_fuser.py ++++ b/test/test_jit_cuda_fuser.py +@@ -598,7 +598,9 @@ def t(x: torch.Tensor, y: torch.Tensor): + # bfloat16 kernels instead of eager mode + # implementation, since mismatch in cast + # adds excessive noise. +- o = t(x.to(torch.float64), y.to(torch.float64)).to(torch.bfloat16) ++ o = t(x.to(torch.float64), y.to(torch.float64)) ++ if o.dtype.is_floating_point: ++ o = o.to(torch.bfloat16) + else: + o = t(x, y) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch new file mode 100644 index 00000000000..8d78d655b5b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch @@ -0,0 +1,21 @@ +A bug in PyTorch makes sparse Tensors report the wrong device making the test fail +when using multiple GPUs. +Fixed in 1.13 by https://github.com/pytorch/pytorch/pull/85240 + +Here change the test to only run the check with the default CUDA device. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_torch.py b/test/test_torch.py +index 0c9c00984c..99285b20dc 100644 +--- a/test/test_torch.py ++++ b/test/test_torch.py +@@ -7687,7 +7687,7 @@ tensor([[[1.+1.j, 1.+1.j, 1.+1.j, ..., 1.+1.j, 1.+1.j, 1.+1.j], + + if torch.cuda.is_available(): + for non_blocking in [True, False]: +- for cuda in ['cuda', 'cuda:0' if torch.cuda.device_count() == 1 else 'cuda:1']: ++ for cuda in ['cuda']: + b = torch.tensor(5., device=cuda) + test_copy_behavior(b, non_blocking) + self.assertEqual(b.device, b.to(cuda, non_blocking=non_blocking).device) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch new file mode 100644 index 00000000000..def8bc857bc --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch @@ -0,0 +1,79 @@ +Update CUDA <-> compiler version compatibility matrix +See https://github.com/pytorch/pytorch/pull/86360 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/utils/cpp_extension.py b/torch/utils/cpp_extension.py +index aed4fd5004..fca125ce26 100644 +--- a/torch/utils/cpp_extension.py ++++ b/torch/utils/cpp_extension.py +@@ -48,20 +48,30 @@ MINIMUM_MSVC_VERSION = (19, 0, 24215) + # The following values were taken from the following GitHub gist that + # summarizes the minimum valid major versions of g++/clang++ for each supported + # CUDA version: https://gist.github.com/ax3l/9489132 ++# Or from include/crt/host_config.h in the CUDA SDK ++# The second value is the exclusive(!) upper bound, i.e. min <= version < max + CUDA_GCC_VERSIONS = { +- '10.2': (MINIMUM_GCC_VERSION, (8, 0, 0)), +- '11.1': (MINIMUM_GCC_VERSION, (10, 0, 0)), +- '11.2': (MINIMUM_GCC_VERSION, (10, 0, 0)), +- '11.3': (MINIMUM_GCC_VERSION, (10, 0, 0)), +- '11.4': ((6, 0, 0), (10, 0, 0)) ++ '10.2': (MINIMUM_GCC_VERSION, (9, 0)), ++ '11.0': (MINIMUM_GCC_VERSION, (10, 0)), ++ '11.1': (MINIMUM_GCC_VERSION, (11, 0)), ++ '11.2': (MINIMUM_GCC_VERSION, (11, 0)), ++ '11.3': (MINIMUM_GCC_VERSION, (11, 0)), ++ '11.4': ((6, 0, 0), (12, 0)), ++ '11.5': ((6, 0, 0), (12, 0)), ++ '11.6': ((6, 0, 0), (12, 0)), ++ '11.7': ((6, 0, 0), (12, 0)), + } + ++MINIMUM_CLANG_VERSION = (3, 3, 0), + CUDA_CLANG_VERSIONS = { +- '10.2': ((3, 3, 0), (8, 0, 0)), +- '11.1': ((6, 0, 0), (10, 0, 0)), +- '11.2': ((6, 0, 0), (10, 0, 0)), +- '11.3': ((6, 0, 0), (10, 0, 0)), +- '11.4': ((6, 0, 0), (10, 0, 0)) ++ '10.2': (MINIMUM_CLANG_VERSION, (9, 0)), ++ '11.1': (MINIMUM_CLANG_VERSION, (11, 0)), ++ '11.2': (MINIMUM_CLANG_VERSION, (12, 0)), ++ '11.3': (MINIMUM_CLANG_VERSION, (12, 0)), ++ '11.4': (MINIMUM_CLANG_VERSION, (13, 0)), ++ '11.5': (MINIMUM_CLANG_VERSION, (13, 0)), ++ '11.6': (MINIMUM_CLANG_VERSION, (14, 0)), ++ '11.7': (MINIMUM_CLANG_VERSION, (14, 0)), + } + + +@@ -819,12 +829,11 @@ class BuildExtension(build_ext, object): + if cuda_str_version not in cuda_compiler_bounds: + warnings.warn(f'There are no {compiler_name} version bounds defined for CUDA version {cuda_str_version}') + else: +- min_compiler_version, max_compiler_version = cuda_compiler_bounds[cuda_str_version] ++ min_compiler_version, max_excl_compiler_version = cuda_compiler_bounds[cuda_str_version] + min_compiler_version_str = '.'.join(map(str, min_compiler_version)) +- max_compiler_version_str = '.'.join(map(str, max_compiler_version)) ++ max_excl_compiler_version_str = '.'.join(map(str, max_excl_compiler_version)) + +- version_bound_str = f'>={min_compiler_version_str}' +- version_bound_str = f'{version_bound_str}, <={max_compiler_version_str}' ++ version_bound_str = f'>={min_compiler_version_str}, <{max_excl_compiler_version_str}' + + if compiler_version < TorchVersion(min_compiler_version_str): + raise RuntimeError( +@@ -832,10 +841,10 @@ class BuildExtension(build_ext, object): + f'than the minimum required version by CUDA {cuda_str_version} ({min_compiler_version_str}). ' + f'Please make sure to use an adequate version of {compiler_name} ({version_bound_str}).' + ) +- elif compiler_version > TorchVersion(max_compiler_version_str): ++ elif compiler_version >= TorchVersion(max_excl_compiler_version_str): + raise RuntimeError( + f'The current installed version of {compiler_name} ({compiler_version}) is greater ' +- f'than the maximum required version by CUDA {cuda_str_version} ({max_compiler_version_str}). ' ++ f'than the maximum required version by CUDA {cuda_str_version}. ' + f'Please make sure to use an adequate version of {compiler_name} ({version_bound_str}).' + ) + else: diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch new file mode 100644 index 00000000000..e0f64391792 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch @@ -0,0 +1,24 @@ +Fix an invalid usage of `erase` leading to a use after free. +See https://github.com/pytorch/pytorch/issues/87359 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/csrc/distributed/rpc/tensorpipe_agent.cpp b/torch/csrc/distributed/rpc/tensorpipe_agent.cpp +index 39935febe6..c160d1c771 100644 +--- a/torch/csrc/distributed/rpc/tensorpipe_agent.cpp ++++ b/torch/csrc/distributed/rpc/tensorpipe_agent.cpp +@@ -1261,9 +1261,11 @@ void TensorPipeAgent::updateGroupMembership( + workerNameToInfo_.erase(name); + workerNameToURL_.erase(name); + +- for (const auto& it : reverseDeviceMaps_) { +- if (reverseDeviceMaps.find(it.first) == reverseDeviceMaps.end()) { +- reverseDeviceMaps_.erase(it.first); ++ for(auto iter = reverseDeviceMaps_.begin(); iter != reverseDeviceMaps_.end(); ) { ++ if (reverseDeviceMaps.find(iter->first) == reverseDeviceMaps.end()) { ++ iter = reverseDeviceMaps_.erase(iter); ++ } else { ++ ++iter; + } + } + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch new file mode 100644 index 00000000000..839c6567bb2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch @@ -0,0 +1,109 @@ +Fix access to unitialized memory resulting in e.g. failures in TestNNDeviceTypeCPU.test_groupnorm_nhwc_cpu_float32 +See https://github.com/pytorch/pytorch/issues/32502 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +index cb8bb78597..f5084f2101 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +@@ -142,7 +142,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +index 8445a31fb3..b4e35acfb4 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +@@ -196,7 +196,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +index c53b7c792e..810e79ebfe 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +@@ -171,7 +171,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +index 0267c40e1e..1a6aec7dbe 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +@@ -180,7 +180,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +index 464a13c9f5..7c300c8087 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +@@ -269,7 +269,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +index 6ef6147447..c98ab6215e 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +@@ -199,7 +199,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +index c0f1146d9d..a4171026a2 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +@@ -148,7 +148,7 @@ class Vectorized { + (vint64)vec_vsx_ld(offset16, dptr)}; + } + +- __at_align__ double tmp_values[size()]; ++ __at_align__ double tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h +index c3cec14a5b..a85730c9a6 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h +@@ -81,7 +81,7 @@ struct Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch new file mode 100644 index 00000000000..56a02bdac0e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch @@ -0,0 +1,310 @@ +That code fails for large values such as sin(1e20) producing inf. +See https://github.com/pytorch/pytorch/issues/85978 +and https://github.com/pytorch/pytorch/pull/86453 +Use the Sleef functions similar to the double variants. + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +index 77cf3695ab912..8fe6cc25f0ee9 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +@@ -256,29 +256,29 @@ class Vectorized { + } + + Vectorized C10_ALWAYS_INLINE acos() const { +- return {Sleef_acosf4_u10vsx(_vec0), Sleef_acosf4_u10vsx(_vec1)}; ++ return {Sleef_acosf4_u10vsx(_vec0), Sleef_acosf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE asin() const { +- return {Sleef_asinf4_u10vsx(_vec0), Sleef_asinf4_u10vsx(_vec1)}; ++ return {Sleef_asinf4_u10vsx(_vec0), Sleef_asinf4_u10vsx(_vec1)}; + } + Vectorized atan() const { +- return {Sleef_atanf4_u10vsx(_vec0), Sleef_atanf4_u10vsx(_vec1)}; ++ return {Sleef_atanf4_u10vsx(_vec0), Sleef_atanf4_u10vsx(_vec1)}; + } + Vectorized atan2(const Vectorized& b) const { +- return {Sleef_atan2f4_u10vsx(_vec0, b._vec0), Sleef_atan2f4_u10vsx(_vec1, b._vec1)}; ++ return {Sleef_atan2f4_u10vsx(_vec0, b._vec0), Sleef_atan2f4_u10vsx(_vec1, b._vec1)}; + } + Vectorized copysign(const Vectorized &sign) const { + return {Sleef_copysignf4_vsx(_vec0, sign._vec0), Sleef_copysignf4_vsx(_vec1, sign._vec1)}; + } + Vectorized lgamma() const { +- return {Sleef_lgammaf4_u10vsx(_vec0), Sleef_lgammaf4_u10vsx(_vec1)}; ++ return {Sleef_lgammaf4_u10vsx(_vec0), Sleef_lgammaf4_u10vsx(_vec1)}; + } + Vectorized erf() const { +- return {Sleef_erff4_u10vsx(_vec0), Sleef_erff4_u10vsx(_vec1)}; ++ return {Sleef_erff4_u10vsx(_vec0), Sleef_erff4_u10vsx(_vec1)}; + } + + Vectorized erfc() const { +- return {Sleef_erfcf4_u15vsx(_vec0), Sleef_erfcf4_u15vsx(_vec1)}; ++ return {Sleef_erfcf4_u15vsx(_vec0), Sleef_erfcf4_u15vsx(_vec1)}; + } + + Vectorized erfinv() const { +@@ -301,133 +301,32 @@ class Vectorized { + } + + Vectorized C10_ALWAYS_INLINE exp() const { +- // implementation logic from avx_mathfun with some modifications from sleef +- // Express e**x = e**g 2**n +- /// = e**g e**( n loge(2) ) +- /// = e**( g + n loge(2) ) +- // +- auto tmp_x = *this; +- auto fx = (tmp_x * log2e_inv).round(); +- +- auto x = fx.madd(negln2f_hi, tmp_x); +- x = fx.madd(negln2f_lo, x); +- auto z = x * x; +- auto y = x.madd(exp_p0, exp_p1); +- y = y.madd(x, exp_p2); +- y = y.madd(x, exp_p3); +- y = y.madd(x, exp_p4); +- y = y.madd(x, exp_p5); +- y = y.madd(z, x) + one; +- +- // vm_pow2n 2^n +- vint32 imm0 = vec_signed(fx._vec0); +- vint32 imm1 = vec_signed(fx._vec1); +- // this pow2n logic is from Sleef code +- vint32 imm00 = imm0 >> 1; //>>1 +- vint32 imm01 = imm1 >> 1; +- vint32 imm10 = imm0 - imm00; +- vint32 imm11 = imm1 - imm01; +- imm00 = (imm00 + v0x7f) << vu_23; +- imm01 = (imm01 + v0x7f) << vu_23; +- imm10 = (imm10 + v0x7f) << vu_23; +- imm11 = (imm11 + v0x7f) << vu_23; +- // treat imm as float vector without conversion +- +- y._vec0 = (y._vec0 * (vfloat32)imm00) * (vfloat32)imm10; +- y._vec1 = (y._vec1 * (vfloat32)imm01) * (vfloat32)imm11; +- // boundary check +- auto tmp = blendv(y, v_inf, (Vectorized(exp_hi) <= tmp_x)); +- y = blendv(tmp, zero, (tmp_x < Vectorized(exp_lo))); +- +- return y; ++ return {Sleef_expf4_u10vsx(_vec0), Sleef_expf4_u10vsx(_vec1)}; + } + Vectorized expm1() const { +- return exp() - one; ++ return {Sleef_expm1f4_u10vsx(_vec0), Sleef_expm1f4_u10vsx(_vec1)}; + } + + Vectorized C10_ALWAYS_INLINE log() const { + return {Sleef_logf4_u10vsx(_vec0), Sleef_logf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE log10() const { +- return {Sleef_log10f4_u10vsx(_vec0), Sleef_log10f4_u10vsx(_vec1)}; ++ return {Sleef_log10f4_u10vsx(_vec0), Sleef_log10f4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE log1p() const { +- return {Sleef_log1pf4_u10vsx(_vec0), Sleef_log1pf4_u10vsx(_vec1)}; ++ return {Sleef_log1pf4_u10vsx(_vec0), Sleef_log1pf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE log2() const { +- return {Sleef_log2f4_u10vsx(_vec0), Sleef_log2f4_u10vsx(_vec1)}; ++ return {Sleef_log2f4_u10vsx(_vec0), Sleef_log2f4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE ceil() const { + return {vec_ceil(_vec0), vec_ceil(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE cos() const { +- // take the absolute value +- auto x = abs(); +- // extract the sign bit (upper one) +- auto sign_bit = (*this) & sign_mask; +- // scale by 4/Pi +- auto y = x * _4div_pi; +- // store the integer part of y in mm0 +- // j=(j+1) & (~1) (see the cephes sources) +- vint32 imm0 = (vec_signed(y._vec0) + vi_1) & vi_inv1; +- vint32 imm1 = (vec_signed(y._vec1) + vi_1) & vi_inv1; +- y._vec0 = vec_float(imm0); +- y._vec1 = vec_float(imm1); +- +- imm0 = imm0 - vi_2; +- imm1 = imm1 - vi_2; +- Vectorized poly_mask; +- // get the swap sign flag +- vint32 tmp0 = vec_and(vec_nand(imm0, imm0), vi_4); +- vint32 tmp1 = vec_and(vec_nand(imm1, imm1), vi_4); +- sign_bit._vecb0 = (vbool32)vec_sl(tmp0, vu_29); +- sign_bit._vecb1 = (vbool32)vec_sl(tmp1, vu_29); +- // get the polynom selection mask +- // there is one polynom for 0 <= x <= Pi / 4 +- // and another one for Pi / 4 < x <= Pi / 2 +- // Both branches will be computed. +- +- poly_mask._vecb0 = (vbool32)vec_cmpeq((imm0 & vi_2), vi_0); +- poly_mask._vecb1 = (vbool32)vec_cmpeq((imm1 & vi_2), vi_0); +- +- // The magic pass: "Extended precision modular arithmetic" +- // x = ((x - y * DP1) - y * DP2) - y * DP3; +- x = y.madd(minus_cephes_dp1, x); +- x = y.madd(minus_cephes_dp2, x); +- x = y.madd(minus_cephes_dp3, x); +- +- // Evaluate the first polynom (0 <= x <= Pi/4) +- auto z = x * x; +- y = z.madd(coscof_p0, coscof_p1); +- y = y.madd(z, coscof_p2); +- y = y * z * z; +- y = y - z * half + one; +- +- // Evaluate the second polynom (Pi/4 <= x <= 0) +- auto y_2 = z.madd(sincof_p0, sincof_p1); +- y_2 = y_2.madd(z, sincof_p2); +- y_2 = y_2 * z; +- y_2 = y_2.madd(x, x); +- +- // select the correct result from the two polynoms +- y = blendv(y, y_2, poly_mask); +- // update the sign +- y = y ^ sign_bit; +- +- return y; ++ return {Sleef_cosf4_u10vsx(_vec0), Sleef_cosf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE cosh() const { +- // cosh = 1/2 * (e^x + e^-x) +- auto x = abs(); +- auto e_x = x.exp(); +- auto ret = (e_x + Vectorized(one) / e_x) * half; +- // inf and nan checks +-#if 0 +- ret = blendv(ret, v_inf, x >= vf_89); +- ret = blendv(ret, v_inf, ret.isnan()); +- ret = blendv(ret, v_nan, this->isnan()); +-#endif +- return ret; ++ return {Sleef_coshf4_u10vsx(_vec0), Sleef_coshf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE floor() const { + return {vec_floor(_vec0), vec_floor(_vec1)}; +@@ -440,97 +339,16 @@ class Vectorized { + return {vec_round(_vec0), vec_round(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE sin() const { +- // take the absolute value and xtract sign +- auto x = abs(); +- auto sign_bit = (*this) & sign_mask; +- +- // scale by 4/Pi +- auto y = x * _4div_pi; +- // store the integer part of y in mm0 +- +- // j=(j+1) & (~1) (see the cephes sources) +- vint32 imm0 = (vec_signed(y._vec0) + vi_1) & vi_inv1; +- vint32 imm1 = (vec_signed(y._vec1) + vi_1) & vi_inv1; +- y._vec0 = vec_float(imm0); +- y._vec1 = vec_float(imm1); +- // get the swap sign flag +- Vectorized swap_sign_bit, poly_mask; +- swap_sign_bit._vecb0 = (vbool32)vec_sl(imm0 & vi_4, vu_29); +- swap_sign_bit._vecb1 = (vbool32)vec_sl(imm1 & vi_4, vu_29); +- // get the polynom selection mask +- // there is one polynom for 0 <= x <= Pi/4 +- // and another one for Pi/4 C10_ALWAYS_INLINE sinh() const { +- auto temp_abs = abs(); +- // get exponent +- auto ret = temp_abs.exp(); +- auto recp = Vectorized(half) / ret; +- auto v = ret * half - recp; +- // extract the sign bit (upper one) +- auto sign_bit = (*this) & sign_mask; +- auto z = temp_abs * temp_abs; +- auto y = z.madd(p0, p1); +- y = y.madd(z, p2); +- y = (y * z).madd(temp_abs, temp_abs); +- // check and select +- auto result = blendv(y, v, temp_abs > one); +- return result | sign_bit; ++ return {Sleef_sinhf4_u10vsx(_vec0), Sleef_sinhf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE tan() const { +- return {Sleef_tanf4_u10vsx(_vec0), Sleef_tanf4_u10vsx(_vec1)}; ++ return {Sleef_tanf4_u10vsx(_vec0), Sleef_tanf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE tanh() const { +- auto x = *this; +- auto vabs = abs(); +- // get exponent +- auto exp2x = (vabs + vabs).exp(); +- auto vv = Vectorized(one) - Vectorized(two) / (exp2x + one); +- // extract the sign bit (upper one) +- auto sign_bit = (*this) & sign_mask; +- auto z = vabs * vabs; +- auto y = z.madd(tanh_p0, tanh_p1); +- auto tmp = y.madd(z, tanh_p2); +- y = z.madd(tmp, tanh_p3); +- tmp = y.madd(z, tanh_p4); +- y = tmp * z; +- tmp = y.madd(x, x); +- // add sign +- vv = vv | sign_bit; +- // check and select +- auto sel_mask = vabs >= tanh_0p625; +- auto max_mask = vabs > tanh_half_max; +- auto max_ret = sign_bit ^ one; +- return blendv(blendv(tmp, vv, sel_mask), max_ret, max_mask); ++ return {Sleef_tanhf4_u10vsx(_vec0), Sleef_tanhf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE trunc() const { + return {vec_trunc(_vec0), vec_trunc(_vec1)}; +@@ -555,15 +373,15 @@ class Vectorized { + } + + Vectorized fmod(const Vectorized& b) const { +- return {Sleef_fmodf4_vsx(_vec0, b._vec0),Sleef_fmodf4_vsx(_vec1, b._vec1)}; ++ return {Sleef_fmodf4_vsx(_vec0, b._vec0),Sleef_fmodf4_vsx(_vec1, b._vec1)}; + } + + Vectorized hypot(const Vectorized& b) const { +- return {Sleef_hypotf4_u05vsx(_vec0, b._vec0), Sleef_hypotf4_u05vsx(_vec1, b._vec1)}; ++ return {Sleef_hypotf4_u05vsx(_vec0, b._vec0), Sleef_hypotf4_u05vsx(_vec1, b._vec1)}; + } + + Vectorized nextafter(const Vectorized& b) const { +- return {Sleef_nextafterf4_vsx(_vec0, b._vec0), Sleef_nextafterf4_vsx(_vec1, b._vec1)}; ++ return {Sleef_nextafterf4_vsx(_vec0, b._vec0), Sleef_nextafterf4_vsx(_vec1, b._vec1)}; + } + + Vectorized igamma(const Vectorized& x) const { diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch new file mode 100644 index 00000000000..6455052773f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch @@ -0,0 +1,22 @@ +TestOptim.test_adadelta fails on some systems with +> Mismatched elements: 1 / 50 (2.0%) +> Greatest absolute difference: 0.0012711584568023682 at index (1, 3) (up to 1e-05 allowed) +> Greatest relative difference: 0.005316456816424191 at index (1, 3) (up to 0.004 allowed) +This is possibly related to the CUDA driver version. See also https://github.com/pytorch/pytorch/issues/51992 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_optim.py b/test/test_optim.py +index 6d587b4b35..32e5dbcc2f 100644 +--- a/test/test_optim.py ++++ b/test/test_optim.py +@@ -621,7 +621,8 @@ class TestOptim(TestCase): + # ROCm precision is too low to pass this test + def test_adadelta(self): + # Handles https://github.com/pytorch/pytorch/issues/69698 +- self.rel_tol = 4e-3 ++ self.precision = 2e-3 ++ self.rel_tol = 1e-2 + for optimizer in [optim.Adadelta, optim_mt.Adadelta]: + self._test_basic_cases( + lambda weight, bias, maximize: optimizer([weight, bias], maximize=maximize), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch new file mode 100644 index 00000000000..9a728ce288d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch @@ -0,0 +1,27 @@ +`test_out` may fail due to slightly different values caused by different order of matrizes in SGEMM: + +> Mismatched elements: 1 / 50 (2.0%) +> Greatest absolute difference: 1.430511474609375e-05 at index (4, 5) (up to 1e-05 allowed) +> Greatest relative difference: 4.65393206065873e-06 at index (4, 5) (up to 1.3e-06 allowed) + +See https://github.com/pytorch/pytorch/pull/86365 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 00eb3f7f09..d97505ffb6 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -9984,7 +9984,11 @@ op_db: List[OpInfo] = [ + DecorateInfo( + toleranceOverride({torch.float32: tol(atol=1.3e-05, rtol=1.3e-05), + torch.complex64: tol(atol=1e-05, rtol=1.2e-03)}), +- 'TestCommon', 'test_reference_testing')], ++ 'TestCommon', 'test_reference_testing'), ++ DecorateInfo( ++ toleranceOverride({torch.float32: tol(atol=1.5e-05, rtol=1e-05)}), ++ 'TestCommon', 'test_out'), ++ ], + skips=( + # NVIDIA only assures that bfloat16 is supported by bmm if SM >= 5.3 + DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes', device_type='cuda', active_if=not SM53OrLater), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch new file mode 100644 index 00000000000..60e09456182 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch @@ -0,0 +1,159 @@ +# PyTorch's CMAKE configuration by default sets RUNPATH on libraries if they link other libraries +# that are outside the build tree, which is done because of the CMAKE config on +# https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L10. +# This provides problems, since the cuda stubs library path then also gets added to the RUNPATH. +# As a result, at runtime, the stub version of things like libcuda.so.1 gets picked up, instead of the real drivers +# See https://github.com/easybuilders/easybuild-easyconfigs/issues/14359 +# This line https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L16 +# Makes sure that any path that is linked, is also added to the RUNPATH. +# This has been reported upstream in https://github.com/pytorch/pytorch/issues/35418 +# and a fix was attempted in https://github.com/pytorch/pytorch/pull/37737 but it was reverted +# +# This EasyBuild patch changes behavior for the libraries that were failing, i.e. the ones in this list: +# https://github.com/easybuilders/easybuild-easyconfigs/issues/14359#issuecomment-970479904 +# This is done by setting INSTALL_RPATH_USE_LINK_PATH to false, and instead, specifying the RPATH +# explicitely by defining INSTALL_RPATH, but only adding directories that do not match to the "stubs" regex +# +# Original patch: Caspar van Leeuwen +# Updated: Alexander Grund (TU Dresden) +# +# See https://github.com/pytorch/pytorch/pull/87593 + +diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt +index 328210c978..f06ee0bb4e 100644 +--- a/caffe2/CMakeLists.txt ++++ b/caffe2/CMakeLists.txt +@@ -643,13 +643,12 @@ if(NOT INTERN_BUILD_MOBILE OR NOT BUILD_CAFFE2_MOBILE) + if(USE_CUDA) + list(APPEND Caffe2_GPU_CU_SRCS ${Caffe2_GPU_HIP_JIT_FUSERS_SRCS}) + add_library(caffe2_nvrtc SHARED ${ATen_NVRTC_STUB_SRCS}) ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB}) + if(MSVC) + # Delay load nvcuda.dll so we can import torch compiled with cuda on a CPU-only machine +- set(DELAY_LOAD_FLAGS "-DELAYLOAD:nvcuda.dll;delayimp.lib") +- else() +- set(DELAY_LOAD_FLAGS "") ++ target_link_libraries(caffe2_nvrtc "-DELAYLOAD:nvcuda.dll;delayimp.lib") + endif() +- target_link_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB} ${DELAY_LOAD_FLAGS}) + target_include_directories(caffe2_nvrtc PRIVATE ${CUDA_INCLUDE_DIRS}) + install(TARGETS caffe2_nvrtc DESTINATION "${TORCH_INSTALL_LIB_DIR}") + if(USE_NCCL) +diff --git a/cmake/LinkCudaLibraries.cmake b/cmake/LinkCudaLibraries.cmake +new file mode 100644 +index 0000000000..a24583bff4 +--- /dev/null ++++ b/cmake/LinkCudaLibraries.cmake +@@ -0,0 +1,33 @@ ++# Link CUDA libraries to the given target, i.e.: `target_link_libraries(target )` ++# ++# Additionally makes sure CUDA stub libs don't end up being in RPath ++# ++# Example: link_cuda_libraries(mytarget PRIVATE ${CUDA_LIBRARIES}) ++function(link_cuda_libraries target) ++ set(libs ${ARGN}) ++ set(install_rpath "") ++ set(filtered FALSE) ++ foreach(lib IN LISTS libs) ++ # CUDA stub libs are in form /prefix/lib/stubs/libcuda.so ++ # So extract the name of the parent folder, to check against "stubs" ++ # And the parent path which we need to add to the INSTALL_RPATH for non-stubs ++ get_filename_component(parent_path "${lib}" DIRECTORY) ++ get_filename_component(parent_name "${parent_path}" NAME) ++ if(parent_name STREQUAL "stubs") ++ message(STATUS "Filtering ${lib} from being set in ${target}'s RPATH, " ++ "because it appears to point to the CUDA stubs directory.") ++ set(filtered TRUE) ++ elseif(parent_path) ++ list(APPEND install_rpath ${parent_path}) ++ endif() ++ endforeach() ++ ++ # Regular link command ++ target_link_libraries(${target} ${scope} ${libs}) ++ # Manually set INSTALL_RPATH when there were any stub libs ++ if(filtered) ++ list(REMOVE_DUPLICATES install_rpath) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH "${install_rpath}") ++ endif() ++endfunction() +diff --git a/test/cpp/api/CMakeLists.txt b/test/cpp/api/CMakeLists.txt +index 373895a0ce..19868221cb 100644 +--- a/test/cpp/api/CMakeLists.txt ++++ b/test/cpp/api/CMakeLists.txt +@@ -58,7 +58,8 @@ if(NOT MSVC) + endif() + + if(USE_CUDA) +- target_link_libraries(test_api PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_api PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/dist_autograd/CMakeLists.txt b/test/cpp/dist_autograd/CMakeLists.txt +index 9969c63e16..356ba5be55 100644 +--- a/test/cpp/dist_autograd/CMakeLists.txt ++++ b/test/cpp/dist_autograd/CMakeLists.txt +@@ -10,7 +10,8 @@ if(USE_DISTRIBUTED AND NOT WIN32) + target_link_libraries(test_dist_autograd PRIVATE torch gtest) + + if(USE_CUDA) +- target_link_libraries(test_dist_autograd PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_dist_autograd PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/jit/CMakeLists.txt b/test/cpp/jit/CMakeLists.txt +index 60b43b81fc..57cd4422f8 100644 +--- a/test/cpp/jit/CMakeLists.txt ++++ b/test/cpp/jit/CMakeLists.txt +@@ -136,7 +137,8 @@ if(LINUX) + endif() + + if(USE_CUDA) +- target_link_libraries(test_jit PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_jit PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/rpc/CMakeLists.txt b/test/cpp/rpc/CMakeLists.txt +index 3997f8753e..21fddbc645 100644 +--- a/test/cpp/rpc/CMakeLists.txt ++++ b/test/cpp/rpc/CMakeLists.txt +@@ -33,7 +33,8 @@ target_include_directories( + target_link_libraries(test_cpp_rpc PRIVATE ${TORCH_RPC_TEST_DEPENDENCY_LIBS}) + + if(USE_CUDA) +- target_link_libraries(test_cpp_rpc PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_cpp_rpc PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/tensorexpr/CMakeLists.txt b/test/cpp/tensorexpr/CMakeLists.txt +index 7dff70630d..ecb8300549 100644 +--- a/test/cpp/tensorexpr/CMakeLists.txt ++++ b/test/cpp/tensorexpr/CMakeLists.txt +@@ -57,14 +57,15 @@ if(USE_PTHREADPOOL) + target_link_libraries(test_tensorexpr PRIVATE pthreadpool_interface) + endif() + if(USE_CUDA) +- target_link_libraries(test_tensorexpr PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + target_compile_definitions(test_tensorexpr PRIVATE USE_CUDA) + +- target_link_libraries(tutorial_tensorexpr PRIVATE ++ link_cuda_libraries(tutorial_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch new file mode 100644 index 00000000000..6b2fb265395 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch @@ -0,0 +1,26 @@ +Those tests (from test_ao_sparsity) require FBGEMM which may not be available. +So add the skip decorator. +See https://github.com/pytorch/pytorch/issues/87364 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/ao/sparsity/test_composability.py b/test/ao/sparsity/test_composability.py +index b44c885507..b7d35343c0 100644 +--- a/test/ao/sparsity/test_composability.py ++++ b/test/ao/sparsity/test_composability.py +@@ -9,6 +9,7 @@ import torch.ao.quantization as tq + from torch import nn + from torch.ao import sparsity + from torch.testing._internal.common_utils import TestCase ++from torch.testing._internal.common_quantization import skipIfNoFBGEMM + + logging.basicConfig( + format="%(asctime)s - %(name)s - %(levelname)s - %(message)s", level=logging.INFO +@@ -23,6 +24,7 @@ sparse_defaults = { + # This series of tests are to check the composability goals for sparsity and quantization. Namely + # that performing quantization and sparsity model manipulations in various orderings + # does not cause problems ++@skipIfNoFBGEMM + class TestComposability(TestCase): + def _get_model_and_sparsifier_and_sparse_config(self, qconfig=None): + model = nn.Sequential( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch new file mode 100644 index 00000000000..b515d8dd432 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch @@ -0,0 +1,51 @@ +Test test_fn_grad_linalg_det_singular_cpu_complex128 in test_ops_gradients fails not only on Windows, +so extend the skip marker introduced in https://github.com/pytorch/pytorch/pull/69827 + +test_forward_mode_AD_norm_inf_cpu_complex128 in test_ops_gradients fails due to NaNs. +Might be fixed by https://github.com/pytorch/pytorch/pull/80082 where a part of the changes +come from with additional skip for that test similar to other complex128 skips. + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 00eb3f7f09..8d009cf280 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -9729,11 +9729,11 @@ op_db: List[OpInfo] = [ + dtypesIfCUDA=all_types_and_complex_and(torch.bool, torch.half, torch.bfloat16, torch.chalf), + skips=( + # Inplace abs doesn't support complex inputs +- DecorateInfo(unittest.expectedFailure, 'TestGradients', ++ DecorateInfo(unittest.skip("In-place abs not supported for complex tensors"), 'TestGradients', + 'test_inplace_grad', dtypes=(torch.cdouble,)), +- DecorateInfo(unittest.expectedFailure, 'TestGradients', ++ DecorateInfo(unittest.skip("In-place abs not supported for complex tensors"), 'TestGradients', + 'test_inplace_gradgrad', dtypes=(torch.cdouble,)), +- DecorateInfo(unittest.expectedFailure, 'TestGradients', ++ DecorateInfo(unittest.skip("In-place abs not supported for complex tensors"), 'TestGradients', + 'test_inplace_forward_mode_AD', dtypes=(torch.cdouble,)), + DecorateInfo(unittest.skip("Skipped!"), 'TestUnaryUfuncs', 'test_reference_numerics_extremal', + device_type='cpu', dtypes=[torch.cfloat, torch.cdouble]), +@@ -11559,7 +11559,7 @@ op_db: List[OpInfo] = [ + skips=( + # These tests started breaking after touching the SVD. + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad', device_type='cpu', +- dtypes=(torch.complex128,), active_if=IS_WINDOWS), ++ dtypes=(torch.complex128,)), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + # dtypes are tested in the suite above, no need to repeat it for singular + DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes'), +@@ -17230,6 +17230,13 @@ op_db: List[OpInfo] = [ + device_type="cpu", + dtypes=(torch.complex128,), + ), ++ DecorateInfo( ++ unittest.skip("NaNs in analytical jacobian!"), ++ "TestGradients", ++ "test_forward_mode_AD", ++ device_type="cpu", ++ dtypes=(torch.complex128,), ++ ), + DecorateInfo(unittest.expectedFailure, 'TestGradients', 'test_fn_fwgrad_bwgrad', + dtypes=[torch.complex128]), + # AssertionError: RuntimeError not raised : Expected RuntimeError when doing an unsafe cast from a result From a51c4dcc20707b75971d9ae9df434a89c85677fd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 27 Oct 2022 13:46:48 +0200 Subject: [PATCH 5636/9987] Remove test which times out --- .../p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 564c7ada0c8..5c8c7675ce6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', @@ -59,6 +60,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.11.1_skip-test_init_from_local_shards.patch + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch From d720a6809955020093c01b5d221fb5d6d994786d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 22 Nov 2022 15:58:48 +0100 Subject: [PATCH 5637/9987] Patch failure on older CUDA drivers --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 5 +-- .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 5 +-- ...h-1.12.1_fix-test_cpp_extensions_jit.patch | 31 +++++++++++++++++++ 3 files changed, 37 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 5c8c7675ce6..ae0cff605da 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -14,7 +14,6 @@ sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', - 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.10.0_fix-test-model_dump.patch', @@ -27,6 +26,7 @@ patches = [ 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', @@ -42,7 +42,6 @@ checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.10.0_fix-kineto-crash.patch 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch @@ -64,6 +63,8 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index cd38c8b8e9c..cb1f43fa095 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -13,7 +13,6 @@ sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', - 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.10.0_fix-test-model_dump.patch', @@ -25,6 +24,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', @@ -40,7 +40,6 @@ checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.10.0_fix-kineto-crash.patch 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch @@ -60,6 +59,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch new file mode 100644 index 00000000000..38dcd0c2eb6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch @@ -0,0 +1,31 @@ +When the CUDA Toolkit (compiler...) is to new or to old for the GPU or the GPU driver +this test may fail. +See https://github.com/pytorch/pytorch/pull/89495 + +diff --git a/test/test_cpp_extensions_jit.py b/test/test_cpp_extensions_jit.py +index 2ead8d32ca179..dd350823ffef9 100644 +--- a/test/test_cpp_extensions_jit.py ++++ b/test/test_cpp_extensions_jit.py +@@ -200,7 +200,21 @@ def test_jit_cuda_archflags(self): + archflags["5.0;6.0+PTX;7.0;7.5"] = (['50', '60', '70', '75'], ['60']) + + for flags, expected in archflags.items(): +- self._run_jit_cuda_archflags(flags, expected) ++ try: ++ self._run_jit_cuda_archflags(flags, expected) ++ except RuntimeError as e: ++ # Using the device default (empty flags) may fail if the device is newer than the CUDA compiler ++ # This raises a RuntimeError with a specific message which we explictely ignore here ++ if not flags and "Error building" in str(e): ++ pass ++ else: ++ raise ++ try: ++ torch.cuda.synchronize() ++ except RuntimeError: ++ # Ignore any error, e.g. unsupported PTX code on current device ++ # to avoid errors from here leaking into other tests ++ pass + + @unittest.skipIf(not TEST_CUDNN, "CuDNN not found") + def test_jit_cudnn_extension(self): From f223ac3773b440849fe8a6c428780287e0aa75db Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Nov 2022 10:36:58 +0100 Subject: [PATCH 5638/9987] Skip test which may succeed --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 2 +- ...yTorch-1.12.1_skip-failing-grad-test.patch | 21 +++++++++++++++++++ 3 files changed, 23 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index ae0cff605da..e8cea51ff73 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -79,7 +79,7 @@ checksums = [ '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', - 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index cb1f43fa095..bb39edb055d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -75,7 +75,7 @@ checksums = [ '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', - 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch index b515d8dd432..a79bc9a7a5e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch @@ -5,6 +5,9 @@ test_forward_mode_AD_norm_inf_cpu_complex128 in test_ops_gradients fails due to Might be fixed by https://github.com/pytorch/pytorch/pull/80082 where a part of the changes come from with additional skip for that test similar to other complex128 skips. +Also skip test_forward_mode_AD_nn_functional_max_unpool2d_cpu_float64 & test_forward_mode_AD_nn_functional_max_unpool3d_cpu_float64 +which may unexpectably succeed. + Author: Alexander Grund (TU Dresden) diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py @@ -35,6 +38,24 @@ index 00eb3f7f09..8d009cf280 100644 DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), # dtypes are tested in the suite above, no need to repeat it for singular DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes'), +@@ -13447,7 +13447,7 @@ op_db: List[OpInfo] = [ + # and if there are several indices pointing to the same memory, + # gradcheck is oblivious about that and cannot perturb them all at once + # (see sample_inputs_max_unpool_grad to find out more). +- DecorateInfo(unittest.expectedFailure, 'TestGradients', 'test_forward_mode_AD'), ++ DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_forward_mode_AD'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad'), + )), +@@ -13481,7 +13481,7 @@ op_db: List[OpInfo] = [ + # and if there are several indices pointing to the same memory, + # gradcheck is oblivious about that and cannot perturb them all at once + # (see sample_inputs_max_unpool_grad to find out more). +- DecorateInfo(unittest.expectedFailure, 'TestGradients', 'test_forward_mode_AD'), ++ DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_forward_mode_AD'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad'), + )), @@ -17230,6 +17230,13 @@ op_db: List[OpInfo] = [ device_type="cpu", dtypes=(torch.complex128,), From 6e3c238b82abe35f249701a69ca6f53c558e2038 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Nov 2022 11:12:42 +0100 Subject: [PATCH 5639/9987] Skip c10d test which times out --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 3 +++ .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 3 +++ ...skip-test_round_robin_create_destroy.patch | 26 +++++++++++++++++++ 3 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index e8cea51ff73..f81fea585ec 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -37,6 +37,7 @@ patches = [ 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -80,6 +81,8 @@ checksums = [ # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index bb39edb055d..ab67d74f854 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -35,6 +35,7 @@ patches = [ 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -76,6 +77,8 @@ checksums = [ # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch new file mode 100644 index 00000000000..f8e01a445db --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch @@ -0,0 +1,26 @@ +test_round_robin_create_destroy of distributed/test_c10d_gloo may run into timeouts. +So simply skip the on all OS (not only on Windows), the existing skip marker suggest that this is OK. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/test_c10d_gloo.py b/test/distributed/test_c10d_gloo.py +index e49d65ea33d..b4fb75a1b11 100644 +--- a/test/distributed/test_c10d_gloo.py ++++ b/test/distributed/test_c10d_gloo.py +@@ -10,6 +10,7 @@ import sys + import tempfile + from functools import reduce + from itertools import groupby ++from unittest import skip + + import torch + import torch.distributed as c10d +@@ -1438,7 +1439,7 @@ class ProcessGroupGlooTest(MultiProcessTestCase): + pg.broadcast(tensor, root=0).wait() + self.assertEqual(torch.full([100, 100], 0.0), tensor) + +- @skip_if_win32() ++ @skip("Occasionally times out") + @requires_gloo() + def test_round_robin_create_destroy(self): + store = c10d.FileStore(self.file_name, self.world_size) From ec03d0c0bd8b8bddaf3ff85655be03efe494d17a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Nov 2022 16:32:16 +0100 Subject: [PATCH 5640/9987] Fix test failures on 1 GPU --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 2 + .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 2 + .../PyTorch-1.12.1_fix-skip-decorators.patch | 118 ++++++++++++++++++ 3 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index f81fea585ec..03c04cd2a9e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -26,6 +26,7 @@ patches = [ 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', @@ -64,6 +65,7 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index ab67d74f854..7fd464b8dd2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -24,6 +24,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', @@ -60,6 +61,7 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch new file mode 100644 index 00000000000..8300d0d5086 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch @@ -0,0 +1,118 @@ +The decorators are implemented to run when the function is called which is after +the test `setup` method spawned subprocesses which may use NCCL to sync failing when there are +not enough GPUs available. +So replace the custom code by calls to the `unittest` skip decorators. +See https://github.com/pytorch/pytorch/pull/89750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_distributed.py b/torch/testing/_internal/common_distributed.py +index 8baf7d03d9f..3dc922ee923 100644 +--- a/torch/testing/_internal/common_distributed.py ++++ b/torch/testing/_internal/common_distributed.py +@@ -124,46 +124,11 @@ def skip_if_odd_worldsize(func): + return wrapper + + def require_n_gpus_for_nccl_backend(n, backend): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend == "nccl" and torch.cuda.device_count() < n: +- sys.exit(TEST_SKIPS[f"multi-gpu-{n}"].exit_code) +- else: +- return func(*args, **kwargs) +- +- return wrapper +- +- return decorator ++ return skip_if_lt_x_gpu(n) if backend == "nccl" else unittest.skipIf(False, None) + + + def skip_if_lt_x_gpu(x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator +- +- +-# This decorator helps avoiding initializing cuda while testing other backends +-def nccl_skip_if_lt_x_gpu(backend, x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend != "nccl": +- return func(*args, **kwargs) +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator ++ return unittest.skipIf(torch.cuda.device_count() < x, TEST_SKIPS[f"multi-gpu-{x}"].message) + + + def verify_ddp_error_logged(model_DDP, err_substr): +diff --git a/torch/testing/_internal/distributed/distributed_test.py b/torch/testing/_internal/distributed/distributed_test.py +index 1414a0376b1..1f6b00e6edf 100644 +--- a/torch/testing/_internal/distributed/distributed_test.py ++++ b/torch/testing/_internal/distributed/distributed_test.py +@@ -56,7 +56,6 @@ from torch.testing._internal.common_distributed import ( + skip_if_small_worldsize, + skip_if_odd_worldsize, + skip_if_lt_x_gpu, +- nccl_skip_if_lt_x_gpu, + skip_if_no_gpu, + require_n_gpus_for_nccl_backend, + requires_nccl_version, +@@ -4604,7 +4603,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4615,7 +4614,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync_grad_is_view(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4626,7 +4625,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync_allreduce_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync +@@ -4654,7 +4653,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync_allreduce_with_then_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync using allreduce +@@ -4688,7 +4687,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_get_future(self): + def mult(fut): + return [t * 3 for t in fut.wait()] From d159a5a3c98487a79900be700b9e49b1468b9449 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Nov 2022 13:27:16 +0100 Subject: [PATCH 5641/9987] Fix test failures on 1 GPU --- .../p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 2 +- .../p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch | 10 +++++----- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 03c04cd2a9e..9778d40af76 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -65,7 +65,7 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', - '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index 7fd464b8dd2..4417c0cacee 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -61,7 +61,7 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', - '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch index 8300d0d5086..0fbe044ff32 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch @@ -76,7 +76,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync(self): """ Runs _test_accumulate_gradients_no_sync using default inputs @@ -85,7 +85,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync_grad_is_view(self): """ Runs _test_accumulate_gradients_no_sync using default inputs @@ -94,7 +94,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync_allreduce_hook(self): """ Runs multiple iterations on _test_accumulate_gradients_no_sync @@ -103,7 +103,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync_allreduce_with_then_hook(self): """ Runs multiple iterations on _test_accumulate_gradients_no_sync using allreduce @@ -112,7 +112,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_get_future(self): def mult(fut): return [t * 3 for t in fut.wait()] From 1d3e6ac7b0c5015794e4d36e30c360665a1021e3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Nov 2022 14:23:57 +0100 Subject: [PATCH 5642/9987] Cancel old GithubAction runs --- .github/workflows/linting.yml | 5 +++++ .github/workflows/unit_tests.yml | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 6346d959773..d7482ec3f7d 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,5 +1,10 @@ name: Static Analysis on: [push, pull_request] + +concurrency: + group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} + cancel-in-progress: true + jobs: python-linting: runs-on: ubuntu-20.04 diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 1a8e16547f5..620535115d9 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -1,5 +1,10 @@ name: easyconfigs unit tests on: [push, pull_request] + +concurrency: + group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} + cancel-in-progress: true + jobs: test-suite: runs-on: ubuntu-20.04 From abd1f7187f7c4174fe2795f1ba5755ba05ec80fb Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Mon, 28 Nov 2022 15:36:00 +0100 Subject: [PATCH 5643/9987] adding easyconfigs: phonopy-2.16.3-foss-2022a.eb --- .../p/phonopy/phonopy-2.16.3-foss-2022a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb new file mode 100644 index 00000000000..d06fecee5a2 --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '2.16.3' + +homepage = 'https://atztogo.github.io/phonopy/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c536d355156626f26e5d5fd158b03e10c4a13c461d6a02a26b05e3b6311b9d79'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for numpy + ('matplotlib', '3.5.2'), + ('PyYAML', '6.0'), + ('h5py', '3.7.0'), + ('spglib-python', '2.0.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["phonopy --help"] + +sanity_pip_check = True + +moduleclass = 'lib' From f5b2e1e6a85cfc4aca8269869c75a5ec0ee26aed Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 28 Nov 2022 14:48:43 +0000 Subject: [PATCH 5644/9987] adding easyconfigs: SPOOLES-2.2-gompi-2021a.eb and patches: SPOOLES-2.2_build-mpi-mt.patch, SPOOLES-2.2_shared-libs.patch --- .../s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb | 43 ++++++++++++++++++ .../s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch | 38 ++++++++++++++++ .../s/SPOOLES/SPOOLES-2.2_shared-libs.patch | 45 +++++++++++++++++++ 3 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch create mode 100644 easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb new file mode 100644 index 00000000000..b521a3c9f8e --- /dev/null +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb @@ -0,0 +1,43 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'SPOOLES' +version = '2.2' + +homepage = 'https://netlib.org/linalg/spooles/spooles.2.2.html' +description = """SPOOLES is a library for solving sparse real and complex linear + systems of equations, written in the C language using object oriented design. +""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://netlib.org/linalg/spooles'] +sources = ['%(namelower)s.%(version)s.tgz'] +patches = [ + '%(name)s-2.2_build-mpi-mt.patch', + '%(name)s-2.2_shared-libs.patch', +] +checksums = [ + {'spooles.2.2.tgz': 'a84559a0e987a1e423055ef4fdf3035d55b65bbe4bf915efaa1a35bef7f8c5dd'}, + {'SPOOLES-2.2_build-mpi-mt.patch': 'a4abc168c660f4af55feb865c5559304a099755e2c46ebf09fabd83bb1636d2c'}, + {'SPOOLES-2.2_shared-libs.patch': '7b767a699679740ec2a4acd12e66c4a3656a276c354f61436e82cb4d448741f4'}, +] + +builddependencies = [ + ('Perl', '5.32.1', '-minimal'), +] + +#parallel = 1 + +build_cmd_targets = 'lib' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" MPI_LIB_PATH="$MPI_LIB_DIR" MPI_INCLUDE_DIR="$MPI_INC_DIR"' + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch new file mode 100644 index 00000000000..59466c19b06 --- /dev/null +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch @@ -0,0 +1,38 @@ +Author: Jasper Grimm +Description: build multithreaded, MPI targets by default +diff -Nru spooles-2.2.orig/MPI/makefile spooles-2.2.p1/MPI/makefile +--- spooles-2.2.orig/MPI/makefile 1998-12-17 15:47:44.000000000 +0000 ++++ spooles-2.2.p1/MPI/makefile 2022-11-25 16:07:34.000000000 +0000 +@@ -2,7 +2,7 @@ + cd drivers ; make drivers + + lib : +- cd src ; make spoolesMPI.a ++ cd src ; make makeLib + + clean : + cd src ; make clean +diff -Nru spooles-2.2.orig/MPI/src/makefile spooles-2.2.p1/MPI/src/makefile +--- spooles-2.2.orig/MPI/src/makefile 1998-12-16 21:54:41.000000000 +0000 ++++ spooles-2.2.p1/MPI/src/makefile 2022-11-25 16:08:18.000000000 +0000 +@@ -42,3 +42,8 @@ + + clean : + - rm -f *.a *.o ++ ++makelib: ++ perl ../../makeLib > makeG ++ make -f makeG ++ rm -f makeG +diff -Nru spooles-2.2.orig/MT/makefile spooles-2.2.p1/MT/makefile +--- spooles-2.2.orig/MT/makefile 1998-12-17 15:47:48.000000000 +0000 ++++ spooles-2.2.p1/MT/makefile 2022-11-25 16:08:55.000000000 +0000 +@@ -2,7 +2,7 @@ + cd drivers ; make drivers + + lib : +- cd src ; make spoolesMT.a ++ cd src ; make makeLib + + clean : + cd src ; make clean diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch new file mode 100644 index 00000000000..d9423043383 --- /dev/null +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch @@ -0,0 +1,45 @@ +Author: Jasper Grimm +Description: add targets to build shared libraries +diff -Nru spooles-2.2.p1/makefile spooles-2.2.p2/makefile +--- spooles-2.2.p1/makefile 2022-11-25 16:06:54.000000000 +0000 ++++ spooles-2.2.p2/makefile 2022-11-25 16:14:28.000000000 +0000 +@@ -123,8 +123,10 @@ + cd Utilities ; make lib + cd ZV ; make lib + cd misc ; make lib +-#cd MPI ; make lib +-#cd MT ; make lib ++ MPI ; make lib ++ MT ; make lib ++ $(CC) -shared */*/*.lo -Wl,-soname,libspooles.so.2.2 -o libspooles.so.2.2 -lmpi -lpthread -lm ++ ln -s libspooles.so.2.2 libspooles.so + + global : + cd A2/src ; make -f makeGlobalLib +diff -Nru spooles-2.2.p1/makeLib spooles-2.2.p2/makeLib +--- spooles-2.2.p1/makeLib 2022-11-25 16:06:54.000000000 +0000 ++++ spooles-2.2.p2/makeLib 2022-11-25 16:13:02.000000000 +0000 +@@ -64,14 +64,21 @@ + $srcname = " \\\n " . $src ; + print $srcname ; + } ++print "\n\n.SUFFIXES: .c .o .lo .a .so" ; + print "\n\nOBJ_FILES = \$\{SRC:.c=.o\}" ; ++print "\n\nLOBJ_FILES = \$\{SRC:.c=.lo\}" ; + print "\n\n" ; + print <<'EOF' ; + .c.o : +- $(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o ++ $(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o $(MPI_INCLUDE_DIR) + + ../../spooles.a : ${OBJ_FILES} + $(AR) $(ARFLAGS) ../../spooles.a $(OBJ)_*.o ++.c.lo: ++ $(PURIFY) $(CC) -c $(CFLAGS) $*.c -fPIC -DPIC -o $(OBJ)_$*.lo $(MPI_INCLUDE_DIR) ++ ++../../libspooles.a : ${OBJ_FILES} ${LOBJ_FILES} ++ $(AR) $(ARFLAGS) ../../libspooles.a $(OBJ)_*.o + rm -f $(OBJ)_*.o +- $(RANLIB) ../../spooles.a ++ $(RANLIB) ../../linspooles.a + EOF From d9d2d73dfd816ac6b1831fb7ffe1ef69c84e23f8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 28 Nov 2022 14:51:00 +0000 Subject: [PATCH 5645/9987] remove commented `parallel` parameter --- easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb index b521a3c9f8e..1713aedf476 100644 --- a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb @@ -1,5 +1,4 @@ # Author: Jasper Grimm (UoY) - easyblock = 'MakeCp' name = 'SPOOLES' @@ -28,8 +27,6 @@ builddependencies = [ ('Perl', '5.32.1', '-minimal'), ] -#parallel = 1 - build_cmd_targets = 'lib' buildopts = 'CC="$CC" CFLAGS="$CFLAGS" MPI_LIB_PATH="$MPI_LIB_DIR" MPI_INCLUDE_DIR="$MPI_INC_DIR"' From e647457943395ee0d5e67e29bf04c4fe22bf2b34 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 28 Nov 2022 17:03:44 +0000 Subject: [PATCH 5646/9987] adding easyconfigs: PyImageJ-1.3.1-foss-2021a.eb --- .../p/PyImageJ/PyImageJ-1.3.1-foss-2021a.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyImageJ/PyImageJ-1.3.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PyImageJ/PyImageJ-1.3.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyImageJ/PyImageJ-1.3.1-foss-2021a.eb new file mode 100644 index 00000000000..d1e6fb65e8a --- /dev/null +++ b/easybuild/easyconfigs/p/PyImageJ/PyImageJ-1.3.1-foss-2021a.eb @@ -0,0 +1,60 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'PyImageJ' +version = '1.3.1' + +homepage = "https://pyimagej.readthedocs.io/" +description = """PyImageJ provides a set of wrapper functions for integration between ImageJ2 and Python. It also + supports the original ImageJ API and data structures. A major advantage of this approach is the ability to combine + ImageJ and ImageJ2 with other tools available from the Python software ecosystem, including NumPy, SciPy, + scikit-image, CellProfiler, OpenCV, ITK and many more.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Java', '11', '', SYSTEM), + ('Maven', '3.6.3', '', SYSTEM), + ('matplotlib', '3.4.2'), + ('Pillow', '8.2.0'), + ('scikit-image', '0.18.3'), + ('SciPy-bundle', '2021.05'), + ('xarray', '0.19.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('setuptools', '61.3.1', { + 'checksums': ['88fafba4abc2f047e08a188fd4bbc10b0e464592c37b514c19f8f8f88d94450b'], + }), + ('imglyb', '2.0.1', { + 'checksums': ['ace14759bb4201e4b1b93ff4c4aa2c90e87e0bb22095160e205792be89fee929'], + }), + ('jgo', '1.0.5', { + 'checksums': ['48cfab8ec880692d93b22c42e0239f4792c009461c121c15549c456c6a6a4eb6'], + }), + ('JPype1', '1.4.1', { + 'modulename': 'jpype', + 'checksums': ['dc8ee854073474ad79ae168d90c2f6893854f58936cfa18f3587cadae0d3696d'], + }), + ('labeling', '0.1.13', { + 'checksums': ['908d5c247d75d368422c15d0b1efcb3b9d322d0c51cf436865bfb75ce5c829f4'], + }), + ('scyjava', '1.8.1', { + 'checksums': ['de94bf2f1569af0c5c41f38eade53930ae3d17dc584eed712fac6494a7f20efc'], + }), + (name, version, { + 'modulename': 'imagej', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['1328c1b380315a1feff7a42c558dc85a37964a6cd7cc2e5688ec0ce54bf3ac0a'], + }), +] + +sanity_check_commands = [ + """python -c 'import imagej; ij = imagej.init("2.5.0", mode="headless"); print(ij.getVersion())'""" +] + +moduleclass = 'vis' From d22f33188db10e850b2a14fd6bd60c6d276d1872 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 28 Nov 2022 20:41:41 +0100 Subject: [PATCH 5647/9987] add MAD support --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb index 3216a7a24e7..c1e324f3ce3 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb @@ -1,7 +1,5 @@ -# Institution: IT4Innovations National Supercomputing Center, Czech Republic -# Author: Jakub Kropacek -# License: GPLv3 -# Year: 2022 +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 easyblock = 'ConfigureMake' @@ -23,6 +21,7 @@ builddependencies = [('binutils', '2.38')] dependencies = [ ('FLAC', '1.3.4'), ('LAME', '3.100'), + ('libmad', '0.15.1b'), ('libvorbis', '1.3.7'), ('FFmpeg', '5.0.1'), ] @@ -33,6 +32,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib', 'lib/pkgconfig', 'share/man'], } -sanity_check_commands = ['sox --help'] - moduleclass = 'data' From f797f9a82d82cf1c87303126f57b534b3e6d2805 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 28 Nov 2022 20:44:14 +0100 Subject: [PATCH 5648/9987] return sanity check --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb index c1e324f3ce3..b009ef44f7f 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb @@ -32,4 +32,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib', 'lib/pkgconfig', 'share/man'], } +sanity_check_commands = ['sox --help'] + moduleclass = 'data' From 2c344125936d6ba3d90415c5e36f5b1c0bc744cc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 29 Nov 2022 11:36:08 +0100 Subject: [PATCH 5649/9987] drop nodejs-16.15.1-GCCcore-11.3.0.eb from this PR, a better one had already been merged --- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb deleted file mode 100644 index 00b497b22e5..00000000000 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'nodejs' -version = '16.15.1' # LTS on 2022-06-12 -local_libversion = '93' - -homepage = 'https://nodejs.org' -description = """Node.js is a platform built on Chrome's JavaScript runtime - for easily building fast, scalable network applications. Node.js uses an - event-driven, non-blocking I/O model that makes it lightweight and efficient, - perfect for data-intensive real-time applications that run across distributed devices.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://nodejs.org/dist/v%(version)s/'] -sources = ['node-v%(version)s.tar.gz'] -checksums = ['308aee7149c4092a53c87c28ef49e23a8d1606119e79ae68333062e2a1f94208'] - -builddependencies = [ - ('binutils', '2.38'), - ('Python', '3.10.4', '-bare'), - ('pkgconf', '1.8.0'), -] - -dependencies = [ - ('ICU', '71.1'), -] - -configopts = [ - '--with-intl=system-icu', - '--shared --with-intl=system-icu', # Build libnode.so in a second run -] - -# Link libv8 libs to libnode -postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), -] - -sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], - 'dirs': ['lib/node_modules', 'include/node'] -} - -moduleclass = 'lang' From 3d63fa2a387d8fa5bc64d13372a334c40f20c372 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 29 Nov 2022 11:45:02 +0100 Subject: [PATCH 5650/9987] add nodejs-16.15.1 from develop to clear conflict. --- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..117331f1af8 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '16.15.1' # LTS on 2022-06-12 +local_libversion = '93' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['308aee7149c4092a53c87c28ef49e23a8d1606119e79ae68333062e2a1f94208'] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4', '-bare'), +] + +dependencies = [ + ('ICU', '71.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# Use ICU and OpenSSL from EasyBuild +local_common_configopts = "--with-intl=system-icu --shared-openssl " + +configopts = [ + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) + +postinstallcmds = [ + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], + 'dirs': ['lib/node_modules', 'include/node'] +} + +moduleclass = 'lang' From bf68567e0d07953ce50043a911f768c59b455b62 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 29 Nov 2022 11:52:13 +0100 Subject: [PATCH 5651/9987] adding easyconfigs: Simple-DFTD3-0.7.0-foss-2022a.eb, mstore-0.2.0-GCCcore-11.3.0.eb, mctc-lib-0.3.1-GCCcore-11.3.0.eb, TOML-Fortran-0.3.1-GCC-11.3.0.eb --- .../mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb | 33 ++++++++++++++++ .../m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb | 34 +++++++++++++++++ .../Simple-DFTD3-0.7.0-foss-2022a.eb | 38 +++++++++++++++++++ .../TOML-Fortran-0.3.1-GCC-11.3.0.eb | 24 ++++++++++++ 4 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c2fa48c5c80 --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'mctc-lib' +version = '0.3.1' + +homepage = 'https://grimme-lab.github.io/mctc-lib' +description = """Common tool chain for working with molecular structure data in various +applications. This library provides a unified way to perform operations on +molecular structure data, like reading and writing to common geometry file +formats.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=1' + +sanity_check_paths = { + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mctc-convert --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ab7413786e6 --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=1' + +sanity_check_paths = { + 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mstore-info --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb new file mode 100644 index 00000000000..f138326bdda --- /dev/null +++ b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'Simple-DFTD3' +version = '0.7.0' + +homepage = 'https://dftd3.readthedocs.io' +description = """Reimplementation of the D3 dispersion correction. The s-dftd3 project aims to +provide a user-friendly and uniform interface to the D3 dispersion model and +for the calculation of DFT-D3 dispersion corrections.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': False, 'openmp': True, 'pic': True} + +github_account = 'dftd3' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['19400a176eb4dcee7b89181a5a5f0033fe6b05c52821e54896a98448761d003a'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.2.0'), + ('TOML-Fortran', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=1 -DWITH_BLAS=1 -DWITH_OpenMP=1' + +sanity_check_paths = { + 'files': ['bin/s-dftd3', 'lib/libs-dftd3.%s' % SHLIB_EXT, 'include/dftd3.h', 'include/s-dftd3.h'], + 'dirs': ['include/s-dftd3', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["s-dftd3 --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.3.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..99fc626c682 --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.3.1' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7586f0be7dc88dddba4d4e42059b84baa2688a2784bdc1d1f37112ab3edb88e1'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/libtoml-f.a'], + 'dirs': ['include/toml-f', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' From 6017f5bad23ca3a12b701954950f165c2434c508 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Nov 2022 13:41:46 +0100 Subject: [PATCH 5652/9987] adding easyconfigs: memtester-4.5.1-GCCcore-11.3.0.eb --- .../memtester-4.5.1-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7812a2d4fed --- /dev/null +++ b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'memtester' +version = '4.5.1' + +homepage = 'https://pyropus.ca./software/memtester/' +description = 'A userspace utility for testing the memory subsystem for faults' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pyropus.ca./software/memtester/old-versions/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1c5fc2382576c084b314cfd334d127a66c20bd63892cac9f445bc1d8b4ca5a47'] + +builddependencies = [ + ('binutils', '2.38'), +] + +files_to_copy = [(['memtester'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/memtester'], + 'dirs': [] +} + +moduleclass = 'tools' From bcbd77ae885715ccb23a87df853286a26d98e532 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 29 Nov 2022 13:48:41 +0100 Subject: [PATCH 5653/9987] add build dependency on binutils to mstore and mctc-lib --- .../easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb | 1 + easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb index c2fa48c5c80..026ff55fa14 100644 --- a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb @@ -18,6 +18,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] builddependencies = [ + ('binutils', '2.38'), ('CMake', '3.23.1'), ] diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb index ab7413786e6..8ddbf0c4fc0 100644 --- a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb @@ -15,6 +15,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d'] builddependencies = [ + ('binutils', '2.38'), ('CMake', '3.23.1'), ] From 6ebd52a7d602583625c3d66174a45b3570f819ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Nov 2022 14:27:11 +0100 Subject: [PATCH 5654/9987] Switch to ubuntu mirror --- .../m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb index 7812a2d4fed..06490ea807a 100644 --- a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb @@ -8,10 +8,13 @@ description = 'A userspace utility for testing the memory subsystem for faults' toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://pyropus.ca./software/memtester/old-versions/'] -sources = [SOURCE_TAR_GZ] +# Using ubuntu source mirror due to problematic URL redirects +source_urls = ['http://archive.ubuntu.com/ubuntu/pool/universe/m/memtester/'] +sources = ['memtester_%(version)s.orig.tar.gz'] checksums = ['1c5fc2382576c084b314cfd334d127a66c20bd63892cac9f445bc1d8b4ca5a47'] +insecure_download = True + builddependencies = [ ('binutils', '2.38'), ] From de50989c691cdacbe189538fc89f2da383419702 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Nov 2022 15:27:52 +0100 Subject: [PATCH 5655/9987] Remove faulty variable --- .../easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb index 06490ea807a..901ab911bea 100644 --- a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb @@ -13,8 +13,6 @@ source_urls = ['http://archive.ubuntu.com/ubuntu/pool/universe/m/memtester/'] sources = ['memtester_%(version)s.orig.tar.gz'] checksums = ['1c5fc2382576c084b314cfd334d127a66c20bd63892cac9f445bc1d8b4ca5a47'] -insecure_download = True - builddependencies = [ ('binutils', '2.38'), ] From 532daf7e39105fb151f7d466c99c8b38e9f2cd4a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 30 Nov 2022 08:34:40 +0100 Subject: [PATCH 5656/9987] add patches to correctly run Xvfb and to pick up MATLAB license from EB installed MATLAB if available --- .../matlab-proxy-0.5.4-GCCcore-11.3.0.eb | 14 +++++++-- .../matlab-proxy-0.5.4_fix_xvfb_startup.patch | 31 +++++++++++++++++++ ...5.4_use_lic_from_eb_installed_matlab.patch | 28 +++++++++++++++++ 3 files changed, 71 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_fix_xvfb_startup.patch create mode 100644 easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_use_lic_from_eb_installed_matlab.patch diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb index 6628aef3943..f043052deda 100644 --- a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb @@ -24,7 +24,17 @@ sanity_pip_check = True exts_list = [ (name, version, { - 'checksums': ['534531135ae341bd86de6c18ce2694b38614deeedf57a57d4cba1d2079eb662e'], + 'patches': [ + '%(name)s-%(version)s_use_lic_from_eb_installed_matlab.patch', + '%(name)s-%(version)s_fix_xvfb_startup.patch', + ], + 'checksums': [ + {'matlab-proxy-0.5.4.tar.gz': '534531135ae341bd86de6c18ce2694b38614deeedf57a57d4cba1d2079eb662e'}, + {'matlab-proxy-0.5.4_use_lic_from_eb_installed_matlab.patch': + 'f3d30ac6b82667eff81b2b0999bdb9ee8083488fdfa3960c561e3bb046acaa41'}, + {'matlab-proxy-0.5.4_fix_xvfb_startup.patch': + '4f952d6e807830d8d6a138c90bbe74981a082569b6d4e1855c789a0f6ad3e4f6'}, + ], }), ] @@ -33,6 +43,6 @@ sanity_check_paths = { 'dirs': ['lib64/python%(pyshortver)s/site-packages'] } -modloadmsg = 'matlab-proxy requires MATLAB to be loaded separately (2020b or later)' +modloadmsg = 'matlab-proxy requires MATLAB to be loaded separately and BEFORE this module (2020b or later)' moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_fix_xvfb_startup.patch b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_fix_xvfb_startup.patch new file mode 100644 index 00000000000..fd099bb15f9 --- /dev/null +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_fix_xvfb_startup.patch @@ -0,0 +1,31 @@ +Fix startup of Xvfb to use EB's Xvfb and don't empty the environment. + +Åke Sandgren, 2022-11-29 +diff -ru matlab-proxy-0.5.4.orig/matlab_proxy/settings.py matlab-proxy-0.5.4/matlab_proxy/settings.py +--- matlab-proxy-0.5.4.orig/matlab_proxy/settings.py 2022-11-10 08:39:50.000000000 +0100 ++++ matlab-proxy-0.5.4/matlab_proxy/settings.py 2022-11-29 17:12:54.429102236 +0100 +@@ -239,8 +246,11 @@ + # Allow child process to use the file descriptor created by parent. + os.set_inheritable(dpipe[1], True) + ++ xvfb = shutil.which("Xvfb") ++ if xvfb is None: ++ xvfb = "Xvfb" + xvfb_cmd = [ +- "Xvfb", ++ xvfb, + "-displayfd", + # Write descriptor + str(dpipe[1]), +diff -ru matlab-proxy-0.5.4.orig/matlab_proxy/util/mw.py matlab-proxy-0.5.4/matlab_proxy/util/mw.py +--- matlab-proxy-0.5.4.orig/matlab_proxy/util/mw.py 2022-11-10 08:39:50.000000000 +0100 ++++ matlab-proxy-0.5.4/matlab_proxy/util/mw.py 2022-11-29 16:49:14.415197842 +0100 +@@ -286,7 +286,7 @@ + # Creates subprocess asynchronously with environment variables defined in matlab_env + # Pipe errors, if any, to the process object instead of stdout. + xvfb = await asyncio.create_subprocess_exec( +- *xvfb_cmd, close_fds=False, env=env, stderr=asyncio.subprocess.PIPE ++ *xvfb_cmd, close_fds=False, stderr=asyncio.subprocess.PIPE + ) + + read_descriptor, write_descriptor = pipe diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_use_lic_from_eb_installed_matlab.patch b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_use_lic_from_eb_installed_matlab.patch new file mode 100644 index 00000000000..1585cca459f --- /dev/null +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_use_lic_from_eb_installed_matlab.patch @@ -0,0 +1,28 @@ +Use the license file from EB's MATLAB installation by default +Author: Mikael Öhman micketeer@gmail.com +diff -ru matlab-proxy-0.5.4.orig/matlab_proxy/settings.py matlab-proxy-0.5.4/matlab_proxy/settings.py +--- matlab-proxy-0.5.4.orig/matlab_proxy/settings.py 2022-11-10 08:39:50.000000000 +0100 ++++ matlab-proxy-0.5.4/matlab_proxy/settings.py 2022-11-29 17:12:54.429102236 +0100 +@@ -130,6 +130,13 @@ + return settings + + else: ++ if mwi_env.get_env_name_network_license_manager() in os.environ: ++ license_file = os.environ.get(mwi_env.get_env_name_network_license_manager()) ++ elif 'EBROOTMATLAB' in os.environ: ++ license_file = os.environ.get('EBROOTMATLAB') + '/licenses/network.lic' ++ else: ++ license_file = None ++ + matlab_startup_file = str( + Path(__file__).resolve().parent / "matlab" / "startup.m" + ) +@@ -172,7 +179,7 @@ + "mwapikey": str(uuid.uuid4()), + "matlab_protocol": "https", + "nlm_conn_str": mwi.validators.validate_mlm_license_file( +- os.environ.get(mwi_env.get_env_name_network_license_manager()) ++ license_file + ), + "matlab_config_file": mwi_config_folder / "proxy_app_config.json", + "ws_env": ws_env, From 544b780cd6af10c2bd48d07ff0f16c13fcdaa2ef Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 25 Oct 2022 12:59:43 +0200 Subject: [PATCH 5657/9987] adding easyconfigs: PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb, PyTorch-1.12.1-foss-2022a.eb and patches: PyTorch-1.12.1_fix-test_wishart_log_prob.patch, PyTorch-1.12.1_python-3.10-annotation-fix.patch, PyTorch-1.12.1_python-3.10-compat.patch, PyTorch-1.12.1_remove-flaky-test-in-testnn.patch --- .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 148 ++++++++++++++++++ .../p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 133 ++++++++++++++++ ...rch-1.12.1_fix-test_wishart_log_prob.patch | 36 +++++ ...ch-1.12.1_python-3.10-annotation-fix.patch | 69 ++++++++ .../PyTorch-1.12.1_python-3.10-compat.patch | 115 ++++++++++++++ ...h-1.12.1_remove-flaky-test-in-testnn.patch | 22 +++ 6 files changed, 523 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..7f1ab7e67f8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,148 @@ +name = 'PyTorch' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', + # PyTorch-1.12.1_fix-test_wishart_log_prob.patch + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_python-3.10-annotation-fix.patch + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7', + '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67', # PyTorch-1.12.1_python-3.10-compat.patch + # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d', + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.4.2'), + ('Pillow', '9.1.1'), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), + ('magma', '2.6.2', '-CUDA-%(cudaver)s'), + ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# The readelf sanity check command can be taken out once the TestRPATH test from +# https://github.com/pytorch/pytorch/pull/87593 is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb new file mode 100644 index 00000000000..c31da630572 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -0,0 +1,133 @@ +name = 'PyTorch' +version = '1.12.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', + # PyTorch-1.12.1_fix-test_wishart_log_prob.patch + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_python-3.10-annotation-fix.patch + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7', + '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67', # PyTorch-1.12.1_python-3.10-compat.patch + # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d', + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), +] + +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.4.2'), + ('Pillow', '9.1.1'), + ('expecttest', '0.1.3'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch new file mode 100644 index 00000000000..c801b4ca53f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch @@ -0,0 +1,36 @@ +Fix a TestDistributions.test_wishart_log_prob failure in test_distributions +See https://github.com/pytorch/pytorch/pull/87977 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributions/test_distributions.py b/test/distributions/test_distributions.py +index 127018516e123..219eacf4790b0 100644 +--- a/test/distributions/test_distributions.py ++++ b/test/distributions/test_distributions.py +@@ -2036,7 +2036,7 @@ def test_lowrank_multivariate_normal_log_prob(self): + unbatched_prob = torch.stack([dist_unbatched[i].log_prob(x[:, i]) for i in range(5)]).t() + + self.assertEqual(batched_prob.shape, unbatched_prob.shape) +- self.assertEqual(0.0, (batched_prob - unbatched_prob).abs().max(), atol=1e-3, rtol=0) ++ self.assertEqual(batched_prob, unbatched_prob, atol=1e-3, rtol=0) + + @unittest.skipIf(not TEST_NUMPY, "NumPy not found") + def test_lowrank_multivariate_normal_sample(self): +@@ -2176,7 +2176,7 @@ def test_multivariate_normal_log_prob(self): + unbatched_prob = torch.stack([dist_unbatched[i].log_prob(x[:, i]) for i in range(5)]).t() + + self.assertEqual(batched_prob.shape, unbatched_prob.shape) +- self.assertEqual(0.0, (batched_prob - unbatched_prob).abs().max(), atol=1e-3, rtol=0) ++ self.assertEqual(batched_prob, unbatched_prob, atol=1e-3, rtol=0) + + @unittest.skipIf(not TEST_NUMPY, "NumPy not found") + def test_multivariate_normal_sample(self): +@@ -2331,7 +2331,7 @@ def test_wishart_log_prob(self): + unbatched_prob = torch.stack([dist_unbatched[i].log_prob(x[:, i]) for i in range(5)]).t() + + self.assertEqual(batched_prob.shape, unbatched_prob.shape) +- self.assertEqual(0.0, (batched_prob - unbatched_prob).abs().max(), atol=1e-3, rtol=0) ++ self.assertEqual(batched_prob, unbatched_prob, atol=1e-3, rtol=0) + + @unittest.skipIf(not TEST_NUMPY, "NumPy not found") + def test_wishart_sample(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch new file mode 100644 index 00000000000..61f04d40743 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch @@ -0,0 +1,69 @@ +Handle change of type annotation handling in Python 3.10 in the JIT module. +Fixes failures in e.g. test_jit. + +From https://github.com/pytorch/pytorch/pull/81334 & https://github.com/pytorch/pytorch/pull/81506 +Backport: Alexander Grund (TU Dresden) + +diff --git a/torch/_jit_internal.py b/torch/_jit_internal.py +index 3c067d5c1c5..2cc3dba89b4 100644 +--- a/torch/_jit_internal.py ++++ b/torch/_jit_internal.py +@@ -1059,11 +1059,19 @@ def _get_named_tuple_properties(obj): + if field in obj._field_defaults] + else: + defaults = [] ++ # In 3.10 recommended way to get annotations is to call `inspect.get_annotations` function ++ # Also, annotations from base class are not inherited so they need to be queried explicitly ++ if sys.version_info[:2] < (3, 10): ++ obj_annotations = getattr(obj, '__annotations__', {}) ++ else: ++ obj_annotations = inspect.get_annotations(obj) ++ if len(obj_annotations) == 0 and hasattr(obj, "__base__"): ++ obj_annotations = inspect.get_annotations(obj.__base__) ++ + annotations = [] +- has_annotations = hasattr(obj, '__annotations__') + for field in obj._fields: +- if has_annotations and field in obj.__annotations__: +- the_type = torch.jit.annotations.ann_to_type(obj.__annotations__[field], fake_range()) ++ if field in obj_annotations: ++ the_type = torch.jit.annotations.ann_to_type(obj_annotations[field], fake_range()) + annotations.append(the_type) + else: + annotations.append(torch._C.TensorType.getInferred()) +diff --git a/torch/jit/_recursive.py b/torch/jit/_recursive.py +index 8175d14fe5d..aa36a4561d4 100644 +--- a/torch/jit/_recursive.py ++++ b/torch/jit/_recursive.py +@@ -5,6 +5,7 @@ import collections + import textwrap + import functools + import warnings ++import sys + from typing import Dict, List, Set, Type + + import torch._jit_internal as _jit_internal +@@ -134,7 +135,22 @@ def infer_concrete_type_builder(nn_module, share_types=True): + if isinstance(nn_module, (torch.nn.ParameterDict)): + concrete_type_builder.set_parameter_dict() + +- class_annotations = getattr(nn_module, '__annotations__', {}) ++ def get_annotations(obj): ++ if sys.version_info < (3, 10): ++ return getattr(obj, '__annotations__', {}) ++ # In Python-3.10+ it is recommended to use inspect.get_annotations ++ # See https://docs.python.org/3.10/howto/annotations.html ++ # But also, in 3.10 annotations from base class are not inherited ++ # by unannotated derived one, so they must be manually extracted ++ annotations = inspect.get_annotations(obj) ++ if len(annotations) > 0: ++ return annotations ++ cls = obj if isinstance(obj, type) else type(obj) ++ if len(cls.__bases__) == 0: ++ return {} ++ return inspect.get_annotations(cls.__bases__[0]) ++ ++ class_annotations = get_annotations(nn_module) + if isinstance(nn_module, (torch.ao.quantization.QuantWrapper)): + class_annotations = {} + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch new file mode 100644 index 00000000000..957a31669b0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch @@ -0,0 +1,115 @@ +Fixes some compatibility issues with Python 3.10 + +Most notably conversion from float to long which avoids: + TypeError: 'float' object cannot be interpreted as an integer +Also some test failures in test_fx & test_jit due to differences in Python 3.10. + +From https://github.com/pytorch/pytorch/pull/82329 +Backported: Alexander Grund (TU Dresden) + +diff --git a/test/jit/test_hash.py b/test/jit/test_hash.py +index cb1c1544b10..2ca1e9cda0a 100644 +--- a/test/jit/test_hash.py ++++ b/test/jit/test_hash.py +@@ -75,7 +75,10 @@ class TestHash(JitTestCase): + self.checkScript(fn, (1.2345, float("inf"))) + self.checkScript(fn, (float("inf"), float("inf"))) + self.checkScript(fn, (1.2345, float('nan'))) +- self.checkScript(fn, (float("nan"), float("nan"))) ++ if sys.version_info < (3, 10): ++ # Hash of two nans are not guaranteed to be equal. From https://docs.python.org/3/whatsnew/3.10.html : ++ # Hashes of NaN values of both float type and decimal.Decimal type now depend on object identity. ++ self.checkScript(fn, (float("nan"), float("nan"))) + self.checkScript(fn, (float("nan"), float("inf"))) + + def test_hash_int(self): +diff --git a/test/test_fx.py b/test/test_fx.py +index 625614d29a8..307b629cab3 100644 +--- a/test/test_fx.py ++++ b/test/test_fx.py +@@ -3280,6 +3280,7 @@ class TestFX(JitTestCase): + .run(scripted.code) + + @unittest.skipIf(IS_WINDOWS, "Python Windows bug? https://bugs.python.org/issue45108") ++ @unittest.skipIf(sys.version_info >= (3, 10), "Does not work on Python-3.10") + def test_assert(self): + def f(x): + assert x > 1 +@@ -4017,7 +4018,7 @@ class TestFunctionalTracing(JitTestCase): + + def functional_test(self): + if func_name in self.UNTRACEABLE_FUNCTIONALS_PY38 and \ +- sys.version_info >= (3, 8) and sys.version_info < (3, 10): ++ sys.version_info >= (3, 8) and sys.version_info < (3, 11): + exc, err = self.UNTRACEABLE_FUNCTIONALS_PY38[func_name] + with self.assertRaisesRegex(exc, err): + symbolic_trace(fn) +diff --git a/test/test_jit.py b/test/test_jit.py +index 7dbae135a9a..ea436482a55 100644 +--- a/test/test_jit.py ++++ b/test/test_jit.py +@@ -7450,6 +7450,9 @@ a") + # tensor from empty list is type float in python and annotated type in torchscript + if "annotate" in li and "dtype" not in option: + continue ++ # Skip unsigned tensor initializaton for signed values on 3.10 ++ if sys.version_info[:2] >= (3, 10) and "torch.uint8" in option and "-" in li: ++ continue + code = tensor_template.format(list_create=li, tensor_op=op, options=option) + scope = {} + exec(code, globals(), scope) +diff --git a/torch/csrc/utils/python_scalars.h b/torch/csrc/utils/python_scalars.h +index 7f454bdff82..7df0662fa2c 100644 +--- a/torch/csrc/utils/python_scalars.h ++++ b/torch/csrc/utils/python_scalars.h +@@ -1,6 +1,7 @@ + #pragma once + + #include ++#include + #include + + #include +@@ -8,13 +9,37 @@ + + namespace torch { namespace utils { + ++template ++inline T unpackIntegral(PyObject* obj, const char* type) { ++#if PY_VERSION_HEX >= 0x030a00f0 ++ // In Python-3.10 floats can no longer be silently converted to integers ++ // Keep backward compatible behavior for now ++ if (PyFloat_Check(obj)) { ++ return c10::checked_convert(THPUtils_unpackDouble(obj), type); ++ } ++ return c10::checked_convert(THPUtils_unpackLong(obj), type); ++#else ++ return static_cast(THPUtils_unpackLong(obj)); ++#endif ++} ++ + inline void store_scalar(void* data, at::ScalarType scalarType, PyObject* obj) { + switch (scalarType) { +- case at::kByte: *(uint8_t*)data = (uint8_t)THPUtils_unpackLong(obj); break; +- case at::kChar: *(int8_t*)data = (int8_t)THPUtils_unpackLong(obj); break; +- case at::kShort: *(int16_t*)data = (int16_t)THPUtils_unpackLong(obj); break; +- case at::kInt: *(int32_t*)data = (int32_t)THPUtils_unpackLong(obj); break; +- case at::kLong: *(int64_t*)data = THPUtils_unpackLong(obj); break; ++ case at::kByte: ++ *(uint8_t*)data = unpackIntegral(obj, "uint8"); ++ break; ++ case at::kChar: ++ *(int8_t*)data = unpackIntegral(obj, "int8"); ++ break; ++ case at::kShort: ++ *(int16_t*)data = unpackIntegral(obj, "int16"); ++ break; ++ case at::kInt: ++ *(int32_t*)data = unpackIntegral(obj, "int32"); ++ break; ++ case at::kLong: ++ *(int64_t*)data = unpackIntegral(obj, "int64"); ++ break; + case at::kHalf: + *(at::Half*)data = at::convert(THPUtils_unpackDouble(obj)); + break; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch new file mode 100644 index 00000000000..31d44fb01d1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch @@ -0,0 +1,22 @@ +This test is flaky when run with the type float16. +I.e. TestNNDeviceTypeCPU.test_embedding_bag_device_cpu_int32_int32_float16 & + TestNNDeviceTypeCPU.test_embedding_bag_device_cpu_int64_int64_float16 +fail. +See https://github.com/pytorch/pytorch/issues/86638 +So remove the half precision test. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_nn.py b/test/test_nn.py +index aad884ebd4f..b514f72a3e9 100644 +--- a/test/test_nn.py ++++ b/test/test_nn.py +@@ -18236,7 +18236,7 @@ class TestNNDeviceType(NNTestCase): + self.assertRaises(RuntimeError, lambda: es(input.view(-1), offset)) + + @skipMeta +- @dtypes(*itertools.product((torch.int, torch.long), (torch.int, torch.long), (torch.float, torch.double, torch.half))) ++ @dtypes(*itertools.product((torch.int, torch.long), (torch.int, torch.long), (torch.float, torch.double))) + def test_embedding_bag_device(self, device, dtypes): + self._test_EmbeddingBag(device, 'sum', False, wdtype=dtypes[2], dtype=dtypes[0], odtype=dtypes[1]) + self._test_EmbeddingBag(device, 'mean', False, wdtype=dtypes[2], dtype=dtypes[0], odtype=dtypes[1]) From 8ee368d5a36f73e2e13a2da77a18c0f4d6238746 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Wed, 30 Nov 2022 10:09:28 +0100 Subject: [PATCH 5658/9987] Add Molden-7.1 --- .../m/Molden/Molden-7.1-GCCcore-11.3.0.eb | 48 +++++++++++ .../Molden/Molden-7.1_fix_arg_handling.patch | 24 ++++++ ...olden-7.1_fix_makefile_for_easybuild.patch | 82 +++++++++++++++++++ .../makedepend-1.0.7-GCCcore-11.3.0.eb | 26 ++++++ 4 files changed, 180 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.1_fix_arg_handling.patch create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.1_fix_makefile_for_easybuild.patch create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..305f84282e9 --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'Molden' +version = '7.1' + +homepage = 'https://www3.cmbi.umcn.nl/molden' +description = """Molden is a package for displaying Molecular Density from the + Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical + packages Mopac/Ampac""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden'] +sources = ['%(namelower)s%(version)s.tar.gz'] +patches = [ + 'Molden-7.1_fix_makefile_for_easybuild.patch', + 'Molden-7.1_fix_arg_handling.patch', +] +checksums = [ + '98a39f0aa1667c14c36f40c0251522984245e5ba282af8fbc8a2f06079e40d43', # molden7.1.tar.gz + '78c9dd75fdc4c62392bb4284c377fbfd8bdae51f3f867540266723c3a978789c', # Molden-7.1_fix_makefile_for_easybuild.patch + 'e69941737369ec76049b4bd5d0e008d1e200b7043e44dae83ae058144699e924', # Molden-7.1_fix_arg_handling.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('makedepend', '1.0.7'), +] + +dependencies = [ + ('X11', '20220504'), + ('libglvnd', '1.4.0'), + ('libGLU', '9.0.2'), +] + +buildopts = 'CC="$CC" FC="$F90" FFLAGS="$FFLAGS -fallow-argument-mismatch" all' + +parallel = 1 + +files_to_copy = [(['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']], 'bin'), + 'CopyRight', 'README', 'REGISTER'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']] + ['README', 'REGISTER'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_arg_handling.patch b/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_arg_handling.patch new file mode 100644 index 00000000000..e01ce216125 --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_arg_handling.patch @@ -0,0 +1,24 @@ +# Use F2003 functions for argument handling. +# Author: maxim-masterv (SURF) +diff -Nru molden7.1.orig/src/molden.f molden7.1/src/molden.f +--- molden7.1.orig/src/molden.f 2022-05-06 22:35:25.000000000 +0200 ++++ molden7.1/src/molden.f 2022-11-29 20:17:13.900597108 +0100 +@@ -3813,15 +3813,15 @@ + endif + + iredir = 0 +- nargs = iargc() +- call getarg(0,liris) ++ nargs = COMMAND_ARGUMENT_COUNT() ++ call GET_COMMAND_ARGUMENT(0,liris) + call parsfn(liris,linlen(liris),20) + + ntargs = 0 + n = 0 + if (nargs.gt.0) then + 2013 n = n + 1 +- call getarg(n,liris) ++ call GET_COMMAND_ARGUMENT(n,liris) + if (liris(1:1).eq.'-') then + if (liris(1:2).eq.'-5') ido5d = 1 + if (liris(1:2).eq.'-7') ido7f = 1 diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_makefile_for_easybuild.patch b/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_makefile_for_easybuild.patch new file mode 100644 index 00000000000..b02b9c70f55 --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_makefile_for_easybuild.patch @@ -0,0 +1,82 @@ +# Make makefile EasyBuild friendly. +# Author: maxim-masterov (SURF) +diff -Nru molden7.1.orig/makefile molden7.1/makefile +--- molden7.1.orig/makefile 2022-01-21 12:28:48.000000000 +0100 ++++ molden7.1/makefile 2022-11-29 20:26:40.997854074 +0100 +@@ -13,10 +13,10 @@ + # Disregard compiler warnings on rdmolf.f + # + # +-CC = cc ++#CC = cc + LIBS = -lX11 -lm + LDR = ${FC} +-LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lXmu -lX11 -lm ++LIBSG = -lGLU -lGL -lXmu -lX11 -lm + ARCH := $(shell getconf LONG_BIT) + AFLAG= -m$(ARCH) + EXTEN= +@@ -29,20 +29,6 @@ + uname := $(shell uname -s) + os := + +-ifeq ($(uname), Linux) +- os := $(shell head -n 1 /etc/issue | cut -d" " -f1) +- ifeq ($(os), Ubuntu) +- EXTEN = exten +- EXTENZ = exten2 +- LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lX11 -lm +- endif +- ifeq ($(os), Debian) +- LIBSG = -L/usr/lib/X11 -lGLU -lGL -lX11 -lm +- endif +- +- choosefc := 'yes' +-endif +- + ifneq (,$(findstring CYGWIN,$(uname))) + uname := Linux + choosefc := 'yes' +@@ -52,18 +38,6 @@ + choosefc := 'yes' + endif + +- +-ifneq ($(choosefc), $(empty)) +- comg77 := $(shell which g77 | grep -i g77) +- comgfort := $(shell which gfortran | grep -i gfortran) +- ifneq ($(comg77), $(empty)) +- FC = g77 +- endif +- ifneq ($(comgfort), $(empty)) +- FC = gfortran +- endif +-endif +- + print-% : ; @echo $* = $($*) + # + # Linux version +@@ -108,17 +82,17 @@ + EXT = ${EXTRAZ} + endif + FFLAGS = -g ${AFLAG} +-LIBS = -L/usr/X11R6/lib -lX11 -lm ++LIBS = -lX11 -lm + ifeq ($(AFLAG),"-m64") +-LIBS = -L/usr/X11R6/lib64 -lX11 -lm ++LIBS = -lX11 -lm + endif + LDR = ${FC} -g ${AFLAG} +-CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 ++CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 + ifeq ($(os), Debian) +- CFLAGS = ${AFLAG} ${EXTRAZ} -c -I/usr/include/X11 -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 +- LIBS = -L/usr/lib/X11 -lX11 -lm ++ CFLAGS = ${AFLAG} ${EXTRAZ} -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 ++ LIBS = -lX11 -lm + ifeq ($(AFLAG),"-m64") +- LIBS = -L/usr/X11R6/lib64 -lX11 -lm ++ LIBS = -lX11 -lm + endif + endif + ifeq ($(os), FreeBSD) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..375e2d9f2a7 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.7' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['17c1adf0284aaee473abfff0e8d3e754770615e1275f2a0043b9d97a00ed5cc9'] + +builddependencies = [ + ('binutils', '2.38'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.3'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' From e3b48de3343a89fbb35f09ae7257bf6c54607687 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 30 Nov 2022 10:14:19 +0100 Subject: [PATCH 5659/9987] adding easyconfigs: PyTorch-Geometric-2.1.0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb --- ...0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb new file mode 100644 index 00000000000..27fbf46a606 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '2.1.0' +local_pytorchver = '1.12.1' +versionsuffix = '-PyTorch-%s-CUDA-%%(cudaver)s' % local_pytorchver + +homepage = 'https://github.com/rusty1s/pytorch_geometric' +description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', SYSTEM), + ('PyTorch', local_pytorchver, '-CUDA-%(cudaver)s'), + ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), + ('numba', '0.53.1'), + ('h5py', '3.2.1'), + ('tqdm', '4.61.2'), + ('RDFlib', '6.2.0'), + ('ASE', '3.22.0'), + ('YACS', '0.1.8'), +] + +use_pip = True + +exts_list = [ + ('googledrivedownloader', '0.4', { + 'modulename': 'google_drive_downloader', + 'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'], + }), + ('plyfile', '0.7.4', { + 'checksums': ['9e9a18d22a3158fcd74df38761d43a7facc6df75126f2ab9f4e9a5d4d2188652'], + }), + ('torch_scatter', version, { + 'checksums': ['3a7124c2a033552febbdc72407f7d4d8cb6dce465720e84ab831512e81c1d208'], + }), + ('torch_sparse', '0.6.15', { + 'checksums': ['3a741ae8a7cc19247a44de549fa4d593c4257b5f741e1eb5110b712a14209dd9'], + }), + ('torch_cluster', '1.6.0', { + 'checksums': ['249c1bd8c33a887b22bf569a59d0868545804032123594dd8c76ba1885859c39'], + }), + ('torch_spline_conv', '1.2.1', { + 'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'], + }), + ('python-louvain', '0.16', { + 'modulename': 'community.community_louvain', + 'checksums': ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'], + }), + ('torch_geometric', version, { + 'checksums': ['72653deca925885e4d613eb5c72268bb9710325d9c717516922499fbe1197079'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 7bcc8094ce3db34b1457f35102f1900eccff975a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 30 Nov 2022 10:27:37 +0100 Subject: [PATCH 5660/9987] adding easyconfigs: GlobalArrays-5.8.2-intel-2022a.eb --- .../GlobalArrays-5.8.2-intel-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb new file mode 100644 index 00000000000..4af8e53447d --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.8.2' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] + +configopts = ' --with-mpi --enable-i8' +configopts += ' --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' + +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', + 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 94b168c6396d4713b4e96b679e54bac2b6a127ad Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 30 Nov 2022 10:48:53 +0100 Subject: [PATCH 5661/9987] Fix ftp address --- easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb index 305f84282e9..5a87cef7f18 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb @@ -10,7 +10,7 @@ description = """Molden is a package for displaying Molecular Density from the toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden'] +source_urls = ['https://ftp.science.ru.nl/Molden/'] sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'Molden-7.1_fix_makefile_for_easybuild.patch', From 93fddda86a3291b8dc66f36dfedfe34283b1145d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 30 Nov 2022 10:52:04 +0100 Subject: [PATCH 5662/9987] add missing checksums --- .../easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb index 4af8e53447d..435986d2ef9 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb @@ -11,6 +11,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['51599e4abfe36f05cecfaffa33be19efbe9e9fa42d035fd3f866469b663c22a2'] configopts = ' --with-mpi --enable-i8' configopts += ' --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' From 2d7958b4c6ad394947f684cffab73969af003db5 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 30 Nov 2022 11:38:43 +0100 Subject: [PATCH 5663/9987] adding easyconfigs: OpenMolcas-22.10-intel-2022a.eb, OpenMolcas-22.10-intel-2022a-noGA.eb --- .../OpenMolcas-22.10-intel-2022a-noGA.eb | 47 ++++++++++++++++++ .../OpenMolcas-22.10-intel-2022a.eb | 48 +++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb new file mode 100644 index 00000000000..a173700d990 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'OpenMolcas' +version = '22.10' +versionsuffix = '-noGA' + +homepage = "https://gitlab.com/Molcas/OpenMolcas" +description = """OpenMolcas is a quantum chemistry software package. +This build does not support MPI and can only be run on a single node.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] +sources = ["OpenMolcas-v%(version)s.tar.gz"] +patches = ['OpenMolcas-21.06_mcpdft_deps.patch'] +checksums = [ + {'OpenMolcas-v22.10.tar.gz': 'd1d3d6c9bd69486c36f5285a51ac18e75c03540c5b33751855e94abc764d9658'}, + {'OpenMolcas-21.06_mcpdft_deps.patch': '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a'}, +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('HDF5', '1.12.2'), +] + +build_shared_libs = True + +configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' +configopts += '-DOPENMP=ON -DTOOLS=ON -DFDE=ON' +configopts += '-DMPI=OFF -DGA=OFF ' + +modextrapaths = {'PATH': ''} +modextravars = { + 'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', +} + +sanity_check_paths = { + 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, + 'sbin/help_basis', 'pymolcas'], + 'dirs': ['data/', 'basis_library/'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb new file mode 100644 index 00000000000..62257a69fe8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'OpenMolcas' +version = '22.10' + +homepage = "https://gitlab.com/Molcas/OpenMolcas" +description = "OpenMolcas is a quantum chemistry software package." + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] +sources = ["OpenMolcas-v%(version)s.tar.gz"] +patches = ['OpenMolcas-21.06_mcpdft_deps.patch'] +checksums = [ + {'OpenMolcas-v22.10.tar.gz': 'd1d3d6c9bd69486c36f5285a51ac18e75c03540c5b33751855e94abc764d9658'}, + {'OpenMolcas-21.06_mcpdft_deps.patch': '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a'}, +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('HDF5', '1.12.2'), + ('GlobalArrays', '5.8.2'), +] + +build_shared_libs = True + +preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' +configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' +configopts += '-DOPENMP=ON -DTOOLS=ON -DFDE=ON' +configopts += '-DMPI=ON -DGA=ON ' + +modextrapaths = {'PATH': ''} +modextravars = { + 'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', +} + +sanity_check_paths = { + 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, + 'sbin/help_basis', 'pymolcas'], + 'dirs': ['data/', 'basis_library/'], +} + +moduleclass = 'chem' From 8d27d191d89eb52c703f9b133b39428a3c78a50c Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 30 Nov 2022 13:38:57 +0100 Subject: [PATCH 5664/9987] adding easyconfigs: MEMOTE-0.13.0-foss-2021a.eb --- .../m/MEMOTE/MEMOTE-0.13.0-foss-2021a.eb | 134 ++++++++++++++++++ 1 file changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEMOTE/MEMOTE-0.13.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MEMOTE/MEMOTE-0.13.0-foss-2021a.eb b/easybuild/easyconfigs/m/MEMOTE/MEMOTE-0.13.0-foss-2021a.eb new file mode 100644 index 00000000000..9483459e6fd --- /dev/null +++ b/easybuild/easyconfigs/m/MEMOTE/MEMOTE-0.13.0-foss-2021a.eb @@ -0,0 +1,134 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'MEMOTE' +version = '0.13.0' + +homepage = 'https://github.com/opencobra/memote' +description = """The genome-scale metabolic model test suite""" +# software_license = 'LicenseApachev2' + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('COBRApy', '0.26.0'), + ('GitPython', '3.1.18'), + ('boto3', '1.20.13'), + ('openpyxl', '3.0.7'), + ('PyYAML', '5.4.1'), +] + +use_pip = True + +exts_list = [ + ('click-configfile', '0.2.3', { + 'checksums': ['95beec13bee950e98f43c81dcdabef4f644091559ea66298f9dadf59351d90d1'], + }), + ('click-log', '0.4.0', { + 'checksums': ['3970f8570ac54491237bcdb3d8ab5e3eef6c057df29f8c3d1151a51a9c23b975'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('jinja2-time', '0.2.0', { + 'checksums': ['d14eaa4d315e7688daa4969f616f226614350c48730bfa1692d2caebd8c90d40'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '7.0.0', { + 'modulename': 'slugify', + 'checksums': ['7a0f21a39fa6c1c4bf2e5984c9b9ae944483fd10b54804cb0e23a3ccd4954f0b'], + }), + ('cookiecutter', '2.1.1', { + 'checksums': ['f3982be8d9c53dac1261864013fdec7f83afd2e42ede6f6dd069c5e149c540d5'], + }), + ('numpydoc', '1.1.0', { + 'checksums': ['c36fd6cb7ffdc9b4e165a43f67bf6271a7b024d0bb6b00ac468c9e2bfc76448e'], + }), + ('click-default-group', '1.2.2', { + 'checksums': ['d9560e8e8dfa44b3562fbc9425042a0fd6d21956fcc2db0077f63f34253ab904'], + }), + ('jsonpointer', '2.3', { + 'checksums': ['97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a'], + }), + ('datapackage', '1.15.2', { + 'checksums': ['1e91a18c866914dea0acfe2aec785e6ec583c33766b0682c740b30bb7de88c58'], + }), + ('simpleeval', '0.9.12', { + 'checksums': ['3e0be507486d4e21cf9d08847c7e57dd61a1603950399985f7c5a0be7fd33e36'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + ('greenlet', '2.0.1', { + 'checksums': ['42e602564460da0e8ee67cb6d7236363ee5e131aa15943b6670e44e5c2ed0f67'], + }), + ('SQLAlchemy', '1.4.44', { + 'modulename': 'sqlalchemy', + 'checksums': ['2dda5f96719ae89b3ec0f1b79698d86eb9aecb1d54e990abb3fdd92c04b46a90'], + }), + ('unicodecsv', '0.14.1', { + 'checksums': ['018c08037d48649a0412063ff4eda26eaa81eff1546dbffa51fa5293276ff7fc'], + }), + ('ijson', '3.1.4', { + 'checksums': ['1d1003ae3c6115ec9b587d29dd136860a81a23c7626b682e2b5b12c9fd30e4ea'], + }), + ('jsonlines', '3.1.0', { + 'checksums': ['2579cb488d96f815b0eb81629e3e6b0332da0962a18fa3532958f7ba14a5c37f'], + }), + ('linear-tsv', '1.1.0', { + 'modulename': 'tsv', + 'checksums': ['b504d78f4075615ae75de86a16e5680701a441fc84da2a2cf9f94351ab1ccbf5'], + }), + ('tabulator', '1.53.5', { + 'checksums': ['0e2887d0b36483a292e75b118d7f03e710c1337435553b5f62d2a7a891b7fe55'], + }), + ('cached-property', '1.5.2', { + 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('tableschema', '1.20.2', { + 'checksums': ['cfa3b0aa1c0941002384c6288794f9488cb5ea9188cf84ac700d17758cb036e7'], + }), + ('goodtables', '2.5.4', { + 'checksums': ['67c51ac98967684763adb6406f92a683571d144b3a80095b0351a65f49848027'], + }), + ('pylru', '1.2.1', { + 'checksums': ['47ad140a63ab9389648dadfbb4330700e0ffeeb28ec04664ee47d37ed133b0f4'], + }), + ('pyperclip', '1.6.0', { + 'checksums': ['ce829433a9af640e08ee89b20f7c62132714bcc5d77df114044d0fccb8c3b3b8'], + }), + ('travis-encrypt', '1.1.2', { + 'modulename': 'travis', + 'checksums': ['0eaec20d99fb7a6051dae39195a51d81c365097675ad921d6c6381eabf014ce5'], + }), + ('memote', version, { + 'checksums': ['574620e67e461c6a2003ecd2c9bda01cafe5919c4c6f1653e382b9d74d8af05c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/memote'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["memote"] + +sanity_pip_check = True + +moduleclass = 'bio' From 5c8a45e5eafabd1f491f8661cfafd8b68c25afb3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Nov 2022 15:54:42 +0100 Subject: [PATCH 5665/9987] add numbat extension and requires dependencies to R-bundle-Bioconductor 3.15 + R 4.2.1 --- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 12 +++++++++ .../easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 27 +++++++++++++++++++ 2 files changed, 39 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 118a0158da3..5566af30766 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1101,6 +1101,18 @@ exts_list = [ ('scDblFinder', '1.10.0', { 'checksums': ['c0834495a342c6467d64dc899ba5913354ea5d53037c9be95e639950db6e2478'], }), + ('treeio', '1.20.2', { + 'checksums': ['a103a6953abf2014bd1bb8b2da4f2d7375bab338724d0bf864085981a85fd5cb'], + }), + ('ggtree', '3.4.4', { + 'checksums': ['c59f4879b4e4ee1a24d61bbec9bfddced3a7a6a747c9bc537bf2c84c2ca43840'], + }), + ('scistreer', '1.0.1', { + 'checksums': ['cb2461cb97a844a1cbdd9e5ecc1961ada0fc3ef186313c73cb07658a887a16dd'], + }), + ('numbat', '1.1.0', { + 'checksums': ['3cdda07de7329e6c886a1f60b2978bb776b04133080e97d82d5772fd666efc2c'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 3e4080c1ebf..3065e42243c 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3367,6 +3367,33 @@ exts_list = [ ('HGNChelper', '0.8.1', { 'checksums': ['aa3f0b3a8691ed93d63bec8f36d2954c6fcfd0b8b3efc705379248544c999363'], }), + ('logger', '0.2.2', { + 'checksums': ['4f1be7d4381f2fc591f19fdbfb8f3cccbf26c9fdbae104612f6e6d5762a97e22'], + }), + ('parallelDist', '0.2.6', { + 'checksums': ['30c6b3b85cf78c04a7dcd17ea7ed64356971f6ce48d15794078a18c53b249e06'], + }), + ('roptim', '0.1.6', { + 'checksums': ['7ef0c2a2ddb3703efaabf337fa0026485875d5ffb35ba3ef5d60eb0c62c30686'], + }), + ('yulab.utils', '0.0.5', { + 'checksums': ['6ecd4dc5dae40e86b7a462fdac3ab8c0b276dcae5a284eb43390a05b01e3056b'], + }), + ('ggfun', '0.0.9', { + 'checksums': ['5c740e9d1e73b77658f41ed65e21492f4e71b12c7c9ff4b9e52ebf5f8f197612'], + }), + ('gridGraphics', '0.5-1', { + 'checksums': ['29086e94e63891884c933b186b35511aac2a2f9c56967a72e4050e2980e7da8b'], + }), + ('ggplotify', '0.1.0', { + 'checksums': ['178f73d6d3dc391c3efb1a62c95fe38587044f9e3288dffb915d3687941bb38a'], + }), + ('aplot', '0.1.9', { + 'checksums': ['af0763620a757571caac769bad5398c22a4890af6cb5646ac5fa9039a114bb12'], + }), + ('tidytree', '0.4.1', { + 'checksums': ['fbc4364d17e1b1c26ed06af0cdf36c88a5bc562fdbd4731ab179e30bba4009eb'], + }), ] moduleclass = 'lang' From f1201d60610dd411c8364e2d990ddddcbf554730 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 30 Nov 2022 18:41:41 +0100 Subject: [PATCH 5666/9987] adding easyconfigs: STAR-CCM+-17.06.007.eb, STAR-CCM+-17.06.007-r8.eb --- .../s/STAR-CCM+/STAR-CCM+-17.06.007-r8.eb | 14 ++++++++++++++ .../easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007.eb | 13 +++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007-r8.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007.eb diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007-r8.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007-r8.eb new file mode 100644 index 00000000000..4a95d4c1766 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007-r8.eb @@ -0,0 +1,14 @@ +name = 'STAR-CCM+' +version = '17.06.007' +versionsuffix = '-r8' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +sources = ['%%(name)s%%(version)s_01_linux-x86_64%s.tar.gz' % versionsuffix] +checksums = ['d6417d2b778afb5e7222d0bf174e335c158b418f530f2e860cae32d1a48e4bfa'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007.eb new file mode 100644 index 00000000000..bace577350a --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007.eb @@ -0,0 +1,13 @@ +name = 'STAR-CCM+' +version = '17.06.007' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +sources = ['%(name)s%(version)s_01_linux-x86_64.tar.gz'] +checksums = ['b8c9d142deffde4ff9e9d8524cc2dc20e9f0035238b0ecebb8ea25e594c9165b'] + +moduleclass = 'cae' From 38f3860ad81cc321a663b646e60b0e93f2ea0c97 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 30 Nov 2022 18:11:26 +0000 Subject: [PATCH 5667/9987] adding easyconfigs: TensorFlow-2.8.4-foss-2021b.eb and patches: TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch --- .../TensorFlow/TensorFlow-2.8.4-foss-2021b.eb | 202 ++++++++++++++++++ ....8.4_remove-libclang-and-io-gcs-deps.patch | 34 +++ 2 files changed, 236 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb new file mode 100644 index 00000000000..15c5fd729ce --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb @@ -0,0 +1,202 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.8.4' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '4.2.2'), + ('protobuf', '3.17.3'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.33.1', '-nodocs'), + ('pybind11', '2.7.1'), + ('UnZip', '6.0'), + ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed +] +dependencies = [ + ('Python', '3.9.6'), + ('h5py', '3.6.0'), + ('cURL', '7.78.0'), + ('dill', '0.3.4'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.5.0'), + ('ICU', '69.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.29'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.36'), + ('protobuf-python', '3.17.3'), + ('flatbuffers-python', '2.0'), + ('libpng', '1.6.37'), + ('snappy', '1.1.9'), + ('zlib', '1.2.11'), + ('networkx', '2.6.3'), # required for pythran +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('tensorflow_estimator', '2.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['bee8e0520c60ae7eaf6ca8cb46c5a9f4b45725531380db8fbe38fcb48478b6bb'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('Werkzeug', '2.1.2', { + 'checksums': ['1ce08e8093ed67d638d63879fd1ba3735817f7a80de3674d293f5984f25fb6e6'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('Markdown', '3.3.7', { + 'checksums': ['cbb516f16218e643d8e0a95b309f77eb118cb138d39a4f27851e6a63581db874'], + }), + ('grpcio', '1.46.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['4835b0f5fedbee3a3d6eea48f4e65dffd30b52c078690fa97ddc9fcea1e3b35d'], + }), + ('oauthlib', '3.2.0', { + 'checksums': ['23a8208d75b902797ea29fd31fa80a15ed9dc2c6c16fe73f5d346f83f6fa27a2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('rsa', '4.8', { + 'checksums': ['5c6bd9dc7a543b7fe4304a631f8a8a3b674e2bbfc49c2ae96200cdbe55df6b17'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('cachetools', '5.1.0', { + 'checksums': ['8b3b8fa53f564762e5b221e9896798951e7f915513abf2ba072ce0f07f3f5a98'], + }), + ('google-auth', '2.6.6', { + 'modulename': 'google.auth', + 'checksums': ['1ba4938e032b73deb51e59c4656a00e0939cf0b1112575099f136babb4563312'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('tensorboard', '2.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['65a338e4424e9079f2604923bdbe301792adce2ace1be68da6b3ddf005170def'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('keras', '2.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['744d39dc6577dcd80ff4a4d41549e92b77d6a17e0edd58a431d30656e29bc94e'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.5.2', { + 'checksums': ['c55683ad725f5c00a41bc7db0225223e8be024b1fa564d039ed3390e4fd48fb3'], + }), + ('absl-py', '1.0.0', { + 'modulename': 'absl', + 'checksums': ['ac511215c01ee9ae47b19716599e8ccfa746f2e18de72bdf641b79b22afa27ea'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch', + 'TensorFlow-2.7.1_fix_cpu_count.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + '-//tensorflow/python/data/experimental/kernel_tests/service:fault_tolerance_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small --run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + 'checksums': [ + {'v2.8.4.tar.gz': 'c08a222792bdbff9da299c7885561ee27b95d414d1111c426efac4ccdce92cde'}, + {'TensorFlow-2.1.0_fix-cuda-build.patch': + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a'}, + {'TensorFlow-2.4.0_add-ldl.patch': '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.5.0_add-support-for-large-core-systems.patch': + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636'}, + {'TensorFlow-2.5.0_disable-avx512-extensions.patch': + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03'}, + {'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch': + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75'}, + {'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch': + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8'}, + {'TensorFlow-2.5.0_fix-crash-on-shutdown.patch': + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd'}, + {'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch': + 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483'}, + {'TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch': + '10a6daad2ef65d649a6d4a6659f97f833359b3c35d3ce15e63d2db2e331a6a35'}, + {'TensorFlow-2.7.1_fix_cpu_count.patch': + '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch new file mode 100644 index 00000000000..b9f3afe50d0 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch @@ -0,0 +1,34 @@ +This combines two patches from TensorFlow 2.7.1. + +tensorflow-io-gcs-filesystem is not available as a binary for all architectures and +building it requires TensorFlow to be installed, i.e. there is a cyclic dependency. +As it is not actually required (but optional) remove it from `REQUIRED_PACKAGES`. +See https://github.com/tensorflow/tensorflow/issues/56636 + +libclang was introduced in +https://github.com/tensorflow/tensorflow/commit/c211472000ff57bac7fcec9b0465cf73b37bf135 +> This is in preparation to open-source TF's TFRT backend. +> TFRT generates code using libclang python bindings as part of the build. +Hence it is not currently used and as it is not (easily) available for all architectures +simply remove it. + +Patch added by Simon Branford (University of Birmingham) + +--- tensorflow/tools/pip_package/setup.py.orig 2022-11-29 16:42:19.016145000 +0000 ++++ tensorflow/tools/pip_package/setup.py 2022-11-29 16:42:39.287641518 +0000 +@@ -78,7 +78,6 @@ + 'google_pasta >= 0.1.1', + 'h5py >= 2.9.0', + 'keras_preprocessing >= 1.1.1', # 1.1.0 needs tensorflow==1.7 +- 'libclang >= 9.0.1', + 'numpy >= 1.20', + 'opt_einsum >= 2.3.2', + # TODO(b/182876485): Protobuf 3.20 results in linker errors on Windows +@@ -101,7 +100,6 @@ + 'tensorboard >= 2.8, < 2.9', + 'tensorflow-estimator >= 2.8, < 2.9', + 'keras >= 2.8.0rc0, < 2.9', +- 'tensorflow-io-gcs-filesystem >= 0.23.1', + ] + + From 86b2154c791af929a207ef03fc95b6d7e2335cf6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 30 Nov 2022 18:28:13 +0000 Subject: [PATCH 5668/9987] split long lines --- .../easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb index 15c5fd729ce..5e83ea300e9 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb @@ -148,7 +148,8 @@ exts_list = [ 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', - 'test_tag_filters_gpu': 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' + '-benchmark-test,-v1only'), 'test_targets': [ '//tensorflow/core/...', '-//tensorflow/core:example_java_proto', @@ -170,7 +171,8 @@ exts_list = [ '-//tensorflow/python/data/experimental/kernel_tests/service:fault_tolerance_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", - 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small --run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", 'with_xla': True, 'checksums': [ {'v2.8.4.tar.gz': 'c08a222792bdbff9da299c7885561ee27b95d414d1111c426efac4ccdce92cde'}, From 6dcc9281a466822d9b15dd444c9b9ba98951b9f0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 30 Nov 2022 18:33:02 +0000 Subject: [PATCH 5669/9987] return comments that --inject-checksums removed --- .../t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb index 5e83ea300e9..a3e3a25f20d 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb @@ -157,17 +157,24 @@ exts_list = [ '//tensorflow/cc/...', '//tensorflow/c/...', '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway '-//tensorflow/c/eager:c_api_test_gpu', '-//tensorflow/c/eager:c_api_distributed_test', '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 '-//tensorflow/c/eager:c_api_cluster_test_gpu', '-//tensorflow/c/eager:c_api_remote_function_test_gpu', '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 '-//tensorflow/core/common_runtime:mkl_layout_pass_test', '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + # All tests in this directory fail with segfault (TensorFlow Graph IR) '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + # Fails on e.g. AMD EPYC and known to be flaky on Mac: https://github.com/tensorflow/tensorflow/issues/56717 '-//tensorflow/python/data/experimental/kernel_tests/service:fault_tolerance_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", From bb01ff5e5f8401f9ddc48f0b641117784f36da77 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 1 Dec 2022 10:33:34 +0100 Subject: [PATCH 5670/9987] adding easyconfigs: Alfred-0.2.6-GCC-11.2.0.eb --- .../a/Alfred/Alfred-0.2.6-GCC-11.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/Alfred/Alfred-0.2.6-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Alfred/Alfred-0.2.6-GCC-11.2.0.eb b/easybuild/easyconfigs/a/Alfred/Alfred-0.2.6-GCC-11.2.0.eb new file mode 100644 index 00000000000..63a34e4004d --- /dev/null +++ b/easybuild/easyconfigs/a/Alfred/Alfred-0.2.6-GCC-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Alfred' +version = '0.2.6' + +homepage = "https://www.gear-genomics.com/alfred/" +description = """Alfred is an efficient and versatile command-line application + that computes multi-sample quality control metrics in a read-group aware manner. + Alfred supports read counting, feature annotation and haplotype-resolved consensus + computation using multiple sequence alignments.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'tobiasrausch' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['2f92cc1acc1f059a75468fca49f755c25947d59f39f2225abaaa4d145ac971a8'] + +dependencies = [ + ('Boost', '1.77.0'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.14'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('zstd', '1.5.0'), +] + +files_to_copy = [(['src/%(namelower)s'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From c42a0661329ff63b1e3134267ebb81de54f1608f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Dec 2022 10:34:30 +0100 Subject: [PATCH 5671/9987] adding easyconfigs: Bonnie++-2.00a-GCC-10.3.0.eb --- .../b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb new file mode 100644 index 00000000000..b4663ebc3f5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'Bonnie++' +version = '2.00a' + +homepage = 'https://www.coker.com.au/bonnie++' +description = """Bonnie++-1.97: Enhanced performance Test of Filesystem I/O""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://www.coker.com.au/bonnie++/'] +sources = [SOURCELOWER_TGZ] +checksums = ['a8d33bbd81bc7eb559ce5bf6e584b9b53faea39ccfb4ae92e58f27257e468f0e'] + +sanity_check_paths = { + 'files': ['sbin/bonnie++'], + 'dirs': [] +} + +sanity_check_commands = ["bonnie++ --help 2>&1 | grep '^bonnie'"] + +moduleclass = 'tools' From d60aefdb6ee0fe3ae9548440999ed054d58cfd13 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 1 Dec 2022 09:54:46 +0000 Subject: [PATCH 5672/9987] adding easyconfigs: tensorflow-probability-0.16.0-foss-2021b.eb --- ...ensorflow-probability-0.16.0-foss-2021b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.16.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.16.0-foss-2021b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.16.0-foss-2021b.eb new file mode 100644 index 00000000000..05bea7aff46 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.16.0-foss-2021b.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'PythonBundle' + +name = 'tensorflow-probability' +version = '0.16.0' + +homepage = 'https://www.tensorflow.org/probability' +description = """TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'pic': True} + +dependencies = [ + ('Python', '3.9.6'), + ('TensorFlow', '2.8.4'), + ('dm-tree', '0.1.6'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + (name, version, { + 'installopts': '--install-option="--release"', + 'modulename': 'tensorflow_probability', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/probability/archive/'], + 'checksums': ['0c8b8bb00403af56979f5c5cfda6fb3ea6f3e5efc4530ab66889415d230ebd81'], + }), +] + +sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] + +sanity_pip_check = True + +moduleclass = 'lib' From eb30861033549b9a0861dcf3b1b8b26a62420699 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 1 Dec 2022 12:45:45 +0100 Subject: [PATCH 5673/9987] Downgrade version of GA to match what is already used in other PRs for this toolchain version --- .../easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb index 62257a69fe8..06c24894075 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb @@ -22,7 +22,7 @@ builddependencies = [('CMake', '3.23.1')] dependencies = [ ('Python', '3.10.4'), ('HDF5', '1.12.2'), - ('GlobalArrays', '5.8.2'), + ('GlobalArrays', '5.8.1'), ] build_shared_libs = True From 4e61d4f5ff141bb13f6488310c7b2fac0aeafb56 Mon Sep 17 00:00:00 2001 From: Maxim Date: Thu, 1 Dec 2022 15:03:20 +0100 Subject: [PATCH 5674/9987] Update OpenMolcas-22.06-intel-2022a.eb --- .../o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb index 77b806ac4f4..0cbe3d6e3df 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb @@ -17,20 +17,21 @@ checksums = [ '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a', # OpenMolcas-21.06_mcpdft_deps.patch ] +builddependencies = [('CMake', '3.23.1')] + dependencies = [ ('GlobalArrays', '5.8.1'), ('HDF5', '1.12.2'), ('Python', '3.10.4'), ] -builddependencies = [('CMake', '3.23.1')] - separate_build_dir = True +build_shared_libs = True preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' configopts += '-DMPI=ON -DOPENMP=ON -DGA=ON ' -configopts += '-DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON' +configopts += '-DTOOLS=ON -DFDE=ON' modextrapaths = {'PATH': ''} modextravars = { From fffe2f973ee41c2365a3381c69df7f7856ce2988 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 1 Dec 2022 17:05:43 +0100 Subject: [PATCH 5675/9987] delete patch (already added by PR #16166) --- ...remove_undeclared_redundant_variable.patch | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch b/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch deleted file mode 100644 index 3bfe94fd93a..00000000000 --- a/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch +++ /dev/null @@ -1,27 +0,0 @@ -Remove the undeclared (and unused) variable i from the private clause -in an OpenMP pragma, which otherwise results in an error: - - 93 | !$omp parallel do private(ihkl,i,f,angle) - | 1 -Error: Symbol i at (1) has no IMPLICIT type - -Bob Dröge, University of Groningen, 2022-08-18 ---- amber22_src.orig/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:24.807724049 +0200 -+++ amber22_src/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:42.039809811 +0200 -@@ -90,7 +90,7 @@ - call check_precondition(size(frac, 2) == size(scatter_type_index)) - call check_precondition(size(hkl, 2) == size(atomic_scatter_factor, 1)) - -- !$omp parallel do private(ihkl,i,f,angle) -+ !$omp parallel do private(ihkl,f,angle) - do ihkl = 1, size(hkl, 2) - - ! Fhkl = SUM( fj * exp(2 * M_PI * i * (h * xj + k * yj + l * zj)) ), -@@ -127,4 +127,4 @@ - end subroutine calc_f_non_bulk - - --end module xray_non_bulk_impl_cpu_module -\ No newline at end of file -+end module xray_non_bulk_impl_cpu_module - From 0f955aeeb754a9b070da9f2eedd4161c299ae07d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 1 Dec 2022 17:07:39 +0100 Subject: [PATCH 5676/9987] Use SYSTEM instead of True for system-level deps --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 9d5139c40a3..036301c8c41 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -88,7 +88,7 @@ dependencies = [ ('PnetCDF', '1.12.3'), ('Tkinter', '3.9.6'), ('X11', '20210802'), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), ] From b5810670afcfdb8ed9c7860fa649b9789fba7d87 Mon Sep 17 00:00:00 2001 From: Maxim Date: Thu, 1 Dec 2022 17:13:19 +0100 Subject: [PATCH 5677/9987] Update OpenMolcas-22.06-intel-2022a.eb --- .../easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb index 0cbe3d6e3df..b8d19e00410 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb @@ -25,7 +25,6 @@ dependencies = [ ('Python', '3.10.4'), ] -separate_build_dir = True build_shared_libs = True preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' From 4f5688325d003ac34702632cfde3697cc0ca7915 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 1 Dec 2022 19:15:38 +0000 Subject: [PATCH 5678/9987] Update easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb --- easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb index b4663ebc3f5..6876b4e9f65 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb @@ -13,7 +13,7 @@ name = 'Bonnie++' version = '2.00a' homepage = 'https://www.coker.com.au/bonnie++' -description = """Bonnie++-1.97: Enhanced performance Test of Filesystem I/O""" +description = """Enhanced performance Test of Filesystem I/O""" toolchain = {'name': 'GCC', 'version': '10.3.0'} From 9a70cfc6df30558484d2421d2d6b32d81b352ce6 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 1 Dec 2022 22:15:30 +0100 Subject: [PATCH 5679/9987] adding easyconfigs: pysteps-1.7.1-foss-2022a.eb and patches: pysteps-1.7.1_h5py-3.7_compat.patch --- .../p/pysteps/pysteps-1.7.1-foss-2022a.eb | 52 +++++++++++++++++++ .../pysteps-1.7.1_h5py-3.7_compat.patch | 17 ++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pysteps/pysteps-1.7.1_h5py-3.7_compat.patch diff --git a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb new file mode 100644 index 00000000000..1716b3638df --- /dev/null +++ b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'pysteps' +version = '1.7.1' + +homepage = 'https://pysteps.github.io/' +description = """ +Pysteps is an open-source and community-driven Python library for probabilistic +precipitation nowcasting, i.e. short-term ensemble prediction systems.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('OpenCV', '4.6.0', '-contrib'), + ('Pillow', '9.1.1'), + ('pyproj', '3.4.0'), + ('matplotlib', '3.5.2'), + ('dask', '2022.10.0'), + ('netcdf4-python', '1.6.1'), + ('xarray', '2022.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('jsmin', '3.0.1', { + 'checksums': ['c0959a121ef94542e807a674142606f7e90214a2b3d1eb17300244bbb5cc2bfc'], + }), + ('pyFFTW', '0.13.0', { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'checksums': ['da85102405c0bd95d57eb19e99b01a0729d8406cb204c3900894b873784253da'], + }), + (name, version, { + 'patches': ['pysteps-1.7.1_h5py-3.7_compat.patch'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pySTEPS/pysteps/archive/'], + 'checksums': [ + {'v1.7.1.tar.gz': '5063d7546d9995ec6ca52a5b4e50ef3f3c1ae43088a55e370af4aec18162a22f'}, + {'pysteps-1.7.1_h5py-3.7_compat.patch': 'c2b1a47d7151a7f4072dce797c6303314c0d8fd7683b0001deb43f24357ed977'}, + ], + }), + ('pysteps-nwp-importers', '6ca1582', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/pySTEPS/pysteps-nwp-importers/archive/'], + 'checksums': ['e9aea5f1c49dadf0bc878822cd9403db93cf473c8ad21d8bfda799136c87f4db'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1_h5py-3.7_compat.patch b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1_h5py-3.7_compat.patch new file mode 100644 index 00000000000..853055ec24e --- /dev/null +++ b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1_h5py-3.7_compat.patch @@ -0,0 +1,17 @@ +Fix compatibility with h5py v3.7 +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur pysteps-1.7.1.orig/pysteps/io/importers.py pysteps-1.7.1/pysteps/io/importers.py +--- pysteps-1.7.1.orig/pysteps/io/importers.py 2022-09-25 22:49:54.000000000 +0200 ++++ pysteps-1.7.1/pysteps/io/importers.py 2022-11-25 13:00:14.948382946 +0100 +@@ -1377,7 +1377,10 @@ + raise IOError("requested quantity %s not found" % qty) + + where = f["where"] +- proj4str = where.attrs["projdef"].decode() ++ proj4str = where.attrs["projdef"] ++ if(not isinstance(proj4str, str)): ++ proj4str = proj4str.decode() ++ + pr = pyproj.Proj(proj4str) + + ll_lat = where.attrs["LL_lat"] From b8ab8ca6c3eaac0827add186726786641960b781 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 1 Dec 2022 22:45:19 +0100 Subject: [PATCH 5680/9987] fix xarray version --- easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb index 1716b3638df..6c52576341f 100644 --- a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb @@ -19,7 +19,7 @@ dependencies = [ ('matplotlib', '3.5.2'), ('dask', '2022.10.0'), ('netcdf4-python', '1.6.1'), - ('xarray', '2022.9.0'), + ('xarray', '2022.6.0'), ] use_pip = True From 25727ca728bf3a1a5514bb9ffd0195bbdfc079ce Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 2 Dec 2022 09:28:33 +0100 Subject: [PATCH 5681/9987] fix homepage --- easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb index a6c09399b71..4f00955fdf9 100644 --- a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb @@ -5,7 +5,7 @@ name = 'n2v' version = '0.3.2' versionsuffix = '-CUDA-%(cudaver)s' -homepage = 'https://github.com/juglab/cryoCARE_pip' +homepage = 'https://github.com/juglab/n2v' description = """ Noise2Void - Learning Denoising from Single Noisy Images The field of image denoising is currently dominated by discriminative deep From 4b97835c4ce4af35f5412aa7cc7772c2bf18b855 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 2 Dec 2022 10:19:00 +0100 Subject: [PATCH 5682/9987] use correct order for patch checksums --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 036301c8c41..c649a8f5035 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -61,8 +61,8 @@ checksums = [ 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch # AmberTools-22_fix_missing_error_check_on_test_run.patch 'a86eee60bd65c16a849469e303cb99dfc207cbadd2ae9e70b9ff580ced785475', - 'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e', # Amber-22_reduce_precision_of_kmmd_test.patch '3fc08a2cf61f3eefd094554e60c88b14c9f5071f94e0a0a15c6b55fe321bfc78', # AmberTools-22_fix_cuda_version_check.patch + 'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e', # Amber-22_reduce_precision_of_kmmd_test.patch # Amber-22_remove_undeclared_redundant_variable.patch 'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb', ] From bb109fa47fc3d769e1830d032623b0216cae6f55 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 2 Dec 2022 12:31:55 +0100 Subject: [PATCH 5683/9987] Git subtree support Git subtree is part of git since 1.7, and is default on OS git - we shouldn't have less functionality --- easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb index 7760dcfd6bd..001f08105d6 100644 --- a/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb @@ -39,6 +39,8 @@ preconfigopts = 'make configure && ' # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" +postinstallcmds = ['cd contrib/subtree; make install'] + sanity_check_paths = { 'files': ['bin/git'], 'dirs': ['libexec/git-core', 'share'], From 901cd22c51d1eeced500c1a792ca5a09b1951049 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 2 Dec 2022 12:35:20 +0100 Subject: [PATCH 5684/9987] Git subtree support Git subtree is part of git since 1.7, and it gets installed by default on the OS package of git. --- easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb index 214a4cc7228..658c91a6dd5 100644 --- a/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb @@ -39,6 +39,8 @@ preconfigopts = 'make configure && ' # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" +postinstallcmds = ['cd contrib/subtree; make install'] + sanity_check_paths = { 'files': ['bin/git'], 'dirs': ['libexec/git-core', 'share'], From 4cf2c16db72886057c5a2fa8d22fb47cd81f1f96 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 2 Dec 2022 15:30:57 +0100 Subject: [PATCH 5685/9987] adding easyconfigs: cuDNN-8.7.0.84-CUDA-11.8.0.eb --- .../c/cuDNN/cuDNN-8.7.0.84-CUDA-11.8.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.7.0.84-CUDA-11.8.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.7.0.84-CUDA-11.8.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.7.0.84-CUDA-11.8.0.eb new file mode 100644 index 00000000000..8443701d7c4 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.7.0.84-CUDA-11.8.0.eb @@ -0,0 +1,40 @@ +name = 'cuDNN' +version = '8.7.0.84' +versionsuffix = '-CUDA-%(cudaver)s' +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN is tied to specific to CUDA versions, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +local_cuda_major = '11' + +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/%%(cudashortver)s/' % local_short_ver # noqa: E501 +] +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = [{ + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '976c4cba7233c97ae74006afab5172976300ba40f5b250a21f8cf71f59c9f76d', + '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '0433d6d8b6841298e049e8a542750aa330a6e046a52ad95fae0c2f75dabe5575', + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'cf967f78dbf6c075243cc83aa18759e370db3754aa15b12a0a14e8bf67a3a9d4', +}] + +dependencies = [('CUDA', '11.8.0')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From c02eb63373defb8485ec294b7a3430a5bc4c706b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 2 Dec 2022 20:57:38 +0100 Subject: [PATCH 5686/9987] adding easyconfigs: mold-1.7.1-GCCcore-12.2.0.eb --- .../m/mold/mold-1.7.1-GCCcore-12.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7345b723f61 --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'mold' +version = '1.7.1' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fa2558664db79a1e20f09162578632fa856b3cde966fbcb23084c352b827dfa9'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = "-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=c++" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' From 0f49063a158908cb1fef76b756e274302f32cd49 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 2 Dec 2022 23:08:03 +0100 Subject: [PATCH 5687/9987] update easyconfigs: NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb --- .../NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb | 46 ++++++++++--------- 1 file changed, 24 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb index ba7dbd9499e..e59c093c9fa 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb @@ -27,34 +27,36 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', versionsuffix), ('NCCL', '2.10.3', versionsuffix), ] skipsteps = ['configure'] -prebuildopts = 'export NVSHMEM_USE_GDRCOPY=1 && ' -prebuildopts += 'export GDRCOPY_HOME=${EBROOTGDRCOPY} && ' - -prebuildopts += 'export MPI_HOME=${EBROOTOPENMPI} && ' -prebuildopts += 'export NVSHMEM_MPI_SUPPORT=1 && ' -prebuildopts += 'export NVSHMEMTEST_USE_MPI_LAUNCHER=1 && ' - -prebuildopts += 'export NCCL_HOME=${EBROOTNCCL} && ' -prebuildopts += 'export NVSHMEM_USE_NCCL=1 && ' - -prebuildopts += 'export NVSHMEM_BUILDDIR=%(builddir)s && ' -prebuildopts += 'export NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj && ' -prebuildopts += 'export NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj && ' -prebuildopts += 'export NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj && ' -prebuildopts += 'export NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj && ' - -prebuildopts += 'export NVSHMEM_PREFIX=%(installdir)s && ' -prebuildopts += 'export NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples && ' -prebuildopts += 'export NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest && ' -prebuildopts += 'export NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest && ' -prebuildopts += 'export NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test && ' +prebuildopts = 'export %s &&' % ' '.join([ + 'NVSHMEM_USE_GDRCOPY=1', + 'GDRCOPY_HOME=${EBROOTGDRCOPY}', + + 'MPI_HOME=${EBROOTOPENMPI}', + 'NVSHMEM_MPI_SUPPORT=1', + 'NVSHMEMTEST_USE_MPI_LAUNCHER=1', + + 'NCCL_HOME=${EBROOTNCCL}', + 'NVSHMEM_USE_NCCL=1', + + 'NVSHMEM_BUILDDIR=%(builddir)s', + 'NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj', + 'NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj', + 'NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj', + 'NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj', + + 'NVSHMEM_PREFIX=%(installdir)s', + 'NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples', + 'NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest', + 'NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest', + 'NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test', +]) preinstallopts = prebuildopts From 8e0c5fd34382a07bc887b96c140df72f09123581 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 2 Dec 2022 23:28:15 +0100 Subject: [PATCH 5688/9987] adding easyconfigs: NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb --- .../NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..0876e2e7643 --- /dev/null +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb @@ -0,0 +1,70 @@ +easyblock = 'ConfigureMake' + +name = 'NVSHMEM' +version = '2.7.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nvshmem' +description = """NVSHMEM is a parallel programming interface based on OpenSHMEM that provides +efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a +global address space for data that spans the memory of multiple GPUs and can be +accessed with fine-grained GPU-initiated operations, CPU-initiated operations, +and operations on CUDA streams. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +download_instructions = """The sources of NVSHMEM can be downloaded at NVIDIA's webpage when you have signed up for +their (free) developer program: +https://developer.nvidia.com/nvshmem-downloads""" + +sources = ['%(namelower)s_src_%(version)s-6.txz'] +checksums = ['23ed9b0187104dc87d5d2bc1394b6f5ff29e8c19138dc019d940b109ede699df'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('NCCL', '2.12.12', versionsuffix), +] + +skipsteps = ['configure'] + +prebuildopts = 'export %s &&' % ' '.join([ + 'NVSHMEM_USE_GDRCOPY=1', + 'GDRCOPY_HOME=${EBROOTGDRCOPY}', + + 'MPI_HOME=${EBROOTOPENMPI}', + 'NVSHMEM_MPI_SUPPORT=1', + 'NVSHMEMTEST_USE_MPI_LAUNCHER=1', + + 'NCCL_HOME=${EBROOTNCCL}', + 'NVSHMEM_USE_NCCL=1', + + 'NVSHMEM_BUILDDIR=%(builddir)s', + 'NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj', + 'NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj', + 'NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj', + 'NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj', + + 'NVSHMEM_PREFIX=%(installdir)s', + 'NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples', + 'NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest', + 'NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest', + 'NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test', +]) + +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['lib/libnvshmem.a', 'lib/nvshmem_bootstrap_mpi.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +modextravars = {'NVSHMEM_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 8e84eb93b72ca85a67339a41e2e4a6ea04ab63d0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 3 Dec 2022 23:24:22 +0100 Subject: [PATCH 5689/9987] update mold-1.7.1-GCCcore-12.2.0.eb: remove not needed configsopts --- easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb index 7345b723f61..9dac36ca914 100644 --- a/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb @@ -21,8 +21,6 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] -configopts = "-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=c++" - runtest = 'test' sanity_check_paths = { From 17e9a433cab17c63b650b749ed0f749074def2f3 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 4 Dec 2022 12:44:53 +0000 Subject: [PATCH 5690/9987] testsuite exception --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9e66b9f8b2a..3160d1b9ad9 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -582,6 +582,8 @@ def check_dep_vars(self, gen, dep, dep_vars): ('2.5.0;', ['AlphaFold-2.1.2-']), # medaka 1.5.0 (foss/2021a) depends on TensorFlow >=2.5.2, <2.6.0 ('2.5.3;', ['medaka-1.5.0-']), + # tensorflow-probability version to TF version + ('2.8.4;', ['tensorflow-probability-0.16.0-']), ], # smooth-topk uses a newer version of torchvision 'torchvision': [('0.11.3;', ['smooth-topk-1.0-20210817-'])], From 0e44f70703a3ab2f09aa2627ae75e119b4d3e58c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 5 Dec 2022 08:11:10 +0100 Subject: [PATCH 5691/9987] rename sources on download --- .../easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb index 6c52576341f..241d7b89116 100644 --- a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb @@ -35,16 +35,16 @@ exts_list = [ }), (name, version, { 'patches': ['pysteps-1.7.1_h5py-3.7_compat.patch'], - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/pySTEPS/pysteps/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': [ - {'v1.7.1.tar.gz': '5063d7546d9995ec6ca52a5b4e50ef3f3c1ae43088a55e370af4aec18162a22f'}, + {'pysteps-1.7.1.tar.gz': '5063d7546d9995ec6ca52a5b4e50ef3f3c1ae43088a55e370af4aec18162a22f'}, {'pysteps-1.7.1_h5py-3.7_compat.patch': 'c2b1a47d7151a7f4072dce797c6303314c0d8fd7683b0001deb43f24357ed977'}, ], }), - ('pysteps-nwp-importers', '6ca1582', { - 'source_tmpl': '%(version)s.tar.gz', + ('pysteps-nwp-importers', '20220124', { 'source_urls': ['https://github.com/pySTEPS/pysteps-nwp-importers/archive/'], + 'sources': [{'download_filename': '6ca1582.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['e9aea5f1c49dadf0bc878822cd9403db93cf473c8ad21d8bfda799136c87f4db'], }), ] From 208570f5ae1971ea5935822a09ab1dd4c2a466ce Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 5 Dec 2022 11:10:44 +0100 Subject: [PATCH 5692/9987] fix homepage --- easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb index 5a87cef7f18..af605779f96 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'MakeCp' name = 'Molden' version = '7.1' -homepage = 'https://www3.cmbi.umcn.nl/molden' +homepage = 'https://www.theochem.ru.nl/molden/' description = """Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac""" From 41bf0895e03a05391cbd1510136f6a9cb213ff36 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 5 Dec 2022 12:23:22 +0100 Subject: [PATCH 5693/9987] make sure configopts does not end up with missing space between options. --- .../OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb | 13 ++++++++++--- .../o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb | 13 ++++++++++--- 2 files changed, 20 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb index a173700d990..fb6ba76e942 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb @@ -27,9 +27,16 @@ dependencies = [ build_shared_libs = True -configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' -configopts += '-DOPENMP=ON -DTOOLS=ON -DFDE=ON' -configopts += '-DMPI=OFF -DGA=OFF ' +_copts = [ + '-DLINALG=MKL', + '-DMKLROOT=$MKLROOT', + '-DOPENMP=ON', + '-DTOOLS=ON', + '-DFDE=ON', + '-DMPI=OFF', + '-DGA=OFF', +] +configopts = ' '.join(_copts) modextrapaths = {'PATH': ''} modextravars = { diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb index 06c24894075..412aae94403 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb @@ -28,9 +28,16 @@ dependencies = [ build_shared_libs = True preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' -configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' -configopts += '-DOPENMP=ON -DTOOLS=ON -DFDE=ON' -configopts += '-DMPI=ON -DGA=ON ' +_copts = [ + '-DLINALG=MKL', + '-DMKLROOT=$MKLROOT', + '-DOPENMP=ON', + '-DTOOLS=ON', + '-DFDE=ON', + '-DMPI=ON', + '-DGA=ON', +] +configopts = ' '.join(_copts) modextrapaths = {'PATH': ''} modextravars = { From 452419edf55084e67600bda613c37c90273b91e4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 5 Dec 2022 16:23:57 +0100 Subject: [PATCH 5694/9987] Skip remaining PyTorch 1.12.1 test timeout --- .../p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index 7f1ab7e67f8..d70fb060378 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -24,6 +24,7 @@ patches = [ 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -64,6 +65,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.11.1_skip-test_init_from_local_shards.patch + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch From 240d54c072800c73d07b29e08973917fc5e6613c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 5 Dec 2022 17:58:38 +0000 Subject: [PATCH 5695/9987] adding easyconfigs: MOB-suite-3.1.0-foss-2019b-Python-3.7.4.eb, ETE-3.1.2-foss-2019b-Python-3.7.4.eb --- .../ETE/ETE-3.1.2-foss-2019b-Python-3.7.4.eb | 35 +++++++++++++++++ ...MOB-suite-3.1.0-foss-2019b-Python-3.7.4.eb | 38 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/m/MOB-suite/MOB-suite-3.1.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..18293697388 --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +checksums = ['4fc987b8c529889d6608fab1101f1455cb5cbd42722788de6aea9c7d0a8e59e9'] + +dependencies = [ + ('lxml', '4.4.2'), + ('Python', '3.7.4'), + ('PyQt5', '5.13.2', versionsuffix), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MOB-suite/MOB-suite-3.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOB-suite/MOB-suite-3.1.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..be9c4937022 --- /dev/null +++ b/easybuild/easyconfigs/m/MOB-suite/MOB-suite-3.1.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'MOB-suite' +version = '3.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/phac-nml/mob-suite' +description = "Software tools for clustering, reconstruction and typing of plasmids from draft assemblies" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('Biopython', '1.75', versionsuffix), + ('PycURL', '7.43.0.5', versionsuffix), + ('PyTables', '3.6.1', versionsuffix), + ('ETE', '3.1.2', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mob-suite', version, { + 'sources': ['mob_suite-%(version)s.tar.gz'], + 'checksums': ['03b502673dd115ccceaf912330cb7f4e38b77c9ab895119891ecf8ef0e115f91'], + }), +] + +sanity_check_paths = { + 'files': ['bin/mob_init'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['mob_init -V'] + +moduleclass = 'bio' From dd4cbe8810d95c17642d6416639aba75f0ec7540 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 5 Dec 2022 18:27:37 +0000 Subject: [PATCH 5696/9987] adding easyconfigs: XGBoost-1.7.1-foss-2022a.eb --- .../x/XGBoost/XGBoost-1.7.1-foss-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.1-foss-2022a.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.1-foss-2022a.eb new file mode 100644 index 00000000000..36425089ffc --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.1-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '1.7.1' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb302c5c33e14bab94603940987940f29203ecb8767a7a719daf579fbfaace64'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# use the parallel parameter from EB instead of total procs in the system +preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&" + +moduleclass = 'lib' From d4c8979e46f2bb5c2065e99e9e03c179baec11c7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 6 Dec 2022 12:58:28 +0100 Subject: [PATCH 5697/9987] adding easyconfigs: SAP-1.1.3-GCC-11.3.0.eb --- .../easyconfigs/s/SAP/SAP-1.1.3-GCC-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAP/SAP-1.1.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SAP/SAP-1.1.3-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SAP/SAP-1.1.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..0b8512ddefa --- /dev/null +++ b/easybuild/easyconfigs/s/SAP/SAP-1.1.3-GCC-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'SAP' +version = '1.1.3' + +homepage = 'https://github.com/mathbio-nimr-mrc-ac-uk/SAP' +description = "SAP is a pairwise structure alignment via double dynamic programming" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'mathbio-nimr-mrc-ac-uk' +source_urls = [GITHUB_SOURCE] +sources = ['v.%(version)s.tar.gz'] +checksums = ['1ee5025f8a900cd9d9c490f7038b98d80a619e3015f2dc97b869ea3033c459e0'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Perl', '5.34.1'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/sap'], + 'dirs': [], +} + +moduleclass = 'bio' From 7e18786d5bbe93fbf3713c3292dab0efce325436 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 6 Dec 2022 17:23:10 +0100 Subject: [PATCH 5698/9987] adding easyconfigs: DendroPy-4.5.2-GCCcore-11.3.0.eb --- .../DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1ffdbf30d5e --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.5.2' + +homepage = 'https://dendropy.org/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["sumtrees.py --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From e580ce3034dd84c87617e784fcddad7c820f8035 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 6 Dec 2022 17:24:05 +0100 Subject: [PATCH 5699/9987] adding easyconfigs: arpack-ng-3.8.0-foss-2022a.eb --- .../a/arpack-ng/arpack-ng-3.8.0-foss-2022a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022a.eb new file mode 100644 index 00000000000..7aba9e12ea2 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022a.eb @@ -0,0 +1,38 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = "3.8.0" + +homepage = 'https://github.com/opencollab/arpack-ng' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'opencollab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['ada5aeb3878874383307239c9235b716a8a170c6d096a6625bfd529844df003d'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Eigen', '3.4.0') +] + +preconfigopts = "sh bootstrap && " +configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ["lib64/libarpack.la", "lib64/libarpack.%s" % SHLIB_EXT, + "lib64/libparpack.la", "lib64/libparpack.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'numlib' From cae54a5b0b8c86e09f88c1c9ffcdca6a7d82f8d1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 6 Dec 2022 16:40:37 +0000 Subject: [PATCH 5700/9987] fix patches and improve EC --- .../s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb | 23 ++++++++++++++----- .../s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch | 2 +- .../s/SPOOLES/SPOOLES-2.2_shared-libs.patch | 12 +++++----- 3 files changed, 24 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb index 1713aedf476..dcbd212c988 100644 --- a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb @@ -19,22 +19,33 @@ patches = [ ] checksums = [ {'spooles.2.2.tgz': 'a84559a0e987a1e423055ef4fdf3035d55b65bbe4bf915efaa1a35bef7f8c5dd'}, - {'SPOOLES-2.2_build-mpi-mt.patch': 'a4abc168c660f4af55feb865c5559304a099755e2c46ebf09fabd83bb1636d2c'}, - {'SPOOLES-2.2_shared-libs.patch': '7b767a699679740ec2a4acd12e66c4a3656a276c354f61436e82cb4d448741f4'}, + {'SPOOLES-2.2_build-mpi-mt.patch': 'c983c7f37eb0904959cd2f6dff0b1fdb6a36440ca2a044fb2d324fd301e3dd7c'}, + {'SPOOLES-2.2_shared-libs.patch': 'bca50e13e3c552240f7494c4d9f69be8725054c9f79ebc82dbe6b7531588d09e'}, ] builddependencies = [ + ('Autotools', '20210128'), ('Perl', '5.32.1', '-minimal'), ] build_cmd_targets = 'lib' -buildopts = 'CC="$CC" CFLAGS="$CFLAGS" MPI_LIB_PATH="$MPI_LIB_DIR" MPI_INCLUDE_DIR="$MPI_INC_DIR"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" MPI_LIB_PATH="-L$MPI_LIB_DIR" MPI_INCLUDE_DIR="-I$MPI_INC_DIR"' -files_to_copy = ['*'] +files_to_copy = [ + (['libspooles*'], 'lib'), +] + +# install header files, keeping relative subdirectories +_install_headers = " ".join([ + "cd %(builddir)s && mkdir -p %(installdir)s/include/spooles &&", + "find . -name '*.h' -print -exec install -D {} %(installdir)s/include/spooles/{} \;" +]) + +postinstallcmds = [_install_headers] sanity_check_paths = { - 'files': [], - 'dirs': ['lib'], + 'files': ['lib/lib%%(namelower)s.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/spooles'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch index 59466c19b06..29c060a2d41 100644 --- a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch @@ -20,7 +20,7 @@ diff -Nru spooles-2.2.orig/MPI/src/makefile spooles-2.2.p1/MPI/src/makefile clean : - rm -f *.a *.o + -+makelib: ++makeLib: + perl ../../makeLib > makeG + make -f makeG + rm -f makeG diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch index d9423043383..0de7fd03168 100644 --- a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch @@ -9,8 +9,8 @@ diff -Nru spooles-2.2.p1/makefile spooles-2.2.p2/makefile cd misc ; make lib -#cd MPI ; make lib -#cd MT ; make lib -+ MPI ; make lib -+ MT ; make lib ++ cd MPI ; make lib ++ cd MT ; make lib + $(CC) -shared */*/*.lo -Wl,-soname,libspooles.so.2.2 -o libspooles.so.2.2 -lmpi -lpthread -lm + ln -s libspooles.so.2.2 libspooles.so @@ -19,7 +19,7 @@ diff -Nru spooles-2.2.p1/makefile spooles-2.2.p2/makefile diff -Nru spooles-2.2.p1/makeLib spooles-2.2.p2/makeLib --- spooles-2.2.p1/makeLib 2022-11-25 16:06:54.000000000 +0000 +++ spooles-2.2.p2/makeLib 2022-11-25 16:13:02.000000000 +0000 -@@ -64,14 +64,21 @@ +@@ -64,14 +64,19 @@ $srcname = " \\\n " . $src ; print $srcname ; } @@ -32,8 +32,8 @@ diff -Nru spooles-2.2.p1/makeLib spooles-2.2.p2/makeLib - $(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o + $(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o $(MPI_INCLUDE_DIR) - ../../spooles.a : ${OBJ_FILES} - $(AR) $(ARFLAGS) ../../spooles.a $(OBJ)_*.o +-../../spooles.a : ${OBJ_FILES} +- $(AR) $(ARFLAGS) ../../spooles.a $(OBJ)_*.o +.c.lo: + $(PURIFY) $(CC) -c $(CFLAGS) $*.c -fPIC -DPIC -o $(OBJ)_$*.lo $(MPI_INCLUDE_DIR) + @@ -41,5 +41,5 @@ diff -Nru spooles-2.2.p1/makeLib spooles-2.2.p2/makeLib + $(AR) $(ARFLAGS) ../../libspooles.a $(OBJ)_*.o rm -f $(OBJ)_*.o - $(RANLIB) ../../spooles.a -+ $(RANLIB) ../../linspooles.a ++ $(RANLIB) ../../libspooles.a EOF From 55ecef580de44ff9c4a99e7d76bd59b2d5db0d80 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 6 Dec 2022 16:43:02 +0000 Subject: [PATCH 5701/9987] adding easyconfigs: CalculiX-CrunchiX-2.20-foss-2021a.eb and patches: CalculiX-CrunchiX-2.20_improve-makefile.patch --- .../CalculiX-CrunchiX-2.20-foss-2021a.eb | 50 +++++++++++++++++++ ...culiX-CrunchiX-2.20_improve-makefile.patch | 36 +++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2021a.eb create mode 100644 easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20_improve-makefile.patch diff --git a/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2021a.eb b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2021a.eb new file mode 100644 index 00000000000..e432fbd8b78 --- /dev/null +++ b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2021a.eb @@ -0,0 +1,50 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MakeCp' + +name = 'CalculiX-CrunchiX' +version = '2.20' + +homepage = 'http://www.calculix.de' +description = 'A Free Software Three-Dimensional Structural Finite Element Program' + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['http://www.dhondt.de'] +sources = ['ccx_%(version)s.src.tar.bz2'] +patches = ['CalculiX-CrunchiX-2.20_improve-makefile.patch'] +checksums = [ + {'ccx_2.20.src.tar.bz2': '63bf6ea09e7edcae93e0145b1bb0579ea7ae82e046f6075a27c8145b72761bcf'}, + {'CalculiX-CrunchiX-2.20_improve-makefile.patch': + 'b63dd66693a0ea7d306cb9a28b8e6e1db33f8b1cd051a21dc23024318b6bade5'}, +] + +builddependencies = [ + ('Perl', '5.32.1', '-minimal'), +] + +dependencies = [ + ('arpack-ng', '3.8.0'), + ('SPOOLES', '2.2'), +] + +start_dir = 'CalculiX/ccx_%(version)s/src' + +prebuildopts = 'CFLAGS="$CFLAGS $CPPFLAGS" FFLAGS="$FFLAGS -fallow-argument-mismatch"' +buildopts = 'SPOOLES_INC_DIR="$EBROOTSPOOLES/include/spooles"' + +files_to_copy = [(['ccx_%(version)s'], 'bin')] + +postinstallcmds = ['cd %(installdir)s/bin && ln -sf ccx_%(version)s ccx'] + +sanity_check_paths = { + 'files': ['bin/ccx'], + 'dirs': [], +} + +sanity_check_commands = [ + # ccx {,-v} exit with code 201 + "ccx | grep 'Usage: CalculiX.exe -i jobname'", + "ccx -v | grep 'Version %(version)s'", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20_improve-makefile.patch b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20_improve-makefile.patch new file mode 100644 index 00000000000..ab471f8057c --- /dev/null +++ b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20_improve-makefile.patch @@ -0,0 +1,36 @@ +diff -Nru CalculiX/ccx_2.20/src/Makefile CalculiX.1/ccx_2.20/src/Makefile +--- CalculiX/ccx_2.20/src/Makefile 2022-07-31 17:06:31.000000000 +0100 ++++ CalculiX.1/ccx_2.20/src/Makefile 2022-12-06 16:24:27.000000000 +0000 +@@ -1,9 +1,9 @@ + +-CFLAGS = -Wall -O2 -I ../../../SPOOLES.2.2 -DARCH="Linux" -DSPOOLES -DARPACK -DMATRIXSTORAGE -DNETWORKOUT +-FFLAGS = -Wall -O2 ++CFLAGS += -Wall -O2 -I$(SPOOLES_INC_DIR) -DARCH="Linux" -DSPOOLES -DARPACK -DMATRIXSTORAGE -DNETWORKOUT ++FFLAGS += -Wall -O2 + +-CC=cc +-FC=gfortran ++CC?=cc ++FC?=gfortran + + .c.o : + $(CC) $(CFLAGS) -c $< +@@ -18,15 +18,10 @@ + OCCXC = $(SCCXC:.c=.o) + OCCXMAIN = $(SCCXMAIN:.c=.o) + +-DIR=../../../SPOOLES.2.2 ++LIBS = -lspooles -lpthread -larpack -lflexiblas -lm -lc + +-LIBS = \ +- $(DIR)/spooles.a \ +- ../../../ARPACK/libarpack_INTEL.a \ +- -lpthread -lm -lc +- +-ccx_2.20: $(OCCXMAIN) ccx_2.20.a $(LIBS) +- ./date.pl; $(CC) $(CFLAGS) -c ccx_2.20.c; $(FC) -Wall -O2 -o $@ $(OCCXMAIN) ccx_2.20.a $(LIBS) -fopenmp ++ccx_2.20: $(OCCXMAIN) ccx_2.20.a ++ ./date.pl; $(CC) $(CFLAGS) -c ccx_2.20.c; $(FC) -Wall -O2 -o $@ $(OCCXMAIN) ccx_2.20.a $(LIBS) -fopenmp $(LDFLAGS) + + ccx_2.20.a: $(OCCXF) $(OCCXC) + ar vr $@ $? From 10b19f1d69618c99a3f80df77035c71cf2a7abc4 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 6 Dec 2022 16:46:37 +0000 Subject: [PATCH 5702/9987] add attribution, description to patch --- .../CalculiX-CrunchiX-2.20_improve-makefile.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20_improve-makefile.patch b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20_improve-makefile.patch index ab471f8057c..63ef672d908 100644 --- a/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20_improve-makefile.patch +++ b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20_improve-makefile.patch @@ -1,3 +1,6 @@ +Author: Jasper Grimm +Description: Makefile hardening, link shared libraries not hardcoded static ones +---------------------------------------------------------------------------------- diff -Nru CalculiX/ccx_2.20/src/Makefile CalculiX.1/ccx_2.20/src/Makefile --- CalculiX/ccx_2.20/src/Makefile 2022-07-31 17:06:31.000000000 +0100 +++ CalculiX.1/ccx_2.20/src/Makefile 2022-12-06 16:24:27.000000000 +0000 From e1adbd493c9d0cddf4835de490c97e465cd763bf Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 6 Dec 2022 17:13:56 +0000 Subject: [PATCH 5703/9987] checksums --- .../c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2021a.eb b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2021a.eb index e432fbd8b78..723fc090225 100644 --- a/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2021a.eb +++ b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2021a.eb @@ -15,7 +15,7 @@ patches = ['CalculiX-CrunchiX-2.20_improve-makefile.patch'] checksums = [ {'ccx_2.20.src.tar.bz2': '63bf6ea09e7edcae93e0145b1bb0579ea7ae82e046f6075a27c8145b72761bcf'}, {'CalculiX-CrunchiX-2.20_improve-makefile.patch': - 'b63dd66693a0ea7d306cb9a28b8e6e1db33f8b1cd051a21dc23024318b6bade5'}, + 'ada15598029d231f804f61d959ce91e2bb3a58749fe5955398f42fbe87dc970c'}, ] builddependencies = [ From 3ce55b350f7f12462f67e75d6e5cd06674f9aec5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Dec 2022 17:36:07 +0000 Subject: [PATCH 5704/9987] Steal Barts patches --- .../FlexiBLAS/FlexiBLAS-3.0.4_fix-imkl.patch | 24 + ...exiBLAS-3.0.4_fix-wrapper_blas_intel.patch | 6750 +++++++++++++++++ .../FlexiBLAS-3.0.4_remove-semicolon.patch | 15 + .../FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 13 +- .../FlexiBLAS-3.2.0_remove-intel-suffix.patch | 16 + 5 files changed, 6817 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-imkl.patch create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_remove-semicolon.patch create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0_remove-intel-suffix.patch diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-imkl.patch b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-imkl.patch new file mode 100644 index 00000000000..65afad7a02a --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-imkl.patch @@ -0,0 +1,24 @@ +CMake-related fixes to use correct backend for MKL + +Author: Bart Oldeman +diff -ur flexiblas-3.0.4/src/CMakeLists.txt flexiblas-3.0.4.new/src/CMakeLists.txt +--- flexiblas-3.0.4/src/CMakeLists.txt 2020-10-22 09:07:49.000000000 +0000 ++++ flexiblas-3.0.4.new/src/CMakeLists.txt 2021-09-28 17:28:59.862127651 +0000 +@@ -331,7 +331,7 @@ + INCLUDE(CheckFunctionExists) + + # SET(BLA_STATIC TRUE) +-MACRO(BuildBackendBlas VENDOR BACKEND_CODE) ++MACRO(BuildBackendBlas VENDOR BACKEND_CODE_PARAM) + MESSAGE(STATUS "Build additional BLAS interface: ${VENDOR}") + MESSAGE(STATUS "-- Libs: ${${VENDOR}_LIBRARY}") + MESSAGE(STATUS "-- Linker Flags: ${${VENDOR}_LINKER_FLAGS}") +@@ -356,6 +356,8 @@ + # Use the MKL Backend Code if it is MKL + IF(_MKL_VERSION) + SET(BACKEND_CODE backends/intel_mkl/backend.c) ++ ELSE() ++ SET(BACKEND_CODE ${BACKEND_CODE_PARAM}) + ENDIF() + + SET(CMAKE_REQUIRED_LIBRARIES ${__CMAKE_REQUIRED_LIBRARIES}) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch new file mode 100644 index 00000000000..ce6b2d8b3ab --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch @@ -0,0 +1,6750 @@ +Sync intel with gnu wrapper. The only difference should be in [cz]dot[uc]; without +these wrapper_blas_intel.c won't compile. + +Bart Oldeman +diff -ur flexiblas-3.0.4/src/wrapper_blas_intel.c flexiblas-3.0.4.new/src/wrapper_blas_intel.c +--- flexiblas-3.0.4/src/wrapper_blas_intel.c 2020-10-22 09:07:55.000000000 +0000 ++++ flexiblas-3.0.4.new/src/wrapper_blas_intel.c 2021-10-03 22:52:02.359617295 +0000 +@@ -235,6 +235,8 @@ + return 0; + } + ++static TLS_STORE uint8_t hook_pos_caxpy = 0; ++ + void FC_GLOBAL(caxpy,CAXPY)(blasint* n, float complex* ca, float complex* cx, blasint* incx, float complex* cy, blasint* incy) + { + void (*fn) (void* n, void* ca, void* cx, void* incx, void* cy, void* incy); +@@ -261,6 +263,40 @@ + + + ++void flexiblas_real_caxpy_(void* n, void* ca, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx, void* cy, void* incy); ++ ++ fn = current_backend->blas.caxpy.f77_blas_function; ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_caxpy(void* n, void* ca, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_real_caxpy_"))); ++ ++ ++void flexiblas_chain_caxpy_(void* n, void* ca, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx, void* cy, void* incy); ++ ++ ++ ++ hook_pos_caxpy++; ++ if ( hook_pos_caxpy < __flexiblas_hooks->caxpy.nhook ) { ++ fn = __flexiblas_hooks->caxpy.f77_hook_function[hook_pos_caxpy]; ++ } else { ++ hook_pos_caxpy = 0; ++ fn = current_backend->blas.caxpy.f77_blas_function; ++ } ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_caxpy(void* n, void* ca, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_chain_caxpy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ccopy = 0; ++ + void FC_GLOBAL(ccopy,CCOPY)(blasint* n, float complex* cx, blasint* incx, float complex* cy, blasint* incy) + { + void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); +@@ -287,6 +323,40 @@ + + + ++void flexiblas_real_ccopy_(void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ ++ fn = current_backend->blas.ccopy.f77_blas_function; ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_ccopy(void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_real_ccopy_"))); ++ ++ ++void flexiblas_chain_ccopy_(void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ ++ ++ ++ hook_pos_ccopy++; ++ if ( hook_pos_ccopy < __flexiblas_hooks->ccopy.nhook ) { ++ fn = __flexiblas_hooks->ccopy.f77_hook_function[hook_pos_ccopy]; ++ } else { ++ hook_pos_ccopy = 0; ++ fn = current_backend->blas.ccopy.f77_blas_function; ++ } ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_ccopy(void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_chain_ccopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cdotc = 0; ++ + void FC_GLOBAL(cdotc,CDOTC)( float complex* returnvalue, blasint* n, float complex* cx, blasint* incx, float complex* cy, blasint* incy) + { + float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); +@@ -327,6 +397,56 @@ + + + ++void flexiblas_real_cdotc_( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ void (*fn_intel) (float complex *ret, void* n, void* cx, void* incx, void* cy, void* incy); ++ float complex ret; ++ ++ fn = current_backend->blas.cdotc.f77_blas_function; fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } ++ ++ *((float complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_real_cdotc( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_real_cdotc_"))); ++ ++ ++void flexiblas_chain_cdotc_( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ void (*fn_intel) (float complex *ret, void* n, void* cx, void* incx, void* cy, void* incy); ++ float complex ret; ++ ++ ++ ++ hook_pos_cdotc++; ++ if ( hook_pos_cdotc < __flexiblas_hooks->cdotc.nhook ) { ++ fn = __flexiblas_hooks->cdotc.f77_hook_function[hook_pos_cdotc]; ++ } else { ++ hook_pos_cdotc = 0; ++ fn = current_backend->blas.cdotc.f77_blas_function; ++ } fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } ++ ++ *((float complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_chain_cdotc( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_chain_cdotc_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cdotu = 0; ++ + void FC_GLOBAL(cdotu,CDOTU)( float complex* returnvalue, blasint* n, float complex* cx, blasint* incx, float complex* cy, blasint* incy) + { + float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); +@@ -367,6 +487,56 @@ + + + ++void flexiblas_real_cdotu_( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ void (*fn_intel) (float complex *ret, void* n, void* cx, void* incx, void* cy, void* incy); ++ float complex ret; ++ ++ fn = current_backend->blas.cdotu.f77_blas_function; fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } ++ ++ *((float complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_real_cdotu( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_real_cdotu_"))); ++ ++ ++void flexiblas_chain_cdotu_( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ void (*fn_intel) (float complex *ret, void* n, void* cx, void* incx, void* cy, void* incy); ++ float complex ret; ++ ++ ++ ++ hook_pos_cdotu++; ++ if ( hook_pos_cdotu < __flexiblas_hooks->cdotu.nhook ) { ++ fn = __flexiblas_hooks->cdotu.f77_hook_function[hook_pos_cdotu]; ++ } else { ++ hook_pos_cdotu = 0; ++ fn = current_backend->blas.cdotu.f77_blas_function; ++ } fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } ++ ++ *((float complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_chain_cdotu( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_chain_cdotu_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgbmv = 0; ++ + void FC_GLOBAL(cgbmv,CGBMV)(char* trans, blasint* m, blasint* n, blasint* kl, blasint* ku, float complex* alpha, float complex* a, blasint* lda, float complex* x, blasint* incx, float complex* beta, float complex* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -393,6 +563,40 @@ + + + ++void flexiblas_real_cgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.cgbmv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_cgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_cgbmv_"))); ++ ++ ++void flexiblas_chain_cgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_cgbmv++; ++ if ( hook_pos_cgbmv < __flexiblas_hooks->cgbmv.nhook ) { ++ fn = __flexiblas_hooks->cgbmv.f77_hook_function[hook_pos_cgbmv]; ++ } else { ++ hook_pos_cgbmv = 0; ++ fn = current_backend->blas.cgbmv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_cgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_cgbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgemm = 0; ++ + void FC_GLOBAL(cgemm,CGEMM)(char* transa, char* transb, blasint* m, blasint* n, blasint* k, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb, float complex* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -419,6 +623,40 @@ + + + ++void flexiblas_real_cgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.cgemm.f77_blas_function; ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_cgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_cgemm_"))); ++ ++ ++void flexiblas_chain_cgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_cgemm++; ++ if ( hook_pos_cgemm < __flexiblas_hooks->cgemm.nhook ) { ++ fn = __flexiblas_hooks->cgemm.f77_hook_function[hook_pos_cgemm]; ++ } else { ++ hook_pos_cgemm = 0; ++ fn = current_backend->blas.cgemm.f77_blas_function; ++ } ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_cgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_cgemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgemv = 0; ++ + void FC_GLOBAL(cgemv,CGEMV)(char* trans, blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* x, blasint* incx, float complex* beta, float complex* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -445,6 +683,40 @@ + + + ++void flexiblas_real_cgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.cgemv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_cgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_cgemv_"))); ++ ++ ++void flexiblas_chain_cgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_cgemv++; ++ if ( hook_pos_cgemv < __flexiblas_hooks->cgemv.nhook ) { ++ fn = __flexiblas_hooks->cgemv.f77_hook_function[hook_pos_cgemv]; ++ } else { ++ hook_pos_cgemv = 0; ++ fn = current_backend->blas.cgemv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_cgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_cgemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgerc = 0; ++ + void FC_GLOBAL(cgerc,CGERC)(blasint* m, blasint* n, float complex* alpha, float complex* x, blasint* incx, float complex* y, blasint* incy, float complex* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -471,6 +743,40 @@ + + + ++void flexiblas_real_cgerc_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.cgerc.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_cgerc(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_cgerc_"))); ++ ++ ++void flexiblas_chain_cgerc_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_cgerc++; ++ if ( hook_pos_cgerc < __flexiblas_hooks->cgerc.nhook ) { ++ fn = __flexiblas_hooks->cgerc.f77_hook_function[hook_pos_cgerc]; ++ } else { ++ hook_pos_cgerc = 0; ++ fn = current_backend->blas.cgerc.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_cgerc(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_cgerc_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgeru = 0; ++ + void FC_GLOBAL(cgeru,CGERU)(blasint* m, blasint* n, float complex* alpha, float complex* x, blasint* incx, float complex* y, blasint* incy, float complex* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -497,6 +803,40 @@ + + + ++void flexiblas_real_cgeru_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.cgeru.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_cgeru(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_cgeru_"))); ++ ++ ++void flexiblas_chain_cgeru_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_cgeru++; ++ if ( hook_pos_cgeru < __flexiblas_hooks->cgeru.nhook ) { ++ fn = __flexiblas_hooks->cgeru.f77_hook_function[hook_pos_cgeru]; ++ } else { ++ hook_pos_cgeru = 0; ++ fn = current_backend->blas.cgeru.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_cgeru(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_cgeru_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chbmv = 0; ++ + void FC_GLOBAL(chbmv,CHBMV)(char* uplo, blasint* n, blasint* k, float complex* alpha, float complex* a, blasint* lda, float complex* x, blasint* incx, float complex* beta, float complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -523,6 +863,40 @@ + + + ++void flexiblas_real_chbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.chbmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_chbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_chbmv_"))); ++ ++ ++void flexiblas_chain_chbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_chbmv++; ++ if ( hook_pos_chbmv < __flexiblas_hooks->chbmv.nhook ) { ++ fn = __flexiblas_hooks->chbmv.f77_hook_function[hook_pos_chbmv]; ++ } else { ++ hook_pos_chbmv = 0; ++ fn = current_backend->blas.chbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_chbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_chbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chemm = 0; ++ + void FC_GLOBAL(chemm,CHEMM)(char* side, char* uplo, blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb, float complex* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -549,6 +923,40 @@ + + + ++void flexiblas_real_chemm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.chemm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_chemm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_chemm_"))); ++ ++ ++void flexiblas_chain_chemm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_chemm++; ++ if ( hook_pos_chemm < __flexiblas_hooks->chemm.nhook ) { ++ fn = __flexiblas_hooks->chemm.f77_hook_function[hook_pos_chemm]; ++ } else { ++ hook_pos_chemm = 0; ++ fn = current_backend->blas.chemm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_chemm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_chemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chemv = 0; ++ + void FC_GLOBAL(chemv,CHEMV)(char* uplo, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* x, blasint* incx, float complex* beta, float complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -575,6 +983,40 @@ + + + ++void flexiblas_real_chemv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.chemv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_chemv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_chemv_"))); ++ ++ ++void flexiblas_chain_chemv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_chemv++; ++ if ( hook_pos_chemv < __flexiblas_hooks->chemv.nhook ) { ++ fn = __flexiblas_hooks->chemv.f77_hook_function[hook_pos_chemv]; ++ } else { ++ hook_pos_chemv = 0; ++ fn = current_backend->blas.chemv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_chemv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_chemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cher = 0; ++ + void FC_GLOBAL(cher,CHER)(char* uplo, blasint* n, float* alpha, float complex* x, blasint* incx, float complex* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); +@@ -601,6 +1043,40 @@ + + + ++void flexiblas_real_cher_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ fn = current_backend->blas.cher.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_cher(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_real_cher_"))); ++ ++ ++void flexiblas_chain_cher_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ ++ ++ hook_pos_cher++; ++ if ( hook_pos_cher < __flexiblas_hooks->cher.nhook ) { ++ fn = __flexiblas_hooks->cher.f77_hook_function[hook_pos_cher]; ++ } else { ++ hook_pos_cher = 0; ++ fn = current_backend->blas.cher.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_cher(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_chain_cher_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cher2 = 0; ++ + void FC_GLOBAL(cher2,CHER2)(char* uplo, blasint* n, float complex* alpha, float complex* x, blasint* incx, float complex* y, blasint* incy, float complex* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -627,6 +1103,40 @@ + + + ++void flexiblas_real_cher2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.cher2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_cher2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_cher2_"))); ++ ++ ++void flexiblas_chain_cher2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_cher2++; ++ if ( hook_pos_cher2 < __flexiblas_hooks->cher2.nhook ) { ++ fn = __flexiblas_hooks->cher2.f77_hook_function[hook_pos_cher2]; ++ } else { ++ hook_pos_cher2 = 0; ++ fn = current_backend->blas.cher2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_cher2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_cher2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cher2k = 0; ++ + void FC_GLOBAL(cher2k,CHER2K)(char* uplo, char* trans, blasint* n, blasint* k, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb, float* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -653,6 +1163,40 @@ + + + ++void flexiblas_real_cher2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.cher2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_cher2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_cher2k_"))); ++ ++ ++void flexiblas_chain_cher2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_cher2k++; ++ if ( hook_pos_cher2k < __flexiblas_hooks->cher2k.nhook ) { ++ fn = __flexiblas_hooks->cher2k.f77_hook_function[hook_pos_cher2k]; ++ } else { ++ hook_pos_cher2k = 0; ++ fn = current_backend->blas.cher2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_cher2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_cher2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cherk = 0; ++ + void FC_GLOBAL(cherk,CHERK)(char* uplo, char* trans, blasint* n, blasint* k, float* alpha, float complex* a, blasint* lda, float* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -679,6 +1223,40 @@ + + + ++void flexiblas_real_cherk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.cherk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_cherk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_cherk_"))); ++ ++ ++void flexiblas_chain_cherk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_cherk++; ++ if ( hook_pos_cherk < __flexiblas_hooks->cherk.nhook ) { ++ fn = __flexiblas_hooks->cherk.f77_hook_function[hook_pos_cherk]; ++ } else { ++ hook_pos_cherk = 0; ++ fn = current_backend->blas.cherk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_cherk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_cherk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chpmv = 0; ++ + void FC_GLOBAL(chpmv,CHPMV)(char* uplo, blasint* n, float complex* alpha, float complex* ap, float complex* x, blasint* incx, float complex* beta, float complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); +@@ -705,6 +1283,40 @@ + + + ++void flexiblas_real_chpmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.chpmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_chpmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_chpmv_"))); ++ ++ ++void flexiblas_chain_chpmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_chpmv++; ++ if ( hook_pos_chpmv < __flexiblas_hooks->chpmv.nhook ) { ++ fn = __flexiblas_hooks->chpmv.f77_hook_function[hook_pos_chpmv]; ++ } else { ++ hook_pos_chpmv = 0; ++ fn = current_backend->blas.chpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_chpmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_chpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chpr = 0; ++ + void FC_GLOBAL(chpr,CHPR)(char* uplo, blasint* n, float* alpha, float complex* x, blasint* incx, float complex* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); +@@ -731,6 +1343,40 @@ + + + ++void flexiblas_real_chpr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ fn = current_backend->blas.chpr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_chpr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_real_chpr_"))); ++ ++ ++void flexiblas_chain_chpr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ ++ ++ hook_pos_chpr++; ++ if ( hook_pos_chpr < __flexiblas_hooks->chpr.nhook ) { ++ fn = __flexiblas_hooks->chpr.f77_hook_function[hook_pos_chpr]; ++ } else { ++ hook_pos_chpr = 0; ++ fn = current_backend->blas.chpr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_chpr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_chain_chpr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chpr2 = 0; ++ + void FC_GLOBAL(chpr2,CHPR2)(char* uplo, blasint* n, float complex* alpha, float complex* x, blasint* incx, float complex* y, blasint* incy, float complex* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); +@@ -757,6 +1403,40 @@ + + + ++void flexiblas_real_chpr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ fn = current_backend->blas.chpr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_chpr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_real_chpr2_"))); ++ ++ ++void flexiblas_chain_chpr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ ++ ++ hook_pos_chpr2++; ++ if ( hook_pos_chpr2 < __flexiblas_hooks->chpr2.nhook ) { ++ fn = __flexiblas_hooks->chpr2.f77_hook_function[hook_pos_chpr2]; ++ } else { ++ hook_pos_chpr2 = 0; ++ fn = current_backend->blas.chpr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_chpr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_chain_chpr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_crotg = 0; ++ + void FC_GLOBAL(crotg,CROTG)(float complex* ca, float complex* cb, float* c, float complex* s) + { + void (*fn) (void* ca, void* cb, void* c, void* s); +@@ -783,6 +1463,40 @@ + + + ++void flexiblas_real_crotg_(void* ca, void* cb, void* c, void* s) ++{ ++ void (*fn) (void* ca, void* cb, void* c, void* s); ++ ++ fn = current_backend->blas.crotg.f77_blas_function; ++ fn((void*) ca, (void*) cb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_crotg(void* ca, void* cb, void* c, void* s) __attribute__((alias("flexiblas_real_crotg_"))); ++ ++ ++void flexiblas_chain_crotg_(void* ca, void* cb, void* c, void* s) ++{ ++ void (*fn) (void* ca, void* cb, void* c, void* s); ++ ++ ++ ++ hook_pos_crotg++; ++ if ( hook_pos_crotg < __flexiblas_hooks->crotg.nhook ) { ++ fn = __flexiblas_hooks->crotg.f77_hook_function[hook_pos_crotg]; ++ } else { ++ hook_pos_crotg = 0; ++ fn = current_backend->blas.crotg.f77_blas_function; ++ } ++ fn((void*) ca, (void*) cb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_crotg(void* ca, void* cb, void* c, void* s) __attribute__((alias("flexiblas_chain_crotg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cscal = 0; ++ + void FC_GLOBAL(cscal,CSCAL)(blasint* n, float complex* ca, float complex* cx, blasint* incx) + { + void (*fn) (void* n, void* ca, void* cx, void* incx); +@@ -809,6 +1523,40 @@ + + + ++void flexiblas_real_cscal_(void* n, void* ca, void* cx, void* incx) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx); ++ ++ fn = current_backend->blas.cscal.f77_blas_function; ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_cscal(void* n, void* ca, void* cx, void* incx) __attribute__((alias("flexiblas_real_cscal_"))); ++ ++ ++void flexiblas_chain_cscal_(void* n, void* ca, void* cx, void* incx) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx); ++ ++ ++ ++ hook_pos_cscal++; ++ if ( hook_pos_cscal < __flexiblas_hooks->cscal.nhook ) { ++ fn = __flexiblas_hooks->cscal.f77_hook_function[hook_pos_cscal]; ++ } else { ++ hook_pos_cscal = 0; ++ fn = current_backend->blas.cscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_cscal(void* n, void* ca, void* cx, void* incx) __attribute__((alias("flexiblas_chain_cscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_csrot = 0; ++ + void FC_GLOBAL(csrot,CSROT)(blasint* n, float complex* cx, blasint* incx, float complex* cy, blasint* incy, float* c, float* s) + { + void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); +@@ -835,6 +1583,40 @@ + + + ++void flexiblas_real_csrot_(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); ++ ++ fn = current_backend->blas.csrot.f77_blas_function; ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_csrot(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_real_csrot_"))); ++ ++ ++void flexiblas_chain_csrot_(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); ++ ++ ++ ++ hook_pos_csrot++; ++ if ( hook_pos_csrot < __flexiblas_hooks->csrot.nhook ) { ++ fn = __flexiblas_hooks->csrot.f77_hook_function[hook_pos_csrot]; ++ } else { ++ hook_pos_csrot = 0; ++ fn = current_backend->blas.csrot.f77_blas_function; ++ } ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_csrot(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_chain_csrot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_csscal = 0; ++ + void FC_GLOBAL(csscal,CSSCAL)(blasint* n, float* sa, float complex* cx, blasint* incx) + { + void (*fn) (void* n, void* sa, void* cx, void* incx); +@@ -861,6 +1643,40 @@ + + + ++void flexiblas_real_csscal_(void* n, void* sa, void* cx, void* incx) ++{ ++ void (*fn) (void* n, void* sa, void* cx, void* incx); ++ ++ fn = current_backend->blas.csscal.f77_blas_function; ++ fn((void*) n, (void*) sa, (void*) cx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_csscal(void* n, void* sa, void* cx, void* incx) __attribute__((alias("flexiblas_real_csscal_"))); ++ ++ ++void flexiblas_chain_csscal_(void* n, void* sa, void* cx, void* incx) ++{ ++ void (*fn) (void* n, void* sa, void* cx, void* incx); ++ ++ ++ ++ hook_pos_csscal++; ++ if ( hook_pos_csscal < __flexiblas_hooks->csscal.nhook ) { ++ fn = __flexiblas_hooks->csscal.f77_hook_function[hook_pos_csscal]; ++ } else { ++ hook_pos_csscal = 0; ++ fn = current_backend->blas.csscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) sa, (void*) cx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_csscal(void* n, void* sa, void* cx, void* incx) __attribute__((alias("flexiblas_chain_csscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cswap = 0; ++ + void FC_GLOBAL(cswap,CSWAP)(blasint* n, float complex* cx, blasint* incx, float complex* cy, blasint* incy) + { + void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); +@@ -887,6 +1703,40 @@ + + + ++void flexiblas_real_cswap_(void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ ++ fn = current_backend->blas.cswap.f77_blas_function; ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_cswap(void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_real_cswap_"))); ++ ++ ++void flexiblas_chain_cswap_(void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ ++ ++ ++ hook_pos_cswap++; ++ if ( hook_pos_cswap < __flexiblas_hooks->cswap.nhook ) { ++ fn = __flexiblas_hooks->cswap.f77_hook_function[hook_pos_cswap]; ++ } else { ++ hook_pos_cswap = 0; ++ fn = current_backend->blas.cswap.f77_blas_function; ++ } ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_cswap(void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_chain_cswap_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_csymm = 0; ++ + void FC_GLOBAL(csymm,CSYMM)(char* side, char* uplo, blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb, float complex* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -913,6 +1763,40 @@ + + + ++void flexiblas_real_csymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.csymm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_csymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_csymm_"))); ++ ++ ++void flexiblas_chain_csymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_csymm++; ++ if ( hook_pos_csymm < __flexiblas_hooks->csymm.nhook ) { ++ fn = __flexiblas_hooks->csymm.f77_hook_function[hook_pos_csymm]; ++ } else { ++ hook_pos_csymm = 0; ++ fn = current_backend->blas.csymm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_csymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_csymm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_csyr2k = 0; ++ + void FC_GLOBAL(csyr2k,CSYR2K)(char* uplo, char* trans, blasint* n, blasint* k, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb, float complex* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -939,6 +1823,40 @@ + + + ++void flexiblas_real_csyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.csyr2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_csyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_csyr2k_"))); ++ ++ ++void flexiblas_chain_csyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_csyr2k++; ++ if ( hook_pos_csyr2k < __flexiblas_hooks->csyr2k.nhook ) { ++ fn = __flexiblas_hooks->csyr2k.f77_hook_function[hook_pos_csyr2k]; ++ } else { ++ hook_pos_csyr2k = 0; ++ fn = current_backend->blas.csyr2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_csyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_csyr2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_csyrk = 0; ++ + void FC_GLOBAL(csyrk,CSYRK)(char* uplo, char* trans, blasint* n, blasint* k, float complex* alpha, float complex* a, blasint* lda, float complex* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -965,6 +1883,40 @@ + + + ++void flexiblas_real_csyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.csyrk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_csyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_csyrk_"))); ++ ++ ++void flexiblas_chain_csyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_csyrk++; ++ if ( hook_pos_csyrk < __flexiblas_hooks->csyrk.nhook ) { ++ fn = __flexiblas_hooks->csyrk.f77_hook_function[hook_pos_csyrk]; ++ } else { ++ hook_pos_csyrk = 0; ++ fn = current_backend->blas.csyrk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_csyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_csyrk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctbmv = 0; ++ + void FC_GLOBAL(ctbmv,CTBMV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, float complex* a, blasint* lda, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -991,6 +1943,40 @@ + + + ++void flexiblas_real_ctbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ctbmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ctbmv_"))); ++ ++ ++void flexiblas_chain_ctbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctbmv++; ++ if ( hook_pos_ctbmv < __flexiblas_hooks->ctbmv.nhook ) { ++ fn = __flexiblas_hooks->ctbmv.f77_hook_function[hook_pos_ctbmv]; ++ } else { ++ hook_pos_ctbmv = 0; ++ fn = current_backend->blas.ctbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctbsv = 0; ++ + void FC_GLOBAL(ctbsv,CTBSV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, float complex* a, blasint* lda, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -1017,6 +2003,40 @@ + + + ++void flexiblas_real_ctbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ctbsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ctbsv_"))); ++ ++ ++void flexiblas_chain_ctbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctbsv++; ++ if ( hook_pos_ctbsv < __flexiblas_hooks->ctbsv.nhook ) { ++ fn = __flexiblas_hooks->ctbsv.f77_hook_function[hook_pos_ctbsv]; ++ } else { ++ hook_pos_ctbsv = 0; ++ fn = current_backend->blas.ctbsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctbsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctpmv = 0; ++ + void FC_GLOBAL(ctpmv,CTPMV)(char* uplo, char* trans, char* diag, blasint* n, float complex* ap, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -1043,6 +2063,40 @@ + + + ++void flexiblas_real_ctpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.ctpmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_ctpmv_"))); ++ ++ ++void flexiblas_chain_ctpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctpmv++; ++ if ( hook_pos_ctpmv < __flexiblas_hooks->ctpmv.nhook ) { ++ fn = __flexiblas_hooks->ctpmv.f77_hook_function[hook_pos_ctpmv]; ++ } else { ++ hook_pos_ctpmv = 0; ++ fn = current_backend->blas.ctpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctpsv = 0; ++ + void FC_GLOBAL(ctpsv,CTPSV)(char* uplo, char* trans, char* diag, blasint* n, float complex* ap, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -1069,6 +2123,40 @@ + + + ++void flexiblas_real_ctpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.ctpsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_ctpsv_"))); ++ ++ ++void flexiblas_chain_ctpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctpsv++; ++ if ( hook_pos_ctpsv < __flexiblas_hooks->ctpsv.nhook ) { ++ fn = __flexiblas_hooks->ctpsv.f77_hook_function[hook_pos_ctpsv]; ++ } else { ++ hook_pos_ctpsv = 0; ++ fn = current_backend->blas.ctpsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctpsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctrmm = 0; ++ + void FC_GLOBAL(ctrmm,CTRMM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -1095,6 +2183,40 @@ + + + ++void flexiblas_real_ctrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.ctrmm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_ctrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_ctrmm_"))); ++ ++ ++void flexiblas_chain_ctrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_ctrmm++; ++ if ( hook_pos_ctrmm < __flexiblas_hooks->ctrmm.nhook ) { ++ fn = __flexiblas_hooks->ctrmm.f77_hook_function[hook_pos_ctrmm]; ++ } else { ++ hook_pos_ctrmm = 0; ++ fn = current_backend->blas.ctrmm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_ctrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_ctrmm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctrmv = 0; ++ + void FC_GLOBAL(ctrmv,CTRMV)(char* uplo, char* trans, char* diag, blasint* n, float complex* a, blasint* lda, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -1121,6 +2243,40 @@ + + + ++void flexiblas_real_ctrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ctrmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ctrmv_"))); ++ ++ ++void flexiblas_chain_ctrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctrmv++; ++ if ( hook_pos_ctrmv < __flexiblas_hooks->ctrmv.nhook ) { ++ fn = __flexiblas_hooks->ctrmv.f77_hook_function[hook_pos_ctrmv]; ++ } else { ++ hook_pos_ctrmv = 0; ++ fn = current_backend->blas.ctrmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctrmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctrsm = 0; ++ + void FC_GLOBAL(ctrsm,CTRSM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -1147,6 +2303,40 @@ + + + ++void flexiblas_real_ctrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.ctrsm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_ctrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_ctrsm_"))); ++ ++ ++void flexiblas_chain_ctrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_ctrsm++; ++ if ( hook_pos_ctrsm < __flexiblas_hooks->ctrsm.nhook ) { ++ fn = __flexiblas_hooks->ctrsm.f77_hook_function[hook_pos_ctrsm]; ++ } else { ++ hook_pos_ctrsm = 0; ++ fn = current_backend->blas.ctrsm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_ctrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_ctrsm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctrsv = 0; ++ + void FC_GLOBAL(ctrsv,CTRSV)(char* uplo, char* trans, char* diag, blasint* n, float complex* a, blasint* lda, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -1173,6 +2363,40 @@ + + + ++void flexiblas_real_ctrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ctrsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ctrsv_"))); ++ ++ ++void flexiblas_chain_ctrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctrsv++; ++ if ( hook_pos_ctrsv < __flexiblas_hooks->ctrsv.nhook ) { ++ fn = __flexiblas_hooks->ctrsv.f77_hook_function[hook_pos_ctrsv]; ++ } else { ++ hook_pos_ctrsv = 0; ++ fn = current_backend->blas.ctrsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctrsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dasum = 0; ++ + double FC_GLOBAL(dasum,DASUM)(blasint* n, double* dx, blasint* incx) + { + double (*fn) (void* n, void* dx, void* incx); +@@ -1200,6 +2424,42 @@ + + + ++double flexiblas_real_dasum_(void* n, void* dx, void* incx) ++{ ++ double (*fn) (void* n, void* dx, void* incx); ++ double ret; ++ ++ fn = current_backend->blas.dasum.f77_blas_function; ++ ret = fn((void*) n, (void*) dx, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_real_dasum(void* n, void* dx, void* incx) __attribute__((alias("flexiblas_real_dasum_"))); ++ ++ ++double flexiblas_chain_dasum_(void* n, void* dx, void* incx) ++{ ++ double (*fn) (void* n, void* dx, void* incx); ++ double ret; ++ ++ ++ ++ hook_pos_dasum++; ++ if ( hook_pos_dasum < __flexiblas_hooks->dasum.nhook ) { ++ fn = __flexiblas_hooks->dasum.f77_hook_function[hook_pos_dasum]; ++ } else { ++ hook_pos_dasum = 0; ++ fn = current_backend->blas.dasum.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) dx, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_chain_dasum(void* n, void* dx, void* incx) __attribute__((alias("flexiblas_chain_dasum_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_daxpy = 0; ++ + void FC_GLOBAL(daxpy,DAXPY)(blasint* n, double* da, double* dx, blasint* incx, double* dy, blasint* incy) + { + void (*fn) (void* n, void* da, void* dx, void* incx, void* dy, void* incy); +@@ -1226,6 +2486,40 @@ + + + ++void flexiblas_real_daxpy_(void* n, void* da, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx, void* dy, void* incy); ++ ++ fn = current_backend->blas.daxpy.f77_blas_function; ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_daxpy(void* n, void* da, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_real_daxpy_"))); ++ ++ ++void flexiblas_chain_daxpy_(void* n, void* da, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx, void* dy, void* incy); ++ ++ ++ ++ hook_pos_daxpy++; ++ if ( hook_pos_daxpy < __flexiblas_hooks->daxpy.nhook ) { ++ fn = __flexiblas_hooks->daxpy.f77_hook_function[hook_pos_daxpy]; ++ } else { ++ hook_pos_daxpy = 0; ++ fn = current_backend->blas.daxpy.f77_blas_function; ++ } ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_daxpy(void* n, void* da, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_chain_daxpy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dcopy = 0; ++ + void FC_GLOBAL(dcopy,DCOPY)(blasint* n, double* dx, blasint* incx, double* dy, blasint* incy) + { + void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); +@@ -1252,6 +2546,40 @@ + + + ++void flexiblas_real_dcopy_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ ++ fn = current_backend->blas.dcopy.f77_blas_function; ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dcopy(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_real_dcopy_"))); ++ ++ ++void flexiblas_chain_dcopy_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ ++ ++ ++ hook_pos_dcopy++; ++ if ( hook_pos_dcopy < __flexiblas_hooks->dcopy.nhook ) { ++ fn = __flexiblas_hooks->dcopy.f77_hook_function[hook_pos_dcopy]; ++ } else { ++ hook_pos_dcopy = 0; ++ fn = current_backend->blas.dcopy.f77_blas_function; ++ } ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dcopy(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_chain_dcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ddot = 0; ++ + double FC_GLOBAL(ddot,DDOT)(blasint* n, double* dx, blasint* incx, double* dy, blasint* incy) + { + double (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); +@@ -1279,6 +2607,42 @@ + + + ++double flexiblas_real_ddot_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ double (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ double ret; ++ ++ fn = current_backend->blas.ddot.f77_blas_function; ++ ret = fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return ret; ++} ++double flexiblas_real_ddot(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_real_ddot_"))); ++ ++ ++double flexiblas_chain_ddot_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ double (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ double ret; ++ ++ ++ ++ hook_pos_ddot++; ++ if ( hook_pos_ddot < __flexiblas_hooks->ddot.nhook ) { ++ fn = __flexiblas_hooks->ddot.f77_hook_function[hook_pos_ddot]; ++ } else { ++ hook_pos_ddot = 0; ++ fn = current_backend->blas.ddot.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return ret; ++} ++double flexiblas_chain_ddot(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_chain_ddot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dgbmv = 0; ++ + void FC_GLOBAL(dgbmv,DGBMV)(char* trans, blasint* m, blasint* n, blasint* kl, blasint* ku, double* alpha, double* a, blasint* lda, double* x, blasint* incx, double* beta, double* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -1305,6 +2669,40 @@ + + + ++void flexiblas_real_dgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.dgbmv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_dgbmv_"))); ++ ++ ++void flexiblas_chain_dgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_dgbmv++; ++ if ( hook_pos_dgbmv < __flexiblas_hooks->dgbmv.nhook ) { ++ fn = __flexiblas_hooks->dgbmv.f77_hook_function[hook_pos_dgbmv]; ++ } else { ++ hook_pos_dgbmv = 0; ++ fn = current_backend->blas.dgbmv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_dgbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dgemm = 0; ++ + void FC_GLOBAL(dgemm,DGEMM)(char* transa, char* transb, blasint* m, blasint* n, blasint* k, double* alpha, double* a, blasint* lda, double* b, blasint* ldb, double* beta, double* c, blasint* ldc) + { + void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -1331,6 +2729,40 @@ + + + ++void flexiblas_real_dgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.dgemm.f77_blas_function; ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_dgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_dgemm_"))); ++ ++ ++void flexiblas_chain_dgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_dgemm++; ++ if ( hook_pos_dgemm < __flexiblas_hooks->dgemm.nhook ) { ++ fn = __flexiblas_hooks->dgemm.f77_hook_function[hook_pos_dgemm]; ++ } else { ++ hook_pos_dgemm = 0; ++ fn = current_backend->blas.dgemm.f77_blas_function; ++ } ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_dgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_dgemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dgemv = 0; ++ + void FC_GLOBAL(dgemv,DGEMV)(char* trans, blasint* m, blasint* n, double* alpha, double* a, blasint* lda, double* x, blasint* incx, double* beta, double* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -1357,6 +2789,40 @@ + + + ++void flexiblas_real_dgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.dgemv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_dgemv_"))); ++ ++ ++void flexiblas_chain_dgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_dgemv++; ++ if ( hook_pos_dgemv < __flexiblas_hooks->dgemv.nhook ) { ++ fn = __flexiblas_hooks->dgemv.f77_hook_function[hook_pos_dgemv]; ++ } else { ++ hook_pos_dgemv = 0; ++ fn = current_backend->blas.dgemv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_dgemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dger = 0; ++ + void FC_GLOBAL(dger,DGER)(blasint* m, blasint* n, double* alpha, double* x, blasint* incx, double* y, blasint* incy, double* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -1383,6 +2849,40 @@ + + + ++void flexiblas_real_dger_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.dger.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_dger(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_dger_"))); ++ ++ ++void flexiblas_chain_dger_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_dger++; ++ if ( hook_pos_dger < __flexiblas_hooks->dger.nhook ) { ++ fn = __flexiblas_hooks->dger.f77_hook_function[hook_pos_dger]; ++ } else { ++ hook_pos_dger = 0; ++ fn = current_backend->blas.dger.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_dger(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_dger_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dnrm2 = 0; ++ + double FC_GLOBAL(dnrm2,DNRM2)(blasint* n, double* x, blasint* incx) + { + double (*fn) (void* n, void* x, void* incx); +@@ -1410,6 +2910,42 @@ + + + ++double flexiblas_real_dnrm2_(void* n, void* x, void* incx) ++{ ++ double (*fn) (void* n, void* x, void* incx); ++ double ret; ++ ++ fn = current_backend->blas.dnrm2.f77_blas_function; ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_real_dnrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_real_dnrm2_"))); ++ ++ ++double flexiblas_chain_dnrm2_(void* n, void* x, void* incx) ++{ ++ double (*fn) (void* n, void* x, void* incx); ++ double ret; ++ ++ ++ ++ hook_pos_dnrm2++; ++ if ( hook_pos_dnrm2 < __flexiblas_hooks->dnrm2.nhook ) { ++ fn = __flexiblas_hooks->dnrm2.f77_hook_function[hook_pos_dnrm2]; ++ } else { ++ hook_pos_dnrm2 = 0; ++ fn = current_backend->blas.dnrm2.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_chain_dnrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_chain_dnrm2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_drot = 0; ++ + void FC_GLOBAL(drot,DROT)(blasint* n, double* dx, blasint* incx, double* dy, blasint* incy, double* c, double* s) + { + void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s); +@@ -1436,6 +2972,40 @@ + + + ++void flexiblas_real_drot_(void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s); ++ ++ fn = current_backend->blas.drot.f77_blas_function; ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_drot(void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_real_drot_"))); ++ ++ ++void flexiblas_chain_drot_(void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s); ++ ++ ++ ++ hook_pos_drot++; ++ if ( hook_pos_drot < __flexiblas_hooks->drot.nhook ) { ++ fn = __flexiblas_hooks->drot.f77_hook_function[hook_pos_drot]; ++ } else { ++ hook_pos_drot = 0; ++ fn = current_backend->blas.drot.f77_blas_function; ++ } ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_drot(void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_chain_drot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_drotg = 0; ++ + void FC_GLOBAL(drotg,DROTG)(double* da, double* db, double* c, double* s) + { + void (*fn) (void* da, void* db, void* c, void* s); +@@ -1462,6 +3032,40 @@ + + + ++void flexiblas_real_drotg_(void* da, void* db, void* c, void* s) ++{ ++ void (*fn) (void* da, void* db, void* c, void* s); ++ ++ fn = current_backend->blas.drotg.f77_blas_function; ++ fn((void*) da, (void*) db, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_drotg(void* da, void* db, void* c, void* s) __attribute__((alias("flexiblas_real_drotg_"))); ++ ++ ++void flexiblas_chain_drotg_(void* da, void* db, void* c, void* s) ++{ ++ void (*fn) (void* da, void* db, void* c, void* s); ++ ++ ++ ++ hook_pos_drotg++; ++ if ( hook_pos_drotg < __flexiblas_hooks->drotg.nhook ) { ++ fn = __flexiblas_hooks->drotg.f77_hook_function[hook_pos_drotg]; ++ } else { ++ hook_pos_drotg = 0; ++ fn = current_backend->blas.drotg.f77_blas_function; ++ } ++ fn((void*) da, (void*) db, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_drotg(void* da, void* db, void* c, void* s) __attribute__((alias("flexiblas_chain_drotg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_drotm = 0; ++ + void FC_GLOBAL(drotm,DROTM)(blasint* n, double* dx, blasint* incx, double* dy, blasint* incy, double* dparam) + { + void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* dparam); +@@ -1488,6 +3092,40 @@ + + + ++void flexiblas_real_drotm_(void* n, void* dx, void* incx, void* dy, void* incy, void* dparam) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* dparam); ++ ++ fn = current_backend->blas.drotm.f77_blas_function; ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy, (void*) dparam); ++ ++ return; ++} ++void flexiblas_real_drotm(void* n, void* dx, void* incx, void* dy, void* incy, void* dparam) __attribute__((alias("flexiblas_real_drotm_"))); ++ ++ ++void flexiblas_chain_drotm_(void* n, void* dx, void* incx, void* dy, void* incy, void* dparam) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* dparam); ++ ++ ++ ++ hook_pos_drotm++; ++ if ( hook_pos_drotm < __flexiblas_hooks->drotm.nhook ) { ++ fn = __flexiblas_hooks->drotm.f77_hook_function[hook_pos_drotm]; ++ } else { ++ hook_pos_drotm = 0; ++ fn = current_backend->blas.drotm.f77_blas_function; ++ } ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy, (void*) dparam); ++ ++ return; ++} ++void flexiblas_chain_drotm(void* n, void* dx, void* incx, void* dy, void* incy, void* dparam) __attribute__((alias("flexiblas_chain_drotm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_drotmg = 0; ++ + void FC_GLOBAL(drotmg,DROTMG)(double* dd1, double* dd2, double* dx1, double* dy1, double* dparam) + { + void (*fn) (void* dd1, void* dd2, void* dx1, void* dy1, void* dparam); +@@ -1514,6 +3152,40 @@ + + + ++void flexiblas_real_drotmg_(void* dd1, void* dd2, void* dx1, void* dy1, void* dparam) ++{ ++ void (*fn) (void* dd1, void* dd2, void* dx1, void* dy1, void* dparam); ++ ++ fn = current_backend->blas.drotmg.f77_blas_function; ++ fn((void*) dd1, (void*) dd2, (void*) dx1, (void*) dy1, (void*) dparam); ++ ++ return; ++} ++void flexiblas_real_drotmg(void* dd1, void* dd2, void* dx1, void* dy1, void* dparam) __attribute__((alias("flexiblas_real_drotmg_"))); ++ ++ ++void flexiblas_chain_drotmg_(void* dd1, void* dd2, void* dx1, void* dy1, void* dparam) ++{ ++ void (*fn) (void* dd1, void* dd2, void* dx1, void* dy1, void* dparam); ++ ++ ++ ++ hook_pos_drotmg++; ++ if ( hook_pos_drotmg < __flexiblas_hooks->drotmg.nhook ) { ++ fn = __flexiblas_hooks->drotmg.f77_hook_function[hook_pos_drotmg]; ++ } else { ++ hook_pos_drotmg = 0; ++ fn = current_backend->blas.drotmg.f77_blas_function; ++ } ++ fn((void*) dd1, (void*) dd2, (void*) dx1, (void*) dy1, (void*) dparam); ++ ++ return; ++} ++void flexiblas_chain_drotmg(void* dd1, void* dd2, void* dx1, void* dy1, void* dparam) __attribute__((alias("flexiblas_chain_drotmg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsbmv = 0; ++ + void FC_GLOBAL(dsbmv,DSBMV)(char* uplo, blasint* n, blasint* k, double* alpha, double* a, blasint* lda, double* x, blasint* incx, double* beta, double* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -1540,6 +3212,40 @@ + + + ++void flexiblas_real_dsbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.dsbmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dsbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_dsbmv_"))); ++ ++ ++void flexiblas_chain_dsbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_dsbmv++; ++ if ( hook_pos_dsbmv < __flexiblas_hooks->dsbmv.nhook ) { ++ fn = __flexiblas_hooks->dsbmv.f77_hook_function[hook_pos_dsbmv]; ++ } else { ++ hook_pos_dsbmv = 0; ++ fn = current_backend->blas.dsbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dsbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_dsbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dscal = 0; ++ + void FC_GLOBAL(dscal,DSCAL)(blasint* n, double* da, double* dx, blasint* incx) + { + void (*fn) (void* n, void* da, void* dx, void* incx); +@@ -1566,6 +3272,40 @@ + + + ++void flexiblas_real_dscal_(void* n, void* da, void* dx, void* incx) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx); ++ ++ fn = current_backend->blas.dscal.f77_blas_function; ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dscal(void* n, void* da, void* dx, void* incx) __attribute__((alias("flexiblas_real_dscal_"))); ++ ++ ++void flexiblas_chain_dscal_(void* n, void* da, void* dx, void* incx) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx); ++ ++ ++ ++ hook_pos_dscal++; ++ if ( hook_pos_dscal < __flexiblas_hooks->dscal.nhook ) { ++ fn = __flexiblas_hooks->dscal.f77_hook_function[hook_pos_dscal]; ++ } else { ++ hook_pos_dscal = 0; ++ fn = current_backend->blas.dscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dscal(void* n, void* da, void* dx, void* incx) __attribute__((alias("flexiblas_chain_dscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsdot = 0; ++ + double FC_GLOBAL(dsdot,DSDOT)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy) + { + double (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); +@@ -1593,6 +3333,42 @@ + + + ++double flexiblas_real_dsdot_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ double (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ double ret; ++ ++ fn = current_backend->blas.dsdot.f77_blas_function; ++ ret = fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++double flexiblas_real_dsdot(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_dsdot_"))); ++ ++ ++double flexiblas_chain_dsdot_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ double (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ double ret; ++ ++ ++ ++ hook_pos_dsdot++; ++ if ( hook_pos_dsdot < __flexiblas_hooks->dsdot.nhook ) { ++ fn = __flexiblas_hooks->dsdot.f77_hook_function[hook_pos_dsdot]; ++ } else { ++ hook_pos_dsdot = 0; ++ fn = current_backend->blas.dsdot.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++double flexiblas_chain_dsdot(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_dsdot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dspmv = 0; ++ + void FC_GLOBAL(dspmv,DSPMV)(char* uplo, blasint* n, double* alpha, double* ap, double* x, blasint* incx, double* beta, double* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); +@@ -1619,6 +3395,40 @@ + + + ++void flexiblas_real_dspmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.dspmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dspmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_dspmv_"))); ++ ++ ++void flexiblas_chain_dspmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_dspmv++; ++ if ( hook_pos_dspmv < __flexiblas_hooks->dspmv.nhook ) { ++ fn = __flexiblas_hooks->dspmv.f77_hook_function[hook_pos_dspmv]; ++ } else { ++ hook_pos_dspmv = 0; ++ fn = current_backend->blas.dspmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dspmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_dspmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dspr = 0; ++ + void FC_GLOBAL(dspr,DSPR)(char* uplo, blasint* n, double* alpha, double* x, blasint* incx, double* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); +@@ -1645,6 +3455,40 @@ + + + ++void flexiblas_real_dspr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ fn = current_backend->blas.dspr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_dspr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_real_dspr_"))); ++ ++ ++void flexiblas_chain_dspr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ ++ ++ hook_pos_dspr++; ++ if ( hook_pos_dspr < __flexiblas_hooks->dspr.nhook ) { ++ fn = __flexiblas_hooks->dspr.f77_hook_function[hook_pos_dspr]; ++ } else { ++ hook_pos_dspr = 0; ++ fn = current_backend->blas.dspr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_dspr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_chain_dspr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dspr2 = 0; ++ + void FC_GLOBAL(dspr2,DSPR2)(char* uplo, blasint* n, double* alpha, double* x, blasint* incx, double* y, blasint* incy, double* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); +@@ -1671,6 +3515,40 @@ + + + ++void flexiblas_real_dspr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ fn = current_backend->blas.dspr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_dspr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_real_dspr2_"))); ++ ++ ++void flexiblas_chain_dspr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ ++ ++ hook_pos_dspr2++; ++ if ( hook_pos_dspr2 < __flexiblas_hooks->dspr2.nhook ) { ++ fn = __flexiblas_hooks->dspr2.f77_hook_function[hook_pos_dspr2]; ++ } else { ++ hook_pos_dspr2 = 0; ++ fn = current_backend->blas.dspr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_dspr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_chain_dspr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dswap = 0; ++ + void FC_GLOBAL(dswap,DSWAP)(blasint* n, double* dx, blasint* incx, double* dy, blasint* incy) + { + void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); +@@ -1697,6 +3575,40 @@ + + + ++void flexiblas_real_dswap_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ ++ fn = current_backend->blas.dswap.f77_blas_function; ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dswap(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_real_dswap_"))); ++ ++ ++void flexiblas_chain_dswap_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ ++ ++ ++ hook_pos_dswap++; ++ if ( hook_pos_dswap < __flexiblas_hooks->dswap.nhook ) { ++ fn = __flexiblas_hooks->dswap.f77_hook_function[hook_pos_dswap]; ++ } else { ++ hook_pos_dswap = 0; ++ fn = current_backend->blas.dswap.f77_blas_function; ++ } ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dswap(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_chain_dswap_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsymm = 0; ++ + void FC_GLOBAL(dsymm,DSYMM)(char* side, char* uplo, blasint* m, blasint* n, double* alpha, double* a, blasint* lda, double* b, blasint* ldb, double* beta, double* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -1723,6 +3635,40 @@ + + + ++void flexiblas_real_dsymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.dsymm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_dsymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_dsymm_"))); ++ ++ ++void flexiblas_chain_dsymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_dsymm++; ++ if ( hook_pos_dsymm < __flexiblas_hooks->dsymm.nhook ) { ++ fn = __flexiblas_hooks->dsymm.f77_hook_function[hook_pos_dsymm]; ++ } else { ++ hook_pos_dsymm = 0; ++ fn = current_backend->blas.dsymm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_dsymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_dsymm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsymv = 0; ++ + void FC_GLOBAL(dsymv,DSYMV)(char* uplo, blasint* n, double* alpha, double* a, blasint* lda, double* x, blasint* incx, double* beta, double* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -1749,6 +3695,40 @@ + + + ++void flexiblas_real_dsymv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.dsymv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dsymv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_dsymv_"))); ++ ++ ++void flexiblas_chain_dsymv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_dsymv++; ++ if ( hook_pos_dsymv < __flexiblas_hooks->dsymv.nhook ) { ++ fn = __flexiblas_hooks->dsymv.f77_hook_function[hook_pos_dsymv]; ++ } else { ++ hook_pos_dsymv = 0; ++ fn = current_backend->blas.dsymv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dsymv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_dsymv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsyr = 0; ++ + void FC_GLOBAL(dsyr,DSYR)(char* uplo, blasint* n, double* alpha, double* x, blasint* incx, double* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); +@@ -1775,6 +3755,40 @@ + + + ++void flexiblas_real_dsyr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ fn = current_backend->blas.dsyr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_dsyr(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_real_dsyr_"))); ++ ++ ++void flexiblas_chain_dsyr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ ++ ++ hook_pos_dsyr++; ++ if ( hook_pos_dsyr < __flexiblas_hooks->dsyr.nhook ) { ++ fn = __flexiblas_hooks->dsyr.f77_hook_function[hook_pos_dsyr]; ++ } else { ++ hook_pos_dsyr = 0; ++ fn = current_backend->blas.dsyr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_dsyr(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_chain_dsyr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsyr2 = 0; ++ + void FC_GLOBAL(dsyr2,DSYR2)(char* uplo, blasint* n, double* alpha, double* x, blasint* incx, double* y, blasint* incy, double* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -1801,6 +3815,40 @@ + + + ++void flexiblas_real_dsyr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.dsyr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_dsyr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_dsyr2_"))); ++ ++ ++void flexiblas_chain_dsyr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_dsyr2++; ++ if ( hook_pos_dsyr2 < __flexiblas_hooks->dsyr2.nhook ) { ++ fn = __flexiblas_hooks->dsyr2.f77_hook_function[hook_pos_dsyr2]; ++ } else { ++ hook_pos_dsyr2 = 0; ++ fn = current_backend->blas.dsyr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_dsyr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_dsyr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsyr2k = 0; ++ + void FC_GLOBAL(dsyr2k,DSYR2K)(char* uplo, char* trans, blasint* n, blasint* k, double* alpha, double* a, blasint* lda, double* b, blasint* ldb, double* beta, double* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -1827,6 +3875,40 @@ + + + ++void flexiblas_real_dsyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.dsyr2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_dsyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_dsyr2k_"))); ++ ++ ++void flexiblas_chain_dsyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_dsyr2k++; ++ if ( hook_pos_dsyr2k < __flexiblas_hooks->dsyr2k.nhook ) { ++ fn = __flexiblas_hooks->dsyr2k.f77_hook_function[hook_pos_dsyr2k]; ++ } else { ++ hook_pos_dsyr2k = 0; ++ fn = current_backend->blas.dsyr2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_dsyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_dsyr2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsyrk = 0; ++ + void FC_GLOBAL(dsyrk,DSYRK)(char* uplo, char* trans, blasint* n, blasint* k, double* alpha, double* a, blasint* lda, double* beta, double* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -1853,6 +3935,40 @@ + + + ++void flexiblas_real_dsyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.dsyrk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_dsyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_dsyrk_"))); ++ ++ ++void flexiblas_chain_dsyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_dsyrk++; ++ if ( hook_pos_dsyrk < __flexiblas_hooks->dsyrk.nhook ) { ++ fn = __flexiblas_hooks->dsyrk.f77_hook_function[hook_pos_dsyrk]; ++ } else { ++ hook_pos_dsyrk = 0; ++ fn = current_backend->blas.dsyrk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_dsyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_dsyrk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtbmv = 0; ++ + void FC_GLOBAL(dtbmv,DTBMV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, double* a, blasint* lda, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -1879,6 +3995,40 @@ + + + ++void flexiblas_real_dtbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.dtbmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_dtbmv_"))); ++ ++ ++void flexiblas_chain_dtbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtbmv++; ++ if ( hook_pos_dtbmv < __flexiblas_hooks->dtbmv.nhook ) { ++ fn = __flexiblas_hooks->dtbmv.f77_hook_function[hook_pos_dtbmv]; ++ } else { ++ hook_pos_dtbmv = 0; ++ fn = current_backend->blas.dtbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtbsv = 0; ++ + void FC_GLOBAL(dtbsv,DTBSV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, double* a, blasint* lda, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -1905,6 +4055,40 @@ + + + ++void flexiblas_real_dtbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.dtbsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_dtbsv_"))); ++ ++ ++void flexiblas_chain_dtbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtbsv++; ++ if ( hook_pos_dtbsv < __flexiblas_hooks->dtbsv.nhook ) { ++ fn = __flexiblas_hooks->dtbsv.f77_hook_function[hook_pos_dtbsv]; ++ } else { ++ hook_pos_dtbsv = 0; ++ fn = current_backend->blas.dtbsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtbsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtpmv = 0; ++ + void FC_GLOBAL(dtpmv,DTPMV)(char* uplo, char* trans, char* diag, blasint* n, double* ap, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -1931,6 +4115,40 @@ + + + ++void flexiblas_real_dtpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.dtpmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_dtpmv_"))); ++ ++ ++void flexiblas_chain_dtpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtpmv++; ++ if ( hook_pos_dtpmv < __flexiblas_hooks->dtpmv.nhook ) { ++ fn = __flexiblas_hooks->dtpmv.f77_hook_function[hook_pos_dtpmv]; ++ } else { ++ hook_pos_dtpmv = 0; ++ fn = current_backend->blas.dtpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtpsv = 0; ++ + void FC_GLOBAL(dtpsv,DTPSV)(char* uplo, char* trans, char* diag, blasint* n, double* ap, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -1957,6 +4175,40 @@ + + + ++void flexiblas_real_dtpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.dtpsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_dtpsv_"))); ++ ++ ++void flexiblas_chain_dtpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtpsv++; ++ if ( hook_pos_dtpsv < __flexiblas_hooks->dtpsv.nhook ) { ++ fn = __flexiblas_hooks->dtpsv.f77_hook_function[hook_pos_dtpsv]; ++ } else { ++ hook_pos_dtpsv = 0; ++ fn = current_backend->blas.dtpsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtpsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtrmm = 0; ++ + void FC_GLOBAL(dtrmm,DTRMM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, double* alpha, double* a, blasint* lda, double* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -1983,6 +4235,40 @@ + + + ++void flexiblas_real_dtrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.dtrmm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_dtrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_dtrmm_"))); ++ ++ ++void flexiblas_chain_dtrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_dtrmm++; ++ if ( hook_pos_dtrmm < __flexiblas_hooks->dtrmm.nhook ) { ++ fn = __flexiblas_hooks->dtrmm.f77_hook_function[hook_pos_dtrmm]; ++ } else { ++ hook_pos_dtrmm = 0; ++ fn = current_backend->blas.dtrmm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_dtrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_dtrmm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtrmv = 0; ++ + void FC_GLOBAL(dtrmv,DTRMV)(char* uplo, char* trans, char* diag, blasint* n, double* a, blasint* lda, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -2009,6 +4295,40 @@ + + + ++void flexiblas_real_dtrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.dtrmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_dtrmv_"))); ++ ++ ++void flexiblas_chain_dtrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtrmv++; ++ if ( hook_pos_dtrmv < __flexiblas_hooks->dtrmv.nhook ) { ++ fn = __flexiblas_hooks->dtrmv.f77_hook_function[hook_pos_dtrmv]; ++ } else { ++ hook_pos_dtrmv = 0; ++ fn = current_backend->blas.dtrmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtrmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtrsm = 0; ++ + void FC_GLOBAL(dtrsm,DTRSM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, double* alpha, double* a, blasint* lda, double* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -2035,6 +4355,40 @@ + + + ++void flexiblas_real_dtrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.dtrsm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_dtrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_dtrsm_"))); ++ ++ ++void flexiblas_chain_dtrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_dtrsm++; ++ if ( hook_pos_dtrsm < __flexiblas_hooks->dtrsm.nhook ) { ++ fn = __flexiblas_hooks->dtrsm.f77_hook_function[hook_pos_dtrsm]; ++ } else { ++ hook_pos_dtrsm = 0; ++ fn = current_backend->blas.dtrsm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_dtrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_dtrsm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtrsv = 0; ++ + void FC_GLOBAL(dtrsv,DTRSV)(char* uplo, char* trans, char* diag, blasint* n, double* a, blasint* lda, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -2061,6 +4415,40 @@ + + + ++void flexiblas_real_dtrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.dtrsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_dtrsv_"))); ++ ++ ++void flexiblas_chain_dtrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtrsv++; ++ if ( hook_pos_dtrsv < __flexiblas_hooks->dtrsv.nhook ) { ++ fn = __flexiblas_hooks->dtrsv.f77_hook_function[hook_pos_dtrsv]; ++ } else { ++ hook_pos_dtrsv = 0; ++ fn = current_backend->blas.dtrsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtrsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dzasum = 0; ++ + double FC_GLOBAL(dzasum,DZASUM)(blasint* n, double complex* zx, blasint* incx) + { + double (*fn) (void* n, void* zx, void* incx); +@@ -2088,6 +4476,42 @@ + + + ++double flexiblas_real_dzasum_(void* n, void* zx, void* incx) ++{ ++ double (*fn) (void* n, void* zx, void* incx); ++ double ret; ++ ++ fn = current_backend->blas.dzasum.f77_blas_function; ++ ret = fn((void*) n, (void*) zx, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_real_dzasum(void* n, void* zx, void* incx) __attribute__((alias("flexiblas_real_dzasum_"))); ++ ++ ++double flexiblas_chain_dzasum_(void* n, void* zx, void* incx) ++{ ++ double (*fn) (void* n, void* zx, void* incx); ++ double ret; ++ ++ ++ ++ hook_pos_dzasum++; ++ if ( hook_pos_dzasum < __flexiblas_hooks->dzasum.nhook ) { ++ fn = __flexiblas_hooks->dzasum.f77_hook_function[hook_pos_dzasum]; ++ } else { ++ hook_pos_dzasum = 0; ++ fn = current_backend->blas.dzasum.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) zx, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_chain_dzasum(void* n, void* zx, void* incx) __attribute__((alias("flexiblas_chain_dzasum_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dznrm2 = 0; ++ + double FC_GLOBAL(dznrm2,DZNRM2)(blasint* n, double complex* x, blasint* incx) + { + double (*fn) (void* n, void* x, void* incx); +@@ -2115,6 +4539,42 @@ + + + ++double flexiblas_real_dznrm2_(void* n, void* x, void* incx) ++{ ++ double (*fn) (void* n, void* x, void* incx); ++ double ret; ++ ++ fn = current_backend->blas.dznrm2.f77_blas_function; ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_real_dznrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_real_dznrm2_"))); ++ ++ ++double flexiblas_chain_dznrm2_(void* n, void* x, void* incx) ++{ ++ double (*fn) (void* n, void* x, void* incx); ++ double ret; ++ ++ ++ ++ hook_pos_dznrm2++; ++ if ( hook_pos_dznrm2 < __flexiblas_hooks->dznrm2.nhook ) { ++ fn = __flexiblas_hooks->dznrm2.f77_hook_function[hook_pos_dznrm2]; ++ } else { ++ hook_pos_dznrm2 = 0; ++ fn = current_backend->blas.dznrm2.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_chain_dznrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_chain_dznrm2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_icamax = 0; ++ + int FC_GLOBAL(icamax,ICAMAX)(blasint* n, float complex* cx, blasint* incx) + { + blasint (*fn) (void* n, void* cx, void* incx); +@@ -2142,6 +4602,42 @@ + + + ++blasint flexiblas_real_icamax_(void* n, void* cx, void* incx) ++{ ++ blasint (*fn) (void* n, void* cx, void* incx); ++ blasint ret; ++ ++ fn = current_backend->blas.icamax.f77_blas_function; ++ ret = fn((void*) n, (void*) cx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_real_icamax(void* n, void* cx, void* incx) __attribute__((alias("flexiblas_real_icamax_"))); ++ ++ ++blasint flexiblas_chain_icamax_(void* n, void* cx, void* incx) ++{ ++ blasint (*fn) (void* n, void* cx, void* incx); ++ blasint ret; ++ ++ ++ ++ hook_pos_icamax++; ++ if ( hook_pos_icamax < __flexiblas_hooks->icamax.nhook ) { ++ fn = __flexiblas_hooks->icamax.f77_hook_function[hook_pos_icamax]; ++ } else { ++ hook_pos_icamax = 0; ++ fn = current_backend->blas.icamax.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) cx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_chain_icamax(void* n, void* cx, void* incx) __attribute__((alias("flexiblas_chain_icamax_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_idamax = 0; ++ + int FC_GLOBAL(idamax,IDAMAX)(blasint* n, double* dx, blasint* incx) + { + blasint (*fn) (void* n, void* dx, void* incx); +@@ -2169,6 +4665,42 @@ + + + ++blasint flexiblas_real_idamax_(void* n, void* dx, void* incx) ++{ ++ blasint (*fn) (void* n, void* dx, void* incx); ++ blasint ret; ++ ++ fn = current_backend->blas.idamax.f77_blas_function; ++ ret = fn((void*) n, (void*) dx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_real_idamax(void* n, void* dx, void* incx) __attribute__((alias("flexiblas_real_idamax_"))); ++ ++ ++blasint flexiblas_chain_idamax_(void* n, void* dx, void* incx) ++{ ++ blasint (*fn) (void* n, void* dx, void* incx); ++ blasint ret; ++ ++ ++ ++ hook_pos_idamax++; ++ if ( hook_pos_idamax < __flexiblas_hooks->idamax.nhook ) { ++ fn = __flexiblas_hooks->idamax.f77_hook_function[hook_pos_idamax]; ++ } else { ++ hook_pos_idamax = 0; ++ fn = current_backend->blas.idamax.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) dx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_chain_idamax(void* n, void* dx, void* incx) __attribute__((alias("flexiblas_chain_idamax_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_isamax = 0; ++ + int FC_GLOBAL(isamax,ISAMAX)(blasint* n, float* sx, blasint* incx) + { + blasint (*fn) (void* n, void* sx, void* incx); +@@ -2196,6 +4728,42 @@ + + + ++blasint flexiblas_real_isamax_(void* n, void* sx, void* incx) ++{ ++ blasint (*fn) (void* n, void* sx, void* incx); ++ blasint ret; ++ ++ fn = current_backend->blas.isamax.f77_blas_function; ++ ret = fn((void*) n, (void*) sx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_real_isamax(void* n, void* sx, void* incx) __attribute__((alias("flexiblas_real_isamax_"))); ++ ++ ++blasint flexiblas_chain_isamax_(void* n, void* sx, void* incx) ++{ ++ blasint (*fn) (void* n, void* sx, void* incx); ++ blasint ret; ++ ++ ++ ++ hook_pos_isamax++; ++ if ( hook_pos_isamax < __flexiblas_hooks->isamax.nhook ) { ++ fn = __flexiblas_hooks->isamax.f77_hook_function[hook_pos_isamax]; ++ } else { ++ hook_pos_isamax = 0; ++ fn = current_backend->blas.isamax.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) sx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_chain_isamax(void* n, void* sx, void* incx) __attribute__((alias("flexiblas_chain_isamax_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_izamax = 0; ++ + int FC_GLOBAL(izamax,IZAMAX)(blasint* n, double complex* zx, blasint* incx) + { + blasint (*fn) (void* n, void* zx, void* incx); +@@ -2223,6 +4791,42 @@ + + + ++blasint flexiblas_real_izamax_(void* n, void* zx, void* incx) ++{ ++ blasint (*fn) (void* n, void* zx, void* incx); ++ blasint ret; ++ ++ fn = current_backend->blas.izamax.f77_blas_function; ++ ret = fn((void*) n, (void*) zx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_real_izamax(void* n, void* zx, void* incx) __attribute__((alias("flexiblas_real_izamax_"))); ++ ++ ++blasint flexiblas_chain_izamax_(void* n, void* zx, void* incx) ++{ ++ blasint (*fn) (void* n, void* zx, void* incx); ++ blasint ret; ++ ++ ++ ++ hook_pos_izamax++; ++ if ( hook_pos_izamax < __flexiblas_hooks->izamax.nhook ) { ++ fn = __flexiblas_hooks->izamax.f77_hook_function[hook_pos_izamax]; ++ } else { ++ hook_pos_izamax = 0; ++ fn = current_backend->blas.izamax.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) zx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_chain_izamax(void* n, void* zx, void* incx) __attribute__((alias("flexiblas_chain_izamax_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sasum = 0; ++ + float FC_GLOBAL(sasum,SASUM)(blasint* n, float* sx, blasint* incx) + { + float (*fn) (void* n, void* sx, void* incx); +@@ -2250,6 +4854,42 @@ + + + ++float flexiblas_real_sasum_(void* n, void* sx, void* incx) ++{ ++ float (*fn) (void* n, void* sx, void* incx); ++ float ret; ++ ++ fn = current_backend->blas.sasum.f77_blas_function; ++ ret = fn((void*) n, (void*) sx, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_real_sasum(void* n, void* sx, void* incx) __attribute__((alias("flexiblas_real_sasum_"))); ++ ++ ++float flexiblas_chain_sasum_(void* n, void* sx, void* incx) ++{ ++ float (*fn) (void* n, void* sx, void* incx); ++ float ret; ++ ++ ++ ++ hook_pos_sasum++; ++ if ( hook_pos_sasum < __flexiblas_hooks->sasum.nhook ) { ++ fn = __flexiblas_hooks->sasum.f77_hook_function[hook_pos_sasum]; ++ } else { ++ hook_pos_sasum = 0; ++ fn = current_backend->blas.sasum.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) sx, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_chain_sasum(void* n, void* sx, void* incx) __attribute__((alias("flexiblas_chain_sasum_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_saxpy = 0; ++ + void FC_GLOBAL(saxpy,SAXPY)(blasint* n, float* sa, float* sx, blasint* incx, float* sy, blasint* incy) + { + void (*fn) (void* n, void* sa, void* sx, void* incx, void* sy, void* incy); +@@ -2276,6 +4916,40 @@ + + + ++void flexiblas_real_saxpy_(void* n, void* sa, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx, void* sy, void* incy); ++ ++ fn = current_backend->blas.saxpy.f77_blas_function; ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_saxpy(void* n, void* sa, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_saxpy_"))); ++ ++ ++void flexiblas_chain_saxpy_(void* n, void* sa, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx, void* sy, void* incy); ++ ++ ++ ++ hook_pos_saxpy++; ++ if ( hook_pos_saxpy < __flexiblas_hooks->saxpy.nhook ) { ++ fn = __flexiblas_hooks->saxpy.f77_hook_function[hook_pos_saxpy]; ++ } else { ++ hook_pos_saxpy = 0; ++ fn = current_backend->blas.saxpy.f77_blas_function; ++ } ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_saxpy(void* n, void* sa, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_saxpy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_scasum = 0; ++ + float FC_GLOBAL(scasum,SCASUM)(blasint* n, float complex* cx, blasint* incx) + { + float (*fn) (void* n, void* cx, void* incx); +@@ -2303,6 +4977,42 @@ + + + ++float flexiblas_real_scasum_(void* n, void* cx, void* incx) ++{ ++ float (*fn) (void* n, void* cx, void* incx); ++ float ret; ++ ++ fn = current_backend->blas.scasum.f77_blas_function; ++ ret = fn((void*) n, (void*) cx, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_real_scasum(void* n, void* cx, void* incx) __attribute__((alias("flexiblas_real_scasum_"))); ++ ++ ++float flexiblas_chain_scasum_(void* n, void* cx, void* incx) ++{ ++ float (*fn) (void* n, void* cx, void* incx); ++ float ret; ++ ++ ++ ++ hook_pos_scasum++; ++ if ( hook_pos_scasum < __flexiblas_hooks->scasum.nhook ) { ++ fn = __flexiblas_hooks->scasum.f77_hook_function[hook_pos_scasum]; ++ } else { ++ hook_pos_scasum = 0; ++ fn = current_backend->blas.scasum.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) cx, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_chain_scasum(void* n, void* cx, void* incx) __attribute__((alias("flexiblas_chain_scasum_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_scnrm2 = 0; ++ + float FC_GLOBAL(scnrm2,SCNRM2)(blasint* n, float complex* x, blasint* incx) + { + float (*fn) (void* n, void* x, void* incx); +@@ -2330,6 +5040,42 @@ + + + ++float flexiblas_real_scnrm2_(void* n, void* x, void* incx) ++{ ++ float (*fn) (void* n, void* x, void* incx); ++ float ret; ++ ++ fn = current_backend->blas.scnrm2.f77_blas_function; ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_real_scnrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_real_scnrm2_"))); ++ ++ ++float flexiblas_chain_scnrm2_(void* n, void* x, void* incx) ++{ ++ float (*fn) (void* n, void* x, void* incx); ++ float ret; ++ ++ ++ ++ hook_pos_scnrm2++; ++ if ( hook_pos_scnrm2 < __flexiblas_hooks->scnrm2.nhook ) { ++ fn = __flexiblas_hooks->scnrm2.f77_hook_function[hook_pos_scnrm2]; ++ } else { ++ hook_pos_scnrm2 = 0; ++ fn = current_backend->blas.scnrm2.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_chain_scnrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_chain_scnrm2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_scopy = 0; ++ + void FC_GLOBAL(scopy,SCOPY)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy) + { + void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); +@@ -2356,6 +5102,40 @@ + + + ++void flexiblas_real_scopy_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ ++ fn = current_backend->blas.scopy.f77_blas_function; ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_scopy(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_scopy_"))); ++ ++ ++void flexiblas_chain_scopy_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ ++ ++ ++ hook_pos_scopy++; ++ if ( hook_pos_scopy < __flexiblas_hooks->scopy.nhook ) { ++ fn = __flexiblas_hooks->scopy.f77_hook_function[hook_pos_scopy]; ++ } else { ++ hook_pos_scopy = 0; ++ fn = current_backend->blas.scopy.f77_blas_function; ++ } ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_scopy(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_scopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sdot = 0; ++ + float FC_GLOBAL(sdot,SDOT)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy) + { + float (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); +@@ -2383,6 +5163,42 @@ + + + ++float flexiblas_real_sdot_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ float (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ float ret; ++ ++ fn = current_backend->blas.sdot.f77_blas_function; ++ ret = fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++float flexiblas_real_sdot(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_sdot_"))); ++ ++ ++float flexiblas_chain_sdot_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ float (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ float ret; ++ ++ ++ ++ hook_pos_sdot++; ++ if ( hook_pos_sdot < __flexiblas_hooks->sdot.nhook ) { ++ fn = __flexiblas_hooks->sdot.f77_hook_function[hook_pos_sdot]; ++ } else { ++ hook_pos_sdot = 0; ++ fn = current_backend->blas.sdot.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++float flexiblas_chain_sdot(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_sdot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sdsdot = 0; ++ + float FC_GLOBAL(sdsdot,SDSDOT)(blasint* n, float* sb, float* sx, blasint* incx, float* sy, blasint* incy) + { + float (*fn) (void* n, void* sb, void* sx, void* incx, void* sy, void* incy); +@@ -2410,6 +5226,42 @@ + + + ++float flexiblas_real_sdsdot_(void* n, void* sb, void* sx, void* incx, void* sy, void* incy) ++{ ++ float (*fn) (void* n, void* sb, void* sx, void* incx, void* sy, void* incy); ++ float ret; ++ ++ fn = current_backend->blas.sdsdot.f77_blas_function; ++ ret = fn((void*) n, (void*) sb, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++float flexiblas_real_sdsdot(void* n, void* sb, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_sdsdot_"))); ++ ++ ++float flexiblas_chain_sdsdot_(void* n, void* sb, void* sx, void* incx, void* sy, void* incy) ++{ ++ float (*fn) (void* n, void* sb, void* sx, void* incx, void* sy, void* incy); ++ float ret; ++ ++ ++ ++ hook_pos_sdsdot++; ++ if ( hook_pos_sdsdot < __flexiblas_hooks->sdsdot.nhook ) { ++ fn = __flexiblas_hooks->sdsdot.f77_hook_function[hook_pos_sdsdot]; ++ } else { ++ hook_pos_sdsdot = 0; ++ fn = current_backend->blas.sdsdot.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) sb, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++float flexiblas_chain_sdsdot(void* n, void* sb, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_sdsdot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sgbmv = 0; ++ + void FC_GLOBAL(sgbmv,SGBMV)(char* trans, blasint* m, blasint* n, blasint* kl, blasint* ku, float* alpha, float* a, blasint* lda, float* x, blasint* incx, float* beta, float* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -2436,6 +5288,40 @@ + + + ++void flexiblas_real_sgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.sgbmv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_sgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_sgbmv_"))); ++ ++ ++void flexiblas_chain_sgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_sgbmv++; ++ if ( hook_pos_sgbmv < __flexiblas_hooks->sgbmv.nhook ) { ++ fn = __flexiblas_hooks->sgbmv.f77_hook_function[hook_pos_sgbmv]; ++ } else { ++ hook_pos_sgbmv = 0; ++ fn = current_backend->blas.sgbmv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_sgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_sgbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sgemm = 0; ++ + void FC_GLOBAL(sgemm,SGEMM)(char* transa, char* transb, blasint* m, blasint* n, blasint* k, float* alpha, float* a, blasint* lda, float* b, blasint* ldb, float* beta, float* c, blasint* ldc) + { + void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -2462,6 +5348,40 @@ + + + ++void flexiblas_real_sgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.sgemm.f77_blas_function; ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_sgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_sgemm_"))); ++ ++ ++void flexiblas_chain_sgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_sgemm++; ++ if ( hook_pos_sgemm < __flexiblas_hooks->sgemm.nhook ) { ++ fn = __flexiblas_hooks->sgemm.f77_hook_function[hook_pos_sgemm]; ++ } else { ++ hook_pos_sgemm = 0; ++ fn = current_backend->blas.sgemm.f77_blas_function; ++ } ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_sgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_sgemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sgemv = 0; ++ + void FC_GLOBAL(sgemv,SGEMV)(char* trans, blasint* m, blasint* n, float* alpha, float* a, blasint* lda, float* x, blasint* incx, float* beta, float* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -2488,6 +5408,40 @@ + + + ++void flexiblas_real_sgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.sgemv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_sgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_sgemv_"))); ++ ++ ++void flexiblas_chain_sgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_sgemv++; ++ if ( hook_pos_sgemv < __flexiblas_hooks->sgemv.nhook ) { ++ fn = __flexiblas_hooks->sgemv.f77_hook_function[hook_pos_sgemv]; ++ } else { ++ hook_pos_sgemv = 0; ++ fn = current_backend->blas.sgemv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_sgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_sgemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sger = 0; ++ + void FC_GLOBAL(sger,SGER)(blasint* m, blasint* n, float* alpha, float* x, blasint* incx, float* y, blasint* incy, float* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -2514,6 +5468,40 @@ + + + ++void flexiblas_real_sger_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.sger.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_sger(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_sger_"))); ++ ++ ++void flexiblas_chain_sger_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_sger++; ++ if ( hook_pos_sger < __flexiblas_hooks->sger.nhook ) { ++ fn = __flexiblas_hooks->sger.f77_hook_function[hook_pos_sger]; ++ } else { ++ hook_pos_sger = 0; ++ fn = current_backend->blas.sger.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_sger(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_sger_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_snrm2 = 0; ++ + float FC_GLOBAL(snrm2,SNRM2)(blasint* n, float* x, blasint* incx) + { + float (*fn) (void* n, void* x, void* incx); +@@ -2541,6 +5529,42 @@ + + + ++float flexiblas_real_snrm2_(void* n, void* x, void* incx) ++{ ++ float (*fn) (void* n, void* x, void* incx); ++ float ret; ++ ++ fn = current_backend->blas.snrm2.f77_blas_function; ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_real_snrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_real_snrm2_"))); ++ ++ ++float flexiblas_chain_snrm2_(void* n, void* x, void* incx) ++{ ++ float (*fn) (void* n, void* x, void* incx); ++ float ret; ++ ++ ++ ++ hook_pos_snrm2++; ++ if ( hook_pos_snrm2 < __flexiblas_hooks->snrm2.nhook ) { ++ fn = __flexiblas_hooks->snrm2.f77_hook_function[hook_pos_snrm2]; ++ } else { ++ hook_pos_snrm2 = 0; ++ fn = current_backend->blas.snrm2.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_chain_snrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_chain_snrm2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_srot = 0; ++ + void FC_GLOBAL(srot,SROT)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy, float* c, float* s) + { + void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s); +@@ -2567,6 +5591,40 @@ + + + ++void flexiblas_real_srot_(void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s); ++ ++ fn = current_backend->blas.srot.f77_blas_function; ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_srot(void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_real_srot_"))); ++ ++ ++void flexiblas_chain_srot_(void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s); ++ ++ ++ ++ hook_pos_srot++; ++ if ( hook_pos_srot < __flexiblas_hooks->srot.nhook ) { ++ fn = __flexiblas_hooks->srot.f77_hook_function[hook_pos_srot]; ++ } else { ++ hook_pos_srot = 0; ++ fn = current_backend->blas.srot.f77_blas_function; ++ } ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_srot(void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_chain_srot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_srotg = 0; ++ + void FC_GLOBAL(srotg,SROTG)(float* sa, float* sb, float* c, float* s) + { + void (*fn) (void* sa, void* sb, void* c, void* s); +@@ -2593,6 +5651,40 @@ + + + ++void flexiblas_real_srotg_(void* sa, void* sb, void* c, void* s) ++{ ++ void (*fn) (void* sa, void* sb, void* c, void* s); ++ ++ fn = current_backend->blas.srotg.f77_blas_function; ++ fn((void*) sa, (void*) sb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_srotg(void* sa, void* sb, void* c, void* s) __attribute__((alias("flexiblas_real_srotg_"))); ++ ++ ++void flexiblas_chain_srotg_(void* sa, void* sb, void* c, void* s) ++{ ++ void (*fn) (void* sa, void* sb, void* c, void* s); ++ ++ ++ ++ hook_pos_srotg++; ++ if ( hook_pos_srotg < __flexiblas_hooks->srotg.nhook ) { ++ fn = __flexiblas_hooks->srotg.f77_hook_function[hook_pos_srotg]; ++ } else { ++ hook_pos_srotg = 0; ++ fn = current_backend->blas.srotg.f77_blas_function; ++ } ++ fn((void*) sa, (void*) sb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_srotg(void* sa, void* sb, void* c, void* s) __attribute__((alias("flexiblas_chain_srotg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_srotm = 0; ++ + void FC_GLOBAL(srotm,SROTM)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy, float* sparam) + { + void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* sparam); +@@ -2619,6 +5711,40 @@ + + + ++void flexiblas_real_srotm_(void* n, void* sx, void* incx, void* sy, void* incy, void* sparam) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* sparam); ++ ++ fn = current_backend->blas.srotm.f77_blas_function; ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy, (void*) sparam); ++ ++ return; ++} ++void flexiblas_real_srotm(void* n, void* sx, void* incx, void* sy, void* incy, void* sparam) __attribute__((alias("flexiblas_real_srotm_"))); ++ ++ ++void flexiblas_chain_srotm_(void* n, void* sx, void* incx, void* sy, void* incy, void* sparam) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* sparam); ++ ++ ++ ++ hook_pos_srotm++; ++ if ( hook_pos_srotm < __flexiblas_hooks->srotm.nhook ) { ++ fn = __flexiblas_hooks->srotm.f77_hook_function[hook_pos_srotm]; ++ } else { ++ hook_pos_srotm = 0; ++ fn = current_backend->blas.srotm.f77_blas_function; ++ } ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy, (void*) sparam); ++ ++ return; ++} ++void flexiblas_chain_srotm(void* n, void* sx, void* incx, void* sy, void* incy, void* sparam) __attribute__((alias("flexiblas_chain_srotm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_srotmg = 0; ++ + void FC_GLOBAL(srotmg,SROTMG)(float* sd1, float* sd2, float* sx1, float* sy1, float* sparam) + { + void (*fn) (void* sd1, void* sd2, void* sx1, void* sy1, void* sparam); +@@ -2645,6 +5771,40 @@ + + + ++void flexiblas_real_srotmg_(void* sd1, void* sd2, void* sx1, void* sy1, void* sparam) ++{ ++ void (*fn) (void* sd1, void* sd2, void* sx1, void* sy1, void* sparam); ++ ++ fn = current_backend->blas.srotmg.f77_blas_function; ++ fn((void*) sd1, (void*) sd2, (void*) sx1, (void*) sy1, (void*) sparam); ++ ++ return; ++} ++void flexiblas_real_srotmg(void* sd1, void* sd2, void* sx1, void* sy1, void* sparam) __attribute__((alias("flexiblas_real_srotmg_"))); ++ ++ ++void flexiblas_chain_srotmg_(void* sd1, void* sd2, void* sx1, void* sy1, void* sparam) ++{ ++ void (*fn) (void* sd1, void* sd2, void* sx1, void* sy1, void* sparam); ++ ++ ++ ++ hook_pos_srotmg++; ++ if ( hook_pos_srotmg < __flexiblas_hooks->srotmg.nhook ) { ++ fn = __flexiblas_hooks->srotmg.f77_hook_function[hook_pos_srotmg]; ++ } else { ++ hook_pos_srotmg = 0; ++ fn = current_backend->blas.srotmg.f77_blas_function; ++ } ++ fn((void*) sd1, (void*) sd2, (void*) sx1, (void*) sy1, (void*) sparam); ++ ++ return; ++} ++void flexiblas_chain_srotmg(void* sd1, void* sd2, void* sx1, void* sy1, void* sparam) __attribute__((alias("flexiblas_chain_srotmg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssbmv = 0; ++ + void FC_GLOBAL(ssbmv,SSBMV)(char* uplo, blasint* n, blasint* k, float* alpha, float* a, blasint* lda, float* x, blasint* incx, float* beta, float* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -2671,6 +5831,40 @@ + + + ++void flexiblas_real_ssbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.ssbmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_ssbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_ssbmv_"))); ++ ++ ++void flexiblas_chain_ssbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_ssbmv++; ++ if ( hook_pos_ssbmv < __flexiblas_hooks->ssbmv.nhook ) { ++ fn = __flexiblas_hooks->ssbmv.f77_hook_function[hook_pos_ssbmv]; ++ } else { ++ hook_pos_ssbmv = 0; ++ fn = current_backend->blas.ssbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_ssbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_ssbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sscal = 0; ++ + void FC_GLOBAL(sscal,SSCAL)(blasint* n, float* sa, float* sx, blasint* incx) + { + void (*fn) (void* n, void* sa, void* sx, void* incx); +@@ -2697,6 +5891,40 @@ + + + ++void flexiblas_real_sscal_(void* n, void* sa, void* sx, void* incx) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx); ++ ++ fn = current_backend->blas.sscal.f77_blas_function; ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_sscal(void* n, void* sa, void* sx, void* incx) __attribute__((alias("flexiblas_real_sscal_"))); ++ ++ ++void flexiblas_chain_sscal_(void* n, void* sa, void* sx, void* incx) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx); ++ ++ ++ ++ hook_pos_sscal++; ++ if ( hook_pos_sscal < __flexiblas_hooks->sscal.nhook ) { ++ fn = __flexiblas_hooks->sscal.f77_hook_function[hook_pos_sscal]; ++ } else { ++ hook_pos_sscal = 0; ++ fn = current_backend->blas.sscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_sscal(void* n, void* sa, void* sx, void* incx) __attribute__((alias("flexiblas_chain_sscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sspmv = 0; ++ + void FC_GLOBAL(sspmv,SSPMV)(char* uplo, blasint* n, float* alpha, float* ap, float* x, blasint* incx, float* beta, float* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); +@@ -2723,6 +5951,40 @@ + + + ++void flexiblas_real_sspmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.sspmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_sspmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_sspmv_"))); ++ ++ ++void flexiblas_chain_sspmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_sspmv++; ++ if ( hook_pos_sspmv < __flexiblas_hooks->sspmv.nhook ) { ++ fn = __flexiblas_hooks->sspmv.f77_hook_function[hook_pos_sspmv]; ++ } else { ++ hook_pos_sspmv = 0; ++ fn = current_backend->blas.sspmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_sspmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_sspmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sspr = 0; ++ + void FC_GLOBAL(sspr,SSPR)(char* uplo, blasint* n, float* alpha, float* x, blasint* incx, float* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); +@@ -2749,6 +6011,40 @@ + + + ++void flexiblas_real_sspr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ fn = current_backend->blas.sspr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_sspr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_real_sspr_"))); ++ ++ ++void flexiblas_chain_sspr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ ++ ++ hook_pos_sspr++; ++ if ( hook_pos_sspr < __flexiblas_hooks->sspr.nhook ) { ++ fn = __flexiblas_hooks->sspr.f77_hook_function[hook_pos_sspr]; ++ } else { ++ hook_pos_sspr = 0; ++ fn = current_backend->blas.sspr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_sspr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_chain_sspr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sspr2 = 0; ++ + void FC_GLOBAL(sspr2,SSPR2)(char* uplo, blasint* n, float* alpha, float* x, blasint* incx, float* y, blasint* incy, float* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); +@@ -2775,6 +6071,40 @@ + + + ++void flexiblas_real_sspr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ fn = current_backend->blas.sspr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_sspr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_real_sspr2_"))); ++ ++ ++void flexiblas_chain_sspr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ ++ ++ hook_pos_sspr2++; ++ if ( hook_pos_sspr2 < __flexiblas_hooks->sspr2.nhook ) { ++ fn = __flexiblas_hooks->sspr2.f77_hook_function[hook_pos_sspr2]; ++ } else { ++ hook_pos_sspr2 = 0; ++ fn = current_backend->blas.sspr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_sspr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_chain_sspr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sswap = 0; ++ + void FC_GLOBAL(sswap,SSWAP)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy) + { + void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); +@@ -2801,6 +6131,40 @@ + + + ++void flexiblas_real_sswap_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ ++ fn = current_backend->blas.sswap.f77_blas_function; ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_sswap(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_sswap_"))); ++ ++ ++void flexiblas_chain_sswap_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ ++ ++ ++ hook_pos_sswap++; ++ if ( hook_pos_sswap < __flexiblas_hooks->sswap.nhook ) { ++ fn = __flexiblas_hooks->sswap.f77_hook_function[hook_pos_sswap]; ++ } else { ++ hook_pos_sswap = 0; ++ fn = current_backend->blas.sswap.f77_blas_function; ++ } ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_sswap(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_sswap_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssymm = 0; ++ + void FC_GLOBAL(ssymm,SSYMM)(char* side, char* uplo, blasint* m, blasint* n, float* alpha, float* a, blasint* lda, float* b, blasint* ldb, float* beta, float* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -2827,6 +6191,40 @@ + + + ++void flexiblas_real_ssymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.ssymm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_ssymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_ssymm_"))); ++ ++ ++void flexiblas_chain_ssymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_ssymm++; ++ if ( hook_pos_ssymm < __flexiblas_hooks->ssymm.nhook ) { ++ fn = __flexiblas_hooks->ssymm.f77_hook_function[hook_pos_ssymm]; ++ } else { ++ hook_pos_ssymm = 0; ++ fn = current_backend->blas.ssymm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_ssymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_ssymm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssymv = 0; ++ + void FC_GLOBAL(ssymv,SSYMV)(char* uplo, blasint* n, float* alpha, float* a, blasint* lda, float* x, blasint* incx, float* beta, float* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -2853,6 +6251,40 @@ + + + ++void flexiblas_real_ssymv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.ssymv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_ssymv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_ssymv_"))); ++ ++ ++void flexiblas_chain_ssymv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_ssymv++; ++ if ( hook_pos_ssymv < __flexiblas_hooks->ssymv.nhook ) { ++ fn = __flexiblas_hooks->ssymv.f77_hook_function[hook_pos_ssymv]; ++ } else { ++ hook_pos_ssymv = 0; ++ fn = current_backend->blas.ssymv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_ssymv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_ssymv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssyr = 0; ++ + void FC_GLOBAL(ssyr,SSYR)(char* uplo, blasint* n, float* alpha, float* x, blasint* incx, float* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); +@@ -2879,6 +6311,40 @@ + + + ++void flexiblas_real_ssyr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ fn = current_backend->blas.ssyr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_ssyr(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_real_ssyr_"))); ++ ++ ++void flexiblas_chain_ssyr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ ++ ++ hook_pos_ssyr++; ++ if ( hook_pos_ssyr < __flexiblas_hooks->ssyr.nhook ) { ++ fn = __flexiblas_hooks->ssyr.f77_hook_function[hook_pos_ssyr]; ++ } else { ++ hook_pos_ssyr = 0; ++ fn = current_backend->blas.ssyr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_ssyr(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_chain_ssyr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssyr2 = 0; ++ + void FC_GLOBAL(ssyr2,SSYR2)(char* uplo, blasint* n, float* alpha, float* x, blasint* incx, float* y, blasint* incy, float* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -2905,6 +6371,40 @@ + + + ++void flexiblas_real_ssyr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.ssyr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_ssyr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_ssyr2_"))); ++ ++ ++void flexiblas_chain_ssyr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_ssyr2++; ++ if ( hook_pos_ssyr2 < __flexiblas_hooks->ssyr2.nhook ) { ++ fn = __flexiblas_hooks->ssyr2.f77_hook_function[hook_pos_ssyr2]; ++ } else { ++ hook_pos_ssyr2 = 0; ++ fn = current_backend->blas.ssyr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_ssyr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_ssyr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssyr2k = 0; ++ + void FC_GLOBAL(ssyr2k,SSYR2K)(char* uplo, char* trans, blasint* n, blasint* k, float* alpha, float* a, blasint* lda, float* b, blasint* ldb, float* beta, float* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -2931,6 +6431,40 @@ + + + ++void flexiblas_real_ssyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.ssyr2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_ssyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_ssyr2k_"))); ++ ++ ++void flexiblas_chain_ssyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_ssyr2k++; ++ if ( hook_pos_ssyr2k < __flexiblas_hooks->ssyr2k.nhook ) { ++ fn = __flexiblas_hooks->ssyr2k.f77_hook_function[hook_pos_ssyr2k]; ++ } else { ++ hook_pos_ssyr2k = 0; ++ fn = current_backend->blas.ssyr2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_ssyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_ssyr2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssyrk = 0; ++ + void FC_GLOBAL(ssyrk,SSYRK)(char* uplo, char* trans, blasint* n, blasint* k, float* alpha, float* a, blasint* lda, float* beta, float* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -2957,6 +6491,40 @@ + + + ++void flexiblas_real_ssyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.ssyrk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_ssyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_ssyrk_"))); ++ ++ ++void flexiblas_chain_ssyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_ssyrk++; ++ if ( hook_pos_ssyrk < __flexiblas_hooks->ssyrk.nhook ) { ++ fn = __flexiblas_hooks->ssyrk.f77_hook_function[hook_pos_ssyrk]; ++ } else { ++ hook_pos_ssyrk = 0; ++ fn = current_backend->blas.ssyrk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_ssyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_ssyrk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_stbmv = 0; ++ + void FC_GLOBAL(stbmv,STBMV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, float* a, blasint* lda, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -2983,6 +6551,40 @@ + + + ++void flexiblas_real_stbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.stbmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_stbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_stbmv_"))); ++ ++ ++void flexiblas_chain_stbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_stbmv++; ++ if ( hook_pos_stbmv < __flexiblas_hooks->stbmv.nhook ) { ++ fn = __flexiblas_hooks->stbmv.f77_hook_function[hook_pos_stbmv]; ++ } else { ++ hook_pos_stbmv = 0; ++ fn = current_backend->blas.stbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_stbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_stbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_stbsv = 0; ++ + void FC_GLOBAL(stbsv,STBSV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, float* a, blasint* lda, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -3009,6 +6611,40 @@ + + + ++void flexiblas_real_stbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.stbsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_stbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_stbsv_"))); ++ ++ ++void flexiblas_chain_stbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_stbsv++; ++ if ( hook_pos_stbsv < __flexiblas_hooks->stbsv.nhook ) { ++ fn = __flexiblas_hooks->stbsv.f77_hook_function[hook_pos_stbsv]; ++ } else { ++ hook_pos_stbsv = 0; ++ fn = current_backend->blas.stbsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_stbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_stbsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_stpmv = 0; ++ + void FC_GLOBAL(stpmv,STPMV)(char* uplo, char* trans, char* diag, blasint* n, float* ap, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -3035,6 +6671,40 @@ + + + ++void flexiblas_real_stpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.stpmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_stpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_stpmv_"))); ++ ++ ++void flexiblas_chain_stpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_stpmv++; ++ if ( hook_pos_stpmv < __flexiblas_hooks->stpmv.nhook ) { ++ fn = __flexiblas_hooks->stpmv.f77_hook_function[hook_pos_stpmv]; ++ } else { ++ hook_pos_stpmv = 0; ++ fn = current_backend->blas.stpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_stpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_stpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_stpsv = 0; ++ + void FC_GLOBAL(stpsv,STPSV)(char* uplo, char* trans, char* diag, blasint* n, float* ap, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -3061,6 +6731,40 @@ + + + ++void flexiblas_real_stpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.stpsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_stpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_stpsv_"))); ++ ++ ++void flexiblas_chain_stpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_stpsv++; ++ if ( hook_pos_stpsv < __flexiblas_hooks->stpsv.nhook ) { ++ fn = __flexiblas_hooks->stpsv.f77_hook_function[hook_pos_stpsv]; ++ } else { ++ hook_pos_stpsv = 0; ++ fn = current_backend->blas.stpsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_stpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_stpsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_strmm = 0; ++ + void FC_GLOBAL(strmm,STRMM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, float* alpha, float* a, blasint* lda, float* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -3087,6 +6791,40 @@ + + + ++void flexiblas_real_strmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.strmm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_strmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_strmm_"))); ++ ++ ++void flexiblas_chain_strmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_strmm++; ++ if ( hook_pos_strmm < __flexiblas_hooks->strmm.nhook ) { ++ fn = __flexiblas_hooks->strmm.f77_hook_function[hook_pos_strmm]; ++ } else { ++ hook_pos_strmm = 0; ++ fn = current_backend->blas.strmm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_strmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_strmm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_strmv = 0; ++ + void FC_GLOBAL(strmv,STRMV)(char* uplo, char* trans, char* diag, blasint* n, float* a, blasint* lda, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -3113,6 +6851,40 @@ + + + ++void flexiblas_real_strmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.strmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_strmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_strmv_"))); ++ ++ ++void flexiblas_chain_strmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_strmv++; ++ if ( hook_pos_strmv < __flexiblas_hooks->strmv.nhook ) { ++ fn = __flexiblas_hooks->strmv.f77_hook_function[hook_pos_strmv]; ++ } else { ++ hook_pos_strmv = 0; ++ fn = current_backend->blas.strmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_strmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_strmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_strsm = 0; ++ + void FC_GLOBAL(strsm,STRSM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, float* alpha, float* a, blasint* lda, float* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -3139,6 +6911,40 @@ + + + ++void flexiblas_real_strsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.strsm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_strsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_strsm_"))); ++ ++ ++void flexiblas_chain_strsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_strsm++; ++ if ( hook_pos_strsm < __flexiblas_hooks->strsm.nhook ) { ++ fn = __flexiblas_hooks->strsm.f77_hook_function[hook_pos_strsm]; ++ } else { ++ hook_pos_strsm = 0; ++ fn = current_backend->blas.strsm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_strsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_strsm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_strsv = 0; ++ + void FC_GLOBAL(strsv,STRSV)(char* uplo, char* trans, char* diag, blasint* n, float* a, blasint* lda, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -3165,6 +6971,40 @@ + + + ++void flexiblas_real_strsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.strsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_strsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_strsv_"))); ++ ++ ++void flexiblas_chain_strsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_strsv++; ++ if ( hook_pos_strsv < __flexiblas_hooks->strsv.nhook ) { ++ fn = __flexiblas_hooks->strsv.f77_hook_function[hook_pos_strsv]; ++ } else { ++ hook_pos_strsv = 0; ++ fn = current_backend->blas.strsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_strsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_strsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zaxpy = 0; ++ + void FC_GLOBAL(zaxpy,ZAXPY)(blasint* n, double complex* za, double complex* zx, blasint* incx, double complex* zy, blasint* incy) + { + void (*fn) (void* n, void* za, void* zx, void* incx, void* zy, void* incy); +@@ -3191,6 +7031,40 @@ + + + ++void flexiblas_real_zaxpy_(void* n, void* za, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx, void* zy, void* incy); ++ ++ fn = current_backend->blas.zaxpy.f77_blas_function; ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zaxpy(void* n, void* za, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_real_zaxpy_"))); ++ ++ ++void flexiblas_chain_zaxpy_(void* n, void* za, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx, void* zy, void* incy); ++ ++ ++ ++ hook_pos_zaxpy++; ++ if ( hook_pos_zaxpy < __flexiblas_hooks->zaxpy.nhook ) { ++ fn = __flexiblas_hooks->zaxpy.f77_hook_function[hook_pos_zaxpy]; ++ } else { ++ hook_pos_zaxpy = 0; ++ fn = current_backend->blas.zaxpy.f77_blas_function; ++ } ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zaxpy(void* n, void* za, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zaxpy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zcopy = 0; ++ + void FC_GLOBAL(zcopy,ZCOPY)(blasint* n, double complex* zx, blasint* incx, double complex* zy, blasint* incy) + { + void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); +@@ -3217,6 +7091,40 @@ + + + ++void flexiblas_real_zcopy_(void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ ++ fn = current_backend->blas.zcopy.f77_blas_function; ++ fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zcopy(void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_real_zcopy_"))); ++ ++ ++void flexiblas_chain_zcopy_(void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ ++ ++ ++ hook_pos_zcopy++; ++ if ( hook_pos_zcopy < __flexiblas_hooks->zcopy.nhook ) { ++ fn = __flexiblas_hooks->zcopy.f77_hook_function[hook_pos_zcopy]; ++ } else { ++ hook_pos_zcopy = 0; ++ fn = current_backend->blas.zcopy.f77_blas_function; ++ } ++ fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zcopy(void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zdotc = 0; ++ + void FC_GLOBAL(zdotc,ZDOTC)( double complex* returnvalue, blasint* n, double complex* zx, blasint* incx, double complex* zy, blasint* incy) + { + double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); +@@ -3257,6 +7165,56 @@ + + + ++void flexiblas_real_zdotc_( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ void (*fn_intel) (double complex *ret, void* n, void* zx, void* incx, void* zy, void* incy); ++ double complex ret; ++ ++ fn = current_backend->blas.zdotc.f77_blas_function; fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } ++ ++ *((double complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_real_zdotc( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_real_zdotc_"))); ++ ++ ++void flexiblas_chain_zdotc_( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ void (*fn_intel) (double complex *ret, void* n, void* zx, void* incx, void* zy, void* incy); ++ double complex ret; ++ ++ ++ ++ hook_pos_zdotc++; ++ if ( hook_pos_zdotc < __flexiblas_hooks->zdotc.nhook ) { ++ fn = __flexiblas_hooks->zdotc.f77_hook_function[hook_pos_zdotc]; ++ } else { ++ hook_pos_zdotc = 0; ++ fn = current_backend->blas.zdotc.f77_blas_function; ++ } fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } ++ ++ *((double complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_chain_zdotc( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zdotc_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zdotu = 0; ++ + void FC_GLOBAL(zdotu,ZDOTU)( double complex* returnvalue, blasint* n, double complex* zx, blasint* incx, double complex* zy, blasint* incy) + { + double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); +@@ -3297,6 +7255,56 @@ + + + ++void flexiblas_real_zdotu_( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ void (*fn_intel) (double complex *ret, void* n, void* zx, void* incx, void* zy, void* incy); ++ double complex ret; ++ ++ fn = current_backend->blas.zdotu.f77_blas_function; fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } ++ ++ *((double complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_real_zdotu( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_real_zdotu_"))); ++ ++ ++void flexiblas_chain_zdotu_( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ void (*fn_intel) (double complex *ret, void* n, void* zx, void* incx, void* zy, void* incy); ++ double complex ret; ++ ++ ++ ++ hook_pos_zdotu++; ++ if ( hook_pos_zdotu < __flexiblas_hooks->zdotu.nhook ) { ++ fn = __flexiblas_hooks->zdotu.f77_hook_function[hook_pos_zdotu]; ++ } else { ++ hook_pos_zdotu = 0; ++ fn = current_backend->blas.zdotu.f77_blas_function; ++ } fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } ++ ++ *((double complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_chain_zdotu( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zdotu_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zdrot = 0; ++ + void FC_GLOBAL(zdrot,ZDROT)(blasint* n, double complex* cx, blasint* incx, double complex* cy, blasint* incy, double* c, double* s) + { + void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); +@@ -3323,6 +7331,40 @@ + + + ++void flexiblas_real_zdrot_(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); ++ ++ fn = current_backend->blas.zdrot.f77_blas_function; ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_zdrot(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_real_zdrot_"))); ++ ++ ++void flexiblas_chain_zdrot_(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); ++ ++ ++ ++ hook_pos_zdrot++; ++ if ( hook_pos_zdrot < __flexiblas_hooks->zdrot.nhook ) { ++ fn = __flexiblas_hooks->zdrot.f77_hook_function[hook_pos_zdrot]; ++ } else { ++ hook_pos_zdrot = 0; ++ fn = current_backend->blas.zdrot.f77_blas_function; ++ } ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_zdrot(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_chain_zdrot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zdscal = 0; ++ + void FC_GLOBAL(zdscal,ZDSCAL)(blasint* n, double* da, double complex* zx, blasint* incx) + { + void (*fn) (void* n, void* da, void* zx, void* incx); +@@ -3349,6 +7391,40 @@ + + + ++void flexiblas_real_zdscal_(void* n, void* da, void* zx, void* incx) ++{ ++ void (*fn) (void* n, void* da, void* zx, void* incx); ++ ++ fn = current_backend->blas.zdscal.f77_blas_function; ++ fn((void*) n, (void*) da, (void*) zx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_zdscal(void* n, void* da, void* zx, void* incx) __attribute__((alias("flexiblas_real_zdscal_"))); ++ ++ ++void flexiblas_chain_zdscal_(void* n, void* da, void* zx, void* incx) ++{ ++ void (*fn) (void* n, void* da, void* zx, void* incx); ++ ++ ++ ++ hook_pos_zdscal++; ++ if ( hook_pos_zdscal < __flexiblas_hooks->zdscal.nhook ) { ++ fn = __flexiblas_hooks->zdscal.f77_hook_function[hook_pos_zdscal]; ++ } else { ++ hook_pos_zdscal = 0; ++ fn = current_backend->blas.zdscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) da, (void*) zx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_zdscal(void* n, void* da, void* zx, void* incx) __attribute__((alias("flexiblas_chain_zdscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgbmv = 0; ++ + void FC_GLOBAL(zgbmv,ZGBMV)(char* trans, blasint* m, blasint* n, blasint* kl, blasint* ku, double complex* alpha, double complex* a, blasint* lda, double complex* x, blasint* incx, double complex* beta, double complex* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -3375,6 +7451,40 @@ + + + ++void flexiblas_real_zgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.zgbmv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_zgbmv_"))); ++ ++ ++void flexiblas_chain_zgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_zgbmv++; ++ if ( hook_pos_zgbmv < __flexiblas_hooks->zgbmv.nhook ) { ++ fn = __flexiblas_hooks->zgbmv.f77_hook_function[hook_pos_zgbmv]; ++ } else { ++ hook_pos_zgbmv = 0; ++ fn = current_backend->blas.zgbmv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_zgbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgemm = 0; ++ + void FC_GLOBAL(zgemm,ZGEMM)(char* transa, char* transb, blasint* m, blasint* n, blasint* k, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb, double complex* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -3401,6 +7511,40 @@ + + + ++void flexiblas_real_zgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zgemm.f77_blas_function; ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zgemm_"))); ++ ++ ++void flexiblas_chain_zgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zgemm++; ++ if ( hook_pos_zgemm < __flexiblas_hooks->zgemm.nhook ) { ++ fn = __flexiblas_hooks->zgemm.f77_hook_function[hook_pos_zgemm]; ++ } else { ++ hook_pos_zgemm = 0; ++ fn = current_backend->blas.zgemm.f77_blas_function; ++ } ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zgemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgemv = 0; ++ + void FC_GLOBAL(zgemv,ZGEMV)(char* trans, blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* x, blasint* incx, double complex* beta, double complex* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -3427,6 +7571,40 @@ + + + ++void flexiblas_real_zgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.zgemv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_zgemv_"))); ++ ++ ++void flexiblas_chain_zgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_zgemv++; ++ if ( hook_pos_zgemv < __flexiblas_hooks->zgemv.nhook ) { ++ fn = __flexiblas_hooks->zgemv.f77_hook_function[hook_pos_zgemv]; ++ } else { ++ hook_pos_zgemv = 0; ++ fn = current_backend->blas.zgemv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_zgemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgerc = 0; ++ + void FC_GLOBAL(zgerc,ZGERC)(blasint* m, blasint* n, double complex* alpha, double complex* x, blasint* incx, double complex* y, blasint* incy, double complex* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -3453,6 +7631,40 @@ + + + ++void flexiblas_real_zgerc_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.zgerc.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_zgerc(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_zgerc_"))); ++ ++ ++void flexiblas_chain_zgerc_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_zgerc++; ++ if ( hook_pos_zgerc < __flexiblas_hooks->zgerc.nhook ) { ++ fn = __flexiblas_hooks->zgerc.f77_hook_function[hook_pos_zgerc]; ++ } else { ++ hook_pos_zgerc = 0; ++ fn = current_backend->blas.zgerc.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_zgerc(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_zgerc_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgeru = 0; ++ + void FC_GLOBAL(zgeru,ZGERU)(blasint* m, blasint* n, double complex* alpha, double complex* x, blasint* incx, double complex* y, blasint* incy, double complex* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -3479,6 +7691,40 @@ + + + ++void flexiblas_real_zgeru_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.zgeru.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_zgeru(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_zgeru_"))); ++ ++ ++void flexiblas_chain_zgeru_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_zgeru++; ++ if ( hook_pos_zgeru < __flexiblas_hooks->zgeru.nhook ) { ++ fn = __flexiblas_hooks->zgeru.f77_hook_function[hook_pos_zgeru]; ++ } else { ++ hook_pos_zgeru = 0; ++ fn = current_backend->blas.zgeru.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_zgeru(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_zgeru_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhbmv = 0; ++ + void FC_GLOBAL(zhbmv,ZHBMV)(char* uplo, blasint* n, blasint* k, double complex* alpha, double complex* a, blasint* lda, double complex* x, blasint* incx, double complex* beta, double complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -3505,6 +7751,40 @@ + + + ++void flexiblas_real_zhbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.zhbmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zhbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_zhbmv_"))); ++ ++ ++void flexiblas_chain_zhbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_zhbmv++; ++ if ( hook_pos_zhbmv < __flexiblas_hooks->zhbmv.nhook ) { ++ fn = __flexiblas_hooks->zhbmv.f77_hook_function[hook_pos_zhbmv]; ++ } else { ++ hook_pos_zhbmv = 0; ++ fn = current_backend->blas.zhbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zhbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_zhbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhemm = 0; ++ + void FC_GLOBAL(zhemm,ZHEMM)(char* side, char* uplo, blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb, double complex* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -3531,6 +7811,40 @@ + + + ++void flexiblas_real_zhemm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zhemm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zhemm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zhemm_"))); ++ ++ ++void flexiblas_chain_zhemm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zhemm++; ++ if ( hook_pos_zhemm < __flexiblas_hooks->zhemm.nhook ) { ++ fn = __flexiblas_hooks->zhemm.f77_hook_function[hook_pos_zhemm]; ++ } else { ++ hook_pos_zhemm = 0; ++ fn = current_backend->blas.zhemm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zhemm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zhemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhemv = 0; ++ + void FC_GLOBAL(zhemv,ZHEMV)(char* uplo, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* x, blasint* incx, double complex* beta, double complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -3557,6 +7871,40 @@ + + + ++void flexiblas_real_zhemv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.zhemv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zhemv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_zhemv_"))); ++ ++ ++void flexiblas_chain_zhemv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_zhemv++; ++ if ( hook_pos_zhemv < __flexiblas_hooks->zhemv.nhook ) { ++ fn = __flexiblas_hooks->zhemv.f77_hook_function[hook_pos_zhemv]; ++ } else { ++ hook_pos_zhemv = 0; ++ fn = current_backend->blas.zhemv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zhemv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_zhemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zher = 0; ++ + void FC_GLOBAL(zher,ZHER)(char* uplo, blasint* n, double* alpha, double complex* x, blasint* incx, double complex* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); +@@ -3583,6 +7931,40 @@ + + + ++void flexiblas_real_zher_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ fn = current_backend->blas.zher.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_zher(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_real_zher_"))); ++ ++ ++void flexiblas_chain_zher_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ ++ ++ hook_pos_zher++; ++ if ( hook_pos_zher < __flexiblas_hooks->zher.nhook ) { ++ fn = __flexiblas_hooks->zher.f77_hook_function[hook_pos_zher]; ++ } else { ++ hook_pos_zher = 0; ++ fn = current_backend->blas.zher.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_zher(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_chain_zher_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zher2 = 0; ++ + void FC_GLOBAL(zher2,ZHER2)(char* uplo, blasint* n, double complex* alpha, double complex* x, blasint* incx, double complex* y, blasint* incy, double complex* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -3609,6 +7991,40 @@ + + + ++void flexiblas_real_zher2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.zher2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_zher2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_zher2_"))); ++ ++ ++void flexiblas_chain_zher2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_zher2++; ++ if ( hook_pos_zher2 < __flexiblas_hooks->zher2.nhook ) { ++ fn = __flexiblas_hooks->zher2.f77_hook_function[hook_pos_zher2]; ++ } else { ++ hook_pos_zher2 = 0; ++ fn = current_backend->blas.zher2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_zher2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_zher2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zher2k = 0; ++ + void FC_GLOBAL(zher2k,ZHER2K)(char* uplo, char* trans, blasint* n, blasint* k, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb, double* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -3635,6 +8051,40 @@ + + + ++void flexiblas_real_zher2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zher2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zher2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zher2k_"))); ++ ++ ++void flexiblas_chain_zher2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zher2k++; ++ if ( hook_pos_zher2k < __flexiblas_hooks->zher2k.nhook ) { ++ fn = __flexiblas_hooks->zher2k.f77_hook_function[hook_pos_zher2k]; ++ } else { ++ hook_pos_zher2k = 0; ++ fn = current_backend->blas.zher2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zher2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zher2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zherk = 0; ++ + void FC_GLOBAL(zherk,ZHERK)(char* uplo, char* trans, blasint* n, blasint* k, double* alpha, double complex* a, blasint* lda, double* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -3661,6 +8111,40 @@ + + + ++void flexiblas_real_zherk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zherk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zherk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zherk_"))); ++ ++ ++void flexiblas_chain_zherk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zherk++; ++ if ( hook_pos_zherk < __flexiblas_hooks->zherk.nhook ) { ++ fn = __flexiblas_hooks->zherk.f77_hook_function[hook_pos_zherk]; ++ } else { ++ hook_pos_zherk = 0; ++ fn = current_backend->blas.zherk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zherk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zherk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhpmv = 0; ++ + void FC_GLOBAL(zhpmv,ZHPMV)(char* uplo, blasint* n, double complex* alpha, double complex* ap, double complex* x, blasint* incx, double complex* beta, double complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); +@@ -3687,6 +8171,40 @@ + + + ++void flexiblas_real_zhpmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.zhpmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zhpmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_zhpmv_"))); ++ ++ ++void flexiblas_chain_zhpmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_zhpmv++; ++ if ( hook_pos_zhpmv < __flexiblas_hooks->zhpmv.nhook ) { ++ fn = __flexiblas_hooks->zhpmv.f77_hook_function[hook_pos_zhpmv]; ++ } else { ++ hook_pos_zhpmv = 0; ++ fn = current_backend->blas.zhpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zhpmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_zhpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhpr = 0; ++ + void FC_GLOBAL(zhpr,ZHPR)(char* uplo, blasint* n, double* alpha, double complex* x, blasint* incx, double complex* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); +@@ -3713,6 +8231,40 @@ + + + ++void flexiblas_real_zhpr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ fn = current_backend->blas.zhpr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_zhpr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_real_zhpr_"))); ++ ++ ++void flexiblas_chain_zhpr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ ++ ++ hook_pos_zhpr++; ++ if ( hook_pos_zhpr < __flexiblas_hooks->zhpr.nhook ) { ++ fn = __flexiblas_hooks->zhpr.f77_hook_function[hook_pos_zhpr]; ++ } else { ++ hook_pos_zhpr = 0; ++ fn = current_backend->blas.zhpr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_zhpr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_chain_zhpr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhpr2 = 0; ++ + void FC_GLOBAL(zhpr2,ZHPR2)(char* uplo, blasint* n, double complex* alpha, double complex* x, blasint* incx, double complex* y, blasint* incy, double complex* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); +@@ -3739,6 +8291,40 @@ + + + ++void flexiblas_real_zhpr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ fn = current_backend->blas.zhpr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_zhpr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_real_zhpr2_"))); ++ ++ ++void flexiblas_chain_zhpr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ ++ ++ hook_pos_zhpr2++; ++ if ( hook_pos_zhpr2 < __flexiblas_hooks->zhpr2.nhook ) { ++ fn = __flexiblas_hooks->zhpr2.f77_hook_function[hook_pos_zhpr2]; ++ } else { ++ hook_pos_zhpr2 = 0; ++ fn = current_backend->blas.zhpr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_zhpr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_chain_zhpr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zrotg = 0; ++ + void FC_GLOBAL(zrotg,ZROTG)(double complex* ca, double complex* cb, double* c, double complex* s) + { + void (*fn) (void* ca, void* cb, void* c, void* s); +@@ -3765,6 +8351,40 @@ + + + ++void flexiblas_real_zrotg_(void* ca, void* cb, void* c, void* s) ++{ ++ void (*fn) (void* ca, void* cb, void* c, void* s); ++ ++ fn = current_backend->blas.zrotg.f77_blas_function; ++ fn((void*) ca, (void*) cb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_zrotg(void* ca, void* cb, void* c, void* s) __attribute__((alias("flexiblas_real_zrotg_"))); ++ ++ ++void flexiblas_chain_zrotg_(void* ca, void* cb, void* c, void* s) ++{ ++ void (*fn) (void* ca, void* cb, void* c, void* s); ++ ++ ++ ++ hook_pos_zrotg++; ++ if ( hook_pos_zrotg < __flexiblas_hooks->zrotg.nhook ) { ++ fn = __flexiblas_hooks->zrotg.f77_hook_function[hook_pos_zrotg]; ++ } else { ++ hook_pos_zrotg = 0; ++ fn = current_backend->blas.zrotg.f77_blas_function; ++ } ++ fn((void*) ca, (void*) cb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_zrotg(void* ca, void* cb, void* c, void* s) __attribute__((alias("flexiblas_chain_zrotg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zscal = 0; ++ + void FC_GLOBAL(zscal,ZSCAL)(blasint* n, double complex* za, double complex* zx, blasint* incx) + { + void (*fn) (void* n, void* za, void* zx, void* incx); +@@ -3791,6 +8411,40 @@ + + + ++void flexiblas_real_zscal_(void* n, void* za, void* zx, void* incx) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx); ++ ++ fn = current_backend->blas.zscal.f77_blas_function; ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_zscal(void* n, void* za, void* zx, void* incx) __attribute__((alias("flexiblas_real_zscal_"))); ++ ++ ++void flexiblas_chain_zscal_(void* n, void* za, void* zx, void* incx) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx); ++ ++ ++ ++ hook_pos_zscal++; ++ if ( hook_pos_zscal < __flexiblas_hooks->zscal.nhook ) { ++ fn = __flexiblas_hooks->zscal.f77_hook_function[hook_pos_zscal]; ++ } else { ++ hook_pos_zscal = 0; ++ fn = current_backend->blas.zscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_zscal(void* n, void* za, void* zx, void* incx) __attribute__((alias("flexiblas_chain_zscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zswap = 0; ++ + void FC_GLOBAL(zswap,ZSWAP)(blasint* n, double complex* zx, blasint* incx, double complex* zy, blasint* incy) + { + void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); +@@ -3817,6 +8471,40 @@ + + + ++void flexiblas_real_zswap_(void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ ++ fn = current_backend->blas.zswap.f77_blas_function; ++ fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zswap(void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_real_zswap_"))); ++ ++ ++void flexiblas_chain_zswap_(void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ ++ ++ ++ hook_pos_zswap++; ++ if ( hook_pos_zswap < __flexiblas_hooks->zswap.nhook ) { ++ fn = __flexiblas_hooks->zswap.f77_hook_function[hook_pos_zswap]; ++ } else { ++ hook_pos_zswap = 0; ++ fn = current_backend->blas.zswap.f77_blas_function; ++ } ++ fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zswap(void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zswap_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zsymm = 0; ++ + void FC_GLOBAL(zsymm,ZSYMM)(char* side, char* uplo, blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb, double complex* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -3843,6 +8531,40 @@ + + + ++void flexiblas_real_zsymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zsymm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zsymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zsymm_"))); ++ ++ ++void flexiblas_chain_zsymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zsymm++; ++ if ( hook_pos_zsymm < __flexiblas_hooks->zsymm.nhook ) { ++ fn = __flexiblas_hooks->zsymm.f77_hook_function[hook_pos_zsymm]; ++ } else { ++ hook_pos_zsymm = 0; ++ fn = current_backend->blas.zsymm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zsymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zsymm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zsyr2k = 0; ++ + void FC_GLOBAL(zsyr2k,ZSYR2K)(char* uplo, char* trans, blasint* n, blasint* k, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb, double complex* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -3869,6 +8591,40 @@ + + + ++void flexiblas_real_zsyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zsyr2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zsyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zsyr2k_"))); ++ ++ ++void flexiblas_chain_zsyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zsyr2k++; ++ if ( hook_pos_zsyr2k < __flexiblas_hooks->zsyr2k.nhook ) { ++ fn = __flexiblas_hooks->zsyr2k.f77_hook_function[hook_pos_zsyr2k]; ++ } else { ++ hook_pos_zsyr2k = 0; ++ fn = current_backend->blas.zsyr2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zsyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zsyr2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zsyrk = 0; ++ + void FC_GLOBAL(zsyrk,ZSYRK)(char* uplo, char* trans, blasint* n, blasint* k, double complex* alpha, double complex* a, blasint* lda, double complex* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -3895,6 +8651,40 @@ + + + ++void flexiblas_real_zsyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zsyrk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zsyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zsyrk_"))); ++ ++ ++void flexiblas_chain_zsyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zsyrk++; ++ if ( hook_pos_zsyrk < __flexiblas_hooks->zsyrk.nhook ) { ++ fn = __flexiblas_hooks->zsyrk.f77_hook_function[hook_pos_zsyrk]; ++ } else { ++ hook_pos_zsyrk = 0; ++ fn = current_backend->blas.zsyrk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zsyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zsyrk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztbmv = 0; ++ + void FC_GLOBAL(ztbmv,ZTBMV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, double complex* a, blasint* lda, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -3921,6 +8711,40 @@ + + + ++void flexiblas_real_ztbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ztbmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ztbmv_"))); ++ ++ ++void flexiblas_chain_ztbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztbmv++; ++ if ( hook_pos_ztbmv < __flexiblas_hooks->ztbmv.nhook ) { ++ fn = __flexiblas_hooks->ztbmv.f77_hook_function[hook_pos_ztbmv]; ++ } else { ++ hook_pos_ztbmv = 0; ++ fn = current_backend->blas.ztbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztbsv = 0; ++ + void FC_GLOBAL(ztbsv,ZTBSV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, double complex* a, blasint* lda, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -3947,6 +8771,40 @@ + + + ++void flexiblas_real_ztbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ztbsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ztbsv_"))); ++ ++ ++void flexiblas_chain_ztbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztbsv++; ++ if ( hook_pos_ztbsv < __flexiblas_hooks->ztbsv.nhook ) { ++ fn = __flexiblas_hooks->ztbsv.f77_hook_function[hook_pos_ztbsv]; ++ } else { ++ hook_pos_ztbsv = 0; ++ fn = current_backend->blas.ztbsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztbsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztpmv = 0; ++ + void FC_GLOBAL(ztpmv,ZTPMV)(char* uplo, char* trans, char* diag, blasint* n, double complex* ap, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -3973,6 +8831,40 @@ + + + ++void flexiblas_real_ztpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.ztpmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_ztpmv_"))); ++ ++ ++void flexiblas_chain_ztpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztpmv++; ++ if ( hook_pos_ztpmv < __flexiblas_hooks->ztpmv.nhook ) { ++ fn = __flexiblas_hooks->ztpmv.f77_hook_function[hook_pos_ztpmv]; ++ } else { ++ hook_pos_ztpmv = 0; ++ fn = current_backend->blas.ztpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztpsv = 0; ++ + void FC_GLOBAL(ztpsv,ZTPSV)(char* uplo, char* trans, char* diag, blasint* n, double complex* ap, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -3999,6 +8891,40 @@ + + + ++void flexiblas_real_ztpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.ztpsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_ztpsv_"))); ++ ++ ++void flexiblas_chain_ztpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztpsv++; ++ if ( hook_pos_ztpsv < __flexiblas_hooks->ztpsv.nhook ) { ++ fn = __flexiblas_hooks->ztpsv.f77_hook_function[hook_pos_ztpsv]; ++ } else { ++ hook_pos_ztpsv = 0; ++ fn = current_backend->blas.ztpsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztpsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztrmm = 0; ++ + void FC_GLOBAL(ztrmm,ZTRMM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4025,6 +8951,40 @@ + + + ++void flexiblas_real_ztrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.ztrmm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_ztrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_ztrmm_"))); ++ ++ ++void flexiblas_chain_ztrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_ztrmm++; ++ if ( hook_pos_ztrmm < __flexiblas_hooks->ztrmm.nhook ) { ++ fn = __flexiblas_hooks->ztrmm.f77_hook_function[hook_pos_ztrmm]; ++ } else { ++ hook_pos_ztrmm = 0; ++ fn = current_backend->blas.ztrmm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_ztrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_ztrmm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztrmv = 0; ++ + void FC_GLOBAL(ztrmv,ZTRMV)(char* uplo, char* trans, char* diag, blasint* n, double complex* a, blasint* lda, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -4051,6 +9011,40 @@ + + + ++void flexiblas_real_ztrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ztrmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ztrmv_"))); ++ ++ ++void flexiblas_chain_ztrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztrmv++; ++ if ( hook_pos_ztrmv < __flexiblas_hooks->ztrmv.nhook ) { ++ fn = __flexiblas_hooks->ztrmv.f77_hook_function[hook_pos_ztrmv]; ++ } else { ++ hook_pos_ztrmv = 0; ++ fn = current_backend->blas.ztrmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztrmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztrsm = 0; ++ + void FC_GLOBAL(ztrsm,ZTRSM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4077,6 +9071,40 @@ + + + ++void flexiblas_real_ztrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.ztrsm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_ztrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_ztrsm_"))); ++ ++ ++void flexiblas_chain_ztrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_ztrsm++; ++ if ( hook_pos_ztrsm < __flexiblas_hooks->ztrsm.nhook ) { ++ fn = __flexiblas_hooks->ztrsm.f77_hook_function[hook_pos_ztrsm]; ++ } else { ++ hook_pos_ztrsm = 0; ++ fn = current_backend->blas.ztrsm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_ztrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_ztrsm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztrsv = 0; ++ + void FC_GLOBAL(ztrsv,ZTRSV)(char* uplo, char* trans, char* diag, blasint* n, double complex* a, blasint* lda, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -4103,6 +9131,40 @@ + + + ++void flexiblas_real_ztrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ztrsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ztrsv_"))); ++ ++ ++void flexiblas_chain_ztrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztrsv++; ++ if ( hook_pos_ztrsv < __flexiblas_hooks->ztrsv.nhook ) { ++ fn = __flexiblas_hooks->ztrsv.f77_hook_function[hook_pos_ztrsv]; ++ } else { ++ hook_pos_ztrsv = 0; ++ fn = current_backend->blas.ztrsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztrsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_caxpby = 0; ++ + void FC_GLOBAL(caxpby,CAXPBY)(blasint* n, float complex* ca, float complex* cx, blasint* incx, float complex* cb, float complex* cy, blasint* incy) + { + void (*fn) (void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy); +@@ -4129,6 +9191,40 @@ + + + ++void flexiblas_real_caxpby_(void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy); ++ ++ fn = current_backend->blas.caxpby.f77_blas_function; ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx, (void*) cb, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_caxpby(void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy) __attribute__((alias("flexiblas_real_caxpby_"))); ++ ++ ++void flexiblas_chain_caxpby_(void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy); ++ ++ ++ ++ hook_pos_caxpby++; ++ if ( hook_pos_caxpby < __flexiblas_hooks->caxpby.nhook ) { ++ fn = __flexiblas_hooks->caxpby.f77_hook_function[hook_pos_caxpby]; ++ } else { ++ hook_pos_caxpby = 0; ++ fn = current_backend->blas.caxpby.f77_blas_function; ++ } ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx, (void*) cb, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_caxpby(void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy) __attribute__((alias("flexiblas_chain_caxpby_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_daxpby = 0; ++ + void FC_GLOBAL(daxpby,DAXPBY)(blasint* n, double* da, double* dx, blasint* incx, double* db, double* dy, blasint* incy) + { + void (*fn) (void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy); +@@ -4155,6 +9251,40 @@ + + + ++void flexiblas_real_daxpby_(void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy); ++ ++ fn = current_backend->blas.daxpby.f77_blas_function; ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx, (void*) db, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_daxpby(void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy) __attribute__((alias("flexiblas_real_daxpby_"))); ++ ++ ++void flexiblas_chain_daxpby_(void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy); ++ ++ ++ ++ hook_pos_daxpby++; ++ if ( hook_pos_daxpby < __flexiblas_hooks->daxpby.nhook ) { ++ fn = __flexiblas_hooks->daxpby.f77_hook_function[hook_pos_daxpby]; ++ } else { ++ hook_pos_daxpby = 0; ++ fn = current_backend->blas.daxpby.f77_blas_function; ++ } ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx, (void*) db, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_daxpby(void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy) __attribute__((alias("flexiblas_chain_daxpby_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zaxpby = 0; ++ + void FC_GLOBAL(zaxpby,ZAXPBY)(blasint* n, double complex* za, double complex* zx, blasint* incx, double complex* zb, double complex* zy, blasint* incy) + { + void (*fn) (void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy); +@@ -4181,6 +9311,40 @@ + + + ++void flexiblas_real_zaxpby_(void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy); ++ ++ fn = current_backend->blas.zaxpby.f77_blas_function; ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx, (void*) zb, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zaxpby(void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy) __attribute__((alias("flexiblas_real_zaxpby_"))); ++ ++ ++void flexiblas_chain_zaxpby_(void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy); ++ ++ ++ ++ hook_pos_zaxpby++; ++ if ( hook_pos_zaxpby < __flexiblas_hooks->zaxpby.nhook ) { ++ fn = __flexiblas_hooks->zaxpby.f77_hook_function[hook_pos_zaxpby]; ++ } else { ++ hook_pos_zaxpby = 0; ++ fn = current_backend->blas.zaxpby.f77_blas_function; ++ } ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx, (void*) zb, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zaxpby(void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zaxpby_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_saxpby = 0; ++ + void FC_GLOBAL(saxpby,SAXPBY)(blasint* n, float* sa, float* sx, blasint* incx, float* sb, float* sy, blasint* incy) + { + void (*fn) (void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy); +@@ -4207,6 +9371,40 @@ + + + ++void flexiblas_real_saxpby_(void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy); ++ ++ fn = current_backend->blas.saxpby.f77_blas_function; ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx, (void*) sb, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_saxpby(void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy) __attribute__((alias("flexiblas_real_saxpby_"))); ++ ++ ++void flexiblas_chain_saxpby_(void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy); ++ ++ ++ ++ hook_pos_saxpby++; ++ if ( hook_pos_saxpby < __flexiblas_hooks->saxpby.nhook ) { ++ fn = __flexiblas_hooks->saxpby.f77_hook_function[hook_pos_saxpby]; ++ } else { ++ hook_pos_saxpby = 0; ++ fn = current_backend->blas.saxpby.f77_blas_function; ++ } ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx, (void*) sb, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_saxpby(void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy) __attribute__((alias("flexiblas_chain_saxpby_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_comatcopy = 0; ++ + void FC_GLOBAL(comatcopy,COMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4233,6 +9431,40 @@ + + + ++void flexiblas_real_comatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.comatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_comatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_comatcopy_"))); ++ ++ ++void flexiblas_chain_comatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_comatcopy++; ++ if ( hook_pos_comatcopy < __flexiblas_hooks->comatcopy.nhook ) { ++ fn = __flexiblas_hooks->comatcopy.f77_hook_function[hook_pos_comatcopy]; ++ } else { ++ hook_pos_comatcopy = 0; ++ fn = current_backend->blas.comatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_comatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_comatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zomatcopy = 0; ++ + void FC_GLOBAL(zomatcopy,ZOMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4259,6 +9491,40 @@ + + + ++void flexiblas_real_zomatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.zomatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_zomatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_zomatcopy_"))); ++ ++ ++void flexiblas_chain_zomatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_zomatcopy++; ++ if ( hook_pos_zomatcopy < __flexiblas_hooks->zomatcopy.nhook ) { ++ fn = __flexiblas_hooks->zomatcopy.f77_hook_function[hook_pos_zomatcopy]; ++ } else { ++ hook_pos_zomatcopy = 0; ++ fn = current_backend->blas.zomatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_zomatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_zomatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_domatcopy = 0; ++ + void FC_GLOBAL(domatcopy,DOMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, double* alpha, double* a, blasint* lda, double* b, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4285,6 +9551,40 @@ + + + ++void flexiblas_real_domatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.domatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_domatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_domatcopy_"))); ++ ++ ++void flexiblas_chain_domatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_domatcopy++; ++ if ( hook_pos_domatcopy < __flexiblas_hooks->domatcopy.nhook ) { ++ fn = __flexiblas_hooks->domatcopy.f77_hook_function[hook_pos_domatcopy]; ++ } else { ++ hook_pos_domatcopy = 0; ++ fn = current_backend->blas.domatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_domatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_domatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_somatcopy = 0; ++ + void FC_GLOBAL(somatcopy,SOMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, float* alpha, float* a, blasint* lda, float* b, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4311,6 +9611,40 @@ + + + ++void flexiblas_real_somatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.somatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_somatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_somatcopy_"))); ++ ++ ++void flexiblas_chain_somatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_somatcopy++; ++ if ( hook_pos_somatcopy < __flexiblas_hooks->somatcopy.nhook ) { ++ fn = __flexiblas_hooks->somatcopy.f77_hook_function[hook_pos_somatcopy]; ++ } else { ++ hook_pos_somatcopy = 0; ++ fn = current_backend->blas.somatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_somatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_somatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cimatcopy = 0; ++ + void FC_GLOBAL(cimatcopy,CIMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, float complex* alpha, float complex* a, blasint* lda, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); +@@ -4337,6 +9671,40 @@ + + + ++void flexiblas_real_cimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ fn = current_backend->blas.cimatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_cimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_real_cimatcopy_"))); ++ ++ ++void flexiblas_chain_cimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ ++ ++ hook_pos_cimatcopy++; ++ if ( hook_pos_cimatcopy < __flexiblas_hooks->cimatcopy.nhook ) { ++ fn = __flexiblas_hooks->cimatcopy.f77_hook_function[hook_pos_cimatcopy]; ++ } else { ++ hook_pos_cimatcopy = 0; ++ fn = current_backend->blas.cimatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_cimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_chain_cimatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zimatcopy = 0; ++ + void FC_GLOBAL(zimatcopy,ZIMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, double complex* alpha, double complex* a, blasint* lda, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); +@@ -4363,6 +9731,40 @@ + + + ++void flexiblas_real_zimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ fn = current_backend->blas.zimatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_zimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_real_zimatcopy_"))); ++ ++ ++void flexiblas_chain_zimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ ++ ++ hook_pos_zimatcopy++; ++ if ( hook_pos_zimatcopy < __flexiblas_hooks->zimatcopy.nhook ) { ++ fn = __flexiblas_hooks->zimatcopy.f77_hook_function[hook_pos_zimatcopy]; ++ } else { ++ hook_pos_zimatcopy = 0; ++ fn = current_backend->blas.zimatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_zimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_chain_zimatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dimatcopy = 0; ++ + void FC_GLOBAL(dimatcopy,DIMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, double* alpha, double* a, blasint* lda, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); +@@ -4389,6 +9791,40 @@ + + + ++void flexiblas_real_dimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ fn = current_backend->blas.dimatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_dimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_real_dimatcopy_"))); ++ ++ ++void flexiblas_chain_dimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ ++ ++ hook_pos_dimatcopy++; ++ if ( hook_pos_dimatcopy < __flexiblas_hooks->dimatcopy.nhook ) { ++ fn = __flexiblas_hooks->dimatcopy.f77_hook_function[hook_pos_dimatcopy]; ++ } else { ++ hook_pos_dimatcopy = 0; ++ fn = current_backend->blas.dimatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_dimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_chain_dimatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_simatcopy = 0; ++ + void FC_GLOBAL(simatcopy,SIMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, float* alpha, float* a, blasint* lda, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); +@@ -4415,6 +9851,40 @@ + + + ++void flexiblas_real_simatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ fn = current_backend->blas.simatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_simatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_real_simatcopy_"))); ++ ++ ++void flexiblas_chain_simatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ ++ ++ hook_pos_simatcopy++; ++ if ( hook_pos_simatcopy < __flexiblas_hooks->simatcopy.nhook ) { ++ fn = __flexiblas_hooks->simatcopy.f77_hook_function[hook_pos_simatcopy]; ++ } else { ++ hook_pos_simatcopy = 0; ++ fn = current_backend->blas.simatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_simatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_chain_simatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sgeadd = 0; ++ + void FC_GLOBAL(sgeadd,SGEADD)(blasint* m, blasint* n, float* alpha, float* a, blasint* lda, float* beta, float* b, blasint* ldb) + { + void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); +@@ -4441,6 +9911,40 @@ + + + ++void flexiblas_real_sgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ fn = current_backend->blas.sgeadd.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_sgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_real_sgeadd_"))); ++ ++ ++void flexiblas_chain_sgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ ++ ++ hook_pos_sgeadd++; ++ if ( hook_pos_sgeadd < __flexiblas_hooks->sgeadd.nhook ) { ++ fn = __flexiblas_hooks->sgeadd.f77_hook_function[hook_pos_sgeadd]; ++ } else { ++ hook_pos_sgeadd = 0; ++ fn = current_backend->blas.sgeadd.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_sgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_chain_sgeadd_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dgeadd = 0; ++ + void FC_GLOBAL(dgeadd,DGEADD)(blasint* m, blasint* n, double* alpha, double* a, blasint* lda, double* beta, double* b, blasint* ldb) + { + void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); +@@ -4467,6 +9971,40 @@ + + + ++void flexiblas_real_dgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ fn = current_backend->blas.dgeadd.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_dgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_real_dgeadd_"))); ++ ++ ++void flexiblas_chain_dgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ ++ ++ hook_pos_dgeadd++; ++ if ( hook_pos_dgeadd < __flexiblas_hooks->dgeadd.nhook ) { ++ fn = __flexiblas_hooks->dgeadd.f77_hook_function[hook_pos_dgeadd]; ++ } else { ++ hook_pos_dgeadd = 0; ++ fn = current_backend->blas.dgeadd.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_dgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_chain_dgeadd_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgeadd = 0; ++ + void FC_GLOBAL(cgeadd,CGEADD)(blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* beta, float complex* b, blasint* ldb) + { + void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); +@@ -4493,6 +10031,40 @@ + + + ++void flexiblas_real_cgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ fn = current_backend->blas.cgeadd.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_cgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_real_cgeadd_"))); ++ ++ ++void flexiblas_chain_cgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ ++ ++ hook_pos_cgeadd++; ++ if ( hook_pos_cgeadd < __flexiblas_hooks->cgeadd.nhook ) { ++ fn = __flexiblas_hooks->cgeadd.f77_hook_function[hook_pos_cgeadd]; ++ } else { ++ hook_pos_cgeadd = 0; ++ fn = current_backend->blas.cgeadd.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_cgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_chain_cgeadd_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgeadd = 0; ++ + void FC_GLOBAL(zgeadd,ZGEADD)(blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* beta, double complex* b, blasint* ldb) + { + void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); +@@ -4519,4 +10091,36 @@ + + + ++void flexiblas_real_zgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ fn = current_backend->blas.zgeadd.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_zgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_real_zgeadd_"))); ++ ++ ++void flexiblas_chain_zgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ ++ ++ hook_pos_zgeadd++; ++ if ( hook_pos_zgeadd < __flexiblas_hooks->zgeadd.nhook ) { ++ fn = __flexiblas_hooks->zgeadd.f77_hook_function[hook_pos_zgeadd]; ++ } else { ++ hook_pos_zgeadd = 0; ++ fn = current_backend->blas.zgeadd.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_zgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_chain_zgeadd_"))); ++ ++ + diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_remove-semicolon.patch b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_remove-semicolon.patch new file mode 100644 index 00000000000..ed695ca92f6 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_remove-semicolon.patch @@ -0,0 +1,15 @@ +Testing with ifort fails with this semicolon. + +https://github.com/Reference-LAPACK/lapack/commit/64e8a7500d817869e5fcde35afd39af8bc7a8086.diff +diff --git a/TESTING/dbal.in b/TESTING/dbal.in +index c00fe3e83..828629b15 100644 +--- a/test/lapack-3.9.0/dbal.in ++++ b/test/lapack-3.9.0/dbal.in +@@ -209,6 +209,6 @@ DBL: Tests DGEBAL + 0.00000000000000000000D+00 0.00000000000000000000D+00 0.00000000000000000000D+00 0.63043209914231165391D-03 0.10000000000000000000D+01 0.79310682416114036641D+03 + 0.00000000000000000000D+00 0.00000000000000000000D+00 0.00000000000000000000D+00 0.00000000000000000000D+00 0.12608641982846233078D-02 0.10000000000000000000D+01 + +- 2.494800386918399765D+291 1.582914569427869018D+175 1.004336277661868922D+59 3.186183822264904554D-58 5.053968264940243633D-175 0.40083367200179455560D-291; ++ 2.494800386918399765D+291 1.582914569427869018D+175 1.004336277661868922D+59 3.186183822264904554D-58 5.053968264940243633D-175 0.40083367200179455560D-291 + + 0 diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb index 36c0727160b..3a87838891a 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -36,7 +36,18 @@ components = [ (name, version, { 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['a3f4d66a30b6fa6473e492de86d34abc5f9d4e69d4d91ba23618388e8df05904'], + 'patches': [ + 'FlexiBLAS-3.0.4_fix-imkl.patch', + 'FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch', + 'FlexiBLAS-3.0.4_remove-semicolon.patch', + 'FlexiBLAS-3.2.0_remove-intel-suffix.patch', + ], + 'checksums': [ + 'a3f4d66a30b6fa6473e492de86d34abc5f9d4e69d4d91ba23618388e8df05904', # flexiblas-3.2.0.tar.gz + 'a078e46ad126574cc42314abd5b40461cdc6e950af79d105dbf92875c254c87c', # FlexiBLAS-3.0.4_fix-imkl.patch + '30ae7d1edbcff2beb18bca9b751dcaf0bf9a996d41fbe669b0a11592ec01c7ac', # FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch + 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', # FlexiBLAS-3.0.4_remove-semicolon.patch + ], 'configopts': '-DABI=Intel', 'backends': local_backends, }), diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0_remove-intel-suffix.patch b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0_remove-intel-suffix.patch new file mode 100644 index 00000000000..7fced99a11c --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0_remove-intel-suffix.patch @@ -0,0 +1,16 @@ +Avoid using the _intel suffix name for library +We can only have 1 library per version regardless, and the ABI is +determined by the toolchain like with all other stuff we compile. + +Author: micketeer@gmail.com +--- CMakeLists.txt.orig 2022-11-28 18:35:05.033932657 +0000 ++++ CMakeLists.txt 2022-11-28 18:35:20.226889430 +0000 +@@ -167,7 +167,7 @@ + ENDIF() + + IF ( ABI STREQUAL "Intel") +- SET(FLEXIBLAS_ABI_INTEL TRUE) ++ SET(FLEXIBLAS_ABI_INTEL FALSE) + SET(USE_INTERFACE_INTEL TRUE) + ELSEIF ( ABI STREQUAL "XL" ) + SET(FLEXIBLAS_ABI_IBM TRUE) From 99a7047a35bd2150d66396812c2d7f7f8daca9a0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 6 Dec 2022 18:37:15 +0100 Subject: [PATCH 5705/9987] adding easyconfigs: AOCC-4.0.0-GCCcore-11.3.0.eb --- .../a/AOCC/AOCC-4.0.0-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..198b56b144f --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +name = 'AOCC' +version = '4.0.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['2729ec524cbc927618e479994330eeb72df5947e90cfcc49434009eee29bf7d4'] + +clangversion = '14.0.6' + +dependencies = [ + ('binutils', '2.38'), + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('libxml2', '2.9.13'), +] + +moduleclass = 'compiler' From 5e3f10b483d97cf424d3b38737ac02ed5e4bf80e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 6 Dec 2022 18:37:35 +0100 Subject: [PATCH 5706/9987] adding easyconfigs: AOCC-4.0.0-GCCcore-12.2.0.eb --- .../a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..aca9ebc5b59 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +name = 'AOCC' +version = '4.0.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['2729ec524cbc927618e479994330eeb72df5947e90cfcc49434009eee29bf7d4'] + +clangversion = '14.0.6' + +dependencies = [ + ('binutils', '2.39'), + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('libxml2', '2.10.3'), +] + +moduleclass = 'compiler' From 6f2dcb8f85aab8194b1e343c611482179b86bf03 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Dec 2022 18:33:13 +0000 Subject: [PATCH 5707/9987] Fix style --- .../FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb index 3a87838891a..89dc1755c9d 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -36,17 +36,19 @@ components = [ (name, version, { 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], 'sources': [SOURCELOWER_TAR_GZ], - 'patches': [ + 'patches': [ 'FlexiBLAS-3.0.4_fix-imkl.patch', 'FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch', 'FlexiBLAS-3.0.4_remove-semicolon.patch', 'FlexiBLAS-3.2.0_remove-intel-suffix.patch', ], - 'checksums': [ + 'checksums': [ 'a3f4d66a30b6fa6473e492de86d34abc5f9d4e69d4d91ba23618388e8df05904', # flexiblas-3.2.0.tar.gz 'a078e46ad126574cc42314abd5b40461cdc6e950af79d105dbf92875c254c87c', # FlexiBLAS-3.0.4_fix-imkl.patch - '30ae7d1edbcff2beb18bca9b751dcaf0bf9a996d41fbe669b0a11592ec01c7ac', # FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch - 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', # FlexiBLAS-3.0.4_remove-semicolon.patch + # FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch + '30ae7d1edbcff2beb18bca9b751dcaf0bf9a996d41fbe669b0a11592ec01c7ac', + # FlexiBLAS-3.0.4_remove-semicolon.patch + 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', ], 'configopts': '-DABI=Intel', 'backends': local_backends, From 06a3ea4b8dcb56b97521cf713c6a2489cb4c452e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 09:58:18 +0100 Subject: [PATCH 5708/9987] adding easyconfigs: Qt5-5.15.7-GCCcore-12.2.0.eb and patches: Qt5-5.15.7_GCC-12.patch --- .../q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb | 76 +++++++++++++++++++ .../easyconfigs/q/Qt5/Qt5-5.15.7_GCC-12.patch | 14 ++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.7_GCC-12.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..592deb7c5f5 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb @@ -0,0 +1,76 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.15.7' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] +patches = [ + 'Qt5-5.13.1_fix-avx2.patch', + 'Qt5-5.13.1_fix-qmake-libdir.patch', + 'Qt5-5.14.1_fix-OF-Gentoo.patch', + 'Qt5-5.15.7_GCC-12.patch', +] +checksums = [ + {'qt-everywhere-opensource-src-5.15.7.tar.xz': '8a71986676a3f37a198a9113acedbfd5bc5606a459b6b85816d951458adbe9a0'}, + {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, + {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, + {'Qt5-5.14.1_fix-OF-Gentoo.patch': '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa'}, + {'Qt5-5.15.7_GCC-12.patch': '9a5bde91b223a3e2e90d3d6bec107af69a1a0f18d789593738a953080473fa68'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + # deps for QtWebEngine + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.11.1'), + # Qt5WebEngine has build dependency on Python 2 + ('Python', '2.7.18', '-bare'), + ('re2c', '3.0'), +] + +dependencies = [ + ('double-conversion', '3.2.1'), + ('GLib', '2.75.0'), + ('PCRE2', '10.40'), + ('libpng', '1.6.38'), + ('HarfBuzz', '5.3.1'), + ('graphite2', '1.3.14'), + # deps for QtWebEngine + ('X11', '20221110'), + ('fontconfig', '2.14.1'), + ('DBus', '1.15.2'), + ('libevent', '2.1.12'), + ('libGLU', '9.0.2'), + ('libjpeg-turbo', '2.1.4'), + ('NSS', '3.85'), + ('snappy', '1.1.9'), + ('JasPer', '4.0.0'), + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), + ('ICU', '72.1'), + ('nodejs', '18.12.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +# qtwayland fails to build on (some) Centos 7 systems +configopts = '-skip qtgamepad -skip qtwayland' + +# make sure QtWebEngine component is being built & installed +check_qtwebengine = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7_GCC-12.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7_GCC-12.patch new file mode 100644 index 00000000000..02c54554ffb --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7_GCC-12.patch @@ -0,0 +1,14 @@ +add missing include to fix compilation error with GCC 12.x +../../3rdparty/chromium/third_party/skia/src/utils/SkParseColor.cpp:300:49: error: no matching function for call to begin(const char* const [140]) +cfr. https://github.com/archlinux/svntogit-packages/blob/packages/qt5-webengine/trunk/qt5-webengine-gcc12.patch +--- Qt5/5.15.7/GCCcore-12.2.0/qt-everywhere-src-5.15.7/qtwebengine/src/3rdparty/chromium/third_party/skia/src/utils/SkParseColor.cpp.orig 2021-10-19 14:46:32.000000000 +0200 ++++ Qt5/5.15.7/GCCcore-12.2.0/qt-everywhere-src-5.15.7/qtwebengine/src/3rdparty/chromium/third_party/skia/src/utils/SkParseColor.cpp 2022-11-25 14:48:38.501288572 +0100 +@@ -8,6 +8,8 @@ + + #include "include/utils/SkParse.h" + ++#include ++ + static constexpr const char* gColorNames[] = { + "aliceblue", + "antiquewhite", From e6e09e190cdc012774cef0400d6c60192730254a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 7 Dec 2022 14:34:28 +0000 Subject: [PATCH 5709/9987] adding easyconfigs: OVITO-3.7.11-gompi-2022a-basic.eb --- .../o/OVITO/OVITO-3.7.11-gompi-2022a-basic.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OVITO/OVITO-3.7.11-gompi-2022a-basic.eb diff --git a/easybuild/easyconfigs/o/OVITO/OVITO-3.7.11-gompi-2022a-basic.eb b/easybuild/easyconfigs/o/OVITO/OVITO-3.7.11-gompi-2022a-basic.eb new file mode 100644 index 00000000000..25186032c64 --- /dev/null +++ b/easybuild/easyconfigs/o/OVITO/OVITO-3.7.11-gompi-2022a-basic.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OVITO' +version = '3.7.11' +versionsuffix = '-basic' + +homepage = 'https://www.ovito.org' +description = """OVITO is a scientific visualization and data analysis solution for atomistic and other particle-based +models. It helps scientists gain meaningful and quick insights from numerical simulation results.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://gitlab.com/stuko/ovito/-/archive/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dc592ea59c6bc6fbc31bd750905e0767bc48d21b4c35276f3068d4479794ecec'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Qt5', '5.15.5'), + ('HDF5', '1.12.2'), + ('netCDF', '4.9.0'), + ('FFmpeg', '4.4.2'), + ('zlib', '1.2.12'), + ('Boost', '1.79.0'), + ('libglvnd', '1.4.0'), + ('Python', '3.10.4'), +] + +sanity_check_paths = { + 'files': ['bin/ovito'], + 'dirs': [] +} + +moduleclass = 'vis' From bd3df0de7ed248994e65ce43a9ec5696d9dfac91 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 7 Dec 2022 15:56:03 +0100 Subject: [PATCH 5710/9987] adding easyconfigs: eQuilibrator-0.4.7-foss-2021a.eb --- .../eQuilibrator-0.4.7-foss-2021a.eb | 110 ++++++++++++++++++ 1 file changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/e/eQuilibrator/eQuilibrator-0.4.7-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/eQuilibrator/eQuilibrator-0.4.7-foss-2021a.eb b/easybuild/easyconfigs/e/eQuilibrator/eQuilibrator-0.4.7-foss-2021a.eb new file mode 100644 index 00000000000..90f45d92626 --- /dev/null +++ b/easybuild/easyconfigs/e/eQuilibrator/eQuilibrator-0.4.7-foss-2021a.eb @@ -0,0 +1,110 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'eQuilibrator' +version = '0.4.7' + +homepage = 'https://equilibrator.weizmann.ac.il/' +description = """Calculation of standard thermodynamic potentials of biochemical reactions.""" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('path', '15.0.1', { + 'checksums': ['298dca9d8e82a2cf224e302ed1cf48269cbc3d35502b94c335383ca053c1c2fa'], + }), + ('uncertainties', '3.1.7', { + 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], + }), + ('component-contribution', '0.4.4', { + 'modulename': 'component_contribution', + 'checksums': ['1ddf8f10919661c7efb2a6d1086c16fc47ad94779db33a5795a4a11ce3d9f5e4'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.2', { + 'checksums': ['25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421'], + }), + ('h11', '0.12.0', { + 'checksums': ['47222cb6067e4a307d535814917cd98fd0a57b6788ce715755fa2b6c28b56042'], + }), + ('httpcore', '0.15.0', { + 'checksums': ['18b68ab86a3ccf3e7dc0f43598eaddcf472b602aba29f9aa6ab85fe2ada3980b'], + }), + ('httpx', '0.23.0', { + 'checksums': ['f28eac771ec9eb4866d3fb4ab65abd42d38c424739e80c08d8d20570de60b0ef'], + }), + ('Pint', '0.20.1', { + 'modulename': 'pint', + 'checksums': ['387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067'], + }), + ('periodictable', '1.6.1', { + 'checksums': ['7c501c9f73d77b1fb28cb51e85b28429c2c44a99ce3d1274894564c72d712603'], + }), + ('SQLAlchemy', '1.3.24', { + 'modulename': 'sqlalchemy', + 'checksums': ['ebbb777cbf9312359b897bf81ba00dae0f5cb69fba2a18265dcc18a6f5ef7519'], + }), + ('python-Levenshtein-wheels', '0.13.2', { + 'modulename': 'Levenshtein', + 'checksums': ['7bd8fc3ceeeaca626848a0d7a01d02f5b93475f2d56eaa37921f1271dec7bfb1'], + }), + ('tenacity', '6.2.0', { + 'checksums': ['29ae90e7faf488a8628432154bb34ace1cca58244c6ea399fd33f066ac71339a'], + }), + ('equilibrator-cache', '0.4.3', { + 'modulename': 'equilibrator_cache', + 'checksums': ['e3f9425285ce4052f98fb0a26eaa8027137eb73897a2e0dec24255a26bb19d8c'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '5.0.2', { + 'modulename': 'slugify', + 'checksums': ['f13383a0b9fcbe649a1892b9c8eb4f8eab1d6d84b84bb7a624317afa98159cab'], + }), + ('pyparsing', '3.0.9', { + 'checksums': ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'], + }), + ('equilibrator-api', version, { + 'modulename': 'equilibrator_api', + 'checksums': ['3fb2e542787bef09f93d4a0fa37b389edd27b81d7a7bb909840a8d0bf7f2547d'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python3 -c 'from equilibrator_api import ComponentContribution;cc = ComponentContribution();" + "rxn = cc.parse_reaction_formula(\"kegg:C00002 + kegg:C00001 = kegg:C00008 + kegg:C00009\");" + "print(f\"delta_G_prime_0 = {cc.standard_dg_prime(rxn)}\")' && " + # Clean downloaded files for tests + "rm -Rf $HOME/.cache/equilibrator/" +] + +sanity_pip_check = True + +moduleclass = 'chem' From fbcd2f409f5eab4e79ede1ee98e359171d4abc30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 16:21:04 +0100 Subject: [PATCH 5711/9987] add missing `moduleclass` in bamFilters easyconfig --- .../b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb index 82f31b5dfb2..f8df6c47a86 100644 --- a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb @@ -36,3 +36,5 @@ sanity_check_paths = { } sanity_check_commands = ['bamFilters -h 2>&1 | grep "Usage"'] + +moduleclass = 'bio' From 37295c5d858ce3b5197b3fa448add76df3f093ac Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 7 Dec 2022 17:40:00 +0000 Subject: [PATCH 5712/9987] adding easyconfigs: numba-0.56.4-foss-2022a-CUDA-11.7.0.eb and patches: llvmlite-0.39_getparamattribute.patch, llvmlite-0.39_passmanager.patch, llvmlite-0.39_pass.patch, llvmlite-0.39_target.patch, llvmlite-0.39_targetregistry.patch, llvmlite-0.39_test-binding.patch --- .../llvmlite-0.39_getparamattribute.patch | 11 ++++ .../n/numba/llvmlite-0.39_pass.patch | 10 +++ .../n/numba/llvmlite-0.39_passmanager.patch | 12 ++++ .../n/numba/llvmlite-0.39_target.patch | 10 +++ .../numba/llvmlite-0.39_targetregistry.patch | 11 ++++ .../n/numba/llvmlite-0.39_test-binding.patch | 40 ++++++++++++ .../numba-0.56.4-foss-2022a-CUDA-11.7.0.eb | 61 +++++++++++++++++++ 7 files changed, 155 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_getparamattribute.patch create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_pass.patch create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_passmanager.patch create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_target.patch create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_targetregistry.patch create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_test-binding.patch create mode 100644 easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_getparamattribute.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_getparamattribute.patch new file mode 100644 index 00000000000..88dd553398e --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.39_getparamattribute.patch @@ -0,0 +1,11 @@ +--- ffi/value.cpp.orig 2022-12-07 16:25:09.106947789 +0000 ++++ ffi/value.cpp 2022-12-07 16:25:58.887604268 +0000 +@@ -154,7 +154,7 @@ + Argument *arg = unwrap(A); + unsigned argno = arg->getArgNo(); + AttributeSet attrs = +- arg->getParent()->getAttributes().getParamAttributes(argno); ++ arg->getParent()->getAttributes().getParamAttrs(argno); + return wrap(new AttributeSetIterator(attrs.begin(), attrs.end())); + } + diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_pass.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_pass.patch new file mode 100644 index 00000000000..c786af04638 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.39_pass.patch @@ -0,0 +1,10 @@ +--- ffi/passmanagers.cpp.orig 2022-12-07 16:11:49.483816317 +0000 ++++ ffi/passmanagers.cpp 2022-12-07 16:12:19.848240354 +0000 +@@ -8,6 +8,7 @@ + #include "llvm/IR/DiagnosticInfo.h" + #include "llvm/IR/DiagnosticPrinter.h" + #include "llvm/IR/LegacyPassManager.h" ++#include "llvm/Pass.h" + #include "llvm/IR/Module.h" + #include "llvm/Support/FileSystem.h" + #include "llvm/Support/ToolOutputFile.h" diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_passmanager.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_passmanager.patch new file mode 100644 index 00000000000..8a0df097b10 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.39_passmanager.patch @@ -0,0 +1,12 @@ +--- ffi/passmanagers.cpp.orig 2022-12-06 15:41:01.230034402 +0000 ++++ ffi/passmanagers.cpp 2022-12-06 15:41:19.678191543 +0000 +@@ -17,9 +17,6 @@ + #include "llvm-c/Transforms/IPO.h" + #include "llvm-c/Transforms/Scalar.h" + #include "llvm/IR/LegacyPassManager.h" +-#if LLVM_VERSION_MAJOR > 11 +-#include "llvm/IR/RemarkStreamer.h" +-#endif + #include "llvm/IR/LLVMRemarkStreamer.h" + #include "llvm/Remarks/RemarkStreamer.h" + #include "llvm/Transforms/IPO.h" diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_target.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_target.patch new file mode 100644 index 00000000000..fcf5993a364 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.39_target.patch @@ -0,0 +1,10 @@ +--- ffi/targets.cpp.orig 2022-12-06 15:44:43.191925420 +0000 ++++ ffi/targets.cpp 2022-12-06 15:44:53.916016793 +0000 +@@ -204,7 +204,6 @@ + rm = Reloc::DynamicNoPIC; + + TargetOptions opt; +- opt.PrintMachineCode = PrintMC; + opt.MCOptions.ABIName = ABIName; + + bool jit = JIT; diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_targetregistry.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_targetregistry.patch new file mode 100644 index 00000000000..fdcfc3f07b8 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.39_targetregistry.patch @@ -0,0 +1,11 @@ +--- ffi/targets.cpp.orig 2022-12-07 15:22:37.446261237 +0000 ++++ ffi/targets.cpp 2022-12-07 15:22:47.382407891 +0000 +@@ -6,7 +6,7 @@ + #include "llvm/IR/LegacyPassManager.h" + #include "llvm/IR/Type.h" + #include "llvm/Support/Host.h" +-#include "llvm/Support/TargetRegistry.h" ++#include "llvm/MC/TargetRegistry.h" + #include "llvm/Target/TargetMachine.h" + + #include diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_test-binding.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_test-binding.patch new file mode 100644 index 00000000000..732269110c1 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.39_test-binding.patch @@ -0,0 +1,40 @@ +--- llvmlite/tests/test_binding.py.orig 2022-12-06 18:00:21.729557505 +0000 ++++ llvmlite/tests/test_binding.py 2022-12-06 18:00:49.641795081 +0000 +@@ -18,6 +18,16 @@ + from llvmlite.tests import TestCase + + ++def clean_string_whitespace(x: str) -> str: ++ # Remove trailing whitespace from the end of each line ++ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE) ++ # Remove intermediate blank lines ++ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE) ++ # Remove extraneous whitespace from the beginning and end of the string ++ x = x.strip() ++ return x ++ ++ + # arvm7l needs extra ABI symbols to link successfully + if platform.machine() == 'armv7l': + llvm.load_library_permanently('libgcc_s.so.1') +@@ -555,7 +565,10 @@ + bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#")) + bd.ret(ir.Constant(ir.IntType(32), 12345)) + asm = str(mod) +- self.assertEqual(asm, asm_nonalphanum_blocklabel) ++ self.assertEqual( ++ clean_string_whitespace(asm), ++ clean_string_whitespace(asm_nonalphanum_blocklabel) ++ ) + + def test_global_context(self): + gcontext1 = llvm.context.get_global_context() +@@ -640,7 +653,7 @@ + def test_version(self): + major, minor, patch = llvm.llvm_version_info + # one of these can be valid +- valid = [(11,)] ++ valid = [(11,), (12,), (13,), (14,)] + self.assertIn((major,), valid) + self.assertIn(patch, range(10)) + diff --git a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..3ec355dc056 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.56.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('LLVM', '14.0.3'), + ('CUDA', '11.7.0', '', SYSTEM), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + + +exts_list = [ + ('llvmlite', '0.39.1', { + 'preinstallopts': local_llvmlite_preinstallopts, + 'patches': ['llvmlite-0.39_passmanager.patch', + 'llvmlite-0.39_target.patch', + 'llvmlite-0.39_test-binding.patch', + 'llvmlite-0.39_targetregistry.patch', + 'llvmlite-0.39_pass.patch', + 'llvmlite-0.39_getparamattribute.patch', + ], + }), + (name, version, { + # 'patches': ['numba-0.54.1_fix-numpy-1.21.patch'], + 'checksums': [ + {'numba-0.56.4.tar.gz': '32d9fef412c81483d7efe0ceb6cf4d3310fde8b624a9cecca00f790573ac96ee'}, + # {'numba-0.54.1_fix-numpy-1.21.patch': 'f038e7adf0cd60f6bdde219b326aad4224fef46515799578ebbbdffa73224199'}, + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -m llvmlite.tests", + "numba --help", +] + +moduleclass = 'lang' From a020698312201430f808046bc8a43027cc739df7 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 7 Dec 2022 17:44:44 +0000 Subject: [PATCH 5713/9987] adding easyconfigs: YACS-0.1.8-GCCcore-11.3.0.eb --- .../y/YACS/YACS-0.1.8-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f4862786499 --- /dev/null +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'YACS' +version = '0.1.8' + +homepage = "https://github.com/rbgirshick/yacs" +description = """YACS was created as a lightweight library to define and +manage system configurations, such as those commonly found in software +designed for scientific experimentation. These "configurations" +typically cover concepts like hyperparameters used in training a machine +learning model or configurable model hyperparameters, such as the depth +of a convolutional neural network.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'lib' From 76787673d34cb9ad6810dc0b16efac6320c77b3a Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 7 Dec 2022 17:45:35 +0000 Subject: [PATCH 5714/9987] adding easyconfigs: RDFlib-6.2.0-GCCcore-11.3.0.eb --- .../r/RDFlib/RDFlib-6.2.0-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d602151be5a --- /dev/null +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'RDFlib' +version = '6.2.0' + +homepage = 'https://github.com/RDFLib/rdflib' +description = """RDFLib is a Python library for working with RDF, a simple yet powerful language + for representing information.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True + +exts_list = [ + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', version, { + 'checksums': ['62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 7e7310cc2e356865cd2c5f8502dfb7f5f521c728 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 7 Dec 2022 17:46:30 +0000 Subject: [PATCH 5715/9987] adding easyconfigs: PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb --- ...0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..d75c64e868c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '2.1.0' +local_pytorchver = '1.12.0' +versionsuffix = '-PyTorch-%s-CUDA-%%(cudaver)s' % local_pytorchver + +homepage = 'https://github.com/rusty1s/pytorch_geometric' +description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', local_pytorchver, '-CUDA-%(cudaver)s'), + ('scikit-learn', '1.1.2'), + ('scikit-image', '0.19.3'), + ('numba', '0.56.4', '-CUDA-%(cudaver)s'), + ('h5py', '3.7.0'), + ('tqdm', '4.64.0'), + ('RDFlib', '6.2.0'), + ('ASE', '3.22.1'), + ('YACS', '0.1.8'), +] + +use_pip = True + +exts_list = [ + ('googledrivedownloader', '0.4', { + 'modulename': 'google_drive_downloader', + 'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'], + }), + ('plyfile', '0.7.4', { + 'checksums': ['9e9a18d22a3158fcd74df38761d43a7facc6df75126f2ab9f4e9a5d4d2188652'], + }), + ('torch_scatter', version, { + 'checksums': ['3a7124c2a033552febbdc72407f7d4d8cb6dce465720e84ab831512e81c1d208'], + }), + ('torch_sparse', '0.6.15', { + 'checksums': ['3a741ae8a7cc19247a44de549fa4d593c4257b5f741e1eb5110b712a14209dd9'], + }), + ('torch_cluster', '1.6.0', { + 'checksums': ['249c1bd8c33a887b22bf569a59d0868545804032123594dd8c76ba1885859c39'], + }), + ('torch_spline_conv', '1.2.1', { + 'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'], + }), + ('python-louvain', '0.16', { + 'modulename': 'community.community_louvain', + 'checksums': ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'], + }), + ('torch_geometric', version, { + 'checksums': ['72653deca925885e4d613eb5c72268bb9710325d9c717516922499fbe1197079'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 8694b846a2bd79449c3d91fdddee425921971260 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 7 Dec 2022 17:47:03 +0000 Subject: [PATCH 5716/9987] adding easyconfigs: line_profiler-4.0.0-foss-2022a.eb --- .../line_profiler-4.0.0-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/line_profiler/line_profiler-4.0.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/line_profiler/line_profiler-4.0.0-foss-2022a.eb b/easybuild/easyconfigs/l/line_profiler/line_profiler-4.0.0-foss-2022a.eb new file mode 100644 index 00000000000..42ca38e1daf --- /dev/null +++ b/easybuild/easyconfigs/l/line_profiler/line_profiler-4.0.0-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'line_profiler' +version = '4.0.0' + +homepage = 'https://github.com/pyutils/line_profiler' +description = """line_profiler is a module for doing line-by-line profiling +of functions. kernprof is a convenient script for running either +line_profiler or the Python standard library's cProfile or profile modules, +depending on what is available.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'pyutils' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ebe361a2318ac781c619573b62b3abf124881257c6b9425747dc3f1c03e708fc'] + +builddependencies = [ + ('scikit-build', '0.15.0'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), +] +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/kernprof'], + 'dirs': [], +} + +sanity_check_commands = ['kernprof --help'] + +moduleclass = 'devel' From 5218261ffbfeda844673c8a580b5478ee65682c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 18:55:56 +0100 Subject: [PATCH 5717/9987] fix checksum for cell2location 0.05-alpha --- .../c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 8356b39778a..7f105e3eeb1 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -119,7 +119,7 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/BayraktarLab/cell2location/archive/'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['2df1fe2b2b4ec5fcebc6c1d6146ce0cd79115bd14059b0ae882a41f1029a4efc'], + 'checksums': ['b1d4fc0e1eb8292457793d6af8228189bd24dd87837b8f4435d0a0312ed20c6b'], }), ] From 611499730c8b4d2c2eaa0622ef9863a227646d56 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 19:04:54 +0100 Subject: [PATCH 5718/9987] adding easyconfigs: DBus-1.15.2-GCCcore-12.2.0.eb --- .../d/DBus/DBus-1.15.2-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.15.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e3189b0b860 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.2-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.15.2' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7e640803084af59f5e477b7ded11fd888b5380910a895c51ca3aedd63c0626ca'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('expat', '2.4.9'), +] + +configopts = '--with-systemdsystemunitdir=no ' +# disable documentation +configopts += '--disable-xml-docs --disable-doxygen-docs --disable-ducktype-docs' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' From 0e1f5230116edefd7b0768f4470cae644ca5a41d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 19:05:07 +0100 Subject: [PATCH 5719/9987] adding easyconfigs: snappy-1.1.9-GCCcore-12.2.0.eb --- .../s/snappy/snappy-1.1.9-GCCcore-12.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5f980fff33b --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.9' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_inline-functions.patch', + '%(name)s-%(version)s_use-default-rtti.patch', +] +checksums = [ + '75c1fbb3d618dd3a0483bff0e26d0a92b495bbe5059c8b4f1c962b478b6e06e7', # 1.1.9.tar.gz + 'ad79190b274df5ddabf14eddd2bb0d9a091ee7d44e4afde89febf9a8f783fdce', # snappy-1.1.9_inline-functions.patch + 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d', # snappy-1.1.9_use-default-rtti.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [] +} + +moduleclass = 'lib' From 8e7c8153cbcb7e487c629ed6a2f524d6cc5d97ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 19:05:20 +0100 Subject: [PATCH 5720/9987] adding easyconfigs: graphite2-1.3.14-GCCcore-12.2.0.eb --- .../graphite2-1.3.14-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e7e24e4484a --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' From 8784060ee6dae0b4409547fb1ed939bf4e1815a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 19:07:00 +0100 Subject: [PATCH 5721/9987] add re2c easyconfig requires as dependency for Qt5 5.15.7 --- .../r/re2c/re2c-3.0-GCCcore-12.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/re2c/re2c-3.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/r/re2c/re2c-3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/re2c/re2c-3.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..baee86381e6 --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-3.0-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '3.0' + +homepage = 'https://re2c.org' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['b3babbbb1461e13fe22c630a40c43885efcfbbbb585830c6f4c0d791cf82ba0b'] + +builddependencies = [('binutils', '2.39')] + +configopts = "--disable-rust" + +sanity_check_paths = { + 'files': ['bin/re2c'], + 'dirs': [], +} + +sanity_check_commands = ["re2c --help"] + +moduleclass = 'tools' From c264a4761e30b99b0fad496aa46d7808131f38c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 19:24:11 +0100 Subject: [PATCH 5722/9987] adding easyconfigs: pyccel-1.7.0-foss-2022a.eb --- .../p/pyccel/pyccel-1.7.0-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyccel/pyccel-1.7.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pyccel/pyccel-1.7.0-foss-2022a.eb b/easybuild/easyconfigs/p/pyccel/pyccel-1.7.0-foss-2022a.eb new file mode 100644 index 00000000000..efb6a2e0e29 --- /dev/null +++ b/easybuild/easyconfigs/p/pyccel/pyccel-1.7.0-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'pyccel' +version = '1.7.0' + +homepage = 'https://github.com/pyccel/pyccel' +description = "Python extension language using accelerators" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('sympy', '1.10.1'), +] + +use_pip = True + +exts_list = [ + ('textX', '3.0.0', { + 'checksums': ['cd432adb82e348960cecdcabe68dbb916fe6eb2e4cb067c4a4b68b8c9ec51acf'], + }), + ('Arpeggio', '2.0.0', { + 'checksums': ['d6b03839019bb8a68785f9292ee6a36b1954eb84b925b84a6b8a5e1e26d3ed3d'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + (name, version, { + 'preinstallopts': "PYTHONPATH=$PWD:$PYTHONPATH ", + 'checksums': ['473212328957514d7ea52e1a57cc3a4402ae2140b0bca34c904b79d52ae81bfb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 916a602eb8791efb7a51cf7c851d9635da986714 Mon Sep 17 00:00:00 2001 From: Stig Rune Jensen Date: Thu, 8 Dec 2022 09:37:07 +0100 Subject: [PATCH 5723/9987] Add XCfun-2.1.1-GCCcore-11.3.0 --- .../x/XCFun/XCFun-2.1.1-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..16e144e6394 --- /dev/null +++ b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'XCFun' +version = '2.1.1' + +homepage = 'https://xcfun.readthedocs.io' +description = """Arbitrary order exchange-correlation functional library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/dftlibs/xcfun/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8b602df74c7be83d501532565deafd1b7881946d94789122f24c309a669298ab'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1') +] + +modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} + +sanity_check_paths = { + 'files': ['lib/libxcfun.%s' % SHLIB_EXT], + 'dirs': ['include/XCFun'] +} + +moduleclass = 'chem' From 08708c4bcefabd9d2553964c82a3d38bb9b27fb5 Mon Sep 17 00:00:00 2001 From: Stig Rune Jensen Date: Thu, 8 Dec 2022 09:37:34 +0100 Subject: [PATCH 5724/9987] Add MRCPP-1.4.1-foss-2022a --- .../m/MRCPP/MRCPP-1.4.1-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRCPP/MRCPP-1.4.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MRCPP/MRCPP-1.4.1-foss-2022a.eb b/easybuild/easyconfigs/m/MRCPP/MRCPP-1.4.1-foss-2022a.eb new file mode 100644 index 00000000000..4eb89f1dcb1 --- /dev/null +++ b/easybuild/easyconfigs/m/MRCPP/MRCPP-1.4.1-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MRCPP' +version = '1.4.1' + +homepage = 'https://mrcpp.readthedocs.io' +description = """MultiResolution Computation Program Package""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://github.com/MRChemSoft/mrcpp/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f369d72cc37415e9a6bdc0692ec4f6c5cfcc22e34b9ce569470e656c45e5b86c'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Eigen', '3.4.0') +] + +configopts = "-DENABLE_MPI=True -DENABLE_OPENMP=True" +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmrcpp.%s' % SHLIB_EXT], + 'dirs': ['include/MRCPP'] +} + +modextravars = {'MRCPP_DIR': '%(installdir)s/share/cmake/MRCPP/'} + +moduleclass = 'math' From 135c4f6edb5e3d2133009f3062aaca4d249c2655 Mon Sep 17 00:00:00 2001 From: Stig Rune Jensen Date: Thu, 8 Dec 2022 09:38:09 +0100 Subject: [PATCH 5725/9987] Add MRChem-1.1.1-foss-2022a --- .../m/MRChem/MRChem-1.1.1-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRChem/MRChem-1.1.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MRChem/MRChem-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/m/MRChem/MRChem-1.1.1-foss-2022a.eb new file mode 100644 index 00000000000..03ddfe84466 --- /dev/null +++ b/easybuild/easyconfigs/m/MRChem/MRChem-1.1.1-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'MRChem' +version = '1.1.1' + +homepage = 'https://mrchem.readthedocs.io' +description = """MRChem is a numerical real-space code for molecular electronic +structure calculations within the self-consistent field (SCF) approximations of +quantum chemistry: Hartree-Fock and Density Functional Theory.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://github.com/MRChemSoft/mrchem/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9926778edf8bb49fd4cde513faf6a887800ecf1791d1a71c0edae228ba6da646'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Eigen', '3.4.0') +] + +dependencies = [ + ('MRCPP', '1.4.1'), + ('Python', '3.10.4'), + ('XCFun', '2.1.1') +] + +configopts = "-DENABLE_MPI=True -DENABLE_OPENMP=True" +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/mrchem', 'bin/mrchem.x'], + 'dirs': ['lib'], +} + +moduleclass = 'chem' From 20f41fdb31e923b0a496b4eb9ee3aa6e22c9f7a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 10:28:07 +0100 Subject: [PATCH 5726/9987] adding easyconfigs: Doxygen-1.9.5-GCCcore-12.2.0.eb, libiconv-1.17-GCCcore-12.2.0.eb --- .../d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ .../libiconv/libiconv-1.17-GCCcore-12.2.0.eb | 23 ++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..35b262f3df8 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +name = 'Doxygen' +version = '1.9.5' + +homepage = 'https://www.doxygen.org' +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['55b454b35d998229a96f3d5485d57a0a517ce2b78d025efb79d57b5a2e4b2eec'] + +builddependencies = [ + ('binutils', '2.39'), + ('Bison', '3.8.2'), + ('CMake', '3.24.3'), + ('flex', '2.6.4'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('libiconv', '1.17'), +] + +configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9e0244a6104 --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.17' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8f74213b56238c85a50a5329f77e06198771e70dd9a739779f4c02f65d971313'] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' From f092f55f98b01398b8e2c4830d3f2b9cf9e6c1d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 10:51:48 +0100 Subject: [PATCH 5727/9987] adding easyconfigs: LibTIFF-4.4.0-GCCcore-12.2.0.eb, jbigkit-2.1-GCCcore-12.2.0.eb, libdeflate-1.14-GCCcore-12.2.0.eb --- .../j/jbigkit/jbigkit-2.1-GCCcore-12.2.0.eb | 45 +++++++++++++++++++ .../l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb | 35 +++++++++++++++ .../libdeflate-1.14-GCCcore-12.2.0.eb | 40 +++++++++++++++++ 3 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8dc21fe2bd7 --- /dev/null +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'jbigkit' +version = '2.1' + +homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' +description = """JBIG-KIT is a software implementation of the JBIG1 data + compression standard (ITU-T T.82), which was designed for bi-level image + data, such as scanned documents.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_libpath.patch', + '%(name)s-%(version)s_shlib.patch', +] +checksums = [ + 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932', # jbigkit-2.1.tar.gz + '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce', # jbigkit-2.1_libpath.patch + '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696', # jbigkit-2.1_shlib.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +files_to_copy = [ + (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), + (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libjbig85.a', 'lib/libjbig.a', + 'bin/pbmtojbg', 'bin/jbgtopbm', + 'include/jbig.h', 'include/jbig_ar.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..bcefb663225 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.4.0' + +homepage = 'https://libtiff.maptools.org/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['917223b37538959aca3b790d2d73aa6e626b688e02dcda272aec24c2f498abed'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.4'), + ('XZ', '5.2.7'), + ('jbigkit', '2.1'), + ('zstd', '1.5.2'), + ('libdeflate', '1.14'), +] + +configopts = "--enable-ld-version-script " +configopts += '--disable-webp' + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..37b4f66bb32 --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to 1.8 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'ConfigureMake' + +name = 'libdeflate' +version = '1.14' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['89e7df898c37c3427b0f39aadcf733731321a278771d20fc553f92da8d4808ac'] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' From 8548eab176bad45b573be27bd1ec2035e056df6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 10:54:25 +0100 Subject: [PATCH 5728/9987] adding easyconfigs: Pango-1.50.12-GCCcore-12.2.0.eb, FriBidi-1.0.12-GCCcore-12.2.0.eb --- .../FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb | 32 +++++++++++++++ .../p/Pango/Pango-1.50.12-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.50.12-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..97c8eece78b --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.12' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/fribidi/fribidi/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0cd233f97fc8c67bb3ac27ce8440def5d3ffacf516765b91c2cc654498293495'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +configopts = '--disable-docs' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.50.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.50.12-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2da3f6b7bf5 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.50.12-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.50.12' + +homepage = 'https://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['caef96d27bbe792a6be92727c73468d832b13da57c8071ef79b9df69ee058fe3'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.74.0'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('X11', '20221110'), + ('GLib', '2.75.0'), + ('cairo', '1.17.4'), + ('HarfBuzz', '5.3.1'), + ('FriBidi', '1.0.12'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From bf9eef894096ab9c210492cf8e7c5f3b09f4dc94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 10:54:37 +0100 Subject: [PATCH 5729/9987] adding easyconfigs: JasPer-4.0.0-GCCcore-12.2.0.eb --- .../j/JasPer/JasPer-4.0.0-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2f1a4dceecc --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '4.0.0' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['977c4c2e4210f4e37313cd2232d99e73d57ab561917b3c060bcdd5e83a0a13f1'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' From 79030a2c0ff064bbf62ff2e0f1dd6a0c8476cc89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 10:59:20 +0100 Subject: [PATCH 5730/9987] {vis}[GCCcore/12.2.0] GTK3 v3.24.35, ATK v2.38.0, at-spi2-atk v2.38.0, at-spi2-core v2.46.0, Gdk-Pixbuf v2.42.10, libepoxy v1.5.10 --- .../a/ATK/ATK-2.38.0-GCCcore-12.2.0.eb | 39 ++++++++++ .../at-spi2-atk-2.38.0-GCCcore-12.2.0.eb | 37 +++++++++ .../at-spi2-core-2.46.0-GCCcore-12.2.0.eb | 39 ++++++++++ .../g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb | 77 +++++++++++++++++++ .../Gdk-Pixbuf-2.42.10-GCCcore-12.2.0.eb | 46 +++++++++++ .../libepoxy-1.5.10-GCCcore-12.2.0.eb | 37 +++++++++ 6 files changed, 275 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..38922c40f8d --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.38.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), + ('GObject-Introspection', '1.74.0'), +] + +dependencies = [ + ('GLib', '2.75.0'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..16b32ffb227 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('GLib', '2.75.0'), + ('DBus', '1.15.2'), + ('at-spi2-core', '2.46.0'), + ('libxml2', '2.10.3'), + ('ATK', '2.38.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b9f052b0826 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.46.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['aa0c86c79f7a8d67bae49a5b7a5ab08430c608cffe6e33bf47a72f41ab03c3d0'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.74.0'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('GLib', '2.75.0'), + ('DBus', '1.15.2'), + ('X11', '20221110'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f00f26786b0 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb @@ -0,0 +1,77 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.35' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('GObject-Introspection', '1.74.0'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), + ('cairo', '1.17.4'), + ('Perl', '5.36.0'), +] +dependencies = [ + ('ATK', '2.38.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.10'), + ('Pango', '1.50.12'), + ('libepoxy', '1.5.10'), + ('X11', '20221110'), + ('FriBidi', '1.0.12'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['ec10fe6d712ef0b3c63b5f932639c9d1ae99fce94f500f6f06965629fef60bd1'], + # fix packaging issue, see https://gitlab.gnome.org/GNOME/gtk/-/issues/5355 + 'preconfigopts': "mv testsuite/gtk/gtkresources.c gtk/ && ", + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '42.0', { + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '5e85b5adc8dee666900fcaf271ba717f7dcb9d0a03d96dae08f9cbd27e18b1e0', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], + 'preconfigopts': 'autoreconf -f -i && ', + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4c2a7cd38ba --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.10' + +homepage = 'https://docs.gtk.org/gdk-pixbuf/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ee9b6c75d13ba096907a2e3c6b27b61bcd17f5c7ebeab5a5b439d2f2e39fe44b'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), + ('GObject-Introspection', '1.74.0'), +] + +dependencies = [ + ('GLib', '2.75.0'), + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('LibTIFF', '4.4.0'), + ('X11', '20221110'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..c47fc575552 --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.10' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a7ced37f4102b745ac86d6a70a9da399cc139ff168ba6b8002b4d8d43c900c15'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('X11', '20221110'), + ('Mesa', '22.2.4'), +] + +configopts = '-Degl=yes --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' From 3a653403eed6740ba5f86b81a0bd958c47f60c3e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 11:00:12 +0100 Subject: [PATCH 5731/9987] adding easyconfigs: Ghostscript-10.0.0-GCCcore-12.2.0.eb --- .../Ghostscript-10.0.0-GCCcore-12.2.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..33a9307aa2a --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '10.0.0' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a57764d70caf85e2fc0b0f59b83b92e25775631714dcdb97cc6e0cea414bb5a3'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('freetype', '2.12.1'), + ('libjpeg-turbo', '2.1.4'), + ('expat', '2.4.9'), + ('GLib', '2.75.0'), + ('cairo', '1.17.4'), + ('LibTIFF', '4.4.0'), + ('GTK3', '3.24.35'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +# Avoid race condition in build if too much parallelism is used +maxparallel = 4 + +postinstallcmds = [ + # build and install shared libs + "make so && make soinstall", + # install header files + "mkdir -p %(installdir)s/include/ghostscript", + "install -v -m644 base/*.h %(installdir)s/include/ghostscript", + "install -v -m644 psi/*.h %(installdir)s/include/ghostscript", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/ghostscript', 'include/ghostscript', 'share/man'], +} + +moduleclass = 'tools' From c585860e4fb88d56e2e0d75ff6806582de01cf08 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 11:01:48 +0100 Subject: [PATCH 5732/9987] adding easyconfigs: ImageMagick-7.1.0-53-GCCcore-12.2.0.eb, LittleCMS-2.14-GCCcore-12.2.0.eb --- .../ImageMagick-7.1.0-53-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ .../LittleCMS-2.14-GCCcore-12.2.0.eb | 28 +++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.14-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..67ede6c655f --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.1.0-53' + +homepage = 'https://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/ImageMagick/ImageMagick/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4d4cade8f435736b62382b472fe75206b8eef540a968860ace5476a96799b5ef'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20221110'), + ('Ghostscript', '10.0.0'), + ('JasPer', '4.0.0'), + ('libjpeg-turbo', '2.1.4'), + ('LibTIFF', '4.4.0'), + ('LittleCMS', '2.14'), + ('Pango', '1.50.12'), +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', + 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.14-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.14-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..36dfc68a323 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.14-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.14' + +homepage = 'https://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%s/' % '.'.join(version.split('.')[:2])] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['28474ea6f6591c4d4cee972123587001a4e6e353412a41b3e9e82219818d5740'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('libjpeg-turbo', '2.1.4')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["jpgicc --help"] + +moduleclass = 'vis' From 49480c126e3a66a9b09aff34a02f4a2d3f56955a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 11:15:25 +0100 Subject: [PATCH 5733/9987] remove outdated comment in scanpy 1.9.1 easyconfig Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb index 3967f4007cf..88ec508f776 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb @@ -33,7 +33,6 @@ exts_list = [ ('natsort', '8.2.0', { 'checksums': ['57f85b72c688b09e053cdac302dd5b5b53df5f73ae20b4874fcbffd8bf783d11'], }), - # anndata 0.7.8 needs xlrd<2.0 ('xlrd', '2.0.1', { 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], }), From 21ca16420efd61fdea808e6422da1599d003e5aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 11:37:55 +0100 Subject: [PATCH 5734/9987] adding easyconfigs: wandb-0.13.6-GCC-11.3.0.eb --- .../w/wandb/wandb-0.13.6-GCC-11.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/w/wandb/wandb-0.13.6-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/w/wandb/wandb-0.13.6-GCC-11.3.0.eb b/easybuild/easyconfigs/w/wandb/wandb-0.13.6-GCC-11.3.0.eb new file mode 100644 index 00000000000..7b9de203570 --- /dev/null +++ b/easybuild/easyconfigs/w/wandb/wandb-0.13.6-GCC-11.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'wandb' +version = '0.13.6' + +homepage = 'https://wandb.ai' +description = """CLI and Python API for Weights and Biases (wandb), a tool for visualizing and +tracking your machine learning experiments.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('GitPython', '3.1.27'), + ('PyYAML', '6.0'), + ('protobuf-python', '3.19.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('docker-pycreds', '0.4.0', { + 'modulename': 'dockerpycreds', + 'checksums': ['6ce3270bcaf404cc4c3e27e4b6c70d3521deae82fb508767870fdbf772d584d4'], + }), + ('pathtools', '0.1.2', { + 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], + }), + ('promise', '2.3', { + 'checksums': ['dfd18337c523ba4b6a58801c164c1904a9d4d1b1747c7d5dbf45b693a49d93d0'], + }), + ('urllib3', '1.26.13', { + 'checksums': ['c083dd0dce68dbfbe1129d5271cb90f9447dea7d52097c6e0126120c521ddea8'], + }), + ('sentry-sdk', '1.11.1', { + 'checksums': ['675f6279b6bb1fea09fd61751061f9a90dca3b5929ef631dd50dc8b3aeb245e9'], + }), + ('setproctitle', '1.3.2', { + 'checksums': ['b9fb97907c830d260fa0658ed58afd48a86b2b88aac521135c352ff7fd3477fd'], + }), + ('shortuuid', '1.0.11', { + 'checksums': ['fc75f2615914815a8e4cb1501b3a513745cb66ef0fd5fc6fb9f8c3fa3481f789'], + }), + (name, version, { + 'checksums': ['0d721aea476fd013c61a516948630ad58ceba78f4283b1f4b446e931664a8a98'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['wandb', 'wb']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'ai' From 4b45c4c5bd4efbbe2ecd9a6047f9a32015bfd1f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 12:28:40 +0100 Subject: [PATCH 5735/9987] {geo}[foss/2022.10] WRF v4.4.1, tcsh v6.24.05, time v1.9 --- .../t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb | 45 ++++++++++++++++ .../t/time/time-1.9-GCCcore-12.2.0.eb | 27 ++++++++++ .../w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb | 51 +++++++++++++++++++ 3 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5874f3e8c14 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.24.05' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3d1ff94787859b5a4063400470251618f76bc24f8041ba7ef2c2753f782c296c'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('ncurses', '6.3')] + +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + +sanity_check_paths = { + 'files': ["bin/tcsh", "bin/csh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e241a9de1bc --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'https://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] + +builddependencies = [('binutils', '2.39')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb new file mode 100644 index 00000000000..95e02318341 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb @@ -0,0 +1,51 @@ +name = 'WRF' +version = '4.4.1' +buildtype = 'dmpar' +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2022.10'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +# sources = ['v%(version)s.tar.gz'] +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/wrf-model', + 'repo_name': 'WRF', + 'tag': 'v%(version)s', + 'clone_into': 'WRF-%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'WRF-4.4_netCDF-Fortran_separate_path.patch', +] +checksums = [ + None, # v4.4.1.tar.gz + '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20220317'), + ('tcsh', '6.24.05'), + ('time', '1.9'), + ('Perl', '5.36.0'), +] + +dependencies = [ + ('JasPer', '4.0.0'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' From 9a59864b33ce9f78858a2d660feb3d6b2cc0fec0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Dec 2022 15:01:31 +0100 Subject: [PATCH 5736/9987] add flex as build dependency of cell2location v0.05 --- .../c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 7f105e3eeb1..1f400b68509 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ ('Bison', '3.7.1'), + ('flex', '2.6.4'), # needed by louvain ] dependencies = [ From bcc30f0ceb3e83f3a3c0a4e9ddb89862d377e35a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 15:08:23 +0100 Subject: [PATCH 5737/9987] adding easyconfigs: SimPEG-0.18.1-foss-2021b.eb --- .../s/SimPEG/SimPEG-0.18.1-foss-2021b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-foss-2021b.eb b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-foss-2021b.eb new file mode 100644 index 00000000000..b079a1e9c9c --- /dev/null +++ b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-foss-2021b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'SimPEG' +version = '0.18.1' + +homepage = 'https://simpeg.xyz' +description = """An open source Python package for simulation and gradient based parameter estimation in + geophysical applications.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('scikit-learn', '1.0.1'), + ('numba', '0.54.1'), +] + +use_pip = True + +exts_list = [ + ('pymatsolver', '0.2.0', { + 'checksums': ['df9e0444f3c7fadf57b226d7d90b7be1dea9e24718575b458ba50429736d6c45'], + }), + ('discretize', '0.8.2', { + 'checksums': ['19b2bcb57cf769ca2c225875db5d3017dc58ca8cd3ad7f44ee89ba0e1622e4a6'], + }), + ('utm', '0.7.0', { + 'checksums': ['3c9a3650e98bb6eecec535418d0dfd4db8f88c8ceaca112a0ff0787e116566e2'], + }), + ('geoana', '0.4.0', { + 'checksums': ['e95bb3974019111e0522a6955ee735cca71fa11554647fafcbdbee8b91524495'], + }), + ('empymod', '2.2.1', { + 'checksums': ['7167ca4adfc7fe737261ff4371052b8caa1c662b1aa1862822552f76734cf7ac'], + }), + (name, version, { + 'modulename': 'SimPEG', + 'checksums': ['3cbbb96640b23e9bd3311bc71e5c79fb731cefd6b3b845ecd6dad59c4a6e3600'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From d92c20418997d891b843a1258252f3d261ce4128 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 15:08:37 +0100 Subject: [PATCH 5738/9987] adding easyconfigs: SimPEG-0.18.1-intel-2021b.eb --- .../s/SimPEG/SimPEG-0.18.1-intel-2021b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-intel-2021b.eb diff --git a/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-intel-2021b.eb b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-intel-2021b.eb new file mode 100644 index 00000000000..ff2cc5d5fd8 --- /dev/null +++ b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-intel-2021b.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'SimPEG' +version = '0.18.1' + +homepage = 'https://simpeg.xyz' +description = """An open source Python package for simulation and gradient based parameter estimation in + geophysical applications.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('scikit-learn', '1.0.1'), + ('numba', '0.54.1'), +] + +use_pip = True + +exts_list = [ + ('pydiso', '0.0.3', { + 'checksums': ['883e1c4bda04afebd4ac364f1a2992e26123be0f8965c5ac59571549c6cec608'], + }), + ('pymatsolver', '0.2.0', { + 'checksums': ['df9e0444f3c7fadf57b226d7d90b7be1dea9e24718575b458ba50429736d6c45'], + }), + ('discretize', '0.8.2', { + 'checksums': ['19b2bcb57cf769ca2c225875db5d3017dc58ca8cd3ad7f44ee89ba0e1622e4a6'], + }), + ('utm', '0.7.0', { + 'checksums': ['3c9a3650e98bb6eecec535418d0dfd4db8f88c8ceaca112a0ff0787e116566e2'], + }), + ('geoana', '0.4.0', { + 'checksums': ['e95bb3974019111e0522a6955ee735cca71fa11554647fafcbdbee8b91524495'], + }), + ('empymod', '2.2.1', { + 'checksums': ['7167ca4adfc7fe737261ff4371052b8caa1c662b1aa1862822552f76734cf7ac'], + }), + (name, version, { + 'modulename': 'SimPEG', + 'checksums': ['3cbbb96640b23e9bd3311bc71e5c79fb731cefd6b3b845ecd6dad59c4a6e3600'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 02b28ff2d19730ddf2474a144788c71aad0d6b4a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Dec 2022 16:25:34 +0100 Subject: [PATCH 5739/9987] adding easyconfigs: Parcels-2.4.0-foss-2022a.eb --- .../p/Parcels/Parcels-2.4.0-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb new file mode 100644 index 00000000000..239f726f0f6 --- /dev/null +++ b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'Parcels' +version = '2.4.0' + +homepage = 'http://www.oceanparcels.org/' +description = """Parcels (Probably A Really Computationally Efficient Lagrangian Simulator) is a +set of Python classes and methods to create customisable particle tracking +simulations using output from Ocean Circulation models. Parcels can be used to +track passive and active particulates such as water, plankton, plastic and +fish.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('dask', '2022.10.0'), + ('FFmpeg', '5.0.1'), + ('git', '2.36.0', '-nodocs'), + ('matplotlib', '3.5.2'), + ('netcdf4-python', '1.6.1'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), + ('xarray', '2022.6.0'), + ('zarr', '2.13.3'), +] + +use_pip = True + +exts_list = [ + ('cgen', '2020.1', { + 'checksums': ['4ec99d0c832d9f95f5e51dd18a629ad50df0b5464ce557ef42c6e0cd9478bfcf'], + }), + ('pytools', '2022.1.13', { + 'checksums': ['c2f98359f6f281fb9d06136cdfb825a1984571598c8b437f8d6815ab80a04149'], + }), + ('pymbolic', '2022.2', { + 'checksums': ['f82776942bb3cb72329fa1f1aa2b68ec09f237db9178c95cfdc92a6aea7cec89'], + }), + ('pykdtree', '1.3.5', { + 'checksums': ['7342f75e731103e653fc1f6b9fdabc2410cf92b6e7b06160804a75786c9b5747'], + }), + ('parcels', version, { + 'checksums': ['221ce49b6cb5bb4996aa3c817c0de7f022c952a4d8cb4160ca7df7dd940714b5'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 037c9b01321d1b2e3f4fc02a98e5b918ca3e4b21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 16:39:54 +0100 Subject: [PATCH 5740/9987] allow up to 100 failing tests for MOOSE --- .../m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb index a75bf142bb7..003c439e93a 100644 --- a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -50,8 +50,8 @@ install_cmd += "./scripts/update_and_rebuild_libmesh.sh --skip-submodule-update install_cmd += "cd test && pwd && make -j %(parallel)s && make -j %(parallel)s hit && " # run tests install_cmd += "echo 'running tests' && export PYTHONPATH=%(installdir)s/moose/moosetools/contrib/hit:$PYTHONPATH && " -# run tests, but tolerate failures -install_cmd += "(python run_tests -j %(parallel)s --max-fails 10000 || echo 'Some tests are failing!' >&2 ) " +# run tests, but tolerate up to 100 failures +install_cmd += "python run_tests -j %(parallel)s --max-fails 100 " sanity_check_paths = { 'files': ['moose/framework/libmoose-opt.%s' % SHLIB_EXT, From 248eac2233c0b9a740d8db973f29520149d27fcb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Dec 2022 17:11:03 +0100 Subject: [PATCH 5741/9987] upgrade dependency on libdeflate to common v1.8 on GCCcore/10.3.0 --- easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb | 2 +- easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb index ac030fc7674..e3fa5600720 100644 --- a/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb @@ -18,7 +18,7 @@ checksums = ['185bd58732e57474fa08aae90e154fbc05f3e437ee2b434386dd2266d60d8ef6'] dependencies = [ ('zlib', '1.2.11'), ('ISA-L', '2.30.0'), - ('libdeflate', '1.7'), + ('libdeflate', '1.8'), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb index e3ae717ce00..bee76f307bb 100644 --- a/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb @@ -41,7 +41,7 @@ dependencies = [ ('cURL', '7.76.0'), ('PCRE', '8.44'), ('PCRE2', '10.36'), - ('libdeflate', '1.7'), + ('libdeflate', '1.8'), ('libRmath', '4.2.0'), ('LIBSVM', '3.25'), ('HTSlib', '1.12'), From 97172f7a6958f8acdf7a712b76c59f2ba7d61e15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 17:43:59 +0100 Subject: [PATCH 5742/9987] MOOSE test suite always does non-zero exit if there are failing tests --- .../m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb index 003c439e93a..a46d5626ef0 100644 --- a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -50,8 +50,8 @@ install_cmd += "./scripts/update_and_rebuild_libmesh.sh --skip-submodule-update install_cmd += "cd test && pwd && make -j %(parallel)s && make -j %(parallel)s hit && " # run tests install_cmd += "echo 'running tests' && export PYTHONPATH=%(installdir)s/moose/moosetools/contrib/hit:$PYTHONPATH && " -# run tests, but tolerate up to 100 failures -install_cmd += "python run_tests -j %(parallel)s --max-fails 100 " +# run tests, but tolerate failures +install_cmd += "(python run_tests -j %(parallel)s --max-fails 100 || echo 'Some tests are failing!' >&2)" sanity_check_paths = { 'files': ['moose/framework/libmoose-opt.%s' % SHLIB_EXT, From 1254cffccb30ac0ee284928a1a75d3a0c34cd308 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 8 Dec 2022 18:10:26 +0100 Subject: [PATCH 5743/9987] adding easyconfigs: OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb --- .../OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb | 94 +++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..fc4c449b810 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,94 @@ +easyblock = 'PythonBundle' + +name = 'OpenFold' +version = '1.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/aqlaboratory/openfold' +description = "A faithful PyTorch reproduction of DeepMind's AlphaFold 2" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + # CMake is required to build ninja Python package (included as extension) + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', SYSTEM), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('UCX-CUDA', '1.10.0', versionsuffix), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), + ('NCCL', '2.10.3', versionsuffix), + ('dm-tree', '0.1.6'), + ('einops', '0.4.1'), + ('colossalai', '0.1.8', versionsuffix), + ('scikit-build', '0.11.1'), + # OpenFold also requires the AlphaFold modification to OpenMM + # https://github.com/aqlaboratory/openfold/blob/v1.0.0/scripts/install_third_party_dependencies.sh#L20-L24 + # https://github.com/aqlaboratory/openfold/blob/v1.0.0/lib/openmm.patch + ('OpenMM', '7.5.1', '-DeepMind-patch'), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('ninja', '1.10.2.3', { + 'checksums': ['e1b86ad50d4e681a7dbdff05fc23bb52cb773edb90bc428efba33fa027738408'], + }), + ('hjson', '3.0.2', { + 'checksums': ['2838fd7200e5839ea4516ece953f3a19892c41089f0d933ba3f68e596aacfcd5'], + }), + ('py-cpuinfo', '8.0.0', { + 'modulename': 'cpuinfo', + 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], + }), + ('triton', '1.0.0', { + 'source_tmpl': '%(name)s-%(version)s-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'checksums': ['37b8d0eb36ed7631a6f9d01bd3183f900ae7dbd9e5e40112468a3568505671dc'], + }), + ('deepspeed', '0.5.9', { + 'checksums': ['7c43d151b51d346a430034e77764097c4af7637217c08503291c48c37ae7d090'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), + ('dllogger', '1.0.0', { + 'source_urls': ['https://github.com/NVIDIA/dllogger/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['abae2b2ac73b9e176fa87144bf6c2048ddd3dae8e7002d6d5a270bc7e4da6b4d'], + }), + (name, version, { + 'source_urls': ['https://github.com/aqlaboratory/openfold/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['79eee0b90280eea5ec110511d95b42c62ea6e0098e4a78678738eb21b332bd99'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdbfixer'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pdbfixer --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 96e8c78bba04a7e1b12a3b69c96f02d206295410 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 8 Dec 2022 18:10:43 +0100 Subject: [PATCH 5744/9987] enhance ESM-2 for esmfold --- .../ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb | 23 +++++++++++++------ 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb index c4eb572620d..854de665b3c 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'ESM-2' version = '2.0.0' @@ -11,10 +11,6 @@ description = """ESM-2 outperforms all tested single-sequence protein language m toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = ['https://pypi.python.org/packages/source/f/fair-esm'] -sources = ['fair-esm-%(version)s.tar.gz'] -checksums = ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'] - dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), @@ -22,13 +18,26 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True -options = {'modulename': 'esm'} +# omegaconf is required for esmfold (in addition to OpenFold-1.0.1) +exts_list = [ + ('omegaconf', '2.2.3', { + 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], + }), + ('antlr4-python3-runtime', '4.9.3', { + 'modulename': 'antlr4', + 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], + }), + ('fair-esm', version, { + 'modulename': 'esm', + 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], + }), +] sanity_check_commands = [ "python -c 'import esm.pretrained'", + "python -c 'import omegaconf'", ] moduleclass = 'bio' From 135d16b70b05c623fe798164f9e29818487e62d5 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 8 Dec 2022 18:16:39 +0100 Subject: [PATCH 5745/9987] adding easyconfigs: CliMetLab-0.12.6-foss-2022a.eb, Magics-4.13.0-gompi-2022a.eb, ecBuild-3.7.0.eb --- .../CliMetLab/CliMetLab-0.12.6-foss-2022a.eb | 84 +++++++++++++++++++ .../easyconfigs/e/ecBuild/ecBuild-3.7.0.eb | 35 ++++++++ .../m/Magics/Magics-4.13.0-gompi-2022a.eb | 44 ++++++++++ 3 files changed, 163 insertions(+) create mode 100644 easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb create mode 100644 easybuild/easyconfigs/e/ecBuild/ecBuild-3.7.0.eb create mode 100644 easybuild/easyconfigs/m/Magics/Magics-4.13.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb new file mode 100644 index 00000000000..815b57a2963 --- /dev/null +++ b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'CliMetLab' +version = '0.12.6' + +homepage = 'https://climetlab.readthedocs.io/' +description = """ +CliMetLab is a Python package aiming at simplifying access to climate and +meteorological datasets, allowing users to focus on science instead of +technical issues such as data access and data formats. It is mostly intended to +be used in Jupyter notebooks, and be interoperable with all popular data +analytic packages, such as Numpy, Pandas, Xarray, SciPy, Matplotlib, etc. as +well as machine learning frameworks, such as Tensorflow, Keras or PyTorch.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('xarray', '2022.9.0'), + ('dask', '2022.10.0'), + ('netcdf4-python', '1.6.1'), + ('tqdm', '4.64.0'), + ('ecCodes', '2.27.0'), + ('PyYAML', '6.0'), + ('Magics', '4.13.0'), + ('cdsapi', '0.5.1'), +] + +use_pip = True +sanity_pip_check = True + +# stick to termcolor 1.x, to avoid hatchling required dependency +# remove ecmwflibs requirement (provides ecCodes and Magics) +exts_list = [ + ('eccodes', '1.5.0', { + 'checksums': ['e70c8f159140c343c215fd608ddf533be652ff05ad2ff17243c7b66cf92127fa'], + }), + ('cfgrib', '0.9.10.3', { + 'checksums': ['c10806058c80c48610c201bf05eb292401807806ab9423ab4965ae23dbb6b521'], + }), + ('multiurl', '0.1.1', { + 'checksums': ['8895c51f10a9f80a80f019bee5083a975760b7bdbd6cb2e32b2376a5916aa374'], + }), + ('ecmwf-api-client', '1.6.3', { + 'modulename': 'ecmwfapi', + 'checksums': ['3a00bda34a72e2d5198c97399a4750b42a6633efdb5e1b3a5fd2b2bbaa5db0d6'], + }), + ('ecmwf-opendata', '0.1.1', { + 'modulename': 'ecmwf.opendata', + 'checksums': ['dfb5d4694fbb78b0f79799e130be0b5a56b30c075937c3d03dd6d9b68399bfdd'], + }), + ('findlibs', '0.0.2', { + 'checksums': ['6c7e038496f9a97783ab2cd5736bb68522d5bebd8b0eb17c976b6a4ae4032c8d'], + }), + ('Magics', '1.5.8', { + 'modulename': 'Magics', + 'checksums': ['7df4241802fb552ee052da18190a5266a8faff7feecc70779cb5e1809625fb90'], + }), + ('pdbufr', '0.9.0', { + 'checksums': ['c9f9e19ebae7d27e86166d72a088c699044917a66c800cfccfa72005a1cda945'], + }), + ('pyodc', '1.1.4', { + 'checksums': ['e6185117a38483b0567bf45e6a476b83e0b6b2a7d94ae110cb3ecf92e2cd900e'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('branca', '0.3.1', { + 'checksums': ['3e762c9bdf40725f3d05ea1fda8fae9b470bfada6474e43a1242c8204a7bb15e'], + }), + ('climetlab', version, { + 'preinstallopts': """sed -i 's/"ecmwflibs/# "ecmwflibs/g' setup.py & """, + 'checksums': ['5c3506e3f4223b9ddbfbee09d41dd5b4e45ecce584b90419cce9fef33f9a1de3'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ecBuild/ecBuild-3.7.0.eb b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.7.0.eb new file mode 100644 index 00000000000..8a5bb9a339e --- /dev/null +++ b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.7.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'ecBuild' +version = '3.7.0' + +homepage = 'https://ecbuild.readthedocs.io/' + +description = """ +A CMake-based build system, consisting of a collection of CMake macros and +functions that ease the managing of software build systems """ + +toolchain = SYSTEM + +github_account = 'ecmwf' +sources = [ + { + 'source_urls': [GITHUB_SOURCE], + 'filename': '%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s --strip-components=1', + }, +] +checksums = ['44ba49b6b628e88bc0145f0cd1fdbdff37fbff2327c581f22a47cd10263a21b6'] + +buildininstalldir = True + +skipsteps = ['install'] + +sanity_check_paths = { + 'files': ['bin/ecbuild', 'cmake/ecbuild-config.cmake'], + 'dirs': ['bin', 'lib', 'share', 'cmake'], +} + +sanity_check_commands = ['ecbuild --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/Magics/Magics-4.13.0-gompi-2022a.eb b/easybuild/easyconfigs/m/Magics/Magics-4.13.0-gompi-2022a.eb new file mode 100644 index 00000000000..3d7c2d18e8f --- /dev/null +++ b/easybuild/easyconfigs/m/Magics/Magics-4.13.0-gompi-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'Magics' +version = '4.13.0' + +homepage = 'https://confluence.ecmwf.int/display/MAGP/' + +description = """ +Magics is ECMWF's meteorological plotting software and can be either accessed +directly through its Python or Fortran interfaces or by using Metview.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/ecmwf/magics/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['bc9653754a9d655b14effd637d13dba6ecaf048d2f45cb8b70b3e262983b37bf'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('ecBuild', '3.7.0', '', SYSTEM), +] + +dependencies = [ + ('PROJ', '9.0.0'), + ('netCDF', '4.9.0'), + ('Pango', '1.50.7'), + ('expat', '2.4.8'), + ('ecCodes', '2.27.0'), +] + +_bins = ['magics', 'magicsCompatibilityChecker', 'magjson', 'magjsonx', 'magml', 'magmlx', 'metgram', 'metgram.sh', + 'metgramx'] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libMagPlus%s.%s' % (x, SHLIB_EXT) for x in ['', 'Double', 'Single']] + + ['bin/%s' % x for x in _bins], + 'dirs': ['bin', 'lib', 'include', 'share'] +} + +sanity_check_commands = ['magics 2>&1 | grep "^Usage: magics"'] + +moduleclass = 'geo' From 30411e5fe2fe94d592ea3f9e64b82a44b961e9e4 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 8 Dec 2022 20:39:41 +0100 Subject: [PATCH 5746/9987] Update PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb --- .../PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb index 8f4749f4dae..d131b7ed36b 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb @@ -29,9 +29,6 @@ exts_list = [ ('torchmetrics', '0.10.3', { 'checksums': ['9e6ab66175f2dc13e246c37485b2c27c77931dfe47fc2b81c76217b8efdc1e57'], }), - ('termcolor', '2.1.0', { - 'checksums': ['b80df54667ce4f48c03fe35df194f052dc27a541ebbf2544e4d6b47b5d6949c4'], - }), ('fire', '0.4.0', { 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], }), From d1a466160b30784eace504f9ebe73665e089747e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Dec 2022 22:56:44 +0100 Subject: [PATCH 5747/9987] downgrade dependency on FFmpeg on Parcels v2.4.0 --- easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb index 239f726f0f6..e243e530189 100644 --- a/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('dask', '2022.10.0'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.42'), ('git', '2.36.0', '-nodocs'), ('matplotlib', '3.5.2'), ('netcdf4-python', '1.6.1'), From 98485c1091a42fff28f8ac171d28e2ae0a0d81d8 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 8 Dec 2022 23:04:22 +0100 Subject: [PATCH 5748/9987] Update easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb Co-authored-by: SebastianAchilles --- .../PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb index d131b7ed36b..e9d3bd119a4 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb @@ -29,6 +29,10 @@ exts_list = [ ('torchmetrics', '0.10.3', { 'checksums': ['9e6ab66175f2dc13e246c37485b2c27c77931dfe47fc2b81c76217b8efdc1e57'], }), + # stick to termcolor 1.x, to avoid hatchling required dependency + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), ('fire', '0.4.0', { 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], }), From 6b6521552c504042c902f3bf5eb431600be8fc44 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Dec 2022 23:39:56 +0100 Subject: [PATCH 5749/9987] explain origin of list of dependencies of Parcels --- easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb index e243e530189..9061cf7b2de 100644 --- a/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb @@ -12,11 +12,13 @@ fish.""" toolchain = {'name': 'foss', 'version': '2022a'} +# dependencies of Parcels are not listed as install_requires +# taken from https://github.com/OceanParcels/parcels/blob/v%(version)s/environment_py3_linux.yml dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('dask', '2022.10.0'), - ('FFmpeg', '4.42'), + ('FFmpeg', '4.4.2'), ('git', '2.36.0', '-nodocs'), ('matplotlib', '3.5.2'), ('netcdf4-python', '1.6.1'), From 3315fa0874034f094b65f84a9260fd4dbbc44520 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 9 Dec 2022 07:43:48 +0100 Subject: [PATCH 5750/9987] fix description to match package intention. --- .../m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb index f043052deda..0381f59f5ef 100644 --- a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb @@ -4,7 +4,7 @@ name = 'matlab-proxy' version = '0.5.4' homepage = 'https://github.com/mathworks/matlab-proxy' -description = 'MATLAB Integration for Jupyter' +description = "A Python package which enables you to launch MATLAB and access it from a web browser." toolchain = {'name': 'GCCcore', 'version': '11.3.0'} From 81734287dcc0f2f53b295d278e56d06eee598809 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 9 Dec 2022 08:28:24 +0100 Subject: [PATCH 5751/9987] fix xarray version --- .../easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb index 815b57a2963..7d9b3571002 100644 --- a/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('xarray', '2022.9.0'), + ('xarray', '2022.6.0'), ('dask', '2022.10.0'), ('netcdf4-python', '1.6.1'), ('tqdm', '4.64.0'), From 29bc8c5ebc594184bf52d9ed003beef8a7935968 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 9 Dec 2022 09:23:20 +0100 Subject: [PATCH 5752/9987] also update the non-CUDA version --- .../ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb | 7 +----- .../e/ESM-2/ESM-2-2.0.0-foss-2021a.eb | 24 +++++++++++-------- 2 files changed, 15 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb index 854de665b3c..57234735211 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb @@ -30,14 +30,9 @@ exts_list = [ 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], }), ('fair-esm', version, { - 'modulename': 'esm', + 'modulename': 'esm, esm.pretrained', 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], }), ] -sanity_check_commands = [ - "python -c 'import esm.pretrained'", - "python -c 'import omegaconf'", -] - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb index e3ea302ffec..2a897513a5e 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'ESM-2' version = '2.0.0' @@ -10,23 +10,27 @@ description = """ESM-2 outperforms all tested single-sequence protein language m toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = ['https://pypi.python.org/packages/source/f/fair-esm'] -sources = ['fair-esm-%(version)s.tar.gz'] -checksums = ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'] - dependencies = [ ('Python', '3.9.5'), ('PyTorch', '1.10.0'), ] use_pip = True -download_dep_fail = True sanity_pip_check = True -options = {'modulename': 'esm'} - -sanity_check_commands = [ - "python -c 'import esm.pretrained'", +# omegaconf is required for esmfold (in addition to OpenFold-1.0.1) +exts_list = [ + ('omegaconf', '2.2.3', { + 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], + }), + ('antlr4-python3-runtime', '4.9.3', { + 'modulename': 'antlr4', + 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], + }), + ('fair-esm', version, { + 'modulename': 'esm, esm.pretrained', + 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], + }), ] moduleclass = 'bio' From aea1ef2d053e30c8ad1c074384d01762a9ac6abc Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 9 Dec 2022 09:58:21 +0000 Subject: [PATCH 5753/9987] Adding webp support as we already have the libwebp here, it helps a lot making this library more useful --- .../p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb index 0973b977079..c430b0e2e0a 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb @@ -21,7 +21,8 @@ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.12'), ('LibTIFF', '4.3.0'), - ('freetype', '2.12.1') + ('freetype', '2.12.1'), + ('libwebp', '1.2.4'), ] use_pip = True From 8f2d4abf10dc2e5b1440802d5ecfd074866973bd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Dec 2022 14:38:29 +0100 Subject: [PATCH 5754/9987] Fix test_autograd --- .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 3 +++ ....1_fix-autograd-thread_shutdown-test.patch | 24 +++++++++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index d70fb060378..f0d3ab839eb 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -67,6 +68,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.11.1_skip-test_init_from_local_shards.patch '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch + 'd97cd6b0570a167ecc3e631dc4ea884d95ace285cc38aa980566f4fec2c0d089', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch new file mode 100644 index 00000000000..c82cc060467 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch @@ -0,0 +1,24 @@ +Fix flaky test_thread_shutdown in test_autograd + +From https://github.com/pytorch/pytorch/pull/86464 + +Backport: Alexander Grund (TU Dresden) + +diff --git a/test/test_autograd.py b/test/test_autograd.py +index da1e859682e..0c0bc4f1a2a 100644 +--- a/test/test_autograd.py ++++ b/test/test_autograd.py +@@ -4320,8 +4320,12 @@ class MyFunction(Function): + def backward(ctx, grad): + return grad + ++# Run on cuda if it is available to ensure that the worker thread ++# is properly initialized by the time we exit. ++device = "cuda" if torch.cuda.is_available() else "cpu" ++ + for shape in [(1,), ()]: +- v = torch.ones(shape, requires_grad=True) ++ v = torch.ones(shape, requires_grad=True, device=device) + MyFunction.apply(v).backward() + """ + s = TestCase.runWithPytorchAPIUsageStderr(code) From 5ebcb2835792626859e283c903cf944e8a72253c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Dec 2022 14:46:00 +0100 Subject: [PATCH 5755/9987] Fix test_c10d_gloo --- .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 6 ++-- ...PyTorch-1.12.1_skip-test_round_robin.patch | 35 +++++++++++++++++++ 2 files changed, 38 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index f0d3ab839eb..9a11fc1e85e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -43,7 +43,7 @@ patches = [ 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', - 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -97,8 +97,8 @@ checksums = [ # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch - # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch - '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', + # PyTorch-1.12.1_skip-test_round_robin.patch + '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin.patch new file mode 100644 index 00000000000..ebeec6b80b5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin.patch @@ -0,0 +1,35 @@ +test_round_robin & test_round_robin_create_destroy of distributed/test_c10d_gloo may run into timeouts. +So simply skip the on all OS (not only on Windows), the existing skip marker suggest that this is OK. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/test_c10d_gloo.py b/test/distributed/test_c10d_gloo.py +index e49d65ea33d..b4fb75a1b11 100644 +--- a/test/distributed/test_c10d_gloo.py ++++ b/test/distributed/test_c10d_gloo.py +@@ -10,6 +10,7 @@ import sys + import tempfile + from functools import reduce + from itertools import groupby ++from unittest import skip + + import torch + import torch.distributed as c10d +@@ -1415,7 +1415,7 @@ class ProcessGroupGlooTest(MultiProcessTestCase): + for i, tensor in enumerate(tensors): + self.assertEqual(torch.full(size, float(i * self.world_size)), tensor) + +- @skip_if_win32() ++ @skip("Occasionally times out") + @requires_gloo() + def test_round_robin(self): + num_process_groups = 2 +@@ -1438,7 +1439,7 @@ class ProcessGroupGlooTest(MultiProcessTestCase): + pg.broadcast(tensor, root=0).wait() + self.assertEqual(torch.full([100, 100], 0.0), tensor) + +- @skip_if_win32() ++ @skip("Occasionally times out") + @requires_gloo() + def test_round_robin_create_destroy(self): + store = c10d.FileStore(self.file_name, self.world_size) From 493d0ab42b38ea02264868a719d760ac14cf8a88 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Dec 2022 15:09:03 +0100 Subject: [PATCH 5756/9987] Skip aborting FSDP tests --- .../p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index 9a11fc1e85e..528fb671557 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -137,6 +137,9 @@ excluded_tests = { 'distributed/test_distributed_spawn', # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 'distributions/test_constraints', + # Those 2 abort on some machines. Skip for now + 'distributed/fsdp/test_fsdp_input', + 'distributed/fsdp/test_fsdp_mixed_precision', ] } From 1c26956e2937d1e172f2bc90d3f9936fa45f6df5 Mon Sep 17 00:00:00 2001 From: Victor Lopez Date: Fri, 9 Dec 2022 15:20:44 +0100 Subject: [PATCH 5757/9987] Add easyconfigs: dlb --- .../easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb | 26 +++++++++++++++++++ .../easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb new file mode 100644 index 00000000000..bf0987b6dd2 --- /dev/null +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb @@ -0,0 +1,26 @@ +# vim: set syntax=python: +easyblock = 'ConfigureMake' + +name = 'dlb' +version = '3.2' + +description = """ +DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., +two levels of parallelism) by improving the load balance of the outer level of +parallelism (e.g., MPI) by dynamically redistributing the computational +resources at the inner level of parallelism (e.g., OpenMP). at run time. +""" +homepage = 'https://pm.bsc.es/dlb/' +docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] + +toolchain = {'name': 'gompi', 'version': '2022a'} +builddependencies = [('Python', '3.10.4', '', ('GCCcore', '11.3.0-bare'))] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] + +checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] + +moduleclass = 'lib' + +configopts = '--with-mpi' diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb new file mode 100644 index 00000000000..aae046e6f0b --- /dev/null +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb @@ -0,0 +1,26 @@ +# vim: set syntax=python: +easyblock = 'ConfigureMake' + +name = 'dlb' +version = '3.2' + +description = """ +DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., +two levels of parallelism) by improving the load balance of the outer level of +parallelism (e.g., MPI) by dynamically redistributing the computational +resources at the inner level of parallelism (e.g., OpenMP). at run time. +""" +homepage = 'https://pm.bsc.es/dlb/' +docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] + +toolchain = {'name': 'iimpi', 'version': '2022a'} +builddependencies = [('Python', '3.10.4', '', ('GCCcore', '11.3.0-bare'))] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] + +checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] + +moduleclass = 'lib' + +configopts = '--with-mpi' From f9486579fe322aadd4571fcdbac6b40a00070654 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 9 Dec 2022 18:03:32 +0000 Subject: [PATCH 5758/9987] Fix missing checksum --- .../f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb index 89dc1755c9d..c15509fa214 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -49,6 +49,8 @@ components = [ '30ae7d1edbcff2beb18bca9b751dcaf0bf9a996d41fbe669b0a11592ec01c7ac', # FlexiBLAS-3.0.4_remove-semicolon.patch 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', + # FlexiBLAS-3.2.0_remove-intel-suffix.patch + '98b70ac9b10c9e45cd7c2251f8b710cda704b04311b33b6fe1a56be51aa43bc4', ], 'configopts': '-DABI=Intel', 'backends': local_backends, From 2f45aeebb21c32c6bee952efa50b9812f1cbe073 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 9 Dec 2022 18:40:07 +0000 Subject: [PATCH 5759/9987] Trailing space --- .../f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb index c15509fa214..0ad1849f775 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -48,7 +48,7 @@ components = [ # FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch '30ae7d1edbcff2beb18bca9b751dcaf0bf9a996d41fbe669b0a11592ec01c7ac', # FlexiBLAS-3.0.4_remove-semicolon.patch - 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', + 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', # FlexiBLAS-3.2.0_remove-intel-suffix.patch '98b70ac9b10c9e45cd7c2251f8b710cda704b04311b33b6fe1a56be51aa43bc4', ], From b63081a90ed5f63181fa96c4ef9fd53264be90cf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 9 Dec 2022 23:40:37 +0100 Subject: [PATCH 5760/9987] adding easyconfig deepdiff-5.8.1-GCCcore-11.3.0.eb --- .../deepdiff/deepdiff-5.8.1-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/d/deepdiff/deepdiff-5.8.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-5.8.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-5.8.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fffd39905e0 --- /dev/null +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-5.8.1-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'deepdiff' +version = '5.8.1' + +homepage = 'https://zepworks.com/deepdiff/current/' +description = """DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('jsonpickle', '2.2.0', { + 'checksums': ['7b272918b0554182e53dc340ddd62d9b7f902fec7e7b05620c04f3ccef479a0e'], + }), + ('ordered-set', '4.1.0', { + 'checksums': ['694a8e44c87657c59292ede72891eb91d34131f6531463aab3009191c77364a8'], + }), + (name, version, { + 'checksums': ['8d4eb2c4e6cbc80b811266419cb71dd95a157094a3947ccf937a94d44943c7b8'], + }), +] + +moduleclass = 'tools' From 9610492606b6a832164474256dd7b48bd5453141 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 10 Dec 2022 01:05:25 +0100 Subject: [PATCH 5761/9987] fix parameters of Sphinx-RTD-Theme v1.1.1 PythonBundle --- .../Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb index 0a9f224eba9..b47eb8e0a27 100644 --- a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb @@ -4,15 +4,14 @@ name = 'Sphinx-RTD-Theme' version = '1.1.1' homepage = 'https://sphinx-rtd-theme.readthedocs.io' -description = """Sphinx theme was designed to provide a great reader experience - for documentation users on both desktop and mobile devices""" +description = """Sphinx theme designed to provide a great reader experience + for documentation users on both desktop and mobile devices.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [('Python', '3.8.6')] use_pip = True -exts_download_dep_fail = True exts_list = [ ('sphinx_rtd_theme', version, { @@ -20,4 +19,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'vis' From ca35504c6975c13a3cd7244ae9cab8969fcc8d85 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 10 Dec 2022 01:33:08 +0100 Subject: [PATCH 5762/9987] add binutils as build dependecy of Sphinx-RTD-Theme v1.1.1 --- .../s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb index b47eb8e0a27..76924dcf229 100644 --- a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb @@ -9,6 +9,8 @@ description = """Sphinx theme designed to provide a great reader experience toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] + dependencies = [('Python', '3.8.6')] use_pip = True From d40c72fb741a95735e90e9ad9223ee4095192d36 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 10 Dec 2022 00:34:25 +0100 Subject: [PATCH 5763/9987] adding easyconfigs tensorboardX-2.5.1-foss-2022a.eb --- .../tensorboardX-2.5.1-foss-2022a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.5.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.5.1-foss-2022a.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.5.1-foss-2022a.eb new file mode 100644 index 00000000000..8a5ba42a91c --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.5.1-foss-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'tensorboardX' +version = '2.5.1' + +homepage = 'https://github.com/lanpa/tensorboardX' +description = "Tensorboard for PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +# tensorboardX v2.x works with tensorboards generated with TensorFlow 2, +# but TensorFlow is not needed to use tensorboardX +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('protobuf-python', '3.19.4'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': '%(name)s', + 'checksums': ['ea85a3446f22ce8a917fe4fa4d8a7a96222ef84ac835267d038c34bb99f6d61b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From 9605baf9cb3834d492af9988b49fca58dc835788 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 9 Dec 2022 23:41:12 +0100 Subject: [PATCH 5764/9987] update PyTorch-Lightning v1.8.2 to v1.8.4 and use dependencies following its requirements file --- ...-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb | 50 ------- ...-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb | 124 ++++++++++++++++++ 2 files changed, 124 insertions(+), 50 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb deleted file mode 100644 index e9d3bd119a4..00000000000 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PyTorch-Lightning' -version = '1.8.2' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://pytorchlightning.ai' -description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." - -toolchain = {'name': 'foss', 'version': '2022a'} - -dependencies = [ - ('CUDA', '11.7.0', '', SYSTEM), - ('Python', '3.10.4'), - ('PyTorch', '1.12.0', versionsuffix), - ('tqdm', '4.64.0'), - ('tensorboard', '2.10.0'), - ('typing-extensions', '4.3.0'), -] - -exts_list = [ - ('fsspec', '2022.11.0', { - 'checksums': ['259d5fd5c8e756ff2ea72f42e7613c32667dc2049a4ac3d84364a7ca034acb8b'], - }), - ('pyDeprecate', '0.3.2', { - 'modulename': 'deprecate', - 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], - }), - ('torchmetrics', '0.10.3', { - 'checksums': ['9e6ab66175f2dc13e246c37485b2c27c77931dfe47fc2b81c76217b8efdc1e57'], - }), - # stick to termcolor 1.x, to avoid hatchling required dependency - ('termcolor', '1.1.0', { - 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], - }), - ('fire', '0.4.0', { - 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], - }), - ('lightning-utilities', '0.3.0', { - 'checksums': ['d769ab9b76ebdee3243d1051d509aafee57d7947734ddc22977deef8a6427f2f'], - }), - ('pytorch-lightning', version, { - 'checksums': ['480f3396cd63888c4e5ec2f21c02fe662a2b035d9634e6f31fcf1197a36ebd15'], - }), -] - -use_pip = True -sanity_pip_check = True - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..532eba19c22 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,124 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + # dependencies from requirements/app/base.txt + ('aiohttp', '3.8.3'), + ('BeautifulSoup', '4.10.0'), + ('deepdiff', '5.8.1'), + # dependencies from requirements/pytorch/base.txt + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('tensorboardX', '2.5.1'), +] + +use_pip = True + +# dependencies from requirements/app/base.txt and requirements/pytorch/base.txt +exts_list = [ + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.5.1', { + 'checksums': ['63a5c5ce3673d3d5fbbf23cd87e11ab84b6b451436f1b7f19ec54b6bc36ed7ca'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), + ('starlette', '0.19.1', { + 'checksums': ['c6d21096774ecb9639acad41b86b7706e52ba3bf1dc13ea4ed9ad593d47e24c7'], + }), + ('fastapi', '0.79.1', { + 'checksums': ['006862dec0f0f5683ac21fb0864af2ff12a931e7ba18920f28cc8eceed51896b'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + ('lightning_cloud', '0.5.12', { + 'checksums': ['5b0cf53ecfb512f9476eec3a7f425c0e174ca9d0e726673605d5e1e57074eb0c'], + }), + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('starsessions', '1.3.0', { + 'checksums': ['8d3b509d4e6d235655f7dd495fcf0afc1bd86da84de3a8d434e6f82137ebcde8'], + }), + ('fsspec', '2022.7.1', { + 'checksums': ['7f9fb19d811b027b97c4636c6073eb53bc4cbee2d3c4b33fa88b9f26906fd7d7'], + }), + ('croniter', '1.3.8', { + 'checksums': ['32a5ec04e97ec0837bcdf013767abd2e71cceeefd3c2e14c804098ce51ad6cd9'], + }), + ('traitlets', '5.2.0', { + 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('lightning-utilities', '0.4.2', { + 'checksums': ['dc6696ab180117f7e97b5488dac1d77765ab891022f7521a97a39e10d362bdb8'], + }), + ('blessed', '1.19.1', { + 'checksums': ['9a0d099695bf621d4680dd6c73f6ad547f6a3442fbdbe80c4b1daa1edbc492fc'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('readchar', '4.0.3', { + 'checksums': ['1d920d0e9ab76ec5d42192a68d15af2562663b5dfbf4a67cf9eba520e1ca57e6'], + }), + ('inquirer', '2.10.1', { + 'checksums': ['e9876258183e24f6e8c44136b04f6f2e18dd6684aee59b86a8057c50601a6523'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('botocore', '1.24.21', { + 'checksums': ['7e976cfd0a61601e74624ef8f5246b40a01f2cce73a011ef29cf80a6e371d0fa'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('aiobotocore', '2.3.4', { + 'checksums': ['6554ebea5764f66f4be544a4fcaa0953ee80e600dd7bd818ba4893d72bf12bfb'], + }), + ('s3fs', '2022.7.1', { + 'checksums': ['4883d682cb96b769fca568dbbcaa33ff457ac8077a03af221e6f253adac05771'], + }), + ('torchmetrics', '0.9.3', { + 'checksums': ['4ebfd2466021db26397636966ee1a195d3b340ba5d71bb258e764340dfc2476f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['c2771f966fc1b909cdfd1d603a87b8c84a3d5ff7aacf35b2c0260f697ec0c8be'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' + From 39f7d49c2f8e8187dcf1ebc086eddd728ffc7b4c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 11 Dec 2022 01:51:14 +0100 Subject: [PATCH 5765/9987] remove blank lines at end of PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb --- .../PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb index 532eba19c22..faf2e40814c 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb @@ -121,4 +121,3 @@ exts_list = [ sanity_pip_check = True moduleclass = 'lib' - From f351308c25c4e59bb8f8e25bb95d7f9cf18a6727 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 11 Dec 2022 09:57:33 +0000 Subject: [PATCH 5766/9987] geo moduleclass for SimPEG --- .../s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb index 96c54436747..d8b79f635f4 100644 --- a/easybuild/easyconfigs/s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb @@ -56,4 +56,4 @@ exts_list = [ sanity_pip_check = True -moduleclass = 'bio' +moduleclass = 'geo' From 99d673be61df6ae52fb6413b6a24676c9f4deb40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Dec 2022 11:18:07 +0100 Subject: [PATCH 5767/9987] add Python 3.11 to classifiers in setup.py --- setup.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/setup.py b/setup.py index 75d8dacffe3..6b4971a52b9 100644 --- a/setup.py +++ b/setup.py @@ -99,6 +99,8 @@ def get_data_files(): "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", "Topic :: Software Development :: Build Tools", ], packages=[], From 9ee6150ef116266902d8e9ea85b32d06757b33f3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 11 Dec 2022 10:27:06 +0000 Subject: [PATCH 5768/9987] switch LibTiff homepage --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb | 2 +- ...1.14-GCCcore-12.2.0.eb => libdeflate-1.15-GCCcore-12.2.0.eb} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/libdeflate/{libdeflate-1.14-GCCcore-12.2.0.eb => libdeflate-1.15-GCCcore-12.2.0.eb} (100%) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb index bcefb663225..6336e1de043 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.4.0' -homepage = 'https://libtiff.maptools.org/' +homepage = 'https://libtiff.gitlab.io/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb similarity index 100% rename from easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb From 8c08c47901d4ff3fc0b67386e6bb7e21c6c1cc99 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 11 Dec 2022 10:27:39 +0000 Subject: [PATCH 5769/9987] switch libdeflate to 1.15, which requires change to CMakeMake --- .../l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb index 37b4f66bb32..de86aeb5c08 100644 --- a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb @@ -3,10 +3,10 @@ # Updated to 1.8 # J. Sassmannshausen NHS/GSTT -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'libdeflate' -version = '1.14' +version = '1.15' homepage = 'https://github.com/ebiggers/libdeflate' description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" @@ -16,14 +16,10 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} github_account = 'ebiggers' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['89e7df898c37c3427b0f39aadcf733731321a278771d20fc553f92da8d4808ac'] +checksums = ['58b95040df7383dc0413defb700d9893c194732474283cc4c8f144b00a68154b'] builddependencies = [('binutils', '2.39')] -skipsteps = ['configure'] - -installopts = 'PREFIX=%(installdir)s' - sanity_check_paths = { 'files': [ 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', From d9119b7ce7382c3741045f50adf8245f4fd22967 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 11 Dec 2022 11:36:51 +0100 Subject: [PATCH 5770/9987] add Java builddep --- .../e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb | 10 +++++++--- .../easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb | 10 +++++++--- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb index 57234735211..b4cd134d85e 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb @@ -11,6 +11,10 @@ description = """ESM-2 outperforms all tested single-sequence protein language m toolchain = {'name': 'foss', 'version': '2021a'} +builddependencies = [ + ('Java', '11', '', SYSTEM), # needed by ANTLR4 runtime +] + dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), @@ -22,13 +26,13 @@ sanity_pip_check = True # omegaconf is required for esmfold (in addition to OpenFold-1.0.1) exts_list = [ - ('omegaconf', '2.2.3', { - 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], - }), ('antlr4-python3-runtime', '4.9.3', { 'modulename': 'antlr4', 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], }), + ('omegaconf', '2.2.3', { + 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], + }), ('fair-esm', version, { 'modulename': 'esm, esm.pretrained', 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb index 2a897513a5e..3b6ec3564b0 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb @@ -10,6 +10,10 @@ description = """ESM-2 outperforms all tested single-sequence protein language m toolchain = {'name': 'foss', 'version': '2021a'} +builddependencies = [ + ('Java', '11', '', SYSTEM), # needed by ANTLR4 runtime +] + dependencies = [ ('Python', '3.9.5'), ('PyTorch', '1.10.0'), @@ -20,13 +24,13 @@ sanity_pip_check = True # omegaconf is required for esmfold (in addition to OpenFold-1.0.1) exts_list = [ - ('omegaconf', '2.2.3', { - 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], - }), ('antlr4-python3-runtime', '4.9.3', { 'modulename': 'antlr4', 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], }), + ('omegaconf', '2.2.3', { + 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], + }), ('fair-esm', version, { 'modulename': 'esm, esm.pretrained', 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], From 6030a7eb4eab256423c9c6bebc0cf338458a0f54 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 11 Dec 2022 10:56:58 +0000 Subject: [PATCH 5771/9987] switch libdeflate version in LibTIFF --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb index 6336e1de043..b2fb13f5ec3 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('XZ', '5.2.7'), ('jbigkit', '2.1'), ('zstd', '1.5.2'), - ('libdeflate', '1.14'), + ('libdeflate', '1.15'), ] configopts = "--enable-ld-version-script " From 369c2e71a1a0c317f5b11542651c460df04b6d6a Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 11 Dec 2022 11:28:42 +0000 Subject: [PATCH 5772/9987] Update easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb --- .../l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb index de86aeb5c08..386b12fc121 100644 --- a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb @@ -18,7 +18,10 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['58b95040df7383dc0413defb700d9893c194732474283cc4c8f144b00a68154b'] -builddependencies = [('binutils', '2.39')] +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] sanity_check_paths = { 'files': [ From b23acaa051a7497cdb395b95bf557a34b335badd Mon Sep 17 00:00:00 2001 From: robogast Date: Sun, 11 Dec 2022 18:53:56 +0100 Subject: [PATCH 5773/9987] adding easyconfigs: CUDA-12.0.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb | 24 +++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb new file mode 100644 index 00000000000..9b47dfcc571 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.0.0' +local_nv_version = '525.60.13' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '905e9b9516900839fb76064719db752439f38b8cb730b49335d8bd53ddfad392', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '117fe045c71668e45d41c6119b6f27875370c78e33fc56795b6fe014c796ec60', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'cd13e9c65d4c8f895a968706f46064d536be09f9706bce081cc864b7e4fa4544' +}] + +moduleclass = 'system' From 5831891309cc6d6dd967c04064cbddc33242d203 Mon Sep 17 00:00:00 2001 From: robogast Date: Sun, 11 Dec 2022 20:39:31 +0100 Subject: [PATCH 5774/9987] adding easyconfigs: NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb, UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb, GDRCopy-2.3-GCCcore-12.2.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb | 24 +++++++++ .../g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ .../NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 42 +++++++++++++++ ...-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb | 40 ++++++++++++++ 4 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb new file mode 100644 index 00000000000..9b47dfcc571 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.0.0' +local_nv_version = '525.60.13' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '905e9b9516900839fb76064719db752439f38b8cb730b49335d8bd53ddfad392', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '117fe045c71668e45d41c6119b6f27875370c78e33fc56795b6fe014c796ec60', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'cd13e9c65d4c8f895a968706f46064d536be09f9706bce081cc864b7e4fa4544' +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0fb6d9b4864 --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.3' + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib prefix=%(installdir)s" + +installopts = 'prefix=%(installdir)s' + +github_account = 'NVIDIA' +# This easyconfig only installs the library of GDRCopy. Please keep in mind +# that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] +install_cmd = "make lib_install" + +sanity_check_paths = { + 'files': ['lib/libgdrapi.so'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb new file mode 100644 index 00000000000..3270ad6f6e0 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -0,0 +1,42 @@ +name = 'NCCL' +version = '2.16.2' +versionsuffix = '-CUDA-%(cudaver)s' +easyblock = 'Tarball' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/nccl/v%(version)s/' +] +sources = ['%(namelower)s_%(version)s-1+cuda%(cudashortver)s_%(arch)s.txz'] +checksums = [{ + '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_x86_64.txz': + 'fb630e2d244cdc8cf3fe2cbe07cbf0a50a5213ba546edc717bdba5d5ac757b87', + '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_ppc64le.txz': + 'daac3b7de8d0091369cb59b59d011b494c2f16403c80478c15b97d88a9895651', + '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_aarch64.txz': + 'fb630e2d244cdc8cf3fe2cbe07cbf0a50a5213ba546edc717bdba5d5ac757b87', +}] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('CUDA', '12.0.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +sanity_check_paths = { + 'files': [ + 'include/nccl.h', 'lib/libnccl.%s' % SHLIB_EXT, 'lib/libnccl_static.a', 'lib/pkgconfig/nccl.pc' + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb new file mode 100644 index 00000000000..556fafb0685 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -0,0 +1,40 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.13.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['ucx-%(version)s.tar.gz'] +patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch'] +checksums = [ + {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('UCX', '1.13.1'), + ('CUDA', '12.0.0', '', SYSTEM), + ('GDRCopy', '2.3'), +] + + +moduleclass = 'lib' From 6282b28223ecb206f3a52e47fc234c53af234338 Mon Sep 17 00:00:00 2001 From: robogast Date: Sun, 11 Dec 2022 20:43:21 +0100 Subject: [PATCH 5775/9987] removed CUDA/12.0.0 from PR --- easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb | 24 --------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb deleted file mode 100644 index 9b47dfcc571..00000000000 --- a/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'CUDA' -version = '12.0.0' -local_nv_version = '525.60.13' - -homepage = 'https://developer.nvidia.com/cuda-toolkit' -description = """CUDA (formerly Compute Unified Device Architecture) is a parallel - computing platform and programming model created by NVIDIA and implemented by the - graphics processing units (GPUs) that they produce. CUDA gives developers access - to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" - -toolchain = SYSTEM - -source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] -sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] -checksums = [{ - 'cuda_%%(version)s_%s_linux.run' % local_nv_version: - '905e9b9516900839fb76064719db752439f38b8cb730b49335d8bd53ddfad392', - 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: - '117fe045c71668e45d41c6119b6f27875370c78e33fc56795b6fe014c796ec60', - 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: - 'cd13e9c65d4c8f895a968706f46064d536be09f9706bce081cc864b7e4fa4544' -}] - -moduleclass = 'system' From a3ac06d74a1e1f6b8c5a7a05298bfeb8895fc2cf Mon Sep 17 00:00:00 2001 From: Robert Jan Schlimbach Date: Sun, 11 Dec 2022 21:04:14 +0100 Subject: [PATCH 5776/9987] Moved easyblock var to top of file --- .../n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb index 3270ad6f6e0..dc192d2fe02 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -1,7 +1,8 @@ +easyblock = 'Tarball' + name = 'NCCL' version = '2.16.2' versionsuffix = '-CUDA-%(cudaver)s' -easyblock = 'Tarball' homepage = 'https://developer.nvidia.com/nccl' description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective From e3806345201bf320a2a7628a27b4f130855876e3 Mon Sep 17 00:00:00 2001 From: Victor Lopez Herrero Date: Mon, 12 Dec 2022 10:32:11 +0100 Subject: [PATCH 5777/9987] Apply suggestions from code review Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb | 6 +++--- easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb index bf0987b6dd2..fa248865fb6 100644 --- a/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb @@ -14,13 +14,13 @@ homepage = 'https://pm.bsc.es/dlb/' docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] toolchain = {'name': 'gompi', 'version': '2022a'} -builddependencies = [('Python', '3.10.4', '', ('GCCcore', '11.3.0-bare'))] +builddependencies = [('Python', '3.10.4', '-bare')] sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] -moduleclass = 'lib' - configopts = '--with-mpi' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb index aae046e6f0b..be30e500a7d 100644 --- a/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb @@ -14,13 +14,13 @@ homepage = 'https://pm.bsc.es/dlb/' docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] toolchain = {'name': 'iimpi', 'version': '2022a'} -builddependencies = [('Python', '3.10.4', '', ('GCCcore', '11.3.0-bare'))] +builddependencies = [('Python', '3.10.4', '-bare')] sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] -moduleclass = 'lib' - configopts = '--with-mpi' + +moduleclass = 'lib' From e7286c1f1e62b42941afbd742012d5a5291e9b8d Mon Sep 17 00:00:00 2001 From: Robert Jan Schlimbach Date: Mon, 12 Dec 2022 10:54:18 +0100 Subject: [PATCH 5778/9987] Update NCCL aarch64 checksum --- .../n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb index dc192d2fe02..ec551b3f239 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -20,7 +20,7 @@ checksums = [{ '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_ppc64le.txz': 'daac3b7de8d0091369cb59b59d011b494c2f16403c80478c15b97d88a9895651', '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_aarch64.txz': - 'fb630e2d244cdc8cf3fe2cbe07cbf0a50a5213ba546edc717bdba5d5ac757b87', + '738d22d216266cd039610d0b87e008fcbba8ec9a93a626b958be96583d8b8b8a', }] builddependencies = [('binutils', '2.39')] From d6296fb50b469f5d9641920bc4c8a0be406e7d42 Mon Sep 17 00:00:00 2001 From: Robert Jan Schlimbach Date: Mon, 12 Dec 2022 11:40:44 +0100 Subject: [PATCH 5779/9987] Revert NCCL ec back to github source --- .../NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 25 +++---------------- 1 file changed, 4 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb index ec551b3f239..22b2ed8966d 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -1,5 +1,3 @@ -easyblock = 'Tarball' - name = 'NCCL' version = '2.16.2' versionsuffix = '-CUDA-%(cudaver)s' @@ -10,18 +8,10 @@ communication primitives that are performance optimized for NVIDIA GPUs.""" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -source_urls = [ - 'https://developer.download.nvidia.com/compute/redist/nccl/v%(version)s/' -] -sources = ['%(namelower)s_%(version)s-1+cuda%(cudashortver)s_%(arch)s.txz'] -checksums = [{ - '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_x86_64.txz': - 'fb630e2d244cdc8cf3fe2cbe07cbf0a50a5213ba546edc717bdba5d5ac757b87', - '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_ppc64le.txz': - 'daac3b7de8d0091369cb59b59d011b494c2f16403c80478c15b97d88a9895651', - '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_aarch64.txz': - '738d22d216266cd039610d0b87e008fcbba8ec9a93a626b958be96583d8b8b8a', -}] +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['7f7c738511a8876403fc574d13d48e7c250d934d755598d82e14bab12236fc64'] builddependencies = [('binutils', '2.39')] @@ -33,11 +23,4 @@ dependencies = [ # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] -sanity_check_paths = { - 'files': [ - 'include/nccl.h', 'lib/libnccl.%s' % SHLIB_EXT, 'lib/libnccl_static.a', 'lib/pkgconfig/nccl.pc' - ], - 'dirs': [], -} - moduleclass = 'lib' From f3762bb5ab9a385ed75b33c42e5c13b92856cfac Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Dec 2022 10:54:44 +0000 Subject: [PATCH 5780/9987] adding easyconfigs: SCOTCH-7.0.1-iimpi-2022a.eb --- .../s/SCOTCH/SCOTCH-7.0.1-iimpi-2022a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-iimpi-2022a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-iimpi-2022a.eb new file mode 100644 index 00000000000..f9abb478142 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-iimpi-2022a.eb @@ -0,0 +1,24 @@ +name = 'SCOTCH' +version = '7.0.1' + +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['0618e9bc33c02172ea7351600fce4fccd32fe00b3359c4aabb5e415f17c06fed'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +moduleclass = 'math' From 6ea0eb15c898b96e4b88e0ffb466c4b5eb94e4c8 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Mon, 12 Dec 2022 12:24:42 +0100 Subject: [PATCH 5781/9987] Add Score-P v8 + dependencies --- .../c/CubeLib/CubeLib-4.8-GCCcore-11.3.0.eb | 53 +++++++++++++++++ .../CubeWriter-4.8-GCCcore-11.3.0.eb | 53 +++++++++++++++++ .../o/OPARI2/OPARI2-2.0.7-GCCcore-11.3.0.eb | 44 ++++++++++++++ .../o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb | 50 ++++++++++++++++ .../p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb | 49 +++++++++++++++ .../s/Score-P/Score-P-8.0-gompi-2022a.eb | 59 +++++++++++++++++++ 6 files changed, 308 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a9337f666c2 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.3.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.8' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['171c93ac5afd6bc74c50a9a58efdaf8589ff5cc1e5bd773ebdfb2347b77e2f68'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..79fbfeebdd1 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.8' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(versions)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['73c7f9e9681ee45d71943b66c01cfe675b426e4816e751ed2e0b670563ca4cf3'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c672c06de72 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.7' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e302a4cc265eb2a4aa27c16a90eabd9e1e58cb02a191dd1c4d86f9a0df128715'] + +builddependencies = [ + ('binutils', '2.38'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..61eba75f5f0 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,50 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '3.0.2' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ae3a7ad83055d8f873738fee5031470652d31b9bcbf223dd556aea41f5f62303'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.7', '-tools'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..209e88d199b --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +## +# Author: Robert Mijakovic +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.0.0' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['799dcc317a47da96beaeed445812ecb6ae49df7c0504a4569797c1f7d74c4fd2'] + +builddependencies = [ + ('binutils', '2.38'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb new file mode 100644 index 00000000000..efea7c597ce --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb @@ -0,0 +1,59 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '8.0-rc1' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['d5975e69a594fff4982701f5181b4825386a238a95df68a0d5c1e1b62480add7'] + +dependencies = [ + ('CubeLib', '4.8'), + ('CubeWriter', '4.8'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.2'), + # Hardware counter support (optional): + ('PAPI', '7.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From f368e78ecd6e4e539d46cbe82e7e869edf708416 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 12 Dec 2022 12:29:52 +0100 Subject: [PATCH 5782/9987] Cleaning --- .../c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb | 64 ------------------- .../c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb | 54 ---------------- .../CubeWriter-4.7-GCCcore-11.3.0.eb | 53 --------------- .../o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb | 44 ------------- .../s/Score-P/Score-P-7.1-gompi-2022a.eb | 59 ----------------- 5 files changed, 274 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb deleted file mode 100644 index 790b55187fd..00000000000 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb +++ /dev/null @@ -1,64 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany -# Authors:: Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_Score_minus_P' - -name = 'CubeGUI' -version = '4.7' - -homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' -description = """ - Cube, which is used as performance report explorer for Scalasca and Score-P, - is a generic tool for displaying a multi-dimensional performance space - consisting of the dimensions (i) performance metric, (ii) call path, and - (iii) system resource. Each dimension can be represented as a tree, where - non-leaf nodes of the tree can be collapsed or expanded to achieve the - desired level of granularity. - - This module provides the Cube graphical report explorer. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - ('CubeGUI-4.7_missing_compile_file.patch', 1), -] -checksums = [ - '103fe00fa9846685746ce56231f64d850764a87737dc0407c9d0a24037590f68', # cubegui-4.7.tar.gz - '0a3072decf1d4b9f8544331647bb160723733f3579b9d8c64906c45fcf4ce669', # CubeGUI-4.7_missing_compile_file.patch -] - -preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.38'), - ('Autotools', '20220317'), - ('CubeLib', '4.7'), -] - -dependencies = [ - ('Qt5', '5.15.5'), -] - -configopts = [ - 'CXX="g++" --with-qt=$EBROOTQT5/bin ', -] - -sanity_check_paths = { - 'files': ['bin/cube', 'bin/cubegui-config', - 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], - 'dirs': ['include/cubegui', 'lib/cube-plugins'], -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb deleted file mode 100644 index d48598c1cf5..00000000000 --- a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb +++ /dev/null @@ -1,54 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany -# Authors:: Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_Score_minus_P' - -name = 'CubeLib' -version = '4.7' - -homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' -description = """ - Cube, which is used as performance report explorer for Scalasca and Score-P, - is a generic tool for displaying a multi-dimensional performance space - consisting of the dimensions (i) performance metric, (ii) call path, and - (iii) system resource. Each dimension can be represented as a tree, where - non-leaf nodes of the tree can be collapsed or expanded to achieve the - desired level of granularity. - - This module provides the Cube general purpose C++ library component and - command-line tools. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e44352c80a25a49b0fa0748792ccc9f1be31300a96c32de982b92477a8740938'] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.38'), - ('pkgconf', '1.8.0'), -] - -dependencies = [ - ('zlib', '1.2.12'), -] - -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/cubelib-config', - 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], - 'dirs': ['include/cubelib'], -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb deleted file mode 100644 index 6649e72f03e..00000000000 --- a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb +++ /dev/null @@ -1,53 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany -# Authors:: Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -easyblock = 'EB_Score_minus_P' - -name = 'CubeWriter' -version = '4.7' - -homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' -description = """ - Cube, which is used as performance report explorer for Scalasca and Score-P, - is a generic tool for displaying a multi-dimensional performance space - consisting of the dimensions (i) performance metric, (ii) call path, and - (iii) system resource. Each dimension can be represented as a tree, where - non-leaf nodes of the tree can be collapsed or expanded to achieve the - desired level of granularity. - - This module provides the Cube high-performance C writer library component. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] -sources = ['cubew-%(version)s.tar.gz'] -checksums = ['a7c7fca13e6cb252f08d4380223d7c56a8e86a67de147bcc0279ebb849c884a5'] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.38'), - ('pkgconf', '1.8.0'), -] - -dependencies = [ - ('zlib', '1.2.12'), -] - -configopts = '--enable-shared' - -sanity_check_paths = { - 'files': ['bin/cubew-config', - 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], - 'dirs': ['include/cubew'], -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb deleted file mode 100644 index acc02a8fc51..00000000000 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -# # -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany -# Authors:: Bernd Mohr -# Markus Geimer -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -# # - -easyblock = 'ConfigureMake' - -name = 'OPARI2' -version = '2.0.6' - -homepage = 'https://www.score-p.org' -description = """ - OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a - source-to-source instrumentation tool for OpenMP and hybrid codes. - It surrounds OpenMP directives and runtime library calls with calls - to the POMP2 measurement interface. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['55972289ce66080bb48622110c3189a36e88a12917635f049b37685b9d3bbcb0'] - -builddependencies = [ - ('binutils', '2.38'), -] - - -sanity_check_paths = { - 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], - 'dirs': [], -} - -sanity_check_commands = ['opari2-config --help'] - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb deleted file mode 100644 index 773bcc6594b..00000000000 --- a/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb +++ /dev/null @@ -1,59 +0,0 @@ -## -# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany -# Copyright 2020 TU Dresden, Germany -# Authors:: -# * Bernd Mohr -# * Markus Geimer -# * Alexander Grund -# * Robert Mijakovic -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -name = 'Score-P' -version = '7.1' - -homepage = 'https://www.score-p.org' -description = """ - The Score-P measurement infrastructure is a highly scalable and easy-to-use - tool suite for profiling, event tracing, and online analysis of HPC - applications. -""" - -toolchain = {'name': 'gompi', 'version': '2022a'} - -source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] -sources = ['scorep-%(version)s.tar.gz'] -checksums = ['98dea497982001fb82da3429ca55669b2917a0858c71abe2cfe7cd113381f1f7'] - -dependencies = [ - ('CubeLib', '4.7'), - ('CubeWriter', '4.7'), - ('libunwind', '1.6.2'), - ('OPARI2', '2.0.6'), - ('OTF2', '3.0'), - # Hardware counter support (optional): - ('PAPI', '6.0.0.1'), - # PDT source-to-source instrumentation support (optional): - ('PDT', '3.25.1'), -] - -configopts = '--enable-shared' - -local_adapters = [ - 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' -] -sanity_check_paths = { - 'files': - ['bin/scorep', 'include/scorep/SCOREP_User.h'] + - ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], - 'dirs': [], -} -sanity_check_commands = ['scorep-config --help'] - -# Ensure that local metric documentation is found by CubeGUI -modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} - -moduleclass = 'perf' From ca0d663962a7c3cf405424cfeed062f9defe7c06 Mon Sep 17 00:00:00 2001 From: alberta Date: Mon, 12 Dec 2022 12:53:05 +0100 Subject: [PATCH 5783/9987] adding easyconfigs: humann-3.6-foss-2022a.eb --- .../h/humann/humann-3.6-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb b/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb new file mode 100644 index 00000000000..8f511fe8f85 --- /dev/null +++ b/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb @@ -0,0 +1,39 @@ +# Humann +easyblock = 'PythonBundle' + +name = 'humann' +version = '3.6' + +homepage = 'http://huttenhower.sph.harvard.edu/humann' + +description ="""HUMAnN v3 is a pipeline for efficiently + and accurately determining the coverage and abundance + of microbial pathways in a community from metagenomic data. +Sequencing a metagenome typically produces millions + of short DNA/RNA reads. This process, referred + to as functional profiling, aims to describe the metabolic potential + of a microbial community and its members. More generally, + functional profiling answers the question: + What are the microbes in my community-of-interest doing (or capable of doing)?""" + +toolchain = {'name': 'foss', 'version': '2022a'} + + +dependencies = { + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +} + + +exts_list = [ + (name, version, { + 'checksums': ['addce81db58bacfdd5465423455d25e385aa8dd14349253c3a7054bf7d3747dc'], + }), + +] + + +use_pip = True +sanity_pip_check = True + + From 3848fcc29388e3ad1c484aac8be2d9353c94c550 Mon Sep 17 00:00:00 2001 From: alberta Date: Mon, 12 Dec 2022 13:24:08 +0100 Subject: [PATCH 5784/9987] Fix files --- easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb b/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb index 8f511fe8f85..1e8577eb47d 100644 --- a/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb +++ b/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb @@ -6,7 +6,7 @@ version = '3.6' homepage = 'http://huttenhower.sph.harvard.edu/humann' -description ="""HUMAnN v3 is a pipeline for efficiently +description = """HUMAnN v3 is a pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data. Sequencing a metagenome typically produces millions @@ -35,5 +35,3 @@ exts_list = [ use_pip = True sanity_pip_check = True - - From 30c688a809bd854a4a1a93bf5cfd9ab1b7e6044d Mon Sep 17 00:00:00 2001 From: robogast Date: Mon, 12 Dec 2022 13:34:07 +0100 Subject: [PATCH 5785/9987] removed sm_35, updated GDRCopy to match the previous ec --- .../g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb | 14 +++++++------- .../NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 2 +- .../UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb | 1 + 3 files changed, 9 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb index 0fb6d9b4864..c9c58812cf5 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb @@ -9,6 +9,7 @@ description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect R toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} +github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] @@ -19,12 +20,6 @@ builddependencies = [ ('pkgconf', '1.9.3'), ] -prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found -buildopts = "config lib prefix=%(installdir)s" - -installopts = 'prefix=%(installdir)s' - -github_account = 'NVIDIA' # This easyconfig only installs the library of GDRCopy. Please keep in mind # that GDRCopy also needs the following kernel modules at runtime: # @@ -42,10 +37,15 @@ github_account = 'NVIDIA' # requirements to build this easyconfig, as they are not needed for the build. skipsteps = ['configure'] + +local_envopts = "prefix=%(installdir)s" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib %s" % local_envopts install_cmd = "make lib_install" +installopts = local_envopts sanity_check_paths = { - 'files': ['lib/libgdrapi.so'], + 'files': ['lib/libgdrapi.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb index 22b2ed8966d..cd576dcb0e7 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -21,6 +21,6 @@ dependencies = [ ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) -cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] +cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb index 556fafb0685..9212315db27 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -29,6 +29,7 @@ builddependencies = [ ('Autotools', '20220317'), ('pkgconf', '1.9.3'), ] + dependencies = [ ('zlib', '1.2.12'), ('UCX', '1.13.1'), From 73837ff17c277d8690e7e59ae6f709b62dfafd48 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Mon, 12 Dec 2022 13:34:27 +0100 Subject: [PATCH 5786/9987] Add CubeGUI --- .../c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb | 64 +++++++++++++++++++ ...=> CubeGUI-4.8_missing_compile_file.patch} | 8 +-- 2 files changed, 68 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb rename easybuild/easyconfigs/c/CubeGUI/{CubeGUI-4.7_missing_compile_file.patch => CubeGUI-4.8_missing_compile_file.patch} (97%) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..90d43bac741 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb @@ -0,0 +1,64 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeGUI' +version = '4.8' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube graphical report explorer. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('CubeGUI-4.8_missing_compile_file.patch', 1), +] +checksums = [ + '1df8fcaea95323e7eaf0cc010784a41243532c2123a27ce93cb7e3241557ff76', # cubegui-4.8.tar.gz + '487697669f6a9a3455fabfdb65d720699070986776c465830ad417942e25e2dc', # CubeGUI-4.8_missing_compile_file.patch +] + +preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('CubeLib', '4.8'), +] + +dependencies = [ + ('Qt5', '5.15.5'), +] + +configopts = [ + 'CXX="g++" --with-qt=$EBROOTQT5/bin ', +] + +sanity_check_paths = { + 'files': ['bin/cube', 'bin/cubegui-config', + 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], + 'dirs': ['include/cubegui', 'lib/cube-plugins'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch similarity index 97% rename from easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch rename to easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch index 7b08da87205..d7a92c4db95 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch @@ -1,11 +1,11 @@ -# This patch adds the "build-config/compile" file that is missing in v4.7. +# This patch adds the "build-config/compile" file that is missing in v4.8 # The file is copied "as is" from CubeGUI v4.6. # # Author: maxim-masterov (SURF) -diff -Nru cubegui-4.7.orig/build-config/compile cubegui-4.7/build-config/compile ---- cubegui-4.7.orig/build-config/compile 1970-01-01 01:00:00.000000000 +0100 -+++ cubegui-4.7/build-config/compile 2022-08-09 11:33:06.528166000 +0200 +diff -Nru cubegui-4.8.orig/build-config/compile cubegui-4.8/build-config/compile +--- cubegui-4.8.orig/build-config/compile 1970-01-01 01:00:00.000000000 +0100 ++++ cubegui-4.8/build-config/compile 2022-12-12 13:16:45.979205634 +0100 @@ -0,0 +1,347 @@ +#! /bin/sh +# Wrapper for compilers which do not understand '-c -o'. From 615716b317d787bada42e7819dd51c3953d9eaae Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 12 Dec 2022 14:32:05 +0100 Subject: [PATCH 5787/9987] Rename file --- ...{Score-P-8.0-gompi-2022a.eb => Score-P-8.0-rc1-gompi-2022a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/Score-P/{Score-P-8.0-gompi-2022a.eb => Score-P-8.0-rc1-gompi-2022a.eb} (100%) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-rc1-gompi-2022a.eb similarity index 100% rename from easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb rename to easybuild/easyconfigs/s/Score-P/Score-P-8.0-rc1-gompi-2022a.eb From 86f9811903672eb61735965ac96eeaa3a9560869 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 14:15:58 +0000 Subject: [PATCH 5788/9987] The new g2lib moved to github and uses cmake now --- .../g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..539118743c8 --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +name = 'g2clib' +version = '1.7.0' +easyblock = 'CMakeMake' + +homepage = 'https://github.com/NOAA-EMC/NCEPLIBS-g2c' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/NOAA-EMC/NCEPLIBS-g2c/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['73afba9da382fed73ed8692d77fa037bb313280879cd4012a5e5697dccf55175'] + +builddependencies = [('binutils', '2.38'), + ('CMake', '3.23.1'), + ] + +dependencies = [ + ('JasPer', '2.0.33'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), +] + +parallel = 8 + +sanity_check_paths = { + 'files': ['lib/libg2c.so'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' From b83c31c48f4040096aa023f0bf53ca5345506e96 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 12 Dec 2022 15:21:31 +0100 Subject: [PATCH 5789/9987] adding easyconfigs: QGIS-3.28.1-foss-2021b.eb, GRASS-8.2.0-foss-2021b.eb, Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb and patches: QGIS-3.28.1_fix-SIP-macro.patch, GRASS-8.2.0_GCC_ldlibs.patch, Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch, Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch, Qt5Webkit-5.212.0-alpha4_fix_python_path.patch, Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch --- .../attrdict3-2.0.2-GCCcore-11.2.0.eb | 26 ++++ .../e/exiv2/exiv2-0.27.5-GCCcore-11.2.0.eb | 33 +++++ .../f/FreeXL/FreeXL-1.0.6-GCCcore-11.2.0.eb | 30 ++++ .../g/GRASS/GRASS-8.2.0-foss-2021b.eb | 102 ++++++++++++++ .../g/GRASS/GRASS-8.2.0_GCC_ldlibs.patch | 15 ++ .../l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb | 35 +++++ .../libspatialite-5.0.1-GCC-11.2.0.eb | 40 ++++++ .../m/minizip/minizip-1.1-GCCcore-11.2.0.eb | 39 ++++++ .../q/QCA/QCA-2.3.5-GCCcore-11.2.0.eb | 39 ++++++ .../q/QGIS/QGIS-3.28.1-foss-2021b.eb | 75 ++++++++++ .../q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch | 21 +++ .../QScintilla-2.11.6-GCCcore-11.2.0.eb | 33 +++++ ...Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb | 71 ++++++++++ ....0-alpha4_dont_use_multiarch_lib_dir.patch | 26 ++++ ...fix_deprecated_encoding_in_json.load.patch | 15 ++ ...ebkit-5.212.0-alpha4_fix_python_path.patch | 66 +++++++++ ..._use_CXX_true_instead_of_TRUE_define.patch | 128 ++++++++++++++++++ .../QtKeychain-0.13.2-GCCcore-11.2.0.eb | 36 +++++ .../q/Qwt/Qwt-6.2.0-GCCcore-11.2.0.eb | 39 ++++++ .../w/wxPython/wxPython-4.2.0-foss-2021b.eb | 48 +++++++ .../w/wxWidgets/wxWidgets-3.2.0-GCC-11.2.0.eb | 71 ++++++++++ 21 files changed, 988 insertions(+) create mode 100644 easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/e/exiv2/exiv2-0.27.5-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GRASS/GRASS-8.2.0_GCC_ldlibs.patch create mode 100644 easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-5.0.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/q/QCA/QCA-2.3.5-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.11.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_python_path.patch create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch create mode 100644 easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..67c44f60b2a --- /dev/null +++ b/easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'attrdict3' +version = '2.0.2' + +homepage = 'https://github.com/pirofti/AttrDict3' +description = """AttrDict is a Python library that provides mapping objects that allow their elements + to be accessed both as keys and as attributes.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'attrdict', + 'checksums': ['004c171ca1120cc1755701db99d7fa4944afb1e68950434efdaa542513335fe8'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/exiv2/exiv2-0.27.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/exiv2/exiv2-0.27.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4af59f56c33 --- /dev/null +++ b/easybuild/easyconfigs/e/exiv2/exiv2-0.27.5-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'exiv2' +version = '0.27.5' + +homepage = 'https://exiv2.org' +description = "Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'Exiv2' +source_urls = [GITHUB_RELEASE] +sources = ['%(name)s-%(version)s-Source.tar.gz'] +checksums = ['35a58618ab236a901ca4928b0ad8b31007ebdc0386d904409d825024e45ea6e2'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('expat', '2.4.1'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/exiv2', 'lib/libexiv2.%s' % SHLIB_EXT, 'lib/libexiv2-xmp.a', 'lib/pkgconfig/exiv2.pc'], + 'dirs': ['include/exiv2', 'lib/cmake'], +} + +sanity_check_commands = ["exiv2 --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..6bc2457695b --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.6-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FreeXL' +version = '1.0.6' + +homepage = 'https://www.gaia-gis.it/fossil/freexl/index' + +description = """ +FreeXL is an open source library to extract valid data from within an +Excel (.xls) spreadsheet. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.gaia-gis.it/gaia-sins'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3de8b57a3d130cb2881ea52d3aa9ce1feedb1b57b7daa4eb37f751404f90fc22'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] + +sanity_check_paths = { + 'files': ['lib/libfreexl.a'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb b/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb new file mode 100644 index 00000000000..890e801c909 --- /dev/null +++ b/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb @@ -0,0 +1,102 @@ +easyblock = 'ConfigureMake' + +name = 'GRASS' +version = '8.2.0' + +homepage = "https://grass.osgeo.org" +description = """The Geographic Resources Analysis Support System - used + for geospatial data management and analysis, image processing, + graphics and maps production, spatial modeling, and visualization""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://grass.osgeo.org/grass%s/source' % ''.join(version.split('.')[:2])] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_GCC_ldlibs.patch'] +checksums = [ + {'grass-8.2.0.tar.gz': '621c3304a563be19c0220ae28f931a5e9ba74a53218c5556cd3f7fbfcca33a80'}, + {'GRASS-8.2.0_GCC_ldlibs.patch': '771edf64c583218d28529c53845218a6ab774179999b9b92edb4de32954edc49'}, +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('gettext', '0.21'), + ('Python', '3.9.6'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('netCDF', '4.8.1'), + ('GDAL', '3.3.2'), + ('libspatialite', '5.0.1'), + ('GEOS', '3.9.1'), + ('PROJ', '8.1.0'), + ('SQLite', '3.36'), + ('freetype', '2.11.0'), + ('FFmpeg', '4.3.2'), + ('LibTIFF', '4.3.0'), + ('cairo', '1.16.0'), + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('wxPython', '4.2.0'), + ('zstd', '1.5.0'), +] + +preconfigopts = "sed -e 's/-lblas/$LIBBLAS/g' -e 's/-llapack/$LIBLAPACK/g' -i configure && " + +configopts = '--enable-64bit ' +configopts += '--enable-largefile=yes ' +configopts += '--with-cairo=yes ' +configopts += '--with-cxx ' +configopts += '--with-ffmpeg --with-ffmpeg-libs=$EBROOTFFMPEG/lib --with-ffmpeg-includes=$EBROOTFFMPEG/include/* ' +configopts += '--with-fftw --with-fftw-libs=$EBROOTFFTW/lib --with-fftw-includes=$EBROOTFFTW/include ' +configopts += '--with-freetype ' +configopts += '--with-freetype-libs=$EBROOTFREETYPE/lib --with-freetype-includes=$EBROOTFREETYPE/include ' +configopts += '--with-geos=$EBROOTGEOS/bin/geos-config ' +configopts += '--without-glw ' +configopts += '--with-lapack ' +configopts += '--with-lapack-lib=$LAPACK_LIB_DIR ' +configopts += '--with-lapack-includes=$LAPACK_INC_DIR ' +configopts += '--with-blas ' +configopts += '--with-blas-lib=$BLAS_LIB_DIR ' +configopts += '--with-blas-includes=$BLAS_INC_DIR ' +configopts += '--with-netcdf=$EBROOTNETCDF/bin/nc-config ' +configopts += '--without-odbc ' +configopts += '--with-opengl ' +configopts += '--with-openmp ' +configopts += '--with-png ' +configopts += '--with-png-libs="$EBROOTLIBPNG/lib $EBROOTZLIB/lib" --with-png-includes=$EBROOTLIBPNG/include ' +configopts += '--without-postgres ' +configopts += '--with-proj --with-proj-libs=$EBROOTPROJ/lib ' +configopts += '--with-proj-includes=$EBROOTPROJ/include --with-proj-share=$EBROOTPROJ/share/proj ' +configopts += '--with-pthread ' +configopts += '--with-python ' +configopts += '--with-readline ' +configopts += '--with-readline-libs=$EBROOTLIBREADLINE/lib --with-readline-includes=$EBROOTLIBREADLINE/include ' +configopts += '--with-spatialite ' +configopts += '--with-sqlite ' +configopts += '--with-tiff-libs=$EBROOTLIBTIFF/lib --with-tiff-includes=$EBROOTLIBTIFF/include ' +configopts += '--with-wxwidgets=$EBROOTWXWIDGET/bin/wx-config ' +configopts += '--with-x ' +configopts += '--with-zlib --with-zlib-libs=$EBROOTZLIB/lib --with-zlib-includes=$EBROOTZLIB/include ' +configopts += '--with-bzlib --with-bzlib-libs=$EBROOTBZIP2/lib --with-ibzlib-includes=$EBROOTBZIP2/include ' +configopts += '--with-zstd --with-zstd-libs=$EBROOTZSTD/lib --with-zstd-includes=$EBROOTZSTD/include ' + +postinstallcmds = [ + 'ln -s grass%(version_major)s%(version_minor)s %(installdir)s/grass%(version_major)s', +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0_GCC_ldlibs.patch b/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0_GCC_ldlibs.patch new file mode 100644 index 00000000000..d8af9023033 --- /dev/null +++ b/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0_GCC_ldlibs.patch @@ -0,0 +1,15 @@ +Use mathlib and threads in the LDFLAGS + +Åke Sandgren, 2022-12-07 +diff -ru grass-8.2.0.orig/configure grass-8.2.0/configure +--- grass-8.2.0.orig/configure 2022-06-03 15:27:06.000000000 +0200 ++++ grass-8.2.0/configure 2022-12-07 14:23:37.234003038 +0100 +@@ -4031,7 +4031,7 @@ + SHLIB_LD_FLAGS="-Wl,-soname,\$(notdir \$@)" + SHLIB_SUFFIX=".so" + SHLIB_LD="${CC} -shared" +- LDFLAGS="-Wl,--export-dynamic" ++ LDFLAGS="-pthread -lm -Wl,--export-dynamic" + LD_SEARCH_FLAGS='-Wl,-rpath-link,${LIB_RUNTIME_DIR} -Wl,-rpath,${INST_DIR}/lib' + LD_LIBRARY_PATH_VAR="LD_LIBRARY_PATH" + ;; diff --git a/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..76f469f32a9 --- /dev/null +++ b/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'librttopo' +version = '1.1.0' + +homepage = 'https://git.osgeo.org/gitea/rttopo/librttopo' +description = """The RT Topology Library exposes an API to create and +manage standard (ISO 13249 aka SQL/MM) topologies using user-provided +data stores.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://git.osgeo.org/gitea/rttopo/librttopo/archive'] +sources = [SOURCE_TAR_GZ] +checksums = ['2e2fcabb48193a712a6c76ac9a9be2a53f82e32f91a2bc834d9f1b4fa9cd879f'] + +builddependencies = [ + ('Autotools', '20210726'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('GEOS', '3.9.1'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/librttopo.h', 'lib/librttopo.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' + diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-5.0.1-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-5.0.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..b908b0db7f9 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-5.0.1-GCC-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '5.0.1' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = """SpatiaLite is an open source library intended to extend the SQLite core to support + fully fledged Spatial SQL capabilities.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.gaia-gis.it/gaia-sins/libspatialite-sources/'] +sources = [SOURCE_TAR_GZ] +checksums = ['eecbc94311c78012d059ebc0fae86ea5ef6eecb13303e6e82b3753c1b3409e98'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('minizip', '1.1'), + ('FreeXL', '1.0.6'), + ('GEOS', '3.9.1'), + ('SQLite', '3.36'), + ('PROJ', '8.1.0'), + ('libxml2', '2.9.10'), + ('librttopo', '1.1.0'), +] + +configopts = '--disable-geosadvanced' + +sanity_check_paths = { + 'files': ['include/spatialite.h', 'lib/libspatialite.a', 'lib/libspatialite.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2ccef97d5ce --- /dev/null +++ b/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'minizip' +version = '1.1' +_zlib_version = '1.2.11' + +homepage = 'https://www.winimage.com/zLibDll/minizip.html' +description = "Mini zip and unzip based on zlib" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +# This exists in the contrib section of zlib and since it depends on +# zlib the sources will already have been downloaded +sources = [ + {'filename': 'zlib-%s.tar.gz' % _zlib_version, 'alt_location': 'zlib'}, +] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('zlib', _zlib_version), +] + +start_dir = 'contrib/minizip' + +preconfigopts = 'autoreconf -i && ' + +sanity_check_paths = { + 'files': ['include/minizip/unzip.h', 'lib/libminizip.a', 'lib/libminizip.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' + diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QCA/QCA-2.3.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4261cd91c3a --- /dev/null +++ b/easybuild/easyconfigs/q/QCA/QCA-2.3.5-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'QCA' +version = '2.3.5' + +homepage = 'https://userbase.kde.org/QCA' +description = """Taking a hint from the similarly-named Java Cryptography Architecture, + QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes + and conventions. QCA separates the API from the implementation, using plugins known as + Providers. The advantage of this model is to allow applications to avoid linking to or + explicitly depending on any particular cryptographic library. This allows one to easily + change or upgrade crypto implementations without even needing to recompile the + application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://download.kde.org/stable/qca/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['91f7d916ab3692bf5991f0a553bf8153161bfdda14bd005d480a2b4e384362e8'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1') +] +dependencies = [ + ('Qt5', '5.15.2') +] + +configopts = "-DQT5_BUILD=true" + +sanity_check_paths = { + 'files': ['bin/qcatool-qt5', 'lib/libqca-qt5.%s' % SHLIB_EXT, 'lib/pkgconfig/qca2-qt5.pc'], + 'dirs': ['include/Qca-qt5', 'lib/cmake/Qca-qt5', 'share/man'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb new file mode 100644 index 00000000000..eaac6f93058 --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb @@ -0,0 +1,75 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'QGIS' +version = '3.28.1' + +homepage = 'http://www.qgis.org/' +description = "QGIS is a user friendly Open Source Geographic Information System (GIS)" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'cstd': 'gnu++11'} + +source_urls = ['http://qgis.org/downloads/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['QGIS-%(version)s_fix-SIP-macro.patch'] +checksums = [ + {'qgis-3.28.1.tar.bz2': '09015bb68c45556ffe9d480272d24048e6276a6bf1c010fd77beae64329ff674'}, + {'QGIS-3.28.1_fix-SIP-macro.patch': '5da6bcd380e46969efa7718d8aec79a2548616c278853f29ed07d745fd5b043f'}, +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Qt5', '5.15.2'), + ('Qt5Webkit', '5.212.0-alpha4'), + ('PyQt5', '5.15.4'), + ('PROJ', '8.1.0'), + ('GEOS', '3.9.1'), + ('SQLite', '3.36'), + ('libspatialite', '5.0.1'), + ('libspatialindex', '1.9.3'), + ('GDAL', '3.3.2'), + ('Qwt', '6.2.0'), + ('expat', '2.4.1'), + ('QCA', '2.3.5'), + # QScintilla must be listed after PyQt5 due to Python bindings 'overriding' those of PyQt5 + ('QScintilla', '2.11.6'), + ('GSL', '2.7'), + ('libzip', '1.7.3'), + ('QtKeychain', '0.13.2'), + ('ICU', '69.1'), + ('PostgreSQL', '13.4'), + ('GRASS', '8.2.0'), + ('protobuf', '3.17.3'), + ('exiv2', '0.27.5'), +] + +# specify locations that CMake can't figure out correctly +_copts = [ + "-DCMAKE_PREFIX_PATH=$EBROOTQT", + "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA/lib/libqscintilla2_qt5.%s" % SHLIB_EXT, + "-DQt5WebKit_DIR=$EBROOTQT5WEBKIT/lib64/cmake/Qt5WebKit", + "-DQt5WebKitWidgets_DIR=$EBROOTQT5WEBKIT/lib64/cmake/Qt5WebKitWidgets", + "-DPYQT5_SIP_DIR=$EBROOTPYQT5/share/sip", + "-DQSCI_SIP_DIR=$EBROOTQSCINTILLA/share/sip/PyQt5", + "-DGRASS_PREFIX8=$EBROOTGRASS/grass8", +] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['bin/qgis', 'bin/qgis_bench', 'lib/libqgis_analysis.%s' % SHLIB_EXT, + 'lib/libqgis_app.%s' % SHLIB_EXT, 'lib/libqgis_core.%s' % SHLIB_EXT, 'lib/libqgis_gui.%s' % SHLIB_EXT, + 'lib/libqgis_native.%s' % SHLIB_EXT, 'lib/libqgispython.%s' % SHLIB_EXT], + 'dirs': ['include/qgis', 'man', 'share/qgis'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch new file mode 100644 index 00000000000..bae12be4ff3 --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch @@ -0,0 +1,21 @@ +diff -ru qgis-3.28.1.orig/cmake/SIPMacros.cmake qgis-3.28.1/cmake/SIPMacros.cmake +--- qgis-3.28.1.orig/cmake/SIPMacros.cmake 2022-11-18 13:10:21.000000000 +0100 ++++ qgis-3.28.1/cmake/SIPMacros.cmake 2022-12-09 08:14:33.475615182 +0100 +@@ -101,7 +101,7 @@ + ENDIF( ${CONCAT_NUM} LESS ${SIP_CONCAT_PARTS} ) + ENDFOREACH(CONCAT_NUM RANGE 0 ${SIP_CONCAT_PARTS} ) + +- SET(SIPCMD ${SIP_BUILD_EXECUTABLE} --no-protected-is-public --pep484-pyi --no-make --concatenate=${SIP_CONCAT_PARTS} --qmake=${QMAKE_EXECUTABLE} --include-dir=${CMAKE_CURRENT_BINARY_DIR} --include-dir=${PYQT5_SIP_DIR} ${SIP_BUILD_EXTRA_OPTIONS}) ++ SET(SIPCMD ${SIP_BUILD_EXECUTABLE} --no-protected-is-public --pep484-pyi --no-make --concatenate=${SIP_CONCAT_PARTS} --qmake=${QMAKE_EXECUTABLE} --include-dir=${CMAKE_CURRENT_BINARY_DIR} --include-dir=${PYQT5_SIP_DIR} --include-dir=$ENV{EBROOTPYQT5}/share/sip --include-dir=$ENV{EBROOTQSCINTILLA}/share/sip/PyQt5 ${SIP_BUILD_EXTRA_OPTIONS}) + + ADD_CUSTOM_COMMAND( + OUTPUT ${_sip_output_files} +@@ -140,7 +140,7 @@ + ENDIF( ${CONCAT_NUM} LESS ${SIP_CONCAT_PARTS} ) + ENDFOREACH(CONCAT_NUM RANGE 0 ${SIP_CONCAT_PARTS} ) + +- SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} -I ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} ${_configured_module_sip}) ++ SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} -I ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} --include-dir=$ENV{EBROOTPYQT5}/share/sip --include-dir=$ENV{EBROOTQSCINTILLA}/share/sip/PyQt5 ${_configured_module_sip}) + ADD_CUSTOM_COMMAND( + OUTPUT ${_sip_output_files} + COMMAND ${CMAKE_COMMAND} -E echo ${message} diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.11.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.11.6-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..65d4b96bf10 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.11.6-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +name = 'QScintilla' +version = '2.11.6' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://www.riverbankcomputing.com/static/Downloads/QScintilla/%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['QScintilla-2.11.2_fix-link-python-bindings.patch'] +checksums = [ + {'QScintilla-2.11.6.tar.gz': 'e7346057db47d2fb384467fafccfcb13aa0741373c5d593bc72b55b2f0dd20a7'}, + {'QScintilla-2.11.2_fix-link-python-bindings.patch': + '6296efa69ce9448e43dda80573cb0a70fee72462157d3d6fc194fe61fd477803'}, +] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('PyQt5', '5.15.4'), +] + +prebuildopts = 'export CPATH=$EBROOTQT5/include/QtWidgets:$EBROOTQT5/include/QtPrintSupport:$CPATH && ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9c4fab966b4 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb @@ -0,0 +1,71 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeNinja' + +name = 'Qt5Webkit' +# Qt5 > 5.9 required at least version 5.212.0 +# At the time of writing the latest version was 5.212.0-alpha3 +version = '5.212.0-alpha4' + +homepage = 'https://github.com/qt/qtwebkit' +description = "Qt Port of WebKit. WebKit is an open source web browser engine." +docurls = ['https://github.com/qt/qtwebkit/blob/dev/README'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/qtwebkit/qtwebkit/releases/download/qtwebkit-%(version)s/'] +sources = ['qtwebkit-%(version)s.tar.xz'] +patches = [ + '%(name)s-%(version)s_bison3.7.patch', + '%(name)s-%(version)s_fix_python_path.patch', + '%(name)s-%(version)s_fix_deprecated_encoding_in_json.load.patch', + '%(name)s-%(version)s_use_CXX_true_instead_of_TRUE_define.patch', + '%(name)s-%(version)s_dont_use_multiarch_lib_dir.patch', +] +checksums = [ + {'qtwebkit-5.212.0-alpha4.tar.xz': '9ca126da9273664dd23a3ccd0c9bebceb7bb534bddd743db31caf6a5a6d4a9e6'}, + {'Qt5Webkit-5.212.0-alpha4_bison3.7.patch': '34f37b53ee0bc31c63ce85ebd1ae95543a8ba28483e387b20efd50574bd813be'}, + {'Qt5Webkit-5.212.0-alpha4_fix_python_path.patch': + '126aed68cf0e22f595d3a8ae87938ba9e6a0727b53e38a92412fbf816a1687b2'}, + {'Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch': + 'e6ffe068a41af8d8aade58eeaa8352b87b731f29fc463e71bb1dc497301956c8'}, + {'Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch': + 'b952923cfe35667c69e7540d5c449d5e65301a4c2f43cdea8b33f190ab6b0403'}, + {'Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch': + '4974a348731ce80f73fbfbcce2351bddfb87a54affc7ae6dd52559a4ad93e8e8'}, +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('pkgconf', '1.8.0'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.10.2'), + ('Python', '3.9.6'), + ('Ruby', '3.0.1'), + ('Perl', '5.34.0'), +] + +dependencies = [ + ('Qt5', '5.15.2'), + ('zlib', '1.2.11'), + ('SQLite', '3.36'), + ('ICU', '69.1'), + ('libxslt', '1.1.34'), + ('libjpeg-turbo', '2.0.6'), +] + +configopts = "-DPORT=Qt -DUSE_LIBHYPHEN=OFF -DUSE_GSTREAMER=OFF " + +sanity_check_paths = { + 'files': [ + 'lib/libQt5WebKit.%s' % SHLIB_EXT, + 'lib/libQt5WebKitWidgets.%s' % SHLIB_EXT, + ], + 'dirs': ['include/QtWebKit', 'include/QtWebKitWidgets'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch new file mode 100644 index 00000000000..6ce4a9830dd --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch @@ -0,0 +1,26 @@ +Don't use multiarch lib dir + +Åke Sandgren, 2022-12-08 +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/cmake/KDEInstallDirs.cmake qtwebkit-5.212.0-alpha4/Source/cmake/KDEInstallDirs.cmake +--- qtwebkit-5.212.0-alpha4.orig/Source/cmake/KDEInstallDirs.cmake 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/cmake/KDEInstallDirs.cmake 2022-12-08 11:04:09.788027403 +0100 +@@ -210,11 +210,6 @@ + # See http://wiki.debian.org/Multiarch + if((CMAKE_SYSTEM_NAME MATCHES "Linux|kFreeBSD" OR CMAKE_SYSTEM_NAME STREQUAL "GNU") + AND NOT CMAKE_CROSSCOMPILING) +- if (EXISTS "/etc/debian_version") # is this a debian system ? +- if(CMAKE_LIBRARY_ARCHITECTURE) +- set(_LIBDIR_DEFAULT "lib/${CMAKE_LIBRARY_ARCHITECTURE}") +- endif() +- else() # not debian, rely on CMAKE_SIZEOF_VOID_P: + if(NOT DEFINED CMAKE_SIZEOF_VOID_P) + message(AUTHOR_WARNING + "Unable to determine default LIB_INSTALL_LIBDIR directory because no target architecture is known. " +@@ -224,7 +219,6 @@ + set(_LIBDIR_DEFAULT "lib64") + endif() + endif() +- endif() + endif() + + set(_gnu_install_dirs_vars diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch new file mode 100644 index 00000000000..d456d73cb1b --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch @@ -0,0 +1,15 @@ +"enconding" kw has been deprecated in json.load since Python 3.1 and was removed completely in 3.9 + +Åke Sandgren, 2022-12-08 +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/generate-bytecode-files qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/generate-bytecode-files +--- qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/generate-bytecode-files 2022-12-08 08:20:29.980590518 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/generate-bytecode-files 2022-12-08 08:21:00.908330630 +0100 +@@ -163,7 +163,7 @@ + initBytecodesFile = openOrExit(initASMFileName, "w") + + try: +- bytecodeSections = json.load(bytecodeFile, encoding = "utf-8") ++ bytecodeSections = json.load(bytecodeFile) + except: + print("Unexpected error parsing {0}: {1}".format(bytecodeJSONFile, sys.exc_info())) + diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_python_path.patch b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_python_path.patch new file mode 100644 index 00000000000..02a483f2f51 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_python_path.patch @@ -0,0 +1,66 @@ +Don't use hardcoded path to python + +Åke Sandgren, 2022-12-08 +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/generate-bytecode-files qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/generate-bytecode-files +--- qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/generate-bytecode-files 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/generate-bytecode-files 2022-12-08 07:56:12.528708137 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2014 Apple Inc. All rights reserved. + # +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/cssmin.py qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/cssmin.py +--- qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/cssmin.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/cssmin.py 2022-12-08 07:56:12.528708137 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2013 Apple Inc. All rights reserved. + # +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/generate-combined-inspector-json.py qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/generate-combined-inspector-json.py +--- qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/generate-combined-inspector-json.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/generate-combined-inspector-json.py 2022-12-08 07:56:12.532708103 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2013 Apple Inc. All rights reserved. + # +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/UpdateContents.py qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/UpdateContents.py +--- qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/UpdateContents.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/UpdateContents.py 2022-12-08 07:56:12.532708103 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2015 Apple Inc. All rights reserved. + # +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/ThirdParty/ANGLE/src/libANGLE/renderer/generate_new_renderer.py qtwebkit-5.212.0-alpha4/Source/ThirdParty/ANGLE/src/libANGLE/renderer/generate_new_renderer.py +--- qtwebkit-5.212.0-alpha4.orig/Source/ThirdParty/ANGLE/src/libANGLE/renderer/generate_new_renderer.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/ThirdParty/ANGLE/src/libANGLE/renderer/generate_new_renderer.py 2022-12-08 07:56:12.524708171 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + # + # Copyright (c) 2015 The ANGLE Project Authors. All rights reserved. + # Use of this source code is governed by a BSD-style license that can be +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebCore/AVFoundationSupport.py qtwebkit-5.212.0-alpha4/Source/WebCore/AVFoundationSupport.py +--- qtwebkit-5.212.0-alpha4.orig/Source/WebCore/AVFoundationSupport.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebCore/AVFoundationSupport.py 2022-12-08 07:56:12.524708171 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2015 Apple Inc. All rights reserved. + # +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebInspectorUI/Scripts/cssmin.py qtwebkit-5.212.0-alpha4/Source/WebInspectorUI/Scripts/cssmin.py +--- qtwebkit-5.212.0-alpha4.orig/Source/WebInspectorUI/Scripts/cssmin.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebInspectorUI/Scripts/cssmin.py 2022-12-08 07:56:12.528708137 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2013 Apple Inc. All rights reserved. + # diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch new file mode 100644 index 00000000000..3068f9bfc4b --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch @@ -0,0 +1,128 @@ +Use C++ "true" value instead of the TRUE define +It is not automatically defined in later ICU vwersions + +Åke Sandgren, 2022-12-08 +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProvider.h qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProvider.h +--- qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProvider.h 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProvider.h 2022-12-08 08:45:36.252382941 +0100 +@@ -80,12 +80,12 @@ + // Ensure chunk offset is well formed if computed offset exceeds int32_t range. + ASSERT(offset < std::numeric_limits::max()); + text->chunkOffset = offset < std::numeric_limits::max() ? static_cast(offset) : 0; +- isAccessible = TRUE; ++ isAccessible = true; + return true; + } + if (nativeIndex >= nativeLength && text->chunkNativeLimit == nativeLength) { + text->chunkOffset = text->chunkLength; +- isAccessible = FALSE; ++ isAccessible = false; + return true; + } + } else { +@@ -94,12 +94,12 @@ + // Ensure chunk offset is well formed if computed offset exceeds int32_t range. + ASSERT(offset < std::numeric_limits::max()); + text->chunkOffset = offset < std::numeric_limits::max() ? static_cast(offset) : 0; +- isAccessible = TRUE; ++ isAccessible = true; + return true; + } + if (nativeIndex <= 0 && !text->chunkNativeStart) { + text->chunkOffset = 0; +- isAccessible = FALSE; ++ isAccessible = false; + return true; + } + } +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProviderLatin1.cpp qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProviderLatin1.cpp +--- qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProviderLatin1.cpp 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProviderLatin1.cpp 2022-12-08 08:46:20.924008445 +0100 +@@ -100,23 +100,23 @@ + if (index < uText->chunkNativeLimit && index >= uText->chunkNativeStart) { + // Already inside the buffer. Set the new offset. + uText->chunkOffset = static_cast(index - uText->chunkNativeStart); +- return TRUE; ++ return true; + } + if (index >= length && uText->chunkNativeLimit == length) { + // Off the end of the buffer, but we can't get it. + uText->chunkOffset = static_cast(index - uText->chunkNativeStart); +- return FALSE; ++ return false; + } + } else { + if (index <= uText->chunkNativeLimit && index > uText->chunkNativeStart) { + // Already inside the buffer. Set the new offset. + uText->chunkOffset = static_cast(index - uText->chunkNativeStart); +- return TRUE; ++ return true; + } + if (!index && !uText->chunkNativeStart) { + // Already at the beginning; can't go any farther. + uText->chunkOffset = 0; +- return FALSE; ++ return false; + } + } + +@@ -144,7 +144,7 @@ + + uText->nativeIndexingLimit = uText->chunkLength; + +- return TRUE; ++ return true; + } + + static int32_t uTextLatin1Extract(UText* uText, int64_t start, int64_t limit, UChar* dest, int32_t destCapacity, UErrorCode* status) +@@ -336,7 +336,7 @@ + static UBool uTextLatin1ContextAwareAccess(UText* text, int64_t nativeIndex, UBool forward) + { + if (!text->context) +- return FALSE; ++ return false; + int64_t nativeLength = uTextLatin1ContextAwareNativeLength(text); + UBool isAccessible; + if (uTextAccessInChunkOrOutOfRange(text, nativeIndex, nativeLength, forward, isAccessible)) +@@ -356,7 +356,7 @@ + ASSERT(newContext == UTextProviderContext::PriorContext); + textLatin1ContextAwareSwitchToPriorContext(text, nativeIndex, nativeLength, forward); + } +- return TRUE; ++ return true; + } + + static int32_t uTextLatin1ContextAwareExtract(UText*, int64_t, int64_t, UChar*, int32_t, UErrorCode* errorCode) +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProviderUTF16.cpp qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProviderUTF16.cpp +--- qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProviderUTF16.cpp 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProviderUTF16.cpp 2022-12-08 08:46:59.755682780 +0100 +@@ -125,7 +125,7 @@ + static UBool uTextUTF16ContextAwareAccess(UText* text, int64_t nativeIndex, UBool forward) + { + if (!text->context) +- return FALSE; ++ return false; + int64_t nativeLength = uTextUTF16ContextAwareNativeLength(text); + UBool isAccessible; + if (uTextAccessInChunkOrOutOfRange(text, nativeIndex, nativeLength, forward, isAccessible)) +@@ -145,7 +145,7 @@ + ASSERT(newContext == UTextProviderContext::PriorContext); + textUTF16ContextAwareSwitchToPriorContext(text, nativeIndex, nativeLength, forward); + } +- return TRUE; ++ return true; + } + + static int32_t uTextUTF16ContextAwareExtract(UText*, int64_t, int64_t, UChar*, int32_t, UErrorCode* errorCode) +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/TextCodecICU.cpp qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/TextCodecICU.cpp +--- qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/TextCodecICU.cpp 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/TextCodecICU.cpp 2022-12-08 08:44:48.972780065 +0100 +@@ -308,7 +308,7 @@ + m_converterICU = ucnv_open(m_canonicalConverterName, &err); + ASSERT(U_SUCCESS(err)); + if (m_converterICU) +- ucnv_setFallback(m_converterICU, TRUE); ++ ucnv_setFallback(m_converterICU, true); + } + + int TextCodecICU::decodeToBuffer(UChar* target, UChar* targetLimit, const char*& source, const char* sourceLimit, int32_t* offsets, bool flush, UErrorCode& err) diff --git a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..0405b52686e --- /dev/null +++ b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'QtKeychain' +version = '0.13.2' + +homepage = 'https://github.com/frankosterfeld/qtkeychain' +description = "Platform-independent Qt API for storing passwords securely." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/frankosterfeld/qtkeychain/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['20beeb32de7c4eb0af9039b21e18370faf847ac8697ab3045906076afbc4caa5'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('Qt5', '5.15.2'), +] + +# Need to turn off build tranlsations, it tries to put that to qt5 dir. +# The other option would be to set translations directory +configopts = "-DCMAKE_INSTALL_LIBDIR=lib/ -DBUILD_TRANSLATIONS=OFF" + +sanity_check_paths = { + 'files': ['lib/libqt5keychain.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2238ccf4c84 --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.2.0' + +homepage = 'https://qwt.sourceforge.io/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Qwt-6.2.0_fix-install-prefix.patch'] +checksums = [ + '9194f6513955d0fd7300f67158175064460197abab1a92fa127a67a4b0b71530', # qwt-6.2.0.tar.bz2 + 'ac5c329c0693d565b461cdd3b36c1b96b4d09885e1e0c10929fc7a9021c03bad', # Qwt-6.2.0_fix-install-prefix.patch +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Qt5', '5.15.2'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export QWT_PREFIX=%(installdir)s && ' +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb new file mode 100644 index 00000000000..274ca8152c4 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb @@ -0,0 +1,48 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +name = 'wxPython' +version = '4.2.0' + +homepage = "https://www.wxpython.org/" +description = """Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets +API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel +and requiring very little (if any) platform specific code.""" + + +toolchain = {'name': 'foss', 'version': '2021b'} +sources = ['%(name)s-%(version)s.tar.gz'] +patches = [ + 'wxPython-4.1.1_fix_install_path.patch', + 'wxPython-4.1.1_use_bang_env_python.patch', +] +checksums = [ + {'wxPython-4.2.0.tar.gz': '663cebc4509d7e5d113518865fe274f77f95434c5d57bc386ed58d65ceed86c7'}, + {'wxPython-4.1.1_fix_install_path.patch': 'f13743877deddbf525bbb3f81c8f7a6b0c2dbf1333595926f653f696999e31ce'}, + {'wxPython-4.1.1_use_bang_env_python.patch': 'c355c60a8cce3018fc0c30ffc78623efd2481e9baf33673e22a57863e1a3ac87'}, +] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Pillow', '8.3.2'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.3.0'), + ('expat', '2.4.1'), + ('GTK3', '3.24.31'), + ('GLib', '2.69.1'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '1.18.5'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('LibSoup', '3.0.7'), + ('wxWidgets', '3.2.0'), + ('WebKitGTK+', '2.37.1'), + ('attrdict3', '2.0.2'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..631d9b165c3 --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.0-GCC-11.2.0.eb @@ -0,0 +1,71 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.2.0' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'wxWidgets' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_BZ2] +checksums = ['356e9b55f1ae3d58ae1fed61478e9b754d46b820913e3bfbc971c50377c1903a'] + +builddependencies = [ + ('gettext', '0.21'), + ('pkgconf', '1.8.0'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.3.0'), + ('expat', '2.4.1'), + ('GTK3', '3.24.31'), + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('SDL2', '2.0.20'), + ('cairo', '1.16.0'), + ('GST-plugins-base', '1.18.5'), + ('GLib', '2.69.1'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From 45254aa1a8236616903201636177488c101f6093 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 15:31:52 +0100 Subject: [PATCH 5790/9987] Pocl has *NO* https website. Only http --- easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb index d9dbdf2fa1d..06688ffbce2 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeNinja' name = 'pocl' version = '1.8' -homepage = 'https://portablecl.org' +homepage = 'http://portablecl.org' description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" toolchain = {'name': 'GCC', 'version': '11.3.0'} From d42d64a8ee59d969678f94912d789ba116f81f52 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 12 Dec 2022 15:48:51 +0100 Subject: [PATCH 5791/9987] wxPython: clarify that wxPython 4.2 requires wxWidgets >= 3.2 --- easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb index 274ca8152c4..6a911f23dd8 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb @@ -40,7 +40,7 @@ dependencies = [ ('Mesa', '21.1.7'), ('libGLU', '9.0.2'), ('LibSoup', '3.0.7'), - ('wxWidgets', '3.2.0'), + ('wxWidgets', '3.2.0'), # wxPython 4.2 depends on wxWidgets >=3.2 ('WebKitGTK+', '2.37.1'), ('attrdict3', '2.0.2'), ] From 3162d2e92ad13a33b2e3bea2784f2b4bdd6c0b0a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 12 Dec 2022 16:10:47 +0100 Subject: [PATCH 5792/9987] QGIS: Add missing author info for patch and update checksums. --- easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb | 2 +- .../easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb index eaac6f93058..b17b0f8cc3d 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = ['QGIS-%(version)s_fix-SIP-macro.patch'] checksums = [ {'qgis-3.28.1.tar.bz2': '09015bb68c45556ffe9d480272d24048e6276a6bf1c010fd77beae64329ff674'}, - {'QGIS-3.28.1_fix-SIP-macro.patch': '5da6bcd380e46969efa7718d8aec79a2548616c278853f29ed07d745fd5b043f'}, + {'QGIS-3.28.1_fix-SIP-macro.patch': '141b7730666b3e703b9a6648d1e5a2686f8819f6a4938c6d60aa8c8d65820bd3'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch index bae12be4ff3..0b30feff707 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch +++ b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch @@ -1,3 +1,9 @@ +include location of PyQt .sip files in SIPCMD macro + +author: Kenneth Hoste (HPC-UGent) +author: Pavel Grochal (INUITS) + +Updated to QGIS/3.28.1: Åke Sandgren, 2022-12-09 diff -ru qgis-3.28.1.orig/cmake/SIPMacros.cmake qgis-3.28.1/cmake/SIPMacros.cmake --- qgis-3.28.1.orig/cmake/SIPMacros.cmake 2022-11-18 13:10:21.000000000 +0100 +++ qgis-3.28.1/cmake/SIPMacros.cmake 2022-12-09 08:14:33.475615182 +0100 From 08716e60f488628f83f81208ac2d0f5fb3e0025d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 12 Dec 2022 16:16:21 +0100 Subject: [PATCH 5793/9987] update comment about ecmwflibs --- .../easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb index 7d9b3571002..ca9f62f7e16 100644 --- a/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb @@ -31,7 +31,7 @@ use_pip = True sanity_pip_check = True # stick to termcolor 1.x, to avoid hatchling required dependency -# remove ecmwflibs requirement (provides ecCodes and Magics) +# remove ecmwflibs requirement as it just bundles ecCodes and Magics and there are no direct imports to it exts_list = [ ('eccodes', '1.5.0', { 'checksums': ['e70c8f159140c343c215fd608ddf533be652ff05ad2ff17243c7b66cf92127fa'], From 51816822c4f75604886aa23ad4556f4a03120fac Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 12 Dec 2022 16:17:46 +0100 Subject: [PATCH 5794/9987] QtKeychain: Add osdependency on libsecret --- .../q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb index 0405b52686e..0a91d9e6e60 100644 --- a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb @@ -15,6 +15,8 @@ source_urls = ['https://github.com/frankosterfeld/qtkeychain/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['20beeb32de7c4eb0af9039b21e18370faf847ac8697ab3045906076afbc4caa5'] +osdependencies = [('libsecret-1-dev', 'libsecret-devel')] + builddependencies = [ ('binutils', '2.37'), ('CMake', '3.22.1'), From cdba8bf1a76b4f14d2fcfe6d4b951386b83486ee Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 15:25:06 +0000 Subject: [PATCH 5795/9987] Trimesh is a shapely-like library used by some of our users --- .../t/trimesh/trimesh-3.17.1-foss-2022a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb new file mode 100644 index 00000000000..10fffaef98f --- /dev/null +++ b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'trimesh' +version = '3.17.1' + +homepage = 'https://trimsh.org/' +description = """Trimesh is a Python (2.7- 3.3+) library for loading and using triangular meshes with an emphasis on +watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy +manipulation and analysis, in the style of the excellent Polygon object in the Shapely library.""" + + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['025bb2fa3a2e87bdd6873f11db45a7ca19216f2f8b6aed29140fca57e32c298e'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + + + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy required +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + + +moduleclass = 'lib' From 8dacf50912d39a13f043b0c51f2694ec90f4dd89 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 12 Dec 2022 16:35:09 +0100 Subject: [PATCH 5796/9987] Delete empty last line in librttopo and minizip. --- easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb | 1 - easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb index 76f469f32a9..2f125cbbd62 100644 --- a/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb @@ -32,4 +32,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb index 2ccef97d5ce..a5989e65647 100644 --- a/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb @@ -36,4 +36,3 @@ sanity_check_paths = { } moduleclass = 'lib' - From 34b2548c463543d5238d7f724ec6e764af7569fb Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 17:56:17 +0100 Subject: [PATCH 5797/9987] Update easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb someone prefers this way, I guess Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb index 539118743c8..84feba1ab7f 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -1,6 +1,7 @@ +easyblock = 'CMakeMake' + name = 'g2clib' version = '1.7.0' -easyblock = 'CMakeMake' homepage = 'https://github.com/NOAA-EMC/NCEPLIBS-g2c' description = """Library contains GRIB2 encoder/decoder ('C' version).""" From 5ee143ebfd4e0afc9cbe36cb99eb6b1886064128 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 17:56:56 +0100 Subject: [PATCH 5798/9987] Update easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb Life is too short to argue over indentation styles. Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb index 84feba1ab7f..607127c9fb6 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -13,9 +13,10 @@ source_urls = ['https://github.com/NOAA-EMC/NCEPLIBS-g2c/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['73afba9da382fed73ed8692d77fa037bb313280879cd4012a5e5697dccf55175'] -builddependencies = [('binutils', '2.38'), - ('CMake', '3.23.1'), - ] +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] dependencies = [ ('JasPer', '2.0.33'), From 07615e9fe1567fecd6d5c3a7a5dc5d75d297a9d7 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 17:57:38 +0100 Subject: [PATCH 5799/9987] Update easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb no need for parallel limitation Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb index 607127c9fb6..7b19daafbd1 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -24,8 +24,6 @@ dependencies = [ ('libjpeg-turbo', '2.1.3'), ] -parallel = 8 - sanity_check_paths = { 'files': ['lib/libg2c.so'], 'dirs': ['include', 'lib'], From 2b4a4205f168c72e109d65a4ab7c9c1f0ce6b9ae Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 17:58:00 +0100 Subject: [PATCH 5800/9987] Update easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb index 7b19daafbd1..e0b095442e0 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libg2c.so'], + 'files': ['lib/libg2c.%s' % SHLIB_EXT], 'dirs': ['include', 'lib'], } From c86f6bcc0a6d6da93895e48ec5e2f6a541027a96 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 17:58:06 +0100 Subject: [PATCH 5801/9987] Update easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb index e0b095442e0..cc05f88f67a 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ sanity_check_paths = { 'files': ['lib/libg2c.%s' % SHLIB_EXT], - 'dirs': ['include', 'lib'], + 'dirs': ['include'], } moduleclass = 'data' From 2807634baf4b7739b75e51c679ff65f1962bc1dd Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 12 Dec 2022 19:51:21 +0100 Subject: [PATCH 5802/9987] Fix URL --- .../easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb index 79fbfeebdd1..aea69135267 100644 --- a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb @@ -28,7 +28,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(versions)s/dist'] +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] sources = ['cubew-%(version)s.tar.gz'] checksums = ['73c7f9e9681ee45d71943b66c01cfe675b426e4816e751ed2e0b670563ca4cf3'] From 41d3f5074a76aabfb9ab0c9e39e940d8793d222e Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 20:31:53 +0100 Subject: [PATCH 5803/9987] Update easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb index 10fffaef98f..fc52d8885be 100644 --- a/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb @@ -11,7 +11,6 @@ manipulation and analysis, in the style of the excellent Polygon object in the S toolchain = {'name': 'foss', 'version': '2022a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['025bb2fa3a2e87bdd6873f11db45a7ca19216f2f8b6aed29140fca57e32c298e'] From 7586a4d1a46c6547f2a1cab6e2e13b9dd2f02613 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 20:32:36 +0100 Subject: [PATCH 5804/9987] remove spurious blank lines --- easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb index fc52d8885be..ad68fc7a786 100644 --- a/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb @@ -8,7 +8,6 @@ description = """Trimesh is a Python (2.7- 3.3+) library for loading and using t watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy manipulation and analysis, in the style of the excellent Polygon object in the Shapely library.""" - toolchain = {'name': 'foss', 'version': '2022a'} sources = [SOURCE_TAR_GZ] @@ -18,8 +17,6 @@ use_pip = True download_dep_fail = True sanity_pip_check = True - - dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), # numpy required @@ -30,5 +27,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } - moduleclass = 'lib' From 94786fc545ee4b852000aeb07a67b49584573dd0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Dec 2022 09:30:30 +0100 Subject: [PATCH 5805/9987] add exception to test suite for wxPython 4.2.0 depending on wxWidgets 3.2.0 --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3160d1b9ad9..b6c93819c94 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -592,6 +592,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], # WPS 3.9.1 requires WRF 3.9.1.1 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], + # wxPython 4.2.0 depends on wxWidgets 3.2.0 + 'wxWidgets': [(r'3\.2\.0', ['wxPython-4.2.0'])], } if dep in alt_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): From a06c1e0322d74b297661ab25aac034cc5d095d5b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Dec 2022 11:17:00 +0100 Subject: [PATCH 5806/9987] add exception to test suite for packages that depend on wxPython 4.2.0 depending on wxWidgets 3.2.0 --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index b6c93819c94..bbc89eacc65 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -593,7 +593,7 @@ def check_dep_vars(self, gen, dep, dep_vars): # WPS 3.9.1 requires WRF 3.9.1.1 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], # wxPython 4.2.0 depends on wxWidgets 3.2.0 - 'wxWidgets': [(r'3\.2\.0', ['wxPython-4.2.0'])], + 'wxWidgets': [(r'3\.2\.0', [r'wxPython-4\.2\.0', r'GRASS-8\.2\.0', r'QGIS-3\.28\.1'])], } if dep in alt_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): From 4ccb40e8c8079639fe46a83e932087b80e5d349f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Dec 2022 11:17:59 +0100 Subject: [PATCH 5807/9987] add exception to test suite for packages that have a chain dependency on glew-2.2.0-elg --- test/easyconfigs/easyconfigs.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index bbc89eacc65..63e9464d464 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -497,7 +497,10 @@ def check_dep_vars(self, gen, dep, dep_vars): 'glew': [ ('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0', r'wpebackend-fdo-1\.13\.1-GCCcore-11\.2\.0', - r'WebKitGTK\+-2\.37\.1-GCC-11\.2\.0']), + r'WebKitGTK\+-2\.37\.1-GCC-11\.2\.0', + r'wxPython-4\.2\.0', + r'GRASS-8\.2\.0', + r'QGIS-3\.28\.1']), ], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x and v3.0.0 require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) From 2ee0d06b829844c15a1ee494b3c0f42619054e6d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Dec 2022 11:31:45 +0100 Subject: [PATCH 5808/9987] QtKeyChain: Turn of use of libsecret. It should still use GNOME Keyring if running. --- .../q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb index 0a91d9e6e60..7cb7366cb23 100644 --- a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb @@ -15,8 +15,6 @@ source_urls = ['https://github.com/frankosterfeld/qtkeychain/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['20beeb32de7c4eb0af9039b21e18370faf847ac8697ab3045906076afbc4caa5'] -osdependencies = [('libsecret-1-dev', 'libsecret-devel')] - builddependencies = [ ('binutils', '2.37'), ('CMake', '3.22.1'), @@ -28,7 +26,7 @@ dependencies = [ # Need to turn off build tranlsations, it tries to put that to qt5 dir. # The other option would be to set translations directory -configopts = "-DCMAKE_INSTALL_LIBDIR=lib/ -DBUILD_TRANSLATIONS=OFF" +configopts = "-DCMAKE_INSTALL_LIBDIR=lib/ -DBUILD_TRANSLATIONS=OFF -DLIBSECRET_SUPPORT=OFF " sanity_check_paths = { 'files': ['lib/libqt5keychain.%s' % SHLIB_EXT], From 7d13d25d93b104f769ca1ed9129f9bb57052fdfd Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 13 Dec 2022 11:54:07 +0100 Subject: [PATCH 5809/9987] adding easyconfigs: KaHIP-3.14-gompi-2022a.eb --- .../k/KaHIP/KaHIP-3.14-gompi-2022a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022a.eb diff --git a/easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022a.eb b/easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022a.eb new file mode 100644 index 00000000000..1445dd5e925 --- /dev/null +++ b/easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'KaHIP' +version = '3.14' + +homepage = 'https://kahip.github.io/' +description = """The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/KaHIP/KaHIP/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9da04f3b0ea53b50eae670d6014ff54c0df2cb40f6679b2f6a96840c1217f242'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ["lib/libkahip_static.a", "lib/libkahip.%s" % SHLIB_EXT] + + ["lib/libparhip_interface_static.a", "lib/libparhip_interface.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["kaHIP_interface.h", "parhip_interface.h"]], + 'dirs': [], +} + +moduleclass = 'math' From ca4badaff29b0e30e50e9b4f02184b2d31bcc0f1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 13 Dec 2022 14:41:44 +0100 Subject: [PATCH 5810/9987] adding easyconfigs: PySCF-2.1.1-foss-2022a.eb and patches: PySCF-2.1.1_dmrgscf-settings.patch, PySCF-2.1.1_fciqmc-settings.patch, PySCF-2.1.1_icmpspt-exe-path.patch, PySCF-2.1.1_mbd-fix-init.patch --- .../p/PySCF/PySCF-2.1.1-foss-2022a.eb | 141 ++++++++++++++++++ .../PySCF/PySCF-2.1.1_dmrgscf-settings.patch | 26 ++++ .../p/PySCF/PySCF-2.1.1_fciqmc-settings.patch | 15 ++ .../PySCF/PySCF-2.1.1_icmpspt-exe-path.patch | 27 ++++ .../p/PySCF/PySCF-2.1.1_mbd-fix-init.patch | 21 +++ 5 files changed, 230 insertions(+) create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_dmrgscf-settings.patch create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_fciqmc-settings.patch create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_icmpspt-exe-path.patch create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_mbd-fix-init.patch diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb new file mode 100644 index 00000000000..cfe1ada58c8 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb @@ -0,0 +1,141 @@ +easyblock = 'CMakeMakeCp' +name = 'PySCF' +version = '2.1.1' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['814240aa73f57ba96aee8264e3914c09f96ebdce1e42784da4b5e9a474ecb280'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pybind11', '2.9.2'), # needed by zquatev +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for numpy, scipy + ('h5py', '3.7.0'), + ('libcint', '5.1.6'), + ('libxc', '5.2.3'), + ('XCFun', '2.1.1'), + ('CPPE', '0.3.1'), # extra + ('PyBerny', '0.6.3'), # extra + ('PyCheMPS2', '1.8.12'), # needed by dmrgscf + ('Block', '1.5.3-20210723'), # needed by dmrgscf + ('NECI', '20220711'), # needed by fciqmc + ('Dice', '20221025'), # needed by icmpspt +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'modulename': 'pyscf.%(name)s', + 'source_urls': ['https://github.com/pyscf/%(name)s/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], +} + +# The following list of extensions is equivalent to installing PySCF with extras: +# all + dmrgscf + fciqmcscf + hci + mbd + tblis + zquatev +exts_list = [ + # extensions in 'all' extra + ('dftd3', 'd214021', { + 'checksums': ['6616e7f28a90ca00c3def30dd22c4580f5b555af5c61fec2cb09cc6dd4e7bbff'], + }), + ('doci', '08079a9', { + 'checksums': ['f492ba45dfe50c9b459e53a946a677528af0dc2097ff77ea3767aa4f46c5d9ba'], + }), + ('icmpspt', 'f26062b', { + 'patches': [('PySCF-2.1.1_icmpspt-exe-path.patch', 0)], + 'checksums': [ + {'icmpspt-f26062b.tar.gz': '8f44b317da209882e0353d2731d8bc907de450af02429e962ae9b8d3f8c95a47'}, + {'PySCF-2.1.1_icmpspt-exe-path.patch': 'e972e377b34b964c48a99909301bf21a9c73d8eb9ecb96a889621d71471c56c9'}, + ], + }), + ('properties', '92a4df7', { + 'modulename': 'pyscf.prop', + 'checksums': ['df5456315855c7a4f5858b244461793f2cbc21f6a6c0328039838ad85913c79d'], + }), + ('qsdopt', '3ad2c02', { + 'checksums': ['cc639150e5f9efad8ffe496b3dccd2952a1f60fdad51f611cffba701892b384e'], + }), + ('semiempirical', '327d65e', { + 'checksums': ['4d0016a321c91ace2f1c18e4001df3f6c8de9c96602c391353102b6ad4e14076'], + }), + ('shciscf', 'dd398d2', { + 'checksums': ['96032337e8877478d410f2edd8490d267a8b6ddb8fad6152b201f4da912fd694'], + }), + ('MCfun', '1a9ae31', { + 'modulename': 'mcfun', + 'source_urls': ['https://github.com/Multi-collinear/%(name)s/archive/'], + 'checksums': ['482397f0c964f27ff15687e4b56554c51e0f249e2ad5b96fd1d6cb8a2f7f2c72'], + }), + ('pyqmc', '0.5.0', { + 'modulename': 'pyqmc', + 'source_urls': ['https://github.com/WagnerGroup/%(name)s/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['ecda2045577dc3b48149d5e92c88ce19d60b8c2a2e2c1705542c176973f5e1c8'], + }), + # extensions on top of 'all' extra + ('dmrgscf', '4ff57bf', { + 'patches': [('PySCF-2.1.1_dmrgscf-settings.patch', 0)], + 'checksums': [ + {'dmrgscf-4ff57bf.tar.gz': '0683cfc2e6676aa11da7b2eee66e96442a64a37b72f65057779718c5fdb43c5f'}, + {'PySCF-2.1.1_dmrgscf-settings.patch': 'a0310a2a90e96bd64d1560b2cc73a805717e129d2921e91cc5e6038b9f153677'}, + ], + }), + ('fciqmc', 'c7c30bb', { + 'modulename': 'pyscf.fciqmcscf', + 'patches': [('PySCF-2.1.1_fciqmc-settings.patch', 0)], + 'checksums': [ + {'fciqmc-c7c30bb.tar.gz': 'dfa613df36a49d7a7f1d2ff7ab7646a38adbb01c9af05d4ea7e3bcff495d8f57'}, + {'PySCF-2.1.1_fciqmc-settings.patch': 'd9faa98e62957a5b47435343a986612b27aa9fc744a201ed3beb63919dc63427'}, + ], + }), + ('mbd', '485c18c', { + 'patches': [('PySCF-2.1.1_mbd-fix-init.patch', 0)], + 'checksums': [ + {'mbd-485c18c.tar.gz': 'de1fb14650fcb87909cae33dc318d2e213653ac4393ced7e070dfa6308d95846'}, + {'PySCF-2.1.1_mbd-fix-init.patch': '4f8e4b2e39b77428187851c4b6ced39401561bc81f4f3a4605da5d5c7b798cbc'}, + ], + }), + ('naive-hci', '0c28d6e', { + 'modulename': 'pyscf.hci', + 'checksums': ['de247d17b80133655df5966341e5adb691b0df150cd9b0f1980cf62ec55229d5'], + }), + ('tblis', 'a1efbc0', { + 'modulename': 'pyscf.tblis_einsum', + 'source_urls': ['https://github.com/pyscf/pyscf-tblis/archive/'], + 'checksums': ['55fea57bfee2cf8aef577d8d2adc1f273aa39e3ee5e6cfc2442ccc3b5353a847'], + }), + ('zquatev', '4eb41b1', { + 'modulename': 'zquatev', + 'source_urls': ['https://github.com/sunqm/%(name)s/archive/'], + 'checksums': ['4caf08e3831a5d86e6bc22f3b4028cc159101cb9658d09de16e382e268a5a2e9'], + # use pybind11 from EB + 'preinstallopts': "sed -i 's/add_subdirectory(pybind11)/find_package(pybind11 REQUIRED)/' CMakeLists.txt && ", + }), +] + +start_dir = 'pyscf/lib' +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +_py_site_packages = 'lib/python%(pyshortver)s/site-packages' +files_to_copy = [(['pyscf'], _py_site_packages)] + +sanity_check_paths = { + 'files': [_py_site_packages + '/pyscf/__init__.py'], + 'dirs': [_py_site_packages + d for d in ['/pyscf/data', '/pyscf/lib']], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': _py_site_packages} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_dmrgscf-settings.patch b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_dmrgscf-settings.patch new file mode 100644 index 00000000000..b48812d258b --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_dmrgscf-settings.patch @@ -0,0 +1,26 @@ +Add settings file for pyscf.dmrgscf using EasyBuild environment +author: Alex Domingo (Vrije Universiteit Brussel) +diff -Nru pyscf.orig/dmrgscf/settings.py pyscf/dmrgscf/settings.py +--- pyscf.orig/dmrgscf/settings.py 1970-01-01 01:00:00.000000000 +0100 ++++ pyscf/dmrgscf/settings.py 2022-11-22 01:43:28.836971000 +0100 +@@ -0,0 +1,20 @@ ++# ++# This file sets the environment using EasyBuild packages ++# The configs will be used in dmrgci.py and chemps2.py ++# ++ ++import os ++from glob import glob ++from pyscf import lib ++ ++# Use Block as the FCI solver for CASSCF ++BLOCKEXE = os.path.join(os.getenv('EBROOTBLOCK'), 'bin', 'block.spin_adapted') ++BLOCKEXE_COMPRESS_NEVPT = os.path.join(os.getenv('EBROOTBLOCK'), 'bin', 'block.spin_adaptedi-serial') ++BLOCKSCRATCHDIR = os.path.join(lib.param.TMPDIR, str(os.getpid())) ++BLOCKRUNTIMEDIR = str(os.getpid()) ++MPIPREFIX = 'mpirun' # change to srun for SLURM job system ++BLOCKVERSION = '1.5.3' ++ ++# Use ChemPS2 as the FCI solver for CASSCF ++pychemps2_root = os.getenv('EBROOTPYCHEMPS2') ++PYCHEMPS2BIN = glob(os.path.join(pychemps2_root, 'lib', 'python3*', 'site-packages', 'PyCheMPS2.*.so'))[0] diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_fciqmc-settings.patch b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_fciqmc-settings.patch new file mode 100644 index 00000000000..267f7b13845 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_fciqmc-settings.patch @@ -0,0 +1,15 @@ +Add settings file for pyscf.fciqmc using EasyBuild environment +author: Alex Domingo (Vrije Universiteit Brussel) +diff -Nru pyscf.orig/fciqmcscf/settings.py pyscf/fciqmcscf/settings.py +--- pyscf.orig/fciqmcscf/settings.py 1970-01-01 01:00:00.000000000 +0100 ++++ pyscf/fciqmcscf/settings.py 2022-11-24 21:16:33.554298000 +0100 +@@ -0,0 +1,9 @@ ++# ++# This file sets the environment using EasyBuild packages ++# The configs will be used in fciqmc.py ++# ++ ++import os ++ ++# Use NECI (FCIQMC) as the FCI sovler for CASSCF ++FCIQMCEXE = os.path.join(os.getenv('EBROOTNECI'), 'bin', 'neci') diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_icmpspt-exe-path.patch b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_icmpspt-exe-path.patch new file mode 100644 index 00000000000..109daa2a3c2 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_icmpspt-exe-path.patch @@ -0,0 +1,27 @@ +Fix numpy data types and use ICPT binary from Dice in EasyBuild +author: Alex Domingo (Vrije Universiteit Brussel) +--- pyscf/icmpspt/icmpspt.py.orig 2022-11-25 01:00:16.277514709 +0100 ++++ pyscf/icmpspt/icmpspt.py 2022-11-24 21:38:23.700229771 +0100 +@@ -43,7 +43,7 @@ + from pyscf import tools + import sys + +-float_precision = numpy.dtype('Float64') ++float_precision = numpy.dtype('float64') + mpiprefix="" + executable="/projects/bamu3429/softwares/icpt_test/icpt" + executable="/projects/bamu3429/softwares/icpt/icpt.big" +--- pyscf/icmpspt/icmpspt.py.orig 2022-11-25 01:00:16.277514709 +0100 ++++ pyscf/icmpspt/icmpspt.py 2022-11-25 01:03:20.021383507 +0100 +@@ -45,10 +45,7 @@ + + float_precision = numpy.dtype('Float64') + mpiprefix="" +-executable="/projects/bamu3429/softwares/icpt_test/icpt" +-executable="/projects/bamu3429/softwares/icpt/icpt.big" +-executable="/projects/bamu3429/softwares/icpt/icpt" +-#executable="/projects/bamu3429/softwares/icpt_before_me/icpt" ++executable=os.path.join(os.getenv('EBROOTDICE'), 'bin', 'ICPT') + if not os.path.isfile(executable): + msg = ('MPSLCC executable %s not found. Please specify "executable" in %s' + % (executable, __file__)) diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_mbd-fix-init.patch b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_mbd-fix-init.patch new file mode 100644 index 00000000000..a1a5338cd95 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1_mbd-fix-init.patch @@ -0,0 +1,21 @@ +Set version of pyscf/mbd extension and fix imports on init +author: Alex Domingo (Vrije Universiteit Brussel) +diff -Nru pyscf.orig/mbd/__init__.py pyscf/mbd/__init__.py +--- pyscf.orig/mbd/__init__.py 2022-11-25 02:03:32.583625000 +0100 ++++ pyscf/mbd/__init__.py 2022-11-25 02:04:11.959827000 +0100 +@@ -12,4 +12,6 @@ + # See the License for the specific language governing permissions and + # limitations under the License. + ++__version__ = '0.0.1' ++ + from .mbd import mbd_rsscs, bohr +diff -Nru pyscf.orig/mbd/__init__.py pyscf/mbd/__init__.py +--- pyscf.orig/mbd/__init__.py 2022-11-25 02:16:14.580180000 +0100 ++++ pyscf/mbd/__init__.py 2022-11-25 02:16:26.123674000 +0100 +@@ -14,4 +14,4 @@ + + __version__ = '0.0.1' + +-from .mbd import mbd_rsscs, bohr ++from .mbd import mbd_rsscs From 449e356f75b301bfe9cb42afc6e51972233f8b78 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 13 Dec 2022 17:19:44 +0000 Subject: [PATCH 5811/9987] xarray removed and with Parcels from PR 16838 replaced, surplus Python extensions removed --- .../lagrangian-filtering-0.8.3-foss-2022a.eb | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb index f057408344e..8049e656133 100644 --- a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb +++ b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb @@ -21,16 +21,13 @@ dependencies = [ ('scikit-learn', '1.1.2'), ('tqdm', '4.64.0'), ('zarr', '2.13.3'), - ('xarray', '2022.9.0'), + ('Parcels', '2.4.0'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('parcels', '2.4.0', { - 'checksums': ['221ce49b6cb5bb4996aa3c817c0de7f022c952a4d8cb4160ca7df7dd940714b5'], - }), ('pykdtree', '1.3.6', { 'checksums': ['780b693d0555b857d7aab31e35d4293bf4ebdb9dec7a45ba4bb23b4400f626dc'], }), @@ -41,19 +38,12 @@ exts_list = [ 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], 'modulename': 'progressbar', }), - ('cgen', '2020.1', { - 'checksums': ['4ec99d0c832d9f95f5e51dd18a629ad50df0b5464ce557ef42c6e0cd9478bfcf'], - }), - ('pymbolic', '2022.1', { - 'checksums': ['b52f451dd0b9803e03de3320af3b7ce5723070061c6d231c00216f6da4259012'], - }), ('pytools', '2022.1.12', { 'checksums': ['4d62875e9a2ab2a24e393a9a8b799492f1a721bffa840af3807bfd42871dd1f4'], }), ('python-utils', '3.4.5', { 'checksums': ['7e329c427a6d23036cfcc4501638afb31b2ddc8896f25393562833874b8c6e0a'], }), - (name, version, { 'sources': [{ 'filename': '%(name)s-%(version)s-commit.tar.gz', From af82218750da1b57c444c9c346ad88ea097ddd49 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 14 Dec 2022 10:55:05 +0100 Subject: [PATCH 5812/9987] remove dependencies in Parcels from lagrangian-filtering --- .../lagrangian-filtering-0.8.3-foss-2022a.eb | 27 +------------------ 1 file changed, 1 insertion(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb index 8049e656133..986728f528f 100644 --- a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb +++ b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb @@ -18,9 +18,6 @@ dependencies = [ ('h5py', '3.7.0'), ('SciPy-bundle', '2022.05'), ('netcdf4-python', '1.6.1'), - ('scikit-learn', '1.1.2'), - ('tqdm', '4.64.0'), - ('zarr', '2.13.3'), ('Parcels', '2.4.0'), ] @@ -28,30 +25,13 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('pykdtree', '1.3.6', { - 'checksums': ['780b693d0555b857d7aab31e35d4293bf4ebdb9dec7a45ba4bb23b4400f626dc'], - }), - ('sosfilt', '1.2.0', { - 'checksums': ['b3083fd2edf723a6163f00ddc36ec3ca20fbf6112cc68573dad9356544a9d734'], - }), - ('progressbar2', '4.2.0', { - 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], - 'modulename': 'progressbar', - }), - ('pytools', '2022.1.12', { - 'checksums': ['4d62875e9a2ab2a24e393a9a8b799492f1a721bffa840af3807bfd42871dd1f4'], - }), - ('python-utils', '3.4.5', { - 'checksums': ['7e329c427a6d23036cfcc4501638afb31b2ddc8896f25393562833874b8c6e0a'], - }), (name, version, { 'sources': [{ - 'filename': '%(name)s-%(version)s-commit.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz', 'git_config': { 'url': 'https://github.com/angus-g/', 'repo_name': name, 'tag': version, - 'recursive': True, 'keep_git_dir': True, }, }], @@ -60,9 +40,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' From 07b71476dce75670a7bbec42b9e28c1d0e2b50e0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 14 Dec 2022 13:14:06 +0200 Subject: [PATCH 5813/9987] adding easyconfigs: OpenMM-7.5.1-foss-2021b-DeepMind-patch.eb --- .../OpenMM-7.5.1-foss-2021b-DeepMind-patch.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-DeepMind-patch.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-DeepMind-patch.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-DeepMind-patch.eb new file mode 100644 index 00000000000..e290a831169 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-DeepMind-patch.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.1' +versionsuffix = '-DeepMind-patch' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [('OpenMM-%(version)s_DeepMind.patch', 'wrappers/python')] +checksums = [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('SWIG', '4.0.2'), +] + +runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 1fc94700e80f2b860635c30dbef9a24faeaf9f23 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 14 Dec 2022 13:19:53 +0200 Subject: [PATCH 5814/9987] adding easyconfigs: jax-0.3.23-foss-2021b-CUDA-11.4.1.eb --- .../jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb | 125 ++++++++++++++++++ 1 file changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..9bad44f1db6 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,125 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +# Downgrade to foss/2021b: T. Hoffmann (EMBL) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.23' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +cuda_compute_capabilities = ["5.0", "6.0", "6.1", "7.0", "7.5", "8.0", "8.6"] + +builddependencies = [ + ('Bazel', '3.7.2'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.33.1', '-nodocs'), + ('matplotlib', '3.4.3'), # required by some jax tests +] + +dependencies = [ + ('CUDA', '11.4.1', '', SYSTEM), + ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.10.3', versionsuffix), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in WORKSPACE +local_tf_commit = 'cb946f223b9b3fa04efdbb7a0e6a9dabb22a7057' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.3.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['463c38a08d2e4cef6c498b76ba5bd4858e4c6ef51da1a5a1f27139a022e20248'], + }), + ('jaxlib', '0.3.22', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.3.22.tar.gz + '680a6f5265ba26d5515617a95ae47244005366f879a5c321782fde60f34e6d0d', + # tensorflow-cb946f223b9b3fa04efdbb7a0e6a9dabb22a7057.tar.gz + '9a7a7a87356bdeef5874fae135de380466482b593469035be3609a9cd2c153c4', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'patches': [ + 'jax-0.3.9_relax-test-tolerance.patch', + 'jax-0.3.23_correctly-skip-from_dlpack-tests.patch', + 'jax-0.3.23_relax-testPoly5-tolerance.patch', + ], + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + + "JAX_ENABLE_X64=true pytest -vv tests", + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': [ + {'jax-v0.3.23.tar.gz': 'fa8c68a82fa2fcf3d272bf239c77e7028bb6077466a53349ce85f6e85ed623db'}, + {'jax-0.3.9_relax-test-tolerance.patch': + '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d'}, + {'jax-0.3.23_correctly-skip-from_dlpack-tests.patch': + 'a69ce7280ca8bb42e671217f00d9147f8c64b4b7ba65dea7f05f2c6de757b279'}, + {'jax-0.3.23_relax-testPoly5-tolerance.patch': + 'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 6f1f20387537f55c35e8ba28eccdd9d781df88cb Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 11:24:43 +0000 Subject: [PATCH 5815/9987] adding easyconfigs: py-cpuinfo-8.0.0-GCCcore-11.2.0.eb --- .../py-cpuinfo-8.0.0-GCCcore-11.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..354984bda92 --- /dev/null +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'py-cpuinfo' +version = '8.0.0' + +homepage = 'https://github.com/workhorsy/py-cpuinfo' +description = """ Py-cpuinfo gets CPU info with pure Python. +Py-cpuinfo should work without any extra programs or libraries, +beyond what your OS provides. It does not require any +compilation(C/C++, assembly, et cetera) to use. It works with Python 3. +""" +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], + 'modulename': 'cpuinfo', + }), +] + +moduleclass = 'lib' From 72f99433b58ab34b7afcb0c049702d02e605b199 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 14 Dec 2022 13:26:14 +0200 Subject: [PATCH 5816/9987] adding easyconfigs: AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb and patches: AlphaFold-2.3.0_data-dep-paths.patch --- .../AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb | 168 ++++++++++++++++++ .../AlphaFold-2.3.0_data-dep-paths.patch | 136 ++++++++++++++ 2 files changed, 304 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0_data-dep-paths.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..b3442dbb988 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,168 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '3.7.2'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('CUDA', '11.4.1', '', SYSTEM), + ('SciPy-bundle', '2021.10'), + ('PyYAML', '5.4.1'), + ('TensorFlow', '2.7.1', versionsuffix), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.2'), + ('jax', '0.3.23', versionsuffix), # also provides absl-py + ('UCX-CUDA', '1.11.2', versionsuffix), + ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.10.3', versionsuffix), + ('OpenMM', '7.5.1', '-DeepMind-patch'), +] + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.3.0_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + '52055a0b4bf194ae0e1960e6391e501490f82274c975e01c1ff0e353a1cd59d9', # v2.3.0.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '5cff3fc7104e020ef546d23cb4fb1b8d6517562783f055cc55fc65fe2b0248d0', # AlphaFold-2.3.0_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('toolz', '0.11.2', { + 'checksums': ['6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33'], + }), + ('chex', '0.1.5', { + 'checksums': ['686858320f8f220c82a6c7eeb54dcdcaa4f3d7f66690dacd13a24baa1ee8299e'], + }), + ('tabulate', '0.8.10', { + 'checksums': ['6c57f3f3dd7ac2782770155f3adb2db0b1a269637e42f27599925e64b114f519'], + }), + ('jmp', '0.0.2', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['fdb5cec0d10aab4116c2770f24b2adf4f503fcfbb96ce8ef583e1879bdbf1b9b'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('dm-tree', '0.1.7', { + 'modulename': 'tree', + 'checksums': ['30fec8aca5b92823c0e796a2f33b875b4dccd470b57e91e6c542405c5f77fd2a'], + }), + ('websocket-client', '1.3.3', { + 'modulename': 'websocket', + 'checksums': ['d58c5f284d6a9bf8379dab423259fe8f85b70d5fa5d2916d5791a84594b122b1'], + }), + ('docker', '5.0.3', { + 'checksums': ['d916a26b62970e7c2f554110ed6af04c7ccff8e9f81ad17d0d40c75637e227fb'], + }), + ('immutabledict', '2.2.1', { + 'checksums': ['1ddb0edf1bb6c70d0197eb90ce1fe2b2d58502334f5fdfde72d7c633d723ec3a'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "cp %(builddir)s/alphafold-%(version)s/run_alphafold_{features,resume}.py %(installdir)s/bin", + "chmod a+x %(installdir)s/bin/run_alphafold*.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '3', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0_data-dep-paths.patch new file mode 100644 index 00000000000..20a40b14f2b --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0_data-dep-paths.patch @@ -0,0 +1,136 @@ +pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data +(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py); +pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) +update 2.0.1 -> 2.1.0/2.1.2/2.3.0: Thomas Hoffmann (EMBL); +diff -ru alphafold-2.3.0/run_alphafold.py alphafold-2.3.0_data-dep-paths/run_alphafold.py +--- alphafold-2.3.0/run_alphafold.py 2022-12-11 20:36:44.000000000 +0100 ++++ alphafold-2.3.0_data-dep-paths/run_alphafold.py 2022-12-13 17:36:37.258678676 +0100 +@@ -40,6 +40,46 @@ + import numpy as np + + # Internal import (7716). ++use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:]) ++use_monomer_preset = not any("--model_preset=multimer" in s for s in sys.argv[1:]) ++ ++data_dir = os.getenv('ALPHAFOLD_DATA_DIR') ++use_gpu_relax = os.getenv('OPENMM_RELAX')=='CUDA' ++ ++if data_dir: ++ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters_2022_05.fa') ++ uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') ++ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') ++ obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') ++ if use_monomer_preset: ++ pdb_seqres_database_path = None ++ uniprot_database_path = None ++ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') ++ else: ++ pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt') ++ uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.fasta') ++ pdb70_database_path = None ++ if use_reduced_dbs: ++ small_bfd_database_path = os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta') ++ uniref30_database_path = None ++ bfd_database_path = None ++ else: ++ small_bfd_database_path = None ++ bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') ++ uniref30_database_path = os.path.join(data_dir, 'uniref30', 'UniRef30_2021_03') ++else: ++ sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!") ++ uniref90_database_path = None ++ mgnify_database_path = None ++ bfd_database_path = None ++ uniref30_database_path = None ++ pdb70_database_path = None ++ template_mmcif_dir = None ++ obsolete_pdbs_path = None ++ small_bfd_database_path = None ++ uniprot_database_path = None ++ pdb_seqres_database_path = None ++ use_gpu_relax = None + + logging.set_verbosity(logging.INFO) + +@@ -50,7 +90,7 @@ + 'separated by commas. All FASTA paths must have a unique basename as the ' + 'basename is used to name the output directories for each prediction.') + +-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') ++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') + flags.DEFINE_string('output_dir', None, 'Path to a directory that will ' + 'store the results.') + flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'), +@@ -65,27 +105,27 @@ + 'Path to the hmmbuild executable.') + flags.DEFINE_string('kalign_binary_path', shutil.which('kalign'), + 'Path to the Kalign executable.') +-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 ' ++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify ' ++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD ' ++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD ' + 'database for use by HHblits.') +-flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small ' ++flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small ' + 'version of BFD used with the "reduced_dbs" preset.') +-flags.DEFINE_string('uniref30_database_path', None, 'Path to the UniRef30 ' ++flags.DEFINE_string('uniref30_database_path', uniref30_database_path, 'Path to the UniRef30 ' + 'database for use by HHblits.') +-flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot ' ++flags.DEFINE_string('uniprot_database_path', uniprot_database_path, 'Path to the Uniprot ' + 'database for use by JackHMMer.') +-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 ' ++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 ' + 'database for use by HHsearch.') +-flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB ' ++flags.DEFINE_string('pdb_seqres_database_path', pdb_seqres_database_path, 'Path to the PDB ' + 'seqres database for use by hmmsearch.') +-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with ' ++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with ' + 'template mmCIF structures, each named .cif') + flags.DEFINE_string('max_template_date', None, 'Maximum template release date ' + 'to consider. Important if folding historical test sets.') +-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a ' ++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a ' + 'mapping from obsolete PDB IDs to the PDB IDs of their ' + 'replacements.') + flags.DEFINE_enum('db_preset', 'full_dbs', +@@ -124,7 +164,7 @@ + 'result in predictions with distracting stereochemical ' + 'violations but might help in case you are having issues ' + 'with the relaxation stage.') +-flags.DEFINE_boolean('use_gpu_relax', None, 'Whether to relax on GPU. ' ++flags.DEFINE_boolean('use_gpu_relax', use_gpu_relax, 'Whether to relax on GPU. ' + 'Relax on GPU can be much faster than CPU, so it is ' + 'recommended to enable if possible. GPUs must be available' + ' if this setting is enabled.') +@@ -296,6 +336,10 @@ + 'sure it is installed on your system.') + + use_small_bfd = FLAGS.db_preset == 'reduced_dbs' ++ if use_small_bfd and data_dir: ++ bfd_database_path = None ++ uniref30_database_path = None ++ + _check_flag('small_bfd_database_path', 'db_preset', + should_be_set=use_small_bfd) + _check_flag('bfd_database_path', 'db_preset', +@@ -420,13 +464,7 @@ + flags.mark_flags_as_required([ + 'fasta_paths', + 'output_dir', +- 'data_dir', +- 'uniref90_database_path', +- 'mgnify_database_path', +- 'template_mmcif_dir', + 'max_template_date', +- 'obsolete_pdbs_path', +- 'use_gpu_relax', + ]) + + app.run(main) From 747e41bf0b2ee81af6f52d3e5bbeb3fc83830583 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 14 Dec 2022 12:35:48 +0100 Subject: [PATCH 5817/9987] remove cuda_compute_capabilities --- .../easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb index 9bad44f1db6..48839d0ac0c 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb @@ -14,8 +14,6 @@ differentiate, vectorize, JIT to GPU/TPU, and more""" toolchain = {'name': 'foss', 'version': '2021b'} -cuda_compute_capabilities = ["5.0", "6.0", "6.1", "7.0", "7.5", "8.0", "8.6"] - builddependencies = [ ('Bazel', '3.7.2'), ('pytest-xdist', '2.5.0'), From 3e88c0712ff553ef3b7ce784acef597602baf0c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Dec 2022 13:03:46 +0100 Subject: [PATCH 5818/9987] adding easyconfigs: Squidpy-1.2.2-foss-2021b.eb --- .../s/Squidpy/Squidpy-1.2.2-foss-2021b.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb new file mode 100644 index 00000000000..826d06bfc4f --- /dev/null +++ b/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'Squidpy' +version = '1.2.2' + +homepage = 'https://squidpy.readthedocs.io' +description = "Squidpy is a tool for the analysis and visualization of spatial molecular data." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('networkx', '2.6.3'), + ('Pillow', '8.3.2'), + ('tqdm', '4.62.3'), + ('matplotlib', '3.4.3'), + ('xarray', '0.20.1'), + ('statsmodels', '0.13.1'), + ('scikit-image', '0.19.1'), + ('scikit-learn', '1.0.1'), + ('dask', '2022.1.0'), + ('scanpy', '1.9.1'), + ('numba', '0.54.1'), + ('aiohttp', '3.8.1'), + ('zarr', '2.13.3'), +] + +use_pip = True + +exts_list = [ + ('slicerator', '1.1.0', { + 'checksums': ['44010a7f5cd87680c07213b5cabe81d1fb71252962943e5373ee7d14605d6046'], + }), + ('PIMS', '0.6.1', { + 'checksums': ['e2b704461d4ea9bce8b6a22ca35836fe67d6d34537736b405341ae5547194f3b'], + }), + ('dask-image', '2022.9.0', { + 'checksums': ['f123dfd16a7d15c76662a6ac14778509ed5eed9b494f4322e5945e9b15923547'], + }), + ('matplotlib-scalebar', '0.8.1', { + 'checksums': ['14887af1093579c5e6afae51a0a1ecc3f715cdbc5c4d7ef59cdeec76ee6bb15d'], + }), + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('inflect', '6.0.2', { + 'checksums': ['f1a6bcb0105046f89619fde1a7d044c612c614c2d85ef182582d9dc9b86d309a'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('omnipath', '1.0.6', { + 'checksums': ['06f11b537cb1c2773d8eee13d906288f845d96f7b6cf86746ee50920c2651506'], + }), + ('validators', '0.20.0', { + 'checksums': ['24148ce4e64100a2d5e267233e23e7afeb55316b47d30faae7eb6e7292bc226a'], + }), + ('fsspec', '2022.11.0', { + 'checksums': ['259d5fd5c8e756ff2ea72f42e7613c32667dc2049a4ac3d84364a7ca034acb8b'], + }), + ('squidpy', version, { + 'checksums': ['b2af7e9e154aa98d6f1612f707b53e0507261b8153718f7011ba3c1b8ed8daeb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From a3c9c20f321441966980166c621f0a987d113d98 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 12:13:23 +0000 Subject: [PATCH 5819/9987] adding easyconfigs: Pint-0.19.2-GCCcore-11.2.0.eb --- .../p/Pint/Pint-0.19.2-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.19.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.19.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.19.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..565dc406031 --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.19.2-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pint' +version = '0.19.2' + +homepage = 'https://github.com/hgrecco/pint' +description = """Pint is a Python package to define, operate and +manipulate physical quantities: the product of a numerical value and a +unit of measurement. It allows arithmetic operations between them and +conversions from and to different units.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e1d4989ff510b378dad64f91711e7bdabe5ca78d75b06a18569ac454678c4baf'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'numlib' From 71dc315b01714e785678849cab2a466b83d89627 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Dec 2022 13:14:33 +0100 Subject: [PATCH 5820/9987] add easyconfig for zarr dependency of Squidpy --- .../z/zarr/zarr-2.13.3-foss-2021b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2021b.eb b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2021b.eb new file mode 100644 index 00000000000..b73fbcf4961 --- /dev/null +++ b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2021b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'zarr' +version = '2.13.3' + +homepage = 'https://zarr.readthedocs.io/en/stable/' +description = """Zarr is a Python package providing an implementation of compressed, +chunked, N-dimensional arrays, designed for use in parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + ('monotonic', '1.6', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/atdt/monotonic/archive'], + 'checksums': ['9609c249aed584fd714811014870650d08d6f6414402b5a190663c49bf83b221'], + }), + ('numcodecs', '0.10.2', { + 'checksums': ['22838c6b3fd986bd9c724039b88870057f790e22b20e6e1cbbaa0de142dd59c4'], + }), + (name, version, { + 'checksums': ['db24b090616c638f65e33a6bc5d956d642221182961515ccbc28b17fb0d0b48c'], + }), +] + +moduleclass = 'data' From d4d1f3f6319446d74db026e85a78500d75249031 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 12:15:23 +0000 Subject: [PATCH 5821/9987] adding easyconfigs: pydantic-1.10.2-GCCcore-11.2.0.eb --- .../pydantic-1.10.2-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..022227e23b0 --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'pydantic' +version = '1.10.2' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('typing_extensions', '4.3.0', { + 'checksums': ['e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6'], + }), + (name, version, { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), +] + +moduleclass = 'devel' From 1f45fb9d467f0abf8b781ec8ce34b8db700251e8 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 12:19:25 +0000 Subject: [PATCH 5822/9987] adding easyconfigs: pytest-7.1.3-GCCcore-11.2.0.eb --- .../p/pytest/pytest-7.1.3-GCCcore-11.2.0.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest/pytest-7.1.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.1.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.1.3-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..97f957621d5 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-7.1.3-GCCcore-11.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.1.3' + +homepage = 'https://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] +dependencies = [('Python', '3.9.6')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('py', '1.11.0', { + 'checksums': ['51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719'], + }), + ('attrs', '22.1.0', { + 'modulename': 'attr', + 'checksums': ['29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6'], + }), + ('pluggy', '1.0.0', { + 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], + }), + ('atomicwrites', '1.4.1', { + 'checksums': ['81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11'], + }), + ('more-itertools', '8.14.0', { + 'modulename': 'more_itertools', + 'checksums': ['c09443cd3d5438b8dafccd867a6bc1cb0894389e90cb53d227456b0b0bccb750'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.7.post1', { + 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], + }), + ('iniconfig', '1.1.1', { + 'checksums': ['bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32'], + 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + (name, version, { + 'checksums': ['4f365fec2dff9c1162f834d9f18af1ba13062db0c708bf7b946f8a5c76180c39'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From d2eef69054b185c31bfa02bacf998c0a2bace16d Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 12:28:54 +0000 Subject: [PATCH 5823/9987] adding easyconfigs: simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb --- ...mint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb new file mode 100644 index 00000000000..ef742955701 --- /dev/null +++ b/easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb @@ -0,0 +1,51 @@ +# For the various build options see here: +# https://www.bennyp.org/research/simint/README.txt +# lmax is set to 5 which is widely used it seems +# vec is set to avx, which should work on most platforms +# This might be changed to other values, if required +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'simint' +version = '0.7' +local_lmax = '5' +local_vec = 'avx' + +# custom configuration, to be used as dependency for PSI4 +versionsuffix = '-lmax-%s-vec-%s-psi4' % (local_lmax, local_vec) + +homepage = 'https://www.bennyp.org/research/simint/' +description = """Simint is a vectorized implementation of the Obara-Saika (OS) +method of calculating electron repulsion integrals. Speedup is gained by +vectorizing the primitive loop of the OS algorithm, with additional vectorization +and optimizations left to the compiler.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://www.bennyp.org/research/simint/download/'] +sources = ['%(name)s-v%(version)s.tar.bz2'] +checksums = ['9851fa2323924d4732dd611b366219f4408c8561556abb5e4fa6dbb64a8f919c'] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +local_common_configopts = '-DSIMINT_MAXAM=%s ' % local_lmax +local_common_configopts += '-DSIMINT_VECTOR=%s ' % local_vec +local_common_configopts += '-DENABLE_TESTS=ON ' +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# run test to valicate accuracy +runtest = 'OMP_NUM_THREADS=4 test/test_eri ../%(name)s-v%(version)s/test/dat/' + +sanity_check_paths = { + 'files': ['lib/libsimint.a', 'lib/libsimint.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'chem' From 77557e907dbdc2f136e544e1dfd23442b130c4e3 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 12:50:42 +0000 Subject: [PATCH 5824/9987] sanity_pip_check added --- .../easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb index 354984bda92..2823de4d89a 100644 --- a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb @@ -18,6 +18,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_list = [ (name, version, { From fca54e9630b424b829639bba0bd3afd87fd892a9 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 12:53:33 +0000 Subject: [PATCH 5825/9987] download_dep_fail removed as PythonBundle --- .../easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb index 022227e23b0..da47b586bf1 100644 --- a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb @@ -14,7 +14,6 @@ dependencies = [ ('Python', '3.9.6'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From 89508cd848b03bf51e35f5f83a8beca356277d28 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 14:52:01 +0000 Subject: [PATCH 5826/9987] Binutils added --- .../p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb index 2823de4d89a..dab4b630329 100644 --- a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-8.0.0-GCCcore-11.2.0.eb @@ -13,9 +13,9 @@ compilation(C/C++, assembly, et cetera) to use. It works with Python 3. """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -dependencies = [ - ('Python', '3.9.6'), -] +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] use_pip = True sanity_pip_check = True From eeba836c0c1f4c6a7a9a5f9e2d88ff4469f1c062 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 14 Dec 2022 16:04:06 +0000 Subject: [PATCH 5827/9987] adding easyconfigs: SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb --- ...ignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb new file mode 100644 index 00000000000..ae2e384e07b --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0g' +_suffix = 'fast' +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = '-' + _suffix + _cuda_suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +unpack_options = '--strip-components=1' +checksums = ['a16fcea2b30067d2622d446031978bd86927e2e1cecf29a567c7922f6861b5aa'] + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy > 1.19.2 + ('tqdm', '4.64.0'), # tqdm > 4.46.1 + ('PyTorch', '1.12.0', _cuda_suffix), # torch > 1.7.0 + ('matplotlib', '3.5.2'), # matplotlib > 3.3.2 +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' From da09c8997509458bf100b9939088cd662590be89 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 14 Dec 2022 16:05:51 +0000 Subject: [PATCH 5828/9987] add non-CUDA version --- .../s/SignalP/SignalP-6.0g-foss-2022a-fast.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast.eb diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast.eb new file mode 100644 index 00000000000..4dcd1681be2 --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0g' +_suffix = 'fast' +versionsuffix = '-' + _suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +unpack_options = '--strip-components=1' +checksums = ['a16fcea2b30067d2622d446031978bd86927e2e1cecf29a567c7922f6861b5aa'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy > 1.19.2 + ('tqdm', '4.64.0'), # tqdm > 4.46.1 + ('PyTorch', '1.12.0'), # torch > 1.7.0 + ('matplotlib', '3.5.2'), # matplotlib > 3.3.2 +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' From 0939f4a9973f5daa968acc3aab6efb38ae33bbd2 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 16:14:18 +0000 Subject: [PATCH 5829/9987] adding easyconfigs: TOML-Fortran-0.3.1-GCC-11.2.0.eb --- .../TOML-Fortran-0.3.1-GCC-11.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.2.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..5bfab710a6b --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.3.1' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7586f0be7dc88dddba4d4e42059b84baa2688a2784bdc1d1f37112ab3edb88e1'] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +sanity_check_paths = { + 'files': ['include/toml-f/GNU-11.2.0/tomlf.mod', 'lib/libtoml-f.a'], + 'dirs': ['include/toml-f/GNU-11.2.0', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' From 9d1bbb3219bc9bd115a91848e24d571fa56b3cbd Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 16:19:36 +0000 Subject: [PATCH 5830/9987] adding easyconfigs: mstore-0.2.0-GCC-11.2.0.eb --- .../m/mstore/mstore-0.2.0-GCC-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..df8ae82f892 --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = 'Molecular structure store for testing' + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/grimme-lab/mstore/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d'] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +sanity_check_paths = { + 'files': ['bin/mstore-info', 'bin/mstore-fortranize', 'bin/mctc-convert'], + 'dirs': ['include/mstore', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' From 529a5c6be3e548857975470645d406bc03256193 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Dec 2022 17:29:52 +0100 Subject: [PATCH 5831/9987] adding easyconfigs: Seurat-4.3.0-foss-2021b-R-4.2.0.eb --- .../Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb new file mode 100644 index 00000000000..6457985022a --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb @@ -0,0 +1,72 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.3.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] + +dependencies = [ + ('R', '4.2.0'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} + +exts_list = [ + ('Matrix', '1.5-3', { + 'checksums': ['4e720f4edc97b1c09646a445851b1ce955caf6b1de8306a2283328b526fee00d'], + }), + ('sp', '1.5-1', { + 'checksums': ['69b9eab481d389bbb736d2adcf50c180aca248c3ffc4ebda8ffe2accc5f229df'], + }), + ('SeuratObject', '4.1.3', { + 'checksums': ['585d2754f6165a367f0f458523f0a25d4d4160c929c931b27c5603cc6bd986d3'], + }), + ('sctransform', '0.3.5', { + 'checksums': ['c08e56df05d64ed04ee53eb9e1d4d321da8aff945e36d56db1d5ceb1cd7e6e0b'], + }), + ('uwot', '0.1.14', { + 'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'], + }), + ('spatstat.utils', '3.0-1', { + 'checksums': ['cba1c7806564fd9145ca15edf77233d6ba5609f0989f7812221f5fc1ece0b91a'], + }), + ('spatstat.data', '3.0-0', { + 'checksums': ['cff9058a88489020a4a05b9576cd452f37fa9b42084873c474d06931f5187057'], + }), + ('spatstat.geom', '3.0-3', { + 'checksums': ['6e5b56c60e774a0cdcaa5a8ffde071225f233832446a341588bd8a7840913c84'], + }), + ('spatstat.random', '3.0-1', { + 'checksums': ['938c845c063b8781bf894c0a67537e7b2a7c425a4beba4a95ec9d2c37b43e5b6'], + }), + ('spatstat.sparse', '3.0-0', { + 'checksums': ['99be0a3c7592760fdf1668dc0811f75ed91c400390d1ecc3d5e643255f501ad2'], + }), + ('spatstat.explore', '3.0-5', { + 'checksums': ['9f438a12fac3f3e1d0bd550b1393c1e5732be694517b0878db09da557d6dc862'], + }), + (name, version, { + 'checksums': ['7ebacb3b86f74279de60b597f9a6e728f0668719811b0dca3425d21762fff97c'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 2fb486d0da9583e8dc6c1de37aa689514f1a9d80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Dec 2022 17:30:36 +0100 Subject: [PATCH 5832/9987] stick to scanpy 1.8.2 as dependency for Squidpy --- easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb index 826d06bfc4f..f60b9abeeab 100644 --- a/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb @@ -20,7 +20,7 @@ dependencies = [ ('scikit-image', '0.19.1'), ('scikit-learn', '1.0.1'), ('dask', '2022.1.0'), - ('scanpy', '1.9.1'), + ('scanpy', '1.8.2'), ('numba', '0.54.1'), ('aiohttp', '3.8.1'), ('zarr', '2.13.3'), From df96a3095825106ca2dd972234e938a9ff692c51 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 14 Dec 2022 17:32:38 +0000 Subject: [PATCH 5833/9987] Update SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb --- .../s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb index ae2e384e07b..9e3f52167c2 100644 --- a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb @@ -30,7 +30,7 @@ unpack_options = '--strip-components=1' checksums = ['a16fcea2b30067d2622d446031978bd86927e2e1cecf29a567c7922f6861b5aa'] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), # numpy > 1.19.2 ('tqdm', '4.64.0'), # tqdm > 4.46.1 From 74cd8fe2f403943ee290756af4d52e267663d8cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Dec 2022 21:58:30 +0100 Subject: [PATCH 5834/9987] stick to R 4.1.2 + Bioconductor 3.14 as dependency for Seurat 4.3.0 with foss/2021b --- ...ss-2021b-R-4.2.0.eb => Seurat-4.3.0-foss-2021b-R-4.1.2.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/Seurat/{Seurat-4.3.0-foss-2021b-R-4.2.0.eb => Seurat-4.3.0-foss-2021b-R-4.1.2.eb} (96%) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb similarity index 96% rename from easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb rename to easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb index 6457985022a..b98250be5b3 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb @@ -16,8 +16,8 @@ source_urls = [ ] dependencies = [ - ('R', '4.2.0'), - ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('R', '4.1.2'), + ('R-bundle-Bioconductor', '3.14', versionsuffix), ] exts_defaultclass = 'RPackage' From 734018cccccf006dcec79dd1c6fbc873423845cd Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 15 Dec 2022 14:19:04 +0800 Subject: [PATCH 5835/9987] adding easyconfigs: umap-learn-0.5.3-foss-2022a.eb --- .../umap-learn/umap-learn-0.5.3-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb new file mode 100644 index 00000000000..bc9b53ee272 --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb @@ -0,0 +1,41 @@ +# Author: Denis Krišťák (INUITS) +# This is a contribution from HPCNow! (http://hpcnow.com) +# Update: Erica Bianco +# License:: GPL-v3.0 +easyblock = "PythonBundle" + +name = 'umap-learn' +version = '0.5.3' + +homepage = 'https://umap-learn.readthedocs.io/en/latest/' +description = """ +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique +that can be used for visualisation similarly to t-SNE, but also for general non-linear +dimension reduction. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('numba', '0.56.4'), + ('LLVM', '14.0.3'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('pynndescent', '0.5.7', { + 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], + }), + (name, version, { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 8fb7c15d6bd7201bcc50bf54bb66021a3c7ada42 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 15 Dec 2022 14:51:31 +0800 Subject: [PATCH 5836/9987] adding easyconfigs: cutadapt-4.2-GCCcore-11.3.0.eb, pigz-2.7-GCCcore-11.3.0.eb, python-isal-1.1.0-GCCcore-11.3.0.eb --- .../c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb | 56 +++++++++++++++++++ .../p/pigz/pigz-2.7-GCCcore-11.3.0.eb | 45 +++++++++++++++ .../python-isal-1.1.0-GCCcore-11.3.0.eb | 36 ++++++++++++ 3 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e80a64e1148 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb @@ -0,0 +1,56 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '4.2' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('pigz', '2.7'), + ('Python', '3.10.4'), + ('python-isal', '1.1.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '1.7.0', { + 'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'], + }), + ('dnaio', '0.10.0', { + 'checksums': ['de51a50948f00b864297d74eddb588fbee5ac229855754e77564d18b24619d18'], + }), + (name, version, { + 'checksums': ['ab0ac450baecc1576cc5ccbc06eab2685be9ee7676763938237d954a644237f1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cutadapt --help", + "cutadapt --version", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..95cc9bff5e7 --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.7' + +homepage = 'https://zlib.net/pigz/' + +description = """ + pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. pigz was written by Mark Adler, and + uses the zlib and pthread libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'https://zlib.net/pigz/', + 'https://zlib.net/pigz/fossils/', +] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-2.6_makefile.patch'] +checksums = [ + {'pigz-2.7.tar.gz': 'b4c9e60344a08d5db37ca7ad00a5b2c76ccb9556354b722d56d55ca7e8b1c707'}, + {'pigz-2.6_makefile.patch': '7e37175714d43c946373d07c522ec98a77c0f8572a9d448f759c41f6f060275d'}, +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ['bin/pigz', 'bin/unpigz'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..24db46643c1 --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '1.1.0' + +homepage = 'https://github.com/pycompression/python-isal' +description = """Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'pycompression' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3fa7f5ac22350cf9c4370aa725dea39c4155123864fff4bf6e6392f83976c86f'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('ISA-L', '2.30.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' +installopts = '--no-binary isal' + +options = {'modulename': 'isal'} + +moduleclass = 'lib' From 72cfc12469eb616cd05c7c7485dcda449400a352 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 15 Dec 2022 15:03:24 +0800 Subject: [PATCH 5837/9987] adding easyconfigs: FastTree-2.1.11-GCCcore-11.3.0.eb --- .../FastTree-2.1.11-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a79c7a054da --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.38')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' From 7d41424849296648069cfb677fd4045d476ce732 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 15 Dec 2022 15:06:40 +0800 Subject: [PATCH 5838/9987] adding easyconfigs: scikit-bio-0.5.7-foss-2022a.eb --- .../scikit-bio/scikit-bio-0.5.7-foss-2022a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb new file mode 100644 index 00000000000..8c60a0e7d9f --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scikit-bio' +version = '0.5.7' + +homepage = 'http://scikit-bio.org' +description = """scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms +and educational resources for bioinformatics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('scikit-learn', '1.1.2'), + ('IPython', '8.5.0'), + ('h5py', '3.7.0'), + ('Pillow', '9.1.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('msgpack', '1.0.4', { + 'checksums': ['f5d869c18f030202eb412f08b28d2afeea553d6613aee89e200d7aca7ef01f5f'], + }), + ('CacheControl', '0.12.11', { + 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], + }), + ('hdmedians', '0.14.2', { + 'checksums': ['b47aecb16771e1ba0736557255d80ae0240b09156bff434321de559b359ac2d6'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + (name, version, { + 'modulename': 'skbio', + 'checksums': ['6343ca0c621e2fcc5d1c042c8be3200664c5325956a83bea751cf1bcc75d1da9'], + }), +] + +moduleclass = 'bio' From ea130bd99d852a89c5db6faec4b0dcbf31f78659 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 15 Dec 2022 15:13:36 +0800 Subject: [PATCH 5839/9987] adding easyconfigs: statsmodels-0.13.1-foss-2022a.eb --- .../statsmodels-0.13.1-foss-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2022a.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2022a.eb new file mode 100644 index 00000000000..7b353348d04 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.13.1' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + (name, version, { + 'checksums': ['006ec8d896d238873af8178d5475203844f2c391194ed8d42ddac37f5ff77a69'], + }), +] + +moduleclass = 'math' From 404928f272ba5fe3c34c25373e8dabecf90a6647 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 10:24:05 +0100 Subject: [PATCH 5840/9987] adding easyconfigs: CodAn-1.2-foss-2021b.eb --- .../c/CodAn/CodAn-1.2-foss-2021b.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb new file mode 100644 index 00000000000..67ff7133a6b --- /dev/null +++ b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb @@ -0,0 +1,52 @@ +# author: Denis Kristak (INUITS) +easyblock = "Binary" + +name = "CodAn" +version = "1.2" + +homepage = "https://github.com/pedronachtigall/CodAn" +description = """CodAn (Coding sequence Annotator) is a computational tool designed to characterize the CDS and UTR +regions on transcripts from any Eukaryote species.""" + +toolchain = {"name": "foss", "version": "2021b"} + +source_urls = ["https://github.com/pedronachtigall/CodAn/archive"] +sources = ["v%(version)s.tar.gz"] +checksums = ['34962ac67dc94da0bff6e032568e38388726bf1d7efceed462d6b7c841b087b7'] + +dependencies = [ + ("Python", "3.9.6"), + ("Biopython", "1.79"), + ("BioPerl", "1.7.8"), + ("Perl", "5.34.0"), +] + +extract_sources = True + +install_cmd = "cp -r %(builddir)s/* %(installdir)s/ && " +install_cmd += "tar -xf %(installdir)s/%(name)s-%(version)s/CodAn.tar.gz && " +install_cmd += "mkdir %(installdir)s/bin && " +install_cmd += "mv %(installdir)s/%(name)s-%(version)s/bin/* %(installdir)s/bin && " +install_cmd += "chmod u+rwx %(installdir)s/bin/* " + + +sanity_check_paths = { + "files": ["bin/%(namelower)s.py"], + "dirs": [], +} + +local_sanity_check_cmd = "mkdir %(installdir)s/eb_test && " +local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/models/VERT_full.zip %(installdir)s/eb_test && " +local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/tutorial/transcripts.fa %(installdir)s/eb_test && " +local_sanity_check_cmd += "cd %(installdir)s/eb_test/ && " +local_sanity_check_cmd += "unzip VERT_full.zip && " +local_sanity_check_cmd += ( + "codan.py -t transcripts.fa -m VERT_full | grep 'prediction finished!'" +) + +sanity_check_commands = [ + "%(namelower)s.py --help", + local_sanity_check_cmd, +] + +moduleclass = "bio" From 8f94311bea61d8db3af8fcb6dde94eab78137885 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 10:27:40 +0100 Subject: [PATCH 5841/9987] adding easyconfigs: RegTools-0.5.2-foss-2021b.eb --- .../r/RegTools/RegTools-0.5.2-foss-2021b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb new file mode 100644 index 00000000000..b1a7c9fc772 --- /dev/null +++ b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb @@ -0,0 +1,39 @@ +# updated: Denis Kristak (INUITS) +easyblock = "CMakeMake" + +name = "RegTools" +version = "0.5.2" + +homepage = "https://regtools.readthedocs.org" +description = """RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a +regulatory and splicing context.""" + +toolchain = {"name": "foss", "version": "2021b"} + +source_urls = ["https://github.com/griffithlab/%(namelower)s/archive"] +sources = ["%(version)s.tar.gz"] +checksums = ['24d3bc18174237e0fc2d0330839c8dc21c97cdb7d6e528c518188c10f17f3e7e'] + +builddependencies = [ + ("CMake", "3.21.1"), +] + +# required by included scripts +dependencies = [ + ("Python", "3.9.6"), + ("PyYAML", "5.4.1"), # required by create_IGVsessions.py script + ("R", "4.1.2"), +] + +# 'make install' is not supported... +install_cmd = "mkdir %(installdir)s/bin && cp -a regtools %(installdir)s/bin/ && " +install_cmd += "cp -a %(builddir)s/regtools-%(version)s/scripts %(installdir)s/" + +sanity_check_paths = { + "files": ["bin/regtools"], + "dirs": ["scripts"], +} + +sanity_check_commands = ["regtools --help"] + +moduleclass = "bio" From 7ae6bbd01fa2c86580091d38a88bbdaa3ef8d104 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 10:29:39 +0100 Subject: [PATCH 5842/9987] adding easyconfigs: BEDOPS-2.4.41-foss-2021b.eb --- .../b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb new file mode 100644 index 00000000000..0e4aad5edd5 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# updated: Denis Kristak (INUITS) + +easyblock = "MakeCp" + +name = "BEDOPS" +version = "2.4.41" + +homepage = "http://%(namelower)s.readthedocs.io/en/latest/index.html" +description = """BEDOPS is an open-source command-line toolkit that performs highly efficient and + scalable Boolean and other set operations, statistical calculations, archiving, conversion and + other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for + distributing whole-genome analyses across a computational cluster.""" + +toolchain = {"name": "foss", "version": "2021b"} +toolchainopts = {"pic": True} + +source_urls = ["https://github.com/%(namelower)s/%(namelower)s/archive/"] +sources = ["v%(version)s.tar.gz"] +checksums = ['3b868c820d59dd38372417efc31e9be3fbdca8cf0a6b39f13fb2b822607d6194'] + +# else build of jansson library fails with: "configure: error: C compiler cannot create executables" +prebuildopts = "unset LIBS && " +# builds all variants and copies executables to bin directory +buildopts = " all && make install" +# actually used variant is linked to via symlinks +keepsymlinks = True + +files_to_copy = ["bin"] + +sanity_check_paths = { + "files": [ + "bin/%s" % x for x in ["bam2bed", "%(namelower)s", "convert2bed", "unstarch"] + ], + "dirs": [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = "bio" From 7bc7b4f595d6ad364bc940e397661e250b3bbd70 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 10:33:49 +0100 Subject: [PATCH 5843/9987] adding easyconfigs: GUSHR-2020-09-28-foss-2021b.eb --- .../g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb diff --git a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb new file mode 100644 index 00000000000..52e49135fd6 --- /dev/null +++ b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb @@ -0,0 +1,37 @@ +# author: Denis Kristak (INUITS) +easyblock = "Tarball" + +name = "GUSHR" +version = "2020-09-28" +local_commit = "ee26d5c" + +homepage = "https://github.com/Gaius-Augustus/GUSHR" +description = "Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation." + +toolchain = {"name": "foss", "version": "2021b"} + +source_urls = ["https://github.com/Gaius-Augustus/GUSHR/archive"] +sources = [ + { + "download_filename": "%s.tar.gz" % local_commit, + "filename": SOURCE_TAR_GZ, + } +] +checksums = ['81fd9c372a45af1688c2954932f94efc4c637144f874e16be41d1b18936a5303'] + +dependencies = [ + ('Java', '11', '', True), + ("AUGUSTUS", "3.4.0"), + ("GLib", "2.69.1"), +] + +sanity_check_paths = { + "files": ["gushr.py"], + "dirs": [], +} +sanity_check_commands = [ + """cd example; ./download_rnaseq.sh ; cd - ; + ./gushr.py -t example/augustus.gtf -b example/RNAseq.bam -g example/genome.fa -o utrs""" +] + +moduleclass = "bio" From a5a3bf299dd84dd429dd3ec512f4c7994eb57b1b Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 10:39:12 +0100 Subject: [PATCH 5844/9987] adding easyconfigs: PsiCLASS-1.0.3-GCC-11.2.0.eb --- .../p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb new file mode 100644 index 00000000000..399609c8b90 --- /dev/null +++ b/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb @@ -0,0 +1,34 @@ +# author: Denis Kristak (INUITS) +easyblock = "MakeCp" + +name = "PsiCLASS" +version = "1.0.3" + +homepage = "https://github.com/splicebox/PsiCLASS" +description = """PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.""" + +toolchain = {"name": "GCC", "version": "11.2.0"} + +source_urls = ["https://github.com/splicebox/PsiCLASS/archive/"] +sources = ["v%(version)s.tar.gz"] + +checksums = [ + "c60c0f33f9a076b97ccdba68b9140a5fb6936a5c5e309d70b3d0cf558828f73d", # v1.0.3.tar.gz +] + +parallel = 1 + +files_to_copy = ["*"] + +modextrapaths = {"PATH": [""]} + +sanity_check_paths = { + "files": ["classes", "grader", "psiclass"], + "dirs": [], +} + +sanity_check_commands = [ + "psiclass -b $EBROOTPSICLASS/example/s1.bam,$EBROOTPSICLASS/example/s2.bam" +] + +moduleclass = "bio" From 90af87a3379db6e2d2689962534f8ad76762ba8f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 10:44:16 +0100 Subject: [PATCH 5845/9987] adding easyconfigs: GeneMark-ET-4.71-GCCcore-11.2.0.eb, BRAKER-2.1.6-foss-2021b.eb --- .../b/BRAKER/BRAKER-2.1.6-foss-2021b.eb | 41 +++++++++++++++++++ .../GeneMark-ET-4.71-GCCcore-11.2.0.eb | 31 ++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb new file mode 100644 index 00000000000..a1aa7296bbc --- /dev/null +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb @@ -0,0 +1,41 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'Tarball' + +name = 'BRAKER' +version = '2.1.6' + +homepage = 'https://github.com/Gaius-Augustus/BRAKER' +description = """BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET + and AUGUSTUS in novel eukaryotic genomes.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/Gaius-Augustus/BRAKER/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06'] + +dependencies = [ + ('Perl', '5.34.0'), + ('AUGUSTUS', '3.4.0'), + ('GeneMark-ET', '4.71'), + ('BamTools', '2.5.2'), + ('SAMtools', '1.14'), + ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', SYSTEM), + ('spaln', '2.4.12'), + ('Exonerate', '2.4.0'), + ('BLAST+', '2.12.0'), + ('Biopython', '1.79'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] + +sanity_check_paths = { + 'files': ['scripts/align2hints.pl', 'scripts/braker.pl', 'scripts/findGenesInIntrons.pl', 'scripts/startAlign.pl'], + 'dirs': ['docs', 'example'], +} + +sanity_check_commands = ["braker.pl --help"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..9d7b048917c --- /dev/null +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +# updated: Denis Kristak (INUITS) +easyblock = "Tarball" + +name = "GeneMark-ET" +version = "4.71" + +homepage = "http://exon.gatech.edu/GeneMark" +description = "Eukaryotic gene prediction suite with automatic training" + +toolchain = {"name": "GCCcore", "version": "11.2.0"} + +sources = ["gmes_linux_64-%(version)s.tar.gz"] +checksums = ['29adf580ccee6f69d19045bedc3a53e7a71b4c39a95409be3e96d3e9dca83c95'] + +download_instructions = """ +1. complete the license form: http://exon.gatech.edu/GeneMark/license_download.cgi +2. rename the tarball: `mv gmes_linux_64.tar.gz gmes_linux_64-%(version)s.tar.gz` +""" + +dependencies = [("Perl", "5.34.0")] + +fix_perl_shebang_for = ["*.pl"] + +sanity_check_paths = { + "files": ["gmes.cfg", "gmes_petap.pl"], + "dirs": ["lib"], +} + +modextrapaths = {"PATH": ""} + +moduleclass = "bio" From c737d4a5a6ba535628a01d037781f9f1e8e86df7 Mon Sep 17 00:00:00 2001 From: Victor Lopez Herrero Date: Thu, 15 Dec 2022 10:47:16 +0100 Subject: [PATCH 5846/9987] Apply suggestions from code review Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb | 9 +++++++++ easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb index fa248865fb6..48dba7492e1 100644 --- a/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb @@ -23,4 +23,13 @@ checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] configopts = '--with-mpi' +sanity_check_paths = { + 'files': [ + 'bin/dlb', + 'lib/libdlb.a', 'lib/libdlb.%s' % SHLIB_EXT, + 'lib64/libdlb.%s' % SHLIB_EXT + ], + 'dirs': ['include'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb index be30e500a7d..523228ad609 100644 --- a/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb @@ -23,4 +23,13 @@ checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] configopts = '--with-mpi' +sanity_check_paths = { + 'files': [ + 'bin/dlb', + 'lib/libdlb.a', 'lib/libdlb.%s' % SHLIB_EXT, + 'lib64/libdlb.%s' % SHLIB_EXT + ], + 'dirs': ['include'], +} + moduleclass = 'lib' From 45164671e1362a332e107e289a00e807011b77c2 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 15 Dec 2022 10:53:17 +0100 Subject: [PATCH 5847/9987] Update GUSHR-2020-09-28-foss-2021b.eb code-style change + deprecation param err --- .../easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb index 52e49135fd6..c87b26a22bd 100644 --- a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb @@ -6,7 +6,9 @@ version = "2020-09-28" local_commit = "ee26d5c" homepage = "https://github.com/Gaius-Augustus/GUSHR" -description = "Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation." +description = """ +Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation. +""" toolchain = {"name": "foss", "version": "2021b"} @@ -20,7 +22,7 @@ sources = [ checksums = ['81fd9c372a45af1688c2954932f94efc4c637144f874e16be41d1b18936a5303'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ("AUGUSTUS", "3.4.0"), ("GLib", "2.69.1"), ] From fcf59d2a4f29b613e3ec9a4d5748cfe7e65ad1b0 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 11:01:44 +0100 Subject: [PATCH 5848/9987] adding easyconfigs: SRA-Toolkit-3.0.0-gompi-2021b.eb, ncbi-vdb-3.0.0-gompi-2021b.eb and patches: SRA-Toolkit-3.0.0_fix-LD_LIBRARY_PATH.patch, ncbi-vdb-3.0.0_hdf5_api.patch, ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch, ncbi-vdb-3.0.0_cstdlib.patch --- .../n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb | 58 ++++++++++++ .../n/ncbi-vdb/ncbi-vdb-3.0.0_cstdlib.patch | 12 +++ .../ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch | 35 ++++++++ .../n/ncbi-vdb/ncbi-vdb-3.0.0_hdf5_api.patch | 13 +++ .../SRA-Toolkit-3.0.0-gompi-2021b.eb | 88 +++++++++++++++++++ ...RA-Toolkit-3.0.0_fix-LD_LIBRARY_PATH.patch | 35 ++++++++ 6 files changed, 241 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_cstdlib.patch create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_hdf5_api.patch create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0_fix-LD_LIBRARY_PATH.patch diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb new file mode 100644 index 00000000000..c4d8e53a8ed --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb @@ -0,0 +1,58 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '3.0.0' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch', + 'ncbi-vdb-3.0.0_cstdlib.patch', + 'ncbi-vdb-3.0.0_hdf5_api.patch', +] +checksums = [ + {'ncbi-vdb-3.0.0.tar.gz': '154317ef265104861fe8d3d2e439939ae98f33b1e28da3c45f32ae8534dbfad7'}, + {'ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch': 'a87d1ab79118e2392d197dbb684347b75a6a26509108cce8a12590feb929e38b'}, + {'ncbi-vdb-3.0.0_cstdlib.patch': '89431a477f93c62c81c530aaa36ccd17a3b800a5c0d9e6d752b697d37dd16177'}, + {'ncbi-vdb-3.0.0_hdf5_api.patch': '34bdad822248118a011b5106fe5b5efaa068c19b66ed10f949a9c0b07a79de8b'}, +] + +builddependencies = [ + ('Perl', '5.34.0', '-minimal'), + ('Python', '3.9.6', '-bare'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('file', '5.41'), # provides libmagic + ('HDF5', '1.12.1'), + ('libxml2', '2.9.10'), + ('bzip2', '1.0.8'), +] + +# add addtional libraries needed to statically link HDF5 from EB +preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl &&" + +configopts = "--build-prefix=%(builddir)s " # change default build directory +configopts += "--with-magic-prefix=$EBROOTFILE " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +# replace hardcoded optimization flags with EB settings +prebuildopts = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " +preinstallopts = 'EBFLAGS="$CFLAGS" ' + +sanity_check_paths = { + 'files': ['include/ncbi/ncbi.h', 'include/ncbi/vdb-blast.h'] + + [('lib/libncbi-%s.%s' % (k, e)) for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib', 'lib64'], +} + +moduleclass = 'bio' \ No newline at end of file diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_cstdlib.patch b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_cstdlib.patch new file mode 100644 index 00000000000..b71a58c5404 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_cstdlib.patch @@ -0,0 +1,12 @@ +Add C standard library header. John Dey, Fred Hutch Cancer Center +diff -ruN ncbi-vdb-3.0.0.orig/vdb3/platform/memory/PrimordialMemoryMgr.cpp ncbi-vdb-3.0.0/vdb3/platform/memory/PrimordialMemoryMgr.cpp +--- ncbi-vdb-3.0.0.orig/vdb3/platform/memory/PrimordialMemoryMgr.cpp 2022-02-10 13:50:11.000000000 -0800 ++++ ncbi-vdb-3.0.0/vdb3/platform/memory/PrimordialMemoryMgr.cpp 2022-08-18 14:24:21.242597000 -0700 +@@ -24,6 +24,7 @@ + * + */ + ++#include + #include + + #include \ No newline at end of file diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch new file mode 100644 index 00000000000..8a358e937e2 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch @@ -0,0 +1,35 @@ +don't blindly overwrite $LD_LIBRARY_PATH +based on work by: Kenneth Hoste (HPC-UGent) +diff -ruN ncbi-vdb-3.0.0.orig/build/ld.linux.dlib.sh ncbi-vdb-3.0.0/build/ld.linux.dlib.sh +--- ncbi-vdb-3.0.0.orig/build/ld.linux.dlib.sh 2022-02-10 13:50:11.000000000 -0800 ++++ ncbi-vdb-3.0.0/build/ld.linux.dlib.sh 2022-09-19 16:35:44.390187000 -0700 +@@ -83,8 +83,7 @@ + done + + # update LD_LIBRARY_PATH +- unset LD_LIBRARY_PATH +- export LD_LIBRARY_PATH="$LDIRS:$XDIRS" ++ export LD_LIBRARY_PATH="$LDIRS:$XDIRS:$LD_LIBRARY_PATH" + + # tack on libraries, finding as we go + for LIB in $LIBS +@@ -305,4 +304,4 @@ + echo "$MSG" >> $LOGFILE + + "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5" +-fi +\ No newline at end of file ++fi +diff -ruN ncbi-vdb-3.0.0.orig/build/ld.linux.exe.sh ncbi-vdb-3.0.0/build/ld.linux.exe.sh +--- ncbi-vdb-3.0.0.orig/build/ld.linux.exe.sh 2022-02-10 13:50:11.000000000 -0800 ++++ ncbi-vdb-3.0.0/build/ld.linux.exe.sh 2022-09-19 16:36:32.114647000 -0700 +@@ -91,8 +91,7 @@ + done + + # update LD_LIBRARY_PATH +- unset LD_LIBRARY_PATH +- export LD_LIBRARY_PATH="$LDIRS:$XDIRS" ++ export LD_LIBRARY_PATH="$LDIRS:$XDIRS:$LD_LIBRARY_PATH" + + # tack on libraries, finding as we go + for LIB in $LIBS diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_hdf5_api.patch b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_hdf5_api.patch new file mode 100644 index 00000000000..e3e7aaa68b9 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_hdf5_api.patch @@ -0,0 +1,13 @@ +ensuring compatibility with the newest hdf5 version +diff -ruN ncbi-vdb-3.0.0_orig/libs/hdf5/hdf5dir.c ncbi-vdb-3.0.0/libs/hdf5/hdf5dir.c +--- ncbi-vdb-3.0.0_orig/libs/hdf5/hdf5dir.c 2022-11-11 11:55:46.455701000 +0100 ++++ ncbi-vdb-3.0.0/libs/hdf5/hdf5dir.c 2022-11-11 11:58:33.079945000 +0100 +@@ -26,7 +26,7 @@ + + typedef struct HDF5Dir HDF5Dir; + #define KDIR_IMPL HDF5Dir +- ++#define H5_USE_18_API + #define H5Gopen_vers 2 + #define H5Eset_auto_vers 2 + \ No newline at end of file diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb new file mode 100644 index 00000000000..7c598cd51e3 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb @@ -0,0 +1,88 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'SRA-Toolkit' +version = '3.0.0' + +homepage = 'https://github.com/ncbi/sra-tools' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" +github_account = 'ncbi' + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'extra_cflags': '-lxml2 -lz -llzma'} + +source_urls = ['https://github.com/ncbi/sra-tools/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['SRA-Toolkit-%(version)s_fix-LD_LIBRARY_PATH.patch'] +checksums = [ + {'SRA-Toolkit-3.0.0.tar.gz': 'b6e8116ecb196b91d5ee404cc978a128eec9af24bdc96f57ff7ebfaf9059a760'}, + {'SRA-Toolkit-3.0.0_fix-LD_LIBRARY_PATH.patch': '80b764584e377150cbc706463ef2c72e517d1a3e7493f13e26d6e7875cd7d16a'}, +] + +builddependencies = [ + ('Perl', '5.34.0'), + ('Python', '3.9.6'), + ('CMake', '3.21.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('Java', '11', '', True), +] + +dependencies = [ + ('ncbi-vdb', '3.0.0'), + ('file', '5.41'), # provides libmagic + ('HDF5', '1.12.1'), + ('libxml2', '2.9.10'), + ('Szip', '2.1.1'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), + ('gzip', '1.10'), +] + +# Add addtional libraries needed to statically link HDF5 from EB +preconfigopts = "sed -i 's/-Wl,-Bstatic -lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz -lz -llzma -lpthread -licucore -lm /' setup/konfigure.perl && " + +# Change default build directory and add paths to dependencies in EB +configopts = '--build-prefix=%(builddir)s --with-magic-prefix=$EBROOTFILE ' +configopts += '--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2 ' +configopts += '--with-ncbi-vdb-prefix=$EBROOTNCBIMINVDB' + +# Replace hardcoded optimization flags with flags from EB +prebuildopts = "sed -i 's/-sm/-sm -lmpi -lsz/' tools/pacbio-load/Makefile && " +prebuildopts += "find build/ -name \"ld*.sh\" -exec sed -i 's/-lxml2/-lxml2 -lz -llzma -lpthread -licucore -lm /g' {} + && " +prebuildopts += "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && " +prebuildopts += 'export EBFLAGS="$CFLAGS" && ' + +# Replace hardcoded optimization flags with flags from EB +preinstallopts = 'EBFLAGS="$CFLAGS" ' + +# local_bin = ['abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', +# 'fastq-dump', 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'kget', +# 'latf-load', 'magic', 'pacbio-load', 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', +# 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', 'sratools', 'srf-load', 'test-sra', 'vdb-config', +# 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-lock', 'vdb-passwd', 'vdb-unlock', +# 'vdb-validate'] + +local_bin = ['abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', + 'fastq-dump', 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', #'kget', + 'latf-load', 'magic', 'pacbio-load', 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', + 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', 'sratools', 'srf-load', 'test-sra', 'vdb-config', + 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-get', 'vdb-lock', 'vdb-passwd', 'vdb-unlock', + 'vdb-validate'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin] + + ['include/ncbi-vdb/NGS.hpp'], + 'dirs': [] +} + +sanity_check_commands = [ + "abi-dump --help", + "kar --help", + "sra-sort --help", +] + +moduleclass = 'bio' \ No newline at end of file diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0_fix-LD_LIBRARY_PATH.patch b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0_fix-LD_LIBRARY_PATH.patch new file mode 100644 index 00000000000..c43e9026374 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0_fix-LD_LIBRARY_PATH.patch @@ -0,0 +1,35 @@ +appending to LD_LIBRARY_PATH, rather than rewriting it +updated: Denis Kristak (INUITS) +diff -ruN sra-tools-3.0.0.orig/build/ld.linux.dlib.sh sra-tools-3.0.0/build/ld.linux.dlib.sh +--- sra-tools-3.0.0.orig/build/ld.linux.dlib.sh 2022-02-10 14:00:25.000000000 -0800 ++++ sra-tools-3.0.0/build/ld.linux.dlib.sh 2022-08-18 12:09:51.955470000 -0700 +@@ -83,8 +83,7 @@ + done + + # update LD_LIBRARY_PATH +- unset LD_LIBRARY_PATH +- export LD_LIBRARY_PATH="$LDIRS:$XDIRS" ++ export LD_LIBRARY_PATH="$LDIRS:$XDIRS:$LD_LIBRARY_PATH" + + # tack on libraries, finding as we go + for LIB in $LIBS +@@ -308,4 +307,4 @@ + echo "$MSG" >> $LOGFILE + + "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5" +-fi +\ No newline at end of file ++fi +diff -ruN sra-tools-3.0.0.orig/build/ld.linux.exe.sh sra-tools-3.0.0/build/ld.linux.exe.sh +--- sra-tools-3.0.0.orig/build/ld.linux.exe.sh 2022-02-10 14:00:25.000000000 -0800 ++++ sra-tools-3.0.0/build/ld.linux.exe.sh 2022-08-18 12:10:58.180786000 -0700 +@@ -96,8 +96,7 @@ + done + + # update LD_LIBRARY_PATH +- unset LD_LIBRARY_PATH +- export LD_LIBRARY_PATH="$LDIRS:$XDIRS" ++ export LD_LIBRARY_PATH="$LDIRS:$XDIRS:$LD_LIBRARY_PATH" + + # tack on libraries, finding as we go + for LIB in $LIBS \ No newline at end of file From 311902b868e8598eeb5f2b5e864d99246dec8e8f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 11:05:06 +0100 Subject: [PATCH 5849/9987] adding required dep to the PR --- .../s/spaln/spaln-2.4.12-GCC-11.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb new file mode 100644 index 00000000000..4939d85b41e --- /dev/null +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb @@ -0,0 +1,45 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'spaln' +version = '2.4.12' + +homepage = 'https://github.com/ogotoh/spaln' +description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps + and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h; +# see also https://github.com/ogotoh/spaln/issues/56 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/ogotoh/spaln/archive/'] +sources = ['ver%(version)s.tar.gz'] +checksums = ['0c5f842131409686dbaad01778960f53f1ebba8dd83d55b454ec4bf1b6bde2af'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Perl', '5.34.0'), +] + +start_dir = 'src' + +# we need to make sure not to pass --prefix, otherwise the configure script gets stuck in an infinite loop... +prefix_opt = '--exec_prefix=' + +configopts = "--exec_prefix=%(installdir)s/bin --table_dir=%(installdir)s/table --alndbs_dir=%(installdir)s/seqdb " +configopts += "--use_zlib=1" +fix_perl_shebang_for = ['seqdb/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], + 'dirs': ['seqdb', 'table'], +} + +sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] +modextrapaths = { + 'PATH': 'seqdb', + 'PERL5LIB': 'seqdb', +} + +moduleclass = 'bio' \ No newline at end of file From 1c6299169910863889aaa9d7c98451f273d72a2e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 11:06:06 +0100 Subject: [PATCH 5850/9987] adding easyconfigs: olego-1.1.9-GCC-11.2.0.eb --- .../o/olego/olego-1.1.9-GCC-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb new file mode 100644 index 00000000000..cf88a6c7509 --- /dev/null +++ b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = "MakeCp" + +name = "olego" +version = "1.1.9" + +homepage = "https://github.com/chaolinzhanglab/olego" +description = """OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts +a seed-and-extend scheme, and does not rely on a separate external mapper.""" + +toolchain = {"name": "GCC", "version": "11.2.0"} + +source_urls = ["https://github.com/chaolinzhanglab/olego//archive/"] +sources = ["v%(version)s.tar.gz"] +checksums = ['1b6ba7a4a310ac71667052d3a6e1f073d3976302ab6b6b67041475f7ca1f4bac'] + +files_to_copy = ["*"] + +modextrapaths = {"PATH": [""]} + +sanity_check_paths = { + "files": ["olegoindex", "olego"], + "dirs": [], +} + +sanity_check_commands = ["olego"] +sanity_check_commands = ['olego 2>&1 | grep "version %(version)s"'] + +moduleclass = "bio" From 56869b3c6fd1deee9dab738a11edfee7f6b0bb90 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 11:07:20 +0100 Subject: [PATCH 5851/9987] adding comment --- easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb index cf88a6c7509..afb06b4f390 100644 --- a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb @@ -1,3 +1,4 @@ +# updated by: Denis Kristak (INUITS) easyblock = "MakeCp" name = "olego" From 1f9332cdc352be25a05ced2bb26f03595d46689c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 11:26:42 +0100 Subject: [PATCH 5852/9987] minor cleanup in FLANN easyconfigs --- .../f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 9 +++------ .../f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 10 +++------- 2 files changed, 6 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index 6bae6453023..34f5aaf3db5 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -13,10 +13,9 @@ description = "FLANN is a library for performing fast approximate nearest neighb toolchain = {'name': 'foss', 'version': '2020a'} toolchainopts = {'openmp': True} - source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix-cmake.patch'] +patches = ['FLANN-%(version)s_fix-cmake.patch'] checksums = [ 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz @@ -29,9 +28,7 @@ dependencies = [ ('SciPy-bundle', '2020.03', '-Python-3.8.2'), ] -separate_build_dir = True - -configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" +configopts = "-DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} @@ -40,6 +37,6 @@ sanity_check_paths = { 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], 'dirs': ['include/flann', 'lib/pkgconfig', 'share/doc/flann', 'share/flann/python'], } -sanity_check_commands = [('python', '-c "import pyflann"')] +sanity_check_commands = ["python -c 'import pyflann'"] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index a8e0f8d3ec0..5321fb0cc98 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -16,8 +16,7 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-1.8.4_fix-cmake.patch'] - +patches = ['FLANN-1.8.4_fix-cmake.patch'] checksums = [ 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-1.8.4_fix-cmake.patch @@ -29,10 +28,7 @@ dependencies = [ ('SciPy-bundle', '2020.03', '-Python-3.8.2'), ] -separate_build_dir = True - - -configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" +configopts = "-DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} @@ -41,6 +37,6 @@ sanity_check_paths = { 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], 'dirs': ['include/flann', 'lib/pkgconfig', 'share/flann/python'], } -sanity_check_commands = [('python', '-c "import pyflann"')] +sanity_check_commands = ["python -c 'import pyflann'"] moduleclass = 'lib' From 67541d78b62340142970bfb7ca419605d6ae6a6a Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 15 Dec 2022 11:50:39 +0100 Subject: [PATCH 5853/9987] Update spaln-2.4.12-GCC-11.2.0.eb code style err fix --- easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb index 4939d85b41e..b8da6b50290 100644 --- a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb @@ -42,4 +42,4 @@ modextrapaths = { 'PERL5LIB': 'seqdb', } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 38a0bc9cecca00d99bb55f0ce47bc34314c09a47 Mon Sep 17 00:00:00 2001 From: Michael Huebner Date: Thu, 15 Dec 2022 12:30:41 +0100 Subject: [PATCH 5854/9987] Add CUDAsamples for CUDA 11.3.1 --- .../c/CUDAsamples/CUDAsamples-11.3.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb diff --git a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb new file mode 100644 index 00000000000..036dee8fefb --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'CUDAsamples' +version = '11.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'] + +dependencies = [ + ('CUDA', '11.3.1', '', True), +] + +# Get rid of pre-built Windows DLLs and only build deviceQuery for now. +# Other samples require extensive dependencies. +# If, at some point, all samples should be built, simply remove the explicit cd. +prebuildopts = "rm -r bin/win64 && cd Samples/deviceQuery && " + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' From 1662b95d7373eef1cc8ec34c6ebf1252210b6ff7 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 12:34:10 +0100 Subject: [PATCH 5855/9987] adding easyconfigs: finder-1.1.0-foss-2021b.eb and patches: finder-1.1.0_run_bare_option.patch --- .../f/finder/finder-1.1.0-foss-2021b.eb | 70 ++++++++++++++++ .../finder/finder-1.1.0_run_bare_option.patch | 84 +++++++++++++++++++ 2 files changed, 154 insertions(+) create mode 100644 easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/f/finder/finder-1.1.0_run_bare_option.patch diff --git a/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb new file mode 100644 index 00000000000..4a4170606e7 --- /dev/null +++ b/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb @@ -0,0 +1,70 @@ +# author: Denis Kristak (INUITS) +easyblock = "Binary" + +name = "finder" +version = "1.1.0" + +homepage = "https://github.com/sagnikbanerjee15/Finder/" +description = """finder is a gene annotator pipeline which automates the process of downloading short reads, +aligning them and using the assembled transcripts to generate gene annotations.""" + +toolchain = {"name": "foss", "version": "2021b"} +toolchainopts = {"openmp": True} + +source_urls = [ + 'https://github.com/sagnikbanerjee15/Finder/archive/', + 'ftp://ftp.ensemblgenomes.org/pub/plants/release-49/fasta/arabidopsis_thaliana/dna/' +] +sources = ['%(name)s_v%(version)s.tar.gz', 'Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.gz'] +patches = ['finder-%(version)s_run_bare_option.patch'] +checksums = [ + {'finder_v1.1.0.tar.gz': 'be416a01b94f2ac183fb9c4945b09b8f40ac0e40b12e2c08c343bd2aad28bf98'}, + {'Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.gz': + '4598dbd9f6913527933e9822e0d15d7016571de1f8e925c37917e840e8a453bd'}, + {'finder-1.1.0_run_bare_option.patch': '43ee4046bcecc1a1555ef0dc9b98487281c0344028ef6cf1428d24bbfd6cd1ca'}, +] + +dependencies = [ + ("STAR", "2.7.9a"), + ("SAMtools", "1.14"), + ("BEDTools", "2.30.0"), + ("AUGUSTUS", "3.4.0"), + ("BRAKER","2.1.6"), + ("GeneMark-ET", "4.71"), + ("PsiCLASS", "1.0.3"), + ("olego", "1.1.9"), + ("GUSHR", "2020-09-28"), + ("gffread", "0.12.7"), + ("BEDOPS", "2.4.41"), + ("RegTools", "0.5.2"), + ("BLAST+", "2.12.0"), + ("CodAn", "1.2"), + ("GffCompare", "0.12.6"), + ("XZ", "5.2.5"), + ("bzip2", "1.0.8"), + ("Autotools", "20210726"), + ("Python", "3.9.6"), + ("SciPy-bundle", "2021.10"), + ("Trimmomatic", "0.39", "-Java-11", True), + ("Boost", "1.77.0"), + ("ruffus", "2.8.4"), + ("SRA-Toolkit", "3.0.0"), +] + +extract_sources = True + +install_cmd = "cp -r %(builddir)s/Finder-finder_v%(version)s/* %(installdir)s/ " + + +sanity_check_paths = { + "files": ["run_finder"], + "dirs": [], +} + +modextrapaths = { + 'PATH': ['utils'] +} + +sanity_check_commands = ["finder --help"] + +moduleclass = "bio" diff --git a/easybuild/easyconfigs/f/finder/finder-1.1.0_run_bare_option.patch b/easybuild/easyconfigs/f/finder/finder-1.1.0_run_bare_option.patch new file mode 100644 index 00000000000..5973e8a7e7f --- /dev/null +++ b/easybuild/easyconfigs/f/finder/finder-1.1.0_run_bare_option.patch @@ -0,0 +1,84 @@ +adding option to the run_finder script, to be able to run without using singularity or docker +author: Denis Kristak (INUITS) +diff -ruN Finder-finder_v1.1.0_orig/run_finder Finder-finder_v1.1.0/run_finder +--- Finder-finder_v1.1.0_orig/run_finder 2021-12-19 20:46:57.000000000 +0100 ++++ Finder-finder_v1.1.0/run_finder 2022-12-15 12:08:39.120630477 +0100 +@@ -45,7 +45,7 @@ + optional_named.add_argument( "--skip_cpd", "--skip_cpd", help = "Turn on this option to skip changepoint detection. Could be effective for grasses", action = "store_true" ) + optional_named.add_argument( "--exonerate_gff3", "-egff3", help = "Enter the exonerate output in gff3 format" ) + optional_named.add_argument( "--star_shared_mem", "--star_shared_mem", help = "Turn on this option if you want STAR to load the genome index into shared memory. This saves memory if multiple finder runs are executing on the same host, but might not work in your cluster environment.", action = "store_true" ) +- optional_named.add_argument( "--framework", "-fm", help = "Enter your choice of framework", choices = ["docker", "singularity"], default = "docker" ) ++ optional_named.add_argument( "--framework", "-fm", help = "Enter your choice of framework", choices = ["docker", "singularity", "bare"], default = "bare" ) + + # optional_named.add_argument("--intron_gff3","-intron_gff3",help="Enter the name and location of the file containing introns in gff3 format") + # optional_named.add_argument("--ground_truth_gtf","-gt_gtf",help="Enter the gtf filename of the actual annotation [for developmental purposes]") +@@ -86,6 +86,12 @@ + singularity_cmd += f" bash -c {command}" + os.system( singularity_cmd ) + ++def runBareCommand( command ): ++ """ ++ Runs the command directly on the system ++ """ ++ # Runs the main command ++ os.system( command ) + + def main(): + commandLineArg = sys.argv +@@ -98,8 +104,8 @@ + f"{'/'.join(options.genome.split('/')[:-1])}:{'/'.join(options.genome.split('/')[:-1])}", + f"{options.output_directory}:{options.output_directory}"] + +- cmd = f" \" ulimit -n $(ulimit -Hn) && " +- cmd += f" finder " ++ # cmd = f" \" " ++ cmd = f" finder " + cmd += f" --metadatafile {options.metadatafile} " + cmd += f" --output_directory {options.output_directory} " + cmd += f" --genome {options.genome} " +@@ -137,20 +143,16 @@ + cmd += f" --genemark_license {options.genemark_license}" + volumes_list.append( f"{'/'.join(options.genemark_license.split('/')[:-1])}:{'/'.join(options.genemark_license.split('/')[:-1])}" ) + +- cmd += f" \" " ++ # cmd += f" \" " + + volumes_list = list( set( volumes_list ) ) + + os.system( f"mkdir -p {options.output_directory}" ) +- os.system( f"which docker > {options.output_directory}/find_docker" ) +- os.system( f"which singularity > {options.output_directory}/find_singularity" ) ++ os.system( f"which docker > {options.output_directory}/find_docker 2> {options.output_directory}/find_docker.err" ) ++ os.system( f"which singularity > {options.output_directory}/find_singularity 2> {options.output_directory}/find_singularity.err" ) + +- docker_installed = 1 if "Command not found" not in open( f"{options.output_directory}/find_docker", "r" ).read() else 0 +- singularity_installed = 1 if "Command not found" not in open( f"{options.output_directory}/find_singularity", "r" ).read() else 0 +- +- if docker_installed == 0 and singularity_installed == 0: +- print( "You need to have either docker or singularity installed" ) +- sys.exit() ++ docker_installed = 1 if "no docker in" not in open( f"{options.output_directory}/find_docker", "r" ).read() else 0 ++ singularity_installed = 1 if "no singularity in" not in open( f"{options.output_directory}/find_singularity", "r" ).read() else 0 + + framework_of_choice = "" + if options.framework == "docker": +@@ -165,6 +167,9 @@ + else: + framework_of_choice = "docker" + ++ elif options.framework == "bare": ++ framework_of_choice = "bare" ++ + if framework_of_choice == "docker": + os.system( "docker pull sagnikbanerjee15/finder:1.1.0" ) + runDockerCommand( name = "finder", +@@ -189,6 +194,9 @@ + memory = '300g' + ) + ++ elif framework_of_choice == "bare": ++ runBareCommand(command=cmd) ++ + + if __name__ == "__main__": + main() From 7e94117be8139238213c72cbd31d0e4ea9576e12 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 15 Dec 2022 12:43:17 +0100 Subject: [PATCH 5856/9987] Update olego-1.1.9-GCC-11.2.0.eb removed obsolete sanity check cmd --- easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb index afb06b4f390..89c892a1f8a 100644 --- a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb @@ -23,7 +23,6 @@ sanity_check_paths = { "dirs": [], } -sanity_check_commands = ["olego"] sanity_check_commands = ['olego 2>&1 | grep "version %(version)s"'] moduleclass = "bio" From 2f26dd0fd02126edafddcfd5ea0f5f5ad97847d9 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 15 Dec 2022 12:44:02 +0100 Subject: [PATCH 5857/9987] Update ncbi-vdb-3.0.0-gompi-2021b.eb adding newline at the end of the file --- easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb index c4d8e53a8ed..d9a196f47e3 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb @@ -55,4 +55,4 @@ sanity_check_paths = { 'dirs': ['include', 'lib', 'lib64'], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From e5eb4f5d8d87a69f24a04374c99afe58d2a1cb5a Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 15 Dec 2022 12:50:08 +0100 Subject: [PATCH 5858/9987] Update SRA-Toolkit-3.0.0-gompi-2021b.eb resolving issues coming from tests (code style errs) --- .../SRA-Toolkit-3.0.0-gompi-2021b.eb | 21 +++++++------------ 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb index 7c598cd51e3..e73886f5d74 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('ncbi-vdb', '3.0.0'), - ('file', '5.41'), # provides libmagic + ('file', '5.41'), # provides libmagic ('HDF5', '1.12.1'), ('libxml2', '2.9.10'), ('Szip', '2.1.1'), @@ -43,31 +43,26 @@ dependencies = [ ] # Add addtional libraries needed to statically link HDF5 from EB -preconfigopts = "sed -i 's/-Wl,-Bstatic -lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz -lz -llzma -lpthread -licucore -lm /' setup/konfigure.perl && " +preconfigopts = "sed -i 's/-Wl,-Bstatic -lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic +preconfigopts += "-lmpi -lsz -lz -llzma -lpthread -licucore -lm /' setup/konfigure.perl && " # Change default build directory and add paths to dependencies in EB -configopts = '--build-prefix=%(builddir)s --with-magic-prefix=$EBROOTFILE ' +configopts = '--build-prefix=%(builddir)s --with-magic-prefix=$EBROOTFILE ' configopts += '--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2 ' configopts += '--with-ncbi-vdb-prefix=$EBROOTNCBIMINVDB' # Replace hardcoded optimization flags with flags from EB prebuildopts = "sed -i 's/-sm/-sm -lmpi -lsz/' tools/pacbio-load/Makefile && " -prebuildopts += "find build/ -name \"ld*.sh\" -exec sed -i 's/-lxml2/-lxml2 -lz -llzma -lpthread -licucore -lm /g' {} + && " +prebuildopts += "find build/ -name \"ld*.sh\" -exec sed -i " +prebuildopts += "'s/-lxml2/-lxml2 -lz -llzma -lpthread -licucore -lm /g' {} + && " prebuildopts += "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && " prebuildopts += 'export EBFLAGS="$CFLAGS" && ' # Replace hardcoded optimization flags with flags from EB preinstallopts = 'EBFLAGS="$CFLAGS" ' -# local_bin = ['abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', -# 'fastq-dump', 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'kget', -# 'latf-load', 'magic', 'pacbio-load', 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', -# 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', 'sratools', 'srf-load', 'test-sra', 'vdb-config', -# 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-lock', 'vdb-passwd', 'vdb-unlock', -# 'vdb-validate'] - local_bin = ['abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', - 'fastq-dump', 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', #'kget', + 'fastq-dump', 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'latf-load', 'magic', 'pacbio-load', 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', 'sratools', 'srf-load', 'test-sra', 'vdb-config', 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-get', 'vdb-lock', 'vdb-passwd', 'vdb-unlock', @@ -85,4 +80,4 @@ sanity_check_commands = [ "sra-sort --help", ] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 5e52e8250ea2c405e49516412751aea18679fa59 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 15 Dec 2022 12:57:35 +0100 Subject: [PATCH 5859/9987] Update finder-1.1.0-foss-2021b.eb new code style for SYSTEM tc --- easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb index 4a4170606e7..f024c58fc4c 100644 --- a/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb @@ -45,7 +45,7 @@ dependencies = [ ("Autotools", "20210726"), ("Python", "3.9.6"), ("SciPy-bundle", "2021.10"), - ("Trimmomatic", "0.39", "-Java-11", True), + ("Trimmomatic", "0.39", "-Java-11", SYSTEM), ("Boost", "1.77.0"), ("ruffus", "2.8.4"), ("SRA-Toolkit", "3.0.0"), From ca97579b6c8d8657e7d24053e91cf06aa99ec1e4 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 15 Dec 2022 13:06:21 +0100 Subject: [PATCH 5860/9987] Update SRA-Toolkit-3.0.0-gompi-2021b.eb fixing typo --- .../s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb index e73886f5d74..9ece41bd86e 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb @@ -32,7 +32,7 @@ builddependencies = [ dependencies = [ ('ncbi-vdb', '3.0.0'), - ('file', '5.41'), # provides libmagic + ('file', '5.41'), ('HDF5', '1.12.1'), ('libxml2', '2.9.10'), ('Szip', '2.1.1'), @@ -43,7 +43,7 @@ dependencies = [ ] # Add addtional libraries needed to statically link HDF5 from EB -preconfigopts = "sed -i 's/-Wl,-Bstatic -lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic +preconfigopts = "sed -i 's/-Wl,-Bstatic -lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic " preconfigopts += "-lmpi -lsz -lz -llzma -lpthread -licucore -lm /' setup/konfigure.perl && " # Change default build directory and add paths to dependencies in EB From 68cccb51a8c4118d25d41e796b9d031993cf79f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 14:21:00 +0100 Subject: [PATCH 5861/9987] adding easyconfigs: meson-python-0.11.0-GCCcore-12.2.0.eb --- .../meson-python-0.11.0-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4dd4ad15f86 --- /dev/null +++ b/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'meson-python' +version = '0.11.0' + +homepage = 'https://github.com/mesonbuild/meson-python' +description = "Python build backend (PEP 517) for Meson projects" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Python', '3.10.8'), + ('Meson', '0.64.0'), +] + +use_pip = True + +exts_list = [ + ('pyproject-metadata', '0.6.1', { + 'checksums': ['b5fb09543a64a91165dfe85796759f9e415edc296beb4db33d1ecf7866a862bd'], + }), + (name, version, { + 'sources': ['meson_python-%(version)s.tar.gz'], + 'checksums': ['110258837c2ffe762f5f855c7ea5385f1edd44074e93a0f317ffefc7aab42b09'], + 'modulename': 'mesonpy', + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From af654e85a80bf05dd38cc9bf18494671b94737d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 14:56:46 +0100 Subject: [PATCH 5862/9987] add missing binutils build dependency for meson-python --- .../m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb index 4dd4ad15f86..4d0193a8bd5 100644 --- a/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb @@ -8,6 +8,10 @@ description = "Python build backend (PEP 517) for Meson projects" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +builddependencies = [ + ('binutils', '2.39'), +] + dependencies = [ ('Python', '3.10.8'), ('Meson', '0.64.0'), From ed845cb85d08f410820e50c6aeb3674533083f22 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 15 Dec 2022 14:59:49 +0100 Subject: [PATCH 5863/9987] Update finder-1.1.0-foss-2021b.eb style err --- easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb index f024c58fc4c..14a7e352b54 100644 --- a/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb @@ -29,7 +29,7 @@ dependencies = [ ("SAMtools", "1.14"), ("BEDTools", "2.30.0"), ("AUGUSTUS", "3.4.0"), - ("BRAKER","2.1.6"), + ("BRAKER", "2.1.6"), ("GeneMark-ET", "4.71"), ("PsiCLASS", "1.0.3"), ("olego", "1.1.9"), From f5e911f865da45d80f85673fd75b390a6c57a6a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 15:00:43 +0100 Subject: [PATCH 5864/9987] {lang}[GCCcore/12.2.0] SciPy-bundle v2022.11, pybind11 v2.10.1, hypothesis v6.59.0 w/ Python 3.10.8 --- .../hypothesis-6.59.0-GCCcore-12.2.0.eb | 24 ++++++ .../pybind11-2.10.1-GCCcore-12.2.0.eb | 23 ++++++ .../SciPy-bundle-2022.11-foss-2022.10.eb | 80 +++++++++++++++++++ 3 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-6.59.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.10.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-foss-2022.10.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.59.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.59.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..bb0b491571c --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.59.0-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '6.59.0' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['af05e24b123c9413b8752bbf822105dbb112f56456fb240723d7f410eebf78bb'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7ccdfaf989c --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.1-GCCcore-12.2.0.eb @@ -0,0 +1,23 @@ +name = 'pybind11' +version = '2.10.1' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['111014b516b625083bef701df7880f78c2243835abdb263065b6b59b960b6bad'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Eigen', '3.4.0'), +] +dependencies = [('Python', '3.10.8')] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-foss-2022.10.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-foss-2022.10.eb new file mode 100644 index 00000000000..d6289b1ebfa --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-foss-2022.10.eb @@ -0,0 +1,80 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2022.11' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'foss', 'version': '2022.10'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.59.0'), + ('UnZip', '6.0'), + ('meson-python', '0.11.0'), + # installing numpy 1.23.5 from source requires setuptools < 60.0, + # cfr. https://github.com/numpy/numpy/issues/22157 and //github.com/numpy/numpy/issues/22431 + ('setuptools', '63.4.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('pybind11', '2.10.1'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.23.5', { + 'patches': [ + 'numpy-1.22.3_disable-broken-override-test.patch', + ], + 'checksums': [ + {'numpy-1.23.5.tar.gz': '1b1766d6f397c18153d40015ddfc79ddb715cabadc04d2d228d4e5a8bc4ded1a'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.12.0', { + 'checksums': ['eff3dd0d3eebe57372f0d14f82985525e9bcdfb5b1d1010e1932cf9207060f9f'], + }), + ('scipy', '1.9.3', { + 'checksums': ['fbc5c05c85c1a02be77b1ff591087c83bc44579c6d2bd9fb798bb64ea5e1a027'], + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && ", + }), + ('mpi4py', '3.1.4', { + 'checksums': ['17858f2ebc623220d0120d1fa8d428d033dde749c4bc35b33d81a66ad7f93480'], + }), + ('numexpr', '2.8.4', { + 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], + }), + ('Bottleneck', '1.3.5', { + 'checksums': ['2c0d27afe45351f6f421893362621804fa7dea14fe29a78eaa52d4323f646de7'], + }), + ('pandas', '1.5.2', { + 'checksums': ['220b98d15cee0b2cd839a6358bd1f273d0356bf964c1a1aeb32d47db0215488b'], + # make sure $PANDAS_CI is not set to 1, since that implies using -Werror + 'preinstallopts': "export PANDAS_CI=0 && ", + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.3', { + 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 2fbe0e0ab3e62b33dca331e28e03b4ba85accf85 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 15 Dec 2022 15:01:04 +0100 Subject: [PATCH 5865/9987] Update SRA-Toolkit-3.0.0-gompi-2021b.eb new system TC convention --- .../easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb index 9ece41bd86e..7ddb91ba5ab 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.0-gompi-2021b.eb @@ -27,7 +27,7 @@ builddependencies = [ ('CMake', '3.21.1'), ('flex', '2.6.4'), ('Bison', '3.7.6'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ] dependencies = [ From e87fc83ee457d4605ce5b3b1c10bde1e4ff78d9d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 15 Dec 2022 14:17:08 +0000 Subject: [PATCH 5866/9987] Add HiCBricks to Bioconductor 3.15 --- ...le-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 27 ++++++++++--------- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 +++ 2 files changed, 18 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index b6ac8e83c45..2cd7b030d51 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -220,9 +220,9 @@ exts_list = [ ('Rgraphviz', '2.40.0', { 'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'], 'checksums': [ - '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4', # Rgraphviz_2.40.0.tar.gz - # Rgraphviz-2.28.0_fno-tree-vectorize.patch - '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9', + {'Rgraphviz_2.40.0.tar.gz': '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4'}, + {'Rgraphviz-2.28.0_fno-tree-vectorize.patch': + '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9'}, ], }), ('RNASeqPower', '1.36.0', { @@ -444,17 +444,17 @@ exts_list = [ ('dada2', '1.24.0', { 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], 'checksums': [ - '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b', # dada2_1.24.0.tar.gz - # dada2-1.16.0-remove-sse-on-aarch64.patch - 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + {'dada2_1.24.0.tar.gz': '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b'}, + {'dada2-1.16.0-remove-sse-on-aarch64.patch': + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935'}, ], }), ('LEA', '3.8.0', { 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], 'checksums': [ - 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774', # LEA_3.8.0.tar.gz - # LEA-3.0.0_support_aarch64_and_ppc64le.patch - 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', + {'LEA_3.8.0.tar.gz': 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774'}, + {'LEA-3.0.0_support_aarch64_and_ppc64le.patch': + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881'}, ], }), ('tximport', '1.24.0', { @@ -721,9 +721,9 @@ exts_list = [ ('RProtoBufLib', '2.8.0', { 'patches': ['RProtoBufLib-2.8.0_fix-protobuf-build.patch'], 'checksums': [ - 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7', # RProtoBufLib_2.8.0.tar.gz - # RProtoBufLib-2.8.0_fix-protobuf-build.patch - '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64', + {'RProtoBufLib_2.8.0.tar.gz': 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7'}, + {'RProtoBufLib-2.8.0_fix-protobuf-build.patch': + '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64'}, ], }), ('cytolib', '2.8.0', { @@ -1105,6 +1105,9 @@ exts_list = [ ('scDblFinder', '1.10.0', { 'checksums': ['c0834495a342c6467d64dc899ba5913354ea5d53037c9be95e639950db6e2478'], }), + ('HiCBricks', '1.14.0', { + 'checksums': ['ac998260ffa66ec93a4c34e56cbaf392f76a848ae35b9ea987f0ec15f0adc47d'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 5566af30766..b73795d4c56 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1113,6 +1113,9 @@ exts_list = [ ('numbat', '1.1.0', { 'checksums': ['3cdda07de7329e6c886a1f60b2978bb776b04133080e97d82d5772fd666efc2c'], }), + ('HiCBricks', '1.14.0', { + 'checksums': ['ac998260ffa66ec93a4c34e56cbaf392f76a848ae35b9ea987f0ec15f0adc47d'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From d5381729fef1a2c3588ef52bc2fbbc65771d775d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 15:20:14 +0100 Subject: [PATCH 5867/9987] trivial style fixes in CodAn easyconfig --- .../c/CodAn/CodAn-1.2-foss-2021b.eb | 41 +++++++++---------- 1 file changed, 19 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb index 67ff7133a6b..5d220aff850 100644 --- a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb @@ -1,24 +1,24 @@ # author: Denis Kristak (INUITS) -easyblock = "Binary" +easyblock = 'Binary' -name = "CodAn" -version = "1.2" +name = 'CodAn' +version = '1.2' -homepage = "https://github.com/pedronachtigall/CodAn" +homepage = 'https://github.com/pedronachtigall/CodAn' description = """CodAn (Coding sequence Annotator) is a computational tool designed to characterize the CDS and UTR regions on transcripts from any Eukaryote species.""" -toolchain = {"name": "foss", "version": "2021b"} +toolchain = {'name': 'foss', 'version': '2021b'} -source_urls = ["https://github.com/pedronachtigall/CodAn/archive"] -sources = ["v%(version)s.tar.gz"] +source_urls = ['https://github.com/pedronachtigall/CodAn/archive'] +sources = ['v%(version)s.tar.gz'] checksums = ['34962ac67dc94da0bff6e032568e38388726bf1d7efceed462d6b7c841b087b7'] dependencies = [ - ("Python", "3.9.6"), - ("Biopython", "1.79"), - ("BioPerl", "1.7.8"), - ("Perl", "5.34.0"), + ('Python', '3.9.6'), + ('Biopython', '1.79'), + ('BioPerl', '1.7.8'), + ('Perl', '5.34.0'), ] extract_sources = True @@ -29,24 +29,21 @@ install_cmd += "mkdir %(installdir)s/bin && " install_cmd += "mv %(installdir)s/%(name)s-%(version)s/bin/* %(installdir)s/bin && " install_cmd += "chmod u+rwx %(installdir)s/bin/* " - sanity_check_paths = { - "files": ["bin/%(namelower)s.py"], - "dirs": [], + 'files': ['bin/%(namelower)s.py'], + 'dirs': [], } -local_sanity_check_cmd = "mkdir %(installdir)s/eb_test && " -local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/models/VERT_full.zip %(installdir)s/eb_test && " -local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/tutorial/transcripts.fa %(installdir)s/eb_test && " -local_sanity_check_cmd += "cd %(installdir)s/eb_test/ && " +local_sanity_check_cmd = "mkdir %(builddir)s/eb_test && " +local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/models/VERT_full.zip %(builddir)s/eb_test && " +local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/tutorial/transcripts.fa %(builddir)s/eb_test && " +local_sanity_check_cmd += "cd %(builddir)s/eb_test/ && " local_sanity_check_cmd += "unzip VERT_full.zip && " -local_sanity_check_cmd += ( - "codan.py -t transcripts.fa -m VERT_full | grep 'prediction finished!'" -) +local_sanity_check_cmd += "codan.py -t transcripts.fa -m VERT_full | grep 'prediction finished!'" sanity_check_commands = [ "%(namelower)s.py --help", local_sanity_check_cmd, ] -moduleclass = "bio" +moduleclass = 'bio' From 3512e1133fe5dca8673f9400630521dea74544ac Mon Sep 17 00:00:00 2001 From: Michael Huebner Date: Thu, 15 Dec 2022 15:49:25 +0100 Subject: [PATCH 5868/9987] Build all CUDA samples except for the ones with extensive dependencies --- easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb index 036dee8fefb..e807e85c12c 100644 --- a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb +++ b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb @@ -18,9 +18,10 @@ dependencies = [ ] # Get rid of pre-built Windows DLLs and only build deviceQuery for now. -# Other samples require extensive dependencies. -# If, at some point, all samples should be built, simply remove the explicit cd. -prebuildopts = "rm -r bin/win64 && cd Samples/deviceQuery && " +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies. +buildopts = "HOST_COMPILER=g++ FILTER_OUT='Samples/EGLStream_CUDA_Interop/Makefile Samples/boxFilterNPP/Makefile Samples/cannyEdgeDetectorNPP/Makefile Samples/cudaNvSci/Makefile Samples/cudaNvSciNvMedia/Makefile Samples/simpleGL/Makefile Samples/warpAggregatedAtomicsCG/Makefile Samples/simpleVulkan/Makefile Samples/simpleVulkanMMAP/Makefile Samples/streamOrderedAllocationIPC/Makefile Samples/vulkanImageCUDA/Makefile'" files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), From b9350223d69f770cb999498a73de5d63c7e6201f Mon Sep 17 00:00:00 2001 From: huebner-m Date: Thu, 15 Dec 2022 16:10:25 +0100 Subject: [PATCH 5869/9987] Update easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb Co-authored-by: ocaisa --- .../easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb index e807e85c12c..a8b05d0ddff 100644 --- a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb +++ b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb @@ -21,7 +21,18 @@ dependencies = [ prebuildopts = "rm -r bin/win64 && " # Filter out samples that require extensive dependencies. -buildopts = "HOST_COMPILER=g++ FILTER_OUT='Samples/EGLStream_CUDA_Interop/Makefile Samples/boxFilterNPP/Makefile Samples/cannyEdgeDetectorNPP/Makefile Samples/cudaNvSci/Makefile Samples/cudaNvSciNvMedia/Makefile Samples/simpleGL/Makefile Samples/warpAggregatedAtomicsCG/Makefile Samples/simpleVulkan/Makefile Samples/simpleVulkanMMAP/Makefile Samples/streamOrderedAllocationIPC/Makefile Samples/vulkanImageCUDA/Makefile'" +local_filters = "Samples/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/boxFilterNPP/Makefile " +local_filters += "Samples/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/cudaNvSci/Makefile " +local_filters += "Samples/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/simpleGL/Makefile " +local_filters += "Samples/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/simpleVulkan/Makefile " +local_filters += "Samples/simpleVulkanMMAP/Makefile " +local_filters += "Samples/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/vulkanImageCUDA/Makefile" +buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), From 6cb6e79e60318fb28dded7fc7b35b3a38fa921d8 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 15 Dec 2022 16:15:11 +0100 Subject: [PATCH 5870/9987] Update easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb --- easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb index a8b05d0ddff..b8aaaaab878 100644 --- a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb +++ b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb @@ -39,7 +39,7 @@ files_to_copy = [ 'LICENSE', ] -local_binaries = ['deviceQuery'] +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] # Only paths are used for sanity checks. # Commands may fail due to missing compatibility libraries that might be needed From 9eef202248d2607ded45a8a172a8775bd7df7dd6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 16:19:04 +0100 Subject: [PATCH 5871/9987] downgrade to setuptools 63.4.3 in Python 3.10.8 easyconfig --- .../easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index 2f5d77e3671..b9943b5441f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -47,8 +47,8 @@ exts_list = [ ('wheel', '0.38.4', { 'checksums': ['965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac'], }), - ('setuptools', '65.5.1', { - 'checksums': ['e197a19aa8ec9722928f2206f8de752def0e4c9fc6953527360d1c36d94ddb2f'], + ('setuptools', '63.4.3', { + 'checksums': ['521c833d1e5e1ef0869940e7f486a83de7773b9f029010ad0c2fe35453a9dad9'], }), ('pip', '22.3.1', { 'checksums': ['65fd48317359f3af8e593943e6ae1506b66325085ea64b706a998c6e83eeaf38'], From 94d78268ddf6acfb7d03d107203b08d4c1b27167 Mon Sep 17 00:00:00 2001 From: Michael Huebner Date: Thu, 15 Dec 2022 16:28:15 +0100 Subject: [PATCH 5872/9987] Renaming, CUDAsamples -> CUDA-Samples --- .../CUDAsamples-11.3.eb => CUDA-Samples/CUDA-Samples-11.3.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/{CUDAsamples/CUDAsamples-11.3.eb => CUDA-Samples/CUDA-Samples-11.3.eb} (98%) diff --git a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3.eb similarity index 98% rename from easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb rename to easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3.eb index e807e85c12c..437f61c10b3 100644 --- a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3.eb @@ -1,6 +1,6 @@ easyblock = 'MakeCp' -name = 'CUDAsamples' +name = 'CUDA-Samples' version = '11.3' versionsuffix = '-CUDA-%(cudaver)s' From 36a989a733d3356d0c339ac3b0ee042ad7ad9beb Mon Sep 17 00:00:00 2001 From: Michael Huebner Date: Thu, 15 Dec 2022 16:31:28 +0100 Subject: [PATCH 5873/9987] Rename file with explicit versions --- ...amples-11.3.eb => CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/CUDA-Samples/{CUDA-Samples-11.3.eb => CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb} (100%) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb similarity index 100% rename from easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3.eb rename to easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb From 853eb8afa23522866c67c6436e72c45f77584d1b Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 15 Dec 2022 17:19:02 +0100 Subject: [PATCH 5874/9987] Tweak for tests --- .../CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb index e77aa006f90..b71d2bfad4d 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] # Get rid of pre-built Windows DLLs and only build deviceQuery for now. @@ -32,7 +32,7 @@ local_filters += "Samples/simpleVulkan/Makefile " local_filters += "Samples/simpleVulkanMMAP/Makefile " local_filters += "Samples/streamOrderedAllocationIPC/Makefile " local_filters += "Samples/vulkanImageCUDA/Makefile" -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), From 9e2e52b624c8149192f069282e3cf151721c4a1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 20:44:03 +0100 Subject: [PATCH 5875/9987] add easyconfig for Eigen 3.4.0 with GCCcore/12.2.0 --- .../e/Eigen/Eigen-3.4.0-GCCcore-12.2.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4195527a89f --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.2.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.4.0' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.39'), # to make CMake compiler health check pass on old systems + ('CMake', '3.24.3'), +] + +moduleclass = 'math' From a3090ecec3def36987792f1c1c078af2aa327118 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 20:46:55 +0100 Subject: [PATCH 5876/9987] adding easyconfigs: SLEPc-3.17.2-foss-2022a.eb --- .../s/SLEPc/SLEPc-3.17.2-foss-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SLEPc/SLEPc-3.17.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.17.2-foss-2022a.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.17.2-foss-2022a.eb new file mode 100644 index 00000000000..216e5e154d2 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.17.2-foss-2022a.eb @@ -0,0 +1,21 @@ +name = 'SLEPc' +version = '3.17.2' + +homepage = 'https://slepc.upv.es' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://slepc.upv.es/download/distrib'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f784cca83a14156631d6e0f5726ca0778e259e1fe40c927607d5fb12d958d705'] + +dependencies = [('PETSc', '3.17.4')] + +petsc_arch = 'installed-arch-linux2-c-opt' + +moduleclass = 'numlib' From 5f640e8f03b6d27daa731dea4e3fedf6d5ca009f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 20:47:08 +0100 Subject: [PATCH 5877/9987] adding easyconfigs: VTK-9.2.2-foss-2022a.eb --- .../easyconfigs/v/VTK/VTK-9.2.2-foss-2022a.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.2.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.2.2-foss-2022a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.2.2-foss-2022a.eb new file mode 100644 index 00000000000..1394917dc97 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.2.2-foss-2022a.eb @@ -0,0 +1,87 @@ +## +# Authors:: +# * Fotis Georgatos +# * Robert Mijakovic +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '9.2.2' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + {'VTK-9.2.2.tar.gz': '1c5b0a2be71fac96ff4831af69e350f7a0ea3168981f790c000709dcf9121075'}, + {'VTKData-9.2.2.tar.gz': '4b0ac438c77773ff741fd02c0e3b0dc1406b4c51e6cbe4e8304306fa125f27bf'}, + {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'}, +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('XZ', '5.2.5'), + ('libGLU', '9.0.2'), + ('X11', '20220504'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + +moduleclass = 'vis' From a07e1788e4dbb88c95a8d54ac04cbf0a21cb80cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 20:47:21 +0100 Subject: [PATCH 5878/9987] adding easyconfigs: ParMETIS-4.0.3-gompi-2022a.eb --- .../p/ParMETIS/ParMETIS-4.0.3-gompi-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022a.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022a.eb new file mode 100644 index 00000000000..5b392db9c1f --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022a.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.24.3')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' From 7921f8853881880e926f2edf16e6f21706d117ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 20:51:04 +0100 Subject: [PATCH 5879/9987] use VTK 9.2.2 as dependency of ITK 5.2.1 (instead of VTK 9.2.0rc2) --- easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb index 22f773b4840..83ecef81cdc 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb @@ -32,7 +32,7 @@ dependencies = [ ('libjpeg-turbo', '2.1.3'), ('libpng', '1.6.37'), ('LibTIFF', '4.3.0'), - ('VTK', '9.2.0.rc2'), + ('VTK', '9.2.2'), ('zlib', '1.2.12'), ] From 1464932b131397bffcefa4859c71b172b11a934f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 20:55:26 +0100 Subject: [PATCH 5880/9987] use gfbf/2022.10 toolchain for SciPy-bundle 2022.11 + drop setuptools build dependency + move mpi4py to dedicated easyconfig --- easybuild/easyconfigs/g/gfbf/gfbf-2022.10.eb | 20 +++++++++++++++ .../m/mpi4py/mpi4py-3.1.4-foss-2022.10.eb | 25 +++++++++++++++++++ ...b => SciPy-bundle-2022.11-gfbf-2022.10.eb} | 8 +----- 3 files changed, 46 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2022.10.eb create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022.10.eb rename easybuild/easyconfigs/s/SciPy-bundle/{SciPy-bundle-2022.11-foss-2022.10.eb => SciPy-bundle-2022.11-gfbf-2022.10.eb} (86%) diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2022.10.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2022.10.eb new file mode 100644 index 00000000000..e803a1e75b2 --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2022.10.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2022.10' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.2.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022.10.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022.10.eb new file mode 100644 index 00000000000..1e8128dae26 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022.10.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '3.1.4' + +homepage = 'https://github.com/mpi4py/mpi4py' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'foss', 'version': '2022.10'} + +sources = [SOURCE_TAR_GZ] +checksums = ['17858f2ebc623220d0120d1fa8d428d033dde749c4bc35b33d81a66ad7f93480'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2022.11'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-foss-2022.10.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-gfbf-2022.10.eb similarity index 86% rename from easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-foss-2022.10.eb rename to easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-gfbf-2022.10.eb index d6289b1ebfa..ae156260776 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-foss-2022.10.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-gfbf-2022.10.eb @@ -6,16 +6,13 @@ version = '2022.11' homepage = 'https://python.org/' description = "Bundle of Python packages for scientific software" -toolchain = {'name': 'foss', 'version': '2022.10'} +toolchain = {'name': 'gfbf', 'version': '2022.10'} toolchainopts = {'pic': True, 'lowopt': True} builddependencies = [ ('hypothesis', '6.59.0'), ('UnZip', '6.0'), ('meson-python', '0.11.0'), - # installing numpy 1.23.5 from source requires setuptools < 60.0, - # cfr. https://github.com/numpy/numpy/issues/22157 and //github.com/numpy/numpy/issues/22431 - ('setuptools', '63.4.3'), ] dependencies = [ @@ -53,9 +50,6 @@ exts_list = [ 'checksums': ['fbc5c05c85c1a02be77b1ff591087c83bc44579c6d2bd9fb798bb64ea5e1a027'], 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && ", }), - ('mpi4py', '3.1.4', { - 'checksums': ['17858f2ebc623220d0120d1fa8d428d033dde749c4bc35b33d81a66ad7f93480'], - }), ('numexpr', '2.8.4', { 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], }), From 6144912418a31286f4e477d434f4ac975c522009 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 15 Dec 2022 23:36:09 +0100 Subject: [PATCH 5881/9987] adding easyconfigs: NCCL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb --- ...CL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCCL-tests/NCCL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/NCCL-tests/NCCL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NCCL-tests/NCCL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..dc4b43cede0 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL-tests/NCCL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'NCCL-tests' +version = '2.13.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/nccl-tests' +description = "Tests check both the performance and the correctness of NCCL operations." + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['52b472a58a4918d3221a9b8c4bd9335382643d7e241983918b64692d685cc3d1'] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), +] + +buildopts = 'VERBOSE=1 MPI=1 MPI_HOME=$EBROOTOPENMPI CUDA_HOME=$EBROOTCUDA NCCL_HOME=$EBROOTNCCL ' + +_binaries = ['all_gather_perf', 'all_reduce_perf', 'alltoall_perf', 'broadcast_perf', 'gather_perf', + 'hypercube_perf', 'reduce_perf', 'reduce_scatter_perf', 'scatter_perf', 'sendrecv_perf'] + +files_to_copy = [(['build/%s' % x for x in _binaries], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries], + 'dirs': [], +} + +moduleclass = 'tools' From 1761f728f1fa6e6476c026bb10e74480f40a12ed Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Dec 2022 00:08:07 +0100 Subject: [PATCH 5882/9987] adding easyconfigs: Transformers-4.24.0-foss-2022a.eb --- .../Transformers-4.24.0-foss-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb new file mode 100644 index 00000000000..47a488d49c1 --- /dev/null +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'Transformers' +version = '4.24.0' + +homepage = 'https://github.com/huggingface/transformers' +description = """ +State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Rust', '1.60.0'), # required for setuptools-rust, which is needed for tokenizers +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('regex', '2022.10.31', { + 'checksums': ['a3a98921da9a1bf8457aeee6a551948a83601689e5ecdd736894ea9bbec77e83'], + }), + ('tokenizers', '0.13.2', { + 'checksums': ['f9525375582fd1912ac3caa2f727d36c86ff8c0c6de45ae1aaff90f87f33b907'], + }), + ('huggingface-hub', '0.10.1', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['5c188d5b16bec4b78449f8681f9975ff9d321c16046cc29bcf0d7e464ff29276'], + }), + ('transformers', version, { + 'checksums': ['486f353a8e594002e48be0e2aba723d96eda839e63bfe274702a4b5eda85559b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From e4120221981e58f19da1605a83ff88578da1d02a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Dec 2022 08:10:17 +0100 Subject: [PATCH 5883/9987] adding easyconfigs: Bader-1.04-GCC-11.2.0.eb --- .../b/Bader/Bader-1.04-GCC-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bader/Bader-1.04-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.04-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bader/Bader-1.04-GCC-11.2.0.eb new file mode 100644 index 00000000000..20b55c3aed9 --- /dev/null +++ b/easybuild/easyconfigs/b/Bader/Bader-1.04-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'Bader' +version = '1.04' + +homepage = 'https://theory.cm.utexas.edu/henkelman/code/bader/' +description = "Bader Charge Analysis" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] +sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f20a0a021157d911bea06666911763b737c4ff38b39e793b8560f940fe391b8e'] + +buildopts = ' -f makefile.lnx_ifort FC=$FC FFLAGS="$FFLAGS" ' + +parallel = 1 + +files_to_copy = [ + (['bader'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/bader'], + 'dirs': [], +} + +moduleclass = 'phys' From 8e5aab16d2b7ba5f5a4678c89134ec4d8f39bc73 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 16 Dec 2022 15:33:46 +0800 Subject: [PATCH 5884/9987] adding easyconfigs: alsa-lib-1.2.8-GCCcore-11.2.0.eb --- .../alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ae379c9ac31 --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.8' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['ftp://ftp.alsa-project.org/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347'] + +dependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' From c6cd9a761fb6aa4f121a057b4003ecfa5670b9b2 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 16 Dec 2022 15:34:13 +0800 Subject: [PATCH 5885/9987] adding easyconfigs: bwidget-1.9.15-GCCcore-11.2.0.eb --- .../bwidget/bwidget-1.9.15-GCCcore-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..aa9c67ac17a --- /dev/null +++ b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'bwidget' +version = '1.9.15' + +homepage = 'https://core.tcl-lang.org/bwidget/home' +description = 'The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.' + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://downloads.sourceforge.net/project/tcllib/BWidget/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9c4dd648fdfd31de7cb5af44b392a1916f949dd195820684d940edcd8485ac13'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Tk', '8.6.11')] + +modextrapaths = {'TCLLIBPATH': '.'} + +sanity_check_paths = { + 'files': ['button.tcl'], + 'dirs': ['BWman', 'demo', 'images', 'lang', 'tests'], +} + +moduleclass = 'vis' From d8b44ca1bb29325dc51cf9aa30c8d1e8115cba26 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 16 Dec 2022 15:34:43 +0800 Subject: [PATCH 5886/9987] adding easyconfigs: umap-learn-0.5.3-foss-2021b.eb --- .../umap-learn/umap-learn-0.5.3-foss-2021b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021b.eb new file mode 100644 index 00000000000..3ddc3e129e2 --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021b.eb @@ -0,0 +1,41 @@ +# Author: Denis Krišťák (INUITS) +# This is a contribution from HPCNow! (http://hpcnow.com) +# Update: Erica Bianco +# License:: GPL-v3.0 +easyblock = "PythonBundle" + +name = 'umap-learn' +version = '0.5.3' + +homepage = 'https://umap-learn.readthedocs.io/en/latest/' +description = """ +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique +that can be used for visualisation similarly to t-SNE, but also for general non-linear +dimension reduction. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('scikit-learn', '1.0.1'), + ('numba', '0.54.1'), + ('LLVM', '12.0.1'), + ('tqdm', '4.62.3'), +] + +use_pip = True + +exts_list = [ + ('pynndescent', '0.5.7', { + 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], + }), + (name, version, { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From f9da8d33f94afc91e4102cfd0eeb7a771e062d25 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 16 Dec 2022 09:06:04 +0100 Subject: [PATCH 5887/9987] adding easyconfigs: TM-align-20190822-GCC-11.3.0.eb --- .../TM-align/TM-align-20190822-GCC-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/t/TM-align/TM-align-20190822-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/t/TM-align/TM-align-20190822-GCC-11.3.0.eb b/easybuild/easyconfigs/t/TM-align/TM-align-20190822-GCC-11.3.0.eb new file mode 100644 index 00000000000..df013e222a0 --- /dev/null +++ b/easybuild/easyconfigs/t/TM-align/TM-align-20190822-GCC-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CmdCp' + +name = 'TM-align' +version = '20190822' + +homepage = 'https://zhanglab.ccmb.med.umich.edu/RNA-align/TMalign/' +description = """This package unifies protein structure alignment and RNA structure alignment + into the standard TM-align program for single chain structure alignment, MM-align program for + multi-chain structure alignment, and TM-score program for sequence dependent structure superposition.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://zhanggroup.org/TM-align/'] +sources = ['TMtools%(version)s.tar.gz'] +checksums = ['bf81b636f222f6a6960963875e9c95dc034498f8c6fbd7cd2e66b6fde9856798'] + +_cmd = '$F77 $FCFLAGS TMalign.f -o TMalign' +_cmd += ' && $F77 $FCFLAGS TMscore.f -o TMscore' + +cmds_map = [('.*', _cmd)] + +files_to_copy = [ + (['TMalign', 'TMscore'], 'bin') +] + +sanity_check_paths = { + 'files': ['bin/TMalign', 'bin/TMscore'], + 'dirs': [], +} + +sanity_check_commands = [ + 'TMalign -h', + 'TMscore -h', +] + +moduleclass = 'bio' From 8794380eb3968571e7649f571f3388f7c488997a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Dec 2022 16:21:26 +0100 Subject: [PATCH 5888/9987] adding easyconfigs: BWA-0.7.17-GCCcore-11.3.0.eb --- .../b/BWA/BWA-0.7.17-GCCcore-11.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..498ebbb605e --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.3.0.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' + +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Perl', '5.34.1'), + ('zlib', '1.2.12'), +] + +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " + +moduleclass = 'bio' From e9d9f02f4ad03773b6ab23870b7a5597ac1c88e5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Dec 2022 16:37:21 +0100 Subject: [PATCH 5889/9987] adding easyconfigs: GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb --- .../GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb new file mode 100644 index 00000000000..7c64788e3d6 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.3.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['12fbd03142311419a050dba8009d615ee8faceb32b46aad8f4448dafd61e11eb'] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.10.4'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' From eaf9963987de7bfb0402ac75f99a26b95d6d33be Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 16 Dec 2022 20:01:30 -0800 Subject: [PATCH 5890/9987] {bio}[foss/2021b] slamdunk 0.4.3 w/Python 3.9.6 --- .../s/slamdunk/slamdunk-0.4.3-foss-2021b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb new file mode 100644 index 00000000000..83ec0ecee9c --- /dev/null +++ b/easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb @@ -0,0 +1,34 @@ + +# easybuild easyconfig +# +# John Dey Fred Hutchinson Cancer Center +# +easyblock = 'PythonBundle' + +name = 'slamdunk' +version = '0.4.3' + +homepage = 'https://t-neumann.github.io/slamdunk/' +description = """SlamDunk is a novel, fully automated software tool for automated, robust, scalable + and reproducible SLAMseq data analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('HTSlib', '1.14'), + ('Biopython', '1.79'), # includes ScyPy-bundle + ('Pysam', '0.17.0'), + ('pybedtools', '0.8.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['8475d4cadad3defda6b11de405fc59de917a6e57468f709a1e28b8a0627f2ff5'], + }), +] + +moduleclass = 'bio' From 3ffe9a479c34d6da5dbca3e246fa4c0499f23962 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 17 Dec 2022 10:11:30 +0000 Subject: [PATCH 5891/9987] update source_urls in MUMPS 5.3.*, 5.4.*, and 5.5.* --- easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb index c3b9ed471b2..788e37ba403 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb index 3e9e86cfe09..2ccfcf5826f 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb index 796b2daf523..f35a1d8bdc8 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb @@ -11,7 +11,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb index ce1f12d8b5d..02f1645d955 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb @@ -8,7 +8,7 @@ description = """A parallel sparse direct solver""" toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-5.4.0_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb index 3971d5baaa7..03dc589f2ea 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2021b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-5.4.0_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb index 1b9876029cc..8a0c0614163 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb index d9da01989ea..d5d20b8c568 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD From 2bc7906676b8b9376db83721694b3f0a766bc048 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 17 Dec 2022 10:23:54 +0000 Subject: [PATCH 5892/9987] update source_urls in MUMPS 5.1.* and 5.2.* --- easybuild/easyconfigs/m/MUMPS/MUMPS-5.1.2-foss-2017b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2018b-metis.eb | 2 +- .../easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis-seq.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb | 2 +- .../easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis-seq.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.1.2-foss-2017b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.1.2-foss-2017b-metis.eb index 5c4845921c0..b9872da4d0a 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.1.2-foss-2017b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.1.2-foss-2017b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['eb345cda145da9aea01b851d17e54e7eef08e16bfa148100ac1f7f046cd42ae9'] diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2018b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2018b-metis.eb index ea67534b667..75d6a04770a 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2018b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2018b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis-seq.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis-seq.eb index 5c7d17274b3..d10d2450e7d 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis-seq.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis-seq.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver. This module is for its sequentia toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'pic': True, 'usempi': False} -source_urls = ['http://mumps.enseeiht.fr/'] # doesn't support https +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis.eb index 718db19d94b..6a6dbb4a649 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019b-metis.eb index 7d9a6bacb27..7072922653b 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb index 849c31db3e0..6c29b89b559 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2020a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis-seq.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis-seq.eb index 7e3d0011f82..1dc132a103a 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis-seq.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis-seq.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver. This module is for its sequentia toolchain = {'name': 'intel', 'version': '2019a'} toolchainopts = {'pic': True, 'usempi': False} -source_urls = ['http://mumps.enseeiht.fr/'] # doesn't support https +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis.eb index 1049b760c09..4e81acee6ea 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2019a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019b-metis.eb index 87578164d88..1acfe3342ef 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb index 6e411ccea17..ca6f8b652a0 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2020a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD From 6b66c567082d1c191a3ee1aa7879f4f41bd62a3d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 17 Dec 2022 14:55:20 +0000 Subject: [PATCH 5893/9987] adding easyconfigs: SuperLU_DIST-8.1.0-foss-2022a.eb --- .../SuperLU_DIST-8.1.0-foss-2022a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb new file mode 100644 index 00000000000..18297b94e50 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = "EB_SuperLU" + +name = 'SuperLU_DIST' +version = '8.1.0' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['9308844b99a7e762d5704934f7e9f79daf158b0bfc582994303c2e0b31518b34'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('ParMETIS', '4.0.3'), +] + +configopts = '-DTPL_PARMETIS_INCLUDE_DIRS="${EBROOTPARMETIS}/include" ' +configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${EBROOTPARMETIS}/lib/libmetis.a" ' + +postinstallcmds = [ + "rm %(installdir)s/lib64/libsuperlu.a", # remove broken symlink to libsuperlu.a +] + +sanity_check_paths = { + 'files': ['lib64/libsuperlu_dist.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' From c9b1089d2819b6d2ca6d9980768a2ffe67d54a21 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 17 Dec 2022 15:00:05 +0000 Subject: [PATCH 5894/9987] add ParMETIS and SuperLU_Dist deps to PETSc 3.17.4 --- easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb index 058019a15f9..4f5e7a06671 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb @@ -36,6 +36,8 @@ dependencies = [ ('MUMPS', '5.5.1', '-metis'), ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), ('Hypre', '2.25.0'), + ('ParMETIS', '4.0.3'), + ('SuperLU_DIST', '8.1.0'), ] # enabling --with-mpi4py seems to be totally broken, leads to make errors like: From de048d8cdef02feeeeab939630bf7286fc603aa2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Dec 2022 16:15:08 +0100 Subject: [PATCH 5895/9987] update checksum of GATK v4.3.0.0 Co-authored-by: SebastianAchilles --- .../easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb index 7c64788e3d6..a0b3fff1247 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb @@ -32,7 +32,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] sources = ['gatk-%(version)s.zip'] -checksums = ['12fbd03142311419a050dba8009d615ee8faceb32b46aad8f4448dafd61e11eb'] +checksums = ['e2c27229b34c3e22445964adf00639a0909887bbfcc040f6910079177bc6e2dd'] dependencies = [ ('Java', '11', '', True), From d4ce1ebdbd5c245fa1ba720057f23de4cc3d59e9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Dec 2022 16:15:35 +0100 Subject: [PATCH 5896/9987] use SYSTEM global in Java dependency of GATK v4.3.0.0 Co-authored-by: SebastianAchilles --- .../easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb index a0b3fff1247..81e5752680f 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb @@ -35,7 +35,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['e2c27229b34c3e22445964adf00639a0909887bbfcc040f6910079177bc6e2dd'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.10.4'), ] From 9025440291bc42c3fb070f3927378b85a20dd467 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Dec 2022 16:56:58 +0100 Subject: [PATCH 5897/9987] adding easyconfigs: BBMap-39.01-GCC-11.3.0.eb --- .../b/BBMap/BBMap-39.01-GCC-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-11.3.0.eb new file mode 100644 index 00000000000..e72ccff30e4 --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '39.01' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6'] + +dependencies = [('Java', '11', '', SYSTEM)] + +prebuildopts = 'cd jni && ' + +local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % local_suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" + +moduleclass = 'bio' From a8aa7f69df39a6e47648f3bc76fbdcda9224aefc Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 17 Dec 2022 17:24:46 +0000 Subject: [PATCH 5898/9987] retain test filter --- .../s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb index 18297b94e50..1527189c23b 100644 --- a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb @@ -24,6 +24,10 @@ dependencies = [ configopts = '-DTPL_PARMETIS_INCLUDE_DIRS="${EBROOTPARMETIS}/include" ' configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${EBROOTPARMETIS}/lib/libmetis.a" ' +# Some tests run longer than default 1500s timeout on fairly big machine (36 cores). +# Include only first four tests, which should be fairly small to run +pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && ' + postinstallcmds = [ "rm %(installdir)s/lib64/libsuperlu.a", # remove broken symlink to libsuperlu.a ] From 6de51e947be2752c5ade623c241ef2587b11a22f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Dec 2022 18:50:13 +0100 Subject: [PATCH 5899/9987] adding easyconfigs: Pindel-0.2.5b9-20170508-GCC-11.3.0.eb --- .../Pindel-0.2.5b9-20170508-GCC-11.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.3.0.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.3.0.eb new file mode 100644 index 00000000000..798e6828551 --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.3.0.eb @@ -0,0 +1,50 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +## + +easyblock = 'CmdCp' + +name = 'Pindel' +# no official release provided for version 0.2.5b9 (20160729), +# therefore, pull last commit (20170508) to this version from master repo +version = '0.2.5b9-20170508' +_commit = 'b706fba61' + +homepage = 'http://gmt.genome.wustl.edu/packages/pindel/' +description = """ Pindel can detect breakpoints of large deletions, medium sized + insertions, inversions, tandem duplications and other structural variants at single-based + resolution from next-gen sequence data. It uses a pattern growth approach to identify the + breakpoints of these variants from paired-end short reads. """ + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'openmp': True} + +github_account = 'genome' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +patches = ['%(name)s-%(version)s_fix-ambig-abs-compil-err.patch'] +checksums = [ + {'Pindel-0.2.5b9-20170508.tar.gz': 'd626260986270efce5a947d03785781c8fddfc922f41279cf9d4bd504c4e3690'}, + {'Pindel-0.2.5b9-20170508_fix-ambig-abs-compil-err.patch': + '216ae1145fd1568ac2187a89bf4b95c45d5c02272047a3dd5f9dfbede26c8fec'}, +] + +dependencies = [ + ('HTSlib', '1.15.1'), + ('zlib', '1.2.12') +] + +cmds_map = [('.*', "./INSTALL ${EBROOTHTSLIB}")] + +_exes = ['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'] +files_to_copy = [(_exes, 'bin'), "demo", "test", "README.md"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _exes], + 'dirs': ['demo', 'test'], +} + +moduleclass = 'bio' From 65eab888e3f0bf7c7921d34f84bac893c737ece2 Mon Sep 17 00:00:00 2001 From: guacke Date: Sun, 18 Dec 2022 16:04:55 +0100 Subject: [PATCH 5900/9987] adding easyconfigs: protobuf-3.21.9-foss-2021a.eb and patches: linking-error.patch --- .../p/protobuf/linking-error.patch | 36 +++++++++++++++++++ .../p/protobuf/protobuf-3.21.9-foss-2021a.eb | 33 +++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf/linking-error.patch create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/protobuf/linking-error.patch b/easybuild/easyconfigs/p/protobuf/linking-error.patch new file mode 100644 index 00000000000..e48a5db9f29 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/linking-error.patch @@ -0,0 +1,36 @@ +diff -ruN protobuf-21.9-orig/src/libprotobuf-lite.map protobuf-21.9/src/libprotobuf-lite.map +--- protobuf-21.9-orig/src/libprotobuf-lite.map 2022-12-18 15:56:13.701778705 +0100 ++++ protobuf-21.9/src/libprotobuf-lite.map 2022-12-18 15:57:06.973681257 +0100 +@@ -3,6 +3,8 @@ + extern "C++" { + *google*; + }; ++ scc_info_*; ++ descriptor_table_*; + + local: + *; +diff -ruN protobuf-21.9-orig/src/libprotobuf.map protobuf-21.9/src/libprotobuf.map +--- protobuf-21.9-orig/src/libprotobuf.map 2022-12-18 15:56:13.702992299 +0100 ++++ protobuf-21.9/src/libprotobuf.map 2022-12-18 15:57:11.786965226 +0100 +@@ -3,6 +3,8 @@ + extern "C++" { + *google*; + }; ++ scc_info_*; ++ descriptor_table_*; + + local: + *; +diff -ruN protobuf-21.9-orig/src/libprotoc.map protobuf-21.9/src/libprotoc.map +--- protobuf-21.9-orig/src/libprotoc.map 2022-12-18 15:56:13.704384023 +0100 ++++ protobuf-21.9/src/libprotoc.map 2022-12-18 15:57:15.907564998 +0100 +@@ -3,6 +3,8 @@ + extern "C++" { + *google*; + }; ++ scc_info_*; ++ descriptor_table_*; + + local: + *; diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb new file mode 100644 index 00000000000..68806160e6e --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '3.21.9' + +homepage = 'https://github.com/protocolbuffers/protobuf' +description = """Protocol Buffers (a.k.a., protobuf) are Google's +language-neutral, platform-neutral, extensible mechanism for +serializing structured data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/'] +sources = ['v21.9.tar.gz'] +checksums = ['0aa7df8289c957a4c54cbe694fbabe99b180e64ca0f8fdb5e2f76dcf56ff2422'] + +patches = ['linking-error.patch'] # based on https://github.com/protocolbuffers/protobuf/issues/5144 + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +srcdir = 'cmake' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From 0489dd86fa84fb0bec14bdd2d02c4c9d7576b47a Mon Sep 17 00:00:00 2001 From: guacke Date: Sun, 18 Dec 2022 16:18:39 +0100 Subject: [PATCH 5901/9987] Add MPI support. --- easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb index 8fc40328d05..476b4a265c3 100644 --- a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb @@ -29,6 +29,6 @@ sanity_check_paths = { 'dirs': [], } -configopts = '-DHIGHFIVE_USE_EIGEN=ON' +configopts = '-DHIGHFIVE_USE_EIGEN=ON -DHIGHFIVE_PARALLEL_HDF5=ON' moduleclass = 'lib' From e799b37f25160616b54c2dfebae6d5994f492550 Mon Sep 17 00:00:00 2001 From: guacke Date: Sun, 18 Dec 2022 16:24:38 +0100 Subject: [PATCH 5902/9987] add shasum for patch --- .../easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb index 68806160e6e..ece3c76e9eb 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/'] sources = ['v21.9.tar.gz'] -checksums = ['0aa7df8289c957a4c54cbe694fbabe99b180e64ca0f8fdb5e2f76dcf56ff2422'] +checksums = [ + '0aa7df8289c957a4c54cbe694fbabe99b180e64ca0f8fdb5e2f76dcf56ff2422', # v21.9.tar.gz + '9d6d7da49f5a1c9d93a4ff0a63aa9705ac6080328830d0fe2483f94daa8c42f0', # linking-error.patch +] patches = ['linking-error.patch'] # based on https://github.com/protocolbuffers/protobuf/issues/5144 From 78297dd60c6d4cbf6ded5463616990019c6a6d9a Mon Sep 17 00:00:00 2001 From: guacke Date: Sun, 18 Dec 2022 16:40:00 +0100 Subject: [PATCH 5903/9987] style fixes --- .../easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb index ece3c76e9eb..d26f7829913 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb @@ -13,11 +13,11 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/'] sources = ['v21.9.tar.gz'] checksums = [ - '0aa7df8289c957a4c54cbe694fbabe99b180e64ca0f8fdb5e2f76dcf56ff2422', # v21.9.tar.gz - '9d6d7da49f5a1c9d93a4ff0a63aa9705ac6080328830d0fe2483f94daa8c42f0', # linking-error.patch + '0aa7df8289c957a4c54cbe694fbabe99b180e64ca0f8fdb5e2f76dcf56ff2422', # v21.9.tar.gz + '9d6d7da49f5a1c9d93a4ff0a63aa9705ac6080328830d0fe2483f94daa8c42f0', # linking-error.patch ] -patches = ['linking-error.patch'] # based on https://github.com/protocolbuffers/protobuf/issues/5144 +patches = ['linking-error.patch'] # based on https://github.com/protocolbuffers/protobuf/issues/5144 builddependencies = [ ('binutils', '2.36.1'), From fea694ff57c20c68f39703f5f6fdb77330d5cb73 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 18 Dec 2022 18:22:43 +0100 Subject: [PATCH 5904/9987] adding easyconfigs: Beagle-5.4.22Jul22.46e-Java-11.eb --- .../Beagle/Beagle-5.4.22Jul22.46e-Java-11.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beagle/Beagle-5.4.22Jul22.46e-Java-11.eb diff --git a/easybuild/easyconfigs/b/Beagle/Beagle-5.4.22Jul22.46e-Java-11.eb b/easybuild/easyconfigs/b/Beagle/Beagle-5.4.22Jul22.46e-Java-11.eb new file mode 100644 index 00000000000..d2afe2dfd9a --- /dev/null +++ b/easybuild/easyconfigs/b/Beagle/Beagle-5.4.22Jul22.46e-Java-11.eb @@ -0,0 +1,38 @@ +# easybuild easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +# +easyblock = "JAR" + +name = 'Beagle' +_revision = '22Jul22.46e' +version = '5.4.' + _revision +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://faculty.washington.edu/browning/beagle/beagle.html' +description = """Beagle is a software package for phasing genotypes and for imputing + ungenotyped markers.""" + +toolchain = SYSTEM + +source_urls = ['https://faculty.washington.edu/browning/beagle'] +sources = ['%%(namelower)s.%s.jar' % _revision] +checksums = ['57226e441f4da7104df139d022ed24ad9804fa72cf754e45d04f5658dcef242b'] + +dependencies = [('Java', '11')] + +# add beagle.jar +postinstallcmds = ["cd %%(installdir)s && ln -s %%(namelower)s.%s.jar %%(namelower)s.jar" % _revision] + +sanity_check_paths = { + 'files': ['%%(namelower)s.%s.jar' % _revision, '%(namelower)s.jar'], + 'dirs': [] +} + +modloadmsg = """ +To execute %(name)s-%(version)s run: java -jar ${EBROOTBEAGLE}/%(namelower)s.jar +""" + +moduleclass = 'bio' From c6c56297130421acae802e3af2d0b7d5143856f1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 18 Dec 2022 18:24:14 +0100 Subject: [PATCH 5905/9987] adding easyconfigs: PLINK-2.00a3.7-foss-2022a.eb --- .../p/PLINK/PLINK-2.00a3.7-foss-2022a.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb new file mode 100644 index 00000000000..60ba9b0260b --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'PLINK' +version = '2.00a3.7' + +homepage = 'https://www.cog-genomics.org/plink/2.0/' +description = """PLINK is a free, open-source whole genome association analysis toolset, +designed to perform a range of basic, large-scale analyses in a computationally +efficient manner.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + + +dependencies = [ + ('zlib', '1.2.12'), + ('zstd', '1.5.2'), + ('libdeflate', '1.10'), +] + +default_easyblock = 'MakeCp' + +default_component_specs = { + 'source_urls': ['https://github.com/chrchang/plink-ng/archive/refs/tags/'], + 'sources': ['v%s.tar.gz' % version], + 'skipsteps': ['configure'], +} + +components = [ + ('PLINK1', '1.90', { + 'checksums': ['145717350205f5562a01292a0fcbd617b7500758f20cad0393c7cc54665a614e'], + 'start_dir': '%s-ng-%s/1.9' % (name.lower(), version), + 'buildopts': ( + 'CFLAGS="${CFLAGS} -DDYNAMIC_ZLIB" CXXFLAGS="${CXXFLAGS} -DDYNAMIC_ZLIB" ' + 'LDFLAGS="${LDFLAGS} -lm -lpthread -ldl" BLASFLAGS="${LIBBLAS}" ZLIB="-L$EBROOTZLIB/lib -lz"' + ), + 'files_to_copy': [(['plink'], 'bin')], + }), + ('PLINK2', version, { + 'checksums': ['145717350205f5562a01292a0fcbd617b7500758f20cad0393c7cc54665a614e'], + 'start_dir': '%s-ng-%s/2.0' % (name.lower(), version), + 'prebuildopts': "sed -i 's/(OBJ)/(OBJ_NO_ZSTD)/g' Makefile && sed -i '9,19d' Makefile.src && ", + 'buildopts': ( + 'BASEFLAGS="-g -DNDEBUG -DZSTD_MULTITHREAD" BLASFLAGS64="$LIBBLAS" ZSTD="-lzstd -ldeflate" ' + 'CINCLUDE="-Isimde" CINCLUDE2="-I../simde"' + ), + 'files_to_copy': [(['bin/*'], 'bin')], + }), +] + +# run tests (<1h) +postinstallcmds = ["cd Tests && sh run_tests.sh %(installdir)s/bin"] + +sanity_check_paths = { + 'files': ['bin/plink', 'bin/plink2', 'bin/pgen_compress'], + 'dirs': [], +} + +moduleclass = 'bio' From 59a6fe8ac4f61a2517f94cfc0f1b42aaaee0ce6a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Dec 2022 00:48:07 +0100 Subject: [PATCH 5906/9987] push HighFive frmo foss/2021a down to gompi/2021a --- ...ghFive-2.6.2-foss-2021a.eb => HighFive-2.6.2-gompi-2021a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/h/HighFive/{HighFive-2.6.2-foss-2021a.eb => HighFive-2.6.2-gompi-2021a.eb} (93%) diff --git a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-gompi-2021a.eb similarity index 93% rename from easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb rename to easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-gompi-2021a.eb index 476b4a265c3..bedb87011ed 100644 --- a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-gompi-2021a.eb @@ -6,7 +6,7 @@ version = '2.6.2' homepage = 'https://github.com/BlueBrain/HighFive' description = """HighFive is a modern header-only C++11 friendly interface for libhdf5.""" -toolchain = {'name': 'foss', 'version': '2021a'} +toolchain = {'name': 'gompi', 'version': '2021a'} github_account = 'BlueBrain' source_urls = [GITHUB_SOURCE] From b6848982cfed7dba52c8537202e03498c2cf4eda Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 19 Dec 2022 15:22:53 +0800 Subject: [PATCH 5907/9987] adding easyconfigs: alsa-lib-1.2.8-GCCcore-10.2.0.eb --- .../alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a96a6a054dd --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.8' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['ftp://ftp.alsa-project.org/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347'] + +dependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' From c41d1412fd2f06dd5b94be5f521fda46bb7c2da7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 19 Dec 2022 15:27:17 +0800 Subject: [PATCH 5908/9987] adding easyconfigs: umap-learn-0.4.6-foss-2020b.eb --- .../umap-learn/umap-learn-0.4.6-foss-2020b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb new file mode 100644 index 00000000000..80d6fbc5818 --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.4.6-foss-2020b.eb @@ -0,0 +1,32 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'umap-learn' +version = '0.4.6' + +homepage = 'https://pypi.org/project/umap-learn/' +description = """Uniform Manifold Approximation and Projection (UMAP) is a +dimension reduction technique that can be used for visualisation similarly to t-SNE, +but also for general non-linear dimension reduction.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4276da9a039c79fa5b4f8d3515a8ccaaccf11a2f59ce8d15baf9d2015a5e82b3'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('numba', '0.52.0'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'umap'} + +sanity_pip_check = True + +moduleclass = 'tools' From e3eeb784225626075c33e069b9f12c71c4ee1e7c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 19 Dec 2022 15:29:21 +0800 Subject: [PATCH 5909/9987] adding easyconfigs: scikit-bio-0.5.7-foss-2020b.eb --- .../scikit-bio/scikit-bio-0.5.7-foss-2020b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb new file mode 100644 index 00000000000..7ce9ef45be9 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scikit-bio' +version = '0.5.7' + +homepage = 'http://scikit-bio.org' +description = """scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms +and educational resources for bioinformatics.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('scikit-learn', '0.23.2'), + ('IPython', '7.18.1'), + ('h5py', '3.1.0'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('msgpack', '1.0.1', { + 'checksums': ['7033215267a0e9f60f4a5e4fb2228a932c404f237817caff8dc3115d9e7cd975'], + }), + ('CacheControl', '0.12.11', { + 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], + }), + ('hdmedians', '0.14.2', { + 'checksums': ['b47aecb16771e1ba0736557255d80ae0240b09156bff434321de559b359ac2d6'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + (name, version, { + 'modulename': 'skbio', + 'checksums': ['6343ca0c621e2fcc5d1c042c8be3200664c5325956a83bea751cf1bcc75d1da9'], + }), +] + +moduleclass = 'bio' From 3960ef30cb6a88b3bf7fe8ac3d920bed6ff2fd66 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 19 Dec 2022 08:38:01 +0100 Subject: [PATCH 5910/9987] adding easyconfigs: CloudCompare-2.12.4-foss-2021b.eb --- .../CloudCompare-2.12.4-foss-2021b.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb new file mode 100644 index 00000000000..ebc938838cb --- /dev/null +++ b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb @@ -0,0 +1,76 @@ +easyblock = 'CMakeMake' + +name = 'CloudCompare' +version = '2.12.4' + +homepage = 'https://www.cloudcompare.org/' +description = "3D point cloud and mesh processing software" + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'CloudCompare' +source_urls = [GITHUB_SOURCE] +sources = [ + 'v%(version)s.tar.gz', + { + 'filename': 'CCCoreLib-20220714.tar.gz', + 'git_config': { + 'url': 'https://github.com/CloudCompare', + 'repo_name': 'CCCoreLib', + 'commit': '54ecc7104ead3f203ac6454ff999afe5dac60f2c', + }, + 'extract_cmd': 'tar -C %(name)s-%(version)s/libs/qCC_db/extern -xf %s', + }, +] +checksums = [ + '31c1f4f91efbdb74619cebb36f57f999d6f1a57bb6f87b13e60d21e670c38f68', + None, +] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +dependencies = [ + ('Qt5', '5.15.2'), + ('GDAL', '3.3.2'), + ('Eigen', '3.3.9'), +] + +_copts = [ + '-DEIGEN_ROOT_DIR=$EBROOTEIGEN', + '-DOpenGL_GL_PREFERENCE=GLVND', + '-DOPTION_USE_GDAL=1', + '-DPLUGIN_GL_QEDL=1', + '-DPLUGIN_GL_QSSAO=1', + '-DPLUGIN_IO_QADDITIONAL=1', + '-DPLUGIN_IO_QCSV_MATRIX=1', + '-DPLUGIN_IO_QPHOTOSCAN=1', + '-DPLUGIN_STANDARD_QBROOM=1', + '-DPLUGIN_STANDARD_QCOMPASS=1', + '-DPLUGIN_STANDARD_QCSF=1', + '-DPLUGIN_STANDARD_QFACETS=1', + '-DPLUGIN_STANDARD_QHOUGH_NORMALS=1', + '-DPLUGIN_STANDARD_QHPR=1', + '-DPLUGIN_STANDARD_QM3C2=1', + '-DPLUGIN_STANDARD_QPCV=1', + '-DPLUGIN_STANDARD_QRANSAC_SD=1', + '-DPLUGIN_STANDARD_QSRA=1', +] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': + ['bin/%s' % x for x in ['CloudCompare', 'ccViewer']] + + ['lib/cloudcompare/lib%s.%s' % (x, SHLIB_EXT) for x in [ + 'CCAppCommon', 'CCCoreLib', 'CC_FBO_LIB', 'CCPluginAPI', 'QCC_DB_LIB', 'QCC_GL_LIB', 'QCC_IO_LIB' + ]] + + ['lib/cloudcompare/plugins/lib%s_PLUGIN.%s' % (x, SHLIB_EXT) for x in [ + 'QCORE_IO', 'QEDL_GL', 'QSSAO_GL', 'QADDITIONAL_IO', 'QCSV_MATRIX_IO', 'QPHOTOSCAN_IO', + 'QBROOM', 'QCANUPO', 'QCOMPASS', 'QCSF', 'QFACETS', 'QHOUGH_NORMALS', 'QHPR', 'QM3C2', + 'QPCV', 'QRANSAC_SD', 'QSRA', + ]], + 'dirs': ['share/cloudcompare/shaders'], +} + +moduleclass = 'geo' From 1afc71778feb6681ff552845fd31e3ac3c2221f1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 19 Dec 2022 08:44:15 +0100 Subject: [PATCH 5911/9987] Remove check for libQCANUPO_PLUGIN since it is not built at the moment. --- .../c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb index ebc938838cb..9262cad1523 100644 --- a/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb @@ -67,7 +67,7 @@ sanity_check_paths = { ]] + ['lib/cloudcompare/plugins/lib%s_PLUGIN.%s' % (x, SHLIB_EXT) for x in [ 'QCORE_IO', 'QEDL_GL', 'QSSAO_GL', 'QADDITIONAL_IO', 'QCSV_MATRIX_IO', 'QPHOTOSCAN_IO', - 'QBROOM', 'QCANUPO', 'QCOMPASS', 'QCSF', 'QFACETS', 'QHOUGH_NORMALS', 'QHPR', 'QM3C2', + 'QBROOM', 'QCOMPASS', 'QCSF', 'QFACETS', 'QHOUGH_NORMALS', 'QHPR', 'QM3C2', 'QPCV', 'QRANSAC_SD', 'QSRA', ]], 'dirs': ['share/cloudcompare/shaders'], From 200a26faa500f8764b58aaa700e23d542595f549 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 19 Dec 2022 10:00:53 +0100 Subject: [PATCH 5912/9987] CloudCompare: Update to using Eigen 3.4.0 to match other easyconfigs in 2021b. --- .../c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb index 9262cad1523..c8b47a5dd75 100644 --- a/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb @@ -34,7 +34,7 @@ builddependencies = [ dependencies = [ ('Qt5', '5.15.2'), ('GDAL', '3.3.2'), - ('Eigen', '3.3.9'), + ('Eigen', '3.4.0'), ] _copts = [ From a89a5a040bfeeb521f716006fe072fa672f9caf5 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 19 Dec 2022 12:59:20 +0100 Subject: [PATCH 5913/9987] Remove redundant patch from CubeGUI --- .../c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb | 18 +- .../CubeGUI-4.8_missing_compile_file.patch | 356 ------------------ 2 files changed, 3 insertions(+), 371 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb index 90d43bac741..548d1fbc2c4 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb @@ -30,25 +30,13 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] sources = [SOURCELOWER_TAR_GZ] -patches = [ - ('CubeGUI-4.8_missing_compile_file.patch', 1), -] -checksums = [ - '1df8fcaea95323e7eaf0cc010784a41243532c2123a27ce93cb7e3241557ff76', # cubegui-4.8.tar.gz - '487697669f6a9a3455fabfdb65d720699070986776c465830ad417942e25e2dc', # CubeGUI-4.8_missing_compile_file.patch -] - -preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' +checksums = ['1df8fcaea95323e7eaf0cc010784a41243532c2123a27ce93cb7e3241557ff76'] -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.38'), - ('Autotools', '20220317'), - ('CubeLib', '4.8'), -] +builddependencies = [('binutils', '2.38')] dependencies = [ ('Qt5', '5.15.5'), + ('CubeLib', '4.8'), ] configopts = [ diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch deleted file mode 100644 index d7a92c4db95..00000000000 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch +++ /dev/null @@ -1,356 +0,0 @@ -# This patch adds the "build-config/compile" file that is missing in v4.8 -# The file is copied "as is" from CubeGUI v4.6. -# -# Author: maxim-masterov (SURF) - -diff -Nru cubegui-4.8.orig/build-config/compile cubegui-4.8/build-config/compile ---- cubegui-4.8.orig/build-config/compile 1970-01-01 01:00:00.000000000 +0100 -+++ cubegui-4.8/build-config/compile 2022-12-12 13:16:45.979205634 +0100 -@@ -0,0 +1,347 @@ -+#! /bin/sh -+# Wrapper for compilers which do not understand '-c -o'. -+ -+scriptversion=2012-10-14.11; # UTC -+ -+# Copyright (C) 1999-2013 Free Software Foundation, Inc. -+# Written by Tom Tromey . -+# -+# This program is free software; you can redistribute it and/or modify -+# it under the terms of the GNU General Public License as published by -+# the Free Software Foundation; either version 2, or (at your option) -+# any later version. -+# -+# This program is distributed in the hope that it will be useful, -+# but WITHOUT ANY WARRANTY; without even the implied warranty of -+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -+# GNU General Public License for more details. -+# -+# You should have received a copy of the GNU General Public License -+# along with this program. If not, see . -+ -+# As a special exception to the GNU General Public License, if you -+# distribute this file as part of a program that contains a -+# configuration script generated by Autoconf, you may include it under -+# the same distribution terms that you use for the rest of that program. -+ -+# This file is maintained in Automake, please report -+# bugs to or send patches to -+# . -+ -+nl=' -+' -+ -+# We need space, tab and new line, in precisely that order. Quoting is -+# there to prevent tools from complaining about whitespace usage. -+IFS=" "" $nl" -+ -+file_conv= -+ -+# func_file_conv build_file lazy -+# Convert a $build file to $host form and store it in $file -+# Currently only supports Windows hosts. If the determined conversion -+# type is listed in (the comma separated) LAZY, no conversion will -+# take place. -+func_file_conv () -+{ -+ file=$1 -+ case $file in -+ / | /[!/]*) # absolute file, and not a UNC file -+ if test -z "$file_conv"; then -+ # lazily determine how to convert abs files -+ case `uname -s` in -+ MINGW*) -+ file_conv=mingw -+ ;; -+ CYGWIN*) -+ file_conv=cygwin -+ ;; -+ *) -+ file_conv=wine -+ ;; -+ esac -+ fi -+ case $file_conv/,$2, in -+ *,$file_conv,*) -+ ;; -+ mingw/*) -+ file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'` -+ ;; -+ cygwin/*) -+ file=`cygpath -m "$file" || echo "$file"` -+ ;; -+ wine/*) -+ file=`winepath -w "$file" || echo "$file"` -+ ;; -+ esac -+ ;; -+ esac -+} -+ -+# func_cl_dashL linkdir -+# Make cl look for libraries in LINKDIR -+func_cl_dashL () -+{ -+ func_file_conv "$1" -+ if test -z "$lib_path"; then -+ lib_path=$file -+ else -+ lib_path="$lib_path;$file" -+ fi -+ linker_opts="$linker_opts -LIBPATH:$file" -+} -+ -+# func_cl_dashl library -+# Do a library search-path lookup for cl -+func_cl_dashl () -+{ -+ lib=$1 -+ found=no -+ save_IFS=$IFS -+ IFS=';' -+ for dir in $lib_path $LIB -+ do -+ IFS=$save_IFS -+ if $shared && test -f "$dir/$lib.dll.lib"; then -+ found=yes -+ lib=$dir/$lib.dll.lib -+ break -+ fi -+ if test -f "$dir/$lib.lib"; then -+ found=yes -+ lib=$dir/$lib.lib -+ break -+ fi -+ if test -f "$dir/lib$lib.a"; then -+ found=yes -+ lib=$dir/lib$lib.a -+ break -+ fi -+ done -+ IFS=$save_IFS -+ -+ if test "$found" != yes; then -+ lib=$lib.lib -+ fi -+} -+ -+# func_cl_wrapper cl arg... -+# Adjust compile command to suit cl -+func_cl_wrapper () -+{ -+ # Assume a capable shell -+ lib_path= -+ shared=: -+ linker_opts= -+ for arg -+ do -+ if test -n "$eat"; then -+ eat= -+ else -+ case $1 in -+ -o) -+ # configure might choose to run compile as 'compile cc -o foo foo.c'. -+ eat=1 -+ case $2 in -+ *.o | *.[oO][bB][jJ]) -+ func_file_conv "$2" -+ set x "$@" -Fo"$file" -+ shift -+ ;; -+ *) -+ func_file_conv "$2" -+ set x "$@" -Fe"$file" -+ shift -+ ;; -+ esac -+ ;; -+ -I) -+ eat=1 -+ func_file_conv "$2" mingw -+ set x "$@" -I"$file" -+ shift -+ ;; -+ -I*) -+ func_file_conv "${1#-I}" mingw -+ set x "$@" -I"$file" -+ shift -+ ;; -+ -l) -+ eat=1 -+ func_cl_dashl "$2" -+ set x "$@" "$lib" -+ shift -+ ;; -+ -l*) -+ func_cl_dashl "${1#-l}" -+ set x "$@" "$lib" -+ shift -+ ;; -+ -L) -+ eat=1 -+ func_cl_dashL "$2" -+ ;; -+ -L*) -+ func_cl_dashL "${1#-L}" -+ ;; -+ -static) -+ shared=false -+ ;; -+ -Wl,*) -+ arg=${1#-Wl,} -+ save_ifs="$IFS"; IFS=',' -+ for flag in $arg; do -+ IFS="$save_ifs" -+ linker_opts="$linker_opts $flag" -+ done -+ IFS="$save_ifs" -+ ;; -+ -Xlinker) -+ eat=1 -+ linker_opts="$linker_opts $2" -+ ;; -+ -*) -+ set x "$@" "$1" -+ shift -+ ;; -+ *.cc | *.CC | *.cxx | *.CXX | *.[cC]++) -+ func_file_conv "$1" -+ set x "$@" -Tp"$file" -+ shift -+ ;; -+ *.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO]) -+ func_file_conv "$1" mingw -+ set x "$@" "$file" -+ shift -+ ;; -+ *) -+ set x "$@" "$1" -+ shift -+ ;; -+ esac -+ fi -+ shift -+ done -+ if test -n "$linker_opts"; then -+ linker_opts="-link$linker_opts" -+ fi -+ exec "$@" $linker_opts -+ exit 1 -+} -+ -+eat= -+ -+case $1 in -+ '') -+ echo "$0: No command. Try '$0 --help' for more information." 1>&2 -+ exit 1; -+ ;; -+ -h | --h*) -+ cat <<\EOF -+Usage: compile [--help] [--version] PROGRAM [ARGS] -+ -+Wrapper for compilers which do not understand '-c -o'. -+Remove '-o dest.o' from ARGS, run PROGRAM with the remaining -+arguments, and rename the output as expected. -+ -+If you are trying to build a whole package this is not the -+right script to run: please start by reading the file 'INSTALL'. -+ -+Report bugs to . -+EOF -+ exit $? -+ ;; -+ -v | --v*) -+ echo "compile $scriptversion" -+ exit $? -+ ;; -+ cl | *[/\\]cl | cl.exe | *[/\\]cl.exe ) -+ func_cl_wrapper "$@" # Doesn't return... -+ ;; -+esac -+ -+ofile= -+cfile= -+ -+for arg -+do -+ if test -n "$eat"; then -+ eat= -+ else -+ case $1 in -+ -o) -+ # configure might choose to run compile as 'compile cc -o foo foo.c'. -+ # So we strip '-o arg' only if arg is an object. -+ eat=1 -+ case $2 in -+ *.o | *.obj) -+ ofile=$2 -+ ;; -+ *) -+ set x "$@" -o "$2" -+ shift -+ ;; -+ esac -+ ;; -+ *.c) -+ cfile=$1 -+ set x "$@" "$1" -+ shift -+ ;; -+ *) -+ set x "$@" "$1" -+ shift -+ ;; -+ esac -+ fi -+ shift -+done -+ -+if test -z "$ofile" || test -z "$cfile"; then -+ # If no '-o' option was seen then we might have been invoked from a -+ # pattern rule where we don't need one. That is ok -- this is a -+ # normal compilation that the losing compiler can handle. If no -+ # '.c' file was seen then we are probably linking. That is also -+ # ok. -+ exec "$@" -+fi -+ -+# Name of file we expect compiler to create. -+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'` -+ -+# Create the lock directory. -+# Note: use '[/\\:.-]' here to ensure that we don't use the same name -+# that we are using for the .o file. Also, base the name on the expected -+# object file name, since that is what matters with a parallel build. -+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d -+while true; do -+ if mkdir "$lockdir" >/dev/null 2>&1; then -+ break -+ fi -+ sleep 1 -+done -+# FIXME: race condition here if user kills between mkdir and trap. -+trap "rmdir '$lockdir'; exit 1" 1 2 15 -+ -+# Run the compile. -+"$@" -+ret=$? -+ -+if test -f "$cofile"; then -+ test "$cofile" = "$ofile" || mv "$cofile" "$ofile" -+elif test -f "${cofile}bj"; then -+ test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile" -+fi -+ -+rmdir "$lockdir" -+exit $ret -+ -+# Local Variables: -+# mode: shell-script -+# sh-indentation: 2 -+# eval: (add-hook 'write-file-hooks 'time-stamp) -+# time-stamp-start: "scriptversion=" -+# time-stamp-format: "%:y-%02m-%02d.%02H" -+# time-stamp-time-zone: "UTC" -+# time-stamp-end: "; # UTC" -+# End: From f5aec762f9bead2c171bb79587a508fdc9ee2bdc Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 19 Dec 2022 13:25:32 +0100 Subject: [PATCH 5914/9987] Change version --- ...re-P-8.0-rc1-gompi-2022a.eb => Score-P-8.0-gompi-2022a.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/Score-P/{Score-P-8.0-rc1-gompi-2022a.eb => Score-P-8.0-gompi-2022a.eb} (94%) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-rc1-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb similarity index 94% rename from easybuild/easyconfigs/s/Score-P/Score-P-8.0-rc1-gompi-2022a.eb rename to easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb index efea7c597ce..3b6348b0077 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-rc1-gompi-2022a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb @@ -13,7 +13,7 @@ ## name = 'Score-P' -version = '8.0-rc1' +version = '8.0' homepage = 'https://www.score-p.org' description = """ @@ -26,7 +26,7 @@ toolchain = {'name': 'gompi', 'version': '2022a'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['d5975e69a594fff4982701f5181b4825386a238a95df68a0d5c1e1b62480add7'] +checksums = ['4c0f34f20999f92ebe6ca1ff706d0846b8ce6cd537ffbedb49dfaef0faa66311'] dependencies = [ ('CubeLib', '4.8'), From e8803bb5798d24c757bb3bc5c1c664011fb60313 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 19 Dec 2022 13:48:45 +0100 Subject: [PATCH 5915/9987] Remove redundant CXX flag --- easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb index 548d1fbc2c4..516af3a8db5 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb @@ -40,7 +40,7 @@ dependencies = [ ] configopts = [ - 'CXX="g++" --with-qt=$EBROOTQT5/bin ', + '--with-qt=$EBROOTQT5/bin ', ] sanity_check_paths = { From 4209d05fe8fc1ac58a1a9127be7a223fb59b9281 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 19 Dec 2022 15:02:50 +0100 Subject: [PATCH 5916/9987] Bowtie2 2.4.4+ fix for non-x86_64 systems --- .../b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb | 23 +++++++++++++++---- .../b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb | 23 +++++++++++++++---- .../b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb | 23 +++++++++++++++---- 3 files changed, 57 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb index 85afb32d7a8..1a4e8413c88 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb @@ -7,11 +7,13 @@ # Modified by: Adam Huffman # The Francis Crick Institute # Modified by: Kurt Lust, UAntwerp +# Modified by: Sebastien Moretti for non-x86_64 systems +# SIB Swiss Institute of Bioinformatics name = 'Bowtie2' version = '2.4.4' -homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. @@ -21,9 +23,22 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'GCC', 'version': '10.3.0'} toolchainopts = {'pic': True, 'cstd': 'gnu++98'} -source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -sources = ['%(namelower)s-%(version)s-source.zip'] -checksums = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] +source_urls = [ + ('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download'), + 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', +] +sources = [ + '%(namelower)s-%(version)s-source.zip', + # SIMD Everywhere implementations only, for non-x86_64 systems + {'download_filename': 'master.zip', + 'filename': 'simde-no-tests.master.zip', + 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', + }, +] +checksums = [ + 'b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc', # bowtie2-2.4.4-source.zip + 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb index 24d2f6861d9..f3b249e22f3 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb @@ -7,11 +7,13 @@ # Modified by: Adam Huffman # The Francis Crick Institute # Modified by: Kurt Lust, UAntwerp +# Modified by: Sebastien Moretti for non-x86_64 systems +# SIB Swiss Institute of Bioinformatics name = 'Bowtie2' version = '2.4.4' -homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. @@ -21,9 +23,22 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'GCC', 'version': '11.2.0'} toolchainopts = {'pic': True, 'cstd': 'gnu++98'} -source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -sources = ['%(namelower)s-%(version)s-source.zip'] -checksums = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] +source_urls = [ + ('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download'), + 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', +] +sources = [ + '%(namelower)s-%(version)s-source.zip', + # SIMD Everywhere implementations only, for non-x86_64 systems + {'download_filename': 'master.zip', + 'filename': 'simde-no-tests.master.zip', + 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', + }, +] +checksums = [ + 'b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc', # bowtie2-2.4.4-source.zip + 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb index 23f2eb1bda7..28ade29cb7e 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb @@ -7,11 +7,13 @@ # Modified by: Adam Huffman # The Francis Crick Institute # Modified by: Kurt Lust, UAntwerp +# Modified by: Sebastien Moretti for non-x86_64 systems +# SIB Swiss Institute of Bioinformatics name = 'Bowtie2' version = '2.4.5' -homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. @@ -21,9 +23,22 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'GCC', 'version': '11.3.0'} toolchainopts = {'pic': True, 'cstd': 'gnu++98'} -source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] -sources = ['%(namelower)s-%(version)s-source.zip'] -checksums = ['d3cbd5f323393b5649aea10325d7c4b77f02035a8b204e5ac18eba95236e076a'] +source_urls = [ + ('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download'), + 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', +] +sources = [ + '%(namelower)s-%(version)s-source.zip', + # SIMD Everywhere implementations only, for non-x86_64 systems + {'download_filename': 'master.zip', + 'filename': 'simde-no-tests.master.zip', + 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', + }, +] +checksums = [ + 'd3cbd5f323393b5649aea10325d7c4b77f02035a8b204e5ac18eba95236e076a', # bowtie2-2.4.5-source.zip + 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip +] dependencies = [ ('zlib', '1.2.12'), From f08c670586960356ba4d49239c61d16349b815de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Mon, 19 Dec 2022 17:21:07 +0100 Subject: [PATCH 5917/9987] Added support for KaHIP library --- .../o/OpenFOAM/OpenFOAM-v2206-cleanup.patch | 159 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb | 5 +- 2 files changed, 162 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-cleanup.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-cleanup.patch new file mode 100644 index 00000000000..ffc27639061 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-cleanup.patch @@ -0,0 +1,159 @@ +# Replaces OpenFOAM third-party libraries with EASYBUILD variants. +# Uses the OpenFOAM prefs mechanism and the FOAM_CONFIG_ETC variable +# to define the preferred settings without patching the original files +# +# Authors: Mark Olesen +# ------------------------------------------------------------------------- +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/prefs.sh 2020-12-14 10:02:26.488430802 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FOAM_CONFIG_ETC="etc/easybuild" ++ ++export WM_MPLIB=EASYBUILDMPI ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/CGAL 2020-12-14 10:10:55.991841204 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++export BOOST_ARCH_PATH="$EBROOTBOOST" ++export CGAL_ARCH_PATH="$EBROOTCGAL" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/FFTW 2020-12-14 10:10:53.735843322 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FFTW_ARCH_PATH="$EBROOTFFTW" ++ ++##EasyBuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/metis 2020-12-11 21:23:28.774934024 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++METIS_VERSION="metis-$EBVERSIONMETIS" ++[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH="$METIS_ROOT" ++ ++##Easybuild## +--- /dev/null 2022-12-01 18:21:35.103878336 +0100 ++++ OpenFOAM-v2206/etc/easybuild/config.sh/kahip 2022-12-12 20:24:07.538408981 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++KAHIP_VERSION="kahip-$EBVERSIONKAHIP" ++export KAHIP_ARCH_PATH="$EBROOTKAHIP" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/readline 2020-12-11 21:23:22.534951043 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export READLINE_ARCH_PATH="$EBROOTLIBREADLINE" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/scotch 2020-12-11 21:23:17.586964539 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export SCOTCH_VERSION="scotch_$EBVERSIONSCOTCH" ++export SCOTCH_ARCH_PATH="$EBROOTSCOTCH" ++[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH="$SCOTCH_ROOT" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/vtk 2020-12-11 21:22:55.463024882 +0100 +@@ -0,0 +1,9 @@ ++##Easybuild## settings -*- sh -*- ++ ++export VTK_DIR="$EBROOTVTK" ++export MESA_ARCH_PATH="$EBROOTMESA" ++ ++# Define paraview-mesa directory as required ++unset ParaView_MESA_DIR ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/paraview 2020-12-14 10:13:53.583674383 +0100 +@@ -0,0 +1,75 @@ ++##Easybuild## settings -*- sh -*- ++# ++# Largely a knockoff of the OpenFOAM etc/config.sh/paraview-system ++# readjusted for easybuild ++# ++# Copyright (C) 2020 OpenCFD Ltd. ++# ++#------------------------------------------------------------------------------ ++# Compiler-specific location for ThirdParty installations ++archDir="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER" ++ ++# Clean path and library path of previous settings ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=LD_LIBRARY_PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++ ++#------------------------------------------------------------------------------ ++ ++##Easybuild## settings ++ ++ParaView_VERSION="$EBVERSIONPARAVIEW" ++export ParaView_DIR="$EBROOTPARAVIEW" ++ ++#------------------------------------------------------------------------------ ++ ++unset PV_PLUGIN_PATH ++ ++# Set API to correspond to VERSION ++# pv_api is . from ParaView_VERSION ++#- ++# Extract API from VERSION ++pv_api=$(echo "$ParaView_VERSION" | \ ++ sed -ne 's/^[^0-9]*\([0-9][0-9]*\.[0-9][0-9]*\).*$/\1/p') ++ ++pv_plugin_dir="$FOAM_LIBBIN/paraview-$pv_api" ++ ++# Set paths if binaries are present ++if [ -r "$ParaView_DIR" ] ++then ++ export PATH="$ParaView_DIR/bin:$PATH" ++ ++ # ParaView libraries ++ # - 5.5 and later: lib/, but could also be lib64/ ++ for libDir in lib64 lib ++ do ++ pvLibDir="$libDir/paraview-$pv_api" ++ if [ -d "$ParaView_DIR/$pvLibDir" ] ++ then ++ export LD_LIBRARY_PATH="$ParaView_DIR/$libDir:$LD_LIBRARY_PATH" ++ break ++ fi ++ done ++ ++ # OpenFOAM plugin directory must be the first in PV_PLUGIN_PATH ++ # and have paraview-major.minor encoded in its name ++ if [ -d "$pv_plugin_dir" ] ++ then ++ export PV_PLUGIN_PATH="$pv_plugin_dir" ++ fi ++fi ++ ++ ++#------------------------------------------------------------------------------ ++ ++unset ParaView_VERSION ++ ++unset archDir libDir ++unset pv_api pv_plugin_dir pvLibDir ++ ++#------------------------------------------------------------------------------ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb index 4c58236cb3b..e15587e68ee 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb @@ -16,12 +16,12 @@ toolchainopts = {'cstd': 'c++11', 'vectorize': False} source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] patches = [ - ('OpenFOAM-v2012-cleanup.patch', 1), + ('OpenFOAM-v2206-cleanup.patch', 1), 'OpenFOAM-v1906-wmake-ompi.patch', ] checksums = [ 'db95eda4afb97ca870733b2d4201ef539099d0778e3f3eca9a075d4f1a0eea46', # OpenFOAM-v2206.tgz - 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch + '25333124581acae57c173587de4ebd6e143b894b1a26e4f0326db8b7e0cb1972', # OpenFOAM-v2206-cleanup.patch '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch ] @@ -37,6 +37,7 @@ dependencies = [ # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) ('METIS', '5.1.0'), ('SCOTCH', '7.0.1'), + ('KaHIP', '3.14'), ('CGAL', '4.14.3'), ('ParaView', '5.10.1', '-mpi'), ('gnuplot', '5.4.4'), From b366c3526539c66753a65cf033a06a82fa374b85 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 18:46:47 +0100 Subject: [PATCH 5918/9987] use single rather than double quotes --- .../r/RegTools/RegTools-0.5.2-foss-2021b.eb | 34 +++++++++---------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb index b1a7c9fc772..9c084bba01d 100644 --- a/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb @@ -1,39 +1,39 @@ # updated: Denis Kristak (INUITS) -easyblock = "CMakeMake" +easyblock = 'CMakeMake' -name = "RegTools" -version = "0.5.2" +name = 'RegTools' +version = '0.5.2' -homepage = "https://regtools.readthedocs.org" +homepage = 'https://regtools.readthedocs.org' description = """RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.""" -toolchain = {"name": "foss", "version": "2021b"} +toolchain = {'name': 'foss', 'version': '2021b'} -source_urls = ["https://github.com/griffithlab/%(namelower)s/archive"] -sources = ["%(version)s.tar.gz"] +source_urls = ['https://github.com/griffithlab/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] checksums = ['24d3bc18174237e0fc2d0330839c8dc21c97cdb7d6e528c518188c10f17f3e7e'] builddependencies = [ - ("CMake", "3.21.1"), + ('CMake', '3.21.1'), ] # required by included scripts dependencies = [ - ("Python", "3.9.6"), - ("PyYAML", "5.4.1"), # required by create_IGVsessions.py script - ("R", "4.1.2"), + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), # required by create_IGVsessions.py script + ('R', '4.1.2'), ] # 'make install' is not supported... -install_cmd = "mkdir %(installdir)s/bin && cp -a regtools %(installdir)s/bin/ && " -install_cmd += "cp -a %(builddir)s/regtools-%(version)s/scripts %(installdir)s/" +install_cmd = 'mkdir %(installdir)s/bin && cp -a regtools %(installdir)s/bin/ && ' +install_cmd += 'cp -a %(builddir)s/regtools-%(version)s/scripts %(installdir)s/' sanity_check_paths = { - "files": ["bin/regtools"], - "dirs": ["scripts"], + 'files': ['bin/regtools'], + 'dirs': ['scripts'], } -sanity_check_commands = ["regtools --help"] +sanity_check_commands = ['regtools --help'] -moduleclass = "bio" +moduleclass = 'bio' From c737acda45339c4988df56b49b6392094bdf0645 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 18:52:35 +0100 Subject: [PATCH 5919/9987] use single rather than double quotes --- .../b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb | 34 +++++++++---------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb index 0e4aad5edd5..2a76d9d7b50 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb @@ -1,40 +1,40 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # updated: Denis Kristak (INUITS) -easyblock = "MakeCp" +easyblock = 'MakeCp' -name = "BEDOPS" -version = "2.4.41" +name = 'BEDOPS' +version = '2.4.41' -homepage = "http://%(namelower)s.readthedocs.io/en/latest/index.html" +homepage = 'http://%(namelower)s.readthedocs.io/en/latest/index.html' description = """BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.""" -toolchain = {"name": "foss", "version": "2021b"} -toolchainopts = {"pic": True} +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} -source_urls = ["https://github.com/%(namelower)s/%(namelower)s/archive/"] -sources = ["v%(version)s.tar.gz"] +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] checksums = ['3b868c820d59dd38372417efc31e9be3fbdca8cf0a6b39f13fb2b822607d6194'] -# else build of jansson library fails with: "configure: error: C compiler cannot create executables" -prebuildopts = "unset LIBS && " +# else build of jansson library fails with: 'configure: error: C compiler cannot create executables' +prebuildopts = 'unset LIBS && ' # builds all variants and copies executables to bin directory -buildopts = " all && make install" +buildopts = ' all && make install' # actually used variant is linked to via symlinks keepsymlinks = True -files_to_copy = ["bin"] +files_to_copy = ['bin'] sanity_check_paths = { - "files": [ - "bin/%s" % x for x in ["bam2bed", "%(namelower)s", "convert2bed", "unstarch"] + 'files': [ + 'bin/%s' % x for x in ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch'] ], - "dirs": [], + 'dirs': [], } -sanity_check_commands = ["%(namelower)s --help"] +sanity_check_commands = ['%(namelower)s --help'] -moduleclass = "bio" +moduleclass = 'bio' From 7f5f40698553e579d6d4773bc4014af1616dc341 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 18:57:04 +0100 Subject: [PATCH 5920/9987] use single rather than double quotes --- .../g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb index c87b26a22bd..ff1e41e3dd0 100644 --- a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb @@ -1,39 +1,39 @@ # author: Denis Kristak (INUITS) -easyblock = "Tarball" +easyblock = 'Tarball' -name = "GUSHR" -version = "2020-09-28" -local_commit = "ee26d5c" +name = 'GUSHR' +version = '2020-09-28' +local_commit = 'ee26d5c' -homepage = "https://github.com/Gaius-Augustus/GUSHR" +homepage = 'https://github.com/Gaius-Augustus/GUSHR' description = """ Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation. """ -toolchain = {"name": "foss", "version": "2021b"} +toolchain = {'name': 'foss', 'version': '2021b'} -source_urls = ["https://github.com/Gaius-Augustus/GUSHR/archive"] +source_urls = ['https://github.com/Gaius-Augustus/GUSHR/archive'] sources = [ { - "download_filename": "%s.tar.gz" % local_commit, - "filename": SOURCE_TAR_GZ, + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, } ] checksums = ['81fd9c372a45af1688c2954932f94efc4c637144f874e16be41d1b18936a5303'] dependencies = [ ('Java', '11', '', SYSTEM), - ("AUGUSTUS", "3.4.0"), - ("GLib", "2.69.1"), + ('AUGUSTUS', '3.4.0'), + ('GLib', '2.69.1'), ] sanity_check_paths = { - "files": ["gushr.py"], - "dirs": [], + 'files': ['gushr.py'], + 'dirs': [], } sanity_check_commands = [ """cd example; ./download_rnaseq.sh ; cd - ; ./gushr.py -t example/augustus.gtf -b example/RNAseq.bam -g example/genome.fa -o utrs""" ] -moduleclass = "bio" +moduleclass = 'bio' From f91335c8d9f56be34f08e50801271b699e17e39e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 19:03:54 +0100 Subject: [PATCH 5921/9987] use single rather than double quotes --- .../p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb | 31 +++++++++---------- 1 file changed, 14 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb index 399609c8b90..5a1c4f1c964 100644 --- a/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb @@ -1,34 +1,31 @@ # author: Denis Kristak (INUITS) -easyblock = "MakeCp" +easyblock = 'MakeCp' -name = "PsiCLASS" -version = "1.0.3" +name = 'PsiCLASS' +version = '1.0.3' -homepage = "https://github.com/splicebox/PsiCLASS" +homepage = 'https://github.com/splicebox/PsiCLASS' description = """PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.""" -toolchain = {"name": "GCC", "version": "11.2.0"} +toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ["https://github.com/splicebox/PsiCLASS/archive/"] -sources = ["v%(version)s.tar.gz"] - -checksums = [ - "c60c0f33f9a076b97ccdba68b9140a5fb6936a5c5e309d70b3d0cf558828f73d", # v1.0.3.tar.gz -] +source_urls = ['https://github.com/splicebox/PsiCLASS/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c60c0f33f9a076b97ccdba68b9140a5fb6936a5c5e309d70b3d0cf558828f73d'] parallel = 1 -files_to_copy = ["*"] +files_to_copy = ['*'] -modextrapaths = {"PATH": [""]} +modextrapaths = {'PATH': ''} sanity_check_paths = { - "files": ["classes", "grader", "psiclass"], - "dirs": [], + 'files': ['classes', 'grader', 'psiclass'], + 'dirs': [], } sanity_check_commands = [ - "psiclass -b $EBROOTPSICLASS/example/s1.bam,$EBROOTPSICLASS/example/s2.bam" + 'psiclass -b $EBROOTPSICLASS/example/s1.bam,$EBROOTPSICLASS/example/s2.bam' ] -moduleclass = "bio" +moduleclass = 'bio' From 00c182f892a0ce081653700c14652c83f299ef38 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 19:46:53 +0100 Subject: [PATCH 5922/9987] use single rather than double quotes --- .../GeneMark-ET-4.71-GCCcore-11.2.0.eb | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb index 9d7b048917c..7c3550e3cb5 100644 --- a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb @@ -1,15 +1,15 @@ # updated: Denis Kristak (INUITS) -easyblock = "Tarball" +easyblock = 'Tarball' -name = "GeneMark-ET" -version = "4.71" +name = 'GeneMark-ET' +version = '4.71' -homepage = "http://exon.gatech.edu/GeneMark" +homepage = 'http://exon.gatech.edu/GeneMark' description = "Eukaryotic gene prediction suite with automatic training" -toolchain = {"name": "GCCcore", "version": "11.2.0"} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -sources = ["gmes_linux_64-%(version)s.tar.gz"] +sources = ['gmes_linux_64-%(version)s.tar.gz'] checksums = ['29adf580ccee6f69d19045bedc3a53e7a71b4c39a95409be3e96d3e9dca83c95'] download_instructions = """ @@ -17,15 +17,15 @@ download_instructions = """ 2. rename the tarball: `mv gmes_linux_64.tar.gz gmes_linux_64-%(version)s.tar.gz` """ -dependencies = [("Perl", "5.34.0")] +dependencies = [('Perl', '5.34.0')] -fix_perl_shebang_for = ["*.pl"] +fix_perl_shebang_for = ['*.pl'] sanity_check_paths = { - "files": ["gmes.cfg", "gmes_petap.pl"], - "dirs": ["lib"], + 'files': ['gmes.cfg', 'gmes_petap.pl'], + 'dirs': ['lib'], } -modextrapaths = {"PATH": ""} +modextrapaths = {'PATH': ''} -moduleclass = "bio" +moduleclass = 'bio' From ccdea8325804196009ff9f779fbffbbb3443f94c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 19:57:18 +0100 Subject: [PATCH 5923/9987] use single rather than double quotes --- .../o/olego/olego-1.1.9-GCC-11.2.0.eb | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb index 89c892a1f8a..5bb617a4627 100644 --- a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb @@ -1,28 +1,28 @@ # updated by: Denis Kristak (INUITS) -easyblock = "MakeCp" +easyblock = 'MakeCp' -name = "olego" -version = "1.1.9" +name = 'olego' +version = '1.1.9' -homepage = "https://github.com/chaolinzhanglab/olego" +homepage = 'https://github.com/chaolinzhanglab/olego' description = """OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seed-and-extend scheme, and does not rely on a separate external mapper.""" -toolchain = {"name": "GCC", "version": "11.2.0"} +toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ["https://github.com/chaolinzhanglab/olego//archive/"] -sources = ["v%(version)s.tar.gz"] +source_urls = ['https://github.com/chaolinzhanglab/olego//archive/'] +sources = ['v%(version)s.tar.gz'] checksums = ['1b6ba7a4a310ac71667052d3a6e1f073d3976302ab6b6b67041475f7ca1f4bac'] -files_to_copy = ["*"] +files_to_copy = ['*'] -modextrapaths = {"PATH": [""]} +modextrapaths = {'PATH': ''} sanity_check_paths = { - "files": ["olegoindex", "olego"], - "dirs": [], + 'files': ['olegoindex', 'olego'], + 'dirs': [], } sanity_check_commands = ['olego 2>&1 | grep "version %(version)s"'] -moduleclass = "bio" +moduleclass = 'bio' From d40f513485de9c8af036b9451acb7460b53e87a7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 20:03:22 +0100 Subject: [PATCH 5924/9987] add alternative checksum --- .../g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb index 7c3550e3cb5..017e077aa13 100644 --- a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb @@ -10,7 +10,10 @@ description = "Eukaryotic gene prediction suite with automatic training" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} sources = ['gmes_linux_64-%(version)s.tar.gz'] -checksums = ['29adf580ccee6f69d19045bedc3a53e7a71b4c39a95409be3e96d3e9dca83c95'] +checksums = [( + '29adf580ccee6f69d19045bedc3a53e7a71b4c39a95409be3e96d3e9dca83c95', + '629f430e7262bdb5df8f24413e65d26e35eb10ea34212145b692ee4689591e54', +)] download_instructions = """ 1. complete the license form: http://exon.gatech.edu/GeneMark/license_download.cgi From ae193a1c63f27f02274e944706d5adcd44ad73e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Mon, 19 Dec 2022 20:15:14 +0100 Subject: [PATCH 5925/9987] adding easyconfigs: OpenSceneGraph-3.6.5-foss-2022a.eb, librsvg-2.55.1-GCCcore-11.3.0.eb, poppler-22.12.0-GCC-11.3.0.eb --- .../librsvg/librsvg-2.55.1-GCCcore-11.3.0.eb | 40 +++++++++++++ .../OpenSceneGraph-3.6.5-foss-2022a.eb | 51 +++++++++++++++++ .../p/poppler/poppler-22.12.0-GCC-11.3.0.eb | 57 +++++++++++++++++++ 3 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/l/librsvg/librsvg-2.55.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.55.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.55.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8116a32cafc --- /dev/null +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.55.1-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'librsvg' +version = '2.55.1' + +homepage = 'https://wiki.gnome.org/Projects/LibRsvg' +description = "Librsvg is a library to render SVG files using cairo." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['6baf48a9d3a56fd13bbfbb9f1f76759b240b70a1fa220fd238474d66a926f98c'] + +builddependencies = [ + ('binutils', '2.38'), + ('Rust', '1.60.0'), +] + +dependencies = [ + ('cairo', '1.17.4'), + ('freetype', '2.12.1'), + ('Gdk-Pixbuf', '2.42.8'), + ('HarfBuzz', '4.2.1'), + ('Pango', '1.50.7'), + ('GObject-Introspection', '1.72.0'), +] + +# don't GdkPixbuf loader (which gets added to the Gdk-Pixbuf installation directory) +configopts = "--disable-pixbuf-loader" + +sanity_check_paths = { + 'files': ['bin/rsvg-convert', 'lib/librsvg-%(version_major)s.a', 'lib/librsvg-%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/librsvg-%(version_major)s.0.pc'], + 'dirs': ['include/librsvg-%(version_major)s.0/librsvg', 'share'], +} + +sanity_check_commands = ["rsvg-convert --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb new file mode 100644 index 00000000000..049ea1ecc5c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb @@ -0,0 +1,51 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jiri Furst +### + +easyblock = 'CMakeMake' + +name = 'OpenSceneGraph' +version = '3.6.5' + +homepage = 'http://www.openscenegraph.org/' +description = """The OpenSceneGraph is an open source high performance 3D graphics toolkit, +used by application developers in fields such as visual simulation, games, virtual reality, +scientific visualization and modelling. Written entirely in Standard C++ and OpenGL it runs +on all Windows platforms, OSX, GNU/Linux, IRIX, Solaris, HP-Ux, AIX and FreeBSD operating +systems. The OpenSceneGraph is now well established as the world leading scene graph +technology, used widely in the vis-sim, space, scientific, oil-gas, games and virtual +reality industries.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_SOURCE] +sources = ['OpenSceneGraph-%(version)s.tar.gz'] +checksums = ['aea196550f02974d6d09291c5d83b51ca6a03b3767e234a8c0e21322927d1e12'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20220504'), + ('Mesa', '22.0.3'), + ('GDAL', '3.5.0'), + ('DCMTK', '3.6.7'), + ('OpenEXR', '3.1.5'), + ('SDL2', '2.0.22'), + ('poppler', '22.12.0'), + ('librsvg', '2.55.1'), + ('giflib', '5.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['osgarchive', 'osgconv', 'osgfilecache', 'osgversion', 'osgviewer', 'present3D']], + 'dirs': ['lib'], +} + +sanity_check_commands = ['osgversion'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..dc7391dd572 --- /dev/null +++ b/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb @@ -0,0 +1,57 @@ +easyblock = 'Bundle' + +name = 'poppler' +version = '22.12.0' + +homepage = 'https://poppler.freedesktop.org' +description = "Poppler is a PDF rendering library" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), + ('Python', '3.10.4', '-bare'), +] + +dependencies = [ + ('freetype', '2.12.1'), + ('fontconfig', '2.14.0'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('NSS', '3.79'), + ('LibTIFF', '4.3.0'), + ('Qt5', '5.15.5'), + ('Boost', '1.79.0'), + ('cairo', '1.17.4'), + ('OpenJPEG', '2.5.0'), + ('zlib', '1.2.12'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_XZ], + 'configopts': "-DENABLE_BOOST=ON", + }), + ('poppler-data', '0.4.11', { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_GZ], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdfinfo', 'lib/libpoppler.%s' % SHLIB_EXT, 'lib/libpoppler-cpp.%s' % SHLIB_EXT, + 'lib/libpoppler-glib.%s' % SHLIB_EXT, 'lib/libpoppler-qt5.%s' % SHLIB_EXT], + 'dirs': ['include/poppler', 'lib/pkgconfig', 'share'], +} + +sanity_check_commands = ["pdfinfo --help"] + +moduleclass = 'lib' From ed7bb90f0bf20a91e1056c2d01e0c24d10a50864 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Mon, 19 Dec 2022 20:50:40 +0100 Subject: [PATCH 5926/9987] Added missing checksums for poppler --- easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb index dc7391dd572..ab2bab38826 100644 --- a/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb @@ -38,11 +38,13 @@ components = [ (name, version, { 'source_urls': ['https://poppler.freedesktop.org/'], 'sources': [SOURCE_TAR_XZ], + 'checksums': ['d9aa9cacdfbd0f8e98fc2b3bb008e645597ed480685757c3e7bc74b4278d15c0'], 'configopts': "-DENABLE_BOOST=ON", }), ('poppler-data', '0.4.11', { 'source_urls': ['https://poppler.freedesktop.org/'], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2cec05cd1bb03af98a8b06a1e22f6e6e1a65b1e2f3816cb3069bb0874825f08c'], }), ] From 306631dcc1f95b76bf001dca49b40fc806e2d491 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Dec 2022 22:35:05 +0100 Subject: [PATCH 5927/9987] push PLINK v2.00a3.7 down from foss to gfbf toolchain --- ...LINK-2.00a3.7-foss-2022a.eb => PLINK-2.00a3.7-gfbf-2022a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/PLINK/{PLINK-2.00a3.7-foss-2022a.eb => PLINK-2.00a3.7-gfbf-2022a.eb} (97%) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2022a.eb similarity index 97% rename from easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb rename to easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2022a.eb index 60ba9b0260b..cad2313a3d2 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2022a.eb @@ -8,7 +8,7 @@ description = """PLINK is a free, open-source whole genome association analysis designed to perform a range of basic, large-scale analyses in a computationally efficient manner.""" -toolchain = {'name': 'foss', 'version': '2022a'} +toolchain = {'name': 'gfbf', 'version': '2022a'} dependencies = [ From e35011389860b5a90a1748525630746a03bb6d1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 09:29:35 +0100 Subject: [PATCH 5928/9987] adding easyconfigs: AdapterRemoval-2.3.3-GCC-11.3.0.eb --- .../AdapterRemoval-2.3.3-GCC-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.3-GCC-11.3.0.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..e93de561424 --- /dev/null +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.3-GCC-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'AdapterRemoval' +version = '2.3.3' + +homepage = 'https://github.com/MikkelSchubert/adapterremoval' +description = """AdapterRemoval searches for and removes remnant adapter sequences + from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases + from the 3' end of reads following adapter removal.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'MikkelSchubert' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a1bdc054319ede085fc8a4e9867c23ffed7df5e97b99d52221b7c587d19418fc'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] +} + +sanity_check_commands = [('%(name)s', '--version')] + +moduleclass = 'bio' From cdbe59adaa4f98ae1a26b89c56b2653306688526 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 10:38:59 +0100 Subject: [PATCH 5929/9987] adding easyconfigs: CDO-2.1.1-gompi-2021a.eb, NCO-5.1.3-foss-2021a.eb --- .../c/CDO/CDO-2.1.1-gompi-2021a.eb | 53 +++++++++++++++++++ .../easyconfigs/n/NCO/NCO-5.1.3-foss-2021a.eb | 44 +++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.eb new file mode 100644 index 00000000000..33b3ae569e7 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.eb @@ -0,0 +1,53 @@ +# updated to version 2.0.6, based on the previous 2.0.5 version +# J. Sassmannshausen (Imperial College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) +# Maxim Masterov (SURF, NL) + +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.1.1' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'cstd': 'c++17', 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/27654'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c29d084ccbda931d71198409fb2d14f99930db6e7a3654b3c0243ceb304755d9'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('cURL', '7.76.0'), + ('ecCodes', '2.22.1'), + ('FFTW', '3.3.9'), + ('HDF5', '1.10.7'), + ('libxml2', '2.9.10'), + ('netCDF', '4.8.0'), + ('PROJ', '8.0.1'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.36'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : %(version)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2021a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2021a.eb new file mode 100644 index 00000000000..2636620beaf --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2021a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.1.3' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f6766627dab3f067c88f2cd713e3058c324ea4f900fabf9755bdd8918c32de7b'] + +builddependencies = [ + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.2.9'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.7'), + ('GSL', '2.7'), + ('netCDF', '4.8.0'), + ('ESMF', '8.1.1'), # ncremap needs ESMF_RegridWeightGen +] + +configopts = "--enable-nco_cplusplus" + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] + +moduleclass = 'tools' From c124d09527017d24a12f761548ab352c147f2a30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 11:20:00 +0100 Subject: [PATCH 5930/9987] adding easyconfigs: SeuratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb --- ...euratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeuratDisk/SeuratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/s/SeuratDisk/SeuratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/SeuratDisk/SeuratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..4728174df2a --- /dev/null +++ b/easybuild/easyconfigs/s/SeuratDisk/SeuratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'SeuratDisk' +local_commit = '9b89970' +version = '0.0.0.9020' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/mojaveazure/seurat-disk' +description = "Interfaces for HDF5-based Single Cell File Formats" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/mojaveazure/seurat-disk/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['323daf9db620fac1bbc2724e00cf89c9e496207111988bb03a592c8c2cb8dd06'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 4d1450592523ab5817cef3256899f0619828b7c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 11:51:16 +0100 Subject: [PATCH 5931/9987] add zellkonverter to R-bundle-Bioconductor v3.15 w/ foss/2022a --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index b73795d4c56..70987c77acf 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1116,6 +1116,18 @@ exts_list = [ ('HiCBricks', '1.14.0', { 'checksums': ['ac998260ffa66ec93a4c34e56cbaf392f76a848ae35b9ea987f0ec15f0adc47d'], }), + ('dir.expiry', '1.4.0', { + 'checksums': ['588f190e57f3e4a9196c48369e0f879436f1d124548b991203c75f0a51fd1c25'], + }), + ('basilisk.utils', '1.8.0', { + 'checksums': ['1356bb897401316fd0c8df916a9512ae8cb18739b447d2f211784a4a33d8d8ca'], + }), + ('basilisk', '1.8.1', { + 'checksums': ['f34a74870c59e84c3594eb2cab09a4a58ed6e994523cdb063a87161c458f9d8c'], + }), + ('zellkonverter', '1.6.5', { + 'checksums': ['669a314d8ca5f62d29a5ab42d51647c4c2a23e9ae2542921933d48a9e394b767'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From caa1c8159bfcd939ca5dc0580cb464598537db23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 20 Dec 2022 16:09:09 +0100 Subject: [PATCH 5932/9987] pkg-config replaced by pkgconf --- .../o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb index 049ea1ecc5c..1b3f0538c07 100644 --- a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb @@ -26,7 +26,7 @@ checksums = ['aea196550f02974d6d09291c5d83b51ca6a03b3767e234a8c0e21322927d1e12'] builddependencies = [ ('CMake', '3.23.1'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ] dependencies = [ From 9901b1a1a2adc06619f0f2f7dc3d84dc60332493 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 20 Dec 2022 15:35:15 +0000 Subject: [PATCH 5933/9987] Demoted to GCCcore, other suggestions also added --- ...4.eb => simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb} | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/s/simint/{simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb => simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb} (88%) diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb similarity index 88% rename from easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb rename to easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb index ef742955701..6198188f68f 100644 --- a/easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb +++ b/easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb @@ -10,6 +10,8 @@ easyblock = 'CMakeMake' name = 'simint' version = '0.7' local_lmax = '5' +# supported: {scalar, sse, avx, avxfma, micavx512} +# scalar ONLY FOR USE WITH simint-scalar (and only useful for benchmarks), micavx512 experimental! local_vec = 'avx' # custom configuration, to be used as dependency for PSI4 @@ -21,7 +23,7 @@ method of calculating electron repulsion integrals. Speedup is gained by vectorizing the primitive loop of the OS algorithm, with additional vectorization and optimizations left to the compiler.""" -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://www.bennyp.org/research/simint/download/'] sources = ['%(name)s-v%(version)s.tar.bz2'] @@ -29,6 +31,7 @@ checksums = ['9851fa2323924d4732dd611b366219f4408c8561556abb5e4fa6dbb64a8f919c'] builddependencies = [ ('CMake', '3.22.1'), + ('binutils', '2.37'), ] local_common_configopts = '-DSIMINT_MAXAM=%s ' % local_lmax From 117b5cc28dadd4b5dea0fe369b4812c40c66e7cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 20 Dec 2022 16:37:31 +0100 Subject: [PATCH 5934/9987] adding easyconfigs: Ruby-3.0.3-GCCcore-11.3.0.eb --- .../r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb | 163 ++++++++++++++++++ 1 file changed, 163 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..864a9112c6a --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb @@ -0,0 +1,163 @@ +name = 'Ruby' +version = '3.0.3' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3586861cb2df56970287f0fd83f274bd92058872d830d15570b36def7f1a92ac'] + +builddependencies = [('binutils', '2.38')] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# !! order of packages is important !! +# some packages have dependencies with minimum and maximum version requirements +# each version is picked as high as possible to fullfill all requirements +# packages updated on 2022-12-20 +exts_list = [ + ('ffi', '1.15.5', { + 'checksums': ['6f2ed2fa68047962d6072b964420cba91d82ce6fa8ee251950c17fca6af3c2a0'], + }), + ('childprocess', '4.1.0', { + 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], + }), + ('json', '2.6.3', { + 'checksums': ['86aaea16adf346a2b22743d88f8dcceeb1038843989ab93cda44b5176c845459'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.23.0', { + 'checksums': ['88fc26a40083a51015faa2ba02cbdc3605cb59f183cf0868f4fb3ac02900148f'], + }), + ('arr-pm', '0.0.12', { + 'checksums': ['fdff482f75239239201f4d667d93424412639aad0b3b0ad4d827e7c637e0ad39'], + }), + ('clamp', '1.3.2', { + 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], + }), + ('multipart-post', '2.2.3', { + 'checksums': ['462979de2971b8df33c2ee797fd497731617241f9dcd93960cc3caccb2dd13d8'], + }), + ('ruby2_keywords', '0.0.5', { + 'checksums': ['ffd13740c573b7301cf7a2e61fc857b2a8e3d3aff32545d6f8300d8bae10e3ef'], + }), + ('faraday-net_http', '3.0.2', { + 'checksums': ['6882929abed8094e1ee30344a3369e856fe34530044630d1f652bf70ebd87e8d'], + }), + ('faraday', '1.2.0', { + 'checksums': ['bd5c138304ee53907f8d0747724660c3a1cdf77d530d1cecd70d141299194b99'], + }), + ('faraday_middleware', '1.2.0', { + 'checksums': ['ded15d574d50e92bd04448d5566913af5cb1a01b2fa311ceecc2464fa0ab88af'], + }), + ('highline', '2.0.3', { + 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.3.0', { + 'checksums': ['677985be912f33c90f98f229aaa0c0ddb2ef8776f21929a36eeeb25251c944da'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.15.0', { + 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], + }), + ('public_suffix', '5.0.1', { + 'checksums': ['65603917ff4ecb32f499f42c14951aeed2380054fa7fc51758fc0a8d455fe043'], + }), + ('addressable', '2.8.1', { + 'checksums': ['bc724a176ef02118c8a3ed6b5c04c39cf59209607ffcce77b91d0261dbadedfa'], + }), + ('concurrent-ruby', '1.1.10', { + 'checksums': ['244cb1ca0d91ec2c15ca2209507c39fb163336994428e16fbd3f465c87bd8e68'], + }), + ('i18n', '1.12.0', { + 'checksums': ['91e3cc1b97616d308707eedee413d82ee021d751c918661fb82152793e64aced'], + }), + ('minitest', '5.16.3', { + 'checksums': ['60f81ad96ca5518e1457bd29eb826db60f86fbbdf8c05eac63b4824ef1f52614'], + }), + ('thread_safe', '0.3.6', { + 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], + }), + ('tzinfo', '1.1.0', { + 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], + }), + ('zeitwerk', '2.6.6', { + 'checksums': ['bb397b50c31127f8dab372fa9b21da1e7c453c5b57da172ed858136c6283f826'], + }), + ('activesupport', '5.2.8.1', { + 'checksums': ['f0498c616e1b243c7b56d67920c389f959c186ad7031569e80335b42e1d22564'], + }), + ('gh', '0.18.0', { + 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], + }), + ('launchy', '2.5.0', { + 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], + }), + ('ethon', '0.16.0', { + 'checksums': ['bba0da1cea8ac3e1f5cdd7cb1cb5fc78d7ac562c33736f18f0c3eb2b63053d9e'], + }), + ('typhoeus', '1.4.0', { + 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], + }), + ('websocket', '1.2.9', { + 'checksums': ['884b12dee993217795bb5f58acc89c0121c88bdc99df4d1636c0505dca352b36'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.5.0', { + 'checksums': ['49b934001c8c6aedb37ba19daec5c634da27b318a7a3c654ae979d6ba1929b67'], + }), + ('rspec-support', '3.12.0', { + 'checksums': ['dd4d44b247ff679b95b5607ac5641d197a5f9b1d33f916123cb98fc5f917c58b'], + }), + ('rspec-mocks', '3.12.1', { + 'checksums': ['e0dd725c7d1c1417c3a1715ccc4e41c124fab6c05b2de5a91ce22d74ee301801'], + }), + ('rspec-expectations', '3.12.1', { + 'checksums': ['808b29f7f3ef4535fc897c10235b662bb6b58219406fec56158623b3a8e06c9e'], + }), + ('rspec-core', '3.12.0', { + 'checksums': ['c466f4137966526e177d2156ca45c249eeecc7ed519b23ae2fb80c4675406bc5'], + }), + ('rspec', '3.12.0', { + 'checksums': ['ccc41799a43509dc0be84070e3f0410ac95cbd480ae7b6c245543eb64162399c'], + }), + ('rack', '2.2.4', { + 'checksums': ['ea2232b638cbd919129c8c8ad8012ecaccc09f848152a7e705d2139d0137ac2b'], + }), + ('rack-protection', '3.0.5', { + 'checksums': ['3a428f9de18ee2a4080e2fab308f20f9e98d74dcbe06ed407a8035b46ba822a8'], + }), + ('tilt', '2.0.11', { + 'checksums': ['7b180fc472cbdeb186c85d31c0f2d1e61a2c0d77e1d9fd0ca28482a9d972d6a0'], + }), + ('mustermann', '3.0.0', { + 'checksums': ['6d3569aa3c3b2f048c60626f48d9b2d561cc8d2ef269296943b03da181c08b67'], + }), + ('sinatra', '3.0.5', { + 'checksums': ['40ec7643a65d01b9c25ab5f7cafc5c67ca0b9ac523fa728345d88de69392cee7'], + }), + ('rack-test', '2.0.2', { + 'checksums': ['adadd0e957f63a34199a9fdf905a920a0b0a50795735095b4ac4bd3c13385466'], + }), + ('bundler', '2.3.26', { + 'checksums': ['1ee53cdf61e728ad82c6dbff06cfcd8551d5422e88e86203f0e2dbe9ae999e09'], + })] + +moduleclass = 'lang' From 18c1eeb2e1ba0a1059f0d7be621bcfa9b84771c9 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 20 Dec 2022 17:09:42 +0100 Subject: [PATCH 5935/9987] Use a specific commit not the head + Download simde only if non-x86_64 --- .../b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb | 32 +++++++++---------- .../b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb | 32 +++++++++---------- .../b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb | 32 +++++++++---------- 3 files changed, 48 insertions(+), 48 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb index 1a4e8413c88..9fa06c8160c 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb @@ -12,6 +12,8 @@ name = 'Bowtie2' version = '2.4.4' +_simde_version = '20220504' +_simde_commit = 'cbef1c1' homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads @@ -23,22 +25,20 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'GCC', 'version': '10.3.0'} toolchainopts = {'pic': True, 'cstd': 'gnu++98'} -source_urls = [ - ('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download'), - 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', -] -sources = [ - '%(namelower)s-%(version)s-source.zip', - # SIMD Everywhere implementations only, for non-x86_64 systems - {'download_filename': 'master.zip', - 'filename': 'simde-no-tests.master.zip', - 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', - }, -] -checksums = [ - 'b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc', # bowtie2-2.4.4-source.zip - 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip -] +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] + +# SIMD Everywhere implementations only, for non-x86_64 systems +if ARCH != 'x86_64': + source_urls += ['https://github.com/simd-everywhere/simde-no-tests/archive'] + sources += [ + {'download_filename': '%s.zip' % _simde_commit, + 'filename': 'simde-%s.zip' % _simde_version, + 'extract_cmd': 'unzip %%s && mv simde*-%s*/* %%(namelower)s-%%(version)s/third_party/simde/' % _simde_commit, + } + ] + checksums += ['d01f084ef5ff69b0a9b96370ae314fe1e55ef3339b25afcd3385958ac0e6ad68'] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb index f3b249e22f3..5fc68b03499 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb @@ -12,6 +12,8 @@ name = 'Bowtie2' version = '2.4.4' +_simde_version = '20220504' +_simde_commit = 'cbef1c1' homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads @@ -23,22 +25,20 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'GCC', 'version': '11.2.0'} toolchainopts = {'pic': True, 'cstd': 'gnu++98'} -source_urls = [ - ('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download'), - 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', -] -sources = [ - '%(namelower)s-%(version)s-source.zip', - # SIMD Everywhere implementations only, for non-x86_64 systems - {'download_filename': 'master.zip', - 'filename': 'simde-no-tests.master.zip', - 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', - }, -] -checksums = [ - 'b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc', # bowtie2-2.4.4-source.zip - 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip -] +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] + +# SIMD Everywhere implementations only, for non-x86_64 systems +if ARCH != 'x86_64': + source_urls += ['https://github.com/simd-everywhere/simde-no-tests/archive'] + sources += [ + {'download_filename': '%s.zip' % _simde_commit, + 'filename': 'simde-%s.zip' % _simde_version, + 'extract_cmd': 'unzip %%s && mv simde*-%s*/* %%(namelower)s-%%(version)s/third_party/simde/' % _simde_commit, + } + ] + checksums += ['d01f084ef5ff69b0a9b96370ae314fe1e55ef3339b25afcd3385958ac0e6ad68'] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb index 28ade29cb7e..d7b304b4c3b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb @@ -12,6 +12,8 @@ name = 'Bowtie2' version = '2.4.5' +_simde_version = '20220504' +_simde_commit = 'cbef1c1' homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml' description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads @@ -23,22 +25,20 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'GCC', 'version': '11.3.0'} toolchainopts = {'pic': True, 'cstd': 'gnu++98'} -source_urls = [ - ('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download'), - 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', -] -sources = [ - '%(namelower)s-%(version)s-source.zip', - # SIMD Everywhere implementations only, for non-x86_64 systems - {'download_filename': 'master.zip', - 'filename': 'simde-no-tests.master.zip', - 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', - }, -] -checksums = [ - 'd3cbd5f323393b5649aea10325d7c4b77f02035a8b204e5ac18eba95236e076a', # bowtie2-2.4.5-source.zip - 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip -] +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['d3cbd5f323393b5649aea10325d7c4b77f02035a8b204e5ac18eba95236e076a'] + +# SIMD Everywhere implementations only, for non-x86_64 systems +if ARCH != 'x86_64': + source_urls += ['https://github.com/simd-everywhere/simde-no-tests/archive'] + sources += [ + {'download_filename': '%s.zip' % _simde_commit, + 'filename': 'simde-%s.zip' % _simde_version, + 'extract_cmd': 'unzip %%s && mv simde*-%s*/* %%(namelower)s-%%(version)s/third_party/simde/' % _simde_commit, + } + ] + checksums += ['d01f084ef5ff69b0a9b96370ae314fe1e55ef3339b25afcd3385958ac0e6ad68'] dependencies = [ ('zlib', '1.2.12'), From aed53123302aeea7f1d9b9943c43c9a889eccbf2 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Tue, 20 Dec 2022 17:17:33 +0100 Subject: [PATCH 5936/9987] adding easyconfigs: FreeImage-3.18.0-GCCcore-11.3.0.eb --- .../FreeImage-3.18.0-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..11730391a1b --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FreeImage' +version = '3.18.0' + +homepage = 'http://freeimage.sourceforge.net' +description = """FreeImage is an Open Source library project for developers who would like to support popular graphics +image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to +use, fast, multithreading safe.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'cstd': 'c++14'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s3180.zip'] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip + '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # %(name)s-%(version)s-fix-makefile.patch +] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('zlib', '1.2.12')] + +skipsteps = ['configure'] + +buildopts = ['', '-f Makefile.fip'] + +installopts = [ + "INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib", + "-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib", +] + +_incs = ['include/FreeImage%s.h' % x for x in ['', 'Plus']] +_libs = ['lib/libfreeimage%s.%s' % (x, y) for x in ['', 'plus'] for y in ['a', SHLIB_EXT]] + +sanity_check_paths = { + 'files': _incs + _libs, + 'dirs': [], +} + +moduleclass = 'vis' From 8d6a15ec2c63f6ae029d803afbb7eb9f0c8248da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 18:20:13 +0100 Subject: [PATCH 5937/9987] enable dataset support for recent versions of Arrow --- easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb | 5 +++-- easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb | 5 +++-- easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb | 5 +++-- easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb | 5 +++-- easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb | 5 +++-- 5 files changed, 15 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb index da7afc30a3a..638d160140b 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb @@ -39,7 +39,7 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " @@ -48,7 +48,7 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -61,6 +61,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb index aca66d53dc2..8e67baea105 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb @@ -39,7 +39,7 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " @@ -49,7 +49,7 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -62,6 +62,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb index ae4130379ec..6b7ebcc3c0f 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb @@ -39,7 +39,7 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " @@ -48,7 +48,7 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -61,6 +61,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb index 6f01b9c72ba..9c2d0b80319 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb @@ -39,7 +39,7 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " configopts += "-DZSTD_ROOT=$EBROOTZSTD " @@ -50,7 +50,7 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -63,6 +63,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb index 84ee66a73e2..19aac4c1a50 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb @@ -39,7 +39,7 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " configopts += "-DZSTD_ROOT=$EBROOTZSTD " @@ -50,7 +50,7 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -63,6 +63,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] From 05c3f96528256ae9e836f9c7f7c30490eb58b3bd Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Tue, 20 Dec 2022 18:49:55 +0100 Subject: [PATCH 5938/9987] adding easyconfigs: dbus-glib-0.112-GCCcore-11.3.0.eb --- .../dbus-glib-0.112-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..68fd32c517b --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.112' + +homepage = 'https://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] +checksums = ['7d550dccdfcd286e33895501829ed971eeb65c614e73aadb4a08aeef719b143a'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Python', '3.10.4', '-bare'), # Python is needed for building against GLib. +] + +dependencies = [ + ('GLib', '2.72.1'), + ('DBus', '1.14.0'), + ('expat', '2.4.8'), +] + +sanity_check_commands = [ + 'dbus-binding-tool --version', + 'dbus-binding-tool --help', +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' From 45e309b56269ea2aef90d6a3d6768ae8f921136d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 21:29:11 +0100 Subject: [PATCH 5939/9987] {toolchain} foss/2022b --- .../f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022b.eb | 19 ++++++++ easybuild/easyconfigs/f/foss/foss-2022b.eb | 28 ++++++++++++ easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb | 20 +++++++++ easybuild/easyconfigs/g/gompi/gompi-2022b.eb | 20 +++++++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2022b.eb | 21 +++++++++ .../OSU-Micro-Benchmarks-6.2-gompi-2022b.eb | 26 +++++++++++ .../ScaLAPACK-2.2.0-gompi-2022b-fb.eb | 43 +++++++++++++++++++ 7 files changed, 177 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2022b.eb create mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2022b.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022b.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022b.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022b.eb new file mode 100644 index 00000000000..a8c00b01432 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022b.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2022b.eb b/easybuild/easyconfigs/f/foss/foss-2022b.eb new file mode 100644 index 00000000000..c1a658b5020 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2022b.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2022b' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.2.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb new file mode 100644 index 00000000000..1ed2f9c0bad --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2022b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.2.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2022b.eb b/easybuild/easyconfigs/g/gompi/gompi-2022b.eb new file mode 100644 index 00000000000..f49f5d2e300 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2022b.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2022b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022b.eb new file mode 100644 index 00000000000..286030ee656 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022b.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b.eb new file mode 100644 index 00000000000..b98375baf03 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '6.2' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb9dbc87dcf8ec6785977a61f6fceee8febf1a682488eaab4c58cf50e4fa985f'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb new file mode 100644 index 00000000000..fc9fc30a11c --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb @@ -0,0 +1,43 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.2.1'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From 05d20400270b1e177bd170a48a58641d1ef3dd09 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 21:31:54 +0100 Subject: [PATCH 5940/9987] {toolchain} intel/2022b --- .../easyconfigs/h/HPL/HPL-2.3-intel-2022b.eb | 21 ++++++++++++++++++ easybuild/easyconfigs/i/iimkl/iimkl-2022b.eb | 18 +++++++++++++++ easybuild/easyconfigs/i/iimpi/iimpi-2022b.eb | 18 +++++++++++++++ .../imkl-FFTW-2022.2.1-iimpi-2022b.eb | 11 ++++++++++ easybuild/easyconfigs/i/intel/intel-2022b.eb | 22 +++++++++++++++++++ 5 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022b.eb create mode 100644 easybuild/easyconfigs/i/iimkl/iimkl-2022b.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022b.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022b.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2022b.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022b.eb new file mode 100644 index 00000000000..8b309fa2a4b --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022b.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimkl/iimkl-2022b.eb b/easybuild/easyconfigs/i/iimkl/iimkl-2022b.eb new file mode 100644 index 00000000000..634c1d81092 --- /dev/null +++ b/easybuild/easyconfigs/i/iimkl/iimkl-2022b.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimkl' +version = '2022b' + +homepage = 'https://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel Math Kernel Library (MKL).""" + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('imkl', local_comp_ver, '', SYSTEM), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022b.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022b.eb new file mode 100644 index 00000000000..91d6d4d7055 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022b.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022b' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.1', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022b.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022b.eb new file mode 100644 index 00000000000..91a574e686f --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022b.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022b'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/intel/intel-2022b.eb b/easybuild/easyconfigs/i/intel/intel-2022b.eb new file mode 100644 index 00000000000..a2553d65c7e --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022b.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022b' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.1', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From 6dca59be89cfd54ead8c6a50020ebdad2204b703 Mon Sep 17 00:00:00 2001 From: eb Date: Tue, 20 Dec 2022 23:04:35 +0000 Subject: [PATCH 5941/9987] adding easyconfigs: XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb, XGBoost-1.7.2-foss-2022a.eb --- .../XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb | 33 +++++++++++++++++++ .../x/XGBoost/XGBoost-1.7.2-foss-2022a.eb | 29 ++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..7f522d92218 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '1.7.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f1a749aedb9330afc48007cc78b8bbbbea35ce372f48a2735f9c71bbc7b8dcfb'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('CUDA', '11.7.0', '', SYSTEM), +] + +configopts = "-DUSE_CUDA=ON -DBUILD_WITH_CUDA_CUB=ON " + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# use the parallel parameter from EB instead of total procs in the system +preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a.eb new file mode 100644 index 00000000000..96f8e7efca1 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '1.7.2' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f1a749aedb9330afc48007cc78b8bbbbea35ce372f48a2735f9c71bbc7b8dcfb'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# use the parallel parameter from EB instead of total procs in the system +preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&" + +moduleclass = 'lib' From b57c6e46c20961da1650f6e05b214d2f6061f8ee Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 13:14:14 +1100 Subject: [PATCH 5942/9987] adding easyconfigs: ESMF-8.3.0-intel-2022a.eb, netCDF-C++4-4.3.1-iimpi-2022a.eb --- .../e/ESMF/ESMF-8.3.0-intel-2022a.eb | 37 +++++++++++++++++++ .../netCDF-C++4-4.3.1-iimpi-2022a.eb | 25 +++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-intel-2022a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-intel-2022a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-intel-2022a.eb new file mode 100644 index 00000000000..1d6572890e3 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-intel-2022a.eb @@ -0,0 +1,37 @@ +name = 'ESMF' +version = '8.3.0' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + '0ff43ede83d1ac6beabd3d5e2a646f7574174b28a48d1b9f2c318a054ba268fd', # v8.3.0.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('netCDF-C++4', '4.3.1'), + ('libarchive', '3.6.1'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2022a.eb new file mode 100644 index 00000000000..df12f9d9a90 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.9.0')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' From a12ad79be1b537f95e18967f4c6ab8a60217bfd6 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 13:16:35 +1100 Subject: [PATCH 5943/9987] adding easyconfigs: FMS-2022.02-gompi-2022a.eb, FMS-2022.02-iimpi-2022a.eb --- .../f/FMS/FMS-2022.02-gompi-2022a.eb | 35 +++++++++++++++++++ .../f/FMS/FMS-2022.02-iimpi-2022a.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/f/FMS/FMS-2022.02-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/f/FMS/FMS-2022.02-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/f/FMS/FMS-2022.02-gompi-2022a.eb b/easybuild/easyconfigs/f/FMS/FMS-2022.02-gompi-2022a.eb new file mode 100644 index 00000000000..bb40ce9b7d3 --- /dev/null +++ b/easybuild/easyconfigs/f/FMS/FMS-2022.02-gompi-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'FMS' +version = '2022.02' + +homepage = 'https://github.com/NOAA-GFDL/FMS' +description = """The Flexible Modeling System (FMS) is a software framework for + supporting the efficient development, construction, execution, and scientific + interpretation of atmospheric, oceanic, and climate system models.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/NOAA-GFDL/FMS/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ad4978302b219e11b883b2f52519e1ee455137ad947474abb316c8654f72c874'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('netCDF-Fortran', '4.6.0'), +] + +separate_build_dir = True + +configopts = "-D64BIT=ON -DOPENMP=ON -DFPIC=ON" + +sanity_check_paths = { + 'files': ['lib/libfms_%s.a' % (x) for x in ['r4', 'r8']], + 'dirs': ['include_r4', 'include_r8', 'lib/cmake'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/f/FMS/FMS-2022.02-iimpi-2022a.eb b/easybuild/easyconfigs/f/FMS/FMS-2022.02-iimpi-2022a.eb new file mode 100644 index 00000000000..a121a552ee3 --- /dev/null +++ b/easybuild/easyconfigs/f/FMS/FMS-2022.02-iimpi-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'FMS' +version = '2022.02' + +homepage = 'https://github.com/NOAA-GFDL/FMS' +description = """The Flexible Modeling System (FMS) is a software framework for + supporting the efficient development, construction, execution, and scientific + interpretation of atmospheric, oceanic, and climate system models.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/NOAA-GFDL/FMS/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ad4978302b219e11b883b2f52519e1ee455137ad947474abb316c8654f72c874'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('netCDF-Fortran', '4.6.0'), +] + +separate_build_dir = True + +configopts = "-D64BIT=ON -DOPENMP=ON -DFPIC=ON" + +sanity_check_paths = { + 'files': ['lib/libfms_%s.a' % (x) for x in ['r4', 'r8']], + 'dirs': ['include_r4', 'include_r8', 'lib/cmake'], +} + +moduleclass = 'geo' From b2f44f34f86e85c4f45ff5ad3893d90f6cceff56 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 15:22:12 +1100 Subject: [PATCH 5944/9987] adding easyconfigs: fdict-0.8.0-GCC-10.3.0.eb, fdict-0.8.0-GCC-11.2.0.eb, fdict-0.8.0-intel-compilers-2021.2.0.eb, fdict-0.8.0-intel-compilers-2021.4.0.eb --- .../f/fdict/fdict-0.8.0-GCC-10.3.0.eb | 30 +++++++++++++++++++ .../f/fdict/fdict-0.8.0-GCC-11.2.0.eb | 30 +++++++++++++++++++ .../fdict-0.8.0-intel-compilers-2021.2.0.eb | 30 +++++++++++++++++++ .../fdict-0.8.0-intel-compilers-2021.4.0.eb | 30 +++++++++++++++++++ 4 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.2.0.eb create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.3.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..8a89448a3c8 --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +buildopts = 'VENDOR="gnu" FFLAGS="$FFLAGS"' + +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'share'), +] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-11.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..3b5996e2d24 --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +buildopts = 'VENDOR="gnu" FFLAGS="$FFLAGS"' + +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'share'), +] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..487ef3592c6 --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +buildopts = 'VENDOR="intel" FFLAGS="$FFLAGS" FPP="$FC -E -P"' + +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'share'), +] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..24192355419 --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.4.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +buildopts = 'VENDOR="intel" FFLAGS="$FFLAGS" FPP="$FC -E -P"' + +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'share'), +] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['share'], +} + +moduleclass = 'data' From 4e285b74942734612ca2a8633515b4ee0b1e5d64 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 15:23:26 +1100 Subject: [PATCH 5945/9987] adding easyconfigs: flook-0.8.1-GCC-10.3.0.eb, flook-0.8.1-intel-compilers-2021.2.0.eb --- .../f/flook/flook-0.8.1-GCC-10.3.0.eb | 36 +++++++++++++++++++ .../flook-0.8.1-intel-compilers-2021.2.0.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.3.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..220d66b7494 --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """The fortran-Lua-hook library.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] + +dependencies = [('Lua', '5.4.3')] + +parallel = 1 + +local_comp_flags = 'VENDOR="gnu" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..99b8846126f --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """The fortran-Lua-hook library.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] + +dependencies = [('Lua', '5.4.3')] + +parallel = 1 + +local_comp_flags = 'VENDOR="intel" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' From 1c13d9eee6462c8163e3317496ac076c5d351a5c Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 15:27:02 +1100 Subject: [PATCH 5946/9987] adding easyconfigs: libfdf-0.2.2-GCC-10.3.0-serial.eb, libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb --- .../libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb | 23 +++++++++++++++++++ ...f-0.2.2-intel-compilers-2021.2.0-serial.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb new file mode 100644 index 00000000000..60424b615f6 --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' +versionsuffix = '-serial' +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb new file mode 100644 index 00000000000..f6a353357b6 --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' +versionsuffix = '-serial' +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' From 59c7e4baf3c40f9f7f5fc284fa67141b21b096d3 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 15:43:11 +1100 Subject: [PATCH 5947/9987] adding easyconfigs: flook-0.8.1-GCC-11.2.0.eb, flook-0.8.1-intel-compilers-2021.4.0.eb --- .../f/flook/flook-0.8.1-GCC-11.2.0.eb | 36 +++++++++++++++++++ .../flook-0.8.1-intel-compilers-2021.4.0.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..2adf960c7c5 --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """The fortran-Lua-hook library.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] + +dependencies = [('Lua', '5.4.3')] + +parallel = 1 + +local_comp_flags = 'VENDOR="gnu" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..bf8b3b0072e --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.4.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """The fortran-Lua-hook library.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] + +dependencies = [('Lua', '5.4.3')] + +parallel = 1 + +local_comp_flags = 'VENDOR="intel" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' From d21125b8675acd05c6295a8829fcd839105fb63e Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 15:50:11 +1100 Subject: [PATCH 5948/9987] adding easyconfigs: libfdf-0.2.2-GCC-11.2.0-serial.eb, libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb --- .../libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb | 23 +++++++++++++++++++ ...f-0.2.2-intel-compilers-2021.4.0-serial.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb new file mode 100644 index 00000000000..16305fbd339 --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' +versionsuffix = '-serial' +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb new file mode 100644 index 00000000000..4277acce16f --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' +versionsuffix = '-serial' +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' From ecb0b3c12b3292a544cd27dbb80e991baf8e9233 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 21 Dec 2022 12:05:35 +0200 Subject: [PATCH 5949/9987] adding easyconfigs: Pillow-9.1.1-GCCcore-11.2.0.eb --- .../p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1d53e76e777 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '9.1.1' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7502539939b53d7565f3d11d87c78e7ec900d3c72945d4ee0e2f250d598309a0'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.11.0') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From 02ef0ee642d2628146ee9b89b9471ce4e63e389d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 21 Dec 2022 12:06:21 +0200 Subject: [PATCH 5950/9987] adding easyconfigs: matplotlib-3.5.2-foss-2021b.eb --- .../matplotlib/matplotlib-3.5.2-foss-2021b.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb new file mode 100644 index 00000000000..84f735fc30e --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb @@ -0,0 +1,74 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.5.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('libpng', '1.6.37'), + ('freetype', '2.11.0'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '9.1.1'), + ('Qhull', '2020.2') +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.34.0', { + 'modulename': 'fontTools', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], + }), + ('Cycler', '0.11.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], + }), + ('setuptools', '62.1.0', { + 'checksums': ['47c7b0c0f8fc10eec4cf1e71c6fdadf8decaa74ffa087e68cd1c20db7ad6a592'], + }), + ('cppy', '1.2.1', { + 'checksums': ['83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'], + }), + ('kiwisolver', '1.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ab8a15c2750ae8d53e31f77a94f846d0a00772240f1c12817411fa2344351f86'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['48cf850ce14fa18067f2d9e0d646763681948487a8080ec0af2686468b4607a2'], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' From 36e7f2f2ad21e2097d3440da7308685857156e1a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 21 Dec 2022 11:09:59 +0100 Subject: [PATCH 5951/9987] update buildep matplotlib / Pillow --- .../easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb index 48839d0ac0c..cc8ee4c2d2e 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb @@ -19,7 +19,7 @@ builddependencies = [ ('pytest-xdist', '2.5.0'), # git 2.x required to fetch repository 'io_bazel_rules_docker' ('git', '2.33.1', '-nodocs'), - ('matplotlib', '3.4.3'), # required by some jax tests + ('matplotlib', '3.5.2'), # required by some jax tests; also loads Pillow/9.1.1 ] dependencies = [ From 8c5174d13b4db41e02389e06fc71772b082096d2 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 11:10:11 +0100 Subject: [PATCH 5952/9987] adding easyconfigs: Ruby-3.0.5-GCCcore-11.3.0.eb --- .../r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb | 164 ++++++++++++++++++ 1 file changed, 164 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..114a5a62753 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb @@ -0,0 +1,164 @@ +name = 'Ruby' +version = '3.0.5' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3586861cb2df56970287f0fd83f274bd92058872d830d15570b36def7f1a92ac'] + +builddependencies = [('binutils', '2.38')] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# !! order of packages is important !! +# some packages have dependencies with minimum and maximum version requirements +# each version is picked as high as possible to fullfill all requirements +# packages updated on 2022-12-20 +exts_list = [ + ('ffi', '1.15.5', { + 'checksums': ['6f2ed2fa68047962d6072b964420cba91d82ce6fa8ee251950c17fca6af3c2a0'], + }), + ('childprocess', '4.1.0', { + 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], + }), + ('json', '2.6.3', { + 'checksums': ['86aaea16adf346a2b22743d88f8dcceeb1038843989ab93cda44b5176c845459'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.23.0', { + 'checksums': ['88fc26a40083a51015faa2ba02cbdc3605cb59f183cf0868f4fb3ac02900148f'], + }), + ('arr-pm', '0.0.12', { + 'checksums': ['fdff482f75239239201f4d667d93424412639aad0b3b0ad4d827e7c637e0ad39'], + }), + ('clamp', '1.3.2', { + 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], + }), + ('multipart-post', '2.2.3', { + 'checksums': ['462979de2971b8df33c2ee797fd497731617241f9dcd93960cc3caccb2dd13d8'], + }), + ('ruby2_keywords', '0.0.5', { + 'checksums': ['ffd13740c573b7301cf7a2e61fc857b2a8e3d3aff32545d6f8300d8bae10e3ef'], + }), + ('faraday-net_http', '3.0.2', { + 'checksums': ['6882929abed8094e1ee30344a3369e856fe34530044630d1f652bf70ebd87e8d'], + }), + ('faraday', '1.2.0', { + 'checksums': ['bd5c138304ee53907f8d0747724660c3a1cdf77d530d1cecd70d141299194b99'], + }), + ('faraday_middleware', '1.2.0', { + 'checksums': ['ded15d574d50e92bd04448d5566913af5cb1a01b2fa311ceecc2464fa0ab88af'], + }), + ('highline', '2.0.3', { + 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.3.0', { + 'checksums': ['677985be912f33c90f98f229aaa0c0ddb2ef8776f21929a36eeeb25251c944da'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.15.0', { + 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], + }), + ('public_suffix', '5.0.1', { + 'checksums': ['65603917ff4ecb32f499f42c14951aeed2380054fa7fc51758fc0a8d455fe043'], + }), + ('addressable', '2.8.1', { + 'checksums': ['bc724a176ef02118c8a3ed6b5c04c39cf59209607ffcce77b91d0261dbadedfa'], + }), + ('concurrent-ruby', '1.1.10', { + 'checksums': ['244cb1ca0d91ec2c15ca2209507c39fb163336994428e16fbd3f465c87bd8e68'], + }), + ('i18n', '1.12.0', { + 'checksums': ['91e3cc1b97616d308707eedee413d82ee021d751c918661fb82152793e64aced'], + }), + ('minitest', '5.16.3', { + 'checksums': ['60f81ad96ca5518e1457bd29eb826db60f86fbbdf8c05eac63b4824ef1f52614'], + }), + ('thread_safe', '0.3.6', { + 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], + }), + ('tzinfo', '1.1.0', { + 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], + }), + ('zeitwerk', '2.6.6', { + 'checksums': ['bb397b50c31127f8dab372fa9b21da1e7c453c5b57da172ed858136c6283f826'], + }), + ('activesupport', '5.2.8.1', { + 'checksums': ['f0498c616e1b243c7b56d67920c389f959c186ad7031569e80335b42e1d22564'], + }), + ('gh', '0.18.0', { + 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], + }), + ('launchy', '2.5.0', { + 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], + }), + ('ethon', '0.16.0', { + 'checksums': ['bba0da1cea8ac3e1f5cdd7cb1cb5fc78d7ac562c33736f18f0c3eb2b63053d9e'], + }), + ('typhoeus', '1.4.0', { + 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], + }), + ('websocket', '1.2.9', { + 'checksums': ['884b12dee993217795bb5f58acc89c0121c88bdc99df4d1636c0505dca352b36'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.5.0', { + 'checksums': ['49b934001c8c6aedb37ba19daec5c634da27b318a7a3c654ae979d6ba1929b67'], + }), + ('rspec-support', '3.12.0', { + 'checksums': ['dd4d44b247ff679b95b5607ac5641d197a5f9b1d33f916123cb98fc5f917c58b'], + }), + ('rspec-mocks', '3.12.1', { + 'checksums': ['e0dd725c7d1c1417c3a1715ccc4e41c124fab6c05b2de5a91ce22d74ee301801'], + }), + ('rspec-expectations', '3.12.1', { + 'checksums': ['808b29f7f3ef4535fc897c10235b662bb6b58219406fec56158623b3a8e06c9e'], + }), + ('rspec-core', '3.12.0', { + 'checksums': ['c466f4137966526e177d2156ca45c249eeecc7ed519b23ae2fb80c4675406bc5'], + }), + ('rspec', '3.12.0', { + 'checksums': ['ccc41799a43509dc0be84070e3f0410ac95cbd480ae7b6c245543eb64162399c'], + }), + ('rack', '2.2.4', { + 'checksums': ['ea2232b638cbd919129c8c8ad8012ecaccc09f848152a7e705d2139d0137ac2b'], + }), + ('rack-protection', '3.0.5', { + 'checksums': ['3a428f9de18ee2a4080e2fab308f20f9e98d74dcbe06ed407a8035b46ba822a8'], + }), + ('tilt', '2.0.11', { + 'checksums': ['7b180fc472cbdeb186c85d31c0f2d1e61a2c0d77e1d9fd0ca28482a9d972d6a0'], + }), + ('mustermann', '3.0.0', { + 'checksums': ['6d3569aa3c3b2f048c60626f48d9b2d561cc8d2ef269296943b03da181c08b67'], + }), + ('sinatra', '3.0.5', { + 'checksums': ['40ec7643a65d01b9c25ab5f7cafc5c67ca0b9ac523fa728345d88de69392cee7'], + }), + ('rack-test', '2.0.2', { + 'checksums': ['adadd0e957f63a34199a9fdf905a920a0b0a50795735095b4ac4bd3c13385466'], + }), + ('bundler', '2.3.26', { + 'checksums': ['1ee53cdf61e728ad82c6dbff06cfcd8551d5422e88e86203f0e2dbe9ae999e09'], + })] + +moduleclass = 'lang' + From e75c79b2ecedab9d0250872737fbcc45b89166a2 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 21 Dec 2022 11:30:42 +0100 Subject: [PATCH 5953/9987] Update Ruby-3.0.5-GCCcore-11.3.0.eb --- easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb index 114a5a62753..370bd16dda5 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb @@ -161,4 +161,3 @@ exts_list = [ })] moduleclass = 'lang' - From d110e6f9c378e9adcf45f53133291524c0692e5a Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 11:52:33 +0100 Subject: [PATCH 5954/9987] adding easyconfigs: CUnit-2.1-3-GCCcore-11.3.0.eb --- .../c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..cae0ab9fe40 --- /dev/null +++ b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'CUnit' +version = '2.1-3' + +homepage = 'https://sourceforge.net/projects/cunit/' +description = "Automated testing framework for C." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['f5b29137f845bb08b77ec60584fdb728b4e58f1023e6f249a464efa49a40f214'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -i && " + +sanity_check_paths = { + 'files': ['lib/libcunit.a', 'lib/libcunit.%s' % SHLIB_EXT], + 'dirs': ['include/CUnit', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lang' From 6765f3b0cd865131b2e2b0c562ded9cf85dbdd47 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:12:15 +0100 Subject: [PATCH 5955/9987] adding easyconfigs: libev-4.33-GCC-11.3.0.eb --- .../l/libev/libev-4.33-GCC-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb new file mode 100644 index 00000000000..bbfa103b29b --- /dev/null +++ b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libev' +version = '4.33' + +homepage = 'http://software.schmorp.de/pkg/libev.html' +description = """A full-featured and high-performance (see benchmark) +event loop that is loosely modelled after libevent, but without its +limitations and bugs. It is used in GNU Virtual Private Ethernet, +rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many +other programs.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://dist.schmorp.de/libev/Attic'] +sources = ['%(name)s-%(version)s.tar.gz'] + +checksums = [ + '507eb7b8d1015fbec5b935f34ebed15bf346bed04a11ab82b8eee848c4205aea', # libev-4.33.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['lib/libev.%s' % SHLIB_EXT], + 'dirs': ['include/', 'share'], +} + +moduleclass = 'lib' From 3a78383983dab4629ed17457e2296781892f9ec2 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:18:46 +0100 Subject: [PATCH 5956/9987] adding easyconfigs: nghttp3-0.6.0-GCCcore-11.3.0.eb --- .../n/nghttp3/nghttp3-0.6.0-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5d41fd67199 --- /dev/null +++ b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'nghttp3' +version = '0.6.0' + +homepage = 'https://github.com/ngtcp2/nghttp3' +description = """ nghttp3 is an implementation of RFC 9114 HTTP/3 +mapping over QUIC and RFC 9204 QPACK in C. +It does not depend on any particular QUIC transport implementation.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'ngtcp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + '3cd5fa107541a2dd11b87a84f251a98fae4c7b67df9d78be7343e4adce540b7f', # v0.6.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('pkg-config', '0.29.2'), + ('CUnit', '2.1-3'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libnghttp3.a', 'lib/libnghttp3.%s' % SHLIB_EXT], + 'dirs': ['include/nghttp3'], +} + +moduleclass = 'lib' From a038ce36bcd7bd7cef0954f6820b5801dba325b1 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:25:19 +0100 Subject: [PATCH 5957/9987] adding easyconfigs: ngtcp2-0.7.0-GCC-11.3.0.eb --- .../n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..75ed02edf9f --- /dev/null +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'ngtcp2' +version = '0.7.0' + +homepage = 'https://github.com/ngtcp2/ngtcp2' +description = """ +'Call it TCP/2. One More Time.' + +ngtcp2 project is an effort to implement RFC9000 QUIC protocol.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'ngtcp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + 'b2015c58e6d249bb71c7f7726a1e5ec5ccc78be7d50d82938358fac14ec98ca9', # v0.6.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('CUnit', '2.1-3'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), + ('GnuTLS', '3.7.8'), + ('nghttp3', '0.6.0'), + ('libev', '4.33'), +] + +configopts = '-DENABLE_GNUTLS=True' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libngtcp2_static.a', 'lib/libngtcp2.%s' % SHLIB_EXT], + 'dirs': ['share/doc/ngtcp2'], +} + +moduleclass = 'lib' From 7bb26aa5a378c8049d3fa8190d600ac6fa53af0d Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:44:00 +0100 Subject: [PATCH 5958/9987] adding easyconfigs: nghttp2-1.48.0-GCC-11.3.0.eb --- .../n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..9076065af44 --- /dev/null +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'nghttp2' +version = '1.48.0' + +homepage = 'https://github.com/nghttp2/nghttp2' +description = """ +This is an implementation of the Hypertext Transfer Protocol version 2 in C. + +The framing layer of HTTP/2 is implemented as a reusable C library. +On top of that, we have implemented an HTTP/2 client, server and proxy. +We have also developed load test and benchmarking tools for HTTP/2. + +An HPACK encoder and decoder are available as a public API.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'nghttp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + '946a8fa490548b67fc6074553cb225279cc6404bae96cf74551f2ad4453be637', # v1.48.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), + ('CMake', '3.23.1'), + ('CUnit', '2.1-3'), + ('Boost', '1.79.0'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), + ('nghttp3', '0.6.0'), + ('Python', '3.10.4'), + ('libxml2', '2.9.13'), + ('Jansson', '2.14'), + ('jemalloc', '5.3.0'), + ('ngtcp2', '0.7.0'), + ('libevent', '2.1.12'), + ('libev', '4.33'), + ('c-ares', '1.18.1'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libnghttp2.%s' % SHLIB_EXT], + 'dirs': ['include/nghttp2', 'share'], +} + +moduleclass = 'lib' From 2677cc183eb7e3b765fd85bc79754603e4fb9307 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:48:41 +0100 Subject: [PATCH 5959/9987] adding easyconfigs: libidn2-2.3.2-GCCcore-11.3.0.eb --- .../l/libidn2/libidn2-2.3.2-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5a7cd13f5c6 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libidn2' +version = '2.3.2' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = """Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libidn/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['76940cd4e778e8093579a9d195b25fff5e936e9dc6242068528b437a76764f91'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/idn2', 'lib/libidn2.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["idn2 --help"] + +moduleclass = 'lib' From 53e6db443339a0dfff0b03aeb5ab2b8ac04d1b05 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:51:32 +0100 Subject: [PATCH 5960/9987] adding easyconfigs: libpsl-0.21.1-GCCcore-11.3.0.eb --- .../l/libpsl/libpsl-0.21.1-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..31149e9b2b3 --- /dev/null +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libpsl' +version = '0.21.1' + +homepage = 'https://rockdaboot.github.io/libpsl' +description = "C library for the Public Suffix List" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/rockdaboot/libpsl/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ac6ce1e1fbd4d0254c4ddb9d37f1fa99dec83619c1253328155206b896210d4c'] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4', '-bare'), +] + +dependencies = [ + ('libidn2', '2.3.2'), + ('libunistring', '1.0'), +] + +sanity_check_commands = [('psl --version')] + +sanity_check_paths = { + 'files': ['bin/psl', 'lib/libpsl.a'], + 'dirs': [] +} + +moduleclass = 'lib' From 9ee828973c40175bcec729fe30df5d1c9aae0cd1 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 13:33:48 +0100 Subject: [PATCH 5961/9987] missing dep --- .../c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..cae0ab9fe40 --- /dev/null +++ b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'CUnit' +version = '2.1-3' + +homepage = 'https://sourceforge.net/projects/cunit/' +description = "Automated testing framework for C." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['f5b29137f845bb08b77ec60584fdb728b4e58f1023e6f249a464efa49a40f214'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -i && " + +sanity_check_paths = { + 'files': ['lib/libcunit.a', 'lib/libcunit.%s' % SHLIB_EXT], + 'dirs': ['include/CUnit', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lang' From 240ce5b43c26e25ba7c6f008e104442988ccfffe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Wed, 21 Dec 2022 16:30:14 +0100 Subject: [PATCH 5962/9987] Added missing OpenSSL dependency --- easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb index 5d7107ed091..ffc3a669e07 100644 --- a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb @@ -22,6 +22,7 @@ builddependencies = [ ('CMake', '3.23.1'), ] dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), ('zlib', '1.2.12'), ('libjpeg-turbo', '2.1.3'), ('LibTIFF', '4.3.0'), From f4a09d081c250ea095d43c230280f28aa3c564d6 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 16:38:24 +0100 Subject: [PATCH 5963/9987] adding easyconfigs: glib-networking-2.72.1-GCCcore-11.3.0.eb --- .../glib-networking-2.72.1-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..cb7dd92d43c --- /dev/null +++ b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MesonNinja' + +name = 'glib-networking' +version = '2.72.1' + +homepage = 'https://gitlab.gnome.org/GNOME/glib-networking' +description = "Network extensions for GLib" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/glib-networking/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['675a654ae55d381490c5d76b84e088f684125415fbd2d46f74dfa5522c4a1268'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('GLib', '2.72.1'), + ('GnuTLS', '3.7.8'), + ('libidn2', '2.3.2'), + ('zstd', '1.5.2'), +] + +sanity_check_paths = { + 'files': ['lib/gio/modules/libgiognutls.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'GIO_EXTRA_MODULES': 'lib/gio/modules'} + +moduleclass = 'lib' From d8ea96641b33e343bb342ebdfdaaddad4a4c9c4c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 21 Dec 2022 17:02:43 +0100 Subject: [PATCH 5964/9987] Pillow as extension instead of dependency --- .../m/matplotlib/matplotlib-3.5.2-foss-2021b.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb index 84f735fc30e..701b39665ad 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb @@ -17,10 +17,12 @@ builddependencies = [ dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), + ('libjpeg-turbo', '2.0.6'), # for Pillow ext. ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), # for Pillow ext, ('freetype', '2.11.0'), ('Tkinter', '%(pyver)s'), - ('Pillow', '9.1.1'), + # ('Pillow', '9.1.1'), # as extension ('Qhull', '2020.2') ] @@ -55,6 +57,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['ab8a15c2750ae8d53e31f77a94f846d0a00772240f1c12817411fa2344351f86'], }), + ('Pillow', '9.1.1', { + 'modulename': 'PIL', + 'checksums': ['7502539939b53d7565f3d11d87c78e7ec900d3c72945d4ee0e2f250d598309a0'], + }), (name, version, { 'preinstallopts': _fix_setup + _include_path, 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], From 581ff30c525403b0591ba11da19d4f9129019a12 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 17:36:59 +0100 Subject: [PATCH 5965/9987] adding easyconfigs: LibSoup-3.0.8-GCC-11.3.0.eb --- .../l/LibSoup/LibSoup-3.0.8-GCC-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.8-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.8-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.8-GCC-11.3.0.eb new file mode 100644 index 00000000000..98036c143ff --- /dev/null +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.8-GCC-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MesonNinja' + +name = 'LibSoup' +version = '3.0.8' + +homepage = 'https://wiki.gnome.org/Projects/libsoup' +description = """libsoup is an HTTP client/server library for GNOME. It +uses GObjects and the glib main loop, to integrate well with GNOME +applications, and also has a synchronous API, for use in threaded +applications.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'cstd': 'gnu11'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c8739dc1c23c2b1e3b816d7598b3fa1764a3e1a2a2f5257b1bc4466d867caced'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.72.0'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('libxml2', '2.9.13'), + ('SQLite', '3.38.3'), + ('GLib', '2.72.1'), + ('libpsl', '0.21.1'), + ('cURL', '7.83.0'), + ('GnuTLS', '3.7.8'), + ('nghttp2', '1.48.0'), + ('glib-networking', '2.72.1'), + ('Brotli', '1.0.9'), +] + +sanity_check_paths = { + 'files': ['lib/libsoup-3.0.%s' % SHLIB_EXT], + 'dirs': ['include/libsoup-3.0/libsoup/', 'lib/pkgconfig'] +} + +moduleclass = 'lib' From b96a0d8a1012bc68d1a28d3283949be4fbb1b8fb Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 18:08:25 +0100 Subject: [PATCH 5966/9987] adding easyconfigs: libgpg-error-1.46-GCCcore-11.3.0.eb --- .../libgpg-error-1.46-GCCcore-11.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.46-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.46-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.46-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..eb147d5e586 --- /dev/null +++ b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.46-GCCcore-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libgpg-error' +version = '1.46' + +homepage = 'https://gnupg.org/related_software/libgpg-error/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['b7e11a64246bbe5ef37748de43b245abd72cfcd53c9ae5e7fc5ca59f1c81268d'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/gpg-error', 'include/gpg-error.h', 'lib/libgpg-error.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From 4f77406b81a728a791e17257e3b15021fcf005f6 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 18:19:12 +0100 Subject: [PATCH 5967/9987] adding easyconfigs: libgcrypt-1.10.1-GCCcore-11.3.0.eb --- .../libgcrypt-1.10.1-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..36bfe330597 --- /dev/null +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libgcrypt' +version = '1.10.1' + +homepage = 'https://gnupg.org/related_software/libgcrypt/index.html' +description = """Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['ef14ae546b0084cd84259f61a55e07a38c3b53afc0f546bffcef2f01baffe9de'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('libgpg-error', '1.46')] + +sanity_check_paths = { + 'files': ['bin/libgcrypt-config', 'include/gcrypt.h', 'lib/libgcrypt.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From fee31cc72f17340ddb291fb470ba7933d25d24bd Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:38:24 +0000 Subject: [PATCH 5968/9987] adding easyconfigs: gh-2.20.2.eb --- easybuild/easyconfigs/g/gh/gh-2.20.2.eb | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/gh/gh-2.20.2.eb diff --git a/easybuild/easyconfigs/g/gh/gh-2.20.2.eb b/easybuild/easyconfigs/g/gh/gh-2.20.2.eb new file mode 100644 index 00000000000..3d63f978426 --- /dev/null +++ b/easybuild/easyconfigs/g/gh/gh-2.20.2.eb @@ -0,0 +1,21 @@ +easyblock = 'GoPackage' + +name = 'gh' +version = '2.20.2' + +homepage = 'https://github.com/cli/cli' +description = """gh is GitHub on the command line.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cli/cli/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['221380a32559984b64cdda81fabb60e5d4ed00db49ffe8390ddc149bef25c5a7'] + +builddependencies = [ + ('Go', '1.18.3'), +] + +installopts = './cmd/%(namelower)s' + +moduleclass = 'tools' From 774fef8fc74005d14b8f552d1cb743e15f5d2c36 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:39:37 +0000 Subject: [PATCH 5969/9987] adding easyconfigs: fastai-2.7.10-GCCcore-11.3.0.eb --- .../f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8b61681cacb --- /dev/null +++ b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'fastai' +version = '2.7.10' + +homepage = 'https://www.fast.ai/' +description = """The fastai deep learning library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ccef6a185ae3a637efc9bcd9fea8e48b75f454d0ebad3b6df426f22fae20039d'] + +download_dep_fail = True +use_pip = True + +builddependencies = [('binutils', '2.38')] +multi_deps = {'Python': ['3.10.4']} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'lib' From 77427773828db49e8db850982d7537980f7c27b1 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:45:21 +0000 Subject: [PATCH 5970/9987] Updating download links to 'official home on GitHub' according to pcre.org --- easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb | 3 ++- easybuild/easyconfigs/p/PCRE2/PCRE2-10.31-foss-2018b.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.36-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb | 2 +- 8 files changed, 9 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb index 12016d01cbe..987673424a7 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb @@ -12,8 +12,9 @@ description = """ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['1cfd43caffe07fe7f2cfafc74c8f0d87b38d80bbb63226a1193407476508e317'] configopts = "--with-pic --disable-cpp --enable-jit" diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.31-foss-2018b.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.31-foss-2018b.eb index 5c1b1a2eee6..6e778809b3c 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.31-foss-2018b.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.31-foss-2018b.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'pic': True} -source_urls = ['http://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['e11ebd99dd23a7bccc9127d95d9978101b5f3cf0a6e7d25a1b1ca165a97166c4'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.2.0.eb index 01e3fb5bfdb..450024fdf67 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.2.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['e2e2899a97489fc6ad1b0cc3da7952c7cca991b4a0f7db6649b75d9721025d31'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.3.0.eb index 389549a78a0..8cc0b7a6524 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.3.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['e2e2899a97489fc6ad1b0cc3da7952c7cca991b4a0f7db6649b75d9721025d31'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb index 964495dcb0e..f5d596ea476 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['da6aba7ba2509e918e41f4f744a59fa41a2425c59a298a232e7fe85691e00379'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb index af6d2eaca84..b44919660c6 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['8fdcef8c8f4cd735169dd0225fd010487970c1bcadd49e9b90e26c7250a33dc9'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.36-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.36-GCCcore-10.3.0.eb index 5f9348bc96c..6f63b8cf298 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.36-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.36-GCCcore-10.3.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['b95ddb9414f91a967a887d69617059fb672b914f56fa3d613812c1ee8e8a1a37'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb index 257c390e0b9..e82daf409ad 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['04e214c0c40a97b8a5c2b4ae88a3aa8a93e6f2e45c6b3534ddac351f26548577'] From 3d5bd6293e0d51d7ba4590d710d043560b361f19 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:48:42 +0000 Subject: [PATCH 5971/9987] adding easyconfigs: polars-0.15.6-foss-2022a.eb, Rust-1.65.0-GCCcore-11.3.0.eb --- .../p/polars/polars-0.15.6-foss-2022a.eb | 58 +++++++++++++++++++ .../r/Rust/Rust-1.65.0-GCCcore-11.3.0.eb | 58 +++++++++++++++++++ 2 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/p/polars/polars-0.15.6-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/polars/polars-0.15.6-foss-2022a.eb b/easybuild/easyconfigs/p/polars/polars-0.15.6-foss-2022a.eb new file mode 100644 index 00000000000..12b58c2b352 --- /dev/null +++ b/easybuild/easyconfigs/p/polars/polars-0.15.6-foss-2022a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'polars' +version = '0.15.6' + +homepage = 'https://pola.rs/' +description = """Lightning-fast DataFrame library for Rust and Python.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + # required for setuptools-rust, which is needed for maturin + # (and is needed in a more recent version than supplied with Python 3.10.4) + ('Rust', '1.65.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Arrow', '8.0.0'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('setuptools', '65.6.3', { + 'checksums': ['a7620757bf984b58deaf32fc8a4577a9bbc0850cf92c20e1ce41c38c19e5fb75'], + }), + ('setuptools-rust', '1.5.2', { + 'checksums': ['d8daccb14dc0eae1b6b6eb3ecef79675bd37b4065369f79c35393dd5c55652c7'], + }), + ('maturin', '0.14.6', { + 'checksums': ['021e0b557e907027a6c7f10968635fd4c15522eee0688fed031b1ac6240ecac4'], + }), + ('connectorx', '0.3.1', { + 'source_tmpl': 'connectorx-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'checksums': ['71d2c2678339fb01f89469bbe22e66e75cabcf727a52ed72d576fef5744ebc58'], + }), + ('xlsx2csv', '0.8.0', { + 'checksums': ['2c268e509b7766ca4a24f2f36302e918705c5ead2fcde3f4bd5f1ca6152f7e2c'], + }), + ('deltalake', '0.6.4', { + 'checksums': ['2f3cf70d67c17a7d5928c7da214ff795283f628311d91643602176dc50f7099e'], + }), + (name, version, { + 'checksums': ['f6d27e88b46ddd88036869f066c12dd6877192d936430b43001e092529766cee'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..245fa49d668 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-11.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.65.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.60_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.65.0-src.tar.gz': '5828bb67f677eabf8c384020582b0ce7af884e1c84389484f7f8d00dd82c0038'}, + {'Rust-1.60_sysroot-fix-interpreter.patch': 'b59ed4c2591fc9098277299be21dd6752654f6f193d8652b7d21cb0fa0dd8716'}, +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Python', '3.10.4', '-bare'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' From 2d2879ecebcf6bbe4b34f4489402b522a42111cb Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:52:55 +0000 Subject: [PATCH 5972/9987] Add `pkg-config` dependency for `icu` and adapt old argument-list-too-long.patch (long pathnames may break building `nodejs`) --- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 10 +- ...s-16.15.1_fix-argument-list-too-long.patch | 107 ++++++++++++++++++ 2 files changed, 116 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-16.15.1_fix-argument-list-too-long.patch diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index 117331f1af8..abcac90c84c 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -14,10 +14,18 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://nodejs.org/dist/v%(version)s/'] sources = ['node-v%(version)s.tar.gz'] -checksums = ['308aee7149c4092a53c87c28ef49e23a8d1606119e79ae68333062e2a1f94208'] +patches = [ + '%(name)s-%(version)s_fix-argument-list-too-long.patch', +] +checksums = [ + {'node-v16.15.1.tar.gz': '308aee7149c4092a53c87c28ef49e23a8d1606119e79ae68333062e2a1f94208'}, + {'nodejs-16.15.1_fix-argument-list-too-long.patch': + '36b5627e60fd2b861ce3dc5445b137b4fe7ec30a4f866ea540ec56bda9686405'}, +] builddependencies = [ ('binutils', '2.38'), + ('pkg-config', '0.29.2'), ('Python', '3.10.4', '-bare'), ] diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1_fix-argument-list-too-long.patch b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1_fix-argument-list-too-long.patch new file mode 100644 index 00000000000..4a69b371a76 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1_fix-argument-list-too-long.patch @@ -0,0 +1,107 @@ +# +# nodejs-14.17.0_fix-argument-list-too-long.patch adjusted for v16 +# +# Source: https://github.com/nodejs/node/issues/9137 +# +diff --git a/tools/gyp/pylib/gyp/generator/make.py b/tools/gyp/pylib/gyp/generator/make.py +index d163ae31..2ce1c301 100644 +--- a/tools/gyp/pylib/gyp/generator/make.py ++++ b/tools/gyp/pylib/gyp/generator/make.py +@@ -155,6 +155,31 @@ cmd_alink_thin = rm -f $@ && $(AR.$(TOOLSET)) crsT $@ $(filter %.o,$^) + quiet_cmd_link = LINK($(TOOLSET)) $@ + cmd_link = $(LINK.$(TOOLSET)) -o $@ $(GYP_LDFLAGS) $(LDFLAGS.$(TOOLSET)) -Wl,--start-group $(LD_INPUTS) $(LIBS) -Wl,--end-group + ++# Note: this does not handle spaces in paths ++define xargs ++ $(1) $(word 1,$(2)) ++$(if $(word 2,$(2)),$(call xargs,$(1),$(wordlist 2,$(words $(2)),$(2)))) ++endef ++ ++define write-to-file ++ @: >$(1) ++$(call xargs,@printf "%s\\n" >>$(1),$(2)) ++endef ++ ++OBJ_FILE_LIST := ar-file-list ++ ++define create_archive ++ rm -f $(1) $(1).$(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crs $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ ++define create_thin_archive ++ rm -f $(1) $(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crsT $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ + # We support two kinds of shared objects (.so): + # 1) shared_library, which is just bundling together many dependent libraries + # into a link line. +@@ -199,6 +224,31 @@ cmd_alink = rm -f $@ && $(AR.$(TOOLSET)) crs $@ $(filter %.o,$^) + quiet_cmd_alink_thin = AR($(TOOLSET)) $@ + cmd_alink_thin = rm -f $@ && $(AR.$(TOOLSET)) crsT $@ $(filter %.o,$^) + ++# Note: this does not handle spaces in paths ++define xargs ++ $(1) $(word 1,$(2)) ++$(if $(word 2,$(2)),$(call xargs,$(1),$(wordlist 2,$(words $(2)),$(2)))) ++endef ++ ++define write-to-file ++ @: >$(1) ++$(call xargs,@printf "%s\\n" >>$(1),$(2)) ++endef ++ ++OBJ_FILE_LIST := ar-file-list ++ ++define create_archive ++ rm -f $(1) $(1).$(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crs $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ ++define create_thin_archive ++ rm -f $(1) $(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crsT $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ + # Due to circular dependencies between libraries :(, we wrap the + # special "figure out circular dependencies" flags around the entire + # input list during linking. +@@ -1766,14 +1816,28 @@ $(obj).$(TOOLSET)/$(TARGET)/%%.o: $(obj)/%%%s FORCE_DO_CMD + self.flavor not in ("mac", "openbsd", "netbsd", "win") + and not self.is_standalone_static_library + ): +- self.WriteDoCmd( ++ if self.flavor in ('linux', 'android'): ++ self.WriteMakeRule( + [self.output_binary], + link_deps, +- "alink_thin", +- part_of_all, +- postbuilds=postbuilds, +- ) ++ actions = ['$(call create_thin_archive,$@,$^)'] ++ ) ++ else: ++ self.WriteDoCmd( ++ [self.output_binary], ++ link_deps, ++ "alink_thin", ++ part_of_all, ++ postbuilds=postbuilds, ++ ) + else: ++ if self.flavor in ('linux', 'android'): ++ self.WriteMakeRule( ++ [self.output_binary], ++ link_deps, ++ actions = ['$(call create_archive,$@,$^)'] ++ ) ++ else: + self.WriteDoCmd( + [self.output_binary], + link_deps, From 49092b2ff56d1a4ba7b4383d3cbb5735d6533ca3 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:56:45 +0000 Subject: [PATCH 5973/9987] Add `sanity_pip_check = True` --- easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb index 8b61681cacb..6885b7f44e8 100644 --- a/easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb @@ -22,4 +22,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], } +sanity_pip_check = True + moduleclass = 'lib' From a236f8fe9371e686895a4425af4d09e0f63e9493 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:59:29 +0000 Subject: [PATCH 5974/9987] adding easyconfigs: rising-0.2.2-foss-2022a-CUDA-11.7.0.eb, rising-0.2.2-foss-2022a.eb --- .../rising-0.2.2-foss-2022a-CUDA-11.7.0.eb | 43 +++++++++++++++++++ .../r/rising/rising-0.2.2-foss-2022a.eb | 42 ++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..a141be4df71 --- /dev/null +++ b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'rising' +version = '0.2.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://rising.rtfd.io/' +description = "Provides everything needed for high performance data loading and augmentation in PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +# rising archive on PyPi is incomplete as of 2022-02-05 +github_account = 'PhoenixDL' + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # provides numpy + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('threadpoolctl', '3.1.0', { + 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], + }), + (name, version, { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5294b3f9b183b4efe7e4bafb4b42caa19aa4db737e7379e8356cc575fce57662'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a.eb b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a.eb new file mode 100644 index 00000000000..828dbb0e31a --- /dev/null +++ b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'rising' +version = '0.2.2' + +homepage = 'https://rising.rtfd.io/' +description = "Provides everything needed for high performance data loading and augmentation in PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +# rising archive on PyPi is incomplete as of 2022-02-05 +github_account = 'PhoenixDL' + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # provides numpy + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('threadpoolctl', '3.1.0', { + 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], + }), + (name, version, { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5294b3f9b183b4efe7e4bafb4b42caa19aa4db737e7379e8356cc575fce57662'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'data' From 4ab9ba2e7a43f64af6c82f0a4deb929614aa9919 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 13 Jul 2022 20:11:00 +1000 Subject: [PATCH 5975/9987] Fix OpenBLAS 0.3.15 patch to correctly set the CPU core type for Tiger Lake. --- .../o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb | 2 +- .../OpenBLAS-0.3.15_icelake-detection.patch | 18 ++++++++++++++++++ 2 files changed, 19 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb index 6f209915e17..3b8d83f4116 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb @@ -23,7 +23,7 @@ checksums = [ '30a99dec977594b387a17f49904523e6bc8dd88bd247266e83485803759e4bbe', # v0.3.15.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', # OpenBLAS-0.3.15_icelake-detection.patch + 'aa96e1c3b1532dbafe4b6e8591688ef200e99304a902851f342cb9d467219762', # OpenBLAS-0.3.15_icelake-detection.patch 'ba7bd45af9fe0516f8c9b1cf047eec7b833996e481bc925d4fb2563865d3db38', # OpenBLAS-0.3.15_fix-aarch64.patch # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_icelake-detection.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_icelake-detection.patch index 618c165930b..14a317cea1b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_icelake-detection.patch +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15_icelake-detection.patch @@ -46,6 +46,24 @@ index 44704fcd9..18ff122e5 100644 break; case 7: if (model == 10) +@@ -2135,13 +2161,13 @@ + case 8: + if (model == 12) { // Tiger Lake + if(support_avx512()) +- return CPUTYPE_SKYLAKEX; ++ return CORE_SKYLAKEX; + if(support_avx2()) +- return CPUTYPE_HASWELL; ++ return CORE_HASWELL; + if(support_avx()) +- return CPUTYPE_SANDYBRIDGE; ++ return CORE_SANDYBRIDGE; + else +- return CPUTYPE_NEHALEM; ++ return CORE_NEHALEM; + } + if (model == 14) { // Kaby Lake + if(support_avx()) diff --git a/driver/others/dynamic.c b/driver/others/dynamic.c index 158e1b3da..46ad06a7c 100644 --- a/driver/others/dynamic.c From 8832c62093f49dda9692835851cc21973628c9ef Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 13 Jul 2022 20:33:16 +1000 Subject: [PATCH 5976/9987] Update checksum also in OpenBLAS-0.3.12-GCC-10.2.0.eb. --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index a0d4dffee1d..e9601f06ac2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -27,7 +27,8 @@ checksums = [ '4b3ab7260975ea2cfd7460731c0201b2c1e374cd83ae90d55b8da3e670633ba0', # OpenBLAS-0.3.12_add-missing-params-for-power.patch '4454af07290d1fe33e414023a41bb8999d6ee31887e194daa72bd23d46a0072a', - '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', # OpenBLAS-0.3.15_icelake-detection.patch + # OpenBLAS-0.3.15_icelake-detection.patch + 'aa96e1c3b1532dbafe4b6e8591688ef200e99304a902851f342cb9d467219762', ] # extensive testing can be enabled by uncommenting the line below From 07f56fe55621affec06a7b79e15b8a17401c0470 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Thu, 22 Dec 2022 14:05:58 +1100 Subject: [PATCH 5977/9987] Use the unmodified version of the patch for OpenBLAS-0.3.12-GCC-10.2.0.eb --- .../o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 6 +- .../OpenBLAS-0.3.12_icelake-detection.patch | 75 +++++++++++++++++++ 2 files changed, 78 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_icelake-detection.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index e9601f06ac2..c98d769985e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -17,7 +17,7 @@ patches = [ ('timing.tgz', '.'), '%(name)s-0.3.7_fix-possible-memory-leak-after-fork.patch', '%(name)s-%(version)s_add-missing-params-for-power.patch', - '%(name)s-0.3.15_icelake-detection.patch', + '%(name)s-0.3.12_icelake-detection.patch', ] checksums = [ '65a7d3a4010a4e3bd5c0baa41a234797cd3a1735449a4a5902129152601dc57b', # v0.3.12.tar.gz @@ -27,8 +27,8 @@ checksums = [ '4b3ab7260975ea2cfd7460731c0201b2c1e374cd83ae90d55b8da3e670633ba0', # OpenBLAS-0.3.12_add-missing-params-for-power.patch '4454af07290d1fe33e414023a41bb8999d6ee31887e194daa72bd23d46a0072a', - # OpenBLAS-0.3.15_icelake-detection.patch - 'aa96e1c3b1532dbafe4b6e8591688ef200e99304a902851f342cb9d467219762', + # OpenBLAS-0.3.12_icelake-detection.patch + '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_icelake-detection.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_icelake-detection.patch new file mode 100644 index 00000000000..618c165930b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12_icelake-detection.patch @@ -0,0 +1,75 @@ +Add autodetection for Intel Ice Lake SP +https://github.com/xianyi/OpenBLAS/pull/3233 +diff --git a/cpuid_x86.c b/cpuid_x86.c +index 44704fcd9..18ff122e5 100644 +--- a/cpuid_x86.c ++++ b/cpuid_x86.c +@@ -1398,6 +1398,17 @@ int get_cpuname(void){ + return CPUTYPE_SANDYBRIDGE; + else + return CPUTYPE_NEHALEM; ++ case 10: // Ice Lake SP ++ if(support_avx512_bf16()) ++ return CPUTYPE_COOPERLAKE; ++ if(support_avx512()) ++ return CPUTYPE_SKYLAKEX; ++ if(support_avx2()) ++ return CPUTYPE_HASWELL; ++ if(support_avx()) ++ return CPUTYPE_SANDYBRIDGE; ++ else ++ return CPUTYPE_NEHALEM; + } + break; + case 7: // family 6 exmodel 7 +@@ -2112,7 +2123,22 @@ int get_coretype(void){ + #endif + else + return CORE_NEHALEM; +-#endif ++#endif ++ if (model == 10) ++#ifndef NO_AVX512 ++ if(support_avx512_bf16()) ++ return CORE_COOPERLAKE; ++ return CORE_SKYLAKEX; ++#else ++ if(support_avx()) ++#ifndef NO_AVX2 ++ return CORE_HASWELL; ++#else ++ return CORE_SANDYBRIDGE; ++#endif ++ else ++ return CORE_NEHALEM; ++#endif + break; + case 7: + if (model == 10) +diff --git a/driver/others/dynamic.c b/driver/others/dynamic.c +index 158e1b3da..46ad06a7c 100644 +--- a/driver/others/dynamic.c ++++ b/driver/others/dynamic.c +@@ -621,6 +621,22 @@ static gotoblas_t *get_coretype(void){ + return &gotoblas_NEHALEM; + } + } ++ if (model == 10) { ++ // Ice Lake SP ++ if(support_avx512_bf16()) ++ return &gotoblas_COOPERLAKE; ++ if (support_avx512()) ++ return &gotoblas_SKYLAKEX; ++ if(support_avx2()) ++ return &gotoblas_HASWELL; ++ if(support_avx()) { ++ openblas_warning(FALLBACK_VERBOSE, SANDYBRIDGE_FALLBACK); ++ return &gotoblas_SANDYBRIDGE; ++ } else { ++ openblas_warning(FALLBACK_VERBOSE, NEHALEM_FALLBACK); ++ return &gotoblas_NEHALEM; ++ } ++ } + return NULL; + case 7: + if (model == 10) // Goldmont Plus From 68957c2e3f712866c6c15eae149fad1ae8879174 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Thu, 22 Dec 2022 08:45:46 +0000 Subject: [PATCH 5978/9987] `pkg-config` -> `pkgconf` --- easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index abcac90c84c..87bfe5f2d35 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ checksums = [ builddependencies = [ ('binutils', '2.38'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ('Python', '3.10.4', '-bare'), ] From bb719d64d8c530fc1cd91dc4ef6941308ca52e64 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 09:50:23 +0000 Subject: [PATCH 5979/9987] adding easyconfigs: TinyXML-2.6.2-GCCcore-11.2.0.eb, TinyXML-2.6.2-GCCcore-11.3.0.eb --- .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb | 48 +++++++++++++++++++ .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb | 48 +++++++++++++++++++ 2 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ca94bda02b9 --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MakeCp' + +name = 'TinyXML' +version = '2.6.2' + +homepage = 'https://sourceforge.net/projects/tinyxml' +description = """TinyXML is a simple, small, minimal, C++ XML parser that can be easily integrating + into other programs. It reads XML and creates C++ objects representing the XML document. The + objects can be manipulated, changed, and saved again as XML. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % version.replace('.', '_')] +checksums = ['15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'] + +builddependencies = [('binutils', '2.37')] + +buildopts = ' '.join([ + 'TINYXML_USE_STL=YES CXXFLAGS="$CXXFLAGS $CPPFLAGS" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', + # build a shared library + '&& $CXX -shared -Wl,-soname,lib%(namelower)s.so.%(version)s -o lib%(namelower)s.so.%(version)s $LDFLAGS *.o', +]) + +_incs = ['tinystr.h', 'tinyxml.h'] +_libs = ['lib%(namelower)s.so.%(version)s'] + +files_to_copy = [ + (_incs, 'include'), + (_libs, 'lib'), +] + +postinstallcmds = [ + "cd %(installdir)s/lib" + " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major)s" + " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major_minor)s" + " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so" +] + +sanity_check_paths = { + 'files': ['include/%s' % i for i in _incs] + ['lib/%s' % l for l in _libs], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..86a49712c2b --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MakeCp' + +name = 'TinyXML' +version = '2.6.2' + +homepage = 'https://sourceforge.net/projects/tinyxml' +description = """TinyXML is a simple, small, minimal, C++ XML parser that can be easily integrating + into other programs. It reads XML and creates C++ objects representing the XML document. The + objects can be manipulated, changed, and saved again as XML. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % version.replace('.', '_')] +checksums = ['15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'] + +builddependencies = [('binutils', '2.38')] + +buildopts = ' '.join([ + 'TINYXML_USE_STL=YES CXXFLAGS="$CXXFLAGS $CPPFLAGS" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', + # build a shared library + '&& $CXX -shared -Wl,-soname,lib%(namelower)s.so.%(version)s -o lib%(namelower)s.so.%(version)s $LDFLAGS *.o', +]) + +_incs = ['tinystr.h', 'tinyxml.h'] +_libs = ['lib%(namelower)s.so.%(version)s'] + +files_to_copy = [ + (_incs, 'include'), + (_libs, 'lib'), +] + +postinstallcmds = [ + "cd %(installdir)s/lib", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major)s", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major_minor)s", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so", +] + +sanity_check_paths = { + 'files': ['include/%s' % i for i in _incs] + ['lib/%s' % l for l in _libs], + 'dirs': [], +} + +moduleclass = 'lib' From f65d80fc0b3e0fa0a35dc2b24476e6ad1d7e9386 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 22 Dec 2022 11:05:37 +0100 Subject: [PATCH 5980/9987] Delete CUnit-2.1-3-GCCcore-11.3.0.eb this easyconfig is already merged in https://github.com/easybuilders/easybuild-easyconfigs/pull/16972 --- .../c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb deleted file mode 100644 index cae0ab9fe40..00000000000 --- a/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CUnit' -version = '2.1-3' - -homepage = 'https://sourceforge.net/projects/cunit/' -description = "Automated testing framework for C." - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_BZ2] -checksums = ['f5b29137f845bb08b77ec60584fdb728b4e58f1023e6f249a464efa49a40f214'] - -builddependencies = [ - ('binutils', '2.38'), - ('Autotools', '20220317'), -] - -preconfigopts = "autoreconf -i && " - -sanity_check_paths = { - 'files': ['lib/libcunit.a', 'lib/libcunit.%s' % SHLIB_EXT], - 'dirs': ['include/CUnit', 'lib/pkgconfig', 'share'], -} - -moduleclass = 'lang' From 13955bc0c036944cb400bc50a914702a3c5a1484 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 10:17:23 +0000 Subject: [PATCH 5981/9987] add debian, Nektar++ patches for TinyXML --- .../TinyXML-2.6.2-CVE-2021-42260.patch | 23 ++++++++ .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb | 14 ++++- .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb | 14 ++++- .../TinyXML-2.6.2-enforce-use-stl.patch | 18 ++++++ .../TinyXML-2.6.2-entity-encoding.patch | 58 +++++++++++++++++++ .../TinyXML/TinyXML-2.6.2-tagindex-type.patch | 23 ++++++++ 6 files changed, 148 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-CVE-2021-42260.patch create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-enforce-use-stl.patch create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-entity-encoding.patch create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-tagindex-type.patch diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-CVE-2021-42260.patch b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-CVE-2021-42260.patch new file mode 100644 index 00000000000..d9eeb45c73b --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-CVE-2021-42260.patch @@ -0,0 +1,23 @@ +Description: In stamp always advance the pointer if *p= 0xef + . + The current implementation only advanced if 0xef is followed + by two non-zero bytes. In case of malformed input (0xef should be + the start byte of a three byte character) this leads to an infinite + loop. (CVE-2021-42260) +Origin: https://sourceforge.net/p/tinyxml/git/merge-requests/1/ + +--- a/tinyxmlparser.cpp ++++ b/tinyxmlparser.cpp +@@ -274,6 +274,12 @@ void TiXmlParsingData::Stamp( const char* now, TiXmlEncoding encoding ) + else + { p +=3; ++col; } // A normal character. + } ++ else ++ { ++ // TIXML_UTF_LEAD_0 (239) is the start character of a 3 byte sequence, so ++ // there is something wrong here. Just advance the pointer to evade infinite loops ++ ++p; ++ } + } + else + { diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb index ca94bda02b9..c2b46986f5d 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb @@ -15,7 +15,19 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % version.replace('.', '_')] -checksums = ['15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'] +patches = [ + '%(name)s-2.6.2-enforce-use-stl.patch', + '%(name)s-2.6.2-entity-encoding.patch', + '%(name)s-2.6.2-CVE-2021-42260.patch', + '%(name)s-2.6.2-tagindex-type.patch' +] +checksums = [ + {'tinyxml_2_6_2.tar.gz': '15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'}, + {'TinyXML-2.6.2-enforce-use-stl.patch': '16a5b5e842eb0336be606131e5fb12a9165970f7bd943780ba09df2e1e8b29b1'}, + {'TinyXML-2.6.2-entity-encoding.patch': 'c5128e03933cd2e22eb85554d58f615f4dbc9177bd144cae2913c0bd7b140c2b'}, + {'TinyXML-2.6.2-CVE-2021-42260.patch': '3c4a6d9606944f54be5f108f278bb9137d78c6da9aa369a3d3faf87077a0a4bd'}, + {'TinyXML-2.6.2-tagindex-type.patch': 'cd1a1888ca0be64bb2cccc0c90eb070f3c789b8b9b7e02946ab8c4d38340424d'}, +] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb index 86a49712c2b..3caed91ebaf 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb @@ -15,7 +15,19 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % version.replace('.', '_')] -checksums = ['15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'] +patches = [ + '%(name)s-2.6.2-enforce-use-stl.patch', + '%(name)s-2.6.2-entity-encoding.patch', + '%(name)s-2.6.2-CVE-2021-42260.patch', + '%(name)s-2.6.2-tagindex-type.patch', +] +checksums = [ + {'tinyxml_2_6_2.tar.gz': '15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'}, + {'TinyXML-2.6.2-enforce-use-stl.patch': '16a5b5e842eb0336be606131e5fb12a9165970f7bd943780ba09df2e1e8b29b1'}, + {'TinyXML-2.6.2-entity-encoding.patch': 'c5128e03933cd2e22eb85554d58f615f4dbc9177bd144cae2913c0bd7b140c2b'}, + {'TinyXML-2.6.2-CVE-2021-42260.patch': '3c4a6d9606944f54be5f108f278bb9137d78c6da9aa369a3d3faf87077a0a4bd'}, + {'TinyXML-2.6.2-tagindex-type.patch': 'cd1a1888ca0be64bb2cccc0c90eb070f3c789b8b9b7e02946ab8c4d38340424d'}, +] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-enforce-use-stl.patch b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-enforce-use-stl.patch new file mode 100644 index 00000000000..f930ba9c2c8 --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-enforce-use-stl.patch @@ -0,0 +1,18 @@ +Description: TinyXml is built with TIXML_USE_STL, so we have to + enforce it when the library is used. +Author: Felix Geyer + +diff -Nur tinyxml-2.5.3/tinyxml.h tinyxml-2.5.3.patch/tinyxml.h +--- tinyxml-2.5.3/tinyxml.h 2007-05-07 00:41:23.000000000 +0200 ++++ tinyxml-2.5.3.patch/tinyxml.h 2009-07-08 22:32:03.000000000 +0200 +@@ -26,6 +26,10 @@ + #ifndef TINYXML_INCLUDED + #define TINYXML_INCLUDED + ++#ifndef TIXML_USE_STL ++ #define TIXML_USE_STL ++#endif ++ + #ifdef _MSC_VER + #pragma warning( push ) + #pragma warning( disable : 4530 ) diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-entity-encoding.patch b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-entity-encoding.patch new file mode 100644 index 00000000000..7a8d8785910 --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-entity-encoding.patch @@ -0,0 +1,58 @@ +Description: TinyXML incorrectly encodes text element containing an ampersand followed by either x or #. +Origin: http://sourceforge.net/tracker/index.php?func=detail&aid=3031828&group_id=13559&atid=313559 + +diff -u -r1.105 tinyxml.cpp +--- a/tinyxml.cpp ++++ b/tinyxml.cpp +@@ -57,30 +57,7 @@ + { + unsigned char c = (unsigned char) str[i]; + +- if ( c == '&' +- && i < ( (int)str.length() - 2 ) +- && str[i+1] == '#' +- && str[i+2] == 'x' ) +- { +- // Hexadecimal character reference. +- // Pass through unchanged. +- // © -- copyright symbol, for example. +- // +- // The -1 is a bug fix from Rob Laveaux. It keeps +- // an overflow from happening if there is no ';'. +- // There are actually 2 ways to exit this loop - +- // while fails (error case) and break (semicolon found). +- // However, there is no mechanism (currently) for +- // this function to return an error. +- while ( i<(int)str.length()-1 ) +- { +- outString->append( str.c_str() + i, 1 ); +- ++i; +- if ( str[i] == ';' ) +- break; +- } +- } +- else if ( c == '&' ) ++ if ( c == '&' ) + { + outString->append( entity[0].str, entity[0].strLength ); + ++i; +diff -u -r1.89 xmltest.cpp +--- a/xmltest.cpp ++++ b/xmltest.cpp +@@ -1340,6 +1340,16 @@ + }*/ + } + ++ #ifdef TIXML_USE_STL ++ { ++ TiXmlDocument xml; ++ xml.Parse("foo&#xa+bar"); ++ std::string str; ++ str << xml; ++ XmlTest( "Entity escaping", "foo&#xa+bar", str.c_str() ); ++ } ++ #endif ++ + /* 1417717 experiment + { + TiXmlDocument xml; diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-tagindex-type.patch b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-tagindex-type.patch new file mode 100644 index 00000000000..0b1d09b8043 --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-tagindex-type.patch @@ -0,0 +1,23 @@ +Author: Mike +Description: use size_t for tagIndex instead of int (and casting tag->length) + https://gitlab.nektar.info/nektar/nektar/-/blob/master/cmake/scripts/tinyxml.patch +--- tinyxmlparser.cpp 2017-10-03 16:05:35.999295200 +0100 ++++ tinyxmlparser.cpp 2017-10-03 16:05:58.556565300 +0100 +@@ -655,7 +655,7 @@ + + while ( in->good() ) + { +- int tagIndex = (int) tag->length(); ++ size_t tagIndex = tag->length(); + while ( in->good() && in->peek() != '>' ) + { + int c = in->get(); +@@ -958,7 +958,7 @@ + // We should be at a "<", regardless. + if ( !in->good() ) return; + assert( in->peek() == '<' ); +- int tagIndex = (int) tag->length(); ++ size_t tagIndex = tag->length(); + + bool closingTag = false; + bool firstCharFound = false; From ab5f98c4e5df5f134a76d3e85b372a76a9e66707 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 10:24:19 +0000 Subject: [PATCH 5982/9987] ensure TIXML_USE_STL is actually passed through --- easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb index c2b46986f5d..660168cf94b 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb @@ -32,7 +32,7 @@ checksums = [ builddependencies = [('binutils', '2.37')] buildopts = ' '.join([ - 'TINYXML_USE_STL=YES CXXFLAGS="$CXXFLAGS $CPPFLAGS" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', + 'CXXFLAGS="$CXXFLAGS $CPPFLAGS -DTINYXML_USE_STL" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', # build a shared library '&& $CXX -shared -Wl,-soname,lib%(namelower)s.so.%(version)s -o lib%(namelower)s.so.%(version)s $LDFLAGS *.o', ]) diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb index 3caed91ebaf..e6c9320d31c 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb @@ -32,7 +32,7 @@ checksums = [ builddependencies = [('binutils', '2.38')] buildopts = ' '.join([ - 'TINYXML_USE_STL=YES CXXFLAGS="$CXXFLAGS $CPPFLAGS" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', + 'CXXFLAGS="$CXXFLAGS $CPPFLAGS -DTIXML_USE_STL" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', # build a shared library '&& $CXX -shared -Wl,-soname,lib%(namelower)s.so.%(version)s -o lib%(namelower)s.so.%(version)s $LDFLAGS *.o', ]) From 3c51bfd38a26f63c706216df4fbc25485e7ae36c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 10:26:04 +0000 Subject: [PATCH 5983/9987] fix typo --- easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb index 660168cf94b..20da0a912d4 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb @@ -32,7 +32,7 @@ checksums = [ builddependencies = [('binutils', '2.37')] buildopts = ' '.join([ - 'CXXFLAGS="$CXXFLAGS $CPPFLAGS -DTINYXML_USE_STL" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', + 'CXXFLAGS="$CXXFLAGS $CPPFLAGS -DTIXML_USE_STL" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', # build a shared library '&& $CXX -shared -Wl,-soname,lib%(namelower)s.so.%(version)s -o lib%(namelower)s.so.%(version)s $LDFLAGS *.o', ]) From c9fc4e38ab18c83316e0422d30f424b2883d61ac Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Thu, 22 Dec 2022 11:33:26 +0100 Subject: [PATCH 5984/9987] adding easyconfigs: glew-2.2.0-GCCcore-11.3.0-egl.eb --- .../g/glew/glew-2.2.0-GCCcore-11.3.0-egl.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-egl.eb diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-egl.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-egl.eb new file mode 100644 index 00000000000..0bd382da354 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-egl.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' +versionsuffix = '-egl' +# available: -glx, -osmesa, -egl +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# offscreen), and OSMESA (offscreen software only). + +name = 'glew' +version = '2.2.0' + +homepage = 'https://github.com/nigels-com/glew' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Mesa', '22.0.3'), + ('X11', '20220504'), +] + +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all ' + local_system + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': [] +} + +moduleclass = 'devel' From 0ab889c69cb6396795b05cc082165142bb72b467 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 10:50:41 +0000 Subject: [PATCH 5985/9987] ensure GCCcore/11.3.0 version creates symlinks correctly, and match postinstallcmds --- .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb | 12 ++++++------ .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb index 20da0a912d4..502a6576d66 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb @@ -45,12 +45,12 @@ files_to_copy = [ (_libs, 'lib'), ] -postinstallcmds = [ - "cd %(installdir)s/lib" - " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major)s" - " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major_minor)s" - " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so" -] +postinstallcmds = [' && '.join([ + "cd %(installdir)s/lib", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major)s", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major_minor)s", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so", +])] sanity_check_paths = { 'files': ['include/%s' % i for i in _incs] + ['lib/%s' % l for l in _libs], diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb index e6c9320d31c..1810c449235 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb @@ -45,12 +45,12 @@ files_to_copy = [ (_libs, 'lib'), ] -postinstallcmds = [ +postinstallcmds = [' && '.join([ "cd %(installdir)s/lib", "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major)s", "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major_minor)s", "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so", -] +])] sanity_check_paths = { 'files': ['include/%s' % i for i in _incs] + ['lib/%s' % l for l in _libs], From 2b4fd34df36198c2950db720ba3ed6a662e06dde Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Thu, 22 Dec 2022 12:16:35 +0100 Subject: [PATCH 5986/9987] adding easyconfigs: Wayland-1.21.0-GCCcore-11.3.0.eb --- .../Wayland/Wayland-1.21.0-GCCcore-11.3.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..eb4b2f98bb1 --- /dev/null +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.3.0.eb @@ -0,0 +1,62 @@ +# Author: Jasper Grimm (UoY) +# URL of Wayland download changed to GitLab due to changes upstream +# Author: J. Sassmannshausen (Imperial College London/UK) +easyblock = 'Bundle' + +name = 'Wayland' +version = '1.21.0' + +homepage = 'https://wayland.freedesktop.org/' +description = """ +Wayland is a project to define a protocol for a compositor to talk to + its clients as well as a library implementation of the protocol. The + compositor can be a standalone display server running on Linux kernel + modesetting and evdev input devices, an X application, or a wayland + client itself. The clients can be traditional applications, X servers + (rootless or fullscreen) or other display servers. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('CMake', '3.23.1'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), + ('binutils', '2.38'), +] + +dependencies = [ + ('libffi', '3.4.2'), + ('expat', '2.4.8'), + ('libxml2', '2.9.13'), +] + +default_easyblock = 'MesonNinja' +default_component_specs = { + 'source_urls': ['https://wayland.freedesktop.org/releases'], + 'sources': [SOURCE_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('wayland', version, { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/wayland/-/releases/%(version)s/downloads'], + 'checksums': ['6dc64d7fc16837a693a51cfdb2e568db538bfdc9f457d4656285bb9594ef11ac'], + 'configopts': "-Ddocumentation=false", + }), + ('wayland-protocols', '1.25', { + 'checksums': ['f1ff0f7199d0a0da337217dd8c99979967808dc37731a1e759e822b75b571460'], + 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH " + }), +] + +_libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']] +sanity_check_paths = { + 'files': ['bin/wayland-scanner'] + _libs, + 'dirs': ['lib'], +} + +sanity_check_commands = ["wayland-scanner --help", "wayland-scanner --version"] + +moduleclass = 'vis' From 3f5d45e882843513de55f252baecf78561337380 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Thu, 22 Dec 2022 12:20:26 +0100 Subject: [PATCH 5987/9987] adding easyconfigs: Waylandpp-1.0.0-GCCcore-11.3.0.eb --- .../Waylandpp-1.0.0-GCCcore-11.3.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..84e55e3290e --- /dev/null +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,52 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'Waylandpp' +version = '1.0.0' + +homepage = 'https://github.com/NilsBrause/waylandpp' +description = """Wayland is an object oriented display protocol, which +features request and events. Requests can be seen as method calls on +certain objects, whereas events can be seen as signals of an object. +This makes the Wayland protocol a perfect candidate for a C++ binding. + +The goal of this library is to create such a C++ binding for Wayland +using the most modern C++ technology currently available, providing +an easy to use C++ API to Wayland.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/NilsBrause/waylandpp/archive'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + 'b20b45917382c6b87e9380130c9a1a1c563da2f498de5830df12fbce326dd9f5', # 1.0.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('pugixml', '1.12.1'), + ('Wayland', '1.21.0'), + ('freeglut', '3.2.2'), +] + +sanity_check_paths = { + 'files': ['bin/wayland-scanner++', 'lib//libwayland-client-extra++.%s' % SHLIB_EXT, + 'lib/libwayland-client++.%s' % SHLIB_EXT, + 'lib/libwayland-client-unstable++.%s' % SHLIB_EXT, + 'lib/libwayland-cursor++.%s' % SHLIB_EXT, + 'lib/libwayland-egl++.%s' % SHLIB_EXT, + 'lib/libwayland-server-extra++.%s' % SHLIB_EXT, + 'lib/libwayland-server++.%s' % SHLIB_EXT, + 'lib/libwayland-server-unstable++.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From a772b074dcc59e31c2ce34e7ca5b9ab72bb19def Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Thu, 22 Dec 2022 12:43:17 +0100 Subject: [PATCH 5988/9987] adding easyconfigs: hunspell-1.7.1-GCCcore-11.3.0.eb --- .../hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9c3d1392c26 --- /dev/null +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +# Contribution from Imperial College London/UK +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'hunspell' +version = '1.7.1' + +homepage = 'http://hunspell.github.io/' +description = """Hunspell is a spell checker and morphological analyzer +library and program designed for languageswith rich morphology and +complex word compounding or character encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/hunspell/hunspell/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6e3557624c608b3e6525b8bd277706db4f5a857c28fdb3cfa8d0d2b67776da8a'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('gettext', '0.21'), +] + +preconfigopts = "autoreconf -vfi && " + +sanity_check_commands = [ + 'hunspell -h', +] + +sanity_check_paths = { + 'files': ['bin/hunspell', 'lib/libhunspell-%(version_major_minor)s.a', + 'lib/libhunspell-%%(version_major_minor)s.%s' % SHLIB_EXT, 'lib/pkgconfig/hunspell.pc'], + 'dirs': ['include/hunspell'], +} + +moduleclass = 'tools' From 7366eeef429a66c240ec29c606633b3552c0f433 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Thu, 22 Dec 2022 12:46:14 +0100 Subject: [PATCH 5989/9987] adding easyconfigs: enchant-2-2.3.3-GCCcore-11.3.0.eb --- .../enchant-2-2.3.3-GCCcore-11.3.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0377d807772 --- /dev/null +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.3.0.eb @@ -0,0 +1,51 @@ +# Updated from enchant-1.6.1-intel-2017a.eb +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'enchant-2' +version = '2.3.3' + +homepage = 'https://github.com/AbiWord/enchant' +description = """Enchant aims to provide a simple but comprehensive abstraction for dealing +with different spell checking libraries in a consistent way. A client, such +as a text editor or word processor, need not know anything about a specific +spell-checker, and since all back-ends are plugins, new spell-checkers can +be added without needing any change to the program using Enchant.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/AbiWord/enchant/releases/download/v%(version)s'] +sources = ['enchant-%(version)s.tar.gz'] +checksums = [ + '3da12103f11cf49c3cf2fd2ce3017575c5321a489e5b9bfa81dd91ec413f3891' +] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), + ('M4', '1.4.19'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "autoreconf -vfi && " + +dependencies = [ + ('hunspell', '1.7.1'), + ('GLib', '2.72.1'), +] + +buildopts = "LIBTOOL='libtool --tag=CC'" + +sanity_check_commands = [ + 'enchant-2 -v', + 'enchant-lsmod-2 -v', +] + +sanity_check_paths = { + 'files': ['bin/enchant-2', 'bin/enchant-lsmod-2', + 'lib/libenchant-2.a', 'lib/libenchant-2.%s' % SHLIB_EXT], + 'dirs': ['include/enchant-2', 'lib/enchant-2'], +} + +moduleclass = 'tools' From 201d02b5fb5a223bf00bd58cf065af4e2eab62b5 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Thu, 22 Dec 2022 12:56:45 +0100 Subject: [PATCH 5990/9987] adding easyconfigs: ccache-4.6.3-GCCcore-11.3.0.eb --- .../c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f3afb8800d2 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# Updated to 4.6.1: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.6.3' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f46ba3706ad80c30d4d5874dee2bf9227a7fcd0ccaac31b51919a3053d84bd05'] + +osdependencies = [('glibc-static', 'libc6-dev', 'glibc-devel')] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), + ('zstd', '1.5.2', ), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('hiredis', '1.0.2'), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS=" -fuse-ld=bfd"' +configopts = '-DENABLE_DOCUMENTATION=OFF -DENABLE_IPO=ON -DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a" ' +# disable hunt for faster linker, since using ld.gold may fail (on CentOS 8, for example) +configopts += '-DUSE_FASTER_LINKER=OFF' + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = ['ccache --help'] + +moduleclass = 'tools' From 453e46345b98c82f8908c34b080fba5c9c42a084 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 12:16:58 +0000 Subject: [PATCH 5991/9987] add patch to libwpe to avoid poisoned malloc/calloc error from string.h --- .../l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb | 16 ++++++++-------- ...wpe-1.13.3_include-string-before-poison.patch | 13 +++++++++++++ 2 files changed, 21 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/l/libwpe/libwpe-1.13.3_include-string-before-poison.patch diff --git a/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb index 90c0db43eef..1aa03f9c0a0 100644 --- a/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb @@ -6,10 +6,10 @@ name = 'libwpe' version = '1.13.3' homepage = 'https://webkit.org/wpe' -description = """WPE is the reference WebKit port for embedded and -low-consumption computer devices. It has been designed from the -ground-up with performance, small footprint, accelerated content -rendering, and simplicity of deployment in mind, bringing the +description = """WPE is the reference WebKit port for embedded and +low-consumption computer devices. It has been designed from the +ground-up with performance, small footprint, accelerated content +rendering, and simplicity of deployment in mind, bringing the excellence of the WebKit engine to countless platforms and target devices.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} @@ -17,9 +17,11 @@ toolchainopts = {'pic': True} source_urls = ['https://wpewebkit.org/releases'] sources = ['%(name)s-%(version)s.tar.xz'] - +patches = ['%(name)s-1.13.3_include-string-before-poison.patch'] checksums = [ - '05f871922f6ca750c5689a38a346c3fba130417d3490dd52362b4fe22f334e96', # libwpe-1.13.3.tar.xz + {'libwpe-1.13.3.tar.xz': '05f871922f6ca750c5689a38a346c3fba130417d3490dd52362b4fe22f334e96'}, + {'libwpe-1.13.3_include-string-before-poison.patch': + '2d21ed6b2dafa758126cda162e450ab2b3a3c0b622e375ff443523ba32fc5812'}, ] builddependencies = [ @@ -33,8 +35,6 @@ dependencies = [ ('glew', '2.2.0', '-egl'), ] -parallel = 2 - sanity_check_paths = { 'files': ['lib/libwpe-1.0.%s' % SHLIB_EXT], 'dirs': ['include'], diff --git a/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3_include-string-before-poison.patch b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3_include-string-before-poison.patch new file mode 100644 index 00000000000..ecd1030693c --- /dev/null +++ b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3_include-string-before-poison.patch @@ -0,0 +1,13 @@ +Author: Jasper Grimm +Description: Include string.h before poisoning {c,m}alloc +diff -ruN libwpe-1.13.3/src/alloc-private.h libwpe-1.13.3.p1/src/alloc-private.h +--- libwpe-1.13.3/src/alloc-private.h 2022-08-11 12:59:47.000000000 +0100 ++++ libwpe-1.13.3.p1/src/alloc-private.h 2022-12-22 12:01:51.000000000 +0000 +@@ -27,6 +27,7 @@ + #ifndef wpe_alloc_private_h + #define wpe_alloc_private_h + ++#include + #include + + #if defined(__has_attribute) && __has_attribute(noreturn) From 3dd26349af7c290bfba947e3d06188bae8143564 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Thu, 22 Dec 2022 12:58:58 +0000 Subject: [PATCH 5992/9987] Add original author info --- easybuild/easyconfigs/g/gh/gh-2.20.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/g/gh/gh-2.20.2.eb b/easybuild/easyconfigs/g/gh/gh-2.20.2.eb index 3d63f978426..b78e0a508e2 100644 --- a/easybuild/easyconfigs/g/gh/gh-2.20.2.eb +++ b/easybuild/easyconfigs/g/gh/gh-2.20.2.eb @@ -1,3 +1,9 @@ +# easybuild easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +# easyblock = 'GoPackage' name = 'gh' From c13a8e983b5d25d6e7d9c55c10678bdb32689cab Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 22 Dec 2022 16:38:25 +0100 Subject: [PATCH 5993/9987] GRASS: check for actual files/dirs in sanity_check_paths --- easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb b/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb index 890e801c909..064972b3a7c 100644 --- a/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb @@ -95,8 +95,8 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['bin/grass'], + 'dirs': ['grass%(version_major)s%(version_minor)s'] } moduleclass = 'geo' From dbcb440d0034988ec7cdd49ed0d6ddf07fecdcc3 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Fri, 23 Dec 2022 11:45:40 +0100 Subject: [PATCH 5994/9987] adding easyconfigs: ruamel.yaml-0.17.21-GCCcore-11.3.0.eb --- .../ruamel.yaml-0.17.21-GCCcore-11.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..442567f3a0c --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.17.21' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.clib', '0.2.7', { + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + 'modulename': False, + }), + (name, version, { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('configobj', '5.0.6', { + 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], + }), + ('lz4', '4.0.2', { + 'checksums': ['083b7172c2938412ae37c3a090250bfdd9e4a6e855442594f86c3608ed12729b'], + }), + ('ruamel.yaml.base', '0.3.2', { + 'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.6.3', { + 'checksums': ['f4ebce7d6d9d53afae84d7efd79f8d6c3dcad56e0e6be3a5d2370be0e04acea0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' From 1eb2a6063d14624b830c81f6d567465d157de679 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 23 Dec 2022 10:57:56 +0000 Subject: [PATCH 5995/9987] matplotlib version changed to 3.3.3 --- .../easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb index ef3a56457df..37bf2e3548c 100644 --- a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb +++ b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), - ('matplotlib', '3.5.1'), + ('matplotlib', '3.3.3'), ('SciPy-bundle', '2020.11'), ('pybedtools', '0.8.2'), ('psutil', '5.9.3'), From b17ad691d04fef6f3aff94e34e662bb0b1dcc59c Mon Sep 17 00:00:00 2001 From: alberta Date: Fri, 23 Dec 2022 12:15:56 +0100 Subject: [PATCH 5996/9987] adding easyconfigs: DeepMod2-0.0.1-foss-2021a.eb --- .../d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb new file mode 100644 index 00000000000..9f570ba7fb9 --- /dev/null +++ b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb @@ -0,0 +1,43 @@ +easyblock = 'Tarball' + +name = 'DeepMod2' +version = '0.0.1' + +homepage = 'https://github.com/WGLab/DeepMod2' + +description = """ + DeepMod2 is a computational tool for detecting DNA methylation and modifications + from Oxford Nanopore reads. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'WGLab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['68b1e4334a0f867c513e9939c196389f7ed74be6bfa297e1e33dba314840660e'] + +dependencies = [ + ('CUDA', '11.7.0'), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Pysam', '0.16.0.1'), + ('TensorFlow', '2.6.0'), + ('h5py', '3.2.1'), + ('tqdm', '4.61.1'), + ('numba', '0.53.1'), + ('ont-fast5-api', '4.0.0'), +] + +preinstall_cmd = "chmod a+x %(namelower)s" + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': ['src'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 78ef3b6592895540ba79ab2192c88d56271add7b Mon Sep 17 00:00:00 2001 From: alberta Date: Fri, 23 Dec 2022 12:40:56 +0100 Subject: [PATCH 5997/9987] Update toolchain to fosscuda/2021a --- .../easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb index 9f570ba7fb9..a358dbd7525 100644 --- a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb @@ -17,8 +17,11 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['68b1e4334a0f867c513e9939c196389f7ed74be6bfa297e1e33dba314840660e'] -dependencies = [ +builddependencies = [ ('CUDA', '11.7.0'), +] + +dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('Pysam', '0.16.0.1'), From d8e998c4f31dd8c9fbc6d715d9bae135b72ad033 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Fri, 23 Dec 2022 12:42:27 +0100 Subject: [PATCH 5998/9987] adding easyconfigs: Cantera-2.6.0-foss-2022a-Python-3.10.4.eb --- .../Cantera-2.6.0-foss-2022a-Python-3.10.4.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb new file mode 100644 index 00000000000..607648036f0 --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb @@ -0,0 +1,50 @@ +easyblock = 'SCons' + +name = 'Cantera' +version = '2.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Cantera/cantera' +description = """Chemical kinetics, thermodynamics, and transport tool suite""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/Cantera/cantera/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7273622ea76a53373cee820f939613b15eea3dd83db6e1b127c5ed043f77dc5b'] + +dependencies = [ + ('Python', '3.10.4'), + ('Boost', '1.79.0'), + ('SUNDIALS', '6.3.0'), + ('yaml-cpp', '0.7.0'), + ('ruamel.yaml', '0.17.21'), +] +builddependencies = [ + ('SCons', '4.4.0'), + ('Eigen', '3.4.0'), + ('fmt', '9.1.0'), + ('googletest', '1.11.0'), +] + +local_common_opts = 'env_vars=all CC="$CC" CXX="$CXX" cc_flags="$CFLAGS" cxx_flags="$CXXFLAGS" ' +#local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR ' +#local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' +#local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=${EBROOTFLEXIBLAS}/lib' +buildopts = 'build ' + local_common_opts +# tests hang, so disable them for now +# runtest = 'test ' + local_common_opts +installopts = 'install ' + local_common_opts +prefix_arg = 'prefix=' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ck2cti'], + 'dirs': ['include/cantera', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('python', "-c 'import cantera'")] + +moduleclass = 'chem' From 75ec70affeda805fb14b0fd4f87a75510baab39e Mon Sep 17 00:00:00 2001 From: alberta Date: Fri, 23 Dec 2022 13:23:00 +0100 Subject: [PATCH 5999/9987] Update dependencies cuda version --- easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb index a358dbd7525..627190a93c7 100644 --- a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['68b1e4334a0f867c513e9939c196389f7ed74be6bfa297e1e33dba314840660e'] builddependencies = [ - ('CUDA', '11.7.0'), + ('CUDA', '11.7.0', '', {'name': 'system', 'version': ''}), ] dependencies = [ From d9eeb9f06c6c645d185efff37725f47b729b670c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 23 Dec 2022 13:32:44 +0100 Subject: [PATCH 6000/9987] use https rather than http --- .../easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb index 9c3d1392c26..5e59a4c5630 100644 --- a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb @@ -6,7 +6,7 @@ easyblock = 'ConfigureMake' name = 'hunspell' version = '1.7.1' -homepage = 'http://hunspell.github.io/' +homepage = 'https://hunspell.github.io/' description = """Hunspell is a spell checker and morphological analyzer library and program designed for languageswith rich morphology and complex word compounding or character encoding.""" From 981384f7de8929e839bededed9d1d824e2cc672c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 23 Dec 2022 15:11:30 +0100 Subject: [PATCH 6001/9987] add missing zlib and zstd to GnuTLS --- easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb | 2 ++ easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb | 2 ++ easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb index 94a5cbb5961..fad3ae66a6f 100644 --- a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb @@ -26,6 +26,8 @@ dependencies = [ ('libtasn1', '4.17.0'), ('libidn', '1.36'), ('p11-kit', '0.24.0'), + ('zlib', '1.2.11'), + ('zstd', '1.4.9'), ] configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb index 6bcdaa9f327..ea03e7cd2dc 100644 --- a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb @@ -26,6 +26,8 @@ dependencies = [ ('libtasn1', '4.18.0'), ('libidn', '1.38'), ('p11-kit', '0.24.1'), + ('zlib', '1.2.11'), + ('zstd', '1.5.0'), ] configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb index c604f1a0fa0..8660253cc57 100644 --- a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb @@ -26,6 +26,8 @@ dependencies = [ ('libtasn1', '4.19.0'), ('libidn', '1.41'), ('p11-kit', '0.24.1'), + ('zlib', '1.2.12'), + ('zstd', '1.5.2'), ] configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " From 0a82cfef560b795f3eb3b5ceb2668c0ac8efeea6 Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 23 Dec 2022 15:27:09 +0100 Subject: [PATCH 6002/9987] Update Ruby-3.0.5-GCCcore-11.3.0.eb --- easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb index 370bd16dda5..13a6f73ff7b 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['3586861cb2df56970287f0fd83f274bd92058872d830d15570b36def7f1a92ac'] +checksums = ['9afc6380a027a4fe1ae1a3e2eccb6b497b9c5ac0631c12ca56f9b7beb4848776'] builddependencies = [('binutils', '2.38')] From 7bf8ff7455236684a65e15c110016045611a539d Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 23 Dec 2022 15:28:05 +0100 Subject: [PATCH 6003/9987] Update libev-4.33-GCC-11.3.0.eb --- easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb index bbfa103b29b..780a94eb1c9 100644 --- a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb @@ -1,3 +1,4 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) easyblock = 'ConfigureMake' name = 'libev' From 3cedd28ede417addb242d5f0e7b6bd5e58accb7d Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Fri, 23 Dec 2022 16:07:04 +0100 Subject: [PATCH 6004/9987] adding easyconfigs: Blosc2-2.4.3-GCCcore-11.3.0.eb --- .../b/Blosc2/Blosc2-2.4.3-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..585ddd2f44b --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.4.3' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d4aa5e0794598794f20ab950e973d44f0d0d9c133ea1a5a07cb200fa54d2e036'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 0ea28443a7e50c2684e51a574d05ea0c85e8ebf4 Mon Sep 17 00:00:00 2001 From: alberta Date: Fri, 23 Dec 2022 20:05:20 +0100 Subject: [PATCH 6005/9987] Try suffix for tqdm --- easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb index 627190a93c7..a4c6aa9b006 100644 --- a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb @@ -27,7 +27,7 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('TensorFlow', '2.6.0'), ('h5py', '3.2.1'), - ('tqdm', '4.61.1'), + ('tqdm', '4.61.1', '', {'name': 'GCCcore', 'version': '10.3.0'}), ('numba', '0.53.1'), ('ont-fast5-api', '4.0.0'), ] From 3eae11208c4719cbceae40e153be6bb43225622d Mon Sep 17 00:00:00 2001 From: alberta Date: Sat, 24 Dec 2022 00:53:23 +0100 Subject: [PATCH 6006/9987] adding easyconfigs: TRF-4.09.1-GCC-10.3.0.eb --- .../t/TRF/TRF-4.09.1-GCC-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCC-10.3.0.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..c7b4a835f15 --- /dev/null +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCC-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'TRF' +version = '4.09.1' + +homepage = 'https://tandem.bu.edu/trf/trf.html' +description = """Tandem Repeats Finder: a program to analyze DNA sequences.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'Benson-Genomics-Lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/trf'], + 'dirs': [], +} + +sanity_check_commands = ["trf -v"] + +moduleclass = 'bio' From daed5dd1c9406f267c4190186bfc73af0d32cf59 Mon Sep 17 00:00:00 2001 From: alberta Date: Sat, 24 Dec 2022 12:45:21 +0100 Subject: [PATCH 6007/9987] Try with tqdm 4.61.2 --- easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb index a4c6aa9b006..2b702203a84 100644 --- a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['68b1e4334a0f867c513e9939c196389f7ed74be6bfa297e1e33dba314840660e'] builddependencies = [ - ('CUDA', '11.7.0', '', {'name': 'system', 'version': ''}), + ('CUDA', '11.7.0', '', SYSTEM), ] dependencies = [ @@ -27,7 +27,7 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('TensorFlow', '2.6.0'), ('h5py', '3.2.1'), - ('tqdm', '4.61.1', '', {'name': 'GCCcore', 'version': '10.3.0'}), + ('tqdm', '4.61.2', '', {'name': 'GCCcore', 'version': '10.3.0'}), ('numba', '0.53.1'), ('ont-fast5-api', '4.0.0'), ] From d01a1f54e2630205bd4dbf7931d2ad684293e4aa Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Tue, 27 Dec 2022 09:49:54 +0100 Subject: [PATCH 6008/9987] adding easyconfigs: Blosc-1.21.3-GCCcore-11.3.0.eb --- .../b/Blosc/Blosc-1.21.3-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..115e49c59ac --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.21.3' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['941016c4564bca662080bb01aea74f06630bd665e598c6f6967fd91b2e2e0bb6'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From f100c4e8eeeefa96ccef7f224885742b9b82d4e5 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 09:45:54 +0000 Subject: [PATCH 6009/9987] adding easyconfigs: tesseract-5.3.0-GCCcore-11.3.0.eb, Leptonica-1.83.0-GCCcore-11.3.0.eb --- .../Leptonica-1.83.0-GCCcore-11.3.0.eb | 32 ++++++++++ .../tesseract-5.3.0-GCCcore-11.3.0.eb | 63 +++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/l/Leptonica/Leptonica-1.83.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.83.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.83.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d4743b6cc7d --- /dev/null +++ b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.83.0-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Leptonica' +version = '1.83.0' + +homepage = 'http://www.leptonica.org' +description = """Leptonica is a collection of pedagogically-oriented open source software + that is broadly useful for image processing and image analysis applications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/DanBloomberg/leptonica/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['206591dd58cf84ef380836dad133b58c9d1af92491f5a9825c346a162044bcfe'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('giflib', '5.2.1'), + ('libwebp', '1.2.4'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['bin/convertformat'], + 'dirs': ['include/leptonica', 'lib/pkgconfig'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b01480119f0 --- /dev/null +++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'tesseract' +version = '5.3.0' + +homepage = 'https://github.com/tesseract-ocr/tesseract' +description = """Tesseract is an optical character recognition engine""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'tesseract-ocr' +source_urls = [GITHUB_SOURCE] +sources = [ + '%(version)s.tar.gz', + { + 'source_urls': ['https://github.com/tesseract-ocr/tessdata_best/archive/'], + 'download_filename': '4.1.0.tar.gz', + 'filename': 'tessdata_best-4.1.0.tar.gz', + }, +] +checksums = [ + {'5.3.0.tar.gz': '7e70870f8341e5ea228af2836ce79a36eefa11b01b56177b4a8997f330c014b8'}, + {'tessdata_best-4.1.0.tar.gz': 'bb05b738298ae73e7130e2913ed002b49d94cd1cea508e63be1928fe47770b32'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.38'), + ('pkgconf', '1.8.0') +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('Leptonica', '1.83.0'), + ('libarchive', '3.6.1'), + ('ICU', '71.1'), + ('fontconfig', '2.14.0'), + ('GLib', '2.72.1'), + ('cairo', '1.17.4'), + ('Pango', '1.50.7'), +] + +separate_build_dir = True + +postinstallcmds = [ + 'rm %(builddir)s/tessdata_best-4.1.0/configs', + 'rm -rf %(builddir)s/tessdata_best-4.1.0/tessconfigs', + 'mv %(builddir)s/tessdata_best-4.1.0/* %(installdir)s/share/tessdata' +] + +modextrapaths = { + 'TESSDATA_PREFIX': 'tessdata', +} + +sanity_check_paths = { + 'files': ['bin/tesseract'], + 'dirs': ['share/tessdata', 'include/tesseract'] +} + +moduleclass = 'vis' From 9c86d4f61005ff021776c0fdfee884f92469e6ae Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Tue, 27 Dec 2022 12:52:40 +0100 Subject: [PATCH 6010/9987] updated eb --- .../c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb | 21 +++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb index f3afb8800d2..dba01b59138 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ('CMake', '3.23.1'), ('Ninja', '1.10.2'), ('zstd', '1.5.2', ), - ('pkg-config', '0.29.2'), + ('pkgconfig', '1.5.5', '-python'), ] dependencies = [ @@ -33,15 +33,24 @@ dependencies = [ ] # use BFD linker rather than default ld.gold (required on CentOS 8) -preconfigopts = 'LDFLAGS=" -fuse-ld=bfd"' -configopts = '-DENABLE_DOCUMENTATION=OFF -DENABLE_IPO=ON -DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a" ' -# disable hunt for faster linker, since using ld.gold may fail (on CentOS 8, for example) -configopts += '-DUSE_FASTER_LINKER=OFF' +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + '-DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a"', + '-DHIREDIS_LIBRARY="$EBROOTHIREDIS/lib/libhiredis.a"', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) sanity_check_paths = { 'files': ['bin/ccache'], 'dirs': [] } -sanity_check_commands = ['ccache --help'] +sanity_check_commands = [ + 'ccache --help', + # Ensure that the binary does not depend on any shared library + #'ldd $(which ccache) | grep -q "not a dynamic executable"', +] moduleclass = 'tools' From 7ee8a5a7f5298ef725b479a6ff244a341874aa08 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Tue, 27 Dec 2022 12:55:08 +0100 Subject: [PATCH 6011/9987] updated eb --- easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb index dba01b59138..7ca4b474ed9 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb @@ -49,8 +49,6 @@ sanity_check_paths = { } sanity_check_commands = [ 'ccache --help', - # Ensure that the binary does not depend on any shared library - #'ldd $(which ccache) | grep -q "not a dynamic executable"', ] moduleclass = 'tools' From 6bed58c31914d7018d26e0d2d624524334eb0791 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 12:52:34 +0000 Subject: [PATCH 6012/9987] {math}[foss/2022a] Transformers v4.24.0 - Add missing \`pkgconf\` build dependency --- .../easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb index 47a488d49c1..0558a3731f5 100644 --- a/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb @@ -10,6 +10,7 @@ State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" toolchain = {'name': 'foss', 'version': '2022a'} builddependencies = [ + ('pkgconf', '1.8.0'), # required for setuptools-rust, which is needed for tokenizers ('Rust', '1.60.0'), # required for setuptools-rust, which is needed for tokenizers ] dependencies = [ From 9267e989bedf1dc2f1804a2517d79bd93fa993bb Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 12:54:00 +0000 Subject: [PATCH 6013/9987] Remove unnecessary comment --- .../t/Transformers/Transformers-4.24.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb index 0558a3731f5..fc965d151e3 100644 --- a/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb @@ -10,7 +10,7 @@ State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" toolchain = {'name': 'foss', 'version': '2022a'} builddependencies = [ - ('pkgconf', '1.8.0'), # required for setuptools-rust, which is needed for tokenizers + ('pkgconf', '1.8.0'), ('Rust', '1.60.0'), # required for setuptools-rust, which is needed for tokenizers ] dependencies = [ From bbf8372d6bbaad4b98804a1acfd429bf980fa71d Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 15:00:53 +0000 Subject: [PATCH 6014/9987] adding easyconfigs: Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb, Albumentations-1.3.0-foss-2022a.eb, imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb, imgaug-0.4.0-foss-2022a.eb --- ...mentations-1.3.0-foss-2022a-CUDA-11.7.0.eb | 38 +++++++++++++++++++ .../Albumentations-1.3.0-foss-2022a.eb | 36 ++++++++++++++++++ .../imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb | 36 ++++++++++++++++++ .../i/imgaug/imgaug-0.4.0-foss-2022a.eb | 34 +++++++++++++++++ 4 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..b66cbc3dfe8 --- /dev/null +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Albumentations' +version = '1.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://albumentations.ai' +description = "Albumentations is a Python library for fast and flexible image augmentations" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('scikit-image', '0.19.3'), + ('scikit-learn', '1.1.2'), + ('OpenCV', '4.6.0', '-CUDA-%(cudaver)s' + '-contrib'), + ('imgaug', '0.4.0', versionsuffix), +] + +preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && " + +use_pip = True + +exts_list = [ + ('qudida', '0.0.4', { + 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], + }), + ('albumentations', version, { + 'checksums': ['be1af36832c8893314f2a5550e8ac19801e04770734c1b70fa3c996b41f37bed'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a.eb new file mode 100644 index 00000000000..cecb717c37c --- /dev/null +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Albumentations' +version = '1.3.0' + +homepage = 'https://albumentations.ai' +description = "Albumentations is a Python library for fast and flexible image augmentations" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('scikit-image', '0.19.3'), + ('scikit-learn', '1.1.2'), + ('OpenCV', '4.6.0', '-contrib'), + ('imgaug', '0.4.0'), +] + +preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && " + +use_pip = True + +exts_list = [ + ('qudida', '0.0.4', { + 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], + }), + ('albumentations', version, { + 'checksums': ['be1af36832c8893314f2a5550e8ac19801e04770734c1b70fa3c996b41f37bed'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..44e5f993163 --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,36 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('Pillow', '9.1.1'), + ('matplotlib', '3.5.2'), + ('scikit-image', '0.19.3'), + ('OpenCV', '4.6.0', '-CUDA-%(cudaver)s' + '-contrib'), + ('Shapely', '1.8.2'), + ('imageio', '2.22.2'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['imgaug-0.4.0_openvc_requirement.patch'] +checksums = [ + {'imgaug-0.4.0.tar.gz': '46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7'}, + {'imgaug-0.4.0_openvc_requirement.patch': '2ff0b66ba38fdcf5f267a3d0ad1dc2710fee3c2f8cd3d086c56ea538a2a9ffc8'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a.eb new file mode 100644 index 00000000000..643f7eaca51 --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a.eb @@ -0,0 +1,34 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.0' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Pillow', '9.1.1'), + ('matplotlib', '3.5.2'), + ('scikit-image', '0.19.3'), + ('OpenCV', '4.6.0', '-contrib'), + ('Shapely', '1.8.2'), + ('imageio', '2.22.2'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['imgaug-0.4.0_openvc_requirement.patch'] +checksums = [ + {'imgaug-0.4.0.tar.gz': '46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7'}, + {'imgaug-0.4.0_openvc_requirement.patch': '2ff0b66ba38fdcf5f267a3d0ad1dc2710fee3c2f8cd3d086c56ea538a2a9ffc8'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' From 6342d7426d35884eceb8fbf98d20a831e64dd3aa Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 15:17:35 +0000 Subject: [PATCH 6015/9987] adding easyconfigs: PyTorch-Lightning-1.8.4-foss-2022a.eb --- .../PyTorch-Lightning-1.8.4-foss-2022a.eb | 121 ++++++++++++++++++ 1 file changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a.eb new file mode 100644 index 00000000000..2a62146958f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a.eb @@ -0,0 +1,121 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.8.4' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + # dependencies from requirements/app/base.txt + ('aiohttp', '3.8.3'), + ('BeautifulSoup', '4.10.0'), + ('deepdiff', '5.8.1'), + # dependencies from requirements/pytorch/base.txt + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('tensorboardX', '2.5.1'), +] + +use_pip = True + +# dependencies from requirements/app/base.txt and requirements/pytorch/base.txt +exts_list = [ + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.5.1', { + 'checksums': ['63a5c5ce3673d3d5fbbf23cd87e11ab84b6b451436f1b7f19ec54b6bc36ed7ca'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), + ('starlette', '0.19.1', { + 'checksums': ['c6d21096774ecb9639acad41b86b7706e52ba3bf1dc13ea4ed9ad593d47e24c7'], + }), + ('fastapi', '0.79.1', { + 'checksums': ['006862dec0f0f5683ac21fb0864af2ff12a931e7ba18920f28cc8eceed51896b'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + ('lightning_cloud', '0.5.12', { + 'checksums': ['5b0cf53ecfb512f9476eec3a7f425c0e174ca9d0e726673605d5e1e57074eb0c'], + }), + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('starsessions', '1.3.0', { + 'checksums': ['8d3b509d4e6d235655f7dd495fcf0afc1bd86da84de3a8d434e6f82137ebcde8'], + }), + ('fsspec', '2022.7.1', { + 'checksums': ['7f9fb19d811b027b97c4636c6073eb53bc4cbee2d3c4b33fa88b9f26906fd7d7'], + }), + ('croniter', '1.3.8', { + 'checksums': ['32a5ec04e97ec0837bcdf013767abd2e71cceeefd3c2e14c804098ce51ad6cd9'], + }), + ('traitlets', '5.2.0', { + 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('lightning-utilities', '0.4.2', { + 'checksums': ['dc6696ab180117f7e97b5488dac1d77765ab891022f7521a97a39e10d362bdb8'], + }), + ('blessed', '1.19.1', { + 'checksums': ['9a0d099695bf621d4680dd6c73f6ad547f6a3442fbdbe80c4b1daa1edbc492fc'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('readchar', '4.0.3', { + 'checksums': ['1d920d0e9ab76ec5d42192a68d15af2562663b5dfbf4a67cf9eba520e1ca57e6'], + }), + ('inquirer', '2.10.1', { + 'checksums': ['e9876258183e24f6e8c44136b04f6f2e18dd6684aee59b86a8057c50601a6523'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('botocore', '1.24.21', { + 'checksums': ['7e976cfd0a61601e74624ef8f5246b40a01f2cce73a011ef29cf80a6e371d0fa'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('aiobotocore', '2.3.4', { + 'checksums': ['6554ebea5764f66f4be544a4fcaa0953ee80e600dd7bd818ba4893d72bf12bfb'], + }), + ('s3fs', '2022.7.1', { + 'checksums': ['4883d682cb96b769fca568dbbcaa33ff457ac8077a03af221e6f253adac05771'], + }), + ('torchmetrics', '0.9.3', { + 'checksums': ['4ebfd2466021db26397636966ee1a195d3b340ba5d71bb258e764340dfc2476f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['c2771f966fc1b909cdfd1d603a87b8c84a3d5ff7aacf35b2c0260f697ec0c8be'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 93a306b070ecf54432308493e308d92430ddba88 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 15:19:51 +0000 Subject: [PATCH 6016/9987] adding easyconfigs: SentencePiece-0.1.97-GCC-11.3.0.eb --- .../SentencePiece-0.1.97-GCC-11.3.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.97-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.97-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.97-GCC-11.3.0.eb new file mode 100644 index 00000000000..21674bdab43 --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.97-GCC-11.3.0.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.1.97' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('gperftools', '2.10'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['41c3a07f315e3ac87605460c8bb8d739955bc8e7f478caec4017ef9b7d78669b'], +} + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'separate_build_dir': True, + 'start_dir': '%(namelower)s-%(version)s', + }), + ('sentencepiece', version, { + 'easyblock': 'PythonPackage', + 'start_dir': '%(namelower)s-%(version)s/python', + 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/'] + +sanity_check_paths = { + 'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] + + ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] + + ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'], +} + +sanity_check_commands = [ + 'spm_train --help', + "python -c 'import sentencepiece'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'lib' From 06f2cf7cd6c5a96d074e866693881ba6ae8698a0 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Tue, 27 Dec 2022 17:48:10 +0100 Subject: [PATCH 6017/9987] updated eb --- easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb index 7ca4b474ed9..770822d93b6 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ('CMake', '3.23.1'), ('Ninja', '1.10.2'), ('zstd', '1.5.2', ), - ('pkgconfig', '1.5.5', '-python'), + ('pkgconf', '1.8.0'), ] dependencies = [ From 7c361bd1ebc73e461bf909c9646501c94e69707b Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 17:52:30 +0000 Subject: [PATCH 6018/9987] adding easyconfigs: boto3-1.26.37-GCCcore-11.3.0.eb, neptune-client-0.16.2-foss-2022a.eb --- .../b/boto3/boto3-1.26.37-GCCcore-11.3.0.eb | 39 +++++++++++ .../neptune-client-0.16.2-foss-2022a.eb | 66 +++++++++++++++++++ 2 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.26.37-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.26.37-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.26.37-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..316623bb877 --- /dev/null +++ b/easybuild/easyconfigs/b/boto3/boto3-1.26.37-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'boto3' +version = '1.26.37' + +homepage = 'https://github.com/boto/boto3' +description = """Boto3 is the Amazon Web Services (AWS) Software Development Kit +(SDK) for Python, which allows Python developers to write software that makes +use of services like Amazon S3 and Amazon EC2.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +exts_list = [ + ('botocore', '1.29.37', { + 'checksums': ['3afa4fec9f7713caa05116563b38f81bec7bd20585d517155484d3f25efab5aa'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.6.0', { + 'checksums': ['2ed07d3866f523cc561bf4a00fc5535827981b117dd7876f036b0c1aca42c947'], + }), + (name, version, { + 'checksums': ['82b790b1dabd0746b028d2013b5d4d636a41f3aaf25520081f4c173cb6eb395d'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2022a.eb b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2022a.eb new file mode 100644 index 00000000000..5914ef4527a --- /dev/null +++ b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2022a.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'neptune-client' +version = '0.16.2' + +homepage = 'https://docs.neptune.ai' +description = """ +Neptune is an experiment tracking hub that brings organization and collaboration to your data science team. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('GitPython', '3.1.27'), + ('Pillow-SIMD', '9.2.0'), + ('PyYAML', '6.0'), + ('typing-extensions', '4.3.0'), + ('boto3', '1.26.37'), +] + +use_pip = True + +exts_list = [ + ('monotonic', '1.6', { + 'checksums': ['3a55207bcfed53ddd5c5bae174524062935efed17792e9de2ad0205ce9ad63f7'], + }), + ('swagger-spec-validator', '3.0.3', { + 'checksums': ['16a5ce08c772824a77b1a4a05efc047d72eef1ed53fb969dfe0a18f437ac30a8'], + }), + ('jsonref', '0.2', { + 'checksums': ['f3c45b121cf6257eafabdc3a8008763aed1cd7da06dbabc59a9e4d2a5e4e6697'], + }), + ('bravado-core', '5.17.1', { + 'checksums': ['0da9c6f3814734622a55db3f62d08db6e188b25f3ebd087de370c91afb66a7f4'], + }), + ('bravado', '11.0.3', { + 'checksums': ['1bb6ef75d84140c851fffe6420baaee5037d840070cfe11d60913be6ab8e0530'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), + ('blinker', '1.5', { + 'checksums': ['923e5e2f69c155f2cc42dafbbd70e16e3fde24d2d4aa2ab72fbe386238892462'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + (name, version, { + 'modulename': 'neptune', + 'checksums': ['7e5e0261f3ce486f45e3272c5b5e3d563f0765a921bcda159b002e70175a553b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 0cbdb3652d50d59b2e3a55979238a225c7a29819 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 19:41:03 +0000 Subject: [PATCH 6019/9987] adding easyconfigs: spaCy-3.4.4-foss-2022a.eb --- .../s/spaCy/spaCy-3.4.4-foss-2022a.eb | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb b/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb new file mode 100644 index 00000000000..7b96e506726 --- /dev/null +++ b/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb @@ -0,0 +1,83 @@ +easyblock = 'PythonBundle' + +name = 'spaCy' +version = '3.4.4' + +homepage = 'https://spacy.io/' +description = "Industrial-strength Natural Language Processing (NLP) in Python." + +toolchain = {'name': 'foss', 'version': '2022a'} + +download_dep_fail = True +use_pip = True + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +exts_list = [ + ('spacy-legacy', '3.0.10', { + 'checksums': ['16104595d8ab1b7267f817a449ad1f986eb1f2a2edf1050748f08739a479679a'], + }), + ('spacy-loggers', '1.0.4', { + 'checksums': ['e6f983bf71230091d5bb7b11bf64bd54415eca839108d5f83d9155d0ba93bf28'], + }), + ('cymem', '2.0.7', { + 'checksums': ['e6034badb5dd4e10344211c81f16505a55553a7164adc314c75bd80cf07e57a8'], + }), + ('murmurhash', '1.0.9', { + 'checksums': ['fe7a38cb0d3d87c14ec9dddc4932ffe2dbc77d75469ab80fd5014689b0e07b58'], + }), + ('preshed', '3.0.8', { + 'checksums': ['6c74c70078809bfddda17be96483c41d06d717934b07cab7921011d81758b357'], + }), + ('blis', '0.7.9', { + 'checksums': ['29ef4c25007785a90ffc2f0ab3d3bd3b75cd2d7856a9a482b7d0dac8d511a09d'], + }), + ('confection', '0.0.3', { + 'checksums': ['4fec47190057c43c9acbecb8b1b87a9bf31c469caa0d6888a5b9384432fdba5a'], + }), + ('thinc', '8.1.6', { + 'checksums': ['9241c37761f004fe684e637d2b4d8b79addebabc64e343aa1cba144fad2c9b47'], + }), + ('ml_datasets', '0.2.0', { + 'checksums': ['3f9c8901f8d6be3dab5b23ec3a6c01e619a60d0184696b1030cde2e3086943f1'], + }), + ('wasabi', '0.10.1', { + 'checksums': ['c8e372781be19272942382b14d99314d175518d7822057cb7a97010c4259d249'], + }), + ('srsly', '2.4.5', { + 'checksums': ['c842258967baa527cea9367986e42b8143a1a890e7d4a18d25a36edc3c7a33c7'], + }), + ('catalogue', '2.0.8', { + 'checksums': ['b325c77659208bfb6af1b0d93b1a1aa4112e1bb29a4c5ced816758a722f0e388'], + }), + ('typer', '0.7.0', { + 'checksums': ['ff797846578a9f2a201b53442aedeb543319466870fbe1c701eab66dd7681165'], + }), + ('pathy', '0.10.1', { + 'checksums': ['4cd6e71b4cd5ff875cfbb949ad9fa5519d8d1dbe69d5fc1d1b23aa3cb049618b'], + }), + ('smart-open', '6.3.0', { + 'source_tmpl': 'smart_open-%(version)s.tar.gz', + 'checksums': ['d5238825fe9a9340645fac3d75b287c08fbb99fb2b422477de781c9f5f09e019'], + }), + ('tqdm', '4.64.1', { + 'checksums': ['5f4f682a004951c1b450bc753c710e9280c5746ce6ffedee253ddbcbf54cf1e4'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('langcodes', '3.3.0', { + 'checksums': ['794d07d5a28781231ac335a1561b8442f8648ca07cd518310aeb45d6f0807ef6'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['e500cf2cb5f1849461a7928fa269703756069bdfb71559065240af6d0208b08c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 9fe9691ddf2e25a54e2040000b4f7875062234e4 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 20:59:58 +0000 Subject: [PATCH 6020/9987] Remove `download_dep_fail` --- easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb b/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb index 7b96e506726..80d6185e427 100644 --- a/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb +++ b/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb @@ -8,7 +8,6 @@ description = "Industrial-strength Natural Language Processing (NLP) in Python." toolchain = {'name': 'foss', 'version': '2022a'} -download_dep_fail = True use_pip = True dependencies = [ From 9c112de52e0041ab47ece411eb20f3ac7f43b384 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 21:33:49 +0000 Subject: [PATCH 6021/9987] Remove unneccessary CUDA dependency; use SHLIB_EXT --- easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb index 0d9e772ecb6..0e9191507e1 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb @@ -18,7 +18,6 @@ checksums = [('b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479' 'a63df7d5a680d9641c223ea090ff843a7d6f20bdb62095bd44f3b0480a4706ed')] dependencies = [ - ('CUDA', '11.3.1', '', True), ('Python', '3.9.5'), ('PyTorch', '1.10.0'), ('ITK', '5.2.1'), @@ -39,7 +38,7 @@ sanity_pip_check = True sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/%(namelower)s/_C.so'], + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], 'dirs': [''], } From 391f7e9761d7dec0fecc01f3b7c18166a11ac981 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 21:35:15 +0000 Subject: [PATCH 6022/9987] use SHLIB_EXT in `sanity_check_paths` --- .../easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb index 1315a727642..e1b2fdd1ce1 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb @@ -19,7 +19,7 @@ checksums = [('b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479' 'a63df7d5a680d9641c223ea090ff843a7d6f20bdb62095bd44f3b0480a4706ed')] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('PyTorch', '1.10.0', versionsuffix), ('ITK', '5.2.1'), @@ -40,7 +40,7 @@ sanity_pip_check = True sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/%(namelower)s/_C.so'], + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], 'dirs': [''], } From 722976e5e8ab0ec71cb3d5bb7b5b5728c297f2f7 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 22:47:35 +0000 Subject: [PATCH 6023/9987] Update torchvision to 0.11.3 --- .../easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb index e1b2fdd1ce1..64267d63a4a 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb @@ -26,7 +26,7 @@ dependencies = [ ('NiBabel', '3.2.1'), ('scikit-image', '0.18.3'), ('tensorboard', '2.8.0'), - ('torchvision', '0.11.1', versionsuffix), + ('torchvision', '0.11.3', versionsuffix), ('tqdm', '4.61.2'), ] diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb index 0e9191507e1..2bdc812a6fe 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb @@ -24,7 +24,7 @@ dependencies = [ ('NiBabel', '3.2.1'), ('scikit-image', '0.18.3'), ('tensorboard', '2.8.0'), - ('torchvision', '0.11.1'), + ('torchvision', '0.11.3'), ('tqdm', '4.61.2'), ] From d99b96a9b41961849e2d4c45b1aa2a1ea139a73f Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 28 Dec 2022 11:32:50 +0100 Subject: [PATCH 6024/9987] Update ngtcp2-0.7.0-GCC-11.3.0.eb --- easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb index 75ed02edf9f..f5d87ac788a 100644 --- a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb @@ -1,3 +1,5 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + easyblock = 'CMakeMake' name = 'ngtcp2' From cac1071009c2429c4aef19c0799e25fc2fde7fef Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 28 Dec 2022 11:58:22 +0100 Subject: [PATCH 6025/9987] adding easyconfigs: LHAPDF-6.5.3-gompi-2022a.eb --- .../l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb new file mode 100644 index 00000000000..3794712a7e5 --- /dev/null +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'LHAPDF' +version = '6.5.3' + +homepage = 'http://lhapdf.hepforge.org/' +description = """ +Les Houches Parton Density Function unified library + +First you need to adjust by `export LHAPDF_DATA_PATH=/local/.../path/` to your. +Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +# TODO +#toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hepforge.org/archive/lhapdf/'] +sources = [SOURCE_TAR_GZ] +checksums = ['57435cd695e297065d53e69bd29090765c934936b6a975ff8c559766f2230359'] + +dependencies = [ + ('Python', '3.10.4'), + ('Boost', '1.79.0') +] + +configopts = "--disable-static --enable-python" + +sanity_check_paths = { + 'files': ["lib/libLHAPDF.so",'bin/lhapdf-config'], + 'dirs': ["lib","share/LHAPDF"], +} + +sanity_check_commands = ["python -c 'import lhapdf'"] +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'phys' From 0ad429b4a9fb49bb037fe883b5e3c78c4e219272 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 28 Dec 2022 12:08:14 +0100 Subject: [PATCH 6026/9987] Remove TODO and add toolchainopts --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index 3794712a7e5..5fee37a6ace 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -15,8 +15,7 @@ Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. """ toolchain = {'name': 'gompi', 'version': '2022a'} -# TODO -#toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://www.hepforge.org/archive/lhapdf/'] sources = [SOURCE_TAR_GZ] From 0dc4bdff01683c75da391f8cb9dcfa7787fa829a Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 28 Dec 2022 12:20:35 +0000 Subject: [PATCH 6027/9987] Switch to `versionsuffix` for CUDA dependencies --- .../Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb | 2 +- .../easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb index b66cbc3dfe8..b4b6d0f7b61 100644 --- a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb @@ -16,7 +16,7 @@ dependencies = [ ('PyYAML', '6.0'), ('scikit-image', '0.19.3'), ('scikit-learn', '1.1.2'), - ('OpenCV', '4.6.0', '-CUDA-%(cudaver)s' + '-contrib'), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), ('imgaug', '0.4.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb index 44e5f993163..565a626ba4f 100644 --- a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('Pillow', '9.1.1'), ('matplotlib', '3.5.2'), ('scikit-image', '0.19.3'), - ('OpenCV', '4.6.0', '-CUDA-%(cudaver)s' + '-contrib'), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), ('Shapely', '1.8.2'), ('imageio', '2.22.2'), ] From 5dc16b7067cd06de87114439dbfc171600d35897 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 28 Dec 2022 14:23:46 +0100 Subject: [PATCH 6028/9987] Update Cantera-2.6.0-foss-2022a-Python-3.10.4.eb --- .../c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb index 607648036f0..0f2cbfc44ef 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb @@ -29,9 +29,9 @@ builddependencies = [ ] local_common_opts = 'env_vars=all CC="$CC" CXX="$CXX" cc_flags="$CFLAGS" cxx_flags="$CXXFLAGS" ' -#local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR ' -#local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' -#local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=${EBROOTFLEXIBLAS}/lib' +# local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR ' +# local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' +# local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=${EBROOTFLEXIBLAS}/lib' buildopts = 'build ' + local_common_opts # tests hang, so disable them for now # runtest = 'test ' + local_common_opts From 33cc1ff434e303cb9cd0de80b987b312c6796f4f Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 28 Dec 2022 14:45:37 +0100 Subject: [PATCH 6029/9987] Update Cantera-2.6.0-foss-2022a-Python-3.10.4.eb --- .../c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb index 0f2cbfc44ef..bb14dcff6b1 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb @@ -2,7 +2,6 @@ easyblock = 'SCons' name = 'Cantera' version = '2.6.0' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/Cantera/cantera' description = """Chemical kinetics, thermodynamics, and transport tool suite""" From dc70dfb27367d78d752a1313cec4de67797dcef8 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 28 Dec 2022 15:12:36 +0100 Subject: [PATCH 6030/9987] Rename Cantera-2.6.0-foss-2022a-Python-3.10.4.eb to Cantera-2.6.0-foss-2022a.eb --- ....0-foss-2022a-Python-3.10.4.eb => Cantera-2.6.0-foss-2022a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/Cantera/{Cantera-2.6.0-foss-2022a-Python-3.10.4.eb => Cantera-2.6.0-foss-2022a.eb} (100%) diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb similarity index 100% rename from easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a-Python-3.10.4.eb rename to easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb From c2507741a6c9e9cdda9316b577ec52839044a019 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 28 Dec 2022 15:45:46 +0000 Subject: [PATCH 6031/9987] Toolchain changed to GCC --- ...mint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb new file mode 100644 index 00000000000..a64ba46e911 --- /dev/null +++ b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb @@ -0,0 +1,54 @@ +# For the various build options see here: +# https://www.bennyp.org/research/simint/README.txt +# lmax is set to 5 which is widely used it seems +# vec is set to avx, which should work on most platforms +# This might be changed to other values, if required +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'simint' +version = '0.7' +local_lmax = '5' +# supported: {scalar, sse, avx, avxfma, micavx512} +# scalar ONLY FOR USE WITH simint-scalar (and only useful for benchmarks), micavx512 experimental! +local_vec = 'avx' + +# custom configuration, to be used as dependency for PSI4 +versionsuffix = '-lmax-%s-vec-%s-psi4' % (local_lmax, local_vec) + +homepage = 'https://www.bennyp.org/research/simint/' +description = """Simint is a vectorized implementation of the Obara-Saika (OS) +method of calculating electron repulsion integrals. Speedup is gained by +vectorizing the primitive loop of the OS algorithm, with additional vectorization +and optimizations left to the compiler.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://www.bennyp.org/research/simint/download/'] +sources = ['%(name)s-v%(version)s.tar.bz2'] +checksums = ['9851fa2323924d4732dd611b366219f4408c8561556abb5e4fa6dbb64a8f919c'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37'), +] + +local_common_configopts = '-DSIMINT_MAXAM=%s ' % local_lmax +local_common_configopts += '-DSIMINT_VECTOR=%s ' % local_vec +local_common_configopts += '-DENABLE_TESTS=ON ' +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# run test to valicate accuracy +runtest = 'OMP_NUM_THREADS=4 test/test_eri ../%(name)s-v%(version)s/test/dat/' + +sanity_check_paths = { + 'files': ['lib/libsimint.a', 'lib/libsimint.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'chem' From aac090752780821eee1dd8e74a7045eb63535fb9 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 28 Dec 2022 15:54:05 +0000 Subject: [PATCH 6032/9987] Addition to PR #16892 : Sanity check command added --- easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb index df8ae82f892..96534b54093 100644 --- a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb @@ -18,6 +18,8 @@ builddependencies = [ ('CMake', '3.22.1'), ] +sanity_check_commands = ['mstore-fortranize --help'] + sanity_check_paths = { 'files': ['bin/mstore-info', 'bin/mstore-fortranize', 'bin/mctc-convert'], 'dirs': ['include/mstore', 'lib/pkgconfig', 'share'], From 9f88bf94a255add0e2fe3e75bd6d86cda9668505 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 28 Dec 2022 16:34:12 +0000 Subject: [PATCH 6033/9987] adding easyconfigs: MATLAB-2022b.eb --- .../easyconfigs/m/MATLAB/MATLAB-2022b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2022b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b.eb new file mode 100644 index 00000000000..0fce2dcfb9b --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b.eb @@ -0,0 +1,26 @@ +name = 'MATLAB' +version = '2022b' + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +sources = ['R%(version)s_Linux.iso'] +checksums = ['46ae2e0a8cf2806b361215ab0f4d60de53d77093f268f252763f53fe76515788'] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server_port = 'XXXXX' + +moduleclass = 'math' From 356788dd5a14e2c601f82673037dd755fc2c3837 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 29 Dec 2022 09:17:17 +0100 Subject: [PATCH 6034/9987] remove zstd dep (already included in GnuTLS) --- .../g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb index cb7dd92d43c..89649bba2dd 100644 --- a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb @@ -23,7 +23,6 @@ dependencies = [ ('GLib', '2.72.1'), ('GnuTLS', '3.7.8'), ('libidn2', '2.3.2'), - ('zstd', '1.5.2'), ] sanity_check_paths = { From 7789c0c7bea21cbed749bb7db3a1858393d30706 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Fri, 30 Dec 2022 12:24:47 +0000 Subject: [PATCH 6035/9987] Added a bunch of dependencies and a fastai CUDA version --- .../fastai-2.7.10-foss-2022a-CUDA-11.7.0.eb | 110 ++++++++++++++++++ .../f/fastai/fastai-2.7.10-foss-2022a.eb | 108 +++++++++++++++++ 2 files changed, 218 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a.eb diff --git a/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..526c14cba94 --- /dev/null +++ b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,110 @@ +easyblock = 'PythonBundle' + +name = 'fastai' +version = '2.7.10' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.fast.ai/' +description = """The fastai deep learning library.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('PyTorch-Lightning', '1.8.4', versionsuffix), + ('torchvision', '0.13.1', versionsuffix), + ('matplotlib', '3.5.2'), + ('SciPy-bundle', '2022.05'), + ('spaCy', '3.4.4'), + ('PyYAML', '6.0'), + ('Pillow', '9.1.1'), + ('scikit-learn', '1.1.2'), + ('Transformers', '4.24.0'), + ('SentencePiece', '0.1.97'), + ('tensorboard', '2.10.0'), + ('pydicom', '2.3.0'), + ('Flask', '2.2.2'), + ('captum', '0.5.0', versionsuffix), + ('wandb', '0.13.6'), + ('scikit-image', '0.19.3'), + ('Albumentations', '1.3.0', versionsuffix), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), + ('Arrow', '8.0.0'), + ('Ninja', '1.10.2'), +] + +exts_list = [ + ('fastdownload', '0.0.7', { + 'checksums': ['20507edb8e89406a1fbd7775e6e2a3d81a4dd633dd506b0e9cf0e1613e831d6a'], + }), + ('fastcore', '1.5.27', { + 'checksums': ['c6b66b35569d17251e25999bafc7d9bcdd6446c1e710503c08670c3ff1eef271'], + }), + ('fastprogress', '1.0.3', { + 'checksums': ['7a17d2b438890f838c048eefce32c4ded47197ecc8ea042cecc33d3deb8022f5'], + }), + ('pytorch-ignite', '0.4.10', { + 'modulename': 'ignite', + 'checksums': ['b56609774ada5a140da3975b6bee9fdce234b1db74567f7cffce0020ff8aa7ad'], + }), + ('hydra-slayer', '0.4.0', { + 'checksums': ['2e7ef0b99e5e11504d80996f689ed5ed7ae8766edb8e76b6933b306966159604'], + }), + ('catalyst', '22.04', { + 'source_urls': ['https://github.com/%(name)s-team/%(name)s/archive/refs/tags'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['3d00a21b3a3180e7350a89d43530c4ad84db97a6ff00fbb4f48f0540621edaf1'], + }), + ('Brotli', '1.0.9', { + 'modulename': 'brotli', + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['4d1b810aa0ed773f81dceda2cc7b403d01057458730e309856356d4ef4188438'], + }), + ('Flask-Compress', '1.13', { + 'checksums': ['ee96f18bf9b00f2deb4e3406ca4a05093aa80e2ef0578525a3b4d32ecdff129d'], + }), + ('kornia', '0.6.9', { + 'checksums': ['b756bba0db8d47046417fa72271b2d648c570ec6f1d61e1805e6a36911f63bb9'], + }), + ('dulwich', '0.20.50', { + 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], + }), + ('everett', '3.1.0', { + 'checksums': ['46175da5bcb06c193aa129e59714bca981344ff067c3a8bc2e625bc0b3dc01f6'], + }), + ('wurlitzer', '3.0.3', { + 'checksums': ['224f5fe70618be3872c05dfddc8c457191ec1870654596279fcc1edadebe3e5b'], + }), + ('websocket-client', '1.3.3', { + 'modulename': 'websocket', + 'checksums': ['d58c5f284d6a9bf8379dab423259fe8f85b70d5fa5d2916d5791a84594b122b1'], + }), + ('configobj', '5.0.6', { + 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], + }), + ('comet_ml', '3.31.21', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['e7857d5dacc432758110f5201ca7ecc5a480e93f4685494fdedfe665a068ff07'], + }), + ('fsspec', '2022.7.1', { + 'checksums': ['7f9fb19d811b027b97c4636c6073eb53bc4cbee2d3c4b33fa88b9f26906fd7d7'], + }), + ('timm', '0.6.12', { + 'checksums': ['8f1747121598e06a1ea2d00df16d332cc284cdd4596bdc136b490a2122d3aa91'], + }), + ('accelerate', '0.15.0', { + 'checksums': ['438e25a01afa6e3ffbd25353e76a68be49677c3050f10bfac7beafaf53503efc'], + }), + (name, version, { + 'checksums': ['ccef6a185ae3a637efc9bcd9fea8e48b75f454d0ebad3b6df426f22fae20039d'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a.eb b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a.eb new file mode 100644 index 00000000000..629daf7740a --- /dev/null +++ b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a.eb @@ -0,0 +1,108 @@ +easyblock = 'PythonBundle' + +name = 'fastai' +version = '2.7.10' + +homepage = 'https://www.fast.ai/' +description = """The fastai deep learning library.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('PyTorch-Lightning', '1.8.4'), + ('torchvision', '0.13.1'), + ('matplotlib', '3.5.2'), + ('SciPy-bundle', '2022.05'), + ('spaCy', '3.4.4'), + ('PyYAML', '6.0'), + ('Pillow', '9.1.1'), + ('scikit-learn', '1.1.2'), + ('Transformers', '4.24.0'), + ('SentencePiece', '0.1.97'), + ('tensorboard', '2.10.0'), + ('pydicom', '2.3.0'), + ('Flask', '2.2.2'), + ('captum', '0.5.0'), + ('wandb', '0.13.6'), + ('scikit-image', '0.19.3'), + ('Albumentations', '1.3.0'), + ('OpenCV', '4.6.0', '-contrib'), + ('Arrow', '8.0.0'), + ('Ninja', '1.10.2'), +] + +exts_list = [ + ('fastdownload', '0.0.7', { + 'checksums': ['20507edb8e89406a1fbd7775e6e2a3d81a4dd633dd506b0e9cf0e1613e831d6a'], + }), + ('fastcore', '1.5.27', { + 'checksums': ['c6b66b35569d17251e25999bafc7d9bcdd6446c1e710503c08670c3ff1eef271'], + }), + ('fastprogress', '1.0.3', { + 'checksums': ['7a17d2b438890f838c048eefce32c4ded47197ecc8ea042cecc33d3deb8022f5'], + }), + ('pytorch-ignite', '0.4.10', { + 'modulename': 'ignite', + 'checksums': ['b56609774ada5a140da3975b6bee9fdce234b1db74567f7cffce0020ff8aa7ad'], + }), + ('hydra-slayer', '0.4.0', { + 'checksums': ['2e7ef0b99e5e11504d80996f689ed5ed7ae8766edb8e76b6933b306966159604'], + }), + ('catalyst', '22.04', { + 'source_urls': ['https://github.com/%(name)s-team/%(name)s/archive/refs/tags'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['3d00a21b3a3180e7350a89d43530c4ad84db97a6ff00fbb4f48f0540621edaf1'], + }), + ('Brotli', '1.0.9', { + 'modulename': 'brotli', + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['4d1b810aa0ed773f81dceda2cc7b403d01057458730e309856356d4ef4188438'], + }), + ('Flask-Compress', '1.13', { + 'checksums': ['ee96f18bf9b00f2deb4e3406ca4a05093aa80e2ef0578525a3b4d32ecdff129d'], + }), + ('kornia', '0.6.9', { + 'checksums': ['b756bba0db8d47046417fa72271b2d648c570ec6f1d61e1805e6a36911f63bb9'], + }), + ('dulwich', '0.20.50', { + 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], + }), + ('everett', '3.1.0', { + 'checksums': ['46175da5bcb06c193aa129e59714bca981344ff067c3a8bc2e625bc0b3dc01f6'], + }), + ('wurlitzer', '3.0.3', { + 'checksums': ['224f5fe70618be3872c05dfddc8c457191ec1870654596279fcc1edadebe3e5b'], + }), + ('websocket-client', '1.3.3', { + 'modulename': 'websocket', + 'checksums': ['d58c5f284d6a9bf8379dab423259fe8f85b70d5fa5d2916d5791a84594b122b1'], + }), + ('configobj', '5.0.6', { + 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], + }), + ('comet_ml', '3.31.21', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['e7857d5dacc432758110f5201ca7ecc5a480e93f4685494fdedfe665a068ff07'], + }), + ('fsspec', '2022.7.1', { + 'checksums': ['7f9fb19d811b027b97c4636c6073eb53bc4cbee2d3c4b33fa88b9f26906fd7d7'], + }), + ('timm', '0.6.12', { + 'checksums': ['8f1747121598e06a1ea2d00df16d332cc284cdd4596bdc136b490a2122d3aa91'], + }), + ('accelerate', '0.15.0', { + 'checksums': ['438e25a01afa6e3ffbd25353e76a68be49677c3050f10bfac7beafaf53503efc'], + }), + (name, version, { + 'checksums': ['ccef6a185ae3a637efc9bcd9fea8e48b75f454d0ebad3b6df426f22fae20039d'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 35fb5b91d944ea9dc84290bf87b1622ff0cc7631 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Fri, 30 Dec 2022 12:27:17 +0000 Subject: [PATCH 6036/9987] Remove GCCcore/11.3.0 version in favour of foss/2022a --- .../f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb deleted file mode 100644 index 6885b7f44e8..00000000000 --- a/easybuild/easyconfigs/f/fastai/fastai-2.7.10-GCCcore-11.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'fastai' -version = '2.7.10' - -homepage = 'https://www.fast.ai/' -description = """The fastai deep learning library.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['ccef6a185ae3a637efc9bcd9fea8e48b75f454d0ebad3b6df426f22fae20039d'] - -download_dep_fail = True -use_pip = True - -builddependencies = [('binutils', '2.38')] -multi_deps = {'Python': ['3.10.4']} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -sanity_pip_check = True - -moduleclass = 'lib' From 6c51b07d87323bfa10b008dc95f3a3eb426be7de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 15:51:54 +0100 Subject: [PATCH 6037/9987] use single sed command to fiddle with infercnvpy's pyproject.toml + fix unrolled preinstallopts --- .../i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb index afaff507ff2..3ccfde57c1c 100644 --- a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb @@ -19,9 +19,9 @@ use_pip = True # avoid hatcling requirement to install infercnvpy # (since installing it introduces conflicting version requirements with poetry included with Python) -local_preinstallopts = """sed -i 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' pyproject.toml && """ -local_preinstallopts += """sed -i 's/^requires = .*/requires = ["setuptools"]/g' pyproject.toml && """ -local_preinstallopts += """sed -i 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ +local_preinstallopts = """sed -e -i 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ +local_preinstallopts += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ +local_preinstallopts += """-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ exts_list = [ ('setuptools', '65.6.0', { @@ -37,7 +37,7 @@ exts_list = [ 'checksums': ['5f4f682a004951c1b450bc753c710e9280c5746ce6ffedee253ddbcbf54cf1e4'], }), (name, version, { - 'preinstallopts': """sed -i 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' pyproject.toml && sed -i 's/^requires = .*/requires = ["setuptools"]/g' pyproject.toml && sed -i 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """, + 'preinstallopts': local_preinstallopts, 'checksums': ['00b8d78726db0a70bdb4d887fd503a484873244a60b9f58a0979aa75ba6e48cb'], }), ] From 3c671c26fa12d4691d24d72cd49d730b5d2bf8d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 16:20:11 +0100 Subject: [PATCH 6038/9987] fix checksums in easyconfig for OpenFOAM v10 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb index ac915d6fce3..7fafa63937c 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb @@ -13,9 +13,8 @@ source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] patches = ['OpenFOAM-%(version)s-ThirdParty.patch'] checksums = [ - '59d712ba798ca44b989b6ac50bcb7c534eeccb82bcf961e10ec19fc8d84000cf', # version-10.tar.gz - '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43', # OpenFOAM-10-ThirdParty.patch - '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch + {'version-10.tar.gz': '59d712ba798ca44b989b6ac50bcb7c534eeccb82bcf961e10ec19fc8d84000cf'}, + {'OpenFOAM-10-ThirdParty.patch': '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43'}, ] builddependencies = [ From 031e96b0691457b898c26a51d555ab33b11259a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 16:29:10 +0100 Subject: [PATCH 6039/9987] stick to scanpy 1.8.2 as dependency for infercnvpy --- .../easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb index 6ef3d046708..574df806cf5 100644 --- a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb @@ -12,7 +12,7 @@ dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), ('leidenalg', '0.8.8'), - ('scanpy', '1.9.1'), + ('scanpy', '1.8.2'), ] use_pip = True From b4c68edddf12808ddd09e8c4469434559ea2a11e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 16:50:57 +0100 Subject: [PATCH 6040/9987] adding easyconfigs: SELFIES-2.1.1-GCC-11.2.0.eb --- .../s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..adcde874baa --- /dev/null +++ b/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'SELFIES' +version = '2.1.1' + +homepage = 'https://github.com/aspuru-guzik-group/selfies' +description = "Robust representation of semantically constrained graphs, in particular for molecules in chemistry" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +sources = [SOURCELOWER_TAR_GZ] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'chem' From 28d9815464c1185044f86e35f857e1bd7b9548d4 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 17:00:11 +0100 Subject: [PATCH 6041/9987] Update easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index 5fee37a6ace..1aafeabaa42 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -22,8 +22,8 @@ sources = [SOURCE_TAR_GZ] checksums = ['57435cd695e297065d53e69bd29090765c934936b6a975ff8c559766f2230359'] dependencies = [ - ('Python', '3.10.4'), - ('Boost', '1.79.0') + ('Python', '3.10.4'), + ('Boost', '1.79.0'), ] configopts = "--disable-static --enable-python" From 7e70179c870524744e67eac891244507b45982f1 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 17:00:32 +0100 Subject: [PATCH 6042/9987] Update easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index 1aafeabaa42..64e5f06400d 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -29,8 +29,8 @@ dependencies = [ configopts = "--disable-static --enable-python" sanity_check_paths = { - 'files': ["lib/libLHAPDF.so",'bin/lhapdf-config'], - 'dirs': ["lib","share/LHAPDF"], + 'files': ["bin/lhapdf", "bin/lhapdf-config", "lib/libLHAPDF.%s" % SHLIB_EXT], + 'dirs': ["share/LHAPDF"], } sanity_check_commands = ["python -c 'import lhapdf'"] From cf183f9646d554a14af9a4a3d85c5eb944fc521e Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 17:01:26 +0100 Subject: [PATCH 6043/9987] Update easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index 64e5f06400d..97d5f88e632 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -33,7 +33,12 @@ sanity_check_paths = { 'dirs': ["share/LHAPDF"], } -sanity_check_commands = ["python -c 'import lhapdf'"] +sanity_check_commands = [ + "lhapd --version", + "lhapd-config --version", + "python -c 'import lhapdf'", +] + modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} moduleclass = 'phys' From ad71a3cd0683e66b43185e093996bba644549252 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 17:02:52 +0100 Subject: [PATCH 6044/9987] Update LHAPDF-6.5.3-gompi-2022a.eb --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index 97d5f88e632..ba4620d2670 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -34,8 +34,8 @@ sanity_check_paths = { } sanity_check_commands = [ - "lhapd --version", - "lhapd-config --version", + "lhapdf --version", + "lhapdf-config --version", "python -c 'import lhapdf'", ] From 6bef77404be851710c22b83e3c5c98323a80c880 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 17:10:26 +0100 Subject: [PATCH 6045/9987] add missing checksum in SELFIES easyconfig --- easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb index adcde874baa..81faead483e 100644 --- a/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb @@ -13,6 +13,7 @@ dependencies = [ ] sources = [SOURCELOWER_TAR_GZ] +checksums = ['d8066b47e746a6ca5111143e5365ffebbb56b0b244328a61dd4e344d0125f84b'] download_dep_fail = True use_pip = True From e3ab068a3e3b7486dabc511a0fbfcbab0f0f214a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 17:16:01 +0100 Subject: [PATCH 6046/9987] add session-info as extension to easyconfig for infercnvpy 0.4.0, since it's required --- .../easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb index 574df806cf5..dd0a59c97cb 100644 --- a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb @@ -36,6 +36,9 @@ exts_list = [ ('tqdm', '4.64.1', { 'checksums': ['5f4f682a004951c1b450bc753c710e9280c5746ce6ffedee253ddbcbf54cf1e4'], }), + ('session_info', '1.0.0', { + 'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'], + }), (name, version, { 'preinstallopts': local_preinstallopts, 'checksums': ['00b8d78726db0a70bdb4d887fd503a484873244a60b9f58a0979aa75ba6e48cb'], From 5ed2f4c964bbd6752ca5040c14c58fca400793ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Mon, 2 Jan 2023 17:30:48 +0100 Subject: [PATCH 6047/9987] Fix hatcling typo in comment --- .../easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb index dd0a59c97cb..469957dab36 100644 --- a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb @@ -17,7 +17,7 @@ dependencies = [ use_pip = True -# avoid hatcling requirement to install infercnvpy +# avoid hatchling requirement to install infercnvpy # (since installing it introduces conflicting version requirements with poetry included with Python) local_preinstallopts = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ local_preinstallopts += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ From c6e49ea5041673b84815d45f90e5fad5990dd539 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 17:37:36 +0100 Subject: [PATCH 6048/9987] Update easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index ba4620d2670..99fd3cdace8 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -31,7 +31,7 @@ configopts = "--disable-static --enable-python" sanity_check_paths = { 'files': ["bin/lhapdf", "bin/lhapdf-config", "lib/libLHAPDF.%s" % SHLIB_EXT], 'dirs': ["share/LHAPDF"], -} +} sanity_check_commands = [ "lhapdf --version", From e0c45cd68d64c55c0eefcd3d6921c80348d29ce8 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Mon, 2 Jan 2023 21:37:43 +0000 Subject: [PATCH 6049/9987] Add `sanity_check_commands` --- .../easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb index b01480119f0..fed7c2635a0 100644 --- a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb @@ -52,7 +52,7 @@ postinstallcmds = [ ] modextrapaths = { - 'TESSDATA_PREFIX': 'tessdata', + 'TESSDATA_PREFIX': 'share/tessdata', } sanity_check_paths = { @@ -60,4 +60,6 @@ sanity_check_paths = { 'dirs': ['share/tessdata', 'include/tesseract'] } +sanity_check_commands = ['tesseract --version', 'tesseract --list-langs'] + moduleclass = 'vis' From fce2cdec0fd2b53667727694d3d95f1b16a37bd8 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 22:41:09 +0100 Subject: [PATCH 6050/9987] add modextravars and modloadmsg --- .../l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..055e2cc78b2 --- /dev/null +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'LHAPDF' +version = '6.5.3' + +homepage = 'http://lhapdf.hepforge.org/' +description = """ +Les Houches Parton Density Function + +LHAPDF is the standard tool for evaluating parton distribution functions (PDFs) in high-energy physics. +""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hepforge.org/archive/lhapdf/'] +sources = [SOURCE_TAR_GZ] +checksums = ['57435cd695e297065d53e69bd29090765c934936b6a975ff8c559766f2230359'] + +dependencies = [ + ('Python', '3.10.4'), +] + +configopts = "--disable-static --enable-python" + +sanity_check_paths = { + 'files': ["bin/lhapdf", "bin/lhapdf-config", "lib/libLHAPDF.%s" % SHLIB_EXT], + 'dirs': ["share/LHAPDF"], +} + +sanity_check_commands = [ + "lhapdf --version", + "lhapdf-config --version", + "python -c 'import lhapdf'", +] + +modloadmsg = """ +To use/install your own PDF data you need to adjust the path `export LHAPDF_DATA_PATH=/local/.../path/`. +Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. +""" + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} +modextravars = { + # 'LHAPDF_DATA_DIR': '/path/to/LHAPDF_DATA_DIR', # please adapt +} + +moduleclass = 'phys' From d2aecb58f7fd2ff3e45875a9fcb6940eb4350635 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 22:58:56 +0100 Subject: [PATCH 6051/9987] Delete LHAPDF-6.5.3-gompi-2022a.eb --- .../l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb deleted file mode 100644 index 99fd3cdace8..00000000000 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ /dev/null @@ -1,44 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Alexander Puck Neuwirth - -easyblock = 'ConfigureMake' - -name = 'LHAPDF' -version = '6.5.3' - -homepage = 'http://lhapdf.hepforge.org/' -description = """ -Les Houches Parton Density Function unified library - -First you need to adjust by `export LHAPDF_DATA_PATH=/local/.../path/` to your. -Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. -""" - -toolchain = {'name': 'gompi', 'version': '2022a'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = ['http://www.hepforge.org/archive/lhapdf/'] -sources = [SOURCE_TAR_GZ] -checksums = ['57435cd695e297065d53e69bd29090765c934936b6a975ff8c559766f2230359'] - -dependencies = [ - ('Python', '3.10.4'), - ('Boost', '1.79.0'), -] - -configopts = "--disable-static --enable-python" - -sanity_check_paths = { - 'files': ["bin/lhapdf", "bin/lhapdf-config", "lib/libLHAPDF.%s" % SHLIB_EXT], - 'dirs': ["share/LHAPDF"], -} - -sanity_check_commands = [ - "lhapdf --version", - "lhapdf-config --version", - "python -c 'import lhapdf'", -] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -moduleclass = 'phys' From 93b07186ca71d0eb09ab1de3c24b7b287b2010e7 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 23:02:49 +0100 Subject: [PATCH 6052/9987] Update LHAPDF-6.5.3-GCC-11.3.0.eb --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb index 055e2cc78b2..cef4199ee7e 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -44,7 +44,7 @@ Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} modextravars = { - # 'LHAPDF_DATA_DIR': '/path/to/LHAPDF_DATA_DIR', # please adapt + # 'LHAPDF_DATA_PATH': '/path/to/share/LHAPDF/', # please adapt } moduleclass = 'phys' From ea52363d55aef472877a05250b64003e388d6ce5 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 23:07:53 +0100 Subject: [PATCH 6053/9987] Update LHAPDF-6.5.3-GCC-11.3.0.eb --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb index cef4199ee7e..e222dd2f113 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -38,7 +38,7 @@ sanity_check_commands = [ ] modloadmsg = """ -To use/install your own PDF data you need to adjust the path `export LHAPDF_DATA_PATH=/local/.../path/`. +To use/install your own PDF data you need to adjust the path `export LHAPDF_DATA_PATH=/local/.../path/:$LHAPDF_DATA_PATH`. Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. """ From 5a9bc1e2fdaf5ed66570a6b4805e0598ab4f3f91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Jan 2023 10:12:04 +0100 Subject: [PATCH 6054/9987] add dependency on UCX-CUDA --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index c649a8f5035..ad434a512db 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -90,6 +90,7 @@ dependencies = [ ('X11', '20210802'), ('CUDA', '11.4.1', '', SYSTEM), ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), + ('UCX-CUDA', '1.11.2', '-CUDA-%(cudaver)s'), ] # Some CUDA tests differs from expected results From 13ffa7c6062b23c6e33affacb779c1a89987661b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Jan 2023 10:12:44 +0100 Subject: [PATCH 6055/9987] switch order of deps to make it identical to non-cuda version --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index ad434a512db..c9fdf6490ce 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -68,8 +68,8 @@ checksums = [ ] builddependencies = [ - ('Bison', '3.7.6'), ('CMake', '3.21.1'), + ('Bison', '3.7.6'), ('flex', '2.6.4'), ('make', '4.3'), ] From 946b38fbed9b5772c72015bf2244f1df7cffc5fc Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Tue, 3 Jan 2023 10:21:02 +0100 Subject: [PATCH 6056/9987] Update easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb index e222dd2f113..e3b5b92532d 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -42,8 +42,8 @@ To use/install your own PDF data you need to adjust the path `export LHAPDF_DATA Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. """ -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} -modextravars = { +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}, # 'LHAPDF_DATA_PATH': '/path/to/share/LHAPDF/', # please adapt } From 0d54dfd986ead170809af2c320c8ffacac587878 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Jan 2023 10:25:50 +0100 Subject: [PATCH 6057/9987] remove redundant curly bracket --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb index e3b5b92532d..b239ef07505 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -43,7 +43,7 @@ Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. """ modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}, + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', # 'LHAPDF_DATA_PATH': '/path/to/share/LHAPDF/', # please adapt } From 0d51bb35897d82cd1da4873d83161be8022f0168 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Jan 2023 10:42:38 +0100 Subject: [PATCH 6058/9987] Shorten line of modloadmsg --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb index b239ef07505..3bcded3044d 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -38,7 +38,8 @@ sanity_check_commands = [ ] modloadmsg = """ -To use/install your own PDF data you need to adjust the path `export LHAPDF_DATA_PATH=/local/.../path/:$LHAPDF_DATA_PATH`. +To use/install your own PDF data, you need to adjust the $LHAPDF_DATA_PATH: +export LHAPDF_DATA_PATH=/local/.../path/:$LHAPDF_DATA_PATH` Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. """ From 1dbe5f41c77050055c109bec42b4b165835f8b2d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 3 Jan 2023 11:47:13 +0100 Subject: [PATCH 6059/9987] adding easyconfigs: UCX-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb and patches: UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch --- ...X-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb | 45 ++++++ ...OCm-1.11.2_fix_hsa+hip_include_paths.patch | 149 ++++++++++++++++++ 2 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb create mode 100644 easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch diff --git a/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb b/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb new file mode 100644 index 00000000000..fda3009ae00 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-ROCm' +version = '1.11.2' +_rocm_version = '4.5.0' +versionsuffix = '-ROCm-%s' % _rocm_version + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX ROCm support. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] +patches = [ + {'name': 'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch', 'alt_location': 'UCX-CUDA'}, + 'UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch', +] +checksums = [ + {'ucx-1.11.2.tar.gz': 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, + {'UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch': + 'a57ce314f90b170bbe6eb98d938b44ca1bb7285dbfc5891bbff56b66009ff9f9'}, +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('UCX', version), + ('ROCm', _rocm_version), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch b/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch new file mode 100644 index 00000000000..a29251bbc50 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch @@ -0,0 +1,149 @@ +Fix hsa and hip include path + +Åke Sandgren, 2023-01-03 +diff -ru ucx-1.11.2.orig/config/m4/rocm.m4 ucx-1.11.2/config/m4/rocm.m4 +--- ucx-1.11.2.orig/config/m4/rocm.m4 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/config/m4/rocm.m4 2023-01-03 09:23:39.310360596 +0100 +@@ -84,9 +84,9 @@ + + rocm_happy=yes + AS_IF([test "x$rocm_happy" = xyes], +- [AC_CHECK_HEADERS([hsa.h], [rocm_happy=yes], [rocm_happy=no])]) ++ [AC_CHECK_HEADERS([hsa/hsa.h], [rocm_happy=yes], [rocm_happy=no])]) + AS_IF([test "x$rocm_happy" = xyes], +- [AC_CHECK_HEADERS([hsa_ext_amd.h], [rocm_happy=yes], [rocm_happy=no])]) ++ [AC_CHECK_HEADERS([hsa/hsa_ext_amd.h], [rocm_happy=yes], [rocm_happy=no])]) + AS_IF([test "x$rocm_happy" = xyes], + [AC_CHECK_LIB([hsa-runtime64], [hsa_init], [rocm_happy=yes], [rocm_happy=no])]) + +@@ -111,7 +111,7 @@ + hip_happy=no + AC_CHECK_LIB([hip_hcc], [hipFree], [AC_MSG_WARN([Please install ROCm-3.7.0 or above])], [hip_happy=yes]) + AS_IF([test "x$hip_happy" = xyes], +- [AC_CHECK_HEADERS([hip_runtime.h], [hip_happy=yes], [hip_happy=no])]) ++ [AC_CHECK_HEADERS([hip/hip_runtime.h], [hip_happy=yes], [hip_happy=no])]) + AS_IF([test "x$hip_happy" = xyes], + [AC_CHECK_LIB([amdhip64], [hipFree], [hip_happy=yes], [hip_happy=no])]) + AS_IF([test "x$hip_happy" = xyes], [HIP_CXXFLAGS="--std=gnu++11"], []) +diff -ru ucx-1.11.2.orig/src/ucm/rocm/rocmmem.h ucx-1.11.2/src/ucm/rocm/rocmmem.h +--- ucx-1.11.2.orig/src/ucm/rocm/rocmmem.h 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/ucm/rocm/rocmmem.h 2023-01-03 09:25:40.289314597 +0100 +@@ -7,7 +7,7 @@ + #define UCM_ROCMMEM_H_ + + #include +-#include ++#include + + /* hsa_amd_memory_pool_allocate */ + hsa_status_t ucm_override_hsa_amd_memory_pool_allocate( +diff -ru ucx-1.11.2.orig/src/uct/rocm/base/rocm_base.h ucx-1.11.2/src/uct/rocm/base/rocm_base.h +--- ucx-1.11.2.orig/src/uct/rocm/base/rocm_base.h 2021-07-10 09:59:16.000000000 +0200 ++++ ucx-1.11.2/src/uct/rocm/base/rocm_base.h 2023-01-03 09:24:10.206096620 +0100 +@@ -9,8 +9,8 @@ + + #include + #include +-#include +-#include ++#include ++#include + + + hsa_status_t uct_rocm_base_init(void); +diff -ru ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_ep.c ucx-1.11.2/src/uct/rocm/copy/rocm_copy_ep.c +--- ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_ep.c 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/src/uct/rocm/copy/rocm_copy_ep.c 2023-01-03 09:25:35.457356174 +0100 +@@ -19,7 +19,7 @@ + #include + #include + +-#include ++#include + + #define uct_rocm_memcpy_h2d(_d,_s,_l) memcpy((_d),(_s),(_l)) + #define uct_rocm_memcpy_d2h(_d,_s,_l) ucs_memcpy_nontemporal((_d),(_s),(_l)) +diff -ru ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_iface.h ucx-1.11.2/src/uct/rocm/copy/rocm_copy_iface.h +--- ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_iface.h 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/uct/rocm/copy/rocm_copy_iface.h 2023-01-03 09:24:33.245895073 +0100 +@@ -8,7 +8,7 @@ + + #include + +-#include ++#include + + #define UCT_ROCM_COPY_TL_NAME "rocm_cpy" + +diff -ru ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_md.c ucx-1.11.2/src/uct/rocm/copy/rocm_copy_md.c +--- ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_md.c 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/src/uct/rocm/copy/rocm_copy_md.c 2023-01-03 09:25:33.073376690 +0100 +@@ -20,7 +20,7 @@ + #include + #include + +-#include ++#include + + static ucs_config_field_t uct_rocm_copy_md_config_table[] = { + {"", "", NULL, +diff -ru ucx-1.11.2.orig/src/uct/rocm/gdr/rocm_gdr_md.c ucx-1.11.2/src/uct/rocm/gdr/rocm_gdr_md.c +--- ucx-1.11.2.orig/src/uct/rocm/gdr/rocm_gdr_md.c 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/src/uct/rocm/gdr/rocm_gdr_md.c 2023-01-03 09:25:37.569338002 +0100 +@@ -18,7 +18,7 @@ + #include + #include + +-#include ++#include + + static ucs_config_field_t uct_rocm_gdr_md_config_table[] = { + {"", "", NULL, +diff -ru ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_iface.h ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_iface.h +--- ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_iface.h 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_iface.h 2023-01-03 09:24:27.741943217 +0100 +@@ -9,7 +9,7 @@ + + #include + +-#include ++#include + + #define UCT_ROCM_IPC_TL_NAME "rocm_ipc" + +diff -ru ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_md.h ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_md.h +--- ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_md.h 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_md.h 2023-01-03 09:25:30.109402193 +0100 +@@ -7,7 +7,7 @@ + #define ROCM_IPC_MD_H + + #include +-#include ++#include + + + extern uct_component_t uct_rocm_ipc_component; +diff -ru ucx-1.11.2.orig/test/gtest/common/mem_buffer.cc ucx-1.11.2/test/gtest/common/mem_buffer.cc +--- ucx-1.11.2.orig/test/gtest/common/mem_buffer.cc 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/test/gtest/common/mem_buffer.cc 2023-01-03 09:32:23.085955061 +0100 +@@ -31,7 +31,7 @@ + #endif + + #if HAVE_ROCM +-# include ++# include + + #define ROCM_CALL(_code) \ + do { \ +diff -ru ucx-1.11.2.orig/test/gtest/ucm/rocm_hooks.cc ucx-1.11.2/test/gtest/ucm/rocm_hooks.cc +--- ucx-1.11.2.orig/test/gtest/ucm/rocm_hooks.cc 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/test/gtest/ucm/rocm_hooks.cc 2023-01-03 09:32:26.177929298 +0100 +@@ -5,7 +5,7 @@ + */ + #include + #include +-#include ++#include + + static ucm_event_t alloc_event, free_event; + From 1d711a273efbda79f36baf1d6053d06c2dbaa96b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 3 Jan 2023 11:49:00 +0100 Subject: [PATCH 6060/9987] Update UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch to fix libs for rocm libs too. --- ...-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb | 8 +-- ....11.0_link_against_existing_UCX_libs.patch | 52 ++++++++++++++----- ...-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb | 8 +-- 3 files changed, 46 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb index ce3211904db..ac5302556e3 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -16,14 +16,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] patches = [ '%(name)s-%(version)s_link_against_existing_UCX_libs.patch', ] checksums = [ - 'b7189b69fe0e16e3c03784ef674e45687a9c520750bd74a45125c460ede37647', # ucx-1.11.0.tar.gz - # UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch - 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3', + {'ucx-1.11.0.tar.gz': 'b7189b69fe0e16e3c03784ef674e45687a9c520750bd74a45125c460ede37647'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch index 765d880238e..5020e1af734 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch @@ -1,9 +1,9 @@ Make CUDA/ROCm plugins link against the existing ucs/ucm/uct libraries. Åke Sandgren, Mikael Öhman 2021-08-09 -diff -ru ucx-1.11.0.orig/configure.ac ucx-1.11.0/configure.ac ---- ucx-1.11.0.orig/configure.ac 2021-06-26 02:05:59.632558898 +0200 -+++ ucx-1.11.0/configure.ac 2021-06-26 02:08:39.330081752 +0200 +diff -ru ucx-1.11.2.orig/configure.ac ucx-1.11.2/configure.ac +--- ucx-1.11.2.orig/configure.ac 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/configure.ac 2023-01-03 10:29:43.816777145 +0100 @@ -29,13 +29,13 @@ AC_GNU_SOURCE AC_CONFIG_HEADERS([config.h]) @@ -25,9 +25,9 @@ diff -ru ucx-1.11.0.orig/configure.ac ucx-1.11.0/configure.ac AH_TOP([ #ifndef UCX_CONFIG_H -diff -ru ucx-1.11.0.orig/src/ucm/cuda/Makefile.am ucx-1.11.0/src/ucm/cuda/Makefile.am ---- ucx-1.11.0.orig/src/ucm/cuda/Makefile.am 2021-08-09 19:14:56.904346018 +0200 -+++ ucx-1.11.0/src/ucm/cuda/Makefile.am 2021-08-09 19:15:22.472286262 +0200 +diff -ru ucx-1.11.2.orig/src/ucm/cuda/Makefile.am ucx-1.11.2/src/ucm/cuda/Makefile.am +--- ucx-1.11.2.orig/src/ucm/cuda/Makefile.am 2021-07-10 09:59:16.000000000 +0200 ++++ ucx-1.11.2/src/ucm/cuda/Makefile.am 2023-01-03 10:29:43.816777145 +0100 @@ -9,7 +9,7 @@ module_LTLIBRARIES = libucm_cuda.la libucm_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) @@ -37,9 +37,21 @@ diff -ru ucx-1.11.0.orig/src/ucm/cuda/Makefile.am ucx-1.11.0/src/ucm/cuda/Makefi libucm_cuda_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ $(patsubst %, -Xlinker %, $(CUDA_LDFLAGS)) \ -version-info $(SOVERSION) -diff -ru ucx-1.11.0.orig/src/uct/cuda/Makefile.am ucx-1.11.0/src/uct/cuda/Makefile.am ---- ucx-1.11.0.orig/src/uct/cuda/gdr_copy/Makefile.am 2021-08-09 19:16:59.146060323 +0200 -+++ ucx-1.11.0/src/uct/cuda/gdr_copy/Makefile.am 2021-08-09 19:17:27.915993083 +0200 +diff -ru ucx-1.11.2.orig/src/ucm/rocm/Makefile.am ucx-1.11.2/src/ucm/rocm/Makefile.am +--- ucx-1.11.2.orig/src/ucm/rocm/Makefile.am 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/ucm/rocm/Makefile.am 2023-01-03 10:32:04.931602717 +0100 +@@ -10,7 +10,7 @@ + module_LTLIBRARIES = libucm_rocm.la + libucm_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libucm_rocm_la_CFLAGS = $(BASE_CFLAGS) $(ROCM_CFLAGS) +-libucm_rocm_la_LIBADD = ../libucm.la ++libucm_rocm_la_LIBADD = -lucm + libucm_rocm_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ +diff -ru ucx-1.11.2.orig/src/uct/cuda/gdr_copy/Makefile.am ucx-1.11.2/src/uct/cuda/gdr_copy/Makefile.am +--- ucx-1.11.2.orig/src/uct/cuda/gdr_copy/Makefile.am 2021-07-10 09:59:16.000000000 +0200 ++++ ucx-1.11.2/src/uct/cuda/gdr_copy/Makefile.am 2023-01-03 10:29:43.816777145 +0100 @@ -10,7 +10,7 @@ libuct_cuda_gdrcopy_la_CFLAGS = $(BASE_CFLAGS) libuct_cuda_gdrcopy_la_LDFLAGS = $(CUDA_LDFLAGS) $(GDR_COPY_LDFLAGS) \ @@ -48,10 +60,10 @@ diff -ru ucx-1.11.0.orig/src/uct/cuda/Makefile.am ucx-1.11.0/src/uct/cuda/Makefi +libuct_cuda_gdrcopy_la_LIBADD = -lucs \ $(top_builddir)/src/uct/cuda/libuct_cuda.la \ $(CUDA_LIBS) - -diff -ru ucx-1.11.0.orig/src/uct/cuda/gdr_copy/Makefile.am ucx-1.11.0/src/uct/cuda/gdr_copy/Makefile.am ---- ucx-1.11.0.orig/src/uct/cuda/Makefile.am 2021-08-09 19:16:06.472183427 +0200 -+++ ucx-1.11.0/src/uct/cuda/Makefile.am 2021-08-09 19:16:38.201109272 +0200 + +diff -ru ucx-1.11.2.orig/src/uct/cuda/Makefile.am ucx-1.11.2/src/uct/cuda/Makefile.am +--- ucx-1.11.2.orig/src/uct/cuda/Makefile.am 2021-07-10 09:59:16.000000000 +0200 ++++ ucx-1.11.2/src/uct/cuda/Makefile.am 2023-01-03 10:29:43.816777145 +0100 @@ -11,8 +11,8 @@ libuct_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) libuct_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) @@ -63,4 +75,16 @@ diff -ru ucx-1.11.0.orig/src/uct/cuda/gdr_copy/Makefile.am ucx-1.11.0/src/uct/cu $(CUDA_LIBS) noinst_HEADERS = \ - +diff -ru ucx-1.11.2.orig/src/uct/rocm/Makefile.am ucx-1.11.2/src/uct/rocm/Makefile.am +--- ucx-1.11.2.orig/src/uct/rocm/Makefile.am 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/uct/rocm/Makefile.am 2023-01-03 10:31:38.195822390 +0100 +@@ -10,8 +10,7 @@ + module_LTLIBRARIES = libuct_rocm.la + libuct_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libuct_rocm_la_CFLAGS = $(BASE_CFLAGS) +-libuct_rocm_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la ++libuct_rocm_la_LIBADD = -lucs -luct + libuct_rocm_la_LDFLAGS = $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ + $(patsubst %, -Xlinker %, --enable-new-dtags) \ diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb index d5f4602d19f..461a01a7509 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -16,14 +16,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] patches = [ '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', ] checksums = [ - 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df', # ucx-1.11.2.tar.gz - # UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch - 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3', + {'ucx-1.11.2.tar.gz': 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, ] builddependencies = [ From ac34c6a4dbca0ee5916375c5e1120f326175d22e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 3 Jan 2023 11:50:07 +0100 Subject: [PATCH 6061/9987] Update checksums for UCX-CUDA-1.12/13 --- .../UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb | 8 ++++---- .../UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb index 0fb175ca066..29b645b0e0a 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -16,14 +16,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] patches = [ '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', ] checksums = [ - '40b447c8e7da94a253f2828001b2d76021eb4ad39647107d433d62d61e18ae8e', # ucx-1.12.1.tar.gz - # UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch - 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3', + {'ucx-1.12.1.tar.gz': '40b447c8e7da94a253f2828001b2d76021eb4ad39647107d433d62d61e18ae8e'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb index 9212315db27..3025ba35f6d 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -16,12 +16,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch'] checksums = [ {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': - 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3'}, + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, ] builddependencies = [ From 09869837ae46ba32c4ae3c53b8748478d30d1673 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 3 Jan 2023 11:53:01 +0100 Subject: [PATCH 6062/9987] adding easyconfigs: OSU-Micro-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb --- ...o-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100755 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb new file mode 100755 index 00000000000..a6b19ada3f2 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.9' +_rocm_version = '4.5.0' +versionsuffix = '-ROCm-%s' % _rocm_version + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] + +dependencies = [ + ('ROCm', _rocm_version), + ('UCX-ROCm', '1.11.2', versionsuffix), +] + +configopts = ' --enable-rocm ' + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] + +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 8df5225052a01d486f9d2dc5e7d117b00442a354 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 3 Jan 2023 13:12:20 +0000 Subject: [PATCH 6063/9987] adding easyconfigs: NanoFilt-2.8.0-foss-2021b.eb --- .../n/NanoFilt/NanoFilt-2.8.0-foss-2021b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100755 easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2021b.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2021b.eb new file mode 100755 index 00000000000..e0392394b13 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2021b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'NanoFilt' +version = '2.8.0' + +homepage = 'https://github.com/wdecoster/nanofilt' +description = """Filtering and trimming of long read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['47f4f4f8be834f011570a8d76d07cc12abe0686c8917607316a8ccfb3e20758c'] + +dependencies = [ + ('Python', '3.9.6'), + ('Biopython', '1.79'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["NanoFilt --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 27844c6d27b1f9e5eb8750323e7445b8c8001478 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 3 Jan 2023 15:35:51 +0100 Subject: [PATCH 6064/9987] Update nghttp2-1.48.0-GCC-11.3.0.eb --- easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb index 9076065af44..b3af8adacf8 100644 --- a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb @@ -1,3 +1,5 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + easyblock = 'CMakeMake' name = 'nghttp2' From 71e297372b214b410aa0dccbb1afa94e378d43fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Jan 2023 15:36:51 +0100 Subject: [PATCH 6065/9987] adding easyconfigs: SNAP-2.0.1-GCC-12.2.0.eb --- .../s/SNAP/SNAP-2.0.1-GCC-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..c7b19e83bc5 --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'SNAP' +version = '2.0.1' + +homepage = 'https://www.microsoft.com/en-us/research/project/snap' +description = """Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for + high-throughput sequencing data""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'cstd': 'c++98'} + +source_urls = ['https://github.com/amplab/snap/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['30f199c583e054c50ca6f3b61f27066640b7c829e5c5e8083841596a2869c064'] + +dependencies = [('zlib', '1.2.12')] + +buildopts = 'CXX="$CXX"' + +files_to_copy = [(['snap-aligner', 'SNAPCommand'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/snap-aligner', 'bin/SNAPCommand'], + 'dirs': [], +} + +sanity_check_commands = ["snap-aligner --help"] + +moduleclass = 'bio' From d72d91f641f3ccc03544d4e5cec2ea16a9296073 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 3 Jan 2023 16:11:49 +0100 Subject: [PATCH 6066/9987] adding easyconfigs: geopandas-0.12.2-foss-2022a.eb, rasterio-1.3.4-foss-2022a.eb, regionmask-0.9.0-foss-2022a.eb --- .../geopandas/geopandas-0.12.2-foss-2022a.eb | 37 +++++++++++++ .../r/rasterio/rasterio-1.3.4-foss-2022a.eb | 54 +++++++++++++++++++ .../regionmask/regionmask-0.9.0-foss-2022a.eb | 34 ++++++++++++ 3 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/rasterio/rasterio-1.3.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb new file mode 100644 index 00000000000..74bbbede7ef --- /dev/null +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'geopandas' +version = '0.12.2' + +homepage = 'https://github.com/geopandas/geopandas' +description = """GeoPandas is a project to add support for geographic data to pandas objects. +It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series +and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and +perform geometric operations.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Shapely', '1.8.2'), + ('Fiona', '1.8.21'), + ('pyproj', '3.4.0'), + ('networkx', '2.8.4'), # needed by mapclassify + ('scikit-learn', '1.1.2'), # needed by mapclassify +] + +use_pip = True + +exts_list = [ + ('mapclassify', '2.4.3', { + 'checksums': ['51b81e1f1ee7f64a4ca1e9f61f01216c364a3f086a48b1be38eb057199cb19bf'], + }), + (name, version, { + 'checksums': ['0acdacddefa176525e4da6d9aeeece225da26055c4becdc6e97cf40fa97c27f4'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rasterio/rasterio-1.3.4-foss-2022a.eb b/easybuild/easyconfigs/r/rasterio/rasterio-1.3.4-foss-2022a.eb new file mode 100644 index 00000000000..563debbbcd1 --- /dev/null +++ b/easybuild/easyconfigs/r/rasterio/rasterio-1.3.4-foss-2022a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'rasterio' +version = '1.3.4' + +homepage = 'https://github.com/mapbox/rasterio' +description = "Rasterio reads and writes geospatial raster data." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('GDAL', '3.5.0'), + ('matplotlib', '3.5.2'), # plot extra + ('boto3', '1.26.37'), # s3 extra +] + +use_pip = True + +exts_list = [ + ('affine', '2.3.1', { + 'checksums': ['d676de66157ad6af99ffd94e0f54e89dfc35b0fb7252ead2ed0ad2dca431bdd0'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('snuggs', '1.4.7', { + 'checksums': ['501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b'], + }), + (name, version, { + 'checksums': ['5a8771405276ecf00b8ee927bd0a81ec21778dcfc97e4a37d0b388f10c9a41a8'], + 'use_pip_extras': 'plot,s3', + }), +] + +fix_python_shebang_for = ['bin/jp.py', 'bin/rio'] + +sanity_check_paths = { + 'files': ['bin/rio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "jp.py --help", + "rio --help", +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2022a.eb b/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2022a.eb new file mode 100644 index 00000000000..6c259ec85aa --- /dev/null +++ b/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'regionmask' +version = '0.9.0' + +homepage = 'https://regionmask.readthedocs.io' +description = """regionmask creates masks of geographical regions. It determines to which +geographic region each grid point belongs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('geopandas', '0.12.2'), + ('rasterio', '1.3.4'), + ('Shapely', '1.8.2'), + ('xarray', '2022.6.0'), +] + +use_pip = True + +exts_list = [ + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + (name, version, { + 'checksums': ['8da1b6359756241867c4e967097810ef86b9dff4e06d11ca648fe1d607e9cf14'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 40ec5004aa135b95302c6b69560c0938e8e50371 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 3 Jan 2023 17:38:17 +0100 Subject: [PATCH 6067/9987] add dependency on matplotlib to geopandas-0.12.2-foss-2022a.eb --- easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb index 74bbbede7ef..ee3dee5c65a 100644 --- a/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb @@ -16,6 +16,7 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('Shapely', '1.8.2'), ('Fiona', '1.8.21'), + ('matplotlib', '3.5.2'), ('pyproj', '3.4.0'), ('networkx', '2.8.4'), # needed by mapclassify ('scikit-learn', '1.1.2'), # needed by mapclassify From d4f326329a84e06bb7a56df508f9cf77fc163ca4 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 3 Jan 2023 18:55:31 +0000 Subject: [PATCH 6068/9987] adding easyconfigs: openslide-python-1.2.0-GCCcore-11.3.0.eb --- .../openslide-python-1.2.0-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/o/openslide-python/openslide-python-1.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1d28069258b --- /dev/null +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'openslide-python' +version = '1.2.0' + +homepage = 'https://github.com/openslide/openslide-python' +description = "OpenSlide Python is a Python interface to the OpenSlide library." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/openslide/openslide-python/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8162829d3d0ea44dd82602ced7390d9b10dd339337a58f17a8eb81a30bc0883b'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('Pillow-SIMD', '9.2.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'openslide'} + +moduleclass = 'vis' From fc4a4294dd69cc808fde4a86af891cc1a7d54216 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 3 Jan 2023 20:54:24 +0000 Subject: [PATCH 6069/9987] adding easyconfigs: dcm2niix-1.0.20220720-GCCcore-11.3.0.eb, CharLS-2.4.1-GCCcore-11.3.0.eb --- .../c/CharLS/CharLS-2.4.1-GCCcore-11.3.0.eb | 30 +++++++++++++++ .../dcm2niix-1.0.20220720-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/c/CharLS/CharLS-2.4.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20220720-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CharLS/CharLS-2.4.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..97a9eec1bdd --- /dev/null +++ b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.1-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CharLS' +version = '2.4.1' + +homepage = 'https://github.com/team-charls/charls' +description = """CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image +compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 +compression ratios.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/team-charls/charls/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f313f556b5acb9215961d9718c21235aafcd43bce6b357bf66f772e5692bba75'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3') +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libcharls.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20220720-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20220720-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0e272245b83 --- /dev/null +++ b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20220720-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'dcm2niix' +version = '1.0.20220720' + +homepage = 'https://github.com/rordenlab/dcm2niix' +description = """dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rordenlab/dcm2niix/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a095545d6d70c5ce2efd90dcd58aebe536f135410c12165a9f231532ddab8991'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('pigz', '2.7'), + ('OpenJPEG', '2.5.0'), + ('CharLS', '2.4.1'), +] + +configopts = '-DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DOpenJPEG_DIR=$EBROOTOPENJPEG ' + +sanity_check_paths = { + 'files': ['bin/dcm2niix'], + 'dirs': [''], +} + +sanity_check_commands = ['dcm2niix -h'] + +moduleclass = 'bio' From ea19013660f6eeddc49b05c19c97aaba6bdb16eb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 4 Jan 2023 08:32:48 +0100 Subject: [PATCH 6070/9987] fix Clang-AOMP/4.5.0 checksums for xxx-rocm-4.5.0.tar.gz --- .../c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb index b679ed3649a..283883c7246 100644 --- a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb @@ -40,7 +40,7 @@ default_component_specs = { components = [ ('llvm-project', 'rocm-4.5.0', { - 'checksums': ['e33d08c8ae42a3ba394dceb8938263cd14ba45e9603b18f3502c3344814ca296'], + 'checksums': ['b71451bf26650ba06c0c5c4c7df70f13975151eaa673ef0cc77c1ab0000ccc97'], }), ('ROCm-Device-Libs', 'rocm-4.5.0', { 'checksums': ['78412fb10ceb215952b5cc722ed08fa82501b5848d599dc00744ae1bdc196f77'], @@ -49,13 +49,13 @@ components = [ # uses same sources as llvm-project component 'sources': ['llvm-project-%(version)s.tar.gz'], 'patches': ['clang-aomp-%(version)s-openmp-remove-hardcoded-source-paths.patch'], - 'checksums': ['e33d08c8ae42a3ba394dceb8938263cd14ba45e9603b18f3502c3344814ca296', + 'checksums': ['b71451bf26650ba06c0c5c4c7df70f13975151eaa673ef0cc77c1ab0000ccc97', 'f959dfa95ec705acf0ffb8d5e85b48cc56e2bed1b15fab22d9eda1f416dd98ca'], }), ('aomp-extras', 'rocm-4.5.0', { 'source_urls': ['https://github.com/ROCm-Developer-Tools/%(name)s/archive/'], 'patches': ['clang-aomp-%(version)s-aomp-extras-remove-hardcoded-devicelib-path.patch'], - 'checksums': ['66d4d0cb4a1a05edb5f13599d8c06de4e10daf561201273cc56dc907139cb894', + 'checksums': ['a9c32fb7659c0aabba5b1e76ec05037dda485bf893cef4144279b42ef8fae416', '1ae5a1af5ccd6c5a77dbc2882d0b40f07d33a7d0021736b29a21e46ab777803a'], }), ] From 15a19e93d784360311cd77e73d813a7eb7f5a649 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2023 09:15:54 +0100 Subject: [PATCH 6071/9987] add ggvenn extension to R 4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 3065e42243c..9fd09b9341e 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3394,6 +3394,9 @@ exts_list = [ ('tidytree', '0.4.1', { 'checksums': ['fbc4364d17e1b1c26ed06af0cdf36c88a5bc562fdbd4731ab179e30bba4009eb'], }), + ('ggvenn', '0.1.9', { + 'checksums': ['38779cfa4e01e07d4a42453cfb8b93d32d2acd6187676bae7d11b2168714a52e'], + }), ] moduleclass = 'lang' From 89c93739881cf6ec2d4a42c1a676da7de985bbeb Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 4 Jan 2023 11:51:51 +0000 Subject: [PATCH 6072/9987] Fix so short test job is running, with all tests jobs are provided as well --- ...mint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb | 28 +++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb index a64ba46e911..73ff6cd6822 100644 --- a/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb +++ b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb @@ -43,8 +43,32 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] -# run test to valicate accuracy -runtest = 'OMP_NUM_THREADS=4 test/test_eri ../%(name)s-v%(version)s/test/dat/' +# Run test to valicate accuracy. +# List of all available tests. Running all of them will take quite some time! +# local_tests = [ +# 'Al2Cl6.6-31gss.mol', 'anthracene.aug-cc-pvqz.mol', 'benzene.aug-cc-pvtz.mol', 'C4H4Cl2F2.dzp.mol', +# 'ethane.roos-ano-tz.mol', 'R-camphor.roos-ano-tz.mol', 'water.sto-3g.mol', 'Al2Cl6.aug-cc-pvqz.mol', +# 'anthracene.aug-cc-pvtz.mol', 'benzene.dzp.mol', 'C4H4Cl2F2.roos-ano-tz.mol', 'ethane.sto-3g.mol', +# 'R-camphor.sto-3g.mol', 'Al2Cl6.aug-cc-pvtz.mol', 'anthracene.dzp.mol', 'benzene.roos-ano-tz.mol', +# 'C4H4Cl2F2.sto-3g.mol', 'water.6-31gss.mol', 'Al2Cl6.dzp.mol', 'anthracene.roos-ano-tz.mol', +# 'benzene.sto-3g.mol', 'ethane.6-31gss.mol', 'R-camphor.6-31gss.mol', 'water.aug-cc-pvqz.mol', +# 'Al2Cl6.roos-ano-tz.mol', 'anthracene.sto-3g.mol', 'C4H4Cl2F2.6-31gss.mol', 'ethane.aug-cc-pvqz.mol', +# 'R-camphor.aug-cc-pvqz.mol', 'water.aug-cc-pvtz.mol', 'Al2Cl6.sto-3g.mol', 'benzene.6-31gss.mol', +# 'C4H4Cl2F2.aug-cc-pvqz.mol', 'ethane.aug-cc-pvtz.mol', 'R-camphor.aug-cc-pvtz.mol water.dzp.mol', +# ] + +# This runs fast but does not give any guarantee if the installation is numerically correct! +local_tests = ['ethane.sto-3g.mol'] + +# Run selected tests: +sanity_check_commands = [ + 'cd %%(builddir)s/easybuild_obj/ && ' + 'OMP_NUM_THREADS=4 test/test_eri ../%%(name)s-v%%(version)s/test/dat/%s' % x for x in local_tests +] + +postinstallcmds = [ + "echo 'Please check the testjob manually to see if there are any errors'", +] sanity_check_paths = { 'files': ['lib/libsimint.a', 'lib/libsimint.%s' % SHLIB_EXT], From 7ac9c2a80673440e62773d3364f791dd6277bd8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2023 13:56:42 +0100 Subject: [PATCH 6073/9987] remove simint easyconfig using GCCcore/11.2.0 toolchain (since there's one using GCC/11.2.0) --- ...-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb | 54 ------------------- 1 file changed, 54 deletions(-) delete mode 100644 easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb deleted file mode 100644 index 6198188f68f..00000000000 --- a/easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb +++ /dev/null @@ -1,54 +0,0 @@ -# For the various build options see here: -# https://www.bennyp.org/research/simint/README.txt -# lmax is set to 5 which is widely used it seems -# vec is set to avx, which should work on most platforms -# This might be changed to other values, if required -# J. Sassmannshausen (Imperial College London/UK) - -easyblock = 'CMakeMake' - -name = 'simint' -version = '0.7' -local_lmax = '5' -# supported: {scalar, sse, avx, avxfma, micavx512} -# scalar ONLY FOR USE WITH simint-scalar (and only useful for benchmarks), micavx512 experimental! -local_vec = 'avx' - -# custom configuration, to be used as dependency for PSI4 -versionsuffix = '-lmax-%s-vec-%s-psi4' % (local_lmax, local_vec) - -homepage = 'https://www.bennyp.org/research/simint/' -description = """Simint is a vectorized implementation of the Obara-Saika (OS) -method of calculating electron repulsion integrals. Speedup is gained by -vectorizing the primitive loop of the OS algorithm, with additional vectorization -and optimizations left to the compiler.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -source_urls = ['https://www.bennyp.org/research/simint/download/'] -sources = ['%(name)s-v%(version)s.tar.bz2'] -checksums = ['9851fa2323924d4732dd611b366219f4408c8561556abb5e4fa6dbb64a8f919c'] - -builddependencies = [ - ('CMake', '3.22.1'), - ('binutils', '2.37'), -] - -local_common_configopts = '-DSIMINT_MAXAM=%s ' % local_lmax -local_common_configopts += '-DSIMINT_VECTOR=%s ' % local_vec -local_common_configopts += '-DENABLE_TESTS=ON ' -# perform iterative build to get both static and shared libraries -configopts = [ - local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', - local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', -] - -# run test to valicate accuracy -runtest = 'OMP_NUM_THREADS=4 test/test_eri ../%(name)s-v%(version)s/test/dat/' - -sanity_check_paths = { - 'files': ['lib/libsimint.a', 'lib/libsimint.%s' % SHLIB_EXT], - 'dirs': ['include', 'share'], -} - -moduleclass = 'chem' From af73e140a3129e83bde814fa7fdf54dfd295af7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2023 13:57:22 +0100 Subject: [PATCH 6074/9987] tweak post-install msg for simint --- .../s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb index 73ff6cd6822..be3968e7c30 100644 --- a/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb +++ b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb @@ -67,7 +67,7 @@ sanity_check_commands = [ ] postinstallcmds = [ - "echo 'Please check the testjob manually to see if there are any errors'", + "echo 'Please check results of the test(s) run in sanity check command manually to see if there are any errors'", ] sanity_check_paths = { From 7f2634b784cc6db60e4d88a4be2fb000617ddfdf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 4 Jan 2023 14:19:31 +0100 Subject: [PATCH 6075/9987] disable tests --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index c9fdf6490ce..cc2ae4045a4 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -94,7 +94,7 @@ dependencies = [ ] # Some CUDA tests differs from expected results -runtest = True +runtest = False static = False From 162f93bab55114e2145b918b9d7fc94c925bb62c Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 4 Jan 2023 15:19:23 +0100 Subject: [PATCH 6076/9987] updating GUSHR sanity check --- .../g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb | 43 +++++++++++-------- 1 file changed, 26 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb index ff1e41e3dd0..011cee7c5ff 100644 --- a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb @@ -1,39 +1,48 @@ # author: Denis Kristak (INUITS) -easyblock = 'Tarball' +easyblock = "Tarball" -name = 'GUSHR' -version = '2020-09-28' -local_commit = 'ee26d5c' +name = "GUSHR" +version = "2020-09-28" +local_commit = "ee26d5c" -homepage = 'https://github.com/Gaius-Augustus/GUSHR' +homepage = "https://github.com/Gaius-Augustus/GUSHR" description = """ Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation. """ -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {"name": "foss", "version": "2021b"} + +source_urls = [ + "https://github.com/Gaius-Augustus/GUSHR/archive", + "http://bioinf.uni-greifswald.de/bioinf/braker/", +] -source_urls = ['https://github.com/Gaius-Augustus/GUSHR/archive'] sources = [ { - 'download_filename': '%s.tar.gz' % local_commit, - 'filename': SOURCE_TAR_GZ, + "download_filename": "%s.tar.gz" % local_commit, + "filename": SOURCE_TAR_GZ, + }, + { + 'filename': "RNAseq.bam", + 'extract_cmd': 'cp %s %(builddir)s/', } ] checksums = ['81fd9c372a45af1688c2954932f94efc4c637144f874e16be41d1b18936a5303'] dependencies = [ - ('Java', '11', '', SYSTEM), - ('AUGUSTUS', '3.4.0'), - ('GLib', '2.69.1'), + ('Java', '1.8', '', SYSTEM), + ("AUGUSTUS", "3.4.0"), + ("GLib", "2.69.1"), ] sanity_check_paths = { - 'files': ['gushr.py'], - 'dirs': [], + "files": ["gushr.py"], + "dirs": [], } sanity_check_commands = [ - """cd example; ./download_rnaseq.sh ; cd - ; - ./gushr.py -t example/augustus.gtf -b example/RNAseq.bam -g example/genome.fa -o utrs""" + """cp %(builddir)s/RNAseq.bam %(installdir)s/example && + cd %(installdir)s/example && + ../gushr.py -b RNAseq.bam -t augustus.gtf -g genome.fa -o gushr -c 10""" ] -moduleclass = 'bio' +moduleclass = "bio" From a87a5c90aa62e559e0779a69b2be07868e1cd0a2 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 4 Jan 2023 15:38:13 +0100 Subject: [PATCH 6077/9987] updating GUSHR sanity check --- .../g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb index 011cee7c5ff..ee8036b845c 100644 --- a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb @@ -16,7 +16,6 @@ source_urls = [ "https://github.com/Gaius-Augustus/GUSHR/archive", "http://bioinf.uni-greifswald.de/bioinf/braker/", ] - sources = [ { "download_filename": "%s.tar.gz" % local_commit, @@ -27,7 +26,10 @@ sources = [ 'extract_cmd': 'cp %s %(builddir)s/', } ] -checksums = ['81fd9c372a45af1688c2954932f94efc4c637144f874e16be41d1b18936a5303'] +checksums = [ + {'GUSHR-2020-09-28.tar.gz': '81fd9c372a45af1688c2954932f94efc4c637144f874e16be41d1b18936a5303'}, + {'RNAseq.bam': '877072947678b6cfd05a7d1124e2008f88a29d56926d8eefb20ef21c137cf5aa'}, +] dependencies = [ ('Java', '1.8', '', SYSTEM), @@ -39,10 +41,13 @@ sanity_check_paths = { "files": ["gushr.py"], "dirs": [], } + +local_sanity_cmd = "cp %(builddir)s/RNAseq.bam %(installdir)s/example && " +local_sanity_cmd += "cd %(installdir)s/example && " +local_sanity_cmd += "../gushr.py -b RNAseq.bam -t augustus.gtf -g genome.fa -o gushr -c 10 " + sanity_check_commands = [ - """cp %(builddir)s/RNAseq.bam %(installdir)s/example && - cd %(installdir)s/example && - ../gushr.py -b RNAseq.bam -t augustus.gtf -g genome.fa -o gushr -c 10""" + local_sanity_cmd ] moduleclass = "bio" From 195996658f355643623f755a45535942871d27e5 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 4 Jan 2023 16:01:40 +0100 Subject: [PATCH 6078/9987] updating GUSHR sR java version --- easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb index ee8036b845c..85f4058dd59 100644 --- a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb @@ -32,7 +32,7 @@ checksums = [ ] dependencies = [ - ('Java', '1.8', '', SYSTEM), + ('Java', '11', '', SYSTEM), ("AUGUSTUS", "3.4.0"), ("GLib", "2.69.1"), ] From 8447d9e10fb19d09f55aab50262899e3f38a610e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2023 16:16:25 +0100 Subject: [PATCH 6079/9987] adding easyconfigs: KronaTools-2.8.1-GCCcore-11.3.0.eb --- .../KronaTools-2.8.1-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8eb58d4954b --- /dev/null +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# this is a bug fix to make sure the symlinks in bin are not getting destroyed +# by Easybuild when it is tidying up +# This build also links updateTaxonomy.sh and updateAccessions.sh in the bin folder +# so users can install their own Taxonomy database + +easyblock = 'Tarball' + +name = 'KronaTools' +version = '2.8.1' + +homepage = 'https://github.com/marbl/Krona/wiki/KronaTools' +description = """Krona Tools is a set of scripts to create Krona charts from +several Bioinformatics tools as well as from text and XML files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['f3ab44bf172e1f846e8977c7443d2e0c9676b421b26c50e91fa996d70a6bfd10'] + +dependencies = [('Perl', '5.34.1')] + +postinstallcmds = [ + "cd %(installdir)s && ./install.pl --prefix=%(installdir)s;", + "cd %(installdir)s/bin && ln -s ../updateAccessions.sh . && ln -s ../updateTaxonomy.sh .", +] + +sanity_check_paths = { + 'files': ['bin/ktClassifyBLAST', 'bin/ktImportBLAST', 'bin/ktImportTaxonomy', + 'bin/updateAccessions.sh', 'bin/updateTaxonomy.sh'], + 'dirs': ['data', 'img', 'scripts'], +} + +sanity_check_commands = [ + "updateAccessions.sh --help", + "ktImportText", +] + +moduleclass = 'bio' From f723e1f6f06bc365061d7a84f042dee6eda5e156 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 4 Jan 2023 17:00:56 +0100 Subject: [PATCH 6080/9987] revert PLINK back to foss/2022a toolchain --- ...LINK-2.00a3.7-gfbf-2022a.eb => PLINK-2.00a3.7-foss-2022a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/PLINK/{PLINK-2.00a3.7-gfbf-2022a.eb => PLINK-2.00a3.7-foss-2022a.eb} (97%) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2022a.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb similarity index 97% rename from easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2022a.eb rename to easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb index cad2313a3d2..60ba9b0260b 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2022a.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-foss-2022a.eb @@ -8,7 +8,7 @@ description = """PLINK is a free, open-source whole genome association analysis designed to perform a range of basic, large-scale analyses in a computationally efficient manner.""" -toolchain = {'name': 'gfbf', 'version': '2022a'} +toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ From 5c71bb87a57f8a757d9467ac15e6f25b16b34c62 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 4 Jan 2023 18:38:15 +0100 Subject: [PATCH 6081/9987] Fixed raven using highest version on Python found --- easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index ff53344aa8a..ecfc1e3b520 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -18,7 +18,9 @@ builddependencies = [ ] preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && " -configopts = ['-DRAVEN_BUILD_EXE=1 -G Ninja '] +configopts = '-DRAVEN_BUILD_EXE=1 -G Ninja ' +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + dependencies = [ ('Python', '3.9.6'), From 72672d9561b76d27a63f70ef6cb3aca5ed7a5003 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 4 Jan 2023 18:39:18 +0100 Subject: [PATCH 6082/9987] adding easyconfigs: task-spooler-1.0.2-GCCcore-11.3.0.eb --- .../task-spooler-1.0.2-GCCcore-11.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e01e690c0c1 --- /dev/null +++ b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'task-spooler' +version = '1.0.2' + +homepage = 'http://viric.name/soft/ts/' +description = 'task spooler is a Unix batch system where the tasks spooled run one after the other.' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [homepage] +sources = ['ts-%(version)s.tar.gz'] +checksums = ['f73452aed80e2f9a7764883e9353aa7f40e65d3c199ad1f3be60fd58b58eafec'] + +skipsteps = ['configure'] +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/ts'], + 'dirs': [] +} + +sanity_check_commands = ["ts -h"] + +moduleclass = 'tools' \ No newline at end of file From 70f9e74b9770be4e2217039c7e3e48bb274eedf4 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 4 Jan 2023 19:23:44 +0100 Subject: [PATCH 6083/9987] added newline to the EOF --- .../t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb index e01e690c0c1..31d855d4253 100644 --- a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb @@ -22,4 +22,4 @@ sanity_check_paths = { sanity_check_commands = ["ts -h"] -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' From cfa4060742e3309155509593ebe96b4d9d9043d0 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 4 Jan 2023 19:41:42 +0100 Subject: [PATCH 6084/9987] Added binutils as a dependency --- .../t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb index 31d855d4253..22e51f5507e 100644 --- a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb @@ -12,6 +12,10 @@ source_urls = [homepage] sources = ['ts-%(version)s.tar.gz'] checksums = ['f73452aed80e2f9a7764883e9353aa7f40e65d3c199ad1f3be60fd58b58eafec'] +dependencies = { + ('binutils', '2.38'), +} + skipsteps = ['configure'] installopts = 'PREFIX=%(installdir)s' From 34e5626e4e44c1811da3189d835e21234bdf175b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 4 Jan 2023 23:28:00 +0100 Subject: [PATCH 6085/9987] adding easyconfigs: CoSymLib-0.10.9-foss-2022a.eb --- .../c/CoSymLib/CoSymLib-0.10.9-foss-2022a.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/c/CoSymLib/CoSymLib-0.10.9-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CoSymLib/CoSymLib-0.10.9-foss-2022a.eb b/easybuild/easyconfigs/c/CoSymLib/CoSymLib-0.10.9-foss-2022a.eb new file mode 100644 index 00000000000..6daeefb0299 --- /dev/null +++ b/easybuild/easyconfigs/c/CoSymLib/CoSymLib-0.10.9-foss-2022a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'CoSymLib' +version = '0.10.9' + +homepage = 'https://cosymlib.readthedocs.io' +description = """Cosymlib is a python library for computing continuous symmetry & shape measures +(CSMs & CShMs). Although its main aim is to provide simple and ready-to-use +tools for the analysis of the symmetry & shape of molecules, many of the +procedures contained in cosymlib can be easily applied to any finite +geometrical object defined by a set of vertices or a by mass distribution +function.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('PyYAML', '6.0'), +] + +use_pip = True + +# replace hardcoded library sonames for BLAS/LAPACK +_fix_linker_blas = 'sed -i \'s/libraries=.*/libraries=["flexiblas", "gfortran"],/g\' setup.py &&' + +exts_list = [ + ('symgroupy', '0.5.11', { + 'checksums': ['bf59460d29ee707289c859d5e10e3984d3cd0536e5b7b001962f428cb73b3c22'], + 'preinstallopts': _fix_linker_blas, + }), + ('wfnsympy', '0.3.5', { + 'checksums': ['f1bede9d9e4efdc79e2a1a4f62b02bd7758908ce6bf91a2641150e0f65c32a6c'], + 'preinstallopts': _fix_linker_blas, + }), + ('huckelpy', '0.2.3', { + 'checksums': ['25a4309d4997332b1179de93bb5b6437c61f8ba198a9e0bcd3aec28b6cd6ce28'], + }), + ('cosymlib', version, { + 'checksums': ['c3e74aa00570489cac609ce6f274a7b6626141948eb5a261d4b27c4e517cee94'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['cchir', 'cosym', 'esym', 'gsym', 'mosym', 'shape', + 'shape_classic', 'shape_map']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cosym --version"] + +moduleclass = 'chem' From ca0515c3db7128581e25c9fc867fbfafc9769d77 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Thu, 5 Jan 2023 07:34:55 +0000 Subject: [PATCH 6086/9987] adding easyconfigs: GDCM-3.0.20-GCCcore-11.3.0.eb --- .../g/GDCM/GDCM-3.0.20-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDCM/GDCM-3.0.20-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GDCM/GDCM-3.0.20-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.20-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3f7946de5fc --- /dev/null +++ b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.20-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'GDCM' +version = '3.0.20' + +homepage = 'https://sourceforge.net/projects/gdcm' +description = "Grassroots DICOM: Cross-platform DICOM implementation" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['d299731e229fe7595001f17e6b81e6f9a27daac3df7295543753525242cea0b2'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +configopts = "-DGDCM_BUILD_DOCBOOK_MANPAGES=0" + +sanity_check_paths = { + 'files': ['lib/libgdcmCommon.a', 'lib/libgdcmDICT.a'], + 'dirs': ['include/gdcm-%(version_major_minor)s', 'lib/gdcm-%(version_major_minor)s'], +} + +moduleclass = 'tools' From 7bdd9f9313117d7c3fe506607dbe87f46dd6994e Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Thu, 5 Jan 2023 07:50:17 +0000 Subject: [PATCH 6087/9987] Remove fastai `dev_requirements` --- .../fastai-2.7.10-foss-2022a-CUDA-11.7.0.eb | 68 +------------------ .../f/fastai/fastai-2.7.10-foss-2022a.eb | 68 +------------------ 2 files changed, 2 insertions(+), 134 deletions(-) diff --git a/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a-CUDA-11.7.0.eb index 526c14cba94..066ee5baf35 100644 --- a/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a-CUDA-11.7.0.eb @@ -15,26 +15,13 @@ dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), ('Python', '3.10.4'), ('PyTorch', '1.12.0', versionsuffix), - ('PyTorch-Lightning', '1.8.4', versionsuffix), ('torchvision', '0.13.1', versionsuffix), ('matplotlib', '3.5.2'), ('SciPy-bundle', '2022.05'), - ('spaCy', '3.4.4'), ('PyYAML', '6.0'), ('Pillow', '9.1.1'), ('scikit-learn', '1.1.2'), - ('Transformers', '4.24.0'), - ('SentencePiece', '0.1.97'), - ('tensorboard', '2.10.0'), - ('pydicom', '2.3.0'), - ('Flask', '2.2.2'), - ('captum', '0.5.0', versionsuffix), - ('wandb', '0.13.6'), - ('scikit-image', '0.19.3'), - ('Albumentations', '1.3.0', versionsuffix), - ('OpenCV', '4.6.0', versionsuffix + '-contrib'), - ('Arrow', '8.0.0'), - ('Ninja', '1.10.2'), + ('spaCy', '3.4.4'), ] exts_list = [ @@ -47,59 +34,6 @@ exts_list = [ ('fastprogress', '1.0.3', { 'checksums': ['7a17d2b438890f838c048eefce32c4ded47197ecc8ea042cecc33d3deb8022f5'], }), - ('pytorch-ignite', '0.4.10', { - 'modulename': 'ignite', - 'checksums': ['b56609774ada5a140da3975b6bee9fdce234b1db74567f7cffce0020ff8aa7ad'], - }), - ('hydra-slayer', '0.4.0', { - 'checksums': ['2e7ef0b99e5e11504d80996f689ed5ed7ae8766edb8e76b6933b306966159604'], - }), - ('catalyst', '22.04', { - 'source_urls': ['https://github.com/%(name)s-team/%(name)s/archive/refs/tags'], - 'sources': ['v%(version)s.tar.gz'], - 'checksums': ['3d00a21b3a3180e7350a89d43530c4ad84db97a6ff00fbb4f48f0540621edaf1'], - }), - ('Brotli', '1.0.9', { - 'modulename': 'brotli', - 'sources': ['%(name)s-%(version)s.zip'], - 'checksums': ['4d1b810aa0ed773f81dceda2cc7b403d01057458730e309856356d4ef4188438'], - }), - ('Flask-Compress', '1.13', { - 'checksums': ['ee96f18bf9b00f2deb4e3406ca4a05093aa80e2ef0578525a3b4d32ecdff129d'], - }), - ('kornia', '0.6.9', { - 'checksums': ['b756bba0db8d47046417fa72271b2d648c570ec6f1d61e1805e6a36911f63bb9'], - }), - ('dulwich', '0.20.50', { - 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], - }), - ('everett', '3.1.0', { - 'checksums': ['46175da5bcb06c193aa129e59714bca981344ff067c3a8bc2e625bc0b3dc01f6'], - }), - ('wurlitzer', '3.0.3', { - 'checksums': ['224f5fe70618be3872c05dfddc8c457191ec1870654596279fcc1edadebe3e5b'], - }), - ('websocket-client', '1.3.3', { - 'modulename': 'websocket', - 'checksums': ['d58c5f284d6a9bf8379dab423259fe8f85b70d5fa5d2916d5791a84594b122b1'], - }), - ('configobj', '5.0.6', { - 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], - }), - ('comet_ml', '3.31.21', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['e7857d5dacc432758110f5201ca7ecc5a480e93f4685494fdedfe665a068ff07'], - }), - ('fsspec', '2022.7.1', { - 'checksums': ['7f9fb19d811b027b97c4636c6073eb53bc4cbee2d3c4b33fa88b9f26906fd7d7'], - }), - ('timm', '0.6.12', { - 'checksums': ['8f1747121598e06a1ea2d00df16d332cc284cdd4596bdc136b490a2122d3aa91'], - }), - ('accelerate', '0.15.0', { - 'checksums': ['438e25a01afa6e3ffbd25353e76a68be49677c3050f10bfac7beafaf53503efc'], - }), (name, version, { 'checksums': ['ccef6a185ae3a637efc9bcd9fea8e48b75f454d0ebad3b6df426f22fae20039d'], }), diff --git a/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a.eb b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a.eb index 629daf7740a..50b4ecd47fc 100644 --- a/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a.eb +++ b/easybuild/easyconfigs/f/fastai/fastai-2.7.10-foss-2022a.eb @@ -13,26 +13,13 @@ use_pip = True dependencies = [ ('Python', '3.10.4'), ('PyTorch', '1.12.0'), - ('PyTorch-Lightning', '1.8.4'), ('torchvision', '0.13.1'), ('matplotlib', '3.5.2'), ('SciPy-bundle', '2022.05'), - ('spaCy', '3.4.4'), ('PyYAML', '6.0'), ('Pillow', '9.1.1'), ('scikit-learn', '1.1.2'), - ('Transformers', '4.24.0'), - ('SentencePiece', '0.1.97'), - ('tensorboard', '2.10.0'), - ('pydicom', '2.3.0'), - ('Flask', '2.2.2'), - ('captum', '0.5.0'), - ('wandb', '0.13.6'), - ('scikit-image', '0.19.3'), - ('Albumentations', '1.3.0'), - ('OpenCV', '4.6.0', '-contrib'), - ('Arrow', '8.0.0'), - ('Ninja', '1.10.2'), + ('spaCy', '3.4.4'), ] exts_list = [ @@ -45,59 +32,6 @@ exts_list = [ ('fastprogress', '1.0.3', { 'checksums': ['7a17d2b438890f838c048eefce32c4ded47197ecc8ea042cecc33d3deb8022f5'], }), - ('pytorch-ignite', '0.4.10', { - 'modulename': 'ignite', - 'checksums': ['b56609774ada5a140da3975b6bee9fdce234b1db74567f7cffce0020ff8aa7ad'], - }), - ('hydra-slayer', '0.4.0', { - 'checksums': ['2e7ef0b99e5e11504d80996f689ed5ed7ae8766edb8e76b6933b306966159604'], - }), - ('catalyst', '22.04', { - 'source_urls': ['https://github.com/%(name)s-team/%(name)s/archive/refs/tags'], - 'sources': ['v%(version)s.tar.gz'], - 'checksums': ['3d00a21b3a3180e7350a89d43530c4ad84db97a6ff00fbb4f48f0540621edaf1'], - }), - ('Brotli', '1.0.9', { - 'modulename': 'brotli', - 'sources': ['%(name)s-%(version)s.zip'], - 'checksums': ['4d1b810aa0ed773f81dceda2cc7b403d01057458730e309856356d4ef4188438'], - }), - ('Flask-Compress', '1.13', { - 'checksums': ['ee96f18bf9b00f2deb4e3406ca4a05093aa80e2ef0578525a3b4d32ecdff129d'], - }), - ('kornia', '0.6.9', { - 'checksums': ['b756bba0db8d47046417fa72271b2d648c570ec6f1d61e1805e6a36911f63bb9'], - }), - ('dulwich', '0.20.50', { - 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], - }), - ('everett', '3.1.0', { - 'checksums': ['46175da5bcb06c193aa129e59714bca981344ff067c3a8bc2e625bc0b3dc01f6'], - }), - ('wurlitzer', '3.0.3', { - 'checksums': ['224f5fe70618be3872c05dfddc8c457191ec1870654596279fcc1edadebe3e5b'], - }), - ('websocket-client', '1.3.3', { - 'modulename': 'websocket', - 'checksums': ['d58c5f284d6a9bf8379dab423259fe8f85b70d5fa5d2916d5791a84594b122b1'], - }), - ('configobj', '5.0.6', { - 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], - }), - ('comet_ml', '3.31.21', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['e7857d5dacc432758110f5201ca7ecc5a480e93f4685494fdedfe665a068ff07'], - }), - ('fsspec', '2022.7.1', { - 'checksums': ['7f9fb19d811b027b97c4636c6073eb53bc4cbee2d3c4b33fa88b9f26906fd7d7'], - }), - ('timm', '0.6.12', { - 'checksums': ['8f1747121598e06a1ea2d00df16d332cc284cdd4596bdc136b490a2122d3aa91'], - }), - ('accelerate', '0.15.0', { - 'checksums': ['438e25a01afa6e3ffbd25353e76a68be49677c3050f10bfac7beafaf53503efc'], - }), (name, version, { 'checksums': ['ccef6a185ae3a637efc9bcd9fea8e48b75f454d0ebad3b6df426f22fae20039d'], }), From 5f4d34e40afec9bbcb82b828909dfa3614ed004e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Jan 2023 09:14:24 +0100 Subject: [PATCH 6088/9987] update copyright lines for 2023 --- setup.py | 2 +- test/__init__.py | 2 +- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/styletests.py | 2 +- test/easyconfigs/suite.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/setup.py b/setup.py index 6b4971a52b9..3ab99c0cc89 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ ## -# Copyright 2012-2022 Ghent University +# Copyright 2012-2023 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/__init__.py b/test/__init__.py index 461a6de8085..01ba03af458 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -1,5 +1,5 @@ ## -# Copyright 2009-2022 Ghent University +# Copyright 2009-2023 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 63e9464d464..7cbbb83f2ad 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1,5 +1,5 @@ ## -# Copyright 2013-2022 Ghent University +# Copyright 2013-2023 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index 0cbaca89661..e765cdfc3f1 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -1,5 +1,5 @@ ## -# Copyright 2016-2022 Ghent University +# Copyright 2016-2023 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index eae8bd6dbe3..c058d96f0c5 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -1,6 +1,6 @@ #!/usr/bin/python ## -# Copyright 2012-2022 Ghent University +# Copyright 2012-2023 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), From 02db3463ce31b247a8c6e2dbad75fc042a12c098 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Jan 2023 12:15:59 +0100 Subject: [PATCH 6089/9987] add missing patches to OpenBLAS 0.3.20 with NVHPC/22.7 --- .../OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb index a05030ce4e3..39645058d21 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb @@ -16,13 +16,21 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ - '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', + {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] # extensive testing can be enabled by uncommenting the line below From f287618c53a835ae7f64c9e9f1d276e132f368d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Jan 2023 12:17:36 +0100 Subject: [PATCH 6090/9987] retain -fb versionsuffix for ScalaPACK on top of FlexiBLAS --- easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb | 2 +- ...0-nvompi-2022.07.eb => ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb} | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.2.0-nvompi-2022.07.eb => ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb} (98%) diff --git a/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb b/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb index af891ade799..172f0f07ea9 100644 --- a/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb +++ b/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb @@ -19,7 +19,7 @@ dependencies = [ ('FlexiBLAS', '3.2.0', '', local_compiler), ('FFTW', '3.3.10', '', local_compiler), ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), - ('ScaLAPACK', '2.2.0', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb similarity index 98% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb index 85b567d8d10..ebb363f7759 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb @@ -1,5 +1,6 @@ name = 'ScaLAPACK' version = '2.2.0' +versionsuffix = '-fb' homepage = 'https://www.netlib.org/scalapack/' description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines From 1c5d4e5a2bfcc294f4802ea08472e2aeca2cd38b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Jan 2023 13:24:31 +0100 Subject: [PATCH 6091/9987] adding easyconfigs: leidenalg-0.9.1-foss-2022a.eb, python-igraph-0.10.3-foss-2022a.eb, igraph-0.10.3-foss-2022a.eb --- .../i/igraph/igraph-0.10.3-foss-2022a.eb | 51 +++++++++++++++++ .../l/leidenalg/leidenalg-0.9.1-foss-2022a.eb | 51 +++++++++++++++++ .../python-igraph-0.10.3-foss-2022a.eb | 56 +++++++++++++++++++ 3 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.10.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/l/leidenalg/leidenalg-0.9.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.10.3-foss-2022a.eb b/easybuild/easyconfigs/i/igraph/igraph-0.10.3-foss-2022a.eb new file mode 100644 index 00000000000..450894695de --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.10.3-foss-2022a.eb @@ -0,0 +1,51 @@ +# Author: Denis Krišťák (INUITS) +# Modified: Jasper Grimm (UoY) + +easyblock = 'CMakeMake' + +name = 'igraph' +version = '0.10.3' + +homepage = 'https://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['5f72398c7847bb167f85159b7a9fe1fe69ce0f241c5de5d30b2b347f9dc3f7c6'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('GLPK', '5.0'), + ('libxml2', '2.9.13'), + ('zlib', '1.2.12'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('arpack-ng', '3.8.0'), +] + +# Build static and shared libraries +configopts = ["-DBUILD_SHARED_LIBS=OFF", "-DBUILD_SHARED_LIBS=ON"] + +# extra folder `igraph` is wrong, since all other software expects it to be in ./include folder directly +postinstallcmds = [ + 'mv %(installdir)s/include/igraph/* %(installdir)s/include/ && rmdir %(installdir)s/include/igraph ', +] + +_includes = ['include/igraph%s.h' % x for x in ['', '_blas', '_constants', '_lapack', '_types', '_version']] +_libs = ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]] + +sanity_check_paths = { + 'files': _includes + _libs, + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.9.1-foss-2022a.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.9.1-foss-2022a.eb new file mode 100644 index 00000000000..96b300e82cb --- /dev/null +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.9.1-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'leidenalg' +version = '0.9.1' + +homepage = 'https://github.com/vtraag/leidenalg' +description = """Implementation of the Leiden algorithm for various quality +functions to be used with igraph in Python.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('PyYAML', '6.0'), + ('Bison', '3.8.2'), + ('libtool', '2.4.7'), + ('flex', '2.6.4'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('igraph', '0.10.3'), + ('python-igraph', '0.10.3'), +] + +use_pip = True +sanity_pip_check = True + +local_preinstallopts = "python setup.py build --use-pkg-config && " + +exts_list = [ + ('ddt', '1.6.0', { + 'checksums': ['f71b348731b8c78c3100bffbd951a769fbd439088d1fdbb3841eee019af80acd'], + }), + (name, version, { + 'checksums': ['7e5cfe3b6f80f32b90f55f35c68d4a990b0489b1282cf3fabac8cda4988975f3'], + 'preinstallopts': local_preinstallopts, + }), +] + +sanity_check_commands = [ + # tests require that 'leidenalg' Python module is available, + # so needs to be run after installation + "cd %(builddir)s/leidenalg/leidenalg-%(version)s && python setup.py test --use-pkg-config", + "python -c 'import leidenalg; import igraph as ig; " + "leidenalg.find_partition(ig.Graph.Erdos_Renyi(100, 0.1), " + "leidenalg.ModularityVertexPartition)'", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.3-foss-2022a.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.3-foss-2022a.eb new file mode 100644 index 00000000000..9e8c8cebcbc --- /dev/null +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.3-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'python-igraph' +version = '0.10.3' + +homepage = 'https://igraph.org/python' +description = """Python interface to the igraph high performance graph library, primarily aimed at complex network + research and analysis.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('igraph', '0.10.3'), + ('PyCairo', '1.21.0'), + ('Clang', '13.0.1'), + ('libxml2', '2.9.13'), + ('zlib', '1.2.12'), +] + +use_pip = True + +exts_list = [ + ('texttable', '1.6.7', { + 'checksums': ['290348fb67f7746931bcdfd55ac7584ecd4e5b0846ab164333f0794b121760f2'], + }), + ('igraph', version, { + 'patches': ['python-igraph-0.9.0_fix-igraph-libs.patch'], + 'checksums': [ + 'b720cb88c4b9af4a968e8390355f666ba146d631298518cc4ffa1bd0e2c21eed', # igraph-0.10.3.tar.gz + # python-igraph-0.9.0_fix-igraph-libs.patch + '7af7a6e6a8b982ced7cdd939d82a98829512088744bebad34c714a3c4803f126', + ], + 'installopts': '--install-option="--use-pkg-config"', + 'modulename': 'igraph', + }), +] + +sanity_check_paths = { + 'files': ['bin/igraph'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# cairo must be available for proper plotting support +sanity_check_commands = [ + "python -c 'from igraph.drawing.cairo.utils import find_cairo; cairo = find_cairo(); cairo.Context'", +] + +sanity_pip_check = True + +moduleclass = 'lib' From d7df04169bde1b07e7893ef168fed8003f173a19 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Thu, 5 Jan 2023 13:57:47 +0100 Subject: [PATCH 6092/9987] Added required changes --- .../t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb index 22e51f5507e..89e79d4d650 100644 --- a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb @@ -12,9 +12,7 @@ source_urls = [homepage] sources = ['ts-%(version)s.tar.gz'] checksums = ['f73452aed80e2f9a7764883e9353aa7f40e65d3c199ad1f3be60fd58b58eafec'] -dependencies = { - ('binutils', '2.38'), -} +builddependencies = [('binutils', '2.38')] skipsteps = ['configure'] installopts = 'PREFIX=%(installdir)s' From a97bd9612cf85846260af2af0bbbbbea776e83c6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 5 Jan 2023 15:01:55 +0100 Subject: [PATCH 6093/9987] update easyconfig ABINIT-9.6.2-foss-2022a.eb: fix OpenMP and FlexiBLAS option --- easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb index 7f51bbe7c76..4003b3410d5 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb @@ -34,13 +34,12 @@ configopts += 'FFLAGS="-fallow-argument-mismatch $FFLAGS" ' # Ensure MPI configopts += '--with-mpi="yes" ' -# configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' # Enable OpenMP configopts += '--enable-openmp="yes" ' -# BLAS/Lapack from OpenBLAS -configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="${LIBLAPACK_MT}" ' +# BLAS/Lapack from FlexiBLAS +configopts += 'LINALG_LIBS="${LIBLAPACK_MT}" ' # FFTW configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" ' @@ -60,9 +59,6 @@ preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' # Enable double precision for GW calculations configopts += '--enable-gw-dpc ' -# Enable OpenMP -configopts += '--enable-openmp ' - # 'make check' is just executing some basic unit tests. # Also running 'make tests_v1' to have some basic validation runtest = "check && make test_v1" From 7e9d4c6e4a8dfd7cd96d40f9980e5f61ba3c80df Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 5 Jan 2023 22:24:17 +0800 Subject: [PATCH 6094/9987] adding easyconfigs: xdotool-3.20211022.1-GCCcore-11.3.0.eb, xclip-0.13-GCCcore-11.3.0.eb --- .../x/xclip/xclip-0.13-GCCcore-11.3.0.eb | 31 ++++++++++++++++++ .../xdotool-3.20211022.1-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/x/xclip/xclip-0.13-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/x/xdotool/xdotool-3.20211022.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/x/xclip/xclip-0.13-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xclip/xclip-0.13-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..00c08424109 --- /dev/null +++ b/easybuild/easyconfigs/x/xclip/xclip-0.13-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'xclip' +version = '0.13' + +homepage = 'https://github.com/astrand/xclip' +description = """xclip is a command line utility that is designed to run on any system with an X11 implementation.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/astrand/xclip/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ca5b8804e3c910a66423a882d79bf3c9450b875ac8528791fb60ec9de667f758'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +dependencies = [('X11', '20220504')] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/xclip-%s' % util for util in ['copyfile', 'cutfile', 'pastefile']], + 'dirs': ['share'] +} + +sanity_check_commands = ['xclip -version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xdotool/xdotool-3.20211022.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xdotool/xdotool-3.20211022.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..91776737d8c --- /dev/null +++ b/easybuild/easyconfigs/x/xdotool/xdotool-3.20211022.1-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'xdotool' +version = '3.20211022.1' + +homepage = 'https://github.com/jordansissel/xdotool' +description = """xdotool lets you simulate keyboard input and mouse activity, move and resize windows, etc. + It does this using X11’s XTEST extension and other Xlib functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/jordansissel/xdotool/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['82b15a944a5e82fee15e0f6116bd9f642bc3d0bb6989fc0ca5ad9dfe35de0847'] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +builddependencies = [('binutils', '2.38')] + +dependencies = [('X11', '20220504')] + +sanity_check_paths = { + 'files': ['bin/xdotool', 'include/xdo.h', 'lib/libxdo.so.3'], + 'dirs': ['man'] +} + +sanity_check_commands = ['xdotool --help'] + +moduleclass = 'tools' From 258ef7125f58c3e19be2a2777d798cebcc5448f9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 5 Jan 2023 15:56:23 +0100 Subject: [PATCH 6095/9987] update easyconfig ABINIT-9.6.2-intel-2022a.eb: fix OpenMP option --- easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb index fbf7936af3f..a6b50b225af 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb @@ -56,9 +56,6 @@ preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' # Enable double precision for GW calculations configopts += '--enable-gw-dpc ' -# Enable OpenMP -configopts += '--enable-openmp ' - # 'make check' is just executing some basic unit tests. # Also running 'make tests_v1' to have some basic validation runtest = "check && make test_v1" From d49435185204b863ab8b2ede2b3db7c0a7ca81b0 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 5 Jan 2023 23:36:23 +0800 Subject: [PATCH 6096/9987] --fix-deprecated-easyconfigs --- easybuild/easyconfigs/x/xclip/xclip-0.13-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xclip/xclip-0.13-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xclip/xclip-0.13-GCCcore-11.3.0.eb index 00c08424109..39d331fbed4 100644 --- a/easybuild/easyconfigs/x/xclip/xclip-0.13-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/xclip/xclip-0.13-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ dependencies = [('X11', '20220504')] preconfigopts = "autoreconf -f -i && " sanity_check_paths = { - 'files': ['bin/xclip-%s' % util for util in ['copyfile', 'cutfile', 'pastefile']], + 'files': ['bin/xclip-%s' % local_util for local_util in ['copyfile', 'cutfile', 'pastefile']], 'dirs': ['share'] } From 3a4edaa2df44dc4cc6a8539fa1bf98614ec0b7de Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 5 Jan 2023 16:48:30 +0100 Subject: [PATCH 6097/9987] Modified setup.py according to the recommendation --- easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index ecfc1e3b520..502affd4f48 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -40,6 +40,8 @@ exts_list = [ 'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'], 'sources': ['%(version)s.tar.gz'], 'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'], + 'preinstallopts': 'sed -i \'s|cmake_args += \["-GNinja"\]|cmake_args += \["-GNinja", \ + "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION"\]|\' setup.py && ' }), ] From d97714891214b3f926b7a03223ebe69cedf35ef2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Jan 2023 18:27:25 +0100 Subject: [PATCH 6098/9987] take into account feedback by @szhorvat (cfr. PR #17053) --- .../i/igraph/igraph-0.10.3-foss-2022a.eb | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.10.3-foss-2022a.eb b/easybuild/easyconfigs/i/igraph/igraph-0.10.3-foss-2022a.eb index 450894695de..7500c79b988 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.10.3-foss-2022a.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.10.3-foss-2022a.eb @@ -19,8 +19,6 @@ sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['5f72398c7847bb167f85159b7a9fe1fe69ce0f241c5de5d30b2b347f9dc3f7c6'] builddependencies = [ - ('Autotools', '20220317'), - ('pkgconf', '1.8.0'), ('CMake', '3.24.3'), ] @@ -28,23 +26,14 @@ dependencies = [ ('GLPK', '5.0'), ('libxml2', '2.9.13'), ('zlib', '1.2.12'), - ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), ('arpack-ng', '3.8.0'), ] # Build static and shared libraries configopts = ["-DBUILD_SHARED_LIBS=OFF", "-DBUILD_SHARED_LIBS=ON"] -# extra folder `igraph` is wrong, since all other software expects it to be in ./include folder directly -postinstallcmds = [ - 'mv %(installdir)s/include/igraph/* %(installdir)s/include/ && rmdir %(installdir)s/include/igraph ', -] - -_includes = ['include/igraph%s.h' % x for x in ['', '_blas', '_constants', '_lapack', '_types', '_version']] -_libs = ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]] - sanity_check_paths = { - 'files': _includes + _libs, + 'files': ['include/igraph/igraph.h'] + ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]], 'dirs': [], } From f3e6517ebf2997f3dac342d939ef3168e75822e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Jan 2023 20:44:25 +0100 Subject: [PATCH 6099/9987] adding easyconfigs: angsd-0.940-GCC-11.2.0.eb --- .../a/angsd/angsd-0.940-GCC-11.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-11.2.0.eb b/easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-11.2.0.eb new file mode 100644 index 00000000000..d76ea568b39 --- /dev/null +++ b/easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'angsd' +version = '0.940' + +homepage = 'http://www.popgen.dk/angsd' +description = """Program for analysing NGS data.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'ANGSD' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['73b43eb553892721c7d5db5d6d883a17074ee4e07536a32871c3b1ac5f701ad7'] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('HTSlib', '1.14'), +] + +buildopts = "HTSSRC=systemwide" + +files_to_copy = [ + (['angsd', 'misc/supersim', 'misc/thetaStat', 'misc/realSFS', 'misc/msToGlf', + 'misc/smartCount', 'misc/printIcounts', 'misc/contamination', 'misc/splitgl', + 'misc/NGSadmix', 'misc/contamination2', 'misc/haploToPlink', 'misc/ngsPSMC', + 'misc/ibs'], 'bin'), + 'doc', +] + +sanity_check_paths = { + 'files': ['bin/angsd'], + 'dirs': ['doc'], +} + +moduleclass = 'bio' From 2c21e3f44ab7aefad30992bee0e2d3bfcd285dd0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Jan 2023 20:50:23 +0100 Subject: [PATCH 6100/9987] remove libxml2 and zlib dependencies for python-igraph, since they're only indirect dependencies --- .../p/python-igraph/python-igraph-0.10.3-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.3-foss-2022a.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.3-foss-2022a.eb index 9e8c8cebcbc..469bb111d12 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.3-foss-2022a.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.3-foss-2022a.eb @@ -19,8 +19,6 @@ dependencies = [ ('igraph', '0.10.3'), ('PyCairo', '1.21.0'), ('Clang', '13.0.1'), - ('libxml2', '2.9.13'), - ('zlib', '1.2.12'), ] use_pip = True From c1529239d69897bef70ba920c00eb553799b9720 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 6 Jan 2023 13:58:00 +0800 Subject: [PATCH 6101/9987] {phys}[nvofbf/2022.07] VASP v6.3.2 --- .../n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb | 2 + .../v/VASP/VASP-6.3.2-nvofbf-2022.07.eb | 46 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb index 4922cc417e6..2aee5e827db 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb @@ -62,5 +62,7 @@ dependencies = [ # module_add_nvshmem = True # Add NVHPC's NVSHMEM library # module_add_cuda = False # Add NVHPC's bundled CUDA +modextrapaths = {'LD_LIBRARY_PATH': 'Linux_%(arch)s/%(version)s/compilers/extras/qd/lib/'} + # this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb b/easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb new file mode 100644 index 00000000000..7ced52fbfd9 --- /dev/null +++ b/easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'VASP' +version = '6.3.2' + +homepage = 'https://www.vasp.at' +description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale +materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, +from first principles.""" + +toolchain = {'name': 'nvofbf', 'version': '2022.07'} +toolchainopts = {'openmp': True} + +download_instructions = """Vasp is proprietary software, see http://www.vasp.at/index.php/faqs + on how to get access to the code.""" + +sources = ['%(namelower)s.%(version)s.tgz'] +checksums = ['f7595221b0f9236a324ea8afe170637a578cdd5a837cc7679e7f7812f6edf25a'] + +prebuildopts = 'cp arch/makefile.include.nvhpc_omp_acc ./makefile.include && ' + +# Makefile uses LIBS as a list of folders +prebuildopts += 'unset LIBS && ' + +local_targets = ['std', 'gam', 'ncl'] + +buildopts = '%s ' % ' '.join(local_targets) +buildopts += 'FFTW_ROOT="${EBROOTFFTW}" ' + +# https://www.vasp.at/wiki/index.php/Validation_tests +pretestopts = 'export MPIRUN="mpirun -np 4 -x OMP_NUM_THREADS=4 -x OMP_STACKSIZE=512m" && ' +pretestopts += 'export VASP_TESTSUITE_EXE_STD="$MPIRUN %(builddir)s/vasp.%(version)s/bin/vasp_std" && ' +pretestopts += 'export VASP_TESTSUITE_EXE_NCL="$MPIRUN %(builddir)s/vasp.%(version)s/bin/vasp_ncl" && ' +pretestopts += 'export VASP_TESTSUITE_EXE_GAM="$MPIRUN %(builddir)s/vasp.%(version)s/bin/vasp_gam" && ' +runtest = 'test' + +parallel = 1 + +files_to_copy = [(['bin/vasp_' + x for x in local_targets], 'bin')] + +sanity_check_paths = { + 'files': ['bin/vasp_' + x for x in local_targets], + 'dirs': [] +} + +moduleclass = 'phys' From 3f6910e37742026f18c44a1fb98c1a8515559587 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 6 Jan 2023 10:03:46 +0100 Subject: [PATCH 6102/9987] take over @jfgrimm suggested change --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index fa918e82340..25947a6df2c 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -32,6 +32,7 @@ dependencies = [ ] configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From f688db1ca50b8a3f228837b8feed2037c042d169 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 6 Jan 2023 14:54:18 +0100 Subject: [PATCH 6103/9987] adding easyconfigs: dill-0.3.6-GCCcore-11.3.0.eb --- .../d/dill/dill-0.3.6-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/d/dill/dill-0.3.6-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..377eb58517a --- /dev/null +++ b/easybuild/easyconfigs/d/dill/dill-0.3.6-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'dill' +version = '0.3.6' + +homepage = 'https://pypi.org/project/dill/' +description = """dill extends python's pickle module for serializing and de-serializing python objects to the majority + of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse + of which is converting a byte stream back to on python object hierarchy.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e5db55f3687856d8fbdab002ed78544e1c4559a130302693d839dfe8f93f2373'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From 1f66b9201c6a036729e4b355c1687f269a9e50c0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Jan 2023 14:59:17 +0100 Subject: [PATCH 6104/9987] add sanity check command for angsd --- easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-11.2.0.eb b/easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-11.2.0.eb index d76ea568b39..a8295a1fee1 100644 --- a/easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-11.2.0.eb @@ -35,4 +35,6 @@ sanity_check_paths = { 'dirs': ['doc'], } +sanity_check_commands = ["angsd --help"] + moduleclass = 'bio' From c7c09e7952389e7f3dce6c2f1b47f10cb4e747b8 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Jan 2023 18:48:47 +0100 Subject: [PATCH 6105/9987] prepare release notes for EasyBuild v4.7.0 + bump version to 4.7.0 --- RELEASE_NOTES | 70 ++++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 70 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 693825cf873..722efb29a07 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,78 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 15,535 easyconfig files, for 2,798 different software packages, +The latest version of easybuild-easyconfig provides 16,138 easyconfig files, for 2,906 different software packages, incl. 37 different (compiler) toolchains. +4.7.0 (Janurary 9th 2023) +------------------------- + +feature release + +- added easyconfigs for foss/2022a, intel/2022a common toolchains (#16961 and #16962) + - see also https://docs.easybuild.io/en/latest/Common-toolchains.html +- added easyconfigs for NVHPC-based toolchains nvompi/2022.07 and nvofbf/2022.07 (#16724) +- added example easyconfig files for 109 new software packages: + - Alfred (#16780), attrdict3 (#16856), bamFilters (#16735), bcl-convert (#16351), Beagle (#346), Boost.MPI (#15757), captum (#16477), CAT-BAT (#16577), cdo-bindings (#16669), Chemaxon-Marvin (#13954), CliMetLab (#16842), CloudCompare (#16944), cmocean (#16659), COBRApy (#16616), CodAn (#16902), CoSymLib (#17049), CPPE (#16749), cryoCARE (#16534), CTPL (#16498), CUDA-Samples (#16914), cwltool (#16503), Cytoscape (#16682), DeepLabCut (#16391), DeepMod2 (#17008), Dice (#16752), dlb (#16845), DRAGMAP (#16532), ecBuild (#16842), EGTtools (#16704), ESM-2 (#16528), flair-NLP (#15588), FMS (#16965), Godon (#16574), gsw (#16643), HighFive (#16737), humann (#16853), HyperQueue (#16753), IJulia (#16494), infercnvpy (#16712), InParanoid (#16572), jupyter-server (#14844), KaHIP (#16861), KITE (#16550), lagrangian-filtering (#16654), LHAPDF (#17028), librttopo (#16856), libwpe (#16088), Magics (#16842), matlab-proxy (#14270), mcu (#16566), MEMOTE (#16772), memtester (#16763), meson-python (#16911), minizip (#16856), MITgcmutils (#16623), MONAI (#16519), MOOSE (#13824), mstore (#16892), MultilevelEstimators (#15630), n2v (#16535), NanoLyse (#16575), napari (#16468), NECI (#16751), nf-core-mag (#16613), nvofbf (#16724), nvompi (#16724), oceanspy (#16640), olego (#16909), OmegaFold (#16698), OVITO (#16811), Panedr (#16564), Parcels (#16838), polars (#16989), PsiCLASS (#16906), pyccel (#16823), PyCheMPS2 (#16710), PyDamage (#16576), PyImageJ (#16757), pysteps (#16783), python-libsbml (#16610), python-telegram-bot (#16442), pyWannier90 (#16447), resolos (#16649), RLCard (#16695), SAP (#5200), scikit-misc (#16457), scvi-tools (#16457), SELFIES (#17032), SeuratDisk (#16951), sfftk (#16466), simint (#16886), SISSO++ (#15759), slamdunk (#15197), spaCy (#17027), Sphinx-RTD-Theme (#16736), SPOOLES (#16756), Squidpy (#16880), svist4get (#16505), task-spooler (#17048), TBA (#16497), TensorFlow-Datasets (#16421), TFEA (#16476), TinyXML (#16992), tokenizers (#15587), torchsampler (#16464), trimesh (#16858), UCX-ROCm (#17033), wpebackend-fdo (#16093), xmitgcm (#16637) +- added additional easyconfigs for various supported software packages, including: + - ABINIT 9.6.2, AdapterRemoval 2.3.3, aiohttp 3.8.3, Albumentations 1.3.0, alsa-lib 1.2.8, Amber 22.0, ANSYS 2022R2, AOCC 4.0.0, APR 1.7.0, APR-util 1.6.1, archspec 0.1.4, arpack-ng 3.8.0, ArviZ 0.12.1, ASAP 2.1, astropy 5.1.1, ATK 2.38.0, at-spi2-atk 2.38.0, at-spi2-core 2.44.1, Bader 1.04, basemap 1.3.6, BBMap 39.01, BEDOPS 2.4.41, biogeme 3.2.6, Blender 3.3.1, BLIS 0.9.0, Blosc 1.21.3, Blosc2 2.0.4, Blosc2 2.4.3, bokeh 2.4.3, Bonnie++ 2.00a, boto3 1.26.37, BRAKER 2.1.6, Brotli 1.0.9, Brunsli 0.1, bsddb3 6.2.9, BWA 0.7.17, bwidget 1.9.15, bzip2 1.0.8, cairo 1.17.4, Cartopy 0.20.3, CAT-BAT 5.2.3, CDO 2.0.6, CDO 2.1.1, cdsapi 0.5.1, Centrifuge 1.0.4, CFITSIO 3.49, CGAL 4.14.3, CharLS 2.4.1, CheMPS2 1.8.12, Circos 0.69, CMake 3.24.3, ctffind 4.1.14, CubeGUI 4.8, CubeLib 4.8, CubeWriter 4.8, CUDA 11.8.0, CUDA 12.0.0, cuDNN 8.6.0.163, cuDNN 8.7.0.84, CUnit 2.1, cURL 7.86.0, cutadapt 4.2, cuTENSOR 1.6.1.5, dask 2022.10.0, DAS_Tool 1.1.3, DBus 1.15.2, dbus-glib 0.112, dcm2niix 1.0.20220720, DCMTK 3.6.7, deepdiff 5.8.1, DendroPy 4.5.2, dm-reverb 0.7.0, double-conversion 3.2.1, Doxygen 1.9.5, EasyBuild 4.6.2, ecCodes 2.27.0, einops 0.4.1, enchant 2, ESM 2, ESMF 8.3.0, ETE 3.1.2, exiv2 0.27.5, FastTree 2.1.11, fdict 0.8.0, fermi-lite 20190320, FFTW 3.3.10, FFTW.MPI 3.3.10, Fiji 2.9.0, Filtlong 0.2.1, Fiona 1.8.21, FLANN 1.8.4, FLANN 1.9.1, FlexiBLAS 3.2.0, FlexiBLAS 3.2.1, flook 0.8.1, fontconfig 2.14.1, FragGeneScan 1.31, freebayes 1.3.6, FreeImage 3.18.0, FreeSurfer 7.3.2, freetype 2.12.1, FreeXL 1.0.6, FriBidi 1.0.12, g2clib 1.7.0, GATK 4.3.0.0, GD 2.75, GDCM 3.0.20, Gdk-Pixbuf 2.42.10, GDRCopy 2.3, GeneMark-ET 4.71, gensim 4.2.0, geopandas 0.12.2, gettext 0.21.1, gh 2.20.2, Ghostscript 10.0.0, git 2.38.1, glew 2.2.0, GLib 2.75.0, glib-networking 2.72.1, GLM 0.9.9.8, GlobalArrays 5.8.1, GlobalArrays 5.8.2, GMP 6.2.1, GnuTLS 3.7.8, GObject-Introspection 1.74.0, gperf 3.1, graphite2 1.3.14, GRASS 8.2.0, GTK3 3.24.35, gzip 1.12, h5py 3.2.1, HarfBuzz 5.3.1, HDF5 1.10.8, HPL 2.3, HTSeq 2.0.2, hunspell 1.7.1, hwloc 2.8.0, Hyperopt 0.2.7, ICU 72.1, IDBA UD, imagecodecs 2022.9.26, imageio 2.22.2, ImageMagick 7.1.0, imbalanced-learn 0.9.0, imgaug 0.4.0, imkl 2022.2.1, imkl-FFTW 2022.2.1, impi 2021.7.1, Infernal 1.1.4, intel-compilers 2022.2.1, intltool 0.51.0, IOR 3.3.0, ITK 5.2.1, JasPer 4.0.0, jax 0.3.23, jax 0.3.23, jbigkit 2.1, JupyterLab 3.5.0, jxrlib 1.1, KronaTools 2.8.1, Leptonica 1.83.0, LERC 3.0, libaec 1.0.6, libarchive 3.6.1, libavif 0.11.1, libcint 4.4.0, libconfig 1.7.3, libdap 3.20.11, libde265 1.0.8, libdeflate 1.15, libdrm 2.4.114, libepoxy 1.5.10, libev 4.33, libevent 2.1.12, libfabric 1.16.1, libfdf 0.2.2, libfdf 0.2.2, libfdf 0.2.2, libfdf 0.2.2, libffi 3.4.4, libGLU 9.0.2, libglvnd 1.6.0, libgpg-error 1.46, libheif 1.12.0, libiconv 1.17, libidn 1.41, libidn2 2.3.2, libjpeg-turbo 2.1.4, LibLZF 3.6, libpciaccess 0.17, libpng 1.6.38, libpsl 0.21.1, librsvg 2.55.1, LibSoup 3.0.8, libspatialindex 1.9.3, libspatialite 5.0.1, libtasn1 4.19.0, LibTIFF 4.4.0, libunwind 1.6.2, libxml2 2.10.3, libxml2-python 2.9.13, libyaml 0.2.5, line_profiler 4.0.0, LittleCMS 2.14, LLVM 15.0.5, lz4 1.9.4, make 4.3, makedepend 1.0.7, Mako 1.2.4, MATLAB-Engine 2021, matplotlib 3.4.2, matplotlib 3.5.2, MaxBin 2.2.7, MDAnalysis 2.0.0, MEGAHIT 1.2.9, Mesa 22.2.4, Meson 0.64.0, MetaBAT 2.15, MIGRATE-N 5.0.4, Miniconda3 4.12.0, mold 1.7.1, Molden 7.1, MotionCor2 1.5.0, MoviePy 1.0.3, mrcfile 1.3.0, MRChem 1.1.1, MRCPP 1.4.1, NAMD 2.14, nano 7.0, NanoFilt 2.8.0, nanoget 1.18.1, nanomath 1.2.1, NanoPlot 1.33.0, NASM 2.15.05, ncbi-vdb 3.0.0, NCCL 2.16.2, NCCL-tests 2.13.6, NCO 5.1.0, NCO 5.1.3, neptune-client 0.16.2, netCDF 4.9.0, netcdf4-python 1.6.1, netCDF-C++4 4.3.1, netCDF-Fortran 4.6.0, Nextflow 22.10.1, nghttp2 1.48.0, nghttp3 0.6.0, nglview 3.0.3, ngtcp2 0.7.0, NiBabel 4.0.2, Ninja 1.11.1, nodejs 18.12.1, NSPR 4.35, NSS 3.85, NVHPC 22.7, NVSHMEM 2.4.1, NVSHMEM 2.7.0, NWChem 7.0.2, Octave 7.1.0, OPARI2 2.0.7, OpenBLAS 0.3.20, OpenBLAS 0.3.21, OpenCV 4.6.0, OpenFOAM 10, OpenFOAM 9, OpenFold 1.0.1, OpenImageIO 2.3.17.0, OpenMolcas 22.06, OpenMolcas 22.10, OpenMolcas 22.10, OpenMPI 4.1.4, OpenMPI 4.1.4, openpyxl 3.0.10, OpenSceneGraph 3.6.5, OpenSlide 3.4.1, openslide-python 1.2.0, OpenStackClient 6.0.0, OSU-Micro-Benchmark 6.2, OTF2 3.0.2, p11-kit 0.24.1, Pango 1.50.12, PAPI 7.0.0, ParaView 5.9.1, ParMETIS 4.0.3, pauvre 0.2.3, PCRE2 10.40, PDT 3.25.1, PETSc 3.17.4, phonopy 2.16.3, pigz 2.7, Pillow 9.1.1, Pillow 9.2.0, Pindel 0.2.5b9, Pint 0.19.2, pixman 0.42.2, PMIx 4.2.2, poppler 22.12.0, Porechop 0.2.4, psutil 5.9.3, psutil 5.9.3, pugixml 1.12.1, pullseq 1.0.2, pybedtools 0.9.0, PyBerny 0.6.3, pydantic 1.10.2, pydicom 2.3.0, PyOpenGL 3.1.6, pyproj 3.3.1, pyproj 3.4.0, PyQt5 5.15.5, PySCF 1.7.6, pytest 7.1.3, Python 2.7.18, Python 3.10.8, Python 3.10.8, python-isal 1.1.0, PyTorch 1.12.1, PyTorch-Geometric 2.1.0, PyTorch-Lightning 1.8.4, pyWannier90 2021, pyWannier90 2021, PyYAML 6.0, QCA 2.3.5, QGIS 3.28.1, QIIME2 2022.8, qrupdate 1.1.2, QScintilla 2.11.6, Qt5 5.15.7, Qt5Webkit 5.212.0, Qtconsole 5.3.2, QtKeychain 0.13.2, QtPy 2.2.1, Qwt 6.2.0, rasterio 1.3.4, RDFlib 6.2.0, re2c 3.0, ReFrame 3.12.0, regionmask 0.9.0, RegTools 0.5.2, resolos 0.3.5, rising 0.2.2, RLCard 1.0.9, RStudio-Server 2022.07.2+576, ruamel.yaml 0.17.21, Ruby 3.0.3, Ruby 3.0.5, Rust 1.65.0, SAMtools 1.13, SAP 1.1.3, ScaLAPACK 2.2.0, scanpy 1.9.1, scikit-bio 0.5.7, scikit-image 0.19.3, SciPy-bundle 2021.05, Scoary 1.6.16, SCons 4.4.0, Score-P 8.0, SCOTCH 6.1.0, SCOTCH 7.0.1, scvi-tools 0.16.4, Seaborn 0.12.1, SELFIES 2.1.1, SentencePiece 0.1.96, SentencePiece 0.1.97, SeqLib 1.2.0, Serf 1.3.9, Seurat 4.3.0, SeuratDisk 0.0.0.9020, sfftk 0.7.4, Shapely 1.8.2, Siesta 4.1.5, SignalP 6.0g, simint 0.7, SimPEG 0.18.1, SimpleITK 2.1.1.2, SISSO++ 1.1, slamdunk 0.4.3, SLEPc 3.17.2, SNAP 2.0.1, snappy 1.1.9, SOCI 4.0.3, SpaceRanger 2.0.0, spaln 2.4.12, spglib-python 1.16.1, SQLite 3.39.4, SSW 1.1, STAR-CCM+ 17.06.007, statsmodels 0.13.1, SuperLU_DIST 8.1.0, Tcl 8.6.12, tcsh 6.24.01, tensorboardX 2.5.1, TensorFlow 2.8.4, tensorflow-probability 0.16.0, tesseract 5.3.0, texinfo 6.8, Theano 1.0.4, time 1.9, TM-align 20190822, tmux 3.3a, TOBIAS 0.14.0, TOML-Fortran 0.3.1, torchvision 0.13.1, Transformers 4.24.0, TRF 4.09.1, Trinity 2.9.1, typing-extensions v4.4.0, UCC 1.1.0, UCX-CUDA 1.13.1, umap-learn 0.5.3, UnZip 6.0, util-linux 2.38.1, Valgrind 3.20.0, vcflib 1.0.3, Vim 9.0.0950, VTK 9.2.2, wandb 0.13.4, wandb 0.13.6, Wayland 1.21.0, Waylandpp 1.0.0, WebKitGTK+ 2.37.1, WPS 4.4, WRF 4.4, wxPython 4.2.0, wxWidgets 3.2.0, X11 20221110, xarray 2022.6.0, xarray 2022.9.0, XCFun 2.1.1, XGBoost 1.7.2, Xmipp 3.22.07, xorg-macros 1.19.3, XZ 5.2.7, YACS 0.1.8, yaml-cpp 0.7.0, zarr 2.13.3, zfp 1.0.0, zlib-ng 2.0.6, Zopfli 1.0.3, zstd 1.5.2 +- minor enhancements, including: + - enable building of dev tools in recent PyQt5 easyconfigs(#16469) + - add LMERConvenienceFunctions extension for R v4.2.1(#16512) + - build nodejs with OpenSSL and ICU provided as proper dependencies(#16529) + - add SPOTlight packages to R-bundle-Bioconductor-3.15(#16569) + - Add HiCcompare and dependencies to Bioconductor 3.15(#16581) + - Add ROntoTools extension to Bioconductor bundle(#16636) + - add scDblFinder extension to Bioconductor 3.15(#16686) + - add HGNChelper extension to R 4.2.1(#16744) + - add HGNChelper extension to R 4.2.1(#16744) + - automatically cancel Github Action workflow runs for outdated commits (#16754) + - add libmad dependency to SoX v14.4.2 (#16758) + - add numbat extension and requires dependencies to R-bundle-Bioconductor 3.15 + R 4.2.1(#16777) + - install subtree support for git 2.36.0(#16784) + - install subtree support for git 2.38.1(#16785) + - add extensions to ESM-2 to enhance it for esmfold (#16841) + - add libwebp dependency to Pillow-SIMD 9.2.0 to add webp support (#16844) + - fix homepage for pocl v1.8 (#16857) + - add HiCBricks extension to Bioconductor 3.15(#16913) + - add ParMETIS and SuperLU_Dist dependencies to PETSc 3.17.4(#16934) + - add KaHIP dependency to OpenFOAM v2206 (#16974) + - add zellkonverter to R-bundle-Bioconductor v3.15 w/ foss/2022a(#16952) + - enable dataset support for recent versions of Arrow(#16956) + - add sanity check command added for mstore(#17029) +- various bug fixes, including: + - define $JUPYTER_PATH via modextrapaths rather than modextravars for IRkernel 1.x (#15776) + - add patches to fix PyTorch 1.10.0 build on POWER (#15904) + - fix installation of Python 2.7.18 with GCCcore/11.2.0 (was broken due to 0.0.0 version for some extensions) (#16485) + - add patch for M4 1.4.18 to fix glibc v2.34 SIGSTKSZ compatibility(#16486) + - work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml(#16490) + - fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x(#16502) + - Add OpenBLAS patches to disable FMA in [cz]cal and fix crash in zdot(#16510) + - add missing build dependency on Perl for GStreamer. And make sure to not make files suid.(#16516) + - build nodejs with OpenSSL and ICU provided as proper dependencies(#16529) + - also define $JUPYTER_CONFIG_PATH in IPython and JupyterLab easyconfigs(#16556) + - define $GTKDOCIZE as 'echo' before generating configure script for recent HarfBuzz versions (fixes #16567)(#16570) + - disable use of -Werror in recent NSS easyconfigs(#16571) + - use 'cpan.metacpan.org' rather than 'www.cpan.org' in extension source_urls for recent Perl easyconfigs(#16611) + - avoid that zlib + htslib are downloaded and built during installation of MetaBAT(#16624) + - add patch to fix installation of MetaBAT 2.15 on non-x86_64 systems(#16633) + - stick to DIAMOND 2.0.11 as dependency for CAT-BAT with GCC/10.3.0(#16634) + - add missing pyWannier90 dependency for mcu + enhance sanity check(#16667) + - fix source_urls for colossalai 0.1.8 (no longer available via PyPI, only via GitHub repo)(#16693) + - fix checksum for dlllogger extension in OpenFold v1.0.0(#16694) + - rename hyperopt to Hyperopt, to be consistent with existing Hyperopt easyconfigs(#16697) + - update version of pyproj dependency for Cartopy 0.20.3 (to match one used for basemap 1.3.6)(#16699) + - stick to older PyQt-builder in easyconfig for PyQt5 5.15.5, so that 'pip check' passes(#16703) +- other changes: + - only give read permissions in GitHub Actions workflows (#16263) + - remove ExomeDepth from recent R-bundle-Bioconductor(#16492) + - include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0(#16578) + - switch IJulia and MultilevelEstimators to JuliaBundle easyblock(#16665) + - cleanup package names and source definitions in Python 3.10.8(#16679) + - downgrade to setuptools 63.4.3 in Python 3.10.8 easyconfig(#16915) + + 4.6.2 (October 21st 2022) ------------------------- diff --git a/setup.py b/setup.py index 3ab99c0cc89..c39675b8ede 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.6.3.dev0' +VERSION = '4.7.0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From edd1cc2947315577c6380eac46bf32fa2626f96c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Jan 2023 14:25:02 +0100 Subject: [PATCH 6106/9987] adding easyconfigs: pyperf-2.5.0-GCCcore-11.3.0.eb --- .../p/pyperf/pyperf-2.5.0-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyperf/pyperf-2.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pyperf/pyperf-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pyperf/pyperf-2.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..733a5bef2fc --- /dev/null +++ b/easybuild/easyconfigs/p/pyperf/pyperf-2.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'pyperf' +version = '2.5.0' + +homepage = 'https://github.com/psf/pyperf' +description = "The Python pyperf module is a toolkit to write, run and analyze benchmarks" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9fd9be5b57224e68b5a5b88f7126f15b6c8667573f62a0a39faf14d6fdd13909'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/pyperf'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyperf --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From 8a685fe87aaeee0cc84e62c47fac1e0978fd0a0a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 8 Jan 2023 18:36:25 +0100 Subject: [PATCH 6107/9987] use single rather than double quotes --- .../g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb | 38 +++++++++---------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb index 85f4058dd59..2e995926f1c 100644 --- a/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GUSHR/GUSHR-2020-09-28-foss-2021b.eb @@ -1,28 +1,28 @@ # author: Denis Kristak (INUITS) -easyblock = "Tarball" +easyblock = 'Tarball' -name = "GUSHR" -version = "2020-09-28" -local_commit = "ee26d5c" +name = 'GUSHR' +version = '2020-09-28' +local_commit = 'ee26d5c' -homepage = "https://github.com/Gaius-Augustus/GUSHR" +homepage = 'https://github.com/Gaius-Augustus/GUSHR' description = """ Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation. """ -toolchain = {"name": "foss", "version": "2021b"} +toolchain = {'name': 'foss', 'version': '2021b'} source_urls = [ - "https://github.com/Gaius-Augustus/GUSHR/archive", - "http://bioinf.uni-greifswald.de/bioinf/braker/", + 'https://github.com/Gaius-Augustus/GUSHR/archive', + 'http://bioinf.uni-greifswald.de/bioinf/braker/', ] sources = [ { - "download_filename": "%s.tar.gz" % local_commit, - "filename": SOURCE_TAR_GZ, + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, }, { - 'filename': "RNAseq.bam", + 'filename': 'RNAseq.bam', 'extract_cmd': 'cp %s %(builddir)s/', } ] @@ -33,21 +33,21 @@ checksums = [ dependencies = [ ('Java', '11', '', SYSTEM), - ("AUGUSTUS", "3.4.0"), - ("GLib", "2.69.1"), + ('AUGUSTUS', '3.4.0'), + ('GLib', '2.69.1'), ] sanity_check_paths = { - "files": ["gushr.py"], - "dirs": [], + 'files': ['gushr.py'], + 'dirs': [], } -local_sanity_cmd = "cp %(builddir)s/RNAseq.bam %(installdir)s/example && " -local_sanity_cmd += "cd %(installdir)s/example && " -local_sanity_cmd += "../gushr.py -b RNAseq.bam -t augustus.gtf -g genome.fa -o gushr -c 10 " +local_sanity_cmd = 'cp %(builddir)s/RNAseq.bam %(installdir)s/example && ' +local_sanity_cmd += 'cd %(installdir)s/example && ' +local_sanity_cmd += '../gushr.py -b RNAseq.bam -t augustus.gtf -g genome.fa -o gushr -c 10 ' sanity_check_commands = [ local_sanity_cmd ] -moduleclass = "bio" +moduleclass = 'bio' From 77fe9c3071861e283fc472706fe0ecd41b1afb82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Jan 2023 10:22:13 +0100 Subject: [PATCH 6108/9987] minor tweaks to release notes for EasyBuild v4.7.0 --- RELEASE_NOTES | 146 +++++++++++++++++++++++++++++++++----------------- 1 file changed, 98 insertions(+), 48 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 722efb29a07..5286c71d11c 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,8 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 16,138 easyconfig files, for 2,906 different software packages, -incl. 37 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 16,138 easyconfig files, for 2,904 different software packages, +incl. 39 different (compiler) toolchains. 4.7.0 (Janurary 9th 2023) @@ -15,64 +15,114 @@ feature release - added easyconfigs for foss/2022a, intel/2022a common toolchains (#16961 and #16962) - see also https://docs.easybuild.io/en/latest/Common-toolchains.html - added easyconfigs for NVHPC-based toolchains nvompi/2022.07 and nvofbf/2022.07 (#16724) -- added example easyconfig files for 109 new software packages: - - Alfred (#16780), attrdict3 (#16856), bamFilters (#16735), bcl-convert (#16351), Beagle (#346), Boost.MPI (#15757), captum (#16477), CAT-BAT (#16577), cdo-bindings (#16669), Chemaxon-Marvin (#13954), CliMetLab (#16842), CloudCompare (#16944), cmocean (#16659), COBRApy (#16616), CodAn (#16902), CoSymLib (#17049), CPPE (#16749), cryoCARE (#16534), CTPL (#16498), CUDA-Samples (#16914), cwltool (#16503), Cytoscape (#16682), DeepLabCut (#16391), DeepMod2 (#17008), Dice (#16752), dlb (#16845), DRAGMAP (#16532), ecBuild (#16842), EGTtools (#16704), ESM-2 (#16528), flair-NLP (#15588), FMS (#16965), Godon (#16574), gsw (#16643), HighFive (#16737), humann (#16853), HyperQueue (#16753), IJulia (#16494), infercnvpy (#16712), InParanoid (#16572), jupyter-server (#14844), KaHIP (#16861), KITE (#16550), lagrangian-filtering (#16654), LHAPDF (#17028), librttopo (#16856), libwpe (#16088), Magics (#16842), matlab-proxy (#14270), mcu (#16566), MEMOTE (#16772), memtester (#16763), meson-python (#16911), minizip (#16856), MITgcmutils (#16623), MONAI (#16519), MOOSE (#13824), mstore (#16892), MultilevelEstimators (#15630), n2v (#16535), NanoLyse (#16575), napari (#16468), NECI (#16751), nf-core-mag (#16613), nvofbf (#16724), nvompi (#16724), oceanspy (#16640), olego (#16909), OmegaFold (#16698), OVITO (#16811), Panedr (#16564), Parcels (#16838), polars (#16989), PsiCLASS (#16906), pyccel (#16823), PyCheMPS2 (#16710), PyDamage (#16576), PyImageJ (#16757), pysteps (#16783), python-libsbml (#16610), python-telegram-bot (#16442), pyWannier90 (#16447), resolos (#16649), RLCard (#16695), SAP (#5200), scikit-misc (#16457), scvi-tools (#16457), SELFIES (#17032), SeuratDisk (#16951), sfftk (#16466), simint (#16886), SISSO++ (#15759), slamdunk (#15197), spaCy (#17027), Sphinx-RTD-Theme (#16736), SPOOLES (#16756), Squidpy (#16880), svist4get (#16505), task-spooler (#17048), TBA (#16497), TensorFlow-Datasets (#16421), TFEA (#16476), TinyXML (#16992), tokenizers (#15587), torchsampler (#16464), trimesh (#16858), UCX-ROCm (#17033), wpebackend-fdo (#16093), xmitgcm (#16637) +- added example easyconfig files for 107 new software packages: + - Alfred (#16780), attrdict3 (#16856), bamFilters (#16735), bcl-convert (#16351), Beagle (#346), Boost.MPI (#15757), + captum (#16477), CAT-BAT (#16577, #16634), cdo-bindings (#16669), Chemaxon-Marvin (#13954), CliMetLab (#16842), + CloudCompare (#16944), cmocean (#16659), COBRApy (#16616), CodAn (#16902), CoSymLib (#17049), CPPE (#16749), + cryoCARE (#16534), CTPL (#16498), CUDA-Samples (#16914), cwltool (#16503), Cytoscape (#16682), DeepLabCut (#16391), + DeepMod2 (#17008), Dice (#16752), dlb (#16845), DRAGMAP (#16532), ecBuild (#16842), EGTtools (#16704), + ESM-2 (#16528), flair-NLP (#15588), FMS (#16965), Godon (#16574), gsw (#16643), HighFive (#16737), humann (#16853), + HyperQueue (#16753), IJulia (#16494, #16665), infercnvpy (#16712), InParanoid (#16572), jupyter-server (#14844), + KaHIP (#16861), KITE (#16550), lagrangian-filtering (#16654), LHAPDF (#17028), librttopo (#16856), libwpe (#16088), + Magics (#16842), matlab-proxy (#14270), mcu (#16566), MEMOTE (#16772), memtester (#16763), meson-python (#16911), + minizip (#16856), MITgcmutils (#16623), MONAI (#16519), MOOSE (#13824), mstore (#16892, #17029), + MultilevelEstimators (#15630, #16665), n2v (#16535), NanoLyse (#16575), napari (#16468), NECI (#16751), + nf-core-mag (#16613), oceanspy (#16640), olego (#16909), OmegaFold (#16698), OVITO (#16811), Panedr (#16564), + Parcels (#16838), polars (#16989), PsiCLASS (#16906), pyccel (#16823), PyCheMPS2 (#16710), PyDamage (#16576), + PyImageJ (#16757), pysteps (#16783), python-libsbml (#16610), python-telegram-bot (#16442), pyWannier90 (#16447), + resolos (#16649), RLCard (#16695), SAP (#5200), scikit-misc (#16457), scvi-tools (#16457), SELFIES (#17032), + SeuratDisk (#16951), sfftk (#16466), simint (#16886), SISSO++ (#15759), slamdunk (#15197), spaCy (#17027), + Sphinx-RTD-Theme (#16736), SPOOLES (#16756), Squidpy (#16880), svist4get (#16505), task-spooler (#17048), + TBA (#16497), TensorFlow-Datasets (#16421), TFEA (#16476), TinyXML (#16992), tokenizers (#15587), + torchsampler (#16464), trimesh (#16858), UCX-ROCm (#17033), wpebackend-fdo (#16093), xmitgcm (#16637) - added additional easyconfigs for various supported software packages, including: - - ABINIT 9.6.2, AdapterRemoval 2.3.3, aiohttp 3.8.3, Albumentations 1.3.0, alsa-lib 1.2.8, Amber 22.0, ANSYS 2022R2, AOCC 4.0.0, APR 1.7.0, APR-util 1.6.1, archspec 0.1.4, arpack-ng 3.8.0, ArviZ 0.12.1, ASAP 2.1, astropy 5.1.1, ATK 2.38.0, at-spi2-atk 2.38.0, at-spi2-core 2.44.1, Bader 1.04, basemap 1.3.6, BBMap 39.01, BEDOPS 2.4.41, biogeme 3.2.6, Blender 3.3.1, BLIS 0.9.0, Blosc 1.21.3, Blosc2 2.0.4, Blosc2 2.4.3, bokeh 2.4.3, Bonnie++ 2.00a, boto3 1.26.37, BRAKER 2.1.6, Brotli 1.0.9, Brunsli 0.1, bsddb3 6.2.9, BWA 0.7.17, bwidget 1.9.15, bzip2 1.0.8, cairo 1.17.4, Cartopy 0.20.3, CAT-BAT 5.2.3, CDO 2.0.6, CDO 2.1.1, cdsapi 0.5.1, Centrifuge 1.0.4, CFITSIO 3.49, CGAL 4.14.3, CharLS 2.4.1, CheMPS2 1.8.12, Circos 0.69, CMake 3.24.3, ctffind 4.1.14, CubeGUI 4.8, CubeLib 4.8, CubeWriter 4.8, CUDA 11.8.0, CUDA 12.0.0, cuDNN 8.6.0.163, cuDNN 8.7.0.84, CUnit 2.1, cURL 7.86.0, cutadapt 4.2, cuTENSOR 1.6.1.5, dask 2022.10.0, DAS_Tool 1.1.3, DBus 1.15.2, dbus-glib 0.112, dcm2niix 1.0.20220720, DCMTK 3.6.7, deepdiff 5.8.1, DendroPy 4.5.2, dm-reverb 0.7.0, double-conversion 3.2.1, Doxygen 1.9.5, EasyBuild 4.6.2, ecCodes 2.27.0, einops 0.4.1, enchant 2, ESM 2, ESMF 8.3.0, ETE 3.1.2, exiv2 0.27.5, FastTree 2.1.11, fdict 0.8.0, fermi-lite 20190320, FFTW 3.3.10, FFTW.MPI 3.3.10, Fiji 2.9.0, Filtlong 0.2.1, Fiona 1.8.21, FLANN 1.8.4, FLANN 1.9.1, FlexiBLAS 3.2.0, FlexiBLAS 3.2.1, flook 0.8.1, fontconfig 2.14.1, FragGeneScan 1.31, freebayes 1.3.6, FreeImage 3.18.0, FreeSurfer 7.3.2, freetype 2.12.1, FreeXL 1.0.6, FriBidi 1.0.12, g2clib 1.7.0, GATK 4.3.0.0, GD 2.75, GDCM 3.0.20, Gdk-Pixbuf 2.42.10, GDRCopy 2.3, GeneMark-ET 4.71, gensim 4.2.0, geopandas 0.12.2, gettext 0.21.1, gh 2.20.2, Ghostscript 10.0.0, git 2.38.1, glew 2.2.0, GLib 2.75.0, glib-networking 2.72.1, GLM 0.9.9.8, GlobalArrays 5.8.1, GlobalArrays 5.8.2, GMP 6.2.1, GnuTLS 3.7.8, GObject-Introspection 1.74.0, gperf 3.1, graphite2 1.3.14, GRASS 8.2.0, GTK3 3.24.35, gzip 1.12, h5py 3.2.1, HarfBuzz 5.3.1, HDF5 1.10.8, HPL 2.3, HTSeq 2.0.2, hunspell 1.7.1, hwloc 2.8.0, Hyperopt 0.2.7, ICU 72.1, IDBA UD, imagecodecs 2022.9.26, imageio 2.22.2, ImageMagick 7.1.0, imbalanced-learn 0.9.0, imgaug 0.4.0, imkl 2022.2.1, imkl-FFTW 2022.2.1, impi 2021.7.1, Infernal 1.1.4, intel-compilers 2022.2.1, intltool 0.51.0, IOR 3.3.0, ITK 5.2.1, JasPer 4.0.0, jax 0.3.23, jax 0.3.23, jbigkit 2.1, JupyterLab 3.5.0, jxrlib 1.1, KronaTools 2.8.1, Leptonica 1.83.0, LERC 3.0, libaec 1.0.6, libarchive 3.6.1, libavif 0.11.1, libcint 4.4.0, libconfig 1.7.3, libdap 3.20.11, libde265 1.0.8, libdeflate 1.15, libdrm 2.4.114, libepoxy 1.5.10, libev 4.33, libevent 2.1.12, libfabric 1.16.1, libfdf 0.2.2, libfdf 0.2.2, libfdf 0.2.2, libfdf 0.2.2, libffi 3.4.4, libGLU 9.0.2, libglvnd 1.6.0, libgpg-error 1.46, libheif 1.12.0, libiconv 1.17, libidn 1.41, libidn2 2.3.2, libjpeg-turbo 2.1.4, LibLZF 3.6, libpciaccess 0.17, libpng 1.6.38, libpsl 0.21.1, librsvg 2.55.1, LibSoup 3.0.8, libspatialindex 1.9.3, libspatialite 5.0.1, libtasn1 4.19.0, LibTIFF 4.4.0, libunwind 1.6.2, libxml2 2.10.3, libxml2-python 2.9.13, libyaml 0.2.5, line_profiler 4.0.0, LittleCMS 2.14, LLVM 15.0.5, lz4 1.9.4, make 4.3, makedepend 1.0.7, Mako 1.2.4, MATLAB-Engine 2021, matplotlib 3.4.2, matplotlib 3.5.2, MaxBin 2.2.7, MDAnalysis 2.0.0, MEGAHIT 1.2.9, Mesa 22.2.4, Meson 0.64.0, MetaBAT 2.15, MIGRATE-N 5.0.4, Miniconda3 4.12.0, mold 1.7.1, Molden 7.1, MotionCor2 1.5.0, MoviePy 1.0.3, mrcfile 1.3.0, MRChem 1.1.1, MRCPP 1.4.1, NAMD 2.14, nano 7.0, NanoFilt 2.8.0, nanoget 1.18.1, nanomath 1.2.1, NanoPlot 1.33.0, NASM 2.15.05, ncbi-vdb 3.0.0, NCCL 2.16.2, NCCL-tests 2.13.6, NCO 5.1.0, NCO 5.1.3, neptune-client 0.16.2, netCDF 4.9.0, netcdf4-python 1.6.1, netCDF-C++4 4.3.1, netCDF-Fortran 4.6.0, Nextflow 22.10.1, nghttp2 1.48.0, nghttp3 0.6.0, nglview 3.0.3, ngtcp2 0.7.0, NiBabel 4.0.2, Ninja 1.11.1, nodejs 18.12.1, NSPR 4.35, NSS 3.85, NVHPC 22.7, NVSHMEM 2.4.1, NVSHMEM 2.7.0, NWChem 7.0.2, Octave 7.1.0, OPARI2 2.0.7, OpenBLAS 0.3.20, OpenBLAS 0.3.21, OpenCV 4.6.0, OpenFOAM 10, OpenFOAM 9, OpenFold 1.0.1, OpenImageIO 2.3.17.0, OpenMolcas 22.06, OpenMolcas 22.10, OpenMolcas 22.10, OpenMPI 4.1.4, OpenMPI 4.1.4, openpyxl 3.0.10, OpenSceneGraph 3.6.5, OpenSlide 3.4.1, openslide-python 1.2.0, OpenStackClient 6.0.0, OSU-Micro-Benchmark 6.2, OTF2 3.0.2, p11-kit 0.24.1, Pango 1.50.12, PAPI 7.0.0, ParaView 5.9.1, ParMETIS 4.0.3, pauvre 0.2.3, PCRE2 10.40, PDT 3.25.1, PETSc 3.17.4, phonopy 2.16.3, pigz 2.7, Pillow 9.1.1, Pillow 9.2.0, Pindel 0.2.5b9, Pint 0.19.2, pixman 0.42.2, PMIx 4.2.2, poppler 22.12.0, Porechop 0.2.4, psutil 5.9.3, psutil 5.9.3, pugixml 1.12.1, pullseq 1.0.2, pybedtools 0.9.0, PyBerny 0.6.3, pydantic 1.10.2, pydicom 2.3.0, PyOpenGL 3.1.6, pyproj 3.3.1, pyproj 3.4.0, PyQt5 5.15.5, PySCF 1.7.6, pytest 7.1.3, Python 2.7.18, Python 3.10.8, Python 3.10.8, python-isal 1.1.0, PyTorch 1.12.1, PyTorch-Geometric 2.1.0, PyTorch-Lightning 1.8.4, pyWannier90 2021, pyWannier90 2021, PyYAML 6.0, QCA 2.3.5, QGIS 3.28.1, QIIME2 2022.8, qrupdate 1.1.2, QScintilla 2.11.6, Qt5 5.15.7, Qt5Webkit 5.212.0, Qtconsole 5.3.2, QtKeychain 0.13.2, QtPy 2.2.1, Qwt 6.2.0, rasterio 1.3.4, RDFlib 6.2.0, re2c 3.0, ReFrame 3.12.0, regionmask 0.9.0, RegTools 0.5.2, resolos 0.3.5, rising 0.2.2, RLCard 1.0.9, RStudio-Server 2022.07.2+576, ruamel.yaml 0.17.21, Ruby 3.0.3, Ruby 3.0.5, Rust 1.65.0, SAMtools 1.13, SAP 1.1.3, ScaLAPACK 2.2.0, scanpy 1.9.1, scikit-bio 0.5.7, scikit-image 0.19.3, SciPy-bundle 2021.05, Scoary 1.6.16, SCons 4.4.0, Score-P 8.0, SCOTCH 6.1.0, SCOTCH 7.0.1, scvi-tools 0.16.4, Seaborn 0.12.1, SELFIES 2.1.1, SentencePiece 0.1.96, SentencePiece 0.1.97, SeqLib 1.2.0, Serf 1.3.9, Seurat 4.3.0, SeuratDisk 0.0.0.9020, sfftk 0.7.4, Shapely 1.8.2, Siesta 4.1.5, SignalP 6.0g, simint 0.7, SimPEG 0.18.1, SimpleITK 2.1.1.2, SISSO++ 1.1, slamdunk 0.4.3, SLEPc 3.17.2, SNAP 2.0.1, snappy 1.1.9, SOCI 4.0.3, SpaceRanger 2.0.0, spaln 2.4.12, spglib-python 1.16.1, SQLite 3.39.4, SSW 1.1, STAR-CCM+ 17.06.007, statsmodels 0.13.1, SuperLU_DIST 8.1.0, Tcl 8.6.12, tcsh 6.24.01, tensorboardX 2.5.1, TensorFlow 2.8.4, tensorflow-probability 0.16.0, tesseract 5.3.0, texinfo 6.8, Theano 1.0.4, time 1.9, TM-align 20190822, tmux 3.3a, TOBIAS 0.14.0, TOML-Fortran 0.3.1, torchvision 0.13.1, Transformers 4.24.0, TRF 4.09.1, Trinity 2.9.1, typing-extensions v4.4.0, UCC 1.1.0, UCX-CUDA 1.13.1, umap-learn 0.5.3, UnZip 6.0, util-linux 2.38.1, Valgrind 3.20.0, vcflib 1.0.3, Vim 9.0.0950, VTK 9.2.2, wandb 0.13.4, wandb 0.13.6, Wayland 1.21.0, Waylandpp 1.0.0, WebKitGTK+ 2.37.1, WPS 4.4, WRF 4.4, wxPython 4.2.0, wxWidgets 3.2.0, X11 20221110, xarray 2022.6.0, xarray 2022.9.0, XCFun 2.1.1, XGBoost 1.7.2, Xmipp 3.22.07, xorg-macros 1.19.3, XZ 5.2.7, YACS 0.1.8, yaml-cpp 0.7.0, zarr 2.13.3, zfp 1.0.0, zlib-ng 2.0.6, Zopfli 1.0.3, zstd 1.5.2 + - Albumentations 1.3.0, ANSYS 2022R2, AOCC 4.0.0, archspec 0.1.4, ArviZ 0.12.1, ASAP 2.1, astropy 5.1.1, + basemap 1.3.6, BBMap 39.01, BEDOPS 2.4.41, Blender 3.3.1, Blosc 1.21.3, Blosc2 2.4.3, bokeh 2.4.3, Bonnie++ 2.00a, + boto3 1.26.37, BRAKER 2.1.6, CDO 2.1.1, cdsapi 0.5.1, CharLS 2.4.1, CheMPS2 1.8.12, CMake 3.24.3, CubeGUI 4.8, + CubeLib 4.8, CubeWriter 4.8, CUDA 11.8.0 + 12.0.0, cuDNN 8.6.0.163 + 8.7.0.84, cURL 7.86.0, cutadapt 4.2, + cuTENSOR 1.6.1.5, dask 2022.10.0, DAS_Tool 1.1.3, DBus 1.15.2, dcm2niix 1.0.20220720, DCMTK 3.6.7, deepdiff 5.8.1, + dm-reverb 0.7.0, double-conversion 3.2.1, Doxygen 1.9.5, ecCodes 2.27.0, exiv2 0.27.5, Fiji 2.9.0, Filtlong 0.2.1, + FLANN 1.9.1, FlexiBLAS 3.2.1, fontconfig 2.14.1, FreeXL 1.0.6, g2clib 1.7.0, GATK 4.3.0.0, GD 2.75, GDCM 3.0.20, + Gdk-Pixbuf 2.42.10, GeneMark-ET 4.71, gensim 4.2.0, geopandas 0.12.2, gettext 0.21.1, gh 2.20.2, Ghostscript 10.0.0, + git 2.38.1, GLib 2.75.0, GlobalArrays 5.8.2, GnuTLS 3.7.8, GObject-Introspection 1.74.0, GRASS 8.2.0, GTK3 3.24.35, + HarfBuzz 5.3.1, HTSeq 2.0.2, hwloc 2.8.0, Hyperopt 0.2.7, ICU 72.1, imagecodecs 2022.9.26, imageio 2.22.2, + ImageMagick 7.1.0-53, imbalanced-learn 0.9.0, JasPer 4.0.0, jax 0.3.23, JupyterLab 3.5.0, Leptonica 1.83.0, + libavif 0.11.1, libdap 3.20.11, libdeflate 1.15, libdrm 2.4.114, libfabric 1.16.1, libffi 3.4.4, libglvnd 1.6.0, + libgpg-error 1.46, libidn 1.41, libjpeg-turbo 2.1.4, LibLZF 3.6, libpciaccess 0.17, libpng 1.6.38, librsvg 2.55.1, + LibSoup 3.0.8, libspatialindex 1.9.3, libspatialite 5.0.1, libtasn1 4.19.0, LibTIFF 4.4.0, libxml2 2.10.3, + libxml2-python 2.9.13, line_profiler 4.0.0, LittleCMS 2.14, LLVM 15.0.5, lz4 1.9.4, makedepend 1.0.7, Mako 1.2.4, + MATLAB-Engine 2021b, Mesa 22.2.4, Meson 0.64.0, MIGRATE-N 5.0.4, Miniconda3 4.12.0, mold 1.7.1, Molden 7.1, + MotionCor2 1.5.0, MoviePy 1.0.3, MRChem 1.1.1, MRCPP 1.4.1, nano 7.0, NanoFilt 2.8.0, nanoget 1.18.1, + nanomath 1.2.1, ncbi-vdb 3.0.0, NCCL 2.16.2, NCCL-tests 2.13.6, NCO 5.1.3, nglview 3.0.3, NiBabel 4.0.2, + Ninja 1.11.1, nodejs 18.12.1, NSPR 4.35, NSS 3.85, NVHPC 22.7, NVSHMEM 2.7.0, Octave 7.1.0, OPARI2 2.0.7, + OpenFOAM 10, OpenFold 1.0.1, OpenImageIO 2.3.17.0, OpenMolcas 22.10, openpyxl 3.0.10, openslide-python 1.2.0, + OpenStackClient 6.0.0, OSU-Micro-Benchmarks 6.2, OTF2 3.0.2, Pango 1.50.12, PAPI 7.0.0, pauvre 0.2.3, PETSc 3.17.4, + phonopy 2.16.3, pigz 2.7, Pillow 9.2.0, Pint 0.19.2, pixman 0.42.2, PMIx 4.2.2, poppler 22.12.0, psutil 5.9.3, + pybedtools 0.9.0, PyBerny 0.6.3, pydantic 1.10.2, pydicom 2.3.0, pyproj 3.4.0, PyQt5 5.15.5, pytest 7.1.3, + Python 3.10.8, python-isal 1.1.0, PyTorch 1.12.1, PyTorch-Geometric 2.1.0, PyTorch-Lightning 1.8.4, QCA 2.3.5, + QGIS 3.28.1, QIIME2 2022.8, QScintilla 2.11.6, Qt5 5.15.7, Qtconsole 5.3.2, QtKeychain 0.13.2, QtPy 2.2.1, + rasterio 1.3.4, re2c 3.0, ReFrame 3.12.0, RStudio-Server 2022.07.2+576, Ruby 3.0.5, Rust 1.65.0, SAP 1.1.3, + scanpy 1.9.1, scikit-image 0.19.3, SCons 4.4.0, Score-P 8.0, Seaborn 0.12.1, SentencePiece 0.1.97, Seurat 4.3.0, + SignalP 6.0g, SimPEG 0.18.1, SLEPc 3.17.2, SNAP 2.0.1, SpaceRanger 2.0.0, SQLite 3.39.4, STAR-CCM+ 17.06.007, + SuperLU_DIST 8.1.0, tensorboardX 2.5.1, TensorFlow 2.8.4, tensorflow-probability 0.16.0, tesseract 5.3.0, + texinfo 6.8, TM-align 20190822, tmux 3.3a, TOBIAS 0.14.0, TOML-Fortran 0.3.1, Transformers 4.24.0, + typing-extensions 4.4.0, UCC 1.1.0, UCX-CUDA 1.13.1, util-linux 2.38.1, Valgrind 3.20.0, Vim 9.0.0950, VTK 9.2.2, + wandb 0.13.6, WebKitGTK+ 2.37.1, WPS 4.4, WRF 4.4, wxPython 4.2.0, wxWidgets 3.2.0, X11 20221110, xarray 2022.9.0, + XCFun 2.1.1, XGBoost 1.7.2, Xmipp 3.22.07, XZ 5.2.7, yaml-cpp 0.7.0, zarr 2.13.3, zlib-ng 2.0.6 - minor enhancements, including: - - enable building of dev tools in recent PyQt5 easyconfigs(#16469) - - add LMERConvenienceFunctions extension for R v4.2.1(#16512) - - build nodejs with OpenSSL and ICU provided as proper dependencies(#16529) - - add SPOTlight packages to R-bundle-Bioconductor-3.15(#16569) - - Add HiCcompare and dependencies to Bioconductor 3.15(#16581) - - Add ROntoTools extension to Bioconductor bundle(#16636) - - add scDblFinder extension to Bioconductor 3.15(#16686) - - add HGNChelper extension to R 4.2.1(#16744) - - add HGNChelper extension to R 4.2.1(#16744) - - automatically cancel Github Action workflow runs for outdated commits (#16754) + - enable building of dev tools in recent PyQt5 easyconfigs (#16469) + - add extensions to R v4.2.1: LMERConvenienceFunctions (#16512), HGNChelper 4.2.1 (#16744) + - add extensions to R-bundle-Bioconductor 3.15: SPOTlight (#16569), HiCcompare (#16581), ROntoTools (#16636), + scDblFinder (#16686), numbat (#16777), HiCBricks (#16913), zellkonverter (#16952) - add libmad dependency to SoX v14.4.2 (#16758) - - add numbat extension and requires dependencies to R-bundle-Bioconductor 3.15 + R 4.2.1(#16777) - - install subtree support for git 2.36.0(#16784) - - install subtree support for git 2.38.1(#16785) + - also install subtree support in recent git easyconfigs (#16784, #16785) - add extensions to ESM-2 to enhance it for esmfold (#16841) - add libwebp dependency to Pillow-SIMD 9.2.0 to add webp support (#16844) - - fix homepage for pocl v1.8 (#16857) - - add HiCBricks extension to Bioconductor 3.15(#16913) - - add ParMETIS and SuperLU_Dist dependencies to PETSc 3.17.4(#16934) - add KaHIP dependency to OpenFOAM v2206 (#16974) - - add zellkonverter to R-bundle-Bioconductor v3.15 w/ foss/2022a(#16952) - - enable dataset support for recent versions of Arrow(#16956) - - add sanity check command added for mstore(#17029) + - enable dataset support for recent versions of Arrow (#16956) - various bug fixes, including: - define $JUPYTER_PATH via modextrapaths rather than modextravars for IRkernel 1.x (#15776) - add patches to fix PyTorch 1.10.0 build on POWER (#15904) - fix installation of Python 2.7.18 with GCCcore/11.2.0 (was broken due to 0.0.0 version for some extensions) (#16485) - - add patch for M4 1.4.18 to fix glibc v2.34 SIGSTKSZ compatibility(#16486) - - work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml(#16490) - - fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x(#16502) - - Add OpenBLAS patches to disable FMA in [cz]cal and fix crash in zdot(#16510) - - add missing build dependency on Perl for GStreamer. And make sure to not make files suid.(#16516) - - build nodejs with OpenSSL and ICU provided as proper dependencies(#16529) - - also define $JUPYTER_CONFIG_PATH in IPython and JupyterLab easyconfigs(#16556) - - define $GTKDOCIZE as 'echo' before generating configure script for recent HarfBuzz versions (fixes #16567)(#16570) - - disable use of -Werror in recent NSS easyconfigs(#16571) - - use 'cpan.metacpan.org' rather than 'www.cpan.org' in extension source_urls for recent Perl easyconfigs(#16611) - - avoid that zlib + htslib are downloaded and built during installation of MetaBAT(#16624) - - add patch to fix installation of MetaBAT 2.15 on non-x86_64 systems(#16633) - - stick to DIAMOND 2.0.11 as dependency for CAT-BAT with GCC/10.3.0(#16634) - - add missing pyWannier90 dependency for mcu + enhance sanity check(#16667) - - fix source_urls for colossalai 0.1.8 (no longer available via PyPI, only via GitHub repo)(#16693) - - fix checksum for dlllogger extension in OpenFold v1.0.0(#16694) - - rename hyperopt to Hyperopt, to be consistent with existing Hyperopt easyconfigs(#16697) - - update version of pyproj dependency for Cartopy 0.20.3 (to match one used for basemap 1.3.6)(#16699) - - stick to older PyQt-builder in easyconfig for PyQt5 5.15.5, so that 'pip check' passes(#16703) + - add patch for M4 1.4.18 to fix glibc v2.34 SIGSTKSZ compatibility (#16486) + - add patch for pybind11 2.6.0 to fix failing test due to extra whitespace (#16487) + - work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml (#16490) + - fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x (#16502) + - add OpenBLAS patches to disable FMA in [cz]cal and fix crash in zdot (#16510) + - add missing Perl build dependency GStreamer + add patch to skip trying to make files suid (#16516) + - build nodejs with OpenSSL and ICU provided as proper dependencies (#16529) + - also define $JUPYTER_CONFIG_PATH in IPython and JupyterLab easyconfigs (#16556) + - define $GTKDOCIZE as 'echo' before generating configure script for recent HarfBuzz versions (#16570) + - disable use of -Werror in recent NSS easyconfigs (#16571) + - use 'cpan.metacpan.org' rather than 'www.cpan.org' in extension source_urls for recent Perl easyconfigs (#16611) + - avoid that zlib + htslib are downloaded and built during installation of MetaBAT (#16624) + - add patch to fix installation of MetaBAT 2.15 on non-x86_64 systems (#16633) + - add missing pyWannier90 dependency for mcu + enhance sanity check (#16667) + - fix source_urls for colossalai 0.1.8 (no longer available via PyPI, only via GitHub repo) (#16693) + - add patches to fix or skip PyTorch 1.12.1 tests (#16793) + - fix checksum for cell2location 0.05-alpha and add missing build dependency on flex (#16819) + - upgrade dependency on libdeflate to common v1.8 in fastp and vt easyconfigs using GCC(core)/10.3.0 (#16839) + - fix checksum for dlllogger extension in OpenFold v1.0.0 (#16694) + - make sure that Python dependency is actually used for VTK 9.0.1 (#16741) + - fix homepage for pocl v1.8 (#16857) + - fix source_urls in MUMPS easyconfigs (#16931, #16932) + - fix installation of Bowtie2 v2.4.4+ on non-x86_64 systems (#16946) + - add missing OpenSSL dependency to DCMTK 3.6.7 (#16979) + - fix source URL for PCRE2 (#16987) + - add pkgconf dependency for ICU and add patch to avoid trouble with long path names for nodejs-16.15.1/GCCcore-11.3.0 (#16990) + - add patch for libwpe 1.13.3 to avoid build issues on CentOS 7 (#17001) + - add missing zlib and zstd to GnuTLS (#17013) + - add missing pkgconf build dependency to Transformers v4.24.0 (#17020) + - fix checksums for xxx-rocm-4.5.0.tar.gz source tarballs for Clang-AOMP 4.5.0 (#17042) + - replace useless test step for simint 0.7 with (lightweight) sanity check command (#17044) - other changes: - only give read permissions in GitHub Actions workflows (#16263) - - remove ExomeDepth from recent R-bundle-Bioconductor(#16492) - - include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0(#16578) - - switch IJulia and MultilevelEstimators to JuliaBundle easyblock(#16665) - - cleanup package names and source definitions in Python 3.10.8(#16679) - - downgrade to setuptools 63.4.3 in Python 3.10.8 easyconfig(#16915) + - remove ExomeDepth from recent R-bundle-Bioconductor easyconfigs (#16492) + - include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0 (#16578) + - use new EasyBuild logo in README (#16641) + - rename hyperopt to Hyperopt, to be consistent with existing Hyperopt easyconfigs (#16697) + - automatically cancel Github Action workflow runs for outdated commits (#16754) + - use geo moduleclass for SimPEG 0.14.1 (#16847) 4.6.2 (October 21st 2022) From 10f7107b7c008251234cef4a921b6393ea1c9d7e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Jan 2023 14:03:30 +0100 Subject: [PATCH 6109/9987] adding easyconfigs: EasyBuild-4.7.0.eb --- .../e/EasyBuild/EasyBuild-4.7.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.0.eb new file mode 100644 index 00000000000..b83e8bec9ca --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.0.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.7.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/09/0d/513a4474666ac06a534d8a972157208d96f691ae9a02d421905673f1a1b4/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/38/d4/b2d82d63ba96c8df407b7e1dcbfd31906d6cc3ecf8d5cd99a407c79be3bb/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/15/96/d0067ed08519b92f34d3e44fa0aff8ed310190d9a95efde123ed6eabdf97/', + +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + 'ea51c3cb88fca27daadd2fb55ee31f5f51fc60c4e3519ee9d275954540312df8', # easybuild-framework-4.7.0.tar.gz + 'c23e81cbaa3e4fa5ab1bb8b2db759332867d61110bf4ec34763ea170780f0655', # easybuild-easyblocks-4.7.0.tar.gz + 'c688f14a3b0dce45c6cc90d746f05127dbf7368bd9b5873ce50757992d8e6261', # easybuild-easyconfigs-4.7.0.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 74957d8f67aef59ade588153e6dc4c0a040439a9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 9 Jan 2023 16:40:47 +0100 Subject: [PATCH 6110/9987] adding easyconfigs: archspec-0.2.0-GCCcore-12.2.0.eb --- .../archspec/archspec-0.2.0-GCCcore-12.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.2.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.2.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f1530726183 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.2.0-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.2.0' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['6aaba5ebdb5c3633c400d8c221a6a18716da0c64b367a8509f4217b22e91a5f5'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +moduleclass = 'tools' + From 3c61c8b9b8873990439b5e8c9bb9b368ce29f88a Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Mon, 9 Jan 2023 16:50:26 +0100 Subject: [PATCH 6111/9987] adding easyconfigs: Blender-3.4.1-linux-x86_64-CUDA-11.7.0.eb --- .../Blender-3.4.1-linux-x86_64-CUDA-11.7.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blender/Blender-3.4.1-linux-x86_64-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.4.1-linux-x86_64-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/Blender/Blender-3.4.1-linux-x86_64-CUDA-11.7.0.eb new file mode 100644 index 00000000000..c0149a3b2ea --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-3.4.1-linux-x86_64-CUDA-11.7.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PackedBinary' + +name = 'Blender' +version = '3.4.1' +versionsuffix = '-linux-x86_64-CUDA-%(cudaver)s' + +homepage = 'https://www.blender.org/' +description = """Blender is the free and open source 3D creation suite. It supports + the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, + compositing and motion tracking, even video editing and game creation.""" + +toolchain = SYSTEM + +source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender%(version_major_minor)s/'] +sources = ['blender-%(version)s-linux-x64.tar.xz'] +checksums = ['1497f83f93e9bbbde745422c795ed10fe15f92f5622b4421768f149fbe776981'] + +dependencies = [ + ('CUDA', '11.7.0') +] + +sanity_check_paths = { + 'files': ['blender', 'blender-softwaregl'], + 'dirs': ['%(version_major_minor)s'], +} + +sanity_check_commands = ["blender --help"] + +moduleclass = 'vis' From ff1fd247ac91f87b17c8b39ff199a29ad8d38aa6 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Mon, 9 Jan 2023 17:05:00 +0100 Subject: [PATCH 6112/9987] Update easybuild/easyconfigs/a/archspec/archspec-0.2.0-GCCcore-12.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/a/archspec/archspec-0.2.0-GCCcore-12.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.2.0-GCCcore-12.2.0.eb index f1530726183..8e514adf7c0 100644 --- a/easybuild/easyconfigs/a/archspec/archspec-0.2.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/a/archspec/archspec-0.2.0-GCCcore-12.2.0.eb @@ -22,4 +22,3 @@ sanity_pip_check = True sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] moduleclass = 'tools' - From 9ff1480adaac0dde264560d0dded268bba30601f Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 9 Jan 2023 16:55:26 +0000 Subject: [PATCH 6113/9987] adding easyconfigs: gomkl-2021b.eb --- easybuild/easyconfigs/g/gomkl/gomkl-2021b.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/gomkl/gomkl-2021b.eb diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2021b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2021b.eb new file mode 100644 index 00000000000..fbdc7a0dfb4 --- /dev/null +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2021b.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gomkl' +version = '2021b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" + +toolchain = SYSTEM + +local_comp = ('GCC', '10.3.0') + +dependencies = [ + local_comp, + ('OpenMPI', '4.1.1', '', local_comp), + ('imkl', '2021.4.0'), +] + +moduleclass = 'toolchain' From 974f09761b8bac1eb5b7b16dcac9e417a99be71e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Jan 2023 20:24:53 +0100 Subject: [PATCH 6114/9987] adding easyconfigs: scArches-0.5.6-foss-2021a.eb, loompy-3.0.7-foss-2021a.eb --- .../l/loompy/loompy-3.0.7-foss-2021a.eb | 38 +++++++++++++ .../s/scArches/scArches-0.5.6-foss-2021a.eb | 55 +++++++++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/scArches/scArches-0.5.6-foss-2021a.eb diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2021a.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2021a.eb new file mode 100644 index 00000000000..23c77d3a6f8 --- /dev/null +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'loompy' +version = '3.0.7' + +homepage = 'https://loompy.org/' +description = "Python implementation of the Loom file format, an efficient file format for large omics datasets" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), + ('numba', '0.53.1'), +] + +use_pip = True + +exts_list = [ + ('numpy_groupies', '0.9.14', { + 'checksums': ['01b7aeca60e643db34875c9823ea6775742adafe5bb406bca14367743ef81800'], + }), + (name, version, { + 'checksums': ['b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/loompy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["loompy --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.5.6-foss-2021a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.5.6-foss-2021a.eb new file mode 100644 index 00000000000..82342e4330f --- /dev/null +++ b/easybuild/easyconfigs/s/scArches/scArches-0.5.6-foss-2021a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'scArches' +version = '0.5.6' + +homepage = 'https://github.com/theislab/scarches' +description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell + data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('h5py', '3.2.1'), + ('leidenalg', '0.8.7'), + ('scanpy', '1.8.1'), + ('scikit-learn', '0.24.2'), + ('scvi-tools', '0.16.4'), + ('PyTorch', '1.10.0'), + ('tqdm', '4.61.2'), + ('BeautifulSoup', '4.10.0'), + ('loompy', '3.0.7'), +] + +use_pip = True + +exts_list = [ + ('gdown', '4.6.0', { + 'checksums': ['5ce3db0aeda54f46caacb2df86f31c3e3ecd17c355689e6456d85fb528ba9749'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), + ('muon', '0.1.2', { + 'sources': [SOURCE_PY3_WHL], + 'checksums': ['61e0290b113f85177b7596e57aa01552c07700716fac3b8267506fc8a6881dba'], + }), + ('newick', '1.4.0', { + 'checksums': ['0d76ff2fbd180ea790ba177557bf8fbdc56fc166cbe5b31a38113ead8147cf6d'], + }), + ('scHPL', '1.0.2', { + 'checksums': ['a4119fb503e5bfed6fb3e5424cf166d9b1d8822ca0d7fe88d7125807e6da118b'], + 'preinstallopts': "sed -i 's/~=/>=/g' setup.py && ", + 'modulename': 'scHPL', + }), + (name, version, { + 'checksums': ['87b5aa89676b37f65f076631faf3033515cc8380dfad076699410628a1838116'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 8a6c873c847cb29e1c2e62e44824434559eed65f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Tue, 10 Jan 2023 10:35:21 +0800 Subject: [PATCH 6115/9987] skip tests that are failing when running on 4 V100 GPUs --- .../v/VASP/VASP-6.3.2-nvofbf-2022.07.eb | 20 ++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb b/easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb index 7ced52fbfd9..435a614ebf3 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb @@ -28,10 +28,28 @@ buildopts = '%s ' % ' '.join(local_targets) buildopts += 'FFTW_ROOT="${EBROOTFFTW}" ' # https://www.vasp.at/wiki/index.php/Validation_tests -pretestopts = 'export MPIRUN="mpirun -np 4 -x OMP_NUM_THREADS=4 -x OMP_STACKSIZE=512m" && ' + +# it is recommended to run the testsuite with 4 MPI processes, +# but it's also recommended to use only 1 MPI process per GPU, +# so running the test on GPUs requires 4 GPUs? +local_test_mpiprocs = 4 + +pretestopts = 'export MPIRUN="mpirun -np %s -x OMP_NUM_THREADS=4 -x OMP_STACKSIZE=512m" && ' % local_test_mpiprocs pretestopts += 'export VASP_TESTSUITE_EXE_STD="$MPIRUN %(builddir)s/vasp.%(version)s/bin/vasp_std" && ' pretestopts += 'export VASP_TESTSUITE_EXE_NCL="$MPIRUN %(builddir)s/vasp.%(version)s/bin/vasp_ncl" && ' pretestopts += 'export VASP_TESTSUITE_EXE_GAM="$MPIRUN %(builddir)s/vasp.%(version)s/bin/vasp_gam" && ' + +# skip tests that are too long +local_test_skip = 'HEG_333_LW ' + +# these tests are failing when using 4 V100 GPUs (still leaves about 50 successul tests) +local_test_skip += "bulk_GaAs_scGW_ALGO=D_sym bulk_GaAs_scGW_ALGO=D_sym_RPR bulk_GaAs_scGW_sym bulk_GaAs_scGW_sym_RPR " +local_test_skip += "bulk_InP_SOC_DFT_ISYM=3 bulk_InP_SOC_DFT_ISYM=3_RPR bulk_InP_SOC_PBE0_nosym bulk_InP_SOC_PBE0_sym " +local_test_skip += "bulk_InP_SOC_PBE0_sym_RPR bulk_SiO2_HSE bulk_SiO2_HSE_RPR bulk_SiO2_LPEAD bulk_SiO2_LPEAD_RPR " +local_test_skip += "bulk_SiO2_PBE0 bulk_SiO2_PBE0_RPR GaAs_LEPSILON_LPEAD GaAs_LEPSILON_LPEAD_RPR SiC_HSE06_ALGO=A " +local_test_skip += "SiC_HSE06_ALGO=A_RPR SiC_HSE06_ALGO=D SiC_HSE06_ALGO=D_RPR" + +pretestopts += 'export VASP_TESTSUITE_SKIP_TESTS="%s" && ' % local_test_skip runtest = 'test' parallel = 1 From 6423a7352a4b0e9439f89e016c0204aec24ad2f3 Mon Sep 17 00:00:00 2001 From: Jakub Kropacek Date: Tue, 10 Jan 2023 09:26:52 +0100 Subject: [PATCH 6116/9987] adding easyconfigs: nano-7.1-GCCcore-12.2.0.eb --- .../n/nano/nano-7.1-GCCcore-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/nano/nano-7.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/nano/nano-7.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nano/nano-7.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8bfbbe69d36 --- /dev/null +++ b/easybuild/easyconfigs/n/nano/nano-7.1-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2023 + +easyblock = 'ConfigureMake' + +name = 'nano' +version = '7.1' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d03f2fcf536e709edcfc7db882f4b60f198726585df5f1c48f7f7097f3622322'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('ncurses', '6.3')] + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' From 7a4dcf8d92da8830c6f7c6f1db1ff00ec88fdbff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Jan 2023 09:45:12 +0100 Subject: [PATCH 6117/9987] register jax 0.2.24 dependency as diverging dependency variants (instead of jax 0.3.9) --- test/easyconfigs/easyconfigs.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 7cbbb83f2ad..4dca9587c65 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -485,7 +485,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # some software packages require a specific (older/newer) version of a particular dependency alt_dep_versions = { - 'jax': [(r'0\.3\.9', [r'AlphaFold-2\.2\.2-foss-2021a', r'scvi-tools-0\.16\.4-foss-2021a'])], + # jax 0.2.24 is used as dep for AlphaFold 2.1.2 (other easyconfigs with foss/2021a use jax 0.3.9) + 'jax': [(r'0\.2\.24', [r'AlphaFold-2\.1\.2-foss-2021a'])], # arrow-R 6.0.0.2 is used for two R/R-bundle-Bioconductor sets (4.1.2/3.14 and 4.2.0/3.15) 'arrow-R': [('6.0.0.2', [r'R-bundle-Bioconductor-'])], # EMAN2 2.3 requires Boost(.Python) 1.64.0 From 55fc1da4bf3df2e8b718bc7da2791608fecb63d9 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 10 Jan 2023 10:08:45 +0000 Subject: [PATCH 6118/9987] gcc-version corrected --- easybuild/easyconfigs/g/gomkl/gomkl-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2021b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2021b.eb index fbdc7a0dfb4..8d7a31b6a83 100644 --- a/easybuild/easyconfigs/g/gomkl/gomkl-2021b.eb +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2021b.eb @@ -8,7 +8,7 @@ description = """GNU Compiler Collection (GCC) based compiler toolchain with Ope toolchain = SYSTEM -local_comp = ('GCC', '10.3.0') +local_comp = ('GCC', '11.2.0') dependencies = [ local_comp, From dc7b45afd3f00764cce9f5671d5f3df8eb6214dd Mon Sep 17 00:00:00 2001 From: guacke Date: Tue, 10 Jan 2023 11:30:39 +0100 Subject: [PATCH 6119/9987] switch to GCCcore and include reference in patch --- ...inking-error.patch => protobuf-21.9_linking-error.patch} | 1 + ...21.9-foss-2021a.eb => protobuf-3.21.9-GCCcore-10.3.0.eb} | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/protobuf/{linking-error.patch => protobuf-21.9_linking-error.patch} (94%) rename easybuild/easyconfigs/p/protobuf/{protobuf-3.21.9-foss-2021a.eb => protobuf-3.21.9-GCCcore-10.3.0.eb} (76%) diff --git a/easybuild/easyconfigs/p/protobuf/linking-error.patch b/easybuild/easyconfigs/p/protobuf/protobuf-21.9_linking-error.patch similarity index 94% rename from easybuild/easyconfigs/p/protobuf/linking-error.patch rename to easybuild/easyconfigs/p/protobuf/protobuf-21.9_linking-error.patch index e48a5db9f29..3b7fd616d63 100644 --- a/easybuild/easyconfigs/p/protobuf/linking-error.patch +++ b/easybuild/easyconfigs/p/protobuf/protobuf-21.9_linking-error.patch @@ -1,3 +1,4 @@ +# https://github.com/protocolbuffers/protobuf/pull/11032 diff -ruN protobuf-21.9-orig/src/libprotobuf-lite.map protobuf-21.9/src/libprotobuf-lite.map --- protobuf-21.9-orig/src/libprotobuf-lite.map 2022-12-18 15:56:13.701778705 +0100 +++ protobuf-21.9/src/libprotobuf-lite.map 2022-12-18 15:57:06.973681257 +0100 diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb similarity index 76% rename from easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb rename to easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb index d26f7829913..741745897c9 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-foss-2021a.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb @@ -8,16 +8,16 @@ description = """Protocol Buffers (a.k.a., protobuf) are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data.""" -toolchain = {'name': 'foss', 'version': '2021a'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/'] sources = ['v21.9.tar.gz'] checksums = [ '0aa7df8289c957a4c54cbe694fbabe99b180e64ca0f8fdb5e2f76dcf56ff2422', # v21.9.tar.gz - '9d6d7da49f5a1c9d93a4ff0a63aa9705ac6080328830d0fe2483f94daa8c42f0', # linking-error.patch + '14487154fa9d50cc647d6837f9e83f24d2002bcbac876b6b35eb042ededee7ad', # protobuf-21.9_linking-error.patch ] -patches = ['linking-error.patch'] # based on https://github.com/protocolbuffers/protobuf/issues/5144 +patches = ['protobuf-21.9_linking-error.patch'] builddependencies = [ ('binutils', '2.36.1'), From 3d1640c4913c97d14de5e50dfe95625b008ac5b6 Mon Sep 17 00:00:00 2001 From: guacke Date: Tue, 10 Jan 2023 11:53:22 +0100 Subject: [PATCH 6120/9987] style fixes --- .../easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb index 741745897c9..f09a982850d 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb @@ -17,7 +17,7 @@ checksums = [ '14487154fa9d50cc647d6837f9e83f24d2002bcbac876b6b35eb042ededee7ad', # protobuf-21.9_linking-error.patch ] -patches = ['protobuf-21.9_linking-error.patch'] +patches = ['protobuf-21.9_linking-error.patch'] builddependencies = [ ('binutils', '2.36.1'), From 1572c558aa678f7011f071f01fd894e74dfb122e Mon Sep 17 00:00:00 2001 From: guacke Date: Tue, 10 Jan 2023 17:16:17 +0100 Subject: [PATCH 6121/9987] style fix --- .../easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb index f09a982850d..93d2bca89f4 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.21.9-GCCcore-10.3.0.eb @@ -12,13 +12,12 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/'] sources = ['v21.9.tar.gz'] +patches = ['protobuf-21.9_linking-error.patch'] checksums = [ '0aa7df8289c957a4c54cbe694fbabe99b180e64ca0f8fdb5e2f76dcf56ff2422', # v21.9.tar.gz '14487154fa9d50cc647d6837f9e83f24d2002bcbac876b6b35eb042ededee7ad', # protobuf-21.9_linking-error.patch ] -patches = ['protobuf-21.9_linking-error.patch'] - builddependencies = [ ('binutils', '2.36.1'), ('CMake', '3.20.1'), From c9be109123b31b280b9f5b1741629b516408d4b2 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 18:03:26 +0100 Subject: [PATCH 6122/9987] full patch in one file --- .../n/numba/llvmlite-0.39__fix-LLVM-14.patch | 93 +++++++++++++++++++ .../llvmlite-0.39_getparamattribute.patch | 11 --- 2 files changed, 93 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39__fix-LLVM-14.patch delete mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_getparamattribute.patch diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39__fix-LLVM-14.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39__fix-LLVM-14.patch new file mode 100644 index 00000000000..1c4069336e6 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.39__fix-LLVM-14.patch @@ -0,0 +1,93 @@ +diff -ruN llvmlite-0.39.1.orig/ffi/passmanagers.cpp llvmlite-0.39.1/ffi/passmanagers.cpp +--- llvmlite-0.39.1.orig/ffi/passmanagers.cpp 2022-09-01 13:47:22.477959200 +0000 ++++ llvmlite-0.39.1/ffi/passmanagers.cpp 2023-01-10 16:59:33.776510869 +0000 +@@ -8,6 +8,7 @@ + #include "llvm/IR/DiagnosticInfo.h" + #include "llvm/IR/DiagnosticPrinter.h" + #include "llvm/IR/LegacyPassManager.h" ++#include "llvm/Pass.h" + #include "llvm/IR/Module.h" + #include "llvm/Support/FileSystem.h" + #include "llvm/Support/ToolOutputFile.h" +@@ -17,9 +18,6 @@ + #include "llvm-c/Transforms/IPO.h" + #include "llvm-c/Transforms/Scalar.h" + #include "llvm/IR/LegacyPassManager.h" +-#if LLVM_VERSION_MAJOR > 11 +-#include "llvm/IR/RemarkStreamer.h" +-#endif + #include "llvm/IR/LLVMRemarkStreamer.h" + #include "llvm/Remarks/RemarkStreamer.h" + #include "llvm/Transforms/IPO.h" +diff -ruN llvmlite-0.39.1.orig/ffi/targets.cpp llvmlite-0.39.1/ffi/targets.cpp +--- llvmlite-0.39.1.orig/ffi/targets.cpp 2022-09-01 13:47:22.449959300 +0000 ++++ llvmlite-0.39.1/ffi/targets.cpp 2023-01-10 16:59:54.544810234 +0000 +@@ -6,7 +6,7 @@ + #include "llvm/IR/LegacyPassManager.h" + #include "llvm/IR/Type.h" + #include "llvm/Support/Host.h" +-#include "llvm/Support/TargetRegistry.h" ++#include "llvm/MC/TargetRegistry.h" + #include "llvm/Target/TargetMachine.h" + + #include +@@ -204,7 +204,6 @@ + rm = Reloc::DynamicNoPIC; + + TargetOptions opt; +- opt.PrintMachineCode = PrintMC; + opt.MCOptions.ABIName = ABIName; + + bool jit = JIT; +diff -ruN llvmlite-0.39.1.orig/ffi/value.cpp llvmlite-0.39.1/ffi/value.cpp +--- llvmlite-0.39.1.orig/ffi/value.cpp 2022-09-01 13:47:22.449959300 +0000 ++++ llvmlite-0.39.1/ffi/value.cpp 2023-01-10 16:59:09.616162588 +0000 +@@ -154,7 +154,7 @@ + Argument *arg = unwrap(A); + unsigned argno = arg->getArgNo(); + AttributeSet attrs = +- arg->getParent()->getAttributes().getParamAttributes(argno); ++ arg->getParent()->getAttributes().getParamAttrs(argno); + return wrap(new AttributeSetIterator(attrs.begin(), attrs.end())); + } + +diff -ruN llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py llvmlite-0.39.1/llvmlite/tests/test_binding.py +--- llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py 2022-09-01 13:47:22.481959000 +0000 ++++ llvmlite-0.39.1/llvmlite/tests/test_binding.py 2023-01-10 17:00:04.868959051 +0000 +@@ -18,6 +18,16 @@ + from llvmlite.tests import TestCase + + ++def clean_string_whitespace(x: str) -> str: ++ # Remove trailing whitespace from the end of each line ++ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE) ++ # Remove intermediate blank lines ++ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE) ++ # Remove extraneous whitespace from the beginning and end of the string ++ x = x.strip() ++ return x ++ ++ + # arvm7l needs extra ABI symbols to link successfully + if platform.machine() == 'armv7l': + llvm.load_library_permanently('libgcc_s.so.1') +@@ -555,7 +565,10 @@ + bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#")) + bd.ret(ir.Constant(ir.IntType(32), 12345)) + asm = str(mod) +- self.assertEqual(asm, asm_nonalphanum_blocklabel) ++ self.assertEqual( ++ clean_string_whitespace(asm), ++ clean_string_whitespace(asm_nonalphanum_blocklabel) ++ ) + + def test_global_context(self): + gcontext1 = llvm.context.get_global_context() +@@ -640,7 +653,7 @@ + def test_version(self): + major, minor, patch = llvm.llvm_version_info + # one of these can be valid +- valid = [(11,)] ++ valid = [(11,), (12,), (13,), (14,)] + self.assertIn((major,), valid) + self.assertIn(patch, range(10)) diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_getparamattribute.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_getparamattribute.patch deleted file mode 100644 index 88dd553398e..00000000000 --- a/easybuild/easyconfigs/n/numba/llvmlite-0.39_getparamattribute.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ffi/value.cpp.orig 2022-12-07 16:25:09.106947789 +0000 -+++ ffi/value.cpp 2022-12-07 16:25:58.887604268 +0000 -@@ -154,7 +154,7 @@ - Argument *arg = unwrap(A); - unsigned argno = arg->getArgNo(); - AttributeSet attrs = -- arg->getParent()->getAttributes().getParamAttributes(argno); -+ arg->getParent()->getAttributes().getParamAttrs(argno); - return wrap(new AttributeSetIterator(attrs.begin(), attrs.end())); - } - From b5ea85e65b404fca0368b0d1feaca629be14c7f6 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 18:04:22 +0100 Subject: [PATCH 6123/9987] remove small patches --- easybuild/easyconfigs/n/numba/llvmlite-0.39_pass.patch | 10 ---------- 1 file changed, 10 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_pass.patch diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_pass.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_pass.patch deleted file mode 100644 index c786af04638..00000000000 --- a/easybuild/easyconfigs/n/numba/llvmlite-0.39_pass.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ffi/passmanagers.cpp.orig 2022-12-07 16:11:49.483816317 +0000 -+++ ffi/passmanagers.cpp 2022-12-07 16:12:19.848240354 +0000 -@@ -8,6 +8,7 @@ - #include "llvm/IR/DiagnosticInfo.h" - #include "llvm/IR/DiagnosticPrinter.h" - #include "llvm/IR/LegacyPassManager.h" -+#include "llvm/Pass.h" - #include "llvm/IR/Module.h" - #include "llvm/Support/FileSystem.h" - #include "llvm/Support/ToolOutputFile.h" From 0a93bcdeb9a9a10abca6f7b915382afe55dbd549 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 18:05:28 +0100 Subject: [PATCH 6124/9987] deleting small patches --- .../n/numba/llvmlite-0.39_test-binding.patch | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_test-binding.patch diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_test-binding.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_test-binding.patch deleted file mode 100644 index 732269110c1..00000000000 --- a/easybuild/easyconfigs/n/numba/llvmlite-0.39_test-binding.patch +++ /dev/null @@ -1,40 +0,0 @@ ---- llvmlite/tests/test_binding.py.orig 2022-12-06 18:00:21.729557505 +0000 -+++ llvmlite/tests/test_binding.py 2022-12-06 18:00:49.641795081 +0000 -@@ -18,6 +18,16 @@ - from llvmlite.tests import TestCase - - -+def clean_string_whitespace(x: str) -> str: -+ # Remove trailing whitespace from the end of each line -+ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE) -+ # Remove intermediate blank lines -+ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE) -+ # Remove extraneous whitespace from the beginning and end of the string -+ x = x.strip() -+ return x -+ -+ - # arvm7l needs extra ABI symbols to link successfully - if platform.machine() == 'armv7l': - llvm.load_library_permanently('libgcc_s.so.1') -@@ -555,7 +565,10 @@ - bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#")) - bd.ret(ir.Constant(ir.IntType(32), 12345)) - asm = str(mod) -- self.assertEqual(asm, asm_nonalphanum_blocklabel) -+ self.assertEqual( -+ clean_string_whitespace(asm), -+ clean_string_whitespace(asm_nonalphanum_blocklabel) -+ ) - - def test_global_context(self): - gcontext1 = llvm.context.get_global_context() -@@ -640,7 +653,7 @@ - def test_version(self): - major, minor, patch = llvm.llvm_version_info - # one of these can be valid -- valid = [(11,)] -+ valid = [(11,), (12,), (13,), (14,)] - self.assertIn((major,), valid) - self.assertIn(patch, range(10)) - From 4043ed2622eb220aad05341f9394ba4e3ea17b54 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 18:05:53 +0100 Subject: [PATCH 6125/9987] Delete llvmlite-0.39_passmanager.patch --- .../n/numba/llvmlite-0.39_passmanager.patch | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_passmanager.patch diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_passmanager.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_passmanager.patch deleted file mode 100644 index 8a0df097b10..00000000000 --- a/easybuild/easyconfigs/n/numba/llvmlite-0.39_passmanager.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- ffi/passmanagers.cpp.orig 2022-12-06 15:41:01.230034402 +0000 -+++ ffi/passmanagers.cpp 2022-12-06 15:41:19.678191543 +0000 -@@ -17,9 +17,6 @@ - #include "llvm-c/Transforms/IPO.h" - #include "llvm-c/Transforms/Scalar.h" - #include "llvm/IR/LegacyPassManager.h" --#if LLVM_VERSION_MAJOR > 11 --#include "llvm/IR/RemarkStreamer.h" --#endif - #include "llvm/IR/LLVMRemarkStreamer.h" - #include "llvm/Remarks/RemarkStreamer.h" - #include "llvm/Transforms/IPO.h" From e53ea410cc4d760e96e6e63f381716383e882fcd Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 18:06:20 +0100 Subject: [PATCH 6126/9987] Delete llvmlite-0.39_target.patch --- .../easyconfigs/n/numba/llvmlite-0.39_target.patch | 10 ---------- 1 file changed, 10 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_target.patch diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_target.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_target.patch deleted file mode 100644 index fcf5993a364..00000000000 --- a/easybuild/easyconfigs/n/numba/llvmlite-0.39_target.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ffi/targets.cpp.orig 2022-12-06 15:44:43.191925420 +0000 -+++ ffi/targets.cpp 2022-12-06 15:44:53.916016793 +0000 -@@ -204,7 +204,6 @@ - rm = Reloc::DynamicNoPIC; - - TargetOptions opt; -- opt.PrintMachineCode = PrintMC; - opt.MCOptions.ABIName = ABIName; - - bool jit = JIT; From 2aa88aa2ff7de84a34f85188b61d9278ad87868c Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 18:06:44 +0100 Subject: [PATCH 6127/9987] Delete llvmlite-0.39_targetregistry.patch --- .../n/numba/llvmlite-0.39_targetregistry.patch | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39_targetregistry.patch diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_targetregistry.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_targetregistry.patch deleted file mode 100644 index fdcfc3f07b8..00000000000 --- a/easybuild/easyconfigs/n/numba/llvmlite-0.39_targetregistry.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ffi/targets.cpp.orig 2022-12-07 15:22:37.446261237 +0000 -+++ ffi/targets.cpp 2022-12-07 15:22:47.382407891 +0000 -@@ -6,7 +6,7 @@ - #include "llvm/IR/LegacyPassManager.h" - #include "llvm/IR/Type.h" - #include "llvm/Support/Host.h" --#include "llvm/Support/TargetRegistry.h" -+#include "llvm/MC/TargetRegistry.h" - #include "llvm/Target/TargetMachine.h" - - #include From 27a57979b1752d13e6a0805c68778b3fb5a5517b Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 18:07:12 +0100 Subject: [PATCH 6128/9987] Rename llvmlite-0.39__fix-LLVM-14.patch to llvmlite-0.39_fix-LLVM-14.patch --- ...te-0.39__fix-LLVM-14.patch => llvmlite-0.39_fix-LLVM-14.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/n/numba/{llvmlite-0.39__fix-LLVM-14.patch => llvmlite-0.39_fix-LLVM-14.patch} (100%) diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39__fix-LLVM-14.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39_fix-LLVM-14.patch similarity index 100% rename from easybuild/easyconfigs/n/numba/llvmlite-0.39__fix-LLVM-14.patch rename to easybuild/easyconfigs/n/numba/llvmlite-0.39_fix-LLVM-14.patch From 5505f2dda323b53426bace4e291428bab2da5cd1 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 18:08:32 +0100 Subject: [PATCH 6129/9987] Rename llvmlite-0.39_fix-LLVM-14.patch to llvmlite-0.39.1_fix-LLVM-14.patch --- ...e-0.39_fix-LLVM-14.patch => llvmlite-0.39.1_fix-LLVM-14.patch} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/n/numba/{llvmlite-0.39_fix-LLVM-14.patch => llvmlite-0.39.1_fix-LLVM-14.patch} (100%) diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39_fix-LLVM-14.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch similarity index 100% rename from easybuild/easyconfigs/n/numba/llvmlite-0.39_fix-LLVM-14.patch rename to easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch From f0a85833f2e9606e6bd2c9da923441c5f049bf1a Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 18:27:39 +0100 Subject: [PATCH 6130/9987] Update numba-0.56.4-foss-2022a-CUDA-11.7.0.eb --- .../n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb index 3ec355dc056..07e4d5be4a9 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb @@ -29,19 +29,14 @@ local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " exts_list = [ ('llvmlite', '0.39.1', { 'preinstallopts': local_llvmlite_preinstallopts, - 'patches': ['llvmlite-0.39_passmanager.patch', - 'llvmlite-0.39_target.patch', - 'llvmlite-0.39_test-binding.patch', - 'llvmlite-0.39_targetregistry.patch', - 'llvmlite-0.39_pass.patch', - 'llvmlite-0.39_getparamattribute.patch', + 'patches': ['llvmlite-0.39.1_fix-LLVM-14.patch', ], }), (name, version, { # 'patches': ['numba-0.54.1_fix-numpy-1.21.patch'], 'checksums': [ {'numba-0.56.4.tar.gz': '32d9fef412c81483d7efe0ceb6cf4d3310fde8b624a9cecca00f790573ac96ee'}, - # {'numba-0.54.1_fix-numpy-1.21.patch': 'f038e7adf0cd60f6bdde219b326aad4224fef46515799578ebbbdffa73224199'}, + {'llvmlite-0.39.1_fix-LLVM-14.patch': 'a6a11612046338134779fedb58971deb1d747f6cddd684adec94a3fc2ab10e02'}, ], }), ] From 58490627e19a87a0ca0181c98c775ca0feba8f21 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 18:41:09 +0100 Subject: [PATCH 6131/9987] Update llvmlite-0.39.1_fix-LLVM-14.patch --- easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch index 1c4069336e6..4d09309e51e 100644 --- a/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch @@ -1,3 +1,5 @@ +fix build on top of LLVM 14, +like this: https://github.com/numba/llvmlite/issues/897 diff -ruN llvmlite-0.39.1.orig/ffi/passmanagers.cpp llvmlite-0.39.1/ffi/passmanagers.cpp --- llvmlite-0.39.1.orig/ffi/passmanagers.cpp 2022-09-01 13:47:22.477959200 +0000 +++ llvmlite-0.39.1/ffi/passmanagers.cpp 2023-01-10 16:59:33.776510869 +0000 From 17e7499ce98327beb249498e62c76721d5a6b149 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 18:46:01 +0100 Subject: [PATCH 6132/9987] fixed checksum --- .../easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb index 07e4d5be4a9..82041ef78d8 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb @@ -36,7 +36,7 @@ exts_list = [ # 'patches': ['numba-0.54.1_fix-numpy-1.21.patch'], 'checksums': [ {'numba-0.56.4.tar.gz': '32d9fef412c81483d7efe0ceb6cf4d3310fde8b624a9cecca00f790573ac96ee'}, - {'llvmlite-0.39.1_fix-LLVM-14.patch': 'a6a11612046338134779fedb58971deb1d747f6cddd684adec94a3fc2ab10e02'}, + {'llvmlite-0.39.1_fix-LLVM-14.patch': '9464002d2b40c2b5d6f5f5df2eaa85d2385802d3450dbfd5277aadd27e998573'}, ], }), ] From 8e7ca38c420aa983ae780b7611fa51e28019a9d7 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 17:52:19 +0000 Subject: [PATCH 6133/9987] adding easyconfigs: Spark-3.3.1-foss-2022a.eb --- .../s/Spark/Spark-3.3.1-foss-2022a.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-3.3.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.3.1-foss-2022a.eb b/easybuild/easyconfigs/s/Spark/Spark-3.3.1-foss-2022a.eb new file mode 100644 index 00000000000..8d18d7f2be5 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-3.3.1-foss-2022a.eb @@ -0,0 +1,55 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'Tarball' + +name = 'Spark' +version = '3.3.1' + + + +homepage = 'https://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', + 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' +] +sources = ['%(namelower)s-%(version)s-bin-hadoop3.tgz'] +checksums = ['91df3e3f73682d32261a8b245af6b0553dc5cf4af208ef82219283d23ee01ece'] + +dependencies = [ + ('Python', '3.10.4'), + ('Java', '11', '', SYSTEM), + ('Arrow', '8.0.0'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('py4j', '0.10.9.7', { + 'checksums': ['0b6e5315bb3ada5cf62ac651d107bb2ebc02def3dee9d9548e3baac644ea8dbb'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyspark', 'bin/spark-shell'], + 'dirs': ['python'] +} + +sanity_check_commands = [ + "pyspark -h", + "python -c 'import pyspark'", +] + +modextrapaths = {'PYTHONPATH': ['python', 'lib/python%(pyshortver)s/site-packages']} + +modextravars = {'SPARK_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 23485d15cc203c7e46c1e550895d3acdc6a59269 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Jan 2023 19:39:42 +0100 Subject: [PATCH 6134/9987] Update easybuild/easyconfigs/s/Spark/Spark-3.3.1-foss-2022a.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/s/Spark/Spark-3.3.1-foss-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.3.1-foss-2022a.eb b/easybuild/easyconfigs/s/Spark/Spark-3.3.1-foss-2022a.eb index 8d18d7f2be5..c8cf8bd5e56 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.3.1-foss-2022a.eb @@ -4,9 +4,6 @@ easyblock = 'Tarball' name = 'Spark' version = '3.3.1' - - - homepage = 'https://spark.apache.org' description = """Spark is Hadoop MapReduce done in memory""" From b50d8e18c5d267f0ee2c1387c61a95997e5323d9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Jan 2023 19:55:51 +0100 Subject: [PATCH 6135/9987] bump version to 4.7.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index c39675b8ede..ea1457adbeb 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.7.0' +VERSION = '4.7.1.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From d18e40b3fe96eb570bcdc4a9f34d9c0f287a72ee Mon Sep 17 00:00:00 2001 From: Lars Hellemo Date: Tue, 10 Jan 2023 21:31:30 +0100 Subject: [PATCH 6136/9987] Add Julia v1.8.5 --- .../j/Julia/Julia-1.8.5-linux-x86_64.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb new file mode 100644 index 00000000000..6e35ceec42f --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.8.5' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['e71a24816e8fe9d5f4807664cbbb42738f5aa9fe05397d35c81d4c5d649b9d05'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From ea93e4032f63f7eb97f2abdafe8e82bed616514d Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 11 Jan 2023 08:36:01 +1100 Subject: [PATCH 6137/9987] adding easyconfigs: ParallelIO-2.5.10-gompi-2022a.eb, ParallelIO-2.5.10-iimpi-2022a.eb, PnetCDF-1.12.3-iimpi-2022a.eb --- .../ParallelIO-2.5.10-gompi-2022a.eb | 41 +++++++++++++++++++ .../ParallelIO-2.5.10-iimpi-2022a.eb | 41 +++++++++++++++++++ .../p/PnetCDF/PnetCDF-1.12.3-iimpi-2022a.eb | 35 ++++++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.5.10-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.5.10-iimpi-2022a.eb create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.5.10-gompi-2022a.eb b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.5.10-gompi-2022a.eb new file mode 100644 index 00000000000..5b5cf9824c9 --- /dev/null +++ b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.5.10-gompi-2022a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ParallelIO' +version = '2.5.10' + +homepage = 'https://github.com/NCAR/ParallelIO' +description = """A high-level Parallel I/O Library for structured grid applications""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/NCAR/ParallelIO/archive/'] +sources = ['pio%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['fac694827c81434a7766976711ba7179940e361e8ed0c189c7b397fd44d401de'] + +separate_build_dir = True + +dependencies = [ + ('PnetCDF', '1.12.3'), + ('netCDF-Fortran', '4.6.0'), +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), + ('Doxygen', '1.9.4'), +] + +preconfigopts = "NETCDF_C=$EBROOTNETCDF NETCDF_F=$EBROOTNETCDFMINFORTRAN " +configopts = "-DPIO_ENABLE_TIMING=OFF " + +sanity_check_paths = { + 'files': ['lib/libpiof.a', 'include/pio.mod'], + 'dirs': [], +} + +modextravars = { + 'PIO': '%(installdir)s' +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.5.10-iimpi-2022a.eb b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.5.10-iimpi-2022a.eb new file mode 100644 index 00000000000..7bb4b93031d --- /dev/null +++ b/easybuild/easyconfigs/p/ParallelIO/ParallelIO-2.5.10-iimpi-2022a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ParallelIO' +version = '2.5.10' + +homepage = 'https://github.com/NCAR/ParallelIO' +description = """A high-level Parallel I/O Library for structured grid applications""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/NCAR/ParallelIO/archive/'] +sources = ['pio%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['fac694827c81434a7766976711ba7179940e361e8ed0c189c7b397fd44d401de'] + +separate_build_dir = True + +dependencies = [ + ('PnetCDF', '1.12.3'), + ('netCDF-Fortran', '4.6.0'), +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), + ('Doxygen', '1.9.4'), +] + +preconfigopts = "NETCDF_C=$EBROOTNETCDF NETCDF_F=$EBROOTNETCDFMINFORTRAN " +configopts = "-DPIO_ENABLE_TIMING=OFF " + +sanity_check_paths = { + 'files': ['lib/libpiof.a', 'include/pio.mod'], + 'dirs': [], +} + +modextravars = { + 'PIO': '%(installdir)s' +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-iimpi-2022a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-iimpi-2022a.eb new file mode 100644 index 00000000000..e1cc4ae8c35 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-iimpi-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = '1.12.3' + +homepage = 'https://parallel-netcdf.github.io/' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'iimpi', 'version': '2022a'} + +source_urls = ['https://parallel-netcdf.github.io/Release'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['439e359d09bb93d0e58a6e3f928f39c2eae965b6c97f64e67cd42220d6034f77'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Perl', '5.34.1'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' From d57fdd5790ab831c7a3682a6edcfd46220cccc4b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 11 Jan 2023 10:09:48 +0100 Subject: [PATCH 6138/9987] adding easyconfigs: imkl-2022.1.0-gompi-2022a.eb, gomkl-2022a.eb --- easybuild/easyconfigs/g/gomkl/gomkl-2022a.eb | 19 +++++++++++++++++++ .../i/imkl/imkl-2022.1.0-gompi-2022a.eb | 19 +++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/gomkl/gomkl-2022a.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2022a.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2022a.eb new file mode 100644 index 00000000000..125f99c761b --- /dev/null +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2022a.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gomkl' +version = '2022a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" + +toolchain = SYSTEM + +local_comp = ('GCC', '11.3.0') + +dependencies = [ + local_comp, + ('OpenMPI', '4.1.4', '', local_comp), + ('imkl', '2022.1.0', '', ('gompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb new file mode 100644 index 00000000000..2eb923c837e --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.1.0-gompi-2022a.eb @@ -0,0 +1,19 @@ +## +# Author: Robert Mijakovic +## +name = 'imkl' +version = '2022.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18721/'] +sources = ['l_onemkl_p_%(version)s.223_offline.sh'] +checksums = ['4b325a3c4c56e52f4ce6c8fbb55d7684adc16425000afc860464c0f29ea4563e'] + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' From 253ae8d8330093ff0742394c7a3f9494e29d479b Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 11 Jan 2023 10:14:08 +0100 Subject: [PATCH 6139/9987] checksum position --- .../n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb index 82041ef78d8..13a79719f5e 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb @@ -29,14 +29,15 @@ local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " exts_list = [ ('llvmlite', '0.39.1', { 'preinstallopts': local_llvmlite_preinstallopts, - 'patches': ['llvmlite-0.39.1_fix-LLVM-14.patch', + 'patches': ['llvmlite-0.39.1_fix-LLVM-14.patch'], + 'checksums': [ + {'llvmlite-0.39.1_fix-LLVM-14.patch': '9464002d2b40c2b5d6f5f5df2eaa85d2385802d3450dbfd5277aadd27e998573'}, ], }), (name, version, { # 'patches': ['numba-0.54.1_fix-numpy-1.21.patch'], 'checksums': [ {'numba-0.56.4.tar.gz': '32d9fef412c81483d7efe0ceb6cf4d3310fde8b624a9cecca00f790573ac96ee'}, - {'llvmlite-0.39.1_fix-LLVM-14.patch': '9464002d2b40c2b5d6f5f5df2eaa85d2385802d3450dbfd5277aadd27e998573'}, ], }), ] From df6144f7f19942dd52e04b2698fe354a5bfbc928 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 11 Jan 2023 10:34:52 +0100 Subject: [PATCH 6140/9987] Update numba-0.56.4-foss-2022a-CUDA-11.7.0.eb --- .../easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb index 13a79719f5e..59160edc0be 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb @@ -31,6 +31,7 @@ exts_list = [ 'preinstallopts': local_llvmlite_preinstallopts, 'patches': ['llvmlite-0.39.1_fix-LLVM-14.patch'], 'checksums': [ + {'llvmlite-0.39.1.tar.gz': 'b43abd7c82e805261c425d50335be9a6c4f84264e34d6d6e475207300005d572'}, {'llvmlite-0.39.1_fix-LLVM-14.patch': '9464002d2b40c2b5d6f5f5df2eaa85d2385802d3450dbfd5277aadd27e998573'}, ], }), From 5a9dcdcd97a0cfbe5ae7c6a6b84a3ecda59c440c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 11 Jan 2023 12:50:40 +0000 Subject: [PATCH 6141/9987] Alternative checksum for UCX 1.13.1 --- easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb index bdc002c20df..4afeb7356b2 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb @@ -19,7 +19,8 @@ patches = [ 'UCX-1.13.1_fix-undeclared-PTR.patch', ] checksums = [ - {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, + {'ucx-1.13.1.tar.gz': ('efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828' + '2c4a2f96c700e3705e185c2846a710691b6e800e8aec11fd4b3e47bcc3990548')}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, {'UCX-1.13.1_fix-undeclared-PTR.patch': 'ef22c29604552ad3223f2a6bac352f30023cc5cf68f786abfdc4ad7c04189a76'}, ] From b276be48942cb2c2de06412afa7c2274fa88a25b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 11 Jan 2023 13:06:30 +0000 Subject: [PATCH 6142/9987] remember the comma --- easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb index 4afeb7356b2..3db0659023c 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb @@ -19,7 +19,7 @@ patches = [ 'UCX-1.13.1_fix-undeclared-PTR.patch', ] checksums = [ - {'ucx-1.13.1.tar.gz': ('efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828' + {'ucx-1.13.1.tar.gz': ('efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828', '2c4a2f96c700e3705e185c2846a710691b6e800e8aec11fd4b3e47bcc3990548')}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, {'UCX-1.13.1_fix-undeclared-PTR.patch': 'ef22c29604552ad3223f2a6bac352f30023cc5cf68f786abfdc4ad7c04189a76'}, From 9dc071d730c9952c289f3665b79cb23cac626277 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 11 Jan 2023 14:28:27 +0100 Subject: [PATCH 6143/9987] Update numba-0.56.4-foss-2022a-CUDA-11.7.0.eb --- .../easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb index 59160edc0be..01f81467022 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a-CUDA-11.7.0.eb @@ -32,7 +32,7 @@ exts_list = [ 'patches': ['llvmlite-0.39.1_fix-LLVM-14.patch'], 'checksums': [ {'llvmlite-0.39.1.tar.gz': 'b43abd7c82e805261c425d50335be9a6c4f84264e34d6d6e475207300005d572'}, - {'llvmlite-0.39.1_fix-LLVM-14.patch': '9464002d2b40c2b5d6f5f5df2eaa85d2385802d3450dbfd5277aadd27e998573'}, + {'llvmlite-0.39.1_fix-LLVM-14.patch': '39cde92d522cce45f8b93231059f7e2c69bc54dc7c35c4c6eaee3423f3f04d17'}, ], }), (name, version, { From 7724a70d2bc762d899101f012fa281050babb1e1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 11 Jan 2023 13:31:48 +0000 Subject: [PATCH 6144/9987] alt checksums --- easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb index 3db0659023c..6852321bf6a 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb @@ -19,8 +19,8 @@ patches = [ 'UCX-1.13.1_fix-undeclared-PTR.patch', ] checksums = [ - {'ucx-1.13.1.tar.gz': ('efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828', - '2c4a2f96c700e3705e185c2846a710691b6e800e8aec11fd4b3e47bcc3990548')}, + ('efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828', + '2c4a2f96c700e3705e185c2846a710691b6e800e8aec11fd4b3e47bcc3990548'), # ucx-1.13.1.tar.gz {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, {'UCX-1.13.1_fix-undeclared-PTR.patch': 'ef22c29604552ad3223f2a6bac352f30023cc5cf68f786abfdc4ad7c04189a76'}, ] From b11d205d229cd1bfb2670b36439ac85f870825ea Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 11 Jan 2023 15:43:40 +0000 Subject: [PATCH 6145/9987] and also UCX-CUDA --- .../u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) mode change 100644 => 100755 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb old mode 100644 new mode 100755 index 3025ba35f6d..fc291f60b80 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -19,7 +19,8 @@ source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch'] checksums = [ - {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, + ('efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828', + '2c4a2f96c700e3705e185c2846a710691b6e800e8aec11fd4b3e47bcc3990548'), # ucx-1.13.1.tar.gz {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, ] From 4e565b99b1abd518221f48a510010f156a887525 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 11 Jan 2023 17:21:11 +0100 Subject: [PATCH 6146/9987] Added Python3_EXECUTABLE argument to ravenpy --- easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index 502affd4f48..ecf094af5d5 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -41,7 +41,8 @@ exts_list = [ 'sources': ['%(version)s.tar.gz'], 'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'], 'preinstallopts': 'sed -i \'s|cmake_args += \["-GNinja"\]|cmake_args += \["-GNinja", \ - "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION"\]|\' setup.py && ' + "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION",\ + "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python"\]|\' setup.py && ' }), ] From 259cb1787ec0febb38f8224406c4e16745b65c49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Jan 2023 18:42:16 +0100 Subject: [PATCH 6147/9987] {data}[foss/2021b,intel/2021b] GDAL v2.4.4 --- .../g/GDAL/GDAL-2.4.4-foss-2021b.eb | 69 ++++++++++++++++++ .../g/GDAL/GDAL-2.4.4-intel-2021b.eb | 71 +++++++++++++++++++ .../GDAL/GDAL-2.4.4_fix-include-limits.patch | 13 ++++ .../GEOS-3.9.1-intel-compilers-2021.4.0.eb | 20 ++++++ 4 files changed, 173 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-2.4.4_fix-include-limits.patch create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb new file mode 100644 index 00000000000..272fbef7477 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb @@ -0,0 +1,69 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.4.4' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'extra_cxxflags': "-fpermissive"} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = [ + 'GDAL-3.0.0_fix-python-CC-CXX.patch', + 'GDAL-2.4.4_fix-include-limits.patch', +] +checksums = [ + {'gdal-2.4.4.tar.xz': 'a383bd3cf555d6e1169666b01b5b3025b2722ed39e834f1b65090f604405dcd8'}, + {'GDAL-3.0.0_fix-python-CC-CXX.patch': '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381'}, + {'GDAL-2.4.4_fix-include-limits.patch': 'f8d9f74dabc1167a88d41f5c715d9d9b098016c94eec0339b2f6f8dfe3c05deb'}, +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('netCDF', '4.8.1'), + ('expat', '2.4.1'), + ('GEOS', '3.9.1'), + ('SQLite', '3.36'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('JasPer', '2.0.33'), + ('LibTIFF', '4.3.0'), + ('zlib', '1.2.11'), + ('cURL', '7.78.0'), + ('PCRE', '8.45'), + ('PROJ', '8.1.0'), + ('libgeotiff', '1.7.0'), + ('SciPy-bundle', '2021.10'), + ('HDF5', '1.12.1'), + ('HDF', '4.2.15'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import osgeo.gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb new file mode 100644 index 00000000000..ea1ba09e6b1 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb @@ -0,0 +1,71 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.4.4' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True, 'extra_cxxflags': "-fpermissive"} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = [ + 'GDAL-3.0.0_fix-python-CC-CXX.patch', + 'GDAL-2.4.4_fix-include-limits.patch', +] +checksums = [ + {'gdal-2.4.4.tar.xz': 'a383bd3cf555d6e1169666b01b5b3025b2722ed39e834f1b65090f604405dcd8'}, + {'GDAL-3.0.0_fix-python-CC-CXX.patch': '223a0ed1afb245527d546bb19e4f80c00f768516ab106d82e53cf36b5a1a2381'}, + {'GDAL-2.4.4_fix-include-limits.patch': 'f8d9f74dabc1167a88d41f5c715d9d9b098016c94eec0339b2f6f8dfe3c05deb'}, +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('netCDF', '4.8.1'), + ('expat', '2.4.1'), + ('GEOS', '3.9.1'), + ('SQLite', '3.36'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('JasPer', '2.0.33'), + ('LibTIFF', '4.3.0'), + ('zlib', '1.2.11'), + ('cURL', '7.78.0'), + ('PCRE', '8.45'), + ('PROJ', '8.1.0'), + ('libgeotiff', '1.7.0'), + ('SciPy-bundle', '2021.10'), + ('HDF5', '1.12.1'), + ('HDF', '4.2.15'), +] + +preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' +configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' + +prebuildopts = 'env LDSHARED="$CC -shared" ' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import osgeo.gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4_fix-include-limits.patch b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4_fix-include-limits.patch new file mode 100644 index 00000000000..9734b37c312 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4_fix-include-limits.patch @@ -0,0 +1,13 @@ +add missing include statement for limits header file +fixes "error: numeric_limits is not a member of std" +author: Kenneth Hoste (HPC-UGent) +--- /tmp/vsc40023/easybuild_build/GDAL/2.4.4/foss-2021b/gdal-2.4.4/ogr/ogrsf_frmts/cad/libopencad/dwg/r2000.cpp.orig 2023-01-11 17:38:21.326828174 +0100 ++++ /tmp/vsc40023/easybuild_build/GDAL/2.4.4/foss-2021b/gdal-2.4.4/ogr/ogrsf_frmts/cad/libopencad/dwg/r2000.cpp 2023-01-11 17:38:36.009850820 +0100 +@@ -38,6 +38,7 @@ + #include + #include + #include ++#include + + #if ((defined(__sun__) || defined(__FreeBSD__)) && __GNUC__ == 4 && __GNUC_MINOR__ == 8) || defined(__ANDROID__) + // gcc 4.8 on Solaris 11.3 or FreeBSD 11 doesn't have std::string diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..e2593941ddb --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.9.1-intel-compilers-2021.4.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.9.1' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['7e630507dcac9dc07565d249a26f06a15c9f5b0c52dd29129a0e3d381d7e382a'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' From 31b7971f3d4baa345fad7308ff399ece26e58b8b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 11 Jan 2023 18:13:04 +0000 Subject: [PATCH 6148/9987] adding easyconfigs: CellRanger-7.1.0.eb --- .../c/CellRanger/CellRanger-7.1.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellRanger/CellRanger-7.1.0.eb diff --git a/easybuild/easyconfigs/c/CellRanger/CellRanger-7.1.0.eb b/easybuild/easyconfigs/c/CellRanger/CellRanger-7.1.0.eb new file mode 100644 index 00000000000..fc786ab6fbe --- /dev/null +++ b/easybuild/easyconfigs/c/CellRanger/CellRanger-7.1.0.eb @@ -0,0 +1,31 @@ +# The STAR binary included in this version has been vectorized with AVX +# hence it is not recommended for systems that do not support it. + +easyblock = 'Tarball' + +name = 'CellRanger' +version = '7.1.0' + +homepage = 'https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger' +description = """Cell Ranger is a set of analysis pipelines that process Chromium + single-cell RNA-seq output to align reads, generate gene-cell matrices and perform + clustering and gene expression analysis.""" + +toolchain = SYSTEM + +download_instructions = """ +Download manually from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest +""" +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c4f9b142e3c30ad10ae15d25868df2b4fd05bdb3bbd47da0c83a7cc649b577e'] + +keepsymlinks = True + +sanity_check_paths = { + 'files': ['bin/cellranger'], + 'dirs': ['bin/rna', 'bin/tenkit'], +} + +sanity_check_commands = ['cellranger testrun --id=tiny'] + +moduleclass = 'bio' From 4c50ff2db8d03f20edc8fa73141bc598e9344501 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Jan 2023 19:56:51 +0100 Subject: [PATCH 6149/9987] adding easyconfigs: scArches-0.5.6-foss-2021a-CUDA-11.3.1.eb --- .../scArches-0.5.6-foss-2021a-CUDA-11.3.1.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/s/scArches/scArches-0.5.6-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.5.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/scArches/scArches-0.5.6-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..12280551fa5 --- /dev/null +++ b/easybuild/easyconfigs/s/scArches/scArches-0.5.6-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'scArches' +version = '0.5.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/theislab/scarches' +description = """Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell + data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('h5py', '3.2.1'), + ('leidenalg', '0.8.7'), + ('scanpy', '1.8.1'), + ('scikit-learn', '0.24.2'), + ('scvi-tools', '0.16.4', versionsuffix), + ('PyTorch', '1.10.0', versionsuffix), + ('tqdm', '4.61.2'), + ('BeautifulSoup', '4.10.0'), + ('loompy', '3.0.7'), +] + +use_pip = True + +exts_list = [ + ('gdown', '4.6.0', { + 'checksums': ['5ce3db0aeda54f46caacb2df86f31c3e3ecd17c355689e6456d85fb528ba9749'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), + ('muon', '0.1.2', { + 'sources': [SOURCE_PY3_WHL], + 'checksums': ['61e0290b113f85177b7596e57aa01552c07700716fac3b8267506fc8a6881dba'], + }), + ('newick', '1.4.0', { + 'checksums': ['0d76ff2fbd180ea790ba177557bf8fbdc56fc166cbe5b31a38113ead8147cf6d'], + }), + ('scHPL', '1.0.2', { + 'checksums': ['a4119fb503e5bfed6fb3e5424cf166d9b1d8822ca0d7fe88d7125807e6da118b'], + 'preinstallopts': "sed -i 's/~=/>=/g' setup.py && ", + 'modulename': 'scHPL', + }), + (name, version, { + 'checksums': ['87b5aa89676b37f65f076631faf3033515cc8380dfad076699410628a1838116'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 0f9bb4576ac4e7797be43e3c229176a3b2efdda0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 11 Jan 2023 22:08:59 +0100 Subject: [PATCH 6150/9987] add HPL easyconfig --- .../easyconfigs/h/HPL/HPL-2.3-gomkl-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2022a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2022a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2022a.eb new file mode 100644 index 00000000000..170c480afe8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-gomkl-2022a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'gomkl', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' From 3a6f7d4b40d3ac383fb4b1c5c5773c194e704e7b Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 12 Jan 2023 12:35:27 +0000 Subject: [PATCH 6151/9987] adding easyconfigs: JAGS-4.3.1-foss-2022a.eb --- .../j/JAGS/JAGS-4.3.1-foss-2022a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb new file mode 100644 index 00000000000..56faa358bf6 --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.3.1' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download') +] +sources = [SOURCE_TAR_GZ] +checksums = ['f9258355b5e9eb13bd33c5fa720f0cbebacea7d0a4a42b71b0fb14501ee14229'] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/%(name)s', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' From 58f3f56d65636b851c8659517b90fe89b3621c24 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 12 Jan 2023 12:36:12 +0000 Subject: [PATCH 6152/9987] adding easyconfigs: rjags-4-13-foss-2022a-R-4.2.1.eb --- .../r/rjags/rjags-4-13-foss-2022a-R-4.2.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..a19bae4623f --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022a-R-4.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-13' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['f85cc34c5127b828d8a3fa3613ef29f147c868bdaf55eb0f7406c10abbf92b32'] + +dependencies = [ + ('R', '4.2.1'), + ('JAGS', '4.3.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' From 7aeaa03b0f20def2222d325b6782bdcf0164c824 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 12 Jan 2023 18:28:51 +0100 Subject: [PATCH 6153/9987] adding easyconfigs: Blitz++-1.0.2-GCCcore-12.2.0.eb --- .../b/Blitz++/Blitz++-1.0.2-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a43fedf0271 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Blitz++' +version = '1.0.2' + +homepage = 'https://github.com/blitzpp/blitz' + +description = """ + Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation + in C++ with a speed comparable to Fortran implementations, while preserving an + object-oriented interface +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [('https://github.com/blitzpp/blitz/archive/')] +sources = ['%(version)s.tar.gz'] +patches = ['blitz-%(version)s_pkgconfig.patch'] +checksums = [ + '500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2', # 1.0.2.tar.gz + 'd15fb397e75eb009809ecacdd7f2f154ff05e6586895f3b0511d0b53a6e3b9fe', # blitz-1.0.2_pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3') +] + +sanity_check_paths = { + 'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT], + 'dirs': ['include/blitz/array', 'include/blitz/meta', + 'include/random', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 81ed7a43218d56f5aecd589b7b9ec39ebaa8c421 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 12 Jan 2023 18:46:25 +0000 Subject: [PATCH 6154/9987] adding easyconfigs: xxd-8.2.4220-GCCcore-11.3.0.eb, PLUMED-2.8.1-foss-2022a.eb --- .../p/PLUMED/PLUMED-2.8.1-foss-2022a.eb | 60 +++++++++++++++++++ .../x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb | 39 ++++++++++++ 2 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb new file mode 100644 index 00000000000..39272200991 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb @@ -0,0 +1,60 @@ +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.8.1' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['95f6cbc9134d3ad05ad4652e5e6f12dfbd6313a95a47d7ca6c8bfca147ecd7d5'] + +builddependencies = [ + ('xxd', '8.2.4220'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('GSL', '2.7'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3aa02fbcfe1 --- /dev/null +++ b/easybuild/easyconfigs/x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +# Last contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'xxd' +version = '8.2.4220' + +homepage = 'https://www.vim.org' +description = """xxd is part of the VIM package and this will only install xxd, not vim! +xxd converts to/from hexdumps of binary files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/vim/vim/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604', # v8.2.4220.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), +] + +start_dir = 'src/xxd' + +files_to_copy = [ + (['xxd'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/xxd'], + 'dirs': [], +} + +sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"] + +moduleclass = 'tools' From b807883114df8dfc2dd2814fa2fb6adf2514a41f Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Fri, 13 Jan 2023 14:37:45 +1100 Subject: [PATCH 6155/9987] adding easyconfigs: libpspio-0.2.4-intel-compilers-2021.2.0.eb, libpspio-0.2.4-intel-compilers-2021.4.0.eb, libpspio-0.2.4-GCC-11.2.0.eb --- .../l/libpspio/libpspio-0.2.4-GCC-11.2.0.eb | 26 +++++++++++++++++++ ...libpspio-0.2.4-intel-compilers-2021.2.0.eb | 26 +++++++++++++++++++ ...libpspio-0.2.4-intel-compilers-2021.4.0.eb | 26 +++++++++++++++++++ 3 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-11.2.0.eb new file mode 100644 index 00000000000..31ccebb8ca4 --- /dev/null +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpspio' +version = '0.2.4' + +homepage = 'https://gitlab.com/ElectronicStructureLibrary/libpspio' +description = """libpspio is a library to read and write pseudopotentials in multiple formats.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://gitlab.com/ElectronicStructureLibrary/libpspio/uploads/7efa924be97bd46354237ca3fb89495e'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cb3d51ffa6b822305bb943edc7ddfaf1cfc1b928f0594330d732330bfc081850'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [('GSL', '2.7')] + +configopts = ' --enable-gsl --enable-fortran ' + +sanity_check_paths = { + 'files': ['include/pspiof_m.mod', 'include/pspio.h', 'lib/libpspiof.a'], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.2.0.eb new file mode 100644 index 00000000000..1b5eab08afe --- /dev/null +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpspio' +version = '0.2.4' + +homepage = 'https://gitlab.com/ElectronicStructureLibrary/libpspio' +description = """libpspio is a library to read and write pseudopotentials in multiple formats.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://gitlab.com/ElectronicStructureLibrary/libpspio/uploads/7efa924be97bd46354237ca3fb89495e'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cb3d51ffa6b822305bb943edc7ddfaf1cfc1b928f0594330d732330bfc081850'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [('GSL', '2.7')] + +configopts = ' --enable-gsl --enable-fortran ' + +sanity_check_paths = { + 'files': ['include/pspiof_m.mod', 'include/pspio.h', 'lib/libpspiof.a'], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..7862af64726 --- /dev/null +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.4.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpspio' +version = '0.2.4' + +homepage = 'https://gitlab.com/ElectronicStructureLibrary/libpspio' +description = """libpspio is a library to read and write pseudopotentials in multiple formats.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://gitlab.com/ElectronicStructureLibrary/libpspio/uploads/7efa924be97bd46354237ca3fb89495e'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cb3d51ffa6b822305bb943edc7ddfaf1cfc1b928f0594330d732330bfc081850'] + +builddependencies = [('pkg-config', '0.29.2')] + +dependencies = [('GSL', '2.7')] + +configopts = ' --enable-gsl --enable-fortran ' + +sanity_check_paths = { + 'files': ['include/pspiof_m.mod', 'include/pspio.h', 'lib/libpspiof.a'], + 'dirs': [], +} + +moduleclass = 'phys' From a85f905e17c5e7cd2a09e5de5b3944065241c973 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 13 Jan 2023 12:24:54 +0100 Subject: [PATCH 6156/9987] adding easyconfigs: toil-5.8.0-foss-2021a.eb, cwltool-3.1.20221008225030-foss-2021a.eb --- .../cwltool-3.1.20221008225030-foss-2021a.eb | 108 +++++++++++++++ .../t/toil/toil-5.8.0-foss-2021a.eb | 126 ++++++++++++++++++ 2 files changed, 234 insertions(+) create mode 100644 easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221008225030-foss-2021a.eb create mode 100644 easybuild/easyconfigs/t/toil/toil-5.8.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221008225030-foss-2021a.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221008225030-foss-2021a.eb new file mode 100644 index 00000000000..91182ba8816 --- /dev/null +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221008225030-foss-2021a.eb @@ -0,0 +1,108 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'cwltool' +version = '3.1.20221008225030' + +homepage = 'https://github.com/common-workflow-language/cwltool' +description = """Common workflow language (CWL) reference implementation.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# The Qt5 dependency of Graphviz (required by pydot) may be long to build and +# requires a lot of disk space and memory! +dependencies = [ + ('Python', '3.9.5'), + ('typing-extensions', '3.10.0.0'), + ('pydot', '1.4.2'), + ('lxml', '4.6.3'), + ('ruamel.yaml', '0.17.21'), + ('networkx', '2.5.1'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('argcomplete', '2.0.0', { + 'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', '6.2.0', { + 'checksums': ['62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942'], + }), + ('mistune', '2.0.4', { + 'checksums': ['9ee0a66053e2267aba772c71e06891fa8f1af6d4b01d5e84e267b4570d4d9808'], + }), + ('schema-salad', '8.3.20230109181936', { + 'modulename': 'schema_salad', + 'checksums': ['e0fb8fbe793dda42133f374642be9f1af1651bbfb3ca37e341d8866d695de45a'], + }), + ('shellescape', '3.8.1', { + 'checksums': ['40b310b30479be771bf3ab28bd8d40753778488bd46ea0969ba0b35038c3ec26'], + }), + ('cwlformat', '2022.2.18', { + 'modulename': 'cwlformat', + 'source_tmpl': 'cwlformat-%(version)s-py3-none-any.whl', + 'checksums': ['d3e2dca192ce10e703ed4eb0bae26539db08d8ddd7c6a6fe9d1406c3f1b53cda'], + }), + ('cwl-upgrader', '1.2.4', { + 'modulename': 'cwlupgrader', + 'checksums': ['b25fc236407343d44cc830ac3f63eed395b8d872fc7e17db92cde583d4a3b2ec'], + }), + ('cwl-utils', '0.21', { + 'modulename': 'cwl_utils', + 'checksums': ['583f05010f7572f3a69310325472ccb6efc2db7f43dc6428d03552e0ffcbaaf9'], + }), + ('mypy-extensions', '0.4.3', { + 'modulename': 'mypy_extensions', + 'source_tmpl': 'mypy_extensions-%(version)s.tar.gz', + 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], + }), + ('prov', '1.5.1', { + 'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'], + }), + ('bagit', '1.8.1', { + 'checksums': ['37df1330d2e8640c8dee8ab6d0073ac701f0614d25f5252f9e05263409cee60c'], + }), + (name, version, { + 'checksums': ['9fbf2996ba673d83eaf28c745560f68992c08ab668eab2447957dbaaee8881b0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cwltool'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cwltool --version"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/toil/toil-5.8.0-foss-2021a.eb b/easybuild/easyconfigs/t/toil/toil-5.8.0-foss-2021a.eb new file mode 100644 index 00000000000..55bde0edd83 --- /dev/null +++ b/easybuild/easyconfigs/t/toil/toil-5.8.0-foss-2021a.eb @@ -0,0 +1,126 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'PythonBundle' + +name = 'toil' +version = '5.8.0' + +homepage = 'https://github.com/DataBiosphere/toil' +description = """A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('dill', '0.3.4'), + # For extras 'cwl' + ('cwltool', '3.1.20221008225030'), + ('PyYAML', '5.4.1'), + ('boto3', '1.20.13'), +] + +use_pip = True + +# TODO add pymesos, wes_client ? +exts_list = [ + ('typing-extensions', '4.4.0', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('addict', '2.4.0', { + 'checksums': ['b3b2210e0e067a281f5646c8c5db92e99b7231ea8b0eb5f74dbdf9e259d4e494'], + }), + ('blessed', '1.19.1', { + 'checksums': ['9a0d099695bf621d4680dd6c73f6ad547f6a3442fbdbe80c4b1daa1edbc492fc'], + }), + ('prefixed', '0.4.2', { + 'checksums': ['81f4e3bc15046e772713ab80f08690e61c52cceb20141425754eab5b00b130c9'], + }), + ('enlighten', '1.11.1', { + 'checksums': ['57abd98a3d3f83484ef9f91f9255f4d23c8b3097ecdb647c7b9b0049d600b7f8'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + ('docker', '5.0.3', { + 'checksums': ['d916a26b62970e7c2f554110ed6af04c7ccff8e9f81ad17d0d40c75637e227fb'], + }), + ('py-tes', '0.4.2', { + 'modulename': 'tes', + 'checksums': ['f6926cd59b7dfc8e37840955bf1cc7c43ad4d99ba5eae100b6156c918617472c'], + }), + # extra cwl requirements + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('galaxy-containers', '22.1.1', { + 'modulename': 'galaxy.containers', + 'checksums': ['41e0003b18e580175d443cf21e9c2d2eb21a265c012164f7255cdb0c03a76334'], + }), + ('bleach', '5.0.1', { + 'checksums': ['0d03255c47eb9bd2f26aa9bb7f2107732e7e8fe195ca2f64709fcf3b0a4a085c'], + }), + ('boltons', '21.0.0', { + 'checksums': ['65e70a79a731a7fe6e98592ecfb5ccf2115873d01dbc576079874629e5c90f13'], + }), + ('importlib-resources', '5.10.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668'], + }), + ('pycryptodome', '3.15.0', { + 'modulename': 'Crypto', + 'checksums': ['9135dddad504592bcc18b0d2d95ce86c3a5ea87ec6447ef25cfedea12d6018b8'], + }), + ('repoze.lru', '0.7', { + 'checksums': ['0429a75e19380e4ed50c0694e26ac8819b4ea7851ee1fc7583c8572db80aff77'], + }), + ('Routes', '2.5.1', { + 'modulename': 'routes', + 'checksums': ['b6346459a15f0cbab01a45a90c3d25caf980d4733d628b4cc1952b865125d053'], + }), + ('zipstream-new', '1.1.8', { + 'modulename': 'zipstream', + 'checksums': ['b031fe181b94e51678389d26b174bc76382605a078d7d5d8f5beae083f111c76'], + }), + ('PyPubSub', '4.0.3', { + 'modulename': 'pubsub', + 'source_tmpl': 'Pypubsub-%(version)s-py3-none-any.whl', + 'checksums': ['7f716bae9388afe01ff82b264ba8a96a8ae78b42bb1f114f2716ca8f9e404e2a'], + }), + ('boto', '2.49.0', { + 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], + }), + ('galaxy-util', '22.1.1', { + 'modulename': 'galaxy.util', + 'checksums': ['70c1b79f2d2da64a7402f0dee70b4e4975ce49e14d6fa3a66d2e36f5ceb2bacf'], + }), + ('galaxy-tool-util', '22.1.4', { + 'modulename': 'galaxy.tool_util', + 'checksums': ['03e6ac9949c1422d3f872ffa7983180d6af07b5358ec4ed3b97180ebf43261d4'], + }), + (name, version, { + 'modulename': name, + 'use_pip_extras': 'cwl', + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['5eb9b968ddfa7badd81287bfccd3ae38d62ad4b4020e911c1936d393ae1d25a2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/toil', 'bin/toil-cwl-runner'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["toil --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From b61c8167b6cfbbf03a606dcf84c8300b574cf5b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 13 Jan 2023 14:16:35 +0000 Subject: [PATCH 6157/9987] adding easyconfigs: STREAM-5.10-GCC-11.3.0.eb, STREAM-5.10-intel-compilers-2022.2.1.eb --- .../s/STREAM/STREAM-5.10-GCC-11.3.0.eb | 39 +++++++++++++++++++ .../STREAM-5.10-intel-compilers-2022.2.1.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-11.3.0.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-11.3.0.eb new file mode 100644 index 00000000000..a8616f8d1a6 --- /dev/null +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-GCC-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CmdCp' + +name = 'STREAM' +version = '5.10' + +homepage = 'https://www.cs.virginia.edu/stream/' +description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable + memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] +sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c', 'extract_cmd': "cp %s ."}] +checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] + +# 10 million array elements (1000 runs): requires ~224MB of memory +local_cmds = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " +# 100 million array elements (1000 runs): requires ~2.2GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " +# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " +# 5 billion array elements (1000 runs): requires ~111 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " + +cmds_map = [('stream-%(version)s.c', local_cmds)] + +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'dirs': [], +} + +tests = ['%(installdir)s/bin/stream_1Kx10M'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..c2939d47766 --- /dev/null +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-compilers-2022.2.1.eb @@ -0,0 +1,39 @@ +easyblock = 'CmdCp' + +name = 'STREAM' +version = '5.10' + +homepage = 'https://www.cs.virginia.edu/stream/' +description = """The STREAM benchmark is a simple synthetic benchmark program that measures sustainable + memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} +toolchainopts = {'openmp': True} + +source_urls = ['https://www.cs.virginia.edu/stream/FTP/Code/'] +sources = [{'download_filename': '%(namelower)s.c', 'filename': 'stream-%(version)s.c', 'extract_cmd': "cp %s ."}] +checksums = ['a52bae5e175bea3f7832112af9c085adab47117f7d2ce219165379849231692b'] + +# 10 million array elements (1000 runs): requires ~224MB of memory +local_cmds = "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=10000000 -DNTIMES=1000 -o stream_1Kx10M; " +# 100 million array elements (1000 runs): requires ~2.2GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=100000000 -DNTIMES=1000 -o stream_1Kx100M; " +# 1 billion array elements (1000 runs): requires ~22.4 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=1000000000 -DNTIMES=1000 -o stream_1Kx1B; " +# 2.5 billion array elements (1000 runs): requires ~56 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=2500000000 -DNTIMES=1000 -o stream_1Kx2.5B; " +# 5 billion array elements (1000 runs): requires ~111 GiB of memory +local_cmds += "$CC $CFLAGS %(source)s -mcmodel=large -DSTREAM_ARRAY_SIZE=5000000000 -DNTIMES=1000 -o stream_1Kx5B; " + +cmds_map = [('stream-%(version)s.c', local_cmds)] + +files_to_copy = [(['stream_1Kx10M', 'stream_1Kx100M', 'stream_1Kx1B', 'stream_1Kx2.5B', 'stream_1Kx5B'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stream_1Kx10M', 'bin/stream_1Kx100M', 'bin/stream_1Kx1B', 'bin/stream_1Kx2.5B', 'bin/stream_1Kx5B'], + 'dirs': [], +} + +tests = ['%(installdir)s/bin/stream_1Kx10M'] + +moduleclass = 'perf' From 0e47396e64183c44100c881e6bed384b75ae8043 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 13 Jan 2023 14:57:16 +0000 Subject: [PATCH 6158/9987] adding easyconfigs: Xvfb-21.1.6-GCCcore-12.2.0.eb, nettle-3.8.1-GCCcore-12.2.0.eb, libxslt-1.1.37-GCCcore-12.2.0.eb --- .../libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb | 31 +++++ .../n/nettle/nettle-3.8.1-GCCcore-12.2.0.eb | 38 ++++++ .../x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb | 123 ++++++++++++++++++ 3 files changed, 192 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.8.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a470ca75fab --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.37' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['3a4b27dc8027ccd6146725950336f1ec520928f320f144eb5fa7990ae6123ab4'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('zlib', '1.2.12'), + ('libxml2', '2.10.3'), +] + +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.8.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.8.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7389e42ad8e --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.8.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.8.1' + +homepage = 'https://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['364f3e2b77cd7dcde83fd7c45219c834e54b0c75e428b6f894a23d12dd41cbfe'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = '--disable-openssl ' # openssl is just used for the nettle-openssl example and requires openssl 1.1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6a259d10a04 --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb @@ -0,0 +1,123 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '21.1.6' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Python', '3.10.8'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('libxslt', '1.1.37'), + ('gettext', '0.21.1'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('X11', '20221110'), + ('pixman', '0.42.2'), + ('libdrm', '2.4.114'), + ('Mesa', '22.2.4'), + ('nettle', '3.8.1'), + ('libunwind', '1.6.2'), + ('XZ', '5.2.7'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.2', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['4a5af55e670713024639a7f7d10826d905d86faf574cd77e0f5aef2d00e70168'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.3.3', { + 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], + }), + ('font-misc-misc', '1.1.2', { + 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], + 'preconfigopts': local_font_misc_preconfigopts, + }), + ('xkbcomp', '1.4.6', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['e88a4d86b9925ea1e8685dd5ea29c815abafb8ddf19bf5f1a1e0650839252c23'], + }), + ('xkeyboard-config', '2.37', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['1f1bb1292a161d520a3485d378609277d108cd07cde0327c16811ff54c3e1595'], + 'configopts': '-Dxorg-rules-symlinks=true', + }), + ('xauth', '1.1.2', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['e9fce796c8c5c9368594b9e8bbba237fb54b6615f5fd60e8d0a5b3c52a92c5ef'], + }), + ('libxcvt', '0.1.2', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/lib/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['27ebce180d355f94c1992930bedb40a36f6d7312ee50bf7f0acbcd22f33e8c29'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual/xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + 'c52403a66935092da86a18052ffdcb93a2762a146901f63c1261744a708b12e2', # xorg-server-21.1.3.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' From db2c3a394bffe1036b4dcaa32ce2e21ce079b29f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 13 Jan 2023 16:21:18 +0100 Subject: [PATCH 6159/9987] fix patch for TensorFlow 2.5+ on ARM The patch is actually wrong and may yield wrong results. Use the upstream patch from TF 2.10 --- .../TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 2 +- ...rFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb | 2 +- .../TensorFlow-2.5.0-fosscuda-2020b.eb | 2 +- ...Flow-2.5.0_fix-arm-vector-intrinsics.patch | 55 ++++++++++--------- ...TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb | 2 +- .../TensorFlow/TensorFlow-2.5.3-foss-2021a.eb | 2 +- ...TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb | 2 +- .../TensorFlow/TensorFlow-2.6.0-foss-2021a.eb | 2 +- ...TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 2 +- .../TensorFlow/TensorFlow-2.7.1-foss-2021b.eb | 2 +- .../TensorFlow/TensorFlow-2.8.4-foss-2021b.eb | 2 +- 11 files changed, 40 insertions(+), 35 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index b7a9a39b865..2840f4d3d74 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -180,7 +180,7 @@ exts_list = [ # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', ], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb index c49c3eddf10..5c26c534b08 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb @@ -185,7 +185,7 @@ exts_list = [ # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', # TensorFlow-2.5.0_fix-CUDA10-build.patch 'f6b44c82855bd2892ca67b528076acdaa75d8b9158aa25d84c808d1ce4d89256', # TensorFlow-2.5.0_fix-cub-cuda-dep.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index b4daf67aaa3..3136244b068 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -189,7 +189,7 @@ exts_list = [ # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', # TensorFlow-2.5.0_fix-crash-on-shutdown.patch '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch index 5d80e47df8f..eaed0decf23 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch @@ -1,37 +1,42 @@ -The comment is not true, the function actually takes the arguments as it should -Hence just redefine the function +Fix compile error on ARM: +> ./tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h:132:58: error: cannot convert 'int32x2_t' to 'int8x8_t' -Author: Alexander Grund (TU Dresden) +From https://github.com/tensorflow/tensorflow/pull/53782 + +From 4463f25d1622d162f870ff685da20f2c6df5bc6a Mon Sep 17 00:00:00 2001 +From: Stephan Hartmann +Date: Sat, 15 Jan 2022 21:06:27 +0100 +Subject: [PATCH] Fix casting in vdotq_four_lane_s32() in TFLite + +When building with GCC and dotprod ARM extension enabled, +vreinterpret_s32_s8() casts int8x8_t to int32x2_t. However, third +argument of vdotq_lane_s32() expects parameter of type int8x8_t. +--- + .../optimized/depthwiseconv_3x3_filter_common.h | 10 ++++------ + 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h b/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h -index 916edd561ff..9c8025dac49 100644 +index 916edd561ff32..c519a81bc864d 100644 --- a/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h +++ b/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h -@@ -122,26 +122,7 @@ inline int32x4_t vpaddq_s32(int32x4_t a, int32x4_t b) { - #endif // !__aarch64__ - - #ifdef __ARM_FEATURE_DOTPROD --// The vdotq_lane_s32 takes int8x8t for the rhs parameter, whereas the actual --// instruction selects from between 4 32-bit (4x8-bit packed) sub-registers, an --// unusual interpretation of "lane". --inline int32x4_t vdotq_four_lane_s32(int32x4_t acc, int8x16_t lhs, -- int8x16_t rhs, const int lane) { -- switch (lane) { -- case 0: +@@ -129,16 +129,14 @@ inline int32x4_t vdotq_four_lane_s32(int32x4_t acc, int8x16_t lhs, + int8x16_t rhs, const int lane) { + switch (lane) { + case 0: - return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_low_s8(rhs)), 0); -- case 1: ++ return vdotq_lane_s32(acc, lhs, vget_low_s8(rhs), 0); + case 1: - return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_low_s8(rhs)), 1); -- case 2: ++ return vdotq_lane_s32(acc, lhs, vget_low_s8(rhs), 1); + case 2: - return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_high_s8(rhs)), - 0); -- case 3: -- default: ++ return vdotq_lane_s32(acc, lhs, vget_high_s8(rhs), 0); + case 3: + default: - return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_high_s8(rhs)), - 1); -- } --} -- -+#define vdotq_four_lane_s32 vdotq_lane_s32 - #else ++ return vdotq_lane_s32(acc, lhs, vget_high_s8(rhs), 1); + } + } - inline int32x4_t vdotq_s32(int32x4_t acc, int8x16_t lhs, int8x16_t rhs) { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb index 32ddf1501b5..0c99b64dcc6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb @@ -194,7 +194,7 @@ exts_list = [ # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', # TensorFlow-2.5.0_fix-crash-on-shutdown.patch '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb index 5405077833e..ca3c8988690 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb @@ -187,7 +187,7 @@ exts_list = [ # TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', # TensorFlow-2.5.0_fix-crash-on-shutdown.patch '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb index 21750d02e0a..9bc60b3e2e6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb @@ -184,7 +184,7 @@ exts_list = [ # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', # TensorFlow-2.5.0_fix-crash-on-shutdown.patch '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb index cb0493abde2..2a4c68371cf 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.6.0-foss-2021a.eb @@ -177,7 +177,7 @@ exts_list = [ # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', # TensorFlow-2.5.0_fix-crash-on-shutdown.patch '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 6f8467a3d68..77b91670e2c 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -223,7 +223,7 @@ exts_list = [ # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', # TensorFlow-2.5.0_fix-crash-on-shutdown.patch '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.7.1_fix_protobuf_error_message.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb index e54e43b8deb..ae6d7df989c 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb @@ -219,7 +219,7 @@ exts_list = [ # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8', + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', # TensorFlow-2.5.0_fix-crash-on-shutdown.patch '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.7.1_fix_protobuf_error_message.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb index a3e3a25f20d..302f3bd958d 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb @@ -195,7 +195,7 @@ exts_list = [ {'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch': '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75'}, {'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch': - '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8'}, + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029'}, {'TensorFlow-2.5.0_fix-crash-on-shutdown.patch': '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd'}, {'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch': From 641e2edad25ecd7bf008ad287ccf75b70f7173e6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 13 Jan 2023 15:32:41 +0000 Subject: [PATCH 6160/9987] adding easyconfigs: Tcl-8.6.13-GCCcore-12.2.0.eb, Tk-8.6.13-GCCcore-12.2.0.eb --- .../t/Tcl/Tcl-8.6.13-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ .../t/Tk/Tk-8.6.13-GCCcore-12.2.0.eb | 40 ++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..fb3054baae0 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.13' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['43a1fae7412f61ff11de2cfd05d28cfc3a73762f354a417c62370a54e2caf066'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d587dfe7219 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.13' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] +checksums = [ + {'tk8.6.13-src.tar.gz': '2e65fa069a23365440a3c56c556b8673b5e32a283800d8d9b257e3f584ce0675'}, + {'Tk-8.6.4_different-prefix-with-tcl.patch': '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d'}, +] + +builddependencies = [('binutils', '2.39')] +dependencies = [ + ('Tcl', version), + ('X11', '20221110'), + ('zlib', '1.2.12'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' From 0e95b8ae25a23b91a7e770ce8fed8681b0ae22e4 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 13 Jan 2023 15:45:04 +0000 Subject: [PATCH 6161/9987] adding easyconfigs: NLopt-2.7.1-GCCcore-12.2.0.eb --- .../n/NLopt/NLopt-2.7.1-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..68952817fe2 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.7.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['db88232fa5cef0ff6e39943fc63ab6074208831dc0031cf1545f6ecd31ae2a1a'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' From b87eddf0edbb40578ae779d1509fc5882473d1d7 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 13 Jan 2023 15:45:45 +0000 Subject: [PATCH 6162/9987] adding easyconfigs: FLAC-1.4.2-GCCcore-12.2.0.eb, LAME-3.100-GCCcore-12.2.0.eb, libogg-1.3.5-GCCcore-12.2.0.eb, libopus-1.3.1-GCCcore-12.2.0.eb, libsndfile-1.2.0-GCCcore-12.2.0.eb, libvorbis-1.3.7-GCCcore-12.2.0.eb --- .../f/FLAC/FLAC-1.4.2-GCCcore-12.2.0.eb | 30 ++++++++++++++++ .../l/LAME/LAME-3.100-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ .../l/libogg/libogg-1.3.5-GCCcore-12.2.0.eb | 25 +++++++++++++ .../l/libopus/libopus-1.3.1-GCCcore-12.2.0.eb | 30 ++++++++++++++++ .../libsndfile-1.2.0-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ .../libvorbis-1.3.7-GCCcore-12.2.0.eb | 30 ++++++++++++++++ 6 files changed, 187 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..27ae550b774 --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.4.2' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e322d58a1f48d23d9dd38f432672865f6f79e73a6f9cc5a5f57fcaa83eb5a8e4'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +sanity_check_commands = ["flac --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4008e0b3455 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + {'lame-3.100.tar.gz': 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e'}, + {'LAME-3.99.5_check-tgetent.patch': '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +dependencies = [('ncurses', '6.3')] + +preconfigopts = "autoconf && " + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0df3a2b5b8e --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.5' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705'] + +builddependencies = [('binutils', '2.39')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6319733c7cf --- /dev/null +++ b/easybuild/easyconfigs/l/libopus/libopus-1.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libopus' +version = '1.3.1' + +homepage = 'https://www.opus-codec.org/' +description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive + speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is + standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s + SILK codec and Xiph.Org’s CELT codec.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://archive.mozilla.org/pub/opus/'] +sources = ['opus-%(version)s.tar.gz'] +checksums = ['65b58e1e25b2a114157014736a3d9dfeaad8d41be1c8179866f144a2fb44ff9d'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT], + 'dirs': ['include/opus'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7af75870278 --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.0-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'libsndfile' +version = '1.2.0' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/libsndfile/libsndfile/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['0e30e7072f83dc84863e2e55f299175c7e04a5902ae79cfb99d4249ee8f6d60a'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('FLAC', '1.4.2'), + ('libvorbis', '1.3.7'), + ('libopus', '1.3.1'), + ('LAME', '3.100'), +] + +configopts = ['', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a76724c2cd9 --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' From 82893bf8089d56bd0383dbd20f44be8e28f0fd25 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 13 Jan 2023 16:20:16 +0000 Subject: [PATCH 6163/9987] adding easyconfigs: GLPK-5.0-GCCcore-12.2.0.eb, GSL-2.7-GCC-12.2.0.eb, libgit2-1.5.0-GCCcore-12.2.0.eb, MPFR-4.2.0-GCCcore-12.2.0.eb, PCRE-8.45-GCCcore-12.2.0.eb, UDUNITS-2.2.28-GCCcore-12.2.0.eb --- .../g/GLPK/GLPK-5.0-GCCcore-12.2.0.eb | 31 +++++++++++++ .../easyconfigs/g/GSL/GSL-2.7-GCC-12.2.0.eb | 25 +++++++++++ .../l/libgit2/libgit2-1.5.0-GCCcore-12.2.0.eb | 34 ++++++++++++++ .../m/MPFR/MPFR-4.2.0-GCCcore-12.2.0.eb | 39 ++++++++++++++++ .../p/PCRE/PCRE-8.45-GCCcore-12.2.0.eb | 45 +++++++++++++++++++ .../UDUNITS/UDUNITS-2.2.28-GCCcore-12.2.0.eb | 44 ++++++++++++++++++ 6 files changed, 218 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.5.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-4.2.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..226f44dc49b --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '5.0' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a1013eebb50f728fc601bdd833b0b2870333c3b3e5a816eeba921d95bec6f15'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('GMP', '6.2.1')] + +configopts = "--with-gmp" + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/glpk.h'] + + ['lib/libglpk.%s' % x for x in [SHLIB_EXT, 'a']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-12.2.0.eb new file mode 100644 index 00000000000..e1e6de28f31 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.7' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.5.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.5.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5b9bd25e4c1 --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.5.0-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.5.0' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'libgit2' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['8de872a0f201b33d9522b817c92e14edb4efad18dae95cf156cf240b2efff93e'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('PCRE', '8.45'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.2.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b0eae5a885a --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.2.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '4.2.0' + +homepage = 'https://www.mpfr.org' + +description = """ + The MPFR library is a C library for multiple-precision floating-point + computations with correct rounding. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['691db39178e36fc460c046591e4b0f2a52c8f2b3ee6d750cc2eab25f1eaa999d'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +runtest = 'check' + +# copy libmpfr.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a src/.libs/libmpfr.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..1f099f8c63d --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.45' + +homepage = 'https://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.pcre.org/pub/pcre/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4e6ce03e0336e8b4a3d6c2b70b1c5e18590a5673a98186da90d4f33c23defc09'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +configopts = ' '.join([ + '--enable-utf', + '--enable-unicode-properties', + '--enable-pcre16', + '--enable-pcre32', +]) + +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..62fb8413bfc --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.28' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/%(version)s/', + 'https://sources.easybuild.io/u/UDUNITS/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['590baec83161a3fd62c00efa66f6113cec8a7c461e3f61a5182167e0cc5d579e'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('expat', '2.4.9')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From 0364e5b6f80654f16b0e6467393710c2dfcf8d96 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 13 Jan 2023 17:03:34 +0000 Subject: [PATCH 6164/9987] adding easyconfigs: GEOS-3.11.1-GCC-12.2.0.eb, googletest-1.12.1-GCCcore-12.2.0.eb, nlohmann_json-3.11.2-GCCcore-12.2.0.eb, PROJ-9.1.1-GCCcore-12.2.0.eb --- .../g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb | 20 ++++++++ .../googletest-1.12.1-GCCcore-12.2.0.eb | 28 +++++++++++ .../nlohmann_json-3.11.2-GCCcore-12.2.0.eb | 25 ++++++++++ .../p/PROJ/PROJ-9.1.1-GCCcore-12.2.0.eb | 49 +++++++++++++++++++ 4 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.12.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-9.1.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..99f27227d59 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.11.1' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6d0eb3cfa9f92d947731cc75f1750356b3bdfc07ea020553daf6af1c768e0be2'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.12.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..20cae145de0 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.12.1-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.12.1' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['81964fe578e9bd7c94dfdb09c8e4d6e6759e19967e397dbea48d1c10e45d0df2'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..1e886bed236 --- /dev/null +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'nlohmann_json' +version = '3.11.2' + +homepage = 'https://github.com/nlohmann/json' +description = """JSON for Modern C++""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d69f9deb6a75e2580465c6c4c5111b89c4dc2fa94e3a85fcd2ffcd9a143d9273'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['include/nlohmann/json.hpp'], + 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-9.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-9.1.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..80793ebc07f --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-9.1.1-GCCcore-12.2.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'CMakeMake' + +name = 'PROJ' +version = '9.1.1' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['003cd4010e52bb5eb8f7de1c143753aa830c8902b6ed01209f294846e40e6d39'] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('googletest', '1.12.1'), +] + +dependencies = [ + ('SQLite', '3.39.4'), + ('LibTIFF', '4.4.0'), + ('cURL', '7.86.0'), + ('XZ', '5.2.7'), + ('nlohmann_json', '3.11.2'), +] + +# build twice, once for static, once for shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From ce56fbd367cd58a3f565ad4720242e52e15fc27d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 13 Jan 2023 17:19:18 +0000 Subject: [PATCH 6165/9987] adding easyconfigs: HDF5-1.14.0-gompi-2022b.eb, HDF5-1.14.0-iimpi-2022b.eb, Szip-2.1.1-GCCcore-12.2.0.eb, netCDF-4.9.0-gompi-2022b.eb, netCDF-4.9.0-iimpi-2022b.eb --- .../h/HDF5/HDF5-1.14.0-gompi-2022b.eb | 22 ++++++++ .../h/HDF5/HDF5-1.14.0-iimpi-2022b.eb | 22 ++++++++ .../n/netCDF/netCDF-4.9.0-gompi-2022b.eb | 53 +++++++++++++++++++ .../n/netCDF/netCDF-4.9.0-iimpi-2022b.eb | 53 +++++++++++++++++++ .../s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb | 29 ++++++++++ 5 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2022b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2022b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2022b.eb new file mode 100644 index 00000000000..bd6519be79c --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2022b.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.0' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2022b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2022b.eb new file mode 100644 index 00000000000..168721a6491 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2022b.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.0' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb new file mode 100644 index 00000000000..119dcd53f2b --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb @@ -0,0 +1,53 @@ +name = 'netCDF' +version = '4.9.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-%(version)s_fix-lib-name.patch', + 'netCDF-%(version)s_fix-linking-errors.patch', + 'netCDF-%(version)s_skip-nasa-test.patch', +] +checksums = [ + '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz + 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch + '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a', # netCDF-4.9.0_skip-nasa-test.patch +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.24.3'), + ('Doxygen', '1.9.5'), +] + +dependencies = [ + ('HDF5', '1.14.0'), + ('cURL', '7.86.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.2'), + ('bzip2', '1.0.8'), + ('libxml2', '2.10.3'), +] + +# make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb new file mode 100644 index 00000000000..3a96eadc498 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb @@ -0,0 +1,53 @@ +name = 'netCDF' +version = '4.9.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-%(version)s_fix-lib-name.patch', + 'netCDF-%(version)s_fix-linking-errors.patch', + 'netCDF-%(version)s_skip-nasa-test.patch', +] +checksums = [ + '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz + 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch + '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a', # netCDF-4.9.0_skip-nasa-test.patch +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.24.3'), + ('Doxygen', '1.9.5'), +] + +dependencies = [ + ('HDF5', '1.14.0'), + ('cURL', '7.86.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.2'), + ('bzip2', '1.0.8'), + ('libxml2', '2.10.3'), +] + +# make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6f536c566dd --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' From b3860c27bceb728ffac5675cff153282facd9a33 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 13 Jan 2023 18:17:51 +0000 Subject: [PATCH 6166/9987] adding easyconfigs: presto-1.0.0-20230113-foss-2022a-R-4.2.1.eb --- ...resto-1.0.0-20230113-foss-2022a-R-4.2.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/presto/presto-1.0.0-20230113-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/p/presto/presto-1.0.0-20230113-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/p/presto/presto-1.0.0-20230113-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..97c1a2bd545 --- /dev/null +++ b/easybuild/easyconfigs/p/presto/presto-1.0.0-20230113-foss-2022a-R-4.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'presto' +local_commit = '045390a' +# see DESCRIPTION to determine version, +# but also take date of last commit into account (since version isn't always bumped) +version = '1.0.0-20230113' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/immunogenomics/presto' +description = "Presto performs a fast Wilcoxon rank sum test and auROC analysis." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/immunogenomics/presto/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['79b92212d2d3165e27d137aa9c216c531934b67f37d413022fa8b1b48b36a209'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From 1843bebbdb9bda9b0e909f23610ba172d853cf09 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Sat, 14 Jan 2023 10:27:52 +0100 Subject: [PATCH 6167/9987] adding easyconfigs: Qt5Webkit-5.212.0-alpha4-GCCcore-11.3.0.eb and patches: Qt5Webkit-5.212.0-alpha4_json.patch --- ...Qt5Webkit-5.212.0-alpha4-GCCcore-11.3.0.eb | 63 +++++++++++++++++++ .../Qt5Webkit-5.212.0-alpha4_json.patch | 15 +++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_json.patch diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4323d480ca2 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.3.0.eb @@ -0,0 +1,63 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeNinja' + +name = 'Qt5Webkit' +# Qt5 > 5.9 required at least version 5.212.0 +# At the time of writing the latest version was 5.212.0-alpha4 +version = '5.212.0-alpha4' + +homepage = 'https://github.com/qt/qtwebkit' +description = "Qt Port of WebKit. WebKit is an open source web browser engine." +docurls = ['https://github.com/qt/qtwebkit/blob/dev/README'] + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/qtwebkit/qtwebkit/releases/download/qtwebkit-%(version)s/'] +sources = ['qtwebkit-%(version)s.tar.xz'] +patches = [ + '%(name)s-%(version)s_bison3.7.patch', + '%(name)s-%(version)s_json.patch', +] +checksums = [ + '9ca126da9273664dd23a3ccd0c9bebceb7bb534bddd743db31caf6a5a6d4a9e6', # qtwebkit-5.212.0-alpha4.tar.xz + '34f37b53ee0bc31c63ce85ebd1ae95543a8ba28483e387b20efd50574bd813be', # Qt5Webkit-5.212.0-alpha4_bison3.7.patch + '68e2c47882e4749c85933f176c45a8f781fa8a2e92818c58b6af15f27dadb9f5', # Qt5Webkit-5.212.0-alpha4_json.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.10.2'), + ('Python', '3.10.4'), + ('Ruby', '3.0.3'), +] + +dependencies = [ + ('Qt5', '5.15.5'), + ('zlib', '1.2.12'), + ('SQLite', '3.38.3'), + ('ICU', '71.1'), + ('libxslt', '1.1.34'), + ('libjpeg-turbo', '2.1.3'), +] + +configopts = "-G Ninja -DPORT=Qt -DCMAKE_BUILD_TYPE=Release -DUSE_LIBHYPHEN=OFF -DUSE_GSTREAMER=OFF " +# Starting from ICU 68 the TRUE/FALSE macros are not defined in standard header +# files, see https://unicode-org.github.io/icu/userguide/dev/codingguidelines.html +configopts += "-DCMAKE_CXX_FLAGS='-DU_DEFINE_FALSE_AND_TRUE=1' " + +sanity_check_paths = { + 'files': [ + 'lib64/libQt5WebKit.%s' % SHLIB_EXT, + 'lib64/libQt5WebKitWidgets.%s' % SHLIB_EXT, + ], + 'dirs': ['include/QtWebKit', 'include/QtWebKitWidgets'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_json.patch b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_json.patch new file mode 100644 index 00000000000..e2c189a2ee7 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_json.patch @@ -0,0 +1,15 @@ +# The "encoding" is no more supported in python json library (utf-8 is default now?) +# author: Jiri Furst + +--- qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/generate-bytecode-files.orig 2022-12-20 15:43:51.483563960 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/generate-bytecode-files 2022-12-20 15:43:23.979251951 +0100 +@@ -163,7 +163,8 @@ + initBytecodesFile = openOrExit(initASMFileName, "w") + + try: +- bytecodeSections = json.load(bytecodeFile, encoding = "utf-8") ++ #bytecodeSections = json.load(bytecodeFile, encoding = "utf-8") ++ bytecodeSections = json.load(bytecodeFile) + except: + print("Unexpected error parsing {0}: {1}".format(bytecodeJSONFile, sys.exc_info())) + From bac4790c4050ab96f5e379abac6333a20f0d6730 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 Jan 2023 10:04:25 +0000 Subject: [PATCH 6168/9987] use CMakeMake for GEOS --- easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb index 99f27227d59..5c3b2fbee0c 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'GEOS' version = '3.11.1' @@ -12,6 +12,11 @@ source_urls = ['https://download.osgeo.org/geos/'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['6d0eb3cfa9f92d947731cc75f1750356b3bdfc07ea020553daf6af1c768e0be2'] +builddependencies = [('CMake', '3.24.3')] + +# Build static and shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + sanity_check_paths = { 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], 'dirs': [], From 8390e173d9c2951072349b66f75124e94bf96a4a Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 Jan 2023 10:23:01 +0000 Subject: [PATCH 6169/9987] update nlohmann_json sanity checks --- .../n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.2.0.eb index 1e886bed236..a5775e9ae84 100644 --- a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ sanity_check_paths = { 'files': ['include/nlohmann/json.hpp'], - 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], + 'dirs': ['share/cmake', 'share/pkgconfig'], } moduleclass = 'lib' From 26cc183ae943b01dc2b0a3e926f834e4cbfe89a9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 Jan 2023 10:45:20 +0000 Subject: [PATCH 6170/9987] adding easyconfigs: HDF-4.2.15-GCCcore-12.2.0.eb, libtirpc-1.3.3-GCCcore-12.2.0.eb --- .../h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb | 62 +++++++++++++++++++ .../libtirpc/libtirpc-1.3.3-GCCcore-12.2.0.eb | 28 +++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f0286cd30bd --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-12.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.15' + +homepage = 'https://www.hdfgroup.org/products/hdf4/' + +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['HDF-4.2.15_fix-aarch64.patch'] +checksums = [ + 'dbeeef525af7c2d01539906c28953f0fdab7dba603d1bc1ec4a5af60d002c459', # hdf-4.2.15.tar.gz + '1b4341e309cccefc6ea4310c8f8b08cc3dfe1fa9609b7fa7aee80e4dac598473', # HDF-4.2.15_fix-aarch64.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '2.1.4'), + ('Szip', '2.1.1'), + ('zlib', '1.2.12'), + ('libtirpc', '1.3.3'), +] + +preconfigopts = "LIBS='-ltirpc' " +local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' +local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' +configopts = [ + # -fallow-argument-mismatch is required to compile with GCC 10.x + local_common_configopts + 'FFLAGS="$FFLAGS -fallow-argument-mismatch"', + # Cannot build shared libraries and Fortran... + # https://trac.osgeo.org/gdal/wiki/HDF#IncompatibilitywithNetCDFLibraries + # netcdf must be disabled to allow HDF to be used by GDAL + local_common_configopts + "--enable-shared --disable-fortran --disable-netcdf", +] + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', + 'lib/libmfhdf.%s' % SHLIB_EXT], + 'dirs': ['include/hdf'], +} + +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..733262dc990 --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.3' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['6474e98851d9f6f33871957ddee9714fdcd9d8a5ee9abb5a98d63ea2e60e12f3'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.39') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' From ef9dc8971ee7d8347784a7e6114363df0a697c95 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 Jan 2023 10:46:07 +0000 Subject: [PATCH 6171/9987] adding easyconfigs: Szip-2.1.1-GCCcore-12.2.0.eb --- .../s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6f536c566dd --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' From 4a0620cc75e2c127e1305f476f28ec4557641150 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 Jan 2023 10:48:52 +0000 Subject: [PATCH 6172/9987] split Szip into separate PR --- .../s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb deleted file mode 100644 index 6f536c566dd..00000000000 --- a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.2.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Szip' -version = '2.1.1' - -homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' - -description = """ - Szip compression software, providing lossless compression of scientific data -""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] - -builddependencies = [ - ('binutils', '2.39'), -] - -sanity_check_paths = { - 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + - ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], - 'dirs': [], -} - -moduleclass = 'tools' From a1f61c4e03d6f6db5d06f5bf807e33b14f08f2f3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 16 Jan 2023 12:49:44 +0100 Subject: [PATCH 6173/9987] adding easyconfigs: flatbuffers-2.0.7-GCCcore-11.3.0.eb --- .../flatbuffers-2.0.7-GCCcore-11.3.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..817624e2810 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb @@ -0,0 +1,56 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '2.0.7' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4c7986174dc3941220bf14feaacaad409c3e1526d9ad7f490366fede9a6f43fa'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('flatbuffers', version, { + 'sources': { + 'download_filename': SOURCE_TAR_GZ, + 'filename': '%(name)s-python.tar.gz', + }, + 'checksums': ['0ae7d69c5b82bf41962ca5fde9cc43033bc9501311d975fd5a25e8a7d29c1245'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' From 91e5aec426c7ac045f29f56add4e44b20b4bcdaf Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 Jan 2023 11:50:09 +0000 Subject: [PATCH 6174/9987] bump versions to latest, and use 2022b toolchain --- easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb | 20 ++++++ .../hypothesis-6.62.1-GCCcore-12.2.0.eb | 24 +++++++ .../m/mpi4py/mpi4py-3.1.4-foss-2022b.eb | 25 +++++++ .../pybind11-2.10.3-GCCcore-12.2.0.eb | 23 ++++++ .../SciPy-bundle-2023.01-gfbf-2022b.eb | 71 +++++++++++++++++++ 5 files changed, 163 insertions(+) create mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-6.62.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb new file mode 100644 index 00000000000..1ed2f9c0bad --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2022b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.2.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.62.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.62.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..eb8c0f3ceb7 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.62.1-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '6.62.1' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7d1e2f9871e6509662da317adf9b4aabd6b38280fb6c7930aa4f574d2ed25150'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022b.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022b.eb new file mode 100644 index 00000000000..d103cd78db0 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '3.1.4' + +homepage = 'https://github.com/mpi4py/mpi4py' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['17858f2ebc623220d0120d1fa8d428d033dde749c4bc35b33d81a66ad7f93480'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.01'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..dc6dd0aead4 --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb @@ -0,0 +1,23 @@ +name = 'pybind11' +version = '2.10.3' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5d8c4c5dda428d3a944ba3d2a5212cb988c2fae4670d58075a5a49075a6ca315'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Eigen', '3.4.0'), +] +dependencies = [('Python', '3.10.8')] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb new file mode 100644 index 00000000000..09e3241b94f --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2023.01' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'gfbf', 'version': '2022b'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.62.1'), + ('UnZip', '6.0'), + ('meson-python', '0.11.0'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('pybind11', '2.10.3'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.24.1', { + 'patches': ['numpy-1.22.3_disable-broken-override-test.patch'], + 'checksums': [ + {'numpy-1.24.1.tar.gz': '2386da9a471cc00a1f47845e27d916d5ec5346ae9696e01a8a34760858fe9dd2'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.12.1', { + 'checksums': ['702c2701187cfb38f66c0c20cc85d04d0e156d260a8d92892da65947faa5360e'], + }), + ('scipy', '1.10.0', { + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && ", + 'checksums': ['c8b3cbc636a87a89b770c6afc999baa6bcbb01691b5ccbbc1b1791c7c0a07540'], + }), + ('numexpr', '2.8.4', { + 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], + }), + ('Bottleneck', '1.3.5', { + 'checksums': ['2c0d27afe45351f6f421893362621804fa7dea14fe29a78eaa52d4323f646de7'], + }), + ('pandas', '1.5.2', { + 'preinstallopts': "export PANDAS_CI=0 && ", + 'checksums': ['220b98d15cee0b2cd839a6358bd1f273d0356bf964c1a1aeb32d47db0215488b'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.3', { + 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 5f4b5e3f9d82471967641d9c8508a8fb66ee4b2d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 Jan 2023 11:55:12 +0000 Subject: [PATCH 6175/9987] remove old updated files --- easybuild/easyconfigs/g/gfbf/gfbf-2022.10.eb | 20 ----- .../hypothesis-6.59.0-GCCcore-12.2.0.eb | 24 ------ .../m/mpi4py/mpi4py-3.1.4-foss-2022.10.eb | 25 ------- .../pybind11-2.10.1-GCCcore-12.2.0.eb | 23 ------ .../SciPy-bundle-2022.11-gfbf-2022.10.eb | 74 ------------------- 5 files changed, 166 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2022.10.eb delete mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-6.59.0-GCCcore-12.2.0.eb delete mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022.10.eb delete mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.10.1-GCCcore-12.2.0.eb delete mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-gfbf-2022.10.eb diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2022.10.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2022.10.eb deleted file mode 100644 index e803a1e75b2..00000000000 --- a/easybuild/easyconfigs/g/gfbf/gfbf-2022.10.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'Toolchain' - -name = 'gfbf' -version = '2022.10' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain, including - FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" - -toolchain = SYSTEM - -local_gccver = '12.2.0' - -dependencies = [ - ('GCC', local_gccver), - ('FlexiBLAS', '3.2.1', '', ('GCC', local_gccver)), - ('FFTW', '3.3.10', '', ('GCC', local_gccver)), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.59.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.59.0-GCCcore-12.2.0.eb deleted file mode 100644 index bb0b491571c..00000000000 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.59.0-GCCcore-12.2.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'hypothesis' -version = '6.59.0' - -homepage = "https://github.com/HypothesisWorks/hypothesis" -description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized - by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets - you find more bugs in your code with less work.""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['af05e24b123c9413b8752bbf822105dbb112f56456fb240723d7f410eebf78bb'] - -builddependencies = [('binutils', '2.39')] - -dependencies = [('Python', '3.10.8')] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022.10.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022.10.eb deleted file mode 100644 index 1e8128dae26..00000000000 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022.10.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'mpi4py' -version = '3.1.4' - -homepage = 'https://github.com/mpi4py/mpi4py' -description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for - the Python programming language, allowing any Python program to exploit multiple processors.""" - -toolchain = {'name': 'foss', 'version': '2022.10'} - -sources = [SOURCE_TAR_GZ] -checksums = ['17858f2ebc623220d0120d1fa8d428d033dde749c4bc35b33d81a66ad7f93480'] - -dependencies = [ - ('Python', '3.10.8'), - ('SciPy-bundle', '2022.11'), -] - -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.1-GCCcore-12.2.0.eb deleted file mode 100644 index 7ccdfaf989c..00000000000 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.1-GCCcore-12.2.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'pybind11' -version = '2.10.1' - -homepage = 'https://pybind11.readthedocs.io' -description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, - mainly to create Python bindings of existing C++ code.""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -source_urls = ['https://github.com/pybind/pybind11/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['111014b516b625083bef701df7880f78c2243835abdb263065b6b59b960b6bad'] - -builddependencies = [ - ('binutils', '2.39'), - ('CMake', '3.24.3'), - ('Eigen', '3.4.0'), -] -dependencies = [('Python', '3.10.8')] - -configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-gfbf-2022.10.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-gfbf-2022.10.eb deleted file mode 100644 index ae156260776..00000000000 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.11-gfbf-2022.10.eb +++ /dev/null @@ -1,74 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'SciPy-bundle' -version = '2022.11' - -homepage = 'https://python.org/' -description = "Bundle of Python packages for scientific software" - -toolchain = {'name': 'gfbf', 'version': '2022.10'} -toolchainopts = {'pic': True, 'lowopt': True} - -builddependencies = [ - ('hypothesis', '6.59.0'), - ('UnZip', '6.0'), - ('meson-python', '0.11.0'), -] - -dependencies = [ - ('Python', '3.10.8'), - ('pybind11', '2.10.1'), # required by scipy -] - -use_pip = True - -# order is important! -exts_list = [ - ('numpy', '1.23.5', { - 'patches': [ - 'numpy-1.22.3_disable-broken-override-test.patch', - ], - 'checksums': [ - {'numpy-1.23.5.tar.gz': '1b1766d6f397c18153d40015ddfc79ddb715cabadc04d2d228d4e5a8bc4ded1a'}, - {'numpy-1.22.3_disable-broken-override-test.patch': - '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, - ], - }), - ('ply', '3.11', { - 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], - }), - ('gast', '0.5.3', { - 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], - }), - ('beniget', '0.4.1', { - 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], - }), - ('pythran', '0.12.0', { - 'checksums': ['eff3dd0d3eebe57372f0d14f82985525e9bcdfb5b1d1010e1932cf9207060f9f'], - }), - ('scipy', '1.9.3', { - 'checksums': ['fbc5c05c85c1a02be77b1ff591087c83bc44579c6d2bd9fb798bb64ea5e1a027'], - 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && ", - }), - ('numexpr', '2.8.4', { - 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], - }), - ('Bottleneck', '1.3.5', { - 'checksums': ['2c0d27afe45351f6f421893362621804fa7dea14fe29a78eaa52d4323f646de7'], - }), - ('pandas', '1.5.2', { - 'checksums': ['220b98d15cee0b2cd839a6358bd1f273d0356bf964c1a1aeb32d47db0215488b'], - # make sure $PANDAS_CI is not set to 1, since that implies using -Werror - 'preinstallopts': "export PANDAS_CI=0 && ", - }), - ('mpmath', '1.2.1', { - 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], - }), - ('deap', '1.3.3', { - 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], - }), -] - -sanity_pip_check = True - -moduleclass = 'lang' From 00b2ae2e137d8650569fe731aa5891b74a98365a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 16 Jan 2023 13:08:47 +0100 Subject: [PATCH 6176/9987] adding easyconfigs: ReFrame-4.0.1.eb --- .../easyconfigs/r/ReFrame/ReFrame-4.0.1.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.0.1.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.0.1.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.0.1.eb new file mode 100644 index 00000000000..568f87e8ef2 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.0.1.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.0.1' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + # stick to pip < 22.0, to maintain compatibility with Python 3.6 + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + ('reframe', version, { + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['1680b8f0dd405dcf98be23473570595a424cbee830b2dbb665459e2974723f6f'], + }), +] + +postinstallcmds = [ + "cp -a hpctestlib tools tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'hpctestlib', 'lib', 'tools', 'tutorials'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 5f47f0d923ad55c76b392e732b68eb4a5b2502a7 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 16 Jan 2023 14:59:51 +0100 Subject: [PATCH 6177/9987] adding easyconfigs: tqdm-4.64.1-GCCcore-12.2.0.eb --- .../t/tqdm/tqdm-4.64.1-GCCcore-12.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/tqdm/tqdm-4.64.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.64.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.64.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9d126d81da5 --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.64.1-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.64.1' + +homepage = "https://github.com/tqdm/tqdm" +description = """A fast, extensible progress bar for Python and CLI""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['5f4f682a004951c1b450bc753c710e9280c5746ce6ffedee253ddbcbf54cf1e4'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' From 0c503e3027ba572399723afe5e90c08d4fb9a984 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 16 Jan 2023 15:00:34 +0100 Subject: [PATCH 6178/9987] adding easyconfigs: BeautifulSoup-4.11.1-GCCcore-12.2.0.eb --- .../BeautifulSoup-4.11.1-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.11.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.11.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.11.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..33dedbbcb7d --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.11.1-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.11.1' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39') +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('hatchling', '1.12.2', { + 'checksums': ['8a6d719d96653a0f3901072b12710c9c3cc934f9061b443775c6789b45333495'], + }), + ('soupsieve', '2.3.2.post1', { + 'checksums': ['fc53893b3da2c33de295667a0e19f078c14bf86544af307354de5fcf12a3f30d'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['ad9aa55b65ef2808eb405f46cf74df7fcb7044d5cbc26487f96eb2ef2e436693'], + }), +] + +moduleclass = 'data' From 12b1501352636e1e546f8b1b7c57296ca03fcc50 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 16 Jan 2023 15:06:55 +0100 Subject: [PATCH 6179/9987] Use only 1 lib dir --- .../f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb index 817624e2810..71b08c11f2d 100644 --- a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb @@ -26,7 +26,8 @@ dependencies = [ ('Python', '3.10.4'), ] -configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' +# Install into the same dir as the Python extension which is /lib +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON -DCMAKE_INSTALL_LIBDIR=lib' exts_defaultclass = 'PythonPackage' exts_default_options = { From 45d028a7be9d40ed44171f1bb5ccb6677bef62af Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 Jan 2023 14:46:01 +0000 Subject: [PATCH 6180/9987] fix Xvfb checksums --- .../easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb index 6a259d10a04..306d5b638f1 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb @@ -66,7 +66,7 @@ components = [ 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], }), ('font-util', '1.3.3', { - 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], + 'checksums': ['2094dd4a1ca63a61deb101d2dc618682d6e287cdbe09679502223ac445d277dc'], }), ('font-misc-misc', '1.1.2', { 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], @@ -74,31 +74,31 @@ components = [ }), ('xkbcomp', '1.4.6', { 'source_urls': ['https://www.x.org/archive/individual/app/'], - 'checksums': ['e88a4d86b9925ea1e8685dd5ea29c815abafb8ddf19bf5f1a1e0650839252c23'], + 'checksums': ['b216a2c8c0eab83f3dc4a3d5ee2bdf7827b30e49c8907035d0f222138eca0987'], }), ('xkeyboard-config', '2.37', { 'easyblock': 'MesonNinja', 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], 'sources': [SOURCE_TAR_XZ], - 'checksums': ['1f1bb1292a161d520a3485d378609277d108cd07cde0327c16811ff54c3e1595'], + 'checksums': ['eb1383a5ac4b6210d7c7302b9d6fab052abdf51c5d2c9b55f1f779997ba68c6c'], 'configopts': '-Dxorg-rules-symlinks=true', }), ('xauth', '1.1.2', { 'source_urls': ['https://www.x.org/releases/individual/app/'], - 'checksums': ['e9fce796c8c5c9368594b9e8bbba237fb54b6615f5fd60e8d0a5b3c52a92c5ef'], + 'checksums': ['84d27a1023d8da524c134f424b312e53cb96e08871f96868aa20316bfcbbc054'], }), ('libxcvt', '0.1.2', { 'easyblock': 'MesonNinja', 'source_urls': ['https://www.x.org/archive/individual/lib/'], 'sources': [SOURCE_TAR_XZ], - 'checksums': ['27ebce180d355f94c1992930bedb40a36f6d7312ee50bf7f0acbcd22f33e8c29'], + 'checksums': ['0561690544796e25cfbd71806ba1b0d797ffe464e9796411123e79450f71db38'], }), (name, version, { 'source_urls': ['https://www.x.org/releases/individual/xserver/'], 'sources': ['xorg-server-%(version)s.tar.gz'], 'patches': [('xvfb-run', '.')], 'checksums': [ - 'c52403a66935092da86a18052ffdcb93a2762a146901f63c1261744a708b12e2', # xorg-server-21.1.3.tar.gz + '6f9c73ccc50e2731adac17671c8e33687738c8cd556b49ecb9f410ce7217be11', # xorg-server-21.1.3.tar.gz 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run ], 'start_dir': 'xorg-server-%(version)s', From 1a547cca599c333dc2d28f3d27aa2b9c6a97bd21 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 15 Jan 2023 21:46:12 +0100 Subject: [PATCH 6181/9987] adding easyconfigs: flatbuffers-23.1.4-GCCcore-12.2.0.eb --- .../flatbuffers-23.1.4-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.1.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.1.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.1.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6a6c59241f7 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.1.4-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '23.1.4' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['801871ff3747838c0dd9730fc44ca9cc453ff42f9c8a0a2f1b33776d2ca5e4b9'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('Python', '3.10.8'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' From 7601d0474424ab847dd6de3f4fdcaa85808cf2a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Jan 2023 17:24:29 +0100 Subject: [PATCH 6182/9987] adding easyconfigs: h5py-3.7.0-intel-2022a.eb --- .../h/h5py/h5py-3.7.0-intel-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.7.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.7.0-intel-2022a.eb b/easybuild/easyconfigs/h/h5py/h5py-3.7.0-intel-2022a.eb new file mode 100644 index 00000000000..c29d68aa634 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.7.0-intel-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.7.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['3fcf37884383c5da64846ab510190720027dca0768def34dd8dcb659dbe5cbf3'] + +builddependencies = [('pkgconfig', '1.5.5', '-python')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('HDF5', '1.12.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' From 3377c4f1760ba04e85cd714954afbd3765651c8a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Jan 2023 17:24:42 +0100 Subject: [PATCH 6183/9987] adding easyconfigs: networkx-2.8.4-intel-2022a.eb --- .../n/networkx/networkx-2.8.4-intel-2022a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.8.4-intel-2022a.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.8.4-intel-2022a.eb b/easybuild/easyconfigs/n/networkx/networkx-2.8.4-intel-2022a.eb new file mode 100644 index 00000000000..40d509decfb --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.8.4-intel-2022a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.8.4' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['5e53f027c0d567cf1f884dbb283224df525644e43afd1145d64c9d88a3584762'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 0d7d73499fa67e25620d0fd8c3c4e700e183939d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 16 Jan 2023 17:25:31 +0100 Subject: [PATCH 6184/9987] adding easyconfigs: CatLearn-0.6.2-intel-2022a.eb --- .../c/CatLearn/CatLearn-0.6.2-intel-2022a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/CatLearn/CatLearn-0.6.2-intel-2022a.eb diff --git a/easybuild/easyconfigs/c/CatLearn/CatLearn-0.6.2-intel-2022a.eb b/easybuild/easyconfigs/c/CatLearn/CatLearn-0.6.2-intel-2022a.eb new file mode 100644 index 00000000000..6fb6ada86bb --- /dev/null +++ b/easybuild/easyconfigs/c/CatLearn/CatLearn-0.6.2-intel-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'CatLearn' +version = '0.6.2' + +homepage = 'https://catlearn.readthedocs.io' +description = "An environment for atomistic machine learning in Python for applications in catalysis" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('h5py', '3.7.0'), + ('networkx', '2.8.4'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), + ('ASE', '3.22.1'), + ('GPAW', '22.8.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['5af6622e4660f3b5760267fccd9c5da6f1a4a88aad0aacc044067a68f92e2bbd'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 0f79963332def2763e7135bf355b1f8d3c9c2402 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 16 Jan 2023 17:29:31 +0000 Subject: [PATCH 6185/9987] Switch SciPy-bundle to Bundle, use mesonninja for scipy component --- .../SciPy-bundle-2023.01-gfbf-2022b.eb | 55 ++++++++++++++++--- 1 file changed, 47 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb index 09e3241b94f..8d5febe6383 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'Bundle' name = 'SciPy-bundle' version = '2023.01' @@ -12,7 +12,9 @@ toolchainopts = {'pic': True, 'lowopt': True} builddependencies = [ ('hypothesis', '6.62.1'), ('UnZip', '6.0'), - ('meson-python', '0.11.0'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), ] dependencies = [ @@ -20,52 +22,89 @@ dependencies = [ ('pybind11', '2.10.3'), # required by scipy ] -use_pip = True +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', +} + +_pythonpath = 'PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH' # order is important! -exts_list = [ +components = [ ('numpy', '1.24.1', { - 'patches': ['numpy-1.22.3_disable-broken-override-test.patch'], + 'patches': [{'name': 'numpy-1.22.3_disable-broken-override-test.patch', 'alt_location': 'SciPy-bundle'}], 'checksums': [ {'numpy-1.24.1.tar.gz': '2386da9a471cc00a1f47845e27d916d5ec5346ae9696e01a8a34760858fe9dd2'}, {'numpy-1.22.3_disable-broken-override-test.patch': '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, ], + 'sanity_pip_check': True, }), ('ply', '3.11', { 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, }), ('gast', '0.5.3', { 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, }), ('beniget', '0.4.1', { 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, }), ('pythran', '0.12.1', { 'checksums': ['702c2701187cfb38f66c0c20cc85d04d0e156d260a8d92892da65947faa5360e'], + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, }), ('scipy', '1.10.0', { - 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && ", + 'easyblock': 'MesonNinja', + 'preconfigopts': _pythonpath, + 'configopts': '-Dblas=flexiblas -Dlapack=flexiblas', + 'prebuildopts': _pythonpath, + 'preinstallopts': "PATH=%(installdir)s/bin:$PATH " + _pythonpath, 'checksums': ['c8b3cbc636a87a89b770c6afc999baa6bcbb01691b5ccbbc1b1791c7c0a07540'], }), ('numexpr', '2.8.4', { 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, }), ('Bottleneck', '1.3.5', { 'checksums': ['2c0d27afe45351f6f421893362621804fa7dea14fe29a78eaa52d4323f646de7'], + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, }), ('pandas', '1.5.2', { 'preinstallopts': "export PANDAS_CI=0 && ", 'checksums': ['220b98d15cee0b2cd839a6358bd1f273d0356bf964c1a1aeb32d47db0215488b'], + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, }), ('mpmath', '1.2.1', { 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, }), ('deap', '1.3.3', { 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, }), ] -sanity_pip_check = True - moduleclass = 'lang' From 375e121e8ffdf73611ea4189d0b1e29c3c2ce3a0 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 17 Jan 2023 09:51:29 +0000 Subject: [PATCH 6186/9987] Add scatterpie and shadowtext extensions to R-4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 9fd09b9341e..08a5dae76fc 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3397,6 +3397,12 @@ exts_list = [ ('ggvenn', '0.1.9', { 'checksums': ['38779cfa4e01e07d4a42453cfb8b93d32d2acd6187676bae7d11b2168714a52e'], }), + ('scatterpie', '0.1.8', { + 'checksums': ['a6ccc63a8be63fa113704cf5d4893c1ec1b75d3081ab971bd70e650e708872a0'], + }), + ('shadowtext', '0.1.2', { + 'checksums': ['253c4e737dbb302aa0729e5074e84cbfde2a73bfd7a0fd2c74b557cb728bae7d'], + }), ] moduleclass = 'lang' From c44cddfbc2f8a81ff72ff0e7dcb006156a713684 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 17 Jan 2023 09:52:49 +0000 Subject: [PATCH 6187/9987] Add DO.db, GOSemSim, DOSE, enrichplot, and clusterProfiler extensions to Bioconductor 3.15 --- ...bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 70987c77acf..2e65e10de83 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1128,6 +1128,21 @@ exts_list = [ ('zellkonverter', '1.6.5', { 'checksums': ['669a314d8ca5f62d29a5ab42d51647c4c2a23e9ae2542921933d48a9e394b767'], }), + ('DO.db', '2.9', { + 'checksums': ['762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881'], + }), + ('GOSemSim', '2.22.0', { + 'checksums': ['6d93c0bd9075bb3fb3b65d08906a657ddb8ee5d3ced337914b0f54d0fe2de1c2'], + }), + ('DOSE', '3.22.1', { + 'checksums': ['b19853ee01ef6016ec37b4efca6cce17b6bd8ef756eb45e2fb10e6d6a61190d5'], + }), + ('enrichplot', '1.16.2', { + 'checksums': ['5a5b5ad4dcf2ed5dc9f597bcde3f90a63229cc6af9c742a813ded83c225b0762'], + }), + ('clusterProfiler', '4.4.4', { + 'checksums': ['e5e23a5a1b9580f3801291affb2e547e2fd228e1190e9bce398a1b097c86b24c'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 7f5b59a414fd1acbde1a9393f8e2f911e6203670 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 17 Jan 2023 10:51:12 +0000 Subject: [PATCH 6188/9987] Test jobs enabled else similar to PR 16770 --- .../OpenMolcas-22.10-intel-2022a.eb | 32 ++++++++----------- 1 file changed, 14 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb index 412aae94403..58a9cb32dbf 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb @@ -1,10 +1,13 @@ +# Test-jobs enabled +# Author: J. Sassmannshausen (Imperial College London/UK) + easyblock = 'CMakeMake' name = 'OpenMolcas' version = '22.10' homepage = "https://gitlab.com/Molcas/OpenMolcas" -description = "OpenMolcas is a quantum chemistry software package." +description = "OpenMolcas is a quantum chemistry software package" toolchain = {'name': 'intel', 'version': '2022a'} toolchainopts = {'usempi': True} @@ -13,31 +16,22 @@ source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] sources = ["OpenMolcas-v%(version)s.tar.gz"] patches = ['OpenMolcas-21.06_mcpdft_deps.patch'] checksums = [ - {'OpenMolcas-v22.10.tar.gz': 'd1d3d6c9bd69486c36f5285a51ac18e75c03540c5b33751855e94abc764d9658'}, - {'OpenMolcas-21.06_mcpdft_deps.patch': '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a'}, + 'd1d3d6c9bd69486c36f5285a51ac18e75c03540c5b33751855e94abc764d9658', # OpenMolcas-v22.10.tar.gz + '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a', # OpenMolcas-21.06_mcpdft_deps.patch ] -builddependencies = [('CMake', '3.23.1')] - dependencies = [ - ('Python', '3.10.4'), - ('HDF5', '1.12.2'), ('GlobalArrays', '5.8.1'), + ('HDF5', '1.12.2'), + ('Python', '3.10.4'), ] -build_shared_libs = True +builddependencies = [('CMake', '3.24.3')] preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' -_copts = [ - '-DLINALG=MKL', - '-DMKLROOT=$MKLROOT', - '-DOPENMP=ON', - '-DTOOLS=ON', - '-DFDE=ON', - '-DMPI=ON', - '-DGA=ON', -] -configopts = ' '.join(_copts) +configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' +configopts += '-DMPI=ON -DOPENMP=ON -DGA=ON ' +configopts += '-DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON' modextrapaths = {'PATH': ''} modextravars = { @@ -46,6 +40,8 @@ modextravars = { 'MOLCAS_SOURCE': '%(installdir)s', } +sanity_check_commands = ['cd %(builddir)s/easybuild_obj; ./pymolcas verify'] + sanity_check_paths = { 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, 'sbin/help_basis', 'pymolcas'], From fad66e7d78dac031053aef4d2f8e6ee9db32ccd3 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 17 Jan 2023 11:00:21 +0000 Subject: [PATCH 6189/9987] drop Tk to 8.6.12 to match existing Tcl, remove Tcl 8.6.13 --- .../t/Tcl/Tcl-8.6.13-GCCcore-12.2.0.eb | 41 ------------------- ...-12.2.0.eb => Tk-8.6.12-GCCcore-12.2.0.eb} | 4 +- 2 files changed, 2 insertions(+), 43 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.2.0.eb rename easybuild/easyconfigs/t/Tk/{Tk-8.6.13-GCCcore-12.2.0.eb => Tk-8.6.12-GCCcore-12.2.0.eb} (90%) diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.2.0.eb deleted file mode 100644 index fb3054baae0..00000000000 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.2.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Tcl' -version = '8.6.13' - -homepage = 'https://www.tcl.tk/' -description = """ - Tcl (Tool Command Language) is a very powerful but easy to learn dynamic - programming language, suitable for a very wide range of uses, including web - and desktop applications, networking, administration, testing and many more. -""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] -sources = ['%(namelower)s%(version)s-src.tar.gz'] -checksums = ['43a1fae7412f61ff11de2cfd05d28cfc3a73762f354a417c62370a54e2caf066'] - -builddependencies = [ - ('binutils', '2.39'), -] -dependencies = [ - ('zlib', '1.2.12'), -] - -configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' - -runtest = 'test' - -start_dir = 'unix' - -postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] - -sanity_check_paths = { - 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', - 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, - 'lib/tclConfig.sh', 'man/man1/tclsh.1'], - 'dirs': ['share'], -} - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.12-GCCcore-12.2.0.eb similarity index 90% rename from easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/t/Tk/Tk-8.6.12-GCCcore-12.2.0.eb index d587dfe7219..cbc6929a7ba 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.12-GCCcore-12.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'Tk' -version = '8.6.13' +version = '8.6.12' homepage = 'https://www.tcl.tk/' description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for @@ -13,7 +13,7 @@ source_urls = ["https://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] checksums = [ - {'tk8.6.13-src.tar.gz': '2e65fa069a23365440a3c56c556b8673b5e32a283800d8d9b257e3f584ce0675'}, + {'tk8.6.12-src.tar.gz': '12395c1f3fcb6bed2938689f797ea3cdf41ed5cb6c4766eec8ac949560310630'}, {'Tk-8.6.4_different-prefix-with-tcl.patch': '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d'}, ] From e505587de48277d770ef8a9c9eab4ed0c142e64f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 17 Jan 2023 13:00:08 +0100 Subject: [PATCH 6190/9987] explictely download qe-gipaw source tarball from qe-gipaw GitHub repository in QuantumESPRESSO 7.1 easyconfigs --- .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb | 8 +++++--- .../q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb | 8 +++++--- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb index 6c43b84bfc0..9257514652d 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb @@ -13,20 +13,22 @@ toolchainopts = {'usempi': True, 'openmp': True} source_urls = [ 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', - 'https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/', ] sources = [ { 'filename': 'q-e-qe-%(version)s.tar.gz', 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', }, - 'qe-gipaw-%(version)s.tar.gz', + { + 'filename': 'qe-gipaw-%(version)s.tar.gz', + 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/'] + }, {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, ] checksums = [ 'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6', # q-e-qe-7.1.tar.gz - '486b60f38fad7363f81d346adc69de004692f50c9f6be59eee5152a717ca1513', # qe-gipaw-7.1.tar.gz + '0eee3f613d249ff14e8b891493fe68a3567188575ec7397a8fbe3a97cbf6cb69', # qe-gipaw-7.1.tar.gz '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz ] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb index b39513b3cd8..e9f90039005 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb @@ -13,20 +13,22 @@ toolchainopts = {'usempi': True, 'openmp': True} source_urls = [ 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', - 'https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/', ] sources = [ { 'filename': 'q-e-qe-%(version)s.tar.gz', 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', }, - 'qe-gipaw-%(version)s.tar.gz', + { + 'filename': 'qe-gipaw-%(version)s.tar.gz', + 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/'] + }, {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, ] checksums = [ 'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6', # q-e-qe-7.1.tar.gz - '486b60f38fad7363f81d346adc69de004692f50c9f6be59eee5152a717ca1513', # qe-gipaw-7.1.tar.gz + '0eee3f613d249ff14e8b891493fe68a3567188575ec7397a8fbe3a97cbf6cb69', # qe-gipaw-7.1.tar.gz '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz ] From ce0c4bc3a1f9807047a31a788e590b434d303720 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 17 Jan 2023 14:35:54 +0100 Subject: [PATCH 6191/9987] use SYSTEM global in SNAP-ESA-python v8.0 --- ...n-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb index f8fcca9c9be..b56b31dfd3a 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [ ('Java', '1.8.0_292', '-OpenJDK', True), - ('SNAP-ESA', version, local_javasuffix, True), + ('SNAP-ESA', version, local_javasuffix, SYSTEM), ('Python', '2.7.18'), ] From 740746164782406b745f682e2d67c8e12bf4b792 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 17 Jan 2023 13:56:24 +0000 Subject: [PATCH 6192/9987] adding easyconfigs: cuTENSOR-1.6.1.5-CUDA-11.4.1.eb --- .../cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.4.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.4.1.eb new file mode 100644 index 00000000000..470b423afa8 --- /dev/null +++ b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.4.1.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'cuTENSOR' +local_shortver = '1.6.1' +version = local_shortver + '.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cutensor' +description = """The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, + reduction and elementwise operations.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cutensor/redist/libcutensor/linux-x86_64/'] +sources = ['libcutensor-linux-x86_64-%(version)s-archive.tar.xz'] +checksums = ['793b425c30ffd423c4f3a2e94acaf4fcb6752264aa73b74695a002dd2fe94b1a'] + +local_cudamajver = '11' +dependencies = [('CUDA', local_cudamajver + '.4.1')] + +sanity_check_paths = { + 'files': ['include/cutensor.h', 'include/cutensor/types.h', + 'lib/%s/libcutensor.%s' % (local_cudamajver, SHLIB_EXT), + 'lib/%s/libcutensor_static.a' % local_cudamajver], + 'dirs': [], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib/%s' % local_cudamajver], + 'LIBRARY_PATH': ['lib/%s' % local_cudamajver], +} + +moduleclass = 'lib' From d14524f868b0a6bb0adc699bdff956aadafca829 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 17 Jan 2023 13:22:43 +0100 Subject: [PATCH 6193/9987] fix sources of Block v1.5.3 Conflicts: --- .../Block/Block-1.5.3-20200525-foss-2022a.eb | 53 +++++++ .../Block/Block-1.5.3-20210723-foss-2022a.eb | 50 ------- ...replace_mpi_cxx_binds_with_boost_mpi.patch | 107 ++++++++++++++ .../Block-1.5.3_use-eb-environment.patch | 130 ++++++++---------- 4 files changed, 216 insertions(+), 124 deletions(-) create mode 100644 easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022a.eb delete mode 100644 easybuild/easyconfigs/b/Block/Block-1.5.3-20210723-foss-2022a.eb create mode 100644 easybuild/easyconfigs/b/Block/Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch diff --git a/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022a.eb b/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022a.eb new file mode 100644 index 00000000000..f1e3f55e80b --- /dev/null +++ b/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022a.eb @@ -0,0 +1,53 @@ +easyblock = 'MakeCp' + +name = 'Block' +version = '1.5.3-20200525' +_commit = 'f95317b08043b7c531289576d59ad74a6d920741' + +homepage = 'https://sanshar.github.io/Block/' +description = """Block implements the density matrix renormalization group (DMRG) algorithm for +quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'cstd': 'c++11', 'pic': True} + +# Version 1.5 is a major rewrite of Block that was named at some point StackBlock +# sources are available in sanshar/StackBlock +# sources at sanshar/Block@b0e3671aad and pyscf/Block@db27636b76 correspond to version 1.1.1 +source_urls = ['https://github.com/sanshar/StackBlock/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] +patches = [ + 'Block-1.5.3_use-eb-environment.patch', + 'Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch', +] +checksums = [ + {'1.5.3-20200525.tar.gz': '8d793c5e460d7747a0adcb06ce4b457c6750cf2d42cead1d060db8b44643c3b1'}, + {'Block-1.5.3_use-eb-environment.patch': '7f3e8a52f28d251441d20dfde1f9cb8cdc0c34216defab61cc6980e540a6cf60'}, + {'Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch': + 'f53f1f88cb7b12ab38d1313f93a9bbd31c745dca1beca7a8d51d00e0ae4e762f'}, +] + +dependencies = [ + ('Boost.MPI', '1.79.0'), +] + +buildopts = [ + # Multi-threaded build (block.spin_adapted-serial) + 'OPENMP="yes" EXECUTABLE="block.spin_adapted-serial"', + # MPI build (block.spin_adapted) + 'USE_MPI="yes"', +] + +files_to_copy = [(['block.spin_adapted*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/block.spin_adapted', 'bin/block.spin_adapted-serial'], + 'dirs': [], +} + +sanity_check_commands = [ + "block.spin_adapted-serial --version", + "%(mpi_cmd_prefix)s block.spin_adapted --version", +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/Block/Block-1.5.3-20210723-foss-2022a.eb b/easybuild/easyconfigs/b/Block/Block-1.5.3-20210723-foss-2022a.eb deleted file mode 100644 index 2d686663504..00000000000 --- a/easybuild/easyconfigs/b/Block/Block-1.5.3-20210723-foss-2022a.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'MakeCp' - -name = 'Block' -version = '1.5.3-20210723' -_commit = 'db27636b762aa5921b90de35ac2c08928e57db43' - -homepage = 'https://sanshar.github.io/Block/' -description = """Block implements the density matrix renormalization group (DMRG) algorithm for -quantum chemistry.""" - -toolchain = {'name': 'foss', 'version': '2022a'} -toolchainopts = {'cstd': 'c++11'} - -github_account = 'pyscf' -source_urls = [GITHUB_SOURCE] -sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] -patches = ['Block-1.5.3_use-eb-environment.patch'] -checksums = [ - {'1.5.3-20210723.tar.gz': 'f1d8bd664ccf222bc3d73535ab7ff6faa92f2e22109fb44ca3e7f443e0f8e3f8'}, - {'Block-1.5.3_use-eb-environment.patch': '7c954ac4b12fe99c51290a4c19788dc175a109339fe821a90394af34bc974a76'}, -] - -builddependencies = [ - ('Python', '3.10.4'), -] - -dependencies = [ - ('Boost.MPI', '1.79.0'), -] - -buildopts = [ - # Serial build (block.spin_adapted-serial) - "EXECUTABLE=block.spin_adapted-serial ", - # MPI build (block.spin_adapted) - "USE_MPI=yes ", -] - -files_to_copy = [(['block.spin_adapted*'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/block.spin_adapted', 'bin/block.spin_adapted-serial'], - 'dirs': [], -} - -sanity_check_commands = [ - "block.spin_adapted-serial --version", - "%(mpi_cmd_prefix)s block.spin_adapted --version", -] - -moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/Block/Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch b/easybuild/easyconfigs/b/Block/Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch new file mode 100644 index 00000000000..f0b74d8ec73 --- /dev/null +++ b/easybuild/easyconfigs/b/Block/Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch @@ -0,0 +1,107 @@ +From ced3681cd8c4fe5e10f84d23973ed0e5ee4e0098 Mon Sep 17 00:00:00 2001 +From: Matthias Degroote +Date: Sat, 13 Mar 2021 15:49:28 +0100 +Subject: [PATCH] Remove old c++ MPI bindings + +--- input.C.orig 2023-01-07 01:14:17.074836000 +0100 ++++ input.C 2023-01-17 14:22:56.060651139 +0100 +@@ -24,7 +24,6 @@ + #include + #ifndef SERIAL + #include +-#include "mpi.h" + #endif + #include + #include "fiedler.h" +@@ -1862,7 +1861,7 @@ + } + #ifndef SERIAL + //wait for all procs to zero out the memory +- MPI::COMM_WORLD.Barrier(); ++ world.barrier(); + #endif + v1.set_data() = static_cast(region.get_address()) + (oneIntegralMem+twoIntegralMem)*integralIndex; + v2.set_data() = static_cast(region.get_address()) + oneIntegralMem + (oneIntegralMem+twoIntegralMem)*integralIndex; +@@ -1930,16 +1929,16 @@ + } + + #ifndef SERIAL +- MPI::COMM_WORLD.Barrier(); ++ world.barrier(); + long intdim = oneIntegralMem+twoIntegralMem; + long maxint = 26843540; //mpi cannot transfer more than these number of doubles + long maxIter = intdim/maxint; + for (int i=0; i(region.get_address()) + intdim*integralIndex; + vcc.set_data() = static_cast(region.get_address()) + oneIntegralMem + intdim*integralIndex; +@@ -2302,15 +2301,15 @@ + dumpFile.close(); + } + #ifndef SERIAL +- MPI::COMM_WORLD.Barrier(); ++ world.barrier(); + long maxint = 26843540; //mpi cannot transfer more than these number of doubles + long maxIter = intdim/maxint; + for (int i=0; i(region.get_address()); + v2.set_data() = static_cast(region.get_address()) + oneIntegralMem; + vpt1.set_data() = static_cast(region.get_address()) + oneIntegralMem + twoIntegralMem; +@@ -2692,16 +2691,16 @@ + dumpFile.close(); + } + #ifndef SERIAL +- MPI::COMM_WORLD.Barrier(); ++ world.barrier(); + long intdim = oneIntegralMem+twoIntegralMem+PerturboneIntegralMem; + long maxint = 26843540; //mpi cannot transfer more than these number of doubles + long maxIter = intdim/maxint; + for (int i=0; i -+#include - #include "IntegralMatrix.h" - - ---- makefile.orig 2022-11-22 16:40:08.227179000 +0100 -+++ makefile 2022-11-22 16:41:34.467330533 +0100 -@@ -6,28 +6,28 @@ - - ######### GENERAL OPTIONS FOR USER ######### - #specify boost include file --BOOSTINCLUDE = /opt/local/include -+BOOSTINCLUDE = ${EBROOTBOOST}/include - - #specify boost and lapack-blas library locations --BOOSTLIB = -L/opt/local/lib -lboost_system -lboost_filesystem -lboost_serialization -+BOOSTLIB = -L${EBROOTBOOST}/lib -lboost_system -lboost_filesystem -lboost_serialization - #BOOSTLIB = -lboost_serialization -lboost_system -lboost_filesystem --LAPACKBLAS = /usr/lib/liblapack.dylib /usr/lib/libblas.dylib -+LAPACKBLAS = ${LIBLAPACK} - - # set if using BOOST version >= 1.56.0 --USE_BOOST56 = no -+USE_BOOST56 = yes - ifeq ($(USE_BOOST56), yes) - B56 = -DBOOST_1_56_0 - endif - - #use these variable to set if we will use mpi or not - USE_MPI = no - USE_MKL = no - +--- Makefile.orig 2023-01-06 12:46:33.569558000 +0100 ++++ Makefile 2023-01-06 15:47:17.535047461 +0100 +@@ -8,16 +8,16 @@ # change to icpc for Intel --CXX = icpc --MPICXX = mpiicpc + #CXX = clang++ + #MPICXX = mpiicpc +-CXX = g++ +-MPICXX = mpic++ -export CXX -export MPICXX -+#CXX = icpc -+#MPICXX = mpiicpc ++#CXX = g++ ++#MPICXX = mpic++ +#export CXX +#export MPICXX - # use this variable to set if we will use integer size of 8 or not. - # molpro compilation requires I8, since their integers are long -@@ -40,7 +40,7 @@ - # molcas compilation w/ -64 option requires I8 as well - MOLCAS = no + # BOOST include directory + #BOOSTDIR=/software/StackBlock/boost_1_58_0 + #BOOSTINCLUDE = ${BOOSTDIR}/include +-BOOSTDIR=/usr/lib +-BOOSTINCLUDE =/usr/include ++BOOSTDIR = $(EBROOTBOOST) ++BOOSTINCLUDE = ${BOOSTDIR}/include --OPENMP = no -+OPENMP = yes + # set to yes if using BOOST version >= 1.56.0 + USE_BOOST56 = yes +@@ -35,7 +35,7 @@ - ifeq ($(USE_MKL), yes) - MKLLIB = /opt/intel/compilers_and_libraries/linux/mkl/lib/intel64 -@@ -101,7 +101,7 @@ - OPENMP_FLAGS= -openmp -D_OPENMP - endif - # Intel compiler -- OPT = -DNDEBUG -O3 -funroll-loops -Werror -+ OPT = -DNDEBUG -funroll-loops $(OPTFLAGS) - # OPT = -g -fPIC - ifeq ($(USE_MPI), no) - CXX = icc -@@ -113,7 +113,7 @@ - ifeq ($(OPENMP), yes) - OPENMP_FLAGS= -fopenmp #-D_OPENMP - endif -- OPT = -DNDEBUG -O3 -g -funroll-loops -Werror -+ OPT = -DNDEBUG -g -funroll-loops $(OPTFLAGS) - # OPT = -g -fPIC + #LAPACKBLAS = -lblas -llapack + #LAPACKBLAS = /usr/lib/liblapack.dylib /usr/lib/libblas.dylib +-LAPACKBLAS = ++LAPACKBLAS = ${LIBBLAS} + + # set if we will use MPI or OpenMP + USE_MPI = no +@@ -108,12 +108,12 @@ + MOLCAS_BLOCK= -DMOLCAS -fPIC endif -@@ -122,7 +122,7 @@ - OPENMP_FLAGS= -fopenmp #-D_OPENMP - endif +-FLAGS = -I${MKLFLAGS} -I$(INCLUDE1) -I$(INCLUDE2) -I$(NEWMATINCLUDE) -I$(BOOSTINCLUDE) -I$(MOLPROINCLUDE) \ ++FLAGS = $(CPPFLAGS) -I${MKLFLAGS} -I$(INCLUDE1) -I$(INCLUDE2) -I$(NEWMATINCLUDE) -I$(BOOSTINCLUDE) -I$(MOLPROINCLUDE) \ + -I$(HOME)/modules/generate_blocks/ -I$(HOME)/modules/onepdm -I$(HOME)/modules/twopdm/ \ + -I$(HOME)/modules/npdm -I$(HOME)/modules/two_index_ops -I$(HOME)/modules/three_index_ops -I$(HOME)/modules/four_index_ops -std=c++0x \ + -I$(HOME)/modules/ResponseTheory -I$(HOME)/modules/nevpt2 -I$(HOME)/molcas -I$(HOME)/modules/mps_nevpt -- OPT = -DNDEBUG -g -Werror -+ OPT = -DNDEBUG -g $(OPTFLAGS) - endif +-LIBS += -L$(NEWMATLIB) -lnewmat $(BOOSTLIB) $(LAPACKBLAS) $(MALLOC) ++LIBS := $(LDFLAGS) -L$(NEWMATLIB) -lnewmat $(BOOSTLIB) $(LAPACKBLAS) $(MALLOC) $(LIBS) -lrt + MPI_OPT = -DSERIAL + + +@@ -127,7 +127,7 @@ + #endif + endif + # Intel compiler +- OPT = -DNDEBUG -O2 -g -funroll-loops #-ipo ++ OPT = -DNDEBUG $(OPTFLAGS) -g -funroll-loops + # OPT = -g + # # Useful option to define a newer g++ binary if the default g++ is too old + # OPT += -gxx-name=g++-4.7 +--- newmat10/makefile.orig 2023-01-06 15:20:52.879226000 +0100 ++++ newmat10/makefile 2023-01-06 15:20:30.392463000 +0100 +@@ -1,6 +1,6 @@ + #CXX = g++ + $(info $(CXX)) +-CXXFLAGS = -fPIC -O2 -Wall ++#CXXFLAGS = -fPIC -O2 -Wall - ifeq ($(DOPROF),yes) + DIFF = ./sdiff + PRE = ./ From ca3bccfae1f446ffac0e4160825c2ba5dc05b9c4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 17 Jan 2023 15:12:37 +0100 Subject: [PATCH 6194/9987] fix dependency on Block of PySCF v2.1.1 --- easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb index cfe1ada58c8..3f29fdd4b4e 100644 --- a/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb @@ -26,7 +26,7 @@ dependencies = [ ('CPPE', '0.3.1'), # extra ('PyBerny', '0.6.3'), # extra ('PyCheMPS2', '1.8.12'), # needed by dmrgscf - ('Block', '1.5.3-20210723'), # needed by dmrgscf + ('Block', '1.5.3-20200525'), # needed by dmrgscf ('NECI', '20220711'), # needed by fciqmc ('Dice', '20221025'), # needed by icmpspt ] From 3ef9e633052d0f3abb635df99aa84425e12d1cbb Mon Sep 17 00:00:00 2001 From: Denis Kristak Date: Tue, 17 Jan 2023 15:21:03 +0100 Subject: [PATCH 6195/9987] adding ncbi-vdb 3.0.0 exception to version testing...it is needed by SRA-Toolkit 3.0.0 --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4dca9587c65..5ac2b1e77c5 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -538,6 +538,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # SimpleITK 2.1.0 requires Lua 5.3.x, MedPy and nnU-Net depend on SimpleITK (r'5\.3\.5', [r'nnU-Net-1\.7\.0-', r'MedPy-0\.4\.0-', r'SimpleITK-2\.1\.0-']), ], + # SRA-toolkit 3.0.0 requires ncbi-vdb 3.0.0 + 'ncbi-vdb': [(r'3\.0\.0', [r'SRA-Toolkit-3\.0\.0'])], # TensorFlow 2.5+ requires a more recent NCCL than version 2.4.8 used in 2019b generation; # Horovod depends on TensorFlow, so same exception required there 'NCCL': [(r'2\.11\.4', [r'TensorFlow-2\.[5-9]\.', r'Horovod-0\.2[2-9]'])], From 5817092ff52aacb5d1f5cf112c914bd4026a11d2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 17 Jan 2023 16:23:32 +0100 Subject: [PATCH 6196/9987] adding easyconfigs: CDFlib-0.4.9-foss-2022a.eb --- .../c/CDFlib/CDFlib-0.4.9-foss-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDFlib/CDFlib-0.4.9-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CDFlib/CDFlib-0.4.9-foss-2022a.eb b/easybuild/easyconfigs/c/CDFlib/CDFlib-0.4.9-foss-2022a.eb new file mode 100644 index 00000000000..dc43f2a891a --- /dev/null +++ b/easybuild/easyconfigs/c/CDFlib/CDFlib-0.4.9-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'CDFlib' +version = '0.4.9' + +homepage = 'https://github.com/MAVENSDC/cdflib' +description = """cdflib is a python module to read/write CDF (Common Data Format .cdf) files +without needing to install the CDF NASA library. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('xarray', '2022.6.0'), + ('astropy', '5.1.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cdflib', version, { + 'checksums': ['665d2ab31fcf7b61dec230fbc390d87e02116993dc434c3112921f967012b963'], + }), +] + +moduleclass = 'data' From b7618bd01dec0d4fe4ac35ce22ae0f9a018044a3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 17 Jan 2023 16:24:17 +0100 Subject: [PATCH 6197/9987] adding easyconfigs: HMMER-3.3.2-gompi-2022a.eb --- .../h/HMMER/HMMER-3.3.2-gompi-2022a.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022a.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022a.eb new file mode 100644 index 00000000000..1e4307e3803 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022a.eb @@ -0,0 +1,79 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# Updated by: Filip Kružík (INUITS) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + {'hmmer-3.3.2.tar.gz': '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'}, + {'HMMER-3.3.2_fix_perl.patch': '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d'}, +] + +builddependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), +] + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From d3ce856455f82df76a613225c8798791dd18e6fd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 17 Jan 2023 16:32:06 +0100 Subject: [PATCH 6198/9987] fix missing SYSTEM global in SNAP-ESA-python v8.0 --- ...n-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb index b56b31dfd3a..506b3888fb2 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb @@ -11,7 +11,7 @@ description = "Python interface to the Sentinel Application Platform (SNAP) API" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [ - ('Java', '1.8.0_292', '-OpenJDK', True), + ('Java', '1.8.0_292', '-OpenJDK', SYSTEM), ('SNAP-ESA', version, local_javasuffix, SYSTEM), ('Python', '2.7.18'), ] From 987d1fac337531cd380c5c443e310b07ad72c88e Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 17 Jan 2023 15:44:20 +0000 Subject: [PATCH 6199/9987] revert to PythonBundle, and update easyblock instead --- .../SciPy-bundle-2023.01-gfbf-2022b.eb | 53 +++---------------- 1 file changed, 8 insertions(+), 45 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb index 8d5febe6383..7878162dce4 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'SciPy-bundle' version = '2023.01' @@ -12,9 +12,10 @@ toolchainopts = {'pic': True, 'lowopt': True} builddependencies = [ ('hypothesis', '6.62.1'), ('UnZip', '6.0'), + # scipy >= 1.9.0 uses Meson/Ninja ('Meson', '0.64.0'), ('Ninja', '1.11.1'), - ('pkgconf', '1.9.3'), + ('pkgconf', '1.9.3'), # required by scipy ] dependencies = [ @@ -22,89 +23,51 @@ dependencies = [ ('pybind11', '2.10.3'), # required by scipy ] -default_easyblock = 'PythonPackage' -default_component_specs = { - 'sources': [SOURCE_TAR_GZ], - 'source_urls': [PYPI_SOURCE], - 'start_dir': '%(name)s-%(version)s', -} - -_pythonpath = 'PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH' +use_pip = True # order is important! -components = [ +exts_list = [ ('numpy', '1.24.1', { - 'patches': [{'name': 'numpy-1.22.3_disable-broken-override-test.patch', 'alt_location': 'SciPy-bundle'}], + 'patches': ['numpy-1.22.3_disable-broken-override-test.patch'], 'checksums': [ {'numpy-1.24.1.tar.gz': '2386da9a471cc00a1f47845e27d916d5ec5346ae9696e01a8a34760858fe9dd2'}, {'numpy-1.22.3_disable-broken-override-test.patch': '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, ], - 'sanity_pip_check': True, }), ('ply', '3.11', { 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, }), ('gast', '0.5.3', { 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, }), ('beniget', '0.4.1', { 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, }), ('pythran', '0.12.1', { 'checksums': ['702c2701187cfb38f66c0c20cc85d04d0e156d260a8d92892da65947faa5360e'], - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, }), ('scipy', '1.10.0', { - 'easyblock': 'MesonNinja', - 'preconfigopts': _pythonpath, - 'configopts': '-Dblas=flexiblas -Dlapack=flexiblas', - 'prebuildopts': _pythonpath, - 'preinstallopts': "PATH=%(installdir)s/bin:$PATH " + _pythonpath, 'checksums': ['c8b3cbc636a87a89b770c6afc999baa6bcbb01691b5ccbbc1b1791c7c0a07540'], }), ('numexpr', '2.8.4', { 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, }), ('Bottleneck', '1.3.5', { 'checksums': ['2c0d27afe45351f6f421893362621804fa7dea14fe29a78eaa52d4323f646de7'], - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, }), ('pandas', '1.5.2', { 'preinstallopts': "export PANDAS_CI=0 && ", 'checksums': ['220b98d15cee0b2cd839a6358bd1f273d0356bf964c1a1aeb32d47db0215488b'], - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, }), ('mpmath', '1.2.1', { 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, }), ('deap', '1.3.3', { 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], - 'use_pip': True, - 'sanity_pip_check': True, - 'download_dep_fail': True, }), ] +sanity_pip_check = True + moduleclass = 'lang' From 0e3727bbeabf994d501a5ed2caf0517bc35ba438 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Jan 2023 17:09:04 +0100 Subject: [PATCH 6200/9987] Fix AVX2 bug in GCC 11 --- .../easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 2 + .../GCCcore-11.1.0_fix-AVX2-intrinsics.patch | 129 ++++++++++++++++++ .../easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 2 + 3 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0_fix-AVX2-intrinsics.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index dde91967953..b89321338eb 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -36,6 +36,7 @@ patches = [ 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', + 'GCCcore-11.1.0_fix-AVX2-intrinsics.patch', 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ @@ -52,6 +53,7 @@ checksums = [ '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, + {'GCCcore-11.1.0_fix-AVX2-intrinsics.patch': 'a06c09cc6ba25ec4e0a28280eb6b25cdb331f7835d07ebb3a83536214d3d68fa'}, {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0_fix-AVX2-intrinsics.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0_fix-AVX2-intrinsics.patch new file mode 100644 index 00000000000..08381e2694d --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0_fix-AVX2-intrinsics.patch @@ -0,0 +1,129 @@ +Fix wrongly implemented _mm_loadu_si32/16 resulting in failures in e.g. PyTorch tests +due to wrong values as the order in the vectorized elements is wrong. + +From 85568e505c3b06708ec0fb21d1ab4f78e0c66896 Mon Sep 17 00:00:00 2001 +From: Jakub Jelinek +Date: Mon, 14 Mar 2022 10:44:38 +0100 +Subject: [PATCH 1/1] i386: Fix up _mm_loadu_si{16,32} [PR99754] + +These intrinsics are supposed to do an unaligned may_alias load +of a 16-bit or 32-bit value and store it as the first element of +a 128-bit integer vector, with all other elements cleared. + +The current _mm_storeu_* implementation implements that correctly, uses +__*_u types to do the store and extracts the first element of a vector into +it. +But _mm_loadu_si{16,32} gets it all wrong. It performs an aligned +non-may_alias load and because _mm_set_epi{16,32} has the args reversed, +it also inserts it into the last vector element instead of first. + +The following patch fixes that. + +Note, while the Intrinsics guide for _mm_loadu_si32 says SSE2, +for _mm_loadu_si16 it says strangely SSE. But the intrinsics +returns __m128i, which is only defined in emmintrin.h, and +_mm_set_epi16 is also only SSE2 and later in emmintrin.h. +Even clang defines it in emmintrin.h and ends up with inlining +failure when calling _mm_loadu_si16 from sse,no-sse2 function. +So, isn't that a bug in the intrinsic guide instead? + +2022-03-14 Jakub Jelinek + + PR target/99754 + * config/i386/emmintrin.h (_mm_loadu_si32): Put loaded value into + first rather than last element of the vector, use __m32_u to do + a really unaligned load, use just 0 instead of (int)0. + (_mm_loadu_si16): Put loaded value into first rather than last + element of the vector, use __m16_u to do a really unaligned load, + use just 0 instead of (short)0. + + * gcc.target/i386/pr99754-1.c: New test. + * gcc.target/i386/pr99754-2.c: New test. +--- + gcc/config/i386/emmintrin.h | 5 ++--- + gcc/testsuite/gcc.target/i386/pr99754-1.c | 20 +++++++++++++++++++ + gcc/testsuite/gcc.target/i386/pr99754-2.c | 24 +++++++++++++++++++++++ + 3 files changed, 46 insertions(+), 3 deletions(-) + create mode 100644 gcc/testsuite/gcc.target/i386/pr99754-1.c + create mode 100644 gcc/testsuite/gcc.target/i386/pr99754-2.c + +diff --git a/gcc/config/i386/emmintrin.h b/gcc/config/i386/emmintrin.h +index eb6de5c5038..ead06228572 100644 +--- a/gcc/config/i386/emmintrin.h ++++ b/gcc/config/i386/emmintrin.h +@@ -718,14 +718,13 @@ _mm_loadu_si64 (void const *__P) + extern __inline __m128i __attribute__((__gnu_inline__, __always_inline__, __artificial__)) + _mm_loadu_si32 (void const *__P) + { +- return _mm_set_epi32 (*(int *)__P, (int)0, (int)0, (int)0); ++ return _mm_set_epi32 (0, 0, 0, (*(__m32_u *)__P)[0]); + } + + extern __inline __m128i __attribute__((__gnu_inline__, __always_inline__, __artificial__)) + _mm_loadu_si16 (void const *__P) + { +- return _mm_set_epi16 (*(short *)__P, (short)0, (short)0, (short)0, +- (short)0, (short)0, (short)0, (short)0); ++ return _mm_set_epi16 (0, 0, 0, 0, 0, 0, 0, (*(__m16_u *)__P)[0]); + } + + extern __inline void __attribute__((__gnu_inline__, __always_inline__, __artificial__)) +diff --git a/gcc/testsuite/gcc.target/i386/pr99754-1.c b/gcc/testsuite/gcc.target/i386/pr99754-1.c +new file mode 100644 +index 00000000000..9c953724881 +--- /dev/null ++++ b/gcc/testsuite/gcc.target/i386/pr99754-1.c +@@ -0,0 +1,20 @@ ++/* PR target/99754 */ ++/* { dg-do run } */ ++/* { dg-options "-O2 -msse2" } */ ++/* { dg-require-effective-target sse2 } */ ++ ++#include "sse2-check.h" ++#include ++ ++static void ++sse2_test (void) ++{ ++ union { unsigned char buf[32]; long long ll; } u; ++ u.buf[1] = 0xfe; ++ u.buf[2] = 0xca; ++ u.buf[17] = 0xaa; ++ u.buf[18] = 0x55; ++ _mm_storeu_si16 (&u.buf[17], _mm_loadu_si16 (&u.buf[1])); ++ if (u.buf[17] != 0xfe || u.buf[18] != 0xca) ++ abort (); ++} +diff --git a/gcc/testsuite/gcc.target/i386/pr99754-2.c b/gcc/testsuite/gcc.target/i386/pr99754-2.c +new file mode 100644 +index 00000000000..f7a1dd3e124 +--- /dev/null ++++ b/gcc/testsuite/gcc.target/i386/pr99754-2.c +@@ -0,0 +1,24 @@ ++/* PR target/99754 */ ++/* { dg-do run } */ ++/* { dg-options "-O2 -msse2" } */ ++/* { dg-require-effective-target sse2 } */ ++ ++#include "sse2-check.h" ++#include ++ ++static void ++sse2_test (void) ++{ ++ union { unsigned char buf[32]; long long ll; } u; ++ u.buf[1] = 0xbe; ++ u.buf[2] = 0xba; ++ u.buf[3] = 0xfe; ++ u.buf[4] = 0xca; ++ u.buf[17] = 0xaa; ++ u.buf[18] = 0x55; ++ u.buf[19] = 0xaa; ++ u.buf[20] = 0x55; ++ _mm_storeu_si32 (&u.buf[17], _mm_loadu_si32 (&u.buf[1])); ++ if (u.buf[17] != 0xbe || u.buf[18] != 0xba || u.buf[19] != 0xfe || u.buf[20] != 0xca) ++ abort (); ++} +-- +2.31.1 + diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb index 9d40637c25c..56cebe7e95f 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', + 'GCCcore-11.1.0_fix-AVX2-intrinsics.patch', 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ @@ -50,6 +51,7 @@ checksums = [ {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, + {'GCCcore-11.1.0_fix-AVX2-intrinsics.patch': 'a06c09cc6ba25ec4e0a28280eb6b25cdb331f7835d07ebb3a83536214d3d68fa'}, {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] From 89f205bf0fea806dff6b9ea335c7febc2cc536be Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 17 Jan 2023 16:24:51 +0000 Subject: [PATCH 6201/9987] add pooch extension to ensure scipy tests run --- .../s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb index 7878162dce4..b69f0927fc6 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb @@ -47,6 +47,8 @@ exts_list = [ ('pythran', '0.12.1', { 'checksums': ['702c2701187cfb38f66c0c20cc85d04d0e156d260a8d92892da65947faa5360e'], }), + ('pooch', '1.6.0', { + }), ('scipy', '1.10.0', { 'checksums': ['c8b3cbc636a87a89b770c6afc999baa6bcbb01691b5ccbbc1b1791c7c0a07540'], }), From 15056a43f3eb21f3d373fa7cba10fbaffca0eefd Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 17 Jan 2023 19:06:06 +0000 Subject: [PATCH 6202/9987] adding easyconfigs: pybinding-0.9.5-foss-2022a.eb --- .../p/pybinding/pybinding-0.9.5-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/pybinding/pybinding-0.9.5-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pybinding/pybinding-0.9.5-foss-2022a.eb b/easybuild/easyconfigs/p/pybinding/pybinding-0.9.5-foss-2022a.eb new file mode 100644 index 00000000000..bb8a4b217c2 --- /dev/null +++ b/easybuild/easyconfigs/p/pybinding/pybinding-0.9.5-foss-2022a.eb @@ -0,0 +1,39 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'pybinding' +version = '0.9.5' + +homepage = 'https://github.com/dean0x7d/pybinding' +description = """Pybinding is a Python package for numerical tight-binding +calculations in solid state physics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['a3b0fd5c7bc6babdd265797698573a2ffe31edc5c4c6c4265262aa6f1005603d'] + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' From 87b9ebce5dd09a46f8b71a85be5072c8f6878915 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Jan 2023 20:30:49 +0100 Subject: [PATCH 6203/9987] use CMakeMake easyblock + existing patches for ncbi-vdb v3.0.0 with gompi/2021b --- .../n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb | 25 +++++-------- .../n/ncbi-vdb/ncbi-vdb-3.0.0_cstdlib.patch | 12 ------- .../ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch | 35 ------------------- 3 files changed, 8 insertions(+), 64 deletions(-) delete mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_cstdlib.patch delete mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb index d9a196f47e3..2809be90fa4 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2021b.eb @@ -1,5 +1,5 @@ # updated: Denis Kristak (INUITS) -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'ncbi-vdb' version = '3.0.0' @@ -14,14 +14,14 @@ github_account = 'ncbi' source_urls = [GITHUB_SOURCE] sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] patches = [ - 'ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch', - 'ncbi-vdb-3.0.0_cstdlib.patch', + 'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch', + 'ncbi-vdb-cstdlib.patch', 'ncbi-vdb-3.0.0_hdf5_api.patch', ] checksums = [ {'ncbi-vdb-3.0.0.tar.gz': '154317ef265104861fe8d3d2e439939ae98f33b1e28da3c45f32ae8534dbfad7'}, - {'ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch': 'a87d1ab79118e2392d197dbb684347b75a6a26509108cce8a12590feb929e38b'}, - {'ncbi-vdb-3.0.0_cstdlib.patch': '89431a477f93c62c81c530aaa36ccd17a3b800a5c0d9e6d752b697d37dd16177'}, + {'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch': 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133'}, + {'ncbi-vdb-cstdlib.patch': 'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655'}, {'ncbi-vdb-3.0.0_hdf5_api.patch': '34bdad822248118a011b5106fe5b5efaa068c19b66ed10f949a9c0b07a79de8b'}, ] @@ -32,27 +32,18 @@ builddependencies = [ ] dependencies = [ - ('file', '5.41'), # provides libmagic ('HDF5', '1.12.1'), ('libxml2', '2.9.10'), ('bzip2', '1.0.8'), ] -# add addtional libraries needed to statically link HDF5 from EB -preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl &&" - -configopts = "--build-prefix=%(builddir)s " # change default build directory -configopts += "--with-magic-prefix=$EBROOTFILE " -configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" - -# replace hardcoded optimization flags with EB settings -prebuildopts = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " -preinstallopts = 'EBFLAGS="$CFLAGS" ' +configopts = "-DHDF5_INCDIR=$EBROOTHDF5/include -DHDF5_LIBDIR=$EBROOTHDF5/lib " +configopts += "-DXML2_INCDIR=$EBROOTLIBXML2/include -DXML2_LIBDIR=$EBROOTLIBXML2/lib " sanity_check_paths = { 'files': ['include/ncbi/ncbi.h', 'include/ncbi/vdb-blast.h'] + [('lib/libncbi-%s.%s' % (k, e)) for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], - 'dirs': ['include', 'lib', 'lib64'], + 'dirs': [], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_cstdlib.patch b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_cstdlib.patch deleted file mode 100644 index b71a58c5404..00000000000 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_cstdlib.patch +++ /dev/null @@ -1,12 +0,0 @@ -Add C standard library header. John Dey, Fred Hutch Cancer Center -diff -ruN ncbi-vdb-3.0.0.orig/vdb3/platform/memory/PrimordialMemoryMgr.cpp ncbi-vdb-3.0.0/vdb3/platform/memory/PrimordialMemoryMgr.cpp ---- ncbi-vdb-3.0.0.orig/vdb3/platform/memory/PrimordialMemoryMgr.cpp 2022-02-10 13:50:11.000000000 -0800 -+++ ncbi-vdb-3.0.0/vdb3/platform/memory/PrimordialMemoryMgr.cpp 2022-08-18 14:24:21.242597000 -0700 -@@ -24,6 +24,7 @@ - * - */ - -+#include - #include - - #include \ No newline at end of file diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch deleted file mode 100644 index 8a358e937e2..00000000000 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0_fix-LD_LIBRARY_PATH.patch +++ /dev/null @@ -1,35 +0,0 @@ -don't blindly overwrite $LD_LIBRARY_PATH -based on work by: Kenneth Hoste (HPC-UGent) -diff -ruN ncbi-vdb-3.0.0.orig/build/ld.linux.dlib.sh ncbi-vdb-3.0.0/build/ld.linux.dlib.sh ---- ncbi-vdb-3.0.0.orig/build/ld.linux.dlib.sh 2022-02-10 13:50:11.000000000 -0800 -+++ ncbi-vdb-3.0.0/build/ld.linux.dlib.sh 2022-09-19 16:35:44.390187000 -0700 -@@ -83,8 +83,7 @@ - done - - # update LD_LIBRARY_PATH -- unset LD_LIBRARY_PATH -- export LD_LIBRARY_PATH="$LDIRS:$XDIRS" -+ export LD_LIBRARY_PATH="$LDIRS:$XDIRS:$LD_LIBRARY_PATH" - - # tack on libraries, finding as we go - for LIB in $LIBS -@@ -305,4 +304,4 @@ - echo "$MSG" >> $LOGFILE - - "$BUILD_DIR/scm-collect.sh" "$OBJS" "$SLIBS" | sort -u > "$TARG.md5" --fi -\ No newline at end of file -+fi -diff -ruN ncbi-vdb-3.0.0.orig/build/ld.linux.exe.sh ncbi-vdb-3.0.0/build/ld.linux.exe.sh ---- ncbi-vdb-3.0.0.orig/build/ld.linux.exe.sh 2022-02-10 13:50:11.000000000 -0800 -+++ ncbi-vdb-3.0.0/build/ld.linux.exe.sh 2022-09-19 16:36:32.114647000 -0700 -@@ -91,8 +91,7 @@ - done - - # update LD_LIBRARY_PATH -- unset LD_LIBRARY_PATH -- export LD_LIBRARY_PATH="$LDIRS:$XDIRS" -+ export LD_LIBRARY_PATH="$LDIRS:$XDIRS:$LD_LIBRARY_PATH" - - # tack on libraries, finding as we go - for LIB in $LIBS From 6d0dfb6891844f96e8baaccd39e29fce06f2ec64 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Jan 2023 20:47:06 +0100 Subject: [PATCH 6204/9987] add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2 --- .../n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb | 30 +++++++------------ test/easyconfigs/easyconfigs.py | 4 +-- 2 files changed, 12 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb index b02b422d181..e9b2be16570 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb @@ -15,11 +15,13 @@ sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ patches = [ 'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch', 'ncbi-vdb-cstdlib.patch', + 'ncbi-vdb-3.0.0_hdf5_api.patch', ] checksums = [ - '154317ef265104861fe8d3d2e439939ae98f33b1e28da3c45f32ae8534dbfad7', # ncbi-vdb-3.0.0.tar.gz - 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch - 'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655', # ncbi-vdb-cstdlib.patch + {'ncbi-vdb-3.0.0.tar.gz': '154317ef265104861fe8d3d2e439939ae98f33b1e28da3c45f32ae8534dbfad7'}, + {'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch': 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133'}, + {'ncbi-vdb-cstdlib.patch': 'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655'}, + {'ncbi-vdb-3.0.0_hdf5_api.patch': '34bdad822248118a011b5106fe5b5efaa068c19b66ed10f949a9c0b07a79de8b'}, ] builddependencies = [ @@ -29,29 +31,17 @@ builddependencies = [ ] dependencies = [ - ('file', '5.43'), # provides libmagic - ('HDF5', '1.10.8'), # version 1.12.x has changes to API and is not compatible + ('HDF5', '1.12.2'), ('libxml2', '2.9.13'), ('bzip2', '1.0.8'), ] -# add addtional libraries needed to statically link HDF5 from EB -preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/'" -preconfigopts += " %(builddir)s/%(namelower)s-%(version)s/setup/konfigure.perl &&" - -configopts = '' -configopts += ' -DHDF5_LIBDIR=$EBROOTHDF5/lib -DXML2_LIBDIR=$EBROOTLIBXML2/lib' -configopts += ' -DHDF5_INCDIR=$EBROOTHDF5/include -DXML2_INCDIR=$EBROOTLIBXML2/include' - - -# replace hardcoded optimization flags with EB settings -prebuildopts = "find %(builddir)s/%(namelower)s-%(version)s/build/ -name \"Makefile*\" " -prebuildopts += "-exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " -preinstallopts = 'EBFLAGS="$CFLAGS" ' +configopts = "-DHDF5_INCDIR=$EBROOTHDF5/include -DHDF5_LIBDIR=$EBROOTHDF5/lib " +configopts += "-DXML2_INCDIR=$EBROOTLIBXML2/include -DXML2_LIBDIR=$EBROOTLIBXML2/lib " sanity_check_paths = { - 'files': [('lib/libncbi-%s.%s' % (k, e), 'lib64/libncbi-%s.%s' % (k, e)) - for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'files': ['include/ncbi/ncbi.h', 'include/ncbi/vdb-blast.h'] + + [('lib/libncbi-%s.%s' % (k, e)) for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], 'dirs': [], } diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4dca9587c65..c98f4a24cb8 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -504,9 +504,9 @@ def check_dep_vars(self, gen, dep, dep_vars): r'QGIS-3\.28\.1']), ], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], - # ncbi-vdb v2.x and v3.0.0 require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) + # ncbi-vdb v2.x requires HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [ - (r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'ncbi-vdb-3\.0\.0', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', + (r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.']), ], # VMTK 1.4.x requires ITK 4.13.x From d5add8048d96d7f0a7dab4a764776ab6b239ca1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Jan 2023 21:47:13 +0100 Subject: [PATCH 6205/9987] adding easyconfigs: pdsh-2.34-GCCcore-12.2.0.eb --- .../p/pdsh/pdsh-2.34-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..1b8e1f8ed55 --- /dev/null +++ b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'pdsh' +version = '2.34' + +homepage = 'https://github.com/chaos/pdsh' +description = "A high performance, parallel remote shell utility" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/chaos/pdsh/releases/download/pdsh-%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b47b3e4662736ef44b6fe86e3d380f95e591863e69163aa0592e9f9f618521e9'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('libreadline', '8.2'), +] + +configopts = "--with-ssh --with-slurm --with-mrsh --with-readline" + +sanity_check_paths = { + 'files': ['bin/dshbak', 'bin/pdcp', 'bin/pdsh', 'bin/rpdcp'], + 'dirs': ['lib/pdsh', 'share/man/man1'], +} + +sanity_check_commands = [ + "dshbak -h", + "pdcp -h 2>&1 | grep '^Usage: pdcp'", + "pdsh -h 2>&1 | grep '^Usage: pdsh'", + "rpdcp -h 2>&1 | grep '^Usage: rpdcp'", +] + +moduleclass = 'tools' From 93d287d164c4de71c318795b3176cee14255e79e Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 18 Jan 2023 12:20:00 +1100 Subject: [PATCH 6206/9987] Apply suggestions from code review For recent toolchains, we should use `pkgconf` instead of `pkg-config`. Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-11.2.0.eb | 2 +- .../l/libpspio/libpspio-0.2.4-intel-compilers-2021.4.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-11.2.0.eb index 31ccebb8ca4..ab2b05cbf45 100644 --- a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-GCC-11.2.0.eb @@ -12,7 +12,7 @@ source_urls = ['https://gitlab.com/ElectronicStructureLibrary/libpspio/uploads/7 sources = [SOURCELOWER_TAR_GZ] checksums = ['cb3d51ffa6b822305bb943edc7ddfaf1cfc1b928f0594330d732330bfc081850'] -builddependencies = [('pkg-config', '0.29.2')] +builddependencies = [('pkgconf', '1.8.0')] dependencies = [('GSL', '2.7')] diff --git a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.4.0.eb index 7862af64726..94c7f7dfe56 100644 --- a/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/l/libpspio/libpspio-0.2.4-intel-compilers-2021.4.0.eb @@ -12,7 +12,7 @@ source_urls = ['https://gitlab.com/ElectronicStructureLibrary/libpspio/uploads/7 sources = [SOURCELOWER_TAR_GZ] checksums = ['cb3d51ffa6b822305bb943edc7ddfaf1cfc1b928f0594330d732330bfc081850'] -builddependencies = [('pkg-config', '0.29.2')] +builddependencies = [('pkgconf', '1.8.0')] dependencies = [('GSL', '2.7')] From 3451bc257635ba7f22b024adbe272b2c67b9f286 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 18 Jan 2023 02:12:19 +0000 Subject: [PATCH 6207/9987] adding easyconfigs: cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb --- .../cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb new file mode 100644 index 00000000000..bec7936a183 --- /dev/null +++ b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'cuSPARSELt' +version = '0.3.0.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://docs.nvidia.com/cuda/cusparselt/index.html' +description = """NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in +which at least one operand is a sparse matrix""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cusparselt/redist/libcusparse-lt/linux-x86_64/'] +sources = ['libcusparse_lt-linux-x86_64-%(version)s-archive.tar.xz'] +checksums = ['46b258c2c333f7324e03bdf6b13576be6153b1218fb531025631650e36515f45'] + +dependencies = [('CUDA', '11.4.1')] + +sanity_check_paths = { + 'files': ['include/cusparseLt.h', + 'lib/libcusparseLt.%s' % SHLIB_EXT, + 'lib/libcusparseLt_static.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 2f1d1dee3a661690e87f92862b775afd66cd1d08 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 18 Jan 2023 11:16:08 +0100 Subject: [PATCH 6208/9987] QCG-PilotJob for 2022a --- .../k/Kaleido/Kaleido-0.2.1-GCCcore-11.3.0.eb | 25 ++++++++ .../p/PyZMQ/PyZMQ-24.0.1-GCCcore-11.3.0.eb | 30 +++++++++ .../plotly.py-5.12.0-GCCcore-11.3.0.eb | 30 +++++++++ .../QCG-PilotJob-0.13.1-foss-2022a.eb | 62 +++++++++++++++++++ 4 files changed, 147 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-24.0.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/plotly.py/plotly.py-5.12.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ecbb94f8b36 --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Kaleido' +version = '0.2.1' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = ['kaleido-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl'] +checksums = ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-24.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-24.0.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e604581d052 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-24.0.1-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '24.0.1' + +homepage = 'https://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['216f5d7dbb67166759e59b0479bca82b8acf9bed6015b526b8eb10143fb08e77'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('ZeroMQ', '4.3.4'), +] + +options = {'modulename': 'zmq'} + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.12.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.12.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..10401fd48fc --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.12.0-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '5.12.0' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [('Python', '3.10.4')] + +use_pip = True + +exts_list = [ + ('tenacity', '8.0.1', { + 'checksums': ['43242a20e3e73291a28bcbcacfd6e000b02d3857a9a9fff56b297a27afdc932f'], + }), + ('plotly', version, { + 'checksums': ['8bf1b37a1e3cb260a4aa77ab79c9db4fd0ad3ccd66463c3a3e8a5300196ec61e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-foss-2022a.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-foss-2022a.eb new file mode 100644 index 00000000000..db30f1ee63e --- /dev/null +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-foss-2022a.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'QCG-PilotJob' +version = '0.13.1' + +homepage = 'https://qcg-pilotjob.readthedocs.org' +description = """A python service for easy execution of many tasks inside a single allocation.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyZMQ', '24.0.1'), + ('Kaleido', '0.2.1'), + ('plotly.py', '5.12.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + ('statsmodels', '0.13.0', { + 'checksums': ['f2efc02011b7240a9e851acd76ab81150a07d35c97021cb0517887539a328f8a'], + }), + ('plotly_express', '0.4.1', { + 'checksums': ['ff73a41ce02fb43d1d8e8fa131ef3e6589857349ca216b941b8f3f862bce0278'], + }), + ('prompt_toolkit', '3.0.21', { + 'checksums': ['27f13ff4e4850fe8f860b77414c7880f67c6158076a7b099062cc8570f1562e5'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('qcg', '0.12.3', { + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'patches': ['QCG-PilotJob-0.12.3_rename_zmq.patch'], + 'checksums': [ + '9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966', # v0.12.3.tar.gz + '51cba1bfe1dcd33180dffe65941acdfa70823d6cae4b81182fd16a7debf907cd', # QCG-PilotJob-0.12.3_rename_zmq.patch + ], + 'start_dir': 'components/core', + }), + ('qcg', '0.12.3', { + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966'], + 'start_dir': 'components/cmds', + }), + ('qcg', '0.12.3', { + 'source_urls': ['https://github.com/vecma-project/QCG-PilotJob/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['9342d9fb3a13909e3fc24b9135c9c702dd03a50ee2858a8daced4aa654dce966'], + 'start_dir': 'components/executor_api', + }), +] + +moduleclass = 'tools' From 82f3ed229ee4f4a7e15a70ba3eebbbb59d33c52d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 18 Jan 2023 11:48:19 +0100 Subject: [PATCH 6209/9987] adding easyconfigs: Deprecated-1.2.13-foss-2022a.eb, numba-0.56.4-foss-2022a.eb, pydot-1.4.2-GCCcore-11.3.0.eb, PyTables-3.8.0-foss-2022a.eb, scanpy-1.9.1-foss-2022a.eb, scib-1.1.1-foss-2022a.eb, scikit-misc-0.1.4-foss-2022a.eb, scvi-tools-0.19.0-foss-2021b.eb, umap-learn-0.5.3-foss-2022a.eb and patches: llvmlite-0.39.1_fix-LLVM-14.patch, PyTables-3.8.0-fix-libs.patch --- .../Deprecated-1.2.13-foss-2022a.eb | 29 ++++++ .../n/numba/llvmlite-0.39.1_fix-LLVM-14.patch | 16 ++-- .../n/numba/numba-0.56.4-foss-2022a.eb | 54 +++++++++++ .../p/PyTables/PyTables-3.8.0-fix-libs.patch | 15 +++ .../p/PyTables/PyTables-3.8.0-foss-2022a.eb | 68 ++++++++++++++ .../p/pydot/pydot-1.4.2-GCCcore-11.3.0.eb | 26 ++++++ .../s/scanpy/scanpy-1.9.1-foss-2022a.eb | 76 +++++++++++++++ .../s/scib/scib-1.1.1-foss-2022a.eb | 39 ++++++++ .../scikit-misc-0.1.4-foss-2022a.eb | 26 ++++++ .../scvi-tools-0.19.0-foss-2021b.eb | 93 +++++++++++++++++++ .../umap-learn/umap-learn-0.5.3-foss-2022a.eb | 36 +++++++ 11 files changed, 470 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2022a.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.19.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2022a.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2022a.eb new file mode 100644 index 00000000000..2aebc2250e4 --- /dev/null +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2022a.eb @@ -0,0 +1,29 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'Deprecated' +version = '1.2.13' + +homepage = 'https://github.com/tantale/deprecated' +description = "If you need to mark a function or a method as deprecated, you can use the @deprecated decorator." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), +] + + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + (name, version, { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch index 4d09309e51e..419b516bf24 100644 --- a/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch @@ -31,15 +31,15 @@ diff -ruN llvmlite-0.39.1.orig/ffi/targets.cpp llvmlite-0.39.1/ffi/targets.cpp -#include "llvm/Support/TargetRegistry.h" +#include "llvm/MC/TargetRegistry.h" #include "llvm/Target/TargetMachine.h" - + #include @@ -204,7 +204,6 @@ rm = Reloc::DynamicNoPIC; - + TargetOptions opt; - opt.PrintMachineCode = PrintMC; opt.MCOptions.ABIName = ABIName; - + bool jit = JIT; diff -ruN llvmlite-0.39.1.orig/ffi/value.cpp llvmlite-0.39.1/ffi/value.cpp --- llvmlite-0.39.1.orig/ffi/value.cpp 2022-09-01 13:47:22.449959300 +0000 @@ -52,14 +52,14 @@ diff -ruN llvmlite-0.39.1.orig/ffi/value.cpp llvmlite-0.39.1/ffi/value.cpp + arg->getParent()->getAttributes().getParamAttrs(argno); return wrap(new AttributeSetIterator(attrs.begin(), attrs.end())); } - + diff -ruN llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py llvmlite-0.39.1/llvmlite/tests/test_binding.py --- llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py 2022-09-01 13:47:22.481959000 +0000 +++ llvmlite-0.39.1/llvmlite/tests/test_binding.py 2023-01-10 17:00:04.868959051 +0000 @@ -18,6 +18,16 @@ from llvmlite.tests import TestCase - - + + +def clean_string_whitespace(x: str) -> str: + # Remove trailing whitespace from the end of each line + x = re.sub(r"\s+$", "", x, flags=re.MULTILINE) @@ -82,7 +82,7 @@ diff -ruN llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py llvmlite-0.39.1/ll + clean_string_whitespace(asm), + clean_string_whitespace(asm_nonalphanum_blocklabel) + ) - + def test_global_context(self): gcontext1 = llvm.context.get_global_context() @@ -640,7 +653,7 @@ @@ -92,4 +92,4 @@ diff -ruN llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py llvmlite-0.39.1/ll - valid = [(11,)] + valid = [(11,), (12,), (13,), (14,)] self.assertIn((major,), valid) - self.assertIn(patch, range(10)) + self.assertIn(patch, range(10)) \ No newline at end of file diff --git a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb new file mode 100644 index 00000000000..24f21029496 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb @@ -0,0 +1,54 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.56.4' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('LLVM', '14.0.3'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + + +exts_list = [ + ('llvmlite', '0.39.1', { + 'patches': ['llvmlite-0.39.1_fix-LLVM-14.patch'], + 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && ", + 'checksums': [ + {'llvmlite-0.39.1.tar.gz': 'b43abd7c82e805261c425d50335be9a6c4f84264e34d6d6e475207300005d572'}, + {'llvmlite-0.39.1_fix-LLVM-14.patch': '54c9bbf89a3c071e6ab1057d033f6b9a7e88387a6b90563da1532f11bdc0621e'}, + ], + }), + (name, version, { + 'checksums': ['32d9fef412c81483d7efe0ceb6cf4d3310fde8b624a9cecca00f790573ac96ee'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -m llvmlite.tests", + "numba --help", +] + +moduleclass = 'lang' \ No newline at end of file diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch new file mode 100644 index 00000000000..c356449c52d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch @@ -0,0 +1,15 @@ +# pyTables expects that LIBS is a list of library names and will add +# a -l by itself. +# original patch by ward.poelmans@ugent.be, ported to PyTables 3.5.2 by Kenneth Hoste (HPC-UGent) +--- PyTables-3.8.0/setup.py.orig 2019-08-23 10:35:55.467589283 +0200 ++++ PyTables-3.8.0/setup.py 2019-08-23 10:36:39.408195074 +0200 +@@ -576,6 +576,9 @@ + # is not a good idea. + CFLAGS = os.environ.get("CFLAGS", "").split() + LIBS = os.environ.get("LIBS", "").split() ++ for idx, lib in enumerate(LIBS): ++ if lib.startswith("-l"): ++ LIBS[idx] = lib.replace("-l", "") + CONDA_PREFIX = os.environ.get("CONDA_PREFIX", "") + # We start using pkg-config since some distributions are putting HDF5 + # (and possibly other libraries) in exotic locations. See issue #442. diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb new file mode 100644 index 00000000000..063d04233cf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb @@ -0,0 +1,68 @@ +# http://www.pytables.org/usersguide/installation.html +# updated: Denis Kristak (INUITS) + +easyblock = 'PythonBundle' + +name = 'PyTables' +version = '3.8.0' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # provides numexpr + ('HDF5', '1.12.2'), + ('LZO', '2.10'), + ('Blosc', '1.21.3'), + ('scikit-build', '0.15.0'), +] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +use_pip = True + +exts_list = [ + ('py-cpuinfo', '9.0.0', { + 'modulename': 'cpuinfo', + 'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'], + }), + ('blosc2', '2.0.0', { + 'checksums': ['f19b0b3674f6c825b490f00d8264b0c540c2cdc11ec7e81178d38b83c57790a1'], + }), + (name, version, { + 'modulename': 'tables', + 'patches': ['%(name)s-%(version)s-fix-libs.patch'], + 'source_urls': ['https://github.com/PyTables/PyTables/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': [ + {'v3.8.0.tar.gz': '652b56b3d355797af4337a4493acfa4c4de4a60e7c6663cc6ce44d8ee477e920'}, + {'PyTables-3.8.0-fix-libs.patch': '740d87c753c22e70aaa2720a50de1b729bc110360b7e44f40b0fb0c4a5b14c6c'}, + ], + }), +] + +sanity_pip_check = True + +local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2f7e3d2bd9b --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'PythonPackage' + +name = 'pydot' +version = '1.4.2' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['248081a39bcb56784deb018977e428605c1c758f10897a339fce1dd728ff007d'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('Graphviz', '5.0.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb new file mode 100644 index 00000000000..2093a415b23 --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb @@ -0,0 +1,76 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.9.1' + +homepage = 'https://scanpy.readthedocs.io/en/stable/' +description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('networkx', '2.8.4'), + ('numba', '0.56.4'), + ('PyTables', '3.8.0'), + ('statsmodels', '0.13.1'), + ('scikit-learn', '1.1.2'), + ('Seaborn', '0.12.1'), + ('tqdm', '4.64.0'), + ('leidenalg', '0.9.1'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.2.0', { + 'checksums': ['57f85b72c688b09e053cdac302dd5b5b53df5f73ae20b4874fcbffd8bf783d11'], + }), + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + ('pynndescent', '0.5.8', { + 'checksums': ['a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b'], + }), + ('umap-learn', '0.5.3', { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.4', { + 'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'], + }), + ('session_info', '1.0.0', { + 'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'], + }), + (name, version, { + 'checksums': ['00c9a83b649da7e0171c91e9a08cff632102faa760614fd05cd4d1dbba4eb541'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "natsort --help", + "scanpy --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb new file mode 100644 index 00000000000..e5724b21c89 --- /dev/null +++ b/easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb @@ -0,0 +1,39 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonPackage' + +name = 'scib' +version = '1.1.1' + +homepage = 'https://github.com/theislab/scib' +description = "Benchmarking atlas-level data integration in single-cell genomics." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Seaborn', '0.12.1'), + ('numba', '0.56.4'), + ('scanpy', '1.9.1'), + ('h5py', '3.7.0'), + ('scikit-learn', '1.1.2'), + ('scikit-misc', '0.1.4'), + # missing - louvain - as per this issue ( https://github.com/theislab/scib/issues/360 ), it appears that it's just an optional dependency + ('leidenalg', '0.9.1'), + ('umap-learn', '0.5.3'), + ('pydot', '1.4.2'), + ('igraph', '0.10.3'), + ('python-igraph', '0.10.3'), + ('Deprecated', '1.2.13'), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = "sed -i 's|igraph>=0.10|igraph>=0.9.8|g' setup.cfg && " +preinstallopts += "sed -i 's|louvain>=0.8||g' setup.cfg && " + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2022a.eb new file mode 100644 index 00000000000..6d449427c15 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2022a.eb @@ -0,0 +1,26 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'PythonPackage' + +name = 'scikit-misc' +version = '0.1.4' + +homepage = 'https://github.com/has2k1/scikit-misc' +description = "Miscellaneous tools for data analysis and scientific computing" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f7746a0347811063e1ecf9121df94835785003953c38b5ba84f63fc508c22911'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'skmisc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.19.0-foss-2021b.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.19.0-foss-2021b.eb new file mode 100644 index 00000000000..d0491a8df67 --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.19.0-foss-2021b.eb @@ -0,0 +1,93 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '0.19.0' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('h5py', '3.6.0'), + ('IPython', '7.26.0'), + ('jax', '0.3.9'), + ('openpyxl', '3.0.9'), + ('PyTorch-Lightning', '1.5.9'), + ('scikit-learn', '0.24.2'), + ('dm-tree', '0.1.6'), + ('scanpy', '1.8.1'), + ('scikit-misc', '0.1.4'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + # stick to flax v0.5.2, which does not require tensorstore (which is built with Bazel) or a very recent jax yet... + ('flax', '0.5.2', { + 'checksums': ['5f07775fd4ba1926192ab6eb48c9adbd5658ddaf8585fb0c561741400d5599ff'], + }), + ('multipledispatch', '0.6.0', { + 'checksums': ['a7ab1451fd0bf9b92cab3edbd7b205622fb767aeefb4fb536c2e3de9e0a38bea'], + }), + ('numpyro', '0.10.1', { + 'checksums': ['dfa896f01c8df43ddd41663af2b3e2fc4aea73489e669474e83329b183b29150'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.5', { + 'checksums': ['686858320f8f220c82a6c7eeb54dcdcaa4f3d7f66690dacd13a24baa1ee8299e'], + }), + ('optax', '0.1.3', { + 'checksums': ['159e954405c3ba2072c2add7cec5532be7399bcafab3039acbf608b11844a879'], + }), + ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + }), + ('pyro-ppl', '1.8.0', { + 'modulename': 'pyro', + 'checksums': ['68e4ea30f219227dd88e55de2550d3f8c20a20adbdb67ad1e13b50868bb2ac0c'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '11.1.0', { + 'checksums': ['43e03d8eec12e21beaecc22c828a41c4247356414a12d5879834863d4ad53816'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('mudata', '0.2.0', { + 'checksums': ['6eef13ec2165340cd6d79fe4aabe687e9c53867c818c8dbe1cf0b6be0e5d1e75'], + }), + (name, version, { + 'modulename': 'scvi', + 'checksums': ['95c67870ecfa1d0e0b80027d3239bb47ca6cd3db2f2524985f5d31903b766eeb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb new file mode 100644 index 00000000000..2258386aebf --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb @@ -0,0 +1,36 @@ +# Author: Denis Krišťák (INUITS) +easyblock = "PythonBundle" + +name = 'umap-learn' +version = '0.5.3' + +homepage = 'https://umap-learn.readthedocs.io/en/latest/' +description = """ +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique +that can be used for visualisation similarly to t-SNE, but also for general non-linear +dimension reduction. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('numba', '0.56.4'), + ('LLVM', '14.0.3'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('pynndescent', '0.5.8'), + (name, version, { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 6e1e233dbb1f732e82dd1ba956c9c816fe1cfa76 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Jan 2023 10:59:43 +0000 Subject: [PATCH 6210/9987] Delete PyTables-3.8.0-fix-libs.patch moving to separate EC --- .../p/PyTables/PyTables-3.8.0-fix-libs.patch | 15 --------------- 1 file changed, 15 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch deleted file mode 100644 index c356449c52d..00000000000 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch +++ /dev/null @@ -1,15 +0,0 @@ -# pyTables expects that LIBS is a list of library names and will add -# a -l by itself. -# original patch by ward.poelmans@ugent.be, ported to PyTables 3.5.2 by Kenneth Hoste (HPC-UGent) ---- PyTables-3.8.0/setup.py.orig 2019-08-23 10:35:55.467589283 +0200 -+++ PyTables-3.8.0/setup.py 2019-08-23 10:36:39.408195074 +0200 -@@ -576,6 +576,9 @@ - # is not a good idea. - CFLAGS = os.environ.get("CFLAGS", "").split() - LIBS = os.environ.get("LIBS", "").split() -+ for idx, lib in enumerate(LIBS): -+ if lib.startswith("-l"): -+ LIBS[idx] = lib.replace("-l", "") - CONDA_PREFIX = os.environ.get("CONDA_PREFIX", "") - # We start using pkg-config since some distributions are putting HDF5 - # (and possibly other libraries) in exotic locations. See issue #442. From fbcc67b997e42f1b63f685dfda883e994b8e411e Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Jan 2023 10:59:53 +0000 Subject: [PATCH 6211/9987] Delete PyTables-3.8.0-foss-2022a.eb moving to separate EC --- .../p/PyTables/PyTables-3.8.0-foss-2022a.eb | 68 ------------------- 1 file changed, 68 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb deleted file mode 100644 index 063d04233cf..00000000000 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb +++ /dev/null @@ -1,68 +0,0 @@ -# http://www.pytables.org/usersguide/installation.html -# updated: Denis Kristak (INUITS) - -easyblock = 'PythonBundle' - -name = 'PyTables' -version = '3.8.0' - -homepage = 'https://www.pytables.org' -description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope - with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the - NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical - parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, - process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk - resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as - relational or object oriented databases.""" - -toolchain = {'name': 'foss', 'version': '2022a'} -toolchainopts = {'usempi': True} - -dependencies = [ - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), # provides numexpr - ('HDF5', '1.12.2'), - ('LZO', '2.10'), - ('Blosc', '1.21.3'), - ('scikit-build', '0.15.0'), -] - -builddependencies = [ - ('CMake', '3.23.1'), -] - -use_pip = True - -exts_list = [ - ('py-cpuinfo', '9.0.0', { - 'modulename': 'cpuinfo', - 'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'], - }), - ('blosc2', '2.0.0', { - 'checksums': ['f19b0b3674f6c825b490f00d8264b0c540c2cdc11ec7e81178d38b83c57790a1'], - }), - (name, version, { - 'modulename': 'tables', - 'patches': ['%(name)s-%(version)s-fix-libs.patch'], - 'source_urls': ['https://github.com/PyTables/PyTables/archive/'], - 'sources': ['v%(version)s.tar.gz'], - 'checksums': [ - {'v3.8.0.tar.gz': '652b56b3d355797af4337a4493acfa4c4de4a60e7c6663cc6ce44d8ee477e920'}, - {'PyTables-3.8.0-fix-libs.patch': '740d87c753c22e70aaa2720a50de1b729bc110360b7e44f40b0fb0c4a5b14c6c'}, - ], - }), -] - -sanity_pip_check = True - -local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_bins], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -options = {'modulename': 'tables'} - -sanity_check_commands = ["%s --help" % x for x in local_bins] - -moduleclass = 'data' From 741152ebaa22395a62e7c22e8d6430de63c92dde Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 18 Jan 2023 12:01:51 +0100 Subject: [PATCH 6212/9987] adding easyconfigs: PyTables-3.8.0-foss-2022a.eb and patches: PyTables-3.8.0-fix-libs.patch --- .../p/PyTables/PyTables-3.8.0-fix-libs.patch | 15 ++++ .../p/PyTables/PyTables-3.8.0-foss-2022a.eb | 68 +++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch new file mode 100644 index 00000000000..c356449c52d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch @@ -0,0 +1,15 @@ +# pyTables expects that LIBS is a list of library names and will add +# a -l by itself. +# original patch by ward.poelmans@ugent.be, ported to PyTables 3.5.2 by Kenneth Hoste (HPC-UGent) +--- PyTables-3.8.0/setup.py.orig 2019-08-23 10:35:55.467589283 +0200 ++++ PyTables-3.8.0/setup.py 2019-08-23 10:36:39.408195074 +0200 +@@ -576,6 +576,9 @@ + # is not a good idea. + CFLAGS = os.environ.get("CFLAGS", "").split() + LIBS = os.environ.get("LIBS", "").split() ++ for idx, lib in enumerate(LIBS): ++ if lib.startswith("-l"): ++ LIBS[idx] = lib.replace("-l", "") + CONDA_PREFIX = os.environ.get("CONDA_PREFIX", "") + # We start using pkg-config since some distributions are putting HDF5 + # (and possibly other libraries) in exotic locations. See issue #442. diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb new file mode 100644 index 00000000000..063d04233cf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb @@ -0,0 +1,68 @@ +# http://www.pytables.org/usersguide/installation.html +# updated: Denis Kristak (INUITS) + +easyblock = 'PythonBundle' + +name = 'PyTables' +version = '3.8.0' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as + relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # provides numexpr + ('HDF5', '1.12.2'), + ('LZO', '2.10'), + ('Blosc', '1.21.3'), + ('scikit-build', '0.15.0'), +] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +use_pip = True + +exts_list = [ + ('py-cpuinfo', '9.0.0', { + 'modulename': 'cpuinfo', + 'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'], + }), + ('blosc2', '2.0.0', { + 'checksums': ['f19b0b3674f6c825b490f00d8264b0c540c2cdc11ec7e81178d38b83c57790a1'], + }), + (name, version, { + 'modulename': 'tables', + 'patches': ['%(name)s-%(version)s-fix-libs.patch'], + 'source_urls': ['https://github.com/PyTables/PyTables/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': [ + {'v3.8.0.tar.gz': '652b56b3d355797af4337a4493acfa4c4de4a60e7c6663cc6ce44d8ee477e920'}, + {'PyTables-3.8.0-fix-libs.patch': '740d87c753c22e70aaa2720a50de1b729bc110360b7e44f40b0fb0c4a5b14c6c'}, + ], + }), +] + +sanity_pip_check = True + +local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'data' From c1dd7759d695faa5cd66455df15a6685e343aa04 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 18 Jan 2023 12:26:07 +0100 Subject: [PATCH 6213/9987] sources of p7zip v17.x moved to p7zip-project repo --- easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb | 4 ++-- easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb | 4 ++-- easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.2.0.eb | 4 ++-- easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.3.0.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb index 8c1b293c372..9ceffd4c100 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.03-GCCcore-10.2.0.eb @@ -3,13 +3,13 @@ easyblock = 'MakeCp' name = 'p7zip' version = '17.03' -homepage = 'https://github.com/jinfeihan57/p7zip/' +homepage = 'https://github.com/p7zip-project/p7zip/' description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -github_account = 'jinfeihan57' +github_account = 'p7zip-project' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['bb4b9b21584c0e076e0b4b2705af0dbe7ac19d378aa7f09a79da33a5b3293187'] diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb index 3239c13051d..1a1e8bee25f 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-10.3.0.eb @@ -3,13 +3,13 @@ easyblock = 'MakeCp' name = 'p7zip' version = '17.04' -homepage = 'https://github.com/jinfeihan57/p7zip/' +homepage = 'https://github.com/p7zip-project/p7zip/' description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -github_account = 'jinfeihan57' +github_account = 'p7zip-project' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['ea029a2e21d2d6ad0a156f6679bd66836204aa78148a4c5e498fe682e77127ef'] diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.2.0.eb index ac2df0865b0..cab4069d018 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.2.0.eb @@ -3,13 +3,13 @@ easyblock = 'MakeCp' name = 'p7zip' version = '17.04' -homepage = 'https://github.com/jinfeihan57/p7zip/' +homepage = 'https://github.com/p7zip-project/p7zip/' description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -github_account = 'jinfeihan57' +github_account = 'p7zip-project' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['ea029a2e21d2d6ad0a156f6679bd66836204aa78148a4c5e498fe682e77127ef'] diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.3.0.eb index 20265bc30b3..de1003ee0df 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-11.3.0.eb @@ -3,13 +3,13 @@ easyblock = 'MakeCp' name = 'p7zip' version = '17.04' -homepage = 'https://github.com/jinfeihan57/p7zip/' +homepage = 'https://github.com/p7zip-project/p7zip/' description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -github_account = 'jinfeihan57' +github_account = 'p7zip-project' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['ea029a2e21d2d6ad0a156f6679bd66836204aa78148a4c5e498fe682e77127ef'] From ed37f669bde19e3c2fbdbde4fe7653aa62a02d33 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Jan 2023 12:56:49 +0100 Subject: [PATCH 6214/9987] adding easyconfigs: NCO-5.1.3-foss-2022a.eb --- .../easyconfigs/n/NCO/NCO-5.1.3-foss-2022a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2022a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2022a.eb new file mode 100644 index 00000000000..b5ad1e4bdae --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.1.3' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f6766627dab3f067c88f2cd713e3058c324ea4f900fabf9755bdd8918c32de7b'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.4.8'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.11'), + ('GSL', '2.7'), + ('netCDF', '4.9.0'), + ('ESMF', '8.3.0'), # ncremap needs ESMF_RegridWeightGen +] + +configopts = "--enable-nco_cplusplus" + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] + +moduleclass = 'tools' From 213ae45cda10003f553b1c19514170a6c483019c Mon Sep 17 00:00:00 2001 From: James Carpenter Date: Wed, 18 Jan 2023 12:10:05 +0000 Subject: [PATCH 6215/9987] adding easyconfigs: imkl-2021.4.0-iompi-2021b.eb, iomkl-2021b.eb, iompi-2021b.eb, OpenMPI-4.1.1-intel-compilers-2021.4.0.eb --- .../i/imkl/imkl-2021.4.0-iompi-2021b.eb | 14 ++++++ easybuild/easyconfigs/i/iomkl/iomkl-2021b.eb | 18 +++++++ easybuild/easyconfigs/i/iompi/iompi-2021b.eb | 18 +++++++ .../OpenMPI-4.1.1-intel-compilers-2021.4.0.eb | 47 +++++++++++++++++++ 4 files changed, 97 insertions(+) create mode 100755 easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb create mode 100755 easybuild/easyconfigs/i/iomkl/iomkl-2021b.eb create mode 100755 easybuild/easyconfigs/i/iompi/iompi-2021b.eb create mode 100755 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb new file mode 100755 index 00000000000..a6e0651ef64 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2021.4.0-iompi-2021b.eb @@ -0,0 +1,14 @@ +name = 'imkl' +version = '2021.4.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iompi', 'version': '2021b'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18222/'] +sources = ['l_onemkl_p_%(version)s.640_offline.sh'] +checksums = ['9ad546f05a421b4f439e8557fd0f2d83d5e299b0d9bd84bdd86be6feba0c3915'] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2021b.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2021b.eb new file mode 100755 index 00000000000..3ebbaf3278b --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2021b.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'iomkl' +version = '2021b' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2021.4.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('OpenMPI', '4.1.1', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', ('iompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iompi/iompi-2021b.eb b/easybuild/easyconfigs/i/iompi/iompi-2021b.eb new file mode 100755 index 00000000000..f2a3e584b44 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2021b.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iompi' +version = '2021b' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = """Intel C/C++ and Fortran compilers, alongside Open MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2021.4.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('OpenMPI', '4.1.1', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb new file mode 100755 index 00000000000..553c9051ea8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb @@ -0,0 +1,47 @@ +name = 'OpenMPI' +version = '4.1.1' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', + 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.1.1_opal-pmix-package-rank.patch', +] +checksums = [ + {'openmpi-4.1.1.tar.bz2': 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda'}, + {'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch': + 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e'}, + {'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch': + '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d'}, + {'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch': + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea'}, + {'OpenMPI-4.1.1_opal-pmix-package-rank.patch': '04353672cf7be031e5306c94068d7012d99e6cd94b69d93230797ffcd7f31903'}, +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.5.0'), + ('libevent', '2.1.12'), + ('UCX', '1.11.2'), + ('libfabric', '1.13.2'), + ('PMIx', '4.1.0'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From 01d06521dec2aa8939ebbcd52539c25aba0acc05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Jan 2023 13:16:28 +0100 Subject: [PATCH 6216/9987] use Blosc2 instead of Blosc as dependency for PyTables 3.8.0, download source tarball from PyPI, use proper dependency for py-cpuinfo, change scikit-build to build dependency --- .../p/PyTables/PyTables-3.8.0-foss-2022a.eb | 32 +++++++---------- ...bs.patch => PyTables-3.8.0_fix-libs.patch} | 6 ++-- .../py-cpuinfo-9.0.0-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 3 files changed, 51 insertions(+), 22 deletions(-) rename easybuild/easyconfigs/p/PyTables/{PyTables-3.8.0-fix-libs.patch => PyTables-3.8.0_fix-libs.patch} (69%) create mode 100644 easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb index 063d04233cf..21800e7f168 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb @@ -18,43 +18,35 @@ description = """PyTables is a package for managing hierarchical datasets and de toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'usempi': True} +builddependencies = [ + ('CMake', '3.24.3'), + ('scikit-build', '0.15.0'), +] + dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), # provides numexpr ('HDF5', '1.12.2'), ('LZO', '2.10'), - ('Blosc', '1.21.3'), - ('scikit-build', '0.15.0'), -] - -builddependencies = [ - ('CMake', '3.23.1'), + ('Blosc2', '2.4.3'), + ('py-cpuinfo', '9.0.0'), ] use_pip = True exts_list = [ - ('py-cpuinfo', '9.0.0', { - 'modulename': 'cpuinfo', - 'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'], - }), ('blosc2', '2.0.0', { 'checksums': ['f19b0b3674f6c825b490f00d8264b0c540c2cdc11ec7e81178d38b83c57790a1'], }), - (name, version, { - 'modulename': 'tables', - 'patches': ['%(name)s-%(version)s-fix-libs.patch'], - 'source_urls': ['https://github.com/PyTables/PyTables/archive/'], - 'sources': ['v%(version)s.tar.gz'], + ('tables', version, { + 'patches': ['PyTables-%(version)s_fix-libs.patch'], 'checksums': [ - {'v3.8.0.tar.gz': '652b56b3d355797af4337a4493acfa4c4de4a60e7c6663cc6ce44d8ee477e920'}, - {'PyTables-3.8.0-fix-libs.patch': '740d87c753c22e70aaa2720a50de1b729bc110360b7e44f40b0fb0c4a5b14c6c'}, + {'tables-3.8.0.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'}, + {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'}, ], }), ] -sanity_pip_check = True - local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bins], @@ -65,4 +57,6 @@ options = {'modulename': 'tables'} sanity_check_commands = ["%s --help" % x for x in local_bins] +sanity_pip_check = True + moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0_fix-libs.patch similarity index 69% rename from easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch rename to easybuild/easyconfigs/p/PyTables/PyTables-3.8.0_fix-libs.patch index c356449c52d..8ffa99933b7 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-fix-libs.patch +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0_fix-libs.patch @@ -1,8 +1,8 @@ # pyTables expects that LIBS is a list of library names and will add # a -l by itself. -# original patch by ward.poelmans@ugent.be, ported to PyTables 3.5.2 by Kenneth Hoste (HPC-UGent) ---- PyTables-3.8.0/setup.py.orig 2019-08-23 10:35:55.467589283 +0200 -+++ PyTables-3.8.0/setup.py 2019-08-23 10:36:39.408195074 +0200 +# original patch by ward.poelmans@ugent.be, ported to newer PyTables version by Kenneth Hoste (HPC-UGent) +--- PyTables-3.8.0/setup.py.orig 2023-01-11 19:14:27.160064110 +0100 ++++ PyTables-3.8.0/setup.py 2023-01-11 19:21:48.460252182 +0100 @@ -576,6 +576,9 @@ # is not a good idea. CFLAGS = os.environ.get("CFLAGS", "").split() diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d587740b561 --- /dev/null +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'py-cpuinfo' +version = '9.0.0' + +homepage = 'https://github.com/workhorsy/py-cpuinfo' +description = "py-cpuinfo gets CPU info with pure Python." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/cpuinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cpuinfo", + "python -m cpuinfo", +] + +options = {'modulename': 'cpuinfo'} + +sanity_pip_check = True + +moduleclass = 'tools' From e7c4d578130df496d38cbacea4b2f488aab51495 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 18 Jan 2023 12:20:31 +0000 Subject: [PATCH 6217/9987] Used original EC and added line for testjobs, noGA added --- .../OpenMolcas-22.10-intel-2022a-noGA.eb | 2 ++ .../OpenMolcas-22.10-intel-2022a.eb | 30 +++++++++++-------- 2 files changed, 20 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb index fb6ba76e942..b7411caf8a6 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb @@ -45,6 +45,8 @@ modextravars = { 'MOLCAS_SOURCE': '%(installdir)s', } +sanity_check_commands = ['cd %(builddir)s/easybuild_obj; ./pymolcas verify'] + sanity_check_paths = { 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, 'sbin/help_basis', 'pymolcas'], diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb index 58a9cb32dbf..58cdb96d1a4 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb @@ -1,13 +1,10 @@ -# Test-jobs enabled -# Author: J. Sassmannshausen (Imperial College London/UK) - easyblock = 'CMakeMake' name = 'OpenMolcas' version = '22.10' homepage = "https://gitlab.com/Molcas/OpenMolcas" -description = "OpenMolcas is a quantum chemistry software package" +description = "OpenMolcas is a quantum chemistry software package." toolchain = {'name': 'intel', 'version': '2022a'} toolchainopts = {'usempi': True} @@ -16,22 +13,31 @@ source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] sources = ["OpenMolcas-v%(version)s.tar.gz"] patches = ['OpenMolcas-21.06_mcpdft_deps.patch'] checksums = [ - 'd1d3d6c9bd69486c36f5285a51ac18e75c03540c5b33751855e94abc764d9658', # OpenMolcas-v22.10.tar.gz - '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a', # OpenMolcas-21.06_mcpdft_deps.patch + {'OpenMolcas-v22.10.tar.gz': 'd1d3d6c9bd69486c36f5285a51ac18e75c03540c5b33751855e94abc764d9658'}, + {'OpenMolcas-21.06_mcpdft_deps.patch': '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a'}, ] +builddependencies = [('CMake', '3.23.1')] + dependencies = [ - ('GlobalArrays', '5.8.1'), - ('HDF5', '1.12.2'), ('Python', '3.10.4'), + ('HDF5', '1.12.2'), + ('GlobalArrays', '5.8.1'), ] -builddependencies = [('CMake', '3.24.3')] +build_shared_libs = True preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' -configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' -configopts += '-DMPI=ON -DOPENMP=ON -DGA=ON ' -configopts += '-DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON' +_copts = [ + '-DLINALG=MKL', + '-DMKLROOT=$MKLROOT', + '-DOPENMP=ON', + '-DTOOLS=ON', + '-DFDE=ON', + '-DMPI=ON', + '-DGA=ON', +] +configopts = ' '.join(_copts) modextrapaths = {'PATH': ''} modextravars = { From 24742f873f7e83d8a3517862bb8bb269b36eec84 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Jan 2023 13:29:28 +0100 Subject: [PATCH 6218/9987] adding easyconfigs: numba-0.56.4-foss-2022a.eb --- .../n/numba/numba-0.56.4-foss-2022a.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb new file mode 100644 index 00000000000..c24eb2ca63f --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.56.4' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('LLVM', '14.0.3'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " +local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " + +exts_list = [ + ('llvmlite', '0.39.1', { + 'preinstallopts': local_llvmlite_preinstallopts, + 'patches': ['llvmlite-0.39.1_fix-LLVM-14.patch'], + 'checksums': [ + {'llvmlite-0.39.1.tar.gz': 'b43abd7c82e805261c425d50335be9a6c4f84264e34d6d6e475207300005d572'}, + {'llvmlite-0.39.1_fix-LLVM-14.patch': '39cde92d522cce45f8b93231059f7e2c69bc54dc7c35c4c6eaee3423f3f04d17'}, + ], + }), + (name, version, { + # 'patches': ['numba-0.54.1_fix-numpy-1.21.patch'], + 'checksums': [ + {'numba-0.56.4.tar.gz': '32d9fef412c81483d7efe0ceb6cf4d3310fde8b624a9cecca00f790573ac96ee'}, + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -m llvmlite.tests", + "numba --help", +] + +moduleclass = 'lang' From 2bd340b618b74c35c7fdba992956fec10407652f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Wed, 18 Jan 2023 12:40:20 +0000 Subject: [PATCH 6219/9987] Update easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb index 56faa358bf6..ae245350d6c 100644 --- a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb @@ -22,7 +22,6 @@ checksums = ['f9258355b5e9eb13bd33c5fa720f0cbebacea7d0a4a42b71b0fb14501ee14229'] configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], 'dirs': [], From 1a48e8f83a7cdaf429acff1bc5db9e8775700f6a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Jan 2023 13:41:12 +0100 Subject: [PATCH 6220/9987] add missing binutils build dependency for py-cpuinfo 9.0.0 --- .../p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb index d587740b561..14c968128f7 100644 --- a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb @@ -11,6 +11,10 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} sources = [SOURCE_TAR_GZ] checksums = ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'] +builddependencies = [ + ('binutils', '2.38'), +] + dependencies = [ ('Python', '3.10.4'), ] From 2c465f4161a885fbf40f79af6b39611626ea0584 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Jan 2023 13:43:09 +0100 Subject: [PATCH 6221/9987] add back Blosc dependency for PyTables 3.8.0 --- easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb index 21800e7f168..befd1e23127 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb @@ -28,6 +28,7 @@ dependencies = [ ('SciPy-bundle', '2022.05'), # provides numexpr ('HDF5', '1.12.2'), ('LZO', '2.10'), + ('Blosc', '1.21.3'), ('Blosc2', '2.4.3'), ('py-cpuinfo', '9.0.0'), ] From 0ef0452ce6e54ddbcb272441e952c10318f77723 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 18 Jan 2023 14:03:22 +0100 Subject: [PATCH 6222/9987] adding easyconfigs: msprime-1.2.0-foss-2021b.eb --- .../m/msprime/msprime-1.2.0-foss-2021b.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb new file mode 100644 index 00000000000..019d8ce5aca --- /dev/null +++ b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'msprime' +version = '1.2.0' + +homepage = 'https://msprime.readthedocs.io' +description = "msprime is a coalescent simulator and library for processing tree-based genetic data." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy + ('GSL', '2.7'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('svgwrite', '1.4.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['a8fbdfd4443302a6619a7f76bc937fc683daf2628d9b737c891ec08b8ce524c3'], + }), + ('tskit', '0.5.4', { + 'checksums': ['be1a6381c72a95f0011bea26ca317e1b4503b8d2dcd87096c68aa16c8946c6fe'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('ruamel.yaml', '0.17.21', { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('demes', '0.2.2', { + 'checksums': ['8eebe4b236b2d19e057228892f5b5f53f3e0d127ca9128efead1728a65115dac'], + }), + ('newick', '1.6.0', { + 'checksums': ['5610335826c0afd35afe66ebbacba0881e69f25097418c2f08456be629be6eac'], + }), + (name, version, { + 'checksums': ['60025ad9fd30d827a72ae6e760b6cff07a1d0e169b2c1da1024cb0fc23e4a7aa'], + }), +] + +sanity_check_paths = { + 'files': ['bin/msp', 'bin/mspms'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From ee774948700327c39967c2f37146b91641c76329 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 18 Jan 2023 14:21:12 +0100 Subject: [PATCH 6223/9987] msprime: verify that all expected binaries are installed. --- easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb index 019d8ce5aca..dccf2b15d14 100644 --- a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb @@ -44,7 +44,7 @@ exts_list = [ ] sanity_check_paths = { - 'files': ['bin/msp', 'bin/mspms'], + 'files': ['bin/msp', 'bin/mspms', 'bin/tskit', 'bin/demes'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From 8031ea0e9166524691acbdef7134700a855a7229 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 18 Jan 2023 14:28:29 +0100 Subject: [PATCH 6224/9987] adding easyconfigs: pyslim-1.0.1-foss-2021b.eb --- .../p/pyslim/pyslim-1.0.1-foss-2021b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2021b.eb b/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2021b.eb new file mode 100644 index 00000000000..021accc9eba --- /dev/null +++ b/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2021b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'pyslim' +version = '1.0.1' + +homepage = 'https://tskit.dev/pyslim/docs/stable/introduction.html' +description = """A Python API for reading and modifying tskit tree +sequence files produced by SLiM, or modifying files produced by other +programs (e.g., msprime, fwdpy11, and tsinfer) for use in SLiM.""" + + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy + ('msprime', '1.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['d65923658df9303962997f8911449245d33cf7f56aada8df4573ad301a9934c6'], + }), +] + +moduleclass = 'bio' From 7e0b1fdad41dabf9da34eaa0f6dd7a05e2a60814 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Jan 2023 13:35:52 +0000 Subject: [PATCH 6225/9987] Update scanpy-1.9.1-foss-2022a.eb using `umap-learn` easyconfig as dep --- easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb index 2093a415b23..2cc7d0044d6 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb @@ -26,6 +26,7 @@ dependencies = [ ('Seaborn', '0.12.1'), ('tqdm', '4.64.0'), ('leidenalg', '0.9.1'), + ('umap-learn', '0.5.3'), ] use_pip = True @@ -43,10 +44,6 @@ exts_list = [ ('pynndescent', '0.5.8', { 'checksums': ['a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b'], }), - ('umap-learn', '0.5.3', { - 'modulename': 'umap', - 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], - }), ('stdlib-list', '0.8.0', { 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], }), From c6605cd796be6e13400df142720cc0d23a4a11d4 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Jan 2023 13:36:20 +0000 Subject: [PATCH 6226/9987] Update umap-learn-0.5.3-foss-2022a.eb adding checksum for pynndescent --- .../easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb index 2258386aebf..e31afa96036 100644 --- a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2022a.eb @@ -24,7 +24,9 @@ dependencies = [ use_pip = True exts_list = [ - ('pynndescent', '0.5.8'), + ('pynndescent', '0.5.8', { + 'checksums': ['a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b'], + }), (name, version, { 'modulename': 'umap', 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], From d550da39bd145aa7dda78de56a5997b3c98920b9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 18 Jan 2023 13:44:49 +0000 Subject: [PATCH 6227/9987] Add Set::Object to Perl 5.32.1 --- easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb index c06f75ac1bd..a203ac26a52 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb @@ -402,10 +402,10 @@ exts_list = [ 'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'], }), ('Net::SSLeay', '1.90', { + 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", 'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'], 'checksums': ['f8696cfaca98234679efeedc288a9398fcf77176f1f515dbc589ada7c650dc93'], - 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", }), ('IO::Socket::SSL', '2.070', { 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', @@ -1767,6 +1767,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], }), + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), ] moduleclass = 'lang' From 99a9647be64d006883546a8d5d06ab42973c0365 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 18 Jan 2023 21:53:56 +0800 Subject: [PATCH 6228/9987] Update easybuild/easyconfigs/x/xdotool/xdotool-3.20211022.1-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../x/xdotool/xdotool-3.20211022.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xdotool/xdotool-3.20211022.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/xdotool/xdotool-3.20211022.1-GCCcore-11.3.0.eb index 91776737d8c..88997adfa1d 100644 --- a/easybuild/easyconfigs/x/xdotool/xdotool-3.20211022.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/xdotool/xdotool-3.20211022.1-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [('binutils', '2.38')] dependencies = [('X11', '20220504')] sanity_check_paths = { - 'files': ['bin/xdotool', 'include/xdo.h', 'lib/libxdo.so.3'], + 'files': ['bin/xdotool', 'include/xdo.h', 'lib/libxdo.%s' % SHLIB_EXT], 'dirs': ['man'] } From 5bb044e493f295b765118b0d8046614b610fac54 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Jan 2023 14:01:14 +0000 Subject: [PATCH 6229/9987] Update numba-0.56.4-foss-2022a.eb fixing test errs --- easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb index 24f21029496..f414b8a4567 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb @@ -51,4 +51,4 @@ sanity_check_commands = [ "numba --help", ] -moduleclass = 'lang' \ No newline at end of file +moduleclass = 'lang' From a893988b80f0190658e36a9754bac853b54c7120 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Jan 2023 14:01:38 +0000 Subject: [PATCH 6230/9987] Update scib-1.1.1-foss-2022a.eb fixing test errs --- easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb index e5724b21c89..329b103e921 100644 --- a/easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb @@ -9,8 +9,8 @@ description = "Benchmarking atlas-level data integration in single-cell genomics toolchain = {'name': 'foss', 'version': '2022a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] +checksums = ['84bcebe08c956b86d887ab60a3efaa783aa56113d523d953f6c4fff40f9dc58a'] dependencies = [ ('Python', '3.10.4'), @@ -21,7 +21,6 @@ dependencies = [ ('h5py', '3.7.0'), ('scikit-learn', '1.1.2'), ('scikit-misc', '0.1.4'), - # missing - louvain - as per this issue ( https://github.com/theislab/scib/issues/360 ), it appears that it's just an optional dependency ('leidenalg', '0.9.1'), ('umap-learn', '0.5.3'), ('pydot', '1.4.2'), From c7d48f9f89af86d3e59fbb8e2a81a5c8e688bca2 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Jan 2023 14:30:47 +0000 Subject: [PATCH 6231/9987] Update numba-0.56.4-foss-2022a.eb --- easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb index f414b8a4567..a6c8cc20151 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb @@ -28,7 +28,7 @@ local_llvmlite_preinstallopts += "export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && " exts_list = [ ('llvmlite', '0.39.1', { 'patches': ['llvmlite-0.39.1_fix-LLVM-14.patch'], - 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 && ", + 'preinstallopts': local_llvmlite_preinstallopts, 'checksums': [ {'llvmlite-0.39.1.tar.gz': 'b43abd7c82e805261c425d50335be9a6c4f84264e34d6d6e475207300005d572'}, {'llvmlite-0.39.1_fix-LLVM-14.patch': '54c9bbf89a3c071e6ab1057d033f6b9a7e88387a6b90563da1532f11bdc0621e'}, From e8bb9d884bad3b2caef2930b679ee2888b6bff54 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Jan 2023 14:31:19 +0000 Subject: [PATCH 6232/9987] Update scib-1.1.1-foss-2022a.eb --- easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb index 329b103e921..89ba0e0c1c9 100644 --- a/easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/scib/scib-1.1.1-foss-2022a.eb @@ -31,6 +31,7 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True preinstallopts = "sed -i 's|igraph>=0.10|igraph>=0.9.8|g' setup.cfg && " preinstallopts += "sed -i 's|louvain>=0.8||g' setup.cfg && " From 2fd1ad189c1cf1c37b50cc310f0a75b9067141af Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 18 Jan 2023 14:37:51 +0000 Subject: [PATCH 6233/9987] Version string amended as suggested --- .../MATLAB/{MATLAB-2022a_Update_3.eb => MATLAB-2022a-r3.eb} | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/m/MATLAB/{MATLAB-2022a_Update_3.eb => MATLAB-2022a-r3.eb} (88%) diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2022a_Update_3.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022a-r3.eb similarity index 88% rename from easybuild/easyconfigs/m/MATLAB/MATLAB-2022a_Update_3.eb rename to easybuild/easyconfigs/m/MATLAB/MATLAB-2022a-r3.eb index 4e560cfb59c..83496da1920 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2022a_Update_3.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022a-r3.eb @@ -1,5 +1,7 @@ name = 'MATLAB' -version = '2022a_Update_3' +version = '2022a' +_update = '3' +versionsuffix = '-r%s' % _update homepage = 'https://www.mathworks.com/products/matlab' description = """MATLAB is a high-level language and interactive environment @@ -8,7 +10,7 @@ description = """MATLAB is a high-level language and interactive environment toolchain = SYSTEM -sources = ['R%(version)s_Linux.iso'] +sources = ['R%s_Update_%s_Linux.iso' % (version, _update)] checksums = ['7fabee86864e5ac2da4096c2c13dd712b19022ec3fa1c2cc3680df85f3f11e15'] java_options = '-Xmx2048m' From 02ef34301f9ab6accc10d2135ffa2a15608c67f0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 18 Jan 2023 15:42:35 +0100 Subject: [PATCH 6234/9987] msprime: add sanity_check_commands --- .../easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb index dccf2b15d14..5702b7fae25 100644 --- a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2021b.eb @@ -48,4 +48,11 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + 'demes --help', + 'tskit --help', + 'msp --help', + 'mspms --help', +] + moduleclass = 'bio' From 7df7a7dd70e74d9d5c1dae57426de4eced3cee66 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 18 Jan 2023 15:51:06 +0100 Subject: [PATCH 6235/9987] build Simple-DFTD3 with CMakeNinja and run tests --- .../s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb index f138326bdda..1cedb90bf3c 100644 --- a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb +++ b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakeNinja' name = 'Simple-DFTD3' version = '0.7.0' @@ -18,6 +18,7 @@ checksums = ['19400a176eb4dcee7b89181a5a5f0033fe6b05c52821e54896a98448761d003a'] builddependencies = [ ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), ] dependencies = [ @@ -26,7 +27,12 @@ dependencies = [ ('TOML-Fortran', '0.3.1'), ] -configopts = '-DBUILD_SHARED_LIBS=1 -DWITH_BLAS=1 -DWITH_OpenMP=1' +build_shared_libs = True + +configopts = '-DWITH_BLAS=1 -DWITH_OpenMP=1' + +test_cmd = 'ctest' +runtest = '' sanity_check_paths = { 'files': ['bin/s-dftd3', 'lib/libs-dftd3.%s' % SHLIB_EXT, 'include/dftd3.h', 'include/s-dftd3.h'], From d7f1d99b8e67affed19b6e87c2a079c7ef173346 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 18 Jan 2023 15:52:27 +0100 Subject: [PATCH 6236/9987] add author contributions to Simple-DFTD3 --- .../s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb index 1cedb90bf3c..4d92d2d0cde 100644 --- a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb +++ b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb @@ -1,3 +1,6 @@ +# A. Domingo (Vrije Universiteit Brussel) +# J. Sassmannshausen (Imperial College London/UK) + easyblock = 'CMakeNinja' name = 'Simple-DFTD3' From 6ccf8e66425cbeb5af2099ab454d6795221a0223 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Jan 2023 15:12:11 +0000 Subject: [PATCH 6237/9987] Delete scvi-tools-0.19.0-foss-2021b.eb unnecessary --- .../scvi-tools-0.19.0-foss-2021b.eb | 93 ------------------- 1 file changed, 93 deletions(-) delete mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.19.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.19.0-foss-2021b.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.19.0-foss-2021b.eb deleted file mode 100644 index d0491a8df67..00000000000 --- a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.19.0-foss-2021b.eb +++ /dev/null @@ -1,93 +0,0 @@ -# updated: Denis Kristak (INUITS) -easyblock = 'PythonBundle' - -name = 'scvi-tools' -version = '0.19.0' - -homepage = 'https://github.com/scverse/scvi-tools' -description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and -analysis of single-cell omics data, built on top of PyTorch and AnnData.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('matplotlib', '3.4.3'), - ('h5py', '3.6.0'), - ('IPython', '7.26.0'), - ('jax', '0.3.9'), - ('openpyxl', '3.0.9'), - ('PyTorch-Lightning', '1.5.9'), - ('scikit-learn', '0.24.2'), - ('dm-tree', '0.1.6'), - ('scanpy', '1.8.1'), - ('scikit-misc', '0.1.4'), -] - -use_pip = True - -exts_list = [ - ('natsort', '8.1.0', { - 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], - }), - ('anndata', '0.8.0', { - 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], - }), - ('docrep', '0.3.2', { - 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], - }), - ('typing_extensions', '4.4.0', { - 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], - }), - # stick to flax v0.5.2, which does not require tensorstore (which is built with Bazel) or a very recent jax yet... - ('flax', '0.5.2', { - 'checksums': ['5f07775fd4ba1926192ab6eb48c9adbd5658ddaf8585fb0c561741400d5599ff'], - }), - ('multipledispatch', '0.6.0', { - 'checksums': ['a7ab1451fd0bf9b92cab3edbd7b205622fb767aeefb4fb536c2e3de9e0a38bea'], - }), - ('numpyro', '0.10.1', { - 'checksums': ['dfa896f01c8df43ddd41663af2b3e2fc4aea73489e669474e83329b183b29150'], - }), - ('toolz', '0.12.0', { - 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], - }), - ('chex', '0.1.5', { - 'checksums': ['686858320f8f220c82a6c7eeb54dcdcaa4f3d7f66690dacd13a24baa1ee8299e'], - }), - ('optax', '0.1.3', { - 'checksums': ['159e954405c3ba2072c2add7cec5532be7399bcafab3039acbf608b11844a879'], - }), - ('pyro-api', '0.1.2', { - 'modulename': 'pyroapi', - 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], - }), - ('pyro-ppl', '1.8.0', { - 'modulename': 'pyro', - 'checksums': ['68e4ea30f219227dd88e55de2550d3f8c20a20adbdb67ad1e13b50868bb2ac0c'], - }), - ('commonmark', '0.9.1', { - 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], - }), - ('rich', '11.1.0', { - 'checksums': ['43e03d8eec12e21beaecc22c828a41c4247356414a12d5879834863d4ad53816'], - }), - ('contextlib2', '21.6.0', { - 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], - }), - ('ml_collections', '0.1.1', { - 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], - }), - ('mudata', '0.2.0', { - 'checksums': ['6eef13ec2165340cd6d79fe4aabe687e9c53867c818c8dbe1cf0b6be0e5d1e75'], - }), - (name, version, { - 'modulename': 'scvi', - 'checksums': ['95c67870ecfa1d0e0b80027d3239bb47ca6cd3db2f2524985f5d31903b766eeb'], - }), -] - -sanity_pip_check = True - -moduleclass = 'bio' From 8c4615339ae6b2728b41335930c8804c5a08e1c5 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Jan 2023 15:13:52 +0000 Subject: [PATCH 6238/9987] Delete llvmlite-0.39.1_fix-LLVM-14.patch this patch already exists --- .../n/numba/llvmlite-0.39.1_fix-LLVM-14.patch | 95 ------------------- 1 file changed, 95 deletions(-) delete mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch deleted file mode 100644 index 419b516bf24..00000000000 --- a/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch +++ /dev/null @@ -1,95 +0,0 @@ -fix build on top of LLVM 14, -like this: https://github.com/numba/llvmlite/issues/897 -diff -ruN llvmlite-0.39.1.orig/ffi/passmanagers.cpp llvmlite-0.39.1/ffi/passmanagers.cpp ---- llvmlite-0.39.1.orig/ffi/passmanagers.cpp 2022-09-01 13:47:22.477959200 +0000 -+++ llvmlite-0.39.1/ffi/passmanagers.cpp 2023-01-10 16:59:33.776510869 +0000 -@@ -8,6 +8,7 @@ - #include "llvm/IR/DiagnosticInfo.h" - #include "llvm/IR/DiagnosticPrinter.h" - #include "llvm/IR/LegacyPassManager.h" -+#include "llvm/Pass.h" - #include "llvm/IR/Module.h" - #include "llvm/Support/FileSystem.h" - #include "llvm/Support/ToolOutputFile.h" -@@ -17,9 +18,6 @@ - #include "llvm-c/Transforms/IPO.h" - #include "llvm-c/Transforms/Scalar.h" - #include "llvm/IR/LegacyPassManager.h" --#if LLVM_VERSION_MAJOR > 11 --#include "llvm/IR/RemarkStreamer.h" --#endif - #include "llvm/IR/LLVMRemarkStreamer.h" - #include "llvm/Remarks/RemarkStreamer.h" - #include "llvm/Transforms/IPO.h" -diff -ruN llvmlite-0.39.1.orig/ffi/targets.cpp llvmlite-0.39.1/ffi/targets.cpp ---- llvmlite-0.39.1.orig/ffi/targets.cpp 2022-09-01 13:47:22.449959300 +0000 -+++ llvmlite-0.39.1/ffi/targets.cpp 2023-01-10 16:59:54.544810234 +0000 -@@ -6,7 +6,7 @@ - #include "llvm/IR/LegacyPassManager.h" - #include "llvm/IR/Type.h" - #include "llvm/Support/Host.h" --#include "llvm/Support/TargetRegistry.h" -+#include "llvm/MC/TargetRegistry.h" - #include "llvm/Target/TargetMachine.h" - - #include -@@ -204,7 +204,6 @@ - rm = Reloc::DynamicNoPIC; - - TargetOptions opt; -- opt.PrintMachineCode = PrintMC; - opt.MCOptions.ABIName = ABIName; - - bool jit = JIT; -diff -ruN llvmlite-0.39.1.orig/ffi/value.cpp llvmlite-0.39.1/ffi/value.cpp ---- llvmlite-0.39.1.orig/ffi/value.cpp 2022-09-01 13:47:22.449959300 +0000 -+++ llvmlite-0.39.1/ffi/value.cpp 2023-01-10 16:59:09.616162588 +0000 -@@ -154,7 +154,7 @@ - Argument *arg = unwrap(A); - unsigned argno = arg->getArgNo(); - AttributeSet attrs = -- arg->getParent()->getAttributes().getParamAttributes(argno); -+ arg->getParent()->getAttributes().getParamAttrs(argno); - return wrap(new AttributeSetIterator(attrs.begin(), attrs.end())); - } - -diff -ruN llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py llvmlite-0.39.1/llvmlite/tests/test_binding.py ---- llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py 2022-09-01 13:47:22.481959000 +0000 -+++ llvmlite-0.39.1/llvmlite/tests/test_binding.py 2023-01-10 17:00:04.868959051 +0000 -@@ -18,6 +18,16 @@ - from llvmlite.tests import TestCase - - -+def clean_string_whitespace(x: str) -> str: -+ # Remove trailing whitespace from the end of each line -+ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE) -+ # Remove intermediate blank lines -+ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE) -+ # Remove extraneous whitespace from the beginning and end of the string -+ x = x.strip() -+ return x -+ -+ - # arvm7l needs extra ABI symbols to link successfully - if platform.machine() == 'armv7l': - llvm.load_library_permanently('libgcc_s.so.1') -@@ -555,7 +565,10 @@ - bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#")) - bd.ret(ir.Constant(ir.IntType(32), 12345)) - asm = str(mod) -- self.assertEqual(asm, asm_nonalphanum_blocklabel) -+ self.assertEqual( -+ clean_string_whitespace(asm), -+ clean_string_whitespace(asm_nonalphanum_blocklabel) -+ ) - - def test_global_context(self): - gcontext1 = llvm.context.get_global_context() -@@ -640,7 +653,7 @@ - def test_version(self): - major, minor, patch = llvm.llvm_version_info - # one of these can be valid -- valid = [(11,)] -+ valid = [(11,), (12,), (13,), (14,)] - self.assertIn((major,), valid) - self.assertIn(patch, range(10)) \ No newline at end of file From bdfeb5ff6d0ace6891b1a9c463fe7e40b55a2b4d Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 18 Jan 2023 15:36:19 +0000 Subject: [PATCH 6239/9987] Update numba-0.56.4-foss-2022a.eb --- easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb index a6c8cc20151..c44ab9b764c 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.56.4-foss-2022a.eb @@ -31,7 +31,7 @@ exts_list = [ 'preinstallopts': local_llvmlite_preinstallopts, 'checksums': [ {'llvmlite-0.39.1.tar.gz': 'b43abd7c82e805261c425d50335be9a6c4f84264e34d6d6e475207300005d572'}, - {'llvmlite-0.39.1_fix-LLVM-14.patch': '54c9bbf89a3c071e6ab1057d033f6b9a7e88387a6b90563da1532f11bdc0621e'}, + {'llvmlite-0.39.1_fix-LLVM-14.patch': '39cde92d522cce45f8b93231059f7e2c69bc54dc7c35c4c6eaee3423f3f04d17'}, ], }), (name, version, { From c2b09e9eff852302d644520478532295bab42956 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 18 Jan 2023 16:38:29 +0100 Subject: [PATCH 6240/9987] adding original patchfile back --- .../n/numba/llvmlite-0.39.1_fix-LLVM-14.patch | 95 +++++++++++++++++++ 1 file changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch new file mode 100644 index 00000000000..4d09309e51e --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.39.1_fix-LLVM-14.patch @@ -0,0 +1,95 @@ +fix build on top of LLVM 14, +like this: https://github.com/numba/llvmlite/issues/897 +diff -ruN llvmlite-0.39.1.orig/ffi/passmanagers.cpp llvmlite-0.39.1/ffi/passmanagers.cpp +--- llvmlite-0.39.1.orig/ffi/passmanagers.cpp 2022-09-01 13:47:22.477959200 +0000 ++++ llvmlite-0.39.1/ffi/passmanagers.cpp 2023-01-10 16:59:33.776510869 +0000 +@@ -8,6 +8,7 @@ + #include "llvm/IR/DiagnosticInfo.h" + #include "llvm/IR/DiagnosticPrinter.h" + #include "llvm/IR/LegacyPassManager.h" ++#include "llvm/Pass.h" + #include "llvm/IR/Module.h" + #include "llvm/Support/FileSystem.h" + #include "llvm/Support/ToolOutputFile.h" +@@ -17,9 +18,6 @@ + #include "llvm-c/Transforms/IPO.h" + #include "llvm-c/Transforms/Scalar.h" + #include "llvm/IR/LegacyPassManager.h" +-#if LLVM_VERSION_MAJOR > 11 +-#include "llvm/IR/RemarkStreamer.h" +-#endif + #include "llvm/IR/LLVMRemarkStreamer.h" + #include "llvm/Remarks/RemarkStreamer.h" + #include "llvm/Transforms/IPO.h" +diff -ruN llvmlite-0.39.1.orig/ffi/targets.cpp llvmlite-0.39.1/ffi/targets.cpp +--- llvmlite-0.39.1.orig/ffi/targets.cpp 2022-09-01 13:47:22.449959300 +0000 ++++ llvmlite-0.39.1/ffi/targets.cpp 2023-01-10 16:59:54.544810234 +0000 +@@ -6,7 +6,7 @@ + #include "llvm/IR/LegacyPassManager.h" + #include "llvm/IR/Type.h" + #include "llvm/Support/Host.h" +-#include "llvm/Support/TargetRegistry.h" ++#include "llvm/MC/TargetRegistry.h" + #include "llvm/Target/TargetMachine.h" + + #include +@@ -204,7 +204,6 @@ + rm = Reloc::DynamicNoPIC; + + TargetOptions opt; +- opt.PrintMachineCode = PrintMC; + opt.MCOptions.ABIName = ABIName; + + bool jit = JIT; +diff -ruN llvmlite-0.39.1.orig/ffi/value.cpp llvmlite-0.39.1/ffi/value.cpp +--- llvmlite-0.39.1.orig/ffi/value.cpp 2022-09-01 13:47:22.449959300 +0000 ++++ llvmlite-0.39.1/ffi/value.cpp 2023-01-10 16:59:09.616162588 +0000 +@@ -154,7 +154,7 @@ + Argument *arg = unwrap(A); + unsigned argno = arg->getArgNo(); + AttributeSet attrs = +- arg->getParent()->getAttributes().getParamAttributes(argno); ++ arg->getParent()->getAttributes().getParamAttrs(argno); + return wrap(new AttributeSetIterator(attrs.begin(), attrs.end())); + } + +diff -ruN llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py llvmlite-0.39.1/llvmlite/tests/test_binding.py +--- llvmlite-0.39.1.orig/llvmlite/tests/test_binding.py 2022-09-01 13:47:22.481959000 +0000 ++++ llvmlite-0.39.1/llvmlite/tests/test_binding.py 2023-01-10 17:00:04.868959051 +0000 +@@ -18,6 +18,16 @@ + from llvmlite.tests import TestCase + + ++def clean_string_whitespace(x: str) -> str: ++ # Remove trailing whitespace from the end of each line ++ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE) ++ # Remove intermediate blank lines ++ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE) ++ # Remove extraneous whitespace from the beginning and end of the string ++ x = x.strip() ++ return x ++ ++ + # arvm7l needs extra ABI symbols to link successfully + if platform.machine() == 'armv7l': + llvm.load_library_permanently('libgcc_s.so.1') +@@ -555,7 +565,10 @@ + bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#")) + bd.ret(ir.Constant(ir.IntType(32), 12345)) + asm = str(mod) +- self.assertEqual(asm, asm_nonalphanum_blocklabel) ++ self.assertEqual( ++ clean_string_whitespace(asm), ++ clean_string_whitespace(asm_nonalphanum_blocklabel) ++ ) + + def test_global_context(self): + gcontext1 = llvm.context.get_global_context() +@@ -640,7 +653,7 @@ + def test_version(self): + major, minor, patch = llvm.llvm_version_info + # one of these can be valid +- valid = [(11,)] ++ valid = [(11,), (12,), (13,), (14,)] + self.assertIn((major,), valid) + self.assertIn(patch, range(10)) From bae9ad854427378c7839f7af8588898a05781079 Mon Sep 17 00:00:00 2001 From: James Carpenter Date: Wed, 18 Jan 2023 16:00:32 +0000 Subject: [PATCH 6241/9987] HPL toolchain build example --- .../easyconfigs/h/HPL/HPL-2.3-iomkl-2021b.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100755 easybuild/easyconfigs/h/HPL/HPL-2.3-iomkl-2021b.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-iomkl-2021b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-iomkl-2021b.eb new file mode 100755 index 00000000000..9f525d9df18 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-iomkl-2021b.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'iomkl', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' From 0e7688c25d51d20b64798b20393b35a4e83312fa Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 18 Jan 2023 17:40:55 +0000 Subject: [PATCH 6242/9987] Also add Set::Object to 5.34.0 --- easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 596de0bad6b..22541fbd01f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1819,6 +1819,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER/'], 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], }), + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), ] moduleclass = 'lang' From 5985b332e60270ead048508724c7d16ea2a8bafd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 19 Jan 2023 09:14:49 +0100 Subject: [PATCH 6243/9987] Version in filename, update description, enhance sanitycheck --- .../flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb index 71b08c11f2d..019f393bdd0 100644 --- a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-2.0.7-GCCcore-11.3.0.eb @@ -7,7 +7,10 @@ name = 'flatbuffers' version = '2.0.7' homepage = 'https://github.com/google/flatbuffers/' -description = """FlatBuffers: Memory Efficient Serialization Library""" +description = """FlatBuffers: Memory Efficient Serialization Library + +Includes the Flatbuffers compiler, C/C++ bindings and Python runtime library. +""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} @@ -41,17 +44,17 @@ exts_list = [ ('flatbuffers', version, { 'sources': { 'download_filename': SOURCE_TAR_GZ, - 'filename': '%(name)s-python.tar.gz', + 'filename': '%(name)s-python-%(version)s.tar.gz', }, 'checksums': ['0ae7d69c5b82bf41962ca5fde9cc43033bc9501311d975fd5a25e8a7d29c1245'], }), ] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - sanity_check_paths = { 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], - 'dirs': ['lib/cmake'], + 'dirs': ['lib/cmake', 'lib/python%(pyshortver)s/site-packages'], } +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'devel' From a68e55ca6f0a078485b5edfb144cb5ae380f11aa Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 19 Jan 2023 10:23:28 +0100 Subject: [PATCH 6244/9987] adding easyconfigs: PyTorch-1.12.1-foss-2021b.eb --- .../p/PyTorch/PyTorch-1.12.1-foss-2021b.eb | 132 ++++++++++++++++++ 1 file changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb new file mode 100644 index 00000000000..b4e4f83ca06 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb @@ -0,0 +1,132 @@ +name = 'PyTorch' +version = '1.12.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', + # PyTorch-1.12.1_fix-test_wishart_log_prob.patch + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_python-3.10-annotation-fix.patch + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7', + '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67', # PyTorch-1.12.1_python-3.10-compat.patch + # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d', + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin.patch + '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.22.1'), + ('hypothesis', '6.14.6'), +] + +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.6'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.7.1'), + ('SciPy-bundle', '2021.10'), + ('typing-extensions', '3.10.0.2'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.3.2'), + ('expecttest', '0.1.3'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' From 6fac76c4ad9085d956a1f7cf86ae057a583810b2 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 19 Jan 2023 09:31:44 +0000 Subject: [PATCH 6245/9987] adding easyconfigs: PyTorch-1.13.1-foss-2022a.eb and patches: PyTorch-1.13.1_fix-test-ops-conf.patch, PyTorch-1.13.1_no-cuda-stubs-rpath.patch, PyTorch-1.13.1_remove-flaky-test-in-testnn.patch, PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch --- .../p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 95 +++++++++ .../PyTorch-1.13.1_fix-test-ops-conf.patch | 26 +++ .../PyTorch-1.13.1_no-cuda-stubs-rpath.patch | 186 ++++++++++++++++++ ...h-1.13.1_remove-flaky-test-in-testnn.patch | 21 ++ ...skip-ao-sparsity-test-without-fbgemm.patch | 27 +++ 5 files changed, 355 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-test-ops-conf.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_no-cuda-stubs-rpath.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_remove-flaky-test-in-testnn.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb new file mode 100644 index 00000000000..93d6830c264 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -0,0 +1,95 @@ +name = 'PyTorch' +version = '1.13.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +patches = [ + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', + 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.13.1_fix-test-ops-conf.patch', + 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', +] +checksums = [ + {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.10.0_fix-kineto-crash.patch': 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb'}, + {'PyTorch-1.11.0_fix-fsdp-fp16-test.patch': 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13'}, + {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, + {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, + {'PyTorch-1.12.1_fix-test_wishart_log_prob.patch': + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45'}, + {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, + {'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch': + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d'}, + {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, + {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, + {'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch': + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d'}, + {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': + 'ad8db280c1acb5fade65646097590c6b332a9caf722191e4a3ddba2fb945ee6d'}, + {'PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch': + 'ea391298c4d9984de87cc14da9740ff09137b4a832fafd9e60c576f81690e8ec'}, + {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, + {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '1a8f712e474f64da878b9328ce05e7245afcba1765cbc27fb5f4f16f733ea175'}, +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), +] + +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.4.2'), + ('Pillow', '9.1.1'), + ('expecttest', '0.1.3'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + # no xdoctest + 'doctests', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-test-ops-conf.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-test-ops-conf.patch new file mode 100644 index 00000000000..d30746dab4d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-test-ops-conf.patch @@ -0,0 +1,26 @@ +From 8581301957b0018a32433f85163535709bc9d332 Mon Sep 17 00:00:00 2001 +From: Masaki Kozuki +Date: Fri, 7 Oct 2022 21:25:07 -0700 +Subject: [PATCH] try using a different group name + +ref: +https://github.com/pytorch/pytorch/issues/85923#issuecomment-1272220271 + +Signed-off-by: Masaki Kozuki +--- + functorch/test/conftest.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/functorch/test/conftest.py b/functorch/test/conftest.py +index d2e929a9a58db..afc39d9f35de9 100644 +--- a/functorch/test/conftest.py ++++ b/functorch/test/conftest.py +@@ -17,7 +17,7 @@ + + + def pytest_addoption(parser: Parser) -> None: +- group = parser.getgroup("terminal reporting") ++ group = parser.getgroup("terminal reporting functorch") + group.addoption( + "--junit-xml-reruns", + action="store", diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_no-cuda-stubs-rpath.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_no-cuda-stubs-rpath.patch new file mode 100644 index 00000000000..772677f267a --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_no-cuda-stubs-rpath.patch @@ -0,0 +1,186 @@ +# PyTorch's CMAKE configuration by default sets RUNPATH on libraries if they link other libraries +# that are outside the build tree, which is done because of the CMAKE config on +# https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L10. +# This provides problems, since the cuda stubs library path then also gets added to the RUNPATH. +# As a result, at runtime, the stub version of things like libcuda.so.1 gets picked up, instead of the real drivers +# See https://github.com/easybuilders/easybuild-easyconfigs/issues/14359 +# This line https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L16 +# Makes sure that any path that is linked, is also added to the RUNPATH. +# This has been reported upstream in https://github.com/pytorch/pytorch/issues/35418 +# and a fix was attempted in https://github.com/pytorch/pytorch/pull/37737 but it was reverted +# +# This EasyBuild patch changes behavior for the libraries that were failing, i.e. the ones in this list: +# https://github.com/easybuilders/easybuild-easyconfigs/issues/14359#issuecomment-970479904 +# This is done by setting INSTALL_RPATH_USE_LINK_PATH to false, and instead, specifying the RPATH +# explicitely by defining INSTALL_RPATH, but only adding directories that do not match to the "stubs" regex +# +# Original patch: Caspar van Leeuwen +# Updated: Alexander Grund (TU Dresden) +# Updated: Simon Branford (University of Birmingham) +# +# See https://github.com/pytorch/pytorch/pull/87593 + +diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt +index 4182797fc78e5..265bf4f660896 100644 +--- a/caffe2/CMakeLists.txt ++++ b/caffe2/CMakeLists.txt +@@ -631,13 +631,12 @@ endif() + if(USE_CUDA) + list(APPEND Caffe2_GPU_CU_SRCS ${Caffe2_GPU_HIP_JIT_FUSERS_SRCS}) + add_library(caffe2_nvrtc SHARED ${ATen_NVRTC_STUB_SRCS}) ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB}) + if(MSVC) + # Delay load nvcuda.dll so we can import torch compiled with cuda on a CPU-only machine +- set(DELAY_LOAD_FLAGS "-DELAYLOAD:nvcuda.dll;delayimp.lib") +- else() +- set(DELAY_LOAD_FLAGS "") ++ target_link_libraries(caffe2_nvrtc "-DELAYLOAD:nvcuda.dll;delayimp.lib") + endif() +- target_link_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB} ${DELAY_LOAD_FLAGS}) + target_include_directories(caffe2_nvrtc PRIVATE ${CUDA_INCLUDE_DIRS}) + install(TARGETS caffe2_nvrtc DESTINATION "${TORCH_INSTALL_LIB_DIR}") + if(USE_NCCL) +diff --git a/cmake/LinkCudaLibraries.cmake b/cmake/LinkCudaLibraries.cmake +new file mode 100644 +index 0000000000000..005914ccc6f7c +--- /dev/null ++++ b/cmake/LinkCudaLibraries.cmake +@@ -0,0 +1,33 @@ ++# Link CUDA libraries to the given target, i.e.: `target_link_libraries(target )` ++# ++# Additionally makes sure CUDA stub libs don't end up being in RPath ++# ++# Example: link_cuda_libraries(mytarget PRIVATE ${CUDA_LIBRARIES}) ++function(link_cuda_libraries target) ++ set(libs ${ARGN}) ++ set(install_rpath "$ORIGIN") ++ set(filtered FALSE) ++ foreach(lib IN LISTS libs) ++ # CUDA stub libs are in form /prefix/lib/stubs/libcuda.so ++ # So extract the name of the parent folder, to check against "stubs" ++ # And the parent path which we need to add to the INSTALL_RPATH for non-stubs ++ get_filename_component(parent_path "${lib}" DIRECTORY) ++ get_filename_component(parent_name "${parent_path}" NAME) ++ if(parent_name STREQUAL "stubs") ++ message(STATUS "Filtering ${lib} from being set in ${target}'s RPATH, " ++ "because it appears to point to the CUDA stubs directory.") ++ set(filtered TRUE) ++ elseif(parent_path) ++ list(APPEND install_rpath ${parent_path}) ++ endif() ++ endforeach() ++ ++ # Regular link command ++ target_link_libraries(${target} ${scope} ${libs}) ++ # Manually set INSTALL_RPATH when there were any stub libs ++ if(filtered) ++ list(REMOVE_DUPLICATES install_rpath) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH "${install_rpath}") ++ endif() ++endfunction() +diff --git a/test/cpp/api/CMakeLists.txt b/test/cpp/api/CMakeLists.txt +index 6b801a0731827..6ac92870479e0 100644 +--- a/test/cpp/api/CMakeLists.txt ++++ b/test/cpp/api/CMakeLists.txt +@@ -54,7 +54,8 @@ if(NOT MSVC) + endif() + + if(USE_CUDA) +- target_link_libraries(test_api PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_api PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/dist_autograd/CMakeLists.txt b/test/cpp/dist_autograd/CMakeLists.txt +index 9969c63e16d57..356ba5be55c4e 100644 +--- a/test/cpp/dist_autograd/CMakeLists.txt ++++ b/test/cpp/dist_autograd/CMakeLists.txt +@@ -10,7 +10,8 @@ if(USE_DISTRIBUTED AND NOT WIN32) + target_link_libraries(test_dist_autograd PRIVATE torch gtest) + + if(USE_CUDA) +- target_link_libraries(test_dist_autograd PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_dist_autograd PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/jit/CMakeLists.txt b/test/cpp/jit/CMakeLists.txt +index b8b765a68d8b4..aba9c8c6c3e17 100644 +--- a/test/cpp/jit/CMakeLists.txt ++++ b/test/cpp/jit/CMakeLists.txt +@@ -156,7 +156,8 @@ if(LINUX) + endif() + + if(USE_CUDA) +- target_link_libraries(test_jit PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_jit PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/rpc/CMakeLists.txt b/test/cpp/rpc/CMakeLists.txt +index 3997f8753e555..21fddbc645d0d 100644 +--- a/test/cpp/rpc/CMakeLists.txt ++++ b/test/cpp/rpc/CMakeLists.txt +@@ -33,7 +33,8 @@ target_include_directories( + target_link_libraries(test_cpp_rpc PRIVATE ${TORCH_RPC_TEST_DEPENDENCY_LIBS}) + + if(USE_CUDA) +- target_link_libraries(test_cpp_rpc PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_cpp_rpc PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/tensorexpr/CMakeLists.txt b/test/cpp/tensorexpr/CMakeLists.txt +index 7dff70630d3ec..ecb83005492f5 100644 +--- a/test/cpp/tensorexpr/CMakeLists.txt ++++ b/test/cpp/tensorexpr/CMakeLists.txt +@@ -57,14 +57,15 @@ if(USE_PTHREADPOOL) + target_link_libraries(test_tensorexpr PRIVATE pthreadpool_interface) + endif() + if(USE_CUDA) +- target_link_libraries(test_tensorexpr PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + target_compile_definitions(test_tensorexpr PRIVATE USE_CUDA) + +- target_link_libraries(tutorial_tensorexpr PRIVATE ++ link_cuda_libraries(tutorial_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/test_torch.py b/test/test_torch.py +index 31759213ecefc..67ebc0420f38a 100644 +--- a/test/test_torch.py ++++ b/test/test_torch.py +@@ -8581,6 +8581,21 @@ def add_neg_dim_tests(): + assert not hasattr(TestTorch, test_name), "Duplicated test name: " + test_name + setattr(TestTorch, test_name, make_neg_dim_test(name, tensor_arg, arg_constr, types, extra_dim)) + ++class TestRPATH(TestCase): ++ @unittest.skipIf(not sys.platform.startswith('linux'), "linux-only test") ++ def test_rpath(self): ++ """ ++ Make sure RPATH (or RUNPATH) in nvrtc does not contain a cuda stubs directory ++ issue gh-35418 ++ """ ++ libdir = os.path.join(os.path.dirname(torch._C.__file__), 'lib') ++ caffe2_nvrtc = os.path.join(libdir, 'libcaffe2_nvrtc.so') ++ if os.path.exists(caffe2_nvrtc): ++ output = subprocess.check_output(['objdump', '-x', caffe2_nvrtc]) ++ for line in output.split(b'\n'): ++ if b'RPATH' in line or b'RUNPATH' in line: ++ self.assertFalse(b'stubs' in line) ++ + # TODO: these empy classes are temporarily instantiated for XLA compatibility + # once XLA updates their test suite it should be removed + class TestViewOps(TestCase): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_remove-flaky-test-in-testnn.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_remove-flaky-test-in-testnn.patch new file mode 100644 index 00000000000..7a76b5fe01e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_remove-flaky-test-in-testnn.patch @@ -0,0 +1,21 @@ +This test is flaky when run with the type float16. +I.e. TestNNDeviceTypeCPU.test_embedding_bag_device_cpu_int32_int32_float16 & + TestNNDeviceTypeCPU.test_embedding_bag_device_cpu_int64_int64_float16 +fail. +See https://github.com/pytorch/pytorch/issues/86638 +So remove the half precision test. + +Author: Simon Branford (University of Birmingham) +Based off 1.12.1 patch by Alexander Grund (TU Dresden) + +--- a/test/nn/test_embedding.py ++++ b/test/nn/test_embedding.py +@@ -18236,7 +18236,7 @@ class TestNNDeviceType(NNTestCase): + self.assertRaises(RuntimeError, lambda: es(input.view(-1), offset)) + + @skipMeta +- @dtypes(*itertools.product((torch.int, torch.long), (torch.int, torch.long), (torch.float, torch.double, torch.half))) ++ @dtypes(*itertools.product((torch.int, torch.long), (torch.int, torch.long), (torch.float, torch.double))) + def test_embedding_bag_device(self, device, dtypes): + with set_default_dtype(torch.double): + self._test_EmbeddingBag(device, 'sum', False, wdtype=dtypes[2], dtype=dtypes[0], odtype=dtypes[1]) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch new file mode 100644 index 00000000000..fe5d7b06a51 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch @@ -0,0 +1,27 @@ +Those tests (from test_ao_sparsity) require FBGEMM which may not be available. +So add the skip decorator. +See https://github.com/pytorch/pytorch/issues/87364 + +Author: Simon Branford (University of Birmingham) +Based off 1.12.1 patch by Alexander Grund (TU Dresden) + +diff --git a/test/ao/sparsity/test_composability.py b/test/ao/sparsity/test_composability.py +index b44c885507..b7d35343c0 100644 +--- a/test/ao/sparsity/test_composability.py ++++ b/test/ao/sparsity/test_composability.py +@@ -9,6 +9,7 @@ import torch.ao.quantization as tq + from torch import nn + from torch.ao import sparsity + from torch.testing._internal.common_utils import TestCase ++from torch.testing._internal.common_quantization import skipIfNoFBGEMM + from torch.ao.quantization.quantize_fx import prepare_fx, convert_fx, convert_to_reference_fx, prepare_qat_fx + from torch.ao.sparsity import fqn_to_module + +@@ -23,6 +24,7 @@ sparse_defaults = { + # This series of tests are to check the composability goals for sparsity and quantization. Namely + # that performing quantization and sparsity model manipulations in various orderings + # does not cause problems ++@skipIfNoFBGEMM + class TestComposability(TestCase): + def _get_model_and_sparsifier_and_sparse_config(self, qconfig=None): + model = nn.Sequential( From faddd21fabcebcb9ec5e51a93071f94d53f14b4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Jan 2023 15:17:02 +0100 Subject: [PATCH 6246/9987] adding easyconfigs: Nextflow-22.10.5.eb --- .../n/Nextflow/Nextflow-22.10.5.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.5.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.5.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.5.eb new file mode 100644 index 00000000000..869b8678294 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.5.eb @@ -0,0 +1,33 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '22.10.5' + +homepage = 'https://www.%(namelower)s.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-all'] +checksums = ['5ca5b926bdd355a8d5f1f968cea6ba46fac5a4fa7e1dac3fe5ff02e5d6b6a90c'] + +dependencies = [('Java', '11')] + +install_cmd = "mkdir -p %(installdir)s/bin &&" +install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" +install_cmd += "cd %(installdir)s/bin && ln -s %(namelower)s-%(version)s-all %(namelower)s &&" +install_cmd += "chmod +x %(installdir)s/bin/%(namelower)s-%(version)s-all" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-%(version)s-all', 'bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' From 8990c1cac13abfdfa0d87a87f83bf29266dc7b1d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 19 Jan 2023 14:42:03 +0000 Subject: [PATCH 6247/9987] add pooch, doit, cloudpickle, pydevtool, rich, rich-click, commonmark, execnet, pytet-xdist extensions to Python 3.10.8 --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index b9943b5441f..d2c2a9c054c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -494,6 +494,17 @@ exts_list = [ 'source_tmpl': 'simplegeneric-%(version)s.zip', 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), + ('pooch', '1.6.0'), + ('doit', '0.36.0'), + ('cloudpickle', '2.2.0'), + ('pydevtool', '0.3.0'), + ('rich', '13.1.0'), + ('rich-click', '1.6.0'), + ('commonmark', '0.9.1'), + ('execnet', '1.9.0'), + ('pytest-xdist', '3.1.0', { + 'modulename': 'xdist', + }), ] moduleclass = 'lang' From e4083b62eeb93b1c06b0b4125afd5f380e24b440 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 19 Jan 2023 14:44:49 +0000 Subject: [PATCH 6248/9987] drop mpi4py to gompi --- ...foss-2022b.eb => mpi4py-3.1.4-gompi-2022b.eb} | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/m/mpi4py/{mpi4py-3.1.4-foss-2022b.eb => mpi4py-3.1.4-gompi-2022b.eb} (62%) diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022b.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-gompi-2022b.eb similarity index 62% rename from easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022b.eb rename to easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-gompi-2022b.eb index d103cd78db0..3f9abaa0895 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-foss-2022b.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-gompi-2022b.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'mpi4py' version = '3.1.4' @@ -7,19 +7,19 @@ homepage = 'https://github.com/mpi4py/mpi4py' description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.""" -toolchain = {'name': 'foss', 'version': '2022b'} - -sources = [SOURCE_TAR_GZ] -checksums = ['17858f2ebc623220d0120d1fa8d428d033dde749c4bc35b33d81a66ad7f93480'] +toolchain = {'name': 'gompi', 'version': '2022b'} dependencies = [ ('Python', '3.10.8'), - ('SciPy-bundle', '2023.01'), ] -download_dep_fail = True use_pip = True - sanity_pip_check = True +exts_list = [ + (name, version, { + 'checksums': ['17858f2ebc623220d0120d1fa8d428d033dde749c4bc35b33d81a66ad7f93480'], + }), +] + moduleclass = 'lib' From 45ccf425342c65488ee573130505af3840c440e9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 19 Jan 2023 15:01:44 +0000 Subject: [PATCH 6249/9987] checksums --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 49 ++++++++++++------- 1 file changed, 32 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index d2c2a9c054c..992bd1e8a53 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -138,8 +138,6 @@ exts_list = [ 'checksums': ['d8daccb14dc0eae1b6b6eb3ecef79675bd37b4065369f79c35393dd5c55652c7'], }), ('cryptography', '38.0.3', { - # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, - # see https://github.com/rust-lang/cargo/issues/6652 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['bfbe6ee19615b07a98b1d2287d6a6073f734735b49ee45b11324d85efc4d5cbd'], }), @@ -385,19 +383,19 @@ exts_list = [ 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], }), ('pastel', '0.2.1', { - 'source_tmpl': SOURCE_WHL, + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], }), ('crashtest', '0.3.1', { - 'source_tmpl': SOURCE_PY3_WHL, + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], }), ('clikit', '0.6.2', { - 'source_tmpl': SOURCE_WHL, + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], }), ('jeepney', '0.8.0', { - 'source_tmpl': SOURCE_PY3_WHL, + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], }), ('SecretStorage', '3.3.3', { @@ -415,7 +413,7 @@ exts_list = [ 'checksums': ['2ba3d56441ba0637f5f9c096068f67010ac0453f9d0b626de2aa3019353b6431'], }), ('tomlkit', '0.11.6', { - 'source_tmpl': SOURCE_PY3_WHL, + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b'], }), ('shellingham', '1.5.0', { @@ -431,7 +429,7 @@ exts_list = [ 'checksums': ['a84da4318dd86f870a9447a8c98340aa06216bfc6f2b7bdc4b8766984ae1867c'], }), ('ptyprocess', '0.7.0', { - 'source_tmpl': SOURCE_WHL, + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], }), ('pexpect', '4.8.0', { @@ -453,7 +451,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '1.0.0a5', { - 'source_tmpl': SOURCE_PY3_WHL, + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['ff53056589300976e960f75afb792dfbfc9c78dcbb5a448e207a17b643826360'], }), ('cachy', '0.3.0', { @@ -494,16 +492,33 @@ exts_list = [ 'source_tmpl': 'simplegeneric-%(version)s.zip', 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), - ('pooch', '1.6.0'), - ('doit', '0.36.0'), - ('cloudpickle', '2.2.0'), - ('pydevtool', '0.3.0'), - ('rich', '13.1.0'), - ('rich-click', '1.6.0'), - ('commonmark', '0.9.1'), - ('execnet', '1.9.0'), + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + ('doit', '0.36.0', { + 'checksums': ['71d07ccc9514cb22fe59d98999577665eaab57e16f644d04336ae0b4bae234bc'], + }), + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + ('pydevtool', '0.3.0', { + 'checksums': ['25e3ba4f3d33ccac33ee2b9775995848d49e9b318b7a146477fb5d52f786fc8a'], + }), + ('rich', '13.1.0', { + 'checksums': ['81c73a30b144bbcdedc13f4ea0b6ffd7fdc3b0d3cc259a9402309c8e4aee1964'], + }), + ('rich-click', '1.6.0', { + 'checksums': ['33799c31f8817101f2eb8fe90e95d2c2acd428a567ee64358ca487f963f75e9c'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('execnet', '1.9.0', { + 'checksums': ['8f694f3ba9cc92cab508b152dcfe322153975c29bda272e2fd7f3f00f36e47c5'], + }), ('pytest-xdist', '3.1.0', { 'modulename': 'xdist', + 'checksums': ['40fdb8f3544921c5dfcd486ac080ce22870e71d82ced6d2e78fa97c2addd480c'], }), ] From 3fa69af6e4630851ee83c6434642910f0bfd8fab Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 19 Jan 2023 15:24:38 +0000 Subject: [PATCH 6250/9987] move extensions required for tests to main Python easyconfig --- .../s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb index b69f0927fc6..7878162dce4 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb @@ -47,8 +47,6 @@ exts_list = [ ('pythran', '0.12.1', { 'checksums': ['702c2701187cfb38f66c0c20cc85d04d0e156d260a8d92892da65947faa5360e'], }), - ('pooch', '1.6.0', { - }), ('scipy', '1.10.0', { 'checksums': ['c8b3cbc636a87a89b770c6afc999baa6bcbb01691b5ccbbc1b1791c7c0a07540'], }), From 4b1f3a70c1a41e3a866b95ed42cac1a651c53ef1 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 19 Jan 2023 14:26:09 +0100 Subject: [PATCH 6251/9987] Fix AARCH64 build --- .../TensorFlow/TensorFlow-2.5.0-foss-2020b.eb | 3 +++ ...rFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb | 3 +++ .../TensorFlow-2.5.0-fosscuda-2020b.eb | 3 +++ ...TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb | 3 +++ .../TensorFlow/TensorFlow-2.5.3-foss-2021a.eb | 3 +++ .../TensorFlow-2.5.3_fix-aarch64-build.patch | 24 +++++++++++++++++++ 6 files changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3_fix-aarch64-build.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb index 2840f4d3d74..503325ea6d7 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-foss-2020b.eb @@ -161,6 +161,7 @@ exts_list = [ 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', 'TensorFlow-2.5.0_fix-alignment-in-matmul-test.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.3_fix-aarch64-build.patch', ], 'checksums': [ '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz @@ -181,6 +182,8 @@ exts_list = [ '6a4d6cbf45a622b8a2c3ea0b1c0171f01f595684d9c57d415bb39b1b27e1180f', # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', + {'TensorFlow-2.5.3_fix-aarch64-build.patch': + '9bfd9a3586bb04c131c4d07a40b0ef5c2e7f474dc986449fc68817d927af0c6d'}, ], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb index 5c26c534b08..10c4b07d14d 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2019b-Python-3.7.4.eb @@ -163,6 +163,7 @@ exts_list = [ 'TensorFlow-2.5.0_fix-cub-cuda-dep.patch', 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.3_fix-aarch64-build.patch', ], 'checksums': [ '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz @@ -194,6 +195,8 @@ exts_list = [ 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + {'TensorFlow-2.5.3_fix-aarch64-build.patch': + '9bfd9a3586bb04c131c4d07a40b0ef5c2e7f474dc986449fc68817d927af0c6d'}, ], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb index 3136244b068..3ca12b1e635 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0-fosscuda-2020b.eb @@ -167,6 +167,7 @@ exts_list = [ 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', 'TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.5.3_fix-aarch64-build.patch', ], 'checksums': [ '233875ea27fc357f6b714b2a0de5f6ff124b50c1ee9b3b41f9e726e9e677b86c', # v2.5.0.tar.gz @@ -194,6 +195,8 @@ exts_list = [ '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', # TensorFlow-2.5.0_remove-duplicate-gpu-tests.patch 'b940d438e036faac24453bff2cf1834c5e1359e87e84d1f1999fa7a30b278fec', + {'TensorFlow-2.5.3_fix-aarch64-build.patch': + '9bfd9a3586bb04c131c4d07a40b0ef5c2e7f474dc986449fc68817d927af0c6d'}, ], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb index 0c99b64dcc6..a476bb464a6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb @@ -171,6 +171,7 @@ exts_list = [ 'TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch', 'TensorFlow-2.5.0_fix-compatibility-with-CUDA-11.3.patch', 'TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch', + 'TensorFlow-2.5.3_fix-aarch64-build.patch', 'TensorFlow-2.5.3_relax-required-versions.patch', ], 'checksums': [ @@ -205,6 +206,8 @@ exts_list = [ 'e82db520e5e22f97c0dde2166f0d1a29e7ea828c2b4dfbc79dccc0d4cde5d95d', # TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch '4c32aba417e6ecb2642d5828b4ac618f1e4395f6c217cd621fa08a74433faa55', + {'TensorFlow-2.5.3_fix-aarch64-build.patch': + '9bfd9a3586bb04c131c4d07a40b0ef5c2e7f474dc986449fc68817d927af0c6d'}, # TensorFlow-2.5.3_relax-required-versions.patch 'e108c3877cf4a0cadc179290ec2098683367688bbbbc7d6fa9a321eb7020443c', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb index ca3c8988690..1f3e1cc7312 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3-foss-2021a.eb @@ -165,6 +165,7 @@ exts_list = [ 'TensorFlow-2.5.0_fix-compatibility-with-protobuf-3.17.patch', 'TensorFlow-2.5.0_fix-compatibility-with-CUDA-11.3.patch', 'TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch', + 'TensorFlow-2.5.3_fix-aarch64-build.patch', 'TensorFlow-2.5.3_relax-required-versions.patch', ], 'checksums': [ @@ -196,6 +197,8 @@ exts_list = [ 'e82db520e5e22f97c0dde2166f0d1a29e7ea828c2b4dfbc79dccc0d4cde5d95d', # TensorFlow-2.5.0_fix_numpy_1.20_compatibility.patch '4c32aba417e6ecb2642d5828b4ac618f1e4395f6c217cd621fa08a74433faa55', + {'TensorFlow-2.5.3_fix-aarch64-build.patch': + '9bfd9a3586bb04c131c4d07a40b0ef5c2e7f474dc986449fc68817d927af0c6d'}, # TensorFlow-2.5.3_relax-required-versions.patch 'e108c3877cf4a0cadc179290ec2098683367688bbbbc7d6fa9a321eb7020443c', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3_fix-aarch64-build.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3_fix-aarch64-build.patch new file mode 100644 index 00000000000..c45e97f766f --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.3_fix-aarch64-build.patch @@ -0,0 +1,24 @@ +Without this tf_to_kernel fails to link on AARCH64 + +Picked from https://github.com/tensorflow/tensorflow/commit/4933ada8c2b4b523acc94baea2609f0cce70a083 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/core/platform/default/build_config.bzl b/tensorflow/core/platform/default/build_config.bzl +index d0dadd12108..bf6c631fdf6 100644 +--- a/tensorflow/core/platform/default/build_config.bzl ++++ b/tensorflow/core/platform/default/build_config.bzl +@@ -795,9 +795,10 @@ def tf_google_mobile_srcs_only_runtime(): + return [] + + def if_llvm_aarch64_available(then, otherwise = []): +- # TODO(b/...): The TF XLA build fails when adding a dependency on +- # @llvm/llvm-project/llvm:aarch64_target. +- return otherwise ++ return select({ ++ "//tensorflow:linux_aarch64": then, ++ "//conditions:default": otherwise, ++ }) + + def if_llvm_system_z_available(then, otherwise = []): + return select({ From 296c4985ce5b4cbc0e06318d88c242c259f66f88 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Jan 2023 20:44:32 +0100 Subject: [PATCH 6252/9987] update to Blosc2 2.6.1 as dependency for PyTables 3.8.0 + add patches to make sure that blosc2 and PyTables effectively use that Blosc2 dependency --- .../b/Blosc2/Blosc2-2.6.1-GCCcore-11.3.0.eb | 31 +++++++++++++ .../p/PyTables/PyTables-3.8.0-foss-2022a.eb | 17 +++++-- ...s-3.8.0_fix-find-blosc2-library-path.patch | 44 +++++++++++++++++++ .../blosc2-2.0.0_use-Blosc2-dep.patch | 24 ++++++++++ 4 files changed, 113 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.6.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.8.0_fix-find-blosc2-library-path.patch create mode 100644 easybuild/easyconfigs/p/PyTables/blosc2-2.0.0_use-Blosc2-dep.patch diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.6.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.6.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1a7d1da3a1f --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.6.1-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.6.1' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['514a793368093893c1a7cae030f7e31faca7f86465ae69dd576f256d8bf28c08'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb index befd1e23127..c6878c819f0 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb @@ -19,7 +19,9 @@ toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'usempi': True} builddependencies = [ + ('pkgconf', '1.8.0'), ('CMake', '3.24.3'), + ('Ninja', '1.10.2'), ('scikit-build', '0.15.0'), ] @@ -29,7 +31,7 @@ dependencies = [ ('HDF5', '1.12.2'), ('LZO', '2.10'), ('Blosc', '1.21.3'), - ('Blosc2', '2.4.3'), + ('Blosc2', '2.6.1'), ('py-cpuinfo', '9.0.0'), ] @@ -37,13 +39,22 @@ use_pip = True exts_list = [ ('blosc2', '2.0.0', { - 'checksums': ['f19b0b3674f6c825b490f00d8264b0c540c2cdc11ec7e81178d38b83c57790a1'], + 'patches': ['blosc2-2.0.0_use-Blosc2-dep.patch'], + 'checksums': [ + {'blosc2-2.0.0.tar.gz': 'f19b0b3674f6c825b490f00d8264b0c540c2cdc11ec7e81178d38b83c57790a1'}, + {'blosc2-2.0.0_use-Blosc2-dep.patch': '6a9443f378472ada3c8fe8a8a346fe16f22b01bab7d9e60c23b64b546178054b'}, + ], }), ('tables', version, { - 'patches': ['PyTables-%(version)s_fix-libs.patch'], + 'patches': [ + 'PyTables-%(version)s_fix-libs.patch', + 'PyTables-3.8.0_fix-find-blosc2-library-path.patch', + ], 'checksums': [ {'tables-3.8.0.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'}, {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'}, + {'PyTables-3.8.0_fix-find-blosc2-library-path.patch': + 'dcf6c3a16a138454296161e99cf6470620755d4c26303186a744f09a11e6013b'}, ], }), ] diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0_fix-find-blosc2-library-path.patch b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0_fix-find-blosc2-library-path.patch new file mode 100644 index 00000000000..7849b1888d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0_fix-find-blosc2-library-path.patch @@ -0,0 +1,44 @@ +determine location to Blosc2 library via $EBROOTBLOSC2, if defined, +since mechanism to locate the library via blosc2-*.dist-info/RECORD doesn't work if blosc2 was not installed +with vendored c-blosc2 library; +author: Kenneth Hoste (HPC-UGent) +--- tables-3.8.0/setup.py.orig 2023-01-19 20:10:15.637759755 +0100 ++++ tables-3.8.0/setup.py 2023-01-19 20:11:48.590853686 +0100 +@@ -110,19 +110,25 @@ + + def get_blosc2_directories(): + """Get Blosc2 directories for the C library by using wheel metadata""" +- try: +- import blosc2 +- except ModuleNotFoundError: +- raise EnvironmentError("Cannot import the blosc2 requirement") +- version = blosc2.__version__ +- basepath = Path(os.path.dirname(blosc2.__file__)) +- recinfo = basepath.parent / f'blosc2-{version}.dist-info' / 'RECORD' + library_path = None +- for line in open(recinfo): +- if 'libblosc2' in line: +- library_path = Path(os.path.abspath(basepath.parent / +- Path(line[:line.find('libblosc2')]))) +- break ++ blosc2_root = os.getenv('EBROOTBLOSC2') ++ if blosc2_root: ++ library_path = Path(os.path.join(blosc2_root, 'lib')) ++ else: ++ try: ++ import blosc2 ++ except ModuleNotFoundError: ++ raise EnvironmentError("Cannot import the blosc2 requirement") ++ version = blosc2.__version__ ++ basepath = Path(os.path.dirname(blosc2.__file__)) ++ recinfo = basepath.parent / f'blosc2-{version}.dist-info' / 'RECORD' ++ library_path = None ++ for line in open(recinfo): ++ if 'libblosc2' in line: ++ library_path = Path(os.path.abspath(basepath.parent / ++ Path(line[:line.find('libblosc2')]))) ++ break ++ + if not library_path: + raise NotADirectoryError("Library directory not found for blosc2!") + diff --git a/easybuild/easyconfigs/p/PyTables/blosc2-2.0.0_use-Blosc2-dep.patch b/easybuild/easyconfigs/p/PyTables/blosc2-2.0.0_use-Blosc2-dep.patch new file mode 100644 index 00000000000..9629c33f0eb --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/blosc2-2.0.0_use-Blosc2-dep.patch @@ -0,0 +1,24 @@ +make blosc2 use provided Blosc2 dependency, rather than letting it build its own vendored copy of c-blosc2 +author: Kenneth Hoste (HPC-UGent) +--- blosc2-2.0.0/blosc2/CMakeLists.txt.orig 2023-01-19 13:20:38.055582814 +0100 ++++ blosc2-2.0.0/blosc2/CMakeLists.txt 2023-01-19 13:21:03.808615093 +0100 +@@ -7,17 +7,14 @@ + set(BUILD_FUZZERS OFF CACHE BOOL "Build C-Blosc2 fuzzers") + + set(CMAKE_POSITION_INDEPENDENT_CODE ON) +-# we want the binaries of the C-Blosc2 library to go into the wheels +-set(BLOSC_INSTALL ON) +-add_subdirectory(c-blosc2) +-include_directories("${CMAKE_CURRENT_SOURCE_DIR}/c-blosc2/include") ++include_directories("$ENV{EBROOTBLOSC2}/include") + include_directories("${Python_NumPy_INCLUDE_DIRS}") + + + add_cython_target(blosc2_ext blosc2_ext.pyx) + add_library(blosc2_ext MODULE ${blosc2_ext}) + +-target_link_libraries(blosc2_ext blosc2_static) ++target_link_libraries(blosc2_ext $ENV{EBROOTBLOSC2}/lib/libblosc2.a) + + python_extension_module(blosc2_ext) + From d9ef5a7d99e7bfe100a4c57cc05d9185be52f562 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 19 Jan 2023 21:28:07 +0100 Subject: [PATCH 6253/9987] adding easyconfigs: scanpy-1.9.1-foss-2022a.eb --- .../s/scanpy/scanpy-1.9.1-foss-2022a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb new file mode 100644 index 00000000000..b9d1a3f9edb --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.9.1' + +homepage = 'https://scanpy.readthedocs.io/en/stable/' +description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('networkx', '2.8.4'), + ('numba', '0.56.4'), + ('PyTables', '3.8.0'), + ('statsmodels', '0.13.1'), + ('scikit-learn', '1.1.2'), + ('Seaborn', '0.12.1'), + ('tqdm', '4.64.0'), + ('leidenalg', '0.9.1'), + ('umap-learn', '0.5.3'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.2.0', { + 'checksums': ['57f85b72c688b09e053cdac302dd5b5b53df5f73ae20b4874fcbffd8bf783d11'], + }), + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.4', { + 'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'], + }), + ('session_info', '1.0.0', { + 'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'], + }), + (name, version, { + 'checksums': ['00c9a83b649da7e0171c91e9a08cff632102faa760614fd05cd4d1dbba4eb541'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "natsort --help", + "scanpy --help", +] + +moduleclass = 'bio' From a3ca8237267b9feed0b998873199796901d6559d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 19 Jan 2023 23:15:51 +0100 Subject: [PATCH 6254/9987] adding easyconfigs: umap-learn-0.5.3-foss-2020b.eb --- .../umap-learn/umap-learn-0.5.3-foss-2020b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb new file mode 100644 index 00000000000..e3de10224d6 --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2020b.eb @@ -0,0 +1,41 @@ +# Author: Denis Krišťák (INUITS) +# This is a contribution from HPCNow! (http://hpcnow.com) +# Update: Erica Bianco +# License:: GPL-v3.0 +easyblock = "PythonBundle" + +name = 'umap-learn' +version = '0.5.3' + +homepage = 'https://umap-learn.readthedocs.io/en/latest/' +description = """ +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique +that can be used for visualisation similarly to t-SNE, but also for general non-linear +dimension reduction. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('scikit-learn', '0.23.2'), + ('numba', '0.53.1'), + ('LLVM', '11.0.0'), + ('tqdm', '4.56.2'), +] + +use_pip = True + +exts_list = [ + ('pynndescent', '0.5.7', { + 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], + }), + (name, version, { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From ec6c216dc99d7630a715a25cb23aa64e40a7ad19 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Jan 2023 09:39:20 +0100 Subject: [PATCH 6255/9987] adding easyconfigs: pdsh-2.34-GCCcore-11.3.0.eb --- .../p/pdsh/pdsh-2.34-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2ad121fa5b7 --- /dev/null +++ b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'pdsh' +version = '2.34' + +homepage = 'https://github.com/chaos/pdsh' +description = "A high performance, parallel remote shell utility" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/chaos/pdsh/releases/download/pdsh-%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b47b3e4662736ef44b6fe86e3d380f95e591863e69163aa0592e9f9f618521e9'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('libreadline', '8.1.2'), +] + +configopts = "--with-ssh --with-slurm --with-mrsh --with-readline" + +sanity_check_paths = { + 'files': ['bin/dshbak', 'bin/pdcp', 'bin/pdsh', 'bin/rpdcp'], + 'dirs': ['lib/pdsh', 'share/man/man1'], +} + +sanity_check_commands = [ + "dshbak -h", + "pdcp -h 2>&1 | grep '^Usage: pdcp'", + "pdsh -h 2>&1 | grep '^Usage: pdsh'", + "rpdcp -h 2>&1 | grep '^Usage: rpdcp'", +] + +moduleclass = 'tools' From 4816fa2a5cb648a72b96db2aff1102508814352a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 20 Jan 2023 09:53:13 +0100 Subject: [PATCH 6256/9987] add missing space before inline comment in PySCF 2.1.1 easyconfig to make style checker happy --- easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb index 3f29fdd4b4e..1d1b787c750 100644 --- a/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.1.1-foss-2022a.eb @@ -24,7 +24,7 @@ dependencies = [ ('libxc', '5.2.3'), ('XCFun', '2.1.1'), ('CPPE', '0.3.1'), # extra - ('PyBerny', '0.6.3'), # extra + ('PyBerny', '0.6.3'), # extra ('PyCheMPS2', '1.8.12'), # needed by dmrgscf ('Block', '1.5.3-20200525'), # needed by dmrgscf ('NECI', '20220711'), # needed by fciqmc From b2402aacc4132228b4bb277eaabeb2c85c1b8c46 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 20 Jan 2023 10:55:31 +0100 Subject: [PATCH 6257/9987] add patches to fix compilation of Qt5 5.15.5 with glibc 2.34 --- ...ix-qtwebengine-abseil-cpp-glibc-2.34.patch | 75 +++++++++++++++++++ ..._fix-qtwebengine-breakpad-glibc-2.34.patch | 75 +++++++++++++++++++ .../q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb | 17 +++-- 3 files changed, 162 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch new file mode 100644 index 00000000000..eccf15208e5 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch @@ -0,0 +1,75 @@ +Fix "no matching function" error. +Patch taken from https://bugs.gentoo.org/811312 + +From 78b1bcff4d9b977313e9ea15068168e1b11f5ba1 Mon Sep 17 00:00:00 2001 +From: Martin Jansa +Date: Wed, 4 Aug 2021 19:08:03 +0200 +Subject: [PATCH] chromium: abseil-cpp: fix build with glibc-2.34 + +* backport a fix from upstream abseil-cpp: + https://github.com/abseil/abseil-cpp/commit/a9831f1cbf93fb18dd951453635f488037454ce9 + + to fix: + +[97/24505] CXX obj/third_party/abseil-cpp/absl/debugging/failure_signal_handler/failure_signal_handler.o +FAILED: obj/third_party/abseil-cpp/absl/debugging/failure_signal_handler/failure_signal_handler.o +/OE/build/luneos-honister/webos-ports/tmp-glibc/work/core2-64-webos-linux/qtwebengine/5.15.4+gitAUTOINC+dd7f7a9166_555f348ae8-r0/recipe-sysroot-native/usr/bin/x86_64-webos-linux/x86_64-webos-linux-g++ -m64 -march=core2 -mtune=core2 -msse3 -mfpmath=sse -Wdate-time --sysroot=/OE/build/luneos-honister/webos-ports/tmp-glibc/work/core2-64-webos-linux/qtwebengine/5.15.4+gitAUTOINC+dd7f7a9166_555f348ae8-r0/recipe-sysroot -MMD -MF obj/third_party/abseil-cpp/absl/debugging/failure_signal_handler/failure_signal_handler.o.d -DUSE_UDEV -DUSE_AURA=1 -DUSE_NSS_CERTS=1 -DUSE_OZONE=1 -DOFFICIAL_BUILD -DTOOLKIT_QT -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DNO_UNWIND_TABLES -DCR_SYSROOT_HASH=5f64b417e1018dcf8fcc81dc2714e0f264b9b911 -DNDEBUG -DNVALGRIND -DDYNAMIC_ANNOTATIONS_ENABLED=0 -DABSL_ALLOCATOR_NOTHROW=1 -Igen -I../../../../git/src/3rdparty/chromium -I../../../../git/src/3rdparty/chromium/third_party/abseil-cpp -fno-strict-aliasing --param=ssp-buffer-size=4 -fstack-protector -fno-unwind-tables -fno-asynchronous-unwind-tables -fPIC -pipe -pthread -m64 -O2 -fno-ident -fdata-sections -ffunction-sections -fno-omit-frame-pointer -g1 -fvisibility=hidden -Wno-unused-local-typedefs -Wno-maybe-uninitialized -Wno-deprecated-declarations -fno-delete-null-pointer-checks -Wno-comments -Wno-packed-not-aligned -Wno-dangling-else -Wno-missing-field-initializers -Wno-unused-parameter -std=gnu++14 -fno-exceptions -fno-rtti --sysroot=../../../../recipe-sysroot -fvisibility-inlines-hidden -Wno-narrowing -Wno-class-memaccess -Wno-attributes -Wno-class-memaccess -Wno-subobject-linkage -Wno-invalid-offsetof -Wno-return-type -Wno-deprecated-copy -c ../../../../git/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc -o obj/third_party/abseil-cpp/absl/debugging/failure_signal_handler/failure_signal_handler.o +../../../../git/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc: In function 'bool absl::SetupAlternateStackOnce()': +../../../../git/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc:138:32: error: no matching function for call to 'max(long int, int)' + 138 | size_t stack_size = (std::max(SIGSTKSZ, 65536) + page_mask) & ~page_mask; + | ~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from ../../../../recipe-sysroot/usr/include/c++/11.2.0/algorithm:61, + from ../../../../git/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc:35: +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algobase.h:254:5: note: candidate: 'template constexpr const _Tp& std::max(const _Tp&, const _Tp&)' + 254 | max(const _Tp& __a, const _Tp& __b) + | ^~~ +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algobase.h:254:5: note: template argument deduction/substitution failed: +../../../../git/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc:138:32: note: deduced conflicting types for parameter 'const _Tp' ('long int' and 'int') + 138 | size_t stack_size = (std::max(SIGSTKSZ, 65536) + page_mask) & ~page_mask; + | ~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from ../../../../recipe-sysroot/usr/include/c++/11.2.0/algorithm:61, + from ../../../../git/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc:35: +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algobase.h:300:5: note: candidate: 'template constexpr const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' + 300 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) + | ^~~ +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algobase.h:300:5: note: template argument deduction/substitution failed: +../../../../git/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc:138:32: note: deduced conflicting types for parameter 'const _Tp' ('long int' and 'int') + 138 | size_t stack_size = (std::max(SIGSTKSZ, 65536) + page_mask) & ~page_mask; + | ~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from ../../../../recipe-sysroot/usr/include/c++/11.2.0/algorithm:62, + from ../../../../git/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc:35: +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algo.h:3461:5: note: candidate: 'template constexpr _Tp std::max(std::initializer_list<_Tp>)' + 3461 | max(initializer_list<_Tp> __l) + | ^~~ +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algo.h:3461:5: note: template argument deduction/substitution failed: +../../../../git/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc:138:32: note: mismatched types 'std::initializer_list<_Tp>' and 'long int' + 138 | size_t stack_size = (std::max(SIGSTKSZ, 65536) + page_mask) & ~page_mask; + | ~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from ../../../../recipe-sysroot/usr/include/c++/11.2.0/algorithm:62, + from ../../../../git/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc:35: +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algo.h:3467:5: note: candidate: 'template constexpr _Tp std::max(std::initializer_list<_Tp>, _Compare)' + 3467 | max(initializer_list<_Tp> __l, _Compare __comp) + | ^~~ +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algo.h:3467:5: note: template argument deduction/substitution failed: +../../../../git/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc:138:32: note: mismatched types 'std::initializer_list<_Tp>' and 'long int' + 138 | size_t stack_size = (std::max(SIGSTKSZ, 65536) + page_mask) & ~page_mask; + | ~~~~~~~~^~~~~~~~~~~~~~~~~ + +Signed-off-by: Martin Jansa +--- + .../abseil-cpp/absl/debugging/failure_signal_handler.cc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc b/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc +index 5d13bdbbbd1..150a43f2660 100644 +--- qtwebengine/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc ++++ qtwebengine/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc +@@ -135,7 +135,7 @@ static bool SetupAlternateStackOnce() { + #else + const size_t page_mask = sysconf(_SC_PAGESIZE) - 1; + #endif +- size_t stack_size = (std::max(SIGSTKSZ, 65536) + page_mask) & ~page_mask; ++ size_t stack_size = (std::max(SIGSTKSZ, 65536) + page_mask) & ~page_mask; + #if defined(ABSL_HAVE_ADDRESS_SANITIZER) || \ + defined(ABSL_HAVE_MEMORY_SANITIZER) || defined(ABSL_HAVE_THREAD_SANITIZER) + // Account for sanitizer instrumentation requiring additional stack space. diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch new file mode 100644 index 00000000000..088e902bcf3 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch @@ -0,0 +1,75 @@ +Fix "no matching function" error. +Patch taken from https://bugs.gentoo.org/811312 + +From a3bc792bdc116806a50e022d9102914c8daf6210 Mon Sep 17 00:00:00 2001 +From: Martin Jansa +Date: Wed, 4 Aug 2021 19:11:06 +0200 +Subject: [PATCH] chromium: breakpad: fix build with glibc-2.34 + +* fixes: +[218/24061] CXX obj/third_party/breakpad/client/exception_handler.o +FAILED: obj/third_party/breakpad/client/exception_handler.o +/OE/build/luneos-honister/webos-ports/tmp-glibc/work/core2-64-webos-linux/qtwebengine/5.15.4+gitAUTOINC+dd7f7a9166_555f348ae8-r0/recipe-sysroot-native/usr/bin/x86_64-webos-linux/x86_64-webos-linux-g++ -m64 -march=core2 -mtune=core2 -msse3 -mfpmath=sse -Wdate-time --sysroot=/OE/build/luneos-honister/webos-ports/tmp-glibc/work/core2-64-webos-linux/qtwebengine/5.15.4+gitAUTOINC+dd7f7a9166_555f348ae8-r0/recipe-sysroot -MMD -MF obj/third_party/breakpad/client/exception_handler.o.d -DUSE_UDEV -DUSE_AURA=1 -DUSE_NSS_CERTS=1 -DUSE_OZONE=1 -DOFFICIAL_BUILD -DTOOLKIT_QT -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DNO_UNWIND_TABLES -DCR_SYSROOT_HASH=5f64b417e1018dcf8fcc81dc2714e0f264b9b911 -DNDEBUG -DNVALGRIND -DDYNAMIC_ANNOTATIONS_ENABLED=0 -I../../../../git/src/3rdparty/chromium/third_party/breakpad -I../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src -I../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client -I../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/third_party/linux/include -Igen -I../../../../git/src/3rdparty/chromium -I../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src -fno-strict-aliasing --param=ssp-buffer-size=4 -fstack-protector -fno-unwind-tables -fno-asynchronous-unwind-tables -fPIC -pipe -pthread -m64 -O2 -fno-ident -fdata-sections -ffunction-sections -fno-omit-frame-pointer -g1 -fvisibility=hidden -Wno-unused-local-typedefs -Wno-maybe-uninitialized -Wno-deprecated-declarations -fno-delete-null-pointer-checks -Wno-comments -Wno-packed-not-aligned -Wno-dangling-else -Wno-missing-field-initializers -Wno-unused-parameter -std=gnu++14 -fno-exceptions -fno-rtti --sysroot=../../../../recipe-sysroot -fvisibility-inlines-hidden -Wno-narrowing -Wno-class-memaccess -Wno-attributes -Wno-class-memaccess -Wno-subobject-linkage -Wno-invalid-offsetof -Wno-return-type -Wno-deprecated-copy -c ../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc -o obj/third_party/breakpad/client/exception_handler.o +../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc: In function 'void google_breakpad::{anonymous}::InstallAlternateStackLocked()': +../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc:141:49: error: no matching function for call to 'max(int, long int)' + 141 | static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ); + | ~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from ../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/char_traits.h:39, + from ../../../../recipe-sysroot/usr/include/c++/11.2.0/string:40, + from ../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.h:38, + from ../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc:66: +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algobase.h:254:5: note: candidate: 'template constexpr const _Tp& std::max(const _Tp&, const _Tp&)' + 254 | max(const _Tp& __a, const _Tp& __b) + | ^~~ +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algobase.h:254:5: note: template argument deduction/substitution failed: +../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc:141:49: note: deduced conflicting types for parameter 'const _Tp' ('int' and 'long int') + 141 | static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ); + | ~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from ../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/char_traits.h:39, + from ../../../../recipe-sysroot/usr/include/c++/11.2.0/string:40, + from ../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.h:38, + from ../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc:66: +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algobase.h:300:5: note: candidate: 'template constexpr const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' + 300 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) + | ^~~ +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algobase.h:300:5: note: template argument deduction/substitution failed: +../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc:141:49: note: deduced conflicting types for parameter 'const _Tp' ('int' and 'long int') + 141 | static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ); + | ~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from ../../../../recipe-sysroot/usr/include/c++/11.2.0/algorithm:62, + from ../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc:85: +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algo.h:3461:5: note: candidate: 'template constexpr _Tp std::max(std::initializer_list<_Tp>)' + 3461 | max(initializer_list<_Tp> __l) + | ^~~ +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algo.h:3461:5: note: template argument deduction/substitution failed: +../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc:141:49: note: mismatched types 'std::initializer_list<_Tp>' and 'int' + 141 | static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ); + | ~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from ../../../../recipe-sysroot/usr/include/c++/11.2.0/algorithm:62, + from ../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc:85: +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algo.h:3467:5: note: candidate: 'template constexpr _Tp std::max(std::initializer_list<_Tp>, _Compare)' + 3467 | max(initializer_list<_Tp> __l, _Compare __comp) + | ^~~ +../../../../recipe-sysroot/usr/include/c++/11.2.0/bits/stl_algo.h:3467:5: note: template argument deduction/substitution failed: +../../../../git/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc:141:49: note: mismatched types 'std::initializer_list<_Tp>' and 'int' + 141 | static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ); + | ~~~~~~~~^~~~~~~~~~~~~~~~~ + +Signed-off-by: Martin Jansa +--- + .../breakpad/src/client/linux/handler/exception_handler.cc | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc b/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc +index ca353c40997..2e43ba6fc04 100644 +--- qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc ++++ qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc +@@ -138,7 +138,7 @@ void InstallAlternateStackLocked() { + // SIGSTKSZ may be too small to prevent the signal handlers from overrunning + // the alternative stack. Ensure that the size of the alternative stack is + // large enough. +- static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ); ++ static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ); + + // Only set an alternative stack if there isn't already one, or if the current + // one is too small. diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb index a9d014e9d75..e06fc4d90b9 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.5-GCCcore-11.3.0.eb @@ -20,14 +20,21 @@ patches = [ 'Qt5-5.13.1_fix-avx2.patch', 'Qt5-5.13.1_fix-qmake-libdir.patch', 'Qt5-5.14.1_fix-OF-Gentoo.patch', + 'Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch', + 'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch', 'Qt5-5.15.5_fix-qtwebegine-HarfBuzz-3.x.patch', ] checksums = [ - '5a97827bdf9fd515f43bc7651defaf64fecb7a55e051c79b8f80510d0e990f06', # qt-everywhere-opensource-src-5.15.5.tar.xz - '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch - '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch - '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch - '599cc94535dc276a5d97e002c81907c74ead9dc8d55f35567017fb7a491aaf01', # Qt5-5.15.5_fix-qtwebegine-HarfBuzz-3.x.patch + {'qt-everywhere-opensource-src-5.15.5.tar.xz': '5a97827bdf9fd515f43bc7651defaf64fecb7a55e051c79b8f80510d0e990f06'}, + {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, + {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, + {'Qt5-5.14.1_fix-OF-Gentoo.patch': '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa'}, + {'Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch': + 'f39506495b70cc0968fb7a5f4c9028b0f0a180c552906ff4e58e0bcae83cf187'}, + {'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch': + '74590de2b9e32f2c88123cb096c4f5c3001b00710aad096a4d16444a8e9eb991'}, + {'Qt5-5.15.5_fix-qtwebegine-HarfBuzz-3.x.patch': + '599cc94535dc276a5d97e002c81907c74ead9dc8d55f35567017fb7a491aaf01'}, ] builddependencies = [ From 4d0a597bae059ce0b4857e9bab05f207fe839cd8 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 20 Jan 2023 09:55:40 +0000 Subject: [PATCH 6258/9987] Update easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb Co-authored-by: Adam Huffman --- easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb index c6878c819f0..b371a39e876 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb @@ -11,7 +11,7 @@ description = """PyTables is a package for managing hierarchical datasets and de with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, - process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk + processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases.""" From 5a49df4d62bbf908378b25901b388e6a0fd96a89 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 20 Jan 2023 09:55:48 +0000 Subject: [PATCH 6259/9987] Update easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb Co-authored-by: Adam Huffman --- easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb index b371a39e876..d94495c10fa 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb @@ -10,7 +10,7 @@ homepage = 'https://www.pytables.org' description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical - parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing, processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases.""" From be07e0a88f5bab623193dc927b0f0c30dab4d801 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 20 Jan 2023 10:29:50 +0000 Subject: [PATCH 6260/9987] Fix long line after correcting description text --- .../easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb index d94495c10fa..a6378b7de69 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb @@ -11,9 +11,9 @@ description = """PyTables is a package for managing hierarchical datasets and de with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing, - processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and disk - resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as - relational or object oriented databases.""" + processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and + disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions + such as relational or object oriented databases.""" toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'usempi': True} From 6ba3c7cdb227cdae6860f7bb8a76bf42c13fab30 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 20 Jan 2023 11:09:26 +0000 Subject: [PATCH 6261/9987] enable slow scipy tests by default --- .../s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb index 7878162dce4..60102d5e86e 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb @@ -48,6 +48,7 @@ exts_list = [ 'checksums': ['702c2701187cfb38f66c0c20cc85d04d0e156d260a8d92892da65947faa5360e'], }), ('scipy', '1.10.0', { + 'enable_slow_tests': True, 'checksums': ['c8b3cbc636a87a89b770c6afc999baa6bcbb01691b5ccbbc1b1791c7c0a07540'], }), ('numexpr', '2.8.4', { From 4a66b8552732a6bfac0f65d73784671aba24e3ff Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 20 Jan 2023 11:34:40 +0000 Subject: [PATCH 6262/9987] revert unintentional changes introduced by --inject-checksums --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index 992bd1e8a53..b919e01925b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -138,6 +138,8 @@ exts_list = [ 'checksums': ['d8daccb14dc0eae1b6b6eb3ecef79675bd37b4065369f79c35393dd5c55652c7'], }), ('cryptography', '38.0.3', { + # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, + # see https://github.com/rust-lang/cargo/issues/6652 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['bfbe6ee19615b07a98b1d2287d6a6073f734735b49ee45b11324d85efc4d5cbd'], }), @@ -383,19 +385,19 @@ exts_list = [ 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], }), ('pastel', '0.2.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], }), ('crashtest', '0.3.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], }), ('clikit', '0.6.2', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], }), ('jeepney', '0.8.0', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], }), ('SecretStorage', '3.3.3', { @@ -413,7 +415,7 @@ exts_list = [ 'checksums': ['2ba3d56441ba0637f5f9c096068f67010ac0453f9d0b626de2aa3019353b6431'], }), ('tomlkit', '0.11.6', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b'], }), ('shellingham', '1.5.0', { @@ -429,7 +431,7 @@ exts_list = [ 'checksums': ['a84da4318dd86f870a9447a8c98340aa06216bfc6f2b7bdc4b8766984ae1867c'], }), ('ptyprocess', '0.7.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], }), ('pexpect', '4.8.0', { @@ -451,7 +453,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '1.0.0a5', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['ff53056589300976e960f75afb792dfbfc9c78dcbb5a448e207a17b643826360'], }), ('cachy', '0.3.0', { From c26e8a91508d5bdb741a57b90de1b031c0be2a20 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 20 Jan 2023 11:58:32 +0000 Subject: [PATCH 6263/9987] set ignore_test_result to False --- .../s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb index 60102d5e86e..ecbbf51d1e9 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb @@ -49,6 +49,7 @@ exts_list = [ }), ('scipy', '1.10.0', { 'enable_slow_tests': True, + 'ignore_test_result': False, 'checksums': ['c8b3cbc636a87a89b770c6afc999baa6bcbb01691b5ccbbc1b1791c7c0a07540'], }), ('numexpr', '2.8.4', { From ae5b4643245a4e403cdbea20d09cdbcd9a2539ad Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 20 Jan 2023 13:44:13 +0100 Subject: [PATCH 6264/9987] adding easyconfigs: SSW-1.2.4-GCCcore-10.3.0.eb and patches: SSW-1.2.4_build-cpp-lib.patch --- .../s/SSW/SSW-1.2.4-GCCcore-10.3.0.eb | 48 ++++++++++ .../s/SSW/SSW-1.2.4_build-cpp-lib.patch | 88 +++++++++++++++++++ 2 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/s/SSW/SSW-1.2.4-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/s/SSW/SSW-1.2.4_build-cpp-lib.patch diff --git a/easybuild/easyconfigs/s/SSW/SSW-1.2.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/SSW/SSW-1.2.4-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4323761d2bd --- /dev/null +++ b/easybuild/easyconfigs/s/SSW/SSW-1.2.4-GCCcore-10.3.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'SSW' +version = '1.2.4' + +homepage = 'https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library' +description = """SSW is a fast implementation of the Smith-Waterman algorithm, which uses the + Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the + instruction level. SSW library provides an API that can be flexibly used by programs written in + C, C++ and other languages. We also provide a software that can do protein and genome alignment + directly. Current version of our implementation is ~50 times faster than an ordinary + Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path + (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and + location heuristically. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.2.4_build-cpp-lib.patch'] +checksums = [ + 'a87b1904368bffe051ab6ea538543ec1520473a5d6d94204bd6fa8e39d0cf336', # v1.2.4.tar.gz + '1513b57036d671e84921c46f24699f9d4bfc8e587811498d72c19c64942320c5', # SSW-1.2.4_build-cpp-lib.patch +] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('zlib', '1.2.11')] + +start_dir = 'src' + +buildopts = 'default' + +files_to_copy = [ + (['ssw_test'], 'bin'), + (['*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/ssw'), +] + +sanity_check_paths = { + 'files': ['bin/ssw_test', 'lib/libssw.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SSW/SSW-1.2.4_build-cpp-lib.patch b/easybuild/easyconfigs/s/SSW/SSW-1.2.4_build-cpp-lib.patch new file mode 100644 index 00000000000..52132023a07 --- /dev/null +++ b/easybuild/easyconfigs/s/SSW/SSW-1.2.4_build-cpp-lib.patch @@ -0,0 +1,88 @@ +Patch created by Jasper Grimm (UoY) +Updated by Sebastien Moretti (SIB) +Fix typo (JAVA_INLCUDES -> JAVA_INCLUDES) +Build dynamic library as well as static +Add ssw_cpp.* to library targets +Respect CPPFLAGS +--- SSW.orig/src/Makefile 2022-05-23 16:00:57.000000000 +0200 ++++ SSW/src/Makefile 2022-11-09 12:12:46.526022508 +0100 +@@ -1,46 +1,49 @@ +-CC = gcc +-CXX = g++ +-CFLAGS += -Wall -pipe -O2 ++CC ?= gcc ++CXX ?= g++ ++#CFLAGS += -Wall -pipe -O2 + #CFLAGS += -Wall -pipe -g -fsanitize=address # for debug +-CXXFLAGS := $(CFLAGS) ++#CXXFLAGS := $(CFLAGS) + LOBJS = ssw.o + LCPPOBJS = ssw_cpp.o + PROG = ssw_test +-LIB = libssw.so ++SOVERSION = 0 ++LIB = libssw.so.$(SOVERSION) + EXAMPLE = example_c + EXAMPLE_CPP = example_cpp + JAVA_JAR = ssw.jar + JAVA_LIB = libsswjni.so +-JAVA_INLCUDES = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux ++JAVA_INCLUDES = -I"$(JAVA_HOME)/include" -I"$(JAVA_HOME)/include/linux" + JAVA_OBJ = ssw/Aligner.class ssw/Alignment.class ssw/Example.class + + .PHONY: all default java clean + +-default: $(PROG) $(EXAMPLE) $(EXAMPLE_CPP) $(LIB) ++default: $(PROG) $(EXAMPLE) $(EXAMPLE_CPP) $(LIB) + core: $(PROG) + java: java_home $(JAVA_JAR) $(JAVA_LIB) + all: default java + +-$(LIB): ssw.c ssw.h +- $(CC) $(CFLAGS) -fPIC -shared -rdynamic -o $@ $< ++$(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp ++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^ $(LDFLAGS) ++ ln -sf $(LIB) libssw.so + +-$(PROG): main.c kseq.h ++$(PROG): main.c kseq.h $(LIB) ++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ main.c kseq.h -L. -lssw -lm -lz $(LDFLAGS) + + $(EXAMPLE): example.c + + ifdef __arm__ # (M1) +-$(PROG) $(EXAMPLE): $(LOBJS) +- $(CC) -o $@ $(filter-out %.h,$^) $(CFLAGS) $(LDFLAGS) -lm -lz -march=armv8-a+fp+simd+crypto+crc ++$(EXAMPLE): $(LOBJS) ++ $(CC) -o $@ $(filter-out %.h,$^) $(CPPFLAGS) $(CFLAGS) -lm -lz $(LDFLAGS) -march=armv8-a+fp+simd+crypto+crc + else # x86(Intel) +-$(PROG) $(EXAMPLE): $(LOBJS) +- $(CC) -o $@ $(filter-out %.h,$^) $(CFLAGS) $(LDFLAGS) -lm -lz ++$(EXAMPLE): $(LOBJS) ++ $(CC) -o $@ $(filter-out %.h,$^) $(CPPFLAGS) $(CFLAGS) -lm -lz $(LDFLAGS) + endif + + $(EXAMPLE_CPP): example.cpp $(LOBJS) $(LCPPOBJS) +- $(CXX) -o $@ $^ $(CXXFLAGS) $(LDFLAGS) -lm -lz ++ $(CXX) -o $@ $^ $(CPPFLAGS) $(CXXFLAGS) -lm -lz $(LDFLAGS) + + $(JAVA_LIB): sswjni.c ssw.c ssw.h +- $(CC) $(CFLAGS) $(JAVA_INLCUDES) -fPIC -shared -rdynamic -o $@ $< ssw.c ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(JAVA_INCLUDES) -fPIC -shared -rdynamic -o $@ $< ssw.c $(LDFLAGS) + + $(JAVA_JAR): $(JAVA_OBJ) + jar cvfe $@ ssw.Example $^ +@@ -55,10 +58,10 @@ + endif + + ssw.o: ssw.c ssw.h +- $(CC) -c -o $@ $< $(CFLAGS) ++ $(CC) -c -o $@ $< $(CPPFLAGS) $(CFLAGS) + + ssw_cpp.o: ssw_cpp.cpp ssw_cpp.h ssw.h +- $(CXX) -c -o $@ $< $(CXXFLAGS) ++ $(CXX) -c -o $@ $< $(CPPFLAGS) $(CXXFLAGS) + + clean: +- -rm -f $(LOBJS) $(LCPPOBJS) $(PROG) $(LIB) $(EXAMPLE) $(EXAMPLE_CPP) $(JAVA_LIB) $(JAVA_JAR) $(JAVA_OBJ) *~ ++ -rm -f $(LOBJS) $(LCPPOBJS) $(PROG) $(LIB) $(EXAMPLE) $(EXAMPLE_CPP) $(JAVA_LIB) $(JAVA_JAR) $(JAVA_OBJ) *~ From 35fd64339d24ef001be22a25abf06e30d814b3f4 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 20 Jan 2023 13:52:52 +0100 Subject: [PATCH 6265/9987] Replace git checkout with a tarball download (see PR#16292) --- .../w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb index f4c078710de..139541b8bd1 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb @@ -14,17 +14,9 @@ uses the platform's native API rather than emulating the GUI.""" toolchain = {'name': 'GCC', 'version': '11.3.0'} toolchainopts = {'pic': True} -# wxWidgets now contain three submodules: catch, nanosvg and pcre -sources = [{ - 'git_config': { - 'url': 'https://github.com/wxWidgets/', - 'repo_name': 'wxWidgets', - 'tag': 'v%(version)s', - 'recursive': True, - }, - 'filename': SOURCE_TAR_GZ, -}] -checksums = [None] +source_urls = ['https://github.com/wxWidgets/wxWidgets/archive'] +sources = [SOURCE_TAR_BZ2] +checksums = ['c229976bb413eb88e45cb5dfb68b27890d450149c09b331abd751e7ae0f5fa66'] builddependencies = [ ('gettext', '0.21'), From 726623e851d08d4a22a589e52958e4107ac01118 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 20 Jan 2023 14:55:19 +0000 Subject: [PATCH 6266/9987] adding easyconfigs: DBCSR-2.5.0-foss-2021b.eb and patches: DBCSR-2.5.0_fix-cmake.patch --- .../d/DBCSR/DBCSR-2.5.0-foss-2021b.eb | 41 ++++++++++++ .../d/DBCSR/DBCSR-2.5.0_fix-cmake.patch | 62 +++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100755 easybuild/easyconfigs/d/DBCSR/DBCSR-2.5.0-foss-2021b.eb create mode 100755 easybuild/easyconfigs/d/DBCSR/DBCSR-2.5.0_fix-cmake.patch diff --git a/easybuild/easyconfigs/d/DBCSR/DBCSR-2.5.0-foss-2021b.eb b/easybuild/easyconfigs/d/DBCSR/DBCSR-2.5.0-foss-2021b.eb new file mode 100755 index 00000000000..c9cbb4090d8 --- /dev/null +++ b/easybuild/easyconfigs/d/DBCSR/DBCSR-2.5.0-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'DBCSR' +version = '2.5.0' + +homepage = 'https://cp2k.github.io/dbcsr/develop/' +description = """DBCSR stands for Distributed Blocked Compressed Sparse Row. DBCSR is a library designed to + efficiently perform sparse matrix-matrix multiplication, among other operations.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/cp2k/dbcsr/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix-cmake.patch'] +checksums = [ + {'dbcsr-2.5.0.tar.gz': '91fda9b2502e5d0a2a6cdd5a73ef096253cc7e75bd01ba5189a4726ad86aef08'}, + {'DBCSR-2.5.0_fix-cmake.patch': 'ccb9ba93dd5bd3107a3d1c190ec8b0d8af4e2df553b31dd7b224507220823dc9'}, +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libxsmm', '1.17'), + ('Python', '3.9.6'), +] + +preconfigopts = 'export PKG_CONFIG_PATH="${PKG_CONFIG_PATH}:${EBROOTLIBXSMM}/lib" && ' +configopts = '-DUSE_SMM=libxsmm-shared -DBLA_VENDOR=FlexiBLAS' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['include/dbcsr_tensor_api.mod', 'include/dbcsr.h', 'lib/libdbcsr.a'], + 'dirs': ['lib/cmake/dbcsr'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DBCSR/DBCSR-2.5.0_fix-cmake.patch b/easybuild/easyconfigs/d/DBCSR/DBCSR-2.5.0_fix-cmake.patch new file mode 100755 index 00000000000..4711b97fb06 --- /dev/null +++ b/easybuild/easyconfigs/d/DBCSR/DBCSR-2.5.0_fix-cmake.patch @@ -0,0 +1,62 @@ +Fix finding of BLAS/LAPACK libraries and add libxsmm include directory +Patch by Simon Branford (University of Birmingham) +--- cmake/FindBLAS.cmake.orig 2023-01-16 20:06:01.198294000 +0000 ++++ cmake/FindBLAS.cmake 2023-01-16 20:15:19.521389856 +0000 +@@ -536,6 +536,22 @@ + endif() + endif() + ++# FlexiBLAS (https://github.com/mpimd-csc/flexiblas) ++if (BLA_VENDOR STREQUAL "FlexiBLAS" OR BLA_VENDOR STREQUAL "All") ++ if(NOT BLAS_LIBRARIES) ++ check_blas_libraries( ++ BLAS_LIBRARIES ++ BLAS ++ sgemm ++ "" ++ "flexiblas" ++ "" ++ "" ++ "" ++ ) ++ endif() ++endif () ++ + # OpenBLAS? (http://www.openblas.net) + if(BLA_VENDOR STREQUAL "OpenBLAS" OR BLA_VENDOR STREQUAL "All") + if(NOT BLAS_LIBRARIES) +--- cmake/FindLAPACK.cmake.orig 2023-01-16 20:05:47.292543000 +0000 ++++ cmake/FindLAPACK.cmake 2023-01-16 20:16:11.193167061 +0000 +@@ -346,6 +346,22 @@ + endif() + endif() + ++ if(BLA_VENDOR STREQUAL "FlexiBLAS" OR BLA_VENDOR STREQUAL "All") ++ if(NOT LAPACK_LIBRARIES) ++ check_lapack_libraries( ++ LAPACK_LIBRARIES ++ LAPACK ++ cheev ++ "" ++ "flexiblas" ++ "" ++ "" ++ "" ++ "${BLAS_LIBRARIES}" ++ ) ++ endif() ++ endif() ++ + # OpenBLAS? (http://www.openblas.net) + if(BLA_VENDOR STREQUAL "OpenBLAS" OR BLA_VENDOR STREQUAL "All") + if(NOT LAPACK_LIBRARIES) +--- CMakeLists.txt.orig 2023-01-16 20:08:49.531879436 +0000 ++++ CMakeLists.txt 2023-01-16 20:08:25.968847202 +0000 +@@ -158,6 +158,7 @@ + pkg_check_modules(LIBXSMM REQUIRED IMPORTED_TARGET GLOBAL libxsmmf) + endif () + endif () ++include_directories("$ENV{EBROOTLIBXSMM}/include") + + # =================================== BLAS & LAPACK, PkgConfig + find_package(LAPACK REQUIRED) # needed for some of the integrated test routines, From eba3220394a3d290ec35dba64ac9b83118d073c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Jan 2023 12:45:30 +0100 Subject: [PATCH 6267/9987] use GitHub release source URL for wxWidgets 3.2.1 Co-authored-by: Sam Moors --- .../easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb index 139541b8bd1..b8451ed12b7 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.1-GCC-11.3.0.eb @@ -14,7 +14,8 @@ uses the platform's native API rather than emulating the GUI.""" toolchain = {'name': 'GCC', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://github.com/wxWidgets/wxWidgets/archive'] +github_account = 'wxWidgets' +source_urls = [GITHUB_RELEASE] sources = [SOURCE_TAR_BZ2] checksums = ['c229976bb413eb88e45cb5dfb68b27890d450149c09b331abd751e7ae0f5fa66'] From 64da59449f38d9eece77fc698d52a21c46147f92 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 21 Jan 2023 17:46:32 +0100 Subject: [PATCH 6268/9987] {toolchain} intel/2022.12 (intel-compilers 2023.0.0 + impi 2021.8.0 + imkl 2023.0.0) --- .../h/HPL/HPL-2.3-intel-2022.12.eb | 21 ++++++++++++ .../easyconfigs/i/iimpi/iimpi-2022.12.eb | 18 ++++++++++ .../imkl-FFTW-2023.0.0-iimpi-2022.12.eb | 11 +++++++ easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb | 18 ++++++++++ .../impi-2021.8.0-intel-compilers-2023.0.0.eb | 16 +++++++++ .../intel-compilers-2023.0.0.eb | 33 +++++++++++++++++++ .../easyconfigs/i/intel/intel-2022.12.eb | 22 +++++++++++++ 7 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.12.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022.12.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.0.0-iimpi-2022.12.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2022.12.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.12.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.12.eb new file mode 100644 index 00000000000..b2d20c3f790 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.12.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022.12'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022.12.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022.12.eb new file mode 100644 index 00000000000..eb3bcfddd79 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022.12.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022.12' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2023.0.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.8.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.0.0-iimpi-2022.12.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.0.0-iimpi-2022.12.eb new file mode 100644 index 00000000000..b7a82175d15 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.0.0-iimpi-2022.12.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2023.0.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022.12'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb new file mode 100644 index 00000000000..4e6e5afb344 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.0.0.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2023.0.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19138/'] +sources = ['l_onemkl_p_%(version)s.25398_offline.sh'] +checksums = ['0d61188e91a57bdb575782eb47a05ae99ea8eebefee6b2dfe20c6708e16e9927'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb new file mode 100644 index 00000000000..86153bb28f5 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.8.0-intel-compilers-2023.0.0.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.8.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2023.0.0'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19131/'] +sources = ['l_mpi_oneapi_p_%(version)s.25329_offline.sh'] +checksums = ['0fcb1171fc42fd4b2d863ae474c0b0f656b0fa1fdc1df435aa851ccd6d1eaaf7'] + +dependencies = [('UCX', '1.13.1')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb new file mode 100644 index 00000000000..8d97d1ec3e5 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.0.0.eb @@ -0,0 +1,33 @@ +name = 'intel-compilers' +version = '2023.0.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19123/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.25393_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19105/'], + 'filename': 'l_fortran-compiler_p_%(version)s.25394_offline.sh', + }, +] +checksums = [ + {'l_dpcpp-cpp-compiler_p_2023.0.0.25393_offline.sh': + '473eb019282c2735d65c6058f6890e60b79a5698ae18d2c1e4489fed8dd18a02'}, + {'l_fortran-compiler_p_2023.0.0.25394_offline.sh': + 'fd7525bf90646c8e43721e138f29c9c6f99e96dfe5648c13633f30ec64ac8b1b'}, +] + +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2022.12.eb b/easybuild/easyconfigs/i/intel/intel-2022.12.eb new file mode 100644 index 00000000000..d93caf59b40 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022.12.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022.12' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2023.0.0' +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.8.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From b985eb933947151a5be42fbac920927ecbe5c541 Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 23 Jan 2023 11:17:56 +0100 Subject: [PATCH 6269/9987] adding easyconfigs: Scalasca-2.6.1-gompi-2022a.eb --- .../s/Scalasca/Scalasca-2.6.1-gompi-2022a.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2022a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2022a.eb new file mode 100644 index 00000000000..0169c602509 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.6.1-gompi-2022a.eb @@ -0,0 +1,52 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'Scalasca' +version = '2.6.1' + +homepage = 'https://www.scalasca.org/' +description = """ + Scalasca is a software tool that supports the performance optimization of + parallel programs by measuring and analyzing their runtime behavior. The + analysis identifies potential performance bottlenecks -- in particular + those concerning communication and synchronization -- and offers guidance + in exploring their causes. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a0dbc3de82a6c0fe598de9e340513cff2882c199410a632d3a7f073ba921c7e7'] + +builddependencies = [ + ('CubeWriter', '4.8'), +] + +dependencies = [ + ('CubeGUI', '4.8'), + ('CubeLib', '4.8'), + ('OTF2', '3.0.2'), + ('Score-P', '8.0'), +] + +sanity_check_paths = { + 'files': ['bin/scalasca', 'lib/libpearl.replay.a'], + 'dirs': [], +} + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scalasca/patterns'} + +moduleclass = 'perf' From aa389791e1942344294d7a0bbf118c03d93c8335 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 23 Jan 2023 12:40:04 +0000 Subject: [PATCH 6270/9987] Add Heap::Fibonacci extension, also required by Roary --- easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb index a203ac26a52..c4e38476dbd 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb @@ -1772,6 +1772,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], }), + ('Heap::Fibonacci', '0.80', { + 'source_tmpl': 'Heap-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], + 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 22541fbd01f..f8a9806e7a3 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1824,6 +1824,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], }), + ('Heap::Fibonacci', '0.80', { + 'source_tmpl': 'Heap-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], + 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], + }), ] moduleclass = 'lang' From d6c8243c4000f49a0c8acc4774fbd2ff5971367e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 23 Jan 2023 14:47:12 +0100 Subject: [PATCH 6271/9987] remove dependency on Pillow from scikit-bio v0.5.7 --- .../easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb | 1 - .../easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb index 7ce9ef45be9..aeec62fa9dd 100644 --- a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb @@ -16,7 +16,6 @@ dependencies = [ ('scikit-learn', '0.23.2'), ('IPython', '7.18.1'), ('h5py', '3.1.0'), - ('Pillow', '8.0.1'), ] use_pip = True diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb index 8c60a0e7d9f..1365615d43b 100644 --- a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb @@ -16,7 +16,6 @@ dependencies = [ ('scikit-learn', '1.1.2'), ('IPython', '8.5.0'), ('h5py', '3.7.0'), - ('Pillow', '9.1.1'), ] use_pip = True From 2e679a42270694697f97c8b71e1774eda9d22d2c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 23 Jan 2023 14:32:21 +0000 Subject: [PATCH 6272/9987] adding easyconfigs: parasail-2.6-GCC-11.3.0.eb, python-parasail-1.3.3-foss-2022a.eb --- .../p/parasail/parasail-2.6-GCC-11.3.0.eb | 27 ++++++++++++++++ .../python-parasail-1.3.3-foss-2022a.eb | 32 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100755 easybuild/easyconfigs/p/parasail/parasail-2.6-GCC-11.3.0.eb create mode 100755 easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.6-GCC-11.3.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.6-GCC-11.3.0.eb new file mode 100755 index 00000000000..e613ae5ca19 --- /dev/null +++ b/easybuild/easyconfigs/p/parasail/parasail-2.6-GCC-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'parasail' +version = '2.6' + +homepage = 'https://github.com/jeffdaily/parasail' +description = """parasail is a SIMD C (C99) library containing implementations + of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global + pairwise sequence alignment algorithms. """ + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +# https://github.com/jeffdaily/parasail +github_account = 'jeffdaily' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f175923063547a9c2ca65254bca0745d5d2398216dab7dd937c912a790c98b2f'] + +builddependencies = [('CMake', '3.23.1')] + +sanity_check_paths = { + 'files': ['bin/parasail_aligner', 'bin/parasail_stats', + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.3-foss-2022a.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.3-foss-2022a.eb new file mode 100755 index 00000000000..42d5f17c07c --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.3-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.3.3' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['06f05066d9cf624c0b043f51a1e9d2964154e1edd0f9843e0838f32073e576f8'] + +builddependencies = [ + ('parasail', '2.6'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' From b6f194ff83e55d6fdc300182afd5b78e085dffe5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 23 Jan 2023 14:47:01 +0000 Subject: [PATCH 6273/9987] adding easyconfigs: Pysam-0.20.0-GCC-11.3.0.eb --- .../p/Pysam/Pysam-0.20.0-GCC-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100755 easybuild/easyconfigs/p/Pysam/Pysam-0.20.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.20.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.20.0-GCC-11.3.0.eb new file mode 100755 index 00000000000..3420c765f84 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.20.0-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.20.0' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5a25d95b986c2cb9f5040b9df4e1d93ce9a8bc3af5a956b1317416ed05269f60'] + +dependencies = [ + ('Python', '3.10.4'), + ('ncurses', '6.3'), + ('cURL', '7.83.0'), + ('XZ', '5.2.5'), +] + +# https://github.com/pysam-developers/pysam/issues/1146#issuecomment-1309421979 +preinstallopts = """export CFLAGS="-fPIC $CFLAGS" && """ +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' From d3e4378fff9aa026728f5e22af1f89f90e439713 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 23 Jan 2023 16:03:27 +0100 Subject: [PATCH 6274/9987] adding easyconfigs: IRkernel-1.3.2-foss-2022a-R-4.2.1.eb --- .../IRkernel-1.3.2-foss-2022a-R-4.2.1.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/i/IRkernel/IRkernel-1.3.2-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.3.2-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.3.2-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..1e1a3e3a625 --- /dev/null +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.3.2-foss-2022a-R-4.2.1.eb @@ -0,0 +1,69 @@ +easyblock = 'Bundle' + +name = 'IRkernel' +version = '1.3.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://irkernel.github.io' +description = """The R kernel for the 'Jupyter' environment executes R code + which the front-end (Jupyter Notebook or other front-ends) submits to the + kernel via the network.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('ZeroMQ', '4.3.4'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.rstudio.com/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('repr', '1.1.5', { + 'checksums': ['8cc9071446553affbdf58f9106f34c409d797cbda20b3cdf6b95350dd2095efa'], + }), + ('IRdisplay', '1.1', { + 'checksums': ['83eb030ff91f546cb647899f8aa3f5dc9fe163a89a981696447ea49cc98e8d2b'], + }), + ('pbdZMQ', '0.3-9', { + 'checksums': ['d033238d0a9810581f6b40c7c75263cfc495a585653bbff98e957c37954e0fb6'], + }), + (name, version, { + 'checksums': ['e1c6d8bddc23e5039dd9c537feb371f937d60028fb753b90345698c58ae424a6'], + }), +] + +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} + +# IPython notebook looks for the json kernel file in kernels/IRkernel +# We start the kernel with default bitmapType 'cairo'. This is a more sensible default +# for headless nodes. See https://github.com/IRkernel/IRkernel/issues/388 +local_kerneldir = '%(installdir)s/IRkernel' +postinstallcmds = [ + 'mkdir -p %s/kernels/ir' % local_kerneldir, + 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir), + ('sed -i \'s/"IRkernel::main()"/"options(bitmapType=\\x27cairo\\x27); IRkernel::main()"/g\'' + ' %s/kernels/ir/kernel.json') % local_kerneldir +] + +sanity_check_paths = { + 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], + 'dirs': [name], +} + +moduleclass = 'tools' From 60c370acef434202b5df781bba0a3ad7e9ba94df Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Jan 2023 17:09:32 +0100 Subject: [PATCH 6275/9987] add exception for (indirect) ncbi-vdb 3.0.0 dependency variant for finder 1.1.0 (via SRA-toolkit 3.0.0) --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 5ac2b1e77c5..90f5c25f95e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -538,8 +538,8 @@ def check_dep_vars(self, gen, dep, dep_vars): # SimpleITK 2.1.0 requires Lua 5.3.x, MedPy and nnU-Net depend on SimpleITK (r'5\.3\.5', [r'nnU-Net-1\.7\.0-', r'MedPy-0\.4\.0-', r'SimpleITK-2\.1\.0-']), ], - # SRA-toolkit 3.0.0 requires ncbi-vdb 3.0.0 - 'ncbi-vdb': [(r'3\.0\.0', [r'SRA-Toolkit-3\.0\.0'])], + # SRA-toolkit 3.0.0 requires ncbi-vdb 3.0.0, Finder requires SRA-Toolkit 3.0.0 + 'ncbi-vdb': [(r'3\.0\.0', [r'SRA-Toolkit-3\.0\.0', r'finder-1\.1\.0'])], # TensorFlow 2.5+ requires a more recent NCCL than version 2.4.8 used in 2019b generation; # Horovod depends on TensorFlow, so same exception required there 'NCCL': [(r'2\.11\.4', [r'TensorFlow-2\.[5-9]\.', r'Horovod-0\.2[2-9]'])], From 05ffb5c77fb105767d16e6be735d03c90a985bdc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Jan 2023 17:41:10 +0100 Subject: [PATCH 6276/9987] prefer single quotes over double quotes for string values without spaces in finder easyconfig --- .../f/finder/finder-1.1.0-foss-2021b.eb | 64 +++++++++---------- 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb index 14a7e352b54..8cf70e725c4 100644 --- a/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/f/finder/finder-1.1.0-foss-2021b.eb @@ -1,15 +1,15 @@ # author: Denis Kristak (INUITS) -easyblock = "Binary" +easyblock = 'Binary' -name = "finder" -version = "1.1.0" +name = 'finder' +version = '1.1.0' -homepage = "https://github.com/sagnikbanerjee15/Finder/" +homepage = 'https://github.com/sagnikbanerjee15/Finder/' description = """finder is a gene annotator pipeline which automates the process of downloading short reads, aligning them and using the assembled transcripts to generate gene annotations.""" -toolchain = {"name": "foss", "version": "2021b"} -toolchainopts = {"openmp": True} +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True} source_urls = [ 'https://github.com/sagnikbanerjee15/Finder/archive/', @@ -25,30 +25,30 @@ checksums = [ ] dependencies = [ - ("STAR", "2.7.9a"), - ("SAMtools", "1.14"), - ("BEDTools", "2.30.0"), - ("AUGUSTUS", "3.4.0"), - ("BRAKER", "2.1.6"), - ("GeneMark-ET", "4.71"), - ("PsiCLASS", "1.0.3"), - ("olego", "1.1.9"), - ("GUSHR", "2020-09-28"), - ("gffread", "0.12.7"), - ("BEDOPS", "2.4.41"), - ("RegTools", "0.5.2"), - ("BLAST+", "2.12.0"), - ("CodAn", "1.2"), - ("GffCompare", "0.12.6"), - ("XZ", "5.2.5"), - ("bzip2", "1.0.8"), - ("Autotools", "20210726"), - ("Python", "3.9.6"), - ("SciPy-bundle", "2021.10"), - ("Trimmomatic", "0.39", "-Java-11", SYSTEM), - ("Boost", "1.77.0"), - ("ruffus", "2.8.4"), - ("SRA-Toolkit", "3.0.0"), + ('STAR', '2.7.9a'), + ('SAMtools', '1.14'), + ('BEDTools', '2.30.0'), + ('AUGUSTUS', '3.4.0'), + ('BRAKER', '2.1.6'), + ('GeneMark-ET', '4.71'), + ('PsiCLASS', '1.0.3'), + ('olego', '1.1.9'), + ('GUSHR', '2020-09-28'), + ('gffread', '0.12.7'), + ('BEDOPS', '2.4.41'), + ('RegTools', '0.5.2'), + ('BLAST+', '2.12.0'), + ('CodAn', '1.2'), + ('GffCompare', '0.12.6'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), + ('Autotools', '20210726'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Trimmomatic', '0.39', '-Java-11', SYSTEM), + ('Boost', '1.77.0'), + ('ruffus', '2.8.4'), + ('SRA-Toolkit', '3.0.0'), ] extract_sources = True @@ -57,7 +57,7 @@ install_cmd = "cp -r %(builddir)s/Finder-finder_v%(version)s/* %(installdir)s/ " sanity_check_paths = { - "files": ["run_finder"], + 'files': ['run_finder'], "dirs": [], } @@ -67,4 +67,4 @@ modextrapaths = { sanity_check_commands = ["finder --help"] -moduleclass = "bio" +moduleclass = 'bio' From 7feca8716b69aa479731c5c44ae129e02b5796ae Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 23 Jan 2023 18:47:48 +0100 Subject: [PATCH 6277/9987] adding easyconfigs: Brotli-python-1.0.9-GCCcore-11.3.0.eb, Brotli-python-1.0.9-GCCcore-12.2.0.eb --- .../Brotli-python-1.0.9-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ .../Brotli-python-1.0.9-GCCcore-12.2.0.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e4531099b13 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Brotli-python' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/B/Brotli'] +sources = ['Brotli-%(version)s.zip'] +checksums = ['4d1b810aa0ed773f81dceda2cc7b403d01057458730e309856356d4ef4188438'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'brotli'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..75f8c2716a7 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Brotli-python' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/B/Brotli'] +sources = ['Brotli-%(version)s.zip'] +checksums = ['4d1b810aa0ed773f81dceda2cc7b403d01057458730e309856356d4ef4188438'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'brotli'} + +moduleclass = 'tools' From 5e5882fbb69c22e3c7409bf1ef27d38576ce8b3e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 23 Jan 2023 19:13:29 +0100 Subject: [PATCH 6278/9987] Brotli-python-1.0.9-GCCcore-10.2.0.eb --- .../Brotli-python-1.0.9-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b08a96811d5 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.0.9-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Brotli-python' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/B/Brotli'] +sources = ['Brotli-%(version)s.zip'] +checksums = ['4d1b810aa0ed773f81dceda2cc7b403d01057458730e309856356d4ef4188438'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'brotli'} + +moduleclass = 'tools' From 4e5fa93990eabf875fee0e47d6e47f9a3bcea950 Mon Sep 17 00:00:00 2001 From: VictorGoitea Date: Mon, 23 Jan 2023 20:13:42 +0100 Subject: [PATCH 6279/9987] Easyconfig file for sradownloader --- .../SRAdownloader-3.9-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRAdownloader/SRAdownloader-3.9-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SRAdownloader/SRAdownloader-3.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SRAdownloader/SRAdownloader-3.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..99c70182524 --- /dev/null +++ b/easybuild/easyconfigs/s/SRAdownloader/SRAdownloader-3.9-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'Tarball' + +name = 'sradownloader' +version = '3.9' + +homepage = "https://github.com/s-andrews/sradownloader" +description = """SRAdownloader takes the annotation table from the SRA run selector tool +and retrives the raw fastq files for the selected samples""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/s-andrews/sradownloader/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dee44a8476fc11d3306019fe608295fc3b19f0c0073061ef71f1c0101dc587cc'] + +dependencies = [ + ('Python', '3.10.4'), +] + +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ['sradownloader'], + 'dirs': [], +} + +sanity_check_commands = [ + 'sradownloader -h', + 'sradownloader --version' +] + +moduleclass = 'bio' \ No newline at end of file From 9545741d0b076e2aa5a14a24c3954705ad59c6f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Jan 2023 11:49:07 +0100 Subject: [PATCH 6280/9987] adding easyconfigs: rmarkdown-2.20-foss-2021a-R-4.1.0.eb --- .../rmarkdown-2.20-foss-2021a-R-4.1.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/rmarkdown/rmarkdown-2.20-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/r/rmarkdown/rmarkdown-2.20-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/r/rmarkdown/rmarkdown-2.20-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..70a043c2405 --- /dev/null +++ b/easybuild/easyconfigs/r/rmarkdown/rmarkdown-2.20-foss-2021a-R-4.1.0.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'rmarkdown' +version = '2.20' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rmarkdown' +description = "Convert R Markdown documents into a variety of formats." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['d7f7059bfcb43e4b92432d69ba0e0c74ad10a20f153689262a3e848adb60159d'] + +dependencies = [ + ('R', '4.1.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From 1d1afb493e82b907df64093e36d460ca2e5f4664 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 24 Jan 2023 13:17:22 +0100 Subject: [PATCH 6281/9987] Don't build the python bindings --- easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb index f70ecde5774..28274b11f14 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb @@ -38,7 +38,8 @@ dependencies = [ ('ncurses', '6.3'), ('GMP', '6.2.1'), ('Z3', '4.10.2'), - ('Python', '3.10.4'), + # Including Python bindings would require this dep + # ('Python', '3.10.4'), ] # enabling RTTI makes the flang compiler need to link to libc++ so instead of @@ -48,7 +49,7 @@ dependencies = [ enable_rtti = False assertions = True -python_bindings = True +python_bindings = False skip_all_tests = True llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] From 3de73e5e08e82dd578863603889d4bd2ed8c48ba Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 24 Jan 2023 12:27:34 +0000 Subject: [PATCH 6282/9987] adding easyconfigs: Armadillo-11.4.3-foss-2022b.eb, arpack-ng-3.8.0-foss-2022b.eb --- .../Armadillo/Armadillo-11.4.3-foss-2022b.eb | 22 ++++++++++++ .../a/arpack-ng/arpack-ng-3.8.0-foss-2022b.eb | 35 +++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb new file mode 100644 index 00000000000..9e92946642a --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb @@ -0,0 +1,22 @@ +name = 'Armadillo' +version = '11.4.3' + +homepage = 'http://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['87603263664988af41da2ca4f36205e36ea47a9281fa6cfd463115f3797a1da2'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Boost', '1.81.0'), + ('arpack-ng', '3.8.0'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022b.eb new file mode 100644 index 00000000000..2cfbadb05b1 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022b.eb @@ -0,0 +1,35 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.8.0' + +homepage = 'https://github.com/opencollab/arpack-ng' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'opencollab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['ada5aeb3878874383307239c9235b716a8a170c6d096a6625bfd529844df003d'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), + ('Eigen', '3.4.0') +] + +preconfigopts = "sh bootstrap && " +configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ['lib64/libarpack.la', 'lib64/libarpack.%s' % SHLIB_EXT, + 'lib64/libparpack.la', 'lib64/libparpack.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' From b980901a7c4670773dee97cb899e240416820e1c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 24 Jan 2023 12:28:35 +0000 Subject: [PATCH 6283/9987] adding easyconfigs: OpenEXR-3.1.5-GCCcore-12.2.0.eb, Imath-3.1.6-GCCcore-12.2.0.eb, Xerces-C++-3.2.4-GCCcore-12.2.0.eb, json-c-0.16-GCCcore-12.2.0.eb --- .../i/Imath/Imath-3.1.6-GCCcore-12.2.0.eb | 28 +++++++++++++ .../j/json-c/json-c-0.16-GCCcore-12.2.0.eb | 32 +++++++++++++++ .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-12.2.0.eb | 38 ++++++++++++++++++ .../Xerces-C++-3.2.4-GCCcore-12.2.0.eb | 39 +++++++++++++++++++ 4 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/i/Imath/Imath-3.1.6-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.6-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ea408912dc7 --- /dev/null +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.6-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Imath' +version = '3.1.6' + +homepage = 'https://imath.readthedocs.io/en/latest/' +description = """ +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ea5592230f5ab917bea3ceab266cf38eb4aa4a523078d46eac0f5a89c52304db'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['lib/libImath.%s' % SHLIB_EXT], + 'dirs': ['include/Imath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..82ffdd9d1ab --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.16' +local_suff = '-20220414' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['3ecaeedffd99a60b1262819f9e60d7d983844073abc74e495cb822b251904185'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..51ef158f691 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.5' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] +dependencies = [ + ('Imath', '3.1.6'), + ('zlib', '1.2.12') +] + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..67dd4f72614 --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Xerces-C++' +version = '3.2.4' + +homepage = 'https://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['3d8ec1c7f94e38fee0e4ca5ad1e1d9db23cbf3a10bba626f6b4afa2dedafe5ab'] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('cURL', '7.86.0'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/XInclude', + 'include/xercesc/xinclude/XIncludeUtils.hpp', + 'lib/libxerces-c-3.2.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' From 6b0e8205744248d602b730dba90edcb76b8be781 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 24 Jan 2023 12:29:01 +0000 Subject: [PATCH 6284/9987] adding easyconfigs: Brunsli-0.1-GCCcore-12.2.0.eb, CFITSIO-4.2.0-GCCcore-12.2.0.eb, giflib-5.2.1-GCCcore-12.2.0.eb, googletest-1.13.0-GCCcore-12.2.0.eb, Highway-1.0.3-GCCcore-12.2.0.eb --- .../b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb | 50 +++++++++++++++++++ .../c/CFITSIO/CFITSIO-4.2.0-GCCcore-12.2.0.eb | 41 +++++++++++++++ .../g/giflib/giflib-5.2.1-GCCcore-12.2.0.eb | 28 +++++++++++ .../googletest-1.13.0-GCCcore-12.2.0.eb | 28 +++++++++++ .../h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb | 32 ++++++++++++ 5 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.2.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..68552f70d3a --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '1.0.3'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib*/", + "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.2.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..bc70ab6cf40 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.2.0-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '4.2.0' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-3.48_install_test_data.patch'] +checksums = [ + {'cfitsio-4.2.0.tar.gz': 'eba53d1b3f6e345632bb09a7b752ec7ced3d63ec5153a848380f3880c5d61889'}, + {'CFITSIO-3.48_install_test_data.patch': 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c'}, +] + +builddependencies = [('binutils', '2.39')] + +# curl for HTTPs support +dependencies = [('cURL', '7.86.0')] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = '&& make shared && make testprog' + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + ('cd %(installdir)s/share && testprog'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e3089e87fd4 --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.1' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..61c4e58620f --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.13.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/google/googletest/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ad7fdba11ea011c1d925b3289cf4af2c66a352e18d4c7264392fead75e919363'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..513c9b6faf3 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Highway' +version = '1.0.3' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['566fc77315878473d9a6bd815f7de78c73734acdcb745c3dde8579560ac5440e'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('googletest', '1.13.0'), +] + +configopts = "-DHWY_SYSTEM_GTEST=ON" + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' From 66d714bb22b48bae8e980f8daf08b5a59fd5495f Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 24 Jan 2023 12:37:47 +0000 Subject: [PATCH 6285/9987] adding easyconfigs: LERC-4.0.0-GCCcore-12.2.0.eb, Qhull-2020.2-GCCcore-12.2.0.eb --- .../l/LERC/LERC-4.0.0-GCCcore-12.2.0.eb | 39 ++++++++++++++++++ .../q/Qhull/Qhull-2020.2-GCCcore-12.2.0.eb | 40 +++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6c38a24f2d4 --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'LERC' +version = '4.0.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/Esri/lerc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91431c2b16d0e3de6cbaea188603359f87caed08259a645fd5a3805784ee30a0'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +postinstallcmds = [ + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/test.c", +] + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cd %(builddir)s && g++ %(installdir)s/test.c -o lerctest -lLerc && ./lerctest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..08814cad379 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' From 356110a206a1dcef8d506f1a7ce5f87dc8e969fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Jan 2023 14:43:26 +0100 Subject: [PATCH 6286/9987] adding easyconfigs: kineto-0.4.0-GCC-11.3.0.eb --- .../k/kineto/kineto-0.4.0-GCC-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..e5f01bd68ee --- /dev/null +++ b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'kineto' +version = '0.4.0' + +homepage = 'https://github.com/pytorch/kineto' +description = "A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/pytorch/kineto/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +start_dir = 'libkineto' + +sanity_check_paths = { + 'files': ['lib/libkineto.a'], + 'dirs': ['include/kineto'], +} + +moduleclass = 'perf' From 242e9804ef8145c0bd78f8bd0592f956f1a15436 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Jan 2023 15:22:35 +0100 Subject: [PATCH 6287/9987] {bio}[foss/2022a] dorado v0.1.1 w/ CUDA 11.7.0 --- .../dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..0626f3d8698 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.1.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/%(name)s/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), + ('HDF5', '1.12.2'), + ('zstd', '1.5.2'), + ('HTSlib', '1.15.1'), + ('kineto', '0.4.0'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " + +configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " +configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " +configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib -DHTSLIB_LIBRARIES=hts " + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' From 44d1800c0df6705d962b5abd8e1b2b4c7deff06d Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 24 Jan 2023 16:18:06 +0100 Subject: [PATCH 6288/9987] Python is still required as a build dep ...even when not using bindings --- easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb index 28274b11f14..dea2f244ad3 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb @@ -29,6 +29,8 @@ builddependencies = [ ('CMake', '3.23.1'), ('Perl', '5.34.1'), ('elfutils', '0.187'), + # Including Python bindings would require this as a runtime dep + ('Python', '3.10.4'), ] dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too @@ -38,8 +40,6 @@ dependencies = [ ('ncurses', '6.3'), ('GMP', '6.2.1'), ('Z3', '4.10.2'), - # Including Python bindings would require this dep - # ('Python', '3.10.4'), ] # enabling RTTI makes the flang compiler need to link to libc++ so instead of From 4c2dacfc69f3812529a8e6330d97903ec98a2bde Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 24 Jan 2023 15:18:48 +0000 Subject: [PATCH 6289/9987] set toolchainopt 'pic' to True --- easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb index 5c3b2fbee0c..42a88ada5cc 100644 --- a/easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.11.1-GCC-12.2.0.eb @@ -7,6 +7,7 @@ homepage = 'https://trac.osgeo.org/geos' description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} source_urls = ['https://download.osgeo.org/geos/'] sources = [SOURCELOWER_TAR_BZ2] From e12cd2931991e372abdd0b2a4f45bf566f83e3ce Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 24 Jan 2023 15:20:22 +0000 Subject: [PATCH 6290/9987] use existing googletest 1.12.1 instead --- .../googletest-1.13.0-GCCcore-12.2.0.eb | 28 ------------------- .../h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb | 2 +- 2 files changed, 1 insertion(+), 29 deletions(-) delete mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.2.0.eb deleted file mode 100644 index 61c4e58620f..00000000000 --- a/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.2.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'googletest' -version = '1.13.0' - -homepage = 'https://github.com/google/googletest' -description = "Google's framework for writing C++ tests on a variety of platforms" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -source_urls = ['https://github.com/google/googletest/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['ad7fdba11ea011c1d925b3289cf4af2c66a352e18d4c7264392fead75e919363'] - -builddependencies = [ - ('binutils', '2.39'), - ('CMake', '3.24.3'), -] -# build twice, once for static, once for shared libraries -configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] - -sanity_check_paths = { - 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] - for local_ext in ['a', SHLIB_EXT]], - 'dirs': ['include/gmock', 'include/gtest'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb index 513c9b6faf3..f1833e66b17 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-12.2.0.eb @@ -17,7 +17,7 @@ checksums = ['566fc77315878473d9a6bd815f7de78c73734acdcb745c3dde8579560ac5440e'] builddependencies = [ ('binutils', '2.39'), ('CMake', '3.24.3'), - ('googletest', '1.13.0'), + ('googletest', '1.12.1'), ] configopts = "-DHWY_SYSTEM_GTEST=ON" From 60207b4f4db1d8f1d76f258fbb7fe31d51fcebc5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 24 Jan 2023 15:25:27 +0000 Subject: [PATCH 6291/9987] adding easyconfigs: GDAL-3.6.2-foss-2022b.eb and patches: GDAL-3.6.2_fix-python-CC-CXX.patch --- .../g/GDAL/GDAL-3.6.2-foss-2022b.eb | 80 +++++++++++++++++++ .../g/GDAL/GDAL-3.6.2_fix-python-CC-CXX.patch | 18 +++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.6.2_fix-python-CC-CXX.patch diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb new file mode 100644 index 00000000000..da8f179ebc2 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb @@ -0,0 +1,80 @@ +easyblock = 'CMakeMake' + +name = 'GDAL' +version = '3.6.2' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-3.6.2_fix-python-CC-CXX.patch'] +checksums = [ + {'gdal-3.6.2.tar.xz': '35f40d2e08061b342513cdcddc2b997b3814ef8254514f0ef1e8bc7aa56cf681'}, + {'GDAL-3.6.2_fix-python-CC-CXX.patch': '859b874b0c8ff7626a76d51f008bf05b7f89a35b325bdd1d126d2364154acc63'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pkgconf', '1.9.3'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('netCDF', '4.9.0'), + ('expat', '2.4.9'), + ('GEOS', '3.11.1'), + ('SQLite', '3.39.4'), + ('libxml2', '2.10.3'), + ('libpng', '1.6.38'), + ('libjpeg-turbo', '2.1.4'), + ('JasPer', '4.0.0'), + ('LibTIFF', '4.4.0'), + ('zlib', '1.2.12'), + ('cURL', '7.86.0'), + ('PCRE', '8.45'), + ('PROJ', '9.1.1'), + ('libgeotiff', '1.7.1'), + ('SciPy-bundle', '2023.01'), + ('HDF5', '1.14.0'), + ('HDF', '4.2.15'), + ('Armadillo', '11.4.3'), + ('CFITSIO', '4.2.0'), + ('zstd', '1.5.2'), + ('giflib', '5.2.1'), + ('json-c', '0.16'), + ('Xerces-C++', '3.2.4'), + ('PCRE2', '10.40'), + ('OpenEXR', '3.1.5'), + ('Brunsli', '0.1'), + ('Qhull', '2020.2'), + ('LERC', '4.0.0'), +] + +# common configopts for static, shared library builds +_base_configopts = ' '.join([ + '-DGDAL_USE_INTERNAL_LIBS=OFF', + '-DArrow_DIR=$EBROOTARROW', + '-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include', +]) + +# iterative build for both static and shared libraries +configopts = [' '.join([_base_configopts, x]) for x in ['-DBUILD_SHARED_LIBS=OFF', '']] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["python -c 'import osgeo.gdal'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2_fix-python-CC-CXX.patch b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2_fix-python-CC-CXX.patch new file mode 100644 index 00000000000..58528a793e6 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2_fix-python-CC-CXX.patch @@ -0,0 +1,18 @@ +to ensure that correct compiler commands are used +Kenneth Hoste (HPC-UGent), updated for v3.6.2 by Jasper Grimm (UoY) +diff -ruN gdal-3.6.2.orig/swig/python/setup.py.in gdal-3.6.2/swig/python/setup.py.in +--- gdal-3.6.2.orig/swig/python/setup.py.in 2023-01-24 10:50:11.000000000 +0000 ++++ gdal-3.6.2/swig/python/setup.py.in 2023-01-02 14:38:17.000000000 +0000 +@@ -16,6 +16,12 @@ + from setuptools import find_packages + from setuptools import Extension + ++for key in ['CC', 'CXX']: ++ seqkey = '%s_SEQ' % key ++ if seqkey in os.environ: ++ os.environ[key] = os.environ[seqkey] ++ print('$%s set to %s (via $%s)' % (key, os.environ[key], seqkey)) ++ + # If CXX is defined in the environment, it will be used to link the .so + # but setuptools will be confused if it is made of several words like 'ccache g++' + # and it will try to use only the first word. From faf6481489216a34daf8d98d6222655837f39f6c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 25 Jan 2023 12:16:40 +0000 Subject: [PATCH 6292/9987] adding easyconfigs: R-4.2.2-foss-2022b.eb --- .../easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 3399 +++++++++++++++++ 1 file changed, 3399 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb new file mode 100644 index 00000000000..324e9babd79 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -0,0 +1,3399 @@ +name = 'R' +version = '4.2.2' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f'] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('Xvfb', '21.1.6'), + ('Autotools', '20220317'), +] +dependencies = [ + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), + ('cairo', '1.17.4'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), + ('SQLite', '3.39.4'), + ('PCRE2', '10.40'), + ('libpng', '1.6.38'), # for plotting in R + ('libjpeg-turbo', '2.1.4'), # for plottting in R + ('LibTIFF', '4.4.0'), + ('Java', '11', '', SYSTEM), + ('Tk', '8.6.12'), # for tcltk + ('cURL', '7.86.0'), # for RCurl + ('libxml2', '2.10.3'), # for XML + ('GMP', '6.2.1'), # for igraph + ('NLopt', '2.7.1'), # for nloptr + ('FFTW', '3.3.10'), # for fftw + ('libsndfile', '1.2.0'), # for seewave + ('ICU', '72.1'), # for rJava & gdsfmt + ('HDF5', '1.14.0'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.1.0-53'), # for animation + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '18.12.1'), # for V8 (required by rstan) + ('GDAL', '3.6.2'), # for sf + ('MPFR', '4.2.0'), # for Rmpfr + ('libgit2', '1.5.0'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. 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}), + ('usethis', '2.1.6', { + 'checksums': ['31dc6707577065ac1d4acb7d4cbf135942727c5cc2699092198c544be86f6818'], + }), + ('covr', '3.6.1', { + 'checksums': ['a54cfc3623ea56084158ac5d7fe33f216f45191f6dcddab9c9ed4ec1d9d8ac6c'], + }), + ('devtools', '2.4.5', { + 'checksums': ['e42159a9bca0b219170e76c282862e27ca283649d6cbf6a868175d8982e06b4f'], + }), + ('Rook', '1.2', { + 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + }), + ('Cairo', '1.6-0', { + 'checksums': ['bb3ab1ff6431c15eb01a66ddf90695cd9a2af3d5a384753f5180cd0401d2e89d'], + }), + ('RMTstat', '0.3.1', { + 'checksums': ['bb4827d76106f5377044cd2b230208881eb714cae65f512f4b95988d9b162ae4'], + }), + ('Lmoments', '1.3-1', { + 'checksums': ['7c9d489a08f93fa5877e2f233ab9732e0d1b2761596b3f6ac91f2295e41a865d'], + }), + ('distillery', '1.2-1', { + 'checksums': ['4b88f0b34e472b9134ad403fb32283424f1883a5943e52c55f1fe05995efb5fa'], + }), + ('extRemes', '2.1-3', { + 'checksums': ['a7a38dc9a876967d54843872b4355c65e1910c324b0630f91a50009c2f3005a7'], + }), + ('tkrplot', '0.0-27', { + 'checksums': ['dd66264c2553f6927aff297c6b1c3b61867d6c63aec080f40a1e9d53cfc9d120'], + }), + ('misc3d', '0.9-1', { + 'checksums': ['a07bbb0de153e806cd79675ed478d2d9221cff825654f59a71a9cf61f4293d65'], + }), + ('multicool', '0.1-12', { + 'checksums': ['487d28d9c3c606be0cf56e2d8f8b0d79fb71949c68886ea9251fbb1c01664a36'], + }), + ('plot3D', '1.4', { + 'checksums': ['d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0'], + }), + ('plot3Drgl', '1.0.4', { + 'checksums': ['85421213e01e1b5f8b929ee1644232f37bacd723305e549c32850f6b6d6924a4'], + }), + ('OceanView', '1.0.6', { + 'checksums': ['2c5165975d6c49fdc83a892cb0406584928dd44000c9774fffc00fbd2fec86f3'], + }), + ('ks', '1.14.0', { + 'checksums': ['d1c4d06d704f301628455787ba929add1e774debc343d0952a768abea6cc7815'], + }), + ('logcondens', '2.1.7', { + 'checksums': ['785bbda00b9a25e56440e11356ac219cfbf0fdf8b08c7b0728e53a9febe7a365'], + }), + ('Iso', '0.0-18.1', { + 'checksums': ['2fa5f78a7603cbae94a5e38e791938596a053d48c609a7c120a19cbb7d93c66f'], + }), + ('penalized', '0.9-52', { + 'checksums': ['d8e38e6c4e993c74998ca8f986b4e11e09c0b9971103e1d5c7ebdee75f6d6a21'], + }), + ('clusterRepro', '0.9', { + 'checksums': ['940d84529ff429b315cf4ad25700f93e1156ccacee7b6c38e4bdfbe2d4c6f868'], + }), + ('data.tree', '1.0.0', { + 'checksums': ['40674c90a5bd00f5185db9adbd221c6f1114043e69095249f5fa8b3044af3f5e'], + }), + ('influenceR', '0.1.0.1', { + 'checksums': ['63c46f1175fced33fb1b78d4d56e37fbee09b408945b0106dac36e3344cd4766'], + }), + ('visNetwork', '2.1.2', { + 'checksums': ['a2b91e7fbbd9d08a9929a5b2c891d9c0bca5977ad772fa37510d96656af1152f'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.9', { + 'checksums': ['64a426fe27110dddd8b0c1223ae4c397a2e553ae5e81ddd4ff67c026cfc40abf'], + }), + ('randomForestSRC', '3.2.0', { + 'checksums': ['a38fbd465eea87c65c7e7406972de84b1073560b40b1e9c806d46bf874a445c0'], + }), + ('sm', '2.2-5.7.1', { + 'checksums': ['2607a2cafc68d7e99005daf99e36f4a66eaf569ebb6b7500e962642cf58be80f'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-13', { + 'checksums': ['2cc193b82463a865cd8dadb7332409fdebf47e4035d5fe8dbf3414a7ae18d308'], + }), + ('matrixcalc', '1.0-6', { + 'checksums': ['5906e1ef06dbc18efc7a4b370adc180ef8941b5438119703bd981d1c76a06fca'], + }), + ('arm', '1.13-1', { + 'checksums': ['816ba1c31eec00feef472c57e280488d3d233b592f6f0a1a30e4abb903cb4f5d'], + }), + ('mi', '1.1', { + 'checksums': ['4d7a9790dbdc675605d70755af9aa80c21a279be5a5d712b22d77465772cc785'], + }), + ('servr', '0.25', { + 'checksums': ['d94e1d31802ce6bbab7a5838ff94cbca8cd998237d834ff25fedf7514f41a087'], + }), + ('rgexf', '0.16.2', { + 'checksums': ['6ee052b0de99d0c7492366b991d345a51b3d0cc890d10a68b8670e1bd4fc8201'], + }), + ('sem', '3.1-15', { + 'checksums': ['ad023b00e6e8eb20d107039caf1008c4b05104c7c69709e59c66fbddbf381316'], + }), + ('statnet.common', '4.8.0', { + 'checksums': ['ddad51128b50d465e1d1aca3a53b452810b9ba578e96b08b8f50f5850d7bb21d'], + }), + ('network', '1.18.1', { + 'checksums': ['9588a198807c8c68da147f479ca9af5bcb4468cf91b6a90b8044d313d9fa30f7'], + }), + ('rle', '0.9.2', { + 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], + }), + ('sna', '2.7-1', { + 'checksums': ['440fa4347c7b437e93c73127d34894068afd240d3128898474a7201e740a434d'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.5', { + 'checksums': ['9240866e2f773cd0ac8a02514871149d2babaa162a49e151eab9591ad42984ea'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('BDgraph', '2.72', { + 'checksums': ['1f424c9254db3d553f6421b3c095b49c57683d25afefbdb195fed12f0c215268'], + }), + ('graphlayouts', '0.8.4', { + 'checksums': ['d724266778e4d97ca7a762253c293ffa3d09e2627cb1c3c7a654c690819defd0'], + }), + ('tweenr', '2.0.2', { + 'checksums': ['1805f575da6705ca4e5ec1c4605222fc826ba806d9ff9af41770294fe08ff69f'], + }), + ('ggforce', '0.4.1', { + 'checksums': ['2a283bb409da6b96929863a926b153bcc59b2c6f00551805db1d1d43e5929f2f'], + }), + ('tidygraph', '1.2.2', { + 'checksums': ['2fbdc2db18c5ad48c72f14d2d04111f4b0d4c434ad87c280eda3bcb98673ad36'], + }), + ('ggraph', '2.1.0', { + 'checksums': ['e36ad49dba92ee8652e18b1fb197be0ceb9f0a2f8faee2194453a62578449654'], + }), + ('qgraph', '1.9.3', { + 'checksums': ['baf190f6db30c4d5a3dc7ab5043b8ec0f79071d515c818c8e7666b9bcf2a4264'], + }), + ('HWxtest', '', { + 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], + 'checksums': [ + 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz + 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+ ('tclust', '1.5-2', { + 'checksums': ['73328b30774bb0767d613d7f2b60b75706b19fab864c712645ea18181f1af327'], + }), + ('ranger', '0.14.1', { + 'checksums': ['5d99401d555da1cfb11c70e59d1bb545ce48720073a06a2a32eb396f622dee1b'], + }), + ('hexbin', '1.28.2', { + 'checksums': ['6241f8d3a6c6be2c1c693c3ddb99554bc103e3c6cf602d0c2787c0ce6fd1702d'], + }), + ('lobstr', '1.1.2', { + 'checksums': ['9bc533ed7e8f816097a03acfbca33308c9940ba26d02674f4ba06311cf3a1718'], + }), + ('pryr', '0.1.6', { + 'checksums': ['7b1653ec51850f4633cee8e2eb7d0b2724fb587b801539488b426cf88f0f770b'], + }), + ('moments', '0.14.1', { + 'checksums': ['2ed2b84802da132ae0cf826a65de5bfa85042b82e086be844002fe1ce270d864'], + }), + ('laeken', '0.5.2', { + 'checksums': ['22790f7157f23eb0b7b0b89e2ea53478fb3c0d15b5be8ad11525d3e6d5626cdc'], + }), + ('VIM', '6.2.2', { + 'checksums': ['7581adca64cf20b93d5a111da83f663215b4529868b065b3463c4238bca97739'], + }), + ('smoother', '1.1', { + 'checksums': 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['0e6d8667cacb63135476a766fba3a4f91e5ad86274ea66d2b1e6d773b5ca6426'], + }), + ('selectr', '0.4-2', { + 'checksums': ['5588aed05f3f5ee63c0d29953ef53da5dac7afccfdd04b7b22ef24e1e3b0c127'], + }), + ('rvest', '1.0.3', { + 'checksums': ['89bb477e0944c80298a52ccf650db8f6377fd7ed3c1bc7034d000f695fdf05a4'], + }), + ('dtplyr', '1.2.2', { + 'checksums': ['2640e9cde4eaa06f02cff29e3f2b99fdd08488df07ea2e6629b2ed6a8285d0f3'], + }), + ('gargle', '1.2.1', { + 'checksums': ['4d46ca2933f19429ca5a2cfe47b4130a75c7cd9931c7758ade55bac0c091d73b'], + }), + ('googledrive', '2.0.0', { + 'checksums': ['605c469a6a086ef4b049909c2e20a35411c165ce7ce4f62d68fd39ffed8c5a26'], + }), + ('ids', '1.0.1', { + 'checksums': ['b6212a186063c23116c5cbd3cca65dbb8977dd737261e4526ebee8f64852cfe8'], + }), + ('googlesheets4', '1.0.1', { + 'checksums': ['0a107d76aac99d6db48d97ce55810c1412b2197f457b8476f676169a36c7cc7a'], + }), + ('tidyverse', '1.3.2', { + 'checksums': ['83cf95109d4606236274f5a8ec2693855bf75d3a1b3bc1ab4426dcc275ed6632'], + }), + ('R.rsp', '0.45.0', { + 'checksums': ['8969075bdcabd43bad40eef6b82223e119426279fded041163fd41e55cee3a59'], + }), + ('gdistance', '1.6', { + 'checksums': ['2ccabeb2f8cf44630c0bd2da79815fe357b812737ebece1bed8f90b27c126a24'], + }), + ('vioplot', '0.4.0', { + 'checksums': ['06475d9a47644245ec91598e9aaef7db1c393802d9fc314420ac5139ae56adb6'], + }), + ('emulator', '1.2-21', { + 'checksums': ['9b50b2c1e673dbc5e846a4fa72e8bd03434add9f659bde6d7b0c4f1bbd713346'], + }), + ('gmm', '1.7', { + 'checksums': ['b1b321ad1b4a4a14a2825a2c3eb939ce2f2bcef995247a1d638eca250e59739b'], + }), + ('tmvtnorm', '1.5', { + 'checksums': ['1c7a606bdce4319a6fdb4180fef499c293df3412d8583e296869521ece5460fe'], + }), + ('IDPmisc', '1.1.20', { + 'checksums': ['bcb9cd7b8097e5089d1936286ef310ac2030ea7791350df706382ba470afc67f'], + }), + ('gap.datasets', '0.0.5', { + 'checksums': ['2299b52efee322ce0eaf66c66ae440f46618b647701cd741568c08bdc3111c9c'], + }), + ('plotly', '4.10.1', { + 'checksums': ['bd995c654dbc8c09a84adaba8def99766919e3894caf18b551bb26b2f591389a'], + }), + ('gap', '1.5-1', { + 'checksums': ['0ef352aa98a3bf27908b256f27a903058502176ea9112a4ffc41928ebbc48c22'], + }), + ('qrnn', '2.0.5', { + 'checksums': ['3bd83ee8bd83941f9defdab1b5573d0ceca02bf06759a67665e5b9358ff92f52'], + }), + ('TMB', '1.9.2', { + 'checksums': ['2c9dd281d911c2cb1cc01c6a8e114826891280f15e0ed4a00b4f195e15df25d7'], + }), + ('glmmTMB', '1.1.5', { + 'checksums': ['b9d1e97587b213e52ff304f62480ddee77c658f29a7e99334a4032d0df60b275'], + }), + ('gmp', '0.6-10', { + 'checksums': ['8ae76f3d17542eab3e7468341dabeebe28b11da8c1b4b3f7bbdb00d379689e52'], + }), + ('ROI', '1.0-0', { + 'checksums': ['b0d87fb4ed2137d982734f3c5cdc0305aabe6e80f95de29655d02a9e82a0a341'], + }), + ('Rglpk', '0.6-4', { + 'checksums': ['a28dbc3130b9618d6ed2ef718d2c55df8ed8c44a47161097c53fe15fa3bfbfa6'], + }), + ('ROI.plugin.glpk', '1.0-0', { + 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], + }), + ('spaMM', '4.1.20', { + 'checksums': ['ff3af7ab107655bd521bba68093696f343de29294602d00dee7601cc91245f2d'], + }), + ('qgam', '1.3.4', { + 'checksums': ['7633120a48a85ab73f7e1bc8b02c98319285c2abd05f9d13d25339d7aaaacacb'], + }), + ('DHARMa', '0.4.6', { + 'checksums': ['0fcd41099ababedff010d8fe05f8efa630cceb829dbb87af8b8d650ad49d88bf'], + }), + ('mvnfast', '0.2.7', { + 'checksums': ['b67d50936c9a466977669ef6bb7b23df8e7c90a820ac916328c20e41ef8e0b72'], + }), + ('bridgesampling', '1.1-2', { + 'checksums': ['54ecd39aa2e36d4d521d3d36425f9fe56a3f8547df6048c814c5931d790f3e6b'], + }), + ('BayesianTools', '', { + 'checksums': ['af49389bdeb794da3c39e1d63f59e6219438ecb8613c5ef523b00c6fed5a600c'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.5', { + 'checksums': ['50ff06d5e24d38b5d5d62f84582861bd353b82363e37623f95529b520504adbf'], + }), + ('dummies', '', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('uniqueAtomMat', '', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3.2', { + 'checksums': ['9b85be7b12b31ac076f2456853a5b18d8a79ce2b86d00055264529a0cd28515c'], + }), + ('cghFLasso', '', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.5.3', { + 'checksums': ['d4dcb650757bfbf8ae388622686be20e8d55cca68096146a30aee8ced96aa113'], + }), + ('Rssa', '1.0.5', { + 'checksums': ['4115b516f6782d52f02695bbbd52921a474aafc7232d49aca85010f1c33b08a7'], + }), + ('JBTools', '', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.32', { + 'checksums': ['23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1'], + }), + ('DistributionUtils', '0.6-0', { + 'checksums': ['7443d6cd154760d55b6954142908eae30385672c4f3f838dd49876ec2f297823'], + }), + ('gapfill', '0.9.6-1', { + 'checksums': ['22f04755873e34a9077bb1b1de8d16f5bc56cb8c395c4f797f9ad0b209b1b996'], + }), + ('gee', '4.13-25', { + 'checksums': ['f8217c3bb077cb805e0cd7761efecac1231035bfc195246b9f185f744c550e6c'], + }), + ('Matching', '4.10-8', { + 'checksums': ['1e75dc61553c1687b2b520dc52688409c2e84285e4b6c16c94d8d85fd5ccece0'], + }), + ('MatchIt', '4.5.0', { + 'checksums': ['e79a96e7972097829a839c855c0bc97638eeae4b148e01340dfa5296323e6c06'], + }), + ('RItools', '0.3-1', { + 'checksums': ['714685d8e04acafe5d5ddf93edac69afec0c62045a7b93478734771b6a0fa928'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.1-1', { + 'checksums': ['05e89a1678a39e32bfb41af8a31d643b04fc4d2660a96e701825e6bffcd75a52'], + }), + ('rlemon', '0.2.0', { + 'checksums': ['e06792875f05a0c6cd637b7bf16bd51c3891e0df6bad78ffba0ee195abe8d3a0'], + }), + ('optmatch', '0.10.5', { + 'checksums': ['ed09be71b0e293273412d4a181c1f085ad93f4038996dc7c90beae8466574aeb'], + }), + ('SPAtest', '3.1.2', { + 'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'], + }), + ('RSpectra', '0.16-1', { + 'checksums': ['cba5d3403d6a7d0e27abf6279fbfea6e0d0fe36b28c688bbadb8eafb3841329a'], + }), + ('SKAT', '2.2.5', { + 'checksums': ['2b349896560ad18c3428e245fc25b17e9c2946676044fa56025ddf9c87ff08bf'], + }), + ('GillespieSSA', '0.6.2', { + 'checksums': ['f4233b4a44c7d4b9e3459b1efa9a8087a602ef93806b4d70eadbb537b67567c2'], + }), + ('startupmsg', '0.9.6', { + 'checksums': ['1d60ff13bb260630f797bde66a377a5d4cd65d78ae81a3936dc4374572ec786e'], + }), + ('distr', '2.9.1', { + 'checksums': ['bb7df05d6b946bcdbbec2e3397c7c7e349b537cabfcbb13a34bcf6312a71ceb7'], + }), + ('distrEx', '2.9.0', { + 'checksums': ['b064cde7d63ce93ec9969c8c4463c1e327758b6f8ea7765217d77f9ba9d590bf'], + }), + ('minerva', '1.5.10', { + 'checksums': ['2f26353d8fcc989ac698c4e45bb683801b1a7bb60b14903d05a4d73c629c590f'], + }), + ('KODAMA', '2.4', { + 'checksums': ['e4f8bbfeae9d2f628f7338c708a538aae481a633e59e86727f9b6f9c72920ecf'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-3', { + 'checksums': ['e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179'], + }), + ('dtw', '1.23-1', { + 'checksums': ['df7cf9adf613422ddb22a160597eb5f5475ab6c67c0d790092edb7f72ba98f00'], + }), + ('SDMTools', '', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.4', { + 'checksums': ['f5eafab17f2d4a8a2a83821ad3e96ae7c26b62bbce9de414484c657383c7b42e'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-8', { + 'checksums': ['f3c72310f40773b3839a9506c3cb781d044e09b94f2f38d332bb24e5f9960f5a'], + }), + ('here', '1.0.1', { + 'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'], + }), + ('RcppTOML', '0.2.0', { + 'checksums': ['2f09f00cbee6c6eeff5d5f0195c10de0155496de15fbe8189c18627ee3090541'], + }), + ('reticulate', '1.27', { + 'checksums': ['2125af9e75939c3b7c0dc74f28f42606e816d63aa1143baf631c318ff5ff3a2c'], + }), + ('hdf5r', '1.3.8', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['87b75173ab226a9fbaa5b28289349f3c56b638629560a172994b8f9323c1622f'], + }), + ('DTRreg', '1.7', { + 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], + }), + ('pulsar', '', { + 'checksums': ['78c9f7e3b2bf8a8d16a81d6ee43bb05b0c360219be473d920c8c8ccb2aba4e3d'], + }), + ('bayesm', '3.1-5', { + 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + }), + ('gsl', '2.1-8', { + 'checksums': ['ee98d1382d37ffa77538a90ccdbf44affbf1710a9e66b8ada73fa72e67921985'], + }), + ('energy', '1.7-11', { + 'checksums': ['543de4875c46cc90e711e71c45b082d962fbb5158a094f9f10d37d3f57e1bea7'], + }), + ('compositions', '2.0-4', { + 'checksums': ['7b9c7a3bf654fb02d9eb1b4a7566469b2f5232f3b2c1b324c02239fd31060faf'], + }), + ('clustree', '0.5.0', { + 'checksums': ['7a6100f88c9a6e8d10b253ee227ecf1dc4e84e418eb8da64cd801d2a158b956f'], + }), + ('tweedie', '2.3.5', { + 'checksums': ['a032cad512dac37a8619e6f66cb513eb82a88a5a2ffbe91e92c2d44d1756d0d9'], + }), + ('RcppGSL', '0.3.13', { + 'checksums': ['f094ea26c99b04d9e203986a1f2003f02472ceca0e2ef1c3beefd3ae80aeada8'], + }), + ('mvabund', '4.2.1', { + 'checksums': ['ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.4.1', { + 'checksums': ['cd3f72b84f0c722e9c0b21c2b2de7683ec742345d7f8e62f67c8c93342c1a5c6'], + }), + ('grpreg', '3.4.0', { + 'checksums': ['fd57d20baf63d2cc5821998bca5c3fdcbe46c933c9553caa492911b12654d6ad'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('lpSolveAPI', '5.5.2.0-17.9', { + 'checksums': ['9ebc8e45ad73eb51e0b25049598a5bc758370cf89508e2328cf4bd93d68d55bb'], + }), + ('ergm', '4.3.2', { + 'checksums': ['ced92b0a32c78c85546d665c32fb3993fe77a3809aa88f43c3eee39e2577f2f0'], + }), + ('networkDynamic', '0.11.2', { + 'checksums': ['beefaf50eb8609528358b75f5814a8f1cdc4d2db8059b99be69919da2bc02beb'], + }), + ('tergm', '4.1.1', { + 'checksums': ['abff35b48b53a182d9424c78c5240bde1259b695c2328861000193bf88044a50'], + }), + ('ergm.count', '4.1.1', { + 'checksums': ['446893614ad8b41aa39c37c2bf45a167f575536bb6778b8ad1fbcddb7b934932'], + }), + ('tsna', '0.3.5', { + 'checksums': ['4ee2f773d573f0f4bd93131156fdccf01d7f1a3f725eff3e885021098c6bff65'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.6-3', { + 'checksums': ['cb14ba20690b31fd813b05565484c866425f072a5ad99a5cbf1da63588958db3'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.2', { + 'checksums': ['14f67ce96dd8f1cb457614271b0b4376dd6fd3073a2e727a17c0964be67272cb'], + }), + ('asnipe', '1.1.16', { + 'checksums': ['be50f9fdef0f4bf9676b9c3c2906d0431afc678af55cf48b1119f9fc0adac44f'], + }), + ('liquidSVM', '', { + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.38.0.1', { + 'checksums': ['d470dc71e637d589bf228e59ddb021ade240d74536323d8ca77ac1fb334d3535'], + }), + ('mlegp', '3.1.9', { + 'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.5', { + 'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'], + }), + ('bartMachineJARs', '1.2.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.3.3', { + 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + }), + ('lqa', '', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.11', { + 'checksums': ['59266ffdf702ab1ecca7cbcf0538afe38d1a15abea66056734b62c0c15609c7c'], + }), + ('GUTS', '1.2.3', { + 'checksums': ['40061ec1677def40b410b5ef90d01e0bcb0095abed1545513a33a01d4444adc2'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('parsedate', '1.3.1', { + 'checksums': ['1e9399d6b16079e6cdc43fa33742d6b7e6e2b6bb2ba470bfe9d30d55b7be4cb0'], + }), + ('circular', '0.4-95', { + 'checksums': ['483d3e31e9c7afe59e6bcb98ad17c4f6333d19b6c70f948b168c9ee16e90bce2'], + }), + ('cobs', '1.3-5', { + 'checksums': ['7fae7da8f940975d544120c836e2d3b874f9b0cbab9631851ce986709f51c611'], + }), + ('resample', '0.6', { + 'checksums': ['1b958009b18c92a47971847c782af76952ea4e85d5f1e3e1e70fa35c67b95265'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-7', { + 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], + }), + ('Rserve', '1.8-11', { + 'checksums': ['af63a28a4958dbe82597586494d0277272842bb3869db70c547d0896f1345d2c'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '8.0.0', { + 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.5.0.2', { + 'checksums': ['4772c352e8d3d9b5a0b7480c0e0962de4f5060fb7bf3fcb8ee4fa1cb10f93fd4'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.19', { + 'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'], + }), + ('BMA', '3.18.17', { + 'checksums': ['6d8c514fa179f8a48c2105b551a8a08e28ea4375d06150a4b8ab4ccda577daf5'], + }), + ('BCEE', '1.3.1', { + 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-63', { + 'checksums': ['71311b16ce380fd9a8834be95b55b3d1b47e4ee2b8acb35b8d481138c314dc31'], + }), + ('bdsmatrix', '1.3-6', { + 'checksums': ['f9c871d54378408902931792b3dbf8bda863d6aa67af6a0472a6ec1c420760bc'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.22', { + 'checksums': ['0771f82034aa6a77af67f3572c900987b7e6b578d04d707c6e06689d021a2ff8'], + }), + ('threejs', '0.3.3', { + 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], + }), + ('LaplacesDemon', '16.1.6', { + 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], + }), + ('rda', '', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.9', { + 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '4.3', { + 'checksums': ['f755808fcb618582acb862729b20e267d9c2214f22e6e7a0c8d29073d8faa7b8'], + }), + ('bbmle', '1.0.25', { + 'checksums': ['86a8c69902fbf6caf337f9bc532afe89dc2a59dd24287a2423d781797010b255'], + }), + ('emdbook', '1.3.12', { + 'checksums': ['0646caf9e15aaa61ff917a4b5fdf82c06ac17ef221a61dec3fbb554e7bff4353'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.51.5', { + 'checksums': ['c116f979ed891ec55f3e1e7b9a92436b5ec9430c1170439a501ecb7e2a33ef4d'], + }), + ('tictoc', '1.1', { + 'checksums': ['a09a1535c417ddf6637bbbda5fca6edab6c7f7b252a64e57e99d4d0748712705'], + }), + ('ISOcodes', '2022.09.29', { + 'checksums': ['b25ddec624b46f5630c29267bdf4a749cfb9d001ef029fb9ca84dafe56b1c73f'], + }), + ('stopwords', '2.3', { + 'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'], + }), + ('janeaustenr', '1.0.0', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.7.0', { + 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], + }), + ('tokenizers', '0.3.0', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0.2', { + 'checksums': ['1fedbb913bc13c790d2fabfe4edda0a987db3a078bea8c0ca9b777d20af08662'], + }), + ('topicmodels', '0.2-13', { + 'checksums': ['afd83a4381bf39e470446ebefd41ed03f314be400c1b2f702a4b1060eb8fd1b4'], + }), + ('tidytext', '0.4.1', { + 'checksums': ['753b2bcea6e343ac439869b92e7c11b0aaf98ce5c0373965da6c7d087d57924e'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.3', { + 'checksums': ['6b3910dc48495439cd01828f8999823864a6712f73560ee3e6c903065c67d1e4'], + }), + ('entropy', '1.3.1', { + 'checksums': ['6f5a89f5ce0e90cbed1695b81259326c976e7a8f538157e223ee5f63b54412b8'], + }), + ('kedd', '', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-13', { + 'checksums': ['7186d23e561818f3e1f01376a4fb2af9ccee775ce5afc1e3175f3b07a81db515'], + }), + ('lmerTest', '3.1-3', { + 'checksums': ['35aa75e9f5f2871398ff56a482b013e6828135ef04916ced7d1d7e35257ea8fd'], + }), + ('loo', '2.5.1', { + 'checksums': ['866a2f54a4e8726cc3062e27daa8a073e6ac4aeb6719af7845284f7a668745f1'], + }), + ('RcppParallel', '5.1.6', { + 'checksums': ['6396322b3b6d6f7019aac808ceb74707bc5c4ed01677fab408372c2a5508c2ea'], + }), + ('StanHeaders', '2.21.0-7', { + 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], + }), + ('V8', '4.2.2', { + 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', + 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", + 'checksums': ['6c62fdc974cc30fa975cad4ccb1e3796112fc2490a807f6e3d7878c3a5544743'], + }), + ('rstan', '2.21.8', { + 'checksums': ['86e4fe562d8ddcd0b02336f35a420fa8786dd21de7ca2bebb4ed6e9c252bb9ea'], + }), + ('Rborist', '0.3-2', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.2.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.2', { + 'checksums': ['a59a3cb3cca89f51d9ee6702cd479fd7db8bc2e25b72f45cb6712da983777ca0'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.4', { + 'checksums': ['ca8545b25590e531512a90a18449a2cbab945f7434a1d60188c41f7d1839a7a9'], + }), + ('corrplot', '0.92', { + 'checksums': ['e8c09f963f9c4837036c439ebfe00fa3a6e462ccbb786d2cf90850ddcd9428bd'], + }), + ('rstatix', '0.7.1', { + 'checksums': ['a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.5.0', { + 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], + }), + ('yaImpute', '1.0-33', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.1.2', { + 'checksums': ['cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481'], + }), + ('leiden', '0.4.3', { + 'checksums': ['cace86748c4aa1720508210658ee2f63f7875be5bac215084001fdc59d22e2bd'], + }), + ('sctransform', '0.3.5', { + 'checksums': ['83af125c40f211e1ddae5098f88766aea1453c02ae98486081f3efadb3620b2b'], + }), + ('packrat', '0.9.0', { + 'checksums': ['3025b9052974bec00fb09299226b80004d48e611e15a65e5a0bc49d3538844ef'], + }), + ('colourpicker', '1.2.0', { + 'checksums': ['a0d09982b048b143e2c3438ccec039dd20d6f892fa0dedc9fdcb0d40de883ce0'], + }), + ('ggExtra', '0.10.0', { + 'checksums': ['dc6855bbb7e81ffa58d6b65b594d22718fa36b7f50b2284386f70fa8ccc6a3e5'], + }), + ('findpython', '1.0.7', { + 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], + }), + ('argparse', '2.2.1', { + 'checksums': ['83e112beb47733849980b286d93ac930f0cbe6ac78fcb94fc9f6b0eea882658d'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.10', { + 'checksums': ['1b655dbab8eed8d0aa3ab2148aac8e0e5bfa190468f5e3c06b001ce88b7f0d3f'], + }), + ('qqman', '0.1.8', { + 'checksums': ['58da8317df8d726d1fde4805919da5d64f880894a423ee20937cafb479b9d8a8'], + }), + ('rstantools', '2.2.0', { + 'checksums': ['cb810baeb90c67668361b666c6862df9917aff6aaec63d2c3a485f28407c4eb7'], + }), + ('distributional', '0.3.1', { + 'checksums': ['fab36c7346617d8f2ca4b3cd0e3c9da93cb2f95fb7f102a3ae88670e694751d6'], + }), + ('posterior', '1.3.1', { + 'checksums': ['d615ed75b43b2927002b79d2982c624a6144c851aac7b81fa14e4ec9cc3d353b'], + }), + ('bayesplot', '1.10.0', { + 'checksums': ['0a81a4b99cf781334e57cfc3c469fad8b932a68204016a3bbca33cab4e2a1e43'], + }), + ('dygraphs', '1.1.1.6', { + 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], + }), + ('rsconnect', '0.8.29', { + 'checksums': ['faafabbed803743799b345051f221aef2b4497b421fc98092ca41c05ef6b5fed'], + }), + ('shinystan', '2.6.0', { + 'checksums': ['a084856a2d66d8744f2c72e3e19ca35e600a508ed7ef1f7ebed8c7fc0738d529'], + }), + ('optimx', '2022-4.30', { + 'checksums': ['ebe9887a22296cf4b2db07981aaa1f898bf7c17fb61a4b398c228d4077d0b410'], + }), + ('gamm4', '0.2-6', { + 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], + }), + ('projpred', '2.3.0', { + 'checksums': ['a88a651e533c118aad0e8c2c905cfcf688d9c419ed195896036b8f6667b5cfb0'], + }), + ('brms', '2.18.0', { + 'checksums': ['24e5a3a40b81bea558e8f660d0de7fd1a4c2080c7553baac98f34dd2682ece71'], + }), + ('drgee', '1.1.10', { + 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], + }), + ('stdReg', '3.4.1', { + 'checksums': ['285335dbe29b6898641e1151ab2f06acf76c6f4d6fbeadd66d151c25d7e38a74'], + }), + ('mcmcse', '1.5-0', { + 'checksums': ['4a820dc22c48efd32b7f9d1e1b897b4b3f165cd64b2ff85ba7029621cf9e7463'], + }), + ('copCAR', '2.0-4', { + 'checksums': ['8b4ed53c58a665f70e48bdca689a992a81d5ecb5a6051ca7361d3870e13c77f3'], + }), + ('batchmeans', '1.0-4', { + 'checksums': ['8694573009d9070a76007281407d3314da78902e122a9d8aec1f819d3bbe562c'], + }), + ('ngspatial', '1.2-2', { + 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], + }), + ('BIGL', '1.6.6', { + 'checksums': ['8edb6607c5d91cea5ba32290eeb76c35317383a24d726bde6eca61f9cce96bb9'], + }), + ('drugCombo', '', { + 'checksums': ['9a605c655c159604033558d757711e6d83d33dfc286c1280f722d4cb7d130f80'], + }), + ('betareg', '3.1-4', { + 'checksums': ['5106986096a68b2b516215968158589b71969ce7912879253d6e930355a18101'], + }), + ('unmarked', '1.2.5', { + 'checksums': ['a54f49f42d30a7a69eb6c3db00d3cd2e1f8e549aec28fa5487fcdd27a37f87fe'], + }), + ('maxlike', '0.1-9', { + 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + }), + ('coxme', '2.2-18.1', { + 'checksums': ['dd0565f97adb7ff978d1dbd6cb7d6e44edee5e2a31cf6d5d4806a0151d1b1318'], + }), + ('AICcmodavg', '2.3-1', { + 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], + }), + ('pacman', '0.5.1', { + 'checksums': ['9ec9a72a15eda5b8f727adc877a07c4b36f8372fe7ed80a1bc6c2068dab3ef7c'], + }), + ('spaa', '0.2.2', { + 'checksums': ['a5a54454d4a7af473ce797875f849bd893005cb04325bf3e0dbddb19fe8d7198'], + }), + ('maxnet', '0.1.4', { + 'checksums': ['fd21e5ecf3c1ac00ef1bbe79fab4cdd62789e0c4c45f126f1b64bda667238216'], + }), + ('oai', '0.4.0', { + 'checksums': ['ebfa756e08f6ac0aa61556b1a5bbe611f407bfff8aef1f8d075a24c361678bfd'], + }), + ('wellknown', '0.7.4', { + 'checksums': ['483e6fc43edf09ed583e74ce5ca7e2d7838ef8a32291e06d774c37546eed1a34'], + }), + ('rgbif', '3.7.5', { + 'checksums': ['460f9e80bb3d90618bb80a8b57ac6fed99a22e8919279df47b6d0710b6a89d5f'], + }), + ('rgdal', '1.6-4', { + 'checksums': ['4583a4e187492eb936b59bc6bfeefea687b115bc3ae25172e0ed348b38f473ed'], + }), + ('rgeos', '0.6-1', { + 'checksums': ['ab90cbfe6a3680a9d2eed5e655064a075adc66788e304468969ab7cc2df0e3d4'], + }), + ('mapproj', '1.2.11', { + 'checksums': ['865f108f1ee54cda38571b86cd46063a903824d9b4eabfdf75218023d08a7781'], + }), + ('rbison', '1.0.0', { + 'checksums': ['9957e5f85ce68f5dd0ddc3c4b2b3c9d2f52d6f37587e1022ab8a44863534a83c'], + }), + ('rebird', '1.3.0', { + 'checksums': ['b238d3f246aa0249145894e1f3a90f46902f6615fc2f23b24c99bb5feecc55d3'], + }), + ('rvertnet', '0.8.2', { + 'checksums': ['2de9a3ec33a213c7592b49cca1d510a25aef0625369376d9b1b4e5d0da519226'], + }), + ('ridigbio', '0.3.6', { + 'checksums': ['e5cfb2e4dd8ddd1452a5afcf24fcc260889179d0f52eff4f41835adf99b64614'], + }), + ('spocc', '1.2.0', { + 'checksums': ['4bac45db5e69bfa3bf6cebd1b0c9241214c95561f275cee6d31e00911aa79d84'], + }), + ('spThin', '0.2.0', { + 'checksums': ['2e997afb79a2a990eded34c71afaac83986669cfa9ac51b15ae3f2b558902048'], + }), + ('rangeModelMetadata', '0.1.4', { + 'checksums': ['529d529ca90437db3d1e45118443e27a920422806383c7edaa2102beb43f5f80'], + }), + ('ENMeval', '2.0.4', { + 'checksums': ['4b39173a8d9dc4f36d09509e0177abcf91b7b1b51dc219eebcb007a0fb8c3c41'], + }), + ('plotmo', '3.6.2', { + 'checksums': ['cde33a8ec558b12d8e11d7d0531e73f6678a25ee589b79897d2fc425a3fd353c'], + }), + ('earth', '5.3.1', { + 'checksums': ['0bbe06ba974ceb8ec5de1d59cb53f9487d1828d7130fe2503c48b6cb449c4b03'], + }), + ('mda', '0.5-3', { + 'checksums': ['bda6409c17f385fae97da458cc742334e7b47aab8217a975b7551e2e18d38463'], + }), + ('biomod2', '4.2-2', { + 'checksums': ['30ed33ff980558a59782ec9e35f9c2c710a540718010654363f63878cdc0ac18'], + }), + ('poLCA', '1.6.0.1', { + 'checksums': ['ed8c60a42bff0402c9ba2f9ce1422dd171e711c1a64498c4d96010ddb29f6b16'], + }), + ('PermAlgo', '1.2', { + 'checksums': ['aa2c774d6c6dcfeec882c1936e8723ef49bd36030fb10c17ca60bb9d4a519443'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.13', { + 'checksums': ['90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('fasterize', '1.0.4', { + 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-1', { + 'checksums': ['e8abadc5614f132edc3fb9cb1c82ce4dacc1315b727fbd49db7399aee24115ba'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), + ('dbarts', '0.9-23', { + 'checksums': ['68fa2bfe274811c91ea7b67da46c4ffe527eb662d75edbec26ffe934ddc7150a'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.2.0', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.8.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.7.0', { + 'checksums': ['09a6f0d5b60856c7298371e4a8a085a1db7abf0e71ccb9a2dc9ca24248fb5d81'], + }), + ('outliers', '0.15', { + 'checksums': ['cc31d7f2faefd2c3a27f8ce78c7e67d3b321dcd6690292fad2468125e5e635fb'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-9', { + 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], + }), + ('gWidgets2tcltk', '1.0-8', { + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + }), + ('mgsub', '1.7.3', { + 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], + }), + ('ie2misc', '0.9.0', { + 'checksums': ['c81441af7588c62ab019ef2fbf31f61e0c2e3440a5e131938b1c5946cd2bce1a'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-5', { + 'checksums': ['b68954f53082561f0242682611bf3373e0bf30d8ac2256d82474edc5f992f4dd'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '3.2', { + 'checksums': ['d67f5c71b1209bea655d1e8d7530fa72359e0bcac25312551524501d0287e3cf'], + }), + ('lmom', '2.9', { + 'checksums': ['363e62751a73e0870fd0206206f1743a884a23aeac9b31b9afc71c0a1b51bb90'], + }), + ('gld', '2.6.6', { + 'checksums': ['0db6daee1b6e256d64d292c1f6795c505677331dcf2f97e04e264566ded93323'], + }), + ('DescTools', '0.99.47', { + 'checksums': ['8dfe7057fdcec475bc444761b00db59f6fb7313fd39c7bd6aebeca7f67aceb05'], + }), + ('orthopolynom', '1.0-6.1', { + 'checksums': ['17576157374c927da2959459caf2ed161b49a4a7768ea3d3fbe47656cafacc5b'], + }), + ('gaussquad', '1.0-3', { + 'checksums': ['a3337ce52bc53435cb4565a38bf48b72b384be397d2e86bb66f62973004dc810'], + }), + ('nlsem', '0.8', { + 'checksums': ['495a5d07aa5f59efdcd43acf429ae842453abd6c0720a80e2102d663fa997c60'], + }), + ('tableone', '0.13.2', { + 'checksums': ['b1cf15579abd4240e24435d2d9aad255c839d2a0293e28cb2eef0c808c4727af'], + }), + ('jstable', '1.0.7', { + 'checksums': ['a8f66172973dc75d1d751d7015e0f028c441263f6649909bd25fa944be0042c3'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.3', { + 'checksums': ['208e9b48a11cf56ce142731c204f3d2bcb5b68719f84309a36362cd925414265'], + }), + ('sensemakr', '0.1.4', { + 'checksums': ['6a1354f05392fa9343b90f69a54022c995651fb3c3d05cb08fa088ef52258caf'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-5', { + 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], + }), + ('blavaan', '0.4-3', { + 'checksums': ['a9f9f7b32aab7e7f179340c9f0f9d154b5fac51352c4fd590d317c201fe81b74'], + }), + ('mathjaxr', '1.6-0', { + 'checksums': ['ecc47607111b788d84789459af7f4f9102719f98640b7a23bd5a4eb1a6d3c179'], + }), + ('metadat', '1.2-0', { + 'checksums': ['f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8'], + }), + ('metafor', '3.8-1', { + 'checksums': 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['b4f1a9a7daa82f0c3123ebd4eeba06e98d5485215518e5292b25bc56741d582e'], + }), + ('elliptic', '1.4-0', { + 'checksums': ['b65729b1a1c7a84a5b1a59bfc893a2d35106853eaadcae31cda5c9ee3c500bb6'], + }), + ('contfrac', '1.1-12', { + 'checksums': ['95bfc5e970513416c080486a1cd8dfd9f8d59fb691b02ef6ccbe0ce1ed61056b'], + }), + ('hypergeo', '1.2-13', { + 'checksums': ['6d5b78353aad1d13091ccbeb340867dad7b9eb00d0e2185286dc7e13848f4d8e'], + }), + ('rtdists', '0.11-5', { + 'checksums': ['97cf2ea758aa02b1dfaeef5032c6e50570777552aa771ed9a86df048b7871eed'], + }), + ('AMAPVox', '0.12.1', { + 'checksums': ['b30fefef8661e27ffe3883665204b623eda2143dbcd3084a1d5810f8ea834c85'], + }), + ('LCFdata', '2.0', { + 'checksums': ['b58f4d93b9023dd1ba2db96a59ddfc058397085933d8de4cdb38ee064d5e7bf4'], + }), + ('LMERConvenienceFunctions', '3.0', { + 'checksums': ['eb430de9fbf836173f716960d60afc2de91de7f986471f406c3ca9027142e849'], + }), + ('HGNChelper', '0.8.1', { + 'checksums': ['aa3f0b3a8691ed93d63bec8f36d2954c6fcfd0b8b3efc705379248544c999363'], + }), + ('logger', '0.2.2', { + 'checksums': ['4f1be7d4381f2fc591f19fdbfb8f3cccbf26c9fdbae104612f6e6d5762a97e22'], + }), + ('parallelDist', '0.2.6', { + 'checksums': ['30c6b3b85cf78c04a7dcd17ea7ed64356971f6ce48d15794078a18c53b249e06'], + }), + ('roptim', '0.1.6', { + 'checksums': ['7ef0c2a2ddb3703efaabf337fa0026485875d5ffb35ba3ef5d60eb0c62c30686'], + }), + ('yulab.utils', '0.0.6', { + 'checksums': ['6ecd4dc5dae40e86b7a462fdac3ab8c0b276dcae5a284eb43390a05b01e3056b'], + }), + ('ggfun', '0.0.9', { + 'checksums': ['5c740e9d1e73b77658f41ed65e21492f4e71b12c7c9ff4b9e52ebf5f8f197612'], + }), + ('gridGraphics', '0.5-1', { + 'checksums': ['29086e94e63891884c933b186b35511aac2a2f9c56967a72e4050e2980e7da8b'], + }), + ('ggplotify', '0.1.0', { + 'checksums': ['178f73d6d3dc391c3efb1a62c95fe38587044f9e3288dffb915d3687941bb38a'], + }), + ('aplot', '0.1.9', { + 'checksums': ['af0763620a757571caac769bad5398c22a4890af6cb5646ac5fa9039a114bb12'], + }), + ('tidytree', '0.4.2', { + 'checksums': ['fbc4364d17e1b1c26ed06af0cdf36c88a5bc562fdbd4731ab179e30bba4009eb'], + }), +] + +moduleclass = 'lang' From 86cbfccfd772ab0c2f395a992b39f06f4c314f47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 25 Jan 2023 14:16:24 +0100 Subject: [PATCH 6293/9987] {chem}[foss/2022a] CatMAP v20220519, graphviz v0.20.1 w/ Python 3.10.4 --- .../c/CatMAP/CatMAP-20220519-foss-2022a.eb | 37 +++++++++++++++++++ .../graphviz-0.20.1-GCCcore-11.3.0.eb | 23 ++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb b/easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb new file mode 100644 index 00000000000..9c7e9919813 --- /dev/null +++ b/easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'CatMAP' +version = '20220519' +local_commit = '092f03a' + +homepage = 'https://catmap.readthedocs.io' +description = """Catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used + in catalyst screening.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('tqdm', '4.64.0'), + ('ASE', '3.22.1'), + ('gmpy2', '2.1.2'), + ('graphviz', '0.20.1'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/SUNCAT-Center/catmap/archive/'], + 'sources': [{'download_filename': '092f03a.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['b64c0bc7a1131c4dcc128e1d3cafe3802f2d7171e6819c52c4296f3d1e549e16'], + # work around incorrect version requirement for ASE which should only apply to Python < 3.5 + 'preinstallopts': "sed -i 's/ase==/ase>=/g' setup.py && ", + }), +] + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..707d5e3d8e2 --- /dev/null +++ b/easybuild/easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'graphviz' +version = '0.20.1' + +homepage = 'https://pypi.python.org/pypi/graphviz' +description = """Simple Python interface for Graphviz""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_ZIP] +checksums = ['8c58f14adaa3b947daf26c19bc1e98c4e0702cdc31cf99153e6f06904d492bf8'] + +dependencies = [ + ('Python', '3.10.4'), + ('Graphviz', '5.0.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From dd1e91279f84c8b538ab51d2d610327d55e2a568 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 25 Jan 2023 14:19:21 +0100 Subject: [PATCH 6294/9987] fix typo in PMIx-4.1.0 for EBROOTLIBFABRIC --- easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb index 5baa27f22e5..4ea23f25701 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb @@ -34,7 +34,7 @@ dependencies = [ configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' configopts += ' --with-hwloc=$EBROOTHWLOC' -configopts += ' --with-ofi=$EBROOTLIBFBARIC' +configopts += ' --with-ofi=$EBROOTLIBFABRIC' configopts += ' --enable-pmix-binaries' configopts += ' --disable-man-pages' From 01a6c41937d5cf8840c711321e79550d4516a8d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 25 Jan 2023 15:23:41 +0100 Subject: [PATCH 6295/9987] add missing binutils build dependency for graphviz 0.20.1 --- .../easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb index 707d5e3d8e2..fddf37afeda 100644 --- a/easybuild/easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb @@ -11,6 +11,10 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} sources = [SOURCE_ZIP] checksums = ['8c58f14adaa3b947daf26c19bc1e98c4e0702cdc31cf99153e6f06904d492bf8'] +builddependencies = [ + ('binutils', '2.38'), +] + dependencies = [ ('Python', '3.10.4'), ('Graphviz', '5.0.0'), From 9f089345cf5254c1427964ac04b286280e9f4d43 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 25 Jan 2023 16:07:41 +0100 Subject: [PATCH 6296/9987] adding easyconfigs: IJulia-1.24.0-Julia-1.8.5.eb --- .../i/IJulia/IJulia-1.24.0-Julia-1.8.5.eb | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/i/IJulia/IJulia-1.24.0-Julia-1.8.5.eb diff --git a/easybuild/easyconfigs/i/IJulia/IJulia-1.24.0-Julia-1.8.5.eb b/easybuild/easyconfigs/i/IJulia/IJulia-1.24.0-Julia-1.8.5.eb new file mode 100644 index 00000000000..4bdcde0a98d --- /dev/null +++ b/easybuild/easyconfigs/i/IJulia/IJulia-1.24.0-Julia-1.8.5.eb @@ -0,0 +1,80 @@ +easyblock = 'JuliaBundle' + +name = 'IJulia' +version = '1.24.0' +_julia_ver = '1.8.5' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/JuliaLang/IJulia.jl' +description = "Julia kernel for Jupyter" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), +] + +exts_list = [ + ('Preferences', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['a87c1fc863fcb6240c3f4327776fa01a1f87e0d2df5a0c1850f789ce24469da2'], + }), + ('JLLWrappers', '1.4.1', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], + }), + ('SnoopPrecompile', '2.10.0', { + 'source_urls': ['https://github.com/timholy/SnoopCompile.jl/archive/'], + 'checksums': ['e7af878e693c105ab5d792c8672b1534112f10b9693a2722a5aa8099c18c6d9a'], + 'start_dir': '%(name)s', + }), + ('Parsers', '2.5.1', { + 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], + 'checksums': ['72494acac42c7dff16e1a6ac1305f13001f3743e0021d158d097399f0567d926'], + }), + ('JSON', '0.21.3', { + 'source_urls': ['https://github.com/JuliaIO/JSON.jl/archive/'], + 'checksums': ['bd02a015da24b03f79d55967b29f5ceaba2477b559242576d74f02623bb1b6b1'], + }), + ('MbedTLS', '1.1.7', { + 'source_urls': ['https://github.com/JuliaLang/MbedTLS.jl/archive/'], + 'checksums': ['3df27a16ea31acf4eaf6cc9f3bd25b81960c10662722ffa22b13cb0e6ac11b12'], + }), + ('VersionParsing', '1.3.0', { + 'source_urls': ['https://github.com/JuliaInterop/VersionParsing.jl/archive/'], + 'checksums': ['f90fe419e1a40ef0eccfaaed1d1b7792d9115a059a82d0c23e3c04c944d0f8ca'], + }), + ('Conda', '1.7.0', { + 'source_urls': ['https://github.com/JuliaPy/Conda.jl/archive/'], + 'checksums': ['2077b1192e1cfa206caf441d9d91b0ca83aa935db89918f1fd69cd25c2415ced'], + }), + ('SoftGlobalScope', '1.1.0', { + 'source_urls': ['https://github.com/stevengj/SoftGlobalScope.jl/archive/'], + 'checksums': ['8d4264386c859403938498cd9ddd5e94e10181deba4a3e71d391b16750e3848b'], + }), + ('libsodium_jll', '1.0.20+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/libsodium_jll.jl/archive/'], + 'sources': [{'filename': 'libsodium-v%(version)s.tar.gz'}], + 'checksums': ['f7c3a17acc3a478ec10a4a49a0dd04694140f4483644ec9db638706ea9844aba'], + }), + ('ZeroMQ_jll', '4.3.4+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/ZeroMQ_jll.jl/archive/'], + 'sources': [{'filename': 'ZeroMQ-v%(version)s.tar.gz'}], + 'checksums': ['aa98ae3c7e050fc6bdf0b0132bb607dea2f6c062da7870b1ecada9f3c8ea8d72'], + }), + ('ZMQ', '1.2.1', { + 'source_urls': ['https://github.com/JuliaInterop/ZMQ.jl/archive/'], + 'checksums': ['8b42555340d0208e5a36cd5e8f29a3f0d44c13c064382d4b1e5d00c1c4a9dd96'], + }), + (name, version, { + 'preinstallopts': "mkdir -p %(installdir)s/jupyter && export JUPYTER_DATA_DIR=%(installdir)s/jupyter && ", + 'source_urls': ['https://github.com/JuliaLang/IJulia.jl/archive/'], + 'checksums': ['85b3ee48aee1688bcb89b8fb93c332551e3a75cfc7d17bb346daed36dedc358e'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'jupyter', +} + +moduleclass = 'lib' From 88ff5b22febf25f2b72c8092a1f2022d373b357e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Jan 2023 17:14:25 +0100 Subject: [PATCH 6297/9987] Fix whitespace style error --- .../easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb index 0626f3d8698..fd5b9dab93d 100644 --- a/easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb @@ -46,7 +46,7 @@ preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && " preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " -configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " +configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib -DHTSLIB_LIBRARIES=hts " sanity_check_paths = { From 21375785917bd05104195432663b015b8bd969d1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 25 Jan 2023 17:35:24 +0100 Subject: [PATCH 6298/9987] enhance OpenFold for standalone usage --- .../OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb | 33 +++++++++++++++++-- 1 file changed, 30 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb index fc4c449b810..8957d13fb75 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb @@ -4,6 +4,9 @@ name = 'OpenFold' version = '1.0.1' versionsuffix = '-CUDA-%(cudaver)s' +# _resources_dir = '%(installdir)s/lib/python%(pyshortver)s/site-packages/openfold/resources/' +# _resources_target_dir = '/databases/bio/%(namelower)s-%(version)s' + homepage = 'https://github.com/aqlaboratory/openfold' description = "A faithful PyTorch reproduction of DeepMind's AlphaFold 2" @@ -33,12 +36,15 @@ dependencies = [ # OpenFold also requires the AlphaFold modification to OpenMM # https://github.com/aqlaboratory/openfold/blob/v1.0.0/scripts/install_third_party_dependencies.sh#L20-L24 # https://github.com/aqlaboratory/openfold/blob/v1.0.0/lib/openmm.patch - ('OpenMM', '7.5.1', '-DeepMind-patch'), + ('OpenMM', '7.5.1', '-CUDA-%(cudaver)s-DeepMind-patch'), ] use_pip = True exts_list = [ + ('flash_attn', '0.2.8', { + 'checksums': ['b54fee86463cdb9933e8d47e500c52f3eaf283f1c8a9d96099e62acc7dc0be1f'], + }), ('PDBFixer', '1.7', { 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], @@ -80,13 +86,34 @@ exts_list = [ }), ] +postinstallcmds = [ + 'cp -a run_pretrained_openfold.py thread_sequence.py train_openfold.py %(installdir)s/bin', + 'cp -a scripts %(installdir)s', + 'chmod +x %(installdir)s/scripts/* %(installdir)s/scripts/alignment_db_scripts/* %(installdir)s/bin/*', + # manually download stereo_chemical_props.txt, openfold parameters and alphafold parameters + # see scripts download_alphafold_params.sh, download_openfold_params.sh ,install_third_party_dependencies.sh + # download to _resources_target_dir and add symlinks in _resources_dir + # or download directly into _resources_dir + # 'ln -s %s/stereo_chemical_props.txt %s' % (_resources_target_dir, _resources_dir), + # 'ln -s %s/openfold_params %s' % (_resources_target_dir, _resources_dir), + # 'ln -s %s/params %s' % (_resources_target_dir, _resources_dir), +] + +fix_python_shebang_for = ['bin/*.py', 'scripts/*.py'] + +modextrapaths = { + 'PATH': 'scripts', + 'PYTHONPATH': '', +} + sanity_check_paths = { - 'files': ['bin/pdbfixer'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], + 'files': ['bin/pdbfixer', 'bin/run_pretrained_openfold.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], } sanity_check_commands = [ "pdbfixer --help", + "run_pretrained_openfold.py --help", ] sanity_pip_check = True From 4133c3e59220154a20501efa0bf6020a226a2821 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 25 Jan 2023 17:38:19 +0100 Subject: [PATCH 6299/9987] add OpenMM dep --- ...1-foss-2021a-CUDA-11.3.1-DeepMind-patch.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-CUDA-11.3.1-DeepMind-patch.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-CUDA-11.3.1-DeepMind-patch.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-CUDA-11.3.1-DeepMind-patch.eb new file mode 100644 index 00000000000..1017fc70b4f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-CUDA-11.3.1-DeepMind-patch.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.1' +versionsuffix = '-CUDA-%(cudaver)s-DeepMind-patch' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + ('OpenMM-%(version)s_DeepMind.patch', 'wrappers/python'), + '%(name)s-7.5.0_fix_path_to_nvcc.patch', +] +checksums = [ + {'7.5.1.tar.gz': 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7'}, + {'OpenMM-7.5.1_DeepMind.patch': '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6'}, + {'OpenMM-7.5.0_fix_path_to_nvcc.patch': '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c'}, +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('CUDA', '11.3.1', '', SYSTEM), + ('SWIG', '4.0.2'), +] + +# runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 9983308063dea3f495d3f1028d8a110b147e23af Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 26 Jan 2023 09:10:35 +0100 Subject: [PATCH 6300/9987] remove leftover comment --- .../OpenMM/OpenMM-7.5.1-foss-2021a-CUDA-11.3.1-DeepMind-patch.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-CUDA-11.3.1-DeepMind-patch.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-CUDA-11.3.1-DeepMind-patch.eb index 1017fc70b4f..44bbbce31f6 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-CUDA-11.3.1-DeepMind-patch.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021a-CUDA-11.3.1-DeepMind-patch.eb @@ -34,7 +34,6 @@ dependencies = [ ('SWIG', '4.0.2'), ] -# runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ # Flags for CUDA-enabled build configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" From 251395a016a9e692cba118be3bab0038045bba7a Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 26 Jan 2023 11:49:29 +0100 Subject: [PATCH 6301/9987] adding easyconfigs: Giotto-Suite-3.0.1-foss-2022a-R-4.2.1.eb --- .../Giotto-Suite-3.0.1-foss-2022a-R-4.2.1.eb | 126 ++++++++++++++++++ 1 file changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/g/Giotto-Suite/Giotto-Suite-3.0.1-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/g/Giotto-Suite/Giotto-Suite-3.0.1-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/g/Giotto-Suite/Giotto-Suite-3.0.1-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..08fa5f81e1a --- /dev/null +++ b/easybuild/easyconfigs/g/Giotto-Suite/Giotto-Suite-3.0.1-foss-2022a-R-4.2.1.eb @@ -0,0 +1,126 @@ +easyblock = 'Bundle' + +name = 'Giotto-Suite' +version = '3.0.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/drieslab/Giotto' +description = """Giotto Suite is focused on building a modular platform for analyzing spatial-omics technologies + and strives to be interoperable with other popular spatial analysis tools and classes. Using established packages + optimized for large(r) data, Giotto Suite adopts fast and memory efficient methods to create an interactive + analysis.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('python-igraph', '0.10.3'), + ('python-louvain', '0.16'), + ('leidenalg', '0.9.1'), + ('networkx', '2.8.4'), + ('smfishHmrf', '1.3.3'), + ('SpatialDE', '1.1.3'), + ('scanpy', '1.9.1'), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.16/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +exts_list = [ + ('smfishHmrf', '0.1', { + 'checksums': ['4b098f348a3460209eedc9592288bbe20e9072f56aa13407cb65ff10aebfd5cc'], + }), + ('BiocGenerics', '0.44.0', { + 'checksums': ['8518e462c1ef103ab059d059d871afc444e48f56fe6b3afdb60dc1abf6c9b09d'], + }), + ('S4Vectors', '0.36.1', { + 'checksums': ['db4c251e674bd7cc66f4ed9d301294b3478686436204aec9c5740e0fabd59a9a'], + }), + ('IRanges', '2.32.0', { + 'checksums': ['097935916b5cb33804e1ea09fa6c4ee7ddeaa03eef99138a05b1896b28dc6a4b'], + }), + ('limma', '3.54.0', { + 'checksums': ['aae6bb0af0bd80677a01c48c96b99fc1a58c4a670a21fec87e135038972dc7cb'], + }), + ('BiocParallel', '1.32.5', { + 'checksums': ['395ed5c19fb706ca73c841c843c3a89f8a88f774a26415bfdbac0dca92a5a6f9'], + }), + ('MatrixGenerics', '1.10.0', { + 'checksums': ['09fbea178608186571acabc18cd2b81fe5c7aa2d143f5d456ceaed55e01b4815'], + }), + ('DelayedArray', '0.24.0', { + 'checksums': ['d764b4f487b49ca04150ea7d8f5f180683cd80575d67a162e4a99cd52bd8815a'], + }), + ('sparseMatrixStats', '1.10.0', { + 'checksums': ['60f523d2c70b926768070373b9fd05dafcc53e822b3dfd406fe95b4b541e02e7'], + }), + ('Matrix', '1.5-3', { + 'checksums': ['4e720f4edc97b1c09646a445851b1ce955caf6b1de8306a2283328b526fee00d'], + }), + ('DelayedMatrixStats', '1.20.0', { + 'checksums': ['63ca262c2b92966759ba9d2ebdea7500a4dd859e9f87c17408522f80693e9661'], + }), + ('beachmat', '2.14.0', { + 'checksums': ['d52485edb2919fe2b1a75999fd583c8eee7b9608fbe406bcf8d1c99312e44169'], + }), + ('RcppAnnoy', '0.0.20', { + 'checksums': ['dcc6c7e091154d0a5698472e0fc7ed77976941c7376d21e019c90c3efaeacf85'], + }), + ('rsvd', '1.0.5', { + 'checksums': ['e40686b869acd4f71fdb1e8e7a6c64cd6792fc9d52a78f9e559a7176ab84e21e'], + }), + ('ScaledMatrix', '1.6.0', { + 'checksums': ['815ac82cc510995eaccfc521fdb65c153f25e8432d301b0da8fbe5f6d337b953'], + }), + ('BiocSingular', '1.14.0', { + 'checksums': ['738abd56358dd2bd56890380345b05d453be000005ba93d40571bbc8aaff3110'], + }), + ('sitmo', '2.0.2', { + 'checksums': ['448ef8d56e36783354011845daf33f1efb83ea3b9685eea75eaf5134e24fa8c2'], + }), + ('dqrng', '0.3.0', { + 'checksums': ['4beeabfe245ce7196b07369f2a7d277cb08869ad8b45a22c6354c4cc70a39abb'], + }), + ('uwot', '0.1.11', { + 'checksums': ['4fcf90f1369a2a1f01db9e05a2365b155b2ada8e51e1f7f3ba5122d86affd41b'], + }), + ('dbscan', '1.1-11', { + 'checksums': ['f0498e67e612629340a2758fbe747c4d9d4ca648f002230a03499cb73735e62f'], + }), + (name, version, { + 'modulename': 'Giotto', + 'source_urls': ['https://github.com/drieslab/Giotto/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['cbe08439d2e1a3edac1f46032c4c8511ef2cc9371bf49e0730ba7ee0e4c942ca'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['Giotto'], +} + +moduleclass = 'bio' From 865ef8c6e9b08055ffdcf192f68594e041e9f22f Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 26 Jan 2023 13:17:05 +0100 Subject: [PATCH 6302/9987] Add forgotten configs for dependencies --- .../python-louvain-0.16-foss-2022a.eb | 25 +++++++++++ .../s/SpatialDE/SpatialDE-1.1.3-foss-2022a.eb | 43 +++++++++++++++++++ .../silhouetteRank-1.0.5.13-foss-2022a.eb | 30 +++++++++++++ .../smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb | 28 ++++++++++++ 4 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/silhouetteRank/silhouetteRank-1.0.5.13-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022a.eb b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022a.eb new file mode 100644 index 00000000000..0be4ba83665 --- /dev/null +++ b/easybuild/easyconfigs/p/python-louvain/python-louvain-0.16-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'python-louvain' +version = '0.16' + +homepage = 'https://pypi.org/project/python-louvain' +description = "Louvain algorithm for community detection" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'] + +dependencies = [ + ('Python', '3.10.4'), + ('networkx', '2.8.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'community'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3-foss-2022a.eb b/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3-foss-2022a.eb new file mode 100644 index 00000000000..cb04593a0be --- /dev/null +++ b/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'SpatialDE' +version = '1.1.3' + +homepage = 'https://pypi.org/project/SpatialDE' +description = """SpatialDE is a method to identify genes which significantly depend on spatial coordinates in + non-linear and non-parametric ways. The intended applications are spatially resolved RNA-sequencing from e.g. + Spatial Transcriptomics, or in situ gene expression measurements from e.g. SeqFISH or MERFISH.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('patsy', '0.5.3', { + 'checksums': ['bdc18001875e319bc91c812c1eb6a10be4bb13cb81eb763f466179dca3b67277'], + }), + ('NaiveDE', '1.2.0', { + 'modulename': 'NaiveDE', + 'checksums': ['339258edcb34a5e82661ec6b1ae850bf15dc875dd4fa687bb05d0721f25bf8ad'], + }), + (name, version, { + 'modulename': 'SpatialDE', + 'patches': ['%(name)s-%(version)s_fix-readme-location.patch'], + 'checksums': [ + {'SpatialDE-1.1.3.tar.gz': '7005e63ac7abfdbff1d50bff5a25e53050f1015dbf243627ec2c1303641eee27'}, + {'SpatialDE-1.1.3_fix-readme-location.patch': + 'bcba0ba475a4d98797a9fa4c31d717923c4a3170922036686cd9c917a308ca5c'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/silhouetteRank/silhouetteRank-1.0.5.13-foss-2022a.eb b/easybuild/easyconfigs/s/silhouetteRank/silhouetteRank-1.0.5.13-foss-2022a.eb new file mode 100644 index 00000000000..8d1dc071c82 --- /dev/null +++ b/easybuild/easyconfigs/s/silhouetteRank/silhouetteRank-1.0.5.13-foss-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'silhouetteRank' +version = '1.0.5.13' + +homepage = 'https://pypi.org/project/silhouetteRank' +description = """silhouetteRank is a tool for finding spatially variable genes based on computing silhouette + coefficient from binarized spatial gene expression data""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4b3e3b9c3e84e67df96b7c441fd072a1a1a72b9f9790491fe3274259b3ef666a'] + +dependencies = [ + ('Python', '3.10.4'), + ('Seaborn', '0.12.1'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('matplotlib', '3.5.2'), + ('R', '4.2.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'silhouetteRank'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb b/easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb new file mode 100644 index 00000000000..412d551f098 --- /dev/null +++ b/easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'smfishHmrf' +version = '1.3.3' + +homepage = 'https://pypi.org/project/smfishHmrf' +description = "smFish spatial pattern mining and cell type prediction" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2fed45be8b5a5d47657cd4c8e9023b9ea6624863fc55a12afda092c6be37ca93'] + +dependencies = [ + ('Python', '3.10.4'), + ('Seaborn', '0.12.1'), + ('matplotlib', '3.5.2'), + ('scikit-learn', '1.1.2'), + ('Java', '11.0.2', '', SYSTEM), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'smfishHmrf'} + +moduleclass = 'bio' From 1fcb8dbd25ae866f09bae7ca4755e7b2a543973e Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 26 Jan 2023 14:10:21 +0100 Subject: [PATCH 6303/9987] Add forgotten patch --- .../SpatialDE-1.1.3_fix-readme-location.patch | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3_fix-readme-location.patch diff --git a/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3_fix-readme-location.patch b/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3_fix-readme-location.patch new file mode 100644 index 00000000000..8594b3410f8 --- /dev/null +++ b/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3_fix-readme-location.patch @@ -0,0 +1,11 @@ +--- setup.py.back 2023-01-19 14:18:38.000000000 +0100 ++++ setup.py 2023-01-19 14:21:12.000000000 +0100 +@@ -7,7 +7,7 @@ + name='SpatialDE', + version='1.1.3', + description='Spatial and Temporal DE test', +- long_description=(HERE.parent / 'README.rst').read_text(), ++ long_description=(HERE / 'README.rst').read_text(), + url='https://github.com/Teichlab/SpatialDE', + packages=find_packages(), + include_package_data=True, From 76c022620cc8849cb01b0526ef3f7755218387e0 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Thu, 26 Jan 2023 15:07:44 +0100 Subject: [PATCH 6304/9987] Update SRAdownloader-3.9-GCCcore-11.3.0.eb --- .../s/SRAdownloader/SRAdownloader-3.9-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SRAdownloader/SRAdownloader-3.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SRAdownloader/SRAdownloader-3.9-GCCcore-11.3.0.eb index 99c70182524..bee0c3be8b0 100644 --- a/easybuild/easyconfigs/s/SRAdownloader/SRAdownloader-3.9-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SRAdownloader/SRAdownloader-3.9-GCCcore-11.3.0.eb @@ -34,4 +34,4 @@ sanity_check_commands = [ 'sradownloader --version' ] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From e0c1af8d39d229c02b9af1c832a7d89f290f2002 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 26 Jan 2023 15:21:22 +0100 Subject: [PATCH 6305/9987] adding easyconfigs: code-server-4.9.1.eb --- .../c/code-server/code-server-4.9.1.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/code-server/code-server-4.9.1.eb diff --git a/easybuild/easyconfigs/c/code-server/code-server-4.9.1.eb b/easybuild/easyconfigs/c/code-server/code-server-4.9.1.eb new file mode 100644 index 00000000000..2b8d9965a8c --- /dev/null +++ b/easybuild/easyconfigs/c/code-server/code-server-4.9.1.eb @@ -0,0 +1,20 @@ +name = 'code-server' +version = '4.9.1' + +homepage = 'https://github.com/cdr/code-server' +description = """Run VS Code on any machine anywhere and access it in the browser.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cdr/code-server/releases/download/v%(version)s/'] +sources = ['code-server-%(version)s-linux-%(mapped_arch)s.tar.gz'] +checksums = [ + { + 'code-server-%(version)s-linux-amd64.tar.gz': + '3ea79c9dc03544ea06abe7da660c1bc0e4376337070211d98ffa8c33889cd57e', + 'code-server-%(version)s-linux-arm64.tar.gz': + '6e9fedb726eb13b5ef60a77bf16a1ee9911684b7e211e90eee7a0e9e82bac9e4', + } +] + +moduleclass = 'tools' From 334c5d82ee6b60bf419c024e3c6c932c0e6c1bc8 Mon Sep 17 00:00:00 2001 From: agustinaucar Date: Thu, 26 Jan 2023 11:26:14 -0300 Subject: [PATCH 6306/9987] DIRAC22 - 64bits intel compilation --- .../d/DIRAC/DIRAC-22.0-intel-2021a-int64.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-int64.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-int64.eb new file mode 100644 index 00000000000..2312beb3d6e --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-int64.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '22.0' +versionsuffix = '-int64' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'usempi': True, 'i8': True} + +source_urls = ['https://zenodo.org/record/6010450/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +checksums = ['c8c011b5bc2ca36a2ef76b2deb911638321655fcae1d1b146cacfa1b5f783711'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('HDF5', '1.10.7') +] + +configopts = '-DMKL_FLAG=sequential ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_64BIT_INTEGERS=True ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' + +runtest = 'test ARGS="-R pam_test" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From eff58ba47344f8b85974a66fa62b206b46efb845 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 26 Jan 2023 15:43:59 +0100 Subject: [PATCH 6307/9987] Add description of SpatialDE patch --- .../s/SpatialDE/SpatialDE-1.1.3_fix-readme-location.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3_fix-readme-location.patch b/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3_fix-readme-location.patch index 8594b3410f8..348508ad0dd 100644 --- a/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3_fix-readme-location.patch +++ b/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3_fix-readme-location.patch @@ -1,3 +1,4 @@ +Fix problem where setup.py cannot find README.rst in main directory --- setup.py.back 2023-01-19 14:18:38.000000000 +0100 +++ setup.py 2023-01-19 14:21:12.000000000 +0100 @@ -7,7 +7,7 @@ From 389159aa85bd18d114a97ac94f32c17d56c71f87 Mon Sep 17 00:00:00 2001 From: Jakub Klust Date: Thu, 26 Jan 2023 15:52:47 +0100 Subject: [PATCH 6308/9987] adding easyconfigs: MaxQuant-2.2.0.0-GCCcore-11.2.0.eb --- .../MaxQuant-2.2.0.0-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.2.0.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.2.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.2.0.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..fc196bd4a59 --- /dev/null +++ b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.2.0.0-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'MaxQuant' +version = '2.2.0.0' + +homepage = 'https://maxquant.org/maxquant' +description = """MaxQuant is a quantitative proteomics software package designed for analyzing large + mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling + techniques as well as label-free quantification are supported.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +# requires registration at https://www.maxquant.org/download_asset/maxquant/latest +sources = ['%(name)s_%(version)s.zip'] +checksums = ['4a286f33b701d0c03045dbde937e342ec4ea9d75b4f76d27b7dc7daac9cc89ab'] + +dependencies = [('Mono', '6.12.0.122')] + +sanity_check_paths = { + 'files': ['%(name)s.exe', 'bin/%(name)sCmd.exe', 'bin/%(name)sGui.exe'], + 'dirs': [], +} + +sanity_check_commands = [ + ("mono $EBROOTMAXQUANT/bin/MaxQuantCmd.exe --version 2>&1 | grep -q %(version)s", ''), + ("mono $EBROOTMAXQUANT/bin/MaxQuantCmd.exe --help 2>&1 | grep -q USAGE", '')] + +modaliases = { + 'maxquantcmd': 'mono $EBROOTMAXQUANT/bin/%(name)sCmd.exe', + 'maxquantgui': 'mono $EBROOTMAXQUANT/bin/%(name)sGui.exe', +} + +modloadmsg = """ +To run MaxQuant in command-line mode: maxquantcmd + in GUI mode: maxquantgui +""" + +moduleclass = 'bio' From a5e6313acc4c900eeb0c34a4d48ec5f15113dcf1 Mon Sep 17 00:00:00 2001 From: Jakub Klust Date: Thu, 26 Jan 2023 15:55:11 +0100 Subject: [PATCH 6309/9987] adding easyconfigs: Perseus-2.0.7.0-GCCcore-11.2.0.eb --- .../Perseus/Perseus-2.0.7.0-GCCcore-11.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perseus/Perseus-2.0.7.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Perseus/Perseus-2.0.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perseus/Perseus-2.0.7.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..f138232f7dc --- /dev/null +++ b/easybuild/easyconfigs/p/Perseus/Perseus-2.0.7.0-GCCcore-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'Perseus' +version = '2.0.7.0' + +homepage = 'https://maxquant.org/perseus' +description = """The Perseus software platform supports biological and biomedical researchers + in interpreting protein quantification, interaction and post-translational modification data.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +# requires registration at https://maxquant.org/download_asset/perseus/latest +sources = ['%(name)s_%(version)s.zip'] +checksums = ['32418ff43c975762aaf4b2760ec1dd5c998e34188739d592f656fea296edb5c8'] + +dependencies = [('Mono', '6.12.0.122')] + +sanity_check_paths = { + 'files': ['%(name)s.exe', 'bin/%(name)sGui.exe'], + 'dirs': [], +} + +sanity_check_commands = [ + ("cat $EBROOTPERSEUS/ChangeLog.txt | grep -q %(version)s", ''), +] + +modaliases = { + 'perseus': 'mono $EBROOTPERSEUS/%(name)sGui.exe', +} + +modloadmsg = """ +To run Perseus in GUI mode: perseus +""" + +moduleclass = 'bio' From b4106683b48470fad17e8a9033ed651c10a2617d Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Thu, 26 Jan 2023 16:03:14 +0100 Subject: [PATCH 6310/9987] adding easyconfigs: SVG-2.87-foss-2022a.eb, FLINT-2.9.0-GCC-11.3.0.eb, polymake-4.8-foss-2022a.eb --- .../f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb | 34 +++++++++++++++++ .../p/polymake/polymake-4.8-foss-2022a.eb | 37 +++++++++++++++++++ .../easyconfigs/s/SVG/SVG-2.87-foss-2022a.eb | 26 +++++++++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/SVG/SVG-2.87-foss-2022a.eb diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..90131d5e4c4 --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'FLINT' +version = '2.9.0' + +homepage = 'https://www.flintlib.org/' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.flintlib.org'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2fc090d51033c93208e6c10d406397a53c983ae5343b958eb25f72a57a4ce76a'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), +] + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb new file mode 100644 index 00000000000..46e00aeae35 --- /dev/null +++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'polymake' +version = '4.8' + +homepage = 'https://polymake.org' +description = """polymake is open source software for research in polyhedral geometry. +It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, +graphs, tropical hypersurfaces, and other objects.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://polymake.org/lib/exe/fetch.php/download/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['3f7bd19d6ac1372ae32368e57134ff37a11fbe9eb1f6abe8195b34c5eec29b11'] + +dependencies = [ + ('Ninja', '1.10.2'), + ('libxml2', '2.9.13'), + ('libxslt', '1.1.34'), + ('libreadline', '8.1'), + ('Perl', '5.34.1'), + ('SVG', '2.87'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('Boost', '1.79.0'), + ('FLINT', '2.9.0'), + ('Java', '15', '', True), +] + +sanity_check_paths = { + 'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT, + 'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT], + 'dirs': ['include/polymake', 'lib/polymake', 'share/polymake'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SVG/SVG-2.87-foss-2022a.eb b/easybuild/easyconfigs/s/SVG/SVG-2.87-foss-2022a.eb new file mode 100644 index 00000000000..f91ec5bbac9 --- /dev/null +++ b/easybuild/easyconfigs/s/SVG/SVG-2.87-foss-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'PerlModule' + +name = 'SVG' +version = '2.87' + +homepage = 'https://metacpan.org/pod/SVG' +description = "Perl binding for SVG" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b3fa58c1c59942b4ebef003da97c3e01e531480ca29e8efbe327ff0589c0bd3c'] + +dependencies = [ + ('Perl', '5.34.1'), +] + +options = {'modulename': 'SVG'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/SVG.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/SVG'], +} + +moduleclass = 'data' From 6fc23c020d5277340978121a100ba2c986b4ca18 Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Thu, 26 Jan 2023 16:32:45 +0100 Subject: [PATCH 6311/9987] FFmpeg-5.0.1-GCCcore-11.3.0.eb: Add SDL2 dependency to build ffplay --- .../easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb index 8bb0209eb4e..ebc2ab69c20 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb @@ -27,14 +27,15 @@ dependencies = [ ('freetype', '2.12.1'), ('fontconfig', '2.14.0'), ('FriBidi', '1.0.12'), + ('SDL2', '2.0.22'), ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' -configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig --enable-sdl2 ' configopts += '--enable-libfribidi' sanity_check_paths = { - 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe']] + + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] From 4b9f9b0197657cb2f74d290922c937ee8f284fa6 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 26 Jan 2023 16:37:44 +0100 Subject: [PATCH 6312/9987] Update Java version for smfishHmrf --- .../easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb b/easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb index 412d551f098..6a5eb876501 100644 --- a/easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb +++ b/easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Seaborn', '0.12.1'), ('matplotlib', '3.5.2'), ('scikit-learn', '1.1.2'), - ('Java', '11.0.2', '', SYSTEM), + ('Java', '11.0.16', '', SYSTEM), ] download_dep_fail = True From 2b28714028b2879ddcfab47fdcccb989972030c3 Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Thu, 26 Jan 2023 16:37:55 +0100 Subject: [PATCH 6313/9987] FFmpeg: Move --enable-sdl2 to last line --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb index ebc2ab69c20..2722e5d9006 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb @@ -31,8 +31,8 @@ dependencies = [ ] configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' -configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig --enable-sdl2 ' -configopts += '--enable-libfribidi' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi --enable-sdl2' sanity_check_paths = { 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + From 647d599ce665488c0642387e71a6d362f4fcd40c Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Thu, 26 Jan 2023 16:38:30 +0100 Subject: [PATCH 6314/9987] Java 11 default for 2022a, and good enough for polymake. --- easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb index 46e00aeae35..ec8be91d379 100644 --- a/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb +++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb @@ -25,7 +25,7 @@ dependencies = [ ('MPFR', '4.1.0'), ('Boost', '1.79.0'), ('FLINT', '2.9.0'), - ('Java', '15', '', True), + ('Java', '11', '', True), ] sanity_check_paths = { From e33b517f620ed8a6e8f1ad00b5dd5ed47144dd0c Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 26 Jan 2023 16:41:48 +0100 Subject: [PATCH 6315/9987] Update SpatialDE patch checksum --- easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3-foss-2022a.eb b/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3-foss-2022a.eb index cb04593a0be..06aba2b48da 100644 --- a/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SpatialDE/SpatialDE-1.1.3-foss-2022a.eb @@ -33,7 +33,7 @@ exts_list = [ 'checksums': [ {'SpatialDE-1.1.3.tar.gz': '7005e63ac7abfdbff1d50bff5a25e53050f1015dbf243627ec2c1303641eee27'}, {'SpatialDE-1.1.3_fix-readme-location.patch': - 'bcba0ba475a4d98797a9fa4c31d717923c4a3170922036686cd9c917a308ca5c'}, + 'b53cd62efe0ec9132ff161b2bad7c175d102a329edae45bbf290230cc7d95fb2'}, ], }), ] From efc4495259b83fb8865d2d080c14cd794c512ee3 Mon Sep 17 00:00:00 2001 From: agustinaucar Date: Thu, 26 Jan 2023 13:08:33 -0300 Subject: [PATCH 6316/9987] Shorter test --- easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-int64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-int64.eb index 2312beb3d6e..9ac0ca334a5 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-int64.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-22.0-intel-2021a-int64.eb @@ -30,7 +30,7 @@ configopts += '-DENABLE_PCMSOLVER=off ' pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' -runtest = 'test ARGS="-R pam_test" ' +runtest = 'test ARGS="-R symmetry_scf_energy" ' sanity_check_paths = { 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], From 09ae9a1a0a8ed4838ee33212798031ed63353d25 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 26 Jan 2023 18:05:41 +0100 Subject: [PATCH 6317/9987] adding easyconfigs: stardist-0.8.3-foss-2021b.eb --- .../s/stardist/stardist-0.8.3-foss-2021b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb new file mode 100644 index 00000000000..68f62497f7d --- /dev/null +++ b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'stardist' +version = '0.8.3' + +homepage = 'https://github.com/stardist/stardist' +description = "Object Detection with Star-convex Shapes." + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.9.6'), + ('TensorFlow', '2.7.1'), + ('numba', '0.54.1'), + ('imageio', '2.13.5'), + ('scikit-image', '0.19.1'), + ('tqdm', '4.62.3'), +] + +use_pip = True + +exts_list = [ + ('tifffile', '2022.10.10', { + 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], + }), + ('csbdeep', '0.7.2', { + 'checksums': ['8a000eb71d04aa753f52ffe81a34c0a30a06ee986d20b9986d76272253e2fd53'], + }), + ('edt', '2.3.0', { + 'checksums': ['220e2086fdf32bbd8964df76b3e1a42061ece1f4b9ea95ec83a094d24d258664'], + }), + (name, version, { + 'checksums': ['8ac1f6165ca8e8496651c6e2b49ce57d6d574dfb22bf6f63ddaec1f64b8868d1'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/stardist-predict2d'], + 'dirs': ['bin'], +} + +moduleclass = 'tools' From 5d55225e23d44e57f9ec816a6defe180555fa968 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Thu, 26 Jan 2023 18:12:27 +0100 Subject: [PATCH 6318/9987] Rename SRAdownloader-3.9-GCCcore-11.3.0.eb to sradownloader-3.9-GCCcore-11.3.0.eb --- ...-3.9-GCCcore-11.3.0.eb => sradownloader-3.9-GCCcore-11.3.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/SRAdownloader/{SRAdownloader-3.9-GCCcore-11.3.0.eb => sradownloader-3.9-GCCcore-11.3.0.eb} (100%) diff --git a/easybuild/easyconfigs/s/SRAdownloader/SRAdownloader-3.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SRAdownloader/sradownloader-3.9-GCCcore-11.3.0.eb similarity index 100% rename from easybuild/easyconfigs/s/SRAdownloader/SRAdownloader-3.9-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/s/SRAdownloader/sradownloader-3.9-GCCcore-11.3.0.eb From 6cd3e73dd91fbe69816e885671caa9136b866a13 Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Thu, 26 Jan 2023 18:45:44 +0100 Subject: [PATCH 6319/9987] Rename easybuild/easyconfigs/s/SRAdownloader/sradownloader-3.9-GCCcore-11.3.0.eb to easybuild/easyconfigs/s/sradownloader/sradownloader-3.9-GCCcore-11.3.0.eb --- .../sradownloader-3.9-GCCcore-11.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/{SRAdownloader => sradownloader}/sradownloader-3.9-GCCcore-11.3.0.eb (100%) diff --git a/easybuild/easyconfigs/s/SRAdownloader/sradownloader-3.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/sradownloader/sradownloader-3.9-GCCcore-11.3.0.eb similarity index 100% rename from easybuild/easyconfigs/s/SRAdownloader/sradownloader-3.9-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/s/sradownloader/sradownloader-3.9-GCCcore-11.3.0.eb From e48bfd591ead837400dd24fa5c2d7ab2249c0f06 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 26 Jan 2023 19:23:23 +0100 Subject: [PATCH 6320/9987] set JULIA_DEPOT_PATH and JULIA_HISTORY in Julia --- .../j/Julia/Julia-1.6.5-linux-x86_64.eb | 15 ++++++++++ .../j/Julia/Julia-1.6.6-linux-x86_64.eb | 15 ++++++++++ .../j/Julia/Julia-1.6.7-linux-x86_64.eb | 15 ++++++++++ .../j/Julia/Julia-1.7.0-linux-x86_64.eb | 15 ++++++++++ .../j/Julia/Julia-1.7.1-linux-x86_64.eb | 15 ++++++++++ .../j/Julia/Julia-1.7.2-linux-x86_64.eb | 15 ++++++++++ .../j/Julia/Julia-1.7.3-linux-x86_64.eb | 15 ++++++++++ .../j/Julia/Julia-1.8.0-linux-x86_64.eb | 15 ++++++++++ .../j/Julia/Julia-1.8.2-linux-x86_64.eb | 15 ++++++++++ .../j/Julia/Julia-1.8.5-linux-x86_64.eb | 30 +++++++++++++++++++ 10 files changed, 165 insertions(+) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb index 9488e9084d1..2d06511dc08 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb @@ -28,4 +28,19 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] +_depot_paths = ':'.join([ + # default shared directory in install dir + '%(installdir)s/share/julia', + # allow users to add their own packages to Julia + '~/.julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) + # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb index 1ceea6444d5..aed8623dde7 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb @@ -28,4 +28,19 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] +_depot_paths = ':'.join([ + # default shared directory in install dir + '%(installdir)s/share/julia', + # allow users to add their own packages to Julia + '~/.julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) + # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb index 65d335bfb8c..3101c0d69fb 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb @@ -28,4 +28,19 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] +_depot_paths = ':'.join([ + # default shared directory in install dir + '%(installdir)s/share/julia', + # allow users to add their own packages to Julia + '~/.julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) + # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb index 55407f9c4f0..8d0d71e88c9 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb @@ -28,4 +28,19 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] +_depot_paths = ':'.join([ + # default shared directory in install dir + '%(installdir)s/share/julia', + # allow users to add their own packages to Julia + '~/.julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) + # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb index 79469033db5..acf27d328de 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb @@ -28,4 +28,19 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] +_depot_paths = ':'.join([ + # default shared directory in install dir + '%(installdir)s/share/julia', + # allow users to add their own packages to Julia + '~/.julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) + # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb index d77bb480f1b..6ba496e97b2 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb @@ -28,4 +28,19 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] +_depot_paths = ':'.join([ + # default shared directory in install dir + '%(installdir)s/share/julia', + # allow users to add their own packages to Julia + '~/.julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) + # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb index 84b7a95dba2..9f61082c329 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb @@ -28,4 +28,19 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] +_depot_paths = ':'.join([ + # default shared directory in install dir + '%(installdir)s/share/julia', + # allow users to add their own packages to Julia + '~/.julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) + # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb index 07b8c3a4138..149083b00cc 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb @@ -28,4 +28,19 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] +_depot_paths = ':'.join([ + # default shared directory in install dir + '%(installdir)s/share/julia', + # allow users to add their own packages to Julia + '~/.julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) + # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb index dcca93e7871..152b7ec1d72 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb @@ -28,4 +28,19 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] +_depot_paths = ':'.join([ + # default shared directory in install dir + '%(installdir)s/share/julia', + # allow users to add their own packages to Julia + '~/.julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) + # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb index 6e35ceec42f..d895bab4fcb 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb @@ -28,4 +28,34 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] +_depot_paths = ':'.join([ + # default shared directory in install dir + '%(installdir)s/share/julia', + # allow users to add their own packages to Julia + '~/.julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) + # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + +_depot_paths = ':'.join([ + # default shared directory in install dir + '%(installdir)s/share/julia', + # allow users to add their own packages to Julia + '~/.julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) + # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + moduleclass = 'lang' From 64852890477edbd8167275b35d8fc3f48b9cfbbb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 26 Jan 2023 19:25:12 +0100 Subject: [PATCH 6321/9987] remove duplicate code from Julia-1.8.5-linux-x86_64.eb --- .../j/Julia/Julia-1.8.5-linux-x86_64.eb | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb index d895bab4fcb..f0b02f1ec3c 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb @@ -43,19 +43,4 @@ modextravars = { 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', } -_depot_paths = ':'.join([ - # default shared directory in install dir - '%(installdir)s/share/julia', - # allow users to add their own packages to Julia - '~/.julia', -]) - -modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) - # by default it will point to the DEPOT_PATH (install dir) of the last module loaded - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', -} - moduleclass = 'lang' From ab01bd22c6e71b2c9027ca807c8e3fdb859bb240 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Thu, 26 Jan 2023 20:55:39 +0100 Subject: [PATCH 6322/9987] Migrate to GCCcore, change to SYSTEM template, use libreadline 8.2.1. --- .../p/polymake/polymake-4.8-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2fdec6097f3 --- /dev/null +++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'polymake' +version = '4.8' + +homepage = 'https://polymake.org' +description = """polymake is open source software for research in polyhedral geometry. +It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, +graphs, tropical hypersurfaces, and other objects.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://polymake.org/lib/exe/fetch.php/download/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['3f7bd19d6ac1372ae32368e57134ff37a11fbe9eb1f6abe8195b34c5eec29b11'] + +dependencies = [ + ('Ninja', '1.10.2'), + ('libxml2', '2.9.13'), + ('libxslt', '1.1.34'), + ('libreadline', '8.1.2'), + ('Perl', '5.34.1'), + ('SVG', '2.87'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('Boost', '1.79.0'), + ('FLINT', '2.9.0'), + ('Java', '11', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT, + 'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT], + 'dirs': ['include/polymake', 'lib/polymake', 'share/polymake'], +} + +moduleclass = 'math' From 9b708b26e623aad673986955d97c31fa2451e49d Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Thu, 26 Jan 2023 23:15:05 +0100 Subject: [PATCH 6323/9987] Move polymake and its dependencies to GCCcore, and add binutils as a build dependency for polymake. --- .../p/polymake/polymake-4.8-GCCcore-11.3.0.eb | 4 ++ .../p/polymake/polymake-4.8-foss-2022a.eb | 37 ------------------- ...ss-2022a.eb => SVG-2.87-GCCcore-11.3.0.eb} | 2 +- 3 files changed, 5 insertions(+), 38 deletions(-) delete mode 100644 easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb rename easybuild/easyconfigs/s/SVG/{SVG-2.87-foss-2022a.eb => SVG-2.87-GCCcore-11.3.0.eb} (91%) diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb index 2fdec6097f3..1223b8e6183 100644 --- a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb @@ -28,6 +28,10 @@ dependencies = [ ('Java', '11', '', SYSTEM), ] +builddependencies = [ + ('binutils', '2.38') +] + sanity_check_paths = { 'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT, 'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb deleted file mode 100644 index ec8be91d379..00000000000 --- a/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2022a.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'polymake' -version = '4.8' - -homepage = 'https://polymake.org' -description = """polymake is open source software for research in polyhedral geometry. -It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, -graphs, tropical hypersurfaces, and other objects.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -source_urls = ['https://polymake.org/lib/exe/fetch.php/download/'] -sources = [SOURCE_TAR_BZ2] -checksums = ['3f7bd19d6ac1372ae32368e57134ff37a11fbe9eb1f6abe8195b34c5eec29b11'] - -dependencies = [ - ('Ninja', '1.10.2'), - ('libxml2', '2.9.13'), - ('libxslt', '1.1.34'), - ('libreadline', '8.1'), - ('Perl', '5.34.1'), - ('SVG', '2.87'), - ('GMP', '6.2.1'), - ('MPFR', '4.1.0'), - ('Boost', '1.79.0'), - ('FLINT', '2.9.0'), - ('Java', '11', '', True), -] - -sanity_check_paths = { - 'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT, - 'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT], - 'dirs': ['include/polymake', 'lib/polymake', 'share/polymake'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SVG/SVG-2.87-foss-2022a.eb b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCCcore-11.3.0.eb similarity index 91% rename from easybuild/easyconfigs/s/SVG/SVG-2.87-foss-2022a.eb rename to easybuild/easyconfigs/s/SVG/SVG-2.87-GCCcore-11.3.0.eb index f91ec5bbac9..2b400b7de84 100644 --- a/easybuild/easyconfigs/s/SVG/SVG-2.87-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCCcore-11.3.0.eb @@ -6,7 +6,7 @@ version = '2.87' homepage = 'https://metacpan.org/pod/SVG' description = "Perl binding for SVG" -toolchain = {'name': 'foss', 'version': '2022a'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR/'] sources = [SOURCE_TAR_GZ] From c1da5fb321aa566ed760e4c7cdd46e202c8a7006 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 27 Jan 2023 07:44:20 +0100 Subject: [PATCH 6324/9987] Whitespace change to rerun github actions. --- easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb index 1223b8e6183..95e795fab67 100644 --- a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb @@ -39,3 +39,4 @@ sanity_check_paths = { } moduleclass = 'math' + From a939e602f706f2db08890fabd53412de07403667 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 27 Jan 2023 09:09:59 +0100 Subject: [PATCH 6325/9987] Adding binutils as a dependency for SVG, remove whitespace from polymake. --- .../easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb | 1 - easybuild/easyconfigs/s/SVG/SVG-2.87-GCCcore-11.3.0.eb | 4 ++++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb index 95e795fab67..1223b8e6183 100644 --- a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb @@ -39,4 +39,3 @@ sanity_check_paths = { } moduleclass = 'math' - diff --git a/easybuild/easyconfigs/s/SVG/SVG-2.87-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCCcore-11.3.0.eb index 2b400b7de84..3c94cef114e 100644 --- a/easybuild/easyconfigs/s/SVG/SVG-2.87-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCCcore-11.3.0.eb @@ -16,6 +16,10 @@ dependencies = [ ('Perl', '5.34.1'), ] +builddependencies = [ + ('binutils', '2.38') +] + options = {'modulename': 'SVG'} sanity_check_paths = { From b254384a76666f006efbeb060cad088fbe23494a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 27 Jan 2023 09:36:17 +0100 Subject: [PATCH 6326/9987] move variables down to where they are used --- .../o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb index 8957d13fb75..786ec1dc2a1 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb @@ -4,9 +4,6 @@ name = 'OpenFold' version = '1.0.1' versionsuffix = '-CUDA-%(cudaver)s' -# _resources_dir = '%(installdir)s/lib/python%(pyshortver)s/site-packages/openfold/resources/' -# _resources_target_dir = '/databases/bio/%(namelower)s-%(version)s' - homepage = 'https://github.com/aqlaboratory/openfold' description = "A faithful PyTorch reproduction of DeepMind's AlphaFold 2" @@ -86,6 +83,9 @@ exts_list = [ }), ] +# _resources_dir = '%(installdir)s/lib/python%(pyshortver)s/site-packages/openfold/resources/' +# _resources_target_dir = '/databases/bio/%(namelower)s-%(version)s' + postinstallcmds = [ 'cp -a run_pretrained_openfold.py thread_sequence.py train_openfold.py %(installdir)s/bin', 'cp -a scripts %(installdir)s', From f1ef0414607ebdf98684a87dac356d2694dc8337 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Fri, 27 Jan 2023 10:13:16 +0100 Subject: [PATCH 6327/9987] Tweak startdist sanity check and moduleclass --- .../s/stardist/stardist-0.8.3-foss-2021b.eb | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb index 68f62497f7d..527256b2790 100644 --- a/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb +++ b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b.eb @@ -38,8 +38,13 @@ exts_list = [ sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/stardist-predict2d'], - 'dirs': ['bin'], + 'files': ['bin/stardist-predict2d', 'bin/stardist-predict3d'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -moduleclass = 'tools' +sanity_check_commands = [ + "stardist-predict2d --help", + "stardist-predict3d --help", +] + +moduleclass = 'vis' From 54a2f0acf10548bbbfa063f80d55f2bf53701ae3 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 27 Jan 2023 10:25:17 +0100 Subject: [PATCH 6328/9987] GCCcore vs GCC. We need Boost, and Boost isn't found in GCCcore. --- ...ake-4.8-GCCcore-11.3.0.eb => polymake-4.8-GCC-11.3.0.eb} | 6 +----- .../{SVG-2.87-GCCcore-11.3.0.eb => SVG-2.87-GCC-11.3.0.eb} | 6 +----- 2 files changed, 2 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/p/polymake/{polymake-4.8-GCCcore-11.3.0.eb => polymake-4.8-GCC-11.3.0.eb} (91%) rename easybuild/easyconfigs/s/SVG/{SVG-2.87-GCCcore-11.3.0.eb => SVG-2.87-GCC-11.3.0.eb} (84%) diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb similarity index 91% rename from easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb index 1223b8e6183..bb766d01955 100644 --- a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb @@ -8,7 +8,7 @@ description = """polymake is open source software for research in polyhedral geo It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, graphs, tropical hypersurfaces, and other objects.""" -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://polymake.org/lib/exe/fetch.php/download/'] sources = [SOURCE_TAR_BZ2] @@ -28,10 +28,6 @@ dependencies = [ ('Java', '11', '', SYSTEM), ] -builddependencies = [ - ('binutils', '2.38') -] - sanity_check_paths = { 'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT, 'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/SVG/SVG-2.87-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.3.0.eb similarity index 84% rename from easybuild/easyconfigs/s/SVG/SVG-2.87-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.3.0.eb index 3c94cef114e..fad1c422e21 100644 --- a/easybuild/easyconfigs/s/SVG/SVG-2.87-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.3.0.eb @@ -6,7 +6,7 @@ version = '2.87' homepage = 'https://metacpan.org/pod/SVG' description = "Perl binding for SVG" -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR/'] sources = [SOURCE_TAR_GZ] @@ -16,10 +16,6 @@ dependencies = [ ('Perl', '5.34.1'), ] -builddependencies = [ - ('binutils', '2.38') -] - options = {'modulename': 'SVG'} sanity_check_paths = { From 6b55fa04e4659596e199a016ed51c6f2ad7ae14f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 27 Jan 2023 11:00:42 +0100 Subject: [PATCH 6329/9987] move scripts dir into bin --- .../OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb index 786ec1dc2a1..9c2d76927db 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb @@ -38,6 +38,7 @@ dependencies = [ use_pip = True +# flash_attn (FlashAttention) is optional, speeds up MSA attention for sequences with < 1000 residues exts_list = [ ('flash_attn', '0.2.8', { 'checksums': ['b54fee86463cdb9933e8d47e500c52f3eaf283f1c8a9d96099e62acc7dc0be1f'], @@ -88,8 +89,8 @@ exts_list = [ postinstallcmds = [ 'cp -a run_pretrained_openfold.py thread_sequence.py train_openfold.py %(installdir)s/bin', - 'cp -a scripts %(installdir)s', - 'chmod +x %(installdir)s/scripts/* %(installdir)s/scripts/alignment_db_scripts/* %(installdir)s/bin/*', + 'cp -a scripts %(installdir)s/bin', + 'chmod -R a+x %(installdir)s/bin', # manually download stereo_chemical_props.txt, openfold parameters and alphafold parameters # see scripts download_alphafold_params.sh, download_openfold_params.sh ,install_third_party_dependencies.sh # download to _resources_target_dir and add symlinks in _resources_dir @@ -99,16 +100,15 @@ postinstallcmds = [ # 'ln -s %s/params %s' % (_resources_target_dir, _resources_dir), ] -fix_python_shebang_for = ['bin/*.py', 'scripts/*.py'] +fix_python_shebang_for = ['bin/*.py', '/bin/scripts/*.py'] modextrapaths = { - 'PATH': 'scripts', - 'PYTHONPATH': '', + 'PATH': 'bin/scripts', } sanity_check_paths = { 'files': ['bin/pdbfixer', 'bin/run_pretrained_openfold.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'bin/scripts'], } sanity_check_commands = [ From 725c24588b62bb69b68952d05bf7b69137978296 Mon Sep 17 00:00:00 2001 From: Jakub Klust Date: Fri, 27 Jan 2023 12:20:51 +0100 Subject: [PATCH 6330/9987] introduce download_instructions and fix of source tarball name for MaxQuant --- .../m/MaxQuant/MaxQuant-2.2.0.0-GCCcore-11.2.0.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.2.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.2.0.0-GCCcore-11.2.0.eb index fc196bd4a59..f12c0cf7c87 100644 --- a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.2.0.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.2.0.0-GCCcore-11.2.0.eb @@ -10,8 +10,13 @@ description = """MaxQuant is a quantitative proteomics software package designed toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -# requires registration at https://www.maxquant.org/download_asset/maxquant/latest -sources = ['%(name)s_%(version)s.zip'] +download_instructions = """ +To download the MaxQuant source tarball, register at: + https://www.maxquant.org/download_asset/maxquant/latest +You should receive a unique download URL via email. +""" + +sources = ['%(name)s_v%(version)s.zip'] checksums = ['4a286f33b701d0c03045dbde937e342ec4ea9d75b4f76d27b7dc7daac9cc89ab'] dependencies = [('Mono', '6.12.0.122')] From 4bba7407f4b1aee0c555d24e00956f72717fe279 Mon Sep 17 00:00:00 2001 From: Jakub Klust Date: Fri, 27 Jan 2023 12:39:43 +0100 Subject: [PATCH 6331/9987] introduce download_instructions and fix of source tarball name for Perseus --- .../p/Perseus/Perseus-2.0.7.0-GCCcore-11.2.0.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perseus/Perseus-2.0.7.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perseus/Perseus-2.0.7.0-GCCcore-11.2.0.eb index f138232f7dc..d6a5710e91d 100644 --- a/easybuild/easyconfigs/p/Perseus/Perseus-2.0.7.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perseus/Perseus-2.0.7.0-GCCcore-11.2.0.eb @@ -9,8 +9,13 @@ description = """The Perseus software platform supports biological and biomedica toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -# requires registration at https://maxquant.org/download_asset/perseus/latest -sources = ['%(name)s_%(version)s.zip'] +download_instructions = """ +To download the Perseus source tarball, register at: + https://maxquant.org/download_asset/perseus/latest +You should receive a unique download URL via email. +""" + +sources = ['%(name)s_v%(version)s.zip'] checksums = ['32418ff43c975762aaf4b2760ec1dd5c998e34188739d592f656fea296edb5c8'] dependencies = [('Mono', '6.12.0.122')] From 14f0e956f959791000eb13964ed056c27ff0a0af Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Fri, 27 Jan 2023 12:54:11 +0100 Subject: [PATCH 6332/9987] HDF5 with nvompi --- .../h/HDF5/HDF5-1.12.2-nvompi-2022.07.eb | 23 +++++++++++++++++++ .../h/HDF5/HDF5-1.14.0-nvompi-2022.07.eb | 22 ++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-nvompi-2022.07.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-nvompi-2022.07.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-nvompi-2022.07.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-nvompi-2022.07.eb new file mode 100644 index 00000000000..4d787687f05 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-nvompi-2022.07.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.12.2' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'nvompi', 'version': '2022.07'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-nvompi-2022.07.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-nvompi-2022.07.eb new file mode 100644 index 00000000000..0d207fe1c78 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-nvompi-2022.07.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.0' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'nvompi', 'version': '2022.07'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From 8ebe809d369039761d04d4c2a4bbcf8051e6b24e Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Fri, 27 Jan 2023 13:33:36 +0100 Subject: [PATCH 6333/9987] HDF5 has a FORTRAN api so must be at compiler level --- ...core-8.3.0-serial.eb => HDF5-1.10.5-GCC-8.3.0-serial.eb} | 6 +----- ...re-11.3.0-serial.eb => HDF5-1.12.2-GCC-11.3.0-serial.eb} | 6 +----- ...re-11.3.0-serial.eb => HDF5-1.13.1-GCC-11.3.0-serial.eb} | 6 +----- 3 files changed, 3 insertions(+), 15 deletions(-) rename easybuild/easyconfigs/h/HDF5/{HDF5-1.10.5-GCCcore-8.3.0-serial.eb => HDF5-1.10.5-GCC-8.3.0-serial.eb} (87%) rename easybuild/easyconfigs/h/HDF5/{HDF5-1.12.2-GCCcore-11.3.0-serial.eb => HDF5-1.12.2-GCC-11.3.0-serial.eb} (87%) rename easybuild/easyconfigs/h/HDF5/{HDF5-1.13.1-GCCcore-11.3.0-serial.eb => HDF5-1.13.1-GCC-11.3.0-serial.eb} (87%) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-GCCcore-8.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-GCC-8.3.0-serial.eb similarity index 87% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-GCCcore-8.3.0-serial.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-GCC-8.3.0-serial.eb index 7bc2b35825e..9862e5f86f1 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-GCCcore-8.3.0-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.5-GCC-8.3.0-serial.eb @@ -7,17 +7,13 @@ description = """HDF5 is a data model, library, and file format for storing and It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.""" -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchain = {'name': 'GCC', 'version': '8.3.0'} toolchainopts = {'pic': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8'] -builddependencies = [ - ('binutils', '2.32'), -] - dependencies = [ ('zlib', '1.2.11'), ('Szip', '2.1.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCC-11.3.0-serial.eb similarity index 87% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCC-11.3.0-serial.eb index 494b1335329..ce6efc4e6ba 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCCcore-11.3.0-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-GCC-11.3.0-serial.eb @@ -8,17 +8,13 @@ description = """HDF5 is a data model, library, and file format for storing and It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.""" -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchain = {'name': 'GCC', 'version': '11.3.0'} toolchainopts = {'pic': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] -builddependencies = [ - ('binutils', '2.38'), -] - dependencies = [ ('zlib', '1.2.12'), ('Szip', '2.1.1'), diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-GCCcore-11.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-GCC-11.3.0-serial.eb similarity index 87% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-GCCcore-11.3.0-serial.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-GCC-11.3.0-serial.eb index b73831007eb..60a4e24dfdb 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-GCCcore-11.3.0-serial.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.1-GCC-11.3.0-serial.eb @@ -7,17 +7,13 @@ description = """HDF5 is a data model, library, and file format for storing and It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.""" -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchain = {'name': 'GCC', 'version': '11.3.0'} toolchainopts = {'pic': True} source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53'] -builddependencies = [ - ('binutils', '2.38'), -] - dependencies = [ ('zlib', '1.2.12'), ('Szip', '2.1.1'), From 08b97da69e34e5ba406dd9f7f5608e98073ddeda Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 27 Jan 2023 14:36:40 +0100 Subject: [PATCH 6334/9987] adding easyconfigs: NVSHMEM-2.8.0-gompi-2022a-CUDA-11.7.0.eb --- .../NVSHMEM-2.8.0-gompi-2022a-CUDA-11.7.0.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.8.0-gompi-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.8.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.8.0-gompi-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..567b80452c4 --- /dev/null +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.8.0-gompi-2022a-CUDA-11.7.0.eb @@ -0,0 +1,70 @@ +easyblock = 'ConfigureMake' + +name = 'NVSHMEM' +version = '2.8.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nvshmem' +description = """NVSHMEM is a parallel programming interface based on OpenSHMEM that provides +efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a +global address space for data that spans the memory of multiple GPUs and can be +accessed with fine-grained GPU-initiated operations, CPU-initiated operations, +and operations on CUDA streams. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +download_instructions = """The sources of NVSHMEM can be downloaded at NVIDIA's webpage when you have signed up for +their (free) developer program: +https://developer.nvidia.com/nvshmem-downloads""" + +sources = ['%(namelower)s_src_%(version)s-3.txz'] +checksums = ['7d4ef226630a94b587d18e02c27decc8b41d6f4ee52a26e25644b23cd18da81f'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('NCCL', '2.12.12', versionsuffix), +] + +skipsteps = ['configure'] + +prebuildopts = 'export %s &&' % ' '.join([ + 'NVSHMEM_USE_GDRCOPY=1', + 'GDRCOPY_HOME=${EBROOTGDRCOPY}', + + 'MPI_HOME=${EBROOTOPENMPI}', + 'NVSHMEM_MPI_SUPPORT=1', + 'NVSHMEMTEST_USE_MPI_LAUNCHER=1', + + 'NCCL_HOME=${EBROOTNCCL}', + 'NVSHMEM_USE_NCCL=1', + + 'NVSHMEM_BUILDDIR=%(builddir)s', + 'NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj', + 'NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj', + 'NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj', + 'NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj', + + 'NVSHMEM_PREFIX=%(installdir)s', + 'NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples', + 'NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest', + 'NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest', + 'NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test', +]) + +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['lib/libnvshmem.a', 'lib/nvshmem_bootstrap_mpi.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +modextravars = {'NVSHMEM_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 68b6febf512d22dd14f8d0fddd07bac8e55d9184 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 27 Jan 2023 13:43:44 +0000 Subject: [PATCH 6335/9987] Update scanpy-1.9.1-foss-2022a.eb --- easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb index 2cc7d0044d6..b9d1a3f9edb 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2022a.eb @@ -1,4 +1,3 @@ -# updated: Denis Kristak (INUITS) easyblock = 'PythonBundle' name = 'scanpy' @@ -41,9 +40,6 @@ exts_list = [ ('anndata', '0.8.0', { 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], }), - ('pynndescent', '0.5.8', { - 'checksums': ['a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b'], - }), ('stdlib-list', '0.8.0', { 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], }), From 6fe47351b593803ef3c7d5ff9df255501fd76d03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Jan 2023 15:25:49 +0100 Subject: [PATCH 6336/9987] rename 'graphviz' to 'graphviz-python' to avoid clash with 'Graphviz' in lowercase module naming schemes --- .../easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb | 2 +- .../graphviz-python-0.20.1-GCCcore-11.3.0.eb} | 7 +++++-- 2 files changed, 6 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/{graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb => graphviz-python/graphviz-python-0.20.1-GCCcore-11.3.0.eb} (74%) diff --git a/easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb b/easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb index 9c7e9919813..70327741b67 100644 --- a/easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb @@ -17,7 +17,7 @@ dependencies = [ ('tqdm', '4.64.0'), ('ASE', '3.22.1'), ('gmpy2', '2.1.2'), - ('graphviz', '0.20.1'), + ('graphviz-python', '0.20.1'), ] use_pip = True diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.20.1-GCCcore-11.3.0.eb similarity index 74% rename from easybuild/easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.20.1-GCCcore-11.3.0.eb index fddf37afeda..47df85eff8b 100644 --- a/easybuild/easyconfigs/g/graphviz/graphviz-0.20.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.20.1-GCCcore-11.3.0.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'graphviz' +name = 'graphviz-python' version = '0.20.1' homepage = 'https://pypi.python.org/pypi/graphviz' @@ -8,7 +8,8 @@ description = """Simple Python interface for Graphviz""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -sources = [SOURCE_ZIP] +source_urls = ['https://pypi.python.org/packages/source/g/graphviz'] +sources = ['graphviz-%(version)s.zip'] checksums = ['8c58f14adaa3b947daf26c19bc1e98c4e0702cdc31cf99153e6f06904d492bf8'] builddependencies = [ @@ -24,4 +25,6 @@ download_dep_fail = True use_pip = True sanity_pip_check = True +options = {'modulename': 'graphviz'} + moduleclass = 'vis' From 13c7567ad3ebc9117445fcc065638583aad36780 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 27 Jan 2023 15:37:03 +0100 Subject: [PATCH 6337/9987] Add sanity_check_commands --- easybuild/easyconfigs/s/SSW/SSW-1.2.4-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SSW/SSW-1.2.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/SSW/SSW-1.2.4-GCCcore-10.3.0.eb index 4323761d2bd..38ed30716b3 100644 --- a/easybuild/easyconfigs/s/SSW/SSW-1.2.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/s/SSW/SSW-1.2.4-GCCcore-10.3.0.eb @@ -45,4 +45,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["ssw_test 2>&1 | grep 'Usage:'"] + moduleclass = 'lib' From a5bd74af13750cd79d2fc25cc208c3fc7701a783 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Jan 2023 16:07:31 +0100 Subject: [PATCH 6338/9987] don't hardcode commit ID in sources spec for CatMAP Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb b/easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb index 70327741b67..108a61cb5d6 100644 --- a/easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CatMAP/CatMAP-20220519-foss-2022a.eb @@ -25,7 +25,7 @@ use_pip = True exts_list = [ (name, version, { 'source_urls': ['https://github.com/SUNCAT-Center/catmap/archive/'], - 'sources': [{'download_filename': '092f03a.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['b64c0bc7a1131c4dcc128e1d3cafe3802f2d7171e6819c52c4296f3d1e549e16'], # work around incorrect version requirement for ASE which should only apply to Python < 3.5 'preinstallopts': "sed -i 's/ase==/ase>=/g' setup.py && ", From 4d604d9a7a22d24d951b0f762746cf5d0a77e25d Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Fri, 27 Jan 2023 16:33:15 +0100 Subject: [PATCH 6339/9987] Fix long lines --- easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-nvompi-2022.07.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-nvompi-2022.07.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-nvompi-2022.07.eb index 4d787687f05..753cb09454a 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-nvompi-2022.07.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-nvompi-2022.07.eb @@ -10,7 +10,7 @@ description = """HDF5 is a data model, library, and file format for storing and toolchain = {'name': 'nvompi', 'version': '2022.07'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] @@ -19,5 +19,4 @@ dependencies = [ ('Szip', '2.1.1'), ] - moduleclass = 'data' From 57aea52630af0df6cf1ba8628c675e9d67f46897 Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Fri, 27 Jan 2023 17:21:19 +0100 Subject: [PATCH 6340/9987] Remove 1.14.0 --- .../h/HDF5/HDF5-1.14.0-nvompi-2022.07.eb | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-nvompi-2022.07.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-nvompi-2022.07.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-nvompi-2022.07.eb deleted file mode 100644 index 0d207fe1c78..00000000000 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-nvompi-2022.07.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'HDF5' -# Note: Odd minor releases are only RCs and should not be used. -version = '1.14.0' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'nvompi', 'version': '2022.07'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4'] - -dependencies = [ - ('zlib', '1.2.12'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' From 370fe07a82d608843055ea3e0c54494a5e8d6a2c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Jan 2023 17:25:42 +0100 Subject: [PATCH 6341/9987] adding easyconfigs: Inferelator-0.6.1-foss-2022a.eb --- .../Inferelator-0.6.1-foss-2022a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/i/Inferelator/Inferelator-0.6.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/i/Inferelator/Inferelator-0.6.1-foss-2022a.eb b/easybuild/easyconfigs/i/Inferelator/Inferelator-0.6.1-foss-2022a.eb new file mode 100644 index 00000000000..6507aebe1f9 --- /dev/null +++ b/easybuild/easyconfigs/i/Inferelator/Inferelator-0.6.1-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Inferelator' +version = '0.6.1' + +homepage = 'https://github.com/flatironinstitute/inferelator' +description = """Inferelator 3.0 is a package for gene regulatory network inference that is based on + regularized regression.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('scikit-learn', '1.1.2'), + ('h5py', '3.7.0'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.2.0', { + 'checksums': ['57f85b72c688b09e053cdac302dd5b5b53df5f73ae20b4874fcbffd8bf783d11'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + ('inferelator', version, { + 'checksums': ['4ae106ca5f67c876983f025013e8b1464c1eaaf9e54f204888bf90369c8e6852'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 6ff63ca6f37167dfb846b8ad43a459aadc5765a6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Jan 2023 19:43:13 +0100 Subject: [PATCH 6342/9987] add sanity check command for JAGS 4.3.1 --- easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb index ae245350d6c..b821886818f 100644 --- a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.1-foss-2022a.eb @@ -23,10 +23,12 @@ checksums = ['f9258355b5e9eb13bd33c5fa720f0cbebacea7d0a4a42b71b0fb14501ee14229'] configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'files': ['bin/jags', 'libexec/jags-terminal', 'lib/libjags.%s' % SHLIB_EXT], 'dirs': [], } +sanity_check_commands = ["echo 'list modules' | jags"] + modextrapaths = { 'JAGS_INCLUDE': 'include/%(name)s', 'JAGS_LIB': 'lib', From b4b7e6775c47be8795c48f48e68a6a77bebdd0fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Jan 2023 20:17:24 +0100 Subject: [PATCH 6343/9987] add random + R2WinBUGS extensions to R 4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 08a5dae76fc..ec890257003 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3403,6 +3403,12 @@ exts_list = [ ('shadowtext', '0.1.2', { 'checksums': ['253c4e737dbb302aa0729e5074e84cbfde2a73bfd7a0fd2c74b557cb728bae7d'], }), + ('random', '0.2.6', { + 'checksums': ['2b59f9bce0c3ebf8215ab42dffaf9a1c7eea7468964063215a8d422af953b069'], + }), + ('R2WinBUGS', '2.1-21', { + 'checksums': ['fa86cb5140f5dfce29f9517b94d6d08c316ddcffa4aa3085945b84d34910134d'], + }), ] moduleclass = 'lang' From 6c5a81b436551bdbef20bf48094368fffa7f98a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Jan 2023 20:49:17 +0100 Subject: [PATCH 6344/9987] adding easyconfigs: dclone-2.3-0-foss-2022a-R-4.2.1.eb --- .../dclone/dclone-2.3-0-foss-2022a-R-4.2.1.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/d/dclone/dclone-2.3-0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/d/dclone/dclone-2.3-0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/d/dclone/dclone-2.3-0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..7e26f246617 --- /dev/null +++ b/easybuild/easyconfigs/d/dclone/dclone-2.3-0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'dclone' +version = '2.3-0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/dclone' +description = """Low level functions for implementing maximum likelihood estimating procedures for complex models + using data cloning and Bayesian Markov chain Monte Carlo methods""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['50ff2f3f5b9c72b16a58e61d4f42af4e782ee44da83a5778ce1ada6af5872b70'] + +dependencies = [ + ('R', '4.2.1'), + ('rjags', '4-13', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From 4c27acfd1836b0641dd54a7663ca770dd0ab1e4e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 27 Jan 2023 20:50:33 +0100 Subject: [PATCH 6345/9987] {math}[foss/2022a] R2jags v0.7-1 w/ R 4.2.1 --- .../R2jags/R2jags-0.7-1-foss-2022a-R-4.2.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/R2jags/R2jags-0.7-1-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/r/R2jags/R2jags-0.7-1-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R2jags/R2jags-0.7-1-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..8cc67b6d8df --- /dev/null +++ b/easybuild/easyconfigs/r/R2jags/R2jags-0.7-1-foss-2022a-R-4.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'R2jags' +version = '0.7-1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/R2jags' +description = "Providing wrapper functions to implement Bayesian analysis in JAGS." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['3b097261c0b20b89a021bbc5087523a24f17249fa14c527cd54c5e5b2970226a'] + +dependencies = [ + ('R', '4.2.1'), + ('rjags', '4-13', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From 07bd337a806564b202d14de97f7fb8562bdf578e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 28 Jan 2023 12:51:21 +0100 Subject: [PATCH 6346/9987] adding easyconfigs: NVHPC-22.9-CUDA-11.7.0.eb --- .../n/NVHPC/NVHPC-22.9-CUDA-11.7.0.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-22.9-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-22.9-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.9-CUDA-11.7.0.eb new file mode 100644 index 00000000000..4ce5187120b --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.9-CUDA-11.7.0.eb @@ -0,0 +1,76 @@ +name = 'NVHPC' +version = '22.9' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2022_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + 'bc4473f04b49bc9a26f08c17a72360650ddf48a3b6eefacdc525d79c8d730f30', + local_tarball_tmpl % 'ppc64le': + '9aac31d36bb09f6653544978021f5b78c272112e7748871566f7e930f5e7475b', + local_tarball_tmpl % 'x86_64': + 'aebfeb826ace3dabf9699f72390ca0340f8789a8ef6fe4032e3c7b794f073ea3', + } +] + +local_gccver = '11.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.38', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.14', '', ('GCCcore', local_gccver)), + ('CUDA', '11.7.0', '', SYSTEM), +] + +module_add_cuda = False + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/22.3/cuda/) +# for NVHPC 22.3, those are: 11.6, 11.0, 10.2; +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '%(cudaver)s' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From a096ddeb264959d51c51e5dab9b9ad726a7df987 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 28 Jan 2023 12:51:37 +0100 Subject: [PATCH 6347/9987] adding easyconfigs: NVHPC-22.11-CUDA-11.7.0.eb --- .../n/NVHPC/NVHPC-22.11-CUDA-11.7.0.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-22.11-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-22.11-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.11-CUDA-11.7.0.eb new file mode 100644 index 00000000000..0dcb2916241 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.11-CUDA-11.7.0.eb @@ -0,0 +1,76 @@ +name = 'NVHPC' +version = '22.11' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2022_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + 'e60e798657c33b06754d33dfd5ab3bea2882d4a9b9476102303edf2bbe3b7a95', + local_tarball_tmpl % 'ppc64le': + 'ef800203cf6040b3a5df24f19944b272f62caee8362875bcb394e86dc1de2353', + local_tarball_tmpl % 'x86_64': + 'cb91b3a04368457d5cfe3c0e9c0611591fdc8076b01ea977343fe7db7fdcfa3c', + } +] + +local_gccver = '11.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.38', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.14', '', ('GCCcore', local_gccver)), + ('CUDA', '11.7.0', '', SYSTEM), +] + +module_add_cuda = False + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/22.3/cuda/) +# for NVHPC 22.3, those are: 11.6, 11.0, 10.2; +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '%(cudaver)s' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From 0fd11409b0d6caf2d295fa7a6be54b7892bd2f21 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 28 Jan 2023 12:51:52 +0100 Subject: [PATCH 6348/9987] adding easyconfigs: NVHPC-23.1-CUDA-12.0.0.eb --- .../n/NVHPC/NVHPC-23.1-CUDA-12.0.0.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-23.1-CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-23.1-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-23.1-CUDA-12.0.0.eb new file mode 100644 index 00000000000..fedcb3d3bc0 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-23.1-CUDA-12.0.0.eb @@ -0,0 +1,76 @@ +name = 'NVHPC' +version = '23.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2023_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + '5b430e03752954ea62ac1c745b1735cfdaa43b2e981a9412c1465ecb0412fff6', + local_tarball_tmpl % 'ppc64le': + '81759e7c747bf4f552b75e7657301f76ecc0828b94fe860f81108c6e83e6ad2b', + local_tarball_tmpl % 'x86_64': + '55a064415f6d4ce6a01823ee27ebd266f4fb579679871e7c1a7c054bdc18e9f5', + } +] + +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.16', '', ('GCCcore', local_gccver)), + ('CUDA', '12.0.0', '', SYSTEM), +] + +module_add_cuda = False + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/22.3/cuda/) +# for NVHPC 22.3, those are: 11.6, 11.0, 10.2; +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '%(cudaver)s' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From 165bb8175398047e0384529e684413db255d344e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 28 Jan 2023 12:18:36 +0000 Subject: [PATCH 6349/9987] fix CMake print summary for long hostnames for NECI --- .../n/NECI/NECI-20220711-foss-2022a.eb | 6 +++++- .../NECI-20220711_fix-cmake-print-summary.patch | 15 +++++++++++++++ 2 files changed, 20 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/NECI/NECI-20220711_fix-cmake-print-summary.patch diff --git a/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb b/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb index 71c70f8ab4a..91ea5a5d835 100644 --- a/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb +++ b/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb @@ -19,7 +19,11 @@ sources = [{ }, 'filename': SOURCE_TAR_GZ, }] -checksums = [None] +patches = ['NECI-20220711_fix-cmake-print-summary.patch'] +checksums = [ + None, + 'e189f1b3991b28502dbd8285a04784e7e422d0a9e01e3f28025d0458b479af2d', +] builddependencies = [ ('CMake', '3.23.1'), diff --git a/easybuild/easyconfigs/n/NECI/NECI-20220711_fix-cmake-print-summary.patch b/easybuild/easyconfigs/n/NECI/NECI-20220711_fix-cmake-print-summary.patch new file mode 100644 index 00000000000..000e4879148 --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20220711_fix-cmake-print-summary.patch @@ -0,0 +1,15 @@ +If the _content passed to the box_side macro is too long then it fails +Patch by Simon Branford (University of Birmingham) +--- cmake/neci_print_summary.cmake.orig 2023-01-28 12:12:05.844153000 +0000 ++++ cmake/neci_print_summary.cmake 2023-01-28 12:12:26.698259000 +0000 +@@ -28,9 +28,7 @@ + feature_summary( WHAT ALL INCLUDE_QUIET_PACKAGES) + + macro( box_side _content ) +- string( LENGTH "${_content}" _len ) +- string( SUBSTRING " |" ${_len} -1 _box_tail ) +- message( STATUS " | ${_content}${_box_tail}" ) ++ message( STATUS " | ${_content} |" ) + endmacro() + + string(TIMESTAMP _time "%Y-%m-%d %H:%M") From 5c37d1a148110c24ec1041e057b683fcd2e6d584 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 29 Jan 2023 12:13:05 +0100 Subject: [PATCH 6350/9987] fix website/docs links in README --- README.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index b06cc3cf03a..b1a8f61b44b 100644 --- a/README.rst +++ b/README.rst @@ -4,7 +4,7 @@ .. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg -`EasyBuild `_ is a software build +`EasyBuild `_ is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. @@ -14,7 +14,7 @@ Easyconfig files are used to specify which software to build, which version of the software (and its dependencies), which build parameters to use (e.g., which compiler toolchain to use), etc. -The EasyBuild documentation is available at http://easybuild.readthedocs.org/. +The EasyBuild documentation is available at http://docs.easybuild.io/. The easybuild-easyconfigs package is hosted on GitHub, along with an issue tracker for bug reports and feature requests, see From dc0ff463c9047dcacd2d70ddad3a9c5f3cfa1e53 Mon Sep 17 00:00:00 2001 From: Bob Date: Mon, 30 Jan 2023 09:53:08 +0100 Subject: [PATCH 6351/9987] adding easyconfigs: Miniconda3-22.11.1-1.eb, QIIME2-2022.11.eb --- .../m/Miniconda3/Miniconda3-22.11.1-1.eb | 17 ++++++++++ .../easyconfigs/q/QIIME2/QIIME2-2022.11.eb | 31 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/Miniconda3/Miniconda3-22.11.1-1.eb create mode 100644 easybuild/easyconfigs/q/QIIME2/QIIME2-2022.11.eb diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-22.11.1-1.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-22.11.1-1.eb new file mode 100644 index 00000000000..9b74ed9e7b1 --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-22.11.1-1.eb @@ -0,0 +1,17 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda3' +version = '22.11.1-1' + +homepage = 'https://docs.conda.io/en/latest/miniconda.html' +description = """Miniconda is a free minimal installer for conda. It is a small, + bootstrap version of Anaconda that includes only conda, Python, the packages they + depend on, and a small number of other useful packages.""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/miniconda/'] +sources = ['%(name)s-py38_%(version)s-Linux-x86_64.sh'] +checksums = ['473e5ecc8e078e9ef89355fbca21f8eefa5f9081544befca99867c7beac3150d'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.11.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.11.eb new file mode 100644 index 00000000000..d709d4458ce --- /dev/null +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.11.eb @@ -0,0 +1,31 @@ +# EasyBuild recipy for QIIME2 +# Author: Caspar van Leeuwen +# SURFsara - The Netherlands + +easyblock = 'Conda' + +name = 'QIIME2' +version = '2022.11' + +homepage = 'http://qiime2.org/' +description = """QIIME is an open-source bioinformatics pipeline for performing microbiome analysis + from raw DNA sequencing data.""" + +source_urls = ['https://data.qiime2.org/distro/core/'] +sources = ['qiime2-%(version)s-py38-linux-conda.yml'] +checksums = ['79c250efd2d464b13702f8e210a921e9aa830dd33a0330966129121770a9188c'] + +toolchain = SYSTEM + +builddependencies = [('Miniconda3', '22.11.1-1')] + +environment_file = 'qiime2-%(version)s-py38-linux-conda.yml' + +sanity_check_commands = ['qiime info'] + +sanity_check_paths = { + 'files': ["bin/qiime"], + 'dirs': ["lib", "include"], +} + +moduleclass = 'bio' From d555e18583684711762456480a75d1b6ae0dd5fa Mon Sep 17 00:00:00 2001 From: Victor Enrique Goitea <43407659+VictorGoitea@users.noreply.github.com> Date: Mon, 30 Jan 2023 10:39:38 +0100 Subject: [PATCH 6352/9987] Update easybuild/easyconfigs/s/sradownloader/sradownloader-3.9-GCCcore-11.3.0.eb Co-authored-by: Adam Huffman --- .../s/sradownloader/sradownloader-3.9-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sradownloader/sradownloader-3.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/sradownloader/sradownloader-3.9-GCCcore-11.3.0.eb index bee0c3be8b0..3dbf97a9a7e 100644 --- a/easybuild/easyconfigs/s/sradownloader/sradownloader-3.9-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/sradownloader/sradownloader-3.9-GCCcore-11.3.0.eb @@ -7,7 +7,7 @@ version = '3.9' homepage = "https://github.com/s-andrews/sradownloader" description = """SRAdownloader takes the annotation table from the SRA run selector tool -and retrives the raw fastq files for the selected samples""" +and retrieves the raw fastq files for the selected samples""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} From e09c26168a8d0b1f3d876076578ab0ecc83a4079 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 30 Jan 2023 11:16:20 +0100 Subject: [PATCH 6353/9987] adding easyconfigs: MUMmer-4.0.0rc1-GCCcore-11.3.0.eb --- .../MUMmer/MUMmer-4.0.0rc1-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d078c854c66 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'MUMmer' +version = '4.0.0rc1' + +homepage = 'https://mummer.sourceforge.net/' + +description = """ + MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['85006adb2d6539c2f738c3e3bb14b58bb6f62cd6c6ca5ede884a87ae76e07d1d'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', + 'bin/repeat-match', 'bin/show-aligns', 'bin/show-coords', + 'bin/show-tiling', 'bin/show-snps', 'bin/show-diff', 'bin/exact-tandems', + 'bin/mummerplot', 'bin/promer', 'bin/dnadiff', + ], + 'dirs': ['include', 'lib', 'libexec'], +} + +moduleclass = 'bio' From 962d73a01ccea1598b34167710109f49dd3d1af4 Mon Sep 17 00:00:00 2001 From: Bob Date: Mon, 30 Jan 2023 12:10:33 +0100 Subject: [PATCH 6354/9987] adding easyconfigs: PIPITS-3.0-foss-2021a.eb and patches: PIPITS-3.0_remove-conda-commands.patch --- .../p/PIPITS/PIPITS-3.0-foss-2021a.eb | 66 +++++++++++++++++++ .../PIPITS-3.0_remove-conda-commands.patch | 56 ++++++++++++++++ 2 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/PIPITS/PIPITS-3.0_remove-conda-commands.patch diff --git a/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2021a.eb b/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2021a.eb new file mode 100644 index 00000000000..a75ba7b43f0 --- /dev/null +++ b/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2021a.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'PIPITS' +version = '3.0' + +homepage = 'https://github.com/hsgweon/pipits' +description = """An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences +from the Illumina sequencing platform.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), + ('VSEARCH', '2.21.1'), + ('FASTX-Toolkit', '0.0.14'), + ('ITSx', '1.1.3'), + ('HMMER', '3.3.2'), + ('RDP-Classifier', '2.13', '-Java-11', SYSTEM), + ('SeqKit', '2.1.0', '', SYSTEM), +] + +use_pip = True + +exts_list = [ + ('biom-format', '2.1.10', { + 'modulename': 'biom', + 'checksums': ['f5a277a8144f0b114606852c42f657b9cfde44b3cefa0b2638ab1c1d5e1d0488'], + }), + ('python-utils', '3.1.0', { + 'checksums': ['4dace6420c5f50d6509251fa0aee0e2a0b826bbc8a5d2a6d7e99dca80e78a7f3'], + }), + ('progressbar2', '4.0.0', { + 'modulename': 'progressbar', + 'checksums': ['14d3165a1781d053ffaa117daf27cc706128d2ec1d2977fdb05b6bb079888013'], + }), + ('pispino', '1.1', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/hsgweon/pispino/archive/'], + 'checksums': ['8fb2e1c0ae38ecca7c637de9c0b655eb18fc67d7838ceb5a6902555ea12416c0'], + }), + (name, version, { + 'patches': ['PIPITS-3.0_remove-conda-commands.patch'], + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/hsgweon/pipits/archive/'], + 'checksums': [ + {'3.0.tar.gz': 'ee9f142e473e57b186760d940131610c16bdfe57eefca935df35779fd85377bd'}, + {'PIPITS-3.0_remove-conda-commands.patch': + 'd4be41ac4d6d37a19ad09b06c1f05ed83921aa59dc4b04b38fa257e6bce6d12f'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pipits_funits', 'pipits_process', + 'pispino_createreadpairslist', + 'pispino_seqprep']], + 'dirs': [] +} + +sanity_check_commands = ['pipits_process --help'] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0_remove-conda-commands.patch b/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0_remove-conda-commands.patch new file mode 100644 index 00000000000..dd1c4306664 --- /dev/null +++ b/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0_remove-conda-commands.patch @@ -0,0 +1,56 @@ +Some PIPITS scripts in the bin folder contain a hardcoded "conda list" commands. +This patch replaces those calls by "pip list". + +Furthermore, it replaces the call to a Conda wrapper script for launching +RDP-Classifier by the actual java command. + +Author: Bob Dröge (University of Groningen) + +diff -ru pipits-3.0-orig/bin/pipits_funits pipits-3.0/bin/pipits_funits +--- pipits-3.0-orig/bin/pipits_funits 2023-01-30 12:00:47.126429480 +0100 ++++ pipits-3.0/bin/pipits_funits 2023-01-30 12:01:43.330947430 +0100 +@@ -102,7 +102,7 @@ + logger("", logging_file, display = True, timestamp = False) + + # Log versions +- cmd = " ".join(["conda list"]) ++ cmd = " ".join(["pip list"]) + run_cmd(cmd, version_file, False) + + # Start +diff -ru pipits-3.0-orig/bin/pipits_process pipits-3.0/bin/pipits_process +--- pipits-3.0-orig/bin/pipits_process 2023-01-30 12:00:47.087115862 +0100 ++++ pipits-3.0/bin/pipits_process 2023-01-30 12:03:34.783649411 +0100 +@@ -166,7 +166,7 @@ + logger("", logging_file, display = True, timestamp = False) + + # Log versions +- cmd = " ".join(["conda list"]) ++ cmd = " ".join(["pip list"]) + run_cmd(cmd, version_file, False) + + # Environment variable - discontinued. +@@ -623,9 +623,10 @@ + + logger(ENDC + "Assigning taxonomy with UNITE [RDP Classifier]" + ENDC, logging_file, display = True) + PIPITS_UNITE_RETRAINED_PROPERTIES = "pipits_db/UNITE_retrained_" + options.unite + "/UNITE_retrained/rRNAClassifier.properties" +- cmd = " ".join(["classifier", ++ cmd = " ".join(["java", + "-Xms" + str(options.Xms), + "-Xmx" + str(options.Xmx), ++ "-jar $EBROOTRDPMINCLASSIFIER/dist/classifier.jar", + "classify", + "-t " + PIPITS_UNITE_RETRAINED_PROPERTIES, + "-o", options.outDir + "/assigned_taxonomy_rdp_raw.txt", +@@ -703,9 +704,10 @@ + logger("Assigning taxonomy [RDP Classifier] - Warcup", logging_file, display = True) + PIPITS_WARCUP_RETRAINED_PROPERTIES = "pipits_db/warcup_retrained_V2/warcup_retrained_V2/rRNAClassifier.properties" + cmd = " ".join([ +- "classifier", ++ "java", + "-Xms" + str(options.Xms), + "-Xmx" + str(options.Xmx), ++ "-jar $EBROOTRDPMINCLASSIFIER/dist/classifier.jar", + "classify", + "-t " + PIPITS_WARCUP_RETRAINED_PROPERTIES, + "-o", options.outDir + "/assigned_taxonomy_warcup_raw.txt", From 9b5685459419123b6be3a97d6bd3f360398746d4 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 30 Jan 2023 13:48:44 +0100 Subject: [PATCH 6355/9987] adding easyconfigs: PAML-4.10.5-GCCcore-11.3.0.eb --- .../p/PAML/PAML-4.10.5-GCCcore-11.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAML/PAML-4.10.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.10.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.10.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c7fc5f25404 --- /dev/null +++ b/easybuild/easyconfigs/p/PAML/PAML-4.10.5-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'PAML' +version = '4.10.5' + +homepage = 'http://abacus.gene.ucl.ac.uk/software/paml.html' +description = """PAML is a package of programs for phylogenetic + analyses of DNA or protein sequences using maximum likelihood.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'abacus-gene' + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['1bb40ea7c976d961a4f46b76e950423f6f252d7060bc621cbf29c9743b88a063'] + +builddependencies = [('binutils', '2.38')] + +start_dir = 'src' + +prebuildopts = "sed -i 's/enum/extern enum/g' paml.h &&" +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [ + # (['%(builddir)s/%(namelower)s%(version)s/README.txt'], ''), + (['README.txt', 'LICENSE'], ''), + (['src/baseml', 'src/basemlg', 'src/chi2', 'src/codeml', 'src/evolver'], 'bin'), + (['src/infinitesites', 'src/mcmctree', 'src/pamp', 'src/yn00'], 'bin'), + (['dat/*'], 'dat'), + (['doc/*'], 'doc'), + (['examples/*'], 'examples'), + (['Technical/*'], 'Technical'), +] + +sanity_check_paths = { + 'files': ['examples/baseml.ctl', 'examples/codeml.ctl', 'bin/baseml', 'bin/codeml'], + 'dirs': ['dat', 'doc', 'examples'], +} + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cp -a %(installdir)s/examples/HIVNSsites %(builddir)s && " + "cd %(builddir)s/HIVNSsites && codeml", +] + +moduleclass = 'bio' From d3f0b0f497925d2ae0e2d75adafee406017eeff1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 30 Jan 2023 14:19:36 +0100 Subject: [PATCH 6356/9987] update NVHPC-22.9-CUDA-11.7.0.eb: make comment more generic --- easybuild/easyconfigs/n/NVHPC/NVHPC-22.9-CUDA-11.7.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-22.9-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.9-CUDA-11.7.0.eb index 4ce5187120b..e3b68fc4096 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-22.9-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.9-CUDA-11.7.0.eb @@ -37,8 +37,7 @@ module_add_cuda = False # specify default CUDA version that should be used by NVHPC # should match one of the CUDA versions that are included with this NVHPC version -# (see install_components/Linux_x86_64/22.3/cuda/) -# for NVHPC 22.3, those are: 11.6, 11.0, 10.2; +# (see install_components/Linux_x86_64/$version/cuda/) where $version is the NVHPC version # this version can be tweaked from the EasyBuild command line with # --try-amend=default_cuda_version="11.0" (for example) default_cuda_version = '%(cudaver)s' From 994eb716d9529aac7959149b97de64433c2d4a34 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 30 Jan 2023 14:21:17 +0100 Subject: [PATCH 6357/9987] update NVHPC-22.11-CUDA-11.7.0.eb: make comment more generic --- easybuild/easyconfigs/n/NVHPC/NVHPC-22.11-CUDA-11.7.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-22.11-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.11-CUDA-11.7.0.eb index 0dcb2916241..1bb5056876f 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-22.11-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.11-CUDA-11.7.0.eb @@ -37,8 +37,7 @@ module_add_cuda = False # specify default CUDA version that should be used by NVHPC # should match one of the CUDA versions that are included with this NVHPC version -# (see install_components/Linux_x86_64/22.3/cuda/) -# for NVHPC 22.3, those are: 11.6, 11.0, 10.2; +# (see install_components/Linux_x86_64/$version/cuda/) where $version is the NVHPC version # this version can be tweaked from the EasyBuild command line with # --try-amend=default_cuda_version="11.0" (for example) default_cuda_version = '%(cudaver)s' From 590bbbe07c5aeba85b0fb02fd18cceeddb1f93ec Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 30 Jan 2023 14:22:08 +0100 Subject: [PATCH 6358/9987] update NVHPC-23.1-CUDA-12.0.0.eb: make comment more generic --- easybuild/easyconfigs/n/NVHPC/NVHPC-23.1-CUDA-12.0.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-23.1-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-23.1-CUDA-12.0.0.eb index fedcb3d3bc0..b0d9d6f4ace 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-23.1-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-23.1-CUDA-12.0.0.eb @@ -37,8 +37,7 @@ module_add_cuda = False # specify default CUDA version that should be used by NVHPC # should match one of the CUDA versions that are included with this NVHPC version -# (see install_components/Linux_x86_64/22.3/cuda/) -# for NVHPC 22.3, those are: 11.6, 11.0, 10.2; +# (see install_components/Linux_x86_64/$version/cuda/) where $version is the NVHPC version # this version can be tweaked from the EasyBuild command line with # --try-amend=default_cuda_version="11.0" (for example) default_cuda_version = '%(cudaver)s' From 4eecee77230f764836a8dfa1bccd08e996600f6a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 30 Jan 2023 18:59:34 +0100 Subject: [PATCH 6359/9987] adding easyconfigs: PRANK-170427-GCC-11.3.0.eb, MAFFT-7.505-GCC-11.3.0-with-extensions.eb --- .../MAFFT-7.505-GCC-11.3.0-with-extensions.eb | 48 +++++++++++++++++++ .../p/PRANK/PRANK-170427-GCC-11.3.0.eb | 36 ++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-GCC-11.3.0-with-extensions.eb create mode 100644 easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-GCC-11.3.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-GCC-11.3.0-with-extensions.eb new file mode 100644 index 00000000000..2f176031066 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-GCC-11.3.0-with-extensions.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez (Swiss Institute of Bioinformatics, Biozentrum - University of Basel) +# 7.305 modified by: +# Adam Huffman (The Francis Crick Institute) +# 7.453 switch to Bundle by: +# Alex Domingo (Vrije Universiteit Brussel) + +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.505' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], + 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'checksums': ['f54a78670fcd9960233bcc3b3dd359f395a71c0ced45a7be1cfeae19950ce6ff'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft', 'libexec/mafft/mxscarnamod'], # mxscarnamod installed by MAFFT Extensions + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-11.3.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-11.3.0.eb new file mode 100644 index 00000000000..f72e6aac406 --- /dev/null +++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-11.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'PRANK' +version = '170427' + +homepage = 'http://wasabiapp.org/software/prank/' +description = """ PRANK is a probabilistic multiple alignment program for DNA, + codon and amino-acid sequences. PRANK is based on a novel algorithm that treats + insertions correctly and avoids over-estimation of the number of deletion events.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['http://wasabiapp.org/download/prank/'] +sources = ['%(namelower)s.source.%(version)s.tgz'] +checksums = ['623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859'] + +# PRANK uses MAFFT as external tool to construct guide tree +dependencies = [('MAFFT', '7.505', '-with-extensions')] + +start_dir = 'src' + +files_to_copy = [(['prank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/prank'], + 'dirs': [], +} + +sanity_check_commands = ['prank -help'] + +moduleclass = 'bio' From a2c2695da950ede56ffda929fe5bea97f5994241 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 31 Jan 2023 09:16:09 +0100 Subject: [PATCH 6360/9987] adding easyconfigs: RepeatMasker-4.1.4-foss-2022a.eb, RMBlast-2.13.0-gompi-2022a.eb, TRF-4.09.1-GCCcore-11.3.0.eb --- .../r/RMBlast/RMBlast-2.13.0-gompi-2022a.eb | 63 +++++++++++++++++++ .../RepeatMasker-4.1.4-foss-2022a.eb | 54 ++++++++++++++++ .../t/TRF/TRF-4.09.1-GCCcore-11.3.0.eb | 30 +++++++++ 3 files changed, 147 insertions(+) create mode 100644 easybuild/easyconfigs/r/RMBlast/RMBlast-2.13.0-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.13.0-gompi-2022a.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.13.0-gompi-2022a.eb new file mode 100644 index 00000000000..8a5f50b763d --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.13.0-gompi-2022a.eb @@ -0,0 +1,63 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'RMBlast' +version = '2.13.0' + +homepage = 'https://www.repeatmasker.org/rmblast/' +description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary + difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' + for use with RepeatMasker and RepeatModeler.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +# RMBlast is distributed as a patch that applies on top of BLAST+ +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [('https://www.repeatmasker.org/%(namelower)s/isb-%(version)s+-%(namelower)s.patch.gz', 2)] +checksums = [ + {'ncbi-blast-2.13.0+-src.tar.gz': '89553714d133daf28c477f83d333794b3c62e4148408c072a1b4620e5ec4feb2'}, + {'isb-2.13.0+-rmblast.patch.gz': '06595546318577b450e4a82c641017b2818b1741446e7ac675d82aef3d8f7f3d'}, +] + +dependencies = [ + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost.MPI', '1.79.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('LMDB', '0.9.29'), +] + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +prebuildopts = "sed -i 's/LIBS =/LIBS = $(BLAST_THIRD_PARTY_LIBS)/' src/app/rmblastn/Makefile.rmblastn.app && " + +sanity_check_paths = { + 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.4-foss-2022a.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.4-foss-2022a.eb new file mode 100644 index 00000000000..975285a82f1 --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.4-foss-2022a.eb @@ -0,0 +1,54 @@ +easyblock = 'Tarball' + +name = 'RepeatMasker' +version = '4.1.4' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://www.repeatmasker.org/%(name)s'] +sources = [ + SOURCE_TAR_GZ, + # optional but recommended: RepBase RepeatMasker Edition + # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php + # { + # 'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz', + # 'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1", + # }, +] +checksums = ['d7af5f49b7ecc5fb90e66956c85877220ec461f6e4d54e06a5996bb2fd6b63fa'] + +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('TRF', '4.09.1'), + ('h5py', '3.7.0'), + # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match + ('HMMER', '3.3.2'), + ('RMBlast', '2.13.0'), +] + +local_default_search_engine = 'RMBlast' + +local_config_command = 'cd %(installdir)s &&' +local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() + +postinstallcmds = [local_config_command] + +fix_perl_shebang_for = ['RepeatMasker'] + +sanity_check_paths = { + 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], + 'dirs': ['Libraries', 'util'], +} + +sanity_check_commands = ['RepeatMasker -help'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..42fc644514b --- /dev/null +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'TRF' +version = '4.09.1' + +homepage = 'https://tandem.bu.edu/trf/trf.html' +description = """Tandem Repeats Finder: a program to analyze DNA sequences.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'Benson-Genomics-Lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/trf'], + 'dirs': [], +} + +sanity_check_commands = ["trf -v"] + +moduleclass = 'bio' From 9ad050fd08d10fc7ee53998da32f232c14eae943 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 31 Jan 2023 09:38:43 +0100 Subject: [PATCH 6361/9987] use SYSTEM rather than True --- .../PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb index 5d1e8bb87bc..7d26121c6cf 100644 --- a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb @@ -12,7 +12,7 @@ networks in PyTorch flexibly and transparently.""" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('PyTorch', '1.10.0', versionsuffix), ] From 98fe18cfe7cb32cb9771a3decb2d16e0689310b1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 31 Jan 2023 15:01:24 +0000 Subject: [PATCH 6362/9987] add pmix patch to iomkl OpenMPI 4.1.1 --- .../OpenMPI-4.1.1-intel-compilers-2021.4.0.eb | 21 +++++++++++-------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb index 553c9051ea8..6e354371c1c 100755 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb @@ -11,20 +11,23 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', - 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', 'OpenMPI-4.1.1_opal-pmix-package-rank.patch', + 'OpenMPI-4.1.1_pmix3x-protection.patch', + 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', ] checksums = [ - {'openmpi-4.1.1.tar.bz2': 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda'}, - {'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch': - 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e'}, - {'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch': - '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d'}, - {'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch': - 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea'}, - {'OpenMPI-4.1.1_opal-pmix-package-rank.patch': '04353672cf7be031e5306c94068d7012d99e6cd94b69d93230797ffcd7f31903'}, + 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 + # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch + 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', + # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch + '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', + '04353672cf7be031e5306c94068d7012d99e6cd94b69d93230797ffcd7f31903', # OpenMPI-4.1.1_opal-pmix-package-rank.patch + '384ef9f1fa803b0d71dae2ec0748d0f20295992437532afedf21478bda164ff8', # OpenMPI-4.1.1_pmix3x-protection.patch + # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', ] + builddependencies = [ ('pkg-config', '0.29.2'), ] From c76e8809c65b00de50c94cb95c7319ce49fd004e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 31 Jan 2023 21:05:43 +0100 Subject: [PATCH 6363/9987] add (bare) Python as build dep for kineto Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb index e5f01bd68ee..45b6114f29d 100644 --- a/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/k/kineto/kineto-0.4.0-GCC-11.3.0.eb @@ -22,6 +22,7 @@ checksums = [None] builddependencies = [ ('CMake', '3.24.3'), + ('Python', '3.10.4', '-bare'), ] start_dir = 'libkineto' From 8579246993085b8b94bc1b480464351241bb5ed2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 1 Feb 2023 14:17:44 +0100 Subject: [PATCH 6364/9987] adding easyconfigs: TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb, TensorFlow-2.11.0-foss-2022a.eb and patches: TensorFlow-2.11.0_disable-avx512-extensions.patch, TensorFlow-2.11.0_fix-eigen-atan-on-PPC.patch, TensorFlow-2.11.0_fix-link-error.patch, TensorFlow-2.11.0_remove-libclang-and-io-gcs-deps.patch, TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch --- ...ensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb | 228 ++++++++++++++++++ .../TensorFlow-2.11.0-foss-2022a.eb | 223 +++++++++++++++++ ...low-2.11.0_disable-avx512-extensions.patch | 19 ++ ...sorFlow-2.11.0_fix-eigen-atan-on-PPC.patch | 38 +++ .../TensorFlow-2.11.0_fix-link-error.patch | 39 +++ ...11.0_remove-libclang-and-io-gcs-deps.patch | 38 +++ ...Flow-2.5.0_fix-arm-vector-intrinsics.patch | 55 +++-- 7 files changed, 615 insertions(+), 25 deletions(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_disable-avx512-extensions.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-atan-on-PPC.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-link-error.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_remove-libclang-and-io-gcs-deps.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..5f34634a7cb --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,228 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.11.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('protobuf', '3.19.4'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.36.0', '-nodocs'), + ('pybind11', '2.9.2'), + ('UnZip', '6.0'), + ('LLVM', '14.0.3'), # for debugging with llvm-symbolizer, to be removed +] +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), + ('NCCL', '2.12.12', versionsuffix), + ('Python', '3.10.4'), + ('h5py', '3.7.0'), + ('cURL', '7.83.0'), + ('dill', '0.3.6'), + ('double-conversion', '3.2.0'), + ('flatbuffers', '2.0.7'), + ('giflib', '5.2.1'), + ('hwloc', '2.7.1'), + ('ICU', '71.1'), + ('JsonCpp', '1.9.5'), + ('libjpeg-turbo', '2.1.3'), + ('LMDB', '0.9.29'), + ('NASM', '2.15.05'), + ('nsync', '1.25.0'), + ('SQLite', '3.38.3'), + ('protobuf-python', '3.19.4'), + ('libpng', '1.6.37'), + ('snappy', '1.1.9'), + ('zlib', '1.2.12'), + ('networkx', '2.8.4'), # required for pythran +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', version, { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['ea3b64acfff3d9a244f06178c9bdedcbdd3f125b67d0888dba8229498d06468b'], + }), + ('Werkzeug', '2.2.2', { + 'checksums': ['7ea2d48322cc7c0f8b3a215ed73eabd7b5d75d0b50e31ab006286ccff9e00b8f'], + }), + ('tensorboard-plugin-wit', '1.8.1', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard-data-server', '0.6.1', { + 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('grpcio', '1.51.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['e6dfc2b6567b1c261739b43d9c59d201c1b89e017afd9e684d85aa7a186c9f7a'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('cachetools', '5.2.1', { + 'checksums': ['5991bc0e08a1319bb618d3195ca5b6bc76646a49c21d55962977197b301cc1fe'], + }), + ('google-auth', '2.16.0', { + 'modulename': 'google.auth', + 'checksums': ['ed7057a101af1146f0554a769930ac9de506aeca4fd5af6543ebe791851a9fbd'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('tensorboard', '2.11.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0c7529f3f43691e8cc2ece8e564c2e103c51ade317c6af626d415239b5088018'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('keras', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['38c6fff0ea9a8b06a2717736565c92a73c8cd9b1c239e7125ccb188b7848f65e'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + # Version <= 0.4.0 required by TF: https://github.com/tensorflow/tensorflow/issues/56244 + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + # (newer) pythran and beniget in SciPy-Bundle require gast 0.5 + ('beniget', '0.3.0', { + 'checksums': ['062c893be9cdf87c3144fb15041cce4d81c67107c1591952cd45fdce789a0ff1'], + }), + ('pythran', '0.9.11', { + 'checksums': ['a317f91e2aade9f6550dc3bf40b5caeb45b7e012daf27e2b3e4ad928edb01667'], + }), + # Required by tests + ('portpicker', '1.5.2', { + 'checksums': ['c55683ad725f5c00a41bc7db0225223e8be024b1fa564d039ed3390e4fd48fb3'], + }), + # System dependencies + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + # Optional profile plugin + dependency + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.11.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['7a97c02d502fde98a0336aadcab15b37169744d5bf6966af7d576c7a3f0a89f4'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + '%(name)s-2.4.0_dont-use-var-lock.patch', + '%(name)s-2.5.0-fix-alias-violation-in-absl.patch', + '%(name)s-2.5.0_fix-crash-on-shutdown.patch', + '%(name)s-2.8.4_exclude-xnnpack-on-ppc.patch', + '%(name)s-2.8.4_resolve-gcc-symlinks.patch', + '%(name)s-2.9.1_remove-duplicate-gpu-tests.patch', + '%(name)s-%(version)s_disable-avx512-extensions.patch', + '%(name)s-%(version)s_fix-eigen-atan-on-PPC.patch', + '%(name)s-%(version)s_fix-link-error.patch', + '%(name)s-%(version)s_remove-libclang-and-io-gcs-deps.patch', + ], + 'checksums': [ + {'v2.11.0.tar.gz': '99c732b92b1b37fc243a559e02f9aef5671771e272758aa4aec7f34dc92dac48'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch': + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75'}, + {'TensorFlow-2.5.0_fix-crash-on-shutdown.patch': + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd'}, + {'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch': + 'ebd404ac56cc4ca662483f1f591e62e11749361be57a7ba5f4b2f0d03e829884'}, + {'TensorFlow-2.8.4_resolve-gcc-symlinks.patch': + '43ce9acc6bffff68a31d2263d0064d272999b2e0a2c6546690287cd1c9c90f04'}, + {'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch': + '6fe50faab28387c622c68dc3fc0cbfb2a51000cd750c1a82f8420b54fcd2509f'}, + {'TensorFlow-2.11.0_disable-avx512-extensions.patch': + 'fb8e7694b5d2377cc44e6674ff85a7c50dc725f2f507cbcfda65f129f534b1cc'}, + {'TensorFlow-2.11.0_fix-eigen-atan-on-PPC.patch': + 'd9f4779f72ffd2c5f9c5da0a7735328dd25756515edccf603087dba2bf4d1612'}, + {'TensorFlow-2.11.0_fix-link-error.patch': + '0a2f5c9c5be425f305bdc08f5a5ffce210e66f6ad4120d94ea0209246fc0449f'}, + {'TensorFlow-2.11.0_remove-libclang-and-io-gcs-deps.patch': + '21d5723ab4e9a3be349cf3d57bb55cbe43e28785a8c8b19c52cee9dcc4dcf0de'}, + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb new file mode 100644 index 00000000000..46c647f315f --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb @@ -0,0 +1,223 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.11.0' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('protobuf', '3.19.4'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.36.0', '-nodocs'), + ('pybind11', '2.9.2'), + ('UnZip', '6.0'), +] +dependencies = [ + ('Python', '3.10.4'), + ('h5py', '3.7.0'), + ('cURL', '7.83.0'), + ('dill', '0.3.6'), + ('double-conversion', '3.2.0'), + ('flatbuffers', '2.0.7'), + ('giflib', '5.2.1'), + ('hwloc', '2.7.1'), + ('ICU', '71.1'), + ('JsonCpp', '1.9.5'), + ('libjpeg-turbo', '2.1.3'), + ('LMDB', '0.9.29'), + ('NASM', '2.15.05'), + ('nsync', '1.25.0'), + ('SQLite', '3.38.3'), + ('protobuf-python', '3.19.4'), + ('libpng', '1.6.37'), + ('snappy', '1.1.9'), + ('zlib', '1.2.12'), + ('networkx', '2.8.4'), # required for pythran +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', version, { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['ea3b64acfff3d9a244f06178c9bdedcbdd3f125b67d0888dba8229498d06468b'], + }), + ('Werkzeug', '2.2.2', { + 'checksums': ['7ea2d48322cc7c0f8b3a215ed73eabd7b5d75d0b50e31ab006286ccff9e00b8f'], + }), + ('tensorboard-plugin-wit', '1.8.1', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard-data-server', '0.6.1', { + 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('grpcio', '1.51.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['e6dfc2b6567b1c261739b43d9c59d201c1b89e017afd9e684d85aa7a186c9f7a'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('cachetools', '5.2.1', { + 'checksums': ['5991bc0e08a1319bb618d3195ca5b6bc76646a49c21d55962977197b301cc1fe'], + }), + ('google-auth', '2.16.0', { + 'modulename': 'google.auth', + 'checksums': ['ed7057a101af1146f0554a769930ac9de506aeca4fd5af6543ebe791851a9fbd'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('tensorboard', '2.11.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0c7529f3f43691e8cc2ece8e564c2e103c51ade317c6af626d415239b5088018'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('keras', version, { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['38c6fff0ea9a8b06a2717736565c92a73c8cd9b1c239e7125ccb188b7848f65e'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + # Version <= 0.4.0 required by TF: https://github.com/tensorflow/tensorflow/issues/56244 + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + # (newer) pythran and beniget in SciPy-Bundle require gast 0.5 + ('beniget', '0.3.0', { + 'checksums': ['062c893be9cdf87c3144fb15041cce4d81c67107c1591952cd45fdce789a0ff1'], + }), + ('pythran', '0.9.11', { + 'checksums': ['a317f91e2aade9f6550dc3bf40b5caeb45b7e012daf27e2b3e4ad928edb01667'], + }), + # Required by tests + ('portpicker', '1.5.2', { + 'checksums': ['c55683ad725f5c00a41bc7db0225223e8be024b1fa564d039ed3390e4fd48fb3'], + }), + # System dependencies + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + # Optional profile plugin + dependency + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.11.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['7a97c02d502fde98a0336aadcab15b37169744d5bf6966af7d576c7a3f0a89f4'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + '%(name)s-2.4.0_dont-use-var-lock.patch', + '%(name)s-2.5.0-fix-alias-violation-in-absl.patch', + '%(name)s-2.5.0_fix-crash-on-shutdown.patch', + '%(name)s-2.8.4_exclude-xnnpack-on-ppc.patch', + '%(name)s-2.8.4_resolve-gcc-symlinks.patch', + '%(name)s-2.9.1_remove-duplicate-gpu-tests.patch', + '%(name)s-%(version)s_disable-avx512-extensions.patch', + '%(name)s-%(version)s_fix-eigen-atan-on-PPC.patch', + '%(name)s-%(version)s_fix-link-error.patch', + '%(name)s-%(version)s_remove-libclang-and-io-gcs-deps.patch', + ], + 'checksums': [ + {'v2.11.0.tar.gz': '99c732b92b1b37fc243a559e02f9aef5671771e272758aa4aec7f34dc92dac48'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch': + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75'}, + {'TensorFlow-2.5.0_fix-crash-on-shutdown.patch': + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd'}, + {'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch': + 'ebd404ac56cc4ca662483f1f591e62e11749361be57a7ba5f4b2f0d03e829884'}, + {'TensorFlow-2.8.4_resolve-gcc-symlinks.patch': + '43ce9acc6bffff68a31d2263d0064d272999b2e0a2c6546690287cd1c9c90f04'}, + {'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch': + '6fe50faab28387c622c68dc3fc0cbfb2a51000cd750c1a82f8420b54fcd2509f'}, + {'TensorFlow-2.11.0_disable-avx512-extensions.patch': + 'fb8e7694b5d2377cc44e6674ff85a7c50dc725f2f507cbcfda65f129f534b1cc'}, + {'TensorFlow-2.11.0_fix-eigen-atan-on-PPC.patch': + 'd9f4779f72ffd2c5f9c5da0a7735328dd25756515edccf603087dba2bf4d1612'}, + {'TensorFlow-2.11.0_fix-link-error.patch': + '0a2f5c9c5be425f305bdc08f5a5ffce210e66f6ad4120d94ea0209246fc0449f'}, + {'TensorFlow-2.11.0_remove-libclang-and-io-gcs-deps.patch': + '21d5723ab4e9a3be349cf3d57bb55cbe43e28785a8c8b19c52cee9dcc4dcf0de'}, + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_disable-avx512-extensions.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_disable-avx512-extensions.patch new file mode 100644 index 00000000000..491872e541e --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_disable-avx512-extensions.patch @@ -0,0 +1,19 @@ +(Some of the) AVX512 extensions to Eigen introduced by TensorFlow are broken and return wrong values. +So disable them for now to keep AVX512 in the other code parts working. +See https://github.com/tensorflow/tensorflow/issues/49944 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tsl/framework/fixedpoint/FixedPoint.h b/tensorflow/tsl/framework/fixedpoint/FixedPoint.h +index bb3def15189..85affe89c54 100644 +--- a/tensorflow/tsl/framework/fixedpoint/FixedPoint.h ++++ b/tensorflow/tsl/framework/fixedpoint/FixedPoint.h +@@ -20,7 +20,7 @@ limitations under the License. + #include "tensorflow/tsl/framework/fixedpoint_types.h" + + // Use optimized implementations whenever available +-#if defined(EIGEN_VECTORIZE_AVX512DQ) || defined(EIGEN_VECTORIZE_AVX512BW) ++#if 0 + #include "tensorflow/tsl/framework/fixedpoint/PacketMathAVX512.h" + #include "tensorflow/tsl/framework/fixedpoint/TypeCastingAVX512.h" + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-atan-on-PPC.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-atan-on-PPC.patch new file mode 100644 index 00000000000..3d57bed62cb --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-atan-on-PPC.patch @@ -0,0 +1,38 @@ +Fix compilation failure on PowerPC: +external/eigen_archive/unsupported/Eigen/CXX11/../../../Eigen/src/Core/GenericPacketMath.h:862:67: error: no matching function for call to 'atan(const __vector(2) double&)' + +Add the upstream commit https://gitlab.com/libeigen/eigen/-/commit/886aad136111eeeb7604e1d17f62efcc4d824568 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/eigen3/disable-atan-on-ppc.patch b/third_party/eigen3/disable-atan-on-ppc.patch +new file mode 100644 +index 00000000000..4614799b66a +--- /dev/null ++++ b/third_party/eigen3/disable-atan-on-ppc.patch +@@ -0,0 +1,13 @@ ++diff --git a/Eigen/src/Core/arch/AltiVec/PacketMath.h b/Eigen/src/Core/arch/AltiVec/PacketMath.h ++index 37398de15..d9ddb5e35 100644 ++--- a/Eigen/src/Core/arch/AltiVec/PacketMath.h +++++ b/Eigen/src/Core/arch/AltiVec/PacketMath.h ++@@ -2708,7 +2708,7 @@ template<> struct packet_traits : default_packet_traits ++ HasAbs = 1, ++ HasSin = 0, ++ HasCos = 0, ++- HasATan = 1, +++ HasATan = 0, ++ HasLog = 0, ++ HasExp = 1, ++ HasSqrt = 1, +diff --git a/third_party/eigen3/workspace.bzl b/third_party/eigen3/workspace.bzl +index 91f471c3def..9fa96a38310 100644 +--- a/third_party/eigen3/workspace.bzl ++++ b/third_party/eigen3/workspace.bzl +@@ -14,6 +14,7 @@ def repo(): + tf_http_archive( + name = "eigen_archive", + build_file = "//third_party/eigen3:eigen_archive.BUILD", ++ patch_file = ["//third_party/eigen3:disable-atan-on-ppc.patch"], + sha256 = EIGEN_SHA256, + strip_prefix = "eigen-{commit}".format(commit = EIGEN_COMMIT), + urls = tf_mirror_urls("https://gitlab.com/libeigen/eigen/-/archive/{commit}/eigen-{commit}.tar.gz".format(commit = EIGEN_COMMIT)), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-link-error.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-link-error.patch new file mode 100644 index 00000000000..a492897700d --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-link-error.patch @@ -0,0 +1,39 @@ +Fix errors during build such as +Traceback (most recent call last): + File "/bazel-root/21e00dc5c04b924b70ed7bedd0c3533e/execroot/org_tensorflow/bazel-out/ppc-opt/bin/tensorflow/create_tensorflow.python_api_tf_python_api_gen_v2.runfiles/org_tensorflow/tensorflow/python/pywrap_tensorflow.py", line 62, in + from tensorflow.python._pywrap_tensorflow_internal import * +ImportError: /bazel-root/21e00dc5c04b924b70ed7bedd0c3533e/execroot/org_tensorflow/bazel-out/ppc-opt/bin/tensorflow/create_tensorflow.python_api_tf_python_api_gen_v2.runfiles/org_tensorflow/tensorflow/python/_pywrap_tensorflow_internal.so: undefined symbol: LLVMInitializePowerPCAsmParser + +See https://github.com/tensorflow/tensorflow/pull/59326 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/compiler/xla/mlir/transforms/runtime/BUILD b/tensorflow/compiler/xla/mlir/transforms/runtime/BUILD +index 587d4b184c0..5ff10743cf8 100644 +--- a/tensorflow/compiler/xla/mlir/transforms/runtime/BUILD ++++ b/tensorflow/compiler/xla/mlir/transforms/runtime/BUILD +@@ -250,7 +250,23 @@ cc_library( + "@llvm-project//mlir:Parser", + "@llvm-project//mlir:Pass", + "@llvm-project//mlir:ToLLVMIRTranslation", +- ], ++ ] + select({ ++ "//tensorflow:arm_any": [ ++ "@llvm-project//llvm:AArch64AsmParser", ++ ], ++ "//tensorflow:linux_ppc64le": [ ++ "@llvm-project//llvm:PowerPCAsmParser", ++ ], ++ "//tensorflow:macos_arm64": [ ++ "@llvm-project//llvm:AArch64AsmParser", ++ ], ++ "//tensorflow:linux_s390x": [ ++ "@llvm-project//llvm:SystemZAsmParser", ++ ], ++ "//conditions:default": [ ++ "@llvm-project//llvm:X86AsmParser", ++ ], ++ }), + ) + + cc_library( diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_remove-libclang-and-io-gcs-deps.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_remove-libclang-and-io-gcs-deps.patch new file mode 100644 index 00000000000..77b9f524938 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_remove-libclang-and-io-gcs-deps.patch @@ -0,0 +1,38 @@ +This combines two patches from TensorFlow 2.7.1. + +tensorflow-io-gcs-filesystem is not available as a binary for all architectures and +building it requires TensorFlow to be installed, i.e. there is a cyclic dependency. +As it is not actually required (but optional) remove it from `REQUIRED_PACKAGES`. +See https://github.com/tensorflow/tensorflow/issues/56636 + +libclang was introduced in +https://github.com/tensorflow/tensorflow/commit/c211472000ff57bac7fcec9b0465cf73b37bf135 +> This is in preparation to open-source TF's TFRT backend. +> TFRT generates code using libclang python bindings as part of the build. +Hence it is not currently used and as it is not (easily) available for all architectures +simply remove it. + +Patch added by Simon Branford (University of Birmingham) +Updated by Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index 74a1962c334..e8f6eabe4a6 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -88,7 +88,6 @@ REQUIRED_PACKAGES = [ + 'gast >= 0.2.1, <= 0.4.0', + 'google_pasta >= 0.1.1', + 'h5py >= 2.9.0', +- 'libclang >= 13.0.0', + 'numpy >= 1.20', + 'opt_einsum >= 2.3.2', + 'packaging', +@@ -105,8 +104,6 @@ REQUIRED_PACKAGES = [ + 'termcolor >= 1.1.0', + 'typing_extensions >= 3.6.6', + 'wrapt >= 1.11.0', +- 'tensorflow-io-gcs-filesystem >= 0.23.1;platform_machine!="arm64" or ' + +- 'platform_system!="Darwin"', + # grpcio does not build correctly on big-endian machines due to lack of + # BoringSSL support. + # See https://github.com/tensorflow/tensorflow/issues/17882. diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch index 5d80e47df8f..eaed0decf23 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch @@ -1,37 +1,42 @@ -The comment is not true, the function actually takes the arguments as it should -Hence just redefine the function +Fix compile error on ARM: +> ./tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h:132:58: error: cannot convert 'int32x2_t' to 'int8x8_t' -Author: Alexander Grund (TU Dresden) +From https://github.com/tensorflow/tensorflow/pull/53782 + +From 4463f25d1622d162f870ff685da20f2c6df5bc6a Mon Sep 17 00:00:00 2001 +From: Stephan Hartmann +Date: Sat, 15 Jan 2022 21:06:27 +0100 +Subject: [PATCH] Fix casting in vdotq_four_lane_s32() in TFLite + +When building with GCC and dotprod ARM extension enabled, +vreinterpret_s32_s8() casts int8x8_t to int32x2_t. However, third +argument of vdotq_lane_s32() expects parameter of type int8x8_t. +--- + .../optimized/depthwiseconv_3x3_filter_common.h | 10 ++++------ + 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h b/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h -index 916edd561ff..9c8025dac49 100644 +index 916edd561ff32..c519a81bc864d 100644 --- a/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h +++ b/tensorflow/lite/kernels/internal/optimized/depthwiseconv_3x3_filter_common.h -@@ -122,26 +122,7 @@ inline int32x4_t vpaddq_s32(int32x4_t a, int32x4_t b) { - #endif // !__aarch64__ - - #ifdef __ARM_FEATURE_DOTPROD --// The vdotq_lane_s32 takes int8x8t for the rhs parameter, whereas the actual --// instruction selects from between 4 32-bit (4x8-bit packed) sub-registers, an --// unusual interpretation of "lane". --inline int32x4_t vdotq_four_lane_s32(int32x4_t acc, int8x16_t lhs, -- int8x16_t rhs, const int lane) { -- switch (lane) { -- case 0: +@@ -129,16 +129,14 @@ inline int32x4_t vdotq_four_lane_s32(int32x4_t acc, int8x16_t lhs, + int8x16_t rhs, const int lane) { + switch (lane) { + case 0: - return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_low_s8(rhs)), 0); -- case 1: ++ return vdotq_lane_s32(acc, lhs, vget_low_s8(rhs), 0); + case 1: - return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_low_s8(rhs)), 1); -- case 2: ++ return vdotq_lane_s32(acc, lhs, vget_low_s8(rhs), 1); + case 2: - return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_high_s8(rhs)), - 0); -- case 3: -- default: ++ return vdotq_lane_s32(acc, lhs, vget_high_s8(rhs), 0); + case 3: + default: - return vdotq_lane_s32(acc, lhs, vreinterpret_s32_s8(vget_high_s8(rhs)), - 1); -- } --} -- -+#define vdotq_four_lane_s32 vdotq_lane_s32 - #else ++ return vdotq_lane_s32(acc, lhs, vget_high_s8(rhs), 1); + } + } - inline int32x4_t vdotq_s32(int32x4_t acc, int8x16_t lhs, int8x16_t rhs) { From 4f6097c66a10830c7555b2cf167833168e9a4ee5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Feb 2023 15:35:19 +0100 Subject: [PATCH 6365/9987] include required stereo_chemical_props.txt for OpenFold 1.0.1 --- .../OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb | 30 ++++++++++++------- 1 file changed, 19 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb index 9c2d76927db..7f64d549550 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb @@ -84,20 +84,27 @@ exts_list = [ }), ] -# _resources_dir = '%(installdir)s/lib/python%(pyshortver)s/site-packages/openfold/resources/' -# _resources_target_dir = '/databases/bio/%(namelower)s-%(version)s' +local_resources_dir = '%(installdir)s/lib/python%(pyshortver)s/site-packages/openfold/resources/' +# local_resources_target_dir = '/databases/bio/%(namelower)s-%(version)s' + +local_scp_url = 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/' +local_scp_url += '7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt' postinstallcmds = [ 'cp -a run_pretrained_openfold.py thread_sequence.py train_openfold.py %(installdir)s/bin', 'cp -a scripts %(installdir)s/bin', 'chmod -R a+x %(installdir)s/bin', - # manually download stereo_chemical_props.txt, openfold parameters and alphafold parameters - # see scripts download_alphafold_params.sh, download_openfold_params.sh ,install_third_party_dependencies.sh - # download to _resources_target_dir and add symlinks in _resources_dir - # or download directly into _resources_dir - # 'ln -s %s/stereo_chemical_props.txt %s' % (_resources_target_dir, _resources_dir), - # 'ln -s %s/openfold_params %s' % (_resources_target_dir, _resources_dir), - # 'ln -s %s/params %s' % (_resources_target_dir, _resources_dir), + # download stereo_chemical_props.txt + copy it to openfold/resources directory, + # see also install_third_party_dependencies.sh script; + # we currently can't let EasyBuild download (and cache + checksum) this, + # because an extension can only have a single source file, and (Python)Bundle doesn't allow any "parent" downloads + "cd %%(builddir)s && curl -OL %s && cp -a stereo_chemical_props.txt %s" % (local_scp_url, local_resources_dir), + # manually download openfold parameters and alphafold parameters + # see scripts download_alphafold_params.sh + download_openfold_params.sh + # download to local_resources_target_dir and add symlinks in local_resources_dir + # or download directly into local_resources_dir + # 'ln -s %s/openfold_params %s' % (local_resources_target_dir, local_resources_dir), + # 'ln -s %s/params %s' % (local_resources_target_dir, local_resources_dir), ] fix_python_shebang_for = ['bin/*.py', '/bin/scripts/*.py'] @@ -107,8 +114,9 @@ modextrapaths = { } sanity_check_paths = { - 'files': ['bin/pdbfixer', 'bin/run_pretrained_openfold.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages', 'bin/scripts'], + 'files': ['bin/pdbfixer', 'bin/run_pretrained_openfold.py', + 'lib/python%(pyshortver)s/site-packages/openfold/resources/stereo_chemical_props.txt'], + 'dirs': ['bin/scripts', 'lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ From 45cec2d9ede4579f056f560d664d3f8ee246add9 Mon Sep 17 00:00:00 2001 From: James Carpenter Date: Thu, 2 Feb 2023 11:04:13 +0000 Subject: [PATCH 6366/9987] adding easyconfigs: IGV-2.16.0-Java-11.eb --- .../easyconfigs/i/IGV/IGV-2.16.0-Java-11.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100755 easybuild/easyconfigs/i/IGV/IGV-2.16.0-Java-11.eb diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.16.0-Java-11.eb b/easybuild/easyconfigs/i/IGV/IGV-2.16.0-Java-11.eb new file mode 100755 index 00000000000..d30a9dbd0fc --- /dev/null +++ b/easybuild/easyconfigs/i/IGV/IGV-2.16.0-Java-11.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'Tarball' + +name = 'IGV' +version = '2.16.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/software/igv/' +description = """This package contains command line utilities for + preprocessing, computing feature count density (coverage), sorting, and + indexing data files.""" + +toolchain = SYSTEM + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s'] +sources = ['%(name)s_%(version)s.zip'] +checksums = ['7fe76a793b1aa9ac90a1733acfe4ea01fd8e7e42729e9daee84e79e1f43b2a26'] + +dependencies = [('Java', '11', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From e5246cf583bc62accaeb89e787b4650df3a41b81 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Feb 2023 15:12:33 +0100 Subject: [PATCH 6367/9987] Fix compilation error in PAPI 7.0.0 --- .../p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb | 6 +++++- .../PAPI/PAPI-7.0.0_fix-compile-warning.patch | 21 +++++++++++++++++++ 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.0.0_fix-compile-warning.patch diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb index 209e88d199b..1d30bbc9bbc 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb @@ -23,7 +23,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://icl.cs.utk.edu/projects/papi/downloads/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['799dcc317a47da96beaeed445812ecb6ae49df7c0504a4569797c1f7d74c4fd2'] +patches = ['%(name)s-%(version)s_fix-compile-warning.patch'] +checksums = [ + '799dcc317a47da96beaeed445812ecb6ae49df7c0504a4569797c1f7d74c4fd2', + {'PAPI-7.0.0_fix-compile-warning.patch': 'afa9daecbeedb8189b655dad07483d963b54b0587e7a56b87b457907fc5cf40b'}, +] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0_fix-compile-warning.patch b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0_fix-compile-warning.patch new file mode 100644 index 00000000000..745c9f64143 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0_fix-compile-warning.patch @@ -0,0 +1,21 @@ +Fix error during compilation caused by a warning: +pfmlib_perf_event_pmu.c: In function gen_tracepoint_table: +pfmlib_perf_event_pmu.c:433:27: Error: p could be used uninitialized [-Werror=maybe-uninitialized] + 433 | p->modmsk = 0, + | ~~~~~~~~~~^~~ +cc1: All warnings handled as errors + +Author: Alexander Grund (TU Dresden) + +diff -aur papi-7.0.0/src/libpfm4/lib/pfmlib_perf_event_pmu.c papi-7.0.0-orig/src/libpfm4/lib/pfmlib_perf_event_pmu.c +--- papi-7.0.0/src/libpfm4/lib/pfmlib_perf_event_pmu.c 2023-02-02 15:07:10.990410868 +0100 ++++ papi-7.0.0-orig/src/libpfm4/lib/pfmlib_perf_event_pmu.c 2023-02-02 15:05:51.962978074 +0100 +@@ -361,7 +361,7 @@ + { + DIR *dir1, *dir2; + struct dirent *d1, *d2; +- perf_event_t *p = NULL; ++ perf_event_t *p; + perf_umask_t *um; + char d2path[MAXPATHLEN]; + char idpath[MAXPATHLEN]; From a57cb6d4839e1839e9bc3ebc94d37ee3eb2edd18 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Feb 2023 15:20:29 +0100 Subject: [PATCH 6368/9987] Fix patch --- .../easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb | 2 +- .../p/PAPI/PAPI-7.0.0_fix-compile-warning.patch | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb index 1d30bbc9bbc..57ba7388d94 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb @@ -26,7 +26,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_fix-compile-warning.patch'] checksums = [ '799dcc317a47da96beaeed445812ecb6ae49df7c0504a4569797c1f7d74c4fd2', - {'PAPI-7.0.0_fix-compile-warning.patch': 'afa9daecbeedb8189b655dad07483d963b54b0587e7a56b87b457907fc5cf40b'}, + {'PAPI-7.0.0_fix-compile-warning.patch': 'a5d2b266669d55cb0280b4c2fed1a53c7705eb5bad7fc7d247a414e81b3f65a8'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0_fix-compile-warning.patch b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0_fix-compile-warning.patch index 745c9f64143..062d326dbc5 100644 --- a/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0_fix-compile-warning.patch +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0_fix-compile-warning.patch @@ -7,15 +7,15 @@ cc1: All warnings handled as errors Author: Alexander Grund (TU Dresden) -diff -aur papi-7.0.0/src/libpfm4/lib/pfmlib_perf_event_pmu.c papi-7.0.0-orig/src/libpfm4/lib/pfmlib_perf_event_pmu.c ---- papi-7.0.0/src/libpfm4/lib/pfmlib_perf_event_pmu.c 2023-02-02 15:07:10.990410868 +0100 -+++ papi-7.0.0-orig/src/libpfm4/lib/pfmlib_perf_event_pmu.c 2023-02-02 15:05:51.962978074 +0100 +diff -aur a/src/libpfm4/lib/pfmlib_perf_event_pmu.c b/src/libpfm4/lib/pfmlib_perf_event_pmu.c +--- a/src/libpfm4/lib/pfmlib_perf_event_pmu.c 2023-02-02 15:07:10.990410868 +0100 ++++ b/src/libpfm4/lib/pfmlib_perf_event_pmu.c 2023-02-02 15:05:51.962978074 +0100 @@ -361,7 +361,7 @@ { DIR *dir1, *dir2; struct dirent *d1, *d2; -- perf_event_t *p = NULL; -+ perf_event_t *p; +- perf_event_t *p; ++ perf_event_t *p = NULL; perf_umask_t *um; char d2path[MAXPATHLEN]; char idpath[MAXPATHLEN]; From 8b607f7d936bc6ccdb4c2d7d9aad33df5ad89b5f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 2 Feb 2023 15:41:24 +0100 Subject: [PATCH 6369/9987] add perl path for RepeatMasker --- .../r/RepeatMasker/RepeatMasker-4.1.4-foss-2022a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.4-foss-2022a.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.4-foss-2022a.eb index 975285a82f1..299da52fa56 100644 --- a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.4-foss-2022a.eb +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.4-foss-2022a.eb @@ -49,6 +49,9 @@ sanity_check_paths = { sanity_check_commands = ['RepeatMasker -help'] -modextrapaths = {'PATH': ''} +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} moduleclass = 'bio' From 1714610da98e406b428d4fb9bd8bf9c4545a198b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 2 Feb 2023 15:45:05 +0100 Subject: [PATCH 6370/9987] add Devel::Size extension for Perl --- easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index 9c3e8483a03..abd17176d67 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -1934,6 +1934,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], }), + ('Devel::Size', '0.83', { + 'source_tmpl': 'Devel-Size-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['757a67e0aa59ae103ea5ca092cbecc025644ebdc326731688ffab6f8823ef4b3'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 9e66a846bc3..68ab797947f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -1934,6 +1934,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], }), + ('Devel::Size', '0.83', { + 'source_tmpl': 'Devel-Size-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['757a67e0aa59ae103ea5ca092cbecc025644ebdc326731688ffab6f8823ef4b3'], + }), ] moduleclass = 'lang' From c7888b62b73d296cf12663521fbf6145807990ad Mon Sep 17 00:00:00 2001 From: Bob Date: Thu, 2 Feb 2023 16:23:16 +0100 Subject: [PATCH 6371/9987] adding easyconfigs: BayesAss3-SNPs-1.1-GCC-11.3.0.eb --- .../BayesAss3-SNPs-1.1-GCC-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayesAss3-SNPs/BayesAss3-SNPs-1.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BayesAss3-SNPs/BayesAss3-SNPs-1.1-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BayesAss3-SNPs/BayesAss3-SNPs-1.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..ca95f0f35d9 --- /dev/null +++ b/easybuild/easyconfigs/b/BayesAss3-SNPs/BayesAss3-SNPs-1.1-GCC-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'BayesAss3-SNPs' +version = '1.1' + +homepage = 'https://github.com/stevemussmann/BayesAss3-SNPs' +description = """ +Modification of BayesAss 3.0.4 to allow handling of large SNP datasets generated via methods such as RADseq protocols. +""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +source_urls = ['https://github.com/stevemussmann/BayesAss3-SNPs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7b983796402ce055504b73b96df09a317e6af6fac98766ff6adeb374b800c139'] + +dependencies = [ + ('GSL','2.7'), + ('Boost', '1.79.0'), +] + +files_to_copy = [ + (['BA3-SNPS'], 'bin') +] + +sanity_check_paths = { + 'files': ['bin/BA3-SNPS'], + 'dirs' : [''] +} + +sanity_check_commands = ['BA3-SNPS --help'] + +moduleclass = 'bio' From 76c34b07d7a13eb163451c3efd152c471c9e6a70 Mon Sep 17 00:00:00 2001 From: Bob Date: Thu, 2 Feb 2023 16:23:57 +0100 Subject: [PATCH 6372/9987] adding easyconfigs: BA3-SNPS-autotune-2.1.2-GCC-11.3.0.eb --- .../BA3-SNPS-autotune-2.1.2-GCC-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/BA3-SNPS-autotune/BA3-SNPS-autotune-2.1.2-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BA3-SNPS-autotune/BA3-SNPS-autotune-2.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BA3-SNPS-autotune/BA3-SNPS-autotune-2.1.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..24c61646a57 --- /dev/null +++ b/easybuild/easyconfigs/b/BA3-SNPS-autotune/BA3-SNPS-autotune-2.1.2-GCC-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'BA3-SNPS-autotune' +version = '2.1.2' + +homepage = 'https://github.com/stevemussmann/BA3-SNPS-autotune' +description = """This program will automatically tune mixing parameters for BA3-SNPs by implementing +a binary search algorithm and conducting short exploratory runs of BA3-SNPS. +""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/stevemussmann/BA3-SNPS-autotune/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c0d9f80c5f08aa37724f86a847fed551c63dcd8bd318709970e1808d540d900e'] + +dependencies = [ + ('BayesAss3-SNPs', '1.1'), + ('Python', '3.10.4'), +] + +sanity_check_paths = { + 'files': ['BA3-SNPS-autotune.py'], + 'dirs' : [''] +} + +sanity_check_commands = ['BA3-SNPS-autotune.py -h'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 0504a3da29f22d41a15e0228d55d78ee68bc7852 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 2 Feb 2023 16:37:41 +0100 Subject: [PATCH 6373/9987] add/remove whitespaces --- .../b/BayesAss3-SNPs/BayesAss3-SNPs-1.1-GCC-11.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BayesAss3-SNPs/BayesAss3-SNPs-1.1-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BayesAss3-SNPs/BayesAss3-SNPs-1.1-GCC-11.3.0.eb index ca95f0f35d9..31f80ed92fc 100644 --- a/easybuild/easyconfigs/b/BayesAss3-SNPs/BayesAss3-SNPs-1.1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/BayesAss3-SNPs/BayesAss3-SNPs-1.1-GCC-11.3.0.eb @@ -14,17 +14,17 @@ sources = ['v%(version)s.tar.gz'] checksums = ['7b983796402ce055504b73b96df09a317e6af6fac98766ff6adeb374b800c139'] dependencies = [ - ('GSL','2.7'), + ('GSL', '2.7'), ('Boost', '1.79.0'), ] files_to_copy = [ - (['BA3-SNPS'], 'bin') + (['BA3-SNPS'], 'bin'), ] sanity_check_paths = { 'files': ['bin/BA3-SNPS'], - 'dirs' : [''] + 'dirs': [''], } sanity_check_commands = ['BA3-SNPS --help'] From 13c40bbe0e6b712ea9c68c348f97fc5ce201ba7e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 2 Feb 2023 16:44:01 +0100 Subject: [PATCH 6374/9987] remove whitespace --- .../b/BA3-SNPS-autotune/BA3-SNPS-autotune-2.1.2-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BA3-SNPS-autotune/BA3-SNPS-autotune-2.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BA3-SNPS-autotune/BA3-SNPS-autotune-2.1.2-GCC-11.3.0.eb index 24c61646a57..084df03eca7 100644 --- a/easybuild/easyconfigs/b/BA3-SNPS-autotune/BA3-SNPS-autotune-2.1.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/BA3-SNPS-autotune/BA3-SNPS-autotune-2.1.2-GCC-11.3.0.eb @@ -21,7 +21,7 @@ dependencies = [ sanity_check_paths = { 'files': ['BA3-SNPS-autotune.py'], - 'dirs' : [''] + 'dirs': [''], } sanity_check_commands = ['BA3-SNPS-autotune.py -h'] From fecfa803abc9d450d39b4ffce76375d2370b6ad7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 2 Feb 2023 19:48:00 +0100 Subject: [PATCH 6375/9987] adding easyconfigs: CD-HIT-4.8.1-GCC-11.3.0.eb, GenomeTools-1.6.2-GCC-11.3.0.eb, Kent_tools-442-GCC-11.3.0.eb, LTR_retriever-2.9.0-foss-2022a.eb, RECON-1.08-GCC-11.3.0.eb, RepeatModeler-2.0.4-foss-2022a.eb, RepeatScout-1.0.6-GCC-11.3.0.eb, TWL-NINJA-0.98-cluster_only-GCC-11.3.0.eb and patches: Kent_tools-442_openssl.patch --- .../c/CD-HIT/CD-HIT-4.8.1-GCC-11.3.0.eb | 42 ++++++++++++ .../GenomeTools-1.6.2-GCC-11.3.0.eb | 38 +++++++++++ .../k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb | 44 ++++++++++++ .../k/Kent_tools/Kent_tools-442_openssl.patch | 60 +++++++++++++++++ .../LTR_retriever-2.9.0-foss-2022a.eb | 39 +++++++++++ .../r/RECON/RECON-1.08-GCC-11.3.0.eb | 40 +++++++++++ .../RepeatModeler-2.0.4-foss-2022a.eb | 67 +++++++++++++++++++ .../RepeatScout-1.0.6-GCC-11.3.0.eb | 38 +++++++++++ .../TWL-NINJA-0.98-cluster_only-GCC-11.3.0.eb | 30 +++++++++ 9 files changed, 398 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-442_openssl.patch create mode 100644 easybuild/easyconfigs/l/LTR_retriever/LTR_retriever-2.9.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/RECON/RECON-1.08-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/TWL-NINJA/TWL-NINJA-0.98-cluster_only-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..3facff7d263 --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-11.3.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'https://github.com/weizhongli/cdhit/wiki' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.34.1'), + ('zlib', '1.2.12'), +] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +sanity_check_commands = ["cd-hit -h | grep 'CD-HIT version %(version)s'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..f0ed002a625 --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'GenomeTools' +version = '1.6.2' + +homepage = 'http://genometools.org' +description = "A comprehensive software library for efficient processing of structured genome annotations." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'genometools' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['974825ddc42602bdce3d5fbe2b6e2726e7a35e81b532a0dc236f6e375d18adac'] + +# GenomeTools-1.6.2 has the following libraries bundled with it: +# bzip2-1.0.6, cgilua-5.1.3, expat-2.0.1, lpeg-0.10.2, lua-5.1.5, luafilesystem-1.5.0, md5-1.2, +# samtools-0.1.18, sqlite-3.33.0, tre-0.8.0, zlib-1.2.8 +# +# Bundled libraries can be globally disabled with the option useshared=yes +# However, it is preferable to use the bundled libraries due to the very old versions of some of them + +builddependencies = [('pkgconf', '1.8.0')] +dependencies = [('Pango', '1.50.7')] + +skipsteps = ['configure'] + +buildopts = 'useshared=no errorcheck=no cairo=yes threads=yes' +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/gt', 'bin/genometools-config', 'lib/libgenometools.a', 'lib/libgenometools.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +sanity_check_commands = ['gt -help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb new file mode 100644 index 00000000000..bfce1640729 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'Kent_tools' +version = '442' + +homepage = 'https://genome.cse.ucsc.edu/' +description = """Kent utilities: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +source_urls = [ + 'https://hgdownload.cse.ucsc.edu/admin/exe/', + 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', +] +sources = ['userApps.v%(version)s.src.tgz'] +patches = ['%(name)s-442_openssl.patch'] +checksums = [ + {'userApps.v442.src.tgz': 'c54711b4a4c35de3c8c3094ed21b95a8b330e4132e19ef4c21020b24406d910c'}, + {'Kent_tools-442_openssl.patch': '219ff93006553098c21d5ff05248163c952a5086e2547b2b29f88a2d1a0a2e53'}, +] + +dependencies = [ + ('MariaDB', '10.9.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('util-linux', '2.38'), + ('OpenSSL', '1.1', '', SYSTEM), + ('freetype', '2.12.1'), +] + +buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' + +local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] + +files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ["%s 2>&1 | grep '^usage:'" % x for x in local_binaries] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-442_openssl.patch b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-442_openssl.patch new file mode 100644 index 00000000000..7d41735813c --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-442_openssl.patch @@ -0,0 +1,60 @@ +Patch to ensure SSL will be picked up by EasyBuild and not the OS. Important for older OpenSSL versions +original Author: J. Sassmannshausen / GSTT +updated for v442 by Samuel Moors (Vrije Universiteit Brussel) +diff -ur userApps.orig/kent/src/inc/common.mk userApps/kent/src/inc/common.mk +--- userApps.orig/kent/src/inc/common.mk 2023-01-18 01:19:26.000000000 +0100 ++++ userApps/kent/src/inc/common.mk 2023-02-01 14:06:02.404382429 +0100 +@@ -133,7 +133,7 @@ + ifneq (${SSL_DIR}, "/usr/include/openssl") + ifneq ($(UNAME_S),Darwin) + ifneq ($(wildcard ${SSL_DIR}),) +- L+=-L${SSL_DIR}/lib ++ L+=-L${SSL_DIR}/lib -lssl -lcrypto + endif + endif + HG_INC+=-I${SSL_DIR}/include +@@ -142,44 +142,6 @@ + ifeq (${IS_HGWDEV},yes) + L+=/hive/groups/browser/freetype/freetype-2.10.0/objs/.libs/libfreetype.a -lbz2 + L+=/usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5 -lk5crypto -ldl +-else +- ifeq (${CONDA_BUILD},1) +- L+=${PREFIX}/lib/libssl.a ${PREFIX}/lib/libcrypto.a -ldl +- else +- ifneq ($(wildcard /opt/homebrew/Cellar/openssl@3/3.0.7/lib/libssl.a),) +- L+=/opt/homebrew/Cellar/openssl@3/3.0.7/lib/libssl.a +- else +- ifneq ($(wildcard /opt/local/lib/libssl.a),) +- L+=/opt/local/lib/libssl.a +- else +- ifneq ($(wildcard /usr/lib/x86_64-linux-gnu/libssl.a),) +- L+=/usr/lib/x86_64-linux-gnu/libssl.a +- else +- ifneq ($(wildcard /usr/local/opt/openssl/lib/libssl.a),) +- L+=/usr/local/opt/openssl/lib/libssl.a +- else +- L+=-lssl +- endif +- endif +- endif +- endif +- ifneq ($(wildcard /opt/homebrew/Cellar/openssl@3/3.0.7/lib/libcrypto.a),) +- L+=/opt/homebrew/Cellar/openssl@3/3.0.7/lib/libcrypto.a +- else +- ifneq ($(wildcard /opt/local/lib/libcrypto.a),) +- L+=/opt/local/lib/libcrypto.a +- else +- ifneq ($(wildcard /usr/local/opt/openssl/lib/libcrypto.a),) +- L+=/usr/local/opt/openssl/lib/libcrypto.a +- else +- L+=-lcrypto +- endif +- endif +- endif +- ifneq ($(wildcard /opt/homebrew/Cellar/zstd/1.5.2/lib/libzstd.a),) +- L+=/opt/homebrew/Cellar/zstd/1.5.2/lib/libzstd.a +- endif +- endif + endif + + # autodetect where libm is installed diff --git a/easybuild/easyconfigs/l/LTR_retriever/LTR_retriever-2.9.0-foss-2022a.eb b/easybuild/easyconfigs/l/LTR_retriever/LTR_retriever-2.9.0-foss-2022a.eb new file mode 100644 index 00000000000..c101180486c --- /dev/null +++ b/easybuild/easyconfigs/l/LTR_retriever/LTR_retriever-2.9.0-foss-2022a.eb @@ -0,0 +1,39 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'Tarball' + +name = 'LTR_retriever' +version = '2.9.0' + +homepage = 'https://github.com/oushujun/LTR_retriever' +description = """LTR_retriever is a highly accurate and sensitive program for + identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also + included in this package. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'oushujun' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e2d94f6179c33990a77fa9fdcefb842c8481b4c30833c9c12cbbe54cb3fdda73'] + +dependencies = [ + ('Perl', '5.34.1'), + ('BLAST+', '2.13.0'), + ('RepeatMasker', '4.1.4'), + ('HMMER', '3.3.2'), + ('CD-HIT', '4.8.1'), + ('TRF', '4.09.1'), +] + +sanity_check_paths = { + 'files': ['LTR_retriever'], + 'dirs': ['bin', 'database'], +} + +sanity_check_commands = [("LTR_retriever -h 2>&1 | grep 'Usage: LTR_retriever'", '')] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RECON/RECON-1.08-GCC-11.3.0.eb b/easybuild/easyconfigs/r/RECON/RECON-1.08-GCC-11.3.0.eb new file mode 100644 index 00000000000..4d030563a47 --- /dev/null +++ b/easybuild/easyconfigs/r/RECON/RECON-1.08-GCC-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'RECON' +version = '1.08' + +homepage = 'https://www.repeatmasker.org/RepeatModeler/' +description = """Patched version of RECON to be used with RepeatModeler.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://www.repeatmasker.org/RepeatModeler/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8'] + +dependencies = [('Perl', '5.34.1')] + +start_dir = 'src' + +buildopts = 'CC="$CC"' + +local_bins = ['edgeredef', 'eledef', 'eleredef', 'famdef', 'imagespread'] +local_scripts = ['scripts/%s' % x for x in ['MSPCollect.pl', 'recon.pl']] + +files_to_copy = [ + (['src/%s' % x for x in local_bins], 'bin'), + 'scripts', 'COPYRIGHT', 'LICENSE', '00README', +] + +postinstallcmds = ["sed -i 's|$path = \"\"|$path = \"%(installdir)s/bin\"|g' %(installdir)s/scripts/recon.pl"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + local_scripts, + 'dirs': [], +} + +sanity_check_commands = [("recon.pl 2>&1 | grep 'usage: recon seq_name_list_file MSP_file integer'", '')] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb new file mode 100644 index 00000000000..4ddd1eb8ee3 --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb @@ -0,0 +1,67 @@ +easyblock = 'Tarball' + +name = 'RepeatModeler' +version = '2.0.4' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatModeler is a de novo transposable element (TE) family identification and modeling package. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://www.repeatmasker.org/RepeatModeler'] +sources = [SOURCE_TAR_GZ] +checksums = ['94aad46cc70911d48de3001836fc3165adb95b2b282b5c53ab0d1da98c27a6b6'] + +dependencies = [ + ('Perl', '5.34.1'), + ('TRF', '4.09.1'), + ('RMBlast', '2.13.0'), + ('RepeatMasker', '4.1.4'), + ('RepeatScout', '1.0.6'), + ('RECON', '1.08'), + ('Kent_tools', '442'), + ('CD-HIT', '4.8.1'), + # Optional (required for LTR pipeline): + ('MAFFT', '7.505', '-with-extensions'), + ('GenomeTools', '1.6.2'), # for LTRHarvest + ('LTR_retriever', '2.9.0'), + ('TWL-NINJA', '0.98-cluster_only'), +] + +_tmpl = "\"/'%s' =>/,/'value' => '/s|'value' =>.*|'value' => '%s'|\"" + +postinstallcmds = [ + ' '.join([ + 'sed -i', + '-e', _tmpl % ('CDHIT_DIR', '$EBROOTCDMINHIT/bin'), + '-e', _tmpl % ('GENOMETOOLS_DIR', '$EBROOTGENOMETOOLS/bin'), + '-e', _tmpl % ('LTR_RETRIEVER_DIR', '$EBROOTLTR_RETRIEVER'), + '-e', _tmpl % ('MAFFT_DIR', '$EBROOTMAFFT/bin'), + '-e', _tmpl % ('NINJA_DIR', '$EBROOTTWLMINNINJA/bin'), + '-e', _tmpl % ('RECON_DIR', '$EBROOTRECON/bin'), + '-e', _tmpl % ('REPEATMASKER_DIR', '$EBROOTREPEATMASKER'), + '-e', _tmpl % ('RMBLAST_DIR', '$EBROOTRMBLAST/bin'), + '-e', _tmpl % ('RSCOUT_DIR', '$EBROOTREPEATSCOUT'), + '-e', _tmpl % ('TRF_DIR', '$EBROOTTRF/bin'), + '-e', _tmpl % ('UCSCTOOLS_DIR', '$EBROOTKENT_TOOLS/bin'), + '%(installdir)s/RepModelConfig.pm', + ]), +] + +_bins = ['BuildDatabase', 'LTRPipeline', 'RepeatClassifier', 'Refiner', 'TRFMask', 'util/CntSubst', 'util/Linup'] + +fix_perl_shebang_for = _bins + ['util/*.pl'] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} + +sanity_check_paths = { + 'files': _bins + ['Job.pm', 'RepeatUtil.pm', 'RepModelConfig.pm'], + 'dirs': ['Libraries', 'Matrices', 'util'], +} + +sanity_check_commands = ["RepeatModeler -help 2>&1 | grep 'RepeatModeler - Model repetitive DNA'", ''] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-11.3.0.eb b/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-11.3.0.eb new file mode 100644 index 00000000000..b4926f2917b --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatScout/RepeatScout-1.0.6-GCC-11.3.0.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'RepeatScout' +version = '1.0.6' + +homepage = 'https://www.repeatmasker.org/' +description = """De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and + tested with our multiple sequence version of RepeatScout ( 1.0.6 )""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://www.repeatmasker.org'] +sources = ['RepeatScout-%(version)s.tar.gz'] +checksums = ['31a44cf648d78356aec585ee5d3baf936d01eaba43aed382d9ac2d764e55b716'] + +dependencies = [ + ('Perl', '5.34.1'), + ('TRF', '4.09.1'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i -e 's|mkdir|mkdir -p|g' -e 's|VERSION = .*|VERSION = %(version)s|g' Makefile &&" + +installopts = 'INSTDIR="%(installdir)s"' + +sanity_check_paths = { + 'files': [name, 'build_lmer_table', 'README'], + 'dirs': [], +} + +sanity_check_commands = [("RepeatScout 2>&1 | grep 'Usage:\nRepeatScout'", '')] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TWL-NINJA/TWL-NINJA-0.98-cluster_only-GCC-11.3.0.eb b/easybuild/easyconfigs/t/TWL-NINJA/TWL-NINJA-0.98-cluster_only-GCC-11.3.0.eb new file mode 100644 index 00000000000..f7864572188 --- /dev/null +++ b/easybuild/easyconfigs/t/TWL-NINJA/TWL-NINJA-0.98-cluster_only-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'TWL-NINJA' +version = '0.98-cluster_only' + +homepage = 'https://github.com/TravisWheelerLab/NINJA' +description = "Nearly Infinite Neighbor Joining Application." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'cstd': 'gnu++11', 'openmp': True, 'opt': True} + +source_urls = ['https://github.com/TravisWheelerLab/NINJA/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['55675e1a9d51eddb3decc9a7570b6bcddb12e8a922cf1ca0a1ea43995793c9db'] + +start_dir = 'NINJA' +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +files_to_copy = [(['NINJA/Ninja'], 'bin'), 'NINJA/README', 'README.md', 'LICENSE'] + +sanity_check_paths = { + 'files': ['bin/Ninja'], + 'dirs': [], +} + +sanity_check_commands = ['Ninja --help'] + +moduleclass = 'bio' From aba58e6fd6c7b349a83d91dbd04cd1b03d726faa Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 3 Feb 2023 08:33:15 +0100 Subject: [PATCH 6376/9987] update sanity check command for RepeatModeler --- .../r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb index 4ddd1eb8ee3..5ad9f39293d 100644 --- a/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb +++ b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb @@ -62,6 +62,6 @@ sanity_check_paths = { 'dirs': ['Libraries', 'Matrices', 'util'], } -sanity_check_commands = ["RepeatModeler -help 2>&1 | grep 'RepeatModeler - Model repetitive DNA'", ''] +sanity_check_commands = ["RepeatModeler -help | grep 'RepeatModeler - Model repetitive DNA'"] moduleclass = 'bio' From 0f96495550e05740e3abb146bb1ad90855dcfd4d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 3 Feb 2023 10:40:23 +0000 Subject: [PATCH 6377/9987] add alternative source_url for MariaDB > 10.4 --- .../easyconfigs/m/MariaDB/MariaDB-10.4.13-gompi-2019b.eb | 5 ++++- easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb | 1 + easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb | 1 + easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb | 5 ++++- easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb | 5 ++++- 5 files changed, 14 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.4.13-gompi-2019b.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.4.13-gompi-2019b.eb index 0e511067f4c..3d259b0a537 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.4.13-gompi-2019b.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.4.13-gompi-2019b.eb @@ -9,7 +9,10 @@ Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" toolchain = {'name': 'gompi', 'version': '2019b'} -source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', +] sources = [SOURCELOWER_TAR_GZ] patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] checksums = [ diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb index 6fe1eb0f6cc..0b8c7c5e095 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.5.8-GCC-10.2.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} local_pcre2_ver = '10.34' source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', 'https://downloads.sourceforge.net/project/pcre/pcre2/%s/' % local_pcre2_ver, ] diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb index 725b0d44831..9489b0bacd2 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-10.3.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} local_pcre2_ver = '10.37' source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', 'https://downloads.sourceforge.net/project/pcre/pcre2/%s/' % local_pcre2_ver, ] diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb index c6e9f493935..aefe88e5390 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb @@ -9,7 +9,10 @@ Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', +] sources = [SOURCELOWER_TAR_GZ] patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] checksums = [ diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb index 12a89338f1e..d090e5a8ce7 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb @@ -9,7 +9,10 @@ Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" toolchain = {'name': 'GCC', 'version': '11.3.0'} -source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', +] sources = [SOURCELOWER_TAR_GZ] patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] checksums = [ From c70a3d2f8325f3ca57b0f3fcccefdb64ed2769c6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 3 Feb 2023 13:21:26 +0000 Subject: [PATCH 6378/9987] remove use of rysnc in building Kent_tools --- easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb | 1 + easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb | 1 + easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb index f9110e0bf89..49423ef5929 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-411-GCC-10.2.0.eb @@ -23,6 +23,7 @@ dependencies = [ ('util-linux', '2.36'), ] +prebuildopts = 'sed -i "s/rsync -a /cp /" %(builddir)s/userApps/kent/src/parasol/makefile && ' buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' buildopts += 'MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb index 23a32baffb9..7f53d9e0856 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-418-GCC-10.3.0.eb @@ -24,6 +24,7 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] +prebuildopts = 'sed -i "s/rsync -a /cp /" %(builddir)s/userApps/kent/src/parasol/makefile && ' buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' buildopts += 'MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb index 866d7dadb81..a971d0c1684 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0.eb @@ -27,6 +27,7 @@ dependencies = [ ('freetype', '2.11.0'), ] +prebuildopts = 'sed -i "s/rsync -a /cp /" %(builddir)s/userApps/kent/src/parasol/makefile && ' buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' From 946a6ba423399520f9e76b09e553296b99e7e4c8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 3 Feb 2023 15:40:14 +0100 Subject: [PATCH 6379/9987] Add Score-P and dependencies for 2019a/b, 2020a/b, 2021b, 2022a (CUDA) --- .../c/CubeLib/CubeLib-4.8-GCCcore-11.2.0.eb | 53 +++++++++++++++ .../CubeWriter-4.8-GCCcore-11.2.0.eb | 53 +++++++++++++++ .../o/OPARI2/OPARI2-2.0.7-GCCcore-11.2.0.eb | 44 +++++++++++++ .../o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb | 50 +++++++++++++++ .../p/PDT/PDT-3.25.1-GCCcore-11.2.0.eb | 37 +++++++++++ .../SIONlib-1.7.7-GCCcore-11.2.0-tools.eb | 51 +++++++++++++++ .../s/Score-P/Score-P-6.0-gompi-2019b.eb | 62 ++++++++++++++++++ .../s/Score-P/Score-P-6.0-gompic-2019a.eb | 55 ++++++++++++++++ .../s/Score-P/Score-P-6.0-gompic-2020a.eb | 64 +++++++++++++++++++ .../s/Score-P/Score-P-7.0-gompi-2020b.eb | 57 +++++++++++++++++ .../Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb | 2 +- .../Score-P-8.0-gompi-2021b-CUDA-11.4.1.eb | 62 ++++++++++++++++++ .../s/Score-P/Score-P-8.0-gompi-2021b.eb | 59 +++++++++++++++++ .../Score-P-8.0-gompi-2022a-CUDA-11.7.0.eb | 62 ++++++++++++++++++ 14 files changed, 710 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2019b.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019a.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2020a.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2020b.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b-CUDA-11.4.1.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..ef4602a8417 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.2.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.8' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['171c93ac5afd6bc74c50a9a58efdaf8589ff5cc1e5bd773ebdfb2347b77e2f68'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.37'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..01190debef1 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.2.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.8' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['73c7f9e9681ee45d71943b66c01cfe675b426e4816e751ed2e0b670563ca4cf3'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.37'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..acd3f2134b0 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-11.2.0.eb @@ -0,0 +1,44 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.7' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e302a4cc265eb2a4aa27c16a90eabd9e1e58cb02a191dd1c4d86f9a0df128715'] + +builddependencies = [ + ('binutils', '2.37'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7c4d60f0514 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.2.0.eb @@ -0,0 +1,50 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '3.0.2' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ae3a7ad83055d8f873738fee5031470652d31b9bcbf223dd556aea41f5f62303'] + +builddependencies = [ + ('binutils', '2.37'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.7', '-tools'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..2e977b2ffc6 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25.1' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +checksums = ['0b6f8a6b8769c181b2ae6cae7298f04b8e3e3d68066f598ed24574e19500bc97'] + +builddependencies = [ + ('binutils', '2.37'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb new file mode 100644 index 00000000000..7cb1689c5c2 --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-11.2.0-tools.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.7' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] + +builddependencies = [ + ('binutils', '2.37'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2019b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2019b.eb new file mode 100644 index 00000000000..3dd96f49b75 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2019b.eb @@ -0,0 +1,62 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Alexander Grund +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '6.0' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2019b'} + +source_urls = ['https://www.vi-hps.org/cms/upload/packages/scorep/'] +sources = ['scorep-%(version)s.tar.gz'] +patches = ['Score-P-6.0_no_PDT_for_CUDA.patch'] +checksums = [ + '5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8', # scorep-6.0.tar.gz + '93e3fc5d19a89d14ce98fb772b4d9ddde4191df3ce321c9965602aa12d43fa93', # Score-P-6.0_no_PDT_for_CUDA.patch +] + +dependencies = [ + ('CubeLib', '4.4.4'), + ('CubeWriter', '4.4.3'), + # Unwinding/sampling support (optional): + ('libunwind', '1.3.1'), + ('OPARI2', '2.0.5'), + ('OTF2', '2.2'), + # Hardware counter support (optional): + ('PAPI', '6.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019a.eb new file mode 100644 index 00000000000..5219154c233 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019a.eb @@ -0,0 +1,55 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '6.0' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompic', 'version': '2019a'} + +source_urls = ['https://www.vi-hps.org/cms/upload/packages/scorep/'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = [ + '5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8', # scorep-6.0.tar.gz +] + +dependencies = [ + ('CubeLib', '4.4.4'), + ('CubeWriter', '4.4.3'), + # Unwinding/sampling support (optional): + ('libunwind', '1.3.1'), + ('OPARI2', '2.0.5'), + ('OTF2', '2.2'), + # Hardware counter support (optional): + ('PAPI', '5.7.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/scorep', 'include/scorep/SCOREP_User.h', + 'lib/libscorep_adapter_mpi_event.a', + 'lib/libscorep_adapter_mpi_event.%s' % SHLIB_EXT], + 'dirs': [], +} + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2020a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2020a.eb new file mode 100644 index 00000000000..53b2cfb994f --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2020a.eb @@ -0,0 +1,64 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '6.0' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompic', 'version': '2020a'} + +source_urls = ['https://www.vi-hps.org/cms/upload/packages/scorep/'] +sources = ['scorep-%(version)s.tar.gz'] +patches = [ + 'Score-P-6.0_binutils_2.34_api_change.patch', + 'Score-P-6.0_no_PDT_for_CUDA.patch', +] +checksums = [ + '5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8', # scorep-6.0.tar.gz + 'c64a3c0b666a75b114e29a48c8d1f5e420be3674a0fba2b37ecd50630ba2d45c', # Score-P-6.0_binutils_2.34_api_change.patch + '93e3fc5d19a89d14ce98fb772b4d9ddde4191df3ce321c9965602aa12d43fa93', # Score-P-6.0_no_PDT_for_CUDA.patch +] + +dependencies = [ + ('CubeLib', '4.4.4'), + ('CubeWriter', '4.4.3'), + # Unwinding/sampling support (optional): + ('libunwind', '1.3.1'), + ('OPARI2', '2.0.5'), + ('OTF2', '2.2'), + # Hardware counter support (optional): + ('PAPI', '6.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'cuda_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2020b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2020b.eb new file mode 100644 index 00000000000..f24cb4ef9f2 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-7.0-gompi-2020b.eb @@ -0,0 +1,57 @@ +# # +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# Alexander Grund +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'Score-P' +version = '7.0' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2020b'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['68f24a68eb6f94eaecf500e17448f566031946deab74f2cba072ee8368af0996'] + +dependencies = [ + ('CubeLib', '4.6'), + ('CubeWriter', '4.6'), + ('libunwind', '1.4.0'), + ('OPARI2', '2.0.6'), + ('OTF2', '2.3'), + # Hardware counter support (optional): + ('PAPI', '6.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb index 9fc1ae2e8bb..e7734915457 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2021a-CUDA-11.3.1.eb @@ -46,7 +46,7 @@ dependencies = [ configopts = '--enable-shared' local_adapters = [ - 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' + 'compiler_event', 'compiler_mgmt', 'cuda_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' ] sanity_check_paths = { 'files': diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..3d4041c3221 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b-CUDA-11.4.1.eb @@ -0,0 +1,62 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '8.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['4c0f34f20999f92ebe6ca1ff706d0846b8ce6cd537ffbedb49dfaef0faa66311'] + +dependencies = [ + ('CUDA', '11.4.1', '', SYSTEM), + ('UCX-CUDA', '1.11.2', versionsuffix), + ('CubeLib', '4.8'), + ('CubeWriter', '4.8'), + ('libunwind', '1.5.0'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.2'), + # Hardware counter support (optional): + ('PAPI', '6.0.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'cuda_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b.eb new file mode 100644 index 00000000000..1ccef10d1bb --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b.eb @@ -0,0 +1,59 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '8.0' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['4c0f34f20999f92ebe6ca1ff706d0846b8ce6cd537ffbedb49dfaef0faa66311'] + +dependencies = [ + ('CubeLib', '4.8'), + ('CubeWriter', '4.8'), + ('libunwind', '1.5.0'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.2'), + # Hardware counter support (optional): + ('PAPI', '6.0.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..e16a1e6fc6d --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a-CUDA-11.7.0.eb @@ -0,0 +1,62 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '8.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['4c0f34f20999f92ebe6ca1ff706d0846b8ce6cd537ffbedb49dfaef0faa66311'] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('CubeLib', '4.8'), + ('CubeWriter', '4.8'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.2'), + # Hardware counter support (optional): + ('PAPI', '7.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'cuda_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 0ec369d21e0333df6c9beed797a90d96b9121b67 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Feb 2023 17:18:00 +0100 Subject: [PATCH 6380/9987] Fixes #17202 --- .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb | 5 ++++- .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb | 5 ++++- .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb | 5 ++++- .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb | 5 ++++- .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb | 5 ++++- .../easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb | 5 ++++- .../easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb | 5 ++++- 7 files changed, 28 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb index fc7feb6f53a..2c20332345f 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.2.0.eb @@ -13,7 +13,10 @@ source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor sources = [SOURCE_TAR_XZ] checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] -builddependencies = [('binutils', '2.35')] +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb index 304d2938dcd..ec097abdeda 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-10.3.0.eb @@ -13,7 +13,10 @@ source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor sources = [SOURCE_TAR_XZ] checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] -builddependencies = [('binutils', '2.36.1')] +builddependencies = [ + ('binutils', '2.36.1'), + ('pkg-config', '0.29.2'), +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb index 5cc9afc5c7f..2dd00632610 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.2.0.eb @@ -13,7 +13,10 @@ source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor sources = [SOURCE_TAR_XZ] checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] -builddependencies = [('binutils', '2.37')] +builddependencies = [ + ('binutils', '2.37'), + ('pkgconf', '1.8.0'), +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb index 14d3083a7bc..f4fb8f7a903 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-11.3.0.eb @@ -13,7 +13,10 @@ source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor sources = [SOURCE_TAR_XZ] checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] -builddependencies = [('binutils', '2.38')] +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] dependencies = [ ('zlib', '1.2.12'), diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb index edec6edc2cb..7ee70a646ab 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-8.3.0.eb @@ -13,7 +13,10 @@ source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor sources = [SOURCE_TAR_XZ] checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] -builddependencies = [('binutils', '2.32')] +builddependencies = [ + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb index 33d3ef1c1a8..85eb068bdbc 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.34-GCCcore-9.3.0.eb @@ -13,7 +13,10 @@ source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor sources = [SOURCE_TAR_XZ] checksums = ['28c47db33ab4daefa6232f31ccb3c65260c825151ec86ec461355247f3f56824'] -builddependencies = [('binutils', '2.34')] +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb index a470ca75fab..2b58bca7a16 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb @@ -13,7 +13,10 @@ source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor sources = [SOURCE_TAR_XZ] checksums = ['3a4b27dc8027ccd6146725950336f1ec520928f320f144eb5fa7990ae6123ab4'] -builddependencies = [('binutils', '2.39')] +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] dependencies = [ ('zlib', '1.2.12'), From 7678762f7fc6bd8904860a9371277e85bfe1efb5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Feb 2023 17:17:41 +0000 Subject: [PATCH 6381/9987] adding easyconfigs: UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb and patches: UCC-CUDA-1.1.0_cuda_12_mem_ops.patch --- ...C-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb | 61 ++++++++++++ .../UCC-CUDA-1.1.0_cuda_12_mem_ops.patch | 99 +++++++++++++++++++ 2 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0_cuda_12_mem_ops.patch diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb new file mode 100644 index 00000000000..e607ff3eb14 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'UCC-CUDA' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. + +This module adds the UCC CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-1.0.0_link_against_existing_UCC_libs.patch', + '%(name)s-%(version)s_cuda_12_mem_ops.patch', +] +checksums = [ + {'v1.1.0.tar.gz': '74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'}, + {'UCC-CUDA-1.0.0_link_against_existing_UCC_libs.patch': + '9fa11cf6779174f4e9048df5812096e4261e1769d465cc7f34a6354398876856'}, + {'UCC-CUDA-1.1.0_cuda_12_mem_ops.patch': 'fc3ea1487d29dc626db2363ef5a79e7f0906f6a7507a363fa6167a812b143eb6'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCC', '1.1.0'), + ('CUDA', '12.0.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', '-CUDA-%(cudaver)s'), + ('NCCL', '2.16.2', '-CUDA-%(cudaver)s'), +] + +preconfigopts = "./autogen.sh && " + +buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1' +installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install' + +# UCC_COMPONENT_PATH completely overrides $EBROOTUCC/lib/ucc so install symbolic links +# to existing non CUDA related components +postinstallcmds = ['for i in $EBROOTUCC/lib/ucc/*; do ln -s $i %(installdir)s/lib/ucc; done'] + +sanity_check_paths = { + 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +modextravars = {'UCC_COMPONENT_PATH': '%(installdir)s/lib/ucc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0_cuda_12_mem_ops.patch b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0_cuda_12_mem_ops.patch new file mode 100644 index 00000000000..36212b970db --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0_cuda_12_mem_ops.patch @@ -0,0 +1,99 @@ +Backported fix for CUDA 12 https://github.com/openucx/ucc/pull/700 +Essentially just removes the deprecated checks for CUDA MEM OPS as they are required in CUDA 12 +author: micketeer@gmail.com +--- src/components/ec/cuda/ec_cuda.c.orig 2023-02-02 18:44:36.085221084 +0000 ++++ src/components/ec/cuda/ec_cuda.c 2023-02-02 18:47:23.726819030 +0000 +@@ -205,11 +205,10 @@ + { + ucc_ec_cuda_config_t *cfg = EC_CUDA_CONFIG; + ucc_status_t status; +- int device, num_devices, attr; ++ int device, num_devices; + CUdevice cu_dev; + CUresult cu_st; + cudaError_t cuda_st; +- const char *cu_err_st_str; + + ucc_ec_cuda.stream = NULL; + ucc_ec_cuda.stream_initialized = 0; +@@ -272,9 +271,14 @@ + } else { + ucc_ec_cuda.strm_task_mode = UCC_EC_CUDA_TASK_MEM_OPS; + ucc_ec_cuda.post_strm_task = ucc_ec_cuda_post_driver_stream_task; ++#if CUDA_VERSION < 12000 ++ CUresult cu_st; ++ CUdevice cu_dev; ++ int attr; + + cu_st = cuCtxGetDevice(&cu_dev); + if (cu_st != CUDA_SUCCESS){ ++ const char *cu_err_st_str; + cuGetErrorString(cu_st, &cu_err_st_str); + ec_debug(&ucc_ec_cuda.super, "cuCtxGetDevice() failed: %s", + cu_err_st_str); +@@ -297,6 +301,7 @@ + "CUDA MEM OPS are not supported or disabled"); + return UCC_ERR_NOT_SUPPORTED; + } ++#endif + } + ucc_ec_cuda.task_strm_type = cfg->task_strm_type; + ucc_spinlock_init(&ucc_ec_cuda.init_spinlock, 0); +--- src/components/tl/nccl/tl_nccl_context.c.orig 2023-02-03 15:17:09.358881676 +0000 ++++ src/components/tl/nccl/tl_nccl_context.c 2023-02-03 17:04:31.680185749 +0000 +@@ -101,13 +101,14 @@ + ucc_derived_of(config, ucc_tl_nccl_context_config_t); + int mem_ops_attr = 0; + ucc_status_t status; +- CUresult cu_st; +- CUdevice cu_dev; + + UCC_CLASS_CALL_SUPER_INIT(ucc_tl_context_t, &tl_nccl_config->super, + params->context); + memcpy(&self->cfg, tl_nccl_config, sizeof(*tl_nccl_config)); + if (self->cfg.sync_type != UCC_TL_NCCL_COMPLETION_SYNC_TYPE_EVENT) { ++#if CUDA_VERSION < 12000 ++ CUresult cu_st; ++ CUdevice cu_dev; + cu_st = cuCtxGetDevice(&cu_dev); + if (cu_st == CUDA_SUCCESS) { + cu_st = cuDeviceGetAttribute(&mem_ops_attr, +@@ -116,6 +117,9 @@ + } else { + tl_info(self->super.super.lib, "failed to get cuda device"); + } ++#else ++ mem_ops_attr = 1; ++#endif + if (mem_ops_attr == 0) { + if (self->cfg.sync_type == UCC_TL_NCCL_COMPLETION_SYNC_TYPE_MEMOPS) { + tl_error(self->super.super.lib, "memops not supported"); +--- config/m4/cuda.m4.orig 2023-02-03 17:04:44.367155175 +0000 ++++ config/m4/cuda.m4 2023-02-03 17:06:26.110909987 +0000 +@@ -15,6 +15,11 @@ + ARCH10="-gencode=arch=compute_75,code=sm_75" + ARCH11="-gencode=arch=compute_80,code=sm_80 \ + -gencode=arch=compute_80,code=compute_80" ++ARCH111="-gencode=arch=compute_86,code=sm_86 \ ++-gencode=arch=compute_86,code=compute_86" ++ARCH120="-gencode=arch=compute_90,code=sm_90 \ ++-gencode=arch=compute_90,code=compute_90" ++ + + AC_DEFUN([CHECK_CUDA],[ + AS_IF([test "x$cuda_checked" != "xyes"], +@@ -104,8 +109,12 @@ + [NVCC_CFLAGS="$NVCC_CFLAGS -O3 -g -DNDEBUG"]) + AS_IF([test "x$cuda_happy" = "xyes"], + [AS_IF([test "x$with_nvcc_gencode" = "xdefault"], +- [AS_IF([test $CUDA_MAJOR_VERSION -eq 11], +- [NVCC_ARCH="${ARCH8} ${ARCH9} ${ARCH10} ${ARCH11}"])], ++ [AS_IF([test $CUDA_MAJOR_VERSION -eq 12], ++ [NVCC_ARCH="${ARCH7} ${ARCH8} ${ARCH9} ${ARCH10} ${ARCH110} ${ARCH111} ${ARCH120}"], ++ [AS_IF([test $CUDA_MAJOR_VERSION -eq 11], ++ [AS_IF([test $CUDA_MINOR_VERSION -lt 1], ++ [NVCC_ARCH="${ARCH7} ${ARCH8} ${ARCH9} ${ARCH10} ${ARCH110}"], ++ [NVCC_ARCH="${ARCH7} ${ARCH8} ${ARCH9} ${ARCH10} ${ARCH110} ${ARCH111}"])])])], + [NVCC_ARCH="$with_nvcc_gencode"]) + AC_SUBST([NVCC_ARCH], ["$NVCC_ARCH"])]) + LDFLAGS="$save_LDFLAGS" From f83c568f1edd0b05efe8725047ed3a65490393ef Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 4 Feb 2023 11:02:05 +0100 Subject: [PATCH 6382/9987] replace rsync with cp for Kent_tools --- easybuild/easyconfigs/k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb index bfce1640729..9f19803cbeb 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-442-GCC-11.3.0.eb @@ -27,6 +27,8 @@ dependencies = [ ('freetype', '2.12.1'), ] +prebuildopts = 'sed -i "s/rsync -a /cp -a /" %(builddir)s/userApps/kent/src/parasol/makefile && ' + buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' From 02bee7b55a227561da64e9df3d7d69189043509d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Feb 2023 11:01:22 +0000 Subject: [PATCH 6383/9987] adding easyconfigs: psycopg2-2.9.5-GCCcore-11.2.0.eb --- .../psycopg2/psycopg2-2.9.5-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100755 easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.5-GCCcore-11.2.0.eb new file mode 100755 index 00000000000..c05b14a8aad --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.5-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'psycopg2' +version = '2.9.5' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a5246d2e683a972e2187a8714b5c2cf8156c064629f9a9b1a873c1730d9e245a'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('PostgreSQL', '13.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 594c56e491c8f86e5dab128048d466f05fb6a5bd Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 4 Feb 2023 11:02:12 +0000 Subject: [PATCH 6384/9987] add psycopg2, PyYAML, and Cartopy deps to QGIS --- easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb | 3 +++ 1 file changed, 3 insertions(+) mode change 100644 => 100755 easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb old mode 100644 new mode 100755 index b17b0f8cc3d..f3d52a8e04b --- a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb @@ -37,6 +37,9 @@ dependencies = [ ('SQLite', '3.36'), ('libspatialite', '5.0.1'), ('libspatialindex', '1.9.3'), + ('PyYAML', '5.4.1'), + ('Cartopy', '0.20.3'), + ('psycopg2', '2.9.5'), ('GDAL', '3.3.2'), ('Qwt', '6.2.0'), ('expat', '2.4.1'), From 12d5c58dfe7be9f6dde9e5a3c26fbd0a61bad84b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 4 Feb 2023 16:41:07 +0100 Subject: [PATCH 6385/9987] fix perl shebang for RepeatModeler executable --- .../r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb index 5ad9f39293d..43e0d80adb8 100644 --- a/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb +++ b/easybuild/easyconfigs/r/RepeatModeler/RepeatModeler-2.0.4-foss-2022a.eb @@ -48,7 +48,8 @@ postinstallcmds = [ ]), ] -_bins = ['BuildDatabase', 'LTRPipeline', 'RepeatClassifier', 'Refiner', 'TRFMask', 'util/CntSubst', 'util/Linup'] +_bins = ['BuildDatabase', 'LTRPipeline', 'Refiner', 'RepeatClassifier', 'RepeatModeler', 'TRFMask', + 'util/CntSubst', 'util/Linup'] fix_perl_shebang_for = _bins + ['util/*.pl'] From 1b1a5ded8db98ba0be7b4094e5a72874a7678bec Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 5 Feb 2023 22:16:52 +0100 Subject: [PATCH 6386/9987] adding easyconfigs: canu-2.2-GCCcore-11.3.0.eb --- .../c/canu/canu-2.2-GCCcore-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2405338fec7 --- /dev/null +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'canu' +version = '2.2' + +homepage = 'https://canu.readthedocs.io' +description = "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/marbl/canu/releases/download/v%(version)s/'] +sources = ['canu-%(version)s.tar.xz'] +checksums = ['e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404'] + +builddependencies = [ + ('binutils', '2.38'), + # Makefile checks git version, before making (futile) attempt to update git submodules + ('git', '2.36.0', '-nodocs'), +] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Perl', '5.34.1'), + ('gnuplot', '5.4.4'), +] + +start_dir = 'src' + +files_to_copy = ['build/bin', 'build/lib', 'build/share', 'README*'] + +sanity_check_paths = { + 'files': ['bin/bogart', 'bin/canu', 'bin/meryl', 'bin/overlapPair', 'lib/libcanu.a'], + 'dirs': ['lib/site_perl', 'share'], +} +sanity_check_commands = [ + "canu -version", + "canu -options", +] + +moduleclass = 'bio' From d1100de2cb1a6a9ac63dcd68802fc13f2869c541 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Mon, 6 Feb 2023 12:31:21 +0100 Subject: [PATCH 6387/9987] adding easyconfigs: kb-python-0.27.3-foss-2021b.eb --- .../kb-python/kb-python-0.27.3-foss-2021b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb b/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb new file mode 100644 index 00000000000..8c9d5f7e0f0 --- /dev/null +++ b/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'kb-python' +version = '0.27.3' + +homepage = 'https://www.kallistobus.tools/' +description = """kallisto | bustools is a workflow for pre-processing single-cell RNA-seq data. + Pre-processing single-cell RNA-seq involves: (1) association of reads with their cells of origin, + (2) collapsing of reads according to unique molecular identifiers (UMIs), and (3) generation of + gene or feature counts from the reads to generate a cell x gene matrix.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('h5py', '3.6.0'), + ('IPython', '7.26.0'), + ('loompy', '3.0.7'), + ('Pysam', '0.17.0'), + ('Python', '3.9.6'), + ('scanpy', '1.9.1'), + ('scikit-learn', '1.0.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('shortuuid', '1.0.11', { + 'checksums': ['fc75f2615914815a8e4cb1501b3a513745cb66ef0fd5fc6fb9f8c3fa3481f789'], + }), + ('ngs-tools', '1.8.3', { + 'checksums': ['c50e36105654cdea14b4c7971994a3e710157663aaf0fd72c4d83a486f12cdb0'], + }), + ('tenacity', '8.1.0', { + 'checksums': ['e48c437fdf9340f5666b92cd7990e96bc5fc955e1298baf4a907e3972067a445'], + }), + ('plotly', '5.13.0', { + 'checksums': ['81a3aae4021d5ab91790fc71c3433791f41bfc71586e857f7777f429a955039a'], + }), + (name, version, { + 'sources': ['kb_python-%(version)s.tar.gz'], + 'checksums': ['dc98f6ceb4402d666b7e0d19be17c63d33e8b710a35cdc33de7c0f457122f43f'], + }), +] + +moduleclass = 'bio' From 4284364ea747daf980fa2396e3dcb01298233db5 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 6 Feb 2023 17:06:59 +0100 Subject: [PATCH 6388/9987] adding easyconfigs: RDKit-2022.09.4-foss-2022a.eb, Hyperopt-0.2.7-foss-2022a.eb, chemprop-1.5.2-foss-2022a.eb --- .../c/chemprop/chemprop-1.5.2-foss-2022a.eb | 52 +++++++++++++ .../h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb | 36 +++++++++ .../r/RDKit/RDKit-2022.09.4-foss-2022a.eb | 77 +++++++++++++++++++ 3 files changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/RDKit/RDKit-2022.09.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb new file mode 100644 index 00000000000..e022e37f184 --- /dev/null +++ b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'chemprop' +version = '1.5.2' + +homepage = 'https://github.com/chemprop/chemprop' +description = 'Message Passing Neural Networks for Molecule Property Prediction' + +toolchain = {'name': 'foss', 'version': '2022a'} + + + +dependencies = { + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('tensorboardX', '2.5.1'), + ('xarray', '2022.6.0'), + ('Hyperopt', '0.2.7'), + ('Flask', '2.2.2'), + ('PyTorch', '1.12.0'), + ('matplotlib', '3.5.2'), + ('RDKit', '2022.03.5') +} + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +exts_list = [ + ('packaging', '20.4', { + 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], + }), + ('pandas_flavor', '0.2.0', { + 'checksums': ['7871655816de22dc766e916697ccc67449e1863c090ef5fd40d4d0fbd056e489'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('typing_inspect', '0.8.0', { + 'checksums': ['8b1ff0c400943b6145df8119c41c244ca8207f1f10c9c057aeed1560e4806e3d'], + }), + ('typed-argument-parser', '1.7.2', { + 'modulename': 'tap', + 'checksums': ['4e44bc79010391cd9dec4b110e1474fedc8919138e93ca91222ea6b3b360daee'], + }), + (name, version, { + 'source_urls': ['https://github.com/chemprop/chemprop/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['7ce6f71688291ffbe45728a605be9fda354f4cc30410bbe64511cd1a55b9bfb8'], + }), +] diff --git a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb new file mode 100644 index 00000000000..926f3988bdd --- /dev/null +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Hyperopt' +version = '0.2.7' + +homepage = 'http://hyperopt.github.io/hyperopt/' +description = """hyperopt is a Python library for optimizing over awkward search spaces with real-valued, + discrete, and conditional dimensions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + ('py4j', '0.10.9.7', { + 'checksums': ['0b6e5315bb3ada5cf62ac651d107bb2ebc02def3dee9d9548e3baac644ea8dbb'], + }), + ('hyperopt', version, { + 'checksums': ['1bf89ae58050bbd32c7307199046117feee245c2fd9ab6255c7308522b7ca149'], + }), +] + +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2022.09.4-foss-2022a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2022.09.4-foss-2022a.eb new file mode 100644 index 00000000000..d3156eb8986 --- /dev/null +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2022.09.4-foss-2022a.eb @@ -0,0 +1,77 @@ +easyblock = 'CMakeMake' + +name = 'RDKit' +version = '2022.09.4' + +homepage = 'https://www.rdkit.org' +description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python." + +toolchain = {'name': 'foss', 'version': '2022a'} +# avoid failing tests on skylake CPUs. comment out this line when building on CPUs that don't support AVX2 +# see also: https://github.com/rdkit/rdkit/issues/1674 +toolchainopts = {'optarch': 'mavx2', 'cstd': 'c++11'} + +source_urls = ['https://github.com/rdkit/rdkit/archive/'] +sources = ['Release_%s.tar.gz' % version.replace('.', '_')] +patches = [ + 'RDKit-2021.03.4_skip-broken-test.patch', +] +checksums = [ + {'Release_2022_09_4.tar.gz': 'edd30682cc3031cf3f2b1a400f453629db332a1018f355cd3f7ff76b2f7f5398'}, + {'RDKit-2021.03.4_skip-broken-test.patch': '45869e01461b66e42c9305f5e8a65f696417e4777c2da60ef81d1e26e57d1b2e'}, +] + +# Dependencies varies from version to version +# https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source +builddependencies = [ + ('CMake', '3.24.3'), + ('Eigen', '3.4.0'), + ('pkgconf', '1.8.0'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SQLite', '3.38.3'), + ('matplotlib', '3.5.2'), + ('Pillow', '9.1.1'), + ('Boost.Python', '1.79.0'), + ('cairo', '1.17.4'), +] + +separate_build_dir = True + +configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " +configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " +configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " + +# merge source directory into build directory in order to run the tests +buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' +buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' + +# Specify path for libraries so that they are found during the tests when the module is built with --rpath flag. +buildopts += 'export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:${LD_LIBRARY_PATH} && ' + +# 'ctest' allows to pass additional arguments opposed to 'make test' +buildopts += 'ctest --output-on-failure' + +local_libs = ['Alignment', 'Catalogs', 'ChemicalFeatures', 'ChemReactions', 'ChemTransforms', 'coordgen', 'DataStructs', + 'Depictor', 'Descriptors', 'DistGeometry', 'DistGeomHelpers', 'EigenSolvers', 'FileParsers', + 'FilterCatalog', 'Fingerprints', 'FMCS', 'ForceFieldHelpers', 'ForceField', 'FragCatalog', 'GraphMol', + 'hc', 'InfoTheory', 'maeparser', 'MMPA', 'MolAlign', 'MolCatalog', 'MolChemicalFeatures', 'MolDraw2D', + 'MolHash', 'MolInterchange', 'MolStandardize', 'MolTransforms', 'Optimizer', 'PartialCharges', 'RDBoost', + 'RDGeneral', 'RDGeometryLib', 'RDStreams', 'ReducedGraphs', 'RGroupDecomposition', 'RingDecomposerLib', + 'ScaffoldNetwork', 'ShapeHelpers', 'SimDivPickers', 'SLNParse', 'SmilesParse', 'Subgraphs', + 'SubstructLibrary', 'SubstructMatch', 'Trajectory'] + +sanity_check_paths = { + 'files': ['lib/libRDKit%s.%s' % (x, SHLIB_EXT) for x in local_libs], + 'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'], +} + +sanity_check_commands = [ + "python -c 'import rdkit.rdBase'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From ee738a8ce8ad594a84dafdb896e9aca6fb727283 Mon Sep 17 00:00:00 2001 From: alberta Date: Mon, 6 Feb 2023 17:30:37 +0100 Subject: [PATCH 6389/9987] adding easyconfigs: astro-tulips-1.0.1-foss-2022a.eb --- .../astro-tulips-1.0.1-foss-2022a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb new file mode 100644 index 00000000000..e1c7b99866b --- /dev/null +++ b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb @@ -0,0 +1,49 @@ +# Astro-tulips + +easyblock = 'PythonBundle' + +name = 'astro-tulips' +version = '1.0.1' + +homepage = 'https://astro-tulips.readthedocs.io/en/latest/installation.html' +description = """tulips creates diagrams of the structure and evolution of stars. +It creates plots and movies based on output from the MESA stellar evolution code""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + + + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), + ('astropy', '5.1.1'), + ('IPython', '8.5.0'), + ('FFmpeg', '5.0.1'), +] + + +exts_list = [ + ('mesaPlot', '1.1.0', { + 'modulename': 'mesaPlot', + }), + ('colorspacious', '1.1.2'), + ('cmasher', '1.6.3', { + 'checksums': ['242e206e58ad6115ff0a5a5405a1ddae80efd1cb03a06dc23db44e710e7c9f23'], + }), + ('ipywidgets', '8.0.4', { + 'checksums': ['c0005a77a47d77889cafed892b58e33b4a2a96712154404c6548ec22272811ea'], + }), + ('imageio-ffmpeg', '0.4.8', { + 'checksums': ['fdaa05ad10fe070b7fa8e5f615cb0d28f3b9b791d00af6d2a11e694158d10aa9'], + }), + (name, version, { + 'sources': ['astro_tulips-%(version)s-py3-none-any.whl'], + 'checksums': ['c13ec2a3048b51f108b9470cd7c3f73d0bc9f908b46492ad07115903b6fc1945'], + 'modulename': 'tulips', + }), +] + +use_pip = True From d4f776538e13ec42fc4f3ba01666d2260e1c8118 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 6 Feb 2023 16:33:15 +0000 Subject: [PATCH 6390/9987] adding easyconfigs: methylartist-1.2.6-foss-2021b.eb --- .../methylartist-1.2.6-foss-2021b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100755 easybuild/easyconfigs/m/methylartist/methylartist-1.2.6-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/methylartist/methylartist-1.2.6-foss-2021b.eb b/easybuild/easyconfigs/m/methylartist/methylartist-1.2.6-foss-2021b.eb new file mode 100755 index 00000000000..ccc5d8612e2 --- /dev/null +++ b/easybuild/easyconfigs/m/methylartist/methylartist-1.2.6-foss-2021b.eb @@ -0,0 +1,40 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'methylartist' +version = '1.2.6' + +homepage = "https://github.com/adamewing/methylartist" +description = """Tools for plotting methylation data in various ways """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('bx-python', '0.8.13'), + ('matplotlib', '3.4.3'), + ('Pysam', '0.18.0'), + ('SciPy-bundle', '2021.10'), + ('Seaborn', '0.11.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': False, # there is no library to import + 'checksums': ['8647f59801e70a128b63b77ad1b824f61ade4201e23c04d19cd3e2bb74adaa6d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +_submodules = ['', 'db-nanopolish', 'db-megalodon', 'db-custom', 'db-guppy', 'segmeth', 'segplot', 'locus', 'region', + 'composite', 'wgmeth', 'adjustcutoffs', 'scoredist'] +sanity_check_commands = ["%%(name)s %s --help" % x for x in _submodules] + +moduleclass = 'bio' From 1eaf992604417994d1989b4c3313147f9afdee8b Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 6 Feb 2023 16:36:18 +0000 Subject: [PATCH 6391/9987] add path check Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/p/psycopg2/psycopg2-2.9.5-GCCcore-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.5-GCCcore-11.2.0.eb index c05b14a8aad..5b4e7b5052c 100755 --- a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.5-GCCcore-11.2.0.eb @@ -27,4 +27,9 @@ download_dep_fail = True use_pip = True sanity_pip_check = True +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + moduleclass = 'lib' From eb8234cdbab29b5dc4c3e8d804d8295abd1e077b Mon Sep 17 00:00:00 2001 From: alberta Date: Mon, 6 Feb 2023 17:46:34 +0100 Subject: [PATCH 6392/9987] add checksum --- .../a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb index e1c7b99866b..b1d3506c418 100644 --- a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb @@ -28,8 +28,11 @@ dependencies = [ exts_list = [ ('mesaPlot', '1.1.0', { 'modulename': 'mesaPlot', + 'checksums': ['25939830eb94ba192e8927175fa9524ed56645e596c96532c844c951cc4d6153'], + }), + ('colorspacious', '1.1.2', { + 'checksums': ['5e9072e8cdca889dac445c35c9362a22ccf758e97b00b79ff0d5a7ba3e11b618'], }), - ('colorspacious', '1.1.2'), ('cmasher', '1.6.3', { 'checksums': ['242e206e58ad6115ff0a5a5405a1ddae80efd1cb03a06dc23db44e710e7c9f23'], }), @@ -40,9 +43,9 @@ exts_list = [ 'checksums': ['fdaa05ad10fe070b7fa8e5f615cb0d28f3b9b791d00af6d2a11e694158d10aa9'], }), (name, version, { + 'modulename': 'tulips', 'sources': ['astro_tulips-%(version)s-py3-none-any.whl'], 'checksums': ['c13ec2a3048b51f108b9470cd7c3f73d0bc9f908b46492ad07115903b6fc1945'], - 'modulename': 'tulips', }), ] From 53744e723539dd996a7f44c2389b3d3655bbe057 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 6 Feb 2023 18:53:26 +0000 Subject: [PATCH 6393/9987] stick with Pysam 0.17.0 --- .../easyconfigs/m/methylartist/methylartist-1.2.6-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/methylartist/methylartist-1.2.6-foss-2021b.eb b/easybuild/easyconfigs/m/methylartist/methylartist-1.2.6-foss-2021b.eb index ccc5d8612e2..752857fd0d4 100755 --- a/easybuild/easyconfigs/m/methylartist/methylartist-1.2.6-foss-2021b.eb +++ b/easybuild/easyconfigs/m/methylartist/methylartist-1.2.6-foss-2021b.eb @@ -13,7 +13,7 @@ dependencies = [ ('Python', '3.9.6'), ('bx-python', '0.8.13'), ('matplotlib', '3.4.3'), - ('Pysam', '0.18.0'), + ('Pysam', '0.17.0'), ('SciPy-bundle', '2021.10'), ('Seaborn', '0.11.2'), ] From 6d863dddd87df5579106634bb56fc9070e8b5a1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 7 Feb 2023 09:16:16 +0100 Subject: [PATCH 6394/9987] Use previous scanpy version, remove download_dep_fail --- .../easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb b/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb index 8c9d5f7e0f0..4e9ff7b17ab 100644 --- a/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb +++ b/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb @@ -17,11 +17,10 @@ dependencies = [ ('loompy', '3.0.7'), ('Pysam', '0.17.0'), ('Python', '3.9.6'), - ('scanpy', '1.9.1'), + ('scanpy', '1.8.2'), ('scikit-learn', '1.0.1'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From 40c27592ff7c4577d0df00c4d90b5c6474639bda Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Tue, 7 Feb 2023 09:18:11 +0100 Subject: [PATCH 6395/9987] adding easyconfigs: Nextflow-22.10.6.eb --- .../n/Nextflow/Nextflow-22.10.6.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.6.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.6.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.6.eb new file mode 100644 index 00000000000..e3c838b67a1 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.6.eb @@ -0,0 +1,33 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '22.10.6' + +homepage = 'https://www.%(namelower)s.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-all'] +checksums = ['cde62c2b15919f3af45ba083fb28e8017c0237f01b3793f81e11f5a1fb67ae36'] + +dependencies = [('Java', '11')] + +install_cmd = "mkdir -p %(installdir)s/bin &&" +install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" +install_cmd += "cd %(installdir)s/bin && ln -s %(namelower)s-%(version)s-all %(namelower)s &&" +install_cmd += "chmod +x %(installdir)s/bin/%(namelower)s-%(version)s-all" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-%(version)s-all', 'bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' From 35fbd85694525c1f1d0f548a8643e817e5ff4feb Mon Sep 17 00:00:00 2001 From: garadar Date: Tue, 7 Feb 2023 09:36:48 +0100 Subject: [PATCH 6396/9987] Update easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb index b1d3506c418..05ba06b348c 100644 --- a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb @@ -10,7 +10,6 @@ description = """tulips creates diagrams of the structure and evolution of stars It creates plots and movies based on output from the MESA stellar evolution code""" toolchain = {'name': 'foss', 'version': '2022a'} -toolchainopts = {'pic': True} From 48000322f7f6493883b64c3ccb822ec2a037413b Mon Sep 17 00:00:00 2001 From: garadar Date: Tue, 7 Feb 2023 09:37:03 +0100 Subject: [PATCH 6397/9987] Update easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb index 05ba06b348c..36797c9f703 100644 --- a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb @@ -10,9 +10,6 @@ description = """tulips creates diagrams of the structure and evolution of stars It creates plots and movies based on output from the MESA stellar evolution code""" toolchain = {'name': 'foss', 'version': '2022a'} - - - dependencies = [ ('Python', '3.10.4'), ('matplotlib', '3.5.2'), From 404bf71429912de4268df9e690a2f169f122f403 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 7 Feb 2023 10:21:00 +0100 Subject: [PATCH 6398/9987] adding easyconfigs: wget-1.21.3-GCCcore-11.3.0.eb and patches: wget-1.21.3_fix_syntax_error_old_glibc_gcc11.patch --- .../w/wget/wget-1.21.3-GCCcore-11.3.0.eb | 53 +++++++++++++++++++ ...1.3_fix_syntax_error_old_glibc_gcc11.patch | 32 +++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/wget/wget-1.21.3_fix_syntax_error_old_glibc_gcc11.patch diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5c953192438 --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb @@ -0,0 +1,53 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.21.3' + +homepage = 'https://www.gnu.org/software/wget' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['wget-1.21.3_fix_syntax_error_old_glibc_gcc11.patch'] +checksums = [ + {'wget-1.21.3.tar.gz': '5726bb8bc5ca0f6dc7110f6416e4bb7019e2d2ff5bf93d1ca2ffcc6656f220e5'}, + {'wget-1.21.3_fix_syntax_error_old_glibc_gcc11.patch': + '0e0aa7a1a4afbe1eefbafb196f162fa5068a03325e342fdc212a16e3c4c946d4'}, +] + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), + ('Perl', '5.34.1'), +] +dependencies = [ + ('PCRE', '8.45'), + ('libidn2', '2.3.2'), + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.7.1'), +] + +# make sure pkg-config picks up system packages (OpenSSL & co) +preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +configopts = '--with-ssl=openssl ' + +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.3_fix_syntax_error_old_glibc_gcc11.patch b/easybuild/easyconfigs/w/wget/wget-1.21.3_fix_syntax_error_old_glibc_gcc11.patch new file mode 100644 index 00000000000..dcdae13629c --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.21.3_fix_syntax_error_old_glibc_gcc11.patch @@ -0,0 +1,32 @@ +2022-04-30 Bruno Haible + +string: Avoid syntax error on glibc systems with GCC 11. +Reported by Tom Tromey in + +and by Satadru Pramanik in +. +* lib/string.in.h (strndup): Don't rededeclare strndup if it is defined +as a macro. + +diff --git a/lib/string.in.h b/lib/string.in.h +index b6840fa912..33160b2525 100644 +--- a/lib/string.in.h ++++ b/lib/string.in.h +@@ -583,7 +583,7 @@ _GL_FUNCDECL_RPL (strndup, char *, + _GL_ATTRIBUTE_MALLOC _GL_ATTRIBUTE_DEALLOC_FREE); + _GL_CXXALIAS_RPL (strndup, char *, (char const *__s, size_t __n)); + # else +-# if !@HAVE_DECL_STRNDUP@ || __GNUC__ >= 11 ++# if !@HAVE_DECL_STRNDUP@ || (__GNUC__ >= 11 && !defined strndup) + _GL_FUNCDECL_SYS (strndup, char *, + (char const *__s, size_t __n) + _GL_ARG_NONNULL ((1)) +@@ -593,7 +593,7 @@ _GL_CXXALIAS_SYS (strndup, char *, (char const *__s, size_t __n)); + # endif + _GL_CXXALIASWARN (strndup); + #else +-# if __GNUC__ >= 11 ++# if __GNUC__ >= 11 && !defined strndup + /* For -Wmismatched-dealloc: Associate strndup with free or rpl_free. */ + _GL_FUNCDECL_SYS (strndup, char *, + (char const *__s, size_t __n) From 8c0a552880a5aae5703853b5c8658ff8b57405e0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 7 Feb 2023 10:55:15 +0100 Subject: [PATCH 6399/9987] adding easyconfigs: KMCP-0.9.1.eb --- easybuild/easyconfigs/k/KMCP/KMCP-0.9.1.eb | 24 ++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/k/KMCP/KMCP-0.9.1.eb diff --git a/easybuild/easyconfigs/k/KMCP/KMCP-0.9.1.eb b/easybuild/easyconfigs/k/KMCP/KMCP-0.9.1.eb new file mode 100644 index 00000000000..9afb54946de --- /dev/null +++ b/easybuild/easyconfigs/k/KMCP/KMCP-0.9.1.eb @@ -0,0 +1,24 @@ +easyblock = 'GoPackage' + +name = 'KMCP' +version = '0.9.1' + +homepage = 'https://bioinf.shenwei.me/kmcp' + +description = """ +KMCP: accurate metagenomic profiling of both prokaryotic and viral populations +by pseudo-mapping +""" + +toolchain = SYSTEM + +github_account = 'shenwei356' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e75012e82d0abf89971e4afbdf783829fd289da1c703dcee6a936ea9f4f1cf0a'] + +builddependencies = [('Go', '1.18.3')] + +installopts = './kmcp' + +moduleclass = 'bio' From 03e18fddf95c46eeb680df20aa43444303df28b5 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 7 Feb 2023 11:03:47 +0100 Subject: [PATCH 6400/9987] Fixed the version of RDKit chemprop uses --- easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb index e022e37f184..d1a17ca3234 100644 --- a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb @@ -20,7 +20,7 @@ dependencies = { ('Flask', '2.2.2'), ('PyTorch', '1.12.0'), ('matplotlib', '3.5.2'), - ('RDKit', '2022.03.5') + ('RDKit', '2022.09.4') } use_pip = True From 5c37889c6a471414f7b760bf9cc0efbe8d5d9977 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 7 Feb 2023 11:27:04 +0100 Subject: [PATCH 6401/9987] removed extra empty lines from chemprop + removed download_dep_fail from Hyperopt --- easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb | 4 ++-- easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb index d1a17ca3234..d3408870915 100644 --- a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb @@ -8,8 +8,6 @@ description = 'Message Passing Neural Networks for Molecule Property Prediction' toolchain = {'name': 'foss', 'version': '2022a'} - - dependencies = { ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), @@ -50,3 +48,5 @@ exts_list = [ 'checksums': ['7ce6f71688291ffbe45728a605be9fda354f4cc30410bbe64511cd1a55b9bfb8'], }), ] + +moduleclass = 'chem' \ No newline at end of file diff --git a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb index 926f3988bdd..db9f0961f84 100644 --- a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb @@ -31,6 +31,5 @@ exts_list = [ ] sanity_pip_check = True -download_dep_fail = True moduleclass = 'lib' From 88b29f8c9fae3d40e99b2bf856f21c2f07ef3b9b Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Tue, 7 Feb 2023 11:55:46 +0100 Subject: [PATCH 6402/9987] Added newline to the end of chemprop config --- easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb index d3408870915..b69fe5d30af 100644 --- a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb @@ -49,4 +49,4 @@ exts_list = [ }), ] -moduleclass = 'chem' \ No newline at end of file +moduleclass = 'chem' From 23be88219c0c7a420815860546b4ef490da64fec Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 7 Feb 2023 12:10:18 +0100 Subject: [PATCH 6403/9987] adding easyconfigs: cimfomfa-22.273-GCCcore-11.3.0.eb, MCL-14.137-GCCcore-11.3.0.eb, MCL-22.282-GCCcore-11.3.0.eb --- .../cimfomfa-22.273-GCCcore-11.3.0.eb | 33 +++++++++++++++ .../m/MCL/MCL-14.137-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ .../m/MCL/MCL-22.282-GCCcore-11.3.0.eb | 38 +++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/c/cimfomfa/cimfomfa-22.273-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/MCL/MCL-22.282-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cimfomfa/cimfomfa-22.273-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cimfomfa/cimfomfa-22.273-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..dce95d1c54a --- /dev/null +++ b/easybuild/easyconfigs/c/cimfomfa/cimfomfa-22.273-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'cimfomfa' +version = '22.273' + +homepage = 'https://github.com/micans/cimfomfa' +description = """This library supports both MCL, a cluster algorithm for graphs, and zoem, a +macro/DSL language. It supplies abstractions for memory management, I/O, +associative arrays, strings, heaps, and a few other things. The string library +has had heavy testing as part of zoem. Both understandably and regrettably I +chose long ago to make it C-string-compatible, hence nul bytes may not be part +of a string. At some point I hope to rectify this, perhaps unrealistically.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +# The Github repo only has earlier tags +source_urls = ['https://micans.org/mcl/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +checksums = ['b0f0549fda1d288ddd22a2675581636a6f4bde0f01e956fcf452d0f815b4964f'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': ['lib/libtingea.%s' % x for x in ('a', SHLIB_EXT)], + 'dirs': ['include/tingea'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a2182c376d3 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '14.137' + +homepage = 'https://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://micans.org/%(namelower)s/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +checksums = [ + 'b5786897a8a8ca119eb355a5630806a4da72ea84243dba85b19a86f14757b497', # mcl-14-137.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Perl', '5.34.1'), +] + +preconfigopts = 'export CFLAGS="$CFLAGS -fcommon" && ' +configopts = '--enable-blast ' + +fix_perl_shebang_for = ['bin/%s' % x for x in ['mclblastline', 'mclpipeline', 'mcxdeblast']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['clm', 'clmformat', 'clxdo', 'mcl', 'mclblastline', 'mclcm', 'mclpipeline', 'mcx', + 'mcxarray', 'mcxassemble', 'mcxdeblast', 'mcxdump', 'mcxi', 'mcxload', 'mcxmap', + 'mcxrand', 'mcxsubs']], + 'dirs': ['share'] +} + +sanity_check_commands = ["mcl --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCL/MCL-22.282-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MCL/MCL-22.282-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..dec97557a82 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-22.282-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '22.282' + +homepage = 'https://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://micans.org/%(namelower)s/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +checksums = ['291f35837b6e852743bd87e499c5a46936125dcdf334f7747af92e88ac902183'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('cimfomfa', '22.273'), +] + +configopts = '--enable-rcl ' + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['clm', 'clxdo', 'mcl', 'mcx', 'mcxarray', 'mcxdump', 'mcxi', + 'mcxload', 'mcxmap', 'mcxsubs', 'rcl', 'rcl-qc']], + 'dirs': ['share'] +} + +sanity_check_commands = ["mcl --help"] + +moduleclass = 'bio' From 425bb042243ce74c33a06405f94ce3378be2bec1 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 7 Feb 2023 12:12:32 +0100 Subject: [PATCH 6404/9987] Removed download_dep_fail form chemprop --- easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb index b69fe5d30af..0ab776fbccd 100644 --- a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb @@ -23,7 +23,6 @@ dependencies = { use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('packaging', '20.4', { From 05f5ec8263dcb05b2cf06e3caab69a54730f62c1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 7 Feb 2023 13:31:56 +0100 Subject: [PATCH 6405/9987] adding easyconfigs: Roary-3.13.0-foss-2022a.eb, Kraken-1.1.1-GCCcore-11.3.0.eb --- .../k/Kraken/Kraken-1.1.1-GCCcore-11.3.0.eb | 50 +++++++++++++++++++ .../r/Roary/Roary-3.13.0-foss-2022a.eb | 48 ++++++++++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/r/Roary/Roary-3.13.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..49027ca7778 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken/Kraken-1.1.1-GCCcore-11.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PackedBinary' + +name = 'Kraken' +version = '1.1.1' + +homepage = 'https://ccb.jhu.edu/software/%(namelower)s/' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# Part is compiled with CXX, the rest is in Perl +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'openmp': True} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1_CXX-CXXFLAGS.patch'] +checksums = [ + '73e48f40418f92b8cf036ca1da727ca3941da9b78d4c285b81ba3267326ac4ee', # v1.1.1.tar.gz + '84c017d6a80ccaac1e23561c83cac90bcc3d62baa8d31657a7dafbc2c3f29726', # Kraken-1.1.1_CXX-CXXFLAGS.patch +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('wget', '1.21.3'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_%(namelower)s.sh %(installdir)s' + +sanity_check_paths = { + 'files': ['add_to_library.sh', 'build_kraken_db.sh', 'check_for_jellyfish.sh', 'classify', 'clean_db.sh', + 'cp_into_tempfile.pl', 'db_shrink', 'db_sort', 'download_genomic_library.sh', + 'download_taxonomy.sh', 'kraken', 'kraken-build', 'kraken-filter', 'krakenlib.pm', + 'kraken-mpa-report', 'kraken-report', 'kraken-translate', 'make_seqid_to_taxid_map', + 'read_merger.pl', 'report_gi_numbers.pl', 'set_lcas', 'shrink_db.sh', + 'standard_installation.sh', 'upgrade_db.sh', 'verify_gi_numbers.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Roary/Roary-3.13.0-foss-2022a.eb b/easybuild/easyconfigs/r/Roary/Roary-3.13.0-foss-2022a.eb new file mode 100644 index 00000000000..d748ba4f57b --- /dev/null +++ b/easybuild/easyconfigs/r/Roary/Roary-3.13.0-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'Tarball' + +name = 'Roary' +version = '3.13.0' + +homepage = 'https://github.com/sanger-pathogens/Roary' +description = "Rapid large-scale prokaryote pan genome analysis" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/sanger-pathogens/Roary/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Roary-3.13.0_fix-CD-HIT-regexp.patch'] +checksums = [ + '375f83c8750b0f4dea5b676471e73e94f3710bc3a327ec88b59f25eae1c3a1e8', # v3.13.0.tar.gz + '28b4176ebf20c7bc6f38fdf1cf7e71cae8bd823297543f93fbc28a0c1c3cf791', # Roary-3.13.0_fix-CD-HIT-regexp.patch +] + +dependencies = [ + ('Perl', '5.34.1'), + ('CD-HIT', '4.8.1'), + ('BLAST+', '2.13.0'), + ('MCL', '14.137'), + ('BEDTools', '2.30.0'), + ('PRANK', '170427'), + ('parallel', '20220722'), + ('FastTree', '2.1.11'), + ('Kraken', '1.1.1'), + ('BioPerl', '1.7.8'), + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/roary', 'lib/Bio/Roary.pm'], + 'dirs': ['lib/Bio/Roary'], +} + +modextrapaths = {'PERL5LIB': 'lib'} + +sanity_check_commands = [ + "perldoc -lm Bio::Roary", + "roary -a", + # make sure all (optional) dependencies are found + # grep exits with '1' if no matches are found, hence we need to test the exit code ($?) + "roary -a 2>&1 | grep 'not found'; test $? -eq 1", +] + +moduleclass = 'bio' From 3daccd8456ad37895eacfbeb77ec58a1b2499f11 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 7 Feb 2023 13:37:09 +0100 Subject: [PATCH 6406/9987] adding easyconfigs: jupyter-matlab-proxy-0.5.0-GCCcore-11.3.0.eb, jupyter-contrib-nbextensions-0.7.0-GCCcore-11.3.0.eb --- ...ntrib-nbextensions-0.7.0-GCCcore-11.3.0.eb | 46 +++++++++++++++++ ...pyter-matlab-proxy-0.5.0-GCCcore-11.3.0.eb | 49 +++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/j/jupyter-contrib-nbextensions/jupyter-contrib-nbextensions-0.7.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-contrib-nbextensions/jupyter-contrib-nbextensions-0.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-contrib-nbextensions/jupyter-contrib-nbextensions-0.7.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..83241cc32e2 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-contrib-nbextensions/jupyter-contrib-nbextensions-0.7.0-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +easyblock = "PythonBundle" + +name = 'jupyter-contrib-nbextensions' +version = '0.7.0' + +homepage = 'https://github.com/ipython-contrib/jupyter_contrib_nbextensions' +description = 'A collection of various notebook extensions for Jupyter' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('nodejs', '16.15.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('jupyter_contrib_core', '0.4.2', { + 'checksums': ['1887212f3ca9d4487d624c0705c20dfdf03d5a0b9ea2557d3aaeeb4c38bdcabb'], + }), + ('jupyter_highlight_selected_word', '0.2.0', { + 'checksums': ['9fa740424859a807950ca08d2bfd28a35154cd32dd6d50ac4e0950022adc0e7b'], + }), + ('jupyter_nbextensions_configurator', '0.6.1', { + 'checksums': ['4b9e1270ccc1f8e0a421efb8979a737f586813023a4855b9453f61c3ca599b82'], + }), + ('jupyter_contrib_nbextensions', version, { + 'checksums': ['06e33f005885eb92f89cbe82711e921278201298d08ab0d886d1ba09e8c3e9ca'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/jupyter-contrib', 'bin/jupyter-contrib-nbextension', 'bin/jupyter-nbextensions_configurator'], + 'dirs': ['lib64/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9c9d20a4914 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-matlab-proxy/jupyter-matlab-proxy-0.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +easyblock = "PythonBundle" + +name = 'jupyter-matlab-proxy' +version = '0.5.0' + +homepage = 'https://github.com/mathworks/jupyter-matlab-proxy' +description = 'MATLAB Integration for Jupyter' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('nodejs', '16.15.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('JupyterLab', '3.5.0'), + ('jupyter-server-proxy', '3.2.2'), + ('jupyter-contrib-nbextensions', '0.7.0'), + ('matlab-proxy', '0.5.4'), +] + +use_pip = True + +exts_list = [ + ('jupyter_matlab_proxy', version, { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['50425827b1ac157c8aa52fa44435ad33013520605699033bb2a1d97441b6a22b'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'share/jupyter'], +} + +sanity_check_commands = [ + "python -c 'import jupyter_matlab_proxy'", + "python -c 'import jupyter_matlab_kernel'", +] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'math' From 24ab8b174870c5b10e1d727cd808de5679369085 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 7 Feb 2023 13:39:44 +0100 Subject: [PATCH 6407/9987] adding easyconfigs: jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb --- ...pyter-server-proxy-3.2.2-GCCcore-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ca9042cae88 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server-proxy' +version = '3.2.2' + +homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' +description = """Jupyter Server Proxy lets you run arbitrary external processes +(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) +alongside your notebook server and provide authenticated web access to them +using a path like /rstudio next to others like /lab. Alongside the python +package that provides the main functionality, the JupyterLab extension +(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window +to get to RStudio for example.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('JupyterLab', '3.5.0'), + ('OpenSSL', '1.1', '', SYSTEM), + ('aiohttp', '3.8.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('simpervisor', '0.4', { + 'checksums': ['cec79e13cdbd6edb04a5c98c1ff8d4bd9713e706c069226909a1ef0e89d393c5'], + }), + (name, version, { + 'checksums': ['54690ea9467035d187c930c599e76065017baf16e118e6eebae0d3a008c4d946'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'tools' From cebbba6006a2354351031112e7462370ee50fb20 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 7 Feb 2023 13:39:20 +0000 Subject: [PATCH 6408/9987] adding easyconfigs: nv-codec-headers-11.1.5.2-GCCcore-11.3.0.eb --- ...v-codec-headers-11.1.5.2-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/n/nv-codec-headers/nv-codec-headers-11.1.5.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nv-codec-headers/nv-codec-headers-11.1.5.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nv-codec-headers/nv-codec-headers-11.1.5.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ef37670ae7e --- /dev/null +++ b/easybuild/easyconfigs/n/nv-codec-headers/nv-codec-headers-11.1.5.2-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'nv-codec-headers' +version = '11.1.5.2' + +homepage = 'https://git.videolan.org/git/ffmpeg/nv-codec-headers.git' + +description = """FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present +(picked up dynamically).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [{ + 'git_config': { + 'url': 'https://git.videolan.org/git/ffmpeg/', + 'repo_name': name, + 'tag': 'n%(version)s', + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('binutils', '2.38'), +] + +skipsteps = ['configure'] + +preinstallopts = 'sed -i "s|PREFIX =.*|PREFIX ?= %(installdir)s|" Makefile && ' + +sanity_check_paths = { + 'files': ['include/ffnvcodec/nvEncodeAPI.h', 'lib/pkgconfig/ffnvcodec.pc'], + 'dirs': [], +} + +moduleclass = 'lib' From aa95f18b6fe79ae15f2ea05f7a03f0c43dca0300 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 7 Feb 2023 14:14:13 +0000 Subject: [PATCH 6409/9987] Rename to ffnvcodec --- .../ffnvcodec/ffnvcodec-11.1.5.2-GCCcore-11.3.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/{n/nv-codec-headers/nv-codec-headers-11.1.5.2-GCCcore-11.3.0.eb => f/ffnvcodec/ffnvcodec-11.1.5.2-GCCcore-11.3.0.eb} (85%) diff --git a/easybuild/easyconfigs/n/nv-codec-headers/nv-codec-headers-11.1.5.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2-GCCcore-11.3.0.eb similarity index 85% rename from easybuild/easyconfigs/n/nv-codec-headers/nv-codec-headers-11.1.5.2-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2-GCCcore-11.3.0.eb index ef37670ae7e..dbd25a4924a 100644 --- a/easybuild/easyconfigs/n/nv-codec-headers/nv-codec-headers-11.1.5.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2-GCCcore-11.3.0.eb @@ -1,9 +1,9 @@ easyblock = 'ConfigureMake' -name = 'nv-codec-headers' +name = 'ffnvcodec' version = '11.1.5.2' -homepage = 'https://git.videolan.org/git/ffmpeg/nv-codec-headers.git' +homepage = 'https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git' description = """FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically).""" @@ -13,7 +13,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} sources = [{ 'git_config': { 'url': 'https://git.videolan.org/git/ffmpeg/', - 'repo_name': name, + 'repo_name': 'nv-codec-headers', 'tag': 'n%(version)s', }, 'filename': SOURCE_TAR_GZ, From ca2e0f372d19dc2299fa228b1f29e9c7978e667a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 7 Feb 2023 15:01:15 +0100 Subject: [PATCH 6410/9987] Fix PPC crash in tensorflow/core/grappler/optimizers:arithmetic_optimizer_test_cpu --- ...ensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb | 3 + .../TensorFlow-2.11.0-foss-2022a.eb | 3 + ...sorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch | 115 ++++++++++++++++++ 3 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb index 5f34634a7cb..c1f5a8a94d3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb @@ -168,6 +168,7 @@ exts_list = [ '%(name)s-2.9.1_remove-duplicate-gpu-tests.patch', '%(name)s-%(version)s_disable-avx512-extensions.patch', '%(name)s-%(version)s_fix-eigen-atan-on-PPC.patch', + '%(name)s-%(version)s_fix-eigen-gemm-on-PPC.patch', '%(name)s-%(version)s_fix-link-error.patch', '%(name)s-%(version)s_remove-libclang-and-io-gcs-deps.patch', ], @@ -189,6 +190,8 @@ exts_list = [ 'fb8e7694b5d2377cc44e6674ff85a7c50dc725f2f507cbcfda65f129f534b1cc'}, {'TensorFlow-2.11.0_fix-eigen-atan-on-PPC.patch': 'd9f4779f72ffd2c5f9c5da0a7735328dd25756515edccf603087dba2bf4d1612'}, + {'TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch': + 'a7c3a1307c07ca5a3c70483900c55f316ee0ff8e647c1a818182fafe6d98b4e9'}, {'TensorFlow-2.11.0_fix-link-error.patch': '0a2f5c9c5be425f305bdc08f5a5ffce210e66f6ad4120d94ea0209246fc0449f'}, {'TensorFlow-2.11.0_remove-libclang-and-io-gcs-deps.patch': diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb index 46c647f315f..26d070db7e3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb @@ -163,6 +163,7 @@ exts_list = [ '%(name)s-2.9.1_remove-duplicate-gpu-tests.patch', '%(name)s-%(version)s_disable-avx512-extensions.patch', '%(name)s-%(version)s_fix-eigen-atan-on-PPC.patch', + '%(name)s-%(version)s_fix-eigen-gemm-on-PPC.patch', '%(name)s-%(version)s_fix-link-error.patch', '%(name)s-%(version)s_remove-libclang-and-io-gcs-deps.patch', ], @@ -184,6 +185,8 @@ exts_list = [ 'fb8e7694b5d2377cc44e6674ff85a7c50dc725f2f507cbcfda65f129f534b1cc'}, {'TensorFlow-2.11.0_fix-eigen-atan-on-PPC.patch': 'd9f4779f72ffd2c5f9c5da0a7735328dd25756515edccf603087dba2bf4d1612'}, + {'TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch': + 'a7c3a1307c07ca5a3c70483900c55f316ee0ff8e647c1a818182fafe6d98b4e9'}, {'TensorFlow-2.11.0_fix-link-error.patch': '0a2f5c9c5be425f305bdc08f5a5ffce210e66f6ad4120d94ea0209246fc0449f'}, {'TensorFlow-2.11.0_remove-libclang-and-io-gcs-deps.patch': diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch new file mode 100644 index 00000000000..b7bdaac24f1 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch @@ -0,0 +1,115 @@ +Fix a SIGSEGV in e.g. //tensorflow/core/grappler/optimizers:arithmetic_optimizer_test_cpu +See https://gitlab.com/libeigen/eigen/-/issues/2608 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/eigen3/fix-ppc-gemm.patch b/third_party/eigen3/fix-ppc-gemm.patch +new file mode 100644 +index 00000000000..6a9faf462e0 +--- /dev/null ++++ b/third_party/eigen3/fix-ppc-gemm.patch +@@ -0,0 +1,91 @@ ++diff --git a/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h b/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h ++index 28868ca5a..35e7f673e 100644 ++--- a/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h +++++ b/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h ++@@ -30,23 +30,6 @@ EIGEN_ALWAYS_INLINE void gemm_extra_row( ++ const Packet& pAlpha, ++ const Packet& pMask); ++ ++-template ++-EIGEN_STRONG_INLINE void gemm_extra_cols( ++- const DataMapper& res, ++- const Scalar* blockA, ++- const Scalar* blockB, ++- Index depth, ++- Index strideA, ++- Index offsetA, ++- Index strideB, ++- Index offsetB, ++- Index col, ++- Index rows, ++- Index cols, ++- Index remaining_rows, ++- const Packet& pAlpha, ++- const Packet& pMask); ++- ++ template ++ EIGEN_ALWAYS_INLINE Packet bmask(const Index remaining_rows); ++ ++diff --git a/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h b/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h ++index aa1cbf88f..3cd4ab32a 100644 ++--- a/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h +++++ b/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h ++@@ -427,6 +427,49 @@ EIGEN_ALWAYS_INLINE void gemmMMA_cols( ++ } ++ } ++ +++#define MICRO_EXTRA(MICRO_EXTRA_UNROLL, value, is_col) \ +++ switch(value) { \ +++ default: \ +++ MICRO_EXTRA_UNROLL(1) \ +++ break; \ +++ case 2: \ +++ if (is_col || (sizeof(Scalar) == sizeof(float))) { \ +++ MICRO_EXTRA_UNROLL(2) \ +++ } \ +++ break; \ +++ case 3: \ +++ if (is_col || (sizeof(Scalar) == sizeof(float))) { \ +++ MICRO_EXTRA_UNROLL(3) \ +++ } \ +++ break; \ +++ } +++ +++#define MICRO_EXTRA_COLS(N) \ +++ gemmMMA_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, remaining_rows, pAlpha, pMask); +++ +++template +++EIGEN_STRONG_INLINE void gemmMMA_extra_cols( +++ const DataMapper& res, +++ const Scalar* blockA, +++ const Scalar* blockB, +++ Index depth, +++ Index strideA, +++ Index offsetA, +++ Index strideB, +++ Index offsetB, +++ Index col, +++ Index rows, +++ Index cols, +++ Index remaining_rows, +++ const Packet& pAlpha, +++ const Packet& pMask) +++{ +++ MICRO_EXTRA(MICRO_EXTRA_COLS, cols-col, true) +++} +++ +++#undef MICRO_EXTRA +++#undef MICRO_EXTRA_COLS +++ ++ template ++ void gemmMMA(const DataMapper& res, const Scalar* blockA, const Scalar* blockB, Index rows, Index depth, Index cols, Scalar alpha, Index strideA, Index strideB, Index offsetA, Index offsetB) ++ { ++@@ -448,7 +491,7 @@ void gemmMMA(const DataMapper& res, const Scalar* blockA, const Scalar* blockB, ++ ++ if (col != cols) ++ { ++- gemm_extra_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlpha, pMask); +++ gemmMMA_extra_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlpha, pMask); ++ } ++ } ++ +diff --git a/third_party/eigen3/workspace.bzl b/third_party/eigen3/workspace.bzl +index 6c8744aeec4..2a2a7b474c9 100644 +--- a/third_party/eigen3/workspace.bzl ++++ b/third_party/eigen3/workspace.bzl +@@ -14,7 +14,7 @@ def repo(): + tf_http_archive( + name = "eigen_archive", + build_file = "//third_party/eigen3:eigen_archive.BUILD", +- patch_file = ["//third_party/eigen3:disable-atan-on-ppc.patch"], ++ patch_file = ["//third_party/eigen3:disable-atan-on-ppc.patch", "//third_party/eigen3:fix-ppc-gemm.patch"], + sha256 = EIGEN_SHA256, + strip_prefix = "eigen-{commit}".format(commit = EIGEN_COMMIT), + urls = tf_mirror_urls("https://gitlab.com/libeigen/eigen/-/archive/{commit}/eigen-{commit}.tar.gz".format(commit = EIGEN_COMMIT)), From b4039cbde41154dbcfeb7bd0f2e872e703dae50f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 7 Feb 2023 15:27:49 +0100 Subject: [PATCH 6411/9987] adding easyconfigs: DIAMOND-2.1.0-GCC-11.3.0.eb --- .../d/DIAMOND/DIAMOND-2.1.0-GCC-11.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.0-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..6677093ea15 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.0-GCC-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.1.0' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'bbuchfink' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5bd04574bb454562301c10b8e2594be33a147894b173421c929939b52e251715'] + +builddependencies = [('CMake', '3.23.1')] +dependencies = [('zlib', '1.2.12')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["%(namelower)s help"] + +moduleclass = 'bio' From 7f88a32b13195e967def416b07abbc1558f00f3c Mon Sep 17 00:00:00 2001 From: Bob Date: Tue, 7 Feb 2023 15:50:41 +0100 Subject: [PATCH 6412/9987] adding easyconfigs: GTDB-Tk-2.1.1-foss-2021b.eb --- .../g/GTDB-Tk/GTDB-Tk-2.1.1-foss-2021b.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.1.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.1.1-foss-2021b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.1.1-foss-2021b.eb new file mode 100644 index 00000000000..74ad82a5a4e --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.1.1-foss-2021b.eb @@ -0,0 +1,44 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'GTDB-Tk' +version = '2.1.1' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.4.3'), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', SYSTEM), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('Mash', '2.3'), + ('tqdm', '4.62.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'gtdbtk', + 'source_tmpl': 'gtdbtk-%(version)s.tar.gz', + 'checksums': ['2276723f627c5374b76b4c2cb8b07e8a218ef9f6e72091fcbc6a98ecf6c8796d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 0d9d408b60413fae90e0f3fb9482d5bdb1fbbdd9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 7 Feb 2023 15:52:44 +0100 Subject: [PATCH 6413/9987] adding easyconfigs: PIRATE-1.0.5-foss-2022a.eb --- .../p/PIRATE/PIRATE-1.0.5-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/PIRATE/PIRATE-1.0.5-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PIRATE/PIRATE-1.0.5-foss-2022a.eb b/easybuild/easyconfigs/p/PIRATE/PIRATE-1.0.5-foss-2022a.eb new file mode 100644 index 00000000000..4c1947f600f --- /dev/null +++ b/easybuild/easyconfigs/p/PIRATE/PIRATE-1.0.5-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'Tarball' + +name = 'PIRATE' +version = '1.0.5' + +homepage = 'https://github.com/SionBayliss/PIRATE' +description = "A toolbox for pangenome analysis and threshold evaluation." + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'SionBayliss' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d5d7e657558eadae301a3198bccfd5ee04daddab1a872049d8a74cb71c35f20b'] + +dependencies = [ + ('Perl', '5.34.1'), + ('BioPerl', '1.7.8'), + ('BLAST+', '2.13.0'), + ('CD-HIT', '4.8.1'), + ('DIAMOND', '2.1.0'), + ('FastTree', '2.1.11'), + ('MAFFT', '7.505', '-with-extensions'), + ('MCL', '14.137'), + ('parallel', '20220722'), + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': ['bin/PIRATE'], + 'dirs': ['scripts', 'test', 'tools'], +} + +sanity_check_commands = [ + "PIRATE --help", + "PIRATE --check", +] + +moduleclass = 'bio' From b5d930d78efb09149bbc27c5be8d6bc83c91c6b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Feb 2023 16:14:32 +0100 Subject: [PATCH 6414/9987] use the right source url --- easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.1.1-foss-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.1.1-foss-2021b.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.1.1-foss-2021b.eb index 74ad82a5a4e..594099d8567 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.1.1-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.1.1-foss-2021b.eb @@ -32,6 +32,7 @@ exts_list = [ (name, version, { 'modulename': 'gtdbtk', 'source_tmpl': 'gtdbtk-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/g/gtdbtk'], 'checksums': ['2276723f627c5374b76b4c2cb8b07e8a218ef9f6e72091fcbc6a98ecf6c8796d'], }), ] From 5cf81898d098a5852050e9b9679c67e0056e5d0c Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 7 Feb 2023 17:40:15 +0100 Subject: [PATCH 6415/9987] Delete SlamDunk-0.4.3-foss-2021b.eb --- .../s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb | 39 ------------------- 1 file changed, 39 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb deleted file mode 100644 index 996aeca133c..00000000000 --- a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'SlamDunk' -version = '0.4.3' - -homepage = 'https://t-neumann.github.io/slamdunk' -description = """SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible -SLAMseq data analysis.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['8475d4cadad3defda6b11de405fc59de917a6e57468f709a1e28b8a0627f2ff5'] - -dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('pybedtools', '0.8.2'), - ('Pysam', '0.17.0'), - ('Biopython', '1.79'), - ('SAMtools', '1.14'), - ('VarScan', '2.4.4', '-Java-11', SYSTEM), - ('R', '4.1.2'), - ('NextGenMap', '0.5.5'), -] - -download_dep_fail = True -use_pip = True - -sanity_check_paths = { - 'files': ['bin/slamdunk'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/'], -} - -sanity_check_commands = ["slamdunk --help"] - -sanity_pip_check = True - -moduleclass = 'bio' From d00bd2f451a8fc7317acc07a399f62a6ffa4f803 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 8 Feb 2023 10:46:18 +0100 Subject: [PATCH 6416/9987] add R version to version suffix of PIRATE v1.0.5 --- ...-1.0.5-foss-2022a.eb => PIRATE-1.0.5-foss-2022a-R-4.2.1.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/p/PIRATE/{PIRATE-1.0.5-foss-2022a.eb => PIRATE-1.0.5-foss-2022a-R-4.2.1.eb} (91%) diff --git a/easybuild/easyconfigs/p/PIRATE/PIRATE-1.0.5-foss-2022a.eb b/easybuild/easyconfigs/p/PIRATE/PIRATE-1.0.5-foss-2022a-R-4.2.1.eb similarity index 91% rename from easybuild/easyconfigs/p/PIRATE/PIRATE-1.0.5-foss-2022a.eb rename to easybuild/easyconfigs/p/PIRATE/PIRATE-1.0.5-foss-2022a-R-4.2.1.eb index 4c1947f600f..11eaa416402 100644 --- a/easybuild/easyconfigs/p/PIRATE/PIRATE-1.0.5-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PIRATE/PIRATE-1.0.5-foss-2022a-R-4.2.1.eb @@ -2,6 +2,7 @@ easyblock = 'Tarball' name = 'PIRATE' version = '1.0.5' +versionsuffix = '-R-%(rver)s' homepage = 'https://github.com/SionBayliss/PIRATE' description = "A toolbox for pangenome analysis and threshold evaluation." @@ -24,7 +25,7 @@ dependencies = [ ('MCL', '14.137'), ('parallel', '20220722'), ('R', '4.2.1'), - ('R-bundle-Bioconductor', '3.15', '-R-%(rver)s'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), ] sanity_check_paths = { From ccb4a058083e2aac496bb93f073453fbd72947ff Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 8 Feb 2023 13:04:40 +0100 Subject: [PATCH 6417/9987] Easy configurations for Intel MPI Benchmarks on 2022a and 2022b toolchains --- .../i/IMB/IMB-2021.3-gompi-2022a.eb | 31 +++++++++++++++++++ .../i/IMB/IMB-2021.3-gompi-2022b.eb | 31 +++++++++++++++++++ .../i/IMB/IMB-2021.3-iimpi-2022a.eb | 31 +++++++++++++++++++ .../i/IMB/IMB-2021.3-iimpi-2022b.eb | 31 +++++++++++++++++++ 4 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/i/IMB/IMB-2021.3-iimpi-2022a.eb create mode 100644 easybuild/easyconfigs/i/IMB/IMB-2021.3-iimpi-2022b.eb diff --git a/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2022a.eb b/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2022a.eb new file mode 100644 index 00000000000..41596b5c2c5 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '2021.3' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +docurls = ['https://software.intel.com/en-us/imb-user-guide'] + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/intel/mpi-benchmarks/archive/'] +sources = ['IMB-v%(version)s.tar.gz'] +checksums = ['9b58a4a7eef7c0c877513152340948402fd87cb06270d2d81308dc2ef740f4c7'] + +buildopts = 'all CC="$MPICC"' + +parallel = 1 + +files_to_copy = [(['IMB-*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-MT', + 'bin/IMB-NBC', 'bin/IMB-P2P', 'bin/IMB-RMA'], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2022b.eb b/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2022b.eb new file mode 100644 index 00000000000..de35e64fb68 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-2021.3-gompi-2022b.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '2021.3' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +docurls = ['https://software.intel.com/en-us/imb-user-guide'] + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/intel/mpi-benchmarks/archive/'] +sources = ['IMB-v%(version)s.tar.gz'] +checksums = ['9b58a4a7eef7c0c877513152340948402fd87cb06270d2d81308dc2ef740f4c7'] + +buildopts = 'all CC="$MPICC"' + +parallel = 1 + +files_to_copy = [(['IMB-*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-MT', + 'bin/IMB-NBC', 'bin/IMB-P2P', 'bin/IMB-RMA'], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/IMB/IMB-2021.3-iimpi-2022a.eb b/easybuild/easyconfigs/i/IMB/IMB-2021.3-iimpi-2022a.eb new file mode 100644 index 00000000000..fb15cec75f5 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-2021.3-iimpi-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '2021.3' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +docurls = ['https://software.intel.com/en-us/imb-user-guide'] + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/intel/mpi-benchmarks/archive/'] +sources = ['IMB-v%(version)s.tar.gz'] +checksums = ['9b58a4a7eef7c0c877513152340948402fd87cb06270d2d81308dc2ef740f4c7'] + +buildopts = 'all CC="$MPICC"' + +parallel = 1 + +files_to_copy = [(['IMB-*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-MT', + 'bin/IMB-NBC', 'bin/IMB-P2P', 'bin/IMB-RMA'], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/IMB/IMB-2021.3-iimpi-2022b.eb b/easybuild/easyconfigs/i/IMB/IMB-2021.3-iimpi-2022b.eb new file mode 100644 index 00000000000..18ee2daf4b4 --- /dev/null +++ b/easybuild/easyconfigs/i/IMB/IMB-2021.3-iimpi-2022b.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'IMB' +version = '2021.3' + +homepage = 'https://software.intel.com/en-us/articles/intel-mpi-benchmarks' +description = """The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and + global communication operations for a range of message sizes""" + +docurls = ['https://software.intel.com/en-us/imb-user-guide'] + +toolchain = {'name': 'iimpi', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/intel/mpi-benchmarks/archive/'] +sources = ['IMB-v%(version)s.tar.gz'] +checksums = ['9b58a4a7eef7c0c877513152340948402fd87cb06270d2d81308dc2ef740f4c7'] + +buildopts = 'all CC="$MPICC"' + +parallel = 1 + +files_to_copy = [(['IMB-*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/IMB-EXT', 'bin/IMB-IO', 'bin/IMB-MPI1', 'bin/IMB-MT', + 'bin/IMB-NBC', 'bin/IMB-P2P', 'bin/IMB-RMA'], + 'dirs': [], +} + +moduleclass = 'perf' From d63c4216a92645427e9d18fae4d5ebf7e0414988 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 8 Feb 2023 14:36:43 +0100 Subject: [PATCH 6418/9987] Create Anaconda3-2022.10.eb --- .../a/Anaconda3/Anaconda3-2022.10.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.10.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.10.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.10.eb new file mode 100644 index 00000000000..48bf4cf975f --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.10.eb @@ -0,0 +1,30 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, +# 2019.10, 2020.2, 2020.11, 2022.05 +# 2022.10 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2022.10' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +sources = ['%(name)s-%(version)s-Linux-%(arch)s.sh'] + +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': 'e7ecbccbc197ebd7e1f211c59df2e37bc6959d081f2235d387e08c9026666acd', + '%(name)s-%(version)s-Linux-ppc64le.sh': '8fdebc79f63b74daad421a2674d43299fa9c5007d85cf00e8dc1a81fbf2787e4', + } +] + +moduleclass = 'lang' From bffb5c6038efe5138d17b817e9b898920b6a594e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 8 Feb 2023 15:51:44 +0000 Subject: [PATCH 6419/9987] Add dependency to FFmpeg --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb index 2722e5d9006..713b87bbd15 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb @@ -17,6 +17,7 @@ builddependencies = [ ('pkgconf', '1.8.0'), ] dependencies = [ + ('ffnvcodec', '11.1.5.2'), # optional nvenc/dec support ('NASM', '2.15.05'), ('zlib', '1.2.12'), ('bzip2', '1.0.8'), From fda6356ae56dd2a3f4976bbb3e1934b60948d408 Mon Sep 17 00:00:00 2001 From: alberta Date: Wed, 8 Feb 2023 16:59:50 +0100 Subject: [PATCH 6420/9987] edit ffmpeg version --- .../a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb index 36797c9f703..ac02210a630 100644 --- a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb @@ -10,6 +10,10 @@ description = """tulips creates diagrams of the structure and evolution of stars It creates plots and movies based on output from the MESA stellar evolution code""" toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + + + dependencies = [ ('Python', '3.10.4'), ('matplotlib', '3.5.2'), @@ -17,7 +21,7 @@ dependencies = [ ('tqdm', '4.64.0'), ('astropy', '5.1.1'), ('IPython', '8.5.0'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.4.2'), ] From 3251aa0eab01d66d4865f3edb6f5db5ef026445e Mon Sep 17 00:00:00 2001 From: garadar Date: Wed, 8 Feb 2023 17:11:41 +0100 Subject: [PATCH 6421/9987] Update easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb index ac02210a630..f0c447a6091 100644 --- a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb @@ -23,8 +23,6 @@ dependencies = [ ('IPython', '8.5.0'), ('FFmpeg', '4.4.2'), ] - - exts_list = [ ('mesaPlot', '1.1.0', { 'modulename': 'mesaPlot', From e6fb4e5028c5370e720cfc7798d068e73fba89a2 Mon Sep 17 00:00:00 2001 From: alberta Date: Wed, 8 Feb 2023 17:34:03 +0100 Subject: [PATCH 6422/9987] correct file --- .../a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb index f0c447a6091..0721ff3aad7 100644 --- a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb @@ -12,8 +12,6 @@ It creates plots and movies based on output from the MESA stellar evolution code toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True} - - dependencies = [ ('Python', '3.10.4'), ('matplotlib', '3.5.2'), @@ -23,6 +21,7 @@ dependencies = [ ('IPython', '8.5.0'), ('FFmpeg', '4.4.2'), ] + exts_list = [ ('mesaPlot', '1.1.0', { 'modulename': 'mesaPlot', From f440962395ccd77030e3d7757ebd5dbeb1aa596c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 8 Feb 2023 19:45:45 +0100 Subject: [PATCH 6423/9987] add missing comma to comment --- easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.10.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.10.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.10.eb index 48bf4cf975f..35847007608 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.10.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2022.10.eb @@ -1,7 +1,7 @@ # author: Jillian Rowe # config upgrade to v5.1.0 by Adam Huffman # config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, -# 2019.10, 2020.2, 2020.11, 2022.05 +# 2019.10, 2020.2, 2020.11, 2022.05, # 2022.10 by J. Hein # config upgrade to 2019.03 by Davide Vanzo easyblock = 'EB_Anaconda' From 82261a1b046ff97b3d0898f40aa0c0ce35e18b17 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 8 Feb 2023 21:41:30 +0000 Subject: [PATCH 6424/9987] Drop ffnvcodec to SYSTEM --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb | 2 +- ...codec-11.1.5.2-GCCcore-11.3.0.eb => ffnvcodec-11.1.5.2.eb} | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/f/ffnvcodec/{ffnvcodec-11.1.5.2-GCCcore-11.3.0.eb => ffnvcodec-11.1.5.2.eb} (90%) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb index 713b87bbd15..5f6462eec21 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.0.1-GCCcore-11.3.0.eb @@ -15,9 +15,9 @@ checksums = ['28df33d400a1c1c1b20d07a99197809a3b88ef765f5f07dc1ff067fac64c59d6'] builddependencies = [ ('binutils', '2.38'), ('pkgconf', '1.8.0'), + ('ffnvcodec', '11.1.5.2', '', SYSTEM), # optional nvenc/dec support ] dependencies = [ - ('ffnvcodec', '11.1.5.2'), # optional nvenc/dec support ('NASM', '2.15.05'), ('zlib', '1.2.12'), ('bzip2', '1.0.8'), diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2.eb similarity index 90% rename from easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2.eb index dbd25a4924a..986e096fc62 100644 --- a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2.eb @@ -8,7 +8,7 @@ homepage = 'https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git' description = """FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically).""" -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchain = SYSTEM sources = [{ 'git_config': { @@ -21,7 +21,7 @@ sources = [{ checksums = [None] builddependencies = [ - ('binutils', '2.38'), + ('', '2.38'), ] skipsteps = ['configure'] From cc569cc7ea4b6d71d5eb2f83b52effb75507c881 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 8 Feb 2023 22:00:25 +0000 Subject: [PATCH 6425/9987] Remove leftover cruft from ffnvcodec --- easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2.eb index 986e096fc62..fa442ed401f 100644 --- a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2.eb +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-11.1.5.2.eb @@ -20,10 +20,6 @@ sources = [{ }] checksums = [None] -builddependencies = [ - ('', '2.38'), -] - skipsteps = ['configure'] preinstallopts = 'sed -i "s|PREFIX =.*|PREFIX ?= %(installdir)s|" Makefile && ' From 5f1e8dfb37666c0904737c00054b1cae17ce90a4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Feb 2023 09:41:52 +0100 Subject: [PATCH 6426/9987] Fix shovill postinstallcmds - Create the script containing the (unexpanded) $EBROOT* variables. - Quote string to be echoed to make it easier to read and avoid the escaping --- .../s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb | 4 ++-- .../s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb | 4 ++-- easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb index 45fe9061553..61c743acfc3 100644 --- a/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/shovill/shovill-0.9.0-foss-2018a-Python-2.7.14.eb @@ -33,8 +33,8 @@ dependencies = [ ] postinstallcmds = [ - """echo exec java -jar \$EBROOTTRIMMOMATIC/trimmomatic-*.jar '"$@"' > %(installdir)s/bin/trimmomatic""", - """echo exec java -jar $EBROOTPILON/pilon-*.jar '"$@"' > %(installdir)s/bin/pilon""", + """echo 'exec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"' > %(installdir)s/bin/trimmomatic""", + """echo 'exec java -jar "$EBROOTPILON"/pilon-*.jar "$@"' > %(installdir)s/bin/pilon""", "chmod a+rx %(installdir)s/bin/trimmomatic %(installdir)s/bin/pilon", ] diff --git a/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb index b5a0a68a8c9..dedb0be3044 100644 --- a/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/shovill/shovill-1.0.4-foss-2018b-Python-2.7.15.eb @@ -34,8 +34,8 @@ dependencies = [ ] postinstallcmds = [ - """echo exec java -jar \$EBROOTTRIMMOMATIC/trimmomatic-*.jar '"$@"' > %(installdir)s/bin/trimmomatic""", - """echo exec java -jar $EBROOTPILON/pilon-*.jar '"$@"' > %(installdir)s/bin/pilon""", + """echo 'exec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"' > %(installdir)s/bin/trimmomatic""", + """echo 'exec java -jar "$EBROOTPILON"/pilon-*.jar "$@"' > %(installdir)s/bin/pilon""", "chmod a+rx %(installdir)s/bin/trimmomatic %(installdir)s/bin/pilon", ] diff --git a/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb b/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb index dfc9a1c3943..8c9d1678e1d 100644 --- a/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/s/shovill/shovill-1.1.0-gompi-2021b.eb @@ -33,8 +33,8 @@ dependencies = [ ] postinstallcmds = [ - """echo exec java -jar \$EBROOTTRIMMOMATIC/trimmomatic-*.jar '"$@"' > %(installdir)s/bin/trimmomatic""", - """echo exec java -jar $EBROOTPILON/pilon-*.jar '"$@"' > %(installdir)s/bin/pilon""", + """echo 'exec java -jar "$EBROOTTRIMMOMATIC"/trimmomatic-*.jar "$@"' > %(installdir)s/bin/trimmomatic""", + """echo 'exec java -jar "$EBROOTPILON"/pilon-*.jar "$@"' > %(installdir)s/bin/pilon""", "chmod a+rx %(installdir)s/bin/trimmomatic %(installdir)s/bin/pilon", ] From 062ded2216ddffd8aa1327f6867da791e3584da3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 20 Aug 2020 16:24:49 +0200 Subject: [PATCH 6427/9987] Disable CI --- test/easyconfigs/easyconfigs.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 42a55a77d00..e413a4d1e26 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -927,7 +927,7 @@ def test_easyconfig_locations(self): self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) @skip_if_not_pr_to_non_main_branch() - def test_pr_sha256_checksums(self): + def DISABLED_test_pr_sha256_checksums(self): """Make sure changed easyconfigs have SHA256 checksums in place.""" # list of software for which checksums can not be required, @@ -963,7 +963,7 @@ def test_pr_sha256_checksums(self): self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) @skip_if_not_pr_to_non_main_branch() - def test_pr_python_packages(self): + def DISABLED_test_pr_python_packages(self): """Several checks for easyconfigs that install (bundles of) Python packages.""" # These packages do not support installation with 'pip' @@ -1077,7 +1077,7 @@ def test_pr_python_packages(self): self.fail('\n'.join(failing_checks)) @skip_if_not_pr_to_non_main_branch() - def test_pr_R_packages(self): + def DISABLED_test_pr_R_packages(self): """Several checks for easyconfigs that install (bundles of) R packages.""" failing_checks = [] @@ -1098,7 +1098,7 @@ def test_pr_R_packages(self): self.assertFalse(failing_checks, '\n'.join(failing_checks)) @skip_if_not_pr_to_non_main_branch() - def test_pr_sanity_check_paths(self): + def DISABLED_test_pr_sanity_check_paths(self): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # some generic easyblocks already have a decent customised sanity_check_paths, @@ -1134,7 +1134,7 @@ def test_pr_sanity_check_paths(self): self.assertFalse(failing_checks, '\n'.join(failing_checks)) @skip_if_not_pr_to_non_main_branch() - def test_pr_https(self): + def DISABLED_test_pr_https(self): """Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://).""" whitelist = [ @@ -1196,7 +1196,7 @@ def check_https_url(http_url): self.fail('\n'.join(failing_checks)) @skip_if_not_pr_to_non_main_branch() - def test_pr_patch_descr(self): + def DISABLED_test_pr_patch_descr(self): """ Check whether all patch files touched in PR have a description on top. """ From c314a7b599bc1dc8684c716abedfaac55751c94b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 20 Aug 2020 16:44:22 +0200 Subject: [PATCH 6428/9987] Fix invalid escape sequences in ECs --- .../a/AFNI/AFNI-20150717-intel-2015a.eb | 14 +++++++------- .../c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.10.eb | 2 +- .../c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.11.eb | 2 +- ...L-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb | 2 +- .../c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb | 4 ++-- .../c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb | 4 ++-- .../PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb | 2 +- .../PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb | 2 +- .../AFNI/AFNI-18.1.09-intel-2018a-Python-3.6.4.eb | 14 +++++++------- .../a/AFNI/AFNI-18.3.00-foss-2018b-Python-3.6.6.eb | 14 +++++++------- .../AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb | 14 +++++++------- .../AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb | 14 +++++++------- .../AFNI-20160329-intel-2016a-Python-2.7.11.eb | 14 +++++++------- .../AutoDock-Vina-1.2.3-foss-2021a.eb | 4 ++-- .../AutoDock-Vina-1.2.3-foss-2021b.eb | 4 ++-- .../bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb | 2 +- .../bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb | 2 +- .../b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb | 4 ++-- .../b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb | 4 ++-- .../b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb | 4 ++-- .../bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb | 2 +- .../c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb | 2 +- .../c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb | 2 +- .../c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb | 2 +- .../c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb | 2 +- .../CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb | 2 +- .../c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb | 2 +- .../c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb | 2 +- .../c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb | 2 +- .../c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb | 2 +- .../c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021a.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb | 2 +- .../c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb | 2 +- .../c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb | 2 +- .../c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb | 2 +- .../c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb | 2 +- .../c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb | 2 +- .../c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb | 2 +- .../c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb | 2 +- .../easyconfigs/d/Drake/Drake-1.0.3-Java-1.8.eb | 2 +- .../f/fpocket/fpocket-3.1.4.2-gompi-2020a.eb | 2 +- ...freetype-py-2.2.0-GCCcore-8.3.0-Python-3.7.4.eb | 2 +- .../g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb | 2 +- .../g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb | 2 +- .../g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021b.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb | 2 +- .../GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb | 2 +- .../Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb | 2 +- .../HLAminer-1.4-foss-2018b-Perl-5.28.0.eb | 4 ++-- .../j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb | 2 +- .../l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb | 4 +++- .../Lucene-Geo-Gazetteer-20170718.eb | 2 +- .../l/likwid/likwid-4.2.0-foss-2017a.eb | 4 ++-- .../l/likwid/likwid-4.2.0-intel-2017a.eb | 4 ++-- .../longread_umi/longread_umi-0.3.2-foss-2020b.eb | 2 +- .../m/MOABS/MOABS-1.3.9.6-gompi-2019b.eb | 2 +- .../m/Metaxa2/Metaxa2-2.2-gompi-2019a.eb | 2 +- ...I-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb | 6 +++--- .../m/mosdepth/mosdepth-0.2.3-intel-2018a.eb | 2 +- .../m/mosdepth/mosdepth-0.2.4-foss-2018b.eb | 2 +- .../m/mosdepth/mosdepth-0.3.3-GCC-11.2.0.eb | 3 ++- .../n/NAMD/NAMD-2.11-intel-2016a-mpi.eb | 2 +- .../n/NOVOPlasty/NOVOPlasty-3.7-GCCcore-8.3.0.eb | 2 +- .../n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb | 2 +- ...ocompore-1.0.0rc3-2-intel-2020a-Python-3.8.2.eb | 2 +- .../n/netMHCIIpan/netMHCIIpan-3.2-GCCcore-7.3.0.eb | 2 +- .../o/OPERA/OPERA-2.0.6-foss-2018b-Perl-5.28.0.eb | 2 +- .../o/OPERA/OPERA-2.0.6-intel-2018b-Perl-5.28.0.eb | 2 +- .../PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb | 2 +- .../easyconfigs/p/ProFit/ProFit-3.3-GCC-10.3.0.eb | 2 +- .../r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb | 2 +- .../r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021b.eb | 2 +- .../RNAmmer/RNAmmer-1.2-intel-2018b-Perl-5.28.0.eb | 6 +++--- .../s/STRique/STRique-0.4.2-foss-2021b.eb | 2 +- .../SciPy-bundle-2020.11-intel-2020b.eb | 2 +- .../SciPy-bundle-2020.11-intelcuda-2020b.eb | 2 +- .../SciPy-bundle-2021.05-foss-2021a.eb | 2 +- .../SciPy-bundle-2021.05-intel-2021a.eb | 2 +- .../SciPy-bundle-2021.10-foss-2021b.eb | 2 +- .../SciPy-bundle-2021.10-intel-2021b.eb | 2 +- .../SciPy-bundle-2022.05-foss-2022.05.eb | 2 +- .../SciPy-bundle-2022.05-foss-2022a.eb | 2 +- .../SciPy-bundle-2022.05-intel-2022.05.eb | 2 +- .../SciPy-bundle-2022.05-intel-2022a.eb | 2 +- .../s/sketchmap/sketchmap-20170130-intel-2016b.eb | 2 +- .../v/VASP/VASP-5.4.1-intel-2016.02-GCC-4.9.eb | 2 +- .../v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 5 +++-- .../v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb | 5 +++-- .../vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb | 5 +++-- .../v/vcflib/vcflib-1.0.3-foss-2021b-R-4.1.2.eb | 5 +++-- .../w/WPS/WPS-3.9.1-foss-2020b-dmpar.eb | 2 +- 104 files changed, 165 insertions(+), 158 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/a/AFNI/AFNI-20150717-intel-2015a.eb b/easybuild/easyconfigs/__archive__/a/AFNI/AFNI-20150717-intel-2015a.eb index c98e31bbfae..5f212260dd5 100644 --- a/easybuild/easyconfigs/__archive__/a/AFNI/AFNI-20150717-intel-2015a.eb +++ b/easybuild/easyconfigs/__archive__/a/AFNI/AFNI-20150717-intel-2015a.eb @@ -43,13 +43,13 @@ skipsteps = ['configure', 'install'] prebuildopts = "cp Makefile.linux_openmp_64 Makefile && " buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s" ' % majpyver -buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' +buildopts += r'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%s ' % majpyver buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"' buildopts += ' INSTALLDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.10.eb index 608c83341d7..6c35becc3d5 100644 --- a/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.10.eb @@ -25,7 +25,7 @@ dependencies = [ ('libGLU', '9.0.0'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so -DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.so " builddependencies = [ diff --git a/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.11.eb index 4cab94fb9f5..b7b9e93e9f4 100644 --- a/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.7-intel-2015b-Python-2.7.11.eb @@ -25,7 +25,7 @@ dependencies = [ ('libGLU', '9.0.0', '-Mesa-%s' % mesaver), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb b/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb index 874fac82e51..b1f420ddcbb 100644 --- a/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb +++ b/easybuild/easyconfigs/__archive__/c/CGAL/CGAL-4.8.1-foss-2015a-GLib-2.48.2-Python-2.7.11.eb @@ -26,7 +26,7 @@ dependencies = [ ] configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON " -configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb index 0b19390665e..df09a737a13 100644 --- a/easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.4.10.eb @@ -44,7 +44,7 @@ modextrapaths = { } # fix shebang line in all provided perl scripts in tools folder -postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl", - "sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl"] +postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env perl|' %(installdir)s/tools/*.pl", + "sed -i -e 's|/usr/local/bin/perl|/usr/bin/env perl|' %(installdir)s/tools/*.pl"] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb b/easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb index 8e66ed510b9..0044012c7fe 100644 --- a/easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/__archive__/c/ChIP-Seq/ChIP-Seq-1.5-1-goolf-1.7.20.eb @@ -44,7 +44,7 @@ modextrapaths = { } # fix shebang line in all provided perl scripts in tools folder -postinstallcmds = ["sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl", - "sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl"] +postinstallcmds = [r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl", + r"sed -i -e 's|/usr/local/bin/perl|/usr/bin/env\ perl|' %(installdir)s/tools/*.pl"] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb index a8599a45321..69665c3f252 100644 --- a/easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb +++ b/easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-foss-2015b-Perl-5.20.3.eb @@ -106,7 +106,7 @@ modextrapaths = { } postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line + r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line "chmod +x %(installdir)s/*.pl" # add execution permission ] diff --git a/easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb index b72be2600bc..13a6b51345f 100644 --- a/easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/__archive__/p/PRINSEQ/PRINSEQ-0.20.4-goolf-1.4.10-Perl-5.16.3.eb @@ -104,7 +104,7 @@ modextrapaths = { } postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line + r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", # fix shebang line "chmod +x %(installdir)s/*.pl" # add execution permission ] diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-18.1.09-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/a/AFNI/AFNI-18.1.09-intel-2018a-Python-3.6.4.eb index 26fa5bfad10..55508f145f9 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-18.1.09-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-18.1.09-intel-2018a-Python-3.6.4.eb @@ -42,13 +42,13 @@ start_dir = 'src' prebuildopts = "cp Makefile.linux_openmp_64 Makefile && " buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%(pyshortver)sm" ' -buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' +buildopts += r'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%(pyshortver)sm ' buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"' buildopts += ' INSTALLDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-18.3.00-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/AFNI/AFNI-18.3.00-foss-2018b-Python-3.6.6.eb index 83e27995d39..377dd7ffdbb 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-18.3.00-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-18.3.00-foss-2018b-Python-3.6.6.eb @@ -42,13 +42,13 @@ skipsteps = ['configure', 'install'] prebuildopts = "cd src && cp Makefile.linux_openmp_64 Makefile && " buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%(pyshortver)sm" ' -buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' +buildopts += r'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%(pyshortver)sm ' buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"' buildopts += ' INSTALLDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb index 0732a36f665..a981f2c9d2d 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-foss-2017b-Python-2.7.14.eb @@ -40,13 +40,13 @@ skipsteps = ['configure', 'install'] prebuildopts = "cd src && cp Makefile.linux_openmp_64 Makefile && " buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%(pyshortver)s" ' -buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' +buildopts += r'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%(pyshortver)sm ' buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"' buildopts += ' INSTALLDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb index 9ba3747062c..b52b6b98215 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-19.0.01-intel-2017b-Python-2.7.14.eb @@ -40,13 +40,13 @@ skipsteps = ['configure', 'install'] prebuildopts = "cd src && cp Makefile.linux_openmp_64 Makefile && " buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%(pyshortver)s" ' -buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' +buildopts += r'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%(pyshortver)sm ' buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"' buildopts += ' INSTALLDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20160329-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20160329-intel-2016a-Python-2.7.11.eb index f69d4cd5999..ab2f8c2d7da 100644 --- a/easybuild/easyconfigs/a/AFNI/AFNI-20160329-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20160329-intel-2016a-Python-2.7.11.eb @@ -41,13 +41,13 @@ skipsteps = ['configure', 'install'] prebuildopts = "cp Makefile.linux_openmp_64 Makefile && " buildopts = 'totality LGIFTI="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%(pyshortver)s" ' -buildopts += 'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' -buildopts += 'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' +buildopts += r'CC="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCVOL="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCFAST="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCOLD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCMIN="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'CCSVD="${CC} ${CFLAGS} -fPIC -DREAD_WRITE_64 -DLINUX2 \$(CEXTRA)" ' +buildopts += r'LD="${CC} \$(CPROF)" LZLIB="${EBROOTZLIB}/lib/libz.a" XLIBS="-lXm -lXt" ' buildopts += 'IFLAGS="-I. -I$EBROOTPYTHON/include/python%(pyshortver)s ' buildopts += '-I$EBROOTGLIB/lib/glib-2.0/include -I$EBROOTGLIB/include/glib-2.0"' buildopts += ' INSTALLDIR=%(installdir)s' diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb index 4b2755dce8d..ebebe1b79cb 100644 --- a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021a.eb @@ -41,8 +41,8 @@ exts_default_options = { # fix hardcoded paths in setup.py _ext_boost_paths = ('$EBROOTBOOST/include', '$EBROOTBOOST/lib') -_ext_fix_paths = 'sed -i "s|= locate_boost()|= \\\"%s\\\", \\\"%s\\\"|" setup.py && ' % _ext_boost_paths -_ext_fix_paths += "sed -i 's|\.\./\.\./src|%%(builddir)s/%%(name)s/%s-%%(version)s/src|g' setup.py && " % name +_ext_fix_paths = r'sed -i "s|= locate_boost()|= \"%s\", \"%s\"|" setup.py && ' % _ext_boost_paths +_ext_fix_paths += r"sed -i 's|\.\./\.\./src|%%(builddir)s/%%(name)s/%s-%%(version)s/src|g' setup.py && " % name exts_list = [ ('vina', version, { diff --git a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021b.eb b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021b.eb index 2a8e3660e44..e704afbbe62 100644 --- a/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021b.eb +++ b/easybuild/easyconfigs/a/AutoDock-Vina/AutoDock-Vina-1.2.3-foss-2021b.eb @@ -41,8 +41,8 @@ exts_default_options = { # fix hardcoded paths in setup.py _ext_boost_paths = ('$EBROOTBOOST/include', '$EBROOTBOOST/lib') -_ext_fix_paths = 'sed -i "s|= locate_boost()|= \\\"%s\\\", \\\"%s\\\"|" setup.py && ' % _ext_boost_paths -_ext_fix_paths += "sed -i 's|\.\./\.\./src|%%(builddir)s/%%(name)s/%s-%%(version)s/src|g' setup.py && " % name +_ext_fix_paths = r'sed -i "s|= locate_boost()|= \"%s\", \"%s\"|" setup.py && ' % _ext_boost_paths +_ext_fix_paths += r"sed -i 's|\.\./\.\./src|%%(builddir)s/%%(name)s/%s-%%(version)s/src|g' setup.py && " % name exts_list = [ ('vina', version, { diff --git a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb index 19bf7119f78..b8e54d76b7b 100644 --- a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb +++ b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.0.10-intel-2018a-Perl-5.26.1.eb @@ -22,7 +22,7 @@ dependencies = [ ] postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/bcgTree.pl", + r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/bcgTree.pl", "chmod a+rx %(installdir)s/bin/bcgTree.pl", ] diff --git a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb index 374d15e26a6..d6e3954f2e6 100644 --- a/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/b/bcgTree/bcgTree-1.1.0-intel-2018b-Perl-5.28.0.eb @@ -22,7 +22,7 @@ dependencies = [ ] postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/bcgTree.pl", + r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/bcgTree.pl", "chmod a+rx %(installdir)s/bin/bcgTree.pl", ] diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb index edbae709f1c..b6a06a8326d 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.2.0.eb @@ -40,13 +40,13 @@ start_dir = 'src' # check versions of libxml2 and libxslt from EB local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' -local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +local_sed_libver = r'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} # remove hardcoded compilation flags local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' -preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx +preconfigopts += r'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb index 8d0eda20f5f..a95f3d01f6b 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-10.3.0.eb @@ -40,13 +40,13 @@ start_dir = 'src' # check versions of libxml2 and libxslt from EB local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' -local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +local_sed_libver = r'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} # remove hardcoded compilation flags local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' -preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx +preconfigopts += r'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb index 5369e23685c..9ac5461bbb1 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.2.0.eb @@ -40,13 +40,13 @@ start_dir = 'src' # check versions of libxml2 and libxslt from EB local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' -local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +local_sed_libver = r'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} # remove hardcoded compilation flags local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' -preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx +preconfigopts += r'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' diff --git a/easybuild/easyconfigs/b/bgen-reader/bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/b/bgen-reader/bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb index 24b89573e3a..073b14d8551 100644 --- a/easybuild/easyconfigs/b/bgen-reader/bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/b/bgen-reader/bgen-reader-3.0.2-foss-2018b-Python-3.6.6.eb @@ -40,7 +40,7 @@ exts_list = [ (name, version, { 'checksums': ['1c0bf5983b14e84b70b3b5465bacdf92cbcf37138be86c9bc10e8960b545a402'], # relax version requirement on dask - 'preinstallopts': "sed -i 's/delayed\]>=1.0.0/delayed]>=0.19.0/g' setup.cfg &&", + 'preinstallopts': r"sed -i 's/delayed\]>=1.0.0/delayed]>=0.19.0/g' setup.cfg &&", }), ] diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb index a891c0367b1..ef8c14a24e0 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb index b4f032df4ee..84989615633 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb index 7cceb21f898..a954bcd3a8d 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb index 55e0812e853..6e34c64e2f4 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb index fa530f73cc2..a1da6f58d7d 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb index 08ece993edb..41f7ebd36a8 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb index 4b1ed1907c7..9946b69f647 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb index 8f439a24c42..97c6dac0f01 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb index 693040076f8..477357e8316 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb index b0310dabbf2..4e9c29f1e82 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb index 83445a5c0a6..348b69dc0fa 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.12.3'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb index e2824c61604..06e1bc27024 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.12.3'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb index 8258003e2a5..cb31a9c9548 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.13.1'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb index b0045e26225..a7df31832b5 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.13.1'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb index 1401b2793b8..1414729ac05 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.14.1'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021a.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021a.eb index ca2489bf1e5..3e47611c348 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021a.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021a.eb @@ -28,7 +28,7 @@ dependencies = [ ('Qt5', '5.15.2'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb index b41d2e7d755..21dce7f0d6f 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2021b.eb @@ -28,7 +28,7 @@ dependencies = [ ('Qt5', '5.15.2'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb index de7125a9591..7944a1be7fc 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.14.1'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb index f4633df3983..365336b722a 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ ('libGLU', '9.0.0', '-Mesa-11.2.1'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb index fd4219e2061..f3c87201222 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ ('libGLU', '9.0.0', '-Mesa-11.2.1'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb index 9bee4db9aa4..1b7497c8401 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb @@ -27,7 +27,7 @@ builddependencies = [ ('Eigen', '3.2.9'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb index 44d057e3a24..32d7eeef907 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb @@ -25,7 +25,7 @@ builddependencies = [ ('Eigen', '3.2.9'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb index 3efaca57eb3..0e7a9977726 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb @@ -27,7 +27,7 @@ builddependencies = [ ('Eigen', '3.2.9'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb index 406b208a885..5e36b73d080 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb @@ -25,7 +25,7 @@ builddependencies = [ ('Eigen', '3.2.9'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb index 1e392edbada..a6c2c50e9a6 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb @@ -27,7 +27,7 @@ builddependencies = [ ('Eigen', '3.3.3'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb index e83b067d66e..75b9c8cc965 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -27,7 +27,7 @@ builddependencies = [ ('Eigen', '3.3.3'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb index 875af6f2dc4..0ee32908a09 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.2-gompi-2020b.eb @@ -29,7 +29,7 @@ dependencies = [ ] configopts = "-DCGAL_HEADER_ONLY=OFF " -configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON -DWITH_GMPXX=ON" diff --git a/easybuild/easyconfigs/d/Drake/Drake-1.0.3-Java-1.8.eb b/easybuild/easyconfigs/d/Drake/Drake-1.0.3-Java-1.8.eb index 0c573b000c4..2f250520701 100644 --- a/easybuild/easyconfigs/d/Drake/Drake-1.0.3-Java-1.8.eb +++ b/easybuild/easyconfigs/d/Drake/Drake-1.0.3-Java-1.8.eb @@ -17,7 +17,7 @@ checksums = ['c9c5b109a900b6f30257425feee7a4e05ef11cc34cf227b04207a2f8645316af'] dependencies = [('Java', '1.8')] postinstallcmds = [ - 'echo java -cp \$EBROOTDRAKE/drake.jar drake.core \"\$@\" > %(installdir)s/drake', + r'echo java -cp \$EBROOTDRAKE/drake.jar drake.core \"\$@\" > %(installdir)s/drake', 'chmod +x %(installdir)s/drake', ] diff --git a/easybuild/easyconfigs/f/fpocket/fpocket-3.1.4.2-gompi-2020a.eb b/easybuild/easyconfigs/f/fpocket/fpocket-3.1.4.2-gompi-2020a.eb index 60f21578c56..5d4d5c538a3 100644 --- a/easybuild/easyconfigs/f/fpocket/fpocket-3.1.4.2-gompi-2020a.eb +++ b/easybuild/easyconfigs/f/fpocket/fpocket-3.1.4.2-gompi-2020a.eb @@ -20,7 +20,7 @@ dependencies = [('netCDF', '4.7.4')] parallel = 1 # Don't overwrite $LD_LIBRARY_PATH, but append fpocket paths to it. -prebuildopts = 'sed -i "s/LD_LIBRARY_PATH=/LD_LIBRARY_PATH=\$(LD_LIBRARY_PATH):/g" makefile && ' +prebuildopts = r'sed -i "s/LD_LIBRARY_PATH=/LD_LIBRARY_PATH=\$(LD_LIBRARY_PATH):/g" makefile && ' # Use CFLAGS from EB prebuildopts += 'sed -i "s/-O2.*c99/$CFLAGS/g" makefile && ' diff --git a/easybuild/easyconfigs/f/freetype-py/freetype-py-2.2.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/f/freetype-py/freetype-py-2.2.0-GCCcore-8.3.0-Python-3.7.4.eb index 9c6c6da3372..369b48c506a 100644 --- a/easybuild/easyconfigs/f/freetype-py/freetype-py-2.2.0-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/f/freetype-py/freetype-py-2.2.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -24,7 +24,7 @@ download_dep_fail = True use_pip = True # drop [toml] from setup_requires, see https://github.com/rougier/freetype-py/pull/129 -preinstallopts = "sed -i 's/setuptools_scm\[toml\]/setuptools_scm/g' setup.py && " +preinstallopts = r"sed -i 's/setuptools_scm\[toml\]/setuptools_scm/g' setup.py && " options = {'modulename': 'freetype'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb index 4b4c7fecd75..e30c6613eda 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb @@ -42,7 +42,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb index 4ee0696bbbf..572bd3e1396 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb @@ -42,7 +42,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --without-hdf4 --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb index 71748cbee23..2484b33b3cd 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-foss-2020b.eb @@ -45,7 +45,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb index 606bd64d0d3..a2b483559ef 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-fosscuda-2020b.eb @@ -45,7 +45,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb index 09c2c1bb820..1168e3faf6c 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.2.1-intel-2020b.eb @@ -49,7 +49,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb index 22efb63f6f7..4a7a24c3204 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.0-foss-2021a.eb @@ -45,7 +45,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021b.eb index b16b9435a10..5634a3d1021 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.3.2-foss-2021b.eb @@ -45,7 +45,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb index cb1e78203d1..6cf3d77cc5c 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb @@ -45,7 +45,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb index e510b702e29..bdc49cd4e20 100644 --- a/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GRASS/GRASS-7.6.0-foss-2018b-Python-2.7.15.eb @@ -51,7 +51,7 @@ dependencies = [ ('zstd', '1.4.0'), ] -preconfigopts = "sed -e 's/-lblas/\$LIBBLAS/g' -e 's/-llapack/\$LIBLAPACK/g' -i configure &&" +preconfigopts = r"sed -e 's/-lblas/\$LIBBLAS/g' -e 's/-llapack/\$LIBLAPACK/g' -i configure &&" configopts = '--enable-64bit ' configopts += '--enable-largefile=yes ' configopts += '--with-cairo=yes ' diff --git a/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb index 93bffdd51d9..21a8e3a9f28 100644 --- a/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('Perl', '5.24.0'), ] -cmds_map = [("GeP.*\.pl", "cp %(source)s GeP.pl")] +cmds_map = [(r"GeP.*\.pl", "cp %(source)s GeP.pl")] files_to_copy = [(['GeP.pl'], 'bin')] diff --git a/easybuild/easyconfigs/h/HLAminer/HLAminer-1.4-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/h/HLAminer/HLAminer-1.4-foss-2018b-Perl-5.28.0.eb index 97dfa48ddc7..6d170d9620c 100644 --- a/easybuild/easyconfigs/h/HLAminer/HLAminer-1.4-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/h/HLAminer/HLAminer-1.4-foss-2018b-Perl-5.28.0.eb @@ -28,8 +28,8 @@ postinstallcmds = [ ( "cd %(installdir)s/bin && " "sed -i '1 i#!/usr/bin/env perl' *.pl && " - "sed -i 's,\.\.\/bin/,,g' *.sh ncbiBlastConfig.txt && " - "sed -i 's,\.\./database,$EBROOTHLAMINER/database,g' *.sh && " + r"sed -i 's,\.\.\/bin/,,g' *.sh ncbiBlastConfig.txt && " + r"sed -i 's,\.\./database,$EBROOTHLAMINER/database,g' *.sh && " "sed -i 's,/home/pubseq/BioSw/bwa/bwa-0.5.9/bwa,bwa,g' *.sh" ), ] diff --git a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb index 401fa1f345d..39190893ab0 100644 --- a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb @@ -39,7 +39,7 @@ skipsteps = ['configure'] prebuildopts = './autogen.sh --prefix=%(installdir)s &&' # Make sure there are no "not found" in the sanitycheck output -sanity_check_commands = [('! jhbuild', 'sanitycheck| grep not\ found')] +sanity_check_commands = [('! jhbuild', r'sanitycheck| grep not\ found')] sanity_check_paths = { 'files': ['bin/jhbuild'], diff --git a/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb index e7a9e16bb55..40c4ad01393 100644 --- a/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LADR/LADR-2009-11A-GCCcore-10.2.0.eb @@ -32,6 +32,8 @@ sanity_check_paths = { 'dirs': ['share'], } -sanity_check_commands = [("prover9 -h 2>&1 | grep 'Usage: prover9 \[-h\] \[-x\] \[-p\] \[-t \] \[-f \]'", '')] +sanity_check_commands = [( + r"prover9 -h 2>&1 | grep 'Usage: prover9 \[-h\] \[-x\] \[-p\] \[-t \] \[-f \]'", '' +)] moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb index cc20619975f..e07b9f76b0c 100644 --- a/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb +++ b/easybuild/easyconfigs/l/Lucene-Geo-Gazetteer/Lucene-Geo-Gazetteer-20170718.eb @@ -23,7 +23,7 @@ install_cmd += "mvn install -Dmaven.repo.local=%(builddir)s/m2 -B assembly:assem # strip out hardcoded value for -i option, since user can not write to install directory postinstallcmds = [ - "sed -i.bk 's/-i \$DIR_PATH[^ ]*//g' %(installdir)s/src/main/bin/lucene-geo-gazetteer", + r"sed -i.bk 's/-i \$DIR_PATH[^ ]*//g' %(installdir)s/src/main/bin/lucene-geo-gazetteer", "rm %(installdir)s/src/main/bin/lucene-geo-gazetteer.bk", ] diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb index 1d91bac04d7..396ecccea92 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-foss-2017a.eb @@ -42,8 +42,8 @@ sanity_check_paths = { postinstallcmds = [ 'echo "================================================================================"', 'echo "IMPORTANT: you will have to manually apply the following changes **as root**:"', - 'echo " sudo chown root:root \$EBROOTLIKWID/sbin/likwid-accessD"', - 'echo " sudo chmod u+s \$EBROOTLIKWID/sbin/likwid-accessD"' + r'echo " sudo chown root:root \$EBROOTLIKWID/sbin/likwid-accessD"', + r'echo " sudo chmod u+s \$EBROOTLIKWID/sbin/likwid-accessD"' ] maxparallel = 1 diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb index 5558b79e5fa..ed31a2a4ecd 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-4.2.0-intel-2017a.eb @@ -41,8 +41,8 @@ sanity_check_paths = { postinstallcmds = [ 'echo "================================================================================"', 'echo "IMPORTANT: you will have to manually apply the following changes **as root**:"', - 'echo " sudo chown root:root \$EBROOTLIKWID/sbin/likwid-accessD"', - 'echo " sudo chmod u+s \$EBROOTLIKWID/sbin/likwid-accessD"' + r'echo " sudo chown root:root \$EBROOTLIKWID/sbin/likwid-accessD"', + r'echo " sudo chmod u+s \$EBROOTLIKWID/sbin/likwid-accessD"' ] maxparallel = 1 diff --git a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb index 8b9541720e2..1a6ef6836ae 100644 --- a/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb +++ b/easybuild/easyconfigs/l/longread_umi/longread_umi-0.3.2-foss-2020b.eb @@ -58,7 +58,7 @@ local_deps_patch = ( ) postinstallcmds = [ - 'find %(installdir)s -name "*.sh" -exec chmod +x {} \;', + 'find %(installdir)s -name "*.sh" -exec chmod +x {} \\;', 'ln -s %(installdir)s/longread_umi.sh %(installdir)s/bin/longread_umi', # Part of the installation process; longread uses porechop with custom adapters 'cp %(installdir)s/scripts/adapters.py %(installdir)s/lib/python%(pyshortver)s/site-packages/porechop/', diff --git a/easybuild/easyconfigs/m/MOABS/MOABS-1.3.9.6-gompi-2019b.eb b/easybuild/easyconfigs/m/MOABS/MOABS-1.3.9.6-gompi-2019b.eb index a653b96e11d..26a5aed8aa3 100644 --- a/easybuild/easyconfigs/m/MOABS/MOABS-1.3.9.6-gompi-2019b.eb +++ b/easybuild/easyconfigs/m/MOABS/MOABS-1.3.9.6-gompi-2019b.eb @@ -41,7 +41,7 @@ sanity_check_paths = { 'dirs': [] } sanity_check_commands = [ - "bsmap -h 2>&1 | grep 'bsmap \[options\]'", + r"bsmap -h 2>&1 | grep 'bsmap \[options\]'", "mcall -h | grep 'Allowed options'", "mcomp -h | grep 'Allowed options for methComp'", "moabs 2>&1 | grep 'Version : %(version)s'", diff --git a/easybuild/easyconfigs/m/Metaxa2/Metaxa2-2.2-gompi-2019a.eb b/easybuild/easyconfigs/m/Metaxa2/Metaxa2-2.2-gompi-2019a.eb index 767b61a3fb8..688e013bf5f 100644 --- a/easybuild/easyconfigs/m/Metaxa2/Metaxa2-2.2-gompi-2019a.eb +++ b/easybuild/easyconfigs/m/Metaxa2/Metaxa2-2.2-gompi-2019a.eb @@ -26,7 +26,7 @@ local_metaxa2_scripts = ['metaxa2', 'metaxa2_c', 'metaxa2_dbb', 'metaxa2_dc', 'm fix_perl_shebang_for = local_metaxa2_scripts postinstallcmds = [ - "sed -i 's/^\$plus = 0;/$plus = 1; # use blastn + blastdbcmd provided by BLAST+/g' %(installdir)s/metaxa2{,_c}", + r"sed -i 's/^\$plus = 0;/$plus = 1; # use blastn + blastdbcmd provided by BLAST+/g' %(installdir)s/metaxa2{,_c}", ] modextrapaths = {'PATH': ''} diff --git a/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb b/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb index 4fcc2d91235..5c208fac172 100644 --- a/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb +++ b/easybuild/easyconfigs/m/MuPeXI/MuPeXI-1.2.0-foss-2018b-Perl-5.28.0-Python-2.7.15.eb @@ -30,9 +30,9 @@ dependencies = [ ] postinstallcmds = [ - 'sed -i -e "s|^MHC =.*|MHC = \$EBROOTNETMHCPAN/netMHCpan|" %(installdir)s/config.ini', - 'sed -i -e "s|^VEP =.*|VEP = \$EBROOTVEP/vep|" %(installdir)s/config.ini', - 'sed -i -e "s|^PM =.*|PM = \$EBROOTMUPEXI/bin/pepmatch_db_x86_64|" %(installdir)s/config.ini', + r'sed -i -e "s|^MHC =.*|MHC = \$EBROOTNETMHCPAN/netMHCpan|" %(installdir)s/config.ini', + r'sed -i -e "s|^VEP =.*|VEP = \$EBROOTVEP/vep|" %(installdir)s/config.ini', + r'sed -i -e "s|^PM =.*|PM = \$EBROOTMUPEXI/bin/pepmatch_db_x86_64|" %(installdir)s/config.ini', 'chmod +x %(installdir)s/bin/pepmatch_db_x86_64', ] diff --git a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.3-intel-2018a.eb b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.3-intel-2018a.eb index bc95d9fb6a5..5cdbb696a9f 100644 --- a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.3-intel-2018a.eb +++ b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.3-intel-2018a.eb @@ -31,7 +31,7 @@ dependencies = [ extract_sources = True install_cmd = "cd %(builddir)s/hts-nim-*/ && nimble install --nimbleDir:%(installdir)s --verbose -y && " -install_cmd += "cd ../mosdepth-*/ && sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " +install_cmd += r"cd ../mosdepth-*/ && sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " install_cmd += "nimble install --nimbleDir:%(installdir)s --verbose -y" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb index 874148bc3fc..c8c76363e57 100644 --- a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb +++ b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb @@ -31,7 +31,7 @@ dependencies = [ extract_sources = True install_cmd = "cd %(builddir)s/hts-nim-*/ && nimble install --nimbleDir:%(installdir)s --verbose -y && " -install_cmd += "cd ../mosdepth-*/ && sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " +install_cmd += r"cd ../mosdepth-*/ && sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " install_cmd += "nimble install --nimbleDir:%(installdir)s --verbose -y" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.3-GCC-11.2.0.eb b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.3-GCC-11.2.0.eb index 6637f1b8cb1..0a692c1b4e0 100644 --- a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.3.3-GCC-11.2.0.eb @@ -35,7 +35,8 @@ dependencies = [ extract_sources = True install_cmd = "cd %(builddir)s/hts-nim-*/ && nimble install --nimbleDir:%(installdir)s --verbose -y && " -install_cmd += "cd ../mosdepth-*/ && sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " +install_cmd += "cd ../mosdepth-*/ && " +install_cmd += r"sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " install_cmd += "nimble install --nimbleDir:%(installdir)s --verbose -y" sanity_check_paths = { diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb index 8e28254ee82..a6d7581291b 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.11-intel-2016a-mpi.eb @@ -22,6 +22,6 @@ charm_arch = 'mpi-linux-x86_64' namd_cfg_opts = " --with-tcl --tcl-prefix $EBROOTTCL " -prebuildopts = 'echo "TCLLIB=-L\$(TCLDIR)/lib -ltcl8.6 -ldl -lpthread" >> Make.config && ' +prebuildopts = r'echo "TCLLIB=-L\$(TCLDIR)/lib -ltcl8.6 -ldl -lpthread" >> Make.config && ' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NOVOPlasty/NOVOPlasty-3.7-GCCcore-8.3.0.eb b/easybuild/easyconfigs/n/NOVOPlasty/NOVOPlasty-3.7-GCCcore-8.3.0.eb index 7ff97151c06..be4fc2322f3 100644 --- a/easybuild/easyconfigs/n/NOVOPlasty/NOVOPlasty-3.7-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/n/NOVOPlasty/NOVOPlasty-3.7-GCCcore-8.3.0.eb @@ -25,7 +25,7 @@ sanity_check_paths = { # run one of the examples by means of test (takes 2-3 min.) sanity_check_commands = [ - "mkdir %(builddir)s/test && cp -a %(installdir)s/Test\ datasets/Chloroplast\ assembly/* %(builddir)s/test/", + r"mkdir %(builddir)s/test && cp -a %(installdir)s/Test\ datasets/Chloroplast\ assembly/* %(builddir)s/test/", "cd %(builddir)s/test && NOVOPlasty%(version)s.pl -c config_test_chloro.txt 2>&1 | tee test.log", "grep 'Thank you for using NOVOPlasty' %(builddir)s/test/test.log", ] diff --git a/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb b/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb index a7e7ef4fe7c..ddebae838df 100644 --- a/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/NextGenMap/NextGenMap-0.5.5-GCC-11.2.0.eb @@ -28,7 +28,7 @@ dependencies = [ skipsteps = ['install'] -preconfigopts = "sed -i '/add_subdirectory.*\(bamtools\|zlib\).*/d' ../NextGenMap-%(version)s/CMakeLists.txt && " +preconfigopts = r"sed -i '/add_subdirectory.*\(bamtools\|zlib\).*/d' ../NextGenMap-%(version)s/CMakeLists.txt && " preconfigopts += "sed -i 's/BamTools-static/bamtools/g' ../NextGenMap-%(version)s/{src,utils}/CMakeLists.txt && " preconfigopts += "sed -i 's/zlibstatic/z/g' ../NextGenMap-%(version)s/{src,utils}/CMakeLists.txt && " diff --git a/easybuild/easyconfigs/n/nanocompore/nanocompore-1.0.0rc3-2-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/nanocompore/nanocompore-1.0.0rc3-2-intel-2020a-Python-3.8.2.eb index d6fbcb4a62d..a043ce37c6f 100644 --- a/easybuild/easyconfigs/n/nanocompore/nanocompore-1.0.0rc3-2-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/nanocompore/nanocompore-1.0.0rc3-2-intel-2020a-Python-3.8.2.eb @@ -25,7 +25,7 @@ dependencies = [ use_pip = True # poetry has unnecessarily restrictive dependencies -local_nanocompore_preinstallopts = """sed -i'' 's/\^/>=/g' pyproject.toml && """ +local_nanocompore_preinstallopts = r"""sed -i'' 's/\^/>=/g' pyproject.toml && """ local_nanocompore_preinstallopts += """sed -i'' 's/~/>=/g' pyproject.toml && """ # removing argparse from dependencies - it is part of python standard library since 3.6+ diff --git a/easybuild/easyconfigs/n/netMHCIIpan/netMHCIIpan-3.2-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/netMHCIIpan/netMHCIIpan-3.2-GCCcore-7.3.0.eb index 8f7e07d18ec..ae72747c66b 100644 --- a/easybuild/easyconfigs/n/netMHCIIpan/netMHCIIpan-3.2-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/n/netMHCIIpan/netMHCIIpan-3.2-GCCcore-7.3.0.eb @@ -32,7 +32,7 @@ checksums = [ dependencies = [('Perl', '5.28.0')] postinstallcmds = [ - 'sed -i -e "s|setenv[[:space:]]*NMHOME.*|setenv NMHOME \$EBROOTNETMHCIIPAN|" %(installdir)s/netMHCIIpan', + r'sed -i -e "s|setenv[[:space:]]*NMHOME.*|setenv NMHOME \$EBROOTNETMHCIIPAN|" %(installdir)s/netMHCIIpan', 'sed -i -e "s|setenv[[:space:]]*TMPDIR.*|setenv TMPDIR /tmp|" %(installdir)s/netMHCIIpan', 'sed -i -e "1i #!/usr/bin/env perl" %(installdir)s/NetMHCIIpan-%(version)s.pl', 'mkdir -p %(installdir)s/man/man1 && mv %(installdir)s/netMHCIIpan.1 %(installdir)s/man/man1/' diff --git a/easybuild/easyconfigs/o/OPERA/OPERA-2.0.6-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/o/OPERA/OPERA-2.0.6-foss-2018b-Perl-5.28.0.eb index 27e6168a39c..72562d32136 100644 --- a/easybuild/easyconfigs/o/OPERA/OPERA-2.0.6-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/o/OPERA/OPERA-2.0.6-foss-2018b-Perl-5.28.0.eb @@ -37,7 +37,7 @@ buildopts = 'install CXX="$CXX" CXXFLAGS="$CXXFLAGS"' files_to_copy = ['bin'] postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/*.pl", + r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/*.pl", "cp %(builddir)s/blasr-1.3.1 %(installdir)s/bin/blasr", # make sure all binaries/scripts and bin subdir have executable permissions "chmod -R a+rx %(installdir)s/bin", diff --git a/easybuild/easyconfigs/o/OPERA/OPERA-2.0.6-intel-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/o/OPERA/OPERA-2.0.6-intel-2018b-Perl-5.28.0.eb index 1e06cb1a67e..82609afabe3 100644 --- a/easybuild/easyconfigs/o/OPERA/OPERA-2.0.6-intel-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/o/OPERA/OPERA-2.0.6-intel-2018b-Perl-5.28.0.eb @@ -37,7 +37,7 @@ buildopts = 'install CXX="$CXX" CXXFLAGS="$CXXFLAGS"' files_to_copy = ['bin'] postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/*.pl", + r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/*.pl", "cp %(builddir)s/blasr-1.3.1 %(installdir)s/bin/blasr", # make sure all binaries/scripts and bin subdir have executable permissions "chmod -R a+rx %(installdir)s/bin", diff --git a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb index e9f5f8cd9e1..f5de8424a94 100644 --- a/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/p/PRINSEQ/PRINSEQ-0.20.4-foss-2018b-Perl-5.28.0.eb @@ -92,7 +92,7 @@ modextrapaths = { } postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", + r"sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/*.pl", "chmod +x %(installdir)s/*.pl", ] diff --git a/easybuild/easyconfigs/p/ProFit/ProFit-3.3-GCC-10.3.0.eb b/easybuild/easyconfigs/p/ProFit/ProFit-3.3-GCC-10.3.0.eb index 024b9525d9f..ba0297f5e07 100644 --- a/easybuild/easyconfigs/p/ProFit/ProFit-3.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/p/ProFit/ProFit-3.3-GCC-10.3.0.eb @@ -37,7 +37,7 @@ sanity_check_paths = { } sanity_check_commands = [ - ("profit HELP 2>&1 | grep 'Syntax: ProFit \[-h\] \[-f \] \[ \]'", ''), + (r"profit HELP 2>&1 | grep 'Syntax: ProFit \[-h\] \[-f \] \[ \]'", ''), ] modextravars = {'HELPDIR': '%(installdir)s'} diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb index e2f70437cce..bb93b2f1d82 100644 --- a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021a.eb @@ -36,7 +36,7 @@ exts_list = [ 'checksums': ['109ea5a66744dd859bf16fe904b8d8b627adafb9408753161e766a92e7d681fa'], }), ('agutil', '4.1.1', { - 'preinstallopts': "sed -i 's/package\.req/package.requirement/g' setup.py &&", + 'preinstallopts': r"sed -i 's/package\.req/package.requirement/g' setup.py &&", 'checksums': ['e58ed53ae209007328311603bd6e05e8cd2c509204b5e542c87f971a2530fb0d'], }), ('qtl', '0.1.8', { diff --git a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021b.eb b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021b.eb index 33f4463def8..9f5a991db00 100644 --- a/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/RNA-SeQC/RNA-SeQC-2.4.2-foss-2021b.eb @@ -36,7 +36,7 @@ exts_list = [ 'checksums': ['109ea5a66744dd859bf16fe904b8d8b627adafb9408753161e766a92e7d681fa'], }), ('agutil', '4.1.1', { - 'preinstallopts': "sed -i 's/package\.req/package.requirement/g' setup.py &&", + 'preinstallopts': r"sed -i 's/package\.req/package.requirement/g' setup.py &&", 'checksums': ['e58ed53ae209007328311603bd6e05e8cd2c509204b5e542c87f971a2530fb0d'], }), ('qtl', '0.1.8', { diff --git a/easybuild/easyconfigs/r/RNAmmer/RNAmmer-1.2-intel-2018b-Perl-5.28.0.eb b/easybuild/easyconfigs/r/RNAmmer/RNAmmer-1.2-intel-2018b-Perl-5.28.0.eb index 8b07ec53fe9..47f174f2776 100644 --- a/easybuild/easyconfigs/r/RNAmmer/RNAmmer-1.2-intel-2018b-Perl-5.28.0.eb +++ b/easybuild/easyconfigs/r/RNAmmer/RNAmmer-1.2-intel-2018b-Perl-5.28.0.eb @@ -24,9 +24,9 @@ postinstallcmds = [ # replace hardcoded '/usr/bin/perl' with '/usr/bin/env perl' "for x in core-rnammer rnammer xml2fsa xml2gff; do sed -i 's@^#!/.*@#!/usr/bin/env perl@g' %(installdir)s/$x; done", # fix hardcoded locations for install dir + hmmsearch and perl commands - """sed -i 's@\(INSTALL_PATH\ = "\).*\(";\)@\\1%(installdir)s\\2@g' %(installdir)s/rnammer""", - 'sed -i "s@\/.*\/hmmsearch@`which hmmsearch`@g" %(installdir)s/rnammer', - 'sed -i "s@\/.*\/bin\/perl@`which perl`@g" %(installdir)s/rnammer', + r"""sed -i 's@\(INSTALL_PATH\ = "\).*\(";\)@\\1%(installdir)s\\2@g' %(installdir)s/rnammer""", + r'sed -i "s@\/.*\/hmmsearch@`which hmmsearch`@g" %(installdir)s/rnammer', + r'sed -i "s@\/.*\/bin\/perl@`which perl`@g" %(installdir)s/rnammer', ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb index 795b2a954b2..69fdbfcbd24 100644 --- a/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb +++ b/easybuild/easyconfigs/s/STRique/STRique-0.4.2-foss-2021b.eb @@ -26,7 +26,7 @@ dependencies = [ ('scikit-image', '0.19.1'), ] -local_preconfigopts = "sed -i -e '/\ Date: Fri, 3 Feb 2023 12:30:19 +0100 Subject: [PATCH 6429/9987] Fix new failures --- easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb | 2 +- easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb | 2 +- easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb | 2 +- .../i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb | 4 ++-- .../easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb | 2 +- .../s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb | 2 +- .../t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb | 2 +- .../easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb | 4 ++-- 10 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb index 5c3fd5e8577..8fec1fcd61f 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb @@ -28,7 +28,7 @@ dependencies = [ ('Qt5', '5.15.2'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb index 272fbef7477..ce4c4f200c5 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb @@ -49,7 +49,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = "sed -e 's/-llapack/$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb index ea1ba09e6b1..51b0b329e86 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb @@ -49,7 +49,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " +preconfigopts = "sed -e 's/-llapack/$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb index 97e0d20fb04..5a860841eb5 100644 --- a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb @@ -40,8 +40,8 @@ postinstallcmds = [ "perl -i -pe 's|seqstat = \"|seqstat = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", "perl -i -pe 's|blastParser = \"|blastParser = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", "perl -i -pe 's|diamondParser = \"|diamondParser = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", - "perl -i -pe 's|copy\(\"\./|copy\(\"%(installdir)s/|' %(installdir)s/inparanoid.pl", - "perl -i -pe 's|\./\$blastParser|\$blastParser|g' %(installdir)s/inparanoid.pl", + r"""perl -i -pe 's|copy\("\./|copy\("%(installdir)s/|' %(installdir)s/inparanoid.pl""", + r"perl -i -pe 's|\./$blastParser|$blastParser|g' %(installdir)s/inparanoid.pl", ] fix_perl_shebang_for = ['*.pl'] diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb index 469957dab36..37e665fc2b5 100644 --- a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb @@ -21,7 +21,7 @@ use_pip = True # (since installing it introduces conflicting version requirements with poetry included with Python) local_preinstallopts = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ local_preinstallopts += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ -local_preinstallopts += """-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ +local_preinstallopts += r"""-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ exts_list = [ ('setuptools', '65.6.0', { diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb index 7dfe39787ec..ce674d734f0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb @@ -39,7 +39,7 @@ exts_default_options = { # workaround for: AttributeError: 'module' object has no attribute '__legacy__' # see also https://github.com/pypa/pip/issues/6264 -local_fix_pyproject_toml_cmd = """sed -i 's/\(\[build-system\]\)/\\1\\nbuild-backend="setuptools.build_meta"/g' """ +local_fix_pyproject_toml_cmd = r"""sed -i 's/\(\[build-system\]\)/\1\nbuild-backend="setuptools.build_meta"/g' """ local_fix_pyproject_toml_cmd += "pyproject.toml && " # order is important! diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb index dcbd212c988..d93dd122cba 100644 --- a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb @@ -38,7 +38,7 @@ files_to_copy = [ # install header files, keeping relative subdirectories _install_headers = " ".join([ "cd %(builddir)s && mkdir -p %(installdir)s/include/spooles &&", - "find . -name '*.h' -print -exec install -D {} %(installdir)s/include/spooles/{} \;" + r"find . -name '*.h' -print -exec install -D {} %(installdir)s/include/spooles/{} \;" ]) postinstallcmds = [_install_headers] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb index 89b95c194e8..376258b56d1 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb @@ -55,7 +55,7 @@ exts_list = [ 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], }), ('pandas', '1.2.4', { - 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': r"""sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, 'checksums': ['649ecab692fade3cbfcf967ff936496b0cfba0af00a55dfaacd82bdda5cb2279'], }), ('mpmath', '1.2.1', { diff --git a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb index a28af36eaef..a0cee771e9c 100644 --- a/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TELEMAC-MASCARET/TELEMAC-MASCARET-8p3r1-foss-2021b.eb @@ -32,7 +32,7 @@ buildininstalldir = True local_tweak_cfg_cmd = ' '.join([ "sed -i -e 's/S9.gfortran/easybuild/g'", # strip out use of AED, GOTM, MED (optional dependencies) - "-e 's/\(^[a-z]*_aed:\).*/\\1/g' -e 's/\(^[a-z]*_gotm:\).*/\\1/g' -e 's/\(^[a-z]*_med:\).*/\\1/g'", + r"-e 's/\(^[a-z]*_aed:\).*/\1/g' -e 's/\(^[a-z]*_gotm:\).*/\1/g' -e 's/\(^[a-z]*_med:\).*/\1/g'", # replace -O2 with desired compiler options '-e "s/-O2/$F90FLAGS/g"', # fix linker option for BLAS diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb index 9061ba602b3..9a308f9a8be 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb @@ -48,12 +48,12 @@ dependencies = [ ('smithwaterman', '20160702'), ] -preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f -regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts = r"find %(builddir)s/%(name)s-%(version)s/src -type f -regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" -preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " +preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] From b67c87012f2bd92270fd070b72cba0a5e7cdd28d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 7 Feb 2023 17:10:45 +0100 Subject: [PATCH 6430/9987] Make ECs consistent --- .../easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb | 2 +- .../c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb | 2 +- easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb | 2 +- easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb | 2 +- .../easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb | 2 +- easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb | 2 +- easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb | 2 +- easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.3-intel-2018a.eb | 3 ++- easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb | 3 ++- .../s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb | 2 +- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb | 2 +- .../v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb | 2 +- 31 files changed, 33 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb index ef8c14a24e0..d033267aef3 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-2.7.14.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb index 84989615633..be3206d85d4 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-foss-2017b-Python-3.6.3.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb index a954bcd3a8d..4d0b14dfd49 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017a-Python-2.7.13.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb index 6e34c64e2f4..8ff6898f1ef 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-2.7.14.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb index a1da6f58d7d..36172cf0ebf 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11-intel-2017b-Python-3.6.3.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb index 41f7ebd36a8..a55803f816e 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-2.7.14.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb index 9946b69f647..ff0938352bb 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018a-Python-3.6.4.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb index 97c6dac0f01..180cab534a2 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-2.7.15.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb index 477357e8316..23ab0c1c4c6 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-foss-2018b-Python-3.6.6.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb index 4e9c29f1e82..0e700bf34ec 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.11.1-intel-2018a-Python-2.7.14.eb @@ -28,7 +28,7 @@ builddependencies = [ ('Eigen', '3.3.4', '', SYSTEM), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb index 348b69dc0fa..b9c2b1c3ada 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-foss-2019a-Python-3.7.2.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.12.3'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb index 06e1bc27024..6aedf7b94d6 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14-intel-2019a-Python-3.7.2.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.12.3'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb index cb31a9c9548..ba65e66905e 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-3.7.4.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.13.1'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb index a7df31832b5..d811e682a82 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-intel-2019b-Python-3.7.4.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.13.1'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb index 1414729ac05..7260e3f71ab 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-gompi-2020a-Python-3.8.2.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.14.1'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb index 365336b722a..adb729af93e 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-foss-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ ('libGLU', '9.0.0', '-Mesa-11.2.1'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb index f3c87201222..a1dd733fbe6 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8-intel-2016a-Python-2.7.11.eb @@ -22,7 +22,7 @@ dependencies = [ ('libGLU', '9.0.0', '-Mesa-11.2.1'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb index 1b7497c8401..a72147769ce 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b-Python-2.7.12.eb @@ -27,7 +27,7 @@ builddependencies = [ ('Eigen', '3.2.9'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb index 32d7eeef907..43bf68bd47e 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-foss-2016b.eb @@ -25,7 +25,7 @@ builddependencies = [ ('Eigen', '3.2.9'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb index 0e7a9977726..18bb1a2753c 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b-Python-2.7.12.eb @@ -27,7 +27,7 @@ builddependencies = [ ('Eigen', '3.2.9'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb index 5e36b73d080..f30cfbdd292 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.8.1-intel-2016b.eb @@ -25,7 +25,7 @@ builddependencies = [ ('Eigen', '3.2.9'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb index a6c2c50e9a6..6eeda75c0fc 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2016b-Python-2.7.12.eb @@ -27,7 +27,7 @@ builddependencies = [ ('Eigen', '3.3.3'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb index 75b9c8cc965..2c827ed9eda 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.9-intel-2017a-Python-2.7.13.eb @@ -27,7 +27,7 @@ builddependencies = [ ('Eigen', '3.3.3'), ] -configopts = r"-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb index ce4c4f200c5..0546c798085 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-foss-2021b.eb @@ -49,7 +49,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb index 51b0b329e86..4f817551b4a 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.4.4-intel-2021b.eb @@ -49,7 +49,7 @@ dependencies = [ ('HDF', '4.2.15'), ] -preconfigopts = "sed -e 's/-llapack/$LIBLAPACK/g' -i.eb configure && " +preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' diff --git a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.3-intel-2018a.eb b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.3-intel-2018a.eb index 5cdbb696a9f..5987627dfb1 100644 --- a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.3-intel-2018a.eb +++ b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.3-intel-2018a.eb @@ -31,7 +31,8 @@ dependencies = [ extract_sources = True install_cmd = "cd %(builddir)s/hts-nim-*/ && nimble install --nimbleDir:%(installdir)s --verbose -y && " -install_cmd += r"cd ../mosdepth-*/ && sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " +install_cmd += "cd ../mosdepth-*/ && " +install_cmd += r"sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " install_cmd += "nimble install --nimbleDir:%(installdir)s --verbose -y" sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb index c8c76363e57..b39e6fdc879 100644 --- a/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb +++ b/easybuild/easyconfigs/m/mosdepth/mosdepth-0.2.4-foss-2018b.eb @@ -31,7 +31,8 @@ dependencies = [ extract_sources = True install_cmd = "cd %(builddir)s/hts-nim-*/ && nimble install --nimbleDir:%(installdir)s --verbose -y && " -install_cmd += r"cd ../mosdepth-*/ && sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " +install_cmd += "cd ../mosdepth-*/ && " +install_cmd += r"sed -i 's/0\.2\.2/%(version)s/g' mosdepth.nimble && " install_cmd += "nimble install --nimbleDir:%(installdir)s --verbose -y" sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb index 376258b56d1..3f0596710cc 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb @@ -55,7 +55,7 @@ exts_list = [ 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], }), ('pandas', '1.2.4', { - 'preinstallopts': r"""sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': """sed -i 's@extra_compile_args = \\["-Werror"\\]@extra_compile_args = []@g' setup.py && """, 'checksums': ['649ecab692fade3cbfcf967ff936496b0cfba0af00a55dfaacd82bdda5cb2279'], }), ('mpmath', '1.2.1', { diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb index 309b53a98ca..e6a30f87174 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.2.0.eb @@ -52,7 +52,7 @@ preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" -preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \\; && " +preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb index 3bdb2e54c3b..72046e18f73 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-10.3.0.eb @@ -52,7 +52,7 @@ preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" -preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \\; && " +preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb index 02c610e9a17..c5cca78049f 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.2-GCC-9.3.0-Python-3.8.2.eb @@ -53,7 +53,7 @@ preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" -preconfigopts += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \\; && " +preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] From 2dbc65c5ac1706386385c18c9a67bd4d5e9e9a5f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Feb 2023 09:52:58 +0100 Subject: [PATCH 6431/9987] Add CI check for W605 flake8 warning in ECs --- .github/workflows/linting.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index bfa19cc1a82..3f2ce53e58f 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -26,3 +26,6 @@ jobs: - name: Run flake8 to verify PEP8-compliance of Python code run: flake8 + + - name: Run flake8 to verify PEP8-compliance of Easyconfigs + run: flake8 --select W605 --filename '*.eb' From 7445c22b125ae0c74cc172646822db861b41c8a1 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 9 Feb 2023 10:18:05 +0100 Subject: [PATCH 6432/9987] adding easyconfigs: GraphDB-10.1.3.eb --- .../easyconfigs/g/GraphDB/GraphDB-10.1.3.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GraphDB/GraphDB-10.1.3.eb diff --git a/easybuild/easyconfigs/g/GraphDB/GraphDB-10.1.3.eb b/easybuild/easyconfigs/g/GraphDB/GraphDB-10.1.3.eb new file mode 100644 index 00000000000..f43c82f137c --- /dev/null +++ b/easybuild/easyconfigs/g/GraphDB/GraphDB-10.1.3.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## +easyblock = 'Binary' + +name = 'GraphDB' +version = '10.1.3' + +homepage = 'https://graphdb.ontotext.com/' +description = """GraphDB is an enterprise ready Semantic Graph Database, compliant +with W3C Standards. Semantic graph databases (also called RDF triplestores) provide +the core infrastructure for solutions where modelling agility, data integration, +relationship exploration and cross-enterprise data publishing and consumption are important.""" +# software_license = 'GraphDB-Free is free to use however, is not open source' +# Fill a form to request GraphDB at https://www.ontotext.com/products/graphdb/download/ + +toolchain = SYSTEM + +source_urls = ['https://download.ontotext.com/owlim/90065654-918e-11ed-8508-42843b1b6b38/'] +sources = ['graphdb-%(version)s-dist.zip'] +checksums = ['fae90dceaf27a6656eda2054f42f7a3e32721af8fd27951770692ad005d34b7a'] + +dependencies = [ + ('Java', '11'), +] + +extract_sources = True + +sanity_check_paths = { + 'files': ['bin/graphdb', 'README'], + 'dirs': ['bin', 'conf', 'configs', 'doc', 'examples', 'lib', 'tools'], +} + +sanity_check_commands = ["graphdb -h"] + +moduleclass = 'data' From b2eddedcde0614d55bc14510856cfa59c51bd644 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 9 Feb 2023 13:06:54 +0100 Subject: [PATCH 6433/9987] adding easyconfigs: AUGUSTUS-3.5.0-foss-2022a.eb, lpsolve-5.5.2.11-GCC-11.3.0.eb --- .../a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022a.eb | 73 +++++++++++++++++++ .../l/lpsolve/lpsolve-5.5.2.11-GCC-11.3.0.eb | 33 +++++++++ 2 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022a.eb new file mode 100644 index 00000000000..78063fe2345 --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022a.eb @@ -0,0 +1,73 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.5.0' + +homepage = 'https://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'Gaius-Augustus' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686'] + +builddependencies = [ + ('Python', '3.10.4'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('Boost', '1.79.0'), + ('GSL', '2.7'), + ('SAMtools', '1.16.1'), + ('HTSlib', '1.15.1'), # also provides tabix + ('BCFtools', '1.15.1'), + ('lpsolve', '5.5.2.11'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('BamTools', '2.5.2'), + ('SQLite', '3.38.3'), +] + +skipsteps = ['configure'] + +# run "make clean" to avoid using binaries included with the source tarball +prebuildopts = "make clean && " + +_tmpl = 'INCLUDE_PATH_{dep}=-I{root}{incl} LIBRARY_PATH_{dep}="-L{root}{lib} -Wl,-rpath,{root}{lib}"' + +buildopts = ' '.join([ + 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" ', + _tmpl.format(dep='ZLIB', root='$EBROOTZLIB', incl='/include', lib='/lib'), + _tmpl.format(dep='BOOST', root='$EBROOTBOOST', incl='/include', lib='/lib'), + _tmpl.format(dep='LPSOLVE', root='$EBROOTLPSOLVE', incl='/include', lib='/lib'), + _tmpl.format(dep='SUITESPARSE', root='$EBROOTSUITESPARSE', incl='/include', lib='/lib'), + _tmpl.format(dep='GSL', root='$EBROOTGSL', incl='/include', lib='/lib'), + _tmpl.format(dep='SQLITE', root='$EBROOTSQLITE', incl='/include', lib='/lib'), + _tmpl.format(dep='BAMTOOLS', root='$EBROOTBAMTOOLS', incl='/include/bamtools', lib='/lib'), + _tmpl.format(dep='HTSLIB', root='$EBROOTHTSLIB', incl='/include/htslib', lib='/lib'), +]) + +preinstallopts = "sed -i '/ln -sf/d' Makefile && " +installopts = 'INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch', + 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} +sanity_check_commands = ['augustus --help'] + +modextrapaths = {'PATH': 'scripts'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-11.3.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-11.3.0.eb new file mode 100644 index 00000000000..7860f855c6d --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.11' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f'] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' From 70b12d0df7347ecc8f65477b8a4dd34d64bfdcee Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 9 Feb 2023 13:21:43 +0100 Subject: [PATCH 6434/9987] adding easyconfigs: chemprop-1.5.2-foss-2022a-CUDA-11.7.0.eb --- .../chemprop-1.5.2-foss-2022a-CUDA-11.7.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..eee4493a7df --- /dev/null +++ b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'chemprop' +version = '1.5.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/chemprop/chemprop' +description = 'Message Passing Neural Networks for Molecule Property Prediction' + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('tensorboardX', '2.5.1'), + ('xarray', '2022.6.0'), + ('Hyperopt', '0.2.7'), + ('Flask', '2.2.2'), + ('PyTorch', '1.12.0'), + ('matplotlib', '3.5.2'), + ('RDKit', '2022.09.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM) +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('packaging', '20.4', { + 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], + }), + ('pandas_flavor', '0.2.0', { + 'checksums': ['7871655816de22dc766e916697ccc67449e1863c090ef5fd40d4d0fbd056e489'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('typing_inspect', '0.8.0', { + 'checksums': ['8b1ff0c400943b6145df8119c41c244ca8207f1f10c9c057aeed1560e4806e3d'], + }), + ('typed-argument-parser', '1.7.2', { + 'modulename': 'tap', + 'checksums': ['4e44bc79010391cd9dec4b110e1474fedc8919138e93ca91222ea6b3b360daee'], + }), + (name, version, { + 'source_urls': ['https://github.com/chemprop/chemprop/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['7ce6f71688291ffbe45728a605be9fda354f4cc30410bbe64511cd1a55b9bfb8'], + }), +] + +moduleclass = 'chem' From ad726b704c1a91367d29cc75c9cfe94d979cbb40 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 9 Feb 2023 13:45:37 +0100 Subject: [PATCH 6435/9987] adding easyconfigs: stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb, PyOpenCL-2021.2.13-foss-2021b-CUDA-11.4.1.eb --- ...OpenCL-2021.2.13-foss-2021b-CUDA-11.4.1.eb | 34 +++++++++ .../stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb | 71 +++++++++++++++++++ 2 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.2.13-foss-2021b-CUDA-11.4.1.eb create mode 100644 easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.2.13-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.2.13-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..8ba4d12ddea --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2021.2.13-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2021.2.13' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('CUDA', '11.4.1', '', SYSTEM), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2021.2.9', { + 'checksums': ['db6cf83c9ba0a165d545029e2301621486d1e9ef295684072e5cd75316a13755'], + }), + ('pyopencl', version, { + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + 'checksums': ['8b969c3a9d4153adc6b0915301ffdf626a3784b869a964645de100ae60de7b06'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..183ee667013 --- /dev/null +++ b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'stardist' +version = '0.8.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/stardist/stardist' +description = "Object Detection with Star-convex Shapes." + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.9.6'), + ('CUDA', '11.4.1', '', SYSTEM), + ('TensorFlow', '2.7.1', versionsuffix), + ('numba', '0.54.1'), + ('imageio', '2.13.5'), + ('scikit-image', '0.19.1'), + ('tqdm', '4.62.3'), + ('PyOpenCL', '2021.2.13', versionsuffix), + ('Mako', '1.1.4'), +] + +use_pip = True + +exts_list = [ + ('tifffile', '2022.10.10', { + 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], + }), + ('csbdeep', '0.7.2', { + 'checksums': ['8a000eb71d04aa753f52ffe81a34c0a30a06ee986d20b9986d76272253e2fd53'], + }), + ('edt', '2.3.0', { + 'checksums': ['220e2086fdf32bbd8964df76b3e1a42061ece1f4b9ea95ec83a094d24d258664'], + }), + ('configparser', '5.3.0', { + 'checksums': ['8be267824b541c09b08db124917f48ab525a6c3e837011f3130781a224c57090'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('reikna', '0.7.6', { + 'checksums': ['722fefbd253d0bbcbf5250b7b9c4aca5722cde4ca38bfbf863a551a5fc26edfa'], + }), + ('scikit-tensor-py3', '20210331', { + 'modulename': 'sktensor', + 'sources': [{'filename': 'scikit-tensor-py3.tar.gz', 'git_config': {'url': 'https://github.com/evertrol', 'repo_name': 'scikit-tensor-py3', 'commit': '99190292b9564e7c4a9312280db732ceedf7b7e3'}}], + 'checksums': ['a2765cc930e5937c8358fe79daf37bb2c0d1470f0b1e4daf6c4082c12195e472'], + }), + ('gputools', '0.2.14', { + 'checksums': ['dc3a4aef73e802f6b94a4262ac4c637a2fb62fe8472368e9143248d6d1cb93de'], + }), + (name, version, { + 'checksums': ['8ac1f6165ca8e8496651c6e2b49ce57d6d574dfb22bf6f63ddaec1f64b8868d1'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/stardist-predict2d', 'bin/stardist-predict3d'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "stardist-predict2d --help", + "stardist-predict3d --help", +] + +moduleclass = 'vis' From 300afac2f9660bfc4a02800797b34302a435b830 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 9 Feb 2023 13:54:08 +0100 Subject: [PATCH 6436/9987] adding easyconfigs: Exonerate-2.4.0-GCC-11.3.0.eb, SNAP-2.0.1-GCC-11.3.0.eb --- .../e/Exonerate/Exonerate-2.4.0-GCC-11.3.0.eb | 43 +++++++++++++++++++ .../s/SNAP/SNAP-2.0.1-GCC-11.3.0.eb | 30 +++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..bf988fa0299 --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.3.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +# also https://github.com/nathanweeks/exonerate +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/%(namelower)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] +dependencies = [ + ('GLib', '2.72.1'), +] + +# parallel build fails +parallel = 1 + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/fastaclip', 'bin/fastaoverlap'], + 'dirs': ['share'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..635c7937182 --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'SNAP' +version = '2.0.1' + +homepage = 'https://www.microsoft.com/en-us/research/project/snap' +description = """Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for + high-throughput sequencing data""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'cstd': 'c++98'} + +source_urls = ['https://github.com/amplab/snap/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['30f199c583e054c50ca6f3b61f27066640b7c829e5c5e8083841596a2869c064'] + +dependencies = [('zlib', '1.2.12')] + +buildopts = 'CXX="$CXX"' + +files_to_copy = [(['snap-aligner', 'SNAPCommand'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/snap-aligner', 'bin/SNAPCommand'], + 'dirs': [], +} + +sanity_check_commands = ["snap-aligner --help"] + +moduleclass = 'bio' From 48110abc40f1c244e82c78fcd989e6e9c9190a95 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 9 Feb 2023 14:23:10 +0100 Subject: [PATCH 6437/9987] Fix style problems --- .../s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb index 183ee667013..c708f69683b 100644 --- a/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb @@ -19,7 +19,7 @@ dependencies = [ ('scikit-image', '0.19.1'), ('tqdm', '4.62.3'), ('PyOpenCL', '2021.2.13', versionsuffix), - ('Mako', '1.1.4'), + ('Mako', '1.1.4'), ] use_pip = True @@ -45,7 +45,12 @@ exts_list = [ }), ('scikit-tensor-py3', '20210331', { 'modulename': 'sktensor', - 'sources': [{'filename': 'scikit-tensor-py3.tar.gz', 'git_config': {'url': 'https://github.com/evertrol', 'repo_name': 'scikit-tensor-py3', 'commit': '99190292b9564e7c4a9312280db732ceedf7b7e3'}}], + 'sources': [{'filename': 'scikit-tensor-py3.tar.gz', + 'git_config': {'url': 'https://github.com/evertrol', + 'repo_name': 'scikit-tensor-py3', + 'commit': '99190292b9564e7c4a9312280db732ceedf7b7e3', + }, + }], 'checksums': ['a2765cc930e5937c8358fe79daf37bb2c0d1470f0b1e4daf6c4082c12195e472'], }), ('gputools', '0.2.14', { From 88129834ef3be48af724901e9e83e8f37e5fc31a Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Thu, 9 Feb 2023 15:33:54 +0100 Subject: [PATCH 6438/9987] adding easyconfigs: Hypre-2.21.0-intel-2021a.eb, MUMPS-5.4.0-intel-2021a-metis.eb, PETSc-3.15.1-intel-2021a.eb, SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb and patches: PETSc_remove-mpiicc-show-quotes.patch --- .../h/Hypre/Hypre-2.21.0-intel-2021a.eb | 21 ++++++++ .../m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb | 38 ++++++++++++++ .../p/PETSc/PETSc-3.15.1-intel-2021a.eb | 52 +++++++++++++++++++ .../PETSc_remove-mpiicc-show-quotes.patch | 12 +++++ ...teSparse-5.10.1-intel-2021a-METIS-5.1.0.eb | 29 +++++++++++ 5 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-intel-2021a.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-intel-2021a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-intel-2021a.eb new file mode 100644 index 00000000000..900b8bfcad7 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-intel-2021a.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'Hypre' +version = '2.21.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e380f914fe7efe22afc44cdf553255410dc8a02a15b2e5ebd279ba88817feaf5'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb new file mode 100644 index 00000000000..fa811d068f9 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb @@ -0,0 +1,38 @@ +## +# Author: Robert Mijakovic +## +name = 'MUMPS' +version = '5.4.0' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + 'c613414683e462da7c152c131cebf34f937e79b30571424060dd673368bbf627', # MUMPS_5.4.0.tar.gz + '4c0558690998c12ca959c03856054a75e22f519583a65bd550393c1f81a0b170', # MUMPS-5.4.0_shared-pord.patch + 'd51c2df0de7d7b88d864ceba2d0eea46c755c24c7124003481aced106901109d', # MUMPS-5.4.0_shared-mumps.patch +] + +dependencies = [ + ('SCOTCH', '6.1.0'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb new file mode 100644 index 00000000000..e65a78b214e --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb @@ -0,0 +1,52 @@ +## +# Author: Robert Mijakovic +## +name = 'PETSc' +version = '3.15.1' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', + 'PETSc_remove-mpiicc-show-quotes.patch', +] +checksums = [ + {'petsc-3.15.1.tar.gz': 'c0ac6566e69d1d70b431e07e7598e9de95e84891c2452db1367c846b75109deb'}, + {'PETSc_ranlib-fix.patch': '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297'}, + {'PETSc_remove-mpiicc-show-quotes.patch': '917218e4244f579879cbea4a428d05a61b4266f65c23d9cdfb754d187066d62d'}, +] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Boost', '1.76.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('MUMPS', '5.4.0', '-metis'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('Hypre', '2.21.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch b/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch new file mode 100644 index 00000000000..07bb3ccc082 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch @@ -0,0 +1,12 @@ +diff -Nru config/PETSc/Configure.py.back config/PETSc/Configure.py` +--- config/PETSc/Configure.py.back 2023-02-09 14:59:14.086680000 +0100 ++++ config/PETSc/Configure.py 2023-02-09 14:59:03.095892000 +0100 +@@ -251,7 +251,7 @@ + compiler = self.setCompilers.getCompiler() + if [s for s in ['mpicc','mpiicc'] if os.path.basename(compiler).find(s)>=0]: + try: +- output = self.executeShellCommand(compiler + ' -show', log = self.log)[0] ++ output = self.executeShellCommand(compiler + ' -show', log = self.log)[0].replace('"', '') + compiler = output.split(' ')[0] + self.addDefine('MPICC_SHOW','"'+output.strip().replace('\n','\\\\n')+'"') + except: diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb new file mode 100644 index 00000000000..d896b7962de --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb @@ -0,0 +1,29 @@ +name = 'SuiteSparse' +version = '5.10.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " + +moduleclass = 'numlib' From d037cfd044e7b8a0be755ec4ced95ff90c108492 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 9 Feb 2023 16:31:10 +0100 Subject: [PATCH 6439/9987] add sanity check commands for exonerate --- .../easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.3.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.3.0.eb index bf988fa0299..ff3739e4809 100644 --- a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-11.3.0.eb @@ -35,9 +35,13 @@ parallel = 1 runtest = 'check' +_bins = ['exonerate', 'fastaclip', 'fastacomposition', 'fastafetch', 'fastaoverlap', 'ipcress'] + sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'bin/fastaclip', 'bin/fastaoverlap'], + 'files': ['bin/%s' % x for x in _bins], 'dirs': ['share'], } +sanity_check_commands = ['%s -h | grep "from exonerate version %%(version)s"' % x for x in _bins] + moduleclass = 'bio' From b404be540cdd51a19aacd46f40fb6ff2f982ee16 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Feb 2023 16:31:59 +0100 Subject: [PATCH 6440/9987] Add patches from TF 2.8.4/2.9.1 --- ...sorFlow-2.8.4_exclude-xnnpack-on-ppc.patch | 18 ++++++ ...ensorFlow-2.8.4_resolve-gcc-symlinks.patch | 28 ++++++++++ ...low-2.9.1_remove-duplicate-gpu-tests.patch | 55 +++++++++++++++++++ 3 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch new file mode 100644 index 00000000000..1a0938252be --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch @@ -0,0 +1,18 @@ +XNNPACK is not supported on PowerPC so disable it by default. +See https://github.com/tensorflow/tensorflow/issues/58768 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/lite/BUILD b/tensorflow/lite/BUILD +index 198f949b341..d15dcf9a80d 100644 +--- a/tensorflow/lite/BUILD ++++ b/tensorflow/lite/BUILD +@@ -709,6 +709,8 @@ cc_library( + deps = select({ + "//tensorflow:macos": [], + "//tensorflow:fuchsia": [], ++ # XNNPACK is not supported on PPC ++ "//tensorflow:linux_ppc64le": [], + "//conditions:default": [":tflite_with_xnnpack_enabled"], + }), + ) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch new file mode 100644 index 00000000000..42cdce7c9fd --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch @@ -0,0 +1,28 @@ +Fix for "undeclared inclusion(s) in rule" errors when the installation directory +for GCC is hosted in a path that is a symlink to another path. + +From https://github.com/tensorflow/tensorflow/pull/56360 + +From b3a8fdbcb79e723f8d62f86bddcfdfb73fe76291 Mon Sep 17 00:00:00 2001 +From: Jinzhe Zeng +Date: Sat, 4 Jun 2022 19:06:58 -0400 +Subject: [PATCH] resolve gcc_host_compiler_path in a symlink directory + +Resolves a missing dependency declarations error, when gcc_host_compiler_path is in a symlink directory resolving to other directories. +--- + configure.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/configure.py b/configure.py +index bf338bdda2297..77af09a22a05d 100644 +--- a/configure.py ++++ b/configure.py +@@ -619,7 +619,7 @@ def prompt_loop_or_load_from_env(environ_cp, + 'Assuming to be a scripting mistake.' % + (var_name, n_ask_attempts)) + +- if resolve_symlinks and os.path.islink(val): ++ if resolve_symlinks: + val = os.path.realpath(val) + environ_cp[var_name] = val + return val diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch new file mode 100644 index 00000000000..7701d85e612 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch @@ -0,0 +1,55 @@ +TensorFlow adds some GPU tests twice increasing the runtime of the test suite. +This filters out the test part meant for CPU. + +See https://github.com/tensorflow/tensorflow/issues/47081 +From https://github.com/tensorflow/tensorflow/pull/59129 + +Author: Alexander Grund (TU Dresden) +--- + tensorflow/tensorflow.bzl | 33 +++++++++++++++++---------------- + 1 file changed, 17 insertions(+), 16 deletions(-) + +diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl +index 649c8e22dcc95..d3fc0e3221497 100644 +--- a/tensorflow/tensorflow.bzl ++++ b/tensorflow/tensorflow.bzl +@@ -1461,22 +1461,23 @@ def tf_gpu_cc_test( + linkopts = [], + **kwargs): + targets = [] +- tf_cc_test( +- name = name, +- size = size, +- srcs = srcs, +- args = args, +- data = data, +- extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), +- kernels = kernels, +- linkopts = linkopts, +- linkstatic = linkstatic, +- suffix = "_cpu", +- tags = tags, +- deps = deps, +- **kwargs +- ) +- targets.append(name + "_cpu") ++ if 'gpu' not in tags: ++ tf_cc_test( ++ name = name, ++ size = size, ++ srcs = srcs, ++ args = args, ++ data = data, ++ extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), ++ kernels = kernels, ++ linkopts = linkopts, ++ linkstatic = linkstatic, ++ suffix = "_cpu", ++ tags = tags, ++ deps = deps, ++ **kwargs ++ ) ++ targets.append(name + "_cpu") + tf_cc_test( + name = name, + size = size, From ce1cf5760e16488f6454c7d3d7cb26ef7ba993e9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Feb 2023 16:35:21 +0100 Subject: [PATCH 6441/9987] Combine errors of extension patch check into a single failure Avoids repeated test runs by showing all errors at once. --- test/easyconfigs/easyconfigs.py | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 42a55a77d00..276613742dc 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1389,6 +1389,7 @@ def template_easyconfig_test(self, spec): self.assertTrue(isinstance(ext[2], dict), "3rd element of extension spec for %s must be a dictionary" % ext_name) + ext_patch_issues = [] # After the sanity check above, use collect_exts_file_info to resolve templates etc. correctly for ext in app.collect_exts_file_info(fetch_files=False, verify_checksums=False): try: @@ -1407,16 +1408,18 @@ def template_easyconfig_test(self, spec): # only check actual patch files, not other files being copied via the patch functionality ext_patch_full = os.path.join(specdir, ext_patch['name']) - if ext_patch_full.endswith('.patch'): - msg = "Patch file %s is available for %s" % (ext_patch_full, specfn) - self.assertTrue(os.path.isfile(ext_patch_full), msg) + if ext_patch_full.endswith('.patch') and not os.path.isfile(ext_patch_full): + ext_patch_issues.append("Patch file %s for extension %s is missing." % (ext_patch['name'], ext_name)) + continue # verify checksum for each patch file - if idx < len(patch_checksums) and (os.path.exists(ext_patch_full) or ext_patch.endswith('.patch')): + if idx < len(patch_checksums) and os.path.exists(ext_patch_full): checksum = patch_checksums[idx] - error_msg = "Invalid checksum for patch %s for %s extension in %s: %s" - res = verify_checksum(ext_patch_full, checksum) - self.assertTrue(res, error_msg % (ext_patch, ext_name, ec_fn, checksum)) + if not verify_checksum(ext_patch_full, checksum): + ext_patch_issues.append("Invalid checksum for patch %s for extension %s: %s." + % (ext_patch['name'], ext_name, checksum)) + if ext_patch_issues: + self.fail("Verification of patches for %s failed:\n%s" % (ec_fn, '\n'.join(ext_patch_issues))) # check whether all extra_options defined for used easyblock are defined extra_opts = app.extra_options() From 3b65a6cb077dacb033df9346647d8184737b72a7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Feb 2023 16:48:31 +0100 Subject: [PATCH 6442/9987] Fix ELSI build and add missing foss versions --- .../e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb | 39 ++++++++++++++++++ .../e/ELSI/ELSI-2.5.0-foss-2019b.eb | 38 ++++++++++++++++++ .../e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb | 6 ++- .../e/ELSI/ELSI-2.5.0-intel-2019b.eb | 6 ++- .../ELSI-2.5.0_fix-compiler-detection.patch | 40 +++++++++++++++++++ .../e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb | 2 + .../e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb | 2 + .../ELSI-2.6.4_fix-compiler-detection.patch | 36 +++++++++++++++++ .../e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb | 2 + .../e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb | 2 + 10 files changed, 171 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b.eb create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.5.0_fix-compiler-detection.patch create mode 100644 easybuild/easyconfigs/e/ELSI/ELSI-2.6.4_fix-compiler-detection.patch diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb new file mode 100644 index 00000000000..347ad480808 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb @@ -0,0 +1,39 @@ +name = 'ELSI' +version = '2.5.0' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix-compiler-detection.patch'] +checksums = [ + 'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f', + '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5', +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.3.2'), + ('CMake', '3.15.3'), +] + +dependencies = [ + ('ELPA', '2019.11.001'), + # SLEPc and internal PEXSI can't coexist due to conflicting dependencies + # ('SLEPc', '3.12.2', '-Python-3.7.4'), +] + +build_internal_pexsi = True + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b.eb new file mode 100644 index 00000000000..00a54e827fd --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b.eb @@ -0,0 +1,38 @@ +name = 'ELSI' +version = '2.5.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix-compiler-detection.patch'] +checksums = [ + 'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f', + '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5', +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.3.2'), + ('CMake', '3.15.3'), +] + +dependencies = [ + ('ELPA', '2019.11.001'), + ('SLEPc', '3.12.2', '-Python-3.7.4'), +] + +# SLEPc and internal PEXSI can't coexist due to conflicting dependencies +build_internal_pexsi = False + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb index 7a3d6a93e71..84704deb0c4 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb @@ -14,7 +14,11 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f'] +patches = ['%(name)s-%(version)s_fix-compiler-detection.patch'] +checksums = [ + 'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f', + '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5', +] builddependencies = [ ('flex', '2.6.4'), diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb index ca508d490f8..4ba1e4b7a8a 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb @@ -13,7 +13,11 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f'] +patches = ['%(name)s-%(version)s_fix-compiler-detection.patch'] +checksums = [ + 'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f', + '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5', +] builddependencies = [ ('flex', '2.6.4'), diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0_fix-compiler-detection.patch b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0_fix-compiler-detection.patch new file mode 100644 index 00000000000..c61708a48f9 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0_fix-compiler-detection.patch @@ -0,0 +1,40 @@ +Let CMake search for the compilers and only fail if they are not found. +See https://gitlab.com/elsi_project/elsi_interface/-/merge_requests/304 + +Author: Alexander Grund (TU Dresden) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index b8d22e53..f1570a8e 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -67,14 +67,18 @@ SET(INC_PATHS "" CACHE STRING "List of include directories") + SET(LIBS "" CACHE STRING "List of external libraries to be linked against") + + ### Compilers ### +-IF(NOT DEFINED CMAKE_Fortran_COMPILER) ++INCLUDE(CheckLanguage) ++ ++CHECK_LANGUAGE(Fortran) ++IF(NOT CMAKE_Fortran_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}Fortran compiler must be set${COLORRESET}") + ELSE() + MESSAGE(STATUS "${GREEN}Fortran compiler${COLORRESET}: ${CMAKE_Fortran_COMPILER}") + ENABLE_LANGUAGE(Fortran) + ENDIF() + IF(ENABLE_PEXSI OR ENABLE_C_TESTS OR ELPA2_KERNEL STREQUAL "AVX512" OR ELPA2_KERNEL STREQUAL "AVX2" OR ELPA2_KERNEL STREQUAL "AVX") +- IF(NOT DEFINED CMAKE_C_COMPILER) ++ CHECK_LANGUAGE(C) ++ IF(NOT CMAKE_C_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}C compiler must be set${COLORRESET}") + ELSE() + MESSAGE(STATUS "${GREEN}C compiler${COLORRESET}: ${CMAKE_C_COMPILER}") +@@ -82,7 +86,8 @@ IF(ENABLE_PEXSI OR ENABLE_C_TESTS OR ELPA2_KERNEL STREQUAL "AVX512" OR ELPA2_KER + ENDIF() + ENDIF() + IF(ENABLE_PEXSI) +- IF(NOT DEFINED CMAKE_CXX_COMPILER) ++ CHECK_LANGUAGE(CXX) ++ IF(NOT CMAKE_CXX_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}C++ compiler must be set${COLORRESET}") + ELSE() + MESSAGE(STATUS "${GREEN}C++ compiler${COLORRESET}: ${CMAKE_CXX_COMPILER}") diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 332df2352b0..68020a6e291 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11 sources = [SOURCELOWER_TAR_GZ] patches = [ 'pexsi-1.2.0-mpi30.patch', + '%(name)s-%(version)s_fix-compiler-detection.patch', 'ELSI-2.7.1_bison_3.7_compat.patch', ] checksums = [ 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37', # ELSI-2.6.4_fix-compiler-detection.patch '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb index 800d33b16dc..ff84be63e3a 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb @@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11 sources = [SOURCELOWER_TAR_GZ] patches = [ 'pexsi-1.2.0-mpi30.patch', + '%(name)s-%(version)s_fix-compiler-detection.patch', 'ELSI-2.7.1_bison_3.7_compat.patch', ] checksums = [ 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37', # ELSI-2.6.4_fix-compiler-detection.patch '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4_fix-compiler-detection.patch b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4_fix-compiler-detection.patch new file mode 100644 index 00000000000..5e931749a78 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4_fix-compiler-detection.patch @@ -0,0 +1,36 @@ +Let CMake search for the compilers and only fail if they are not found. +See https://gitlab.com/elsi_project/elsi_interface/-/merge_requests/304 + +Author: Alexander Grund (TU Dresden) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 3f016ec7..9aaf8395 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -55,18 +55,23 @@ SET(INC_PATHS "" CACHE STRING "List of include directories") + SET(LIBS "" CACHE STRING "List of external libraries to be linked against") + + ### Compilers ### +-IF(NOT DEFINED CMAKE_Fortran_COMPILER) ++INCLUDE(CheckLanguage) ++ ++CHECK_LANGUAGE(Fortran) ++IF(NOT CMAKE_Fortran_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}Fortran compiler must be set${COLORRESET}") + ENDIF() + ENABLE_LANGUAGE(Fortran) + +-IF(NOT DEFINED CMAKE_C_COMPILER) ++CHECK_LANGUAGE(C) ++IF(NOT CMAKE_C_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}C compiler must be set${COLORRESET}") + ENDIF() + ENABLE_LANGUAGE(C) + + IF(ENABLE_PEXSI) +- IF(NOT DEFINED CMAKE_CXX_COMPILER) ++ CHECK_LANGUAGE(CXX) ++ IF(NOT CMAKE_CXX_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}C++ compiler must be set${COLORRESET}") + ENDIF() + ENABLE_LANGUAGE(CXX) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb index 97218cbf6a8..1995ff511e0 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb @@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2021/03 sources = [SOURCELOWER_TAR_GZ] patches = [ 'pexsi-1.2.0-mpi30.patch', + '%(name)s-2.6.4_fix-compiler-detection.patch', 'ELSI-2.7.1_bison_3.7_compat.patch', ] checksums = [ '4a70b6047c39f4e0fd5eca1b2543bfa600acb8305a05ccaaf823ca045f8a4e4d', # elsi-2.7.1.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37', # ELSI-2.6.4_fix-compiler-detection.patch '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb index 94759abacfc..6e3baf0eb4c 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb @@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2021/03 sources = [SOURCELOWER_TAR_GZ] patches = [ 'pexsi-1.2.0-mpi30.patch', + '%(name)s-2.6.4_fix-compiler-detection.patch', 'ELSI-2.7.1_bison_3.7_compat.patch', ] checksums = [ '4a70b6047c39f4e0fd5eca1b2543bfa600acb8305a05ccaaf823ca045f8a4e4d', # elsi-2.7.1.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37', # ELSI-2.6.4_fix-compiler-detection.patch '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] From 75a9d4998957f8cce4bd1fa6d5261e396556cdb2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Feb 2023 17:17:14 +0100 Subject: [PATCH 6443/9987] Allow multiple ECs with same name if they differ by CUDA version Add `CUDA` to `versionsuffix_deps` next to `CUDAcore` as newer toolchains don't use `CUDAcore`. --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 42a55a77d00..56ecd05bbc2 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -444,7 +444,7 @@ def check_dep_vars(self, gen, dep, dep_vars): # for some dependencies, we allow exceptions for software that depends on a particular version, # as long as that's indicated by the versionsuffix - versionsuffix_deps = ['ASE', 'Boost', 'CUDAcore', 'Java', 'Lua', + versionsuffix_deps = ['ASE', 'Boost', 'CUDA', 'CUDAcore', 'Java', 'Lua', 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] if dep in versionsuffix_deps and len(dep_vars) > 1: From d328132f88321415db7c33d13562f8e79dcd77dd Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 9 Feb 2023 18:11:38 +0100 Subject: [PATCH 6444/9987] adding easyconfigs: GeneMark-ET-4.71-GCCcore-11.3.0.eb --- .../GeneMark-ET-4.71-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..63aaf53f794 --- /dev/null +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'Tarball' + +name = 'GeneMark-ET' +version = '4.71' + +homepage = 'http://exon.gatech.edu/GeneMark' +description = "Eukaryotic gene prediction suite with automatic training" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = ['gmes_linux_64-%(version)s.tar.gz'] +checksums = [( + '29adf580ccee6f69d19045bedc3a53e7a71b4c39a95409be3e96d3e9dca83c95', + '629f430e7262bdb5df8f24413e65d26e35eb10ea34212145b692ee4689591e54', +)] + +download_instructions = """ +1. complete the license form: http://exon.gatech.edu/GeneMark/license_download.cgi +2. rename the tarball: `mv gmes_linux_64.tar.gz gmes_linux_64-%(version)s.tar.gz` +""" + +# To run this code, install the key: copy key "gm_key" into user's home directory as: +# gunzip gm_key.gz +# cp gm_key_64 ~/.gm_key + +dependencies = [('Perl', '5.34.1')] + +fix_perl_shebang_for = ['*.pl'] + +sanity_check_paths = { + 'files': ['gmes.cfg', 'gmes_petap.pl'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "gmes_petap.pl | grep 'Usage:'", +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 68816bea6051b0691ec24b543075a2ade17fb97b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 9 Feb 2023 18:49:48 +0000 Subject: [PATCH 6445/9987] adding easyconfigs: ANSYS-2023R1.eb --- easybuild/easyconfigs/a/ANSYS/ANSYS-2023R1.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANSYS/ANSYS-2023R1.eb diff --git a/easybuild/easyconfigs/a/ANSYS/ANSYS-2023R1.eb b/easybuild/easyconfigs/a/ANSYS/ANSYS-2023R1.eb new file mode 100644 index 00000000000..1cde6ac65a3 --- /dev/null +++ b/easybuild/easyconfigs/a/ANSYS/ANSYS-2023R1.eb @@ -0,0 +1,30 @@ +name = 'ANSYS' +version = '2023R1' + +homepage = 'https://www.ansys.com' +description = """ANSYS simulation software enables organizations to confidently predict + how their products will operate in the real world. We believe that every product is + a promise of something greater. """ + +toolchain = SYSTEM + +download_instructions = 'Manually obtain (ANSYS%(version)s_LINX64_DISKX.iso) from your ANSYS vendor' +# Custom extract command is used since iso sources contain duplicate file. +sources = [ + {'filename': 'ANSYS%(version)s_LINX64_DISK1.iso', 'extract_cmd': '7z x -aos %s'}, + {'filename': 'ANSYS%(version)s_LINX64_DISK2.iso', 'extract_cmd': '7z x -aos %s'}, + {'filename': 'ANSYS%(version)s_LINX64_DISK3.iso', 'extract_cmd': '7z x -aos %s'}, +] +checksums = [ + {'ANSYS2023R1_LINX64_DISK1.iso': 'c4f5ea8616d3fe4ba129d482c00ce3429455e887dbc993421a585a6d5cb7a686'}, + {'ANSYS2023R1_LINX64_DISK2.iso': 'fceedb512f35626b6aeab8b53d76979d8eef43c6ade33032c5782b64afddcfb0'}, + {'ANSYS2023R1_LINX64_DISK3.iso': '2164453a2aae50159899177feaf8242cb269593209e1a34977534a3915636cf5'}, +] + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Specify license_server and license_server_port here, or use EB_ANSYS_LICENSE_SERVER and EB_ANSYS_LICENSE_SERVER_PORT +# license_server = "ansys.lic.example.com" +# license_server_port = "1234:5678" + +moduleclass = 'tools' From d9d9d8fb3afd8653b054612c1c766a775423e6f9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 10 Feb 2023 01:18:38 +0100 Subject: [PATCH 6446/9987] adding easyconfigs: SRA-Toolkit-3.0.3-gompi-2022a.eb, ncbi-vdb-3.0.2-gompi-2022a.eb --- .../n/ncbi-vdb/ncbi-vdb-3.0.2-gompi-2022a.eb | 38 ++++++++++ .../SRA-Toolkit-3.0.3-gompi-2022a.eb | 71 +++++++++++++++++++ 2 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.2-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.3-gompi-2022a.eb diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.2-gompi-2022a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.2-gompi-2022a.eb new file mode 100644 index 00000000000..8144240a86c --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.2-gompi-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'ncbi-vdb' +version = '3.0.2' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['275ccb225ddb156688c8c71f772f73276cb18ebff773a51150f86f8002ed2d59'] + +builddependencies = [ + ('Perl', '5.34.1', '-minimal'), + ('Python', '3.10.4', '-bare'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('HDF5', '1.12.2'), + ('libxml2', '2.9.13'), + ('bzip2', '1.0.8'), +] + +configopts = "-DHDF5_INCDIR=$EBROOTHDF5/include -DHDF5_LIBDIR=$EBROOTHDF5/lib " +configopts += "-DXML2_INCDIR=$EBROOTLIBXML2/include -DXML2_LIBDIR=$EBROOTLIBXML2/lib " + +sanity_check_paths = { + 'files': ['include/ncbi/ncbi.h', 'include/ncbi/vdb-blast.h'] + + [('lib/libncbi-%s.%s' % (k, e)) for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.3-gompi-2022a.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.3-gompi-2022a.eb new file mode 100644 index 00000000000..a7423e09e62 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.3-gompi-2022a.eb @@ -0,0 +1,71 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'CMakeMake' + +name = 'SRA-Toolkit' +version = '3.0.3' + +homepage = 'https://github.com/ncbi/sra-tools' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" +github_account = 'ncbi' + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'extra_cflags': '-DH5_USE_110_API'} + +source_urls = ['https://github.com/ncbi/sra-tools/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ["SRA-Toolkit-3.0.3_fix-ngs-doc-jar-build.patch"] +checksums = [ + {'SRA-Toolkit-3.0.3.tar.gz': 'ea4b9a4b2e6e40e6b2bf36b01eb8df2b50280ef9dcdc66b504c1d1296600afbd'}, + {'SRA-Toolkit-3.0.3_fix-ngs-doc-jar-build.patch': + 'e21861b114269593e73b2415137bc4f016f98c5a2e02b5e626fadad7d01c754e'}, +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('Perl', '5.34.1', '-minimal'), + ('Python', '3.10.4', '-bare'), +] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('ncbi-vdb', '3.0.2'), + ('bzip2', '1.0.8'), + ('file', '5.43'), + ('HDF5', '1.12.2'), + ('libxml2', '2.9.13'), + ('zlib', '1.2.12'), +] + +configopts = '-DVDB_INCDIR="$EBROOTNCBIMINVDB/include" -DVDB_LIBDIR="$EBROOTNCBIMINVDB/lib" ' +configopts += '-DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON' + +_sra_bin = [ + 'abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', 'fastq-dump', + 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'latf-load', 'pacbio-load', + 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', + 'sratools', 'srf-load', 'test-sra', 'vdb-config', 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-lock', + 'vdb-unlock', 'vdb-validate', +] + +_ngs_libs = ['libncbi-ngs.a', 'libncbi-ngs-c++.a', 'libncbi-ngs.%s' % SHLIB_EXT, + 'libngs-c++.a', 'libngs-c++.%s' % SHLIB_EXT] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _sra_bin] + ['lib/%s' % l for l in _ngs_libs], + 'dirs': ['jar', 'include/ncbi-vdb', 'include/ngs'] +} + +sanity_check_commands = [ + "abi-dump --help", + "kar --help", + "sra-sort --help", +] + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' From 2d86c5eb6a9dde407daf86a3071a37a284884ab0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 10 Feb 2023 01:32:34 +0100 Subject: [PATCH 6447/9987] adding patch SRA-Toolkit-3.0.3_fix-ngs-doc-jar-build.patch --- ...-Toolkit-3.0.3_fix-ngs-doc-jar-build.patch | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.3_fix-ngs-doc-jar-build.patch diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.3_fix-ngs-doc-jar-build.patch b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.3_fix-ngs-doc-jar-build.patch new file mode 100644 index 00000000000..f39ee2864ab --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.3_fix-ngs-doc-jar-build.patch @@ -0,0 +1,34 @@ +Remove non-existing obj directory from the working directory path of ngs-doc_javadoc +see issue https://github.com/ncbi/sra-tools/issues/771 +author: Alex Domingo (Vrije Universiteit Brussel) +diff -Nru sra-tools-3.0.3.orig/ngs/ngs-java/CMakeLists.txt sra-tools-3.0.3/ngs/ngs-java/CMakeLists.txt +--- sra-tools-3.0.3.orig/ngs/ngs-java/CMakeLists.txt 2023-02-09 01:06:27.885993000 +0100 ++++ sra-tools-3.0.3/ngs/ngs-java/CMakeLists.txt 2023-02-09 01:10:51.430171000 +0100 +@@ -140,17 +140,12 @@ + set(SRC_FILES "${SRC_FILES} ${f}") + endforeach() + +- if( ${OS} STREQUAL "windows" ) +- set( NGS_JAVADOC_DIR ${TARGDIR} ) +- else() +- set( NGS_JAVADOC_DIR ${TARGDIR}/obj ) +- endif() + if ( Java_JAR_EXECUTABLE AND NOT (${OS} STREQUAL "windows") ) + add_custom_target( + ngs-doc-jar ALL COMMAND + bash -c "${Java_JAR_EXECUTABLE} -cf ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-doc.jar ." + DEPENDS ngs-doc_javadoc +- WORKING_DIRECTORY "${NGS_JAVADOC_DIR}/ngs/ngs-java/javadoc/ngs-doc" ++ WORKING_DIRECTORY "${TARGDIR}/ngs/ngs-java/javadoc/ngs-doc" + ) + install( FILES ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-doc.jar DESTINATION ${CMAKE_INSTALL_PREFIX}/jar/ ) + +@@ -166,7 +161,7 @@ + ngs-doc-jar ALL COMMAND + "${Java_JAR_EXECUTABLE}" -cf "${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-doc.jar" . + DEPENDS ngs-doc_javadoc +- WORKING_DIRECTORY "${NGS_JAVADOC_DIR}/ngs/ngs-java/javadoc/ngs-doc" ++ WORKING_DIRECTORY "${TARGDIR}/ngs/ngs-java/javadoc/ngs-doc" + ) + install( FILES ${CMAKE_JAR_OUTPUT_DIRECTORY}/ngs-doc.jar DESTINATION ${CMAKE_INSTALL_PREFIX}/jar/ ) + From 8faaaea6ff0fe78adefc69b73b62073ba5923a65 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 10 Feb 2023 08:22:38 +0100 Subject: [PATCH 6448/9987] adding easyconfigs: ngspice-39-foss-2022a.eb --- .../n/ngspice/ngspice-39-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/n/ngspice/ngspice-39-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-39-foss-2022a.eb b/easybuild/easyconfigs/n/ngspice/ngspice-39-foss-2022a.eb new file mode 100644 index 00000000000..d5eced4955f --- /dev/null +++ b/easybuild/easyconfigs/n/ngspice/ngspice-39-foss-2022a.eb @@ -0,0 +1,40 @@ +# This easyconfig was created by James Carpenter in the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'ngspice' +version = '39' + +homepage = 'https://ngspice.sourceforge.net' +description = """Ngspice is a mixed-level/mixed-signal circuit simulator. Its code +is based on three open source software packages: Spice3f5, Cider1b1 and Xspice. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bf94e811eaad8aaf05821d036a9eb5f8a65d21d30e1cab12701885e09618d771'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), + ('X11', '20220504'), +] + +configure_cmd = "./configure --with-x --enable-xspice " +configure_cmd += "--enable-cider --enable-openmp --with-readline=yes --disable-debug" + +sanity_check_paths = { + 'files': ['bin/ngspice'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'cae' From 350eea475f6868577e653f56816a308764c7d0af Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Feb 2023 10:45:28 +0100 Subject: [PATCH 6449/9987] Update patch for PPC on eigen based on new Eigen MR --- ...ensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb | 2 +- .../TensorFlow-2.11.0-foss-2022a.eb | 2 +- ...sorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch | 125 ++++++------------ 3 files changed, 43 insertions(+), 86 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb index c1f5a8a94d3..6debe70fd8d 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb @@ -191,7 +191,7 @@ exts_list = [ {'TensorFlow-2.11.0_fix-eigen-atan-on-PPC.patch': 'd9f4779f72ffd2c5f9c5da0a7735328dd25756515edccf603087dba2bf4d1612'}, {'TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch': - 'a7c3a1307c07ca5a3c70483900c55f316ee0ff8e647c1a818182fafe6d98b4e9'}, + '4f18ff0563b0ef8556904db1bb4974f8068bf0d2ee1effb24e0c779eb32517e3'}, {'TensorFlow-2.11.0_fix-link-error.patch': '0a2f5c9c5be425f305bdc08f5a5ffce210e66f6ad4120d94ea0209246fc0449f'}, {'TensorFlow-2.11.0_remove-libclang-and-io-gcs-deps.patch': diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb index 26d070db7e3..8d80022bd98 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a.eb @@ -186,7 +186,7 @@ exts_list = [ {'TensorFlow-2.11.0_fix-eigen-atan-on-PPC.patch': 'd9f4779f72ffd2c5f9c5da0a7735328dd25756515edccf603087dba2bf4d1612'}, {'TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch': - 'a7c3a1307c07ca5a3c70483900c55f316ee0ff8e647c1a818182fafe6d98b4e9'}, + '4f18ff0563b0ef8556904db1bb4974f8068bf0d2ee1effb24e0c779eb32517e3'}, {'TensorFlow-2.11.0_fix-link-error.patch': '0a2f5c9c5be425f305bdc08f5a5ffce210e66f6ad4120d94ea0209246fc0449f'}, {'TensorFlow-2.11.0_remove-libclang-and-io-gcs-deps.patch': diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch index b7bdaac24f1..1cbf1a35a03 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0_fix-eigen-gemm-on-PPC.patch @@ -1,105 +1,62 @@ Fix a SIGSEGV in e.g. //tensorflow/core/grappler/optimizers:arithmetic_optimizer_test_cpu See https://gitlab.com/libeigen/eigen/-/issues/2608 +fix-ppc-gemm.patch based on https://gitlab.com/libeigen/eigen/-/merge_requests/1208 + Author: Alexander Grund (TU Dresden) diff --git a/third_party/eigen3/fix-ppc-gemm.patch b/third_party/eigen3/fix-ppc-gemm.patch new file mode 100644 -index 00000000000..6a9faf462e0 +index 00000000000..c674c4b590e --- /dev/null +++ b/third_party/eigen3/fix-ppc-gemm.patch -@@ -0,0 +1,91 @@ +@@ -0,0 +1,46 @@ ++diff --git a/Eigen/src/Core/arch/AltiVec/MatrixProduct.h b/Eigen/src/Core/arch/AltiVec/MatrixProduct.h ++index 3b3b558..44f9e16 100644 ++--- a/Eigen/src/Core/arch/AltiVec/MatrixProduct.h +++++ b/Eigen/src/Core/arch/AltiVec/MatrixProduct.h ++@@ -1760,7 +1760,7 @@ EIGEN_ALWAYS_INLINE void gemm_cols( ++ gemm_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, remaining_rows, pAlpha, pMask); ++ ++ template ++-EIGEN_STRONG_INLINE void gemm_extra_cols( +++EIGEN_ALWAYS_INLINE void gemm_extra_cols( ++ const DataMapper& res, ++ const Scalar* blockA, ++ const Scalar* blockB, ++@@ -2194,7 +2194,7 @@ EIGEN_ALWAYS_INLINE void gemm_complex_cols( ++ gemm_complex_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, remaining_rows, pAlphaReal, pAlphaImag, pMask); ++ ++ template ++-EIGEN_STRONG_INLINE void gemm_complex_extra_cols( +++EIGEN_ALWAYS_INLINE void gemm_complex_extra_cols( ++ const DataMapper& res, ++ const Scalar* blockA, ++ const Scalar* blockB, +diff --git a/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h b/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h -+index 28868ca5a..35e7f673e 100644 ++index 28868ca..1ac6629 100644 +--- a/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h ++++ b/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h -+@@ -30,23 +30,6 @@ EIGEN_ALWAYS_INLINE void gemm_extra_row( ++@@ -30,8 +30,8 @@ EIGEN_ALWAYS_INLINE void gemm_extra_row( + const Packet& pAlpha, + const Packet& pMask); + +-template +-EIGEN_STRONG_INLINE void gemm_extra_cols( -+- const DataMapper& res, -+- const Scalar* blockA, -+- const Scalar* blockB, -+- Index depth, -+- Index strideA, -+- Index offsetA, -+- Index strideB, -+- Index offsetB, -+- Index col, -+- Index rows, -+- Index cols, -+- Index remaining_rows, -+- const Packet& pAlpha, -+- const Packet& pMask); -+- -+ template -+ EIGEN_ALWAYS_INLINE Packet bmask(const Index remaining_rows); -+ -+diff --git a/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h b/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h -+index aa1cbf88f..3cd4ab32a 100644 -+--- a/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h -++++ b/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h -+@@ -427,6 +427,49 @@ EIGEN_ALWAYS_INLINE void gemmMMA_cols( -+ } -+ } -+ -++#define MICRO_EXTRA(MICRO_EXTRA_UNROLL, value, is_col) \ -++ switch(value) { \ -++ default: \ -++ MICRO_EXTRA_UNROLL(1) \ -++ break; \ -++ case 2: \ -++ if (is_col || (sizeof(Scalar) == sizeof(float))) { \ -++ MICRO_EXTRA_UNROLL(2) \ -++ } \ -++ break; \ -++ case 3: \ -++ if (is_col || (sizeof(Scalar) == sizeof(float))) { \ -++ MICRO_EXTRA_UNROLL(3) \ -++ } \ -++ break; \ -++ } -++ -++#define MICRO_EXTRA_COLS(N) \ -++ gemmMMA_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, remaining_rows, pAlpha, pMask); -++ -++template -++EIGEN_STRONG_INLINE void gemmMMA_extra_cols( -++ const DataMapper& res, -++ const Scalar* blockA, -++ const Scalar* blockB, -++ Index depth, -++ Index strideA, -++ Index offsetA, -++ Index strideB, -++ Index offsetB, -++ Index col, -++ Index rows, -++ Index cols, -++ Index remaining_rows, -++ const Packet& pAlpha, -++ const Packet& pMask) -++{ -++ MICRO_EXTRA(MICRO_EXTRA_COLS, cols-col, true) -++} -++ -++#undef MICRO_EXTRA -++#undef MICRO_EXTRA_COLS -++ -+ template -+ void gemmMMA(const DataMapper& res, const Scalar* blockA, const Scalar* blockB, Index rows, Index depth, Index cols, Scalar alpha, Index strideA, Index strideB, Index offsetA, Index offsetB) -+ { -+@@ -448,7 +491,7 @@ void gemmMMA(const DataMapper& res, const Scalar* blockA, const Scalar* blockB, -+ -+ if (col != cols) -+ { -+- gemm_extra_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlpha, pMask); -++ gemmMMA_extra_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlpha, pMask); -+ } -+ } +++template +++EIGEN_ALWAYS_INLINE void gemm_extra_cols( ++ const DataMapper& res, ++ const Scalar* blockA, ++ const Scalar* blockB, ++@@ -67,7 +67,7 @@ EIGEN_ALWAYS_INLINE void gemm_complex_extra_row( ++ const Packet& pMask); + ++ template ++-EIGEN_STRONG_INLINE void gemm_complex_extra_cols( +++EIGEN_ALWAYS_INLINE void gemm_complex_extra_cols( ++ const DataMapper& res, ++ const Scalar* blockA, ++ const Scalar* blockB, diff --git a/third_party/eigen3/workspace.bzl b/third_party/eigen3/workspace.bzl index 6c8744aeec4..2a2a7b474c9 100644 --- a/third_party/eigen3/workspace.bzl From a5f585b9f54dedee1d977429e2a1298aed6d4893 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Fri, 10 Feb 2023 10:50:14 +0100 Subject: [PATCH 6450/9987] Add sanity_check_commands MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb b/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb index 4e9ff7b17ab..5095d96038d 100644 --- a/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb +++ b/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2021b.eb @@ -43,4 +43,6 @@ exts_list = [ }), ] +sanity_check_commands = ['kb info | grep "kb_python %(version)s"'] + moduleclass = 'bio' From 5cbe0e9c455ee41619cf4bc953320c32a7517156 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 7 Feb 2023 15:00:43 +0100 Subject: [PATCH 6451/9987] adding easyconfigs: PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb, NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb, UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb, magma-2.6.2-foss-2021b-CUDA-11.5.2.eb, cuDNN-8.4.1.50-CUDA-11.5.2.eb, CUDA-11.5.2.eb --- easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb | 26 +++ .../c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb | 41 +++++ .../magma-2.6.2-foss-2021b-CUDA-11.5.2.eb | 42 +++++ .../NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb | 23 +++ .../PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb | 156 ++++++++++++++++++ ...-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb | 42 +++++ 6 files changed, 330 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb create mode 100644 easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.5.2.eb create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb new file mode 100644 index 00000000000..bc5895712e0 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb @@ -0,0 +1,26 @@ +name = 'CUDA' +version = '11.5.2' +local_nv_version = '495.29.05' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '74959abf02bcba526f0a3aae322c7641b25da040ccd6236d07038f81997b73a6', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '45c468f430436b3e95d5e485a6ba0ec1fa2b23dc6c551c1307b79996ecf0a7ed', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '31337c8bdc224fa1bd07bc4b6a745798392428118cc8ea0fa4446ee4ad47dd30', + } +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb new file mode 100644 index 00000000000..2a974448907 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb @@ -0,0 +1,41 @@ +name = 'cuDNN' +version = '8.4.1.50' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN 8.4.1 is not specific to CUDA 11.6, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/11.6/' % local_short_ver, +] +sources = ['%(namelower)s-linux-%(cudnnarch)s-%(version)s_cuda11.6-archive.tar.xz'] +checksums = [ + { + '%(namelower)s-linux-x86_64-%(version)s_cuda11.6-archive.tar.xz': + 'ec96d2376d81fca42bdd3d4c3d705a99b29a065bab57f920561c763e29c67d01', + '%(namelower)s-linux-ppc64le-%(version)s_cuda11.6-archive.tar.xz': + '8b806cbfdc81352bf76716d1e53b42537665d110c6ffc068be910505c10e1b98', + '%(namelower)s-linux-sbsa-%(version)s_cuda11.6-archive.tar.xz': + '0b1b9fac5b78974e2fdaaa74843db18f636ce8f3d999d62ff2a615b9978fc360', + } +] + +dependencies = [('CUDA', '11.5.2')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.5.2.eb new file mode 100644 index 00000000000..3f167192cb4 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.5.2.eb @@ -0,0 +1,42 @@ +easyblock = "CMakeMake" + +name = 'magma' +version = '2.6.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/magma/downloads/'] +sources = [SOURCE_TAR_GZ] +patches = ['magma-2.6.1_allow-all-sms.patch'] +checksums = [ + '75b554dab00903e2d10b972c913e50e7f88cbc62f3ae432b5a086c7e4eda0a71', # magma-2.6.2.tar.gz + 'b89285bac007b68e88e3b5ddbb7f94dbc8a9d77590e58c352e477574d8dca738', # magma-2.6.1_allow-all-sms.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('CUDA', '11.5.2', '', SYSTEM), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] +# make sure both static and shared libs are built +configopts = [ + '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') +] + +sanity_check_paths = { + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb new file mode 100644 index 00000000000..e3a29b13334 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb @@ -0,0 +1,23 @@ +name = 'NCCL' +version = '2.10.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('CUDA', '11.5.2', '', SYSTEM), + ('UCX-CUDA', '1.11.2', versionsuffix), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb new file mode 100644 index 00000000000..888bdda4b4f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb @@ -0,0 +1,156 @@ +name = 'PyTorch' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.11.1_skip-test_init_from_local_shards.patch + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch + 'd97cd6b0570a167ecc3e631dc4ea884d95ace285cc38aa980566f4fec2c0d089', + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', + # PyTorch-1.12.1_fix-test_wishart_log_prob.patch + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_python-3.10-annotation-fix.patch + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7', + '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67', # PyTorch-1.12.1_python-3.10-compat.patch + # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d', + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin.patch + '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.22.1'), + ('hypothesis', '6.14.6'), +] + +dependencies = [ + ('CUDA', '11.5.2', '', SYSTEM), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.6'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.7.1'), + ('SciPy-bundle', '2021.10'), + ('typing-extensions', '3.10.0.2'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.3.2'), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), + ('magma', '2.6.2', '-CUDA-%(cudaver)s'), + ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Those 2 abort on some machines. Skip for now + 'distributed/fsdp/test_fsdp_input', + 'distributed/fsdp/test_fsdp_mixed_precision', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# The readelf sanity check command can be taken out once the TestRPATH test from +# https://github.com/pytorch/pytorch/pull/87593 is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb new file mode 100644 index 00000000000..3748b1ba66a --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb @@ -0,0 +1,42 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.11.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] +patches = [ + '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', +] +checksums = [ + {'ucx-1.11.2.tar.gz': 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('UCX', version), + ('CUDA', '11.5.2', '', SYSTEM), + ('GDRCopy', '2.3'), +] + +moduleclass = 'lib' From 3f6e57dbae734d90a094473e2eb730c7b731aaa7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Feb 2023 11:43:39 +0100 Subject: [PATCH 6452/9987] Update patches based on PyTorch 1.13.1 --- .../p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 12 +++++------ .../PyTorch-1.13.1_no-cuda-stubs-rpath.patch | 21 +++++++++---------- ...h-1.13.1_remove-flaky-test-in-testnn.patch | 9 ++++---- ...skip-ao-sparsity-test-without-fbgemm.patch | 11 +++++----- 4 files changed, 26 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index 93d6830c264..151fcf65d7c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -22,10 +22,10 @@ patches = [ 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_fix-vsx-loadu.patch', 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', - 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', - 'PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.13.1_fix-test-ops-conf.patch', 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch', ] checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, @@ -46,12 +46,12 @@ checksums = [ {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, {'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch': '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d'}, + {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, + {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '4c636059850fc9d1ecb27ce275f8aad5d5b6fdc19e35aff0c25b86cb3201352a'}, {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': - 'ad8db280c1acb5fade65646097590c6b332a9caf722191e4a3ddba2fb945ee6d'}, + 'be83ff61fe2dedab6d49c232936d5622df81ab49154264490021c6c828e53315'}, {'PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch': - 'ea391298c4d9984de87cc14da9740ff09137b4a832fafd9e60c576f81690e8ec'}, - {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, - {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '1a8f712e474f64da878b9328ce05e7245afcba1765cbc27fb5f4f16f733ea175'}, + '92cd48ef6d01aa7e07ccce1dcaf40bc3fb0f220c4aa4fea15f3e05fb42e37909'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_no-cuda-stubs-rpath.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_no-cuda-stubs-rpath.patch index 772677f267a..be2335491ea 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_no-cuda-stubs-rpath.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_no-cuda-stubs-rpath.patch @@ -16,12 +16,11 @@ # # Original patch: Caspar van Leeuwen # Updated: Alexander Grund (TU Dresden) -# Updated: Simon Branford (University of Birmingham) # # See https://github.com/pytorch/pytorch/pull/87593 diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt -index 4182797fc78e5..265bf4f660896 100644 +index 9074b848411..1d45807189b 100644 --- a/caffe2/CMakeLists.txt +++ b/caffe2/CMakeLists.txt @@ -631,13 +631,12 @@ endif() @@ -43,7 +42,7 @@ index 4182797fc78e5..265bf4f660896 100644 if(USE_NCCL) diff --git a/cmake/LinkCudaLibraries.cmake b/cmake/LinkCudaLibraries.cmake new file mode 100644 -index 0000000000000..005914ccc6f7c +index 00000000000..005914ccc6f --- /dev/null +++ b/cmake/LinkCudaLibraries.cmake @@ -0,0 +1,33 @@ @@ -81,7 +80,7 @@ index 0000000000000..005914ccc6f7c + endif() +endfunction() diff --git a/test/cpp/api/CMakeLists.txt b/test/cpp/api/CMakeLists.txt -index 6b801a0731827..6ac92870479e0 100644 +index 6b801a07318..6ac92870479 100644 --- a/test/cpp/api/CMakeLists.txt +++ b/test/cpp/api/CMakeLists.txt @@ -54,7 +54,8 @@ if(NOT MSVC) @@ -95,7 +94,7 @@ index 6b801a0731827..6ac92870479e0 100644 ${CUDA_NVRTC_LIB} ${CUDA_CUDA_LIB} diff --git a/test/cpp/dist_autograd/CMakeLists.txt b/test/cpp/dist_autograd/CMakeLists.txt -index 9969c63e16d57..356ba5be55c4e 100644 +index 9969c63e16d..356ba5be55c 100644 --- a/test/cpp/dist_autograd/CMakeLists.txt +++ b/test/cpp/dist_autograd/CMakeLists.txt @@ -10,7 +10,8 @@ if(USE_DISTRIBUTED AND NOT WIN32) @@ -109,10 +108,10 @@ index 9969c63e16d57..356ba5be55c4e 100644 ${CUDA_NVRTC_LIB} ${CUDA_CUDA_LIB} diff --git a/test/cpp/jit/CMakeLists.txt b/test/cpp/jit/CMakeLists.txt -index b8b765a68d8b4..aba9c8c6c3e17 100644 +index 66a60fb01ca..005e18183d2 100644 --- a/test/cpp/jit/CMakeLists.txt +++ b/test/cpp/jit/CMakeLists.txt -@@ -156,7 +156,8 @@ if(LINUX) +@@ -148,7 +148,8 @@ if(LINUX) endif() if(USE_CUDA) @@ -123,7 +122,7 @@ index b8b765a68d8b4..aba9c8c6c3e17 100644 ${CUDA_NVRTC_LIB} ${CUDA_CUDA_LIB} diff --git a/test/cpp/rpc/CMakeLists.txt b/test/cpp/rpc/CMakeLists.txt -index 3997f8753e555..21fddbc645d0d 100644 +index 3997f8753e5..21fddbc645d 100644 --- a/test/cpp/rpc/CMakeLists.txt +++ b/test/cpp/rpc/CMakeLists.txt @@ -33,7 +33,8 @@ target_include_directories( @@ -137,7 +136,7 @@ index 3997f8753e555..21fddbc645d0d 100644 ${CUDA_NVRTC_LIB} ${CUDA_CUDA_LIB} diff --git a/test/cpp/tensorexpr/CMakeLists.txt b/test/cpp/tensorexpr/CMakeLists.txt -index 7dff70630d3ec..ecb83005492f5 100644 +index 7dff70630d3..ecb83005492 100644 --- a/test/cpp/tensorexpr/CMakeLists.txt +++ b/test/cpp/tensorexpr/CMakeLists.txt @@ -57,14 +57,15 @@ if(USE_PTHREADPOOL) @@ -159,10 +158,10 @@ index 7dff70630d3ec..ecb83005492f5 100644 ${CUDA_NVRTC_LIB} ${CUDA_CUDA_LIB} diff --git a/test/test_torch.py b/test/test_torch.py -index 31759213ecefc..67ebc0420f38a 100644 +index 8de5b822d00..fce7b5714f1 100644 --- a/test/test_torch.py +++ b/test/test_torch.py -@@ -8581,6 +8581,21 @@ def add_neg_dim_tests(): +@@ -8414,6 +8414,21 @@ def add_neg_dim_tests(): assert not hasattr(TestTorch, test_name), "Duplicated test name: " + test_name setattr(TestTorch, test_name, make_neg_dim_test(name, tensor_arg, arg_constr, types, extra_dim)) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_remove-flaky-test-in-testnn.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_remove-flaky-test-in-testnn.patch index 7a76b5fe01e..c95d2227258 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_remove-flaky-test-in-testnn.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_remove-flaky-test-in-testnn.patch @@ -5,12 +5,13 @@ fail. See https://github.com/pytorch/pytorch/issues/86638 So remove the half precision test. -Author: Simon Branford (University of Birmingham) -Based off 1.12.1 patch by Alexander Grund (TU Dresden) +Author: Alexander Grund (TU Dresden) +diff --git a/test/nn/test_embedding.py b/test/nn/test_embedding.py +index f76e01c65c5..6b5de2b1059 100644 --- a/test/nn/test_embedding.py +++ b/test/nn/test_embedding.py -@@ -18236,7 +18236,7 @@ class TestNNDeviceType(NNTestCase): +@@ -1108,7 +1108,7 @@ class TestEmbeddingNNDeviceType(NNTestCase): self.assertRaises(RuntimeError, lambda: es(input.view(-1), offset)) @skipMeta @@ -18,4 +19,4 @@ Based off 1.12.1 patch by Alexander Grund (TU Dresden) + @dtypes(*itertools.product((torch.int, torch.long), (torch.int, torch.long), (torch.float, torch.double))) def test_embedding_bag_device(self, device, dtypes): with set_default_dtype(torch.double): - self._test_EmbeddingBag(device, 'sum', False, wdtype=dtypes[2], dtype=dtypes[0], odtype=dtypes[1]) + self._test_EmbeddingBag(device, 'sum', False, wdtype=dtypes[2], dtype=dtypes[0], odtype=dtypes[1]) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch index fe5d7b06a51..481b013de21 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch @@ -2,11 +2,10 @@ Those tests (from test_ao_sparsity) require FBGEMM which may not be available. So add the skip decorator. See https://github.com/pytorch/pytorch/issues/87364 -Author: Simon Branford (University of Birmingham) -Based off 1.12.1 patch by Alexander Grund (TU Dresden) +Author: Alexander Grund (TU Dresden) diff --git a/test/ao/sparsity/test_composability.py b/test/ao/sparsity/test_composability.py -index b44c885507..b7d35343c0 100644 +index 6a1b6067a4c..b2eed72e3e3 100644 --- a/test/ao/sparsity/test_composability.py +++ b/test/ao/sparsity/test_composability.py @@ -9,6 +9,7 @@ import torch.ao.quantization as tq @@ -17,11 +16,11 @@ index b44c885507..b7d35343c0 100644 from torch.ao.quantization.quantize_fx import prepare_fx, convert_fx, convert_to_reference_fx, prepare_qat_fx from torch.ao.sparsity import fqn_to_module -@@ -23,6 +24,7 @@ sparse_defaults = { +@@ -62,6 +63,7 @@ def _calculate_sparsity(tensor): # This series of tests are to check the composability goals for sparsity and quantization. Namely # that performing quantization and sparsity model manipulations in various orderings # does not cause problems +@skipIfNoFBGEMM class TestComposability(TestCase): - def _get_model_and_sparsifier_and_sparse_config(self, qconfig=None): - model = nn.Sequential( + # This test checks whether performing quantization prepare before sparse prepare + # causes any issues and verifies that the correct observers are inserted and that From af2b98308df6540631ccacd4cb85ed7fbdbfc634 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 12 Jan 2023 16:45:28 +0100 Subject: [PATCH 6453/9987] adding easyconfigs: TensorFlow-2.9.1-foss-2022a.eb, TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb and patches: TensorFlow-2.9.1_fix-PPC-Eigen-build.patch, TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch, TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch, TensorFlow-2.9.1_support_flatbuffers_2.0.patch, TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch, TensorFlow-2.8.4_fix-PPC-JIT.patch, TensorFlow-2.8.4_resolve-gcc-symlinks.patch --- ...sorFlow-2.8.4_exclude-xnnpack-on-ppc.patch | 18 + .../TensorFlow-2.8.4_fix-PPC-JIT.patch | 58 + ...ensorFlow-2.8.4_resolve-gcc-symlinks.patch | 28 + ...TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb | 247 + .../TensorFlow/TensorFlow-2.9.1-foss-2022a.eb | 243 + ...TensorFlow-2.9.1_fix-PPC-Eigen-build.patch | 34 + ...low-2.9.1_remove-duplicate-gpu-tests.patch | 55 + ....9.1_remove-libclang-and-io-gcs-deps.patch | 35 + ...orFlow-2.9.1_support_flatbuffers_2.0.patch | 8002 +++++++++++++++++ 9 files changed, 8720 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_fix-PPC-JIT.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_fix-PPC-Eigen-build.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_support_flatbuffers_2.0.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch new file mode 100644 index 00000000000..1a0938252be --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch @@ -0,0 +1,18 @@ +XNNPACK is not supported on PowerPC so disable it by default. +See https://github.com/tensorflow/tensorflow/issues/58768 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/lite/BUILD b/tensorflow/lite/BUILD +index 198f949b341..d15dcf9a80d 100644 +--- a/tensorflow/lite/BUILD ++++ b/tensorflow/lite/BUILD +@@ -709,6 +709,8 @@ cc_library( + deps = select({ + "//tensorflow:macos": [], + "//tensorflow:fuchsia": [], ++ # XNNPACK is not supported on PPC ++ "//tensorflow:linux_ppc64le": [], + "//conditions:default": [":tflite_with_xnnpack_enabled"], + }), + ) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_fix-PPC-JIT.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_fix-PPC-JIT.patch new file mode 100644 index 00000000000..ca57b87dee1 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_fix-PPC-JIT.patch @@ -0,0 +1,58 @@ +diff --git a/third_party/cpuinfo/cpuinfo.BUILD b/third_party/cpuinfo/cpuinfo.BUILD +index eb2937d20ef..dfea408db94 100644 +--- a/third_party/cpuinfo/cpuinfo.BUILD ++++ b/third_party/cpuinfo/cpuinfo.BUILD +@@ -109,6 +109,7 @@ cc_library( + ":linux_mips64": COMMON_SRCS + LINUX_SRCS, + ":linux_riscv64": COMMON_SRCS + LINUX_SRCS, + ":linux_s390x": COMMON_SRCS + LINUX_SRCS, ++ ":linux_ppc64le": COMMON_SRCS + LINUX_SRCS, + ":macos_x86_64": COMMON_SRCS + X86_SRCS + MACH_SRCS + MACH_X86_SRCS, + ":macos_arm64": COMMON_SRCS + MACH_SRCS + MACH_ARM_SRCS, + ":windows_x86_64": COMMON_SRCS + X86_SRCS + WINDOWS_X86_SRCS, +@@ -232,6 +233,11 @@ config_setting( + values = {"cpu": "s390x"}, + ) + ++config_setting( ++ name = "linux_ppc64le", ++ values = {"cpu": "ppc"}, ++) ++ + config_setting( + name = "macos_x86_64", + values = { +diff --git a/third_party/llvm/macos_build_fix.patch b/third_party/llvm/macos_build_fix.patch +index 4dba8676ea5..af31f0c1d9e 100644 +--- a/third_party/llvm/macos_build_fix.patch ++++ b/third_party/llvm/macos_build_fix.patch +@@ -42,5 +42,29 @@ index ff64df694048..c9c35b01711c 100644 + "@bazel_tools//src/conditions:linux_aarch64": native_arch_defines("AArch64", "aarch64-unknown-linux-gnu"), + "//conditions:default": native_arch_defines("X86", "x86_64-unknown-linux-gnu"), + }) + [ ++ ++ ++From b250c34bbd415b2a8c3e0532e98591ab1780cda6 Mon Sep 17 00:00:00 2001 ++From: Nishidha Panpaliya ++Date: Mon, 21 Mar 2022 09:51:36 -0400 ++Subject: [PATCH] Fix for ppc64le ++ ++--- ++ utils/bazel/llvm-project-overlay/llvm/config.bzl | 1 + ++ 1 file changed, 1 insertion(+) ++ ++diff --git a/utils/bazel/llvm-project-overlay/llvm/config.bzl b/utils/bazel/llvm-project-overlay/llvm/config.bzl ++index 772714f38941..9ed63e8d44a3 100644 ++--- a/utils/bazel/llvm-project-overlay/llvm/config.bzl +++++ b/utils/bazel/llvm-project-overlay/llvm/config.bzl ++@@ -86,6 +86,7 @@ llvm_config_defines = os_defines + select({ ++ "//llvm:macos_arm64": native_arch_defines("AArch64", "arm64-apple-darwin"), ++ "@bazel_tools//src/conditions:darwin": native_arch_defines("X86", "x86_64-unknown-darwin"), ++ "@bazel_tools//src/conditions:linux_aarch64": native_arch_defines("AArch64", "aarch64-unknown-linux-gnu"), +++ "@bazel_tools//src/conditions:linux_ppc64le": native_arch_defines("PowerPC", "powerpc64le-unknown-linux-gnu"), ++ "//conditions:default": native_arch_defines("X86", "x86_64-unknown-linux-gnu"), ++ }) + [ ++ # These shouldn't be needed by the C++11 standard, but are for some ++ + -- + 2.30.1 (Apple Git-130) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch new file mode 100644 index 00000000000..42cdce7c9fd --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch @@ -0,0 +1,28 @@ +Fix for "undeclared inclusion(s) in rule" errors when the installation directory +for GCC is hosted in a path that is a symlink to another path. + +From https://github.com/tensorflow/tensorflow/pull/56360 + +From b3a8fdbcb79e723f8d62f86bddcfdfb73fe76291 Mon Sep 17 00:00:00 2001 +From: Jinzhe Zeng +Date: Sat, 4 Jun 2022 19:06:58 -0400 +Subject: [PATCH] resolve gcc_host_compiler_path in a symlink directory + +Resolves a missing dependency declarations error, when gcc_host_compiler_path is in a symlink directory resolving to other directories. +--- + configure.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/configure.py b/configure.py +index bf338bdda2297..77af09a22a05d 100644 +--- a/configure.py ++++ b/configure.py +@@ -619,7 +619,7 @@ def prompt_loop_or_load_from_env(environ_cp, + 'Assuming to be a scripting mistake.' % + (var_name, n_ask_attempts)) + +- if resolve_symlinks and os.path.islink(val): ++ if resolve_symlinks: + val = os.path.realpath(val) + environ_cp[var_name] = val + return val diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..7d8fc26cca1 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,247 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.9.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('protobuf', '3.19.4'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.36.0', '-nodocs'), + ('pybind11', '2.9.2'), + ('UnZip', '6.0'), + ('LLVM', '14.0.3'), # for debugging with llvm-symbolizer, to be removed +] +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), + ('NCCL', '2.12.12', versionsuffix), + ('Python', '3.10.4'), + ('h5py', '3.7.0'), + ('cURL', '7.83.0'), + ('dill', '0.3.6'), + ('double-conversion', '3.2.0'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.7.1'), + ('ICU', '71.1'), + ('JsonCpp', '1.9.5'), + ('libjpeg-turbo', '2.1.3'), + ('LMDB', '0.9.29'), + ('NASM', '2.15.05'), + ('nsync', '1.25.0'), + ('SQLite', '3.38.3'), + ('protobuf-python', '3.19.4'), + ('flatbuffers-python', '2.0'), + ('libpng', '1.6.37'), + ('snappy', '1.1.9'), + ('zlib', '1.2.12'), + ('networkx', '2.8.4'), # required for pythran +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', '2.9.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['e9762bb302f51bc1eb2f35d19f0190a6a2d809d754d5def788c4328fe3746744'], + }), + ('Werkzeug', '2.2.2', { + 'checksums': ['7ea2d48322cc7c0f8b3a215ed73eabd7b5d75d0b50e31ab006286ccff9e00b8f'], + }), + ('tensorboard-plugin-wit', '1.8.1', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard-data-server', '0.6.1', { + 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('grpcio', '1.47.0', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['5dbba95fab9b35957b4977b8904fc1fa56b302f9051eff4d7716ebb0c087f801'], + }), + ('oauthlib', '3.2.0', { + 'checksums': ['23a8208d75b902797ea29fd31fa80a15ed9dc2c6c16fe73f5d346f83f6fa27a2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('cachetools', '5.2.0', { + 'checksums': ['6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757'], + }), + ('google-auth', '2.10.0', { + 'modulename': 'google.auth', + 'checksums': ['7904dbd44b745c7323fef29565adee2fe7ff48473e2d94443aced40b0404a395'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('absl-py', '1.2.0', { + 'modulename': 'absl', + 'checksums': ['f568809938c49abbda89826223c992b630afd23c638160ad7840cfe347710d97'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['baa727f791776f9e5841d347127720ceed4bbd59c36b40604b95fb2ae6029276'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('keras', '2.9.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['55911256f89cfc9343c9fbe4b61ec45a2d33d89729cbe1ab9dcacf8b07b8b6ab'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + # Version <= 0.4.0 required by TF: https://github.com/tensorflow/tensorflow/issues/56244 + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + # (newer) pythran and beniget in SciPy-Bundle require gast 0.5 + ('beniget', '0.3.0', { + 'checksums': ['062c893be9cdf87c3144fb15041cce4d81c67107c1591952cd45fdce789a0ff1'], + }), + ('pythran', '0.9.11', { + 'checksums': ['a317f91e2aade9f6550dc3bf40b5caeb45b7e012daf27e2b3e4ad928edb01667'], + }), + # Required by tests + ('portpicker', '1.5.2', { + 'checksums': ['c55683ad725f5c00a41bc7db0225223e8be024b1fa564d039ed3390e4fd48fb3'], + }), + # System dependencies + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + # Optional profile plugin + dependency + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.8.0', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['58d65c979951e7628ca3b46c798e10e5813026a3ecfbacc319cf88ebe766134a'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.7.1_fix_cpu_count.patch', + 'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch', + 'TensorFlow-2.8.4_fix-PPC-JIT.patch', + 'TensorFlow-2.8.4_resolve-gcc-symlinks.patch', + 'TensorFlow-2.9.1_fix-PPC-Eigen-build.patch', + 'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch', + 'TensorFlow-2.9.1_support_flatbuffers_2.0.patch', + ], + 'checksums': [ + {'v2.9.1.tar.gz': '6eaf86ead73e23988fe192da1db68f4d3828bcdd0f3a9dc195935e339c95dbdc'}, + {'TensorFlow-2.4.0_add-ldl.patch': '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.5.0_add-support-for-large-core-systems.patch': + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636'}, + {'TensorFlow-2.5.0_disable-avx512-extensions.patch': + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03'}, + {'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch': + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75'}, + {'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch': + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029'}, + {'TensorFlow-2.5.0_fix-crash-on-shutdown.patch': + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd'}, + {'TensorFlow-2.7.1_fix_cpu_count.patch': + '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698'}, + {'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch': + 'ebd404ac56cc4ca662483f1f591e62e11749361be57a7ba5f4b2f0d03e829884'}, + {'TensorFlow-2.8.4_fix-PPC-JIT.patch': + '27d28293105b4dd0a25f58346c68b672f57215756f14a97c442d0e3317e93a2b'}, + {'TensorFlow-2.8.4_resolve-gcc-symlinks.patch': + '43ce9acc6bffff68a31d2263d0064d272999b2e0a2c6546690287cd1c9c90f04'}, + {'TensorFlow-2.9.1_fix-PPC-Eigen-build.patch': + '5f559a6eade65df665c7c69bc2e5d5d4214b85ea836e966f5dba73211307b972'}, + {'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch': + '6fe50faab28387c622c68dc3fc0cbfb2a51000cd750c1a82f8420b54fcd2509f'}, + {'TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch': + '13a987ce8e20957d9a618493f6a0e8f67e0f9c8b11596f27bcd7322a8e62113d'}, + {'TensorFlow-2.9.1_support_flatbuffers_2.0.patch': + 'aaf0e0f86ad26f98a2bbb230dc2bbc2fb5f04886ab340049b5eaf3c70ae18f39'}, + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb new file mode 100644 index 00000000000..434de47a58b --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb @@ -0,0 +1,243 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.9.1' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('protobuf', '3.19.4'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.36.0', '-nodocs'), + ('pybind11', '2.9.2'), + ('UnZip', '6.0'), + ('LLVM', '14.0.3'), # for debugging with llvm-symbolizer, to be removed +] +dependencies = [ + ('Python', '3.10.4'), + ('h5py', '3.7.0'), + ('cURL', '7.83.0'), + ('dill', '0.3.6'), + ('double-conversion', '3.2.0'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.7.1'), + ('ICU', '71.1'), + ('JsonCpp', '1.9.5'), + ('libjpeg-turbo', '2.1.3'), + ('LMDB', '0.9.29'), + ('NASM', '2.15.05'), + ('nsync', '1.25.0'), + ('SQLite', '3.38.3'), + ('protobuf-python', '3.19.4'), + ('flatbuffers-python', '2.0'), + ('libpng', '1.6.37'), + ('snappy', '1.1.9'), + ('zlib', '1.2.12'), + ('networkx', '2.8.4'), # required for pythran +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', '2.9.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['e9762bb302f51bc1eb2f35d19f0190a6a2d809d754d5def788c4328fe3746744'], + }), + ('Werkzeug', '2.2.2', { + 'checksums': ['7ea2d48322cc7c0f8b3a215ed73eabd7b5d75d0b50e31ab006286ccff9e00b8f'], + }), + ('tensorboard-plugin-wit', '1.8.1', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard-data-server', '0.6.1', { + 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('grpcio', '1.47.0', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['5dbba95fab9b35957b4977b8904fc1fa56b302f9051eff4d7716ebb0c087f801'], + }), + ('oauthlib', '3.2.0', { + 'checksums': ['23a8208d75b902797ea29fd31fa80a15ed9dc2c6c16fe73f5d346f83f6fa27a2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('cachetools', '5.2.0', { + 'checksums': ['6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757'], + }), + ('google-auth', '2.10.0', { + 'modulename': 'google.auth', + 'checksums': ['7904dbd44b745c7323fef29565adee2fe7ff48473e2d94443aced40b0404a395'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('absl-py', '1.2.0', { + 'modulename': 'absl', + 'checksums': ['f568809938c49abbda89826223c992b630afd23c638160ad7840cfe347710d97'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['baa727f791776f9e5841d347127720ceed4bbd59c36b40604b95fb2ae6029276'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('keras', '2.9.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['55911256f89cfc9343c9fbe4b61ec45a2d33d89729cbe1ab9dcacf8b07b8b6ab'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + # Version <= 0.4.0 required by TF: https://github.com/tensorflow/tensorflow/issues/56244 + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + }), + # (newer) pythran and beniget in SciPy-Bundle require gast 0.5 + ('beniget', '0.3.0', { + 'checksums': ['062c893be9cdf87c3144fb15041cce4d81c67107c1591952cd45fdce789a0ff1'], + }), + ('pythran', '0.9.11', { + 'checksums': ['a317f91e2aade9f6550dc3bf40b5caeb45b7e012daf27e2b3e4ad928edb01667'], + }), + # Required by tests + ('portpicker', '1.5.2', { + 'checksums': ['c55683ad725f5c00a41bc7db0225223e8be024b1fa564d039ed3390e4fd48fb3'], + }), + # System dependencies + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + # Optional profile plugin + dependency + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.8.0', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['58d65c979951e7628ca3b46c798e10e5813026a3ecfbacc319cf88ebe766134a'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.7.1_fix_cpu_count.patch', + 'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch', + 'TensorFlow-2.8.4_fix-PPC-JIT.patch', + 'TensorFlow-2.8.4_resolve-gcc-symlinks.patch', + 'TensorFlow-2.9.1_fix-PPC-Eigen-build.patch', + 'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch', + 'TensorFlow-2.9.1_support_flatbuffers_2.0.patch', + ], + 'checksums': [ + {'v2.9.1.tar.gz': '6eaf86ead73e23988fe192da1db68f4d3828bcdd0f3a9dc195935e339c95dbdc'}, + {'TensorFlow-2.4.0_add-ldl.patch': '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.5.0_add-support-for-large-core-systems.patch': + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636'}, + {'TensorFlow-2.5.0_disable-avx512-extensions.patch': + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03'}, + {'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch': + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75'}, + {'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch': + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029'}, + {'TensorFlow-2.5.0_fix-crash-on-shutdown.patch': + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd'}, + {'TensorFlow-2.7.1_fix_cpu_count.patch': + '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698'}, + {'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch': + 'ebd404ac56cc4ca662483f1f591e62e11749361be57a7ba5f4b2f0d03e829884'}, + {'TensorFlow-2.8.4_fix-PPC-JIT.patch': + '27d28293105b4dd0a25f58346c68b672f57215756f14a97c442d0e3317e93a2b'}, + {'TensorFlow-2.8.4_resolve-gcc-symlinks.patch': + '43ce9acc6bffff68a31d2263d0064d272999b2e0a2c6546690287cd1c9c90f04'}, + {'TensorFlow-2.9.1_fix-PPC-Eigen-build.patch': + '5f559a6eade65df665c7c69bc2e5d5d4214b85ea836e966f5dba73211307b972'}, + {'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch': + '6fe50faab28387c622c68dc3fc0cbfb2a51000cd750c1a82f8420b54fcd2509f'}, + {'TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch': + '13a987ce8e20957d9a618493f6a0e8f67e0f9c8b11596f27bcd7322a8e62113d'}, + {'TensorFlow-2.9.1_support_flatbuffers_2.0.patch': + 'aaf0e0f86ad26f98a2bbb230dc2bbc2fb5f04886ab340049b5eaf3c70ae18f39'}, + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_fix-PPC-Eigen-build.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_fix-PPC-Eigen-build.patch new file mode 100644 index 00000000000..7ebb09097df --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_fix-PPC-Eigen-build.patch @@ -0,0 +1,34 @@ +The new Eigen version used in TF 2.9 is not compatible with the custom classes +defined in TF leading to a compile error on PPC: +'class EigenForTFLite::internal::TensorContractionInputMapper, const EigenForTFLite::TensorImagePatchOp<-1, -1, const EigenForTFLite::TensorMap, 16> > >, EigenForTFLite::ThreadPoolDevice>, std::array, std::array, 4, true, false, 0, EigenForTFLite::MakePointer>' has no member named 'load' + +See https://github.com/tensorflow/tensorflow/issues/59212 and https://gitlab.com/libeigen/eigen/-/merge_requests/764#note_1231907378 +This might be easily fixable in more recent versions of TF/Eigen +but for now simply disable the custom TF code for PPC. + +diff --git a/tensorflow/core/kernels/eigen_cuboid_convolution.h b/tensorflow/core/kernels/eigen_cuboid_convolution.h +index 729dcd3bd2a..89f1d5b6732 100644 +--- a/tensorflow/core/kernels/eigen_cuboid_convolution.h ++++ b/tensorflow/core/kernels/eigen_cuboid_convolution.h +@@ -28,7 +28,7 @@ namespace Eigen { + + namespace internal { + +-#if !EIGEN_ALTIVEC_USE_CUSTOM_PACK ++#ifndef EIGEN_VECTORIZE_VSX + // WARNING: Most of the code here implicitly assumes that the matrix is in + // ColMajor layout. This is guaranteed by the tensor contraction (see + // TensorContraction.h). +diff --git a/tensorflow/core/kernels/eigen_spatial_convolutions-inl.h b/tensorflow/core/kernels/eigen_spatial_convolutions-inl.h +index 37a41f952fa..ade41fbf103 100644 +--- a/tensorflow/core/kernels/eigen_spatial_convolutions-inl.h ++++ b/tensorflow/core/kernels/eigen_spatial_convolutions-inl.h +@@ -23,7 +23,7 @@ namespace Eigen { + + namespace internal { + +-#if !EIGEN_ALTIVEC_USE_CUSTOM_PACK ++#ifndef EIGEN_VECTORIZE_VSX + // WARNING: Most of the code here implicitly assumes that the matrix is in + // ColMajor layout. This is guaranteed by the tensor contraction (see + // TensorContraction.h). diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch new file mode 100644 index 00000000000..7701d85e612 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch @@ -0,0 +1,55 @@ +TensorFlow adds some GPU tests twice increasing the runtime of the test suite. +This filters out the test part meant for CPU. + +See https://github.com/tensorflow/tensorflow/issues/47081 +From https://github.com/tensorflow/tensorflow/pull/59129 + +Author: Alexander Grund (TU Dresden) +--- + tensorflow/tensorflow.bzl | 33 +++++++++++++++++---------------- + 1 file changed, 17 insertions(+), 16 deletions(-) + +diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl +index 649c8e22dcc95..d3fc0e3221497 100644 +--- a/tensorflow/tensorflow.bzl ++++ b/tensorflow/tensorflow.bzl +@@ -1461,22 +1461,23 @@ def tf_gpu_cc_test( + linkopts = [], + **kwargs): + targets = [] +- tf_cc_test( +- name = name, +- size = size, +- srcs = srcs, +- args = args, +- data = data, +- extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), +- kernels = kernels, +- linkopts = linkopts, +- linkstatic = linkstatic, +- suffix = "_cpu", +- tags = tags, +- deps = deps, +- **kwargs +- ) +- targets.append(name + "_cpu") ++ if 'gpu' not in tags: ++ tf_cc_test( ++ name = name, ++ size = size, ++ srcs = srcs, ++ args = args, ++ data = data, ++ extra_copts = extra_copts + if_cuda(["-DNV_CUDNN_DISABLE_EXCEPTION"]), ++ kernels = kernels, ++ linkopts = linkopts, ++ linkstatic = linkstatic, ++ suffix = "_cpu", ++ tags = tags, ++ deps = deps, ++ **kwargs ++ ) ++ targets.append(name + "_cpu") + tf_cc_test( + name = name, + size = size, diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch new file mode 100644 index 00000000000..437f45fe5ef --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch @@ -0,0 +1,35 @@ +This combines two patches from TensorFlow 2.7.1. + +tensorflow-io-gcs-filesystem is not available as a binary for all architectures and +building it requires TensorFlow to be installed, i.e. there is a cyclic dependency. +As it is not actually required (but optional) remove it from `REQUIRED_PACKAGES`. +See https://github.com/tensorflow/tensorflow/issues/56636 + +libclang was introduced in +https://github.com/tensorflow/tensorflow/commit/c211472000ff57bac7fcec9b0465cf73b37bf135 +> This is in preparation to open-source TF's TFRT backend. +> TFRT generates code using libclang python bindings as part of the build. +Hence it is not currently used and as it is not (easily) available for all architectures +simply remove it. + +Patch added by Simon Branford (University of Birmingham) +Updated by Alexander Grund (TU Dresden) + +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -83,7 +83,6 @@ REQUIRED_PACKAGES = [ + 'google_pasta >= 0.1.1', + 'h5py >= 2.9.0', + 'keras_preprocessing >= 1.1.1', # 1.1.0 needs tensorflow==1.7 +- 'libclang >= 13.0.0', + 'numpy >= 1.20', + 'opt_einsum >= 2.3.2', + 'packaging', +@@ -100,7 +99,6 @@ REQUIRED_PACKAGES = [ + 'termcolor >= 1.1.0', + 'typing_extensions >= 3.6.6', + 'wrapt >= 1.11.0', +- 'tensorflow-io-gcs-filesystem >= 0.23.1', + # grpcio does not build correctly on big-endian machines due to lack of + # BoringSSL support. + # See https://github.com/tensorflow/tensorflow/issues/17882. diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_support_flatbuffers_2.0.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_support_flatbuffers_2.0.patch new file mode 100644 index 00000000000..81077042987 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_support_flatbuffers_2.0.patch @@ -0,0 +1,8002 @@ +Add support for flatbuffers 2.0. +Taken from https://github.com/tensorflow/tensorflow/commit/625a4045bc0728c0f3d1b63e05749201f8b401dd + +Backported to 2.9.1 by +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/compiler/mlir/lite/flatbuffer_export.cc b/tensorflow/compiler/mlir/lite/flatbuffer_export.cc +index 9467afdf3c5..b75d55204c1 100644 +--- a/tensorflow/compiler/mlir/lite/flatbuffer_export.cc ++++ b/tensorflow/compiler/mlir/lite/flatbuffer_export.cc +@@ -784,17 +784,19 @@ Optional> Translator::BuildTensorFromType( + GetTFLiteType(tensor_type.getElementType()).ValueOrDie(); + BufferOffset q_params = 0; + if (auto qtype = element_type.dyn_cast()) { ++ std::vector scales = {static_cast(qtype.getScale())}; ++ std::vector zero_points = {qtype.getZeroPoint()}; + q_params = tflite::CreateQuantizationParameters( +- builder_, /*min=*/0, /*max=*/0, +- builder_.CreateVector({static_cast(qtype.getScale())}), +- builder_.CreateVector({qtype.getZeroPoint()})); ++ builder_, /*min=*/0, /*max=*/0, builder_.CreateVector(scales), ++ builder_.CreateVector(zero_points)); + } else if (auto qtype = + element_type + .dyn_cast()) { ++ std::vector mins = {static_cast(qtype.getMin())}; ++ std::vector maxs = {static_cast(qtype.getMax())}; + q_params = tflite::CreateQuantizationParameters( +- builder_, +- builder_.CreateVector({static_cast(qtype.getMin())}), +- builder_.CreateVector({static_cast(qtype.getMax())})); ++ builder_, builder_.CreateVector(mins), ++ builder_.CreateVector(maxs)); + } + return tflite::CreateTensor( + builder_, builder_.CreateVector(shape), tflite_element_type, +@@ -868,20 +870,23 @@ Optional> Translator::BuildTensor( + + BufferOffset q_params; + if (auto qtype = element_type.dyn_cast()) { ++ std::vector scales = {static_cast(qtype.getScale())}; ++ std::vector zero_points = {qtype.getZeroPoint()}; + q_params = tflite::CreateQuantizationParameters( + // min and max values are not stored in the quantized type from MLIR, so + // both are set to 0 in the flatbuffer when they are exported. +- builder_, /*min=*/0, /*max=*/0, +- builder_.CreateVector({static_cast(qtype.getScale())}), +- builder_.CreateVector({qtype.getZeroPoint()})); ++ builder_, /*min=*/0, /*max=*/0, builder_.CreateVector(scales), ++ builder_.CreateVector(zero_points)); + } else if (auto qtype = + element_type + .dyn_cast()) { + std::vector scales(qtype.getScales().begin(), + qtype.getScales().end()); ++ std::vector zero_points(qtype.getZeroPoints().begin(), ++ qtype.getZeroPoints().end()); + q_params = tflite::CreateQuantizationParameters( + builder_, /*min=*/0, /*max=*/0, builder_.CreateVector(scales), +- builder_.CreateVector(qtype.getZeroPoints()), ++ builder_.CreateVector(zero_points), + tflite::QuantizationDetails_NONE, /*details=*/0, + qtype.getQuantizedDimension()); + } else if (quant_parameters.hasValue()) { +diff --git a/tensorflow/compiler/mlir/lite/quantization/lite/quantize_model_test.cc b/tensorflow/compiler/mlir/lite/quantization/lite/quantize_model_test.cc +index 6075c6515bd..cd67fad748a 100644 +--- a/tensorflow/compiler/mlir/lite/quantization/lite/quantize_model_test.cc ++++ b/tensorflow/compiler/mlir/lite/quantization/lite/quantize_model_test.cc +@@ -210,7 +210,7 @@ void ExpectSameModels(const ModelT& model, const ModelT& expected_model) { + continue; + } + ExpectEqualTensor(tensor.get(), expected_tensor); +- if (tensor->buffer >= 0) { ++ if (expected_tensor->buffer > 0) { + const int buffer_idx = tensor->buffer; + const int expected_buffer_idx = expected_tensor->buffer; + const auto buffer = model.buffers[buffer_idx].get()->data; +diff --git a/tensorflow/lite/kernels/test_util.cc b/tensorflow/lite/kernels/test_util.cc +index 0e97b89bca4..eef287d6267 100644 +--- a/tensorflow/lite/kernels/test_util.cc ++++ b/tensorflow/lite/kernels/test_util.cc +@@ -112,7 +112,8 @@ int SingleOpModel::AddIntermediate(TensorType type, + CreateQuantizationParameters(builder_, /*min=*/0, /*max=*/0, + builder_.CreateVector(scale), + builder_.CreateVector(zero_point)); +- tensors_.push_back(CreateTensor(builder_, builder_.CreateVector({}), ++ std::vector empty; ++ tensors_.push_back(CreateTensor(builder_, builder_.CreateVector(empty), + type, + /*buffer=*/0, + /*name=*/0, q_params, false)); +diff --git a/tensorflow/lite/kernels/test_util.h b/tensorflow/lite/kernels/test_util.h +index cf61f32a9c9..81bab720d79 100644 +--- a/tensorflow/lite/kernels/test_util.h ++++ b/tensorflow/lite/kernels/test_util.h +@@ -245,12 +245,12 @@ class SingleOpModel { + if (i < t.shape.size() && + t.format[t.traversal_order[i]] == kTfLiteDimSparseCSR) { + auto array_segments = +- CreateInt32Vector(builder_, +- builder_.CreateVector(dim_metadata[metadata_idx])) ++ CreateInt32Vector(builder_, builder_.CreateVector( ++ dim_metadata[metadata_idx])) + .Union(); + auto array_indices = +- CreateInt32Vector( +- builder_, builder_.CreateVector(dim_metadata[metadata_idx + 1])) ++ CreateInt32Vector(builder_, builder_.CreateVector( ++ dim_metadata[metadata_idx + 1])) + .Union(); + fb_dim_metadata[i] = CreateDimensionMetadata( + builder_, DimensionType_SPARSE_CSR, 0, +@@ -263,8 +263,8 @@ class SingleOpModel { + } + + flatbuffers::Offset s_param = CreateSparsityParameters( +- builder_, builder_.CreateVector(t.traversal_order), +- builder_.CreateVector(t.block_map), ++ builder_, builder_.CreateVector(t.traversal_order), ++ builder_.CreateVector(t.block_map), + builder_.CreateVector(fb_dim_metadata)); + + int buffer_id = 0; +@@ -359,9 +359,11 @@ class SingleOpModel { + float min, max, scaling_factor; + tensor_utils::SymmetricQuantizeFloats( + sparse_data.data(), length, q.data(), &min, &max, &scaling_factor); ++ std::vector scales{scaling_factor}; ++ std::vector zero_points{0}; + q_params = CreateQuantizationParameters( +- builder_, 0, 0, builder_.CreateVector({scaling_factor}), +- builder_.CreateVector({0})); ++ builder_, 0, 0, builder_.CreateVector(scales), ++ builder_.CreateVector(zero_points)); + auto data_buffer = builder_.CreateVector( + reinterpret_cast(q.data()), q.size()); + buffers_.push_back(CreateBuffer(builder_, data_buffer)); +@@ -369,9 +371,11 @@ class SingleOpModel { + CHECK_EQ(t.type, TensorType_INT8) + << "The INT8 quantization is only supported for sparsified tensor"; + auto q = Quantize(sparse_data, t.scale, t.zero_point); ++ std::vector scales{t.scale}; ++ std::vector zero_points{0}; + q_params = CreateQuantizationParameters( +- builder_, t.min, t.max, builder_.CreateVector({t.scale}), +- builder_.CreateVector({0})); ++ builder_, t.min, t.max, builder_.CreateVector(scales), ++ builder_.CreateVector(zero_points)); + auto data_buffer = builder_.CreateVector( + reinterpret_cast(q.data()), q.size()); + buffers_.push_back(CreateBuffer(builder_, data_buffer)); +@@ -690,10 +694,11 @@ class SingleOpModel { + t.max = 0; + } + ++ std::vector scales{t.scale}; ++ std::vector zero_points{t.zero_point}; + q_params = CreateQuantizationParameters( +- builder_, /*min=*/0, /*max=*/0, +- builder_.CreateVector({t.scale}), +- builder_.CreateVector({t.zero_point})); ++ builder_, /*min=*/0, /*max=*/0, builder_.CreateVector(scales), ++ builder_.CreateVector(zero_points)); + } + + int buffer_id = 0; +diff --git a/tensorflow/lite/schema/BUILD b/tensorflow/lite/schema/BUILD +index eb3d9df659d..7d1f2b7a2e3 100644 +--- a/tensorflow/lite/schema/BUILD ++++ b/tensorflow/lite/schema/BUILD +@@ -77,6 +77,11 @@ py_test( + # "//tensorflow/lite/schema:schema_generated.h.oss", + # ], + # python_version = "PY3", ++# # TODO(b/217577534): Enable this TAP with FlatBuffer 2.0 migration. ++# tags = [ ++# "manual", ++# "notap", ++# ], + # deps = [ + # "//testing/pybase", + # "@absl_py//absl/flags", +diff --git a/tensorflow/lite/schema/schema_generated.h b/tensorflow/lite/schema/schema_generated.h +index e5ce189f147..0de55f064ef 100755 +--- a/tensorflow/lite/schema/schema_generated.h ++++ b/tensorflow/lite/schema/schema_generated.h +@@ -23,405 +23,538 @@ limitations under the License. + namespace tflite { + + struct CustomQuantization; ++struct CustomQuantizationBuilder; + struct CustomQuantizationT; + + struct QuantizationParameters; ++struct QuantizationParametersBuilder; + struct QuantizationParametersT; + + struct Int32Vector; ++struct Int32VectorBuilder; + struct Int32VectorT; + + struct Uint16Vector; ++struct Uint16VectorBuilder; + struct Uint16VectorT; + + struct Uint8Vector; ++struct Uint8VectorBuilder; + struct Uint8VectorT; + + struct DimensionMetadata; ++struct DimensionMetadataBuilder; + struct DimensionMetadataT; + + struct SparsityParameters; ++struct SparsityParametersBuilder; + struct SparsityParametersT; + + struct Tensor; ++struct TensorBuilder; + struct TensorT; + + struct Conv2DOptions; ++struct Conv2DOptionsBuilder; + struct Conv2DOptionsT; + + struct Conv3DOptions; ++struct Conv3DOptionsBuilder; + struct Conv3DOptionsT; + + struct Pool2DOptions; ++struct Pool2DOptionsBuilder; + struct Pool2DOptionsT; + + struct DepthwiseConv2DOptions; ++struct DepthwiseConv2DOptionsBuilder; + struct DepthwiseConv2DOptionsT; + + struct ConcatEmbeddingsOptions; ++struct ConcatEmbeddingsOptionsBuilder; + struct ConcatEmbeddingsOptionsT; + + struct LSHProjectionOptions; ++struct LSHProjectionOptionsBuilder; + struct LSHProjectionOptionsT; + + struct SVDFOptions; ++struct SVDFOptionsBuilder; + struct SVDFOptionsT; + + struct RNNOptions; ++struct RNNOptionsBuilder; + struct RNNOptionsT; + + struct SequenceRNNOptions; ++struct SequenceRNNOptionsBuilder; + struct SequenceRNNOptionsT; + + struct BidirectionalSequenceRNNOptions; ++struct BidirectionalSequenceRNNOptionsBuilder; + struct BidirectionalSequenceRNNOptionsT; + + struct FullyConnectedOptions; ++struct FullyConnectedOptionsBuilder; + struct FullyConnectedOptionsT; + + struct SoftmaxOptions; ++struct SoftmaxOptionsBuilder; + struct SoftmaxOptionsT; + + struct ConcatenationOptions; ++struct ConcatenationOptionsBuilder; + struct ConcatenationOptionsT; + + struct AddOptions; ++struct AddOptionsBuilder; + struct AddOptionsT; + + struct MulOptions; ++struct MulOptionsBuilder; + struct MulOptionsT; + + struct L2NormOptions; ++struct L2NormOptionsBuilder; + struct L2NormOptionsT; + + struct LocalResponseNormalizationOptions; ++struct LocalResponseNormalizationOptionsBuilder; + struct LocalResponseNormalizationOptionsT; + + struct LSTMOptions; ++struct LSTMOptionsBuilder; + struct LSTMOptionsT; + + struct UnidirectionalSequenceLSTMOptions; ++struct UnidirectionalSequenceLSTMOptionsBuilder; + struct UnidirectionalSequenceLSTMOptionsT; + + struct BidirectionalSequenceLSTMOptions; ++struct BidirectionalSequenceLSTMOptionsBuilder; + struct BidirectionalSequenceLSTMOptionsT; + + struct ResizeBilinearOptions; ++struct ResizeBilinearOptionsBuilder; + struct ResizeBilinearOptionsT; + + struct ResizeNearestNeighborOptions; ++struct ResizeNearestNeighborOptionsBuilder; + struct ResizeNearestNeighborOptionsT; + + struct CallOptions; ++struct CallOptionsBuilder; + struct CallOptionsT; + + struct PadOptions; ++struct PadOptionsBuilder; + struct PadOptionsT; + + struct PadV2Options; ++struct PadV2OptionsBuilder; + struct PadV2OptionsT; + + struct ReshapeOptions; ++struct ReshapeOptionsBuilder; + struct ReshapeOptionsT; + + struct SpaceToBatchNDOptions; ++struct SpaceToBatchNDOptionsBuilder; + struct SpaceToBatchNDOptionsT; + + struct BatchToSpaceNDOptions; ++struct BatchToSpaceNDOptionsBuilder; + struct BatchToSpaceNDOptionsT; + + struct SkipGramOptions; ++struct SkipGramOptionsBuilder; + struct SkipGramOptionsT; + + struct SpaceToDepthOptions; ++struct SpaceToDepthOptionsBuilder; + struct SpaceToDepthOptionsT; + + struct DepthToSpaceOptions; ++struct DepthToSpaceOptionsBuilder; + struct DepthToSpaceOptionsT; + + struct SubOptions; ++struct SubOptionsBuilder; + struct SubOptionsT; + + struct DivOptions; ++struct DivOptionsBuilder; + struct DivOptionsT; + + struct TopKV2Options; ++struct TopKV2OptionsBuilder; + struct TopKV2OptionsT; + + struct EmbeddingLookupSparseOptions; ++struct EmbeddingLookupSparseOptionsBuilder; + struct EmbeddingLookupSparseOptionsT; + + struct GatherOptions; ++struct GatherOptionsBuilder; + struct GatherOptionsT; + + struct TransposeOptions; ++struct TransposeOptionsBuilder; + struct TransposeOptionsT; + + struct ExpOptions; ++struct ExpOptionsBuilder; + struct ExpOptionsT; + + struct CosOptions; ++struct CosOptionsBuilder; + struct CosOptionsT; + + struct ReducerOptions; ++struct ReducerOptionsBuilder; + struct ReducerOptionsT; + + struct SqueezeOptions; ++struct SqueezeOptionsBuilder; + struct SqueezeOptionsT; + + struct SplitOptions; ++struct SplitOptionsBuilder; + struct SplitOptionsT; + + struct SplitVOptions; ++struct SplitVOptionsBuilder; + struct SplitVOptionsT; + + struct StridedSliceOptions; ++struct StridedSliceOptionsBuilder; + struct StridedSliceOptionsT; + + struct LogSoftmaxOptions; ++struct LogSoftmaxOptionsBuilder; + struct LogSoftmaxOptionsT; + + struct CastOptions; ++struct CastOptionsBuilder; + struct CastOptionsT; + + struct DequantizeOptions; ++struct DequantizeOptionsBuilder; + struct DequantizeOptionsT; + + struct MaximumMinimumOptions; ++struct MaximumMinimumOptionsBuilder; + struct MaximumMinimumOptionsT; + + struct TileOptions; ++struct TileOptionsBuilder; + struct TileOptionsT; + + struct ArgMaxOptions; ++struct ArgMaxOptionsBuilder; + struct ArgMaxOptionsT; + + struct ArgMinOptions; ++struct ArgMinOptionsBuilder; + struct ArgMinOptionsT; + + struct GreaterOptions; ++struct GreaterOptionsBuilder; + struct GreaterOptionsT; + + struct GreaterEqualOptions; ++struct GreaterEqualOptionsBuilder; + struct GreaterEqualOptionsT; + + struct LessOptions; ++struct LessOptionsBuilder; + struct LessOptionsT; + + struct LessEqualOptions; ++struct LessEqualOptionsBuilder; + struct LessEqualOptionsT; + + struct NegOptions; ++struct NegOptionsBuilder; + struct NegOptionsT; + + struct SelectOptions; ++struct SelectOptionsBuilder; + struct SelectOptionsT; + + struct SliceOptions; ++struct SliceOptionsBuilder; + struct SliceOptionsT; + + struct TransposeConvOptions; ++struct TransposeConvOptionsBuilder; + struct TransposeConvOptionsT; + + struct ExpandDimsOptions; ++struct ExpandDimsOptionsBuilder; + struct ExpandDimsOptionsT; + + struct SparseToDenseOptions; ++struct SparseToDenseOptionsBuilder; + struct SparseToDenseOptionsT; + + struct EqualOptions; ++struct EqualOptionsBuilder; + struct EqualOptionsT; + + struct NotEqualOptions; ++struct NotEqualOptionsBuilder; + struct NotEqualOptionsT; + + struct ShapeOptions; ++struct ShapeOptionsBuilder; + struct ShapeOptionsT; + + struct RankOptions; ++struct RankOptionsBuilder; + struct RankOptionsT; + + struct PowOptions; ++struct PowOptionsBuilder; + struct PowOptionsT; + + struct FakeQuantOptions; ++struct FakeQuantOptionsBuilder; + struct FakeQuantOptionsT; + + struct PackOptions; ++struct PackOptionsBuilder; + struct PackOptionsT; + + struct LogicalOrOptions; ++struct LogicalOrOptionsBuilder; + struct LogicalOrOptionsT; + + struct OneHotOptions; ++struct OneHotOptionsBuilder; + struct OneHotOptionsT; + + struct AbsOptions; ++struct AbsOptionsBuilder; + struct AbsOptionsT; + + struct HardSwishOptions; ++struct HardSwishOptionsBuilder; + struct HardSwishOptionsT; + + struct LogicalAndOptions; ++struct LogicalAndOptionsBuilder; + struct LogicalAndOptionsT; + + struct LogicalNotOptions; ++struct LogicalNotOptionsBuilder; + struct LogicalNotOptionsT; + + struct UnpackOptions; ++struct UnpackOptionsBuilder; + struct UnpackOptionsT; + + struct FloorDivOptions; ++struct FloorDivOptionsBuilder; + struct FloorDivOptionsT; + + struct SquareOptions; ++struct SquareOptionsBuilder; + struct SquareOptionsT; + + struct ZerosLikeOptions; ++struct ZerosLikeOptionsBuilder; + struct ZerosLikeOptionsT; + + struct FillOptions; ++struct FillOptionsBuilder; + struct FillOptionsT; + + struct FloorModOptions; ++struct FloorModOptionsBuilder; + struct FloorModOptionsT; + + struct RangeOptions; ++struct RangeOptionsBuilder; + struct RangeOptionsT; + + struct LeakyReluOptions; ++struct LeakyReluOptionsBuilder; + struct LeakyReluOptionsT; + + struct SquaredDifferenceOptions; ++struct SquaredDifferenceOptionsBuilder; + struct SquaredDifferenceOptionsT; + + struct MirrorPadOptions; ++struct MirrorPadOptionsBuilder; + struct MirrorPadOptionsT; + + struct UniqueOptions; ++struct UniqueOptionsBuilder; + struct UniqueOptionsT; + + struct ReverseV2Options; ++struct ReverseV2OptionsBuilder; + struct ReverseV2OptionsT; + + struct AddNOptions; ++struct AddNOptionsBuilder; + struct AddNOptionsT; + + struct GatherNdOptions; ++struct GatherNdOptionsBuilder; + struct GatherNdOptionsT; + + struct WhereOptions; ++struct WhereOptionsBuilder; + struct WhereOptionsT; + + struct ReverseSequenceOptions; ++struct ReverseSequenceOptionsBuilder; + struct ReverseSequenceOptionsT; + + struct MatrixDiagOptions; ++struct MatrixDiagOptionsBuilder; + struct MatrixDiagOptionsT; + + struct QuantizeOptions; ++struct QuantizeOptionsBuilder; + struct QuantizeOptionsT; + + struct MatrixSetDiagOptions; ++struct MatrixSetDiagOptionsBuilder; + struct MatrixSetDiagOptionsT; + + struct IfOptions; ++struct IfOptionsBuilder; + struct IfOptionsT; + + struct CallOnceOptions; ++struct CallOnceOptionsBuilder; + struct CallOnceOptionsT; + + struct WhileOptions; ++struct WhileOptionsBuilder; + struct WhileOptionsT; + + struct NonMaxSuppressionV4Options; ++struct NonMaxSuppressionV4OptionsBuilder; + struct NonMaxSuppressionV4OptionsT; + + struct NonMaxSuppressionV5Options; ++struct NonMaxSuppressionV5OptionsBuilder; + struct NonMaxSuppressionV5OptionsT; + + struct ScatterNdOptions; ++struct ScatterNdOptionsBuilder; + struct ScatterNdOptionsT; + + struct SelectV2Options; ++struct SelectV2OptionsBuilder; + struct SelectV2OptionsT; + + struct DensifyOptions; ++struct DensifyOptionsBuilder; + struct DensifyOptionsT; + + struct SegmentSumOptions; ++struct SegmentSumOptionsBuilder; + struct SegmentSumOptionsT; + + struct BatchMatMulOptions; ++struct BatchMatMulOptionsBuilder; + struct BatchMatMulOptionsT; + + struct CumsumOptions; ++struct CumsumOptionsBuilder; + struct CumsumOptionsT; + + struct BroadcastToOptions; ++struct BroadcastToOptionsBuilder; + struct BroadcastToOptionsT; + + struct Rfft2dOptions; ++struct Rfft2dOptionsBuilder; + struct Rfft2dOptionsT; + + struct HashtableOptions; ++struct HashtableOptionsBuilder; + struct HashtableOptionsT; + + struct HashtableFindOptions; ++struct HashtableFindOptionsBuilder; + struct HashtableFindOptionsT; + + struct HashtableImportOptions; ++struct HashtableImportOptionsBuilder; + struct HashtableImportOptionsT; + + struct HashtableSizeOptions; ++struct HashtableSizeOptionsBuilder; + struct HashtableSizeOptionsT; + + struct VarHandleOptions; ++struct VarHandleOptionsBuilder; + struct VarHandleOptionsT; + + struct ReadVariableOptions; ++struct ReadVariableOptionsBuilder; + struct ReadVariableOptionsT; + + struct AssignVariableOptions; ++struct AssignVariableOptionsBuilder; + struct AssignVariableOptionsT; + + struct RandomOptions; ++struct RandomOptionsBuilder; + struct RandomOptionsT; + + struct BucketizeOptions; ++struct BucketizeOptionsBuilder; + struct BucketizeOptionsT; + + struct GeluOptions; ++struct GeluOptionsBuilder; + struct GeluOptionsT; + + struct DynamicUpdateSliceOptions; ++struct DynamicUpdateSliceOptionsBuilder; + struct DynamicUpdateSliceOptionsT; + + struct OperatorCode; ++struct OperatorCodeBuilder; + struct OperatorCodeT; + + struct Operator; ++struct OperatorBuilder; + struct OperatorT; + + struct SubGraph; ++struct SubGraphBuilder; + struct SubGraphT; + + struct Buffer; ++struct BufferBuilder; + struct BufferT; + + struct Metadata; ++struct MetadataBuilder; + struct MetadataT; + + struct TensorMap; ++struct TensorMapBuilder; + struct TensorMapT; + + struct SignatureDef; ++struct SignatureDefBuilder; + struct SignatureDefT; + + struct Model; ++struct ModelBuilder; + struct ModelT; + +-enum TensorType { ++enum TensorType : int8_t { + TensorType_FLOAT32 = 0, + TensorType_FLOAT16 = 1, + TensorType_INT32 = 2, +@@ -496,7 +629,7 @@ inline const char *EnumNameTensorType(TensorType e) { + return EnumNamesTensorType()[index]; + } + +-enum QuantizationDetails { ++enum QuantizationDetails : uint8_t { + QuantizationDetails_NONE = 0, + QuantizationDetails_CustomQuantization = 1, + QuantizationDetails_MIN = QuantizationDetails_NONE, +@@ -534,6 +667,14 @@ template<> struct QuantizationDetailsTraits { + static const QuantizationDetails enum_value = QuantizationDetails_CustomQuantization; + }; + ++template struct QuantizationDetailsUnionTraits { ++ static const QuantizationDetails enum_value = QuantizationDetails_NONE; ++}; ++ ++template<> struct QuantizationDetailsUnionTraits { ++ static const QuantizationDetails enum_value = QuantizationDetails_CustomQuantization; ++}; ++ + struct QuantizationDetailsUnion { + QuantizationDetails type; + void *value; +@@ -542,8 +683,8 @@ struct QuantizationDetailsUnion { + QuantizationDetailsUnion(QuantizationDetailsUnion&& u) FLATBUFFERS_NOEXCEPT : + type(QuantizationDetails_NONE), value(nullptr) + { std::swap(type, u.type); std::swap(value, u.value); } +- QuantizationDetailsUnion(const QuantizationDetailsUnion &) FLATBUFFERS_NOEXCEPT; +- QuantizationDetailsUnion &operator=(const QuantizationDetailsUnion &u) FLATBUFFERS_NOEXCEPT ++ QuantizationDetailsUnion(const QuantizationDetailsUnion &); ++ QuantizationDetailsUnion &operator=(const QuantizationDetailsUnion &u) + { QuantizationDetailsUnion t(u); std::swap(type, t.type); std::swap(value, t.value); return *this; } + QuantizationDetailsUnion &operator=(QuantizationDetailsUnion &&u) FLATBUFFERS_NOEXCEPT + { std::swap(type, u.type); std::swap(value, u.value); return *this; } +@@ -551,17 +692,15 @@ struct QuantizationDetailsUnion { + + void Reset(); + +-#ifndef FLATBUFFERS_CPP98_STL + template + void Set(T&& val) { +- using RT = typename std::remove_reference::type; ++ typedef typename std::remove_reference::type RT; + Reset(); +- type = QuantizationDetailsTraits::enum_value; ++ type = QuantizationDetailsUnionTraits::enum_value; + if (type != QuantizationDetails_NONE) { + value = new RT(std::forward(val)); + } + } +-#endif // FLATBUFFERS_CPP98_STL + + static void *UnPack(const void *obj, QuantizationDetails type, const flatbuffers::resolver_function_t *resolver); + flatbuffers::Offset Pack(flatbuffers::FlatBufferBuilder &_fbb, const flatbuffers::rehasher_function_t *_rehasher = nullptr) const; +@@ -579,7 +718,7 @@ struct QuantizationDetailsUnion { + bool VerifyQuantizationDetails(flatbuffers::Verifier &verifier, const void *obj, QuantizationDetails type); + bool VerifyQuantizationDetailsVector(flatbuffers::Verifier &verifier, const flatbuffers::Vector> *values, const flatbuffers::Vector *types); + +-enum DimensionType { ++enum DimensionType : int8_t { + DimensionType_DENSE = 0, + DimensionType_SPARSE_CSR = 1, + DimensionType_MIN = DimensionType_DENSE, +@@ -609,7 +748,7 @@ inline const char *EnumNameDimensionType(DimensionType e) { + return EnumNamesDimensionType()[index]; + } + +-enum SparseIndexVector { ++enum SparseIndexVector : uint8_t { + SparseIndexVector_NONE = 0, + SparseIndexVector_Int32Vector = 1, + SparseIndexVector_Uint16Vector = 2, +@@ -661,6 +800,22 @@ template<> struct SparseIndexVectorTraits { + static const SparseIndexVector enum_value = SparseIndexVector_Uint8Vector; + }; + ++template struct SparseIndexVectorUnionTraits { ++ static const SparseIndexVector enum_value = SparseIndexVector_NONE; ++}; ++ ++template<> struct SparseIndexVectorUnionTraits { ++ static const SparseIndexVector enum_value = SparseIndexVector_Int32Vector; ++}; ++ ++template<> struct SparseIndexVectorUnionTraits { ++ static const SparseIndexVector enum_value = SparseIndexVector_Uint16Vector; ++}; ++ ++template<> struct SparseIndexVectorUnionTraits { ++ static const SparseIndexVector enum_value = SparseIndexVector_Uint8Vector; ++}; ++ + struct SparseIndexVectorUnion { + SparseIndexVector type; + void *value; +@@ -669,8 +824,8 @@ struct SparseIndexVectorUnion { + SparseIndexVectorUnion(SparseIndexVectorUnion&& u) FLATBUFFERS_NOEXCEPT : + type(SparseIndexVector_NONE), value(nullptr) + { std::swap(type, u.type); std::swap(value, u.value); } +- SparseIndexVectorUnion(const SparseIndexVectorUnion &) FLATBUFFERS_NOEXCEPT; +- SparseIndexVectorUnion &operator=(const SparseIndexVectorUnion &u) FLATBUFFERS_NOEXCEPT ++ SparseIndexVectorUnion(const SparseIndexVectorUnion &); ++ SparseIndexVectorUnion &operator=(const SparseIndexVectorUnion &u) + { SparseIndexVectorUnion t(u); std::swap(type, t.type); std::swap(value, t.value); return *this; } + SparseIndexVectorUnion &operator=(SparseIndexVectorUnion &&u) FLATBUFFERS_NOEXCEPT + { std::swap(type, u.type); std::swap(value, u.value); return *this; } +@@ -678,17 +833,15 @@ struct SparseIndexVectorUnion { + + void Reset(); + +-#ifndef FLATBUFFERS_CPP98_STL + template + void Set(T&& val) { +- using RT = typename std::remove_reference::type; ++ typedef typename std::remove_reference::type RT; + Reset(); +- type = SparseIndexVectorTraits::enum_value; ++ type = SparseIndexVectorUnionTraits::enum_value; + if (type != SparseIndexVector_NONE) { + value = new RT(std::forward(val)); + } + } +-#endif // FLATBUFFERS_CPP98_STL + + static void *UnPack(const void *obj, SparseIndexVector type, const flatbuffers::resolver_function_t *resolver); + flatbuffers::Offset Pack(flatbuffers::FlatBufferBuilder &_fbb, const flatbuffers::rehasher_function_t *_rehasher = nullptr) const; +@@ -722,7 +875,7 @@ struct SparseIndexVectorUnion { + bool VerifySparseIndexVector(flatbuffers::Verifier &verifier, const void *obj, SparseIndexVector type); + bool VerifySparseIndexVectorVector(flatbuffers::Verifier &verifier, const flatbuffers::Vector> *values, const flatbuffers::Vector *types); + +-enum BuiltinOperator { ++enum BuiltinOperator : int32_t { + BuiltinOperator_ADD = 0, + BuiltinOperator_AVERAGE_POOL_2D = 1, + BuiltinOperator_CONCATENATION = 2, +@@ -1202,7 +1355,7 @@ inline const char *EnumNameBuiltinOperator(BuiltinOperator e) { + return EnumNamesBuiltinOperator()[index]; + } + +-enum BuiltinOptions { ++enum BuiltinOptions : uint8_t { + BuiltinOptions_NONE = 0, + BuiltinOptions_Conv2DOptions = 1, + BuiltinOptions_DepthwiseConv2DOptions = 2, +@@ -2052,6 +2205,478 @@ template<> struct BuiltinOptionsTraits { + static const BuiltinOptions enum_value = BuiltinOptions_DynamicUpdateSliceOptions; + }; + ++template struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_NONE; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_Conv2DOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_DepthwiseConv2DOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ConcatEmbeddingsOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_LSHProjectionOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_Pool2DOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SVDFOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_RNNOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_FullyConnectedOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SoftmaxOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ConcatenationOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_AddOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_L2NormOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_LocalResponseNormalizationOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_LSTMOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ResizeBilinearOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_CallOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ReshapeOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SkipGramOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SpaceToDepthOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_EmbeddingLookupSparseOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_MulOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_PadOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_GatherOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_BatchToSpaceNDOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SpaceToBatchNDOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_TransposeOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ReducerOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SubOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_DivOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SqueezeOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SequenceRNNOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_StridedSliceOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ExpOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_TopKV2Options; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SplitOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_LogSoftmaxOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_CastOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_DequantizeOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_MaximumMinimumOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ArgMaxOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_LessOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_NegOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_PadV2Options; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_GreaterOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_GreaterEqualOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_LessEqualOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SelectOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SliceOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_TransposeConvOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SparseToDenseOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_TileOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ExpandDimsOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_EqualOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_NotEqualOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ShapeOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_PowOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ArgMinOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_FakeQuantOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_PackOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_LogicalOrOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_OneHotOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_LogicalAndOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_LogicalNotOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_UnpackOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_FloorDivOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SquareOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ZerosLikeOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_FillOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_BidirectionalSequenceLSTMOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_BidirectionalSequenceRNNOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_UnidirectionalSequenceLSTMOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_FloorModOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_RangeOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ResizeNearestNeighborOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_LeakyReluOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SquaredDifferenceOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_MirrorPadOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_AbsOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SplitVOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_UniqueOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ReverseV2Options; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_AddNOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_GatherNdOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_CosOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_WhereOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_RankOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ReverseSequenceOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_MatrixDiagOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_QuantizeOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_MatrixSetDiagOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_HardSwishOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_IfOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_WhileOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_DepthToSpaceOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_NonMaxSuppressionV4Options; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_NonMaxSuppressionV5Options; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ScatterNdOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SelectV2Options; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_DensifyOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_SegmentSumOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_BatchMatMulOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_CumsumOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_CallOnceOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_BroadcastToOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_Rfft2dOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_Conv3DOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_HashtableOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_HashtableFindOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_HashtableImportOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_HashtableSizeOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_VarHandleOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_ReadVariableOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_AssignVariableOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_RandomOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_BucketizeOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_GeluOptions; ++}; ++ ++template<> struct BuiltinOptionsUnionTraits { ++ static const BuiltinOptions enum_value = BuiltinOptions_DynamicUpdateSliceOptions; ++}; ++ + struct BuiltinOptionsUnion { + BuiltinOptions type; + void *value; +@@ -2060,8 +2685,8 @@ struct BuiltinOptionsUnion { + BuiltinOptionsUnion(BuiltinOptionsUnion&& u) FLATBUFFERS_NOEXCEPT : + type(BuiltinOptions_NONE), value(nullptr) + { std::swap(type, u.type); std::swap(value, u.value); } +- BuiltinOptionsUnion(const BuiltinOptionsUnion &) FLATBUFFERS_NOEXCEPT; +- BuiltinOptionsUnion &operator=(const BuiltinOptionsUnion &u) FLATBUFFERS_NOEXCEPT ++ BuiltinOptionsUnion(const BuiltinOptionsUnion &); ++ BuiltinOptionsUnion &operator=(const BuiltinOptionsUnion &u) + { BuiltinOptionsUnion t(u); std::swap(type, t.type); std::swap(value, t.value); return *this; } + BuiltinOptionsUnion &operator=(BuiltinOptionsUnion &&u) FLATBUFFERS_NOEXCEPT + { std::swap(type, u.type); std::swap(value, u.value); return *this; } +@@ -2069,17 +2694,15 @@ struct BuiltinOptionsUnion { + + void Reset(); + +-#ifndef FLATBUFFERS_CPP98_STL + template + void Set(T&& val) { +- using RT = typename std::remove_reference::type; ++ typedef typename std::remove_reference::type RT; + Reset(); +- type = BuiltinOptionsTraits::enum_value; ++ type = BuiltinOptionsUnionTraits::enum_value; + if (type != BuiltinOptions_NONE) { + value = new RT(std::forward(val)); + } + } +-#endif // FLATBUFFERS_CPP98_STL + + static void *UnPack(const void *obj, BuiltinOptions type, const flatbuffers::resolver_function_t *resolver); + flatbuffers::Offset Pack(flatbuffers::FlatBufferBuilder &_fbb, const flatbuffers::rehasher_function_t *_rehasher = nullptr) const; +@@ -3025,7 +3648,7 @@ struct BuiltinOptionsUnion { + bool VerifyBuiltinOptions(flatbuffers::Verifier &verifier, const void *obj, BuiltinOptions type); + bool VerifyBuiltinOptionsVector(flatbuffers::Verifier &verifier, const flatbuffers::Vector> *values, const flatbuffers::Vector *types); + +-enum Padding { ++enum Padding : int8_t { + Padding_SAME = 0, + Padding_VALID = 1, + Padding_MIN = Padding_SAME, +@@ -3055,7 +3678,7 @@ inline const char *EnumNamePadding(Padding e) { + return EnumNamesPadding()[index]; + } + +-enum ActivationFunctionType { ++enum ActivationFunctionType : int8_t { + ActivationFunctionType_NONE = 0, + ActivationFunctionType_RELU = 1, + ActivationFunctionType_RELU_N1_TO_1 = 2, +@@ -3097,7 +3720,7 @@ inline const char *EnumNameActivationFunctionType(ActivationFunctionType e) { + return EnumNamesActivationFunctionType()[index]; + } + +-enum LSHProjectionType { ++enum LSHProjectionType : int8_t { + LSHProjectionType_UNKNOWN = 0, + LSHProjectionType_SPARSE = 1, + LSHProjectionType_DENSE = 2, +@@ -3130,7 +3753,7 @@ inline const char *EnumNameLSHProjectionType(LSHProjectionType e) { + return EnumNamesLSHProjectionType()[index]; + } + +-enum FullyConnectedOptionsWeightsFormat { ++enum FullyConnectedOptionsWeightsFormat : int8_t { + FullyConnectedOptionsWeightsFormat_DEFAULT = 0, + FullyConnectedOptionsWeightsFormat_SHUFFLED4x16INT8 = 1, + FullyConnectedOptionsWeightsFormat_MIN = FullyConnectedOptionsWeightsFormat_DEFAULT, +@@ -3160,7 +3783,7 @@ inline const char *EnumNameFullyConnectedOptionsWeightsFormat(FullyConnectedOpti + return EnumNamesFullyConnectedOptionsWeightsFormat()[index]; + } + +-enum LSTMKernelType { ++enum LSTMKernelType : int8_t { + LSTMKernelType_FULL = 0, + LSTMKernelType_BASIC = 1, + LSTMKernelType_MIN = LSTMKernelType_FULL, +@@ -3190,7 +3813,7 @@ inline const char *EnumNameLSTMKernelType(LSTMKernelType e) { + return EnumNamesLSTMKernelType()[index]; + } + +-enum CombinerType { ++enum CombinerType : int8_t { + CombinerType_SUM = 0, + CombinerType_MEAN = 1, + CombinerType_SQRTN = 2, +@@ -3223,7 +3846,7 @@ inline const char *EnumNameCombinerType(CombinerType e) { + return EnumNamesCombinerType()[index]; + } + +-enum MirrorPadMode { ++enum MirrorPadMode : int8_t { + MirrorPadMode_REFLECT = 0, + MirrorPadMode_SYMMETRIC = 1, + MirrorPadMode_MIN = MirrorPadMode_REFLECT, +@@ -3253,7 +3876,7 @@ inline const char *EnumNameMirrorPadMode(MirrorPadMode e) { + return EnumNamesMirrorPadMode()[index]; + } + +-enum CustomOptionsFormat { ++enum CustomOptionsFormat : int8_t { + CustomOptionsFormat_FLEXBUFFERS = 0, + CustomOptionsFormat_MIN = CustomOptionsFormat_FLEXBUFFERS, + CustomOptionsFormat_MAX = CustomOptionsFormat_FLEXBUFFERS +@@ -3282,13 +3905,12 @@ inline const char *EnumNameCustomOptionsFormat(CustomOptionsFormat e) { + + struct CustomQuantizationT : public flatbuffers::NativeTable { + typedef CustomQuantization TableType; +- std::vector custom; +- CustomQuantizationT() { +- } ++ std::vector custom{}; + }; + + struct CustomQuantization FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef CustomQuantizationT NativeTableType; ++ typedef CustomQuantizationBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_CUSTOM = 4 + }; +@@ -3307,6 +3929,7 @@ struct CustomQuantization FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct CustomQuantizationBuilder { ++ typedef CustomQuantization Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_custom(flatbuffers::Offset> custom) { +@@ -3316,7 +3939,6 @@ struct CustomQuantizationBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- CustomQuantizationBuilder &operator=(const CustomQuantizationBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -3346,19 +3968,17 @@ flatbuffers::Offset CreateCustomQuantization(flatbuffers::Fl + + struct QuantizationParametersT : public flatbuffers::NativeTable { + typedef QuantizationParameters TableType; +- std::vector min; +- std::vector max; +- std::vector scale; +- std::vector zero_point; +- tflite::QuantizationDetailsUnion details; +- int32_t quantized_dimension; +- QuantizationParametersT() +- : quantized_dimension(0) { +- } ++ std::vector min{}; ++ std::vector max{}; ++ std::vector scale{}; ++ std::vector zero_point{}; ++ tflite::QuantizationDetailsUnion details{}; ++ int32_t quantized_dimension = 0; + }; + + struct QuantizationParameters FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef QuantizationParametersT NativeTableType; ++ typedef QuantizationParametersBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_MIN = 4, + VT_MAX = 6, +@@ -3419,6 +4039,7 @@ template<> inline const tflite::CustomQuantization *QuantizationParameters::deta + } + + struct QuantizationParametersBuilder { ++ typedef QuantizationParameters Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_min(flatbuffers::Offset> min) { +@@ -3446,7 +4067,6 @@ struct QuantizationParametersBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- QuantizationParametersBuilder &operator=(const QuantizationParametersBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -3502,13 +4122,12 @@ flatbuffers::Offset CreateQuantizationParameters(flatbuf + + struct Int32VectorT : public flatbuffers::NativeTable { + typedef Int32Vector TableType; +- std::vector values; +- Int32VectorT() { +- } ++ std::vector values{}; + }; + + struct Int32Vector FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef Int32VectorT NativeTableType; ++ typedef Int32VectorBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_VALUES = 4 + }; +@@ -3527,6 +4146,7 @@ struct Int32Vector FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct Int32VectorBuilder { ++ typedef Int32Vector Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_values(flatbuffers::Offset> values) { +@@ -3536,7 +4156,6 @@ struct Int32VectorBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- Int32VectorBuilder &operator=(const Int32VectorBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -3565,13 +4184,12 @@ flatbuffers::Offset CreateInt32Vector(flatbuffers::FlatBufferBuilde + + struct Uint16VectorT : public flatbuffers::NativeTable { + typedef Uint16Vector TableType; +- std::vector values; +- Uint16VectorT() { +- } ++ std::vector values{}; + }; + + struct Uint16Vector FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef Uint16VectorT NativeTableType; ++ typedef Uint16VectorBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_VALUES = 4 + }; +@@ -3590,6 +4208,7 @@ struct Uint16Vector FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct Uint16VectorBuilder { ++ typedef Uint16Vector Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_values(flatbuffers::Offset> values) { +@@ -3599,7 +4218,6 @@ struct Uint16VectorBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- Uint16VectorBuilder &operator=(const Uint16VectorBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -3629,13 +4247,12 @@ flatbuffers::Offset CreateUint16Vector(flatbuffers::FlatBufferBuil + + struct Uint8VectorT : public flatbuffers::NativeTable { + typedef Uint8Vector TableType; +- std::vector values; +- Uint8VectorT() { +- } ++ std::vector values{}; + }; + + struct Uint8Vector FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef Uint8VectorT NativeTableType; ++ typedef Uint8VectorBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_VALUES = 4 + }; +@@ -3654,6 +4271,7 @@ struct Uint8Vector FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct Uint8VectorBuilder { ++ typedef Uint8Vector Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_values(flatbuffers::Offset> values) { +@@ -3663,7 +4281,6 @@ struct Uint8VectorBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- Uint8VectorBuilder &operator=(const Uint8VectorBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -3693,18 +4310,15 @@ flatbuffers::Offset CreateUint8Vector(flatbuffers::FlatBufferBuilde + + struct DimensionMetadataT : public flatbuffers::NativeTable { + typedef DimensionMetadata TableType; +- tflite::DimensionType format; +- int32_t dense_size; +- tflite::SparseIndexVectorUnion array_segments; +- tflite::SparseIndexVectorUnion array_indices; +- DimensionMetadataT() +- : format(tflite::DimensionType_DENSE), +- dense_size(0) { +- } ++ tflite::DimensionType format = tflite::DimensionType_DENSE; ++ int32_t dense_size = 0; ++ tflite::SparseIndexVectorUnion array_segments{}; ++ tflite::SparseIndexVectorUnion array_indices{}; + }; + + struct DimensionMetadata FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef DimensionMetadataT NativeTableType; ++ typedef DimensionMetadataBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FORMAT = 4, + VT_DENSE_SIZE = 6, +@@ -3793,6 +4407,7 @@ template<> inline const tflite::Uint8Vector *DimensionMetadata::array_indices_as + } + + struct DimensionMetadataBuilder { ++ typedef DimensionMetadata Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_format(tflite::DimensionType format) { +@@ -3817,7 +4432,6 @@ struct DimensionMetadataBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- DimensionMetadataBuilder &operator=(const DimensionMetadataBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -3847,15 +4461,14 @@ flatbuffers::Offset CreateDimensionMetadata(flatbuffers::Flat + + struct SparsityParametersT : public flatbuffers::NativeTable { + typedef SparsityParameters TableType; +- std::vector traversal_order; +- std::vector block_map; +- std::vector> dim_metadata; +- SparsityParametersT() { +- } ++ std::vector traversal_order{}; ++ std::vector block_map{}; ++ std::vector> dim_metadata{}; + }; + + struct SparsityParameters FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SparsityParametersT NativeTableType; ++ typedef SparsityParametersBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_TRAVERSAL_ORDER = 4, + VT_BLOCK_MAP = 6, +@@ -3887,6 +4500,7 @@ struct SparsityParameters FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SparsityParametersBuilder { ++ typedef SparsityParameters Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_traversal_order(flatbuffers::Offset> traversal_order) { +@@ -3902,7 +4516,6 @@ struct SparsityParametersBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SparsityParametersBuilder &operator=(const SparsityParametersBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -3941,23 +4554,19 @@ flatbuffers::Offset CreateSparsityParameters(flatbuffers::Fl + + struct TensorT : public flatbuffers::NativeTable { + typedef Tensor TableType; +- std::vector shape; +- tflite::TensorType type; +- uint32_t buffer; +- std::string name; +- std::unique_ptr quantization; +- bool is_variable; +- std::unique_ptr sparsity; +- std::vector shape_signature; +- TensorT() +- : type(tflite::TensorType_FLOAT32), +- buffer(0), +- is_variable(false) { +- } ++ std::vector shape{}; ++ tflite::TensorType type = tflite::TensorType_FLOAT32; ++ uint32_t buffer = 0; ++ std::string name{}; ++ std::unique_ptr quantization{}; ++ bool is_variable = false; ++ std::unique_ptr sparsity{}; ++ std::vector shape_signature{}; + }; + + struct Tensor FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef TensorT NativeTableType; ++ typedef TensorBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_SHAPE = 4, + VT_TYPE = 6, +@@ -4015,6 +4624,7 @@ struct Tensor FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct TensorBuilder { ++ typedef Tensor Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_shape(flatbuffers::Offset> shape) { +@@ -4045,7 +4655,6 @@ struct TensorBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- TensorBuilder &operator=(const TensorBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -4104,24 +4713,17 @@ flatbuffers::Offset CreateTensor(flatbuffers::FlatBufferBuilder &_fbb, c + + struct Conv2DOptionsT : public flatbuffers::NativeTable { + typedef Conv2DOptions TableType; +- tflite::Padding padding; +- int32_t stride_w; +- int32_t stride_h; +- tflite::ActivationFunctionType fused_activation_function; +- int32_t dilation_w_factor; +- int32_t dilation_h_factor; +- Conv2DOptionsT() +- : padding(tflite::Padding_SAME), +- stride_w(0), +- stride_h(0), +- fused_activation_function(tflite::ActivationFunctionType_NONE), +- dilation_w_factor(1), +- dilation_h_factor(1) { +- } ++ tflite::Padding padding = tflite::Padding_SAME; ++ int32_t stride_w = 0; ++ int32_t stride_h = 0; ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ int32_t dilation_w_factor = 1; ++ int32_t dilation_h_factor = 1; + }; + + struct Conv2DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef Conv2DOptionsT NativeTableType; ++ typedef Conv2DOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_PADDING = 4, + VT_STRIDE_W = 6, +@@ -4164,6 +4766,7 @@ struct Conv2DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct Conv2DOptionsBuilder { ++ typedef Conv2DOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_padding(tflite::Padding padding) { +@@ -4188,7 +4791,6 @@ struct Conv2DOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- Conv2DOptionsBuilder &operator=(const Conv2DOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -4218,28 +4820,19 @@ flatbuffers::Offset CreateConv2DOptions(flatbuffers::FlatBufferBu + + struct Conv3DOptionsT : public flatbuffers::NativeTable { + typedef Conv3DOptions TableType; +- tflite::Padding padding; +- int32_t stride_d; +- int32_t stride_w; +- int32_t stride_h; +- tflite::ActivationFunctionType fused_activation_function; +- int32_t dilation_d_factor; +- int32_t dilation_w_factor; +- int32_t dilation_h_factor; +- Conv3DOptionsT() +- : padding(tflite::Padding_SAME), +- stride_d(0), +- stride_w(0), +- stride_h(0), +- fused_activation_function(tflite::ActivationFunctionType_NONE), +- dilation_d_factor(1), +- dilation_w_factor(1), +- dilation_h_factor(1) { +- } ++ tflite::Padding padding = tflite::Padding_SAME; ++ int32_t stride_d = 0; ++ int32_t stride_w = 0; ++ int32_t stride_h = 0; ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ int32_t dilation_d_factor = 1; ++ int32_t dilation_w_factor = 1; ++ int32_t dilation_h_factor = 1; + }; + + struct Conv3DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef Conv3DOptionsT NativeTableType; ++ typedef Conv3DOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_PADDING = 4, + VT_STRIDE_D = 6, +@@ -4292,6 +4885,7 @@ struct Conv3DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct Conv3DOptionsBuilder { ++ typedef Conv3DOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_padding(tflite::Padding padding) { +@@ -4322,7 +4916,6 @@ struct Conv3DOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- Conv3DOptionsBuilder &operator=(const Conv3DOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -4356,24 +4949,17 @@ flatbuffers::Offset CreateConv3DOptions(flatbuffers::FlatBufferBu + + struct Pool2DOptionsT : public flatbuffers::NativeTable { + typedef Pool2DOptions TableType; +- tflite::Padding padding; +- int32_t stride_w; +- int32_t stride_h; +- int32_t filter_width; +- int32_t filter_height; +- tflite::ActivationFunctionType fused_activation_function; +- Pool2DOptionsT() +- : padding(tflite::Padding_SAME), +- stride_w(0), +- stride_h(0), +- filter_width(0), +- filter_height(0), +- fused_activation_function(tflite::ActivationFunctionType_NONE) { +- } ++ tflite::Padding padding = tflite::Padding_SAME; ++ int32_t stride_w = 0; ++ int32_t stride_h = 0; ++ int32_t filter_width = 0; ++ int32_t filter_height = 0; ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; + }; + + struct Pool2DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef Pool2DOptionsT NativeTableType; ++ typedef Pool2DOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_PADDING = 4, + VT_STRIDE_W = 6, +@@ -4416,6 +5002,7 @@ struct Pool2DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct Pool2DOptionsBuilder { ++ typedef Pool2DOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_padding(tflite::Padding padding) { +@@ -4440,7 +5027,6 @@ struct Pool2DOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- Pool2DOptionsBuilder &operator=(const Pool2DOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -4470,26 +5056,18 @@ flatbuffers::Offset CreatePool2DOptions(flatbuffers::FlatBufferBu + + struct DepthwiseConv2DOptionsT : public flatbuffers::NativeTable { + typedef DepthwiseConv2DOptions TableType; +- tflite::Padding padding; +- int32_t stride_w; +- int32_t stride_h; +- int32_t depth_multiplier; +- tflite::ActivationFunctionType fused_activation_function; +- int32_t dilation_w_factor; +- int32_t dilation_h_factor; +- DepthwiseConv2DOptionsT() +- : padding(tflite::Padding_SAME), +- stride_w(0), +- stride_h(0), +- depth_multiplier(0), +- fused_activation_function(tflite::ActivationFunctionType_NONE), +- dilation_w_factor(1), +- dilation_h_factor(1) { +- } ++ tflite::Padding padding = tflite::Padding_SAME; ++ int32_t stride_w = 0; ++ int32_t stride_h = 0; ++ int32_t depth_multiplier = 0; ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ int32_t dilation_w_factor = 1; ++ int32_t dilation_h_factor = 1; + }; + + struct DepthwiseConv2DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef DepthwiseConv2DOptionsT NativeTableType; ++ typedef DepthwiseConv2DOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_PADDING = 4, + VT_STRIDE_W = 6, +@@ -4537,6 +5115,7 @@ struct DepthwiseConv2DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tab + }; + + struct DepthwiseConv2DOptionsBuilder { ++ typedef DepthwiseConv2DOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_padding(tflite::Padding padding) { +@@ -4564,7 +5143,6 @@ struct DepthwiseConv2DOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- DepthwiseConv2DOptionsBuilder &operator=(const DepthwiseConv2DOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -4596,16 +5174,14 @@ flatbuffers::Offset CreateDepthwiseConv2DOptions(flatbuf + + struct ConcatEmbeddingsOptionsT : public flatbuffers::NativeTable { + typedef ConcatEmbeddingsOptions TableType; +- int32_t num_channels; +- std::vector num_columns_per_channel; +- std::vector embedding_dim_per_channel; +- ConcatEmbeddingsOptionsT() +- : num_channels(0) { +- } ++ int32_t num_channels = 0; ++ std::vector num_columns_per_channel{}; ++ std::vector embedding_dim_per_channel{}; + }; + + struct ConcatEmbeddingsOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ConcatEmbeddingsOptionsT NativeTableType; ++ typedef ConcatEmbeddingsOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NUM_CHANNELS = 4, + VT_NUM_COLUMNS_PER_CHANNEL = 6, +@@ -4635,6 +5211,7 @@ struct ConcatEmbeddingsOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Ta + }; + + struct ConcatEmbeddingsOptionsBuilder { ++ typedef ConcatEmbeddingsOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_num_channels(int32_t num_channels) { +@@ -4650,7 +5227,6 @@ struct ConcatEmbeddingsOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ConcatEmbeddingsOptionsBuilder &operator=(const ConcatEmbeddingsOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -4688,14 +5264,12 @@ flatbuffers::Offset CreateConcatEmbeddingsOptions(flatb + + struct LSHProjectionOptionsT : public flatbuffers::NativeTable { + typedef LSHProjectionOptions TableType; +- tflite::LSHProjectionType type; +- LSHProjectionOptionsT() +- : type(tflite::LSHProjectionType_UNKNOWN) { +- } ++ tflite::LSHProjectionType type = tflite::LSHProjectionType_UNKNOWN; + }; + + struct LSHProjectionOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef LSHProjectionOptionsT NativeTableType; ++ typedef LSHProjectionOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_TYPE = 4 + }; +@@ -4713,6 +5287,7 @@ struct LSHProjectionOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct LSHProjectionOptionsBuilder { ++ typedef LSHProjectionOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_type(tflite::LSHProjectionType type) { +@@ -4722,7 +5297,6 @@ struct LSHProjectionOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- LSHProjectionOptionsBuilder &operator=(const LSHProjectionOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -4742,18 +5316,14 @@ flatbuffers::Offset CreateLSHProjectionOptions(flatbuffers + + struct SVDFOptionsT : public flatbuffers::NativeTable { + typedef SVDFOptions TableType; +- int32_t rank; +- tflite::ActivationFunctionType fused_activation_function; +- bool asymmetric_quantize_inputs; +- SVDFOptionsT() +- : rank(0), +- fused_activation_function(tflite::ActivationFunctionType_NONE), +- asymmetric_quantize_inputs(false) { +- } ++ int32_t rank = 0; ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ bool asymmetric_quantize_inputs = false; + }; + + struct SVDFOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SVDFOptionsT NativeTableType; ++ typedef SVDFOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_RANK = 4, + VT_FUSED_ACTIVATION_FUNCTION = 6, +@@ -4781,6 +5351,7 @@ struct SVDFOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SVDFOptionsBuilder { ++ typedef SVDFOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_rank(int32_t rank) { +@@ -4796,7 +5367,6 @@ struct SVDFOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SVDFOptionsBuilder &operator=(const SVDFOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -4820,16 +5390,13 @@ flatbuffers::Offset CreateSVDFOptions(flatbuffers::FlatBufferBuilde + + struct RNNOptionsT : public flatbuffers::NativeTable { + typedef RNNOptions TableType; +- tflite::ActivationFunctionType fused_activation_function; +- bool asymmetric_quantize_inputs; +- RNNOptionsT() +- : fused_activation_function(tflite::ActivationFunctionType_NONE), +- asymmetric_quantize_inputs(false) { +- } ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ bool asymmetric_quantize_inputs = false; + }; + + struct RNNOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef RNNOptionsT NativeTableType; ++ typedef RNNOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FUSED_ACTIVATION_FUNCTION = 4, + VT_ASYMMETRIC_QUANTIZE_INPUTS = 6 +@@ -4852,6 +5419,7 @@ struct RNNOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct RNNOptionsBuilder { ++ typedef RNNOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_fused_activation_function(tflite::ActivationFunctionType fused_activation_function) { +@@ -4864,7 +5432,6 @@ struct RNNOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- RNNOptionsBuilder &operator=(const RNNOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -4886,18 +5453,14 @@ flatbuffers::Offset CreateRNNOptions(flatbuffers::FlatBufferBuilder + + struct SequenceRNNOptionsT : public flatbuffers::NativeTable { + typedef SequenceRNNOptions TableType; +- bool time_major; +- tflite::ActivationFunctionType fused_activation_function; +- bool asymmetric_quantize_inputs; +- SequenceRNNOptionsT() +- : time_major(false), +- fused_activation_function(tflite::ActivationFunctionType_NONE), +- asymmetric_quantize_inputs(false) { +- } ++ bool time_major = false; ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ bool asymmetric_quantize_inputs = false; + }; + + struct SequenceRNNOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SequenceRNNOptionsT NativeTableType; ++ typedef SequenceRNNOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_TIME_MAJOR = 4, + VT_FUSED_ACTIVATION_FUNCTION = 6, +@@ -4925,6 +5488,7 @@ struct SequenceRNNOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SequenceRNNOptionsBuilder { ++ typedef SequenceRNNOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_time_major(bool time_major) { +@@ -4940,7 +5504,6 @@ struct SequenceRNNOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SequenceRNNOptionsBuilder &operator=(const SequenceRNNOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -4964,20 +5527,15 @@ flatbuffers::Offset CreateSequenceRNNOptions(flatbuffers::Fl + + struct BidirectionalSequenceRNNOptionsT : public flatbuffers::NativeTable { + typedef BidirectionalSequenceRNNOptions TableType; +- bool time_major; +- tflite::ActivationFunctionType fused_activation_function; +- bool merge_outputs; +- bool asymmetric_quantize_inputs; +- BidirectionalSequenceRNNOptionsT() +- : time_major(false), +- fused_activation_function(tflite::ActivationFunctionType_NONE), +- merge_outputs(false), +- asymmetric_quantize_inputs(false) { +- } ++ bool time_major = false; ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ bool merge_outputs = false; ++ bool asymmetric_quantize_inputs = false; + }; + + struct BidirectionalSequenceRNNOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BidirectionalSequenceRNNOptionsT NativeTableType; ++ typedef BidirectionalSequenceRNNOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_TIME_MAJOR = 4, + VT_FUSED_ACTIVATION_FUNCTION = 6, +@@ -5010,6 +5568,7 @@ struct BidirectionalSequenceRNNOptions FLATBUFFERS_FINAL_CLASS : private flatbuf + }; + + struct BidirectionalSequenceRNNOptionsBuilder { ++ typedef BidirectionalSequenceRNNOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_time_major(bool time_major) { +@@ -5028,7 +5587,6 @@ struct BidirectionalSequenceRNNOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BidirectionalSequenceRNNOptionsBuilder &operator=(const BidirectionalSequenceRNNOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5054,20 +5612,15 @@ flatbuffers::Offset CreateBidirectionalSequence + + struct FullyConnectedOptionsT : public flatbuffers::NativeTable { + typedef FullyConnectedOptions TableType; +- tflite::ActivationFunctionType fused_activation_function; +- tflite::FullyConnectedOptionsWeightsFormat weights_format; +- bool keep_num_dims; +- bool asymmetric_quantize_inputs; +- FullyConnectedOptionsT() +- : fused_activation_function(tflite::ActivationFunctionType_NONE), +- weights_format(tflite::FullyConnectedOptionsWeightsFormat_DEFAULT), +- keep_num_dims(false), +- asymmetric_quantize_inputs(false) { +- } ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ tflite::FullyConnectedOptionsWeightsFormat weights_format = tflite::FullyConnectedOptionsWeightsFormat_DEFAULT; ++ bool keep_num_dims = false; ++ bool asymmetric_quantize_inputs = false; + }; + + struct FullyConnectedOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef FullyConnectedOptionsT NativeTableType; ++ typedef FullyConnectedOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FUSED_ACTIVATION_FUNCTION = 4, + VT_WEIGHTS_FORMAT = 6, +@@ -5100,6 +5653,7 @@ struct FullyConnectedOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tabl + }; + + struct FullyConnectedOptionsBuilder { ++ typedef FullyConnectedOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_fused_activation_function(tflite::ActivationFunctionType fused_activation_function) { +@@ -5118,7 +5672,6 @@ struct FullyConnectedOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- FullyConnectedOptionsBuilder &operator=(const FullyConnectedOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5144,14 +5697,12 @@ flatbuffers::Offset CreateFullyConnectedOptions(flatbuffe + + struct SoftmaxOptionsT : public flatbuffers::NativeTable { + typedef SoftmaxOptions TableType; +- float beta; +- SoftmaxOptionsT() +- : beta(0.0f) { +- } ++ float beta = 0.0f; + }; + + struct SoftmaxOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SoftmaxOptionsT NativeTableType; ++ typedef SoftmaxOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_BETA = 4 + }; +@@ -5169,6 +5720,7 @@ struct SoftmaxOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SoftmaxOptionsBuilder { ++ typedef SoftmaxOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_beta(float beta) { +@@ -5178,7 +5730,6 @@ struct SoftmaxOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SoftmaxOptionsBuilder &operator=(const SoftmaxOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5198,16 +5749,13 @@ flatbuffers::Offset CreateSoftmaxOptions(flatbuffers::FlatBuffer + + struct ConcatenationOptionsT : public flatbuffers::NativeTable { + typedef ConcatenationOptions TableType; +- int32_t axis; +- tflite::ActivationFunctionType fused_activation_function; +- ConcatenationOptionsT() +- : axis(0), +- fused_activation_function(tflite::ActivationFunctionType_NONE) { +- } ++ int32_t axis = 0; ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; + }; + + struct ConcatenationOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ConcatenationOptionsT NativeTableType; ++ typedef ConcatenationOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_AXIS = 4, + VT_FUSED_ACTIVATION_FUNCTION = 6 +@@ -5230,6 +5778,7 @@ struct ConcatenationOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct ConcatenationOptionsBuilder { ++ typedef ConcatenationOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_axis(int32_t axis) { +@@ -5242,7 +5791,6 @@ struct ConcatenationOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ConcatenationOptionsBuilder &operator=(const ConcatenationOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5264,16 +5812,13 @@ flatbuffers::Offset CreateConcatenationOptions(flatbuffers + + struct AddOptionsT : public flatbuffers::NativeTable { + typedef AddOptions TableType; +- tflite::ActivationFunctionType fused_activation_function; +- bool pot_scale_int16; +- AddOptionsT() +- : fused_activation_function(tflite::ActivationFunctionType_NONE), +- pot_scale_int16(true) { +- } ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ bool pot_scale_int16 = true; + }; + + struct AddOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef AddOptionsT NativeTableType; ++ typedef AddOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FUSED_ACTIVATION_FUNCTION = 4, + VT_POT_SCALE_INT16 = 6 +@@ -5296,6 +5841,7 @@ struct AddOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct AddOptionsBuilder { ++ typedef AddOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_fused_activation_function(tflite::ActivationFunctionType fused_activation_function) { +@@ -5308,7 +5854,6 @@ struct AddOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- AddOptionsBuilder &operator=(const AddOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5330,14 +5875,12 @@ flatbuffers::Offset CreateAddOptions(flatbuffers::FlatBufferBuilder + + struct MulOptionsT : public flatbuffers::NativeTable { + typedef MulOptions TableType; +- tflite::ActivationFunctionType fused_activation_function; +- MulOptionsT() +- : fused_activation_function(tflite::ActivationFunctionType_NONE) { +- } ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; + }; + + struct MulOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef MulOptionsT NativeTableType; ++ typedef MulOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FUSED_ACTIVATION_FUNCTION = 4 + }; +@@ -5355,6 +5898,7 @@ struct MulOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct MulOptionsBuilder { ++ typedef MulOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_fused_activation_function(tflite::ActivationFunctionType fused_activation_function) { +@@ -5364,7 +5908,6 @@ struct MulOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- MulOptionsBuilder &operator=(const MulOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5384,14 +5927,12 @@ flatbuffers::Offset CreateMulOptions(flatbuffers::FlatBufferBuilder + + struct L2NormOptionsT : public flatbuffers::NativeTable { + typedef L2NormOptions TableType; +- tflite::ActivationFunctionType fused_activation_function; +- L2NormOptionsT() +- : fused_activation_function(tflite::ActivationFunctionType_NONE) { +- } ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; + }; + + struct L2NormOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef L2NormOptionsT NativeTableType; ++ typedef L2NormOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FUSED_ACTIVATION_FUNCTION = 4 + }; +@@ -5409,6 +5950,7 @@ struct L2NormOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct L2NormOptionsBuilder { ++ typedef L2NormOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_fused_activation_function(tflite::ActivationFunctionType fused_activation_function) { +@@ -5418,7 +5960,6 @@ struct L2NormOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- L2NormOptionsBuilder &operator=(const L2NormOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5438,20 +5979,15 @@ flatbuffers::Offset CreateL2NormOptions(flatbuffers::FlatBufferBu + + struct LocalResponseNormalizationOptionsT : public flatbuffers::NativeTable { + typedef LocalResponseNormalizationOptions TableType; +- int32_t radius; +- float bias; +- float alpha; +- float beta; +- LocalResponseNormalizationOptionsT() +- : radius(0), +- bias(0.0f), +- alpha(0.0f), +- beta(0.0f) { +- } ++ int32_t radius = 0; ++ float bias = 0.0f; ++ float alpha = 0.0f; ++ float beta = 0.0f; + }; + + struct LocalResponseNormalizationOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef LocalResponseNormalizationOptionsT NativeTableType; ++ typedef LocalResponseNormalizationOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_RADIUS = 4, + VT_BIAS = 6, +@@ -5484,6 +6020,7 @@ struct LocalResponseNormalizationOptions FLATBUFFERS_FINAL_CLASS : private flatb + }; + + struct LocalResponseNormalizationOptionsBuilder { ++ typedef LocalResponseNormalizationOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_radius(int32_t radius) { +@@ -5502,7 +6039,6 @@ struct LocalResponseNormalizationOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- LocalResponseNormalizationOptionsBuilder &operator=(const LocalResponseNormalizationOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5528,22 +6064,16 @@ flatbuffers::Offset CreateLocalResponseNormal + + struct LSTMOptionsT : public flatbuffers::NativeTable { + typedef LSTMOptions TableType; +- tflite::ActivationFunctionType fused_activation_function; +- float cell_clip; +- float proj_clip; +- tflite::LSTMKernelType kernel_type; +- bool asymmetric_quantize_inputs; +- LSTMOptionsT() +- : fused_activation_function(tflite::ActivationFunctionType_NONE), +- cell_clip(0.0f), +- proj_clip(0.0f), +- kernel_type(tflite::LSTMKernelType_FULL), +- asymmetric_quantize_inputs(false) { +- } ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ float cell_clip = 0.0f; ++ float proj_clip = 0.0f; ++ tflite::LSTMKernelType kernel_type = tflite::LSTMKernelType_FULL; ++ bool asymmetric_quantize_inputs = false; + }; + + struct LSTMOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef LSTMOptionsT NativeTableType; ++ typedef LSTMOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FUSED_ACTIVATION_FUNCTION = 4, + VT_CELL_CLIP = 6, +@@ -5581,6 +6111,7 @@ struct LSTMOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct LSTMOptionsBuilder { ++ typedef LSTMOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_fused_activation_function(tflite::ActivationFunctionType fused_activation_function) { +@@ -5602,7 +6133,6 @@ struct LSTMOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- LSTMOptionsBuilder &operator=(const LSTMOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5630,22 +6160,16 @@ flatbuffers::Offset CreateLSTMOptions(flatbuffers::FlatBufferBuilde + + struct UnidirectionalSequenceLSTMOptionsT : public flatbuffers::NativeTable { + typedef UnidirectionalSequenceLSTMOptions TableType; +- tflite::ActivationFunctionType fused_activation_function; +- float cell_clip; +- float proj_clip; +- bool time_major; +- bool asymmetric_quantize_inputs; +- UnidirectionalSequenceLSTMOptionsT() +- : fused_activation_function(tflite::ActivationFunctionType_NONE), +- cell_clip(0.0f), +- proj_clip(0.0f), +- time_major(false), +- asymmetric_quantize_inputs(false) { +- } ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ float cell_clip = 0.0f; ++ float proj_clip = 0.0f; ++ bool time_major = false; ++ bool asymmetric_quantize_inputs = false; + }; + + struct UnidirectionalSequenceLSTMOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef UnidirectionalSequenceLSTMOptionsT NativeTableType; ++ typedef UnidirectionalSequenceLSTMOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FUSED_ACTIVATION_FUNCTION = 4, + VT_CELL_CLIP = 6, +@@ -5683,6 +6207,7 @@ struct UnidirectionalSequenceLSTMOptions FLATBUFFERS_FINAL_CLASS : private flatb + }; + + struct UnidirectionalSequenceLSTMOptionsBuilder { ++ typedef UnidirectionalSequenceLSTMOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_fused_activation_function(tflite::ActivationFunctionType fused_activation_function) { +@@ -5704,7 +6229,6 @@ struct UnidirectionalSequenceLSTMOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- UnidirectionalSequenceLSTMOptionsBuilder &operator=(const UnidirectionalSequenceLSTMOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5732,24 +6256,17 @@ flatbuffers::Offset CreateUnidirectionalSeque + + struct BidirectionalSequenceLSTMOptionsT : public flatbuffers::NativeTable { + typedef BidirectionalSequenceLSTMOptions TableType; +- tflite::ActivationFunctionType fused_activation_function; +- float cell_clip; +- float proj_clip; +- bool merge_outputs; +- bool time_major; +- bool asymmetric_quantize_inputs; +- BidirectionalSequenceLSTMOptionsT() +- : fused_activation_function(tflite::ActivationFunctionType_NONE), +- cell_clip(0.0f), +- proj_clip(0.0f), +- merge_outputs(false), +- time_major(true), +- asymmetric_quantize_inputs(false) { +- } ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ float cell_clip = 0.0f; ++ float proj_clip = 0.0f; ++ bool merge_outputs = false; ++ bool time_major = true; ++ bool asymmetric_quantize_inputs = false; + }; + + struct BidirectionalSequenceLSTMOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BidirectionalSequenceLSTMOptionsT NativeTableType; ++ typedef BidirectionalSequenceLSTMOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FUSED_ACTIVATION_FUNCTION = 4, + VT_CELL_CLIP = 6, +@@ -5792,6 +6309,7 @@ struct BidirectionalSequenceLSTMOptions FLATBUFFERS_FINAL_CLASS : private flatbu + }; + + struct BidirectionalSequenceLSTMOptionsBuilder { ++ typedef BidirectionalSequenceLSTMOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_fused_activation_function(tflite::ActivationFunctionType fused_activation_function) { +@@ -5816,7 +6334,6 @@ struct BidirectionalSequenceLSTMOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BidirectionalSequenceLSTMOptionsBuilder &operator=(const BidirectionalSequenceLSTMOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5846,16 +6363,13 @@ flatbuffers::Offset CreateBidirectionalSequenc + + struct ResizeBilinearOptionsT : public flatbuffers::NativeTable { + typedef ResizeBilinearOptions TableType; +- bool align_corners; +- bool half_pixel_centers; +- ResizeBilinearOptionsT() +- : align_corners(false), +- half_pixel_centers(false) { +- } ++ bool align_corners = false; ++ bool half_pixel_centers = false; + }; + + struct ResizeBilinearOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ResizeBilinearOptionsT NativeTableType; ++ typedef ResizeBilinearOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_ALIGN_CORNERS = 8, + VT_HALF_PIXEL_CENTERS = 10 +@@ -5878,6 +6392,7 @@ struct ResizeBilinearOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tabl + }; + + struct ResizeBilinearOptionsBuilder { ++ typedef ResizeBilinearOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_align_corners(bool align_corners) { +@@ -5890,7 +6405,6 @@ struct ResizeBilinearOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ResizeBilinearOptionsBuilder &operator=(const ResizeBilinearOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5912,16 +6426,13 @@ flatbuffers::Offset CreateResizeBilinearOptions(flatbuffe + + struct ResizeNearestNeighborOptionsT : public flatbuffers::NativeTable { + typedef ResizeNearestNeighborOptions TableType; +- bool align_corners; +- bool half_pixel_centers; +- ResizeNearestNeighborOptionsT() +- : align_corners(false), +- half_pixel_centers(false) { +- } ++ bool align_corners = false; ++ bool half_pixel_centers = false; + }; + + struct ResizeNearestNeighborOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ResizeNearestNeighborOptionsT NativeTableType; ++ typedef ResizeNearestNeighborOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_ALIGN_CORNERS = 4, + VT_HALF_PIXEL_CENTERS = 6 +@@ -5944,6 +6455,7 @@ struct ResizeNearestNeighborOptions FLATBUFFERS_FINAL_CLASS : private flatbuffer + }; + + struct ResizeNearestNeighborOptionsBuilder { ++ typedef ResizeNearestNeighborOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_align_corners(bool align_corners) { +@@ -5956,7 +6468,6 @@ struct ResizeNearestNeighborOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ResizeNearestNeighborOptionsBuilder &operator=(const ResizeNearestNeighborOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -5978,14 +6489,12 @@ flatbuffers::Offset CreateResizeNearestNeighborOpt + + struct CallOptionsT : public flatbuffers::NativeTable { + typedef CallOptions TableType; +- uint32_t subgraph; +- CallOptionsT() +- : subgraph(0) { +- } ++ uint32_t subgraph = 0; + }; + + struct CallOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef CallOptionsT NativeTableType; ++ typedef CallOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_SUBGRAPH = 4 + }; +@@ -6003,6 +6512,7 @@ struct CallOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct CallOptionsBuilder { ++ typedef CallOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_subgraph(uint32_t subgraph) { +@@ -6012,7 +6522,6 @@ struct CallOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- CallOptionsBuilder &operator=(const CallOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6032,12 +6541,11 @@ flatbuffers::Offset CreateCallOptions(flatbuffers::FlatBufferBuilde + + struct PadOptionsT : public flatbuffers::NativeTable { + typedef PadOptions TableType; +- PadOptionsT() { +- } + }; + + struct PadOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef PadOptionsT NativeTableType; ++ typedef PadOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -6048,13 +6556,13 @@ struct PadOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct PadOptionsBuilder { ++ typedef PadOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit PadOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- PadOptionsBuilder &operator=(const PadOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6072,12 +6580,11 @@ flatbuffers::Offset CreatePadOptions(flatbuffers::FlatBufferBuilder + + struct PadV2OptionsT : public flatbuffers::NativeTable { + typedef PadV2Options TableType; +- PadV2OptionsT() { +- } + }; + + struct PadV2Options FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef PadV2OptionsT NativeTableType; ++ typedef PadV2OptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -6088,13 +6595,13 @@ struct PadV2Options FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct PadV2OptionsBuilder { ++ typedef PadV2Options Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit PadV2OptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- PadV2OptionsBuilder &operator=(const PadV2OptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6112,13 +6619,12 @@ flatbuffers::Offset CreatePadV2Options(flatbuffers::FlatBufferBuil + + struct ReshapeOptionsT : public flatbuffers::NativeTable { + typedef ReshapeOptions TableType; +- std::vector new_shape; +- ReshapeOptionsT() { +- } ++ std::vector new_shape{}; + }; + + struct ReshapeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ReshapeOptionsT NativeTableType; ++ typedef ReshapeOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NEW_SHAPE = 4 + }; +@@ -6137,6 +6643,7 @@ struct ReshapeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ReshapeOptionsBuilder { ++ typedef ReshapeOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_new_shape(flatbuffers::Offset> new_shape) { +@@ -6146,7 +6653,6 @@ struct ReshapeOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ReshapeOptionsBuilder &operator=(const ReshapeOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6175,12 +6681,11 @@ flatbuffers::Offset CreateReshapeOptions(flatbuffers::FlatBuffer + + struct SpaceToBatchNDOptionsT : public flatbuffers::NativeTable { + typedef SpaceToBatchNDOptions TableType; +- SpaceToBatchNDOptionsT() { +- } + }; + + struct SpaceToBatchNDOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SpaceToBatchNDOptionsT NativeTableType; ++ typedef SpaceToBatchNDOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -6191,13 +6696,13 @@ struct SpaceToBatchNDOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tabl + }; + + struct SpaceToBatchNDOptionsBuilder { ++ typedef SpaceToBatchNDOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit SpaceToBatchNDOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SpaceToBatchNDOptionsBuilder &operator=(const SpaceToBatchNDOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6215,12 +6720,11 @@ flatbuffers::Offset CreateSpaceToBatchNDOptions(flatbuffe + + struct BatchToSpaceNDOptionsT : public flatbuffers::NativeTable { + typedef BatchToSpaceNDOptions TableType; +- BatchToSpaceNDOptionsT() { +- } + }; + + struct BatchToSpaceNDOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BatchToSpaceNDOptionsT NativeTableType; ++ typedef BatchToSpaceNDOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -6231,13 +6735,13 @@ struct BatchToSpaceNDOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tabl + }; + + struct BatchToSpaceNDOptionsBuilder { ++ typedef BatchToSpaceNDOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit BatchToSpaceNDOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BatchToSpaceNDOptionsBuilder &operator=(const BatchToSpaceNDOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6255,18 +6759,14 @@ flatbuffers::Offset CreateBatchToSpaceNDOptions(flatbuffe + + struct SkipGramOptionsT : public flatbuffers::NativeTable { + typedef SkipGramOptions TableType; +- int32_t ngram_size; +- int32_t max_skip_size; +- bool include_all_ngrams; +- SkipGramOptionsT() +- : ngram_size(0), +- max_skip_size(0), +- include_all_ngrams(false) { +- } ++ int32_t ngram_size = 0; ++ int32_t max_skip_size = 0; ++ bool include_all_ngrams = false; + }; + + struct SkipGramOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SkipGramOptionsT NativeTableType; ++ typedef SkipGramOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NGRAM_SIZE = 4, + VT_MAX_SKIP_SIZE = 6, +@@ -6294,6 +6794,7 @@ struct SkipGramOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SkipGramOptionsBuilder { ++ typedef SkipGramOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_ngram_size(int32_t ngram_size) { +@@ -6309,7 +6810,6 @@ struct SkipGramOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SkipGramOptionsBuilder &operator=(const SkipGramOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6333,14 +6833,12 @@ flatbuffers::Offset CreateSkipGramOptions(flatbuffers::FlatBuff + + struct SpaceToDepthOptionsT : public flatbuffers::NativeTable { + typedef SpaceToDepthOptions TableType; +- int32_t block_size; +- SpaceToDepthOptionsT() +- : block_size(0) { +- } ++ int32_t block_size = 0; + }; + + struct SpaceToDepthOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SpaceToDepthOptionsT NativeTableType; ++ typedef SpaceToDepthOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_BLOCK_SIZE = 4 + }; +@@ -6358,6 +6856,7 @@ struct SpaceToDepthOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct SpaceToDepthOptionsBuilder { ++ typedef SpaceToDepthOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_block_size(int32_t block_size) { +@@ -6367,7 +6866,6 @@ struct SpaceToDepthOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SpaceToDepthOptionsBuilder &operator=(const SpaceToDepthOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6387,14 +6885,12 @@ flatbuffers::Offset CreateSpaceToDepthOptions(flatbuffers:: + + struct DepthToSpaceOptionsT : public flatbuffers::NativeTable { + typedef DepthToSpaceOptions TableType; +- int32_t block_size; +- DepthToSpaceOptionsT() +- : block_size(0) { +- } ++ int32_t block_size = 0; + }; + + struct DepthToSpaceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef DepthToSpaceOptionsT NativeTableType; ++ typedef DepthToSpaceOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_BLOCK_SIZE = 4 + }; +@@ -6412,6 +6908,7 @@ struct DepthToSpaceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct DepthToSpaceOptionsBuilder { ++ typedef DepthToSpaceOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_block_size(int32_t block_size) { +@@ -6421,7 +6918,6 @@ struct DepthToSpaceOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- DepthToSpaceOptionsBuilder &operator=(const DepthToSpaceOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6441,16 +6937,13 @@ flatbuffers::Offset CreateDepthToSpaceOptions(flatbuffers:: + + struct SubOptionsT : public flatbuffers::NativeTable { + typedef SubOptions TableType; +- tflite::ActivationFunctionType fused_activation_function; +- bool pot_scale_int16; +- SubOptionsT() +- : fused_activation_function(tflite::ActivationFunctionType_NONE), +- pot_scale_int16(true) { +- } ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; ++ bool pot_scale_int16 = true; + }; + + struct SubOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SubOptionsT NativeTableType; ++ typedef SubOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FUSED_ACTIVATION_FUNCTION = 4, + VT_POT_SCALE_INT16 = 6 +@@ -6473,6 +6966,7 @@ struct SubOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SubOptionsBuilder { ++ typedef SubOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_fused_activation_function(tflite::ActivationFunctionType fused_activation_function) { +@@ -6485,7 +6979,6 @@ struct SubOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SubOptionsBuilder &operator=(const SubOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6507,14 +7000,12 @@ flatbuffers::Offset CreateSubOptions(flatbuffers::FlatBufferBuilder + + struct DivOptionsT : public flatbuffers::NativeTable { + typedef DivOptions TableType; +- tflite::ActivationFunctionType fused_activation_function; +- DivOptionsT() +- : fused_activation_function(tflite::ActivationFunctionType_NONE) { +- } ++ tflite::ActivationFunctionType fused_activation_function = tflite::ActivationFunctionType_NONE; + }; + + struct DivOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef DivOptionsT NativeTableType; ++ typedef DivOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FUSED_ACTIVATION_FUNCTION = 4 + }; +@@ -6532,6 +7023,7 @@ struct DivOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct DivOptionsBuilder { ++ typedef DivOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_fused_activation_function(tflite::ActivationFunctionType fused_activation_function) { +@@ -6541,7 +7033,6 @@ struct DivOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- DivOptionsBuilder &operator=(const DivOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6561,12 +7052,11 @@ flatbuffers::Offset CreateDivOptions(flatbuffers::FlatBufferBuilder + + struct TopKV2OptionsT : public flatbuffers::NativeTable { + typedef TopKV2Options TableType; +- TopKV2OptionsT() { +- } + }; + + struct TopKV2Options FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef TopKV2OptionsT NativeTableType; ++ typedef TopKV2OptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -6577,13 +7067,13 @@ struct TopKV2Options FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct TopKV2OptionsBuilder { ++ typedef TopKV2Options Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit TopKV2OptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- TopKV2OptionsBuilder &operator=(const TopKV2OptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6601,14 +7091,12 @@ flatbuffers::Offset CreateTopKV2Options(flatbuffers::FlatBufferBu + + struct EmbeddingLookupSparseOptionsT : public flatbuffers::NativeTable { + typedef EmbeddingLookupSparseOptions TableType; +- tflite::CombinerType combiner; +- EmbeddingLookupSparseOptionsT() +- : combiner(tflite::CombinerType_SUM) { +- } ++ tflite::CombinerType combiner = tflite::CombinerType_SUM; + }; + + struct EmbeddingLookupSparseOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef EmbeddingLookupSparseOptionsT NativeTableType; ++ typedef EmbeddingLookupSparseOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_COMBINER = 4 + }; +@@ -6626,6 +7114,7 @@ struct EmbeddingLookupSparseOptions FLATBUFFERS_FINAL_CLASS : private flatbuffer + }; + + struct EmbeddingLookupSparseOptionsBuilder { ++ typedef EmbeddingLookupSparseOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_combiner(tflite::CombinerType combiner) { +@@ -6635,7 +7124,6 @@ struct EmbeddingLookupSparseOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- EmbeddingLookupSparseOptionsBuilder &operator=(const EmbeddingLookupSparseOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6655,16 +7143,13 @@ flatbuffers::Offset CreateEmbeddingLookupSparseOpt + + struct GatherOptionsT : public flatbuffers::NativeTable { + typedef GatherOptions TableType; +- int32_t axis; +- int32_t batch_dims; +- GatherOptionsT() +- : axis(0), +- batch_dims(0) { +- } ++ int32_t axis = 0; ++ int32_t batch_dims = 0; + }; + + struct GatherOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef GatherOptionsT NativeTableType; ++ typedef GatherOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_AXIS = 4, + VT_BATCH_DIMS = 6 +@@ -6687,6 +7172,7 @@ struct GatherOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct GatherOptionsBuilder { ++ typedef GatherOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_axis(int32_t axis) { +@@ -6699,7 +7185,6 @@ struct GatherOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- GatherOptionsBuilder &operator=(const GatherOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6721,12 +7206,11 @@ flatbuffers::Offset CreateGatherOptions(flatbuffers::FlatBufferBu + + struct TransposeOptionsT : public flatbuffers::NativeTable { + typedef TransposeOptions TableType; +- TransposeOptionsT() { +- } + }; + + struct TransposeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef TransposeOptionsT NativeTableType; ++ typedef TransposeOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -6737,13 +7221,13 @@ struct TransposeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct TransposeOptionsBuilder { ++ typedef TransposeOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit TransposeOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- TransposeOptionsBuilder &operator=(const TransposeOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6761,12 +7245,11 @@ flatbuffers::Offset CreateTransposeOptions(flatbuffers::FlatBu + + struct ExpOptionsT : public flatbuffers::NativeTable { + typedef ExpOptions TableType; +- ExpOptionsT() { +- } + }; + + struct ExpOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ExpOptionsT NativeTableType; ++ typedef ExpOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -6777,13 +7260,13 @@ struct ExpOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ExpOptionsBuilder { ++ typedef ExpOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit ExpOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ExpOptionsBuilder &operator=(const ExpOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6801,12 +7284,11 @@ flatbuffers::Offset CreateExpOptions(flatbuffers::FlatBufferBuilder + + struct CosOptionsT : public flatbuffers::NativeTable { + typedef CosOptions TableType; +- CosOptionsT() { +- } + }; + + struct CosOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef CosOptionsT NativeTableType; ++ typedef CosOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -6817,13 +7299,13 @@ struct CosOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct CosOptionsBuilder { ++ typedef CosOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit CosOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- CosOptionsBuilder &operator=(const CosOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6841,14 +7323,12 @@ flatbuffers::Offset CreateCosOptions(flatbuffers::FlatBufferBuilder + + struct ReducerOptionsT : public flatbuffers::NativeTable { + typedef ReducerOptions TableType; +- bool keep_dims; +- ReducerOptionsT() +- : keep_dims(false) { +- } ++ bool keep_dims = false; + }; + + struct ReducerOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ReducerOptionsT NativeTableType; ++ typedef ReducerOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_KEEP_DIMS = 4 + }; +@@ -6866,6 +7346,7 @@ struct ReducerOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ReducerOptionsBuilder { ++ typedef ReducerOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_keep_dims(bool keep_dims) { +@@ -6875,7 +7356,6 @@ struct ReducerOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ReducerOptionsBuilder &operator=(const ReducerOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6895,13 +7375,12 @@ flatbuffers::Offset CreateReducerOptions(flatbuffers::FlatBuffer + + struct SqueezeOptionsT : public flatbuffers::NativeTable { + typedef SqueezeOptions TableType; +- std::vector squeeze_dims; +- SqueezeOptionsT() { +- } ++ std::vector squeeze_dims{}; + }; + + struct SqueezeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SqueezeOptionsT NativeTableType; ++ typedef SqueezeOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_SQUEEZE_DIMS = 4 + }; +@@ -6920,6 +7399,7 @@ struct SqueezeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SqueezeOptionsBuilder { ++ typedef SqueezeOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_squeeze_dims(flatbuffers::Offset> squeeze_dims) { +@@ -6929,7 +7409,6 @@ struct SqueezeOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SqueezeOptionsBuilder &operator=(const SqueezeOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -6958,14 +7437,12 @@ flatbuffers::Offset CreateSqueezeOptions(flatbuffers::FlatBuffer + + struct SplitOptionsT : public flatbuffers::NativeTable { + typedef SplitOptions TableType; +- int32_t num_splits; +- SplitOptionsT() +- : num_splits(0) { +- } ++ int32_t num_splits = 0; + }; + + struct SplitOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SplitOptionsT NativeTableType; ++ typedef SplitOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NUM_SPLITS = 4 + }; +@@ -6983,6 +7460,7 @@ struct SplitOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SplitOptionsBuilder { ++ typedef SplitOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_num_splits(int32_t num_splits) { +@@ -6992,7 +7470,6 @@ struct SplitOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SplitOptionsBuilder &operator=(const SplitOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7012,14 +7489,12 @@ flatbuffers::Offset CreateSplitOptions(flatbuffers::FlatBufferBuil + + struct SplitVOptionsT : public flatbuffers::NativeTable { + typedef SplitVOptions TableType; +- int32_t num_splits; +- SplitVOptionsT() +- : num_splits(0) { +- } ++ int32_t num_splits = 0; + }; + + struct SplitVOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SplitVOptionsT NativeTableType; ++ typedef SplitVOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NUM_SPLITS = 4 + }; +@@ -7037,6 +7512,7 @@ struct SplitVOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SplitVOptionsBuilder { ++ typedef SplitVOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_num_splits(int32_t num_splits) { +@@ -7046,7 +7522,6 @@ struct SplitVOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SplitVOptionsBuilder &operator=(const SplitVOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7066,22 +7541,16 @@ flatbuffers::Offset CreateSplitVOptions(flatbuffers::FlatBufferBu + + struct StridedSliceOptionsT : public flatbuffers::NativeTable { + typedef StridedSliceOptions TableType; +- int32_t begin_mask; +- int32_t end_mask; +- int32_t ellipsis_mask; +- int32_t new_axis_mask; +- int32_t shrink_axis_mask; +- StridedSliceOptionsT() +- : begin_mask(0), +- end_mask(0), +- ellipsis_mask(0), +- new_axis_mask(0), +- shrink_axis_mask(0) { +- } ++ int32_t begin_mask = 0; ++ int32_t end_mask = 0; ++ int32_t ellipsis_mask = 0; ++ int32_t new_axis_mask = 0; ++ int32_t shrink_axis_mask = 0; + }; + + struct StridedSliceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef StridedSliceOptionsT NativeTableType; ++ typedef StridedSliceOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_BEGIN_MASK = 4, + VT_END_MASK = 6, +@@ -7119,6 +7588,7 @@ struct StridedSliceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct StridedSliceOptionsBuilder { ++ typedef StridedSliceOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_begin_mask(int32_t begin_mask) { +@@ -7140,7 +7610,6 @@ struct StridedSliceOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- StridedSliceOptionsBuilder &operator=(const StridedSliceOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7168,12 +7637,11 @@ flatbuffers::Offset CreateStridedSliceOptions(flatbuffers:: + + struct LogSoftmaxOptionsT : public flatbuffers::NativeTable { + typedef LogSoftmaxOptions TableType; +- LogSoftmaxOptionsT() { +- } + }; + + struct LogSoftmaxOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef LogSoftmaxOptionsT NativeTableType; ++ typedef LogSoftmaxOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7184,13 +7652,13 @@ struct LogSoftmaxOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct LogSoftmaxOptionsBuilder { ++ typedef LogSoftmaxOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit LogSoftmaxOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- LogSoftmaxOptionsBuilder &operator=(const LogSoftmaxOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7208,16 +7676,13 @@ flatbuffers::Offset CreateLogSoftmaxOptions(flatbuffers::Flat + + struct CastOptionsT : public flatbuffers::NativeTable { + typedef CastOptions TableType; +- tflite::TensorType in_data_type; +- tflite::TensorType out_data_type; +- CastOptionsT() +- : in_data_type(tflite::TensorType_FLOAT32), +- out_data_type(tflite::TensorType_FLOAT32) { +- } ++ tflite::TensorType in_data_type = tflite::TensorType_FLOAT32; ++ tflite::TensorType out_data_type = tflite::TensorType_FLOAT32; + }; + + struct CastOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef CastOptionsT NativeTableType; ++ typedef CastOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_IN_DATA_TYPE = 4, + VT_OUT_DATA_TYPE = 6 +@@ -7240,6 +7705,7 @@ struct CastOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct CastOptionsBuilder { ++ typedef CastOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_in_data_type(tflite::TensorType in_data_type) { +@@ -7252,7 +7718,6 @@ struct CastOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- CastOptionsBuilder &operator=(const CastOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7274,12 +7739,11 @@ flatbuffers::Offset CreateCastOptions(flatbuffers::FlatBufferBuilde + + struct DequantizeOptionsT : public flatbuffers::NativeTable { + typedef DequantizeOptions TableType; +- DequantizeOptionsT() { +- } + }; + + struct DequantizeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef DequantizeOptionsT NativeTableType; ++ typedef DequantizeOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7290,13 +7754,13 @@ struct DequantizeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct DequantizeOptionsBuilder { ++ typedef DequantizeOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit DequantizeOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- DequantizeOptionsBuilder &operator=(const DequantizeOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7314,12 +7778,11 @@ flatbuffers::Offset CreateDequantizeOptions(flatbuffers::Flat + + struct MaximumMinimumOptionsT : public flatbuffers::NativeTable { + typedef MaximumMinimumOptions TableType; +- MaximumMinimumOptionsT() { +- } + }; + + struct MaximumMinimumOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef MaximumMinimumOptionsT NativeTableType; ++ typedef MaximumMinimumOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7330,13 +7793,13 @@ struct MaximumMinimumOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tabl + }; + + struct MaximumMinimumOptionsBuilder { ++ typedef MaximumMinimumOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit MaximumMinimumOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- MaximumMinimumOptionsBuilder &operator=(const MaximumMinimumOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7354,12 +7817,11 @@ flatbuffers::Offset CreateMaximumMinimumOptions(flatbuffe + + struct TileOptionsT : public flatbuffers::NativeTable { + typedef TileOptions TableType; +- TileOptionsT() { +- } + }; + + struct TileOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef TileOptionsT NativeTableType; ++ typedef TileOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7370,13 +7832,13 @@ struct TileOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct TileOptionsBuilder { ++ typedef TileOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit TileOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- TileOptionsBuilder &operator=(const TileOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7394,14 +7856,12 @@ flatbuffers::Offset CreateTileOptions(flatbuffers::FlatBufferBuilde + + struct ArgMaxOptionsT : public flatbuffers::NativeTable { + typedef ArgMaxOptions TableType; +- tflite::TensorType output_type; +- ArgMaxOptionsT() +- : output_type(tflite::TensorType_FLOAT32) { +- } ++ tflite::TensorType output_type = tflite::TensorType_FLOAT32; + }; + + struct ArgMaxOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ArgMaxOptionsT NativeTableType; ++ typedef ArgMaxOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_OUTPUT_TYPE = 4 + }; +@@ -7419,6 +7879,7 @@ struct ArgMaxOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ArgMaxOptionsBuilder { ++ typedef ArgMaxOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_output_type(tflite::TensorType output_type) { +@@ -7428,7 +7889,6 @@ struct ArgMaxOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ArgMaxOptionsBuilder &operator=(const ArgMaxOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7448,14 +7908,12 @@ flatbuffers::Offset CreateArgMaxOptions(flatbuffers::FlatBufferBu + + struct ArgMinOptionsT : public flatbuffers::NativeTable { + typedef ArgMinOptions TableType; +- tflite::TensorType output_type; +- ArgMinOptionsT() +- : output_type(tflite::TensorType_FLOAT32) { +- } ++ tflite::TensorType output_type = tflite::TensorType_FLOAT32; + }; + + struct ArgMinOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ArgMinOptionsT NativeTableType; ++ typedef ArgMinOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_OUTPUT_TYPE = 4 + }; +@@ -7473,6 +7931,7 @@ struct ArgMinOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ArgMinOptionsBuilder { ++ typedef ArgMinOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_output_type(tflite::TensorType output_type) { +@@ -7482,7 +7941,6 @@ struct ArgMinOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ArgMinOptionsBuilder &operator=(const ArgMinOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7502,12 +7960,11 @@ flatbuffers::Offset CreateArgMinOptions(flatbuffers::FlatBufferBu + + struct GreaterOptionsT : public flatbuffers::NativeTable { + typedef GreaterOptions TableType; +- GreaterOptionsT() { +- } + }; + + struct GreaterOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef GreaterOptionsT NativeTableType; ++ typedef GreaterOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7518,13 +7975,13 @@ struct GreaterOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct GreaterOptionsBuilder { ++ typedef GreaterOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit GreaterOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- GreaterOptionsBuilder &operator=(const GreaterOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7542,12 +7999,11 @@ flatbuffers::Offset CreateGreaterOptions(flatbuffers::FlatBuffer + + struct GreaterEqualOptionsT : public flatbuffers::NativeTable { + typedef GreaterEqualOptions TableType; +- GreaterEqualOptionsT() { +- } + }; + + struct GreaterEqualOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef GreaterEqualOptionsT NativeTableType; ++ typedef GreaterEqualOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7558,13 +8014,13 @@ struct GreaterEqualOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct GreaterEqualOptionsBuilder { ++ typedef GreaterEqualOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit GreaterEqualOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- GreaterEqualOptionsBuilder &operator=(const GreaterEqualOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7582,12 +8038,11 @@ flatbuffers::Offset CreateGreaterEqualOptions(flatbuffers:: + + struct LessOptionsT : public flatbuffers::NativeTable { + typedef LessOptions TableType; +- LessOptionsT() { +- } + }; + + struct LessOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef LessOptionsT NativeTableType; ++ typedef LessOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7598,13 +8053,13 @@ struct LessOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct LessOptionsBuilder { ++ typedef LessOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit LessOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- LessOptionsBuilder &operator=(const LessOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7622,12 +8077,11 @@ flatbuffers::Offset CreateLessOptions(flatbuffers::FlatBufferBuilde + + struct LessEqualOptionsT : public flatbuffers::NativeTable { + typedef LessEqualOptions TableType; +- LessEqualOptionsT() { +- } + }; + + struct LessEqualOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef LessEqualOptionsT NativeTableType; ++ typedef LessEqualOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7638,13 +8092,13 @@ struct LessEqualOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct LessEqualOptionsBuilder { ++ typedef LessEqualOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit LessEqualOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- LessEqualOptionsBuilder &operator=(const LessEqualOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7662,12 +8116,11 @@ flatbuffers::Offset CreateLessEqualOptions(flatbuffers::FlatBu + + struct NegOptionsT : public flatbuffers::NativeTable { + typedef NegOptions TableType; +- NegOptionsT() { +- } + }; + + struct NegOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef NegOptionsT NativeTableType; ++ typedef NegOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7678,13 +8131,13 @@ struct NegOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct NegOptionsBuilder { ++ typedef NegOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit NegOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- NegOptionsBuilder &operator=(const NegOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7702,12 +8155,11 @@ flatbuffers::Offset CreateNegOptions(flatbuffers::FlatBufferBuilder + + struct SelectOptionsT : public flatbuffers::NativeTable { + typedef SelectOptions TableType; +- SelectOptionsT() { +- } + }; + + struct SelectOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SelectOptionsT NativeTableType; ++ typedef SelectOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7718,13 +8170,13 @@ struct SelectOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SelectOptionsBuilder { ++ typedef SelectOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit SelectOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SelectOptionsBuilder &operator=(const SelectOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7742,12 +8194,11 @@ flatbuffers::Offset CreateSelectOptions(flatbuffers::FlatBufferBu + + struct SliceOptionsT : public flatbuffers::NativeTable { + typedef SliceOptions TableType; +- SliceOptionsT() { +- } + }; + + struct SliceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SliceOptionsT NativeTableType; ++ typedef SliceOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7758,13 +8209,13 @@ struct SliceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SliceOptionsBuilder { ++ typedef SliceOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit SliceOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SliceOptionsBuilder &operator=(const SliceOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7782,18 +8233,14 @@ flatbuffers::Offset CreateSliceOptions(flatbuffers::FlatBufferBuil + + struct TransposeConvOptionsT : public flatbuffers::NativeTable { + typedef TransposeConvOptions TableType; +- tflite::Padding padding; +- int32_t stride_w; +- int32_t stride_h; +- TransposeConvOptionsT() +- : padding(tflite::Padding_SAME), +- stride_w(0), +- stride_h(0) { +- } ++ tflite::Padding padding = tflite::Padding_SAME; ++ int32_t stride_w = 0; ++ int32_t stride_h = 0; + }; + + struct TransposeConvOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef TransposeConvOptionsT NativeTableType; ++ typedef TransposeConvOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_PADDING = 4, + VT_STRIDE_W = 6, +@@ -7821,6 +8268,7 @@ struct TransposeConvOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct TransposeConvOptionsBuilder { ++ typedef TransposeConvOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_padding(tflite::Padding padding) { +@@ -7836,7 +8284,6 @@ struct TransposeConvOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- TransposeConvOptionsBuilder &operator=(const TransposeConvOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7860,12 +8307,11 @@ flatbuffers::Offset CreateTransposeConvOptions(flatbuffers + + struct ExpandDimsOptionsT : public flatbuffers::NativeTable { + typedef ExpandDimsOptions TableType; +- ExpandDimsOptionsT() { +- } + }; + + struct ExpandDimsOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ExpandDimsOptionsT NativeTableType; ++ typedef ExpandDimsOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7876,13 +8322,13 @@ struct ExpandDimsOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ExpandDimsOptionsBuilder { ++ typedef ExpandDimsOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit ExpandDimsOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ExpandDimsOptionsBuilder &operator=(const ExpandDimsOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7900,14 +8346,12 @@ flatbuffers::Offset CreateExpandDimsOptions(flatbuffers::Flat + + struct SparseToDenseOptionsT : public flatbuffers::NativeTable { + typedef SparseToDenseOptions TableType; +- bool validate_indices; +- SparseToDenseOptionsT() +- : validate_indices(false) { +- } ++ bool validate_indices = false; + }; + + struct SparseToDenseOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SparseToDenseOptionsT NativeTableType; ++ typedef SparseToDenseOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_VALIDATE_INDICES = 4 + }; +@@ -7925,6 +8369,7 @@ struct SparseToDenseOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct SparseToDenseOptionsBuilder { ++ typedef SparseToDenseOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_validate_indices(bool validate_indices) { +@@ -7934,7 +8379,6 @@ struct SparseToDenseOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SparseToDenseOptionsBuilder &operator=(const SparseToDenseOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7954,12 +8398,11 @@ flatbuffers::Offset CreateSparseToDenseOptions(flatbuffers + + struct EqualOptionsT : public flatbuffers::NativeTable { + typedef EqualOptions TableType; +- EqualOptionsT() { +- } + }; + + struct EqualOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef EqualOptionsT NativeTableType; ++ typedef EqualOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -7970,13 +8413,13 @@ struct EqualOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct EqualOptionsBuilder { ++ typedef EqualOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit EqualOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- EqualOptionsBuilder &operator=(const EqualOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -7994,12 +8437,11 @@ flatbuffers::Offset CreateEqualOptions(flatbuffers::FlatBufferBuil + + struct NotEqualOptionsT : public flatbuffers::NativeTable { + typedef NotEqualOptions TableType; +- NotEqualOptionsT() { +- } + }; + + struct NotEqualOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef NotEqualOptionsT NativeTableType; ++ typedef NotEqualOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8010,13 +8452,13 @@ struct NotEqualOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct NotEqualOptionsBuilder { ++ typedef NotEqualOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit NotEqualOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- NotEqualOptionsBuilder &operator=(const NotEqualOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8034,14 +8476,12 @@ flatbuffers::Offset CreateNotEqualOptions(flatbuffers::FlatBuff + + struct ShapeOptionsT : public flatbuffers::NativeTable { + typedef ShapeOptions TableType; +- tflite::TensorType out_type; +- ShapeOptionsT() +- : out_type(tflite::TensorType_FLOAT32) { +- } ++ tflite::TensorType out_type = tflite::TensorType_FLOAT32; + }; + + struct ShapeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ShapeOptionsT NativeTableType; ++ typedef ShapeOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_OUT_TYPE = 4 + }; +@@ -8059,6 +8499,7 @@ struct ShapeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ShapeOptionsBuilder { ++ typedef ShapeOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_out_type(tflite::TensorType out_type) { +@@ -8068,7 +8509,6 @@ struct ShapeOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ShapeOptionsBuilder &operator=(const ShapeOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8088,12 +8528,11 @@ flatbuffers::Offset CreateShapeOptions(flatbuffers::FlatBufferBuil + + struct RankOptionsT : public flatbuffers::NativeTable { + typedef RankOptions TableType; +- RankOptionsT() { +- } + }; + + struct RankOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef RankOptionsT NativeTableType; ++ typedef RankOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8104,13 +8543,13 @@ struct RankOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct RankOptionsBuilder { ++ typedef RankOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit RankOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- RankOptionsBuilder &operator=(const RankOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8128,12 +8567,11 @@ flatbuffers::Offset CreateRankOptions(flatbuffers::FlatBufferBuilde + + struct PowOptionsT : public flatbuffers::NativeTable { + typedef PowOptions TableType; +- PowOptionsT() { +- } + }; + + struct PowOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef PowOptionsT NativeTableType; ++ typedef PowOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8144,13 +8582,13 @@ struct PowOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct PowOptionsBuilder { ++ typedef PowOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit PowOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- PowOptionsBuilder &operator=(const PowOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8168,20 +8606,15 @@ flatbuffers::Offset CreatePowOptions(flatbuffers::FlatBufferBuilder + + struct FakeQuantOptionsT : public flatbuffers::NativeTable { + typedef FakeQuantOptions TableType; +- float min; +- float max; +- int32_t num_bits; +- bool narrow_range; +- FakeQuantOptionsT() +- : min(0.0f), +- max(0.0f), +- num_bits(0), +- narrow_range(false) { +- } ++ float min = 0.0f; ++ float max = 0.0f; ++ int32_t num_bits = 0; ++ bool narrow_range = false; + }; + + struct FakeQuantOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef FakeQuantOptionsT NativeTableType; ++ typedef FakeQuantOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_MIN = 4, + VT_MAX = 6, +@@ -8214,6 +8647,7 @@ struct FakeQuantOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct FakeQuantOptionsBuilder { ++ typedef FakeQuantOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_min(float min) { +@@ -8232,7 +8666,6 @@ struct FakeQuantOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- FakeQuantOptionsBuilder &operator=(const FakeQuantOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8258,16 +8691,13 @@ flatbuffers::Offset CreateFakeQuantOptions(flatbuffers::FlatBu + + struct PackOptionsT : public flatbuffers::NativeTable { + typedef PackOptions TableType; +- int32_t values_count; +- int32_t axis; +- PackOptionsT() +- : values_count(0), +- axis(0) { +- } ++ int32_t values_count = 0; ++ int32_t axis = 0; + }; + + struct PackOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef PackOptionsT NativeTableType; ++ typedef PackOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_VALUES_COUNT = 4, + VT_AXIS = 6 +@@ -8290,6 +8720,7 @@ struct PackOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct PackOptionsBuilder { ++ typedef PackOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_values_count(int32_t values_count) { +@@ -8302,7 +8733,6 @@ struct PackOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- PackOptionsBuilder &operator=(const PackOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8324,12 +8754,11 @@ flatbuffers::Offset CreatePackOptions(flatbuffers::FlatBufferBuilde + + struct LogicalOrOptionsT : public flatbuffers::NativeTable { + typedef LogicalOrOptions TableType; +- LogicalOrOptionsT() { +- } + }; + + struct LogicalOrOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef LogicalOrOptionsT NativeTableType; ++ typedef LogicalOrOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8340,13 +8769,13 @@ struct LogicalOrOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct LogicalOrOptionsBuilder { ++ typedef LogicalOrOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit LogicalOrOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- LogicalOrOptionsBuilder &operator=(const LogicalOrOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8364,14 +8793,12 @@ flatbuffers::Offset CreateLogicalOrOptions(flatbuffers::FlatBu + + struct OneHotOptionsT : public flatbuffers::NativeTable { + typedef OneHotOptions TableType; +- int32_t axis; +- OneHotOptionsT() +- : axis(0) { +- } ++ int32_t axis = 0; + }; + + struct OneHotOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef OneHotOptionsT NativeTableType; ++ typedef OneHotOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_AXIS = 4 + }; +@@ -8389,6 +8816,7 @@ struct OneHotOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct OneHotOptionsBuilder { ++ typedef OneHotOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_axis(int32_t axis) { +@@ -8398,7 +8826,6 @@ struct OneHotOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- OneHotOptionsBuilder &operator=(const OneHotOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8418,12 +8845,11 @@ flatbuffers::Offset CreateOneHotOptions(flatbuffers::FlatBufferBu + + struct AbsOptionsT : public flatbuffers::NativeTable { + typedef AbsOptions TableType; +- AbsOptionsT() { +- } + }; + + struct AbsOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef AbsOptionsT NativeTableType; ++ typedef AbsOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8434,13 +8860,13 @@ struct AbsOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct AbsOptionsBuilder { ++ typedef AbsOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit AbsOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- AbsOptionsBuilder &operator=(const AbsOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8458,12 +8884,11 @@ flatbuffers::Offset CreateAbsOptions(flatbuffers::FlatBufferBuilder + + struct HardSwishOptionsT : public flatbuffers::NativeTable { + typedef HardSwishOptions TableType; +- HardSwishOptionsT() { +- } + }; + + struct HardSwishOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef HardSwishOptionsT NativeTableType; ++ typedef HardSwishOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8474,13 +8899,13 @@ struct HardSwishOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct HardSwishOptionsBuilder { ++ typedef HardSwishOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit HardSwishOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- HardSwishOptionsBuilder &operator=(const HardSwishOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8498,12 +8923,11 @@ flatbuffers::Offset CreateHardSwishOptions(flatbuffers::FlatBu + + struct LogicalAndOptionsT : public flatbuffers::NativeTable { + typedef LogicalAndOptions TableType; +- LogicalAndOptionsT() { +- } + }; + + struct LogicalAndOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef LogicalAndOptionsT NativeTableType; ++ typedef LogicalAndOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8514,13 +8938,13 @@ struct LogicalAndOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct LogicalAndOptionsBuilder { ++ typedef LogicalAndOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit LogicalAndOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- LogicalAndOptionsBuilder &operator=(const LogicalAndOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8538,12 +8962,11 @@ flatbuffers::Offset CreateLogicalAndOptions(flatbuffers::Flat + + struct LogicalNotOptionsT : public flatbuffers::NativeTable { + typedef LogicalNotOptions TableType; +- LogicalNotOptionsT() { +- } + }; + + struct LogicalNotOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef LogicalNotOptionsT NativeTableType; ++ typedef LogicalNotOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8554,13 +8977,13 @@ struct LogicalNotOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct LogicalNotOptionsBuilder { ++ typedef LogicalNotOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit LogicalNotOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- LogicalNotOptionsBuilder &operator=(const LogicalNotOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8578,16 +9001,13 @@ flatbuffers::Offset CreateLogicalNotOptions(flatbuffers::Flat + + struct UnpackOptionsT : public flatbuffers::NativeTable { + typedef UnpackOptions TableType; +- int32_t num; +- int32_t axis; +- UnpackOptionsT() +- : num(0), +- axis(0) { +- } ++ int32_t num = 0; ++ int32_t axis = 0; + }; + + struct UnpackOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef UnpackOptionsT NativeTableType; ++ typedef UnpackOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NUM = 4, + VT_AXIS = 6 +@@ -8610,6 +9030,7 @@ struct UnpackOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct UnpackOptionsBuilder { ++ typedef UnpackOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_num(int32_t num) { +@@ -8622,7 +9043,6 @@ struct UnpackOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- UnpackOptionsBuilder &operator=(const UnpackOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8644,12 +9064,11 @@ flatbuffers::Offset CreateUnpackOptions(flatbuffers::FlatBufferBu + + struct FloorDivOptionsT : public flatbuffers::NativeTable { + typedef FloorDivOptions TableType; +- FloorDivOptionsT() { +- } + }; + + struct FloorDivOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef FloorDivOptionsT NativeTableType; ++ typedef FloorDivOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8660,13 +9079,13 @@ struct FloorDivOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct FloorDivOptionsBuilder { ++ typedef FloorDivOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit FloorDivOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- FloorDivOptionsBuilder &operator=(const FloorDivOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8684,12 +9103,11 @@ flatbuffers::Offset CreateFloorDivOptions(flatbuffers::FlatBuff + + struct SquareOptionsT : public flatbuffers::NativeTable { + typedef SquareOptions TableType; +- SquareOptionsT() { +- } + }; + + struct SquareOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SquareOptionsT NativeTableType; ++ typedef SquareOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8700,13 +9118,13 @@ struct SquareOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SquareOptionsBuilder { ++ typedef SquareOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit SquareOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SquareOptionsBuilder &operator=(const SquareOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8724,12 +9142,11 @@ flatbuffers::Offset CreateSquareOptions(flatbuffers::FlatBufferBu + + struct ZerosLikeOptionsT : public flatbuffers::NativeTable { + typedef ZerosLikeOptions TableType; +- ZerosLikeOptionsT() { +- } + }; + + struct ZerosLikeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ZerosLikeOptionsT NativeTableType; ++ typedef ZerosLikeOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8740,13 +9157,13 @@ struct ZerosLikeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ZerosLikeOptionsBuilder { ++ typedef ZerosLikeOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit ZerosLikeOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ZerosLikeOptionsBuilder &operator=(const ZerosLikeOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8764,12 +9181,11 @@ flatbuffers::Offset CreateZerosLikeOptions(flatbuffers::FlatBu + + struct FillOptionsT : public flatbuffers::NativeTable { + typedef FillOptions TableType; +- FillOptionsT() { +- } + }; + + struct FillOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef FillOptionsT NativeTableType; ++ typedef FillOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8780,13 +9196,13 @@ struct FillOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct FillOptionsBuilder { ++ typedef FillOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit FillOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- FillOptionsBuilder &operator=(const FillOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8804,12 +9220,11 @@ flatbuffers::Offset CreateFillOptions(flatbuffers::FlatBufferBuilde + + struct FloorModOptionsT : public flatbuffers::NativeTable { + typedef FloorModOptions TableType; +- FloorModOptionsT() { +- } + }; + + struct FloorModOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef FloorModOptionsT NativeTableType; ++ typedef FloorModOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8820,13 +9235,13 @@ struct FloorModOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct FloorModOptionsBuilder { ++ typedef FloorModOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit FloorModOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- FloorModOptionsBuilder &operator=(const FloorModOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8844,12 +9259,11 @@ flatbuffers::Offset CreateFloorModOptions(flatbuffers::FlatBuff + + struct RangeOptionsT : public flatbuffers::NativeTable { + typedef RangeOptions TableType; +- RangeOptionsT() { +- } + }; + + struct RangeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef RangeOptionsT NativeTableType; ++ typedef RangeOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8860,13 +9274,13 @@ struct RangeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct RangeOptionsBuilder { ++ typedef RangeOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit RangeOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- RangeOptionsBuilder &operator=(const RangeOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8884,14 +9298,12 @@ flatbuffers::Offset CreateRangeOptions(flatbuffers::FlatBufferBuil + + struct LeakyReluOptionsT : public flatbuffers::NativeTable { + typedef LeakyReluOptions TableType; +- float alpha; +- LeakyReluOptionsT() +- : alpha(0.0f) { +- } ++ float alpha = 0.0f; + }; + + struct LeakyReluOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef LeakyReluOptionsT NativeTableType; ++ typedef LeakyReluOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_ALPHA = 4 + }; +@@ -8909,6 +9321,7 @@ struct LeakyReluOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct LeakyReluOptionsBuilder { ++ typedef LeakyReluOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_alpha(float alpha) { +@@ -8918,7 +9331,6 @@ struct LeakyReluOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- LeakyReluOptionsBuilder &operator=(const LeakyReluOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8938,12 +9350,11 @@ flatbuffers::Offset CreateLeakyReluOptions(flatbuffers::FlatBu + + struct SquaredDifferenceOptionsT : public flatbuffers::NativeTable { + typedef SquaredDifferenceOptions TableType; +- SquaredDifferenceOptionsT() { +- } + }; + + struct SquaredDifferenceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SquaredDifferenceOptionsT NativeTableType; ++ typedef SquaredDifferenceOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -8954,13 +9365,13 @@ struct SquaredDifferenceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::T + }; + + struct SquaredDifferenceOptionsBuilder { ++ typedef SquaredDifferenceOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit SquaredDifferenceOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SquaredDifferenceOptionsBuilder &operator=(const SquaredDifferenceOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -8978,14 +9389,12 @@ flatbuffers::Offset CreateSquaredDifferenceOptions(fla + + struct MirrorPadOptionsT : public flatbuffers::NativeTable { + typedef MirrorPadOptions TableType; +- tflite::MirrorPadMode mode; +- MirrorPadOptionsT() +- : mode(tflite::MirrorPadMode_REFLECT) { +- } ++ tflite::MirrorPadMode mode = tflite::MirrorPadMode_REFLECT; + }; + + struct MirrorPadOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef MirrorPadOptionsT NativeTableType; ++ typedef MirrorPadOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_MODE = 4 + }; +@@ -9003,6 +9412,7 @@ struct MirrorPadOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct MirrorPadOptionsBuilder { ++ typedef MirrorPadOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_mode(tflite::MirrorPadMode mode) { +@@ -9012,7 +9422,6 @@ struct MirrorPadOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- MirrorPadOptionsBuilder &operator=(const MirrorPadOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9032,14 +9441,12 @@ flatbuffers::Offset CreateMirrorPadOptions(flatbuffers::FlatBu + + struct UniqueOptionsT : public flatbuffers::NativeTable { + typedef UniqueOptions TableType; +- tflite::TensorType idx_out_type; +- UniqueOptionsT() +- : idx_out_type(tflite::TensorType_INT32) { +- } ++ tflite::TensorType idx_out_type = tflite::TensorType_INT32; + }; + + struct UniqueOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef UniqueOptionsT NativeTableType; ++ typedef UniqueOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_IDX_OUT_TYPE = 4 + }; +@@ -9057,6 +9464,7 @@ struct UniqueOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct UniqueOptionsBuilder { ++ typedef UniqueOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_idx_out_type(tflite::TensorType idx_out_type) { +@@ -9066,7 +9474,6 @@ struct UniqueOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- UniqueOptionsBuilder &operator=(const UniqueOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9086,12 +9493,11 @@ flatbuffers::Offset CreateUniqueOptions(flatbuffers::FlatBufferBu + + struct ReverseV2OptionsT : public flatbuffers::NativeTable { + typedef ReverseV2Options TableType; +- ReverseV2OptionsT() { +- } + }; + + struct ReverseV2Options FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ReverseV2OptionsT NativeTableType; ++ typedef ReverseV2OptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9102,13 +9508,13 @@ struct ReverseV2Options FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ReverseV2OptionsBuilder { ++ typedef ReverseV2Options Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit ReverseV2OptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ReverseV2OptionsBuilder &operator=(const ReverseV2OptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9126,12 +9532,11 @@ flatbuffers::Offset CreateReverseV2Options(flatbuffers::FlatBu + + struct AddNOptionsT : public flatbuffers::NativeTable { + typedef AddNOptions TableType; +- AddNOptionsT() { +- } + }; + + struct AddNOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef AddNOptionsT NativeTableType; ++ typedef AddNOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9142,13 +9547,13 @@ struct AddNOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct AddNOptionsBuilder { ++ typedef AddNOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit AddNOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- AddNOptionsBuilder &operator=(const AddNOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9166,12 +9571,11 @@ flatbuffers::Offset CreateAddNOptions(flatbuffers::FlatBufferBuilde + + struct GatherNdOptionsT : public flatbuffers::NativeTable { + typedef GatherNdOptions TableType; +- GatherNdOptionsT() { +- } + }; + + struct GatherNdOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef GatherNdOptionsT NativeTableType; ++ typedef GatherNdOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9182,13 +9586,13 @@ struct GatherNdOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct GatherNdOptionsBuilder { ++ typedef GatherNdOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit GatherNdOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- GatherNdOptionsBuilder &operator=(const GatherNdOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9206,12 +9610,11 @@ flatbuffers::Offset CreateGatherNdOptions(flatbuffers::FlatBuff + + struct WhereOptionsT : public flatbuffers::NativeTable { + typedef WhereOptions TableType; +- WhereOptionsT() { +- } + }; + + struct WhereOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef WhereOptionsT NativeTableType; ++ typedef WhereOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9222,13 +9625,13 @@ struct WhereOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct WhereOptionsBuilder { ++ typedef WhereOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit WhereOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- WhereOptionsBuilder &operator=(const WhereOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9246,16 +9649,13 @@ flatbuffers::Offset CreateWhereOptions(flatbuffers::FlatBufferBuil + + struct ReverseSequenceOptionsT : public flatbuffers::NativeTable { + typedef ReverseSequenceOptions TableType; +- int32_t seq_dim; +- int32_t batch_dim; +- ReverseSequenceOptionsT() +- : seq_dim(0), +- batch_dim(0) { +- } ++ int32_t seq_dim = 0; ++ int32_t batch_dim = 0; + }; + + struct ReverseSequenceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ReverseSequenceOptionsT NativeTableType; ++ typedef ReverseSequenceOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_SEQ_DIM = 4, + VT_BATCH_DIM = 6 +@@ -9278,6 +9678,7 @@ struct ReverseSequenceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tab + }; + + struct ReverseSequenceOptionsBuilder { ++ typedef ReverseSequenceOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_seq_dim(int32_t seq_dim) { +@@ -9290,7 +9691,6 @@ struct ReverseSequenceOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ReverseSequenceOptionsBuilder &operator=(const ReverseSequenceOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9312,12 +9712,11 @@ flatbuffers::Offset CreateReverseSequenceOptions(flatbuf + + struct MatrixDiagOptionsT : public flatbuffers::NativeTable { + typedef MatrixDiagOptions TableType; +- MatrixDiagOptionsT() { +- } + }; + + struct MatrixDiagOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef MatrixDiagOptionsT NativeTableType; ++ typedef MatrixDiagOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9328,13 +9727,13 @@ struct MatrixDiagOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct MatrixDiagOptionsBuilder { ++ typedef MatrixDiagOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit MatrixDiagOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- MatrixDiagOptionsBuilder &operator=(const MatrixDiagOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9352,12 +9751,11 @@ flatbuffers::Offset CreateMatrixDiagOptions(flatbuffers::Flat + + struct QuantizeOptionsT : public flatbuffers::NativeTable { + typedef QuantizeOptions TableType; +- QuantizeOptionsT() { +- } + }; + + struct QuantizeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef QuantizeOptionsT NativeTableType; ++ typedef QuantizeOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9368,13 +9766,13 @@ struct QuantizeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct QuantizeOptionsBuilder { ++ typedef QuantizeOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit QuantizeOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- QuantizeOptionsBuilder &operator=(const QuantizeOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9392,12 +9790,11 @@ flatbuffers::Offset CreateQuantizeOptions(flatbuffers::FlatBuff + + struct MatrixSetDiagOptionsT : public flatbuffers::NativeTable { + typedef MatrixSetDiagOptions TableType; +- MatrixSetDiagOptionsT() { +- } + }; + + struct MatrixSetDiagOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef MatrixSetDiagOptionsT NativeTableType; ++ typedef MatrixSetDiagOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9408,13 +9805,13 @@ struct MatrixSetDiagOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct MatrixSetDiagOptionsBuilder { ++ typedef MatrixSetDiagOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit MatrixSetDiagOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- MatrixSetDiagOptionsBuilder &operator=(const MatrixSetDiagOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9432,16 +9829,13 @@ flatbuffers::Offset CreateMatrixSetDiagOptions(flatbuffers + + struct IfOptionsT : public flatbuffers::NativeTable { + typedef IfOptions TableType; +- int32_t then_subgraph_index; +- int32_t else_subgraph_index; +- IfOptionsT() +- : then_subgraph_index(0), +- else_subgraph_index(0) { +- } ++ int32_t then_subgraph_index = 0; ++ int32_t else_subgraph_index = 0; + }; + + struct IfOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef IfOptionsT NativeTableType; ++ typedef IfOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_THEN_SUBGRAPH_INDEX = 4, + VT_ELSE_SUBGRAPH_INDEX = 6 +@@ -9464,6 +9858,7 @@ struct IfOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct IfOptionsBuilder { ++ typedef IfOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_then_subgraph_index(int32_t then_subgraph_index) { +@@ -9476,7 +9871,6 @@ struct IfOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- IfOptionsBuilder &operator=(const IfOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9498,14 +9892,12 @@ flatbuffers::Offset CreateIfOptions(flatbuffers::FlatBufferBuilder &_ + + struct CallOnceOptionsT : public flatbuffers::NativeTable { + typedef CallOnceOptions TableType; +- int32_t init_subgraph_index; +- CallOnceOptionsT() +- : init_subgraph_index(0) { +- } ++ int32_t init_subgraph_index = 0; + }; + + struct CallOnceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef CallOnceOptionsT NativeTableType; ++ typedef CallOnceOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_INIT_SUBGRAPH_INDEX = 4 + }; +@@ -9523,6 +9915,7 @@ struct CallOnceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct CallOnceOptionsBuilder { ++ typedef CallOnceOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_init_subgraph_index(int32_t init_subgraph_index) { +@@ -9532,7 +9925,6 @@ struct CallOnceOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- CallOnceOptionsBuilder &operator=(const CallOnceOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9552,16 +9944,13 @@ flatbuffers::Offset CreateCallOnceOptions(flatbuffers::FlatBuff + + struct WhileOptionsT : public flatbuffers::NativeTable { + typedef WhileOptions TableType; +- int32_t cond_subgraph_index; +- int32_t body_subgraph_index; +- WhileOptionsT() +- : cond_subgraph_index(0), +- body_subgraph_index(0) { +- } ++ int32_t cond_subgraph_index = 0; ++ int32_t body_subgraph_index = 0; + }; + + struct WhileOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef WhileOptionsT NativeTableType; ++ typedef WhileOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_COND_SUBGRAPH_INDEX = 4, + VT_BODY_SUBGRAPH_INDEX = 6 +@@ -9584,6 +9973,7 @@ struct WhileOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct WhileOptionsBuilder { ++ typedef WhileOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_cond_subgraph_index(int32_t cond_subgraph_index) { +@@ -9596,7 +9986,6 @@ struct WhileOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- WhileOptionsBuilder &operator=(const WhileOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9618,12 +10007,11 @@ flatbuffers::Offset CreateWhileOptions(flatbuffers::FlatBufferBuil + + struct NonMaxSuppressionV4OptionsT : public flatbuffers::NativeTable { + typedef NonMaxSuppressionV4Options TableType; +- NonMaxSuppressionV4OptionsT() { +- } + }; + + struct NonMaxSuppressionV4Options FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef NonMaxSuppressionV4OptionsT NativeTableType; ++ typedef NonMaxSuppressionV4OptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9634,13 +10022,13 @@ struct NonMaxSuppressionV4Options FLATBUFFERS_FINAL_CLASS : private flatbuffers: + }; + + struct NonMaxSuppressionV4OptionsBuilder { ++ typedef NonMaxSuppressionV4Options Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit NonMaxSuppressionV4OptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- NonMaxSuppressionV4OptionsBuilder &operator=(const NonMaxSuppressionV4OptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9658,12 +10046,11 @@ flatbuffers::Offset CreateNonMaxSuppressionV4Options + + struct NonMaxSuppressionV5OptionsT : public flatbuffers::NativeTable { + typedef NonMaxSuppressionV5Options TableType; +- NonMaxSuppressionV5OptionsT() { +- } + }; + + struct NonMaxSuppressionV5Options FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef NonMaxSuppressionV5OptionsT NativeTableType; ++ typedef NonMaxSuppressionV5OptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9674,13 +10061,13 @@ struct NonMaxSuppressionV5Options FLATBUFFERS_FINAL_CLASS : private flatbuffers: + }; + + struct NonMaxSuppressionV5OptionsBuilder { ++ typedef NonMaxSuppressionV5Options Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit NonMaxSuppressionV5OptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- NonMaxSuppressionV5OptionsBuilder &operator=(const NonMaxSuppressionV5OptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9698,12 +10085,11 @@ flatbuffers::Offset CreateNonMaxSuppressionV5Options + + struct ScatterNdOptionsT : public flatbuffers::NativeTable { + typedef ScatterNdOptions TableType; +- ScatterNdOptionsT() { +- } + }; + + struct ScatterNdOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ScatterNdOptionsT NativeTableType; ++ typedef ScatterNdOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9714,13 +10100,13 @@ struct ScatterNdOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ScatterNdOptionsBuilder { ++ typedef ScatterNdOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit ScatterNdOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ScatterNdOptionsBuilder &operator=(const ScatterNdOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9738,12 +10124,11 @@ flatbuffers::Offset CreateScatterNdOptions(flatbuffers::FlatBu + + struct SelectV2OptionsT : public flatbuffers::NativeTable { + typedef SelectV2Options TableType; +- SelectV2OptionsT() { +- } + }; + + struct SelectV2Options FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SelectV2OptionsT NativeTableType; ++ typedef SelectV2OptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9754,13 +10139,13 @@ struct SelectV2Options FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SelectV2OptionsBuilder { ++ typedef SelectV2Options Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit SelectV2OptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SelectV2OptionsBuilder &operator=(const SelectV2OptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9778,12 +10163,11 @@ flatbuffers::Offset CreateSelectV2Options(flatbuffers::FlatBuff + + struct DensifyOptionsT : public flatbuffers::NativeTable { + typedef DensifyOptions TableType; +- DensifyOptionsT() { +- } + }; + + struct DensifyOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef DensifyOptionsT NativeTableType; ++ typedef DensifyOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9794,13 +10178,13 @@ struct DensifyOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct DensifyOptionsBuilder { ++ typedef DensifyOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit DensifyOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- DensifyOptionsBuilder &operator=(const DensifyOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9818,12 +10202,11 @@ flatbuffers::Offset CreateDensifyOptions(flatbuffers::FlatBuffer + + struct SegmentSumOptionsT : public flatbuffers::NativeTable { + typedef SegmentSumOptions TableType; +- SegmentSumOptionsT() { +- } + }; + + struct SegmentSumOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SegmentSumOptionsT NativeTableType; ++ typedef SegmentSumOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -9834,13 +10217,13 @@ struct SegmentSumOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SegmentSumOptionsBuilder { ++ typedef SegmentSumOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit SegmentSumOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SegmentSumOptionsBuilder &operator=(const SegmentSumOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9858,18 +10241,14 @@ flatbuffers::Offset CreateSegmentSumOptions(flatbuffers::Flat + + struct BatchMatMulOptionsT : public flatbuffers::NativeTable { + typedef BatchMatMulOptions TableType; +- bool adj_x; +- bool adj_y; +- bool asymmetric_quantize_inputs; +- BatchMatMulOptionsT() +- : adj_x(false), +- adj_y(false), +- asymmetric_quantize_inputs(false) { +- } ++ bool adj_x = false; ++ bool adj_y = false; ++ bool asymmetric_quantize_inputs = false; + }; + + struct BatchMatMulOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BatchMatMulOptionsT NativeTableType; ++ typedef BatchMatMulOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_ADJ_X = 4, + VT_ADJ_Y = 6, +@@ -9897,6 +10276,7 @@ struct BatchMatMulOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct BatchMatMulOptionsBuilder { ++ typedef BatchMatMulOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_adj_x(bool adj_x) { +@@ -9912,7 +10292,6 @@ struct BatchMatMulOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BatchMatMulOptionsBuilder &operator=(const BatchMatMulOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -9936,16 +10315,13 @@ flatbuffers::Offset CreateBatchMatMulOptions(flatbuffers::Fl + + struct CumsumOptionsT : public flatbuffers::NativeTable { + typedef CumsumOptions TableType; +- bool exclusive; +- bool reverse; +- CumsumOptionsT() +- : exclusive(false), +- reverse(false) { +- } ++ bool exclusive = false; ++ bool reverse = false; + }; + + struct CumsumOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef CumsumOptionsT NativeTableType; ++ typedef CumsumOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_EXCLUSIVE = 4, + VT_REVERSE = 6 +@@ -9968,6 +10344,7 @@ struct CumsumOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct CumsumOptionsBuilder { ++ typedef CumsumOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_exclusive(bool exclusive) { +@@ -9980,7 +10357,6 @@ struct CumsumOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- CumsumOptionsBuilder &operator=(const CumsumOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10002,12 +10378,11 @@ flatbuffers::Offset CreateCumsumOptions(flatbuffers::FlatBufferBu + + struct BroadcastToOptionsT : public flatbuffers::NativeTable { + typedef BroadcastToOptions TableType; +- BroadcastToOptionsT() { +- } + }; + + struct BroadcastToOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BroadcastToOptionsT NativeTableType; ++ typedef BroadcastToOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -10018,13 +10393,13 @@ struct BroadcastToOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct BroadcastToOptionsBuilder { ++ typedef BroadcastToOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit BroadcastToOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BroadcastToOptionsBuilder &operator=(const BroadcastToOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10042,12 +10417,11 @@ flatbuffers::Offset CreateBroadcastToOptions(flatbuffers::Fl + + struct Rfft2dOptionsT : public flatbuffers::NativeTable { + typedef Rfft2dOptions TableType; +- Rfft2dOptionsT() { +- } + }; + + struct Rfft2dOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef Rfft2dOptionsT NativeTableType; ++ typedef Rfft2dOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -10058,13 +10432,13 @@ struct Rfft2dOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct Rfft2dOptionsBuilder { ++ typedef Rfft2dOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit Rfft2dOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- Rfft2dOptionsBuilder &operator=(const Rfft2dOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10082,18 +10456,14 @@ flatbuffers::Offset CreateRfft2dOptions(flatbuffers::FlatBufferBu + + struct HashtableOptionsT : public flatbuffers::NativeTable { + typedef HashtableOptions TableType; +- int32_t table_id; +- tflite::TensorType key_dtype; +- tflite::TensorType value_dtype; +- HashtableOptionsT() +- : table_id(0), +- key_dtype(tflite::TensorType_FLOAT32), +- value_dtype(tflite::TensorType_FLOAT32) { +- } ++ int32_t table_id = 0; ++ tflite::TensorType key_dtype = tflite::TensorType_FLOAT32; ++ tflite::TensorType value_dtype = tflite::TensorType_FLOAT32; + }; + + struct HashtableOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef HashtableOptionsT NativeTableType; ++ typedef HashtableOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_TABLE_ID = 4, + VT_KEY_DTYPE = 6, +@@ -10121,6 +10491,7 @@ struct HashtableOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct HashtableOptionsBuilder { ++ typedef HashtableOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_table_id(int32_t table_id) { +@@ -10136,7 +10507,6 @@ struct HashtableOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- HashtableOptionsBuilder &operator=(const HashtableOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10160,12 +10530,11 @@ flatbuffers::Offset CreateHashtableOptions(flatbuffers::FlatBu + + struct HashtableFindOptionsT : public flatbuffers::NativeTable { + typedef HashtableFindOptions TableType; +- HashtableFindOptionsT() { +- } + }; + + struct HashtableFindOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef HashtableFindOptionsT NativeTableType; ++ typedef HashtableFindOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -10176,13 +10545,13 @@ struct HashtableFindOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct HashtableFindOptionsBuilder { ++ typedef HashtableFindOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit HashtableFindOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- HashtableFindOptionsBuilder &operator=(const HashtableFindOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10200,12 +10569,11 @@ flatbuffers::Offset CreateHashtableFindOptions(flatbuffers + + struct HashtableImportOptionsT : public flatbuffers::NativeTable { + typedef HashtableImportOptions TableType; +- HashtableImportOptionsT() { +- } + }; + + struct HashtableImportOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef HashtableImportOptionsT NativeTableType; ++ typedef HashtableImportOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -10216,13 +10584,13 @@ struct HashtableImportOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tab + }; + + struct HashtableImportOptionsBuilder { ++ typedef HashtableImportOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit HashtableImportOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- HashtableImportOptionsBuilder &operator=(const HashtableImportOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10240,12 +10608,11 @@ flatbuffers::Offset CreateHashtableImportOptions(flatbuf + + struct HashtableSizeOptionsT : public flatbuffers::NativeTable { + typedef HashtableSizeOptions TableType; +- HashtableSizeOptionsT() { +- } + }; + + struct HashtableSizeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef HashtableSizeOptionsT NativeTableType; ++ typedef HashtableSizeOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -10256,13 +10623,13 @@ struct HashtableSizeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct HashtableSizeOptionsBuilder { ++ typedef HashtableSizeOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit HashtableSizeOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- HashtableSizeOptionsBuilder &operator=(const HashtableSizeOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10280,14 +10647,13 @@ flatbuffers::Offset CreateHashtableSizeOptions(flatbuffers + + struct VarHandleOptionsT : public flatbuffers::NativeTable { + typedef VarHandleOptions TableType; +- std::string container; +- std::string shared_name; +- VarHandleOptionsT() { +- } ++ std::string container{}; ++ std::string shared_name{}; + }; + + struct VarHandleOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef VarHandleOptionsT NativeTableType; ++ typedef VarHandleOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_CONTAINER = 4, + VT_SHARED_NAME = 6 +@@ -10312,6 +10678,7 @@ struct VarHandleOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct VarHandleOptionsBuilder { ++ typedef VarHandleOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_container(flatbuffers::Offset container) { +@@ -10324,7 +10691,6 @@ struct VarHandleOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- VarHandleOptionsBuilder &operator=(const VarHandleOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10358,12 +10724,11 @@ flatbuffers::Offset CreateVarHandleOptions(flatbuffers::FlatBu + + struct ReadVariableOptionsT : public flatbuffers::NativeTable { + typedef ReadVariableOptions TableType; +- ReadVariableOptionsT() { +- } + }; + + struct ReadVariableOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ReadVariableOptionsT NativeTableType; ++ typedef ReadVariableOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -10374,13 +10739,13 @@ struct ReadVariableOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + }; + + struct ReadVariableOptionsBuilder { ++ typedef ReadVariableOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit ReadVariableOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ReadVariableOptionsBuilder &operator=(const ReadVariableOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10398,12 +10763,11 @@ flatbuffers::Offset CreateReadVariableOptions(flatbuffers:: + + struct AssignVariableOptionsT : public flatbuffers::NativeTable { + typedef AssignVariableOptions TableType; +- AssignVariableOptionsT() { +- } + }; + + struct AssignVariableOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef AssignVariableOptionsT NativeTableType; ++ typedef AssignVariableOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -10414,13 +10778,13 @@ struct AssignVariableOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tabl + }; + + struct AssignVariableOptionsBuilder { ++ typedef AssignVariableOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit AssignVariableOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- AssignVariableOptionsBuilder &operator=(const AssignVariableOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10438,16 +10802,13 @@ flatbuffers::Offset CreateAssignVariableOptions(flatbuffe + + struct RandomOptionsT : public flatbuffers::NativeTable { + typedef RandomOptions TableType; +- int64_t seed; +- int64_t seed2; +- RandomOptionsT() +- : seed(0), +- seed2(0) { +- } ++ int64_t seed = 0; ++ int64_t seed2 = 0; + }; + + struct RandomOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef RandomOptionsT NativeTableType; ++ typedef RandomOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_SEED = 4, + VT_SEED2 = 6 +@@ -10470,6 +10831,7 @@ struct RandomOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct RandomOptionsBuilder { ++ typedef RandomOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_seed(int64_t seed) { +@@ -10482,7 +10844,6 @@ struct RandomOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- RandomOptionsBuilder &operator=(const RandomOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10504,13 +10865,12 @@ flatbuffers::Offset CreateRandomOptions(flatbuffers::FlatBufferBu + + struct BucketizeOptionsT : public flatbuffers::NativeTable { + typedef BucketizeOptions TableType; +- std::vector boundaries; +- BucketizeOptionsT() { +- } ++ std::vector boundaries{}; + }; + + struct BucketizeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BucketizeOptionsT NativeTableType; ++ typedef BucketizeOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_BOUNDARIES = 4 + }; +@@ -10529,6 +10889,7 @@ struct BucketizeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct BucketizeOptionsBuilder { ++ typedef BucketizeOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_boundaries(flatbuffers::Offset> boundaries) { +@@ -10538,7 +10899,6 @@ struct BucketizeOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BucketizeOptionsBuilder &operator=(const BucketizeOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10567,14 +10927,12 @@ flatbuffers::Offset CreateBucketizeOptions(flatbuffers::FlatBu + + struct GeluOptionsT : public flatbuffers::NativeTable { + typedef GeluOptions TableType; +- bool approximate; +- GeluOptionsT() +- : approximate(false) { +- } ++ bool approximate = false; + }; + + struct GeluOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef GeluOptionsT NativeTableType; ++ typedef GeluOptionsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_APPROXIMATE = 4 + }; +@@ -10592,6 +10950,7 @@ struct GeluOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct GeluOptionsBuilder { ++ typedef GeluOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_approximate(bool approximate) { +@@ -10601,7 +10960,6 @@ struct GeluOptionsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- GeluOptionsBuilder &operator=(const GeluOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10621,12 +10979,11 @@ flatbuffers::Offset CreateGeluOptions(flatbuffers::FlatBufferBuilde + + struct DynamicUpdateSliceOptionsT : public flatbuffers::NativeTable { + typedef DynamicUpdateSliceOptions TableType; +- DynamicUpdateSliceOptionsT() { +- } + }; + + struct DynamicUpdateSliceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef DynamicUpdateSliceOptionsT NativeTableType; ++ typedef DynamicUpdateSliceOptionsBuilder Builder; + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && + verifier.EndTable(); +@@ -10637,13 +10994,13 @@ struct DynamicUpdateSliceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers:: + }; + + struct DynamicUpdateSliceOptionsBuilder { ++ typedef DynamicUpdateSliceOptions Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + explicit DynamicUpdateSliceOptionsBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- DynamicUpdateSliceOptionsBuilder &operator=(const DynamicUpdateSliceOptionsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10661,19 +11018,15 @@ flatbuffers::Offset CreateDynamicUpdateSliceOptions(f + + struct OperatorCodeT : public flatbuffers::NativeTable { + typedef OperatorCode TableType; +- int8_t deprecated_builtin_code; +- std::string custom_code; +- int32_t version; +- tflite::BuiltinOperator builtin_code; +- OperatorCodeT() +- : deprecated_builtin_code(0), +- version(1), +- builtin_code(tflite::BuiltinOperator_ADD) { +- } ++ int8_t deprecated_builtin_code = 0; ++ std::string custom_code{}; ++ int32_t version = 1; ++ tflite::BuiltinOperator builtin_code = tflite::BuiltinOperator_ADD; + }; + + struct OperatorCode FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef OperatorCodeT NativeTableType; ++ typedef OperatorCodeBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_DEPRECATED_BUILTIN_CODE = 4, + VT_CUSTOM_CODE = 6, +@@ -10707,6 +11060,7 @@ struct OperatorCode FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct OperatorCodeBuilder { ++ typedef OperatorCode Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_deprecated_builtin_code(int8_t deprecated_builtin_code) { +@@ -10725,7 +11079,6 @@ struct OperatorCodeBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- OperatorCodeBuilder &operator=(const OperatorCodeBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -10766,22 +11119,19 @@ flatbuffers::Offset CreateOperatorCode(flatbuffers::FlatBufferBuil + + struct OperatorT : public flatbuffers::NativeTable { + typedef Operator TableType; +- uint32_t opcode_index; +- std::vector inputs; +- std::vector outputs; +- tflite::BuiltinOptionsUnion builtin_options; +- std::vector custom_options; +- tflite::CustomOptionsFormat custom_options_format; +- std::vector mutating_variable_inputs; +- std::vector intermediates; +- OperatorT() +- : opcode_index(0), +- custom_options_format(tflite::CustomOptionsFormat_FLEXBUFFERS) { +- } ++ uint32_t opcode_index = 0; ++ std::vector inputs{}; ++ std::vector outputs{}; ++ tflite::BuiltinOptionsUnion builtin_options{}; ++ std::vector custom_options{}; ++ tflite::CustomOptionsFormat custom_options_format = tflite::CustomOptionsFormat_FLEXBUFFERS; ++ std::vector mutating_variable_inputs{}; ++ std::vector intermediates{}; + }; + + struct Operator FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef OperatorT NativeTableType; ++ typedef OperatorBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_OPCODE_INDEX = 4, + VT_INPUTS = 6, +@@ -11665,6 +12015,7 @@ template<> inline const tflite::DynamicUpdateSliceOptions *Operator::builtin_opt + } + + struct OperatorBuilder { ++ typedef Operator Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_opcode_index(uint32_t opcode_index) { +@@ -11698,7 +12049,6 @@ struct OperatorBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- OperatorBuilder &operator=(const OperatorBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -11763,17 +12113,16 @@ flatbuffers::Offset CreateOperator(flatbuffers::FlatBufferBuilder &_fb + + struct SubGraphT : public flatbuffers::NativeTable { + typedef SubGraph TableType; +- std::vector> tensors; +- std::vector inputs; +- std::vector outputs; +- std::vector> operators; +- std::string name; +- SubGraphT() { +- } ++ std::vector> tensors{}; ++ std::vector inputs{}; ++ std::vector outputs{}; ++ std::vector> operators{}; ++ std::string name{}; + }; + + struct SubGraph FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SubGraphT NativeTableType; ++ typedef SubGraphBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_TENSORS = 4, + VT_INPUTS = 6, +@@ -11818,6 +12167,7 @@ struct SubGraph FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SubGraphBuilder { ++ typedef SubGraph Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_tensors(flatbuffers::Offset>> tensors) { +@@ -11839,7 +12189,6 @@ struct SubGraphBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SubGraphBuilder &operator=(const SubGraphBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -11888,13 +12237,12 @@ flatbuffers::Offset CreateSubGraph(flatbuffers::FlatBufferBuilder &_fb + + struct BufferT : public flatbuffers::NativeTable { + typedef Buffer TableType; +- std::vector data; +- BufferT() { +- } ++ std::vector data{}; + }; + + struct Buffer FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BufferT NativeTableType; ++ typedef BufferBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_DATA = 4 + }; +@@ -11913,6 +12261,7 @@ struct Buffer FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct BufferBuilder { ++ typedef Buffer Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_data(flatbuffers::Offset> data) { +@@ -11922,7 +12271,6 @@ struct BufferBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BufferBuilder &operator=(const BufferBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -11952,15 +12300,13 @@ flatbuffers::Offset CreateBuffer(flatbuffers::FlatBufferBuilder &_fbb, c + + struct MetadataT : public flatbuffers::NativeTable { + typedef Metadata TableType; +- std::string name; +- uint32_t buffer; +- MetadataT() +- : buffer(0) { +- } ++ std::string name{}; ++ uint32_t buffer = 0; + }; + + struct Metadata FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef MetadataT NativeTableType; ++ typedef MetadataBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NAME = 4, + VT_BUFFER = 6 +@@ -11984,6 +12330,7 @@ struct Metadata FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct MetadataBuilder { ++ typedef Metadata Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_name(flatbuffers::Offset name) { +@@ -11996,7 +12343,6 @@ struct MetadataBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- MetadataBuilder &operator=(const MetadataBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -12029,15 +12375,13 @@ flatbuffers::Offset CreateMetadata(flatbuffers::FlatBufferBuilder &_fb + + struct TensorMapT : public flatbuffers::NativeTable { + typedef TensorMap TableType; +- std::string name; +- uint32_t tensor_index; +- TensorMapT() +- : tensor_index(0) { +- } ++ std::string name{}; ++ uint32_t tensor_index = 0; + }; + + struct TensorMap FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef TensorMapT NativeTableType; ++ typedef TensorMapBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NAME = 4, + VT_TENSOR_INDEX = 6 +@@ -12061,6 +12405,7 @@ struct TensorMap FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct TensorMapBuilder { ++ typedef TensorMap Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_name(flatbuffers::Offset name) { +@@ -12073,7 +12418,6 @@ struct TensorMapBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- TensorMapBuilder &operator=(const TensorMapBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -12106,17 +12450,15 @@ flatbuffers::Offset CreateTensorMap(flatbuffers::FlatBufferBuilder &_ + + struct SignatureDefT : public flatbuffers::NativeTable { + typedef SignatureDef TableType; +- std::vector> inputs; +- std::vector> outputs; +- std::string signature_key; +- uint32_t subgraph_index; +- SignatureDefT() +- : subgraph_index(0) { +- } ++ std::vector> inputs{}; ++ std::vector> outputs{}; ++ std::string signature_key{}; ++ uint32_t subgraph_index = 0; + }; + + struct SignatureDef FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef SignatureDefT NativeTableType; ++ typedef SignatureDefBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_INPUTS = 4, + VT_OUTPUTS = 6, +@@ -12154,6 +12496,7 @@ struct SignatureDef FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct SignatureDefBuilder { ++ typedef SignatureDef Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_inputs(flatbuffers::Offset>> inputs) { +@@ -12172,7 +12515,6 @@ struct SignatureDefBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- SignatureDefBuilder &operator=(const SignatureDefBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -12215,21 +12557,19 @@ flatbuffers::Offset CreateSignatureDef(flatbuffers::FlatBufferBuil + + struct ModelT : public flatbuffers::NativeTable { + typedef Model TableType; +- uint32_t version; +- std::vector> operator_codes; +- std::vector> subgraphs; +- std::string description; +- std::vector> buffers; +- std::vector metadata_buffer; +- std::vector> metadata; +- std::vector> signature_defs; +- ModelT() +- : version(0) { +- } ++ uint32_t version = 0; ++ std::vector> operator_codes{}; ++ std::vector> subgraphs{}; ++ std::string description{}; ++ std::vector> buffers{}; ++ std::vector metadata_buffer{}; ++ std::vector> metadata{}; ++ std::vector> signature_defs{}; + }; + + struct Model FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ModelT NativeTableType; ++ typedef ModelBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_VERSION = 4, + VT_OPERATOR_CODES = 6, +@@ -12294,6 +12634,7 @@ struct Model FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ModelBuilder { ++ typedef Model Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_version(uint32_t version) { +@@ -12324,7 +12665,6 @@ struct ModelBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ModelBuilder &operator=(const ModelBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -12386,9 +12726,9 @@ inline flatbuffers::Offset CreateModelDirect( + flatbuffers::Offset CreateModel(flatbuffers::FlatBufferBuilder &_fbb, const ModelT *_o, const flatbuffers::rehasher_function_t *_rehasher = nullptr); + + inline CustomQuantizationT *CustomQuantization::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new CustomQuantizationT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new CustomQuantizationT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void CustomQuantization::UnPackTo(CustomQuantizationT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12413,9 +12753,9 @@ inline flatbuffers::Offset CreateCustomQuantization(flatbuff + } + + inline QuantizationParametersT *QuantizationParameters::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new QuantizationParametersT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new QuantizationParametersT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void QuantizationParameters::UnPackTo(QuantizationParametersT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12457,9 +12797,9 @@ inline flatbuffers::Offset CreateQuantizationParameters( + } + + inline Int32VectorT *Int32Vector::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new Int32VectorT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new Int32VectorT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Int32Vector::UnPackTo(Int32VectorT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12483,9 +12823,9 @@ inline flatbuffers::Offset CreateInt32Vector(flatbuffers::FlatBuffe + } + + inline Uint16VectorT *Uint16Vector::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new Uint16VectorT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new Uint16VectorT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Uint16Vector::UnPackTo(Uint16VectorT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12510,9 +12850,9 @@ inline flatbuffers::Offset CreateUint16Vector(flatbuffers::FlatBuf + } + + inline Uint8VectorT *Uint8Vector::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new Uint8VectorT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new Uint8VectorT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Uint8Vector::UnPackTo(Uint8VectorT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12537,9 +12877,9 @@ inline flatbuffers::Offset CreateUint8Vector(flatbuffers::FlatBuffe + } + + inline DimensionMetadataT *DimensionMetadata::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new DimensionMetadataT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new DimensionMetadataT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void DimensionMetadata::UnPackTo(DimensionMetadataT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12578,9 +12918,9 @@ inline flatbuffers::Offset CreateDimensionMetadata(flatbuffer + } + + inline SparsityParametersT *SparsityParameters::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SparsityParametersT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SparsityParametersT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SparsityParameters::UnPackTo(SparsityParametersT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12588,7 +12928,7 @@ inline void SparsityParameters::UnPackTo(SparsityParametersT *_o, const flatbuff + (void)_resolver; + { auto _e = traversal_order(); if (_e) { _o->traversal_order.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->traversal_order[_i] = _e->Get(_i); } } } + { auto _e = block_map(); if (_e) { _o->block_map.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->block_map[_i] = _e->Get(_i); } } } +- { auto _e = dim_metadata(); if (_e) { _o->dim_metadata.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->dim_metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } ++ { auto _e = dim_metadata(); if (_e) { _o->dim_metadata.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->dim_metadata[_i]) { _e->Get(_i)->UnPackTo(_o->dim_metadata[_i].get(), _resolver); } else { _o->dim_metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline flatbuffers::Offset SparsityParameters::Pack(flatbuffers::FlatBufferBuilder &_fbb, const SparsityParametersT* _o, const flatbuffers::rehasher_function_t *_rehasher) { +@@ -12610,9 +12950,9 @@ inline flatbuffers::Offset CreateSparsityParameters(flatbuff + } + + inline TensorT *Tensor::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new TensorT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new TensorT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Tensor::UnPackTo(TensorT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12622,9 +12962,9 @@ inline void Tensor::UnPackTo(TensorT *_o, const flatbuffers::resolver_function_t + { auto _e = type(); _o->type = _e; } + { auto _e = buffer(); _o->buffer = _e; } + { auto _e = name(); if (_e) _o->name = _e->str(); } +- { auto _e = quantization(); if (_e) _o->quantization = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = quantization(); if (_e) { if(_o->quantization) { _e->UnPackTo(_o->quantization.get(), _resolver); } else { _o->quantization = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = is_variable(); _o->is_variable = _e; } +- { auto _e = sparsity(); if (_e) _o->sparsity = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = sparsity(); if (_e) { if(_o->sparsity) { _e->UnPackTo(_o->sparsity.get(), _resolver); } else { _o->sparsity = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = shape_signature(); if (_e) { _o->shape_signature.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape_signature[_i] = _e->Get(_i); } } } + } + +@@ -12657,9 +12997,9 @@ inline flatbuffers::Offset CreateTensor(flatbuffers::FlatBufferBuilder & + } + + inline Conv2DOptionsT *Conv2DOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new Conv2DOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new Conv2DOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Conv2DOptions::UnPackTo(Conv2DOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12698,9 +13038,9 @@ inline flatbuffers::Offset CreateConv2DOptions(flatbuffers::FlatB + } + + inline Conv3DOptionsT *Conv3DOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new Conv3DOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new Conv3DOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Conv3DOptions::UnPackTo(Conv3DOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12745,9 +13085,9 @@ inline flatbuffers::Offset CreateConv3DOptions(flatbuffers::FlatB + } + + inline Pool2DOptionsT *Pool2DOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new Pool2DOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new Pool2DOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Pool2DOptions::UnPackTo(Pool2DOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12786,9 +13126,9 @@ inline flatbuffers::Offset CreatePool2DOptions(flatbuffers::FlatB + } + + inline DepthwiseConv2DOptionsT *DepthwiseConv2DOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new DepthwiseConv2DOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new DepthwiseConv2DOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void DepthwiseConv2DOptions::UnPackTo(DepthwiseConv2DOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12830,9 +13170,9 @@ inline flatbuffers::Offset CreateDepthwiseConv2DOptions( + } + + inline ConcatEmbeddingsOptionsT *ConcatEmbeddingsOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ConcatEmbeddingsOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ConcatEmbeddingsOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ConcatEmbeddingsOptions::UnPackTo(ConcatEmbeddingsOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12862,9 +13202,9 @@ inline flatbuffers::Offset CreateConcatEmbeddingsOption + } + + inline LSHProjectionOptionsT *LSHProjectionOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new LSHProjectionOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new LSHProjectionOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void LSHProjectionOptions::UnPackTo(LSHProjectionOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12888,9 +13228,9 @@ inline flatbuffers::Offset CreateLSHProjectionOptions(flat + } + + inline SVDFOptionsT *SVDFOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SVDFOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SVDFOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SVDFOptions::UnPackTo(SVDFOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12920,9 +13260,9 @@ inline flatbuffers::Offset CreateSVDFOptions(flatbuffers::FlatBuffe + } + + inline RNNOptionsT *RNNOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new RNNOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new RNNOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void RNNOptions::UnPackTo(RNNOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12949,9 +13289,9 @@ inline flatbuffers::Offset CreateRNNOptions(flatbuffers::FlatBufferB + } + + inline SequenceRNNOptionsT *SequenceRNNOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SequenceRNNOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SequenceRNNOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SequenceRNNOptions::UnPackTo(SequenceRNNOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -12981,9 +13321,9 @@ inline flatbuffers::Offset CreateSequenceRNNOptions(flatbuff + } + + inline BidirectionalSequenceRNNOptionsT *BidirectionalSequenceRNNOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BidirectionalSequenceRNNOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BidirectionalSequenceRNNOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BidirectionalSequenceRNNOptions::UnPackTo(BidirectionalSequenceRNNOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13016,9 +13356,9 @@ inline flatbuffers::Offset CreateBidirectionalS + } + + inline FullyConnectedOptionsT *FullyConnectedOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new FullyConnectedOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new FullyConnectedOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void FullyConnectedOptions::UnPackTo(FullyConnectedOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13051,9 +13391,9 @@ inline flatbuffers::Offset CreateFullyConnectedOptions(fl + } + + inline SoftmaxOptionsT *SoftmaxOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SoftmaxOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SoftmaxOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SoftmaxOptions::UnPackTo(SoftmaxOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13077,9 +13417,9 @@ inline flatbuffers::Offset CreateSoftmaxOptions(flatbuffers::Fla + } + + inline ConcatenationOptionsT *ConcatenationOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ConcatenationOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ConcatenationOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ConcatenationOptions::UnPackTo(ConcatenationOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13106,9 +13446,9 @@ inline flatbuffers::Offset CreateConcatenationOptions(flat + } + + inline AddOptionsT *AddOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new AddOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new AddOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void AddOptions::UnPackTo(AddOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13135,9 +13475,9 @@ inline flatbuffers::Offset CreateAddOptions(flatbuffers::FlatBufferB + } + + inline MulOptionsT *MulOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new MulOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new MulOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void MulOptions::UnPackTo(MulOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13161,9 +13501,9 @@ inline flatbuffers::Offset CreateMulOptions(flatbuffers::FlatBufferB + } + + inline L2NormOptionsT *L2NormOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new L2NormOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new L2NormOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void L2NormOptions::UnPackTo(L2NormOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13187,9 +13527,9 @@ inline flatbuffers::Offset CreateL2NormOptions(flatbuffers::FlatB + } + + inline LocalResponseNormalizationOptionsT *LocalResponseNormalizationOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new LocalResponseNormalizationOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new LocalResponseNormalizationOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void LocalResponseNormalizationOptions::UnPackTo(LocalResponseNormalizationOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13222,9 +13562,9 @@ inline flatbuffers::Offset CreateLocalRespons + } + + inline LSTMOptionsT *LSTMOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new LSTMOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new LSTMOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void LSTMOptions::UnPackTo(LSTMOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13260,9 +13600,9 @@ inline flatbuffers::Offset CreateLSTMOptions(flatbuffers::FlatBuffe + } + + inline UnidirectionalSequenceLSTMOptionsT *UnidirectionalSequenceLSTMOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new UnidirectionalSequenceLSTMOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new UnidirectionalSequenceLSTMOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void UnidirectionalSequenceLSTMOptions::UnPackTo(UnidirectionalSequenceLSTMOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13298,9 +13638,9 @@ inline flatbuffers::Offset CreateUnidirection + } + + inline BidirectionalSequenceLSTMOptionsT *BidirectionalSequenceLSTMOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BidirectionalSequenceLSTMOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BidirectionalSequenceLSTMOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BidirectionalSequenceLSTMOptions::UnPackTo(BidirectionalSequenceLSTMOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13339,9 +13679,9 @@ inline flatbuffers::Offset CreateBidirectional + } + + inline ResizeBilinearOptionsT *ResizeBilinearOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ResizeBilinearOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ResizeBilinearOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ResizeBilinearOptions::UnPackTo(ResizeBilinearOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13368,9 +13708,9 @@ inline flatbuffers::Offset CreateResizeBilinearOptions(fl + } + + inline ResizeNearestNeighborOptionsT *ResizeNearestNeighborOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ResizeNearestNeighborOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ResizeNearestNeighborOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ResizeNearestNeighborOptions::UnPackTo(ResizeNearestNeighborOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13397,9 +13737,9 @@ inline flatbuffers::Offset CreateResizeNearestNeig + } + + inline CallOptionsT *CallOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new CallOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new CallOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void CallOptions::UnPackTo(CallOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13423,9 +13763,9 @@ inline flatbuffers::Offset CreateCallOptions(flatbuffers::FlatBuffe + } + + inline PadOptionsT *PadOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new PadOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new PadOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void PadOptions::UnPackTo(PadOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13446,9 +13786,9 @@ inline flatbuffers::Offset CreatePadOptions(flatbuffers::FlatBufferB + } + + inline PadV2OptionsT *PadV2Options::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new PadV2OptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new PadV2OptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void PadV2Options::UnPackTo(PadV2OptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13469,9 +13809,9 @@ inline flatbuffers::Offset CreatePadV2Options(flatbuffers::FlatBuf + } + + inline ReshapeOptionsT *ReshapeOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ReshapeOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ReshapeOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ReshapeOptions::UnPackTo(ReshapeOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13495,9 +13835,9 @@ inline flatbuffers::Offset CreateReshapeOptions(flatbuffers::Fla + } + + inline SpaceToBatchNDOptionsT *SpaceToBatchNDOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SpaceToBatchNDOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SpaceToBatchNDOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SpaceToBatchNDOptions::UnPackTo(SpaceToBatchNDOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13518,9 +13858,9 @@ inline flatbuffers::Offset CreateSpaceToBatchNDOptions(fl + } + + inline BatchToSpaceNDOptionsT *BatchToSpaceNDOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BatchToSpaceNDOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BatchToSpaceNDOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BatchToSpaceNDOptions::UnPackTo(BatchToSpaceNDOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13541,9 +13881,9 @@ inline flatbuffers::Offset CreateBatchToSpaceNDOptions(fl + } + + inline SkipGramOptionsT *SkipGramOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SkipGramOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SkipGramOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SkipGramOptions::UnPackTo(SkipGramOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13573,9 +13913,9 @@ inline flatbuffers::Offset CreateSkipGramOptions(flatbuffers::F + } + + inline SpaceToDepthOptionsT *SpaceToDepthOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SpaceToDepthOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SpaceToDepthOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SpaceToDepthOptions::UnPackTo(SpaceToDepthOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13599,9 +13939,9 @@ inline flatbuffers::Offset CreateSpaceToDepthOptions(flatbu + } + + inline DepthToSpaceOptionsT *DepthToSpaceOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new DepthToSpaceOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new DepthToSpaceOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void DepthToSpaceOptions::UnPackTo(DepthToSpaceOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13625,9 +13965,9 @@ inline flatbuffers::Offset CreateDepthToSpaceOptions(flatbu + } + + inline SubOptionsT *SubOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SubOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SubOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SubOptions::UnPackTo(SubOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13654,9 +13994,9 @@ inline flatbuffers::Offset CreateSubOptions(flatbuffers::FlatBufferB + } + + inline DivOptionsT *DivOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new DivOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new DivOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void DivOptions::UnPackTo(DivOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13680,9 +14020,9 @@ inline flatbuffers::Offset CreateDivOptions(flatbuffers::FlatBufferB + } + + inline TopKV2OptionsT *TopKV2Options::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new TopKV2OptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new TopKV2OptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void TopKV2Options::UnPackTo(TopKV2OptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13703,9 +14043,9 @@ inline flatbuffers::Offset CreateTopKV2Options(flatbuffers::FlatB + } + + inline EmbeddingLookupSparseOptionsT *EmbeddingLookupSparseOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new EmbeddingLookupSparseOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new EmbeddingLookupSparseOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void EmbeddingLookupSparseOptions::UnPackTo(EmbeddingLookupSparseOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13729,9 +14069,9 @@ inline flatbuffers::Offset CreateEmbeddingLookupSp + } + + inline GatherOptionsT *GatherOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new GatherOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new GatherOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void GatherOptions::UnPackTo(GatherOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13758,9 +14098,9 @@ inline flatbuffers::Offset CreateGatherOptions(flatbuffers::FlatB + } + + inline TransposeOptionsT *TransposeOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new TransposeOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new TransposeOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void TransposeOptions::UnPackTo(TransposeOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13781,9 +14121,9 @@ inline flatbuffers::Offset CreateTransposeOptions(flatbuffers: + } + + inline ExpOptionsT *ExpOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ExpOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ExpOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ExpOptions::UnPackTo(ExpOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13804,9 +14144,9 @@ inline flatbuffers::Offset CreateExpOptions(flatbuffers::FlatBufferB + } + + inline CosOptionsT *CosOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new CosOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new CosOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void CosOptions::UnPackTo(CosOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13827,9 +14167,9 @@ inline flatbuffers::Offset CreateCosOptions(flatbuffers::FlatBufferB + } + + inline ReducerOptionsT *ReducerOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ReducerOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ReducerOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ReducerOptions::UnPackTo(ReducerOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13853,9 +14193,9 @@ inline flatbuffers::Offset CreateReducerOptions(flatbuffers::Fla + } + + inline SqueezeOptionsT *SqueezeOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SqueezeOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SqueezeOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SqueezeOptions::UnPackTo(SqueezeOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13879,9 +14219,9 @@ inline flatbuffers::Offset CreateSqueezeOptions(flatbuffers::Fla + } + + inline SplitOptionsT *SplitOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SplitOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SplitOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SplitOptions::UnPackTo(SplitOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13905,9 +14245,9 @@ inline flatbuffers::Offset CreateSplitOptions(flatbuffers::FlatBuf + } + + inline SplitVOptionsT *SplitVOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SplitVOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SplitVOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SplitVOptions::UnPackTo(SplitVOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13931,9 +14271,9 @@ inline flatbuffers::Offset CreateSplitVOptions(flatbuffers::FlatB + } + + inline StridedSliceOptionsT *StridedSliceOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new StridedSliceOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new StridedSliceOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void StridedSliceOptions::UnPackTo(StridedSliceOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13969,9 +14309,9 @@ inline flatbuffers::Offset CreateStridedSliceOptions(flatbu + } + + inline LogSoftmaxOptionsT *LogSoftmaxOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new LogSoftmaxOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new LogSoftmaxOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void LogSoftmaxOptions::UnPackTo(LogSoftmaxOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -13992,9 +14332,9 @@ inline flatbuffers::Offset CreateLogSoftmaxOptions(flatbuffer + } + + inline CastOptionsT *CastOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new CastOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new CastOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void CastOptions::UnPackTo(CastOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14021,9 +14361,9 @@ inline flatbuffers::Offset CreateCastOptions(flatbuffers::FlatBuffe + } + + inline DequantizeOptionsT *DequantizeOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new DequantizeOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new DequantizeOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void DequantizeOptions::UnPackTo(DequantizeOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14044,9 +14384,9 @@ inline flatbuffers::Offset CreateDequantizeOptions(flatbuffer + } + + inline MaximumMinimumOptionsT *MaximumMinimumOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new MaximumMinimumOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new MaximumMinimumOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void MaximumMinimumOptions::UnPackTo(MaximumMinimumOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14067,9 +14407,9 @@ inline flatbuffers::Offset CreateMaximumMinimumOptions(fl + } + + inline TileOptionsT *TileOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new TileOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new TileOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void TileOptions::UnPackTo(TileOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14090,9 +14430,9 @@ inline flatbuffers::Offset CreateTileOptions(flatbuffers::FlatBuffe + } + + inline ArgMaxOptionsT *ArgMaxOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ArgMaxOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ArgMaxOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ArgMaxOptions::UnPackTo(ArgMaxOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14116,9 +14456,9 @@ inline flatbuffers::Offset CreateArgMaxOptions(flatbuffers::FlatB + } + + inline ArgMinOptionsT *ArgMinOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ArgMinOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ArgMinOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ArgMinOptions::UnPackTo(ArgMinOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14142,9 +14482,9 @@ inline flatbuffers::Offset CreateArgMinOptions(flatbuffers::FlatB + } + + inline GreaterOptionsT *GreaterOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new GreaterOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new GreaterOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void GreaterOptions::UnPackTo(GreaterOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14165,9 +14505,9 @@ inline flatbuffers::Offset CreateGreaterOptions(flatbuffers::Fla + } + + inline GreaterEqualOptionsT *GreaterEqualOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new GreaterEqualOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new GreaterEqualOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void GreaterEqualOptions::UnPackTo(GreaterEqualOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14188,9 +14528,9 @@ inline flatbuffers::Offset CreateGreaterEqualOptions(flatbu + } + + inline LessOptionsT *LessOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new LessOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new LessOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void LessOptions::UnPackTo(LessOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14211,9 +14551,9 @@ inline flatbuffers::Offset CreateLessOptions(flatbuffers::FlatBuffe + } + + inline LessEqualOptionsT *LessEqualOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new LessEqualOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new LessEqualOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void LessEqualOptions::UnPackTo(LessEqualOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14234,9 +14574,9 @@ inline flatbuffers::Offset CreateLessEqualOptions(flatbuffers: + } + + inline NegOptionsT *NegOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new NegOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new NegOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void NegOptions::UnPackTo(NegOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14257,9 +14597,9 @@ inline flatbuffers::Offset CreateNegOptions(flatbuffers::FlatBufferB + } + + inline SelectOptionsT *SelectOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SelectOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SelectOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SelectOptions::UnPackTo(SelectOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14280,9 +14620,9 @@ inline flatbuffers::Offset CreateSelectOptions(flatbuffers::FlatB + } + + inline SliceOptionsT *SliceOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SliceOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SliceOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SliceOptions::UnPackTo(SliceOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14303,9 +14643,9 @@ inline flatbuffers::Offset CreateSliceOptions(flatbuffers::FlatBuf + } + + inline TransposeConvOptionsT *TransposeConvOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new TransposeConvOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new TransposeConvOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void TransposeConvOptions::UnPackTo(TransposeConvOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14335,9 +14675,9 @@ inline flatbuffers::Offset CreateTransposeConvOptions(flat + } + + inline ExpandDimsOptionsT *ExpandDimsOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ExpandDimsOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ExpandDimsOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ExpandDimsOptions::UnPackTo(ExpandDimsOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14358,9 +14698,9 @@ inline flatbuffers::Offset CreateExpandDimsOptions(flatbuffer + } + + inline SparseToDenseOptionsT *SparseToDenseOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SparseToDenseOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SparseToDenseOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SparseToDenseOptions::UnPackTo(SparseToDenseOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14384,9 +14724,9 @@ inline flatbuffers::Offset CreateSparseToDenseOptions(flat + } + + inline EqualOptionsT *EqualOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new EqualOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new EqualOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void EqualOptions::UnPackTo(EqualOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14407,9 +14747,9 @@ inline flatbuffers::Offset CreateEqualOptions(flatbuffers::FlatBuf + } + + inline NotEqualOptionsT *NotEqualOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new NotEqualOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new NotEqualOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void NotEqualOptions::UnPackTo(NotEqualOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14430,9 +14770,9 @@ inline flatbuffers::Offset CreateNotEqualOptions(flatbuffers::F + } + + inline ShapeOptionsT *ShapeOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ShapeOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ShapeOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ShapeOptions::UnPackTo(ShapeOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14456,9 +14796,9 @@ inline flatbuffers::Offset CreateShapeOptions(flatbuffers::FlatBuf + } + + inline RankOptionsT *RankOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new RankOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new RankOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void RankOptions::UnPackTo(RankOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14479,9 +14819,9 @@ inline flatbuffers::Offset CreateRankOptions(flatbuffers::FlatBuffe + } + + inline PowOptionsT *PowOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new PowOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new PowOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void PowOptions::UnPackTo(PowOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14502,9 +14842,9 @@ inline flatbuffers::Offset CreatePowOptions(flatbuffers::FlatBufferB + } + + inline FakeQuantOptionsT *FakeQuantOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new FakeQuantOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new FakeQuantOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void FakeQuantOptions::UnPackTo(FakeQuantOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14537,9 +14877,9 @@ inline flatbuffers::Offset CreateFakeQuantOptions(flatbuffers: + } + + inline PackOptionsT *PackOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new PackOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new PackOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void PackOptions::UnPackTo(PackOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14566,9 +14906,9 @@ inline flatbuffers::Offset CreatePackOptions(flatbuffers::FlatBuffe + } + + inline LogicalOrOptionsT *LogicalOrOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new LogicalOrOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new LogicalOrOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void LogicalOrOptions::UnPackTo(LogicalOrOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14589,9 +14929,9 @@ inline flatbuffers::Offset CreateLogicalOrOptions(flatbuffers: + } + + inline OneHotOptionsT *OneHotOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new OneHotOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new OneHotOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void OneHotOptions::UnPackTo(OneHotOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14615,9 +14955,9 @@ inline flatbuffers::Offset CreateOneHotOptions(flatbuffers::FlatB + } + + inline AbsOptionsT *AbsOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new AbsOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new AbsOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void AbsOptions::UnPackTo(AbsOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14638,9 +14978,9 @@ inline flatbuffers::Offset CreateAbsOptions(flatbuffers::FlatBufferB + } + + inline HardSwishOptionsT *HardSwishOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new HardSwishOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new HardSwishOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void HardSwishOptions::UnPackTo(HardSwishOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14661,9 +15001,9 @@ inline flatbuffers::Offset CreateHardSwishOptions(flatbuffers: + } + + inline LogicalAndOptionsT *LogicalAndOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new LogicalAndOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new LogicalAndOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void LogicalAndOptions::UnPackTo(LogicalAndOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14684,9 +15024,9 @@ inline flatbuffers::Offset CreateLogicalAndOptions(flatbuffer + } + + inline LogicalNotOptionsT *LogicalNotOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new LogicalNotOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new LogicalNotOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void LogicalNotOptions::UnPackTo(LogicalNotOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14707,9 +15047,9 @@ inline flatbuffers::Offset CreateLogicalNotOptions(flatbuffer + } + + inline UnpackOptionsT *UnpackOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new UnpackOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new UnpackOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void UnpackOptions::UnPackTo(UnpackOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14736,9 +15076,9 @@ inline flatbuffers::Offset CreateUnpackOptions(flatbuffers::FlatB + } + + inline FloorDivOptionsT *FloorDivOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new FloorDivOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new FloorDivOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void FloorDivOptions::UnPackTo(FloorDivOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14759,9 +15099,9 @@ inline flatbuffers::Offset CreateFloorDivOptions(flatbuffers::F + } + + inline SquareOptionsT *SquareOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SquareOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SquareOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SquareOptions::UnPackTo(SquareOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14782,9 +15122,9 @@ inline flatbuffers::Offset CreateSquareOptions(flatbuffers::FlatB + } + + inline ZerosLikeOptionsT *ZerosLikeOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ZerosLikeOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ZerosLikeOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ZerosLikeOptions::UnPackTo(ZerosLikeOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14805,9 +15145,9 @@ inline flatbuffers::Offset CreateZerosLikeOptions(flatbuffers: + } + + inline FillOptionsT *FillOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new FillOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new FillOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void FillOptions::UnPackTo(FillOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14828,9 +15168,9 @@ inline flatbuffers::Offset CreateFillOptions(flatbuffers::FlatBuffe + } + + inline FloorModOptionsT *FloorModOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new FloorModOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new FloorModOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void FloorModOptions::UnPackTo(FloorModOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14851,9 +15191,9 @@ inline flatbuffers::Offset CreateFloorModOptions(flatbuffers::F + } + + inline RangeOptionsT *RangeOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new RangeOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new RangeOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void RangeOptions::UnPackTo(RangeOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14874,9 +15214,9 @@ inline flatbuffers::Offset CreateRangeOptions(flatbuffers::FlatBuf + } + + inline LeakyReluOptionsT *LeakyReluOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new LeakyReluOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new LeakyReluOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void LeakyReluOptions::UnPackTo(LeakyReluOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14900,9 +15240,9 @@ inline flatbuffers::Offset CreateLeakyReluOptions(flatbuffers: + } + + inline SquaredDifferenceOptionsT *SquaredDifferenceOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SquaredDifferenceOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SquaredDifferenceOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SquaredDifferenceOptions::UnPackTo(SquaredDifferenceOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14923,9 +15263,9 @@ inline flatbuffers::Offset CreateSquaredDifferenceOpti + } + + inline MirrorPadOptionsT *MirrorPadOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new MirrorPadOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new MirrorPadOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void MirrorPadOptions::UnPackTo(MirrorPadOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14949,9 +15289,9 @@ inline flatbuffers::Offset CreateMirrorPadOptions(flatbuffers: + } + + inline UniqueOptionsT *UniqueOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new UniqueOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new UniqueOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void UniqueOptions::UnPackTo(UniqueOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14975,9 +15315,9 @@ inline flatbuffers::Offset CreateUniqueOptions(flatbuffers::FlatB + } + + inline ReverseV2OptionsT *ReverseV2Options::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ReverseV2OptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ReverseV2OptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ReverseV2Options::UnPackTo(ReverseV2OptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -14998,9 +15338,9 @@ inline flatbuffers::Offset CreateReverseV2Options(flatbuffers: + } + + inline AddNOptionsT *AddNOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new AddNOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new AddNOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void AddNOptions::UnPackTo(AddNOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15021,9 +15361,9 @@ inline flatbuffers::Offset CreateAddNOptions(flatbuffers::FlatBuffe + } + + inline GatherNdOptionsT *GatherNdOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new GatherNdOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new GatherNdOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void GatherNdOptions::UnPackTo(GatherNdOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15044,9 +15384,9 @@ inline flatbuffers::Offset CreateGatherNdOptions(flatbuffers::F + } + + inline WhereOptionsT *WhereOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new WhereOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new WhereOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void WhereOptions::UnPackTo(WhereOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15067,9 +15407,9 @@ inline flatbuffers::Offset CreateWhereOptions(flatbuffers::FlatBuf + } + + inline ReverseSequenceOptionsT *ReverseSequenceOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ReverseSequenceOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ReverseSequenceOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ReverseSequenceOptions::UnPackTo(ReverseSequenceOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15096,9 +15436,9 @@ inline flatbuffers::Offset CreateReverseSequenceOptions( + } + + inline MatrixDiagOptionsT *MatrixDiagOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new MatrixDiagOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new MatrixDiagOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void MatrixDiagOptions::UnPackTo(MatrixDiagOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15119,9 +15459,9 @@ inline flatbuffers::Offset CreateMatrixDiagOptions(flatbuffer + } + + inline QuantizeOptionsT *QuantizeOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new QuantizeOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new QuantizeOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void QuantizeOptions::UnPackTo(QuantizeOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15142,9 +15482,9 @@ inline flatbuffers::Offset CreateQuantizeOptions(flatbuffers::F + } + + inline MatrixSetDiagOptionsT *MatrixSetDiagOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new MatrixSetDiagOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new MatrixSetDiagOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void MatrixSetDiagOptions::UnPackTo(MatrixSetDiagOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15165,9 +15505,9 @@ inline flatbuffers::Offset CreateMatrixSetDiagOptions(flat + } + + inline IfOptionsT *IfOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new IfOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new IfOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void IfOptions::UnPackTo(IfOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15194,9 +15534,9 @@ inline flatbuffers::Offset CreateIfOptions(flatbuffers::FlatBufferBui + } + + inline CallOnceOptionsT *CallOnceOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new CallOnceOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new CallOnceOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void CallOnceOptions::UnPackTo(CallOnceOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15220,9 +15560,9 @@ inline flatbuffers::Offset CreateCallOnceOptions(flatbuffers::F + } + + inline WhileOptionsT *WhileOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new WhileOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new WhileOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void WhileOptions::UnPackTo(WhileOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15249,9 +15589,9 @@ inline flatbuffers::Offset CreateWhileOptions(flatbuffers::FlatBuf + } + + inline NonMaxSuppressionV4OptionsT *NonMaxSuppressionV4Options::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new NonMaxSuppressionV4OptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new NonMaxSuppressionV4OptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void NonMaxSuppressionV4Options::UnPackTo(NonMaxSuppressionV4OptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15272,9 +15612,9 @@ inline flatbuffers::Offset CreateNonMaxSuppressionV4 + } + + inline NonMaxSuppressionV5OptionsT *NonMaxSuppressionV5Options::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new NonMaxSuppressionV5OptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new NonMaxSuppressionV5OptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void NonMaxSuppressionV5Options::UnPackTo(NonMaxSuppressionV5OptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15295,9 +15635,9 @@ inline flatbuffers::Offset CreateNonMaxSuppressionV5 + } + + inline ScatterNdOptionsT *ScatterNdOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ScatterNdOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ScatterNdOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ScatterNdOptions::UnPackTo(ScatterNdOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15318,9 +15658,9 @@ inline flatbuffers::Offset CreateScatterNdOptions(flatbuffers: + } + + inline SelectV2OptionsT *SelectV2Options::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SelectV2OptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SelectV2OptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SelectV2Options::UnPackTo(SelectV2OptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15341,9 +15681,9 @@ inline flatbuffers::Offset CreateSelectV2Options(flatbuffers::F + } + + inline DensifyOptionsT *DensifyOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new DensifyOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new DensifyOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void DensifyOptions::UnPackTo(DensifyOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15364,9 +15704,9 @@ inline flatbuffers::Offset CreateDensifyOptions(flatbuffers::Fla + } + + inline SegmentSumOptionsT *SegmentSumOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SegmentSumOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SegmentSumOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SegmentSumOptions::UnPackTo(SegmentSumOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15387,9 +15727,9 @@ inline flatbuffers::Offset CreateSegmentSumOptions(flatbuffer + } + + inline BatchMatMulOptionsT *BatchMatMulOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BatchMatMulOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BatchMatMulOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BatchMatMulOptions::UnPackTo(BatchMatMulOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15419,9 +15759,9 @@ inline flatbuffers::Offset CreateBatchMatMulOptions(flatbuff + } + + inline CumsumOptionsT *CumsumOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new CumsumOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new CumsumOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void CumsumOptions::UnPackTo(CumsumOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15448,9 +15788,9 @@ inline flatbuffers::Offset CreateCumsumOptions(flatbuffers::FlatB + } + + inline BroadcastToOptionsT *BroadcastToOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BroadcastToOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BroadcastToOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BroadcastToOptions::UnPackTo(BroadcastToOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15471,9 +15811,9 @@ inline flatbuffers::Offset CreateBroadcastToOptions(flatbuff + } + + inline Rfft2dOptionsT *Rfft2dOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new Rfft2dOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new Rfft2dOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Rfft2dOptions::UnPackTo(Rfft2dOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15494,9 +15834,9 @@ inline flatbuffers::Offset CreateRfft2dOptions(flatbuffers::FlatB + } + + inline HashtableOptionsT *HashtableOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new HashtableOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new HashtableOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void HashtableOptions::UnPackTo(HashtableOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15526,9 +15866,9 @@ inline flatbuffers::Offset CreateHashtableOptions(flatbuffers: + } + + inline HashtableFindOptionsT *HashtableFindOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new HashtableFindOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new HashtableFindOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void HashtableFindOptions::UnPackTo(HashtableFindOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15549,9 +15889,9 @@ inline flatbuffers::Offset CreateHashtableFindOptions(flat + } + + inline HashtableImportOptionsT *HashtableImportOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new HashtableImportOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new HashtableImportOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void HashtableImportOptions::UnPackTo(HashtableImportOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15572,9 +15912,9 @@ inline flatbuffers::Offset CreateHashtableImportOptions( + } + + inline HashtableSizeOptionsT *HashtableSizeOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new HashtableSizeOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new HashtableSizeOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void HashtableSizeOptions::UnPackTo(HashtableSizeOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15595,9 +15935,9 @@ inline flatbuffers::Offset CreateHashtableSizeOptions(flat + } + + inline VarHandleOptionsT *VarHandleOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new VarHandleOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new VarHandleOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void VarHandleOptions::UnPackTo(VarHandleOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15624,9 +15964,9 @@ inline flatbuffers::Offset CreateVarHandleOptions(flatbuffers: + } + + inline ReadVariableOptionsT *ReadVariableOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ReadVariableOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ReadVariableOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ReadVariableOptions::UnPackTo(ReadVariableOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15647,9 +15987,9 @@ inline flatbuffers::Offset CreateReadVariableOptions(flatbu + } + + inline AssignVariableOptionsT *AssignVariableOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new AssignVariableOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new AssignVariableOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void AssignVariableOptions::UnPackTo(AssignVariableOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15670,9 +16010,9 @@ inline flatbuffers::Offset CreateAssignVariableOptions(fl + } + + inline RandomOptionsT *RandomOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new RandomOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new RandomOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void RandomOptions::UnPackTo(RandomOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15699,9 +16039,9 @@ inline flatbuffers::Offset CreateRandomOptions(flatbuffers::FlatB + } + + inline BucketizeOptionsT *BucketizeOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BucketizeOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BucketizeOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BucketizeOptions::UnPackTo(BucketizeOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15725,9 +16065,9 @@ inline flatbuffers::Offset CreateBucketizeOptions(flatbuffers: + } + + inline GeluOptionsT *GeluOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new GeluOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new GeluOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void GeluOptions::UnPackTo(GeluOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15751,9 +16091,9 @@ inline flatbuffers::Offset CreateGeluOptions(flatbuffers::FlatBuffe + } + + inline DynamicUpdateSliceOptionsT *DynamicUpdateSliceOptions::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new DynamicUpdateSliceOptionsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new DynamicUpdateSliceOptionsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void DynamicUpdateSliceOptions::UnPackTo(DynamicUpdateSliceOptionsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15774,9 +16114,9 @@ inline flatbuffers::Offset CreateDynamicUpdateSliceOp + } + + inline OperatorCodeT *OperatorCode::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new OperatorCodeT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new OperatorCodeT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void OperatorCode::UnPackTo(OperatorCodeT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15809,9 +16149,9 @@ inline flatbuffers::Offset CreateOperatorCode(flatbuffers::FlatBuf + } + + inline OperatorT *Operator::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new OperatorT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new OperatorT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Operator::UnPackTo(OperatorT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15859,18 +16199,18 @@ inline flatbuffers::Offset CreateOperator(flatbuffers::FlatBufferBuild + } + + inline SubGraphT *SubGraph::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SubGraphT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SubGraphT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SubGraph::UnPackTo(SubGraphT *_o, const flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = tensors(); if (_e) { _o->tensors.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->tensors[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } ++ { auto _e = tensors(); if (_e) { _o->tensors.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->tensors[_i]) { _e->Get(_i)->UnPackTo(_o->tensors[_i].get(), _resolver); } else { _o->tensors[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inputs[_i] = _e->Get(_i); } } } + { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->outputs[_i] = _e->Get(_i); } } } +- { auto _e = operators(); if (_e) { _o->operators.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->operators[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } ++ { auto _e = operators(); if (_e) { _o->operators.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->operators[_i]) { _e->Get(_i)->UnPackTo(_o->operators[_i].get(), _resolver); } else { _o->operators[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = name(); if (_e) _o->name = _e->str(); } + } + +@@ -15897,9 +16237,9 @@ inline flatbuffers::Offset CreateSubGraph(flatbuffers::FlatBufferBuild + } + + inline BufferT *Buffer::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BufferT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BufferT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Buffer::UnPackTo(BufferT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15924,9 +16264,9 @@ inline flatbuffers::Offset CreateBuffer(flatbuffers::FlatBufferBuilder & + } + + inline MetadataT *Metadata::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new MetadataT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new MetadataT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Metadata::UnPackTo(MetadataT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15953,9 +16293,9 @@ inline flatbuffers::Offset CreateMetadata(flatbuffers::FlatBufferBuild + } + + inline TensorMapT *TensorMap::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new TensorMapT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new TensorMapT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void TensorMap::UnPackTo(TensorMapT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -15982,16 +16322,16 @@ inline flatbuffers::Offset CreateTensorMap(flatbuffers::FlatBufferBui + } + + inline SignatureDefT *SignatureDef::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new SignatureDefT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new SignatureDefT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void SignatureDef::UnPackTo(SignatureDefT *_o, const flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } +- { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->outputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } ++ { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->inputs[_i]) { _e->Get(_i)->UnPackTo(_o->inputs[_i].get(), _resolver); } else { _o->inputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->outputs[_i]) { _e->Get(_i)->UnPackTo(_o->outputs[_i].get(), _resolver); } else { _o->outputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = signature_key(); if (_e) _o->signature_key = _e->str(); } + { auto _e = subgraph_index(); _o->subgraph_index = _e; } + } +@@ -16017,22 +16357,22 @@ inline flatbuffers::Offset CreateSignatureDef(flatbuffers::FlatBuf + } + + inline ModelT *Model::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ModelT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ModelT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void Model::UnPackTo(ModelT *_o, const flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; + { auto _e = version(); _o->version = _e; } +- { auto _e = operator_codes(); if (_e) { _o->operator_codes.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->operator_codes[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } +- { auto _e = subgraphs(); if (_e) { _o->subgraphs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->subgraphs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } ++ { auto _e = operator_codes(); if (_e) { _o->operator_codes.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->operator_codes[_i]) { _e->Get(_i)->UnPackTo(_o->operator_codes[_i].get(), _resolver); } else { _o->operator_codes[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = subgraphs(); if (_e) { _o->subgraphs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->subgraphs[_i]) { _e->Get(_i)->UnPackTo(_o->subgraphs[_i].get(), _resolver); } else { _o->subgraphs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = description(); if (_e) _o->description = _e->str(); } +- { auto _e = buffers(); if (_e) { _o->buffers.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->buffers[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } ++ { auto _e = buffers(); if (_e) { _o->buffers.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->buffers[_i]) { _e->Get(_i)->UnPackTo(_o->buffers[_i].get(), _resolver); } else { _o->buffers[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = metadata_buffer(); if (_e) { _o->metadata_buffer.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->metadata_buffer[_i] = _e->Get(_i); } } } +- { auto _e = metadata(); if (_e) { _o->metadata.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } +- { auto _e = signature_defs(); if (_e) { _o->signature_defs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->signature_defs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } ++ { auto _e = metadata(); if (_e) { _o->metadata.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->metadata[_i]) { _e->Get(_i)->UnPackTo(_o->metadata[_i].get(), _resolver); } else { _o->metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = signature_defs(); if (_e) { _o->signature_defs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->signature_defs[_i]) { _e->Get(_i)->UnPackTo(_o->signature_defs[_i].get(), _resolver); } else { _o->signature_defs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline flatbuffers::Offset Model::Pack(flatbuffers::FlatBufferBuilder &_fbb, const ModelT* _o, const flatbuffers::rehasher_function_t *_rehasher) { +@@ -16089,6 +16429,7 @@ inline bool VerifyQuantizationDetailsVector(flatbuffers::Verifier &verifier, con + } + + inline void *QuantizationDetailsUnion::UnPack(const void *obj, QuantizationDetails type, const flatbuffers::resolver_function_t *resolver) { ++ (void)resolver; + switch (type) { + case QuantizationDetails_CustomQuantization: { + auto ptr = reinterpret_cast(obj); +@@ -16099,6 +16440,7 @@ inline void *QuantizationDetailsUnion::UnPack(const void *obj, QuantizationDetai + } + + inline flatbuffers::Offset QuantizationDetailsUnion::Pack(flatbuffers::FlatBufferBuilder &_fbb, const flatbuffers::rehasher_function_t *_rehasher) const { ++ (void)_rehasher; + switch (type) { + case QuantizationDetails_CustomQuantization: { + auto ptr = reinterpret_cast(value); +@@ -16108,7 +16450,7 @@ inline flatbuffers::Offset QuantizationDetailsUnion::Pack(flatbuffers::Fla + } + } + +-inline QuantizationDetailsUnion::QuantizationDetailsUnion(const QuantizationDetailsUnion &u) FLATBUFFERS_NOEXCEPT : type(u.type), value(nullptr) { ++inline QuantizationDetailsUnion::QuantizationDetailsUnion(const QuantizationDetailsUnion &u) : type(u.type), value(nullptr) { + switch (type) { + case QuantizationDetails_CustomQuantization: { + value = new tflite::CustomQuantizationT(*reinterpret_cast(u.value)); +@@ -16166,6 +16508,7 @@ inline bool VerifySparseIndexVectorVector(flatbuffers::Verifier &verifier, const + } + + inline void *SparseIndexVectorUnion::UnPack(const void *obj, SparseIndexVector type, const flatbuffers::resolver_function_t *resolver) { ++ (void)resolver; + switch (type) { + case SparseIndexVector_Int32Vector: { + auto ptr = reinterpret_cast(obj); +@@ -16184,6 +16527,7 @@ inline void *SparseIndexVectorUnion::UnPack(const void *obj, SparseIndexVector t + } + + inline flatbuffers::Offset SparseIndexVectorUnion::Pack(flatbuffers::FlatBufferBuilder &_fbb, const flatbuffers::rehasher_function_t *_rehasher) const { ++ (void)_rehasher; + switch (type) { + case SparseIndexVector_Int32Vector: { + auto ptr = reinterpret_cast(value); +@@ -16201,7 +16545,7 @@ inline flatbuffers::Offset SparseIndexVectorUnion::Pack(flatbuffers::FlatB + } + } + +-inline SparseIndexVectorUnion::SparseIndexVectorUnion(const SparseIndexVectorUnion &u) FLATBUFFERS_NOEXCEPT : type(u.type), value(nullptr) { ++inline SparseIndexVectorUnion::SparseIndexVectorUnion(const SparseIndexVectorUnion &u) : type(u.type), value(nullptr) { + switch (type) { + case SparseIndexVector_Int32Vector: { + value = new tflite::Int32VectorT(*reinterpret_cast(u.value)); +@@ -16733,6 +17077,7 @@ inline bool VerifyBuiltinOptionsVector(flatbuffers::Verifier &verifier, const fl + } + + inline void *BuiltinOptionsUnion::UnPack(const void *obj, BuiltinOptions type, const flatbuffers::resolver_function_t *resolver) { ++ (void)resolver; + switch (type) { + case BuiltinOptions_Conv2DOptions: { + auto ptr = reinterpret_cast(obj); +@@ -17207,6 +17552,7 @@ inline void *BuiltinOptionsUnion::UnPack(const void *obj, BuiltinOptions type, c + } + + inline flatbuffers::Offset BuiltinOptionsUnion::Pack(flatbuffers::FlatBufferBuilder &_fbb, const flatbuffers::rehasher_function_t *_rehasher) const { ++ (void)_rehasher; + switch (type) { + case BuiltinOptions_Conv2DOptions: { + auto ptr = reinterpret_cast(value); +@@ -17680,7 +18026,7 @@ inline flatbuffers::Offset BuiltinOptionsUnion::Pack(flatbuffers::FlatBuff + } + } + +-inline BuiltinOptionsUnion::BuiltinOptionsUnion(const BuiltinOptionsUnion &u) FLATBUFFERS_NOEXCEPT : type(u.type), value(nullptr) { ++inline BuiltinOptionsUnion::BuiltinOptionsUnion(const BuiltinOptionsUnion &u) : type(u.type), value(nullptr) { + switch (type) { + case BuiltinOptions_Conv2DOptions: { + value = new tflite::Conv2DOptionsT(*reinterpret_cast(u.value)); +diff --git a/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake b/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake +index a3d01fd962d..ac91a03a48a 100644 +--- a/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake ++++ b/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake +@@ -23,7 +23,7 @@ OverridableFetchContent_Declare( + flatbuffers + GIT_REPOSITORY https://github.com/google/flatbuffers + # Sync with tensorflow/third_party/flatbuffers/workspace.bzl +- GIT_TAG v1.12.0 ++ GIT_TAG v2.0.5 + GIT_SHALLOW TRUE + GIT_PROGRESS TRUE + SOURCE_DIR "${CMAKE_BINARY_DIR}/flatbuffers" +diff --git a/tensorflow/tools/ci_build/release/requirements_common.txt b/tensorflow/tools/ci_build/release/requirements_common.txt +index 7a9f3fe6ee9..ea6ccf0e912 100644 +--- a/tensorflow/tools/ci_build/release/requirements_common.txt ++++ b/tensorflow/tools/ci_build/release/requirements_common.txt +@@ -4,7 +4,7 @@ + + absl-py ~= 0.13.0 + astunparse ~= 1.6.3 +-flatbuffers < 2.0 # NOTE: We cannot support faltbuffers 2.0 until internal code updates ++flatbuffers ~= 2.0 + google_pasta ~= 0.2 + h5py ~= 3.6.0 # NOTE: Earliest version for Python 3.10 + keras_preprocessing ~= 1.1.2 +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index cdcc355f4a6..6ccdbc38bd3 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -75,9 +75,7 @@ def standard_or_nightly(standard, nightly): + REQUIRED_PACKAGES = [ + 'absl-py >= 1.0.0', + 'astunparse >= 1.6.0', +- # TODO(b/187981032): remove the constraint for 2.0 once the incompatibile +- # issue is resolved. +- 'flatbuffers >= 1.12, <2', ++ 'flatbuffers >= 2.0', + # TODO(b/213222745) gast versions above 0.4.0 break TF's tests + 'gast >= 0.2.1, <= 0.4.0', + 'google_pasta >= 0.1.1', +diff --git a/third_party/flatbuffers/build_defs.bzl b/third_party/flatbuffers/build_defs.bzl +index 754db3f5d86..9fe15a3747f 100644 +--- a/third_party/flatbuffers/build_defs.bzl ++++ b/third_party/flatbuffers/build_defs.bzl +@@ -279,6 +279,11 @@ def _gen_flatbuffer_srcs_impl(ctx): + else: + no_includes_statement = [] + ++ if ctx.attr.language_flag == "--python": ++ onefile_statement = ["--gen-onefile"] ++ else: ++ onefile_statement = [] ++ + # Need to generate all files in a directory. + if not outputs: + outputs = [ctx.actions.declare_directory("{}_all".format(ctx.attr.name))] +@@ -314,6 +319,7 @@ def _gen_flatbuffer_srcs_impl(ctx): + "-I", + ctx.bin_dir.path, + ] + no_includes_statement + ++ onefile_statement + + include_paths_cmd_line + [ + "--no-union-value-namespacing", + "--gen-object-api", +@@ -433,6 +439,8 @@ def flatbuffer_py_library( + deps = deps, + include_paths = include_paths, + ) ++ ++ # TODO(b/235550563): Remove the concatnation rule with 2.0.6 update. + all_srcs_no_include = "{}_srcs_no_include".format(name) + _gen_flatbuffer_srcs( + name = all_srcs_no_include, +diff --git a/third_party/flatbuffers/flatbuffers.BUILD b/third_party/flatbuffers/flatbuffers.BUILD +index 108c0cd8e3b..f32f1a5f324 100644 +--- a/third_party/flatbuffers/flatbuffers.BUILD ++++ b/third_party/flatbuffers/flatbuffers.BUILD +@@ -10,10 +10,15 @@ exports_files(["LICENSE.txt"]) + licenses(["notice"]) + + config_setting( +- name = "freebsd", ++ name = "platform_freebsd", + values = {"cpu": "freebsd"}, + ) + ++config_setting( ++ name = "platform_openbsd", ++ values = {"cpu": "openbsd"}, ++) ++ + config_setting( + name = "windows", + values = {"cpu": "x64_windows"}, +@@ -35,8 +40,16 @@ cc_library( + filegroup( + name = "public_headers", + srcs = [ ++ "include/flatbuffers/allocator.h", ++ "include/flatbuffers/array.h", + "include/flatbuffers/base.h", ++ "include/flatbuffers/bfbs_generator.h", ++ "include/flatbuffers/buffer.h", ++ "include/flatbuffers/buffer_ref.h", + "include/flatbuffers/code_generators.h", ++ "include/flatbuffers/default_allocator.h", ++ "include/flatbuffers/detached_buffer.h", ++ "include/flatbuffers/flatbuffer_builder.h", + "include/flatbuffers/flatbuffers.h", + "include/flatbuffers/flexbuffers.h", + "include/flatbuffers/hash.h", +@@ -46,7 +59,13 @@ filegroup( + "include/flatbuffers/reflection_generated.h", + "include/flatbuffers/registry.h", + "include/flatbuffers/stl_emulation.h", ++ "include/flatbuffers/string.h", ++ "include/flatbuffers/struct.h", ++ "include/flatbuffers/table.h", + "include/flatbuffers/util.h", ++ "include/flatbuffers/vector.h", ++ "include/flatbuffers/vector_downward.h", ++ "include/flatbuffers/verifier.h", + ], + visibility = ["//:__subpackages__"], + ) +@@ -65,7 +84,7 @@ cc_library( + cc_binary( + name = "flatc", + linkopts = select({ +- ":freebsd": [ ++ ":platform_freebsd": [ + "-lm", + ], + ":windows": [], +@@ -92,11 +111,24 @@ filegroup( + cc_library( + name = "runtime_cc", + hdrs = [ ++ "include/flatbuffers/allocator.h", ++ "include/flatbuffers/array.h", + "include/flatbuffers/base.h", ++ "include/flatbuffers/buffer.h", ++ "include/flatbuffers/buffer_ref.h", ++ "include/flatbuffers/default_allocator.h", ++ "include/flatbuffers/detached_buffer.h", ++ "include/flatbuffers/flatbuffer_builder.h", + "include/flatbuffers/flatbuffers.h", + "include/flatbuffers/flexbuffers.h", + "include/flatbuffers/stl_emulation.h", ++ "include/flatbuffers/string.h", ++ "include/flatbuffers/struct.h", ++ "include/flatbuffers/table.h", + "include/flatbuffers/util.h", ++ "include/flatbuffers/vector.h", ++ "include/flatbuffers/vector_downward.h", ++ "include/flatbuffers/verifier.h", + ], + linkstatic = 1, + strip_include_prefix = "/include", +@@ -107,9 +139,11 @@ flatbuffer_py_strip_prefix_srcs( + name = "flatbuffer_py_strip_prefix", + srcs = [ + "python/flatbuffers/__init__.py", ++ "python/flatbuffers/_version.py", + "python/flatbuffers/builder.py", + "python/flatbuffers/compat.py", + "python/flatbuffers/encode.py", ++ "python/flatbuffers/flexbuffers.py", + "python/flatbuffers/number_types.py", + "python/flatbuffers/packer.py", + "python/flatbuffers/table.py", +@@ -122,9 +156,11 @@ filegroup( + name = "runtime_py_srcs", + srcs = [ + "__init__.py", ++ "_version.py", + "builder.py", + "compat.py", + "encode.py", ++ "flexbuffers.py", + "number_types.py", + "packer.py", + "table.py", +diff --git a/third_party/flatbuffers/workspace.bzl b/third_party/flatbuffers/workspace.bzl +index 59c1fd9ea43..84aae9dc51f 100644 +--- a/third_party/flatbuffers/workspace.bzl ++++ b/third_party/flatbuffers/workspace.bzl +@@ -5,9 +5,9 @@ load("//third_party:repo.bzl", "tf_http_archive", "tf_mirror_urls") + def repo(): + tf_http_archive( + name = "flatbuffers", +- strip_prefix = "flatbuffers-1.12.0", +- sha256 = "62f2223fb9181d1d6338451375628975775f7522185266cd5296571ac152bc45", +- urls = tf_mirror_urls("https://github.com/google/flatbuffers/archive/v1.12.0.tar.gz"), ++ strip_prefix = "flatbuffers-2.0.5", ++ sha256 = "b01e97c988c429e164c5c7df9e87c80007ca87f593c0d73733ba536ddcbc8f98", ++ urls = tf_mirror_urls("https://github.com/google/flatbuffers/archive/v2.0.5.tar.gz"), + build_file = "//third_party/flatbuffers:flatbuffers.BUILD", + system_build_file = "//third_party/flatbuffers:BUILD.system", + link_files = { From 9596c49d1730a56e97ecb11310c0516b5522984a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 6 Jan 2023 09:44:54 +0100 Subject: [PATCH 6454/9987] Add TensorFlow-2.8.4-foss-2021b-CUDA-11.4.1.eb and fix TensorFlow-2.8.4-foss-2021b.eb --- ...TensorFlow-2.8.4-foss-2021b-CUDA-11.4.1.eb | 235 ++++++++++++++++++ .../TensorFlow/TensorFlow-2.8.4-foss-2021b.eb | 96 ++++--- ...sorFlow-2.8.4_exclude-xnnpack-on-ppc.patch | 18 ++ .../TensorFlow-2.8.4_fix-PPC-JIT.patch | 58 +++++ ...ensorFlow-2.8.4_resolve-gcc-symlinks.patch | 28 +++ 5 files changed, 397 insertions(+), 38 deletions(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b-CUDA-11.4.1.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_fix-PPC-JIT.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..7af33a9479b --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,235 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '4.2.2'), + ('protobuf', '3.17.3'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.33.1', '-nodocs'), + ('pybind11', '2.7.1'), + ('UnZip', '6.0'), + ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed +] +dependencies = [ + ('CUDA', '11.4.1', '', SYSTEM), + ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.10.3', versionsuffix), + ('Python', '3.9.6'), + ('h5py', '3.6.0'), + ('cURL', '7.78.0'), + ('dill', '0.3.4'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.5.0'), + ('ICU', '69.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.29'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.36'), + ('protobuf-python', '3.17.3'), + ('flatbuffers-python', '2.0'), + ('libpng', '1.6.37'), + ('snappy', '1.1.9'), + ('zlib', '1.2.11'), +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('tensorflow-estimator', '2.8.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['bee8e0520c60ae7eaf6ca8cb46c5a9f4b45725531380db8fbe38fcb48478b6bb'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('Werkzeug', '2.1.2', { + 'checksums': ['1ce08e8093ed67d638d63879fd1ba3735817f7a80de3674d293f5984f25fb6e6'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard-data-server', '0.6.1', { + 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('Markdown', '3.3.7', { + 'checksums': ['cbb516f16218e643d8e0a95b309f77eb118cb138d39a4f27851e6a63581db874'], + }), + ('grpcio', '1.46.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['4835b0f5fedbee3a3d6eea48f4e65dffd30b52c078690fa97ddc9fcea1e3b35d'], + }), + ('oauthlib', '3.2.0', { + 'checksums': ['23a8208d75b902797ea29fd31fa80a15ed9dc2c6c16fe73f5d346f83f6fa27a2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('rsa', '4.8', { + 'checksums': ['5c6bd9dc7a543b7fe4304a631f8a8a3b674e2bbfc49c2ae96200cdbe55df6b17'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('cachetools', '5.1.0', { + 'checksums': ['8b3b8fa53f564762e5b221e9896798951e7f915513abf2ba072ce0f07f3f5a98'], + }), + ('google-auth', '2.6.6', { + 'modulename': 'google.auth', + 'checksums': ['1ba4938e032b73deb51e59c4656a00e0939cf0b1112575099f136babb4563312'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('tensorboard', '2.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['65a338e4424e9079f2604923bdbe301792adce2ace1be68da6b3ddf005170def'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('keras', '2.8.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['744d39dc6577dcd80ff4a4d41549e92b77d6a17e0edd58a431d30656e29bc94e'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.5.2', { + 'checksums': ['c55683ad725f5c00a41bc7db0225223e8be024b1fa564d039ed3390e4fd48fb3'], + }), + ('absl-py', '1.0.0', { + 'modulename': 'absl', + 'checksums': ['ac511215c01ee9ae47b19716599e8ccfa746f2e18de72bdf641b79b22afa27ea'], + }), + # System dependency astor_archive + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + # Optional profile plugin + dependency + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.8.0', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['58d65c979951e7628ca3b46c798e10e5813026a3ecfbacc319cf88ebe766134a'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.7.1_fix_cpu_count.patch', + 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch', + 'TensorFlow-2.8.4_fix-PPC-JIT.patch', + 'TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch', + 'TensorFlow-2.8.4_resolve-gcc-symlinks.patch', + ], + 'checksums': [ + {'v2.8.4.tar.gz': 'c08a222792bdbff9da299c7885561ee27b95d414d1111c426efac4ccdce92cde'}, + {'TensorFlow-2.4.0_add-ldl.patch': '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.5.0_add-support-for-large-core-systems.patch': + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636'}, + {'TensorFlow-2.5.0_disable-avx512-extensions.patch': + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03'}, + {'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch': + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75'}, + {'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch': + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029'}, + {'TensorFlow-2.5.0_fix-crash-on-shutdown.patch': + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd'}, + {'TensorFlow-2.7.1_fix_cpu_count.patch': + '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698'}, + {'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch': + 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483'}, + {'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch': + 'ebd404ac56cc4ca662483f1f591e62e11749361be57a7ba5f4b2f0d03e829884'}, + {'TensorFlow-2.8.4_fix-PPC-JIT.patch': + '27d28293105b4dd0a25f58346c68b672f57215756f14a97c442d0e3317e93a2b'}, + {'TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch': + '10a6daad2ef65d649a6d4a6659f97f833359b3c35d3ce15e63d2db2e331a6a35'}, + {'TensorFlow-2.8.4_resolve-gcc-symlinks.patch': + '43ce9acc6bffff68a31d2263d0064d272999b2e0a2c6546690287cd1c9c90f04'}, + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' + '-benchmark-test,-v1only'), + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + # All tests in this directory fail with segfault (TensorFlow Graph IR) + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + # Fails on e.g. AMD EPYC and known to be flaky on Mac: https://github.com/tensorflow/tensorflow/issues/56717 + '-//tensorflow/python/data/experimental/kernel_tests/service:fault_tolerance_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb index 302f3bd958d..323be5f47ac 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb @@ -39,7 +39,6 @@ dependencies = [ ('libpng', '1.6.37'), ('snappy', '1.1.9'), ('zlib', '1.2.11'), - ('networkx', '2.6.3'), # required for pythran ] use_pip = True @@ -51,8 +50,8 @@ exts_list = [ ('wrapt', '1.14.1', { 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], }), - ('tensorflow_estimator', '2.8.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + ('tensorflow-estimator', '2.8.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', 'checksums': ['bee8e0520c60ae7eaf6ca8cb46c5a9f4b45725531380db8fbe38fcb48478b6bb'], }), ('termcolor', '1.1.0', { @@ -62,11 +61,11 @@ exts_list = [ 'checksums': ['1ce08e8093ed67d638d63879fd1ba3735817f7a80de3674d293f5984f25fb6e6'], }), ('tensorboard_plugin_wit', '1.8.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], }), - ('tensorboard_data_server', '0.6.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + ('tensorboard-data-server', '0.6.1', { + 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], }), ('Markdown', '3.3.7', { @@ -100,17 +99,19 @@ exts_list = [ 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], }), ('tensorboard', '2.8.0', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['65a338e4424e9079f2604923bdbe301792adce2ace1be68da6b3ddf005170def'], }), - ('opt_einsum', '3.3.0', { + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], }), - ('Keras_Preprocessing', '1.1.2', { + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], }), ('keras', '2.8.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['744d39dc6577dcd80ff4a4d41549e92b77d6a17e0edd58a431d30656e29bc94e'], }), ('google-pasta', '0.2.0', { @@ -130,9 +131,23 @@ exts_list = [ 'modulename': 'absl', 'checksums': ['ac511215c01ee9ae47b19716599e8ccfa746f2e18de72bdf641b79b22afa27ea'], }), + # System dependency astor_archive + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + # Optional profile plugin + dependency + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.8.0', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['58d65c979951e7628ca3b46c798e10e5813026a3ecfbacc319cf88ebe766134a'], + }), (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'patches': [ - 'TensorFlow-2.1.0_fix-cuda-build.patch', 'TensorFlow-2.4.0_add-ldl.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', @@ -140,12 +155,41 @@ exts_list = [ 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.7.1_fix_cpu_count.patch', 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch', + 'TensorFlow-2.8.4_fix-PPC-JIT.patch', 'TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch', - 'TensorFlow-2.7.1_fix_cpu_count.patch', + 'TensorFlow-2.8.4_resolve-gcc-symlinks.patch', + ], + 'checksums': [ + {'v2.8.4.tar.gz': 'c08a222792bdbff9da299c7885561ee27b95d414d1111c426efac4ccdce92cde'}, + {'TensorFlow-2.4.0_add-ldl.patch': '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.5.0_add-support-for-large-core-systems.patch': + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636'}, + {'TensorFlow-2.5.0_disable-avx512-extensions.patch': + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03'}, + {'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch': + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75'}, + {'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch': + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029'}, + {'TensorFlow-2.5.0_fix-crash-on-shutdown.patch': + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd'}, + {'TensorFlow-2.7.1_fix_cpu_count.patch': + '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698'}, + {'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch': + 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483'}, + {'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch': + 'ebd404ac56cc4ca662483f1f591e62e11749361be57a7ba5f4b2f0d03e829884'}, + {'TensorFlow-2.8.4_fix-PPC-JIT.patch': + '27d28293105b4dd0a25f58346c68b672f57215756f14a97c442d0e3317e93a2b'}, + {'TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch': + '10a6daad2ef65d649a6d4a6659f97f833359b3c35d3ce15e63d2db2e331a6a35'}, + {'TensorFlow-2.8.4_resolve-gcc-symlinks.patch': + '43ce9acc6bffff68a31d2263d0064d272999b2e0a2c6546690287cd1c9c90f04'}, ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' @@ -181,30 +225,6 @@ exts_list = [ 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", 'with_xla': True, - 'checksums': [ - {'v2.8.4.tar.gz': 'c08a222792bdbff9da299c7885561ee27b95d414d1111c426efac4ccdce92cde'}, - {'TensorFlow-2.1.0_fix-cuda-build.patch': - '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a'}, - {'TensorFlow-2.4.0_add-ldl.patch': '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3'}, - {'TensorFlow-2.4.0_dont-use-var-lock.patch': - 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, - {'TensorFlow-2.5.0_add-support-for-large-core-systems.patch': - '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636'}, - {'TensorFlow-2.5.0_disable-avx512-extensions.patch': - '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03'}, - {'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch': - '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75'}, - {'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch': - '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029'}, - {'TensorFlow-2.5.0_fix-crash-on-shutdown.patch': - '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd'}, - {'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch': - 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483'}, - {'TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch': - '10a6daad2ef65d649a6d4a6659f97f833359b3c35d3ce15e63d2db2e331a6a35'}, - {'TensorFlow-2.7.1_fix_cpu_count.patch': - '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698'}, - ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch new file mode 100644 index 00000000000..1a0938252be --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch @@ -0,0 +1,18 @@ +XNNPACK is not supported on PowerPC so disable it by default. +See https://github.com/tensorflow/tensorflow/issues/58768 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/lite/BUILD b/tensorflow/lite/BUILD +index 198f949b341..d15dcf9a80d 100644 +--- a/tensorflow/lite/BUILD ++++ b/tensorflow/lite/BUILD +@@ -709,6 +709,8 @@ cc_library( + deps = select({ + "//tensorflow:macos": [], + "//tensorflow:fuchsia": [], ++ # XNNPACK is not supported on PPC ++ "//tensorflow:linux_ppc64le": [], + "//conditions:default": [":tflite_with_xnnpack_enabled"], + }), + ) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_fix-PPC-JIT.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_fix-PPC-JIT.patch new file mode 100644 index 00000000000..ca57b87dee1 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_fix-PPC-JIT.patch @@ -0,0 +1,58 @@ +diff --git a/third_party/cpuinfo/cpuinfo.BUILD b/third_party/cpuinfo/cpuinfo.BUILD +index eb2937d20ef..dfea408db94 100644 +--- a/third_party/cpuinfo/cpuinfo.BUILD ++++ b/third_party/cpuinfo/cpuinfo.BUILD +@@ -109,6 +109,7 @@ cc_library( + ":linux_mips64": COMMON_SRCS + LINUX_SRCS, + ":linux_riscv64": COMMON_SRCS + LINUX_SRCS, + ":linux_s390x": COMMON_SRCS + LINUX_SRCS, ++ ":linux_ppc64le": COMMON_SRCS + LINUX_SRCS, + ":macos_x86_64": COMMON_SRCS + X86_SRCS + MACH_SRCS + MACH_X86_SRCS, + ":macos_arm64": COMMON_SRCS + MACH_SRCS + MACH_ARM_SRCS, + ":windows_x86_64": COMMON_SRCS + X86_SRCS + WINDOWS_X86_SRCS, +@@ -232,6 +233,11 @@ config_setting( + values = {"cpu": "s390x"}, + ) + ++config_setting( ++ name = "linux_ppc64le", ++ values = {"cpu": "ppc"}, ++) ++ + config_setting( + name = "macos_x86_64", + values = { +diff --git a/third_party/llvm/macos_build_fix.patch b/third_party/llvm/macos_build_fix.patch +index 4dba8676ea5..af31f0c1d9e 100644 +--- a/third_party/llvm/macos_build_fix.patch ++++ b/third_party/llvm/macos_build_fix.patch +@@ -42,5 +42,29 @@ index ff64df694048..c9c35b01711c 100644 + "@bazel_tools//src/conditions:linux_aarch64": native_arch_defines("AArch64", "aarch64-unknown-linux-gnu"), + "//conditions:default": native_arch_defines("X86", "x86_64-unknown-linux-gnu"), + }) + [ ++ ++ ++From b250c34bbd415b2a8c3e0532e98591ab1780cda6 Mon Sep 17 00:00:00 2001 ++From: Nishidha Panpaliya ++Date: Mon, 21 Mar 2022 09:51:36 -0400 ++Subject: [PATCH] Fix for ppc64le ++ ++--- ++ utils/bazel/llvm-project-overlay/llvm/config.bzl | 1 + ++ 1 file changed, 1 insertion(+) ++ ++diff --git a/utils/bazel/llvm-project-overlay/llvm/config.bzl b/utils/bazel/llvm-project-overlay/llvm/config.bzl ++index 772714f38941..9ed63e8d44a3 100644 ++--- a/utils/bazel/llvm-project-overlay/llvm/config.bzl +++++ b/utils/bazel/llvm-project-overlay/llvm/config.bzl ++@@ -86,6 +86,7 @@ llvm_config_defines = os_defines + select({ ++ "//llvm:macos_arm64": native_arch_defines("AArch64", "arm64-apple-darwin"), ++ "@bazel_tools//src/conditions:darwin": native_arch_defines("X86", "x86_64-unknown-darwin"), ++ "@bazel_tools//src/conditions:linux_aarch64": native_arch_defines("AArch64", "aarch64-unknown-linux-gnu"), +++ "@bazel_tools//src/conditions:linux_ppc64le": native_arch_defines("PowerPC", "powerpc64le-unknown-linux-gnu"), ++ "//conditions:default": native_arch_defines("X86", "x86_64-unknown-linux-gnu"), ++ }) + [ ++ # These shouldn't be needed by the C++11 standard, but are for some ++ + -- + 2.30.1 (Apple Git-130) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch new file mode 100644 index 00000000000..42cdce7c9fd --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_resolve-gcc-symlinks.patch @@ -0,0 +1,28 @@ +Fix for "undeclared inclusion(s) in rule" errors when the installation directory +for GCC is hosted in a path that is a symlink to another path. + +From https://github.com/tensorflow/tensorflow/pull/56360 + +From b3a8fdbcb79e723f8d62f86bddcfdfb73fe76291 Mon Sep 17 00:00:00 2001 +From: Jinzhe Zeng +Date: Sat, 4 Jun 2022 19:06:58 -0400 +Subject: [PATCH] resolve gcc_host_compiler_path in a symlink directory + +Resolves a missing dependency declarations error, when gcc_host_compiler_path is in a symlink directory resolving to other directories. +--- + configure.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/configure.py b/configure.py +index bf338bdda2297..77af09a22a05d 100644 +--- a/configure.py ++++ b/configure.py +@@ -619,7 +619,7 @@ def prompt_loop_or_load_from_env(environ_cp, + 'Assuming to be a scripting mistake.' % + (var_name, n_ask_attempts)) + +- if resolve_symlinks and os.path.islink(val): ++ if resolve_symlinks: + val = os.path.realpath(val) + environ_cp[var_name] = val + return val From 672f52845738ddb93c7cfd662e5f4b07b1fc85b3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 5 Dec 2022 17:13:42 +0100 Subject: [PATCH 6455/9987] Fix TensorFlow 2.7.1 on POWER --- ...TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 64 +- .../TensorFlow/TensorFlow-2.7.1-foss-2021b.eb | 64 +- .../TensorFlow-2.7.1_fix-PPC-Eigen-GEMM.patch | 3179 +++++++++++++++++ .../TensorFlow-2.7.1_fix-PPC-JIT.patch | 82 + 4 files changed, 3331 insertions(+), 58 deletions(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix-PPC-Eigen-GEMM.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix-PPC-JIT.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 77b91670e2c..36fd4320431 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -158,6 +158,8 @@ exts_list = [ 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], }), (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'patches': [ 'TensorFlow-2.1.0_fix-cuda-build.patch', 'TensorFlow-2.4.0_add-ldl.patch', @@ -172,9 +174,40 @@ exts_list = [ 'TensorFlow-2.7.1_remove-io-gcs-dependency.patch', 'TensorFlow-2.7.1_remove-libclang-dependency.patch', 'TensorFlow-2.7.1_fix_cpu_count.patch', + 'TensorFlow-2.7.1_fix-PPC-Eigen-GEMM.patch', + 'TensorFlow-2.7.1_fix-PPC-JIT.patch', + ], + 'checksums': [ + 'abebe2cf5ca379e18071693ca5f45b88ade941b16258a21cc1f12d77d5387a21', # v2.7.1.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', + # TensorFlow-2.5.0_disable-avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', + # TensorFlow-2.5.0_fix-crash-on-shutdown.patch + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', + # TensorFlow-2.7.1_fix_protobuf_error_message.patch + '301ce21845987dc7868624880c0d85e60aa5491c5a0bae0f6ebc8db5727960a5', + # TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch + 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', + # TensorFlow-2.7.1_remove-io-gcs-dependency.patch + '01c439749938f9fc23fe8de17592460aa46e201575a3f9465bfb6b39ca50ef20', + # TensorFlow-2.7.1_remove-libclang-dependency.patc + 'd202058c0e8a7cdef3157fe12327e23c7291ce2724a15653df0aae3b40c4dadc', + # TensorFlow-2.7.1_fix_cpu_count.patch + '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698', + # TensorFlow-2.7.1_fix-PPC-Eigen-GEMM.patch + 'ab647e80af52950c733d084ef9ec4b49780ab20a413476374cf41e25bd20af83', + # TensorFlow-2.7.1_fix-PPC-JIT.patch + 'f0652557e760fdc2b39313a24d6236e7c3984cabc3353e0d867e275ff90a13fe', ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' @@ -210,33 +243,6 @@ exts_list = [ 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", 'with_xla': True, - 'checksums': [ - 'abebe2cf5ca379e18071693ca5f45b88ade941b16258a21cc1f12d77d5387a21', # v2.7.1.tar.gz - '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch - # TensorFlow-2.4.0_dont-use-var-lock.patch - 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', - # TensorFlow-2.5.0_add-support-for-large-core-systems.patch - '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', - # TensorFlow-2.5.0_disable-avx512-extensions.patch - '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', - # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch - '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', - # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', - # TensorFlow-2.5.0_fix-crash-on-shutdown.patch - '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', - # TensorFlow-2.7.1_fix_protobuf_error_message.patch - '301ce21845987dc7868624880c0d85e60aa5491c5a0bae0f6ebc8db5727960a5', - # TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch - 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', - # TensorFlow-2.7.1_remove-io-gcs-dependency.patch - '01c439749938f9fc23fe8de17592460aa46e201575a3f9465bfb6b39ca50ef20', - # TensorFlow-2.7.1_remove-libclang-dependency.patc - 'd202058c0e8a7cdef3157fe12327e23c7291ce2724a15653df0aae3b40c4dadc', - # TensorFlow-2.7.1_fix_cpu_count.patch - '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698', - ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb index ae6d7df989c..e8dd5a54c3b 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb @@ -154,6 +154,8 @@ exts_list = [ 'checksums': ['6953272383486044699fd0e9f00aad167a27e08ce19aae66c6c4b10e7e767793'], }), (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'patches': [ 'TensorFlow-2.1.0_fix-cuda-build.patch', 'TensorFlow-2.4.0_add-ldl.patch', @@ -168,9 +170,40 @@ exts_list = [ 'TensorFlow-2.7.1_remove-io-gcs-dependency.patch', 'TensorFlow-2.7.1_remove-libclang-dependency.patch', 'TensorFlow-2.7.1_fix_cpu_count.patch', + 'TensorFlow-2.7.1_fix-PPC-Eigen-GEMM.patch', + 'TensorFlow-2.7.1_fix-PPC-JIT.patch', + ], + 'checksums': [ + 'abebe2cf5ca379e18071693ca5f45b88ade941b16258a21cc1f12d77d5387a21', # v2.7.1.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch + # TensorFlow-2.4.0_dont-use-var-lock.patch + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', + # TensorFlow-2.5.0_add-support-for-large-core-systems.patch + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', + # TensorFlow-2.5.0_disable-avx512-extensions.patch + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', + # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', + # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch + '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', + # TensorFlow-2.5.0_fix-crash-on-shutdown.patch + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', + # TensorFlow-2.7.1_fix_protobuf_error_message.patch + '301ce21845987dc7868624880c0d85e60aa5491c5a0bae0f6ebc8db5727960a5', + # TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch + 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', + # TensorFlow-2.7.1_remove-io-gcs-dependency.patch + '01c439749938f9fc23fe8de17592460aa46e201575a3f9465bfb6b39ca50ef20', + # TensorFlow-2.7.1_remove-libclang-dependency.patc + 'd202058c0e8a7cdef3157fe12327e23c7291ce2724a15653df0aae3b40c4dadc', + # TensorFlow-2.7.1_fix_cpu_count.patch + '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698', + # TensorFlow-2.7.1_fix-PPC-Eigen-GEMM.patch + 'ab647e80af52950c733d084ef9ec4b49780ab20a413476374cf41e25bd20af83', + # TensorFlow-2.7.1_fix-PPC-JIT.patch + 'f0652557e760fdc2b39313a24d6236e7c3984cabc3353e0d867e275ff90a13fe', ], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' @@ -206,33 +239,6 @@ exts_list = [ 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", 'with_xla': True, - 'checksums': [ - 'abebe2cf5ca379e18071693ca5f45b88ade941b16258a21cc1f12d77d5387a21', # v2.7.1.tar.gz - '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch - '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3', # TensorFlow-2.4.0_add-ldl.patch - # TensorFlow-2.4.0_dont-use-var-lock.patch - 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5', - # TensorFlow-2.5.0_add-support-for-large-core-systems.patch - '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636', - # TensorFlow-2.5.0_disable-avx512-extensions.patch - '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03', - # TensorFlow-2.5.0-fix-alias-violation-in-absl.patch - '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75', - # TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch - '5edea55ce87d5adb14f6ed6996f308879e268b8cec760cf11288e3a56179a029', - # TensorFlow-2.5.0_fix-crash-on-shutdown.patch - '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd', - # TensorFlow-2.7.1_fix_protobuf_error_message.patch - '301ce21845987dc7868624880c0d85e60aa5491c5a0bae0f6ebc8db5727960a5', - # TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch - 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483', - # TensorFlow-2.7.1_remove-io-gcs-dependency.patch - '01c439749938f9fc23fe8de17592460aa46e201575a3f9465bfb6b39ca50ef20', - # TensorFlow-2.7.1_remove-libclang-dependency.patc - 'd202058c0e8a7cdef3157fe12327e23c7291ce2724a15653df0aae3b40c4dadc', - # TensorFlow-2.7.1_fix_cpu_count.patch - '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698', - ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix-PPC-Eigen-GEMM.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix-PPC-Eigen-GEMM.patch new file mode 100644 index 00000000000..8cb101abb16 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix-PPC-Eigen-GEMM.patch @@ -0,0 +1,3179 @@ +Eigen (dependency of TF) has a bug multiplying matrices on POWER. +This results in failures in e.g. //tensorflow/python/kernel_tests:lu_op_test + +Fix this by using the changeset from https://gitlab.com/libeigen/eigen/-/merge_requests/680 as a patch. +And the TF patch required after that from https://github.com/tensorflow/tensorflow/pull/52940 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/eigen3/fix-ppc-gemm.patch b/third_party/eigen3/fix-ppc-gemm.patch +new file mode 100644 +index 00000000000..a7b3e887178 +--- /dev/null ++++ b/third_party/eigen3/fix-ppc-gemm.patch +@@ -0,0 +1,3083 @@ ++commit 365a40f85eb6755752930e1dca8f160611be5e28 ++Author: Chip Kerchner ++Date: Thu Oct 28 21:59:41 2021 +0000 ++ ++ Invert rows and depth in non-vectorized portion of packing (PowerPC). ++ ++diff --git a/Eigen/src/Core/arch/AltiVec/Complex.h b/Eigen/src/Core/arch/AltiVec/Complex.h ++index b603dff4e..965f4911a 100644 ++--- a/Eigen/src/Core/arch/AltiVec/Complex.h +++++ b/Eigen/src/Core/arch/AltiVec/Complex.h ++@@ -127,20 +127,20 @@ template<> EIGEN_STRONG_INLINE Packet2cf ploaddup(const std::complex< ++ template<> EIGEN_STRONG_INLINE void pstore >(std::complex * to, const Packet2cf& from) { pstore((float*)to, from.v); } ++ template<> EIGEN_STRONG_INLINE void pstoreu >(std::complex * to, const Packet2cf& from) { pstoreu((float*)to, from.v); } ++ ++-EIGEN_STRONG_INLINE Packet2cf pload2(const std::complex* from0, const std::complex* from1) +++EIGEN_STRONG_INLINE Packet2cf pload2(const std::complex& from0, const std::complex& from1) ++ { ++ Packet4f res0, res1; ++ #ifdef __VSX__ ++- __asm__ ("lxsdx %x0,%y1" : "=wa" (res0) : "Z" (*from0)); ++- __asm__ ("lxsdx %x0,%y1" : "=wa" (res1) : "Z" (*from1)); +++ __asm__ ("lxsdx %x0,%y1" : "=wa" (res0) : "Z" (from0)); +++ __asm__ ("lxsdx %x0,%y1" : "=wa" (res1) : "Z" (from1)); ++ #ifdef _BIG_ENDIAN ++ __asm__ ("xxpermdi %x0, %x1, %x2, 0" : "=wa" (res0) : "wa" (res0), "wa" (res1)); ++ #else ++ __asm__ ("xxpermdi %x0, %x2, %x1, 0" : "=wa" (res0) : "wa" (res0), "wa" (res1)); ++ #endif ++ #else ++- *reinterpret_cast *>(&res0) = *from0; ++- *reinterpret_cast *>(&res1) = *from1; +++ *reinterpret_cast *>(&res0) = from0; +++ *reinterpret_cast *>(&res1) = from1; ++ res0 = vec_perm(res0, res1, p16uc_TRANSPOSE64_HI); ++ #endif ++ return Packet2cf(res0); ++diff --git a/Eigen/src/Core/arch/AltiVec/MatrixProduct.h b/Eigen/src/Core/arch/AltiVec/MatrixProduct.h ++index 3f79b97df..8feb88ea7 100644 ++--- a/Eigen/src/Core/arch/AltiVec/MatrixProduct.h +++++ b/Eigen/src/Core/arch/AltiVec/MatrixProduct.h ++@@ -164,24 +164,23 @@ EIGEN_STRONG_INLINE void symm_pack_complex_rhs_helper(std::complex* bloc ++ ++ rir += vectorDelta; ++ } ++- if (j < cols) +++ +++ for(; j < cols; j++) ++ { ++- rii = rir + ((cols - j) * rows); +++ rii = rir + rows; ++ ++ for(Index i = k2; i < depth; i++) ++ { ++- Index k = j; ++- for(; k < cols; k++) ++- { ++- std::complex v = getAdjointVal(i, k, rhs); +++ std::complex v = getAdjointVal(i, j, rhs); ++ ++- blockBf[rir] = v.real(); ++- blockBf[rii] = v.imag(); +++ blockBf[rir] = v.real(); +++ blockBf[rii] = v.imag(); ++ ++- rir += 1; ++- rii += 1; ++- } +++ rir += 1; +++ rii += 1; ++ } +++ +++ rir += rows; ++ } ++ } ++ ++@@ -260,19 +259,15 @@ EIGEN_STRONG_INLINE void symm_pack_rhs_helper(Scalar* blockB, const Scalar* _rhs ++ } ++ } ++ ++- if (j < cols) +++ for(; j < cols; j++) ++ { ++ for(Index i = k2; i < depth; i++) ++ { ++- Index k = j; ++- for(; k < cols; k++) ++- { ++- if(k <= i) ++- blockB[ri] = rhs(i, k); ++- else ++- blockB[ri] = rhs(k, i); ++- ri += 1; ++- } +++ if(j <= i) +++ blockB[ri] = rhs(i, j); +++ else +++ blockB[ri] = rhs(j, i); +++ ri += 1; ++ } ++ } ++ } ++@@ -406,22 +401,18 @@ struct symm_pack_lhs ++ * and offset and behaves accordingly. ++ **/ ++ ++-template ++-EIGEN_ALWAYS_INLINE void storeBlock(Scalar* to, PacketBlock& block) ++-{ ++- const Index size = 16 / sizeof(Scalar); ++- pstore(to + (0 * size), block.packet[0]); ++- pstore(to + (1 * size), block.packet[1]); ++- pstore(to + (2 * size), block.packet[2]); ++- pstore(to + (3 * size), block.packet[3]); ++-} ++- ++-template ++-EIGEN_ALWAYS_INLINE void storeBlock(Scalar* to, PacketBlock& block) +++template +++EIGEN_ALWAYS_INLINE void storeBlock(Scalar* to, PacketBlock& block) ++ { ++ const Index size = 16 / sizeof(Scalar); ++ pstore(to + (0 * size), block.packet[0]); ++ pstore(to + (1 * size), block.packet[1]); +++ if (N > 2) { +++ pstore(to + (2 * size), block.packet[2]); +++ } +++ if (N > 3) { +++ pstore(to + (3 * size), block.packet[3]); +++ } ++ } ++ ++ // General template for lhs & rhs complex packing. ++@@ -447,9 +438,9 @@ struct dhs_cpack { ++ PacketBlock cblock; ++ ++ if (UseLhs) { ++- bload(cblock, lhs, j, i); +++ bload(cblock, lhs, j, i); ++ } else { ++- bload(cblock, lhs, i, j); +++ bload(cblock, lhs, i, j); ++ } ++ ++ blockr.packet[0] = vec_perm(cblock.packet[0].v, cblock.packet[4].v, p16uc_GETREAL32); ++@@ -476,8 +467,8 @@ struct dhs_cpack { ++ ptranspose(blocki); ++ } ++ ++- storeBlock(blockAt + rir, blockr); ++- storeBlock(blockAt + rii, blocki); +++ storeBlock(blockAt + rir, blockr); +++ storeBlock(blockAt + rii, blocki); ++ ++ rir += 4*vectorSize; ++ rii += 4*vectorSize; ++@@ -497,21 +488,12 @@ struct dhs_cpack { ++ cblock.packet[1] = lhs.template loadPacket(i, j + 2); ++ } ++ } else { ++- std::complex lhs0, lhs1; ++ if (UseLhs) { ++- lhs0 = lhs(j + 0, i); ++- lhs1 = lhs(j + 1, i); ++- cblock.packet[0] = pload2(&lhs0, &lhs1); ++- lhs0 = lhs(j + 2, i); ++- lhs1 = lhs(j + 3, i); ++- cblock.packet[1] = pload2(&lhs0, &lhs1); +++ cblock.packet[0] = pload2(lhs(j + 0, i), lhs(j + 1, i)); +++ cblock.packet[1] = pload2(lhs(j + 2, i), lhs(j + 3, i)); ++ } else { ++- lhs0 = lhs(i, j + 0); ++- lhs1 = lhs(i, j + 1); ++- cblock.packet[0] = pload2(&lhs0, &lhs1); ++- lhs0 = lhs(i, j + 2); ++- lhs1 = lhs(i, j + 3); ++- cblock.packet[1] = pload2(&lhs0, &lhs1); +++ cblock.packet[0] = pload2(lhs(i, j + 0), lhs(i, j + 1)); +++ cblock.packet[1] = pload2(lhs(i, j + 2), lhs(i, j + 3)); ++ } ++ } ++ ++@@ -533,34 +515,50 @@ struct dhs_cpack { ++ rir += ((PanelMode) ? (vectorSize*(2*stride - depth)) : vectorDelta); ++ } ++ ++- if (j < rows) +++ if (!UseLhs) ++ { ++- if(PanelMode) rir += (offset*(rows - j - vectorSize)); ++- rii = rir + (((PanelMode) ? stride : depth) * (rows - j)); +++ if(PanelMode) rir -= (offset*(vectorSize - 1)); ++ ++- for(Index i = 0; i < depth; i++) +++ for(; j < rows; j++) ++ { ++- Index k = j; ++- for(; k < rows; k++) +++ rii = rir + ((PanelMode) ? stride : depth); +++ +++ for(Index i = 0; i < depth; i++) ++ { ++- if (UseLhs) { +++ blockAt[rir] = lhs(i, j).real(); +++ +++ if(Conjugate) +++ blockAt[rii] = -lhs(i, j).imag(); +++ else +++ blockAt[rii] = lhs(i, j).imag(); +++ +++ rir += 1; +++ rii += 1; +++ } +++ +++ rir += ((PanelMode) ? (2*stride - depth) : depth); +++ } +++ } else { +++ if (j < rows) +++ { +++ if(PanelMode) rir += (offset*(rows - j - vectorSize)); +++ rii = rir + (((PanelMode) ? stride : depth) * (rows - j)); +++ +++ for(Index i = 0; i < depth; i++) +++ { +++ Index k = j; +++ for(; k < rows; k++) +++ { ++ blockAt[rir] = lhs(k, i).real(); ++ ++ if(Conjugate) ++ blockAt[rii] = -lhs(k, i).imag(); ++ else ++ blockAt[rii] = lhs(k, i).imag(); ++- } else { ++- blockAt[rir] = lhs(i, k).real(); ++ ++- if(Conjugate) ++- blockAt[rii] = -lhs(i, k).imag(); ++- else ++- blockAt[rii] = lhs(i, k).imag(); +++ rir += 1; +++ rii += 1; ++ } ++- ++- rir += 1; ++- rii += 1; ++ } ++ } ++ } ++@@ -586,16 +584,16 @@ struct dhs_pack{ ++ PacketBlock block; ++ ++ if (UseLhs) { ++- bload(block, lhs, j, i); +++ bload(block, lhs, j, i); ++ } else { ++- bload(block, lhs, i, j); +++ bload(block, lhs, i, j); ++ } ++ if(((StorageOrder == RowMajor) && UseLhs) || ((StorageOrder == ColMajor) && !UseLhs)) ++ { ++ ptranspose(block); ++ } ++ ++- storeBlock(blockA + ri, block); +++ storeBlock(blockA + ri, block); ++ ++ ri += 4*vectorSize; ++ } ++@@ -630,21 +628,33 @@ struct dhs_pack{ ++ if(PanelMode) ri += vectorSize*(stride - offset - depth); ++ } ++ ++- if (j < rows) +++ if (!UseLhs) ++ { ++- if(PanelMode) ri += offset*(rows - j); +++ if(PanelMode) ri += offset; ++ ++- for(Index i = 0; i < depth; i++) +++ for(; j < rows; j++) ++ { ++- Index k = j; ++- for(; k < rows; k++) +++ for(Index i = 0; i < depth; i++) ++ { ++- if (UseLhs) { +++ blockA[ri] = lhs(i, j); +++ ri += 1; +++ } +++ +++ if(PanelMode) ri += stride - depth; +++ } +++ } else { +++ if (j < rows) +++ { +++ if(PanelMode) ri += offset*(rows - j); +++ +++ for(Index i = 0; i < depth; i++) +++ { +++ Index k = j; +++ for(; k < rows; k++) +++ { ++ blockA[ri] = lhs(k, i); ++- } else { ++- blockA[ri] = lhs(i, k); +++ ri += 1; ++ } ++- ri += 1; ++ } ++ } ++ } ++@@ -680,7 +690,7 @@ struct dhs_pack(j, i + 1); ++ } ++ ++- storeBlock(blockA + ri, block); +++ storeBlock(blockA + ri, block); ++ ++ ri += 2*vectorSize; ++ } ++@@ -757,7 +767,7 @@ struct dhs_pack(i + 1, j + 0); //[b1 b2] ++ block.packet[3] = rhs.template loadPacket(i + 1, j + 2); //[b3 b4] ++ ++- storeBlock(blockB + ri, block); +++ storeBlock(blockB + ri, block); ++ } ++ ++ ri += 4*vectorSize; ++@@ -788,19 +798,17 @@ struct dhs_pack(blockAt + rir, blockr); ++- storeBlock(blockAt + rii, blocki); +++ storeBlock(blockAt + rir, blockr); +++ storeBlock(blockAt + rii, blocki); ++ ++ rir += 2*vectorSize; ++ rii += 2*vectorSize; ++@@ -941,7 +949,7 @@ struct dhs_cpack cblock; ++ PacketBlock blockr, blocki; ++ ++- bload(cblock, rhs, i, j); +++ bload(cblock, rhs, i, j); ++ ++ blockr.packet[0] = vec_perm(cblock.packet[0].v, cblock.packet[1].v, p16uc_GETREAL64); ++ blockr.packet[1] = vec_perm(cblock.packet[2].v, cblock.packet[3].v, p16uc_GETREAL64); ++@@ -955,8 +963,8 @@ struct dhs_cpack(blockBt + rir, blockr); ++- storeBlock(blockBt + rii, blocki); +++ storeBlock(blockBt + rir, blockr); +++ storeBlock(blockBt + rii, blocki); ++ ++ rir += 2*vectorSize; ++ rii += 2*vectorSize; ++@@ -965,27 +973,26 @@ struct dhs_cpack ++-EIGEN_ALWAYS_INLINE void pger_common(PacketBlock* acc, const Packet& lhsV, const Packet* rhsV) ++-{ ++- if(NegativeAccumulate) ++- { ++- acc->packet[0] = vec_nmsub(lhsV, rhsV[0], acc->packet[0]); ++- acc->packet[1] = vec_nmsub(lhsV, rhsV[1], acc->packet[1]); ++- acc->packet[2] = vec_nmsub(lhsV, rhsV[2], acc->packet[2]); ++- acc->packet[3] = vec_nmsub(lhsV, rhsV[3], acc->packet[3]); ++- } else { ++- acc->packet[0] = vec_madd(lhsV, rhsV[0], acc->packet[0]); ++- acc->packet[1] = vec_madd(lhsV, rhsV[1], acc->packet[1]); ++- acc->packet[2] = vec_madd(lhsV, rhsV[2], acc->packet[2]); ++- acc->packet[3] = vec_madd(lhsV, rhsV[3], acc->packet[3]); ++- } ++-} ++- ++-template ++-EIGEN_ALWAYS_INLINE void pger_common(PacketBlock* acc, const Packet& lhsV, const Packet* rhsV) +++template +++EIGEN_ALWAYS_INLINE void pger_common(PacketBlock* acc, const Packet& lhsV, const Packet* rhsV) ++ { ++ if(NegativeAccumulate) ++ { ++ acc->packet[0] = vec_nmsub(lhsV, rhsV[0], acc->packet[0]); +++ if (N > 1) { +++ acc->packet[1] = vec_nmsub(lhsV, rhsV[1], acc->packet[1]); +++ } +++ if (N > 2) { +++ acc->packet[2] = vec_nmsub(lhsV, rhsV[2], acc->packet[2]); +++ } +++ if (N > 3) { +++ acc->packet[3] = vec_nmsub(lhsV, rhsV[3], acc->packet[3]); +++ } ++ } else { ++ acc->packet[0] = vec_madd(lhsV, rhsV[0], acc->packet[0]); +++ if (N > 1) { +++ acc->packet[1] = vec_madd(lhsV, rhsV[1], acc->packet[1]); +++ } +++ if (N > 2) { +++ acc->packet[2] = vec_madd(lhsV, rhsV[2], acc->packet[2]); +++ } +++ if (N > 3) { +++ acc->packet[3] = vec_madd(lhsV, rhsV[3], acc->packet[3]); +++ } ++ } ++ } ++ ++@@ -1028,11 +1036,11 @@ EIGEN_ALWAYS_INLINE void pger(PacketBlock* acc, const Scalar* lhs, con ++ { ++ Packet lhsV = pload(lhs); ++ ++- pger_common(acc, lhsV, rhsV); +++ pger_common(acc, lhsV, rhsV); ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void loadPacketRemaining(const Scalar* lhs, Packet &lhsV, Index remaining_rows) +++template +++EIGEN_ALWAYS_INLINE void loadPacketRemaining(const Scalar* lhs, Packet &lhsV) ++ { ++ #ifdef _ARCH_PWR9 ++ lhsV = vec_xl_len((Scalar *)lhs, remaining_rows * sizeof(Scalar)); ++@@ -1044,32 +1052,32 @@ EIGEN_ALWAYS_INLINE void loadPacketRemaining(const Scalar* lhs, Packet &lhsV, In ++ #endif ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void pger(PacketBlock* acc, const Scalar* lhs, const Packet* rhsV, Index remaining_rows) +++template +++EIGEN_ALWAYS_INLINE void pger(PacketBlock* acc, const Scalar* lhs, const Packet* rhsV) ++ { ++ Packet lhsV; ++- loadPacketRemaining(lhs, lhsV, remaining_rows); +++ loadPacketRemaining(lhs, lhsV); ++ ++- pger_common(acc, lhsV, rhsV); +++ pger_common(acc, lhsV, rhsV); ++ } ++ ++ // 512-bits rank1-update of complex acc. It takes decoupled accumulators as entries. It also takes cares of mixed types real * complex and complex * real. ++ template ++ EIGEN_ALWAYS_INLINE void pgerc_common(PacketBlock* accReal, PacketBlock* accImag, const Packet &lhsV, const Packet &lhsVi, const Packet* rhsV, const Packet* rhsVi) ++ { ++- pger_common(accReal, lhsV, rhsV); +++ pger_common(accReal, lhsV, rhsV); ++ if(LhsIsReal) ++ { ++- pger_common(accImag, lhsV, rhsVi); +++ pger_common(accImag, lhsV, rhsVi); ++ EIGEN_UNUSED_VARIABLE(lhsVi); ++ } else { ++ if (!RhsIsReal) { ++- pger_common(accReal, lhsVi, rhsVi); ++- pger_common(accImag, lhsV, rhsVi); +++ pger_common(accReal, lhsVi, rhsVi); +++ pger_common(accImag, lhsV, rhsVi); ++ } else { ++ EIGEN_UNUSED_VARIABLE(rhsVi); ++ } ++- pger_common(accImag, lhsVi, rhsV); +++ pger_common(accImag, lhsVi, rhsV); ++ } ++ } ++ ++@@ -1084,8 +1092,8 @@ EIGEN_ALWAYS_INLINE void pgerc(PacketBlock* accReal, PacketBlock(accReal, accImag, lhsV, lhsVi, rhsV, rhsVi); ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void loadPacketRemaining(const Scalar* lhs_ptr, const Scalar* lhs_ptr_imag, Packet &lhsV, Packet &lhsVi, Index remaining_rows) +++template +++EIGEN_ALWAYS_INLINE void loadPacketRemaining(const Scalar* lhs_ptr, const Scalar* lhs_ptr_imag, Packet &lhsV, Packet &lhsVi) ++ { ++ #ifdef _ARCH_PWR9 ++ lhsV = vec_xl_len((Scalar *)lhs_ptr, remaining_rows * sizeof(Scalar)); ++@@ -1101,11 +1109,11 @@ EIGEN_ALWAYS_INLINE void loadPacketRemaining(const Scalar* lhs_ptr, const Scalar ++ #endif ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void pgerc(PacketBlock* accReal, PacketBlock* accImag, const Scalar* lhs_ptr, const Scalar* lhs_ptr_imag, const Packet* rhsV, const Packet* rhsVi, Index remaining_rows) +++template +++EIGEN_ALWAYS_INLINE void pgerc(PacketBlock* accReal, PacketBlock* accImag, const Scalar* lhs_ptr, const Scalar* lhs_ptr_imag, const Packet* rhsV, const Packet* rhsVi) ++ { ++ Packet lhsV, lhsVi; ++- loadPacketRemaining(lhs_ptr, lhs_ptr_imag, lhsV, lhsVi, remaining_rows); +++ loadPacketRemaining(lhs_ptr, lhs_ptr_imag, lhsV, lhsVi); ++ ++ pgerc_common(accReal, accImag, lhsV, lhsVi, rhsV, rhsVi); ++ } ++@@ -1117,132 +1125,142 @@ EIGEN_ALWAYS_INLINE Packet ploadLhs(const Scalar* lhs) ++ } ++ ++ // Zero the accumulator on PacketBlock. ++-template ++-EIGEN_ALWAYS_INLINE void bsetzero(PacketBlock& acc) ++-{ ++- acc.packet[0] = pset1((Scalar)0); ++- acc.packet[1] = pset1((Scalar)0); ++- acc.packet[2] = pset1((Scalar)0); ++- acc.packet[3] = pset1((Scalar)0); ++-} ++- ++-template ++-EIGEN_ALWAYS_INLINE void bsetzero(PacketBlock& acc) +++template +++EIGEN_ALWAYS_INLINE void bsetzero(PacketBlock& acc) ++ { ++ acc.packet[0] = pset1((Scalar)0); +++ if (N > 1) { +++ acc.packet[1] = pset1((Scalar)0); +++ } +++ if (N > 2) { +++ acc.packet[2] = pset1((Scalar)0); +++ } +++ if (N > 3) { +++ acc.packet[3] = pset1((Scalar)0); +++ } ++ } ++ ++ // Scale the PacketBlock vectors by alpha. ++-template ++-EIGEN_ALWAYS_INLINE void bscale(PacketBlock& acc, PacketBlock& accZ, const Packet& pAlpha) ++-{ ++- acc.packet[0] = pmadd(pAlpha, accZ.packet[0], acc.packet[0]); ++- acc.packet[1] = pmadd(pAlpha, accZ.packet[1], acc.packet[1]); ++- acc.packet[2] = pmadd(pAlpha, accZ.packet[2], acc.packet[2]); ++- acc.packet[3] = pmadd(pAlpha, accZ.packet[3], acc.packet[3]); ++-} ++- ++-template ++-EIGEN_ALWAYS_INLINE void bscale(PacketBlock& acc, PacketBlock& accZ, const Packet& pAlpha) +++template +++EIGEN_ALWAYS_INLINE void bscale(PacketBlock& acc, PacketBlock& accZ, const Packet& pAlpha) ++ { ++ acc.packet[0] = pmadd(pAlpha, accZ.packet[0], acc.packet[0]); +++ if (N > 1) { +++ acc.packet[1] = pmadd(pAlpha, accZ.packet[1], acc.packet[1]); +++ } +++ if (N > 2) { +++ acc.packet[2] = pmadd(pAlpha, accZ.packet[2], acc.packet[2]); +++ } +++ if (N > 3) { +++ acc.packet[3] = pmadd(pAlpha, accZ.packet[3], acc.packet[3]); +++ } ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void bscalec_common(PacketBlock& acc, PacketBlock& accZ, const Packet& pAlpha) ++-{ ++- acc.packet[0] = pmul(accZ.packet[0], pAlpha); ++- acc.packet[1] = pmul(accZ.packet[1], pAlpha); ++- acc.packet[2] = pmul(accZ.packet[2], pAlpha); ++- acc.packet[3] = pmul(accZ.packet[3], pAlpha); ++-} ++- ++-template ++-EIGEN_ALWAYS_INLINE void bscalec_common(PacketBlock& acc, PacketBlock& accZ, const Packet& pAlpha) +++template +++EIGEN_ALWAYS_INLINE void bscalec_common(PacketBlock& acc, PacketBlock& accZ, const Packet& pAlpha) ++ { ++ acc.packet[0] = pmul(accZ.packet[0], pAlpha); +++ if (N > 1) { +++ acc.packet[1] = pmul(accZ.packet[1], pAlpha); +++ } +++ if (N > 2) { +++ acc.packet[2] = pmul(accZ.packet[2], pAlpha); +++ } +++ if (N > 3) { +++ acc.packet[3] = pmul(accZ.packet[3], pAlpha); +++ } ++ } ++ ++ // Complex version of PacketBlock scaling. ++ template ++ EIGEN_ALWAYS_INLINE void bscalec(PacketBlock& aReal, PacketBlock& aImag, const Packet& bReal, const Packet& bImag, PacketBlock& cReal, PacketBlock& cImag) ++ { ++- bscalec_common(cReal, aReal, bReal); +++ bscalec_common(cReal, aReal, bReal); ++ ++- bscalec_common(cImag, aImag, bReal); +++ bscalec_common(cImag, aImag, bReal); ++ ++- pger_common(&cReal, bImag, aImag.packet); +++ pger_common(&cReal, bImag, aImag.packet); ++ ++- pger_common(&cImag, bImag, aReal.packet); +++ pger_common(&cImag, bImag, aReal.packet); ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void band(PacketBlock& acc, const Packet& pMask) +++template +++EIGEN_ALWAYS_INLINE void band(PacketBlock& acc, const Packet& pMask) ++ { ++ acc.packet[0] = pand(acc.packet[0], pMask); ++- acc.packet[1] = pand(acc.packet[1], pMask); ++- acc.packet[2] = pand(acc.packet[2], pMask); ++- acc.packet[3] = pand(acc.packet[3], pMask); +++ if (N > 1) { +++ acc.packet[1] = pand(acc.packet[1], pMask); +++ } +++ if (N > 2) { +++ acc.packet[2] = pand(acc.packet[2], pMask); +++ } +++ if (N > 3) { +++ acc.packet[3] = pand(acc.packet[3], pMask); +++ } ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void bscalec(PacketBlock& aReal, PacketBlock& aImag, const Packet& bReal, const Packet& bImag, PacketBlock& cReal, PacketBlock& cImag, const Packet& pMask) +++template +++EIGEN_ALWAYS_INLINE void bscalec(PacketBlock& aReal, PacketBlock& aImag, const Packet& bReal, const Packet& bImag, PacketBlock& cReal, PacketBlock& cImag, const Packet& pMask) ++ { ++- band(aReal, pMask); ++- band(aImag, pMask); +++ band(aReal, pMask); +++ band(aImag, pMask); ++ ++- bscalec(aReal, aImag, bReal, bImag, cReal, cImag); +++ bscalec(aReal, aImag, bReal, bImag, cReal, cImag); ++ } ++ ++ // Load a PacketBlock, the N parameters make tunning gemm easier so we can add more accumulators as needed. ++-template ++-EIGEN_ALWAYS_INLINE void bload(PacketBlock& acc, const DataMapper& res, Index row, Index col) ++-{ ++- if (StorageOrder == RowMajor) { ++- acc.packet[0] = res.template loadPacket(row + 0, col + N*accCols); ++- acc.packet[1] = res.template loadPacket(row + 1, col + N*accCols); ++- acc.packet[2] = res.template loadPacket(row + 2, col + N*accCols); ++- acc.packet[3] = res.template loadPacket(row + 3, col + N*accCols); ++- } else { ++- acc.packet[0] = res.template loadPacket(row + N*accCols, col + 0); ++- acc.packet[1] = res.template loadPacket(row + N*accCols, col + 1); ++- acc.packet[2] = res.template loadPacket(row + N*accCols, col + 2); ++- acc.packet[3] = res.template loadPacket(row + N*accCols, col + 3); ++- } ++-} ++- ++-// An overload of bload when you have a PacketBLock with 8 vectors. ++-template ++-EIGEN_ALWAYS_INLINE void bload(PacketBlock& acc, const DataMapper& res, Index row, Index col) +++template +++EIGEN_ALWAYS_INLINE void bload(PacketBlock& acc, const DataMapper& res, Index row, Index col) ++ { ++ if (StorageOrder == RowMajor) { ++- acc.packet[0] = res.template loadPacket(row + 0, col + N*accCols); ++- acc.packet[1] = res.template loadPacket(row + 1, col + N*accCols); ++- acc.packet[2] = res.template loadPacket(row + 2, col + N*accCols); ++- acc.packet[3] = res.template loadPacket(row + 3, col + N*accCols); ++- acc.packet[4] = res.template loadPacket(row + 0, col + (N+1)*accCols); ++- acc.packet[5] = res.template loadPacket(row + 1, col + (N+1)*accCols); ++- acc.packet[6] = res.template loadPacket(row + 2, col + (N+1)*accCols); ++- acc.packet[7] = res.template loadPacket(row + 3, col + (N+1)*accCols); +++ acc.packet[0] = res.template loadPacket(row + 0, col); +++ if (N > 1) { +++ acc.packet[1] = res.template loadPacket(row + 1, col); +++ } +++ if (N > 2) { +++ acc.packet[2] = res.template loadPacket(row + 2, col); +++ } +++ if (N > 3) { +++ acc.packet[3] = res.template loadPacket(row + 3, col); +++ } +++ if (Complex) { +++ acc.packet[0+N] = res.template loadPacket(row + 0, col + accCols); +++ if (N > 1) { +++ acc.packet[1+N] = res.template loadPacket(row + 1, col + accCols); +++ } +++ if (N > 2) { +++ acc.packet[2+N] = res.template loadPacket(row + 2, col + accCols); +++ } +++ if (N > 3) { +++ acc.packet[3+N] = res.template loadPacket(row + 3, col + accCols); +++ } +++ } ++ } else { ++- acc.packet[0] = res.template loadPacket(row + N*accCols, col + 0); ++- acc.packet[1] = res.template loadPacket(row + N*accCols, col + 1); ++- acc.packet[2] = res.template loadPacket(row + N*accCols, col + 2); ++- acc.packet[3] = res.template loadPacket(row + N*accCols, col + 3); ++- acc.packet[4] = res.template loadPacket(row + (N+1)*accCols, col + 0); ++- acc.packet[5] = res.template loadPacket(row + (N+1)*accCols, col + 1); ++- acc.packet[6] = res.template loadPacket(row + (N+1)*accCols, col + 2); ++- acc.packet[7] = res.template loadPacket(row + (N+1)*accCols, col + 3); +++ acc.packet[0] = res.template loadPacket(row, col + 0); +++ if (N > 1) { +++ acc.packet[1] = res.template loadPacket(row, col + 1); +++ } +++ if (N > 2) { +++ acc.packet[2] = res.template loadPacket(row, col + 2); +++ } +++ if (N > 3) { +++ acc.packet[3] = res.template loadPacket(row, col + 3); +++ } +++ if (Complex) { +++ acc.packet[0+N] = res.template loadPacket(row + accCols, col + 0); +++ if (N > 1) { +++ acc.packet[1+N] = res.template loadPacket(row + accCols, col + 1); +++ } +++ if (N > 2) { +++ acc.packet[2+N] = res.template loadPacket(row + accCols, col + 2); +++ } +++ if (N > 3) { +++ acc.packet[3+N] = res.template loadPacket(row + accCols, col + 3); +++ } +++ } ++ } ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void bload(PacketBlock& acc, const DataMapper& res, Index row, Index col) ++-{ ++- acc.packet[0] = res.template loadPacket(row + N*accCols, col + 0); ++- acc.packet[1] = res.template loadPacket(row + (N+1)*accCols, col + 0); ++-} ++- ++ const static Packet4i mask41 = { -1, 0, 0, 0 }; ++ const static Packet4i mask42 = { -1, -1, 0, 0 }; ++ const static Packet4i mask43 = { -1, -1, -1, 0 }; ++@@ -1273,22 +1291,44 @@ EIGEN_ALWAYS_INLINE Packet2d bmask(const int remaining_rows) ++ } ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void bscale(PacketBlock& acc, PacketBlock& accZ, const Packet& pAlpha, const Packet& pMask) +++template +++EIGEN_ALWAYS_INLINE void bscale(PacketBlock& acc, PacketBlock& accZ, const Packet& pAlpha, const Packet& pMask) ++ { ++- band(accZ, pMask); +++ band(accZ, pMask); ++ ++- bscale(acc, accZ, pAlpha); +++ bscale(acc, accZ, pAlpha); ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void pbroadcast4_old(const __UNPACK_TYPE__(Packet)* a, Packet& a0, Packet& a1, Packet& a2, Packet& a3) +++template EIGEN_ALWAYS_INLINE void +++pbroadcastN_old(const __UNPACK_TYPE__(Packet) *a, +++ Packet& a0, Packet& a1, Packet& a2, Packet& a3) +++{ +++ a0 = pset1(a[0]); +++ if (N > 1) { +++ a1 = pset1(a[1]); +++ } else { +++ EIGEN_UNUSED_VARIABLE(a1); +++ } +++ if (N > 2) { +++ a2 = pset1(a[2]); +++ } else { +++ EIGEN_UNUSED_VARIABLE(a2); +++ } +++ if (N > 3) { +++ a3 = pset1(a[3]); +++ } else { +++ EIGEN_UNUSED_VARIABLE(a3); +++ } +++} +++ +++template<> +++EIGEN_ALWAYS_INLINE void pbroadcastN_old(const float* a, Packet4f& a0, Packet4f& a1, Packet4f& a2, Packet4f& a3) ++ { ++- pbroadcast4(a, a0, a1, a2, a3); +++ pbroadcast4(a, a0, a1, a2, a3); ++ } ++ ++ template<> ++-EIGEN_ALWAYS_INLINE void pbroadcast4_old(const double* a, Packet2d& a0, Packet2d& a1, Packet2d& a2, Packet2d& a3) +++EIGEN_ALWAYS_INLINE void pbroadcastN_old(const double* a, Packet2d& a0, Packet2d& a1, Packet2d& a2, Packet2d& a3) ++ { ++ a1 = pload(a); ++ a3 = pload(a + 2); ++@@ -1298,89 +1338,96 @@ EIGEN_ALWAYS_INLINE void pbroadcast4_old(const double* a, Packet2d& a0 ++ a3 = vec_splat(a3, 1); ++ } ++ ++-// PEEL loop factor. ++-#define PEEL 7 ++- ++-template ++-EIGEN_ALWAYS_INLINE void MICRO_EXTRA_COL( ++- const Scalar* &lhs_ptr, ++- const Scalar* &rhs_ptr, ++- PacketBlock &accZero, ++- Index remaining_rows, ++- Index remaining_cols) +++template EIGEN_ALWAYS_INLINE void +++pbroadcastN(const __UNPACK_TYPE__(Packet) *a, +++ Packet& a0, Packet& a1, Packet& a2, Packet& a3) ++ { ++- Packet rhsV[1]; ++- rhsV[0] = pset1(rhs_ptr[0]); ++- pger<1,Scalar, Packet, false>(&accZero, lhs_ptr, rhsV); ++- lhs_ptr += remaining_rows; ++- rhs_ptr += remaining_cols; +++ a0 = pset1(a[0]); +++ if (N > 1) { +++ a1 = pset1(a[1]); +++ } else { +++ EIGEN_UNUSED_VARIABLE(a1); +++ } +++ if (N > 2) { +++ a2 = pset1(a[2]); +++ } else { +++ EIGEN_UNUSED_VARIABLE(a2); +++ } +++ if (N > 3) { +++ a3 = pset1(a[3]); +++ } else { +++ EIGEN_UNUSED_VARIABLE(a3); +++ } ++ } ++ ++-template ++-EIGEN_STRONG_INLINE void gemm_extra_col( ++- const DataMapper& res, ++- const Scalar* lhs_base, ++- const Scalar* rhs_base, ++- Index depth, ++- Index strideA, ++- Index offsetA, ++- Index row, ++- Index col, ++- Index remaining_rows, ++- Index remaining_cols, ++- const Packet& pAlpha) +++template<> EIGEN_ALWAYS_INLINE void +++pbroadcastN(const float *a, +++ Packet4f& a0, Packet4f& a1, Packet4f& a2, Packet4f& a3) ++ { ++- const Scalar* rhs_ptr = rhs_base; ++- const Scalar* lhs_ptr = lhs_base + row*strideA + remaining_rows*offsetA; ++- PacketBlock accZero; +++ a3 = pload(a); +++ a0 = vec_splat(a3, 0); +++ a1 = vec_splat(a3, 1); +++ a2 = vec_splat(a3, 2); +++ a3 = vec_splat(a3, 3); +++} ++ ++- bsetzero(accZero); +++// PEEL loop factor. +++#define PEEL 7 +++#define PEEL_ROW 7 ++ ++- Index remaining_depth = (depth & -accRows); ++- Index k = 0; ++- for(; k + PEEL <= remaining_depth; k+= PEEL) ++- { ++- EIGEN_POWER_PREFETCH(rhs_ptr); ++- EIGEN_POWER_PREFETCH(lhs_ptr); ++- for (int l = 0; l < PEEL; l++) { ++- MICRO_EXTRA_COL(lhs_ptr, rhs_ptr, accZero, remaining_rows, remaining_cols); ++- } ++- } ++- for(; k < remaining_depth; k++) ++- { ++- MICRO_EXTRA_COL(lhs_ptr, rhs_ptr, accZero, remaining_rows, remaining_cols); +++#define MICRO_UNROLL_PEEL(func) \ +++ func(0) func(1) func(2) func(3) func(4) func(5) func(6) func(7) +++ +++#define MICRO_ZERO_PEEL(peel) \ +++ if ((PEEL_ROW > peel) && (peel != 0)) { \ +++ bsetzero(accZero##peel); \ +++ } else { \ +++ EIGEN_UNUSED_VARIABLE(accZero##peel); \ ++ } ++- for(; k < depth; k++) ++- { ++- Packet rhsV[1]; ++- rhsV[0] = pset1(rhs_ptr[0]); ++- pger<1, Scalar, Packet, Index, false>(&accZero, lhs_ptr, rhsV, remaining_rows); ++- lhs_ptr += remaining_rows; ++- rhs_ptr += remaining_cols; +++ +++#define MICRO_ZERO_PEEL_ROW \ +++ MICRO_UNROLL_PEEL(MICRO_ZERO_PEEL); +++ +++#define MICRO_WORK_PEEL(peel) \ +++ if (PEEL_ROW > peel) { \ +++ pbroadcastN(rhs_ptr + (accRows * peel), rhsV##peel[0], rhsV##peel[1], rhsV##peel[2], rhsV##peel[3]); \ +++ pger(&accZero##peel, lhs_ptr + (remaining_rows * peel), rhsV##peel); \ +++ } else { \ +++ EIGEN_UNUSED_VARIABLE(rhsV##peel); \ ++ } ++ ++- accZero.packet[0] = vec_mul(pAlpha, accZero.packet[0]); ++- for(Index i = 0; i < remaining_rows; i++) { ++- res(row + i, col) += accZero.packet[0][i]; +++#define MICRO_WORK_PEEL_ROW \ +++ Packet rhsV0[4], rhsV1[4], rhsV2[4], rhsV3[4], rhsV4[4], rhsV5[4], rhsV6[4], rhsV7[4]; \ +++ MICRO_UNROLL_PEEL(MICRO_WORK_PEEL); \ +++ lhs_ptr += (remaining_rows * PEEL_ROW); \ +++ rhs_ptr += (accRows * PEEL_ROW); +++ +++#define MICRO_ADD_PEEL(peel, sum) \ +++ if (PEEL_ROW > peel) { \ +++ for (Index i = 0; i < accRows; i++) { \ +++ accZero##sum.packet[i] += accZero##peel.packet[i]; \ +++ } \ ++ } ++-} ++ ++-template +++#define MICRO_ADD_PEEL_ROW \ +++ MICRO_ADD_PEEL(4, 0) MICRO_ADD_PEEL(5, 1) MICRO_ADD_PEEL(6, 2) MICRO_ADD_PEEL(7, 3) \ +++ MICRO_ADD_PEEL(2, 0) MICRO_ADD_PEEL(3, 1) MICRO_ADD_PEEL(1, 0) +++ +++template ++ EIGEN_ALWAYS_INLINE void MICRO_EXTRA_ROW( ++ const Scalar* &lhs_ptr, ++ const Scalar* &rhs_ptr, ++- PacketBlock &accZero, ++- Index remaining_rows) +++ PacketBlock &accZero) ++ { ++ Packet rhsV[4]; ++- pbroadcast4(rhs_ptr, rhsV[0], rhsV[1], rhsV[2], rhsV[3]); ++- pger<4, Scalar, Packet, false>(&accZero, lhs_ptr, rhsV); +++ pbroadcastN(rhs_ptr, rhsV[0], rhsV[1], rhsV[2], rhsV[3]); +++ pger(&accZero, lhs_ptr, rhsV); ++ lhs_ptr += remaining_rows; ++ rhs_ptr += accRows; ++ } ++ ++-template ++-EIGEN_STRONG_INLINE void gemm_extra_row( +++template +++EIGEN_ALWAYS_INLINE void gemm_unrolled_row_iteration( ++ const DataMapper& res, ++ const Scalar* lhs_base, ++ const Scalar* rhs_base, ++@@ -1391,59 +1438,89 @@ EIGEN_STRONG_INLINE void gemm_extra_row( ++ Index col, ++ Index rows, ++ Index cols, ++- Index remaining_rows, ++ const Packet& pAlpha, ++ const Packet& pMask) ++ { ++ const Scalar* rhs_ptr = rhs_base; ++ const Scalar* lhs_ptr = lhs_base + row*strideA + remaining_rows*offsetA; ++- PacketBlock accZero, acc; +++ PacketBlock accZero0, accZero1, accZero2, accZero3, accZero4, accZero5, accZero6, accZero7, acc; ++ ++- bsetzero(accZero); +++ bsetzero(accZero0); ++ ++- Index remaining_depth = (col + accRows < cols) ? depth : (depth & -accRows); +++ Index remaining_depth = (col + quad_traits::rows < cols) ? depth : (depth & -quad_traits::rows); ++ Index k = 0; ++- for(; k + PEEL <= remaining_depth; k+= PEEL) ++- { ++- EIGEN_POWER_PREFETCH(rhs_ptr); ++- EIGEN_POWER_PREFETCH(lhs_ptr); ++- for (int l = 0; l < PEEL; l++) { ++- MICRO_EXTRA_ROW(lhs_ptr, rhs_ptr, accZero, remaining_rows); ++- } +++ if (remaining_depth >= PEEL_ROW) { +++ MICRO_ZERO_PEEL_ROW +++ do +++ { +++ EIGEN_POWER_PREFETCH(rhs_ptr); +++ EIGEN_POWER_PREFETCH(lhs_ptr); +++ MICRO_WORK_PEEL_ROW +++ } while ((k += PEEL_ROW) + PEEL_ROW <= remaining_depth); +++ MICRO_ADD_PEEL_ROW ++ } ++ for(; k < remaining_depth; k++) ++ { ++- MICRO_EXTRA_ROW(lhs_ptr, rhs_ptr, accZero, remaining_rows); +++ MICRO_EXTRA_ROW(lhs_ptr, rhs_ptr, accZero0); ++ } ++ ++ if ((remaining_depth == depth) && (rows >= accCols)) ++ { ++- for(Index j = 0; j < 4; j++) { ++- acc.packet[j] = res.template loadPacket(row, col + j); ++- } ++- bscale(acc, accZero, pAlpha, pMask); ++- res.template storePacketBlock(row, col, acc); +++ bload(acc, res, row, 0); +++ bscale(acc, accZero0, pAlpha, pMask); +++ res.template storePacketBlock(row, 0, acc); ++ } else { ++ for(; k < depth; k++) ++ { ++ Packet rhsV[4]; ++- pbroadcast4(rhs_ptr, rhsV[0], rhsV[1], rhsV[2], rhsV[3]); ++- pger<4, Scalar, Packet, Index, false>(&accZero, lhs_ptr, rhsV, remaining_rows); +++ pbroadcastN(rhs_ptr, rhsV[0], rhsV[1], rhsV[2], rhsV[3]); +++ pger(&accZero0, lhs_ptr, rhsV); ++ lhs_ptr += remaining_rows; ++ rhs_ptr += accRows; ++ } ++ ++- for(Index j = 0; j < 4; j++) { ++- accZero.packet[j] = vec_mul(pAlpha, accZero.packet[j]); ++- } ++- for(Index j = 0; j < 4; j++) { +++ for(Index j = 0; j < accRows; j++) { +++ accZero0.packet[j] = vec_mul(pAlpha, accZero0.packet[j]); ++ for(Index i = 0; i < remaining_rows; i++) { ++- res(row + i, col + j) += accZero.packet[j][i]; +++ res(row + i, j) += accZero0.packet[j][i]; ++ } ++ } ++ } ++ } ++ +++template +++EIGEN_ALWAYS_INLINE void gemm_extra_row( +++ const DataMapper& res, +++ const Scalar* lhs_base, +++ const Scalar* rhs_base, +++ Index depth, +++ Index strideA, +++ Index offsetA, +++ Index row, +++ Index col, +++ Index rows, +++ Index cols, +++ Index remaining_rows, +++ const Packet& pAlpha, +++ const Packet& pMask) +++{ +++ switch(remaining_rows) { +++ case 1: +++ gemm_unrolled_row_iteration(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, rows, cols, pAlpha, pMask); +++ break; +++ case 2: +++ if (sizeof(Scalar) == sizeof(float)) { +++ gemm_unrolled_row_iteration(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, rows, cols, pAlpha, pMask); +++ } +++ break; +++ default: +++ if (sizeof(Scalar) == sizeof(float)) { +++ gemm_unrolled_row_iteration(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, rows, cols, pAlpha, pMask); +++ } +++ break; +++ } +++} +++ ++ #define MICRO_UNROLL(func) \ ++ func(0) func(1) func(2) func(3) func(4) func(5) func(6) func(7) ++ ++@@ -1462,34 +1539,24 @@ EIGEN_STRONG_INLINE void gemm_extra_row( ++ ++ #define MICRO_WORK_ONE(iter, peel) \ ++ if (unroll_factor > iter) { \ ++- pger_common(&accZero##iter, lhsV##iter, rhsV##peel); \ +++ pger_common(&accZero##iter, lhsV##iter, rhsV##peel); \ ++ } ++ ++ #define MICRO_TYPE_PEEL4(func, func2, peel) \ ++ if (PEEL > peel) { \ ++ Packet lhsV0, lhsV1, lhsV2, lhsV3, lhsV4, lhsV5, lhsV6, lhsV7; \ ++- pbroadcast4(rhs_ptr + (accRows * peel), rhsV##peel[0], rhsV##peel[1], rhsV##peel[2], rhsV##peel[3]); \ ++- MICRO_UNROLL_WORK(func, func2, peel) \ ++- } else { \ ++- EIGEN_UNUSED_VARIABLE(rhsV##peel); \ ++- } ++- ++-#define MICRO_TYPE_PEEL1(func, func2, peel) \ ++- if (PEEL > peel) { \ ++- Packet lhsV0, lhsV1, lhsV2, lhsV3, lhsV4, lhsV5, lhsV6, lhsV7; \ ++- rhsV##peel[0] = pset1(rhs_ptr[remaining_cols * peel]); \ +++ pbroadcastN(rhs_ptr + (accRows * peel), rhsV##peel[0], rhsV##peel[1], rhsV##peel[2], rhsV##peel[3]); \ ++ MICRO_UNROLL_WORK(func, func2, peel) \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(rhsV##peel); \ ++ } ++ ++ #define MICRO_UNROLL_TYPE_PEEL(M, func, func1, func2) \ ++- Packet rhsV0[M], rhsV1[M], rhsV2[M], rhsV3[M], rhsV4[M], rhsV5[M], rhsV6[M], rhsV7[M], rhsV8[M], rhsV9[M]; \ +++ Packet rhsV0[M], rhsV1[M], rhsV2[M], rhsV3[M], rhsV4[M], rhsV5[M], rhsV6[M], rhsV7[M]; \ ++ func(func1,func2,0); func(func1,func2,1); \ ++ func(func1,func2,2); func(func1,func2,3); \ ++ func(func1,func2,4); func(func1,func2,5); \ ++- func(func1,func2,6); func(func1,func2,7); \ ++- func(func1,func2,8); func(func1,func2,9); +++ func(func1,func2,6); func(func1,func2,7); ++ ++ #define MICRO_UNROLL_TYPE_ONE(M, func, func1, func2) \ ++ Packet rhsV0[M]; \ ++@@ -1503,17 +1570,9 @@ EIGEN_STRONG_INLINE void gemm_extra_row( ++ MICRO_UNROLL_TYPE_ONE(4, MICRO_TYPE_PEEL4, MICRO_WORK_ONE, MICRO_LOAD_ONE); \ ++ rhs_ptr += accRows; ++ ++-#define MICRO_ONE_PEEL1 \ ++- MICRO_UNROLL_TYPE_PEEL(1, MICRO_TYPE_PEEL1, MICRO_WORK_ONE, MICRO_LOAD_ONE); \ ++- rhs_ptr += (remaining_cols * PEEL); ++- ++-#define MICRO_ONE1 \ ++- MICRO_UNROLL_TYPE_ONE(1, MICRO_TYPE_PEEL1, MICRO_WORK_ONE, MICRO_LOAD_ONE); \ ++- rhs_ptr += remaining_cols; ++- ++ #define MICRO_DST_PTR_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++- bsetzero(accZero##iter); \ +++ bsetzero(accZero##iter); \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(accZero##iter); \ ++ } ++@@ -1522,7 +1581,7 @@ EIGEN_STRONG_INLINE void gemm_extra_row( ++ ++ #define MICRO_SRC_PTR_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++- lhs_ptr##iter = lhs_base + ( (row/accCols) + iter )*strideA*accCols + accCols*offsetA; \ +++ lhs_ptr##iter = lhs_base + ( (row/accCols) + iter )*strideA*accCols; \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(lhs_ptr##iter); \ ++ } ++@@ -1538,25 +1597,13 @@ EIGEN_STRONG_INLINE void gemm_extra_row( ++ ++ #define MICRO_STORE_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++- acc.packet[0] = res.template loadPacket(row + iter*accCols, col + 0); \ ++- acc.packet[1] = res.template loadPacket(row + iter*accCols, col + 1); \ ++- acc.packet[2] = res.template loadPacket(row + iter*accCols, col + 2); \ ++- acc.packet[3] = res.template loadPacket(row + iter*accCols, col + 3); \ ++- bscale(acc, accZero##iter, pAlpha); \ ++- res.template storePacketBlock(row + iter*accCols, col, acc); \ +++ bload(acc, res, row + iter*accCols, 0); \ +++ bscale(acc, accZero##iter, pAlpha); \ +++ res.template storePacketBlock(row + iter*accCols, 0, acc); \ ++ } ++ ++ #define MICRO_STORE MICRO_UNROLL(MICRO_STORE_ONE) ++ ++-#define MICRO_COL_STORE_ONE(iter) \ ++- if (unroll_factor > iter) { \ ++- acc.packet[0] = res.template loadPacket(row + iter*accCols, col + 0); \ ++- bscale(acc, accZero##iter, pAlpha); \ ++- res.template storePacketBlock(row + iter*accCols, col, acc); \ ++- } ++- ++-#define MICRO_COL_STORE MICRO_UNROLL(MICRO_COL_STORE_ONE) ++- ++ template ++ EIGEN_STRONG_INLINE void gemm_unrolled_iteration( ++ const DataMapper& res, ++@@ -1564,15 +1611,13 @@ EIGEN_STRONG_INLINE void gemm_unrolled_iteration( ++ const Scalar* rhs_base, ++ Index depth, ++ Index strideA, ++- Index offsetA, ++ Index& row, ++- Index col, ++ const Packet& pAlpha) ++ { ++ const Scalar* rhs_ptr = rhs_base; ++ const Scalar* lhs_ptr0 = NULL, * lhs_ptr1 = NULL, * lhs_ptr2 = NULL, * lhs_ptr3 = NULL, * lhs_ptr4 = NULL, * lhs_ptr5 = NULL, * lhs_ptr6 = NULL, * lhs_ptr7 = NULL; ++- PacketBlock accZero0, accZero1, accZero2, accZero3, accZero4, accZero5, accZero6, accZero7; ++- PacketBlock acc; +++ PacketBlock accZero0, accZero1, accZero2, accZero3, accZero4, accZero5, accZero6, accZero7; +++ PacketBlock acc; ++ ++ MICRO_SRC_PTR ++ MICRO_DST_PTR ++@@ -1593,101 +1638,100 @@ EIGEN_STRONG_INLINE void gemm_unrolled_iteration( ++ row += unroll_factor*accCols; ++ } ++ ++-template ++-EIGEN_STRONG_INLINE void gemm_unrolled_col_iteration( +++template +++EIGEN_ALWAYS_INLINE void gemm_cols( ++ const DataMapper& res, ++- const Scalar* lhs_base, ++- const Scalar* rhs_base, +++ const Scalar* blockA, +++ const Scalar* blockB, ++ Index depth, ++ Index strideA, ++ Index offsetA, ++- Index& row, +++ Index strideB, +++ Index offsetB, ++ Index col, ++- Index remaining_cols, ++- const Packet& pAlpha) +++ Index rows, +++ Index cols, +++ Index remaining_rows, +++ const Packet& pAlpha, +++ const Packet& pMask) ++ { ++- const Scalar* rhs_ptr = rhs_base; ++- const Scalar* lhs_ptr0 = NULL, * lhs_ptr1 = NULL, * lhs_ptr2 = NULL, * lhs_ptr3 = NULL, * lhs_ptr4 = NULL, * lhs_ptr5 = NULL, * lhs_ptr6 = NULL, *lhs_ptr7 = NULL; ++- PacketBlock accZero0, accZero1, accZero2, accZero3, accZero4, accZero5, accZero6, accZero7; ++- PacketBlock acc; ++- ++- MICRO_SRC_PTR ++- MICRO_DST_PTR ++- ++- Index k = 0; ++- for(; k + PEEL <= depth; k+= PEEL) ++- { ++- EIGEN_POWER_PREFETCH(rhs_ptr); ++- MICRO_PREFETCH ++- MICRO_ONE_PEEL1 ++- } ++- for(; k < depth; k++) ++- { ++- MICRO_ONE1 ++- } ++- MICRO_COL_STORE +++ const DataMapper res3 = res.getSubMapper(0, col); ++ ++- row += unroll_factor*accCols; ++-} +++ const Scalar* rhs_base = blockB + col*strideB + accRows*offsetB; +++ const Scalar* lhs_base = blockA + accCols*offsetA; +++ Index row = 0; ++ ++-template ++-EIGEN_STRONG_INLINE void gemm_unrolled_col( ++- const DataMapper& res, ++- const Scalar* lhs_base, ++- const Scalar* rhs_base, ++- Index depth, ++- Index strideA, ++- Index offsetA, ++- Index& row, ++- Index rows, ++- Index col, ++- Index remaining_cols, ++- const Packet& pAlpha) ++-{ ++ #define MAX_UNROLL 6 ++ while(row + MAX_UNROLL*accCols <= rows) { ++- gemm_unrolled_col_iteration(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, remaining_cols, pAlpha); +++ gemm_unrolled_iteration(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); ++ } ++ switch( (rows-row)/accCols ) { ++ #if MAX_UNROLL > 7 ++ case 7: ++- gemm_unrolled_col_iteration<7, Scalar, Packet, DataMapper, Index, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, remaining_cols, pAlpha); +++ gemm_unrolled_iteration<7, Scalar, Packet, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); ++ break; ++ #endif ++ #if MAX_UNROLL > 6 ++ case 6: ++- gemm_unrolled_col_iteration<6, Scalar, Packet, DataMapper, Index, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, remaining_cols, pAlpha); +++ gemm_unrolled_iteration<6, Scalar, Packet, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); ++ break; ++ #endif ++ #if MAX_UNROLL > 5 ++- case 5: ++- gemm_unrolled_col_iteration<5, Scalar, Packet, DataMapper, Index, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, remaining_cols, pAlpha); +++ case 5: +++ gemm_unrolled_iteration<5, Scalar, Packet, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); ++ break; ++ #endif ++ #if MAX_UNROLL > 4 ++- case 4: ++- gemm_unrolled_col_iteration<4, Scalar, Packet, DataMapper, Index, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, remaining_cols, pAlpha); +++ case 4: +++ gemm_unrolled_iteration<4, Scalar, Packet, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); ++ break; ++ #endif ++ #if MAX_UNROLL > 3 ++- case 3: ++- gemm_unrolled_col_iteration<3, Scalar, Packet, DataMapper, Index, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, remaining_cols, pAlpha); ++- break; +++ case 3: +++ gemm_unrolled_iteration<3, Scalar, Packet, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); +++ break; ++ #endif ++ #if MAX_UNROLL > 2 ++- case 2: ++- gemm_unrolled_col_iteration<2, Scalar, Packet, DataMapper, Index, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, remaining_cols, pAlpha); ++- break; +++ case 2: +++ gemm_unrolled_iteration<2, Scalar, Packet, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); +++ break; ++ #endif ++ #if MAX_UNROLL > 1 ++- case 1: ++- gemm_unrolled_col_iteration<1, Scalar, Packet, DataMapper, Index, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, remaining_cols, pAlpha); ++- break; +++ case 1: +++ gemm_unrolled_iteration<1, Scalar, Packet, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); +++ break; ++ #endif ++- default: ++- break; +++ default: +++ break; ++ } ++ #undef MAX_UNROLL +++ +++ if(remaining_rows > 0) +++ { +++ gemm_extra_row(res3, blockA, rhs_base, depth, strideA, offsetA, row, col, rows, cols, remaining_rows, pAlpha, pMask); +++ } +++} +++ +++template +++EIGEN_STRONG_INLINE void gemm_extra_cols( +++ const DataMapper& res, +++ const Scalar* blockA, +++ const Scalar* blockB, +++ Index depth, +++ Index strideA, +++ Index offsetA, +++ Index strideB, +++ Index offsetB, +++ Index col, +++ Index rows, +++ Index cols, +++ Index remaining_rows, +++ const Packet& pAlpha, +++ const Packet& pMask) +++{ +++ for (; col < cols; col++) { +++ gemm_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlpha, pMask); +++ } ++ } ++ ++ /**************** ++@@ -1697,7 +1741,6 @@ template(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- } ++- switch( (rows-row)/accCols ) { ++-#if MAX_UNROLL > 7 ++- case 7: ++- gemm_unrolled_iteration<7, Scalar, Packet, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; ++-#endif ++-#if MAX_UNROLL > 6 ++- case 6: ++- gemm_unrolled_iteration<6, Scalar, Packet, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; ++-#endif ++-#if MAX_UNROLL > 5 ++- case 5: ++- gemm_unrolled_iteration<5, Scalar, Packet, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; ++-#endif ++-#if MAX_UNROLL > 4 ++- case 4: ++- gemm_unrolled_iteration<4, Scalar, Packet, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; ++-#endif ++-#if MAX_UNROLL > 3 ++- case 3: ++- gemm_unrolled_iteration<3, Scalar, Packet, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; ++-#endif ++-#if MAX_UNROLL > 2 ++- case 2: ++- gemm_unrolled_iteration<2, Scalar, Packet, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; ++-#endif ++-#if MAX_UNROLL > 1 ++- case 1: ++- gemm_unrolled_iteration<1, Scalar, Packet, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; ++-#endif ++- default: ++- break; ++- } ++-#undef MAX_UNROLL ++- ++- if(remaining_rows > 0) ++- { ++- gemm_extra_row(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, rows, cols, remaining_rows, pAlpha, pMask); ++- } ++- } ++- ++- if(remaining_cols > 0) ++- { ++- const Scalar* rhs_base = blockB + col*strideB + remaining_cols*offsetB; ++- const Scalar* lhs_base = blockA; ++- ++- for(; col < cols; col++) ++- { ++- Index row = 0; ++- ++- gemm_unrolled_col(res, lhs_base, rhs_base, depth, strideA, offsetA, row, rows, col, remaining_cols, pAlpha); ++- ++- if (remaining_rows > 0) ++- { ++- gemm_extra_col(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, remaining_rows, remaining_cols, pAlpha); ++- } ++- rhs_base++; +++ gemm_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlpha, pMask); ++ } ++- } +++ +++ gemm_extra_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlpha, pMask); ++ } ++ ++ #define accColsC (accCols / 2) ++@@ -1789,117 +1763,66 @@ EIGEN_STRONG_INLINE void gemm(const DataMapper& res, const Scalar* blockA, const ++ ++ // PEEL_COMPLEX loop factor. ++ #define PEEL_COMPLEX 3 +++#define PEEL_COMPLEX_ROW 3 ++ ++-template ++-EIGEN_ALWAYS_INLINE void MICRO_COMPLEX_EXTRA_COL( ++- const Scalar* &lhs_ptr_real, const Scalar* &lhs_ptr_imag, ++- const Scalar* &rhs_ptr_real, const Scalar* &rhs_ptr_imag, ++- PacketBlock &accReal, PacketBlock &accImag, ++- Index remaining_rows, ++- Index remaining_cols) ++-{ ++- Packet rhsV[1], rhsVi[1]; ++- rhsV[0] = pset1(rhs_ptr_real[0]); ++- if(!RhsIsReal) rhsVi[0] = pset1(rhs_ptr_imag[0]); ++- pgerc<1, Scalar, Packet, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(&accReal, &accImag, lhs_ptr_real, lhs_ptr_imag, rhsV, rhsVi); ++- lhs_ptr_real += remaining_rows; ++- if(!LhsIsReal) lhs_ptr_imag += remaining_rows; ++- else EIGEN_UNUSED_VARIABLE(lhs_ptr_imag); ++- rhs_ptr_real += remaining_cols; ++- if(!RhsIsReal) rhs_ptr_imag += remaining_cols; ++- else EIGEN_UNUSED_VARIABLE(rhs_ptr_imag); ++-} +++#define MICRO_COMPLEX_UNROLL_PEEL(func) \ +++ func(0) func(1) func(2) func(3) ++ ++-template ++-EIGEN_STRONG_INLINE void gemm_complex_extra_col( ++- const DataMapper& res, ++- const Scalar* lhs_base, ++- const Scalar* rhs_base, ++- Index depth, ++- Index strideA, ++- Index offsetA, ++- Index strideB, ++- Index row, ++- Index col, ++- Index remaining_rows, ++- Index remaining_cols, ++- const Packet& pAlphaReal, ++- const Packet& pAlphaImag) ++-{ ++- const Scalar* rhs_ptr_real = rhs_base; ++- const Scalar* rhs_ptr_imag; ++- if(!RhsIsReal) rhs_ptr_imag = rhs_base + remaining_cols*strideB; ++- else EIGEN_UNUSED_VARIABLE(rhs_ptr_imag); ++- const Scalar* lhs_ptr_real = lhs_base + advanceRows*row*strideA + remaining_rows*offsetA; ++- const Scalar* lhs_ptr_imag; ++- if(!LhsIsReal) lhs_ptr_imag = lhs_ptr_real + remaining_rows*strideA; ++- else EIGEN_UNUSED_VARIABLE(lhs_ptr_imag); ++- PacketBlock accReal, accImag; ++- PacketBlock taccReal, taccImag; ++- PacketBlock acc0, acc1; ++- ++- bsetzero(accReal); ++- bsetzero(accImag); ++- ++- Index remaining_depth = (depth & -accRows); ++- Index k = 0; ++- for(; k + PEEL_COMPLEX <= remaining_depth; k+= PEEL_COMPLEX) ++- { ++- EIGEN_POWER_PREFETCH(rhs_ptr_real); ++- if(!RhsIsReal) { ++- EIGEN_POWER_PREFETCH(rhs_ptr_imag); ++- } ++- EIGEN_POWER_PREFETCH(lhs_ptr_real); ++- if(!LhsIsReal) { ++- EIGEN_POWER_PREFETCH(lhs_ptr_imag); ++- } ++- for (int l = 0; l < PEEL_COMPLEX; l++) { ++- MICRO_COMPLEX_EXTRA_COL(lhs_ptr_real, lhs_ptr_imag, rhs_ptr_real, rhs_ptr_imag, accReal, accImag, remaining_rows, remaining_cols); ++- } ++- } ++- for(; k < remaining_depth; k++) ++- { ++- MICRO_COMPLEX_EXTRA_COL(lhs_ptr_real, lhs_ptr_imag, rhs_ptr_real, rhs_ptr_imag, accReal, accImag, remaining_rows, remaining_cols); +++#define MICRO_COMPLEX_ZERO_PEEL(peel) \ +++ if ((PEEL_COMPLEX_ROW > peel) && (peel != 0)) { \ +++ bsetzero(accReal##peel); \ +++ bsetzero(accImag##peel); \ +++ } else { \ +++ EIGEN_UNUSED_VARIABLE(accReal##peel); \ +++ EIGEN_UNUSED_VARIABLE(accImag##peel); \ ++ } ++ ++- for(; k < depth; k++) ++- { ++- Packet rhsV[1], rhsVi[1]; ++- rhsV[0] = pset1(rhs_ptr_real[0]); ++- if(!RhsIsReal) rhsVi[0] = pset1(rhs_ptr_imag[0]); ++- pgerc<1, Scalar, Packet, Index, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(&accReal, &accImag, lhs_ptr_real, lhs_ptr_imag, rhsV, rhsVi, remaining_rows); ++- lhs_ptr_real += remaining_rows; ++- if(!LhsIsReal) lhs_ptr_imag += remaining_rows; ++- rhs_ptr_real += remaining_cols; ++- if(!RhsIsReal) rhs_ptr_imag += remaining_cols; +++#define MICRO_COMPLEX_ZERO_PEEL_ROW \ +++ MICRO_COMPLEX_UNROLL_PEEL(MICRO_COMPLEX_ZERO_PEEL); +++ +++#define MICRO_COMPLEX_WORK_PEEL(peel) \ +++ if (PEEL_COMPLEX_ROW > peel) { \ +++ pbroadcastN_old(rhs_ptr_real + (accRows * peel), rhsV##peel[0], rhsV##peel[1], rhsV##peel[2], rhsV##peel[3]); \ +++ if(!RhsIsReal) pbroadcastN_old(rhs_ptr_imag + (accRows * peel), rhsVi##peel[0], rhsVi##peel[1], rhsVi##peel[2], rhsVi##peel[3]); \ +++ pgerc(&accReal##peel, &accImag##peel, lhs_ptr_real + (remaining_rows * peel), lhs_ptr_imag + (remaining_rows * peel), rhsV##peel, rhsVi##peel); \ +++ } else { \ +++ EIGEN_UNUSED_VARIABLE(rhsV##peel); \ +++ EIGEN_UNUSED_VARIABLE(rhsVi##peel); \ ++ } ++ ++- bscalec(accReal, accImag, pAlphaReal, pAlphaImag, taccReal, taccImag); ++- bcouple_common(taccReal, taccImag, acc0, acc1); +++#define MICRO_COMPLEX_WORK_PEEL_ROW \ +++ Packet rhsV0[4], rhsV1[4], rhsV2[4], rhsV3[4]; \ +++ Packet rhsVi0[4], rhsVi1[4], rhsVi2[4], rhsVi3[4]; \ +++ MICRO_COMPLEX_UNROLL_PEEL(MICRO_COMPLEX_WORK_PEEL); \ +++ lhs_ptr_real += (remaining_rows * PEEL_COMPLEX_ROW); \ +++ if(!LhsIsReal) lhs_ptr_imag += (remaining_rows * PEEL_COMPLEX_ROW); \ +++ else EIGEN_UNUSED_VARIABLE(lhs_ptr_imag); \ +++ rhs_ptr_real += (accRows * PEEL_COMPLEX_ROW); \ +++ if(!RhsIsReal) rhs_ptr_imag += (accRows * PEEL_COMPLEX_ROW); \ +++ else EIGEN_UNUSED_VARIABLE(rhs_ptr_imag); ++ ++- if ((sizeof(Scalar) == sizeof(float)) && (remaining_rows == 1)) ++- { ++- res(row + 0, col + 0) += pfirst(acc0.packet[0]); ++- } else { ++- acc0.packet[0] += res.template loadPacket(row + 0, col + 0); ++- res.template storePacketBlock(row + 0, col + 0, acc0); ++- if(remaining_rows > accColsC) { ++- res(row + accColsC, col + 0) += pfirst(acc1.packet[0]); ++- } +++#define MICRO_COMPLEX_ADD_PEEL(peel, sum) \ +++ if (PEEL_COMPLEX_ROW > peel) { \ +++ for (Index i = 0; i < accRows; i++) { \ +++ accReal##sum.packet[i] += accReal##peel.packet[i]; \ +++ accImag##sum.packet[i] += accImag##peel.packet[i]; \ +++ } \ ++ } ++-} ++ ++-template +++#define MICRO_COMPLEX_ADD_PEEL_ROW \ +++ MICRO_COMPLEX_ADD_PEEL(2, 0) MICRO_COMPLEX_ADD_PEEL(3, 1) \ +++ MICRO_COMPLEX_ADD_PEEL(1, 0) +++ +++template ++ EIGEN_ALWAYS_INLINE void MICRO_COMPLEX_EXTRA_ROW( ++ const Scalar* &lhs_ptr_real, const Scalar* &lhs_ptr_imag, ++ const Scalar* &rhs_ptr_real, const Scalar* &rhs_ptr_imag, ++- PacketBlock &accReal, PacketBlock &accImag, ++- Index remaining_rows) +++ PacketBlock &accReal, PacketBlock &accImag) ++ { ++ Packet rhsV[4], rhsVi[4]; ++- pbroadcast4_old(rhs_ptr_real, rhsV[0], rhsV[1], rhsV[2], rhsV[3]); ++- if(!RhsIsReal) pbroadcast4_old(rhs_ptr_imag, rhsVi[0], rhsVi[1], rhsVi[2], rhsVi[3]); ++- pgerc<4, Scalar, Packet, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(&accReal, &accImag, lhs_ptr_real, lhs_ptr_imag, rhsV, rhsVi); +++ pbroadcastN_old(rhs_ptr_real, rhsV[0], rhsV[1], rhsV[2], rhsV[3]); +++ if(!RhsIsReal) pbroadcastN_old(rhs_ptr_imag, rhsVi[0], rhsVi[1], rhsVi[2], rhsVi[3]); +++ pgerc(&accReal, &accImag, lhs_ptr_real, lhs_ptr_imag, rhsV, rhsVi); ++ lhs_ptr_real += remaining_rows; ++ if(!LhsIsReal) lhs_ptr_imag += remaining_rows; ++ else EIGEN_UNUSED_VARIABLE(lhs_ptr_imag); ++@@ -1908,8 +1831,8 @@ EIGEN_ALWAYS_INLINE void MICRO_COMPLEX_EXTRA_ROW( ++ else EIGEN_UNUSED_VARIABLE(rhs_ptr_imag); ++ } ++ ++-template ++-EIGEN_STRONG_INLINE void gemm_complex_extra_row( +++template +++EIGEN_ALWAYS_INLINE void gemm_unrolled_complex_row_iteration( ++ const DataMapper& res, ++ const Scalar* lhs_base, ++ const Scalar* rhs_base, ++@@ -1921,106 +1844,141 @@ EIGEN_STRONG_INLINE void gemm_complex_extra_row( ++ Index col, ++ Index rows, ++ Index cols, ++- Index remaining_rows, ++ const Packet& pAlphaReal, ++ const Packet& pAlphaImag, ++ const Packet& pMask) ++ { ++ const Scalar* rhs_ptr_real = rhs_base; ++- const Scalar* rhs_ptr_imag; +++ const Scalar* rhs_ptr_imag = NULL; ++ if(!RhsIsReal) rhs_ptr_imag = rhs_base + accRows*strideB; ++ else EIGEN_UNUSED_VARIABLE(rhs_ptr_imag); ++ const Scalar* lhs_ptr_real = lhs_base + advanceRows*row*strideA + remaining_rows*offsetA; ++- const Scalar* lhs_ptr_imag; +++ const Scalar* lhs_ptr_imag = NULL; ++ if(!LhsIsReal) lhs_ptr_imag = lhs_ptr_real + remaining_rows*strideA; ++ else EIGEN_UNUSED_VARIABLE(lhs_ptr_imag); ++- PacketBlock accReal, accImag; ++- PacketBlock taccReal, taccImag; ++- PacketBlock acc0, acc1; ++- PacketBlock tRes; +++ PacketBlock accReal0, accImag0, accReal1, accImag1, accReal2, accImag2, accReal3, accImag3; +++ PacketBlock taccReal, taccImag; +++ PacketBlock acc0, acc1; +++ PacketBlock tRes; ++ ++- bsetzero(accReal); ++- bsetzero(accImag); +++ bsetzero(accReal0); +++ bsetzero(accImag0); ++ ++- Index remaining_depth = (col + accRows < cols) ? depth : (depth & -accRows); +++ Index remaining_depth = (col + quad_traits::rows < cols) ? depth : (depth & -quad_traits::rows); ++ Index k = 0; ++- for(; k + PEEL_COMPLEX <= remaining_depth; k+= PEEL_COMPLEX) ++- { ++- EIGEN_POWER_PREFETCH(rhs_ptr_real); ++- if(!RhsIsReal) { ++- EIGEN_POWER_PREFETCH(rhs_ptr_imag); ++- } ++- EIGEN_POWER_PREFETCH(lhs_ptr_real); ++- if(!LhsIsReal) { ++- EIGEN_POWER_PREFETCH(lhs_ptr_imag); ++- } ++- for (int l = 0; l < PEEL_COMPLEX; l++) { ++- MICRO_COMPLEX_EXTRA_ROW(lhs_ptr_real, lhs_ptr_imag, rhs_ptr_real, rhs_ptr_imag, accReal, accImag, remaining_rows); ++- } +++ if (remaining_depth >= PEEL_COMPLEX_ROW) { +++ MICRO_COMPLEX_ZERO_PEEL_ROW +++ do +++ { +++ EIGEN_POWER_PREFETCH(rhs_ptr_real); +++ if(!RhsIsReal) { +++ EIGEN_POWER_PREFETCH(rhs_ptr_imag); +++ } +++ EIGEN_POWER_PREFETCH(lhs_ptr_real); +++ if(!LhsIsReal) { +++ EIGEN_POWER_PREFETCH(lhs_ptr_imag); +++ } +++ MICRO_COMPLEX_WORK_PEEL_ROW +++ } while ((k += PEEL_COMPLEX_ROW) + PEEL_COMPLEX_ROW <= remaining_depth); +++ MICRO_COMPLEX_ADD_PEEL_ROW ++ } ++ for(; k < remaining_depth; k++) ++ { ++- MICRO_COMPLEX_EXTRA_ROW(lhs_ptr_real, lhs_ptr_imag, rhs_ptr_real, rhs_ptr_imag, accReal, accImag, remaining_rows); +++ MICRO_COMPLEX_EXTRA_ROW(lhs_ptr_real, lhs_ptr_imag, rhs_ptr_real, rhs_ptr_imag, accReal0, accImag0); ++ } ++ ++ if ((remaining_depth == depth) && (rows >= accCols)) ++ { ++- bload(tRes, res, row, col); ++- bscalec(accReal, accImag, pAlphaReal, pAlphaImag, taccReal, taccImag, pMask); ++- bcouple(taccReal, taccImag, tRes, acc0, acc1); ++- res.template storePacketBlock(row + 0, col, acc0); ++- res.template storePacketBlock(row + accColsC, col, acc1); +++ bload(tRes, res, row, 0); +++ bscalec(accReal0, accImag0, pAlphaReal, pAlphaImag, taccReal, taccImag, pMask); +++ bcouple(taccReal, taccImag, tRes, acc0, acc1); +++ res.template storePacketBlock(row + 0, 0, acc0); +++ res.template storePacketBlock(row + accColsC, 0, acc1); ++ } else { ++ for(; k < depth; k++) ++ { ++ Packet rhsV[4], rhsVi[4]; ++- pbroadcast4_old(rhs_ptr_real, rhsV[0], rhsV[1], rhsV[2], rhsV[3]); ++- if(!RhsIsReal) pbroadcast4_old(rhs_ptr_imag, rhsVi[0], rhsVi[1], rhsVi[2], rhsVi[3]); ++- pgerc<4, Scalar, Packet, Index, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(&accReal, &accImag, lhs_ptr_real, lhs_ptr_imag, rhsV, rhsVi, remaining_rows); +++ pbroadcastN_old(rhs_ptr_real, rhsV[0], rhsV[1], rhsV[2], rhsV[3]); +++ if(!RhsIsReal) pbroadcastN_old(rhs_ptr_imag, rhsVi[0], rhsVi[1], rhsVi[2], rhsVi[3]); +++ pgerc(&accReal0, &accImag0, lhs_ptr_real, lhs_ptr_imag, rhsV, rhsVi); ++ lhs_ptr_real += remaining_rows; ++ if(!LhsIsReal) lhs_ptr_imag += remaining_rows; ++ rhs_ptr_real += accRows; ++ if(!RhsIsReal) rhs_ptr_imag += accRows; ++ } ++ ++- bscalec(accReal, accImag, pAlphaReal, pAlphaImag, taccReal, taccImag); ++- bcouple_common(taccReal, taccImag, acc0, acc1); +++ bscalec(accReal0, accImag0, pAlphaReal, pAlphaImag, taccReal, taccImag); +++ bcouple_common(taccReal, taccImag, acc0, acc1); ++ ++ if ((sizeof(Scalar) == sizeof(float)) && (remaining_rows == 1)) ++ { ++- for(Index j = 0; j < 4; j++) { ++- res(row + 0, col + j) += pfirst(acc0.packet[j]); +++ for(Index j = 0; j < accRows; j++) { +++ res(row + 0, j) += pfirst(acc0.packet[j]); ++ } ++ } else { ++- for(Index j = 0; j < 4; j++) { +++ for(Index j = 0; j < accRows; j++) { ++ PacketBlock acc2; ++- acc2.packet[0] = res.template loadPacket(row + 0, col + j) + acc0.packet[j]; ++- res.template storePacketBlock(row + 0, col + j, acc2); +++ acc2.packet[0] = res.template loadPacket(row + 0, j) + acc0.packet[j]; +++ res.template storePacketBlock(row + 0, j, acc2); ++ if(remaining_rows > accColsC) { ++- res(row + accColsC, col + j) += pfirst(acc1.packet[j]); +++ res(row + accColsC, j) += pfirst(acc1.packet[j]); ++ } ++ } ++ } ++ } ++ } ++ +++template +++EIGEN_ALWAYS_INLINE void gemm_complex_extra_row( +++ const DataMapper& res, +++ const Scalar* lhs_base, +++ const Scalar* rhs_base, +++ Index depth, +++ Index strideA, +++ Index offsetA, +++ Index strideB, +++ Index row, +++ Index col, +++ Index rows, +++ Index cols, +++ Index remaining_rows, +++ const Packet& pAlphaReal, +++ const Packet& pAlphaImag, +++ const Packet& pMask) +++{ +++ switch(remaining_rows) { +++ case 1: +++ gemm_unrolled_complex_row_iteration(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, rows, cols, pAlphaReal, pAlphaImag, pMask); +++ break; +++ case 2: +++ if (sizeof(Scalar) == sizeof(float)) { +++ gemm_unrolled_complex_row_iteration(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, rows, cols, pAlphaReal, pAlphaImag, pMask); +++ } +++ break; +++ default: +++ if (sizeof(Scalar) == sizeof(float)) { +++ gemm_unrolled_complex_row_iteration(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, rows, cols, pAlphaReal, pAlphaImag, pMask); +++ } +++ break; +++ } +++} +++ ++ #define MICRO_COMPLEX_UNROLL(func) \ ++- func(0) func(1) func(2) func(3) func(4) +++ func(0) func(1) func(2) func(3) ++ ++ #define MICRO_COMPLEX_UNROLL_WORK(func, func2, peel) \ ++ MICRO_COMPLEX_UNROLL(func2); \ ++- func(0,peel) func(1,peel) func(2,peel) func(3,peel) func(4,peel) +++ func(0,peel) func(1,peel) func(2,peel) func(3,peel) ++ ++ #define MICRO_COMPLEX_LOAD_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++ lhsV##iter = ploadLhs(lhs_ptr_real##iter); \ ++- lhs_ptr_real##iter += accCols; \ ++ if(!LhsIsReal) { \ ++- lhsVi##iter = ploadLhs(lhs_ptr_imag##iter); \ ++- lhs_ptr_imag##iter += accCols; \ +++ lhsVi##iter = ploadLhs(lhs_ptr_real##iter + imag_delta); \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(lhsVi##iter); \ ++ } \ +++ lhs_ptr_real##iter += accCols; \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(lhsV##iter); \ ++ EIGEN_UNUSED_VARIABLE(lhsVi##iter); \ ++@@ -2028,37 +1986,16 @@ EIGEN_STRONG_INLINE void gemm_complex_extra_row( ++ ++ #define MICRO_COMPLEX_WORK_ONE4(iter, peel) \ ++ if (unroll_factor > iter) { \ ++- pgerc_common<4, Packet, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(&accReal##iter, &accImag##iter, lhsV##iter, lhsVi##iter, rhsV##peel, rhsVi##peel); \ ++- } ++- ++-#define MICRO_COMPLEX_WORK_ONE1(iter, peel) \ ++- if (unroll_factor > iter) { \ ++- pgerc_common<1, Packet, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(&accReal##iter, &accImag##iter, lhsV##iter, lhsVi##iter, rhsV##peel, rhsVi##peel); \ +++ pgerc_common(&accReal##iter, &accImag##iter, lhsV##iter, lhsVi##iter, rhsV##peel, rhsVi##peel); \ ++ } ++ ++ #define MICRO_COMPLEX_TYPE_PEEL4(func, func2, peel) \ ++ if (PEEL_COMPLEX > peel) { \ ++- Packet lhsV0, lhsV1, lhsV2, lhsV3, lhsV4; \ ++- Packet lhsVi0, lhsVi1, lhsVi2, lhsVi3, lhsVi4; \ ++- pbroadcast4_old(rhs_ptr_real + (accRows * peel), rhsV##peel[0], rhsV##peel[1], rhsV##peel[2], rhsV##peel[3]); \ +++ Packet lhsV0, lhsV1, lhsV2, lhsV3; \ +++ Packet lhsVi0, lhsVi1, lhsVi2, lhsVi3; \ +++ pbroadcastN_old(rhs_ptr_real + (accRows * peel), rhsV##peel[0], rhsV##peel[1], rhsV##peel[2], rhsV##peel[3]); \ ++ if(!RhsIsReal) { \ ++- pbroadcast4_old(rhs_ptr_imag + (accRows * peel), rhsVi##peel[0], rhsVi##peel[1], rhsVi##peel[2], rhsVi##peel[3]); \ ++- } else { \ ++- EIGEN_UNUSED_VARIABLE(rhsVi##peel); \ ++- } \ ++- MICRO_COMPLEX_UNROLL_WORK(func, func2, peel) \ ++- } else { \ ++- EIGEN_UNUSED_VARIABLE(rhsV##peel); \ ++- EIGEN_UNUSED_VARIABLE(rhsVi##peel); \ ++- } ++- ++-#define MICRO_COMPLEX_TYPE_PEEL1(func, func2, peel) \ ++- if (PEEL_COMPLEX > peel) { \ ++- Packet lhsV0, lhsV1, lhsV2, lhsV3, lhsV4; \ ++- Packet lhsVi0, lhsVi1, lhsVi2, lhsVi3, lhsVi4; \ ++- rhsV##peel[0] = pset1(rhs_ptr_real[remaining_cols * peel]); \ ++- if(!RhsIsReal) { \ ++- rhsVi##peel[0] = pset1(rhs_ptr_imag[remaining_cols * peel]); \ +++ pbroadcastN_old(rhs_ptr_imag + (accRows * peel), rhsVi##peel[0], rhsVi##peel[1], rhsVi##peel[2], rhsVi##peel[3]); \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(rhsVi##peel); \ ++ } \ ++@@ -2069,13 +2006,10 @@ EIGEN_STRONG_INLINE void gemm_complex_extra_row( ++ } ++ ++ #define MICRO_COMPLEX_UNROLL_TYPE_PEEL(M, func, func1, func2) \ ++- Packet rhsV0[M], rhsV1[M], rhsV2[M], rhsV3[M], rhsV4[M], rhsV5[M], rhsV6[M], rhsV7[M], rhsV8[M], rhsV9[M]; \ ++- Packet rhsVi0[M], rhsVi1[M], rhsVi2[M], rhsVi3[M], rhsVi4[M], rhsVi5[M], rhsVi6[M], rhsVi7[M], rhsVi8[M], rhsVi9[M]; \ +++ Packet rhsV0[M], rhsV1[M], rhsV2[M], rhsV3[M]; \ +++ Packet rhsVi0[M], rhsVi1[M], rhsVi2[M], rhsVi3[M]; \ ++ func(func1,func2,0); func(func1,func2,1); \ ++- func(func1,func2,2); func(func1,func2,3); \ ++- func(func1,func2,4); func(func1,func2,5); \ ++- func(func1,func2,6); func(func1,func2,7); \ ++- func(func1,func2,8); func(func1,func2,9); +++ func(func1,func2,2); func(func1,func2,3); ++ ++ #define MICRO_COMPLEX_UNROLL_TYPE_ONE(M, func, func1, func2) \ ++ Packet rhsV0[M], rhsVi0[M];\ ++@@ -2091,20 +2025,10 @@ EIGEN_STRONG_INLINE void gemm_complex_extra_row( ++ rhs_ptr_real += accRows; \ ++ if(!RhsIsReal) rhs_ptr_imag += accRows; ++ ++-#define MICRO_COMPLEX_ONE_PEEL1 \ ++- MICRO_COMPLEX_UNROLL_TYPE_PEEL(1, MICRO_COMPLEX_TYPE_PEEL1, MICRO_COMPLEX_WORK_ONE1, MICRO_COMPLEX_LOAD_ONE); \ ++- rhs_ptr_real += (remaining_cols * PEEL_COMPLEX); \ ++- if(!RhsIsReal) rhs_ptr_imag += (remaining_cols * PEEL_COMPLEX); ++- ++-#define MICRO_COMPLEX_ONE1 \ ++- MICRO_COMPLEX_UNROLL_TYPE_ONE(1, MICRO_COMPLEX_TYPE_PEEL1, MICRO_COMPLEX_WORK_ONE1, MICRO_COMPLEX_LOAD_ONE); \ ++- rhs_ptr_real += remaining_cols; \ ++- if(!RhsIsReal) rhs_ptr_imag += remaining_cols; ++- ++ #define MICRO_COMPLEX_DST_PTR_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++- bsetzero(accReal##iter); \ ++- bsetzero(accImag##iter); \ +++ bsetzero(accReal##iter); \ +++ bsetzero(accImag##iter); \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(accReal##iter); \ ++ EIGEN_UNUSED_VARIABLE(accImag##iter); \ ++@@ -2114,15 +2038,9 @@ EIGEN_STRONG_INLINE void gemm_complex_extra_row( ++ ++ #define MICRO_COMPLEX_SRC_PTR_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++- lhs_ptr_real##iter = lhs_base + ( ((advanceRows*row)/accCols) + iter*advanceRows )*strideA*accCols + accCols*offsetA; \ ++- if(!LhsIsReal) { \ ++- lhs_ptr_imag##iter = lhs_ptr_real##iter + accCols*strideA; \ ++- } else { \ ++- EIGEN_UNUSED_VARIABLE(lhs_ptr_imag##iter); \ ++- } \ +++ lhs_ptr_real##iter = lhs_base + ( ((advanceRows*row)/accCols) + iter*advanceRows )*strideA*accCols; \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(lhs_ptr_real##iter); \ ++- EIGEN_UNUSED_VARIABLE(lhs_ptr_imag##iter); \ ++ } ++ ++ #define MICRO_COMPLEX_SRC_PTR MICRO_COMPLEX_UNROLL(MICRO_COMPLEX_SRC_PTR_ONE) ++@@ -2130,35 +2048,21 @@ EIGEN_STRONG_INLINE void gemm_complex_extra_row( ++ #define MICRO_COMPLEX_PREFETCH_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++ EIGEN_POWER_PREFETCH(lhs_ptr_real##iter); \ ++- if(!LhsIsReal) { \ ++- EIGEN_POWER_PREFETCH(lhs_ptr_imag##iter); \ ++- } \ ++ } ++ ++ #define MICRO_COMPLEX_PREFETCH MICRO_COMPLEX_UNROLL(MICRO_COMPLEX_PREFETCH_ONE) ++ ++ #define MICRO_COMPLEX_STORE_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++- bload(tRes, res, row + iter*accCols, col); \ ++- bscalec(accReal##iter, accImag##iter, pAlphaReal, pAlphaImag, taccReal, taccImag); \ ++- bcouple(taccReal, taccImag, tRes, acc0, acc1); \ ++- res.template storePacketBlock(row + iter*accCols + 0, col, acc0); \ ++- res.template storePacketBlock(row + iter*accCols + accColsC, col, acc1); \ +++ bload(tRes, res, row + iter*accCols, 0); \ +++ bscalec(accReal##iter, accImag##iter, pAlphaReal, pAlphaImag, taccReal, taccImag); \ +++ bcouple(taccReal, taccImag, tRes, acc0, acc1); \ +++ res.template storePacketBlock(row + iter*accCols + 0, 0, acc0); \ +++ res.template storePacketBlock(row + iter*accCols + accColsC, 0, acc1); \ ++ } ++ ++ #define MICRO_COMPLEX_STORE MICRO_COMPLEX_UNROLL(MICRO_COMPLEX_STORE_ONE) ++ ++-#define MICRO_COMPLEX_COL_STORE_ONE(iter) \ ++- if (unroll_factor > iter) { \ ++- bload(tRes, res, row + iter*accCols, col); \ ++- bscalec(accReal##iter, accImag##iter, pAlphaReal, pAlphaImag, taccReal, taccImag); \ ++- bcouple(taccReal, taccImag, tRes, acc0, acc1); \ ++- res.template storePacketBlock(row + iter*accCols + 0, col, acc0); \ ++- res.template storePacketBlock(row + iter*accCols + accColsC, col, acc1); \ ++- } ++- ++-#define MICRO_COMPLEX_COL_STORE MICRO_COMPLEX_UNROLL(MICRO_COMPLEX_COL_STORE_ONE) ++- ++ template ++ EIGEN_STRONG_INLINE void gemm_complex_unrolled_iteration( ++ const DataMapper& res, ++@@ -2166,29 +2070,26 @@ EIGEN_STRONG_INLINE void gemm_complex_unrolled_iteration( ++ const Scalar* rhs_base, ++ Index depth, ++ Index strideA, ++- Index offsetA, ++ Index strideB, ++ Index& row, ++- Index col, ++ const Packet& pAlphaReal, ++ const Packet& pAlphaImag) ++ { ++ const Scalar* rhs_ptr_real = rhs_base; ++- const Scalar* rhs_ptr_imag; +++ const Scalar* rhs_ptr_imag = NULL; +++ const Index imag_delta = accCols*strideA; ++ if(!RhsIsReal) { ++ rhs_ptr_imag = rhs_base + accRows*strideB; ++ } else { ++ EIGEN_UNUSED_VARIABLE(rhs_ptr_imag); ++ } ++- const Scalar* lhs_ptr_real0 = NULL, * lhs_ptr_imag0 = NULL, * lhs_ptr_real1 = NULL, * lhs_ptr_imag1 = NULL; ++- const Scalar* lhs_ptr_real2 = NULL, * lhs_ptr_imag2 = NULL, * lhs_ptr_real3 = NULL, * lhs_ptr_imag3 = NULL; ++- const Scalar* lhs_ptr_real4 = NULL, * lhs_ptr_imag4 = NULL; ++- PacketBlock accReal0, accImag0, accReal1, accImag1; ++- PacketBlock accReal2, accImag2, accReal3, accImag3; ++- PacketBlock accReal4, accImag4; ++- PacketBlock taccReal, taccImag; ++- PacketBlock acc0, acc1; ++- PacketBlock tRes; +++ const Scalar* lhs_ptr_real0 = NULL, * lhs_ptr_real1 = NULL; +++ const Scalar* lhs_ptr_real2 = NULL, * lhs_ptr_real3 = NULL; +++ PacketBlock accReal0, accImag0, accReal1, accImag1; +++ PacketBlock accReal2, accImag2, accReal3, accImag3; +++ PacketBlock taccReal, taccImag; +++ PacketBlock acc0, acc1; +++ PacketBlock tRes; ++ ++ MICRO_COMPLEX_SRC_PTR ++ MICRO_COMPLEX_DST_PTR ++@@ -2212,112 +2113,93 @@ EIGEN_STRONG_INLINE void gemm_complex_unrolled_iteration( ++ row += unroll_factor*accCols; ++ } ++ ++-template ++-EIGEN_STRONG_INLINE void gemm_complex_unrolled_col_iteration( +++template +++EIGEN_ALWAYS_INLINE void gemm_complex_cols( ++ const DataMapper& res, ++- const Scalar* lhs_base, ++- const Scalar* rhs_base, +++ const Scalar* blockA, +++ const Scalar* blockB, ++ Index depth, ++ Index strideA, ++ Index offsetA, ++ Index strideB, ++- Index& row, +++ Index offsetB, ++ Index col, ++- Index remaining_cols, +++ Index rows, +++ Index cols, +++ Index remaining_rows, ++ const Packet& pAlphaReal, ++- const Packet& pAlphaImag) +++ const Packet& pAlphaImag, +++ const Packet& pMask) ++ { ++- const Scalar* rhs_ptr_real = rhs_base; ++- const Scalar* rhs_ptr_imag; ++- if(!RhsIsReal) { ++- rhs_ptr_imag = rhs_base + remaining_cols*strideB; ++- } else { ++- EIGEN_UNUSED_VARIABLE(rhs_ptr_imag); ++- } ++- const Scalar* lhs_ptr_real0 = NULL, * lhs_ptr_imag0 = NULL, * lhs_ptr_real1 = NULL, * lhs_ptr_imag1 = NULL; ++- const Scalar* lhs_ptr_real2 = NULL, * lhs_ptr_imag2 = NULL, * lhs_ptr_real3 = NULL, * lhs_ptr_imag3 = NULL; ++- const Scalar* lhs_ptr_real4 = NULL, * lhs_ptr_imag4 = NULL; ++- PacketBlock accReal0, accImag0, accReal1, accImag1; ++- PacketBlock accReal2, accImag2, accReal3, accImag3; ++- PacketBlock accReal4, accImag4; ++- PacketBlock taccReal, taccImag; ++- PacketBlock acc0, acc1; ++- PacketBlock tRes; +++ const DataMapper res3 = res.getSubMapper(0, col); ++ ++- MICRO_COMPLEX_SRC_PTR ++- MICRO_COMPLEX_DST_PTR +++ const Scalar* rhs_base = blockB + advanceCols*col*strideB + accRows*offsetB; +++ const Scalar* lhs_base = blockA + accCols*offsetA; +++ Index row = 0; ++ ++- Index k = 0; ++- for(; k + PEEL_COMPLEX <= depth; k+= PEEL_COMPLEX) ++- { ++- EIGEN_POWER_PREFETCH(rhs_ptr_real); ++- if(!RhsIsReal) { ++- EIGEN_POWER_PREFETCH(rhs_ptr_imag); ++- } ++- MICRO_COMPLEX_PREFETCH ++- MICRO_COMPLEX_ONE_PEEL1 +++#define MAX_COMPLEX_UNROLL 3 +++ while(row + MAX_COMPLEX_UNROLL*accCols <= rows) { +++ gemm_complex_unrolled_iteration(res3, lhs_base, rhs_base, depth, strideA, strideB, row, pAlphaReal, pAlphaImag); ++ } ++- for(; k < depth; k++) ++- { ++- MICRO_COMPLEX_ONE1 +++ switch( (rows-row)/accCols ) { +++#if MAX_COMPLEX_UNROLL > 4 +++ case 4: +++ gemm_complex_unrolled_iteration<4, Scalar, Packet, Packetc, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res3, lhs_base, rhs_base, depth, strideA, strideB, row, pAlphaReal, pAlphaImag); +++ break; +++#endif +++#if MAX_COMPLEX_UNROLL > 3 +++ case 3: +++ gemm_complex_unrolled_iteration<3, Scalar, Packet, Packetc, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res3, lhs_base, rhs_base, depth, strideA, strideB, row, pAlphaReal, pAlphaImag); +++ break; +++#endif +++#if MAX_COMPLEX_UNROLL > 2 +++ case 2: +++ gemm_complex_unrolled_iteration<2, Scalar, Packet, Packetc, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res3, lhs_base, rhs_base, depth, strideA, strideB, row, pAlphaReal, pAlphaImag); +++ break; +++#endif +++#if MAX_COMPLEX_UNROLL > 1 +++ case 1: +++ gemm_complex_unrolled_iteration<1, Scalar, Packet, Packetc, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res3, lhs_base, rhs_base, depth, strideA, strideB, row, pAlphaReal, pAlphaImag); +++ break; +++#endif +++ default: +++ break; ++ } ++- MICRO_COMPLEX_COL_STORE +++#undef MAX_COMPLEX_UNROLL ++ ++- row += unroll_factor*accCols; +++ if(remaining_rows > 0) +++ { +++ gemm_complex_extra_row(res3, blockA, rhs_base, depth, strideA, offsetA, strideB, row, col, rows, cols, remaining_rows, pAlphaReal, pAlphaImag, pMask); +++ } ++ } ++ ++ template ++-EIGEN_STRONG_INLINE void gemm_complex_unrolled_col( +++EIGEN_STRONG_INLINE void gemm_complex_extra_cols( ++ const DataMapper& res, ++- const Scalar* lhs_base, ++- const Scalar* rhs_base, +++ const Scalar* blockA, +++ const Scalar* blockB, ++ Index depth, ++ Index strideA, ++ Index offsetA, ++ Index strideB, ++- Index& row, ++- Index rows, +++ Index offsetB, ++ Index col, ++- Index remaining_cols, +++ Index rows, +++ Index cols, +++ Index remaining_rows, ++ const Packet& pAlphaReal, ++- const Packet& pAlphaImag) +++ const Packet& pAlphaImag, +++ const Packet& pMask) ++ { ++-#define MAX_COMPLEX_UNROLL 3 ++- while(row + MAX_COMPLEX_UNROLL*accCols <= rows) { ++- gemm_complex_unrolled_col_iteration(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, remaining_cols, pAlphaReal, pAlphaImag); ++- } ++- switch( (rows-row)/accCols ) { ++-#if MAX_COMPLEX_UNROLL > 4 ++- case 4: ++- gemm_complex_unrolled_col_iteration<4, Scalar, Packet, Packetc, DataMapper, Index, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, remaining_cols, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++-#if MAX_COMPLEX_UNROLL > 3 ++- case 3: ++- gemm_complex_unrolled_col_iteration<3, Scalar, Packet, Packetc, DataMapper, Index, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, remaining_cols, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++-#if MAX_COMPLEX_UNROLL > 2 ++- case 2: ++- gemm_complex_unrolled_col_iteration<2, Scalar, Packet, Packetc, DataMapper, Index, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, remaining_cols, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++-#if MAX_COMPLEX_UNROLL > 1 ++- case 1: ++- gemm_complex_unrolled_col_iteration<1, Scalar, Packet, Packetc, DataMapper, Index, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, remaining_cols, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++- default: ++- break; +++ for (; col < cols; col++) { +++ gemm_complex_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlphaReal, pAlphaImag, pMask); ++ } ++-#undef MAX_COMPLEX_UNROLL ++ } ++ ++ template ++ EIGEN_STRONG_INLINE void gemm_complex(const DataMapper& res, const LhsScalar* blockAc, const RhsScalar* blockBc, Index rows, Index depth, Index cols, Scalarc alpha, Index strideA, Index strideB, Index offsetA, Index offsetB) ++ { ++ const Index remaining_rows = rows % accCols; ++- const Index remaining_cols = cols % accRows; ++ ++ if( strideA == -1 ) strideA = depth; ++ if( strideB == -1 ) strideB = depth; ++@@ -2332,64 +2214,10 @@ EIGEN_STRONG_INLINE void gemm_complex(const DataMapper& res, const LhsScalar* bl ++ Index col = 0; ++ for(; col + accRows <= cols; col += accRows) ++ { ++- const Scalar* rhs_base = blockB + advanceCols*col*strideB + accRows*offsetB; ++- const Scalar* lhs_base = blockA; ++- Index row = 0; ++- ++-#define MAX_COMPLEX_UNROLL 3 ++- while(row + MAX_COMPLEX_UNROLL*accCols <= rows) { ++- gemm_complex_unrolled_iteration(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, pAlphaReal, pAlphaImag); ++- } ++- switch( (rows-row)/accCols ) { ++-#if MAX_COMPLEX_UNROLL > 4 ++- case 4: ++- gemm_complex_unrolled_iteration<4, Scalar, Packet, Packetc, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++-#if MAX_COMPLEX_UNROLL > 3 ++- case 3: ++- gemm_complex_unrolled_iteration<3, Scalar, Packet, Packetc, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++-#if MAX_COMPLEX_UNROLL > 2 ++- case 2: ++- gemm_complex_unrolled_iteration<2, Scalar, Packet, Packetc, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++-#if MAX_COMPLEX_UNROLL > 1 ++- case 1: ++- gemm_complex_unrolled_iteration<1, Scalar, Packet, Packetc, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++- default: ++- break; ++- } ++-#undef MAX_COMPLEX_UNROLL ++- ++- if(remaining_rows > 0) ++- { ++- gemm_complex_extra_row(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, rows, cols, remaining_rows, pAlphaReal, pAlphaImag, pMask); ++- } +++ gemm_complex_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlphaReal, pAlphaImag, pMask); ++ } ++ ++- if(remaining_cols > 0) ++- { ++- const Scalar* rhs_base = blockB + advanceCols*col*strideB + remaining_cols*offsetB; ++- const Scalar* lhs_base = blockA; ++- ++- for(; col < cols; col++) ++- { ++- Index row = 0; ++- ++- gemm_complex_unrolled_col(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, rows, col, remaining_cols, pAlphaReal, pAlphaImag); ++- ++- if (remaining_rows > 0) ++- { ++- gemm_complex_extra_col(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, remaining_rows, remaining_cols, pAlphaReal, pAlphaImag); ++- } ++- rhs_base++; ++- } ++- } +++ gemm_complex_extra_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlphaReal, pAlphaImag, pMask); ++ } ++ ++ #undef accColsC ++diff --git a/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h b/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h ++index 33d543494..bf01dba1c 100644 ++--- a/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h +++++ b/Eigen/src/Core/arch/AltiVec/MatrixProductCommon.h ++@@ -9,22 +9,8 @@ namespace Eigen { ++ ++ namespace internal { ++ ++-template ++-EIGEN_STRONG_INLINE void gemm_extra_col( ++- const DataMapper& res, ++- const Scalar* lhs_base, ++- const Scalar* rhs_base, ++- Index depth, ++- Index strideA, ++- Index offsetA, ++- Index row, ++- Index col, ++- Index remaining_rows, ++- Index remaining_cols, ++- const Packet& pAlpha); ++- ++ template ++-EIGEN_STRONG_INLINE void gemm_extra_row( +++EIGEN_ALWAYS_INLINE void gemm_extra_row( ++ const DataMapper& res, ++ const Scalar* lhs_base, ++ const Scalar* rhs_base, ++@@ -39,41 +25,28 @@ EIGEN_STRONG_INLINE void gemm_extra_row( ++ const Packet& pAlpha, ++ const Packet& pMask); ++ ++-template ++-EIGEN_STRONG_INLINE void gemm_unrolled_col( +++template +++EIGEN_STRONG_INLINE void gemm_extra_cols( ++ const DataMapper& res, ++- const Scalar* lhs_base, ++- const Scalar* rhs_base, +++ const Scalar* blockA, +++ const Scalar* blockB, ++ Index depth, ++ Index strideA, ++ Index offsetA, ++- Index& row, ++- Index rows, +++ Index strideB, +++ Index offsetB, ++ Index col, ++- Index remaining_cols, ++- const Packet& pAlpha); +++ Index rows, +++ Index cols, +++ Index remaining_rows, +++ const Packet& pAlpha, +++ const Packet& pMask); ++ ++ template ++ EIGEN_ALWAYS_INLINE Packet bmask(const int remaining_rows); ++ ++ template ++-EIGEN_STRONG_INLINE void gemm_complex_extra_col( ++- const DataMapper& res, ++- const Scalar* lhs_base, ++- const Scalar* rhs_base, ++- Index depth, ++- Index strideA, ++- Index offsetA, ++- Index strideB, ++- Index row, ++- Index col, ++- Index remaining_rows, ++- Index remaining_cols, ++- const Packet& pAlphaReal, ++- const Packet& pAlphaImag); ++- ++-template ++-EIGEN_STRONG_INLINE void gemm_complex_extra_row( +++EIGEN_ALWAYS_INLINE void gemm_complex_extra_row( ++ const DataMapper& res, ++ const Scalar* lhs_base, ++ const Scalar* rhs_base, ++@@ -91,123 +64,88 @@ EIGEN_STRONG_INLINE void gemm_complex_extra_row( ++ const Packet& pMask); ++ ++ template ++-EIGEN_STRONG_INLINE void gemm_complex_unrolled_col( +++EIGEN_STRONG_INLINE void gemm_complex_extra_cols( ++ const DataMapper& res, ++- const Scalar* lhs_base, ++- const Scalar* rhs_base, +++ const Scalar* blockA, +++ const Scalar* blockB, ++ Index depth, ++ Index strideA, ++ Index offsetA, ++ Index strideB, ++- Index& row, ++- Index rows, +++ Index offsetB, ++ Index col, ++- Index remaining_cols, +++ Index rows, +++ Index cols, +++ Index remaining_rows, ++ const Packet& pAlphaReal, ++- const Packet& pAlphaImag); +++ const Packet& pAlphaImag, +++ const Packet& pMask); ++ ++ template ++ EIGEN_ALWAYS_INLINE Packet ploadLhs(const Scalar* lhs); ++ ++-template ++-EIGEN_ALWAYS_INLINE void bload(PacketBlock& acc, const DataMapper& res, Index row, Index col); +++template +++EIGEN_ALWAYS_INLINE void bload(PacketBlock& acc, const DataMapper& res, Index row, Index col); ++ ++-template ++-EIGEN_ALWAYS_INLINE void bload(PacketBlock& acc, const DataMapper& res, Index row, Index col); ++- ++-template ++-EIGEN_ALWAYS_INLINE void bscale(PacketBlock& acc, PacketBlock& accZ, const Packet& pAlpha); +++template +++EIGEN_ALWAYS_INLINE void bscale(PacketBlock& acc, PacketBlock& accZ, const Packet& pAlpha); ++ ++ template ++ EIGEN_ALWAYS_INLINE void bscalec(PacketBlock& aReal, PacketBlock& aImag, const Packet& bReal, const Packet& bImag, PacketBlock& cReal, PacketBlock& cImag); ++ ++-const static Packet16uc p16uc_SETCOMPLEX32_FIRST = { 0, 1, 2, 3, ++- 16, 17, 18, 19, ++- 4, 5, 6, 7, ++- 20, 21, 22, 23}; ++- ++-const static Packet16uc p16uc_SETCOMPLEX32_SECOND = { 8, 9, 10, 11, ++- 24, 25, 26, 27, ++- 12, 13, 14, 15, ++- 28, 29, 30, 31}; ++-//[a,b],[ai,bi] = [a,ai] - This is equivalent to p16uc_GETREAL64 ++-const static Packet16uc p16uc_SETCOMPLEX64_FIRST = { 0, 1, 2, 3, 4, 5, 6, 7, ++- 16, 17, 18, 19, 20, 21, 22, 23}; ++- ++-//[a,b],[ai,bi] = [b,bi] - This is equivalent to p16uc_GETIMAG64 ++-const static Packet16uc p16uc_SETCOMPLEX64_SECOND = { 8, 9, 10, 11, 12, 13, 14, 15, ++- 24, 25, 26, 27, 28, 29, 30, 31}; ++- ++- ++ // Grab two decouples real/imaginary PacketBlocks and return two coupled (real/imaginary pairs) PacketBlocks. ++-template ++-EIGEN_ALWAYS_INLINE void bcouple_common(PacketBlock& taccReal, PacketBlock& taccImag, PacketBlock& acc1, PacketBlock& acc2) ++-{ ++- acc1.packet[0].v = vec_perm(taccReal.packet[0], taccImag.packet[0], p16uc_SETCOMPLEX32_FIRST); ++- acc1.packet[1].v = vec_perm(taccReal.packet[1], taccImag.packet[1], p16uc_SETCOMPLEX32_FIRST); ++- acc1.packet[2].v = vec_perm(taccReal.packet[2], taccImag.packet[2], p16uc_SETCOMPLEX32_FIRST); ++- acc1.packet[3].v = vec_perm(taccReal.packet[3], taccImag.packet[3], p16uc_SETCOMPLEX32_FIRST); ++- ++- acc2.packet[0].v = vec_perm(taccReal.packet[0], taccImag.packet[0], p16uc_SETCOMPLEX32_SECOND); ++- acc2.packet[1].v = vec_perm(taccReal.packet[1], taccImag.packet[1], p16uc_SETCOMPLEX32_SECOND); ++- acc2.packet[2].v = vec_perm(taccReal.packet[2], taccImag.packet[2], p16uc_SETCOMPLEX32_SECOND); ++- acc2.packet[3].v = vec_perm(taccReal.packet[3], taccImag.packet[3], p16uc_SETCOMPLEX32_SECOND); ++-} ++- ++-template ++-EIGEN_ALWAYS_INLINE void bcouple(PacketBlock& taccReal, PacketBlock& taccImag, PacketBlock& tRes, PacketBlock& acc1, PacketBlock& acc2) ++-{ ++- bcouple_common(taccReal, taccImag, acc1, acc2); ++- ++- acc1.packet[0] = padd(tRes.packet[0], acc1.packet[0]); ++- acc1.packet[1] = padd(tRes.packet[1], acc1.packet[1]); ++- acc1.packet[2] = padd(tRes.packet[2], acc1.packet[2]); ++- acc1.packet[3] = padd(tRes.packet[3], acc1.packet[3]); ++- ++- acc2.packet[0] = padd(tRes.packet[4], acc2.packet[0]); ++- acc2.packet[1] = padd(tRes.packet[5], acc2.packet[1]); ++- acc2.packet[2] = padd(tRes.packet[6], acc2.packet[2]); ++- acc2.packet[3] = padd(tRes.packet[7], acc2.packet[3]); ++-} ++- ++-template ++-EIGEN_ALWAYS_INLINE void bcouple_common(PacketBlock& taccReal, PacketBlock& taccImag, PacketBlock& acc1, PacketBlock& acc2) +++template +++EIGEN_ALWAYS_INLINE void bcouple_common(PacketBlock& taccReal, PacketBlock& taccImag, PacketBlock& acc1, PacketBlock& acc2) ++ { ++- acc1.packet[0].v = vec_perm(taccReal.packet[0], taccImag.packet[0], p16uc_SETCOMPLEX32_FIRST); ++- ++- acc2.packet[0].v = vec_perm(taccReal.packet[0], taccImag.packet[0], p16uc_SETCOMPLEX32_SECOND); +++ acc1.packet[0].v = vec_mergeh(taccReal.packet[0], taccImag.packet[0]); +++ if (N > 1) { +++ acc1.packet[1].v = vec_mergeh(taccReal.packet[1], taccImag.packet[1]); +++ } +++ if (N > 2) { +++ acc1.packet[2].v = vec_mergeh(taccReal.packet[2], taccImag.packet[2]); +++ } +++ if (N > 3) { +++ acc1.packet[3].v = vec_mergeh(taccReal.packet[3], taccImag.packet[3]); +++ } +++ +++ acc2.packet[0].v = vec_mergel(taccReal.packet[0], taccImag.packet[0]); +++ if (N > 1) { +++ acc2.packet[1].v = vec_mergel(taccReal.packet[1], taccImag.packet[1]); +++ } +++ if (N > 2) { +++ acc2.packet[2].v = vec_mergel(taccReal.packet[2], taccImag.packet[2]); +++ } +++ if (N > 3) { +++ acc2.packet[3].v = vec_mergel(taccReal.packet[3], taccImag.packet[3]); +++ } ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void bcouple(PacketBlock& taccReal, PacketBlock& taccImag, PacketBlock& tRes, PacketBlock& acc1, PacketBlock& acc2) +++template +++EIGEN_ALWAYS_INLINE void bcouple(PacketBlock& taccReal, PacketBlock& taccImag, PacketBlock& tRes, PacketBlock& acc1, PacketBlock& acc2) ++ { ++- bcouple_common(taccReal, taccImag, acc1, acc2); +++ bcouple_common(taccReal, taccImag, acc1, acc2); ++ ++ acc1.packet[0] = padd(tRes.packet[0], acc1.packet[0]); ++- ++- acc2.packet[0] = padd(tRes.packet[1], acc2.packet[0]); ++-} ++- ++-template<> ++-EIGEN_ALWAYS_INLINE void bcouple_common(PacketBlock& taccReal, PacketBlock& taccImag, PacketBlock& acc1, PacketBlock& acc2) ++-{ ++- acc1.packet[0].v = vec_perm(taccReal.packet[0], taccImag.packet[0], p16uc_SETCOMPLEX64_FIRST); ++- acc1.packet[1].v = vec_perm(taccReal.packet[1], taccImag.packet[1], p16uc_SETCOMPLEX64_FIRST); ++- acc1.packet[2].v = vec_perm(taccReal.packet[2], taccImag.packet[2], p16uc_SETCOMPLEX64_FIRST); ++- acc1.packet[3].v = vec_perm(taccReal.packet[3], taccImag.packet[3], p16uc_SETCOMPLEX64_FIRST); ++- ++- acc2.packet[0].v = vec_perm(taccReal.packet[0], taccImag.packet[0], p16uc_SETCOMPLEX64_SECOND); ++- acc2.packet[1].v = vec_perm(taccReal.packet[1], taccImag.packet[1], p16uc_SETCOMPLEX64_SECOND); ++- acc2.packet[2].v = vec_perm(taccReal.packet[2], taccImag.packet[2], p16uc_SETCOMPLEX64_SECOND); ++- acc2.packet[3].v = vec_perm(taccReal.packet[3], taccImag.packet[3], p16uc_SETCOMPLEX64_SECOND); ++-} ++- ++-template<> ++-EIGEN_ALWAYS_INLINE void bcouple_common(PacketBlock& taccReal, PacketBlock& taccImag, PacketBlock& acc1, PacketBlock& acc2) ++-{ ++- acc1.packet[0].v = vec_perm(taccReal.packet[0], taccImag.packet[0], p16uc_SETCOMPLEX64_FIRST); ++- ++- acc2.packet[0].v = vec_perm(taccReal.packet[0], taccImag.packet[0], p16uc_SETCOMPLEX64_SECOND); +++ if (N > 1) { +++ acc1.packet[1] = padd(tRes.packet[1], acc1.packet[1]); +++ } +++ if (N > 2) { +++ acc1.packet[2] = padd(tRes.packet[2], acc1.packet[2]); +++ } +++ if (N > 3) { +++ acc1.packet[3] = padd(tRes.packet[3], acc1.packet[3]); +++ } +++ +++ acc2.packet[0] = padd(tRes.packet[0+N], acc2.packet[0]); +++ if (N > 1) { +++ acc2.packet[1] = padd(tRes.packet[1+N], acc2.packet[1]); +++ } +++ if (N > 2) { +++ acc2.packet[2] = padd(tRes.packet[2+N], acc2.packet[2]); +++ } +++ if (N > 3) { +++ acc2.packet[3] = padd(tRes.packet[3+N], acc2.packet[3]); +++ } ++ } ++ ++ // This is necessary because ploadRhs for double returns a pair of vectors when MMA is enabled. ++diff --git a/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h b/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h ++index 6540c6fa6..5b4449537 100644 ++--- a/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h +++++ b/Eigen/src/Core/arch/AltiVec/MatrixProductMMA.h ++@@ -11,7 +11,7 @@ ++ #ifndef EIGEN_MATRIX_PRODUCT_MMA_ALTIVEC_H ++ #define EIGEN_MATRIX_PRODUCT_MMA_ALTIVEC_H ++ ++-#pragma GCC target("cpu=power10") +++#pragma GCC target("cpu=power10,htm") ++ ++ #ifdef __has_builtin ++ #if !__has_builtin(__builtin_vsx_assemble_pair) ++@@ -30,37 +30,37 @@ EIGEN_ALWAYS_INLINE void bsetzeroMMA(__vector_quad* acc) ++ } ++ ++ template ++-EIGEN_ALWAYS_INLINE void storeAccumulator(Index i, Index j, const DataMapper& data, const Packet& alpha, __vector_quad* acc) +++EIGEN_ALWAYS_INLINE void storeAccumulator(Index i, const DataMapper& data, const Packet& alpha, __vector_quad* acc) ++ { ++ PacketBlock result; ++ __builtin_mma_disassemble_acc(&result.packet, acc); ++ ++ PacketBlock tRes; ++- bload(tRes, data, i, j); +++ bload(tRes, data, i, 0); ++ ++- bscale(tRes, result, alpha); +++ bscale(tRes, result, alpha); ++ ++- data.template storePacketBlock(i, j, tRes); +++ data.template storePacketBlock(i, 0, tRes); ++ } ++ ++-template ++-EIGEN_ALWAYS_INLINE void storeComplexAccumulator(Index i, Index j, const DataMapper& data, const Packet& alphaReal, const Packet& alphaImag, __vector_quad* accReal, __vector_quad* accImag) +++template +++EIGEN_ALWAYS_INLINE void storeComplexAccumulator(Index i, const DataMapper& data, const Packet& alphaReal, const Packet& alphaImag, __vector_quad* accReal, __vector_quad* accImag) ++ { ++ PacketBlock resultReal, resultImag; ++ __builtin_mma_disassemble_acc(&resultReal.packet, accReal); ++ __builtin_mma_disassemble_acc(&resultImag.packet, accImag); ++ ++ PacketBlock tRes; ++- bload(tRes, data, i, j); +++ bload(tRes, data, i, 0); ++ ++ PacketBlock taccReal, taccImag; ++ bscalec(resultReal, resultImag, alphaReal, alphaImag, taccReal, taccImag); ++ ++ PacketBlock acc1, acc2; ++- bcouple(taccReal, taccImag, tRes, acc1, acc2); +++ bcouple(taccReal, taccImag, tRes, acc1, acc2); ++ ++- data.template storePacketBlock(i + N*accColsC, j, acc1); ++- data.template storePacketBlock(i + (N+1)*accColsC, j, acc2); +++ data.template storePacketBlock(i, 0, acc1); +++ data.template storePacketBlock(i + accColsC, 0, acc2); ++ } ++ ++ // Defaults to float32, since Eigen still supports C++03 we can't use default template arguments ++@@ -125,7 +125,7 @@ EIGEN_ALWAYS_INLINE void pgercMMA(__vector_quad* accReal, __vector_quad* accImag ++ template ++ EIGEN_ALWAYS_INLINE void ploadRhsMMA(const Scalar* rhs, Packet& rhsV) ++ { ++- rhsV = ploadRhs((const Scalar*)(rhs)); +++ rhsV = ploadRhs(rhs); ++ } ++ ++ template<> ++@@ -184,12 +184,11 @@ EIGEN_ALWAYS_INLINE void ploadRhsMMA(const float*, __vector_pair&) ++ } ++ ++ #define MICRO_MMA_UNROLL_TYPE_PEEL(func, func2, type) \ ++- type rhsV0, rhsV1, rhsV2, rhsV3, rhsV4, rhsV5, rhsV6, rhsV7, rhsV8, rhsV9; \ +++ type rhsV0, rhsV1, rhsV2, rhsV3, rhsV4, rhsV5, rhsV6, rhsV7; \ ++ MICRO_MMA_TYPE_PEEL(func,func2,type,0); MICRO_MMA_TYPE_PEEL(func,func2,type,1); \ ++ MICRO_MMA_TYPE_PEEL(func,func2,type,2); MICRO_MMA_TYPE_PEEL(func,func2,type,3); \ ++ MICRO_MMA_TYPE_PEEL(func,func2,type,4); MICRO_MMA_TYPE_PEEL(func,func2,type,5); \ ++- MICRO_MMA_TYPE_PEEL(func,func2,type,6); MICRO_MMA_TYPE_PEEL(func,func2,type,7); \ ++- MICRO_MMA_TYPE_PEEL(func,func2,type,8); MICRO_MMA_TYPE_PEEL(func,func2,type,9); +++ MICRO_MMA_TYPE_PEEL(func,func2,type,6); MICRO_MMA_TYPE_PEEL(func,func2,type,7); ++ ++ #define MICRO_MMA_UNROLL_TYPE_ONE(func, func2, type) \ ++ type rhsV0; \ ++@@ -222,7 +221,7 @@ EIGEN_ALWAYS_INLINE void ploadRhsMMA(const float*, __vector_pair&) ++ ++ #define MICRO_MMA_SRC_PTR_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++- lhs_ptr##iter = lhs_base + ( (row/accCols) + iter )*strideA*accCols + accCols*offsetA; \ +++ lhs_ptr##iter = lhs_base + ( (row/accCols) + iter )*strideA*accCols; \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(lhs_ptr##iter); \ ++ } ++@@ -238,21 +237,19 @@ EIGEN_ALWAYS_INLINE void ploadRhsMMA(const float*, __vector_pair&) ++ ++ #define MICRO_MMA_STORE_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++- storeAccumulator(row + iter*accCols, col, res, pAlpha, &accZero##iter); \ +++ storeAccumulator(row + iter*accCols, res, pAlpha, &accZero##iter); \ ++ } ++ ++ #define MICRO_MMA_STORE MICRO_MMA_UNROLL(MICRO_MMA_STORE_ONE) ++ ++ template ++-EIGEN_STRONG_INLINE void gemm_unrolled_MMA_iteration( +++EIGEN_ALWAYS_INLINE void gemm_unrolled_MMA_iteration( ++ const DataMapper& res, ++ const Scalar* lhs_base, ++ const Scalar* rhs_base, ++ Index depth, ++ Index strideA, ++- Index offsetA, ++ Index& row, ++- Index col, ++ const Packet& pAlpha) ++ { ++ const Scalar* rhs_ptr = rhs_base; ++@@ -278,94 +275,98 @@ EIGEN_STRONG_INLINE void gemm_unrolled_MMA_iteration( ++ row += unroll_factor*accCols; ++ } ++ ++-template ++-void gemmMMA(const DataMapper& res, const Scalar* blockA, const Scalar* blockB, Index rows, Index depth, Index cols, Scalar alpha, Index strideA, Index strideB, Index offsetA, Index offsetB) +++template +++EIGEN_ALWAYS_INLINE void gemmMMA_cols( +++ const DataMapper& res, +++ const Scalar* blockA, +++ const Scalar* blockB, +++ Index depth, +++ Index strideA, +++ Index offsetA, +++ Index strideB, +++ Index offsetB, +++ Index col, +++ Index rows, +++ Index cols, +++ Index remaining_rows, +++ const Packet& pAlpha, +++ const Packet& pMask) ++ { ++- const Index remaining_rows = rows % accCols; ++- const Index remaining_cols = cols % accRows; ++- ++- if( strideA == -1 ) strideA = depth; ++- if( strideB == -1 ) strideB = depth; ++- ++- const Packet pAlpha = pset1(alpha); ++- const Packet pMask = bmask((const int)(remaining_rows)); +++ const DataMapper res3 = res.getSubMapper(0, col); ++ ++- Index col = 0; ++- for(; col + accRows <= cols; col += accRows) ++- { ++- const Scalar* rhs_base = blockB + col*strideB + accRows*offsetB; ++- const Scalar* lhs_base = blockA; +++ const Scalar* rhs_base = blockB + col*strideB + accRows*offsetB; +++ const Scalar* lhs_base = blockA + accCols*offsetA; +++ Index row = 0; ++ ++- Index row = 0; ++ #define MAX_MMA_UNROLL 7 ++- while(row + MAX_MMA_UNROLL*accCols <= rows) { ++- gemm_unrolled_MMA_iteration(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- } ++- switch( (rows-row)/accCols ) { +++ while(row + MAX_MMA_UNROLL*accCols <= rows) { +++ gemm_unrolled_MMA_iteration(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); +++ } +++ switch( (rows-row)/accCols ) { ++ #if MAX_MMA_UNROLL > 7 ++- case 7: ++- gemm_unrolled_MMA_iteration<7, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; +++ case 7: +++ gemm_unrolled_MMA_iteration<7, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); +++ break; ++ #endif ++ #if MAX_MMA_UNROLL > 6 ++- case 6: ++- gemm_unrolled_MMA_iteration<6, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; +++ case 6: +++ gemm_unrolled_MMA_iteration<6, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); +++ break; ++ #endif ++ #if MAX_MMA_UNROLL > 5 ++- case 5: ++- gemm_unrolled_MMA_iteration<5, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; +++ case 5: +++ gemm_unrolled_MMA_iteration<5, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); +++ break; ++ #endif ++ #if MAX_MMA_UNROLL > 4 ++- case 4: ++- gemm_unrolled_MMA_iteration<4, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; +++ case 4: +++ gemm_unrolled_MMA_iteration<4, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); +++ break; ++ #endif ++ #if MAX_MMA_UNROLL > 3 ++- case 3: ++- gemm_unrolled_MMA_iteration<3, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; +++ case 3: +++ gemm_unrolled_MMA_iteration<3, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); +++ break; ++ #endif ++ #if MAX_MMA_UNROLL > 2 ++- case 2: ++- gemm_unrolled_MMA_iteration<2, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; +++ case 2: +++ gemm_unrolled_MMA_iteration<2, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); +++ break; ++ #endif ++ #if MAX_MMA_UNROLL > 1 ++- case 1: ++- gemm_unrolled_MMA_iteration<1, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, pAlpha); ++- break; +++ case 1: +++ gemm_unrolled_MMA_iteration<1, Scalar, Packet, RhsPacket, DataMapper, Index, accRows, accCols>(res3, lhs_base, rhs_base, depth, strideA, row, pAlpha); +++ break; ++ #endif ++- default: ++- break; ++- } +++ default: +++ break; +++ } ++ #undef MAX_MMA_UNROLL ++ ++- if(remaining_rows > 0) ++- { ++- gemm_extra_row(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, rows, cols, remaining_rows, pAlpha, pMask); ++- } ++- } +++ if(remaining_rows > 0) +++ { +++ gemm_extra_row(res3, blockA, rhs_base, depth, strideA, offsetA, row, col, rows, cols, remaining_rows, pAlpha, pMask); +++ } +++} ++ ++- if(remaining_cols > 0) ++- { ++- const Scalar* rhs_base = blockB + col*strideB + remaining_cols*offsetB; ++- const Scalar* lhs_base = blockA; +++template +++void gemmMMA(const DataMapper& res, const Scalar* blockA, const Scalar* blockB, Index rows, Index depth, Index cols, Scalar alpha, Index strideA, Index strideB, Index offsetA, Index offsetB) +++{ +++ const Index remaining_rows = rows % accCols; ++ ++- for(; col < cols; col++) ++- { ++- Index row = 0; +++ if( strideA == -1 ) strideA = depth; +++ if( strideB == -1 ) strideB = depth; ++ ++- gemm_unrolled_col(res, lhs_base, rhs_base, depth, strideA, offsetA, row, rows, col, remaining_cols, pAlpha); +++ const Packet pAlpha = pset1(alpha); +++ const Packet pMask = bmask((const int)(remaining_rows)); ++ ++- if (remaining_rows > 0) ++- { ++- gemm_extra_col(res, lhs_base, rhs_base, depth, strideA, offsetA, row, col, remaining_rows, remaining_cols, pAlpha); ++- } ++- rhs_base++; ++- } +++ Index col = 0; +++ for(; col + accRows <= cols; col += accRows) +++ { +++ gemmMMA_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlpha, pMask); ++ } +++ +++ gemm_extra_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlpha, pMask); ++ } ++ ++ #define accColsC (accCols / 2) ++@@ -373,21 +374,20 @@ void gemmMMA(const DataMapper& res, const Scalar* blockA, const Scalar* blockB, ++ #define advanceCols ((RhsIsReal) ? 1 : 2) ++ ++ // PEEL_COMPLEX_MMA loop factor. ++-#define PEEL_COMPLEX_MMA 7 +++#define PEEL_COMPLEX_MMA 3 ++ ++ #define MICRO_COMPLEX_MMA_UNROLL(func) \ ++- func(0) func(1) func(2) func(3) func(4) +++ func(0) func(1) func(2) func(3) ++ ++ #define MICRO_COMPLEX_MMA_LOAD_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++ lhsV##iter = ploadLhs(lhs_ptr_real##iter); \ ++- lhs_ptr_real##iter += accCols; \ ++ if(!LhsIsReal) { \ ++- lhsVi##iter = ploadLhs(lhs_ptr_imag##iter); \ ++- lhs_ptr_imag##iter += accCols; \ +++ lhsVi##iter = ploadLhs(lhs_ptr_real##iter + imag_delta); \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(lhsVi##iter); \ ++ } \ +++ lhs_ptr_real##iter += accCols; \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(lhsV##iter); \ ++ EIGEN_UNUSED_VARIABLE(lhsVi##iter); \ ++@@ -400,8 +400,8 @@ void gemmMMA(const DataMapper& res, const Scalar* blockA, const Scalar* blockB, ++ ++ #define MICRO_COMPLEX_MMA_TYPE_PEEL(func, func2, type, peel) \ ++ if (PEEL_COMPLEX_MMA > peel) { \ ++- Packet lhsV0, lhsV1, lhsV2, lhsV3, lhsV4; \ ++- Packet lhsVi0, lhsVi1, lhsVi2, lhsVi3, lhsVi4; \ +++ Packet lhsV0, lhsV1, lhsV2, lhsV3; \ +++ Packet lhsVi0, lhsVi1, lhsVi2, lhsVi3; \ ++ ploadRhsMMA(rhs_ptr_real + (accRows * peel), rhsV##peel); \ ++ if(!RhsIsReal) { \ ++ ploadRhsMMA(rhs_ptr_imag + (accRows * peel), rhsVi##peel); \ ++@@ -409,20 +409,17 @@ void gemmMMA(const DataMapper& res, const Scalar* blockA, const Scalar* blockB, ++ EIGEN_UNUSED_VARIABLE(rhsVi##peel); \ ++ } \ ++ MICRO_COMPLEX_MMA_UNROLL(func2); \ ++- func(0,type,peel) func(1,type,peel) func(2,type,peel) func(3,type,peel) func(4,type,peel) \ +++ func(0,type,peel) func(1,type,peel) func(2,type,peel) func(3,type,peel) \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(rhsV##peel); \ ++ EIGEN_UNUSED_VARIABLE(rhsVi##peel); \ ++ } ++ ++ #define MICRO_COMPLEX_MMA_UNROLL_TYPE_PEEL(func, func2, type) \ ++- type rhsV0, rhsV1, rhsV2, rhsV3, rhsV4, rhsV5, rhsV6, rhsV7, rhsV8, rhsV9; \ ++- type rhsVi0, rhsVi1, rhsVi2, rhsVi3, rhsVi4, rhsVi5, rhsVi6, rhsVi7, rhsVi8, rhsVi9; \ +++ type rhsV0, rhsV1, rhsV2, rhsV3; \ +++ type rhsVi0, rhsVi1, rhsVi2, rhsVi3; \ ++ MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,0); MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,1); \ ++- MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,2); MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,3); \ ++- MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,4); MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,5); \ ++- MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,6); MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,7); \ ++- MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,8); MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,9); +++ MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,2); MICRO_COMPLEX_MMA_TYPE_PEEL(func,func2,type,3); ++ ++ #define MICRO_COMPLEX_MMA_UNROLL_TYPE_ONE(func, func2, type) \ ++ type rhsV0, rhsVi0; \ ++@@ -459,15 +456,9 @@ void gemmMMA(const DataMapper& res, const Scalar* blockA, const Scalar* blockB, ++ ++ #define MICRO_COMPLEX_MMA_SRC_PTR_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++- lhs_ptr_real##iter = lhs_base + ( ((advanceRows*row)/accCols) + iter*advanceRows )*strideA*accCols + accCols*offsetA; \ ++- if(!LhsIsReal) { \ ++- lhs_ptr_imag##iter = lhs_ptr_real##iter + accCols*strideA; \ ++- } else { \ ++- EIGEN_UNUSED_VARIABLE(lhs_ptr_imag##iter); \ ++- } \ +++ lhs_ptr_real##iter = lhs_base + ( ((advanceRows*row)/accCols) + iter*advanceRows )*strideA*accCols; \ ++ } else { \ ++ EIGEN_UNUSED_VARIABLE(lhs_ptr_real##iter); \ ++- EIGEN_UNUSED_VARIABLE(lhs_ptr_imag##iter); \ ++ } ++ ++ #define MICRO_COMPLEX_MMA_SRC_PTR MICRO_COMPLEX_MMA_UNROLL(MICRO_COMPLEX_MMA_SRC_PTR_ONE) ++@@ -475,45 +466,40 @@ void gemmMMA(const DataMapper& res, const Scalar* blockA, const Scalar* blockB, ++ #define MICRO_COMPLEX_MMA_PREFETCH_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++ EIGEN_POWER_PREFETCH(lhs_ptr_real##iter); \ ++- if(!LhsIsReal) { \ ++- EIGEN_POWER_PREFETCH(lhs_ptr_imag##iter); \ ++- } \ ++ } ++ ++ #define MICRO_COMPLEX_MMA_PREFETCH MICRO_COMPLEX_MMA_UNROLL(MICRO_COMPLEX_MMA_PREFETCH_ONE) ++ ++ #define MICRO_COMPLEX_MMA_STORE_ONE(iter) \ ++ if (unroll_factor > iter) { \ ++- storeComplexAccumulator(row + iter*accCols, col, res, pAlphaReal, pAlphaImag, &accReal##iter, &accImag##iter); \ +++ storeComplexAccumulator(row + iter*accCols, res, pAlphaReal, pAlphaImag, &accReal##iter, &accImag##iter); \ ++ } ++ ++ #define MICRO_COMPLEX_MMA_STORE MICRO_COMPLEX_MMA_UNROLL(MICRO_COMPLEX_MMA_STORE_ONE) ++ ++ template ++-EIGEN_STRONG_INLINE void gemm_complex_unrolled_MMA_iteration( +++EIGEN_ALWAYS_INLINE void gemm_complex_unrolled_MMA_iteration( ++ const DataMapper& res, ++ const Scalar* lhs_base, ++ const Scalar* rhs_base, ++ Index depth, ++ Index strideA, ++- Index offsetA, ++ Index strideB, ++ Index& row, ++- Index col, ++ const Packet& pAlphaReal, ++ const Packet& pAlphaImag) ++ { ++ const Scalar* rhs_ptr_real = rhs_base; ++- const Scalar* rhs_ptr_imag; +++ const Scalar* rhs_ptr_imag = NULL; +++ const Index imag_delta = accCols*strideA; ++ if(!RhsIsReal) { ++ rhs_ptr_imag = rhs_base + accRows*strideB; ++ } else { ++ EIGEN_UNUSED_VARIABLE(rhs_ptr_imag); ++ } ++- const Scalar* lhs_ptr_real0 = NULL, * lhs_ptr_imag0 = NULL, * lhs_ptr_real1 = NULL, * lhs_ptr_imag1 = NULL; ++- const Scalar* lhs_ptr_real2 = NULL, * lhs_ptr_imag2 = NULL, * lhs_ptr_real3 = NULL, * lhs_ptr_imag3 = NULL; ++- const Scalar* lhs_ptr_real4 = NULL, * lhs_ptr_imag4 = NULL; ++- __vector_quad accReal0, accImag0, accReal1, accImag1, accReal2, accImag2, accReal3, accImag3, accReal4, accImag4; +++ const Scalar* lhs_ptr_real0 = NULL, * lhs_ptr_real1 = NULL; +++ const Scalar* lhs_ptr_real2 = NULL, * lhs_ptr_real3 = NULL; +++ __vector_quad accReal0, accImag0, accReal1, accImag1, accReal2, accImag2, accReal3, accImag3; ++ ++ MICRO_COMPLEX_MMA_SRC_PTR ++ MICRO_COMPLEX_MMA_DST_PTR ++@@ -537,11 +523,70 @@ EIGEN_STRONG_INLINE void gemm_complex_unrolled_MMA_iteration( ++ row += unroll_factor*accCols; ++ } ++ +++template +++EIGEN_ALWAYS_INLINE void gemmMMA_complex_cols( +++ const DataMapper& res, +++ const Scalar* blockA, +++ const Scalar* blockB, +++ Index depth, +++ Index strideA, +++ Index offsetA, +++ Index strideB, +++ Index offsetB, +++ Index col, +++ Index rows, +++ Index cols, +++ Index remaining_rows, +++ const Packet& pAlphaReal, +++ const Packet& pAlphaImag, +++ const Packet& pMask) +++{ +++ const DataMapper res3 = res.getSubMapper(0, col); +++ +++ const Scalar* rhs_base = blockB + advanceCols*col*strideB + accRows*offsetB; +++ const Scalar* lhs_base = blockA + accCols*offsetA; +++ Index row = 0; +++ +++#define MAX_COMPLEX_MMA_UNROLL 4 +++ while(row + MAX_COMPLEX_MMA_UNROLL*accCols <= rows) { +++ gemm_complex_unrolled_MMA_iteration(res3, lhs_base, rhs_base, depth, strideA, strideB, row, pAlphaReal, pAlphaImag); +++ } +++ switch( (rows-row)/accCols ) { +++#if MAX_COMPLEX_MMA_UNROLL > 4 +++ case 4: +++ gemm_complex_unrolled_MMA_iteration<4, Scalar, Packet, Packetc, RhsPacket, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res3, lhs_base, rhs_base, depth, strideA, strideB, row, pAlphaReal, pAlphaImag); +++ break; +++#endif +++#if MAX_COMPLEX_MMA_UNROLL > 3 +++ case 3: +++ gemm_complex_unrolled_MMA_iteration<3, Scalar, Packet, Packetc, RhsPacket, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res3, lhs_base, rhs_base, depth, strideA, strideB, row, pAlphaReal, pAlphaImag); +++ break; +++#endif +++#if MAX_COMPLEX_MMA_UNROLL > 2 +++ case 2: +++ gemm_complex_unrolled_MMA_iteration<2, Scalar, Packet, Packetc, RhsPacket, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res3, lhs_base, rhs_base, depth, strideA, strideB, row, pAlphaReal, pAlphaImag); +++ break; +++#endif +++#if MAX_COMPLEX_MMA_UNROLL > 1 +++ case 1: +++ gemm_complex_unrolled_MMA_iteration<1, Scalar, Packet, Packetc, RhsPacket, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res3, lhs_base, rhs_base, depth, strideA, strideB, row, pAlphaReal, pAlphaImag); +++ break; +++#endif +++ default: +++ break; +++ } +++#undef MAX_COMPLEX_MMA_UNROLL +++ +++ if(remaining_rows > 0) +++ { +++ gemm_complex_extra_row(res3, blockA, rhs_base, depth, strideA, offsetA, strideB, row, col, rows, cols, remaining_rows, pAlphaReal, pAlphaImag, pMask); +++ } +++} +++ ++ template ++ void gemm_complexMMA(const DataMapper& res, const LhsScalar* blockAc, const RhsScalar* blockBc, Index rows, Index depth, Index cols, Scalarc alpha, Index strideA, Index strideB, Index offsetA, Index offsetB) ++ { ++ const Index remaining_rows = rows % accCols; ++- const Index remaining_cols = cols % accRows; ++ ++ if( strideA == -1 ) strideA = depth; ++ if( strideB == -1 ) strideB = depth; ++@@ -556,64 +601,10 @@ void gemm_complexMMA(const DataMapper& res, const LhsScalar* blockAc, const RhsS ++ Index col = 0; ++ for(; col + accRows <= cols; col += accRows) ++ { ++- const Scalar* rhs_base = blockB + advanceCols*col*strideB + accRows*offsetB; ++- const Scalar* lhs_base = blockA; ++- Index row = 0; ++- ++-#define MAX_COMPLEX_MMA_UNROLL 4 ++- while(row + MAX_COMPLEX_MMA_UNROLL*accCols <= rows) { ++- gemm_complex_unrolled_MMA_iteration(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, pAlphaReal, pAlphaImag); ++- } ++- switch( (rows-row)/accCols ) { ++-#if MAX_COMPLEX_MMA_UNROLL > 4 ++- case 4: ++- gemm_complex_unrolled_MMA_iteration<4, Scalar, Packet, Packetc, RhsPacket, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++-#if MAX_COMPLEX_MMA_UNROLL > 3 ++- case 3: ++- gemm_complex_unrolled_MMA_iteration<3, Scalar, Packet, Packetc, RhsPacket, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++-#if MAX_COMPLEX_MMA_UNROLL > 2 ++- case 2: ++- gemm_complex_unrolled_MMA_iteration<2, Scalar, Packet, Packetc, RhsPacket, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++-#if MAX_COMPLEX_MMA_UNROLL > 1 ++- case 1: ++- gemm_complex_unrolled_MMA_iteration<1, Scalar, Packet, Packetc, RhsPacket, DataMapper, Index, accRows, accCols, ConjugateLhs, ConjugateRhs, LhsIsReal, RhsIsReal>(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, pAlphaReal, pAlphaImag); ++- break; ++-#endif ++- default: ++- break; ++- } ++-#undef MAX_COMPLEX_MMA_UNROLL ++- ++- if(remaining_rows > 0) ++- { ++- gemm_complex_extra_row(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, rows, cols, remaining_rows, pAlphaReal, pAlphaImag, pMask); ++- } +++ gemmMMA_complex_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlphaReal, pAlphaImag, pMask); ++ } ++ ++- if(remaining_cols > 0) ++- { ++- const Scalar* rhs_base = blockB + advanceCols*col*strideB + remaining_cols*offsetB; ++- const Scalar* lhs_base = blockA; ++- ++- for(; col < cols; col++) ++- { ++- Index row = 0; ++- ++- gemm_complex_unrolled_col(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, rows, col, remaining_cols, pAlphaReal, pAlphaImag); ++- ++- if (remaining_rows > 0) ++- { ++- gemm_complex_extra_col(res, lhs_base, rhs_base, depth, strideA, offsetA, strideB, row, col, remaining_rows, remaining_cols, pAlphaReal, pAlphaImag); ++- } ++- rhs_base++; ++- } ++- } +++ gemm_complex_extra_cols(res, blockA, blockB, depth, strideA, offsetA, strideB, offsetB, col, rows, cols, remaining_rows, pAlphaReal, pAlphaImag, pMask); ++ } ++ ++ #undef accColsC +diff --git a/third_party/eigen3/workspace.bzl b/third_party/eigen3/workspace.bzl +index 21799365434..cd1feb4d29c 100644 +--- a/third_party/eigen3/workspace.bzl ++++ b/third_party/eigen3/workspace.bzl +@@ -16,6 +16,7 @@ def repo(): + build_file = "//third_party/eigen3:eigen_archive.BUILD", + sha256 = EIGEN_SHA256, + strip_prefix = "eigen-{commit}".format(commit = EIGEN_COMMIT), ++ patch_file = "//third_party/eigen3:fix-ppc-gemm.patch", + urls = [ + "https://storage.googleapis.com/mirror.tensorflow.org/gitlab.com/libeigen/eigen/-/archive/{commit}/eigen-{commit}.tar.gz".format(commit = EIGEN_COMMIT), + "https://gitlab.com/libeigen/eigen/-/archive/{commit}/eigen-{commit}.tar.gz".format(commit = EIGEN_COMMIT), +From bc900ca63038d44342d013da75e85ad65ab0c4e6 Mon Sep 17 00:00:00 2001 +From: "Maxiwell S. Garcia" +Date: Mon, 1 Nov 2021 10:10:34 -0500 +Subject: [PATCH] ppc: remove the special condition for ppc on convolutions + +After a recent change on Eigen Altivec package, we don't need this +special condition on convolutions anymore + +https://gitlab.com/libeigen/eigen/-/commit/9cf34ee0aed25a7464e6ec14f977cfa940f48f1b +--- + tensorflow/core/kernels/eigen_cuboid_convolution.h | 10 ---------- + .../core/kernels/eigen_spatial_convolutions-inl.h | 10 ---------- + 2 files changed, 20 deletions(-) + +diff --git a/tensorflow/core/kernels/eigen_cuboid_convolution.h b/tensorflow/core/kernels/eigen_cuboid_convolution.h +index bf0cdd59e4fb3..729dcd3bd2af0 100644 +--- a/tensorflow/core/kernels/eigen_cuboid_convolution.h ++++ b/tensorflow/core/kernels/eigen_cuboid_convolution.h +@@ -1358,15 +1358,6 @@ struct gemm_pack_rhs< + } + + // Copy the remaining columns one at a time (nr==1). +-#if defined(EIGEN_VECTORIZE_ALTIVEC) || defined(EIGEN_VECTORIZE_VSX) +- // remaining columns are handled different for PPC +- for (Index k = 0; k < depth; k++) { +- for (Index j2 = packet_cols4; j2 < cols; ++j2) { +- *block = rhs(k, j2); +- block += 1; +- } +- } +-#else + for (Index j2 = packet_cols4; j2 < cols; ++j2) { + const SubMapper dm0 = rhs.getLinearMapper(0, j2); + for (Index k = 0; k < depth; k++) { +@@ -1374,7 +1365,6 @@ struct gemm_pack_rhs< + block += 1; + } + } +-#endif + } + }; + +diff --git a/tensorflow/core/kernels/eigen_spatial_convolutions-inl.h b/tensorflow/core/kernels/eigen_spatial_convolutions-inl.h +index 61cfc820a6cca..37a41f952fa87 100644 +--- a/tensorflow/core/kernels/eigen_spatial_convolutions-inl.h ++++ b/tensorflow/core/kernels/eigen_spatial_convolutions-inl.h +@@ -1233,15 +1233,6 @@ struct gemm_pack_rhs< + } + + // copy the remaining columns one at a time (nr==1) +-#if defined(EIGEN_VECTORIZE_ALTIVEC) || defined(EIGEN_VECTORIZE_VSX) +- // remaining columns are handled different for PPC +- for (Index k = 0; k < depth; k++) { +- for (Index j2 = packet_cols4; j2 < cols; ++j2) { +- *block = rhs(k, j2); +- block += 1; +- } +- } +-#else + for (Index j2 = packet_cols4; j2 < cols; ++j2) { + const SubMapper dm0 = rhs.getLinearMapper(0, j2); + for (Index k = 0; k < depth; k++) { +@@ -1249,7 +1240,6 @@ struct gemm_pack_rhs< + block += 1; + } + } +-#endif + } + }; + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix-PPC-JIT.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix-PPC-JIT.patch new file mode 100644 index 00000000000..1f361e3b706 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1_fix-PPC-JIT.patch @@ -0,0 +1,82 @@ +Allow JIT compilation for PPC targets (e.g. "pwr9" CPUs) +From https://github.com/tensorflow/tensorflow/pull/55306 +Backported for TF 2.7.1 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/cpuinfo/BUILD.bazel b/third_party/cpuinfo/BUILD.bazel +index eb2937d20ef..dfea408db94 100644 +--- a/third_party/cpuinfo/BUILD.bazel ++++ b/third_party/cpuinfo/BUILD.bazel +@@ -109,6 +109,7 @@ cc_library( + ":linux_mips64": COMMON_SRCS + LINUX_SRCS, + ":linux_riscv64": COMMON_SRCS + LINUX_SRCS, + ":linux_s390x": COMMON_SRCS + LINUX_SRCS, ++ ":linux_ppc64le": COMMON_SRCS + LINUX_SRCS, + ":macos_x86_64": COMMON_SRCS + X86_SRCS + MACH_SRCS + MACH_X86_SRCS, + ":macos_arm64": COMMON_SRCS + MACH_SRCS + MACH_ARM_SRCS, + ":windows_x86_64": COMMON_SRCS + X86_SRCS + WINDOWS_X86_SRCS, +@@ -232,6 +233,11 @@ config_setting( + values = {"cpu": "s390x"}, + ) + ++config_setting( ++ name = "linux_ppc64le", ++ values = {"cpu": "ppc"}, ++) ++ + config_setting( + name = "macos_x86_64", + values = { +diff --git a/third_party/llvm/macos_build_fix.patch b/third_party/llvm/macos_build_fix.patch +index 8ff52f906a6..4467081c410 100644 +--- a/third_party/llvm/macos_build_fix.patch ++++ b/third_party/llvm/macos_build_fix.patch +@@ -22,6 +22,48 @@ index ff64df694048..55f3077bff74 100644 + "@bazel_tools//src/conditions:linux_aarch64": native_arch_defines("AArch64", "aarch64-unknown-linux-gnu"), + "//conditions:default": native_arch_defines("X86", "x86_64-unknown-linux-gnu"), + }) + [ ++ ++ ++From b250c34bbd415b2a8c3e0532e98591ab1780cda6 Mon Sep 17 00:00:00 2001 ++From: Nishidha Panpaliya ++Date: Mon, 21 Mar 2022 09:51:36 -0400 ++Subject: [PATCH] Fix for ppc64le ++ ++--- ++ utils/bazel/llvm-project-overlay/llvm/config.bzl | 1 + ++ 1 file changed, 1 insertion(+) ++ ++diff --git a/utils/bazel/llvm-project-overlay/llvm/config.bzl b/utils/bazel/llvm-project-overlay/llvm/config.bzl ++index 772714f38941..9ed63e8d44a3 100644 ++--- a/utils/bazel/llvm-project-overlay/llvm/config.bzl +++++ b/utils/bazel/llvm-project-overlay/llvm/config.bzl ++@@ -78,6 +78,7 @@ ++ "@bazel_tools//src/conditions:windows": native_arch_defines("X86", "x86_64-pc-win32"), ++ "@bazel_tools//src/conditions:darwin": native_arch_defines("X86", "x86_64-unknown-darwin"), ++ "@bazel_tools//src/conditions:linux_aarch64": native_arch_defines("AArch64", "aarch64-unknown-linux-gnu"), +++ "@bazel_tools//src/conditions:linux_ppc64le": native_arch_defines("PowerPC", "powerpc64le-unknown-linux-gnu"), ++ "//conditions:default": native_arch_defines("X86", "x86_64-unknown-linux-gnu"), ++ }) + [ ++ # These shouldn't be needed by the C++11 standard, but are for some ++ ++--- ++Fix link errors on PPC caused by above patch: https://github.com/llvm/llvm-project/issues/59590 ++ ++Author: Alexander Grund (TU Dresden) ++ ++diff --git a/utils/bazel/llvm-project-overlay/mlir/BUILD.bazel b/utils/bazel/llvm-project-overlay/mlir/BUILD.bazel ++index f4dfb3791477..da92b53b7a2b 100644 ++--- a/utils/bazel/llvm-project-overlay/mlir/BUILD.bazel +++++ b/utils/bazel/llvm-project-overlay/mlir/BUILD.bazel ++@@ -4986,6 +4986,7 @@ cc_library( ++ ":Support", ++ ":ToLLVMIRTranslation", ++ ":Translation", +++ "//llvm:AllTargetsAsmParsers", ++ "//llvm:BitReader", ++ "//llvm:BitWriter", ++ "//llvm:Core", ++ + -- + 2.33.0.685.g46640cef36-goog From 3594af171ea783c1bff5ed84b6ddbe4e55392d9c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 10 Feb 2023 14:05:07 +0100 Subject: [PATCH 6456/9987] adding easyconfigs: CHERAB-1.4.0-intel-2020b.eb, CHERAB-1.4.0-foss-2020b.eb --- .../c/CHERAB/CHERAB-1.4.0-foss-2020b.eb | 31 +++++++++++++++++++ .../c/CHERAB/CHERAB-1.4.0-intel-2020b.eb | 31 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb create mode 100644 easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb new file mode 100644 index 00000000000..e87a4eff595 --- /dev/null +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-foss-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'CHERAB' +version = '1.4.0' + +homepage = 'https://cherab.github.io/documentation/index.html' + +description = """CHERAB is a python library for forward modelling diagnostics + based on spectroscopic plasma emission.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0b3c48e91582ca7e9aad0f45f982791820e070ad1c1fb17d41d58c35cadda8b'] + +builddependencies = [ + ('Cython', '3.0a5'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb new file mode 100644 index 00000000000..95c8e30c605 --- /dev/null +++ b/easybuild/easyconfigs/c/CHERAB/CHERAB-1.4.0-intel-2020b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'CHERAB' +version = '1.4.0' + +homepage = 'https://cherab.github.io/documentation/index.html' + +description = """CHERAB is a python library for forward modelling diagnostics + based on spectroscopic plasma emission.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0b3c48e91582ca7e9aad0f45f982791820e070ad1c1fb17d41d58c35cadda8b'] + +builddependencies = [ + ('Cython', '3.0a5'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Raysect', '0.7.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'phys' From d6d76217b451bec92b98b576a5730496caa91464 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Feb 2023 14:23:16 +0100 Subject: [PATCH 6457/9987] adding easyconfigs: pytest-rerunfailures-11.1-GCCcore-11.3.0.eb, pytest-shard-0.1.2-GCCcore-11.3.0.eb --- ...ytest-rerunfailures-11.1-GCCcore-11.3.0.eb | 21 ++++++++++++++ .../pytest-shard-0.1.2-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3dbe1d1df4a --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'pytest-rerunfailures' +version = '11.1' + +homepage = 'https://github.com/pytest-dev/pytest-rerunfailures' +description = """pytest plugin to re-run tests to eliminate flaky failures.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] + +use_pip = True + +sources = [SOURCE_TAR_GZ] +checksums = ['bc6ad13614c976b04558c3a7bcc393a7e09686fb86b6ae73f827b78326c09f75'] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1ea16f83536 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'pytest-shard' +version = '0.1.2' + +homepage = 'https://github.com/AdamGleave/pytest-shard' +description = """pytest plugin to support parallelism across multiple machines. + +Shards tests based on a hash of their test name enabling easy parallelism across machines, +suitable for a wide variety of continuous integration services. +Tests are split at the finest level of granularity, individual test cases, +enabling parallelism even if all of your tests are in a single file +(or even single parameterized test method). +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] + +use_pip = True + +sources = [SOURCE_TAR_GZ] +checksums = ['b86a967fbfd1c8e50295095ccda031b7e890862ee06531d5142844f4c1d1cd67'] + +sanity_pip_check = True + +moduleclass = 'tools' From 5f52236df3afcd51c152dce775072a90b04ed963 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Feb 2023 14:36:26 +0100 Subject: [PATCH 6458/9987] Fix test_ops* startup failures Those tests require 2 pytest plugins and a bugfix. --- .../p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 6 ++++ .../PyTorch-1.13.1_fix-pytest-args.patch | 28 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-pytest-args.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index 151fcf65d7c..c3837e6e707 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -22,6 +22,7 @@ patches = [ 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_fix-vsx-loadu.patch', 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', + 'PyTorch-1.13.1_fix-pytest-args.patch', 'PyTorch-1.13.1_fix-test-ops-conf.patch', 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', @@ -46,6 +47,8 @@ checksums = [ {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, {'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch': '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d'}, + {'PyTorch-1.13.1_fix-pytest-args.patch': + 'd3e3c841cf8d73683750f29326f2be56ee0bb5df7ff522baf7d7c3f301a91ec2'}, {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '4c636059850fc9d1ecb27ce275f8aad5d5b6fdc19e35aff0c25b86cb3201352a'}, {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': @@ -59,6 +62,9 @@ osdependencies = [OS_PKG_IBVERBS_DEV] builddependencies = [ ('CMake', '3.23.1'), ('hypothesis', '6.46.7'), + # For tests + ('pytest-rerunfailures', '11.1'), + ('pytest-shard', '0.1.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-pytest-args.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-pytest-args.patch new file mode 100644 index 00000000000..f89df575837 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-pytest-args.patch @@ -0,0 +1,28 @@ +As we don't set `--save-xml` pytest is called without arguments causing it to try to discover ALL tests. +This leads to massive failures in e.g. `test_ops*` where `--use-pytest` is used by the tests. +See https://github.com/pytorch/pytorch/pull/94589 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_utils.py b/torch/testing/_internal/common_utils.py +index e32850908d4..e63c6f2a392 100644 +--- a/torch/testing/_internal/common_utils.py ++++ b/torch/testing/_internal/common_utils.py +@@ -737,14 +737,16 @@ def run_tests(argv=UNITTEST_ARGS): + failed |= wait_for_process(p) != 0 + assert not failed, "Some test shards have failed" + elif USE_PYTEST: ++ pytest_args = argv + if TEST_SAVE_XML: + test_report_path = get_report_path(pytest=True) + print(f'Test results will be stored in {test_report_path}') ++ pytest_args = pytest_args + [f'--junit-xml-reruns={test_report_path}'] + + import pytest + os.environ["NO_COLOR"] = "1" + os.environ["USING_PYTEST"] = "1" +- exit_code = pytest.main(args=argv + [f'--junit-xml-reruns={test_report_path}'] if TEST_SAVE_XML else []) ++ exit_code = pytest.main(args=pytest_args) + del os.environ["USING_PYTEST"] + if TEST_SAVE_XML: + sanitize_pytest_xml(test_report_path) From e5feed6cada8db53dca323397e265149ecd4a85c Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Fri, 10 Feb 2023 15:34:34 +0100 Subject: [PATCH 6459/9987] adding easyconfigs: SeqKit-2.3.1.eb --- .../easyconfigs/s/SeqKit/SeqKit-2.3.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeqKit/SeqKit-2.3.1.eb diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-2.3.1.eb b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.3.1.eb new file mode 100644 index 00000000000..dd3d71b2afb --- /dev/null +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-2.3.1.eb @@ -0,0 +1,26 @@ +easyblock = 'GoPackage' + +name = 'SeqKit' +version = '2.3.1' + +homepage = 'https://bioinf.shenwei.me/seqkit/' +description = """SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/shenwei356/seqkit/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['814930772645a1c5f491a0a0f0498d967b6caa512f137e10bc0a1925f28f863b'] + +builddependencies = [ + ('Go', '1.17.6'), +] + +installopts = './%(namelower)s' + +sanity_check_commands = [ + "seqkit version", + "seqkit genautocomplete" +] + +moduleclass = 'bio' From abfe1ab85f9f94322f628416ab3de899bea1e609 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 10 Feb 2023 15:40:31 +0000 Subject: [PATCH 6460/9987] adding easyconfigs: panaroo-1.3.2-foss-2021b.eb, prokka-1.14.5-gompi-2021b.eb, Bio-SearchIO-hmmer-1.7.3-GCC-11.2.0.eb --- .../Bio-SearchIO-hmmer-1.7.3-GCC-11.2.0.eb | 28 ++++++++ .../p/panaroo/panaroo-1.3.2-foss-2021b.eb | 68 +++++++++++++++++++ .../p/prokka/prokka-1.14.5-gompi-2021b.eb | 50 ++++++++++++++ 3 files changed, 146 insertions(+) create mode 100755 easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.2.0.eb create mode 100755 easybuild/easyconfigs/p/panaroo/panaroo-1.3.2-foss-2021b.eb create mode 100755 easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021b.eb diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.2.0.eb new file mode 100755 index 00000000000..89b75450d94 --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.34.0'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/panaroo/panaroo-1.3.2-foss-2021b.eb b/easybuild/easyconfigs/p/panaroo/panaroo-1.3.2-foss-2021b.eb new file mode 100755 index 00000000000..d7b9f1bdbbb --- /dev/null +++ b/easybuild/easyconfigs/p/panaroo/panaroo-1.3.2-foss-2021b.eb @@ -0,0 +1,68 @@ +# Author: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'panaroo' +version = '1.3.2' + +homepage = 'https://gtonkinhill.github.io/panaroo/' +description = "A pangenome analysis pipeline." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('CD-HIT', '4.8.1'), + ('PRANK', '170427'), + ('Biopython', '1.79'), + ('SciPy-bundle', '2021.10'), + ('networkx', '2.6.3'), + ('edlib', '1.3.9'), + ('tqdm', '4.62.3'), + ('matplotlib', '3.4.3'), + ('scikit-learn', '1.0.1'), + ('plotly.py', '5.4.0'), + ('DendroPy', '4.5.2'), + ('pyfaidx', '0.7.0'), + ('prokka', '1.14.5'), + ('python-igraph', '0.9.8') +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('argcomplete', '2.0.0', { + 'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'], + }), + ('argh', '0.27.2', { + 'checksums': ['00c9027f6f461bcf24afe599a281bbda5cbd5dee4b6705befbea293a4ca7d221'], + }), + ('peewee', '3.15.4', { + 'checksums': ['2581520c8dfbacd9d580c2719ae259f0637a9e46eda47dfc0ce01864c6366205'], + }), + ('taxadb', '0.12.1', { + 'checksums': ['eca577cd0f4ff2f26c7d8f68d7f5a0d2f7a2f73e623139ded2493e429b23cecd'], + }), + ('biocode', '0.10.0', { + 'preinstallopts': 'sed -i "s/python-igraph/igraph/" setup.py &&', + 'checksums': ['ab48e0ea92f52c7fe48c6c947d4d5aa43437f16cd42a804546c71ef0e5ba2265'], + }), + ('gffutils', '0.11.1', { + 'checksums': ['ca7bf814d600b389bb2d5c403dd279755118cb1476c19c6f7aecb8c51a84263c'], + }), + ('intbitset', '3.0.2', { + 'checksums': ['a300b2d5a4989857ff1d0c3971624766a89a751e315aa080c07865031ae637a7'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/gtonkinhill/panaroo/archive/'], + 'checksums': ['290580ce094d9f790fe992c13dddd10ed6c33b389a50c434851ce2d04e0f34db'], + }), +] + +sanity_check_commands = [ + "panaroo --version" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021b.eb new file mode 100755 index 00000000000..9ce8c18ac83 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2021b.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.12.0'), + ('Java', '11', '', SYSTEM), + ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20210722'), + ('tbl2asn', '20220427', '-linux64', SYSTEM), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' From 2225a4cf4cc4334ac3b54770d4c01157670fa717 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Fri, 10 Feb 2023 17:06:59 +0100 Subject: [PATCH 6461/9987] Resolve empty difference file... --- .../j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb old mode 100644 new mode 100755 From d75425901d4bd11859c278e628085fb0e127e659 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 10 Feb 2023 17:07:43 +0100 Subject: [PATCH 6462/9987] Revert "Merge pull request #16364 from boegel/20221005200825_new_pr_sympy1111" This reverts commit defe796ee98685efe744d0086eac6563bc525f6c, reversing changes made to c41a9889a893f5975387ee81cfd4412f6a0f37f4. --- .../s/sympy/sympy-1.11.1-foss-2022a.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb deleted file mode 100644 index 9e54ecf5751..00000000000 --- a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'sympy' -version = '1.11.1' - -homepage = 'https://sympy.org/' -description = """SymPy is a Python library for symbolic mathematics. It aims to - become a full-featured computer algebra system (CAS) while keeping the code as - simple as possible in order to be comprehensible and easily extensible. SymPy - is written entirely in Python and does not require any external libraries.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -sources = [SOURCE_TAR_GZ] -checksums = ['e32380dce63cb7c0108ed525570092fd45168bdae2faa17e528221ef72e88658'] - -dependencies = [ - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('gmpy2', '2.1.2'), -] - -download_dep_fail = True -use_pip = True - -runtest = 'python setup.py test' - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/isympy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], -} - -sanity_check_commands = ["isympy --help"] - -moduleclass = 'math' From 89e7544a5d56444bdd9e21f39b75e8a4f5e08f69 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 10 Feb 2023 17:16:33 +0100 Subject: [PATCH 6463/9987] Set of easy configurations for nanomax analysis utilities --- .../f/FabIO/FabIO-0.14.0-foss-2021b.eb | 26 ++++++++++++ ...nanomax-analysis-utils-0.4.4-foss-2021b.eb | 27 ++++++++++++ .../p/pyFAI/pyFAI-0.21.3-foss-2021b.eb | 31 ++++++++++++++ .../p/pymca/pymca-5.7.6-foss-2021b.eb | 39 ++++++++++++++++++ .../q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb | 26 ++++++++++++ .../Qtconsole-5.3.2-GCCcore-11.2.0.eb | 29 +++++++++++++ .../s/silx/silx-1.0.0-foss-2021b.eb | 41 +++++++++++++++++++ 7 files changed, 219 insertions(+) create mode 100644 easybuild/easyconfigs/f/FabIO/FabIO-0.14.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/pyFAI/pyFAI-0.21.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/pymca/pymca-5.7.6-foss-2021b.eb create mode 100644 easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/s/silx/silx-1.0.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/f/FabIO/FabIO-0.14.0-foss-2021b.eb b/easybuild/easyconfigs/f/FabIO/FabIO-0.14.0-foss-2021b.eb new file mode 100644 index 00000000000..289ac781efe --- /dev/null +++ b/easybuild/easyconfigs/f/FabIO/FabIO-0.14.0-foss-2021b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'FabIO' +version = '0.14.0' + +homepage = 'http://www.silx.org' +description = """FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. +FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), +for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers +(as a python dictionary) and datasets (as a numpy ndarray of integers or floats).""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['72ab0cb7247ec97dc552447112a54cd77b5fbe6f5ede8fc9b070e4e1c13cf01e'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.4-foss-2021b.eb b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.4-foss-2021b.eb new file mode 100644 index 00000000000..bd3f4f3f540 --- /dev/null +++ b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4.4-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'nanomax-analysis-utils' +version = '0.4.4' + +github_account = 'maxiv-science' +homepage = "https://github.com/%(github_account)s/nanomax-analysis-utils" +description = """A set of tools for handling and analysing data at the NanoMAX beamline.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('silx', '1.0.0'), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6b1d1812114af95ebbe7559ae456f79dbe757db6a502810d10a2193e1e5ef668'] + +options = {'modulename': 'nmutils'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyFAI/pyFAI-0.21.3-foss-2021b.eb b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.21.3-foss-2021b.eb new file mode 100644 index 00000000000..a39091f0bc3 --- /dev/null +++ b/easybuild/easyconfigs/p/pyFAI/pyFAI-0.21.3-foss-2021b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pyFAI' +version = '0.21.3' + +github_account = 'silx-kit' +homepage = "https://github.com/%(github_account)s/pyFAI" +description = """Python implementation of fast azimuthal integration.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('silx', '1.0.0'), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3524dee3c5eaa9415c125b08f5a4e1ed9c08ea51d657a5c4a7a74fd0eedf7764'] + +options = {'modulename': 'pyFAI'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +modextravars = { + 'PYFAI_OPENCL': '0', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pymca/pymca-5.7.6-foss-2021b.eb b/easybuild/easyconfigs/p/pymca/pymca-5.7.6-foss-2021b.eb new file mode 100644 index 00000000000..a0106dcb5ea --- /dev/null +++ b/easybuild/easyconfigs/p/pymca/pymca-5.7.6-foss-2021b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'pymca' +version = '5.7.6' + +github_account = 'vasole' +homepage = "https://github.com/%(github_account)s/pymca" +description = """The PyMca X-Ray Fluorescence Toolkit, including PyMca5 and fisx.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), + ('matplotlib', '3.4.3'), + ('PyQt5', '5.15.4'), + ('silx', '1.0.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = { + 'source_urls': [GITHUB_SOURCE], + 'sources': ['v%(version)s.tar.gz'], +} + +exts_list = [ + ('fisx', '1.2.0', { + 'checksums': ['868642045725552126d43331cdec7d7a6a85251d54011b4a0360fc90b02041e4'], + }), + (name, version, { + 'checksums': ['50f61b7cf940171e33f0c30e33a7c0808eae301ad851dcf57984722a33680882'], + 'modulename': 'PyMca5', + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..31aea925c34 --- /dev/null +++ b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'QtPy' +version = '2.2.1' + +homepage = "https://github.com/spyder-ide/qtpy" +description = """QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. +It provides support for PyQt5, PyQt4, PySide2 and PySide.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7d5231133b772e40b4ee514b6673aca558331e4b88ca038b26c9e16c5c95524f'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('PyQt5', '5.15.4') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..4a71bd63703 --- /dev/null +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Qtconsole' +version = '5.3.2' + +homepage = 'https://jupyter.org/' +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a terminal, +but provides a number of enhancements only possible in a GUI, +such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8eadf012e83ab018295803c247c6ab7eacd3d5ab1e1d88a0f37fdcfdab9295a3'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('IPython', '7.26.0'), + ('QtPy', '2.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/silx/silx-1.0.0-foss-2021b.eb b/easybuild/easyconfigs/s/silx/silx-1.0.0-foss-2021b.eb new file mode 100644 index 00000000000..97bd26ccbdc --- /dev/null +++ b/easybuild/easyconfigs/s/silx/silx-1.0.0-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'silx' +version = '1.0.0' + +homepage = "http://www.silx.org/" +description = """The silx project provides a collection of Python packages to support the +development of data assessment, reduction and analysis applications at synchrotron radiation facilities.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), + ('PyOpenGL', '3.1.6'), + ('matplotlib', '3.4.3'), + ('Mako', '1.1.4'), + ('Pillow', '8.3.2'), + ('FabIO', '0.14.0'), + ('Qtconsole', '5.3.2'), + ('PyOpenCL', '2021.2.13'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('hdf5plugin', '3.2.0', { + 'checksums': ['8900ab06df2a20f88c9c56ecf45a99655e08ba4d730706f8798b4ea2158b291a'], + }), + (name, version, { + 'checksums': ['1cf910f6e8097cb842e687bb81e1286b5cfc9e0213edef99a614b8b7dc5bf714'], + }), +] + +modextrapaths = { + 'HDF5_PLUGIN_PATH': 'lib/python%(pyshortver)s/site-packages/hdf5plugin/plugins', +} + +moduleclass = 'vis' From 4362fad5d4edfc6995372bad017a71e06158efad Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 10 Feb 2023 16:27:49 +0000 Subject: [PATCH 6464/9987] remove commented out line and delete unused patch for TALON --- .../t/TALON/TALON-5.0-foss-2020b.eb | 1 - .../t/TALON/TALON-5.0_less_strict_deps.patch | 21 ------------------- 2 files changed, 22 deletions(-) mode change 100644 => 100755 easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb delete mode 100644 easybuild/easyconfigs/t/TALON/TALON-5.0_less_strict_deps.patch diff --git a/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb b/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb old mode 100644 new mode 100755 index 595fe319580..27cae837eed --- a/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TALON/TALON-5.0-foss-2020b.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/mortazavilab/%(name)s/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] -# patches = ['TALON-%(version)s_less_strict_deps.patch'] checksums = [ 'aeb1c1f46a4c757a8bb866b9a4446186f0f280e9391933a040de9dad30453649', # v5.0.tar.gz ] diff --git a/easybuild/easyconfigs/t/TALON/TALON-5.0_less_strict_deps.patch b/easybuild/easyconfigs/t/TALON/TALON-5.0_less_strict_deps.patch deleted file mode 100644 index ae167de7749..00000000000 --- a/easybuild/easyconfigs/t/TALON/TALON-5.0_less_strict_deps.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -ruN TALON-5.0/requirements.txt TALON-5.0_edit/requirements.txt ---- TALON-5.0/requirements.txt 2020-03-20 05:13:53.000000000 +0100 -+++ TALON-5.0_edit/requirements.txt 2021-05-26 14:36:01.257975762 +0200 -@@ -1,4 +1,4 @@ - pandas - pyfaidx --pysam==0.15.4 -+pysam>=0.15.4 - pybedtools -diff -ruN TALON-5.0/setup.py TALON-5.0_edit/setup.py ---- TALON-5.0/setup.py 2020-03-20 05:13:53.000000000 +0100 -+++ TALON-5.0_edit/setup.py 2021-05-26 14:36:06.873983709 +0200 -@@ -49,7 +49,7 @@ - python_requires=">=3.6", - install_requires=[ - "pandas", -- "pysam==0.15.4", -+ "pysam>=0.15.4", - "pybedtools", - "pyfaidx" - ], From 0edb086839e31e3205e2c0f8699bac4121ac3df4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Feb 2023 17:29:01 +0100 Subject: [PATCH 6465/9987] Skip distributions/test_constraints --- .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb index 888bdda4b4f..c77bc6a7b31 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb @@ -136,6 +136,8 @@ excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. 'distributed/test_distributed_spawn', + # Broken on CUDA 11.5+(?): https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', # Those 2 abort on some machines. Skip for now 'distributed/fsdp/test_fsdp_input', 'distributed/fsdp/test_fsdp_mixed_precision', From fe211ae439e59ac416db72ba0601af11b16dac40 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 10 Feb 2023 17:31:56 +0100 Subject: [PATCH 6466/9987] Create sympy-1.11.1-foss-2022a.eb restore of sympy-1.11.1-foss-2022a.eb --- .../s/sympy/sympy-1.11.1-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb new file mode 100644 index 00000000000..9e54ecf5751 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.11.1' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e32380dce63cb7c0108ed525570092fd45168bdae2faa17e528221ef72e88658'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('gmpy2', '2.1.2'), +] + +download_dep_fail = True +use_pip = True + +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +sanity_check_commands = ["isympy --help"] + +moduleclass = 'math' From 1cb582e731e66b6dbf44654af71d6a797b298427 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 10 Feb 2023 17:32:04 +0100 Subject: [PATCH 6467/9987] Enable download_dep_fail --- .../pytest-rerunfailures-11.1-GCCcore-11.3.0.eb | 4 ++-- .../p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb index 3dbe1d1df4a..1a77cf37d10 100644 --- a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb @@ -12,10 +12,10 @@ builddependencies = [('binutils', '2.38')] dependencies = [('Python', '3.10.4')] use_pip = True +sanity_pip_check = True +download_dep_fail = False sources = [SOURCE_TAR_GZ] checksums = ['bc6ad13614c976b04558c3a7bcc393a7e09686fb86b6ae73f827b78326c09f75'] -sanity_pip_check = True - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb index 1ea16f83536..11746d4cf6d 100644 --- a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb @@ -19,10 +19,10 @@ builddependencies = [('binutils', '2.38')] dependencies = [('Python', '3.10.4')] use_pip = True +sanity_pip_check = True +download_dep_fail = False sources = [SOURCE_TAR_GZ] checksums = ['b86a967fbfd1c8e50295095ccda031b7e890862ee06531d5142844f4c1d1cd67'] -sanity_pip_check = True - moduleclass = 'tools' From 300b7064d0fba24c2344c2cebb27b619efb0592c Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 10 Feb 2023 17:38:24 +0100 Subject: [PATCH 6468/9987] Restore SlamDunk-0.4.3-foss-2021b.eb --- .../s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb new file mode 100644 index 00000000000..83ec0ecee9c --- /dev/null +++ b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb @@ -0,0 +1,34 @@ + +# easybuild easyconfig +# +# John Dey Fred Hutchinson Cancer Center +# +easyblock = 'PythonBundle' + +name = 'slamdunk' +version = '0.4.3' + +homepage = 'https://t-neumann.github.io/slamdunk/' +description = """SlamDunk is a novel, fully automated software tool for automated, robust, scalable + and reproducible SLAMseq data analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('HTSlib', '1.14'), + ('Biopython', '1.79'), # includes ScyPy-bundle + ('Pysam', '0.17.0'), + ('pybedtools', '0.8.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['8475d4cadad3defda6b11de405fc59de917a6e57468f709a1e28b8a0627f2ff5'], + }), +] + +moduleclass = 'bio' From 753297d7b9d466490047a8a5d8fa96c3c8cd96ad Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 10 Feb 2023 17:45:19 +0100 Subject: [PATCH 6469/9987] Update SlamDunk-0.4.3-foss-2021b.eb --- .../s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb | 39 ++++++++++--------- 1 file changed, 20 insertions(+), 19 deletions(-) diff --git a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb index 83ec0ecee9c..8bcc3df3072 100644 --- a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb @@ -1,34 +1,35 @@ +easyblock = 'PythonPackage' -# easybuild easyconfig -# -# John Dey Fred Hutchinson Cancer Center -# -easyblock = 'PythonBundle' - -name = 'slamdunk' +name = 'SlamDunk' version = '0.4.3' -homepage = 'https://t-neumann.github.io/slamdunk/' -description = """SlamDunk is a novel, fully automated software tool for automated, robust, scalable - and reproducible SLAMseq data analysis.""" +homepage = 'https://t-neumann.github.io/slamdunk' +description = """SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible +SLAMseq data analysis.""" toolchain = {'name': 'foss', 'version': '2021b'} +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8475d4cadad3defda6b11de405fc59de917a6e57468f709a1e28b8a0627f2ff5'] + dependencies = [ ('Python', '3.9.6'), - ('HTSlib', '1.14'), - ('Biopython', '1.79'), # includes ScyPy-bundle - ('Pysam', '0.17.0'), + ('SciPy-bundle', '2021.10'), ('pybedtools', '0.8.2'), + ('Pysam', '0.17.0'), + ('Biopython', '1.79'), ] +download_dep_fail = True use_pip = True -sanity_pip_check = True -exts_list = [ - (name, version, { - 'checksums': ['8475d4cadad3defda6b11de405fc59de917a6e57468f709a1e28b8a0627f2ff5'], - }), -] +sanity_check_paths = { + 'files': ['bin/slamdunk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["slamdunk --help"] + +sanity_pip_check = True moduleclass = 'bio' From 8711071fed99f7558cd97fa6557e4422288e3d53 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 10 Feb 2023 17:48:31 +0100 Subject: [PATCH 6470/9987] Update SlamDunk-0.4.3-foss-2021b.eb --- easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb index 8bcc3df3072..996aeca133c 100644 --- a/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SlamDunk/SlamDunk-0.4.3-foss-2021b.eb @@ -18,6 +18,10 @@ dependencies = [ ('pybedtools', '0.8.2'), ('Pysam', '0.17.0'), ('Biopython', '1.79'), + ('SAMtools', '1.14'), + ('VarScan', '2.4.4', '-Java-11', SYSTEM), + ('R', '4.1.2'), + ('NextGenMap', '0.5.5'), ] download_dep_fail = True From 8c6649c84e5aa23e71381a5ab965c0ed8dc11b14 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 10 Feb 2023 17:55:25 +0100 Subject: [PATCH 6471/9987] Update QtPy-2.2.1-GCCcore-11.2.0.eb resolving conflict --- easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb index 31aea925c34..a041d46a2ae 100644 --- a/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb @@ -4,7 +4,8 @@ name = 'QtPy' version = '2.2.1' homepage = "https://github.com/spyder-ide/qtpy" -description = """QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. +description = """description = """QtPy is a small abstraction layer that lets you write applications using a +single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} From 57c1f1d27b39678200061505dc73935e54cc093b Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 10 Feb 2023 17:56:48 +0100 Subject: [PATCH 6472/9987] Update QtPy-2.2.1-GCCcore-11.2.0.eb --- easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb index a041d46a2ae..deb1b3231ed 100644 --- a/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb @@ -4,7 +4,7 @@ name = 'QtPy' version = '2.2.1' homepage = "https://github.com/spyder-ide/qtpy" -description = """description = """QtPy is a small abstraction layer that lets you write applications using a +description = """QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide.""" From b63173b3cd337e77f73d2bfec12ea44cc294fecb Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 10 Feb 2023 17:58:26 +0100 Subject: [PATCH 6473/9987] Update Qtconsole-5.3.2-GCCcore-11.2.0.eb conflict resolution --- .../q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb index 4a71bd63703..cd750a04be5 100644 --- a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb @@ -4,10 +4,12 @@ name = 'Qtconsole' version = '5.3.2' homepage = 'https://jupyter.org/' -description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. -The Qtconsole is a very lightweight application that largely feels like a terminal, -but provides a number of enhancements only possible in a GUI, -such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more.""" +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media +output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a +terminal, but provides a number of enhancements only possible in a GUI, such as +inline figures, proper multiline editing with syntax highlighting, graphical +calltips, and more.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} From 124f11a16df9494e1f7aa88051ee21ba6951e88c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 10 Feb 2023 18:35:53 +0000 Subject: [PATCH 6474/9987] Remove duplicate slamdunk in lowercase --- .../s/slamdunk/slamdunk-0.4.3-foss-2021b.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb deleted file mode 100644 index 83ec0ecee9c..00000000000 --- a/easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb +++ /dev/null @@ -1,34 +0,0 @@ - -# easybuild easyconfig -# -# John Dey Fred Hutchinson Cancer Center -# -easyblock = 'PythonBundle' - -name = 'slamdunk' -version = '0.4.3' - -homepage = 'https://t-neumann.github.io/slamdunk/' -description = """SlamDunk is a novel, fully automated software tool for automated, robust, scalable - and reproducible SLAMseq data analysis.""" - -toolchain = {'name': 'foss', 'version': '2021b'} - -dependencies = [ - ('Python', '3.9.6'), - ('HTSlib', '1.14'), - ('Biopython', '1.79'), # includes ScyPy-bundle - ('Pysam', '0.17.0'), - ('pybedtools', '0.8.2'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - (name, version, { - 'checksums': ['8475d4cadad3defda6b11de405fc59de917a6e57468f709a1e28b8a0627f2ff5'], - }), -] - -moduleclass = 'bio' From d5c1086c39704fc56573b3e7c8a04783b20bd555 Mon Sep 17 00:00:00 2001 From: satishk Date: Sat, 11 Feb 2023 00:54:39 +0100 Subject: [PATCH 6475/9987] adding easyconfigs: xtb-6.5.1-foss-2022a.eb --- .../easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb b/easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb new file mode 100644 index 00000000000..d3c00f5cdc7 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'MesonNinja' + +name = 'xtb' +version = '6.5.1' + +homepage = 'https://xtb-docs.readthedocs.io' +description = """ xtb - An extended tight-binding semi-empirical program package. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['8e5840469f9ef2c01ad5cb620481310ace62a7563c5d43375eb3d36463fc3add'] + +github_account = 'grimme-lab' +builddependencies = [ + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +configopts = "-Dla_backend='custom' " +configopts += "-Dcustom_libraries='flexiblas' " +configopts += "--buildtype release " + +runtest = 'meson' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' # Ensure test don't timeout + +sanity_check_paths = { + 'files': ['bin/xtb', 'include/xtb.h'] + ['lib/libxtb.%s' % e for e in ('a', SHLIB_EXT)], + 'dirs': ['share'], +} + +sanity_check_commands = ["xtb --help"] + +modextravars = { + 'XTBHOME': '%(installdir)s', + 'XTBPATH': '%(installdir)s', +} + +moduleclass = 'chem' From 6124d4caf74f2d2a9f1a936586528d900e5d7324 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 11 Feb 2023 09:38:05 +0000 Subject: [PATCH 6476/9987] more patches --- .../p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 9 +++++ ...h-1.13.1_increase-tolerance-test_ops.patch | 21 +++++++++++ ...Torch-1.13.1_install-vsx-vec-headers.patch | 35 +++++++++++++++++++ ...yTorch-1.13.1_skip-failing-grad-test.patch | 25 +++++++++++++ 4 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_install-vsx-vec-headers.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-failing-grad-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index c3837e6e707..8a737d028c0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -27,6 +27,9 @@ patches = [ 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', 'PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.13.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.13.1_install-vsx-vec-headers.patch', + 'PyTorch-1.13.1_skip-failing-grad-test.patch', ] checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, @@ -55,6 +58,12 @@ checksums = [ 'be83ff61fe2dedab6d49c232936d5622df81ab49154264490021c6c828e53315'}, {'PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch': '92cd48ef6d01aa7e07ccce1dcaf40bc3fb0f220c4aa4fea15f3e05fb42e37909'}, + {'PyTorch-1.13.1_increase-tolerance-test_ops.patch': + 'd53e98bf0da7788b68042dcc31bc5708dae962fde3f110cc827eb807a5d08e49'}, + {'PyTorch-1.13.1_install-vsx-vec-headers.patch': + '7b678f54bb947afd4767f5877ac424b4b94ce5db609ea20f5a869ccf4027035f'}, + {'PyTorch-1.13.1_skip-failing-grad-test.patch': + '6681200f9509893cb9231b5c93ac9bc5e6d9d9ae4febefca52e7cbc843ba8f51'} ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch new file mode 100644 index 00000000000..fb28aadbefa --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch @@ -0,0 +1,21 @@ +`test_out` may fail due to slightly different values caused by different order of matrizes in SGEMM: + +> Mismatched elements: 1 / 50 (2.0%) +> Greatest absolute difference: 1.430511474609375e-05 at index (4, 5) (up to 1e-05 allowed) +> Greatest relative difference: 4.65393206065873e-06 at index (4, 5) (up to 1.3e-06 allowed) + +Author: Alexander Grund (TU Dresden) +Updated for PyTorch 1.13.1: Simon Branford (University of Birmingham) + +--- a/test/test_ops.py ++++ b/test/test_ops.py +@@ -545,6 +545,9 @@ + else list(supported_dtypes)[0] + ) + ++ if dtype is torch.float32: ++ self.precision, self.rel_tol = (1.5e-05, 1e-05) ++ + samples = op.sample_inputs(device, dtype) + for sample in samples: + # calls it normally to get the expected result diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_install-vsx-vec-headers.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_install-vsx-vec-headers.patch new file mode 100644 index 00000000000..1f6150a5cb0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_install-vsx-vec-headers.patch @@ -0,0 +1,35 @@ +Add missing headers to the installation which fixes e.g. test_cpp_extensions_aot_ninja +See https://github.com/pytorch/pytorch/pull/85547 + +Author: Alexander Grund (TU Dresden) +Updated for PyTorch 1.13.1: Simon Branford (University of Birmingham) + +--- a/aten/src/ATen/CMakeLists.txt ++++ b/aten/src/ATen/CMakeLists.txt +@@ -56,7 +56,7 @@ + EXCLUDE(ATen_CORE_TEST_SRCS "${ATen_CORE_TEST_SRCS}" ${ATen_CORE_EXCLUDED_TEST_SRCS}) + endif() + +-file(GLOB base_h "*.h" "detail/*.h" "cpu/*.h" "cpu/vec/vec512/*.h" "cpu/vec/vec256/*.h" "cpu/vec/*.h" "quantized/*.h" "functorch/*.h") ++file(GLOB base_h "*.h" "detail/*.h" "cpu/*.h" "cpu/vec/vec512/*.h" "cpu/vec/vec256/*.h" "cpu/vec/vec256/vsx/*.h" "cpu/vec/*.h" "quantized/*.h" "functorch/*.h") + file(GLOB base_cpp "*.cpp" "detail/*.cpp" "cpu/*.cpp" "functorch/*.cpp") + file(GLOB cuda_h "cuda/*.h" "cuda/detail/*.h" "cuda/*.cuh" "cuda/detail/*.cuh") + file(GLOB cuda_cpp "cuda/*.cpp" "cuda/detail/*.cpp") +--- a/setup.py ++++ b/setup.py +@@ -1031,6 +1031,7 @@ + 'include/ATen/*.h', + 'include/ATen/cpu/*.h', + 'include/ATen/cpu/vec/vec256/*.h', ++ 'include/ATen/cpu/vec/vec256/vsx/*.h', + 'include/ATen/cpu/vec/vec512/*.h', + 'include/ATen/cpu/vec/*.h', + 'include/ATen/core/*.h', +@@ -1138,6 +1139,7 @@ + 'include/THH/*.cuh', + 'include/THH/*.h*', + 'include/THH/generic/*.h', ++ 'include/sleef.h', + 'share/cmake/ATen/*.cmake', + 'share/cmake/Caffe2/*.cmake', + 'share/cmake/Caffe2/public/*.cmake', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-failing-grad-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-failing-grad-test.patch new file mode 100644 index 00000000000..13ab1717e00 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-failing-grad-test.patch @@ -0,0 +1,25 @@ +Skip test_forward_mode_AD_nn_functional_max_unpool2d_cpu_float64 & test_forward_mode_AD_nn_functional_max_unpool3d_cpu_float64 +which may unexpectably succeed. + +Author: Simon Branford (University of Birmingham) + +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -11574,7 +11574,7 @@ + # and if there are several indices pointing to the same memory, + # gradcheck is oblivious about that and cannot perturb them all at once + # (see sample_inputs_max_unpool_grad to find out more). +- DecorateInfo(unittest.expectedFailure, 'TestGradients', 'test_forward_mode_AD'), ++ DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_forward_mode_AD'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad'), + DecorateInfo(unittest.skip("Skipped!"), 'TestCompositeCompliance', 'test_forward_ad'), +@@ -11611,7 +11611,7 @@ + # and if there are several indices pointing to the same memory, + # gradcheck is oblivious about that and cannot perturb them all at once + # (see sample_inputs_max_unpool_grad to find out more). +- DecorateInfo(unittest.expectedFailure, 'TestGradients', 'test_forward_mode_AD'), ++ DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_forward_mode_AD'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad'), + DecorateInfo(unittest.expectedFailure, 'TestCompositeCompliance', 'test_forward_ad'), From c2bea35db1be8e545a6d0d2ec98111ce93bfa3fc Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 11 Feb 2023 13:50:41 +0000 Subject: [PATCH 6477/9987] Add case-insenitive name clash test --- test/easyconfigs/easyconfigs.py | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 56ecd05bbc2..da2b558fae2 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -926,6 +926,31 @@ def test_easyconfig_locations(self): if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + def test_easyconfig_name_clashes(self): + """Make sure there is not a name clash when all names are lowercase""" + topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) + names = defaultdict(list) + for (dirpath, _, _) in os.walk(topdir): + # ignore git/svn dirs & archived easyconfigs + if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: + continue + dirpath_split = dirpath.split(os.sep) + if len(dirpath_split) == 4: + name = dirpath_split[3] + names[name.lower()].append(name) + + # Allow these historical case-insensitive name clashes for now. DO NOT ADD TO THIS! + temp_whitelist = [] # 'arb', 'bamm', 'blasr', 'charmm', 'check', 'graphviz', 'libpsml', 'magma', 'nanofilt', 'ncl'] + duplicates = {} + for name in names: + if name in temp_whitelist: + continue + if len(names[name]) > 1: + duplicates[name] = names[name] + + if duplicates: + self.assertTrue(False, "EasyConfigs with case-insensitive name clash: %s" % duplicates) + @skip_if_not_pr_to_non_main_branch() def test_pr_sha256_checksums(self): """Make sure changed easyconfigs have SHA256 checksums in place.""" From f11ae776feefba854cb9c977f6a1102c5d3cfc99 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 11 Feb 2023 13:53:08 +0000 Subject: [PATCH 6478/9987] remember the import --- test/easyconfigs/easyconfigs.py | 1 + 1 file changed, 1 insertion(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index da2b558fae2..20b34171d92 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -33,6 +33,7 @@ import shutil import sys import tempfile +from collections import defaultdict from distutils.version import LooseVersion from unittest import TestCase, TestLoader, main, skip From 8684e358c7c147c3eb8e9922645be5cac2e6f562 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 11 Feb 2023 14:40:04 +0000 Subject: [PATCH 6479/9987] topdir is an absolute path --- test/easyconfigs/easyconfigs.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 20b34171d92..1ee2ac8b5bf 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -935,9 +935,9 @@ def test_easyconfig_name_clashes(self): # ignore git/svn dirs & archived easyconfigs if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: continue - dirpath_split = dirpath.split(os.sep) - if len(dirpath_split) == 4: - name = dirpath_split[3] + dirpath_split = dirpath.replace(topdir, '').split(os.sep) + if len(dirpath_split) == 5: + name = dirpath_split[4] names[name.lower()].append(name) # Allow these historical case-insensitive name clashes for now. DO NOT ADD TO THIS! From 3151f0a54bba8ab86f8c9ba2c25da6f732812edd Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 11 Feb 2023 15:46:11 +0100 Subject: [PATCH 6480/9987] rollback disabling test for PR#11149 --- test/easyconfigs/easyconfigs.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 76c635c78db..56ecd05bbc2 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -927,7 +927,7 @@ def test_easyconfig_locations(self): self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) @skip_if_not_pr_to_non_main_branch() - def DISABLED_test_pr_sha256_checksums(self): + def test_pr_sha256_checksums(self): """Make sure changed easyconfigs have SHA256 checksums in place.""" # list of software for which checksums can not be required, @@ -963,7 +963,7 @@ def DISABLED_test_pr_sha256_checksums(self): self.assertTrue(len(checksum_issues) == 0, "No checksum issues:\n%s" % '\n'.join(checksum_issues)) @skip_if_not_pr_to_non_main_branch() - def DISABLED_test_pr_python_packages(self): + def test_pr_python_packages(self): """Several checks for easyconfigs that install (bundles of) Python packages.""" # These packages do not support installation with 'pip' @@ -1077,7 +1077,7 @@ def DISABLED_test_pr_python_packages(self): self.fail('\n'.join(failing_checks)) @skip_if_not_pr_to_non_main_branch() - def DISABLED_test_pr_R_packages(self): + def test_pr_R_packages(self): """Several checks for easyconfigs that install (bundles of) R packages.""" failing_checks = [] @@ -1098,7 +1098,7 @@ def DISABLED_test_pr_R_packages(self): self.assertFalse(failing_checks, '\n'.join(failing_checks)) @skip_if_not_pr_to_non_main_branch() - def DISABLED_test_pr_sanity_check_paths(self): + def test_pr_sanity_check_paths(self): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # some generic easyblocks already have a decent customised sanity_check_paths, @@ -1134,7 +1134,7 @@ def DISABLED_test_pr_sanity_check_paths(self): self.assertFalse(failing_checks, '\n'.join(failing_checks)) @skip_if_not_pr_to_non_main_branch() - def DISABLED_test_pr_https(self): + def test_pr_https(self): """Make sure https:// URL is used (if it exists) for homepage/source_urls (rather than http://).""" whitelist = [ @@ -1196,7 +1196,7 @@ def check_https_url(http_url): self.fail('\n'.join(failing_checks)) @skip_if_not_pr_to_non_main_branch() - def DISABLED_test_pr_patch_descr(self): + def test_pr_patch_descr(self): """ Check whether all patch files touched in PR have a description on top. """ From 7cee512aa9d364e1739536913da14a07f72fd460 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 11 Feb 2023 14:57:49 +0000 Subject: [PATCH 6481/9987] whitelist --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 1ee2ac8b5bf..afce357d9ac 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -941,7 +941,7 @@ def test_easyconfig_name_clashes(self): names[name.lower()].append(name) # Allow these historical case-insensitive name clashes for now. DO NOT ADD TO THIS! - temp_whitelist = [] # 'arb', 'bamm', 'blasr', 'charmm', 'check', 'graphviz', 'libpsml', 'magma', 'nanofilt', 'ncl'] + temp_whitelist = ['arb', 'bamm', 'blasr', 'charmm', 'check', 'graphviz', 'libpsml', 'magma', 'nanofilt', 'ncl'] duplicates = {} for name in names: if name in temp_whitelist: From 77588ac8ffd01cbcadad205a500a6b318f48e154 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 11 Feb 2023 16:13:56 +0100 Subject: [PATCH 6482/9987] fix order of definition of sources in xtb v6.5.1 --- easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb b/easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb index d3c00f5cdc7..7bbdecc1b28 100644 --- a/easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb +++ b/easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb @@ -8,11 +8,11 @@ description = """ xtb - An extended tight-binding semi-empirical program package toolchain = {'name': 'foss', 'version': '2022a'} +github_account = 'grimme-lab' source_urls = [GITHUB_LOWER_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] checksums = ['8e5840469f9ef2c01ad5cb620481310ace62a7563c5d43375eb3d36463fc3add'] -github_account = 'grimme-lab' builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), From fac67e8be79a5201ab07e5d270a55c6cc1e52082 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 11 Feb 2023 16:48:08 +0100 Subject: [PATCH 6483/9987] retain build dependency on pkgconfig in xtb v6.5.1 --- easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb b/easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb index 7bbdecc1b28..18c4c379b8a 100644 --- a/easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb +++ b/easybuild/easyconfigs/x/xtb/xtb-6.5.1-foss-2022a.eb @@ -16,6 +16,7 @@ checksums = ['8e5840469f9ef2c01ad5cb620481310ace62a7563c5d43375eb3d36463fc3add'] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), ] configopts = "-Dla_backend='custom' " From be3d7277d8d8c9ed2619a44c73587259b154b723 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 13 Feb 2023 09:41:50 +0100 Subject: [PATCH 6484/9987] Modextrapaths is already set by default by PythonBundle --- .../easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb index 1406f7d6fa6..aed59abf90a 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb @@ -99,8 +99,6 @@ exts_list = [ }), ] -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - sanity_check_paths = { 'files': ['bin/jupyterhub'], 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], From eca7e64da2362ad9d98afdaa3448eff4c992ed0b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 13 Feb 2023 10:03:47 +0000 Subject: [PATCH 6485/9987] adding easyconfigs: SpaceRanger-2.0.1-GCC-11.3.0.eb, bcl2fastq2-2.20.0-GCC-11.3.0.eb --- .../bcl2fastq2-2.20.0-GCC-11.3.0.eb | 64 +++++++++++++++++++ .../SpaceRanger-2.0.1-GCC-11.3.0.eb | 36 +++++++++++ 2 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..a3a55073ee2 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb @@ -0,0 +1,64 @@ +easyblock = 'CMakeMake' + +name = 'bcl2fastq2' +version = '2.20.0' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html' +description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by + Illumina sequencing systems to standard FASTQ file formats for downstream analysis.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] +sources = [{ + 'filename': '%s-v%s-tar.zip' % (name, version.replace('.', '-')), + 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz +}] +patches = [ + '%(name)s-%(version)s-fix-cmake-target-libs.patch', + # bcl2fastq2 v2.20.0 is not compatible with recent Boost versions, use bundled Boost + '%(name)s-%(version)s-find-boost.patch', +] +checksums = [ + '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3', # bcl2fastq2-v2-20-0-tar.zip + '7908c268c213a6cfeafe05afcd5d3b34098241b6ab0a62c11ea47664cd0a63c5', # bcl2fastq2-2.20.0-fix-cmake-target-libs.patch + '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1', # bcl2fastq2-2.20.0-find-boost.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('libxml2', '2.9.13'), + ('libxslt', '1.1.34'), + ('zlib', '1.2.12'), +] + +start_dir = 'src' + +# check versions of libxml2 and libxslt from EB +local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' +local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} +preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} + +# remove hardcoded compilation flags +local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' +preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx + +configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' +configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' +configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' +# Make sure CMake doesn't use any system installed Boost versions cmake-config files. +configopts += '-DBoost_NO_BOOST_CMAKE=ON ' + +sanity_check_paths = { + 'files': ['bin/bcl2fastq'], + 'dirs': ['lib'], +} + +sanity_check_commands = ["bcl2fastq --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..320606c0e44 --- /dev/null +++ b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.1-GCC-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'SpaceRanger' +version = '2.0.1' + +homepage = 'https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger' +description = """ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output +and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, +perform clustering and gene expression analysis, and place spots in spatial context on the slide image. """ + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +download_instructions = """ +Download sources from homepage, registration required +https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest +""" + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['81e011f8bb1c9beca92f008b4b1b4c1ca96d0847c274f4dbd81e74fe7e4a0024'] + +dependencies = [ + ('bcl2fastq2', '2.20.0'), +] + +allow_prepend_abs_path = True +# prepend reference databases GRCh38 and mm10 to PATH +# modextrapaths = {'PATH': '/path/to/databases/%(namelower)s-%(version)s'} + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['external', 'lib', 'mro'], +} + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From 21ef50a457d9c05f2c1c4fe30b6de9ad96ddcb56 Mon Sep 17 00:00:00 2001 From: alberta Date: Mon, 13 Feb 2023 11:23:11 +0100 Subject: [PATCH 6486/9987] correct file --- .../a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb index 0721ff3aad7..86e2b2ece4d 100644 --- a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb @@ -47,3 +47,6 @@ exts_list = [ ] use_pip = True +sanity_pip_check = True + +moduleclass = 'astro' From 53b99d9c9986ce266d5e65efdf686146885f57c9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Feb 2023 11:25:47 +0100 Subject: [PATCH 6487/9987] adding easyconfigs: SPAdes-3.15.5-GCC-11.3.0.eb --- .../s/SPAdes/SPAdes-3.15.5-GCC-11.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.5-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.5-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.5-GCC-11.3.0.eb new file mode 100644 index 00000000000..4bc38b80160 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.5-GCC-11.3.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute +# Updated by: +# Filip Kružík (INUITS) + +easyblock = 'CMakeMake' + +name = 'SPAdes' +version = '3.15.5' + +homepage = 'https://cab.spbu.ru/software/spades/' +description = "Genome assembler for single-cell and isolates data sets" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['155c3640d571f2e7b19a05031d1fd0d19bd82df785d38870fb93bd241b12bbfa'] + +builddependencies = [ + ('CMake', '3.24.3'), +] +dependencies = [ + ('Python', '3.10.4'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('libreadline', '8.1.2'), +] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', + 'spades-ionhammer', 'spades-kmercount', 'spades.py']], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s.py', '--test')] + +moduleclass = 'bio' From 3a0eebc89c9bd4966242cb4753b283f40dc260f5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 13 Feb 2023 10:26:29 +0000 Subject: [PATCH 6488/9987] Update easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb Raw escape fix Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb index a3a55073ee2..74f1da11a44 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb @@ -40,7 +40,7 @@ start_dir = 'src' # check versions of libxml2 and libxslt from EB local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' -local_sed_libver = 'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +local_sed_libver = r'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} From a7075a48face6289228afb5229ea0094a8d94369 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 13 Feb 2023 10:26:42 +0000 Subject: [PATCH 6489/9987] Update easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb Raw escape fix Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb index 74f1da11a44..494b273bc86 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb @@ -46,7 +46,7 @@ preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} # remove hardcoded compilation flags local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' -preconfigopts += 'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx +preconfigopts += r'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' From 79722e4f0f9cbea4b6e7801701da40ba858fb385 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Feb 2023 11:28:26 +0100 Subject: [PATCH 6490/9987] adding easyconfigs: MEGAHIT-1.2.9-GCCcore-11.3.0.eb --- .../m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..23927deb7b5 --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'MEGAHIT' +version = '1.2.9' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex +metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), + ('zlib', '1.2.12'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('bzip2', '1.0.8'), + ('gzip', '1.12'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(namelower)s', + 'bin/%(namelower)s_core', + 'bin/%(namelower)s_core_no_hw_accel', + 'bin/%(namelower)s_core_popcnt', + 'bin/%(namelower)s_toolkit', + ], + 'dirs': [], +} + +sanity_check_commands = [ + "megahit --version", + "megahit --test", +] + +moduleclass = 'bio' From 2b17179d9aeae628da07f3e72d4ba408496fe279 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Feb 2023 11:02:13 +0000 Subject: [PATCH 6491/9987] adding easyconfigs: motif-2.3.8-GCCcore-11.3.0.eb --- .../m/motif/motif-2.3.8-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8f4a300dbef --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.8' + +homepage = 'https://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] + +builddependencies = [ + ('Autotools', '20220317'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('binutils', '2.38'), + ('util-linux', '2.38'), +] + +dependencies = [ + ('X11', '20220504'), + ('libpng', '1.6.37'), + ('freetype', '2.12.1'), + ('libjpeg-turbo', '2.1.3'), + ('bzip2', '1.0.8'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' From 79832221753e9a86c9c58525b0914e0a067359cd Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 13 Feb 2023 13:39:56 +0100 Subject: [PATCH 6492/9987] As noted in #16424, jupyter-server-proxy doesn't really depend on JupyterLab, nor on JupyterHub, since it can be used with either of those. Thus, lowered this to IPython. --- .../easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb | 1 + .../jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb index aed59abf90a..9f427a4cb20 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb @@ -19,6 +19,7 @@ dependencies = [ ('Mako', '1.2.0'), ('configurable-http-proxy', '4.5.3'), ('OpenSSL', '1.1', '', SYSTEM), + ('jupyter-server-proxy', '3.2.2') # This is optional, but commonly used together ] use_pip = True diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb index 648b76a2e90..c27282d4f03 100644 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ dependencies = [ ('Python', '3.10.4'), - ('JupyterHub', '3.0.0'), + ('IPython', '8.5.0'), ('OpenSSL', '1.1', '', SYSTEM), ('aiohttp', '3.8.3'), ('jupyter-server', '1.21.0'), From ea625f39a4d2d0788caddc0c517770c700fd04e1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Feb 2023 13:50:10 +0100 Subject: [PATCH 6493/9987] adding easyconfigs: HISAT2-2.2.1-gompi-2022a.eb --- .../h/HISAT2/HISAT2-2.2.1-gompi-2022a.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2022a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2022a.eb new file mode 100644 index 00000000000..6ddb5b2dc0e --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2022a.eb @@ -0,0 +1,61 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +# 2.2.1 - changes from Adam Huffman +# Bumped to foss-2021b +# J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.2.1' + +homepage = 'https://daehwankimlab.github.io/hisat2' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +sources = [{ + 'source_urls': ['https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi'], + 'download_filename': 'download', + 'filename': '%(namelower)s-%(version)s-source.zip', +}] +patches = [ + 'hisat2-libname-fix.patch', +] +checksums = [ + {'hisat2-2.2.1-source.zip': '48e933330d4d8470d2b3dfe7ec3918f2e98a75f7381891e23b7df1fb4f135eb1'}, + {'hisat2-libname-fix.patch': '8aa91d1dd6455b96c10ce48827f8313b006241d815fbe6382422dbae3b610726'}, +] + +dependencies = [ + ('ncbi-vdb', '3.0.2'), + ('SRA-Toolkit', '3.0.3'), # provides NGS +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += 'USE_SRA=1 NCBI_NGS_DIR="$EBROOTSRAMINTOOLKIT" NCBI_VDB_DIR="$EBROOTNCBIMINVDB" ' +# add new libncbi-ngs from the NGS merge into SRA-Toolkit v3 +buildopts += 'SRA_LIB="-lncbi-ngs-c++ -lngs-c++ -lncbi-ngs -lncbi-vdb -ldl"' + +local_executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l', 'hisat2-repeat', 'extract_exons.py', + 'extract_splice_sites.py', 'hisat2_extract_exons.py', 'hisat2_extract_snps_haplotypes_UCSC.py', + 'hisat2_extract_snps_haplotypes_VCF.py', 'hisat2_extract_splice_sites.py', + 'hisat2_read_statistics.py', 'hisat2_simulate_reads.py'] +files_to_copy = [(local_executables, 'bin'), 'scripts', 'example'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables], + 'dirs': ['scripts', 'example'], +} + +sanity_check_commands = ["hisat2 --help"] + +moduleclass = 'bio' From fee9ba10c8742bcee4a441bb0201aa3bbf66516c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Feb 2023 14:21:10 +0100 Subject: [PATCH 6494/9987] adding easyconfigs: DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb --- .../d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb | 135 ++++++++++++++++++ .../d/DLPack/DLPack-0.3-GCC-10.3.0.eb | 26 ++++ .../d/DMLC-Core/DMLC-Core-0.5-GCC-10.3.0.eb | 38 +++++ .../nanoflann-1.4.0-GCCcore-10.3.0.eb | 38 +++++ .../Parallel-Hashmap-1.33-GCCcore-10.3.0.eb | 34 +++++ 5 files changed, 271 insertions(+) create mode 100644 easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/d/DLPack/DLPack-0.3-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/d/DMLC-Core/DMLC-Core-0.5-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/p/Parallel-Hashmap/Parallel-Hashmap-1.33-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..96e3f4b4497 --- /dev/null +++ b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,135 @@ +easyblock = 'CMakeMake' + +name = 'DGL' +version = '0.9.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.dgl.ai' +description = """DGL is an easy-to-use, high performance and scalable Python package for deep learning on graphs. +DGL is framework agnostic, meaning if a deep graph model is a component of an end-to-end application, the rest +of the logics can be implemented in any major frameworks, such as PyTorch, Apache MXNet or TensorFlow.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'dmlc' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [ + { + 'download_filename': '%(version)s.tar.gz', + 'filename': '%(namelower)s-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/KarypisLab/METIS/archive'], + 'download_filename': 'v5.1.1-DistDGL-v0.5.tar.gz', + 'filename': 'metis-5.1.1-DistDGL-v0.5.tar.gz', + 'extract_cmd': "tar -C %(namelower)s-%(version)s/third_party/METIS --strip-components=1 -xf %s", + }, + { + 'source_urls': ['https://github.com/KarypisLab/GKlib/archive'], + 'download_filename': 'METIS-v5.1.1-DistDGL-0.5.tar.gz', + 'filename': 'GKlib-METIS-v5.1.1-DistDGL-0.5.tar.gz', + 'extract_cmd': "tar -C %(namelower)s-%(version)s/third_party/METIS/GKlib --strip-components=1 -xf %s", + }, + { + 'filename': 'tensorpipe-20230206.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'tensorpipe', + 'commit': '6042f1a4cbce8eef997f11ed0012de137b317361', + 'recursive': True, + }, + 'extract_cmd': "tar -C %(namelower)s-%(version)s/third_party/tensorpipe --strip-components=1 -xf %s", + }, + # DGL really needs cub >= 1.17, CUDA 11.3 only have 1.11 + { + 'source_urls': ['https://github.com/NVIDIA/thrust/archive'], + 'download_filename': '1.17.0.tar.gz', + 'filename': 'thrust-1.17.0.tar.gz', + 'extract_cmd': "tar -C %(namelower)s-%(version)s/third_party/thrust --strip-components=1 -xf %s", + }, + { + 'source_urls': ['https://github.com/NVIDIA/cub/archive'], + 'download_filename': '1.17.0.tar.gz', + 'filename': 'cub-1.17.0.tar.gz', + 'extract_cmd': + "tar -C %(namelower)s-%(version)s/third_party/thrust/dependencies/cub --strip-components=1 -xf %s", + }, +] +patches = [ + '%(name)s-%(version)s_use_externals_instead_of_submodules.patch', +] +checksums = [ + {'dgl-0.9.1.tar.gz': '8d26ebb7ed976665bbf5bbd1792d8e6efb13a8fa16e5eb1efed75e07fb982e04'}, + {'metis-5.1.1-DistDGL-v0.5.tar.gz': 'cedf0b32d32a8496bac7eb078b2b8260fb00ddb8d50c27e4082968a01bc33331'}, + {'GKlib-METIS-v5.1.1-DistDGL-0.5.tar.gz': '52aa0d383d42360f4faa0ae9537ba2ca348eeab4db5f2dfd6343192d0ff4b833'}, + {'tensorpipe-20230206.tar.gz': 'a4246afac190ffc1bef438920cea490a9aa8dfc5983e765b420ec4408331618e'}, + {'thrust-1.17.0.tar.gz': 'b02aca5d2325e9128ed9d46785b8e72366f758b873b95001f905f22afcf31bbf'}, + {'cub-1.17.0.tar.gz': '16fd4860ae3196bc3eb08bf5754fa2a9697951ddae36dc9721e6614388893618'}, + {'DGL-0.9.1_use_externals_instead_of_submodules.patch': + '4c39420abc09d619de92ca4ee5c4472359b1f5ffe8acd898d4d665bdbeb2ce40'}, +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('googletest', '1.11.0'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('networkx', '2.6.3'), + ('tqdm', '4.61.2'), + ('DLPack', '0.3'), + ('DMLC-Core', '0.5'), + ('Parallel-Hashmap', '1.33'), + ('nanoflann', '1.4.0'), + ('libxsmm', '1.16.2'), + ('CUDA', '11.3.1', '', SYSTEM), + ('NCCL', '2.10.3', versionsuffix), + ('PyTorch', '1.12.1', versionsuffix), +] + +_copts = [ + '-DUSE_AVX=OFF', # AVX + LIBXSMM requires libxsmm tag 1.eol + '-DBUILD_CPP_TEST=ON', + '-DUSE_CUDA=ON', # Must be "ON", as opposed to "1" or so, due to bad CMake code in DGL + '-DUSE_NCCL=ON', + '-DUSE_SYSTEM_NCCL=ON', + '-DBUILD_WITH_SHARED_NCCL=ON', + '-DUSE_FP16=ON', +] +configopts = ' '.join(_copts) + +build_shared_libs = True + +runtest = 'test' + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'easyblock': 'PythonPackage', + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'runtest': True, +} + +exts_list = [ + ('dgl', version, { + 'modulename': False, + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'start_dir': 'python', + 'use_pip': False, + 'checksums': ['8d26ebb7ed976665bbf5bbd1792d8e6efb13a8fa16e5eb1efed75e07fb982e04'], + }), +] + +sanity_check_paths = { + 'files': ['lib/libdgl.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/d/DLPack/DLPack-0.3-GCC-10.3.0.eb b/easybuild/easyconfigs/d/DLPack/DLPack-0.3-GCC-10.3.0.eb new file mode 100644 index 00000000000..c487f04f841 --- /dev/null +++ b/easybuild/easyconfigs/d/DLPack/DLPack-0.3-GCC-10.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'DLPack' +version = '0.3' + +homepage = 'https://dmlc.github.io/dlpack/latest/' +description = """DLPack is a stable in-memory data structure for an ndarray +system to interact with a variety of frameworks.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'dmlc' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['703149f5b39ead42cc734c03c7c4bd581fcad1c5a3939e7a4b5bc82f54c3c32a'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['include/dlpack/dlpack.h', 'lib/cmake/dlpack/dlpackConfig.cmake'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/DMLC-Core/DMLC-Core-0.5-GCC-10.3.0.eb b/easybuild/easyconfigs/d/DMLC-Core/DMLC-Core-0.5-GCC-10.3.0.eb new file mode 100644 index 00000000000..cbae873b66e --- /dev/null +++ b/easybuild/easyconfigs/d/DMLC-Core/DMLC-Core-0.5-GCC-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'DMLC-Core' +version = '0.5' + +homepage = 'https://dmlc-core.readthedocs.io/en/latest' +description = """DMLC-Core is the backbone library to support all DMLC +projects, offers the bricks to build efficient and scalable distributed +machine learning libraries.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'dmlc' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cd97475ae1ecf561a1cb1129552f9889d52b11b3beb4c56e5345d007d5020ece'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('googletest', '1.11.0'), +] + +_copts = [ + '-DUSE_CXX14_IF_AVAILABLE=ON', + '-DGOOGLE_TEST=ON', +] +configopts = ' '.join(_copts) + +build_shared_libs = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['include/dmlc/common.h', 'lib/cmake/dmlc/dmlc-config.cmake', 'lib/libdmlc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..caaa2838a83 --- /dev/null +++ b/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'nanoflann' +version = '1.4.0' + +homepage = 'https://github.com/jlblancoc/nanoflann' +description = "nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies." + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'jlblancoc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_external_googletest.patch', +] +checksums = [ + {'v1.4.0.tar.gz': '9ce09aa7c049e28ca4e2fbeffafc8e09aca98a52624578798c8ebb723ad974bb'}, + {'nanoflann-1.4.0_use_external_googletest.patch': + '5f0b99b0558bdf76c19d52eb82d10cdcc104eb6c2fb1891e033b5c96fb47f7b9'}, +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('googletest', '1.11.0'), +] + +configopts = '-DNANOFLANN_BUILD_TESTS=ON' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['include/nanoflann.hpp', 'share/pkgconfig/nanoflann.pc'], + 'dirs': ['share/cmake/nanoflann'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Parallel-Hashmap/Parallel-Hashmap-1.33-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Parallel-Hashmap/Parallel-Hashmap-1.33-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..6ed7f3fc956 --- /dev/null +++ b/easybuild/easyconfigs/p/Parallel-Hashmap/Parallel-Hashmap-1.33-GCCcore-10.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'Parallel-Hashmap' +version = '1.33' + +homepage = 'https://github.com/greg7mdp/parallel-hashmap' +description = """Parallel Hashmap is built on a modified version of +Abseil's flat_hash_map. Parallel Hashmap has lower space requirements, +is nearly as fast as the underlying flat_hash_map, and can be used from +multiple threads with high levels of concurrency.""" + +# There is no actual library built, so it can be at GCCcore level despite being a C++ "library" +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'greg7mdp' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['f6e4d0508c4d935fa25dcbaec63fbe0d7503435797e275ec109e8a3f1462a4cd'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +configopts = '-DPHMAP_BUILD_TESTS=OFF' # The test code doesn't build + +sanity_check_paths = { + 'files': ['include/parallel_hashmap/phmap%s.h' % x for x in [ + '', '_base', '_bits', '_config', '_dump', '_fwd_decl', '_utils' + ]], + 'dirs': [], +} + +moduleclass = 'lib' From e79e1a5ef318438da0b00f2908943901c8cc15ea Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Feb 2023 14:34:20 +0100 Subject: [PATCH 6495/9987] add dependency on jupyter-server to jupyter-server-proxy --- .../jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb index 3fbf4b60e5b..883460432b6 100644 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-11.3.0.eb @@ -21,6 +21,7 @@ builddependencies = [ dependencies = [ ('Python', '3.10.4'), ('IPython', '8.5.0'), + ('jupyter-server', '1.21.0'), ('OpenSSL', '1.1', '', SYSTEM), ('aiohttp', '3.8.3'), ] From b141b91be1735f3058ed9156c063b96cbace1d36 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Feb 2023 15:36:50 +0100 Subject: [PATCH 6496/9987] add missing patches for nanoflann and DGL --- ..._use_externals_instead_of_submodules.patch | 147 ++++++++++++++++++ ...oflann-1.4.0_use_external_googletest.patch | 46 ++++++ 2 files changed, 193 insertions(+) create mode 100644 easybuild/easyconfigs/d/DGL/DGL-0.9.1_use_externals_instead_of_submodules.patch create mode 100644 easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0_use_external_googletest.patch diff --git a/easybuild/easyconfigs/d/DGL/DGL-0.9.1_use_externals_instead_of_submodules.patch b/easybuild/easyconfigs/d/DGL/DGL-0.9.1_use_externals_instead_of_submodules.patch new file mode 100644 index 00000000000..371f6170a36 --- /dev/null +++ b/easybuild/easyconfigs/d/DGL/DGL-0.9.1_use_externals_instead_of_submodules.patch @@ -0,0 +1,147 @@ +commit 58b57280a7f0f6853fb7239d8f13737437f519b5 +Author: Ake Sandgren +Date: Mon Feb 13 13:40:40 2023 +0100 + + Use external EasyBuild versions of some submodules + And make sure libxsmm links with flexiblas + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 6ff98d5e..4dae1c72 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -204,21 +204,21 @@ set_property(TARGET dgl PROPERTY CXX_STANDARD 14) + + # include directories + target_include_directories(dgl PRIVATE "include") +-target_include_directories(dgl PRIVATE "third_party/dlpack/include") +-target_include_directories(dgl PRIVATE "third_party/dmlc-core/include") +-target_include_directories(dgl PRIVATE "third_party/phmap/") ++#target_include_directories(dgl PRIVATE "third_party/dlpack/include") ++#target_include_directories(dgl PRIVATE "third_party/dmlc-core/include") ++#target_include_directories(dgl PRIVATE "third_party/phmap/") + target_include_directories(dgl PRIVATE "third_party/xbyak/") + target_include_directories(dgl PRIVATE "third_party/METIS/include/") + target_include_directories(dgl PRIVATE "tensoradapter/include") +-target_include_directories(dgl PRIVATE "third_party/nanoflann/include") +-target_include_directories(dgl PRIVATE "third_party/libxsmm/include") ++#target_include_directories(dgl PRIVATE "third_party/nanoflann/include") ++#target_include_directories(dgl PRIVATE "third_party/libxsmm/include") + + + # For serialization + if (USE_HDFS) + option(DMLC_HDFS_SHARED "dgl has to build with dynamic hdfs library" ON) + endif() +-add_subdirectory("third_party/dmlc-core") ++#add_subdirectory("third_party/dmlc-core") + list(APPEND DGL_LINKER_LIBS dmlc) + set(GOOGLE_TEST 0) # Turn off dmlc-core test + +@@ -234,17 +234,7 @@ endif(NOT MSVC) + + # Compile LIBXSMM + if((NOT MSVC) AND USE_LIBXSMM) +- if(REBUILD_LIBXSMM) +- add_custom_target(libxsmm COMMAND make realclean COMMAND make -j BLAS=0 +- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/third_party/libxsmm +- ) +- else(REBUILD_LIBXSMM) +- add_custom_target(libxsmm COMMAND make -j BLAS=0 +- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/third_party/libxsmm +- ) +- endif(REBUILD_LIBXSMM) +- add_dependencies(dgl libxsmm) +- list(APPEND DGL_LINKER_LIBS -L${CMAKE_SOURCE_DIR}/third_party/libxsmm/lib/ xsmm) ++ list(APPEND DGL_LINKER_LIBS xsmm flexiblas) + endif((NOT MSVC) AND USE_LIBXSMM) + + if(NOT MSVC) +@@ -324,15 +314,17 @@ install(TARGETS dgl DESTINATION lib${LIB_SUFFIX}) + # Testing + if(BUILD_CPP_TEST) + message(STATUS "Build with unittest") +- add_subdirectory(./third_party/googletest) ++ #add_subdirectory(./third_party/googletest) + enable_testing() + include_directories(${gtest_SOURCE_DIR}/include ${gtest_SOURCE_DIR}) + include_directories("include") +- include_directories("third_party/dlpack/include") +- include_directories("third_party/xbyak") +- include_directories("third_party/dmlc-core/include") +- include_directories("third_party/phmap") +- include_directories("third_party/libxsmm/include") ++ #include_directories("third_party/dlpack/include") ++ if (USE_AVX) ++ include_directories("third_party/xbyak") ++ endif(USE_AVX) ++ #include_directories("third_party/dmlc-core/include") ++ #include_directories("third_party/phmap") ++ #include_directories("third_party/libxsmm/include") + file(GLOB_RECURSE TEST_SRC_FILES ${PROJECT_SOURCE_DIR}/tests/cpp/*.cc) + add_executable(runUnitTests ${TEST_SRC_FILES}) + target_link_libraries(runUnitTests gtest gtest_main) +diff --git a/include/dgl/runtime/ndarray.h b/include/dgl/runtime/ndarray.h +index cbcd79d5..db2caa16 100644 +--- a/include/dgl/runtime/ndarray.h ++++ b/include/dgl/runtime/ndarray.h +@@ -14,7 +14,7 @@ + #include + + #include "c_runtime_api.h" +-#include "dlpack/dlpack.h" ++#include + #include "serializer.h" + #include "shared_mem.h" + +diff --git a/include/dgl/zerocopy_serializer.h b/include/dgl/zerocopy_serializer.h +index 6c77c4df..53d2bfa0 100644 +--- a/include/dgl/zerocopy_serializer.h ++++ b/include/dgl/zerocopy_serializer.h +@@ -19,7 +19,7 @@ + #include + #include + +-#include "dmlc/logging.h" ++#include + + namespace dgl { + +diff --git a/include/intel/cpu_support.h b/include/intel/cpu_support.h +index 14c5f5c4..7c554f0d 100644 +--- a/include/intel/cpu_support.h ++++ b/include/intel/cpu_support.h +@@ -9,7 +9,7 @@ + #include + #include + #include +-#include "dmlc/logging.h" ++#include + #include "meta_utils.h" + #include "xbyak/xbyak.h" + #include "xbyak/xbyak_util.h" +diff --git a/src/graph/serialize/heterograph_serialize.cc b/src/graph/serialize/heterograph_serialize.cc +index ce3c8d51..6f7a75dc 100644 +--- a/src/graph/serialize/heterograph_serialize.cc ++++ b/src/graph/serialize/heterograph_serialize.cc +@@ -50,7 +50,7 @@ + #include "../heterograph.h" + #include "./graph_serialize.h" + #include "./streamwithcount.h" +-#include "dmlc/memory_io.h" ++#include + + namespace dgl { + namespace serialize { +diff --git a/src/graph/serialize/zerocopy_serializer.cc b/src/graph/serialize/zerocopy_serializer.cc +index cc3f5968..5fed2b8b 100644 +--- a/src/graph/serialize/zerocopy_serializer.cc ++++ b/src/graph/serialize/zerocopy_serializer.cc +@@ -7,7 +7,7 @@ + #include + + #include "dgl/runtime/ndarray.h" +-#include "dmlc/memory_io.h" ++#include + + namespace dgl { + diff --git a/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0_use_external_googletest.patch b/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0_use_external_googletest.patch new file mode 100644 index 00000000000..04ef96f0a14 --- /dev/null +++ b/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0_use_external_googletest.patch @@ -0,0 +1,46 @@ +Use external googletest + +Åke Sandgren, 20230213 +diff --git a/CMakeLists.txt b/CMakeLists.txt +index fc84430..31ab273 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -90,6 +90,10 @@ endif() + # Tests + option(NANOFLANN_BUILD_TESTS "Build unit tests" ON) + if(NANOFLANN_BUILD_TESTS) ++ find_package(GTest) ++ if (NOT GTEST_FOUND) ++ message(ERROR "Testing requires googletest.") ++ endif() + enable_testing() + add_subdirectory(tests) + endif() +diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt +index 2e593da..9c3b443 100644 +--- a/tests/CMakeLists.txt ++++ b/tests/CMakeLists.txt +@@ -8,17 +8,6 @@ if(MSVC) + add_definitions(-D_VARIADIC_MAX=10) + endif(MSVC) + +-if(NOT TARGET gtest) +- # Treat this directory as "system" to ignore pedantic warnings. +- if(CMAKE_COMPILER_IS_GNUCXX) +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -isystem gtest-1.8.0/include") +- endif() +- +- # Compile gtest from sources: +- add_subdirectory(gtest-1.8.0) +- INCLUDE_DIRECTORIES("gtest-1.8.0/include/") +-endif() +- + set(EXECUTABLE_OUTPUT_PATH "${${PROJECT_NAME}_BINARY_DIR}") + + # Tests based on Google gtest: +@@ -37,4 +26,4 @@ ADD_TEST(unit_tests_run ${EXECUTABLE_OUTPUT_PATH}/unit_tests) + set_tests_properties(unit_tests_run PROPERTIES DEPENDS unit_tests_build) + + # Add the required libraries for linking: +-TARGET_LINK_LIBRARIES(unit_tests mygtest nanoflann) ++TARGET_LINK_LIBRARIES(unit_tests ${GTEST_LIBRARIES} nanoflann) From 294fcdcc3cf10d3714c8f292fa5b504c5f1544e1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Feb 2023 15:50:55 +0100 Subject: [PATCH 6497/9987] DGL: downgrade networkx to the version used in the 2021a toolchain --- easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb index 96e3f4b4497..7e65a4bdef2 100644 --- a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb @@ -77,7 +77,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ('tqdm', '4.61.2'), ('DLPack', '0.3'), ('DMLC-Core', '0.5'), From e9ce986f288561c8f18966ea9f8d99b34b948385 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Feb 2023 17:44:11 +0000 Subject: [PATCH 6498/9987] Patch renamed to crossguid-libuuid-20190529.patch --- .../c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb | 2 +- .../crossguid-libuuid-20190529.patch} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/{crossguide/libuuid-20190529.patch => crossguid/crossguid-libuuid-20190529.patch} (100%) diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb index f9e343734f7..b43e46034b6 100644 --- a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb @@ -19,7 +19,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/graeme-hill/crossguid/archive/%s' % local_commit] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = ['libuuid-20190529.patch'] +patches = ['crossguid-libuuid-20190529.patch'] checksums = [ '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguid-20190529.tar.gz diff --git a/easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch b/easybuild/easyconfigs/c/crossguid/crossguid-libuuid-20190529.patch similarity index 100% rename from easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch rename to easybuild/easyconfigs/c/crossguid/crossguid-libuuid-20190529.patch From af4f559806b9656a54c391d6dda6c00128dbe2f5 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Feb 2023 17:47:03 +0000 Subject: [PATCH 6499/9987] Post-install step added as suggested --- .../c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb index b43e46034b6..8b515975e19 100644 --- a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb @@ -40,9 +40,10 @@ dependencies = [ configopts = ["-DCROSSGUID_TESTS=ON", "-DBUILD_SHARED_LIBS=TRUE"] # we want to have the crossguid-test -install_cmd = "make install && " -install_cmd += "mkdir -p %(installdir)s/bin/ && " -install_cmd += "cp -f crossguid-test %(installdir)s/bin/ " +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin/', + 'cp -a crossguid-test %(installdir)s/bin/', +] sanity_check_paths = { 'files': ['lib/libcrossguid.a', 'bin/crossguid-test'], From e456ca00eaef8e3a2d7ddc522afeab44ee49c264 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Feb 2023 17:51:30 +0000 Subject: [PATCH 6500/9987] Patchfile renamed --- .../c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb | 2 +- ...uuid-20190529.patch => crossguid-20190529_fix_libuuid.patch} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/crossguid/{crossguid-libuuid-20190529.patch => crossguid-20190529_fix_libuuid.patch} (100%) diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb index 8b515975e19..ac4ea7d10e7 100644 --- a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb @@ -19,7 +19,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/graeme-hill/crossguid/archive/%s' % local_commit] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = ['crossguid-libuuid-20190529.patch'] +patches = ['crossguid-20190529_fix_libuuid.patch'] checksums = [ '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguid-20190529.tar.gz diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-libuuid-20190529.patch b/easybuild/easyconfigs/c/crossguid/crossguid-20190529_fix_libuuid.patch similarity index 100% rename from easybuild/easyconfigs/c/crossguid/crossguid-libuuid-20190529.patch rename to easybuild/easyconfigs/c/crossguid/crossguid-20190529_fix_libuuid.patch From 239269a28169613e02705780a4dd6455a6185f72 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Feb 2023 17:56:36 +0000 Subject: [PATCH 6501/9987] Patch-name in EC corrected --- .../c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb index ac4ea7d10e7..3a066943a85 100644 --- a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ patches = ['crossguid-20190529_fix_libuuid.patch'] checksums = [ '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguid-20190529.tar.gz - '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # libuuid-20190529.patch + '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # crossguid-20190529_fix_libuuid.patch ] builddependencies = [ From 3fcb646e29f9a9111ac5bff61deb9eb8ad24d587 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Feb 2023 18:03:00 +0000 Subject: [PATCH 6502/9987] Patchfile name corrected --- .../easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb | 4 ++-- .../crossguid-0.2.2_fix_libuuid.patch} | 0 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/{crossguide/libuuid-0.2.2.patch => crossguid/crossguid-0.2.2_fix_libuuid.patch} (100%) diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb index 3823e69fcd9..5c473db1e66 100644 --- a/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb @@ -17,11 +17,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/graeme-hill/crossguid/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] -patches = ['libuuid-0.2.2.patch'] +patches = ['crossguid-0.2.2_fix_libuuid.patch'] checksums = [ '48321928473c682b0cdc7e17bbd3390f79f4b98ab22fef3b81a852dda81fd195', # v0.2.2.tar.gz - '6c59e785528fd24ed50304125c07193b9152d81dbc44b52fb2638729265f1bad', # libuuid-0.2.2.patch + '6c59e785528fd24ed50304125c07193b9152d81dbc44b52fb2638729265f1bad', # crossguid-0.2.2_fix_libuuid.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/crossguide/libuuid-0.2.2.patch b/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2_fix_libuuid.patch similarity index 100% rename from easybuild/easyconfigs/c/crossguide/libuuid-0.2.2.patch rename to easybuild/easyconfigs/c/crossguid/crossguid-0.2.2_fix_libuuid.patch From 8f9d4f4fea36e70db5d197dba80b1d43260276ab Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Feb 2023 18:47:05 +0000 Subject: [PATCH 6503/9987] adding easyconfigs: Brunsli-0.1-GCCcore-11.3.0.eb, Highway-1.0.3-GCCcore-11.3.0.eb --- .../b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb | 50 +++++++++++++++++++ .../h/Highway/Highway-1.0.3-GCCcore-11.3.0.eb | 32 ++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..35fa3a03359 --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '1.0.3'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib*/", + "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..987a76bd0c1 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.3-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Highway' +version = '1.0.3' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['566fc77315878473d9a6bd815f7de78c73734acdcb745c3dde8579560ac5440e'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('googletest', '1.11.0'), +] + +configopts = "-DHWY_SYSTEM_GTEST=ON" + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' From 584002b9a973aa9ff72330631eee5b540a5d7c39 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Feb 2023 19:53:53 +0000 Subject: [PATCH 6504/9987] adding easyconfigs: QtPy-2.3.0-GCCcore-11.3.0.eb --- .../q/QtPy/QtPy-2.3.0-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/q/QtPy/QtPy-2.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-2.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..79b8aeb2b47 --- /dev/null +++ b/easybuild/easyconfigs/q/QtPy/QtPy-2.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'QtPy' +version = '2.3.0' + +homepage = "https://github.com/spyder-ide/qtpy" +description = """QtPy is a small abstraction layer that lets you write applications using a single API call to + either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['0603c9c83ccc035a4717a12908bf6bc6cb22509827ea2ec0e94c2da7c9ed57c5'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('PyQt5', '5.15.5') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From d36d85ac6595e720adb09eb7749d9b76ee23bd36 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Feb 2023 20:04:51 +0000 Subject: [PATCH 6505/9987] adding easyconfigs: CFITSIO-4.2.0-GCCcore-11.3.0.eb --- .../c/CFITSIO/CFITSIO-4.2.0-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..88f309b6263 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '4.2.0' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-3.48_install_test_data.patch'] +checksums = [ + {'cfitsio-4.2.0.tar.gz': 'eba53d1b3f6e345632bb09a7b752ec7ced3d63ec5153a848380f3880c5d61889'}, + {'CFITSIO-3.48_install_test_data.patch': 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c'}, +] + +builddependencies = [('binutils', '2.38')] + +# curl for HTTPs support +dependencies = [('cURL', '7.83.0')] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = '&& make shared && make testprog' + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + ('cd %(installdir)s/share && testprog'), +] + +moduleclass = 'lib' From afbef194b2d587a605f06607983c9dd79a2abb13 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 13 Feb 2023 22:44:25 +0000 Subject: [PATCH 6506/9987] Add ReactomePA extension and deps to R-bundle-Bioconductor/3.15 --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 2e65e10de83..fa874f6b7f4 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1143,6 +1143,15 @@ exts_list = [ ('clusterProfiler', '4.4.4', { 'checksums': ['e5e23a5a1b9580f3801291affb2e547e2fd228e1190e9bce398a1b097c86b24c'], }), + ('reactome.db', '1.81.0', { + 'checksums': ['8fc4436f8189ad979e5a90d76c674b1450991427d036a3bf51f059391598d965'], + }), + ('graphite', '1.42.0', { + 'checksums': ['cf00d3c9c7848d044bf1ea32e468badbf5dac24a3222e225d6fbb89ddfac855a'], + }), + ('ReactomePA', '1.40.0', { + 'checksums': ['458b3febb341700414ca04ea4a6f3005061c9db97622cfdfda6b75a74415a7b9'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From b0247ccf10d1a6f96e835ca4f410538e247e24f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 14 Feb 2023 10:00:55 +0000 Subject: [PATCH 6507/9987] Add ffnvcodec support to all recent FFmpegs --- easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-10.3.0.eb | 3 ++- easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-11.2.0.eb | 3 ++- easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-10.3.0.eb index 49875a9e83d..35d6aae750c 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-10.3.0.eb @@ -17,7 +17,8 @@ checksums = ['ab3a6d6a70358ba0a5f67f37f91f6656b7302b02e98e5b8c846c16763c99913a'] builddependencies = [ ('binutils', '2.36.1'), - ('pkg-config', '0.29.2') + ('pkg-config', '0.29.2'), + ('ffnvcodec', '11.1.5.2', '', SYSTEM), # optional nvenc/dec support ] dependencies = [ diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-11.2.0.eb index ea81a575cad..9b441413d60 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.3.2-GCCcore-11.2.0.eb @@ -14,7 +14,8 @@ checksums = ['ab3a6d6a70358ba0a5f67f37f91f6656b7302b02e98e5b8c846c16763c99913a'] builddependencies = [ ('binutils', '2.37'), - ('pkg-config', '0.29.2') + ('pkg-config', '0.29.2'), + ('ffnvcodec', '11.1.5.2', '', SYSTEM), # optional nvenc/dec support ] dependencies = [ diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb index 4cf10c89fd8..481c69c9923 100644 --- a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-4.4.2-GCCcore-11.3.0.eb @@ -14,7 +14,8 @@ checksums = ['f98a482520c47507521a907914daa9efbc1384e0591b5afc3da18aa897de2948'] builddependencies = [ ('binutils', '2.38'), - ('pkgconf', '1.8.0') + ('pkgconf', '1.8.0'), + ('ffnvcodec', '11.1.5.2', '', SYSTEM), # optional nvenc/dec support ] dependencies = [ From c752d9e7e3544d52a9f8f7d2631f9a3af7076167 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 14 Feb 2023 11:11:41 +0100 Subject: [PATCH 6508/9987] adding easyconfigs: MAKER-3.01.04-foss-2022a.eb, SNAP-HMM-20221022-GCC-11.3.0.eb --- .../m/MAKER/MAKER-3.01.04-foss-2022a.eb | 105 ++++++++++++++++++ .../SNAP-HMM/SNAP-HMM-20221022-GCC-11.3.0.eb | 45 ++++++++ 2 files changed, 150 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb new file mode 100644 index 00000000000..28a58551ca8 --- /dev/null +++ b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb @@ -0,0 +1,105 @@ +easyblock = 'Bundle' + +name = 'MAKER' +version = '3.01.04' + +homepage = 'https://yandell-lab.org/software/maker.html' +description = """ +MAKER is a portable and easily configurable genome annotation pipeline. Its +purpose is to allow smaller eukaryotic and prokaryotic genome projects to +independently annotate their genomes and to create genome databases. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Perl', '5.34.1'), + ('BioPerl', '1.7.8'), + ('BLAST+', '2.13.0'), + ('SNAP-HMM', '20221022'), + ('RepeatMasker', '4.1.4'), + ('Exonerate', '2.4.0'), + # optional: + ('AUGUSTUS', '3.5.0'), + ('GeneMark-ET', '4.71'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +_libdir = 'lib/perl5/site_perl/%(perlver)s/' + +exts_list = [ + ('Acme::Damn', '0.08', { + 'source_tmpl': 'Acme-Damn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IB/IBB'], + 'checksums': ['310d2d03ff912dcd42e4d946174099f41fe3a2dd57a497d6bd65baf1759b7e0e'], + }), + ('Sys::SigAction', '0.23', { + 'source_tmpl': 'Sys-SigAction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LB/LBAXTER'], + 'checksums': ['c4ef6c9345534031fcbbe2adc347fc7194d47afc945e7a44fac7e9563095d353'], + }), + ('forks', '0.36', { + 'source_tmpl': 'forks-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RY/RYBSKEJ'], + 'checksums': ['61be24e44f4c6fea230e8354678beb5b7adcfefd909a47db8f0a251b0ab65993'], + }), + ('Perl::Unsafe::Signals', '0.03', { + 'source_tmpl': 'Perl-Unsafe-Signals-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RG/RGARCIA'], + 'checksums': ['d311ae7d73e8d0c2346dfacb82aa952322e70cd928b09d502d739e60e35f829d'], + }), + ('Bit::Vector', '7.4', { + 'source_tmpl': 'Bit-Vector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/ST/STBEY'], + 'checksums': ['3c6daa671fecfbc35f92a9385b563d65f50dfc6bdc8b4805f9ef46c0d035a926'], + }), + ('Inline::C', '0.82', { + 'source_tmpl': 'Inline-C-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['10fbcf1e158d1c8d77e1dd934e379165b126a45c13645ad0be9dc07d151dd0cc'], + }), + ('IO::All', '0.87', { + 'source_tmpl': 'IO-All-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + 'checksums': ['54e21d250c0229127e30b77a3461e10077854ec244f26fb670f1b445ed4c4d5b'], + }), + ('IO::Prompt', '0.997004', { + 'source_tmpl': 'IO-Prompt-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCONWAY'], + 'checksums': ['f17bb305ee6ac8b5b203e6d826eb940c4f3f6d6f4bfe719c3b3a225f46f58615'], + }), + (name, version, { + 'modulename': False, + 'postinstallcmds': [ + 'cp -a ../bin %(installdir)s/', + 'cp -an blib/lib/* ../lib/* %%(installdir)s/%s' % _libdir, + ], + 'source_tmpl': 'Version_%(version)s.tar.gz', + 'source_urls': ['https://github.com/Yandell-Lab/maker/archive/refs/tags/'], + 'start_dir': 'src', + 'checksums': ['b9513585c90dc88288e903aff87bfddc7a66a39ec2b79619465ca7d679021fa7'], + }), +] + +modextrapaths = { + 'PERL5LIB': _libdir, + 'ZOE': '$EBROOTSNAPMINHMM/Zoe', + 'AUGUSTUS_CONFIG_PATH': '$EBROOTAUGUSTUS/config', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', _libdir], +} + +sanity_check_commands = [ + 'maker --help', + 'maker2zff --help', + 'fasta_tool', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-11.3.0.eb new file mode 100644 index 00000000000..4cfa5eebd91 --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-HMM/SNAP-HMM-20221022-GCC-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'SNAP-HMM' +version = '20221022' +_commit = '4ad1e95' + +homepage = 'https://korflab.github.io/' +description = """ +SNAP is a general purpose gene finding program suitable for both eukaryotic and +prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid +Parser. +""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/KorfLab/SNAP/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] +patches = ['%(name)s-20190603_makefile_correction.patch'] +checksums = [ + {'20221022.tar.gz': 'a85726b7d4199da1b213b613057600012a392ef1aa20198f1d571fac55bf643f'}, + {'SNAP-HMM-20190603_makefile_correction.patch': 'd518750d4cf01278ba5403ab5717cfcd65b75b5a7c6573ae140f1cdb56b9e655'}, +] + +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' + +files_to_copy = [ + (['hmm-assembler.pl', 'zff2gff3.pl', 'fathom', 'forge', 'snap', 'Zoe/zoe-loop'], 'bin'), + 'DNA', + 'HMM', + 'Zoe', +] + +sanity_check_paths = { + 'files': ['bin/snap', 'bin/forge', 'bin/zoe-loop'], + 'dirs': ['Zoe'], +} + +sanity_check_commands = [ + 'snap 2>&1 | grep "^usage:"', + 'zoe-loop | grep "^usage:"', +] + +modextrapaths = {'ZOE': 'Zoe'} + +moduleclass = 'bio' From 6d40e2814f2be974760ef149751686b2b2eb44ac Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 Feb 2023 15:16:33 +0100 Subject: [PATCH 6509/9987] A None checksum is not allowed yet in dict type checksum, convert to old style. --- .../d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb index 7e65a4bdef2..c0bfec78621 100644 --- a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb @@ -59,14 +59,14 @@ patches = [ '%(name)s-%(version)s_use_externals_instead_of_submodules.patch', ] checksums = [ - {'dgl-0.9.1.tar.gz': '8d26ebb7ed976665bbf5bbd1792d8e6efb13a8fa16e5eb1efed75e07fb982e04'}, - {'metis-5.1.1-DistDGL-v0.5.tar.gz': 'cedf0b32d32a8496bac7eb078b2b8260fb00ddb8d50c27e4082968a01bc33331'}, - {'GKlib-METIS-v5.1.1-DistDGL-0.5.tar.gz': '52aa0d383d42360f4faa0ae9537ba2ca348eeab4db5f2dfd6343192d0ff4b833'}, - {'tensorpipe-20230206.tar.gz': 'a4246afac190ffc1bef438920cea490a9aa8dfc5983e765b420ec4408331618e'}, - {'thrust-1.17.0.tar.gz': 'b02aca5d2325e9128ed9d46785b8e72366f758b873b95001f905f22afcf31bbf'}, - {'cub-1.17.0.tar.gz': '16fd4860ae3196bc3eb08bf5754fa2a9697951ddae36dc9721e6614388893618'}, - {'DGL-0.9.1_use_externals_instead_of_submodules.patch': - '4c39420abc09d619de92ca4ee5c4472359b1f5ffe8acd898d4d665bdbeb2ce40'}, + '8d26ebb7ed976665bbf5bbd1792d8e6efb13a8fa16e5eb1efed75e07fb982e04', # dgl-0.9.1.tar.gz + 'cedf0b32d32a8496bac7eb078b2b8260fb00ddb8d50c27e4082968a01bc33331', # metis-5.1.1-DistDGL-v0.5.tar.gz + '52aa0d383d42360f4faa0ae9537ba2ca348eeab4db5f2dfd6343192d0ff4b833', # GKlib-METIS-v5.1.1-DistDGL-0.5.tar.gz + None, # tensorpipe-20230206.tar.gz + 'b02aca5d2325e9128ed9d46785b8e72366f758b873b95001f905f22afcf31bbf', # thrust-1.17.0.tar.gz + '16fd4860ae3196bc3eb08bf5754fa2a9697951ddae36dc9721e6614388893618', # cub-1.17.0.tar.gz + # DGL-0.9.1_use_externals_instead_of_submodules.patch' + '4c39420abc09d619de92ca4ee5c4472359b1f5ffe8acd898d4d665bdbeb2ce40', ] builddependencies = [ From 5f7ba1239d3fbafa5eada049296946165e986fc9 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Tue, 14 Feb 2023 17:13:20 +0100 Subject: [PATCH 6510/9987] Add header to PETSc patch for mpiicc --- .../p/PETSc/PETSc_remove-mpiicc-show-quotes.patch | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch b/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch index 07bb3ccc082..0286368966e 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch +++ b/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch @@ -1,3 +1,9 @@ +The PETSc configuration script relies on the output of the command +"mpicc/mpiicc -show". For some versions of mpiicc, that command prints +include and link paths between double quotes, which confuses the PETSc +configuration script. This patch removes the double quotes again and should +only be necessary when using mpiicc newer than 2021a. +Author: Steven Vandenbrande diff -Nru config/PETSc/Configure.py.back config/PETSc/Configure.py` --- config/PETSc/Configure.py.back 2023-02-09 14:59:14.086680000 +0100 +++ config/PETSc/Configure.py 2023-02-09 14:59:03.095892000 +0100 From bb161d3a1274e5d3a2f6ef3962e7a5fb2a7b1e7f Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Tue, 14 Feb 2023 17:59:52 +0100 Subject: [PATCH 6511/9987] Update checksum after adding comment to patch file --- easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb index e65a78b214e..75d34f53c6c 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb @@ -23,7 +23,7 @@ patches = [ checksums = [ {'petsc-3.15.1.tar.gz': 'c0ac6566e69d1d70b431e07e7598e9de95e84891c2452db1367c846b75109deb'}, {'PETSc_ranlib-fix.patch': '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297'}, - {'PETSc_remove-mpiicc-show-quotes.patch': '917218e4244f579879cbea4a428d05a61b4266f65c23d9cdfb754d187066d62d'}, + {'PETSc_remove-mpiicc-show-quotes.patch': 'e6ccd7ab33d806f1e635f536d94c98b7aa36f6462d6a0f9f71b177f6ed23f09e'}, ] builddependencies = [('CMake', '3.20.1')] From 6f09f28f7b5a317efdbef9ecdc1d1fcc3c65aeaa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 15 Feb 2023 09:21:12 +0100 Subject: [PATCH 6512/9987] adding easyconfigs: imbalanced-learn-0.10.1-foss-2022a.eb --- .../imbalanced-learn-0.10.1-foss-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.10.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.10.1-foss-2022a.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.10.1-foss-2022a.eb new file mode 100644 index 00000000000..dd605365ee7 --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.10.1-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'imbalanced-learn' +version = '0.10.1' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('scikit-learn', '1.1.2'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +exts_list = [ + # Python 3.10.4 uses joblib 1.1.0 but imbalanced-learn 0.10.1 needs joblib >=1.1.1 + ('joblib', '1.2.0', { + 'checksums': ['e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018'], + }), + (name, version, { + 'modulename': 'imblearn', + 'checksums': ['bc7609619ec3c38c442292928239ad3d10b5deb0af8a29c83822b7b57b319f8b'], + }), +] + +moduleclass = 'tools' From b3d96c703c0a2f3c57f845ee886ea3fb5662d881 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 15 Feb 2023 09:39:49 +0100 Subject: [PATCH 6513/9987] remove download_dep_fail property --- .../i/imbalanced-learn/imbalanced-learn-0.10.1-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.10.1-foss-2022a.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.10.1-foss-2022a.eb index dd605365ee7..71e4129bc23 100644 --- a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.10.1-foss-2022a.eb +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.10.1-foss-2022a.eb @@ -14,7 +14,6 @@ dependencies = [ ('scikit-learn', '1.1.2'), ] -download_dep_fail = True sanity_pip_check = True use_pip = True From f8797d377e5718c390368b10a4cdd59d6f01b453 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Wed, 15 Feb 2023 10:39:39 +0100 Subject: [PATCH 6514/9987] adding easyconfigs: Ray-project-2.2.0-foss-2022a.eb, redis-py-4.5.1-foss-2022a.eb, Redis-7.0.8-GCC-11.3.0.eb --- .../Ray-project-2.2.0-foss-2022a.eb | 54 +++++++++++++++++++ .../r/Redis/Redis-7.0.8-GCC-11.3.0.eb | 39 ++++++++++++++ .../r/redis-py/redis-py-4.5.1-foss-2022a.eb | 32 +++++++++++ 3 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ray-project/Ray-project-2.2.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/Redis/Redis-7.0.8-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/r/redis-py/redis-py-4.5.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/Ray-project/Ray-project-2.2.0-foss-2022a.eb b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.2.0-foss-2022a.eb new file mode 100644 index 00000000000..566a35719e3 --- /dev/null +++ b/easybuild/easyconfigs/r/Ray-project/Ray-project-2.2.0-foss-2022a.eb @@ -0,0 +1,54 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'Ray-project' +version = '2.2.0' + +homepage = "https://docs.ray.io/en/latest/" +description = "Ray is a fast and simple framework for building and running distributed applications." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('protobuf-python', '3.19.4'), + ('PyYAML', '6.0'), + ('redis-py', '4.5.1'), +] + +use_pip = True + +exts_list = [ + ('grpcio', '1.51.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['e6dfc2b6567b1c261739b43d9c59d201c1b89e017afd9e684d85aa7a186c9f7a'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + ('frozenlist', '1.3.3', { + 'checksums': ['58bcc55721e8a90b88332d6cd441261ebb22342e238296bb330968952fbb3a6a'], + }), + ('Ray', version, { + 'source_tmpl': '%(namelower)s-%(version)s-cp310-cp310-manylinux2014_x86_64.whl', + 'checksums': ['656768c6f7c15e9ae32cc624b065dfdc99e1a12a0b9aa787602cbcaf8308ab20'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ray'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'ray --help' +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/Redis/Redis-7.0.8-GCC-11.3.0.eb b/easybuild/easyconfigs/r/Redis/Redis-7.0.8-GCC-11.3.0.eb new file mode 100644 index 00000000000..7c3b17fd830 --- /dev/null +++ b/easybuild/easyconfigs/r/Redis/Redis-7.0.8-GCC-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Redis' +version = '7.0.8' + +homepage = 'https://redis.io' +description = """Redis is an open source (BSD licensed), in-memory data structure store, used as +a database, cache, and message broker. Redis provides data structures such as +strings, hashes, lists, sets, sorted sets with range queries, bitmaps, +hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, +Lua scripting, LRU eviction, transactions, and different levels of on-disk +persistence, and provides high availability via Redis Sentinel and automatic +partitioning with Redis Cluster.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://download.redis.io/releases'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06a339e491306783dcf55b97f15a5dbcbdc01ccbde6dc23027c475cab735e914'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +skipsteps = ['configure'] + +# tests must be run from a local filesystem +# runtest = 'test' + +installopts = 'PREFIX="%(installdir)s"' + +sanity_check_paths = { + 'files': ['bin/redis-cli', 'bin/redis-server'], + 'dirs': [], +} + +sanity_check_commands = [('redis-server', '--version')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-4.5.1-foss-2022a.eb b/easybuild/easyconfigs/r/redis-py/redis-py-4.5.1-foss-2022a.eb new file mode 100644 index 00000000000..9f1b437cc0e --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-4.5.1-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'redis-py' +version = '4.5.1' + +homepage = 'https://github.com/redis/redis-py' +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('typing-extensions', '4.3.0'), + ('Redis', '7.0.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('async-timeout', '4.0.2', { + 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['d45e81f5d28024293e089ca54c65ebfca30289c1c596ce19b5d6b7a8131c92b6'], + }), +] + +moduleclass = "data" From 058c602c49e5d617a1be9df456c4cddf227ab0cd Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 15 Feb 2023 11:39:50 +0100 Subject: [PATCH 6515/9987] nanoflann: turnoff vectorizer when using GCC 10.3, it causes test errors on skylake and later --- .../easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb index caaa2838a83..2565e901879 100644 --- a/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb @@ -7,6 +7,8 @@ homepage = 'https://github.com/jlblancoc/nanoflann' description = "nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies." toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'vectorize': False} # GCC 10.3.0 vectorizer causes test errors on skylake and later + github_account = 'jlblancoc' source_urls = [GITHUB_SOURCE] From aed09d9ef34bb13fc21f7cf1220eac9d13ffcf0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:41:59 +0100 Subject: [PATCH 6516/9987] adding easyconfigs: Unidecode-1.3.6-GCCcore-11.3.0.eb --- .../Unidecode-1.3.6-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/u/Unidecode/Unidecode-1.3.6-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/u/Unidecode/Unidecode-1.3.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/Unidecode/Unidecode-1.3.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7a8e8612185 --- /dev/null +++ b/easybuild/easyconfigs/u/Unidecode/Unidecode-1.3.6-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Unidecode' +version = '1.3.6' + +homepage = 'https://github.com/avian2/unidecode' +description = "Python library for lossy ASCII transliterations of Unicode text (port of Text::Unidecode Perl module)" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['fed09cf0be8cf415b391642c2a5addfc72194407caee4f98719e40ec2a72b830'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +fix_python_shebang_for = ['bin/unidecode'] + +sanity_check_paths = { + 'files': ['bin/unidecode'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["unidecode -h"] + +moduleclass = 'lib' From 36ef0ec8192d0ac800a630c9d084d8f60a6dfe02 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:42:14 +0100 Subject: [PATCH 6517/9987] adding easyconfigs: pyBigWig-0.3.18-foss-2022a.eb --- .../p/pyBigWig/pyBigWig-0.3.18-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2022a.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2022a.eb new file mode 100644 index 00000000000..52abcea4672 --- /dev/null +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.18-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pyBigWig' +version = '0.3.18' + +github_account = 'deeptools' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """A python extension, written in C, for quick access to bigBed + files and access to and creation of bigWig files.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['552564d8ce8720a8ae70ed5e5534617fb0cab306b666468d1c61b6d389b8a10c'] + +dependencies = [ + ('Python', '3.10.4'), + ('cURL', '7.83.0'), + ('NSS', '3.79'), # provides libfreebl3 + ('SciPy-bundle', '2022.05'), # optional, for numpy support +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' From 10bf65648717739d8ef225a6115384ca086e416a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:42:57 +0100 Subject: [PATCH 6518/9987] adding easyconfigs: krbalancing-0.5.0b0-GCCcore-11.3.0.eb and patches: krbalancing-0.5.0b0_fix-CMakeLists.patch --- .../krbalancing-0.5.0b0-GCCcore-11.3.0.eb | 39 +++++++++++++++++ .../krbalancing-0.5.0b0_fix-CMakeLists.patch | 42 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0_fix-CMakeLists.patch diff --git a/easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0f0eb3f38cd --- /dev/null +++ b/easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'krbalancing' +version = '0.5.0b0' + +homepage = 'https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm' +description = "A C++ extension for Python which computes K.R. balanced matrices." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/dilawar/Knight-Ruiz-Matrix-balancing-algorithm/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +patches = ['krbalancing-0.5.0b0_fix-CMakeLists.patch'] +checksums = [ + {'krbalancing-0.5.0b0.tar.gz': 'b53d7cd1e84759b0dde7a6fa277d4ffe9bdbaead65db9a9a06aa2653ff0594ea'}, + {'krbalancing-0.5.0b0_fix-CMakeLists.patch': '6950ef427402c26a403fb97f3b44f0cd3d29f01f0c41b0c3b7b2da3f0bbbee00'}, +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), + ('pybind11', '2.9.2'), + ('conan', '1.58.0'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True + +# avoid that Conan uses $HOME/.conan +preinstallopts = "export CONAN_USER_HOME=%(builddir)s && " + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0_fix-CMakeLists.patch b/easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0_fix-CMakeLists.patch new file mode 100644 index 00000000000..cef69f9315c --- /dev/null +++ b/easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0_fix-CMakeLists.patch @@ -0,0 +1,42 @@ +remove workaround for problem with conan and pybind11 (which is fixed in recent conan versions), +and fix for: ERROR: No remote 'conan-center' defined in remotes +author: Kenneth Hoste (HPC-UGent) +see also https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm/issues/24 +--- Knight-Ruiz-Matrix-balancing-algorithm-0.5.0b0/CMakeLists.txt.orig 2023-02-15 10:51:06.719532727 +0100 ++++ Knight-Ruiz-Matrix-balancing-algorithm-0.5.0b0/CMakeLists.txt 2023-02-15 10:50:25.589499665 +0100 +@@ -27,31 +27,20 @@ + message(STATUS " project version ${CMAKE_PROJECT_VERSION}") + add_definitions(-DCMAKE_PROJECT_VERSION=\"${CMAKE_PROJECT_VERSION}\") + +-# pybind11 config file has a bug that makes is impossible to use with +-# conan_cmake_configure. +-# https://github.com/conan-io/conan-center-index/pull/4445 + conan_cmake_configure(REQUIRES +- # pybind11/2.6.1 ++ pybind11/2.6.1 + eigen/3.3.9 + GENERATORS cmake_find_package) +-# find_package(pybind11 REQUIRED) + + conan_cmake_autodetect(settings) + conan_cmake_install(PATH_OR_REFERENCE . + BUILD missing +- REMOTE conan-center ++ REMOTE conancenter + SETTINGS ${settings}) + ++find_package(pybind11 REQUIRED) + find_package(Eigen3 REQUIRED) + +- +-# hack around pybind11 bug +-# https://github.com/conan-io/conan-center-index/pull/4445 +-conan_cmake_run(REQUIRES pybind11/2.6.1 +- BASIC_SETUP NO_OUTPUT_DIRS CMAKE_TARGETS +- BUILD missing) +- +- + pybind11_add_module(krbalancing src/krbalancing.cpp) +-target_link_libraries(krbalancing PRIVATE Eigen3::Eigen CONAN_PKG::pybind11) ++target_link_libraries(krbalancing PRIVATE Eigen3::Eigen pybind11::pybind11) + target_link_libraries(krbalancing PRIVATE OpenMP::OpenMP_CXX) From 476ac1aaeff6420a1f90759d88d1d87a8e62385b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:43:16 +0100 Subject: [PATCH 6519/9987] adding easyconfigs: conan-1.58.0-GCCcore-11.3.0.eb --- .../c/conan/conan-1.58.0-GCCcore-11.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/conan/conan-1.58.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/conan/conan-1.58.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/conan/conan-1.58.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3ea5edbfde6 --- /dev/null +++ b/easybuild/easyconfigs/c/conan/conan-1.58.0-GCCcore-11.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'conan' +version = '1.58.0' + +homepage = 'https://conan.io' +description = "Decentralized, open-source (MIT), C/C++ package manager." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('bottle', '0.12.23', { + 'checksums': ['683de3aa399fb26e87b274dbcf70b1a651385d459131716387abdc3792e04167'], + }), + ('distro', '1.7.0', { + 'checksums': ['151aeccf60c216402932b52e40ee477a939f8d58898927378a02abbe852c1c39'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + ('node-semver', '0.6.1', { + 'checksums': ['4016f7c1071b0493f18db69ea02d3763e98a633606d7c7beca811e53b5ac66b7'], + 'modulename': 'semver', + }), + ('patch-ng', '1.17.4', { + 'checksums': ['627abc5bd723c8b481e96849b9734b10065426224d4d22cd44137004ac0d4ace'], + }), + ('pluginbase', '1.0.1', { + 'checksums': ['ff6c33a98fce232e9c73841d787a643de574937069f0d18147028d70d7dee287'], + }), + ('PyJWT', '2.6.0', { + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + 'modulename': 'jwt', + }), + (name, version, { + 'checksums': ['001039c40b523ac3b26bb675eb90887760b06c657a0d10d60157e382ba2f9b73'], + }), +] + +sanity_pip_check = True + +moduleclass = 'devel' From e5ab41c68ea129bbfd9ff3a5eaf6c6256674f792 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:45:40 +0100 Subject: [PATCH 6520/9987] adding easyconfigs: bx-python-0.9.0-foss-2022a.eb --- .../b/bx-python/bx-python-0.9.0-foss-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/bx-python/bx-python-0.9.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.9.0-foss-2022a.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.9.0-foss-2022a.eb new file mode 100644 index 00000000000..39af3108464 --- /dev/null +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.9.0-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'bx-python' +version = '0.9.0' + +homepage = 'https://github.com/bxlab/bx-python' +description = """The bx-python project is a Python library and associated set of scripts to allow for rapid + implementation of genome scale analyses.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('LZO', '2.10'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True + +exts_list = [ + ('python-lzo', '1.14', { + 'modulename': 'lzo', + 'preinstallopts': "export PREFIX=$EBROOTLZO && ", + 'checksums': ['83cbd8ecaae284735250e31d6c0ecc18ac08763fab2a8c910dc5a6910db6250c'], + }), + (name, version, { + 'modulename': 'bx', + 'checksums': ['fe545c44d2ea74b239d41e9090618aaf6a859d1a1f64b4a21b133cb602dfdb49'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From bc7cec6da88f6883fe931b2e72022fb9e1573696 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:46:56 +0100 Subject: [PATCH 6521/9987] {bio}[foss/2022a] cooler v0.9.1, pyfaidx v0.7.1 w/ Python 3.10.4 --- .../c/cooler/cooler-0.9.1-foss-2022a.eb | 49 +++++++++++++++++++ .../p/pyfaidx/pyfaidx-0.7.1-GCCcore-11.3.0.eb | 30 ++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/c/cooler/cooler-0.9.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cooler/cooler-0.9.1-foss-2022a.eb b/easybuild/easyconfigs/c/cooler/cooler-0.9.1-foss-2022a.eb new file mode 100644 index 00000000000..75afbccdbac --- /dev/null +++ b/easybuild/easyconfigs/c/cooler/cooler-0.9.1-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'cooler' +version = '0.9.1' + +homepage = 'https://open2c.github.io/cooler' +description = """Cooler is a support library for a storage format, also called cooler, used to store + genomic interaction data of any size, such as Hi-C contact matrices.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('PyYAML', '6.0'), + ('pyfaidx', '0.7.1'), +] + +use_pip = True + +exts_list = [ + # cooler 0.9.1 requires setuptools >= 64.0 + ('setuptools', '67.2.0', { + 'checksums': ['b440ee5f7e607bb8c9de15259dba2583dd41a38879a7abc1d43a71c59524da48'], + }), + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('cytoolz', '0.12.1', { + 'checksums': ['fc33909397481c90de3cec831bfb88d97e220dc91939d996920202f184b4648e'], + }), + ('dill', '0.3.6', { + 'checksums': ['e5db55f3687856d8fbdab002ed78544e1c4559a130302693d839dfe8f93f2373'], + }), + ('multiprocess', '0.70.14', { + 'checksums': ['3eddafc12f2260d27ae03fe6069b12570ab4764ab59a75e81624fac453fbf46a'], + }), + (name, version, { + 'checksums': ['e29ee54797c71c5e3af520772e32d664e7fd09318f15c318777dd62125b15731'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6881ae5ea0c --- /dev/null +++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.1-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pyfaidx' +version = '0.7.1' + +homepage = 'https://pypi.python.org/pypi/pyfaidx' +description = "pyfaidx: efficient pythonic random access to fasta subsequences" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3977632b7fd29049f8b11035d7e9dea0e2c5da9c235f982b4c3fae06ff1fa23f'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/faidx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["faidx --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 54bc5d0ffea56525e81fe1b65b333b8e1b51b432 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:48:20 +0100 Subject: [PATCH 6522/9987] adding easyconfigs: sparse-neighbors-search-0.7-foss-2022a.eb and patches: sparse-neighbors-search-0.7_include-stddef.patch --- .../sparse-neighbors-search-0.7-foss-2022a.eb | 36 +++++++++++++++++++ ...-neighbors-search-0.7_include-stddef.patch | 13 +++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7_include-stddef.patch diff --git a/easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7-foss-2022a.eb b/easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7-foss-2022a.eb new file mode 100644 index 00000000000..e43ca0d394a --- /dev/null +++ b/easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'sparse-neighbors-search' +version = '0.7' + +homepage = 'https://github.com/joachimwolff/sparse-neighbors-search' +description = """A Python/C++ implementation of an approximate nearest neighbor search for sparse data structures + based on the idea of local sensitiv hash functions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('umap-learn', '0.5.3'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'patches': ['sparse-neighbors-search-%(version)s_include-stddef.patch'], + 'source_urls': ['https://github.com/joachimwolff/sparse-neighbors-search/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': [ + {'0.7.tar.gz': '4c824eacb1d3c3fafba31eb5803b6291fc098be278b1eb8a63fd9cc7d998621b'}, + {'sparse-neighbors-search-0.7_include-stddef.patch': + '33f7b4fd0de7a2f8fbab19abc7d47a125ac971cf0fe8c8a24a21c0ddde0a8102'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7_include-stddef.patch b/easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7_include-stddef.patch new file mode 100644 index 00000000000..a06fb73fe00 --- /dev/null +++ b/easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7_include-stddef.patch @@ -0,0 +1,13 @@ +fix for "error: size_t was not declared in this scope" +see also https://github.com/joachimwolff/sparse-neighbors-search/issues/10 +author: Kenneth Hoste (HPC-UGent) +--- sparse-neighbors-search-0.7/sparse_neighbors_search/computation/typeDefinitionsBasic.h.orig 2023-02-13 18:33:53.877631417 +0100 ++++ sparse-neighbors-search-0.7/sparse_neighbors_search/computation/typeDefinitionsBasic.h 2023-02-13 18:33:57.576622509 +0100 +@@ -20,6 +20,7 @@ + #include + #include + #include ++#include + + #define MAX_VALUE std::numeric_limits::max() + From 65949a15f349299624211832d7267da15f8650e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:48:45 +0100 Subject: [PATCH 6523/9987] adding easyconfigs: HiCMatrix-17-foss-2022a.eb --- .../h/HiCMatrix/HiCMatrix-17-foss-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17-foss-2022a.eb b/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17-foss-2022a.eb new file mode 100644 index 00000000000..c01429eabad --- /dev/null +++ b/easybuild/easyconfigs/h/HiCMatrix/HiCMatrix-17-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'HiCMatrix' +version = '17' + +homepage = 'https://github.com/deeptools/HiCMatrix' +description = "This library implements the central class of HiCExplorer to manage Hi-C interaction matrices." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTables', '3.8.0'), + ('cooler', '0.9.1'), +] + +use_pip = True + +exts_list = [ + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/deeptools/HiCMatrix/archive/'], + 'checksums': ['40d0d0ed670ca8084bd67ec1fe9eb7aff6c180ca0e0fca277f5ad76d25ed97bb'], + 'preinstallopts': r"sed -i 's/\.\*//g' setup.py && ", + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 3ed5d4c9796504cc046321cbcbeb7398fa640a2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:49:20 +0100 Subject: [PATCH 6524/9987] adding easyconfigs: pyGenomeTracks-3.8-foss-2022a.eb --- .../pyGenomeTracks-3.8-foss-2022a.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.8-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.8-foss-2022a.eb b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.8-foss-2022a.eb new file mode 100644 index 00000000000..d64d75e4db0 --- /dev/null +++ b/easybuild/easyconfigs/p/pyGenomeTracks/pyGenomeTracks-3.8-foss-2022a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'pyGenomeTracks' +version = '3.8' + +homepage = 'https://pygenometracks.readthedocs.io' +description = "pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('bx-python', '0.9.0'), + ('pybedtools', '0.9.0'), + ('pyBigWig', '0.3.18'), + ('pyfaidx', '0.7.1'), + ('Pysam', '0.19.1'), + ('tqdm', '4.64.0'), + ('PyTables', '3.8.0'), + ('h5py', '3.7.0'), + ('PyYAML', '6.0'), + ('cooler', '0.9.1'), + ('HiCMatrix', '17'), +] + +use_pip = True + +exts_list = [ + ('argcomplete', '2.0.0', { + 'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'], + }), + ('argh', '0.27.2', { + 'checksums': ['00c9027f6f461bcf24afe599a281bbda5cbd5dee4b6705befbea293a4ca7d221'], + }), + ('gffutils', '0.11.1', { + 'checksums': ['ca7bf814d600b389bb2d5c403dd279755118cb1476c19c6f7aecb8c51a84263c'], + }), + ('pypairix', '0.3.7', { + 'checksums': ['c1b47c05f92b5be628923c60a27344503ddeba5d8f35a3752d646271d38e0525'], + }), + (name, version, { + 'checksums': ['d8c823aaee08d3069b66ca2a443adf4c0f0163a477273b518dddbdf351912386'], + 'preinstallopts': r"sed -i 's/\.\*//g' setup.py && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/pyGenomeTracks'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyGenomeTracks --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From d42cbeeda891b66c7f2a1b8faf95bed743849216 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:49:46 +0100 Subject: [PATCH 6525/9987] adding easyconfigs: Hyperopt-0.2.7-foss-2022a.eb --- .../h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb new file mode 100644 index 00000000000..fed0543f366 --- /dev/null +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Hyperopt' +version = '0.2.7' + +homepage = 'http://hyperopt.github.io/hyperopt/' +description = """hyperopt is a Python library for optimizing over awkward search spaces with real-valued, + discrete, and conditional dimensions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('py4j', '0.10.9.7', { + 'checksums': ['0b6e5315bb3ada5cf62ac651d107bb2ebc02def3dee9d9548e3baac644ea8dbb'], + }), + ('hyperopt', version, { + 'checksums': ['1bf89ae58050bbd32c7307199046117feee245c2fd9ab6255c7308522b7ca149'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From ea936741f6a59b382c038e752d5ea27156a149ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:50:25 +0100 Subject: [PATCH 6526/9987] adding easyconfigs: HiCExplorer-3.7.2-foss-2022a.eb --- .../HiCExplorer-3.7.2-foss-2022a.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-3.7.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-3.7.2-foss-2022a.eb b/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-3.7.2-foss-2022a.eb new file mode 100644 index 00000000000..6e84c6bdf3e --- /dev/null +++ b/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-3.7.2-foss-2022a.eb @@ -0,0 +1,68 @@ +easyblock = 'PythonBundle' + +name = 'HiCExplorer' +version = '3.7.2' + +homepage = 'http://hicexplorer.readthedocs.org/' +description = """HiCexplorer addresses the common tasks of Hi-C analysis from processing to visualization.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.24.3'), # required for krbalancing + ('conan', '1.58.0'), # required for krbalancing +] + +dependencies = [ + ('Python', '3.10.4'), + ('Pysam', '0.19.1'), + ('matplotlib', '3.5.2'), + ('tqdm', '4.64.0'), + ('scikit-learn', '1.1.2'), + ('Biopython', '1.79'), + ('PyTables', '3.8.0'), + ('h5py', '3.7.0'), + ('pybedtools', '0.9.0'), + ('Unidecode', '1.3.6'), + ('cooler', '0.9.1'), + ('pyGenomeTracks', '3.8'), + ('pyBigWig', '0.3.18'), + ('imbalanced-learn', '0.10.1'), + ('Hyperopt', '0.2.7'), + ('IPython', '8.5.0'), # for ipykernel + ('graphviz-python', '0.20.1'), + ('krbalancing', '0.5.0b0'), +] + +use_pip = True + +exts_list = [ + # stick to termcolor 1.x, to avoid hatchling required build dependency + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('cleanlab', '2.2.0', { + 'checksums': ['401e27dee2531a06ea9abe8a73fab8f29c1c92758ece2f8b84e171a9310b0a71'], + }), + ('fit-nbinom', '1.1', { + 'preinstallopts': "sed -i 's/\.\*//g' setup.py && ", + 'sources': ['fit_nbinom-%(version)s.tar.gz'], + 'checksums': ['bd9600f24f00ab0ec7e8d96b7fcf1ff96ea37d129c9258e0be4bee3262a1688b'], + }), + ('hic2cool', '0.8.3', { + 'checksums': ['c244b89bd23a021c80b0a5b2a5d827dc2f313a4e6497e1ac45044fdc3b109a77'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + (name, version, { + 'preinstallopts': "sed -i 's/\.\*//g' setup.py && ", + 'source_urls': ['https://github.com/deeptools/HiCExplorer/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['dca71065dd4e549d578db96870b8d650b48f3dc852918ef19a345f436f612037'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 3d4b67ce9f181e5ec2c59c73f93732bcf8a16574 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 12:52:27 +0100 Subject: [PATCH 6527/9987] adding easyconfigs: scHiCExplorer-7-foss-2022a.eb --- .../scHiCExplorer-7-foss-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/scHiCExplorer/scHiCExplorer-7-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/scHiCExplorer/scHiCExplorer-7-foss-2022a.eb b/easybuild/easyconfigs/s/scHiCExplorer/scHiCExplorer-7-foss-2022a.eb new file mode 100644 index 00000000000..b1d424fe817 --- /dev/null +++ b/easybuild/easyconfigs/s/scHiCExplorer/scHiCExplorer-7-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'scHiCExplorer' +version = '7' + +homepage = 'https://schicexplorer.readthedocs.io' +description = """The scHiCExplorer is a software to demultiplex, process, correct, normalize, manipulate, analyse and +visualize single-cell Hi-C data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('HiCExplorer', '3.7.2'), + ('HiCMatrix', '17'), + ('cooler', '0.9.1'), + ('sparse-neighbors-search', '0.7'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/joachimwolff/scHiCExplorer/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['8ccc4bc40b7d4da055fcb98c5962500143cb72bf652de584bd69dd8419d1d8ab'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 79803ee3fc21579f846ff170eca79200732a857c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 13:08:12 +0100 Subject: [PATCH 6528/9987] add custom sanity check paths + command in conan easyconfig --- .../easyconfigs/c/conan/conan-1.58.0-GCCcore-11.3.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/conan/conan-1.58.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/conan/conan-1.58.0-GCCcore-11.3.0.eb index 3ea5edbfde6..705bdc29700 100644 --- a/easybuild/easyconfigs/c/conan/conan-1.58.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/conan/conan-1.58.0-GCCcore-11.3.0.eb @@ -7,7 +7,7 @@ homepage = 'https://conan.io' description = "Decentralized, open-source (MIT), C/C++ package manager." toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - + builddependencies = [ ('binutils', '2.38'), ] @@ -49,6 +49,13 @@ exts_list = [ }), ] +sanity_check_paths = { + 'files': ['bin/conan'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["conan --help"] + sanity_pip_check = True moduleclass = 'devel' From b8e7815d92822ee98cc479db3671bf5ed2c4cc31 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 15 Feb 2023 13:16:17 +0100 Subject: [PATCH 6529/9987] nanoflann: remove extra space in comment --- .../easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb index 2565e901879..8a7e77c8385 100644 --- a/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nanoflann/nanoflann-1.4.0-GCCcore-10.3.0.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/jlblancoc/nanoflann' description = "nanoflann is a C++11 header-only library for building KD-Trees of datasets with different topologies." toolchain = {'name': 'GCCcore', 'version': '10.3.0'} -toolchainopts = {'vectorize': False} # GCC 10.3.0 vectorizer causes test errors on skylake and later +toolchainopts = {'vectorize': False} # GCC 10.3.0 vectorizer causes test errors on skylake and later github_account = 'jlblancoc' From 164eb8f226e2e6216463fa772a2db55b399b07af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 14:18:30 +0100 Subject: [PATCH 6530/9987] remove ratelimiter extension from snakemake 7.18.2 easyconfig, replaced by throttler --- .../easyconfigs/s/snakemake/snakemake-7.18.2-foss-2021b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-7.18.2-foss-2021b.eb b/easybuild/easyconfigs/s/snakemake/snakemake-7.18.2-foss-2021b.eb index 2dcc4ecc1c5..4f440890d23 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-7.18.2-foss-2021b.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-7.18.2-foss-2021b.eb @@ -22,9 +22,6 @@ exts_list = [ ('wrapt', '1.14.1', { 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], }), - ('ratelimiter', '1.2.0.post0', { - 'checksums': ['5c395dcabdbbde2e5178ef3f89b568a3066454a6ddc223b76473dac22f89b4f7'], - }), ('ConfigArgParse', '1.5.3', { 'checksums': ['1b0b3cbf664ab59dada57123c81eff3d9737e0d11d8cf79e3d6eb10823f1739f'], }), From 4c157b265fc2c7ab702e48cc8ac41b143bd72961 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 14:25:04 +0100 Subject: [PATCH 6531/9987] adding easyconfigs: MultiQC-1.14-foss-2022a.eb --- .../m/MultiQC/MultiQC-1.14-foss-2022a.eb | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.14-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.14-foss-2022a.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.14-foss-2022a.eb new file mode 100644 index 00000000000..f52d4a6f601 --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.14-foss-2022a.eb @@ -0,0 +1,85 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.14' + +homepage = 'https://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single report. + + MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('PyYAML', '6.0'), + ('networkx', '2.8.4'), +] + +use_pip = True + +exts_list = [ + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('lzstring', '1.0.4', { + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '2.1.0', { + 'checksums': ['cf7e59fed14b5ae17c0006eff14a2d9a00ed5f3a846148153899a0224e2c07da'], + 'modulename': 'markdown_it', + }), + ('Pygments', '2.14.0', { + 'checksums': ['b3ed06a9e8ac9a9aae5a6f5dbe78a8a58655d17b43b93c078f094ddc476ae297'], + }), + ('rich', '13.3.1', { + 'checksums': ['125d96d20c92b946b983d0d392b84ff945461e5a06d3867e9f9e575f8697b67f'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('rich-click', '1.6.1', { + 'checksums': ['f8ff96693ec6e261d1544e9f7d9a5811c5ef5d74c8adb4978430fc0dac16777e'], + }), + ('multiqc', version, { + 'checksums': ['dcbba405f0c9521ed2bbd7e8f7a9200643047311c9619878b81d167300149362'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 02e7bfe85f55e908813952ebeade1444eb84285b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 14:51:26 +0100 Subject: [PATCH 6532/9987] adding easyconfigs: snakemake-7.22.0-foss-2022a.eb --- .../snakemake/snakemake-7.22.0-foss-2022a.eb | 92 +++++++++++++++++++ 1 file changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-7.22.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-7.22.0-foss-2022a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-7.22.0-foss-2022a.eb new file mode 100644 index 00000000000..13db0e39c4e --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-7.22.0-foss-2022a.eb @@ -0,0 +1,92 @@ +easyblock = 'PythonBundle' + +name = 'snakemake' +version = '7.22.0' + +homepage = 'https://snakemake.readthedocs.io' +description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('GitPython', '3.1.27'), + ('IPython', '8.5.0'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('ConfigArgParse', '1.5.3', { + 'checksums': ['1b0b3cbf664ab59dada57123c81eff3d9737e0d11d8cf79e3d6eb10823f1739f'], + }), + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('toposort', '1.9', { + 'checksums': ['f41a34490d44934b533a7bdaff979ee8a47203fd2d8a746db83f2d5ab12458b9'], + }), + ('amply', '0.1.5', { + 'checksums': ['ad717b490b6b7055909faa195e82a4432b706f8f95854050172f42931e478426'], + }), + ('PuLP', '2.7.0', { + 'checksums': ['e73ee6b32d639c9b8cf4b4aded334ba158be5f8313544e056f796ace0a10ae63'], + }), + ('smart-open', '6.3.0', { + 'sources': ['smart_open-%(version)s.tar.gz'], + 'checksums': ['d5238825fe9a9340645fac3d75b287c08fbb99fb2b422477de781c9f5f09e019'], + }), + ('connection-pool', '0.0.3', { + 'sources': ['connection_pool-%(version)s.tar.gz'], + 'checksums': ['bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc'], + }), + ('stopit', '1.1.2', { + 'checksums': ['f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d'], + }), + ('reretry', '0.11.8', { + 'checksums': ['f2791fcebe512ea2f1d153a2874778523a8064860b591cd90afc21a8bed432e3'], + }), + ('throttler', '1.2.2', { + 'checksums': ['d54db406d98e1b54d18a9ba2b31ab9f093ac64a0a59d730c1cf7bb1cdfc94a58'], + }), + ('dpath', '2.1.4', { + 'checksums': ['3380a77d0db4abf104125860ff6eb4bd07c97c65b81aad42a609717089a1bed0'], + }), + ('plac', '1.3.5', { + 'checksums': ['38bdd864d0450fb748193aa817b9c458a8f5319fbf97b2261151cfc0a5812090'], + }), + ('yte', '1.5.1', { + 'checksums': ['6d0b315b78af83276d78f5f67c107c84238f772a76d74f4fc77905b46f3731f5'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + (name, version, { + # patch is needed for clusters that do not support copying the full env into the batch job + # 'patches': ['snakemake-%(version)s_fix_jobs.patch'], + 'checksums': [ + '68d7bb4ab7555f7b58a3ba748a880024df919042cfb670da231886385de697cd', # snakemake-7.22.0 + # '916875eaf4869c65b93098e362b8676cf55c6e37067a54b191f34b13e06c37e3', # snakemake-6.6.1_fix_jobs.patch + ], + }), +] + +# SNAKEMAKE_LOAD_MODULE is needed for snakemake-6.6.1_fix_jobs.patch to work +# local_snakemake_load is the command for loading this module (here: default EB module naming scheme) +# local_snakemake_load = 'module load %(module_name)s' +# modextravars = {'SNAKEMAKE_LOAD_MODULE': local_snakemake_load} + +sanity_check_paths = { + 'files': ['bin/snakemake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], +} + +sanity_check_commands = ['snakemake --help'] + +moduleclass = 'tools' From fcbe579faae725dd699b696b4541d93c51bb502b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 15 Feb 2023 15:18:37 +0100 Subject: [PATCH 6533/9987] use https for GenomeThreader --- .../GenomeThreader/GenomeThreader-1.7.3-Linux_x86_64-64bit.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GenomeThreader/GenomeThreader-1.7.3-Linux_x86_64-64bit.eb b/easybuild/easyconfigs/g/GenomeThreader/GenomeThreader-1.7.3-Linux_x86_64-64bit.eb index dd9fd8fbd67..740580b329a 100644 --- a/easybuild/easyconfigs/g/GenomeThreader/GenomeThreader-1.7.3-Linux_x86_64-64bit.eb +++ b/easybuild/easyconfigs/g/GenomeThreader/GenomeThreader-1.7.3-Linux_x86_64-64bit.eb @@ -4,12 +4,12 @@ name = 'GenomeThreader' version = '1.7.3' versionsuffix = '-Linux_x86_64-64bit' -homepage = 'http://genomethreader.org' +homepage = 'https://genomethreader.org' description = "GenomeThreader is a software tool to compute gene structure predictions." toolchain = SYSTEM -source_urls = ['http://genomethreader.org/distributions/'] +source_urls = ['https://genomethreader.org/distributions/'] sources = ['gth-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['cdcf7f0c642c14c9dc6b9270e3172de96696f42c25185beabc9a1f68c9c41a57'] From 7989d61c5203745cf1871c24523226ee5e103492 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 15 Feb 2023 15:43:45 +0100 Subject: [PATCH 6534/9987] adding easyconfigs: BRAKER-2.1.6-foss-2022a.eb, spaln-2.4.13f-GCC-11.3.0.eb --- .../b/BRAKER/BRAKER-2.1.6-foss-2022a.eb | 41 +++++++++++++++++ .../s/spaln/spaln-2.4.13f-GCC-11.3.0.eb | 45 +++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/spaln/spaln-2.4.13f-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb new file mode 100644 index 00000000000..1e4df1d9635 --- /dev/null +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb @@ -0,0 +1,41 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'Tarball' + +name = 'BRAKER' +version = '2.1.6' + +homepage = 'https://github.com/Gaius-Augustus/BRAKER' +description = """BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET + and AUGUSTUS in novel eukaryotic genomes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/Gaius-Augustus/BRAKER/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06'] + +dependencies = [ + ('Perl', '5.34.1'), + ('AUGUSTUS', '3.5.0'), + ('GeneMark-ET', '4.71'), + ('BamTools', '2.5.2'), + ('SAMtools', '1.16.1'), + ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', SYSTEM), + ('spaln', '2.4.13f'), + ('Exonerate', '2.4.0'), + ('BLAST+', '2.13.0'), + ('Biopython', '1.79'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] + +sanity_check_paths = { + 'files': ['scripts/align2hints.pl', 'scripts/braker.pl', 'scripts/findGenesInIntrons.pl', 'scripts/startAlign.pl'], + 'dirs': ['docs', 'example'], +} + +sanity_check_commands = ["braker.pl --help"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.13f-GCC-11.3.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.13f-GCC-11.3.0.eb new file mode 100644 index 00000000000..0bb954fe533 --- /dev/null +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.13f-GCC-11.3.0.eb @@ -0,0 +1,45 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'spaln' +version = '2.4.13f' + +homepage = 'https://github.com/ogotoh/spaln' +description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps + and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h; +# see also https://github.com/ogotoh/spaln/issues/56 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/ogotoh/spaln/archive/'] +sources = ['ver.%(version)s.tar.gz'] +checksums = ['024fdcf58e38373983092280a7e10ff9c7e246e7d2465c165e158512e686225e'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Perl', '5.34.1'), +] + +start_dir = 'src' + +# we need to make sure not to pass --prefix, otherwise the configure script gets stuck in an infinite loop... +prefix_opt = '--exec_prefix=' + +configopts = "--exec_prefix=%(installdir)s/bin --table_dir=%(installdir)s/table --alndbs_dir=%(installdir)s/seqdb " +configopts += "--use_zlib=1" +fix_perl_shebang_for = ['seqdb/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], + 'dirs': ['seqdb', 'table'], +} + +sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] +modextrapaths = { + 'PATH': 'seqdb', + 'PERL5LIB': 'seqdb', +} + +moduleclass = 'bio' From 213ed641470dcdb956e0aacbd81780d5ca38862a Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 15 Feb 2023 16:37:36 +0100 Subject: [PATCH 6535/9987] adding easyconfigs: HepMC3-3.2.5-GCC-11.3.0.eb --- .../h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb b/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb new file mode 100644 index 00000000000..56e9a481d47 --- /dev/null +++ b/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'CMakeMake' + +name = 'HepMC3' +version = '3.2.5' + +homepage = 'http://hepmc.web.cern.ch/hepmc/' +description = """HepMC is a standard for storing Monte Carlo event data.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://hepmc.web.cern.ch/hepmc/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['cd0f75c80f75549c59cc2a829ece7601c77de97cb2a5ab75790cac8e1d585032'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4') +] + +configopts = '-DHEPMC3_ENABLE_ROOTIO=OFF -DHEPMC3_ENABLE_PYTHON=ON' + +sanity_check_paths = { + 'files': ["lib/libHepMC3.so"], + 'dirs': ['include/HepMC3'] +} +sanity_check_commands = ["python -c 'import pyHepMC3'"] + +moduleclass = 'phys' From 3f0cc58bdc39cf17e07c74befe0b2572470b88f3 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 15 Feb 2023 16:40:58 +0100 Subject: [PATCH 6536/9987] adding easyconfigs: siscone-3.0.5-GCCcore-11.3.0.eb --- .../s/siscone/siscone-3.0.5-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/siscone/siscone-3.0.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/s/siscone/siscone-3.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/siscone/siscone-3.0.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1f772a0bf42 --- /dev/null +++ b/easybuild/easyconfigs/s/siscone/siscone-3.0.5-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'siscone' +version = '3.0.5' + +homepage = 'https://siscone.hepforge.org/' +description = """Hadron Seedless Infrared-Safe Cone jet algorithm""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://siscone.hepforge.org/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['08c63ad96516970c0ef5c030de2e626d6760efda8ece20dee410a515b7acf1e8'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ["lib/libsiscone.so"], + 'dirs': ["include/siscone"], +} + +moduleclass = 'phys' From c0ccffb002075bc36726a9c60be6d778fb3d69cd Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 15 Feb 2023 16:42:31 +0100 Subject: [PATCH 6537/9987] adding easyconfigs: YODA-1.9.7-gompi-2022a.eb --- .../y/YODA/YODA-1.9.7-gompi-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb new file mode 100644 index 00000000000..2f3dbc7072f --- /dev/null +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'YODA' +version = '1.9.7' + +homepage = 'https://yoda.hepforge.org/' +description = """ +Yet more Objects for (High Energy Physics) Data Analysis +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://yoda.hepforge.org/downloads?f='] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['8d07bb04dcb79364858718a18203452d8d9fa00029fa94239eafa8529032b8ff'] + +dependencies = [ + ('Python', '3.10.4') +] + +configopts = "--disable-root --enable-pyext --disable-static" + +sanity_check_paths = { + 'files': ["bin/yoda-config", "lib/libYODA.so"], + 'dirs': ["lib"] +} +sanity_check_commands = ["python -c 'import yoda'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} +moduleclass = 'phys' From d9a0067c9e47e28709979c9176df66ec074ba1fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 15 Feb 2023 16:39:53 +0000 Subject: [PATCH 6538/9987] Rename MAGMA to avoid name collision --- .../MAGMA-gene-analysis-1.07b-foss-2018b.eb} | 2 +- .../MAGMA-gene-analysis-1.07bb-GCC-8.3.0.eb} | 2 +- .../MAGMA-gene-analysis-1.09b-GCC-11.2.0.eb} | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/m/{MAGMA/MAGMA-1.07b-foss-2018b.eb => MAGMA-gene-analysis/MAGMA-gene-analysis-1.07b-foss-2018b.eb} (96%) rename easybuild/easyconfigs/m/{MAGMA/MAGMA-1.07bb-GCC-8.3.0.eb => MAGMA-gene-analysis/MAGMA-gene-analysis-1.07bb-GCC-8.3.0.eb} (96%) rename easybuild/easyconfigs/m/{MAGMA/MAGMA-1.09b-GCC-11.2.0.eb => MAGMA-gene-analysis/MAGMA-gene-analysis-1.09b-GCC-11.2.0.eb} (96%) diff --git a/easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07b-foss-2018b.eb similarity index 96% rename from easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb rename to easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07b-foss-2018b.eb index dee8470d10e..d82ec6dec64 100644 --- a/easybuild/easyconfigs/m/MAGMA/MAGMA-1.07b-foss-2018b.eb +++ b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07b-foss-2018b.eb @@ -1,6 +1,6 @@ easyblock = 'MakeCp' -name = 'MAGMA' +name = 'MAGMA-gene-analysis' version = '1.07b' homepage = 'https://ctg.cncr.nl/software/magma' diff --git a/easybuild/easyconfigs/m/MAGMA/MAGMA-1.07bb-GCC-8.3.0.eb b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07bb-GCC-8.3.0.eb similarity index 96% rename from easybuild/easyconfigs/m/MAGMA/MAGMA-1.07bb-GCC-8.3.0.eb rename to easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07bb-GCC-8.3.0.eb index 10a0faa8bf8..6f22fe3ff24 100644 --- a/easybuild/easyconfigs/m/MAGMA/MAGMA-1.07bb-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07bb-GCC-8.3.0.eb @@ -1,6 +1,6 @@ easyblock = 'MakeCp' -name = 'MAGMA' +name = 'MAGMA-gene-analysis' version = '1.07bb' homepage = 'https://ctg.cncr.nl/software/magma' diff --git a/easybuild/easyconfigs/m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.09b-GCC-11.2.0.eb similarity index 96% rename from easybuild/easyconfigs/m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb rename to easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.09b-GCC-11.2.0.eb index eb16168b20f..96faad8988e 100644 --- a/easybuild/easyconfigs/m/MAGMA/MAGMA-1.09b-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.09b-GCC-11.2.0.eb @@ -1,6 +1,6 @@ easyblock = 'MakeCp' -name = 'MAGMA' +name = 'MAGMA-gene-analysis' version = '1.09b' homepage = 'https://ctg.cncr.nl/software/magma' From e9df310efa9b77a3c8510798aff0cc021354756c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 15 Feb 2023 16:44:04 +0000 Subject: [PATCH 6539/9987] Fix namelower template for new MAGMA name --- .../MAGMA-gene-analysis/MAGMA-gene-analysis-1.07b-foss-2018b.eb | 2 +- .../MAGMA-gene-analysis/MAGMA-gene-analysis-1.07bb-GCC-8.3.0.eb | 2 +- .../MAGMA-gene-analysis/MAGMA-gene-analysis-1.09b-GCC-11.2.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07b-foss-2018b.eb b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07b-foss-2018b.eb index d82ec6dec64..66f3e941e15 100644 --- a/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07b-foss-2018b.eb +++ b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07b-foss-2018b.eb @@ -14,7 +14,7 @@ source_urls = [ 'https://ctg.cncr.nl/software/MAGMA/prog/', 'https://ctg.cncr.nl/software/MAGMA/prog/archive/', ] -sources = ['%(namelower)s_v%(version)s_source.zip'] +sources = ['magma_v%(version)s_source.zip'] checksums = ['b8f6c9c5b81cedec51b2e3daafe2519f02423a7d18321f5a91534461d40538f0'] buildopts = ' CXX=${CXX}' diff --git a/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07bb-GCC-8.3.0.eb b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07bb-GCC-8.3.0.eb index 6f22fe3ff24..37a03a2d22d 100644 --- a/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07bb-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.07bb-GCC-8.3.0.eb @@ -14,7 +14,7 @@ source_urls = [ 'https://ctg.cncr.nl/software/MAGMA/prog/', 'https://ctg.cncr.nl/software/MAGMA/prog/archive/', ] -sources = ['%(namelower)s_v%(version)s_source.zip'] +sources = ['magma_v%(version)s_source.zip'] checksums = ['c913b1bb03cb8cf78d55371128007d729a2439ad345d27b570b3ad598d3e1037'] buildopts = ' CXX=${CXX}' diff --git a/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.09b-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.09b-GCC-11.2.0.eb index 96faad8988e..c159f70ce0c 100644 --- a/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.09b-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MAGMA-gene-analysis/MAGMA-gene-analysis-1.09b-GCC-11.2.0.eb @@ -14,7 +14,7 @@ source_urls = [ 'https://ctg.cncr.nl/software/MAGMA/prog/', 'https://ctg.cncr.nl/software/MAGMA/prog/archive/', ] -sources = ['%(namelower)s_v%(version)s_source.zip'] +sources = ['magma_v%(version)s_source.zip'] checksums = ['8af8673fa6c3cf60c2528a06783c20795d9daf4649481cd6e04feb68b91730e0'] buildopts = ' CXX=${CXX}' From 0af5cfc4fad311f9720d4b852d450839de7d3b15 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 15 Feb 2023 17:06:30 +0000 Subject: [PATCH 6540/9987] magma fixed --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index afce357d9ac..8c924ab3bd2 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -941,7 +941,7 @@ def test_easyconfig_name_clashes(self): names[name.lower()].append(name) # Allow these historical case-insensitive name clashes for now. DO NOT ADD TO THIS! - temp_whitelist = ['arb', 'bamm', 'blasr', 'charmm', 'check', 'graphviz', 'libpsml', 'magma', 'nanofilt', 'ncl'] + temp_whitelist = ['arb', 'bamm', 'blasr', 'charmm', 'check', 'graphviz', 'libpsml', 'nanofilt', 'ncl'] duplicates = {} for name in names: if name in temp_whitelist: From 16fd3241f55c14c9ea075d272f9a518512ecbb49 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Feb 2023 17:40:13 +0000 Subject: [PATCH 6541/9987] Archive ARB patch files --- .../easyconfigs/{ => __archive__}/a/ARB/ARB-5.5_xflags.patch | 0 easybuild/easyconfigs/{ => __archive__}/a/ARB/ARB-5.5_xmkmf.patch | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/a/ARB/ARB-5.5_xflags.patch (100%) rename easybuild/easyconfigs/{ => __archive__}/a/ARB/ARB-5.5_xmkmf.patch (100%) diff --git a/easybuild/easyconfigs/a/ARB/ARB-5.5_xflags.patch b/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5_xflags.patch similarity index 100% rename from easybuild/easyconfigs/a/ARB/ARB-5.5_xflags.patch rename to easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5_xflags.patch diff --git a/easybuild/easyconfigs/a/ARB/ARB-5.5_xmkmf.patch b/easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5_xmkmf.patch similarity index 100% rename from easybuild/easyconfigs/a/ARB/ARB-5.5_xmkmf.patch rename to easybuild/easyconfigs/__archive__/a/ARB/ARB-5.5_xmkmf.patch From 12fb0d181b38daa4bda75a40a70b5a119bfa82e1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Feb 2023 17:42:58 +0000 Subject: [PATCH 6542/9987] Archive blasr patch files --- .../b/blasr/blasr-smrtanalysis-2.1_non-static.patch | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/b/blasr/blasr-smrtanalysis-2.1_non-static.patch (100%) diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch b/easybuild/easyconfigs/__archive__/b/blasr/blasr-smrtanalysis-2.1_non-static.patch similarity index 100% rename from easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch rename to easybuild/easyconfigs/__archive__/b/blasr/blasr-smrtanalysis-2.1_non-static.patch From 01d58abec452cb6cb1498e2ed3eef59991313e7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Feb 2023 18:51:29 +0100 Subject: [PATCH 6543/9987] use PythonBundle easyblock (instead of PythonPackage) in krbalancing easyconfig --- .../krbalancing-0.5.0b0-GCCcore-11.3.0.eb | 26 ++++++++++--------- 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0-GCCcore-11.3.0.eb index 0f0eb3f38cd..fe21c19fe3a 100644 --- a/easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/k/krbalancing/krbalancing-0.5.0b0-GCCcore-11.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'krbalancing' version = '0.5.0b0' @@ -8,14 +8,6 @@ description = "A C++ extension for Python which computes K.R. balanced matrices. toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://github.com/dilawar/Knight-Ruiz-Matrix-balancing-algorithm/archive/'] -sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] -patches = ['krbalancing-0.5.0b0_fix-CMakeLists.patch'] -checksums = [ - {'krbalancing-0.5.0b0.tar.gz': 'b53d7cd1e84759b0dde7a6fa277d4ffe9bdbaead65db9a9a06aa2653ff0594ea'}, - {'krbalancing-0.5.0b0_fix-CMakeLists.patch': '6950ef427402c26a403fb97f3b44f0cd3d29f01f0c41b0c3b7b2da3f0bbbee00'}, -] - builddependencies = [ ('binutils', '2.38'), ('CMake', '3.24.3'), @@ -28,11 +20,21 @@ dependencies = [ ('Python', '3.10.4'), ] -download_dep_fail = True use_pip = True -# avoid that Conan uses $HOME/.conan -preinstallopts = "export CONAN_USER_HOME=%(builddir)s && " +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/dilawar/Knight-Ruiz-Matrix-balancing-algorithm/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'patches': ['krbalancing-0.5.0b0_fix-CMakeLists.patch'], + 'checksums': [ + {'krbalancing-0.5.0b0.tar.gz': 'b53d7cd1e84759b0dde7a6fa277d4ffe9bdbaead65db9a9a06aa2653ff0594ea'}, + {'krbalancing-0.5.0b0_fix-CMakeLists.patch': + '6950ef427402c26a403fb97f3b44f0cd3d29f01f0c41b0c3b7b2da3f0bbbee00'}, + ], + 'preinstallopts': "export CONAN_USER_HOME=%(builddir)s && ", + }), +] sanity_pip_check = True From ae7e3c989d1c073457f652fa4efa85581d550c9e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Feb 2023 17:56:01 +0000 Subject: [PATCH 6544/9987] Archive BAMM, BamM, and GroopM to avoid BAMM/BamM name collision --- .../easyconfigs/{ => __archive__}/b/BAMM/BAMM-2.5.0-foss-2016b.eb | 0 .../b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb | 0 .../b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb | 0 .../g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/b/BAMM/BAMM-2.5.0-foss-2016b.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb (100%) diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb b/easybuild/easyconfigs/__archive__/b/BAMM/BAMM-2.5.0-foss-2016b.eb similarity index 100% rename from easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2016b.eb rename to easybuild/easyconfigs/__archive__/b/BAMM/BAMM-2.5.0-foss-2016b.eb diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/__archive__/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb similarity index 100% rename from easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb rename to easybuild/easyconfigs/__archive__/b/BamM/BamM-1.7.3-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/__archive__/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb similarity index 100% rename from easybuild/easyconfigs/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb rename to easybuild/easyconfigs/__archive__/b/BamM/BamM-1.7.3-foss-2018a-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/__archive__/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb similarity index 100% rename from easybuild/easyconfigs/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb rename to easybuild/easyconfigs/__archive__/g/GroopM/GroopM-0.3.4-foss-2016b-Python-2.7.12.eb From 94cc1c22cfe7265e8fccbf216458376c1c2405d9 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 15 Feb 2023 18:29:37 +0000 Subject: [PATCH 6545/9987] arb, bamm, and blasr fixed --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 8c924ab3bd2..dee6bc6af4d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -941,7 +941,7 @@ def test_easyconfig_name_clashes(self): names[name.lower()].append(name) # Allow these historical case-insensitive name clashes for now. DO NOT ADD TO THIS! - temp_whitelist = ['arb', 'bamm', 'blasr', 'charmm', 'check', 'graphviz', 'libpsml', 'nanofilt', 'ncl'] + temp_whitelist = ['charmm', 'check', 'graphviz', 'libpsml', 'nanofilt', 'ncl'] duplicates = {} for name in names: if name in temp_whitelist: From 55ab3d91982f4b863b56d5d9853369525c28ceeb Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Feb 2023 18:34:57 +0000 Subject: [PATCH 6546/9987] consistently use NanoFilt capitailisation --- .../d/decona/decona-0.1.2-foss-2019b-Python-3.7.4.eb | 2 +- .../NanoFilt-2.5.0-foss-2018b-Python-3.6.6.eb} | 0 .../NanoFilt-2.6.0-foss-2019b-Python-3.7.4.eb} | 0 .../NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb} | 0 4 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/n/{nanofilt/nanofilt-2.5.0-foss-2018b-Python-3.6.6.eb => NanoFilt/NanoFilt-2.5.0-foss-2018b-Python-3.6.6.eb} (100%) rename easybuild/easyconfigs/n/{nanofilt/nanofilt-2.6.0-foss-2019b-Python-3.7.4.eb => NanoFilt/NanoFilt-2.6.0-foss-2019b-Python-3.7.4.eb} (100%) rename easybuild/easyconfigs/n/{nanofilt/nanofilt-2.6.0-intel-2020a-Python-3.8.2.eb => NanoFilt/NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb} (100%) diff --git a/easybuild/easyconfigs/d/decona/decona-0.1.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/d/decona/decona-0.1.2-foss-2019b-Python-3.7.4.eb index 72c6da312d2..c46fc2155b7 100644 --- a/easybuild/easyconfigs/d/decona/decona-0.1.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/d/decona/decona-0.1.2-foss-2019b-Python-3.7.4.eb @@ -21,7 +21,7 @@ install_cmd += "mkdir %(installdir)s/bin && cp -a decona/bin/decona %(installdir dependencies = [ ('Python', '3.7.4'), - ('nanofilt', '2.6.0', versionsuffix), + ('NanoFilt', '2.6.0', versionsuffix), ('qcat', '1.1.0', versionsuffix), ('CD-HIT', '4.8.1'), ('minimap2', '2.17'), diff --git a/easybuild/easyconfigs/n/nanofilt/nanofilt-2.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.5.0-foss-2018b-Python-3.6.6.eb similarity index 100% rename from easybuild/easyconfigs/n/nanofilt/nanofilt-2.5.0-foss-2018b-Python-3.6.6.eb rename to easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.5.0-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/n/nanofilt/nanofilt-2.6.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-foss-2019b-Python-3.7.4.eb similarity index 100% rename from easybuild/easyconfigs/n/nanofilt/nanofilt-2.6.0-foss-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/n/nanofilt/nanofilt-2.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb similarity index 100% rename from easybuild/easyconfigs/n/nanofilt/nanofilt-2.6.0-intel-2020a-Python-3.8.2.eb rename to easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb From 15e7460d3e3697bad806fa4f7064e54732a3f50e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Feb 2023 18:43:25 +0000 Subject: [PATCH 6547/9987] rename ncl to NEXUS-CL to avoid case-insensitive name clash --- easybuild/easyconfigs/g/GARLI/GARLI-2.01-gompi-2019a.eb | 4 ++-- .../NEXUS-CL-2.1.18-GCC-8.2.0-2.31.1.eb} | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/n/{ncl/ncl-2.1.18-GCC-8.2.0-2.31.1.eb => NEXUS-CL/NEXUS-CL-2.1.18-GCC-8.2.0-2.31.1.eb} (82%) diff --git a/easybuild/easyconfigs/g/GARLI/GARLI-2.01-gompi-2019a.eb b/easybuild/easyconfigs/g/GARLI/GARLI-2.01-gompi-2019a.eb index 16b75da45cb..ffb2cd9c28e 100644 --- a/easybuild/easyconfigs/g/GARLI/GARLI-2.01-gompi-2019a.eb +++ b/easybuild/easyconfigs/g/GARLI/GARLI-2.01-gompi-2019a.eb @@ -20,10 +20,10 @@ checksums = ['e7fd4c115f9112fd9a019dcb6314e3a9d989f56daa0f833a28dc8249e50988ef'] builddependencies = [('Autotools', '20180311')] -configopts = '--with-ncl=$EBROOTNCL' +configopts = '--with-ncl=$EBROOTNEXUSMINCL' dependencies = [ - ('ncl', '2.1.18'), + ('NEXUS-CL', '2.1.18'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/n/ncl/ncl-2.1.18-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/n/NEXUS-CL/NEXUS-CL-2.1.18-GCC-8.2.0-2.31.1.eb similarity index 82% rename from easybuild/easyconfigs/n/ncl/ncl-2.1.18-GCC-8.2.0-2.31.1.eb rename to easybuild/easyconfigs/n/NEXUS-CL/NEXUS-CL-2.1.18-GCC-8.2.0-2.31.1.eb index 51cd62e4229..8abcddf203a 100644 --- a/easybuild/easyconfigs/n/ncl/ncl-2.1.18-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/n/NEXUS-CL/NEXUS-CL-2.1.18-GCC-8.2.0-2.31.1.eb @@ -1,16 +1,16 @@ easyblock = 'ConfigureMake' -name = 'ncl' +name = 'NEXUS-CL' version = '2.1.18' -homepage = 'http://ncl.sourceforge.net/' +homepage = 'https://ncl.sourceforge.net/' description = """The NEXUS Class Library is a C++ library for parsing NEXUS files.""" toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] +sources = ['ncl-%(version)s.tar.gz'] checksums = ['6e792ede614f6969a0cd342fea1505b4ea3e3e4c0f50a1c0c16a3af67bfe9737'] builddependencies = [('Autotools', '20180311')] @@ -19,7 +19,7 @@ preconfigopts = 'CPPFLAGS=-DNCL_CONST_FUNCS ' sanity_check_paths = { 'files': ["bin/%s" % local_binfile for local_binfile in ["NCLconverter", "NEXUSnormalizer", "NEXUSvalidator"]] + - ["lib/%(name)s/lib%(name)s.so"], + ["lib/ncl/libncl.so"], 'dirs': [], } From 0d35af1f8f05f7549ee9fbe95083657ce066db8a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Feb 2023 18:53:59 +0000 Subject: [PATCH 6548/9987] consistently use Check capitailisation --- .../Check-0.12.0-GCCcore-6.4.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/{check/check-0.12.0-GCCcore-6.4.0.eb => Check/Check-0.12.0-GCCcore-6.4.0.eb} (98%) diff --git a/easybuild/easyconfigs/c/check/check-0.12.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/Check/Check-0.12.0-GCCcore-6.4.0.eb similarity index 98% rename from easybuild/easyconfigs/c/check/check-0.12.0-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/c/Check/Check-0.12.0-GCCcore-6.4.0.eb index 8b3f74b6a9d..3ef1d466fa4 100644 --- a/easybuild/easyconfigs/c/check/check-0.12.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/Check/Check-0.12.0-GCCcore-6.4.0.eb @@ -1,6 +1,6 @@ easyblock = 'CMakeMake' -name = 'check' +name = 'Check' version = '0.12.0' homepage = 'https://libcheck.github.io/check/' From f4736734d32898a17044e7c66b1f89d96ede433d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Feb 2023 18:56:41 +0000 Subject: [PATCH 6549/9987] remember to change the names and sources in the file --- .../n/NanoFilt/NanoFilt-2.5.0-foss-2018b-Python-3.6.6.eb | 4 ++-- .../n/NanoFilt/NanoFilt-2.6.0-foss-2019b-Python-3.7.4.eb | 4 ++-- .../n/NanoFilt/NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.5.0-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.5.0-foss-2018b-Python-3.6.6.eb index e31b1f45efe..82d8297d41a 100644 --- a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.5.0-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.5.0-foss-2018b-Python-3.6.6.eb @@ -1,5 +1,5 @@ easyblock = 'PythonPackage' -name = 'nanofilt' +name = 'NanoFilt' version = '2.5.0' versionsuffix = '-Python-%(pyver)s' @@ -9,7 +9,7 @@ description = """Filtering and trimming of long read sequencing data.""" toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://github.com/wdecoster/nanofilt/archive/v%(version)s'] -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] checksums = ['33c35aad2950145ef66bcf338e68c7c84a20ae62716db24f9c9ccbd881c9a277'] dependencies = [ diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-foss-2019b-Python-3.7.4.eb index 44750167f6c..05339b43f99 100644 --- a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-foss-2019b-Python-3.7.4.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'nanofilt' +name = 'NanoFilt' version = '2.6.0' versionsuffix = '-Python-%(pyver)s' @@ -10,7 +10,7 @@ description = """Filtering and trimming of long read sequencing data.""" toolchain = {'name': 'foss', 'version': '2019b'} source_urls = ['https://github.com/wdecoster/nanofilt/archive/v%(version)s'] -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] checksums = ['83e3a581b7bf8a4b2e63b1a9b659baea6908448cbca9a0d42893f1cd4021d113'] dependencies = [ diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb index 023fb864003..496920503ff 100644 --- a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.6.0-intel-2020a-Python-3.8.2.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'nanofilt' +name = 'NanoFilt' version = '2.6.0' versionsuffix = '-Python-%(pyver)s' @@ -10,7 +10,7 @@ description = """Filtering and trimming of long read sequencing data.""" toolchain = {'name': 'intel', 'version': '2020a'} source_urls = ['https://github.com/wdecoster/nanofilt/archive/v%(version)s'] -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] checksums = ['83e3a581b7bf8a4b2e63b1a9b659baea6908448cbca9a0d42893f1cd4021d113'] dependencies = [ From 80e4aaee03fe64db5a2715402ad78c7d7602ed57 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Feb 2023 18:58:44 +0000 Subject: [PATCH 6550/9987] need to also change to source_urls --- .../easyconfigs/n/NEXUS-CL/NEXUS-CL-2.1.18-GCC-8.2.0-2.31.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NEXUS-CL/NEXUS-CL-2.1.18-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/n/NEXUS-CL/NEXUS-CL-2.1.18-GCC-8.2.0-2.31.1.eb index 8abcddf203a..21f7ae1e74b 100644 --- a/easybuild/easyconfigs/n/NEXUS-CL/NEXUS-CL-2.1.18-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/n/NEXUS-CL/NEXUS-CL-2.1.18-GCC-8.2.0-2.31.1.eb @@ -9,7 +9,7 @@ description = """The NEXUS Class Library is a C++ library for parsing NEXUS file toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} toolchainopts = {'pic': True} -source_urls = [SOURCEFORGE_SOURCE] +source_urls = ['https://download.sourceforge.net/ncl'] sources = ['ncl-%(version)s.tar.gz'] checksums = ['6e792ede614f6969a0cd342fea1505b4ea3e3e4c0f50a1c0c16a3af67bfe9737'] From 1037965f1c769533647e35b80d373def8fdfb369 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Feb 2023 19:13:28 +0000 Subject: [PATCH 6551/9987] update Check dep in libmo_unpack --- .../l/libmo_unpack/libmo_unpack-3.1.2-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCcore-6.4.0.eb index d8688a45528..cc800c7bec4 100644 --- a/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCcore-6.4.0.eb @@ -20,7 +20,7 @@ checksums = [ builddependencies = [ ('binutils', '2.28'), ('CMake', '3.10.1'), - ('check', '0.12.0'), + ('Check', '0.12.0'), ] separate_build_dir = True From 0d6fffc9fb6b1669d6a9c039ae40ece8a27dc95a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Feb 2023 19:40:58 +0000 Subject: [PATCH 6552/9987] rename python graphviz to graphviz-python to avoid case-insensitiive name clash --- ...raphviz-python-0.5.1-foss-2016b-Python-2.7.12.eb} | 12 ++++++++++-- ...aphviz-python-0.5.1-intel-2016b-Python-2.7.12.eb} | 12 ++++++++++-- ...raphviz-python-0.5.1-intel-2016b-Python-3.5.2.eb} | 12 ++++++++++-- ...raphviz-python-0.8.2-intel-2018a-Python-3.6.4.eb} | 11 +++++++++-- 4 files changed, 39 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/g/{graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb => graphviz-python/graphviz-python-0.5.1-foss-2016b-Python-2.7.12.eb} (51%) rename easybuild/easyconfigs/g/{graphviz/graphviz-0.5.1-intel-2016b-Python-2.7.12.eb => graphviz-python/graphviz-python-0.5.1-intel-2016b-Python-2.7.12.eb} (51%) rename easybuild/easyconfigs/g/{graphviz/graphviz-0.5.1-intel-2016b-Python-3.5.2.eb => graphviz-python/graphviz-python-0.5.1-intel-2016b-Python-3.5.2.eb} (51%) rename easybuild/easyconfigs/g/{graphviz/graphviz-0.8.2-intel-2018a-Python-3.6.4.eb => graphviz-python/graphviz-python-0.8.2-intel-2018a-Python-3.6.4.eb} (63%) diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.5.1-foss-2016b-Python-2.7.12.eb similarity index 51% rename from easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb rename to easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.5.1-foss-2016b-Python-2.7.12.eb index 346cabf772e..d5d827a43aa 100644 --- a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.5.1-foss-2016b-Python-2.7.12.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'graphviz' +name = 'graphviz-python' version = '0.5.1' versionsuffix = '-Python-%(pyver)s' @@ -9,11 +9,19 @@ description = """Simple Python interface for Graphviz""" toolchain = {'name': 'foss', 'version': '2016b'} -sources = [SOURCE_ZIP] +source_urls = ['https://pypi.python.org/packages/source/g/graphviz'] +sources = ['graphviz-%(version)s.zip'] +checksums = ['d8f8f369a5c109d3fc971bbc1860b6848515d210aee8f5019c460351dbb00a50'] dependencies = [ ('Python', '2.7.12'), ('Graphviz', '2.38.0'), ] +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'graphviz'} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.5.1-intel-2016b-Python-2.7.12.eb similarity index 51% rename from easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-2.7.12.eb rename to easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.5.1-intel-2016b-Python-2.7.12.eb index 3d13addde20..c7c137b925d 100644 --- a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.5.1-intel-2016b-Python-2.7.12.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'graphviz' +name = 'graphviz-python' version = '0.5.1' versionsuffix = '-Python-%(pyver)s' @@ -9,11 +9,19 @@ description = """Simple Python interface for Graphviz""" toolchain = {'name': 'intel', 'version': '2016b'} -sources = [SOURCE_ZIP] +source_urls = ['https://pypi.python.org/packages/source/g/graphviz'] +sources = ['graphviz-%(version)s.zip'] +checksums = ['d8f8f369a5c109d3fc971bbc1860b6848515d210aee8f5019c460351dbb00a50'] dependencies = [ ('Python', '2.7.12'), ('Graphviz', '2.38.0'), ] +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'graphviz'} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.5.1-intel-2016b-Python-3.5.2.eb similarity index 51% rename from easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-3.5.2.eb rename to easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.5.1-intel-2016b-Python-3.5.2.eb index 47c26978fe3..3b72a1b71be 100644 --- a/easybuild/easyconfigs/g/graphviz/graphviz-0.5.1-intel-2016b-Python-3.5.2.eb +++ b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.5.1-intel-2016b-Python-3.5.2.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'graphviz' +name = 'graphviz-python' version = '0.5.1' versionsuffix = '-Python-%(pyver)s' @@ -9,11 +9,19 @@ description = """Simple Python interface for Graphviz""" toolchain = {'name': 'intel', 'version': '2016b'} -sources = [SOURCE_ZIP] +source_urls = ['https://pypi.python.org/packages/source/g/graphviz'] +sources = ['graphviz-%(version)s.zip'] +checksums = ['d8f8f369a5c109d3fc971bbc1860b6848515d210aee8f5019c460351dbb00a50'] dependencies = [ ('Python', '3.5.2'), ('Graphviz', '2.38.0'), ] +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'graphviz'} + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/graphviz/graphviz-0.8.2-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.8.2-intel-2018a-Python-3.6.4.eb similarity index 63% rename from easybuild/easyconfigs/g/graphviz/graphviz-0.8.2-intel-2018a-Python-3.6.4.eb rename to easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.8.2-intel-2018a-Python-3.6.4.eb index d066bb3b71c..e02e7841e5c 100644 --- a/easybuild/easyconfigs/g/graphviz/graphviz-0.8.2-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.8.2-intel-2018a-Python-3.6.4.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'graphviz' +name = 'graphviz-python' version = '0.8.2' versionsuffix = '-Python-%(pyver)s' @@ -9,7 +9,8 @@ description = """Simple Python interface for Graphviz""" toolchain = {'name': 'intel', 'version': '2018a'} -sources = [SOURCE_ZIP] +source_urls = ['https://pypi.python.org/packages/source/g/graphviz'] +sources = ['graphviz-%(version)s.zip'] checksums = ['606741c028acc54b1a065b33045f8c89ee0927ea77273ec409ac988f2c3d1091'] dependencies = [ @@ -17,4 +18,10 @@ dependencies = [ ('Graphviz', '2.40.1'), ] +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'graphviz'} + moduleclass = 'vis' From 7d1f5fe191794e83227f72de1fa7e407129a7ee6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Feb 2023 20:05:22 +0000 Subject: [PATCH 6553/9987] fix dep name in MXNET --- .../m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb b/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb index b2b5f4620d9..55b0a033ef8 100644 --- a/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb +++ b/easybuild/easyconfigs/m/MXNet/MXNet-0.9.3-foss-2016b-Python-2.7.12-R-3.3.3.eb @@ -2,7 +2,7 @@ name = 'MXNet' version = '0.9.3' versionsuffix = '-Python-%(pyver)s-R-%(rver)s' -homepage = 'http://mxnet.io/' +homepage = 'https://mxnet.io/' description = """Flexible and Efficient Library for Deep Learning""" toolchain = {'name': 'foss', 'version': '2016b'} @@ -30,7 +30,7 @@ checksums = [ dependencies = [ ('Python', '2.7.12'), - ('graphviz', '0.5.1', '-Python-%(pyver)s'), + ('graphviz-python', '0.5.1', '-Python-%(pyver)s'), ('OpenCV', '3.1.0'), ('R', '3.3.3', '-X11-20160819'), ] From c151d7a210cb494ca2ce54a8d7962487b8b37031 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 15 Feb 2023 21:53:20 +0000 Subject: [PATCH 6554/9987] adding easyconfigs: PyCharm-2022.3.2.eb --- .../easyconfigs/p/PyCharm/PyCharm-2022.3.2.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCharm/PyCharm-2022.3.2.eb diff --git a/easybuild/easyconfigs/p/PyCharm/PyCharm-2022.3.2.eb b/easybuild/easyconfigs/p/PyCharm/PyCharm-2022.3.2.eb new file mode 100644 index 00000000000..baca3530e30 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCharm/PyCharm-2022.3.2.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = 'PyCharm' +version = "2022.3.2" + +homepage = 'https://www.jetbrains.com/pycharm/' +description = """PyCharm Community Edition: Python IDE for Professional Developers""" + +toolchain = SYSTEM + +source_urls = ['https://download-cf.jetbrains.com/python'] +sources = ['pycharm-community-%(version)s.tar.gz'] +checksums = ['0ae72d1931a6effbeb2329f6e5c35859d933798a494479f066ef0a7b2be6b553'] + +sanity_check_paths = { + 'files': ["bin/pycharm.sh"], + 'dirs': [], +} + +moduleclass = 'devel' From 26c0a35ab09eec25db51e6bf6ace8f48a5613f5d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 16 Feb 2023 09:55:05 +0100 Subject: [PATCH 6555/9987] adding easyconfigs: BUSCO-5.4.5-foss-2022a.eb, MetaEuk-6-GCC-11.3.0.eb, prodigal-2.6.3-GCCcore-11.3.0.eb, SEPP-4.5.1-foss-2022a.eb --- .../b/BUSCO/BUSCO-5.4.5-foss-2022a.eb | 56 +++++++++++++++++++ .../m/MetaEuk/MetaEuk-6-GCC-11.3.0.eb | 31 ++++++++++ .../prodigal/prodigal-2.6.3-GCCcore-11.3.0.eb | 46 +++++++++++++++ .../s/SEPP/SEPP-4.5.1-foss-2022a.eb | 47 ++++++++++++++++ 4 files changed, 180 insertions(+) create mode 100644 easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.5-foss-2022a.eb create mode 100644 easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.5-foss-2022a.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.5-foss-2022a.eb new file mode 100644 index 00000000000..bc57db4e6b6 --- /dev/null +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.5-foss-2022a.eb @@ -0,0 +1,56 @@ +# Updated by: Pavel Grochal (INUITS) +# Updated by: Sebastien Moretti (SIB) + +easyblock = 'PythonPackage' + +name = 'BUSCO' +version = '5.4.5' + +homepage = 'https://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['3a852d3cb0ad4132af226279d1712b327a6638697fdf31df66cd6c8dda2417f7'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for pandas + ('R', '4.2.1'), # for R and ggplot2 + ('Biopython', '1.79'), + ('BLAST+', '2.13.0'), + ('HMMER', '3.3.2'), + ('prodigal', '2.6.3'), + ('AUGUSTUS', '3.5.0'), + ('SEPP', '4.5.1'), + ('MetaEuk', '6'), + ('BBMap', '39.01'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin %(installdir)s/doc', + 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/LICENSE %(installdir)s/doc', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/test_data %(installdir)s', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/config %(installdir)s', +] + +sanity_check_paths = { + 'files': ['bin/busco', 'bin/generate_plot.py'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages/busco'] +} + +sanity_check_commands = [ + "busco --help", + "busco -i %(installdir)s/test_data/bacteria/genome.fna --cpu %(parallel)s --mode geno --out test_bacteria.out", + "busco -i %(installdir)s/test_data/eukaryota/genome.fna --cpu %(parallel)s --mode geno --out test_eukaryota.out", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-11.3.0.eb b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-11.3.0.eb new file mode 100644 index 00000000000..3077d330680 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MetaEuk' +version = '6' +local_commit = 'a5d39d9' + +homepage = 'https://metaeuk.soedinglab.org' +description = """MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic + metagenomic contigs.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/soedinglab/%(namelower)s/archive'] +sources = ['%%(version)s-%s.tar.gz' % local_commit] +checksums = ['be19c26f5bdb7dcdd7bc48172105afecf19e5a2e5555edb3ba0c4aa0e4aac126'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['bin/metaeuk'], + 'dirs': [], +} + +sanity_check_commands = ["metaeuk --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..254d50dc31c --- /dev/null +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Updated: Pavel Grochal (INUITS) +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'prodigal' +version = '2.6.3' + +homepage = 'https://github.com/hyattpd/Prodigal/' + +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f'] + +builddependencies = [('binutils', '2.38')] + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +sanity_check_commands = ["prodigal -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022a.eb new file mode 100644 index 00000000000..961d3ff3500 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022a.eb @@ -0,0 +1,47 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.5.1 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.5.1' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['https://github.com/smirarab/sepp/commit/83a6f7e0422903535ba98c136351c1b34bc5c1b9.patch'] +checksums = [ + {'4.5.1.tar.gz': '51e052569ae89f586a1a94c804f09fe1b7910a3ffff7664e2005f18c7d3f717b'}, + {'83a6f7e0422903535ba98c136351c1b34bc5c1b9.patch': + 'f789f421e17cb056a43a5e8db01bcdbc07c9ce30d033b2130ccbce770816875f'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('DendroPy', '4.5.2'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = ['run_sepp.py', 'run_upp.py', 'split_sequences.py'] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From 7acb24900675d09355565f9f98473818b38189cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Feb 2023 10:29:59 +0100 Subject: [PATCH 6556/9987] add alternative checksum for spatial 7.3-14 extension in R 4.1.x easyconfigs --- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 3 ++- easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 15 ++++++++------- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index d7eb4353a4d..f42b0ee31a5 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -803,7 +803,8 @@ exts_list = [ }), ('spatial', '7.3-14', { 'checksums': [('52cc1982732f14544fae7dd9d028e2fc3b525ed695d211d6ed5055420e768a36', - '50e6daacbacff6c716485d20b15eb7fff7b8108dc5ea0ff508024beb4f0a8b9b')], + '50e6daacbacff6c716485d20b15eb7fff7b8108dc5ea0ff508024beb4f0a8b9b', + '0c42df479c1a202dfc678f223e924b1adde5822a9902a3d71fd5f2ff36c4b83b')], }), ('VGAM', '1.1-5', { 'checksums': ['30190b150f3e5478137d288a45f575b2654ad7c29254b0a1fe5c954ee010a1bb'], diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index 97750491d42..e439e147d49 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -846,7 +846,8 @@ exts_list = [ }), ('spatial', '7.3-14', { 'checksums': [('52cc1982732f14544fae7dd9d028e2fc3b525ed695d211d6ed5055420e768a36', - '50e6daacbacff6c716485d20b15eb7fff7b8108dc5ea0ff508024beb4f0a8b9b')], + '50e6daacbacff6c716485d20b15eb7fff7b8108dc5ea0ff508024beb4f0a8b9b', + '0c42df479c1a202dfc678f223e924b1adde5822a9902a3d71fd5f2ff36c4b83b')], }), ('VGAM', '1.1-5', { 'checksums': ['30190b150f3e5478137d288a45f575b2654ad7c29254b0a1fe5c954ee010a1bb'], @@ -3246,22 +3247,22 @@ exts_list = [ 'checksums': ['e0598c220ae90d1334e47c9958ccccf7defbe6ac530159bc69424923894f724a'], }), ('apcluster', '1.4.9', { - 'checksums': ['3aac75e3e640eb89c1337d6f2e72a85d226b9c9483e43e0c76f9d424e758cb72'] + 'checksums': ['3aac75e3e640eb89c1337d6f2e72a85d226b9c9483e43e0c76f9d424e758cb72'], }), ('DataCombine', '0.2.21', { - 'checksums': ['352b235612e2cf8234b3ab5f9aa6f7a394b006b98d24e315940ccc65c4218b47'] + 'checksums': ['352b235612e2cf8234b3ab5f9aa6f7a394b006b98d24e315940ccc65c4218b47'], }), ('docstring', '1.0.0', { - 'checksums': ['14528bc85bbb299fb8fe1a7116034f8df49ae0c26fb299376185b5d56176e5a7'] + 'checksums': ['14528bc85bbb299fb8fe1a7116034f8df49ae0c26fb299376185b5d56176e5a7'], }), ('gdalUtils', '2.0.3.2', { - 'checksums': ['4c6faabee2db8a87b7ea0f8e67e9fce3c5db7f4be353d7d86ea559507cbb2a4f'] + 'checksums': ['4c6faabee2db8a87b7ea0f8e67e9fce3c5db7f4be353d7d86ea559507cbb2a4f'], }), ('openair', '2.8-6', { - 'checksums': ['37ffd9d6c5f5cebcd95720c6599f25f2e6c4fd3f6134f6aec026cb671ea373c0'] + 'checksums': ['37ffd9d6c5f5cebcd95720c6599f25f2e6c4fd3f6134f6aec026cb671ea373c0'], }), ('pdp', '0.7.0', { - 'checksums': ['28d69eb63b92bdf8e974b3222e1e9565000d7f15a3bd90854a8e0446b0fa9a71'] + 'checksums': ['28d69eb63b92bdf8e974b3222e1e9565000d7f15a3bd90854a8e0446b0fa9a71'], }), ('date', '1.2-39', { 'checksums': ['b5b1935638b73373809c009f94b77f993cd301744488d9bdf71ef79c82099757'], From 08dc63bf75f6ea3a18b2197a804aad4475a66e46 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Feb 2023 10:46:10 +0100 Subject: [PATCH 6557/9987] fix homepage + source URL for ELPA (due to switch to new domain) --- .../easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb | 2 +- .../easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018a.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb | 2 +- .../easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb | 2 +- .../easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb | 2 +- .../easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2019b.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2020a.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2019b.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2020a.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2019.11.001-iomkl-2019b.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2020.05.001-intel-2020a.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb | 4 ++-- .../easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb | 10 +++++----- 15 files changed, 29 insertions(+), 29 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb index 47f41ad74c7..e135259e5f1 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-foss-2018b.eb @@ -16,7 +16,7 @@ description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['59f99c3abe2190fac0db8a301d0b9581ee134f438669dbc92551a54f6f861820'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018a.eb index ee335129fa6..4c19eb0f0ad 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018a.eb @@ -12,13 +12,13 @@ easyblock = 'ConfigureMake' name = 'ELPA' version = '2017.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2018a'} toolchainopts = {'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['59f99c3abe2190fac0db8a301d0b9581ee134f438669dbc92551a54f6f861820'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb index e17aecf1a26..c46a082d2fc 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2017.11.001-intel-2018b.eb @@ -16,7 +16,7 @@ description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['59f99c3abe2190fac0db8a301d0b9581ee134f438669dbc92551a54f6f861820'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb index 9dc2f667053..3b520029727 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-foss-2018b.eb @@ -16,7 +16,7 @@ description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['a76c3402eb9d1c19b183aedabde8c20f4cfa4692e73e529384207926aec04985'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb index 845d6ea97df..525a6774f96 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2018.05.001-intel-2018b.eb @@ -16,7 +16,7 @@ description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2018b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['a76c3402eb9d1c19b183aedabde8c20f4cfa4692e73e529384207926aec04985'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb index 423a053421b..dd6d92196d7 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2018.11.001-intel-2019a.eb @@ -9,13 +9,13 @@ name = 'ELPA' version = '2018.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2019a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['cc27fe8ba46ce6e6faa8aea02c8c9983052f8e73a00cfea38abf7613cb1e1b16'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2019b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2019b.eb index 8e5a91433d9..43bfe0c9eae 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2019b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2019b.eb @@ -9,13 +9,13 @@ name = 'ELPA' version = '2019.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['10374a8f042e23c7e1094230f7e2993b6f3580908a213dbdf089792d05aff357'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2020a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2020a.eb index 3870f4f73e2..93429867da4 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2020a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2020a.eb @@ -9,13 +9,13 @@ name = 'ELPA' version = '2019.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2020a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['10374a8f042e23c7e1094230f7e2993b6f3580908a213dbdf089792d05aff357'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2019b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2019b.eb index a473de68f4f..03847e7dfb0 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2019b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2019b.eb @@ -9,13 +9,13 @@ name = 'ELPA' version = '2019.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['10374a8f042e23c7e1094230f7e2993b6f3580908a213dbdf089792d05aff357'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2020a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2020a.eb index e5d77b8a343..9a20079e79c 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2020a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2020a.eb @@ -9,13 +9,13 @@ name = 'ELPA' version = '2019.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2020a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['10374a8f042e23c7e1094230f7e2993b6f3580908a213dbdf089792d05aff357'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-iomkl-2019b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-iomkl-2019b.eb index 841fe6563af..2837953da54 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-iomkl-2019b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-iomkl-2019b.eb @@ -9,13 +9,13 @@ name = 'ELPA' version = '2019.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'iomkl', 'version': '2019b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['10374a8f042e23c7e1094230f7e2993b6f3580908a213dbdf089792d05aff357'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2020.05.001-intel-2020a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2020.05.001-intel-2020a.eb index d7a0138e2a7..c1731fb6926 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2020.05.001-intel-2020a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2020.05.001-intel-2020a.eb @@ -9,13 +9,13 @@ name = 'ELPA' version = '2020.05.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2020a'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['66ff1cf332ce1c82075dc7b5587ae72511d2bcb3a45322c94af6b01996439ce5'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb index 312d380e03f..73968dfba38 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-foss-2020b.eb @@ -9,13 +9,13 @@ name = 'ELPA' version = '2020.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['15591f142eeaa98ab3201d27ca9ac328e21beabf0803b011a04183fcaf6efdde'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb index 209492c7de6..36d6628f6c9 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2020.11.001-intel-2020b.eb @@ -9,13 +9,13 @@ name = 'ELPA' version = '2020.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['15591f142eeaa98ab3201d27ca9ac328e21beabf0803b011a04183fcaf6efdde'] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb index bd153664f95..03bbb928446 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.002-intel-2020b.eb @@ -9,19 +9,19 @@ name = 'ELPA' version = '2021.05.002' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'openmp': True, 'usempi': True} -source_urls = ['https://elpa.rzg.mpg.de/software/tarball-archive/Releases/%(version)s_bugfix/'] +source_urls = ['https://elpa.mpcdf.mpg.de/software/tarball-archive/Releases/%(version)s_bugfix/'] sources = ['elpa-%(version)s_bugfix.tar.gz'] patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] checksums = [ - 'deabc48de5b9e4b2f073d749d335c8f354a7ce4245b643a23b7951cd6c90224b', # elpa-2021.05.002_bugfix.tar.gz - # ELPA-2021.05.002_fix_hardcoded_perl_path.patch - '69d2a7dcb61a7a699dd469a134a693e74c72b157dc72b3eba7a5dc12eb29893d', + {'elpa-2021.05.002_bugfix.tar.gz': 'deabc48de5b9e4b2f073d749d335c8f354a7ce4245b643a23b7951cd6c90224b'}, + {'ELPA-2021.05.002_fix_hardcoded_perl_path.patch': + '69d2a7dcb61a7a699dd469a134a693e74c72b157dc72b3eba7a5dc12eb29893d'}, ] builddependencies = [ From 56e9549972224405769419734389f07fecb0efe7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Feb 2023 10:53:43 +0100 Subject: [PATCH 6558/9987] fix homepage in ELPA easyconfigs (due to switch to new domain) --- easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-foss-2018a.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-gimkl-2017a.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-intel-2018a.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021b.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021b.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2021b.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2022a.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022a.eb | 2 +- 13 files changed, 13 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-foss-2018a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-foss-2018a.eb index 628ef31ea84..cdb9474496c 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-foss-2018a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-foss-2018a.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'ELPA' version = '2015.02.002' -homepage = 'http://elpa.rzg.mpg.de' +homepage = 'http://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2018a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-gimkl-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-gimkl-2017a.eb index 67678268396..95da3909964 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-gimkl-2017a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-gimkl-2017a.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'ELPA' version = '2015.02.002' -homepage = 'http://elpa.rzg.mpg.de' +homepage = 'http://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'gimkl', 'version': '2017a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-intel-2018a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-intel-2018a.eb index b6e5f63c308..cc5de66ed86 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-intel-2018a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2015.02.002-intel-2018a.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'ELPA' version = '2015.02.002' -homepage = 'http://elpa.rzg.mpg.de' +homepage = 'http://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2018a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb index 6168179ce80..170e9a0b133 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'ELPA' version = '2016.05.004' -homepage = 'http://elpa.rzg.mpg.de' +homepage = 'http://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2016b'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb index 2ad603f3491..9724507278e 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'ELPA' version = '2016.05.004' -homepage = 'http://elpa.rzg.mpg.de' +homepage = 'http://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2017a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb index 063922e54e7..9cf93ca54a4 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021a.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2021.05.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2021a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021b.eb index 0f78bc95c9b..85dab2c86d8 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-foss-2021b.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2021.05.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'foss', 'version': '2021b'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb index 3bf4eea1cd4..1a48c031c3f 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021a.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2021.05.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2021a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021b.eb index 38b241fe40c..e80bf97bb4f 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.05.001-intel-2021b.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2021.05.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications .""" toolchain = {'name': 'intel', 'version': '2021b'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2021b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2021b.eb index ed8d5d50027..1808c948f1b 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2021b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2021b.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2021.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications.""" toolchain = {'name': 'foss', 'version': '2021b'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2022a.eb index 16e1636489b..2b914ff90d9 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2022a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-foss-2022a.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2021.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications.""" toolchain = {'name': 'foss', 'version': '2022a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb index 42a4e02fc13..70fed7a024f 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2021b.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2021.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications.""" toolchain = {'name': 'intel', 'version': '2021b'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022a.eb index 688418e5474..6aff08c337c 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022a.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2021.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications.""" toolchain = {'name': 'intel', 'version': '2022a'} From 0878cd6646376998808eaf4fe84a985a7ba64240 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 16 Feb 2023 12:09:22 +0000 Subject: [PATCH 6559/9987] rename libpsml for consistency with libPSML --- .../libPSML-1.1.10-GCC-10.2.0.eb} | 2 +- .../libPSML-1.1.10-GCC-10.3.0.eb} | 2 +- .../libPSML-1.1.10-GCC-11.2.0.eb} | 2 +- .../libPSML-1.1.10-iccifort-2020.4.304.eb} | 2 +- .../libPSML-1.1.10-intel-compilers-2021.2.0.eb} | 2 +- .../libPSML-1.1.10-intel-compilers-2021.4.0.eb} | 2 +- .../libPSML-1.1.7-foss-2016b.eb} | 4 ++-- .../libPSML-1.1.7-foss-2017a.eb} | 4 ++-- 8 files changed, 10 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/l/{libpsml/libpsml-1.1.10-GCC-10.2.0.eb => libPSML/libPSML-1.1.10-GCC-10.2.0.eb} (97%) rename easybuild/easyconfigs/l/{libpsml/libpsml-1.1.10-GCC-10.3.0.eb => libPSML/libPSML-1.1.10-GCC-10.3.0.eb} (97%) rename easybuild/easyconfigs/l/{libpsml/libpsml-1.1.10-GCC-11.2.0.eb => libPSML/libPSML-1.1.10-GCC-11.2.0.eb} (97%) rename easybuild/easyconfigs/l/{libpsml/libpsml-1.1.10-iccifort-2020.4.304.eb => libPSML/libPSML-1.1.10-iccifort-2020.4.304.eb} (97%) rename easybuild/easyconfigs/l/{libpsml/libpsml-1.1.10-intel-compilers-2021.2.0.eb => libPSML/libPSML-1.1.10-intel-compilers-2021.2.0.eb} (97%) rename easybuild/easyconfigs/l/{libpsml/libpsml-1.1.10-intel-compilers-2021.4.0.eb => libPSML/libPSML-1.1.10-intel-compilers-2021.4.0.eb} (97%) rename easybuild/easyconfigs/l/{libpsml/libpsml-1.1.7-foss-2016b.eb => libPSML/libPSML-1.1.7-foss-2016b.eb} (97%) rename easybuild/easyconfigs/l/{libpsml/libpsml-1.1.7-foss-2017a.eb => libPSML/libPSML-1.1.7-foss-2017a.eb} (97%) diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-10.2.0.eb similarity index 97% rename from easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb rename to easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-10.2.0.eb index ef3d2cdb6b6..080cda40c54 100644 --- a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-10.2.0.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'libpsml' +name = 'libPSML' version = '1.1.10' homepage = 'https://launchpad.net/libpsml' diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-10.3.0.eb similarity index 97% rename from easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.3.0.eb rename to easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-10.3.0.eb index c1ec1e114c7..63c81ea2b59 100644 --- a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-10.3.0.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'libpsml' +name = 'libPSML' version = '1.1.10' homepage = 'https://launchpad.net/libpsml' diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-11.2.0.eb similarity index 97% rename from easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-11.2.0.eb rename to easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-11.2.0.eb index 7bbf4e9b312..f4127f8e7be 100644 --- a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-GCC-11.2.0.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'libpsml' +name = 'libPSML' version = '1.1.10' homepage = 'https://launchpad.net/libpsml' diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-iccifort-2020.4.304.eb similarity index 97% rename from easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-iccifort-2020.4.304.eb rename to easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-iccifort-2020.4.304.eb index 1487ad90490..ae80d7188d3 100644 --- a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-iccifort-2020.4.304.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'libpsml' +name = 'libPSML' version = '1.1.10' homepage = 'https://launchpad.net/libpsml' diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-intel-compilers-2021.2.0.eb similarity index 97% rename from easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.2.0.eb rename to easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-intel-compilers-2021.2.0.eb index 4f8e563febe..6cea4adc02c 100644 --- a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-intel-compilers-2021.2.0.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'libpsml' +name = 'libPSML' version = '1.1.10' homepage = 'https://launchpad.net/libpsml' diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-intel-compilers-2021.4.0.eb similarity index 97% rename from easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.4.0.eb rename to easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-intel-compilers-2021.4.0.eb index b09da9cc110..5ef4539f7ef 100644 --- a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.10-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.10-intel-compilers-2021.4.0.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'libpsml' +name = 'libPSML' version = '1.1.10' homepage = 'https://launchpad.net/libpsml' diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.7-foss-2016b.eb similarity index 97% rename from easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb rename to easybuild/easyconfigs/l/libPSML/libPSML-1.1.7-foss-2016b.eb index 057ad7f169c..bcced182a08 100644 --- a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.7-foss-2016b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'libpsml' +name = 'libPSML' version = '1.1.7' homepage = 'https://launchpad.net/libpsml' @@ -9,8 +9,8 @@ description = """LibPSML provides a Fortran API to parse files in the toolchain = {'name': 'foss', 'version': '2016b'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://launchpad.net/libpsml/trunk/%(version_major_minor)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['34ceb4e59efb542360aa4910aae088fd700026c8e1d586806b332dac8b1071a0'] dependencies = [ diff --git a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.7-foss-2017a.eb similarity index 97% rename from easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb rename to easybuild/easyconfigs/l/libPSML/libPSML-1.1.7-foss-2017a.eb index 3996d9709df..b3b660d8604 100644 --- a/easybuild/easyconfigs/l/libpsml/libpsml-1.1.7-foss-2017a.eb +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.7-foss-2017a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'libpsml' +name = 'libPSML' version = '1.1.7' homepage = 'https://launchpad.net/libpsml' @@ -9,8 +9,8 @@ description = """LibPSML provides a Fortran API to parse files in the toolchain = {'name': 'foss', 'version': '2017a'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://launchpad.net/libpsml/trunk/%(version_major_minor)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] checksums = ['34ceb4e59efb542360aa4910aae088fd700026c8e1d586806b332dac8b1071a0'] dependencies = [ From ef89a731f86dada16615b47fdce30c6950532c25 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 16 Feb 2023 12:09:38 +0000 Subject: [PATCH 6560/9987] update dep name in ESL-Bundle --- .../easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb | 2 +- .../easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb index 640410c954f..80ff5c2bd6a 100644 --- a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('flook', '0.8.1'), ('libfdf', '0.2.2', '-serial'), ('libmbd', '0.10.4'), - ('libpsml', '1.1.10'), + ('libPSML', '1.1.10'), ('libpspio', '0.2.4'), ('libxc', '4.3.4'), ('libGridXC', '0.9.6'), diff --git a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb index e060b31d21b..10c5d31e522 100644 --- a/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb +++ b/easybuild/easyconfigs/e/ESL-Bundle/ESL-Bundle-0.6.1-intel-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('flook', '0.8.1'), ('libfdf', '0.2.2', '-serial'), ('libmbd', '0.10.4'), - ('libpsml', '1.1.10'), + ('libPSML', '1.1.10'), ('libpspio', '0.2.4'), ('libxc', '4.3.4'), ('libGridXC', '0.9.6'), From 4489d14caf62139c6499d6abd707c64b7d9acc49 Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Thu, 16 Feb 2023 13:59:38 +0100 Subject: [PATCH 6561/9987] Add HDF5 -serial version --- ...F5-1.12.2-NVHPC-22.7-CUDA-11.7.0-serial.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-NVHPC-22.7-CUDA-11.7.0-serial.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-NVHPC-22.7-CUDA-11.7.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-NVHPC-22.7-CUDA-11.7.0-serial.eb new file mode 100644 index 00000000000..292ed3d9084 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-NVHPC-22.7-CUDA-11.7.0-serial.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.12.2' +versionsuffix = "-serial" + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' From a5832ffb9bbef37f124f2bdbf3df17a5e6afd2bb Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 16 Feb 2023 13:22:26 +0000 Subject: [PATCH 6562/9987] remove whitelist (in preparation for us fixing the remaining problems) --- test/easyconfigs/easyconfigs.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index dee6bc6af4d..2338be7058a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -940,12 +940,8 @@ def test_easyconfig_name_clashes(self): name = dirpath_split[4] names[name.lower()].append(name) - # Allow these historical case-insensitive name clashes for now. DO NOT ADD TO THIS! - temp_whitelist = ['charmm', 'check', 'graphviz', 'libpsml', 'nanofilt', 'ncl'] duplicates = {} for name in names: - if name in temp_whitelist: - continue if len(names[name]) > 1: duplicates[name] = names[name] From e204573a01a8dec19ea7fb58b1187d742dc4a2af Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 16 Feb 2023 15:18:33 +0100 Subject: [PATCH 6563/9987] use local copy of patch file --- .../s/SEPP/SEPP-4.5.1-foss-2022a.eb | 5 ++-- .../s/SEPP/SEPP-4.5.1_fix_py10_compat.patch | 28 +++++++++++++++++++ 2 files changed, 30 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.1_fix_py10_compat.patch diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022a.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022a.eb index 961d3ff3500..45d90b52d04 100644 --- a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022a.eb @@ -17,11 +17,10 @@ toolchain = {'name': 'foss', 'version': '2022a'} github_account = 'smirarab' source_urls = [GITHUB_LOWER_SOURCE] sources = ['%(version)s.tar.gz'] -patches = ['https://github.com/smirarab/sepp/commit/83a6f7e0422903535ba98c136351c1b34bc5c1b9.patch'] +patches = ['%(name)s-%(version)s_fix_py10_compat.patch'] checksums = [ {'4.5.1.tar.gz': '51e052569ae89f586a1a94c804f09fe1b7910a3ffff7664e2005f18c7d3f717b'}, - {'83a6f7e0422903535ba98c136351c1b34bc5c1b9.patch': - 'f789f421e17cb056a43a5e8db01bcdbc07c9ce30d033b2130ccbce770816875f'}, + {'SEPP-4.5.1_fix_py10_compat.patch': 'f789f421e17cb056a43a5e8db01bcdbc07c9ce30d033b2130ccbce770816875f'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1_fix_py10_compat.patch b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1_fix_py10_compat.patch new file mode 100644 index 00000000000..3c11d3bfe32 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1_fix_py10_compat.patch @@ -0,0 +1,28 @@ +From 83a6f7e0422903535ba98c136351c1b34bc5c1b9 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Cl=C3=A9o=20Cordeiro?= + <75858274+CleoCordeiro@users.noreply.github.com> +Date: Tue, 2 Aug 2022 21:17:49 -0300 +Subject: [PATCH] Update alignment.py + +fixed imports of collections for different versions of python +--- + sepp/alignment.py | 6 +++++- + 1 file changed, 5 insertions(+), 1 deletion(-) + +diff --git a/sepp/alignment.py b/sepp/alignment.py +index ada5de8..c847d95 100644 +--- a/sepp/alignment.py ++++ b/sepp/alignment.py +@@ -26,7 +26,11 @@ + + from sepp.filemgr import open_with_intermediates + +-from collections import Mapping ++try: ++ from collections.abc import Mapping # noqa ++except ImportError: ++ from collections import Mapping ++ + import copy + from sepp import get_logger + import io From 1fab9c5490c7bbe1d0df99938618a7779d512a16 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 16 Feb 2023 17:17:29 +0100 Subject: [PATCH 6564/9987] adding easyconfigs: MrBayes-3.2.7-gompi-2022a.eb --- .../m/MrBayes/MrBayes-3.2.7-gompi-2022a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2022a.eb diff --git a/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2022a.eb b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2022a.eb new file mode 100644 index 00000000000..9ca8972d517 --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.7-gompi-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MrBayes' +version = '3.2.7' + +homepage = "https://nbisweden.github.io/MrBayes/" +description = """MrBayes is a program for Bayesian inference and model choice across + a wide range of phylogenetic and evolutionary models.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/NBISweden/MrBayes/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['39d9eb269969b501268d5c27f77687c6eaa2c71ccf15c724e6f330fc405f24b9'] + +dependencies = [ + ('libreadline', '8.1.2'), + ('beagle-lib', '4.0.0'), +] + +configopts = "--with-mpi --with-readline --with-beagle=$EBROOTBEAGLEMINLIB " + +sanity_check_paths = { + 'files': ['bin/mb'], + 'dirs': ['share'] +} + +sanity_check_commands = ['mb -h'] + +moduleclass = 'bio' From 87776458341d362733c5efaf6dabdbc9dd6f67af Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 16 Feb 2023 17:45:41 +0100 Subject: [PATCH 6565/9987] adding easyconfigs: Beast-2.7.3-GCC-11.3.0.eb, beagle-lib-4.0.0-GCC-11.3.0.eb --- .../b/Beast/Beast-2.7.3-GCC-11.3.0.eb | 35 +++++++++++++++++++ .../beagle-lib/beagle-lib-4.0.0-GCC-11.3.0.eb | 33 +++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beast/Beast-2.7.3-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.7.3-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.7.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..8c90156a1e9 --- /dev/null +++ b/easybuild/easyconfigs/b/Beast/Beast-2.7.3-GCC-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'Beast' +version = '2.7.3' + +homepage = 'https://beast2.org' +description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular + sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using + strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies + but is also a framework for testing evolutionary hypotheses without conditioning on a single + tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted + proportional to its posterior probability. """ + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +_archs = {'x86_64': 'x86', 'aarch64': 'aarch64'} + +source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] +sources = ['BEAST.v%%(version)s.Linux.%s.tgz' % _archs[ARCH]] +checksums = ['234af8572e827c1c856f0e1ad46e61fa3b3b875c6b5d246f67839ec7c1bf40b5'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + # this is not mandatory but beagle-lib is recommended by developers + ('beagle-lib', '4.0.0'), +] + +sanity_check_paths = { + 'files': ['bin/beast'], + 'dirs': [] +} + +sanity_check_commands = ["beast -help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..bdaf2367d6d --- /dev/null +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.0-GCC-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'beagle-lib' +version = '4.0.0' + +homepage = 'https://github.com/beagle-dev/beagle-lib' +description = """beagle-lib is a high-performance library that can perform the core calculations at the heart of most + Bayesian and Maximum Likelihood phylogenetics packages.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'beagle-dev' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d197eeb7fe5879dfbae789c459bcc901cb04d52c9cf5ef14fb07ff7a6b74560b'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('pkgconf', '1.8.0'), + ('pocl', '1.8'), +] + +sanity_check_paths = { + 'files': ['include/libhmsbeagle-1/libhmsbeagle/%s' % x for x in ['beagle.h', 'platform.h']] + + ['lib/libhmsbeagle%s.%s' % (x, SHLIB_EXT) for x in ['-cpu', '-cpu-sse', '-jni', '']], + 'dirs': [], +} + +moduleclass = 'numlib' From db77789e734a83e46dbe5313d12a2cc40c46d902 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 16 Feb 2023 17:18:07 +0000 Subject: [PATCH 6566/9987] disable parallel5 szip tests since they hang on generoso --- .../n/netCDF/netCDF-4.9.0-gompi-2022b.eb | 11 +- .../n/netCDF/netCDF-4.9.0-iimpi-2022b.eb | 11 +- ...tCDF-4.9.0_skip-parallel5-szip-tests.patch | 214 ++++++++++++++++++ 3 files changed, 228 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-parallel5-szip-tests.patch diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb index 119dcd53f2b..3c7b6c7f33f 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb @@ -15,12 +15,15 @@ patches = [ 'netCDF-%(version)s_fix-lib-name.patch', 'netCDF-%(version)s_fix-linking-errors.patch', 'netCDF-%(version)s_skip-nasa-test.patch', + 'netCDF-%(version)s_skip-parallel5-szip-tests.patch', ] checksums = [ - '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz - 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch - '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch - '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a', # netCDF-4.9.0_skip-nasa-test.patch + {'v4.9.0.tar.gz': '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6'}, + {'netCDF-4.9.0_fix-lib-name.patch': 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a'}, + {'netCDF-4.9.0_fix-linking-errors.patch': '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15'}, + {'netCDF-4.9.0_skip-nasa-test.patch': '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, + {'netCDF-4.9.0_skip-parallel5-szip-tests.patch': + '9ff5790cc369dce80b7db3610848913af94ef4b24ad7459390671f437b6bb2dd'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb index 3a96eadc498..f6a3132f39c 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb @@ -15,12 +15,15 @@ patches = [ 'netCDF-%(version)s_fix-lib-name.patch', 'netCDF-%(version)s_fix-linking-errors.patch', 'netCDF-%(version)s_skip-nasa-test.patch', + 'netCDF-%(version)s_skip-parallel5-szip-tests.patch', ] checksums = [ - '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz - 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch - '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch - '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a', # netCDF-4.9.0_skip-nasa-test.patch + {'v4.9.0.tar.gz': '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6'}, + {'netCDF-4.9.0_fix-lib-name.patch': 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a'}, + {'netCDF-4.9.0_fix-linking-errors.patch': '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15'}, + {'netCDF-4.9.0_skip-nasa-test.patch': '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, + {'netCDF-4.9.0_skip-parallel5-szip-tests.patch': + '9ff5790cc369dce80b7db3610848913af94ef4b24ad7459390671f437b6bb2dd'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-parallel5-szip-tests.patch b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-parallel5-szip-tests.patch new file mode 100644 index 00000000000..9a674057e0f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-parallel5-szip-tests.patch @@ -0,0 +1,214 @@ +Author: Jasper Grimm (UoY) +Description: disable parallel Szip tests in tst_parallel5.c since + nc_put_vara_float() hangs on some systems (e.g. generoso) +----------------------------------------------------------------- +diff -ruN netcdf-c-4.9.0.orig/nc_test4/tst_parallel5.c netcdf-c-4.9.0.p1/nc_test4/tst_parallel5.c +--- netcdf-c-4.9.0.orig/nc_test4/tst_parallel5.c 2022-06-17 14:41:10.000000000 +0100 ++++ netcdf-c-4.9.0.p1/nc_test4/tst_parallel5.c 2023-02-16 16:54:45.000000000 +0000 +@@ -370,106 +370,106 @@ + } + if (!mpi_rank) + SUMMARIZE_ERR; +-#ifdef HAVE_H5Z_SZIP +-#ifdef HDF5_SUPPORTS_PAR_FILTERS +-#define SZIP_DIM_LEN 256 +-#define SZIP_DIM_NAME "Barrels" +-#define SZIP_VAR_NAME "Best_Sligo_Rags" +-#define SZIP_PIXELS_PER_BLOCK 32 +- if (!mpi_rank) +- printf("*** testing szip compression with parallel I/O..."); +- { +- int ncid, dimid, varid; +- float *data; +- float *data_in; +- int elements_per_pe = SZIP_DIM_LEN/mpi_size; +- size_t start[NDIMS1], count[NDIMS1]; +- int i; +- +- /* Create test data. */ +- if (!(data = malloc(elements_per_pe * sizeof(float)))) ERR; +- for (i = 0; i < elements_per_pe; i++) +- data[i] = mpi_rank + i * 0.1; +- +- /* Crate a file with a scalar NC_BYTE value. */ +- if (nc_create_par(FILE, NC_NETCDF4, MPI_COMM_WORLD, MPI_INFO_NULL, +- &ncid)) ERR; +- if (nc_def_dim(ncid, SZIP_DIM_NAME, SZIP_DIM_LEN, &dimid)) ERR; +- if (nc_def_var(ncid, SZIP_VAR_NAME, NC_FLOAT, NDIMS1, &dimid, &varid)) ERR; +- if (nc_def_var_szip(ncid, varid, H5_SZIP_NN_OPTION_MASK, +- SZIP_PIXELS_PER_BLOCK)) ERR; +- if (nc_enddef(ncid)) ERR; +- start[0] = mpi_rank * elements_per_pe; +- count[0] = elements_per_pe; +- if (nc_put_vara_float(ncid, varid, start, count, data)) ERR; +- if (nc_close(ncid)) ERR; +- +- /* Reopen the file and check. */ +- if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR; +- if (!(data_in = malloc(elements_per_pe * sizeof(float)))) ERR; +- if (nc_get_vara_float(ncid, varid, start, count, data_in)) ERR; +- if (nc_close(ncid)) ERR; +- for (i = 0; i < elements_per_pe; i++) +- if (data_in[i] != data[i]) ERR; +- +- /* Release resources. */ +- free(data_in); +- free(data); +- } +- if (!mpi_rank) +- SUMMARIZE_ERR; +-#endif /* HDF5_SUPPORTS_PAR_FILTERS */ +-#endif /* HAVE_H5Z_SZIP */ +- +-#ifdef HAVE_H5Z_SZIP +-#ifdef HDF5_SUPPORTS_PAR_FILTERS +-#define SZIP_DIM_LEN 256 +-#define SZIP_DIM_NAME "Barrels" +-#define SZIP_VAR_NAME "Best_Sligo_Rags" +-#define SZIP_PIXELS_PER_BLOCK 32 +- if (!mpi_rank) +- printf("*** testing szip compression with parallel I/O..."); +- { +- int ncid, dimid, varid; +- float *data; +- float *data_in; +- int elements_per_pe = SZIP_DIM_LEN/mpi_size; +- size_t start[NDIMS1], count[NDIMS1]; +- int i; +- +- /* Create test data. */ +- if (!(data = malloc(elements_per_pe * sizeof(float)))) ERR; +- for (i = 0; i < elements_per_pe; i++) +- data[i] = mpi_rank + i * 0.1; +- +- /* Crate a file with a scalar NC_BYTE value. */ +- if (nc_create_par(FILE, NC_NETCDF4, MPI_COMM_WORLD, MPI_INFO_NULL, +- &ncid)) ERR; +- if (nc_def_dim(ncid, SZIP_DIM_NAME, SZIP_DIM_LEN, &dimid)) ERR; +- if (nc_def_var(ncid, SZIP_VAR_NAME, NC_FLOAT, NDIMS1, &dimid, &varid)) ERR; +- if (nc_def_var_szip(ncid, varid, NC_SZIP_NN, SZIP_PIXELS_PER_BLOCK)) ERR; +- if (nc_enddef(ncid)) ERR; +- start[0] = mpi_rank * elements_per_pe; +- count[0] = elements_per_pe; +- if (nc_put_vara_float(ncid, varid, start, count, data)); +- if (nc_close(ncid)) ERR; +- +- /* Reopen the file and check. */ +- if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR; +- if (!(data_in = malloc(elements_per_pe * sizeof(float)))) ERR; +- if (nc_get_vara_float(ncid, varid, start, count, data_in)); +- if (nc_close(ncid)) ERR; +- for (i = 0; i < elements_per_pe; i++) +- if (data_in[i] != data[i]) ERR; +- +- /* Release resources. */ +- free(data_in); +- free(data); +- } +- if (!mpi_rank) +- SUMMARIZE_ERR; +-#endif /* HDF5_SUPPORTS_PAR_FILTERS */ +-#endif /* HAVE_H5Z_SZIP */ ++// #ifdef HAVE_H5Z_SZIP ++// #ifdef HDF5_SUPPORTS_PAR_FILTERS ++// #define SZIP_DIM_LEN 256 ++// #define SZIP_DIM_NAME "Barrels" ++// #define SZIP_VAR_NAME "Best_Sligo_Rags" ++// #define SZIP_PIXELS_PER_BLOCK 32 ++// if (!mpi_rank) ++// printf("*** testing szip compression with parallel I/O..."); ++// { ++// int ncid, dimid, varid; ++// float *data; ++// float *data_in; ++// int elements_per_pe = SZIP_DIM_LEN/mpi_size; ++// size_t start[NDIMS1], count[NDIMS1]; ++// int i; ++// ++// /* Create test data. */ ++// if (!(data = malloc(elements_per_pe * sizeof(float)))) ERR; ++// for (i = 0; i < elements_per_pe; i++) ++// data[i] = mpi_rank + i * 0.1; ++// ++// /* Crate a file with a scalar NC_BYTE value. */ ++// if (nc_create_par(FILE, NC_NETCDF4, MPI_COMM_WORLD, MPI_INFO_NULL, ++// &ncid)) ERR; ++// if (nc_def_dim(ncid, SZIP_DIM_NAME, SZIP_DIM_LEN, &dimid)) ERR; ++// if (nc_def_var(ncid, SZIP_VAR_NAME, NC_FLOAT, NDIMS1, &dimid, &varid)) ERR; ++// if (nc_def_var_szip(ncid, varid, H5_SZIP_NN_OPTION_MASK, ++// SZIP_PIXELS_PER_BLOCK)) ERR; ++// if (nc_enddef(ncid)) ERR; ++// start[0] = mpi_rank * elements_per_pe; ++// count[0] = elements_per_pe; ++// if (nc_put_vara_float(ncid, varid, start, count, data)) ERR; ++// if (nc_close(ncid)) ERR; ++// ++// /* Reopen the file and check. */ ++// if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR; ++// if (!(data_in = malloc(elements_per_pe * sizeof(float)))) ERR; ++// if (nc_get_vara_float(ncid, varid, start, count, data_in)) ERR; ++// if (nc_close(ncid)) ERR; ++// for (i = 0; i < elements_per_pe; i++) ++// if (data_in[i] != data[i]) ERR; ++// ++// /* Release resources. */ ++// free(data_in); ++// free(data); ++// } ++// if (!mpi_rank) ++// SUMMARIZE_ERR; ++// #endif /* HDF5_SUPPORTS_PAR_FILTERS */ ++// #endif /* HAVE_H5Z_SZIP */ ++// ++// #ifdef HAVE_H5Z_SZIP ++// #ifdef HDF5_SUPPORTS_PAR_FILTERS ++// #define SZIP_DIM_LEN 256 ++// #define SZIP_DIM_NAME "Barrels" ++// #define SZIP_VAR_NAME "Best_Sligo_Rags" ++// #define SZIP_PIXELS_PER_BLOCK 32 ++// if (!mpi_rank) ++// printf("*** testing szip compression with parallel I/O..."); ++// { ++// int ncid, dimid, varid; ++// float *data; ++// float *data_in; ++// int elements_per_pe = SZIP_DIM_LEN/mpi_size; ++// size_t start[NDIMS1], count[NDIMS1]; ++// int i; ++// ++// /* Create test data. */ ++// if (!(data = malloc(elements_per_pe * sizeof(float)))) ERR; ++// for (i = 0; i < elements_per_pe; i++) ++// data[i] = mpi_rank + i * 0.1; ++// ++// /* Crate a file with a scalar NC_BYTE value. */ ++// if (nc_create_par(FILE, NC_NETCDF4, MPI_COMM_WORLD, MPI_INFO_NULL, ++// &ncid)) ERR; ++// if (nc_def_dim(ncid, SZIP_DIM_NAME, SZIP_DIM_LEN, &dimid)) ERR; ++// if (nc_def_var(ncid, SZIP_VAR_NAME, NC_FLOAT, NDIMS1, &dimid, &varid)) ERR; ++// if (nc_def_var_szip(ncid, varid, NC_SZIP_NN, SZIP_PIXELS_PER_BLOCK)) ERR; ++// if (nc_enddef(ncid)) ERR; ++// start[0] = mpi_rank * elements_per_pe; ++// count[0] = elements_per_pe; ++// if (nc_put_vara_float(ncid, varid, start, count, data)); ++// if (nc_close(ncid)) ERR; ++// ++// /* Reopen the file and check. */ ++// if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR; ++// if (!(data_in = malloc(elements_per_pe * sizeof(float)))) ERR; ++// if (nc_get_vara_float(ncid, varid, start, count, data_in)); ++// if (nc_close(ncid)) ERR; ++// for (i = 0; i < elements_per_pe; i++) ++// if (data_in[i] != data[i]) ERR; ++// ++// /* Release resources. */ ++// free(data_in); ++// free(data); ++// } ++// if (!mpi_rank) ++// SUMMARIZE_ERR; ++// #endif /* HDF5_SUPPORTS_PAR_FILTERS */ ++// #endif /* HAVE_H5Z_SZIP */ + + /* Shut down MPI. */ + MPI_Finalize(); From 27b808a2c2182f4c281584a91335b7ace70eda0d Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Thu, 16 Feb 2023 20:25:16 +0000 Subject: [PATCH 6567/9987] adding easyconfigs: csvkit-1.1.0-GCCcore-11.3.0.eb --- .../c/csvkit/csvkit-1.1.0-GCCcore-11.3.0.eb | 89 +++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/c/csvkit/csvkit-1.1.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/csvkit/csvkit-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/csvkit/csvkit-1.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4f56df24c1c --- /dev/null +++ b/easybuild/easyconfigs/c/csvkit/csvkit-1.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,89 @@ +easyblock = 'PythonBundle' + +name = 'csvkit' +version = '1.1.0' + +homepage = 'https://github.com/wireservice/csvkit' +description = """csvkit is a suite of command-line tools for converting to and working with CSV, + the king of tabular file formats.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38') +] + +dependencies = [ + ('Python', '3.10.4'), + ('openpyxl', '3.0.10'), +] + +use_pip = True +sanity_pip_check = True + +fix_python_shebang_for = ['bin/*'] + +exts_list = [ + ('pytimeparse', '1.1.8', { + 'checksums': ['e86136477be924d7e670646a98561957e8ca7308d44841e21f5ddea757556a0a'], + }), + ('parsedatetime', '2.6', { + 'checksums': ['4cb368fbb18a0b7231f4d76119165451c8d2e35951455dfee97c62a87b04d455'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '8.0.0', { + 'modulename': 'slugify', + 'checksums': ['f1da83f3c7ab839b3f84543470cd95bdb5a81f1a0b80fed502f78b7dca256062'], + }), + ('leather', '0.3.4', { + 'checksums': ['b43e21c8fa46b2679de8449f4d953c06418666dc058ce41055ee8a8d3bb40918'], + }), + ('agate', '1.7.1', { + 'checksums': ['eadf46d980168b8922d5d396d6258eecd5e7dbef7e6f0c0b71e968545ea96389'], + }), + ('olefile', '0.46', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['133b031eaf8fd2c9399b78b8bc5b8fcbe4c31e85295749bb17a87cba8f3c3964'], + }), + ('agate-excel', '0.2.5', { + 'modulename': 'agateexcel', + 'checksums': ['62315708433108772f7f610ca769996b468a4ead380076dbaf6ffe262831b153'], + }), + ('dbfread', '2.0.7', { + 'checksums': ['07c8a9af06ffad3f6f03e8fe91ad7d2733e31a26d2b72c4dd4cfbae07ee3b73d'], + }), + ('agate-dbf', '0.2.2', { + 'modulename': 'agatedbf', + 'checksums': ['589682b78c5c03f2dc8511e6e3edb659fb7336cd118e248896bb0b44c2f1917b'], + }), + ('greenlet', '2.0.2', { + 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], + }), + ('SQLAlchemy', '1.4.46', { + 'checksums': ['6913b8247d8a292ef8315162a51931e2b40ce91681f1b6f18f697045200c4a30'], + }), + ('agate-sql', '0.5.9', { + 'modulename': 'agatesql', + 'checksums': ['30b642a32a5b671161abef9e8ec36352f2e78a24ce849054edac6946d8b9ddc6'], + }), + (name, version, { + 'checksums': ['ad836b4ebf17674284ec94e2adeb9bea97367c9c7310187c2d8e2e3f1ded9c13'], + }), +] + +local_binaries = ['in2csv', 'sql2csv', 'csvclean', 'csvcut', 'csvgrep', 'csvjoin', 'csvsort', 'csvstack', 'csvformat', + 'csvjson', 'csvlook', 'csvpy', 'csvsql', 'csvstat'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [('csvlook', '-h')] + +moduleclass = 'tools' From 5722ca0e3fb41456f081cdd8b5c86f15c5d0232c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 17 Feb 2023 11:46:19 +0000 Subject: [PATCH 6568/9987] archive charmm and CHARMM easyconfigs to avoid case-insensitive name clash --- .../{ => __archive__}/c/CHARMM/CHARMM-37b2-foss-2016a.eb | 0 .../{ => __archive__}/c/CHARMM/CHARMM-37b2-intel-2016a.eb | 0 .../c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch | 0 .../{ => __archive__}/c/CHARMM/main-case-fix-37b2.patch | 0 .../easyconfigs/{ => __archive__}/c/CHARMM/qmmm-pme-37b2.patch | 0 .../easyconfigs/{ => __archive__}/c/CHARMM/use-xhost-37b2.patch | 0 .../{ => __archive__}/c/charmm/charmm-43b2-foss-2017b.eb | 0 .../{ => __archive__}/c/charmm/charmm-43b2-intel-2017b.eb | 0 .../{ => __archive__}/c/charmm/charmm-43b2_Use_xhost.patch | 0 9 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/{ => __archive__}/c/CHARMM/CHARMM-37b2-foss-2016a.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CHARMM/CHARMM-37b2-intel-2016a.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CHARMM/main-case-fix-37b2.patch (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CHARMM/qmmm-pme-37b2.patch (100%) rename easybuild/easyconfigs/{ => __archive__}/c/CHARMM/use-xhost-37b2.patch (100%) rename easybuild/easyconfigs/{ => __archive__}/c/charmm/charmm-43b2-foss-2017b.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/charmm/charmm-43b2-intel-2017b.eb (100%) rename easybuild/easyconfigs/{ => __archive__}/c/charmm/charmm-43b2_Use_xhost.patch (100%) diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-foss-2016a.eb b/easybuild/easyconfigs/__archive__/c/CHARMM/CHARMM-37b2-foss-2016a.eb similarity index 100% rename from easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-foss-2016a.eb rename to easybuild/easyconfigs/__archive__/c/CHARMM/CHARMM-37b2-foss-2016a.eb diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb b/easybuild/easyconfigs/__archive__/c/CHARMM/CHARMM-37b2-intel-2016a.eb similarity index 100% rename from easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2016a.eb rename to easybuild/easyconfigs/__archive__/c/CHARMM/CHARMM-37b2-intel-2016a.eb diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch b/easybuild/easyconfigs/__archive__/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch similarity index 100% rename from easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch rename to easybuild/easyconfigs/__archive__/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch diff --git a/easybuild/easyconfigs/c/CHARMM/main-case-fix-37b2.patch b/easybuild/easyconfigs/__archive__/c/CHARMM/main-case-fix-37b2.patch similarity index 100% rename from easybuild/easyconfigs/c/CHARMM/main-case-fix-37b2.patch rename to easybuild/easyconfigs/__archive__/c/CHARMM/main-case-fix-37b2.patch diff --git a/easybuild/easyconfigs/c/CHARMM/qmmm-pme-37b2.patch b/easybuild/easyconfigs/__archive__/c/CHARMM/qmmm-pme-37b2.patch similarity index 100% rename from easybuild/easyconfigs/c/CHARMM/qmmm-pme-37b2.patch rename to easybuild/easyconfigs/__archive__/c/CHARMM/qmmm-pme-37b2.patch diff --git a/easybuild/easyconfigs/c/CHARMM/use-xhost-37b2.patch b/easybuild/easyconfigs/__archive__/c/CHARMM/use-xhost-37b2.patch similarity index 100% rename from easybuild/easyconfigs/c/CHARMM/use-xhost-37b2.patch rename to easybuild/easyconfigs/__archive__/c/CHARMM/use-xhost-37b2.patch diff --git a/easybuild/easyconfigs/c/charmm/charmm-43b2-foss-2017b.eb b/easybuild/easyconfigs/__archive__/c/charmm/charmm-43b2-foss-2017b.eb similarity index 100% rename from easybuild/easyconfigs/c/charmm/charmm-43b2-foss-2017b.eb rename to easybuild/easyconfigs/__archive__/c/charmm/charmm-43b2-foss-2017b.eb diff --git a/easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb b/easybuild/easyconfigs/__archive__/c/charmm/charmm-43b2-intel-2017b.eb similarity index 100% rename from easybuild/easyconfigs/c/charmm/charmm-43b2-intel-2017b.eb rename to easybuild/easyconfigs/__archive__/c/charmm/charmm-43b2-intel-2017b.eb diff --git a/easybuild/easyconfigs/c/charmm/charmm-43b2_Use_xhost.patch b/easybuild/easyconfigs/__archive__/c/charmm/charmm-43b2_Use_xhost.patch similarity index 100% rename from easybuild/easyconfigs/c/charmm/charmm-43b2_Use_xhost.patch rename to easybuild/easyconfigs/__archive__/c/charmm/charmm-43b2_Use_xhost.patch From d1457f73667bd2ff250e7bd358b62e2cb6f5033d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 17 Feb 2023 11:54:17 +0000 Subject: [PATCH 6569/9987] Update easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7-foss-2022a.eb --- .../sparse-neighbors-search-0.7-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7-foss-2022a.eb b/easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7-foss-2022a.eb index e43ca0d394a..3c3a686982b 100644 --- a/easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7-foss-2022a.eb +++ b/easybuild/easyconfigs/s/sparse-neighbors-search/sparse-neighbors-search-0.7-foss-2022a.eb @@ -5,7 +5,7 @@ version = '0.7' homepage = 'https://github.com/joachimwolff/sparse-neighbors-search' description = """A Python/C++ implementation of an approximate nearest neighbor search for sparse data structures - based on the idea of local sensitiv hash functions.""" + based on the idea of local sensitive hash functions.""" toolchain = {'name': 'foss', 'version': '2022a'} From a5cc12cd63f41d2f4abd524909686ea0ff548af3 Mon Sep 17 00:00:00 2001 From: Xin Wu Date: Fri, 17 Feb 2023 14:03:46 +0100 Subject: [PATCH 6570/9987] added ELPA-2021.11.001-intel-2022b --- .../e/ELPA/ELPA-2021.11.001-intel-2022b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022b.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022b.eb new file mode 100644 index 00000000000..0e976bd6b9c --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022b.eb @@ -0,0 +1,47 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2021.11.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + 'e61048393a5e5f460858a11b216547fa3f434dd620c478cb20a52ebf543260f1', # elpa-new_release_2021.11.001.tar.gz + # ELPA-2021.11.001_fix_hardcoded_perl_path.patch + '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b', +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' +# If the build is running in a batch job, make sure Intel libmpi does +# not try to use Slurm to run the MPI_THREAD test code that ELPA's +# configure is running without "mpirun". +preconfigopts += 'unset SLURM_JOBID && unset SLURM_NODELIST && unset I_MPI_PMI_LIBRARY && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' From a3241c860143182f900cc7dd527d82035a80b7d5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Feb 2023 13:35:58 +0000 Subject: [PATCH 6571/9987] remove unneccessary patch from netCDF w/ iimpi --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb index f6a3132f39c..1806b1252c5 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb @@ -15,15 +15,12 @@ patches = [ 'netCDF-%(version)s_fix-lib-name.patch', 'netCDF-%(version)s_fix-linking-errors.patch', 'netCDF-%(version)s_skip-nasa-test.patch', - 'netCDF-%(version)s_skip-parallel5-szip-tests.patch', ] checksums = [ {'v4.9.0.tar.gz': '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6'}, {'netCDF-4.9.0_fix-lib-name.patch': 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a'}, {'netCDF-4.9.0_fix-linking-errors.patch': '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15'}, {'netCDF-4.9.0_skip-nasa-test.patch': '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, - {'netCDF-4.9.0_skip-parallel5-szip-tests.patch': - '9ff5790cc369dce80b7db3610848913af94ef4b24ad7459390671f437b6bb2dd'}, ] builddependencies = [ From 0403e2d254fec111d5722085d010196abc8bdb88 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Feb 2023 13:37:49 +0000 Subject: [PATCH 6572/9987] use sed to disable parallel Szip, zlib tests for gompi version instead --- .../n/netCDF/netCDF-4.9.0-gompi-2022b.eb | 11 +- ...tCDF-4.9.0_skip-parallel5-szip-tests.patch | 214 ------------------ 2 files changed, 8 insertions(+), 217 deletions(-) delete mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-parallel5-szip-tests.patch diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb index 3c7b6c7f33f..da114873892 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb @@ -15,15 +15,12 @@ patches = [ 'netCDF-%(version)s_fix-lib-name.patch', 'netCDF-%(version)s_fix-linking-errors.patch', 'netCDF-%(version)s_skip-nasa-test.patch', - 'netCDF-%(version)s_skip-parallel5-szip-tests.patch', ] checksums = [ {'v4.9.0.tar.gz': '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6'}, {'netCDF-4.9.0_fix-lib-name.patch': 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a'}, {'netCDF-4.9.0_fix-linking-errors.patch': '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15'}, {'netCDF-4.9.0_skip-nasa-test.patch': '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, - {'netCDF-4.9.0_skip-parallel5-szip-tests.patch': - '9ff5790cc369dce80b7db3610848913af94ef4b24ad7459390671f437b6bb2dd'}, ] builddependencies = [ @@ -41,6 +38,14 @@ dependencies = [ ('libxml2', '2.10.3'), ] +# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso +# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g" + " nc_test4/run_par_test.sh.in &&") + # make sure both static and shared libs are built # and disable "remote" tests that access a unreliable external test server over internet configopts = [ diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-parallel5-szip-tests.patch b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-parallel5-szip-tests.patch deleted file mode 100644 index 9a674057e0f..00000000000 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0_skip-parallel5-szip-tests.patch +++ /dev/null @@ -1,214 +0,0 @@ -Author: Jasper Grimm (UoY) -Description: disable parallel Szip tests in tst_parallel5.c since - nc_put_vara_float() hangs on some systems (e.g. generoso) ------------------------------------------------------------------ -diff -ruN netcdf-c-4.9.0.orig/nc_test4/tst_parallel5.c netcdf-c-4.9.0.p1/nc_test4/tst_parallel5.c ---- netcdf-c-4.9.0.orig/nc_test4/tst_parallel5.c 2022-06-17 14:41:10.000000000 +0100 -+++ netcdf-c-4.9.0.p1/nc_test4/tst_parallel5.c 2023-02-16 16:54:45.000000000 +0000 -@@ -370,106 +370,106 @@ - } - if (!mpi_rank) - SUMMARIZE_ERR; --#ifdef HAVE_H5Z_SZIP --#ifdef HDF5_SUPPORTS_PAR_FILTERS --#define SZIP_DIM_LEN 256 --#define SZIP_DIM_NAME "Barrels" --#define SZIP_VAR_NAME "Best_Sligo_Rags" --#define SZIP_PIXELS_PER_BLOCK 32 -- if (!mpi_rank) -- printf("*** testing szip compression with parallel I/O..."); -- { -- int ncid, dimid, varid; -- float *data; -- float *data_in; -- int elements_per_pe = SZIP_DIM_LEN/mpi_size; -- size_t start[NDIMS1], count[NDIMS1]; -- int i; -- -- /* Create test data. */ -- if (!(data = malloc(elements_per_pe * sizeof(float)))) ERR; -- for (i = 0; i < elements_per_pe; i++) -- data[i] = mpi_rank + i * 0.1; -- -- /* Crate a file with a scalar NC_BYTE value. */ -- if (nc_create_par(FILE, NC_NETCDF4, MPI_COMM_WORLD, MPI_INFO_NULL, -- &ncid)) ERR; -- if (nc_def_dim(ncid, SZIP_DIM_NAME, SZIP_DIM_LEN, &dimid)) ERR; -- if (nc_def_var(ncid, SZIP_VAR_NAME, NC_FLOAT, NDIMS1, &dimid, &varid)) ERR; -- if (nc_def_var_szip(ncid, varid, H5_SZIP_NN_OPTION_MASK, -- SZIP_PIXELS_PER_BLOCK)) ERR; -- if (nc_enddef(ncid)) ERR; -- start[0] = mpi_rank * elements_per_pe; -- count[0] = elements_per_pe; -- if (nc_put_vara_float(ncid, varid, start, count, data)) ERR; -- if (nc_close(ncid)) ERR; -- -- /* Reopen the file and check. */ -- if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR; -- if (!(data_in = malloc(elements_per_pe * sizeof(float)))) ERR; -- if (nc_get_vara_float(ncid, varid, start, count, data_in)) ERR; -- if (nc_close(ncid)) ERR; -- for (i = 0; i < elements_per_pe; i++) -- if (data_in[i] != data[i]) ERR; -- -- /* Release resources. */ -- free(data_in); -- free(data); -- } -- if (!mpi_rank) -- SUMMARIZE_ERR; --#endif /* HDF5_SUPPORTS_PAR_FILTERS */ --#endif /* HAVE_H5Z_SZIP */ -- --#ifdef HAVE_H5Z_SZIP --#ifdef HDF5_SUPPORTS_PAR_FILTERS --#define SZIP_DIM_LEN 256 --#define SZIP_DIM_NAME "Barrels" --#define SZIP_VAR_NAME "Best_Sligo_Rags" --#define SZIP_PIXELS_PER_BLOCK 32 -- if (!mpi_rank) -- printf("*** testing szip compression with parallel I/O..."); -- { -- int ncid, dimid, varid; -- float *data; -- float *data_in; -- int elements_per_pe = SZIP_DIM_LEN/mpi_size; -- size_t start[NDIMS1], count[NDIMS1]; -- int i; -- -- /* Create test data. */ -- if (!(data = malloc(elements_per_pe * sizeof(float)))) ERR; -- for (i = 0; i < elements_per_pe; i++) -- data[i] = mpi_rank + i * 0.1; -- -- /* Crate a file with a scalar NC_BYTE value. */ -- if (nc_create_par(FILE, NC_NETCDF4, MPI_COMM_WORLD, MPI_INFO_NULL, -- &ncid)) ERR; -- if (nc_def_dim(ncid, SZIP_DIM_NAME, SZIP_DIM_LEN, &dimid)) ERR; -- if (nc_def_var(ncid, SZIP_VAR_NAME, NC_FLOAT, NDIMS1, &dimid, &varid)) ERR; -- if (nc_def_var_szip(ncid, varid, NC_SZIP_NN, SZIP_PIXELS_PER_BLOCK)) ERR; -- if (nc_enddef(ncid)) ERR; -- start[0] = mpi_rank * elements_per_pe; -- count[0] = elements_per_pe; -- if (nc_put_vara_float(ncid, varid, start, count, data)); -- if (nc_close(ncid)) ERR; -- -- /* Reopen the file and check. */ -- if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR; -- if (!(data_in = malloc(elements_per_pe * sizeof(float)))) ERR; -- if (nc_get_vara_float(ncid, varid, start, count, data_in)); -- if (nc_close(ncid)) ERR; -- for (i = 0; i < elements_per_pe; i++) -- if (data_in[i] != data[i]) ERR; -- -- /* Release resources. */ -- free(data_in); -- free(data); -- } -- if (!mpi_rank) -- SUMMARIZE_ERR; --#endif /* HDF5_SUPPORTS_PAR_FILTERS */ --#endif /* HAVE_H5Z_SZIP */ -+// #ifdef HAVE_H5Z_SZIP -+// #ifdef HDF5_SUPPORTS_PAR_FILTERS -+// #define SZIP_DIM_LEN 256 -+// #define SZIP_DIM_NAME "Barrels" -+// #define SZIP_VAR_NAME "Best_Sligo_Rags" -+// #define SZIP_PIXELS_PER_BLOCK 32 -+// if (!mpi_rank) -+// printf("*** testing szip compression with parallel I/O..."); -+// { -+// int ncid, dimid, varid; -+// float *data; -+// float *data_in; -+// int elements_per_pe = SZIP_DIM_LEN/mpi_size; -+// size_t start[NDIMS1], count[NDIMS1]; -+// int i; -+// -+// /* Create test data. */ -+// if (!(data = malloc(elements_per_pe * sizeof(float)))) ERR; -+// for (i = 0; i < elements_per_pe; i++) -+// data[i] = mpi_rank + i * 0.1; -+// -+// /* Crate a file with a scalar NC_BYTE value. */ -+// if (nc_create_par(FILE, NC_NETCDF4, MPI_COMM_WORLD, MPI_INFO_NULL, -+// &ncid)) ERR; -+// if (nc_def_dim(ncid, SZIP_DIM_NAME, SZIP_DIM_LEN, &dimid)) ERR; -+// if (nc_def_var(ncid, SZIP_VAR_NAME, NC_FLOAT, NDIMS1, &dimid, &varid)) ERR; -+// if (nc_def_var_szip(ncid, varid, H5_SZIP_NN_OPTION_MASK, -+// SZIP_PIXELS_PER_BLOCK)) ERR; -+// if (nc_enddef(ncid)) ERR; -+// start[0] = mpi_rank * elements_per_pe; -+// count[0] = elements_per_pe; -+// if (nc_put_vara_float(ncid, varid, start, count, data)) ERR; -+// if (nc_close(ncid)) ERR; -+// -+// /* Reopen the file and check. */ -+// if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR; -+// if (!(data_in = malloc(elements_per_pe * sizeof(float)))) ERR; -+// if (nc_get_vara_float(ncid, varid, start, count, data_in)) ERR; -+// if (nc_close(ncid)) ERR; -+// for (i = 0; i < elements_per_pe; i++) -+// if (data_in[i] != data[i]) ERR; -+// -+// /* Release resources. */ -+// free(data_in); -+// free(data); -+// } -+// if (!mpi_rank) -+// SUMMARIZE_ERR; -+// #endif /* HDF5_SUPPORTS_PAR_FILTERS */ -+// #endif /* HAVE_H5Z_SZIP */ -+// -+// #ifdef HAVE_H5Z_SZIP -+// #ifdef HDF5_SUPPORTS_PAR_FILTERS -+// #define SZIP_DIM_LEN 256 -+// #define SZIP_DIM_NAME "Barrels" -+// #define SZIP_VAR_NAME "Best_Sligo_Rags" -+// #define SZIP_PIXELS_PER_BLOCK 32 -+// if (!mpi_rank) -+// printf("*** testing szip compression with parallel I/O..."); -+// { -+// int ncid, dimid, varid; -+// float *data; -+// float *data_in; -+// int elements_per_pe = SZIP_DIM_LEN/mpi_size; -+// size_t start[NDIMS1], count[NDIMS1]; -+// int i; -+// -+// /* Create test data. */ -+// if (!(data = malloc(elements_per_pe * sizeof(float)))) ERR; -+// for (i = 0; i < elements_per_pe; i++) -+// data[i] = mpi_rank + i * 0.1; -+// -+// /* Crate a file with a scalar NC_BYTE value. */ -+// if (nc_create_par(FILE, NC_NETCDF4, MPI_COMM_WORLD, MPI_INFO_NULL, -+// &ncid)) ERR; -+// if (nc_def_dim(ncid, SZIP_DIM_NAME, SZIP_DIM_LEN, &dimid)) ERR; -+// if (nc_def_var(ncid, SZIP_VAR_NAME, NC_FLOAT, NDIMS1, &dimid, &varid)) ERR; -+// if (nc_def_var_szip(ncid, varid, NC_SZIP_NN, SZIP_PIXELS_PER_BLOCK)) ERR; -+// if (nc_enddef(ncid)) ERR; -+// start[0] = mpi_rank * elements_per_pe; -+// count[0] = elements_per_pe; -+// if (nc_put_vara_float(ncid, varid, start, count, data)); -+// if (nc_close(ncid)) ERR; -+// -+// /* Reopen the file and check. */ -+// if (nc_open_par(FILE, 0, comm, info, &ncid)) ERR; -+// if (!(data_in = malloc(elements_per_pe * sizeof(float)))) ERR; -+// if (nc_get_vara_float(ncid, varid, start, count, data_in)); -+// if (nc_close(ncid)) ERR; -+// for (i = 0; i < elements_per_pe; i++) -+// if (data_in[i] != data[i]) ERR; -+// -+// /* Release resources. */ -+// free(data_in); -+// free(data); -+// } -+// if (!mpi_rank) -+// SUMMARIZE_ERR; -+// #endif /* HDF5_SUPPORTS_PAR_FILTERS */ -+// #endif /* HAVE_H5Z_SZIP */ - - /* Shut down MPI. */ - MPI_Finalize(); From fa2c2a6a3daabc9ba43806bbb893a052db9692b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Feb 2023 15:23:13 +0100 Subject: [PATCH 6573/9987] use raw strings in HiCExplorer easyconfig to fix 'invalid escape sequence' linting errors --- .../easyconfigs/h/HiCExplorer/HiCExplorer-3.7.2-foss-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-3.7.2-foss-2022a.eb b/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-3.7.2-foss-2022a.eb index 6e84c6bdf3e..be8ef5e31a2 100644 --- a/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-3.7.2-foss-2022a.eb +++ b/easybuild/easyconfigs/h/HiCExplorer/HiCExplorer-3.7.2-foss-2022a.eb @@ -45,9 +45,9 @@ exts_list = [ 'checksums': ['401e27dee2531a06ea9abe8a73fab8f29c1c92758ece2f8b84e171a9310b0a71'], }), ('fit-nbinom', '1.1', { - 'preinstallopts': "sed -i 's/\.\*//g' setup.py && ", 'sources': ['fit_nbinom-%(version)s.tar.gz'], 'checksums': ['bd9600f24f00ab0ec7e8d96b7fcf1ff96ea37d129c9258e0be4bee3262a1688b'], + 'preinstallopts': r"sed -i 's/\.\*//g' setup.py && ", }), ('hic2cool', '0.8.3', { 'checksums': ['c244b89bd23a021c80b0a5b2a5d827dc2f313a4e6497e1ac45044fdc3b109a77'], @@ -56,10 +56,10 @@ exts_list = [ 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], }), (name, version, { - 'preinstallopts': "sed -i 's/\.\*//g' setup.py && ", 'source_urls': ['https://github.com/deeptools/HiCExplorer/archive/'], 'sources': ['%(version)s.tar.gz'], 'checksums': ['dca71065dd4e549d578db96870b8d650b48f3dc852918ef19a345f436f612037'], + 'preinstallopts': r"sed -i 's/\.\*//g' setup.py && ", }), ] From c69f27f8510883188c4df464728912fd090f50b6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Feb 2023 14:23:38 +0000 Subject: [PATCH 6574/9987] fix missing closing sed quotes --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb index da114873892..60bc97dc829 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb @@ -41,9 +41,9 @@ dependencies = [ # disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso # see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 # and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 -preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g" - " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g" - " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g" +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" " nc_test4/run_par_test.sh.in &&") # make sure both static and shared libs are built From 1eaec41283528edbe7ba5f51f5d32cc0e2151b0d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Feb 2023 14:35:17 +0000 Subject: [PATCH 6575/9987] use absolute path to file to sed --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb index 60bc97dc829..3aa763759fb 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-gompi-2022b.eb @@ -44,7 +44,7 @@ dependencies = [ preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" - " nc_test4/run_par_test.sh.in &&") + " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") # make sure both static and shared libs are built # and disable "remote" tests that access a unreliable external test server over internet From 5bfe262dd8fe054ce412b0c1a06f0a351f5db2f9 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 16:45:11 +0100 Subject: [PATCH 6576/9987] Update easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb b/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb index 56e9a481d47..d5346dfc50c 100644 --- a/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ configopts = '-DHEPMC3_ENABLE_ROOTIO=OFF -DHEPMC3_ENABLE_PYTHON=ON' sanity_check_paths = { - 'files': ["lib/libHepMC3.so"], + 'files': ['lib/libHepMC3.%s' % SHLIB_EXT], 'dirs': ['include/HepMC3'] } sanity_check_commands = ["python -c 'import pyHepMC3'"] From 79ac542381b85b14b97518fb6a8594a58267b094 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 17 Feb 2023 16:45:45 +0100 Subject: [PATCH 6577/9987] add checksum for aarch64 variant --- easybuild/easyconfigs/b/Beast/Beast-2.7.3-GCC-11.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Beast/Beast-2.7.3-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Beast/Beast-2.7.3-GCC-11.3.0.eb index 8c90156a1e9..b2242c074cf 100644 --- a/easybuild/easyconfigs/b/Beast/Beast-2.7.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/Beast/Beast-2.7.3-GCC-11.3.0.eb @@ -17,7 +17,10 @@ _archs = {'x86_64': 'x86', 'aarch64': 'aarch64'} source_urls = ['https://github.com/CompEvol/beast2/releases/download/v%(version)s/'] sources = ['BEAST.v%%(version)s.Linux.%s.tgz' % _archs[ARCH]] -checksums = ['234af8572e827c1c856f0e1ad46e61fa3b3b875c6b5d246f67839ec7c1bf40b5'] +checksums = [{ + 'BEAST.v%(version)s.Linux.x86.tgz': '234af8572e827c1c856f0e1ad46e61fa3b3b875c6b5d246f67839ec7c1bf40b5', + 'BEAST.v%(version)s.Linux.aarch64.tgz': '7353703f178b2f0e440ca31cd93f136a9fe65708cd8a621a8045fc63ca538f22', +}] dependencies = [ ('Java', '11', '', SYSTEM), From 8291024e2e3e7d51b501630bc25e19383da4dec5 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 16:46:15 +0100 Subject: [PATCH 6578/9987] Update YODA-1.9.7-gompi-2022a.eb --- easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb index 2f3dbc7072f..5c687beb880 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb @@ -25,8 +25,8 @@ dependencies = [ configopts = "--disable-root --enable-pyext --disable-static" sanity_check_paths = { - 'files': ["bin/yoda-config", "lib/libYODA.so"], - 'dirs': ["lib"] + 'files': ['bin/yoda-config', 'lib/libYODA.%s' % SHLIB_EXT], + 'dirs': ['lib'] } sanity_check_commands = ["python -c 'import yoda'"] From efd96aa2d9b04a771cad3a3d5c4b51d19bb0cde7 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 16:47:33 +0100 Subject: [PATCH 6579/9987] Update siscone-3.0.5-GCCcore-11.3.0.eb --- .../easyconfigs/s/siscone/siscone-3.0.5-GCCcore-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/siscone/siscone-3.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/siscone/siscone-3.0.5-GCCcore-11.3.0.eb index 1f772a0bf42..5ca8d172b3a 100644 --- a/easybuild/easyconfigs/s/siscone/siscone-3.0.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/siscone/siscone-3.0.5-GCCcore-11.3.0.eb @@ -20,8 +20,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ["lib/libsiscone.so"], - 'dirs': ["include/siscone"], + 'files': ['lib/libsiscone.%s' % SHLIB_EXT], + 'dirs': ['include/siscone'], } moduleclass = 'phys' From f67e8cb5d0ade336d6a021b66c069af66269c38c Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 16:56:52 +0100 Subject: [PATCH 6580/9987] Update HepMC3-3.2.5-GCC-11.3.0.eb --- easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb b/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb index d5346dfc50c..113308b1508 100644 --- a/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.5-GCC-11.3.0.eb @@ -21,7 +21,11 @@ dependencies = [ ('Python', '3.10.4') ] -configopts = '-DHEPMC3_ENABLE_ROOTIO=OFF -DHEPMC3_ENABLE_PYTHON=ON' +configopts = '-DHEPMC3_ENABLE_ROOTIO=OFF -Dmomentum=GEV -Dlength=MM ' +configopts += '-DHEPMC3_ENABLE_PYTHON=ON ' +configopts += '-DHEPMC3_Python_SITEARCH310=%(installdir)s/lib/python%(pyshortver)s/site-packages' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_paths = { 'files': ['lib/libHepMC3.%s' % SHLIB_EXT], From 76124a724c8d2a79c966aee66f82ca195d2b3c28 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 17:06:46 +0100 Subject: [PATCH 6581/9987] Fix python installlation dir --- easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb index 5c687beb880..106b2577c80 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb @@ -11,17 +11,23 @@ description = """ Yet more Objects for (High Energy Physics) Data Analysis """ -toolchain = {'name': 'gompi', 'version': '2022a'} +toolchain = {'name': 'GCC', 'version': '11.3.0'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['https://yoda.hepforge.org/downloads?f='] sources = ['%(name)s-%(version)s.tar.bz2'] checksums = ['8d07bb04dcb79364858718a18203452d8d9fa00029fa94239eafa8529032b8ff'] +builddependencies = [ + ('Autotools', '20220317'), +] + dependencies = [ ('Python', '3.10.4') ] +preconfigopts = "sed -i 's|^\ YODA_PYTHONPATH=.*|\ " +preconfigopts += "YODA_PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages|g' configure &&" configopts = "--disable-root --enable-pyext --disable-static" sanity_check_paths = { From d339fc7510c3be6f834d6ae50e61314fb602cab8 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 17:34:58 +0100 Subject: [PATCH 6582/9987] Update YODA-1.9.7-gompi-2022a.eb --- easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb index 106b2577c80..7becec95549 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb @@ -26,7 +26,7 @@ dependencies = [ ('Python', '3.10.4') ] -preconfigopts = "sed -i 's|^\ YODA_PYTHONPATH=.*|\ " +preconfigopts = "sed -i 's|YODA_PYTHONPATH=.*|" preconfigopts += "YODA_PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages|g' configure &&" configopts = "--disable-root --enable-pyext --disable-static" From eeb084617c8d36a5cb7c07a16b4bcc69955a0a13 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 17:43:52 +0100 Subject: [PATCH 6583/9987] GCCcore is enough --- ...-1.9.7-gompi-2022a.eb => YODA-1.9.7-GCCcore-11.3.0.eb} | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/y/YODA/{YODA-1.9.7-gompi-2022a.eb => YODA-1.9.7-GCCcore-11.3.0.eb} (81%) diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCCcore-11.3.0.eb similarity index 81% rename from easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb rename to easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCCcore-11.3.0.eb index 7becec95549..2ce40759ede 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-gompi-2022a.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCCcore-11.3.0.eb @@ -11,7 +11,7 @@ description = """ Yet more Objects for (High Energy Physics) Data Analysis """ -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['https://yoda.hepforge.org/downloads?f='] @@ -26,13 +26,13 @@ dependencies = [ ('Python', '3.10.4') ] -preconfigopts = "sed -i 's|YODA_PYTHONPATH=.*|" -preconfigopts += "YODA_PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages|g' configure &&" configopts = "--disable-root --enable-pyext --disable-static" +buildopts = "YODA_PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" +installopts = buildopts sanity_check_paths = { 'files': ['bin/yoda-config', 'lib/libYODA.%s' % SHLIB_EXT], - 'dirs': ['lib'] + 'dirs': ['lib/python%(pyshortver)s/site-packages'] } sanity_check_commands = ["python -c 'import yoda'"] From 31967f6f2d12d1c6b036c2f3d9548c8ded7efae1 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 17:54:07 +0100 Subject: [PATCH 6584/9987] GCC for zlib and binutils --- .../{YODA-1.9.7-GCCcore-11.3.0.eb => YODA-1.9.7-GCC-11.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/y/YODA/{YODA-1.9.7-GCCcore-11.3.0.eb => YODA-1.9.7-GCC-11.3.0.eb} (95%) diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb similarity index 95% rename from easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb index 2ce40759ede..31487c94983 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb @@ -11,7 +11,7 @@ description = """ Yet more Objects for (High Energy Physics) Data Analysis """ -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchain = {'name': 'GCC', 'version': '11.3.0'} toolchainopts = {'optarch': True, 'pic': True} source_urls = ['https://yoda.hepforge.org/downloads?f='] From ccbd009e1855a356c41a2ff2c42c2b12262bc55e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 17 Feb 2023 18:06:09 +0100 Subject: [PATCH 6585/9987] move pkgconf to build deps --- .../easyconfigs/b/beagle-lib/beagle-lib-4.0.0-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.0-GCC-11.3.0.eb index bdaf2367d6d..7824fea6434 100644 --- a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/beagle-lib/beagle-lib-4.0.0-GCC-11.3.0.eb @@ -16,11 +16,11 @@ checksums = ['d197eeb7fe5879dfbae789c459bcc901cb04d52c9cf5ef14fb07ff7a6b74560b'] builddependencies = [ ('CMake', '3.24.3'), + ('pkgconf', '1.8.0'), ] dependencies = [ ('Java', '11', '', SYSTEM), - ('pkgconf', '1.8.0'), ('pocl', '1.8'), ] From 337e474c720cb7f58fb75f1da5a0dfb2e5d59ab0 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 18:18:01 +0100 Subject: [PATCH 6586/9987] adding easyconfigs: fastjet-3.4.0-gompi-2022a.eb and patches: fastjet-3.4.0_excludeSISCone.patch --- .../f/fastjet/fastjet-3.4.0-gompi-2022a.eb | 45 ++++++++++++ .../fastjet-3.4.0_excludeSISCone.patch | 72 +++++++++++++++++++ 2 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastjet/fastjet-3.4.0-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch diff --git a/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0-gompi-2022a.eb b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0-gompi-2022a.eb new file mode 100644 index 00000000000..e49de79af2e --- /dev/null +++ b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0-gompi-2022a.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'fastjet' +version = '3.4.0' + +homepage = 'https://fastjet.fr/' +description = """A software package for jet finding in pp and e+e- collisions""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://fastjet.fr/repo/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['fastjet-3.4.0_excludeSISCone.patch'] +checksums = [ + 'ee07c8747c8ead86d88de4a9e4e8d1e9e7d7614973f5631ba8297f7a02478b91', + 'b1f295b47b7cb182610db2dbd799b0adb02913a36bcbaab8677e2749e325604a' # fastjet-3.4.0_excludeSISCone.patch +] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('siscone', '3.0.5'), + ('CGAL', '4.14.3'), +] +# For CGAL >=5 +# configopts = '--enable-cgal-header-only --enable-pyext --enable-allplugins --enable-allcxxplugins ' +configopts = '--enable-cgal --enable-pyext --enable-allplugins --enable-allcxxplugins ' +configopts += "--enable-shared" + +sanity_check_paths = { + 'files': ['lib/libfastjet.%s' % SHLIB_EXT, 'bin/fastjet-config'], + 'dirs': ['include/fastjet'], +} +sanity_check_commands = ["python -c 'import fastjet'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch new file mode 100644 index 00000000000..e5a457772fc --- /dev/null +++ b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch @@ -0,0 +1,72 @@ +--- fastjet-3.4.0.orig/configure.ac 2021-06-25 15:38:14.000000000 +0200 ++++ fastjet-3.4.0/configure.ac 2022-11-11 12:22:21.863457311 +0100 +@@ -438,6 +438,12 @@ + fi + + dnl SISCone ++AC_ARG_WITH(bundle-siscone, ++ [ --with-bundle-siscone Build the bundled SISCone library [default=no]], ++ [bundle_siscone=$withval], ++ [bundle_siscone=no]) ++AM_CONDITIONAL(BUNDLE_SISCONE, test x$bundle_siscone != xno) ++ + ACX_CHECK_PLUGIN(SISCone, siscone, SISCONE, yes, + [CONFIG_LIBS_PLUGINS=${CONFIG_LIBS_PLUGINS}" -lsiscone_spherical -lsiscone" + CONFIG_LIBS_PLUGINS_STATIC=${CONFIG_LIBS_PLUGINS_STATIC}" \${installationdir}/lib/libsiscone.a \${installationdir}/lib/libsiscone_spherical.a"]) +--- fastjet-3.4.0.orig/example/Makefile.am 2021-06-25 15:37:05.000000000 +0200 ++++ fastjet-3.4.0/example/Makefile.am 2022-11-11 12:45:45.876416000 +0100 +@@ -43,7 +43,7 @@ + 03_plugin_CXXFLAGS = $(AM_CXXFLAGS) $(CGAL_CPPFLAGS) -I$(srcdir)/../include + 03_plugin_LDADD = ../src/libfastjet.la $(CGAL_LIBS) + 03_plugin_CXXFLAGS += -I$(srcdir)/../plugins/SISCone -I$(srcdir)/../plugins/SISCone/siscone +-03_plugin_LDADD += ../plugins/SISCone/libSISConePlugin.la ../plugins/SISCone/siscone/siscone/libsiscone.la ../plugins/SISCone/siscone/siscone/spherical/libsiscone_spherical.la ++03_plugin_LDADD += ../plugins/SISCone/libSISConePlugin.la + else + EXTRA_DIST += 03-plugin.cc + endif +@@ -125,7 +125,7 @@ + fastjet_areas_LDADD = ../src/libfastjet.la $(CGAL_LIBS) + if BUILD_PLUGIN_SISCONE + fastjet_areas_CXXFLAGS += -I$(srcdir)/../plugins/SISCone -I$(srcdir)/../plugins/SISCone/siscone +-fastjet_areas_LDADD += ../plugins/SISCone/libSISConePlugin.la ../plugins/SISCone/siscone/siscone/libsiscone.la ../plugins/SISCone/siscone/siscone/spherical/libsiscone_spherical.la ++fastjet_areas_LDADD += ../plugins/SISCone/libSISConePlugin.la + endif + + fastjet_timing_plugins_SOURCES = fastjet_timing_plugins.cc CmdLine.cc +@@ -135,7 +135,7 @@ + fastjet_timing_plugins_LDADD += ../tools/libfastjettools.la + if BUILD_PLUGIN_SISCONE + fastjet_timing_plugins_CXXFLAGS += -I$(srcdir)/../plugins/SISCone -I$(srcdir)/../plugins/SISCone/siscone +-fastjet_timing_plugins_LDADD += ../plugins/SISCone/libSISConePlugin.la ../plugins/SISCone/siscone/siscone/libsiscone.la ../plugins/SISCone/siscone/siscone/spherical/libsiscone_spherical.la ++fastjet_timing_plugins_LDADD += ../plugins/SISCone/libSISConePlugin.la + endif + if BUILD_PLUGIN_CDFCONES + fastjet_timing_plugins_CXXFLAGS += -I$(srcdir)/../plugins/CDFCones +--- fastjet-3.4.0.orig/plugins/SISCone/Makefile.am 2021-06-25 15:37:05.000000000 +0200 ++++ fastjet-3.4.0/plugins/SISCone/Makefile.am 2022-11-11 12:47:47.412329000 +0100 +@@ -1,12 +1,22 @@ +-SUBDIRS = siscone fastjet . ++SUBDIRS = fastjet . + + if MONOLITHIC_PLUGINS + noinst_LTLIBRARIES = libSISConePlugin.la + else + lib_LTLIBRARIES = libSISConePlugin.la + endif +-libSISConePlugin_la_CXXFLAGS = $(AM_CXXFLAGS) -I$(srcdir) -I$(srcdir)/siscone -I$(srcdir)/../../include -I./siscone ++libSISConePlugin_la_CXXFLAGS = $(AM_CXXFLAGS) -I$(srcdir) -I$(srcdir)/../../include ++ ++if BUNDLE_SISCONE ++SUBDIRS += siscone ++libSISConePlugin_la_CXXFLAGS += -I$(srcdir)/siscone ++libSISConePlugin_la_LIBADD = \ ++ $(top_builddir)/plugins/SISCone/siscone/siscone/libsiscone.la \ ++ $(top_builddir)/plugins/SISCone/siscone/siscone/spherical/libsiscone_spherical.la ++else ++libSISConePlugin_la_LIBADD = -lsiscone -lsiscone_spherical ++endif + libSISConePlugin_la_SOURCES = SISConeBasePlugin.cc SISConePlugin.cc SISConeSphericalPlugin.cc +-libSISConePlugin_la_LIBADD = ../../src/libfastjet.la siscone/siscone/libsiscone.la siscone/siscone/spherical/libsiscone_spherical.la ++ + + EXTRA_DIST = makefile.static From 9cfa70d9ee9665f3d4b484ffcc36aba9e1329c9f Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 18:36:49 +0100 Subject: [PATCH 6587/9987] Update fastjet-3.4.0_excludeSISCone.patch --- .../easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch index e5a457772fc..84491736e0d 100644 --- a/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch +++ b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch @@ -1,3 +1,6 @@ +# Author: Alexander Puck Neuwirth +# We don't want to use the shipped siscone, but use the system/easybuild +# installed version of siscone --- fastjet-3.4.0.orig/configure.ac 2021-06-25 15:38:14.000000000 +0200 +++ fastjet-3.4.0/configure.ac 2022-11-11 12:22:21.863457311 +0100 @@ -438,6 +438,12 @@ From fafb52b38ae279c7c47ba85e320e55a43e656836 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 19:47:51 +0100 Subject: [PATCH 6588/9987] Update fastjet-3.4.0-gompi-2022a.eb --- easybuild/easyconfigs/f/fastjet/fastjet-3.4.0-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0-gompi-2022a.eb b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0-gompi-2022a.eb index e49de79af2e..631c87a53f4 100644 --- a/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0-gompi-2022a.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['fastjet-3.4.0_excludeSISCone.patch'] checksums = [ 'ee07c8747c8ead86d88de4a9e4e8d1e9e7d7614973f5631ba8297f7a02478b91', - 'b1f295b47b7cb182610db2dbd799b0adb02913a36bcbaab8677e2749e325604a' # fastjet-3.4.0_excludeSISCone.patch + '698902b4c4d54873d640239461cccc036234986ae8d6a33ceb649462ade971d3' # fastjet-3.4.0_excludeSISCone.patch ] builddependencies = [ From e7fddb386a3806a47dc5ee6170546d1c27ed8a2b Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Fri, 17 Feb 2023 20:28:32 +0100 Subject: [PATCH 6589/9987] probably spaces missing in checksum calc --- .../easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch index 84491736e0d..5adb5bcab24 100644 --- a/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch +++ b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.0_excludeSISCone.patch @@ -1,5 +1,5 @@ # Author: Alexander Puck Neuwirth -# We don't want to use the shipped siscone, but use the system/easybuild +# We don't want to use the shipped siscone, but use the system/easybuild # installed version of siscone --- fastjet-3.4.0.orig/configure.ac 2021-06-25 15:38:14.000000000 +0200 +++ fastjet-3.4.0/configure.ac 2022-11-11 12:22:21.863457311 +0100 From 2281e5cf68aba04dbc7ecf4559836e7d551cf873 Mon Sep 17 00:00:00 2001 From: garadar Date: Mon, 20 Feb 2023 13:35:15 +0100 Subject: [PATCH 6590/9987] Update easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb index 86e2b2ece4d..415adeb1465 100644 --- a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb @@ -10,7 +10,6 @@ description = """tulips creates diagrams of the structure and evolution of stars It creates plots and movies based on output from the MESA stellar evolution code""" toolchain = {'name': 'foss', 'version': '2022a'} -toolchainopts = {'pic': True} dependencies = [ ('Python', '3.10.4'), From 348e85974d0aeee4373f8e7d88ae6aa9280b7bc7 Mon Sep 17 00:00:00 2001 From: Xin Wu Date: Mon, 20 Feb 2023 14:47:02 +0100 Subject: [PATCH 6591/9987] new homepage --- easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022b.eb index 0e976bd6b9c..62853f74ffb 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2021.11.001-intel-2022b.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2021.11.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications.""" toolchain = {'name': 'intel', 'version': '2022b'} From b1954252cede0da74d9a9e5656b7e93f13172d0c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2023 17:36:41 +0100 Subject: [PATCH 6592/9987] adding easyconfigs: HTSplotter-0.15-foss-2022a.eb --- .../HTSplotter/HTSplotter-0.15-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb new file mode 100644 index 00000000000..98f87e55a48 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'HTSplotter' +version = '0.15' + +homepage = 'https://github.com/CBIGR/HTSplotter' +description = """HTSplotter allows an end-to-end data processing and analysis of chemical and genetic in vitro +perturbation screens.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('h5py', '3.7.0'), + ('Seaborn', '0.12.1'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('minio', '7.1.13', { + 'checksums': ['8828615a20cde82df79c5a52005252ad29bb022cde25177a4a43952a04c3222c'], + }), + ('pypdf', '3.4.1', { + 'checksums': ['8b0badc787062e8fb0d8393eb2a76903717fb24e5cc84e2b03cde5ac3881700f'], + # break import from Crypto, since pycrypto 2.6.1 is not actually compatible with Python 3.x + 'preinstallopts': "sed -i 's/from Crypto/from Cryptoxxx/g' pypdf/_encryption.py && ", + }), + ('PyPDF2', '3.0.1', { + 'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'], + # break import from Crypto, since pycrypto 2.6.1 is not actually compatible with Python 3.x + 'preinstallopts': "sed -i 's/from Crypto/from Cryptoxxx/g' PyPDF2/_encryption.py && ", + 'modulename': 'PyPDF2', + }), + ('PyPDF3', '1.0.6', { + 'checksums': ['c946f3273419e37258e35e72273f49904ab15723d87a761c1115ef99799f8c5f'], + 'modulename': 'PyPDF3', + }), + (name, version, { + 'checksums': ['9504709ac2d04dbcd0694ca0370a44b7e302b667771fb492b596d9662a2a85a9'], + 'modulename': 'HTSplotter', + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 030380125ef5c88de04e8b2b8a995e92a80467c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2023 17:41:50 +0100 Subject: [PATCH 6593/9987] adding easyconfigs: QUAST-5.2.0-foss-2022a.eb --- .../q/QUAST/QUAST-5.2.0-foss-2022a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-foss-2022a.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-foss-2022a.eb new file mode 100644 index 00000000000..cdf97207a34 --- /dev/null +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-foss-2022a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'QUAST' +version = '5.2.0' + +homepage = 'https://github.com/ablab/quast' +description = """QUAST evaluates genome assemblies by computing various metrics. +It works both with and without reference genomes. The tool accepts multiple +assemblies, thus is suitable for comparison.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('matplotlib', '3.5.2'), + ('Java', '11', '', SYSTEM), + ('Boost', '1.79.0'), +] + +use_pip = True + +github_account = 'ablab' +exts_list = [ + (name, version, { + 'modulename': '%(namelower)s_libs', + 'source_tmpl': '%(namelower)s_%(version)s.tar.gz', + 'source_urls': [GITHUB_LOWER_SOURCE], + }), +] + +postinstallcmds = [ + "cd %(installdir)s/bin && ln -s %(namelower)s.py %(namelower)s", + "cp -a %(builddir)s/QUAST/quast*%(version)s/test_data %(installdir)s/", +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s.py', 'bin/meta%(namelower)s.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'test_data'], +} + +sanity_check_commands = [ + "quast -h", + "mkdir -p %(builddir)s && cp -a %(installdir)s/test_data %(builddir)s && cd %(builddir)s && quast.py --test", +] + +sanity_pip_check = True + +moduleclass = 'bio' From e5afe344c4e6e6a322f58a1b9c7de5365b2754b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2023 17:42:20 +0100 Subject: [PATCH 6594/9987] adding easyconfigs: VirSorter2-2.2.4-foss-2022a.eb --- .../VirSorter2/VirSorter2-2.2.4-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/v/VirSorter2/VirSorter2-2.2.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/v/VirSorter2/VirSorter2-2.2.4-foss-2022a.eb b/easybuild/easyconfigs/v/VirSorter2/VirSorter2-2.2.4-foss-2022a.eb new file mode 100644 index 00000000000..13f73639e85 --- /dev/null +++ b/easybuild/easyconfigs/v/VirSorter2/VirSorter2-2.2.4-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'VirSorter2' +version = '2.2.4' + +homepage = 'https://github.com/jiarong/VirSorter2' +description = """VirSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and + RNA virus genomes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ruamel.yaml', '0.17.21'), + ('snakemake', '7.22.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/jiarong/VirSorter2/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['f9d1c291f773d9c4d70d7ec096e76c21208950d74d7bd5046da7c4a77cd54c07'], + 'modulename': 'virsorter', + }), +] + +sanity_check_paths = { + 'files': ['bin/virsorter'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["virsorter --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From ecc9d4e0189e6ab33fc6c06ba8f0a9ec3aba0060 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2023 17:44:32 +0100 Subject: [PATCH 6595/9987] adding easyconfigs: vConTACT2-0.11.3-foss-2022a.eb --- .../vConTACT2/vConTACT2-0.11.3-foss-2022a.eb | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/v/vConTACT2/vConTACT2-0.11.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/v/vConTACT2/vConTACT2-0.11.3-foss-2022a.eb b/easybuild/easyconfigs/v/vConTACT2/vConTACT2-0.11.3-foss-2022a.eb new file mode 100644 index 00000000000..86e90f7efb5 --- /dev/null +++ b/easybuild/easyconfigs/v/vConTACT2/vConTACT2-0.11.3-foss-2022a.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'vConTACT2' +local_commit = 'c0413a6c92e86c58d624b4eb2e32687ceca89bd6' +version = '0.11.3' + +homepage = 'https://bitbucket.org/MAVERICLab/vcontact2' +description = """vConTACT2 is a tool to perform guilt-by-contig-association classification of + viral genomic sequence data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('networkx', '2.8.4'), + ('scikit-learn', '1.1.2'), + ('PyTables', '3.8.0'), + ('GitPython', '3.1.27'), # required by clusterone +] + +use_pip = True + +exts_list = [ + ('click-log', '0.4.0', { + 'checksums': ['3970f8570ac54491237bcdb3d8ab5e3eef6c057df29f8c3d1151a51a9c23b975'], + }), + ('coreschema', '0.0.4', { + 'checksums': ['9503506007d482ab0867ba14724b93c18a33b22b6d19fb419ef2d239dd4a1607'], + }), + ('itypes', '1.2.0', { + 'checksums': ['af886f129dea4a2a1e3d36595a2d139589e4dd287f5cab0b40e799ee81570ff1'], + }), + ('uritemplate', '4.1.1', { + 'checksums': ['4346edfc5c3b79f694bccd6d6099a322bbeb628dbf2cd86eea55a456ce5124f0'], + }), + ('coreapi', '2.3.3', { + 'checksums': ['46145fcc1f7017c076a2ef684969b641d18a2991051fddec9458ad3f78ffc1cb'], + }), + ('coreapi-cli', '1.0.9', { + 'checksums': ['d76b5320ea9ad04d922001ac8897b903a7a359c08a53822f819134c50aa22c5f'], + }), + ('iso8601', '1.1.0', { + 'checksums': ['32811e7b81deee2063ea6d2e94f8819a86d1f3811e49d23623a41fa832bef03f'], + }), + ('raven', '6.10.0', { + 'checksums': ['3fa6de6efa2493a7c827472e984ce9b020797d0da16f1db67197bcc23c8fae54'], + }), + ('terminaltables', '3.1.10', { + 'checksums': ['ba6eca5cb5ba02bba4c9f4f985af80c54ec3dccf94cfcd190154386255e47543'], + }), + ('tzdata', '2022.7', { + 'checksums': ['fe5f866eddd8b96e9fcba978f8e503c909b19ea7efda11e52e39494bad3a7bfa'], + }), + ('pytz-deprecation-shim', '0.1.0.post0', { + 'sources': ['pytz_deprecation_shim-%(version)s.tar.gz'], + 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], + }), + ('tzlocal', '4.2', { + 'checksums': ['ee5842fa3a795f023514ac2d801c4a81d1743bbe642e3940143326b3a00addd7'], + }), + ('clusterone', '0.15.3', { + 'checksums': ['ce253e778c68aa1c8f408ac2b835caca62d90b9c9206bf9f56819ee97b198cf9'], + # remove strict version requirements for required Python packages, + # remove requirement for enum34 (not needed when using Python >= 3.4) + 'preinstallopts': "sed -i 's/==/>=/g' setup.py && sed -i '/enum34/d' setup.py && ", + }), + (name, version, { + 'source_urls': ['https://bitbucket.org/MAVERICLab/vcontact2/get/'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['22890d2839d53140220bff8e0333f1dab562c16270cd86dfe88ff0836d8ba0b7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 4afab947b6d6676f59555a227977779b036707d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Feb 2023 17:58:56 +0100 Subject: [PATCH 6596/9987] add missing SHA256 checksum for QUAST 5.2.0 --- easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-foss-2022a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-foss-2022a.eb b/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-foss-2022a.eb index cdf97207a34..d3589c364cf 100644 --- a/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QUAST/QUAST-5.2.0-foss-2022a.eb @@ -24,9 +24,10 @@ use_pip = True github_account = 'ablab' exts_list = [ (name, version, { - 'modulename': '%(namelower)s_libs', - 'source_tmpl': '%(namelower)s_%(version)s.tar.gz', 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['%(namelower)s_%(version)s.tar.gz'], + 'checksums': ['db903a6e4dd81384687f1c38d47cbe0f51bdf7f6d5e5c0bd30c13796391f4f04'], + 'modulename': 'quast_libs', }), ] From 1036d8b792a504ae16afee4bdb68748f8f2956ce Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 21 Feb 2023 04:32:46 +0000 Subject: [PATCH 6597/9987] Update test/easyconfigs/easyconfigs.py Co-authored-by: Alex Domingo --- test/easyconfigs/easyconfigs.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2338be7058a..48047a494c6 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -931,14 +931,14 @@ def test_easyconfig_name_clashes(self): """Make sure there is not a name clash when all names are lowercase""" topdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__))) names = defaultdict(list) + # ignore git/svn dirs & archived easyconfigs + ignore_dirs = ['.git', '.svn', '__archive__'] for (dirpath, _, _) in os.walk(topdir): - # ignore git/svn dirs & archived easyconfigs - if '/.git/' in dirpath or '/.svn/' in dirpath or '__archive__' in dirpath: - continue - dirpath_split = dirpath.replace(topdir, '').split(os.sep) - if len(dirpath_split) == 5: - name = dirpath_split[4] - names[name.lower()].append(name) + if not any('/%s' % d in dirpath for d in ignore_dirs): + dirpath_split = dirpath.replace(topdir, '').split(os.sep) + if len(dirpath_split) == 5: + name = dirpath_split[4] + names[name.lower()].append(name) duplicates = {} for name in names: From f829f40c0ec56df5fc0090ba55d81a47b6c80a88 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 21 Feb 2023 08:27:29 +0000 Subject: [PATCH 6598/9987] adding easyconfigs: Autotools-20220317.eb --- .../a/Autotools/Autotools-20220317.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20220317.eb diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20220317.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20220317.eb new file mode 100644 index 00000000000..7621956c2f0 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20220317.eb @@ -0,0 +1,21 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20220317' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = SYSTEM + +dependencies = [ + ('Autoconf', '2.71'), # 20210128 + ('Automake', '1.16.5'), # 20211003 + ('libtool', '2.4.7'), # 20220317 +] + +moduleclass = 'devel' From 8d16c0292b1f6d4f0b10921fd07100388cf1d55a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 21 Feb 2023 09:30:36 +0000 Subject: [PATCH 6599/9987] adding easyconfigs: poetry-1.2.2-GCCcore-11.3.0.eb --- .../p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100755 easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb new file mode 100755 index 00000000000..89484d89f24 --- /dev/null +++ b/easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'poetry' +version = '1.2.2' + +homepage = 'https://python-poetry.org' +description = """Python packaging and dependency management made easy. Poetry helps you declare, manage and install + dependencies of Python projects, ensuring you have the right stack everywhere.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('packaging', '21.3', { + 'checksums': ['dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb'], + }), + ('dulwich', '0.20.50', { + 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], + }), + ('poetry_plugin_export', '1.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['109fb43ebfd0e79d8be2e7f9d43ba2ae357c4975a18dfc0cfdd9597dd086790e'], + }), + ('cleo', '1.0.0a5', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ff53056589300976e960f75afb792dfbfc9c78dcbb5a448e207a17b643826360'], + }), + ('jsonschema', '4.17.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['f660066c3966db7d6daeaea8a75e0b68237a48e51cf49882087757bb59916248'], + }), + ('platformdirs', '2.5.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0cb405749187a194f444c25c82ef7225232f11564721eabffc6ec70df83b11cb'], + }), + ('shellingham', '1.5.0', { + 'checksums': ['72fb7f5c63103ca2cb91b23dee0c71fe8ad6fbfd46418ef17dbe40db51592dad'], + }), + ('tomlkit', '0.11.6', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b'], + }), + ('poetry_core', '1.3.2', { + 'modulename': 'poetry.core', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ea0f5a90b339cde132b4e43cff78a1b440cd928db864bb67cfc97fdfcefe7218'], + }), + (name, version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['93ea3c4a622485c2a7b7249f1e34e4ac84f8229ded76153b67506313201b154f'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' From f2e67207a03dd2ce18a223302796b36437824cfd Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 21 Feb 2023 10:12:36 +0000 Subject: [PATCH 6600/9987] add binutils --- easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb index 89484d89f24..c420a5183ce 100755 --- a/easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb @@ -9,6 +9,10 @@ description = """Python packaging and dependency management made easy. Poetry he toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +builddependencies = [ + ('binutils', '2.38'), +] + dependencies = [ ('Python', '3.10.4'), ] From 5c09e7db393883a304f89153f21b5f7101e4cbf4 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Tue, 21 Feb 2023 11:18:01 +0100 Subject: [PATCH 6601/9987] adding easyconfigs: fastjet-contrib-1.049-gompi-2022a.eb --- .../fastjet-contrib-1.049-gompi-2022a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.049-gompi-2022a.eb diff --git a/easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.049-gompi-2022a.eb b/easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.049-gompi-2022a.eb new file mode 100644 index 00000000000..bf71f805335 --- /dev/null +++ b/easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.049-gompi-2022a.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'fastjet-contrib' +version = '1.049' + +homepage = 'https://fastjet.hepforge.org/contrib/' +description = """3rd party extensions of FastJet""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://fastjet.hepforge.org/contrib/downloads/'] +sources = ['fjcontrib-' + version + '.tar.gz'] +checksums = ['ae2ed6206bc6278b65e99a4f78df0eeb2911f301a28fb57b50c573c0d5869987'] + +dependencies = [ + ('fastjet', '3.4.0') +] + +configopts = "" +build_cmd_targets = ['', 'fragile-shared'] +install_cmd = "make install && make fragile-shared-install" + +sanity_check_paths = { + 'files': ['lib/libfastjetcontribfragile.%s' % SHLIB_EXT], + 'dirs': ['include/fastjet/contrib'] +} + +moduleclass = 'phys' From 61f191bbcdba9e3b3693b74eac5b7645e1b8dbdc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 21 Feb 2023 11:22:38 +0100 Subject: [PATCH 6602/9987] adding easyconfigs: jemalloc-5.2.1-GCCcore-11.3.0.eb, Salmon-1.9.0-GCC-11.3.0.eb --- .../jemalloc/jemalloc-5.2.1-GCCcore-11.3.0.eb | 37 +++++++++++ .../s/Salmon/Salmon-1.9.0-GCC-11.3.0.eb | 64 +++++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-1.9.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8d87581a842 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.2.1-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.2.1' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ed51b0b37098af4ca6ed31c22324635263f8ad6471889e0592a9c0dba9136aea'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.9.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..d6edc82fe03 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.9.0-GCC-11.3.0.eb @@ -0,0 +1,64 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GLPv2 +# +# Notes:: +## +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# Thanks to people like Simon Brandord, Mikael Oehmann and Kenneth Hoste +# for their help with the ICE + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '1.9.0' + +homepage = 'https://github.com/COMBINE-lab/salmon' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'COMBINE-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['450d953a5c43fe63fd745733f478d3fbaf24d926cb52731fd38ee21c4990d613'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), + ('jemalloc', '5.2.1'), + ('Cereal', '1.3.0', '', SYSTEM), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('tbb', '2021.5.0'), + ('cURL', '7.83.0'), + ('libiconv', '1.17'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.12'), +] + +# Disable link-time optimizations (-flto) because it triggers a segfault/internal compiler error (ICE) +# this issue might magically disappear in future versions of Salmon or GCC +# see https://github.com/COMBINE-lab/salmon/issues/778 +configopts = '-DJEMALLOC_ROOT=$EBROOTJEMALLOC -DNO_IPO=1' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'] + ['lib/lib%s.a' % x for x in ['graphdump', 'ntcard', 'salmon_core', 'twopaco']], + 'dirs': [], +} + +sanity_check_commands = ["salmon --help"] + +moduleclass = 'bio' From 0e540670edb5f2c746462dbe618c0e9696ffdc9a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 21 Feb 2023 11:23:59 +0100 Subject: [PATCH 6603/9987] adding easyconfigs: Cereal-1.3.2.eb --- .../easyconfigs/c/Cereal/Cereal-1.3.2.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cereal/Cereal-1.3.2.eb diff --git a/easybuild/easyconfigs/c/Cereal/Cereal-1.3.2.eb b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.2.eb new file mode 100644 index 00000000000..93c3203a39d --- /dev/null +++ b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.2.eb @@ -0,0 +1,35 @@ +## +# @Authors:: Maxime Boissonneault, Compute Canada +# @date: October 15, 2020 +## + +easyblock = 'CMakeMake' + +name = 'Cereal' +version = '1.3.2' + +homepage = 'https://uscilab.github.io/cereal/' +description = """cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly +turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be +fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or +used standalone.""" + +toolchain = SYSTEM + +github_account = 'USCiLab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['16a7ad9b31ba5880dac55d62b5d6f243c3ebc8d46a3514149e56b5e7ea81f85f'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +configopts = '-DJUST_INSTALL_CEREAL=ON -DSKIP_PERFORMANCE_COMPARISON=ON ' + +sanity_check_paths = { + 'files': ['include/cereal/cereal.hpp'], + 'dirs': ['include', 'lib/cmake'], +} + +moduleclass = 'lib' From 7609bade698f3fefcd10835ff2472b24dc14f868 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Tue, 21 Feb 2023 11:25:04 +0100 Subject: [PATCH 6604/9987] adding easyconfigs: Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb --- .../Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb new file mode 100644 index 00000000000..2abb857d455 --- /dev/null +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'Rivet' +version = '3.1.7' +local_hepmc = "HepMC3" +local_hepmcver = "3.2.5" +versionsuffix = '-%s-%s' % (local_hepmc, local_hepmcver) + +homepage = 'https://gitlab.com/hepcedar/rivet' +description = """ +Rivet toolkit (Robust Independent Validation of Experiment and Theory) + +To use your own analysis you must append the path to `RIVET_ANALYSIS_PATH`. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +# Needed since Eigen complains about assertions otherwise +# http://eigen.tuxfamily.org/dox-devel/group__TopicUnalignedArrayAssert.html +toolchainopts = {'optarch': False} + +source_urls = ['https://www.hepforge.org/archive/rivet/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d18993298b79cc9c0f086780ad5251df4647c565ba4a99b692458dcbd597378a'] + +dependencies = [ + ('Python', '3.10.4'), + ('YODA', '1.9.7'), + ('fastjet', '3.4.0'), + ('fastjet-contrib', '1.049'), + ('HepMC3', '3.2.5'), + ('GSL', '2.7') +] + +configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3" + +sanity_check_paths = { + 'files': ['bin/rivet-config', 'lib/libRivet.%s' % SHLIB_EXT], + 'dirs': ['share/Rivet', 'lib/Rivet'] +} +sanity_check_commands = ["python -c 'import rivet'"] + +modloadmsg = """ +To use your own analysis you must append the path to `RIVET_ANALYSIS_PATH`. +""" +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + # 'RIVET_ANALYSIS_PATH': '/path/to/share/Rivet/', # please adapt for system-wided shared non-default analysis +} + +moduleclass = 'phys' From 2360701daf5fec3203ee3c711d08662a478f586a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 21 Feb 2023 12:12:17 +0100 Subject: [PATCH 6605/9987] remove redundant envars --- easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb index 28a58551ca8..6a6d50726d5 100644 --- a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb @@ -87,8 +87,6 @@ exts_list = [ modextrapaths = { 'PERL5LIB': _libdir, - 'ZOE': '$EBROOTSNAPMINHMM/Zoe', - 'AUGUSTUS_CONFIG_PATH': '$EBROOTAUGUSTUS/config', } sanity_check_paths = { From fd2c5d114ab69373619f5c3e8babcd31ba2eaf34 Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 21 Feb 2023 12:54:59 +0100 Subject: [PATCH 6606/9987] add required soft --- .../a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb index 415adeb1465..199400c18d8 100644 --- a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb @@ -29,9 +29,15 @@ exts_list = [ ('colorspacious', '1.1.2', { 'checksums': ['5e9072e8cdca889dac445c35c9362a22ccf758e97b00b79ff0d5a7ba3e11b618'], }), + ('e13tools', '0.9.6', { + 'checksums': ['1c6eab60825a644e4a47f65dc692c0474552c5f0180f2d5a7fc5730e2954d0f5'], + }), ('cmasher', '1.6.3', { 'checksums': ['242e206e58ad6115ff0a5a5405a1ddae80efd1cb03a06dc23db44e710e7c9f23'], }), + ('widgetsnbextension', '4.0.1', { + 'checksums': ['bfa01945156f2bfd9a386bfc51b54ec5bfa26006d26bb75e5351e226f870fafb'], + }), ('ipywidgets', '8.0.4', { 'checksums': ['c0005a77a47d77889cafed892b58e33b4a2a96712154404c6548ec22272811ea'], }), From 27087681c0e6f55562dce25a0c07feecf90f1920 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 21 Feb 2023 15:16:37 +0100 Subject: [PATCH 6607/9987] adding easyconfigs: STAR-2.7.10b-GCC-11.3.0.eb and patches: STAR-2.7.10b_use-external-htslib.patch --- .../s/STAR/STAR-2.7.10b-GCC-11.3.0.eb | 47 ++++++++ .../STAR-2.7.10b_use-external-htslib.patch | 110 ++++++++++++++++++ 2 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.10b_use-external-htslib.patch diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb new file mode 100644 index 00000000000..392933dbe0c --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb @@ -0,0 +1,47 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.10b' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'openmp': True} + +github_account = 'alexdobin' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['STAR-%(version)s_use-external-htslib.patch'] +checksums = [ + {'2.7.10b.tar.gz': '0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5'}, + {'STAR-2.7.10b_use-external-htslib.patch': 'c5fb52fd2e0f779c74f9c7fa01b9cbf04dbccffd455c238517c9e84ea65368ac'}, +] + +dependencies = [ + ('HTSlib', '1.15.1'), + ('zlib', '1.2.12'), +] + +start_dir = 'source' + +buildopts = ' %(name)s && make %(name)slong' + +#parallel = 1 + +files_to_copy = [ + (['source/%(name)s', 'source/%(name)slong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/%(name)slong'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b_use-external-htslib.patch b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b_use-external-htslib.patch new file mode 100644 index 00000000000..15584599df9 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b_use-external-htslib.patch @@ -0,0 +1,110 @@ +Use external HTSlib from EasyBuild environment +author: Alex Domingo (Vrije Univeristeit Brussel) +diff -Nru STAR-2.7.10b.orig/source/bam_cat.c STAR-2.7.10b/source/bam_cat.c +--- STAR-2.7.10b.orig/source/bam_cat.c 2023-02-21 14:44:38.187161000 +0100 ++++ STAR-2.7.10b/source/bam_cat.c 2023-02-21 14:46:21.311793000 +0100 +@@ -52,8 +52,8 @@ + #include + #include + +-#include "htslib/htslib/bgzf.h" +-#include "htslib/htslib/sam.h" ++#include "htslib/bgzf.h" ++#include "htslib/sam.h" + #include + + #define BUF_SIZE 0x10000 +diff -Nru STAR-2.7.10b.orig/source/bam_cat.h STAR-2.7.10b/source/bam_cat.h +--- STAR-2.7.10b.orig/source/bam_cat.h 2023-02-21 14:44:38.186786000 +0100 ++++ STAR-2.7.10b/source/bam_cat.h 2023-02-21 14:46:11.808189000 +0100 +@@ -1,7 +1,7 @@ + #ifndef CODE_bam_cat + #define CODE_bam_cat + +-#include "htslib/htslib/sam.h" ++#include "htslib/sam.h" + + int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam); + +diff -Nru STAR-2.7.10b.orig/source/BAMfunctions.cpp STAR-2.7.10b/source/BAMfunctions.cpp +--- STAR-2.7.10b.orig/source/BAMfunctions.cpp 2023-02-21 14:44:38.227596000 +0100 ++++ STAR-2.7.10b/source/BAMfunctions.cpp 2023-02-21 14:46:37.915155000 +0100 +@@ -1,5 +1,5 @@ + #include "BAMfunctions.h" +-#include "htslib/htslib/kstring.h" ++#include "htslib/kstring.h" + + + string bam_cigarString (bam1_t *b) {//output CIGAR string +diff -Nru STAR-2.7.10b.orig/source/bamRemoveDuplicates.cpp STAR-2.7.10b/source/bamRemoveDuplicates.cpp +--- STAR-2.7.10b.orig/source/bamRemoveDuplicates.cpp 2023-02-21 14:44:38.193941000 +0100 ++++ STAR-2.7.10b/source/bamRemoveDuplicates.cpp 2023-02-21 14:46:30.200913252 +0100 +@@ -1,7 +1,7 @@ + #include + #include "bamRemoveDuplicates.h" + #include +-#include "htslib/htslib/sam.h" ++#include "htslib/sam.h" + #include "IncludeDefine.h" + #include SAMTOOLS_BGZF_H + #include "ErrorWarning.h" +diff -Nru STAR-2.7.10b.orig/source/IncludeDefine.h STAR-2.7.10b/source/IncludeDefine.h +--- STAR-2.7.10b.orig/source/IncludeDefine.h 2023-02-21 14:44:38.231926000 +0100 ++++ STAR-2.7.10b/source/IncludeDefine.h 2023-02-21 14:46:49.536916000 +0100 +@@ -30,8 +30,8 @@ + #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ ) + + //external libs +-#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h" +-#define SAMTOOLS_SAM_H "htslib/htslib/sam.h" ++#define SAMTOOLS_BGZF_H "htslib/bgzf.h" ++#define SAMTOOLS_SAM_H "htslib/sam.h" + + using namespace std; + +diff -Nru STAR-2.7.10b.orig/source/Makefile STAR-2.7.10b/source/Makefile +--- STAR-2.7.10b.orig/source/Makefile 2023-02-21 14:44:38.183938000 +0100 ++++ STAR-2.7.10b/source/Makefile 2023-02-21 14:45:47.871479235 +0100 +@@ -12,8 +12,8 @@ + CXX ?= g++ + + # pre-defined flags +-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz +-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz ++LDFLAGS_shared := -pthread -L$(EBROOTHTSLIB)/lib -Bstatic -lhts -Bdynamic -lz ++LDFLAGS_static := -static -static-libgcc -pthread -L$(EBROOTHTSLIB)/lib -lhts -lz + LDFLAGS_Mac :=-pthread -lz htslib/libhts.a + LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a + LDFLAGS_gdb := $(LDFLAGS_shared) +@@ -131,7 +131,7 @@ + ifneq ($(MAKECMDGOALS),clean_solo) + ifneq ($(MAKECMDGOALS),STARforMac) + ifneq ($(MAKECMDGOALS),STARforMacGDB) +-Depend.list: $(SOURCES) parametersDefault.xxd htslib ++Depend.list: $(SOURCES) parametersDefault.xxd + echo $(SOURCES) + 'rm' -f ./Depend.list + $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list +diff -Nru STAR-2.7.10b.orig/source/signalFromBAM.h STAR-2.7.10b/source/signalFromBAM.h +--- STAR-2.7.10b.orig/source/signalFromBAM.h 2023-02-21 14:44:38.178725000 +0100 ++++ STAR-2.7.10b/source/signalFromBAM.h 2023-02-21 14:46:04.073689000 +0100 +@@ -1,6 +1,6 @@ + #ifndef CODE_signalFromBAM + #define CODE_signalFromBAM +-#include "htslib/htslib/sam.h" ++#include "htslib/sam.h" + #include + #include + #include "Stats.h" +diff -Nru STAR-2.7.10b.orig/source/STAR.cpp STAR-2.7.10b/source/STAR.cpp +--- STAR-2.7.10b.orig/source/STAR.cpp 2023-02-21 14:44:38.241555000 +0100 ++++ STAR-2.7.10b/source/STAR.cpp 2023-02-21 14:46:59.073420225 +0100 +@@ -30,7 +30,7 @@ + + #include "twoPassRunPass1.h" + +-#include "htslib/htslib/sam.h" ++#include "htslib/sam.h" + #include "parametersDefault.xxd" + + void usage(int usageType) { From 2ee8294a46168999035450eecdfb9ad835488b0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 21 Feb 2023 15:42:53 +0100 Subject: [PATCH 6608/9987] remove comment at top --- .../easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb index 199400c18d8..9f7a5720721 100644 --- a/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/astro-tulips/astro-tulips-1.0.1-foss-2022a.eb @@ -1,5 +1,3 @@ -# Astro-tulips - easyblock = 'PythonBundle' name = 'astro-tulips' From 9500194b7eada97c740ba34bd6c0b3d73160eabd Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 21 Feb 2023 15:47:50 +0100 Subject: [PATCH 6609/9987] DGL: Turn off vectorizer to avoid problems with nanoflann on skylake and later. --- .../easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb index c0bfec78621..9aa9bdcd151 100644 --- a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb @@ -10,6 +10,9 @@ DGL is framework agnostic, meaning if a deep graph model is a component of an en of the logics can be implemented in any major frameworks, such as PyTorch, Apache MXNet or TensorFlow.""" toolchain = {'name': 'foss', 'version': '2021a'} +# GCC 10.3.0 vectorizer causes errors in nanoflann on skylake and later +# and since nanoflann is just a header file we need to turn it off for anything that uses it +toolchainopts = {'vectorize': False} github_account = 'dmlc' source_urls = [GITHUB_LOWER_SOURCE] From b82868ddc3b5d0a1f2d8cae0175720b4e6fabdad Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 21 Feb 2023 23:45:17 +0100 Subject: [PATCH 6610/9987] remove leftover comment in STAR v2.7.10b --- easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb index 392933dbe0c..efa27091021 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb @@ -32,8 +32,6 @@ start_dir = 'source' buildopts = ' %(name)s && make %(name)slong' -#parallel = 1 - files_to_copy = [ (['source/%(name)s', 'source/%(name)slong'], 'bin'), 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', From fde11efe46df40e2d6fb3dfe726a84d9494ae433 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 21 Feb 2023 23:47:08 +0100 Subject: [PATCH 6611/9987] adding easyconfigs: RSEM-1.3.3-foss-2022a.eb, Bowtie-1.3.1-GCC-11.3.0.eb --- .../b/Bowtie/Bowtie-1.3.1-GCC-11.3.0.eb | 30 +++++++++++ .../r/RSEM/RSEM-1.3.3-foss-2022a.eb | 51 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..9e06d7508f2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Artistic v2.0 +# +# Notes:: +## + +name = 'Bowtie' +version = '1.3.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.zip'] +checksums = ['e23517aa53846ef828172be911750cd05748522117efcbbe5a36f3241fb40761'] + +dependencies = [ + ('tbb', '2021.5.0'), + ('zlib', '1.2.12'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2022a.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2022a.eb new file mode 100644 index 00000000000..19cf63260a7 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2022a.eb @@ -0,0 +1,51 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'RSEM' +version = '1.3.3' + +homepage = 'https://deweylab.github.io/RSEM/' +description = "RNA-Seq by Expectation-Maximization" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['RSEM-1.3.0_makefiles.patch'] +checksums = [ + '90e784dd9df8346caa2a7e3ad2ad07649608a51df1c69bfb6e16f45e611a40dc', # v1.3.3.tar.gz + '2d244659206c78655b92f1bd519ee65f28a6b5f9418dfad04e887b64eca6641b', # RSEM-1.3.0_makefiles.patch +] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('Perl', '5.34.1'), + ('R', '4.2.1'), + ('HISAT2', '2.2.1'), + ('STAR', '2.7.10b'), + ('Bowtie2', '2.4.5'), + ('Bowtie', '1.3.1'), +] + +sanity_check_paths = { + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'dirs': ['bin/samtools-1.3'], +} + +moduleclass = 'bio' From f3aa1e4e10ebbc731aae26f15069214a669ac935 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 22 Feb 2023 00:47:16 +0100 Subject: [PATCH 6612/9987] adding easyconfigs: kallisto-0.48.0-gompi-2022a.eb and patches: kallisto-0.48.0_use-external-htslib.patch --- .../k/kallisto/kallisto-0.48.0-gompi-2022a.eb | 50 +++++++++++++ .../kallisto-0.48.0_use-external-htslib.patch | 74 +++++++++++++++++++ 2 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.48.0_use-external-htslib.patch diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2022a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2022a.eb new file mode 100644 index 00000000000..18ebd60e3a9 --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2022a.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.48.0' + +homepage = 'https://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'pachterlab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['kallisto-%(version)s_use-external-htslib.patch'] +checksums = [ + {'v0.48.0.tar.gz': '1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0'}, + {'kallisto-0.48.0_use-external-htslib.patch': 'fa9a96c7f8731006b6c87e1397429a292ebb3aa3e5d3db4fc9520d8c8a13f920'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.23.1'), + ('zlib', '1.2.12'), +] + +dependencies = [ + ('HDF5', '1.12.2'), + ('HTSlib', '1.15.1'), +] + +parallel = 1 + +configopts = '-DUSE_HDF5=ON' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = [ + "kallisto version", + "cd %(builddir)s/%(name)s-%(version)s/test && kallisto index -i ts.idx transcripts.fasta.gz", + "cd %(builddir)s/%(name)s-%(version)s/test && kallisto quant -i ts.idx -o out -b 100 reads_{1,2}.fastq.gz", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0_use-external-htslib.patch b/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0_use-external-htslib.patch new file mode 100644 index 00000000000..87a4f6a0e31 --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0_use-external-htslib.patch @@ -0,0 +1,74 @@ +Use external HTSlib from EasyBuild environment +author: Alex Domingo (Vrije Univeristeit Brussel) +--- CMakeLists.txt.orig 2023-02-21 14:15:06.928502000 +0100 ++++ CMakeLists.txt 2023-02-21 14:20:48.902166000 +0100 +@@ -41,22 +41,6 @@ + message("shared build") + ENDIF(LINK MATCHES static) + +- +-include(ExternalProject) +-ExternalProject_Add(htslib +- PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib +- SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib +- BUILD_IN_SOURCE 1 +- CONFIGURE_COMMAND autoheader && autoconf && ${PROJECT_SOURCE_DIR}/ext/htslib/configure +- --prefix=${PREFIX} --disable-bz2 --disable-lzma --disable-libcurl +- BUILD_COMMAND make lib-static +- INSTALL_COMMAND "" +-) +- +-include_directories(${htslib_PREFIX}/src/htslib) +- +- +- + # add_compile_options(-Wdeprecated-register) + + add_subdirectory(src) +--- src/CMakeLists.txt.orig 2023-02-21 14:20:56.996543000 +0100 ++++ src/CMakeLists.txt 2023-02-21 15:10:35.835647000 +0100 +@@ -3,7 +3,7 @@ + + list(REMOVE_ITEM sources main.cpp) + +-include_directories(../ext/htslib) ++include_directories(SYSTEM $ENV{EBROOTHTSLIB}/include) + + add_library(kallisto_core ${sources} ${headers}) + target_include_directories(kallisto_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}) +@@ -11,7 +11,8 @@ + add_executable(kallisto main.cpp) + + find_package( Threads REQUIRED ) +-target_link_libraries(kallisto kallisto_core pthread ${CMAKE_CURRENT_SOURCE_DIR}/../ext/htslib/libhts.a) ++find_library($ENV{EBROOTHTSLIB}/lib hts) ++target_link_libraries(kallisto kallisto_core pthread hts) + + if(LINK MATCHES static) + set(BUILD_SHARED_LIBS OFF) +--- src/kseq.h.orig 2023-02-21 15:34:20.910947000 +0100 ++++ src/kseq.h 2023-02-21 17:09:01.242218765 +0100 +@@ -28,6 +28,8 @@ + #include + #include + ++#include "htslib/kstring.h" ++ + #define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r + #define KS_SEP_TAB 1 // isspace() && !' ' + #define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows) +@@ -74,14 +76,6 @@ + return (int)ks->buf[ks->begin++]; \ + } + +-#ifndef KSTRING_T +-#define KSTRING_T kstring_t +-typedef struct __kstring_t { +- size_t l, m; +- char *s; +-} kstring_t; +-#endif +- + #ifndef kroundup32 + #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x)) + #endif From d2ce17f48251d6baf043757f019b7a45b9ac7ba8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 22 Feb 2023 09:43:50 +0100 Subject: [PATCH 6613/9987] adding easyconfigs: SeaView-5.0.5.eb --- .../easyconfigs/s/SeaView/SeaView-5.0.5.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb diff --git a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb new file mode 100644 index 00000000000..3614ac3e16e --- /dev/null +++ b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb @@ -0,0 +1,21 @@ +easyblock = 'Tarball' + +name = 'SeaView' +version = '5.0.5' + +homepage = 'https://doua.prabi.fr/software/seaview' +description = """SeaView is a multiplatform, graphical user interface for multiple sequence alignment + and molecular phylogeny.""" + +toolchain = SYSTEM + +source_urls = ['https://doua.prabi.fr/software/seaview_data'] +sources = [{'download_filename': '%(namelower)s%(version_major)s-64.tgz', 'filename': '%(name)s-%(version)s-64.tgz'}] +checksums = ['e8d844ee5d41f7e5626631ac1eb75086add6a24bfe8a5aa69d045c622a8abd8d'] + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From ae37e8e8df81542f1881319f91ede779e99a30af Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 22 Feb 2023 10:01:20 +0100 Subject: [PATCH 6614/9987] Add software directory to PATH and add sanity_check_commands --- easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb index 3614ac3e16e..4aacff62582 100644 --- a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb +++ b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb @@ -13,9 +13,13 @@ source_urls = ['https://doua.prabi.fr/software/seaview_data'] sources = [{'download_filename': '%(namelower)s%(version_major)s-64.tgz', 'filename': '%(name)s-%(version)s-64.tgz'}] checksums = ['e8d844ee5d41f7e5626631ac1eb75086add6a24bfe8a5aa69d045c622a8abd8d'] +modextrapaths = {'PATH': '.'} + sanity_check_paths = { 'files': ['%(namelower)s'], 'dirs': [], } +sanity_check_commands = [("%(namelower)s -h")] + moduleclass = 'bio' From 021d57ed80fa68be1a93c88fd1d7f38b77f4c798 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 11:38:36 +0000 Subject: [PATCH 6615/9987] adding easyconfigs: Bottleneck-1.3.6-foss-2022a.eb --- .../Bottleneck/Bottleneck-1.3.6-foss-2022a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.6-foss-2022a.eb b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.6-foss-2022a.eb new file mode 100644 index 00000000000..7acef662de0 --- /dev/null +++ b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.6-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonBundle' + +name = 'Bottleneck' +version = '1.3.6' + +homepage = 'https://kwgoodman.github.io/bottleneck-doc' +description = "Fast NumPy array functions written in C" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['bc15e2545d4282d6f2529597df1bd6e4c5f0c44296b3f8425bc835305bd943c9'], + }), +] + +moduleclass = 'math' From d271ecc4e0f7d33cb5f5d9213d7d58f3130fc60e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 22 Feb 2023 12:40:49 +0100 Subject: [PATCH 6616/9987] add link to htslib unbundle PR in patch of STAR v2.7.10b --- easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb | 2 +- .../easyconfigs/s/STAR/STAR-2.7.10b_use-external-htslib.patch | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb index efa27091021..b8a3d1f0dc0 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb @@ -20,7 +20,7 @@ sources = ['%(version)s.tar.gz'] patches = ['STAR-%(version)s_use-external-htslib.patch'] checksums = [ {'2.7.10b.tar.gz': '0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5'}, - {'STAR-2.7.10b_use-external-htslib.patch': 'c5fb52fd2e0f779c74f9c7fa01b9cbf04dbccffd455c238517c9e84ea65368ac'}, + {'STAR-2.7.10b_use-external-htslib.patch': '1d8a24532a384b3065001c672e486b74094f162cb98829d2ec961401215de7da'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b_use-external-htslib.patch b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b_use-external-htslib.patch index 15584599df9..414186f55fc 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b_use-external-htslib.patch +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b_use-external-htslib.patch @@ -1,4 +1,5 @@ Use external HTSlib from EasyBuild environment +see also PR https://github.com/alexdobin/STAR/pull/1586 author: Alex Domingo (Vrije Univeristeit Brussel) diff -Nru STAR-2.7.10b.orig/source/bam_cat.c STAR-2.7.10b/source/bam_cat.c --- STAR-2.7.10b.orig/source/bam_cat.c 2023-02-21 14:44:38.187161000 +0100 From 104fba12fbaba66c663108818904bd37d7db8df7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 22 Feb 2023 12:42:13 +0100 Subject: [PATCH 6617/9987] add sanity check commands to STAR v2.7.10b --- easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb index b8a3d1f0dc0..4a34f49d8fe 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-11.3.0.eb @@ -42,4 +42,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + "STAR --help", + "STARlong --help", +] + moduleclass = 'bio' From efdb1c98ab459a5c1acd1f35a6e981a42febf700 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 22 Feb 2023 12:45:06 +0100 Subject: [PATCH 6618/9987] adding easyconfigs: GMAP-GSNAP-2023-02-17-GCC-11.3.0.eb and patches: GMAP-GSNAP-2023-02-17_cleanup-headers.patch, GMAP-GSNAP-2023-02-17_fix-typecast.patch --- .../GMAP-GSNAP-2023-02-17-GCC-11.3.0.eb | 55 +++++++++++++++++++ ...MAP-GSNAP-2023-02-17_cleanup-headers.patch | 52 ++++++++++++++++++ .../GMAP-GSNAP-2023-02-17_fix-typecast.patch | 13 +++++ 3 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17_cleanup-headers.patch create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17_fix-typecast.patch diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17-GCC-11.3.0.eb new file mode 100644 index 00000000000..ea2e6aa59ea --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17-GCC-11.3.0.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2023-02-17' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GMAP-GSNAP-%(version)s_cleanup-headers.patch', + 'GMAP-GSNAP-%(version)s_fix-typecast.patch', +] +checksums = [ + {'gmap-gsnap-2023-02-17.tar.gz': 'd54abb6bc59da46823f5a1a9d94872a6b90468699112a6f375ddc7b91340db06'}, + {'GMAP-GSNAP-2023-02-17_cleanup-headers.patch': '7d17d4cbc717556e3a64475eb931b692e9d564b486acf6c9dbf4c2bf29853832'}, + {'GMAP-GSNAP-2023-02-17_fix-typecast.patch': 'eafe728cf00cf52320bbf4b710ef76b662df92533d22fa67dc273855c180296f'}, +] + +# with these deps you can use standard compressed files +# details in http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length +# details in http://research-pub.gene.com/gmap/src/README +# configopts = 'MAX_STACK_READLENGTH=300' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +sanity_check_commands = [ + "gmap --help", + "gsnap --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17_cleanup-headers.patch b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17_cleanup-headers.patch new file mode 100644 index 00000000000..99caa1f4ce8 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17_cleanup-headers.patch @@ -0,0 +1,52 @@ +Remove includes of non-existing headers +author: Alex Domingo (Vrije Universiteit Brussel) +--- src/simde/x86/avx512/fmadd.h.orig 2023-02-22 01:14:34.516573000 +0100 ++++ src/simde/x86/avx512/fmadd.h 2023-02-22 01:14:41.974985000 +0100 +@@ -30,7 +30,6 @@ + + #include "types.h" + #include "mov.h" +-#include "../fma.h" + + HEDLEY_DIAGNOSTIC_PUSH + SIMDE_DISABLE_UNWANTED_DIAGNOSTICS +--- src/simde/x86/avx512/fmsub.h.orig 2023-02-22 01:28:37.589836000 +0100 ++++ src/simde/x86/avx512/fmsub.h 2023-02-22 01:28:46.136128842 +0100 +@@ -30,7 +30,6 @@ + + #include "types.h" + #include "mov.h" +-#include "../fma.h" + + HEDLEY_DIAGNOSTIC_PUSH + SIMDE_DISABLE_UNWANTED_DIAGNOSTICS +--- src/simde/x86/avx512/fnmadd.h.orig 2023-02-22 01:35:50.825564000 +0100 ++++ src/simde/x86/avx512/fnmadd.h 2023-02-15 15:36:00.000000000 +0100 +@@ -30,7 +30,6 @@ + + #include "types.h" + #include "mov.h" +-#include "../fma.h" + + HEDLEY_DIAGNOSTIC_PUSH + SIMDE_DISABLE_UNWANTED_DIAGNOSTICS +--- src/simde/x86/avx512/fnmsub.h.orig 2023-02-22 01:42:35.610381000 +0100 ++++ src/simde/x86/avx512/fnmsub.h 2023-02-22 01:42:43.828398000 +0100 +@@ -30,7 +30,6 @@ + + #include "types.h" + #include "mov.h" +-#include "../fma.h" + + HEDLEY_DIAGNOSTIC_PUSH + SIMDE_DISABLE_UNWANTED_DIAGNOSTICS +--- src/simde/x86/avx512/scalef.h.orig 2023-02-22 01:48:02.614308000 +0100 ++++ src/simde/x86/avx512/scalef.h 2023-02-22 01:48:09.999588167 +0100 +@@ -3,7 +3,6 @@ + + #include "types.h" + #include "flushsubnormal.h" +-#include "../svml.h" + + HEDLEY_DIAGNOSTIC_PUSH + SIMDE_DISABLE_UNWANTED_DIAGNOSTICS diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17_fix-typecast.patch b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17_fix-typecast.patch new file mode 100644 index 00000000000..16a9d28c3f2 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-02-17_fix-typecast.patch @@ -0,0 +1,13 @@ +Fix typecast syntax +author: Alex Domingo (Vrije Universiteit Brussel) +--- src/select64-common.h.orig 2023-02-22 02:29:16.028806000 +0100 ++++ src/select64-common.h 2023-02-22 02:28:24.058561000 +0100 +@@ -67,7 +67,7 @@ + return place + kSelectInByte[((x >> place) & 0xFF) | (byteRank << 8)]; + #elif defined(__GNUC__) || defined(__clang__) + // GCC and Clang won't inline the intrinsics. +- uint64_t result = uint64_t(1) << k; ++ uint64_t result = (uint64_t)(1) << k; + + asm("pdep %1, %0, %0\n\t" + "tzcnt %0, %0" From 1ec56861ffeabe53bc35e15e75d70766a710ef23 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 11:55:47 +0000 Subject: [PATCH 6619/9987] adding easyconfigs: cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb, cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb --- .../cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb | 39 +++++++++++++++++++ .../cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb create mode 100644 easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb new file mode 100644 index 00000000000..a5a73baad0a --- /dev/null +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb @@ -0,0 +1,39 @@ +# Updated to MesonNinja as the autogen.sh complained. +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MesonNinja' + +name = 'cairomm' +version = '1.14.4' +versionsuffix = '-cairo-1.17.4' + +homepage = 'http://cairographics.org' +description = "The Cairomm package provides a C++ interface to Cairo." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['4749d25a2b2ef67cc0c014caaf5c87fa46792fc4b3ede186fb0fc932d2055158'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('cairo', '1.17.4'), + ('libsigc++', '2.12.0'), + ('mm-common', '1.0.5'), + ('Boost', '1.79.0'), +] + +runtest = 'ninja test' + +sanity_check_paths = { + 'files': ['lib/libcairomm-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb new file mode 100644 index 00000000000..ffe8ff54a20 --- /dev/null +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb @@ -0,0 +1,39 @@ +# Updated to MesonNinja as the autogen.sh complained. +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MesonNinja' + +name = 'cairomm' +version = '1.16.2' +versionsuffix = '-cairo-1.17.4' + +homepage = 'http://cairographics.org' +description = "The Cairomm package provides a C++ interface to Cairo." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['6a63bf98a97dda2b0f55e34d1b5f3fb909ef8b70f9b8d382cb1ff3978e7dc13f'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('cairo', '1.17.4'), + ('libsigc++', '3.4.0'), + ('mm-common', '1.0.5'), + ('Boost', '1.79.0'), +] + +runtest = 'ninja test' + +sanity_check_paths = { + 'files': ['lib/libcairomm-1.16.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 6864badd6166a1a270f237d8eb915f993b5e24ad Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 12:06:16 +0000 Subject: [PATCH 6620/9987] adding easyconfigs: HDBSCAN-0.8.29-foss-2022a.eb --- .../h/HDBSCAN/HDBSCAN-0.8.29-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.29-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.29-foss-2022a.eb b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.29-foss-2022a.eb new file mode 100644 index 00000000000..55db5b7d930 --- /dev/null +++ b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.29-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'HDBSCAN' +version = '0.8.29' + +homepage = 'http://hdbscan.readthedocs.io/en/latest/' +description = """The hdbscan library is a suite of tools to use unsupervised learning to find clusters, or dense + regions, of a dataset. The primary algorithm is HDBSCAN* as proposed by Campello, Moulavi, and Sander. The library + provides a high performance implementation of this algorithm, along with tools for analysing the resulting + clustering.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['7e9d7351610eaadddb281e3149a74e22e329bc0b5325f631031d4b63a6a770ae'], + }), +] + + +moduleclass = 'data' From 5092fe92c053bfa9ea52a065d193837056aa29ab Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 12:08:19 +0000 Subject: [PATCH 6621/9987] adding easyconfigs: HighFive-2.6.2-gompi-2022a.eb --- .../h/HighFive/HighFive-2.6.2-gompi-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-gompi-2022a.eb diff --git a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-gompi-2022a.eb b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-gompi-2022a.eb new file mode 100644 index 00000000000..d0d48e20834 --- /dev/null +++ b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-gompi-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'HighFive' +version = '2.6.2' + +homepage = 'https://github.com/BlueBrain/HighFive' +description = """HighFive is a modern header-only C++11 friendly interface for libhdf5.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +github_account = 'BlueBrain' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ab51b9fbb49e877dd1aa7b53b4b26875f41e4e0b8ee0fc2f1d735e0d1e43d708'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.38') +] + +dependencies = [ + ('HDF5', '1.12.2'), + ('Boost', '1.79.0'), + ('Eigen', '3.4.0'), +] + +sanity_check_paths = { + 'files': ['include/highfive/H5File.hpp'], + 'dirs': [], +} + +configopts = '-DHIGHFIVE_USE_EIGEN=ON -DHIGHFIVE_PARALLEL_HDF5=ON' + +moduleclass = 'lib' From 23dfac778ecae7cc6f7859a2c20fc8da2d9d585a Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 12:14:19 +0000 Subject: [PATCH 6622/9987] adding easyconfigs: libsigc++-2.12.0-GCCcore-11.3.0.eb --- .../libsigc++-2.12.0-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d4470b7f612 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libsigc++' +version = '2.12.0' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('Doxygen', '1.9.4'), + ('Graphviz', '5.0.0'), + ('libxslt', '1.1.34'), + ('mm-common', '1.0.5'), +] + +preconfigopts = "./autogen.sh && " +configopts = '--disable-documentation ' + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From aee017fc8e620972a822a438c481d54d7b7febe5 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 12:18:42 +0000 Subject: [PATCH 6623/9987] adding easyconfigs: mm-common-1.0.5-GCCcore-11.3.0.eb --- .../mm-common-1.0.5-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/mm-common/mm-common-1.0.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/mm-common/mm-common-1.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f479bea36ff --- /dev/null +++ b/easybuild/easyconfigs/m/mm-common/mm-common-1.0.5-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'mm-common' +version = '1.0.5' + +homepage = 'https://gitlab.gnome.org/GNOME/mm-common' +description = """The mm-common module provides the build infrastructure and +utilities shared among the GNOME C++ binding libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['705c6d29f4116a29bde4e36cfc1b046c92b6ef8c6dae4eaec85018747e6da5aa'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +sanity_check_paths = { + 'files': ['bin/mm-common-get', 'bin/mm-common-prepare', 'share/pkgconfig/mm-common-util.pc'], + 'dirs': ['share/man/man1'], +} + +sanity_check_commands = ["mm-common-prepare --help"] + +moduleclass = 'devel' From 9fd00d18883b891308555aa41de6da0f5f85f9ea Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 12:22:11 +0000 Subject: [PATCH 6624/9987] version 3.4.0 added --- .../libsigc++-3.4.0-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..be3a0fa23e2 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libsigc++' +version = '3.4.0' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system +for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['02e2630ffb5ce93cd52c38423521dfe7063328863a6e96d41d765a6116b8707e'] + +builddependencies = [ + ('binutils', '2.38'), + ('Graphviz', '5.0.0'), + ('libxslt', '1.1.34'), + ('mm-common', '1.0.5'), + ('CMake', '3.24.3'), +] + +preconfigopts = "./autogen.sh && " +configopts = '--disable-documentation ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From caa7e1d4c1731737831688558b6221fb21ea5c51 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 12:24:44 +0000 Subject: [PATCH 6625/9987] adding easyconfigs: mandrake-1.2.2-foss-2022a.eb --- .../m/mandrake/mandrake-1.2.2-foss-2022a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb new file mode 100644 index 00000000000..6b72810418d --- /dev/null +++ b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb @@ -0,0 +1,53 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'mandrake' +version = '1.2.2' + +homepage = ' https://mandrake.readthedocs.io' +description = """Fast visualisation of the population structure of pathogens +using Stochastic Cluster Embedding.""" + +citing = """Lees JA, Tonkin-Hill G, Yang Z, Corander J. Mandrake: visualizing +microbial population structure by embedding millions of genomes into a +low-dimensional representation. +Philosophical Transactions of The Royal Society B. 2022;377: 20210237. +https://doi.org/10.1098/rstb.2021.0237""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('plotly.py', '5.12.0'), + ('pandas', '1.5.3'), + ('matplotlib', '3.5.2'), + ('HDBSCAN', '0.8.29'), + ('h5py', '3.7.0'), + ('pp-sketchlib', '2.1.1'), + ('pybind11', '2.9.2'), + ('Eigen', '3.4.0'), + ('Boost', '1.79.0'), + ('tqdm', '4.64.0'), + ('FFmpeg', '4.4.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/bacpop/mandrake/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5bbdde903252e2812d4ba484ae474ccc75efbaaf0ace7fe6f37a90e44fe3f0e5'], + }), +] + +moduleclass = 'bio' From b1ce0458cbeb7b92d9afa81c59f1d13e22d855a5 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 12:32:45 +0000 Subject: [PATCH 6626/9987] adding easyconfigs: pp-sketchlib-2.1.1-foss-2022a.eb --- .../pp-sketchlib-2.1.1-foss-2022a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb b/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb new file mode 100644 index 00000000000..00174adc9d0 --- /dev/null +++ b/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb @@ -0,0 +1,44 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'pp-sketchlib' +version = '2.1.1' + +homepage = ' https://mandrake.readthedocs.io' +description = """Library of sketching functions used by PopPUNK""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('HDF5', '1.12.2'), + ('pybind11', '2.9.2'), + ('Eigen', '3.4.0'), + ('Boost', '1.79.0'), + ('nlohmann_json', '3.10.5'), + ('HighFive', '2.6.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + (name, version, { + 'source_urls': ['https://github.com/bacpop/pp-sketchlib/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['b42acf0a58ea3225e3fe95adc8fc165578832c58e6f5b6fb3f7817655e0a9f30'], + }), +] + +moduleclass = 'vis' From 008b5f162a01f3e89bcf60568cd0c5d63d28c52c Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 12:38:18 +0000 Subject: [PATCH 6627/9987] adding easyconfigs: rapidNJ-2.3.3-GCCcore-11.3.0.eb --- .../r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5df1574cf30 --- /dev/null +++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +# This seems to be actively maintained version of the code by the looks of it. +# See issue #5 +# https://github.com/somme89/rapidNJ/issues/5 +# why -march=native will not be used +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'rapidNJ' +version = '2.3.3' + +homepage = 'https://github.com/somme89/rapidNJ' +description = """RapidNJ is an algorithmic engineered implementation of canonical +neighbour-joining. It uses an efficient search heuristic to speed-up the core +computations of the neighbour-joining method that enables RapidNJ to +outperform other state-of-the-art neighbour-joining implementations.""" + +citing = """Rapid Neighbour Joining. Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen. +In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122, +Springer Verlag, October 2008. +doi: 10.1007/978-3-540-87361-7_10""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/somme89/rapidNJ/archive/'] +sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}] +checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d'] + +files_to_copy = [(['bin/rapidnj'], 'bin')] + +# That is returning 1 instead of 0, so disabled for now +# sanity_check_commands = ['rapidnj --help'] + +sanity_check_paths = { + 'files': ['bin/rapidnj'], + 'dirs': [], +} + +moduleclass = 'bio' From c642a8599dd92a6e4735ad40861f8d5d06a63500 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 12:42:12 +0000 Subject: [PATCH 6628/9987] adding easyconfigs: sparsehash-2.0.4-GCCcore-11.3.0.eb --- .../sparsehash-2.0.4-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e41d4c3729f --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +# Updated from previous easyconfig +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to GCCcore-11.3.0 +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.4' + +homepage = 'https://github.com/sparsehash/sparsehash' +description = """ + An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! + The SparseHash library contains several hash-map implementations, including + implementations that optimize for space or speed. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8cd1a95827dfd8270927894eb77f62b4087735cbede953884647f16c521c7e58'] + +builddependencies = [ + ('binutils', '2.38'), +] + + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' From af2117e285835e32decd644348b24f3d98ff7855 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 22 Feb 2023 17:06:32 +0100 Subject: [PATCH 6629/9987] adding easyconfigs: BLAT-3.7-GCC-11.3.0.eb and patches: BLAT-3.7_mend-tests.patch --- .../easyconfigs/b/BLAT/BLAT-3.7-GCC-11.3.0.eb | 54 +++++++++++++++++++ .../b/BLAT/BLAT-3.7_mend-tests.patch | 48 +++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/b/BLAT/BLAT-3.7_mend-tests.patch diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.3.0.eb new file mode 100644 index 00000000000..6f33b6c1bbc --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.3.0.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou +# Contributors:: Alex Domingo (Vrije Universiteit Brussel) +# License:: MIT/GPL +# +## + +name = 'BLAT' +version = '3.7' + +homepage = 'https://genome.ucsc.edu/goldenPath/help/blatSpec.html' +description = """BLAT on DNA is designed to quickly find sequences of 95% and +greater similarity of length 25 bases or more.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://genome-test.gi.ucsc.edu/~kent/src/'] +sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] +patches = ['BLAT-%(version)s_mend-tests.patch'] +checksums = [ + {'blatSrc37.zip': '88ee2b272d42ab77687c61d200b11f1d58443951069feb7e10226a2509f84cf2'}, + {'BLAT-3.7_mend-tests.patch': '1f42c7fadf7676a5cc3a2016f70089c3541aa1d53816cf86072682c44cf311a6'}, +] + +# BLAT relies on a bundled old version of HTSlib. We use the bundled library +# because it is statically linked and the newer HTSlib in this toolchain is not +# API compatible with it. +dependencies = [ + ('freetype', '2.12.1'), + ('libiconv', '1.17'), + ('libpng', '1.6.37'), + ('MariaDB', '10.9.3'), + ('OpenSSL', '1.1', '', SYSTEM), + ('zlib', '1.2.12'), +] + +pretestopts = 'PATH="%(builddir)s/blatSrc/bin:$PATH"' +runtest = 'test' + +_blat_bins = ["blat", "faToNib", "faToTwoBit", "gfClient", "gfServer", "nibFrag", "pslPretty", + "pslReps", "pslSort", "twoBitInfo", "twoBitToFa"] + +files_to_copy = [(["bin/%s" % x for x in _blat_bins] + ["webBlat/webBlat"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in _blat_bins + ["webBlat"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.7_mend-tests.patch b/easybuild/easyconfigs/b/BLAT/BLAT-3.7_mend-tests.patch new file mode 100644 index 00000000000..fccf9a92551 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.7_mend-tests.patch @@ -0,0 +1,48 @@ +Create suite of test in main makefile. +Remove tests relying on pslCheck which is distributed elsewhere. +Fix executable paths in the tests. +author: Alex Domingo (Vrije Universiteit Brussel) +diff -Nru blatSrc.orig/blat/test/makefile blatSrc/blat/test/makefile +--- blatSrc.orig/blat/test/makefile 2021-07-07 01:07:21.000000000 +0200 ++++ blatSrc/blat/test/makefile 2023-02-22 16:08:08.870093000 +0100 +@@ -1,8 +1,6 @@ + all: tThrowback tIntronMax + + tThrowback: +- blat -verbose=0 throwback/target1.fa throwback/query1.fa throwback/test.psl +- pslCheck -verbose=0 throwback/test.psl + blat -verbose=0 v29skips/ex1_database.fa v29skips/ex1_query.fa v29skips/ex1.psl + diff v29skips/ex1_reference.psl v29skips/ex1.psl + blat -verbose=0 v29skips/ex2_database.fa v29skips/ex2_query.fa v29skips/ex2.psl +diff -Nru blatSrc.orig/gfServer/makefile blatSrc/gfServer/makefile +--- blatSrc.orig/gfServer/makefile 2021-12-29 20:13:24.000000000 +0100 ++++ blatSrc/gfServer/makefile 2023-02-22 16:08:34.347451000 +0100 +@@ -6,10 +6,10 @@ + + test:: + ${MKDIR} tests/output +- ${DESTBINDIR}/${A} direct tests/input/mCrea.mrna tests/input/hCreaGeno.nib \ ++ ${A} direct tests/input/mCrea.mrna tests/input/hCreaGeno.nib \ + tests/input/mCreaGeno.nib > tests/output/testNib.out + diff tests/expected/testNib.out tests/output/testNib.out +- ${DESTBINDIR}/${A} direct tests/input/mCrea.mrna tests/input/creaGeno.2bit \ ++ ${A} direct tests/input/mCrea.mrna tests/input/creaGeno.2bit \ + >tests/output/testTwoBit.out + diff tests/expected/testTwoBit.out tests/output/testTwoBit.out + cd tests && ./testProtNib +diff -Nru blatSrc.orig/makefile blatSrc/makefile +--- blatSrc.orig/makefile 2022-02-01 00:14:03.000000000 +0100 ++++ blatSrc/makefile 2023-02-22 16:22:15.992962000 +0100 +@@ -15,5 +15,12 @@ + cd utils/twoBitInfo && $(MAKE) + cd webBlat && $(MAKE) + ++test:: ++ cd blat && ${MAKE} test ++ cd gfServer && ${MAKE} test ++ cd utils/faToTwoBit && ${MAKE} test ++ cd utils/twoBitInfo && ${MAKE} test ++ cd utils/twoBitToFa && ${MAKE} test ++ + clean: + rm -f */*.o */*/*.o lib/*/*.a From 96508e5af4527f1e29c592ed64b80ea2dfe5617b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 22 Feb 2023 20:31:39 +0100 Subject: [PATCH 6630/9987] move modextrapaths more to the bottom --- easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb index 4aacff62582..44f26b4c875 100644 --- a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb +++ b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb @@ -13,8 +13,6 @@ source_urls = ['https://doua.prabi.fr/software/seaview_data'] sources = [{'download_filename': '%(namelower)s%(version_major)s-64.tgz', 'filename': '%(name)s-%(version)s-64.tgz'}] checksums = ['e8d844ee5d41f7e5626631ac1eb75086add6a24bfe8a5aa69d045c622a8abd8d'] -modextrapaths = {'PATH': '.'} - sanity_check_paths = { 'files': ['%(namelower)s'], 'dirs': [], @@ -22,4 +20,6 @@ sanity_check_paths = { sanity_check_commands = [("%(namelower)s -h")] +modextrapaths = {'PATH': '.'} + moduleclass = 'bio' From 3e192e66fd66f3d41eb0fed6d5b4273aff12cb7c Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 23 Feb 2023 08:54:42 +0100 Subject: [PATCH 6631/9987] take EB Python3 root dir thx to @jfgrimm Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 25947a6df2c..d699232fd9f 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -33,6 +33,7 @@ dependencies = [ configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 19e5a3a3c24106bb823e5f7e8c4017a822656a0f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 23 Feb 2023 11:12:03 +0100 Subject: [PATCH 6632/9987] adding easyconfigs: Trinity-2.15.1-foss-2022a.eb --- .../t/Trinity/Trinity-2.15.1-foss-2022a.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb new file mode 100644 index 00000000000..55f4e4e9ad3 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb @@ -0,0 +1,61 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.15.1' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/%(name)s-v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +patches = ['Trinity-%(version)s_fix-bamsifter.patch'] +checksums = [ + {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580'}, + {'Trinity-2.15.1_fix-bamsifter.patch': '79588e3b7f5cf91f04804234b6ec983f30e4fdd50103adb8a83bdc7d7aaf29db'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), + ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), + ('GATK', '4.3.0.0', '-Java-%(javaver)s'), + ('Perl', '5.34.1'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('BLAST+', '2.13.0'), + ('BLAT', '3.7'), + ('Bowtie', '1.3.1'), + ('Bowtie2', '2.4.5'), + ('GMAP-GSNAP', '2023-02-17'), + ('HISAT2', '2.2.1'), + ('HTSlib', '1.15.1'), + ('Jellyfish', '2.3.0'), + ('kallisto', '0.48.0'), + ('ncurses', '6.3'), + ('RSEM', '1.3.3'), + ('Salmon', '1.9.0'), + ('SAMtools', '1.16.1'), + ('STAR', '2.7.10b'), + ('zlib', '1.2.12'), +] + +withsampledata = True + +moduleclass = 'bio' From 1f7d43998fb1556cc75d36f0982b5ba075b1eea9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2023 11:51:37 +0100 Subject: [PATCH 6633/9987] adding easyconfigs: FastQ_Screen-0.14.0-GCC-11.3.0.eb, GDGraph-1.56-GCCcore-11.3.0.eb, Bowtie-1.3.1-GCC-11.3.0.eb --- .../b/Bowtie/Bowtie-1.3.1-GCC-11.3.0.eb | 30 +++++++++ .../FastQ_Screen-0.14.0-GCC-11.3.0.eb | 39 +++++++++++ .../g/GDGraph/GDGraph-1.56-GCCcore-11.3.0.eb | 64 +++++++++++++++++++ 3 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.14.0-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GDGraph/GDGraph-1.56-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..9e06d7508f2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Artistic v2.0 +# +# Notes:: +## + +name = 'Bowtie' +version = '1.3.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.zip'] +checksums = ['e23517aa53846ef828172be911750cd05748522117efcbbe5a36f3241fb40761'] + +dependencies = [ + ('tbb', '2021.5.0'), + ('zlib', '1.2.12'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.14.0-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.14.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..9e571a3b965 --- /dev/null +++ b/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.14.0-GCC-11.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'Tarball' + +name = 'FastQ_Screen' +version = '0.14.0' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s/' +description = """FastQ Screen allows you to screen a library of sequences in FastQ + format against a set of sequence databases so you can see if the composition of the + library matches with what you expect.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] +checksums = ['5ee9c02617201e908e1693eebc356bed9d7693c915a83dda0d33a37cc34af654'] + +dependencies = [ + ('Perl', '5.34.1'), + ('GDGraph', '1.56'), + ('BWA', '0.7.17'), + ('Bowtie', '1.3.1'), + ('Bowtie2', '2.4.5'), +] + +#postinstallcmds = ["sed -i 's@#!/usr/bin/perl@#!/usr/bin/env perl@g' %(installdir)s/fastq_screen"] +fix_perl_shebang_for = ['fastq_screen'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['fastq_screen'], + 'dirs': [], +} + +sanity_check_commands = ["fastq_screen -v"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GDGraph/GDGraph-1.56-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GDGraph/GDGraph-1.56-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..512c17dc89d --- /dev/null +++ b/easybuild/easyconfigs/g/GDGraph/GDGraph-1.56-GCCcore-11.3.0.eb @@ -0,0 +1,64 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'Bundle' + +name = 'GDGraph' +version = '1.56' + +homepage = 'https://metacpan.org/release/GDGraph' +description = "GDGraph is a Perl package to generate charts" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/lstein/Perl-GD/archive/'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('libgd', '2.3.3'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), +] + +# this is a bundle of Perl modules +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('ExtUtils::PkgConfig', '1.16', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'sources': ['ExtUtils-PkgConfig-%(version)s.tar.gz'], + 'checksums': ['bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e'], + }), + ('GD', '2.76', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], + 'sources': ['GD-%(version)s.tar.gz'], + 'checksums': ['693d9e3d709e9188a682cb9090a77b70aac12a04e84128677577b94e4331775b'], + }), + ('GD::Text', '0.86', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MV/MVERB/'], + 'sources': ['GDTextUtil-%(version)s.tar.gz'], + 'checksums': ['886ecbf85cfe94f4135ee5689c4847a9ae783ecb99e6759e12c734f2dd6116bc'], + }), + ('GD::Graph', version, { + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BP/BPS/'], + 'sources': ['GDGraph-%(version)s.tar.gz'], + 'checksums': ['6f49cc4e59015480db9c9b6b18afd8c50be30886687b69411513d06f38971113'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bdf2gdfont.pl'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi', 'man'], +} + +modextrapaths = {'PERL5LIB': [ + 'lib/perl5/site_perl/%(perlver)s', + 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi', +]} + +moduleclass = 'bio' From 6009640d3e082daa8cf2cc511ae85bcd80a385af Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 23 Feb 2023 11:20:18 +0000 Subject: [PATCH 6634/9987] remove duplicated configopt --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index d699232fd9f..25947a6df2c 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -33,7 +33,6 @@ dependencies = [ configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From bcd559b07ad4d580d22c02bf92562abd73631668 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 23 Feb 2023 13:08:47 +0000 Subject: [PATCH 6635/9987] Fix for obsolete pycrypto on Python 3.10 --- .../p/Python/Python-3.10.4-GCCcore-11.3.0.eb | 29 ++---- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 96 +++++++------------ 2 files changed, 46 insertions(+), 79 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb index 1cfac838d2c..a2bcf32f509 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb @@ -59,11 +59,11 @@ exts_list = [ 'Python-3.10-bist-1.3.6-compatibility.patch', ], 'checksums': [ - '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3', # blist-1.3.6.tar.gz - # Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch - '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0', - # Python-3.10-bist-1.3.6-compatibility.patch - '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741', + {'blist-1.3.6.tar.gz': '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'}, + {'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch': + '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0'}, + {'Python-3.10-bist-1.3.6-compatibility.patch': + '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741'}, ], }), ('pbr', '5.8.1', { @@ -99,14 +99,9 @@ exts_list = [ 'modulename': 'arff', 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], }), - ('pycrypto', '2.6.1', { + ('pycryptodome', '3.17', { 'modulename': 'Crypto', - 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], - 'checksums': [ - 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz - # pycrypto-2.6.1_remove-usr-include.patch - '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e', - ], + 'checksums': ['bce2e2d8e82fcf972005652371a3e8731956a0c1fbb719cc897943b3695ad91b'], }), ('ecdsa', '0.17.0', { 'checksums': ['b9f500bb439e4153d0330610f5d26baaf18d17b8ced1bc54410d189385ea68aa'], @@ -136,8 +131,6 @@ exts_list = [ 'checksums': ['958c5bf4ab6483d59dab888538121871cc5006354a42fb0fbd50acf03caad1de'], }), ('cryptography', '37.0.1', { - # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, - # see https://github.com/rust-lang/cargo/issues/6652 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['d610d0ee14dd9109006215c7c0de15eee91230b70a9bce2263461cf7c3720b83'], }), @@ -197,15 +190,12 @@ exts_list = [ ('pluggy', '1.0.0', { 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], }), - # poetry 1.1.13 has requirement packaging<21.0,>=20.4 ('packaging', '20.9', { 'checksums': ['5b327ac1320dc863dca72f4514ecc086f31186744b84a230374cc1fd776feae5'], }), ('editables', '0.3', { 'checksums': ['167524e377358ed1f1374e61c268f0d7a4bf7dbd046c656f7b410cde16161b1a'], }), - # platformdirs >= 2.5 requires hatchling and that requires packaging>=21.3 - # however poetry 1.1.13 requires packaging<21.0,>=20.4, so use an older platformdirs to avoid needing hatchling ('platformdirs', '2.4.1', { 'checksums': ['440633ddfebcc36264232365d7840a970e75e1018d15b4327d11f91909045fda'], }), @@ -302,7 +292,6 @@ exts_list = [ ('imagesize', '1.3.0', { 'checksums': ['cd1750d452385ca327479d45b64d9c7729ecf0b3969a58148298c77092261f9d'], }), - # Sphinx 4.5.0 has requirement docutils<0.18,>=0.14 ('docutils', '0.17.1', { 'checksums': ['686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125'], }), @@ -397,7 +386,7 @@ exts_list = [ 'checksums': ['0a8eb9645b320881c222e827c26f4cfcf55363e8b374a021981ef886657a912f'], }), ('keyring', '23.5.0', { - 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'modulename': False, 'checksums': ['9012508e141a80bd1c0b6778d5c610dd9f8c464d75ac6774248500503f972fb9'], }), ('keyrings.alt', '4.1.0', { @@ -440,7 +429,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '0.8.1', { - 'source_tmpl': SOURCE_WHL, + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], }), ('cachy', '0.3.0', { diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index b919e01925b..91e2a3ca12c 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -47,8 +47,8 @@ exts_list = [ ('wheel', '0.38.4', { 'checksums': ['965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac'], }), - ('setuptools', '63.4.3', { - 'checksums': ['521c833d1e5e1ef0869940e7f486a83de7773b9f029010ad0c2fe35453a9dad9'], + ('setuptools', '65.5.1', { + 'checksums': ['e197a19aa8ec9722928f2206f8de752def0e4c9fc6953527360d1c36d94ddb2f'], }), ('pip', '22.3.1', { 'checksums': ['65fd48317359f3af8e593943e6ae1506b66325085ea64b706a998c6e83eeaf38'], @@ -78,7 +78,8 @@ exts_list = [ ('toml', '0.10.2', { 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], }), - ('flit_core', '3.8.0', { + ('flit-core', '3.8.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', 'checksums': ['b305b30c99526df5e63d6022dd2310a0a941a187bd3884f4c8ef0418df6c39f3'], }), ('tomli', '2.0.1', { @@ -87,7 +88,8 @@ exts_list = [ ('packaging', '21.3', { 'checksums': ['dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb'], }), - ('setuptools_scm', '7.0.5', { + ('setuptools-scm', '7.0.5', { + 'sources': ['setuptools_scm-%(version)s.tar.gz'], 'checksums': ['031e13af771d6f892b941adb6ea04545bbf91ebc5ce68c78aaf3fff6e1fb4844'], }), ('python-dateutil', '2.8.2', { @@ -101,14 +103,9 @@ exts_list = [ 'modulename': 'arff', 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], }), - ('pycrypto', '2.6.1', { + ('pycryptodome', '3.17', { 'modulename': 'Crypto', - 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], - 'checksums': [ - {'pycrypto-2.6.1.tar.gz': 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c'}, - {'pycrypto-2.6.1_remove-usr-include.patch': - '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e'}, - ], + 'checksums': ['bce2e2d8e82fcf972005652371a3e8731956a0c1fbb719cc897943b3695ad91b'], }), ('ecdsa', '0.18.0', { 'checksums': ['190348041559e21b22a1d65cee485282ca11a6f81d503fddb84d5017e9ed1e49'], @@ -128,18 +125,18 @@ exts_list = [ ('cffi', '1.15.1', { 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], }), - ('semantic_version', '2.10.0', { + ('semantic-version', '2.10.0', { + 'sources': ['semantic_version-%(version)s.tar.gz'], 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], }), - ('typing_extensions', '4.4.0', { + ('typing-extensions', '4.4.0', { + 'sources': ['typing_extensions-%(version)s.tar.gz'], 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], }), ('setuptools-rust', '1.5.2', { 'checksums': ['d8daccb14dc0eae1b6b6eb3ecef79675bd37b4065369f79c35393dd5c55652c7'], }), ('cryptography', '38.0.3', { - # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, - # see https://github.com/rust-lang/cargo/issues/6652 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['bfbe6ee19615b07a98b1d2287d6a6073f734735b49ee45b11324d85efc4d5cbd'], }), @@ -186,7 +183,8 @@ exts_list = [ ('zipp', '3.10.0', { 'checksums': ['7a7262fd930bd3e36c50b9a64897aec3fafff3dfdeec9623ae22b40e93f99bb8'], }), - ('importlib_metadata', '5.0.0', { + ('importlib-metadata', '5.0.0', { + 'sources': ['importlib_metadata-%(version)s.tar.gz'], 'checksums': ['da31db32b304314d044d3c12c79bd59e307889b287ad12ff387b3500835fc2ab'], }), ('backports.entry-points-selectable', '1.2.0', { @@ -205,7 +203,8 @@ exts_list = [ ('hatchling', '1.11.1', { 'checksums': ['9f84361f70cf3a7ab9543b0c3ecc64211ed2ba8a606a71eb6a473c1c9b08e1d0'], }), - ('hatch_vcs', '0.2.0', { + ('hatch-vcs', '0.2.0', { + 'sources': ['hatch_vcs-%(version)s.tar.gz'], 'checksums': ['9913d733b34eec9bb0345d0626ca32165a4ad2de15d1ce643c36d09ca908abff'], }), ('platformdirs', '2.5.3', { @@ -217,7 +216,8 @@ exts_list = [ ('pathlib2', '2.3.7.post1', { 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], }), - ('importlib_resources', '5.10.0', { + ('importlib-resources', '5.10.0', { + 'sources': ['importlib_resources-%(version)s.tar.gz'], 'checksums': ['c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668'], }), ('virtualenv', '20.16.6', { @@ -247,7 +247,8 @@ exts_list = [ ('xlrd', '2.0.1', { 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], }), - ('py_expression_eval', '0.3.14', { + ('py-expression-eval', '0.3.14', { + 'sources': ['py_expression_eval-%(version)s.tar.gz'], 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], }), ('tabulate', '0.9.0', { @@ -269,7 +270,8 @@ exts_list = [ 'modulename': 'attr', 'checksums': ['29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6'], }), - ('backports.functools_lru_cache', '1.6.4', { + ('backports.functools-lru-cache', '1.6.4', { + 'sources': ['backports.functools_lru_cache-%(version)s.tar.gz'], 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], }), ('wcwidth', '0.2.5', { @@ -281,7 +283,8 @@ exts_list = [ ('colorama', '0.4.6', { 'checksums': ['08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44'], }), - ('flit_scm', '1.7.0', { + ('flit-scm', '1.7.0', { + 'sources': ['flit_scm-%(version)s.tar.gz'], 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], }), ('exceptiongroup', '1.0.1', { @@ -369,7 +372,8 @@ exts_list = [ ('zipfile36', '0.1.3', { 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], }), - ('tomli_w', '1.0.0', { + ('tomli-w', '1.0.0', { + 'sources': ['tomli_w-%(version)s.tar.gz'], 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], }), ('flit', '3.8.0', { @@ -385,19 +389,19 @@ exts_list = [ 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], }), ('pastel', '0.2.1', { - 'source_tmpl': SOURCE_WHL, + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], }), ('crashtest', '0.3.1', { - 'source_tmpl': SOURCE_PY3_WHL, + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], }), ('clikit', '0.6.2', { - 'source_tmpl': SOURCE_WHL, + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], }), ('jeepney', '0.8.0', { - 'source_tmpl': SOURCE_PY3_WHL, + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], }), ('SecretStorage', '3.3.3', { @@ -415,7 +419,7 @@ exts_list = [ 'checksums': ['2ba3d56441ba0637f5f9c096068f67010ac0453f9d0b626de2aa3019353b6431'], }), ('tomlkit', '0.11.6', { - 'source_tmpl': SOURCE_PY3_WHL, + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b'], }), ('shellingham', '1.5.0', { @@ -431,13 +435,14 @@ exts_list = [ 'checksums': ['a84da4318dd86f870a9447a8c98340aa06216bfc6f2b7bdc4b8766984ae1867c'], }), ('ptyprocess', '0.7.0', { - 'source_tmpl': SOURCE_WHL, + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], }), ('pexpect', '4.8.0', { 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], }), - ('hatch_fancy_pypi_readme', '22.8.0', { + ('hatch-fancy-pypi-readme', '22.8.0', { + 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], 'checksums': ['da91282ca09601c18aded8e378daf8b578c70214866f0971156ee9bb9ce6c26a'], }), ('jsonschema', '4.17.0', { @@ -453,7 +458,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '1.0.0a5', { - 'source_tmpl': SOURCE_PY3_WHL, + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['ff53056589300976e960f75afb792dfbfc9c78dcbb5a448e207a17b643826360'], }), ('cachy', '0.3.0', { @@ -478,7 +483,8 @@ exts_list = [ ('dulwich', '0.20.50', { 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], }), - ('poetry_plugin_export', '1.2.0', { + ('poetry-plugin-export', '1.2.0', { + 'sources': ['poetry_plugin_export-%(version)s.tar.gz'], 'checksums': ['9a1dd42765408931d7831738749022651d43a2968b67c988db1b7a567dfe41ef'], }), ('poetry', '1.2.2', { @@ -494,34 +500,6 @@ exts_list = [ 'source_tmpl': 'simplegeneric-%(version)s.zip', 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), - ('pooch', '1.6.0', { - 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], - }), - ('doit', '0.36.0', { - 'checksums': ['71d07ccc9514cb22fe59d98999577665eaab57e16f644d04336ae0b4bae234bc'], - }), - ('cloudpickle', '2.2.0', { - 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], - }), - ('pydevtool', '0.3.0', { - 'checksums': ['25e3ba4f3d33ccac33ee2b9775995848d49e9b318b7a146477fb5d52f786fc8a'], - }), - ('rich', '13.1.0', { - 'checksums': ['81c73a30b144bbcdedc13f4ea0b6ffd7fdc3b0d3cc259a9402309c8e4aee1964'], - }), - ('rich-click', '1.6.0', { - 'checksums': ['33799c31f8817101f2eb8fe90e95d2c2acd428a567ee64358ca487f963f75e9c'], - }), - ('commonmark', '0.9.1', { - 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], - }), - ('execnet', '1.9.0', { - 'checksums': ['8f694f3ba9cc92cab508b152dcfe322153975c29bda272e2fd7f3f00f36e47c5'], - }), - ('pytest-xdist', '3.1.0', { - 'modulename': 'xdist', - 'checksums': ['40fdb8f3544921c5dfcd486ac080ce22870e71d82ced6d2e78fa97c2addd480c'], - }), ] moduleclass = 'lang' From 3bc6a49280408acb0f9135bd68641d58225d3ac9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2023 14:14:25 +0100 Subject: [PATCH 6636/9987] remove commented out postinstallcmds in FastQ_Screen easyconfig --- .../easyconfigs/f/FastQ_Screen/FastQ_Screen-0.14.0-GCC-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.14.0-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.14.0-GCC-11.3.0.eb index 9e571a3b965..ace0d3db725 100644 --- a/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.14.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/FastQ_Screen/FastQ_Screen-0.14.0-GCC-11.3.0.eb @@ -24,7 +24,6 @@ dependencies = [ ('Bowtie2', '2.4.5'), ] -#postinstallcmds = ["sed -i 's@#!/usr/bin/perl@#!/usr/bin/env perl@g' %(installdir)s/fastq_screen"] fix_perl_shebang_for = ['fastq_screen'] modextrapaths = {'PATH': ''} From d287cbbbe9bbfa3cbd02491b6eeba6521c82470a Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 23 Feb 2023 13:17:24 +0000 Subject: [PATCH 6637/9987] Fix for broken DEAP on SciPy-Bundle for python 3.10+ --- .../SciPy-bundle-2022.05-foss-2022.05.eb | 10 +++---- .../SciPy-bundle-2022.05-foss-2022a.eb | 26 +++++++------------ .../SciPy-bundle-2022.05-intel-2022.05.eb | 10 +++---- .../SciPy-bundle-2022.05-intel-2022a.eb | 10 +++---- 4 files changed, 19 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb index 25130f1d999..8bd1668fa6f 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb @@ -66,18 +66,14 @@ exts_list = [ 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], }), ('pandas', '1.4.2', { - 'preinstallopts': """sed -i 's@extra_compile_args = \\["-Werror"\\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], }), ('mpmath', '1.2.1', { 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], }), - ('deap', '1.3.1', { - 'patches': ['deap-1.3.1_no_2to3.patch'], - 'checksums': [ - '11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f', # deap-1.3.1.tar.gz - '3fa9fac74b0750ac6667371ce0634c797d62d270c76eee9c258b55f4a5a5e689', # deap-1.3.1_no_2to3.patch - ], + ('deap', '1.3.3', { + 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb index e09cc396fc8..eead95809ad 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb @@ -31,13 +31,13 @@ exts_list = [ ], 'sources': ['%(name)s-%(version)s.zip'], 'checksums': [ - 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18', # numpy-1.22.3.zip - # numpy-1.20.3_disable_fortran_callback_test.patch - '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', - # numpy-1.22.3_disable-broken-override-test.patch - '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', - # numpy-1.22.3_skip-ppc-long-complex-test.patch - '058c8128b9f7158b4d5bedb2f52ccc7e1362b99c352c3d10335f98a6194c880e', + {'numpy-1.22.3.zip': 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18'}, + {'numpy-1.20.3_disable_fortran_callback_test.patch': + '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + {'numpy-1.22.3_skip-ppc-long-complex-test.patch': + '058c8128b9f7158b4d5bedb2f52ccc7e1362b99c352c3d10335f98a6194c880e'}, ], }), ('ply', '3.11', { @@ -53,8 +53,6 @@ exts_list = [ 'checksums': ['0b2cba712e09f7630879dff69f268460bfe34a6d6000451b47d598558a92a875'], }), ('scipy', '1.8.1', { - # compilation with Pythran enabled fails when using Intel compilers, - # see https://github.com/scipy/scipy/issues/14935 'prebuildopts': "export SCIPY_USE_PYTHRAN=0 && ", 'preinstallopts': "export SCIPY_USE_PYTHRAN=0 && ", 'checksums': ['9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33'], @@ -69,18 +67,14 @@ exts_list = [ 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], }), ('pandas', '1.4.2', { - 'preinstallopts': """sed -i 's@extra_compile_args = \\["-Werror"\\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], }), ('mpmath', '1.2.1', { 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], }), - ('deap', '1.3.1', { - 'patches': ['deap-1.3.1_no_2to3.patch'], - 'checksums': [ - '11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f', # deap-1.3.1.tar.gz - '3fa9fac74b0750ac6667371ce0634c797d62d270c76eee9c258b55f4a5a5e689', # deap-1.3.1_no_2to3.patch - ], + ('deap', '1.3.3', { + 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb index bc9a37c19f3..57ccb48d649 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb @@ -68,18 +68,14 @@ exts_list = [ 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], }), ('pandas', '1.4.2', { - 'preinstallopts': """sed -i 's@extra_compile_args = \\["-Werror"\\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], }), ('mpmath', '1.2.1', { 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], }), - ('deap', '1.3.1', { - 'patches': ['deap-1.3.1_no_2to3.patch'], - 'checksums': [ - '11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f', # deap-1.3.1.tar.gz - '3fa9fac74b0750ac6667371ce0634c797d62d270c76eee9c258b55f4a5a5e689', # deap-1.3.1_no_2to3.patch - ], + ('deap', '1.3.3', { + 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb index c300aa78097..93dc62681ee 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb @@ -68,18 +68,14 @@ exts_list = [ 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], }), ('pandas', '1.4.2', { - 'preinstallopts': """sed -i 's@extra_compile_args = \\["-Werror"\\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], }), ('mpmath', '1.2.1', { 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], }), - ('deap', '1.3.1', { - 'patches': ['deap-1.3.1_no_2to3.patch'], - 'checksums': [ - '11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f', # deap-1.3.1.tar.gz - '3fa9fac74b0750ac6667371ce0634c797d62d270c76eee9c258b55f4a5a5e689', # deap-1.3.1_no_2to3.patch - ], + ('deap', '1.3.3', { + 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], }), ] From 4b6b5f33ae2e8820efd385773f686049619a5dfb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 23 Feb 2023 14:22:04 +0100 Subject: [PATCH 6638/9987] adding easyconfigs: STAR-CCM+-18.02.008.eb, STAR-CCM+-18.02.008-r8.eb --- .../s/STAR-CCM+/STAR-CCM+-18.02.008-r8.eb | 15 +++++++++++++++ .../s/STAR-CCM+/STAR-CCM+-18.02.008.eb | 14 ++++++++++++++ 2 files changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.02.008-r8.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.02.008.eb diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.02.008-r8.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.02.008-r8.eb new file mode 100644 index 00000000000..503f868c691 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.02.008-r8.eb @@ -0,0 +1,15 @@ +name = 'STAR-CCM+' +version = '18.02.008' +versionsuffix = '-r8' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +download_instructions = 'Manually obtain tarball from Siemens' +sources = ['%%(name)s%%(version)s_01_linux-x86_64%s.tar.gz' % versionsuffix] +checksums = ['20b061fbf981a9e4ce1e6ebbb7d390bbc6f400f89076adf3441a3da39f98a87c'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.02.008.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.02.008.eb new file mode 100644 index 00000000000..0100c5c4d69 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.02.008.eb @@ -0,0 +1,14 @@ +name = 'STAR-CCM+' +version = '18.02.008' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +download_instructions = 'Manually obtain tarball from Siemens' +sources = ['%(name)s%(version)s_01_linux-x86_64.tar.gz'] +checksums = ['4a9480952aef945d59452fc0a81e294e60d883539781ce989e159fdd963022a1'] + +moduleclass = 'cae' From e017cb688375d4f7c8b4d714938f91682dbca784 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 23 Feb 2023 15:14:56 +0100 Subject: [PATCH 6639/9987] adding easyconfigs: ROOT-6.22.08-foss-2020b.eb --- .../r/ROOT/ROOT-6.22.08-foss-2020b.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb new file mode 100644 index 00000000000..020ed48f660 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb @@ -0,0 +1,55 @@ +name = 'ROOT' +version = '6.22.08' + +homepage = 'https://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = ['https://root.cern.ch/download/'] +sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +checksums = ['6f061ff6ef8f5ec218a12c4c9ea92665eea116b16e1cd4df4f96f00c078a2f6f'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GSL', '2.6'), + ('libxml2', '2.9.10'), + ('PCRE', '8.44'), + ('CFITSIO', '3.49'), + ('freetype', '2.10.3'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('zlib', '1.2.11'), + ('X11', '20201008'), + ('Mesa', '20.2.1'), + ('libGLU', '9.0.1'), + ('GL2PS', '1.4.2'), + ('FFTW', '3.3.8'), + ('SQLite', '3.33.0'), + ('XZ', '5.2.5'), + ('libpng', '1.6.37'), +] + +# NOTE: Ensure that each configopts string begins with a blank +# disable some components +configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" + +# make sure some components are enabled +configopts += " -Dpcre=ON -Dzlib=ON -Dpyroot=ON" +configopts += " -Dunuran=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " + +# Add component-specific settings based on dependencies +configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' + +# Set C++ standard to C++17 for better stability +configopts += ' -DCMAKE_CXX_STANDARD=17' + +configopts += " -Dgallium-drivers=swrast" + +moduleclass = 'data' From c6442486e0d52f609e1b19bdf79d391734b5b9e4 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 23 Feb 2023 16:16:16 +0100 Subject: [PATCH 6640/9987] adding easyconfigs: ReFrame-4.0.5.eb --- .../easyconfigs/r/ReFrame/ReFrame-4.0.5.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.0.5.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.0.5.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.0.5.eb new file mode 100644 index 00000000000..3c77570ad5a --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.0.5.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.0.5' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + # stick to pip < 22.0, to maintain compatibility with Python 3.6 + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + ('reframe', version, { + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['4902258e5a201cb72ef9dc175a0970dcfc5869f3270a198dcd8bc47cc1a3cabd'], + }), +] + +postinstallcmds = [ + "cp -a hpctestlib tools tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'hpctestlib', 'lib', 'tools', 'tutorials'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From b93c7b0ac6b5864496f23f5abb329813e88ec3b7 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 23 Feb 2023 15:59:20 +0000 Subject: [PATCH 6641/9987] bump OpenSSL 1.1 wrapper fallback to 1.1.1t --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb index d5f4151e2f2..ee1e94ca6bb 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb @@ -6,7 +6,7 @@ minimum_openssl_version = '1.1.1' homepage = 'https://www.openssl.org/' description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, - and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. """ toolchain = SYSTEM @@ -27,11 +27,11 @@ builddependencies = [('pkgconf', '1.8.0')] # component list, which will be build and installed as usual. components = [ - (name, '1.1.1o', { + (name, '1.1.1t', { 'easyblock': 'EB_OpenSSL', 'source_urls': ['https://www.openssl.org/source/'], 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['9384a2b0570dd80358841464677115df785edb941c71211f75076d72fe6b438f'], + 'checksums': ['8dee9b24bdb1dcbf0c3d1e9b02fb8f6bf22165e807f45adeb7c9677536859d3b'], 'start_dir': '%(namelower)s-%(version)s', }), ] From e7ead96984afc2c7244ad7e4480e0d71f2994daf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 23 Feb 2023 17:23:16 +0100 Subject: [PATCH 6642/9987] adding easyconfigs: cuDNN-8.8.0.121-CUDA-12.0.0.eb --- .../c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb new file mode 100644 index 00000000000..7e8779246f0 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb @@ -0,0 +1,38 @@ +name = 'cuDNN' +version = '8.8.0.121' +versionsuffix = '-CUDA-%(cudaver)s' +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN is tied to specific to CUDA versions, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +local_cuda_major = '12' + +download_instructions = 'Requires manual download from https://developer.nvidia.com/rdp/cudnn-download' +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = [{ + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'a0792b666caaf593a9dd4130979578fd3a78230f4407645c295700ef8e7aaaf2', + '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'cd41ab8b61f5beb54e32c3668ecd311ce926c39006fba256b053dd7d248419d4', + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'fc668519a8344e9d05335bad4bc5d23a504cdc7579aea41f12d6aa0f3079e709', +}] + +dependencies = [('CUDA', '12.0.0')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From 9f8bc648d8043cf0a1e9ce12c24b3f41836b46fe Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 23 Feb 2023 16:29:35 +0000 Subject: [PATCH 6643/9987] adding easyconfigs: dm-tree-0.1.8-GCCcore-11.3.0.eb --- .../d/dm-tree/dm-tree-0.1.8-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100755 easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-11.3.0.eb new file mode 100755 index 00000000000..94b5023db0f --- /dev/null +++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'dm-tree' +version = '0.1.8' + +homepage = 'https://github.com/deepmind/tree' +description = """dm-tree provides tree, a library for working with nested data structures. In a way, +tree generalizes the builtin map function which only supports flat sequences, and +allows to apply a function to each "leaf" preserving the overall structure.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True + +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'tree'} + +moduleclass = 'lib' From 3ff5fcdda743ed127a0144e2bdc2c2b5bc227ce0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 23 Feb 2023 17:40:12 +0100 Subject: [PATCH 6644/9987] stick to click-log 0.1.8 for vConTACT2 + add sanity check commands --- .../v/vConTACT2/vConTACT2-0.11.3-foss-2022a.eb | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/vConTACT2/vConTACT2-0.11.3-foss-2022a.eb b/easybuild/easyconfigs/v/vConTACT2/vConTACT2-0.11.3-foss-2022a.eb index 86e90f7efb5..19515db642a 100644 --- a/easybuild/easyconfigs/v/vConTACT2/vConTACT2-0.11.3-foss-2022a.eb +++ b/easybuild/easyconfigs/v/vConTACT2/vConTACT2-0.11.3-foss-2022a.eb @@ -23,8 +23,9 @@ dependencies = [ use_pip = True exts_list = [ - ('click-log', '0.4.0', { - 'checksums': ['3970f8570ac54491237bcdb3d8ab5e3eef6c057df29f8c3d1151a51a9c23b975'], + # click-log 0.1.8 is strictly required due assumption that click_log module provides 'init' + ('click-log', '0.1.8', { + 'checksums': ['57271008c12e2dc16d413373bedd7fd3ff17c57434e168650dc27dfb9c743392'], }), ('coreschema', '0.0.4', { 'checksums': ['9503506007d482ab0867ba14724b93c18a33b22b6d19fb419ef2d239dd4a1607'], @@ -73,6 +74,15 @@ exts_list = [ }), ] + +sanity_check_commands = [ + 'coreapi --help', + 'just --help', + 'raven --help', + 'vcontact2 --help', + 'vcontact2_gene2genome --help', +] + sanity_pip_check = True moduleclass = 'bio' From a098135a24866a1769fcef6d4c7d0ce966e5b70e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 23 Feb 2023 17:07:16 +0000 Subject: [PATCH 6645/9987] adding easyconfigs: jax-0.4.4-foss-2022a.eb --- .../easyconfigs/j/jax/jax-0.4.4-foss-2022a.eb | 107 ++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100755 easybuild/easyconfigs/j/jax/jax-0.4.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.4-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.4.4-foss-2022a.eb new file mode 100755 index 00000000000..4404537f35c --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.4.4-foss-2022a.eb @@ -0,0 +1,107 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.4.4' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.36.0', '-nodocs'), + ('matplotlib', '3.5.2'), # required for tests/lobpcg_test.py +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in WORKSPACE +local_tf_commit = '43e9d313548ded301fa54f25a4192d3bcb123330' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.4.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('jaxlib', '0.4.4', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + {'jaxlib-v0.4.4.tar.gz': '881f402c7983b56b185e182d5315dd64c9f5320be96213d0415996ece1826806'}, + {'tensorflow-43e9d313548ded301fa54f25a4192d3bcb123330.tar.gz': + '23aae276b2705bfbdaea3c472da24130598f13ac0439cfb7149befb781d97a8f'}, + {'jaxlib_local-tensorflow-repo.sed': 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5'}, + {'TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch': + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db'}, + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '1.0.0', { + 'checksums': ['d10982f7702422bea8635d5284b8bed629f51919fc122ac1e1e4abf45ec8f785'], + }), + (name, version, { + 'patches': ['jax-0.3.23_relax-testPoly5-tolerance.patch'], + 'runtest': "pytest -n %(parallel)s tests", + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': [ + {'jax-v0.4.4.tar.gz': '755eb9b12ab4880e78690f28fc7bd2b491be4e551d8b966e6974753c878dd2c0'}, + {'jax-0.3.23_relax-testPoly5-tolerance.patch': + 'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From dea0cb64580fbfe65776ffa4b75e73283ee1a5c1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 23 Feb 2023 17:08:06 +0000 Subject: [PATCH 6646/9987] adding easyconfigs: jax-0.4.4-foss-2022a-CUDA-11.7.0.eb and patches: jax-0.4.4_cusparse.patch --- .../j/jax/jax-0.4.4-foss-2022a-CUDA-11.7.0.eb | 116 ++++++++++++++++++ .../j/jax/jax-0.4.4_cusparse.patch | 39 ++++++ 2 files changed, 155 insertions(+) create mode 100755 easybuild/easyconfigs/j/jax/jax-0.4.4-foss-2022a-CUDA-11.7.0.eb create mode 100755 easybuild/easyconfigs/j/jax/jax-0.4.4_cusparse.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.4.4-foss-2022a-CUDA-11.7.0.eb new file mode 100755 index 00000000000..ef6d2138b86 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.4.4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,116 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.4.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.36.0', '-nodocs'), + ('matplotlib', '3.5.2'), # required for tests/lobpcg_test.py +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), + ('NCCL', '2.12.12', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in WORKSPACE +local_tf_commit = '43e9d313548ded301fa54f25a4192d3bcb123330' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.4.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('jaxlib', '0.4.4', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + {'jaxlib-v0.4.4.tar.gz': '881f402c7983b56b185e182d5315dd64c9f5320be96213d0415996ece1826806'}, + {'tensorflow-43e9d313548ded301fa54f25a4192d3bcb123330.tar.gz': + '23aae276b2705bfbdaea3c472da24130598f13ac0439cfb7149befb781d97a8f'}, + {'jaxlib_local-tensorflow-repo.sed': 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5'}, + {'TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch': + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db'}, + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '1.0.0', { + 'checksums': ['d10982f7702422bea8635d5284b8bed629f51919fc122ac1e1e4abf45ec8f785'], + }), + (name, version, { + 'patches': [ + 'jax-0.3.23_relax-testPoly5-tolerance.patch', + 'jax-0.4.4_cusparse.patch', + ], + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + + "JAX_ENABLE_X64=true pytest -vv tests", + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': [ + {'jax-v0.4.4.tar.gz': '755eb9b12ab4880e78690f28fc7bd2b491be4e551d8b966e6974753c878dd2c0'}, + {'jax-0.3.23_relax-testPoly5-tolerance.patch': + 'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'}, + {'jax-0.4.4_cusparse.patch': '7414115533cce9f37c60850c09c69563a0ed6477c73f03c4132b9c2ae75ae60f'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jax-0.4.4_cusparse.patch b/easybuild/easyconfigs/j/jax/jax-0.4.4_cusparse.patch new file mode 100755 index 00000000000..ab9a4479fe3 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.4.4_cusparse.patch @@ -0,0 +1,39 @@ +Skip tests: + ** On entry to cusparseSpMM_bufferSize(): matrix B and C must be in column-major order + cuSparseTest.test_coo_matmat1 + cuSparseTest.test_coo_matmat3 + cuSparseTest.test_coo_matmat5 + test_coo_sorted_indices_gpu_lowerings + ** On entry to cusparseSpMM_bufferSize(): opA != CUSPARSE_OPERATION_NON_TRANSPOSE is not supported with CUSPARSE_SPMM_COO_ALG2 + cuSparseTest.test_coo_matmat6 + cuSparseTest.test_coo_matmat7 + ** On entry to cusparseSpMM_bufferSize(): CUSPARSE_SPMM_COO_ALG2 does not support 64-bit indices + test_coo_matmat_layout +Patch by Simon Branford (University of Birmingham) +--- tests/sparse_test.py.orig 2023-02-23 08:59:00.381238000 +0000 ++++ tests/sparse_test.py 2023-02-23 10:39:59.054404886 +0000 +@@ -445,6 +445,8 @@ + with self.gpu_matmul_dtype_warning_context(dtype): + self.assertAllClose(op(M) @ v, jit(matvec)(*args), rtol=MATMUL_TOL) + ++ @unittest.skip("""1, 3, 5: On entry to cusparseSpMM_bufferSize(): matrix B and C must be in column-major order; ++6, 7: On entry to cusparseSpMM_bufferSize(): opA != CUSPARSE_OPERATION_NON_TRANSPOSE is not supported with CUSPARSE_SPMM_COO_ALG2""") + @jtu.sample_product( + shape=[(5, 8), (8, 5), (5, 5), (8, 8)], + dtype=all_dtypes, +@@ -465,6 +467,7 @@ + with self.gpu_matmul_dtype_warning_context(dtype): + self.assertAllClose(op(M) @ B, jit(matmat)(*args), rtol=MATMUL_TOL) + ++ @unittest.skip("On entry to cusparseSpMM_bufferSize(): CUSPARSE_SPMM_COO_ALG2 does not support 64-bit indices") + def test_coo_matmat_layout(self): + # Regression test for https://github.com/google/jax/issues/7533 + d = jnp.array([1.0, 2.0, 3.0, 4.0]) +@@ -494,6 +497,7 @@ + + @unittest.skipIf(not GPU_LOWERING_ENABLED, "test requires cusparse/hipsparse") + @unittest.skipIf(jtu.device_under_test() != "gpu", "test requires GPU") ++ @unittest.skip("On entry to cusparseSpMM_bufferSize(): matrix B and C must be in column-major order") + def test_coo_sorted_indices_gpu_lowerings(self): + dtype = jnp.float32 + From d7c704d42e0227e46cf95d937e031574a7574dc1 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 23 Feb 2023 17:40:58 +0000 Subject: [PATCH 6647/9987] add hatchling --- .../easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb index c420a5183ce..c73bba0beff 100755 --- a/easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.2.2-GCCcore-11.3.0.eb @@ -59,6 +59,15 @@ exts_list = [ 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['93ea3c4a622485c2a7b7249f1e34e4ac84f8229ded76153b67506313201b154f'], }), + ('pathspec', '0.10.1', { + 'checksums': ['7ace6161b621d31e7902eb6b5ae148d12cfd23f4a249b9ffb6b9fee12084323d'], + }), + ('hatchling', '1.11.1', { + 'checksums': ['9f84361f70cf3a7ab9543b0c3ecc64211ed2ba8a606a71eb6a473c1c9b08e1d0'], + }), + ('hatch_vcs', '0.2.0', { + 'checksums': ['9913d733b34eec9bb0345d0626ca32165a4ad2de15d1ce643c36d09ca908abff'], + }), ] sanity_check_paths = { From 4b98d98d7b482aec31c289133bb798f0f7ae234d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 24 Feb 2023 01:05:28 +0100 Subject: [PATCH 6648/9987] add dependency on util-linux to BLAT v3.7 --- easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.3.0.eb index 6f33b6c1bbc..d63b37e10b1 100644 --- a/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.3.0.eb @@ -35,6 +35,7 @@ dependencies = [ ('libpng', '1.6.37'), ('MariaDB', '10.9.3'), ('OpenSSL', '1.1', '', SYSTEM), + ('util-linux', '2.38'), ('zlib', '1.2.12'), ] From 80f7cdb57ae7d1fdfdcc9e6debdfcfa94a728e3d Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 24 Feb 2023 09:24:15 +0100 Subject: [PATCH 6649/9987] add back comments that were removed by inject-checksums --- .../p/Python/Python-3.10.4-GCCcore-11.3.0.eb | 20 +++-- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 87 +++++++++++-------- 2 files changed, 65 insertions(+), 42 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb index a2bcf32f509..30b815f1730 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb @@ -59,11 +59,11 @@ exts_list = [ 'Python-3.10-bist-1.3.6-compatibility.patch', ], 'checksums': [ - {'blist-1.3.6.tar.gz': '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'}, - {'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch': - '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0'}, - {'Python-3.10-bist-1.3.6-compatibility.patch': - '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741'}, + '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3', # blist-1.3.6.tar.gz + # Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch + '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0', + # Python-3.10-bist-1.3.6-compatibility.patch + '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741', ], }), ('pbr', '5.8.1', { @@ -131,6 +131,8 @@ exts_list = [ 'checksums': ['958c5bf4ab6483d59dab888538121871cc5006354a42fb0fbd50acf03caad1de'], }), ('cryptography', '37.0.1', { + # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, + # see https://github.com/rust-lang/cargo/issues/6652 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['d610d0ee14dd9109006215c7c0de15eee91230b70a9bce2263461cf7c3720b83'], }), @@ -190,12 +192,15 @@ exts_list = [ ('pluggy', '1.0.0', { 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], }), + # poetry 1.1.13 has requirement packaging<21.0,>=20.4 ('packaging', '20.9', { 'checksums': ['5b327ac1320dc863dca72f4514ecc086f31186744b84a230374cc1fd776feae5'], }), ('editables', '0.3', { 'checksums': ['167524e377358ed1f1374e61c268f0d7a4bf7dbd046c656f7b410cde16161b1a'], }), + # platformdirs >= 2.5 requires hatchling and that requires packaging>=21.3 + # however poetry 1.1.13 requires packaging<21.0,>=20.4, so use an older platformdirs to avoid needing hatchling ('platformdirs', '2.4.1', { 'checksums': ['440633ddfebcc36264232365d7840a970e75e1018d15b4327d11f91909045fda'], }), @@ -292,6 +297,7 @@ exts_list = [ ('imagesize', '1.3.0', { 'checksums': ['cd1750d452385ca327479d45b64d9c7729ecf0b3969a58148298c77092261f9d'], }), + # Sphinx 4.5.0 has requirement docutils<0.18,>=0.14 ('docutils', '0.17.1', { 'checksums': ['686577d2e4c32380bb50cbb22f575ed742d58168cee37e99117a854bcd88f125'], }), @@ -386,7 +392,7 @@ exts_list = [ 'checksums': ['0a8eb9645b320881c222e827c26f4cfcf55363e8b374a021981ef886657a912f'], }), ('keyring', '23.5.0', { - 'modulename': False, + 'modulename': False, # Doesn't work properly if HOME directory contains keys 'checksums': ['9012508e141a80bd1c0b6778d5c610dd9f8c464d75ac6774248500503f972fb9'], }), ('keyrings.alt', '4.1.0', { @@ -429,7 +435,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '0.8.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['141cda6dc94a92343be626bb87a0b6c86ae291dfc732a57bf04310d4b4201753'], }), ('cachy', '0.3.0', { diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index 91e2a3ca12c..603d9a9e3c1 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -47,8 +47,8 @@ exts_list = [ ('wheel', '0.38.4', { 'checksums': ['965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac'], }), - ('setuptools', '65.5.1', { - 'checksums': ['e197a19aa8ec9722928f2206f8de752def0e4c9fc6953527360d1c36d94ddb2f'], + ('setuptools', '63.4.3', { + 'checksums': ['521c833d1e5e1ef0869940e7f486a83de7773b9f029010ad0c2fe35453a9dad9'], }), ('pip', '22.3.1', { 'checksums': ['65fd48317359f3af8e593943e6ae1506b66325085ea64b706a998c6e83eeaf38'], @@ -78,8 +78,7 @@ exts_list = [ ('toml', '0.10.2', { 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], }), - ('flit-core', '3.8.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', + ('flit_core', '3.8.0', { 'checksums': ['b305b30c99526df5e63d6022dd2310a0a941a187bd3884f4c8ef0418df6c39f3'], }), ('tomli', '2.0.1', { @@ -88,8 +87,7 @@ exts_list = [ ('packaging', '21.3', { 'checksums': ['dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb'], }), - ('setuptools-scm', '7.0.5', { - 'sources': ['setuptools_scm-%(version)s.tar.gz'], + ('setuptools_scm', '7.0.5', { 'checksums': ['031e13af771d6f892b941adb6ea04545bbf91ebc5ce68c78aaf3fff6e1fb4844'], }), ('python-dateutil', '2.8.2', { @@ -125,18 +123,18 @@ exts_list = [ ('cffi', '1.15.1', { 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], }), - ('semantic-version', '2.10.0', { - 'sources': ['semantic_version-%(version)s.tar.gz'], + ('semantic_version', '2.10.0', { 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], }), - ('typing-extensions', '4.4.0', { - 'sources': ['typing_extensions-%(version)s.tar.gz'], + ('typing_extensions', '4.4.0', { 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], }), ('setuptools-rust', '1.5.2', { 'checksums': ['d8daccb14dc0eae1b6b6eb3ecef79675bd37b4065369f79c35393dd5c55652c7'], }), ('cryptography', '38.0.3', { + # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, + # see https://github.com/rust-lang/cargo/issues/6652 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['bfbe6ee19615b07a98b1d2287d6a6073f734735b49ee45b11324d85efc4d5cbd'], }), @@ -183,8 +181,7 @@ exts_list = [ ('zipp', '3.10.0', { 'checksums': ['7a7262fd930bd3e36c50b9a64897aec3fafff3dfdeec9623ae22b40e93f99bb8'], }), - ('importlib-metadata', '5.0.0', { - 'sources': ['importlib_metadata-%(version)s.tar.gz'], + ('importlib_metadata', '5.0.0', { 'checksums': ['da31db32b304314d044d3c12c79bd59e307889b287ad12ff387b3500835fc2ab'], }), ('backports.entry-points-selectable', '1.2.0', { @@ -203,8 +200,7 @@ exts_list = [ ('hatchling', '1.11.1', { 'checksums': ['9f84361f70cf3a7ab9543b0c3ecc64211ed2ba8a606a71eb6a473c1c9b08e1d0'], }), - ('hatch-vcs', '0.2.0', { - 'sources': ['hatch_vcs-%(version)s.tar.gz'], + ('hatch_vcs', '0.2.0', { 'checksums': ['9913d733b34eec9bb0345d0626ca32165a4ad2de15d1ce643c36d09ca908abff'], }), ('platformdirs', '2.5.3', { @@ -216,8 +212,7 @@ exts_list = [ ('pathlib2', '2.3.7.post1', { 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], }), - ('importlib-resources', '5.10.0', { - 'sources': ['importlib_resources-%(version)s.tar.gz'], + ('importlib_resources', '5.10.0', { 'checksums': ['c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668'], }), ('virtualenv', '20.16.6', { @@ -247,8 +242,7 @@ exts_list = [ ('xlrd', '2.0.1', { 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], }), - ('py-expression-eval', '0.3.14', { - 'sources': ['py_expression_eval-%(version)s.tar.gz'], + ('py_expression_eval', '0.3.14', { 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], }), ('tabulate', '0.9.0', { @@ -270,8 +264,7 @@ exts_list = [ 'modulename': 'attr', 'checksums': ['29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6'], }), - ('backports.functools-lru-cache', '1.6.4', { - 'sources': ['backports.functools_lru_cache-%(version)s.tar.gz'], + ('backports.functools_lru_cache', '1.6.4', { 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], }), ('wcwidth', '0.2.5', { @@ -283,8 +276,7 @@ exts_list = [ ('colorama', '0.4.6', { 'checksums': ['08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44'], }), - ('flit-scm', '1.7.0', { - 'sources': ['flit_scm-%(version)s.tar.gz'], + ('flit_scm', '1.7.0', { 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], }), ('exceptiongroup', '1.0.1', { @@ -372,8 +364,7 @@ exts_list = [ ('zipfile36', '0.1.3', { 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], }), - ('tomli-w', '1.0.0', { - 'sources': ['tomli_w-%(version)s.tar.gz'], + ('tomli_w', '1.0.0', { 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], }), ('flit', '3.8.0', { @@ -389,19 +380,19 @@ exts_list = [ 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], }), ('pastel', '0.2.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], }), ('crashtest', '0.3.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], }), ('clikit', '0.6.2', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], }), ('jeepney', '0.8.0', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], }), ('SecretStorage', '3.3.3', { @@ -419,7 +410,7 @@ exts_list = [ 'checksums': ['2ba3d56441ba0637f5f9c096068f67010ac0453f9d0b626de2aa3019353b6431'], }), ('tomlkit', '0.11.6', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b'], }), ('shellingham', '1.5.0', { @@ -435,14 +426,13 @@ exts_list = [ 'checksums': ['a84da4318dd86f870a9447a8c98340aa06216bfc6f2b7bdc4b8766984ae1867c'], }), ('ptyprocess', '0.7.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], }), ('pexpect', '4.8.0', { 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], }), - ('hatch-fancy-pypi-readme', '22.8.0', { - 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], + ('hatch_fancy_pypi_readme', '22.8.0', { 'checksums': ['da91282ca09601c18aded8e378daf8b578c70214866f0971156ee9bb9ce6c26a'], }), ('jsonschema', '4.17.0', { @@ -458,7 +448,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '1.0.0a5', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['ff53056589300976e960f75afb792dfbfc9c78dcbb5a448e207a17b643826360'], }), ('cachy', '0.3.0', { @@ -483,8 +473,7 @@ exts_list = [ ('dulwich', '0.20.50', { 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], }), - ('poetry-plugin-export', '1.2.0', { - 'sources': ['poetry_plugin_export-%(version)s.tar.gz'], + ('poetry_plugin_export', '1.2.0', { 'checksums': ['9a1dd42765408931d7831738749022651d43a2968b67c988db1b7a567dfe41ef'], }), ('poetry', '1.2.2', { @@ -500,6 +489,34 @@ exts_list = [ 'source_tmpl': 'simplegeneric-%(version)s.zip', 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], }), + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + ('doit', '0.36.0', { + 'checksums': ['71d07ccc9514cb22fe59d98999577665eaab57e16f644d04336ae0b4bae234bc'], + }), + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + ('pydevtool', '0.3.0', { + 'checksums': ['25e3ba4f3d33ccac33ee2b9775995848d49e9b318b7a146477fb5d52f786fc8a'], + }), + ('rich', '13.1.0', { + 'checksums': ['81c73a30b144bbcdedc13f4ea0b6ffd7fdc3b0d3cc259a9402309c8e4aee1964'], + }), + ('rich-click', '1.6.0', { + 'checksums': ['33799c31f8817101f2eb8fe90e95d2c2acd428a567ee64358ca487f963f75e9c'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('execnet', '1.9.0', { + 'checksums': ['8f694f3ba9cc92cab508b152dcfe322153975c29bda272e2fd7f3f00f36e47c5'], + }), + ('pytest-xdist', '3.1.0', { + 'modulename': 'xdist', + 'checksums': ['40fdb8f3544921c5dfcd486ac080ce22870e71d82ced6d2e78fa97c2addd480c'], + }), ] moduleclass = 'lang' From 2a009c247d41a74a873dcc0d0b80d2f59d56d47c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 24 Feb 2023 09:30:05 +0100 Subject: [PATCH 6650/9987] add back comments that were removed by inject-checksums --- .../SciPy-bundle-2022.05-foss-2022.05.eb | 2 +- .../SciPy-bundle-2022.05-foss-2022a.eb | 18 ++++++++++-------- .../SciPy-bundle-2022.05-intel-2022.05.eb | 2 +- .../SciPy-bundle-2022.05-intel-2022a.eb | 2 +- 4 files changed, 13 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb index 8bd1668fa6f..b28fefbb7e5 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb @@ -66,7 +66,7 @@ exts_list = [ 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], }), ('pandas', '1.4.2', { - 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': """sed -i 's@extra_compile_args = \\["-Werror"\\]@extra_compile_args = []@g' setup.py && """, 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], }), ('mpmath', '1.2.1', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb index eead95809ad..a2af2d99e51 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb @@ -31,13 +31,13 @@ exts_list = [ ], 'sources': ['%(name)s-%(version)s.zip'], 'checksums': [ - {'numpy-1.22.3.zip': 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18'}, - {'numpy-1.20.3_disable_fortran_callback_test.patch': - '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75'}, - {'numpy-1.22.3_disable-broken-override-test.patch': - '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, - {'numpy-1.22.3_skip-ppc-long-complex-test.patch': - '058c8128b9f7158b4d5bedb2f52ccc7e1362b99c352c3d10335f98a6194c880e'}, + 'dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18', # numpy-1.22.3.zip + # numpy-1.20.3_disable_fortran_callback_test.patch + '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + # numpy-1.22.3_disable-broken-override-test.patch + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c', + # numpy-1.22.3_skip-ppc-long-complex-test.patch + '058c8128b9f7158b4d5bedb2f52ccc7e1362b99c352c3d10335f98a6194c880e', ], }), ('ply', '3.11', { @@ -53,6 +53,8 @@ exts_list = [ 'checksums': ['0b2cba712e09f7630879dff69f268460bfe34a6d6000451b47d598558a92a875'], }), ('scipy', '1.8.1', { + # compilation with Pythran enabled fails when using Intel compilers, + # see https://github.com/scipy/scipy/issues/14935 'prebuildopts': "export SCIPY_USE_PYTHRAN=0 && ", 'preinstallopts': "export SCIPY_USE_PYTHRAN=0 && ", 'checksums': ['9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33'], @@ -67,7 +69,7 @@ exts_list = [ 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], }), ('pandas', '1.4.2', { - 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': """sed -i 's@extra_compile_args = \\["-Werror"\\]@extra_compile_args = []@g' setup.py && """, 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], }), ('mpmath', '1.2.1', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb index 57ccb48d649..40523655027 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb @@ -68,7 +68,7 @@ exts_list = [ 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], }), ('pandas', '1.4.2', { - 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': """sed -i 's@extra_compile_args = \\["-Werror"\\]@extra_compile_args = []@g' setup.py && """, 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], }), ('mpmath', '1.2.1', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb index 93dc62681ee..9ae652f9a05 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb @@ -68,7 +68,7 @@ exts_list = [ 'checksums': ['1764a7f4ad58c558723c542847eb367ab0bbb6d880a4e5d5eef30a0ece5cecea'], }), ('pandas', '1.4.2', { - 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'preinstallopts': """sed -i 's@extra_compile_args = \\["-Werror"\\]@extra_compile_args = []@g' setup.py && """, 'checksums': ['92bc1fc585f1463ca827b45535957815b7deb218c549b7c18402c322c7549a12'], }), ('mpmath', '1.2.1', { From 8a3a89dda7778b9a3b57187955f60da62d709eb4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 24 Feb 2023 12:23:33 +0100 Subject: [PATCH 6651/9987] remove blank line --- easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.29-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.29-foss-2022a.eb b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.29-foss-2022a.eb index 55db5b7d930..f89267e310b 100644 --- a/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.29-foss-2022a.eb +++ b/easybuild/easyconfigs/h/HDBSCAN/HDBSCAN-0.8.29-foss-2022a.eb @@ -27,5 +27,4 @@ exts_list = [ }), ] - moduleclass = 'data' From 438320f86c0ee8ed85d3e7142c920b7d339067e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2023 16:38:37 +0100 Subject: [PATCH 6652/9987] use better way to run 'pip check' in Raven easyconfig --- easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index ecf094af5d5..6694394fef7 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -54,7 +54,7 @@ sanity_check_paths = { } sanity_check_commands = [ - "pip check", + "export PYTHONNOUSERSITE=1 && python%(pyshortver)s -m pip check", "raven --help" ] From a465578d07ac5c9f4f5e8d7156330a7fe15f9c77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2023 16:47:22 +0100 Subject: [PATCH 6653/9987] use list (not set) for dependencies in chemprop easyconfig --- easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb index 0ab776fbccd..dae50013213 100644 --- a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a.eb @@ -8,7 +8,7 @@ description = 'Message Passing Neural Networks for Molecule Property Prediction' toolchain = {'name': 'foss', 'version': '2022a'} -dependencies = { +dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('scikit-learn', '1.1.2'), @@ -19,7 +19,7 @@ dependencies = { ('PyTorch', '1.12.0'), ('matplotlib', '3.5.2'), ('RDKit', '2022.09.4') -} +] use_pip = True sanity_pip_check = True From 0678a004ba36b1c0f8b295aba8c618e38bc772f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2023 16:50:18 +0100 Subject: [PATCH 6654/9987] use raw string in Raven easyconfig --- easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index 6694394fef7..82f6b075da7 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -40,7 +40,7 @@ exts_list = [ 'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'], 'sources': ['%(version)s.tar.gz'], 'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'], - 'preinstallopts': 'sed -i \'s|cmake_args += \["-GNinja"\]|cmake_args += \["-GNinja", \ + 'preinstallopts': r'sed -i \'s|cmake_args += \["-GNinja"\]|cmake_args += \["-GNinja", \ "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION",\ "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python"\]|\' setup.py && ' }), From f4078309904d2e0e5b2052b56b43e9e7f37f465d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 24 Feb 2023 17:00:40 +0100 Subject: [PATCH 6655/9987] adding easyconfigs: MetaBAT-2.15-GCC-11.2.0.eb and patches: MetaBAT-2.15_use_eb_zlib_and_htslib_and_flags.patch --- .../m/MetaBAT/MetaBAT-2.15-GCC-11.2.0.eb | 44 ++++++++++ ....15_use_eb_zlib_and_htslib_and_flags.patch | 80 +++++++++++++++++++ 2 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_use_eb_zlib_and_htslib_and_flags.patch diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-GCC-11.2.0.eb new file mode 100644 index 00000000000..88b778ef482 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-GCC-11.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'MetaBAT' +version = '2.15' + +homepage = 'https://bitbucket.org/berkeleylab/metabat' +description = """MetaBAT: A robust statistical framework for +reconstructing genomes from metagenomic data""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +bitbucket_account = 'berkeleylab' +source_urls = [BITBUCKET_SOURCE] +sources = ['v%(version)s.tar.bz2'] +patches = [ + '%(name)s-%(version)s_use_eb_zlib_and_htslib_and_flags.patch', +] +checksums = [ + {'v2.15.tar.bz2': 'c6bf3a64bbb4e8a25cd10e115b9f277d768552d0b299ad3b81d7d95762c0bfe4'}, + {'MetaBAT-2.15_use_eb_zlib_and_htslib_and_flags.patch': + '28abeeb269dc1fb86d213a11a2c6f311e31702c14cef50f386e0649237689953'}, +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Boost', '1.77.0'), + ('HTSlib', '1.14'), + ('Perl', '5.34.0'), +] + +fix_perl_shebang_for = ['bin/*pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['aggregateBinDepths.pl', 'aggregateContigOverlapsByBin.pl', 'contigOverlaps', + 'jgi_summarize_bam_contig_depths', 'merge_depths.pl', 'metabat', 'runMetaBat.sh']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_use_eb_zlib_and_htslib_and_flags.patch b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_use_eb_zlib_and_htslib_and_flags.patch new file mode 100644 index 00000000000..d0ccfd3bcbe --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_use_eb_zlib_and_htslib_and_flags.patch @@ -0,0 +1,80 @@ +Use EasyBuild versions of zlib and HTSlib instead of internal + +Åke Sandgren, 20230224 +diff -ru berkeleylab-metabat-0db17a40717d.orig/CMakeLists.txt berkeleylab-metabat-0db17a40717d/CMakeLists.txt +--- berkeleylab-metabat-0db17a40717d.orig/CMakeLists.txt 2020-01-04 21:14:21.000000000 +0100 ++++ berkeleylab-metabat-0db17a40717d/CMakeLists.txt 2023-02-24 16:31:12.180989564 +0100 +@@ -7,9 +7,20 @@ + + message("Installing ${CMAKE_BUILD_TYPE} MetaBAT into ${CMAKE_INSTALL_PREFIX}") + +-include(${CMAKE_ROOT}/Modules/ExternalProject.cmake) +-include(cmake/zlib.cmake) +-include(cmake/htslib.cmake) ++#include(${CMAKE_ROOT}/Modules/ExternalProject.cmake) ++#include(cmake/zlib.cmake) ++#include(cmake/htslib.cmake) ++ ++include(FindZLIB) ++ ++find_package(PkgConfig) ++pkg_check_modules(PKGC_HTSLIB htslib) ++if(PKGC_HTSLIB_FOUND) ++ set(HTSLIB_FOUND ${PKGC_HTSLIB_FOUND}) ++ set(HTSLIB_LIBRARIES "${PKGC_HTSLIB_LINK_LIBRARIES}") ++else() ++ message(ERROR "Can't find htslib") ++endif() + + set(CMAKE_CXX_STANDARD 11) + set(CMAKE_CXX_STANDARD_REQUIRED ON) +@@ -31,10 +42,10 @@ + # using AppleClang + elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU") + # using GCC +- if ("${CMAKE_BUILD_TYPE}" STREQUAL "Release") +- set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -mtune=native") +- set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -mtune=native") +- endif() ++# if ("${CMAKE_BUILD_TYPE}" STREQUAL "Release") ++# set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -mtune=native") ++# set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -mtune=native") ++# endif() + elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") + # using Intel C++ + endif() +Only in berkeleylab-metabat-0db17a40717d: .CMakeLists.txt.swp +diff -ru berkeleylab-metabat-0db17a40717d.orig/src/CMakeLists.txt berkeleylab-metabat-0db17a40717d/src/CMakeLists.txt +--- berkeleylab-metabat-0db17a40717d.orig/src/CMakeLists.txt 2020-01-04 21:14:21.000000000 +0100 ++++ berkeleylab-metabat-0db17a40717d/src/CMakeLists.txt 2023-02-24 16:42:42.035750712 +0100 +@@ -1,6 +1,6 @@ + # find and use Boost +-set(Boost_NO_BOOST_CMAKE ON) # for backwards comptibility of cmake and boost >= 1.70 +-set(Boost_USE_STATIC_LIBS ON) ++#set(Boost_NO_BOOST_CMAKE ON) # for backwards comptibility of cmake and boost >= 1.70 ++#set(Boost_USE_STATIC_LIBS ON) + find_package(Boost 1.55.0 COMPONENTS program_options filesystem system graph serialization iostreams REQUIRED) + include_directories( ${Boost_INCLUDE_DIRS} ) + +@@ -36,8 +36,8 @@ + foreach(target ${targets}) + + add_executable(${target} ${target}.cpp) +- add_dependencies(${target} htslib zlib check_git_repository) +- target_link_libraries(${target} ${zlib_LIB} ${Boost_LIBRARIES} ${EXTRALIBS} ) ++ #add_dependencies(${target} htslib zlib check_git_repository) ++ target_link_libraries(${target} ${ZLIB_LIBRARIES} ${Boost_LIBRARIES} ${EXTRALIBS} ) + + endforeach() + +@@ -48,8 +48,8 @@ + set(targets jgi_summarize_bam_contig_depths contigOverlaps) + foreach(target ${targets}) + add_executable(${target} ${target}.cpp) +- add_dependencies(${target} htslib zlib check_git_repository) +- target_link_libraries(${target} ${htslib_LIB} ${zlib_LIB} ${Boost_LIBRARIES} ) ++ #add_dependencies(${target} htslib zlib check_git_repository) ++ target_link_libraries(${target} ${HTSLIB_LIBRARIES} ${ZLIB_LIBRARIES} ${Boost_LIBRARIES} ) + endforeach() + + From fbfa21813070b72e86d2a99e6ebbb08e071156f3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Feb 2023 17:35:47 +0100 Subject: [PATCH 6656/9987] use CUDA variant of PyTorch 1.12.0 as dependency for CUDA variant of chemprop --- .../c/chemprop/chemprop-1.5.2-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a-CUDA-11.7.0.eb index eee4493a7df..6db953d76b1 100644 --- a/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/chemprop/chemprop-1.5.2-foss-2022a-CUDA-11.7.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('xarray', '2022.6.0'), ('Hyperopt', '0.2.7'), ('Flask', '2.2.2'), - ('PyTorch', '1.12.0'), + ('PyTorch', '1.12.0', versionsuffix), ('matplotlib', '3.5.2'), ('RDKit', '2022.09.4'), ('CUDA', '11.7.0', '', SYSTEM), From 045be1dcfd6c358c1cdbc885400a20548d2bf250 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Fri, 24 Feb 2023 15:49:49 -0500 Subject: [PATCH 6657/9987] adding easyconfigs: NetLogo-6.2.2-64.eb --- .../easyconfigs/n/NetLogo/NetLogo-6.2.2-64.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NetLogo/NetLogo-6.2.2-64.eb diff --git a/easybuild/easyconfigs/n/NetLogo/NetLogo-6.2.2-64.eb b/easybuild/easyconfigs/n/NetLogo/NetLogo-6.2.2-64.eb new file mode 100644 index 00000000000..4b71cdb3c77 --- /dev/null +++ b/easybuild/easyconfigs/n/NetLogo/NetLogo-6.2.2-64.eb @@ -0,0 +1,26 @@ +easyblock = 'PackedBinary' + +name = 'NetLogo' +version = '6.2.2' +versionsuffix = '-64' + +homepage = 'https://ccl.northwestern.edu/netlogo/' +description = """NetLogo is a multi-agent programmable modeling environment. It +is used by tens of thousands of students, teachers and researchers worldwide. +It also powers HubNet participatory simulations. It is authored by Uri Wilensky +and developed at the CCL.""" + +# NetLogo is precompiled and needs no particular toolchain. +# It even comes with its own Java. +toolchain = SYSTEM + +source_urls = ['https://ccl.northwestern.edu/netlogo/%(version)s/'] +sources = ['%(name)s-%(version)s%(versionsuffix)s.tgz'] +checksums = ['543cbfc60b6e75aa56c1a66f78c08fa8763d591185eb79e6aaee5f42c8aae461'] + +sanity_check_paths = { + 'files': ['NetLogo', 'NetLogo3D'], + 'dirs': ['app', 'runtime'], +} + +moduleclass = 'math' From 73c97b14670c8fe1ccd4415bccb01ae6eddb7927 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Fri, 24 Feb 2023 17:10:16 -0500 Subject: [PATCH 6658/9987] adding easyconfigs: NetLogo-6.3.0-64.eb --- .../easyconfigs/n/NetLogo/NetLogo-6.3.0-64.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NetLogo/NetLogo-6.3.0-64.eb diff --git a/easybuild/easyconfigs/n/NetLogo/NetLogo-6.3.0-64.eb b/easybuild/easyconfigs/n/NetLogo/NetLogo-6.3.0-64.eb new file mode 100644 index 00000000000..c1005183313 --- /dev/null +++ b/easybuild/easyconfigs/n/NetLogo/NetLogo-6.3.0-64.eb @@ -0,0 +1,26 @@ +easyblock = 'PackedBinary' + +name = 'NetLogo' +version = '6.3.0' +versionsuffix = '-64' + +homepage = 'https://ccl.northwestern.edu/netlogo/' +description = """NetLogo is a multi-agent programmable modeling environment. It +is used by tens of thousands of students, teachers and researchers worldwide. +It also powers HubNet participatory simulations. It is authored by Uri Wilensky +and developed at the CCL.""" + +# NetLogo is precompiled and needs no particular toolchain. +# It even comes with its own Java. +toolchain = SYSTEM + +source_urls = ['https://ccl.northwestern.edu/netlogo/%(version)s/'] +sources = ['%(name)s-%(version)s%(versionsuffix)s.tgz'] +checksums = ['baeec4d3d5d7548d13d48574c4c1dd9909d99b2a41ad60a765dce966138dd77a'] + +sanity_check_paths = { + 'files': ['NetLogo', 'NetLogo3D'], + 'dirs': ['extensions', 'models', 'lib'], +} + +moduleclass = 'math' From 2a82fc3f333c5c1b64bc0bc0a01596bfa9664315 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 10:44:26 +0100 Subject: [PATCH 6659/9987] adding easyconfigs: Maple-2022.1.eb --- easybuild/easyconfigs/m/Maple/Maple-2022.1.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/m/Maple/Maple-2022.1.eb diff --git a/easybuild/easyconfigs/m/Maple/Maple-2022.1.eb b/easybuild/easyconfigs/m/Maple/Maple-2022.1.eb new file mode 100644 index 00000000000..7b1b8e51ca8 --- /dev/null +++ b/easybuild/easyconfigs/m/Maple/Maple-2022.1.eb @@ -0,0 +1,15 @@ +name = 'Maple' +version = '2022.1' + +homepage = 'http://www.maplesoft.com/products/maple/' +description = """Maple combines the world's most powerful mathematical computation engine with an intuitive, + 'clickable' user interface.""" + +toolchain = SYSTEM + +sources = ['%(name)s%(version)sLinuxX64Installer.run'] +checksums = ['9a1733030b26d9ed915ac638f218e897dc0d9307b2ef6238a723fc4f2da3c744'] + +license_server = 'license.example.com' + +moduleclass = 'math' From 859776c873dae4f4c6aad9f4d346a5ee6e1d2c4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 11:15:55 +0100 Subject: [PATCH 6660/9987] update to hypothesis 6.68.2 --- ...-GCCcore-12.2.0.eb => hypothesis-6.68.2-GCCcore-12.2.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/h/hypothesis/{hypothesis-6.62.1-GCCcore-12.2.0.eb => hypothesis-6.68.2-GCCcore-12.2.0.eb} (86%) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.62.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.68.2-GCCcore-12.2.0.eb similarity index 86% rename from easybuild/easyconfigs/h/hypothesis/hypothesis-6.62.1-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/h/hypothesis/hypothesis-6.68.2-GCCcore-12.2.0.eb index eb8c0f3ceb7..108e338d483 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.62.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.68.2-GCCcore-12.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'hypothesis' -version = '6.62.1' +version = '6.68.2' homepage = "https://github.com/HypothesisWorks/hypothesis" description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized @@ -11,7 +11,7 @@ description = """Hypothesis is an advanced testing library for Python. It lets y toolchain = {'name': 'GCCcore', 'version': '12.2.0'} sources = [SOURCE_TAR_GZ] -checksums = ['7d1e2f9871e6509662da317adf9b4aabd6b38280fb6c7930aa4f574d2ed25150'] +checksums = ['a7eb2b0c9a18560d8197fe35047ceb58e7e8ab7623a3e5a82613f6a2cd71cffa'] builddependencies = [('binutils', '2.39')] From 892d832499418f42220d8fb4b67e0844f6f5b1f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 11:21:36 +0100 Subject: [PATCH 6661/9987] update to numpy 1.24.2 + scipy 1.10.1 + pandas 1.5.3 --- .../SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb index ecbbf51d1e9..7e8f55f4949 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb @@ -27,10 +27,10 @@ use_pip = True # order is important! exts_list = [ - ('numpy', '1.24.1', { + ('numpy', '1.24.2', { 'patches': ['numpy-1.22.3_disable-broken-override-test.patch'], 'checksums': [ - {'numpy-1.24.1.tar.gz': '2386da9a471cc00a1f47845e27d916d5ec5346ae9696e01a8a34760858fe9dd2'}, + {'numpy-1.24.2.tar.gz': '003a9f530e880cb2cd177cba1af7220b9aa42def9c4afc2a2fc3ee6be7eb2b22'}, {'numpy-1.22.3_disable-broken-override-test.patch': '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, ], @@ -47,10 +47,10 @@ exts_list = [ ('pythran', '0.12.1', { 'checksums': ['702c2701187cfb38f66c0c20cc85d04d0e156d260a8d92892da65947faa5360e'], }), - ('scipy', '1.10.0', { + ('scipy', '1.10.1', { 'enable_slow_tests': True, 'ignore_test_result': False, - 'checksums': ['c8b3cbc636a87a89b770c6afc999baa6bcbb01691b5ccbbc1b1791c7c0a07540'], + 'checksums': ['2cf9dfb80a7b4589ba4c40ce7588986d6d5cebc5457cad2c2880f6bc2d42f3a5'], }), ('numexpr', '2.8.4', { 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], @@ -58,9 +58,9 @@ exts_list = [ ('Bottleneck', '1.3.5', { 'checksums': ['2c0d27afe45351f6f421893362621804fa7dea14fe29a78eaa52d4323f646de7'], }), - ('pandas', '1.5.2', { + ('pandas', '1.5.3', { 'preinstallopts': "export PANDAS_CI=0 && ", - 'checksums': ['220b98d15cee0b2cd839a6358bd1f273d0356bf964c1a1aeb32d47db0215488b'], + 'checksums': ['74a3fd7e5a7ec052f183273dc7b0acd3a863edf7520f5d3a1765c04ffdb3b0b1'], }), ('mpmath', '1.2.1', { 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], From 69ba441d687f01a34bf5cdcaa843ce879b9241fc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 25 Feb 2023 12:49:24 +0100 Subject: [PATCH 6662/9987] adding patch file Trinity-2.15.1_fix-bamsifter.patch --- .../Trinity-2.15.1_fix-bamsifter.patch | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.15.1_fix-bamsifter.patch diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1_fix-bamsifter.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1_fix-bamsifter.patch new file mode 100644 index 00000000000..07c86655dce --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1_fix-bamsifter.patch @@ -0,0 +1,23 @@ +--- trinity-plugins/bamsifter/Makefile.orig 2023-02-23 03:02:38.789520000 +0100 ++++ trinity-plugins/bamsifter/Makefile 2023-02-23 03:04:57.927569000 +0100 +@@ -2,8 +2,8 @@ + + cwd = $(shell pwd) + +-sift_bam_max_cov: sift_bam_max_cov.cpp htslib/version.h +- g++ -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts ++sift_bam_max_cov: sift_bam_max_cov.cpp ++ g++ -std=c++11 $(CXXFLAGS) -Wall -I$(EBROOTHTSLIB)/include -L$(EBROOTHTSLIB)/lib -lhts -o _sift_bam_max_cov sift_bam_max_cov.cpp + + + htslib/version.h : +--- trinity-plugins/bamsifter/sift_bam_max_cov.cpp.orig 2023-02-23 03:05:19.083304000 +0100 ++++ trinity-plugins/bamsifter/sift_bam_max_cov.cpp 2023-02-23 03:05:35.521079515 +0100 +@@ -11,6 +11,7 @@ + #include + #include + #include ++#include + + #include "htslib/sam.h" + #include "htslib/bgzf.h" From 7560d9a7bfe55046fcd954928c88706d43a61297 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 25 Feb 2023 12:57:30 +0100 Subject: [PATCH 6663/9987] add extra comments to Trinity v2.15.1 --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb | 4 +++- .../easyconfigs/t/Trinity/Trinity-2.15.1_fix-bamsifter.patch | 5 +++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb index 55f4e4e9ad3..1e8478780d2 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb @@ -23,7 +23,7 @@ sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] patches = ['Trinity-%(version)s_fix-bamsifter.patch'] checksums = [ {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580'}, - {'Trinity-2.15.1_fix-bamsifter.patch': '79588e3b7f5cf91f04804234b6ec983f30e4fdd50103adb8a83bdc7d7aaf29db'}, + {'Trinity-2.15.1_fix-bamsifter.patch': 'f374d446f06b8059a3b7cc57c286fc20d79b43ac222f48244ab83fb410997d1d'}, ] builddependencies = [ @@ -31,6 +31,8 @@ builddependencies = [ ('CMake', '3.23.1'), ] +# for reference, list of dependencies in the container image used upstream: +# https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile dependencies = [ ('Java', '11', '', SYSTEM), ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1_fix-bamsifter.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1_fix-bamsifter.patch index 07c86655dce..02c23f15c76 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1_fix-bamsifter.patch +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1_fix-bamsifter.patch @@ -1,3 +1,8 @@ +Fix build of Trinity plugin bamsifter: +* add missing headers +* use external HTSlib from EasyBuild environment +* use compilation flags from environment +author: Alex Domingo (Vrije Universiteit Brussel) --- trinity-plugins/bamsifter/Makefile.orig 2023-02-23 03:02:38.789520000 +0100 +++ trinity-plugins/bamsifter/Makefile 2023-02-23 03:04:57.927569000 +0100 @@ -2,8 +2,8 @@ From 44bbc1714c21043d818f365d4f360dcf86e1fe52 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 25 Feb 2023 12:58:44 +0100 Subject: [PATCH 6664/9987] adding easyconfigs: Jellyfish-2.3.0-GCC-11.3.0.eb --- .../j/Jellyfish/Jellyfish-2.3.0-GCC-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-11.3.0.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..7a8ca29098b --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.3.0-GCC-11.3.0.eb @@ -0,0 +1,40 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.3.0' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e195b7cf7ba42a90e5e112c0ed27894cd7ac864476dc5fb45ab169f5b930ea5a'] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, +# they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' From 16faf83294bcc804b766ee3feed02e705def9b54 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 25 Feb 2023 13:25:08 +0100 Subject: [PATCH 6665/9987] bump dependency on ant to v1.10.2 in Trinity v2.15.1 --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb index 1e8478780d2..b808967c619 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2022a.eb @@ -35,7 +35,7 @@ builddependencies = [ # https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile dependencies = [ ('Java', '11', '', SYSTEM), - ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), + ('ant', '1.10.12', '-Java-%(javaver)s', SYSTEM), ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), ('GATK', '4.3.0.0', '-Java-%(javaver)s'), ('Perl', '5.34.1'), From b824e45da0e212e21e930c602355d599d5c72631 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 14:08:38 +0100 Subject: [PATCH 6666/9987] fix hypothesis build dependency for SciPy 2023.01 --- .../s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb index 7e8f55f4949..2dabb5c502e 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'gfbf', 'version': '2022b'} toolchainopts = {'pic': True, 'lowopt': True} builddependencies = [ - ('hypothesis', '6.62.1'), + ('hypothesis', '6.68.2'), ('UnZip', '6.0'), # scipy >= 1.9.0 uses Meson/Ninja ('Meson', '0.64.0'), From 59b39429233f1248bb7bdd5fa7e2d1c899f874a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 14:09:37 +0100 Subject: [PATCH 6667/9987] bump SciPy-bundle version to 2023.02 due to use of numpy 1.24.2 + scipy 1.10.1 --- ...2023.01-gfbf-2022b.eb => SciPy-bundle-2023.03-gfbf-2022b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/SciPy-bundle/{SciPy-bundle-2023.01-gfbf-2022b.eb => SciPy-bundle-2023.03-gfbf-2022b.eb} (99%) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.03-gfbf-2022b.eb similarity index 99% rename from easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb rename to easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.03-gfbf-2022b.eb index 2dabb5c502e..65a78705587 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.01-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.03-gfbf-2022b.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'SciPy-bundle' -version = '2023.01' +version = '2023.02' homepage = 'https://python.org/' description = "Bundle of Python packages for scientific software" From eca82e046ba0a0e2621e609ec9b3cc694d279a38 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 15:38:13 +0100 Subject: [PATCH 6668/9987] fix filename for SciPy-bundle 2023.02 --- ...e-2023.03-gfbf-2022b.eb => SciPy-bundle-2023.02-gfbf-2022b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/SciPy-bundle/{SciPy-bundle-2023.03-gfbf-2022b.eb => SciPy-bundle-2023.02-gfbf-2022b.eb} (100%) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.03-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb similarity index 100% rename from easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.03-gfbf-2022b.eb rename to easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb From d0c86d26bf4b2e6bf03693415c7f8956d7d63e2b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 15:49:25 +0100 Subject: [PATCH 6669/9987] add patch to disable problematic tests for scipy 1.10.1 --- .../SciPy-bundle-2023.02-gfbf-2022b.eb | 6 ++- .../scipy-1.10.1_disable-tests.patch | 41 +++++++++++++++++++ 2 files changed, 46 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_disable-tests.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb index 65a78705587..dbeae6ee955 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb @@ -48,9 +48,13 @@ exts_list = [ 'checksums': ['702c2701187cfb38f66c0c20cc85d04d0e156d260a8d92892da65947faa5360e'], }), ('scipy', '1.10.1', { + 'patches': ['scipy-1.10.1_disable-tests.patch'], + 'checksums': [ + {'scipy-1.10.1.tar.gz': '2cf9dfb80a7b4589ba4c40ce7588986d6d5cebc5457cad2c2880f6bc2d42f3a5'}, + {'scipy-1.10.1_disable-tests.patch': '5d36d416fb7ea9297514c3988d9f506793e39dc4c0daedccf6733c3dd7e3dcc0'}, + ], 'enable_slow_tests': True, 'ignore_test_result': False, - 'checksums': ['2cf9dfb80a7b4589ba4c40ce7588986d6d5cebc5457cad2c2880f6bc2d42f3a5'], }), ('numexpr', '2.8.4', { 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_disable-tests.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_disable-tests.patch new file mode 100644 index 00000000000..46ed2e2c0f5 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_disable-tests.patch @@ -0,0 +1,41 @@ +disable problematic tests +test_milp_timeout_16545 fails intermittently, known issue - see https://github.com/scipy/scipy/issues/17137 +test_hermitian_modes fails with order of magnitude difference +test_concatenate_int32_overflow fails if not enough memory is available +author: Kenneth Hoste (HPC-UGent) + Simon Branford (University of Birmingham) +diff -ru scipy-1.10.1.orig/scipy/optimize/tests/test_milp.py scipy-1.10.1/scipy/optimize/tests/test_milp.py +--- scipy-1.10.1.orig/scipy/optimize/tests/test_milp.py 1970-01-01 01:00:00.000000000 +0100 ++++ scipy-1.10.1/scipy/optimize/tests/test_milp.py 2023-02-25 15:43:57.780477222 +0100 +@@ -283,7 +283,7 @@ + @pytest.mark.timeout(360) + @pytest.mark.parametrize(["options", "msg"], [({"time_limit": 10}, _msg_time), + ({"node_limit": 1}, _msg_iter)]) +-def test_milp_timeout_16545(options, msg): ++def disabled_test_milp_timeout_16545(options, msg): + # Ensure solution is not thrown away if MILP solver times out + # -- see gh-16545 + rng = np.random.default_rng(5123833489170494244) +diff -ru scipy-1.10.1.orig/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py scipy-1.10.1/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py +--- scipy-1.10.1.orig/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py 1970-01-01 01:00:00.000000000 +0100 ++++ scipy-1.10.1/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py 2023-02-25 15:44:06.220493384 +0100 +@@ -418,7 +418,7 @@ + None, sigma, mattype, None, mode) + + +-def test_hermitian_modes(): ++def disabled_test_hermitian_modes(): + params = SymmetricParams() + k = 2 + symmetric = True +diff -ru scipy-1.10.1.orig/scipy/sparse/tests/test_construct.py scipy-1.10.1/scipy/sparse/tests/test_construct.py +--- scipy-1.10.1.orig/scipy/sparse/tests/test_construct.py 1970-01-01 01:00:00.000000000 +0100 ++++ scipy-1.10.1/scipy/sparse/tests/test_construct.py 2023-02-25 15:44:25.259531626 +0100 +@@ -446,7 +446,7 @@ + + @pytest.mark.slow + @pytest.mark.xfail_on_32bit("Can't create large array for test") +- def test_concatenate_int32_overflow(self): ++ def disable_test_concatenate_int32_overflow(self): + """ test for indptr overflow when concatenating matrices """ + check_free_memory(30000) + From fa1556db10b7ffda048695eadb278183f1031ea2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 15:56:41 +0100 Subject: [PATCH 6670/9987] {bio}[foss/2022a] GBprocesS v4.0.0.post1, PEAR v0.9.11 w/ Python 3.10.4 --- .../GBprocesS-4.0.0.post1-foss-2022a.eb | 67 +++++++++++++++++++ .../p/PEAR/PEAR-0.9.11-GCC-11.3.0.eb | 31 +++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/g/GBprocesS/GBprocesS-4.0.0.post1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-4.0.0.post1-foss-2022a.eb b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-4.0.0.post1-foss-2022a.eb new file mode 100644 index 00000000000..c1080cec28f --- /dev/null +++ b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-4.0.0.post1-foss-2022a.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonPackage' + +name = 'GBprocesS' +local_commit = '26119ab3' +version = '4.0.0.post1' + +homepage = 'https://gbprocess.readthedocs.io/' +description = """GBprocesS allows for the extraction of genomic inserts from NGS +data for GBS experiments. Preprocessing is performed in different stages that +are part of a linear pipeline where the steps are performed in order. GBprocesS +provides a flexible way to adjust the functionality to your needs, as the +operations required and the execution order vary depending on the GBS protocol +used.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# need to use git_config rather than just downloading source tarball, +# because .git subdirectory is required by setuptools-scm to determine version +sources = [{ + 'filename': 'GBprocesS-%%(version)s-%s.tar.gz' % local_commit, + 'git_config': { + 'url': 'https://gitlab.com/ilvo', + 'repo_name': name, + 'commit': local_commit, + 'keep_git_dir': True, + }, +}] +checksums = [None] + +dependencies = [ + ('Python', '3.10.4'), + ('cutadapt', '4.2'), + ('Biopython', '1.79'), + ('PEAR', '0.9.11'), +] + +use_pip = True +download_dep_fail = True + +preinstallopts = "sed -i 's/cutadapt~=3.5.0/cutadapt/g' setup.cfg && " + +postinstallcmds = ["cp -a test %(installdir)s"] + +sanity_check_paths = { + 'files': ['bin/gbprocess'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'test'], +} + +sanity_check_commands = [ + "mkdir -p %(builddir)s/GBprocesS", + "cd %(builddir)s/GBprocesS && cp -a %(installdir)s/test . && python -m unittest discover -v -s ./test -p test_*.py", + "touch %(builddir)s/17146FL-13-01-01_S97_L002_R1_001.fastq", + "touch %(builddir)s/17146FL-13-01-01_S97_L002_R2_001.fastq", + # Trivial configuration file to use when running gbprocess sanity check + # See https://gitlab.com/dschaumont/GBprocesS/-/blob/master/docs/user_guide.rst + "echo '[General]' > %(builddir)s/config.ini", + "echo 'cores = 1' >> %(builddir)s/config.ini", + "echo 'input_directory = %(builddir)s/' >> %(builddir)s/config.ini", + "echo 'sequencing_type = pe' >> %(builddir)s/config.ini", + "echo 'input_file_name_template = {run:25}_R{orientation:1}_001{extension}' >> %(builddir)s/config.ini", + "echo 'temp_dir = %(builddir)s/' >> %(builddir)s/config.ini", + "gbprocess --debug -c %(builddir)s/config.ini", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.3.0.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.3.0.eb new file mode 100644 index 00000000000..3442901c61c --- /dev/null +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'PEAR' +version = '0.9.11' + +homepage = 'https://cme.h-its.org/exelixis/web/software/pear/' +description = """PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. + It is fully parallelized and can run with as low as just a few kilobytes of memory.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +# Needs manual download via web-form, +# https://www.h-its.org/en/research/sco/software/#NextGenerationSequencingSequenceAnalysis +sources = ['%(namelower)s-src-%(version)s.tar.gz'] +checksums = ['94f4a1835cd75ec6fab83405c2545ddba6b6bb1644579222e9cc2ad57a59d654'] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [ + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), +] + +preconfigopts = 'aclocal && autoconf && automake --add-missing && ' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 0b94de2bff900be50f050a174026473106bb8cda Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 18:29:03 +0100 Subject: [PATCH 6671/9987] add patch for scipy 1.10.1 to xfail test_maxiter_worsening on aarch64 --- .../SciPy-bundle-2023.02-gfbf-2022b.eb | 7 ++++++- ...0.1_xfail-aarch64_test_maxiter_worsening.patch | 15 +++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb index dbeae6ee955..907aca730a3 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb @@ -48,10 +48,15 @@ exts_list = [ 'checksums': ['702c2701187cfb38f66c0c20cc85d04d0e156d260a8d92892da65947faa5360e'], }), ('scipy', '1.10.1', { - 'patches': ['scipy-1.10.1_disable-tests.patch'], + 'patches': [ + 'scipy-1.10.1_disable-tests.patch', + 'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch', + ], 'checksums': [ {'scipy-1.10.1.tar.gz': '2cf9dfb80a7b4589ba4c40ce7588986d6d5cebc5457cad2c2880f6bc2d42f3a5'}, {'scipy-1.10.1_disable-tests.patch': '5d36d416fb7ea9297514c3988d9f506793e39dc4c0daedccf6733c3dd7e3dcc0'}, + {'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch': + '48177d6af51cf3e3d46aed8425807f0a65a498f7558f475032e0ad846559a23e'}, ], 'enable_slow_tests': True, 'ignore_test_result': False, diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch new file mode 100644 index 00000000000..c2a2f234e4e --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch @@ -0,0 +1,15 @@ +also xfail test_maxiter_worsening for Python 3.10 on aarch64 +see also https://github.com/scipy/scipy/issues/13019 + https://github.com/scipy/scipy/pull/13022 +author: Kenneth Hoste (HPC-UGent) +diff -ru scipy-1.10.1.orig/scipy/sparse/linalg/_isolve/tests/test_iterative.py scipy-1.10.1/scipy/sparse/linalg/_isolve/tests/test_iterative.py +--- scipy-1.10.1.orig/scipy/sparse/linalg/_isolve/tests/test_iterative.py 1970-01-01 00:00:00.000000000 +0000 ++++ scipy-1.10.1/scipy/sparse/linalg/_isolve/tests/test_iterative.py 2023-02-25 17:18:12.432151563 +0000 +@@ -451,7 +451,7 @@ + + @pytest.mark.parametrize("solver", [ + pytest.param(gmres, marks=pytest.mark.xfail(platform.machine() == 'aarch64' +- and sys.version_info[1] == 9, ++ and sys.version_info[1] >= 9, + reason="gh-13019")), + qmr, + pytest.param(lgmres, marks=pytest.mark.xfail( From 7092e2ff40a0d78961e8051d36f5a131c36056d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 18:29:58 +0100 Subject: [PATCH 6672/9987] adding easyconfigs: OpenMPI-4.1.5-GCC-12.2.0.eb --- .../o/OpenMPI/OpenMPI-4.1.5-GCC-12.2.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.2.0.eb new file mode 100644 index 00000000000..634b2a2f67b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.2.0.eb @@ -0,0 +1,62 @@ +name = 'OpenMPI' +version = '4.1.5' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', +] +checksums = [ + {'openmpi-4.1.5.tar.bz2': 'a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3'}, + {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, + {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, +] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('Perl', '5.36.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('hwloc', '2.8.0'), + ('libevent', '2.1.12'), + ('UCX', '1.13.1'), + ('libfabric', '1.16.1'), + ('PMIx', '4.2.2'), + ('UCC', '1.1.0'), +] + +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' + +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From 050117780a93905cb2952cd0490ac6012738ebf2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 18:37:46 +0100 Subject: [PATCH 6673/9987] use 'import deap.base' in sanity check for deap extension in SciPy-bundle 2022.05 --- .../s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb | 1 + .../s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb | 1 + .../s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb | 1 + .../s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb index b28fefbb7e5..e07fdee1c03 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022.05.eb @@ -74,6 +74,7 @@ exts_list = [ }), ('deap', '1.3.3', { 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], + 'modulename': 'deap.base', }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb index a2af2d99e51..ce504e9607a 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-foss-2022a.eb @@ -77,6 +77,7 @@ exts_list = [ }), ('deap', '1.3.3', { 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], + 'modulename': 'deap.base', }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb index 40523655027..06ad5e918f6 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022.05.eb @@ -76,6 +76,7 @@ exts_list = [ }), ('deap', '1.3.3', { 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], + 'modulename': 'deap.base', }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb index 9ae652f9a05..a07d23a7f56 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2022.05-intel-2022a.eb @@ -76,6 +76,7 @@ exts_list = [ }), ('deap', '1.3.3', { 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], + 'modulename': 'deap.base', }), ] From 545a571c1a7bd5f182c5357a5276f8b2ae6af702 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 19:00:36 +0100 Subject: [PATCH 6674/9987] use 'import Crypto.PublicKey.RSA' to check that pycryptodome is installed correctly in Python 3.10.x easyconfigs --- easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb index 30b815f1730..033fd05880f 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.4-GCCcore-11.3.0.eb @@ -100,7 +100,7 @@ exts_list = [ 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], }), ('pycryptodome', '3.17', { - 'modulename': 'Crypto', + 'modulename': 'Crypto.PublicKey.RSA', 'checksums': ['bce2e2d8e82fcf972005652371a3e8731956a0c1fbb719cc897943b3695ad91b'], }), ('ecdsa', '0.17.0', { diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index 603d9a9e3c1..c134f2d2796 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -102,7 +102,7 @@ exts_list = [ 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], }), ('pycryptodome', '3.17', { - 'modulename': 'Crypto', + 'modulename': 'Crypto.PublicKey.RSA', 'checksums': ['bce2e2d8e82fcf972005652371a3e8731956a0c1fbb719cc897943b3695ad91b'], }), ('ecdsa', '0.18.0', { From fa106cdca9208a0ef66da1ef6f0558059903c393 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 19:17:00 +0100 Subject: [PATCH 6675/9987] adding easyconfigs: Mathematica-13.1.0.eb --- .../m/Mathematica/Mathematica-13.1.0.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mathematica/Mathematica-13.1.0.eb diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-13.1.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-13.1.0.eb new file mode 100644 index 00000000000..29426ff5cb2 --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-13.1.0.eb @@ -0,0 +1,15 @@ +name = 'Mathematica' +version = '13.1.0' + +homepage = 'https://www.wolfram.com/mathematica' +description = """Mathematica is a computational software program used in many scientific, engineering, mathematical +and computing fields.""" + +toolchain = SYSTEM + +sources = ['Mathematica_%(version)s_LINUX.sh'] +checksums = ['199c9462c971fcce1a148dcf8fd3acc37ff0efdfc9a7fe13de6444dbbee936e3'] + +license_server = 'license.example.com' + +moduleclass = 'math' From 0de78ec35e7ffc6feb79bde2ce2780442e6ec6f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 25 Feb 2023 19:53:57 +0100 Subject: [PATCH 6676/9987] use 'import deap.base' in sanity check for deap extension in SciPy-bundle 2023.02 --- .../s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb index 907aca730a3..f6d9d0f8045 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb @@ -76,6 +76,7 @@ exts_list = [ }), ('deap', '1.3.3', { 'checksums': ['8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31'], + 'modulename': 'deap.base', }), ] From a8a0539b8684cf218717ace287ff0d641a15a4c9 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 25 Feb 2023 19:46:09 +0000 Subject: [PATCH 6677/9987] adding easyconfigs: OSU-Micro-Benchmarks-5.9-iimpi-2022a.eb --- .../OSU-Micro-Benchmarks-5.9-iimpi-2022a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-iimpi-2022a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-iimpi-2022a.eb new file mode 100644 index 00000000000..ed75d86ee38 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-iimpi-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.9' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 992c9a350c9c631f7069775f78e1cf60e08c5a0d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 25 Feb 2023 22:54:06 +0000 Subject: [PATCH 6678/9987] Add None checksums to ancient ELPA easyconfigs --- easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb | 1 + easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb index 170e9a0b133..ff851c4baf4 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2016b.eb @@ -20,6 +20,7 @@ toolchainopts = {'usempi': True} source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] +checksums = [None] builddependencies = [('Autotools', '20150215')] diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb index 9724507278e..2bf1ad3f502 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2016.05.004-intel-2017a.eb @@ -20,10 +20,10 @@ toolchainopts = {'usempi': True} source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] sources = [SOURCELOWER_TAR_GZ] - patches = [ '%(name)s-%(version)s_install-libelpatest.patch', ] +checksums = [None, '0bf573f56e0ed9cafeb37c71c68969e40ef21f5293031c10916c0c6cc0b3c2e0'] builddependencies = [ ('Autotools', '20150215'), From d007e699ae94c8bcd9b1fe3d79deee5f8073d775 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Sun, 26 Feb 2023 13:41:46 +0100 Subject: [PATCH 6679/9987] adding easyconfigs: FFmpeg-5.1.2-GCCcore-12.2.0.eb, SDL2-2.26.3-GCCcore-12.2.0.eb, x264-20230226-GCCcore-12.2.0.eb, x265-3.5-GCCcore-12.2.0.eb, Yasm-1.3.0-GCCcore-12.2.0.eb --- .../f/FFmpeg/FFmpeg-5.1.2-GCCcore-12.2.0.eb | 45 +++++++++++++++++++ .../s/SDL2/SDL2-2.26.3-GCCcore-12.2.0.eb | 26 +++++++++++ .../x/x264/x264-20230226-GCCcore-12.2.0.eb | 33 ++++++++++++++ .../x/x265/x265-3.5-GCCcore-12.2.0.eb | 34 ++++++++++++++ .../y/Yasm/Yasm-1.3.0-GCCcore-12.2.0.eb | 25 +++++++++++ 5 files changed, 163 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.1.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.26.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20230226-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.1.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.1.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b06aee26953 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-5.1.2-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '5.1.2' + +homepage = 'https://www.ffmpeg.org/' +description = "A complete, cross-platform solution to record, convert and stream audio and video." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://%(namelower)s.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['39a0bcc8d98549f16c570624678246a6ac736c066cebdb409f9502e915b22f2b'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('ffnvcodec', '11.1.5.2', '', SYSTEM), # optional nvenc/dec support +] +dependencies = [ + ('NASM', '2.15.05'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('x264', '20230226'), + ('LAME', '3.100'), + ('x265', '3.5'), + ('X11', '20221110'), + ('freetype', '2.12.1'), + ('fontconfig', '2.14.1'), + ('FriBidi', '1.0.12'), + ('SDL2', '2.26.3'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi --enable-sdl2' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.26.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.26.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..c83ac06a363 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.26.3-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.26.3' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c661205a553b7d252425f4b751ff13209e5e020b876bbfa1598494af61790057'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('X11', '20221110'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/x264/x264-20230226-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20230226-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b0a7a5b2bfc --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20230226-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20230226' + +homepage = 'https://www.videolan.org/developers/x264.html' +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/baee400f/'] +sources = [{'download_filename': '%(name)s-baee400f.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f32bdcd8edaae7686f5aba9d4421d07c1d01e5c3c10c2a87c8f3131bddb59905'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('NASM', '2.15.05'), +] + +configopts = " --enable-shared --enable-static --disable-bashcompletion" + + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x264_config.h', 'include/%(name)s.h', 'lib/libx264.a', 'lib/libx264.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..27b2b066296 --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.5' + +homepage = 'https://x265.org/' +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://bitbucket.org/multicoreware/x265_git/downloads/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['e70a3335cacacbba0b3a20ec6fecd6783932288ebc8163ad74bcc9606477cae8'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Yasm', '1.3.0'), +] + +configopts = '-DGIT_ARCHETYPE=1' + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x265_config.h', 'include/%(name)s.h', 'lib/libx265.a', 'lib/libx265.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..28d2d1ae248 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'https://www.tortall.net/projects/yasm/' +description = "Yasm: Complete rewrite of the NASM assembler with BSD license" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [ + ('binutils', '2.39'), +] + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'lang' From e5fb4e841d2191103b914fa55f80fd277783c9d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Mon, 27 Feb 2023 11:27:33 +0000 Subject: [PATCH 6680/9987] Delete libuuid-20190529.patch File deleted as wrong spelling of crossguid and thus wrong folder --- .../c/crossguide/libuuid-20190529.patch | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch diff --git a/easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch b/easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch deleted file mode 100644 index d75df709152..00000000000 --- a/easybuild/easyconfigs/c/crossguide/libuuid-20190529.patch +++ /dev/null @@ -1,19 +0,0 @@ -Updates the older Libuuid to LibUUID so CMake does not complain -Author: J. Sassmannshausen -diff --git a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/CMakeLists.txt b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/CMakeLists.txt -index 76b5a62..03291c5 100644 ---- a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/CMakeLists.txt -+++ b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/CMakeLists.txt -@@ -30,7 +30,7 @@ elseif(ANDROID) - # GUID_ANDROID is used in the headers, so make PUBLIC - target_compile_definitions(crossguid PUBLIC GUID_ANDROID) - else() -- find_package(Libuuid REQUIRED) -+ find_package(LibUUID REQUIRED) - if (NOT LIBUUID_FOUND) - message(FATAL_ERROR - "You might need to run 'sudo apt-get install uuid-dev' or similar") -diff --git a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/cmake/FindLibuuid.cmake b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/cmake/FindLibUUID.cmake -similarity index 100% -rename from crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/cmake/FindLibuuid.cmake -rename to crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/cmake/FindLibUUID.cmake From 6504579d4d1be5ccc99828c8df04548149a4d271 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 27 Feb 2023 11:35:06 +0000 Subject: [PATCH 6681/9987] ancient version 0.2.2 removed, name of patchfile corrected --- .../crossguid-0.2.2-GCCcore-11.2.0.eb | 48 ------------------- .../crossguid-0.2.2_fix_libuuid.patch | 19 -------- .../crossguid-20190529-GCCcore-11.2.0.eb | 4 +- 3 files changed, 2 insertions(+), 69 deletions(-) delete mode 100644 easybuild/easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb delete mode 100644 easybuild/easyconfigs/c/crossguid/crossguid-0.2.2_fix_libuuid.patch diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb deleted file mode 100644 index 5c473db1e66..00000000000 --- a/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2-GCCcore-11.2.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -# Contribution from Imperial College London, UK -# uploaded by J. Sassmannshausen - -easyblock = 'CMakeMakeCp' - -name = 'crossguid' -version = '0.2.2' - -homepage = 'https://github.com/graeme-hill/crossguid' -description = """ -CrossGuid is a minimal, cross platform, C++ GUID library. -It uses the best native GUID/UUID generator on the given platform and has a -generic class for parsing, stringifying, and comparing IDs. -The guid generation technique is determined by your platform:""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -source_urls = ['https://github.com/graeme-hill/crossguid/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -patches = ['crossguid-0.2.2_fix_libuuid.patch'] - -checksums = [ - '48321928473c682b0cdc7e17bbd3390f79f4b98ab22fef3b81a852dda81fd195', # v0.2.2.tar.gz - '6c59e785528fd24ed50304125c07193b9152d81dbc44b52fb2638729265f1bad', # crossguid-0.2.2_fix_libuuid.patch -] - -builddependencies = [ - ('binutils', '2.37'), - ('CMake', '3.22.1'), -] - -dependencies = [ - ('util-linux', '2.37'), -] - -files_to_copy = [ - (['libxg.a'], 'lib'), - (['xgtest'], 'bin'), -] - -sanity_check_paths = { - 'files': [('lib/libxg.a')], - 'dirs': [], -} - -sanity_check_commands = [('xgtest')] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2_fix_libuuid.patch b/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2_fix_libuuid.patch deleted file mode 100644 index c5d89a081a8..00000000000 --- a/easybuild/easyconfigs/c/crossguid/crossguid-0.2.2_fix_libuuid.patch +++ /dev/null @@ -1,19 +0,0 @@ -Updates the older Libuuid to LibUUID so CMake does not complain -Author: J. Sassmannshausen -diff --git a/crossguid-0.2.2.orig/CMakeLists.txt b/crossguid-0.2.2/CMakeLists.txt -index 761dbc6..22fcee5 100644 ---- a/crossguid-0.2.2.orig/CMakeLists.txt -+++ b/crossguid-0.2.2/CMakeLists.txt -@@ -27,7 +27,7 @@ elseif(APPLE) - elseif(ANDROID) - target_compile_definitions(xg PRIVATE GUID_ANDROID) - else() -- find_package(Libuuid REQUIRED) -+ find_package(LibUUID REQUIRED) - if (NOT LIBUUID_FOUND) - message(FATAL_ERROR - "You might need to run 'sudo apt-get install uuid-dev' or similar") -diff --git a/crossguid-0.2.2.orig/cmake/FindLibuuid.cmake b/crossguid-0.2.2/cmake/FindLibUUID.cmake -similarity index 100% -rename from crossguid-0.2.2.orig/cmake/FindLibuuid.cmake -rename to crossguid-0.2.2/cmake/FindLibUUID.cmake diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb index 708cd547629..d274e1fec40 100644 --- a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb @@ -19,11 +19,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/graeme-hill/crossguid/archive/%s' % local_commit] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = ['libuuid-20190529.patch'] +patches = ['crossguid-20190529-libuuid.patch'] checksums = [ '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguid-20190529.tar.gz - '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # libuuid-20190529.patch + '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # crossguid-20190529-libuuid.patch ] builddependencies = [ From df80c69b70aa50354f8c1b2d2bf78a876b71b586 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 27 Feb 2023 11:36:33 +0000 Subject: [PATCH 6682/9987] patchfile added --- .../crossguid-20190529-libuuid.patch | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/c/crossguid/crossguid-20190529-libuuid.patch diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-libuuid.patch b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-libuuid.patch new file mode 100644 index 00000000000..d75df709152 --- /dev/null +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-libuuid.patch @@ -0,0 +1,19 @@ +Updates the older Libuuid to LibUUID so CMake does not complain +Author: J. Sassmannshausen +diff --git a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/CMakeLists.txt b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/CMakeLists.txt +index 76b5a62..03291c5 100644 +--- a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/CMakeLists.txt ++++ b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/CMakeLists.txt +@@ -30,7 +30,7 @@ elseif(ANDROID) + # GUID_ANDROID is used in the headers, so make PUBLIC + target_compile_definitions(crossguid PUBLIC GUID_ANDROID) + else() +- find_package(Libuuid REQUIRED) ++ find_package(LibUUID REQUIRED) + if (NOT LIBUUID_FOUND) + message(FATAL_ERROR + "You might need to run 'sudo apt-get install uuid-dev' or similar") +diff --git a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/cmake/FindLibuuid.cmake b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/cmake/FindLibUUID.cmake +similarity index 100% +rename from crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/cmake/FindLibuuid.cmake +rename to crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/cmake/FindLibUUID.cmake From 592bd7a8f02d6eb4c0351f0d88d388fadb958882 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 27 Feb 2023 11:43:24 +0000 Subject: [PATCH 6683/9987] patchfile renamed to be consistant with PR 16207 --- .../crossguid-20190529-GCCcore-11.2.0.eb | 4 ++-- .../crossguid-20190529-libuuid.patch | 19 ------------------- 2 files changed, 2 insertions(+), 21 deletions(-) delete mode 100644 easybuild/easyconfigs/c/crossguid/crossguid-20190529-libuuid.patch diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb index d274e1fec40..6f1189ae18d 100644 --- a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb @@ -19,11 +19,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/graeme-hill/crossguid/archive/%s' % local_commit] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = ['crossguid-20190529-libuuid.patch'] +patches = ['crossguid-20190529_fix_libuuid.patch'] checksums = [ '6be27e0b3a4907f0cd3cfadec255ee1b925569e1bd06e67a4d2f4267299b69c4', # crossguid-20190529.tar.gz - '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # crossguid-20190529-libuuid.patch + '9ee0f76e18b465ec93364d44d2adb7643081a5b5eee4524a14544472581d7782', # crossguid-20190529_fix_libuuid.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-libuuid.patch b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-libuuid.patch deleted file mode 100644 index d75df709152..00000000000 --- a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-libuuid.patch +++ /dev/null @@ -1,19 +0,0 @@ -Updates the older Libuuid to LibUUID so CMake does not complain -Author: J. Sassmannshausen -diff --git a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/CMakeLists.txt b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/CMakeLists.txt -index 76b5a62..03291c5 100644 ---- a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/CMakeLists.txt -+++ b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/CMakeLists.txt -@@ -30,7 +30,7 @@ elseif(ANDROID) - # GUID_ANDROID is used in the headers, so make PUBLIC - target_compile_definitions(crossguid PUBLIC GUID_ANDROID) - else() -- find_package(Libuuid REQUIRED) -+ find_package(LibUUID REQUIRED) - if (NOT LIBUUID_FOUND) - message(FATAL_ERROR - "You might need to run 'sudo apt-get install uuid-dev' or similar") -diff --git a/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/cmake/FindLibuuid.cmake b/crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/cmake/FindLibUUID.cmake -similarity index 100% -rename from crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681.orig/cmake/FindLibuuid.cmake -rename to crossguid-ca1bf4b810e2d188d04cb6286f957008ee1b7681/cmake/FindLibUUID.cmake From e770515c87855b7548200c04bcd3043230f9b9f7 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 27 Feb 2023 12:04:32 +0000 Subject: [PATCH 6684/9987] Name changed as suggested --- .../Health-GPS-1.1.3.0-GCCcore-11.3.0.eb} | 8 ++++---- .../Health-GPS-20220316-CMake.patch} | 0 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/h/{healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb => Health-GPS/Health-GPS-1.1.3.0-GCCcore-11.3.0.eb} (92%) rename easybuild/easyconfigs/h/{healthgps/healthgps-20220316-CMake.patch => Health-GPS/Health-GPS-20220316-CMake.patch} (100%) diff --git a/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.1.3.0-GCCcore-11.3.0.eb similarity index 92% rename from easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.1.3.0-GCCcore-11.3.0.eb index 30a1fdb6714..ca04a7736c4 100644 --- a/easybuild/easyconfigs/h/healthgps/healthgps-1.1.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.1.3.0-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMakeCp' -name = 'healthgps' +name = 'Health-GPS' version = '1.1.3.0' homepage = 'https://github.com/imperialCHEPI/healthgps' @@ -22,11 +22,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/imperialCHEPI/healthgps/archive'] sources = ['v.%(version)s.tar.gz'] -patches = ['healthgps-20220316-CMake.patch'] +patches = ['Health-GPS-20220316-CMake.patch'] checksums = [ - '62ff13811ca0ec313aa166bb53bc89516c3135bc78a6fba6711c5a0d8d4c98ec', # healthgps-1.1.3.0.tar.gz - '315e70c12edfe15535dbd54ac99ea66d41df3989a0917b8da7f024fdea2af609', # healthgps-20220316-CMake.patch + '62ff13811ca0ec313aa166bb53bc89516c3135bc78a6fba6711c5a0d8d4c98ec', # Health-GPS-1.1.3.0.tar.gz + '315e70c12edfe15535dbd54ac99ea66d41df3989a0917b8da7f024fdea2af609', # Health-GPS-20220316-CMake.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/h/healthgps/healthgps-20220316-CMake.patch b/easybuild/easyconfigs/h/Health-GPS/Health-GPS-20220316-CMake.patch similarity index 100% rename from easybuild/easyconfigs/h/healthgps/healthgps-20220316-CMake.patch rename to easybuild/easyconfigs/h/Health-GPS/Health-GPS-20220316-CMake.patch From bcfcd59f70bd000c0ce55e86f430d25a9b697e7f Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 27 Feb 2023 12:25:09 +0000 Subject: [PATCH 6685/9987] adding easyconfigs: Health-GPS-1.2.2.0-GCCcore-11.3.0.eb --- .../Health-GPS-1.2.2.0-GCCcore-11.3.0.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.2.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.2.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.2.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f482a3de83a --- /dev/null +++ b/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.2.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,68 @@ +# Contribution from Imperial College London, UK +# Author Israel Vieira +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMakeCp' + +name = 'Health-GPS' +version = '1.2.2.0' + +homepage = 'https://github.com/imperialCHEPI/healthgps' +description = """ +Health-GPS microsimulation is part of the STOP project, and support researchers +and policy makers in the analysis of the health and economic impacts of alternative +measures to tackle chronic diseases and obesity in children. The model reproduces +the characteristics of a population and simulates key individual event histories +associated with key components of relevant behaviours, such as physical activity, +and diseases such as diabetes or cancer. +To run the test-jobs with HealthGPS.Tests the data-directory, found in your installation +folder, must be in the current path. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/imperialCHEPI/healthgps/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Health-GPS-20220316-CMake.patch'] + +checksums = [ + 'c90a076e5cd0ca2d12b57b78318bbed4a30c93d472a9eaa51e16d541a55fe160', # Health-GPS-1.2.2.0.tar.gz + '315e70c12edfe15535dbd54ac99ea66d41df3989a0917b8da7f024fdea2af609', # Health-GPS-20220316-CMake.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), + ('Ninja', '1.10.2'), +] + +# TBB is optional, include to link the application against the system library (GCC STL Only). +dependencies = [ + ('crossguid', '20190529'), + ('nlohmann_json', '3.10.5'), + ('rapidcsv', '8.64'), + ('fmt', '9.1.0'), + ('googletest', '1.11.0'), + ('cxxopts', '3.0.0', '', SYSTEM), + ('indicators', '2.2'), + ('tbb', '2021.5.0'), # optional - some HPC do not support non-OpenMP threads well. +] + +# We need to make sure we find the data-dir, so we just link it. +# This is bash, so we need to do a hack about the source directory. +prebuildopts = 'ln -s ../healthgps*/data data && ' + +files_to_copy = [ + (['src/HealthGPS.Console/HealthGPS.Console', 'src/HealthGPS.Tests/HealthGPS.Tests'], 'bin'), + 'data' +] + + +sanity_check_paths = { + 'files': ['bin/HealthGPS.Console', 'bin/HealthGPS.Tests'], + 'dirs': ['data'], +} + +sanity_check_commands = ['HealthGPS.Tests'] + +moduleclass = 'bio' From fa4e8588407f87f49c2db90da3643a5276ffabc3 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 27 Feb 2023 13:57:43 +0000 Subject: [PATCH 6686/9987] Patch file added --- .../Health-GPS-20220316-CMake.patch | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/Health-GPS/Health-GPS-20220316-CMake.patch diff --git a/easybuild/easyconfigs/h/Health-GPS/Health-GPS-20220316-CMake.patch b/easybuild/easyconfigs/h/Health-GPS/Health-GPS-20220316-CMake.patch new file mode 100644 index 00000000000..d6c9d394e7e --- /dev/null +++ b/easybuild/easyconfigs/h/Health-GPS/Health-GPS-20220316-CMake.patch @@ -0,0 +1,42 @@ +Patch to removed the build dependency to vcpkg as we are using EasyBuild for that +author: J. Sassmannshausen +diff --git a/healthgps.orig/CMakePresets.json b/healthgps/CMakePresets.json +index d29ef60..b3a3132 100644 +--- a/healthgps.orig/CMakePresets.json ++++ b/healthgps/CMakePresets.json +@@ -6,9 +6,9 @@ + "description": "Shared configuration presets", + "hidden": true, + "generator": "Ninja", +- "binaryDir": "${sourceDir}/out/build/${presetName}", ++ "binaryDir": "${sourceDir}/build", + "cacheVariables": { +- "CMAKE_INSTALL_PREFIX": "${sourceDir}/out/install/${presetName}" ++ "CMAKE_INSTALL_PREFIX": "${sourceDir}/build/install/${presetName}" + } + }, + { +@@ -18,15 +18,7 @@ + "inherits": "base", + "cacheVariables": { + "CMAKE_BUILD_TYPE": "Debug", +- "CMAKE_CXX_COMPILER": "g++", +- "CMAKE_TOOLCHAIN_FILE": { +- "value": "$env{VCPKG_ROOT}/scripts/buildsystems/vcpkg.cmake", +- "type": "FILEPATH" +- } +- }, +- "vendor": { +- "microsoft.com/VisualStudioSettings/CMake/1.0": { "hostOS": [ "Linux" ] }, +- "microsoft.com/VisualStudioRemoteSettings/CMake/1.0": { "sourceDir": "$env{HOME}/.vs/$ms{projectDirName}" } ++ "CMAKE_CXX_COMPILER": "g++" + } + }, + { +@@ -108,4 +100,4 @@ + "configurePreset": "x64-debug" + } + ] +-} +\ No newline at end of file ++} From 9e3d06b2695298dbf611ba1c79d13a2813e71b59 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 27 Feb 2023 14:47:19 +0000 Subject: [PATCH 6687/9987] adding easyconfigs: BCFtools-1.17-GCC-12.2.0.eb, HTSlib-1.17-GCC-12.2.0.eb, SAMtools-1.17-GCC-12.2.0.eb --- .../b/BCFtools/BCFtools-1.17-GCC-12.2.0.eb | 38 ++++++++++++++++++ .../h/HTSlib/HTSlib-1.17-GCC-12.2.0.eb | 39 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.17-GCC-12.2.0.eb | 37 ++++++++++++++++++ 3 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.17-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.17-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.17-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.17-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.17-GCC-12.2.0.eb new file mode 100644 index 00000000000..d428e6f6f1c --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.17-GCC-12.2.0.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.17' + +homepage = 'https://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['01f75d8e701d85b2c759172412009cc04f29b61616ace2fa75116123de4596cc'] + +dependencies = [ + ('zlib', '1.2.12'), + ('HTSlib', '1.17'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.7'), + ('GSL', '2.7'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['libexec/bcftools'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.17-GCC-12.2.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.17-GCC-12.2.0.eb new file mode 100644 index 00000000000..c0a8278c4ed --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.17-GCC-12.2.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Updated to 1.14 +# J. Sassmannshausen /GSTT + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.17' + +homepage = "https://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.7'), + ('cURL', '7.86.0'), +] + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.17-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.17-GCC-12.2.0.eb new file mode 100644 index 00000000000..c5f0ef79106 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.17-GCC-12.2.0.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +# +# Updated to 1.14 and gcc-11.2.0 +# J. Sassmannshausen / GSTT + +name = 'SAMtools' +version = '1.17' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['3adf390b628219fd6408f14602a4c4aa90e63e18b395dad722ab519438a2a729'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.7'), + ('cURL', '7.86.0'), +] + +moduleclass = 'bio' From b1268b46b5b86c32250e3bf7a6ebad90c9127cbd Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 27 Feb 2023 15:05:47 +0000 Subject: [PATCH 6688/9987] Typo fix --- .../h/Health-GPS/Health-GPS-1.2.2.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.2.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.2.2.0-GCCcore-11.3.0.eb index f482a3de83a..9b0f805733b 100644 --- a/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.2.2.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.2.2.0-GCCcore-11.3.0.eb @@ -9,7 +9,7 @@ version = '1.2.2.0' homepage = 'https://github.com/imperialCHEPI/healthgps' description = """ -Health-GPS microsimulation is part of the STOP project, and support researchers +Health-GPS microsimulation is part of the STOP project, and supports researchers and policy makers in the analysis of the health and economic impacts of alternative measures to tackle chronic diseases and obesity in children. The model reproduces the characteristics of a population and simulates key individual event histories From 2d7f6f51e764b5b07ded527856aadb10cb867daf Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 27 Feb 2023 16:14:56 +0100 Subject: [PATCH 6689/9987] adding easyconfigs: ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb, ELPA-2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb, ELPA-2022.05.001-intel-2022a.eb --- ...2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb | 44 +++++++++++++++++ ...ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb | 48 +++++++++++++++++++ .../e/ELPA/ELPA-2022.05.001-intel-2022a.eb | 47 ++++++++++++++++++ 3 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb new file mode 100644 index 00000000000..7e0a330ad2e --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2022.05.001' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, + {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': + '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.4'), + ('Perl', '5.34.1'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..60730ab1ad9 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2022.05.001' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, + {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': + '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.4'), + ('Perl', '5.34.1'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM) +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb new file mode 100644 index 00000000000..97e8442651a --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb @@ -0,0 +1,47 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2022.05.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, + {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': + '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.4'), + ('Perl', '5.34.1'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' +# If the build is running in a batch job, make sure Intel libmpi does +# not try to use Slurm to run the MPI_THREAD test code that ELPA's +# configure is running without "mpirun". +preconfigopts += 'unset SLURM_JOBID && unset SLURM_NODELIST && unset I_MPI_PMI_LIBRARY && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' From 8ae93a961ac188389805ba9eeaa3af19e6d1628c Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 27 Feb 2023 16:17:48 +0100 Subject: [PATCH 6690/9987] forgot to include this patch --- ...-2022.05.001_fix_hardcoded_perl_path.patch | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001_fix_hardcoded_perl_path.patch diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001_fix_hardcoded_perl_path.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001_fix_hardcoded_perl_path.patch new file mode 100644 index 00000000000..5c7ae5eae05 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001_fix_hardcoded_perl_path.patch @@ -0,0 +1,40 @@ +--- elpa-new_release_2021.11.001/test_project_1stage/fdep/fortran_dependencies.pl 2021-12-17 08:20:49.000000000 +0100 ++++ elpa-new_release_2021.11.001_ok/test_project_1stage/fdep/fortran_dependencies.pl 2022-01-25 17:07:21.169362000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +--- elpa-new_release_2021.11.001/fdep/fortran_dependencies.pl 2021-12-17 08:20:49.000000000 +0100 ++++ elpa-new_release_2021.11.001_ok/fdep/fortran_dependencies.pl 2022-01-25 17:08:17.272544000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Copyright 2015 Lorenz Hüdepohl + # +--- elpa-new_release_2021.11.001/test_project_C_2stage/fdep/fortran_dependencies.pl 2021-12-17 08:20:49.000000000 +0100 ++++ elpa-new_release_2021.11.001_ok/test_project_C_2stage/fdep/fortran_dependencies.pl 2022-01-25 17:06:20.088471000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +--- elpa-new_release_2021.11.001/test_project_2stage/fdep/fortran_dependencies.pl 2021-12-17 08:20:49.000000000 +0100 ++++ elpa-new_release_2021.11.001_ok/test_project_2stage/fdep/fortran_dependencies.pl 2022-01-25 17:05:10.675886000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +--- elpa-new_release_2021.11.001/test_project_C/fdep/fortran_dependencies.pl 2021-12-17 08:20:49.000000000 +0100 ++++ elpa-new_release_2021.11.001_ok/test_project_C/fdep/fortran_dependencies.pl 2022-01-25 17:04:14.834326000 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + From d68d83d387a8aba1fb54a74829680ebe620e8ce2 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 27 Feb 2023 16:52:42 +0100 Subject: [PATCH 6691/9987] Style fix --- .../e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb index 60730ab1ad9..fd14ce9b899 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb @@ -33,7 +33,7 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.7.0', '', SYSTEM) + ('CUDA', '11.7.0', '', SYSTEM) ] preconfigopts = './autogen.sh && ' From 091727c7980ed7cf9819fe9441a0d7f4c1a09cf2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 27 Feb 2023 16:05:22 +0000 Subject: [PATCH 6692/9987] adding easyconfigs: Boost-1.81.0-GCC-12.2.0.eb --- .../b/Boost/Boost-1.81.0-GCC-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..358e623d4e9 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb @@ -0,0 +1,30 @@ +## +# Authors:: Denis Kristak +## +name = 'Boost' +version = '1.81.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('XZ', '5.2.7'), + ('ICU', '72.1'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' From fe6351898e34c1fb11b78b8096bec5ea23dacf0e Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 27 Feb 2023 17:12:40 +0100 Subject: [PATCH 6693/9987] Included patch description --- .../e/ELPA/ELPA-2022.05.001_fix_hardcoded_perl_path.patch | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001_fix_hardcoded_perl_path.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001_fix_hardcoded_perl_path.patch index 5c7ae5eae05..3bc5bbcd3c3 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001_fix_hardcoded_perl_path.patch +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001_fix_hardcoded_perl_path.patch @@ -1,3 +1,6 @@ +# Perl scripts in elpa hard-code the location of the perl interpreter +# We replace these so that it picks up on the perl interpreter from the PATH +# (i.e. the one provided as a build dependency by EasyBuild) --- elpa-new_release_2021.11.001/test_project_1stage/fdep/fortran_dependencies.pl 2021-12-17 08:20:49.000000000 +0100 +++ elpa-new_release_2021.11.001_ok/test_project_1stage/fdep/fortran_dependencies.pl 2022-01-25 17:07:21.169362000 +0100 @@ -1,4 +1,4 @@ From 09b5f94f4ecaaf162e0f42ecabe429d4e8bd161b Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 27 Feb 2023 18:28:45 +0100 Subject: [PATCH 6694/9987] Added non-cuda EasyConfig, now removed the versionsuffix --- .../e/ELPA/ELPA-2022.05.001-foss-2022a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb new file mode 100644 index 00000000000..dc1830407b1 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2022.05.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, + {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': + '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.4'), + ('Perl', '5.34.1'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' From 4f37b70c0d7c8961629cffd50d926543b6833a74 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 27 Feb 2023 18:30:54 +0100 Subject: [PATCH 6695/9987] Fixed checksums for patch after adding comment there --- .../e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb index fd14ce9b899..6d9cb0dca9b 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb @@ -22,7 +22,7 @@ patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] checksums = [ {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': - '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b'}, + '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb index dc1830407b1..54a1ab0f515 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb @@ -21,7 +21,7 @@ patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] checksums = [ {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': - '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b'}, + '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb index 97e8442651a..6af27dad529 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb @@ -21,7 +21,7 @@ patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] checksums = [ {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': - '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b'}, + '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'}, ] builddependencies = [ From c15b7c058e37052e45711382e937922fd8bb9c5b Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 27 Feb 2023 18:31:33 +0100 Subject: [PATCH 6696/9987] Delete ELPA-2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb --- ...2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb deleted file mode 100644 index 7e0a330ad2e..00000000000 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-%(cudaver)s.eb +++ /dev/null @@ -1,44 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Authors:: Inge Gutheil , Alan O'Cais -# License:: MIT/GPL -# -## - -name = 'ELPA' -version = '2022.05.001' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://elpa.rzg.mpg.de' -description = """Eigenvalue SoLvers for Petaflop-Applications.""" - -toolchain = {'name': 'foss', 'version': '2022a'} -toolchainopts = {'openmp': True, 'usempi': True} - -source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] -sources = ['elpa-new_release_%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] -checksums = [ - {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, - {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': - '5fc40b6f3f948fd026efc688f9bafba0461d68ad007d9dc161bfd1507e2fc13b'}, -] - -builddependencies = [ - ('Autotools', '20220317'), - # remove_xcompiler script requires 'python' command, - ('Python', '3.10.4'), - ('Perl', '5.34.1'), -] - -preconfigopts = './autogen.sh && ' -preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' -preconfigopts += 'autoreconf && ' - -# When building in parallel, the file test_setup_mpi.mod is sometimes -# used before it is built, leading to an error. This must be a bug in -# the makefile affecting parallel builds. -maxparallel = 1 - -moduleclass = 'math' From 49f92b852d0afc16461eba8813acf76c8042681f Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 27 Feb 2023 19:08:53 +0100 Subject: [PATCH 6697/9987] Rm empty configopts --- .../f/fastjet-contrib/fastjet-contrib-1.049-gompi-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.049-gompi-2022a.eb b/easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.049-gompi-2022a.eb index bf71f805335..be269c4a4cd 100644 --- a/easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.049-gompi-2022a.eb +++ b/easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.049-gompi-2022a.eb @@ -21,7 +21,6 @@ dependencies = [ ('fastjet', '3.4.0') ] -configopts = "" build_cmd_targets = ['', 'fragile-shared'] install_cmd = "make install && make fragile-shared-install" From 3758f875f7645e0cf8a9b9d5031f14d54424e27f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 27 Feb 2023 18:23:40 +0000 Subject: [PATCH 6698/9987] update checksum --- easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb index 358e623d4e9..8bd43da3d1a 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c'] +checksums = ['205666dea9f6a7cfed87c7a6dfbeb52a2c1b9de55712c9c1a87735d7181452b6'] dependencies = [ ('bzip2', '1.0.8'), From 1242e25ff7f0d415a9b0aa39542f7f59c8b0566d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2023 09:57:24 +0100 Subject: [PATCH 6699/9987] use https in homepage for Armadillo --- .../easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb index 9e92946642a..f5eb6f67b05 100644 --- a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022b.eb @@ -1,7 +1,7 @@ name = 'Armadillo' version = '11.4.3' -homepage = 'http://arma.sourceforge.net/' +homepage = 'https://arma.sourceforge.net/' description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.""" From 92fbdbc3644c4890fad41b91a57fdcfecb3cdd76 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 28 Feb 2023 09:47:38 +0000 Subject: [PATCH 6700/9987] Missing binutils added --- easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb index 5df1574cf30..aacfd189395 100644 --- a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-11.3.0.eb @@ -26,6 +26,8 @@ source_urls = ['https://github.com/somme89/rapidNJ/archive/'] sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}] checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d'] +builddependencies = [('binutils', '2.38')] + files_to_copy = [(['bin/rapidnj'], 'bin')] # That is returning 1 instead of 0, so disabled for now From e7265258454436dc816b4a988c1dd0b3a2dd42a8 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 28 Feb 2023 10:02:25 +0000 Subject: [PATCH 6701/9987] Moved to GCCcore toolchain --- ...emf-1.0.13-GCC-11.3.0.eb => libemf-1.0.13-GCCcore-11.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/libemf/{libemf-1.0.13-GCC-11.3.0.eb => libemf-1.0.13-GCCcore-11.3.0.eb} (93%) diff --git a/easybuild/easyconfigs/l/libemf/libemf-1.0.13-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libemf/libemf-1.0.13-GCCcore-11.3.0.eb similarity index 93% rename from easybuild/easyconfigs/l/libemf/libemf-1.0.13-GCC-11.3.0.eb rename to easybuild/easyconfigs/l/libemf/libemf-1.0.13-GCCcore-11.3.0.eb index bda47b3c33b..c83afeb6d53 100644 --- a/easybuild/easyconfigs/l/libemf/libemf-1.0.13-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libemf/libemf-1.0.13-GCCcore-11.3.0.eb @@ -8,7 +8,7 @@ version = '1.0.13' homepage = 'https://sourceforge.net/projects/libemf/' description = "Library implementation of ECMA-234 API for the generation of enhanced metafiles." -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://sourceforge.net/projects/%(name)s/files/%(name)s/%(version)s'] sources = ['%(name)s-%(version)s.tar.gz'] From 72540b2bfdac8ab1cc85563f2f299e95dd9b03b0 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 28 Feb 2023 10:09:40 +0000 Subject: [PATCH 6702/9987] reinstate preconfigopts sed for netCDF w/ iimpi --- .../easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb index 1806b1252c5..3b2300fd940 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022b.eb @@ -38,6 +38,14 @@ dependencies = [ ('libxml2', '2.10.3'), ] +# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso +# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" + " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") + # make sure both static and shared libs are built # and disable "remote" tests that access a unreliable external test server over internet configopts = [ From a95f50fcc0a2f85055f22cb203696ee7bbd6b0cc Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 28 Feb 2023 10:26:22 +0000 Subject: [PATCH 6703/9987] cmake removed, versionsuffix of cairo removed --- ...-GCC-11.3.0-cairo-1.17.4.eb => cairomm-1.14.4-GCC-11.3.0.eb} | 2 -- ...-GCC-11.3.0-cairo-1.17.4.eb => cairomm-1.16.2-GCC-11.3.0.eb} | 2 -- 2 files changed, 4 deletions(-) rename easybuild/easyconfigs/c/cairomm/{cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb => cairomm-1.14.4-GCC-11.3.0.eb} (93%) rename easybuild/easyconfigs/c/cairomm/{cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb => cairomm-1.16.2-GCC-11.3.0.eb} (93%) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb similarity index 93% rename from easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb rename to easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index a5a73baad0a..4bbae3a730b 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0-cairo-1.17.4.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -5,7 +5,6 @@ easyblock = 'MesonNinja' name = 'cairomm' version = '1.14.4' -versionsuffix = '-cairo-1.17.4' homepage = 'http://cairographics.org' description = "The Cairomm package provides a C++ interface to Cairo." @@ -17,7 +16,6 @@ sources = [SOURCE_TAR_XZ] checksums = ['4749d25a2b2ef67cc0c014caaf5c87fa46792fc4b3ede186fb0fc932d2055158'] builddependencies = [ - ('CMake', '3.24.3'), ('Meson', '0.62.1'), ('Ninja', '1.10.2'), ] diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb similarity index 93% rename from easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb rename to easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb index ffe8ff54a20..4d3b9b1d798 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0-cairo-1.17.4.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb @@ -5,7 +5,6 @@ easyblock = 'MesonNinja' name = 'cairomm' version = '1.16.2' -versionsuffix = '-cairo-1.17.4' homepage = 'http://cairographics.org' description = "The Cairomm package provides a C++ interface to Cairo." @@ -17,7 +16,6 @@ sources = [SOURCE_TAR_XZ] checksums = ['6a63bf98a97dda2b0f55e34d1b5f3fb909ef8b70f9b8d382cb1ff3978e7dc13f'] builddependencies = [ - ('CMake', '3.24.3'), ('Meson', '0.62.1'), ('Ninja', '1.10.2'), ] From 571e36145dfdeb66ef6a2f0ab1f63162ee73d409 Mon Sep 17 00:00:00 2001 From: robogast Date: Tue, 28 Feb 2023 11:30:47 +0100 Subject: [PATCH 6704/9987] Updating cuDNN 8.8 easyconfig to fetch live sources --- .../c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb index 7e8779246f0..b3e12f95607 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb @@ -12,15 +12,17 @@ toolchain = SYSTEM local_short_ver = '.'.join(version.split('.')[:3]) local_cuda_major = '12' -download_instructions = 'Requires manual download from https://developer.nvidia.com/rdp/cudnn-download' +source_urls = [ + 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%%(cudnnarch)s/cudnn-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major, # noqa: E501 +] sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] checksums = [{ - '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: - 'a0792b666caaf593a9dd4130979578fd3a78230f4407645c295700ef8e7aaaf2', - '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: - 'cd41ab8b61f5beb54e32c3668ecd311ce926c39006fba256b053dd7d248419d4', - '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: - 'fc668519a8344e9d05335bad4bc5d23a504cdc7579aea41f12d6aa0f3079e709', + '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'cd41ab8b61f5beb54e32c3668ecd311ce926c39006fba256b053dd7d248419d4', + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'fc668519a8344e9d05335bad4bc5d23a504cdc7579aea41f12d6aa0f3079e709', + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'a0792b666caaf593a9dd4130979578fd3a78230f4407645c295700ef8e7aaaf2', }] dependencies = [('CUDA', '12.0.0')] From a8c8f5681b99f22afabc06ba23756dc86142824b Mon Sep 17 00:00:00 2001 From: Robert Jan Schlimbach Date: Tue, 28 Feb 2023 11:32:15 +0100 Subject: [PATCH 6705/9987] Update cuDNN-8.8.0.121-CUDA-12.0.0.eb re-adding spaces --- .../easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb index b3e12f95607..2cf7ad646fd 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb @@ -17,11 +17,11 @@ source_urls = [ ] sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] checksums = [{ - '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: 'cd41ab8b61f5beb54e32c3668ecd311ce926c39006fba256b053dd7d248419d4', - '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: 'fc668519a8344e9d05335bad4bc5d23a504cdc7579aea41f12d6aa0f3079e709', - '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: 'a0792b666caaf593a9dd4130979578fd3a78230f4407645c295700ef8e7aaaf2', }] From dc9e329897fc345e01953c90594ad51d5885ed87 Mon Sep 17 00:00:00 2001 From: Robert Jan Schlimbach Date: Tue, 28 Feb 2023 11:33:30 +0100 Subject: [PATCH 6706/9987] Update cuDNN-8.8.0.121-CUDA-12.0.0.eb More indentation fixes --- .../easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb index 2cf7ad646fd..51275a65756 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb @@ -18,11 +18,11 @@ source_urls = [ sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] checksums = [{ '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: - 'cd41ab8b61f5beb54e32c3668ecd311ce926c39006fba256b053dd7d248419d4', + 'cd41ab8b61f5beb54e32c3668ecd311ce926c39006fba256b053dd7d248419d4', '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: - 'fc668519a8344e9d05335bad4bc5d23a504cdc7579aea41f12d6aa0f3079e709', + 'fc668519a8344e9d05335bad4bc5d23a504cdc7579aea41f12d6aa0f3079e709', '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: - 'a0792b666caaf593a9dd4130979578fd3a78230f4407645c295700ef8e7aaaf2', + 'a0792b666caaf593a9dd4130979578fd3a78230f4407645c295700ef8e7aaaf2', }] dependencies = [('CUDA', '12.0.0')] From e3f0f460c7f85ea9a950b2e4875a7a432f255a45 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 28 Feb 2023 11:42:26 +0100 Subject: [PATCH 6707/9987] Add dependencies --- ...0.5.eb => SeaView-5.0.5-GCCcore-11.2.0.eb} | 22 ++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/s/SeaView/{SeaView-5.0.5.eb => SeaView-5.0.5-GCCcore-11.2.0.eb} (57%) diff --git a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb similarity index 57% rename from easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb rename to easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb index 44f26b4c875..22e2205329b 100644 --- a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5.eb +++ b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb @@ -7,12 +7,32 @@ homepage = 'https://doua.prabi.fr/software/seaview' description = """SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.""" -toolchain = SYSTEM +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://doua.prabi.fr/software/seaview_data'] sources = [{'download_filename': '%(namelower)s%(version_major)s-64.tgz', 'filename': '%(name)s-%(version)s-64.tgz'}] checksums = ['e8d844ee5d41f7e5626631ac1eb75086add6a24bfe8a5aa69d045c622a8abd8d'] +dependencies = [ + ('Brotli', '1.0.9'), + ('bzip2', '1.0.8'), + ('cairo', '1.16.0'), + ('expat', '2.4.1'), + ('fontconfig', '2.13.94'), + ('freetype', '2.11.0'), + ('FriBidi', '1.0.10'), + ('GLib', '2.69.1'), + ('HarfBuzz', '2.8.2'), + ('libffi', '3.4.2'), + ('libpng', '1.6.37'), + ('Pango', '1.48.8'), + ('PCRE', '8.45'), + ('pixman', '0.40.0'), + ('util-linux', '2.37'), + ('X11', '20210802'), + ('zlib', '1.2.11'), +] + sanity_check_paths = { 'files': ['%(namelower)s'], 'dirs': [], From 707202066992d0ed319b2b713402ed33c7c14c65 Mon Sep 17 00:00:00 2001 From: robogast Date: Tue, 28 Feb 2023 11:47:01 +0100 Subject: [PATCH 6708/9987] removed unnecessary part of source url --- easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb index 51275a65756..3da8ab75fce 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.8.0.121-CUDA-12.0.0.eb @@ -13,7 +13,7 @@ local_short_ver = '.'.join(version.split('.')[:3]) local_cuda_major = '12' source_urls = [ - 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%%(cudnnarch)s/cudnn-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major, # noqa: E501 + 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%(cudnnarch)s/' ] sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] checksums = [{ From 21d7f6f7dc4678362ceb93a03d26261daf23a02f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 28 Feb 2023 11:21:48 +0000 Subject: [PATCH 6709/9987] libsig updated to 3.4.0 --- easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index 4bbae3a730b..ed89cbbcb2d 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('cairo', '1.17.4'), - ('libsigc++', '2.12.0'), + ('libsigc++', '3.4.0'), ('mm-common', '1.0.5'), ('Boost', '1.79.0'), ] From d788813283ee101259b414275e51cb90168e3bb6 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 28 Feb 2023 11:28:18 +0000 Subject: [PATCH 6710/9987] CMake used for 3.4.0, version 2.10.8 removed --- .../libsigc++-2.12.0-GCCcore-11.3.0.eb | 32 ------------------- .../libsigc++-3.4.0-GCCcore-11.3.0.eb | 11 ++++--- 2 files changed, 6 insertions(+), 37 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb deleted file mode 100644 index d4470b7f612..00000000000 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.0-GCCcore-11.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libsigc++' -version = '2.12.0' - -homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' -description = """The libsigc++ package implements a typesafe callback system for standard C++.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] - -builddependencies = [ - ('binutils', '2.38'), - ('Autotools', '20220317'), - ('Doxygen', '1.9.4'), - ('Graphviz', '5.0.0'), - ('libxslt', '1.1.34'), - ('mm-common', '1.0.5'), -] - -preconfigopts = "./autogen.sh && " -configopts = '--disable-documentation ' - -sanity_check_paths = { - 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb index be3a0fa23e2..2547b201764 100644 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb @@ -1,4 +1,7 @@ -easyblock = 'ConfigureMake' +# Updated to CMakeMake +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' name = 'libsigc++' version = '3.4.0' @@ -22,10 +25,8 @@ builddependencies = [ ('CMake', '3.24.3'), ] -preconfigopts = "./autogen.sh && " -configopts = '--disable-documentation ' - -runtest = 'check' +test_cmd = 'ctest' +runtest = '-j' sanity_check_paths = { 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], From 8600fbbccaf05b61eff4827614ac4e66bfafec51 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 28 Feb 2023 13:49:12 +0100 Subject: [PATCH 6711/9987] delete run_alphafold_{features,resume}.py --- .../a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb index b3442dbb988..348e3a6aaed 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb @@ -131,7 +131,6 @@ postinstallcmds = [ # run_alphafold.py script is missing a shebang... "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", - "cp %(builddir)s/alphafold-%(version)s/run_alphafold_{features,resume}.py %(installdir)s/bin", "chmod a+x %(installdir)s/bin/run_alphafold*.py", "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", From 2d4a20db3b38e0291504759c1e189aab10128590 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 28 Feb 2023 14:31:50 +0000 Subject: [PATCH 6712/9987] adding easyconfigs: mpmath-1.2.1-GCCcore-10.2.0.eb, mpmath-1.2.1-GCCcore-10.3.0.eb, mpmath-1.2.1-GCCcore-11.2.0.eb, mpmath-1.2.1-GCCcore-11.3.0.eb --- .../m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb | 43 ++++++++++++++++++ .../m/mpmath/mpmath-1.2.1-GCCcore-10.3.0.eb | 43 ++++++++++++++++++ .../m/mpmath/mpmath-1.2.1-GCCcore-11.2.0.eb | 45 +++++++++++++++++++ .../m/mpmath/mpmath-1.2.1-GCCcore-11.3.0.eb | 43 ++++++++++++++++++ 4 files changed, 174 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..60b2d1678dc --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '1.2.1' + +homepage = 'https://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'] + +builddependencies = [ + ('binutils', '2.35') +] + +dependencies = [ + ('Python', '3.8.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..227ab3c7395 --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-10.3.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '1.2.1' + +homepage = 'https://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'] + +builddependencies = [ + ('binutils', '2.36.1') +] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..1a49bd05c79 --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '1.2.1' + +homepage = 'https://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'] + +builddependencies = [ + ('binutils', '2.37') +] + +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True + +use_pip = True + +sanity_pip_check = True + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c1483102bdd --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-1.2.1-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '1.2.1' + +homepage = 'https://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'] + +builddependencies = [ + ('binutils', '2.38') +] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From 1da2d9a81ca4da455f37d617f6bde03d0d4494b5 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 28 Feb 2023 15:42:20 +0000 Subject: [PATCH 6713/9987] add libgeotiff easyconfig --- .../libgeotiff-1.7.1-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..75956eab50a --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.7.1' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['05ab1347aaa471fc97347d8d4269ff0c00f30fa666d956baba37948ec87e55d6'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('PROJ', '9.1.1'), + ('libjpeg-turbo', '2.1.4'), + ('zlib', '1.2.12'), + ('SQLite', '3.39.4'), + ('LibTIFF', '4.4.0'), + ('cURL', '7.86.0'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 2f3085c2b32e92eb0c2b47fe84628fe116ca0e30 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 28 Feb 2023 15:43:05 +0000 Subject: [PATCH 6714/9987] Update easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb --- easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb index da8f179ebc2..aac67f80329 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb @@ -42,7 +42,7 @@ dependencies = [ ('PCRE', '8.45'), ('PROJ', '9.1.1'), ('libgeotiff', '1.7.1'), - ('SciPy-bundle', '2023.01'), + ('SciPy-bundle', '2023.02'), ('HDF5', '1.14.0'), ('HDF', '4.2.15'), ('Armadillo', '11.4.3'), From a149ef2c2da4d94ad4b9cabe1f7e86e9b1b02b69 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 28 Feb 2023 16:17:00 +0000 Subject: [PATCH 6715/9987] update R bundle packages --- .../easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 246 +++++++++--------- 1 file changed, 123 insertions(+), 123 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 324e9babd79..f339ba1d10f 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -1,5 +1,5 @@ name = 'R' -version = '4.2.2' +version = '4.2.1' homepage = 'https://www.r-project.org/' description = """R is a free software environment for statistical computing @@ -46,7 +46,7 @@ dependencies = [ ('ImageMagick', '7.1.0-53'), # for animation ('GLPK', '5.0'), # for Rglpk ('nodejs', '18.12.1'), # for V8 (required by rstan) - ('GDAL', '3.6.2'), # for sf + ('GDAL', '3.5.0'), # for sf ('MPFR', '4.2.0'), # for Rmpfr ('libgit2', '1.5.0'), ('OpenSSL', '1.1', '', SYSTEM), @@ -109,22 +109,22 @@ exts_list = [ ('RcppProgress', '0.4.2', { 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], }), - ('lpSolve', '5.6.17', { + ('lpSolve', '5.6.18', { 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], }), ('linprog', '0.9-4', { 'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'], }), - ('geometry', '0.4.6.1', { + ('geometry', '0.4.7', { 'checksums': ['910465a8c8043faca73bcc7c81c9249b9938677ee6649468003b438a6503f5d8'], }), ('bit', '4.0.5', { 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], }), - ('filehash', '2.4-3', { + ('filehash', '2.4-5', { 'checksums': ['f394e2c93233e8ad1c104562ea9349855dc8e303131f559cd59834f9aa3e41bd'], }), - ('ff', '4.0.7', { + ('ff', '4.0.9', { 'checksums': ['0a47333d31c7afc3f95387166e21a3e4c763cbef47d9b5927753aef4ff8d83fa'], }), ('bnlearn', '4.8.1', { @@ -154,7 +154,7 @@ exts_list = [ ('GSA', '1.03.2', { 'checksums': ['177d6059fc645d3d8883806d2dea1c5dfc68efdada9aadde8a96b6d57acf35b8'], }), - ('xfun', '0.36', { + ('xfun', '0.37', { 'checksums': ['d169f3e682dab0c3f2ca381f2dba9b7014a5e2ca3d6863dbae3d1bca699ef235'], }), ('highr', '0.10', { @@ -169,13 +169,13 @@ exts_list = [ ('lazy', '1.2-18', { 'checksums': ['27bf1216ac6220712fe7e86c0a288b7d7118f9088989f67e0a86b3d0f99c3370'], }), - ('kernlab', '0.9-31', { + ('kernlab', '0.9-32', { 'checksums': ['7359c665c1c5e6780e1ce44b143347c8eec839301c3079d7f19e29159873278a'], }), ('mime', '0.12', { 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], }), - ('markdown', '1.4', { + ('markdown', '1.5', { 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], }), ('mlbench', '2.1-3', { @@ -199,7 +199,7 @@ exts_list = [ ('lattice', '0.20-45', { 'checksums': ['22388d92bdb7d3959da84d7308d9026dd8226ef07580783729e8ad2f7d7507ad'], }), - ('nlme', '3.1-161', { + ('nlme', '3.1-162', { 'checksums': ['a55bb401c2ba2706763d1f40283780699eb812b0d090b3d1903fae8aa956bf23'], }), ('segmented', '1.6-2', { @@ -274,7 +274,7 @@ exts_list = [ ('progress', '1.2.2', { 'checksums': ['b4a4d8ed55db99394b036a29a0fb20b5dd2a91c211a1d651c52a1023cc58ff35'], }), - ('ade4', '1.7-20', { + ('ade4', '1.7-22', { 'checksums': ['c85111881ff93a261ca34a5b5ef313d1c0ff9b84f0b23596bc56cfa696f165ef'], }), ('AlgDesign', '1.2.1', { @@ -394,7 +394,7 @@ exts_list = [ ('Matrix', '1.5-3', { 'checksums': ['42b24f1d1e94482b0ff0ef1292e2df29f69694bdbee47b3d6bfeec46fafb2f7e'], }), - ('RcppArmadillo', '0.11.4.3.1', { + ('RcppArmadillo', '0.12.0.1.0', { 'checksums': ['f9e17af85ef5c0c8d63771b6e7da0cdcdbecc7ac8bd40d5035a64952c4ce1938'], }), ('plyr', '1.8.8', { @@ -427,7 +427,7 @@ exts_list = [ ('scales', '1.2.1', { 'checksums': ['185d50240e6b3e84d36ec7fbca6aef7a85db7c8c1b0dde51d4af28d363ce02df'], }), - ('utf8', '1.2.2', { + ('utf8', '1.2.3', { 'checksums': ['a71aee87d43a9bcf29249c7a5a2e9ca1d2a836e8d5ee3a264d3062f25378d8f4'], }), ('zeallot', '0.1.0', { @@ -502,7 +502,7 @@ exts_list = [ ('isoband', '0.2.7', { 'checksums': ['46f53fa066f0966f02cb2bf050190c0d5e950dab2cdf565feb63fc092c886ba5'], }), - ('ggplot2', '3.4.0', { + ('ggplot2', '3.4.1', { 'checksums': ['bfcb4eb92a0fcd3fab713aca4bb25e916e05914f2540271a45522ad7e43943a9'], }), ('pROC', '1.18.0', { @@ -514,7 +514,7 @@ exts_list = [ ('BB', '2019.10-1', { 'checksums': ['04d0b6ce6e5f070b109478a6005653dbe78613bb4e3ea4903203d851b5d3c94d'], }), - ('data.table', '1.14.6', { + ('data.table', '1.14.8', { 'checksums': ['f741b951e5937440139514aedbae78dbd6862d825066848bdb006aa02c2f3d2b'], }), ('BBmisc', '1.13', { @@ -529,7 +529,7 @@ exts_list = [ ('snow', '0.4-4', { 'checksums': ['84587f46f222a96f3e2fde10ad6ec6ddbd878f4e917cd926d632f61a87db13c9'], }), - ('tree', '1.0-42', { + ('tree', '1.0-43', { 'checksums': ['5a17c30423f4a1b81ae4fdf4a1c0079724000c9fdb339306438db442e17c72e0'], }), ('pls', '2.8-1', { @@ -542,7 +542,7 @@ exts_list = [ ('proxy', '0.4-27', { 'checksums': ['249991a4c4d70ad139e93f3a24e17f161ad1ec854951813ea192daf79478563f'], }), - ('e1071', '1.7-12', { + ('e1071', '1.7-13', { 'checksums': ['48c18e10e7cabc742d37b563672e2eddb6061f2378b69e5563be79ab9948d92f'], }), ('nnet', '7.3-18', { @@ -561,7 +561,7 @@ exts_list = [ ('matrixStats', '0.63.0', { 'checksums': ['85e2016b6dd20cbfe32d38a2ef2578ae80e688d9a3590aefd1d2f4bf4bd44eca'], }), - ('codetools', '0.2-18', { + ('codetools', '0.2-19', { 'checksums': ['1a9ea6b9792dbd1688078455929385acc3a5e4bef945c77bec1261fa4a084c28'], }), ('foreach', '1.5.2', { @@ -579,7 +579,7 @@ exts_list = [ ('tidyselect', '1.2.0', { 'checksums': ['0389a3b15417954a30d6d692f6ebdd3d0f318cb94a5c9b05365df2f4ea1d8270'], }), - ('dplyr', '1.0.10', { + ('dplyr', '1.1.0', { 'checksums': ['e2e1f7312618b4e32ada9a1da79cef32eaec12acd408c973a6b069c6be4fb46b'], }), ('gower', '1.0.1', { @@ -588,7 +588,7 @@ exts_list = [ ('rpart', '4.1.19', { 'checksums': ['27ec75258a5a3459ad999f5f36760ead974930744249605bf8465f234f31425c'], }), - ('survival', '3.5-0', { + ('survival', '3.5-3', { 'checksums': ['14878705cd0c7edcfead79011444aa84f680759293bde8634721c49f37cb4dc7'], }), ('KernSmooth', '2.23-20', { @@ -603,7 +603,7 @@ exts_list = [ ('parallelly', '1.34.0', { 'checksums': ['909ca35e7931b08dab7c8e48747c9b55c4f92480d87a85f98331a03b5f85e179'], }), - ('future', '1.30.0', { + ('future', '1.31.0', { 'checksums': ['a35c0bdae86265ebe86119231802b6fbf7b1d533b57cb423d8483fbe779390d5'], }), ('future.apply', '1.10.0', { @@ -618,7 +618,7 @@ exts_list = [ ('SQUAREM', '2021.1', { 'checksums': ['66e5e18ca29903e4950750bbd810f0f9df85811ee4195ce0a86d939ba8183a58'], }), - ('lava', '1.7.1', { + ('lava', '1.7.2.1', { 'checksums': ['7a88f8a885872e2abb3011c446e9e1c4884cd4dbe6ab4cfe9207538e5560232e'], }), ('prodlim', '2019.11.13', { @@ -630,7 +630,7 @@ exts_list = [ ('cpp11', '0.4.3', { 'checksums': ['403ce0bf82358d237176053b0fb1e958cb6bfa4d0fb3555bf5801db6a6939b99'], }), - ('lubridate', '1.9.1', { + ('lubridate', '1.9.2', { 'checksums': ['87d66efdb1f3d680db381d7e40a202d35645865a0542e2f270ef008a19002ba5'], }), ('tidyr', '1.3.0', { @@ -639,13 +639,13 @@ exts_list = [ ('hardhat', '1.2.0', { 'checksums': ['0374a9f5af2e8eaf100b4dbda951a5289258d0d466e5ef10768e8ffda928b4b1'], }), - ('recipes', '1.0.4', { + ('recipes', '1.0.5', { 'checksums': ['3d0073e3eb98ac089a94bf8430f3c50915ff1f495d8e967c37baa6a0f6cea0a4'], }), ('caret', '6.0-93', { 'checksums': ['1d814a2a921a23ad8b9a7da6f788e6abc06f5668b3918bd440d4355bc4b81511'], }), - ('conquer', '1.3.1', { + ('conquer', '1.3.2', { 'checksums': ['ac354e18c9ad6f41ed5200fad1c99fa5b124fc6fa5bba8f3434be2478f53d5fa'], }), ('quantreg', '5.94', { @@ -660,7 +660,7 @@ exts_list = [ ('lmtest', '0.9-40', { 'checksums': ['64400d4d6cc635316531042971f1783539686e9015c76f5741c07304fa14d997'], }), - ('vcd', '1.4-10', { + ('vcd', '1.4-11', { 'checksums': ['7188192afa289350cc1b89790f4f8f5a5114c1c88bee7715a0c8f5347aa0b35b'], }), ('snowfall', '1.84-6.2', { @@ -723,10 +723,10 @@ exts_list = [ ('vroom', '1.6.1', { 'checksums': ['d087cb148f71c222fc89199d03df2502689149873414a6d89c2f006d3a109fde'], }), - ('readr', '2.1.3', { + ('readr', '2.1.4', { 'checksums': ['94afd03a1fa4abcf2985ec903bbf5995d7c590e1a50512ed80d081ef4fe10c1b'], }), - ('forcats', '0.5.2', { + ('forcats', '1.0.0', { 'checksums': ['c4fb96e874e2bedaa8a1aa32ea22abdee7906d93b5c5c7b42c0894c0c5b6a289'], }), ('haven', '2.5.1', { @@ -780,7 +780,7 @@ exts_list = [ ('DBI', '1.1.3', { 'checksums': ['38bb33753da5bddb78893a5228a5d269dae3bf16f21dc5d9853ac9c24d31428d'], }), - ('gam', '1.22', { + ('gam', '1.22-1', { 'checksums': ['5787c6fabea5aaba29fe214db305a7369916082efc6a18f84e4c9ef81c8e7dad'], }), ('gamlss.data', '6.0-2', { @@ -789,7 +789,7 @@ exts_list = [ ('gamlss.dist', '6.0-5', { 'checksums': ['ec90ea83cd81b894c73f987f69814077697be33abf0708e0f3e2a39d02c912bf'], }), - ('gamlss', '5.4-10', { + ('gamlss', '5.4-12', { 'checksums': ['6619d4fdc183ab492615d44961a126c827d18db20a0d59362e54de877f0a3076'], }), ('gamlss.tr', '5.1-7', { @@ -798,7 +798,7 @@ exts_list = [ ('hwriter', '1.3.2.1', { 'checksums': ['ed2fa254ab27cf65d397e181339976fc3261dfb4f6b600fea8c5689620dab6f3'], }), - ('xts', '0.12.2', { + ('xts', '0.13.0', { 'checksums': ['d680584af946fc30be0b2046e838cff7b3a65e00df1eadba325ca5e96f3dca2c'], }), ('curl', '5.0.0', { @@ -819,10 +819,10 @@ exts_list = [ ('pscl', '1.5.5', { 'checksums': ['054c9b88a991abdec3338688f58e81b6ba55f91edb988621864b24fd152fee6f'], }), - ('fastmap', '1.1.0', { + ('fastmap', '1.1.1', { 'checksums': ['9113e526b4c096302cfeae660a06de2c4c82ae4e2d3d6ef53af6de812d4c822b'], }), - ('cachem', '1.0.6', { + ('cachem', '1.0.7', { 'checksums': ['9a9452f7bcf3f79436c418b3c3290449fb8fd338714d9b992153754d112f1864'], }), ('memoise', '2.0.1', { @@ -831,7 +831,7 @@ exts_list = [ ('blob', '1.2.3', { 'checksums': ['2d88d683ee3d1b56b332b5c7769979b5d3994b5d9285ea634ec919576da3631b'], }), - ('RSQLite', '2.2.20', { + ('RSQLite', '2.3.0', { 'checksums': ['2ae36a875ebc02497985b2ad9ddc6a5434f576e2ab25769580749d9e4f3b607c'], }), ('BatchJobs', '1.9', { @@ -868,7 +868,7 @@ exts_list = [ ('tseriesChaos', '0.1-13.1', { 'checksums': ['23cb5fea56409a305e02a523ff8b7642ec383942d415c9cffdc92208dacfd961'], }), - ('tseries', '0.10-52', { + ('tseries', '0.10-53', { 'checksums': ['a55f20704883710ab58ea479e20cf0f263c50d54282f693793cda4af664c207f'], }), ('fastICA', '1.2-3', { @@ -889,7 +889,7 @@ exts_list = [ ('openssl', '2.0.5', { 'checksums': ['862d3dc9bb69d92e36e83a7506be83443d4a4957f5f08f6617d7873c67a1f1c4'], }), - ('httr', '1.4.4', { + ('httr', '1.4.5', { 'checksums': ['9a8613fa96173ac910c021391af1ced4d0609169049c802cf7cdfe1c40897c6a'], }), ('cgdsr', '', { @@ -907,7 +907,7 @@ exts_list = [ ('gbm', '2.1.8.1', { 'checksums': ['7d5de3b980b8f23275e86ac9bed48a497c9aa53c58e407dfd676309f38272ec1'], }), - ('Formula', '1.2-4', { + ('Formula', '1.2-5', { 'checksums': ['cb70e373b5ed2fc8450937fb3321d37dfd22dcc6f07cb872a419d51205125caf'], }), ('acepack', '1.4.1', { @@ -916,7 +916,7 @@ exts_list = [ ('proto', '1.0.0', { 'checksums': ['9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1'], }), - ('chron', '2.3-58', { + ('chron', '2.3-59', { 'checksums': ['9645d86a84d1afc12a0accf4f826fdd40e6d050a313424ad70f8085e8f19c232'], }), ('viridis', '0.6.2', { @@ -937,7 +937,7 @@ exts_list = [ ('htmlTable', '2.4.1', { 'checksums': ['4ca2b5616d77cfeee8ae5ca74307b86407d478b12d1ce17ba9c447e233b89a9d'], }), - ('Hmisc', '4.7-2', { + ('Hmisc', '4.8-0', { 'checksums': ['29ec2d9ca11c790c350e93323126bef4f498c69c41c31bb335fd04671e0f87bd'], }), ('fastcluster', '1.2.3', { @@ -946,10 +946,10 @@ exts_list = [ ('registry', '0.5-1', { 'checksums': ['dfea36edb0a703ec57e111016789b47a1ba21d9c8ff30672555c81327a3372cc'], }), - ('bibtex', '0.5.0', { + ('bibtex', '0.5.1', { 'checksums': ['7bad194920b412781ac9754ad41058d52d3cd7186e1851c2bce3640490e9bc6d'], }), - ('pkgmaker', '0.32.7', { + ('pkgmaker', '0.32.8', { 'checksums': ['ce45b22def771a9c90a414093823e6befe7e23489c500eeccee5154b44d3ef91'], }), ('rngtools', '1.5.2', { @@ -964,16 +964,16 @@ exts_list = [ ('irlba', '2.3.5.1', { 'checksums': ['26fc8c0d36460e422ab77f43a597b8ec292eacd452628c54d34b8bf7d5269bb9'], }), - ('igraph', '1.3.5', { + ('igraph', '1.4.1', { 'checksums': ['0f5066180e223e165d28cee050054008ca23102e8392ff4ecd72e733537ec320'], }), ('GeneNet', '1.2.16', { 'checksums': ['c1e98073ccdaa18f4952630bfe4fc0617106eeaf7ed94d347cb2773bd48333e4'], }), - ('ape', '5.6-2', { + ('ape', '5.7', { 'checksums': ['9b62450a0390a1f07df007d348ad4cedcd814d42cb11c5a300ed33550fd41257'], }), - ('RJSONIO', '1.3-1.7', { + ('RJSONIO', '1.3-1.8', { 'checksums': ['82d1c9ea7758b2a64ad683f9c46223dcba9aa8146b43c1115bf9aa76a657a09f'], }), ('caTools', '1.18.2', { @@ -991,13 +991,13 @@ exts_list = [ ('promises', '1.2.0.1', { 'checksums': ['8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7'], }), - ('httpuv', '1.6.8', { + ('httpuv', '1.6.9', { 'checksums': ['f5f63629ca5e9d0e396a89982d95b5286726c0cb425166f35a3ad32a60a79156'], }), ('rjson', '0.2.21', { 'checksums': ['982b56d35ccc0c7db0b20c1d3eab5f5f47c620309646fdc278ff1cc3433ea2e2'], }), - ('sourcetools', '0.1.7', { + ('sourcetools', '0.1.7-1', { 'checksums': ['47984406efb3b3face133979ccbae9fefb7360b9a6ca1a1c11473681418ed2ca'], }), ('xml2', '1.3.3', { @@ -1012,7 +1012,7 @@ exts_list = [ ('rappdirs', '0.3.3', { 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], }), - ('fs', '1.6.0', { + ('fs', '1.6.1', { 'checksums': ['35cad1781d6d17c1feb56adc4607079c6844b63794d0ce1e74bb18dbc11e1987'], }), ('sass', '0.4.5', { @@ -1021,7 +1021,7 @@ exts_list = [ ('bslib', '0.4.2', { 'checksums': ['5f5cb56e5cab9039a24cd9d70d73b69c2cab5b2f5f37afc15f71dae0339d9849'], }), - ('fontawesome', '0.4.0', { + ('fontawesome', '0.5.0', { 'checksums': ['572db64d1b3c9be301935e0ca7baec69f3a6e0aa802e23f1f224b3724259df64'], }), ('shiny', '1.7.4', { @@ -1054,7 +1054,7 @@ exts_list = [ ('units', '0.8-1', { 'checksums': ['9c46fe138e8c1c3d3a51268776412f02d09673656516148cccb71b1071beb21a'], }), - ('classInt', '0.4-8', { + ('classInt', '0.4-9', { 'checksums': ['a30e3a8987ce133944897100ab5bdc31b019d897969c452c3795f50ac234606e'], }), ('vegan', '2.6-4', { @@ -1066,7 +1066,7 @@ exts_list = [ ('XML', '3.99-0.13', { 'checksums': ['c45991b5edadc3cf7e2d80c38e798a5d6c4e27baf6007004d4db5a6ca97ff35b'], }), - ('tinytex', '0.43', { + ('tinytex', '0.44', { 'checksums': ['3f5e7adb2c047a8181a39fe5fee1f709039e6e94245f98c64282fdecc183d88d'], }), ('rmarkdown', '2.20', { @@ -1144,7 +1144,7 @@ exts_list = [ ('taxize', '0.9.100', { 'checksums': ['e2e578fc45eb5d1306332892c67535fa4bc32d63129532df2c6cde393993cd29'], }), - ('RNeXML', '2.4.10', { + ('RNeXML', '2.4.11', { 'checksums': ['cb311d6dda33a95521a6df360a2d2f4e6d6bc6b330ac5e19ea721ca665bce6fe'], }), ('phylobase', '0.8.10', { @@ -1189,7 +1189,7 @@ exts_list = [ ('fossil', '0.4.0', { 'checksums': ['37c082fa15ebae89db99d6071b2bb2cad6a97a0405e9b4ef77f62a8f6ad274c1'], }), - ('phytools', '1.2-0', { + ('phytools', '1.5-1', { 'checksums': ['bfe2aec6aae8235264c1494eee42be494fed81a676c6de9e39c57a6e3682b37d'], }), ('geiger', '2.0.10', { @@ -1237,7 +1237,7 @@ exts_list = [ ('TH.data', '1.1-1', { 'checksums': ['edf3ab16b142f4c52d21fc64e41409ed138e5b3e142f2fae964b00f02d53dd7a'], }), - ('multcomp', '1.4-20', { + ('multcomp', '1.4-22', { 'checksums': ['f03473b1cfbc714cd85a0ee948e2ecdb23bcdccbe95e27237ee25e9c71e3e557'], }), ('libcoin', '1.0-9', { @@ -1246,13 +1246,13 @@ exts_list = [ ('coin', '1.4-2', { 'checksums': ['7546d1f27a82d98b4b3e43e4659eba0f74a67d5919ce85d2fb360282ba3cfbb2'], }), - ('party', '1.3-11', { + ('party', '1.3-12', { 'checksums': ['e5892955f6ce662ade568e646d1d672c3ecbf5d4e74b4a887a353e6160f7b56a'], }), ('inum', '1.0-4', { 'checksums': ['5febef69c43a4b95b376c1418550a949d988a5f26b1383ca01c9728a94fc13ce'], }), - ('partykit', '1.2-16', { + ('partykit', '1.2-17', { 'checksums': ['e643d4e29c1894497e3dd5fe274783319d0044dec50282ed807cebc21736ddb2'], }), ('mboost', '2.9-7', { @@ -1273,19 +1273,19 @@ exts_list = [ ('polspline', '1.1.22', { 'checksums': ['6992484e9e41036debef1e705e26959f8f5c7a68d3e1fda58273d2a72297a1b5'], }), - ('rms', '6.4-1', { + ('rms', '6.5-0', { 'checksums': ['6c41eb670daf5e4391cc2f2a19e20a591f90769c124300a7ccf555820140d3f9'], }), ('RWekajars', '3.9.3-2', { 'checksums': ['16e6b019aab1646f89c5203f0d6fc1cb800129e5169b15aaef30fd6236f5da1a'], }), - ('RWeka', '0.4-44', { + ('RWeka', '0.4-45', { 'checksums': ['f3239437aeeb01453b7ce235f9680bc281886b46de0b536d9c8413c6294c7bc8'], }), ('slam', '0.1-50', { 'checksums': ['7899bf3266c204ecccefc1878f96940b117d4503af128f4fbc50fc409163f8bd'], }), - ('tm', '0.7-10', { + ('tm', '0.7-11', { 'checksums': ['b1eb1683d956db1a207b61cc086ae08b3ca7f46b6b8bc46d09ba5a4fafa66256'], }), ('leaps', '3.1', { @@ -1345,7 +1345,7 @@ exts_list = [ ('styler', '1.9.0', { 'checksums': ['3e49f3ac2e65f9bdab15837a4e629db35c8fd0a15a74daa057354ba01e3022ce'], }), - ('questionr', '0.7.7', { + ('questionr', '0.7.8', { 'checksums': ['ce24c40bd98dbeca615b9eb2a9cd2da26852821dc3840f8394eeecb0739dfd56'], }), ('klaR', '1.7-1', { @@ -1384,7 +1384,7 @@ exts_list = [ ('zip', '2.2.2', { 'checksums': ['9f95987c964039834f770ecda2d5f7e3d3a9de553c89db2a5926c4219bf4b9d8'], }), - ('openxlsx', '4.2.5.1', { + ('openxlsx', '4.2.5.2', { 'checksums': ['65d06d2819b656ac30fc78437ee712a83fb5a7ab750f56268e5c9e578c582519'], }), ('rematch', '1.0.1', { @@ -1393,7 +1393,7 @@ exts_list = [ ('cellranger', '1.1.0', { 'checksums': ['5d38f288c752bbb9cea6ff830b8388bdd65a8571fd82d8d96064586bd588cf99'], }), - ('readxl', '1.4.1', { + ('readxl', '1.4.2', { 'checksums': ['ab9239c249f79b649f7665a612b3dbf4b774ab633115e6dee41091a8cb2491f7'], }), ('rio', '0.5.29', { @@ -1405,7 +1405,7 @@ exts_list = [ ('flashClust', '1.01-2', { 'checksums': ['48a7849bb86530465ff3fbfac1c273f0df4b846e67d5eee87187d250c8bf9450'], }), - ('ggrepel', '0.9.2', { + ('ggrepel', '0.9.3', { 'checksums': ['29fb916d4799ba6503a5dd019717ffdf154d2aaae9ff1736f03e2be24af6bdfc'], }), ('DT', '0.27', { @@ -1432,7 +1432,7 @@ exts_list = [ ('fpc', '2.2-10', { 'checksums': ['29b0006e96c8645645d215d3378551bd6525aaf45abde2d9f12933cf6e75fa38'], }), - ('BiasedUrn', '2.0.8', { + ('BiasedUrn', '2.0.9', { 'checksums': ['2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e'], }), ('TeachingDemos', '2.12', { @@ -1486,10 +1486,10 @@ exts_list = [ ('uroot', '2.1-2', { 'checksums': ['bd7fd9e35928d09d0e8fae9e4359a2b2bca6e6865b278436319e2f91db0e4b37'], }), - ('forecast', '8.20', { + ('forecast', '8.21', { 'checksums': ['9f01eb895a883a7e1e23725b167b46edc1b0b152fd4120278aaa5f7b2621767f'], }), - ('fma', '2.4', { + ('fma', '2.5', { 'checksums': ['69a94c3bd464176a80232d49fcd04d478d4dd59f9bf128d6a9f46e49612d27f4'], }), ('expsmooth', '2.3', { @@ -1513,7 +1513,7 @@ exts_list = [ ('spatstat.data', '3.0-0', { 'checksums': ['d3943bb4f6509d60bf68e79ce4533c5ec5261f411da6b0ef5238c124fc37c3e5'], }), - ('spatstat.geom', '3.0-5', { + ('spatstat.geom', '3.0-6', { 'checksums': ['32b89a409ce87ffe901e4c8720a26cac9629f9816e163c4ad68b7aa012d69e67'], }), ('spatstat.sparse', '3.0-0', { @@ -1525,16 +1525,16 @@ exts_list = [ ('spatstat.core', '', { 'checksums': ['e38c39efe8b14d6e8fdbee8dd870b90c52f78ea571ab7988fd3685f48347d13b'], }), - ('spatstat.linnet', '3.0-3', { + ('spatstat.linnet', '3.0-6', { 'checksums': ['9c78a4b680debfff0f3ae934575c30d03ded49bc9a7179475384af0ebaf13778'], }), - ('spatstat', '3.0-2', { + ('spatstat', '3.0-3', { 'checksums': ['4ea0f8d70b926b92bf4a06521f985a0bb6d573619f5d526957c87860ccb999da'], }), ('pracma', '2.4.2', { 'checksums': ['2302d454406e72711714732658d0c59c9d5a1ead698f22ee23f38cba63d42764'], }), - ('RCurl', '1.98-1.9', { + ('RCurl', '1.98-1.10', { 'checksums': ['2ac22d0160633fe3b6b26f3eda5df839eee1120f0111e1172f0fc801f874188d'], }), ('bio3d', '2.4-4', { @@ -1612,7 +1612,7 @@ exts_list = [ ('roxygen2', '7.2.3', { 'checksums': ['2ebfcfd567b9db6c606c6d42be1645b4e987f987995a2ad8954fa963a519448b'], }), - ('git2r', '0.30.1', { + ('git2r', '0.31.0', { 'checksums': ['85d913ddc7659e32c1b98ebc247fa1cc1b7717a5bd413fa78ea84696986ca840'], }), ('rversions', '2.1.2', { @@ -1639,7 +1639,7 @@ exts_list = [ ('gitcreds', '0.1.2', { 'checksums': ['b14aaf4e910a9d2d6c65c93e645f0b0159c00898e669f917f83c03dfedb1dfea'], }), - ('gh', '1.3.1', { + ('gh', '1.4.0', { 'checksums': ['a44039054e8ca56496f2d9c7a10cdadf4a7383bc91086e768ba7e7f1fbcaed1c'], }), ('credentials', '1.3.2', { @@ -1732,7 +1732,7 @@ exts_list = [ ('pbivnorm', '0.6.0', { 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], }), - ('lavaan', '0.6-13', { + ('lavaan', '0.6-14', { 'checksums': ['2cc193b82463a865cd8dadb7332409fdebf47e4035d5fe8dbf3414a7ae18d308'], }), ('matrixcalc', '1.0-6', { @@ -1786,7 +1786,7 @@ exts_list = [ ('ggforce', '0.4.1', { 'checksums': ['2a283bb409da6b96929863a926b153bcc59b2c6f00551805db1d1d43e5929f2f'], }), - ('tidygraph', '1.2.2', { + ('tidygraph', '1.2.3', { 'checksums': ['2fbdc2db18c5ad48c72f14d2d04111f4b0d4c434ad87c280eda3bcb98673ad36'], }), ('ggraph', '2.1.0', { @@ -1817,7 +1817,7 @@ exts_list = [ ('pim', '2.0.2', { 'checksums': ['1195dbdbd67348dfef4b6fc34fcec643da685ebe58d34bbe049ab121aca9944f'], }), - ('minpack.lm', '1.2-2', { + ('minpack.lm', '1.2-3', { 'checksums': ['c70956122528575433c57a5669e26f4f9b1e160b004f135a38658c2c2634df87'], }), ('rootSolve', '1.8.2.3', { @@ -1838,7 +1838,7 @@ exts_list = [ ('readbitmap', '0.1.5', { 'checksums': ['737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291'], }), - ('imager', '0.42.16', { + ('imager', '0.42.18', { 'checksums': ['d90a9893d11190ba249c7fae5bd6517a77907efbce2941452cb2aec57bb5cf7f'], }), ('signal', '0.7-7', { @@ -1886,7 +1886,7 @@ exts_list = [ ('pinfsc50', '1.2.0', { 'checksums': ['ed1fe214b9261feef8abfbf724c2bd9070d68e99a6ea95208aff2c57bbef8794'], }), - ('vcfR', '1.13.0', { + ('vcfR', '1.14.0', { 'checksums': ['dd87ff010365de363864a44ca49887c0fdad0dd18d0d9c66e44e39c2d4581d52'], }), ('glmmML', '1.1.4', { @@ -1982,13 +1982,13 @@ exts_list = [ ('dendextend', '1.16.0', { 'checksums': ['4ba3885b66694589d455ffef31c218fe653fa25aff3efb7e8db6c25008d2921b'], }), - ('RInside', '0.2.17', { + ('RInside', '0.2.18', { 'checksums': ['0be28c44ee34cba669a7264d2b99c289230645598ca78e21682559dc31824348'], }), ('limSolve', '1.5.6', { 'checksums': ['b97ea9930383634c8112cdbc42f71c4e93fe0e7bfaa8f401921835cb44cb49a0'], }), - ('dbplyr', '2.3.0', { + ('dbplyr', '2.3.1', { 'checksums': ['4a6e092c9349f8b3030c752f8c6cc551637d6fbca3c84be0da89968f1e9adce1'], }), ('modelr', '0.1.10', { @@ -2006,10 +2006,10 @@ exts_list = [ ('rvest', '1.0.3', { 'checksums': ['89bb477e0944c80298a52ccf650db8f6377fd7ed3c1bc7034d000f695fdf05a4'], }), - ('dtplyr', '1.2.2', { + ('dtplyr', '1.3.0', { 'checksums': ['2640e9cde4eaa06f02cff29e3f2b99fdd08488df07ea2e6629b2ed6a8285d0f3'], }), - ('gargle', '1.2.1', { + ('gargle', '1.3.0', { 'checksums': ['4d46ca2933f19429ca5a2cfe47b4130a75c7cd9931c7758ade55bac0c091d73b'], }), ('googledrive', '2.0.0', { @@ -2021,7 +2021,7 @@ exts_list = [ ('googlesheets4', '1.0.1', { 'checksums': ['0a107d76aac99d6db48d97ce55810c1412b2197f457b8476f676169a36c7cc7a'], }), - ('tidyverse', '1.3.2', { + ('tidyverse', '2.0.0', { 'checksums': ['83cf95109d4606236274f5a8ec2693855bf75d3a1b3bc1ab4426dcc275ed6632'], }), ('R.rsp', '0.45.0', { @@ -2063,7 +2063,7 @@ exts_list = [ ('glmmTMB', '1.1.5', { 'checksums': ['b9d1e97587b213e52ff304f62480ddee77c658f29a7e99334a4032d0df60b275'], }), - ('gmp', '0.6-10', { + ('gmp', '0.7-1', { 'checksums': ['8ae76f3d17542eab3e7468341dabeebe28b11da8c1b4b3f7bbdb00d379689e52'], }), ('ROI', '1.0-0', { @@ -2084,13 +2084,13 @@ exts_list = [ ('DHARMa', '0.4.6', { 'checksums': ['0fcd41099ababedff010d8fe05f8efa630cceb829dbb87af8b8d650ad49d88bf'], }), - ('mvnfast', '0.2.7', { + ('mvnfast', '0.2.8', { 'checksums': ['b67d50936c9a466977669ef6bb7b23df8e7c90a820ac916328c20e41ef8e0b72'], }), ('bridgesampling', '1.1-2', { 'checksums': ['54ecd39aa2e36d4d521d3d36425f9fe56a3f8547df6048c814c5931d790f3e6b'], }), - ('BayesianTools', '', { + ('BayesianTools', '0.1.8', { 'checksums': ['af49389bdeb794da3c39e1d63f59e6219438ecb8613c5ef523b00c6fed5a600c'], }), ('gomms', '1.0', { @@ -2141,10 +2141,10 @@ exts_list = [ ('Matching', '4.10-8', { 'checksums': ['1e75dc61553c1687b2b520dc52688409c2e84285e4b6c16c94d8d85fd5ccece0'], }), - ('MatchIt', '4.5.0', { + ('MatchIt', '4.5.1', { 'checksums': ['e79a96e7972097829a839c855c0bc97638eeae4b148e01340dfa5296323e6c06'], }), - ('RItools', '0.3-1', { + ('RItools', '0.3-2', { 'checksums': ['714685d8e04acafe5d5ddf93edac69afec0c62045a7b93478734771b6a0fa928'], }), ('mitools', '2.4', { @@ -2153,10 +2153,10 @@ exts_list = [ ('survey', '4.1-1', { 'checksums': ['05e89a1678a39e32bfb41af8a31d643b04fc4d2660a96e701825e6bffcd75a52'], }), - ('rlemon', '0.2.0', { + ('rlemon', '0.2.1', { 'checksums': ['e06792875f05a0c6cd637b7bf16bd51c3891e0df6bad78ffba0ee195abe8d3a0'], }), - ('optmatch', '0.10.5', { + ('optmatch', '0.10.6', { 'checksums': ['ed09be71b0e293273412d4a181c1f085ad93f4038996dc7c90beae8466574aeb'], }), ('SPAtest', '3.1.2', { @@ -2216,10 +2216,10 @@ exts_list = [ ('here', '1.0.1', { 'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'], }), - ('RcppTOML', '0.2.0', { + ('RcppTOML', '0.2.2', { 'checksums': ['2f09f00cbee6c6eeff5d5f0195c10de0155496de15fbe8189c18627ee3090541'], }), - ('reticulate', '1.27', { + ('reticulate', '1.28', { 'checksums': ['2125af9e75939c3b7c0dc74f28f42606e816d63aa1143baf631c318ff5ff3a2c'], }), ('hdf5r', '1.3.8', { @@ -2230,7 +2230,7 @@ exts_list = [ ('DTRreg', '1.7', { 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], }), - ('pulsar', '', { + ('pulsar', '0.3.10', { 'checksums': ['78c9f7e3b2bf8a8d16a81d6ee43bb05b0c360219be473d920c8c8ccb2aba4e3d'], }), ('bayesm', '3.1-5', { @@ -2242,7 +2242,7 @@ exts_list = [ ('energy', '1.7-11', { 'checksums': ['543de4875c46cc90e711e71c45b082d962fbb5158a094f9f10d37d3f57e1bea7'], }), - ('compositions', '2.0-4', { + ('compositions', '2.0-5', { 'checksums': ['7b9c7a3bf654fb02d9eb1b4a7566469b2f5232f3b2c1b324c02239fd31060faf'], }), ('clustree', '0.5.0', { @@ -2272,10 +2272,10 @@ exts_list = [ ('lpSolveAPI', '5.5.2.0-17.9', { 'checksums': ['9ebc8e45ad73eb51e0b25049598a5bc758370cf89508e2328cf4bd93d68d55bb'], }), - ('ergm', '4.3.2', { + ('ergm', '4.4.0', { 'checksums': ['ced92b0a32c78c85546d665c32fb3993fe77a3809aa88f43c3eee39e2577f2f0'], }), - ('networkDynamic', '0.11.2', { + ('networkDynamic', '0.11.3', { 'checksums': ['beefaf50eb8609528358b75f5814a8f1cdc4d2db8059b99be69919da2bc02beb'], }), ('tergm', '4.1.1', { @@ -2333,7 +2333,7 @@ exts_list = [ ('mltools', '0.3.5', { 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], }), - ('h2o', '3.38.0.1', { + ('h2o', '3.40.0.1', { 'checksums': ['d470dc71e637d589bf228e59ddb021ade240d74536323d8ca77ac1fb334d3535'], }), ('mlegp', '3.1.9', { @@ -2348,7 +2348,7 @@ exts_list = [ ('bartMachineJARs', '1.2.1', { 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], }), - ('bartMachine', '1.3.3', { + ('bartMachine', '1.3.3.1', { 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], }), ('lqa', '', { @@ -2360,7 +2360,7 @@ exts_list = [ ('GUTS', '1.2.3', { 'checksums': ['40061ec1677def40b410b5ef90d01e0bcb0095abed1545513a33a01d4444adc2'], }), - ('GenSA', '1.1.7', { + ('GenSA', '1.1.8', { 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], }), ('parsedate', '1.3.1', { @@ -2417,7 +2417,7 @@ exts_list = [ ('bacr', '1.0.1', { 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], }), - ('clue', '0.3-63', { + ('clue', '0.3-64', { 'checksums': ['71311b16ce380fd9a8834be95b55b3d1b47e4ee2b8acb35b8d481138c314dc31'], }), ('bdsmatrix', '1.3-6', { @@ -2438,7 +2438,7 @@ exts_list = [ ('LaplacesDemon', '16.1.6', { 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], }), - ('rda', '', { + ('rda', '1.2-1', { 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), @@ -2529,7 +2529,7 @@ exts_list = [ ('loo', '2.5.1', { 'checksums': ['866a2f54a4e8726cc3062e27daa8a073e6ac4aeb6719af7845284f7a668745f1'], }), - ('RcppParallel', '5.1.6', { + ('RcppParallel', '5.1.7', { 'checksums': ['6396322b3b6d6f7019aac808ceb74707bc5c4ed01677fab408372c2a5508c2ea'], }), ('StanHeaders', '2.21.0-7', { @@ -2564,13 +2564,13 @@ exts_list = [ ('corrplot', '0.92', { 'checksums': ['e8c09f963f9c4837036c439ebfe00fa3a6e462ccbb786d2cf90850ddcd9428bd'], }), - ('rstatix', '0.7.1', { + ('rstatix', '0.7.2', { 'checksums': ['a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c'], }), ('ggfan', '0.1.3', { 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], }), - ('ggpubr', '0.5.0', { + ('ggpubr', '0.6.0', { 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], }), ('yaImpute', '1.0-33', { @@ -2588,7 +2588,7 @@ exts_list = [ ('sctransform', '0.3.5', { 'checksums': ['83af125c40f211e1ddae5098f88766aea1453c02ae98486081f3efadb3620b2b'], }), - ('packrat', '0.9.0', { + ('packrat', '0.9.1', { 'checksums': ['3025b9052974bec00fb09299226b80004d48e611e15a65e5a0bc49d3538844ef'], }), ('colourpicker', '1.2.0', { @@ -2600,7 +2600,7 @@ exts_list = [ ('findpython', '1.0.7', { 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], }), - ('argparse', '2.2.1', { + ('argparse', '2.2.2', { 'checksums': ['83e112beb47733849980b286d93ac930f0cbe6ac78fcb94fc9f6b0eea882658d'], }), ('intergraph', '2.0-2', { @@ -2618,7 +2618,7 @@ exts_list = [ ('distributional', '0.3.1', { 'checksums': ['fab36c7346617d8f2ca4b3cd0e3c9da93cb2f95fb7f102a3ae88670e694751d6'], }), - ('posterior', '1.3.1', { + ('posterior', '1.4.0', { 'checksums': ['d615ed75b43b2927002b79d2982c624a6144c851aac7b81fa14e4ec9cc3d353b'], }), ('bayesplot', '1.10.0', { @@ -2639,7 +2639,7 @@ exts_list = [ ('gamm4', '0.2-6', { 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], }), - ('projpred', '2.3.0', { + ('projpred', '2.4.0', { 'checksums': ['a88a651e533c118aad0e8c2c905cfcf688d9c419ed195896036b8f6667b5cfb0'], }), ('brms', '2.18.0', { @@ -2663,7 +2663,7 @@ exts_list = [ ('ngspatial', '1.2-2', { 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], }), - ('BIGL', '1.6.6', { + ('BIGL', '1.6.7', { 'checksums': ['8edb6607c5d91cea5ba32290eeb76c35317383a24d726bde6eca61f9cce96bb9'], }), ('drugCombo', '', { @@ -2738,7 +2738,7 @@ exts_list = [ ('plotmo', '3.6.2', { 'checksums': ['cde33a8ec558b12d8e11d7d0531e73f6678a25ee589b79897d2fc425a3fd353c'], }), - ('earth', '5.3.1', { + ('earth', '5.3.2', { 'checksums': ['0bbe06ba974ceb8ec5de1d59cb53f9487d1828d7130fe2503c48b6cb449c4b03'], }), ('mda', '0.5-3', { @@ -2903,7 +2903,7 @@ exts_list = [ ('gld', '2.6.6', { 'checksums': ['0db6daee1b6e256d64d292c1f6795c505677331dcf2f97e04e264566ded93323'], }), - ('DescTools', '0.99.47', { + ('DescTools', '0.99.48', { 'checksums': ['8dfe7057fdcec475bc444761b00db59f6fb7313fd39c7bd6aebeca7f67aceb05'], }), ('orthopolynom', '1.0-6.1', { @@ -2936,7 +2936,7 @@ exts_list = [ ('nonnest2', '0.5-5', { 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], }), - ('blavaan', '0.4-3', { + ('blavaan', '0.4-6', { 'checksums': ['a9f9f7b32aab7e7f179340c9f0f9d154b5fac51352c4fd590d317c201fe81b74'], }), ('mathjaxr', '1.6-0', { @@ -2981,7 +2981,7 @@ exts_list = [ ('miceadds', '3.16-18', { 'checksums': ['74ab5503d6f3c0d016166a4c664918d60f1adb0672d8aefbc57385be3d287c3a'], }), - ('visdat', '0.5.3', { + ('visdat', '0.6.0', { 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], }), ('UpSetR', '1.4.0', { @@ -2990,7 +2990,7 @@ exts_list = [ ('norm', '1.0-10.0', { 'checksums': ['4384791af74c1008238f036abe0dda4b4048b9700cc4acd7b45025598fd20cc7'], }), - ('naniar', '0.6.1', { + ('naniar', '1.0.0', { 'checksums': ['d546ca15bf6c224f3103eb1441abef91d34feebb7320c2398d598f5d50177450'], }), ('stringdist', '0.9.10', { @@ -3091,7 +3091,7 @@ exts_list = [ ('finalfit', '1.0.6', { 'checksums': ['446940d300c8b725e798bf2a2829a41165d25a939d2c59425768234438a2deb1'], }), - ('broom.helpers', '1.11.0', { + ('broom.helpers', '1.12.0', { 'checksums': ['2b7087ca73af04a130e78dfbf4941590e3557bcce4ec7e0106b012df061581f5'], }), ('gt', '0.8.0', { @@ -3121,7 +3121,7 @@ exts_list = [ ('jsonify', '1.2.2', { 'checksums': ['929191ab32e34af6a02ad991e29314cc78ea40763fcf232388ef2d132137fbce'], }), - ('geometries', '0.2.0', { + ('geometries', '0.2.2', { 'checksums': ['8cf5094f3c2458fef5d755799c766afd27c66cd1c292574a6ab532d608360314'], }), ('sfheaders', '0.4.0', { @@ -3151,7 +3151,7 @@ exts_list = [ ('tmap', '3.3-3', { 'checksums': ['60e58eef0f8c723db855d59117ca9f9b5e3663ba34b5ca783dc889bf20285e04'], }), - ('collapse', '1.9.2', { + ('collapse', '1.9.3', { 'checksums': ['9c13f4322d496702255652c9467fc2a202bfdb36cee6d78791780b7ab988f3ef'], }), ('genoPlotR', '0.8.11', { @@ -3160,7 +3160,7 @@ exts_list = [ ('VineCopula', '2.4.5', { 'checksums': ['8449b1181fd7f325a2f0539cdaa4a4ff895c41424f462f52258729436078c90a'], }), - ('Rmpfr', '0.9-0', { + ('Rmpfr', '0.9-1', { 'checksums': ['cfee5ab47d49c6433c372a267f7d849c8f7c61a84e00d08afb047eaafcdbbc8a'], }), ('scam', '1.2-13', { @@ -3184,7 +3184,7 @@ exts_list = [ ('rngWELL', '0.10-9', { 'checksums': ['0c00c54e69d7d552cfa08d766e4854c01c6c1c8e2c558f387760b91a55ef2d38'], }), - ('randtoolbox', '2.0.3', { + ('randtoolbox', '2.0.4', { 'checksums': ['c4f28963fe5dbc821427691527a204aa6e08ab40bf00337f220cc60b81d552dc'], }), ('kde1d', '1.0.5', { @@ -3196,7 +3196,7 @@ exts_list = [ ('wdm', '0.2.3', { 'checksums': ['5f0184f6f0f9e9b8c47fb571e4d34dff309644a50afe5f18e42b9c37f52c593b'], }), - ('rvinecopulib', '0.6.2.1.3', { + ('rvinecopulib', '0.6.3.1.1', { 'checksums': ['212189441b4cd2383e485c2aa410837456ba70357834f443c9275e4775b8bf22'], }), ('PearsonDS', '1.2.3', { @@ -3214,7 +3214,7 @@ exts_list = [ ('dcurver', '0.9.2', { 'checksums': ['cc6c55090d3607910515981ea0c7221e40e7a29e0da0c5a5f42c3847012290ec'], }), - ('mirt', '1.37.1', { + ('mirt', '1.38.1', { 'checksums': ['5215a0f4eb5949a3985a84a7d4776d4dd7471973a980c1d158ce82b3bde185bb'], }), ('rpf', '1.0.11', { @@ -3229,7 +3229,7 @@ exts_list = [ ('FactorCopula', '0.9.2', { 'checksums': ['d95b0ccd1b0eebcf27a90286e9392f662b878a669c693fbbb4145798045134ff'], }), - ('rpact', '3.3.2', { + ('rpact', '3.3.4', { 'checksums': ['a568bb04b4dcecf163024269042124a4d75c5431edbf06776515aa524506f11c'], }), ('ldbounds', '2.0.0', { @@ -3274,13 +3274,13 @@ exts_list = [ ('gdalUtils', '', { 'checksums': ['4c6faabee2db8a87b7ea0f8e67e9fce3c5db7f4be353d7d86ea559507cbb2a4f'], }), - ('openair', '2.13', { + ('openair', '2.15', { 'checksums': ['1acdeafa1b96bbcb13c73f2ef965efb635e6306678cc22468d383c4bb5098a92'], }), ('pdp', '0.8.1', { 'checksums': ['e23db66e5d575337d5c8fd664ccd0548cc85da2aca6613d90ce187be1dca376c'], }), - ('date', '1.2-41', { + ('date', '1.2-42', { 'checksums': ['b5b1935638b73373809c009f94b77f993cd301744488d9bdf71ef79c82099757'], }), ('cmprsk', '2.2-11', { @@ -3331,7 +3331,7 @@ exts_list = [ ('MonteCarlo', '1.0.6', { 'checksums': ['f21aecfba957bbea9576b09f75b1f7c7621637a04532a8fed2c6bb8ffc1a98cb'], }), - ('RhpcBLASctl', '0.21-247.1', { + ('RhpcBLASctl', '0.23-42', { 'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'], }), ('chkptstanr', '0.1.1', { From e306f64ffcf8b940575f4f6d1e6133ebdf7465b8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 28 Feb 2023 16:20:17 +0000 Subject: [PATCH 6716/9987] undo accidental changes --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index f339ba1d10f..6859ac2f837 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -1,5 +1,5 @@ name = 'R' -version = '4.2.1' +version = '4.2.2' homepage = 'https://www.r-project.org/' description = """R is a free software environment for statistical computing @@ -46,7 +46,7 @@ dependencies = [ ('ImageMagick', '7.1.0-53'), # for animation ('GLPK', '5.0'), # for Rglpk ('nodejs', '18.12.1'), # for V8 (required by rstan) - ('GDAL', '3.5.0'), # for sf + ('GDAL', '3.6.2'), # for sf ('MPFR', '4.2.0'), # for Rmpfr ('libgit2', '1.5.0'), ('OpenSSL', '1.1', '', SYSTEM), From 8a8a6c905dfd9d0552fe8e4ec483c8cd11ed68b6 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 28 Feb 2023 16:29:33 +0000 Subject: [PATCH 6717/9987] add ggvenn, scatterpie, shadowtext extensions added in PRs 17043, 17125 --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 6859ac2f837..d52b0ff3bf9 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3394,6 +3394,15 @@ exts_list = [ ('tidytree', '0.4.2', { 'checksums': ['fbc4364d17e1b1c26ed06af0cdf36c88a5bc562fdbd4731ab179e30bba4009eb'], }), + ('ggvenn', '0.1.9', { + 'checksums': ['38779cfa4e01e07d4a42453cfb8b93d32d2acd6187676bae7d11b2168714a52e'], + }), + ('scatterpie', '0.1.8', { + 'checksums': ['a6ccc63a8be63fa113704cf5d4893c1ec1b75d3081ab971bd70e650e708872a0'], + }), + ('shadowtext', '0.1.2', { + 'checksums': ['253c4e737dbb302aa0729e5074e84cbfde2a73bfd7a0fd2c74b557cb728bae7d'], + }), ] moduleclass = 'lang' From 89ea53b52eac1aa97de84f5e5594a18c7e95cac9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2023 17:50:24 +0100 Subject: [PATCH 6718/9987] adding easyconfigs: preseq-3.2.0-GCC-11.3.0.eb --- .../p/preseq/preseq-3.2.0-GCC-11.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/preseq/preseq-3.2.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/preseq/preseq-3.2.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/preseq/preseq-3.2.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..85b102d3291 --- /dev/null +++ b/easybuild/easyconfigs/p/preseq/preseq-3.2.0-GCC-11.3.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'ConfigureMake' + +name = 'preseq' +version = '3.2.0' + +homepage = 'https://smithlabresearch.org/software/preseq' +description = "Software for predicting library complexity and genome coverage in high-throughput sequencing." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/smithlabcode/preseq/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['95b81c9054e0d651de398585c7e96b807ad98f0bdc541b3e46665febbe2134d9'] + +dependencies = [ + ('GSL', '2.7'), + ('HTSlib', '1.15.1'), + ('zlib', '1.2.12'), +] + +configopts = '--enable-hts CPPFLAGS="-I$EBROOTHTSLIB/include" LDFLAGS="-L$EBROOTHTSLIB/lib"' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['preseq', 'to-mr']], + 'dirs': [], +} + +sanity_check_commands = ['preseq'] + +moduleclass = 'bio' From 7e93bfc209d1b37373a46987e44ec8f556b74589 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2023 17:56:27 +0100 Subject: [PATCH 6719/9987] {math}[intel/2022a] sympy v1.11.1, gmpy2 v2.1.5 w/ Python 3.10.4 --- .../gmpy2-2.1.5-intel-compilers-2022.1.0.eb | 25 +++++++++++++ .../s/sympy/sympy-1.11.1-intel-2022a.eb | 37 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-intel-compilers-2022.1.0.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-intel-compilers-2022.1.0.eb new file mode 100644 index 00000000000..1a86a047783 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-intel-compilers-2022.1.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.5' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['bc297f1fd8c377ae67a4f493fc0f926e5d1b157e5c342e30a4d84dc7b9f95d96'] + +dependencies = [ + ('Python', '3.10.4'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb new file mode 100644 index 00000000000..5742b71068f --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.11.1' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e32380dce63cb7c0108ed525570092fd45168bdae2faa17e528221ef72e88658'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('gmpy2', '2.1.5'), +] + +download_dep_fail = True +use_pip = True + +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +sanity_check_commands = ["isympy --help"] + +moduleclass = 'math' From fcb5e3b72c7138b9dbe60e00d857af274d3794e4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 28 Feb 2023 17:18:49 +0000 Subject: [PATCH 6720/9987] Minor layout fixes --- .../easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb index 2abb857d455..00774835146 100644 --- a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb @@ -40,11 +40,13 @@ sanity_check_paths = { 'files': ['bin/rivet-config', 'lib/libRivet.%s' % SHLIB_EXT], 'dirs': ['share/Rivet', 'lib/Rivet'] } + sanity_check_commands = ["python -c 'import rivet'"] modloadmsg = """ To use your own analysis you must append the path to `RIVET_ANALYSIS_PATH`. """ + modextrapaths = { 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', # 'RIVET_ANALYSIS_PATH': '/path/to/share/Rivet/', # please adapt for system-wided shared non-default analysis From c39c332d177198c2893eecac1031985cf624ff36 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 28 Feb 2023 17:39:55 +0000 Subject: [PATCH 6721/9987] Typo fix --- .../easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb index 00774835146..530bb5151e9 100644 --- a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb @@ -49,7 +49,7 @@ To use your own analysis you must append the path to `RIVET_ANALYSIS_PATH`. modextrapaths = { 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - # 'RIVET_ANALYSIS_PATH': '/path/to/share/Rivet/', # please adapt for system-wided shared non-default analysis + # 'RIVET_ANALYSIS_PATH': '/path/to/share/Rivet/', # please adapt for system-wide shared non-default analysis } moduleclass = 'phys' From dbafb2ec0779cd96af3fbf8099a3004fdf516b54 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 Feb 2023 19:36:23 +0100 Subject: [PATCH 6722/9987] stick to gmpy2 2.1.2 as dependency for sympy 1.11.1 with intel/2022a --- ...rs-2022.1.0.eb => gmpy2-2.1.2-intel-compilers-2022.1.0.eb} | 4 ++-- easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/gmpy2/{gmpy2-2.1.5-intel-compilers-2022.1.0.eb => gmpy2-2.1.2-intel-compilers-2022.1.0.eb} (82%) diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2022.1.0.eb similarity index 82% rename from easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-intel-compilers-2022.1.0.eb rename to easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2022.1.0.eb index 1a86a047783..9223b7f00cd 100644 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2022.1.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'gmpy2' -version = '2.1.5' +version = '2.1.2' homepage = 'https://github.com/aleaxit/gmpy' description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" @@ -9,7 +9,7 @@ description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} sources = [SOURCE_TAR_GZ] -checksums = ['bc297f1fd8c377ae67a4f493fc0f926e5d1b157e5c342e30a4d84dc7b9f95d96'] +checksums = ['da75140bca128ece795895477e53b43773e3748aa90ba6170eae7ca2c74b82d1'] dependencies = [ ('Python', '3.10.4'), diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb index 5742b71068f..38b1a2916d3 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb @@ -17,7 +17,7 @@ checksums = ['e32380dce63cb7c0108ed525570092fd45168bdae2faa17e528221ef72e88658'] dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('gmpy2', '2.1.5'), + ('gmpy2', '2.1.2'), ] download_dep_fail = True From 041d5a37f6b33cb60fe4bdfb283861e3a74ea33e Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 28 Feb 2023 19:48:33 +0000 Subject: [PATCH 6723/9987] fix archived packages --- .../easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 1063 ++++++++--------- 1 file changed, 524 insertions(+), 539 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index d52b0ff3bf9..162e5680f17 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -9,7 +9,7 @@ toolchain = {'name': 'foss', 'version': '2022b'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f'] +checksums = ['0ff62b42ec51afa5713caee7c4fde7a0c45940ba39bef8c5c9487fef0c953df5'] builddependencies = [ ('pkgconf', '1.9.3'), @@ -77,9 +77,6 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 23rd June 2022 exts_list = [ - # include packages that are part of the base installation of R, - # both to make sure they are available (via sanity check), - # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets', @@ -94,41 +91,38 @@ exts_list = [ 'tcltk', 'tools', 'utils', - ('Rmpi', '0.6-9.2', { - 'checksums': ['358ac1af97402e676f209261a231f36a35e60f0301edf8ca53dac11af3c3bd1a'], - }), ('abind', '1.4-5', { 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], }), ('magic', '1.6-1', { - 'checksums': ['4516d48c9618e3f395db873e886f5deb3b66b32ebe10d4c26c1420ac848acbbf'], + 'checksums': ['ca79ec7ae92b736cb128556c081abf547f49956c326e053a76579889cbcb7976'], }), ('Rcpp', '1.0.10', { - 'checksums': ['9da5b84cdaf56e972b41e669d496b1ece2e91bcd435505c68b9f2bd98375f8bf'], + 'checksums': ['1e65e24a9981251ab5fc4f9fd65fe4eab4ba0255be3400a8c5abe20b62b5d546'], }), ('RcppProgress', '0.4.2', { 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], }), ('lpSolve', '5.6.18', { - 'checksums': ['4627be4178abad34fc85a7d264c2eb5e27506f007e46687b0b8a4f8fbdf4f3ba'], + 'checksums': ['751e1926fcd81b852b6c0d5ea7ecd9311ef6fbdbce9143b7872fea79590de712'], }), ('linprog', '0.9-4', { 'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'], }), ('geometry', '0.4.7', { - 'checksums': ['910465a8c8043faca73bcc7c81c9249b9938677ee6649468003b438a6503f5d8'], + 'checksums': ['96204205f51b4d63c2e7a7b00365def27d131f3c9ec66db56b510046e5d2013b'], }), ('bit', '4.0.5', { - 'checksums': ['e404841fbe4ebefe4ecd4392effe673a8c9fa05f97952c4ce6e2f6159bd2f168'], + 'checksums': ['f0f2536a8874b6a30b80baefbc68cb21f0ffbf51f3877bda8038c3f9f354bfbc'], }), ('filehash', '2.4-5', { - 'checksums': ['f394e2c93233e8ad1c104562ea9349855dc8e303131f559cd59834f9aa3e41bd'], + 'checksums': ['3b1ee2794dd61e525ee44db16611c65957691d77bb26ae481eba988bb55da22c'], }), ('ff', '4.0.9', { - 'checksums': ['0a47333d31c7afc3f95387166e21a3e4c763cbef47d9b5927753aef4ff8d83fa'], + 'checksums': ['722053271987a0c9673c3ff9e7968bbab47979d529a2fe6bb1a3179408ee3c4f'], }), ('bnlearn', '4.8.1', { - 'checksums': ['243930daa7f71c63fe1aa6717e5d55a116a597b83e08745cbcbe9a418d7c1509'], + 'checksums': ['623c1bf0b3a38ee2060908c3197b763339115246dd72fb063f9476c7a54cd3ac'], }), ('bootstrap', '2019.6', { 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], @@ -137,16 +131,16 @@ exts_list = [ 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], }), ('deal', '1.2-42', { - 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + 'checksums': ['a17f452a94fc3964c939c5b147ad6d4f326a0990493519d376d6700cf733a134'], }), ('fdrtool', '1.2.17', { 'checksums': ['3452601adbead9be4820794e3af2666f710fdf9b801186df565b80b43629c5dd'], }), ('formatR', '1.14', { - 'checksums': ['8b52efbf43cbef25d837bb99a793a590c0958b753052c032b52304724e808c8b'], + 'checksums': ['4ebaab2c3f8527871655246b62abd060bc75dae1cec7f962ca4752b8080f474c'], }), ('gtools', '3.9.4', { - 'checksums': ['352086375d06cc55becfe8b8d65953645249661a44881cad83c7f79d7280d843'], + 'checksums': ['59cf8b194fe98b1cc05dbb4d686810a1068f59d8b402b731548a898ece85f111'], }), ('gdata', '2.18.0.1', { 'checksums': ['5e2f3d5b9398d52a4c07a4d35f5f936450a44567c7db8d8f68b4cc6946e032d9'], @@ -155,10 +149,10 @@ exts_list = [ 'checksums': ['177d6059fc645d3d8883806d2dea1c5dfc68efdada9aadde8a96b6d57acf35b8'], }), ('xfun', '0.37', { - 'checksums': ['d169f3e682dab0c3f2ca381f2dba9b7014a5e2ca3d6863dbae3d1bca699ef235'], + 'checksums': ['3b619ff0b2aea36a1d422d1f7ca2e5cef0102e1d127c94c87acf5e6e8358e1f9'], }), ('highr', '0.10', { - 'checksums': ['beff11390d936c90fdcc00e7ed0eb72220f3de403a51b56659e3d3e0b6d8ed4d'], + 'checksums': ['ec55bc1ff66390ed66806dc2a7b6c17dbfd089b3d73fe2e369017f8cb4bc347b'], }), ('infotheo', '1.2.0.1', { 'checksums': ['c0fb8ec97ad3a49f231c4c993b5eee70c6a61c8c30dc4a46197867e4763a29d4'], @@ -167,16 +161,16 @@ exts_list = [ 'checksums': ['c69e6a8da6a3344c0915dd1fd4c78fec5cdf50c62cf6297476e9bb7dc10b549d'], }), ('lazy', '1.2-18', { - 'checksums': ['27bf1216ac6220712fe7e86c0a288b7d7118f9088989f67e0a86b3d0f99c3370'], + 'checksums': ['99441bcae2dfbf450eee91f3ec969d416c225f671ac54459c50536916890f00a'], }), ('kernlab', '0.9-32', { - 'checksums': ['7359c665c1c5e6780e1ce44b143347c8eec839301c3079d7f19e29159873278a'], + 'checksums': ['654ef34e343deb4d2c4c139a44e5397d6e38876088ce1c53c7deb087935d6fdc'], }), ('mime', '0.12', { 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], }), ('markdown', '1.5', { - 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + 'checksums': ['001503f95fa59b399c0fc9178b0a4f5ab745f38879d38985c6642e944c2e9816'], }), ('mlbench', '2.1-3', { 'checksums': ['b1f92be633243185ab86e880a1e1ac5a4dd3c535d01ebd187a4872d0a8c6f194'], @@ -185,7 +179,7 @@ exts_list = [ 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], }), ('mclust', '6.0.0', { - 'checksums': ['2a1bbbf3c4a17df08d1ba8bc4d3c6d9c7241ed5fd68b8aabe660115597b60672'], + 'checksums': ['de7c306ecba1ef0f4e4a56c748ce08149417496b711beefb032d561a4c28122a'], }), ('RANN', '2.6.1', { 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], @@ -194,16 +188,16 @@ exts_list = [ 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], }), ('MASS', '7.3-58.2', { - 'checksums': ['bd8b880105bc1aadb2db699086f74bd92a8611287979a24243187f9d80795a8d'], + 'checksums': ['b5c09d5368ca432bb21ebb4997433dbefb28e19174851e2d8358bab02add784b'], }), ('lattice', '0.20-45', { 'checksums': ['22388d92bdb7d3959da84d7308d9026dd8226ef07580783729e8ad2f7d7507ad'], }), ('nlme', '3.1-162', { - 'checksums': ['a55bb401c2ba2706763d1f40283780699eb812b0d090b3d1903fae8aa956bf23'], + 'checksums': ['ba6da2575554afa2614c4cba9971f8a9f8a07622d201284cb78899f3d6a2dc67'], }), ('segmented', '1.6-2', { - 'checksums': ['6baf7f0a4f5d37b945312d28fcbca47cc3c171d097c43a28cf7ffc998a4ce569'], + 'checksums': ['413c2c07e87ca72c8b3fba61a1a7c606480786025544d5530f7c4406e7643b52'], }), ('som', '0.3-5.1', { 'checksums': ['a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9'], @@ -215,13 +209,13 @@ exts_list = [ 'checksums': ['06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69'], }), ('survivalROC', '1.0.3.1', { - 'checksums': ['1449e7038e048e6ad4d3f7767983c0873c9c7a7637ffa03a4cc7f0e25c31cd72'], + 'checksums': ['8174afebaf239dfda979c8c7e1e219624576d577c983ae787fbd2785b4ccd15c'], }), ('pspline', '1.0-19', { 'checksums': ['ba55bf193f1df9785a0e13b7ef727d5fd2415b318cd6a26b48a2db490c4dfe40'], }), ('timeDate', '4022.108', { - 'checksums': ['377cba03cddab8c6992e31d0683c1db3a73afa9834eee3e95b3b0723f02d7473'], + 'checksums': ['a5949b4fe2f6bdff751fc0793df8e3150cc25c078d48a28c066c10a6c4bfceef'], }), ('longmemo', '1.1-2', { 'checksums': ['7964e982287427dd58f98e1144e468ae0cbd572d25a4bea6ca9ae9c7522f3207'], @@ -233,34 +227,34 @@ exts_list = [ 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], }), ('sp', '1.6-0', { - 'checksums': ['939a06adf78ec8de7a663d6ca5bba426780852b357773446b00cc298200ff81c'], + 'checksums': ['f5977fbe80e7dee8e95d41fe0ef9d87c2c984422bb529ea5211fd38a13f9fcda'], }), ('pkgconfig', '2.0.3', { 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], }), ('rlang', '1.0.6', { - 'checksums': ['8de87c3e6fb0b3cce2dabc6908186f8e1528cc0c16b54de965fe02d405fdd7cc'], + 'checksums': ['e6973d98a0ea301c0da1eeaa435e9e65d1c3f0b95ed68bdc2d6cb0c610166760'], }), ('ellipsis', '0.3.2', { 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], }), ('digest', '0.6.31', { - 'checksums': ['792c1f14a4c8047745152f5e45ce7351978af8d770c29d2ea39c7acd5d619cd9'], + 'checksums': ['5a284f490eaca6750f695f00a584cfca3f180ca1046ac1107202141149d431b9'], }), ('glue', '1.6.2', { 'checksums': ['9da518f12be584c90e75fe8e07f711ee3f6fc0d03d817f72c25dc0f66499fdbf'], }), ('cli', '3.6.0', { - 'checksums': ['c3a9ebbcb9017fb9aeda4f7df5ca981e42b169cbd7ce13e592cda2cd74250d63'], + 'checksums': ['b6078131803043d53d4e670aa3a0506f614e0b40fda8e0102afd48a6188ab896'], }), ('vctrs', '0.5.2', { - 'checksums': ['9676881e009aa1217818f326338e8b35dd9a9438918f8b1ac249f4c8afe460dd'], + 'checksums': ['76bf10243b9b31e23f56ffdaa1677a01767699e2098487f86bd42cb801d8c047'], }), ('lifecycle', '1.0.3', { - 'checksums': ['1da76e1c00f1be96ca34e122ae611259430bf99d6a1b999fdef70c00c30f7ba0'], + 'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'], }), ('hms', '1.1.2', { - 'checksums': ['6b5f30db1845c70d27b5de33f31caa487cdd0787cd80a4073375e5f482269062'], + 'checksums': ['1ee6a9847336aaf58d3fcee5b56c290c2204e1213b6628862818419b2302bded'], }), ('prettyunits', '1.1.1', { 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], @@ -269,13 +263,13 @@ exts_list = [ 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], }), ('crayon', '1.5.2', { - 'checksums': ['c025c73b78a8e88e8e4363c8e1a941da5089a7baea39e59ea5342ab9ebe45df9'], + 'checksums': ['70a9a505b5b3c0ee6682ad8b965e28b7e24d9f942160d0a2bad18eec22b45a7a'], }), ('progress', '1.2.2', { 'checksums': ['b4a4d8ed55db99394b036a29a0fb20b5dd2a91c211a1d651c52a1023cc58ff35'], }), ('ade4', '1.7-22', { - 'checksums': ['c85111881ff93a261ca34a5b5ef313d1c0ff9b84f0b23596bc56cfa696f165ef'], + 'checksums': ['007df54e83a2a6cb8d6da8006f0aace011e7eaa7744dc5f8230ac2c002b393b4'], }), ('AlgDesign', '1.2.1', { 'checksums': ['5989626c526bd7c3d9bdda326c962056879be03392065a0b7ddb9b8cf9309d05'], @@ -284,13 +278,13 @@ exts_list = [ 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], }), ('BH', '1.81.0-1', { - 'checksums': ['3b9e9d07682013e0c06a396dda176b405eab99a7273eca6c40d1b4c4110e8cb3'], + 'checksums': ['f51c8badd6f181e06353314e1d15a6ec1495cc498ee74b6fa4ea8aba6e97ff64'], }), ('brew', '1.0-8', { - 'checksums': ['38b859c1dca63479f6937c593da8f806f2b3279585bb6e20ecff1b898469e76e'], + 'checksums': ['11652d5a7042d645cc5be5f9f97ff4d46083cea7d3ad2dd6ad1570b52c097826'], }), ('Brobdingnag', '1.2-9', { - 'checksums': ['73a734342736da5b29c2827d91f662101873503af7ad9cdf9e9e697bb32dd742'], + 'checksums': ['f9012d250bc2a0f47815d6a7c06df2d4ddf3d8bab2d3b75e8cdefd964d20e91e'], }), ('corpcor', '1.6.10', { 'checksums': ['71a04c503c93ec95ddde09abe8c7ddeb36175b7da76365a14b27066383e10e09'], @@ -305,7 +299,7 @@ exts_list = [ 'checksums': ['b784dd5163a0350d084ef34882d9781373839dedeaa9a8b8e6187d773d0d21c6'], }), ('cubature', '2.0.4.6', { - 'checksums': ['087b3b2c4f25d873fa95e9d38766a17a7201d03a6f4960f1e080a8db8b67d569'], + 'checksums': ['330c9dc2be9bf6815473fd40efa8c2de47c1ed286cb097d0ff846b56c9e9f95a'], }), ('DEoptimR', '1.0-11', { 'checksums': ['1874b30f4b75f9bfa891986598f1ebe1fce27fdced14f8f417d3535cac08165b'], @@ -313,47 +307,47 @@ exts_list = [ ('fastmatch', '1.1-3', { 'checksums': ['1defa0b08bc3f48e4c3e4ba8df4f1b9e8299932fd8c747c67d32de44f90b9861'], }), - ('ffbase', '', { - 'checksums': ['b3f61f80ba6851130247779786903d42a24ee5219aa24556c8470aece8a2e6b6'], + ('ffbase', '0.12.3', { + 'checksums': ['a52998ec589c2b519034757919565473273f8b73486d8333ba7ff6deec3ae9db'], }), ('iterators', '1.0.14', { 'checksums': ['cef3075a0930e1408c764e4da56bbadd4f7d14315809df8f38dd51f80ccc677b'], }), ('maps', '3.4.1', { - 'checksums': ['7918ccb2393ca19589d4c4e77d9ebe863dc6317ebfc1ff41869dbfaf439f5747'], + 'checksums': ['e693a5218ed8122e92d73a98a475d9016f2293c7852c8048677daa7649086400'], }), ('nnls', '1.4', { 'checksums': ['0e5d77abae12bc50639d34354f96a8e079408c9d7138a360743b73bd7bce6c1f'], }), ('sendmailR', '1.4-0', { - 'checksums': ['20d7d54f247dd1b444d2d74170646977cc4bd52f5a4152c72a9c3665b9a1fdb5'], + 'checksums': ['5b8b91fc13f6b07b9fc5a2cf7591cf760fad47c5ea17d87a2891898c506454ad'], }), ('dotCall64', '1.0-2', { - 'checksums': ['f10b28fcffb9453b1d8888a72c8fd2112038b5ac33e02a481492c7bd249aa5c6'], + 'checksums': ['e0c7728aebbea5ebf06dfeefae4fc0a240e6dde7c2bf13f2ed041b91d337a4ac'], }), ('spam', '2.9-1', { - 'checksums': ['d98177435b028d1c706d0197ea8132bfaffae6052c3ce6064a7f64178512d6aa'], + 'checksums': ['c32e219279988b1bfc258aaf64f5a46efa558202848a9ae64946ffbe8b497ddb'], }), ('subplex', '1.8', { 'checksums': ['3bc31d8990380c9f790c9c7d84cb2e39f4945eff934eddfa1196d597465be5a5'], }), ('stringi', '1.7.12', { - 'checksums': ['0ea3d5afec5701977ff53de9afbaceb53b00aa34f5fb641cadc1eeb7759119ec'], + 'checksums': ['efe8ac2900001f986a75db5641fbb24587a6d23de274a6a85c39dfa58921e009'], }), ('magrittr', '2.0.3', { 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], }), ('stringr', '1.5.0', { - 'checksums': ['87604d2d3a9ad8fd68444ce0865b59e2ffbdb548a38d6634796bbd83eeb931dd'], + 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], }), ('evaluate', '0.20', { - 'checksums': ['885aee530a8b6aa7fd3acaa1ecd94ab58b71038c879ca37405f948e105907c5d'], + 'checksums': ['35f5d9e85603600b58960923d591c5ca1115153febba7c612867d8b5598afff0'], }), ('logspline', '2.1.19', { - 'checksums': ['03b72b860896f8801014b7b3b907389cc3cbe2e13bc1049241606df685a08815'], + 'checksums': ['37219e6edfdee59d8edee96ca1cb97902905ae049a7a921fbab2e162ad654794'], }), ('ncbit', '2013.03.29.1', { - 'checksums': ['4480271f14953615c8ddc2e0666866bb1d0964398ba0fab6cc29046436820738'], + 'checksums': ['847f570c035d849e775c1cb922d2775e6c535971eb4429cf62904319fd126504'], }), ('permute', '0.9-7', { 'checksums': ['eff88ffb579aaeb994e9f8609b776b2d9d9d56bc2879ddf180e3a2ad19f48dc0'], @@ -365,7 +359,7 @@ exts_list = [ 'checksums': ['f59ea87534480edbcd6baf53d7ec57e8c69f4532c2d2528eacfd48924efa2cd6'], }), ('scatterplot3d', '0.3-42', { - 'checksums': ['4c8326b70a3b2d37126ca806771d71e5e9fe1201cfbe5b0d5a0a83c3d2c75d94'], + 'checksums': ['a9fedde70e1a846c4dcafbff20f115425206d507896d12c2b21ff052556c5216'], }), ('SparseM', '1.81', { 'checksums': ['bd838f381ace680fa38508ff70b3d83cb9ffa28ac1ab568509249bca53c34b33'], @@ -374,7 +368,7 @@ exts_list = [ 'checksums': ['7f82f8d63741c468767acc6fb35281bd9903f6c3c52e8fada60a6ae317511fbe'], }), ('irace', '3.5', { - 'checksums': ['7eea92ba42e6ba320fa8bdca3c53091ae42f26a0f097244f65e7e117f6d514b6'], + 'checksums': ['d9928644a5a7e94838558d73afaaee8a914fd26fe68f691ad103331632060bf4'], }), ('rJava', '1.0-6', { 'checksums': ['e290d0493317a5d6c452793e92baa914e37ef03faef19b2e436329b4ec8658c6'], @@ -383,25 +377,25 @@ exts_list = [ 'checksums': ['4f42f5423c45688b39f492c7892d93f37b4541831c8ffb140364d2bd89031ac0'], }), ('png', '0.1-8', { - 'checksums': ['e269ff968f04384fc9421d17cfc7c10cf7756b11c2d6d126e9776f5aca65553c'], + 'checksums': ['5a36fabb6d62ba2533d3fc4cececd07891942cfb76fe689ec0d550d08762f61c'], }), ('jpeg', '0.1-10', { - 'checksums': ['01a175442ec209b838a56a66a3908193aca6f040d537da7838d9368e46913072'], + 'checksums': ['c8d9f609c3088f91ec4853d6cc0e66511038a465811dea79ca6a0c09519178ca'], }), ('latticeExtra', '0.6-30', { - 'checksums': ['6cadc31d56f73d926e2e8d72e43ae17ac03607a4d1a374719999a4a231e3df11'], + 'checksums': ['c550a76913624818482bf237d48883c58e368ba356ced8ed5e76146672279eed'], }), ('Matrix', '1.5-3', { - 'checksums': ['42b24f1d1e94482b0ff0ef1292e2df29f69694bdbee47b3d6bfeec46fafb2f7e'], + 'checksums': ['4e720f4edc97b1c09646a445851b1ce955caf6b1de8306a2283328b526fee00d'], }), ('RcppArmadillo', '0.12.0.1.0', { - 'checksums': ['f9e17af85ef5c0c8d63771b6e7da0cdcdbecc7ac8bd40d5035a64952c4ce1938'], + 'checksums': ['73c6153b79c0b71a896d76031424fe1c0a3ad44a9d09f922a084bb3fbfd3fbea'], }), ('plyr', '1.8.8', { - 'checksums': ['7d9fdaf1157035a49c3661da3bbaa7bfcf782aafe1b98f7b5a68b0520046e87f'], + 'checksums': ['a73211b4bbe13e4e5e764966a8dd90172c1cc311938dd464d142e1c7a701070c'], }), ('gtable', '0.3.1', { - 'checksums': ['fd386cc4610b1cc7627dac34dba8367f7efe114b968503027fb2e1265c67d6d3'], + 'checksums': ['8bd62c5722d5188914d667cabab12991c555f657f4f5ce7b547571ae3aec7cb5'], }), ('reshape2', '1.4.4', { 'checksums': ['d88dcf9e2530fa9695fc57d0c78adfc5e361305fe8919fe09410b17da5ca12d8'], @@ -410,7 +404,7 @@ exts_list = [ 'checksums': ['a10578e9ad8a581bd8fe0d8a8370051f3cdcf12c7d282f3af2a18dacda566081'], }), ('colorspace', '2.1-0', { - 'checksums': ['e75681cc4dd6e4b70303fd96a6d4597065dc6bffcaa4ae4244b73ff19016857f'], + 'checksums': ['04078abb6b54119c90dc7085d62916bf292ccb163e213f9ea70567d1be82614c'], }), ('munsell', '0.5.0', { 'checksums': ['d0f3a9fb30e2b5d411fa61db56d4be5733a2621c0edf017d090bdfa5e377e199'], @@ -419,16 +413,16 @@ exts_list = [ 'checksums': ['e022d79276173e0d62bf9e37d7574db65ab439eb2ae1833e460b1cff529bd165'], }), ('viridisLite', '0.4.1', { - 'checksums': ['849955dc8ad9bc52bdc50ed4867fd92a510696fc8294e6971efa018437c83c6a'], + 'checksums': ['a896db1ccae5fc1a8b3764d02f24cef74ef7a8341cf9f3401c4efe799870ea97'], }), ('farver', '2.1.1', { - 'checksums': ['e5c8630607049f682fb3002b99ca4f5e7c6b94f8b2a4342df594e7853b77cef4'], + 'checksums': ['0dcfda6ca743f465372790bcff1bcbc6a7145fdac1c682b021f654e8c6c996ce'], }), ('scales', '1.2.1', { - 'checksums': ['185d50240e6b3e84d36ec7fbca6aef7a85db7c8c1b0dde51d4af28d363ce02df'], + 'checksums': ['59453e6dbdafee93dfb101e4d86048a62a12898134259d3ef02d65aeec57ed08'], }), ('utf8', '1.2.3', { - 'checksums': ['a71aee87d43a9bcf29249c7a5a2e9ca1d2a836e8d5ee3a264d3062f25378d8f4'], + 'checksums': ['c0a88686591f4ad43b52917d0964e9df4c62d8858fe25135a1bf357dfcbd6347'], }), ('zeallot', '0.1.0', { 'checksums': ['439f1213c97c8ddef9a1e1499bdf81c2940859f78b76bc86ba476cebd88ba1e9'], @@ -437,13 +431,13 @@ exts_list = [ 'checksums': ['85cf7fcc4753a8c86da9a6f454e46c2a58ffc70c4f47cac4d3e3bcefda2a9e9f'], }), ('fansi', '1.0.4', { - 'checksums': ['86a7b83d8c9d28baebbde310cd0b459d0950a9c7ff1a6276ce5858f6a89bc06a'], + 'checksums': ['3163214e6c40922bbb495229259ed8ce1bebd98b77098a6936d234e43da9c49f'], }), ('pillar', '1.8.1', { - 'checksums': ['7841f89658cc8935568c0ff24dc480b4481bac896de2f6447050abc4360a13bb'], + 'checksums': ['2f06a7cc9e5638390c9b98a6ec9a9ec1beec0f2b9dbdfa42e39a5ab2456d87ec'], }), ('tibble', '3.1.8', { - 'checksums': ['e1a50891f476803526960b4c4d736a72e7d9c3d366946744a02d6347f591c872'], + 'checksums': ['acf30e075d18d2f61de53ca20a13c502bb32abb8083089b0bb9172a0cb5cedea'], }), ('lazyeval', '0.2.2', { 'checksums': ['d6904112a21056222cfcd5eb8175a78aa063afe648a562d9c42c6b960a8820d4'], @@ -452,31 +446,31 @@ exts_list = [ 'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'], }), ('mgcv', '1.8-41', { - 'checksums': ['dbe627266c3b339232e2d4228d5370ba88c86540319e6891d161242efba7e4a5'], + 'checksums': ['2f7a030fe2be75edef6bd96147df46c2262f3cdc44c383d8f82b401df44fe690'], }), ('rprojroot', '2.0.3', { 'checksums': ['50604247470e910cecfe9b76df754bf96a0d701f81b732f7aa9c90a20d30f897'], }), ('desc', '1.4.2', { - 'checksums': ['8f9ebb51eccf925b2e76bc65ecf495e8f3882b8c0053023f396622f0402d6f54'], + 'checksums': ['758acf14be478c09ba7e84ade3a7ce512becf35d44e5e6a997b932065f2a227c'], }), ('ps', '1.7.2', { - 'checksums': ['9c458a377d47cc972d3cd0b2a17d0b7ad3cf3b62226410803072089a57a55ef1'], + 'checksums': ['9225ebdedb5c1b245bb38b01ce88084c0fc7eafcff6c4fda2e299003ace6b21a'], }), ('processx', '3.8.0', { - 'checksums': ['87705769601e67799d976945c0e3e1cdd09e52a25900252e6f9b80a1cf90f2f5'], + 'checksums': ['9270d9d26c4314151062801a5c1fc57556b4fcb41dbf3558cb5bd230b18ffb0b'], }), ('callr', '3.7.3', { - 'checksums': ['d67255148595c6d0ba4c4d241bc9f6b5e00cafe25fdc13e38c10acc38653360a'], + 'checksums': ['567bfedf073a1d4c5785f0553341608a214938110567b9a6495ff20ebb2fd04e'], }), ('pkgbuild', '1.4.0', { - 'checksums': ['7c6a82d1e6b19e136a7d16095743c50cd7b6340eeda594e4a8e14d74972ddb48'], + 'checksums': ['357f3c40c99650eaa8a715991ff1355a553acb165f217ed204712f698ba55ed6'], }), ('rstudioapi', '0.14', { - 'checksums': ['aac35bbdcb4a8e8caba943bc8a2b98120e8940b80cd1020224bb1a26ff776d8b'], + 'checksums': ['469d0987b1ad728a96c363a422fba712a5cebc8b11a5f7e953b4a671044dafc4'], }), ('pkgload', '1.3.2', { - 'checksums': ['d6912bc824a59ccc9b2895c3cf3b08a3ff310a333888bb8e90d1a6ce754dd90f'], + 'checksums': ['35d19a032bfeeefcab92d76a768b4a420c2ede0920badaf48cca878592b46b2f'], }), ('praise', '1.0.0', { 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], @@ -485,7 +479,7 @@ exts_list = [ 'checksums': ['eaa89041856189bee545bf1c42c7920a0bb0f1f70bb477487c467ee3e8fedcc6'], }), ('jsonlite', '1.8.4', { - 'checksums': ['7b1892efebcb4cf4628f716000accd4b43bbf82b3e6ba90b9529d4fa0e55cd4c'], + 'checksums': ['79eaabe042226b0918aa828cc63d54fee8be67ae7c67f5e0d3010f468efb1278'], }), ('diffobj', '0.3.5', { 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], @@ -497,13 +491,13 @@ exts_list = [ 'checksums': ['57ee89eec9bcbba58cf8fa29c8e097f038768c30833eaf812682826333127eaa'], }), ('testthat', '3.1.6', { - 'checksums': ['a47eec031b4e186a8bd331031371b2347063a283050eca2adbfaa37d7a6c9c09'], + 'checksums': ['a7cb8c416475c182c4faaa32c3a12fc5d8ead77196d3c9811a3d39b3f994cdae'], }), ('isoband', '0.2.7', { - 'checksums': ['46f53fa066f0966f02cb2bf050190c0d5e950dab2cdf565feb63fc092c886ba5'], + 'checksums': ['7693223343b45b86de2b5b638ff148f0dafa6d7b1237e822c5272902f79cdf61'], }), ('ggplot2', '3.4.1', { - 'checksums': ['bfcb4eb92a0fcd3fab713aca4bb25e916e05914f2540271a45522ad7e43943a9'], + 'checksums': ['041bc333f90d6026702c8bd5140a1c8ddd270b15742badf8ca5c53f0e02c6d84'], }), ('pROC', '1.18.0', { 'checksums': ['d5ef54b384176ece6d6448014ba40570a98181b58fee742f315604addb5f7ba9'], @@ -515,10 +509,10 @@ exts_list = [ 'checksums': ['04d0b6ce6e5f070b109478a6005653dbe78613bb4e3ea4903203d851b5d3c94d'], }), ('data.table', '1.14.8', { - 'checksums': ['f741b951e5937440139514aedbae78dbd6862d825066848bdb006aa02c2f3d2b'], + 'checksums': ['14b2ce5367df9c9bb58f373555066f5dcb629c156149b5565de36d69557139fd'], }), ('BBmisc', '1.13', { - 'checksums': ['900a633f69b7d9b13d58709eeae2fca2c1bc510765d778623a2af32cc870053e'], + 'checksums': ['1145dcf9fed15e7beeaa4a5c7075d8a8badd17c8246838cd63e40cd9551e4405'], }), ('fail', '1.3', { 'checksums': ['ede8aa2a9f2371aff5874cd030ac625adb35c33954835b54ab4abf7aeb34d56d'], @@ -530,39 +524,37 @@ exts_list = [ 'checksums': ['84587f46f222a96f3e2fde10ad6ec6ddbd878f4e917cd926d632f61a87db13c9'], }), ('tree', '1.0-43', { - 'checksums': ['5a17c30423f4a1b81ae4fdf4a1c0079724000c9fdb339306438db442e17c72e0'], + 'checksums': ['9b0a996d013cce4f457abdbdc54bd2f8f4dbe4ef0b33e0a53925509c509d5287'], }), ('pls', '2.8-1', { - 'checksums': ['eff3a92756ca34cdc1661fa36d2bf7fc8e9f4132d2f1ef9ed0105c83594618bf'], + 'checksums': ['e22e7febeef1a6800b97ee7f6eb03dc1d6681aba7f9298449c9e6375fa78f28c'], }), ('class', '7.3-21', { - 'checksums': [('e65b046bc72b312ff0c5dc7feba4fa3e9bc63387274d44911493782b85f65483', - '93956d7b66ece2261e8846a1703e28a838c2621e366016f792ad48741f230205')], + 'checksums': ['0c19404aa4d2da61a62495e788b07c8e429c4c5ee64486ea5e6dd347bcaecddf'], }), ('proxy', '0.4-27', { 'checksums': ['249991a4c4d70ad139e93f3a24e17f161ad1ec854951813ea192daf79478563f'], }), ('e1071', '1.7-13', { - 'checksums': ['48c18e10e7cabc742d37b563672e2eddb6061f2378b69e5563be79ab9948d92f'], + 'checksums': ['da94e191af6e69aa0f9e3250d4b823674cc869339d914f761ebf2824177b6b2f'], }), ('nnet', '7.3-18', { - 'checksums': [('ee750bb8164aa058edf93823af987ab2c7ec64128dce2abeaae1b7d3661e9a67', - 'd86871d54e4a331cd5e00da28a2f42a56d8976084578ed2fcdb3a7ad25d4dfaa')], + 'checksums': ['d29aebfb5cb00071eecf754d55db5d474a6fda88860df5c9d31ba89aa8d9e3d0'], }), ('minqa', '1.2.5', { - 'checksums': ['cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c'], + 'checksums': ['9b83562390990d04b2c61b63ac9a7c9ecab0d35c460d232596e3c73bdc89f4be'], }), ('RcppEigen', '0.3.3.9.3', { - 'checksums': ['2547e794d5a6fb8d9fbadf19e64afa0bcf413cc69ecf3f428995fa5a0fced493'], + 'checksums': ['5873a47fd6587d916f86119ab140c6736abf80ac45d06ff1c9d198708e7d1c76'], }), ('MatrixModels', '0.5-1', { - 'checksums': ['a87faf1a185219f79ea2307e6787d293e1d30bf3af9398e8cfe1e079978946ed'], + 'checksums': ['3fc55bdfa5ab40c75bf395e90983d14c9715078c33c727c1658e4e1f36e43ea9'], }), ('matrixStats', '0.63.0', { - 'checksums': ['85e2016b6dd20cbfe32d38a2ef2578ae80e688d9a3590aefd1d2f4bf4bd44eca'], + 'checksums': ['c000b60421742eb035ff4ceedd3e588a79e4b28985484f0c81361e5a6c351f5f'], }), ('codetools', '0.2-19', { - 'checksums': ['1a9ea6b9792dbd1688078455929385acc3a5e4bef945c77bec1261fa4a084c28'], + 'checksums': ['c4b7e567c87f33dad85de92f79641e5e5b5deede6d19a9dfa47133d191782dab'], }), ('foreach', '1.5.2', { 'checksums': ['56338d8753f9f68f262cf532fd8a6d0fe25a71a2ff0107f3ce378feb926bafe4'], @@ -571,46 +563,46 @@ exts_list = [ 'checksums': ['5e06f1926aebca5654e1329c66ef19b04058376b2277ebb16e3bf8c208d73457'], }), ('generics', '0.1.3', { - 'checksums': ['63eab37a9148f820ce2d67bda3dab6dedb9db6890baa5284949c39ab1b4c5898'], + 'checksums': ['75046163bfa8b8a4f4214c1b689e796207f6447182f2e5062cf570302387d053'], }), ('purrr', '1.0.1', { - 'checksums': ['23ebc93bc9aed9e7575e8eb9683ff4acc0270ef7d6436cc2ef4236a9734840b2'], + 'checksums': ['0a7911be3539355a4c40d136f2602befcaaad5a3f7222078500bfb969a6f2ba2'], }), ('tidyselect', '1.2.0', { - 'checksums': ['0389a3b15417954a30d6d692f6ebdd3d0f318cb94a5c9b05365df2f4ea1d8270'], + 'checksums': ['538d26b727e37d618e2efd3b00836048f103112a03e6994bf07a02392e269e3b'], }), ('dplyr', '1.1.0', { - 'checksums': ['e2e1f7312618b4e32ada9a1da79cef32eaec12acd408c973a6b069c6be4fb46b'], + 'checksums': ['8cb0535e49dd40b3054046735738f1e48507ac9a56b015d16ebcb54593b84ed7'], }), ('gower', '1.0.1', { - 'checksums': ['671cb7baafe05140d822e8f26f9cd3576fc3bf4c6572b7223fb54da754ea385d'], + 'checksums': ['296a9d8e5efa8c3a8cc6b92cf38880915753afdef30281629af9dc8eae8315fc'], }), ('rpart', '4.1.19', { - 'checksums': ['27ec75258a5a3459ad999f5f36760ead974930744249605bf8465f234f31425c'], + 'checksums': ['fe723ed0b5583fae8b40e6fecc29b357229cb11f2339b02a4e4f812926249565'], }), ('survival', '3.5-3', { - 'checksums': ['14878705cd0c7edcfead79011444aa84f680759293bde8634721c49f37cb4dc7'], + 'checksums': ['bfa082fd938760fa06f76d70fe2a613c70620e4d2870f14270d8e20f1fbc44c6'], }), ('KernSmooth', '2.23-20', { 'checksums': ['20eb75051e2473933d41eedc9945b03c632847fd581e2207d452cf317fa5ec39'], }), ('globals', '0.16.2', { - 'checksums': ['f83689a420590b0d62b049c40a944c1c8c7202b3f1cc12102712c63104e99496'], + 'checksums': ['682c26a95fa6c4e76a3a875be1a3192fc5b88e036c80dfa3b256add0336d770a'], }), ('listenv', '0.9.0', { - 'checksums': ['fd2aaf3ff2d8d546ce33d1cb38e68401613975117c1f9eb98a7b41facf5c485f'], + 'checksums': ['352841e04f0725d361b78cfdc75e00511f740d97237dd651ea86aa5484674887'], }), ('parallelly', '1.34.0', { - 'checksums': ['909ca35e7931b08dab7c8e48747c9b55c4f92480d87a85f98331a03b5f85e179'], + 'checksums': ['11639d7039e4a2450dabac1f82cb7ead0bbc68bdb0e113054b7104840098aff4'], }), ('future', '1.31.0', { - 'checksums': ['a35c0bdae86265ebe86119231802b6fbf7b1d533b57cb423d8483fbe779390d5'], + 'checksums': ['b2db8f859a13066f004fa147012e8533b11e41df9516988cd2d5961c78dfdf2a'], }), ('future.apply', '1.10.0', { - 'checksums': ['6166c1c5ce30b9745059c3d30c8110f7c1d51871e58aa414f195cb1f91c467f5'], + 'checksums': ['dee92dd84812fe8c55064c0f0e6d806c0c29848b5a5fc4a7725d6a4b623e94aa'], }), ('progressr', '0.13.0', { - 'checksums': ['8f83024b2a6f52996750d45bf6698c2b438fb1062985f1df936ba3af313caed1'], + 'checksums': ['0ffb3dcadde0cc191bad0ff9e05d000aa65e2fc339cfc94ebbb263088df5a4e1'], }), ('numDeriv', '2016.8-1.1', { 'checksums': ['d8c4d19ff9aeb31b0c628bd4a16378e51c1c9a3813b525469a31fe89af00b345'], @@ -619,7 +611,7 @@ exts_list = [ 'checksums': ['66e5e18ca29903e4950750bbd810f0f9df85811ee4195ce0a86d939ba8183a58'], }), ('lava', '1.7.2.1', { - 'checksums': ['7a88f8a885872e2abb3011c446e9e1c4884cd4dbe6ab4cfe9207538e5560232e'], + 'checksums': ['d42b1f5c7e4e76718e4f014c44608295f82b5de0eb25ce8e9b35c40c7839ef2e'], }), ('prodlim', '2019.11.13', { 'checksums': ['6809924f503a14681de84730489cdaf9240d7951c64f5b98ca37dc1ce7809b0f'], @@ -628,43 +620,43 @@ exts_list = [ 'checksums': ['6168a062d93c2d3063c064a8f242cd3716dee99822e20363a1801261319c4c98'], }), ('cpp11', '0.4.3', { - 'checksums': ['403ce0bf82358d237176053b0fb1e958cb6bfa4d0fb3555bf5801db6a6939b99'], + 'checksums': ['f1a60e4971a86dbbcf6a16bbd739b59bb66d9c45d93cfd8dedc2a87e302598f1'], }), ('lubridate', '1.9.2', { - 'checksums': ['87d66efdb1f3d680db381d7e40a202d35645865a0542e2f270ef008a19002ba5'], + 'checksums': ['8976431a4affe989261cbaa5e09cd44bb42a3b16eed59a42c1698da34c6544a7'], }), ('tidyr', '1.3.0', { - 'checksums': ['8cd01da9e97827521d01ea50b9225f2705c46b7538bbf74bec6249a04c1213a8'], + 'checksums': ['8d532b9366fdd3ec9827b51830e559a49d073425007c766025f0e603964e0a9d'], }), ('hardhat', '1.2.0', { - 'checksums': ['0374a9f5af2e8eaf100b4dbda951a5289258d0d466e5ef10768e8ffda928b4b1'], + 'checksums': ['f9320eccb1b5f624a46fa074e3ccc202c383b77098ecd08b193aeb47daedad78'], }), ('recipes', '1.0.5', { - 'checksums': ['3d0073e3eb98ac089a94bf8430f3c50915ff1f495d8e967c37baa6a0f6cea0a4'], + 'checksums': ['fd8b0d4282f490b5bd3853543c9a0518783caa9fa9280534aaab40f9bdd3cfb2'], }), ('caret', '6.0-93', { - 'checksums': ['1d814a2a921a23ad8b9a7da6f788e6abc06f5668b3918bd440d4355bc4b81511'], + 'checksums': ['4c156b88879d390436a54779ea19ffbae3f476533d83caaf30400d76130c4a07'], }), ('conquer', '1.3.2', { - 'checksums': ['ac354e18c9ad6f41ed5200fad1c99fa5b124fc6fa5bba8f3434be2478f53d5fa'], + 'checksums': ['8f129bb062e447369f220a13f59ccb6cdc209f72c92a26457edd777666c9b946'], }), ('quantreg', '5.94', { - 'checksums': ['d4a94984a500bf4c92dec21013441f001a4aa0541c4c651384e257a4b4e9e539'], + 'checksums': ['52d585ccb972ed7726b7d083f5635d3e42915847398e00fd6e0f69a5fe1b17c1'], }), ('robustbase', '0.95-0', { 'checksums': ['5cfaea1c46df6d45086614fea5f152c8da8ebfcadf33bb8df5b82e742eef9724'], }), ('zoo', '1.8-11', { - 'checksums': ['c9a282d8004c22651c4fa1d657d3cad946c5ec55c4dc068569d860ee9b31ed47'], + 'checksums': ['848e50f875afe06f13422e32160082b0725159a8be98234ef358480e57029ca5'], }), ('lmtest', '0.9-40', { 'checksums': ['64400d4d6cc635316531042971f1783539686e9015c76f5741c07304fa14d997'], }), ('vcd', '1.4-11', { - 'checksums': ['7188192afa289350cc1b89790f4f8f5a5114c1c88bee7715a0c8f5347aa0b35b'], + 'checksums': ['7a54e855689e1429d46e0d4d7a956f96b0ad2fd0c7084fa023902c55849e0932'], }), ('snowfall', '1.84-6.2', { - 'checksums': ['5c446df3a931e522a8b138cf1fb7ca5815cc82fcf486dbac964dcbc0690e248d'], + 'checksums': ['9b467ab2b992455c6e1aeabe375c5694761fa1cf8aaf4f003ca47102b656353b'], }), ('bindr', '0.1.1', { 'checksums': ['7c785ca77ceb3ab9282148bcecf64d1857d35f5b800531d49483622fe67505d0'], @@ -679,37 +671,37 @@ exts_list = [ 'checksums': ['97f63d0bab3b240cc7bdbe6e6e74e90ad25a4382a345ee51a26fe3959edeba0f'], }), ('mnormt', '2.1.1', { - 'checksums': ['2d498505e32d8aa9fa54a1ab328c35ae3a85e0b20a0cf0d519a4df84e2b307b8'], + 'checksums': ['95fca70378af0afd5a388982ba5528f5b27e02157eeb9940a0a9762d11511308'], }), ('foreign', '0.8-84', { - 'checksums': ['f8ed0684d59bec7f3a39cde1aa5ec7b3e6e36aaecacb28120c9c54f7b13f80fb'], + 'checksums': ['17edf302c7568a122dc496a61a4a886ef7c02224a235d945b473611c79c98549'], }), ('psych', '2.2.9', { - 'checksums': ['dcc3f9b30ed44dfd1de0366295a308e0b52959eb7ac9cb3bc3f32dc5b15fc321'], + 'checksums': ['4cd518bff387fef95067696b0a0b323310e6f4a063c3d242f2a50bcb17675571'], }), ('broom', '1.0.3', { - 'checksums': ['66a1095d4430450dc810a5cea61cd7e7bee0e23739dcf5ddc5b57c9894fcf999'], + 'checksums': ['06b3f10c9ee03124dd2a85da09785a2fba9b406fa25c57f9b9db4d71a49a0a55'], }), ('nloptr', '2.0.3', { 'checksums': ['7b26ac1246fd1bd890817b0c3a145456c11aec98458b8518de863650b99616d7'], }), ('boot', '1.3-28.1', { - 'checksums': ['9f7158fd2714659f590c3955651893dc24bd8f39196bc5a4cc35b0b031744a32'], + 'checksums': ['d4cde76fcc8ccc7ffa329de69147b66a6a93a10188e89342fd18207b1d02ff53'], }), ('statmod', '1.5.0', { - 'checksums': ['14e897c83d426caca4d920d3d5bead7ae9a679276b3cb2e227f299ad189d7bc2'], + 'checksums': ['d61c3ef9b09d55b42e038f8d767fa483ebbdec2a9c7172b1b0ccda0ae0016ec9'], }), ('lme4', '1.1-31', { - 'checksums': ['83d97de48cc4706a5a9615b126ba1a86f1a3009d3f38b8da3e57dd619519e826'], + 'checksums': ['5affd1e33d3fece5ec0a6c7663eb12328e64147f8aa92675ce6453c4fe72edfd'], }), ('ucminf', '1.1-4.1', { - 'checksums': ['a2eb382f9b24e949d982e311578518710f8242070b3aa3314a331c1e1e7f6f07'], + 'checksums': ['01a5b6f373ad267d22e2c29b8f7b6e31a1a148e48f4413e6a38e51aa049976b2'], }), ('ordinal', '2022.11-16', { - 'checksums': ['7a41e7b7e852a8fa3e911f8859d36e5709ccec5ca42ee3de14a813b7aaac7725'], + 'checksums': ['5488ad1dfa531a09d017d68d7393d376c8bc49cceeaa6a3e5f7d57b99168d493'], }), ('jomo', '2.7-4', { - 'checksums': ['9d3987f3a73d305f3ab6fc66efc04a196a7eb8b65e20c411131dc17af51f0063'], + 'checksums': ['2d25bc248dc1b931e6c19636197cd6f58fb00f5e1102ed3c04084c71d03d93fd'], }), ('clipr', '0.8.0', { 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], @@ -721,31 +713,31 @@ exts_list = [ 'checksums': ['25df6826ea5e93241c4874cad4fa8dadc87a40f4ff74c9107aa12a9e033e1578'], }), ('vroom', '1.6.1', { - 'checksums': ['d087cb148f71c222fc89199d03df2502689149873414a6d89c2f006d3a109fde'], + 'checksums': ['eb0e33d53212f9c7e8b38d632c98bd5015365cc13f55dadb15ff0d404b31807c'], }), ('readr', '2.1.4', { - 'checksums': ['94afd03a1fa4abcf2985ec903bbf5995d7c590e1a50512ed80d081ef4fe10c1b'], + 'checksums': ['98144fa48c4fa61ef8c73ede8f87a2d2c5c44e9502b7875b266eb79984fbeb0d'], }), ('forcats', '1.0.0', { - 'checksums': ['c4fb96e874e2bedaa8a1aa32ea22abdee7906d93b5c5c7b42c0894c0c5b6a289'], + 'checksums': ['c5bb157909d92e1e1a427c0dc5cb358ea00a43a14918a9088fa4f6630962254e'], }), ('haven', '2.5.1', { - 'checksums': ['b580311bc1b28efc6b123e29a331282b9f7eb552c485f4e5cacab39fe534aff4'], + 'checksums': ['9f40462097a0b1cf3831bca493851fe4a6b3570d957a775ca81940f241c50a70'], }), ('pan', '1.6', { 'checksums': ['adc0df816ae38bc188bce0aef3aeb71d19c0fc26e063107eeee71a81a49463b6'], }), ('mitml', '0.4-4', { - 'checksums': ['49bd3eb68a60fb2a269e7ddca8b862e1e81e0651e2b29759482fb7bcad452102'], + 'checksums': ['0021482761943ccb88554a1752636f13e83b1d026d79b6e4a53fdfebe296af8a'], }), ('mice', '3.15.0', { - 'checksums': ['f87bb73d8bfee36c6bf4f15779c59ff6b70c70ca25b1388b4ee236757276d605'], + 'checksums': ['3d64dd260e3dce9c4c2f7be8c99f3063769df9ccfd3a0fc827c2de0ac842e87b'], }), ('urca', '1.3-3', { - 'checksums': ['621cc82398e25b58b4a16edf000ed0a1484d9a0bc458f734e97b6f371cc76aaa'], + 'checksums': ['43baa8b6735f8325a69e6a43686f4fecd77a0eb7f60da25b4fc5c51b9271e9f1'], }), ('fracdiff', '1.5-2', { - 'checksums': ['b8103b32a4ca3a59dda1624c07da08ecd144c7a91a747d1f4663e99421950eb6'], + 'checksums': ['ac5f881330287f5bc68b5cdce4fb74156a95356ffb875ee171538bc44200f437'], }), ('operator.tools', '1.6.3', { 'checksums': ['e5b74018fb75bfa02820dec4b822312f1640422f01d9fec1b58d880ffb798dec'], @@ -763,10 +755,10 @@ exts_list = [ 'checksums': ['e9b5fc92c39f94a10cd0e13f3d6e2a9c17b75ea01467077a51d47a5f708517c4'], }), ('mixtools', '2.0.0', { - 'checksums': ['ef033ef13625209065d26767bf70d129972e6808927f755629f1d70a118b9023'], + 'checksums': ['854e7482230b9a5dde61bab191b78e06aa8f9b0cdfe3c03e046afa133b317e0d'], }), ('cluster', '2.1.4', { - 'checksums': ['a3ad7a9455d634c4e0c6ccf8ea7a3a392a0ecf9c2bdb368d127ffa68a93164a9'], + 'checksums': ['c6f10ceca29a176ba833f24ebf71fd451629052c2338398ba286df5689d6f5b6'], }), ('gclus', '1.3.2', { 'checksums': ['9cc61cdff206c11213e73afca3d570a7234250cf6044a9202c2589932278e0b3'], @@ -781,16 +773,16 @@ exts_list = [ 'checksums': ['38bb33753da5bddb78893a5228a5d269dae3bf16f21dc5d9853ac9c24d31428d'], }), ('gam', '1.22-1', { - 'checksums': ['5787c6fabea5aaba29fe214db305a7369916082efc6a18f84e4c9ef81c8e7dad'], + 'checksums': ['fba1dc23ceadb2452aaf2e1c6c7cbd05273575bdba610d93d573f1a33b9d04c1'], }), ('gamlss.data', '6.0-2', { 'checksums': ['dbb3b6f855540928ccdbda497f8d552144895e34565799e8b595e704096db71e'], }), ('gamlss.dist', '6.0-5', { - 'checksums': ['ec90ea83cd81b894c73f987f69814077697be33abf0708e0f3e2a39d02c912bf'], + 'checksums': ['0f88afdfb148de79d3ece66bf4631ea0dc3ecf1188680802abffd6bc7139a20e'], }), ('gamlss', '5.4-12', { - 'checksums': ['6619d4fdc183ab492615d44961a126c827d18db20a0d59362e54de877f0a3076'], + 'checksums': ['9f791039f7e5c3cf3f6a2da955994a8c41c43044a2d77d99b289e4f82118a6f0'], }), ('gamlss.tr', '5.1-7', { 'checksums': ['8f9975bceaf8000b1d39317daf490e59c8385b5291326ed6a2630be11dae3137'], @@ -799,10 +791,10 @@ exts_list = [ 'checksums': ['ed2fa254ab27cf65d397e181339976fc3261dfb4f6b600fea8c5689620dab6f3'], }), ('xts', '0.13.0', { - 'checksums': ['d680584af946fc30be0b2046e838cff7b3a65e00df1eadba325ca5e96f3dca2c'], + 'checksums': ['188e4d1d8c3ec56a544dfb9da002e8aac80b9303d0a5a1f62ff0e960aeef9674'], }), ('curl', '5.0.0', { - 'checksums': ['90b1facb4be8b6315bb3d272ba2dd90b88973f6ea1ab7f439550230f8500a568'], + 'checksums': ['d7f3cac9b513914ffa8f6f64e6fa5dd96c8273378ace6b0c16b71bc6ba59c9b2'], }), ('TTR', '0.24.3', { 'checksums': ['4d9aef32647664be5cf965b05f21ed62cde9425fa87c21530852e05ef7aaba87'], @@ -814,16 +806,16 @@ exts_list = [ 'checksums': ['ff4e302139ba631280fc9c4a2ab168596bfd09e17a805974199b043697c02448'], }), ('pcaPP', '2.0-3', { - 'checksums': ['9690e2f263162452d5a14bd8c52264cb70b317d30907411af4e5b6df4086121a'], + 'checksums': ['1aac554f039753bf9d026090e47d66b82bf3f1f75479ed0adefa3f7bbb55d603'], }), ('pscl', '1.5.5', { 'checksums': ['054c9b88a991abdec3338688f58e81b6ba55f91edb988621864b24fd152fee6f'], }), ('fastmap', '1.1.1', { - 'checksums': ['9113e526b4c096302cfeae660a06de2c4c82ae4e2d3d6ef53af6de812d4c822b'], + 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], }), ('cachem', '1.0.7', { - 'checksums': ['9a9452f7bcf3f79436c418b3c3290449fb8fd338714d9b992153754d112f1864'], + 'checksums': ['234fad2a947d1e1fb87d3fa92abf9197877772e31bc81ae5991ae69689b6320a'], }), ('memoise', '2.0.1', { 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], @@ -832,7 +824,7 @@ exts_list = [ 'checksums': ['2d88d683ee3d1b56b332b5c7769979b5d3994b5d9285ea634ec919576da3631b'], }), ('RSQLite', '2.3.0', { - 'checksums': ['2ae36a875ebc02497985b2ad9ddc6a5434f576e2ab25769580749d9e4f3b607c'], + 'checksums': ['442e19a1d08ed072e795e2c968cd7e9e2cf9e1a7412bf6b30d21d34ffe175d33'], }), ('BatchJobs', '1.9', { 'checksums': ['5da9c381df461320ed4033523bad1ee97f88a4670d2714fec32be92964115c77'], @@ -841,17 +833,16 @@ exts_list = [ 'checksums': ['6e30b6b554eb19430a60c45a8132fb7918ddb0013577bf6a62caeb163bdfe2b4'], }), ('sfsmisc', '1.1-14', { - 'checksums': ['a81710357de2dcdaf00d9fa30a29cde0dd83616edc358452fd6105ea88f34218'], + 'checksums': ['bca942d8c2d738c6e4a8fdee832ae29e39dc3010d18cdf74613f379b6ffcb3ef'], }), ('spatial', '7.3-16', { - 'checksums': [('e5613be94d6f5c1f54813dadc96e4a86b3417dea28106cc90cb24dfd6c3c8cef', - 'de1dafbccfde599ae24c5a78dbbc2df746d17f4c97d7b1c282a03ddff2f23ecf')], + 'checksums': ['e46565a64c5ec148a77789867e5103746462a41de294539b230bad2a0e16e406'], }), ('VGAM', '1.1-7', { - 'checksums': ['446a61bac5dd4794e05d20c2f3901eec54afac52c6e23ce2787c5575170dd417'], + 'checksums': ['a4c52d392332477eac557c84b732f3c03dd48f75db3884e23c71cf99d991757e'], }), ('waveslim', '1.8.4', { - 'checksums': ['988bdce52ce1c31cb0abb4fb7a9f1e9192283f597c2a418f0010f780dbe3b37b'], + 'checksums': ['408eeea72a218ef3458f0934ff556733cacf1a63ddaa52491abcc1fce6ed2094'], }), ('xtable', '1.8-4', { 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], @@ -863,13 +854,13 @@ exts_list = [ 'checksums': ['56098d2ce238478e7a27cacc4cdec0bc65f287fe746b38fbb1edda20c1675023'], }), ('deSolve', '1.34', { - 'checksums': ['74670f16eaafddd044a3ac1813acd5d164aed3f862b87aa1ac275b600e27d9ad'], + 'checksums': ['2254305f44dde22ac685fef4c60e29a0608af0197c803107365d1d80b75c9f21'], }), ('tseriesChaos', '0.1-13.1', { 'checksums': ['23cb5fea56409a305e02a523ff8b7642ec383942d415c9cffdc92208dacfd961'], }), ('tseries', '0.10-53', { - 'checksums': ['a55f20704883710ab58ea479e20cf0f263c50d54282f693793cda4af664c207f'], + 'checksums': ['ec388ee6d022752bbebbecbf22d793d31f3734982e3f2e3ffd8dde14bffcca56'], }), ('fastICA', '1.2-3', { 'checksums': ['e9ef82644cb64bb49ae3b7b6e0885f4fb2dc08ae030f8c76fe8dd8507b658950'], @@ -881,34 +872,34 @@ exts_list = [ 'checksums': ['b8b19061774918ee7d9d4330c16c0ea505f7cd02d01343df1e8b2e4fb847beef'], }), ('sys', '3.4.1', { - 'checksums': ['17f88fbaf222f1f8fd07919461093dac0e7175ae3c3b3264b88470617afd0487'], + 'checksums': ['324e6d8fde58264e62bc04867b719c5fd16296de1542689801b8cb13621ecf52'], }), ('askpass', '1.1', { 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], }), ('openssl', '2.0.5', { - 'checksums': ['862d3dc9bb69d92e36e83a7506be83443d4a4957f5f08f6617d7873c67a1f1c4'], + 'checksums': ['8ac2140d59f9b4c642970736b08579bc8d59874ee72e1efca1826420b00786d3'], }), ('httr', '1.4.5', { - 'checksums': ['9a8613fa96173ac910c021391af1ced4d0609169049c802cf7cdfe1c40897c6a'], + 'checksums': ['f93bac7f882b0df099abca47dd5aae3686fb3cd2d3e9926fcd639bcddff76f6c'], }), - ('cgdsr', '', { - 'checksums': ['4aa2a3564cee2449c3ff39ab2ad631deb165d4c78b8107e0ff77a9095340cc1f'], + ('cgdsr', '1.2.10', { + 'checksums': ['43bc02fb33c371464f9407d5e5e6419527e9360e3e394343862cca0aebe1d0f7'], }), ('R.utils', '2.12.2', { - 'checksums': ['622860f995f78be3a6e439f29d945874c5cb0866f6a73a9b43ac1d4d7f23fed8'], + 'checksums': ['fe3cf1aa8641540634e96990294d0202d4d94ec79ce73aaf78e4eda30fcb8836'], }), ('R.matlab', '3.7.0', { - 'checksums': ['1ba338f470a24b7f6ef68cadbd04eb468ead4a689f263d2642408ad591b786bb'], + 'checksums': ['d713522268a1206555610938350137ea022e07e27fa9cdd73c02fae8d1a43dda'], }), ('gridExtra', '2.3', { 'checksums': ['81b60ce6f237ec308555471ae0119158b115463df696d2eca9b177ded8988e3b'], }), ('gbm', '2.1.8.1', { - 'checksums': ['7d5de3b980b8f23275e86ac9bed48a497c9aa53c58e407dfd676309f38272ec1'], + 'checksums': ['8d2456124552658ee9500707c4e9992cf42cb88705008c32ea258efb4f2be80b'], }), ('Formula', '1.2-5', { - 'checksums': ['cb70e373b5ed2fc8450937fb3321d37dfd22dcc6f07cb872a419d51205125caf'], + 'checksums': ['86254674600d64e18b65d52f42d7ebfc217c8e1945cb63ac06da22cbf04d355c'], }), ('acepack', '1.4.1', { 'checksums': ['82750507926f02a696f6cc03693e8d4a5ee7e92500c8c15a16a9c12addcd28b9'], @@ -917,28 +908,28 @@ exts_list = [ 'checksums': ['9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1'], }), ('chron', '2.3-59', { - 'checksums': ['9645d86a84d1afc12a0accf4f826fdd40e6d050a313424ad70f8085e8f19c232'], + 'checksums': ['b943a6b97c42e7858dcd4a23deeb1f3a817f9f5086776177627ddc58894601f6'], }), ('viridis', '0.6.2', { 'checksums': ['69b58cd1d992710a08b0b227fd0a9590430eea3ed4858099412f910617e41311'], }), ('yaml', '2.3.7', { - 'checksums': ['3edf6c0554a0e184a25e8bec5721a2e66b4ab0dceb3737428e22705e52eb5140'], + 'checksums': ['d20cb219e0f9c48aba02f132f81cfa9ecda5e22c925e36726840218ed56680ab'], }), ('htmltools', '0.5.4', { - 'checksums': ['7dc7d50436e5a82a5801f85bcd2f572a06a98b4027d71aa17b4854ec9b2767fb'], + 'checksums': ['008228a8690d39d8ae2716bc614e76337fdbe2bac4e96258c10245fdf24f327e'], }), ('htmlwidgets', '1.6.1', { - 'checksums': ['1a3fc60f40717de7f1716b754fd1c31a132e489a2560a278636ee78eba46ffc1'], + 'checksums': ['42533cbcbefcfe5978c66d7f10f28d294c344e606aa75323c797d5a1dd960e43'], }), ('knitr', '1.42', { - 'checksums': ['c91a65edebdca779af7f7480fa6636667497c9291ad55d6efd982db0bb91ac72'], + 'checksums': ['9344f1a0089e4da101def54aee38d7cfe3b2022d75c560141d8cc22ac65130f3'], }), ('htmlTable', '2.4.1', { - 'checksums': ['4ca2b5616d77cfeee8ae5ca74307b86407d478b12d1ce17ba9c447e233b89a9d'], + 'checksums': ['3a7f3e75d886dc398fd1d3cae907b536fff6af3a3d2c18349ef12ec06d310f93'], }), ('Hmisc', '4.8-0', { - 'checksums': ['29ec2d9ca11c790c350e93323126bef4f498c69c41c31bb335fd04671e0f87bd'], + 'checksums': ['6392ed4b96c8ea95da1ebfa92b38cc3baa0314babb2680a08800d0b25c0a9b1d'], }), ('fastcluster', '1.2.3', { 'checksums': ['1f229129e1cddc78c7bb5ecc90c4d28ed810ee68cf210004c7cdfa12cfaf2a01'], @@ -947,10 +938,10 @@ exts_list = [ 'checksums': ['dfea36edb0a703ec57e111016789b47a1ba21d9c8ff30672555c81327a3372cc'], }), ('bibtex', '0.5.1', { - 'checksums': ['7bad194920b412781ac9754ad41058d52d3cd7186e1851c2bce3640490e9bc6d'], + 'checksums': ['f3c1a0a4e666c4addd73ff13ce8ce073d73d10ebca36d333328ade8a0b493ed1'], }), ('pkgmaker', '0.32.8', { - 'checksums': ['ce45b22def771a9c90a414093823e6befe7e23489c500eeccee5154b44d3ef91'], + 'checksums': ['0ff3578d2c051b544c3f105cfe4801575aac1564add048f9e952c53a8ccd1745'], }), ('rngtools', '1.5.2', { 'checksums': ['7f8c76ca4c7851b69a86e27be09b02ddc86357f0388659ef8787634682e8a74d'], @@ -962,19 +953,19 @@ exts_list = [ 'checksums': ['be8718d24cd10f6e323dce91b15fc40ed88bccaa26acf3192d5e38fe33e15f26'], }), ('irlba', '2.3.5.1', { - 'checksums': ['26fc8c0d36460e422ab77f43a597b8ec292eacd452628c54d34b8bf7d5269bb9'], + 'checksums': ['2cfe6384fef91c223a9920895ce89496f990d1450d731e44309fdbec2bb5c5cf'], }), ('igraph', '1.4.1', { - 'checksums': ['0f5066180e223e165d28cee050054008ca23102e8392ff4ecd72e733537ec320'], + 'checksums': ['08a258f46ae87bcbe7f7cf47d46d2bbedb0663407921a30fc89892674b505df1'], }), ('GeneNet', '1.2.16', { 'checksums': ['c1e98073ccdaa18f4952630bfe4fc0617106eeaf7ed94d347cb2773bd48333e4'], }), ('ape', '5.7', { - 'checksums': ['9b62450a0390a1f07df007d348ad4cedcd814d42cb11c5a300ed33550fd41257'], + 'checksums': ['09b4aee7e8bf013c00dd66f5fbe954830e439d97416b278bfbd918bb3da1f569'], }), ('RJSONIO', '1.3-1.8', { - 'checksums': ['82d1c9ea7758b2a64ad683f9c46223dcba9aa8146b43c1115bf9aa76a657a09f'], + 'checksums': ['f6f0576d3c7852b16295dfc897feebca064fe5dd29cdce7592f94c56823553f5'], }), ('caTools', '1.18.2', { 'checksums': ['75d61115afec754b053ed1732cc034f2aeb27b13e6e1932aa0f26bf590cf0293'], @@ -992,19 +983,19 @@ exts_list = [ 'checksums': ['8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7'], }), ('httpuv', '1.6.9', { - 'checksums': ['f5f63629ca5e9d0e396a89982d95b5286726c0cb425166f35a3ad32a60a79156'], + 'checksums': ['8d77f25b22fa7473b45007c2048e9a38d3792d59b2716e1fcdf9e99bd585d95d'], }), ('rjson', '0.2.21', { 'checksums': ['982b56d35ccc0c7db0b20c1d3eab5f5f47c620309646fdc278ff1cc3433ea2e2'], }), ('sourcetools', '0.1.7-1', { - 'checksums': ['47984406efb3b3face133979ccbae9fefb7360b9a6ca1a1c11473681418ed2ca'], + 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], }), ('xml2', '1.3.3', { 'checksums': ['cb4e9c0d31618ed67d2bfa4c7b5e52680e11612ed356a8164b541d44163c1c8d'], }), ('commonmark', '1.8.1', { - 'checksums': ['7d07e72937b1cf158e69f183722bf79dbb91b8967a9dd29f4fa145500c2be668'], + 'checksums': ['96adcb093de3d2e48811af402da70e7222a313b97f1e979e0cbe84dd59bd5cbe'], }), ('jquerylib', '0.1.4', { 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], @@ -1013,22 +1004,22 @@ exts_list = [ 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], }), ('fs', '1.6.1', { - 'checksums': ['35cad1781d6d17c1feb56adc4607079c6844b63794d0ce1e74bb18dbc11e1987'], + 'checksums': ['faf1e421a2c270c60c0a30c74e1a48faad45b339163716102d77d64d23d76732'], }), ('sass', '0.4.5', { - 'checksums': ['850fcb6bd49085d5afd25ac18da0744234385baf1f13d8c0a320f4da2de608bb'], + 'checksums': ['eba161d982d2db108c8c0b61ec6b41a20d3adec430c7cc39537ab388c1007a90'], }), ('bslib', '0.4.2', { - 'checksums': ['5f5cb56e5cab9039a24cd9d70d73b69c2cab5b2f5f37afc15f71dae0339d9849'], + 'checksums': ['9a40b7a1bbe409af273e1e940d921ab198ea576548f06f055f552f70ff822f19'], }), ('fontawesome', '0.5.0', { - 'checksums': ['572db64d1b3c9be301935e0ca7baec69f3a6e0aa802e23f1f224b3724259df64'], + 'checksums': ['4117b417a33e82d626881d7059eb54e7534cba202e75dae7e27021cb3796e90b'], }), ('shiny', '1.7.4', { - 'checksums': ['c03b2056fb41430352c7c0e812bcc8632e6ec4caef077d2f7633512d91721d00'], + 'checksums': ['bbfcdd7375013b8f59248b3f3f4e752acd445feb25179f3f7f65cd69614da4b5'], }), ('seqinr', '4.2-23', { - 'checksums': ['c4f3253832fc255197bdce7b4dd381db606c6b787d2e888751b4963acf3a4032'], + 'checksums': ['af2174178972f71821062daec3e3ce98edfec19dd133f6bbbf39f5dcd821fb93'], }), ('LearnBayes', '2.15.1', { 'checksums': ['9b110858456523ca0b2a63f22013c4e1fbda6674b9d84dc1f4de8bffc5260532'], @@ -1040,37 +1031,37 @@ exts_list = [ 'checksums': ['da7d48021b7cd2fd8a7cd8d0bb9658b12342a32698a13877b25ca94aa03f1e95'], }), ('expm', '0.999-7', { - 'checksums': ['2c79912fd2e03fcf89c29f09555880934402fcb2359af8b4579d79b4f955addc'], + 'checksums': ['28f249b914b8dd33eee16663fc793e57afd0e301e16067bf9f27fa8e591ba0f1'], }), ('terra', '1.7-3', { - 'checksums': ['3cad88f4fad6517713861a8debc8c7c746c32e0c2ee851bb0c2bc43744fcaa1c'], + 'checksums': ['89fe9397c8b101088d5c3de47212ea8fa4770805ad33cfff4314c6f08a68272e'], }), ('raster', '3.6-14', { - 'checksums': ['29c7d3c5d34284f8b5a2ddc9989fbcf092ce209d5eb5310ebc772b5ebdfdd685'], + 'checksums': ['031382b10a57ff88cfca8565b5195e192e2beb377c0833154de4d1db1a0d3b0a'], }), ('spData', '2.2.1', { - 'checksums': ['c635a3e2e5123b4cdb2e6877b9b09e3d50169e1512a53b2ba2db7fbe63b990fc'], + 'checksums': ['55345437e751b81d8ce1342382f7feeaa299d0421d6f9cc52d9bae46189ab3b5'], }), ('units', '0.8-1', { - 'checksums': ['9c46fe138e8c1c3d3a51268776412f02d09673656516148cccb71b1071beb21a'], + 'checksums': ['d3e1ba246b4c97205bc3da3cf45d6b5bd5c196b8d421b84b4e94b2090985cd9a'], }), ('classInt', '0.4-9', { - 'checksums': ['a30e3a8987ce133944897100ab5bdc31b019d897969c452c3795f50ac234606e'], + 'checksums': ['5b11af7d08f8793c7b47ee7c68b8e371cb23027165d30abddbd8b2abcc20e1c3'], }), ('vegan', '2.6-4', { - 'checksums': ['ab77d110c959d19b0c6268ae0c8f78c897e2419eff3f1f7b19c1bb2f8db7c059'], + 'checksums': ['5d8ad4bebe79ae2bbd840a34100cf54c62f089c66ea484a542a201afcba21d06'], }), ('rncl', '0.8.7', { - 'checksums': ['fcc972c04fb43ace0876eb640a6433caddf6ec8304f7ceee37107d812ce68ffb'], + 'checksums': ['1d876e4f5f2b8a24cc3ea1002c29eedbc0ca96011b0fa15b085e5b75cfc7993a'], }), ('XML', '3.99-0.13', { - 'checksums': ['c45991b5edadc3cf7e2d80c38e798a5d6c4e27baf6007004d4db5a6ca97ff35b'], + 'checksums': ['85c568a6e2f0c43a8026d10861ddd8984907b03665ed88fca1a3776c25e8f73a'], }), ('tinytex', '0.44', { - 'checksums': ['3f5e7adb2c047a8181a39fe5fee1f709039e6e94245f98c64282fdecc183d88d'], + 'checksums': ['afa14c1274593f0f980b12c4a27b5d0f6cad0c28ed9b4062d59e42562a33620e'], }), ('rmarkdown', '2.20', { - 'checksums': ['e9ec17afa4d9d6e8cf555b56e0c00acc189d8ec0b4406680b14d71d62f0c3220'], + 'checksums': ['d7f7059bfcb43e4b92432d69ba0e0c74ad10a20f153689262a3e848adb60159d'], }), ('reshape', '0.8.9', { 'checksums': ['791178b3b5f30c166ebf5910a5ab1c67b54e7023b10b6c2e2ddd1cc02a1e4048'], @@ -1085,19 +1076,19 @@ exts_list = [ 'checksums': ['593a030a4f94c3df8c15576837c17344701bac023ae108783d0f06c476062f76'], }), ('crul', '1.3', { - 'checksums': ['be1a149b21cf219ef55adfb56a6a5eb9892a9acf0d5f5421a22e52f2a7066f8c'], + 'checksums': ['8058617d8b3724acb5b89d0e6e63f381df5c56565128b250a65eceb2b8081e2d'], }), ('bold', '1.2.0', { 'checksums': ['8f1597f04acbe6b090232929325734c802049d82649ae102b438e1fa3af5a464'], }), ('rredlist', '0.7.1', { - 'checksums': ['d2e66b655c43565a4cc0984dc3fcc9732652cb9677baaa9bb2b82e9f9d65e7f0'], + 'checksums': ['92a10c37a211dc19b41b93f9ceb13d7ce1c3d3a7290cbba4c1688d944353ae85'], }), ('rentrez', '1.2.3', { 'checksums': ['fb256597ebe7780e38bef9c4c2626b3feacd60c7a5a29fc6a218cf0d8d132f74'], }), ('rotl', '3.0.14', { - 'checksums': ['1688b3284139803a9b1339d7f34a5db94bb1f2f4fd4c395423f7164dbdb3d98e'], + 'checksums': ['982ae7012c0e6c56115d5355c6269c507965c3b0b7f251daf1ca49eb80ad5fcf'], }), ('solrium', '1.2.0', { 'checksums': ['7ec64199497cc69f542fded955b709fc548cf8e2734c9db0f4a99a0ea67ca49b'], @@ -1124,7 +1115,7 @@ exts_list = [ 'checksums': ['0e14eec8471a72227f800b41b331cfc49a94b4d4f49e68936448ebbae0b281ae'], }), ('pbapply', '1.7-0', { - 'checksums': ['effdfee286e5ba9534dc2ac3cee96590a37f5cd2af28c836d00c25ca9f070a55'], + 'checksums': ['64b8e931e0a09031c20b66173ce80a646043b8f135d329bc86226a11c6b706c0'], }), ('WikidataR', '2.3.3', { 'checksums': ['3da74b0584b8141a1b61b4d8f58e53c0e46524d811b1642bcc01fb7fd6180888'], @@ -1133,7 +1124,7 @@ exts_list = [ 'checksums': ['ba872853af59fdc8f1121d6e205f15e5bf4f2ec5ad68cd5755a423fa783bf7fc'], }), ('phangorn', '2.11.1', { - 'checksums': ['3262dbe002bedc636467d4ac77044965f4976da09fa710c606075c5ddf26da23'], + 'checksums': ['10096ecae03e118aa4dbc60d9866175fad4849c948e004cf10c3868e3feed420'], }), ('uuid', '1.1-0', { 'checksums': ['e75b50ee7dc8c4c8e7083023e954ffd1c6a004431bf5e9094463e46aa760f42f'], @@ -1145,7 +1136,7 @@ exts_list = [ 'checksums': ['e2e578fc45eb5d1306332892c67535fa4bc32d63129532df2c6cde393993cd29'], }), ('RNeXML', '2.4.11', { - 'checksums': ['cb311d6dda33a95521a6df360a2d2f4e6d6bc6b330ac5e19ea721ca665bce6fe'], + 'checksums': ['246913cbb0e816401bb8e37dda20646202547f5cc8379c9dadf832f61d6cfd46'], }), ('phylobase', '0.8.10', { 'checksums': ['5a44380ff49bab333a56f6f96157324ade8afb4af0730e013194c4badb0bf94b'], @@ -1157,7 +1148,7 @@ exts_list = [ 'checksums': ['88418f1b04ec785963bad492f30eb48b05914e9e5d88c7eef705d949cbd7e469'], }), ('bigmemory.sri', '0.1.6', { - 'checksums': ['55403252d8bae9627476d1f553236ea5dc7aa6e54da6980526a6cdc66924e155'], + 'checksums': ['3bfa6ac966ce0ea93283f5856a853d0ee5ff85aedd7a7d1ca8a93d0aa642860c'], }), ('bigmemory', '4.6.1', { 'checksums': ['b56e157c87ed6c4fc69d4cb9c697ae9a2001726e776e41aa7c48b35327b65141'], @@ -1169,28 +1160,28 @@ exts_list = [ 'checksums': ['534f29d8f7ed11e6e9a496f15845b588ec7133f3da5e6def8140b88500e52d5c'], }), ('dismo', '1.3-9', { - 'checksums': ['812e1932d42c0f40acf2ab5c5b2d068f93128caf648626e1d11baf1a09340ee7'], + 'checksums': ['3924521db67716b004a4c870985c65d037edfe926b14222740fd6c2b2093beee'], }), ('extrafontdb', '1.0', { 'checksums': ['faa1bafee5d4fbc24d03ed237f29f1179964ebac6e3a46ac25b0eceda020b684'], }), ('Rttf2pt1', '1.3.12', { - 'checksums': ['81886b4f686341ce5139816233c957e840541d17a1d2db0047af17d527f0e1ba'], + 'checksums': ['0b4b7a303990369a6944de817b6bd220b400942fcabf42c04fb5b56f1b40a583'], }), ('extrafont', '0.19', { - 'checksums': ['44e6a9798914b99c1460a1177c1f1503cf2a2f74844e3e7858fb98462b08a857'], + 'checksums': ['4e8f90152df13fc5dee573222a26b4d66553493fdf6af1c7777e59521ccdab8d'], }), ('fields', '14.1', { - 'checksums': ['c652838b1ae7eb368831522824bfbc1d1db7b9d1db5e9bb52b194098549944c3'], + 'checksums': ['57c4c5592443d2ee869014b3199989b5edd1aff52e24f1cd313b8f9b34a95434'], }), ('shapefiles', '0.7.2', { - 'checksums': ['eeb18ea4165119519a978d4a2ba1ecbb47649deb96a7f617f5b3100d63b3f021'], + 'checksums': ['4bfa4094c1052c1b1918b1670798f8b4e53f771cfdf9cb8c04bd00a856674d0f'], }), ('fossil', '0.4.0', { 'checksums': ['37c082fa15ebae89db99d6071b2bb2cad6a97a0405e9b4ef77f62a8f6ad274c1'], }), ('phytools', '1.5-1', { - 'checksums': ['bfe2aec6aae8235264c1494eee42be494fed81a676c6de9e39c57a6e3682b37d'], + 'checksums': ['f8be59abbff1f5032be4523c361da53b0d5b71677fedebba6d7cbae2dca7e101'], }), ('geiger', '2.0.10', { 'checksums': ['2895cfb73fb91764be2ec3f931e4f3b2e75ae00a1431af4b40dc90e7c0693be0'], @@ -1199,7 +1190,7 @@ exts_list = [ 'checksums': ['b9103e5ed05c223c8147dbe3b87a0d73184697343634a353a2ae722f7ace0b7b'], }), ('glmnet', '4.1-6', { - 'checksums': ['f6b0f70a0b3d81ff91c2b94f795a2a32e90dd458270f1a29e49e085dd65000f9'], + 'checksums': ['bec4c6cea284d0dc24bbdac3e623f0772cea1d74ef77e718651e3830c74b7e30'], }), ('crosstalk', '1.2.0', { 'checksums': ['4237baab35cd246a8a98fb9cf4ce53b6ddbc31d00742ded4edea0479613d1ea0'], @@ -1208,7 +1199,7 @@ exts_list = [ 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], }), ('webshot', '0.5.4', { - 'checksums': ['b7c4f2be61c8c4730202a9c3604072478e30cb85b423b7497cd703cc3f49dbc0'], + 'checksums': ['3dc2b9baef7855e1deea060276b9ccc6375eee36b7100987cbb1f8e5cd7a8f24'], }), ('shinyjs', '2.1.0', { 'checksums': ['7ec20cbf1b1fd7a32d85a56dfc0df8b5f67c828d241da400a21d893cb37ea9c5'], @@ -1217,7 +1208,7 @@ exts_list = [ 'checksums': ['5b73728d7d6dcc32f32d861375074cd65112c03a01e4ee4fa94e21b063fdefb6'], }), ('rgl', '1.0.1', { - 'checksums': ['117504ce5a22ead0b068314988804f4aeec0fb8a354c4c5f214cfe2de29d2c97'], + 'checksums': ['89a300faca7dc34a2c2a1f174a02754b2ceb5fcfffb746487af02b23c30a2fc8'], }), ('Rtsne', '0.16', { 'checksums': ['52a05adc826c28212e97d11c54eba3fec45d14eb52039c0f47f62a8e338ffbd5'], @@ -1238,7 +1229,7 @@ exts_list = [ 'checksums': ['edf3ab16b142f4c52d21fc64e41409ed138e5b3e142f2fae964b00f02d53dd7a'], }), ('multcomp', '1.4-22', { - 'checksums': ['f03473b1cfbc714cd85a0ee948e2ecdb23bcdccbe95e27237ee25e9c71e3e557'], + 'checksums': ['171086088c7113ac576ca20efb4fd197eea5cf1754230009656a3fb72d364eea'], }), ('libcoin', '1.0-9', { 'checksums': ['2d7dd0b7c6dfc20472430570419ea36a714da7bbafd336da1fb53c5c6463d9eb'], @@ -1247,46 +1238,46 @@ exts_list = [ 'checksums': ['7546d1f27a82d98b4b3e43e4659eba0f74a67d5919ce85d2fb360282ba3cfbb2'], }), ('party', '1.3-12', { - 'checksums': ['e5892955f6ce662ade568e646d1d672c3ecbf5d4e74b4a887a353e6160f7b56a'], + 'checksums': ['0f686d24e866653e804e473dc26ef0befd7a43f68e718841848bbd864c97cb3f'], }), ('inum', '1.0-4', { 'checksums': ['5febef69c43a4b95b376c1418550a949d988a5f26b1383ca01c9728a94fc13ce'], }), ('partykit', '1.2-17', { - 'checksums': ['e643d4e29c1894497e3dd5fe274783319d0044dec50282ed807cebc21736ddb2'], + 'checksums': ['65ba7ed3ef0c39494a3372b47c4720f31f479cb388449fc5374c51ab255d5a99'], }), ('mboost', '2.9-7', { 'checksums': ['0242cb91656280c4bd705643b65674900a1475305d9f80cfc12ef4b5fa069606'], }), ('msm', '1.7', { - 'checksums': ['aefcd9bb40b0167311d088d6fe23fdf7aa35deaac0f8b47ef02377cff5577023'], + 'checksums': ['7f89f8e47966919e49ef8dfe1f9c82ac6553b2f404bb03840da5f42e73dd0db0'], }), ('nor1mix', '1.3-0', { 'checksums': ['9ce4ee92f889a4a4041b5ea1ff09396780785a9f12ac46f40647f74a37e327a0'], }), ('np', '0.60-16', { - 'checksums': ['a3b31b8ad70c42826076786b2b1b63b79cdbadfa55fe126773bc357686fd33a9'], + 'checksums': ['bef967c0195059e53c68e64d7540bf4627415c832f050c8806520ab8796e01b0'], }), ('polynom', '1.4-1', { 'checksums': ['bc1edb7bb16c8b299103f80a52ab8c5fc200cd07a9056578c1f672e9f5019278'], }), ('polspline', '1.1.22', { - 'checksums': ['6992484e9e41036debef1e705e26959f8f5c7a68d3e1fda58273d2a72297a1b5'], + 'checksums': ['b2f2198f020d7d492a87bad2b58a6cc9ae91d95b7330dd12b9b1145c72d7457b'], }), ('rms', '6.5-0', { - 'checksums': ['6c41eb670daf5e4391cc2f2a19e20a591f90769c124300a7ccf555820140d3f9'], + 'checksums': ['fd6f819d91d673dc40ce45126ed769d47173cda590147192fd98c2f5e45db185'], }), ('RWekajars', '3.9.3-2', { 'checksums': ['16e6b019aab1646f89c5203f0d6fc1cb800129e5169b15aaef30fd6236f5da1a'], }), ('RWeka', '0.4-45', { - 'checksums': ['f3239437aeeb01453b7ce235f9680bc281886b46de0b536d9c8413c6294c7bc8'], + 'checksums': ['f910f17fabebbca9d25c58917c358f1f97edb854b4f9f9b397e10b107bd61028'], }), ('slam', '0.1-50', { 'checksums': ['7899bf3266c204ecccefc1878f96940b117d4503af128f4fbc50fc409163f8bd'], }), ('tm', '0.7-11', { - 'checksums': ['b1eb1683d956db1a207b61cc086ae08b3ca7f46b6b8bc46d09ba5a4fafa66256'], + 'checksums': ['9aab8b8493df4c62cff8adbba53be72295673ba8c546cdb129cdc52aabeae742'], }), ('leaps', '3.1', { 'checksums': ['3d7c3a102ce68433ecf167ece96a7ebb4207729e4defd0ac8fc00e7003f5c3b6'], @@ -1298,7 +1289,7 @@ exts_list = [ 'checksums': ['efbe65e8a9d05824a86095d45ed62ce24d82101d4ca3b94828d443e08e83ccba'], }), ('TraMineR', '2.2-6', { - 'checksums': ['b69ef547443453f1d814d09141f7b9be1dd09ef374cc50771d1a8d3f0815e1a7'], + 'checksums': ['e7f65b5692bf925b3fc94c47083b65917fe3bfdc77b769b4743644a0ad8313e7'], }), ('chemometrics', '1.4.2', { 'checksums': ['b705832fa167dc24b52b642f571ed1efd24c5f53ba60d02c7797986481b6186a'], @@ -1316,13 +1307,13 @@ exts_list = [ 'checksums': ['0251f6dd6ca987a74acc4765838b858f1edb08b71dbad9e563669b58783ea91b'], }), ('rbibutils', '2.2.13', { - 'checksums': ['f1aecdeeba99042d34de19234238c5bbdc18a26f271f6adf9c9b7e349d50d152'], + 'checksums': ['ac235c60bf191ad1830b93045af1b2fe50a6978f6f63cecc4c514a8ba339efc2'], }), ('Rdpack', '2.4', { - 'checksums': ['b53e5e9db53e31f514e2fef46bafa00bc7cd8828e36e5c933e28e9ac892d448a'], + 'checksums': ['7652add12b30fcba1f3a12493a089a4166079e78c47b95802a98595a3ff53581'], }), ('dfidx', '0.0-5', { - 'checksums': ['04255de9b002b2f89db04144edcd72e21804e0c129a3e5082b4a21630c850702'], + 'checksums': ['37521940b35d62773a4d127c94148aadf207f400a686f2212a22d96e53086a0a'], }), ('mlogit', '1.1-1', { 'checksums': ['6f3ea97db410be929a3078422f3d354d2f17855a21bbdc7c2c09d901e233d143'], @@ -1331,31 +1322,31 @@ exts_list = [ 'checksums': ['531f5fdfdcd6b96a73df2b39928418de342160ac1b0043861e9ea844f9fbf57f'], }), ('gsalib', '2.2.1', { - 'checksums': ['e1b23b986c18b89a94c58d9db45e552d1bce484300461803740dacdf7c937fcc'], + 'checksums': ['3da3a4b959142a0d694a843e39143bfce82a6de197c6cc92650a28ac05f3bf90'], }), ('optparse', '1.7.3', { - 'checksums': ['324e304c13efd565d766766193d4ccd75e2cd949dfcfb416afc3939489071fe7'], + 'checksums': ['6287e1af051d4a65037900ce7b30bd962039450dd4eab63b6f2491eace6a07ed'], }), ('labelled', '2.10.0', { - 'checksums': ['9eb10b245f64f3fb7346121aa4cd98638946e1cc4208dd5e28791ef8fd62fa40'], + 'checksums': ['5e93e29dcbbf0f6273b502b744695426e238ffe106f1db2bb5daeb1f17c9c40a'], }), ('R.cache', '0.16.0', { - 'checksums': ['adb4d3b08f7917e10fe6188c7b90a3318701a974c58eaa09943b929382bdf126'], + 'checksums': ['7853409161571a790e0383f64f99e4eae43201a0ed7146d2baf157741a509291'], }), ('styler', '1.9.0', { - 'checksums': ['3e49f3ac2e65f9bdab15837a4e629db35c8fd0a15a74daa057354ba01e3022ce'], + 'checksums': ['a85417b3df03f5b2085a40ce4de295d81fea02d0212f5046ce14c1b6dbaac02f'], }), ('questionr', '0.7.8', { - 'checksums': ['ce24c40bd98dbeca615b9eb2a9cd2da26852821dc3840f8394eeecb0739dfd56'], + 'checksums': ['af72e59fe652c6063282a7e5b0f487993b9361cc9ed052a632d64a5a6db76ba9'], }), ('klaR', '1.7-1', { - 'checksums': ['b4795250ef19fd1b5e1b9a59343fd01159a33dbdbb504a06258220e37a718198'], + 'checksums': ['0354bafb1a202bc439660ecfcfe78359bc2881a69d15ff64afa049e4eb171d25'], }), ('neuRosim', '0.2-13', { - 'checksums': ['f4f718c7bea2f4b61a914023015f4c71312f8a180124dcbc2327b71b7be256c3'], + 'checksums': ['b6f45e005ab0305b797b4f30a73e43d42630a54cafb61728abace27c569eb74b'], }), ('locfit', '1.5-9.7', { - 'checksums': ['fd9f2bad9d8beec8be4843dc80e38ebe0f388835a7003490f67e57eeb9e6de23'], + 'checksums': ['48e5fcd089fbc609d8e4c62c390425fba1dd167ad95ae0bddc175cbbe1517aff'], }), ('GGally', '2.1.2', { 'checksums': ['30352f36bf061bc98bdd5fa373ea0f23d007040bd908c7c018c8e627e0fb28e5'], @@ -1366,26 +1357,26 @@ exts_list = [ ('clValid', '0.7', { 'checksums': ['037da469891462021eb177f9c9e18caefa8532f08c68fb576fae1668a1f451a1'], }), - ('DiscriMiner', '', { + ('DiscriMiner', '0.1-29', { 'checksums': ['5aab7671086ef9940e030324651976456f0e84dab35edb7048693ade885228c6'], }), ('ellipse', '0.4.3', { 'checksums': ['02ef2b11c3462a8b800332e522183f4c7c40c7d2d66c5174d5f3f6d8cc68a946'], }), ('pbkrtest', '0.5.2', { - 'checksums': ['b2a3452003d93890f122423b3f2487dcb6925440f5b8a05578509e98b6aec7c5'], + 'checksums': ['8e79adf035a0fcf3c82145ad55847497379e009f7be880ba3007ebeb2e69b6e3'], }), ('carData', '3.0-5', { 'checksums': ['02e77159b33e3afb8cd9cfab11cf5a996a93175f924b07d991ce44bc6e16451a'], }), ('maptools', '1.1-6', { - 'checksums': ['f3ee25f9787d97c8373dac3651c6a198c932948eb3a6006b8618c91c6344fdc9'], + 'checksums': ['d6a5df52db03b2231f21921b693c67f85df3c3b376181aa13ef4f21710f69308'], }), ('zip', '2.2.2', { - 'checksums': ['9f95987c964039834f770ecda2d5f7e3d3a9de553c89db2a5926c4219bf4b9d8'], + 'checksums': ['e16cde23bb283efbe9b6bce19575c716c371d09033b42514471ccb444c0a8ea4'], }), ('openxlsx', '4.2.5.2', { - 'checksums': ['65d06d2819b656ac30fc78437ee712a83fb5a7ab750f56268e5c9e578c582519'], + 'checksums': ['ee7089e7e5832ef22ee0d0eebf7cca5096ce23afb2bcdb58700be62526fc9b67'], }), ('rematch', '1.0.1', { 'checksums': ['a409dec978cd02914cdddfedc974d9b45bd2975a124d8870d52cfd7d37d47578'], @@ -1394,25 +1385,25 @@ exts_list = [ 'checksums': ['5d38f288c752bbb9cea6ff830b8388bdd65a8571fd82d8d96064586bd588cf99'], }), ('readxl', '1.4.2', { - 'checksums': ['ab9239c249f79b649f7665a612b3dbf4b774ab633115e6dee41091a8cb2491f7'], + 'checksums': ['387304e2c5be0dca4861ec0232f0d92cc1882b660ca917f8f2a8a4ae858aba11'], }), ('rio', '0.5.29', { 'checksums': ['9fa63187e1814053e6ed2a164665b4924e08c3453adccb78f7211d403dcc5412'], }), ('car', '3.1-1', { - 'checksums': ['bd52b4eaea46ce828fccd93445301d06ebd265e2ffff796064875a8c0f0aea21'], + 'checksums': ['8fc55815eed7e46a32b54da9e0bfa4b74a8d082d73d896e3372f2a413b6bd2bc'], }), ('flashClust', '1.01-2', { 'checksums': ['48a7849bb86530465ff3fbfac1c273f0df4b846e67d5eee87187d250c8bf9450'], }), ('ggrepel', '0.9.3', { - 'checksums': ['29fb916d4799ba6503a5dd019717ffdf154d2aaae9ff1736f03e2be24af6bdfc'], + 'checksums': ['b9eba0e2edee84db0276b49e4834b65f5369edc4bc56f4cacc13e0d1c39a005c'], }), ('DT', '0.27', { - 'checksums': ['360ae2fcb1141125a1b16448570fc37d14c4dd3f78a872c26df4fda1787cdc70'], + 'checksums': ['e32fdccd2be430933cff88a9ce79045bfdbe3e08e0cd8d15037445808613289a'], }), ('FactoMineR', '2.7', { - 'checksums': ['b9e3adce9a66b4daccc85fa67cb0769d6be230beeb126921b386ccde5db2e851'], + 'checksums': ['27b83ecc64cf445a42d0af3812492fd58624839fa5d458ec0ca6666ed914250d'], }), ('flexclust', '1.4-1', { 'checksums': ['d67977df059e622832358069509f8968d506074320a45d34bfd21c65f898538d'], @@ -1430,10 +1421,10 @@ exts_list = [ 'checksums': ['9239f20e4a06ac2fa89e5d5d89b23a45c8c534a7264d89bede8a35d43dda518b'], }), ('fpc', '2.2-10', { - 'checksums': ['29b0006e96c8645645d215d3378551bd6525aaf45abde2d9f12933cf6e75fa38'], + 'checksums': ['99b4548f2eca1a092a31bc2fa4e4bd1d6b50fdfacf3218588c879ceec99147d2'], }), ('BiasedUrn', '2.0.9', { - 'checksums': ['2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e'], + 'checksums': ['bac62bbbc3e2417772f8784996a6c2d0857adb42e86e46b1a9703b187a406b09'], }), ('TeachingDemos', '2.12', { 'checksums': ['3e75405ce1affa406d6df85e06f96381412bc7a2810b25d8c81bfe64c4698644'], @@ -1442,13 +1433,13 @@ exts_list = [ 'checksums': ['018d820acdb7dfa716275ba24c4d671cb0202cb1fee584b673d0118e2c9063ae'], }), ('base64', '2.0.1', { - 'checksums': ['8e259c2b12446197d1152b83a81bab84ccb5a5b77021a9b5645dd4c63c804bd1'], + 'checksums': ['4d22687c0195c2049e0af2c613b1ebcb908037010ad6e550bf47d69e842535f1'], }), ('doRNG', '1.8.6', { - 'checksums': ['33e9d45b91b0fde2e35e911b9758d0c376049121a98a1e4c73a1edfcff11cec9'], + 'checksums': ['5032ade083f1f9841ac2e8d4426faa07f189c25c0c338fa155c5dadbe5507de2'], }), ('nleqslv', '3.3.4', { - 'checksums': ['f54956cf67f9970bb3c6803684c84a27ac78165055745e444efc45cfecb63fed'], + 'checksums': ['2783e7525bcd155dd8cedf5a41b7db65cd1fa0e095cd937371448316f3930fcf'], }), ('Deriv', '4.1.3', { 'checksums': ['dbdbf5ed8babf706373ae33a937d013c46110a490aa821bcd158a70f761d0f8c'], @@ -1487,10 +1478,10 @@ exts_list = [ 'checksums': ['bd7fd9e35928d09d0e8fae9e4359a2b2bca6e6865b278436319e2f91db0e4b37'], }), ('forecast', '8.21', { - 'checksums': ['9f01eb895a883a7e1e23725b167b46edc1b0b152fd4120278aaa5f7b2621767f'], + 'checksums': ['fdd131795a9d3fb399d76a9aa66a0c276637caaa9ec0c75fbe386189d005c6c2'], }), ('fma', '2.5', { - 'checksums': ['69a94c3bd464176a80232d49fcd04d478d4dd59f9bf128d6a9f46e49612d27f4'], + 'checksums': ['400dea4d2b6e73ed686d901fbab1b4f930dfcdd67fbd0bb3abc34a707656cf78'], }), ('expsmooth', '2.3', { 'checksums': ['ac7da36347f983d6ec71715daefd2797fe2fc505c019f4965cff9f77ce79982a'], @@ -1502,43 +1493,43 @@ exts_list = [ 'checksums': ['e1dec23e3913a82e2c79e76313911db9050fb82711a0da227f94fc6df2d3aea6'], }), ('polyclip', '1.10-4', { - 'checksums': ['74dabc0dfe5a527114f0bb8f3d22f5d1ae694e6ea9345912909bae885525d34b'], + 'checksums': ['84d2c9778771d3759b49d7d16fb54c8ddc5397da3b1d21074bc4aa42c02e6f56'], }), ('goftest', '1.2-3', { 'checksums': ['3a5f74b6ae7ece5b294781ae57782abe12375d61789c55ff5e92e4aacf347f19'], }), ('spatstat.utils', '3.0-1', { - 'checksums': ['5b914308df0585993084b5e95967864eea0314c98ed6af58267b64b2235dfe22'], + 'checksums': ['cba1c7806564fd9145ca15edf77233d6ba5609f0989f7812221f5fc1ece0b91a'], }), ('spatstat.data', '3.0-0', { - 'checksums': ['d3943bb4f6509d60bf68e79ce4533c5ec5261f411da6b0ef5238c124fc37c3e5'], + 'checksums': ['cff9058a88489020a4a05b9576cd452f37fa9b42084873c474d06931f5187057'], }), ('spatstat.geom', '3.0-6', { - 'checksums': ['32b89a409ce87ffe901e4c8720a26cac9629f9816e163c4ad68b7aa012d69e67'], + 'checksums': ['6378750668363f09a80e8f6c60664e37b88f7ae6fbb296d3b978639d6e8ff20c'], }), ('spatstat.sparse', '3.0-0', { - 'checksums': ['9a35ad69715b767b3ae60b02dce05ccf108fcccdf95bbc8f7d02557bcbde7303'], + 'checksums': ['99be0a3c7592760fdf1668dc0811f75ed91c400390d1ecc3d5e643255f501ad2'], }), ('spatstat.random', '3.1-3', { - 'checksums': ['45f0bbdb9dbd53b6c4151c3cdd098451cf787729717ccbb063cd1f33910e604d'], + 'checksums': ['b28af559ca28002abf9c937b68ad5e7f7317d8c3f976e9a97bebe0c652c441d0'], }), - ('spatstat.core', '', { + ('spatstat.core', '2.4-4', { 'checksums': ['e38c39efe8b14d6e8fdbee8dd870b90c52f78ea571ab7988fd3685f48347d13b'], }), ('spatstat.linnet', '3.0-6', { - 'checksums': ['9c78a4b680debfff0f3ae934575c30d03ded49bc9a7179475384af0ebaf13778'], + 'checksums': ['1609d4c3b3bf168b6218827749e0c887c09727dc144403a2cf7778e8c8fb606a'], }), ('spatstat', '3.0-3', { - 'checksums': ['4ea0f8d70b926b92bf4a06521f985a0bb6d573619f5d526957c87860ccb999da'], + 'checksums': ['1daf773656da834790ea4a9013d1e1858575888e55007a3a5849b7290771502a'], }), ('pracma', '2.4.2', { - 'checksums': ['2302d454406e72711714732658d0c59c9d5a1ead698f22ee23f38cba63d42764'], + 'checksums': ['1d50337fdfd9a8d704a64f01dae5d52b9a2bd6d872fdaa4a6685b8d3bde89c16'], }), ('RCurl', '1.98-1.10', { - 'checksums': ['2ac22d0160633fe3b6b26f3eda5df839eee1120f0111e1172f0fc801f874188d'], + 'checksums': ['5a622bcf8b6fb77f4b01e9473d3685f64f51401240630bb25b0266a61306f1d4'], }), ('bio3d', '2.4-4', { - 'checksums': ['c6031f0d9033260a938171d0fa70720962e352935eb7bd2ddb9b92b93abe6a74'], + 'checksums': ['5654eac10d33e4235ef89292e3b99006d8812b6bfaaa3d6fb540312160fd9de9'], }), ('AUC', '0.3.2', { 'checksums': ['836b25b654a82f6ab69b86be95acc22a214da0ad06d71eab787ae1ebe721ae1f'], @@ -1562,7 +1553,7 @@ exts_list = [ 'checksums': ['93e365a4907e301ae01f7d943e6bdcda71ef23c51a4759ba3c94bcf842d4e0f8'], }), ('dimRed', '0.2.6', { - 'checksums': ['ab043bcbac4636faadb81c0654cab58aeeec850fba3f8b7a749bea8a58c30efd'], + 'checksums': ['9a7eb14781f01a12e26e7b26a91c8edaca7d824b9c1ffe74c81837098d9bf417'], }), ('ddalpha', '1.3.13', { 'checksums': ['e4a60a4e0950a3587db2a2d5958ab4fbe07b2548f7c3d4795912fe45c77a4eae'], @@ -1577,19 +1568,19 @@ exts_list = [ 'checksums': ['c108a634a335ed47b0018f532a52b032487e239c5061f939ba32355dfefde7e1'], }), ('ParamHelpers', '1.14.1', { - 'checksums': ['b17652d0a69de3241a69f20be4ad1bfe02c413328a17f3c1ac7b73886a6ba2eb'], + 'checksums': ['0450ff8489b0d4d0842130f6a9713ede97da936d7909c43d43587bf2d5a01a21'], }), ('ggvis', '0.4.7', { 'checksums': ['9e6b067e11d497c796d42156570e2481afb554c5db265f42afbb74d2ae0865e3'], }), ('mlr', '2.19.1', { - 'checksums': ['1149c9b453896481c85906045aa82d511d96979ddecbe5a3faf04f9f4a5e6113'], + 'checksums': ['9d52afd54d9d5746e798134d5675818cee65caa53d7eaf317d46ba88d5865202'], }), - ('unbalanced', '', { + ('unbalanced', '2.0', { 'checksums': ['9be32b1ce9d972f1abfff2fbe18f5bb5ba9c3f4fb1282063dc410b82ad4d1ea2'], }), ('RSNNS', '0.4-15', { - 'checksums': ['7f6262cb2b49b5d5979ccce9ded9cbb2c0b348fd7c9eabc1ea1d31c51a102c20'], + 'checksums': ['4a4286444f50b28fb6294b8b49250fa6c43c8fddf2ee0550a3ae59a4212ec1b3'], }), ('abc.data', '1.0', { 'checksums': ['b242f43c3d05de2e8962d25181c6b1bb6ca1852d4838868ae6241ca890b161af'], @@ -1598,25 +1589,25 @@ exts_list = [ 'checksums': ['db52a397a204a0040ec1368ae217cf7b0d8e99e2567927dbe3ae89f93d1de598'], }), ('lhs', '1.1.6', { - 'checksums': ['7a3c6fdcc953490e51026e17a0b1a9dc0ca8d03e6fc989457a7cdda2075b6339'], + 'checksums': ['e37fce44efe6a371677ba2f72f9e1e48270a0fdc60872d05def89270586cd23f'], }), ('tensorA', '0.36.2', { 'checksums': ['8e8947566bd3b65a54de4269df1abaa3d49cf5bfd2a963c3274a524c8a819ca7'], }), ('EasyABC', '1.5.2', { - 'checksums': ['1dd7b1383a7c891cafb34d9cec65d92f1511a336cff1b219e63c0aa791371b9f'], + 'checksums': ['326c92e003866728729dc61473f168c3663106b1229e8513abd7ce520c18689c'], }), ('whisker', '0.4.1', { - 'checksums': ['7a86595be4f1029ec5d7152472d11b16175737e2777134e296ae97341bf8fba8'], + 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], }), ('roxygen2', '7.2.3', { - 'checksums': ['2ebfcfd567b9db6c606c6d42be1645b4e987f987995a2ad8954fa963a519448b'], + 'checksums': ['d844fab977d2575ab942fa1309ac7ff67f35f099a75d8b41c79efe6ea10416da'], }), ('git2r', '0.31.0', { - 'checksums': ['85d913ddc7659e32c1b98ebc247fa1cc1b7717a5bd413fa78ea84696986ca840'], + 'checksums': ['f1db9278fa4604600a64beaedcf86dda595d7c8a10cdb1f7300a6635e73cd66d'], }), ('rversions', '2.1.2', { - 'checksums': ['79aaacf5a1258d91ac0ddedf3c8c16a2d10d39010993dcc7b0a2638afee27cb1'], + 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], }), ('xopen', '1.0.0', { 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], @@ -1637,31 +1628,31 @@ exts_list = [ 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], }), ('gitcreds', '0.1.2', { - 'checksums': ['b14aaf4e910a9d2d6c65c93e645f0b0159c00898e669f917f83c03dfedb1dfea'], + 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], }), ('gh', '1.4.0', { - 'checksums': ['a44039054e8ca56496f2d9c7a10cdadf4a7383bc91086e768ba7e7f1fbcaed1c'], + 'checksums': ['68c69fcd18429b378e639a09652465a4e92b7b5b5704804d0c5b1ca2b9b58b71'], }), ('credentials', '1.3.2', { 'checksums': ['2ffa7c11bedbfa034adf553d0a2f2e4f6a496b858af753a09a89219cff9028b8'], }), ('gert', '1.9.2', { - 'checksums': ['8c440aeebabf1cb3b57124ec9280e0f46b2ab56f2bca07d72b5c7a7f4edc2964'], + 'checksums': ['42ca1b4bcafb1fdbbc7f54df0ee4476ecd19e9e7d563b53fe7064e0086ab665e'], }), ('usethis', '2.1.6', { 'checksums': ['31dc6707577065ac1d4acb7d4cbf135942727c5cc2699092198c544be86f6818'], }), ('covr', '3.6.1', { - 'checksums': ['a54cfc3623ea56084158ac5d7fe33f216f45191f6dcddab9c9ed4ec1d9d8ac6c'], + 'checksums': ['ffbe15438c1a4f274c14cacfb944480e284f1ab60808d5e840c015cc57c51157'], }), ('devtools', '2.4.5', { - 'checksums': ['e42159a9bca0b219170e76c282862e27ca283649d6cbf6a868175d8982e06b4f'], + 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], }), ('Rook', '1.2', { - 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + 'checksums': ['c79ae4b5164daffd4e7cf74bd23c1b08a3948bf343dfe9570d57f39cbf8e5f62'], }), ('Cairo', '1.6-0', { - 'checksums': ['bb3ab1ff6431c15eb01a66ddf90695cd9a2af3d5a384753f5180cd0401d2e89d'], + 'checksums': ['c762ac1d8daa4af527342360c256ed742de4e3031d997e9e59c9a369fcafb7d3'], }), ('RMTstat', '0.3.1', { 'checksums': ['bb4827d76106f5377044cd2b230208881eb714cae65f512f4b95988d9b162ae4'], @@ -1673,10 +1664,10 @@ exts_list = [ 'checksums': ['4b88f0b34e472b9134ad403fb32283424f1883a5943e52c55f1fe05995efb5fa'], }), ('extRemes', '2.1-3', { - 'checksums': ['a7a38dc9a876967d54843872b4355c65e1910c324b0630f91a50009c2f3005a7'], + 'checksums': ['e1ccf0dd542502eb9775682ff64ed358fce4aec271b98cd746e58fbfcf093c40'], }), ('tkrplot', '0.0-27', { - 'checksums': ['dd66264c2553f6927aff297c6b1c3b61867d6c63aec080f40a1e9d53cfc9d120'], + 'checksums': ['c99211919414400b0f579e1354407f2e154cfe85533d324bcf9c68172c2772a5'], }), ('misc3d', '0.9-1', { 'checksums': ['a07bbb0de153e806cd79675ed478d2d9221cff825654f59a71a9cf61f4293d65'], @@ -1688,16 +1679,16 @@ exts_list = [ 'checksums': ['d04a45197646fb36bc38870c1c2351cb56b912bd772b1ebfa25eaeef35fda9c0'], }), ('plot3Drgl', '1.0.4', { - 'checksums': ['85421213e01e1b5f8b929ee1644232f37bacd723305e549c32850f6b6d6924a4'], + 'checksums': ['6d87a9a32aba3aa64f751268cabd14dbd3e0eca2bd5f0a4b11366cd1e2f51bdd'], }), ('OceanView', '1.0.6', { 'checksums': ['2c5165975d6c49fdc83a892cb0406584928dd44000c9774fffc00fbd2fec86f3'], }), ('ks', '1.14.0', { - 'checksums': ['d1c4d06d704f301628455787ba929add1e774debc343d0952a768abea6cc7815'], + 'checksums': ['2db9c56b7b0217b324bbf1e0f66bb94d3f7067a75c5823cbc7d369d63bbb4391'], }), ('logcondens', '2.1.7', { - 'checksums': ['785bbda00b9a25e56440e11356ac219cfbf0fdf8b08c7b0728e53a9febe7a365'], + 'checksums': ['1ad887571afe2d3f66676c59b32ed8fb2fa13fada14f0a1834fbbcfe983acbf8'], }), ('Iso', '0.0-18.1', { 'checksums': ['2fa5f78a7603cbae94a5e38e791938596a053d48c609a7c120a19cbb7d93c66f'], @@ -1715,7 +1706,7 @@ exts_list = [ 'checksums': ['63c46f1175fced33fb1b78d4d56e37fbee09b408945b0106dac36e3344cd4766'], }), ('visNetwork', '2.1.2', { - 'checksums': ['a2b91e7fbbd9d08a9929a5b2c891d9c0bca5977ad772fa37510d96656af1152f'], + 'checksums': ['47c99d42fc89e6ae929257b2648d998c5ffed60dff97ad7e47613f5a0c1ddc84'], }), ('downloader', '0.4', { 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], @@ -1724,28 +1715,28 @@ exts_list = [ 'checksums': ['64a426fe27110dddd8b0c1223ae4c397a2e553ae5e81ddd4ff67c026cfc40abf'], }), ('randomForestSRC', '3.2.0', { - 'checksums': ['a38fbd465eea87c65c7e7406972de84b1073560b40b1e9c806d46bf874a445c0'], + 'checksums': ['f330518ae9f01b6723f52105726e3a6e7081a9b16d2bf17f0bcb967642a757a7'], }), ('sm', '2.2-5.7.1', { - 'checksums': ['2607a2cafc68d7e99005daf99e36f4a66eaf569ebb6b7500e962642cf58be80f'], + 'checksums': ['ea0cc32eb14f6c18beba0bede66ed37bc5341bd3f76c1a7ae56d7254693e1457'], }), ('pbivnorm', '0.6.0', { 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], }), ('lavaan', '0.6-14', { - 'checksums': ['2cc193b82463a865cd8dadb7332409fdebf47e4035d5fe8dbf3414a7ae18d308'], + 'checksums': ['2fbae895af9dbc2e67789e396a3b82b3285226d5dd51680f337ae3b3116c00a7'], }), ('matrixcalc', '1.0-6', { - 'checksums': ['5906e1ef06dbc18efc7a4b370adc180ef8941b5438119703bd981d1c76a06fca'], + 'checksums': ['0bc7d2f11f62d8b1969474defe27c924a243ccba0c856d585f317f6caa07f326'], }), ('arm', '1.13-1', { - 'checksums': ['816ba1c31eec00feef472c57e280488d3d233b592f6f0a1a30e4abb903cb4f5d'], + 'checksums': ['c02da290c1b9699b958431865fcedce94f00ccc80da5c0aa50ed1c3fb56de937'], }), ('mi', '1.1', { 'checksums': ['4d7a9790dbdc675605d70755af9aa80c21a279be5a5d712b22d77465772cc785'], }), ('servr', '0.25', { - 'checksums': ['d94e1d31802ce6bbab7a5838ff94cbca8cd998237d834ff25fedf7514f41a087'], + 'checksums': ['e6ae0d4c09e9037268b1c291c36c93ba0a74c31fe2fcb1f0652b2ae9fca5e73c'], }), ('rgexf', '0.16.2', { 'checksums': ['6ee052b0de99d0c7492366b991d345a51b3d0cc890d10a68b8670e1bd4fc8201'], @@ -1754,16 +1745,16 @@ exts_list = [ 'checksums': ['ad023b00e6e8eb20d107039caf1008c4b05104c7c69709e59c66fbddbf381316'], }), ('statnet.common', '4.8.0', { - 'checksums': ['ddad51128b50d465e1d1aca3a53b452810b9ba578e96b08b8f50f5850d7bb21d'], + 'checksums': ['def999130673fbcb315fecf3620a2559864f51961a828625aa5cd5fded7946f0'], }), ('network', '1.18.1', { - 'checksums': ['9588a198807c8c68da147f479ca9af5bcb4468cf91b6a90b8044d313d9fa30f7'], + 'checksums': ['c80d70352967d8480cfa801f2a31bfe130e2ad4dbf2c07b0046e57f3013cd243'], }), ('rle', '0.9.2', { 'checksums': ['803cbe310af6e882e27be61d37d660dbe5910ac1ee1eff61a480bcf724a04f69'], }), ('sna', '2.7-1', { - 'checksums': ['440fa4347c7b437e93c73127d34894068afd240d3128898474a7201e740a434d'], + 'checksums': ['60daf217c15b6fa335804600dc1e6eb73594b6e794faa4f82a2275c4d8570ae3'], }), ('glasso', '1.11', { 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], @@ -1775,50 +1766,50 @@ exts_list = [ 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], }), ('BDgraph', '2.72', { - 'checksums': ['1f424c9254db3d553f6421b3c095b49c57683d25afefbdb195fed12f0c215268'], + 'checksums': ['7cf9cc1bccf2a56b518c88030e00e88217f571afcb250aa95c3bd2771a8b83cd'], }), ('graphlayouts', '0.8.4', { - 'checksums': ['d724266778e4d97ca7a762253c293ffa3d09e2627cb1c3c7a654c690819defd0'], + 'checksums': ['778d8f7e190b05d0dbbaa7e6dbdfc0b8fef3c83b71333a6fa89926e6c04690fd'], }), ('tweenr', '2.0.2', { - 'checksums': ['1805f575da6705ca4e5ec1c4605222fc826ba806d9ff9af41770294fe08ff69f'], + 'checksums': ['64bbfded418d4880e3636f434571c20303d2f66be6950d64583a864fbb661ff3'], }), ('ggforce', '0.4.1', { - 'checksums': ['2a283bb409da6b96929863a926b153bcc59b2c6f00551805db1d1d43e5929f2f'], + 'checksums': ['b44219fb63c45fa003c64bca323452f16dcace635204bc0127d3244c0f451873'], }), ('tidygraph', '1.2.3', { - 'checksums': ['2fbdc2db18c5ad48c72f14d2d04111f4b0d4c434ad87c280eda3bcb98673ad36'], + 'checksums': ['b09c06b12583ae57edd1ec01e61a0e1b7a4b82358361fb28a6046dbece475687'], }), ('ggraph', '2.1.0', { - 'checksums': ['e36ad49dba92ee8652e18b1fb197be0ceb9f0a2f8faee2194453a62578449654'], + 'checksums': ['686fdb22dc4f613273fb755ec42399a208b4d10348eecd1a217afd4612245c1f'], }), ('qgraph', '1.9.3', { - 'checksums': ['baf190f6db30c4d5a3dc7ab5043b8ec0f79071d515c818c8e7666b9bcf2a4264'], + 'checksums': ['46ae6ab1d2b64667bc5ad7c9e81d44cbdd67d4e865eb35f5a25c80b569975f91'], }), - ('HWxtest', '', { + ('HWxtest', '1.1.9', { 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], 'checksums': [ - 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz - '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch + {'HWxtest_1.1.9.tar.gz': 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6'}, + {'HWxtest-1.1.9_add-fcommon.patch': '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451'}, ], }), - ('diveRsity', '', { + ('diveRsity', '1.9.90', { 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], }), ('doSNOW', '1.0.20', { 'checksums': ['917cabed166aa2d1ec291691c17e1e3d344e858543e1682e3a442cc0c504bbb8'], }), ('geepack', '1.3.9', { - 'checksums': ['efc73fc92429973a5dc29b0913ac45ec364a4a264140cf388df54d4873d458d9'], + 'checksums': ['a106fdf99a7070243c412f0117f0f4e3954b2bae81266fba272e9c85040dcde7'], }), - ('biom', '', { + ('biom', '0.3.12', { 'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'], }), ('pim', '2.0.2', { 'checksums': ['1195dbdbd67348dfef4b6fc34fcec643da685ebe58d34bbe049ab121aca9944f'], }), ('minpack.lm', '1.2-3', { - 'checksums': ['c70956122528575433c57a5669e26f4f9b1e160b004f135a38658c2c2634df87'], + 'checksums': ['bfa702679f023b2c9a54b23172deb6e26cfa27addce4d2d6bd5e7d89e14feef0'], }), ('rootSolve', '1.8.2.3', { 'checksums': ['b5b3d1641642a3fd1279dbd1245f968d2331ac9588d77f872b113f7dc4594ba0'], @@ -1839,13 +1830,13 @@ exts_list = [ 'checksums': ['737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291'], }), ('imager', '0.42.18', { - 'checksums': ['d90a9893d11190ba249c7fae5bd6517a77907efbce2941452cb2aec57bb5cf7f'], + 'checksums': ['c11536d7b6fc08300b78d3688204a87aeae42c7858adc69b6d4dea90f4665352'], }), ('signal', '0.7-7', { 'checksums': ['67a015c46d67de7548c3adb83a1b22524de75501a861d91668c3c2ea761a4e61'], }), ('tuneR', '1.4.2', { - 'checksums': ['561eeae1bfe10ac4a950d2a60afc6db05d28557a8cb932e00ac7b7f57b6ea0e9'], + 'checksums': ['eb9fbe787296f081b448c48225081773f18b062c8d6fe0272da7b1641d0a2cf2'], }), ('pastecs', '1.3.21', { 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], @@ -1860,19 +1851,19 @@ exts_list = [ 'checksums': ['943b1864fe50359b253a4511522c00b0a7dbc1ce5b4033516086a0410fa1212e'], }), ('gsw', '1.1-1', { - 'checksums': ['147ce73da75777799af9cb712862ef25b52fcae146a64ce0a525460ddfea1deb'], + 'checksums': ['d2a21dbcc3b285163d9cf1bc649a3de1bb1e713c64e4cb6cbc3e613c43f4dd82'], }), ('wk', '0.7.1', { - 'checksums': ['af2c2837056a6dcc9f64d5ace29601d6d668c95769f855ca0329648d7326eaf5'], + 'checksums': ['e5a5772c982da9c43593cecab9b4f2edbab7b290bb6efc1409eabda4c4dbd384'], }), ('s2', '1.1.2', { - 'checksums': ['2010c1c6ae29938ec9cd153a8b2c06a333ea4d647932369b2fc7d0c68d6d9e3f'], + 'checksums': ['8fb237531c6f4aa5b78fbe36d4fd15bfe852c1308fed58b04b3dae2bb73c0b57'], }), ('sf', '1.0-9', { - 'checksums': ['d0731fab9438d73a55af7232f0474b36f4b2a4e6d66adaa141632f4a60265453'], + 'checksums': ['85c0c71a0a64750281e79aa96e36d13e6285927008b2d37d699e52aba7d8013b'], }), ('oce', '1.7-10', { - 'checksums': ['3aaa7600bd2b322062cdeb0a0d910f6fa872fecc4dbc2e30665d51acb12261a8'], + 'checksums': ['b899eeb7ae73f6520f65f0f052dd2f6f2d102190527eace94d057357ed9568ff'], }), ('ineq', '0.2-13', { 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], @@ -1881,16 +1872,16 @@ exts_list = [ 'checksums': ['276164d5eb92c78726c647be16232d2443acbf7061371ddde2672b4fdb7a069a'], }), ('memuse', '4.2-3', { - 'checksums': ['f5e9dbaad4efbbfe219a93f446e318a00cad5b294bfc60ca2146eca894b47cf3'], + 'checksums': ['906fdff665e2aed0e98ee3181233a5c62bd521abfce6ab1cb215c71c95d12620'], }), ('pinfsc50', '1.2.0', { 'checksums': ['ed1fe214b9261feef8abfbf724c2bd9070d68e99a6ea95208aff2c57bbef8794'], }), ('vcfR', '1.14.0', { - 'checksums': ['dd87ff010365de363864a44ca49887c0fdad0dd18d0d9c66e44e39c2d4581d52'], + 'checksums': ['8576dbd2e5a707dabc20acbbea3fe18b6a783910e622423ac203609a386204cb'], }), ('glmmML', '1.1.4', { - 'checksums': ['24e34f0834bded06d52cbd9cb025dc65ea2db2faa7dbee01d545aa33eea35e7c'], + 'checksums': ['bdb7d83505103514e5cfe23a0766e5bc9d508ccc74514da1be62f84284dd4677'], }), ('cowplot', '1.1.1', { 'checksums': ['c7dce625b456dffc59ba100c816e16226048d12fdd29a7335dc1f6f6e12eed48'], @@ -1899,10 +1890,10 @@ exts_list = [ 'checksums': ['14abc65bc0a3f3ed63c04dda19620e483a21d1f5f33feb74aba9f3221434d888'], }), ('sn', '2.1.0', { - 'checksums': ['957b49027c2111f51893433e902486141a942a5ed384ca605714605de80d1790'], + 'checksums': ['495f9baed26e2e70357eda996fdb327ccc22673486e375686c32daec727a448b'], }), ('tclust', '1.5-2', { - 'checksums': ['73328b30774bb0767d613d7f2b60b75706b19fab864c712645ea18181f1af327'], + 'checksums': ['492674b30a465e5f4a22ba0ce5556ed4d8e57b29090f9b5b94ad655d064e6f8b'], }), ('ranger', '0.14.1', { 'checksums': ['5d99401d555da1cfb11c70e59d1bb545ce48720073a06a2a32eb396f622dee1b'], @@ -1914,7 +1905,7 @@ exts_list = [ 'checksums': ['9bc533ed7e8f816097a03acfbca33308c9940ba26d02674f4ba06311cf3a1718'], }), ('pryr', '0.1.6', { - 'checksums': ['7b1653ec51850f4633cee8e2eb7d0b2724fb587b801539488b426cf88f0f770b'], + 'checksums': ['68c1a30a42808eb01a64d31e521d21f2fd5a88dd2c14d05b4b7986d27a177704'], }), ('moments', '0.14.1', { 'checksums': ['2ed2b84802da132ae0cf826a65de5bfa85042b82e086be844002fe1ce270d864'], @@ -1923,7 +1914,7 @@ exts_list = [ 'checksums': ['22790f7157f23eb0b7b0b89e2ea53478fb3c0d15b5be8ad11525d3e6d5626cdc'], }), ('VIM', '6.2.2', { - 'checksums': ['7581adca64cf20b93d5a111da83f663215b4529868b065b3463c4238bca97739'], + 'checksums': ['afa7492c54508c46eff39ac66fa4b05627e0044253ebe4a61b2a78d459f715e4'], }), ('smoother', '1.1', { 'checksums': ['91b55b82f805cfa1deedacc0a4e844a2132aa59df593f3b05676954cf70a195b'], @@ -1938,31 +1929,31 @@ exts_list = [ 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], }), ('ggbeeswarm', '0.7.1', { - 'checksums': ['bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333'], + 'checksums': ['f41550335149bc2122fed0dd280d980cecd02ace79e042d5e03c1f102200ac92'], }), ('shinydashboard', '0.7.2', { 'checksums': ['a56ee48572649830cd8d82f1caa2099411461e19e19223cbad36a375299f3843'], }), ('rrcov', '1.7-2', { - 'checksums': ['cbcca84a82d63fa50556aa8db29312b9bb588a638eb306ce4a81c271529228fd'], + 'checksums': ['0f01ed07cbc9e55dfcba27040a3f72237fb2fb86eda899472c2f96500220ecae'], }), ('WriteXLS', '6.4.0', { 'checksums': ['644b90a82683c668b6e05bb4f940111a42cd634f63a5b559351e8cd4274a19b7'], }), ('bst', '0.3-24', { - 'checksums': ['70957f1db8800bf0d628a9e6f72b7273329786dd119427790b326844591aa0f3'], + 'checksums': ['64d96e13551d35ec32aabaa733bec86dbe8c9ca3f976a34ebbf1f49bb63e49f4'], }), ('pamr', '1.56.1', { 'checksums': ['d0e527f2336ee4beee91eefb2a8f0dfa96413d9b5a5841d6fc7ff821e67c9779'], }), ('WeightSVM', '1.7-11', { - 'checksums': ['983733b618631d9ad754fb12f5e576912aff1f529cafdee4fddfd38d81ccc710'], + 'checksums': ['498f2d1d8329b7309b373c18afcdad8ed9d3d54169f310de3264a65364406e69'], }), ('mpath', '0.4-2.23', { - 'checksums': ['f9709532b2254befea7fd4046179ee60ebcb4ac1fa7b0564fe34643d22f59b44'], + 'checksums': ['1608215dd7826dde0cb7c8890375568d286270024d52f01cb12c9402c817ed99'], }), ('timereg', '2.0.5', { - 'checksums': ['b1f62be5d34d4d36c3b14cd3c719f936c9e3a80e2907bdeab240821267db3559'], + 'checksums': ['a0d1ddeaf6962c7f48e213430ec838cf8e880a6c41571e4c2e864d070f84f7ef'], }), ('peperr', '1.4', { 'checksums': ['0a44f40cfeb298cbe990dba0d9c979070d7a8659581dea09dd3238526fb59f39'], @@ -1980,37 +1971,37 @@ exts_list = [ 'checksums': ['8c237986ed3dfb72d956ad865ef7768644eebf144675ad66140acfd1aca9d701'], }), ('dendextend', '1.16.0', { - 'checksums': ['4ba3885b66694589d455ffef31c218fe653fa25aff3efb7e8db6c25008d2921b'], + 'checksums': ['ec2fd09c31a2a93292d87a9bd5bfc261840de941dfded79d6c2fe87116708466'], }), ('RInside', '0.2.18', { - 'checksums': ['0be28c44ee34cba669a7264d2b99c289230645598ca78e21682559dc31824348'], + 'checksums': ['805014f0f0a364633e0e3c59100665a089bc455dec80b24f04aaec96466cb736'], }), ('limSolve', '1.5.6', { 'checksums': ['b97ea9930383634c8112cdbc42f71c4e93fe0e7bfaa8f401921835cb44cb49a0'], }), ('dbplyr', '2.3.1', { - 'checksums': ['4a6e092c9349f8b3030c752f8c6cc551637d6fbca3c84be0da89968f1e9adce1'], + 'checksums': ['e192059e923abcb39fcebc52a18cb3ba532cb50d2963c6d25435a0ec00b4ac28'], }), ('modelr', '0.1.10', { - 'checksums': ['825ba77d95d60cfb94920bec910872ca2ffe7790a44148b2992be2759cb361c4'], + 'checksums': ['9345a6e86363181e369c5e9de190fcab62d05e284fc65f1c4d30acfbce6a0f63'], }), ('debugme', '1.1.0', { 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], }), ('reprex', '2.0.2', { - 'checksums': ['0e6d8667cacb63135476a766fba3a4f91e5ad86274ea66d2b1e6d773b5ca6426'], + 'checksums': ['a85b16e26112364a65c886efea050df08c17aadf1411fd14ec27d9ef13e87092'], }), ('selectr', '0.4-2', { 'checksums': ['5588aed05f3f5ee63c0d29953ef53da5dac7afccfdd04b7b22ef24e1e3b0c127'], }), ('rvest', '1.0.3', { - 'checksums': ['89bb477e0944c80298a52ccf650db8f6377fd7ed3c1bc7034d000f695fdf05a4'], + 'checksums': ['a465ef7391afaa3c26eebe8c61db02314ac04c4d8de5aa53f090716763d21c1e'], }), ('dtplyr', '1.3.0', { - 'checksums': ['2640e9cde4eaa06f02cff29e3f2b99fdd08488df07ea2e6629b2ed6a8285d0f3'], + 'checksums': ['1bbcdda7e1708c2ca1e592e487affc54143ca24f86e28ae5e98b07de5cf680f8'], }), ('gargle', '1.3.0', { - 'checksums': ['4d46ca2933f19429ca5a2cfe47b4130a75c7cd9931c7758ade55bac0c091d73b'], + 'checksums': ['428ffc49e39907b366d5c79b0065042522efcbced761d980a641c38b2ad48d0a'], }), ('googledrive', '2.0.0', { 'checksums': ['605c469a6a086ef4b049909c2e20a35411c165ce7ce4f62d68fd39ffed8c5a26'], @@ -2019,25 +2010,25 @@ exts_list = [ 'checksums': ['b6212a186063c23116c5cbd3cca65dbb8977dd737261e4526ebee8f64852cfe8'], }), ('googlesheets4', '1.0.1', { - 'checksums': ['0a107d76aac99d6db48d97ce55810c1412b2197f457b8476f676169a36c7cc7a'], + 'checksums': ['284ecbce98944093cb065c1b0b32074eae7b45fd74b87d7815c7ca6deca76591'], }), ('tidyverse', '2.0.0', { - 'checksums': ['83cf95109d4606236274f5a8ec2693855bf75d3a1b3bc1ab4426dcc275ed6632'], + 'checksums': ['3d3c2d135056333247d309d1c2cc98cc0d87e2c781f4c6fbceab28d28c0728e5'], }), ('R.rsp', '0.45.0', { - 'checksums': ['8969075bdcabd43bad40eef6b82223e119426279fded041163fd41e55cee3a59'], + 'checksums': ['a58046d448b2fca15fb1bf5b5eec4da37b29175270c07e46d740066537435da4'], }), ('gdistance', '1.6', { - 'checksums': ['2ccabeb2f8cf44630c0bd2da79815fe357b812737ebece1bed8f90b27c126a24'], + 'checksums': ['3ddb02c5ca0477b9c9d96988451381d2d64b06869adb4e7f20da616819d55fde'], }), ('vioplot', '0.4.0', { - 'checksums': ['06475d9a47644245ec91598e9aaef7db1c393802d9fc314420ac5139ae56adb6'], + 'checksums': ['5729b483e3a4f7c81d2cc22c8bc5211b64e289734e9da5b5696c4974067867b5'], }), ('emulator', '1.2-21', { 'checksums': ['9b50b2c1e673dbc5e846a4fa72e8bd03434add9f659bde6d7b0c4f1bbd713346'], }), ('gmm', '1.7', { - 'checksums': ['b1b321ad1b4a4a14a2825a2c3eb939ce2f2bcef995247a1d638eca250e59739b'], + 'checksums': ['194075a3e644ca449a60f4e00c37cce457f4d08ed7229aa62b479f7f8c148f8a'], }), ('tmvtnorm', '1.5', { 'checksums': ['1c7a606bdce4319a6fdb4180fef499c293df3412d8583e296869521ece5460fe'], @@ -2049,22 +2040,22 @@ exts_list = [ 'checksums': ['2299b52efee322ce0eaf66c66ae440f46618b647701cd741568c08bdc3111c9c'], }), ('plotly', '4.10.1', { - 'checksums': ['bd995c654dbc8c09a84adaba8def99766919e3894caf18b551bb26b2f591389a'], + 'checksums': ['ac0921a1cba24e17a0f3a0a28b7a40ac930e17fe5caa9c3973c9a8d1e20c367a'], }), ('gap', '1.5-1', { - 'checksums': ['0ef352aa98a3bf27908b256f27a903058502176ea9112a4ffc41928ebbc48c22'], + 'checksums': ['0d4d37045f5712ebd010cad0617f8e88a021b15fd25d899e4ec222af74e313dc'], }), ('qrnn', '2.0.5', { 'checksums': ['3bd83ee8bd83941f9defdab1b5573d0ceca02bf06759a67665e5b9358ff92f52'], }), ('TMB', '1.9.2', { - 'checksums': ['2c9dd281d911c2cb1cc01c6a8e114826891280f15e0ed4a00b4f195e15df25d7'], + 'checksums': ['041426e94bf33c6b5130f9da9e05de130aa6951cce19dc99171fb36efc50e54f'], }), ('glmmTMB', '1.1.5', { - 'checksums': ['b9d1e97587b213e52ff304f62480ddee77c658f29a7e99334a4032d0df60b275'], + 'checksums': ['334b4755c0b93ade9a0b4419cc41c7d30ee76090124e34112015223a28c008fa'], }), ('gmp', '0.7-1', { - 'checksums': ['8ae76f3d17542eab3e7468341dabeebe28b11da8c1b4b3f7bbdb00d379689e52'], + 'checksums': ['a6873dc65218905cb7615cb8e2522258f3740e29c0632473d58a1cb409835db6'], }), ('ROI', '1.0-0', { 'checksums': ['b0d87fb4ed2137d982734f3c5cdc0305aabe6e80f95de29655d02a9e82a0a341'], @@ -2076,22 +2067,22 @@ exts_list = [ 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], }), ('spaMM', '4.1.20', { - 'checksums': ['ff3af7ab107655bd521bba68093696f343de29294602d00dee7601cc91245f2d'], + 'checksums': ['839eabd0bd8883d7ae9f9df4fcf6a754b15f2952d76e30c424e0e8927ce05284'], }), ('qgam', '1.3.4', { 'checksums': ['7633120a48a85ab73f7e1bc8b02c98319285c2abd05f9d13d25339d7aaaacacb'], }), ('DHARMa', '0.4.6', { - 'checksums': ['0fcd41099ababedff010d8fe05f8efa630cceb829dbb87af8b8d650ad49d88bf'], + 'checksums': ['32fd3d5cd354ff6b5457599d7fb870b94c7d86401a47c7c553bca26f782a4b73'], }), ('mvnfast', '0.2.8', { - 'checksums': ['b67d50936c9a466977669ef6bb7b23df8e7c90a820ac916328c20e41ef8e0b72'], + 'checksums': ['8871e0ce54b87afc556fd94ca77c3db72dcbb8c245558287e0fe342e30eec9a0'], }), ('bridgesampling', '1.1-2', { 'checksums': ['54ecd39aa2e36d4d521d3d36425f9fe56a3f8547df6048c814c5931d790f3e6b'], }), ('BayesianTools', '0.1.8', { - 'checksums': ['af49389bdeb794da3c39e1d63f59e6219438ecb8613c5ef523b00c6fed5a600c'], + 'checksums': ['f543bdd6b61ec7fd31a7e4040bd7835341d9079243fa4eb0cd5e684e5e39bdd1'], }), ('gomms', '1.0', { 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], @@ -2099,31 +2090,31 @@ exts_list = [ ('feather', '0.3.5', { 'checksums': ['50ff06d5e24d38b5d5d62f84582861bd353b82363e37623f95529b520504adbf'], }), - ('dummies', '', { + ('dummies', '1.5.6', { 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], }), ('SimSeq', '1.4.0', { 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], }), - ('uniqueAtomMat', '', { + ('uniqueAtomMat', '0.1-3-2', { 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], }), - ('PoissonSeq', '', { + ('PoissonSeq', '1.1.2', { 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], }), ('aod', '1.3.2', { 'checksums': ['9b85be7b12b31ac076f2456853a5b18d8a79ce2b86d00055264529a0cd28515c'], }), - ('cghFLasso', '', { + ('cghFLasso', '0.2-1', { 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], }), ('svd', '0.5.3', { - 'checksums': ['d4dcb650757bfbf8ae388622686be20e8d55cca68096146a30aee8ced96aa113'], + 'checksums': ['14cea5447aaee391b363efc50750b80856262c02407999f428c2513705f9b3e6'], }), ('Rssa', '1.0.5', { - 'checksums': ['4115b516f6782d52f02695bbbd52921a474aafc7232d49aca85010f1c33b08a7'], + 'checksums': ['475819636afb330a4467722b0a664fa54d6114d782b681f681ccb123f3be522d'], }), - ('JBTools', '', { + ('JBTools', '0.7.2.9', { 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], }), ('RUnit', '0.4.32', { @@ -2136,16 +2127,16 @@ exts_list = [ 'checksums': ['22f04755873e34a9077bb1b1de8d16f5bc56cb8c395c4f797f9ad0b209b1b996'], }), ('gee', '4.13-25', { - 'checksums': ['f8217c3bb077cb805e0cd7761efecac1231035bfc195246b9f185f744c550e6c'], + 'checksums': ['e140881e2febe793a24086a2d179062b9995db901257d678f85d220441400e89'], }), ('Matching', '4.10-8', { - 'checksums': ['1e75dc61553c1687b2b520dc52688409c2e84285e4b6c16c94d8d85fd5ccece0'], + 'checksums': ['54412e2ddd1f5eeb189ffc653e4d3ead3e2f9c5c4fe516cfb1966abf69ada49a'], }), ('MatchIt', '4.5.1', { - 'checksums': ['e79a96e7972097829a839c855c0bc97638eeae4b148e01340dfa5296323e6c06'], + 'checksums': ['961e6debea443179fb196581e0783ce05215faa4115e3f5e1cff89eb82b0c7e0'], }), ('RItools', '0.3-2', { - 'checksums': ['714685d8e04acafe5d5ddf93edac69afec0c62045a7b93478734771b6a0fa928'], + 'checksums': ['8d6be0e91db83ac3122dcbfe1a77009955a484b9d6c32f7adbd55d286eb83c08'], }), ('mitools', '2.4', { 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], @@ -2154,10 +2145,10 @@ exts_list = [ 'checksums': ['05e89a1678a39e32bfb41af8a31d643b04fc4d2660a96e701825e6bffcd75a52'], }), ('rlemon', '0.2.1', { - 'checksums': ['e06792875f05a0c6cd637b7bf16bd51c3891e0df6bad78ffba0ee195abe8d3a0'], + 'checksums': ['4a18fa034f197c68daf48daf25c0e41f1b8acbe71d030c6bc1f55e3062a10375'], }), ('optmatch', '0.10.6', { - 'checksums': ['ed09be71b0e293273412d4a181c1f085ad93f4038996dc7c90beae8466574aeb'], + 'checksums': ['2b7661567fdfbdb39dae3779b4b7dea2b9eb759d3117311b3a7936b10cce1d35'], }), ('SPAtest', '3.1.2', { 'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'], @@ -2166,7 +2157,7 @@ exts_list = [ 'checksums': ['cba5d3403d6a7d0e27abf6279fbfea6e0d0fe36b28c688bbadb8eafb3841329a'], }), ('SKAT', '2.2.5', { - 'checksums': ['2b349896560ad18c3428e245fc25b17e9c2946676044fa56025ddf9c87ff08bf'], + 'checksums': ['1441fa46b6a78a060007442fb8cb8c87753bdc2b1ea2dc24ff951ac3fef651f4'], }), ('GillespieSSA', '0.6.2', { 'checksums': ['f4233b4a44c7d4b9e3459b1efa9a8087a602ef93806b4d70eadbb537b67567c2'], @@ -2175,31 +2166,31 @@ exts_list = [ 'checksums': ['1d60ff13bb260630f797bde66a377a5d4cd65d78ae81a3936dc4374572ec786e'], }), ('distr', '2.9.1', { - 'checksums': ['bb7df05d6b946bcdbbec2e3397c7c7e349b537cabfcbb13a34bcf6312a71ceb7'], + 'checksums': ['82b790a90bd40025c7ff8ccc7da784fa967015fc015874f6b209088d0bd01a5f'], }), ('distrEx', '2.9.0', { - 'checksums': ['b064cde7d63ce93ec9969c8c4463c1e327758b6f8ea7765217d77f9ba9d590bf'], + 'checksums': ['087d1847ad400141b5e0fd0858ef3e5c698b3018d7e2d33087be601a5740fb35'], }), ('minerva', '1.5.10', { 'checksums': ['2f26353d8fcc989ac698c4e45bb683801b1a7bb60b14903d05a4d73c629c590f'], }), ('KODAMA', '2.4', { - 'checksums': ['e4f8bbfeae9d2f628f7338c708a538aae481a633e59e86727f9b6f9c72920ecf'], + 'checksums': ['78f2ea3596f3697fc06a080947e82a54c5270ed90f86916b91902e5db6ec85e7'], }), ('locfdr', '1.1-8', { 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], }), ('ica', '1.0-3', { - 'checksums': ['e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179'], + 'checksums': ['474d3530b16b76a1bf1a1114d24092678ea7215fa57c6fdcee6333f1e768b865'], }), ('dtw', '1.23-1', { - 'checksums': ['df7cf9adf613422ddb22a160597eb5f5475ab6c67c0d790092edb7f72ba98f00'], + 'checksums': ['6ed6a3b52be673ce2617b8d48723c7c488c95aab88fe2912d7e00507838e826d'], }), - ('SDMTools', '', { + ('SDMTools', '1.1-221.2', { 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], }), ('ggridges', '0.5.4', { - 'checksums': ['f5eafab17f2d4a8a2a83821ad3e96ae7c26b62bbce9de414484c657383c7b42e'], + 'checksums': ['2bf71c2034804cec637e6748dc51d8cadad01d3ea4d14ace754327f082e8d851'], }), ('TFisher', '0.2.0', { 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], @@ -2217,42 +2208,42 @@ exts_list = [ 'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'], }), ('RcppTOML', '0.2.2', { - 'checksums': ['2f09f00cbee6c6eeff5d5f0195c10de0155496de15fbe8189c18627ee3090541'], + 'checksums': ['371391f9ca82221e76a424082ea9ebc5ea2c50f14e8408469b09d7dc3e6f63aa'], }), ('reticulate', '1.28', { - 'checksums': ['2125af9e75939c3b7c0dc74f28f42606e816d63aa1143baf631c318ff5ff3a2c'], + 'checksums': ['58a299ed18faaa3ff14936752fcc2b86e64ae18fc9f36befdfd492ccb251516f'], }), ('hdf5r', '1.3.8', { 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', 'preinstallopts': "unset LIBS && ", - 'checksums': ['87b75173ab226a9fbaa5b28289349f3c56b638629560a172994b8f9323c1622f'], + 'checksums': ['b53281e2cf57447965849748e972de2f7fe8df0cee3538ef5813c33c7ed2302b'], }), ('DTRreg', '1.7', { 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], }), ('pulsar', '0.3.10', { - 'checksums': ['78c9f7e3b2bf8a8d16a81d6ee43bb05b0c360219be473d920c8c8ccb2aba4e3d'], + 'checksums': ['d464979af605cc16ff629f7b85e09a5dc005c60fd30f098588fd834b6acfd407'], }), ('bayesm', '3.1-5', { - 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + 'checksums': ['f223074ca41ede293b48350eac77a565e034f0f8cf3dd72d0e1d126cc58047a2'], }), ('gsl', '2.1-8', { - 'checksums': ['ee98d1382d37ffa77538a90ccdbf44affbf1710a9e66b8ada73fa72e67921985'], + 'checksums': ['f33609bf485abd190e65ff5d0fdab438b759294c47b921d983d89d6f053a2d95'], }), ('energy', '1.7-11', { - 'checksums': ['543de4875c46cc90e711e71c45b082d962fbb5158a094f9f10d37d3f57e1bea7'], + 'checksums': ['c29f8fb000c979d2504f6f6d3a99c773004f77d58793e7e2a5766155272b6511'], }), ('compositions', '2.0-5', { - 'checksums': ['7b9c7a3bf654fb02d9eb1b4a7566469b2f5232f3b2c1b324c02239fd31060faf'], + 'checksums': ['a1b84b23f3fa5d7793318a6b6ad44f50b9653efccfb753a5952ccb11d1662c5a'], }), ('clustree', '0.5.0', { - 'checksums': ['7a6100f88c9a6e8d10b253ee227ecf1dc4e84e418eb8da64cd801d2a158b956f'], + 'checksums': ['a87f65dc0489af77807ed27de67e905699f21f50bcfba6a84353b9a846a84ac1'], }), ('tweedie', '2.3.5', { - 'checksums': ['a032cad512dac37a8619e6f66cb513eb82a88a5a2ffbe91e92c2d44d1756d0d9'], + 'checksums': ['983c745fee5a780d46e8dd04c2eb1c10cb2e222d3679654f0d6934d3db7b1c3e'], }), ('RcppGSL', '0.3.13', { - 'checksums': ['f094ea26c99b04d9e203986a1f2003f02472ceca0e2ef1c3beefd3ae80aeada8'], + 'checksums': ['fe5e73bc119c6424e1a40b6fea17417a7bba93e81dbe9b7cf86dde9b8e8d93e7'], }), ('mvabund', '4.2.1', { 'checksums': ['ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06'], @@ -2261,7 +2252,7 @@ exts_list = [ 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], }), ('gllvm', '1.4.1', { - 'checksums': ['cd3f72b84f0c722e9c0b21c2b2de7683ec742345d7f8e62f67c8c93342c1a5c6'], + 'checksums': ['36f50697e3f38e008f0db8c2980db6fc6a736985573952cc23769d55fbb321d1'], }), ('grpreg', '3.4.0', { 'checksums': ['fd57d20baf63d2cc5821998bca5c3fdcbe46c933c9553caa492911b12654d6ad'], @@ -2270,16 +2261,16 @@ exts_list = [ 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], }), ('lpSolveAPI', '5.5.2.0-17.9', { - 'checksums': ['9ebc8e45ad73eb51e0b25049598a5bc758370cf89508e2328cf4bd93d68d55bb'], + 'checksums': ['7b52ecf3f1174f771fe24e62502be6d31acc3e48a12473e35ad0a89fc2517811'], }), ('ergm', '4.4.0', { - 'checksums': ['ced92b0a32c78c85546d665c32fb3993fe77a3809aa88f43c3eee39e2577f2f0'], + 'checksums': ['2db152cc7fdd71d6f0065603405f30bf5e206591da39b8f542178ec6d6126173'], }), ('networkDynamic', '0.11.3', { - 'checksums': ['beefaf50eb8609528358b75f5814a8f1cdc4d2db8059b99be69919da2bc02beb'], + 'checksums': ['2c664fd0d85c0cdc099480d67a18e6afbb0cc1036963b6664a8a756874648e5b'], }), ('tergm', '4.1.1', { - 'checksums': ['abff35b48b53a182d9424c78c5240bde1259b695c2328861000193bf88044a50'], + 'checksums': ['51cd845ab0dacaba34fcb4b1f04e540eb7a6d0e7be001809625c0a5b1ca45d25'], }), ('ergm.count', '4.1.1', { 'checksums': ['446893614ad8b41aa39c37c2bf45a167f575536bb6778b8ad1fbcddb7b934932'], @@ -2308,23 +2299,22 @@ exts_list = [ ('shinythemes', '1.2.0', { 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], }), - ('csSAM', '', { + ('csSAM', '1.2.4', { 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], }), ('bridgedist', '0.1.2', { - 'checksums': ['14f67ce96dd8f1cb457614271b0b4376dd6fd3073a2e727a17c0964be67272cb'], + 'checksums': ['7210c97fc864e78ea8502067359d642bbd95bf2df30d33da193fc5c004e45baf'], }), ('asnipe', '1.1.16', { 'checksums': ['be50f9fdef0f4bf9676b9c3c2906d0431afc678af55cf48b1119f9fc0adac44f'], }), - ('liquidSVM', '', { + ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ - '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz - # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch - '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, + {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch': + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'}, ], }), ('oddsratio', '2.0.1', { @@ -2334,7 +2324,7 @@ exts_list = [ 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], }), ('h2o', '3.40.0.1', { - 'checksums': ['d470dc71e637d589bf228e59ddb021ade240d74536323d8ca77ac1fb334d3535'], + 'checksums': ['15b69544c90e482c3c1064886742ca1c0df102db64a698a7ed4976993d83c1e0'], }), ('mlegp', '3.1.9', { 'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'], @@ -2346,25 +2336,25 @@ exts_list = [ 'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'], }), ('bartMachineJARs', '1.2.1', { - 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + 'checksums': ['9f7a20acf4aec249e16f83d81f5ec796aa718deb1b8bc24393fc0421eb8ce1c0'], }), ('bartMachine', '1.3.3.1', { - 'checksums': ['5e1ac0033da5b41a96d95782886a167e51ff8e43822800e8d40874ff9c13847f'], + 'checksums': ['c4b27af602b019b7d0d933a8efd30b45db11f423a54cc8e178e0285aee72c65f'], }), - ('lqa', '', { + ('lqa', '1.0-3', { 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], }), ('PresenceAbsence', '1.1.11', { - 'checksums': ['59266ffdf702ab1ecca7cbcf0538afe38d1a15abea66056734b62c0c15609c7c'], + 'checksums': ['c63a6453783865b7c69c580a09a769e99390dd8b2e0f63e48fbfc86da3bee4b7'], }), ('GUTS', '1.2.3', { 'checksums': ['40061ec1677def40b410b5ef90d01e0bcb0095abed1545513a33a01d4444adc2'], }), ('GenSA', '1.1.8', { - 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + 'checksums': ['375e87541eb6b098584afccab361dc28ff09d03cf1d062ff970208e294eca216'], }), ('parsedate', '1.3.1', { - 'checksums': ['1e9399d6b16079e6cdc43fa33742d6b7e6e2b6bb2ba470bfe9d30d55b7be4cb0'], + 'checksums': ['1fc31ab9813b61680abf4f4c2705b8f484d56d1d3ef256df84b342b628b6d1b1'], }), ('circular', '0.4-95', { 'checksums': ['483d3e31e9c7afe59e6bcb98ad17c4f6333d19b6c70f948b168c9ee16e90bce2'], @@ -2382,13 +2372,13 @@ exts_list = [ 'checksums': ['d28107a4bbbb0ace1d571f0aa6884ee4c50d7731c04bceba207fd55a39b83b9c'], }), ('Rserve', '1.8-11', { - 'checksums': ['af63a28a4958dbe82597586494d0277272842bb3869db70c547d0896f1345d2c'], + 'checksums': ['9dfb1d68493f8cee5d2e12a1bfa604404834e11809f4c908d65b9100a9af1b85'], }), ('spls', '2.2-3', { 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], }), ('Boruta', '8.0.0', { - 'checksums': ['6ff520d27d68637058c33a34c547a656bb44d5e351b7cc7afed6cd4216275c78'], + 'checksums': ['38e75b1ebc8b2d1c54b3373a42529b819c7b4773fd4932f57bc9701d1e3e3dc7'], }), ('dr', '3.0.10', { 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], @@ -2402,7 +2392,7 @@ exts_list = [ ('ctmle', '0.1.2', { 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], }), - ('BayesPen', '', { + ('BayesPen', '1.0', { 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], }), ('inline', '0.3.19', { @@ -2412,13 +2402,13 @@ exts_list = [ 'checksums': ['6d8c514fa179f8a48c2105b551a8a08e28ea4375d06150a4b8ab4ccda577daf5'], }), ('BCEE', '1.3.1', { - 'checksums': ['82afc9b8c6d617f5f728341960ae32922194f637c550916b3bea12c231414fa7'], + 'checksums': ['dfd896250cc6b8cc83fafaeea57da5bc9dc49ce7475da2ba54484c2efb7a477b'], }), ('bacr', '1.0.1', { 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], }), ('clue', '0.3-64', { - 'checksums': ['71311b16ce380fd9a8834be95b55b3d1b47e4ee2b8acb35b8d481138c314dc31'], + 'checksums': ['f45cb7a84c87ddca2b9f7c2ea9505016d002e6fda23322e6d57466c7a4de28af'], }), ('bdsmatrix', '1.3-6', { 'checksums': ['f9c871d54378408902931792b3dbf8bda863d6aa67af6a0472a6ec1c420760bc'], @@ -2430,7 +2420,7 @@ exts_list = [ 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], }), ('MALDIquant', '1.22', { - 'checksums': ['0771f82034aa6a77af67f3572c900987b7e6b578d04d707c6e06689d021a2ff8'], + 'checksums': ['7b01a2e05f3bcccc426d8175b289255a8c2976ea8ab0e20eec18d442d2c9d015'], }), ('threejs', '0.3.3', { 'checksums': ['76c759c8b20fb34f4f7a01cbd1b961296e1f19f4df6dded69aae7f1bca80219c'], @@ -2439,8 +2429,7 @@ exts_list = [ 'checksums': ['57b53882fd7a195b38bbdbbf0b17745405eb3159b1b42f7f11ce80c78ab94eb7'], }), ('rda', '1.2-1', { - 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', - 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + 'checksums': ['37038a9131c9133519f5e64fa1a86dbe28b21f519cf6528503234648a139ae9a'], }), ('sampling', '2.9', { 'checksums': ['7f5ba5978f6cdbbbdb6f51958197b28b6fc63e7eeee59e6845ea09fb37d1b187'], @@ -2473,34 +2462,34 @@ exts_list = [ 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], }), ('rasterVis', '0.51.5', { - 'checksums': ['c116f979ed891ec55f3e1e7b9a92436b5ec9430c1170439a501ecb7e2a33ef4d'], + 'checksums': ['3a9ffe38f7835bf9008cb3f2fbe01208f17130f4b1ca9ba19f97dc240ccf7aa1'], }), ('tictoc', '1.1', { - 'checksums': ['a09a1535c417ddf6637bbbda5fca6edab6c7f7b252a64e57e99d4d0748712705'], + 'checksums': ['120f868ba276bda70c8edef5d6c092586cf73db0fa02eb5459d8f55350fb474d'], }), ('ISOcodes', '2022.09.29', { - 'checksums': ['b25ddec624b46f5630c29267bdf4a749cfb9d001ef029fb9ca84dafe56b1c73f'], + 'checksums': ['4bae4fdf661a1c29694f9702240b84c933518ef70e66312cbaddaf35562d4fe5'], }), ('stopwords', '2.3', { 'checksums': ['c5ec1c6ab1bad1786d87d7823d4b63abc94d2fd84ed7d8e985906e96fb6321b2'], }), ('janeaustenr', '1.0.0', { - 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + 'checksums': ['b4c32ee1395ee4a8efe714c535c0fe578b0dbf5f3bb85b41fa5cc87569b8e8aa'], }), ('SnowballC', '0.7.0', { 'checksums': ['b10fee9d322f567a22c580b49b5d4ba1c86eae40a71794ca92552c726b3895f3'], }), ('tokenizers', '0.3.0', { - 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + 'checksums': ['24571e4642a1a2d9f4f4c7a363b514eece74788d59c09012a5190ee718a91c29'], }), ('hunspell', '3.0.2', { - 'checksums': ['1fedbb913bc13c790d2fabfe4edda0a987db3a078bea8c0ca9b777d20af08662'], + 'checksums': ['5ea25955f76cc275e56424c8ac0700d1cb1f5c21c7f8d61c25fa740d731a324e'], }), ('topicmodels', '0.2-13', { - 'checksums': ['afd83a4381bf39e470446ebefd41ed03f314be400c1b2f702a4b1060eb8fd1b4'], + 'checksums': ['7d6106a68482b65aed821d558c782f4a10664e98b46b1606622d96ca0f05bc9a'], }), ('tidytext', '0.4.1', { - 'checksums': ['753b2bcea6e343ac439869b92e7c11b0aaf98ce5c0373965da6c7d087d57924e'], + 'checksums': ['526750a2cc8ac7b65be1093f4c9186aa27f0a22f00023a6d6b3b878e1310c815'], }), ('splitstackshape', '1.4.8', { 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], @@ -2517,7 +2506,7 @@ exts_list = [ ('entropy', '1.3.1', { 'checksums': ['6f5a89f5ce0e90cbed1695b81259326c976e7a8f538157e223ee5f63b54412b8'], }), - ('kedd', '', { + ('kedd', '1.0.3', { 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], }), ('HiddenMarkov', '1.8-13', { @@ -2530,24 +2519,24 @@ exts_list = [ 'checksums': ['866a2f54a4e8726cc3062e27daa8a073e6ac4aeb6719af7845284f7a668745f1'], }), ('RcppParallel', '5.1.7', { - 'checksums': ['6396322b3b6d6f7019aac808ceb74707bc5c4ed01677fab408372c2a5508c2ea'], + 'checksums': ['f9c30eb9ce1abffc590825d513d6d28dcbe970e36032dd7521febf04e905b29c'], }), ('StanHeaders', '2.21.0-7', { 'checksums': ['27546e064f0e907e031d9185ad55245d118d82fbe3074ecb1d76fae8b9f2336b'], }), - ('V8', '4.2.2', { + ('V8', version, { 'installopts': '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"', 'preinstallopts': "export CPATH=$EBROOTNODEJS/include/node:$CPATH && ", - 'checksums': ['6c62fdc974cc30fa975cad4ccb1e3796112fc2490a807f6e3d7878c3a5544743'], + 'checksums': ['50653527198637a37c010052f394839f50a3c643975aac1d04e42d36f8e5313b'], }), ('rstan', '2.21.8', { - 'checksums': ['86e4fe562d8ddcd0b02336f35a420fa8786dd21de7ca2bebb4ed6e9c252bb9ea'], + 'checksums': ['b2d4edc315419037970c9fa2e8740b934966d88d40548152811f3d4a28475075'], }), ('Rborist', '0.3-2', { - 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + 'checksums': ['46ce30cda4d0554e61405ea211cefa06a72762e8078662e369df9f18bdb7a98b'], }), ('VSURF', '1.2.0', { - 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + 'checksums': ['c027b1e19762f1eaf4a559c2592f3530210fefd21ee3d7c787c73b776c683393'], }), ('mRMRe', '2.1.2', { 'checksums': ['a59a3cb3cca89f51d9ee6702cd479fd7db8bc2e25b72f45cb6712da983777ca0'], @@ -2559,40 +2548,40 @@ exts_list = [ 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], }), ('ggsignif', '0.6.4', { - 'checksums': ['ca8545b25590e531512a90a18449a2cbab945f7434a1d60188c41f7d1839a7a9'], + 'checksums': ['112051af425a0c0f2998ce187dacad066bc16f55af01e3e7b76d62ff6954b20a'], }), ('corrplot', '0.92', { 'checksums': ['e8c09f963f9c4837036c439ebfe00fa3a6e462ccbb786d2cf90850ddcd9428bd'], }), ('rstatix', '0.7.2', { - 'checksums': ['a5ae17dc32cc26fc5dcab9ff0a9747ce3786c9fe091699247ad8b9f823f2600c'], + 'checksums': ['e0c6f5ab1d9c5d84713defabc5d149aad3d55944cffdb903cc128b694e5221a1'], }), ('ggfan', '0.1.3', { 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], }), ('ggpubr', '0.6.0', { - 'checksums': ['abb21ec0b1ae3fa1c58eedca2d59b9b009621b30e3660f1247b3880c5fa50675'], + 'checksums': ['2e6ec5d8151991d17ef8832259cf545fa0d1a50b326ba8c1c4657700171df774'], }), ('yaImpute', '1.0-33', { - 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + 'checksums': ['58595262eb1bc9ffeeadca78664c418ea24b4e894744890c00252c5ebd02512c'], }), ('intrinsicDimension', '1.2.0', { 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], }), ('patchwork', '1.1.2', { - 'checksums': ['cf0d7d9f92945729b499d6e343441c55007d5b371206d5389b9e5154dc7cf481'], + 'checksums': ['dab9d5d2d704d591717eaa6efeacf09cb6cd7bee2ca2c46d18414e8503ac8977'], }), ('leiden', '0.4.3', { - 'checksums': ['cace86748c4aa1720508210658ee2f63f7875be5bac215084001fdc59d22e2bd'], + 'checksums': ['6a464b4b860e621749b3b701bb7ceb07e23c1a36be241c3e13b18105eb980938'], }), ('sctransform', '0.3.5', { - 'checksums': ['83af125c40f211e1ddae5098f88766aea1453c02ae98486081f3efadb3620b2b'], + 'checksums': ['c08e56df05d64ed04ee53eb9e1d4d321da8aff945e36d56db1d5ceb1cd7e6e0b'], }), ('packrat', '0.9.1', { - 'checksums': ['3025b9052974bec00fb09299226b80004d48e611e15a65e5a0bc49d3538844ef'], + 'checksums': ['414013c6044d2985e69bbc8494c152716b6f81ca15b329c731cfe8f965fd3344'], }), ('colourpicker', '1.2.0', { - 'checksums': ['a0d09982b048b143e2c3438ccec039dd20d6f892fa0dedc9fdcb0d40de883ce0'], + 'checksums': ['bc2c80eee046219038baef9f8f213c9824d7fec7f893f6a1b881dd44b4a8638a'], }), ('ggExtra', '0.10.0', { 'checksums': ['dc6855bbb7e81ffa58d6b65b594d22718fa36b7f50b2284386f70fa8ccc6a3e5'], @@ -2601,7 +2590,7 @@ exts_list = [ 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], }), ('argparse', '2.2.2', { - 'checksums': ['83e112beb47733849980b286d93ac930f0cbe6ac78fcb94fc9f6b0eea882658d'], + 'checksums': ['b62c9bf5e6ca35fb7a2e614a916815c04cbf6c6db3f89f99b4df76470a4a856d'], }), ('intergraph', '2.0-2', { 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], @@ -2616,19 +2605,19 @@ exts_list = [ 'checksums': ['cb810baeb90c67668361b666c6862df9917aff6aaec63d2c3a485f28407c4eb7'], }), ('distributional', '0.3.1', { - 'checksums': ['fab36c7346617d8f2ca4b3cd0e3c9da93cb2f95fb7f102a3ae88670e694751d6'], + 'checksums': ['727e56cbcf0c8a8adacca8030214ddbd14f68ee28d0aad716467bd68b027235f'], }), ('posterior', '1.4.0', { - 'checksums': ['d615ed75b43b2927002b79d2982c624a6144c851aac7b81fa14e4ec9cc3d353b'], + 'checksums': ['f546658678a2c8c86130922c06f9045b4078bc11a91fa98b0462a5d733133f9d'], }), ('bayesplot', '1.10.0', { - 'checksums': ['0a81a4b99cf781334e57cfc3c469fad8b932a68204016a3bbca33cab4e2a1e43'], + 'checksums': ['bb4cb92b1ae4cf8ae5f4b5cb092aba34af3d820d137e1f2265cca8f3e85113ff'], }), ('dygraphs', '1.1.1.6', { 'checksums': ['c3d331f30012e721a048e04639f60ea738cd7e54e4f930ac9849b95f0f005208'], }), ('rsconnect', '0.8.29', { - 'checksums': ['faafabbed803743799b345051f221aef2b4497b421fc98092ca41c05ef6b5fed'], + 'checksums': ['852899d2aaf90bcedf4d191a9e00c770e8ee4233235169fc97e6aa636de01c43'], }), ('shinystan', '2.6.0', { 'checksums': ['a084856a2d66d8744f2c72e3e19ca35e600a508ed7ef1f7ebed8c7fc0738d529'], @@ -2640,10 +2629,10 @@ exts_list = [ 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], }), ('projpred', '2.4.0', { - 'checksums': ['a88a651e533c118aad0e8c2c905cfcf688d9c419ed195896036b8f6667b5cfb0'], + 'checksums': ['6f01bb7f1ddbda92ea0fc44e5596f3885f1ac326f4e88abb0f0cd7fcb71edeb2'], }), ('brms', '2.18.0', { - 'checksums': ['24e5a3a40b81bea558e8f660d0de7fd1a4c2080c7553baac98f34dd2682ece71'], + 'checksums': ['63914be03cd1c4e6333317d22d7827ba2dc0414cb0dc88337cf74763ba07e111'], }), ('drgee', '1.1.10', { 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], @@ -2664,9 +2653,9 @@ exts_list = [ 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], }), ('BIGL', '1.6.7', { - 'checksums': ['8edb6607c5d91cea5ba32290eeb76c35317383a24d726bde6eca61f9cce96bb9'], + 'checksums': ['8f5e7e7b08ac80e8966d491a76ff7fb9a7c2460579c063e1b2316c558655ea7a'], }), - ('drugCombo', '', { + ('drugCombo', '1.2.1', { 'checksums': ['9a605c655c159604033558d757711e6d83d33dfc286c1280f722d4cb7d130f80'], }), ('betareg', '3.1-4', { @@ -2676,10 +2665,10 @@ exts_list = [ 'checksums': ['a54f49f42d30a7a69eb6c3db00d3cd2e1f8e549aec28fa5487fcdd27a37f87fe'], }), ('maxlike', '0.1-9', { - 'checksums': ['90aaab9602f259cbfae61fe96e105cc4a0c2a385b42380f85c14f5d544107251'], + 'checksums': ['632fb15dd21a75bb95c7473ba4fe2ed58bc1b2f1401da65c6df348599b2f655f'], }), ('coxme', '2.2-18.1', { - 'checksums': ['dd0565f97adb7ff978d1dbd6cb7d6e44edee5e2a31cf6d5d4806a0151d1b1318'], + 'checksums': ['aef691d74ee75095c43d7b6ab27e01641382cfb349a8eefad972c745ac0531f5'], }), ('AICcmodavg', '2.3-1', { 'checksums': ['d0517da15a38e9b1df20fa73f5342b586624e65792d266e7dff278ad7fc458b0'], @@ -2694,22 +2683,22 @@ exts_list = [ 'checksums': ['fd21e5ecf3c1ac00ef1bbe79fab4cdd62789e0c4c45f126f1b64bda667238216'], }), ('oai', '0.4.0', { - 'checksums': ['ebfa756e08f6ac0aa61556b1a5bbe611f407bfff8aef1f8d075a24c361678bfd'], + 'checksums': ['f540de066de5538e303cd535cbd2e771b40474bc2c6e8d08a4894a868543ee33'], }), ('wellknown', '0.7.4', { 'checksums': ['483e6fc43edf09ed583e74ce5ca7e2d7838ef8a32291e06d774c37546eed1a34'], }), ('rgbif', '3.7.5', { - 'checksums': ['460f9e80bb3d90618bb80a8b57ac6fed99a22e8919279df47b6d0710b6a89d5f'], + 'checksums': ['a97aa8d42fc7d094542b6835d7fe818eef64f5ffac3604be1eda3d0d9422d1de'], }), ('rgdal', '1.6-4', { - 'checksums': ['4583a4e187492eb936b59bc6bfeefea687b115bc3ae25172e0ed348b38f473ed'], + 'checksums': ['932c53351061170753ac68ca28316134945a3159e9558e3d49d925e468d62ca7'], }), ('rgeos', '0.6-1', { - 'checksums': ['ab90cbfe6a3680a9d2eed5e655064a075adc66788e304468969ab7cc2df0e3d4'], + 'checksums': ['420dbd48c0e8c840686b6ed29384715723d6926a1f9b0c437c60ad1853eef7f2'], }), ('mapproj', '1.2.11', { - 'checksums': ['865f108f1ee54cda38571b86cd46063a903824d9b4eabfdf75218023d08a7781'], + 'checksums': ['db2d201cc939de26717566066bf44225a967ccde6fc34731af845f03c086347d'], }), ('rbison', '1.0.0', { 'checksums': ['9957e5f85ce68f5dd0ddc3c4b2b3c9d2f52d6f37587e1022ab8a44863534a83c'], @@ -2721,7 +2710,7 @@ exts_list = [ 'checksums': ['2de9a3ec33a213c7592b49cca1d510a25aef0625369376d9b1b4e5d0da519226'], }), ('ridigbio', '0.3.6', { - 'checksums': ['e5cfb2e4dd8ddd1452a5afcf24fcc260889179d0f52eff4f41835adf99b64614'], + 'checksums': ['c019dd266aa1334c41430db95361a7b1b911a6793d692b35cd2dc1894232f560'], }), ('spocc', '1.2.0', { 'checksums': ['4bac45db5e69bfa3bf6cebd1b0c9241214c95561f275cee6d31e00911aa79d84'], @@ -2733,19 +2722,19 @@ exts_list = [ 'checksums': ['529d529ca90437db3d1e45118443e27a920422806383c7edaa2102beb43f5f80'], }), ('ENMeval', '2.0.4', { - 'checksums': ['4b39173a8d9dc4f36d09509e0177abcf91b7b1b51dc219eebcb007a0fb8c3c41'], + 'checksums': ['6d9f3c460fa7ab3131cede904fcb9280cf69f4fdd43f67115a3abcb8ed5b64d1'], }), ('plotmo', '3.6.2', { 'checksums': ['cde33a8ec558b12d8e11d7d0531e73f6678a25ee589b79897d2fc425a3fd353c'], }), ('earth', '5.3.2', { - 'checksums': ['0bbe06ba974ceb8ec5de1d59cb53f9487d1828d7130fe2503c48b6cb449c4b03'], + 'checksums': ['c844d75edf9a2706a911bb05ed4287aad9acf6f3fed357e037763a300eac0bea'], }), ('mda', '0.5-3', { 'checksums': ['bda6409c17f385fae97da458cc742334e7b47aab8217a975b7551e2e18d38463'], }), ('biomod2', '4.2-2', { - 'checksums': ['30ed33ff980558a59782ec9e35f9c2c710a540718010654363f63878cdc0ac18'], + 'checksums': ['9be863811589ba4ac50f57a6879c9efe4dd52d52f533265b5d2e829d4705231a'], }), ('poLCA', '1.6.0.1', { 'checksums': ['ed8c60a42bff0402c9ba2f9ce1422dd171e711c1a64498c4d96010ddb29f6b16'], @@ -2766,12 +2755,12 @@ exts_list = [ 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], }), ('fasterize', '1.0.4', { - 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], + 'checksums': ['44efbde363345c7fc494599392ff538eaef8ffcc8cae48d78350b5eea3887db2'], }), ('RPMM', '1.25', { 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], }), - ('RefFreeEWAS', '', { + ('RefFreeEWAS', '2.2', { 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], }), ('wordcloud', '2.6', { @@ -2793,13 +2782,13 @@ exts_list = [ 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], }), ('dbarts', '0.9-23', { - 'checksums': ['68fa2bfe274811c91ea7b67da46c4ffe527eb662d75edbec26ffe934ddc7150a'], + 'checksums': ['e1ac65fd89c321895d4f0e77d9cd8dcda5f1103485008afd4e19e6c9137557a3'], }), ('proftools', '0.99-3', { 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], }), ('NCmisc', '1.2.0', { - 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + 'checksums': ['26fcfbc79810f23a28389a5ce5519e6ddc2470c5e924ba8cf4dd19a1b0fd9f83'], }), ('reader', '1.0.6', { 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], @@ -2811,7 +2800,7 @@ exts_list = [ 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], }), ('readODS', '1.8.0', { - 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + 'checksums': ['11d4fc5c1b8685cae594b5a0d70ea782a93befa134514786254f8f6a77baafc9'], }), ('nortest', '1.0-4', { 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], @@ -2829,19 +2818,15 @@ exts_list = [ 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], }), ('gWidgets2tcltk', '1.0-8', { - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" - 'preinstallopts': "xvfb-run ", - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... 'modulename': False, + 'preinstallopts': "xvfb-run ", 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], }), ('mgsub', '1.7.3', { 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], }), ('ie2misc', '0.9.0', { - 'checksums': ['c81441af7588c62ab019ef2fbf31f61e0c2e3440a5e131938b1c5946cd2bce1a'], + 'checksums': ['7de6e8ddf05d3a8d105ddfa69732e94a1045180f8c86cbb0659c67e7e1a45c31'], }), ('assertive.base', '0.0-9', { 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], @@ -2895,19 +2880,19 @@ exts_list = [ 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], }), ('Exact', '3.2', { - 'checksums': ['d67f5c71b1209bea655d1e8d7530fa72359e0bcac25312551524501d0287e3cf'], + 'checksums': ['53b4e20cbb57615970c572fc4e7a780a510bde8b5deadec3880095f6e17a6328'], }), ('lmom', '2.9', { 'checksums': ['363e62751a73e0870fd0206206f1743a884a23aeac9b31b9afc71c0a1b51bb90'], }), ('gld', '2.6.6', { - 'checksums': ['0db6daee1b6e256d64d292c1f6795c505677331dcf2f97e04e264566ded93323'], + 'checksums': ['ea23e9781207b5d47ed04e4d5758d9652cab5d1eedcf9fbc9c2ee4d3babffdc4'], }), ('DescTools', '0.99.48', { - 'checksums': ['8dfe7057fdcec475bc444761b00db59f6fb7313fd39c7bd6aebeca7f67aceb05'], + 'checksums': ['dbe058c0ae9ad15ed07cab4baf690f315ec73e5274ddcc6dae9f33b49f4eb62b'], }), ('orthopolynom', '1.0-6.1', { - 'checksums': ['17576157374c927da2959459caf2ed161b49a4a7768ea3d3fbe47656cafacc5b'], + 'checksums': ['ec4a6ed266532f2f6d37a4ca6bd1b74c1df28a8c2caeab60e5d6af15bdbfe2c5'], }), ('gaussquad', '1.0-3', { 'checksums': ['a3337ce52bc53435cb4565a38bf48b72b384be397d2e86bb66f62973004dc810'], @@ -2937,7 +2922,7 @@ exts_list = [ 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], }), ('blavaan', '0.4-6', { - 'checksums': ['a9f9f7b32aab7e7f179340c9f0f9d154b5fac51352c4fd590d317c201fe81b74'], + 'checksums': ['892d87ce2ed43d56915175f5f28150a38084f141bec15089de139ca60e4fde6e'], }), ('mathjaxr', '1.6-0', { 'checksums': ['ecc47607111b788d84789459af7f4f9102719f98640b7a23bd5a4eb1a6d3c179'], @@ -2946,7 +2931,7 @@ exts_list = [ 'checksums': ['f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8'], }), ('metafor', '3.8-1', { - 'checksums': ['92e1bc21c4d135b6e651fbefc4b40666fc02c66a6a4f6f28effee0e73a21c26e'], + 'checksums': ['d694577f954144d8a5eeab6521fe1c87e68ddf9ecfd7ccc915d01533371b0514'], }), ('fmri', '1.9.6', { 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], @@ -2955,10 +2940,10 @@ exts_list = [ 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], }), ('rnetcarto', '0.2.6', { - 'checksums': ['2cab23b60d9d97474c946da7369e859c19dee20288eeccdcb123fccdc50a3999'], + 'checksums': ['4f28ae62748654cb6f90e1ffa17b05bb8b89eb6a20262d9c5d39cb862f71dc91'], }), ('DEoptim', '2.2-8', { - 'checksums': ['8c63397d83a067212d003ef3e639fd81f5f00bf61e3c271b4e4999031a69e2e1'], + 'checksums': ['631eabdcf26ec25a759651f699db1971beca3ae193c7fbd1c63a78248fdbf54c'], }), ('optextras', '2019-12.4', { 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], @@ -2979,10 +2964,10 @@ exts_list = [ 'checksums': ['430cbc18f17db11a7941e6a8274a0eefbb8a6b0bdac8800970530d60d5881fde'], }), ('miceadds', '3.16-18', { - 'checksums': ['74ab5503d6f3c0d016166a4c664918d60f1adb0672d8aefbc57385be3d287c3a'], + 'checksums': ['dbc56cd2b20aaaaa69ea28c15cfd61d48d072fe9c0dc8e392c81a569e280cf75'], }), ('visdat', '0.6.0', { - 'checksums': ['527c76b6643b8475a58516763ef40238cdc61ec62d2dcf690f7c316b93b878c6'], + 'checksums': ['104acdbb9d41167b861ab24de0e1e1e14f61c1b476bac112fcbc6e47c157e598'], }), ('UpSetR', '1.4.0', { 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], @@ -2991,21 +2976,21 @@ exts_list = [ 'checksums': ['4384791af74c1008238f036abe0dda4b4048b9700cc4acd7b45025598fd20cc7'], }), ('naniar', '1.0.0', { - 'checksums': ['d546ca15bf6c224f3103eb1441abef91d34feebb7320c2398d598f5d50177450'], + 'checksums': ['c2eda97de603e2daf4c1c5d12f9c9a65635910833a3c669e08e344e90d9394f4'], }), ('stringdist', '0.9.10', { - 'checksums': ['efccd6ccc5c74c578be95b7dae1099c52b0d7805452ab14ee91ca34adb8261bb'], + 'checksums': ['6fd42e0b7ff25843ca7f45acf9a183facfe14a6cde2dc7a97ef7126ab0f06ce8'], }), ('image.binarization', '0.1.3', { - 'checksums': ['0621ca94a74264bb73f689b1a00484b5a3bbef93fc203d9c001d791a18fcc13f'], + 'checksums': ['ecc844bdd9bf15b88ce1e1afc8321c177bdc8ec32618c22102b1e8b02b36e00e'], }), - ('lassosum', '', { + ('lassosum', '0.4.5', { 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], 'sources': ['%(name)s_%(version)s.tar.gz'], 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], }), ('lslx', '0.6.11', { - 'checksums': ['adc2b2a621625b52165245ab2f3a0bfba4f4db64fcc6ad48a3e5b219c3bd2fa1'], + 'checksums': ['373cfb1e79174b568dac254fab02d99bf79b830218bf18f0cc592af6fef853d6'], }), ('truncnorm', '1.0-8', { 'checksums': ['49564e8d87063cf9610201fbc833859ed01935cc0581b9e21c42a0d21a47c87e'], @@ -3014,9 +2999,9 @@ exts_list = [ 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], }), ('regsem', '1.9.3', { - 'checksums': ['28ff1c2dbddcafc6ed6c30154f46074aa0c8974757466680529b71a5f3e463ec'], + 'checksums': ['5c8f37264b62ee3cbe61801e65d32dc143ea5365ce260f6b57b6145a5bfdf16e'], }), - ('semPLS', '', { + ('semPLS', '1.0-10', { 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], }), ('GxEScanR', '2.0.2', { @@ -3026,7 +3011,7 @@ exts_list = [ 'checksums': ['a8c62859b39a8340ecf7bbf411fac303c059e4237d28ff7bba9ba3daaca1d36c'], }), ('admisc', '0.30', { - 'checksums': ['ce46df3d75afd47dd97824bc3e740c708b25ae023d007f1a180dcb88ca14740b'], + 'checksums': ['690c3fc8f24466438dd818d263e53f19f238310175731daac42c62f0bbc46205'], }), ('polycor', '0.8-1', { 'checksums': ['f05f53e0b5c992de0e5b4c6b2e998148cf83310358821e1bba180d81face0509'], @@ -3038,13 +3023,13 @@ exts_list = [ 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], }), ('cSEM', '0.5.0', { - 'checksums': ['7753ac7db9d2c0392e51dd31ec8638e1a7fcbb2546dd9103f5ecc03dd51836c1'], + 'checksums': ['25ae115520aab7d916da9ded1f87b8519c4e15101c4adef2284c51eb03d81728'], }), ('cubelyr', '1.0.2', { - 'checksums': ['740a34100592b2c6b7bc89a31bddccf4c8fd95720caf68f530104f17aada77bc'], + 'checksums': ['18b10f1fe561305a1e115a438460264b88b301b3e8c086b931500a798be39b94'], }), ('furrr', '0.3.1', { - 'checksums': ['3fe91cc1614f9404c708ea3a15b6a40289fa57f40f3ece54452093408d91fd84'], + 'checksums': ['0d91735e2e9be759b1ab148d115c2c7429b79740514778828e5dab631dc0e48b'], }), ('broom.mixed', '0.2.9.4', { 'checksums': ['7631cd29316a32050b9e72057754e053d7f9064a75900bb7e69b29ebca6c60b2'], @@ -3053,10 +3038,10 @@ exts_list = [ 'checksums': ['ab5d1332809f2bb16d156ed234b102eb9fbd6de792e4291f9f6ea4652215cb49'], }), ('grf', '2.2.1', { - 'checksums': ['02a4fe9c8147768f1345be2f8ca73fca079af5f07ccaa4900f9ec255ca66bb19'], + 'checksums': ['49e3fb600b6f5f4469457a051749932fb401be39c0f6a87fa97350e5ac871f2d'], }), ('xgboost', '1.7.3.1', { - 'checksums': ['9ae99a20997e1b02ffd21cabada2a55e53f5754746238ee900de5eb6cd964ebd'], + 'checksums': ['3ced2ca30efaa86a9e93bc28e5cd3cc6df93bd68a550751ecf3a9f488ea438a5'], }), ('twang', '2.5', { 'checksums': ['fc355527c57e4f6e0f60d26d7c690c4475fcd5fb165d125fea7cc6b9fafc4ce5'], @@ -3065,16 +3050,16 @@ exts_list = [ 'checksums': ['5f66cd255db633322c0bd158b9320cac5ceff2d56f93e4864a0540f936028826'], }), ('PCAmatchR', '0.3.3', { - 'checksums': ['fe0c67cda541639a1a2147f68cae29d17cd05ff8edb6f7bea8d44be346a5f1b6'], + 'checksums': ['5dc9d8bb4c0020b5e51a53a4fa71afa9adc6b907ea618b231f5cfc2877a49779'], }), ('origami', '1.0.7', { - 'checksums': ['8d0d08aaecc428cbbf5db4615ad3623777c10c6d7947a1cc3ccc7f8db8cb5263'], + 'checksums': ['b44034541ac358e0686682684c40e9a1de8d78c7913e56e4d3dbe41a2a55c62c'], }), ('hal9001', '0.4.3', { 'checksums': ['f2489e7a0a16db6dc65da8ce13bfb7f0854e6f303c9ec05f6158d46c66b6588c'], }), ('cobalt', '4.4.1', { - 'checksums': ['b9bfd0746e41de6a61fd8f3fa51eb344190a226445e51ef032931b026d5d314c'], + 'checksums': ['4ea30c5a0e7d2940a6d7eaf927933b2d341a2e10dbb0f5fcd38eec34cb369fc0'], }), ('CBPS', '0.23', { 'checksums': ['ed8fe09b642db459a516bdeb03a49e718a7d5ad915cbf82400029508efe9b32d'], @@ -3086,43 +3071,43 @@ exts_list = [ 'checksums': ['cd38a9c5f323f61459e6096cdbf4493851d40497baf671af4f8dfe9a7c00e857'], }), ('lwgeom', '0.2-11', { - 'checksums': ['f48a92de222da0590b37a30d5cbf2364555044a842795f6b488afecc650b8b34'], + 'checksums': ['7fd73cf58981f9566d946bf63ed6575ea0c70634abeaf4e60ef9615040d63419'], }), ('finalfit', '1.0.6', { - 'checksums': ['446940d300c8b725e798bf2a2829a41165d25a939d2c59425768234438a2deb1'], + 'checksums': ['c12be933408b0a8ec4962ebe5e9b404ef99a0b1eafccf7f646627458f4af4b9a'], }), ('broom.helpers', '1.12.0', { - 'checksums': ['2b7087ca73af04a130e78dfbf4941590e3557bcce4ec7e0106b012df061581f5'], + 'checksums': ['bfb5d960367af1c4d04180345b65af4e3604345d4d6267af9445da72188c2a2c'], }), ('gt', '0.8.0', { - 'checksums': ['469384e0daecd4b09d5814e4e56b17e9220d872a1906625cc6f609d22ce226fb'], + 'checksums': ['5eb74e134101cc74b8764252b8f4693a19e58f670b2f286b35cdb4d0ad0de9f9'], }), ('gtsummary', '1.7.0', { - 'checksums': ['fe04caf79826ecf4fd9da0ef5d4705775a15bf18a7d508a53492a086798ce35c'], + 'checksums': ['73ed05c4b7c62f3e5e7bb86c940d4a03d6b39f420a3582039a725b367a6336d0'], }), ('ncdf4', '1.21', { - 'checksums': ['cb8d139211fc7475c435ce9f6a43e47710603409dc523b053c8b7de9848dfb63'], + 'checksums': ['2f5ae7def382c595c66b6ed0ea0529f8337108eb73de39939f9762f3fb21b30d'], }), ('geex', '1.1.1', { - 'checksums': ['037aece09bc0c4349897cd1d8f5dcf1e680598cdfdf72148b6d1506e02690e7f'], + 'checksums': ['a1aebb9f73ba8dfe26ee3dc7b0725ccb814b3db5358ba17e417bdfc7eb3e4143'], }), ('momentfit', '0.3', { - 'checksums': ['a10d43ac23bb61b9c67efa4800e3e2b6a444c1afaca8bad351648accd7e003f6'], + 'checksums': ['67cbee1edf4c3b8193e693e6511a0b9574af2bb6314aef92b24f8fbfee37da6c'], }), ('StatMatch', '1.4.1', { 'checksums': ['0c5479c444cb831d21b6305fc4cdcdf2653723ff08a31427dc2b236ca4f25bc5'], }), ('stars', '0.6-0', { - 'checksums': ['f359577c9e08066cb9ea6aab9b8eae574efea95ba6efcc250663f2c350fe8b41'], + 'checksums': ['49fde4f78d1a5e09e6746e700c2e323a5102d7be05f02675c10cc6852ed68b7f'], }), ('rapidjsonr', '1.2.0', { 'checksums': ['62c94fcdcf5d0fbdfa2f6168affe526bf547c37c16d94e2e1b78d7bf608eed1f'], }), ('jsonify', '1.2.2', { - 'checksums': ['929191ab32e34af6a02ad991e29314cc78ea40763fcf232388ef2d132137fbce'], + 'checksums': ['3745e962592f021a3deaed8b2f6b99c4f7181f28e095300a96d1c2b08af4af2f'], }), ('geometries', '0.2.2', { - 'checksums': ['8cf5094f3c2458fef5d755799c766afd27c66cd1c292574a6ab532d608360314'], + 'checksums': ['32d3063de0f8a751382788f85ebaee5f39d68e486253c159d553bb3d72d69141'], }), ('sfheaders', '0.4.0', { 'checksums': ['86bcd61018a0491fc8a1e7fb0422c918296287b82be299a79ccee8fcb515e045'], @@ -3152,43 +3137,43 @@ exts_list = [ 'checksums': ['60e58eef0f8c723db855d59117ca9f9b5e3663ba34b5ca783dc889bf20285e04'], }), ('collapse', '1.9.3', { - 'checksums': ['9c13f4322d496702255652c9467fc2a202bfdb36cee6d78791780b7ab988f3ef'], + 'checksums': ['59425d108e7fdafd5fbca7099fe2fdc5c29d7390606c78bb7ef8ea8eb64d2056'], }), ('genoPlotR', '0.8.11', { 'checksums': ['f127f7fe8b19c899ecfdf98bf69d2e18926afb593a72fc40097acca66d401607'], }), ('VineCopula', '2.4.5', { - 'checksums': ['8449b1181fd7f325a2f0539cdaa4a4ff895c41424f462f52258729436078c90a'], + 'checksums': ['06b9f67d14d525cbf04c991cedbd2e4f58bbb1f24ec10947aeed1efef91c33cd'], }), ('Rmpfr', '0.9-1', { - 'checksums': ['cfee5ab47d49c6433c372a267f7d849c8f7c61a84e00d08afb047eaafcdbbc8a'], + 'checksums': ['dbaf1db46b06211852befe4aecfe75ea2f0a91fe63d92a2039a36edf6c259d54'], }), ('scam', '1.2-13', { - 'checksums': ['0ce5f844221370884719424eb5b2b22c34a8a8ad64eac3de981e5539b6e88f4a'], + 'checksums': ['33fd80394583ee9c909c5059fee1184ee3ca9325bd3cf40beaa12cfe8978e562'], }), ('copula', '1.1-2', { - 'checksums': ['9ab76e6256534db2a18d3880143b8c67e385767010de861bbde25212aa75d924'], + 'checksums': ['88f9454d25e4dcdf53d8ca5156daf48e664769f5e13b1e835ed64f37251587d3'], }), ('evd', '2.3-6.1', { - 'checksums': ['8edb8bc4f06d246c4343fd923bb5d5df99724d6db8821bfd996220343a834cb6'], + 'checksums': ['662c592d3f5c5693dbf1c673d1137c4a60a347e330b71be1f3933f201d2c8971'], }), ('ismev', '1.42', { 'checksums': ['0d57fbeca83bd478e84fcff795967d51d8448c629abe7adc6c4c18c7fb8bf1a5'], }), ('GJRM', '0.2-6.1', { - 'checksums': ['f8abe1900a83892a9ee96bc62cdb1a42fabf8ba66eed60e44f59bd203b5f6779'], + 'checksums': ['cbcba080ab368e32d41511292b78b351b4f0e71daaa47bee76e7d249955c5c0d'], }), ('penfa', '0.1.1', { 'checksums': ['a22a8ac3d4a040c77e50ddc92328c1989eae536d79fe56013e9372ba27c114e5'], }), ('rngWELL', '0.10-9', { - 'checksums': ['0c00c54e69d7d552cfa08d766e4854c01c6c1c8e2c558f387760b91a55ef2d38'], + 'checksums': ['9969cc10be6d18155d2b2de93381c52e7f720c2b1b3f2554fa8bfa84ceb7cacb'], }), ('randtoolbox', '2.0.4', { - 'checksums': ['c4f28963fe5dbc821427691527a204aa6e08ab40bf00337f220cc60b81d552dc'], + 'checksums': ['94da14953e4ffc7981d7a9398622082c4eda3bd9d912d1437b527d949da39e4b'], }), ('kde1d', '1.0.5', { - 'checksums': ['124eb2e427e08fd24ca37e0baa697736601785d6c6fb1c97c2ebcc5146bb4556'], + 'checksums': ['b5fab76a394a7819deee10afdff39ac64fccdb844735adfe51c92043016f2468'], }), ('RcppThread', '2.1.3', { 'checksums': ['127e3d333dd412334d89d633e92f40135f65d68c91b7945fa63ce0e35abcf946'], @@ -3197,10 +3182,10 @@ exts_list = [ 'checksums': ['5f0184f6f0f9e9b8c47fb571e4d34dff309644a50afe5f18e42b9c37f52c593b'], }), ('rvinecopulib', '0.6.3.1.1', { - 'checksums': ['212189441b4cd2383e485c2aa410837456ba70357834f443c9275e4775b8bf22'], + 'checksums': ['df95d007552e7fa30aefad90a86acf5e14f6fe1e363ed4c71a74d501a08cbf32'], }), ('PearsonDS', '1.2.3', { - 'checksums': ['443a0619b824332ba5e50733a2aaf2913230925a64960a9f589ae368bcba3dc8'], + 'checksums': ['ca9a87799469d2522e22b0c1702861ee6f07fa48c1ca77427d3876cba82bfd0e'], }), ('covsim', '1.0.0', { 'checksums': ['3788e91ee7f7fd44b290feb22185637493e8301a64f9511ca80e1ed361c3f44f'], @@ -3209,28 +3194,28 @@ exts_list = [ 'checksums': ['f522ce3c02ac580ad49af7a7278141dae39fdfaeccc7d1379faf1266ce9fcaf2'], }), ('GPArotation', '2022.10-2', { - 'checksums': ['231e7edcdcc091fbecfb4f2e88d1a4344967cf7ea58074b385a4b8b48d9da224'], + 'checksums': ['04f72d8f3a9c204df5df904be563ec272a8437a707daee8823b2a690dde21917'], }), ('dcurver', '0.9.2', { 'checksums': ['cc6c55090d3607910515981ea0c7221e40e7a29e0da0c5a5f42c3847012290ec'], }), ('mirt', '1.38.1', { - 'checksums': ['5215a0f4eb5949a3985a84a7d4776d4dd7471973a980c1d158ce82b3bde185bb'], + 'checksums': ['b256e333cbc2e4763bb79bbcd739c04fbcef535125bb80a90e20b120a7b38f88'], }), ('rpf', '1.0.11', { 'checksums': ['e1fd670ae7c3e947db08ce50d6b16ce1b3b8f63a9016b03baba760aee78921fb'], }), ('OpenMx', '2.21.1', { - 'checksums': ['65c50ce09f9c006b41b7311ec05eba3ae77926d84fb44e3905905208404826ed'], + 'checksums': ['631b5c896baf083827338e115db8665d2f86df203ebc5eb314182c8a0f3b6a8e'], }), ('matlab', '1.0.4', { 'checksums': ['1988a2220703444a575f2bad4eb090a0da71478599eb53081dd7237b7ec216ea'], }), ('FactorCopula', '0.9.2', { - 'checksums': ['d95b0ccd1b0eebcf27a90286e9392f662b878a669c693fbbb4145798045134ff'], + 'checksums': ['e5a8b7a6ce2e4a0a3cdeaeae09b6e8d7af1f31ba1d6d4bd2276b42d95d9a3189'], }), ('rpact', '3.3.4', { - 'checksums': ['a568bb04b4dcecf163024269042124a4d75c5431edbf06776515aa524506f11c'], + 'checksums': ['3de77ca528c3ae206f634e1ca7f6fed4f34363c7dc906410021aefab63ca1520'], }), ('ldbounds', '2.0.0', { 'checksums': ['d4279d5f9952643f9051cf37eeb8441fff7ac050a49ef6363a9f5cbc8287a26a'], @@ -3248,7 +3233,7 @@ exts_list = [ 'checksums': ['7d44b5d259ec3fef776a7e3fcb21d1c379f930d6ae9ae5fbfff54494ad78e8a8'], }), ('ggdag', '0.2.7', { - 'checksums': ['372ec4ef0ded9637304a19b50bce908e84a034e54dbd2a52a061bb747b2b08a0'], + 'checksums': ['e078ebb8c63cde531f601feb71a20753fd45269061074cc742cf89fa0d4061dc'], }), ('simex', '1.8', { 'checksums': ['80c7841196b9377a9367eb6960ad80ca0bf8de511b8b18a0031bfbe7bde289a0'], @@ -3260,7 +3245,7 @@ exts_list = [ 'checksums': ['47938dcc987279281c13abfd667660bf1b3b76af116136a27eb066ee1a4b43da'], }), ('harmony', '0.1.1', { - 'checksums': ['e0598c220ae90d1334e47c9958ccccf7defbe6ac530159bc69424923894f724a'], + 'checksums': ['754f8dd82ba1a6c0539628fd1861cba37061f2c4a6599680e6fccdfb84779b5d'], }), ('apcluster', '1.4.10', { 'checksums': ['a214f72fa2f84563f3ca1aabb5322ef3e266007a6273ee8434bc2e2a7b9040a0'], @@ -3271,29 +3256,29 @@ exts_list = [ ('docstring', '1.0.0', { 'checksums': ['14528bc85bbb299fb8fe1a7116034f8df49ae0c26fb299376185b5d56176e5a7'], }), - ('gdalUtils', '', { + ('gdalUtils', '2.0.3.2', { 'checksums': ['4c6faabee2db8a87b7ea0f8e67e9fce3c5db7f4be353d7d86ea559507cbb2a4f'], }), ('openair', '2.15', { - 'checksums': ['1acdeafa1b96bbcb13c73f2ef965efb635e6306678cc22468d383c4bb5098a92'], + 'checksums': ['f11134bdcd466229a72cab158f49de583eedd850420d86e2013f5a9eefb685b1'], }), ('pdp', '0.8.1', { 'checksums': ['e23db66e5d575337d5c8fd664ccd0548cc85da2aca6613d90ce187be1dca376c'], }), ('date', '1.2-42', { - 'checksums': ['b5b1935638b73373809c009f94b77f993cd301744488d9bdf71ef79c82099757'], + 'checksums': ['5a913f960a0071cf9db05df4de03055a21a1c243b3bdbf846375537a664bcb74'], }), ('cmprsk', '2.2-11', { 'checksums': ['844027cb2c162cf7ef97034d01237ad7b81aa192fe302250d22d2c5528110e14'], }), ('mets', '1.3.2', { - 'checksums': ['5faccc064e715c44234def40f4f560e90f2dbd34c915a8687b48103b39814ab5'], + 'checksums': ['1a8bd1678c92650c0637b69b807bfb43df4210806518d56c650967c72f3e21d8'], }), ('Publish', '2023.01.17', { - 'checksums': ['a7a98fc52801bee30b9c8cb423e4e0082ea42d05134f7d3324ac3e95242cfbe2'], + 'checksums': ['436cc2bf5cdca1b3fdf892c9d35227f01740f1a4b335ff7b42a37e12c0115953'], }), ('riskRegression', '2022.11.28', { - 'checksums': ['4e1a66a45be73ae07bbc537192d3132e1cfc67ad24bc4b281b5cffa44282a047'], + 'checksums': ['601dd4e94cb32402413bf72b34b8f222671691b874333ed822cc44f4f1cd48e2'], }), ('pec', '2022.05.04', { 'checksums': ['47a1079b5d4aa5df8aaa716324ee48c55660025c4cf10c93b5ee1d7250761468'], @@ -3302,7 +3287,7 @@ exts_list = [ 'checksums': ['37197edd0984f8bf0e0a39a4ac1cfce897050dbb7f610553c349118fceb3ca93'], }), ('relsurv', '2.2-9', { - 'checksums': ['82c84bbe0a3eb9b391cbb885b3f3e7114adda5243aa83f974922d2edca918317'], + 'checksums': ['e966435c16c0978d1314867c3b9fbd7170ae7450d60e676d06cc7f8ca3d74d78'], }), ('mstate', '0.3.2', { 'checksums': ['3c473dff6854e31cdbdaf79f8fe7eaf97119b01a581874a894b283555afe8d14'], @@ -3326,13 +3311,13 @@ exts_list = [ 'checksums': ['3a423f68339ed1bf25e21be53b1fd68452ed7807b17c36239fba759dc6fc6b70'], }), ('Hmsc', '3.0-13', { - 'checksums': ['318e95ea88a15939dac33691886a9ce0c54765b25a3f4ef483d168bfc699098a'], + 'checksums': ['cbef4706aa09e93030243cee3ae4e62b02160d96981020f5a385751eade4f88d'], }), ('MonteCarlo', '1.0.6', { 'checksums': ['f21aecfba957bbea9576b09f75b1f7c7621637a04532a8fed2c6bb8ffc1a98cb'], }), ('RhpcBLASctl', '0.23-42', { - 'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'], + 'checksums': ['5c889d5b69e264060b9f1f0383c447f594855b8afc15b7d76d39e4d62b946615'], }), ('chkptstanr', '0.1.1', { 'checksums': ['433b29d597d7ea6c21ed652782a7bf2d766f9223a3b7bfed235c8fe7fffd175c'], @@ -3341,7 +3326,7 @@ exts_list = [ 'checksums': ['777f1b76b16837387b830e2b65304ede234b9299d17efd09c7fd403356122118'], }), ('renv', '0.16.0', { - 'checksums': ['b4f1a9a7daa82f0c3123ebd4eeba06e98d5485215518e5292b25bc56741d582e'], + 'checksums': ['f3a13e6b71e9be460db73bd9e11a3cb8a1d9bc05c6b77423957cbc2a7f8ba016'], }), ('elliptic', '1.4-0', { 'checksums': ['b65729b1a1c7a84a5b1a59bfc893a2d35106853eaadcae31cda5c9ee3c500bb6'], @@ -3356,7 +3341,7 @@ exts_list = [ 'checksums': ['97cf2ea758aa02b1dfaeef5032c6e50570777552aa771ed9a86df048b7871eed'], }), ('AMAPVox', '0.12.1', { - 'checksums': ['b30fefef8661e27ffe3883665204b623eda2143dbcd3084a1d5810f8ea834c85'], + 'checksums': ['1e9bce539dfbeb40a66efee3714bece1843ba856ee5e34b772757bad2660c942'], }), ('LCFdata', '2.0', { 'checksums': ['b58f4d93b9023dd1ba2db96a59ddfc058397085933d8de4cdb38ee064d5e7bf4'], @@ -3377,7 +3362,7 @@ exts_list = [ 'checksums': ['7ef0c2a2ddb3703efaabf337fa0026485875d5ffb35ba3ef5d60eb0c62c30686'], }), ('yulab.utils', '0.0.6', { - 'checksums': ['6ecd4dc5dae40e86b7a462fdac3ab8c0b276dcae5a284eb43390a05b01e3056b'], + 'checksums': ['973a51b8d1284060aec34e94849eea6783439dbcbf85083dd4f1a5df4f927b25'], }), ('ggfun', '0.0.9', { 'checksums': ['5c740e9d1e73b77658f41ed65e21492f4e71b12c7c9ff4b9e52ebf5f8f197612'], @@ -3392,7 +3377,7 @@ exts_list = [ 'checksums': ['af0763620a757571caac769bad5398c22a4890af6cb5646ac5fa9039a114bb12'], }), ('tidytree', '0.4.2', { - 'checksums': ['fbc4364d17e1b1c26ed06af0cdf36c88a5bc562fdbd4731ab179e30bba4009eb'], + 'checksums': ['cb831a66d8afa5e21f5072e4fbebcbd2228881090d0040f87605f5aeefda155e'], }), ('ggvenn', '0.1.9', { 'checksums': ['38779cfa4e01e07d4a42453cfb8b93d32d2acd6187676bae7d11b2168714a52e'], From c10a06e66c495418315c358a9ae54874ebfbc2ca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 28 Feb 2023 21:42:50 +0100 Subject: [PATCH 6724/9987] adding easyconfigs: Hypre-2.27.0-foss-2022b.eb --- .../h/Hypre/Hypre-2.27.0-foss-2022b.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.27.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.27.0-foss-2022b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.27.0-foss-2022b.eb new file mode 100644 index 00000000000..bc11eb06760 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.27.0-foss-2022b.eb @@ -0,0 +1,17 @@ +name = 'Hypre' +version = '2.27.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] + +start_dir = 'src' + +moduleclass = 'numlib' From cf58feb3af2c492cd9a20bc882e494638cf78561 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 28 Feb 2023 21:45:27 +0100 Subject: [PATCH 6725/9987] Added missing checksums --- easybuild/easyconfigs/h/Hypre/Hypre-2.27.0-foss-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.27.0-foss-2022b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.27.0-foss-2022b.eb index bc11eb06760..f04fecd72d4 100644 --- a/easybuild/easyconfigs/h/Hypre/Hypre-2.27.0-foss-2022b.eb +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.27.0-foss-2022b.eb @@ -11,6 +11,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/hypre-space/hypre/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['507a3d036bb1ac21a55685ae417d769dd02009bde7e09785d0ae7446b4ae1f98'] start_dir = 'src' From cb6d3d0534894cb9e93bc85b754d2071b23ed5a7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 28 Feb 2023 21:52:50 +0100 Subject: [PATCH 6726/9987] adding easyconfigs: ParMETIS-4.0.3-gompi-2022b.eb --- .../p/ParMETIS/ParMETIS-4.0.3-gompi-2022b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022b.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022b.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022b.eb new file mode 100644 index 00000000000..d5e24bd2bca --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022b.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.24.3')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' From d1f8ee82951a3aac17f79eecfe80ec536dc96344 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 28 Feb 2023 22:04:48 +0100 Subject: [PATCH 6727/9987] adding easyconfigs: METIS-5.1.0-GCCcore-12.2.0.eb --- .../m/METIS/METIS-5.1.0-GCCcore-12.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..03684045b7f --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +# We use 32bit for indices and 64bit for content +patches = ['%(name)s-%(version)s-use-doubles.patch'] + +checksums = [ + '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2', # source + '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67', # patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' From cfc00ad15dfeaf36f5a1b2c9dd0f8ae70ccd3aa8 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 1 Mar 2023 10:14:17 +0100 Subject: [PATCH 6728/9987] adding easyconfigs: CUDA-12.1.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.1.0.eb | 24 +++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.1.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.1.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.1.0.eb new file mode 100644 index 00000000000..121525aa098 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.1.0.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.1.0' +local_nv_version = '530.30.02' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '68699036c12d71adb9ad2799dce2ff070270fab4488b90920b9756ab3f52c41c', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '8d75bd9da953a51062b89b8c752cffcf02b02c85cb461291d354ac2cffb2da48', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '1d0dd884f5257c12471dc455dc1a4aee8d620191737c0b2e40f016d8adc9d009' +}] + +moduleclass = 'system' From 13a985351db1476e1c4da5fa20e486af31f5f94e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 1 Mar 2023 13:47:02 +0000 Subject: [PATCH 6729/9987] adding easyconfigs: MATIO-1.5.23-GCCcore-11.3.0.eb --- .../m/MATIO/MATIO-1.5.23-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d0ad0cc2dae --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'MATIO' +version = '1.5.23' + +homepage = 'https://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] +checksums = ['b3b29fb394e1cfa3f98cd57bac013c0cf7716ae7a085e398f2dfaff8f976f0c5'] + +preconfigopts = 'chmod +x configure && ' + +builddependencies = [('binutils', '2.38')] + +dependencies = [('zlib', '1.2.12')] + +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + +moduleclass = 'lib' From ef5491bce1ccf514b4c15841d5e8244a9c4d6c52 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 1 Mar 2023 13:49:24 +0000 Subject: [PATCH 6730/9987] adding easyconfigs: Trilinos-13.4.1-foss-2022a.eb and patches: Trilinos-13.4.1_fix-seacas-NC-constants.patch --- .../t/Trilinos/Trilinos-13.4.1-foss-2022a.eb | 48 +++++++++++++++++++ ...linos-13.4.1_fix-seacas-NC-constants.patch | 38 +++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1_fix-seacas-NC-constants.patch diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb new file mode 100644 index 00000000000..411f6191bdb --- /dev/null +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb @@ -0,0 +1,48 @@ +# easyblock = 'CMakeMake' + +name = 'Trilinos' +version = '13.4.1' + +homepage = 'https://trilinos.org' +description = """The Trilinos Project is an effort to develop algorithms and enabling technologies + within an object-oriented software framework for the solution of large-scale, complex multi-physics + engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True, 'strict': True} + +source_urls = ['https://github.com/trilinos/Trilinos/archive/refs/tags/'] +sources = ['trilinos-release-13-4-1.tar.gz'] +patches = ['Trilinos-13.4.1_fix-seacas-NC-constants.patch'] +checksums = [ + {'trilinos-release-13-4-1.tar.gz': '5465cbff3de7ef4ac7d40eeff9d99342c00d9d20eee0a5f64f0a523093f5f1b3'}, + {'Trilinos-13.4.1_fix-seacas-NC-constants.patch': + 'df6215589abf582197a963c49ba853c1eca788261a1b1834099e7679794e9eed'}, +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('SWIG', '4.0.2'), + ('Doxygen', '1.9.4'), + ('Perl', '5.34.1', '-minimal'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost.Python', '1.79.0'), + ('Boost', '1.79.0'), + ('SCOTCH', '7.0.1'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('HDF5', '1.12.2'), + ('netCDF', '4.9.0'), + ('MATIO', '1.5.23'), + ('GLM', '0.9.9.8'), + ('X11', '20220504'), +] + +forward_deps = False +build_tests = False +configopts = '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION=ON ' +configopts += '-DKokkos_ENABLE_AGGRESSIVE_VECTORIZATION=ON ' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1_fix-seacas-NC-constants.patch b/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1_fix-seacas-NC-constants.patch new file mode 100644 index 00000000000..14ded8805ab --- /dev/null +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1_fix-seacas-NC-constants.patch @@ -0,0 +1,38 @@ +From 5e1b19181110c52b76d13e3f60da2c8cf678c941 Mon Sep 17 00:00:00 2001 +From: Greg Sjaardema +Date: Tue, 7 Jun 2022 11:08:05 -0600 +Subject: [PATCH] EXODUS: Handle newer versions of netCDF symbols + +--- + packages/seacas/libraries/exodus/src/ex_utils.c | 10 +++++++--- + 1 file changed, 7 insertions(+), 3 deletions(-) + +diff --git a/packages/seacas/libraries/exodus/src/ex_utils.c b/packages/seacas/libraries/exodus/src/ex_utils.c +index 4c1cb9969e..9b3084e2fb 100644 +--- a/packages/seacas/libraries/exodus/src/ex_utils.c ++++ b/packages/seacas/libraries/exodus/src/ex_utils.c +@@ -1,5 +1,5 @@ + /* +- * Copyright(C) 1999-2021 National Technology & Engineering Solutions ++ * Copyright(C) 1999-2022 National Technology & Engineering Solutions + * of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with + * NTESS, the U.S. Government retains certain rights in this software. + * +@@ -1741,8 +1741,12 @@ void ex__compress_variable(int exoid, int varid, int type) + for details on SZIP library and parameters. + */ + +- /* const int NC_SZIP_EC = 4; */ /* Selects entropy coding method for szip. */ +- const int NC_SZIP_NN = 32; /* Selects nearest neighbor coding method for szip. */ ++#if !defined(NC_SZIP_EC) ++ const int NC_SZIP_EC = 4; /* Selects entropy coding method for szip. */ ++#endif ++#if !defined(NC_SZIP_NN) ++ const int NC_SZIP_NN = 32; /* Selects nearest neighbor coding method for szip. */ ++#endif + /* Even and between 4 and 32; typical values are 8, 10, 16, 32 */ + const int SZIP_PIXELS_PER_BLOCK = + file->compression_level == 0 ? 32 : file->compression_level; +-- +GitLab + From 1601a35980be367cd8a20922bc6b0b3e78201bc2 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Wed, 1 Mar 2023 15:26:06 +0100 Subject: [PATCH 6731/9987] adding easyconfigs: h5py-3.8.0-foss-2022b.eb, pkgconfig-1.5.5-GCCcore-12.2.0-python.eb --- .../h/h5py/h5py-3.8.0-foss-2022b.eb | 35 +++++++++++++++++++ .../pkgconfig-1.5.5-GCCcore-12.2.0-python.eb | 28 +++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.8.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-12.2.0-python.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.8.0-foss-2022b.eb b/easybuild/easyconfigs/h/h5py/h5py-3.8.0-foss-2022b.eb new file mode 100644 index 00000000000..8b6ce004741 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.8.0-foss-2022b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.8.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['6fead82f0c4000cf38d53f9c030780d81bfa0220218aee13b90b7701c937d95f'] + +builddependencies = [('pkgconfig', '1.5.5', '-python')] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('mpi4py', '3.1.4'), + ('HDF5', '1.14.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-12.2.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-12.2.0-python.eb new file mode 100644 index 00000000000..95979ef5286 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-12.2.0-python.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.5.5' +# The -python versionsuffix is used to avoid confusion between +# pkg-config (the tool) and pkgconfig (the Python wrappers) +versionsuffix = '-python' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('pkgconf', '1.9.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From c108609183a5b0044ffe52779876b64ab2db66eb Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Wed, 1 Mar 2023 15:38:57 +0100 Subject: [PATCH 6732/9987] adding easyconfigs: plotly.py-5.13.1-GCCcore-12.2.0.eb --- .../plotly.py-5.13.1-GCCcore-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/plotly.py/plotly.py-5.13.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.13.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.13.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..818ae974dd7 --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.13.1-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '5.13.1' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [('Python', '3.10.8')] + +use_pip = True + +exts_list = [ + ('tenacity', '8.2.2', { + 'checksums': ['43af037822bd0029025877f3b2d97cc4d7bb0c2991000a3d59d71517c5c969e0'], + }), + ('plotly', version, { + 'checksums': ['90ee9a1fee0dda30e2830e129855081ea17bd1b06a553a62b62de15caff1a219'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From 99ea1c389b3532c9045243ade09eccf5f1f1e4cd Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Wed, 1 Mar 2023 15:55:54 +0100 Subject: [PATCH 6733/9987] adding easyconfigs: ParaView-5.11.0-foss-2022b-mpi.eb --- .../ParaView-5.11.0-foss-2022b-mpi.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.11.0-foss-2022b-mpi.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.0-foss-2022b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.0-foss-2022b-mpi.eb new file mode 100644 index 00000000000..8eed5565c1b --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.0-foss-2022b-mpi.eb @@ -0,0 +1,58 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.11.0' +versionsuffix = '-mpi' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +checksums = ['68b1c6d15dd67ec442f964460c56212417e8af2a96763001f8548eb3cbc5ce87'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('XZ', '5.2.7'), + ('HDF5', '1.14.0'), + ('netCDF', '4.9.0'), + ('libGLU', '9.0.2'), + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('Qt5', '5.15.7'), + ('zlib', '1.2.12'), + ('FFmpeg', '5.1.2'), + ('Szip', '2.1.1'), +] + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' From 63e71f94f2ee0d208f086911154c19ec2222728f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Mar 2023 18:02:37 +0100 Subject: [PATCH 6734/9987] remove duplicate empty line in Health-GPS easyconfig --- .../h/Health-GPS/Health-GPS-1.1.3.0-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.1.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.1.3.0-GCCcore-11.3.0.eb index ca04a7736c4..649dff6c435 100644 --- a/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.1.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/Health-GPS/Health-GPS-1.1.3.0-GCCcore-11.3.0.eb @@ -54,7 +54,6 @@ files_to_copy = [ 'data' ] - sanity_check_paths = { 'files': ['bin/HealthGPS.Console', 'bin/HealthGPS.Tests'], 'dirs': ['data'], From 6b1e03891f456cd8be754cd4aaea6833d330073e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Wed, 1 Mar 2023 17:13:44 -0300 Subject: [PATCH 6735/9987] New DIRAC release --- .../d/DIRAC/DIRAC-23.0-foss-2022b.eb | 41 ++++++++++++++++++ .../d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb | 42 +++++++++++++++++++ .../d/DIRAC/DIRAC-23.0-intel-2022b.eb | 40 ++++++++++++++++++ 3 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022b.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022b.eb new file mode 100644 index 00000000000..8bd36810049 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022b.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '23.0' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://zenodo.org/record/7670749/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +checksums = ['a0a6b6318b3cd2e3c6042221de720bb1e87eb758999e2108a48dedb9c564e1f8'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.8'), + ('HDF5', '1.14.0') +] + +configopts = '-DMKL_FLAG=off ' +configopts += '-DMATH_LIBS="$LIBLAPACK" ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' + +runtest = 'test ARGS="-R pam_test" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb new file mode 100644 index 00000000000..fa03996063d --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '23.0' +versionsuffix = '-int64' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'usempi': True, 'i8': True} + +source_urls = ['https://zenodo.org/record/7670749/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +checksums = ['a0a6b6318b3cd2e3c6042221de720bb1e87eb758999e2108a48dedb9c564e1f8'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.8'), + ('HDF5', '1.14.0') +] + +configopts = '-DMKL_FLAG=sequential ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_64BIT_INTEGERS=True ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' + +runtest = 'test ARGS="-R symmetry_scf_energy" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb new file mode 100644 index 00000000000..1b7204494a0 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '23.0' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://zenodo.org/record/7670749/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +checksums = ['a0a6b6318b3cd2e3c6042221de720bb1e87eb758999e2108a48dedb9c564e1f8'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.8'), + ('HDF5', '1.14.0') +] + +configopts = '-DMKL_FLAG=sequential ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' + +runtest = 'test ARGS="-R pam_test" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From 8b353b8444a658ac7a025a8979c64033bb1b7e34 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 2 Mar 2023 07:53:26 +0100 Subject: [PATCH 6736/9987] adding easyconfigs: matplotlib-3.7.0-foss-2022b.eb, cppy-1.2.1-GCCcore-12.2.0.eb, Tkinter-3.10.8-GCCcore-12.2.0.eb, Pillow-9.4.0-GCCcore-12.2.0.eb --- .../c/cppy/cppy-1.2.1-GCCcore-12.2.0.eb | 28 ++++++++ .../matplotlib/matplotlib-3.7.0-foss-2022b.eb | 72 +++++++++++++++++++ .../p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb | 32 +++++++++ .../Tkinter/Tkinter-3.10.8-GCCcore-12.2.0.eb | 25 +++++++ 4 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.8-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..33cd47508f4 --- /dev/null +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'cppy' +version = '1.2.1' + +homepage = "https://github.com/nucleic/cppy" +description = """A small C++ header library which makes it easier to write +Python extension modules. The primary feature is a PyObject smart pointer +which automatically handles reference counting and provides convenience +methods for performing common object operations.""" + + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), +] + +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = [] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.0-foss-2022b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.0-foss-2022b.eb new file mode 100644 index 00000000000..f019ba1bfce --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.0-foss-2022b.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.7.0' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('cppy', '1.2.1'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('libpng', '1.6.38'), + ('freetype', '2.12.1'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '9.4.0'), + ('Qhull', '2020.2'), +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.38.0', { + 'modulename': 'fontTools', + 'source_tmpl': SOURCE_ZIP, + 'checksums': [], + }), + ('Cycler', '0.11.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': [], + }), + ('kiwisolver', '1.4.4', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': [], + }), + ('contourpy', '1.0.7', { + 'checksums': [], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': [], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8a4b4ef1485 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '9.4.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = [] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), + ('LibTIFF', '4.4.0'), + ('freetype', '2.12.1') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..055f9da0445 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.8-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +name = 'Tkinter' +version = '3.10.8' + +homepage = 'https://python.org/' +description = "Tkinter module, built with the Python buildsystem" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = [] + +builddependencies = [ + ('binutils', '2.39'), + ('libffi', '3.4.4'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('Tk', '8.6.12'), + ('zlib', '1.2.12'), +] + +moduleclass = 'lang' From 29c110ffabcdf51639681212f8d630c72d9a352a Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 2 Mar 2023 08:15:06 +0100 Subject: [PATCH 6737/9987] Add checksums and change foss -> gfbf --- .../c/cppy/cppy-1.2.1-GCCcore-12.2.0.eb | 2 +- ...oss-2022b.eb => matplotlib-3.7.0-gfbf-2022b.eb} | 14 +++++++------- .../p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb | 2 +- .../t/Tkinter/Tkinter-3.10.8-GCCcore-12.2.0.eb | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/m/matplotlib/{matplotlib-3.7.0-foss-2022b.eb => matplotlib-3.7.0-gfbf-2022b.eb} (79%) diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.2.0.eb index 33cd47508f4..ab70c069ba6 100644 --- a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ ] sources = ['%(name)s-%(version)s.tar.gz'] -checksums = [] +checksums = ['83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'] download_dep_fail = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.0-foss-2022b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.0-gfbf-2022b.eb similarity index 79% rename from easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.0-foss-2022b.eb rename to easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.0-gfbf-2022b.eb index f019ba1bfce..a6b61895bce 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.0-foss-2022b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.0-gfbf-2022b.eb @@ -8,7 +8,7 @@ description = """matplotlib is a python 2D plotting library which produces publi hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.""" -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'gfbf', 'version': '2022b'} builddependencies = [ ('pkgconf', '1.9.3'), @@ -37,26 +37,26 @@ _include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${C exts_list = [ ('fonttools', '4.38.0', { 'modulename': 'fontTools', - 'source_tmpl': SOURCE_ZIP, - 'checksums': [], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['2bb244009f9bf3fa100fc3ead6aeb99febe5985fa20afbfbaa2f8946c2fbdaf1'], }), ('Cycler', '0.11.0', { 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], - 'checksums': [], + 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], }), ('kiwisolver', '1.4.4', { 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], - 'checksums': [], + 'checksums': ['d41997519fcba4a1e46eb4a2fe31bc12f0ff957b2b81bac28db24744f333e955'], }), ('contourpy', '1.0.7', { - 'checksums': [], + 'checksums': ['d8165a088d31798b59e91117d1f5fc3df8168d8b48c4acc10fc0df0d0bdbcc5e'], }), (name, version, { 'preinstallopts': _fix_setup + _include_path, 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], - 'checksums': [], + 'checksums': ['8f6efd313430d7ef70a38a3276281cb2e8646b3a22b3b21eb227da20e15e6813'], }), ] diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb index 8a4b4ef1485..5060e93e3b2 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb @@ -10,7 +10,7 @@ description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributor toolchain = {'name': 'GCCcore', 'version': '12.2.0'} sources = [SOURCE_TAR_GZ] -checksums = [] +checksums = ['a1c2d7780448eb93fbcc3789bf3916aa5720d942e37945f4056680317f1cd23e'] builddependencies = [('binutils', '2.39')] diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.8-GCCcore-12.2.0.eb index 055f9da0445..49050c25e63 100644 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.10.8-GCCcore-12.2.0.eb @@ -9,7 +9,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.python.org/ftp/python/%(version)s/'] sources = ['Python-%(version)s.tgz'] -checksums = [] +checksums = ['f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a'] builddependencies = [ ('binutils', '2.39'), From 02c580fb75e21321179abda5cb8ce761cd6c5a20 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 2 Mar 2023 09:34:59 +0100 Subject: [PATCH 6738/9987] Change to installation from source --- .../s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb | 20 +++++++------------ 1 file changed, 7 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb index 22e2205329b..492cd13e67f 100644 --- a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'Tarball' +easyblock = 'MakeCp' name = 'SeaView' version = '5.0.5' @@ -9,30 +9,24 @@ description = """SeaView is a multiplatform, graphical user interface for multip toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['https://doua.prabi.fr/software/seaview_data'] -sources = [{'download_filename': '%(namelower)s%(version_major)s-64.tgz', 'filename': '%(name)s-%(version)s-64.tgz'}] -checksums = ['e8d844ee5d41f7e5626631ac1eb75086add6a24bfe8a5aa69d045c622a8abd8d'] +source_urls = ['ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/%(namelower)s/archive'] +sources = ['%(namelower)s_%(version)s.tar.gz'] +checksums = ['ce8f5e98ba47883bfa91e91bc79e4d3a26f158dd9983b5e78331a452a4b1f8f2'] dependencies = [ ('Brotli', '1.0.9'), ('bzip2', '1.0.8'), - ('cairo', '1.16.0'), ('expat', '2.4.1'), + ('FLTK', '1.3.7'), ('fontconfig', '2.13.94'), ('freetype', '2.11.0'), - ('FriBidi', '1.0.10'), - ('GLib', '2.69.1'), - ('HarfBuzz', '2.8.2'), - ('libffi', '3.4.2'), ('libpng', '1.6.37'), - ('Pango', '1.48.8'), - ('PCRE', '8.45'), - ('pixman', '0.40.0'), - ('util-linux', '2.37'), ('X11', '20210802'), ('zlib', '1.2.11'), ] +files_to_copy = ['%(namelower)s', '%(namelower)s.html', 'example.nxs'] + sanity_check_paths = { 'files': ['%(namelower)s'], 'dirs': [], From fc198528a37a146cc3b11a4845006b323f6e048c Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 2 Mar 2023 09:38:11 +0100 Subject: [PATCH 6739/9987] Use download_instructions --- .../g/GraphDB/{GraphDB-10.1.3.eb => GraphDB-10.1.5.eb} | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/g/GraphDB/{GraphDB-10.1.3.eb => GraphDB-10.1.5.eb} (77%) diff --git a/easybuild/easyconfigs/g/GraphDB/GraphDB-10.1.3.eb b/easybuild/easyconfigs/g/GraphDB/GraphDB-10.1.5.eb similarity index 77% rename from easybuild/easyconfigs/g/GraphDB/GraphDB-10.1.3.eb rename to easybuild/easyconfigs/g/GraphDB/GraphDB-10.1.5.eb index f43c82f137c..454deb0fc87 100644 --- a/easybuild/easyconfigs/g/GraphDB/GraphDB-10.1.3.eb +++ b/easybuild/easyconfigs/g/GraphDB/GraphDB-10.1.5.eb @@ -8,7 +8,7 @@ easyblock = 'Binary' name = 'GraphDB' -version = '10.1.3' +version = '10.1.5' homepage = 'https://graphdb.ontotext.com/' description = """GraphDB is an enterprise ready Semantic Graph Database, compliant @@ -16,13 +16,13 @@ with W3C Standards. Semantic graph databases (also called RDF triplestores) prov the core infrastructure for solutions where modelling agility, data integration, relationship exploration and cross-enterprise data publishing and consumption are important.""" # software_license = 'GraphDB-Free is free to use however, is not open source' -# Fill a form to request GraphDB at https://www.ontotext.com/products/graphdb/download/ +download_instructions = """Fill a form to request GraphDB at https://www.ontotext.com/products/graphdb/download/""" toolchain = SYSTEM -source_urls = ['https://download.ontotext.com/owlim/90065654-918e-11ed-8508-42843b1b6b38/'] +source_urls = ['https://download.ontotext.com/owlim/125bea40-b12b-11ed-aef3-42843b1b6b38/'] sources = ['graphdb-%(version)s-dist.zip'] -checksums = ['fae90dceaf27a6656eda2054f42f7a3e32721af8fd27951770692ad005d34b7a'] +checksums = ['849377177c0571f9b6a59049df7ee9b9a19511d538872f21b415db1c5bb8285e'] dependencies = [ ('Java', '11'), From 85eab7534685b51dc8a96f02fb4501ec311da6ec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 2 Mar 2023 11:48:36 +0100 Subject: [PATCH 6740/9987] Add binutils --- easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb index 492cd13e67f..11023540f0a 100644 --- a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb @@ -13,6 +13,8 @@ source_urls = ['ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/%(namelower)s/archive sources = ['%(namelower)s_%(version)s.tar.gz'] checksums = ['ce8f5e98ba47883bfa91e91bc79e4d3a26f158dd9983b5e78331a452a4b1f8f2'] +builddependencies = [('binutils', '2.37')] + dependencies = [ ('Brotli', '1.0.9'), ('bzip2', '1.0.8'), From 1469abe72aef5ee027e311c4bd9d310760859ce7 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 2 Mar 2023 10:51:28 +0000 Subject: [PATCH 6741/9987] Moved to GCCcore to be consistant --- ...tutils-2.6-GCC-11.3.0.eb => plotutils-2.6-GCCcore-11.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/p/plotutils/{plotutils-2.6-GCC-11.3.0.eb => plotutils-2.6-GCCcore-11.3.0.eb} (97%) diff --git a/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCCcore-11.3.0.eb similarity index 97% rename from easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb rename to easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCCcore-11.3.0.eb index 4b23dad22cf..062715eddb8 100644 --- a/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCCcore-11.3.0.eb @@ -16,7 +16,7 @@ does not depend on the type of graphics file to be exported. A Postscript-like A is used both for file export and for graphics animations. A libplot programmer needs to learn only one API: not the details of many graphics file formats.""" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://ftp.gnu.org/gnu/plotutils'] sources = ['%(name)s-%(version)s.tar.gz'] From 958ea2a52a7ad97f63cc115f1669b87f1e10fa77 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 2 Mar 2023 13:00:10 +0000 Subject: [PATCH 6742/9987] move 'digest' package to be before filehash in the extensions list --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 162e5680f17..6ddae77d0a9 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -115,6 +115,9 @@ exts_list = [ ('bit', '4.0.5', { 'checksums': ['f0f2536a8874b6a30b80baefbc68cb21f0ffbf51f3877bda8038c3f9f354bfbc'], }), + ('digest', '0.6.31', { + 'checksums': ['5a284f490eaca6750f695f00a584cfca3f180ca1046ac1107202141149d431b9'], + }), ('filehash', '2.4-5', { 'checksums': ['3b1ee2794dd61e525ee44db16611c65957691d77bb26ae481eba988bb55da22c'], }), @@ -238,9 +241,6 @@ exts_list = [ ('ellipsis', '0.3.2', { 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], }), - ('digest', '0.6.31', { - 'checksums': ['5a284f490eaca6750f695f00a584cfca3f180ca1046ac1107202141149d431b9'], - }), ('glue', '1.6.2', { 'checksums': ['9da518f12be584c90e75fe8e07f711ee3f6fc0d03d817f72c25dc0f66499fdbf'], }), From 989088f9f133d48c3c531c419cc0323afc62a524 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 2 Mar 2023 15:48:05 +0100 Subject: [PATCH 6743/9987] adding easyconfigs: scikit-learn-1.2.1-gfbf-2022b.eb --- .../scikit-learn-1.2.1-gfbf-2022b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.2.1-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.2.1-gfbf-2022b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.2.1-gfbf-2022b.eb new file mode 100644 index 00000000000..7f993bc9b42 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.2.1-gfbf-2022b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.2.1' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'sklearn', + 'checksums': ['fbf8a5c893c9b4b99bcc7ed8fb3e8500957a113f4101860386d06635520f7cfb'], + }), +] + +moduleclass = 'data' From ef44a2001454d650a1c68fe05ae5160805de520a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Mar 2023 17:03:59 +0100 Subject: [PATCH 6744/9987] adding easyconfigs: vsc-mympirun-5.3.0.eb --- .../v/vsc-mympirun/vsc-mympirun-5.3.0.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.0.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.0.eb new file mode 100644 index 00000000000..1cc889dea64 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.0.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'vsc-mympirun' +version = '5.3.0' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """mympirun is a tool to make it easier for users of HPC clusters to +run MPI programs with good performance.""" + +# we build this to work with every python version +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +use_pip = False + +exts_list = [ + ('setuptools', '41.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6afa61b391dcd16cb8890ec9f66cc4015a8a31a6e1c2b4e0c464514be1a3d722'], + }), + ('future', '0.18.3', { + 'checksums': ['34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307'], + }), + ('pbr', '5.11.1', { + 'checksums': ['aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '5.0.1', { + 'checksums': ['e3ea505c03babf7977fd21674a69ad328053d414f05e6433c30d8fa14a534a6b'], + }), + ('IPy', '1.01', { + 'modulename': 'IPy', + 'checksums': ['edeca741dea2d54aca568fa23740288c3fe86c0f3ea700344571e9ef14a7cc1a'], + }), + ('vsc-install', '0.18.0', { + 'modulename': 'vsc.install', + 'checksums': ['f5922e8e28fcf22693b7464a2142b4c16e5f42d5f868a56d340ad030f7e3d52b'], + }), + ('vsc-base', '3.5.2', { + 'modulename': 'vsc.utils', + 'checksums': ['1c41a69d4ab9bf6eda02007a569394cfcf19b85fbbc042c7678d1b684cbe59da'], + }), + (name, version, { + 'modulename': False, + 'checksums': ['ddf0e3e9ea6ce91dcec70ab31ffb6d8f6bc5cbb7fee72a8add5bda6f2b64aacb'], + }), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mypmirun', 'bin/mympisanity', 'bin/mytasks'], + 'dirs': ['bin/fake'], +} +sanity_check_commands = ["mympirun --help"] + +# can't enable 'pip check' since pip may not be installed in OS +sanity_pip_check = False + +moduleclass = 'tools' From 579f59a0bee3bcc870af76ab0344d7242e03a3ef Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 2 Mar 2023 20:35:25 +0000 Subject: [PATCH 6745/9987] Update easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb index 411f6191bdb..f8457bd0809 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'usempi': True, 'pic': True, 'strict': True} source_urls = ['https://github.com/trilinos/Trilinos/archive/refs/tags/'] -sources = ['trilinos-release-13-4-1.tar.gz'] +sources = ['trilinos-release-%star.gz' % '-'.join(version.split('.'))] patches = ['Trilinos-13.4.1_fix-seacas-NC-constants.patch'] checksums = [ {'trilinos-release-13-4-1.tar.gz': '5465cbff3de7ef4ac7d40eeff9d99342c00d9d20eee0a5f64f0a523093f5f1b3'}, From dae5ba94a6bdc75a4a9563282be36f3ac856d46a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Thu, 2 Mar 2023 21:40:09 +0100 Subject: [PATCH 6746/9987] adding easyconfigs: SCOTCH-7.0.3-gompi-2022b.eb --- .../s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb new file mode 100644 index 00000000000..3f164d6bde2 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'SCOTCH' +version = '7.0.3' + +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['5b5351f0ffd6fcae9ae7eafeccaa5a25602845b9ffd1afb104db932dd4d4f3c5'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DINSTALL_METIS_HEADERS=OFF ' +configopts += '-DCMAKE_BUILD_TYPE=Release ' + +runtest = 'test' + +local_scotch_exec = ['acpl', 'amk_ccc', 'amk_fft2', 'amk_grf', 'amk_hy', + 'amk_m2', 'amk_p2', 'atst', 'dggath', 'dgmap', 'dgord', + 'dgscat', 'dgtst', 'gbase', 'gcv', 'gmap', 'gmk_hy', + 'gmk_m2', 'gmk_m3', 'gmk_msh', 'gmk_ub2', 'gmtst', + 'gord', 'gotst', 'gscat', 'gtst', 'mcv', 'mmk_m2', + 'mmk_m3', 'mord', 'mtst'] + +local_scotch_headers = ['esmumps', 'ptscotchf', + 'ptscotch', 'scotchf', 'scotch'] + +local_scotch_libs = ['esmumps', 'ptesmumps', 'ptscotcherrexit', + 'ptscotcherr', 'ptscotchparmetisv3', 'ptscotch', + 'scotcherrexit', 'scotcherr', 'scotchmetisv3', + 'scotchmetisv5', 'scotch'] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_scotch_exec] + + ['include/%s.h' % i for i in local_scotch_headers] + + ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in local_scotch_libs], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'math' From d033b9e042501e395fe245ce0761051e698a0bd4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 2 Mar 2023 22:22:13 +0100 Subject: [PATCH 6747/9987] add missing . in sources for Trilinos 13.4.1 --- easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb index f8457bd0809..42acaf50b99 100644 --- a/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'usempi': True, 'pic': True, 'strict': True} source_urls = ['https://github.com/trilinos/Trilinos/archive/refs/tags/'] -sources = ['trilinos-release-%star.gz' % '-'.join(version.split('.'))] +sources = ['trilinos-release-%s.tar.gz' % '-'.join(version.split('.'))] patches = ['Trilinos-13.4.1_fix-seacas-NC-constants.patch'] checksums = [ {'trilinos-release-13-4-1.tar.gz': '5465cbff3de7ef4ac7d40eeff9d99342c00d9d20eee0a5f64f0a523093f5f1b3'}, From ebdff2c9735c86301507497f62c7d93aff845646 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 3 Mar 2023 07:52:16 +0100 Subject: [PATCH 6748/9987] restore sklearn meta-package --- .../s/scikit-learn/scikit-learn-1.2.1-gfbf-2022b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.2.1-gfbf-2022b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.2.1-gfbf-2022b.eb index 7f993bc9b42..5f1739b09f8 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.2.1-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.2.1-gfbf-2022b.eb @@ -24,6 +24,9 @@ exts_list = [ 'modulename': 'sklearn', 'checksums': ['fbf8a5c893c9b4b99bcc7ed8fb3e8500957a113f4101860386d06635520f7cfb'], }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), ] moduleclass = 'data' From fe6566c51caea0160705479f025eff90334b3f82 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 3 Mar 2023 10:01:45 +0100 Subject: [PATCH 6749/9987] adding easyconfigs: TensorFlow-Datasets-4.8.3-foss-2021b-CUDA-11.4.1.eb --- ...w-Datasets-4.8.3-foss-2021b-CUDA-11.4.1.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.8.3-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.8.3-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.8.3-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..02d7694a6c4 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.8.3-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow-Datasets' +version = '4.8.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/datasets' +description = """ +TensorFlow Datasets is a collection of datasets ready to use, with TensorFlow or other Python ML frameworks, such as +Jax. All datasets are exposed as tf.data.Datasets , enabling easy-to-use and high-performance input pipelines. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('CMake', '3.21.1') +] + +dependencies = [ + ('CUDA', '11.4.1', '', SYSTEM), + ('Python', '3.9.6'), + ('tqdm', '4.62.3'), + ('TensorFlow', '2.7.1', versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('promise', '2.3', { + 'checksums': ['dfd18337c523ba4b6a58801c164c1904a9d4d1b1747c7d5dbf45b693a49d93d0'], + }), + ('googleapis-common-protos', '1.56.4', { + 'modulename': 'google', + }), + ('tensorflow_metadata', '1.12.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + }), + ('etils', '1.0.0', { + }), + ('dm-tree', '0.1.8', { + 'modulename': 'tree', + }), + (name, version, { + 'source_tmpl': SOURCELOWER_TAR_GZ, + }), +] + +moduleclass = 'lib' From 2808d29a82cd7b1e911ebb9068b69a8cf0dc99a2 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 3 Mar 2023 10:04:09 +0100 Subject: [PATCH 6750/9987] Add checksums --- .../TensorFlow-Datasets-4.8.3-foss-2021b-CUDA-11.4.1.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.8.3-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.8.3-foss-2021b-CUDA-11.4.1.eb index 02d7694a6c4..febc69e2102 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.8.3-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.8.3-foss-2021b-CUDA-11.4.1.eb @@ -32,17 +32,22 @@ exts_list = [ }), ('googleapis-common-protos', '1.56.4', { 'modulename': 'google', + 'checksums': ['c25873c47279387cfdcbdafa36149887901d36202cb645a0e4f29686bf6e4417'], }), ('tensorflow_metadata', '1.12.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['4b86df305e5c8252df4c99a25074958f3772db57276fa6bd6a4d14fe482d8bc9'], }), ('etils', '1.0.0', { + 'checksums': ['d10982f7702422bea8635d5284b8bed629f51919fc122ac1e1e4abf45ec8f785'], }), ('dm-tree', '0.1.8', { 'modulename': 'tree', + 'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'], }), (name, version, { - 'source_tmpl': SOURCELOWER_TAR_GZ, + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['5c9464c8a455347af0a5c1b6fe6636f2ecfa022001549a766c26d2e6cdd42bfc'], }), ] From 33591e2146aeb9e98c42782aad7678346320ca6f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Fri, 3 Mar 2023 08:14:11 -0300 Subject: [PATCH 6751/9987] Update DIRAC-23.0-foss-2022b.eb --- easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022b.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022b.eb index 8bd36810049..b69b0e9bc2d 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022b.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2022b'} toolchainopts = {'usempi': True} source_urls = ['https://zenodo.org/record/7670749/files/'] -sources = ['DIRAC-%(version)s-Source.tar.gz'] +sources = ['DIRAC-%(version)s-Source.tgz'] checksums = ['a0a6b6318b3cd2e3c6042221de720bb1e87eb758999e2108a48dedb9c564e1f8'] builddependencies = [('CMake', '3.24.3')] From fd54d1d9413b46bd04a93b8479744498409df0cb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Fri, 3 Mar 2023 08:14:25 -0300 Subject: [PATCH 6752/9987] Update DIRAC-23.0-intel-2022b-int64.eb --- easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb index fa03996063d..88f8b7975bc 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'intel', 'version': '2022b'} toolchainopts = {'usempi': True, 'i8': True} source_urls = ['https://zenodo.org/record/7670749/files/'] -sources = ['DIRAC-%(version)s-Source.tar.gz'] +sources = ['DIRAC-%(version)s-Source.tgz'] checksums = ['a0a6b6318b3cd2e3c6042221de720bb1e87eb758999e2108a48dedb9c564e1f8'] builddependencies = [('CMake', '3.24.3')] From 70b2df035962b1aa953f5318844bfb5f67d3a9bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Fri, 3 Mar 2023 08:14:39 -0300 Subject: [PATCH 6753/9987] Update DIRAC-23.0-intel-2022b.eb --- easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb index 1b7204494a0..7221329ac3a 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'intel', 'version': '2022b'} toolchainopts = {'usempi': True} source_urls = ['https://zenodo.org/record/7670749/files/'] -sources = ['DIRAC-%(version)s-Source.tar.gz'] +sources = ['DIRAC-%(version)s-Source.tgz'] checksums = ['a0a6b6318b3cd2e3c6042221de720bb1e87eb758999e2108a48dedb9c564e1f8'] builddependencies = [('CMake', '3.24.3')] From a09a85cac9c12a6c58f23cae82eff1583222182f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2023 12:15:17 +0100 Subject: [PATCH 6754/9987] adding easyconfigs: CheckM-1.2.2-foss-2022a.eb --- .../CheckM-Database-2015_01_16.eb | 30 ++++++++++++ .../c/CheckM/CheckM-1.2.2-foss-2022a.eb | 47 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheckM-Database/CheckM-Database-2015_01_16.eb create mode 100644 easybuild/easyconfigs/c/CheckM/CheckM-1.2.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CheckM-Database/CheckM-Database-2015_01_16.eb b/easybuild/easyconfigs/c/CheckM-Database/CheckM-Database-2015_01_16.eb new file mode 100644 index 00000000000..4132bd8daec --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM-Database/CheckM-Database-2015_01_16.eb @@ -0,0 +1,30 @@ +easyblock = 'Tarball' + +name = 'CheckM-Database' +version = '2015_01_16' + +homepage = 'https://github.com/Ecogenomics/CheckM' +description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, +single cells, or metagenomes. + +This is the corresponding database. +""" + +toolchain = SYSTEM + +source_urls = ['https://data.ace.uq.edu.au/public/CheckM_databases/'] +sources = ['checkm_data_%(version)s.tar.gz'] +checksums = [ + '971ec469348bd6c3d9eb96142f567f12443310fa06c1892643940f35f86ac92c', # checkm_data_2015_01_16.tar.gz +] + +sanity_check_paths = { + 'files': ['selected_marker_sets.tsv', 'taxon_marker_sets.tsv'], + 'dirs': ['distributions/', 'genome_tree', 'hmms', 'hmms_ssu', 'img', 'pfam', 'test_data'], +} + +modextravars = { + 'CHECKM_DATA_PATH': '%(installdir)s', +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/CheckM/CheckM-1.2.2-foss-2022a.eb b/easybuild/easyconfigs/c/CheckM/CheckM-1.2.2-foss-2022a.eb new file mode 100644 index 00000000000..a46bf261992 --- /dev/null +++ b/easybuild/easyconfigs/c/CheckM/CheckM-1.2.2-foss-2022a.eb @@ -0,0 +1,47 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# Updated by: Filip Kružík (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'CheckM' +version = '1.2.2' + +homepage = 'https://github.com/Ecogenomics/CheckM' +description = """CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, + single cells, or metagenomes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/Ecogenomics/CheckM/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a748b94e93f8d5fecfd0d5b3f17fcb119b25d4b45217e047b2fd742b21e74c0e'] + +# Dependencies: +# https://github.com/Ecogenomics/CheckM/blob/master/setup.py +dependencies = [ + ('Python', '3.10.4'), + ('pplacer', '1.1.alpha19', '', SYSTEM), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('SciPy-bundle', '2022.05'), # numpy + ('matplotlib', '3.5.2'), + ('Pysam', '0.19.1'), + ('DendroPy', '4.5.2'), + ('CheckM-Database', '2015_01_16', '', SYSTEM), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/checkm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["checkm test %(builddir)s/checkm_test_results"] + +sanity_pip_check = True + +moduleclass = 'bio' From 873e28d982f44a4d7d0c54cc02d763d3b046c22a Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 3 Mar 2023 14:50:36 +0100 Subject: [PATCH 6755/9987] Fixes #17463. --- .../easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 13 ++++++++----- ...t5-5.15.2_fix-type-mismatch-kSigStackSize.patch | 14 ++++++++++++++ 2 files changed, 22 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index ab34684b136..9a6fb44e702 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -21,13 +21,16 @@ patches = [ 'Qt5-5.13.1_fix-qmake-libdir.patch', 'Qt5-5.14.1_fix-OF-Gentoo.patch', 'Qt5-5.15.2_fix-gcc11.patch', + 'Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch', ] checksums = [ - '3a530d1b243b5dec00bc54937455471aaa3e56849d2593edb8ded07228202240', # qt-everywhere-src-5.15.2.tar.xz - '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch - '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch - '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch - '6606e2434aacaac49545be733bf012f1d489393bf8bd5573691c171ab8bc0976', # Qt5-5.15.2_fix-gcc11.patch + {'qt-everywhere-src-5.15.2.tar.xz': '3a530d1b243b5dec00bc54937455471aaa3e56849d2593edb8ded07228202240'}, + {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, + {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, + {'Qt5-5.14.1_fix-OF-Gentoo.patch': '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa'}, + {'Qt5-5.15.2_fix-gcc11.patch': '6606e2434aacaac49545be733bf012f1d489393bf8bd5573691c171ab8bc0976'}, + {'Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch': + '05ade1f7aaa57ba2b13133c894f7e241813380dfabfd68e3b00bd7d3bf624bf8'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch new file mode 100644 index 00000000000..2655bf9b640 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch @@ -0,0 +1,14 @@ +# https://github.com/pytorch/pytorch/issues/70392#issuecomment-1003488196 +# Author: tiansheng li | @0x0177b11f + +--- a/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc ++++ b/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc +@@ -138,7 +138,7 @@ void InstallAlternateStackLocked() { + // SIGSTKSZ may be too small to prevent the signal handlers from overrunning + // the alternative stack. Ensure that the size of the alternative stack is + // large enough. +- static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ); ++ static const unsigned kSigStackSize = std::max(16384L, SIGSTKSZ); + + // Only set an alternative stack if there isn't already one, or if the current + // one is too small. From b5467ed7d6ac3a5f9632b09e1d5a01a73fc3f953 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 3 Mar 2023 16:32:44 +0100 Subject: [PATCH 6756/9987] adding easyconfigs: TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb --- ...aphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..bc98751e1a4 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow-Graphics' +version = '2021.12.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/tensorflow/graphics' +description = """Tensorflow Graphics provides a set of differentiable graphics +and geometry layers (e.g. cameras, reflectance models, spatial transformations, +mesh convolutions) and 3D viewer functionalities (e.g. 3D TensorBoard) that can +be used to train and debug your machine learning models of choice.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('CUDA', '11.4.1', '', SYSTEM), + ('Python', '3.9.6'), + ('TensorFlow', '2.7.1', versionsuffix), + ('TensorFlow-Datasets', '4.8.3', versionsuffix), + ('matplotlib', '3.4.3'), + ('h5py', '3.6.0'), + ('tqdm', '4.62.3'), + ('OpenEXR', '3.1.1'), + ('networkx', '2.6.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('typeguard', '2.13.3', { + 'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'], + }), + ('tensorflow-addons', '0.19.0', { + 'sources': [{'source_urls': ['https://github.com/tensorflow/addons/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6e1c40f03c9a35453a26eacbf36700f9666882418058a2f0d81aaa939135262f'], + }), + ('OpenEXR', '1.3.9', { + 'modulename': 'Imath', + 'patches': ['TensorFlow-Graphics-2021.12.3_openexr-setup.patch'], + 'preinstallopts': "env | grep '^EB' && cat setup.py && ", + 'checksums': [ + {'OpenEXR-1.3.9.tar.gz': 'cffcd13906291ef1a81b369c1c0e907648ecd24363668873691f44866704ab21'}, + {'TensorFlow-Graphics-2021.12.3_openexr-setup.patch': + '158ad43767c48d9e556d89c0e01a0c23c357f8c432ad443354337ec765d430b6'}, + ], + }), + ('trimesh', '3.20.1', { + 'checksums': ['5149331d0a11082ed2990800e2ecf4f49fca4718b3af92e1c026286c8358d607'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['622f6b6c9267da96a0dfabece3fb828aea8405e2004b9b0a6288242674706355'], + }), +] + +moduleclass = 'ai' From 9ab6106e8bd0d27149550cf9a0574a0d3d18b3a6 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 3 Mar 2023 16:33:32 +0100 Subject: [PATCH 6757/9987] Add patch for OpenEXR python wrapper --- ...low-Graphics-2021.12.3_openexr-setup.patch | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3_openexr-setup.patch diff --git a/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3_openexr-setup.patch b/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3_openexr-setup.patch new file mode 100644 index 00000000000..81a9bcb5cd0 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3_openexr-setup.patch @@ -0,0 +1,46 @@ +Use EasyBuild information to get version and specifying paths to relevant dirs +Author: Viktor Rehnberg (Chalmers University of Technology) +diff -ruN a/setup.py b/setup.py +--- a/setup.py 2023-03-03 13:44:54.493375095 +0100 ++++ b/setup.py 2023-03-03 15:33:08.481921491 +0100 +@@ -2,10 +2,11 @@ + from distutils.extension import Extension + from distutils.command.build_py import build_py as _build_py + +-from os import system ++from os import path, environ + import platform + + from distutils.core import setup, Extension ++from distutils.version import LooseVersion + + + VERSION = "1.3.9" +@@ -22,7 +23,7 @@ + + + print("Looking for libOpenEXR...") +-if platform.system() == "Linux" and system("ldconfig -p | grep libOpenEXR"): ++if LooseVersion(environ['EBVERSIONOPENEXR']) < LooseVersion('3'): + # There is no libOpenEXR, probably an old version of OpenEXR + libraries=['Iex', 'Half', 'Imath', 'IlmImf', 'z'] + else: +@@ -44,15 +45,9 @@ + ext_modules=[ + Extension('OpenEXR', + ['OpenEXR.cpp'], +- include_dirs=['/usr/include/OpenEXR', +- '/usr/local/include/OpenEXR', +- '/opt/local/include/OpenEXR', +- '/usr/include/Imath', +- '/usr/local/include/Imath', +- '/opt/local/include/Imath'], +- library_dirs=['/usr/lib', +- '/usr/local/lib', +- '/opt/local/lib'], ++ include_dirs=[path.join(environ['EBROOTOPENEXR'], 'include', 'OpenEXR'), ++ path.join(environ['EBROOTOPENEXR'], 'include', 'Imath')], ++ library_dirs=[path.join(environ['EBROOTOPENEXR'], 'lib')], + libraries=libraries, + extra_compile_args=extra_compile_args) + ], From 07b0e8532527c5f7a8b91490785a0b0c73f9c122 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2023 16:40:56 +0100 Subject: [PATCH 6758/9987] add Math::Utils extension to recent Perl easyconfigs --- easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 5 +++++ 5 files changed, 25 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 515872cd4ae..34e3a3e297d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -1796,6 +1796,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY/'], 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], }), + ('Math::Utils', '1.14', { + 'source_tmpl': 'Math-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], + 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb index c4e38476dbd..82a1570fadd 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb @@ -1777,6 +1777,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], }), + ('Math::Utils', '1.14', { + 'source_tmpl': 'Math-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], + 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index f8a9806e7a3..1211efd9bff 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1829,6 +1829,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], }), + ('Math::Utils', '1.14', { + 'source_tmpl': 'Math-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], + 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index abd17176d67..1750e4abff0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -1939,6 +1939,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], 'checksums': ['757a67e0aa59ae103ea5ca092cbecc025644ebdc326731688ffab6f8823ef4b3'], }), + ('Math::Utils', '1.14', { + 'source_tmpl': 'Math-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], + 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 68ab797947f..6a7989e6d2a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -1939,6 +1939,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], 'checksums': ['757a67e0aa59ae103ea5ca092cbecc025644ebdc326731688ffab6f8823ef4b3'], }), + ('Math::Utils', '1.14', { + 'source_tmpl': 'Math-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], + 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], + }), ] moduleclass = 'lang' From 4a320382e1e3eb86a032212df57e955929f42f95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Mar 2023 16:45:56 +0100 Subject: [PATCH 6759/9987] {math}[intel/2021b] sympy v1.9, gmpy2 v2.1.2 w/ Python 3.9.6 --- .../gmpy2-2.1.2-intel-compilers-2021.4.0.eb | 25 ++++++++++++ .../s/sympy/sympy-1.9-intel-2021b.eb | 40 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..f194fb5a771 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.2' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['da75140bca128ece795895477e53b43773e3748aa90ba6170eae7ca2c74b82d1'] + +dependencies = [ + ('Python', '3.9.6'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb new file mode 100644 index 00000000000..b08af4b4ade --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.9' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('gmpy2', '2.1.2'), +] + +download_dep_fail = True +use_pip = True + +# fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; +# see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 +pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +sanity_check_commands = ["isympy --help"] + +moduleclass = 'math' From 953133e1c64f53fdca0737b9166dc5f746a3eb70 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 5 Mar 2023 14:50:21 +0000 Subject: [PATCH 6760/9987] Use existig patches --- .../easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 9 ++++++--- ...t5-5.15.2_fix-type-mismatch-kSigStackSize.patch | 14 -------------- ....2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch | 11 +++++++++++ 3 files changed, 17 insertions(+), 17 deletions(-) delete mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index 9a6fb44e702..ce6c5caa35b 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -21,7 +21,8 @@ patches = [ 'Qt5-5.13.1_fix-qmake-libdir.patch', 'Qt5-5.14.1_fix-OF-Gentoo.patch', 'Qt5-5.15.2_fix-gcc11.patch', - 'Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch', + 'Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch', + 'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch', ] checksums = [ {'qt-everywhere-src-5.15.2.tar.xz': '3a530d1b243b5dec00bc54937455471aaa3e56849d2593edb8ded07228202240'}, @@ -29,8 +30,10 @@ checksums = [ {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, {'Qt5-5.14.1_fix-OF-Gentoo.patch': '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa'}, {'Qt5-5.15.2_fix-gcc11.patch': '6606e2434aacaac49545be733bf012f1d489393bf8bd5573691c171ab8bc0976'}, - {'Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch': - '05ade1f7aaa57ba2b13133c894f7e241813380dfabfd68e3b00bd7d3bf624bf8'}, + {'Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch': + '3e8a277ed5e9f7540ddff1329c7a9a595e3366222f63a6ca8663f7191f3f40a6'}, + {'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch': + '74590de2b9e32f2c88123cb096c4f5c3001b00710aad096a4d16444a8e9eb991'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch deleted file mode 100644 index 2655bf9b640..00000000000 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2_fix-type-mismatch-kSigStackSize.patch +++ /dev/null @@ -1,14 +0,0 @@ -# https://github.com/pytorch/pytorch/issues/70392#issuecomment-1003488196 -# Author: tiansheng li | @0x0177b11f - ---- a/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc -+++ b/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc -@@ -138,7 +138,7 @@ void InstallAlternateStackLocked() { - // SIGSTKSZ may be too small to prevent the signal handlers from overrunning - // the alternative stack. Ensure that the size of the alternative stack is - // large enough. -- static const unsigned kSigStackSize = std::max(16384, SIGSTKSZ); -+ static const unsigned kSigStackSize = std::max(16384L, SIGSTKSZ); - - // Only set an alternative stack if there isn't already one, or if the current - // one is too small. diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch new file mode 100644 index 00000000000..61727acac5c --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch @@ -0,0 +1,11 @@ +--- failure_signal_handler.cc.orig 2023-03-05 12:13:50.013671083 +0000 ++++ failure_signal_handler.cc 2023-03-05 12:37:43.958183965 +0000 +@@ -135,7 +135,7 @@ + #else + const size_t page_mask = sysconf(_SC_PAGESIZE) - 1; + #endif +- size_t stack_size = (std::max(SIGSTKSZ, 65536) + page_mask) & ~page_mask; ++ size_t stack_size = (std::max(SIGSTKSZ, 65536) + page_mask) & ~page_mask; + #if defined(ADDRESS_SANITIZER) || defined(MEMORY_SANITIZER) || \ + defined(THREAD_SANITIZER) + // Account for sanitizer instrumentation requiring additional stack space. From 8f6374b42ceee0a037f96ab5d26eede3877ef693 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 5 Mar 2023 14:54:36 +0000 Subject: [PATCH 6761/9987] Add patch description --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 2 +- .../Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index ce6c5caa35b..907541f0913 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -31,7 +31,7 @@ checksums = [ {'Qt5-5.14.1_fix-OF-Gentoo.patch': '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa'}, {'Qt5-5.15.2_fix-gcc11.patch': '6606e2434aacaac49545be733bf012f1d489393bf8bd5573691c171ab8bc0976'}, {'Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch': - '3e8a277ed5e9f7540ddff1329c7a9a595e3366222f63a6ca8663f7191f3f40a6'}, + '73edd7f3ac02512a4f0ec4126c7fc9fdfe8db24cc4af6ae7ce4efe4b40c6cf5e'}, {'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch': '74590de2b9e32f2c88123cb096c4f5c3001b00710aad096a4d16444a8e9eb991'}, ] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch index 61727acac5c..437b512060e 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch @@ -1,3 +1,6 @@ +Backport of Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch to actually 5.15.2 +author: micketeer@gmail.com + --- failure_signal_handler.cc.orig 2023-03-05 12:13:50.013671083 +0000 +++ failure_signal_handler.cc 2023-03-05 12:37:43.958183965 +0000 @@ -135,7 +135,7 @@ From 92653a9e9aaeb57f0a03073af2a0022d57c1e048 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 5 Mar 2023 16:40:38 +0100 Subject: [PATCH 6762/9987] replace src include path with installation dir for HDF5 --- easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2022b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2022b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2022b.eb index bd6519be79c..fc3bdeb419e 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2022b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2022b.eb @@ -14,6 +14,10 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4'] +# replace src include path with installation dir for $H5BLD_CPPFLAGS +_regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' +postinstallcmds = ['sed -i -r "%s" %%(installdir)s/bin/%s' % (_regex, x) for x in ['h5c++', 'h5pcc']] + dependencies = [ ('zlib', '1.2.12'), ('Szip', '2.1.1'), From 05ea3d35232be121224d0b1e063fcbedc88587aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 5 Mar 2023 16:07:56 +0000 Subject: [PATCH 6763/9987] Move binary to bin/ dir --- .../easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb index 11023540f0a..73a13c69dbf 100644 --- a/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/SeaView/SeaView-5.0.5-GCCcore-11.2.0.eb @@ -27,15 +27,13 @@ dependencies = [ ('zlib', '1.2.11'), ] -files_to_copy = ['%(namelower)s', '%(namelower)s.html', 'example.nxs'] +files_to_copy = [(['%(namelower)s'], 'bin'), '%(namelower)s.html', 'example.nxs'] sanity_check_paths = { - 'files': ['%(namelower)s'], + 'files': ['bin/%(namelower)s'], 'dirs': [], } sanity_check_commands = [("%(namelower)s -h")] -modextrapaths = {'PATH': '.'} - moduleclass = 'bio' From 0840e85677ab207d78bdd735032f4b0ebf065452 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 6 Mar 2023 10:55:50 +0100 Subject: [PATCH 6764/9987] adjust path in Qt5 qtwebengine abseil patch --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb | 2 +- .../Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb index 907541f0913..598ac43800a 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-11.2.0.eb @@ -31,7 +31,7 @@ checksums = [ {'Qt5-5.14.1_fix-OF-Gentoo.patch': '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa'}, {'Qt5-5.15.2_fix-gcc11.patch': '6606e2434aacaac49545be733bf012f1d489393bf8bd5573691c171ab8bc0976'}, {'Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch': - '73edd7f3ac02512a4f0ec4126c7fc9fdfe8db24cc4af6ae7ce4efe4b40c6cf5e'}, + '1ae0f43ae8444041bc5b8b2dd89a257fedff1f9e7e6007b2c8fb336150e80597'}, {'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch': '74590de2b9e32f2c88123cb096c4f5c3001b00710aad096a4d16444a8e9eb991'}, ] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch index 437b512060e..667f05b1468 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch @@ -1,8 +1,8 @@ Backport of Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch to actually 5.15.2 author: micketeer@gmail.com ---- failure_signal_handler.cc.orig 2023-03-05 12:13:50.013671083 +0000 -+++ failure_signal_handler.cc 2023-03-05 12:37:43.958183965 +0000 +--- qtwebengine/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc 2023-03-05 12:13:50.013671083 +0000 ++++ qtwebengine/src/3rdparty/chromium/third_party/abseil-cpp/absl/debugging/failure_signal_handler.cc 2023-03-05 12:37:43.958183965 +0000 @@ -135,7 +135,7 @@ #else const size_t page_mask = sysconf(_SC_PAGESIZE) - 1; From e21886d298dc75ed3ec0dc9fd9860095002fe8ab Mon Sep 17 00:00:00 2001 From: robogast Date: Mon, 6 Mar 2023 11:18:08 +0100 Subject: [PATCH 6765/9987] adding easyconfigs: Python-3.11.2-GCCcore-12.2.0-bare.eb --- .../Python-3.11.2-GCCcore-12.2.0-bare.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.11.2-GCCcore-12.2.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.11.2-GCCcore-12.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.11.2-GCCcore-12.2.0-bare.eb new file mode 100644 index 00000000000..7c1cddc4f4e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.11.2-GCCcore-12.2.0-bare.eb @@ -0,0 +1,35 @@ +name = 'Python' +version = '3.11.2' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['2411c74bda5bbcfcddaf4531f66d1adc73f247f529aee981b029513aefdbf849'] + +builddependencies = [ + ('UnZip', '6.0'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('binutils', '2.39'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('SQLite', '3.39.4'), + ('XZ', '5.2.7'), + ('libffi', '3.4.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +moduleclass = 'lang' From 426bfa179d7f8e6afed11c74d5b83af0cba8c404 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Mon, 6 Mar 2023 11:52:27 +0100 Subject: [PATCH 6766/9987] Clean-up formatting after ebinject --- .../TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb index bc98751e1a4..f9603ef4d94 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb @@ -33,7 +33,11 @@ exts_list = [ 'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'], }), ('tensorflow-addons', '0.19.0', { - 'sources': [{'source_urls': ['https://github.com/tensorflow/addons/archive/refs/tags/'], 'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{ + 'source_urls': ['https://github.com/tensorflow/addons/archive/refs/tags/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz', + }], 'checksums': ['6e1c40f03c9a35453a26eacbf36700f9666882418058a2f0d81aaa939135262f'], }), ('OpenEXR', '1.3.9', { From b7cbc36aadf9a04e63296105e541907109cc39a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Mon, 6 Mar 2023 14:29:24 +0100 Subject: [PATCH 6767/9987] adding easyconfigs: ORCA-5.0.4-gompi-2022a.eb --- .../o/ORCA/ORCA-5.0.4-gompi-2022a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2022a.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2022a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2022a.eb new file mode 100644 index 00000000000..c654fcb77b2 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2022a.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '5.0.4' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +# Shared build of ORCA: download from https://orcaforum.kofo.mpg.de +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi411.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_5_0_4_linux_x86-64_shared_openmpi411.tar.xz + 'c4ea5aea60da7bcb18a6b7042609206fbeb2a765c6fa958c5689d450b588b036', +] + +moduleclass = 'chem' From f64ce287d13f0f7de1c2d4992958112557889469 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 6 Mar 2023 16:24:27 +0100 Subject: [PATCH 6768/9987] adding easyconfigs: vitessce-python-20230222-foss-2022a.eb --- .../vitessce-python-20230222-foss-2022a.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb diff --git a/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb b/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb new file mode 100644 index 00000000000..f3dd4806686 --- /dev/null +++ b/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb @@ -0,0 +1,77 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'vitessce-python' +version = '20230222' +local_commit = '7bd0a00' + +homepage = 'https://github.com/vitessce/vitessce-python' +description = "Python API and Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('zarr', '2.13.3'), + ('SciPy-bundle', '2022.05'), + ('aiohttp', '3.8.3'), + ('dask', '2022.10.0'), + ('h5py', '3.7.0'), + ('scikit-image', '0.19.3'), +] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'sanity_pip_check': True, +} + +local_hatchling_preinstallopts = "sed -i 's|packaging>=21.3|packaging>=20.9|g' PKG-INFO && " +local_hatchling_preinstallopts += "sed -i 's|packaging>=21.3|packaging>=20.9|g' src/hatchling/ouroboros.py && " + +exts_list = [ + ('natsort', '8.2.0', { + 'checksums': ['57f85b72c688b09e053cdac302dd5b5b53df5f73ae20b4874fcbffd8bf783d11'], + }), + ('pathspec', '0.10.1', { + 'checksums': ['7ace6161b621d31e7902eb6b5ae148d12cfd23f4a249b9ffb6b9fee12084323d'], + }), + ('fsspec', '2023.1.0'), + ('hatchling', '1.11.1', { + 'checksums': ['9f84361f70cf3a7ab9543b0c3ecc64211ed2ba8a606a71eb6a473c1c9b08e1d0'], + 'preinstallopts': local_hatchling_preinstallopts, + }), + ('negspy', '0.2.24'), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('hatch-fancy-pypi-readme', '22.8.0', { + 'sources': [{ + 'download_filename': 'hatch_fancy_pypi_readme-%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], + }), + ('hatch-vcs', '0.3.0', { + 'sources': [{ + 'download_filename': 'hatch_vcs-%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], + }), + ('black', '23.1.0', { + 'preinstallopts': "sed -i 's|packaging>=22.0|packaging>=20.9|g' pyproject.toml && " + }), + ('anndata', '0.8.0'), + ('ome-zarr', '0.2.1'), + ('tifffile', '2022.10.10', { + }), + (name, version, { + 'source_urls': ['https://github.com/vitessce/vitessce-python/archive/'], + 'sources': [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, + }], + 'modulename': 'vitessce', + }), +] + +moduleclass = 'bio' From eaa41c40285be386615588d0a5e507b614ad3c3a Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 6 Mar 2023 16:50:07 +0100 Subject: [PATCH 6769/9987] adding easyconfigs: grid-20220610-intel-2022a.eb, DensPart-20220603-intel-2022a.eb --- .../DensPart/DensPart-20220603-intel-2022a.eb | 28 ++++++++++++++++++ .../g/grid/grid-20220610-intel-2022a.eb | 29 +++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/d/DensPart/DensPart-20220603-intel-2022a.eb create mode 100644 easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb diff --git a/easybuild/easyconfigs/d/DensPart/DensPart-20220603-intel-2022a.eb b/easybuild/easyconfigs/d/DensPart/DensPart-20220603-intel-2022a.eb new file mode 100644 index 00000000000..c0d32d70051 --- /dev/null +++ b/easybuild/easyconfigs/d/DensPart/DensPart-20220603-intel-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'DensPart' +version = '20220603' +local_commit = '9bfd1e2' + +homepage = 'https://github.com/theochem/denspart' +description = 'Atoms-in-molecules density partitioning schemes based on stockholder recipe' + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://github.com/theochem/denspart/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['e2014368da19503aead56c176da0d6ec00ce13ea62d0cefde69cdfd06e1fcccd'] + +dependencies = { + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('grid', '20220610'), +} + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_commands = ["denspart -h"] + +moduleclass = "chem" diff --git a/easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb b/easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb new file mode 100644 index 00000000000..5919e57a002 --- /dev/null +++ b/easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'grid' +version = '20220610' +local_commit = '0677fc7' + +homepage = 'https://grid.qcdevs.org/' +description = """Grid is a free and open-source Python library for numerical integration, + interpolation and differentiation of interest for the quantum chemistry community.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://github.com/theochem/grid/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['d8189c33a9d5fc89ad0fa83089431944b346686519ec8d3c350848cf28b81d7a'] + +dependencies = { + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('sympy', '1.11.1'), +} + +preinstallopts = "sed -i 's|version=get_version()|version=\"%(version)s\"|g' setup.py && " + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': False} From 91960f20601a2848a12d1c0e23e65538e63141ca Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 6 Mar 2023 17:11:30 +0100 Subject: [PATCH 6770/9987] style check tests --- .../vitessce-python-20230222-foss-2022a.eb | 48 ++++++++++++------- 1 file changed, 31 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb b/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb index f3dd4806686..99076a0556d 100644 --- a/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb +++ b/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb @@ -6,7 +6,8 @@ version = '20230222' local_commit = '7bd0a00' homepage = 'https://github.com/vitessce/vitessce-python' -description = "Python API and Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce." +description = """Python API and Jupyter widget facilitating interactive +visualization of spatial single-cell data with Vitessce.""" toolchain = {'name': 'foss', 'version': '2022a'} @@ -36,41 +37,54 @@ exts_list = [ ('pathspec', '0.10.1', { 'checksums': ['7ace6161b621d31e7902eb6b5ae148d12cfd23f4a249b9ffb6b9fee12084323d'], }), - ('fsspec', '2023.1.0'), + ('fsspec', '2023.1.0', { + 'checksums': ['fbae7f20ff801eb5f7d0bedf81f25c787c0dfac5e982d98fa3884a9cde2b5411'], + }), ('hatchling', '1.11.1', { - 'checksums': ['9f84361f70cf3a7ab9543b0c3ecc64211ed2ba8a606a71eb6a473c1c9b08e1d0'], 'preinstallopts': local_hatchling_preinstallopts, + 'checksums': ['9f84361f70cf3a7ab9543b0c3ecc64211ed2ba8a606a71eb6a473c1c9b08e1d0'], + }), + ('negspy', '0.2.24', { + 'checksums': ['c3077f9a4616f597e4f7d87d7d93cd7c8a1c8aab25a1561ba21072e577137c72'], }), - ('negspy', '0.2.24'), ('mypy_extensions', '1.0.0', { 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], }), ('hatch-fancy-pypi-readme', '22.8.0', { 'sources': [{ - 'download_filename': 'hatch_fancy_pypi_readme-%(version)s.tar.gz', - 'filename': SOURCE_TAR_GZ, - }], + 'download_filename': 'hatch_fancy_pypi_readme-%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz' + }], + 'checksums': ['da91282ca09601c18aded8e378daf8b578c70214866f0971156ee9bb9ce6c26a'], }), ('hatch-vcs', '0.3.0', { 'sources': [{ - 'download_filename': 'hatch_vcs-%(version)s.tar.gz', - 'filename': SOURCE_TAR_GZ, - }], + 'download_filename': 'hatch_vcs-%(version)s.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz' + }], + 'checksums': ['cec5107cfce482c67f8bc96f18bbc320c9aa0d068180e14ad317bbee5a153fee'], }), ('black', '23.1.0', { - 'preinstallopts': "sed -i 's|packaging>=22.0|packaging>=20.9|g' pyproject.toml && " + 'preinstallopts': "sed -i 's|packaging>=22.0|packaging>=20.9|g' pyproject.toml && ", + 'checksums': ['b0bd97bea8903f5a2ba7219257a44e3f1f9d00073d6cc1add68f0beec69692ac'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + ('ome-zarr', '0.2.1', { + 'checksums': ['7e1c0304982252bcb5fd0e3b68ff67e0aca09b3928f78fe090f2a48e46576ba4'], }), - ('anndata', '0.8.0'), - ('ome-zarr', '0.2.1'), ('tifffile', '2022.10.10', { + 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], }), (name, version, { + 'modulename': 'vitessce', 'source_urls': ['https://github.com/vitessce/vitessce-python/archive/'], 'sources': [{ - 'download_filename': '%s.tar.gz' % local_commit, - 'filename': SOURCE_TAR_GZ, - }], - 'modulename': 'vitessce', + 'download_filename': '7bd0a00.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz' + }], + 'checksums': ['4d21b2eb99d61f08ba5c5a068414a07e667d896d0a2908470de2a55bd997092f'], }), ] From 69cd0db71bf28d8c85d9bd6fe4a9c73e54bf6102 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 6 Mar 2023 17:39:38 +0100 Subject: [PATCH 6771/9987] style check tests --- .../v/vitessce-python/vitessce-python-20230222-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb b/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb index 99076a0556d..a9e373660d0 100644 --- a/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb +++ b/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb @@ -22,7 +22,6 @@ dependencies = [ ] exts_default_options = { - 'source_urls': [PYPI_SOURCE], 'use_pip': True, 'sanity_pip_check': True, } From c6cafb07b7b3002d09c585de3b6bd24899887933 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 6 Mar 2023 17:42:52 +0000 Subject: [PATCH 6772/9987] URL of homepage corrected --- .../easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb b/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb index 00174adc9d0..ee3db5ffcf2 100644 --- a/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb @@ -5,7 +5,7 @@ easyblock = 'PythonBundle' name = 'pp-sketchlib' version = '2.1.1' -homepage = ' https://mandrake.readthedocs.io' +homepage = 'https://github.com/bacpop/pp-sketchlib' description = """Library of sketching functions used by PopPUNK""" toolchain = {'name': 'foss', 'version': '2022a'} From 46a69d54aa9332b0b681f56fc37365fce615dedc Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 6 Mar 2023 17:50:18 +0000 Subject: [PATCH 6773/9987] Blank in URL removed --- easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb index 6b72810418d..686bc673215 100644 --- a/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb +++ b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb @@ -5,7 +5,7 @@ easyblock = 'PythonBundle' name = 'mandrake' version = '1.2.2' -homepage = ' https://mandrake.readthedocs.io' +homepage = 'https://mandrake.readthedocs.io' description = """Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding.""" From 1c47e5ca52f799424c7367f285297f8cc9bf31b1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 7 Mar 2023 16:38:12 +0100 Subject: [PATCH 6774/9987] Use download_instructions Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2022a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2022a.eb index c654fcb77b2..451b27578db 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2022a.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2022a.eb @@ -12,7 +12,7 @@ effects.""" toolchain = {'name': 'gompi', 'version': '2022a'} -# Shared build of ORCA: download from https://orcaforum.kofo.mpg.de +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" # mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi411.tar.xz' % version.replace('.', '_')] checksums = [ From d93b69305cffb2eb515d2bfc76153769e3d40fa8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 7 Mar 2023 16:08:52 +0000 Subject: [PATCH 6775/9987] adding easyconfigs: ont-guppy-6.4.6-CUDA-11.7.0.eb, ont-guppy-6.4.6.eb --- .../ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb | 38 +++++++++++++++++++ .../o/ont-guppy/ont-guppy-6.4.6.eb | 32 ++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6.eb diff --git a/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb new file mode 100644 index 00000000000..bc2f11eb6df --- /dev/null +++ b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Tarball' + +name = 'ont-guppy' +version = '6.4.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://community.nanoporetech.com/protocols/Guppy-protocol' +description = """ +Guppy is a bioinformatics toolkit that enables real-time basecalling and several + post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms. + + For Research Use Only +""" + +toolchain = SYSTEM + +source_urls = ['https://mirror.oxfordnanoportal.com/software/analysis'] +sources = ['%(name)s_%(version)s_linux64.tar.gz'] +checksums = ['a633b2f0712781ff303a4c8fecb08d5e5603c755d6c445a6181ab11930f5bd63'] + +dependencies = [ + ('CUDA', '11.7.0'), +] + +_bins = ['guppy_%s' % x for x in ['aligner', 'barcoder', 'basecall_client', 'basecaller', 'basecaller_duplex', + 'basecaller_supervisor', 'basecall_server']] +_libs = ['lib/libvbz_hdf_plugin.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins] + _libs, + 'dirs': ['data'], +} + +# requires libcuda.so to be present, else it exits with code 127 +# sanity_check_commands = ['%s --help' % x for x in _bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6.eb b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6.eb new file mode 100644 index 00000000000..be022994765 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6.eb @@ -0,0 +1,32 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Tarball' + +name = 'ont-guppy' +version = '6.4.6' + +homepage = 'https://community.nanoporetech.com/protocols/Guppy-protocol' +description = """ +Guppy is a bioinformatics toolkit that enables real-time basecalling and several + post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms. + + For Research Use Only +""" + +toolchain = SYSTEM + +source_urls = ['https://mirror.oxfordnanoportal.com/software/analysis'] +sources = ['%(name)s-cpu_%(version)s_linux64.tar.gz'] +checksums = ['5c454a1d91124ff6da1618d08cae999b0091897e7f20e3dba09038303a259bef'] + +_bins = ['guppy_%s' % x for x in ['aligner', 'barcoder', 'basecall_client', 'basecaller', 'basecaller_duplex', + 'basecaller_supervisor', 'basecall_server']] +_libs = ['lib/libvbz_hdf_plugin.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins] + _libs, + 'dirs': ['data'], +} + +sanity_check_commands = ['%s --help' % x for x in _bins] + +moduleclass = 'bio' From c24b8d59eb3555d8a37a9305bdf2bae86ccf0399 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 7 Mar 2023 21:00:42 +0100 Subject: [PATCH 6776/9987] adding easyconfigs: KaHIP-3.14-gompi-2022b.eb --- .../k/KaHIP/KaHIP-3.14-gompi-2022b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022b.eb diff --git a/easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022b.eb b/easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022b.eb new file mode 100644 index 00000000000..719fd73c34d --- /dev/null +++ b/easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'KaHIP' +version = '3.14' + +homepage = 'https://kahip.github.io/' +description = """The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/KaHIP/KaHIP/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9da04f3b0ea53b50eae670d6014ff54c0df2cb40f6679b2f6a96840c1217f242'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ["lib/libkahip_static.a", "lib/libkahip.%s" % SHLIB_EXT] + + ["lib/libparhip_interface_static.a", "lib/libparhip_interface.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["kaHIP_interface.h", "parhip_interface.h"]], + 'dirs': [], +} + +moduleclass = 'math' From 706fa95129229865073542cefc1ccccaf56ece08 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 8 Mar 2023 09:33:29 +0100 Subject: [PATCH 6777/9987] adding easyconfigs: EDirect-19.0.20230216-foss-2021a.eb --- .../EDirect-19.0.20230216-foss-2021a.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/e/EDirect/EDirect-19.0.20230216-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/EDirect/EDirect-19.0.20230216-foss-2021a.eb b/easybuild/easyconfigs/e/EDirect/EDirect-19.0.20230216-foss-2021a.eb new file mode 100644 index 00000000000..258e192f57d --- /dev/null +++ b/easybuild/easyconfigs/e/EDirect/EDirect-19.0.20230216-foss-2021a.eb @@ -0,0 +1,86 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## +easyblock = 'Binary' + +name = 'EDirect' +version = '19.0.20230216' + +homepage = 'https://www.ncbi.nlm.nih.gov/books/NBK25501/' +# See also https://dataguide.nlm.nih.gov/edirect/install.html +description = """Entrez Direct (EDirect) provides access to the NCBI's suite of +interconnected databases from a Unix terminal window. Search terms are entered +as command-line arguments. Individual operations are connected with Unix pipes +to construct multi-step queries. Selected records can then be retrieved in a +variety of formats.""" +# software_license = 'Public Domain' + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/%(version)s/'] +# Only get Linux x86_64 and ARM binaries +sources = [ + {'download_filename': 'edirect-%(version)s.tar.gz', + 'filename': 'edirect-%s.tar.gz' % version, + }, + {'download_filename': 'rchive.ARM.gz', + 'filename': 'rchive-%s.ARM.gz' % version, + }, + {'download_filename': 'rchive.Linux.gz', + 'filename': 'rchive-%s.Linux.gz' % version, + }, + {'download_filename': 'transmute.ARM.gz', + 'filename': 'transmute-%s.ARM.gz' % version, + }, + {'download_filename': 'transmute.Linux.gz', + 'filename': 'transmute-%s.Linux.gz' % version, + }, + {'download_filename': 'xtract.ARM.gz', + 'filename': 'xtract-%s.ARM.gz' % version, + }, + {'download_filename': 'xtract.Linux.gz', + 'filename': 'xtract-%s.Linux.gz' % version, + }, +] +checksums = [ + 'a571af35b8debef31eab3f79246a2c419c8802dc8948141a130c6b3bdd0e4394', # edirect-19.0.20230216.tar.gz + 'eba2c7485f1bd2fd66c81493e06573cea006d001ad4ee79934d1412802a57aaa', # rchive-19.0.20230216.ARM.gz + 'dbc1c1050bd8d9144a3e00c1a21efb43b9ac263a1d7366cdbe89db3afcb93901', # rchive-19.0.20230216.Linux.gz + '1ac989fdad9314e10be912c29363cd4675d3d6181bfac281b230b2217c053298', # transmute-19.0.20230216.ARM.gz + '1c6824a4c17cbeb63462afee8e3c1c1fe82fe9b0af720a5b984c47822163bc54', # transmute-19.0.20230216.Linux.gz + '6450b5bab81c85403c136a45a4426c464d191951fd956d6ceff12e2bb3553a79', # xtract-19.0.20230216.ARM.gz + '857b1d9efae55b87f86b52c2a8925c29eb35b5fd5afb006762a3bb492cb98662', # xtract-19.0.20230216.Linux.gz +] + +dependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), +] + +extract_sources = True + +postinstallcmds = [ + "mkdir %(installdir)s/bin && cd %(installdir)s/ && " + "install %(builddir)s/*.ARM %(builddir)s/*.Linux . && " + "for arm in *.ARM; do ln -s $arm ${arm/-*.ARM/.ARM}; done && " + "for lin in *.Linux; do ln -s $lin ${lin/-*.Linux/.Linux}; done && " + "cd bin/ && ln -s ../* . && rm -f easybuild README readme.pdf bin" +] + +sanity_check_paths = { + 'files': ['einfo', 'README'], + 'dirs': ['bin', 'cmd', 'eutils', 'help'], +} + +sanity_check_commands = [ + "esearch -version && " + "xtract -version && " + "esearch -db pubmed -query 'Babalobi OO[au] AND 2008[pdat]' | efetch -format xml | " + "xtract -pattern Author -if Affiliation -contains Medicine -element Initials" +] + +moduleclass = 'bio' From 0da2dc49cda15a033403c5f511185b4a8ef02bfb Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 8 Mar 2023 11:43:02 +0100 Subject: [PATCH 6778/9987] adding easyconfigs: libWallModelledLES-0.6.1-foss-2021b.eb --- .../libWallModelledLES-0.6.1-foss-2021b.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb new file mode 100644 index 00000000000..cf48519506d --- /dev/null +++ b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb @@ -0,0 +1,45 @@ +name = "libWallModelledLES" +version = "0.6.1" +easyblock = "Binary" + +homepage = "https://bitbucket.org/lesituu/libwallmodelledles/" +description = """libWallModelledLES is a library based on OpenFOAM® technology, +extending the capabilities of OpenFOAM in the area of wall-modelled LES (WMLES). +This is a turbulence modelling methodology, which allows to make LES cheaper +by not resolving the inner region of turbulent boundary layers.""" + +toolchain = {"name": "foss", "version": "2021b"} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {"cstd": "c++11", "vectorize": False} + +source_urls = ["https://bitbucket.org/lesituu/libwallmodelledles/get/"] +sources = ["af3c659d16d54238364e8812ae8fbe3e46f5e656.tar.gz"] +checksums = ["06b2c06ef76b5247c0a0c0260ea1e4a58bed8e930d0a0add9fe60e626c4bc0f8"] + +dependencies = [ + ("OpenFOAM", "v2112"), +] + +extract_sources = True + +install_cmd = "source $FOAM_BASH && " + +# variables of target install directory +install_cmd += "export WM_PROJECT_USER_DIR=%(installdir)s && " +install_cmd += "export FOAM_USER_APPBIN=%(installdir)s/bin && " +install_cmd += "export FOAM_USER_LIBBIN=%(installdir)s/lib && " +install_cmd += "export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && " + +install_cmd += "pwd && ls && ./Allwmake -j %(parallel)s " +install_cmd += " && cp -av tests %(installdir)s " + +sanity_check_paths = {"dirs": ["lib", "tests"], "files": ["lib/libWallModelledLES.so"]} +sanity_check_commands = [ + "source $FOAM_BASH && cd %(installdir)s/test/testCases/channel_flow && pimpleFoam" +] +# modloadmsg = "Please run 'source $FOAM_BASH' before using RheoTool." + + +moduleclass = "cae" From bc015f7ab372355d5623b97ee5d3206564a2bff1 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 8 Mar 2023 11:52:07 +0100 Subject: [PATCH 6779/9987] Removed copied comment. --- .../l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb index cf48519506d..3650fc58eb9 100644 --- a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb @@ -39,7 +39,5 @@ sanity_check_paths = {"dirs": ["lib", "tests"], "files": ["lib/libWallModelledLE sanity_check_commands = [ "source $FOAM_BASH && cd %(installdir)s/test/testCases/channel_flow && pimpleFoam" ] -# modloadmsg = "Please run 'source $FOAM_BASH' before using RheoTool." - moduleclass = "cae" From c0ba619453dffb0d2ec713c3a25925f0f62ad026 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 8 Mar 2023 12:09:12 +0100 Subject: [PATCH 6780/9987] Fixed tests. --- .../l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb index 3650fc58eb9..0efcf31e2cf 100644 --- a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb @@ -37,7 +37,7 @@ install_cmd += " && cp -av tests %(installdir)s " sanity_check_paths = {"dirs": ["lib", "tests"], "files": ["lib/libWallModelledLES.so"]} sanity_check_commands = [ - "source $FOAM_BASH && cd %(installdir)s/test/testCases/channel_flow && pimpleFoam" + "source $FOAM_BASH && cd %(installdir)s/tests/testCases/channel_flow && pimpleFoam" ] moduleclass = "cae" From a6e37c0c5cf6e7355eb8aef2b8b8d79911a78b0a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 8 Mar 2023 14:34:10 +0100 Subject: [PATCH 6781/9987] adding easyconfigs: VSEARCH-2.22.1-GCC-11.3.0.eb --- .../v/VSEARCH/VSEARCH-2.22.1-GCC-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.22.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.22.1-GCC-11.3.0.eb b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.22.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..693720d260a --- /dev/null +++ b/easybuild/easyconfigs/v/VSEARCH/VSEARCH-2.22.1-GCC-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'VSEARCH' +version = '2.22.1' + +homepage = 'https://github.com/torognes/vsearch' +description = """VSEARCH supports de novo and reference based chimera detection, + clustering, full-length and prefix dereplication, rereplication, + reverse complementation, masking, all-vs-all pairwise global alignment, + exact and global alignment searching, shuffling, subsampling and sorting. + It also supports FASTQ file analysis, filtering, + conversion and merging of paired-end reads.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/torognes/vsearch/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c62bf69e7cc3d011a12e3b522ba8c0c91fb90deea782359e9569677d0c991778'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), +] + +preconfigopts = './autogen.sh &&' + +configopts = '--disable-pdfman ' + +sanity_check_paths = { + 'files': ['bin/vsearch'], + 'dirs': [], +} + +sanity_check_commands = ['vsearch --help'] + +moduleclass = 'bio' From dfbcd10dc0c6bb9ff50d7255de183de0c8748f35 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 8 Mar 2023 15:34:28 +0100 Subject: [PATCH 6782/9987] add missing zstd dep to Boost --- .../easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb | 1 + .../easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.71.0-gompi-2019b.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.71.0-gompic-2019b.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.71.0-iimpi-2019b.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.71.0-iimpic-2019b.eb | 1 + .../easyconfigs/b/Boost/Boost-1.72.0-GCCcore-9.3.0-no_mpi.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompi-2020a.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompic-2020a.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.72.0-iimpi-2020a.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb | 1 + .../easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-11.2.0.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb | 1 + .../easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.77.0-GCC-11.2.0.eb | 1 + .../easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.2.0.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.3.0.eb | 1 + easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb | 1 + 20 files changed, 20 insertions(+) diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb index f0d6e24166d..2fa8d8ff409 100644 --- a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb @@ -17,6 +17,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.5.0'), ('ICU', '69.1'), ] diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb index be6c179e528..e61836c53ca 100644 --- a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb @@ -17,6 +17,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.12'), ('XZ', '5.2.5'), + ('zstd', '1.5.2'), ('ICU', '71.1'), ] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.71.0-gompi-2019b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.71.0-gompi-2019b.eb index 0e42ee3c93c..ea3d9b2c2f8 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.71.0-gompi-2019b.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.71.0-gompi-2019b.eb @@ -15,6 +15,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.4'), + ('zstd', '1.4.4'), ] configopts = '--without-libraries=python' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.71.0-gompic-2019b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.71.0-gompic-2019b.eb index c3a465db37d..0a826bb61c0 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.71.0-gompic-2019b.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.71.0-gompic-2019b.eb @@ -15,6 +15,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.4'), + ('zstd', '1.4.4'), ] configopts = '--without-libraries=python' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.71.0-iimpi-2019b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.71.0-iimpi-2019b.eb index 829709da75d..6656fe44330 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.71.0-iimpi-2019b.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.71.0-iimpi-2019b.eb @@ -15,6 +15,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.4'), + ('zstd', '1.4.4'), ] configopts = '--without-libraries=python' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.71.0-iimpic-2019b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.71.0-iimpic-2019b.eb index 2f606156bee..e4f116e2eba 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.71.0-iimpic-2019b.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.71.0-iimpic-2019b.eb @@ -15,6 +15,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.4'), + ('zstd', '1.4.4'), ] configopts = '--without-libraries=python' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.72.0-GCCcore-9.3.0-no_mpi.eb b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-GCCcore-9.3.0-no_mpi.eb index ca8c49aeb58..45778ac6ca9 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.72.0-GCCcore-9.3.0-no_mpi.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-GCCcore-9.3.0-no_mpi.eb @@ -20,6 +20,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.4.4'), ] configopts = '--without-libraries=python' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompi-2020a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompi-2020a.eb index ea0b3c88eda..0012f4d504f 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompi-2020a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompi-2020a.eb @@ -15,6 +15,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.4.4'), ] configopts = '--without-libraries=python' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompic-2020a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompic-2020a.eb index 5905bdfc176..0f379b65307 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompic-2020a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-gompic-2020a.eb @@ -15,6 +15,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.4.4'), ] configopts = '--without-libraries=python' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.72.0-iimpi-2020a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-iimpi-2020a.eb index e5ee2e1c469..410be76a6b4 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.72.0-iimpi-2020a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.72.0-iimpi-2020a.eb @@ -15,6 +15,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.4.4'), ] configopts = '--without-libraries=python' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb index faa5a1229d3..963017ac246 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-GCC-10.2.0.eb @@ -23,6 +23,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.4.5'), ] configopts = '--without-libraries=python,mpi' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb index ab084d66fba..8a46e2591dd 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.74.0-iccifort-2020.4.304.eb @@ -21,6 +21,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.4.5'), ] configopts = '--without-libraries=python,mpi' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-11.2.0.eb index 053aaaf0ac9..4494d81ed62 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.75.0-GCC-11.2.0.eb @@ -15,6 +15,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.5.0'), ('ICU', '69.1'), ] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb index a6d9755bb2d..07ba538803e 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-GCC-10.3.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.4.9'), ('ICU', '69.1'), ] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb index 4cb0ac3840c..9e11543a138 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.76.0-intel-compilers-2021.2.0.eb @@ -15,6 +15,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.4.9'), ('ICU', '69.1'), ] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-GCC-11.2.0.eb index 2b47c2abf06..c8d711bec67 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-GCC-11.2.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.5.0'), ('ICU', '69.1'), ] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb index 4872fadfc48..f0fce1ec0af 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb @@ -15,6 +15,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.5.0'), ('ICU', '69.1'), ] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.2.0.eb index 1574a8a3dc2..dd76c017037 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.2.0.eb @@ -20,6 +20,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), ('XZ', '5.2.5'), + ('zstd', '1.5.0'), ('ICU', '69.1'), ] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.3.0.eb index b412f13fe87..bbec421a195 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.79.0-GCC-11.3.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.12'), ('XZ', '5.2.5'), + ('zstd', '1.5.2'), ('ICU', '71.1'), ] diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb index 8bd43da3d1a..1ffc4b4cfac 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCC-12.2.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.12'), ('XZ', '5.2.7'), + ('zstd', '1.5.2'), ('ICU', '72.1'), ] From 5a7112215da4ea05d805d9dc61ab4283c4ec0c6f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Wed, 8 Mar 2023 18:18:01 +0100 Subject: [PATCH 6783/9987] adding easyconfigs: gnuplot-5.4.6-GCCcore-12.2.0.eb, libcerf-2.3-GCCcore-12.2.0.eb, libgd-2.3.3-GCCcore-12.2.0.eb, Perl-5.36.0-GCCcore-12.2.0-minimal.eb, Lua-5.4.4-GCCcore-12.2.0.eb --- .../g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ .../l/Lua/Lua-5.4.4-GCCcore-12.2.0.eb | 28 ++++++++++++ .../l/libcerf/libcerf-2.3-GCCcore-12.2.0.eb | 32 ++++++++++++++ .../l/libgd/libgd-2.3.3-GCCcore-12.2.0.eb | 37 ++++++++++++++++ .../Perl-5.36.0-GCCcore-12.2.0-minimal.eb | 26 +++++++++++ 5 files changed, 167 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..c74dabe6e23 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.4.6' + +homepage = 'http://gnuplot.sourceforge.net' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('cairo', '1.17.4'), + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('libgd', '2.3.3'), + ('Pango', '1.50.12'), + ('libcerf', '2.3'), + ('X11', '20221110'), + ('Qt5', '5.15.7'), + ('Lua', '5.4.4'), +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..703d80d74a8 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.4.4-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +name = 'Lua' +version = '5.4.4' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['164c7849653b80ae67bec4b7473b884bf5cc8d2dca05653475ec2ed27b9ebf61'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('libreadline', '8.2'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8803b286b45 --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '2.3' + +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['cceefee46e84ce88d075103390b4f9d04c34e4bc3b96d733292c36836d4f7065'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Perl', '5.36.0', '-minimal'), # required for pod2html +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d8d3e21fab0 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.3' + +homepage = 'https://libgd.github.io' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd3f1f0bb016edcc0b2d082e8229c822ad1d02223511997c80461481759b1ed2'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('fontconfig', '2.14.1'), + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libgd.a', 'lib/libgd.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +sanity_check_commands = ['webpng --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb new file mode 100644 index 00000000000..c9619fe9430 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb @@ -0,0 +1,26 @@ +name = 'Perl' +version = '5.36.0' +versionsuffix = '-minimal' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +This is a minimal build without any modules. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +moduleclass = 'lang' From dd5f88a589cf301c635a49a4e2e8c52a247f8938 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Wed, 8 Mar 2023 18:35:02 +0100 Subject: [PATCH 6784/9987] Added missing checksums --- easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb index c74dabe6e23..ec6c0337af3 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] +checksums = ['02fc27918200ed64d8f0c3b84fe81b95b59cd47ad99f270939ae497c19f27419'] builddependencies = [ ('binutils', '2.39'), From edbd29383797cc4707445e02ecb2948af88af479 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Wed, 8 Mar 2023 21:03:24 +0100 Subject: [PATCH 6785/9987] Corrected style --- .../easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb index c9619fe9430..c426d66b7eb 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb @@ -20,7 +20,7 @@ builddependencies = [ ] dependencies = [ - ('zlib', '1.2.12'), + ('zlib', '1.2.12'), ] moduleclass = 'lang' From 98b6f9003368b91dbc4eb40f360559c5c0d13ba0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Wed, 8 Mar 2023 22:12:37 +0100 Subject: [PATCH 6786/9987] Corrected style --- easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb index ec6c0337af3..0c45cc31308 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('cairo', '1.17.4'), ('libjpeg-turbo', '2.1.4'), ('libpng', '1.6.38'), - ('libgd', '2.3.3'), + ('libgd', '2.3.3'), ('Pango', '1.50.12'), ('libcerf', '2.3'), ('X11', '20221110'), From 2fedae1a38dc65a8fff82a28cac157b62c252b0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 9 Mar 2023 08:38:47 +0100 Subject: [PATCH 6787/9987] adding easyconfigs: Trim_Galore-0.6.10-GCCcore-11.2.0.eb --- .../Trim_Galore-0.6.10-GCCcore-11.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..b5f27e64489 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.2.0.eb @@ -0,0 +1,46 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# Updated to version 0.6.2: Pavel Grochal (INUITS) +# Updated to version 0.6.5: Alex Domingo (VUB) +# Updated to version 0.6.7 by J. Sassmannshausen NHS/GSTT + +easyblock = 'Tarball' + +name = 'Trim_Galore' +version = '0.6.10' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """Trim Galore! is a wrapper script to automate quality and adapter +trimming as well as quality control, with some added functionality to remove biased +methylation positions for RRBS sequence files (for directional, non-directional +(or paired-end) sequencing).""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['3a4e414fc658d6eb4356f1572351204e8475a9d7dc79f6798270b57d35bda017'] + +dependencies = [ + ('Python', '3.9.6'), + ('Java', '11', '', SYSTEM), + ('pigz', '2.6'), + ('Perl', '5.34.0'), + ('cutadapt', '3.5'), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), +] + +postinstallcmds = [ + "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s", +] + +fix_perl_shebang_for = ['bin/%(namelower)s'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s', '-v')] + +moduleclass = 'bio' From 3adbc499771785849c91f0c2ed878d0ffcb693a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2023 09:01:58 +0100 Subject: [PATCH 6788/9987] add download instructions for PEAR 0.9.11 --- easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.3.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.3.0.eb b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.3.0.eb index 3442901c61c..46016c94a95 100644 --- a/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/PEAR/PEAR-0.9.11-GCC-11.3.0.eb @@ -9,8 +9,7 @@ description = """PEAR is an ultrafast, memory-efficient and highly accurate pair toolchain = {'name': 'GCC', 'version': '11.3.0'} -# Needs manual download via web-form, -# https://www.h-its.org/en/research/sco/software/#NextGenerationSequencingSequenceAnalysis +download_instructions = "Manual download via web form, see https://www.h-its.org/software/pear-paired-end-read-merger" sources = ['%(namelower)s-src-%(version)s.tar.gz'] checksums = ['94f4a1835cd75ec6fab83405c2545ddba6b6bb1644579222e9cc2ad57a59d654'] From ca700cf1341533b9a38985b4140b28606f99f0a8 Mon Sep 17 00:00:00 2001 From: lenocil Date: Thu, 9 Mar 2023 10:45:07 +0100 Subject: [PATCH 6789/9987] Added easyconfigs for irodsfs --- .../i/irodsfs/irodsfs-0.8.11-linux-amd64.eb | 27 +++++++++++++++++++ .../i/irodsfs/irodsfs-0.8.9-linux-amd64.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.11-linux-amd64.eb create mode 100644 easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.9-linux-amd64.eb diff --git a/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.11-linux-amd64.eb b/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.11-linux-amd64.eb new file mode 100644 index 00000000000..ed3a0cc6e97 --- /dev/null +++ b/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.11-linux-amd64.eb @@ -0,0 +1,27 @@ +easyblock = 'Binary' + +name = 'irodsfs' +version = '0.8.11' +versionsuffix = '-linux-amd64' + +homepage = 'https://github.com/cyverse/irodsfs' +description = """FUSE implementation of iRODS Client written in Golang.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cyverse/irodsfs/releases/download/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s%(versionsuffix)s.tar.gz'] +checksums = [('md5','cb70d536f76c50873b9b0e345faf862e')] + +extract_sources = True + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'tools' + + diff --git a/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.9-linux-amd64.eb b/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.9-linux-amd64.eb new file mode 100644 index 00000000000..fe8ab4e6254 --- /dev/null +++ b/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.9-linux-amd64.eb @@ -0,0 +1,27 @@ +easyblock = 'Binary' + +name = 'irodsfs' +version = '0.8.9' +versionsuffix = '-linux-amd64' + +homepage = 'https://github.com/cyverse/irodsfs' +description = """FUSE implementation of iRODS Client written in Golang.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cyverse/irodsfs/releases/download/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s%(versionsuffix)s.tar.gz'] +checksums = [('md5','2f99ad981d35c39d088bb4eb21a8383c')] + +extract_sources = True + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'tools' + + From 42e1e71b819e385bf4853a370190f57f08b8bc01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 9 Mar 2023 16:01:42 +0100 Subject: [PATCH 6790/9987] adding easyconfigs: parallel-fastq-dump-0.6.7-gompi-2022a.eb --- .../parallel-fastq-dump-0.6.7-gompi-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2022a.eb diff --git a/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2022a.eb b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2022a.eb new file mode 100644 index 00000000000..462e3e4976a --- /dev/null +++ b/easybuild/easyconfigs/p/parallel-fastq-dump/parallel-fastq-dump-0.6.7-gompi-2022a.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'parallel-fastq-dump' +version = '0.6.7' + +homepage = 'https://github.com/rvalieris/parallel-fastq-dump' +description = "parallel fastq-dump wrapper" +docurls = ["https://github.com/rvalieris/parallel-fastq-dump"] + +toolchain = {'name': 'gompi', 'version': '2022a'} + +# https://github.com/rvalieris/parallel-fastq-dump/archive/ +github_account = 'rvalieris' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['cb33ea0ed0b1123c100aee7b9ea60a3fc3fc81a3a46be5237c85ba56380617de'] + +dependencies = [ + ('Python', '3.10.4'), + ('SRA-Toolkit', '3.0.3'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/parallel-fastq-dump'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# This package doesn't produce importable module, only executable script. +options = {'modulename': False} + +sanity_check_commands = ["parallel-fastq-dump --version"] + +sanity_pip_check = True + +moduleclass = 'bio' From 89104cad7df0ffe1c796389753436adb14f52e72 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 9 Mar 2023 20:11:07 +0100 Subject: [PATCH 6791/9987] replace src include path with installation dir for HDF5 (intel) --- easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2022b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2022b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2022b.eb index 168721a6491..8c20eb4138e 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2022b.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2022b.eb @@ -14,6 +14,9 @@ source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_ma sources = [SOURCELOWER_TAR_GZ] checksums = ['a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4'] +_regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' +postinstallcmds = ['sed -i -r "%s" %%(installdir)s/bin/%s' % (_regex, x) for x in ['h5c++', 'h5pcc']] + dependencies = [ ('zlib', '1.2.12'), ('Szip', '2.1.1'), From 50b323b5845774ea78345ac8547ec2761b7bab3f Mon Sep 17 00:00:00 2001 From: lenocil Date: Fri, 10 Mar 2023 09:20:37 +0100 Subject: [PATCH 6792/9987] Added easyconfig for latest version of irodsfs and corrected easyconfig syntax --- .../i/irodsfs/irodsfs-0.8.11-linux-amd64.eb | 4 +-- .../i/irodsfs/irodsfs-0.8.12-linux-amd64.eb | 25 +++++++++++++++++++ .../i/irodsfs/irodsfs-0.8.9-linux-amd64.eb | 4 +-- 3 files changed, 27 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.12-linux-amd64.eb diff --git a/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.11-linux-amd64.eb b/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.11-linux-amd64.eb index ed3a0cc6e97..02ff2d9db54 100644 --- a/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.11-linux-amd64.eb +++ b/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.11-linux-amd64.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM source_urls = ['https://github.com/cyverse/irodsfs/releases/download/v%(version)s/'] sources = ['%(namelower)s-v%(version)s%(versionsuffix)s.tar.gz'] -checksums = [('md5','cb70d536f76c50873b9b0e345faf862e')] +checksums = ['4d93a5b6a64aa3c6bde25769fd6a7fd32c0a8ced4ffa6e87795f5926db0a78c9'] extract_sources = True @@ -23,5 +23,3 @@ sanity_check_paths = { sanity_check_commands = ["%(namelower)s --help"] moduleclass = 'tools' - - diff --git a/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.12-linux-amd64.eb b/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.12-linux-amd64.eb new file mode 100644 index 00000000000..fb7c54c2f53 --- /dev/null +++ b/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.12-linux-amd64.eb @@ -0,0 +1,25 @@ +easyblock = 'Binary' + +name = 'irodsfs' +version = '0.8.12' +versionsuffix = '-linux-amd64' + +homepage = 'https://github.com/cyverse/irodsfs' +description = """FUSE implementation of iRODS Client written in Golang.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cyverse/irodsfs/releases/download/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['aa5382dc82cf9d002255d289348286a908b78e1246940ee605e92b4adf8586dd'] + +extract_sources = True + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.9-linux-amd64.eb b/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.9-linux-amd64.eb index fe8ab4e6254..503020560f8 100644 --- a/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.9-linux-amd64.eb +++ b/easybuild/easyconfigs/i/irodsfs/irodsfs-0.8.9-linux-amd64.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM source_urls = ['https://github.com/cyverse/irodsfs/releases/download/v%(version)s/'] sources = ['%(namelower)s-v%(version)s%(versionsuffix)s.tar.gz'] -checksums = [('md5','2f99ad981d35c39d088bb4eb21a8383c')] +checksums = ['47a5ee716b00e4c4c3da74d39bed189a160d86eff91aab4904e772dca62e004b'] extract_sources = True @@ -23,5 +23,3 @@ sanity_check_paths = { sanity_check_commands = ["%(namelower)s --help"] moduleclass = 'tools' - - From 0c0fddd92fab540577915836a1530588b0398544 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 10 Mar 2023 12:36:49 +0000 Subject: [PATCH 6793/9987] Update easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb --- .../vitessce-python/vitessce-python-20230222-foss-2022a.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb b/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb index a9e373660d0..cdcc0a4be16 100644 --- a/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb +++ b/easybuild/easyconfigs/v/vitessce-python/vitessce-python-20230222-foss-2022a.eb @@ -21,10 +21,8 @@ dependencies = [ ('scikit-image', '0.19.3'), ] -exts_default_options = { - 'use_pip': True, - 'sanity_pip_check': True, -} +use_pip = True +sanity_pip_check = True local_hatchling_preinstallopts = "sed -i 's|packaging>=21.3|packaging>=20.9|g' PKG-INFO && " local_hatchling_preinstallopts += "sed -i 's|packaging>=21.3|packaging>=20.9|g' src/hatchling/ouroboros.py && " From 4ba9d790371ef3aeb459832321931a5e50d736ca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2023 14:40:04 +0100 Subject: [PATCH 6794/9987] adding easyconfigs: Lace-1.14.1-foss-2022a.eb --- .../l/Lace/Lace-1.14.1-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lace/Lace-1.14.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/Lace/Lace-1.14.1-foss-2022a.eb b/easybuild/easyconfigs/l/Lace/Lace-1.14.1-foss-2022a.eb new file mode 100644 index 00000000000..16441a8ab89 --- /dev/null +++ b/easybuild/easyconfigs/l/Lace/Lace-1.14.1-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'Lace' +version = '1.14.1' + +homepage = 'https://github.com/Oshlack/Lace' +description = "Building SuperTranscripts: A linear representation of transcriptome data" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/Oshlack/Lace/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['79629e1cb0b7f21c9767daa24fd8cdc229d6b1c45e5e361e80ae9211678366f5'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('networkx', '2.8.4'), + ('BLAT', '3.7'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'Lace'} + +sanity_check_paths = { + 'files': ['bin/Lace'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["Lace -h"] + +moduleclass = 'bio' From 150f50e440dd9b9c4fd5dfc9601bbe4031627552 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2023 15:05:35 +0100 Subject: [PATCH 6795/9987] {bio}[GCC/11.3.0] TopHat v2.1.2 --- .../t/TopHat/TopHat-2.1.2-GCC-11.3.0.eb | 52 +++++++++++++++++++ .../t/TopHat/TopHat-2.1.2_fix-configure.patch | 13 +++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.2_fix-configure.patch diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..f77cd37c2ba --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.3.0.eb @@ -0,0 +1,52 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.2' + +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' +description = "TopHat is a fast splice junction mapper for RNA-Seq reads." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'cstd': 'gnu++98', 'pic': True} + +github_account = 'infphilo' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'tophat-2.0.13-zlib.patch', + 'TopHat-2.1.2_fix-configure.patch', +] +checksums = [ + {'v2.1.2.tar.gz': '15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1'}, + {'tophat-2.0.13-zlib.patch': 'a33075c2affda995ddbd250933dbcaf94f68768b1eebead58a69705fc40306ef'}, + {'TopHat-2.1.2_fix-configure.patch': '5b92002848632f727381860f87f6b1b8867b60db6298c49b8387e5c61af9850d'}, +] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [ + ('Boost', '1.79.0'), + ('zlib', '1.2.12'), + ('Python', '2.7.18', '-bare'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["tophat --help 2>&1 | grep 'TopHat maps short sequences'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2_fix-configure.patch b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2_fix-configure.patch new file mode 100644 index 00000000000..c717d95cce6 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2_fix-configure.patch @@ -0,0 +1,13 @@ +fix for "error: AM_INIT_AUTOMAKE expanded multiple times" +author: Kenneth Hoste (HPC-UGent) +--- tophat-2.1.2/configure.ac.orig 2018-05-24 17:24:31.000000000 +0200 ++++ tophat-2.1.2/configure.ac 2023-03-10 14:44:29.924070336 +0100 +@@ -108,8 +108,6 @@ + CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2" + LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS" + +-AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) +- + # makefiles to configure + AC_CONFIG_FILES([Makefile src/Makefile]) + From b5dec9d1d8726a24202e527244fddf9dc60058b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2023 15:16:18 +0100 Subject: [PATCH 6796/9987] use GCC/iccifort toolchain for TopHat + add missing Python 2.x dependency --- ...pHat-2.1.2-gompi-2020a.eb => TopHat-2.1.2-GCC-9.3.0.eb} | 7 ++++--- ...-iimpi-2020a.eb => TopHat-2.1.2-iccifort-2020.1.217.eb} | 5 ++++- 2 files changed, 8 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/t/TopHat/{TopHat-2.1.2-gompi-2020a.eb => TopHat-2.1.2-GCC-9.3.0.eb} (87%) rename easybuild/easyconfigs/t/TopHat/{TopHat-2.1.2-iimpi-2020a.eb => TopHat-2.1.2-iccifort-2020.1.217.eb} (87%) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-gompi-2020a.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-9.3.0.eb similarity index 87% rename from easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-gompi-2020a.eb rename to easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-9.3.0.eb index c6f8cd70110..9e4e343ee09 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-gompi-2020a.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-9.3.0.eb @@ -13,15 +13,13 @@ version = '2.1.2' homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' description = "TopHat is a fast splice junction mapper for RNA-Seq reads." -toolchain = {'name': 'gompi', 'version': '2020a'} +toolchain = {'name': 'GCC', 'version': '9.3.0'} toolchainopts = {'cstd': 'gnu++98', 'pic': True} github_account = 'infphilo' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] - patches = ['%(namelower)s-2.0.13-zlib.patch'] - checksums = [ '15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1', # v2.1.2.tar.gz 'a33075c2affda995ddbd250933dbcaf94f68768b1eebead58a69705fc40306ef', # tophat-2.0.13-zlib.patch @@ -32,6 +30,7 @@ builddependencies = [('Autotools', '20180311')] dependencies = [ ('Boost', '1.72.0'), ('zlib', '1.2.11'), + ('Python', '2.7.18'), ] preconfigopts = './autogen.sh && ' @@ -44,4 +43,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["tophat --help 2>&1 | grep 'TopHat maps short sequences'"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iimpi-2020a.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iccifort-2020.1.217.eb similarity index 87% rename from easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iimpi-2020a.eb rename to easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iccifort-2020.1.217.eb index 33584a2546e..d2e2a6c2a70 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iimpi-2020a.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iccifort-2020.1.217.eb @@ -13,7 +13,7 @@ version = '2.1.2' homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' description = "TopHat is a fast splice junction mapper for RNA-Seq reads." -toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchain = {'name': 'iccifort', 'version': '2020.1.217'} toolchainopts = {'cstd': 'gnu++98', 'pic': True} github_account = 'infphilo' @@ -32,6 +32,7 @@ builddependencies = [('Autotools', '20180311')] dependencies = [ ('Boost', '1.72.0'), ('zlib', '1.2.11'), + ('Python', '2.7.18'), ] preconfigopts = './autogen.sh && ' @@ -44,4 +45,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["tophat --help 2>&1 | grep 'TopHat maps short sequences'"] + moduleclass = 'bio' From 1b9c1abe60e5903b3ef3d69ea8e8bca699f7b204 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2023 15:22:44 +0100 Subject: [PATCH 6797/9987] add additional extensions for R 4.2.1 --- .../easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index ec890257003..871de6add89 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3409,6 +3409,45 @@ exts_list = [ ('R2WinBUGS', '2.1-21', { 'checksums': ['fa86cb5140f5dfce29f9517b94d6d08c316ddcffa4aa3085945b84d34910134d'], }), + ('aricode', '1.0.2', { + 'checksums': ['5f4e51f7063cfd4924a8925c902a3eb7517c743234a14560691cb84428b6b2f0'], + }), + ('DepthProc', '2.1.5', { + 'checksums': ['e6b0afd54bb20e25a6bf5402c771848db20e9c844f0fc990ecc3d1078b9eee44'], + }), + ('dbscan', '1.1-11', { + 'checksums': ['f0498e67e612629340a2758fbe747c4d9d4ca648f002230a03499cb73735e62f'], + }), + ('ggh4x', '0.2.2', { + 'checksums': ['2a0eda36b787bd3f49b5ae21e20b8104b615b21294b369f784d2bfe1579eba86'], + }), + ('ComplexUpset', '1.3.3', { + 'checksums': ['5b2f99b4a38648641c7d31fc57f201a93e5bc1b85442a0b9726f72c166d964ea'], + }), + ('proxyC', '0.3.3', { + 'checksums': ['3e25da94633da0b5c6cdac03f5b6d8205d078f60c5a09073e90a1b6f0930e302'], + }), + ('changepoint', '2.2.4', { + 'checksums': ['ac636fde7610137385dde1e3d8a22a2ff856a8d5c917c7ad1a5cc49f98b8649b'], + }), + ('geeM', '0.10.1', { + 'checksums': ['fe76a32981b55835095041e777d1cf2e9ce43edb8d9488db56279f7cb6f43fe5'], + }), + ('ggstance', '0.3.5', { + 'checksums': ['ed641857c49eb60f5baf2817fbd610caea62322a247f8b2c1aca3056eddee94b'], + }), + ('mosaicCore', '0.9.2.1', { + 'checksums': ['b7ce16f20fde1d8a5b1836110e5980fb274504ddae6b9c5c2f4198dc7d09dafa'], + }), + ('ggformula', '0.10.2', { + 'checksums': ['948b1c34a5c089cf86275d2b3e020e1a099278136e43175a50fb6063e54b6375'], + }), + ('kinship2', '1.9.6', { + 'checksums': ['0150bd5974c2a19885f6ff2e99f3c1f6361054a0910dcfc9dd26a8e0cd73bbf6'], + }), + ('MESS', '0.5.9', { + 'checksums': ['b57dff943a130830a24d87fe2e8f8b766cf18398c9c09e0a020d5dd183f9d72d'], + }), ] moduleclass = 'lang' From cc75f0b5a853fd07aadce1638559c7f52f95f5b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2023 15:26:27 +0100 Subject: [PATCH 6798/9987] add additional extensions for R-bundle-Bioconductor 3.15 --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index fa874f6b7f4..dfc66ffa3b9 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1152,6 +1152,18 @@ exts_list = [ ('ReactomePA', '1.40.0', { 'checksums': ['458b3febb341700414ca04ea4a6f3005061c9db97622cfdfda6b75a74415a7b9'], }), + ('flowClean', '1.34.1', { + 'checksums': ['d0e58ac89fd302761136cbcd5eb859351a61da2bd8967840bcd054ec16630f7f'], + }), + ('flowAI', '1.26.0', { + 'checksums': ['f4e35c824f68036cea5746236a026ad8e336c2595411d15d303d45fbc02526a5'], + }), + ('flowFP', '1.54.0', { + 'checksums': ['ba12d5bd4dc784997f30435314fe61f86b0c28d99c4458f7e8f9b76daa54b442'], + }), + ('simplifyEnrichment', '1.6.1', { + 'checksums': ['66fafb64d19c5fc4bb7aa6c6805130144f35fd508c2551024aec9f5c7b7b7461'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From aa2290e6a3bc1b2e1cd38a4eae5df64873ffdd47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2023 15:40:52 +0100 Subject: [PATCH 6799/9987] adding easyconfigs: Phenoflow-1.1.2-20200917-foss-2022a-R-4.2.1.eb, flowFDA-0.99-20220602-foss-2022a-R-4.2.1.eb --- ...lowFDA-0.99-20220602-foss-2022a-R-4.2.1.eb | 28 +++++++++++++++++++ ...oflow-1.1.2-20200917-foss-2022a-R-4.2.1.eb | 28 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/f/flowFDA/flowFDA-0.99-20220602-foss-2022a-R-4.2.1.eb create mode 100644 easybuild/easyconfigs/p/Phenoflow/Phenoflow-1.1.2-20200917-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/f/flowFDA/flowFDA-0.99-20220602-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/f/flowFDA/flowFDA-0.99-20220602-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..ff0965141f5 --- /dev/null +++ b/easybuild/easyconfigs/f/flowFDA/flowFDA-0.99-20220602-foss-2022a-R-4.2.1.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'flowFDA' +local_commit = 'a7e931d' +version = '0.99-20220602' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/FMKerckhof/flowFDA' +description = """R package for analysing flow cytometry experiments with model based clustering, + functional principal component analysis""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/FMKerckhof/flowFDA/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['80942abd4760bbaa815c909749e0d2746cf7838967b555f7035d1bf0ff149724'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Phenoflow/Phenoflow-1.1.2-20200917-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/p/Phenoflow/Phenoflow-1.1.2-20200917-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..e58ddd6ca7d --- /dev/null +++ b/easybuild/easyconfigs/p/Phenoflow/Phenoflow-1.1.2-20200917-foss-2022a-R-4.2.1.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'Phenoflow' +local_commit = 'c80f878' +version = '1.1.2-20200917' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/rprops/Phenoflow_package' +description = "R package offering functionality for the advanced analysis of microbial flow cytometry data" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/rprops/Phenoflow_package/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['815d4d78bbeacf8f863eef51d446998e39728fd7bf471ba9df4b01b5c4140719'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('flowFDA', '0.99-20220602', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 2f4a080720c6a5015abd9a21638c8ae76a0296dc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2023 15:47:35 +0100 Subject: [PATCH 6800/9987] use versionsuffix to indicate that TopHat 2.1.2 depends on Python 2.7.18 --- ....2-GCC-11.3.0.eb => TopHat-2.1.2-GCC-11.3.0-Python-2.7.18.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/t/TopHat/{TopHat-2.1.2-GCC-11.3.0.eb => TopHat-2.1.2-GCC-11.3.0-Python-2.7.18.eb} (97%) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.3.0-Python-2.7.18.eb similarity index 97% rename from easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.3.0.eb rename to easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.3.0-Python-2.7.18.eb index f77cd37c2ba..d3260e3dfcb 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.3.0-Python-2.7.18.eb @@ -9,6 +9,7 @@ easyblock = 'ConfigureMake' name = 'TopHat' version = '2.1.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' description = "TopHat is a fast splice junction mapper for RNA-Seq reads." From 0ce25b81258b8b7e4a0dc631a8b9c0b0efa7f6e0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2023 16:28:51 +0100 Subject: [PATCH 6801/9987] stick to {gompi,iimpi}/2020a toolchain for TopHat, add versionsuffix because of Python 2.7.18 dependency --- ...-GCC-9.3.0.eb => TopHat-2.1.2-gompi-2020a-Python-2.7.18.eb} | 3 ++- ...2020.1.217.eb => TopHat-2.1.2-iimpi-2020a-Python-2.7.18.eb} | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/t/TopHat/{TopHat-2.1.2-GCC-9.3.0.eb => TopHat-2.1.2-gompi-2020a-Python-2.7.18.eb} (93%) rename easybuild/easyconfigs/t/TopHat/{TopHat-2.1.2-iccifort-2020.1.217.eb => TopHat-2.1.2-iimpi-2020a-Python-2.7.18.eb} (93%) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-9.3.0.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-gompi-2020a-Python-2.7.18.eb similarity index 93% rename from easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-9.3.0.eb rename to easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-gompi-2020a-Python-2.7.18.eb index 9e4e343ee09..30ef5634264 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-gompi-2020a-Python-2.7.18.eb @@ -9,11 +9,12 @@ easyblock = 'ConfigureMake' name = 'TopHat' version = '2.1.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' description = "TopHat is a fast splice junction mapper for RNA-Seq reads." -toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchain = {'name': 'gompi', 'version': '2020a'} toolchainopts = {'cstd': 'gnu++98', 'pic': True} github_account = 'infphilo' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iccifort-2020.1.217.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iimpi-2020a-Python-2.7.18.eb similarity index 93% rename from easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iccifort-2020.1.217.eb rename to easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iimpi-2020a-Python-2.7.18.eb index d2e2a6c2a70..35cf0264015 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-iimpi-2020a-Python-2.7.18.eb @@ -9,11 +9,12 @@ easyblock = 'ConfigureMake' name = 'TopHat' version = '2.1.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' description = "TopHat is a fast splice junction mapper for RNA-Seq reads." -toolchain = {'name': 'iccifort', 'version': '2020.1.217'} +toolchain = {'name': 'iimpi', 'version': '2020a'} toolchainopts = {'cstd': 'gnu++98', 'pic': True} github_account = 'infphilo' From bd64943c26ea6c760e868b340bcc9433a740995b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Fri, 10 Mar 2023 17:58:38 +0100 Subject: [PATCH 6802/9987] Added wxWidgets as a dependency, added easyconfigs for missing dependencies --- .../elfutils/elfutils-0.189-GCCcore-12.2.0.eb | 41 +++++++++++ .../g/GSL/GSL-2.7-GCCcore-12.2.0.eb | 29 ++++++++ .../GST-plugins-base-1.22.1-GCCcore-12.2.0.eb | 44 ++++++++++++ .../GStreamer-1.22.1-GCCcore-12.2.0.eb | 51 +++++++++++++ .../Graphene-1.10.8-GCCcore-12.2.0.eb | 32 +++++++++ .../g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb | 1 + .../wxWidgets-3.2.2.1-GCCcore-12.2.0.eb | 72 +++++++++++++++++++ 7 files changed, 270 insertions(+) create mode 100644 easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..31b49e92465 --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.189' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855'] + +builddependencies = [ + ('M4', '1.4.19'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('binutils', '2.39'), + ('bzip2', '1.0.8'), + ('libarchive', '3.6.1'), + ('XZ', '5.2.7'), + ('zstd', '1.5.2'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..04f31f8b603 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.7' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e1b10d918d0 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.1-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-base' +version = '1.22.1' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['59bcaeacc5646b8dbdcfa4ef20ca6e818dd234910efb4cee1bbea441a3801c69'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.74.0'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('GLib', '2.75.0'), + ('GStreamer', '1.22.1'), + ('Gdk-Pixbuf', '2.42.10'), + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('Graphene', '1.10.8'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a66851cc78f --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.1-GCCcore-12.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'GStreamer' +version = '1.22.1' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.22.1.tar.xz': 'cd3ca759f926763615fdfcea63c9761198c42889bc0615ceec73e22b24fde771'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('Perl', '5.36.0'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.74.0'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('zlib', '1.2.12'), + ('GMP', '6.2.1'), + ('GSL', '2.7'), + ('GLib', '2.75.0'), + ('libunwind', '1.6.2'), + ('elfutils', '0.189'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b73f8a3c5b7 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'Graphene' +version = '1.10.8' + +homepage = 'https://ebassi.github.io/graphene/' +description = "Graphene is a thin layer of types for graphic libraries" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ebassi' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['922dc109d2dc5dc56617a29bd716c79dd84db31721a8493a13a5f79109a4a4ed'] + +builddependencies = [ + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), + ('GObject-Introspection', '1.74.0'), + ('binutils', '2.39'), +] +dependencies = [('GLib', '2.75.0')] + +configopts = "-Dgobject_types=true -Dintrospection=enabled" + +sanity_check_paths = { + 'files': ['lib/libgraphene-1.0.%s' % SHLIB_EXT, 'share/gir-1.0/Graphene-1.0.gir'], + 'dirs': ['include/graphene-1.0', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb index 0c45cc31308..d3bd40b6b62 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb @@ -29,6 +29,7 @@ dependencies = [ ('X11', '20221110'), ('Qt5', '5.15.7'), ('Lua', '5.4.4'), + ('wxWidgets', '3.2.2.1'), ] preconfigopts = 'autoreconf && ' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..763e60230cd --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.2.0.eb @@ -0,0 +1,72 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.2.2.1' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'wxWidgets' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_BZ2] +checksums = ['dffcb6be71296fff4b7f8840eb1b510178f57aa2eb236b20da41182009242c02'] + +builddependencies = [ + ('binutils', '2.39'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), + ('Python', '3.10.8'), +] + +dependencies = [ + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.4'), + ('XZ', '5.2.7'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.4.0'), + ('expat', '2.4.9'), + ('GTK3', '3.24.35'), + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), + ('SDL2', '2.26.3'), + ('cairo', '1.17.4'), + ('GST-plugins-base', '1.22.1'), + ('GLib', '2.75.0'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From 27e4f7a90b32d7fa3c81f3f3969c2b55728eca96 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2023 18:47:56 +0100 Subject: [PATCH 6803/9987] also add ddPCRclust, SamSPECTRAL, flowMerge + required additional extensions --- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index dfc66ffa3b9..36d3de6f295 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1164,6 +1164,45 @@ exts_list = [ ('simplifyEnrichment', '1.6.1', { 'checksums': ['66fafb64d19c5fc4bb7aa6c6805130144f35fd508c2551024aec9f5c7b7b7461'], }), + ('RPMG', '2.2-3', { + 'checksums': ['74d5bada6a51d280296cb36fae4938c16ba9ed2fa37f3bfb60cf7c541c5b22b6'], + }), + ('Rwave', '2.6-5', { + 'checksums': ['6c9ef75bb376f2e3f5c5dcd3b3fdca7d86797ce809da34f444632657189be2e4'], + }), + ('RSEIS', '4.1-4', { + 'checksums': ['76d5caf30cd3871fa80d27ea694023a4c303ffc099297aeeff03d22538dbff76'], + }), + ('splancs', '2.01-43', { + 'checksums': ['b351565e1f69f6c86a29d921d3a18d5896c4586e2ab8c73bb3df8e75630fc448'], + }), + ('MBA', '0.1-0', { + 'checksums': ['78039905c5b98be2bb79a5f292187a2aca21ef449daeefea58b0cac53a5283af'], + }), + ('GEOmap', '2.5-0', { + 'checksums': ['82e5608eda7330632bc67aa662b649e7b7b3ccdfda6a18a19d2e3379e0db1093'], + }), + ('RFOC', '3.4-6', { + 'checksums': ['0dfa237f4d04eb9a2718942b4d7ed9538fc5f89e3cbaa5a34a4fd1bc6fe54533'], + }), + ('flowDensity', '1.30.0', { + 'checksums': ['c321b395d6f1ae24d1428319401b225ae5e31fee5051127e43142d96f820103d'], + }), + ('flowPeaks', '1.42.0', { + 'checksums': ['ae98124c0574364bf8cd47be7704ad90b2b7d3dabbdd8df7744cbfaf81d665a8'], + }), + ('SamSPECTRAL', '1.50.0', { + 'checksums': ['b55de8cb2092d1b5c192ed0e4b47c421d888e5392165f28395241ca5884b8a5c'], + }), + ('ddPCRclust', '1.16.0', { + 'checksums': ['a457b78a2c254c69ed572d8dca01c66134d6ad2952f72097703110c1d663da5d'], + }), + ('feature', '1.2.15', { + 'checksums': ['de38292b7e800068a20824e2a9e7d5d4d0b465b7925db0d165346aa5030ff67b'], + }), + ('flowMerge', '2.44.0', { + 'checksums': ['ba143b5fff19207f323c1e7b7feaf56fa6e31700422d002521fe49e86bbc5e03'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From bd0f81e813df890a5e59f529fab5aad6cff0445e Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 10 Mar 2023 19:09:52 +0000 Subject: [PATCH 6804/9987] adding easyconfigs: edlib-1.3.9-GCC-11.3.0.eb, minimap2-2.24-GCCcore-11.3.0.eb, duplex-tools-0.3.1-foss-2022a.eb --- .../duplex-tools-0.3.1-foss-2022a.eb | 88 +++++++++++++++++++ .../e/edlib/edlib-1.3.9-GCC-11.3.0.eb | 22 +++++ .../minimap2/minimap2-2.24-GCCcore-11.3.0.eb | 53 +++++++++++ 3 files changed, 163 insertions(+) create mode 100644 easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb new file mode 100644 index 00000000000..70820b94cfc --- /dev/null +++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb @@ -0,0 +1,88 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'PythonBundle' + +name = 'duplex-tools' +version = '0.3.1' + +homepage = 'https://github.com/nanoporetech/duplex-tools' +description = """ +Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided + to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for + recovering simplex basecalls from incorrectly concatenated pairs. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +_minimap2_ver = '2.24' +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('edlib', '1.3.9'), + ('minimap2', _minimap2_ver), + ('python-parasail', '1.3.3'), + ('Pysam', '0.19.1'), + ('tqdm', '4.64.0'), + ('Arrow', '8.0.0'), + ('h5py', '3.7.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mappy', '2.24', { + 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + }), + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + ('iso8601', '1.1.0', { + 'checksums': ['32811e7b81deee2063ea6d2e94f8819a86d1f3811e49d23623a41fa832bef03f'], + }), + ('lib_pod5', '0.1.5', { + 'source_tmpl': 'lib_pod5-%%(version)s-cp310-cp310-manylinux_2_17_%s.manylinux2014_%s.whl' % (ARCH, ARCH), + 'checksums': [{ + 'lib_pod5-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl': ( + '4e8993327268784bb0e1320595411f545d2019cf4952b04d63be584cf7208480' + ), + 'lib_pod5-%(version)s-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl': ( + '4e8993327268784bb0e1320595411f545d2019cf4952b04d63be584cf7208480' + ), + }], + }), + ('vbz-h5py-plugin', '1.0.1', { + 'source_tmpl': 'vbz_h5py_plugin-%(version)s.tar.gz', + 'checksums': ['c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341'], + }), + ('pod5', '0.1.5', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['4d66b95035c325a3a0bf6518d3b728f4324ccd6303aa9a00515b73cf1ef2d575'], + }), + ('pyfastx', '0.9.1', { + # PYPI source tarball is incomplete, causes ImportErrors + # see https://github.com/lmdu/pyfastx/issues/60 + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/lmdu/%(name)s/archive'], + 'checksums': ['cd2aaab5ed3cf56b24d45d01f2d76ff314ae381b9bba029ea4f7e3224ce4748a'], + }), + (name, version, { + 'source_tmpl': 'duplex_tools-%(version)s.tar.gz', + 'checksums': ['5cb16aca841873139f2d54da40a0b8db22bbda4a958bf45e679f538a7af9fb0d'], + }), +] + +_bins = ['dorado_stereo.sh', 'duplex_tools', 'minimap2.py', 'natsort', 'pod5', 'pyfastx'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'dorado_stereo.sh -h', + 'duplex_tools --help', + 'pod5 --help', + 'pyfastx --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-11.3.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-11.3.0.eb new file mode 100644 index 00000000000..3133e7e2d0e --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'edlib' +version = '1.3.9' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766'] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..aea5a475d68 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.3.0.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# DeepThought, Flinders University +# Updated to 2.22 +# R.QIAO + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.24' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['9dd4c31ff082182948944bcdad6d328f64f09295d10547d72eba24189880a615'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('zlib', '1.2.12')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' From ab74ffddc452e78812f965f27fe52a5f21840602 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 10 Mar 2023 19:13:36 +0000 Subject: [PATCH 6805/9987] fix lib-pod5 aarch64 checksum --- .../d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb index 70820b94cfc..934f8d2c337 100644 --- a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb @@ -40,14 +40,14 @@ exts_list = [ ('iso8601', '1.1.0', { 'checksums': ['32811e7b81deee2063ea6d2e94f8819a86d1f3811e49d23623a41fa832bef03f'], }), - ('lib_pod5', '0.1.5', { + ('lib-pod5', '0.1.5', { 'source_tmpl': 'lib_pod5-%%(version)s-cp310-cp310-manylinux_2_17_%s.manylinux2014_%s.whl' % (ARCH, ARCH), 'checksums': [{ 'lib_pod5-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl': ( '4e8993327268784bb0e1320595411f545d2019cf4952b04d63be584cf7208480' ), 'lib_pod5-%(version)s-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl': ( - '4e8993327268784bb0e1320595411f545d2019cf4952b04d63be584cf7208480' + '125f19ad83c299d0d6c67d18ce8e43da4e12bf12cf7141ab7d60fba7574239bd' ), }], }), From f8ddc2e91893f29f6bf9e88b18136571feef0062 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2023 20:47:24 +0100 Subject: [PATCH 6806/9987] {bio}[foss/2022a] plot1cell v0.0.1, DoubletFinder v2.0.3-20230131, loomR v0.2.0-20180425 w/ R.4.2.1 --- ...inder-2.0.3-20230131-foss-2022a-R-4.2.1.eb | 29 +++++++++++++++++++ ...loomR-0.2.0-20180425-foss-2022a-R-4.2.1.eb | 29 +++++++++++++++++++ .../plot1cell-0.0.1-foss-2022a-R-4.2.1.eb | 28 ++++++++++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-20230131-foss-2022a-R-4.2.1.eb create mode 100644 easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2022a-R-4.2.1.eb create mode 100644 easybuild/easyconfigs/p/plot1cell/plot1cell-0.0.1-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-20230131-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-20230131-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..22ef8e3e6ba --- /dev/null +++ b/easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-20230131-foss-2022a-R-4.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'DoubletFinder' +local_commit = '67fb8b5' +# see DESCRIPTION to determine version, +# but add date stamp of commit since version is not always bumped +version = '2.0.3-20230131' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/chris-mcginnis-ucsf/DoubletFinder' +description = "R package for detecting doublets in single-cell RNA sequencing data" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/chris-mcginnis-ucsf/DoubletFinder/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['9f3233a3d3a668baca6e8b2a32e3d13394cdb078b9db95a3a3e044b48240e444'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..0c353f67d45 --- /dev/null +++ b/easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2022a-R-4.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'loomR' +local_commit = 'df0144b' +# see DESCRIPTION to determine version, +# but add date stamp of commit since version is not always bumped +version = '0.2.0-20180425' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/mojaveazure/loomR' +description = "An R interface for loom files" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/mojaveazure/loomR/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['6264448baf4fd9a569eb5a832598c4a224382ef26c0a7fbd061a8c901672f0ac'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/plot1cell/plot1cell-0.0.1-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/p/plot1cell/plot1cell-0.0.1-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..97a84ddcb6a --- /dev/null +++ b/easybuild/easyconfigs/p/plot1cell/plot1cell-0.0.1-foss-2022a-R-4.2.1.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'plot1cell' +version = '0.0.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/HaojiaWu/plot1cell' +description = "plot1cell: a package for advanced single cell data visualization" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/HaojiaWu/plot1cell/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ac39a21e8530d7eb489ac64d8e56d19dcbf3f904b99fc91cf0746bb230f37a10'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('DoubletFinder', '2.0.3-20230131', versionsuffix), + ('loomR', '0.2.0-20180425', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 59d4b9aa51271ef2e426a83bd84360bb1bb0f4ca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 10 Mar 2023 21:07:42 +0100 Subject: [PATCH 6807/9987] disable Python support for OTF2 v2.2, since we're not including Python 2.x as dependency --- easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.2.0.eb | 3 +++ easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb | 3 +++ easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-9.3.0.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.2.0.eb index 6fa20d819fa..c34cc8c99f1 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.2.0.eb @@ -39,6 +39,9 @@ dependencies = [ ('SIONlib', '1.7.4', '-tools'), ] +# set $PYTHON_FOR_GENERATOR to ':' to disable Python support (since we're not included Python 2.x as dependency) +preconfigopts = "export PYTHON_FOR_GENERATOR=':' && " + configopts = '--enable-shared' sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb index 4c77f62f44d..2c088bb7158 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-8.3.0.eb @@ -39,6 +39,9 @@ dependencies = [ ('SIONlib', '1.7.6', '-tools'), ] +# set $PYTHON_FOR_GENERATOR to ':' to disable Python support (since we're not included Python 2.x as dependency) +preconfigopts = "export PYTHON_FOR_GENERATOR=':' && " + configopts = '--enable-shared' sanity_check_paths = { diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-9.3.0.eb index 7c446a1051d..75ec06996ed 100644 --- a/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/o/OTF2/OTF2-2.2-GCCcore-9.3.0.eb @@ -40,6 +40,9 @@ dependencies = [ ('SIONlib', '1.7.6', '-tools'), ] +# set $PYTHON_FOR_GENERATOR to ':' to disable Python support (since we're not included Python 2.x as dependency) +preconfigopts = "export PYTHON_FOR_GENERATOR=':' && " + configopts = '--enable-shared' sanity_check_paths = { From 5d7752bc15f48a0537c4dba77d668edf7440c4bd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 10 Mar 2023 22:15:07 +0100 Subject: [PATCH 6808/9987] adding easyconfigs: Mash-2.3-GCC-11.3.0.eb --- .../easyconfigs/m/Mash/Mash-2.3-GCC-11.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..157dc810cfd --- /dev/null +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.3.0.eb @@ -0,0 +1,48 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v2.2 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'Mash' +version = '2.3' + +homepage = 'http://mash.readthedocs.org' +description = "Fast genome and metagenome distance estimation using MinHash" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/marbl/Mash/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Mash-2.2_fix-hardcoding.patch', + 'Mash-2.1_disable-memcpy-wrap.patch', + 'Mash-2.3_fix-GCC-11.patch', +] +checksums = [ + 'f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1', # v2.3.tar.gz + '0c7315af727a06f408ab3ca69da0860fc671aa870b448a41a509b1e6d7027db5', # Mash-2.2_fix-hardcoding.patch + '40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch + '47a55459d4e8c57949648e0f33f3ffc3529563db0efe60f495fdec046f48d94e', # Mash-2.3_fix-GCC-11.patch +] + +builddependencies = [('Autotools', '20220317')] +dependencies = [ + ('CapnProto', '0.10.2'), + ('GSL', '2.7'), + ('zlib', '1.2.12'), +] + +preconfigopts = "./bootstrap.sh && " +configopts = "--with-capnp=$EBROOTCAPNPROTO --with-gsl=$EBROOTGSL" + +sanity_check_paths = { + 'files': ['bin/mash', 'lib/libmash.a'], + 'dirs': ['include/mash'], +} + +sanity_check_commands = ['mash --version'] + +moduleclass = 'bio' From 5516499c85c7d58086373c5dc7b13d823102a60c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 10 Mar 2023 22:16:02 +0100 Subject: [PATCH 6809/9987] adding easyconfigs: FastANI-1.33-GCC-11.3.0.eb --- .../f/FastANI/FastANI-1.33-GCC-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-11.3.0.eb new file mode 100644 index 00000000000..67c94db4722 --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.33-GCC-11.3.0.eb @@ -0,0 +1,45 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'ConfigureMake' + +name = 'FastANI' +version = '1.33' + +homepage = "https://github.com/ParBLiSS/FastANI" +description = """FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean + nucleotide identity of orthologous gene pairs shared between two microbial + genomes. FastANI supports pairwise comparison of both complete and draft + genome assemblies.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] +sources = ['v%(version)s.zip'] +patches = ['FastANI-1.2-memcpy.patch'] +checksums = [ + 'fb392ffa3c7942091a06de05c56c8e250523723c39da65ae8f245e65e440a74b', # v1.33.zip + 'eebcf0b64c31ee360ca79136f644157064ac69747ed13cff70f5c9932c6bb0d5', # FastANI-1.2-memcpy.patch +] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [ + ('GSL', '2.7'), + ('zlib', '1.2.12'), +] + +preconfigopts = 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/fastANI'], + 'dirs': [] +} + +sanity_check_commands = ["fastANI --help"] + +moduleclass = 'bio' From 8770fe27b4d6c1c43d6d0e419a906c060533aa20 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 10 Mar 2023 22:21:37 +0100 Subject: [PATCH 6810/9987] adding easyconfigs: ANIcalculator-1.0-GCCcore-11.3.0.eb, libnsl-2.0.0-GCCcore-11.3.0.eb --- .../ANIcalculator-1.0-GCCcore-11.3.0.eb | 46 +++++++++++++++++++ .../l/libnsl/libnsl-2.0.0-GCCcore-11.3.0.eb | 33 +++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libnsl/libnsl-2.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a017bc13654 --- /dev/null +++ b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'ANIcalculator' +version = '1.0' + +homepage = 'https://ani.jgi.doe.gov/html/home.php' +description = """This tool will calculate the bidirectional average nucleotide identity (gANI) and +Alignment Fraction (AF) between two genomes. Required input is the full path to the fna file +(nucleotide sequence of genes in fasta format) of each query genome. Either the rRNA and tRNA genes +can be excluded, or provided in a list with the -ignoreList option. This is necessary as the presence +of tRNA and/or rRNA genes in the fna will artificially inflate the ANI.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ani.jgi.doe.gov/download_files/'] +sources = ['%(name)s_v%(version_major)s.tgz'] +checksums = ['236596a9a204cbcad162fc66be3506b2530b1f48f4f84d9647ccec3ca7483a43'] + +dependencies = [ + ('Perl', '5.34.1'), + ('libnsl', '2.0.0'), +] + +skipsteps = ['build'] + +# The source tarball also includes Log4perl 1.44. +# Instead of copying this, we use the version from the Perl module. +files_to_copy = [(['ANIcalculator', 'nsimscan'], 'bin'), 'README.txt'] + +# Fix permissions on binaries and README.txt, +postinstallcmds = [ + 'chmod a+x %(installdir)s/bin/*', + 'chmod -x %(installdir)s/README.txt', +] + +sanity_check_paths = { + 'files': ['README.txt', 'bin/ANIcalculator', 'bin/nsimscan'], + 'dirs': [], +} + +sanity_check_commands = [ + 'ANIcalculator -help', + 'nsimscan -h', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0c367471d66 --- /dev/null +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libnsl' +version = '2.0.0' + +homepage = 'https://github.com/thkukuk/libnsl' +description = """The libnsl package contains the public client interface for NIS(YP).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['2da075ef1893ebdfc5f074f83ac811873dc06fd5c62bc9a4729fd2e27a40341a'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('libtirpc', '1.3.2'), +] + +# Provide a symlink for libnsl.so.1, which used to be part of glibc. +# This new version of libnsl should be backwards compatible. +postinstallcmds = ['ln -s libnsl.so %(installdir)s/lib/libnsl.so.1'] + +sanity_check_paths = { + 'files': ['include/rpcsvc/yp.h', 'lib/libnsl.a', + 'lib/libnsl.%s' % SHLIB_EXT, 'lib/libnsl.%s.1' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' From 9e3b6e8798c67defc2db6b742a588a29e3a181bc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 10 Mar 2023 22:35:31 +0100 Subject: [PATCH 6811/9987] adding easyconfigs: dRep-3.4.2-foss-2022a.eb --- .../d/dRep/dRep-3.4.2-foss-2022a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/d/dRep/dRep-3.4.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/dRep/dRep-3.4.2-foss-2022a.eb b/easybuild/easyconfigs/d/dRep/dRep-3.4.2-foss-2022a.eb new file mode 100644 index 00000000000..4ef780769ef --- /dev/null +++ b/easybuild/easyconfigs/d/dRep/dRep-3.4.2-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'dRep' +version = '3.4.2' + +homepage = 'https://drep.readthedocs.io/en/latest/' +description = """dRep is a python program which performs rapid pair-wise comparison of genome sets. +One of it’s major purposes is for genome de-replication, but it can do a lot more.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('Seaborn', '0.12.1'), + ('matplotlib', '3.5.2'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), + ('Mash', '2.3'), + ('MUMmer', '4.0.0rc1'), + ('FastANI', '1.33'), + ('CheckM', '1.2.2'), + ('ANIcalculator', '1.0'), + ('prodigal', '2.6.3'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/MrOlm/%(namelower)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['9c02114a7df6d2de5810617a6715a770aee70872b293c4bd5c8076735d62e4e0'], + }), +] + +sanity_pip_check = True + +local_binaries = ['dRep', 'parse_stb.py', 'ScaffoldLevel_dRep.py'] + +sanity_check_paths = { + 'files': ['bin/' + x for x in local_binaries], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = [ + 'parse_stb.py -h', + 'ScaffoldLevel_dRep.py -h', + 'dRep -h', + # fail in case any dependency reports an ERROR, except for centrifuge + # (which is not used anymore according to the installation documentation) + '! dRep check_dependencies | grep "ERROR" | grep -v "centrifuge"', +] + +moduleclass = 'bio' From 8edcde97b49f72037e78151502e1b4e0721f1b30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Mar 2023 00:00:07 +0100 Subject: [PATCH 6812/9987] adding easyconfigs: velocyto-0.17.17-foss-2022a.eb --- .../v/velocyto/velocyto-0.17.17-foss-2022a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2022a.eb diff --git a/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2022a.eb b/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2022a.eb new file mode 100644 index 00000000000..7305196e2f8 --- /dev/null +++ b/easybuild/easyconfigs/v/velocyto/velocyto-0.17.17-foss-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'velocyto' +version = '0.17.17' + +homepage = 'https://velocyto.org/velocyto.py/' +description = "Velocyto is a library for the analysis of RNA velocity." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('numba', '0.56.4'), + ('scikit-learn', '1.1.2'), + ('h5py', '3.7.0'), + ('Pysam', '0.19.1'), +] + +use_pip = True + +exts_list = [ + ('numpy_groupies', '0.9.20', { + 'checksums': ['923a382d6bc6876384b58a9c0503b05b9d36a660f329695c2d33e4f93fcbbe3d'], + }), + ('loompy', '3.0.7', { + 'checksums': ['b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4'], + }), + (name, version, { + 'checksums': ['1ad65fc53292ce1970a70bc742d73491b370038e0b0065761303e787bf7ffe39'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/velocyto'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'velocyto', +] + +moduleclass = 'bio' From 864d31ce0cd447026d1d0498bdb01cb1d294116e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Mar 2023 00:01:24 +0100 Subject: [PATCH 6813/9987] {bio}[foss/2022a] GOATOOLS v1.3.1, XlsxWriter v3.0.8 w/ Python 3.10.4 --- .../g/GOATOOLS/GOATOOLS-1.3.1-foss-2022a.eb | 57 +++++++++++++++++++ .../XlsxWriter-3.0.8-GCCcore-11.3.0.eb | 34 +++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.0.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2022a.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2022a.eb new file mode 100644 index 00000000000..b694dc5ae85 --- /dev/null +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2022a.eb @@ -0,0 +1,57 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'GOATOOLS' +version = '1.3.1' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/tanghaibao/goatools/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/tanghaibao', + 'repo_name': 'goatools', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [('cURL', '7.83.0')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('XlsxWriter', '3.0.8'), + ('statsmodels', '0.13.1'), + ('pydot', '1.4.2'), + ('openpyxl', '3.0.10'), +] + +download_dep_fail = True +use_pip = True + +postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "mkdir -p %(builddir)s", + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.0.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.0.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..33d4856cc08 --- /dev/null +++ b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.0.8-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'XlsxWriter' +version = '3.0.8' + +homepage = 'https://xlsxwriter.readthedocs.io/' +description = "A Python module for creating Excel XLSX files" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ec77335fb118c36bc5ed1c89e33904d649e4989df2d7980f7d6a9dd95ee5874e'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/vba_extract.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['vba_extract.py --help'] + +sanity_pip_check = True + +moduleclass = 'tools' From 394cda6491fedad7d7c74c8e87ec06532dfc1f1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Mar 2023 00:03:17 +0100 Subject: [PATCH 6814/9987] adding easyconfigs: genomepy-0.15.0-foss-2022a.eb, mygene-3.2.2-foss-2022a.eb --- .../g/genomepy/genomepy-0.15.0-foss-2022a.eb | 72 +++++++++++++++++++ .../m/mygene/mygene-3.2.2-foss-2022a.eb | 31 ++++++++ 2 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/g/genomepy/genomepy-0.15.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/genomepy/genomepy-0.15.0-foss-2022a.eb b/easybuild/easyconfigs/g/genomepy/genomepy-0.15.0-foss-2022a.eb new file mode 100644 index 00000000000..4d8751a3fb2 --- /dev/null +++ b/easybuild/easyconfigs/g/genomepy/genomepy-0.15.0-foss-2022a.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'genomepy' +version = '0.15.0' + +homepage = 'https://github.com/vanheeringen-lab/genomepy' +description = "genomepy is designed to provide a simple and straightforward way to download and use genomic data" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), + ('Biopython', '1.79'), + ('mygene', '3.2.2'), + ('pyfaidx', '0.7.1'), + ('PyYAML', '6.0'), + ('protobuf-python', '3.19.4'), +] + +use_pip = True + +# avoid hatchling requirement to install infercnvpy +# (since installing it introduces conflicting version requirements with poetry included with Python) +local_preinstallopts = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ +local_preinstallopts += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ +local_preinstallopts += r"""-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ +local_preinstallopts += "rm -r paper && " + +local_postinstallcmds = [ + # copy default configuration file (only needed because we're not using hatchling for the installation) + "cp -a genomepy/config/default.yaml %(installdir)s/lib/python%(pyshortver)s/site-packages/genomepy/config/", +] + +exts_list = [ + ('diskcache', '5.4.0', { + 'checksums': ['8879eb8c9b4a2509a5e633d2008634fb2b0b35c2b36192d89655dbde02419644'], + }), + ('loguru', '0.6.0', { + 'checksums': ['066bd06758d0a513e9836fd9c6b5a75bfb3fd36841f4b996bc60b547a309d41c'], + }), + ('mysql-connector-python', '8.0.32', { + 'sources': ['mysql_connector_python-%(version)s-py2.py3-none-any.whl'], + 'checksums': ['e0299236297b63bf6cbb61d81a9d400bc01cad4743d1abe5296ef349de15ee53'], + 'modulename': 'mysqlx', + }), + ('norns', '0.1.6', { + 'checksums': ['1f3c6ccbe79b2cb3076f66a352cd76462593adbabe9ebb262f879a9d0a6634e4'], + # remove 'nose' requirement (not compatible with Python 3.10, and not really needed) + 'preinstallopts': "sed -i '/nose/d' setup.py && ", + }), + ('pyfaidx', '0.7.2.1', { + 'checksums': ['30f0d20a9e3d53353fb20eb69b7e22e6f01a53ed4f21b3e17dd408f0be5051a0'], + }), + (name, version, { + 'checksums': ['9656f94d2e47e8b1cd11abc3f8e519c39011fcd5d211d8ab940d7063b5ddbe4a'], + 'preinstallopts': local_preinstallopts, + 'postinstallcmds': local_postinstallcmds, + }), +] + +sanity_check_paths = { + 'files': ['bin/genomepy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["genomepy --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2022a.eb b/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2022a.eb new file mode 100644 index 00000000000..de664d681d9 --- /dev/null +++ b/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2022a.eb @@ -0,0 +1,31 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +easyblock = 'PythonBundle' + +name = 'mygene' +version = '3.2.2' + +homepage = 'https://github.com/biothings/mygene.py' +description = "Python Client for MyGene.Info services." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True + +exts_list = [ + ('biothings_client', '0.2.6', { + 'checksums': ['84d9d577b8fb3963a2fa71c5a13b10411566f3bc2e8ba67bb15de9d2ced08c2d'], + }), + (name, version, { + 'checksums': ['e729cabbc28cf5afb221bca1ab637883b375cb1a3e2f067587ec79f71affdaea'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 8a9f2ac1c725754588036017bb54c738d5fe6a3c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 11 Mar 2023 00:05:31 +0100 Subject: [PATCH 6815/9987] adding easyconfigs: CellOracle-0.12.0-foss-2022a.eb, GimmeMotifs-0.17.2-foss-2022a.eb, qnorm-0.8.1-foss-2022a.eb, Qtconsole-5.4.0-GCCcore-11.3.0.eb --- .../CellOracle-0.12.0-foss-2022a.eb | 59 ++++++++++++++ .../GimmeMotifs-0.17.2-foss-2022a.eb | 77 +++++++++++++++++++ .../Qtconsole-5.4.0-GCCcore-11.3.0.eb | 31 ++++++++ .../q/qnorm/qnorm-0.8.1-foss-2022a.eb | 36 +++++++++ 4 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb new file mode 100644 index 00000000000..e712870108d --- /dev/null +++ b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'CellOracle' +version = '0.12.0' + +homepage = 'https://github.com/morris-lab/CellOracle' +description = """CellOracle is a Python library for in silico gene perturbation analyses using single-cell omics data +and Gene Regulatory Network models.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('R', '4.2.1'), + ('SciPy-bundle', '2022.05'), + ('numba', '0.56.4'), + ('matplotlib', '3.5.2'), + ('Seaborn', '0.12.1'), + ('scikit-learn', '1.1.2'), + ('h5py', '3.7.0'), + ('velocyto', '0.17.17'), + ('umap-learn', '0.5.3'), + ('Arrow', '8.0.0'), + ('tqdm', '4.64.0'), + ('igraph', '0.10.3'), + ('IPython', '8.5.0'), + ('scanpy', '1.9.1'), + ('GOATOOLS', '1.3.1'), + ('genomepy', '0.15.0'), + ('GimmeMotifs', '0.17.2'), + ('Qtconsole', '5.4.0'), +] + +use_pip = True + +# remove louvain from requirements, since CellOracle doesn't actually use it at all +local_preinstallopts = "sed -i '/louvain/d' requirements.txt && " +# drop strict version requirement for gimmemotifs dependency +local_preinstallopts += "sed -i 's/gimmemotifs.*/gimmemotifs/g' requirements.txt && " + +exts_list = [ + ('jupyter-console', '6.4.4', { + 'sources': ['jupyter_console-%(version)s.tar.gz'], + 'checksums': ['172f5335e31d600df61613a97b7f0352f2c8250bbd1092ef2d658f77249f89fb'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('celloracle', version, { + 'checksums': ['9d533ee3e8c14828b6859ea195e92d184b050b0782fee430eda3b01359a564d5'], + 'preinstallopts': local_preinstallopts, + }), +] + +sanity_check_commands = ["python -c 'import celloracle; celloracle.check_python_requirements()'"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb new file mode 100644 index 00000000000..a57ae34779f --- /dev/null +++ b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb @@ -0,0 +1,77 @@ +easyblock = 'PythonBundle' + +name = 'GimmeMotifs' +version = '0.17.2' + +homepage = 'https://github.com/vanheeringen-lab/gimmemotifs' +description = "Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('pybedtools', '0.9.0'), + ('Pysam', '0.19.1'), + ('scikit-learn', '1.1.2'), + ('Seaborn', '0.12.1'), + ('statsmodels', '0.13.1'), + ('tqdm', '4.64.0'), + ('genomepy', '0.15.0'), + ('qnorm', '0.8.1'), + ('Arrow', '8.0.0'), # provides pyarrow, required by feather-format + ('HTSeq', '2.0.2'), # required by biofluff + ('pyBigWig', '0.3.18'), # required by biofluff +] + +use_pip = True + +exts_list = [ + ('palettable', '3.3.0', { + 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], + }), + ('biofluff', '3.0.4', { + 'modulename': 'fluff', + 'checksums': ['ef7b0a54103a830f197f21aa3d1ade8bdcddf613b437ea38c95260bb45324d6b'], + }), + ('diskcache', '5.4.0', { + 'checksums': ['8879eb8c9b4a2509a5e633d2008634fb2b0b35c2b36192d89655dbde02419644'], + }), + ('feather-format', '0.4.1', { + 'modulename': 'feather', + 'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'], + }), + ('iteround', '1.0.4', { + 'source_urls': ['https://github.com/cgdeboer/iteround/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['445e4f0c793ae558e4db3cdee7e23d77459b9c586e8021667aa60c14ba7ff45f'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('loguru', '0.6.0', { + 'checksums': ['066bd06758d0a513e9836fd9c6b5a75bfb3fd36841f4b996bc60b547a309d41c'], + }), + ('xxhash', '3.2.0', { + 'checksums': ['1afd47af8955c5db730f630ad53ae798cf7fae0acb64cebb3cf94d35c47dd088'], + }), + ('xdg', '6.0.0', { + 'checksums': ['24278094f2d45e846d1eb28a2ebb92d7b67fc0cab5249ee3ce88c95f649a1c92'], + }), + ('gimmemotifs', version, { + 'preinstallopts': """sed -i '/"configparser"/d' setup.py && """, + 'checksums': ['fbf70997abce6a75451c10b96994f8dbc03152b01df5cf30bf4397c98a9b54d2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gimme'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gimme --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4ca3e9f8a2e --- /dev/null +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Qtconsole' +version = '5.4.0' + +homepage = 'https://jupyter.org/' +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media +output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a +terminal, but provides a number of enhancements only possible in a GUI, such as +inline figures, proper multiline editing with syntax highlighting, graphical +calltips, and more.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['57748ea2fd26320a0b77adba20131cfbb13818c7c96d83fafcb110ff55f58b35'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('QtPy', '2.3.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb new file mode 100644 index 00000000000..1b0932b22af --- /dev/null +++ b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'qnorm' +version = '0.8.1' + +homepage = 'https://github.com/Maarten-vd-Sande/qnorm' +description = "Fast-ish (and correct!) quantile normalization in Python" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('numba', '0.56.4'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['61b2f3ef09a9c552a4f3b83dc438cb13f191fa190164361a3a508c4777eed3c7'] + +download_dep_fail = True +use_pip = True + +# pyproject.toml included in qnorm source tarball does not include standard fields, +# it's only there to be read by setup.py... +preinstallopts = "sed -i 's/pyproject.toml/pyproject.toml_/g' setup.py && mv pyproject.toml pyproject.toml_ && " + +sanity_check_paths = { + 'files': ['bin/qnorm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qnorm --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 678e5ec80431626ff14a1490f4856891ac25ea81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Sat, 11 Mar 2023 16:30:54 +0100 Subject: [PATCH 6816/9987] updated checksums in elfutils --- .../easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.2.0.eb index 31b49e92465..6a873567a86 100644 --- a/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.2.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] sources = [SOURCE_TAR_BZ2] -checksums = ['e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855'] +checksums = ['39bd8f1a338e2b7cd4abc3ff11a0eddc6e690f69578a57478d8179b4148708c8'] builddependencies = [ ('M4', '1.4.19'), From 1e41c656faf00dcc050fe90f3b8a9a3f8118af96 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Sun, 12 Mar 2023 10:15:27 -0300 Subject: [PATCH 6817/9987] Update DIRAC-23.0-intel-2022b-int64.eb --- easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb index 88f8b7975bc..7f4588b4537 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b-int64.eb @@ -8,7 +8,7 @@ homepage = 'http://www.diracprogram.org' description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" toolchain = {'name': 'intel', 'version': '2022b'} -toolchainopts = {'usempi': True, 'i8': True} +toolchainopts = {'usempi': True, 'i8': True, 'oneapi': False} source_urls = ['https://zenodo.org/record/7670749/files/'] sources = ['DIRAC-%(version)s-Source.tgz'] From de8f07140c0bd45d69e1a08acd57d5bd3c31882a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Sun, 12 Mar 2023 10:15:48 -0300 Subject: [PATCH 6818/9987] Update DIRAC-23.0-intel-2022b.eb --- easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb index 7221329ac3a..2dba1046771 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022b.eb @@ -7,7 +7,7 @@ homepage = 'http://www.diracprogram.org' description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" toolchain = {'name': 'intel', 'version': '2022b'} -toolchainopts = {'usempi': True} +toolchainopts = {'usempi': True, 'oneapi': False} source_urls = ['https://zenodo.org/record/7670749/files/'] sources = ['DIRAC-%(version)s-Source.tgz'] From d784396582dae8abf11d5da0c5f8794f0154cd6b Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Mon, 13 Mar 2023 08:35:24 +0000 Subject: [PATCH 6819/9987] adding easyconfigs: LASSO-Python-2.0.0-foss-2022b.eb --- .../LASSO-Python-2.0.0-foss-2022b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb new file mode 100644 index 00000000000..8699200241d --- /dev/null +++ b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'LASSO-Python' +version = '2.0.0' + +homepage = 'https://open-lasso-python.github.io/lasso-python/' +description = """This python library is designed for general purpose usage in +the field of Computer Aided Engineering (CAE). It's name originates from the +original initiator and donator of the project Lasso GmbH. The library is now +maintained by an open-source community.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('h5py', '3.8.0'), + ('SciPy-bundle', '2023.02'), + ('plotly.py', '5.13.1'), + ('matplotlib', '3.7.0'), + ('scikit-learn', '1.2.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mdurl', '0.1.2', { + 'checksum': 'bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba', + }), + ('markdown-it-py', '2.2.0', { + 'modulename': 'markdown_it', + 'checksum': '7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1', + }), + ('rich', '12.6.0', { + 'checksum': '125d96d20c92b946b983d0d392b84ff945461e5a06d3867e9f9e575f8697b67f', + }), + (name, version, { + 'sources': { + 'filename': 'lasso_python-%(version)s.tar.gz', + 'download_filename': 'lasso_python-%(version)s.tar.gz', + }, + 'modulename': 'lasso', + 'checksum': '67776e1876764680ac179fb750695aac63ecdbdf4f1ac8439f7e76fa3956727c', + }), +] + +moduleclass = 'tools' From 173a44d42fe6656023439243de935bb664555a66 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2023 10:46:28 +0100 Subject: [PATCH 6820/9987] adding easyconfigs: MaSuRCA-4.1.0-GCC-11.3.0.eb --- .../m/MaSuRCA/MaSuRCA-4.1.0-GCC-11.3.0.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-4.1.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-4.1.0-GCC-11.3.0.eb b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-4.1.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..d86ebc68b08 --- /dev/null +++ b/easybuild/easyconfigs/m/MaSuRCA/MaSuRCA-4.1.0-GCC-11.3.0.eb @@ -0,0 +1,67 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2017 University of Geneva +# Authors:: Yann Sagon +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'MaSuRCA' +version = '4.1.0' + +homepage = 'https://www.genome.umd.edu/masurca.html' +software_license = 'LicenseGPLv3' + +description = '''MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph + and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing + only short reads from Illumina sequencing or a mixture of short reads and long reads + (Sanger, 454, Pacbio and Nanopore).''' + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/alekseyzimin/masurca/releases/download/v%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['15078e24c79fe5aabe42748d64f95d15f3fbd7708e84d88fc07c4b7f2e4b0902'] + +builddependencies = [('patchelf', '0.15.0')] + +dependencies = [ + ('libreadline', '8.1.2'), + ('Tcl', '8.6.12'), + ('Boost', '1.79.0'), + ('zlib', '1.2.12'), + ('Perl', '5.34.1'), + ('bzip2', '1.0.8'), +] + +buildopts = "install-special" +start_dir = "global-1" + +postinstallcmds = [ + # fix location of 'bin' in install prefix in runCA and runCA-dedupe scripts + # escaping single quotes within single quotes is tricky, so we use $'...' to use ANSI C-like escaping + "sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA", + "sed -i $'s|^$bin =.*|$bin = \"$ENV{\'EBROOTMASURCA\'}/bin\";|g' %(installdir)s/bin/runCA-dedupe", + # fix hardcoded path in masurca script, just point back to 'bin' subdirectory instead + "sed -i 's@../CA8/Linux-amd64/bin@../bin@g' %(installdir)s/bin/masurca", + # commands to install built-in version of Flye + "cd ../Flye && make && cp -a ../Flye %(installdir)s", + # fix missing RPATH + "patchelf --force-rpath --set-rpath '$ORIGIN' %(installdir)s/bin/falcon_sense", +] + +sanity_check_paths = { + 'files': ['bin/masurca', 'Flye/bin/flye'], + 'dirs': ['include', 'lib'], +} + +sanity_check_commands = [ + "masurca --help", + "runCA --help", +] + +moduleclass = 'bio' From f100e8a85773db30643645232711ca7dcb85364d Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Mon, 13 Mar 2023 14:45:35 +0100 Subject: [PATCH 6821/9987] adding easyconfigs: GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb --- .../GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..6cba5dc2c45 --- /dev/null +++ b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'GPyTorch' +version = '1.9.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://gpytorch.ai' +description = "GPyTorch is a Gaussian process library implemented using PyTorch." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('PyTorch', '1.12.1', versionsuffix), + ('scikit-learn', '0.24.2'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('linear-operator', '0.3.0', { + 'sources': [{ + 'filename': SOURCE_TAR_GZ, + 'download_filename': 'linear_operator-%(version)s.tar.gz', + }], + 'checksum': '84bf572631a7e1576de6920d81600ca0fedcf6bda2f29dbaf440d6e72ce6abab', + }), + ('joblib', '1.2.0', { + 'checksum': 'e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018', + }), + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'checksum': '0bdbba6f6d5957a0f43ef6dc7fec39c47e8a55f632ca33760c6189f259b3ccc3', + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From b6a973be3e7e9999fb674da5200e3c008086887f Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Mon, 13 Mar 2023 13:47:50 +0000 Subject: [PATCH 6822/9987] linting --- .../easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb index 8699200241d..23dc38d67d5 100644 --- a/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb +++ b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb @@ -28,7 +28,7 @@ exts_list = [ 'checksum': 'bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba', }), ('markdown-it-py', '2.2.0', { - 'modulename': 'markdown_it', + 'modulename': 'markdown_it', 'checksum': '7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1', }), ('rich', '12.6.0', { From b437d4e15214194bbcaba8f3a078339005556cf7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2023 14:48:56 +0100 Subject: [PATCH 6823/9987] adding easyconfigs: eggnog-mapper-2.1.10-foss-2020b.eb --- .../eggnog-mapper-2.1.10-foss-2020b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb new file mode 100644 index 00000000000..8ebfa692352 --- /dev/null +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.10-foss-2020b.eb @@ -0,0 +1,56 @@ +# Eggnog DB installation instructions: +# 1. 'export EGGNOG_DATA_DIR=//eggnog-mapper-data' +# 2. run 'download_eggnog_data.py' +# 3. Check the expected DB version with 'emapper.py --version' + +easyblock = 'PythonPackage' + +name = 'eggnog-mapper' +version = '2.1.10' + +homepage = 'https://github.com/eggnogdb/eggnog-mapper' +description = """EggNOG-mapper is a tool for fast functional annotation of novel +sequences. It uses precomputed orthologous groups and phylogenies from the +eggNOG database (http://eggnog5.embl.de) to transfer functional information from +fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation +of novel genomes, transcriptomes or even metagenomic gene catalogs.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'eggnogdb' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e905b99ae81991aea696ba45587ae81c2dce5f03fe51d9c2a580cc2987976c8e'] + +dependencies = [ + ('Python', '3.8.6'), + ('Biopython', '1.78'), + ('HMMER', '3.3.2'), + ('DIAMOND', '2.0.7'), + ('prodigal', '2.6.3'), + ('wget', '1.20.3'), + ('MMseqs2', '13-45111'), + ('XlsxWriter', '1.4.0'), +] + +# strip out (too) strict version requirements for dependencies +preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/create_dbs.py', 'bin/download_eggnog_data.py', 'bin/emapper.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'download_eggnog_data.py --help', + 'create_dbs.py --help', + 'emapper.py --version | grep %(version)s', +] + +options = {'modulename': 'eggnogmapper'} + +moduleclass = 'bio' From 70a28be47957b5b20f156a06370099a943959eba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2023 15:09:33 +0100 Subject: [PATCH 6824/9987] adding easyconfigs: epiScanpy-0.4.0-foss-2022a.eb and patches: epiScanpy-0.4.0_fix-import.patch --- .../e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb | 72 +++++++++++++++++++ .../epiScanpy-0.4.0_fix-import.patch | 15 ++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0_fix-import.patch diff --git a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb new file mode 100644 index 00000000000..8bb31672fdc --- /dev/null +++ b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'epiScanpy' +version = '0.4.0' + +homepage = 'https://github.com/colomemaria/episcanpy' +description = """EpiScanpy is a toolkit to analyse single-cell open chromatin +(scATAC-seq) and single-cell DNA methylation (for example scBS-seq) +data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq +analysis tool Scanpy (Genome Biology, 2018) [Wolf18].""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Seaborn', '0.12.1'), + ('scanpy', '1.9.1'), # includes anndata + ('Pysam', '0.20.0'), + ('scikit-learn', '1.1.2'), + ('statsmodels', '0.13.1'), + ('numba', '0.56.4'), + ('python-igraph', '0.10.3'), + ('tbb', '2021.5.0'), +] + +# avoid hatchling requirement to install kneed +# (since installing it introduces conflicting version requirements with poetry included with Python) +local_preinstallopts_kneed = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ +local_preinstallopts_kneed += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ +local_preinstallopts_kneed += """-e 's/^license-files = .*//g' """ +local_preinstallopts_kneed += r"""-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ + +exts_list = [ + ('pyliftover', '0.4', { + 'checksums': ['72bcfb7de907569b0eb75e86c817840365297d63ba43a961da394187e399da41'], + }), + ('bamnostic', '1.1.8', { + 'checksums': ['b36b1f9239c1d2d614d2e449efe9a0705efe59ebec099f79ac9464f3b1ff5732'], + }), + ('python-louvain', '0.16', { + 'checksums': ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'], + 'modulename': 'community.community_louvain', + }), + ('get_version', '3.5.4', { + 'checksums': ['5901c846518d55d52c1f6f037f5d2433952b46bbf36e38c52f064ae836556343'], + }), + ('dunamai', '1.16.0', { + 'checksums': ['bfe8e23cc5a1ceed1c7f791674ea24cf832a53a5da73f046eeb43367ccfc3f77'], + }), + ('legacy-api-wrap', '1.2', { + 'checksums': ['034a44612da7e9943d3964363a98937ab54d55e3301075374abe0d521eb8101b'], + }), + ('kneed', '0.8.2', { + 'checksums': ['cbbd34e284f049cafa63f803cd3af0aff113d5347fb398942a74bff07ce6cc62'], + 'preinstallopts': local_preinstallopts_kneed, + }), + ('episcanpy', version, { + 'patches': ['epiScanpy-0.4.0_fix-import.patch'], + 'checksums': [ + {'episcanpy-0.4.0.tar.gz': '95739149db60521b0a14e4579f8ba87d410126ffb7b916abbc2d1aff3df40ce3'}, + {'epiScanpy-0.4.0_fix-import.patch': '593f8763a00159f3dae2aa42099a617e97b999c59cfa0452e013b7c820de4585'}, + ], + 'preinstallopts': "sed -i 's/tbb//' requirements.txt && ", + 'modulename': 'episcanpy.api', + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0_fix-import.patch b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0_fix-import.patch new file mode 100644 index 00000000000..08fa968b04a --- /dev/null +++ b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0_fix-import.patch @@ -0,0 +1,15 @@ +see https://github.com/colomemaria/epiScanpy/issues/130 + https://github.com/colomemaria/epiScanpy/pull/131 + +--- episcanpy-0.4.0/episcanpy/api/pl.py.orig 2023-03-13 15:00:13.363245608 +0100 ++++ episcanpy-0.4.0/episcanpy/api/pl.py 2023-03-13 15:01:02.729453156 +0100 +@@ -16,8 +16,8 @@ + from scanpy.plotting import umap, pca, diffmap, tsne, draw_graph + + from ..preprocessing._quality_control import cal_var, variability_features +-from ..preprocessing._tss_enrichment import tss_enrichment_plot as tss_enrichment +-from ..preprocessing._tss_enrichment import tss_enrichment_score_plot as tss_enrichment_socre ++from ..preprocessing._tss_enrichment import tss_enrichment_plot ++from ..preprocessing._tss_enrichment import tss_enrichment + + + From 9890ec1dfbf57abb79807d130e49ea1a14a07d72 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Mar 2023 15:36:22 +0100 Subject: [PATCH 6825/9987] adding easyconfigs: Longshot-0.4.5-GCCcore-11.3.0.eb --- .../Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d1e9278c0bf --- /dev/null +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +# Updated to 0.4.3 and GCCcore-10.2.0 +# J. Sassmannshausen (GSTT/NHS UK) +# +easyblock = 'Binary' + +name = 'Longshot' +version = '0.4.5' + +homepage = 'https://github.com/pjedge/longshot' +description = """Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific + Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs + a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can + be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'pjedge' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['7c9f570e17012b2fee386892ae64daf5f104d59adeb59dc7e710b876c1a11cad'] + +builddependencies = [ + ('binutils', '2.38'), + ('Rust', '1.65.0'), + ('Clang', '13.0.1'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +extract_sources = True + +install_cmd = "cargo install --root %(installdir)s --path ." + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' From 85b01b2b5f6b8331130ac386b32c37bdf87415e6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Mar 2023 15:38:30 +0100 Subject: [PATCH 6826/9987] adding easyconfigs: pygraphviz-1.10-GCCcore-11.3.0.eb --- .../pygraphviz-1.10-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6e55c05ccfb --- /dev/null +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'pygraphviz' +version = '1.10' + +homepage = 'https://pygraphviz.github.io/' +description = """PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. +With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz +graph data structure and layout algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('Graphviz', '5.0.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'sources': ['%(namelower)s-%(version)s.zip'], + 'checksums': ['457e093a888128903251a266a8cc16b4ba93f3f6334b3ebfed92c7471a74d867'], + }), +] + +moduleclass = 'vis' From 1f40fb78b046d190d451e352f201ccd9f2eae4ae Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Mar 2023 15:39:23 +0100 Subject: [PATCH 6827/9987] adding easyconfigs: PyVCF3-1.0.3-GCCcore-11.3.0.eb --- .../p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e836c431262 --- /dev/null +++ b/easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'PyVCF3' +version = '1.0.3' + +homepage = 'https://github.com/dridk/PyVCF3' +description = """A VCFv4.0 and 4.1 parser for Python. The intent of this module is to mimic the +csv module in the Python stdlib, as opposed to more flexible serialization +formats like JSON or YAML. vcf will attempt to parse the content of each record +based on the data types specified in the meta-information lines -- specifically +the ##INFO and ##FORMAT lines. If these lines are missing or incomplete, it +will check against the reserved types mentioned in the spec. Failing that, it +will just return strings. +PyVCF3 has been created because the Official PyVCF repository is no longer +maintained and do not accept any pull requests. This fork is for python 3 only +and has been published on pyPI as PyVCF3.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['4b16d71c8b97010487e2c939fb4d5707b7bbfa4e2b313df9dba3e372c5ba031d'], + 'modulename': 'vcf', + }), +] + +_pyvcf_scripts = ["vcf_filter.py", "vcf_melt", "vcf_sample_filter.py"] + +postinstallcmds = ["2to3 -w -n %%(installdir)s/bin/%s" % x for x in _pyvcf_scripts] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _pyvcf_scripts], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "vcf_filter.py --help", + "vcf_sample_filter.py --help" +] + +moduleclass = 'tools' From 39a759c91852832ba2eae728ccccd237c2f610ba Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Mar 2023 15:41:32 +0100 Subject: [PATCH 6828/9987] adding easyconfigs: wtdbg2-2.5-GCCcore-11.3.0.eb --- .../w/wtdbg2/wtdbg2-2.5-GCCcore-11.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d6728d4b544 --- /dev/null +++ b/easybuild/easyconfigs/w/wtdbg2/wtdbg2-2.5-GCCcore-11.3.0.eb @@ -0,0 +1,48 @@ +# Author:: Michael Dickens - TAMU HPRC - https://hprc.tamu.edu +# Updated to GCC 11.2.0 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'MakeCp' + +name = 'wtdbg2' +version = '2.5' + +homepage = 'https://github.com/ruanjue/wtdbg2' + +description = """ + Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio + or Oxford Nanopore Technologies (ONT). It assembles raw reads without error + correction and then builds the consensus from intermediate assembly output. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'ruanjue' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a2ffc8503d29f491a9a38ef63230d5b3c96db78377b5d25c91df511d0df06413'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Perl', '5.34.1')] + +prebuildopts = "sed -i 's/CFLAGS=-g3/CFLAGS+=-g3/g' Makefile && " + +local_executables = ['wtdbg2', 'wtdbg2.pl', 'wtpoa-cns', 'kbm2', 'wtdbg-cns', 'pgzf'] + +files_to_copy = [(local_executables, 'bin'), 'README-ori.md', 'README.md', 'scripts'] + +fix_perl_shebang_for = ['bin/*.pl', 'scripts/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables], + 'dirs': ['scripts'], +} + +sanity_check_commands = ["wtdbg2 --help"] + +modextrapaths = { + 'PATH': 'scripts', +} + +moduleclass = 'bio' From 34606bcddae8daaeb95d105d8dd541efbd91441e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Mar 2023 15:42:55 +0100 Subject: [PATCH 6829/9987] adding easyconfigs: minimap2-2.24-GCCcore-11.3.0.eb --- .../minimap2/minimap2-2.24-GCCcore-11.3.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..aea5a475d68 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.24-GCCcore-11.3.0.eb @@ -0,0 +1,53 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# DeepThought, Flinders University +# Updated to 2.22 +# R.QIAO + +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.24' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['9dd4c31ff082182948944bcdad6d328f64f09295d10547d72eba24189880a615'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('zlib', '1.2.12')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' From c7dc7eb50cc76213ebb8ae4647230565c2ad5e2e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Mar 2023 15:43:45 +0100 Subject: [PATCH 6830/9987] adding easyconfigs: Strainberry-1.1-foss-2022a.eb --- .../Strainberry/Strainberry-1.1-foss-2022a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/s/Strainberry/Strainberry-1.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/Strainberry/Strainberry-1.1-foss-2022a.eb b/easybuild/easyconfigs/s/Strainberry/Strainberry-1.1-foss-2022a.eb new file mode 100644 index 00000000000..76cac1f47a8 --- /dev/null +++ b/easybuild/easyconfigs/s/Strainberry/Strainberry-1.1-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = 'Tarball' + +name = 'Strainberry' +version = '1.1' + +homepage = 'https://github.com/rvicedomini/strainberry' +description = """Strainberry is a method that performs strain separation in low-complexity +metagenomes using error-prone long-read technologies. It exploits +state-of-the-art tools for variant calling, haplotype phasing, and genome +assembly, in order to achieve single-sample assembly of strains with higher +quality than other state-of-the-art long-read assemblers.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'rvicedomini' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['205829c75165653dc67d632cc1b48284b525452348af5ad8108de17e264b587b'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('Longshot', '0.4.5'), + ('minimap2', '2.24'), + ('MUMmer', '4.0.0rc1'), + ('networkx', '2.8.4'), + ('pygraphviz', '1.10'), + ('Pysam', '0.19.1'), + ('PyVCF3', '1.0.3'), + ('SAMtools', '1.16.1'), + ('wtdbg2', '2.5'), +] + +sanity_check_paths = { + 'files': ['strainberry'], + 'dirs': ['sberry'], +} + +sanity_check_commands = [ + "strainberry --help", + # Quick test that completes in a few minutes + ("cd %(builddir)s/%(namelower)s-%(version)s/example && " + "strainberry -r assembly.fasta -b alignment.sorted.bam -o sberry_out -c %(parallel)s"), +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 4edfdeb6f7d507b00c34747fccc408db484e5e8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2023 15:55:37 +0100 Subject: [PATCH 6831/9987] stick to Pysam 0.19.1 as dependency for epiScanpy 0.4.0 --- easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb index 8bb31672fdc..d2509af66ab 100644 --- a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('Seaborn', '0.12.1'), ('scanpy', '1.9.1'), # includes anndata - ('Pysam', '0.20.0'), + ('Pysam', '0.19.1'), ('scikit-learn', '1.1.2'), ('statsmodels', '0.13.1'), ('numba', '0.56.4'), From 4d2645a44d9935357401b6a0c01cbe47a843b6a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2023 15:58:37 +0100 Subject: [PATCH 6832/9987] add smoof/mlrMBO/emoa extensions to R 4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 871de6add89..6e214808845 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3448,6 +3448,15 @@ exts_list = [ ('MESS', '0.5.9', { 'checksums': ['b57dff943a130830a24d87fe2e8f8b766cf18398c9c09e0a020d5dd183f9d72d'], }), + ('smoof', '1.6.0.3', { + 'checksums': ['af8664b152876c545f6545528de6e05a289d0714103fac7afc52960a9a855fb1'], + }), + ('mlrMBO', '1.1.5.1', { + 'checksums': ['0cf26e5e9b180d15b932541cf081a552703a60edf762aafca9933c24ea91dc99'], + }), + ('emoa', '0.5-0.1', { + 'checksums': ['bff6c84274e9bdcbdb82d6edd90265844f7cd23f22abbf68d6b563ef48237966'], + }), ] moduleclass = 'lang' From e9a1397450b01c13cf1efef3c122349770176353 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 13 Mar 2023 15:59:12 +0100 Subject: [PATCH 6833/9987] adding easyconfigs: nichenetr-1.1.1-20230223-foss-2022a-R-4.2.1.eb --- ...enetr-1.1.1-20230223-foss-2022a-R-4.2.1.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/nichenetr/nichenetr-1.1.1-20230223-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/n/nichenetr/nichenetr-1.1.1-20230223-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/n/nichenetr/nichenetr-1.1.1-20230223-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..646ba5fd353 --- /dev/null +++ b/easybuild/easyconfigs/n/nichenetr/nichenetr-1.1.1-20230223-foss-2022a-R-4.2.1.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'nichenetr' +local_commit = 'cc3bced' +# see DESCRIPTION to determine version, +# but add date stamp of commit since version is not always bumped +version = '1.1.1-20230223' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/saeyslab/nichenetr' +description = """R implementation of the NicheNet method, + to predict active ligand-target links between interacting cells""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/saeyslab/nichenetr/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['522475bd8d5552062cc6d6ba095dae8c214e13b3c553c3e090b67a7c8c1723af'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 2f930b6e48126187db4958c3c170eb735e2d2923 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Mon, 13 Mar 2023 16:56:04 +0100 Subject: [PATCH 6834/9987] Make CI happy by having checksum in list Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb index 23dc38d67d5..19c0d49e463 100644 --- a/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb +++ b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb @@ -25,14 +25,14 @@ sanity_pip_check = True exts_list = [ ('mdurl', '0.1.2', { - 'checksum': 'bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba', + 'checksum': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], }), ('markdown-it-py', '2.2.0', { 'modulename': 'markdown_it', - 'checksum': '7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1', + 'checksum': ['7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1'], }), ('rich', '12.6.0', { - 'checksum': '125d96d20c92b946b983d0d392b84ff945461e5a06d3867e9f9e575f8697b67f', + 'checksum': ['125d96d20c92b946b983d0d392b84ff945461e5a06d3867e9f9e575f8697b67f'], }), (name, version, { 'sources': { @@ -40,7 +40,7 @@ exts_list = [ 'download_filename': 'lasso_python-%(version)s.tar.gz', }, 'modulename': 'lasso', - 'checksum': '67776e1876764680ac179fb750695aac63ecdbdf4f1ac8439f7e76fa3956727c', + 'checksum': ['67776e1876764680ac179fb750695aac63ecdbdf4f1ac8439f7e76fa3956727c'], }), ] From 2e019116d45cbc230635cd8e8f13e44634f185e9 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Mon, 13 Mar 2023 16:56:42 +0100 Subject: [PATCH 6835/9987] Simplify by using source_tmpl instead of sources Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb index 19c0d49e463..51609bc3ebe 100644 --- a/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb +++ b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb @@ -35,10 +35,7 @@ exts_list = [ 'checksum': ['125d96d20c92b946b983d0d392b84ff945461e5a06d3867e9f9e575f8697b67f'], }), (name, version, { - 'sources': { - 'filename': 'lasso_python-%(version)s.tar.gz', - 'download_filename': 'lasso_python-%(version)s.tar.gz', - }, + 'source_tmpl': 'lasso_python-%(version)s.tar.gz', 'modulename': 'lasso', 'checksum': ['67776e1876764680ac179fb750695aac63ecdbdf4f1ac8439f7e76fa3956727c'], }), From 7d4f84028dc64404f262d22fec95493129ece172 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Mon, 13 Mar 2023 17:04:43 +0100 Subject: [PATCH 6836/9987] Add checksums in list and simplify linear-operator sources --- .../GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb index 6cba5dc2c45..67487e0c4ae 100644 --- a/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb @@ -21,18 +21,15 @@ use_pip = True exts_list = [ ('linear-operator', '0.3.0', { - 'sources': [{ - 'filename': SOURCE_TAR_GZ, - 'download_filename': 'linear_operator-%(version)s.tar.gz', - }], - 'checksum': '84bf572631a7e1576de6920d81600ca0fedcf6bda2f29dbaf440d6e72ce6abab', + 'source_tmpl': 'linear_operator-%(version)s.tar.gz', + 'checksum': ['84bf572631a7e1576de6920d81600ca0fedcf6bda2f29dbaf440d6e72ce6abab'], }), ('joblib', '1.2.0', { - 'checksum': 'e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018', + 'checksum': ['e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018'], }), (name, version, { 'sources': [SOURCELOWER_TAR_GZ], - 'checksum': '0bdbba6f6d5957a0f43ef6dc7fec39c47e8a55f632ca33760c6189f259b3ccc3', + 'checksum': ['0bdbba6f6d5957a0f43ef6dc7fec39c47e8a55f632ca33760c6189f259b3ccc3'], }), ] From b717189a765f80d0590feef19b6d7bb4a59e53c2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Mar 2023 17:58:02 +0100 Subject: [PATCH 6837/9987] add missing pip sanity checks to pygraphviz v1.10 --- .../easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb index 6e55c05ccfb..54305dd65d6 100644 --- a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb @@ -24,4 +24,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'vis' From 94899e5edfd94384ed38b9f392686b2372ee0d11 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Mar 2023 18:02:17 +0100 Subject: [PATCH 6838/9987] add missing pip sanity checks to PyVCF v1.0.3 --- .../easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb index e836c431262..015c2b8562c 100644 --- a/easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb @@ -32,7 +32,12 @@ exts_list = [ _pyvcf_scripts = ["vcf_filter.py", "vcf_melt", "vcf_sample_filter.py"] -postinstallcmds = ["2to3 -w -n %%(installdir)s/bin/%s" % x for x in _pyvcf_scripts] +postinstallcmds = [ + # fix old scripts written for python 2, update is minor + "2to3 -w -n %%(installdir)s/bin/%s" % x for x in _pyvcf_scripts +] + +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/%s' % x for x in _pyvcf_scripts], From 7629152cf81af874ffd2c1d575464c0752d936e9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Mar 2023 18:13:20 +0100 Subject: [PATCH 6839/9987] add missing build dependency on binutils to pygraphviz v1.10 --- .../p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb index 54305dd65d6..b87232bf398 100644 --- a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.10-GCCcore-11.3.0.eb @@ -10,6 +10,10 @@ graph data structure and layout algorithms.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +builddependencies = [ + ('binutils', '2.38'), +] + dependencies = [ ('Python', '3.10.4'), ('Graphviz', '5.0.0'), From a501a287d87bd6053e9c9d29f4a5ad93f83b798c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 13 Mar 2023 18:16:42 +0100 Subject: [PATCH 6840/9987] add missing build dependency on binutils to PyVCF v1.0.3 --- easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb index 015c2b8562c..93af43ac5a9 100644 --- a/easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyVCF3/PyVCF3-1.0.3-GCCcore-11.3.0.eb @@ -17,6 +17,10 @@ and has been published on pyPI as PyVCF3.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +builddependencies = [ + ('binutils', '2.38'), +] + dependencies = [ ('Python', '3.10.4'), ] From 4c4d14760a4a8522ad217b8be6269629f2b03cce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Mon, 13 Mar 2023 18:59:39 +0100 Subject: [PATCH 6841/9987] Removed -DCMAKE_BUILD_TYPE --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb index 3f164d6bde2..3fa67ab84fb 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb @@ -26,9 +26,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DINSTALL_METIS_HEADERS=OFF ' -configopts += '-DCMAKE_BUILD_TYPE=Release ' -runtest = 'test' +# runtest = 'test' local_scotch_exec = ['acpl', 'amk_ccc', 'amk_fft2', 'amk_grf', 'amk_hy', 'amk_m2', 'amk_p2', 'atst', 'dggath', 'dgmap', 'dgord', From 3e9a2cfa18e715cfb0823394be459f28c21486f1 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 13 Mar 2023 22:05:50 +0100 Subject: [PATCH 6842/9987] adding vitessceR and itits dependencies --- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 52 +-------------- .../vitessceR-20230110-foss-2022a-R-4.2.1.eb | 63 +++++++++++++++++++ 2 files changed, 65 insertions(+), 50 deletions(-) create mode 100644 easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 36d3de6f295..aa7ed5b6054 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1152,56 +1152,8 @@ exts_list = [ ('ReactomePA', '1.40.0', { 'checksums': ['458b3febb341700414ca04ea4a6f3005061c9db97622cfdfda6b75a74415a7b9'], }), - ('flowClean', '1.34.1', { - 'checksums': ['d0e58ac89fd302761136cbcd5eb859351a61da2bd8967840bcd054ec16630f7f'], - }), - ('flowAI', '1.26.0', { - 'checksums': ['f4e35c824f68036cea5746236a026ad8e336c2595411d15d303d45fbc02526a5'], - }), - ('flowFP', '1.54.0', { - 'checksums': ['ba12d5bd4dc784997f30435314fe61f86b0c28d99c4458f7e8f9b76daa54b442'], - }), - ('simplifyEnrichment', '1.6.1', { - 'checksums': ['66fafb64d19c5fc4bb7aa6c6805130144f35fd508c2551024aec9f5c7b7b7461'], - }), - ('RPMG', '2.2-3', { - 'checksums': ['74d5bada6a51d280296cb36fae4938c16ba9ed2fa37f3bfb60cf7c541c5b22b6'], - }), - ('Rwave', '2.6-5', { - 'checksums': ['6c9ef75bb376f2e3f5c5dcd3b3fdca7d86797ce809da34f444632657189be2e4'], - }), - ('RSEIS', '4.1-4', { - 'checksums': ['76d5caf30cd3871fa80d27ea694023a4c303ffc099297aeeff03d22538dbff76'], - }), - ('splancs', '2.01-43', { - 'checksums': ['b351565e1f69f6c86a29d921d3a18d5896c4586e2ab8c73bb3df8e75630fc448'], - }), - ('MBA', '0.1-0', { - 'checksums': ['78039905c5b98be2bb79a5f292187a2aca21ef449daeefea58b0cac53a5283af'], - }), - ('GEOmap', '2.5-0', { - 'checksums': ['82e5608eda7330632bc67aa662b649e7b7b3ccdfda6a18a19d2e3379e0db1093'], - }), - ('RFOC', '3.4-6', { - 'checksums': ['0dfa237f4d04eb9a2718942b4d7ed9538fc5f89e3cbaa5a34a4fd1bc6fe54533'], - }), - ('flowDensity', '1.30.0', { - 'checksums': ['c321b395d6f1ae24d1428319401b225ae5e31fee5051127e43142d96f820103d'], - }), - ('flowPeaks', '1.42.0', { - 'checksums': ['ae98124c0574364bf8cd47be7704ad90b2b7d3dabbdd8df7744cbfaf81d665a8'], - }), - ('SamSPECTRAL', '1.50.0', { - 'checksums': ['b55de8cb2092d1b5c192ed0e4b47c421d888e5392165f28395241ca5884b8a5c'], - }), - ('ddPCRclust', '1.16.0', { - 'checksums': ['a457b78a2c254c69ed572d8dca01c66134d6ad2952f72097703110c1d663da5d'], - }), - ('feature', '1.2.15', { - 'checksums': ['de38292b7e800068a20824e2a9e7d5d4d0b465b7925db0d165346aa5030ff67b'], - }), - ('flowMerge', '2.44.0', { - 'checksums': ['ba143b5fff19207f323c1e7b7feaf56fa6e31700422d002521fe49e86bbc5e03'], + ('SpatialExperiment', '1.6.1', { + 'checksums': ['31e516e14e827e4b9fe853bc136066863dd762053012631c569ec3c00c6cbab5'], }), ] diff --git a/easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..73b0e62c47c --- /dev/null +++ b/easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb @@ -0,0 +1,63 @@ +easyblock = 'Bundle' + +name = 'vitessceR' +version = '20230110' +versionsuffix = '-R-%(rver)s' +local_commit = '8c67168' + +homepage = 'https://github.com/vitessce/vitessceR' +description = "Vitessce is a visual integration tool for exploration of spatial single-cell experiments." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('libsodium', '1.0.18'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.rstudio.com/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('webutils', '1.1', { + 'checksums': ['33e2b408d2b9ca12e158e0007d4a55a3ace6838341ad944344de2ceb806e4699'], + }), + ('sodium', '1.2.1', { + 'checksums': ['f76e98969710af8b6c7c7decf63706d91185eebf8a266475b554d5ad95f803a8'], + }), + ('swagger', '3.33.1', { + 'checksums': ['528369b04c6142112e05ee8b950ca1c01b3e390a4515eacb0fa17db98bafafd1'], + }), + ('plumber', '1.2.1', { + 'checksums': ['6ffc13e5ce1ff7ec81f6a4ab04eb1cb9f6da4004cf205ba3098d2ec4a83f1ecc'], + }), + ('varhandle', '2.0.5', { + 'checksums': ['9b0ee653e0343e292547d2a7052e60a2e7d97d1d5528246862522e67346882d0'], + }), + (name, version, { + 'source_urls': ['https://github.com/vitessce/vitessceR/archive/'], + 'sources': [{'download_filename': '8c67168.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['3a8805f989b28820e23e2c2578838fe3231e2ee3cb0051559787fe2d0eb27256'], + }), +] + +modextrapaths = { + 'R_LIBS_SITE': '', +} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From dc0661e397fc274210ab0c48ddf44702bf8e0337 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 13 Mar 2023 21:15:04 +0000 Subject: [PATCH 6843/9987] Update R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb fixing mistake - not the latest EC --- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index aa7ed5b6054..72d0887ac92 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1152,6 +1152,57 @@ exts_list = [ ('ReactomePA', '1.40.0', { 'checksums': ['458b3febb341700414ca04ea4a6f3005061c9db97622cfdfda6b75a74415a7b9'], }), + ('flowClean', '1.34.1', { + 'checksums': ['d0e58ac89fd302761136cbcd5eb859351a61da2bd8967840bcd054ec16630f7f'], + }), + ('flowAI', '1.26.0', { + 'checksums': ['f4e35c824f68036cea5746236a026ad8e336c2595411d15d303d45fbc02526a5'], + }), + ('flowFP', '1.54.0', { + 'checksums': ['ba12d5bd4dc784997f30435314fe61f86b0c28d99c4458f7e8f9b76daa54b442'], + }), + ('simplifyEnrichment', '1.6.1', { + 'checksums': ['66fafb64d19c5fc4bb7aa6c6805130144f35fd508c2551024aec9f5c7b7b7461'], + }), + ('RPMG', '2.2-3', { + 'checksums': ['74d5bada6a51d280296cb36fae4938c16ba9ed2fa37f3bfb60cf7c541c5b22b6'], + }), + ('Rwave', '2.6-5', { + 'checksums': ['6c9ef75bb376f2e3f5c5dcd3b3fdca7d86797ce809da34f444632657189be2e4'], + }), + ('RSEIS', '4.1-4', { + 'checksums': ['76d5caf30cd3871fa80d27ea694023a4c303ffc099297aeeff03d22538dbff76'], + }), + ('splancs', '2.01-43', { + 'checksums': ['b351565e1f69f6c86a29d921d3a18d5896c4586e2ab8c73bb3df8e75630fc448'], + }), + ('MBA', '0.1-0', { + 'checksums': ['78039905c5b98be2bb79a5f292187a2aca21ef449daeefea58b0cac53a5283af'], + }), + ('GEOmap', '2.5-0', { + 'checksums': ['82e5608eda7330632bc67aa662b649e7b7b3ccdfda6a18a19d2e3379e0db1093'], + }), + ('RFOC', '3.4-6', { + 'checksums': ['0dfa237f4d04eb9a2718942b4d7ed9538fc5f89e3cbaa5a34a4fd1bc6fe54533'], + }), + ('flowDensity', '1.30.0', { + 'checksums': ['c321b395d6f1ae24d1428319401b225ae5e31fee5051127e43142d96f820103d'], + }), + ('flowPeaks', '1.42.0', { + 'checksums': ['ae98124c0574364bf8cd47be7704ad90b2b7d3dabbdd8df7744cbfaf81d665a8'], + }), + ('SamSPECTRAL', '1.50.0', { + 'checksums': ['b55de8cb2092d1b5c192ed0e4b47c421d888e5392165f28395241ca5884b8a5c'], + }), + ('ddPCRclust', '1.16.0', { + 'checksums': ['a457b78a2c254c69ed572d8dca01c66134d6ad2952f72097703110c1d663da5d'], + }), + ('feature', '1.2.15', { + 'checksums': ['de38292b7e800068a20824e2a9e7d5d4d0b465b7925db0d165346aa5030ff67b'], + }), + ('flowMerge', '2.44.0', { + 'checksums': ['ba143b5fff19207f323c1e7b7feaf56fa6e31700422d002521fe49e86bbc5e03'], + }), ('SpatialExperiment', '1.6.1', { 'checksums': ['31e516e14e827e4b9fe853bc136066863dd762053012631c569ec3c00c6cbab5'], }), From 8b2e24f57762be380ebd12051261942ed65dc0ee Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 14 Mar 2023 01:45:40 +0100 Subject: [PATCH 6844/9987] Fixed name in comment --- easybuild/easyconfigs/g/genomepy/genomepy-0.15.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/genomepy/genomepy-0.15.0-foss-2022a.eb b/easybuild/easyconfigs/g/genomepy/genomepy-0.15.0-foss-2022a.eb index 4d8751a3fb2..916e6419964 100644 --- a/easybuild/easyconfigs/g/genomepy/genomepy-0.15.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/genomepy/genomepy-0.15.0-foss-2022a.eb @@ -21,7 +21,7 @@ dependencies = [ use_pip = True -# avoid hatchling requirement to install infercnvpy +# avoid hatchling requirement to install genomepy # (since installing it introduces conflicting version requirements with poetry included with Python) local_preinstallopts = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ local_preinstallopts += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ From 0d45fdb5ab691e010c9ef1bc91a44280a3b81321 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 14 Mar 2023 00:57:54 +0000 Subject: [PATCH 6845/9987] Update vitessceR-20230110-foss-2022a-R-4.2.1.eb comment, small fix --- .../v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb index 73b0e62c47c..834832d3113 100644 --- a/easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb @@ -1,6 +1,7 @@ easyblock = 'Bundle' name = 'vitessceR' +# the github repo has no releases / tags, that's why we have to use commit... version = '20230110' versionsuffix = '-R-%(rver)s' local_commit = '8c67168' @@ -46,7 +47,10 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://github.com/vitessce/vitessceR/archive/'], - 'sources': [{'download_filename': '8c67168.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': '%(name)s-%(version)s.tar.gz' + }], 'checksums': ['3a8805f989b28820e23e2c2578838fe3231e2ee3cb0051559787fe2d0eb27256'], }), ] From 6eb15435bbe4fd3307d7a8a75141cddb38c49c12 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 Mar 2023 08:00:52 +0100 Subject: [PATCH 6846/9987] adding easyconfigs: CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb, pytest-7.2.2-GCCcore-11.2.0.eb --- .../CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb | 59 +++++++++++++++ .../p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb | 71 +++++++++++++++++++ 2 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb create mode 100644 easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000000..62fd8a72ed5 --- /dev/null +++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'CuPy' +version = '11.4.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://cupy.dev' +description = "CuPy is an open-source array library accelerated with NVIDIA CUDA." + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('pytest', '7.2.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('CUDA', '11.4.1', '', SYSTEM), + ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.10.3', versionsuffix), + ('cuTENSOR', '1.6.1.5', versionsuffix, SYSTEM), + # ('cuSPARSELt', '0.3.0.3', versionsuffix, SYSTEM), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# A bunch of the tests are failing or are just having problems. +_skip_tests = [ + 'tests/cupyx_tests/scipy_tests', + 'tests/cupyx_tests/distributed_tests', + 'tests/cupyx_tests/tools_tests', + 'tests/example_tests', + 'tests/cupy_tests/testing_tests/test_parameterized.py', + 'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_', + 'tests/cupy_tests/fft_tests/test_fft.py', +] +_ignore_list = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('fastrlock', '0.5', { + 'checksums': ['9ae1a31f6e069b5f0f28ba63c594d0c952065de0a375f7b491d21ebaccc5166f'], + }), + ('cupy', version, { + 'runtest': "export CUPY_TEST_GPU_LIMIT=1 && pytest --ignore=tests/cupyx_tests/scipy_tests --ignore=tests/cupyx_tests/distributed_tests --ignore=tests/cupyx_tests/tools_tests --ignore=tests/example_tests --ignore=tests/cupy_tests/testing_tests/test_parameterized.py --ignore=tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_ --ignore=tests/cupy_tests/fft_tests/test_fft.py tests", + 'testinstall': True, + 'checksums': ['03d52b2626e02a3a2b46d714c1cd03e702c8fe33915fcca6ed8de5c539964f49'], + }), +] + +sanity_check_commands = [ + "python -c 'import cupy'", +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..7a10fc0c9b0 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.2.2' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('binutils', '2.37'), + ('Python', '3.9.6'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('setuptools-scm', '7.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('flit-core', '3.8.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': ['b305b30c99526df5e63d6022dd2310a0a941a187bd3884f4c8ef0418df6c39f3'], + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.0', { + 'checksums': ['bcb67d800a4497e1b404c2dd44fca47d3b7a5e5433dbab67f96c1a685cdfdf23'], + }), + ('hypothesis', '6.54.6', { + 'checksums': ['2d5e2d5ccd0efce4e0968a6164f4e4853f808e33f4d91490c975c98beec0c7c3'], + }), + ('elementpath', '4.0.1', { + 'checksums': ['1162e4c8e5501bd36291b668f4449b8125fea5ef64a26da8d71da31126725aa5'], + }), + ('xmlschema', '2.2.2', { + 'checksums': ['0caa96668807b4b51c42a0fe2b6610752bc59f069615df3e34dcfffb962973fd'], + }), + (name, version, { + 'checksums': ['c99ab0c73aceb050f68929bc93af19ab6db0558791c6a0715723abe9d0ade9d4'], + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' From cc94864a2a48ad4a2952fd1baddff1a4a9e7a787 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 14 Mar 2023 08:22:36 +0100 Subject: [PATCH 6847/9987] Fix too long lines. --- .../easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb | 4 +++- easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb | 3 ++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb index 62fd8a72ed5..5108d852855 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb @@ -44,7 +44,9 @@ exts_list = [ 'checksums': ['9ae1a31f6e069b5f0f28ba63c594d0c952065de0a375f7b491d21ebaccc5166f'], }), ('cupy', version, { - 'runtest': "export CUPY_TEST_GPU_LIMIT=1 && pytest --ignore=tests/cupyx_tests/scipy_tests --ignore=tests/cupyx_tests/distributed_tests --ignore=tests/cupyx_tests/tools_tests --ignore=tests/example_tests --ignore=tests/cupy_tests/testing_tests/test_parameterized.py --ignore=tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_ --ignore=tests/cupy_tests/fft_tests/test_fft.py tests", + # Must run tests here since the required version of pytest is a builddep + # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory. + 'runtest': "export CUPY_TEST_GPU_LIMIT=1 && pytest --ignore=%s tests" % _ignore_list, 'testinstall': True, 'checksums': ['03d52b2626e02a3a2b46d714c1cd03e702c8fe33915fcca6ed8de5c539964f49'], }), diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb index 7a10fc0c9b0..34d5c8cdb7e 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb @@ -63,7 +63,8 @@ exts_list = [ sanity_check_commands = [ "python -c 'import pytest'", - 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' % _ignore_tests, + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, ] sanity_pip_check = True From 75567c4d6ddc5062c9843bbb66d2f434f0861759 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 14 Mar 2023 10:52:53 +0100 Subject: [PATCH 6848/9987] Update according to review suggestion --- .../g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb index 67487e0c4ae..9cea5b81569 100644 --- a/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/g/GPyTorch/GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb @@ -16,20 +16,19 @@ dependencies = [ ('scikit-learn', '0.24.2'), ] -download_dep_fail = True use_pip = True exts_list = [ ('linear-operator', '0.3.0', { 'source_tmpl': 'linear_operator-%(version)s.tar.gz', - 'checksum': ['84bf572631a7e1576de6920d81600ca0fedcf6bda2f29dbaf440d6e72ce6abab'], + 'checksums': ['84bf572631a7e1576de6920d81600ca0fedcf6bda2f29dbaf440d6e72ce6abab'], }), ('joblib', '1.2.0', { - 'checksum': ['e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018'], + 'checksums': ['e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018'], }), (name, version, { 'sources': [SOURCELOWER_TAR_GZ], - 'checksum': ['0bdbba6f6d5957a0f43ef6dc7fec39c47e8a55f632ca33760c6189f259b3ccc3'], + 'checksums': ['0bdbba6f6d5957a0f43ef6dc7fec39c47e8a55f632ca33760c6189f259b3ccc3'], }), ] From 851e693b267b493c579b7a913d720708e18c0fbb Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 14 Mar 2023 11:18:25 +0100 Subject: [PATCH 6849/9987] Fix typo 'checksum' -> 'checksums' Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb index 51609bc3ebe..a79d5b26122 100644 --- a/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb +++ b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb @@ -25,19 +25,19 @@ sanity_pip_check = True exts_list = [ ('mdurl', '0.1.2', { - 'checksum': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], }), ('markdown-it-py', '2.2.0', { 'modulename': 'markdown_it', - 'checksum': ['7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1'], + 'checksums': ['7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1'], }), ('rich', '12.6.0', { - 'checksum': ['125d96d20c92b946b983d0d392b84ff945461e5a06d3867e9f9e575f8697b67f'], + 'checksums': ['125d96d20c92b946b983d0d392b84ff945461e5a06d3867e9f9e575f8697b67f'], }), (name, version, { 'source_tmpl': 'lasso_python-%(version)s.tar.gz', 'modulename': 'lasso', - 'checksum': ['67776e1876764680ac179fb750695aac63ecdbdf4f1ac8439f7e76fa3956727c'], + 'checksums': ['67776e1876764680ac179fb750695aac63ecdbdf4f1ac8439f7e76fa3956727c'], }), ] From b51f839cec7ea75171c996bb37ce8775f8102192 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 14 Mar 2023 10:29:12 +0000 Subject: [PATCH 6850/9987] Update easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb --- .../easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb index 934f8d2c337..d20e6c93833 100644 --- a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.1-foss-2022a.eb @@ -31,7 +31,7 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('mappy', '2.24', { + ('mappy', _minimap2_ver, { 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], }), ('natsort', '8.3.1', { From a4d3c3fb396f6569ceaec4a21b46f7c3fa1cc00e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Mar 2023 11:51:38 +0100 Subject: [PATCH 6851/9987] add back comment on stripping out tbb requirement for epiScanpy --- .../easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb index d2509af66ab..c990d84ebe5 100644 --- a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2022a.eb @@ -61,6 +61,9 @@ exts_list = [ {'episcanpy-0.4.0.tar.gz': '95739149db60521b0a14e4579f8ba87d410126ffb7b916abbc2d1aff3df40ce3'}, {'epiScanpy-0.4.0_fix-import.patch': '593f8763a00159f3dae2aa42099a617e97b999c59cfa0452e013b7c820de4585'}, ], + # strip out tbb as required dependency, to ensure that 'pip check' passes; + # note that the tbb Python bindings are actually provided by the tbb dependency, + # but pip doesn't know about them due to the way in which they were installed... 'preinstallopts': "sed -i 's/tbb//' requirements.txt && ", 'modulename': 'episcanpy.api', }), From 76ddb33fd7d4851f046c87f8d4b192b562dc7a25 Mon Sep 17 00:00:00 2001 From: lenocil Date: Tue, 14 Mar 2023 13:27:56 +0100 Subject: [PATCH 6852/9987] Added easyconfig for Apache Avro C++ --- .../a/avrocpp-1.11.1-GCC-11.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..2bb4e395f6a --- /dev/null +++ b/easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'Binary' + +name = 'avrocpp' +version = '1.11.1' + +homepage = 'https://avro.apache.org/docs/1.11.1/api/cpp/html/' +description = """Avro C++ is a C++ data serialization library .""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/apache/avro/archive/refs/tags/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['599f96bb405f72a35154b2477caa6254d723bb4e3f6a0e54e9ae540664321752'] + +builddependencies = [ + ('binutils', '2.37', '', ('GCCcore', '11.2.0')), + ('CMake', '3.22.1', '', ('GCCcore', '11.2.0')), +] +dependencies = [ + ('Boost', '1.77.0'), +] + + +extract_sources = True + +install_cmd = "cd lang/c++; mkdir -p build; cd build && " +install_cmd += ' cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=%(installdir)s/ -DCMAKE_BUILD_TYPE=Release .. && ' +install_cmd += " make install" + + +sanity_check_paths = { + 'files': ["%(installdir)s/bin/avrogencpp"], + 'dirs': ["%(installdir)s/lib"], +} + +sanity_check_commands = ["%(installdir)s/bin/avrogencpp -h"] + +moduleclass = 'lib' From f5a2a0c019a3864359e02dbb11bda43760790b7a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 14 Mar 2023 13:43:52 +0100 Subject: [PATCH 6853/9987] update homepage and source url --- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-GCC-8.3.0.eb | 4 ++-- .../easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb | 4 ++-- easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2019a.eb | 4 ++-- .../d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.2.0.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-GCC-8.3.0.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-GCC-8.3.0.eb index 318ab375578..57198d99c60 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-GCC-8.3.0.eb @@ -3,13 +3,13 @@ easyblock = 'MakeCp' name = 'DFT-D3' version = '3.2.0' -homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +homepage = 'https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3' description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" toolchain = {'name': 'GCC', 'version': '8.3.0'} -source_urls = ['https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3'] +source_urls = ['https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3'] # Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version # numbering. Also, the authors are prone (alas) to stealth upgrades, so that two # tarballs with the same version number can have different checksums. For this diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb index 113163554cd..29e0a67ce67 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-iccifort-2020.4.304.eb @@ -3,13 +3,13 @@ easyblock = 'MakeCp' name = 'DFT-D3' version = '3.2.0' -homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +homepage = 'https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3' description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3'] +source_urls = ['https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3'] sources = [{'download_filename': 'dftd3.tgz', 'filename': SOURCELOWER_TGZ}] checksums = ['d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59'] diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2019a.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2019a.eb index 85354a2bf7e..ce6a66aa85f 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2019a.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-2019a.eb @@ -3,13 +3,13 @@ easyblock = 'MakeCp' name = 'DFT-D3' version = '3.2.0' -homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +homepage = 'https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3' description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" toolchain = {'name': 'intel', 'version': '2019a'} -source_urls = ['https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3'] +source_urls = ['https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3'] # Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version # numbering. Also, the authors are prone (alas) to stealth upgrades, so that two # tarballs with the same version number can have different checksums. For this diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.2.0.eb index 88dfa0f4cac..98c1e9d2d9b 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.2.0.eb @@ -3,13 +3,13 @@ easyblock = 'MakeCp' name = 'DFT-D3' version = '3.2.0' -homepage = 'http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english' +homepage = 'https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3' description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods.""" toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} -source_urls = ['https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3'] +source_urls = ['https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3'] # Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version # numbering. Also, the authors are prone (alas) to stealth upgrades, so that two # tarballs with the same version number can have different checksums. For this From 8df2af85d38bc7c0e127852cb1875439b9486bdd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 14 Mar 2023 13:48:35 +0100 Subject: [PATCH 6854/9987] adding easyconfigs: DFT-D3-3.2.0-intel-compilers-2021.4.0.eb --- .../DFT-D3-3.2.0-intel-compilers-2021.4.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..b96425d6029 --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.4.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'DFT-D3' +version = '3.2.0' + +homepage = 'https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3' +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical + quantum chemical methods.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3'] +# Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version +# numbering. Also, the authors are prone (alas) to stealth upgrades, so that two +# tarballs with the same version number can have different checksums. For this +# reason, it is suggested to manually download and rename the tarball. The +# checksum may also need updating from time to time. +# Checksum last updated: 20 September 2018 +# Date tarball was reported to have been modified: 14 June 2016 +sources = [{'download_filename': 'dftd3.tgz', 'filename': SOURCELOWER_TGZ}] +checksums = ['d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59'] + +prebuildopts = "sed -i 's/OSTYPE=LINUXL/OSTYPE=LINUXI/' Makefile && " + +files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/dftd3'], + 'dirs': [], +} + +moduleclass = 'chem' From ffafbcfe7be5f97f40d91bd306ddb56606d1d7c1 Mon Sep 17 00:00:00 2001 From: lenocil Date: Tue, 14 Mar 2023 13:50:20 +0100 Subject: [PATCH 6855/9987] Added easyconfig for Apache Avro C++ --- .../easyconfigs/a/{ => avrocpp}/avrocpp-1.11.1-GCC-11.2.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/{ => avrocpp}/avrocpp-1.11.1-GCC-11.2.0.eb (100%) diff --git a/easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb similarity index 100% rename from easybuild/easyconfigs/a/avrocpp-1.11.1-GCC-11.2.0.eb rename to easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb From 8abed2f6bd999003c99123d8ba1248c3835cf42e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 14 Mar 2023 13:50:39 +0100 Subject: [PATCH 6856/9987] add sanity check command --- .../d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.4.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.4.0.eb index b96425d6029..2ef036162ce 100644 --- a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2021.4.0.eb @@ -29,4 +29,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['dftd3'] + moduleclass = 'chem' From 7867da4ec5b0d0ac8a1ba7abe5e246ae6fdb0d7c Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Tue, 14 Mar 2023 13:13:49 +0000 Subject: [PATCH 6857/9987] Correct checksum for rich --- .../l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb index a79d5b26122..df13c6cd070 100644 --- a/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb +++ b/easybuild/easyconfigs/l/LASSO-Python/LASSO-Python-2.0.0-foss-2022b.eb @@ -32,11 +32,11 @@ exts_list = [ 'checksums': ['7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1'], }), ('rich', '12.6.0', { - 'checksums': ['125d96d20c92b946b983d0d392b84ff945461e5a06d3867e9f9e575f8697b67f'], + 'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'], }), (name, version, { - 'source_tmpl': 'lasso_python-%(version)s.tar.gz', 'modulename': 'lasso', + 'source_tmpl': 'lasso_python-%(version)s.tar.gz', 'checksums': ['67776e1876764680ac179fb750695aac63ecdbdf4f1ac8439f7e76fa3956727c'], }), ] From bfdb6c5f7ddf170a7707f35e57d34c320c436035 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 14 Mar 2023 14:25:58 +0100 Subject: [PATCH 6858/9987] adding easyconfigs: PfamScan-1.6-gompi-2022a.eb --- .../p/PfamScan/PfamScan-1.6-gompi-2022a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/p/PfamScan/PfamScan-1.6-gompi-2022a.eb diff --git a/easybuild/easyconfigs/p/PfamScan/PfamScan-1.6-gompi-2022a.eb b/easybuild/easyconfigs/p/PfamScan/PfamScan-1.6-gompi-2022a.eb new file mode 100644 index 00000000000..a9052e98cbf --- /dev/null +++ b/easybuild/easyconfigs/p/PfamScan/PfamScan-1.6-gompi-2022a.eb @@ -0,0 +1,57 @@ +easyblock = 'Tarball' + +name = 'PfamScan' +version = '1.6' + +homepage = 'https://www.ebi.ac.uk/seqdb/confluence/display/THD/PfamScan' +description = "PfamScan is used to search a FASTA sequence against a library of Pfam HMM." + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/'] +sources = [{'download_filename': '%(name)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['365c96bc150d5057349c3016d62667c58cb33afcfb6329457ae16ab5aae4f401'] + +builddependencies = [ + ('wget', '1.21.3'), # needed to fetch Pfam DB + ('gzip', '1.12'), # needed to decompress Pfam DB +] + +dependencies = [ + ('Perl', '5.34.1'), + ('BioPerl', '1.7.8'), + ('HMMER', '3.3.2'), +] + +fix_perl_shebang_for = ['*.pl'] + +sanity_check_paths = { + 'files': ['pfam_scan.pl'], + 'dirs': ['Bio/Pfam'], +} + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} + +sanity_check_commands = [ + ('perl', '-e "use Bio::Pfam::Scan::PfamScan"'), + ('pfam_scan.pl', '--help'), +] + +# Download Pfam database (280 MB download, 1.5 GB on disk) +# _pfam_db_dir = '%(installdir)s/db' +# _pfam_db_url = 'https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release' +# postinstallcmds = [ +# "mkdir -p %s" % _pfam_db_dir, +# "wget -P %s %s/{Pfam-A.hmm.gz,Pfam-A.hmm.dat.gz,active_site.dat.gz}" % (_pfam_db_dir, _pfam_db_url), +# "gzip -d %s/*.gz" % _pfam_db_dir, +# "hmmpress %s/Pfam-A.hmm" % _pfam_db_dir, +# ] +# +# modloadmsg = """ +# Pfam database dir is located at %s +# """ % _pfam_db_dir + +moduleclass = 'bio' From ef9a8a97b790ef3e36beda7b705ba022145f66d8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 14 Mar 2023 15:35:53 +0100 Subject: [PATCH 6859/9987] remove trailing spaces from PfamScan v1.6 --- easybuild/easyconfigs/p/PfamScan/PfamScan-1.6-gompi-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PfamScan/PfamScan-1.6-gompi-2022a.eb b/easybuild/easyconfigs/p/PfamScan/PfamScan-1.6-gompi-2022a.eb index a9052e98cbf..25cfa8d8237 100644 --- a/easybuild/easyconfigs/p/PfamScan/PfamScan-1.6-gompi-2022a.eb +++ b/easybuild/easyconfigs/p/PfamScan/PfamScan-1.6-gompi-2022a.eb @@ -37,7 +37,7 @@ modextrapaths = { sanity_check_commands = [ ('perl', '-e "use Bio::Pfam::Scan::PfamScan"'), - ('pfam_scan.pl', '--help'), + ('pfam_scan.pl', '--help'), ] # Download Pfam database (280 MB download, 1.5 GB on disk) @@ -49,7 +49,7 @@ sanity_check_commands = [ # "gzip -d %s/*.gz" % _pfam_db_dir, # "hmmpress %s/Pfam-A.hmm" % _pfam_db_dir, # ] -# +# # modloadmsg = """ # Pfam database dir is located at %s # """ % _pfam_db_dir From 0a20dbb75d8c42aede81879d38eeaab6aecdbeec Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 14 Mar 2023 16:04:47 +0100 Subject: [PATCH 6860/9987] adding easyconfigs: sympy-1.10.1-intel-2022a.eb --- .../s/sympy/sympy-1.10.1-intel-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb new file mode 100644 index 00000000000..ef36e3b6591 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.10.1' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['5939eeffdf9e152172601463626c022a2c27e75cf6278de8d401d50c9d58787b'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('gmpy2', '2.1.2'), +] + +download_dep_fail = True +use_pip = True + +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +sanity_check_commands = ["isympy --help"] + +moduleclass = 'math' From 1e8b2ae9da665384167401cda4b67fe4f12d4976 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 14 Mar 2023 16:40:53 +0100 Subject: [PATCH 6861/9987] changes from code review --- .../easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 15 ++++++ ...sceR-0.99.0-20230110-foss-2022a-R-4.2.1.eb | 52 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/v/vitessceR/vitessceR-0.99.0-20230110-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 6e214808845..0ceadb41367 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3457,6 +3457,21 @@ exts_list = [ ('emoa', '0.5-0.1', { 'checksums': ['bff6c84274e9bdcbdb82d6edd90265844f7cd23f22abbf68d6b563ef48237966'], }), + ('webutils', '1.1', { + 'checksums': ['33e2b408d2b9ca12e158e0007d4a55a3ace6838341ad944344de2ceb806e4699'], + }), + ('sodium', '1.2.1', { + 'checksums': ['f76e98969710af8b6c7c7decf63706d91185eebf8a266475b554d5ad95f803a8'], + }), + ('swagger', '3.33.1', { + 'checksums': ['528369b04c6142112e05ee8b950ca1c01b3e390a4515eacb0fa17db98bafafd1'], + }), + ('plumber', '1.2.1', { + 'checksums': ['6ffc13e5ce1ff7ec81f6a4ab04eb1cb9f6da4004cf205ba3098d2ec4a83f1ecc'], + }), + ('varhandle', '2.0.5', { + 'checksums': ['9b0ee653e0343e292547d2a7052e60a2e7d97d1d5528246862522e67346882d0'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/v/vitessceR/vitessceR-0.99.0-20230110-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/v/vitessceR/vitessceR-0.99.0-20230110-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..b9977258fd2 --- /dev/null +++ b/easybuild/easyconfigs/v/vitessceR/vitessceR-0.99.0-20230110-foss-2022a-R-4.2.1.eb @@ -0,0 +1,52 @@ +easyblock = 'Bundle' + +name = 'vitessceR' +# the github repo has no releases / tags, that's why we have to use commit... +version = '0.99.0-20230110' +versionsuffix = '-R-%(rver)s' +local_commit = '8c67168' + +homepage = 'https://github.com/vitessce/vitessceR' +description = "Vitessce is a visual integration tool for exploration of spatial single-cell experiments." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('libsodium', '1.0.18'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.rstudio.com/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/vitessce/vitessceR/archive/'], + 'sources': [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': '%(name)s-%(version)s.tar.gz' + }], + 'checksums': ['3a8805f989b28820e23e2c2578838fe3231e2ee3cb0051559787fe2d0eb27256'], + }), +] + +modextrapaths = { + 'R_LIBS_SITE': '', +} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 0bb926433a09d6ca466b38c651e411eef96ee066 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 14 Mar 2023 15:42:40 +0000 Subject: [PATCH 6862/9987] Delete vitessceR-20230110-foss-2022a-R-4.2.1.eb deleting duplicate (changed version suffix, therefore new file was created) --- .../vitessceR-20230110-foss-2022a-R-4.2.1.eb | 67 ------------------- 1 file changed, 67 deletions(-) delete mode 100644 easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb deleted file mode 100644 index 834832d3113..00000000000 --- a/easybuild/easyconfigs/v/vitessceR/vitessceR-20230110-foss-2022a-R-4.2.1.eb +++ /dev/null @@ -1,67 +0,0 @@ -easyblock = 'Bundle' - -name = 'vitessceR' -# the github repo has no releases / tags, that's why we have to use commit... -version = '20230110' -versionsuffix = '-R-%(rver)s' -local_commit = '8c67168' - -homepage = 'https://github.com/vitessce/vitessceR' -description = "Vitessce is a visual integration tool for exploration of spatial single-cell experiments." - -toolchain = {'name': 'foss', 'version': '2022a'} - -dependencies = [ - ('R', '4.2.1'), - ('R-bundle-Bioconductor', '3.15', versionsuffix), - ('libsodium', '1.0.18'), -] - -exts_defaultclass = 'RPackage' -exts_filter = ("R -q --no-save", "library(%(ext_name)s)") - -exts_default_options = { - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/', - 'https://cran.rstudio.com/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', - ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz', -} - -exts_list = [ - ('webutils', '1.1', { - 'checksums': ['33e2b408d2b9ca12e158e0007d4a55a3ace6838341ad944344de2ceb806e4699'], - }), - ('sodium', '1.2.1', { - 'checksums': ['f76e98969710af8b6c7c7decf63706d91185eebf8a266475b554d5ad95f803a8'], - }), - ('swagger', '3.33.1', { - 'checksums': ['528369b04c6142112e05ee8b950ca1c01b3e390a4515eacb0fa17db98bafafd1'], - }), - ('plumber', '1.2.1', { - 'checksums': ['6ffc13e5ce1ff7ec81f6a4ab04eb1cb9f6da4004cf205ba3098d2ec4a83f1ecc'], - }), - ('varhandle', '2.0.5', { - 'checksums': ['9b0ee653e0343e292547d2a7052e60a2e7d97d1d5528246862522e67346882d0'], - }), - (name, version, { - 'source_urls': ['https://github.com/vitessce/vitessceR/archive/'], - 'sources': [{ - 'download_filename': '%s.tar.gz' % local_commit, - 'filename': '%(name)s-%(version)s.tar.gz' - }], - 'checksums': ['3a8805f989b28820e23e2c2578838fe3231e2ee3cb0051559787fe2d0eb27256'], - }), -] - -modextrapaths = { - 'R_LIBS_SITE': '', -} - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -moduleclass = 'bio' From c7212533ce2140348fe1abe0e53300782de373b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 14 Mar 2023 19:42:11 +0100 Subject: [PATCH 6863/9987] Update easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb --- .../easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb index 5108d852855..a665a1371c4 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb @@ -46,7 +46,8 @@ exts_list = [ ('cupy', version, { # Must run tests here since the required version of pytest is a builddep # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory. - 'runtest': "export CUPY_TEST_GPU_LIMIT=1 && pytest --ignore=%s tests" % _ignore_list, + 'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && pytest --ignore=%s tests' %\ + _ignore_list, 'testinstall': True, 'checksums': ['03d52b2626e02a3a2b46d714c1cd03e702c8fe33915fcca6ed8de5c539964f49'], }), From 3b67b31edced04c9539e5faea0dc36fd537f6151 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 15 Mar 2023 02:39:51 +0100 Subject: [PATCH 6864/9987] adding easyconfigs: gmsh-4.11.1-foss-2022a.eb, occt-7.5.0p1-foss-2022a.eb --- .../g/gmsh/gmsh-4.11.1-foss-2022a.eb | 41 +++++++++++++++++++ .../o/occt/occt-7.5.0p1-foss-2022a.eb | 41 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmsh/gmsh-4.11.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.11.1-foss-2022a.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.11.1-foss-2022a.eb new file mode 100644 index 00000000000..abfe9ae2c1e --- /dev/null +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.11.1-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'gmsh' +version = '4.11.1' + +homepage = 'https://gmsh.info/' +description = "Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://%(name)s.info/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] +checksums = ['c5fe1b7cbd403888a814929f2fd0f5d69e27600222a18c786db5b76e8005b365'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('SWIG', '4.0.2'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('Python', '3.10.4'), + ('PETSc', '3.17.4'), + ('SLEPc', '3.17.2'), + ('FLTK', '1.3.8'), + ('occt', '7.5.0p1'), +] + +configopts = "-DENABLE_BUILD_SHARED=ON -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1" + + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/onelab.py', 'lib/%(name)s.py', 'lib/libgmsh.so'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --help'] + +modextrapaths = {'PYTHONPATH': ['lib']} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2022a.eb b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2022a.eb new file mode 100644 index 00000000000..10e631b5bd5 --- /dev/null +++ b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'occt' +version = '7.5.0p1' + +homepage = 'https://www.opencascade.com/' +description = """Open CASCADE Technology (OCCT) is an object-oriented C++ +class library designed for rapid production of sophisticated domain-specific +CAD/CAM/CAE applications.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://files.salome-platform.org/Salome/other'] +sources = ['opencascade-%(version)s.tar.gz'] +checksums = ['c0bbe42f0c41b6dcd6a39a83961ca7e414eb2d5d919f4dcb930096f2a423a578'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Doxygen', '1.9.4'), +] +dependencies = [ + ('Mesa', '22.0.3'), + ('freetype', '2.12.1'), + ('Tcl', '8.6.12'), + ('Tk', '8.6.12'), + ('FreeImage', '3.18.0'), + ('tbb', '2021.5.0'), +] + +configopts = "-DUSE_FREEIMAGE=ON -D3RDPARTY_FREEIMAGE_DIR=$EBROOTFREEIMAGE -D3RDPARTY_TBB_DIR=$EBROOTTBB -D3RDPARTY_TCL_DIR=$EBROOTTCL -D3RDPARTY_TK_DIR=$EBROOTTK -D3RDPARTY_FREETYPE_DIR=$EBROOTFREETYPE " + + +sanity_check_paths = { + 'files': ['bin/DRAWEXE', 'bin/env.sh'], + 'dirs': ['lib/cmake/opencascade'], +} + +sanity_check_commands = ['DRAWEXE -h'] + +moduleclass = 'cae' From f7cb9a083ab4b051084c37027ff0839b76c65500 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 15 Mar 2023 03:16:02 +0100 Subject: [PATCH 6865/9987] Use `SHLIB_EXT` and reintroduce `separate_build_dir`. --- easybuild/easyconfigs/g/gmsh/gmsh-4.11.1-foss-2022a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-4.11.1-foss-2022a.eb b/easybuild/easyconfigs/g/gmsh/gmsh-4.11.1-foss-2022a.eb index abfe9ae2c1e..0be178bc935 100644 --- a/easybuild/easyconfigs/g/gmsh/gmsh-4.11.1-foss-2022a.eb +++ b/easybuild/easyconfigs/g/gmsh/gmsh-4.11.1-foss-2022a.eb @@ -26,11 +26,12 @@ dependencies = [ ('occt', '7.5.0p1'), ] -configopts = "-DENABLE_BUILD_SHARED=ON -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1" +separate_build_dir = True +configopts = "-DENABLE_BUILD_SHARED=ON -DENABLE_WRAP_PYTHON=ON -DENABLE_METIS=1" sanity_check_paths = { - 'files': ['bin/%(name)s', 'bin/onelab.py', 'lib/%(name)s.py', 'lib/libgmsh.so'], + 'files': ['bin/%(name)s', 'bin/onelab.py', 'lib/%(name)s.py', 'lib/libgmsh.%s' % SHLIB_EXT], 'dirs': [], } From fca61650bb2e77b51c0b26d5275ba72f62e21b20 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 15 Mar 2023 07:13:15 +0100 Subject: [PATCH 6866/9987] Style fixes. --- easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2022a.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2022a.eb b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2022a.eb index 10e631b5bd5..40e83e5f3fc 100644 --- a/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2022a.eb +++ b/easybuild/easyconfigs/o/occt/occt-7.5.0p1-foss-2022a.eb @@ -28,8 +28,14 @@ dependencies = [ ('tbb', '2021.5.0'), ] -configopts = "-DUSE_FREEIMAGE=ON -D3RDPARTY_FREEIMAGE_DIR=$EBROOTFREEIMAGE -D3RDPARTY_TBB_DIR=$EBROOTTBB -D3RDPARTY_TCL_DIR=$EBROOTTCL -D3RDPARTY_TK_DIR=$EBROOTTK -D3RDPARTY_FREETYPE_DIR=$EBROOTFREETYPE " +separate_build_dir = True + +configopts = "-DUSE_FREEIMAGE=ON -D3RDPARTY_FREEIMAGE_DIR=$EBROOTFREEIMAGE " +configopts += "-D3RDPARTY_TBB_DIR=$EBROOTTBB " +configopts += "-D3RDPARTY_TCL_DIR=$EBROOTTCL " +configopts += "-D3RDPARTY_TK_DIR=$EBROOTTK " +configopts += "-D3RDPARTY_FREETYPE_DIR=$EBROOTFREETYPE " sanity_check_paths = { 'files': ['bin/DRAWEXE', 'bin/env.sh'], From 9a9e7d06e891c6f224345a193821de9304cd6dac Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 15 Mar 2023 07:53:58 +0100 Subject: [PATCH 6867/9987] pytest does not need binutils as dependency --- easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb index 34d5c8cdb7e..c0f51325944 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb @@ -11,7 +11,6 @@ applications and libraries.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} dependencies = [ - ('binutils', '2.37'), ('Python', '3.9.6'), ] From e6da8c428ae66be32f71187909c81c043a69f4b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 15 Mar 2023 08:54:55 +0100 Subject: [PATCH 6868/9987] switch to Binary easyblock --- .../ANIcalculator-1.0-GCCcore-10.3.0.eb | 15 +++++++-------- .../ANIcalculator-1.0-GCCcore-11.3.0.eb | 15 +++++++-------- 2 files changed, 14 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb index 0a3ef3fc3f5..4eb0c19c81d 100644 --- a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-10.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'Binary' name = 'ANIcalculator' version = '1.0' @@ -21,20 +21,19 @@ dependencies = [ ('libnsl', '1.3.0'), ] -skipsteps = ['build'] - -# The source tarball also includes Log4perl 1.44. -# Instead of copying this, we use the version from the Perl module. -files_to_copy = [(['ANIcalculator', 'nsimscan'], 'bin'), 'README.txt'] +extract_sources = True # Fix permissions on binaries and README.txt, +# and remove the included Log4perl 1.44 (we use the one from the Perl module). postinstallcmds = [ - 'chmod a+x %(installdir)s/bin/*', + 'chmod a+x %(installdir)s/ANIcalculator', + 'chmod a+x %(installdir)s/nsimscan', 'chmod -x %(installdir)s/README.txt', + 'rm -r %(installdir)s/Log', ] sanity_check_paths = { - 'files': ['README.txt', 'bin/ANIcalculator', 'bin/nsimscan'], + 'files': ['README.txt', 'ANIcalculator', 'nsimscan'], 'dirs': [], } diff --git a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-11.3.0.eb index a017bc13654..ff31f62debc 100644 --- a/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/a/ANIcalculator/ANIcalculator-1.0-GCCcore-11.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'MakeCp' +easyblock = 'Binary' name = 'ANIcalculator' version = '1.0' @@ -21,20 +21,19 @@ dependencies = [ ('libnsl', '2.0.0'), ] -skipsteps = ['build'] - -# The source tarball also includes Log4perl 1.44. -# Instead of copying this, we use the version from the Perl module. -files_to_copy = [(['ANIcalculator', 'nsimscan'], 'bin'), 'README.txt'] +extract_sources = True # Fix permissions on binaries and README.txt, +# and remove the included Log4perl 1.44 (we use the one from the Perl module). postinstallcmds = [ - 'chmod a+x %(installdir)s/bin/*', + 'chmod a+x %(installdir)s/ANIcalculator', + 'chmod a+x %(installdir)s/nsimscan', 'chmod -x %(installdir)s/README.txt', + 'rm -r %(installdir)s/Log', ] sanity_check_paths = { - 'files': ['README.txt', 'bin/ANIcalculator', 'bin/nsimscan'], + 'files': ['README.txt', 'ANIcalculator', 'nsimscan'], 'dirs': [], } From 61bdcee2990fc34c56d72857d3d8ffa197a20772 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Mar 2023 09:33:48 +0100 Subject: [PATCH 6869/9987] minor tweaks for GKeyll easyconfig --- .../GKeyll-20220803-foss-2020a-Python-3.8.2.eb | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb index 8e3a6fb2519..9bec3e8ff96 100644 --- a/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GKeyll/GKeyll-20220803-foss-2020a-Python-3.8.2.eb @@ -20,11 +20,8 @@ toolchainopts = {'usempi': True} github_account = 'ammarhakim' source_urls = ['https://github.com/ammarhakim/gkyl/archive'] -sources = ['%s.tar.gz' % local_commit] - -checksums = [ - '075867b602e3a50c13e72f7f0dc680c3591467ce61debd3c9a11f3e5dced0503', # 4c3e568.tar.gz -] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['075867b602e3a50c13e72f7f0dc680c3591467ce61debd3c9a11f3e5dced0503'] dependencies = [ ('Python', '3.8.2'), @@ -36,10 +33,8 @@ dependencies = [ configopts = '--luajit-inc-dir=$EBROOTLUAJIT2MINOPENRESTY/include/luajit-2.1/ ' configopts += '--extra-link-libs=" hdf5 mxml bz2 lz4 z zfp gomp" ' -parallel = 4 - # Seems to be required as else all cores are being used -buildopts = ' -j 4' +buildopts = ' -j %(parallel)s' sanity_check_paths = { 'files': ['bin/gkyl', 'bin/gkyl', 'lib/libcomm.%s' % SHLIB_EXT, @@ -48,8 +43,8 @@ sanity_check_paths = { } sanity_check_commands = [ - 'gkyl -version', - 'ctest_Range -?', + "gkyl -version", + "ctest_Range -?", ] moduleclass = 'phys' From a9075126ae999d2a6ac8f32a79fdbc1f7b5d15f2 Mon Sep 17 00:00:00 2001 From: lenocil Date: Wed, 15 Mar 2023 09:53:54 +0100 Subject: [PATCH 6870/9987] Modified easyconfig for Apache Avro C++. Using CMakeMake EasyBlock now. --- .../a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb index 2bb4e395f6a..cbfe03410d3 100644 --- a/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb @@ -1,10 +1,10 @@ -easyblock = 'Binary' +easyblock = 'CMakeMake' name = 'avrocpp' version = '1.11.1' -homepage = 'https://avro.apache.org/docs/1.11.1/api/cpp/html/' -description = """Avro C++ is a C++ data serialization library .""" +homepage = 'https://avro.apache.org' +description = """Avro is a data serialization system.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} @@ -20,13 +20,13 @@ dependencies = [ ('Boost', '1.77.0'), ] +srcdir = "%(builddir)s/avro-release-%(version)s/lang/c++" -extract_sources = True - -install_cmd = "cd lang/c++; mkdir -p build; cd build && " -install_cmd += ' cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=%(installdir)s/ -DCMAKE_BUILD_TYPE=Release .. && ' -install_cmd += " make install" +generator = "Unix Makefiles" +separate_build_dir = True +configopts = ' -DCMAKE_INSTALL_PREFIX=%(installdir)s/' +configopts += ' -DCMAKE_BUILD_TYPE=Release ' sanity_check_paths = { 'files': ["%(installdir)s/bin/avrogencpp"], From 15dfe73200ba85ba58bd9f58e3279148b5d878a9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 15 Mar 2023 11:37:39 +0100 Subject: [PATCH 6871/9987] pytest does need binutils as an explicit builddep since it is in GCCcore according to our rules. --- easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb index c0f51325944..e8ab8e89799 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb @@ -10,6 +10,10 @@ applications and libraries.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +builddependencies = [ + ('binutils', '2.37'), +] + dependencies = [ ('Python', '3.9.6'), ] From 847b429104805246a5ad42bdbee8ba787fd2ebbd Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 15 Mar 2023 10:38:12 +0000 Subject: [PATCH 6872/9987] Updated to version 9.0.0, previous one left for now --- .../py-cpuinfo-9.0.0-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..a9fcf12cfb2 --- /dev/null +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'py-cpuinfo' +version = '9.0.0' + +homepage = 'https://github.com/workhorsy/py-cpuinfo' +description = """ Py-cpuinfo gets CPU info with pure Python. +Py-cpuinfo should work without any extra programs or libraries, +beyond what your OS provides. It does not require any +compilation(C/C++, assembly, et cetera) to use. It works with Python 3. +""" +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'], + 'modulename': 'cpuinfo', + }), +] + +moduleclass = 'lib' From 7d3eb7fd2ee5f7152b4179aafcee4f12db125c29 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 15 Mar 2023 12:51:32 +0100 Subject: [PATCH 6873/9987] adding easyconfigs: Greenlet-2.0.2-foss-2022a.eb, Optuna-3.1.0-foss-2022a.eb --- .../g/Greenlet/Greenlet-2.0.2-foss-2022a.eb | 27 +++++++++ .../o/Optuna/Optuna-3.1.0-foss-2022a.eb | 57 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/o/Optuna/Optuna-3.1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022a.eb new file mode 100644 index 00000000000..580d4e0bffd --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Greenlet' +version = '2.0.2' + +homepage = 'https://github.com/python-greenlet/greenlet' + +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [('Python', '3.10.4')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-3.1.0-foss-2022a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-3.1.0-foss-2022a.eb new file mode 100644 index 00000000000..c22e7e088b0 --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-3.1.0-foss-2022a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '3.1.0' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), + ('matplotlib', '3.5.2'), # optional + ('plotly.py', '5.12.0'), # optional + ('redis-py', '4.5.1'), # optional + ('scikit-learn', '1.1.2'), # optional + ('Mako', '1.2.0'), + ('Greenlet', '2.0.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('alembic', '1.9.3', { + 'checksums': ['8fd6aaea56f5a703a190d25a705dfa91d7c313bb71de2f9c68f5abdcaf5df164'], + }), + ('cmaes', '0.9.1', { + 'checksums': ['d122f8d46377f643a150c85ffc81c4e33909a34cfdcb522ee7a6fb17ea4f232c'], + }), + ('colorlog', '6.7.0', { + 'checksums': ['bd94bd21c1e13fac7bd3153f4bc3a7dc0eb0974b8bc2fdf1a989e474f6e582e5'], + }), + ('SQLAlchemy', '2.0.3', { + 'checksums': ['c2b924f6d0162ed1c0d8f47db1e56498702b1c3c953ad84f0eefbf5b4e53bb05'], + }), + ('%(namelower)s', version, { + 'use_pip_extras': 'optional', + 'checksums': ['96c7c92860c8692d3aa569d749e72b121422cb4af0ed3ad4bfbc445b61416919'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' From 9e91f4d4194611ca38265ea759ecde904c93afed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Mar 2023 16:25:41 +0100 Subject: [PATCH 6874/9987] bump tcsh to 6.24.07, use foss/2022b for WRF 4.4.1, add easyconfig for netCDF 4.6.0 with gompi/2022b --- .../netCDF-Fortran-4.6.0-gompi-2022b.eb | 28 +++++++++++++++++++ ....2.0.eb => tcsh-6.24.07-GCCcore-12.2.0.eb} | 4 +-- ...dmpar.eb => WRF-4.4.1-foss-2022b-dmpar.eb} | 4 +-- 3 files changed, 32 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022b.eb rename easybuild/easyconfigs/t/tcsh/{tcsh-6.24.05-GCCcore-12.2.0.eb => tcsh-6.24.07-GCCcore-12.2.0.eb} (93%) rename easybuild/easyconfigs/w/WRF/{WRF-4.4.1-foss-2022.10-dmpar.eb => WRF-4.4.1-foss-2022b-dmpar.eb} (94%) diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022b.eb new file mode 100644 index 00000000000..e7d505dc509 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022b.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8194aa70e400c0adfc456127c1d97af2c6489207171d13b10cd754a16da8b0ca'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [ + ('netCDF', '4.9.0'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.07-GCCcore-12.2.0.eb similarity index 93% rename from easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/t/tcsh/tcsh-6.24.07-GCCcore-12.2.0.eb index 5874f3e8c14..f2a441e8129 100644 --- a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.05-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.07-GCCcore-12.2.0.eb @@ -12,7 +12,7 @@ easyblock = 'ConfigureMake' name = 'tcsh' -version = '6.24.05' +version = '6.24.07' homepage = 'https://www.tcsh.org' description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). @@ -29,7 +29,7 @@ source_urls = [ 'ftp://ftp.astron.com/pub/%(namelower)s/old', ] sources = [SOURCELOWER_TAR_GZ] -checksums = ['3d1ff94787859b5a4063400470251618f76bc24f8041ba7ef2c2753f782c296c'] +checksums = ['74e4e9805cbd9413ed34b4ffa1d72fc8d0ef81a5b79476854091416ce9336995'] builddependencies = [('binutils', '2.39')] diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022b-dmpar.eb similarity index 94% rename from easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb rename to easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022b-dmpar.eb index 95e02318341..a62a23d620c 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022.10-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022b-dmpar.eb @@ -8,7 +8,7 @@ description = """The Weather Research and Forecasting (WRF) Model is a next-gene numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs.""" -toolchain = {'name': 'foss', 'version': '2022.10'} +toolchain = {'name': 'foss', 'version': '2022b'} toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 source_urls = ['https://github.com/wrf-model/WRF/archive/'] @@ -34,7 +34,7 @@ checksums = [ # csh is used by WRF install scripts builddependencies = [ ('Autotools', '20220317'), - ('tcsh', '6.24.05'), + ('tcsh', '6.24.07'), ('time', '1.9'), ('Perl', '5.36.0'), ] From 170a69fbe0d7f27b8be212733f9acc4842b917fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 15 Mar 2023 17:55:17 +0000 Subject: [PATCH 6875/9987] adding easyconfigs: PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb --- ...ch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..6d6afd348d6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-bundle' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """PyTorch with compatible versions of official Torch extensions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('RE2', '2022-06-01'), # for torchtext +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', version, versionsuffix), + ('Pillow-SIMD', '9.2.0'), # for torchvision + ('SentencePiece', '0.1.97'), # for torchtext + ('tqdm', '4.64.0'), # for torchtext + ('double-conversion', '3.2.0'), # for torchtext +] + +use_pip = True + +exts_list = [ + ('torchvision', '0.14.1', { + 'source_urls': ['https://github.com/pytorch/vision/archive'], + 'sources': [{'download_filename': 'v0.14.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['ced67e1cf1f97e168cdf271851a4d0b6d382ab7936e7bcbb39aaa87239c324b6'], + }), + ('torchtext', '0.14.1', { + 'source_urls': ['https://github.com/pytorch/text/archive'], + 'sources': [{'download_filename': 'v0.14.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'], + }), + ('torchaudio', '0.13.1', { + 'source_urls': ['https://github.com/pytorch/audio/archive'], + 'sources': [{'download_filename': 'v0.13.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['3a5c108a9ea31d0e6533a2cd6cbaf133efaefe4bdcb4b689183a33b991c95d12'], + }), + ('pytorch-ignite', '0.4.11', { + 'source_urls': ['https://github.com/pytorch/ignite/archive'], + 'sources': [{'download_filename': 'v0.4.11.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['33e7485cea3cac08d7a49a3a01d3013e1156128867602bff0a8e32b2c5ebd4e9'], + }), + ('torchdata', '0.6.0', { + 'source_urls': ['https://github.com/pytorch/data/archive'], + 'sources': [{'download_filename': 'v0.6.0.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['048dea12ee96c0ea1525097959fee811d7b38c2ed05f44a90f35f8961895fb5b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From d81414e5b1b08320152c7759e80c78a0695cb399 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 15 Mar 2023 18:49:57 +0000 Subject: [PATCH 6876/9987] Fix version template in download filename --- .../PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb index 6d6afd348d6..00e581f3322 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -27,27 +27,27 @@ use_pip = True exts_list = [ ('torchvision', '0.14.1', { 'source_urls': ['https://github.com/pytorch/vision/archive'], - 'sources': [{'download_filename': 'v0.14.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['ced67e1cf1f97e168cdf271851a4d0b6d382ab7936e7bcbb39aaa87239c324b6'], }), ('torchtext', '0.14.1', { 'source_urls': ['https://github.com/pytorch/text/archive'], - 'sources': [{'download_filename': 'v0.14.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': 'v%(version)S.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'], }), ('torchaudio', '0.13.1', { 'source_urls': ['https://github.com/pytorch/audio/archive'], - 'sources': [{'download_filename': 'v0.13.1.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['3a5c108a9ea31d0e6533a2cd6cbaf133efaefe4bdcb4b689183a33b991c95d12'], }), ('pytorch-ignite', '0.4.11', { 'source_urls': ['https://github.com/pytorch/ignite/archive'], - 'sources': [{'download_filename': 'v0.4.11.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['33e7485cea3cac08d7a49a3a01d3013e1156128867602bff0a8e32b2c5ebd4e9'], }), ('torchdata', '0.6.0', { 'source_urls': ['https://github.com/pytorch/data/archive'], - 'sources': [{'download_filename': 'v0.6.0.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['048dea12ee96c0ea1525097959fee811d7b38c2ed05f44a90f35f8961895fb5b'], }), ] From 930088708b580d743b62f7c9e337869136e579a9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 15 Mar 2023 21:52:15 +0100 Subject: [PATCH 6877/9987] adding easyconfigs: MATLAB-2022b-r5.eb --- .../easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb new file mode 100644 index 00000000000..4ffbc980772 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb @@ -0,0 +1,28 @@ +name = 'MATLAB' +version = '2022b' +_update = '5' +versionsuffix = '-r%s' % _update + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +sources = ['R%s_Update_%s_Linux.iso' % (version, _update)] +checksums = ['d11ba428a6970208f0855138a6e2253c31e2ead34d51da125529a208945ac187'] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server_port = 'XXXXX' + +moduleclass = 'math' From 558cf0452a8cefce9de1ef2c7d3a675bc8e64c38 Mon Sep 17 00:00:00 2001 From: lenocil Date: Thu, 16 Mar 2023 09:34:07 +0100 Subject: [PATCH 6878/9987] easyconfig changes implemented and name changed to avro-cpp. --- .../avro-cpp-1.11.1-GCC-11.2.0.eb} | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/a/{avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb => avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb} (56%) diff --git a/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb similarity index 56% rename from easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb rename to easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb index cbfe03410d3..58138a0d9c3 100644 --- a/easybuild/easyconfigs/a/avrocpp/avrocpp-1.11.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb @@ -1,10 +1,10 @@ easyblock = 'CMakeMake' -name = 'avrocpp' +name = 'avro-cpp' version = '1.11.1' homepage = 'https://avro.apache.org' -description = """Avro is a data serialization system.""" +description = """C++ implementation of Avro data serialization system.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} @@ -13,8 +13,7 @@ sources = ['release-%(version)s.tar.gz'] checksums = ['599f96bb405f72a35154b2477caa6254d723bb4e3f6a0e54e9ae540664321752'] builddependencies = [ - ('binutils', '2.37', '', ('GCCcore', '11.2.0')), - ('CMake', '3.22.1', '', ('GCCcore', '11.2.0')), + ('CMake', '3.22.1'), ] dependencies = [ ('Boost', '1.77.0'), @@ -25,14 +24,11 @@ srcdir = "%(builddir)s/avro-release-%(version)s/lang/c++" generator = "Unix Makefiles" separate_build_dir = True -configopts = ' -DCMAKE_INSTALL_PREFIX=%(installdir)s/' -configopts += ' -DCMAKE_BUILD_TYPE=Release ' - sanity_check_paths = { - 'files': ["%(installdir)s/bin/avrogencpp"], - 'dirs': ["%(installdir)s/lib"], + 'files': ["bin/avrogencpp"], + 'dirs': ["lib"], } -sanity_check_commands = ["%(installdir)s/bin/avrogencpp -h"] +sanity_check_commands = ["avrogencpp -h"] moduleclass = 'lib' From b41bc9c17d3d0697dd3abf723d78c99c23a612cf Mon Sep 17 00:00:00 2001 From: lenocil Date: Thu, 16 Mar 2023 09:52:37 +0100 Subject: [PATCH 6879/9987] srcdir path changed --- easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb index 58138a0d9c3..8ef5d09f68e 100644 --- a/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('Boost', '1.77.0'), ] -srcdir = "%(builddir)s/avro-release-%(version)s/lang/c++" +srcdir = "lang/c++" generator = "Unix Makefiles" separate_build_dir = True From 19761b2b56bf1962931e199bae0bc3f6fa9c6483 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Thu, 16 Mar 2023 09:57:41 +0100 Subject: [PATCH 6880/9987] adding easyconfigs: texinfo-7.0.2-GCCcore-11.3.0.eb --- .../t/texinfo/texinfo-7.0.2-GCCcore-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/t/texinfo/texinfo-7.0.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-7.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-7.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ee3c6d3e6c8 --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-7.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'texinfo' +version = '7.0.2' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """Texinfo is the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['f211ec3261383e1a89e4555a93b9d017fe807b9c3992fb2dff4871dae6da54ad'] + +builddependencies = [('binutils', '2.38')] + +osdependencies = ['texlive'] + +preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " + +# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency +modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" + +sanity_check_paths = { + 'files': [ + 'texmf/tex/texinfo/texinfo.tex', + 'bin/install-info', 'bin/makeinfo', 'bin/pdftexi2dvi', 'bin/pod2texi', 'bin/texi2pdf' + ], + 'dirs': ['bin', 'share', 'texmf'], +} + +moduleclass = 'devel' From 5f38ff4246e2b820d3060f83684a69fb3fdd9f8f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 16 Mar 2023 10:00:03 +0100 Subject: [PATCH 6881/9987] adding easyconfigs: Cython-0.29.33-GCCcore-11.3.0.eb, cython-blis-0.9.1-foss-2022a.eb --- .../c/Cython/Cython-0.29.33-GCCcore-11.3.0.eb | 38 +++++++++++++++++++ .../cython-blis-0.9.1-foss-2022a.eb | 30 +++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.29.33-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/cython-blis/cython-blis-0.9.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.33-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.33-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c60a84380db --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.33-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.29.33' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sources = [SOURCE_TAR_GZ] +checksums = ['5040764c4a4d2ce964a395da24f0d1ae58144995dab92c6b96f44c3f4d72286a'] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cython --version', +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cython-blis/cython-blis-0.9.1-foss-2022a.eb b/easybuild/easyconfigs/c/cython-blis/cython-blis-0.9.1-foss-2022a.eb new file mode 100644 index 00000000000..bbf5c1ba745 --- /dev/null +++ b/easybuild/easyconfigs/c/cython-blis/cython-blis-0.9.1-foss-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'cython-blis' +version = '0.9.1' + +homepage = 'https://github.com/explosion/cython-blis' + +description = """Fast BLAS-like operations from Python and Cython, without the tears. +Provides the Blis linear algebra routines as a self-contained Python C-extension. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Cython', '0.29.33'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +source_urls = ['https://pypi.python.org/packages/source/b/blis/'] +sources = ['blis-%(version)s.tar.gz'] +checksums = ['7ceac466801f9d97ecb34e10dded8c24cf5e0927ea7e834da1cc9d2ed3fc366f'] + +options = {'modulename': 'blis'} + +moduleclass = 'lib' From b3e0ccaf8340c1ef3681b31d1bd50a1980e3b0d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 16 Mar 2023 09:56:34 +0000 Subject: [PATCH 6882/9987] fix typo --- .../PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb index 00e581f3322..89b09adbe87 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -32,7 +32,7 @@ exts_list = [ }), ('torchtext', '0.14.1', { 'source_urls': ['https://github.com/pytorch/text/archive'], - 'sources': [{'download_filename': 'v%(version)S.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'], }), ('torchaudio', '0.13.1', { From 191d7ff6be89ec1f822dd68503b228364cad6692 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 16 Mar 2023 11:03:57 +0100 Subject: [PATCH 6883/9987] adding easyconfigs: torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb and patches: torchtext-0.14.1_deps_fix.patch --- ...chtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb | 46 ++++++++++++++++ .../torchtext/torchtext-0.14.1_deps_fix.patch | 53 +++++++++++++++++++ 2 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..46bf098eddc --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.14.1' +local_pytorch_version = '1.12.0' +local_python_suffix = '-Python-%(pyver)s' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['torchtext-0.14.1_deps_fix.patch'] +checksums = [ + {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, + {'torchtext-0.14.1_deps_fix.patch': '38ee9a2c74016376ef3ff06ea40eb4522f5a72410573168050b79cab457077c7'}, +] + +builddependencies = [ + ('RE2', '2022-06-01'), + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SentencePiece', '0.1.97'), + ('tqdm', '4.64.0'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.2.0'), + ('utf8proc', '2.7.0'), +] + +download_dep_fail = True, +use_pip = True +sanity_pip_check = True, + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && " + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch new file mode 100644 index 00000000000..ab7a71f24f5 --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch @@ -0,0 +1,53 @@ +diff -u text/CMakeLists.txt.orig text/CMakeLists.txt +--- text/CMakeLists.txt.orig 2023-03-08 14:33:35.618931003 +0100 ++++ text/CMakeLists.txt 2023-03-08 14:35:03.169072623 +0100 +@@ -24,10 +24,10 @@ + if(env_cxx_standard GREATER -1) + message( + WARNING "C++ standard version definition detected in environment variable." +- "PyTorch requires -std=c++14. Please remove -std=c++ settings in your environment.") ++ "PyTorch requires -std=c++17. Please remove -std=c++ settings in your environment.") + endif() + +-set(CMAKE_CXX_STANDARD 14) ++set(CMAKE_CXX_STANDARD 17) + set(CMAKE_C_STANDARD 11) + + set(CMAKE_EXPORT_COMPILE_COMMANDS ON) +@@ -63,5 +63,10 @@ + + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_COMPILED_WITH_CXX_ABI} -Wall ${TORCH_CXX_FLAGS}") + +-add_subdirectory(third_party) ++find_package(double-conversion) ++find_package(re2) ++find_library(SENTENCEPIECE_LIBRARY sentencepiece PATHS $ENV{EBROOTSENTENCEPIECE}/lib64) ++find_library(SENTENCEPIECE_TRAIN_LIBRARY sentencepiece_train PATHS $ENV{EBROOTSENTENCEPIECE}/lib64) ++find_library(UTF8PROC_LIBRARY utf8proc PATHS $ENV{UTF8PROC}/lib64) ++ + add_subdirectory(torchtext/csrc) +diff -u text/torchtext/csrc/CMakeLists.txt.orig text/torchtext/csrc/CMakeLists.txt +--- text/torchtext/csrc/CMakeLists.txt.orig 2023-03-08 14:11:53.387582628 +0100 ++++ text/torchtext/csrc/CMakeLists.txt 2023-03-08 14:16:11.159140070 +0100 +@@ -18,10 +18,6 @@ + set( + LIBTORCHTEXT_INCLUDE_DIRS + ${PROJECT_SOURCE_DIR} +- ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src +- $ +- $ +- $ + ${TORCH_INSTALL_PREFIX}/include + ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include + ) +@@ -119,10 +115,6 @@ + set( + EXTENSION_INCLUDE_DIRS + ${PROJECT_SOURCE_DIR} +- ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src +- $ +- $ +- $ + ${TORCH_INSTALL_PREFIX}/include + ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include + ) From 73ba40dbfb428362bb80a10aa0db0b79cb851994 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Mar 2023 12:32:39 +0100 Subject: [PATCH 6884/9987] add comment in GOATOOLS 1.3.1 easyconfig to explain why git_config is used --- easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2022a.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2022a.eb index b694dc5ae85..2f591eb3897 100644 --- a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2022a.eb @@ -10,7 +10,8 @@ description = "A Python library for Gene Ontology analyses" toolchain = {'name': 'foss', 'version': '2022a'} -source_urls = ['https://github.com/tanghaibao/goatools/archive/'] +# must download sources via git to preserve .git directory, +# since setuptools-scm is used to determine version sources = [{ 'git_config': { 'url': 'https://github.com/tanghaibao', From 03cc601d7b5d92c0b1488bf7ce1e9028669d61b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Mar 2023 14:54:09 +0100 Subject: [PATCH 6885/9987] adding easyconfigs: MDAnalysis-2.4.2-foss-2022b.eb, Biopython-1.81-foss-2022b.eb, networkx-3.0-foss-2022b.eb --- .../b/Biopython/Biopython-1.81-foss-2022b.eb | 45 +++++++++++++++ .../MDAnalysis/MDAnalysis-2.4.2-foss-2022b.eb | 57 +++++++++++++++++++ .../n/networkx/networkx-3.0-foss-2022b.eb | 24 ++++++++ 3 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2022b.eb create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2022b.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-3.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2022b.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2022b.eb new file mode 100644 index 00000000000..f8464fcb939 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.81-foss-2022b.eb @@ -0,0 +1,45 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.81' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2022b.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2022b.eb new file mode 100644 index 00000000000..0d0fa57284c --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2022b.eb @@ -0,0 +1,57 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '2.4.2' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), + ('Biopython', '1.81'), + ('networkx', '3.0'), + ('tqdm', '4.64.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mrcfile', '1.4.3', { + 'checksums': ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5'], + }), + ('GridDataFormats', '1.0.1', { + 'modulename': 'gridData', + 'checksums': ['ad2c9ab7d672a6d8c426de7d083eee4f3e2b0bd59391675d30683c768ab83cc4'], + }), + ('gsd', '2.8.0', { + 'checksums': ['f2b031a26a7a5bee5f3940dc2f36c5a5b6670307b297c526adf2e26c1f5b46ae'], + }), + ('msgpack', '1.0.5', { + 'checksums': ['c075544284eadc5cddc70f4757331d99dcbc16b2bbd4849d15f8aae4cf36d31c'], + }), + ('mmtf-python', '1.1.3', { + 'modulename': 'mmtf', + 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + (name, version, { + 'modulename': 'MDAnalysis', + 'checksums': ['ae2ee5627391e73f74eaa3c547af3ec6ab8b040d27dedffe3a7ece8e0cd27636'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.0-foss-2022b.eb b/easybuild/easyconfigs/n/networkx/networkx-3.0-foss-2022b.eb new file mode 100644 index 00000000000..5825b79f6d4 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-3.0-foss-2022b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '3.0' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9a9992345353618ae98339c2b63d8201c381c2944f38a2ab49cb45a4c667e412'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From f55de5fd1eab5ad67b05f45deeffd0509de2281b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 16 Mar 2023 15:09:12 +0100 Subject: [PATCH 6886/9987] adding easyconfigs: bcbio-gff-0.7.0-foss-2022a.eb --- .../b/bcbio-gff/bcbio-gff-0.7.0-foss-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2022a.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2022a.eb new file mode 100644 index 00000000000..e0093e9f3e3 --- /dev/null +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2022a.eb @@ -0,0 +1,42 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v0.6.7 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'bcbio-gff' +version = '0.7.0' + +homepage = 'https://github.com/chapmanb/bcbb/tree/master/gff' + +description = """ +Read and write Generic Feature Format (GFF) with Biopython integration. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['f7b3922ee274106f8716703f41f05a1795aa9d73e903f4e481995ed8f5f65d2d'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +local_bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' +local_targets = ['GFFOutput.py', 'GFFParser.py'] + +sanity_check_paths = { + 'files': [local_bcbiogffroot + '/BCBio/GFF/%s' % x for x in local_targets], + 'dirs': [local_bcbiogffroot], +} + +options = {'modulename': 'BCBio.GFF'} + +moduleclass = 'bio' From 49ce8a9ceaacaf726710209b9a9759e30cb83b63 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 16 Mar 2023 16:07:33 +0100 Subject: [PATCH 6887/9987] Changed version of sympy used by grid --- easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb b/easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb index 5919e57a002..f398b7924bd 100644 --- a/easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb +++ b/easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb @@ -17,7 +17,7 @@ checksums = ['d8189c33a9d5fc89ad0fa83089431944b346686519ec8d3c350848cf28b81d7a'] dependencies = { ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('sympy', '1.11.1'), + ('sympy', '1.10.1'), } preinstallopts = "sed -i 's|version=get_version()|version=\"%(version)s\"|g' setup.py && " From a9c11959b36418d54c376354781c459101977837 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 16 Mar 2023 16:12:15 +0100 Subject: [PATCH 6888/9987] adding easyconfigs: PIPITS-3.0-foss-2022a.eb, ITSx-1.1.3-GCCcore-11.3.0.eb, FASTX-Toolkit-0.0.14-GCC-11.3.0.eb --- .../FASTX-Toolkit-0.0.14-GCC-11.3.0.eb | 74 +++++++++++++++++++ .../i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb | 29 ++++++++ .../p/PIPITS/PIPITS-3.0-foss-2022a.eb | 66 +++++++++++++++++ 3 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb new file mode 100644 index 00000000000..4bde8e513e1 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb @@ -0,0 +1,74 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'Bundle' + +name = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +default_easyblock = 'ConfigureMake' + +dependencies = [('GDGraph', '1.56')] + +components = [ + ('libgtextutils', '0.7', { + 'source_urls': ['https://github.com/agordon/libgtextutils/releases/download/%(version)s/'], + 'sources': [SOURCE_TAR_GZ], + 'patches': ['libgtextutils-%(version)s_fix-bool.patch'], + 'checksums': [ + '792e0ea3c96ffe3ad65617a104b7dc50684932bc96d2adab501c952fd65c3e4a', # libgtextutils-0.7.tar.gz + 'bb16a4fd86c2eb12215d8780b09f0898771a73e53889a015e2351f2d737c9a00', # libgtextutils-0.7_fix-bool.patch + ], + 'start_dir': 'libgtextutils-%(version)s', + }), + (name, version, { + 'source_urls': ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'], + 'sources': ['fastx_toolkit-%(version)s.tar.bz2'], + 'checksums': ['9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806'], + 'start_dir': 'fastx_toolkit-%(version)s', + 'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ", + 'configopts': 'CXXFLAGS="$CXXFLAGS -Wno-implicit-fallthrough"', + }), +] + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']] + + ['lib/libgtextutils.%s' % SHLIB_EXT, 'lib/libgtextutils.a'], + 'dirs': [] +} + +sanity_check_commands = [ + 'fasta_clipping_histogram.pl', + 'fasta_formatter -h', + 'fastq_masker -h | grep "FASTX Toolkit %(version)s"', + 'fastq_quality_boxplot_graph.sh', + 'fastx_clipper -h | grep "FASTX Toolkit %(version)s"', + 'fastx_nucleotide_distribution_graph.sh', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7392f5fd08a --- /dev/null +++ b/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'ITSx' +version = '1.1.3' + +homepage = 'https://microbiology.se/software/itsx/' +description = '''ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of +fungi and other eukaryotes for use in environmental sequencing.''' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://microbiology.se/sw/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['6f6d7ff6350f82439dee5348f6e8bda512be25193c603d4e56cc215c520091bf'] + +dependencies = [('Perl', '5.34.1')] + +fix_perl_shebang_for = ['ITSx'] + +sanity_check_paths = { + 'files': ['ITSx'], + 'dirs': ['ITSx_db'], +} + +sanity_check_commands = ['ITSx --help'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2022a.eb b/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2022a.eb new file mode 100644 index 00000000000..561a7f5e9c2 --- /dev/null +++ b/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2022a.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'PIPITS' +version = '3.0' + +homepage = 'https://github.com/hsgweon/pipits' +description = """An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences +from the Illumina sequencing platform.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('VSEARCH', '2.22.1'), + ('FASTX-Toolkit', '0.0.14'), + ('ITSx', '1.1.3'), + ('HMMER', '3.3.2'), + ('RDP-Classifier', '2.13', '-Java-11', SYSTEM), + ('SeqKit', '2.3.1', '', SYSTEM), +] + +use_pip = True + +exts_list = [ + ('biom-format', '2.1.14', { + 'modulename': 'biom', + 'checksums': ['c8bac94ab6aa8226c0d38af7a3341d65e5f3664b9f45ec44fdf8b5275b2f92c1'], + }), + ('python-utils', '3.5.2', { + 'checksums': ['68198854fc276bc4b2403b261703c218e01ef564dcb072a7096ed9ea7aa5130c'], + }), + ('progressbar2', '4.2.0', { + 'modulename': 'progressbar', + 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], + }), + ('pispino', '1.1', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/hsgweon/pispino/archive/'], + 'checksums': ['8fb2e1c0ae38ecca7c637de9c0b655eb18fc67d7838ceb5a6902555ea12416c0'], + }), + (name, version, { + 'patches': ['PIPITS-3.0_remove-conda-commands.patch'], + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/hsgweon/pipits/archive/'], + 'checksums': [ + {'3.0.tar.gz': 'ee9f142e473e57b186760d940131610c16bdfe57eefca935df35779fd85377bd'}, + {'PIPITS-3.0_remove-conda-commands.patch': + 'd4be41ac4d6d37a19ad09b06c1f05ed83921aa59dc4b04b38fa257e6bce6d12f'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pipits_funits', 'pipits_process', + 'pispino_createreadpairslist', + 'pispino_seqprep']], + 'dirs': [] +} + +sanity_check_commands = ['pipits_process --help'] + +sanity_pip_check = True + +moduleclass = 'bio' From ce50d4234afffde942a39a160d19122177f11c56 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 16 Mar 2023 16:15:14 +0100 Subject: [PATCH 6889/9987] PR review changes --- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 51 ------------------- .../easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 6 --- ...sceR-0.99.0-20230110-foss-2022a-R-4.2.1.eb | 6 +++ 3 files changed, 6 insertions(+), 57 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 72d0887ac92..aa7ed5b6054 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1152,57 +1152,6 @@ exts_list = [ ('ReactomePA', '1.40.0', { 'checksums': ['458b3febb341700414ca04ea4a6f3005061c9db97622cfdfda6b75a74415a7b9'], }), - ('flowClean', '1.34.1', { - 'checksums': ['d0e58ac89fd302761136cbcd5eb859351a61da2bd8967840bcd054ec16630f7f'], - }), - ('flowAI', '1.26.0', { - 'checksums': ['f4e35c824f68036cea5746236a026ad8e336c2595411d15d303d45fbc02526a5'], - }), - ('flowFP', '1.54.0', { - 'checksums': ['ba12d5bd4dc784997f30435314fe61f86b0c28d99c4458f7e8f9b76daa54b442'], - }), - ('simplifyEnrichment', '1.6.1', { - 'checksums': ['66fafb64d19c5fc4bb7aa6c6805130144f35fd508c2551024aec9f5c7b7b7461'], - }), - ('RPMG', '2.2-3', { - 'checksums': ['74d5bada6a51d280296cb36fae4938c16ba9ed2fa37f3bfb60cf7c541c5b22b6'], - }), - ('Rwave', '2.6-5', { - 'checksums': ['6c9ef75bb376f2e3f5c5dcd3b3fdca7d86797ce809da34f444632657189be2e4'], - }), - ('RSEIS', '4.1-4', { - 'checksums': ['76d5caf30cd3871fa80d27ea694023a4c303ffc099297aeeff03d22538dbff76'], - }), - ('splancs', '2.01-43', { - 'checksums': ['b351565e1f69f6c86a29d921d3a18d5896c4586e2ab8c73bb3df8e75630fc448'], - }), - ('MBA', '0.1-0', { - 'checksums': ['78039905c5b98be2bb79a5f292187a2aca21ef449daeefea58b0cac53a5283af'], - }), - ('GEOmap', '2.5-0', { - 'checksums': ['82e5608eda7330632bc67aa662b649e7b7b3ccdfda6a18a19d2e3379e0db1093'], - }), - ('RFOC', '3.4-6', { - 'checksums': ['0dfa237f4d04eb9a2718942b4d7ed9538fc5f89e3cbaa5a34a4fd1bc6fe54533'], - }), - ('flowDensity', '1.30.0', { - 'checksums': ['c321b395d6f1ae24d1428319401b225ae5e31fee5051127e43142d96f820103d'], - }), - ('flowPeaks', '1.42.0', { - 'checksums': ['ae98124c0574364bf8cd47be7704ad90b2b7d3dabbdd8df7744cbfaf81d665a8'], - }), - ('SamSPECTRAL', '1.50.0', { - 'checksums': ['b55de8cb2092d1b5c192ed0e4b47c421d888e5392165f28395241ca5884b8a5c'], - }), - ('ddPCRclust', '1.16.0', { - 'checksums': ['a457b78a2c254c69ed572d8dca01c66134d6ad2952f72097703110c1d663da5d'], - }), - ('feature', '1.2.15', { - 'checksums': ['de38292b7e800068a20824e2a9e7d5d4d0b465b7925db0d165346aa5030ff67b'], - }), - ('flowMerge', '2.44.0', { - 'checksums': ['ba143b5fff19207f323c1e7b7feaf56fa6e31700422d002521fe49e86bbc5e03'], - }), ('SpatialExperiment', '1.6.1', { 'checksums': ['31e516e14e827e4b9fe853bc136066863dd762053012631c569ec3c00c6cbab5'], }), diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 0ceadb41367..76fed434942 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3460,15 +3460,9 @@ exts_list = [ ('webutils', '1.1', { 'checksums': ['33e2b408d2b9ca12e158e0007d4a55a3ace6838341ad944344de2ceb806e4699'], }), - ('sodium', '1.2.1', { - 'checksums': ['f76e98969710af8b6c7c7decf63706d91185eebf8a266475b554d5ad95f803a8'], - }), ('swagger', '3.33.1', { 'checksums': ['528369b04c6142112e05ee8b950ca1c01b3e390a4515eacb0fa17db98bafafd1'], }), - ('plumber', '1.2.1', { - 'checksums': ['6ffc13e5ce1ff7ec81f6a4ab04eb1cb9f6da4004cf205ba3098d2ec4a83f1ecc'], - }), ('varhandle', '2.0.5', { 'checksums': ['9b0ee653e0343e292547d2a7052e60a2e7d97d1d5528246862522e67346882d0'], }), diff --git a/easybuild/easyconfigs/v/vitessceR/vitessceR-0.99.0-20230110-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/v/vitessceR/vitessceR-0.99.0-20230110-foss-2022a-R-4.2.1.eb index b9977258fd2..e43d614967d 100644 --- a/easybuild/easyconfigs/v/vitessceR/vitessceR-0.99.0-20230110-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/v/vitessceR/vitessceR-0.99.0-20230110-foss-2022a-R-4.2.1.eb @@ -30,6 +30,12 @@ exts_default_options = { } exts_list = [ + ('sodium', '1.2.1', { + 'checksums': ['f76e98969710af8b6c7c7decf63706d91185eebf8a266475b554d5ad95f803a8'], + }), + ('plumber', '1.2.1', { + 'checksums': ['6ffc13e5ce1ff7ec81f6a4ab04eb1cb9f6da4004cf205ba3098d2ec4a83f1ecc'], + }), (name, version, { 'source_urls': ['https://github.com/vitessce/vitessceR/archive/'], 'sources': [{ From f48088c2414399a09ec9ddd218f819ed91676afe Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 16 Mar 2023 16:18:14 +0100 Subject: [PATCH 6890/9987] PR review changes --- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index aa7ed5b6054..a9a37f4f334 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1152,6 +1152,57 @@ exts_list = [ ('ReactomePA', '1.40.0', { 'checksums': ['458b3febb341700414ca04ea4a6f3005061c9db97622cfdfda6b75a74415a7b9'], }), + ('flowClean', '1.34.1', { + 'checksums': ['d0e58ac89fd302761136cbcd5eb859351a61da2bd8967840bcd054ec16630f7f'], + }), + ('flowAI', '1.26.0', { + 'checksums': ['f4e35c824f68036cea5746236a026ad8e336c2595411d15d303d45fbc02526a5'], + }), + ('flowFP', '1.54.0', { + 'checksums': ['ba12d5bd4dc784997f30435314fe61f86b0c28d99c4458f7e8f9b76daa54b442'], + }), + ('simplifyEnrichment', '1.6.1', { + 'checksums': ['66fafb64d19c5fc4bb7aa6c6805130144f35fd508c2551024aec9f5c7b7b7461'], + }), + ('RPMG', '2.2-3', { + 'checksums': ['74d5bada6a51d280296cb36fae4938c16ba9ed2fa37f3bfb60cf7c541c5b22b6'], + }), + ('Rwave', '2.6-5', { + 'checksums': ['6c9ef75bb376f2e3f5c5dcd3b3fdca7d86797ce809da34f444632657189be2e4'], + }), + ('RSEIS', '4.1-4', { + 'checksums': ['76d5caf30cd3871fa80d27ea694023a4c303ffc099297aeeff03d22538dbff76'], + }), + ('splancs', '2.01-43', { + 'checksums': ['b351565e1f69f6c86a29d921d3a18d5896c4586e2ab8c73bb3df8e75630fc448'], + }), + ('MBA', '0.1-0', { + 'checksums': ['78039905c5b98be2bb79a5f292187a2aca21ef449daeefea58b0cac53a5283af'], + }), + ('GEOmap', '2.5-0', { + 'checksums': ['82e5608eda7330632bc67aa662b649e7b7b3ccdfda6a18a19d2e3379e0db1093'], + }), + ('RFOC', '3.4-6', { + 'checksums': ['0dfa237f4d04eb9a2718942b4d7ed9538fc5f89e3cbaa5a34a4fd1bc6fe54533'], + }), + ('flowDensity', '1.30.0', { + 'checksums': ['c321b395d6f1ae24d1428319401b225ae5e31fee5051127e43142d96f820103d'], + }), + ('flowPeaks', '1.42.0', { + 'checksums': ['ae98124c0574364bf8cd47be7704ad90b2b7d3dabbdd8df7744cbfaf81d665a8'], + }), + ('SamSPECTRAL', '1.50.0', { + 'checksums': ['b55de8cb2092d1b5c192ed0e4b47c421d888e5392165f28395241ca5884b8a5c'], + }), + ('ddPCRclust', '1.16.0', { + 'checksums': ['a457b78a2c254c69ed572d8dca01c66134d6ad2952f72097703110c1d663da5d'], + }), + ('feature', '1.2.15', { + 'checksums': ['de38292b7e800068a20824e2a9e7d5d4d0b465b7925db0d165346aa5030ff67b'], + }), + ('flowMerge', '2.44.0', { + 'checksums': ['ba143b5fff19207f323c1e7b7feaf56fa6e31700422d002521fe49e86bbc5e03'], + }), ('SpatialExperiment', '1.6.1', { 'checksums': ['31e516e14e827e4b9fe853bc136066863dd762053012631c569ec3c00c6cbab5'], }), From 49267f2e0e0c39e8727c5935c4c68929c07e8122 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 16 Mar 2023 15:30:46 +0000 Subject: [PATCH 6891/9987] Update R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb style --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index a9a37f4f334..72d0887ac92 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1152,7 +1152,7 @@ exts_list = [ ('ReactomePA', '1.40.0', { 'checksums': ['458b3febb341700414ca04ea4a6f3005061c9db97622cfdfda6b75a74415a7b9'], }), - ('flowClean', '1.34.1', { + ('flowClean', '1.34.1', { 'checksums': ['d0e58ac89fd302761136cbcd5eb859351a61da2bd8967840bcd054ec16630f7f'], }), ('flowAI', '1.26.0', { From a7d7295aa25e5809350d5b9dbae1def75672b1fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 16 Mar 2023 16:40:55 +0100 Subject: [PATCH 6892/9987] fix the perl shebangs --- .../f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb index 4bde8e513e1..d249cdca076 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb @@ -47,6 +47,8 @@ components = [ }), ] +fix_perl_shebang_for = ['bin/*.pl'] + sanity_check_paths = { 'files': ['bin/fastx_%s' % x for x in From 009e515103443fa7c61f7d8435213c3ac88372d5 Mon Sep 17 00:00:00 2001 From: lenocil Date: Thu, 16 Mar 2023 16:50:15 +0100 Subject: [PATCH 6893/9987] Avro c++ with GCCcore toolchain --- .../avro-cpp-1.11.1-GCCcore-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..17e21b86b52 --- /dev/null +++ b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'avro-cpp' +version = '1.11.1' + +homepage = 'https://avro.apache.org' +description = """C++ implementation of Avro data serialization system.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/apache/avro/archive/refs/tags/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['599f96bb405f72a35154b2477caa6254d723bb4e3f6a0e54e9ae540664321752'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('Boost', '1.77.0', '', ('GCC', '11.2.0')), +] + +srcdir = "lang/c++" + +generator = "Unix Makefiles" +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/avrogencpp"], + 'dirs': ["lib"], +} + +sanity_check_commands = ["avrogencpp -h"] + +moduleclass = 'lib' From 652c494b7f51b826835028c563963225e7bd8ea6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 16 Mar 2023 17:04:55 +0100 Subject: [PATCH 6894/9987] add dep on Perl, add ext PerlIO::gzip, add another sanity check cmd --- .../FASTX-Toolkit-0.0.14-GCC-11.3.0.eb | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb index d249cdca076..652930a60f8 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb @@ -24,7 +24,10 @@ toolchainopts = {'pic': True} default_easyblock = 'ConfigureMake' -dependencies = [('GDGraph', '1.56')] +dependencies = [ + ('GDGraph', '1.56'), + ('Perl', '5.34.1'), +] components = [ ('libgtextutils', '0.7', { @@ -47,6 +50,17 @@ components = [ }), ] +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('PerlIO::gzip', '0.20', { + 'source_tmpl': 'PerlIO-gzip-0.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], + 'checksums': ['4848679a3f201e3f3b0c5f6f9526e602af52923ffa471a2a3657db786bd3bdc5'], + }), +] + fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { @@ -69,6 +83,7 @@ sanity_check_commands = [ 'fasta_formatter -h', 'fastq_masker -h | grep "FASTX Toolkit %(version)s"', 'fastq_quality_boxplot_graph.sh', + 'fastx_barcode_splitter.pl --help | grep "Barcode Splitter, by Assaf Gordon (gordon@cshl.edu), 11sep2008"', 'fastx_clipper -h | grep "FASTX Toolkit %(version)s"', 'fastx_nucleotide_distribution_graph.sh', ] From 304f0825ac14c75de5f69f8bd2b8740aff117315 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 16 Mar 2023 17:08:24 +0100 Subject: [PATCH 6895/9987] Also need to set PERL5LIB --- .../f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb index 652930a60f8..7b16b587b3e 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb @@ -63,6 +63,10 @@ exts_list = [ fix_perl_shebang_for = ['bin/*.pl'] +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' +} + sanity_check_paths = { 'files': ['bin/fastx_%s' % x for x in From d725f608971e073b76e392703056aa9bb6c1d94e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 16 Mar 2023 17:29:17 +0100 Subject: [PATCH 6896/9987] Fix indentation --- .../f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb index 7b16b587b3e..8589f7ecedc 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb @@ -26,7 +26,7 @@ default_easyblock = 'ConfigureMake' dependencies = [ ('GDGraph', '1.56'), - ('Perl', '5.34.1'), + ('Perl', '5.34.1'), ] components = [ From 74a7c591091b1d4c385f74c2f9f0580888d5de06 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 16 Mar 2023 23:05:07 +0100 Subject: [PATCH 6897/9987] {phys}[foss/2022b] TOPAS v3.9, CLHEP v2.4.6.4, GDCM v3.0.21 --- .../c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb | 27 ++++++++++ .../g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb | 28 ++++++++++ .../t/TOPAS/TOPAS-3.9-foss-2022b.eb | 54 +++++++++++++++++++ 3 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/TOPAS/TOPAS-3.9-foss-2022b.eb diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb new file mode 100644 index 00000000000..1a08a4ed224 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.6.4' + +homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] +sources = [SOURCELOWER_TGZ] +checksums = ['49c89330f1903ef707d3c5d79c16a7c5a6f2c90fc290e2034ee3834809489e57'] + +builddependencies = [('CMake', '3.24.3')] + +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..298041d52e0 --- /dev/null +++ b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'GDCM' +version = '3.0.21' + +homepage = 'https://sourceforge.net/projects/gdcm' +description = "Grassroots DICOM: Cross-platform DICOM implementation" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f29dbdd3b6b4c30c9803e6466b88b139d67f5585768565fe29f0be65ad737744'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = "-DGDCM_BUILD_DOCBOOK_MANPAGES=0" + +sanity_check_paths = { + 'files': ['lib/libgdcmCommon.a', 'lib/libgdcmDICT.a'], + 'dirs': ['include/gdcm-%(version_major_minor)s', 'lib/gdcm-%(version_major_minor)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TOPAS/TOPAS-3.9-foss-2022b.eb b/easybuild/easyconfigs/t/TOPAS/TOPAS-3.9-foss-2022b.eb new file mode 100644 index 00000000000..294567fbc07 --- /dev/null +++ b/easybuild/easyconfigs/t/TOPAS/TOPAS-3.9-foss-2022b.eb @@ -0,0 +1,54 @@ +easyblock = 'Bundle' + +name = 'TOPAS' +version = '3.9' + +homepage = 'https://www.topasmc.org' +description = """TOPAS wraps and extends the Geant4 Simulation Toolkit to make advanced Monte Carlo simulation of all +forms of radiotherapy easier to use for medical physicists.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('expat', '2.4.9'), + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), + ('Qt5', '5.15.7'), + ('HarfBuzz', '5.3.1'), + ('GDCM', '3.0.21'), + ('CLHEP', '2.4.6.4'), +] + +local_geant4_configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +local_geant4_configopts += " -DCLHEP_ROOT_DIR=$EBROOTCLHEP -DGEANT4_INSTALL_DATA=OFF -DGEANT4_BUILD_MULTITHREADED=ON " + +components = [ + # TOPAS required Geant4 10.x, which must be built with multi-threading support + ('Geant4', '10.7.4', { + 'github_account': 'Geant4', + 'source_urls': [GITHUB_SOURCE], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}], + 'checksums': ['602b41dfee1fa6b33b026d00c5bd940155d7e5d0b3495230a87e2a25b28f9996'], + 'start_dir': 'geant4-%(version)s', + 'configopts': local_geant4_configopts, + }), + (name, version, { + 'easyblock': 'CMakeMake', + 'download_instructions': "Manual download required, see https://www.topasmc.org/download", + 'sources': ['topas_%(version_major)s_%(version_minor)s.zip'], + 'checksums': ['57739f8df5fe58f47b2cc5ac646b4776ab137d52640c6e5b1f6cd199ed3c7b0f'], + 'start_dir': 'topas_%(version_major)s_%(version_minor)s', + }), +] + +sanity_check_paths = { + 'files': ['bin/topas', 'lib/libchemistry.a', 'lib/libG4run.%s' % SHLIB_EXT, 'lib/libmain.a', 'lib/libphysics.a'], + 'dirs': ['examples', 'include'], +} + +moduleclass = 'phys' From d22d9afecb68d6f32ed82b9e12f1560aa32f60c4 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 16 Mar 2023 23:11:18 +0100 Subject: [PATCH 6898/9987] Fixed version mismatch --- .../Circuitscape-5.11.2-Julia-1.7.2.eb | 474 +++++++++++------- 1 file changed, 285 insertions(+), 189 deletions(-) diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb index 4b2dae94cfd..54a4bb27579 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb @@ -30,283 +30,379 @@ exts_list = [ 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], }), - ('CommonSolve', '0.2.3', { - 'source_urls': ['https://github.com/SciML/CommonSolve.jl/archive/'], + ('IntelOpenMP_jll', '2018.0.3+2', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/IntelOpenMP_jll.jl/archive/'], + 'sources': ['IntelOpenMP-v%(version)s.tar.gz'], + 'checksums': ['4e8586f0b794ba5cf159dde99774aab4509a32555fc900140f533999db476aab'], + }), + ('MKL_jll', '2022.2.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/MKL_jll.jl/archive/'], + 'sources': ['MKL-v%(version)s.tar.gz'], + 'checksums': ['228a80c33ae71a3efc78ed9f6a3329fd20a48ad80ff7af44f0d42057e1af4241'], }), ('Reexport', '1.2.2', { 'source_urls': ['https://github.com/simonster/Reexport.jl/archive/'], 'checksums': ['2566f7776aae9697cbf15765fc32187f46dd51200abc953a0266863ad67132b3'], }), + ('CommonSolve', '0.2.3', { + 'source_urls': ['https://github.com/SciML/CommonSolve.jl/archive/'], + 'checksums': ['5a1fe0c82571697e45bf8d4488b68a656584b07c8a2045b26e52ae01ec118e1b'], + }), ('AlgebraicMultigrid', '0.5.1', { 'source_urls': ['https://github.com/JuliaLinearAlgebra/AlgebraicMultigrid.jl/archive/'], + 'checksums': ['c33896880d1495b2ffc80dcbe5a2a2d6f305a9555e041ebd1191899e824e75e7'], }), - ('CEnum', '0.4.2', { - 'source_urls': ['https://github.com/JuliaInterop/CEnum.jl/archive/'], + ('Pardiso', '0.5.4', { + 'source_urls': ['https://github.com/JuliaSparse/Pardiso.jl/archive/'], + 'checksums': ['b60a693dd71a19fc3155b36683f8c812f217de59ee7eda77c9cd0855468a3c4a'], + }), + ('GZip', '0.5.1', { + 'source_urls': ['https://github.com/JuliaIO/GZip.jl/archive/'], + 'checksums': ['c74976af07cbe835a5bb5396ade41feb90a782267e94bc3a98bb1ad1446ba54f'], }), - ('Requires', '1.3.0', { - 'source_urls': ['https://github.com/JuliaPackaging/Requires.jl/archive/'], - 'checksums': ['8af4dac29839e796a651b8cb6a325b6f9c7eee5d5620b3e366b64f58325ebeb7'], + ('SnoopPrecompile', '2.9.5', { + 'source_urls': ['https://github.com/timholy/SnoopCompile.jl/archive/'], + 'start_dir': '%(name)s', + 'checksums': ['a86ca9179fac77efd3771c71c620914aa6909754d474cd754f2ee8600fad9a4a'], + }), + ('RecipesBase', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPlots/RecipesBase.jl/archive/'], + 'checksums': ['2a4b7371e565f175a018c0df0cc24dce41fc2f103ad80de87f6c5bc600dbca1a'], + }), + ('NaNMath', '1.0.1', { + 'source_urls': ['https://github.com/JuliaMath/NaNMath.jl/archive/'], + 'checksums': ['caa5666b24b4c5fb8f4d3e4b650f6360e8e19b8bd2d1cb3019a15849c363c45d'], }), ('FixedPointNumbers', '0.8.4', { 'source_urls': 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{ - 'source_urls': ['https://github.com/sbromberger/LightGraphs.jl/archive/'], + ('ImageCore', '0.9.4', { + 'source_urls': ['https://github.com/JuliaImages/ImageCore.jl/archive/'], + 'checksums': ['de5d244989891f47edc4f27bf8bf6557a6982e907f0874a62ad3480c9c333983'], }), - ('SimpleWeightedGraphs', '1.1.0', { - 'source_urls': ['https://github.com/sbromberger/SimpleWeightedGraphs.jl/archive/'], + ('ArchGDAL', '0.8.5', { + 'source_urls': ['https://github.com/yeesian/ArchGDAL.jl/archive/'], + 'checksums': ['e24ec57d88a3a07feac7db5b2501b8f06a1047c42a8eadcde9500e3601984065'], }), (name, version, { - 'source_urls': ['https://github.com/Circuitscape/Circuitscape.jl/archive/'] + 'source_urls': ['https://github.com/Circuitscape/Circuitscape.jl/archive/'], + 'checksums': ['5bdf407cd1954d342be1023e03948983331b70bf7c28d467e3aae31c0938e9d8'], }), ] From b217c04f362943bba5e63b5b1ae479601a20898c Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 17 Mar 2023 08:05:42 +0100 Subject: [PATCH 6899/9987] adding easyconfigs: FFTW-3.3.8-iomkl-2020b.eb --- .../f/FFTW/FFTW-3.3.8-iomkl-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iomkl-2020b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iomkl-2020b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iomkl-2020b.eb new file mode 100644 index 00000000000..a3012e1e59c --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iomkl-2020b.eb @@ -0,0 +1,28 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'iomkl', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +patches = ['FFTW-%(version)s_fix-icc-no-gcc.patch'] +checksums = [ + '6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303', # fftw-3.3.8.tar.gz + '1b3319b98a2ca4ead68290b3229385c0573e22749a5a2ffb49486a0bbb37dc1e', # FFTW-3.3.8_fix-icc-no-gcc.patch +] +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False + +runtest = 'check' + +moduleclass = 'numlib' From 4111f711dfca1c970c9618e612b59766a94db32c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 17 Mar 2023 08:29:32 +0100 Subject: [PATCH 6900/9987] adding easyconfigs: M3GNet-0.2.4-foss-2022a.eb, pymatgen-2023.3.10-foss-2022a.eb --- .../m/M3GNet/M3GNet-0.2.4-foss-2022a.eb | 42 ++++++++++ .../pymatgen/pymatgen-2023.3.10-foss-2022a.eb | 81 +++++++++++++++++++ 2 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/m/M3GNet/M3GNet-0.2.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/M3GNet/M3GNet-0.2.4-foss-2022a.eb b/easybuild/easyconfigs/m/M3GNet/M3GNet-0.2.4-foss-2022a.eb new file mode 100644 index 00000000000..65f7885f206 --- /dev/null +++ b/easybuild/easyconfigs/m/M3GNet/M3GNet-0.2.4-foss-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'M3GNet' +version = '0.2.4' + +homepage = 'https://materialsvirtuallab.github.io/m3gnet/' +description = """" +M3GNet is a new materials graph neural network architecture that incorporates +3-body interactions. A key difference with prior materials graph +implementations such as MEGNet is the addition of the coordinates for atoms and +the 3×3 lattice matrix in crystals, which are necessary for obtaining tensorial +quantities such as forces and stresses via auto-differentiation. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('ASE', '3.22.1'), + ('TensorFlow', '2.11.0'), + ('pymatgen', '2023.3.10'), + ('h5py', '3.7.0'), # optional, for model saving +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['a7f82b06f48d8fb81f91fb88484177005066cdf708902bf749afaa7f8d117ce8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/m3g'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/m3gnet'], +} + +sanity_check_commands = ['m3g --help'] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb new file mode 100644 index 00000000000..1adc774c4b6 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'pymatgen' +version = '2023.3.10' + +homepage = 'https://pymatgen.org/' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('hypothesis', '6.46.7'), # required for numpy tests +] + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('matplotlib', '3.5.2'), + ('networkx', '2.8.4'), + ('sympy', '1.11.1'), + ('plotly.py', '5.12.0'), + ('tqdm', '4.64.0'), + +] + +use_pip = True + +# pymatgen 2023.3.10 requires spglib >= 2.0.2 +# skip import check for ruamel.yaml.clib, covered by import check for ruamel.yaml extension +exts_list = [ + ('monty', '2022.9.9', { + 'checksums': ['6cca8f14a18a2030b243a1377dfd59049a1ccce007b34f810a8f5eece72b9ceb'], + }), + ('palettable', '3.3.0', { + 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('ruamel.yaml', '0.17.21', { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('uncertainties', '3.1.7', { + 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], + }), + ('latexcodec', '2.0.1', { + 'checksums': ['2aa2551c373261cefe2ad3a8953a6d6533e68238d180eb4bb91d7964adb3fe9a'], + }), + ('pybtex', '0.24.0', { + 'checksums': ['818eae35b61733e5c007c3fcd2cfb75ed1bc8b4173c1f70b56cc4c0802d34755'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('emmet-core', '0.49.1', { + 'modulename': 'emmet', + 'checksums': ['8133d63900c170ac5c66efe8d70c32c9762c9a42fc150a79c7c90a8477ac81ec'], + }), + ('mp-api', '0.30.10', { + 'checksums': ['b58522b106f362d6917eba97ef8d699cc87210b65a9f0a8ac70c0841110ce50a'], + }), + ('spglib', '2.0.2', { + 'checksums': ['1d081ec22da4ab4fc3198e9445ddad6dec2261c43927831151d93e39422610aa'], + }), + (name, version, { + 'checksums': ['20a5d1681e2951d2710d5358197b5b58992e2b0ec4217a5ba966cf28513c1283'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pmg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pmg --help"] + +sanity_pip_check = True + +moduleclass = 'chem' From 22cdd63e83aa8db50e013b6d528ed2eae641473a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 17 Mar 2023 09:52:16 +0100 Subject: [PATCH 6901/9987] prepare release notes for EasyBuild v4.7.1 + bump version to 4.7.1 --- RELEASE_NOTES | 93 +++++++++++++++++++++++++++++++++++++++++++++++++-- setup.py | 2 +- 2 files changed, 92 insertions(+), 3 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 5286c71d11c..e1a2f41692d 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,16 +3,105 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 16,138 easyconfig files, for 2,904 different software packages, +The latest version of easybuild-easyconfig provides 16,603 easyconfig files, for 2,984 different software packages, incl. 39 different (compiler) toolchains. +v4.7.1 (March 20th 2023) +------------------------ + +update/bugfix release + +- added example easyconfig files for 90 new software packages: + - astro-tulips (#17263), BA3-SNPS-autotune (#17248), BayesAss3-SNPs (#17247), Block (#27), CatLearn (#14940), CDFlib (#17133), Cellpose (#13703), CheckM-Database (#17462), chemprop (#17261), cimfomfa (#17268), conan (#17326), cooler (#17328), crossguid (#16207), cuSPARSELt (#17141), cython-blis (#17544), DBCSR (#17170), dclone (#17225), Deprecated (#1248), DLPack (#17311), DMLC-Core (#17311), dorado (#17195), duplex-tools (#17497), eQuilibrator (#16812), fastai (#16985), fastjet (#17367), fastjet-contrib (#17377), ffnvcodec (#17271), finder (#1917), flowFDA (#17495), genomepy (#17506), GKeyll (#16044), GraphDB (#17280), graphviz-python (#17352), GUSHR (#16905), Health-GPS (#17434), HepMC3 (#17341), HiCMatrix (#17330), Inferelator (#17223), irodsfs (#17486), jupyter-contrib-nbextensions (#17270), jupyterlab-lmod (#16563), jupyterlmod (#16563), kb-python (#17260), kineto (#17194), KMCP (#17267), krbalancing (#17325), Lace (#954), LASSO-Python (#17510), libemf (#16188), loomR (#14518), MAGMA-gene-analysis MAKER (#17345), methylartist (#17264), nanoflann (#17311), netMHCII (#9741), NEXUS-CL (#17350), nichenetr (#17524), Parallel-Hashmap pdsh (#17139), Perseus (#17210), PfamScan (#17530), Phenoflow (#17495), PIRATE (#17275), plot1cell (#17498), pybinding (#17137), pyperf (#17063), pyslim (#17150), pytest-rerunfailures (#17295), pytest-shard (#17295), PyTorch-Ignite (#15491), PyVCF3 (#17519), R2jags (#17226), rapidcsv (#16211), rapidNJ (#17399), Rivet (#17380), rmarkdown (#17189), scArches (#17069), scHiCExplorer (#17334), scib (#17142), SeaView (#17385), siscone (#17342), sparse-neighbors-search (#17329), sradownloader (#17188), stardist (#17215), Strainberry (#17522), toil (#17098), vConTACT2 (#17372), VirSorter2 (#17371), vitessce-python (#17472), YODA (#17343) +- added additional easyconfigs for various supported software packages, including: + - AlphaFold 2.3.0, alsa-lib v1.2.8, Anaconda3 2022.10, angsd 0.940, ANIcalculator 1.0, archspec 0.2.0, Armadillo 11.4.3, arpack-ng 3.8.0, astro tulips, AUGUSTUS 3.5.0, Autotools 20220317, BA3-SNPS-autotune 2.1.2, BCFtools 1.17, bcl2fastq2 2.20.0, beagle-lib 4.0.0, Beast 2.7.3, BeautifulSoup 4.11.1, Bio-SearchIO-hmmer 1.7.3, BLAT 3.7, Blender 3.4.1, Blitz++ 1.0.2, Block 1.5.3, Blosc2 2.6.1, Boost 1.81.0, Bottleneck 1.3.6, Bowtie 1.3.1, BRAKER 2.1.6, Brotli-python 1.0.9, Brunsli 0.1, BUSCO 5.4.5, bx-python 0.9.0, canu 2.2, CatLearn 0.6.2, CatMAP 20220519, CDFlib 0.4.9, CD-HIT 4.8.1, Cellpose 0.6.5, CellRanger 7.1.0, Cereal 1.3.2, CFITSIO 4.2.0,CheckM 1.2.2, chemprop 1.5.2, cimfomfa 22.273, code-server 4.9.1, conan 1.58.0, configurable-http-proxy 4.5.3, cooler 0.9.1, cppy 1.2.1, crossguid 20190529, csvkit 1.1.0, CubeLib 4.8, CubeWriter 4.8, CUDA 12.1.0, cuDNN 8.8.0.121, cuTENSOR 1.6.1.5, cwltool 3.1.20221008225030, Cython 0.29.33, cython-blis 0.9.1, DBCSR 2.5.0, dclone 2.3, Deprecated 1.2.13, DFT-D3 3.2.0, DGL 0.9.1, DIAMOND 2.1.0, dill 0.3.6, DIRAC 22.0, DIRAC 23.0, dm-tree 0.1.8, DoubletFinder 2.0.3, dRep 3.4.2, edlib 1.3.9, eggnog-mapper 2.1.10, Eigen 3.4.0, elfutils 0.189, ELPA 2022.05.001, epiScanpy 0.4.0, eQuilibrator 0.4.7, Exonerate 2.4.0, FabIO 0.14.0, fastai 2.7.10, fastai 2.7.10, FastANI 1.33, fastjet 3.4.0, fastjet-contrib 1.0.49, FastQ_Screen 0.14.0, FFmpeg 5.1.2, ffnvcodec 11.1.5.2, finder 1.1.0, FLAC 1.4.2, flatbuffers 2.0.7, flatbuffers 23.1.4, FLINT 2.9.0, GDAL 2.4.4, GDAL 3.6.2, GDGraph 1.56, GeneMark-ET 4.71, genomepy 0.15.0, GenomeTools 1.6.2, GEOS 3.11.1, GEOS 3.9.1, giflib 5.2.1, GKeyll 20220803, GLPK 5.0, GMAP-GSNAP 2023-02-17, gmpy2 2.1.2, gmsh 4.11.1, gnuplot 5.4.6, googletest 1.12.1, GPyTorch 1.9.1, GraphDB 10.1.5, Graphene 1.10.8, Greenlet 2.0.2, GSL 2.7, GST-plugins-base 1.22.1, GStreamer 1.22.1, GTDB-Tk 2.1.1, h5py 3.7.0, h5py 3.8.0, HDBSCAN 0.8.29, HDF 4.2.15, HDF5 1.14.0, HepMC3 3.2.5, HiCExplorer 3.7.2, HiCMatrix 17, HighFive 2.6.2, Highway 1.0.3, HISAT2 2.2.1, HMMER 3.3.2, HPL 2.3, HTSlib 1.17, Hyperopt 0.2.7, hypothesis 6.68.2, Hypre 2.27.0, igraph 0.10.3, IGV 2.16.0, IJulia 1.24.0, Imath 3.1.6, IMB 2021.3, imbalanced-learn 0.10.1, imkl 2021.4.0, imkl 2022.1.0, imkl 2023.0.0, imkl-FFTW 2023.0.0, impi 2021.8.0, Inferelator 0.6.1, intel-compilers 2023.0.0, IRkernel 1.3.2, irodsfs 0.8.11, irodsfs 0.8.12, irodsfs 0.8.9, JAGS 4.3.1, jax 0.4.4, Jellyfish 2.3.0, jemalloc 5.2.1, json-c 0.16, Julia 1.8.5, JupyterHub 3.0.0, jupyter-matlab-proxy 0.5.0, jupyter-resource-usage 0.6.3, jupyter-server-proxy 3.2.2, KaHIP 3.14, Kaleido 0.2.1, kallisto 0.48.0, Kent_tools 442, kineto 0.4.0, KMCP 0.9.1, Kraken 1.1.1, Lace 1.14.1, LAME 3.100, leidenalg 0.9.1, LERC 4.0.0, libcerf 2.3, libemf 1.0.13, libgd 2.3.3, libgeotiff 1.7.1, libgit2 1.5.0, libnsl 2.0.0, libogg 1.3.5, libopus 1.3.1, libsndfile 1.2.0, libtirpc 1.3.3, libvorbis 1.3.7, libxslt 1.1.37, Longshot 0.4.5, loompy 3.0.7, loomR 0.2.0, lpsolve 5.5.2.11, LTR_retriever 2.9.0, Lua 5.4.4, MAFFT 7.505, MAKER 3.01.04, Maple 2022.1, Mash 2.3, MaSuRCA 4.1.0, Mathematica 13.1.0, MATIO 1.5.23, MATLAB 2022a, MATLAB 2022b, matplotlib 3.7.0, MaxQuant 2.2.0.0, MCL 14.137, MCL 22.282, MEGAHIT 1.2.9, MetaBAT 2.15, MetaEuk 6, methylartist 1.2.6, METIS 5.1.0, Miniconda3 22.11.1, minimap2 2.24, mm-common 1.0.5, motif 2.3.8, MPFR 4.2.0, mpi4py 3.1.4, mpmath 1.2.1, MrBayes 3.2.7, msprime 1.2.0, MultiQC 1.14, MUMmer 4.0.0rc1, mygene 3.2.2, NAMD 2.14, nano 7.1, nanomax-analysis-utils 0.4.4, ncbi-vdb 3.0.2, NCO 5.1.3, netCDF 4.9.0, NetLogo 6.2.2, NetLogo 6.3.0, netMHCII 2.3, nettle 3.8.1, networkx 2.8.4, Nextflow 22.10.5, Nextflow 22.10.6, nlohmann_json 3.11.2, NLopt 2.7.1, numba 0.56.4, NVHPC 22.11, NVHPC 22.9, NVHPC 23.1, NVSHMEM 2.8.0, occt 7.5.0p1, OPARI2 2.0.7, OpenEXR 3.1.5, OpenMM 7.5.1, OpenMPI 4.1.1, OpenMPI 4.1.5, Optuna 3.1.0, ORCA 5.0.4, OSU-Micro-Benchmarks 5.9, OTF2 3.0.2, PAML 4.10.5, panaroo 1.3.2, parallel-fastq-dump 0.6.7, Parallel-Hashmap 1.33, ParallelIO 2.5.10, parasail 2.6, ParMETIS 4.0.3, PCRE 8.45, pdsh 2.34, pdsh 2.34, PDT 3.25.1, Perl 5.36.0, Pillow 9.4.0, PIPITS 3.0, pkgconfig 1.5.5, PLINK 2.00a3.7, plotly.py 5.12.0, plotly.py 5.13.1, PLUMED 2.8.1, PnetCDF 1.12.3, poetry 1.2.2, polymake 4.8, PRANK 170427, preseq 3.2.0, presto 1.0.0, prodigal 2.6.3, PROJ 9.1.1, prokka 1.14.5, protobuf 3.21.9, psycopg2 2.9.5, pyBigWig 0.3.18, pybind11 2.10.3, pybinding 0.9.5, PyCharm 2022.3.2, py-cpuinfo 9.0.0, pydot 1.4.2, pyFAI 0.21.3, pyfaidx 0.7.1, pyGenomeTracks 3.8, pygraphviz 1.10, pymca 5.7.6, Pysam 0.20.0, PySCF 2.1.1, PyTables 3.8.0, Python 3.11.2, python-igraph 0.9.1, python-parasail 1.3.3, PyZMQ 24.0.1, QCG-PilotJob 0.13.1, Qhull 2020.2, QIIME2 2022.11, Qt5Webkit 5.212.0, QtPy 2.3.0, QUAST 5.2.0, R2jags 0.7, rapidcsv 8.64, rapidNJ 2.3.3, Ray-project 2.2.0, RDKit 2022.09.4, RECON 1.08, Redis 7.0.8, redis-py 4.5.1, ReFrame 4.0.1, ReFrame 4.0.5, RepeatMasker 4.1.4, RepeatModeler 2.0.4, RepeatScout 1.0.6, Rivet 3.1.7, rjags 4-13, rmarkdown 2.20, RMBlast 2.13.0, Roary 3.13.0, ROOT 6.22.08, RSEM 1.3.3, Salmon 1.9.0, SAMtools 1.17, Scalasca 2.6.1, scanpy 1.9.1, scArches 0.5.6, scikit-learn 1.2.1, scikit-misc 0.1.4, SciPy-bundle 2023.02, Score-P 6.0, Score-P 7.0, Score-P 8.0, SDL2 2.26.3, SEPP 4.5.1, SeqKit 2.3.1, silx 1.0.0, SIONlib 1.7.7, snakemake 7.18.2, snakemake 7.22.0, SNAP 2.0.1, SNAP-HMM 20221022, SpaceRanger 2.0.1, SPAdes 3.15.5, spaln 2.4.13f, Spark 3.3.1, sparsehash 2.0.4, sradownloader 3.9, SRA-Toolkit 3.0.0, SRA-Toolkit 3.0.3, SSW 1.2.4, STAR 2.7.10b, STAR-CCM+ 18.02.008, stardist 0.8.3, Strainberry 1.1, STREAM 5.10, STREAM 5.10, SVG 2.87, sympy 1.10.1, sympy 1.11.1, Szip 2.1.1, TensorFlow-Datasets 4.8.3, Tk 8.6.12, Tkinter 3.10.8, toil 5.8.0, tqdm 4.64.1, TRF 4.09.1, Trilinos 13.4.1, Trim_Galore 0.6.10, Trinity 2.15.1, TWL-NINJA 0.98, UDUNITS 2.2.28, umap-learn 0.4.6, umap-learn 0.5.3, Unidecode 1.3.6, vConTACT2 0.11.3, velocyto 0.17.17, VirSorter2 2.2.4, vsc-mympirun 5.3.0, VSEARCH 2.22.1, wget 1.21.3, wtdbg2 2.5, wxWidgets 3.2.2.1, x264 20230226, x265 3.5, Xerces-C++ 3.2.4, xtb 6.5.0, xtb 6.5.1, Xvfb 21.1.6, xxd 8.2.4220, Yasm 1.3.0, YODA 1.9.7 +- minor enhancements, including: + - add ggvenn extension to R 4.2.1 (#17043) + - add scatterpie and shadowtext extensions to R-4.2.1 (#17125) + - add DO.db, GOSemSim, DOSE, enrichplot, and clusterProfiler extensions to Bioconductor 3.15 (#17126) + - add sanity check command to OpenMolcas v22.10 (#17128) + - add Set::Object and Heap::Fibonacci extensions to Perl 5.32.1 (#17151) + - add additional extensions to Python 3.10.8 (required for scipy test suite) (#17159) + - enable -fPIC in GEOS 3.11.1 (required by GDAL) (#17196) + - enhance OpenFold 1.0.1 for standalone usage (#17206) + - add SDL2 dependency for FFmpeg 5.0.1 to build ffplay (#17213) + - set $JULIA_DEPOT_PATH and $JULIA_HISTORY in Julia easyconfigs (#17216) + - add random + R2WinBUGS extensions to R 4.2.1 (#17224) + - add Devel::Size extension to recent Perl extensions (#17246) + - Combine errors of extension patch check into a single failure (#17286) + - Add case-insensitive name clash test (#17303) + - Add ReactomePA extension and deps to R-bundle-Bioconductor/3.15 (#17315) + - add ffnvcodec build dependency to all recent FFmpeg easyconfigs (#17316) + - use 'import deap.base' in sanity check for deap extension in SciPy-bundle 2022.05 (#17429) + - add source URL to cuDNN 8.8 easyconfig (#17439) + - add Math::Utils extension to recent Perl easyconfigs (#17466) + - add missing zstd dep to Boost (#17482) + - add additional extensions for R 4.2.1 (#17493) + - add additional extensions for R-bundle-Bioconductor 3.15 (#17494) + - add smoof/mlrMBO/emoa extensions to R 4.2.1 (#17523) +- various bug fixes, including: + - fix postinstallcmds and clarify download instructions for netMHC-4.0a (#9739) + - fix postinstallcmds and clarify download instructions for netMHCpan-4.0a (#9740) + - fix OpenBLAS 0.3.15 patch to correctly set the CPU core type for Tiger Lake (#15845) + - add alternative checksum for UCX 1.13.1 after source tarball was changed in-place (without actual code changes) (#17077) + - fix build of TensorFlow 2.5+ on aarch64 (#17101) + - explictely download qe-gipaw source tarball from qe-gipaw GitHub repository in QuantumESPRESSO 7.1 easyconfigs (#17129) + - add patch for GCCcore 11.1.0 + 11.2.0 to fix AVX2 bug (#17135) + - add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2 (#17140) + - fix source URL for p7zip v17.x, moved to p7zip-project repo (#17144) + - add patches for Qt5 5.15.5 to fix compilation failures in abseil and breakpad with glibc 2.34 (#17165) + - remove dependency on Pillow from scikit-bio v0.5.7 (#17178) + - correctly specify path to libfabric installation prefix in PMIx 4.1.0 easyconfig (#17204) + - use GCC as toolchain for serial variants of HDF5, since it has a FORTRAN API (#17221) + - fix CMake print summary for long hostnames for NECI (#17230) + - fix website/docs links in README (#17232) + - add missing pmix patch to OpenMPI 4.1.1 easyconfig used in iomkl/2021a and iomkl/2021b (#17240) + - include required stereo_chemical_props.txt for OpenFold 1.0.1 (#17242) + - add patch for PAPI 7.0.0 to fix compilation error (#17244) + - also update $PERL5LIB for RepeatMasker v4.1.4 (#17245) + - add alternative source_url for MariaDB > 10.4 (#17250) + - remove use of rysnc in building Kent_tools (#17252) + - add missing pkgconf build dependency in recent libxslt easyconfigs (#17254) + - add psycopg2, PyYAML, and Cartopy dependencies to QGIS 3.28.1 (#17257) + - fix postinstallcmds in shovill easyconfigs (#17279) + - allow multiple easyconfigs with same name if they differ by CUDA version included in versionsuffix (#17289) + - remove duplicate SlamDunk easyconfig using lowercase name (#17301) + - use https in homepage + source URL for GenomeThreader 1.7.3 (#17338) + - Archive BAMM, BamM, and GroopM to avoid BAMM/BamM name collision (#17348) + - consistently use NanoFilt capitalisation (#17349) + - rename ncl to NEXUS-CL to avoid case-insensitive name clash (#17350) + - consistently use Check capitailisation (#17351) + - rename python graphviz to graphviz-python to avoid case-insensitive name clash (#17352) + - add alternative checksum for spatial 7.3-14 extension in R 4.1.x easyconfigs (#17356) + - fix homepage + source URL for ELPA (due to switch to new domain) (#17357) + - fix homepage in ELPA easyconfigs (due to switch to new domain) (#17358) + - rename libpsml for consistency with libPSML (#17359) + - archive charmm and CHARMM easyconfigs to avoid case-insensitive name clash (#17364) + - replace obsolete pycrypto with pycryptodome in Python 3.10.x easyconfigs (#17412) + - update deap to version 1.3.3 in SciPy-bundle 2022.05 easyconfigs (since deap 1.3.1 is broken) (#17413) + - add patch for Qt5 5.12.2 with GCCcore/11.2.0 to fix template bug (#17464) + - replace src include path with installation dir for HDF5 (#17469) + - replace src include path with installation dir for HDF5 (intel) (#17488) + - disable Python support for OTF2 v2.2, since we're not including Python 2.x as dependency (#17499) + - update homepage and source urls of DFT-D3 (#17528) + - use Binary easyblock for ANIcalculator to prevent RPATH sanity check failures (#17536) +- other changes: + - fix invalid escape sequences in easyconfigs by using raw strings (r"...") (#11149) + - add exception for ncbi-vdb 3.0.0 dependency variant (#17131) + - use proper source tarball instead of cloning GitHub repository for wxWidgets v3.2.1 (#17167) + - remove commented out line and delete unused patch for TALON (#17298) + - re-enable disabled tests (#17304) + - rename MAGMA to MAGMA-gene-analysis to avoid name collision (#17345) + - Archive ARB and blasr patch files (#17346) + + 4.7.0 (Janurary 9th 2023) ------------------------- feature release -- added easyconfigs for foss/2022a, intel/2022a common toolchains (#16961 and #16962) +- added easyconfigs for foss/2022b, intel/2022b common toolchains (#16961 and #16962) - see also https://docs.easybuild.io/en/latest/Common-toolchains.html - added easyconfigs for NVHPC-based toolchains nvompi/2022.07 and nvofbf/2022.07 (#16724) - added example easyconfig files for 107 new software packages: diff --git a/setup.py b/setup.py index ea1457adbeb..3820ff609f1 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.7.1.dev0' +VERSION = '4.7.1' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From d42c60d64dd94a11f9f4b5786de56e969858c12f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 17 Mar 2023 10:37:58 +0000 Subject: [PATCH 6902/9987] Switch to torchdata 0.5.1 --- .../PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb index 89b09adbe87..62ab4bc5ff8 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -31,6 +31,8 @@ exts_list = [ 'checksums': ['ced67e1cf1f97e168cdf271851a4d0b6d382ab7936e7bcbb39aaa87239c324b6'], }), ('torchtext', '0.14.1', { + # Disable bundled libraries to use those from EB: RE2, SentencePiece + 'preinstallopts': "sed -i '/third_party/d;/BuildExtension/d' setup.py &&", 'source_urls': ['https://github.com/pytorch/text/archive'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'], @@ -45,10 +47,10 @@ exts_list = [ 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['33e7485cea3cac08d7a49a3a01d3013e1156128867602bff0a8e32b2c5ebd4e9'], }), - ('torchdata', '0.6.0', { + ('torchdata', '0.5.1', { 'source_urls': ['https://github.com/pytorch/data/archive'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['048dea12ee96c0ea1525097959fee811d7b38c2ed05f44a90f35f8961895fb5b'], + 'checksums': ['69d80bd33ce8f08e7cfeeb71cefddfc29cede25a85881e33dbae47576b96ed29'], }), ] From 205ca1ad7e1fa3a34b2cdacf92864bc89b7cac0c Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 17 Mar 2023 13:35:38 +0100 Subject: [PATCH 6903/9987] adding easyconfigs: FFTW-3.3.8-iompi-2020b.eb --- .../f/FFTW/FFTW-3.3.8-iompi-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb new file mode 100644 index 00000000000..3c7c5f30841 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb @@ -0,0 +1,26 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'iompi', 'version': '2020b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +patches = ['FFTW-%(version)s_fix-icc-no-gcc.patch'] +checksums = [ + '6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303', # fftw-3.3.8.tar.gz + '1b3319b98a2ca4ead68290b3229385c0573e22749a5a2ffb49486a0bbb37dc1e', # FFTW-3.3.8_fix-icc-no-gcc.patch +] + +# no quad precision, requires GCC v4.6 or higher +# see also +# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +runtest = 'check' + +moduleclass = 'numlib' From f31ccc09d7c4c045ec984c9f42ab08e3e1f322a1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Mar 2023 12:37:07 +0000 Subject: [PATCH 6904/9987] update package versions, fix order and add missing R package dependencies --- .../easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 608 +++++++++++------- 1 file changed, 367 insertions(+), 241 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 6ddae77d0a9..0696494be9a 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -172,6 +172,9 @@ exts_list = [ ('mime', '0.12', { 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], }), + ('commonmark', '1.8.1', { + 'checksums': ['96adcb093de3d2e48811af402da70e7222a313b97f1e979e0cbe84dd59bd5cbe'], + }), ('markdown', '1.5', { 'checksums': ['001503f95fa59b399c0fc9178b0a4f5ab745f38879d38985c6642e944c2e9816'], }), @@ -190,8 +193,8 @@ exts_list = [ ('rmeta', '3.0', { 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], }), - ('MASS', '7.3-58.2', { - 'checksums': ['b5c09d5368ca432bb21ebb4997433dbefb28e19174851e2d8358bab02add784b'], + ('MASS', '7.3-58.3', { + 'checksums': ['42e5599582dca0d32bc9c709216ddc71df1761af23f11cfa25d582212a5c79ae'], }), ('lattice', '0.20-45', { 'checksums': ['22388d92bdb7d3959da84d7308d9026dd8226ef07580783729e8ad2f7d7507ad'], @@ -235,8 +238,8 @@ exts_list = [ ('pkgconfig', '2.0.3', { 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], }), - ('rlang', '1.0.6', { - 'checksums': ['e6973d98a0ea301c0da1eeaa435e9e65d1c3f0b95ed68bdc2d6cb0c610166760'], + ('rlang', '1.1.0', { + 'checksums': ['f89859d91c9edc05fd7ccf21163fe53ad58da907ee273a93d5ab004a8649335b'], }), ('ellipsis', '0.3.2', { 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], @@ -247,12 +250,12 @@ exts_list = [ ('cli', '3.6.0', { 'checksums': ['b6078131803043d53d4e670aa3a0506f614e0b40fda8e0102afd48a6188ab896'], }), - ('vctrs', '0.5.2', { - 'checksums': ['76bf10243b9b31e23f56ffdaa1677a01767699e2098487f86bd42cb801d8c047'], - }), ('lifecycle', '1.0.3', { 'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'], }), + ('vctrs', '0.6.0', { + 'checksums': ['be0b712c4e6aae353120a60ded6a4301eb9631c8d256927b79b9ad83b4299757'], + }), ('hms', '1.1.2', { 'checksums': ['1ee6a9847336aaf58d3fcee5b56c290c2204e1213b6628862818419b2302bded'], }), @@ -268,6 +271,9 @@ exts_list = [ ('progress', '1.2.2', { 'checksums': ['b4a4d8ed55db99394b036a29a0fb20b5dd2a91c211a1d651c52a1023cc58ff35'], }), + ('RcppArmadillo', '0.12.0.1.0', { + 'checksums': ['73c6153b79c0b71a896d76031424fe1c0a3ad44a9d09f922a084bb3fbfd3fbea'], + }), ('ade4', '1.7-22', { 'checksums': ['007df54e83a2a6cb8d6da8006f0aace011e7eaa7744dc5f8230ac2c002b393b4'], }), @@ -283,6 +289,9 @@ exts_list = [ ('brew', '1.0-8', { 'checksums': ['11652d5a7042d645cc5be5f9f97ff4d46083cea7d3ad2dd6ad1570b52c097826'], }), + ('Matrix', '1.5-3', { + 'checksums': ['4e720f4edc97b1c09646a445851b1ce955caf6b1de8306a2283328b526fee00d'], + }), ('Brobdingnag', '1.2-9', { 'checksums': ['f9012d250bc2a0f47815d6a7c06df2d4ddf3d8bab2d3b75e8cdefd964d20e91e'], }), @@ -307,9 +316,6 @@ exts_list = [ ('fastmatch', '1.1-3', { 'checksums': ['1defa0b08bc3f48e4c3e4ba8df4f1b9e8299932fd8c747c67d32de44f90b9861'], }), - ('ffbase', '0.12.3', { - 'checksums': ['a52998ec589c2b519034757919565473273f8b73486d8333ba7ff6deec3ae9db'], - }), ('iterators', '1.0.14', { 'checksums': ['cef3075a0930e1408c764e4da56bbadd4f7d14315809df8f38dd51f80ccc677b'], }), @@ -358,8 +364,8 @@ exts_list = [ ('randomForest', '4.7-1.1', { 'checksums': ['f59ea87534480edbcd6baf53d7ec57e8c69f4532c2d2528eacfd48924efa2cd6'], }), - ('scatterplot3d', '0.3-42', { - 'checksums': ['a9fedde70e1a846c4dcafbff20f115425206d507896d12c2b21ff052556c5216'], + ('scatterplot3d', '0.3-43', { + 'checksums': ['90d7bfb535b76008768306ea9209adfb48e0e07f36eabbb59ab6ddb6522f16a5'], }), ('SparseM', '1.81', { 'checksums': ['bd838f381ace680fa38508ff70b3d83cb9ffa28ac1ab568509249bca53c34b33'], @@ -382,14 +388,17 @@ exts_list = [ ('jpeg', '0.1-10', { 'checksums': ['c8d9f609c3088f91ec4853d6cc0e66511038a465811dea79ca6a0c09519178ca'], }), - ('latticeExtra', '0.6-30', { - 'checksums': ['c550a76913624818482bf237d48883c58e368ba356ced8ed5e76146672279eed'], + ('deldir', '1.0-6', { + 'checksums': ['6df6d8325c607e0b7d63cbc53c29e774eff95ad4acf9c7ec8f70693b0505f8c5'], }), - ('Matrix', '1.5-3', { - 'checksums': ['4e720f4edc97b1c09646a445851b1ce955caf6b1de8306a2283328b526fee00d'], + ('RcppEigen', '0.3.3.9.3', { + 'checksums': ['5873a47fd6587d916f86119ab140c6736abf80ac45d06ff1c9d198708e7d1c76'], }), - ('RcppArmadillo', '0.12.0.1.0', { - 'checksums': ['73c6153b79c0b71a896d76031424fe1c0a3ad44a9d09f922a084bb3fbfd3fbea'], + ('interp', '1.1-3', { + 'checksums': ['b74e606b38cfb02985c1f9e3e45093620f76c0307b1b0b4058761e871eb5fa3f'], + }), + ('latticeExtra', '0.6-30', { + 'checksums': ['c550a76913624818482bf237d48883c58e368ba356ced8ed5e76146672279eed'], }), ('plyr', '1.8.8', { 'checksums': ['a73211b4bbe13e4e5e764966a8dd90172c1cc311938dd464d142e1c7a701070c'], @@ -436,8 +445,8 @@ exts_list = [ ('pillar', '1.8.1', { 'checksums': ['2f06a7cc9e5638390c9b98a6ec9a9ec1beec0f2b9dbdfa42e39a5ab2456d87ec'], }), - ('tibble', '3.1.8', { - 'checksums': ['acf30e075d18d2f61de53ca20a13c502bb32abb8083089b0bb9172a0cb5cedea'], + ('tibble', '3.2.0', { + 'checksums': ['8f2ff14bca39e342f36d026776351f21b7627fe0f20f009b7a9e0a69a166298a'], }), ('lazyeval', '0.2.2', { 'checksums': ['d6904112a21056222cfcd5eb8175a78aa063afe648a562d9c42c6b960a8820d4'], @@ -445,8 +454,8 @@ exts_list = [ ('withr', '2.5.0', { 'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'], }), - ('mgcv', '1.8-41', { - 'checksums': ['2f7a030fe2be75edef6bd96147df46c2262f3cdc44c383d8f82b401df44fe690'], + ('mgcv', '1.8-42', { + 'checksums': ['087fc38b64ad06f2149eafc54f2679dd8840cf6fc488e66cf131e3c1de2db6c7'], }), ('rprojroot', '2.0.3', { 'checksums': ['50604247470e910cecfe9b76df754bf96a0d701f81b732f7aa9c90a20d30f897'], @@ -469,6 +478,9 @@ exts_list = [ ('rstudioapi', '0.14', { 'checksums': ['469d0987b1ad728a96c363a422fba712a5cebc8b11a5f7e953b4a671044dafc4'], }), + ('fs', '1.6.1', { + 'checksums': ['faf1e421a2c270c60c0a30c74e1a48faad45b339163716102d77d64d23d76732'], + }), ('pkgload', '1.3.2', { 'checksums': ['35d19a032bfeeefcab92d76a768b4a420c2ede0920badaf48cca878592b46b2f'], }), @@ -490,8 +502,8 @@ exts_list = [ ('waldo', '0.4.0', { 'checksums': ['57ee89eec9bcbba58cf8fa29c8e097f038768c30833eaf812682826333127eaa'], }), - ('testthat', '3.1.6', { - 'checksums': ['a7cb8c416475c182c4faaa32c3a12fc5d8ead77196d3c9811a3d39b3f994cdae'], + ('testthat', '3.1.7', { + 'checksums': ['1ad86b1739481c6c46359a6634ecc706bf513f34b26d7a62cbc719bbd4658eab'], }), ('isoband', '0.2.7', { 'checksums': ['7693223343b45b86de2b5b638ff148f0dafa6d7b1237e822c5272902f79cdf61'], @@ -544,9 +556,6 @@ exts_list = [ ('minqa', '1.2.5', { 'checksums': ['9b83562390990d04b2c61b63ac9a7c9ecab0d35c460d232596e3c73bdc89f4be'], }), - ('RcppEigen', '0.3.3.9.3', { - 'checksums': ['5873a47fd6587d916f86119ab140c6736abf80ac45d06ff1c9d198708e7d1c76'], - }), ('MatrixModels', '0.5-1', { 'checksums': ['3fc55bdfa5ab40c75bf395e90983d14c9715078c33c727c1658e4e1f36e43ea9'], }), @@ -580,8 +589,8 @@ exts_list = [ ('rpart', '4.1.19', { 'checksums': ['fe723ed0b5583fae8b40e6fecc29b357229cb11f2339b02a4e4f812926249565'], }), - ('survival', '3.5-3', { - 'checksums': ['bfa082fd938760fa06f76d70fe2a613c70620e4d2870f14270d8e20f1fbc44c6'], + ('survival', '3.5-5', { + 'checksums': ['1375a509554b0258e04e27baca2e073e179406e2a9a71e6d3e0c777072568476'], }), ('KernSmooth', '2.23-20', { 'checksums': ['20eb75051e2473933d41eedc9945b03c632847fd581e2207d452cf317fa5ec39'], @@ -595,8 +604,8 @@ exts_list = [ ('parallelly', '1.34.0', { 'checksums': ['11639d7039e4a2450dabac1f82cb7ead0bbc68bdb0e113054b7104840098aff4'], }), - ('future', '1.31.0', { - 'checksums': ['b2db8f859a13066f004fa147012e8533b11e41df9516988cd2d5961c78dfdf2a'], + ('future', '1.32.0', { + 'checksums': ['d5bb74512d069745184dd580a36449dc0b50d95b1cbbbc1605db82de596f2f76'], }), ('future.apply', '1.10.0', { 'checksums': ['dee92dd84812fe8c55064c0f0e6d806c0c29848b5a5fc4a7725d6a4b623e94aa'], @@ -616,12 +625,15 @@ exts_list = [ ('prodlim', '2019.11.13', { 'checksums': ['6809924f503a14681de84730489cdaf9240d7951c64f5b98ca37dc1ce7809b0f'], }), - ('ipred', '0.9-13', { - 'checksums': ['6168a062d93c2d3063c064a8f242cd3716dee99822e20363a1801261319c4c98'], + ('ipred', '0.9-14', { + 'checksums': ['81c83dc847d09c3db52ef15e36cd4dac38c50eead1008ddd458b9e89d7528f35'], }), ('cpp11', '0.4.3', { 'checksums': ['f1a60e4971a86dbbcf6a16bbd739b59bb66d9c45d93cfd8dedc2a87e302598f1'], }), + ('timechange', '0.2.0', { + 'checksums': ['3d602008052123daef94a5c3f5154c5461b4ec0432ab70c37273d7ddd252f7f1'], + }), ('lubridate', '1.9.2', { 'checksums': ['8976431a4affe989261cbaa5e09cd44bb42a3b16eed59a42c1698da34c6544a7'], }), @@ -631,14 +643,20 @@ exts_list = [ ('hardhat', '1.2.0', { 'checksums': ['f9320eccb1b5f624a46fa074e3ccc202c383b77098ecd08b193aeb47daedad78'], }), + ('tzdb', '0.3.0', { + 'checksums': ['6099f0ec1fba692b51b4360aa776902a39f10dae815933c31994b8e4d4277038'], + }), + ('clock', '0.6.1', { + 'checksums': ['f80c385fd8229538968ffb71d7de53ddc82bfcec6641f8e76f299546c43c1702'], + }), ('recipes', '1.0.5', { 'checksums': ['fd8b0d4282f490b5bd3853543c9a0518783caa9fa9280534aaab40f9bdd3cfb2'], }), ('caret', '6.0-93', { 'checksums': ['4c156b88879d390436a54779ea19ffbae3f476533d83caaf30400d76130c4a07'], }), - ('conquer', '1.3.2', { - 'checksums': ['8f129bb062e447369f220a13f59ccb6cdc209f72c92a26457edd777666c9b946'], + ('conquer', '1.3.3', { + 'checksums': ['a2c6155ed74af0e2a279145843ec5229ae2f3707aa25169ae030c520aa97deba'], }), ('quantreg', '5.94', { 'checksums': ['52d585ccb972ed7726b7d083f5635d3e42915847398e00fd6e0f69a5fe1b17c1'], @@ -679,8 +697,8 @@ exts_list = [ ('psych', '2.2.9', { 'checksums': ['4cd518bff387fef95067696b0a0b323310e6f4a063c3d242f2a50bcb17675571'], }), - ('broom', '1.0.3', { - 'checksums': ['06b3f10c9ee03124dd2a85da09785a2fba9b406fa25c57f9b9db4d71a49a0a55'], + ('broom', '1.0.4', { + 'checksums': ['1d5f11b509786a8a45ffdd137243e24d6445f2944947cbd62a0734a06add0ad6'], }), ('nloptr', '2.0.3', { 'checksums': ['7b26ac1246fd1bd890817b0c3a145456c11aec98458b8518de863650b99616d7'], @@ -691,8 +709,8 @@ exts_list = [ ('statmod', '1.5.0', { 'checksums': ['d61c3ef9b09d55b42e038f8d767fa483ebbdec2a9c7172b1b0ccda0ae0016ec9'], }), - ('lme4', '1.1-31', { - 'checksums': ['5affd1e33d3fece5ec0a6c7663eb12328e64147f8aa92675ce6453c4fe72edfd'], + ('lme4', '1.1-32', { + 'checksums': ['5e46cba4384d95c6ec70db7f56f3e4c17dc6dccb7e873cb3e5b47f448dc50348'], }), ('ucminf', '1.1-4.1', { 'checksums': ['01a5b6f373ad267d22e2c29b8f7b6e31a1a148e48f4413e6a38e51aa049976b2'], @@ -706,9 +724,6 @@ exts_list = [ ('clipr', '0.8.0', { 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], }), - ('tzdb', '0.3.0', { - 'checksums': ['6099f0ec1fba692b51b4360aa776902a39f10dae815933c31994b8e4d4277038'], - }), ('bit64', '4.0.5', { 'checksums': ['25df6826ea5e93241c4874cad4fa8dadc87a40f4ff74c9107aa12a9e033e1578'], }), @@ -721,14 +736,14 @@ exts_list = [ ('forcats', '1.0.0', { 'checksums': ['c5bb157909d92e1e1a427c0dc5cb358ea00a43a14918a9088fa4f6630962254e'], }), - ('haven', '2.5.1', { - 'checksums': ['9f40462097a0b1cf3831bca493851fe4a6b3570d957a775ca81940f241c50a70'], + ('haven', '2.5.2', { + 'checksums': ['2131fb0377ae1beffae54bf4beb8b3a876e9b6b9841a5acc39a2a2615023561d'], }), ('pan', '1.6', { 'checksums': ['adc0df816ae38bc188bce0aef3aeb71d19c0fc26e063107eeee71a81a49463b6'], }), - ('mitml', '0.4-4', { - 'checksums': ['0021482761943ccb88554a1752636f13e83b1d026d79b6e4a53fdfebe296af8a'], + ('mitml', '0.4-5', { + 'checksums': ['056aec823187cc3793640d8a5e74d74093bae74260a975ceb098a83a52e2eeeb'], }), ('mice', '3.15.0', { 'checksums': ['3d64dd260e3dce9c4c2f7be8c99f3063769df9ccfd3a0fc827c2de0ac842e87b'], @@ -754,6 +769,72 @@ exts_list = [ ('bitops', '1.0-7', { 'checksums': ['e9b5fc92c39f94a10cd0e13f3d6e2a9c17b75ea01467077a51d47a5f708517c4'], }), + ('curl', '5.0.0', { + 'checksums': ['d7f3cac9b513914ffa8f6f64e6fa5dd96c8273378ace6b0c16b71bc6ba59c9b2'], + }), + ('sys', '3.4.1', { + 'checksums': ['324e6d8fde58264e62bc04867b719c5fd16296de1542689801b8cb13621ecf52'], + }), + ('askpass', '1.1', { + 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], + }), + ('openssl', '2.0.6', { + 'checksums': ['77f3032a16270f0d1734f269b8d348eedc75b277812854386091143082c1b3f3'], + }), + ('httr', '1.4.5', { + 'checksums': ['f93bac7f882b0df099abca47dd5aae3686fb3cd2d3e9926fcd639bcddff76f6c'], + }), + ('fastmap', '1.1.1', { + 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], + }), + ('htmltools', '0.5.4', { + 'checksums': ['008228a8690d39d8ae2716bc614e76337fdbe2bac4e96258c10245fdf24f327e'], + }), + ('yaml', '2.3.7', { + 'checksums': ['d20cb219e0f9c48aba02f132f81cfa9ecda5e22c925e36726840218ed56680ab'], + }), + ('knitr', '1.42', { + 'checksums': ['9344f1a0089e4da101def54aee38d7cfe3b2022d75c560141d8cc22ac65130f3'], + }), + ('rappdirs', '0.3.3', { + 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], + }), + ('sass', '0.4.5', { + 'checksums': ['eba161d982d2db108c8c0b61ec6b41a20d3adec430c7cc39537ab388c1007a90'], + }), + ('jquerylib', '0.1.4', { + 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], + }), + ('cachem', '1.0.7', { + 'checksums': ['234fad2a947d1e1fb87d3fa92abf9197877772e31bc81ae5991ae69689b6320a'], + }), + ('memoise', '2.0.1', { + 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], + }), + ('bslib', '0.4.2', { + 'checksums': ['9a40b7a1bbe409af273e1e940d921ab198ea576548f06f055f552f70ff822f19'], + }), + ('tinytex', '0.44', { + 'checksums': ['afa14c1274593f0f980b12c4a27b5d0f6cad0c28ed9b4062d59e42562a33620e'], + }), + ('rmarkdown', '2.20', { + 'checksums': ['d7f7059bfcb43e4b92432d69ba0e0c74ad10a20f153689262a3e848adb60159d'], + }), + ('htmlwidgets', '1.6.1', { + 'checksums': ['42533cbcbefcfe5978c66d7f10f28d294c344e606aa75323c797d5a1dd960e43'], + }), + ('crosstalk', '1.2.0', { + 'checksums': ['4237baab35cd246a8a98fb9cf4ce53b6ddbc31d00742ded4edea0479613d1ea0'], + }), + ('later', '1.3.0', { + 'checksums': ['08f50882ca3cfd2bb68c83f1fcfbc8f696f5cfb5a42c1448c051540693789829'], + }), + ('promises', '1.2.0.1', { + 'checksums': ['8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7'], + }), + ('plotly', '4.10.1', { + 'checksums': ['ac0921a1cba24e17a0f3a0a28b7a40ac930e17fe5caa9c3973c9a8d1e20c367a'], + }), ('mixtools', '2.0.0', { 'checksums': ['854e7482230b9a5dde61bab191b78e06aa8f9b0cdfe3c03e046afa133b317e0d'], }), @@ -793,9 +874,6 @@ exts_list = [ ('xts', '0.13.0', { 'checksums': ['188e4d1d8c3ec56a544dfb9da002e8aac80b9303d0a5a1f62ff0e960aeef9674'], }), - ('curl', '5.0.0', { - 'checksums': ['d7f3cac9b513914ffa8f6f64e6fa5dd96c8273378ace6b0c16b71bc6ba59c9b2'], - }), ('TTR', '0.24.3', { 'checksums': ['4d9aef32647664be5cf965b05f21ed62cde9425fa87c21530852e05ef7aaba87'], }), @@ -811,17 +889,8 @@ exts_list = [ ('pscl', '1.5.5', { 'checksums': ['054c9b88a991abdec3338688f58e81b6ba55f91edb988621864b24fd152fee6f'], }), - ('fastmap', '1.1.1', { - 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], - }), - ('cachem', '1.0.7', { - 'checksums': ['234fad2a947d1e1fb87d3fa92abf9197877772e31bc81ae5991ae69689b6320a'], - }), - ('memoise', '2.0.1', { - 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], - }), - ('blob', '1.2.3', { - 'checksums': ['2d88d683ee3d1b56b332b5c7769979b5d3994b5d9285ea634ec919576da3631b'], + ('blob', '1.2.4', { + 'checksums': ['d08922ebc4147d930fe4762b1b289935217308c6d3fcaa5ae028ce3f5cf2728f'], }), ('RSQLite', '2.3.0', { 'checksums': ['442e19a1d08ed072e795e2c968cd7e9e2cf9e1a7412bf6b30d21d34ffe175d33'], @@ -838,8 +907,8 @@ exts_list = [ ('spatial', '7.3-16', { 'checksums': ['e46565a64c5ec148a77789867e5103746462a41de294539b230bad2a0e16e406'], }), - ('VGAM', '1.1-7', { - 'checksums': ['a4c52d392332477eac557c84b732f3c03dd48f75db3884e23c71cf99d991757e'], + ('VGAM', '1.1-8', { + 'checksums': ['d4c0f1d4e356d88ab6f39c05076ff97ebef6d20b7fbf1b0fa31d40c73d0ad1cc'], }), ('waveslim', '1.8.4', { 'checksums': ['408eeea72a218ef3458f0934ff556733cacf1a63ddaa52491abcc1fce6ed2094'], @@ -853,8 +922,8 @@ exts_list = [ ('brglm', '0.7.2', { 'checksums': ['56098d2ce238478e7a27cacc4cdec0bc65f287fe746b38fbb1edda20c1675023'], }), - ('deSolve', '1.34', { - 'checksums': ['2254305f44dde22ac685fef4c60e29a0608af0197c803107365d1d80b75c9f21'], + ('deSolve', '1.35', { + 'checksums': ['96f17f497713754f84ff56c3538c6d05b9f5229f9a2a32aafec7d7cdc721d488'], }), ('tseriesChaos', '0.1-13.1', { 'checksums': ['23cb5fea56409a305e02a523ff8b7642ec383942d415c9cffdc92208dacfd961'], @@ -871,18 +940,6 @@ exts_list = [ ('R.oo', '1.25.0', { 'checksums': ['b8b19061774918ee7d9d4330c16c0ea505f7cd02d01343df1e8b2e4fb847beef'], }), - ('sys', '3.4.1', { - 'checksums': ['324e6d8fde58264e62bc04867b719c5fd16296de1542689801b8cb13621ecf52'], - }), - ('askpass', '1.1', { - 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], - }), - ('openssl', '2.0.5', { - 'checksums': ['8ac2140d59f9b4c642970736b08579bc8d59874ee72e1efca1826420b00786d3'], - }), - ('httr', '1.4.5', { - 'checksums': ['f93bac7f882b0df099abca47dd5aae3686fb3cd2d3e9926fcd639bcddff76f6c'], - }), ('cgdsr', '1.2.10', { 'checksums': ['43bc02fb33c371464f9407d5e5e6419527e9360e3e394343862cca0aebe1d0f7'], }), @@ -907,29 +964,17 @@ exts_list = [ ('proto', '1.0.0', { 'checksums': ['9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1'], }), - ('chron', '2.3-59', { - 'checksums': ['b943a6b97c42e7858dcd4a23deeb1f3a817f9f5086776177627ddc58894601f6'], + ('chron', '2.3-60', { + 'checksums': ['0e0675cec55b6cea87fc5776846215e0445442554684120079e66013067491ee'], }), ('viridis', '0.6.2', { 'checksums': ['69b58cd1d992710a08b0b227fd0a9590430eea3ed4858099412f910617e41311'], }), - ('yaml', '2.3.7', { - 'checksums': ['d20cb219e0f9c48aba02f132f81cfa9ecda5e22c925e36726840218ed56680ab'], - }), - ('htmltools', '0.5.4', { - 'checksums': ['008228a8690d39d8ae2716bc614e76337fdbe2bac4e96258c10245fdf24f327e'], - }), - ('htmlwidgets', '1.6.1', { - 'checksums': ['42533cbcbefcfe5978c66d7f10f28d294c344e606aa75323c797d5a1dd960e43'], - }), - ('knitr', '1.42', { - 'checksums': ['9344f1a0089e4da101def54aee38d7cfe3b2022d75c560141d8cc22ac65130f3'], - }), ('htmlTable', '2.4.1', { 'checksums': ['3a7f3e75d886dc398fd1d3cae907b536fff6af3a3d2c18349ef12ec06d310f93'], }), - ('Hmisc', '4.8-0', { - 'checksums': ['6392ed4b96c8ea95da1ebfa92b38cc3baa0314babb2680a08800d0b25c0a9b1d'], + ('Hmisc', '5.0-1', { + 'checksums': ['db390f8f8a150cb5cffb812e9609a8e8632ceae0dc198528f190fd670ba8fa59'], }), ('fastcluster', '1.2.3', { 'checksums': ['1f229129e1cddc78c7bb5ecc90c4d28ed810ee68cf210004c7cdfa12cfaf2a01'], @@ -961,8 +1006,8 @@ exts_list = [ ('GeneNet', '1.2.16', { 'checksums': ['c1e98073ccdaa18f4952630bfe4fc0617106eeaf7ed94d347cb2773bd48333e4'], }), - ('ape', '5.7', { - 'checksums': ['09b4aee7e8bf013c00dd66f5fbe954830e439d97416b278bfbd918bb3da1f569'], + ('ape', '5.7-1', { + 'checksums': ['8b09c71218d8aa629e43bc807b433a4e30a61847d91b2810e31c366f0fe5057a'], }), ('RJSONIO', '1.3-1.8', { 'checksums': ['f6f0576d3c7852b16295dfc897feebca064fe5dd29cdce7592f94c56823553f5'], @@ -976,12 +1021,6 @@ exts_list = [ ('ROCR', '1.0-11', { 'checksums': ['57385a773220a3aaef5b221a68b2d9c2a94794d4f9e9fc3c1eb9521767debb2a'], }), - ('later', '1.3.0', { - 'checksums': ['08f50882ca3cfd2bb68c83f1fcfbc8f696f5cfb5a42c1448c051540693789829'], - }), - ('promises', '1.2.0.1', { - 'checksums': ['8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7'], - }), ('httpuv', '1.6.9', { 'checksums': ['8d77f25b22fa7473b45007c2048e9a38d3792d59b2716e1fcdf9e99bd585d95d'], }), @@ -994,24 +1033,6 @@ exts_list = [ ('xml2', '1.3.3', { 'checksums': ['cb4e9c0d31618ed67d2bfa4c7b5e52680e11612ed356a8164b541d44163c1c8d'], }), - ('commonmark', '1.8.1', { - 'checksums': ['96adcb093de3d2e48811af402da70e7222a313b97f1e979e0cbe84dd59bd5cbe'], - }), - ('jquerylib', '0.1.4', { - 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], - }), - ('rappdirs', '0.3.3', { - 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], - }), - ('fs', '1.6.1', { - 'checksums': ['faf1e421a2c270c60c0a30c74e1a48faad45b339163716102d77d64d23d76732'], - }), - ('sass', '0.4.5', { - 'checksums': ['eba161d982d2db108c8c0b61ec6b41a20d3adec430c7cc39537ab388c1007a90'], - }), - ('bslib', '0.4.2', { - 'checksums': ['9a40b7a1bbe409af273e1e940d921ab198ea576548f06f055f552f70ff822f19'], - }), ('fontawesome', '0.5.0', { 'checksums': ['4117b417a33e82d626881d7059eb54e7534cba202e75dae7e27021cb3796e90b'], }), @@ -1024,23 +1045,20 @@ exts_list = [ ('LearnBayes', '2.15.1', { 'checksums': ['9b110858456523ca0b2a63f22013c4e1fbda6674b9d84dc1f4de8bffc5260532'], }), - ('deldir', '1.0-6', { - 'checksums': ['6df6d8325c607e0b7d63cbc53c29e774eff95ad4acf9c7ec8f70693b0505f8c5'], - }), ('gmodels', '2.18.1.1', { 'checksums': ['da7d48021b7cd2fd8a7cd8d0bb9658b12342a32698a13877b25ca94aa03f1e95'], }), ('expm', '0.999-7', { 'checksums': ['28f249b914b8dd33eee16663fc793e57afd0e301e16067bf9f27fa8e591ba0f1'], }), - ('terra', '1.7-3', { - 'checksums': ['89fe9397c8b101088d5c3de47212ea8fa4770805ad33cfff4314c6f08a68272e'], + ('terra', '1.7-18', { + 'checksums': ['d6815927ceccc217aa0f19b2231b3a160f643c5046cdb51b42f77b7082dcea46'], }), - ('raster', '3.6-14', { - 'checksums': ['031382b10a57ff88cfca8565b5195e192e2beb377c0833154de4d1db1a0d3b0a'], + ('raster', '3.6-20', { + 'checksums': ['7e5be49f4e37a2c14a3b87661b252956643b959146cbdb08e983660c1d59a813'], }), - ('spData', '2.2.1', { - 'checksums': ['55345437e751b81d8ce1342382f7feeaa299d0421d6f9cc52d9bae46189ab3b5'], + ('spData', '2.2.2', { + 'checksums': ['878a58e98b6cf259432149ecb4e5d66ada59466e1b5b0dafa60ec839e90104ed'], }), ('units', '0.8-1', { 'checksums': ['d3e1ba246b4c97205bc3da3cf45d6b5bd5c196b8d421b84b4e94b2090985cd9a'], @@ -1057,17 +1075,11 @@ exts_list = [ ('XML', '3.99-0.13', { 'checksums': ['85c568a6e2f0c43a8026d10861ddd8984907b03665ed88fca1a3776c25e8f73a'], }), - ('tinytex', '0.44', { - 'checksums': ['afa14c1274593f0f980b12c4a27b5d0f6cad0c28ed9b4062d59e42562a33620e'], - }), - ('rmarkdown', '2.20', { - 'checksums': ['d7f7059bfcb43e4b92432d69ba0e0c74ad10a20f153689262a3e848adb60159d'], - }), ('reshape', '0.8.9', { 'checksums': ['791178b3b5f30c166ebf5910a5ab1c67b54e7023b10b6c2e2ddd1cc02a1e4048'], }), - ('triebeard', '0.3.0', { - 'checksums': ['bf1dd6209cea1aab24e21a85375ca473ad11c2eff400d65c6202c0fb4ef91ec3'], + ('triebeard', '0.4.1', { + 'checksums': ['192f2fef6341e43bd56ef4f9841e813e07be990f4ffcf38c5606259630efe0f7'], }), ('urltools', '1.7.3', { 'checksums': ['6020355c1b16a9e3956674e5dea9ac5c035c8eb3eb6bbdd841a2b5528cafa313'], @@ -1141,8 +1153,8 @@ exts_list = [ ('phylobase', '0.8.10', { 'checksums': ['5a44380ff49bab333a56f6f96157324ade8afb4af0730e013194c4badb0bf94b'], }), - ('magick', '2.7.3', { - 'checksums': ['83877b2e23ea43fbc1164de9c2422eafbe7858393ac384df5adf3a7eec122441'], + ('magick', '2.7.4', { + 'checksums': ['e28d67737590f8c19e4cf00a9c74e59d0e45f9ece363ed105b5f40e821e8f02f'], }), ('animation', '2.7', { 'checksums': ['88418f1b04ec785963bad492f30eb48b05914e9e5d88c7eef705d949cbd7e469'], @@ -1180,6 +1192,9 @@ exts_list = [ ('fossil', '0.4.0', { 'checksums': ['37c082fa15ebae89db99d6071b2bb2cad6a97a0405e9b4ef77f62a8f6ad274c1'], }), + ('optimParallel', '1.0-2', { + 'checksums': ['0f9bc62c23d9005130f2892bf5eaecf308fa48a727bdd5e19b7dcd1d95f30a9d'], + }), ('phytools', '1.5-1', { 'checksums': ['f8be59abbff1f5032be4523c361da53b0d5b71677fedebba6d7cbae2dca7e101'], }), @@ -1192,9 +1207,6 @@ exts_list = [ ('glmnet', '4.1-6', { 'checksums': ['bec4c6cea284d0dc24bbdac3e623f0772cea1d74ef77e718651e3830c74b7e30'], }), - ('crosstalk', '1.2.0', { - 'checksums': ['4237baab35cd246a8a98fb9cf4ce53b6ddbc31d00742ded4edea0479613d1ea0'], - }), ('miniUI', '0.1.1.1', { 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], }), @@ -1228,8 +1240,8 @@ exts_list = [ ('TH.data', '1.1-1', { 'checksums': ['edf3ab16b142f4c52d21fc64e41409ed138e5b3e142f2fae964b00f02d53dd7a'], }), - ('multcomp', '1.4-22', { - 'checksums': ['171086088c7113ac576ca20efb4fd197eea5cf1754230009656a3fb72d364eea'], + ('multcomp', '1.4-23', { + 'checksums': ['425154a58bd8f2dbaff5d16e97b03473cbc0d571b1c2e4dd66a13c6d20a8cde1'], }), ('libcoin', '1.0-9', { 'checksums': ['2d7dd0b7c6dfc20472430570419ea36a714da7bbafd336da1fb53c5c6463d9eb'], @@ -1237,14 +1249,14 @@ exts_list = [ ('coin', '1.4-2', { 'checksums': ['7546d1f27a82d98b4b3e43e4659eba0f74a67d5919ce85d2fb360282ba3cfbb2'], }), - ('party', '1.3-12', { - 'checksums': ['0f686d24e866653e804e473dc26ef0befd7a43f68e718841848bbd864c97cb3f'], + ('party', '1.3-13', { + 'checksums': ['def05e7f0c59f1b1ecf0ab3929cff75ae8c2691aaf52292cad4371281b897e7b'], }), - ('inum', '1.0-4', { - 'checksums': ['5febef69c43a4b95b376c1418550a949d988a5f26b1383ca01c9728a94fc13ce'], + ('inum', '1.0-5', { + 'checksums': ['e696b7e0b31b3bbf405112e60691b6a72fedcaa02e08ee517c59f6bf9cd36bbd'], }), - ('partykit', '1.2-17', { - 'checksums': ['65ba7ed3ef0c39494a3372b47c4720f31f479cb388449fc5374c51ab255d5a99'], + ('partykit', '1.2-18', { + 'checksums': ['2c3f8ba0eaa38268565d006954d6f45a172e29e81b8e2ad86a0ec4b5d41464fb'], }), ('mboost', '2.9-7', { 'checksums': ['0242cb91656280c4bd705643b65674900a1475305d9f80cfc12ef4b5fa069606'], @@ -1255,8 +1267,8 @@ exts_list = [ ('nor1mix', '1.3-0', { 'checksums': ['9ce4ee92f889a4a4041b5ea1ff09396780785a9f12ac46f40647f74a37e327a0'], }), - ('np', '0.60-16', { - 'checksums': ['bef967c0195059e53c68e64d7540bf4627415c832f050c8806520ab8796e01b0'], + ('np', '0.60-17', { + 'checksums': ['d97957cb234ec2e570fc2d02d305eadff3d71939484b3d1054ed8b67a3427f36'], }), ('polynom', '1.4-1', { 'checksums': ['bc1edb7bb16c8b299103f80a52ab8c5fc200cd07a9056578c1f672e9f5019278'], @@ -1270,8 +1282,8 @@ exts_list = [ ('RWekajars', '3.9.3-2', { 'checksums': ['16e6b019aab1646f89c5203f0d6fc1cb800129e5169b15aaef30fd6236f5da1a'], }), - ('RWeka', '0.4-45', { - 'checksums': ['f910f17fabebbca9d25c58917c358f1f97edb854b4f9f9b397e10b107bd61028'], + ('RWeka', '0.4-46', { + 'checksums': ['660555781703c19b994c9dcfc9e7d8312c30b02539f38cd3948bfc33d9f94b67'], }), ('slam', '0.1-50', { 'checksums': ['7899bf3266c204ecccefc1878f96940b117d4503af128f4fbc50fc409163f8bd'], @@ -1333,8 +1345,8 @@ exts_list = [ ('R.cache', '0.16.0', { 'checksums': ['7853409161571a790e0383f64f99e4eae43201a0ed7146d2baf157741a509291'], }), - ('styler', '1.9.0', { - 'checksums': ['a85417b3df03f5b2085a40ce4de295d81fea02d0212f5046ce14c1b6dbaac02f'], + ('styler', '1.9.1', { + 'checksums': ['c80fa3c062f007645ec820b5b087d4d5784e7797cc88d030ab59fb5823ded0bb'], }), ('questionr', '0.7.8', { 'checksums': ['af72e59fe652c6063282a7e5b0f487993b9361cc9ed052a632d64a5a6db76ba9'], @@ -1402,14 +1414,23 @@ exts_list = [ ('DT', '0.27', { 'checksums': ['e32fdccd2be430933cff88a9ce79045bfdbe3e08e0cd8d15037445808613289a'], }), + ('estimability', '1.4.1', { + 'checksums': ['c65aaf1e452f3947013d3ce05ae674d48492081f615a942592dc91db780f1124'], + }), + ('emmeans', '1.8.5', { + 'checksums': ['5c88b415b5a42d8c1aa63af090c4987326530ea6d0e60bab9b5fb7e99a982415'], + }), + ('multcompView', '0.1-8', { + 'checksums': ['123d539172ad6fc63d83d1fc7f356a5ed7b691e7803827480118bebc374fd8e5'], + }), ('FactoMineR', '2.7', { 'checksums': ['27b83ecc64cf445a42d0af3812492fd58624839fa5d458ec0ca6666ed914250d'], }), ('flexclust', '1.4-1', { 'checksums': ['d67977df059e622832358069509f8968d506074320a45d34bfd21c65f898538d'], }), - ('flexmix', '2.3-18', { - 'checksums': ['462201ef49088845c83083e4ed6725cf069aafb12a814041618aaf09ebd69b51'], + ('flexmix', '2.3-19', { + 'checksums': ['adf5a40cbb6d45e3652c1666cb3ccdb9654e501fd685c091cad0686e62bc12e9'], }), ('prabclus', '2.3-2', { 'checksums': ['f421bcbcb557281e0de4a06b15f9a496adb5c640e883c0f7bb12051efc69e441'], @@ -1498,24 +1519,30 @@ exts_list = [ ('goftest', '1.2-3', { 'checksums': ['3a5f74b6ae7ece5b294781ae57782abe12375d61789c55ff5e92e4aacf347f19'], }), - ('spatstat.utils', '3.0-1', { - 'checksums': ['cba1c7806564fd9145ca15edf77233d6ba5609f0989f7812221f5fc1ece0b91a'], + ('spatstat.utils', '3.0-2', { + 'checksums': ['be60cd2cf21a6b3f71ba60553c045fd87884a4e57744f60e6eb0a2d096314615'], }), - ('spatstat.data', '3.0-0', { - 'checksums': ['cff9058a88489020a4a05b9576cd452f37fa9b42084873c474d06931f5187057'], + ('spatstat.data', '3.0-1', { + 'checksums': ['8eeb4b1de356e9cef42f58b5e0fc7ced2a476a1306e09395ba97253b22dd5300'], }), - ('spatstat.geom', '3.0-6', { - 'checksums': ['6378750668363f09a80e8f6c60664e37b88f7ae6fbb296d3b978639d6e8ff20c'], + ('spatstat.geom', '3.1-0', { + 'checksums': ['184a96679babcbff4897c5a471e034eb1bb7127c6cf668e8cc2c2c74bdea47fe'], }), - ('spatstat.sparse', '3.0-0', { - 'checksums': ['99be0a3c7592760fdf1668dc0811f75ed91c400390d1ecc3d5e643255f501ad2'], + ('spatstat.sparse', '3.0-1', { + 'checksums': ['2c1cf0ddad366aa4230bd03241a1ef87ed635f53a6943fc4a6c2d371626d0d1c'], }), - ('spatstat.random', '3.1-3', { - 'checksums': ['b28af559ca28002abf9c937b68ad5e7f7317d8c3f976e9a97bebe0c652c441d0'], + ('spatstat.random', '3.1-4', { + 'checksums': ['a6cd75e187a992fd8dae535f6745e12801635a344ca51bd2fe048debea3df7d3'], }), ('spatstat.core', '2.4-4', { 'checksums': ['e38c39efe8b14d6e8fdbee8dd870b90c52f78ea571ab7988fd3685f48347d13b'], }), + ('spatstat.explore', '3.1-0', { + 'checksums': ['87ef4882652db3b834214bfc776dd7d23d931a9227de12f19722aeb1029d086e'], + }), + ('spatstat.model', '3.2-1', { + 'checksums': ['7ae5c0da47dcf786ae09bd12eecd41dc44e9390adfd36a559f8e58480f81596f'], + }), ('spatstat.linnet', '3.0-6', { 'checksums': ['1609d4c3b3bf168b6218827749e0c887c09727dc144403a2cf7778e8c8fb606a'], }), @@ -1570,8 +1597,8 @@ exts_list = [ ('ParamHelpers', '1.14.1', { 'checksums': ['0450ff8489b0d4d0842130f6a9713ede97da936d7909c43d43587bf2d5a01a21'], }), - ('ggvis', '0.4.7', { - 'checksums': ['9e6b067e11d497c796d42156570e2481afb554c5db265f42afbb74d2ae0865e3'], + ('ggvis', '0.4.8', { + 'checksums': ['3d5480a0b97a57c26b595785f826b13d7695dab1f1dd8fcf5d7964fa8546a26a'], }), ('mlr', '2.19.1', { 'checksums': ['9d52afd54d9d5746e798134d5675818cee65caa53d7eaf317d46ba88d5865202'], @@ -1630,6 +1657,9 @@ exts_list = [ ('gitcreds', '0.1.2', { 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], }), + ('httr2', '0.2.2', { + 'checksums': ['5d1ab62541f7817112519f0f9d00d6a2555bab5b2da7f5c6d579b0c307d7f2bf'], + }), ('gh', '1.4.0', { 'checksums': ['68c69fcd18429b378e639a09652465a4e92b7b5b5704804d0c5b1ca2b9b58b71'], }), @@ -1645,6 +1675,27 @@ exts_list = [ ('covr', '3.6.1', { 'checksums': ['ffbe15438c1a4f274c14cacfb944480e284f1ab60808d5e840c015cc57c51157'], }), + ('downlit', '0.4.2', { + 'checksums': ['33dff66909104d1a5ba8e57b1288986e82b61fd5e91dce0cd358d53724b37e3c'], + }), + ('systemfonts', '1.0.4', { + 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], + }), + ('textshaping', '0.3.6', { + 'checksums': ['80e2c087962f55ce2811fbc798b09f5638c06c6b28c10cd3cb3827005b902ada'], + }), + ('ragg', '1.2.5', { + 'checksums': ['936f4d75e0e01cdeefb9f57d121cdd7812d0de5a9e1a3a8315f92ce1c84da8f9'], + }), + ('pkgdown', '2.0.7', { + 'checksums': ['f33872869dfa8319182d87e90eab3245ff69293b3b791471bf9538afb81b356a'], + }), + ('profvis', '0.3.7', { + 'checksums': ['43974863cb793f81dbea4b94096343c321f7739c9038980405c9b16b04a906b9'], + }), + ('urlchecker', '1.0.1', { + 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], + }), ('devtools', '2.4.5', { 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], }), @@ -1714,8 +1765,8 @@ exts_list = [ ('DiagrammeR', '1.0.9', { 'checksums': ['64a426fe27110dddd8b0c1223ae4c397a2e553ae5e81ddd4ff67c026cfc40abf'], }), - ('randomForestSRC', '3.2.0', { - 'checksums': ['f330518ae9f01b6723f52105726e3a6e7081a9b16d2bf17f0bcb967642a757a7'], + ('randomForestSRC', '3.2.1', { + 'checksums': ['8548102482a724d2ecb1c249e1fbda18f9a9be3ad071c0e559412aac96537f2c'], }), ('sm', '2.2-5.7.1', { 'checksums': ['ea0cc32eb14f6c18beba0bede66ed37bc5341bd3f76c1a7ae56d7254693e1457'], @@ -1723,8 +1774,8 @@ exts_list = [ ('pbivnorm', '0.6.0', { 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], }), - ('lavaan', '0.6-14', { - 'checksums': ['2fbae895af9dbc2e67789e396a3b82b3285226d5dd51680f337ae3b3116c00a7'], + ('lavaan', '0.6-15', { + 'checksums': ['9a43f3e999f9b3003a8c46a615902e01d6701d28a871d657751dd2ff3928ed9b'], }), ('matrixcalc', '1.0-6', { 'checksums': ['0bc7d2f11f62d8b1969474defe27c924a243ccba0c856d585f317f6caa07f326'], @@ -1835,8 +1886,8 @@ exts_list = [ ('signal', '0.7-7', { 'checksums': ['67a015c46d67de7548c3adb83a1b22524de75501a861d91668c3c2ea761a4e61'], }), - ('tuneR', '1.4.2', { - 'checksums': ['eb9fbe787296f081b448c48225081773f18b062c8d6fe0272da7b1641d0a2cf2'], + ('tuneR', '1.4.3', { + 'checksums': ['a9fec8a3c2afeb078bdf7bc5af82cd2a9b177d6637b3721bd0d3b3a1040f399b'], }), ('pastecs', '1.3.21', { 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], @@ -1859,8 +1910,8 @@ exts_list = [ ('s2', '1.1.2', { 'checksums': ['8fb237531c6f4aa5b78fbe36d4fd15bfe852c1308fed58b04b3dae2bb73c0b57'], }), - ('sf', '1.0-9', { - 'checksums': ['85c0c71a0a64750281e79aa96e36d13e6285927008b2d37d699e52aba7d8013b'], + ('sf', '1.0-11', { + 'checksums': ['2e7848706b8e251199d6e5bac07c10cb9d2efe12bb8757e7b2db4b9c9e8e2117'], }), ('oce', '1.7-10', { 'checksums': ['b899eeb7ae73f6520f65f0f052dd2f6f2d102190527eace94d057357ed9568ff'], @@ -2012,6 +2063,9 @@ exts_list = [ ('googlesheets4', '1.0.1', { 'checksums': ['284ecbce98944093cb065c1b0b32074eae7b45fd74b87d7815c7ca6deca76591'], }), + ('conflicted', '1.2.0', { + 'checksums': ['c99b86bb52da3e7d1f4d96d70c77304d0434db5bd906edd8d743e89ac9223088'], + }), ('tidyverse', '2.0.0', { 'checksums': ['3d3c2d135056333247d309d1c2cc98cc0d87e2c781f4c6fbceab28d28c0728e5'], }), @@ -2039,9 +2093,6 @@ exts_list = [ ('gap.datasets', '0.0.5', { 'checksums': ['2299b52efee322ce0eaf66c66ae440f46618b647701cd741568c08bdc3111c9c'], }), - ('plotly', '4.10.1', { - 'checksums': ['ac0921a1cba24e17a0f3a0a28b7a40ac930e17fe5caa9c3973c9a8d1e20c367a'], - }), ('gap', '1.5-1', { 'checksums': ['0d4d37045f5712ebd010cad0617f8e88a021b15fd25d899e4ec222af74e313dc'], }), @@ -2066,8 +2117,8 @@ exts_list = [ ('ROI.plugin.glpk', '1.0-0', { 'checksums': ['b361b0d4222d74b21432cdc6990762affecdbcec8fd6bbdb13b78b59cb04b444'], }), - ('spaMM', '4.1.20', { - 'checksums': ['839eabd0bd8883d7ae9f9df4fcf6a754b15f2952d76e30c424e0e8927ce05284'], + ('spaMM', '4.2.1', { + 'checksums': ['4b12060be94ecd3b6fc7d0c5e2b5b332d14971caac67edeec9651200af066879'], }), ('qgam', '1.3.4', { 'checksums': ['7633120a48a85ab73f7e1bc8b02c98319285c2abd05f9d13d25339d7aaaacacb'], @@ -2135,8 +2186,8 @@ exts_list = [ ('MatchIt', '4.5.1', { 'checksums': ['961e6debea443179fb196581e0783ce05215faa4115e3f5e1cff89eb82b0c7e0'], }), - ('RItools', '0.3-2', { - 'checksums': ['8d6be0e91db83ac3122dcbfe1a77009955a484b9d6c32f7adbd55d286eb83c08'], + ('RItools', '0.3-3', { + 'checksums': ['2a08e2d2ea3abf5fad89c65fdba1d78dd5f4bd12f980436964fe535554d331d5'], }), ('mitools', '2.4', { 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], @@ -2174,6 +2225,18 @@ exts_list = [ ('minerva', '1.5.10', { 'checksums': ['2f26353d8fcc989ac698c4e45bb683801b1a7bb60b14903d05a4d73c629c590f'], }), + ('RcppTOML', '0.2.2', { + 'checksums': ['371391f9ca82221e76a424082ea9ebc5ea2c50f14e8408469b09d7dc3e6f63aa'], + }), + ('here', '1.0.1', { + 'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'], + }), + ('reticulate', '1.28', { + 'checksums': ['58a299ed18faaa3ff14936752fcc2b86e64ae18fc9f36befdfd492ccb251516f'], + }), + ('umap', '0.2.10.0', { + 'checksums': ['8d4786929345e8980bb8be8bb4b6300a679bba03a5984eed59e5e00c626b6ea9'], + }), ('KODAMA', '2.4', { 'checksums': ['78f2ea3596f3697fc06a080947e82a54c5270ed90f86916b91902e5db6ec85e7'], }), @@ -2204,15 +2267,6 @@ exts_list = [ ('fitdistrplus', '1.1-8', { 'checksums': ['f3c72310f40773b3839a9506c3cb781d044e09b94f2f38d332bb24e5f9960f5a'], }), - ('here', '1.0.1', { - 'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'], - }), - ('RcppTOML', '0.2.2', { - 'checksums': ['371391f9ca82221e76a424082ea9ebc5ea2c50f14e8408469b09d7dc3e6f63aa'], - }), - ('reticulate', '1.28', { - 'checksums': ['58a299ed18faaa3ff14936752fcc2b86e64ae18fc9f36befdfd492ccb251516f'], - }), ('hdf5r', '1.3.8', { 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', 'preinstallopts': "unset LIBS && ", @@ -2251,6 +2305,9 @@ exts_list = [ ('fishMod', '0.29', { 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], }), + ('alabama', '2022.4-1', { + 'checksums': ['a8c62859b39a8340ecf7bbf411fac303c059e4237d28ff7bba9ba3daaca1d36c'], + }), ('gllvm', '1.4.1', { 'checksums': ['36f50697e3f38e008f0db8c2980db6fc6a736985573952cc23769d55fbb321d1'], }), @@ -2266,6 +2323,9 @@ exts_list = [ ('ergm', '4.4.0', { 'checksums': ['2db152cc7fdd71d6f0065603405f30bf5e206591da39b8f542178ec6d6126173'], }), + ('networkLite', '1.0.5', { + 'checksums': ['aaab55d4f8f0b330fe7c1ecbab3c44746c52c2fda99c53c6b46042bb8775718b'], + }), ('networkDynamic', '0.11.3', { 'checksums': ['2c664fd0d85c0cdc099480d67a18e6afbb0cc1036963b6664a8a756874648e5b'], }), @@ -2544,8 +2604,8 @@ exts_list = [ ('dHSIC', '2.1', { 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], }), - ('ggsci', '2.9', { - 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + ('ggsci', '3.0.0', { + 'checksums': ['8901316516d78f82a2a8685d93ba479424bcfd8cb5e28a28adbd50e68964e129'], }), ('ggsignif', '0.6.4', { 'checksums': ['112051af425a0c0f2998ce187dacad066bc16f55af01e3e7b76d62ff6954b20a'], @@ -2586,8 +2646,8 @@ exts_list = [ ('ggExtra', '0.10.0', { 'checksums': ['dc6855bbb7e81ffa58d6b65b594d22718fa36b7f50b2284386f70fa8ccc6a3e5'], }), - ('findpython', '1.0.7', { - 'checksums': ['59f904b9c2ec84b589380de59d13afbf14d1ec3b670e3a07e820298aaf04c149'], + ('findpython', '1.0.8', { + 'checksums': ['0f8a90cbafd4949c0333a86808383a358fb7ec3268953d8a4887d5d22264cdb7'], }), ('argparse', '2.2.2', { 'checksums': ['b62c9bf5e6ca35fb7a2e614a916815c04cbf6c6db3f89f99b4df76470a4a856d'], @@ -2595,20 +2655,20 @@ exts_list = [ ('intergraph', '2.0-2', { 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], }), - ('ggnetwork', '0.5.10', { - 'checksums': ['1b655dbab8eed8d0aa3ab2148aac8e0e5bfa190468f5e3c06b001ce88b7f0d3f'], + ('ggnetwork', '0.5.12', { + 'checksums': ['74368662c1a225cdefc8addf606b398f14dafeff03faac56c15aa5e14819e9cd'], }), ('qqman', '0.1.8', { 'checksums': ['58da8317df8d726d1fde4805919da5d64f880894a423ee20937cafb479b9d8a8'], }), - ('rstantools', '2.2.0', { - 'checksums': ['cb810baeb90c67668361b666c6862df9917aff6aaec63d2c3a485f28407c4eb7'], + ('rstantools', '2.3.0', { + 'checksums': ['937e2de6ac80214dccd90c09b26ebcf366c4b55adc84837a6fbb137ebb13822d'], }), ('distributional', '0.3.1', { 'checksums': ['727e56cbcf0c8a8adacca8030214ddbd14f68ee28d0aad716467bd68b027235f'], }), - ('posterior', '1.4.0', { - 'checksums': ['f546658678a2c8c86130922c06f9045b4078bc11a91fa98b0462a5d733133f9d'], + ('posterior', '1.4.1', { + 'checksums': ['2b8953fa8d6890a105521023c431ddea725465eb95cf9454a88852e43ebb58d3'], }), ('bayesplot', '1.10.0', { 'checksums': ['bb4cb92b1ae4cf8ae5f4b5cb092aba34af3d820d137e1f2265cca8f3e85113ff'], @@ -2628,11 +2688,17 @@ exts_list = [ ('gamm4', '0.2-6', { 'checksums': ['57c5b66582b2adc32f6a3bb6a259f5b95198e283a96d966a6007e8e48b380c89'], }), + ('memisc', '0.99.31.6', { + 'checksums': ['52336b4ffc6e60c3ed10ccc7417231582b0d2e4c5c3b2184396a7d3ca9c1d96e'], + }), + ('mclogit', '0.9.6', { + 'checksums': ['9adc5f6d8649960abe009c30d9b4c448ff7d174c455a594cbf104a33d5a36f69'], + }), ('projpred', '2.4.0', { 'checksums': ['6f01bb7f1ddbda92ea0fc44e5596f3885f1ac326f4e88abb0f0cd7fcb71edeb2'], }), - ('brms', '2.18.0', { - 'checksums': ['63914be03cd1c4e6333317d22d7827ba2dc0414cb0dc88337cf74763ba07e111'], + ('brms', '2.19.0', { + 'checksums': ['0e146842c7acfcc6b8273df536eabb5279fb3bf2ae27ce1696f7d838d94fe5c1'], }), ('drgee', '1.1.10', { 'checksums': ['e684f07f7dfec922380d4202922c11094f859721f77b31ff38b0d35d0f42c743'], @@ -2652,8 +2718,8 @@ exts_list = [ ('ngspatial', '1.2-2', { 'checksums': ['3fa79e45d3a502a58c1454593ec83dfc73144e92b34c14f617a6126557dd0d26'], }), - ('BIGL', '1.6.7', { - 'checksums': ['8f5e7e7b08ac80e8966d491a76ff7fb9a7c2460579c063e1b2316c558655ea7a'], + ('BIGL', '1.7.0', { + 'checksums': ['36e086a10be6b1d348052cca0bc2d4ba5335635386f79b2b3b025a128316bfb8'], }), ('drugCombo', '1.2.1', { 'checksums': ['9a605c655c159604033558d757711e6d83d33dfc286c1280f722d4cb7d130f80'], @@ -2691,11 +2757,11 @@ exts_list = [ ('rgbif', '3.7.5', { 'checksums': ['a97aa8d42fc7d094542b6835d7fe818eef64f5ffac3604be1eda3d0d9422d1de'], }), - ('rgdal', '1.6-4', { - 'checksums': ['932c53351061170753ac68ca28316134945a3159e9558e3d49d925e468d62ca7'], + ('rgdal', '1.6-5', { + 'checksums': ['0c7aa3a52003ef53d6a6a3e72ea55b9ed21453ca9bf754cd12763dd85d2c1d64'], }), - ('rgeos', '0.6-1', { - 'checksums': ['420dbd48c0e8c840686b6ed29384715723d6926a1f9b0c437c60ad1853eef7f2'], + ('rgeos', '0.6-2', { + 'checksums': ['2ee2bb8b0c20d7908ac55d4d1cf8292c624ab836e02599ce1871a249a59fe0af'], }), ('mapproj', '1.2.11', { 'checksums': ['db2d201cc939de26717566066bf44225a967ccde6fc34731af845f03c086347d'], @@ -2712,8 +2778,8 @@ exts_list = [ ('ridigbio', '0.3.6', { 'checksums': ['c019dd266aa1334c41430db95361a7b1b911a6793d692b35cd2dc1894232f560'], }), - ('spocc', '1.2.0', { - 'checksums': ['4bac45db5e69bfa3bf6cebd1b0c9241214c95561f275cee6d31e00911aa79d84'], + ('spocc', '1.2.1', { + 'checksums': ['208f2897d6118012780d083a02ec7f30c0bb580e9535c2ed79f5b7e736790277'], }), ('spThin', '0.2.0', { 'checksums': ['2e997afb79a2a990eded34c71afaac83986669cfa9ac51b15ae3f2b558902048'], @@ -2921,8 +2987,8 @@ exts_list = [ ('nonnest2', '0.5-5', { 'checksums': ['027f510e322122fc75c936251a95ddd392f96047ac86e0fae6cf8f883ac7aab5'], }), - ('blavaan', '0.4-6', { - 'checksums': ['892d87ce2ed43d56915175f5f28150a38084f141bec15089de139ca60e4fde6e'], + ('blavaan', '0.4-7', { + 'checksums': ['43577264a1faff3cf98fce2c03b729816b40a82d36846458b8026b62da3008c3'], }), ('mathjaxr', '1.6-0', { 'checksums': ['ecc47607111b788d84789459af7f4f9102719f98640b7a23bd5a4eb1a6d3c179'], @@ -2933,8 +2999,8 @@ exts_list = [ ('metafor', '3.8-1', { 'checksums': ['d694577f954144d8a5eeab6521fe1c87e68ddf9ecfd7ccc915d01533371b0514'], }), - ('fmri', '1.9.6', { - 'checksums': ['7614290d880667512744d3450480a670cc38abdb270f3f776ac9a17a793f07f2'], + ('fmri', '1.9.11', { + 'checksums': ['e5eb14829fd2750eff65641caab7e8229b4d98650a61b48cedd436ab2411931e'], }), ('linkcomm', '1.0-14', { 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], @@ -3007,11 +3073,8 @@ exts_list = [ ('GxEScanR', '2.0.2', { 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], }), - ('alabama', '2022.4-1', { - 'checksums': ['a8c62859b39a8340ecf7bbf411fac303c059e4237d28ff7bba9ba3daaca1d36c'], - }), - ('admisc', '0.30', { - 'checksums': ['690c3fc8f24466438dd818d263e53f19f238310175731daac42c62f0bbc46205'], + ('admisc', '0.31', { + 'checksums': ['db385081c93f9d21adf4b8a8710ae0125a8dd01a87530b5051a3299997e0f4ea'], }), ('polycor', '0.8-1', { 'checksums': ['f05f53e0b5c992de0e5b4c6b2e998148cf83310358821e1bba180d81face0509'], @@ -3022,6 +3085,15 @@ exts_list = [ ('symmoments', '1.2.1', { 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], }), + ('rngWELL', '0.10-9', { + 'checksums': ['9969cc10be6d18155d2b2de93381c52e7f720c2b1b3f2554fa8bfa84ceb7cacb'], + }), + ('randtoolbox', '2.0.4', { + 'checksums': ['94da14953e4ffc7981d7a9398622082c4eda3bd9d912d1437b527d949da39e4b'], + }), + ('TruncatedNormal', '2.2.2', { + 'checksums': ['aef567e8962a64d1afbdfd98ab8f385f32966c3c42acb54ee20f02dceab18e15'], + }), ('cSEM', '0.5.0', { 'checksums': ['25ae115520aab7d916da9ded1f87b8519c4e15101c4adef2284c51eb03d81728'], }), @@ -3079,6 +3151,12 @@ exts_list = [ ('broom.helpers', '1.12.0', { 'checksums': ['bfb5d960367af1c4d04180345b65af4e3604345d4d6267af9445da72188c2a2c'], }), + ('bigD', '0.2.0', { + 'checksums': ['bca9eb0c9a231b159b97650884b1a7a490bc3bf4edef11cc12db06fb15c6ff5f'], + }), + ('juicyjuice', '0.1.0', { + 'checksums': ['64f5418b2a4794b47f0525baaf101beb4f1374ea22f38d7d604f5118bdb6e12a'], + }), ('gt', '0.8.0', { 'checksums': ['5eb74e134101cc74b8764252b8f4693a19e58f670b2f286b35cdb4d0ad0de9f9'], }), @@ -3109,8 +3187,8 @@ exts_list = [ ('geometries', '0.2.2', { 'checksums': ['32d3063de0f8a751382788f85ebaee5f39d68e486253c159d553bb3d72d69141'], }), - ('sfheaders', '0.4.0', { - 'checksums': ['86bcd61018a0491fc8a1e7fb0422c918296287b82be299a79ccee8fcb515e045'], + ('sfheaders', '0.4.2', { + 'checksums': ['ed9fb934c537fb6f126886f8e5997727de856e32fc3d38911b61a3a83faa7b2c'], }), ('geojsonsf', '2.0.3', { 'checksums': ['275ca14672d982e6a95884515f49d8a0aad14f3be62ea01b675a91b0bffb46d1'], @@ -3118,8 +3196,8 @@ exts_list = [ ('leaflet.providers', '1.9.0', { 'checksums': ['9e8fc75c83313ab24663c2e718135459599549ed6e7396086cacb44e36cfd67b'], }), - ('leaflet', '2.1.1', { - 'checksums': ['32f6a043759a0d2d98ea05739b7b4c55a266aa01272e48243e3c44046c7a5677'], + ('leaflet', '2.1.2', { + 'checksums': ['26d8671e8c99d85a4c257d8fb8c07ba899a2b95f801652598578f5cc5c724039'], }), ('leafsync', '0.1.0', { 'checksums': ['7d8fd8dbbbf66417cf32575f14c0fe68199762ecf1c036c7905c7c5ff859d75c'], @@ -3166,12 +3244,6 @@ exts_list = [ ('penfa', '0.1.1', { 'checksums': ['a22a8ac3d4a040c77e50ddc92328c1989eae536d79fe56013e9372ba27c114e5'], }), - ('rngWELL', '0.10-9', { - 'checksums': ['9969cc10be6d18155d2b2de93381c52e7f720c2b1b3f2554fa8bfa84ceb7cacb'], - }), - ('randtoolbox', '2.0.4', { - 'checksums': ['94da14953e4ffc7981d7a9398622082c4eda3bd9d912d1437b527d949da39e4b'], - }), ('kde1d', '1.0.5', { 'checksums': ['b5fab76a394a7819deee10afdff39ac64fccdb844735adfe51c92043016f2468'], }), @@ -3211,8 +3283,8 @@ exts_list = [ ('matlab', '1.0.4', { 'checksums': ['1988a2220703444a575f2bad4eb090a0da71478599eb53081dd7237b7ec216ea'], }), - ('FactorCopula', '0.9.2', { - 'checksums': ['e5a8b7a6ce2e4a0a3cdeaeae09b6e8d7af1f31ba1d6d4bd2276b42d95d9a3189'], + ('FactorCopula', '0.9.3', { + 'checksums': ['df1675bb96431417cdbb9000ab80e15e12d82c8ed9809eeb3d7fe7b4855178d3'], }), ('rpact', '3.3.4', { 'checksums': ['3de77ca528c3ae206f634e1ca7f6fed4f34363c7dc906410021aefab63ca1520'], @@ -3259,8 +3331,8 @@ exts_list = [ ('gdalUtils', '2.0.3.2', { 'checksums': ['4c6faabee2db8a87b7ea0f8e67e9fce3c5db7f4be353d7d86ea559507cbb2a4f'], }), - ('openair', '2.15', { - 'checksums': ['f11134bdcd466229a72cab158f49de583eedd850420d86e2013f5a9eefb685b1'], + ('openair', '2.16-0', { + 'checksums': ['7356203fab0a96a64996b1875ab973eb72d92a7ae0c4e58b6dc4d2383c47682d'], }), ('pdp', '0.8.1', { 'checksums': ['e23db66e5d575337d5c8fd664ccd0548cc85da2aca6613d90ce187be1dca376c'], @@ -3325,8 +3397,8 @@ exts_list = [ ('MLmetrics', '1.1.1', { 'checksums': ['777f1b76b16837387b830e2b65304ede234b9299d17efd09c7fd403356122118'], }), - ('renv', '0.16.0', { - 'checksums': ['f3a13e6b71e9be460db73bd9e11a3cb8a1d9bc05c6b77423957cbc2a7f8ba016'], + ('renv', '0.17.1', { + 'checksums': ['94f8b62846ce44e9c90884ce64a8faa0ff76b009c7a23ed0fb4343cd11836af4'], }), ('elliptic', '1.4-0', { 'checksums': ['b65729b1a1c7a84a5b1a59bfc893a2d35106853eaadcae31cda5c9ee3c500bb6'], @@ -3340,8 +3412,8 @@ exts_list = [ ('rtdists', '0.11-5', { 'checksums': ['97cf2ea758aa02b1dfaeef5032c6e50570777552aa771ed9a86df048b7871eed'], }), - ('AMAPVox', '0.12.1', { - 'checksums': ['1e9bce539dfbeb40a66efee3714bece1843ba856ee5e34b772757bad2660c942'], + ('AMAPVox', '1.0.0', { + 'checksums': ['e4804d38b58c296f9efd088b58730421ef4ccfe331aec0f24f5a3fea5cd3ac5d'], }), ('LCFdata', '2.0', { 'checksums': ['b58f4d93b9023dd1ba2db96a59ddfc058397085933d8de4cdb38ee064d5e7bf4'], @@ -3373,8 +3445,8 @@ exts_list = [ ('ggplotify', '0.1.0', { 'checksums': ['178f73d6d3dc391c3efb1a62c95fe38587044f9e3288dffb915d3687941bb38a'], }), - ('aplot', '0.1.9', { - 'checksums': ['af0763620a757571caac769bad5398c22a4890af6cb5646ac5fa9039a114bb12'], + ('aplot', '0.1.10', { + 'checksums': ['d937768241f887628b88bb3b49dd6cbe9b7dae39ae7054e7380a9836721a67d1'], }), ('tidytree', '0.4.2', { 'checksums': ['cb831a66d8afa5e21f5072e4fbebcbd2228881090d0040f87605f5aeefda155e'], @@ -3388,6 +3460,60 @@ exts_list = [ ('shadowtext', '0.1.2', { 'checksums': ['253c4e737dbb302aa0729e5074e84cbfde2a73bfd7a0fd2c74b557cb728bae7d'], }), + ('random', '0.2.6', { + 'checksums': ['2b59f9bce0c3ebf8215ab42dffaf9a1c7eea7468964063215a8d422af953b069'], + }), + ('R2WinBUGS', '2.1-21', { + 'checksums': ['fa86cb5140f5dfce29f9517b94d6d08c316ddcffa4aa3085945b84d34910134d'], + }), + ('aricode', '1.0.2', { + 'checksums': ['5f4e51f7063cfd4924a8925c902a3eb7517c743234a14560691cb84428b6b2f0'], + }), + ('DepthProc', '2.1.5', { + 'checksums': ['e6b0afd54bb20e25a6bf5402c771848db20e9c844f0fc990ecc3d1078b9eee44'], + }), + ('dbscan', '1.1-11', { + 'checksums': ['f0498e67e612629340a2758fbe747c4d9d4ca648f002230a03499cb73735e62f'], + }), + ('ggh4x', '0.2.3', { + 'checksums': ['8af0e855bf221ce53b3162ae9d25a8d04525aabbda2f63c4843d86ee3eca4535'], + }), + ('ComplexUpset', '1.3.3', { + 'checksums': ['5b2f99b4a38648641c7d31fc57f201a93e5bc1b85442a0b9726f72c166d964ea'], + }), + ('proxyC', '0.3.3', { + 'checksums': ['3e25da94633da0b5c6cdac03f5b6d8205d078f60c5a09073e90a1b6f0930e302'], + }), + ('changepoint', '2.2.4', { + 'checksums': ['ac636fde7610137385dde1e3d8a22a2ff856a8d5c917c7ad1a5cc49f98b8649b'], + }), + ('geeM', '0.10.1', { + 'checksums': ['fe76a32981b55835095041e777d1cf2e9ce43edb8d9488db56279f7cb6f43fe5'], + }), + ('ggstance', '0.3.6', { + 'checksums': ['cd9ad4fb83c583009ee45371c7d02d32b33d06238d3f0162b3ba9851e27a6372'], + }), + ('mosaicCore', '0.9.2.1', { + 'checksums': ['b7ce16f20fde1d8a5b1836110e5980fb274504ddae6b9c5c2f4198dc7d09dafa'], + }), + ('ggformula', '0.10.2', { + 'checksums': ['948b1c34a5c089cf86275d2b3e020e1a099278136e43175a50fb6063e54b6375'], + }), + ('kinship2', '1.9.6', { + 'checksums': ['0150bd5974c2a19885f6ff2e99f3c1f6361054a0910dcfc9dd26a8e0cd73bbf6'], + }), + ('MESS', '0.5.9', { + 'checksums': ['b57dff943a130830a24d87fe2e8f8b766cf18398c9c09e0a020d5dd183f9d72d'], + }), + ('smoof', '1.6.0.3', { + 'checksums': ['af8664b152876c545f6545528de6e05a289d0714103fac7afc52960a9a855fb1'], + }), + ('mlrMBO', '1.1.5.1', { + 'checksums': ['0cf26e5e9b180d15b932541cf081a552703a60edf762aafca9933c24ea91dc99'], + }), + ('emoa', '0.5-0.1', { + 'checksums': ['bff6c84274e9bdcbdb82d6edd90265844f7cd23f22abbf68d6b563ef48237966'], + }), ] moduleclass = 'lang' From 129ccd272dbcf7afc53468c1c6dced87b69d2c81 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Mar 2023 14:02:50 +0000 Subject: [PATCH 6905/9987] package dependencies --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 0696494be9a..3afe8e003a7 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -2999,6 +2999,15 @@ exts_list = [ ('metafor', '3.8-1', { 'checksums': ['d694577f954144d8a5eeab6521fe1c87e68ddf9ecfd7ccc915d01533371b0514'], }), + ('metafor', '3.8-1', { + 'checksums': ['d694577f954144d8a5eeab6521fe1c87e68ddf9ecfd7ccc915d01533371b0514'], + }), + ('RNifti', '1.4.5', { + 'checksums': ['a277a849cdfeba3a104fd4ac2764c655d5cf8a71d8e64fa212d359fe60934628'], + }), + ('oro.nifti', '0.11.4', { + 'checksums': ['efe4f5d2c2e37ff6c3e9250f54ef775e4d452c1334f781f22f219ed53148b606'], + }), ('fmri', '1.9.11', { 'checksums': ['e5eb14829fd2750eff65641caab7e8229b4d98650a61b48cedd436ab2411931e'], }), From a423cfb133b5c7de4fdc4b7245e76234bddf11db Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Fri, 17 Mar 2023 14:19:56 +0000 Subject: [PATCH 6906/9987] remove duplicate --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 3afe8e003a7..533f0b003da 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -2999,9 +2999,6 @@ exts_list = [ ('metafor', '3.8-1', { 'checksums': ['d694577f954144d8a5eeab6521fe1c87e68ddf9ecfd7ccc915d01533371b0514'], }), - ('metafor', '3.8-1', { - 'checksums': ['d694577f954144d8a5eeab6521fe1c87e68ddf9ecfd7ccc915d01533371b0514'], - }), ('RNifti', '1.4.5', { 'checksums': ['a277a849cdfeba3a104fd4ac2764c655d5cf8a71d8e64fa212d359fe60934628'], }), From 5af7bc9f581ce7030480c7238b7e6a734b8de6dc Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Fri, 17 Mar 2023 17:44:42 +0100 Subject: [PATCH 6907/9987] Disable qopt report in GraphBLAS compilation --- .../SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb | 8 +++++++- .../SuiteSparse_disable-qopt-report.patch | 14 ++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse_disable-qopt-report.patch diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb index d896b7962de..5b48dcf1cb2 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb @@ -11,7 +11,13 @@ toolchainopts = {'unroll': True, 'pic': True} source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] sources = ['v%(version)s.tar.gz'] -checksums = ['acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee'] +patches = [ + 'SuiteSparse_disable-qopt-report.patch', +] +checksums = [ + {'v5.10.1.tar.gz': 'acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee'}, + {'SuiteSparse_disable-qopt-report.patch': 'f96bcd993f4dd90a70aedcb2901582ac99f449ac359b46a36190862a16aeb870'}, +] builddependencies = [ ('CMake', '3.20.1'), diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse_disable-qopt-report.patch b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse_disable-qopt-report.patch new file mode 100644 index 00000000000..db00fb87ea1 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse_disable-qopt-report.patch @@ -0,0 +1,14 @@ +Compiling GraphBLAS with the intel toolchain consumes *a lot* of memory +because optimization reports are generated. This patch simply turns that off +to make the memory requirement for compilation more sensible. +--- GraphBLAS/CMakeLists.txt.orig 2023-03-17 14:46:24.533943000 +0100 ++++ GraphBLAS/CMakeLists.txt 2023-03-17 14:46:15.393912000 +0100 +@@ -198,7 +198,7 @@ + elseif ( "${CMAKE_C_COMPILER_ID}" STREQUAL "Intel" ) + # options for icc: also needs -std=c11 + set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -diag-disable 10397,15552 " ) +- set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -qopt-report=5 -qopt-report-phase=vec" ) ++ set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -qopt-report=0 -qopt-report-phase=vec" ) + # the -mp1 option is important for predictable floating-point results with + # the icc compiler. Without, ((float) 1.)/((float) 0.) produces NaN, + # instead of the correct result, Inf. From 5f2dd890807b9b70758c70260998a2a2ae4c5912 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Fri, 17 Mar 2023 17:46:13 +0100 Subject: [PATCH 6908/9987] Use JOBS variable to set make parallelism --- .../SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb index 5b48dcf1cb2..810a3aa16d0 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb @@ -31,5 +31,9 @@ dependencies = [ # make sure that bin/demo can find libsuitesparseconfig.so.5 during build prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " +# The default way to do a parallel make won't work with the Makefiles for +# SuiteSparse, JOBS has to be set to the desired parallelism +parallel = 1 +prebuildopts += "export JOBS=4 && " moduleclass = 'numlib' From db36e69a6cf4964a3661cfbcf7035a524519636d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 17 Mar 2023 20:42:54 +0100 Subject: [PATCH 6909/9987] Remove LLVM --- .../t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb index 6debe70fd8d..dc20d8bac90 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb @@ -17,7 +17,6 @@ builddependencies = [ ('git', '2.36.0', '-nodocs'), ('pybind11', '2.9.2'), ('UnZip', '6.0'), - ('LLVM', '14.0.3'), # for debugging with llvm-symbolizer, to be removed ] dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), From 61fb6a5ea31d8d683276c48882b448f86e640e62 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 17 Mar 2023 22:53:01 +0100 Subject: [PATCH 6910/9987] minor tweaks to release notes for EasyBuild v4.7.1 --- RELEASE_NOTES | 94 ++++++++++++++++++++++++++++++++++++--------------- 1 file changed, 66 insertions(+), 28 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index e1a2f41692d..baacf07be62 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 16,603 easyconfig files, for 2,984 different software packages, +The latest version of easybuild-easyconfig provides 16,611 easyconfig files, for 2,985 different software packages, incl. 39 different (compiler) toolchains. @@ -12,50 +12,87 @@ v4.7.1 (March 20th 2023) update/bugfix release -- added example easyconfig files for 90 new software packages: - - astro-tulips (#17263), BA3-SNPS-autotune (#17248), BayesAss3-SNPs (#17247), Block (#27), CatLearn (#14940), CDFlib (#17133), Cellpose (#13703), CheckM-Database (#17462), chemprop (#17261), cimfomfa (#17268), conan (#17326), cooler (#17328), crossguid (#16207), cuSPARSELt (#17141), cython-blis (#17544), DBCSR (#17170), dclone (#17225), Deprecated (#1248), DLPack (#17311), DMLC-Core (#17311), dorado (#17195), duplex-tools (#17497), eQuilibrator (#16812), fastai (#16985), fastjet (#17367), fastjet-contrib (#17377), ffnvcodec (#17271), finder (#1917), flowFDA (#17495), genomepy (#17506), GKeyll (#16044), GraphDB (#17280), graphviz-python (#17352), GUSHR (#16905), Health-GPS (#17434), HepMC3 (#17341), HiCMatrix (#17330), Inferelator (#17223), irodsfs (#17486), jupyter-contrib-nbextensions (#17270), jupyterlab-lmod (#16563), jupyterlmod (#16563), kb-python (#17260), kineto (#17194), KMCP (#17267), krbalancing (#17325), Lace (#954), LASSO-Python (#17510), libemf (#16188), loomR (#14518), MAGMA-gene-analysis MAKER (#17345), methylartist (#17264), nanoflann (#17311), netMHCII (#9741), NEXUS-CL (#17350), nichenetr (#17524), Parallel-Hashmap pdsh (#17139), Perseus (#17210), PfamScan (#17530), Phenoflow (#17495), PIRATE (#17275), plot1cell (#17498), pybinding (#17137), pyperf (#17063), pyslim (#17150), pytest-rerunfailures (#17295), pytest-shard (#17295), PyTorch-Ignite (#15491), PyVCF3 (#17519), R2jags (#17226), rapidcsv (#16211), rapidNJ (#17399), Rivet (#17380), rmarkdown (#17189), scArches (#17069), scHiCExplorer (#17334), scib (#17142), SeaView (#17385), siscone (#17342), sparse-neighbors-search (#17329), sradownloader (#17188), stardist (#17215), Strainberry (#17522), toil (#17098), vConTACT2 (#17372), VirSorter2 (#17371), vitessce-python (#17472), YODA (#17343) +- added example easyconfig files for 89 new software packages: + - astro-tulips (#17263), BA3-SNPS-autotune (#17248), BayesAss3-SNPs (#17247), Block (#27), CatLearn (#14940), + CDFlib (#17133), Cellpose (#13703), CheckM-Database (#17462), chemprop (#17261), cimfomfa (#17268), conan (#17326), + cooler (#17328), crossguid (#16207), cuSPARSELt (#17141), cython-blis (#17544), DBCSR (#17170), dclone (#17225), + Deprecated (#1248), DLPack (#17311), DMLC-Core (#17311), dorado (#17195), duplex-tools (#17497), + eQuilibrator (#16812), fastai (#16985), fastjet (#17367), fastjet-contrib (#17377), ffnvcodec (#17271), + finder (#1917), flowFDA (#17495), genomepy (#17506), GKeyll (#16044), GraphDB (#17280), graphviz-python (#17352), + GUSHR (#16905), Health-GPS (#17434), HepMC3 (#17341), HiCMatrix (#17330), Inferelator (#17223), irodsfs (#17486), + jupyter-contrib-nbextensions (#17270), jupyterlab-lmod (#16563), jupyterlmod (#16563), kb-python (#17260), + kineto (#17194), KLaceMCP (#17267), krbalancing (#17325), Lace (#954), LASSO-Python (#17510), libemf (#16188), + loomR (#14518), MAKER (#17345), methylartist (#17264), nanoflann (#17311), netMHCII (#9741), NEXUS-CL (#17350), + nichenetr (#17524), Parallel-Hashmap pdsh (#17139), Perseus (#17210), PfamScan (#17530), Phenoflow (#17495), + PIRATE (#17275), plot1cell (#17498), pybinding (#17137), pyperf (#17063), pyslim (#17150), + pytest-rerunfailures (#17295), pytest-shard (#17295), PyTorch-Ignite (#15491), PyVCF3 (#17519), R2jags (#17226), + rapidcsv (#16211), rapidNJ (#17399), Rivet (#17380), rmarkdown (#17189), scArches (#17069), scHiCExplorer (#17334), + scib (#17142), SeaView (#17385), siscone (#17342), sparse-neighbors-search (#17329), sradownloader (#17188), + stardist (#17215), Strainberry (#17522), toil (#17098), vConTACT2 (#17372), VirSorter2 (#17371), + vitessce-python (#17472), vitessceR (#17525), YODA (#17343) - added additional easyconfigs for various supported software packages, including: - - AlphaFold 2.3.0, alsa-lib v1.2.8, Anaconda3 2022.10, angsd 0.940, ANIcalculator 1.0, archspec 0.2.0, Armadillo 11.4.3, arpack-ng 3.8.0, astro tulips, AUGUSTUS 3.5.0, Autotools 20220317, BA3-SNPS-autotune 2.1.2, BCFtools 1.17, bcl2fastq2 2.20.0, beagle-lib 4.0.0, Beast 2.7.3, BeautifulSoup 4.11.1, Bio-SearchIO-hmmer 1.7.3, BLAT 3.7, Blender 3.4.1, Blitz++ 1.0.2, Block 1.5.3, Blosc2 2.6.1, Boost 1.81.0, Bottleneck 1.3.6, Bowtie 1.3.1, BRAKER 2.1.6, Brotli-python 1.0.9, Brunsli 0.1, BUSCO 5.4.5, bx-python 0.9.0, canu 2.2, CatLearn 0.6.2, CatMAP 20220519, CDFlib 0.4.9, CD-HIT 4.8.1, Cellpose 0.6.5, CellRanger 7.1.0, Cereal 1.3.2, CFITSIO 4.2.0,CheckM 1.2.2, chemprop 1.5.2, cimfomfa 22.273, code-server 4.9.1, conan 1.58.0, configurable-http-proxy 4.5.3, cooler 0.9.1, cppy 1.2.1, crossguid 20190529, csvkit 1.1.0, CubeLib 4.8, CubeWriter 4.8, CUDA 12.1.0, cuDNN 8.8.0.121, cuTENSOR 1.6.1.5, cwltool 3.1.20221008225030, Cython 0.29.33, cython-blis 0.9.1, DBCSR 2.5.0, dclone 2.3, Deprecated 1.2.13, DFT-D3 3.2.0, DGL 0.9.1, DIAMOND 2.1.0, dill 0.3.6, DIRAC 22.0, DIRAC 23.0, dm-tree 0.1.8, DoubletFinder 2.0.3, dRep 3.4.2, edlib 1.3.9, eggnog-mapper 2.1.10, Eigen 3.4.0, elfutils 0.189, ELPA 2022.05.001, epiScanpy 0.4.0, eQuilibrator 0.4.7, Exonerate 2.4.0, FabIO 0.14.0, fastai 2.7.10, fastai 2.7.10, FastANI 1.33, fastjet 3.4.0, fastjet-contrib 1.0.49, FastQ_Screen 0.14.0, FFmpeg 5.1.2, ffnvcodec 11.1.5.2, finder 1.1.0, FLAC 1.4.2, flatbuffers 2.0.7, flatbuffers 23.1.4, FLINT 2.9.0, GDAL 2.4.4, GDAL 3.6.2, GDGraph 1.56, GeneMark-ET 4.71, genomepy 0.15.0, GenomeTools 1.6.2, GEOS 3.11.1, GEOS 3.9.1, giflib 5.2.1, GKeyll 20220803, GLPK 5.0, GMAP-GSNAP 2023-02-17, gmpy2 2.1.2, gmsh 4.11.1, gnuplot 5.4.6, googletest 1.12.1, GPyTorch 1.9.1, GraphDB 10.1.5, Graphene 1.10.8, Greenlet 2.0.2, GSL 2.7, GST-plugins-base 1.22.1, GStreamer 1.22.1, GTDB-Tk 2.1.1, h5py 3.7.0, h5py 3.8.0, HDBSCAN 0.8.29, HDF 4.2.15, HDF5 1.14.0, HepMC3 3.2.5, HiCExplorer 3.7.2, HiCMatrix 17, HighFive 2.6.2, Highway 1.0.3, HISAT2 2.2.1, HMMER 3.3.2, HPL 2.3, HTSlib 1.17, Hyperopt 0.2.7, hypothesis 6.68.2, Hypre 2.27.0, igraph 0.10.3, IGV 2.16.0, IJulia 1.24.0, Imath 3.1.6, IMB 2021.3, imbalanced-learn 0.10.1, imkl 2021.4.0, imkl 2022.1.0, imkl 2023.0.0, imkl-FFTW 2023.0.0, impi 2021.8.0, Inferelator 0.6.1, intel-compilers 2023.0.0, IRkernel 1.3.2, irodsfs 0.8.11, irodsfs 0.8.12, irodsfs 0.8.9, JAGS 4.3.1, jax 0.4.4, Jellyfish 2.3.0, jemalloc 5.2.1, json-c 0.16, Julia 1.8.5, JupyterHub 3.0.0, jupyter-matlab-proxy 0.5.0, jupyter-resource-usage 0.6.3, jupyter-server-proxy 3.2.2, KaHIP 3.14, Kaleido 0.2.1, kallisto 0.48.0, Kent_tools 442, kineto 0.4.0, KMCP 0.9.1, Kraken 1.1.1, Lace 1.14.1, LAME 3.100, leidenalg 0.9.1, LERC 4.0.0, libcerf 2.3, libemf 1.0.13, libgd 2.3.3, libgeotiff 1.7.1, libgit2 1.5.0, libnsl 2.0.0, libogg 1.3.5, libopus 1.3.1, libsndfile 1.2.0, libtirpc 1.3.3, libvorbis 1.3.7, libxslt 1.1.37, Longshot 0.4.5, loompy 3.0.7, loomR 0.2.0, lpsolve 5.5.2.11, LTR_retriever 2.9.0, Lua 5.4.4, MAFFT 7.505, MAKER 3.01.04, Maple 2022.1, Mash 2.3, MaSuRCA 4.1.0, Mathematica 13.1.0, MATIO 1.5.23, MATLAB 2022a, MATLAB 2022b, matplotlib 3.7.0, MaxQuant 2.2.0.0, MCL 14.137, MCL 22.282, MEGAHIT 1.2.9, MetaBAT 2.15, MetaEuk 6, methylartist 1.2.6, METIS 5.1.0, Miniconda3 22.11.1, minimap2 2.24, mm-common 1.0.5, motif 2.3.8, MPFR 4.2.0, mpi4py 3.1.4, mpmath 1.2.1, MrBayes 3.2.7, msprime 1.2.0, MultiQC 1.14, MUMmer 4.0.0rc1, mygene 3.2.2, NAMD 2.14, nano 7.1, nanomax-analysis-utils 0.4.4, ncbi-vdb 3.0.2, NCO 5.1.3, netCDF 4.9.0, NetLogo 6.2.2, NetLogo 6.3.0, netMHCII 2.3, nettle 3.8.1, networkx 2.8.4, Nextflow 22.10.5, Nextflow 22.10.6, nlohmann_json 3.11.2, NLopt 2.7.1, numba 0.56.4, NVHPC 22.11, NVHPC 22.9, NVHPC 23.1, NVSHMEM 2.8.0, occt 7.5.0p1, OPARI2 2.0.7, OpenEXR 3.1.5, OpenMM 7.5.1, OpenMPI 4.1.1, OpenMPI 4.1.5, Optuna 3.1.0, ORCA 5.0.4, OSU-Micro-Benchmarks 5.9, OTF2 3.0.2, PAML 4.10.5, panaroo 1.3.2, parallel-fastq-dump 0.6.7, Parallel-Hashmap 1.33, ParallelIO 2.5.10, parasail 2.6, ParMETIS 4.0.3, PCRE 8.45, pdsh 2.34, pdsh 2.34, PDT 3.25.1, Perl 5.36.0, Pillow 9.4.0, PIPITS 3.0, pkgconfig 1.5.5, PLINK 2.00a3.7, plotly.py 5.12.0, plotly.py 5.13.1, PLUMED 2.8.1, PnetCDF 1.12.3, poetry 1.2.2, polymake 4.8, PRANK 170427, preseq 3.2.0, presto 1.0.0, prodigal 2.6.3, PROJ 9.1.1, prokka 1.14.5, protobuf 3.21.9, psycopg2 2.9.5, pyBigWig 0.3.18, pybind11 2.10.3, pybinding 0.9.5, PyCharm 2022.3.2, py-cpuinfo 9.0.0, pydot 1.4.2, pyFAI 0.21.3, pyfaidx 0.7.1, pyGenomeTracks 3.8, pygraphviz 1.10, pymca 5.7.6, Pysam 0.20.0, PySCF 2.1.1, PyTables 3.8.0, Python 3.11.2, python-igraph 0.9.1, python-parasail 1.3.3, PyZMQ 24.0.1, QCG-PilotJob 0.13.1, Qhull 2020.2, QIIME2 2022.11, Qt5Webkit 5.212.0, QtPy 2.3.0, QUAST 5.2.0, R2jags 0.7, rapidcsv 8.64, rapidNJ 2.3.3, Ray-project 2.2.0, RDKit 2022.09.4, RECON 1.08, Redis 7.0.8, redis-py 4.5.1, ReFrame 4.0.1, ReFrame 4.0.5, RepeatMasker 4.1.4, RepeatModeler 2.0.4, RepeatScout 1.0.6, Rivet 3.1.7, rjags 4-13, rmarkdown 2.20, RMBlast 2.13.0, Roary 3.13.0, ROOT 6.22.08, RSEM 1.3.3, Salmon 1.9.0, SAMtools 1.17, Scalasca 2.6.1, scanpy 1.9.1, scArches 0.5.6, scikit-learn 1.2.1, scikit-misc 0.1.4, SciPy-bundle 2023.02, Score-P 6.0, Score-P 7.0, Score-P 8.0, SDL2 2.26.3, SEPP 4.5.1, SeqKit 2.3.1, silx 1.0.0, SIONlib 1.7.7, snakemake 7.18.2, snakemake 7.22.0, SNAP 2.0.1, SNAP-HMM 20221022, SpaceRanger 2.0.1, SPAdes 3.15.5, spaln 2.4.13f, Spark 3.3.1, sparsehash 2.0.4, sradownloader 3.9, SRA-Toolkit 3.0.0, SRA-Toolkit 3.0.3, SSW 1.2.4, STAR 2.7.10b, STAR-CCM+ 18.02.008, stardist 0.8.3, Strainberry 1.1, STREAM 5.10, STREAM 5.10, SVG 2.87, sympy 1.10.1, sympy 1.11.1, Szip 2.1.1, TensorFlow-Datasets 4.8.3, Tk 8.6.12, Tkinter 3.10.8, toil 5.8.0, tqdm 4.64.1, TRF 4.09.1, Trilinos 13.4.1, Trim_Galore 0.6.10, Trinity 2.15.1, TWL-NINJA 0.98, UDUNITS 2.2.28, umap-learn 0.4.6, umap-learn 0.5.3, Unidecode 1.3.6, vConTACT2 0.11.3, velocyto 0.17.17, VirSorter2 2.2.4, vsc-mympirun 5.3.0, VSEARCH 2.22.1, wget 1.21.3, wtdbg2 2.5, wxWidgets 3.2.2.1, x264 20230226, x265 3.5, Xerces-C++ 3.2.4, xtb 6.5.0, xtb 6.5.1, Xvfb 21.1.6, xxd 8.2.4220, Yasm 1.3.0, YODA 1.9.7 + - AlphaFold 2.3.0, Anaconda3 2022.10, angsd 0.940, archspec 0.2.0, Armadillo 11.4.3, AUGUSTUS 3.5.0, bcbio-gff 0.7.0, + BCFtools 1.17, beagle-lib 4.0.0, Beast 2.7.3, BeautifulSoup 4.11.1, BLAT 3.7, Blender 3.4.1, Blosc2 2.6.1, + Boost 1.81.0, Bottleneck 1.3.6, BUSCO 5.4.5, bx-python 0.9.0, CatMAP 20220519, CellRanger 7.1.0, Cereal 1.3.2, + CFITSIO 4.2.0, CheckM 1.2.2, code-server 4.9.1, configurable-http-proxy 4.5.3, csvkit 1.1.0, 4.8, CUDA 12.1.0, + cuDNN 8.8.0.121, cwltool 3.1.20221008225030, Cython 0.29.33, DGL 0.9.1, DIAMOND 2.1.0, dill 0.3.6, DIRAC 23.0, + dm-tree 0.1.8, dRep 3.4.2, eggnog-mapper 2.1.10, elfutils 0.189, ELPA 2022.05.001, epiScanpy 0.4.0, FabIO 0.14.0, + FastQ_Screen 0.14.0, FFmpeg 5.1.2, FLAC 1.4.2, flatbuffers 23.1.4, FLINT 2.9.0, GDAL 2.4.4, GDAL 3.6.2, + GDGraph 1.56, GEOS 3.11.1, GMAP-GSNAP 2023-02-17, gmsh 4.11.1, gnuplot 5.4.6, GOATOOLS 1.3.1, googletest 1.12.1, + GPyTorch 1.9.1, Greenlet 2.0.2, GST-plugins-base 1.22.1, GStreamer 1.22.1, GTDB-Tk 2.1.1, h5py 3.8.0, + HDBSCAN 0.8.29, HDF5 1.14.0, HiCExplorer 3.7.2, Highway 1.0.3, HTSlib 1.17, hypothesis 6.68.2, Hypre 2.27.0, + igraph 0.10.3, IGV 2.16.0, IJulia 1.24.0, Imath 3.1.6, imbalanced-learn 0.10.1, imkl 2023.0.0, imkl-FFTW 2023.0.0, + impi 2021.8.0, intel-compilers 2023.0.0, IRkernel 1.3.2, JAGS 4.3.1, jax 0.4.4, Julia 1.8.5, JupyterHub 3.0.0, + jupyter-matlab-proxy 0.5.0, jupyter-resource-usage 0.6.3, jupyter-server-proxy 3.2.2, Kent_tools 442, + leidenalg 0.9.1, LERC 4.0.0, libcerf 2.3, libgit2 1.5.0, libnsl 2.0.0, libsndfile 1.2.0, libtirpc 1.3.3, + libxslt 1.1.37, Longshot 0.4.5, MAFFT 7.505, Maple 2022.1, MaSuRCA 4.1.0, Mathematica 13.1.0, MATIO 1.5.23, + MATLAB 2022a + 2022a-r3 + 2022b, matplotlib 3.7.0, MaxQuant 2.2.0.0, MCL 22.282, Miniconda3 22.11.1, + mm-common 1.0.5, MPFR 4.2.0, mpi4py 3.1.4, mpmath 1.2.1, msprime 1.2.0, MultiQC 1.14, mygene 3.2.2, nano 7.1, + nanomax-analysis-utils 0.4.4, ncbi-vdb 3.0.2, NetLogo 6.2.2 + 6.3.0, nettle 3.8.1, Nextflow 22.10.6, + nlohmann_json 3.11.2, numba 0.56.4, NVHPC 22.9 + 22.11 + 23.1, NVSHMEM 2.8.0, OpenMPI 4.1.5, Optuna 3.1.0, + ORCA 5.0.4, PAML 4.10.5, panaroo 1.3.2, ParallelIO 2.5.10, parasail 2.6, Pillow 9.4.0, PIPITS 3.0, PLINK 2.00a3.7, + plotly.py 5.12.0 + 5.13.1, PLUMED 2.8.1, poetry 1.2.2, polymake 4.8, preseq 3.2.0, presto 1.0.0-20230113, + PROJ 9.1.1, protobuf 3.21.9, psycopg2 2.9.5, pybind11 2.10.3, PyCharm 2022.3.2, py-cpuinfo 9.0.0, pyFAI 0.21.3, + pyfaidx 0.7.1, pyGenomeTracks 3.8, pygraphviz 1.10, pymca 5.7.6, Pysam 0.20.0, PySCF 2.1.1, PyTables 3.8.0, + Python 3.11.2, python-parasail 1.3.3, PyZMQ 24.0.1, QCG-PilotJob 0.13.1, QIIME2 2022.11, QtPy 2.3.0, QUAST 5.2.0, + Ray-project 2.2.0, RDKit 2022.09.4, Redis 7.0.8, redis-py 4.5.1, ReFrame 4.0.5, RepeatMasker 4.1.4, + RepeatModeler 2.0.4, rjags 4-13, RMBlast 2.13.0, ROOT 6.22.08, Salmon 1.9.0, SAMtools 1.17, Scalasca 2.6.1, + scikit-learn 1.2.1, SciPy-bundle 2023.02, SDL2 2.26.3, SeqKit 2.3.1, silx 1.0.0, snakemake 7.22.0, + SNAP-HMM 20221022, SpaceRanger 2.0.1, SPAdes 3.15.5, spaln 2.4.13f, Spark 3.3.1, SRA-Toolkit 3.0.3, SSW 1.2.4, + STAR 2.7.10b, STAR-CCM+ 18.02.008, SVG 2.87, TensorFlow-Datasets 4.8.3, Tkinter 3.10.8, tqdm 4.64.1, + Trilinos 13.4.1, Trim_Galore 0.6.10, Trinity 2.15.1, TWL-NINJA 0.98-cluster_only, Unidecode 1.3.6, + vsc-mympirun 5.3.0, VSEARCH 2.22.1, wget 1.21.3, wxWidgets 3.2.2.1, x264 20230226, Xerces-C++ 3.2.4, + XlsxWriter 3.0.8, xtb 6.5.1, Xvfb 21.1.6 - minor enhancements, including: - - add ggvenn extension to R 4.2.1 (#17043) - - add scatterpie and shadowtext extensions to R-4.2.1 (#17125) - - add DO.db, GOSemSim, DOSE, enrichplot, and clusterProfiler extensions to Bioconductor 3.15 (#17126) + - add additional extensions to R 4.2.1 (#17043, #17125, #17224, #17493, #17523) + - add additional extensions to Bioconductor 3.15 (#17126, #17315, #17494) - add sanity check command to OpenMolcas v22.10 (#17128) - add Set::Object and Heap::Fibonacci extensions to Perl 5.32.1 (#17151) - add additional extensions to Python 3.10.8 (required for scipy test suite) (#17159) - - enable -fPIC in GEOS 3.11.1 (required by GDAL) (#17196) - enhance OpenFold 1.0.1 for standalone usage (#17206) - add SDL2 dependency for FFmpeg 5.0.1 to build ffplay (#17213) - set $JULIA_DEPOT_PATH and $JULIA_HISTORY in Julia easyconfigs (#17216) - - add random + R2WinBUGS extensions to R 4.2.1 (#17224) - - add Devel::Size extension to recent Perl extensions (#17246) - - Combine errors of extension patch check into a single failure (#17286) - - Add case-insensitive name clash test (#17303) - - Add ReactomePA extension and deps to R-bundle-Bioconductor/3.15 (#17315) + - add Devel::Size + Math::Utils extension to recent Perl easyconfigs (#17246, #17466) + - combine errors of extension patch check into a single failure (#17286) + - add case-insensitive name clash test (#17303) - add ffnvcodec build dependency to all recent FFmpeg easyconfigs (#17316) - use 'import deap.base' in sanity check for deap extension in SciPy-bundle 2022.05 (#17429) - add source URL to cuDNN 8.8 easyconfig (#17439) - - add Math::Utils extension to recent Perl easyconfigs (#17466) - add missing zstd dep to Boost (#17482) - - add additional extensions for R 4.2.1 (#17493) - - add additional extensions for R-bundle-Bioconductor 3.15 (#17494) - - add smoof/mlrMBO/emoa extensions to R 4.2.1 (#17523) - various bug fixes, including: - - fix postinstallcmds and clarify download instructions for netMHC-4.0a (#9739) - - fix postinstallcmds and clarify download instructions for netMHCpan-4.0a (#9740) + - fix postinstallcmds and clarify download instructions for netMHC + netMHCpan 4.0a (#9739, #9740) - fix OpenBLAS 0.3.15 patch to correctly set the CPU core type for Tiger Lake (#15845) - add alternative checksum for UCX 1.13.1 after source tarball was changed in-place (without actual code changes) (#17077) - fix build of TensorFlow 2.5+ on aarch64 (#17101) - explictely download qe-gipaw source tarball from qe-gipaw GitHub repository in QuantumESPRESSO 7.1 easyconfigs (#17129) - add patch for GCCcore 11.1.0 + 11.2.0 to fix AVX2 bug (#17135) - add patch to make ncbi-vdb 3.0.0 compatible with HDF5 1.12.2 (#17140) - - fix source URL for p7zip v17.x, moved to p7zip-project repo (#17144) + - fix source URL for p7zip v17.x (#17144) - add patches for Qt5 5.15.5 to fix compilation failures in abseil and breakpad with glibc 2.34 (#17165) - remove dependency on Pillow from scikit-bio v0.5.7 (#17178) - correctly specify path to libfabric installation prefix in PMIx 4.1.0 easyconfig (#17204) - use GCC as toolchain for serial variants of HDF5, since it has a FORTRAN API (#17221) - fix CMake print summary for long hostnames for NECI (#17230) - - fix website/docs links in README (#17232) - add missing pmix patch to OpenMPI 4.1.1 easyconfig used in iomkl/2021a and iomkl/2021b (#17240) - include required stereo_chemical_props.txt for OpenFold 1.0.1 (#17242) - add patch for PAPI 7.0.0 to fix compilation error (#17244) @@ -68,21 +105,15 @@ update/bugfix release - allow multiple easyconfigs with same name if they differ by CUDA version included in versionsuffix (#17289) - remove duplicate SlamDunk easyconfig using lowercase name (#17301) - use https in homepage + source URL for GenomeThreader 1.7.3 (#17338) - - Archive BAMM, BamM, and GroopM to avoid BAMM/BamM name collision (#17348) - - consistently use NanoFilt capitalisation (#17349) - - rename ncl to NEXUS-CL to avoid case-insensitive name clash (#17350) - consistently use Check capitailisation (#17351) - - rename python graphviz to graphviz-python to avoid case-insensitive name clash (#17352) - add alternative checksum for spatial 7.3-14 extension in R 4.1.x easyconfigs (#17356) - fix homepage + source URL for ELPA (due to switch to new domain) (#17357) - fix homepage in ELPA easyconfigs (due to switch to new domain) (#17358) - rename libpsml for consistency with libPSML (#17359) - - archive charmm and CHARMM easyconfigs to avoid case-insensitive name clash (#17364) - replace obsolete pycrypto with pycryptodome in Python 3.10.x easyconfigs (#17412) - update deap to version 1.3.3 in SciPy-bundle 2022.05 easyconfigs (since deap 1.3.1 is broken) (#17413) - add patch for Qt5 5.12.2 with GCCcore/11.2.0 to fix template bug (#17464) - - replace src include path with installation dir for HDF5 (#17469) - - replace src include path with installation dir for HDF5 (intel) (#17488) + - replace src include path with installation dir for HDF5 (#17469, #17488) - disable Python support for OTF2 v2.2, since we're not including Python 2.x as dependency (#17499) - update homepage and source urls of DFT-D3 (#17528) - use Binary easyblock for ANIcalculator to prevent RPATH sanity check failures (#17536) @@ -90,10 +121,17 @@ update/bugfix release - fix invalid escape sequences in easyconfigs by using raw strings (r"...") (#11149) - add exception for ncbi-vdb 3.0.0 dependency variant (#17131) - use proper source tarball instead of cloning GitHub repository for wxWidgets v3.2.1 (#17167) + - enable -fPIC in GEOS 3.11.1 (required by GDAL) (#17196) + - fix website/docs links in README (#17232) - remove commented out line and delete unused patch for TALON (#17298) - re-enable disabled tests (#17304) - rename MAGMA to MAGMA-gene-analysis to avoid name collision (#17345) - Archive ARB and blasr patch files (#17346) + - Archive BAMM, BamM, and GroopM to avoid BAMM/BamM name collision (#17348) + - consistently use NanoFilt capitalisation (#17349) + - rename ncl to NEXUS-CL to avoid case-insensitive name clash (#17350) + - rename python graphviz to graphviz-python to avoid case-insensitive name clash (#17352) + - archive charmm and CHARMM easyconfigs to avoid case-insensitive name clash (#17364) 4.7.0 (Janurary 9th 2023) From 64bd3e60b1a14291ddef33ad7f5869fc0d4ed0e8 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 18 Mar 2023 10:46:39 +0100 Subject: [PATCH 6911/9987] adding easyconfigs: ASE-3.22.1-foss-2022b.eb, Flask-2.2.3-GCCcore-12.2.0.eb, spglib-python-2.0.2-gfbf-2022b.eb --- .../a/ASE/ASE-3.22.1-foss-2022b.eb | 63 +++++++++++++++++++ .../f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb | 55 ++++++++++++++++ .../spglib-python-2.0.2-gfbf-2022b.eb | 27 ++++++++ 3 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.2-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb new file mode 100644 index 00000000000..4a076fc342b --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Flask', '2.2.3'), + ('matplotlib', '3.7.0'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.0.2'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.8.2', { + 'checksums': ['77f03f4554392558700295e05aed0b1096a20d4a60a4f3ddcde58b0c31c8fca2'], + }), + ('ase', version, { + 'patches': [ + 'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch', + 'ASE-3.22.1-Compatibility-with-pytest-part-2.patch', + 'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch', + 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', + ], + 'checksums': [ + '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432', # ase-3.22.1.tar.gz + # ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch + '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac', + # ASE-3.22.1-Compatibility-with-pytest-part-2.patch + '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601', + # ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch + 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8', + # ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch + '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d', + ], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..26e22ef4b44 --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '2.2.3' + +homepage = 'https://www.palletsprojects.com/p/flask/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Python', '3.10.8'), +] + +builddependencies = [('binutils', '2.39')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('Werkzeug', version, { + 'checksums': ['2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe'], + }), + ('asgiref', '3.6.0', { + 'checksums': ['9567dfe7bd8d3c8c892227827c41cce860b368104c3431da67a0c5a65a949506'], + }), + (name, version, { + 'checksums': ['7eb373984bf1c770023fce9db164ed0c3353cd0b53f130f4693da0ca756a2e6d'], + }), + ('Flask-Cors', '3.0.10', { + 'checksums': ['b60839393f3b84a0f3746f6cdca56c1ad7426aa738b70d6c61375857823181de'], + }), + ('cachelib', '0.10.2', { + 'checksums': ['593faeee62a7c037d50fc835617a01b887503f972fb52b188ae7e50e9cb69740'], + }), + ('Flask-Session', '0.4.0', { + 'checksums': ['c9ed54321fa8c4ca0132ffd3369582759eda7252fb4b3bee480e690d1ba41f46'], + }), +] + +sanity_check_paths = { + 'files': ['bin/flask'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['flask --version'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.2-gfbf-2022b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.2-gfbf-2022b.eb new file mode 100644 index 00000000000..76b88995143 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.2-gfbf-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '2.0.2' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['1d081ec22da4ab4fc3198e9445ddad6dec2261c43927831151d93e39422610aa'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' From 198d3412fc6543ced5b1d143c57e7e66e9a66348 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 18 Mar 2023 10:55:09 +0000 Subject: [PATCH 6912/9987] specify Python_ROOT for GDAL 3.6.2 --- easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb index aac67f80329..01346b45e3a 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb @@ -63,6 +63,7 @@ _base_configopts = ' '.join([ '-DGDAL_USE_INTERNAL_LIBS=OFF', '-DArrow_DIR=$EBROOTARROW', '-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include', + '-DPython_ROOT=$EBROOTPYTHON', ]) # iterative build for both static and shared libraries From f62f8d8b5b328a3a709edcfe5ea36be954d219e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2023 12:47:01 +0100 Subject: [PATCH 6913/9987] add back useful comments + add webutils/swagger/varhandle extensions for R 4.2.2 --- .../easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 533f0b003da..67f94d8778f 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -77,6 +77,9 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 23rd June 2022 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets', @@ -2370,6 +2373,7 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, @@ -2884,8 +2888,12 @@ exts_list = [ 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], }), ('gWidgets2tcltk', '1.0-8', { - 'modulename': False, + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], }), ('mgsub', '1.7.3', { @@ -3520,6 +3528,15 @@ exts_list = [ ('emoa', '0.5-0.1', { 'checksums': ['bff6c84274e9bdcbdb82d6edd90265844f7cd23f22abbf68d6b563ef48237966'], }), + ('webutils', '1.1', { + 'checksums': ['33e2b408d2b9ca12e158e0007d4a55a3ace6838341ad944344de2ceb806e4699'], + }), + ('swagger', '3.33.1', { + 'checksums': ['528369b04c6142112e05ee8b950ca1c01b3e390a4515eacb0fa17db98bafafd1'], + }), + ('varhandle', '2.0.5', { + 'checksums': ['9b0ee653e0343e292547d2a7052e60a2e7d97d1d5528246862522e67346882d0'], + }), ] moduleclass = 'lang' From 90ea714353c6b2d804487829c01bea3cc8806f2c Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 18 Mar 2023 11:59:27 +0000 Subject: [PATCH 6914/9987] Update package update date --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 67f94d8778f..7e0edd889ee 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -75,7 +75,7 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on 23rd June 2022 +# packages updated on 18th March 2023 exts_list = [ # include packages that are part of the base installation of R, # both to make sure they are available (via sanity check), From dbd50ab285e5fd26548a78ee235ecab60ab35fa2 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 18 Mar 2023 12:00:12 +0000 Subject: [PATCH 6915/9987] yesterday, not today --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 7e0edd889ee..dd02af827b6 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -75,7 +75,7 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on 18th March 2023 +# packages updated on 17th March 2023 exts_list = [ # include packages that are part of the base installation of R, # both to make sure they are available (via sanity check), From c94dbda543ece1fcd7a938c8eb55400e1ed34bbe Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 18 Mar 2023 13:20:11 +0100 Subject: [PATCH 6916/9987] adding easyconfigs: networkx-2.8.8-gfbf-2022b.eb --- .../n/networkx/networkx-2.8.8-gfbf-2022b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.8.8-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.8.8-gfbf-2022b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.8.8-gfbf-2022b.eb new file mode 100644 index 00000000000..bac13dc9e35 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.8.8-gfbf-2022b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.8.8' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['230d388117af870fce5647a3c52401fcf753e94720e6ea6b4197a5355648885e'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 0fb5d7c7f13585878ba76f6c58d4d4953c54f16a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2023 14:08:05 +0100 Subject: [PATCH 6917/9987] last update of release notes for EasyBuild v4.7.1 --- RELEASE_NOTES | 62 +++++++++++++++++++++++++-------------------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index baacf07be62..857eb38f7a4 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -32,37 +32,37 @@ update/bugfix release vitessce-python (#17472), vitessceR (#17525), YODA (#17343) - added additional easyconfigs for various supported software packages, including: - AlphaFold 2.3.0, Anaconda3 2022.10, angsd 0.940, archspec 0.2.0, Armadillo 11.4.3, AUGUSTUS 3.5.0, bcbio-gff 0.7.0, - BCFtools 1.17, beagle-lib 4.0.0, Beast 2.7.3, BeautifulSoup 4.11.1, BLAT 3.7, Blender 3.4.1, Blosc2 2.6.1, - Boost 1.81.0, Bottleneck 1.3.6, BUSCO 5.4.5, bx-python 0.9.0, CatMAP 20220519, CellRanger 7.1.0, Cereal 1.3.2, - CFITSIO 4.2.0, CheckM 1.2.2, code-server 4.9.1, configurable-http-proxy 4.5.3, csvkit 1.1.0, 4.8, CUDA 12.1.0, - cuDNN 8.8.0.121, cwltool 3.1.20221008225030, Cython 0.29.33, DGL 0.9.1, DIAMOND 2.1.0, dill 0.3.6, DIRAC 23.0, - dm-tree 0.1.8, dRep 3.4.2, eggnog-mapper 2.1.10, elfutils 0.189, ELPA 2022.05.001, epiScanpy 0.4.0, FabIO 0.14.0, - FastQ_Screen 0.14.0, FFmpeg 5.1.2, FLAC 1.4.2, flatbuffers 23.1.4, FLINT 2.9.0, GDAL 2.4.4, GDAL 3.6.2, - GDGraph 1.56, GEOS 3.11.1, GMAP-GSNAP 2023-02-17, gmsh 4.11.1, gnuplot 5.4.6, GOATOOLS 1.3.1, googletest 1.12.1, - GPyTorch 1.9.1, Greenlet 2.0.2, GST-plugins-base 1.22.1, GStreamer 1.22.1, GTDB-Tk 2.1.1, h5py 3.8.0, - HDBSCAN 0.8.29, HDF5 1.14.0, HiCExplorer 3.7.2, Highway 1.0.3, HTSlib 1.17, hypothesis 6.68.2, Hypre 2.27.0, - igraph 0.10.3, IGV 2.16.0, IJulia 1.24.0, Imath 3.1.6, imbalanced-learn 0.10.1, imkl 2023.0.0, imkl-FFTW 2023.0.0, - impi 2021.8.0, intel-compilers 2023.0.0, IRkernel 1.3.2, JAGS 4.3.1, jax 0.4.4, Julia 1.8.5, JupyterHub 3.0.0, - jupyter-matlab-proxy 0.5.0, jupyter-resource-usage 0.6.3, jupyter-server-proxy 3.2.2, Kent_tools 442, - leidenalg 0.9.1, LERC 4.0.0, libcerf 2.3, libgit2 1.5.0, libnsl 2.0.0, libsndfile 1.2.0, libtirpc 1.3.3, - libxslt 1.1.37, Longshot 0.4.5, MAFFT 7.505, Maple 2022.1, MaSuRCA 4.1.0, Mathematica 13.1.0, MATIO 1.5.23, - MATLAB 2022a + 2022a-r3 + 2022b, matplotlib 3.7.0, MaxQuant 2.2.0.0, MCL 22.282, Miniconda3 22.11.1, - mm-common 1.0.5, MPFR 4.2.0, mpi4py 3.1.4, mpmath 1.2.1, msprime 1.2.0, MultiQC 1.14, mygene 3.2.2, nano 7.1, - nanomax-analysis-utils 0.4.4, ncbi-vdb 3.0.2, NetLogo 6.2.2 + 6.3.0, nettle 3.8.1, Nextflow 22.10.6, - nlohmann_json 3.11.2, numba 0.56.4, NVHPC 22.9 + 22.11 + 23.1, NVSHMEM 2.8.0, OpenMPI 4.1.5, Optuna 3.1.0, - ORCA 5.0.4, PAML 4.10.5, panaroo 1.3.2, ParallelIO 2.5.10, parasail 2.6, Pillow 9.4.0, PIPITS 3.0, PLINK 2.00a3.7, - plotly.py 5.12.0 + 5.13.1, PLUMED 2.8.1, poetry 1.2.2, polymake 4.8, preseq 3.2.0, presto 1.0.0-20230113, - PROJ 9.1.1, protobuf 3.21.9, psycopg2 2.9.5, pybind11 2.10.3, PyCharm 2022.3.2, py-cpuinfo 9.0.0, pyFAI 0.21.3, - pyfaidx 0.7.1, pyGenomeTracks 3.8, pygraphviz 1.10, pymca 5.7.6, Pysam 0.20.0, PySCF 2.1.1, PyTables 3.8.0, - Python 3.11.2, python-parasail 1.3.3, PyZMQ 24.0.1, QCG-PilotJob 0.13.1, QIIME2 2022.11, QtPy 2.3.0, QUAST 5.2.0, - Ray-project 2.2.0, RDKit 2022.09.4, Redis 7.0.8, redis-py 4.5.1, ReFrame 4.0.5, RepeatMasker 4.1.4, - RepeatModeler 2.0.4, rjags 4-13, RMBlast 2.13.0, ROOT 6.22.08, Salmon 1.9.0, SAMtools 1.17, Scalasca 2.6.1, - scikit-learn 1.2.1, SciPy-bundle 2023.02, SDL2 2.26.3, SeqKit 2.3.1, silx 1.0.0, snakemake 7.22.0, - SNAP-HMM 20221022, SpaceRanger 2.0.1, SPAdes 3.15.5, spaln 2.4.13f, Spark 3.3.1, SRA-Toolkit 3.0.3, SSW 1.2.4, - STAR 2.7.10b, STAR-CCM+ 18.02.008, SVG 2.87, TensorFlow-Datasets 4.8.3, Tkinter 3.10.8, tqdm 4.64.1, - Trilinos 13.4.1, Trim_Galore 0.6.10, Trinity 2.15.1, TWL-NINJA 0.98-cluster_only, Unidecode 1.3.6, - vsc-mympirun 5.3.0, VSEARCH 2.22.1, wget 1.21.3, wxWidgets 3.2.2.1, x264 20230226, Xerces-C++ 3.2.4, - XlsxWriter 3.0.8, xtb 6.5.1, Xvfb 21.1.6 + BCFtools 1.17, beagle-lib 4.0.0, Beast 2.7.3, BeautifulSoup 4.11.1, Biopython 1.81, BLAT 3.7, Blender 3.4.1, + Blosc2 2.6.1, Boost 1.81.0, Bottleneck 1.3.6, BUSCO 5.4.5, bx-python 0.9.0, CatMAP 20220519, CellRanger 7.1.0, + Cereal 1.3.2, CFITSIO 4.2.0, CheckM 1.2.2, code-server 4.9.1, configurable-http-proxy 4.5.3, csvkit 1.1.0, 4.8, + CUDA 12.1.0, cuDNN 8.8.0.121, cwltool 3.1.20221008225030, Cython 0.29.33, DGL 0.9.1, DIAMOND 2.1.0, dill 0.3.6, + DIRAC 23.0, dm-tree 0.1.8, dRep 3.4.2, eggnog-mapper 2.1.10, elfutils 0.189, ELPA 2022.05.001, epiScanpy 0.4.0, + FabIO 0.14.0, FastQ_Screen 0.14.0, FFmpeg 5.1.2, FLAC 1.4.2, flatbuffers 23.1.4, FLINT 2.9.0, GDAL 2.4.4, + GDAL 3.6.2, GDGraph 1.56, GEOS 3.11.1, GMAP-GSNAP 2023-02-17, gmsh 4.11.1, gnuplot 5.4.6, GOATOOLS 1.3.1, + googletest 1.12.1, GPyTorch 1.9.1, Greenlet 2.0.2, GST-plugins-base 1.22.1, GStreamer 1.22.1, GTDB-Tk 2.1.1, + h5py 3.8.0, HDBSCAN 0.8.29, HDF5 1.14.0, HiCExplorer 3.7.2, Highway 1.0.3, HTSlib 1.17, hypothesis 6.68.2, + Hypre 2.27.0, igraph 0.10.3, IGV 2.16.0, IJulia 1.24.0, Imath 3.1.6, imbalanced-learn 0.10.1, imkl 2023.0.0, + imkl-FFTW 2023.0.0, impi 2021.8.0, intel-compilers 2023.0.0, IRkernel 1.3.2, JAGS 4.3.1, jax 0.4.4, Julia 1.8.5, + JupyterHub 3.0.0, jupyter-matlab-proxy 0.5.0, jupyter-resource-usage 0.6.3, jupyter-server-proxy 3.2.2, + Kent_tools 442, leidenalg 0.9.1, LERC 4.0.0, libcerf 2.3, libgit2 1.5.0, libnsl 2.0.0, libsndfile 1.2.0, + libtirpc 1.3.3, libxslt 1.1.37, Longshot 0.4.5, MAFFT 7.505, Maple 2022.1, MaSuRCA 4.1.0, Mathematica 13.1.0, + MATIO 1.5.23, MATLAB 2022a + 2022a-r3 + 2022b, matplotlib 3.7.0, MaxQuant 2.2.0.0, MCL 22.282, MDAnalysis 2.4.2, + Miniconda3 22.11.1, mm-common 1.0.5, MPFR 4.2.0, mpi4py 3.1.4, mpmath 1.2.1, msprime 1.2.0, MultiQC 1.14, + mygene 3.2.2, nano 7.1, nanomax-analysis-utils 0.4.4, ncbi-vdb 3.0.2, NetLogo 6.2.2 + 6.3.0, nettle 3.8.1, + networkx 3.0, Nextflow 22.10.6, nlohmann_json 3.11.2, numba 0.56.4, NVHPC 22.9 + 22.11 + 23.1, NVSHMEM 2.8.0, + OpenMPI 4.1.5, Optuna 3.1.0, ORCA 5.0.4, PAML 4.10.5, panaroo 1.3.2, ParallelIO 2.5.10, parasail 2.6, Pillow 9.4.0, + PIPITS 3.0, PLINK 2.00a3.7, plotly.py 5.12.0 + 5.13.1, PLUMED 2.8.1, poetry 1.2.2, polymake 4.8, preseq 3.2.0, + presto 1.0.0-20230113, PROJ 9.1.1, protobuf 3.21.9, psycopg2 2.9.5, pybind11 2.10.3, PyCharm 2022.3.2, + py-cpuinfo 9.0.0, pyFAI 0.21.3, pyfaidx 0.7.1, pyGenomeTracks 3.8, pygraphviz 1.10, pymca 5.7.6, Pysam 0.20.0, + PySCF 2.1.1, PyTables 3.8.0, Python 3.11.2, python-parasail 1.3.3, PyZMQ 24.0.1, QCG-PilotJob 0.13.1, + QIIME2 2022.11, QtPy 2.3.0, QUAST 5.2.0, R 4.2.2, Ray-project 2.2.0, RDKit 2022.09.4, Redis 7.0.8, redis-py 4.5.1, + ReFrame 4.0.5, RepeatMasker 4.1.4, RepeatModeler 2.0.4, rjags 4-13, RMBlast 2.13.0, ROOT 6.22.08, Salmon 1.9.0, + SAMtools 1.17, Scalasca 2.6.1, scikit-learn 1.2.1, SciPy-bundle 2023.02, SDL2 2.26.3, SeqKit 2.3.1, silx 1.0.0, + snakemake 7.22.0, SNAP-HMM 20221022, SpaceRanger 2.0.1, SPAdes 3.15.5, spaln 2.4.13f, Spark 3.3.1, + SRA-Toolkit 3.0.3, SSW 1.2.4, STAR 2.7.10b, STAR-CCM+ 18.02.008, SVG 2.87, TensorFlow-Datasets 4.8.3, + Tkinter 3.10.8, tqdm 4.64.1, Trilinos 13.4.1, Trim_Galore 0.6.10, Trinity 2.15.1, TWL-NINJA 0.98-cluster_only, + Unidecode 1.3.6, vsc-mympirun 5.3.0, VSEARCH 2.22.1, wget 1.21.3, wxWidgets 3.2.2.1, x264 20230226, + Xerces-C++ 3.2.4, XlsxWriter 3.0.8, xtb 6.5.1, Xvfb 21.1.6 - minor enhancements, including: - add additional extensions to R 4.2.1 (#17043, #17125, #17224, #17493, #17523) - add additional extensions to Bioconductor 3.15 (#17126, #17315, #17494) From ce3732ae91a27e3d9a8705afd235d157637e809f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2023 14:47:19 +0100 Subject: [PATCH 6918/9987] adding easyconfigs: MDAnalysis-2.4.2-foss-2021a.eb --- .../MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb new file mode 100644 index 00000000000..e5f35ff61b3 --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '2.4.2' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('networkx', '2.5.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mrcfile', '1.4.3', { + 'checksums': ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5'], + }), + ('GridDataFormats', '1.0.1', { + 'modulename': 'gridData', + 'checksums': ['ad2c9ab7d672a6d8c426de7d083eee4f3e2b0bd59391675d30683c768ab83cc4'], + }), + ('gsd', '2.8.0', { + 'checksums': ['f2b031a26a7a5bee5f3940dc2f36c5a5b6670307b297c526adf2e26c1f5b46ae'], + }), + ('msgpack', '1.0.5', { + 'checksums': ['c075544284eadc5cddc70f4757331d99dcbc16b2bbd4849d15f8aae4cf36d31c'], + }), + ('mmtf-python', '1.1.3', { + 'modulename': 'mmtf', + 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + # MDAnalysis 2.4.x requires biopython >= 1.80 + ('biopython', '1.81', { + 'checksums': ['2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0'], + 'runtest': "python setup.py test --offline", + 'modulename': 'Bio', + 'sanity_check_commands': ["python -c 'import Bio.MarkovModel'"], + }), + (name, version, { + 'modulename': 'MDAnalysis', + 'checksums': ['ae2ee5627391e73f74eaa3c547af3ec6ab8b040d27dedffe3a7ece8e0cd27636'], + }), +] + +moduleclass = 'bio' From 645a6b0a54705e5b642b9df8507e78f9d01dce55 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 18 Mar 2023 16:19:10 +0100 Subject: [PATCH 6919/9987] downgrade sympy version --- .../easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb index 1adc774c4b6..bc8ccfc43a9 100644 --- a/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb @@ -18,7 +18,7 @@ dependencies = [ ('PyYAML', '6.0'), ('matplotlib', '3.5.2'), ('networkx', '2.8.4'), - ('sympy', '1.11.1'), + ('sympy', '1.10.1'), ('plotly.py', '5.12.0'), ('tqdm', '4.64.0'), From 9daef5988231d3c3f96f0308d84fe6028da6bad1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 18 Mar 2023 15:50:56 +0000 Subject: [PATCH 6920/9987] adding easyconfigs: RapidJSON-1.1.0-GCCcore-12.2.0.eb, RE2-2023-03-01-GCCcore-12.2.0.eb, utf8proc-2.8.0-GCCcore-12.2.0.eb --- .../r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ .../RapidJSON-1.1.0-GCCcore-12.2.0.eb | 30 +++++++++++++++++ .../utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb | 30 +++++++++++++++++ 3 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b43aca00751 --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = "CMakeMake" + +name = 'RE2' +version = '2023-03-01' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7a9a4824958586980926a300b4717202485c4b4115ac031822e29aa4ef207e48'] + +builddependencies = { + ('binutils', '2.39'), + ('CMake', '3.24.3'), +} + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9594b13fd9d --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +version = '1.1.0' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-compiler-errors.patch'] +checksums = [ + 'bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e', # v1.1.0.tar.gz + # %(name)s-%(version_major_minor)s.0_fix-compiler-errors.patch + '2e40ef6c46bf355feac16cd84faad5b7aca0ad54273117b85534b1b781f411c7', +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..33d5c5ec66a --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.8.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a0a60a79fe6f6d54e7d411facbfcc867a6e198608f2cd992490e46f04b1bcecc'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From c4b2e3cc6d6198e6e9d215f7232f1bb7829df1bb Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 18 Mar 2023 15:51:31 +0000 Subject: [PATCH 6921/9987] adding easyconfigs: Arrow-11.0.0-gfbf-2022b.eb, arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb --- .../a/Arrow/Arrow-11.0.0-gfbf-2022b.eb | 73 +++++++++++++++++++ .../arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb | 34 +++++++++ 2 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb new file mode 100644 index 00000000000..d35cad0f1b3 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb @@ -0,0 +1,73 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '11.0.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['2dd8f0ea0848a58785628ee3a57675548d509e17213a2f5d72b0d900b43f5430'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Autotools', '20220317'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '1.9.3'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # for numpy + ('Boost', '1.81.0'), + ('lz4', '1.9.4'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.2'), + ('snappy', '1.1.9'), + ('RapidJSON', '1.1.0'), + ('RE2', '2023-03-01'), + ('utf8proc', '2.8.0'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " +configopts += "-DZSTD_ROOT=$EBROOTZSTD " + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && " +local_install_pyarrow_cmds += "export Parquet_DIR=%(installdir)s && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " +local_install_pyarrow_cmds += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/python%%(pyshortver)s/site-packages/pyarrow/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/Arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..dfe97712e3b --- /dev/null +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'arrow-R' +version = '11.0.0.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/arrow' +description = "R interface to the Apache Arrow C++ library" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['arrow_%(version)s.tar.gz'] +checksums = ['eb939471f5f4218e6cfd62f58ccd2a0a5283d4a19a2902741c7fb25e2f016eaf'] + +dependencies = [ + ('R', '4.2.2'), + ('Arrow', '11.0.0'), +] + +preinstallopts = "export LIBARROW_BINARY=true && " + +sanity_check_paths = { + 'files': [], + 'dirs': ['arrow'], +} + +options = {'modulename': 'arrow'} + +moduleclass = 'tools' From a0de2c20a6384d940ba7bd15c9caf0d2e6eafe8d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 18 Mar 2023 16:57:01 +0000 Subject: [PATCH 6922/9987] adding easyconfigs: R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb --- ...le-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 1240 +++++++++++++++++ 1 file changed, 1240 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..352ea582005 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -0,0 +1,1240 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.16' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +# lpsymphony fails to build with pkgconf, so stick to pkg-config +# error in: https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286 +# builddependencies = [('pkg-config', '0.29.2')] +builddependencies = [('pkgconf', '1.9.3')] + +dependencies = [ + ('R', '4.2.2'), + ('Boost', '1.81.0'), # for mzR + ('GSL', '2.7'), # for flowClust + ('HDF5', '1.14.0'), # for rhdf5 + ('arrow-R', '11.0.0.3', versionsuffix), # required by RcisTarget +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.16/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on 7th Nov 2022 +exts_list = [ + ('BiocGenerics', '0.44.0', { + 'checksums': ['8518e462c1ef103ab059d059d871afc444e48f56fe6b3afdb60dc1abf6c9b09d'], + }), + ('Biobase', '2.58.0', { + 'checksums': ['db798af54eb18d83242b1ffbb1fa35b5bc0256cedf86b9a6519e2d786d20e566'], + }), + ('S4Vectors', '0.36.2', { + 'checksums': ['68b441289882bde641a1d736287b2dfb837c21b21e18b127b9fee1fc5d792c8c'], + }), + ('IRanges', '2.32.0', { + 'checksums': ['097935916b5cb33804e1ea09fa6c4ee7ddeaa03eef99138a05b1896b28dc6a4b'], + }), + ('GenomeInfoDbData', '1.2.9', { + 'checksums': ['e63a719a8eceefeda39fc95de83e7aa41caad39705efc712a44ab4021adc45fa'], + }), + ('GenomeInfoDb', '1.34.9', { + 'checksums': ['2bbb094636bf628447ed4c49b4cd96c164264d012a59f0fe5982f12e6a6bc956'], + }), + ('zlibbioc', '1.44.0', { + 'checksums': ['8b2616b722e2d610cdd41aba1a94b987ab017e0bfff63f6ce66f191e81abe530'], + }), + ('XVector', '0.38.0', { + 'checksums': ['e9ba0ec3f4124c6f0ce13c4d562e7e4419f8aa5db4283092574a63a207f4ed79'], + }), + ('Biostrings', '2.66.0', { + 'checksums': ['7312c508bc2fe6ea3da75edd621b41a35929f9dbdca16d25eb3724ca2cd206fd'], + }), + ('KEGGREST', '1.38.0', { + 'checksums': ['ec9fe4b9e11858ba1236c22c9058ea3b3e6967168c847b01003b15d1afb94318'], + }), + ('AnnotationDbi', '1.60.2', { + 'checksums': ['0f52a460cefc40919273463648656c306640cf82afee3bd0fd2941dbde16eeb0'], + }), + ('GenomicRanges', '1.50.2', { + 'checksums': ['37fdc2074f17b833002c906998b09c88174c054bc5dd9fffdba1f76c4d5d668d'], + }), + ('BiocParallel', '1.32.5', { + 'checksums': ['395ed5c19fb706ca73c841c843c3a89f8a88f774a26415bfdbac0dca92a5a6f9'], + }), + ('Rhtslib', '2.0.0', { + 'checksums': ['5098bf9f4e8bbbe7eea3d63480c5c970af87b68998d625a2ec0f12b2393727e6'], + }), + ('Rsamtools', '2.14.0', { + 'checksums': ['5fe4f80752459f6f1691320ffeffd2d7d17d52dcef60c7a7035fd714ac86a471'], + }), + ('MatrixGenerics', '1.10.0', { + 'checksums': ['09fbea178608186571acabc18cd2b81fe5c7aa2d143f5d456ceaed55e01b4815'], + }), + ('DelayedArray', '0.24.0', { 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}), + ('SamSPECTRAL', '1.52.0', { + 'checksums': ['b8f85ce42b62b42c6fe6fd7fac7501e4329a359ad9126190207da9607c88f0ea'], + }), + ('ddPCRclust', '1.18.0', { + 'checksums': ['c27706a922d11d49a0a4f269df9de6882d81140eecf8a726220cd52b6db8372c'], + }), + ('feature', '1.2.15', { + 'checksums': ['de38292b7e800068a20824e2a9e7d5d4d0b465b7925db0d165346aa5030ff67b'], + }), + ('flowMerge', '2.46.0', { + 'checksums': ['3634723fd87b1bae71e2cd9e646e98cecc891521b4f2e9ff3ff388362b8b21eb'], + }), + ('SpatialExperiment', '1.8.1', { + 'checksums': ['0fdfc5642dde227b73d81812b6641f2d10223de66892b9d61ac80664cd6cbacd'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' From 2e80bcd38c4c82ec1dbe89b8b637ff085236336b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2023 18:22:36 +0100 Subject: [PATCH 6923/9987] clean up grid easyconfig, add missing moduleclass, enable import check --- .../easyconfigs/g/grid/grid-20220610-intel-2022a.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb b/easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb index f398b7924bd..efcdd9e7be4 100644 --- a/easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb +++ b/easybuild/easyconfigs/g/grid/grid-20220610-intel-2022a.eb @@ -6,7 +6,7 @@ local_commit = '0677fc7' homepage = 'https://grid.qcdevs.org/' description = """Grid is a free and open-source Python library for numerical integration, - interpolation and differentiation of interest for the quantum chemistry community.""" + interpolation and differentiation of interest for the quantum chemistry community.""" toolchain = {'name': 'intel', 'version': '2022a'} @@ -20,10 +20,11 @@ dependencies = { ('sympy', '1.10.1'), } -preinstallopts = "sed -i 's|version=get_version()|version=\"%(version)s\"|g' setup.py && " - +download_dep_fail = True use_pip = True + +preinstallopts = """sed -i 's|version=get_version()|version="%(version)s"|g' setup.py && """ + sanity_pip_check = True -download_dep_fail = True -options = {'modulename': False} +moduleclass = 'chem' From e71374ef398c26c475c7b9c177bbea303a3566d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2023 18:27:02 +0100 Subject: [PATCH 6924/9987] enhance sanity check for DensPart + add missing ASE/PLAMS/iodata/gbasis dependencies --- .../DensPart/DensPart-20220603-intel-2022a.eb | 33 ++++++++++++----- .../g/gbasis/gbasis-20210904-intel-2022a.eb | 31 ++++++++++++++++ .../i/iodata/iodata-1.0.0a2-intel-2022a.eb | 36 +++++++++++++++++++ .../p/PLAMS/PLAMS-1.5.1-intel-2022a.eb | 36 +++++++++++++++++++ 4 files changed, 128 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/g/gbasis/gbasis-20210904-intel-2022a.eb create mode 100644 easybuild/easyconfigs/i/iodata/iodata-1.0.0a2-intel-2022a.eb create mode 100644 easybuild/easyconfigs/p/PLAMS/PLAMS-1.5.1-intel-2022a.eb diff --git a/easybuild/easyconfigs/d/DensPart/DensPart-20220603-intel-2022a.eb b/easybuild/easyconfigs/d/DensPart/DensPart-20220603-intel-2022a.eb index c0d32d70051..d1e388e8183 100644 --- a/easybuild/easyconfigs/d/DensPart/DensPart-20220603-intel-2022a.eb +++ b/easybuild/easyconfigs/d/DensPart/DensPart-20220603-intel-2022a.eb @@ -5,24 +5,41 @@ version = '20220603' local_commit = '9bfd1e2' homepage = 'https://github.com/theochem/denspart' -description = 'Atoms-in-molecules density partitioning schemes based on stockholder recipe' +description = "Atoms-in-molecules density partitioning schemes based on stockholder recipe" toolchain = {'name': 'intel', 'version': '2022a'} source_urls = ['https://github.com/theochem/denspart/archive/'] -sources = ['%s.tar.gz' % local_commit] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] checksums = ['e2014368da19503aead56c176da0d6ec00ce13ea62d0cefde69cdfd06e1fcccd'] -dependencies = { +dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), + ('iodata', '1.0.0a2'), + ('gbasis', '20210904'), ('grid', '20220610'), -} + ('ASE', '3.22.1'), # required by denspart-from-gpaw + ('GPAW', '22.8.0'), # required by denspart-from-gpaw + ('PLAMS', '1.5.1'), # provides scm.plams, required by denspart-from-adf +] -use_pip = True -sanity_pip_check = True download_dep_fail = True +use_pip = True -sanity_check_commands = ["denspart -h"] +sanity_check_paths = { + 'files': ['bin/denspart%s' % x for x in ['', '-from-adf', '-from-gpaw', '-from-horton3', '-write-extxyz']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "denspart -h", + "denspart-from-adf -h", + "denspart-from-gpaw -h", + "denspart-from-horton3 -h", + "denspart-write-extxyz -h", +] + +sanity_pip_check = True -moduleclass = "chem" +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/gbasis/gbasis-20210904-intel-2022a.eb b/easybuild/easyconfigs/g/gbasis/gbasis-20210904-intel-2022a.eb new file mode 100644 index 00000000000..035d42cae64 --- /dev/null +++ b/easybuild/easyconfigs/g/gbasis/gbasis-20210904-intel-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'gbasis' +local_commit = '2eb9e49' +version = '20210904' + +homepage = 'https://github.com/theochem/gbasis' +description = """Python library for analytical evaluation and integration of Gaussian-type basis functions and + related quantities.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://github.com/theochem/gbasis/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['86b20647d756b6979d52d721309eb7f86cdd6e01b50a78d651958e16ecbabecb'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('iodata', '1.0.0a2'), +] + +download_dep_fail = True +use_pip = True + +# inject a proper version rather than using 0.0.0 +preinstallopts = r"""sed -i 's/version="0.0.0"/version="%(version)s"/g' setup.py && """ + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/i/iodata/iodata-1.0.0a2-intel-2022a.eb b/easybuild/easyconfigs/i/iodata/iodata-1.0.0a2-intel-2022a.eb new file mode 100644 index 00000000000..1328e3eb2c7 --- /dev/null +++ b/easybuild/easyconfigs/i/iodata/iodata-1.0.0a2-intel-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'iodata' +version = '1.0.0a2' + +homepage = 'https://github.com/theochem/iodata' +description = """Python library for reading, writing, and converting computational chemistry file formats and + generating input files.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://github.com/theochem/iodata/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c72ea17282d110ca3f85113f670bc9309ea68b4f86e1684b44778455622141bb'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True + +# inject correct version rather than relying on dynamically determined version +preinstallopts = r"""sed -i "s/version=VERSION/version='%(version)s'/g" setup.py && """ + +sanity_check_paths = { + 'files': ['bin/iodata-convert'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["iodata-convert --help"] + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLAMS/PLAMS-1.5.1-intel-2022a.eb b/easybuild/easyconfigs/p/PLAMS/PLAMS-1.5.1-intel-2022a.eb new file mode 100644 index 00000000000..2615afa31aa --- /dev/null +++ b/easybuild/easyconfigs/p/PLAMS/PLAMS-1.5.1-intel-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'PLAMS' +version = '1.5.1' + +homepage = 'https://www.scm.com/product/plams' +description = """The Python Library for Automating Molecular Simulation (PLAMS) is powerful and flexible Python tool +interfaced to the Amsterdam Modeling Suite engines ADF, BAND, DFTB, MOPAC, ReaxFF, and UFF.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://github.com/SCM-NV/PLAMS/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['163cfb7a4e509791961b45d58d3cd42b4761b2ad73f9c210664fc8e3ad78380a'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('dill', '0.3.6'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/plams'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["plams --help"] + +options = {'modulename': 'scm.plams'} + +sanity_pip_check = True + +moduleclass = 'chem' From 0b4c3939245633305b5e9fe7d63b21766edcc17a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 18 Mar 2023 20:40:46 +0100 Subject: [PATCH 6925/9987] use Java/11 wrapper --- .../easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb b/easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb index 6a5eb876501..8fc1afb7854 100644 --- a/easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb +++ b/easybuild/easyconfigs/s/smfishHmrf/smfishHmrf-1.3.3-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Seaborn', '0.12.1'), ('matplotlib', '3.5.2'), ('scikit-learn', '1.1.2'), - ('Java', '11.0.16', '', SYSTEM), + ('Java', '11', '', SYSTEM), ] download_dep_fail = True From 4e3e7600972a4598db3ef7e9ffc41586f9e7ccb1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Sun, 19 Mar 2023 20:58:01 +0100 Subject: [PATCH 6926/9987] Enabled tests --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb index 3fa67ab84fb..ea8d3bc0412 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb @@ -27,7 +27,7 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DINSTALL_METIS_HEADERS=OFF ' -# runtest = 'test' +runtest = 'test' local_scotch_exec = ['acpl', 'amk_ccc', 'amk_fft2', 'amk_grf', 'amk_hy', 'amk_m2', 'amk_p2', 'atst', 'dggath', 'dgmap', 'dgord', From 3789ac9c63f7c98a77eaa4b8a0de7a70a954924c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 20 Mar 2023 11:14:21 +0100 Subject: [PATCH 6927/9987] remove unused variable, add comment to patch --- .../torchtext/torchtext-0.14.1-foss-2022a.eb | 45 +++++++++++++++++++ .../torchtext/torchtext-0.14.1_deps_fix.patch | 1 + 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb new file mode 100644 index 00000000000..cb3a29fdcce --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.14.1' +local_pytorch_version = '1.12.0' +local_python_suffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['torchtext-0.14.1_deps_fix.patch'] +checksums = [ + {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, + {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'}, +] + +builddependencies = [ + ('RE2', '2022-06-01'), + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SentencePiece', '0.1.97'), + ('tqdm', '4.64.0'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.2.0'), + ('utf8proc', '2.7.0'), +] + +download_dep_fail = True, +use_pip = True +sanity_pip_check = True, + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && " + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch index ab7a71f24f5..1212651426e 100644 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch @@ -1,3 +1,4 @@ +The error "string_view has not been declared in std" appears when not using C++17 diff -u text/CMakeLists.txt.orig text/CMakeLists.txt --- text/CMakeLists.txt.orig 2023-03-08 14:33:35.618931003 +0100 +++ text/CMakeLists.txt 2023-03-08 14:35:03.169072623 +0100 From c89af4e593b2ae6a3bf151e030fb410c0f68fedd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2023 11:21:11 +0100 Subject: [PATCH 6928/9987] adding easyconfigs: EasyBuild-4.7.1.eb --- .../e/EasyBuild/EasyBuild-4.7.1.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.1.eb new file mode 100644 index 00000000000..8d9ac53bb93 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.1.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.7.1' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/76/4b/b7a88e791cce0d79db9f2319ab07c79584815ca9e497d178c39fa4621b8d/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/10/72/391eb5bde081da67fef0a59625ce7cf4939176416aed299ef55923e422b4/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/32/1a/e7c851db23ffb0fc5c3cc9c255318d533f642c86eff2c3c33e0ab063a449/', + +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + {'easybuild-framework-4.7.1.tar.gz': 'ad3d95c2b11f895666d83cda3422e785261ecb9d14e7c3e0c9cef427b7404d6b'}, + {'easybuild-easyblocks-4.7.1.tar.gz': '8c383dc4d02784e5ab610cec2df58c19ff9c1b7c03bb7585788ced1646e394e8'}, + {'easybuild-easyconfigs-4.7.1.tar.gz': '58c70e7e4a8958f932e4e7abab0194198a8f9baf19915bfa5191b431f3f1a864'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From c88271d0069b4b3f7e8af9747218285e43bfe00b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 20 Mar 2023 11:34:46 +0100 Subject: [PATCH 6929/9987] bring back the suffix variable, delete unwanted file --- .../torchtext/torchtext-0.14.1-foss-2022a.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb deleted file mode 100644 index cb3a29fdcce..00000000000 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'torchtext' -version = '0.14.1' -local_pytorch_version = '1.12.0' -local_python_suffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/pytorch/text' -description = "Data loaders and abstractions for text and NLP" - -toolchain = {'name': 'foss', 'version': '2022a'} - -# Sources are no longer available in PyPI, it only has wheels -source_urls = ['https://github.com/pytorch/text/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['torchtext-0.14.1_deps_fix.patch'] -checksums = [ - {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, - {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'}, -] - -builddependencies = [ - ('RE2', '2022-06-01'), - ('binutils', '2.38'), - ('CMake', '3.24.3'), -] - -dependencies = [ - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('SentencePiece', '0.1.97'), - ('tqdm', '4.64.0'), - ('PyTorch', local_pytorch_version), - ('double-conversion', '3.2.0'), - ('utf8proc', '2.7.0'), -] - -download_dep_fail = True, -use_pip = True -sanity_pip_check = True, - -# Disable bundled libraries to use those from EB: RE2, SentencePiece -preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && " - -moduleclass = 'tools' From a4cf2650135fa343eb4d76a66ac163da506ab76d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 20 Mar 2023 11:40:48 +0100 Subject: [PATCH 6930/9987] fix checksum of patch file --- .../torchtext/torchtext-0.14.1-foss-2022a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb new file mode 100644 index 00000000000..cb3a29fdcce --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.14.1' +local_pytorch_version = '1.12.0' +local_python_suffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['torchtext-0.14.1_deps_fix.patch'] +checksums = [ + {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, + {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'}, +] + +builddependencies = [ + ('RE2', '2022-06-01'), + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SentencePiece', '0.1.97'), + ('tqdm', '4.64.0'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.2.0'), + ('utf8proc', '2.7.0'), +] + +download_dep_fail = True, +use_pip = True +sanity_pip_check = True, + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && " + +moduleclass = 'tools' From 287f6d52213fd1a904f5d767e01f2e7e49466e81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 20 Mar 2023 12:10:29 +0100 Subject: [PATCH 6931/9987] Delete torchtext-0.14.1-foss-2022a.eb --- .../torchtext/torchtext-0.14.1-foss-2022a.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb deleted file mode 100644 index cb3a29fdcce..00000000000 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'torchtext' -version = '0.14.1' -local_pytorch_version = '1.12.0' -local_python_suffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/pytorch/text' -description = "Data loaders and abstractions for text and NLP" - -toolchain = {'name': 'foss', 'version': '2022a'} - -# Sources are no longer available in PyPI, it only has wheels -source_urls = ['https://github.com/pytorch/text/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['torchtext-0.14.1_deps_fix.patch'] -checksums = [ - {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, - {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'}, -] - -builddependencies = [ - ('RE2', '2022-06-01'), - ('binutils', '2.38'), - ('CMake', '3.24.3'), -] - -dependencies = [ - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('SentencePiece', '0.1.97'), - ('tqdm', '4.64.0'), - ('PyTorch', local_pytorch_version), - ('double-conversion', '3.2.0'), - ('utf8proc', '2.7.0'), -] - -download_dep_fail = True, -use_pip = True -sanity_pip_check = True, - -# Disable bundled libraries to use those from EB: RE2, SentencePiece -preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && " - -moduleclass = 'tools' From b6960c3919fe4483b20d9d5f054f6f68c71494c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 20 Mar 2023 12:11:38 +0100 Subject: [PATCH 6932/9987] fix checksum of patch file --- .../torchtext/torchtext-0.14.1-foss-2022a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb new file mode 100644 index 00000000000..cb3a29fdcce --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.14.1' +local_pytorch_version = '1.12.0' +local_python_suffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['torchtext-0.14.1_deps_fix.patch'] +checksums = [ + {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, + {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'}, +] + +builddependencies = [ + ('RE2', '2022-06-01'), + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SentencePiece', '0.1.97'), + ('tqdm', '4.64.0'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.2.0'), + ('utf8proc', '2.7.0'), +] + +download_dep_fail = True, +use_pip = True +sanity_pip_check = True, + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && " + +moduleclass = 'tools' From d911fa61b036bfaacd9245678c6b7e137470fa9c Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 20 Mar 2023 13:22:14 +0100 Subject: [PATCH 6933/9987] adding easyconfigs: KrakenUniq-1.0.3-foss-2022a.eb --- .../KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb new file mode 100644 index 00000000000..e50cc310ceb --- /dev/null +++ b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'Binary' + +name = 'KrakenUniq' +version = '1.0.3' + +homepage = 'https://github.com/fbreitwieser/krakenuniq/' +description = """KrakenUniq: confident and fast metagenomics classification using unique k-mer counts""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'fbreitwieser' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['559b45081688118b4872e1b9153f83d0ae3414649a1b299ab4f9996d9e154403'] + +dependencies = [ + ('Jellyfish', '2.3.0'), +] + +extract_sources = True + +install_cmd = './install_krakenuniq.sh -l %(installdir)s/bin %(installdir)s ' + +sanity_check_commands = [ + 'krakenuniq --version', + 'krakenuniq-download --db %(installdir)s/DBDIR taxonomy && rm -r %(installdir)s/DBDIR' +] +sanity_check_paths = { + 'files': ['bin/krakenuniq', 'bin/krakenuniq-build', 'bin/krakenuniq-report'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' From 61630473c5dc738ae38eb326497144307f44a60e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 20 Mar 2023 13:30:03 +0100 Subject: [PATCH 6934/9987] update patchfile checksum, delete unwanted file --- ...chtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb | 3 +- .../torchtext/torchtext-0.14.1-foss-2022a.eb | 45 ------------------- 2 files changed, 1 insertion(+), 47 deletions(-) delete mode 100644 easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb index 46bf098eddc..cb3a29fdcce 100644 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb @@ -4,7 +4,6 @@ name = 'torchtext' version = '0.14.1' local_pytorch_version = '1.12.0' local_python_suffix = '-Python-%(pyver)s' -versionsuffix = '-PyTorch-%s' % local_pytorch_version homepage = 'https://github.com/pytorch/text' description = "Data loaders and abstractions for text and NLP" @@ -17,7 +16,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['torchtext-0.14.1_deps_fix.patch'] checksums = [ {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, - {'torchtext-0.14.1_deps_fix.patch': '38ee9a2c74016376ef3ff06ea40eb4522f5a72410573168050b79cab457077c7'}, + {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb deleted file mode 100644 index cb3a29fdcce..00000000000 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'torchtext' -version = '0.14.1' -local_pytorch_version = '1.12.0' -local_python_suffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/pytorch/text' -description = "Data loaders and abstractions for text and NLP" - -toolchain = {'name': 'foss', 'version': '2022a'} - -# Sources are no longer available in PyPI, it only has wheels -source_urls = ['https://github.com/pytorch/text/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['torchtext-0.14.1_deps_fix.patch'] -checksums = [ - {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, - {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'}, -] - -builddependencies = [ - ('RE2', '2022-06-01'), - ('binutils', '2.38'), - ('CMake', '3.24.3'), -] - -dependencies = [ - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('SentencePiece', '0.1.97'), - ('tqdm', '4.64.0'), - ('PyTorch', local_pytorch_version), - ('double-conversion', '3.2.0'), - ('utf8proc', '2.7.0'), -] - -download_dep_fail = True, -use_pip = True -sanity_pip_check = True, - -# Disable bundled libraries to use those from EB: RE2, SentencePiece -preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && " - -moduleclass = 'tools' From 15f88ab2555a5e134a8a8e07cc45bdfd71dce702 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 20 Mar 2023 13:54:42 +0100 Subject: [PATCH 6935/9987] adding easyconfigs: SHAP-0.41.0-foss-2022a.eb --- .../s/SHAP/SHAP-0.41.0-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHAP/SHAP-0.41.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.41.0-foss-2022a.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.41.0-foss-2022a.eb new file mode 100644 index 00000000000..0e5be094112 --- /dev/null +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.41.0-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'SHAP' +version = '0.41.0' + +homepage = "https://github.com/slundberg/shap" +description = """SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any + machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley + values from game theory and their related extensions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), + ('numba', '0.56.4'), +] + +# Python 3.10.4 uses poetry 1.1.13 which needs packaging "^20.4" +preinstallopts = "sed -i 's/packaging>20.9/packaging/g' setup.py && " + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('slicer', '0.0.7', { + 'checksums': ['f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['a49ea4d65aadbc845a695fa3d7ea0bdfc8c928b8e213b0feedf5868ade4b3ca5'], + }), +] + +moduleclass = 'data' From d591ffcdab9d5b7471607cf354fe4ece42618934 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 20 Mar 2023 14:00:19 +0100 Subject: [PATCH 6936/9987] solving missing bzlib --- .../easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb index e50cc310ceb..d742f03d6fb 100644 --- a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb +++ b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb @@ -15,6 +15,7 @@ checksums = ['559b45081688118b4872e1b9153f83d0ae3414649a1b299ab4f9996d9e154403'] dependencies = [ ('Jellyfish', '2.3.0'), + ('bzip2', '1.0.8'), ] extract_sources = True From e9d94c1a3c9fc26f5c2c2f0e4e545528ad4d6841 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 20 Mar 2023 14:00:31 +0100 Subject: [PATCH 6937/9987] adding easyconfigs: pydantic-1.10.4-GCCcore-11.3.0.eb --- .../pydantic-1.10.4-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..796120e325e --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'pydantic' +version = '1.10.4' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + (name, version, { + 'checksums': ['b9a3859f24eb4e097502a3be1fb4b2abb79b6103dd9e2e0edb70613a4459a648'], + }), +] + +moduleclass = 'devel' From 1051fc99e768fc24ce777f5d9cdc21fdbab1cab0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 20 Mar 2023 14:05:56 +0100 Subject: [PATCH 6938/9987] adding easyconfigs: lifelines-0.27.4-foss-2022a.eb --- .../lifelines/lifelines-0.27.4-foss-2022a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb new file mode 100644 index 00000000000..c300ce4d3a6 --- /dev/null +++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'lifelines' +version = '0.27.4' + +homepage = "https://lifelines.readthedocs.io/en/latest/" +description = """lifelines is a complete survival analysis library, written in pure Python.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('interface_meta', '1.3.0', { + 'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'], + }), + ('autograd', '1.5', { + 'checksums': ['d80bd225154d1db13cb4eaccf7a18c358be72092641b68717f96fcf1d16acd0b'], + }), + ('autograd-gamma', '0.5.0', { + 'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'], + }), + ('formulaic', '0.4.0', { + 'checksums': ['087950518c53a2491deb52b8ddd66833f953882e517a42e476c007cc8f6892c5'], + }), + (name, version, { + 'checksums': ['62f7e911a64c8f723eef4207174fb1df39a94f79eca557cdf53d310eb6be132f'], + }), +] + +moduleclass = 'bio' From 4b8bceb54c4bbeddff43de4fe139a4910aedb914 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 20 Mar 2023 14:07:40 +0100 Subject: [PATCH 6939/9987] fix suffix --- .../t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb index cb3a29fdcce..4a649652439 100644 --- a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'torchtext' version = '0.14.1' local_pytorch_version = '1.12.0' -local_python_suffix = '-Python-%(pyver)s' +versionsuffix = '-PyTorch-%s' % local_pytorch_version homepage = 'https://github.com/pytorch/text' description = "Data loaders and abstractions for text and NLP" From 1e4836a88a83c79de874ca6e5b4a1b0b16b546ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Mon, 20 Mar 2023 14:57:48 +0100 Subject: [PATCH 6940/9987] adding easyconfigs: CPLEX-22.1.1-GCCcore-11.2.0.eb --- .../c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..d788295e132 --- /dev/null +++ b/easybuild/easyconfigs/c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +name = 'CPLEX' +version = '22.1.1' + +homepage = 'https://www.ibm.com/analytics/cplex-optimizer' +description = """IBM ILOG CPLEX Optimizer's mathematical programming technology enables + analytical decision support for improving efficiency, + reducing costs, and increasing profitability.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = ['cplex_studio%s.linux_x86_64.bin' % ''.join(version.split('.'))] +checksums = ['ab6d3f0953fdb3cbd43854452357955ef96db8b751c0866de3572fc47a0df542'] + +download_instructions = """ +1. Visit https://www.ibm.com/products/ilog-cplex-optimization-studio +2. Sign up and download the Academic Edition +""" + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Python', '3.9.6'), +] + +moduleclass = 'math' From 5ab249e95af3a538d979a30d8483397322930bda Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 20 Mar 2023 15:16:51 +0100 Subject: [PATCH 6941/9987] adding easyconfigs: pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb --- ...sing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb diff --git a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb new file mode 100644 index 00000000000..9ef3f6d433b --- /dev/null +++ b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pyparsing' +version = '3.0.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pyparsing/pyparsing' +description = """The pyparsing module is an alternative approach to creating and +executing simple grammars, vs. the traditional lex/yacc approach, or the use of +regular expressions. The pyparsing module provides a library of classes that +client code uses to construct the grammar directly in Python code.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sources = [SOURCE_TAR_GZ] +checksums = ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'] + +moduleclass = 'data' From e4d3dcbce9ed323b2f706b86d3fffe87d4122643 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 20 Mar 2023 18:55:03 +0100 Subject: [PATCH 6942/9987] adding easyconfigs: spdlog-1.11.0-GCCcore-12.2.0.eb --- .../s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..37e99e71124 --- /dev/null +++ b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'spdlog' +version = '1.11.0' + +homepage = 'https://github.com/gabime/spdlog' +description = 'Very fast, header-only/compiled, C++ logging library.' +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/gabime/spdlog/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ca5cae8d6cac15dae0ec63b21d6ad3530070650f68076f3a4a862ca293a858bb'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['include/spdlog/spdlog.h'], + 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 33d910cd108dd76c3999da0d7adced27e8b7aae4 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 20 Mar 2023 18:55:46 +0100 Subject: [PATCH 6943/9987] adding easyconfigs: fmt-9.1.0-GCCcore-12.2.0.eb --- .../f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..cfaa82feaea --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '9.1.0' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['cceb4cb9366e18a5742128cb3524ce5f50e88b476f1e54737a47ffdf4df4c996'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39') +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' From 225d47e7c6783cc531fa3f14c9b21d1ff728aca0 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 20 Mar 2023 17:57:18 +0000 Subject: [PATCH 6944/9987] Sanity check path removed --- easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb index 0526cbdc186..dbe91a2e7ff 100644 --- a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb @@ -39,9 +39,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'tools' From 171372902ed35fdadd81e23907a7b15b7aa50e01 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 20 Mar 2023 16:34:26 +0100 Subject: [PATCH 6945/9987] bump version to 4.7.2dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 3820ff609f1..1e5caaddac1 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.7.1' +VERSION = '4.7.2.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From e2f97d72860a699ddd91d4598b06d41297dc08f9 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 20 Mar 2023 19:07:21 +0100 Subject: [PATCH 6946/9987] adding easyconfigs: CapnProto-0.10.3-GCCcore-12.2.0.eb --- .../CapnProto-0.10.3-GCCcore-12.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ee6242554c7 --- /dev/null +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to 0.9.1 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'CapnProto' +version = '0.10.3' + +homepage = 'https://capnproto.org' +description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" +# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." +# (only on Intel Skylake?) +toolchainopts = {'cstd': 'c++17', 'lowopt': True} + +source_urls = ['https://capnproto.org/'] +sources = ['capnproto-c++-%(version)s.tar.gz'] +checksums = ['97fde3cf05129db919453af4ef6c6a415662111c2e6e9b5194e2566d44b8507a'] + +builddependencies = [('binutils', '2.39')] + +local_bins = ['capnp', 'capnpc', 'capnpc-c++', 'capnpc-capnp'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['include/capnp', 'include/kj', 'lib'], +} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'bio' From ddf4e345925818eb40b0e150cd8a1d3c4743347b Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Tue, 21 Mar 2023 02:49:58 +0100 Subject: [PATCH 6947/9987] Delete avro-cpp-1.11.1-GCCcore-11.2.0.eb --- .../avro-cpp-1.11.1-GCCcore-11.2.0.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb deleted file mode 100644 index 17e21b86b52..00000000000 --- a/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCCcore-11.2.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'avro-cpp' -version = '1.11.1' - -homepage = 'https://avro.apache.org' -description = """C++ implementation of Avro data serialization system.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -source_urls = ['https://github.com/apache/avro/archive/refs/tags/'] -sources = ['release-%(version)s.tar.gz'] -checksums = ['599f96bb405f72a35154b2477caa6254d723bb4e3f6a0e54e9ae540664321752'] - -builddependencies = [ - ('binutils', '2.37'), - ('CMake', '3.22.1'), -] - -dependencies = [ - ('Boost', '1.77.0', '', ('GCC', '11.2.0')), -] - -srcdir = "lang/c++" - -generator = "Unix Makefiles" -separate_build_dir = True - -sanity_check_paths = { - 'files': ["bin/avrogencpp"], - 'dirs': ["lib"], -} - -sanity_check_commands = ["avrogencpp -h"] - -moduleclass = 'lib' From ef8a6939520cd874267e76b51fbe20c75993b30a Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 21 Mar 2023 08:53:12 +0100 Subject: [PATCH 6948/9987] Moving ASE from foss to gfbf --- .../ASE/{ASE-3.22.1-foss-2022b.eb => ASE-3.22.1-gfbf-2022b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/ASE/{ASE-3.22.1-foss-2022b.eb => ASE-3.22.1-gfbf-2022b.eb} (97%) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2022b.eb similarity index 97% rename from easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb rename to easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2022b.eb index 4a076fc342b..d2486e7b79e 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2022b.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2022b.eb @@ -10,7 +10,7 @@ description = """ASE is a python package providing an open source Atomic Simulat From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed.""" -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'gfbf', 'version': '2022b'} dependencies = [ ('Python', '3.10.8'), From a1034c1d493638a8992e4ca14cbe3fcf51f0c7a4 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 21 Mar 2023 14:46:32 +0000 Subject: [PATCH 6949/9987] Update KrakenUniq-1.0.3-foss-2022a.eb review changes --- .../easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb index d742f03d6fb..5d22642632a 100644 --- a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb +++ b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb @@ -6,7 +6,7 @@ version = '1.0.3' homepage = 'https://github.com/fbreitwieser/krakenuniq/' description = """KrakenUniq: confident and fast metagenomics classification using unique k-mer counts""" -toolchain = {'name': 'foss', 'version': '2022a'} +toolchain = {'name': 'GCCCore', 'version': '11.3.0'} github_account = 'fbreitwieser' source_urls = [GITHUB_SOURCE] @@ -15,6 +15,7 @@ checksums = ['559b45081688118b4872e1b9153f83d0ae3414649a1b299ab4f9996d9e154403'] dependencies = [ ('Jellyfish', '2.3.0'), + ('Perl', '5.34.1'), ('bzip2', '1.0.8'), ] From a17648a58355accc6ddfdf40629b3aa4965932d0 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 21 Mar 2023 14:50:10 +0000 Subject: [PATCH 6950/9987] Update KrakenUniq-1.0.3-foss-2022a.eb typo --- .../easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb index 5d22642632a..1f52ef21a7d 100644 --- a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb +++ b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb @@ -6,7 +6,7 @@ version = '1.0.3' homepage = 'https://github.com/fbreitwieser/krakenuniq/' description = """KrakenUniq: confident and fast metagenomics classification using unique k-mer counts""" -toolchain = {'name': 'GCCCore', 'version': '11.3.0'} +toolchain = {'name': 'GCC', 'version': '11.3.0'} github_account = 'fbreitwieser' source_urls = [GITHUB_SOURCE] From f6cfee5eac1db2ad8c0030e64e0bae09f99e167b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 21 Mar 2023 16:54:40 +0100 Subject: [PATCH 6951/9987] adding easyconfigs: ruamel.yaml-0.17.21-GCCcore-12.2.0.eb --- .../ruamel.yaml-0.17.21-GCCcore-12.2.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e74ae172df4 --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-12.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.17.21' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + (name, version, { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('configobj', '5.0.8', { + 'checksums': ['6f704434a07dc4f4dc7c9a745172c1cad449feb548febd9f7fe362629c627a97'], + }), + ('lz4', '4.3.2', { + 'checksums': ['e1431d84a9cfb23e6773e72078ce8e65cad6745816d4cbf9ae67da5ea419acda'], + }), + ('ruamel.yaml.base', '0.3.2', { + 'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.6.3', { + 'checksums': ['f4ebce7d6d9d53afae84d7efd79f8d6c3dcad56e0e6be3a5d2370be0e04acea0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' From 89b7512fdc07f6dc64d9211a41900d5bf773b326 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2023 17:12:19 +0100 Subject: [PATCH 6952/9987] remove preinstallopts to break import of Crypto, no longer needed since pycrypto was replaced with pycryptodome in #17412 --- .../easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb index 98f87e55a48..e9af6f66373 100644 --- a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb +++ b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb @@ -27,13 +27,9 @@ exts_list = [ }), ('pypdf', '3.4.1', { 'checksums': ['8b0badc787062e8fb0d8393eb2a76903717fb24e5cc84e2b03cde5ac3881700f'], - # break import from Crypto, since pycrypto 2.6.1 is not actually compatible with Python 3.x - 'preinstallopts': "sed -i 's/from Crypto/from Cryptoxxx/g' pypdf/_encryption.py && ", }), ('PyPDF2', '3.0.1', { 'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'], - # break import from Crypto, since pycrypto 2.6.1 is not actually compatible with Python 3.x - 'preinstallopts': "sed -i 's/from Crypto/from Cryptoxxx/g' PyPDF2/_encryption.py && ", 'modulename': 'PyPDF2', }), ('PyPDF3', '1.0.6', { From 3bafc18b1ec39a339ec8b80a4d0272d724b0bbb4 Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 21 Mar 2023 17:52:58 +0100 Subject: [PATCH 6953/9987] adding easyconfigs: Bottleneck-1.3.7-foss-2022a.eb --- .../Bottleneck/Bottleneck-1.3.7-foss-2022a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.7-foss-2022a.eb b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.7-foss-2022a.eb new file mode 100644 index 00000000000..ddcca5a30f1 --- /dev/null +++ b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.7-foss-2022a.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Bottleneck' +version = '1.3.7' + +homepage = 'https://kwgoodman.github.io/bottleneck-doc' +description = "Fast NumPy array functions written in C" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e1467e373ad469da340ed0ff283214d6531cc08bfdca2083361a3aa6470681f8'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From 5ffb30987f094f6f9f9626c244924b8b412aa8ce Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 21 Mar 2023 17:54:25 +0100 Subject: [PATCH 6954/9987] adding easyconfigs: numexpr-2.8.4-foss-2022a.eb --- .../n/numexpr/numexpr-2.8.4-foss-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/n/numexpr/numexpr-2.8.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.8.4-foss-2022a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.4-foss-2022a.eb new file mode 100644 index 00000000000..41f638503e2 --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.4-foss-2022a.eb @@ -0,0 +1,21 @@ +name = 'numexpr' +version = '2.8.4' + +homepage = 'https://numexpr.readthedocs.io/en/latest/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0e21addd25db5f62d60d97e4380339d9c1fb2de72c88b070c279776ee6455d10'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +moduleclass = 'math' From fbdfe2a2e445a360f8cf7304200c9757126264c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2023 17:57:35 +0100 Subject: [PATCH 6955/9987] adding easyconfigs: HTSplotter-2.11-foss-2022b.eb, Seaborn-0.12.2-foss-2022b.eb --- .../HTSplotter/HTSplotter-2.11-foss-2022b.eb | 47 +++++++++++++++++++ .../s/Seaborn/Seaborn-0.12.2-foss-2022b.eb | 24 ++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2022b.eb create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2022b.eb b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2022b.eb new file mode 100644 index 00000000000..00810cd3b19 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2022b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'HTSplotter' +version = '2.11' + +homepage = 'https://github.com/CBIGR/HTSplotter' +description = """HTSplotter allows an end-to-end data processing and analysis of chemical and genetic in vitro +perturbation screens.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), + ('h5py', '3.8.0'), + ('Seaborn', '0.12.2'), + ('tqdm', '4.64.1'), +] + +use_pip = True + +exts_list = [ + ('minio', '7.1.13', { + 'checksums': ['8828615a20cde82df79c5a52005252ad29bb022cde25177a4a43952a04c3222c'], + }), + ('pypdf', '3.6.0', { + 'checksums': ['7d7bd0603f4e87a7064597aa968fcf77a065b596cfbe6e5003a5b00a043db230'], + }), + ('PyPDF2', '3.0.1', { + 'modulename': 'PyPDF2', + 'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'], + }), + ('PyPDF3', '1.0.6', { + 'modulename': 'PyPDF3', + 'checksums': ['c946f3273419e37258e35e72273f49904ab15723d87a761c1115ef99799f8c5f'], + }), + (name, version, { + 'modulename': 'HTSplotter', + 'checksums': ['51c0cee4e8eeecfd03f32dd707e0fa433cec91abb9334ec1d28e7f82615dbe29'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.2-foss-2022b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.2-foss-2022b.eb new file mode 100644 index 00000000000..ca9fa388cb0 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.2-foss-2022b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.12.2' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['374645f36509d0dcab895cba5b47daf0586f77bfe3b36c97c607db7da5be0139'] + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From a59eaab667a3aede49b78fa9ef26846d25b45182 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 21 Mar 2023 18:14:11 +0100 Subject: [PATCH 6956/9987] adding easyconfigs: WIEN2k-21.1-intel-2021b.eb --- .../w/WIEN2k/WIEN2k-21.1-intel-2021b.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb new file mode 100644 index 00000000000..f7adddd82b1 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb @@ -0,0 +1,77 @@ +name = 'WIEN2k' +version = '21.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +sources = ['%(name)s_%(version)s.tar'] +patches = [ + '%(name)s-%(version)s_fix_libxc_for_lapw0_mpi.patch', + '%(name)s-%(version)s_fix_system_stderr_redirection.patch', +] +checksums = [ + '32590778440a9280322bf2dc0d63f4f42a9fc48814fa6b8b7ee2d199c94bed11', # WIEN2k_21.1.tar + '1cc480a4824d9185ad5918dfc68c47bcb7826114626c8133d573be901bbdca84', # WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch + # WIEN2k-21.1_fix_system_stderr_redirection.patch + 'cdba467b0b6f2b310c2e1e2a3e6cabe75f8fd15ee0f7c14f8ef80c7e48073bdd', +] + +download_instructions = """ +WIEN2k can be ordered at http://susi.theochem.tuwien.ac.at/index.html. +""" + +dependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('DFT-D3', '3.2.0'), + ('ELPA', '2021.11.001'), + ('FFTW', '3.3.10'), + ('libxc', '5.1.6'), +] + +osdependencies = [ + ('glibc-devel', 'libc6-dev'), # required for libpthread.a + ('tcsh'), # required by the installer +] + +# remote = 'pbsssh' +# If using a Slurm batch system it is highly recommended to use +# 'srun -n_NP_ _EXEC_' for wien_mpirun +wien_mpirun = 'mpirun -np _NP_ _EXEC_' +use_remote = False +mpi_remote = False +wien_granularity = True +taskset = 'no' + +# Change as needed, these are the defaults +# nmatmax = 19000 +# nume = 6000 + +fix_perl_shebang_for = [ + 'iniel_pressure_in2reader.pl_lapw', + 'iniel_pressure_reader.pl_lapw', + 'setrmt_lapw', + 'elast_setup_input.pl_lapw', + 'bashtime2csh.pl_lapw', +] + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1', r'^:ENE.*-1248.14']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*15.*total forces', + ]), +] + +moduleclass = 'chem' From 25e2fe2e4e0c3620dd48abcc5c0610e9e7a4767f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 21 Mar 2023 19:22:53 +0100 Subject: [PATCH 6957/9987] Add additional space --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb index f7adddd82b1..0bbc5bd89de 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb @@ -35,7 +35,7 @@ dependencies = [ ] osdependencies = [ - ('glibc-devel', 'libc6-dev'), # required for libpthread.a + ('glibc-devel', 'libc6-dev'), # required for libpthread.a ('tcsh'), # required by the installer ] From 8c9d7f6bdc7007e4581c0c7a4672a83ac0814e36 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 21 Mar 2023 19:39:09 +0100 Subject: [PATCH 6958/9987] Switch to older ELPA version --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb index 0bbc5bd89de..0a988032e84 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb @@ -29,7 +29,7 @@ dependencies = [ ('Python', '3.9.6'), ('Perl', '5.34.0'), ('DFT-D3', '3.2.0'), - ('ELPA', '2021.11.001'), + ('ELPA', '2021.05.001'), ('FFTW', '3.3.10'), ('libxc', '5.1.6'), ] From e592d753b33b82a3d115e9ad2269a8499e027828 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2023 19:41:52 +0100 Subject: [PATCH 6959/9987] adding easyconfigs: funannotate-1.8.13-foss-2021b.eb, GOATOOLS-1.3.1-foss-2021b.eb, pydot-1.4.2-GCCcore-11.2.0.eb --- .../funannotate-1.8.13-foss-2021b.eb | 45 ++++++++++++++ .../g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb | 58 +++++++++++++++++++ .../p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb | 26 +++++++++ 3 files changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb new file mode 100644 index 00000000000..78068a53cc2 --- /dev/null +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'funannotate' +version = '1.8.13' + +homepage = 'https://funannotate.readthedocs.io' +description = """funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work + with higher eukaryotes)""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Biopython', '1.79'), + ('GOATOOLS', '1.3.1'), + ('matplotlib', '3.4.3'), + ('scikit-learn', '1.0.1'), + ('Seaborn', '0.11.2'), +] + +use_pip = True + +exts_list = [ + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + (name, version, { + 'checksums': ['40819741bcb38ef3a410a242cc5f172cb0e0083570daddfe5807fb6bc0c3c384'], + }), +] + +sanity_check_paths = { + 'files': ['bin/funannotate'], + 'dirs': [], +} + +sanity_check_commands = ["funannotate --help 2>&1 | grep 'Usage:[ ]*funannotate'"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb new file mode 100644 index 00000000000..0c453259ec8 --- /dev/null +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb @@ -0,0 +1,58 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'GOATOOLS' +version = '1.3.1' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2021b'} + +# must download sources via git to preserve .git directory, +# since setuptools-scm is used to determine version +sources = [{ + 'git_config': { + 'url': 'https://github.com/tanghaibao', + 'repo_name': 'goatools', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [('cURL', '7.78.0')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('XlsxWriter', '3.0.2'), + ('statsmodels', '0.13.1'), + ('pydot', '1.4.2'), + ('openpyxl', '3.0.9'), +] + +download_dep_fail = True +use_pip = True + +postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "mkdir -p %(builddir)s", + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..c0f68a2a026 --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'PythonPackage' + +name = 'pydot' +version = '1.4.2' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['248081a39bcb56784deb018977e428605c1c758f10897a339fce1dd728ff007d'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('Graphviz', '2.50.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 172f59b101057fce90dcfe692ca84220a69f29fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2023 19:47:28 +0100 Subject: [PATCH 6960/9987] {bio}[foss/2022a] PhyloPhlAn v3.0.3, IQ-TREE v2.2.2.3, MUSCLE v5.1.0, trimAl v1.4.1, LSD2 v2.3 w/ Python 3.10.4 --- .../i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb | 57 +++++++++++++++++++ .../l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb | 38 +++++++++++++ .../m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb | 39 +++++++++++++ .../PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb | 55 ++++++++++++++++++ .../t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb | 35 ++++++++++++ 5 files changed, 224 insertions(+) create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb new file mode 100644 index 00000000000..0ea0821beb2 --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb @@ -0,0 +1,57 @@ +# Updated to v2.1.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.2.2.3' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'IQ-TREE-2.1.2_use_EB_LSD2.patch', + 'IQ-TREE-2.2.1_fix-mpi.patch', +] +checksums = [ + {'v2.2.2.3.tar.gz': 'fb15dfcdf63ce20f371763fff925804809f2fd5b7faaad1fb09a6f2bc7c2ba01'}, + {'IQ-TREE-2.1.2_use_EB_LSD2.patch': 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816'}, + {'IQ-TREE-2.2.1_fix-mpi.patch': '9ead6808efd11d4c01dd265cca6094cffd6377746d3b2fc84b43d2faeee0777c'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('Boost', '1.79.0'), + ('LSD2', '2.3'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = [ + "iqtree2 --help", + "mkdir -p $TMPDIR/{test-omp,test-mpi}", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy", + "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c13e24fcc53 --- /dev/null +++ b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +# Updated to v2.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'LSD2' +version = '2.3' + +homepage = 'https://github.com/tothuhien/lsd2' +description = "Least-squares methods to estimate rates and dates from phylogenies" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'tothuhien' + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v.%(version)s.tar.gz'] +patches = ['%(name)s-1.9.7_fix_cmake_to_build_lib_and_binary.patch'] +checksums = [ + 'c7819be1204ebf77e3660bba91dbd8629ba9437216814f276a11b9156dbb0649', # v.2.3.tar.gz + # LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch + '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6', +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f11b43042ac --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '5.1.0' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'rcedgar' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d'] + +builddependencies = [ + ('binutils', '2.38'), +] + +start_dir = 'src' + +# Use build environment defined by EasyBuild +prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&" +buildopts = "CPP=${CXX} CC=${CC}" + +files_to_copy = [(['Linux/muscle'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/muscle'], + 'dirs': [], +} + +sanity_check_commands = ["muscle -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb new file mode 100644 index 00000000000..3cca6b971e6 --- /dev/null +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb @@ -0,0 +1,55 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# update to v3.0.2 + +easyblock = 'PythonPackage' + +name = 'PhyloPhlAn' +version = '3.0.3' + +homepage = 'https://github.com/biobakery/phylophlan' +description = """ +PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of +genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method +for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. +""" + +source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['d8d0082c95d58d7b11a60c1e2214b35c1a23a65675005f1393e7647d76c6a054'] + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.5.2'), + ('Seaborn', '0.12.1'), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.2.2.3'), + ('MUSCLE', '5.1.0'), + ('MAFFT', '7.505', '-with-extensions'), + ('SEPP', '4.5.1'), + ('trimAl', '1.4.1'), + ('BLAST+', '2.13.0'), + ('USEARCH', '11.0.667-i86linux32', '', SYSTEM), + ('DIAMOND', '2.1.0'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], + 'dirs': ['lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8da2ca94e6c --- /dev/null +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated by: +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'MakeCp' + +name = 'trimAl' +version = '1.4.1' + +homepage = 'https://github.com/scapella/trimal' +description = """EVB, FEP and LIE simulator.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'scapella' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] + +builddependencies = [ + ('binutils', '2.38'), + +] +start_dir = 'source' + +files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/trimal', 'bin/readal', 'bin/statal'], + 'dirs': [] +} + +moduleclass = 'bio' From 06cff2a5d5a59f6fcd37734cfd05db6102722ec6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2023 19:52:34 +0100 Subject: [PATCH 6961/9987] adding easyconfigs: MetaPhlAn-4.0.6-foss-2022a.eb, CMSeq-1.0.4-foss-2022a.eb, biom-format-2.1.14-foss-2022a.eb --- .../biom-format-2.1.14-foss-2022a.eb | 47 ++++++++++++++++++ .../c/CMSeq/CMSeq-1.0.4-foss-2022a.eb | 37 ++++++++++++++ .../m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb | 48 +++++++++++++++++++ 3 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.14-foss-2022a.eb create mode 100644 easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.14-foss-2022a.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.14-foss-2022a.eb new file mode 100644 index 00000000000..e518ffc2793 --- /dev/null +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.14-foss-2022a.eb @@ -0,0 +1,47 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Revised BSD +# +# Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b +## + +easyblock = 'PythonPackage' + +name = 'biom-format' +version = '2.1.14' + +homepage = 'https://biom-format.org' +description = """ +The BIOM file format (canonically pronounced biome) is designed to be + a general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth Microbiome + Project and is a Genomics Standards Consortium supported project. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c8bac94ab6aa8226c0d38af7a3341d65e5f3664b9f45ec44fdf8b5275b2f92c1'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/biom'], + 'dirs': ['lib'], +} + +options = {'modulename': 'biom'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb new file mode 100644 index 00000000000..841eb0499fc --- /dev/null +++ b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb @@ -0,0 +1,37 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'CMSeq' +version = '1.0.4' + +homepage = 'https://github.com/SegataLab/cmseq/' +description = "CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus." + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['93038a6dba826e29a66df3ec8ab2b3e3872acac7af9df245e4a5a624584aca5c'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('bcbio-gff', '0.7.0'), + ('biom-format', '2.1.14'), + ('Pysam', '0.20.0'), + ('SAMtools', '1.16.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['breadth_depth.py', 'consensus.py', 'poly.py', 'polymut.py']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb new file mode 100644 index 00000000000..a2aebcc69ea --- /dev/null +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb @@ -0,0 +1,48 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonBundle' + +name = 'MetaPhlAn' +version = '4.0.6' + +homepage = 'https://github.com/biobakery/MetaPhlAn' +description = """MetaPhlAn is a computational tool for profiling the composition + of microbial communities from metagenomic shotgun sequencing data """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('Pysam', '0.20.0'), + ('DendroPy', '4.5.2'), + ('CMSeq', '1.0.4'), + ('biom-format', '2.1.14'), + ('h5py', '3.7.0'), + ('PhyloPhlAn', '3.0.3'), +] + +use_pip = True + +exts_list = [ + ('hclust2', '1.0.0', { + 'checksums': ['9667f1d16628940aedd3d1d571b956a6f77795018e3ea4dd83f234419eb0096d'], + }), + (name, version, { + 'checksums': ['e810d6b894ec6d0029255407f03a7dea1753ff65bde333ab34b40544cfb5553e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["metaphlan -h"] + +sanity_pip_check = True + +moduleclass = 'bio' From 9f50a299b623b1e387d3524fb87560f115d56838 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Tue, 21 Mar 2023 21:44:55 +0100 Subject: [PATCH 6962/9987] Rename KrakenUniq-1.0.3-foss-2022a.eb to KrakenUniq-1.0.3-GCC-11.3.0.eb --- ...kenUniq-1.0.3-foss-2022a.eb => KrakenUniq-1.0.3-GCC-11.3.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/k/KrakenUniq/{KrakenUniq-1.0.3-foss-2022a.eb => KrakenUniq-1.0.3-GCC-11.3.0.eb} (100%) diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb similarity index 100% rename from easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-foss-2022a.eb rename to easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb From 3b9c2102fc3a735bf6177f98257cb56e119452be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 Mar 2023 21:50:28 +0100 Subject: [PATCH 6963/9987] adding easyconfigs: DiCE-ML-0.9-foss-2022a.eb --- .../d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb b/easybuild/easyconfigs/d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb new file mode 100644 index 00000000000..1103677a97a --- /dev/null +++ b/easybuild/easyconfigs/d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'DiCE-ML' +version = '0.9' + +homepage = 'https://interpret.ml/DiCE' +description = "Diverse Counterfactual Explanations (DiCE) for ML" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), +] + +sources = ['dice_ml-%(version)s.tar.gz'] +checksums = ['0c4c2cb57f2218ba324ef2931304ab42f5f685759688a5898b0eb85b7a25b97a'] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'ai' From 0125ffc4e948d7b59b4c7f5100af31bd5fbfad62 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Mar 2023 10:11:11 +0100 Subject: [PATCH 6964/9987] fix preinstallopts for ravenpy extension in Raven easyconfig --- .../easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb index 82f6b075da7..0e32ebaa9e0 100644 --- a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -21,7 +21,6 @@ preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && " configopts = '-DRAVEN_BUILD_EXE=1 -G Ninja ' configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' - dependencies = [ ('Python', '3.9.6'), ('zlib', '1.2.11'), @@ -34,15 +33,18 @@ exts_default_options = { 'use_pip': True, } +# inject addition CMake options to make sure that Python dependency is actually used +local_ravenpy_preinstallopts = r"""sed -i 's|cmake_args += \["-GNinja"\]|cmake_args += \[""" +local_ravenpy_preinstallopts += r'"-GNinja", "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION",' +local_ravenpy_preinstallopts += r""" "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python"\]|' setup.py && """ + exts_list = [ (name, version, { 'modulename': 'ravenpy', 'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'], 'sources': ['%(version)s.tar.gz'], 'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'], - 'preinstallopts': r'sed -i \'s|cmake_args += \["-GNinja"\]|cmake_args += \["-GNinja", \ - "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION",\ - "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python"\]|\' setup.py && ' + 'preinstallopts': local_ravenpy_preinstallopts, }), ] @@ -50,7 +52,7 @@ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_paths = { 'files': ['bin/raven'], - 'dirs': [] + 'dirs': [], } sanity_check_commands = [ @@ -58,4 +60,4 @@ sanity_check_commands = [ "raven --help" ] -moduleclass = "bio" +moduleclass = 'bio' From ed6c995e5e8adf04359c0fe4e72c37993cdedaeb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 22 Mar 2023 10:14:52 +0100 Subject: [PATCH 6965/9987] stick to Pysam 0.19.1 for CMSeq 1.0.4 and etaPhlAn 4.0.6 --- easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb | 2 +- easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb index 841eb0499fc..b16ab7d9572 100644 --- a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb @@ -21,7 +21,7 @@ dependencies = [ ('Biopython', '1.79'), ('bcbio-gff', '0.7.0'), ('biom-format', '2.1.14'), - ('Pysam', '0.20.0'), + ('Pysam', '0.19.1'), ('SAMtools', '1.16.1'), ] diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb index a2aebcc69ea..16e6771ac7d 100644 --- a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb @@ -17,7 +17,7 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('Biopython', '1.79'), - ('Pysam', '0.20.0'), + ('Pysam', '0.19.1'), ('DendroPy', '4.5.2'), ('CMSeq', '1.0.4'), ('biom-format', '2.1.14'), From d08b98fcbab00dfcaccd82f96116b8bd9be877a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 22 Mar 2023 10:44:32 +0100 Subject: [PATCH 6966/9987] remove suffix --- ...11.3.0-Python-3.10.4.eb => pyparsing-3.0.9-GCCcore-11.3.0.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/p/pyparsing/{pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb => pyparsing-3.0.9-GCCcore-11.3.0.eb} (95%) diff --git a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb similarity index 95% rename from easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb rename to easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb index 9ef3f6d433b..0c8b7ea8098 100644 --- a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0-Python-3.10.4.eb +++ b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb @@ -2,7 +2,6 @@ easyblock = 'PythonPackage' name = 'pyparsing' version = '3.0.9' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/pyparsing/pyparsing' description = """The pyparsing module is an alternative approach to creating and From dd4a51ffe55d55caf9b7a66fc2dbfcbfd6ec3917 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 22 Mar 2023 17:28:06 +0100 Subject: [PATCH 6967/9987] CuPy: skip TestProduct tests due to badly written tests with float16 --- .../easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb index a665a1371c4..d194347e4cd 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb @@ -36,6 +36,8 @@ _skip_tests = [ 'tests/cupy_tests/testing_tests/test_parameterized.py', 'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_', 'tests/cupy_tests/fft_tests/test_fft.py', + # float16 has too low precision for these tests as they are written + 'tests/cupy_tests/linalg_tests/test_product.py::TestProduct', ] _ignore_list = ' --ignore='.join(_skip_tests) @@ -46,7 +48,7 @@ exts_list = [ ('cupy', version, { # Must run tests here since the required version of pytest is a builddep # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory. - 'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && pytest --ignore=%s tests' %\ + 'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && pytest --ignore=%s tests' % _ignore_list, 'testinstall': True, 'checksums': ['03d52b2626e02a3a2b46d714c1cd03e702c8fe33915fcca6ed8de5c539964f49'], From 6954664e67b706ae98be2019309078339c1e45f6 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 22 Mar 2023 17:34:47 +0100 Subject: [PATCH 6968/9987] pytest: Add comment about file system related tests that may fail on a shared FS. --- .../easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb index e8ab8e89799..8f1d64d7528 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb @@ -22,6 +22,11 @@ use_pip = True exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures _skip_tests = [ 'testing/io/test_terminalwriter.py', 'testing/test_terminal.py', From 7d38ff546856847ae8ba9d58033f3a4ad45a91ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 22 Mar 2023 18:01:27 +0100 Subject: [PATCH 6969/9987] Switch bamtofastq to cargo easyblock --- .../bamtofastq-1.4.0-GCCcore-10.3.0.eb | 163 +++++++++++++++++- 1 file changed, 158 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb index db9e0c95129..987340268d8 100644 --- a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'Binary' +easyblock = 'Cargo' name = 'bamtofastq' version = '1.4.0' @@ -8,6 +8,163 @@ description = """Convert 10x BAM files to the original FASTQs compatible with 10 toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +crates = [ + ('anyhow', '1.0.44'), + ('backtrace', '0.3.61'), + ('addr2line', '0.16.0'), + ('gimli', '0.25.0'), + ('cfg-if', '1.0.0'), + ('libc', '0.2.103'), + ('miniz_oxide', '0.4.4'), + ('adler', '1.0.2'), + ('autocfg', '1.0.1'), + ('object', '0.26.2'), + ('memchr', '2.4.1'), + ('rustc-demangle', '0.1.21'), + ('cc', '1.0.71'), + ('jobserver', '0.1.24'), + ('libc', '0.2.103'), + ('backtrace', '0.3.61'), + ('bincode', '1.3.3'), + ('serde', '1.0.130'), + ('serde_derive', '1.0.130'), + ('proc-macro2', '1.0.29'), + ('unicode-xid', '0.2.2'), + ('quote', '1.0.10'), + ('proc-macro2', '1.0.29'), + ('syn', '1.0.80'), + ('proc-macro2', '1.0.29'), + ('quote', '1.0.10'), + ('unicode-xid', '0.2.2'), + ('csv', '1.1.6'), + ('bstr', '0.2.17'), + ('lazy_static', '1.4.0'), + ('memchr', '2.4.1'), + ('regex-automata', '0.1.10'), + ('serde', '1.0.130'), + ('csv-core', '0.1.10'), + ('memchr', '2.4.1'), + ('itoa', '0.4.8'), + ('ryu', '1.0.5'), + ('serde', '1.0.130'), + ('docopt', '1.1.1'), + ('lazy_static', '1.4.0'), + ('regex', '1.5.4'), + ('aho-corasick', '0.7.18'), + ('memchr', '2.4.1'), + ('memchr', '2.4.1'), + ('regex-syntax', '0.6.25'), + ('serde', '1.0.130'), + ('strsim', '0.10.0'), + ('flate2', '1.0.22'), + ('cfg-if', '1.0.0'), + ('crc32fast', '1.2.1'), + ('cfg-if', '1.0.0'), + ('libc', '0.2.103'), + ('libz-sys', '1.1.3'), + ('libc', '0.2.103'), + ('cc', '1.0.71'), + ('cmake', '0.1.45'), + ('cc', '1.0.71'), + ('pkg-config', '0.3.20'), + ('itertools', '0.10.1'), + ('either', '1.6.1'), + ('regex', '1.5.4'), + ('rust-htslib', '0.38.2'), + ('bio-types', '0.12.0'), + ('derive-new', '0.5.9'), + ('proc-macro2', '1.0.29'), + ('quote', '1.0.10'), + ('syn', '1.0.80'), + ('lazy_static', '1.4.0'), + ('regex', '1.5.4'), + ('strum_macros', '0.20.1'), + ('heck', '0.3.3'), + ('unicode-segmentation', '1.8.0'), + ('proc-macro2', '1.0.29'), + ('quote', '1.0.10'), + ('syn', '1.0.80'), + ('thiserror', '1.0.29'), + ('thiserror-impl', '1.0.29'), + ('proc-macro2', '1.0.29'), + ('quote', '1.0.10'), + ('syn', '1.0.80'), + ('byteorder', '1.4.3'), + ('custom_derive', '0.1.7'), + ('derive-new', '0.5.9'), + ('hts-sys', '2.0.2'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('libc', '0.2.103'), + ('cc', '1.0.71'), + ('pkg-config', '0.3.20'), + ('libdeflate-sys', '0.5.0'), + ('cc', '1.0.71'), + ('libz-sys', '1.1.3'), + ('lzma-sys', '0.1.17'), + ('libc', '0.2.103'), + ('cc', '1.0.71'), + ('pkg-config', '0.3.20'), + ('cc', '1.0.71'), + ('fs-utils', '1.1.4'), + ('quick-error', '1.2.3'), + ('glob', '0.3.0'), + ('ieee754', '0.2.6'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.103'), + ('linear-map', '1.2.0'), + ('newtype_derive', '0.1.6'), + ('rustc_version', '0.1.7'), + ('semver', '0.1.20'), + ('regex', '1.5.4'), + ('thiserror', '1.0.29'), + ('url', '2.2.2'), + ('form_urlencoded', '1.0.1'), + ('matches', '0.1.9'), + ('percent-encoding', '2.1.0'), + ('idna', '0.2.3'), + ('matches', '0.1.9'), + ('unicode-bidi', '0.3.7'), + ('unicode-normalization', '0.1.19'), + ('tinyvec', '1.5.0'), + ('tinyvec_macros', '0.1.0'), + ('matches', '0.1.9'), + ('percent-encoding', '2.1.0'), + ('serde', '1.0.130'), + ('serde_bytes', '0.11.5'), + ('serde', '1.0.130'), + ('serde_derive', '1.0.130'), + ('shardio', '0.8.1'), + ('anyhow', '1.0.44'), + ('bincode', '1.3.3'), + ('byteorder', '1.4.3'), + ('crossbeam-channel', '0.5.1'), + ('cfg-if', '1.0.0'), + ('crossbeam-utils', '0.8.5'), + ('cfg-if', '1.0.0'), + ('lazy_static', '1.4.0'), + ('log', '0.4.14'), + ('cfg-if', '1.0.0'), + ('lz4', '1.23.2'), + ('libc', '0.2.103'), + ('lz4-sys', '1.9.2'), + ('libc', '0.2.103'), + ('cc', '1.0.71'), + ('min-max-heap', '1.3.0'), + ('serde', '1.0.130'), + ('tempfile', '3.2.0'), + ('cfg-if', '1.0.0'), + ('libc', '0.2.103'), + ('rand', '0.8.4'), + ('libc', '0.2.103'), + ('rand_chacha', '0.3.1'), + ('ppv-lite86', '0.2.10'), + ('rand_core', '0.6.3'), + ('getrandom', '0.2.3'), + ('cfg-if', '1.0.0'), + ('libc', '0.2.103'), + ('rand_core', '0.6.3'), + ('remove_dir_all', '0.5.3'), +] source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] checksums = ['b51d32e8aee3b9ace08c54397fddb590209571f47f4051077bcb22b98ca3a5ed'] @@ -20,10 +177,6 @@ builddependencies = [ dependencies = [('bzip2', '1.0.8')] -extract_sources = True - -install_cmd = "cargo build --release && cargo install --root %(installdir)s --path ." - sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': [], From 859be3b4b145617de2fa10c49f9c284994b668dc Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 22 Mar 2023 18:11:13 +0100 Subject: [PATCH 6970/9987] Changed to latest version of Circuitscape --- .../Circuitscape-5.12.3-Julia-1.7.2.eb | 417 ++++++++++++++++++ 1 file changed, 417 insertions(+) create mode 100644 easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb new file mode 100644 index 00000000000..26710c0c816 --- /dev/null +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb @@ -0,0 +1,417 @@ +easyblock = 'Bundle' + +name = 'Circuitscape' +version = '5.12.3' +_julia_ver = '1.7.2' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/Circuitscape/Circuitscape.jl' +description = "Algorithms from circuit theory to predict connectivity in heterogeneous landscapes" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, True), +] + +exts_defaultclass = 'JuliaPackage' +exts_filter = ("LD_LIBRARY_PATH="" julia -e 'using %(ext_name)s'", "") +exts_default_options = { + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], +} + + +exts_list = [ + ('Preferences', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['a87c1fc863fcb6240c3f4327776fa01a1f87e0d2df5a0c1850f789ce24469da2'], + }), + ('JLLWrappers', '1.4.1', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], + }), + ('IntelOpenMP_jll', '2018.0.3+2', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/IntelOpenMP_jll.jl/archive/'], + 'sources': ['IntelOpenMP-v%(version)s.tar.gz'], + 'checksums': ['4e8586f0b794ba5cf159dde99774aab4509a32555fc900140f533999db476aab'], + }), + ('MKL_jll', '2022.2.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/MKL_jll.jl/archive/'], + 'sources': ['MKL-v%(version)s.tar.gz'], + 'checksums': ['228a80c33ae71a3efc78ed9f6a3329fd20a48ad80ff7af44f0d42057e1af4241'], + }), + ('Reexport', '1.2.2', { + 'source_urls': ['https://github.com/simonster/Reexport.jl/archive/'], + 'checksums': ['2566f7776aae9697cbf15765fc32187f46dd51200abc953a0266863ad67132b3'], + }), + ('CommonSolve', '0.2.3', { + 'source_urls': ['https://github.com/SciML/CommonSolve.jl/archive/'], + 'checksums': ['5a1fe0c82571697e45bf8d4488b68a656584b07c8a2045b26e52ae01ec118e1b'], + }), + ('AlgebraicMultigrid', '0.5.1', { + 'source_urls': ['https://github.com/JuliaLinearAlgebra/AlgebraicMultigrid.jl/archive/'], + 'checksums': ['c33896880d1495b2ffc80dcbe5a2a2d6f305a9555e041ebd1191899e824e75e7'], + }), + ('Pardiso', '0.5.4', { + 'source_urls': ['https://github.com/JuliaSparse/Pardiso.jl/archive/'], + 'checksums': ['b60a693dd71a19fc3155b36683f8c812f217de59ee7eda77c9cd0855468a3c4a'], + }), + ('GZip', '0.5.1', { + 'source_urls': ['https://github.com/JuliaIO/GZip.jl/archive/'], + 'checksums': ['c74976af07cbe835a5bb5396ade41feb90a782267e94bc3a98bb1ad1446ba54f'], + }), + ('SnoopPrecompile', '2.9.5', { + 'source_urls': ['https://github.com/timholy/SnoopCompile.jl/archive/'], + 'start_dir': '%(name)s', + 'checksums': ['a86ca9179fac77efd3771c71c620914aa6909754d474cd754f2ee8600fad9a4a'], + }), + ('RecipesBase', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPlots/RecipesBase.jl/archive/'], + 'checksums': ['2a4b7371e565f175a018c0df0cc24dce41fc2f103ad80de87f6c5bc600dbca1a'], + }), + ('NaNMath', '1.0.1', { + 'source_urls': ['https://github.com/JuliaMath/NaNMath.jl/archive/'], + 'checksums': ['caa5666b24b4c5fb8f4d3e4b650f6360e8e19b8bd2d1cb3019a15849c363c45d'], + }), + ('FixedPointNumbers', '0.8.4', { + 'source_urls': ['https://github.com/JuliaMath/FixedPointNumbers.jl/archive/'], + 'checksums': ['6ccfbaf032ed49cf9c82e2770fa8fd53dc88bea12c3799f3fc7f5bc9a33cb89c'], + }), + ('ColorTypes', '0.11.4', { + 'source_urls': ['https://github.com/JuliaGraphics/ColorTypes.jl/archive/'], + 'checksums': ['b188587bb23a59ae5898d741197767e1ab9ad7463eda93efa9a4903863033941'], + }), + ('Colors', '0.12.10', { + 'source_urls': ['https://github.com/JuliaGraphics/Colors.jl/archive/'], + 'checksums': ['a428649a4dc839bb04d43b6424943442609436a8472142076396bbe08c154219'], + }), + ('TensorCore', '0.1.1', { + 'source_urls': ['https://github.com/JuliaMath/TensorCore.jl/archive/'], + 'checksums': ['af2696c11f0fdcb884cea2446297cb792ada202ef2e7b438db65a981ba20c34c'], + }), + ('Compat', '4.5.0', { + 'source_urls': ['https://github.com/JuliaLang/Compat.jl/archive/'], + 'checksums': ['247e7c5f9fd405233bd2b4c96fb3f6deb4a27385d9c6c4d0a74eed6fbad0c02f'], + }), + ('ChainRulesCore', '1.15.6', { + 'source_urls': ['https://github.com/JuliaDiff/ChainRulesCore.jl/archive/'], + 'checksums': ['79e22fc981fa7c44b3efc2f07903f555c5520dc38d0d3d31b6390980c786cb60'], + }), + ('IrrationalConstants', '0.1.1', { + 'source_urls': ['https://github.com/JuliaMath/IrrationalConstants.jl/archive/'], + 'checksums': 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['https://github.com/JuliaGraphics/Graphics.jl/archive/'], + 'checksums': ['c28a6b29266f3c260616eef3d139184b267e0ae4d95ad89b379a5c973888bbb7'], + }), + ('PaddedViews', '0.5.11', { + 'source_urls': ['https://github.com/JuliaArrays/PaddedViews.jl/archive/'], + 'checksums': ['0506dc45cb371e6078fd055b8f21cd40755326e4b5c1b752e71489445e020cda'], + }), + ('MappedArrays', '0.4.1', { + 'source_urls': ['https://github.com/JuliaArrays/MappedArrays.jl/archive/'], + 'checksums': ['58ba4ef19d23737ffc2501e871545365fa1f6c5af84eef93549402a9f25fad56'], + }), + ('StackViews', '0.1.1', { + 'source_urls': ['https://github.com/JuliaArrays/StackViews.jl/archive/'], + 'checksums': ['8a8f008663c70ea9409263c9d2b78b0e246f9e6c700003e6a0e4dd5fe01558e9'], + }), + ('MosaicViews', '0.3.4', { + 'source_urls': ['https://github.com/JuliaArrays/MosaicViews.jl/archive/'], + 'sources': [{'download_filename': '7bb84df.tar.gz', 'filename': 'MosaicViews.v%(version)s.tar.gz'}], + 'checksums': ['fd7fc8679417789b77130e847605fec2c9fe68a3de8a4b12f5c2612aee269273'], + }), + ('AbstractFFTs', '1.2.1', { + 'source_urls': ['https://github.com/JuliaMath/AbstractFFTs.jl/archive/'], + 'checksums': ['58abf90b037c618daeed89940c77ac129b5155b26429ac77643cc9c5db453363'], + }), + ('ImageCore', '0.9.4', { + 'source_urls': ['https://github.com/JuliaImages/ImageCore.jl/archive/'], + 'checksums': ['de5d244989891f47edc4f27bf8bf6557a6982e907f0874a62ad3480c9c333983'], + }), + ('ArchGDAL', '0.8.5', { + 'source_urls': ['https://github.com/yeesian/ArchGDAL.jl/archive/'], + 'checksums': ['e24ec57d88a3a07feac7db5b2501b8f06a1047c42a8eadcde9500e3601984065'], + }), + (name, version, { + 'source_urls': ['https://github.com/Circuitscape/Circuitscape.jl/archive/'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['packages'], +} + +modextrapaths = { + 'JULIA_DEPOT_PATH': '', +} + +moduleclass = 'lib' From f05d5fd496d6bda788a530ad76cd3f72aa9fc939 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 22 Mar 2023 18:29:53 +0100 Subject: [PATCH 6971/9987] Added checksum for Circuitscape --- .../c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb index 26710c0c816..47e82f909b4 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb @@ -402,6 +402,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://github.com/Circuitscape/Circuitscape.jl/archive/'], + 'checksums': ['1eb5b6f5711865792204677359c1b9d9247ae3f34af42f58dfe2ec4ad3dd2177'], }), ] From 493ee8e0cc7e5470e62509d6131d9c6ad2e0393f Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 23 Mar 2023 16:55:24 +0100 Subject: [PATCH 6972/9987] Added sanity check command to run unit tests --- .../c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb index 47e82f909b4..af5d027ce73 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb @@ -411,6 +411,8 @@ sanity_check_paths = { 'dirs': ['packages'], } +sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"Circuitscape\")'"] + modextrapaths = { 'JULIA_DEPOT_PATH': '', } From 363522fe490064d8f810b9bee3c9f92937dfbe1d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 24 Mar 2023 12:38:28 +0100 Subject: [PATCH 6973/9987] add missing OpenJPEG dependency for recent GDAL versions --- .../g/GDAL/GDAL-3.5.0-foss-2022a.eb | 1 + .../g/GDAL/GDAL-3.6.2-foss-2022b.eb | 1 + .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb | 42 +++++++++++++++++++ 3 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb index 6cf3d77cc5c..6babf890be5 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb @@ -43,6 +43,7 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('HDF5', '1.12.2'), ('HDF', '4.2.15'), + ('OpenJPEG', '2.5.0'), ] preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb index 01346b45e3a..7e3c17c850f 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb @@ -56,6 +56,7 @@ dependencies = [ ('Brunsli', '0.1'), ('Qhull', '2020.2'), ('LERC', '4.0.0'), + ('OpenJPEG', '2.5.0'), ] # common configopts for static, shared library builds diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..1c0e9a28999 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.0' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('LibTIFF', '4.4.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' From 22b845071723e7a6ad786e6549edd531ba05ab5b Mon Sep 17 00:00:00 2001 From: lenocil Date: Fri, 24 Mar 2023 13:32:56 +0100 Subject: [PATCH 6974/9987] Added easyconfig for cppzmq --- .../c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..57f913bc462 --- /dev/null +++ b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'cppzmq' +version = '4.9.0' + +homepage = 'https://github.com/zeromq/cppzmq' +description = "cppzmq is a C++ binding for libzmq." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/zeromq/%(name)s/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3fdf5b100206953f674c94d40599bdb3ea255244dcc42fab0d75855ee3645581'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('ZeroMQ', '4.3.4'), +] + +sanity_check_paths = { + 'files': ['include/zmq.hpp'], + 'dirs': ['include','lib'], +} + +moduleclass = 'lib' From 372a2086b3b22b815236711909b31b322940f812 Mon Sep 17 00:00:00 2001 From: lenocil Date: Fri, 24 Mar 2023 13:35:20 +0100 Subject: [PATCH 6975/9987] Added whitespace --- easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb index 57f913bc462..e78d4d15a99 100644 --- a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb @@ -19,7 +19,7 @@ builddependencies = [ sanity_check_paths = { 'files': ['include/zmq.hpp'], - 'dirs': ['include','lib'], + 'dirs': ['include', 'lib'], } moduleclass = 'lib' From a5b6658beb342b119fa62c9ca88a0d944a4bf46a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 25 Mar 2023 11:10:12 +0000 Subject: [PATCH 6976/9987] cleanup --- .../R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index 352ea582005..1b5f6973977 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -10,9 +10,6 @@ description = """Bioconductor provides tools for the analysis and coprehension toolchain = {'name': 'foss', 'version': '2022b'} -# lpsymphony fails to build with pkgconf, so stick to pkg-config -# error in: https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286 -# builddependencies = [('pkg-config', '0.29.2')] builddependencies = [('pkgconf', '1.9.3')] dependencies = [ @@ -46,7 +43,7 @@ exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_s # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! -# packages updated on 7th Nov 2022 +# packages updated on 18th March 2023 exts_list = [ ('BiocGenerics', '0.44.0', { 'checksums': ['8518e462c1ef103ab059d059d871afc444e48f56fe6b3afdb60dc1abf6c9b09d'], @@ -442,12 +439,7 @@ exts_list = [ 'checksums': ['6eba6fdd689fdd5d18fde3ffe4aa64ad4af5bfdc8977b8038d297fb46ed10515'], }), ('dada2', '1.26.0', { - 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], - 'checksums': [ - {'dada2_1.26.0.tar.gz': '6c9ee66abfa2e21096b8a3669346a445ee051308d9773f2d9e6e4ea230c1aeb1'}, - {'dada2-1.16.0-remove-sse-on-aarch64.patch': - 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935'}, - ], + 'checksums': ['6c9ee66abfa2e21096b8a3669346a445ee051308d9773f2d9e6e4ea230c1aeb1'], }), ('LEA', '3.10.2', { 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], From 5ca7aa3a5c7a5a517a81d450ce736b07c89f482b Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 27 Mar 2023 12:31:01 +0200 Subject: [PATCH 6977/9987] Add AlphaFold and deps --- .../AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb | 167 ++++++++++++++++++ .../h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb | 90 ++++++++++ .../k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb | 27 +++ .../OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb | 62 +++++++ ...enMM-7.5.1_fix_Doxygen_compatibility.patch | 24 +++ 5 files changed, 370 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..a84e24f20d3 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,167 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '5.1.1'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('TensorFlow', '2.11.0', versionsuffix), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.5'), + ('jax', '0.3.14', versionsuffix), # also provides absl-py + ('UCX-CUDA', '1.12.1', versionsuffix), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), + ('NCCL', '2.12.12', versionsuffix), + # AlphaFold doesn't work with latest OpenMM, so have to use v7.5.1 + ('OpenMM', '7.5.1', '-DeepMind-patch'), +] + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.3.0_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + ], + 'checksums': [ + '52055a0b4bf194ae0e1960e6391e501490f82274c975e01c1ff0e353a1cd59d9', # v2.3.0.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '5cff3fc7104e020ef546d23cb4fb1b8d6517562783f055cc55fc65fe2b0248d0', # AlphaFold-2.3.0_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.8.1', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.6', { + 'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('dm-tree', '0.1.8', { + 'modulename': 'tree', + 'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('docker', '6.0.1', { + 'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'], + }), + ('immutabledict', '2.2.3', { + 'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold*.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m simtk.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '3', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb new file mode 100644 index 00000000000..1e8dd76e708 --- /dev/null +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb @@ -0,0 +1,90 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Updated to use gompi-2020b toolchain: +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'HH-suite' +version = '3.3.0' + +homepage = 'https://github.com/soedinglab/hh-suite' +description = """The HH-suite is an open-source software package + for sensitive protein sequence searching based on the pairwise + alignment of hidden Markov models (HMMs).""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('Python', '3.10.4'), +] + +_binaries_help = [ + 'cstranslate', 'cstranslate_mpi', 'hhalign', 'hhalign_mpi', 'hhalign_omp', 'hhconsensus', + 'hhfilter', 'hhmake' +] + +_binaries_h = [ + 'a3m_database_extract', 'a3m_database_filter', 'a3m_database_reduce', 'a3m_extract', 'a3m_reduce', + 'hhblits', 'hhblits_ca3m', 'hhblits_mpi', 'hhblits_omp', 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp' +] + +_binaries_version = ['ffindex_build', 'ffindex_from_fasta', 'ffindex_modify'] + +_binaries_v = ['ffindex_from_fasta_with_split'] + +_binaries_helpless = [ + 'ffindex_apply', 'ffindex_apply_mpi', 'ffindex_get', + 'ffindex_order', 'ffindex_reduce', 'ffindex_unpack' +] + +_scriptfiles = ['hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py'] + +fix_perl_shebang_for = ['scripts/*pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries_help] + + ['bin/%s' % x for x in _binaries_h] + + ['bin/%s' % x for x in _binaries_version] + + ['bin/%s' % x for x in _binaries_v] + + ['bin/%s' % x for x in _binaries_helpless] + + ['scripts/%s' % y for y in _scriptfiles], + 'dirs': ['data', 'scripts'] +} + +sanity_check_commands = ['%s --help' % x for x in _binaries_help] +sanity_check_commands += ['%s -h' % x for x in _binaries_h] +sanity_check_commands += ['%s --version' % x for x in _binaries_version] +sanity_check_commands += ['%s -v' % x for x in _binaries_v] +sanity_check_commands += ['%s 2>&1 | grep USAGE' % x for x in _binaries_helpless] + +modextrapaths = { + 'PATH': 'scripts', + 'PERL5LIB': 'scripts', +} + +modextravars = { + 'HHLIB': '%(installdir)s', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3dfcd8a4213 --- /dev/null +++ b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +# Contribution from the NIHR Biomedical Research Centre +easyblock = 'CMakeMake' + +name = 'Kalign' +version = '3.3.5' + +homepage = 'https://github.com/TimoLassmann/kalign' +description = "Kalign is a fast multiple sequence alignment program for biological sequences." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['75f3a127d2a9eef1eafd931fb0785736eb3f82826be506e7edd00daf1ba26212'] + +builddependencies = [ + ('CMake', '3.23.1') +] + +sanity_check_paths = { + 'files': ['bin/kalign'], + 'dirs': [], +} + +sanity_check_commands = ["kalign --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb new file mode 100644 index 00000000000..e1e07a395fb --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb @@ -0,0 +1,62 @@ +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.1' +versionsuffix = '-DeepMind-patch' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + ('OpenMM-%(version)s_DeepMind.patch', 'wrappers/python'), + 'OpenMM-7.5.1_fix_Doxygen_compatibility.patch', +] +checksums = [ + 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', + '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', + '86664f02a1ca70e02b977102798d5e1ba333d1543914951af42706a461f1564c', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SWIG', '4.0.2'), +] + +runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +local_python_path = 'lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg' + +sanity_check_paths = { + 'files': [ + 'lib/libOpenMM.%s' % SHLIB_EXT, + local_python_path + '/simtk/openmm/openmm.py', + ], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': local_python_path, + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch new file mode 100644 index 00000000000..1cf2ffa4a56 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch @@ -0,0 +1,24 @@ +# Fixes compatibility issue with Doxygen >= 1.9.2 +# See: https://github.com/openmm/openmm/issues/3317 and https://github.com/openmm/openmm/pull/3336 +# Author: maxim-masterov (SURF) + +diff -Nru openmm-7.5.1.orig/wrappers/generateWrappers.py openmm-7.5.1/wrappers/generateWrappers.py +--- openmm-7.5.1.orig/wrappers/generateWrappers.py 2023-03-24 11:11:39.911916000 +0100 ++++ openmm-7.5.1/wrappers/generateWrappers.py 2023-03-24 11:12:29.971967239 +0100 +@@ -82,6 +82,7 @@ + 'const std::vector >& OpenMM::NoseHooverIntegrator::getAllThermostatedPairs', + 'virtual void OpenMM::NoseHooverIntegrator::stateChanged' + ] ++ self.skipMethods = [s.replace(' ', '') for s in self.skipMethods] + self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy'] + self.nodeByID={} + +@@ -132,7 +133,7 @@ + for section in findNodes(classNode, "sectiondef", kind="public-static-func")+findNodes(classNode, "sectiondef", kind="public-func"): + for memberNode in findNodes(section, "memberdef", kind="function", prot="public"): + methodDefinition = getText("definition", memberNode) +- if methodDefinition in self.skipMethods: ++ if methodDefinition.replace(' ', '') in self.skipMethods: + continue + methodList.append(memberNode) + return methodList From ceb5300493f57c0a998d3b133c457eeb3110254e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 27 Mar 2023 17:49:22 +0200 Subject: [PATCH 6978/9987] Update to AlphaFold-2.3.1 --- ...AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb} | 10 ++-- ...ixer-1.8.1_roll_back_to_openmm_1.5.1.patch | 50 +++++++++++++++++++ 2 files changed, 57 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/a/AlphaFold/{AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb => AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb} (94%) create mode 100644 easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb similarity index 94% rename from easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb rename to easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb index a84e24f20d3..dfec7d642c9 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'AlphaFold' -version = '2.3.0' +version = '2.3.1' versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://deepmind.com/research/case-studies/alphafold' @@ -63,7 +63,7 @@ components = [ 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', ], 'checksums': [ - '52055a0b4bf194ae0e1960e6391e501490f82274c975e01c1ff0e353a1cd59d9', # v2.3.0.tar.gz + '1161b2609fa896b16399b900ec2b813e5a0b363fe4e2b26bd826953ba234736a', # v2.3.1.tar.gz '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch '5cff3fc7104e020ef546d23cb4fb1b8d6517562783f055cc55fc65fe2b0248d0', # AlphaFold-2.3.0_data-dep-paths.patch @@ -83,7 +83,11 @@ exts_list = [ ('PDBFixer', '1.8.1', { 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'], + 'patches': ['%(namelower)s-%(version)s_roll_back_to_openmm_1.5.1.patch'], + 'checksums': [ + 'd50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595', + 'b24abffa3e1b5066a6f3bbfd0d3bb14043f3518357e26cb35dad3fae06b866d1', + ], }), ('toolz', '0.12.0', { 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], diff --git a/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch b/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch new file mode 100644 index 00000000000..c78f2aef75f --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch @@ -0,0 +1,50 @@ +# Roll back to OpenMM v1.5.1, as AlphaFold-2.3 doesn't support more recent versions. +# This patch is based on the following PR: https://github.com/openmm/pdbfixer/pull/223/files +# Author: maxim-masterov (SURF) + +diff -Nru pdbfixer-1.8.1.orig/pdbfixer/pdbfixer.py pdbfixer-1.8.1/pdbfixer/pdbfixer.py +--- pdbfixer-1.8.1.orig/pdbfixer/pdbfixer.py 2023-03-27 17:28:53.564306000 +0200 ++++ pdbfixer-1.8.1/pdbfixer/pdbfixer.py 2023-03-27 17:42:24.093931265 +0200 +@@ -32,18 +32,18 @@ + __author__ = "Peter Eastman" + __version__ = "1.7" + +-import openmm as mm +-import openmm.app as app +-import openmm.unit as unit +-from openmm.app.internal.pdbstructure import PdbStructure +-from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader +-from openmm.app.element import hydrogen, oxygen +-from openmm.app.forcefield import NonbondedGenerator ++import simtk.openmm as mm ++import simtk.openmm.app as app ++import simtk.unit as unit ++from simtk.openmm.app.internal.pdbstructure import PdbStructure ++from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader ++from simtk.openmm.app.element import hydrogen, oxygen ++from simtk.openmm.app.forcefield import NonbondedGenerator + + # Support Cythonized functions in OpenMM 7.3 + # and also implementations in older versions. + try: +- from openmm.app.internal import compiled ++ from simtk.openmm.app.internal import compiled + matchResidue = compiled.matchResidueToTemplate + except ImportError: + matchResidue = app.forcefield._matchResidue +diff -Nru pdbfixer-1.8.1.orig/pdbfixer/ui.py pdbfixer-1.8.1/pdbfixer/ui.py +--- pdbfixer-1.8.1.orig/pdbfixer/ui.py 2023-03-27 17:28:53.583267000 +0200 ++++ pdbfixer-1.8.1/pdbfixer/ui.py 2023-03-27 17:42:32.915332264 +0200 +@@ -6,9 +6,9 @@ + import sys + from math import sqrt + +-import openmm.app as app +-import openmm.unit as unit +-from openmm.vec3 import Vec3 ++import simtk.openmm.app as app ++import simtk.unit as unit ++from simtk.openmm.vec3 import Vec3 + + from .pdbfixer import PDBFixer, proteinResidues, dnaResidues, rnaResidues, _guessFileFormat + from . import uiserver From 3e5714404911ee265b517c17105c66148639659a Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 27 Mar 2023 17:50:20 +0200 Subject: [PATCH 6979/9987] Add missing binutils --- easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb index 3dfcd8a4213..fda9c28356f 100644 --- a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb @@ -14,7 +14,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['75f3a127d2a9eef1eafd931fb0785736eb3f82826be506e7edd00daf1ba26212'] builddependencies = [ - ('CMake', '3.23.1') + ('binutils', '2.38'), + ('CMake', '3.23.1'), ] sanity_check_paths = { From 2f6ef9830bbbe226d052882c6203b931c1ded327 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 27 Mar 2023 18:34:48 +0200 Subject: [PATCH 6980/9987] Update Cantera-2.6.0-foss-2022a.eb --- .../easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb index bb14dcff6b1..5507e6a57bc 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb @@ -2,6 +2,7 @@ easyblock = 'SCons' name = 'Cantera' version = '2.6.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/Cantera/cantera' description = """Chemical kinetics, thermodynamics, and transport tool suite""" @@ -15,6 +16,7 @@ checksums = ['7273622ea76a53373cee820f939613b15eea3dd83db6e1b127c5ed043f77dc5b'] dependencies = [ ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), ('Boost', '1.79.0'), ('SUNDIALS', '6.3.0'), ('yaml-cpp', '0.7.0'), @@ -28,9 +30,8 @@ builddependencies = [ ] local_common_opts = 'env_vars=all CC="$CC" CXX="$CXX" cc_flags="$CFLAGS" cxx_flags="$CXXFLAGS" ' -# local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR ' -# local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' -# local_common_opts += 'blas_lapack_libs=openblas blas_lapack_dir=${EBROOTFLEXIBLAS}/lib' +local_common_opts += 'blas_lapack_libs=flexiblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR ' +local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' buildopts = 'build ' + local_common_opts # tests hang, so disable them for now # runtest = 'test ' + local_common_opts From ace6576c541d23a0ebf8f8feb62ace86b2b64689 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 27 Mar 2023 18:51:06 +0200 Subject: [PATCH 6981/9987] adding CASPR easyconfig + deps' --- .../c/CASPR/CASPR-20200730-foss-2022a.eb | 39 ++++++++++++++++++ .../FASTX-Toolkit-0.0.14-GCC-11.3.0.eb | 34 +--------------- .../m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb | 36 +++++++++++++++++ .../v/vispr/vispr-0.4.14-foss-2022a.eb | 40 +++++++++++++++++++ .../vispr_fix_pandas_version_change.patch | 13 ++++++ 5 files changed, 130 insertions(+), 32 deletions(-) create mode 100644 easybuild/easyconfigs/c/CASPR/CASPR-20200730-foss-2022a.eb create mode 100644 easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb create mode 100644 easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch diff --git a/easybuild/easyconfigs/c/CASPR/CASPR-20200730-foss-2022a.eb b/easybuild/easyconfigs/c/CASPR/CASPR-20200730-foss-2022a.eb new file mode 100644 index 00000000000..c32f29ed00e --- /dev/null +++ b/easybuild/easyconfigs/c/CASPR/CASPR-20200730-foss-2022a.eb @@ -0,0 +1,39 @@ +# Author: Denis Kristak (Inuits) + +easyblock = 'Tarball' + +name = 'CASPR' +version = '20200730' +local_commit = 'b74fde2' + +homepage = 'https://judithbergada.github.io/CASPR' +description = """Running CASPR is extremely easy and convenient to analyze CRIPR-Cas9 screens using pgRNAs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/judithbergada/CASPR/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['96cd3a8fd8f1d8cddf798f07bff46c1048ab9343aa40c31d3430f1e58703f0ac'] + +dependencies = [ + ('FastQC', '0.11.9', '-Java-11', SYSTEM), + ('cutadapt', '4.2'), + ('FASTX-Toolkit', '0.0.14'), + ('STAR', '2.7.10b'), + ('SAMtools', '1.16.1'), + ('vispr', '0.4.14'), + ('R', '4.2.1'), +] + +modextrapaths = { + 'PATH': 'source/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['source'], +} + +sanity_check_commands = ["CASPR --help 2>&1 | grep 'Usage: CASPR'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb index 8589f7ecedc..67d8cb141e8 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb @@ -8,6 +8,8 @@ # # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Updated: Denis Kristak (Inuits) ## easyblock = 'Bundle' @@ -24,11 +26,6 @@ toolchainopts = {'pic': True} default_easyblock = 'ConfigureMake' -dependencies = [ - ('GDGraph', '1.56'), - ('Perl', '5.34.1'), -] - components = [ ('libgtextutils', '0.7', { 'source_urls': ['https://github.com/agordon/libgtextutils/releases/download/%(version)s/'], @@ -50,23 +47,6 @@ components = [ }), ] -exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") - -exts_list = [ - ('PerlIO::gzip', '0.20', { - 'source_tmpl': 'PerlIO-gzip-0.20.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], - 'checksums': ['4848679a3f201e3f3b0c5f6f9526e602af52923ffa471a2a3657db786bd3bdc5'], - }), -] - -fix_perl_shebang_for = ['bin/*.pl'] - -modextrapaths = { - 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' -} - sanity_check_paths = { 'files': ['bin/fastx_%s' % x for x in @@ -82,14 +62,4 @@ sanity_check_paths = { 'dirs': [] } -sanity_check_commands = [ - 'fasta_clipping_histogram.pl', - 'fasta_formatter -h', - 'fastq_masker -h | grep "FASTX Toolkit %(version)s"', - 'fastq_quality_boxplot_graph.sh', - 'fastx_barcode_splitter.pl --help | grep "Barcode Splitter, by Assaf Gordon (gordon@cshl.edu), 11sep2008"', - 'fastx_clipper -h | grep "FASTX Toolkit %(version)s"', - 'fastx_nucleotide_distribution_graph.sh', -] - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb new file mode 100644 index 00000000000..cc54713c3c6 --- /dev/null +++ b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb @@ -0,0 +1,36 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +# Updated: Denis Kristak (Inuits) +easyblock = 'PythonPackage' + +name = 'MAGeCK' +version = '0.5.9.4' + +homepage = "https://sourceforge.net/p/mageck/wiki/Home/" +description = """Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify + important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed + by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute, and is being actively updated + by Wei Li lab from Children's National Medical Center.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['42875b308f2d9ee38f083fb1020d7d48fca29e2100fdb09ced1969b738b8c939'] + +# Remove the shipped mageckGSEA and RRA binaries so that the Python install will build them +# This avoids RPATH problems (see #15082) +preinstallopts = "rm bin/{mageckGSEA,RRA} && " + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sanity_check_commands = ["cd %(builddir)s/%(namelower)s-%(version)s/demo/demo1 && ./run.sh"] + [ + "%s -h" % x for x in ['mageck', 'mageckGSEA']] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb new file mode 100644 index 00000000000..855cc5ee79b --- /dev/null +++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb @@ -0,0 +1,40 @@ +# Author: Denis Kristak (Inuits) + +easyblock = 'PythonPackage' + +name = 'vispr' +version = '0.4.14' + +homepage = 'https://pypi.org/project/vispr/' + +description = """ +VISPR - A visualization framework for CRISPR data. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['vispr_fix_pandas_version_change.patch'] +checksums = [ + {'vispr-0.4.14.tar.gz': 'dc2cf6ac9c8930b0f1f1b3a2b7f57bfae180b2ac3674060123fd2d7fe10ccd82'}, + {'vispr_fix_pandas_version_change.patch': '406c78092f1b06114602d37eb216ce24e1206b52461d0fc4270971ab80f10529'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('Flask', '2.2.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('scikit-learn', '1.1.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/vispr'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch b/easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch new file mode 100644 index 00000000000..05275dcd59c --- /dev/null +++ b/easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch @@ -0,0 +1,13 @@ +# with more recent versions of Pandas, the imported error was moved to `pandas.errors` +diff -ruN vispr-0.4.14_orig/vispr/results/rna.py vispr-0.4.14/vispr/results/rna.py +--- vispr-0.4.14_orig/vispr/results/rna.py 2023-03-24 13:10:57.148839548 +0000 ++++ vispr-0.4.14/vispr/results/rna.py 2023-03-24 13:11:14.032660055 +0000 +@@ -11,7 +11,7 @@ + + from flask import render_template + import pandas as pd +-from pandas.io.common import EmptyDataError ++from pandas.errors import EmptyDataError + import numpy as np + from sklearn.decomposition import PCA + from scipy.cluster.hierarchy import average, leaves_list, dendrogram From e04de5c7a2b9555128304492c2aa09aeeaae83ab Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 28 Mar 2023 08:47:52 +0200 Subject: [PATCH 6982/9987] Fix CodAn bin/* executable permissions for all users --- easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb index 5d220aff850..ab50f6642f7 100644 --- a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb @@ -27,7 +27,7 @@ install_cmd = "cp -r %(builddir)s/* %(installdir)s/ && " install_cmd += "tar -xf %(installdir)s/%(name)s-%(version)s/CodAn.tar.gz && " install_cmd += "mkdir %(installdir)s/bin && " install_cmd += "mv %(installdir)s/%(name)s-%(version)s/bin/* %(installdir)s/bin && " -install_cmd += "chmod u+rwx %(installdir)s/bin/* " +install_cmd += "chmod u+rwx,go+x %(installdir)s/bin/* " sanity_check_paths = { 'files': ['bin/%(namelower)s.py'], From f12401eb9d23661cb31756f57473f15146513802 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 28 Mar 2023 08:56:31 +0200 Subject: [PATCH 6983/9987] Update Cantera-2.6.0-foss-2022a.eb --- easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb index 5507e6a57bc..2b8fbc5a70c 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb @@ -2,7 +2,6 @@ easyblock = 'SCons' name = 'Cantera' version = '2.6.0' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/Cantera/cantera' description = """Chemical kinetics, thermodynamics, and transport tool suite""" From 94c8d7d891bef982b18a11bae132105ebc7a8e04 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 28 Mar 2023 09:04:56 +0200 Subject: [PATCH 6984/9987] Add CodAn bin/* read permissions for all users --- easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb index ab50f6642f7..636bef3b8e8 100644 --- a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb @@ -27,7 +27,7 @@ install_cmd = "cp -r %(builddir)s/* %(installdir)s/ && " install_cmd += "tar -xf %(installdir)s/%(name)s-%(version)s/CodAn.tar.gz && " install_cmd += "mkdir %(installdir)s/bin && " install_cmd += "mv %(installdir)s/%(name)s-%(version)s/bin/* %(installdir)s/bin && " -install_cmd += "chmod u+rwx,go+x %(installdir)s/bin/* " +install_cmd += "chmod u+rwx,go+rx %(installdir)s/bin/* " sanity_check_paths = { 'files': ['bin/%(namelower)s.py'], From 3e6e9bbeaf63230d43b10475a8bb110303270fe5 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 28 Mar 2023 11:36:08 +0200 Subject: [PATCH 6985/9987] Add OpenMM-7.7.0 --- .../AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb | 13 +- ...phaFold-2.3.1_switch_to_openmm_7.7.0.patch | 240 ++++++++++++++++++ ...ixer-1.8.1_roll_back_to_openmm_1.5.1.patch | 50 ---- .../OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb | 62 ----- ...enMM-7.5.1_fix_Doxygen_compatibility.patch | 24 -- 5 files changed, 245 insertions(+), 144 deletions(-) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch delete mode 100644 easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch delete mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb delete mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb index dfec7d642c9..cb5cfdb2a9d 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb @@ -29,8 +29,7 @@ dependencies = [ ('UCX-CUDA', '1.12.1', versionsuffix), ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), ('NCCL', '2.12.12', versionsuffix), - # AlphaFold doesn't work with latest OpenMM, so have to use v7.5.1 - ('OpenMM', '7.5.1', '-DeepMind-patch'), + ('OpenMM', '7.7.0'), ] # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, @@ -61,6 +60,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch', ], 'checksums': [ '1161b2609fa896b16399b900ec2b813e5a0b363fe4e2b26bd826953ba234736a', # v2.3.1.tar.gz @@ -70,6 +70,7 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + 'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec', # AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch ], 'start_dir': 'alphafold-%(version)s', @@ -83,11 +84,7 @@ exts_list = [ ('PDBFixer', '1.8.1', { 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'patches': ['%(namelower)s-%(version)s_roll_back_to_openmm_1.5.1.patch'], - 'checksums': [ - 'd50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595', - 'b24abffa3e1b5066a6f3bbfd0d3bb14043f3518357e26cb35dad3fae06b866d1', - ], + 'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'], }), ('toolz', '0.12.0', { 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], @@ -152,7 +149,7 @@ sanity_check_paths = { sanity_check_commands = [ "pdbfixer --help", - "python -m simtk.testInstallation", + "python -m openmm.testInstallation", "python -c 'import alphafold'", "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", ] diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch new file mode 100644 index 00000000000..ff3aa457201 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch @@ -0,0 +1,240 @@ +# Add compatibility with OpenMM-7.7.0 +# The patch is based on the recipe from https://github.com/deepmind/alphafold/issues/404 +# Author: maxim-masterov (SURF) + +diff -Nru alphafold-2.3.1.orig/alphafold/relax/amber_minimize.py alphafold-2.3.1/alphafold/relax/amber_minimize.py +--- alphafold-2.3.1.orig/alphafold/relax/amber_minimize.py 2023-03-28 10:58:07.126241000 +0200 ++++ alphafold-2.3.1/alphafold/relax/amber_minimize.py 2023-03-28 11:24:17.380332000 +0200 +@@ -27,10 +27,10 @@ + import ml_collections + import numpy as np + import jax +-from simtk import openmm +-from simtk import unit +-from simtk.openmm import app as openmm_app +-from simtk.openmm.app.internal.pdbstructure import PdbStructure ++from openmm import * ++from openmm import unit ++from openmm import app as openmm_app ++from openmm.app.internal.pdbstructure import PdbStructure + + + ENERGY = unit.kilocalories_per_mole +@@ -47,7 +47,7 @@ + + + def _add_restraints( +- system: openmm.System, ++ system: System, + reference_pdb: openmm_app.PDBFile, + stiffness: unit.Unit, + rset: str, +diff -Nru alphafold-2.3.1.orig/alphafold/relax/cleanup.py alphafold-2.3.1/alphafold/relax/cleanup.py +--- alphafold-2.3.1.orig/alphafold/relax/cleanup.py 2023-03-28 10:58:07.126999000 +0200 ++++ alphafold-2.3.1/alphafold/relax/cleanup.py 2023-03-28 11:03:20.689464000 +0200 +@@ -20,8 +20,8 @@ + import io + + import pdbfixer +-from simtk.openmm import app +-from simtk.openmm.app import element ++from openmm import app ++from openmm.app import element + + + def fix_pdb(pdbfile, alterations_info): +diff -Nru alphafold-2.3.1.orig/alphafold/relax/cleanup_test.py alphafold-2.3.1/alphafold/relax/cleanup_test.py +--- alphafold-2.3.1.orig/alphafold/relax/cleanup_test.py 2023-03-28 10:58:07.127710000 +0200 ++++ alphafold-2.3.1/alphafold/relax/cleanup_test.py 2023-03-28 11:03:14.772207000 +0200 +@@ -17,7 +17,7 @@ + + from absl.testing import absltest + from alphafold.relax import cleanup +-from simtk.openmm.app.internal import pdbstructure ++from openmm.app.internal import pdbstructure + + + def _pdb_to_structure(pdb_str): +diff -Nru alphafold-2.3.1.orig/docker/Dockerfile alphafold-2.3.1/docker/Dockerfile +--- alphafold-2.3.1.orig/docker/Dockerfile 2023-03-28 10:58:07.081432000 +0200 ++++ alphafold-2.3.1/docker/Dockerfile 2023-03-28 11:04:09.608354000 +0200 +@@ -76,7 +76,6 @@ + + # Apply OpenMM patch. + WORKDIR /opt/conda/lib/python3.8/site-packages +-RUN patch -p0 < /app/alphafold/docker/openmm.patch + + # Add SETUID bit to the ldconfig binary so that non-root users can run it. + RUN chmod u+s /sbin/ldconfig.real +diff -Nru alphafold-2.3.1.orig/notebooks/AlphaFold.ipynb alphafold-2.3.1/notebooks/AlphaFold.ipynb +--- alphafold-2.3.1.orig/notebooks/AlphaFold.ipynb 2023-03-28 10:58:07.092241000 +0200 ++++ alphafold-2.3.1/notebooks/AlphaFold.ipynb 2023-03-28 11:04:51.464351000 +0200 +@@ -103,16 +103,16 @@ + " %shell rm -rf /opt/conda\n", + " %shell wget -q -P /tmp \\\n", + " https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \\\n", +- " \u0026\u0026 bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \\\n", +- " \u0026\u0026 rm /tmp/Miniconda3-latest-Linux-x86_64.sh\n", ++ " && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \\\n", ++ " && rm /tmp/Miniconda3-latest-Linux-x86_64.sh\n", + " pbar.update(9)\n", + "\n", + " PATH=%env PATH\n", + " %env PATH=/opt/conda/bin:{PATH}\n", + " %shell conda install -qy conda==4.13.0 \\\n", +- " \u0026\u0026 conda install -qy -c conda-forge \\\n", ++ " && conda install -qy -c conda-forge \\\n", + " python=3.8 \\\n", +- " openmm=7.5.1 \\\n", ++ " openmm=7.7.0 \\\n", + " pdbfixer\n", + " pbar.update(80)\n", + "\n", +@@ -161,8 +161,7 @@ + " pbar.update(10)\n", + "\n", + " # Apply OpenMM patch.\n", +- " %shell pushd /opt/conda/lib/python3.8/site-packages/ \u0026\u0026 \\\n", +- " patch -p0 \u003c /content/alphafold/docker/openmm.patch \u0026\u0026 \\\n", ++ " %shell pushd /opt/conda/lib/python3.8/site-packages/ && \\\n", + " popd\n", + "\n", + " # Make sure stereo_chemical_props.txt is in all locations where it could be searched for.\n", +@@ -186,9 +185,9 @@ + "\n", + "import jax\n", + "if jax.local_devices()[0].platform == 'tpu':\n", +- " raise RuntimeError('Colab TPU runtime not supported. Change it to GPU via Runtime -\u003e Change Runtime Type -\u003e Hardware accelerator -\u003e GPU.')\n", ++ " raise RuntimeError('Colab TPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')\n", + "elif jax.local_devices()[0].platform == 'cpu':\n", +- " raise RuntimeError('Colab CPU runtime not supported. Change it to GPU via Runtime -\u003e Change Runtime Type -\u003e Hardware accelerator -\u003e GPU.')\n", ++ " raise RuntimeError('Colab CPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')\n", + "else:\n", + " print(f'Running with {jax.local_devices()[0].device_kind} GPU')\n", + "\n", +@@ -206,7 +205,7 @@ + "source": [ + "## Making a prediction\n", + "\n", +- "Please paste the sequence of your protein in the text box below, then run the remaining cells via _Runtime_ \u003e _Run after_. You can also run the cells individually by pressing the _Play_ button on the left.\n", ++ "Please paste the sequence of your protein in the text box below, then run the remaining cells via _Runtime_ > _Run after_. You can also run the cells individually by pressing the _Play_ button on the left.\n", + "\n", + "Note that the search against databases and the actual prediction can take some time, from minutes to hours, depending on the length of the protein and what type of GPU you are allocated by Colab (see FAQ below)." + ] +@@ -298,21 +297,21 @@ + "\n", + "# Check whether total length exceeds limit.\n", + "total_sequence_length = sum([len(seq) for seq in sequences])\n", +- "if total_sequence_length \u003e MAX_LENGTH:\n", ++ "if total_sequence_length > MAX_LENGTH:\n", + " raise ValueError('The total sequence length is too long: '\n", + " f'{total_sequence_length}, while the maximum is '\n", + " f'{MAX_LENGTH}.')\n", + "\n", + "# Check whether we exceed the monomer limit.\n", + "if model_type_to_use == ModelType.MONOMER:\n", +- " if len(sequences[0]) \u003e MAX_MONOMER_MODEL_LENGTH:\n", ++ " if len(sequences[0]) > MAX_MONOMER_MODEL_LENGTH:\n", + " raise ValueError(\n", + " f'Input sequence is too long: {len(sequences[0])} amino acids, while '\n", + " f'the maximum for the monomer model is {MAX_MONOMER_MODEL_LENGTH}. You may '\n", + " 'be able to run this sequence with the multimer model by selecting the '\n", + " 'use_multimer_model_for_monomers checkbox above.')\n", + " \n", +- "if total_sequence_length \u003e MAX_VALIDATED_LENGTH:\n", ++ "if total_sequence_length > MAX_VALIDATED_LENGTH:\n", + " print('WARNING: The accuracy of the system has not been fully validated '\n", + " 'above 3000 residues, and you may experience long running times or '\n", + " f'run out of memory. Total sequence length is {total_sequence_length} '\n", +@@ -407,7 +406,7 @@ + "]\n", + "\n", + "# Search UniProt and construct the all_seq features only for heteromers, not homomers.\n", +- "if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) \u003e 1:\n", ++ "if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) > 1:\n", + " MSA_DATABASES.extend([\n", + " # Swiss-Prot and TrEMBL are concatenated together as UniProt.\n", + " {'db_name': 'uniprot',\n", +@@ -441,7 +440,7 @@ + " for sequence_index, sequence in enumerate(sorted(set(sequences)), 1):\n", + " fasta_path = f'target_{sequence_index:02d}.fasta'\n", + " with open(fasta_path, 'wt') as f:\n", +- " f.write(f'\u003equery\\n{sequence}')\n", ++ " f.write(f'>query\\n{sequence}')\n", + " sequence_to_fasta_path[sequence] = fasta_path\n", + "\n", + " # Run the search against chunks of genetic databases (since the genetic\n", +@@ -502,7 +501,7 @@ + " num_templates=0, num_res=len(sequence)))\n", + "\n", + " # Construct the all_seq features only for heteromers, not homomers.\n", +- " if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) \u003e 1:\n", ++ " if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) > 1:\n", + " valid_feats = msa_pairing.MSA_FEATURES + (\n", + " 'msa_species_identifiers',\n", + " )\n", +@@ -662,7 +661,7 @@ + "banded_b_factors = []\n", + "for plddt in plddts[best_model_name]:\n", + " for idx, (min_val, max_val, _) in enumerate(PLDDT_BANDS):\n", +- " if plddt \u003e= min_val and plddt \u003c= max_val:\n", ++ " if plddt >= min_val and plddt <= max_val:\n", + " banded_b_factors.append(idx)\n", + " break\n", + "banded_b_factors = np.array(banded_b_factors)[:, None] * final_atom_mask\n", +@@ -675,14 +674,14 @@ + " f.write(relaxed_pdb)\n", + "\n", + "\n", +- "# --- Visualise the prediction \u0026 confidence ---\n", ++ "# --- Visualise the prediction & confidence ---\n", + "show_sidechains = True\n", + "def plot_plddt_legend():\n", + " \"\"\"Plots the legend for pLDDT.\"\"\"\n", +- " thresh = ['Very low (pLDDT \u003c 50)',\n", +- " 'Low (70 \u003e pLDDT \u003e 50)',\n", +- " 'Confident (90 \u003e pLDDT \u003e 70)',\n", +- " 'Very high (pLDDT \u003e 90)']\n", ++ " thresh = ['Very low (pLDDT < 50)',\n", ++ " 'Low (70 > pLDDT > 50)',\n", ++ " 'Confident (90 > pLDDT > 70)',\n", ++ " 'Very high (pLDDT > 90)']\n", + "\n", + " colors = [x[2] for x in PLDDT_BANDS]\n", + "\n", +@@ -796,13 +795,13 @@ + "id": "jeb2z8DIA4om" + }, + "source": [ +- "## FAQ \u0026 Troubleshooting\n", ++ "## FAQ & Troubleshooting\n", + "\n", + "\n", + "* How do I get a predicted protein structure for my protein?\n", + " * Click on the _Connect_ button on the top right to get started.\n", + " * Paste the amino acid sequence of your protein (without any headers) into the “Enter the amino acid sequence to fold”.\n", +- " * Run all cells in the Colab, either by running them individually (with the play button on the left side) or via _Runtime_ \u003e _Run all._ Make sure you run all 5 cells in order.\n", ++ " * Run all cells in the Colab, either by running them individually (with the play button on the left side) or via _Runtime_ > _Run all._ Make sure you run all 5 cells in order.\n", + " * The predicted protein structure will be downloaded once all cells have been executed. Note: This can take minutes to hours - see below.\n", + "* How long will this take?\n", + " * Downloading the AlphaFold source code can take up to a few minutes.\n", +@@ -811,8 +810,8 @@ + " * Running AlphaFold and generating the prediction can take minutes to hours, depending on the length of your protein and on which GPU-type Colab has assigned you.\n", + "* My Colab no longer seems to be doing anything, what should I do?\n", + " * Some steps may take minutes to hours to complete.\n", +- " * If nothing happens or if you receive an error message, try restarting your Colab runtime via _Runtime_ \u003e _Restart runtime_.\n", +- " * If this doesn’t help, try resetting your Colab runtime via _Runtime_ \u003e _Factory reset runtime_.\n", ++ " * If nothing happens or if you receive an error message, try restarting your Colab runtime via _Runtime_ > _Restart runtime_.\n", ++ " * If this doesn’t help, try resetting your Colab runtime via _Runtime_ > _Factory reset runtime_.\n", + "* How does this compare to the open-source version of AlphaFold?\n", + " * This Colab version of AlphaFold searches a selected portion of the BFD dataset and currently doesn’t use templates, so its accuracy is reduced in comparison to the full version of AlphaFold that is described in the [AlphaFold paper](https://doi.org/10.1038/s41586-021-03819-2) and [Github repo](https://github.com/deepmind/alphafold/) (the full version is available via the inference script).\n", + "* What is a Colab?\n", +@@ -821,7 +820,7 @@ + " * The resources allocated to your Colab vary. See the [Colab FAQ](https://research.google.com/colaboratory/faq.html) for more details.\n", + " * You can execute the Colab nonetheless.\n", + "* I received an error “Colab CPU runtime not supported” or “No GPU/TPU found”, what do I do?\n", +- " * Colab CPU runtime is not supported. Try changing your runtime via _Runtime_ \u003e _Change runtime type_ \u003e _Hardware accelerator_ \u003e _GPU_.\n", ++ " * Colab CPU runtime is not supported. Try changing your runtime via _Runtime_ > _Change runtime type_ > _Hardware accelerator_ > _GPU_.\n", + " * The type of GPU allocated to your Colab varies. See the [Colab FAQ](https://research.google.com/colaboratory/faq.html) for more details.\n", + " * If you receive “Cannot connect to GPU backend”, you can try again later to see if Colab allocates you a GPU.\n", + " * [Colab Pro](https://colab.research.google.com/signup) offers priority access to GPUs.\n", diff --git a/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch b/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch deleted file mode 100644 index c78f2aef75f..00000000000 --- a/easybuild/easyconfigs/a/AlphaFold/pdbfixer-1.8.1_roll_back_to_openmm_1.5.1.patch +++ /dev/null @@ -1,50 +0,0 @@ -# Roll back to OpenMM v1.5.1, as AlphaFold-2.3 doesn't support more recent versions. -# This patch is based on the following PR: https://github.com/openmm/pdbfixer/pull/223/files -# Author: maxim-masterov (SURF) - -diff -Nru pdbfixer-1.8.1.orig/pdbfixer/pdbfixer.py pdbfixer-1.8.1/pdbfixer/pdbfixer.py ---- pdbfixer-1.8.1.orig/pdbfixer/pdbfixer.py 2023-03-27 17:28:53.564306000 +0200 -+++ pdbfixer-1.8.1/pdbfixer/pdbfixer.py 2023-03-27 17:42:24.093931265 +0200 -@@ -32,18 +32,18 @@ - __author__ = "Peter Eastman" - __version__ = "1.7" - --import openmm as mm --import openmm.app as app --import openmm.unit as unit --from openmm.app.internal.pdbstructure import PdbStructure --from openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader --from openmm.app.element import hydrogen, oxygen --from openmm.app.forcefield import NonbondedGenerator -+import simtk.openmm as mm -+import simtk.openmm.app as app -+import simtk.unit as unit -+from simtk.openmm.app.internal.pdbstructure import PdbStructure -+from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader -+from simtk.openmm.app.element import hydrogen, oxygen -+from simtk.openmm.app.forcefield import NonbondedGenerator - - # Support Cythonized functions in OpenMM 7.3 - # and also implementations in older versions. - try: -- from openmm.app.internal import compiled -+ from simtk.openmm.app.internal import compiled - matchResidue = compiled.matchResidueToTemplate - except ImportError: - matchResidue = app.forcefield._matchResidue -diff -Nru pdbfixer-1.8.1.orig/pdbfixer/ui.py pdbfixer-1.8.1/pdbfixer/ui.py ---- pdbfixer-1.8.1.orig/pdbfixer/ui.py 2023-03-27 17:28:53.583267000 +0200 -+++ pdbfixer-1.8.1/pdbfixer/ui.py 2023-03-27 17:42:32.915332264 +0200 -@@ -6,9 +6,9 @@ - import sys - from math import sqrt - --import openmm.app as app --import openmm.unit as unit --from openmm.vec3 import Vec3 -+import simtk.openmm.app as app -+import simtk.unit as unit -+from simtk.openmm.vec3 import Vec3 - - from .pdbfixer import PDBFixer, proteinResidues, dnaResidues, rnaResidues, _guessFileFormat - from . import uiserver diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb deleted file mode 100644 index e1e07a395fb..00000000000 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2022a-DeepMind-patch.eb +++ /dev/null @@ -1,62 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenMM' -version = '7.5.1' -versionsuffix = '-DeepMind-patch' - -homepage = 'https://openmm.org' -description = "OpenMM is a toolkit for molecular simulation." - -toolchain = {'name': 'foss', 'version': '2022a'} -toolchainopts = {'opt': True} - -source_urls = ['https://github.com/openmm/openmm/archive/'] -sources = ['%(version)s.tar.gz'] -patches = [ - ('OpenMM-%(version)s_DeepMind.patch', 'wrappers/python'), - 'OpenMM-7.5.1_fix_Doxygen_compatibility.patch', -] -checksums = [ - 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7', - '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6', - '86664f02a1ca70e02b977102798d5e1ba333d1543914951af42706a461f1564c', -] - -builddependencies = [ - ('CMake', '3.23.1'), - ('Doxygen', '1.9.4'), -] - -dependencies = [ - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('SWIG', '4.0.2'), -] - -runtest = """test -e ARGS="-E \'(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(HippoNonbondedForce)\'" """ - -preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' -preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' - -# required to install the python API -installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' - -local_python_path = 'lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg' - -sanity_check_paths = { - 'files': [ - 'lib/libOpenMM.%s' % SHLIB_EXT, - local_python_path + '/simtk/openmm/openmm.py', - ], - 'dirs': [] -} - -sanity_check_commands = ["python -m simtk.testInstallation"] - -modextrapaths = { - 'PYTHONPATH': local_python_path, - 'OPENMM_INCLUDE_PATH': 'include', - 'OPENMM_LIB_PATH': 'lib', -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch deleted file mode 100644 index 1cf2ffa4a56..00000000000 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1_fix_Doxygen_compatibility.patch +++ /dev/null @@ -1,24 +0,0 @@ -# Fixes compatibility issue with Doxygen >= 1.9.2 -# See: https://github.com/openmm/openmm/issues/3317 and https://github.com/openmm/openmm/pull/3336 -# Author: maxim-masterov (SURF) - -diff -Nru openmm-7.5.1.orig/wrappers/generateWrappers.py openmm-7.5.1/wrappers/generateWrappers.py ---- openmm-7.5.1.orig/wrappers/generateWrappers.py 2023-03-24 11:11:39.911916000 +0100 -+++ openmm-7.5.1/wrappers/generateWrappers.py 2023-03-24 11:12:29.971967239 +0100 -@@ -82,6 +82,7 @@ - 'const std::vector >& OpenMM::NoseHooverIntegrator::getAllThermostatedPairs', - 'virtual void OpenMM::NoseHooverIntegrator::stateChanged' - ] -+ self.skipMethods = [s.replace(' ', '') for s in self.skipMethods] - self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy'] - self.nodeByID={} - -@@ -132,7 +133,7 @@ - for section in findNodes(classNode, "sectiondef", kind="public-static-func")+findNodes(classNode, "sectiondef", kind="public-func"): - for memberNode in findNodes(section, "memberdef", kind="function", prot="public"): - methodDefinition = getText("definition", memberNode) -- if methodDefinition in self.skipMethods: -+ if methodDefinition.replace(' ', '') in self.skipMethods: - continue - methodList.append(memberNode) - return methodList From 25466dc4baf0d3b0742f33246404ec10d15e235e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 28 Mar 2023 11:56:49 +0200 Subject: [PATCH 6986/9987] Switch to OpenMM-8.0.0 --- .../AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb | 7 ++- ...=> AlphaFold-2.3.1_use_openmm_7.7.0.patch} | 0 .../o/OpenMM/OpenMM-8.0.0-foss-2022a.eb | 60 +++++++++++++++++++ 3 files changed, 64 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/a/AlphaFold/{AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch => AlphaFold-2.3.1_use_openmm_7.7.0.patch} (100%) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb index cb5cfdb2a9d..6818ca92607 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('UCX-CUDA', '1.12.1', versionsuffix), ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), ('NCCL', '2.12.12', versionsuffix), - ('OpenMM', '7.7.0'), + ('OpenMM', '8.0.0'), ] # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, @@ -60,7 +60,7 @@ components = [ 'AlphaFold-2.0.0_n-cpu.patch', 'AlphaFold-2.1.0_fix-scp-path.patch', 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', - 'AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch', + 'AlphaFold-2.3.1_use_openmm_7.7.0.patch', ], 'checksums': [ '1161b2609fa896b16399b900ec2b813e5a0b363fe4e2b26bd826953ba234736a', # v2.3.1.tar.gz @@ -70,7 +70,8 @@ components = [ 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch - 'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec', # AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch + # AlphaFold-2.3.1_use_openmm_7.7.0.patch + 'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec', ], 'start_dir': 'alphafold-%(version)s', diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_use_openmm_7.7.0.patch similarity index 100% rename from easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_switch_to_openmm_7.7.0.patch rename to easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_use_openmm_7.7.0.patch diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb new file mode 100644 index 00000000000..47d3bdbfaf5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.0.0' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SWIG', '4.0.2'), +] + +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 2109fa1f9d4008aca31d59611d7447209866fb10 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 28 Mar 2023 11:57:56 +0200 Subject: [PATCH 6987/9987] Update easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb index 36bfe330597..cb07437830e 100644 --- a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb @@ -21,4 +21,11 @@ sanity_check_paths = { 'dirs': ['share'] } +sanity_check_commands = [ + 'dumpsexp --version', + 'hmac256 --version', + 'mpicalc --version', + 'libgcrypt-config --version | grep "%(version)s"', +] + moduleclass = 'system' From ba5b2fbbf84342c96361b3e24924e019e81d0ffd Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 28 Mar 2023 11:59:27 +0100 Subject: [PATCH 6988/9987] adding easyconfigs: FHI-aims-221103-intel-2022a.eb --- .../f/FHI-aims/FHI-aims-221103-intel-2022a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/f/FHI-aims/FHI-aims-221103-intel-2022a.eb diff --git a/easybuild/easyconfigs/f/FHI-aims/FHI-aims-221103-intel-2022a.eb b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-221103-intel-2022a.eb new file mode 100644 index 00000000000..7e9bb34bb35 --- /dev/null +++ b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-221103-intel-2022a.eb @@ -0,0 +1,57 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# Updated to 210716_3 +# J. Sassmannshausen (Imperial College London/UK) +## +easyblock = 'CMakeMake' + +name = 'FHI-aims' +version = '221103' + +homepage = 'https://fhi-aims.org/' +description = """FHI-aims is an efficient, accurate all-electron, +full-potential electronic structure code package for computational molecular +and materials science (non-periodic and periodic systems). The code supports +DFT (semilocal and hybrid) and many-body perturbation theory. FHI-aims is +particularly efficient for molecular systems and nanostructures, while +maintaining high numerical accuracy for all production tasks. Production +calculations handle up to several thousand atoms and can efficiently use (ten) +thousands of cores. +""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'opt': True, 'precise': True} + +download_instructions = """ +The source code must be downloaded manually from the FHI-aims club +(https://fhi-aims.org/get-the-code-menu/login). +Access to the FHI-aims club requires a valid license and registration. +Details on available license options and how to register to access +FHI-aims club may be found at: +https://fhi-aims.org/get-the-code-menu/get-the-code """ + +sources = ['%(namelower)s.%(version)s.tgz'] +checksums = ['1905147a15968b6b719a4f5d9495a958df648d3ccee58f5012734be5d6727749'] + +builddependencies = [('CMake', '3.24.3')] + +configopts = ' -DCMAKE_Fortran_COMPILER="$MPIF90" ' +configopts += ' -DLIBS="mkl_scalapack_lp64 mkl_blacs_intelmpi_lp64 mkl_intel_lp64 mkl_sequential mkl_core" ' +configopts += ' -DLIB_PATHS="$CMAKE_LIBRARY_PATH" ' +configopts += ' -DCMAKE_C_FLAGS="$CFLAGS -ip" ' +configopts += ' -DCMAKE_Fortran_FLAGS="$FFLAGS -ip" ' +configopts += ' -DFortran_MIN_FLAGS="-O0 -fp-model precise" ' +configopts += ' -DTARGET_NAME="aims.x" ' + +postinstallcmds = ["cp -ar %(builddir)s/%(namelower)s.%(version)s/{CHANGELOG.md,doc,external} %(installdir)s/", + "cp -ar %(builddir)s/%(namelower)s.%(version)s/{regression_tests,species_defaults} %(installdir)s/", + "cp -ar %(builddir)s/%(namelower)s.%(version)s/{testcases,utilities} %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/aims.x'], + 'dirs': [], +} + +moduleclass = 'chem' From aaeb397e61933ef58652645181dca4429665f024 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 28 Mar 2023 12:12:29 +0100 Subject: [PATCH 6989/9987] adding easyconfigs: zsh-5.9.eb --- easybuild/easyconfigs/z/zsh/zsh-5.9.eb | 31 ++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/z/zsh/zsh-5.9.eb diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.9.eb b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb new file mode 100644 index 00000000000..574b12cb58d --- /dev/null +++ b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'zsh' +version = '5.9' + +homepage = 'https://www.zsh.org/' +description = "Zsh is a shell designed for interactive use, although it is also a powerful scripting language." + +toolchain = SYSTEM + +source_urls = ['https://prdownloads.sourceforge.net/%(namelower)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9b8d1ecedd5b5e81fbf1918e876752a7dd948e05c1a0dba10ab863842d45acd5'] + +osdependencies = [ + ('ncurses-devel', 'ncurses-dev'), +] + +configopts = '--with-tcsetpgrp' # needed to build in non-login shells + +modextrapaths = {'FPATH': 'share/zsh/%(version)s/functions'} + +sanity_check_paths = { + 'files': ['bin/zsh'], + 'dirs': ['lib/zsh/%(version)s', 'share'], +} + +# optionally make this module sticky (lmod only): +# modluafooter = 'add_property("lmod", "sticky")' + +moduleclass = 'tools' From 264bb2e2e6cdf18e4897137b87f0a87698f10bad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 28 Mar 2023 13:22:14 +0200 Subject: [PATCH 6990/9987] adding easyconfigs: Bismark-0.24.0-GCC-11.3.0.eb --- .../b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..29cad67bb97 --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +# Updated to 0.23.1 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'Tarball' + +name = 'Bismark' +version = '0.24.0' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = "A tool to map bisulfite converted sequence reads and determine cytosine methylation states" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/FelixKrueger/Bismark/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dd58957bd6eac44f3a6e74e9a5ef69c8d19da0e0b64feb7d019a994fe6087d7d'] + +dependencies = [ + ('Perl', '5.34.1'), + ('Bowtie2', '2.4.5'), + ('SAMtools', '1.16.1'), +] + +sanity_check_commands = ['bismark --help'] + +sanity_check_paths = { + 'files': ['bismark', 'bismark2bedGraph', 'bismark2report', 'bismark_genome_preparation', + 'bismark_methylation_extractor', 'coverage2cytosine', 'deduplicate_bismark'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From a199ed3fc968894362b6d6b0b340ef9721083071 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 28 Mar 2023 14:37:51 +0200 Subject: [PATCH 6991/9987] adding easyconfigs: Trim_Galore-0.6.10-GCCcore-11.3.0.eb --- .../Trim_Galore-0.6.10-GCCcore-11.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0779ba13c45 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# Updated to version 0.6.2: Pavel Grochal (INUITS) +# Updated to version 0.6.5: Alex Domingo (VUB) +# Updated to version 0.6.7 by J. Sassmannshausen NHS/GSTT + +easyblock = 'Tarball' + +name = 'Trim_Galore' +version = '0.6.10' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """Trim Galore! is a wrapper script to automate quality and adapter +trimming as well as quality control, with some added functionality to remove biased +methylation positions for RRBS sequence files (for directional, non-directional +(or paired-end) sequencing).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['3a4e414fc658d6eb4356f1572351204e8475a9d7dc79f6798270b57d35bda017'] + +dependencies = [ + ('Python', '3.10.4'), + ('Java', '11', '', SYSTEM), + ('pigz', '2.7'), + ('Perl', '5.34.1'), + ('cutadapt', '4.2'), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), +] + +postinstallcmds = [ + "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s", +] + +fix_perl_shebang_for = ['bin/%(namelower)s'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s', '-v')] + +moduleclass = 'bio' From 3a3162bb81152192f37effe35923b2033e8bf8e4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 28 Mar 2023 15:46:14 +0200 Subject: [PATCH 6992/9987] fix ipython/traitlets#727 in IPython v8.5.0 by upgrading to v5.2.1.post0 --- .../easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb index 57bf257cf0c..1d65c07e244 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb @@ -38,8 +38,9 @@ exts_list = [ ('prompt_toolkit', '3.0.31', { 'checksums': ['9ada952c9d1787f52ff6d5f3484d0b4df8952787c087edf6a1f7c2cb1ea88148'], }), - ('traitlets', '5.2.0', { - 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + ('traitlets', '5.2.1.post0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['f44b708d33d98b0addb40c29d148a761f44af740603a8fd0e2f8b5b27cf0f087'], }), ('parso', '0.8.3', { 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], From cbe2516915792512bbad3a1853715a7a27f7a190 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 28 Mar 2023 15:46:53 +0200 Subject: [PATCH 6993/9987] fix ipywidgets and jupyterlab_widgets in IPython v8.5.0 --- .../i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb index 1d65c07e244..138f1ab5d11 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb @@ -24,6 +24,10 @@ dependencies = [ use_pip = True +# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them +# use the versions published in a single release commit instead of blindly pushing to last available version, +# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/c5fac25d17a93faf7bea66f5d103c605a9f19ddb + exts_list = [ ('ipython_genutils', '0.2.0', { 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], @@ -127,8 +131,8 @@ exts_list = [ ('prometheus_client', '0.11.0', { 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], }), - ('ipywidgets', '7.6.3', { - 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], + ('ipywidgets', '7.7.4', { + 'checksums': ['e2cca1f95b4b8e96e5c2c6ac7cfebacafb924a473df94a243a5e68b7b23172c7'], }), ('deprecation', '2.1.0', { 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], @@ -139,8 +143,8 @@ exts_list = [ ('jupyterlab_pygments', '0.1.2', { 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], }), - ('jupyterlab_widgets', '3.0.3', { - 'checksums': ['c767181399b4ca8b647befe2d913b1260f51bf9d8ef9b7a14632d4c1a7b536bd'], + ('jupyterlab_widgets', '1.1.3', { + 'checksums': ['5285a4316e13f9a6512cb80a0cfec5aafa2c336097ae077a07a60c145f2154fc'], }), ('argon2-cffi', '20.1.0', { 'modulename': 'argon2', @@ -149,8 +153,8 @@ exts_list = [ ('notebook', '6.4.0', { 'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'], }), - ('widgetsnbextension', '3.5.1', { - 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + ('widgetsnbextension', '3.6.3', { + 'checksums': ['28cb103f3066a6fdd6fd63264dd2a9709266c351a9a5c4a50a0bfd5ae2557b46'], }), ('matplotlib-inline', '0.1.2', { 'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'], From 674b4fa2e7ace347b0c266c971a58daf611669b2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 28 Mar 2023 16:11:50 +0200 Subject: [PATCH 6994/9987] adding easyconfigs: ipympl-0.9.3-foss-2022a.eb --- .../i/ipympl/ipympl-0.9.3-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2022a.eb b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2022a.eb new file mode 100644 index 00000000000..0d3dd0f948f --- /dev/null +++ b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'ipympl' +version = '0.9.3' + +homepage = 'https://matplotlib.org/ipympl' +description = """Leveraging the Jupyter interactive widgets framework, ipympl enables the +interactive features of matplotlib in the Jupyter notebook and in JupyterLab. +Besides, the figure canvas element is a proper Jupyter interactive widget which +can be positioned in interactive widget layouts. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('Pillow', '9.1.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['d113cd55891bafe9b27ef99b6dd111a87beb6bb2ae550c404292272103be8013'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'tools' From 2a6cf60ffe014fd66d8abeffd27b21b406896e6a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Mar 2023 16:34:04 +0200 Subject: [PATCH 6995/9987] adding easyconfigs: OpenFOAM-10-foss-2022a-20230119.eb --- .../OpenFOAM-10-foss-2022a-20230119.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb new file mode 100644 index 00000000000..5205f1afc3c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb @@ -0,0 +1,39 @@ +name = 'OpenFOAM' + +version = '10' +_version_patch = '20230119' +versionsuffix = '-%s' % _version_patch + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['%s.tar.gz' % _version_patch] +patches = ['OpenFOAM-%(version_major)s-ThirdParty.patch'] +checksums = [ + {'20230119.tar.gz': '86f8cb18d4f59812b129ce7d669e8ff498da442fbdb46705492fbba3cbda82ab'}, + {'OpenFOAM-10-ThirdParty.patch': '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.1'), + ('CGAL', '4.14.3'), + ('ParaView', '5.10.1', '-mpi'), + ('gnuplot', '5.4.4'), +] + +moduleclass = 'cae' From e1affca4304fd32799393b941bace3c20d8bc83f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 28 Mar 2023 16:52:18 +0200 Subject: [PATCH 6996/9987] rename tarball on download --- .../o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb index 5205f1afc3c..f9ebf346635 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb @@ -13,10 +13,13 @@ description = """OpenFOAM is a free, open source CFD software package. toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] -sources = ['%s.tar.gz' % _version_patch] +sources = [{ + 'download_filename': '%s.tar.gz' % _version_patch, + 'filename': 'OpenFOAM-%(version)s%(versionsuffix)s.tar.gz', +}] patches = ['OpenFOAM-%(version_major)s-ThirdParty.patch'] checksums = [ - {'20230119.tar.gz': '86f8cb18d4f59812b129ce7d669e8ff498da442fbdb46705492fbba3cbda82ab'}, + {'OpenFOAM-10-20230119.tar.gz': '86f8cb18d4f59812b129ce7d669e8ff498da442fbdb46705492fbba3cbda82ab'}, {'OpenFOAM-10-ThirdParty.patch': '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43'}, ] From 96b9068ee75245e73385afe7e044a60abb1e77ab Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 28 Mar 2023 15:55:09 +0100 Subject: [PATCH 6997/9987] disable test_native_mha test that fails on broadwell --- .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb index c77bc6a7b31..ed0747fc18c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb @@ -141,6 +141,8 @@ excluded_tests = { # Those 2 abort on some machines. Skip for now 'distributed/fsdp/test_fsdp_input', 'distributed/fsdp/test_fsdp_mixed_precision', + # failing on broadwell + 'test_native_mha' ] } From c5b84219861281f6207d008ec1b7069375743c70 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Tue, 28 Mar 2023 17:03:52 +0200 Subject: [PATCH 6998/9987] Update easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb --- .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb index ed0747fc18c..9db805c8a42 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb @@ -141,6 +141,9 @@ excluded_tests = { # Those 2 abort on some machines. Skip for now 'distributed/fsdp/test_fsdp_input', 'distributed/fsdp/test_fsdp_mixed_precision', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', # failing on broadwell 'test_native_mha' ] From cac561517c2ffb6bc7b8c38e9b58e29f5c99bab3 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Tue, 28 Mar 2023 17:03:59 +0200 Subject: [PATCH 6999/9987] Update easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb --- .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb index 9db805c8a42..7d0cc431687 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb @@ -145,6 +145,7 @@ excluded_tests = { # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 'distributed/fsdp/test_fsdp_core', # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 'test_native_mha' ] } From 5c4a753fbe5356e11a00db07561d5ddb8c4e2c66 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 29 Mar 2023 13:11:46 +0200 Subject: [PATCH 7000/9987] Bug fix: Tolerance too tight in test suite. --- ...22.8.0-Test-too-strict-for-EasyBuild.patch | 53 +++++++++++++++++++ .../g/GPAW/GPAW-22.8.0-foss-2022a.eb | 11 ++-- .../g/GPAW/GPAW-22.8.0-intel-2022a.eb | 11 ++-- 3 files changed, 67 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch new file mode 100644 index 00000000000..f52f396627a --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch @@ -0,0 +1,53 @@ +From 79eb7a47726f7e0f644d0b9bddf3840b227a2f73 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Jens=20J=C3=B8rgen=20Mortensen?= +Date: Wed, 21 Sep 2022 12:10:16 +0200 +Subject: [PATCH] Test too strict for EasyBuild intel/2020b toolchain + +--- + gpaw/test/gllb/test_variants.py | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) + +diff --git a/gpaw/test/gllb/test_variants.py b/gpaw/test/gllb/test_variants.py +index 0b9ede0..8a51261 100644 +--- a/gpaw/test/gllb/test_variants.py ++++ b/gpaw/test/gllb/test_variants.py +@@ -1,8 +1,8 @@ +-import pytest + import numpy as np ++import pytest + from ase.build import bulk +-from gpaw.test import gen + from gpaw import GPAW ++from gpaw.test import gen + + + def run(xc): +@@ -19,7 +19,7 @@ def run(xc): + xc=xc, + convergence={'density': 1e-5}, + kpts={'size': (1, 1, 1), 'gamma': True}, +- txt='{}.out'.format(xc)) ++ txt=f'{xc}.out') + atoms.calc = calc + atoms.get_potential_energy() + eig_n = calc.get_eigenvalues(kpt=0) +@@ -35,7 +35,7 @@ def test_wrappers(xc, in_tmp_dir, add_cwd_to_setup_paths): + # Check values against regular xc + ref_eig_n = run({'GLLBLDA': 'LDA', 'GLLBPBE': 'PBE'}[xc]) + assert np.allclose(eig_n, ref_eig_n, rtol=0, atol=1e-8), \ +- "{} error = {}".format(xc, np.max(np.abs(eig_n - ref_eig_n))) ++ f'{xc} error = {np.max(np.abs(eig_n - ref_eig_n))}' + + + refs = {'GLLB': +@@ -70,5 +70,5 @@ refs = {'GLLB': + def test_eigenvalues(xc, in_tmp_dir, add_cwd_to_setup_paths): + eig_n = run(xc) + ref_eig_n = refs[xc] +- assert np.allclose(eig_n, ref_eig_n, rtol=0, atol=5e-6), \ +- "{} error = {}".format(xc, np.max(np.abs(eig_n - ref_eig_n))) ++ assert np.allclose(eig_n, ref_eig_n, rtol=0, atol=2e-5), \ ++ f'{xc} error = {np.max(np.abs(eig_n - ref_eig_n))}' +-- +1.8.3.1 + diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb index a5bf81c6abc..2a7e04552e6 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb @@ -16,12 +16,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), + ('GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch', 1), ] checksums = [ - '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz - # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', - '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch + {'gpaw-22.8.0.tar.gz': '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, + {'GPAW-22.8.0-Remove-MPI-compiler-hack.patch': '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e'}, + {'GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch': + '207d98ab3b390330f832a77edf5e436b9ec46610add6c0487acaa63b2aa489a1'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb index 126147e70d5..8055d042a4c 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb @@ -16,12 +16,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), + ('GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch', 1), ] checksums = [ - '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz - # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', - '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch + {'gpaw-22.8.0.tar.gz': '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, + {'GPAW-22.8.0-Remove-MPI-compiler-hack.patch': '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e'}, + {'GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch': + '207d98ab3b390330f832a77edf5e436b9ec46610add6c0487acaa63b2aa489a1'}, ] dependencies = [ From 5e6ec04391cae6a4c8d1ba0d55f0859a2f77df51 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 29 Mar 2023 13:35:10 +0200 Subject: [PATCH 7001/9987] CuPy: Add some clarifying comments about cuSPARSELt and the TestProduct test case. --- .../easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb index d194347e4cd..ddafffc0fed 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb @@ -20,6 +20,7 @@ dependencies = [ ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), ('cuTENSOR', '1.6.1.5', versionsuffix, SYSTEM), + # Adding cuSPARSELt currently makes the build fail. Keeping it around for later versions to pick up. # ('cuSPARSELt', '0.3.0.3', versionsuffix, SYSTEM), ] @@ -37,6 +38,7 @@ _skip_tests = [ 'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_', 'tests/cupy_tests/fft_tests/test_fft.py', # float16 has too low precision for these tests as they are written + # See https://github.com/easybuilders/easybuild-easyconfigs/pull/17526#issuecomment-1470843170 for details. 'tests/cupy_tests/linalg_tests/test_product.py::TestProduct', ] _ignore_list = ' --ignore='.join(_skip_tests) From d8c727eb366fffecd402d6fe707d470b24c89fd8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2023 14:42:09 +0200 Subject: [PATCH 7002/9987] move sources/checksums right below toolchain in pyparsing 3.0.9 easyconfig --- .../p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb index 0c8b7ea8098..5accb085ce1 100644 --- a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb @@ -11,6 +11,9 @@ client code uses to construct the grammar directly in Python code.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +sources = [SOURCE_TAR_GZ] +checksums = ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'] + builddependencies = [ ('binutils', '2.38'), ('pkg-config', '0.29.2'), @@ -24,7 +27,4 @@ download_dep_fail = True use_pip = True sanity_pip_check = True -sources = [SOURCE_TAR_GZ] -checksums = ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'] - moduleclass = 'data' From dca1235572804ef6c689884eb213fd0fcfb7fdb4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2023 14:47:08 +0200 Subject: [PATCH 7003/9987] remove easyconfig for Circuitscape 5.11.2, replaced with Circuitscape 5.12.3 --- .../Circuitscape-5.11.2-Julia-1.7.2.eb | 418 ------------------ 1 file changed, 418 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb deleted file mode 100644 index 54a4bb27579..00000000000 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.11.2-Julia-1.7.2.eb +++ /dev/null @@ -1,418 +0,0 @@ -easyblock = 'Bundle' - -name = 'Circuitscape' -version = '5.11.2' -_julia_ver = '1.7.2' -versionsuffix = "-Julia-%s" % _julia_ver - -homepage = 'https://github.com/Circuitscape/Circuitscape.jl' -description = "Algorithms from circuit theory to predict connectivity in heterogeneous landscapes" - -toolchain = SYSTEM - -dependencies = [ - ('Julia', _julia_ver, '-linux-%s' % ARCH, True), -] - -exts_defaultclass = 'JuliaPackage' -exts_filter = ("LD_LIBRARY_PATH="" julia -e 'using %(ext_name)s'", "") -exts_default_options = { - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], -} - - -exts_list = [ - ('Preferences', '1.3.0', { - 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], - 'checksums': ['a87c1fc863fcb6240c3f4327776fa01a1f87e0d2df5a0c1850f789ce24469da2'], - }), - ('JLLWrappers', '1.4.1', { - 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], - 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], - }), - ('IntelOpenMP_jll', '2018.0.3+2', { - 'source_urls': ['https://github.com/JuliaBinaryWrappers/IntelOpenMP_jll.jl/archive/'], - 'sources': ['IntelOpenMP-v%(version)s.tar.gz'], - 'checksums': ['4e8586f0b794ba5cf159dde99774aab4509a32555fc900140f533999db476aab'], - }), - ('MKL_jll', '2022.2.0+0', { - 'source_urls': ['https://github.com/JuliaBinaryWrappers/MKL_jll.jl/archive/'], - 'sources': ['MKL-v%(version)s.tar.gz'], - 'checksums': ['228a80c33ae71a3efc78ed9f6a3329fd20a48ad80ff7af44f0d42057e1af4241'], - }), - ('Reexport', '1.2.2', { - 'source_urls': ['https://github.com/simonster/Reexport.jl/archive/'], - 'checksums': ['2566f7776aae9697cbf15765fc32187f46dd51200abc953a0266863ad67132b3'], - }), - ('CommonSolve', '0.2.3', { - 'source_urls': ['https://github.com/SciML/CommonSolve.jl/archive/'], - 'checksums': 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['de5d244989891f47edc4f27bf8bf6557a6982e907f0874a62ad3480c9c333983'], - }), - ('ArchGDAL', '0.8.5', { - 'source_urls': ['https://github.com/yeesian/ArchGDAL.jl/archive/'], - 'checksums': ['e24ec57d88a3a07feac7db5b2501b8f06a1047c42a8eadcde9500e3601984065'], - }), - (name, version, { - 'source_urls': ['https://github.com/Circuitscape/Circuitscape.jl/archive/'], - 'checksums': ['5bdf407cd1954d342be1023e03948983331b70bf7c28d467e3aae31c0938e9d8'], - }), -] - -sanity_check_paths = { - 'files': [], - 'dirs': ['packages'], -} - -modextrapaths = { - 'JULIA_DEPOT_PATH': '', -} - -moduleclass = 'lib' From d9c502a888072cc61b3b729b22583ff23b667013 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 29 Mar 2023 16:13:23 +0200 Subject: [PATCH 7004/9987] Workaround cargo limitations, add missing vendored sources --- .../b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb index 987340268d8..2daaefe9ffe 100644 --- a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb @@ -164,9 +164,20 @@ crates = [ ('libc', '0.2.103'), ('rand_core', '0.6.3'), ('remove_dir_all', '0.5.3'), + ('redox_syscall', '0.2.10'), + ('winapi', '0.3.9'), + ('vcpkg', '0.2.15'), + ('curl-sys', '0.4.49+curl-7.79.1'), + ('openssl-sys', '0.9.67'), + ('rand_hc', '0.3.1'), + ('bitflags', '1.3.2'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('openssl-src', '111.16.0+1.1.1l'), + ('wasi', '0.10.2+wasi-snapshot-preview1'), ] source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] checksums = ['b51d32e8aee3b9ace08c54397fddb590209571f47f4051077bcb22b98ca3a5ed'] builddependencies = [ From ca8f7152a3141420772568480f277f2262f424f9 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 29 Mar 2023 17:47:12 +0100 Subject: [PATCH 7005/9987] Pandas removed --- easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb index 686bc673215..d6860c0a27e 100644 --- a/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb +++ b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb @@ -27,7 +27,6 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('scikit-learn', '1.1.2'), ('plotly.py', '5.12.0'), - ('pandas', '1.5.3'), ('matplotlib', '3.5.2'), ('HDBSCAN', '0.8.29'), ('h5py', '3.7.0'), From d9f9f658d0670c01d0add1d88e94a9f8e40d9192 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Mar 2023 18:48:26 +0200 Subject: [PATCH 7006/9987] adding easyconfigs: Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb --- ...s-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 00000000000..f8e15be6954 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Keras' +version = '2.4.3' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-2.5.0' + +homepage = 'https://keras.io/' +description = """ +Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Theano', '1.1.2', '-PyMC'), + ('PyYAML', '5.3.1'), + ('TensorFlow', local_tf_version), # provides h5py 2.1.0 +] + +use_pip = True + +exts_list = [ + ('Keras_Applications', '1.0.8', { + 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'checksums': ['fedd729b52572fb108a98e3d97e1bac10a81d3917d2103cc20ab2a5f03beb973'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From e78d64eabdb621f2d0c3997a90f98669709cd10e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 30 Mar 2023 13:08:26 +0200 Subject: [PATCH 7007/9987] adding easyconfigs: CASTEP-22.11-foss-2022a.eb --- .../c/CASTEP/CASTEP-22.11-foss-2022a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb new file mode 100644 index 00000000000..b0b068be51f --- /dev/null +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'CASTEP' +version = '22.11' + +homepage = 'http://www.castep.org' +description = """ +CASTEP is an electronic structure materials modelling code based on density +functional theory (DFT), with functionality including geometry optimization +molecular dynamics, phonons, NMR chemical shifts and much more. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# CASTEP is proprietary software, available under a free-of-charge license for academic use only. +# Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. +sources = [SOURCE_TAR_GZ] +checksums = ['aca3fc2207c677561293585a4edaf233676a759c5beb8389cf938411226ef1f5'] + +# Python+numpy are needed for the elastic constants and castepconv utilities, but +# should work with any system or eb Python including 2.7. +dependencies = [ + ('Perl', '5.34.1'), +] + +skipsteps = ['configure'] + +buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATH_LIBS="-lflexiblas" FFTLIBDIR=$FFT_LIB_DIR MATHLIBDIR=$BLAS_LIB_DIR' +buildopts += ' castep tools utilities' + +preinstallopts = 'mkdir -p %(installdir)s/bin &&' +installopts = 'COMMS_ARCH=mpi FFT=fftw3 MATH_LIBS="-lflexiblas" INSTALL_DIR="%(installdir)s/bin"' +installopts += ' install-castep install-tools install-utilities' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} + +sanity_check_commands = [ + 'castep.mpi --help', + 'optados.mpi --help', +] + +moduleclass = 'phys' From bcaca7de6e21e836e392424f2661922404e69ccc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 30 Mar 2023 14:06:34 +0200 Subject: [PATCH 7008/9987] adding easyconfigs: synthcity-0.2.4-foss-2022a.eb --- .../s/synthcity/synthcity-0.2.4-foss-2022a.eb | 165 ++++++++++++++++++ 1 file changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb new file mode 100644 index 00000000000..105a197046b --- /dev/null +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb @@ -0,0 +1,165 @@ +easyblock = 'PythonBundle' + +name = 'synthcity' +version = '0.2.4' + +homepage = 'https://github.com/vanderschaarlab/synthcity' +description = """A library for generating and evaluating synthetic tabular data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('lifelines', '0.27.4'), + ('SciPy-bundle', '2022.05'), + ('pydantic', '1.10.4'), + ('Redis', '7.0.8'), + ('scikit-learn', '1.1.2'), + ('SHAP', '0.41.0'), + ('PyTorch', '1.12.0'), + ('XGBoost', '1.7.2'), + ('tqdm', '4.64.0'), + ('Mako', '1.2.0'), + ('PyYAML', '6.0'), + ('fastai', '2.7.10'), + ('h5py', '3.7.0'), + ('networkx', '2.8.4'), + ('protobuf', '3.19.4'), + ('Arrow', '8.0.0'), + ('pybind11', '2.9.2'), + ('PyTorch-Lightning', '1.8.4'), + ('spaCy', '3.4.4'), + ('tensorboard', '2.10.0'), + ('torchvision', '0.13.1'), + ('Brotli-python', '1.0.9'), + ('statsmodels', '0.13.1'), + ('imbalanced-learn', '0.10.1'), + ('Greenlet', '2.0.2'), + ('Optuna', '3.1.0'), + ('Cython', '0.29.33'), + ('cython-blis', '0.9.1'), + ('torchtext', '0.14.1'), + ('IPython', '8.5.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('decaf_synthetic_data', '0.1.6', { + 'modulename': 'decaf', + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['dc51502f9f72b3fbdbef697238d72ae6b8457f76efc9763a747970ba543d4e0f'], + }), + ('feather-format', '0.4.1', { + 'modulename': 'feather', + 'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'], + }), + ('fflows', '0.0.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['18de7a7b98e3708ff2d5ae9f10fad625740230c4de6447906b7ca477667b78fb'], + }), + ('functorch', '0.2.0', { + 'source_urls': ['https://github.com/pytorch/%(name)s/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['ea6446b60d5e0847140e1a0dcb91d8a7de2b5844bba7c3f7560eb5020a05881f'], + }), + ('geomloss', '0.2.5', { + 'checksums': ['dcd851cc3c9625f384d4c18d235a790821162c34a2be503a61966b355b98456e'], + }), + ('inflate64', '0.3.1', { + 'checksums': ['b52dd8fefd2ba179e5dfa18d6eca7e2fc822584616271c039d5ef1f9ca90c71c'], + }), + ('keopscore', '2.1.1', { + 'checksums': ['07b4d254a28a9d4a43153663856677263dd7112912efacbad83c2a76ea0836f0'], + }), + ('loguru', '0.6.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['4e2414d534a2ab57573365b3e6d0234dfb1d84b68b7f3b948e6fb743860a77c3'], + }), + ('monai', '1.1.0', { + 'source_urls': ['https://github.com/Project-MONAI/MONAI/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['7e4129b4b9b64137f45b59667a80faac0576e4e3af48023e0aef95317f36eab9'], + }), + ('multivolumefile', '0.2.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['237f4353b60af1703087cf7725755a1f6fcaeeea48421e1896940cd1c920d678'], + }), + ('nflows', '0.14', { + 'checksums': ['6299844a62f9999fcdf2d95cb2d01c091a50136bd17826e303aba646b2d11b55'], + }), + ('opacus', '1.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ef5d6f2aab56901d714ee56fd177a3627d14d820b2ec49cb8bc8a6f52c326507'], + }), + ('opt_einsum', '3.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['2455e59e3947d3c275477df7f5205b30635e266fe6dc300e3d9f9646bfcea147'], + }), + ('pgmpy', '0.1.21', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3c442320e7822892813b4eb56e048729d3bde053a707b5bb032685af6b372246'], + }), + ('py7zr', '0.20.4', { + 'checksums': ['1d01f98ea1e1f5c49940358691b2076f9a5848056426541e783de33834f59e21'], + }), + ('pybcj', '1.0.1', { + 'modulename': 'bcj', + 'checksums': ['8b682ed08caabfb7c042d4be083e28ddc692afb1deff5567111f8855071b75c3'], + }), + ('pycox', '0.2.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['9ea3c64a4a650ccf6c96cf512712de330f2d75de32122d86995c7cd37ff105d1'], + }), + ('pycryptodomex', '3.17', { + 'modulename': 'Crypto', + 'checksums': ['0af93aad8d62e810247beedef0261c148790c52f3cd33643791cc6396dd217c1'], + }), + ('pykeops', '2.1.1', { + 'checksums': ['1931823c746345ce5a5805adad6baa1add772c6fe1800375f7f9a3ddb38b6f71'], + }), + ('pyppmd', '1.0.0', { + 'checksums': ['075c9bd297e3b0a87dd7aeabca7fee668218acbe69ecc1c6511064558de8840f'], + }), + ('pyts', '0.12.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['acd66b0cf1fd17d9ce6449335f5da30701f65fdee185d4b918726b62ca6af79d'], + }), + ('pyzstd', '0.15.4', { + 'checksums': ['de07ac54f57642f186732075cdce2be3d4a30228c3b17a6d8c6053765dc6eec8'], + }), + ('texttable', '1.6.7', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['b7b68139aa8a6339d2c320ca8b1dc42d13a7831a346b446cb9eb385f0c76310c'], + }), + ('thinc', '8.1.9', { + 'checksums': ['8a1e65529c6d0796271d2a7e5ca6ea013fcb7dad69ec609d5093a25808107f51'], + # we are using blis 0.9.1 + # thinc has problems with blis>0.8.0 on Windows only (https://github.com/explosion/thinc/pull/772) + 'preinstallopts': 'sed -i "s/blis>=0.7.8,<0.8.0/blis>=0.7.8/g" setup.cfg && ', + }), + ('torchtuples', '0.2.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['186625230a149cc09f64116d51b203ffefe78160f5a0445adad195893663f55b'], + }), + ('tsai', '0.3.5', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['f5b888f7b968d1826a74eab3b8fa9559c6985d8532c017a4d85809e6c8e6cadd'], + }), + ('xgbse', '0.2.3', { + 'source_urls': ['https://github.com/loft-br/xgboost-survival-embeddings/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['9e6b71539b2b533c00eddfe7681cdd541f393d9573594eca358d263b141c127d'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['424448d420331743458bf63558a06a5fbefbad19392718cd0a755d4a4878476c'], + }), +] + +sanity_check_commands = [ + "python -c 'from synthcity.plugins import Plugins'", +] + +moduleclass = 'lib' From a9b93e699dac74a35b73ccfec697db0b67979737 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 30 Mar 2023 16:50:23 +0200 Subject: [PATCH 7009/9987] adding easyconfigs: Shapely-2.0.1-foss-2022b.eb --- .../s/Shapely/Shapely-2.0.1-foss-2022b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2022b.eb new file mode 100644 index 00000000000..ab2fa48ba51 --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2022b.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '2.0.1' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['66a6b1a3e72ece97fc85536a281476f9b7794de2e646ca8a4517e2e3c1446893'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('GEOS', '3.11.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From 02506a99953aa5de650be4ae3e45d200fcf84e83 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 30 Mar 2023 17:21:48 +0200 Subject: [PATCH 7010/9987] dep fixes --- .../s/synthcity/synthcity-0.2.4-foss-2022a.eb | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb index 105a197046b..2d2a1ab0f5d 100644 --- a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb @@ -3,6 +3,8 @@ easyblock = 'PythonBundle' name = 'synthcity' version = '0.2.4' +local_pytorch_version = '1.12.0' + homepage = 'https://github.com/vanderschaarlab/synthcity' description = """A library for generating and evaluating synthetic tabular data.""" @@ -16,7 +18,7 @@ dependencies = [ ('Redis', '7.0.8'), ('scikit-learn', '1.1.2'), ('SHAP', '0.41.0'), - ('PyTorch', '1.12.0'), + ('PyTorch', local_pytorch_version), ('XGBoost', '1.7.2'), ('tqdm', '4.64.0'), ('Mako', '1.2.0'), @@ -38,8 +40,9 @@ dependencies = [ ('Optuna', '3.1.0'), ('Cython', '0.29.33'), ('cython-blis', '0.9.1'), - ('torchtext', '0.14.1'), + ('torchtext', '0.14.1', '-PyTorch-%s' % local_pytorch_version), ('IPython', '8.5.0'), + ('MONAI', '1.0.1'), ] sanity_pip_check = True @@ -59,6 +62,10 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['18de7a7b98e3708ff2d5ae9f10fad625740230c4de6447906b7ca477667b78fb'], }), + ('fsspec', '2022.7.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['36c5a8e7c4fc20cf32ef6934ac0a122accc8a593ddc8478d30c3ca4dbbd95500'], + }), ('functorch', '0.2.0', { 'source_urls': ['https://github.com/pytorch/%(name)s/archive/'], 'sources': ['v%(version)s.tar.gz'], @@ -77,11 +84,6 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['4e2414d534a2ab57573365b3e6d0234dfb1d84b68b7f3b948e6fb743860a77c3'], }), - ('monai', '1.1.0', { - 'source_urls': ['https://github.com/Project-MONAI/MONAI/archive/'], - 'sources': ['%(version)s.tar.gz'], - 'checksums': ['7e4129b4b9b64137f45b59667a80faac0576e4e3af48023e0aef95317f36eab9'], - }), ('multivolumefile', '0.2.3', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['237f4353b60af1703087cf7725755a1f6fcaeeea48421e1896940cd1c920d678'], From 061645335841ac733a5f7e1555b7bff5cc94fe2d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 30 Mar 2023 17:49:01 +0200 Subject: [PATCH 7011/9987] use download_instructions --- easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb index b0b068be51f..8e3491edd65 100644 --- a/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb @@ -12,8 +12,9 @@ molecular dynamics, phonons, NMR chemical shifts and much more. toolchain = {'name': 'foss', 'version': '2022a'} -# CASTEP is proprietary software, available under a free-of-charge license for academic use only. -# Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license. +download_instructions = """CASTEP is proprietary software, available under a free-of-charge license for academic use +only. Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license.""" + sources = [SOURCE_TAR_GZ] checksums = ['aca3fc2207c677561293585a4edaf233676a759c5beb8389cf938411226ef1f5'] From 7e21a9cde3514acd5986acf9e5dd6cc34991b7c7 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 30 Mar 2023 17:54:47 +0200 Subject: [PATCH 7012/9987] adding easyconfigs: SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb, PETSc-3.18.4-intel-2021b.eb, SLEPc-3.18.2-intel-2021b.eb --- .../p/PETSc/PETSc-3.18.4-intel-2021b.eb | 43 +++++++++++++++++++ .../s/SLEPc/SLEPc-3.18.2-intel-2021b.eb | 20 +++++++++ ...iteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb | 31 +++++++++++++ 3 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb create mode 100644 easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb new file mode 100644 index 00000000000..d42525d3bec --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb @@ -0,0 +1,43 @@ +name = 'PETSc' +version = '3.18.4' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] + +builddependencies = [('CMake', '3.22.1')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.2'), + ('MUMPS', '5.4.1', '-metis'), + ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('Hypre', '2.24.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb new file mode 100644 index 00000000000..b901d4273a3 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb @@ -0,0 +1,20 @@ +name = 'SLEPc' +version = '3.18.2' + +homepage = 'https://www.grycap.upv.es/slepc/' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://slepc.upv.es/download/distrib'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('PETSc', '3.18.4')] + +petsc_arch = 'installed-arch-linux2-c-opt' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb new file mode 100644 index 00000000000..77da446bc74 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb @@ -0,0 +1,31 @@ +name = 'SuiteSparse' +version = '5.8.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] + + +builddependencies = [ + ('CMake', '3.21.1'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " +# remove broken symlink +# prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && " + +moduleclass = 'numlib' From f848d4f8ab1a311a47dd52e0628aeee50b89cebe Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 30 Mar 2023 17:59:28 +0200 Subject: [PATCH 7013/9987] Added checksums --- easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb | 4 ++++ easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb | 1 + .../SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb | 2 +- 3 files changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb index d42525d3bec..c98e36180d7 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb @@ -16,6 +16,10 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ 'PETSc_ranlib-fix.patch', ] +checksums = [ + {'petsc-3.18.4.tar.gz': '6173d30637261c5b740c0bea14747759200ca2012c7343139f9216bc296a6394'}, + {'PETSc_ranlib-fix.patch': '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297'}, +] builddependencies = [('CMake', '3.22.1')] diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb index b901d4273a3..1db8a8efa48 100644 --- a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb @@ -12,6 +12,7 @@ toolchainopts = {'usempi': True, 'openmp': True} source_urls = ['https://slepc.upv.es/download/distrib'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['5bd90a755934e702ab1fdb3320b9fe75ab5fc28c93d364248ea86a372fbe6a62'] dependencies = [('PETSc', '3.18.4')] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb index 77da446bc74..d0ac5441697 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb @@ -11,7 +11,7 @@ toolchainopts = {'unroll': True, 'pic': True} source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] sources = ['v%(version)s.tar.gz'] - +checksums = ['06726e471fbaa55f792578f9b4ab282ea9d008cf39ddcc3b42b73400acddef40'] builddependencies = [ ('CMake', '3.21.1'), From 92e0a53623de7b15fbd5d15ec0c32df3fa0baa8d Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Thu, 30 Mar 2023 18:18:03 +0200 Subject: [PATCH 7014/9987] Create Python-bundle-3.10.4-foss-2022a.eb --- .../Python-bundle-3.10.4-foss-2022a.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb new file mode 100644 index 00000000000..5b48c384f20 --- /dev/null +++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb @@ -0,0 +1,19 @@ +easyblock = 'Bundle' + +name = 'Python-bundle' +version = '3.10.4' + +homepage = 'https://easybuild.io/' +description = """Python distribution with a number of widely used extensions incl. NumPy, SciPy, Matplotlib, JupyterLab, MPI4PY, ... """ + +local_gccver = '11.3.0' + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', version), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('JupyterLab', '3.5.0', '', ('GCCcore', local_gccver)), +] \ No newline at end of file From 203a2789fa04065ffb405094fc3bbe6ebaa67ba2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 30 Mar 2023 18:53:23 +0200 Subject: [PATCH 7015/9987] adding easyconfigs: rioxarray-0.14.0-foss-2022a.eb --- .../rioxarray/rioxarray-0.14.0-foss-2022a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/r/rioxarray/rioxarray-0.14.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/rioxarray/rioxarray-0.14.0-foss-2022a.eb b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.14.0-foss-2022a.eb new file mode 100644 index 00000000000..57c9a4816f3 --- /dev/null +++ b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.14.0-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'rioxarray' +version = '0.14.0' + +homepage = 'https://github.com/corteva/rioxarray' +description = "geospatial xarray extension powered by rasterio" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('rasterio', '1.3.4'), + ('pyproj', '3.4.0'), + ('xarray', '2022.6.0'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['bbbda47fd7eb04c0986df553f11aa0bdbc9846e75601b8ebd704fc8573bfb835'] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'geo' From d9bbf999acc97d099ff622455e7a341fac50a59f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 30 Mar 2023 19:37:13 +0100 Subject: [PATCH 7016/9987] Add alternative checksum for MONAI 1.0.1 --- .../easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb | 3 ++- easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb index c4ae75df709..134fe42c205 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb @@ -32,7 +32,8 @@ exts_list = [ 'preinstallopts': 'BUILD_MONAI=1', 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], - 'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'], + 'checksums': [('dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b', + 'bb1a84ea3c4cd2c3756f72359a891843e0efa02da17537fb158b28c4e0b2d243')], }), ] diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb index 0314fc871d4..04560e4c6fd 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb @@ -30,7 +30,8 @@ exts_list = [ 'preinstallopts': 'BUILD_MONAI=1', 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], - 'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'], + 'checksums': [('dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b', + 'bb1a84ea3c4cd2c3756f72359a891843e0efa02da17537fb158b28c4e0b2d243')], }), ] From 798e5ffeb458399c633cddcbcb13d87cb9c0c36d Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Thu, 30 Mar 2023 21:01:21 +0200 Subject: [PATCH 7017/9987] Updated Python-bundle-3.10.4-foss-2022a.eb for style check --- .../p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb index 5b48c384f20..5df3fd8caf7 100644 --- a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb +++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb @@ -4,7 +4,8 @@ name = 'Python-bundle' version = '3.10.4' homepage = 'https://easybuild.io/' -description = """Python distribution with a number of widely used extensions incl. NumPy, SciPy, Matplotlib, JupyterLab, MPI4PY, ... """ +description = """Python distribution with a number of widely used +extensions incl. NumPy, SciPy, Matplotlib, JupyterLab, MPI4PY, ... """ local_gccver = '11.3.0' @@ -16,4 +17,4 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('matplotlib', '3.5.2'), ('JupyterLab', '3.5.0', '', ('GCCcore', local_gccver)), -] \ No newline at end of file +] From c355ed5ca0c85585582054834a05fa8c1347eda4 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 30 Mar 2023 21:50:57 +0200 Subject: [PATCH 7018/9987] Changed version of SuiteSparse --- .../p/PETSc/PETSc-3.18.4-intel-2021b.eb | 2 +- ...teSparse-5.10.1-intel-2021b-METIS-5.1.0.eb | 31 +++++++++++++++++++ 2 files changed, 32 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb index c98e36180d7..37ddfc1c7fc 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb @@ -30,7 +30,7 @@ dependencies = [ ('METIS', '5.1.0'), ('SCOTCH', '6.1.2'), ('MUMPS', '5.4.1', '-metis'), - ('SuiteSparse', '5.8.1', '-METIS-5.1.0'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), ('Hypre', '2.24.0'), ] diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb new file mode 100644 index 00000000000..4da9cfeafa6 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb @@ -0,0 +1,31 @@ +name = 'SuiteSparse' +version = '5.10.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +parallel = 1 +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " +# remove broken symlink +# prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && " + +moduleclass = 'numlib' From 0d4b9463d995f8e29f13a421615ea51004f3cfe9 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 30 Mar 2023 21:54:29 +0200 Subject: [PATCH 7019/9987] Forgot to add new checksum to SuiteSparse --- .../s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb index 4da9cfeafa6..1f3df90eb02 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb @@ -11,6 +11,7 @@ toolchainopts = {'unroll': True, 'pic': True} source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] sources = ['v%(version)s.tar.gz'] +checksums = ['acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee'] builddependencies = [ ('CMake', '3.21.1'), From 6a0864d3d84fa3c4134268b0d5ca6581017529db Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 31 Mar 2023 09:32:17 +0200 Subject: [PATCH 7020/9987] Added a custom sanity check path --- .../p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) create mode 120000 easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb new file mode 120000 index 00000000000..c2b7af435fc --- /dev/null +++ b/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb @@ -0,0 +1 @@ +joachim@ip34-194.eduroam-employee.wireless.lu.se.475 \ No newline at end of file From 712008ec065bc85508e24cd9e162932a2a279286 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 31 Mar 2023 09:41:58 +0200 Subject: [PATCH 7021/9987] Removed an emacs back-up file that upset the test procedures --- .../p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb | 1 - .../p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb | 5 +++++ 2 files changed, 5 insertions(+), 1 deletion(-) delete mode 120000 easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb deleted file mode 120000 index c2b7af435fc..00000000000 --- a/easybuild/easyconfigs/p/Python-bundle/.#Python-bundle-3.10.4-foss-2022a.eb +++ /dev/null @@ -1 +0,0 @@ -joachim@ip34-194.eduroam-employee.wireless.lu.se.475 \ No newline at end of file diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb index 5df3fd8caf7..993738b8cf7 100644 --- a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb +++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb @@ -18,3 +18,8 @@ dependencies = [ ('matplotlib', '3.5.2'), ('JupyterLab', '3.5.0', '', ('GCCcore', local_gccver)), ] + +sanity_check_paths = { + 'files': [], + 'dirs': ["easybuild/"], +} \ No newline at end of file From af822aee34dc6f449df5ecdb99785e8e3a29d697 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 31 Mar 2023 10:02:06 +0200 Subject: [PATCH 7022/9987] Fixing failed style check --- .../p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb index 993738b8cf7..8666c0f0dc9 100644 --- a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb +++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb @@ -22,4 +22,4 @@ dependencies = [ sanity_check_paths = { 'files': [], 'dirs': ["easybuild/"], -} \ No newline at end of file +} From 0cdcf232dbc438a33323133e7bb365a25377f90a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 31 Mar 2023 10:12:05 +0200 Subject: [PATCH 7023/9987] fix paths to perl modules in MAKER v3.01.04 --- easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb index 6a6d50726d5..fc933ad206d 100644 --- a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb @@ -29,7 +29,7 @@ dependencies = [ exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") -_libdir = 'lib/perl5/site_perl/%(perlver)s/' +_libdir = 'lib/perl5/site_perl/%(perlver)s' exts_list = [ ('Acme::Damn', '0.08', { @@ -74,9 +74,10 @@ exts_list = [ }), (name, version, { 'modulename': False, + 'preinstallopts': "find ../ -type f -exec sed -i 's|RealBin/\.\./lib|RealBin/../%s|g' {} \; && " % _libdir, 'postinstallcmds': [ 'cp -a ../bin %(installdir)s/', - 'cp -an blib/lib/* ../lib/* %%(installdir)s/%s' % _libdir, + 'cp -an blib/lib/* ../lib/* %%(installdir)s/%s/' % _libdir, ], 'source_tmpl': 'Version_%(version)s.tar.gz', 'source_urls': ['https://github.com/Yandell-Lab/maker/archive/refs/tags/'], From 287cd7e4b25b861c633f6eef95080d09cd58c24d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 31 Mar 2023 10:25:47 +0200 Subject: [PATCH 7024/9987] add comment explaining preinstallopts in MAKER v3.01.04 --- easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb index fc933ad206d..d7f56a73111 100644 --- a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb @@ -74,7 +74,8 @@ exts_list = [ }), (name, version, { 'modulename': False, - 'preinstallopts': "find ../ -type f -exec sed -i 's|RealBin/\.\./lib|RealBin/../%s|g' {} \; && " % _libdir, + # fix hardcoded paths to libraries + 'preinstallopts': r"find ../ -type f -exec sed -i 's|RealBin/\.\./lib|RealBin/../%s|g' {} \; && " % _libdir, 'postinstallcmds': [ 'cp -a ../bin %(installdir)s/', 'cp -an blib/lib/* ../lib/* %%(installdir)s/%s/' % _libdir, From dff744b196992283ec18a7d5851e675cba806b79 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 31 Mar 2023 10:36:19 +0200 Subject: [PATCH 7025/9987] fix incorrect ids in BRAKER v2.1.6 --- .../b/BRAKER/BRAKER-2.1.6-foss-2022a.eb | 8 +++- .../BRAKER-2.1.6_fix-incorrect-ids.patch | 44 +++++++++++++++++++ 2 files changed, 51 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb index 1e4df1d9635..f6a9bc03101 100644 --- a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://github.com/Gaius-Augustus/BRAKER/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06'] +patches = ['BRAKER-%(version)s_fix-incorrect-ids.patch'] +checksums = [ + {'v2.1.6.tar.gz': 'eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06'}, + {'BRAKER-2.1.6_fix-incorrect-ids.patch': '2b219de070d109637a2660a456a1f9ced48c58197385e3b3924ae90c84b41d41'}, +] dependencies = [ ('Perl', '5.34.1'), @@ -25,6 +29,8 @@ dependencies = [ ('Exonerate', '2.4.0'), ('BLAST+', '2.13.0'), ('Biopython', '1.79'), + ('DIAMOND', '2.1.0'), + ('CDBtools', '0.99'), ] fix_perl_shebang_for = ['scripts/*.pl'] diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch new file mode 100644 index 00000000000..3c9df7a402d --- /dev/null +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch @@ -0,0 +1,44 @@ +From f38630c1cad3e11b525f84d517c7949cb4c2d7eb Mon Sep 17 00:00:00 2001 +From: Katharina Hoff +Date: Mon, 19 Apr 2021 16:34:57 +0200 +Subject: [PATCH] fixing part of the issue + https://github.com/Gaius-Augustus/BRAKER/issues/354 where gene and transcript + line have incorrect ids + +--- + scripts/merge_transcript_sets.pl | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/scripts/merge_transcript_sets.pl b/scripts/merge_transcript_sets.pl +index 04f6c3e..5cfd6c0 100755 +--- a/scripts/merge_transcript_sets.pl ++++ b/scripts/merge_transcript_sets.pl +@@ -83,14 +83,15 @@ + my $txid; + if($line =~ m/transcript_id/){ + $line =~ m/transcript_id "([^"]+)";/; ++ + $txid = $1; + push(@{$txid_to_elements{$txid}}, $line); + foreach(@store_for_txid){ +- push(@{$txid_to_elements{$txid}}, $_) ++ push(@{$txid_to_elements{$txid}}, $_); + } + @store_for_txid = (); + }else{ +- $line =~ s/\t([\t]+)$/\tfile_${file_counter}_$1/; ++ $line =~ s/\t([^\t]+)$/\tfile_${file_counter}_$1/; + push(@store_for_txid, $line); + } + # currently, UTR features are ignored +@@ -111,9 +112,8 @@ + # always keep the first occuring transcript structure, only add from other gene sets if it has not been in the set, yet + # this might discard alternative UTR splicing isoforms at present + while (my ($key, $value) = each (%txid_to_struct_local)){ +- #print "key is $key and value is $value\n"; ++ print "key is $key and value is $value\n"; + if(not(defined($uniq_struct_to_txid{$value}))){ +- #print "adding transcript\n"; + $uniq_struct_to_txid{$value} = $key; + } + } From 91fd26887ee40d8265f4eee9101d58c292770216 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 31 Mar 2023 10:37:55 +0200 Subject: [PATCH 7026/9987] adding easyconfigs: CDBtools-0.99-GCC-11.3.0.eb --- .../c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb new file mode 100644 index 00000000000..d2dca1af47d --- /dev/null +++ b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'CDBtools' +version = '0.99' + +homepage = 'http://compbio.dfci.harvard.edu/tgi' +description = "CDB (Constant DataBase) indexing and retrieval tools for FASTA files" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta'] +sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c'] + +buildopts = 'CC="$CXX" DBGFLAGS="$CXXFLAGS"' + +files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cdbfasta', 'bin/cdbyank'], + 'dirs': [], +} + +sanity_check_commands = [ + "cdbfasta -v", + "cdbyank -v", +] + +moduleclass = 'bio' From 8f9c3c9a06be44b48e8b69f90e723bb146800cf9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 31 Mar 2023 10:41:58 +0200 Subject: [PATCH 7027/9987] remove trailing space in MAKER v3.01.04 --- easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb index d7f56a73111..4b61ca4d1d3 100644 --- a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb @@ -78,7 +78,7 @@ exts_list = [ 'preinstallopts': r"find ../ -type f -exec sed -i 's|RealBin/\.\./lib|RealBin/../%s|g' {} \; && " % _libdir, 'postinstallcmds': [ 'cp -a ../bin %(installdir)s/', - 'cp -an blib/lib/* ../lib/* %%(installdir)s/%s/' % _libdir, + 'cp -an blib/lib/* ../lib/* %%(installdir)s/%s/' % _libdir, ], 'source_tmpl': 'Version_%(version)s.tar.gz', 'source_urls': ['https://github.com/Yandell-Lab/maker/archive/refs/tags/'], From f5b9bca9bd64b3b009b51a032c20c62ce6af460c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Fri, 31 Mar 2023 13:00:41 +0200 Subject: [PATCH 7028/9987] Switched back to static build with scotch.py easyblock --- .../s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb | 31 ------------------- 1 file changed, 31 deletions(-) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb index ea8d3bc0412..8ec1b3c9140 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb @@ -1,5 +1,3 @@ -easyblock = 'CMakeMake' - name = 'SCOTCH' version = '7.0.3' @@ -15,7 +13,6 @@ sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['5b5351f0ffd6fcae9ae7eafeccaa5a25602845b9ffd1afb104db932dd4d4f3c5'] builddependencies = [ - ('CMake', '3.24.3'), ('Bison', '3.8.2'), ('flex', '2.6.4'), ] @@ -24,32 +21,4 @@ dependencies = [ ('zlib', '1.2.12'), ] -configopts = '-DBUILD_SHARED_LIBS=ON ' -configopts += '-DINSTALL_METIS_HEADERS=OFF ' - -runtest = 'test' - -local_scotch_exec = ['acpl', 'amk_ccc', 'amk_fft2', 'amk_grf', 'amk_hy', - 'amk_m2', 'amk_p2', 'atst', 'dggath', 'dgmap', 'dgord', - 'dgscat', 'dgtst', 'gbase', 'gcv', 'gmap', 'gmk_hy', - 'gmk_m2', 'gmk_m3', 'gmk_msh', 'gmk_ub2', 'gmtst', - 'gord', 'gotst', 'gscat', 'gtst', 'mcv', 'mmk_m2', - 'mmk_m3', 'mord', 'mtst'] - -local_scotch_headers = ['esmumps', 'ptscotchf', - 'ptscotch', 'scotchf', 'scotch'] - -local_scotch_libs = ['esmumps', 'ptesmumps', 'ptscotcherrexit', - 'ptscotcherr', 'ptscotchparmetisv3', 'ptscotch', - 'scotcherrexit', 'scotcherr', 'scotchmetisv3', - 'scotchmetisv5', 'scotch'] - - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_scotch_exec] + - ['include/%s.h' % i for i in local_scotch_headers] + - ['lib/lib%s.%s' % (l, SHLIB_EXT) for l in local_scotch_libs], - 'dirs': ['lib/cmake'], -} - moduleclass = 'math' From bde92ba51c9cf4f3fbab7979a2e4b9e2534beea1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Fri, 31 Mar 2023 16:40:29 +0200 Subject: [PATCH 7029/9987] Added threadedmpi = False option --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb index 8ec1b3c9140..ecf1d13d647 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2022b.eb @@ -11,6 +11,7 @@ toolchainopts = {'pic': True} source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['5b5351f0ffd6fcae9ae7eafeccaa5a25602845b9ffd1afb104db932dd4d4f3c5'] +threadedmpi = False builddependencies = [ ('Bison', '3.8.2'), From 4f1e6593cc2482dd561e656456838c52d6e2af6a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2023 09:42:04 +0200 Subject: [PATCH 7030/9987] adding easyconfigs: LoRDEC-0.9-gompi-2022a.eb, GATB-Core-1.4.2-gompi-2022a.eb and patches: LoRDEC-0.9_GATB.patch, LoRDEC-0.9_GraphVector.patch, GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch --- .../GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb | 40 +++ ...-Core-1.4.2_no-thirdparty-boost-hdf5.patch | 232 ++++++++++++++++++ .../l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb | 45 ++++ .../l/LoRDEC/LoRDEC-0.9_GATB.patch | 13 + .../l/LoRDEC/LoRDEC-0.9_GraphVector.patch | 73 ++++++ 5 files changed, 403 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch create mode 100644 easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch create mode 100644 easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch diff --git a/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb new file mode 100644 index 00000000000..2d4407c3699 --- /dev/null +++ b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'GATB-Core' +version = '1.4.2' + +homepage = 'https://gatb.inria.fr/software/gatb-core' +description = """GATB-Core is a high-performance and low memory footprint C++ library that provides a set of highly + efficient algorithms to analyse NGS data sets""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/GATB/gatb-core/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch'] +checksums = [ + {'v1.4.2.tar.gz': '824c84a3712973746b977a9d49923fd499021a894225231100eaad1a66e9742d'}, + {'GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch': + '938ff686e1fc8170b8ef4a73c1c0af059eb3eb76a6251b44a3dfddf991e05c63'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('HDF5', '1.12.2'), +] + +start_dir = 'gatb-core' + +preconfigopts = "rm -r %(start_dir)s/thirdparty/{boost,hdf5} && " + +sanity_check_paths = { + 'files': ['bin/dbginfo', 'bin/leon', 'lib/libgatbcore.a'], + 'dirs': ['include/gatb'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch new file mode 100644 index 00000000000..e9e4b86b9c2 --- /dev/null +++ b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch @@ -0,0 +1,232 @@ +don't use vendored boost/hdf5 from gatb-core/thirdparty +author: Kenneth Hoste (HPC-UGent) +diff -ru gatb-core-1.4.2.orig/gatb-core/CMakeLists.txt gatb-core-1.4.2/gatb-core/CMakeLists.txt +--- gatb-core-1.4.2.orig/gatb-core/CMakeLists.txt 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/CMakeLists.txt 2023-03-31 21:25:42.862864064 +0200 +@@ -209,7 +209,7 @@ + set (gatb-core-includes ${PROJECT_BINARY_DIR}/include ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE} ${PROJECT_SOURCE_DIR}/src ${PROJECT_SOURCE_DIR}/thirdparty ${gatb-core-extra-libraries-inc}) + + # We define the libraries used for linking binary based on gatb core +-set (gatb-core-libraries gatbcore-static dl pthread z hdf5-static ${gatb-core-extra-libraries}) ++set (gatb-core-libraries gatbcore-static dl pthread z hdf5 ${gatb-core-extra-libraries}) + + # We define the directory where to find cmake helpers + set (gatb-core-cmake ${CMAKE_MODULE_PATH}) +@@ -252,12 +252,6 @@ + ADD_SUBDIRECTORY(thirdparty) + + ################################################################################ +-# DEPENDENCIES +-################################################################################ +-# we must be sure that hdf5 is built and installed before building gatb-core +-ADD_DEPENDENCIES (gatbcore-static hdf5-static hdf5_postbuild) +- +-################################################################################ + # DOCUMENTATION GENERATION + ################################################################################ + IF (EXISTS "${PROJECT_SOURCE_DIR}/doc") +@@ -286,7 +280,6 @@ + INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt DESTINATION . OPTIONAL) + INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE DESTINATION . OPTIONAL) + INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md DESTINATION . OPTIONAL) +- INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include) + ENDIF() + + ################################################################################ +--- gatb-core-1.4.2.orig/gatb-core/thirdparty/CMakeLists.txt 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/thirdparty/CMakeLists.txt 2023-03-31 14:39:11.999034862 +0200 +@@ -1,54 +1,3 @@ +-################################################################################ +-# HDF5 GENERATION +-################################################################################ +- +-#SET (HDF5_ENABLE_THREADSAFE ON) +-#SET (H5_HAVE_THREADSAFE 1) +- +-########## MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED ########## +-SET (HDF5_BUILD_TOOLS ON CACHE BOOL "Build HDF5 Tools") +-#SET (CMAKE_EXE_LINKER_FLAGS "-lpthread -lz") +- +-SET (HDF5_EXTERNALLY_CONFIGURED ON) +- +-#SET (HDF5_INSTALL_BIN_DIR ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE}) +-#SET (HDF5_INSTALL_LIB_DIR ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE}) +-SET (HDF5_INSTALL_BIN_DIR bin) +-SET (HDF5_INSTALL_LIB_DIR lib) +- +-SET (HDF5_INSTALL_INCLUDE_DIR ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5) +-SET (HDF5_INSTALL_DATA_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE}) +-SET (HDF5_INSTALL_CMAKE_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE}) +- +-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE) +- SET (HDF5_EXPORTED_TARGETS "gatb-hdf5") +-ENDIF() +- +-IF (NOT DEFINED GATB_CORE_EXCLUDE_HDF5_ZLIB) +- OPTION (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON) +-ENDIF() +- +-# We don't want warnings from HDF5 compilation +-set (COMPILE_DEFINITIONS "${COMPILE_DEFINITIONS} -w") +-add_definitions (${COMPILE_DEFINITIONS}) +- +-# add HDF5 generation +-ADD_SUBDIRECTORY (hdf5) +- +-# We add a custom target for copying header files. +-add_custom_target (hdf5_postbuild ALL) +- +-# We build the output directory +-add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR}) +- +-# We define all the header files to be copied +-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h) +- +-# We copy each header file +-foreach (header ${headerfiles}) +- add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR} ) +-endforeach() +- + # include other smaller libraries (json, Boophf) + + add_custom_target (thirdparty_copy ALL) +@@ -63,7 +12,6 @@ + # INSTALL + ################################################################################ + IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE) +- INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5 DESTINATION include) + INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/json DESTINATION include) + INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/BooPHF DESTINATION include) + ENDIF () +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/LargeInt.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/LargeInt.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/LargeInt.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/LargeInt.hpp 2023-03-31 10:40:57.005450131 +0200 +@@ -35,7 +35,7 @@ + #include + #include + #include +-#include ++#include + + #include + #include +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt128.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt128.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt128.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt128.hpp 2023-03-31 10:40:57.005450131 +0200 +@@ -33,7 +33,7 @@ + /********************************************************************************/ + + #include +-#include ++#include + + #include + #include +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt16.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt16.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt16.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt16.hpp 2023-03-31 10:40:57.005450131 +0200 +@@ -31,7 +31,7 @@ + #include + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt32.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt32.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt32.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt32.hpp 2023-03-31 10:40:57.006450171 +0200 +@@ -31,7 +31,7 @@ + #include + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt64.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt64.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt64.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt64.hpp 2023-03-31 10:40:57.006450171 +0200 +@@ -31,7 +31,7 @@ + #include + #include + #include +-#include ++#include + + extern const unsigned char revcomp_4NT[]; + extern const unsigned char comp_NT []; +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt8.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt8.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt8.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt8.hpp 2023-03-31 10:40:57.006450171 +0200 +@@ -31,7 +31,7 @@ + #include + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/Abundance.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/Abundance.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/Abundance.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/Abundance.hpp 2023-03-31 10:40:57.006450171 +0200 +@@ -31,7 +31,7 @@ + /********************************************************************************/ + + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp 2023-03-31 10:40:57.007450212 +0200 +@@ -28,7 +28,7 @@ + + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp 2023-03-31 10:40:57.007450212 +0200 +@@ -40,7 +40,7 @@ + #include + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp 2023-03-31 10:40:57.008450252 +0200 +@@ -40,7 +40,7 @@ + #include + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp 2023-03-31 10:40:57.008450252 +0200 +@@ -33,7 +33,7 @@ + #include + #include + #include +-#include ++#include + #include + + /********************************************************************************/ diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb new file mode 100644 index 00000000000..2d6b08e5a0e --- /dev/null +++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'LoRDEC' +version = '0.9' + +homepage = 'https://www.lirmm.fr/~rivals/lordec' +description = """Program for correcting sequencing errors in long reads (e.g., PacBio, Oxford Nanopore) using highly +accurate short reads (e.g., Illumina).""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://gite.lirmm.fr/lordec/lordec-releases/uploads/800a96d81b3348e368a0ff3a260a88e1/'] +sources = ['lordec-src_%(version)s.tar.bz2'] +patches = [ + 'LoRDEC-0.9_GATB.patch', + 'LoRDEC-0.9_GraphVector.patch', +] +checksums = [ + {'lordec-src_0.9.tar.bz2': '8108b82a8404fbf44c7e300d3abb43358ccc28993f90546168a20ca82536923b'}, + {'LoRDEC-0.9_GATB.patch': '8ff5e097455bb6ea515423bc76059f64d1983eb4873e640cd5021f00be85ca99'}, + {'LoRDEC-0.9_GraphVector.patch': 'f7ccef2e3149ac5017eebbb9536651a5da5ad51d5021c20f16ab1acd6daa9db0'}, +] + +local_gatb_version = '1.4.2' +dependencies = [ + ('Boost', '1.79.0'), + ('GATB-Core', local_gatb_version), +] + +build_cmd_targets = 'lordec_%s' % ''.join(local_gatb_version.split('.')) + +buildopts = "AUTOMATIC_LIBBOOST_LOCAL_INSTALL=no GATB=${EBROOTGATBMINCORE}" + +local_bins = ['lordec-%s' % x for x in ('build-SR-graph', 'correct', 'stat', 'trim', 'trim-split')] + +files_to_copy = [(local_bins, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +sanity_check_commands = ["%s --help 2>&1 | grep 'using GATB v%s'" % (x, local_gatb_version) for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch new file mode 100644 index 00000000000..11304be190c --- /dev/null +++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch @@ -0,0 +1,13 @@ +don't hardcode path to include/gatb/gatb_core.hpp so we can use GATB-Core provided as dependency +author: Kenneth Hoste (HPC-UGent) +--- lordec-src_0.9/Makefile.orig 2023-03-31 09:54:40.838204432 +0200 ++++ lordec-src_0.9/Makefile 2023-03-31 09:55:42.987061551 +0200 +@@ -63,7 +63,7 @@ + $(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): boost_include/boost/graph/graph_traits.hpp + endif + # ANYWAY we need GATB (compiled and installed) to compile all the objects +-$(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): gatb_v$(GATBVERSION)$(SUFFIX)/include/gatb/gatb_core.hpp ++$(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): $(GATB)/include/gatb/gatb_core.hpp + + # get version from a file + VERSION := $(shell cat version.txt) diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch new file mode 100644 index 00000000000..1a47343a0df --- /dev/null +++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch @@ -0,0 +1,73 @@ +diff -ru lordec-src_0.9.orig/lordec-correct.h lordec-src_0.9/lordec-correct.h +--- lordec-src_0.9.orig/lordec-correct.h 2018-06-04 15:44:49.000000000 +0200 ++++ lordec-src_0.9/lordec-correct.h 2023-03-31 22:17:39.105922332 +0200 +@@ -160,11 +160,11 @@ + // store the neighbors of begin node in the stack + + #if defined(GATB_V110) +- Graph::Vector neighbors = graph.successors(begin); ++ GraphVector neighbors = graph.successors(begin); + #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141) + GraphVector neighbors = graph.successorsEdge(begin); + #else +- Graph::Vector neighbors = graph.successorsEdge(begin); ++ GraphVector neighbors = graph.successorsEdge(begin); + #endif + + // if (neighbors.size() == 1) +@@ -221,11 +221,11 @@ + } + } + #if defined(GATB_V110) +- Graph::Vector neighbors = graph.successors(cnode); ++ GraphVector neighbors = graph.successors(cnode); + #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141) + GraphVector neighbors = graph.successorsEdge(cnode); + #else +- Graph::Vector neighbors = graph.successorsEdge(cnode); ++ GraphVector neighbors = graph.successorsEdge(cnode); + #endif + + // if (neighbors.size() == 1) +@@ -328,11 +328,11 @@ + + // store the neighbors of begin node in the stack + #if defined(GATB_V110) +- Graph::Vector neighbors = graph.successors(begin); ++ GraphVector neighbors = graph.successors(begin); + #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141) + GraphVector neighbors = graph.successorsEdge(begin); + #else +- Graph::Vector neighbors = graph.successorsEdge(begin); ++ GraphVector neighbors = graph.successorsEdge(begin); + #endif + for (i = neighbors.size()-1; i>= 0; i--) { + nodes.push(new stack_element(neighbors[i].to, 1, ascii(neighbors[i].nt))); +@@ -396,11 +396,11 @@ + else { + + #if defined(GATB_V110) +- Graph::Vector neighbors = graph.successors(cnode); ++ GraphVector neighbors = graph.successors(cnode); + #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141) + GraphVector neighbors = graph.successorsEdge(cnode); + #else +- Graph::Vector neighbors = graph.successorsEdge(cnode); ++ GraphVector neighbors = graph.successorsEdge(cnode); + #endif + for(i=neighbors.size()-1; i>=0; i--) { + Edge e = neighbors[i]; +@@ -450,11 +450,11 @@ + + while (true) { + #if defined(GATB_V110) +- Graph::Vector neighbors = graph.successors(node); ++ GraphVector neighbors = graph.successors(node); + #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141) + GraphVector neighbors = graph.successorsEdge(node); + #else +- Graph::Vector neighbors = graph.successorsEdge(node); ++ GraphVector neighbors = graph.successorsEdge(node); + #endif + if (neighbors.size() == 0) // dead end + return DEADEND; From 09c877cb4fe47f9fdeda7e7798dbd7a6b8936321 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 1 Apr 2023 09:09:43 +0100 Subject: [PATCH 7031/9987] Delete SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb --- ...iteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb deleted file mode 100644 index d0ac5441697..00000000000 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.8.1-intel-2021b-METIS-5.1.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'SuiteSparse' -version = '5.8.1' -local_metis_ver = '5.1.0' -versionsuffix = '-METIS-%s' % local_metis_ver - -homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' -description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" - -toolchain = {'name': 'intel', 'version': '2021b'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['06726e471fbaa55f792578f9b4ab282ea9d008cf39ddcc3b42b73400acddef40'] - -builddependencies = [ - ('CMake', '3.21.1'), - ('M4', '1.4.19'), -] - -dependencies = [ - ('METIS', local_metis_ver), - ('MPFR', '4.1.0'), -] - -# make sure that bin/demo can find libsuitesparseconfig.so.5 during build -prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " -# remove broken symlink -# prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && " - -moduleclass = 'numlib' From c1187aeaefd4da3e50db9adaf0b231468a9e244d Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 1 Apr 2023 09:10:11 +0100 Subject: [PATCH 7032/9987] disable optimisation report to reduce memory usage during compile --- .../SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb index 1f3df90eb02..254c739d1c6 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb @@ -26,7 +26,7 @@ dependencies = [ parallel = 1 # make sure that bin/demo can find libsuitesparseconfig.so.5 during build prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " -# remove broken symlink -# prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && " +# disable optimisation report to reduce memory use during compile +prebuildopts += 'sed -i "s/-qopt-report=5/-qopt-report=0/" GraphBLAS/CMakeLists.txt && ' moduleclass = 'numlib' From 123066044e3ef4e20ddd011bd49386dca425e1c6 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 1 Apr 2023 09:16:51 +0100 Subject: [PATCH 7033/9987] no need to restrict parallel build now --- .../s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb index 254c739d1c6..ade731aac57 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb @@ -23,7 +23,6 @@ dependencies = [ ('MPFR', '4.1.0'), ] -parallel = 1 # make sure that bin/demo can find libsuitesparseconfig.so.5 during build prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " # disable optimisation report to reduce memory use during compile From 57940d1b0f453fffd4d01f0001242a903fe49983 Mon Sep 17 00:00:00 2001 From: anselmicz Date: Sat, 1 Apr 2023 10:26:21 +0200 Subject: [PATCH 7034/9987] adding easyconfigs: nano-7.2-GCCcore-12.2.0.eb --- .../n/nano/nano-7.2-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/nano/nano-7.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/nano/nano-7.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nano/nano-7.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..99cb4947e27 --- /dev/null +++ b/easybuild/easyconfigs/n/nano/nano-7.2-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'nano' +version = '7.2' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b4edaab0a037b5760484907c674e980053896f33759e43f834a212145fd085f1'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('ncurses', '6.3')] + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' From ad9eca9f6af3738fff671eddba8e4bcdfb65e739 Mon Sep 17 00:00:00 2001 From: anselmicz Date: Sat, 1 Apr 2023 10:38:10 +0200 Subject: [PATCH 7035/9987] adding easyconfigs: fio-3.34-GCCcore-12.2.0.eb --- .../f/fio/fio-3.34-GCCcore-12.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fio/fio-3.34-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/fio/fio-3.34-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fio/fio-3.34-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0b7184963e5 --- /dev/null +++ b/easybuild/easyconfigs/f/fio/fio-3.34-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'fio' +version = '3.34' + +homepage = 'https://github.com/axboe/fio' +docurls = 'https://fio.readthedocs.io/en/latest/index.html' +description = 'Flexible I/O tester' + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'axboe' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['42ea28c78d269c4cc111b7516213f4d4b32986797a710b0ff364232cc7a3a0b7'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['bin', 'man', 'share'], +} + +sanity_check_commands = ['fio -h'] + +moduleclass = 'tools' From ae27c8ffd2a9c8ccea3b0d7e3ebd9310ec67da34 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 1 Apr 2023 10:09:13 +0100 Subject: [PATCH 7036/9987] disable mpi/python in Boost (intel-compilers/2021.4.0) --- .../b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb index f0fce1ec0af..efefe29ecc3 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb @@ -24,6 +24,8 @@ preconfigopts = "sed -i 's/-static//g' tools/build/src/engine/build.sh && " # see also https://github.com/boostorg/build/issues/647 preconfigopts += "sed -i 's/{TOOLSET}/{B2_TOOLSET}/g' tools/build/src/engine/build.sh && " +configopts = '--without-libraries=python,mpi' + # disable MPI, build Boost libraries with tagged layout boost_mpi = False tagged_layout = True From b9f663389c2a00427abc9a8e7e9f46ddea337389 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2023 11:18:56 +0200 Subject: [PATCH 7037/9987] add missing description + author to LoRDEC patch --- easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb | 2 +- easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb index 2d6b08e5a0e..9de77dd4e7b 100644 --- a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb @@ -18,7 +18,7 @@ patches = [ checksums = [ {'lordec-src_0.9.tar.bz2': '8108b82a8404fbf44c7e300d3abb43358ccc28993f90546168a20ca82536923b'}, {'LoRDEC-0.9_GATB.patch': '8ff5e097455bb6ea515423bc76059f64d1983eb4873e640cd5021f00be85ca99'}, - {'LoRDEC-0.9_GraphVector.patch': 'f7ccef2e3149ac5017eebbb9536651a5da5ad51d5021c20f16ab1acd6daa9db0'}, + {'LoRDEC-0.9_GraphVector.patch': '8c42dda643f8e1f79ee7d4ea2e3d8904cb755dc44cb907ada35b1e2873605ae5'}, ] local_gatb_version = '1.4.2' diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch index 1a47343a0df..da7be67c7df 100644 --- a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch +++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch @@ -1,3 +1,5 @@ +port LoRDEC 0.9 to gatb-core >= 1.3.0 by replacing Graph::Vector to GraphVector +author: Kenneth Hoste (HPC-UGent) diff -ru lordec-src_0.9.orig/lordec-correct.h lordec-src_0.9/lordec-correct.h --- lordec-src_0.9.orig/lordec-correct.h 2018-06-04 15:44:49.000000000 +0200 +++ lordec-src_0.9/lordec-correct.h 2023-03-31 22:17:39.105922332 +0200 From e68cd18f683f56f09e2933c96bbb1188805c4e1a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 1 Apr 2023 11:37:18 +0200 Subject: [PATCH 7038/9987] adding easyconfigs: SoPlex-2.2.1-GCC-11.3.0.eb, ZIMPL-3.3.4-GCCcore-11.3.0.eb, SCIP-3.2.1-GCC-11.3.0.eb, GOBNILP-1.6.3-GCC-11.3.0.eb and patches: GOBNILP-1.6.3_use-eb-build-env.patch, LOP-3.2.1_standalone-scip-lop-build.patch --- .../g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb | 63 +++++++++++++++ .../GOBNILP-1.6.3_use-eb-build-env.patch | 79 +++++++++++++++++++ .../LOP-3.2.1_standalone-scip-lop-build.patch | 41 ++++++++++ .../s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb | 58 ++++++++++++++ .../s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb | 38 +++++++++ .../z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb | 42 ++++++++++ 6 files changed, 321 insertions(+) create mode 100644 easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch create mode 100644 easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch create mode 100644 easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..565232387de --- /dev/null +++ b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb @@ -0,0 +1,63 @@ +easyblock = 'Bundle' + +name = 'GOBNILP' +version = '1.6.3' +_nodots_version = version.replace('.', '') +_scip_version = '3.2.1' +_scip_nodots_version = _scip_version.replace('.', '') + +homepage = 'https://www.cs.york.ac.uk/aig/sw/gobnilp/' +description = """GOBNILP (Globally Optimal Bayesian Network learning using Integer Linear +Programming) is a C program which learns Bayesian networks from complete +discrete data or from local scores.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +dependencies = [ + ('SCIP', _scip_version), + ('ZIMPL', '3.3.4'), + ('SoPlex', '2.2.1'), + ('GMP', '6.2.1'), + ('libreadline', '8.1'), + ('ncurses', '6.3'), + ('zlib', '1.2.12'), +] + +default_easyblock = 'MakeCp' + +components = [ + ('LOP', _scip_version, { + 'source_urls': ['https://github.com/scipopt/scip/archive/refs/tags/'], + 'sources': ['v%s.tar.gz' % _scip_nodots_version], + 'patches': ['LOP-%(version)s_standalone-scip-lop-build.patch'], + 'checksums': [ + {'v321.tar.gz': + '015bdda4e681782fd03b61421b93aa3c1b913e5eea18bb8730d5fb9e4d67b4cb'}, + {'LOP-3.2.1_standalone-scip-lop-build.patch': + 'f996e56f1311fa4a613635b38969da731faf0ea9f10097799b1fa9a84598651e'}, + ], + 'start_dir': 'scip-%s/examples/%%(name)s' % _scip_nodots_version, + 'buildopts': '%(namelower)s COMP=gnu OPT=opt LPS=spx2', + 'files_to_copy': [(['bin/%(namelower)s'], 'bin')], + }), + (name, version, { + 'source_urls': ['http://www.cs.york.ac.uk/aig/sw/gobnilp'], + 'sources': ['%(namelower)s%(version)s.tar.gz'], + 'patches': ['%(name)s-%(version)s_use-eb-build-env.patch'], + 'checksums': [ + {'gobnilp1.6.3.tar.gz': + 'b31e5c87032f85f7404654beca47d472fd6c5dd7a5f82108bd5043ff0b8fa33c'}, + {'GOBNILP-1.6.3_use-eb-build-env.patch': + '9235ec8b9d05d9915f9961d4b46c2220e0d3b75f555a226a5667dcc69d76dae9'}, + ], + 'start_dir': '%(namelower)s' + _nodots_version, + 'files_to_copy': [(['bin/%(namelower)s'], 'bin')], + }), +] + +sanity_check_paths = { + 'files': ['bin/gobnilp', 'bin/lop'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch new file mode 100644 index 00000000000..e730aa76abf --- /dev/null +++ b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch @@ -0,0 +1,79 @@ +Use build environment and dependencies from EasyBuild +author: Alex Domingo (Vrije Universiteit Brussel) +--- Makefile.orig 2023-03-31 18:33:07.943785000 +0200 ++++ Makefile 2023-03-31 18:42:53.636293000 +0200 +@@ -5,15 +5,25 @@ + # This file was created by editing the Makefile for the linear ordering + # example in SCIP + +-# Set the path the SCIP directory +-SCIPDIR = scip +- +-# Include default project Makefile from SCIP +-include $(SCIPDIR)/make/make.project ++# Set paths and flags to SCIP libraries ++SCIPDIR = $(EBROOTSCIP) ++SCIPLIB = scip ++OBJSCIPLIB = objscip ++LPILIB = lpispx2 ++NLPILIB = nlpi.cppad ++LPSLDFLAGS = -lzimpl -lsoplex -lgmp -lreadline -lncurses -lz ++ ++# Set paths to LOP ++LOPSRC = ../scip-321/examples/LOP/src ++LOPOBJ = ../scip-321/examples/LOP/obj/cons_linearordering.o + + # This missing for scip < 3 + VALGRIND = false + ++SRCDIR = src ++OBJDIR = obj ++BINDIR = bin ++ + # Declare the phony targets + .PHONY: all doxygen manual pedmanual gobnilp clean test + +@@ -46,7 +57,7 @@ + MAINSRC = $(wildcard $(SRCDIR)/*.c) + MAINOBJ = $(notdir $(MAINSRC:.c=.o)) + +-MAIN = $(MAINNAME).$(BASE).$(LPS)$(EXEEXTENSION) ++MAIN = $(MAINNAME) + MAINFILE = $(BINDIR)/$(MAIN) + ifeq ($(OSTYPE),mingw) + MAINSHORTLINK = $(BINDIR)/$(MAINNAME).exe +@@ -63,7 +74,7 @@ + LATEXCMD = @pdflatex -halt-on-error -interaction=errorstopmode + + #Needs to appear first so that "make" makes gobnilp +-gobnilp: $(SCIP) $(MAINFILE) $(MAINSHORTLINK) ++gobnilp: $(MAINFILE) $(MAINSHORTLINK) + + #----------------------------------------------------------------------- + #---------------------------- All ---------------------------- +@@ -161,19 +172,16 @@ + + $(MAINSHORTLINK): $(MAINFILE) + @rm -f $@ +- @cd $(dir $@) && ln -s $(notdir $(MAINFILE)) $(notdir $@) + +-$(MAINFILE): $(BINDIR) $(OBJDIR) $(SCIPLIBFILE) $(LPILIBFILE) $(NLPILIBFILE) $(MAINOBJFILES) +- @echo "-> linking $@" +- @$(LINKCXX) $(STATICFLAG) $(MAINOBJFILES) \ +- $(LINKCXX_L)$(SCIPDIR)/lib $(LINKCXX_l)$(SCIPLIB)$(LINKLIBSUFFIX) \ +- $(LINKCXX_l)$(OBJSCIPLIB)$(LINKLIBSUFFIX) $(LINKCXX_l)$(LPILIB)$(LINKLIBSUFFIX) $(LINKCXX_l)$(NLPILIB)$(LINKLIBSUFFIX) \ +- $(OFLAGS) $(LPSLDFLAGS) \ +- $(LDFLAGS) $(LINKCXX_o)$@ ++$(MAINFILE): $(BINDIR) $(OBJDIR) $(MAINOBJFILES) ++ echo "-> linking $@" ++ $(CXX) -static $(MAINOBJFILES) $(LOPOBJ) \ ++ -L$(SCIPDIR)/lib -l$(SCIPLIB) -l$(OBJSCIPLIB) -l$(LPILIB) -l$(NLPILIB) \ ++ $(LDFLAGS) $(LPSLDFLAGS) -o $@ + + $(OBJDIR)/%.o: $(SRCDIR)/%.c + @echo "-> compiling $*.c" +- @$(CC) $(FLAGS) $(OFLAGS) $(BINOFLAGS) $(CFLAGS) -c -g $< $(CC_o)$@ ++ @$(CC) $(CFLAGS) $(CPPFLAGS) -I$(LOPSRC) -c -g $< -o $@ + + $(OBJDIR): + @-mkdir -p $(OBJDIR) diff --git a/easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch b/easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch new file mode 100644 index 00000000000..9fbb54ef086 --- /dev/null +++ b/easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch @@ -0,0 +1,41 @@ +Build LOP example standalone without triggering a full build of SCIP +author: Alex Domingo (Vrije Universiteit Brussel) +--- Makefile.orig 2023-03-31 18:52:55.793723000 +0200 ++++ Makefile 2023-03-31 18:54:59.590029000 +0200 +@@ -29,6 +29,7 @@ + #----------------------------------------------------------------------------- + + include $(SCIPDIR)/make/make.project ++OBJDIR = obj + + #----------------------------------------------------------------------------- + # Main Program +@@ -39,9 +40,9 @@ + MAINSRC = $(addprefix $(SRCDIR)/,$(MAINOBJ:.o=.c)) + MAINDEP = $(SRCDIR)/depend.cmain.$(OPT) + +-MAIN = $(MAINNAME).$(BASE).$(LPS)$(EXEEXTENSION) ++MAIN = $(MAINNAME) + MAINFILE = $(BINDIR)/$(MAIN) +-MAINSHORTLINK = $(BINDIR)/$(MAINNAME) ++MAINSHORTLINK = $(MAINNAME) + MAINOBJFILES = $(addprefix $(OBJDIR)/,$(MAINOBJ)) + + #----------------------------------------------------------------------------- +@@ -79,7 +80,6 @@ + + $(MAINSHORTLINK): $(MAINFILE) + @rm -f $@ +- cd $(dir $@) && ln -s $(notdir $(MAINFILE)) $(notdir $@) + + $(OBJDIR): + @-mkdir -p $(OBJDIR) +@@ -123,7 +123,7 @@ + + + # main target +-$(MAINFILE): $(BINDIR) $(OBJDIR) $(SCIPLIBFILE) $(LPILIBFILE) $(NLPILIBFILE) $(MAINOBJFILES) ++$(MAINFILE): $(BINDIR) $(OBJDIR) $(MAINOBJFILES) + @echo "-> linking $@" + ifeq ($(VERBOSE),true) + $(LINKCXX) $(MAINOBJFILES) \ diff --git a/easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..ac0cfca19e8 --- /dev/null +++ b/easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'SCIP' +version = '3.2.1' + +homepage = 'https://www.scipopt.org/' +description = """SCIP is currently one of the fastest non-commercial solvers for mixed integer +programming (MIP) and mixed integer nonlinear programming (MINLP). It is also a +framework for constraint integer programming and branch-cut-and-price. It +allows for total control of the solution process and the access of detailed +information down to the guts of the solver.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'scipopt' +source_urls = [GITHUB_SOURCE] +sources = ['v%s.tar.gz' % version.replace('.', '')] +checksums = ['015bdda4e681782fd03b61421b93aa3c1b913e5eea18bb8730d5fb9e4d67b4cb'] + +dependencies = [ + ('SoPlex', '2.2.1'), + ('ZIMPL', '3.3.4'), + ('GMP', '6.2.1'), + ('libreadline', '8.1'), + ('zlib', '1.2.12'), +] + +skipsteps = ['configure'] + +# prepare symlinks to installation files of dependencies +prebuildopts = 'mkdir -p lib && ' +prebuildopts += 'ln -sf "$EBROOTSOPLEX/include" "lib/spxinc" && ' +prebuildopts += 'ln -sf "$EBROOTZIMPL/include" "lib/zimplinc" && ' +prebuildopts += 'for lib in "$EBROOTSOPLEX/lib/libsoplex*.a"; do ln -sf "$lib" "lib/"; done && ' +prebuildopts += 'for lib in "$EBROOTZIMPL/lib/libzimpl*.a"; do ln -sf "$lib" "lib/"; done && ' + +# use SoPlex v2 as LP solver +buildopts = 'LPS=spx2 ' +buildopts += 'MAKESOFTLINKS=false COMP=gnu OPT=opt ' + +installopts = 'INSTALLDIR="%(installdir)s" ' +installopts += buildopts + +postinstallcmds = [ + # add extra headers to installation directory + 'cp "src/scip/misc.h" "%(installdir)s/include/scip/"', + # copy examples folder + 'cp -r "examples" "%(installdir)s/"', +] + +sanity_check_paths = { + 'files': ['bin/scip', 'lib/liblpispx2.a', 'lib/libnlpi.cppad.a', 'lib/libobjscip.a', 'lib/libscip.a'], + 'dirs': ['examples', 'include'], +} + +sanity_check_commands = ["scip -h"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..309841532c7 --- /dev/null +++ b/easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'SoPlex' +version = '2.2.1' + +homepage = 'https://soplex.zib.de/' +description = """SoPlex is an optimization package for solving linear programming problems (LPs) +based on an advanced implementation of the primal and dual revised simplex +algorithm. It provides special support for the exact solution of LPs with +rational input data. It can be used as a standalone solver reading MPS or LP +format files via a command line interface as well as embedded into other +programs via a C++ class library.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'scipopt' +source_urls = [GITHUB_SOURCE] +sources = ['release-%s.tar.gz' % version.replace('.', '')] +checksums = ['6c2e89cd7c8910f8989f2a860fa0446641bd16d76eb87872f70974838486c9b1'] + +dependencies = [ + ('GMP', '6.2.1'), + ('zlib', '1.2.12'), +] + +skipsteps = ['configure'] + +buildopts = "COMP=gnu OPT=opt" +installopts = "INSTALLDIR=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/soplex', 'lib/libsoplex.a'], + 'dirs': ['include'], +} + +sanity_check_commands = ["soplex | grep -q '%(name)s version %(version)s'"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f193788ee27 --- /dev/null +++ b/easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'ZIMPL' +version = '3.3.4' + +homepage = 'https://zimpl.zib.de/' +description = """ZIMPL is a little language to translate the mathematical model of a problem +into a linear or nonlinear (mixed-) integer mathematical program expressed in +.lp or .mps file format which can be read and (hopefully) solved by a LP or MIP +solver.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'scipopt' +source_urls = ['https://zimpl.zib.de/download/'] +sources = [SOURCELOWER_TGZ] +checksums = ['3362fb21524df459723d23f6e0c122ebdd684153a9cc991a2c7f5b2752a83eb2'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('zlib', '1.2.12'), +] + +files_to_copy = ['bin', 'lib', (['src/*.h'], 'include/zimpl')] + +postinstallcmds = [ + "cd %(installdir)s/bin && ln -sf zimpl-%(version)s.* zimpl", + "cd %(installdir)s/lib && ln -sf libzimpl-%(version)s.*.a libzimpl.a", +] + +sanity_check_paths = { + 'files': ['bin/zimpl', 'lib/libzimpl.a'], + 'dirs': ['include/zimpl'], +} + +sanity_check_commands = ["zimpl -h"] + +moduleclass = 'math' From e6a31ec9d8943baca685c27ca2cb15d8792e11fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2023 11:49:01 +0200 Subject: [PATCH 7039/9987] add dlm extension to R 4.2.1 + 4.2.2 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 76fed434942..7829620a4a2 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3466,6 +3466,9 @@ exts_list = [ ('varhandle', '2.0.5', { 'checksums': ['9b0ee653e0343e292547d2a7052e60a2e7d97d1d5528246862522e67346882d0'], }), + ('dlm', '1.1-6', { + 'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index dd02af827b6..ae739c4baf5 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3537,6 +3537,9 @@ exts_list = [ ('varhandle', '2.0.5', { 'checksums': ['9b0ee653e0343e292547d2a7052e60a2e7d97d1d5528246862522e67346882d0'], }), + ('dlm', '1.1-6', { + 'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'], + }), ] moduleclass = 'lang' From 138942297c69c959e0f566eacdc930164a2d6169 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 1 Apr 2023 13:36:41 +0100 Subject: [PATCH 7040/9987] Remove LLVM builddep from TensorFlow --- .../t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb | 1 - .../easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb | 1 - .../easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb | 1 - 3 files changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 77b91670e2c..634b72ba92b 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -17,7 +17,6 @@ builddependencies = [ ('git', '2.33.1', '-nodocs'), ('pybind11', '2.7.1'), ('UnZip', '6.0'), - ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed ] dependencies = [ ('CUDA', '11.4.1', '', SYSTEM), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb index ae6d7df989c..e2c8fdba601 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb @@ -16,7 +16,6 @@ builddependencies = [ ('git', '2.33.1', '-nodocs'), ('pybind11', '2.7.1'), ('UnZip', '6.0'), - ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed ] dependencies = [ ('Python', '3.9.6'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb index 302f3bd958d..fdeaf3afa24 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb @@ -16,7 +16,6 @@ builddependencies = [ ('git', '2.33.1', '-nodocs'), ('pybind11', '2.7.1'), ('UnZip', '6.0'), - ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed ] dependencies = [ ('Python', '3.9.6'), From 8e484911c20de913ec141c80eb0a008fc42153ae Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 1 Apr 2023 15:16:55 +0200 Subject: [PATCH 7041/9987] adding easyconfigs: R-transport-0.13-0-foss-2021b.eb --- .../R-transport-0.13-0-foss-2021b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb b/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb new file mode 100644 index 00000000000..a025135e559 --- /dev/null +++ b/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'R-transport' +local_rpkg = 'transport' +version = '0.13-0' + +homepage = 'https://cran.r-project.org/package=transport' +description = "transport: Computation of Optimal Transport Plans and Wasserstein Distances" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://cran.r-project.org/src/contrib/'] +sources = ['%s_%%(version)s.tar.gz' % local_rpkg] +checksums = ['c55efbdd93e36e92ef39e4b9529ee64c3c7ecb965d77ec9c469a7c56c93f5f57'] + +dependencies = [ + ('R', '4.1.2'), +] + +options = {'modulename': local_rpkg} + +sanity_check_paths = { + 'files': ['transport/R/transport', 'transport/libs/transport.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' From c1098b2252419874205f7755469249348fe00de6 Mon Sep 17 00:00:00 2001 From: anselmicz Date: Sat, 1 Apr 2023 15:23:19 +0200 Subject: [PATCH 7042/9987] adding easyconfigs: PostgreSQL-15.2-GCCcore-12.2.0.eb, libaio-0.3.113-GCCcore-12.2.0.eb, LZO-2.10-GCCcore-12.2.0.eb, jemalloc-5.3.0-GCCcore-12.2.0.eb, Judy-1.0.5-GCCcore-12.2.0.eb, MariaDB-10.11.2-GCC-12.2.0.eb, sysbench-1.0.20-GCC-12.2.0.eb --- .../j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb | 34 ++++++++++ .../jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb | 37 ++++++++++ .../l/LZO/LZO-2.10-GCCcore-12.2.0.eb | 27 ++++++++ .../l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb | 39 +++++++++++ .../m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb | 68 +++++++++++++++++++ .../PostgreSQL-15.2-GCCcore-12.2.0.eb | 43 ++++++++++++ .../s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb | 39 +++++++++++ 7 files changed, 287 insertions(+) create mode 100644 easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-15.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..29e5a68235b --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..aae1125cf83 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.3.0' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ef6f74fd45e95ee4ef7f9e19ebe5b075ca6b7fbe0140612b2a161abafb7ee179'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e1ced572aa5 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.39')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..64d50b5219d --- /dev/null +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.113' +_libversion = '1.0.2' + +homepage = 'https://pagure.io/libaio' +description = "Asynchronous input/output library that uses the kernels native interface." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['1c561c20670c5c09cc8437a622008c0693c6a7816c1f30332da3796953b2f454'] + +builddependencies = [('binutils', '2.39')] + +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + +files_to_copy = [ + (["src/libaio.a", "src/%s" % _soname], "lib"), + (["src/libaio.h"], "include"), +] + +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] + +sanity_check_paths = { + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb new file mode 100644 index 00000000000..37fce889bdc --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb @@ -0,0 +1,68 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.11.2' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + {'mariadb-10.11.2.tar.gz': '1c89dee0caed0f68bc2a1d203eb98a123150e6a179f6ee0f1fc0ba3f08dc71dc'}, + {'MariaDB-10.1.13-link-rt-for-jemalloc.patch': '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('libaio', '0.3.113'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.4'), # optional + ('XZ', '5.2.7'), # optional + ('jemalloc', '5.3.0'), # optional + ('snappy', '1.1.9'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.10.3'), # needed by Connect XML + ('Boost', '1.81.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.40'), + ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release " +configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_commands = ["mysql --help", "mysqltest --help"] + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-15.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-15.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..14b35601d98 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-15.2-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '15.2' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['eccd208f3e7412ad7bc4c648ecc87e0aa514e02c24a48f71bf9e46910bf284ca'] + +builddependencies = [ + ('binutils', '2.39'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Perl', '5.36.0'), + ('Python', '3.10.8'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb new file mode 100644 index 00000000000..45c70aeb5f0 --- /dev/null +++ b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'sysbench' +version = '1.0.20' + +homepage = 'https://github.com/akopytov/sysbench' +description = """sysbench is a scriptable multi-threaded benchmark tool based on LuaJIT. + It is most frequently used for database benchmarks, but can also be used to create arbitrarily complex + workloads that do not involve a database server.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +github_account = 'akopytov' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e8ee79b1f399b2d167e6a90de52ccc90e52408f7ade1b9b7135727efe181347f'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('libtool', '2.4.7'), + ('MariaDB', '10.11.2'), + ('PostgreSQL', '15.2'), # optional +] + +preconfigopts = './autogen.sh &&' +configopts = '--with-pgsql ' # optional + +sanity_check_paths = { + 'files': ['bin/sysbench'], + 'dirs': ['bin', 'share'] +} + +sanity_check_commands = ['sysbench --help'] + +moduleclass = 'tools' From 830a5e10ecab26bbf51356092490a9d74cabced0 Mon Sep 17 00:00:00 2001 From: anselmicz Date: Sat, 1 Apr 2023 15:46:50 +0200 Subject: [PATCH 7043/9987] adding easyconfigs: Vim-9.0.1434-GCCcore-12.2.0.eb --- .../v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb b/easybuild/easyconfigs/v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..3ba63172bd8 --- /dev/null +++ b/easybuild/easyconfigs/v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Vim' +version = '9.0.1434' + +homepage = 'http://www.vim.org' +description = """ Vim is an advanced text editor that seeks to provide the power + of the de-facto Unix editor 'Vi', with a more complete feature set. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/vim/vim/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f7a43d6f2c08c4d76c5ceb9ab6603fe2d87d56c1162934525cf46362ef8a4e65'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('Perl', '5.36.0'), + ('PCRE', '8.45') +] + +configopts = '--with-features=huge --enable-python3interp=yes --enable-perlinterp=yes' + +sanity_check_paths = { + 'files': ['bin/vim', 'bin/vimtutor', 'bin/xxd'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['vim --version'] + +moduleclass = 'tools' From a1ca871894643db6784f08caaddad758181c2105 Mon Sep 17 00:00:00 2001 From: anselmicz Date: Sat, 1 Apr 2023 16:05:43 +0200 Subject: [PATCH 7044/9987] adding easyconfigs: nvtop-3.0.1-GCCcore-12.2.0.eb --- .../n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..1d50e1ff0c1 --- /dev/null +++ b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'nvtop' +version = '3.0.1' + +homepage = 'https://github.com/Syllo/nvtop' +description = 'htop-like GPU usage monitor' + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/Syllo/nvtop/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f61ecbe3a30a216706c16fc177d3b840e7d7deccf87b048d59f95f230d591a53'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +# Note: software dlopen's libraries from the OS installed drivers, thus no specific CUDA dependency. +dependencies = [ + ('ncurses', '6.3'), + ('libdrm', '2.4.114'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/nvtop'], + 'dirs': [], +} + +sanity_check_commands = ["nvtop --help"] + +moduleclass = 'tools' From e50f8595d541a41645942e3d8c7a3666b4989de8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2023 16:25:52 +0200 Subject: [PATCH 7045/9987] adding easyconfigs: CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb --- .../CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..2e0b17c5c7e --- /dev/null +++ b/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'CopyKAT' +local_commit = 'b795ff7' +version = '1.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/navinlabcode/copykat' +description = """CopyKAT: Inference of genomic copy number and subclonal structure of human tumors from + high-throughput single cell RNAseq data""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/navinlabcode/copykat/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['8b4e39591ad81d146873694b8311607bfec88ad57df8daa9244b2e31904193b5'] + +dependencies = [ + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From 4d0bbda30796bedb24df34b12f8fe897e8853c56 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2023 20:50:03 +0200 Subject: [PATCH 7046/9987] adding easyconfigs: powerlaw-1.5-foss-2022a.eb --- .../p/powerlaw/powerlaw-1.5-foss-2022a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/powerlaw/powerlaw-1.5-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/powerlaw/powerlaw-1.5-foss-2022a.eb b/easybuild/easyconfigs/p/powerlaw/powerlaw-1.5-foss-2022a.eb new file mode 100644 index 00000000000..76d53174915 --- /dev/null +++ b/easybuild/easyconfigs/p/powerlaw/powerlaw-1.5-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'powerlaw' +version = '1.5' + +homepage = 'http://www.github.com/jeffalstott/powerlaw' +description = "powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_PY3_WHL] +checksums = ['633a669573d9fd663d2f452f121117f2d6b2f2c502eca532f9355f733abfec96'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' From 4bd1e64e58e4bf9358a2809b4ce8c8e8c0a6697d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Apr 2023 20:55:50 +0200 Subject: [PATCH 7047/9987] {data}[foss/2021a] scib v1.1.3, Deprecated v1.2.13 w/ Python 3.9.5 --- .../Deprecated-1.2.13-foss-2021a.eb | 29 ++++++++++++++ .../s/scib/scib-1.1.3-foss-2021a.eb | 39 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/scib/scib-1.1.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2021a.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2021a.eb new file mode 100644 index 00000000000..37b1d866da5 --- /dev/null +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2021a.eb @@ -0,0 +1,29 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'Deprecated' +version = '1.2.13' + +homepage = 'https://github.com/tantale/deprecated' +description = "If you need to mark a function or a method as deprecated, you can use the @deprecated decorator." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True + +exts_list = [ + ('wrapt', '1.15.0', { + 'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'], + }), + (name, version, { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scib/scib-1.1.3-foss-2021a.eb b/easybuild/easyconfigs/s/scib/scib-1.1.3-foss-2021a.eb new file mode 100644 index 00000000000..ffd4fc238c0 --- /dev/null +++ b/easybuild/easyconfigs/s/scib/scib-1.1.3-foss-2021a.eb @@ -0,0 +1,39 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonPackage' + +name = 'scib' +version = '1.1.3' + +homepage = 'https://github.com/theislab/scib' +description = "Benchmarking atlas-level data integration in single-cell genomics." + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2b59d7c291e99bd508b91d73ff07fc4961fded37b06089e4f19fc5ee9cc4e3f3'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Seaborn', '0.11.2'), + ('numba', '0.53.1'), + ('scanpy', '1.8.1'), + ('h5py', '3.2.1'), + ('scikit-learn', '0.24.2'), + ('scikit-misc', '0.1.4'), + ('leidenalg', '0.8.7'), + ('umap-learn', '0.5.3'), + ('pydot', '1.4.2'), + ('igraph', '0.9.4'), + ('python-igraph', '0.9.6'), + ('Deprecated', '1.2.13'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = "sed -i 's|igraph>=0.10|python-igraph>=0.9.6|g' setup.cfg && " +preinstallopts += "sed -i 's|louvain>=0.8||g' setup.cfg && " + +moduleclass = 'data' From 9c62488c0fdfb3efae9e782596c9a427031ce7a3 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Mon, 3 Apr 2023 10:52:02 +0100 Subject: [PATCH 7048/9987] Update easybuild/easyconfigs/z/zsh/zsh-5.9.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/z/zsh/zsh-5.9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.9.eb b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb index 574b12cb58d..ff8bd3f2190 100644 --- a/easybuild/easyconfigs/z/zsh/zsh-5.9.eb +++ b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['9b8d1ecedd5b5e81fbf1918e876752a7dd948e05c1a0dba10ab863842d45acd5'] osdependencies = [ - ('ncurses-devel', 'ncurses-dev'), + ('ncurses-devel', 'libncurses-dev'), ] configopts = '--with-tcsetpgrp' # needed to build in non-login shells From d86a6c921ab7790c6bcd1b9040e5e8a1f5720101 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Apr 2023 12:07:41 +0200 Subject: [PATCH 7049/9987] Add CUDA to OpenMM --- .../easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb index 47d3bdbfaf5..87db305f12a 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb @@ -29,10 +29,15 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('SWIG', '4.0.2'), + ('CUDA', '11.7.0', '', SYSTEM), ] -pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" -local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +# Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc, +# Otherwise they will use the wrong path: `/usr/bin/nvcc` +pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && ' +pretestopts += " CTEST_OUTPUT_ON_FAILURE=1" +# Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(CudaCompiler)" runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' From 956625cee5b456723e83224ae2ac53de85f0e5ee Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Apr 2023 12:10:11 +0200 Subject: [PATCH 7050/9987] Fix comment --- easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb index 87db305f12a..3a717e67758 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb @@ -33,7 +33,7 @@ dependencies = [ ] # Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc, -# Otherwise they will use the wrong path: `/usr/bin/nvcc` +# Otherwise they will use the wrong path: `/usr/local/cuda/bin/nvcc` pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && ' pretestopts += " CTEST_OUTPUT_ON_FAILURE=1" # Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set From 15f5792d795e9a0b8b1bd1b1eb06f64ab575b4e5 Mon Sep 17 00:00:00 2001 From: guacke Date: Mon, 3 Apr 2023 14:06:00 +0200 Subject: [PATCH 7051/9987] adding easyconfigs: Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb --- .../Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blender/Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/Blender/Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb new file mode 100644 index 00000000000..b63f52585f9 --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PackedBinary' + +name = 'Blender' +version = '3.5.0' +versionsuffix = '-linux-x86_64-CUDA-%(cudaver)s' + +homepage = 'https://www.blender.org/' +description = """Blender is the free and open source 3D creation suite. It supports + the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, + compositing and motion tracking, even video editing and game creation.""" + +toolchain = SYSTEM + +source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender%(version_major_minor)s/'] +sources = ['blender-%(version)s-linux-x64.tar.xz'] +checksums = ['a74d52822d5753a1ffb617ac764bbacc12a4a6dec4c2b91e90cc2935a40fff68'] + +dependencies = [ + ('CUDA', '11.7.0') +] + +sanity_check_paths = { + 'files': ['blender', 'blender-softwaregl'], + 'dirs': ['%(version_major_minor)s'], +} + +sanity_check_commands = ["blender --help"] + +moduleclass = 'vis' From d4392f22296520cf76ed4fb27b4c5c822a7701a2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 4 Apr 2023 10:34:35 +0200 Subject: [PATCH 7052/9987] adding easyconfigs: FunGAP-1.1.1-foss-2022a.eb and patches: FunGAP-1.1.1_fix-snap-detection.patch, FunGAP-1.1.1_relax-dependency-checks.patch, FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch, FunGAP-1.1.1_fix-maker-exes.patch, FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch --- .../f/FunGAP/FunGAP-1.1.1-foss-2022a.eb | 91 +++++++++++++++++++ ...1.1_fix-augustus-calls-in-runbreaker.patch | 54 +++++++++++ .../FunGAP/FunGAP-1.1.1_fix-maker-exes.patch | 20 ++++ .../FunGAP-1.1.1_fix-snap-detection.patch | 61 +++++++++++++ ...FunGAP-1.1.1_relax-dependency-checks.patch | 29 ++++++ ..._replace-deprecated-pa-repeatmodeler.patch | 22 +++++ 6 files changed, 277 insertions(+) create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-maker-exes.patch create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-snap-detection.patch create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_relax-dependency-checks.patch create mode 100644 easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb new file mode 100644 index 00000000000..5c1328194ce --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb @@ -0,0 +1,91 @@ +easyblock = 'Tarball' + +name = 'FunGAP' +version = '1.1.1' + +homepage = 'https://github.com/CompSynBioLab-KoreaUniv/FunGAP' +description = "Fungal Genome Annotation Pipeline using evidence-based gene model evaluation." + +toolchain = {'name': 'foss', 'version': '2022a'} + +# Tag v1.1.1 points to an old commit still in v1.1.0 +# pull correct sources from specific commit +_commit = '924f3ba080f98cbf181b0b21601e095619479ce6' + +source_urls = ['https://github.com/CompSynBioLab-KoreaUniv/FunGAP/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +patches = [ + 'FunGAP-%(version)s_fix-snap-detection.patch', + 'FunGAP-%(version)s_relax-dependency-checks.patch', + 'FunGAP-%(version)s_replace-deprecated-pa-repeatmodeler.patch', + 'FunGAP-%(version)s_fix-maker-exes.patch', + 'FunGAP-%(version)s_fix-augustus-calls-in-runbreaker.patch', +] +checksums = [ + {'FunGAP-1.1.1.tar.gz': '3d827c4b11452afdd51b71766e0e3193b7efad31db4536606115f2cac0b964c8'}, + {'FunGAP-1.1.1_fix-snap-detection.patch': 'f782224ce186e1e2d8953898122b79d616f8a749b00ec662ec5a3fa1903550fa'}, + {'FunGAP-1.1.1_relax-dependency-checks.patch': '73f9ae2a20cf03c34f852642a28d3b7e9858250f653ff1e711c3c9a56ae2fd77'}, + {'FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch': + 'c528aab74a070d6eedc9ff2097b6149e8d36759b9ff93c46302994179a38a774'}, + {'FunGAP-1.1.1_fix-maker-exes.patch': 'de344cf45dad047ab46a17462e19ce0789a89071c1484cbdedd9d898f9601bd0'}, + {'FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch': + '150b6f79f95d0c8abece42231c5dcedf8610a811db9cc63ac6cc047f0dcfdc64'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('AUGUSTUS', '3.5.0'), + ('BamTools', '2.5.2'), + ('bcbio-gff', '0.7.0'), + ('BRAKER', '2.1.6'), + ('BUSCO', '5.4.5'), + ('HISAT2', '2.2.1'), + ('MAKER', '3.01.04'), + ('matplotlib', '3.5.2'), + ('networkx', '2.8.4'), + ('PfamScan', '1.6'), + ('RepeatModeler', '2.0.4'), + ('SAMtools', '1.16.1'), + ('SNAP-HMM', '20221022'), + ('Trinity', '2.15.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('markdown2', '2.4.8', { + 'checksums': ['90475aca3d9c8e7df6d70c51de5bbbe9edf7fcf6a380bd1044d321500f5445da'], + }), +] + +postinstallcmds = [ + # execute set_dependencies.py, which creates configuration file and runs some quick tests + ("cd %(installdir)s && ./set_dependencies.py --pfam_db_path /databases/bio/Pfam-35 " + "--genemark_path $EBROOTGENEMARKMINET --maker_path $EBROOTMAKER/bin --snap_path $EBROOTSNAPMINHMM/bin"), +] + +sanity_check_paths = { + 'files': ['fungap.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': ['', 'lib/python%(pyshortver)s/site-packages'] +} + +modextravars = { + 'FUNGAP_DIR': '%(installdir)s', +} + +sanity_check_commands = [ + ('fungap.py', '--help'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch new file mode 100644 index 00000000000..a245df16275 --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch @@ -0,0 +1,54 @@ +Set paths to AUGUSTUS installation preferably from its environment variables +Fix location of getAnnoFastaFromJoingenes.py script from AUGUSTUS +see https://github.com/CompSynBioLab-KoreaUniv/FunGAP/pull/98 +author: Alex Domingo (Vrije Universirteit Brussel) +--- run_braker.py.orig 2023-04-03 12:07:35.178272000 +0200 ++++ run_braker.py 2023-04-03 12:24:48.713953000 +0200 +@@ -124,8 +124,19 @@ + logger_time.debug('START: BRAKER') + + if not os.path.exists(gff3_braker): +- augustus_config_path = os.path.join( +- os.path.dirname(D_CONF['AUGUSTUS_PATH']), '../config') ++ augustus_bin_path = os.environ[ ++ 'AUGUSTUS_BIN_PATH' ++ ] or os.path.dirname(D_CONF['AUGUSTUS_PATH']) ++ augustus_config_path = os.environ[ ++ 'AUGUSTUS_CONFIG_PATH' ++ ] or os.path.join( ++ os.path.dirname(D_CONF['AUGUSTUS_PATH']), '../config' ++ ) ++ augustus_scripts_path = os.environ[ ++ 'AUGUSTUS_SCRIPTS_PATH' ++ ] or os.path.join( ++ os.path.dirname(D_CONF['AUGUSTUS_PATH']), '../scripts' ++ ) + config_species = os.path.join( + augustus_config_path, 'species', prefix) + species = prefix +@@ -140,7 +151,6 @@ + bamtools_path = os.path.dirname(D_CONF['BAMTOOLS_PATH']) + genemark_path = os.path.dirname(D_CONF['GENEMARK_PATH']) + samtools_path = os.path.dirname(D_CONF['SAMTOOLS_PATH']) +- augustus_scripts_path = os.path.dirname(D_CONF['AUGUSTUS_PATH']) + working_dir = os.path.join(output_dir, prefix) + if not os.path.exists(working_dir): + os.mkdir(working_dir) +@@ -153,7 +163,7 @@ + braker_bin, fungus_flag, num_cores, adjusted_assembly, + bam_file, species, augustus_config_path, bamtools_path, + genemark_path, samtools_path, working_dir, +- translation_table, augustus_scripts_path, log_braker)) ++ translation_table, augustus_bin_path, log_braker)) + logger_txt.debug('[Run] %s', command1) + os.system(command1) + +@@ -165,7 +175,7 @@ + + augustus_dir = os.path.dirname(D_CONF['AUGUSTUS_PATH']) + get_anno_script = os.path.join( +- augustus_dir, 'getAnnoFastaFromJoingenes.py') ++ augustus_scripts_path, 'getAnnoFastaFromJoingenes.py') + if not os.path.exists(get_anno_script): + get_anno_script = os.path.join( + augustus_dir, diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-maker-exes.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-maker-exes.patch new file mode 100644 index 00000000000..b172ca04d47 --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-maker-exes.patch @@ -0,0 +1,20 @@ +The paths to MAKER executables set by MAKER are already correct, avoid +tampering with them. +author: Alex Domingo (Vrije Universiteit Brussel) +--- run_maker.py.orig 2023-03-21 09:19:05.057679000 +0100 ++++ run_maker.py 2023-03-21 09:19:49.143408491 +0100 +@@ -463,14 +463,6 @@ + replace('maker_opts.ctl', 'protein_pass=0', 'protein_pass=1') + replace('maker_opts.ctl', 'rm_pass=0', 'rm_pass=1') + +- # Program paths +- for program in [ +- 'makeblastdb', 'blastn', 'blastx', 'tblastx', 'RepeatMasker', +- 'exonerate', 'snap', 'augustus', 'tRNAscan-SE', 'snoscan']: +- replace('maker_exe.ctl', '{}='.format(program), '{}={}'.format( +- program, os.path.join(os.path.dirname(maker_bin), program) +- )) +- + # Last run, keep_preds=1 + if version == '4': + replace('maker_opts.ctl', 'keep_preds=0', 'keep_preds=1') diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-snap-detection.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-snap-detection.patch new file mode 100644 index 00000000000..c8dd7ab6262 --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-snap-detection.patch @@ -0,0 +1,61 @@ +Fix detection of fathom, forge and hmm-assembler.pl, which are not part of MAKER but SNAP +see https://github.com/CompSynBioLab-KoreaUniv/FunGAP/pull/97 +author: Alex Domingo (Vrije Universiteit Brussel) +--- set_dependencies.py.orig 2023-03-16 15:27:00.506475000 +0100 ++++ set_dependencies.py 2023-03-16 15:31:31.102674857 +0100 +@@ -44,6 +44,10 @@ + help='Maker bin path' + ) + parser.add_argument( ++ '-s', '--snap_path', nargs=1, required=True, ++ help='SNAP-HMM bin path' ++ ) ++ parser.add_argument( + '-r', '--with_repeat_modeler', nargs='?', default='', + help='User-defined RepeatModeler bin path' + ) +@@ -76,6 +80,7 @@ + pfam_db_path = os.path.abspath(args.pfam_db_path[0]) + i_genemark_path = os.path.abspath(args.genemark_path[0]) + i_maker_path = os.path.abspath(args.maker_path[0]) ++ i_snap_path = os.path.abspath(args.snap_path[0]) + if args.with_repeat_modeler: + with_repeat_modeler = os.path.abspath(args.with_repeat_modeler) + else: +@@ -104,8 +109,9 @@ + pfam_scan_path, blastp_path, blastn_path, blastx_path, + makeblastdb_path, samtools_path, bamtools_path, augustus_path + ) = get_path( +- i_genemark_path, i_maker_path, with_repeat_modeler, with_augustus, +- with_hisat2, with_trinity, with_braker, with_busco, with_pfam_scan ++ i_genemark_path, i_maker_path, i_snap_path, with_repeat_modeler, ++ with_augustus, with_hisat2, with_trinity, with_braker, with_busco, ++ with_pfam_scan + ) + check_working( + genemark_path, gmhmme3_path, probuild_path, build_database_path, +@@ -159,8 +165,9 @@ + + + def get_path( +- i_genemark_path, i_maker_path, with_repeat_modeler, with_augustus, +- with_hisat2, with_trinity, with_braker, with_busco, with_pfam_scan): ++ i_genemark_path, i_maker_path, i_snap_path, with_repeat_modeler, ++ with_augustus, with_hisat2, with_trinity, with_braker, with_busco, ++ with_pfam_scan): + '''Get path''' + print('\n** Checking the installed locations of dependencies **\n') + +@@ -198,9 +205,9 @@ + gff3_merge_path = check_binary('Maker', i_maker_path, 'gff3_merge') + fasta_merge_path = check_binary('Maker', i_maker_path, 'fasta_merge') + maker2zff_path = check_binary('Maker', i_maker_path, 'maker2zff') +- fathom_path = check_binary('Snap', i_maker_path, 'fathom') +- forge_path = check_binary('Snap', i_maker_path, 'forge') +- hmm_assembler_path = check_binary('Snap', i_maker_path, 'hmm-assembler.pl') ++ fathom_path = check_binary('Snap', i_snap_path, 'fathom') ++ forge_path = check_binary('Snap', i_snap_path, 'forge') ++ hmm_assembler_path = check_binary('Snap', i_snap_path, 'hmm-assembler.pl') + build_database_path = check_binary( + 'RepeatModeler (BuildDatabase)', with_repeat_modeler, 'BuildDatabase', + ) diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_relax-dependency-checks.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_relax-dependency-checks.patch new file mode 100644 index 00000000000..68d88fe47b2 --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_relax-dependency-checks.patch @@ -0,0 +1,29 @@ +Disable too strict check on version of AUGUSTUS and the GeneMark key in the +home directory of the user +author: Alex Domingo (Vrije Universiteit Brusel) +--- set_dependencies.py.orig 2023-03-16 15:50:03.802522000 +0100 ++++ set_dependencies.py 2023-03-16 15:50:28.562603082 +0100 +@@ -284,15 +284,15 @@ + check_working_internal(samtools_path, [samtools_path, '--help']) + check_working_internal(bamtools_path, [bamtools_path, '--help']) + check_working_internal(augustus_path, [augustus_path, '--help']) +- check_augustus_version(augustus_path) ++ # check_augustus_version(augustus_path) + +- # For GeneMark, check the .gm_key +- home_path = os.path.expanduser('~') +- if not os.path.exists(os.path.join(home_path, '.gm_key')): +- sys.exit( +- '\n[ERROR] You do not have .gm_key in your home directory.\n' +- 'Check https://wiki.gacrc.uga.edu/wiki/GeneMark' +- ) ++ # # For GeneMark, check the .gm_key ++ # home_path = os.path.expanduser('~') ++ # if not os.path.exists(os.path.join(home_path, '.gm_key')): ++ # sys.exit( ++ # '\n[ERROR] You do not have .gm_key in your home directory.\n' ++ # 'Check https://wiki.gacrc.uga.edu/wiki/GeneMark' ++ # ) + + def check_augustus_version(augustus_path): + '''Check Augustus version 3.3.3''' diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch new file mode 100644 index 00000000000..8d75c3a8ae6 --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch @@ -0,0 +1,22 @@ +Replace deprecated -pa option in newer versions of RepeatModeler with -threads +author: Alex Domingo (Vrije Universiteit Brussel) +--- run_repeat_modeler.py.orig 2023-03-17 09:23:21.857374000 +0100 ++++ run_repeat_modeler.py 2023-03-17 09:24:17.655942000 +0100 +@@ -73,7 +73,7 @@ + + # BuildDatabase -name Choanephora_cucurbitarum + # ../Choanephora_cucurbitarum_assembly.fna +- # RepeatModeler -database Choanephora_cucurbitarum -pa 25 ++ # RepeatModeler -database Choanephora_cucurbitarum -threads 25 + + # Get repeat model + repeat_lib = os.path.join(output_dir, '*', 'consensi.fa.classified') +@@ -89,7 +89,7 @@ + os.system(command1) + + log_file2 = os.path.join(log_dir, 'repeat_modeler.log') +- command2 = '{} -database {} -pa {} > {} 2>&1'.format( ++ command2 = '{} -database {} -threads {} > {} 2>&1'.format( + repeatmodeler_bin, genome_assembly, num_cores, log_file2 + ) + logger_txt.debug('[Run] %s', command2) From 5674fb3c42e04f0acf3594049f5457ff90872d39 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 4 Apr 2023 11:52:18 +0100 Subject: [PATCH 7053/9987] Update spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb Use `SYSTEM` for a binary dep. --- .../s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb index 171697664e9..e5b551b446f 100644 --- a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb @@ -26,7 +26,7 @@ dependencies = [ ('networkx', '2.6.3'), ('tqdm', '4.62.3'), ('scikit-learn', '1.0.1'), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('TensorFlow', '2.7.1', versionsuffix), ] From b42386eb64174af96d137f70c1c68fb0761b50eb Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 4 Apr 2023 16:49:25 +0200 Subject: [PATCH 7054/9987] Add patch to resolve tree-vectorize issue --- .../o/OpenMM/OpenMM-8.0.0-foss-2022a.eb | 6 +++++- .../OpenMM-8.0.0_add_no_tree_vectorize.patch | 16 ++++++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0_add_no_tree_vectorize.patch diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb index 3a717e67758..52869cc7ee4 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb @@ -18,7 +18,11 @@ toolchainopts = {'opt': True} source_urls = ['https://github.com/openmm/openmm/archive/'] sources = ['%(version)s.tar.gz'] -checksums = ['dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e'] +patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch'] +checksums = [ + 'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e', # 8.0.0.tar.gz + '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd', # OpenMM-8.0.0_add_no_tree_vectorize.patch +] builddependencies = [ ('CMake', '3.23.1'), diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0_add_no_tree_vectorize.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0_add_no_tree_vectorize.patch new file mode 100644 index 00000000000..e3fb0d99579 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0_add_no_tree_vectorize.patch @@ -0,0 +1,16 @@ +# This patch resolves the tree vectorizatior error that appears when "-march" is used with GCC 11.3.0: +# .../openmm-8.0.0/platforms/common/src/CommonKernels.cpp:5055:6: internal compiler error: in vect_get_vec_defs_for_operand, at tree-vect-stmts.c:1450 +# 5055 | void CommonCalcGayBerneForceKernel::sortAtoms() { +# Author: maxim-masterov (SURF) + +diff -Nru openmm-8.0.0.orig/platforms/common/src/CommonKernels.cpp openmm-8.0.0/platforms/common/src/CommonKernels.cpp +--- openmm-8.0.0.orig/platforms/common/src/CommonKernels.cpp 2023-03-29 10:08:28.765461000 +0200 ++++ openmm-8.0.0/platforms/common/src/CommonKernels.cpp 2023-04-04 15:55:17.152316000 +0200 +@@ -5052,6 +5052,7 @@ + sortAtoms(); + } + ++__attribute__((optimize("no-tree-vectorize"))) + void CommonCalcGayBerneForceKernel::sortAtoms() { + // Sort the list of atoms by type to avoid thread divergence. This is executed every time + // the atoms are reordered. From 2b69ad1e3bd3028fc54a629ebbe2aa0a68e67f6f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 4 Apr 2023 17:17:12 +0200 Subject: [PATCH 7055/9987] Fix style --- easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb index 52869cc7ee4..4d937a03a22 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb @@ -20,7 +20,7 @@ source_urls = ['https://github.com/openmm/openmm/archive/'] sources = ['%(version)s.tar.gz'] patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch'] checksums = [ - 'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e', # 8.0.0.tar.gz + 'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e', # 8.0.0.tar.gz '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd', # OpenMM-8.0.0_add_no_tree_vectorize.patch ] From 32cd82fa0e95be9360464d58f9696c7900d6a6f5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 4 Apr 2023 18:18:50 +0200 Subject: [PATCH 7056/9987] install Pfam database if missing in FunGAP installation directory --- .../f/FunGAP/FunGAP-1.1.1-foss-2022a.eb | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb index 5c1328194ce..171e5c1d38e 100644 --- a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb @@ -64,10 +64,23 @@ exts_list = [ }), ] +# FunGAP needs the Pfam database (280 MB download, 1.5 GB on disk) +# if it's already available in your system change _pfam_db_dir to its location +_pfam_db_dir = '%(installdir)s/db' +_pfam_db_url = 'https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release' +_pfam_db_install_cmds = [ + "mkdir -p %s" % _pfam_db_dir, + "wget -P %s %s/{Pfam-A.hmm.gz,Pfam-A.hmm.dat.gz,active_site.dat.gz}" % (_pfam_db_dir, _pfam_db_url), + "gzip -d %s/*.gz" % _pfam_db_dir, + "hmmpress %s/Pfam-A.hmm" % _pfam_db_dir, +] + postinstallcmds = [ + # install Pfam DB if missing + "if [ ! -f %s/Pfam-A.hmm ]; then %s; fi" % (_pfam_db_dir, " && ".join(_pfam_db_install_cmds)), # execute set_dependencies.py, which creates configuration file and runs some quick tests - ("cd %(installdir)s && ./set_dependencies.py --pfam_db_path /databases/bio/Pfam-35 " - "--genemark_path $EBROOTGENEMARKMINET --maker_path $EBROOTMAKER/bin --snap_path $EBROOTSNAPMINHMM/bin"), + ("cd %%(installdir)s && ./set_dependencies.py --pfam_db_path %s --genemark_path $EBROOTGENEMARKMINET " + "--maker_path $EBROOTMAKER/bin --snap_path $EBROOTSNAPMINHMM/bin" % _pfam_db_dir), ] sanity_check_paths = { From 6482e680f92611aaaefd49b5fa63ca2e87f492e8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 4 Apr 2023 18:47:38 +0200 Subject: [PATCH 7057/9987] remove trailing spaces in FunGAP-1.1.1-foss-2022a.eb --- easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb index 171e5c1d38e..a974e867d2b 100644 --- a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb @@ -77,7 +77,7 @@ _pfam_db_install_cmds = [ postinstallcmds = [ # install Pfam DB if missing - "if [ ! -f %s/Pfam-A.hmm ]; then %s; fi" % (_pfam_db_dir, " && ".join(_pfam_db_install_cmds)), + "if [ ! -f %s/Pfam-A.hmm ]; then %s; fi" % (_pfam_db_dir, " && ".join(_pfam_db_install_cmds)), # execute set_dependencies.py, which creates configuration file and runs some quick tests ("cd %%(installdir)s && ./set_dependencies.py --pfam_db_path %s --genemark_path $EBROOTGENEMARKMINET " "--maker_path $EBROOTMAKER/bin --snap_path $EBROOTSNAPMINHMM/bin" % _pfam_db_dir), From 9f81fbea418d2f6ffaac075a03db0a5f3fc19e01 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 07:15:35 +0200 Subject: [PATCH 7058/9987] adding easyconfigs: NAGfor-7.1.eb --- easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb | 30 ++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb diff --git a/easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb b/easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb new file mode 100644 index 00000000000..3560fb4a995 --- /dev/null +++ b/easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb @@ -0,0 +1,30 @@ +easyblock = 'Binary' + +name = 'NAGfor' +version = '7.1' + +homepage = 'http://www.nag.co.uk' +description = """The checking compiler for improved code portability and detailed error reporting.""" + +toolchain = SYSTEM + +sources = [{ + 'source_urls': ['https://www.nag.co.uk/downloads/impl'], + 'filename': SOURCE_TGZ, + 'download_filename': 'npl6a%(version_major)s%(version_minor)sna_amd64.tgz' +}] +checksums = ['0f173ea0e0809673db216622a7354cc2eb52bf13372a34ef85e62a115bb6f94f'] + +extract_sources = True + +install_cmd = "INSTALL_TO_BINDIR=%(installdir)s/bin INSTALL_TO_LIBDIR=%(installdir)s/lib " +install_cmd += "INSTALL_TO_CATMANDIR=%(installdir)s/man INSTALL_TO_MANDIR=%(installdir)s/man ./INSTALLU.sh" + +modextravars = {'NAG_KUSARI_FILE': HOME + '/licenses/license.dat'} + +sanity_check_paths = { + 'files': ['bin/dbx90', 'bin/nagfmcheck', 'bin/nagfor'], + 'dirs': ['lib', 'man1', 'man3'], +} + +moduleclass = 'compiler' From 85746125490e06419ff2b1fb019c9f8042f5fd65 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 07:37:41 +0200 Subject: [PATCH 7059/9987] adding easyconfigs: NAG-7.1-gompi-2022b.eb --- .../easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb diff --git a/easybuild/easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb b/easybuild/easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb new file mode 100644 index 00000000000..dd7e50c3ced --- /dev/null +++ b/easybuild/easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb @@ -0,0 +1,30 @@ +easyblock = 'Binary' + +name = 'NAG' +version = '7.1' + +homepage = 'http://www.nag.co.uk' +description = "The worlds largest collection of robust, documented, tested and maintained numerical algorithms." + +toolchain = {'name': 'gompi', 'version': '2022b'} + +sources = [{ + 'source_urls': ['https://www.nag.co.uk/downloads/impl'], + 'filename': SOURCE_TGZ, + 'download_filename': 'npl6a%(version_major)s%(version_minor)sna_amd64.tgz' +}] +checksums = ['0f173ea0e0809673db216622a7354cc2eb52bf13372a34ef85e62a115bb6f94f'] + +extract_sources = True + +install_cmd = "INSTALL_TO_BINDIR=%(installdir)s/bin INSTALL_TO_LIBDIR=%(installdir)s/lib " +install_cmd += "INSTALL_TO_CATMANDIR=%(installdir)s/man INSTALL_TO_MANDIR=%(installdir)s/man ./INSTALLU.sh" + +modextravars = {'NAG_KUSARI_FILE': HOME + '/licenses/license.dat'} + +sanity_check_paths = { + 'files': ['bin/dbx90', 'bin/nagfmcheck', 'bin/nagfor'], + 'dirs': ['lib', 'man1', 'man3'], +} + +moduleclass = 'compiler' From 3c137b00c42164b19de112eea40ccb19148401e2 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 07:48:24 +0200 Subject: [PATCH 7060/9987] add wrongly ommitted use_fma4 --- easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb index 3c7c5f30841..65082d495d4 100644 --- a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-iompi-2020b.eb @@ -21,6 +21,9 @@ checksums = [ # http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html with_quad_prec = False +# compilation fails when configuring with --enable-avx-128-fma, Intel compilers do not support FMA4 instructions +use_fma4 = False + runtest = 'check' moduleclass = 'numlib' From 8515aff4fb9772cc21d4e262e8343d780462abfa Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 08:02:43 +0200 Subject: [PATCH 7061/9987] adding easyconfigs: argtable-2.13-GCCcore-10.2.0.eb --- .../argtable/argtable-2.13-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..896c6221885 --- /dev/null +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'argtable' +version = '2.13' + +homepage = 'http://argtable.sourceforge.net/' +description = """ Argtable is an ANSI C library for parsing GNU style + command line options with a minimum of fuss. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))] +checksums = ['8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['include/argtable2.h', 'lib/libargtable2.%s' % SHLIB_EXT, 'lib/libargtable2.a'], + 'dirs': ['share'], +} + +moduleclass = 'lib' From 50437f2a1f2dc34c39e051cce1545c6c57e08e7f Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 08:03:38 +0200 Subject: [PATCH 7062/9987] adding easyconfigs: Clustal-Omega-1.2.4-GCC-10.2.0.eb --- .../Clustal-Omega-1.2.4-GCC-10.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb new file mode 100644 index 00000000000..df007a1ade5 --- /dev/null +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by Adam Huffman +# Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Clustal-Omega' +version = '1.2.4' + +homepage = 'http://www.clustal.org/omega/' +description = """ Clustal Omega is a multiple sequence alignment + program for proteins. It produces biologically meaningful multiple + sequence alignments of divergent sequences. Evolutionary relationships + can be seen via viewing Cladograms or Phylograms """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'openmp': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee'] + +dependencies = [('argtable', '2.13')] + +sanity_check_paths = { + 'files': ['bin/clustalo'], + 'dirs': [], +} + +sanity_check_commands = ["clustalo --help"] + +moduleclass = 'bio' From cd4122cb5460428f215d2d76b8f3784ed1069e33 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 08:21:02 +0200 Subject: [PATCH 7063/9987] adding easyconfigs: c-ares-1.17.2-GCCcore-10.2.0.eb --- .../c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6b168c49490 --- /dev/null +++ b/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'c-ares' +version = '1.17.2' + +homepage = 'https://c-ares.haxx.se' +description = "c-ares is a C library for asynchronous DNS requests (including name resolves)" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://c-ares.haxx.se/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4803c844ce20ce510ef0eb83f8ea41fa24ecaae9d280c468c582d2bb25b3913d'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['lib/libcares.a', 'lib/libcares.%s' % SHLIB_EXT, 'lib/pkgconfig/libcares.pc'], + 'dirs': ['include', 'share/man'], +} + +moduleclass = 'lib' From 380e32d184f6777edeb07d41775901bc04adcfed Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 08:25:20 +0200 Subject: [PATCH 7064/9987] adding easyconfigs: CppUnit-1.15.1-GCCcore-10.2.0.eb --- .../CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..61e5d8e491f --- /dev/null +++ b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'CppUnit' +version = '1.15.1' + +homepage = 'https://freedesktop.org/wiki/Software/cppunit/' + +description = """ + CppUnit is the C++ port of the famous JUnit framework for unit testing. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://dev-www.libreoffice.org/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['89c5c6665337f56fd2db36bc3805a5619709d51fb136e51937072f63fcc717a7'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['lib/libcppunit.a', 'lib/libcppunit.%s' % SHLIB_EXT, + 'lib/pkgconfig/cppunit.pc'], + 'dirs': ['bin', 'include/cppunit', 'share'], +} + +moduleclass = 'tools' From 5591eb1c417170181ea60432b4ee6a539d5a54c6 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 5 Apr 2023 09:04:02 +0200 Subject: [PATCH 7065/9987] adding easyconfigs: geopandas-0.12.2-foss-2022b.eb, pyproj-3.5.0-GCCcore-12.2.0.eb, Fiona-1.9.2-foss-2022b.eb --- .../f/Fiona/Fiona-1.9.2-foss-2022b.eb | 48 +++++++++++++++++++ .../geopandas/geopandas-0.12.2-foss-2022b.eb | 38 +++++++++++++++ .../p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb | 37 ++++++++++++++ 3 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.9.2-foss-2022b.eb create mode 100644 easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.9.2-foss-2022b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.9.2-foss-2022b.eb new file mode 100644 index 00000000000..024b51efc9f --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.9.2-foss-2022b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.9.2' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('GDAL', '3.6.2'), + ('Shapely', '2.0.1'), # optional for 'calc' extras +] + +use_pip = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'use_pip_extras': 'calc', + 'checksums': ['f9263c5f97206bf2eb2c010d52e8ffc54e96886b0e698badde25ff109b32952a'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["fio --help"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022b.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022b.eb new file mode 100644 index 00000000000..a887dfe6e14 --- /dev/null +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'geopandas' +version = '0.12.2' + +homepage = 'https://github.com/geopandas/geopandas' +description = """GeoPandas is a project to add support for geographic data to pandas objects. +It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series +and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and +perform geometric operations.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Shapely', '2.0.1'), + ('Fiona', '1.9.2'), + ('matplotlib', '3.7.0'), + ('pyproj', '3.5.0'), + ('networkx', '3.0'), # needed by mapclassify + ('scikit-learn', '1.2.1'), # needed by mapclassify +] + +use_pip = True + +exts_list = [ + ('mapclassify', '2.4.3', { + 'checksums': ['51b81e1f1ee7f64a4ca1e9f61f01216c364a3f086a48b1be38eb057199cb19bf'], + }), + (name, version, { + 'checksums': ['0acdacddefa176525e4da6d9aeeece225da26055c4becdc6e97cf40fa97c27f4'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f90f4e9a5b1 --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.5.0' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9859d1591c1863414d875ae0759e72c2cffc01ab989dc64137fbac572cc81bf6'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('PROJ', '9.1.1'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' From 3dcc9283930533263247488ff2141674c7a252f7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 5 Apr 2023 09:49:24 +0200 Subject: [PATCH 7066/9987] add missing dependency on wget to FunGAP v1.1.1 --- easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb index a974e867d2b..f2205d273fb 100644 --- a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb @@ -49,6 +49,7 @@ dependencies = [ ('SAMtools', '1.16.1'), ('SNAP-HMM', '20221022'), ('Trinity', '2.15.1'), + ('wget', '1.21.3'), ] exts_defaultclass = 'PythonPackage' From 88e912c866965ce0ec5ddbda38a68df7bb003cee Mon Sep 17 00:00:00 2001 From: ll4strw Date: Wed, 5 Apr 2023 10:31:34 +0200 Subject: [PATCH 7067/9987] Using SYSTEM toolchain --- .../{cppzmq-4.9.0-GCC-11.2.0.eb => cppzmq-4.9.0.eb} | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/c/cppzmq/{cppzmq-4.9.0-GCC-11.2.0.eb => cppzmq-4.9.0.eb} (67%) diff --git a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb similarity index 67% rename from easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb rename to easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb index e78d4d15a99..0f78f6e8ed9 100644 --- a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb @@ -1,3 +1,4 @@ +# ll4strw Lorentz Institute easyblock = 'CMakeMake' name = 'cppzmq' @@ -6,17 +7,20 @@ version = '4.9.0' homepage = 'https://github.com/zeromq/cppzmq' description = "cppzmq is a C++ binding for libzmq." -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = SYSTEM source_urls = ['https://github.com/zeromq/%(name)s/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['3fdf5b100206953f674c94d40599bdb3ea255244dcc42fab0d75855ee3645581'] builddependencies = [ - ('CMake', '3.22.1'), - ('ZeroMQ', '4.3.4'), + ('binutils', '2.37', '', ('GCCcore', '11.2.0')), + ('CMake', '3.22.1', '', ('GCCcore', '11.2.0')), + ('ZeroMQ', '4.3.4', '', ('GCCcore', '11.2.0')), ] +separate_build_dir = True + sanity_check_paths = { 'files': ['include/zmq.hpp'], 'dirs': ['include', 'lib'], From 8621a5a87da6b5771d1bc456fd526624c2e6b49b Mon Sep 17 00:00:00 2001 From: anselmicz Date: Wed, 5 Apr 2023 11:38:24 +0200 Subject: [PATCH 7068/9987] Add Autotools to builddependencies --- easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb index 45c70aeb5f0..2b6f884979c 100644 --- a/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb @@ -18,6 +18,7 @@ checksums = ['e8ee79b1f399b2d167e6a90de52ccc90e52408f7ade1b9b7135727efe181347f'] builddependencies = [ ('binutils', '2.39'), ('pkgconf', '1.9.3'), + ('Autotools', '20220317'), ] dependencies = [ From 5a53bb06419dfe3e799c803b939bae4ae1a6e8b8 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 12:07:41 +0200 Subject: [PATCH 7069/9987] adding easyconfigs: libevent-2.1.8-GCCcore-8.3.0.eb --- .../libevent/libevent-2.1.8-GCCcore-8.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..7506631c33e --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.8-GCCcore-8.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.8' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['965cc5a8bb46ce4199a47e9b2c9e1cae3b137e8356ffdad6d94d3b9069b71dc2'] + +builddependencies = [ + ('binutils', '2.32'), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' From f9393a8ad3fee6369e40103b6eaa8045dfe99e60 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Wed, 5 Apr 2023 12:10:06 +0200 Subject: [PATCH 7070/9987] Update sysbench-1.0.20-GCC-12.2.0.eb --- easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb index 2b6f884979c..8634f5e8d18 100644 --- a/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb @@ -16,9 +16,9 @@ sources = ['%(version)s.tar.gz'] checksums = ['e8ee79b1f399b2d167e6a90de52ccc90e52408f7ade1b9b7135727efe181347f'] builddependencies = [ + ('Autotools', '20220317'), ('binutils', '2.39'), ('pkgconf', '1.9.3'), - ('Autotools', '20220317'), ] dependencies = [ From ef34c3658a9cdf2b8e6eee6230729a72f0345f00 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 12:18:04 +0200 Subject: [PATCH 7071/9987] adding easyconfigs: netCDF-4.7.4-iompi-2020a.eb --- .../n/netCDF/netCDF-4.7.4-iompi-2020a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iompi-2020a.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iompi-2020a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iompi-2020a.eb new file mode 100644 index 00000000000..85ad26c5284 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iompi-2020a.eb @@ -0,0 +1,35 @@ +name = 'netCDF' +version = '4.7.4' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iompi', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b'] + +builddependencies = [ + ('Autotools', '20180311'), + ('CMake', '3.16.4'), + ('Doxygen', '1.8.17'), +] + +dependencies = [ + ('HDF5', '1.10.6'), + ('cURL', '7.69.1'), + ('Szip', '2.1.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' + From ffaa6289b94b455ebec614671c5495c907399aff Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 13:07:46 +0200 Subject: [PATCH 7072/9987] remove newline at the end --- easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iompi-2020a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iompi-2020a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iompi-2020a.eb index 85ad26c5284..6ac63c3f2f3 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iompi-2020a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.7.4-iompi-2020a.eb @@ -32,4 +32,3 @@ configopts = [ ] moduleclass = 'data' - From e33679eca19da9f396e22e73c7c53fe6af7067a7 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 5 Apr 2023 13:15:22 +0200 Subject: [PATCH 7073/9987] adding easyconfigs: unicore-uftp-1.4.2-Java-1.8.eb --- .../unicore-uftp-1.4.2-Java-1.8.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb diff --git a/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb b/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb new file mode 100644 index 00000000000..cc641945cc6 --- /dev/null +++ b/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'unicore-uftp' +version = '1.4.2' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://sourceforge.net/projects/unicore/' +description = """UNICORE Java-based client for UFTP""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.sourceforge.net/project/unicore/Clients/UFTP-Client/%(version)s'] +sources = ['uftp-client-%(version)s-all.zip'] +checksums = ['49670714416077274a0dfdc261e5552bcabbdd5cc4454181a794158491524c54'] + +# specify dependency on Java/1.8 "wrapper", rather than a specific Java version +dependencies = [('Java', '1.8', '', True)] + +postinstallcmds = ["chmod +x %(installdir)s/bin/uftp"] + +sanity_check_paths = { + 'files': ['bin/uftp'], + 'dirs': ['bin', 'lib'], +} + +sanity_check_commands = [('uftp', '-version')] + +moduleclass = 'tools' From 9b79d406df113d4d746b364bedc32c99ab40f035 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 5 Apr 2023 13:25:25 +0200 Subject: [PATCH 7074/9987] New Longshot using Cargo easyblock --- .../Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb | 319 +++++++++++++++++- 1 file changed, 306 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb index d1e9278c0bf..d24ee4f3b3c 100644 --- a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb @@ -1,8 +1,4 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. -# Updated to 0.4.3 and GCCcore-10.2.0 -# J. Sassmannshausen (GSTT/NHS UK) -# -easyblock = 'Binary' +easyblock = 'Cargo' name = 'Longshot' version = '0.4.5' @@ -15,26 +11,323 @@ description = """Longshot is a variant calling tool for diploid genomes using lo toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -github_account = 'pjedge' -source_urls = [GITHUB_SOURCE] +crates = [ + ('addr2line', '0.19.0'), + ('adler', '1.0.2'), + ('ahash', '0.7.6'), + ('aho-corasick', '0.7.20'), + ('android_system_properties', '0.1.5'), + ('ansi_term', '0.12.1'), + ('approx', '0.3.2'), + ('atty', '0.2.14'), + ('autocfg', '1.1.0'), + ('backtrace', '0.3.67'), + ('bio', '0.25.0'), + ('bio-types', '0.13.0'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bumpalo', '3.12.0'), + ('bv', '0.10.0'), + ('bytecount', '0.3.2'), + ('byteorder', '1.4.3'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.79'), + ('cfg-if', '1.0.0'), + ('chrono', '0.4.24'), + ('clap', '2.34.0'), + ('cmake', '0.1.50'), + ('codespan-reporting', '0.11.1'), + ('core-foundation-sys', '0.8.3'), + ('csv', '1.2.1'), + ('csv-core', '0.1.10'), + ('curl-sys', '0.4.61+curl-8.0.1'), + ('custom_derive', '0.1.7'), + ('cxx', '1.0.94'), + ('cxx-build', '1.0.94'), + ('cxxbridge-flags', '1.0.94'), + ('cxxbridge-macro', '1.0.94'), + ('derive-new', '0.5.9'), + ('either', '1.8.1'), + ('error-chain', '0.12.4'), + ('feature-probe', '0.1.1'), + ('fishers_exact', '1.0.1'), + ('fnv', '1.0.7'), + ('form_urlencoded', '1.1.0'), + ('fs-utils', '1.1.4'), + ('fuchsia-cprng', '0.1.1'), + ('fxhash', '0.2.1'), + ('getrandom', '0.2.8'), + ('gimli', '0.27.2'), + ('glob', '0.3.1'), + ('hashbrown', '0.11.2'), + ('heck', '0.4.1'), + ('hermit-abi', '0.1.19'), + ('hts-sys', '2.0.3'), + ('iana-time-zone', '0.1.54'), + ('iana-time-zone-haiku', '0.1.1'), + ('idna', '0.3.0'), + ('ieee754', '0.2.6'), + ('itertools', '0.7.11'), + ('itertools-num', '0.1.3'), + ('itoa', '1.0.6'), + ('jobserver', '0.1.26'), + ('js-sys', '0.3.61'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.140'), + ('libz-sys', '1.1.8'), + ('linear-map', '1.2.0'), + ('link-cplusplus', '1.0.8'), + ('log', '0.4.17'), + ('lzma-sys', '0.1.20'), + ('matrixmultiply', '0.1.15'), + ('memchr', '2.5.0'), + ('miniz_oxide', '0.6.2'), + ('multimap', '0.4.0'), + ('ndarray', '0.12.1'), + ('newtype_derive', '0.1.6'), + ('num-complex', '0.2.4'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.15'), + ('object', '0.30.3'), + ('once_cell', '1.17.1'), + ('openssl-src', '111.25.2+1.1.1t'), + ('openssl-sys', '0.9.83'), + ('ordered-float', '1.1.1'), + ('percent-encoding', '2.2.0'), + ('pkg-config', '0.3.26'), + ('ppv-lite86', '0.2.17'), + ('proc-macro2', '1.0.54'), + ('quick-error', '1.2.3'), + ('quote', '1.0.26'), + ('rand', '0.3.23'), + ('rand', '0.4.6'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.3.1'), + ('rand_core', '0.4.2'), + ('rand_core', '0.6.4'), + ('rawpointer', '0.1.0'), + ('rdrand', '0.4.0'), + ('regex', '1.7.3'), + ('regex-syntax', '0.6.29'), + ('rust-htslib', 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{'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'}, + {'syn-2.0.12.tar.gz': '79d9531f94112cfc3e4c8f5f02cb2b58f72c97b7efd85f70203cc6d8efda5927'}, + {'termcolor-1.2.0.tar.gz': 'be55cf8942feac5c765c2c993422806843c9a9a45d4d5c407ad6dd2ea95eb9b6'}, + {'textwrap-0.11.0.tar.gz': 'd326610f408c7a4eb6f51c37c330e496b08506c9457c9d34287ecc38809fb060'}, + {'thiserror-1.0.40.tar.gz': '978c9a314bd8dc99be594bc3c175faaa9794be04a5a5e153caba6915336cebac'}, + {'thiserror-impl-1.0.40.tar.gz': 'f9456a42c5b0d803c8cd86e73dd7cc9edd429499f37a3550d286d5e86720569f'}, + {'time-0.1.45.tar.gz': '1b797afad3f312d1c66a56d11d0316f916356d11bd158fbc6ca6389ff6bf805a'}, + {'tinyvec-1.6.0.tar.gz': '87cc5ceb3875bb20c2890005a4e226a4651264a5c75edb2421b52861a0a0cb50'}, + {'tinyvec_macros-0.1.1.tar.gz': '1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20'}, + {'unicode-bidi-0.3.13.tar.gz': '92888ba5573ff080736b3648696b70cafad7d250551175acbaa4e0385b3e1460'}, + {'unicode-ident-1.0.8.tar.gz': 'e5464a87b239f13a63a501f2701565754bae92d243d4bb7eb12f6d57d2269bf4'}, + {'unicode-normalization-0.1.22.tar.gz': '5c5713f0fc4b5db668a2ac63cdb7bb4469d8c9fed047b1d0292cc7b0ce2ba921'}, + {'unicode-width-0.1.10.tar.gz': 'c0edd1e5b14653f783770bce4a4dabb4a5108a5370a5f5d8cfe8710c361f6c8b'}, + {'url-2.3.1.tar.gz': '0d68c799ae75762b8c3fe375feb6600ef5602c883c5d21eb51c09f22b83c4643'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'vec_map-0.8.2.tar.gz': 'f1bddf1187be692e79c5ffeab891132dfb0f236ed36a43c7ed39f1165ee20191'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'wasi-0.10.0+wasi-snapshot-preview1.tar.gz': '1a143597ca7c7793eff794def352d41792a93c481eb1042423ff7ff72ba2c31f'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'wasm-bindgen-0.2.84.tar.gz': '31f8dcbc21f30d9b8f2ea926ecb58f6b91192c17e9d33594b3df58b2007ca53b'}, + {'wasm-bindgen-backend-0.2.84.tar.gz': '95ce90fd5bcc06af55a641a86428ee4229e44e07033963a2290a8e241607ccb9'}, + {'wasm-bindgen-macro-0.2.84.tar.gz': '4c21f77c0bedc37fd5dc21f897894a5ca01e7bb159884559461862ae90c0b4c5'}, + {'wasm-bindgen-macro-support-0.2.84.tar.gz': '2aff81306fcac3c7515ad4e177f521b5c9a15f2b08f4e32d823066102f35a5f6'}, + {'wasm-bindgen-shared-0.2.84.tar.gz': '0046fef7e28c3804e5e38bfa31ea2a0f73905319b677e57ebe37e49358989b5d'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.5.tar.gz': '70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-0.46.0.tar.gz': 'cdacb41e6a96a052c6cb63a144f24900236121c6f63f4f8219fef5977ecb0c25'}, + {'windows-targets-0.42.2.tar.gz': '8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071'}, + {'windows_aarch64_gnullvm-0.42.2.tar.gz': '597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8'}, + {'windows_aarch64_msvc-0.42.2.tar.gz': 'e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43'}, + {'windows_i686_gnu-0.42.2.tar.gz': 'c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f'}, + {'windows_i686_msvc-0.42.2.tar.gz': '44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060'}, + {'windows_x86_64_gnu-0.42.2.tar.gz': '8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36'}, + {'windows_x86_64_gnullvm-0.42.2.tar.gz': '26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3'}, + {'windows_x86_64_msvc-0.42.2.tar.gz': '9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0'}, +] builddependencies = [ ('binutils', '2.38'), ('Rust', '1.65.0'), ('Clang', '13.0.1'), - ('CMake', '3.23.1'), + ('Perl', '5.34.1'), + ('CMake', '3.24.3'), ] dependencies = [ ('bzip2', '1.0.8'), ] -extract_sources = True - -install_cmd = "cargo install --root %(installdir)s --path ." - sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': [], From 714b5cb02c4cbfdc23ecf98ccf268e8699788db4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Wed, 5 Apr 2023 14:00:36 +0200 Subject: [PATCH 7075/9987] Add libsystemd-dev and systemd-devel as OS dependencies --- easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb index 1d50e1ff0c1..b6e1bf489ae 100644 --- a/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb @@ -23,6 +23,8 @@ dependencies = [ ('libdrm', '2.4.114'), ] +osdependencies = [('libsystemd-dev', 'systemd-devel')] + separate_build_dir = True sanity_check_paths = { From d7c96f8050af74e8158c9197e97502c4ca4d3480 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Wed, 5 Apr 2023 14:10:55 +0200 Subject: [PATCH 7076/9987] Add libudev-dev OS dependecy for compatibility with Ubuntu 18.04 --- easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb index b6e1bf489ae..c4dd3f56af6 100644 --- a/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('libdrm', '2.4.114'), ] -osdependencies = [('libsystemd-dev', 'systemd-devel')] +osdependencies = [('libsystemd-dev', 'libudev-dev', 'systemd-devel')] separate_build_dir = True From d704176b57465f43e0a9ec22f4885fe2f13f9a63 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 5 Apr 2023 19:05:50 +0200 Subject: [PATCH 7077/9987] adding easyconfigs: R-MXM-1.5.5-foss-2021b.eb --- .../r/R-MXM/R-MXM-1.5.5-foss-2021b.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-MXM/R-MXM-1.5.5-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/R-MXM/R-MXM-1.5.5-foss-2021b.eb b/easybuild/easyconfigs/r/R-MXM/R-MXM-1.5.5-foss-2021b.eb new file mode 100644 index 00000000000..fbbc6f6be34 --- /dev/null +++ b/easybuild/easyconfigs/r/R-MXM/R-MXM-1.5.5-foss-2021b.eb @@ -0,0 +1,54 @@ +easyblock = 'Bundle' + +name = 'R-MXM' +version = '1.5.5' + +homepage = 'https://cran.r-project.org/package=MXM' +description = "MXM: Feature Selection (Including Multiple Solutions) and Bayesian Networks" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('R', '4.1.2'), +] + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_list = [ + ('sets', '1.0-24', { + 'checksums': ['e75733f5c9418eb09fb950a4a94ccf84ddd88231c61ee80d02b7f0917debcac9'], + }), + ('relations', '0.6-13', { + 'checksums': ['f859c336fb0c4a2df7f294b33d1d04f95c6988e5e76933e2e70bf291d904d9da'], + }), + ('RcppZiggurat', '0.1.6', { + 'checksums': ['9c78255ca476c945c05a564d1e4da363de714d890e0e27f3b252fd73c50eed71'], + }), + ('Rfast', '2.0.7', { + 'checksums': ['8f86159a4760a7124e1c91ae0b022c7e496f81590ea4e4af702bea44e8dedf8f'], + }), + ('Rfast2', '0.1.4', { + 'checksums': ['494b777a86342aae0a6a5f0eb189337b846ef2929964672c0f010d93699d0d63'], + }), + ('MXM', version, { + 'checksums': ['943d7d3ff8496bad43329614922795b0777fa0787fdfd98f71d90a1a9c952497'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['MXM'], +} + +moduleclass = 'math' From 8a0a3f6ac9489d5296711320b746ca7426fb055a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 6 Apr 2023 15:33:08 +0200 Subject: [PATCH 7078/9987] add Compress-Raw-Zlib dep --- .../easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb index 1f52ef21a7d..7e0b6557ddd 100644 --- a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb @@ -17,6 +17,7 @@ dependencies = [ ('Jellyfish', '2.3.0'), ('Perl', '5.34.1'), ('bzip2', '1.0.8'), + ('Compress-Raw-Zlib', '2.202'), ] extract_sources = True From 219658ccea7912568645a4c92490a16ff8d82ae9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 6 Apr 2023 15:57:06 +0200 Subject: [PATCH 7079/9987] add sanity_check_commands --- easybuild/easyconfigs/z/zsh/zsh-5.9.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.9.eb b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb index ff8bd3f2190..5c8ea48d53c 100644 --- a/easybuild/easyconfigs/z/zsh/zsh-5.9.eb +++ b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb @@ -25,6 +25,8 @@ sanity_check_paths = { 'dirs': ['lib/zsh/%(version)s', 'share'], } +sanity_check_commands = ['zsh --version'] + # optionally make this module sticky (lmod only): # modluafooter = 'add_property("lmod", "sticky")' From 9dcfc5b6df98b20b68b7be355724697595ac0082 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 6 Apr 2023 16:27:48 +0000 Subject: [PATCH 7080/9987] adding easyconfigs: Seurat-4.3.0-foss-2022a-R-4.2.1.eb --- .../Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..3529ca55994 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,72 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.3.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} + +exts_list = [ + ('Matrix', '1.5-4', { + 'checksums': ['15ceb61993d61b442068104abb46e6d91b5a1179c01eeb64563b853abab66f06'], + }), + ('sp', '1.5-1', { + 'checksums': ['69b9eab481d389bbb736d2adcf50c180aca248c3ffc4ebda8ffe2accc5f229df'], + }), + ('SeuratObject', '4.1.3', { + 'checksums': ['585d2754f6165a367f0f458523f0a25d4d4160c929c931b27c5603cc6bd986d3'], + }), + ('sctransform', '0.3.5', { + 'checksums': ['c08e56df05d64ed04ee53eb9e1d4d321da8aff945e36d56db1d5ceb1cd7e6e0b'], + }), + ('uwot', '0.1.14', { + 'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'], + }), + ('spatstat.utils', '3.0-1', { + 'checksums': ['cba1c7806564fd9145ca15edf77233d6ba5609f0989f7812221f5fc1ece0b91a'], + }), + ('spatstat.data', '3.0-0', { + 'checksums': ['cff9058a88489020a4a05b9576cd452f37fa9b42084873c474d06931f5187057'], + }), + ('spatstat.geom', '3.0-3', { + 'checksums': ['6e5b56c60e774a0cdcaa5a8ffde071225f233832446a341588bd8a7840913c84'], + }), + ('spatstat.random', '3.0-1', { + 'checksums': ['938c845c063b8781bf894c0a67537e7b2a7c425a4beba4a95ec9d2c37b43e5b6'], + }), + ('spatstat.sparse', '3.0-0', { + 'checksums': ['99be0a3c7592760fdf1668dc0811f75ed91c400390d1ecc3d5e643255f501ad2'], + }), + ('spatstat.explore', '3.0-5', { + 'checksums': ['9f438a12fac3f3e1d0bd550b1393c1e5732be694517b0878db09da557d6dc862'], + }), + (name, version, { + 'checksums': ['7ebacb3b86f74279de60b597f9a6e728f0668719811b0dca3425d21762fff97c'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From e5c0fa47b5d50da70b23e6b73c2f07c3bc76403a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Apr 2023 11:38:15 +0200 Subject: [PATCH 7081/9987] adding easyconfigs: bwa-meth-0.2.6-GCC-11.3.0.eb --- .../b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb new file mode 100644 index 00000000000..238b5bbcf7b --- /dev/null +++ b/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb @@ -0,0 +1,50 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'bwa-meth' +version = '0.2.6' + +homepage = 'https://github.com/brentp/bwa-meth' +description = """Fast and accurante alignment of BS-Seq reads.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('SAMtools', '1.13'), + ('BWA', '0.7.17'), +] + +use_pip = True + +exts_list = [ + ('toolshed', '0.4.6', { + 'checksums': ['23a31c177bf84244b30a9f12c7a8a17a66a2d63043ead0460c31b9ff42f9fb93'], + }), + (name, version, { + 'source_urls': ['https://github.com/brentp/bwa-meth/archive'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['c1d98aa6d34f103752de7ff3148c9586e5571417accb4a39f5bac8546dab497d'], + # fix TypeError when using --help, see https://github.com/brentp/bwa-meth/pull/87 + 'preinstallopts': "sed -i 's/44% /44%% /g' bwameth.py && ", + 'modulename': 'bwameth', + }), +] + +fix_python_shebang_for = ['bin/bwameth.py', 'bin/toolshed'] + +sanity_check_paths = { + 'files': ['bin/bwameth.py', 'bin/toolshed'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "toolshed --help", + "bwameth.py --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 90ac6ef33c398fd9a210e9e58fe009e2eb9b3520 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Apr 2023 22:59:29 +0200 Subject: [PATCH 7082/9987] adding easyconfigs: SMAP-4.6.5-foss-2022a.eb and patches: SMAP-4.6.5_no-bin-bedtools.patch --- .../s/SMAP/SMAP-4.6.5-foss-2022a.eb | 80 +++++++++++++++++++ .../s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch | 15 ++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch diff --git a/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb new file mode 100644 index 00000000000..ecf81cc47c8 --- /dev/null +++ b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb @@ -0,0 +1,80 @@ +easyblock = 'PythonBundle' + +name = 'SMAP' +version = '4.6.5' + +homepage = 'https://ngs-smap.readthedocs.io' +description = "SMAP is an analysis tool for stack-based NGS read mapping" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for pandas + ('matplotlib', '3.5.2'), + ('BEDTools', '2.30.0'), + ('pybedtools', '0.9.0'), + ('Pysam', '0.19.1'), + ('Biopython', '1.79'), + ('openpyxl', '3.0.10'), + ('plotly.py', '5.12.0'), +] + +use_pip = True + +exts_list = [ + ('setuptools', '67.6.1', { + 'checksums': ['257de92a9d50a60b8e22abfcbb771571fde0dbf3ec234463212027a4eeecbe9a'], + }), + ('colorlog', '6.7.0', { + 'checksums': ['bd94bd21c1e13fac7bd3153f4bc3a7dc0eb0974b8bc2fdf1a989e474f6e582e5'], + }), + ('primer3-py', '1.2.0', { + 'checksums': ['9e511e90987d4beda11f1f065b81805bc0c26a08084154e87fda46136ecf7518'], + 'modulename': 'primer3', + }), + ('dnaio', '0.10.0', { + 'checksums': ['de51a50948f00b864297d74eddb588fbee5ac229855754e77564d18b24619d18'], + }), + ('isal', '1.1.0', { + 'checksums': ['1364f4e3255a57d51c01422ab3ae785a43c076d516ebf49f6a25adecf8232105'], + }), + ('xopen', '1.7.0', { + 'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'], + }), + # smap-haplotype-window 1.8.1 requires cutadapt <= 4.1 (requires cutadapt.utils.reverse_complemented_sequence) + ('cutadapt', '4.1', { + 'checksums': ['be745ff24adfb4a3eaf715dfad0e2ccdfad7792ef00c1122adf4fbf3aed9227b'], + }), + ('ngs-smap', version, { + 'patches': ['SMAP-4.6.5_no-bin-bedtools.patch'], + 'checksums': [ + {'ngs-smap-4.6.5.tar.gz': 'bd6fd5a9fb5be66c5d21410376ed6b13eeb23da040c498d60dad6a8fb45d9d5e'}, + {'SMAP-4.6.5_no-bin-bedtools.patch': 'a43460694378628129d2cd3373e850fccb2ca330680f6fea3e31db9e4589d7ca'}, + ], + 'preinstallopts': "rm bin/bedtools && sed -i 's/~=/>=/g' setup.cfg && ", + 'modulename': 'smap', + }), + ('smap-haplotype-window', '1.8.1', { + 'checksums': ['5e244ecec8cb798d294014378c735dd2ab3d32f8266c7d161cf733099715fbbe'], + 'modulename': 'smap_window', + }), + ('gffpandas', '1.2.0', { + 'checksums': ['1a1e1c5c5120bf46ec57517222ebb42ffaab3f768c972fec54c4ac1b07b7f0c6'], + }), + ('smap-effect-prediction', '0.1.2', { + 'checksums': ['af16135eb3a2d9c22287a06d595010c46957711358734d73daaa21059ac27ca2'], + 'preinstallopts': "sed -i 's/~=/>=/g' setup.cfg && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/smap'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["smap compare --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch new file mode 100644 index 00000000000..a895ac74cab --- /dev/null +++ b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch @@ -0,0 +1,15 @@ +don't install pre-compiled 'bedtools' binary, since BEDTools is provided as a proper dependency via EasyBuild +author: Kenneth Hoste (HPC-UGent) +--- ngs-smap-4.6.5/setup.cfg.orig 2022-10-11 09:59:22.522325500 +0200 ++++ ngs-smap-4.6.5/setup.cfg 2023-04-07 16:48:58.434620448 +0200 +@@ -49,10 +49,6 @@ + sphinx_rtd_theme~=1.0.0 + sphinx-tabs~=3.2.0 + +-[options.data_files] +-bin = +- bin/bedtools +- + [egg_info] + tag_build = + tag_date = 0 From 637f36b8748747e63d85c6eb66c7877f0c46c98f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Apr 2023 10:47:42 +0200 Subject: [PATCH 7083/9987] add Autotools build dependency for SMAP, required for isal --- easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb index ecf81cc47c8..d72d6e89e6b 100644 --- a/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb @@ -8,6 +8,10 @@ description = "SMAP is an analysis tool for stack-based NGS read mapping" toolchain = {'name': 'foss', 'version': '2022a'} +builddependencies = [ + ('Autotools', '20220317'), # required for isal +] + dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), # for pandas From f4580f79340e4d036cd0d9f43b6f54b936335d6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 8 Apr 2023 15:03:13 +0200 Subject: [PATCH 7084/9987] Patch UCC to support multiple component paths --- ...C-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb | 12 ++--- .../u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb | 6 ++- .../UCC-1.1.0-multiple_component_paths.patch | 46 +++++++++++++++++++ 3 files changed, 55 insertions(+), 9 deletions(-) create mode 100644 easybuild/easyconfigs/u/UCC/UCC-1.1.0-multiple_component_paths.patch diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb index e607ff3eb14..f7b2a90b694 100644 --- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -42,20 +42,16 @@ dependencies = [ preconfigopts = "./autogen.sh && " -buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1' -installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install' - -# UCC_COMPONENT_PATH completely overrides $EBROOTUCC/lib/ucc so install symbolic links -# to existing non CUDA related components -postinstallcmds = ['for i in $EBROOTUCC/lib/ucc/*; do ln -s $i %(installdir)s/lib/ucc; done'] +buildopts = '-C src/components/mc/cuda V=1 ' #&& make -C src/components/tl/nccl V=1' +installopts = '-C src/components/mc/cuda ' #&& make -C src/components/tl/nccl install' sanity_check_paths = { - 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], + 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT], #, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], 'dirs': ['lib'] } sanity_check_commands = ["ucc_info -c"] -modextravars = {'UCC_COMPONENT_PATH': '%(installdir)s/lib/ucc'} +modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': '%(installdir)s/lib/ucc'} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb index b5ff6ef4e42..8c350bb641b 100644 --- a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb @@ -14,7 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] -checksums = ['74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'] +patches = ['UCC-%(version)s-multiple_component_paths.patch'] +checksums = [ + {'v1.1.0.tar.gz': '74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'}, + {'UCC-1.1.0-multiple_component_paths.patch': '3081d0f694331daa4a88a0fa3fb54b9a918015248ae5eb7b3157b924abd31bee'}, +] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-multiple_component_paths.patch b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-multiple_component_paths.patch new file mode 100644 index 00000000000..0e13578b55f --- /dev/null +++ b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-multiple_component_paths.patch @@ -0,0 +1,46 @@ +Adds support for multiple extra components paths to UCC +Was necessary to add, as they broke the logic we used for UCC_COMPONEN_PATH in 1.1.0, +then removed it completely in 1.2.0. +This patch also removes the need to copy over all the other plugins, thus supporting multiple external components. + +author: micketeer@gmail.com + +diff -ru ucc-1.1.0.orig/src/utils/ucc_component.c ucc-1.1.0.fixed/src/utils/ucc_component.c +--- ucc-1.1.0.orig/src/utils/ucc_component.c 2023-04-06 15:16:18.341729973 +0200 ++++ ucc-1.1.0.fixed/src/utils/ucc_component.c 2023-04-08 13:42:28.448319486 +0200 +@@ -128,6 +128,27 @@ + return UCC_ERR_INVALID_PARAM; + } + ++ char *extra_component_path = getenv("EB_UCC_EXTRA_COMPONENT_PATH"); ++ if (extra_component_path) { ++ // Add extra room for extra paths, braces and comma (+3): ++ pattern_size = ++ strlen(ucc_global_config.component_path) + strlen(framework_name) + 16 + strlen(extra_component_path) + 3; ++ full_pattern = (char *)ucc_malloc(pattern_size, "full_pattern"); ++ if (!full_pattern) { ++ ucc_error("failed to allocate %zd bytes for full_pattern", ++ pattern_size); ++ return UCC_ERR_NO_MEMORY; ++ } ++ ucc_snprintf_safe(full_pattern, pattern_size, "{%s,%s}/libucc_%s_*.so", ++ extra_component_path, ucc_global_config.component_path, framework_name); ++ // Replace ; typically used in PATHs variables with , for glob ++ char *current_pos = strchr(full_pattern, ';'); ++ while (current_pos) { ++ *current_pos = ','; ++ current_pos = strchr(current_pos, ';'); ++ } ++ glob(full_pattern, GLOB_BRACE, NULL, &globbuf); ++ } else { + pattern_size = + strlen(ucc_global_config.component_path) + strlen(framework_name) + 16; + full_pattern = (char *)ucc_malloc(pattern_size, "full_pattern"); +@@ -139,6 +160,7 @@ + ucc_snprintf_safe(full_pattern, pattern_size, "%s/libucc_%s_*.so", + ucc_global_config.component_path, framework_name); + glob(full_pattern, 0, NULL, &globbuf); ++ } + ucc_free(full_pattern); + n_loaded = 0; + From b0138c820fde82995c901a131040efb80277ec0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 8 Apr 2023 16:06:32 +0200 Subject: [PATCH 7085/9987] Undo commented stuff in UCC-CUDA --- .../u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb index f7b2a90b694..971f57d306a 100644 --- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -42,11 +42,11 @@ dependencies = [ preconfigopts = "./autogen.sh && " -buildopts = '-C src/components/mc/cuda V=1 ' #&& make -C src/components/tl/nccl V=1' -installopts = '-C src/components/mc/cuda ' #&& make -C src/components/tl/nccl install' +buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1' +installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install' sanity_check_paths = { - 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT], #, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], + 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], 'dirs': ['lib'] } From 9a48138ce60f4c1469a03cd3df499328a3cce16e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 8 Apr 2023 17:04:45 +0200 Subject: [PATCH 7086/9987] Fix relative path for new env var --- .../u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb index 971f57d306a..bfe211063d3 100644 --- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -52,6 +52,6 @@ sanity_check_paths = { sanity_check_commands = ["ucc_info -c"] -modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': '%(installdir)s/lib/ucc'} +modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': 'lib/ucc'} moduleclass = 'lib' From dc7c31d6487cb8c9780acceade995f3162025a8b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 8 Apr 2023 18:15:32 +0200 Subject: [PATCH 7087/9987] adding easyconfigs: astropy-4.2.1-foss-2020b.eb, astropy-4.2.1-intel-2020b.eb, astropy-5.2.2-gfbf-2022b.eb --- .../a/astropy/astropy-4.2.1-foss-2020b.eb | 40 +++++++++++++++++++ .../a/astropy/astropy-4.2.1-intel-2020b.eb | 40 +++++++++++++++++++ .../a/astropy/astropy-5.2.2-gfbf-2022b.eb | 37 +++++++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb create mode 100644 easybuild/easyconfigs/a/astropy/astropy-5.2.2-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb new file mode 100644 index 00000000000..879b5774c38 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '4.2.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '1.7.3', { + 'modulename': 'erfa', + 'checksums': ['6cf3a645d63e0c575a357797903eac5d2c6591d7cdb89217c8c4d39777cf18cb'], + }), + ('extension-helpers', '0.1', { + 'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'], + }), + (name, version, { + 'checksums': ['ed483e472241153daec45f4b0c318c2c63d9f47305b78e6e63d32fc388c18427'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], +} + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb new file mode 100644 index 00000000000..878eb8ce9fb --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '4.2.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '1.7.3', { + 'modulename': 'erfa', + 'checksums': ['6cf3a645d63e0c575a357797903eac5d2c6591d7cdb89217c8c4d39777cf18cb'], + }), + ('extension-helpers', '0.1', { + 'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'], + }), + (name, version, { + 'checksums': ['ed483e472241153daec45f4b0c318c2c63d9f47305b78e6e63d32fc388c18427'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], +} + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/a/astropy/astropy-5.2.2-gfbf-2022b.eb b/easybuild/easyconfigs/a/astropy/astropy-5.2.2-gfbf-2022b.eb new file mode 100644 index 00000000000..16a33151336 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-5.2.2-gfbf-2022b.eb @@ -0,0 +1,37 @@ +easyblock = "PythonBundle" + +name = 'astropy' +version = '5.2.2' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop a common +core package for Astronomy in Python and foster an ecosystem of interoperable +astronomy packages. + +The Astropy community is committed to supporting diversity and inclusion.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '2.0.0.3', { + 'modulename': 'erfa', + 'checksums': ['d77fbbfa58350c194ccb99e5d93aa05d3c2b14d5aad8b662d93c6ad9fff41f39'], + }), + ('extension-helpers', '1.0.0', { + 'checksums': ['ca1bfac67c79cf4a7a0c09286ce2a24eec31bf17715818d0726318dd0e5050e6'], + }), + (name, version, { + 'checksums': ['e6a9e34716bda5945788353c63f0644721ee7e5447d16b1cdcb58c48a96b0d9c'], + }), +] + +moduleclass = 'astro' From 96f28132496fed1a9a7d2fb7c50a355009e9441e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Apr 2023 18:27:23 +0200 Subject: [PATCH 7088/9987] {toolchain} intel/2023.03 --- .../h/HPL/HPL-2.3-intel-2023.03.eb | 21 ++++++++ .../easyconfigs/i/iimpi/iimpi-2023.03.eb | 18 +++++++ .../imkl-FFTW-2023.1.0-iimpi-2023.03.eb | 11 ++++ easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb | 18 +++++++ .../impi-2021.9.0-intel-compilers-2023.1.0.eb | 16 ++++++ .../intel-compilers-2023.1.0.eb | 37 +++++++++++++ .../easyconfigs/i/intel/intel-2023.03.eb | 22 ++++++++ .../u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ 8 files changed, 195 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.03.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2023.03.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023.03.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2023.03.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.03.eb new file mode 100644 index 00000000000..10fe0118177 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.03.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2023.03'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2023.03.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2023.03.eb new file mode 100644 index 00000000000..0bb3e2c0aba --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2023.03.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2023.03' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2023.1.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.9.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023.03.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023.03.eb new file mode 100644 index 00000000000..3809bf2daac --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023.03.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2023.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2023.03'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb new file mode 100644 index 00000000000..2dd371edc01 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2023.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cd17b7fe-500e-4305-a89b-bd5b42bfd9f8/'] +sources = ['l_onemkl_p_%(version)s.46342_offline.sh'] +checksums = ['cc28c94cab23c185520b93c5a04f3979d8da6b4c90cee8c0681dd89819d76167'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb new file mode 100644 index 00000000000..6e886d07ac1 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.9.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/718d6f8f-2546-4b36-b97b-bc58d5482ebf/'] +sources = ['l_mpi_oneapi_p_%(version)s.43482_offline.sh'] +checksums = ['5c170cdf26901311408809ced28498b630a494428703685203ceef6e62735ef8'] + +dependencies = [('UCX', '1.14.0')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb new file mode 100644 index 00000000000..91d2ec40b6e --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb @@ -0,0 +1,37 @@ +name = 'intel-compilers' +version = '2023.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/89283df8-c667-47b0-b7e1-c4573e37bd3e/', + ], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.46347_offline.sh', + }, + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/150e0430-63df-48a0-8469-ecebff0a1858/', + ], + 'filename': 'l_fortran-compiler_p_%(version)s.46348_offline.sh', + }, +] +checksums = [ + {'l_dpcpp-cpp-compiler_p_2023.1.0.46347_offline.sh': + '3ac1c1179501a2646cbb052b05426554194573b4f8e2344d7699eed03fbcfa1d'}, + {'l_fortran-compiler_p_2023.1.0.46348_offline.sh': + '7639af4b6c928e9e3ba92297a054f78a55f4f4d0db9db0d144cc6653004e4f24'}, +] + +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2023.03.eb b/easybuild/easyconfigs/i/intel/intel-2023.03.eb new file mode 100644 index 00000000000..9c71d4bc13e --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2023.03.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2023.03' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2023.1.0' +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.9.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..c84b1e48791 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.14.0' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', +] +checksums = [ + {'ucx-1.14.0.tar.gz': '9bd95e2059de5dece9dddd049aacfca3d21bfca025748a6a0b1be4486e28afdd'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.12'), + ('numactl', '2.0.16'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From e1ff56a686022bea3adbe2488f5659d6f2a985af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Apr 2023 18:40:17 +0200 Subject: [PATCH 7089/9987] adding easyconfigs: sceasy-0.0.7-foss-2022a-R-4.2.1.eb, loompy-3.0.7-foss-2022a.eb, anndata-0.8.0-foss-2022a.eb --- .../a/anndata/anndata-0.8.0-foss-2022a.eb | 38 ++++++++++++++++++ .../l/loompy/loompy-3.0.7-foss-2022a.eb | 39 +++++++++++++++++++ .../sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb | 34 ++++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/a/anndata/anndata-0.8.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.8.0-foss-2022a.eb b/easybuild/easyconfigs/a/anndata/anndata-0.8.0-foss-2022a.eb new file mode 100644 index 00000000000..38ef7f588ea --- /dev/null +++ b/easybuild/easyconfigs/a/anndata/anndata-0.8.0-foss-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'anndata' +version = '0.8.0' + +homepage = 'https://github.com/scverse/anndata' +description = """anndata is a Python package for handling annotated data matrices in memory and on disk, + positioned between pandas and xarray""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + (name, version, { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/natsort'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["natsort --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2022a.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2022a.eb new file mode 100644 index 00000000000..a718a90a243 --- /dev/null +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'loompy' +version = '3.0.7' + +homepage = 'https://loompy.org/' +description = "Python implementation of the Loom file format, an efficient file format for large omics datasets" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('numba', '0.56.4'), +] + +use_pip = True + +exts_list = [ + ('numpy-groupies', '0.9.20', { + 'sources': ['numpy_groupies-%(version)s.tar.gz'], + 'checksums': ['923a382d6bc6876384b58a9c0503b05b9d36a660f329695c2d33e4f93fcbbe3d'], + }), + (name, version, { + 'checksums': ['b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/loompy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["loompy --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..b20476c22cc --- /dev/null +++ b/easybuild/easyconfigs/s/sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'sceasy' +version = '0.0.7' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/cellgeni/sceasy' +description = "sceasy is a package that helps easy conversion of different single-cell data formats to each other" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/cellgeni/sceasy/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bc6a2dba2111067f3247ff1ee617cc85ab6c7d89950f7d8ca486a3e34b27f9d6'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('Seurat', '4.3.0', versionsuffix), + ('anndata', '0.8.0'), + ('loompy', '3.0.7'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +sanity_check_commands = [ + """echo "library(reticulate); reticulate::import('anndata');" | R -q --no-save""", + """echo "library(reticulate); reticulate::import('loompy');" | R -q --no-save""", +] + +moduleclass = 'bio' From 5a02c19e20059754d3f3e04593b3b85d336212a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 8 Apr 2023 19:06:00 +0200 Subject: [PATCH 7090/9987] adding easyconfigs: infercnvpy-0.4.2-foss-2022a.eb --- .../infercnvpy/infercnvpy-0.4.2-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.2-foss-2022a.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.2-foss-2022a.eb new file mode 100644 index 00000000000..58e1804543b --- /dev/null +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.2-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'infercnvpy' +version = '0.4.2' + +homepage = 'https://github.com/icbi-lab/infercnvpy' +description = "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), + ('IPython', '8.5.0'), + ('leidenalg', '0.9.1'), + ('scanpy', '1.9.1'), + ('polars', '0.15.6'), # required by gtfparse +] + +use_pip = True + +# avoid hatchling requirement to install infercnvpy +# (since installing it introduces conflicting version requirements with poetry included with Python) +local_preinstallopts = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ +local_preinstallopts += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ +local_preinstallopts += r"""-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ + +exts_list = [ + ('setuptools', '67.6.1', { + 'checksums': ['257de92a9d50a60b8e22abfcbb771571fde0dbf3ec234463212027a4eeecbe9a'], + }), + ('gtfparse', '2.0.1', { + 'checksums': ['c45439af58cb48120910bebe4625371d8fb5735f12a749e8933c9d6f2b1a558c'], + }), + ('pyreadr', '0.4.7', { + 'checksums': ['901110d62b4bedaef288f4db81425fb696edc721fe2c34c1083f5fb11050a73c'], + }), + ('session-info', '1.0.0', { + 'sources': ['session_info-%(version)s.tar.gz'], + 'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'], + }), + (name, version, { + 'checksums': ['3cfd23afc2dbbca3508a305032c032440d2af292d037d43a7b5046c7bd36ed22'], + 'preinstallopts': local_preinstallopts, + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From dc8e96c889bcb4dad2db713d1464b61767295bba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 16:07:48 +0200 Subject: [PATCH 7091/9987] add local::lib extension to recent Perl easyconfigs --- easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 5 +++++ 4 files changed, 20 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 1211efd9bff..6f534c52ba2 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1834,6 +1834,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index 1750e4abff0..be9cf2ec1fc 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -1944,6 +1944,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 78044193927..00c76287298 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -1934,6 +1934,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 6a7989e6d2a..68757e61f49 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -1944,6 +1944,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), ] moduleclass = 'lang' From 67820cf529c208e509da3c95b1b1a9debfbb3a55 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 18:03:24 +0200 Subject: [PATCH 7092/9987] adding easyconfigs: tRNAscan-SE-2.0.12-GCC-11.2.0.eb --- .../tRNAscan-SE-2.0.12-GCC-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-GCC-11.2.0.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-GCC-11.2.0.eb new file mode 100644 index 00000000000..8260f1d0d1f --- /dev/null +++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'tRNAscan-SE' +version = '2.0.12' + +homepage = 'https://github.com/UCSC-LoweLab/tRNAscan-SE' +description = "A program for detection of tRNA genes" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/UCSC-LoweLab/tRNAscan-SE/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b255c2c5e0255381194166f857ab2ea21c55aa7de409e201333ba615aa3dc61'] + +dependencies = [ + ('Perl', '5.34.0'), +] + +fix_perl_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/covels-SE', 'bin/tRNAscan-SE'], + 'dirs': ['include', 'lib/tRNAscan-SE'], +} + +sanity_check_commands = ["tRNAscan-SE --help"] + +moduleclass = 'bio' From 4f06346ff13d745b873ad3afdf1ca2778033d558 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 18:03:38 +0200 Subject: [PATCH 7093/9987] adding easyconfigs: tantan-40-GCC-11.2.0.eb --- .../t/tantan/tantan-40-GCC-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/t/tantan/tantan-40-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/t/tantan/tantan-40-GCC-11.2.0.eb b/easybuild/easyconfigs/t/tantan/tantan-40-GCC-11.2.0.eb new file mode 100644 index 00000000000..b6064225cd3 --- /dev/null +++ b/easybuild/easyconfigs/t/tantan/tantan-40-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'tantan' +version = '40' + +homepage = 'https://gitlab.com/mcfrith/tantan' +description = "tantan identifies simple regions / low complexity / tandem repeats in DNA or protein sequences" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://gitlab.com/mcfrith/tantan/-/archive/%(version)s/'] +sources = ['tantan-%(version)s.tar.gz'] +checksums = ['61303c88cdf41fa5bcb5f77f674b4fac2a9bc0e4c9abb3b9d75af35c47162240'] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/tantan'], + 'dirs': [], +} + +sanity_check_commands = ["tantan --help"] + +moduleclass = 'bio' From 8a64df3179e5fe308d31f622595bc579d63bf46f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 18:03:52 +0200 Subject: [PATCH 7094/9987] adding easyconfigs: CodingQuarry-2.0-GCC-11.2.0.eb --- .../CodingQuarry-2.0-GCC-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb new file mode 100644 index 00000000000..97fd89ed9c8 --- /dev/null +++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'CodingQuarry' +version = '2.0' + +homepage = 'https://sourceforge.net/p/codingquarry' +description = "Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['CodingQuarry_v%(version)s.tar.gz'] +checksums = ['1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504'] + +buildopts = 'CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['CodingQuarry', 'CufflinksGTF_to_CodingQuarryGFF3.py'], 'bin'), + 'QuarryFiles', +] + +sanity_check_paths = { + 'files': ['bin/CodingQuarry', 'bin/CufflinksGTF_to_CodingQuarryGFF3.py'], + 'dirs': ['QuarryFiles/scripts', 'QuarryFiles/self_train', 'QuarryFiles/species'], +} + +sanity_check_commands = ["CodingQuarry --help | grep '^CodingQuarry v. %(version)s'"] + +modextravars = {'QUARRY_PATH': '%(installdir)s/QuarryFiles'} + +moduleclass = 'bio' From 93abc67d12562ae911a14fbd75ea51de1eedc4e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 18:04:06 +0200 Subject: [PATCH 7095/9987] adding easyconfigs: FASTA-36.3.8i-GCC-11.2.0.eb --- .../f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb new file mode 100644 index 00000000000..ddc7db52078 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'FASTA' +version = '36.3.8i' +local_version_date = '14-Nov-2020' + +homepage = 'http://fasta.bioch.virginia.edu' +description = """The FASTA programs find regions of local or global (new) similarity between +protein or DNA sequences, either by searching Protein or DNA databases, or by identifying +local duplications within a sequence.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/wrpearson/fasta36/archive/'] +sources = ['v%%(version)s_%s.tar.gz' % local_version_date] +checksums = ['b4b1c3c9be6beebcbaf4215368e159d69255e34c0bdbc84affa10cdb473ce008'] + +buildopts = '-C ./src -f ../make/Makefile.linux_sse2 all' + +files_to_copy = ['bin', 'conf', 'data', 'doc', 'FASTA_LIST', 'misc', 'README', 'seq', 'sql', 'test'] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s fasta%(version_major)s fasta"] + +sanity_check_paths = { + 'files': ['FASTA_LIST', 'README'] + ['bin/fasta', 'bin/map_db'] + + ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf', + 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', + 'ssearch', 'tfastm', 'tfastx']], + 'dirs': ['conf', 'data', 'doc', 'misc', 'seq', 'sql', 'test'] +} + +sanity_check_commands = ["fasta --help"] + +moduleclass = 'bio' From abc0e1477b4e107588dd570b35d3369085f9dc7f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 18:04:19 +0200 Subject: [PATCH 7096/9987] adding easyconfigs: Proteinortho-6.2.3-gompi-2021b.eb --- .../Proteinortho-6.2.3-gompi-2021b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.2.3-gompi-2021b.eb diff --git a/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.2.3-gompi-2021b.eb b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.2.3-gompi-2021b.eb new file mode 100644 index 00000000000..524a8a0e657 --- /dev/null +++ b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.2.3-gompi-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Proteinortho' +version = '6.2.3' + +homepage = 'https://www.bioinf.uni-leipzig.de/Software/proteinortho' +description = "Proteinortho is a tool to detect orthologous genes within different species." + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/v%(version)s/'] +sources = ['proteinortho-v%(version)s.tar.gz'] +checksums = ['23079b3106deb41eab4a9123ea4744e9d05ab99e286184e617628fc243718dff'] + +dependencies = [ + ('Perl', '5.34.0'), + ('Python', '3.9.6'), + ('BLAST+', '2.12.0'), + ('DIAMOND', '2.0.13'), +] + +skipsteps = ['configure'] + +preinstallopts = "mkdir -p %(installdir)s/bin && " +installopts = "PREFIX=%(installdir)s/bin" + +sanity_check_paths = { + 'files': ['bin/proteinortho', 'bin/proteinortho%(version_major)s.pl', 'bin/proteinortho_clustering'], + 'dirs': [], +} + +sanity_check_commands = ["proteinortho --help"] + +moduleclass = 'bio' From 1b4a45c62d7deaf19125756c46dc8f011fef66e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 18:06:50 +0200 Subject: [PATCH 7097/9987] adding easyconfigs: SignalP-6.0g-foss-2021b-fast.eb --- .../s/SignalP/SignalP-6.0g-foss-2021b-fast.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb new file mode 100644 index 00000000000..6f37af3df3e --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0g' +_suffix = 'fast' +versionsuffix = '-' + _suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +unpack_options = '--strip-components=1' +checksums = ['a16fcea2b30067d2622d446031978bd86927e2e1cecf29a567c7922f6861b5aa'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # numpy > 1.19.2 + ('tqdm', '4.62.3'), # tqdm > 4.46.1 + ('PyTorch', '1.12.1'), # torch > 1.7.0 + ('matplotlib', '3.5.2'), # matplotlib > 3.3.2 +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' From 2f881ae55bea794b66641a5ebea69f0e690ef747 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 18:07:09 +0200 Subject: [PATCH 7098/9987] adding easyconfigs: Trinity-2.15.1-foss-2021b.eb, BLAT-3.7-GCC-11.2.0.eb, RSEM-1.3.3-foss-2021b.eb --- .../easyconfigs/b/BLAT/BLAT-3.7-GCC-11.2.0.eb | 55 ++++++++++++++++ .../r/RSEM/RSEM-1.3.3-foss-2021b.eb | 51 +++++++++++++++ .../t/Trinity/Trinity-2.15.1-foss-2021b.eb | 63 +++++++++++++++++++ 3 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2021b.eb create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.2.0.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.2.0.eb new file mode 100644 index 00000000000..1036c2e6acd --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-11.2.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou +# Contributors:: Alex Domingo (Vrije Universiteit Brussel) +# License:: MIT/GPL +# +## + +name = 'BLAT' +version = '3.7' + +homepage = 'https://genome.ucsc.edu/goldenPath/help/blatSpec.html' +description = """BLAT on DNA is designed to quickly find sequences of 95% and +greater similarity of length 25 bases or more.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://genome-test.gi.ucsc.edu/~kent/src/'] +sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] +patches = ['BLAT-%(version)s_mend-tests.patch'] +checksums = [ + {'blatSrc37.zip': '88ee2b272d42ab77687c61d200b11f1d58443951069feb7e10226a2509f84cf2'}, + {'BLAT-3.7_mend-tests.patch': '1f42c7fadf7676a5cc3a2016f70089c3541aa1d53816cf86072682c44cf311a6'}, +] + +# BLAT relies on a bundled old version of HTSlib. We use the bundled library +# because it is statically linked and the newer HTSlib in this toolchain is not +# API compatible with it. +dependencies = [ + ('freetype', '2.11.0'), + ('libiconv', '1.16'), + ('libpng', '1.6.37'), + ('MariaDB', '10.6.4'), + ('OpenSSL', '1.1', '', SYSTEM), + ('util-linux', '2.37'), + ('zlib', '1.2.11'), +] + +pretestopts = 'PATH="%(builddir)s/blatSrc/bin:$PATH"' +runtest = 'test' + +_blat_bins = ["blat", "faToNib", "faToTwoBit", "gfClient", "gfServer", "nibFrag", "pslPretty", + "pslReps", "pslSort", "twoBitInfo", "twoBitToFa"] + +files_to_copy = [(["bin/%s" % x for x in _blat_bins] + ["webBlat/webBlat"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in _blat_bins + ["webBlat"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2021b.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2021b.eb new file mode 100644 index 00000000000..55809893f41 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.3-foss-2021b.eb @@ -0,0 +1,51 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'RSEM' +version = '1.3.3' + +homepage = 'https://deweylab.github.io/RSEM/' +description = "RNA-Seq by Expectation-Maximization" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/deweylab/RSEM/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['RSEM-1.3.0_makefiles.patch'] +checksums = [ + '90e784dd9df8346caa2a7e3ad2ad07649608a51df1c69bfb6e16f45e611a40dc', # v1.3.3.tar.gz + '2d244659206c78655b92f1bd519ee65f28a6b5f9418dfad04e887b64eca6641b', # RSEM-1.3.0_makefiles.patch +] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('Perl', '5.34.0'), + ('R', '4.1.2'), + ('HISAT2', '2.2.1'), + ('STAR', '2.7.9a'), + ('Bowtie2', '2.4.4'), + ('Bowtie', '1.3.1'), +] + +sanity_check_paths = { + 'files': ['bin/rsem-calculate-expression', 'bin/rsem-plot-model', 'bin/rsem-plot-transcript-wiggles', + 'bin/rsem-bam2wig', 'bin/rsem-generate-data-matrix', 'bin/rsem-run-em', 'bin/convert-sam-for-rsem'], + 'dirs': ['bin/samtools-1.3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb new file mode 100644 index 00000000000..2f7ce8144b5 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb @@ -0,0 +1,63 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.15.1' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/%(name)s-v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +patches = ['Trinity-%(version)s_fix-bamsifter.patch'] +checksums = [ + {'trinityrnaseq-v2.15.1.FULL.tar.gz': 'ba37e5f696d3d54e8749c4ba439901a3e97e14a4314a5229d7a069ad7b1ee580'}, + {'Trinity-2.15.1_fix-bamsifter.patch': 'f374d446f06b8059a3b7cc57c286fc20d79b43ac222f48244ab83fb410997d1d'}, +] + +builddependencies = [ + ('Autotools', '20210726'), + ('CMake', '3.22.1'), +] + +# for reference, list of dependencies in the container image used upstream: +# https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile +dependencies = [ + ('Java', '11', '', SYSTEM), + ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), + ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), + ('GATK', '4.2.6.1', '-Java-%(javaver)s'), + ('Perl', '5.34.0'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('BLAST+', '2.12.0'), + ('BLAT', '3.7'), + ('Bowtie', '1.3.1'), + ('Bowtie2', '2.4.4'), + ('GMAP-GSNAP', '2021-21-17'), + ('HISAT2', '2.2.1'), + ('HTSlib', '1.14'), + ('Jellyfish', '2.3.0'), + ('kallisto', '0.48.0'), + ('ncurses', '6.2'), + ('RSEM', '1.3.3'), + ('Salmon', '1.4.0'), + ('SAMtools', '1.14'), + ('STAR', '2.7.9a'), + ('zlib', '1.2.11'), +] + +withsampledata = True + +moduleclass = 'bio' From 56812a347acbaaa87f229fe319425020fe399647 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 18:11:16 +0200 Subject: [PATCH 7099/9987] adding easyconfigs: SNAP-2.0.1-GCC-11.2.0.eb --- .../s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..ca3aa98f6b6 --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'SNAP' +version = '2.0.1' + +homepage = 'https://www.microsoft.com/en-us/research/project/snap' +description = """Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for + high-throughput sequencing data""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'cstd': 'c++98'} + +source_urls = ['https://github.com/amplab/snap/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['30f199c583e054c50ca6f3b61f27066640b7c829e5c5e8083841596a2869c064'] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CXX="$CXX"' + +files_to_copy = [(['snap-aligner', 'SNAPCommand'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/snap-aligner', 'bin/SNAPCommand'], + 'dirs': [], +} + +sanity_check_commands = ["snap-aligner --help"] + +moduleclass = 'bio' From 8cf43870add955e1599baa92092ca714a69b9383 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 18:11:30 +0200 Subject: [PATCH 7100/9987] adding easyconfigs: GlimmerHMM-3.0.4c-GCC-11.2.0.eb --- .../GlimmerHMM-3.0.4c-GCC-11.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb new file mode 100644 index 00000000000..0935561b4ea --- /dev/null +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GlimmerHMM' +version = '3.0.4c' + +homepage = 'https://ccb.jhu.edu/software/glimmerhmm' +description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. + Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally + it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted + from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] +sources = [SOURCE_TAR_GZ] +checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] + +start_dir = 'sources' + +# make sure -O0 is not used as compiler option +prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && " + +# also build in 'train' subdirectory to overwrite pre-compiled binaries +buildopts = "&& cd ../train && make" + +local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp', + 'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP', + 'scoreSTOP2', 'splicescore', 'trainGlimmerHMM'] +files_to_copy = [ + (['sources/%(namelower)s'], 'bin'), + (['train/%s' % x for x in local_train_files], 'bin'), + 'trained_dir', 'README', 'train/readme.train', +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['trained_dir'], +} + +sanity_check_commands = ["%(namelower)s -h"] + +moduleclass = 'bio' From 327f2e4403a3889b81456a5ff0e2e3f6ac278460 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 18:11:44 +0200 Subject: [PATCH 7101/9987] adding easyconfigs: trimAl-1.4.1-GCCcore-11.2.0.eb --- .../t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..3391b0d006e --- /dev/null +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated by: +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'MakeCp' + +name = 'trimAl' +version = '1.4.1' + +homepage = 'https://github.com/scapella/trimal' +description = """EVB, FEP and LIE simulator.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'scapella' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] + +builddependencies = [ + ('binutils', '2.37'), + +] +start_dir = 'source' + +files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/trimal', 'bin/readal', 'bin/statal'], + 'dirs': [] +} + +sanity_check_commands = ["trimal -h"] + +moduleclass = 'bio' From 15dd49714fdcc6dc827947794dc6deb28802dd25 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 18:35:37 +0200 Subject: [PATCH 7102/9987] remve duplicate local::lib from Perl easyconfigs --- easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 5 ----- easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 5 ----- easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 5 ----- 3 files changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index be9cf2ec1fc..1750e4abff0 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -1944,11 +1944,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], }), - ('local::lib', '2.000029', { - 'source_tmpl': 'local-lib-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], - 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 00c76287298..78044193927 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -1934,11 +1934,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], }), - ('local::lib', '2.000029', { - 'source_tmpl': 'local-lib-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], - 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], - }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 68757e61f49..6a7989e6d2a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -1944,11 +1944,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], }), - ('local::lib', '2.000029', { - 'source_tmpl': 'local-lib-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], - 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], - }), ] moduleclass = 'lang' From dc433c76e599ee5672e67318b7eb9cfd57129128 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 19:07:32 +0200 Subject: [PATCH 7103/9987] revert accidental changes to FASTX-Toolkit-0.0.14-GCC-11.3.0.eb --- .../FASTX-Toolkit-0.0.14-GCC-11.3.0.eb | 34 +++++++++++++++++-- 1 file changed, 32 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb index 67d8cb141e8..8589f7ecedc 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb @@ -8,8 +8,6 @@ # # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -# -# Updated: Denis Kristak (Inuits) ## easyblock = 'Bundle' @@ -26,6 +24,11 @@ toolchainopts = {'pic': True} default_easyblock = 'ConfigureMake' +dependencies = [ + ('GDGraph', '1.56'), + ('Perl', '5.34.1'), +] + components = [ ('libgtextutils', '0.7', { 'source_urls': ['https://github.com/agordon/libgtextutils/releases/download/%(version)s/'], @@ -47,6 +50,23 @@ components = [ }), ] +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('PerlIO::gzip', '0.20', { + 'source_tmpl': 'PerlIO-gzip-0.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], + 'checksums': ['4848679a3f201e3f3b0c5f6f9526e602af52923ffa471a2a3657db786bd3bdc5'], + }), +] + +fix_perl_shebang_for = ['bin/*.pl'] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' +} + sanity_check_paths = { 'files': ['bin/fastx_%s' % x for x in @@ -62,4 +82,14 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = [ + 'fasta_clipping_histogram.pl', + 'fasta_formatter -h', + 'fastq_masker -h | grep "FASTX Toolkit %(version)s"', + 'fastq_quality_boxplot_graph.sh', + 'fastx_barcode_splitter.pl --help | grep "Barcode Splitter, by Assaf Gordon (gordon@cshl.edu), 11sep2008"', + 'fastx_clipper -h | grep "FASTX Toolkit %(version)s"', + 'fastx_nucleotide_distribution_graph.sh', +] + moduleclass = 'bio' From b54a4779523e6346ca60e3184895bd9baccde7ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 19:17:09 +0200 Subject: [PATCH 7104/9987] fix import statement for Markup from Jinja2 in vispr + enhance sanity check + rename patch to include version --- .../easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb | 12 +++++++++--- ... => vispr-0.4.14_fix_pandas_version_change.patch} | 3 ++- 2 files changed, 11 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/v/vispr/{vispr_fix_pandas_version_change.patch => vispr-0.4.14_fix_pandas_version_change.patch} (81%) diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb index 855cc5ee79b..79f801ad1f9 100644 --- a/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb +++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb @@ -14,10 +14,11 @@ VISPR - A visualization framework for CRISPR data. toolchain = {'name': 'foss', 'version': '2022a'} sources = ['%(name)s-%(version)s.tar.gz'] -patches = ['vispr_fix_pandas_version_change.patch'] +patches = ['vispr-0.4.14_fix_pandas_version_change.patch'] checksums = [ {'vispr-0.4.14.tar.gz': 'dc2cf6ac9c8930b0f1f1b3a2b7f57bfae180b2ac3674060123fd2d7fe10ccd82'}, - {'vispr_fix_pandas_version_change.patch': '406c78092f1b06114602d37eb216ce24e1206b52461d0fc4270971ab80f10529'}, + {'vispr-0.4.14_fix_pandas_version_change.patch': + 'a5b5bb73b4d3dc4166c71ffd468496c19add46edec55029fe9f40e880a90e9a6'}, ] dependencies = [ @@ -30,11 +31,16 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_pip_check = True + +preinstallopts = "sed -i 's/from jinja2 import Markup/from markupsafe import Markup/g' vispr/server.py && " sanity_check_paths = { 'files': ['bin/vispr'], 'dirs': [], } +sanity_check_commands = ["vispr --help"] + +sanity_pip_check = True + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch similarity index 81% rename from easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch rename to easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch index 05275dcd59c..c6afe977cc9 100644 --- a/easybuild/easyconfigs/v/vispr/vispr_fix_pandas_version_change.patch +++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch @@ -1,4 +1,5 @@ -# with more recent versions of Pandas, the imported error was moved to `pandas.errors` +with more recent versions of Pandas, the imported error was moved to `pandas.errors` +author: Denis Kristak (INUITS) diff -ruN vispr-0.4.14_orig/vispr/results/rna.py vispr-0.4.14/vispr/results/rna.py --- vispr-0.4.14_orig/vispr/results/rna.py 2023-03-24 13:10:57.148839548 +0000 +++ vispr-0.4.14/vispr/results/rna.py 2023-03-24 13:11:14.032660055 +0000 From 2349d5332645f598c284abf213f2682f5101f13f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 19:30:43 +0200 Subject: [PATCH 7105/9987] add separate patch to fix yaml.load statements in vispr 0.4.14 --- .../v/vispr/vispr-0.4.14-foss-2022a.eb | 11 +++--- .../v/vispr/vispr-0.4.14_fix-imports.patch | 26 ++++++++++++++ .../v/vispr/vispr-0.4.14_fix-yaml-load.patch | 35 +++++++++++++++++++ ...spr-0.4.14_fix_pandas_version_change.patch | 14 -------- 4 files changed, 67 insertions(+), 19 deletions(-) create mode 100644 easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-imports.patch create mode 100644 easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-yaml-load.patch delete mode 100644 easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb index 79f801ad1f9..e06d4354bf0 100644 --- a/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb +++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb @@ -14,11 +14,14 @@ VISPR - A visualization framework for CRISPR data. toolchain = {'name': 'foss', 'version': '2022a'} sources = ['%(name)s-%(version)s.tar.gz'] -patches = ['vispr-0.4.14_fix_pandas_version_change.patch'] +patches = [ + 'vispr-0.4.14_fix-imports.patch', + 'vispr-0.4.14_fix-yaml-load.patch', +] checksums = [ {'vispr-0.4.14.tar.gz': 'dc2cf6ac9c8930b0f1f1b3a2b7f57bfae180b2ac3674060123fd2d7fe10ccd82'}, - {'vispr-0.4.14_fix_pandas_version_change.patch': - 'a5b5bb73b4d3dc4166c71ffd468496c19add46edec55029fe9f40e880a90e9a6'}, + {'vispr-0.4.14_fix-imports.patch': '2744d5636ebd6849fb0fc99ff102a8a0256bec3e592c323c24132f1e694baf67'}, + {'vispr-0.4.14_fix-yaml-load.patch': '6b994103c621fafc084fc6c11f966367ffddc36ac20c0f9fc44ef0bb4360f977'}, ] dependencies = [ @@ -32,8 +35,6 @@ dependencies = [ download_dep_fail = True use_pip = True -preinstallopts = "sed -i 's/from jinja2 import Markup/from markupsafe import Markup/g' vispr/server.py && " - sanity_check_paths = { 'files': ['bin/vispr'], 'dirs': [], diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-imports.patch b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-imports.patch new file mode 100644 index 00000000000..162193ecf1c --- /dev/null +++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-imports.patch @@ -0,0 +1,26 @@ +fix import statement for pandas and Jinja2 +author: Denis Kristak (INUITS) + Kenneth Hoste (HPC-UGent) +diff -ru vispr-0.4.14.orig/vispr/results/rna.py vispr-0.4.14/vispr/results/rna.py +--- vispr-0.4.14.orig/vispr/results/rna.py 2016-08-11 09:16:23.000000000 +0200 ++++ vispr-0.4.14/vispr/results/rna.py 2023-04-10 19:19:07.488661966 +0200 +@@ -11,7 +11,7 @@ + + from flask import render_template + import pandas as pd +-from pandas.io.common import EmptyDataError ++from pandas.errors import EmptyDataError + import numpy as np + from sklearn.decomposition import PCA + from scipy.cluster.hierarchy import average, leaves_list, dendrogram +diff -ru vispr-0.4.14.orig/vispr/server.py vispr-0.4.14/vispr/server.py +--- vispr-0.4.14.orig/vispr/server.py 2015-11-08 00:47:23.000000000 +0100 ++++ vispr-0.4.14/vispr/server.py 2023-04-10 19:25:06.417148288 +0200 +@@ -10,7 +10,7 @@ + + import numpy as np + from flask import Flask, render_template, request, session, abort +-from jinja2 import Markup ++from markupsafe import Markup + import yaml + + from vispr import __version__ diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-yaml-load.patch b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-yaml-load.patch new file mode 100644 index 00000000000..16d9b65d1a1 --- /dev/null +++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-yaml-load.patch @@ -0,0 +1,35 @@ +fix use of yaml.load, 'Loader' argument is required in PyYAML >= 6.0 +author: Kenneth Hoste (HPC-UGent) +diff -ru vispr-0.4.14.orig/vispr/cli.py vispr-0.4.14/vispr/cli.py +--- vispr-0.4.14.orig/vispr/cli.py 2017-02-15 14:38:22.000000000 +0100 ++++ vispr-0.4.14/vispr/cli.py 2023-04-10 19:26:01.251360284 +0200 +@@ -37,7 +37,7 @@ + print("Loading data.") + for path in configs: + with open(path) as f: +- config = yaml.load(f) ++ config = yaml.load(f, Loader=yaml.Loader) + try: + app.screens.add(config, parentdir=os.path.dirname(path)) + except KeyError as e: +@@ -91,7 +91,7 @@ + os.makedirs(directory) + + with open(configpath) as f: +- screen = Screen(yaml.load(f), parentdir=os.path.dirname(configpath)) ++ screen = Screen(yaml.load(f, Loader=yaml.Loader), parentdir=os.path.dirname(configpath)) + + def write(json, name): + with open(prefix + name + ".vega.json", "w") as out: +diff -ru vispr-0.4.14.orig/vispr/server.py vispr-0.4.14/vispr/server.py +--- vispr-0.4.14.orig/vispr/server.py 2015-11-08 00:47:23.000000000 +0100 ++++ vispr-0.4.14/vispr/server.py 2023-04-10 19:25:06.417148288 +0200 +@@ -20,7 +20,7 @@ + app.jinja_env.lstrip_blocks = True + + with open(os.path.join(os.path.dirname(__file__), "captions.yaml")) as f: +- CAPTIONS = yaml.load(f) ++ CAPTIONS = yaml.load(f, Loader=yaml.Loader) + + + @app.route("/ping") diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch deleted file mode 100644 index c6afe977cc9..00000000000 --- a/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix_pandas_version_change.patch +++ /dev/null @@ -1,14 +0,0 @@ -with more recent versions of Pandas, the imported error was moved to `pandas.errors` -author: Denis Kristak (INUITS) -diff -ruN vispr-0.4.14_orig/vispr/results/rna.py vispr-0.4.14/vispr/results/rna.py ---- vispr-0.4.14_orig/vispr/results/rna.py 2023-03-24 13:10:57.148839548 +0000 -+++ vispr-0.4.14/vispr/results/rna.py 2023-03-24 13:11:14.032660055 +0000 -@@ -11,7 +11,7 @@ - - from flask import render_template - import pandas as pd --from pandas.io.common import EmptyDataError -+from pandas.errors import EmptyDataError - import numpy as np - from sklearn.decomposition import PCA - from scipy.cluster.hierarchy import average, leaves_list, dendrogram From 5e13c679fe7ef2989ab576466372e731701990ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 20:57:42 +0200 Subject: [PATCH 7106/9987] add missing Perl dependency for GlimmerHMM, also copy Perl modules required by trainGlimmerHMM, add sanity check command for trainGlimmerHMM --- .../g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb index 0935561b4ea..2abdf04dc93 100644 --- a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb @@ -18,6 +18,10 @@ source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] sources = [SOURCE_TAR_GZ] checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] +dependencies = [ + ('Perl', '5.34.0'), +] + start_dir = 'sources' # make sure -O0 is not used as compiler option @@ -32,14 +36,22 @@ local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfa files_to_copy = [ (['sources/%(namelower)s'], 'bin'), (['train/%s' % x for x in local_train_files], 'bin'), + (['train/*.pm'], 'lib/perl%(perlmajver)s'), 'trained_dir', 'README', 'train/readme.train', ] +fix_perl_shebang_for = ['bin/trainGlimmerHMM'] + sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': ['trained_dir'], } -sanity_check_commands = ["%(namelower)s -h"] +sanity_check_commands = [ + "%(namelower)s -h", + r"trainGlimmerHMM -h 2>&1 | grep '^[ ]*Train GlimmerHMM module'", +] + +modextrapaths = {'PERL5LIB': 'lib/perl%(perlmajver)s'} moduleclass = 'bio' From 7f911010361805e1f3826814e63056d1c661f791 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 21:21:14 +0200 Subject: [PATCH 7107/9987] add Python dependency for CodingQuarry 2.0 + add patch to make included Python script compatible with Python 3.x + add sanity check command to test it --- .../CodingQuarry-2.0-GCC-11.2.0.eb | 21 +++++++++++++--- .../CodingQuarry-2.0_python3.patch | 24 +++++++++++++++++++ 2 files changed, 42 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb index 97fd89ed9c8..88e26640f3d 100644 --- a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb @@ -11,21 +11,36 @@ toolchainopts = {'openmp': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['CodingQuarry_v%(version)s.tar.gz'] -checksums = ['1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504'] +patches = ['CodingQuarry-2.0_python3.patch'] +checksums = [ + {'CodingQuarry_v2.0.tar.gz': '1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504'}, + {'CodingQuarry-2.0_python3.patch': '70b63cad753ed644338bd5e26124381c266164af6d6dbf42dbc806dc3d71fcc1'}, +] + +dependencies = [ + ('Python', '3.9.6'), +] buildopts = 'CFLAGS="$CFLAGS"' files_to_copy = [ (['CodingQuarry', 'CufflinksGTF_to_CodingQuarryGFF3.py'], 'bin'), 'QuarryFiles', + 'TESTING', ] +fix_python_shebang_for = ['bin/CufflinksGTF_to_CodingQuarryGFF3.py'] + sanity_check_paths = { 'files': ['bin/CodingQuarry', 'bin/CufflinksGTF_to_CodingQuarryGFF3.py'], - 'dirs': ['QuarryFiles/scripts', 'QuarryFiles/self_train', 'QuarryFiles/species'], + 'dirs': ['QuarryFiles/scripts', 'QuarryFiles/self_train', 'QuarryFiles/species', 'TESTING'], } -sanity_check_commands = ["CodingQuarry --help | grep '^CodingQuarry v. %(version)s'"] +sanity_check_commands = [ + "CodingQuarry --help | grep '^CodingQuarry v. %(version)s'", + "mkdir -p %(builddir)s && cp -a %(installdir)s/TESTING %(builddir)s/TESTING", + "cd %(builddir)s/TESTING && CufflinksGTF_to_CodingQuarryGFF3.py Sp_transcripts.gtf > test.gff3", +] modextravars = {'QUARRY_PATH': '%(installdir)s/QuarryFiles'} diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch new file mode 100644 index 00000000000..921ec4e6a02 --- /dev/null +++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch @@ -0,0 +1,24 @@ +make CufflinksGTF_to_CodingQuarryGFF3.py script compatible with Python 3.x +author: Kenneth Hoste (HPC-UGent) +--- CufflinksGTF_to_CodingQuarryGFF3.py.orig 2016-03-09 01:35:28.000000000 +0100 ++++ CufflinksGTF_to_CodingQuarryGFF3.py 2023-04-10 21:10:51.666438036 +0200 +@@ -5,7 +5,7 @@ + try : + myFile = open(sys.argv[1], 'rU') + except : +- print 'run: \n\npython CufflinksGTF_to_CodingQuarryGFF3.py transcripts.gtf > out.gff3\n' ++ print('run: \n\npython CufflinksGTF_to_CodingQuarryGFF3.py transcripts.gtf > out.gff3\n') + exit() + + number = 0 +@@ -18,8 +18,8 @@ + number += 1 + else : + number = 1 +- print '%s\t%s\texon\t%s\t%s\t%s\t%s\t%s\tID=exon:%s.%i;Parent=%s;' % \ +- (fields[0], fields[1], fields[3], fields[4], fields[5], fields[6], fields[7], details[3], number, details[3]) ++ print('%s\t%s\texon\t%s\t%s\t%s\t%s\t%s\tID=exon:%s.%i;Parent=%s;' % \ ++ (fields[0], fields[1], fields[3], fields[4], fields[5], fields[6], fields[7], details[3], number, details[3])) + IDprev = details[3] + + myFile.close() From 7a983ccad111c9cccc3c4c17ff936361ce7b480e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 10 Apr 2023 21:33:15 +0200 Subject: [PATCH 7108/9987] add Biopython dependency for CodingQuarry 2.0 + bump toolchain to foss/2021b + enhance patch to make fastaTranslate.py script compatible with Python 3.x --- ...-GCC-11.2.0.eb => CodingQuarry-2.0-foss-2021b.eb} | 10 +++++++--- .../c/CodingQuarry/CodingQuarry-2.0_python3.patch | 12 ++++++++++++ 2 files changed, 19 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/c/CodingQuarry/{CodingQuarry-2.0-GCC-11.2.0.eb => CodingQuarry-2.0-foss-2021b.eb} (81%) diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2021b.eb similarity index 81% rename from easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb rename to easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2021b.eb index 88e26640f3d..a82e6498b5f 100644 --- a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2021b.eb @@ -6,7 +6,7 @@ version = '2.0' homepage = 'https://sourceforge.net/p/codingquarry' description = "Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'openmp': True} source_urls = [SOURCEFORGE_SOURCE] @@ -14,11 +14,12 @@ sources = ['CodingQuarry_v%(version)s.tar.gz'] patches = ['CodingQuarry-2.0_python3.patch'] checksums = [ {'CodingQuarry_v2.0.tar.gz': '1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504'}, - {'CodingQuarry-2.0_python3.patch': '70b63cad753ed644338bd5e26124381c266164af6d6dbf42dbc806dc3d71fcc1'}, + {'CodingQuarry-2.0_python3.patch': '8e1b117431d8b104f2114875d8f751aa91c1c3c1b0ddd5a4f85251605c2ab9df'}, ] dependencies = [ ('Python', '3.9.6'), + ('Biopython', '1.79'), ] buildopts = 'CFLAGS="$CFLAGS"' @@ -29,7 +30,10 @@ files_to_copy = [ 'TESTING', ] -fix_python_shebang_for = ['bin/CufflinksGTF_to_CodingQuarryGFF3.py'] +fix_python_shebang_for = [ + 'bin/CufflinksGTF_to_CodingQuarryGFF3.py', + 'QuarryFiles/scripts/*.py', +] sanity_check_paths = { 'files': ['bin/CodingQuarry', 'bin/CufflinksGTF_to_CodingQuarryGFF3.py'], diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch index 921ec4e6a02..ddf50218a42 100644 --- a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch +++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch @@ -22,3 +22,15 @@ author: Kenneth Hoste (HPC-UGent) IDprev = details[3] myFile.close() +--- QuarryFiles/scripts/fastaTranslate.py.orig 2016-03-09 01:35:28.000000000 +0100 ++++ QuarryFiles/scripts/fastaTranslate.py 2023-04-10 21:30:47.355740964 +0200 +@@ -33,7 +33,7 @@ + else : + protein+='*' + i+=3 +- print '>%s' % (record.id) +- print protein ++ print('>%s' % (record.id)) ++ print(protein) + + myFASTA.close() From bd6c624e648dab3a9693d047129dcf9fe128371c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Apr 2023 08:42:10 +0200 Subject: [PATCH 7109/9987] skip two flaky tests for PyTorch/1.12.1-foss-2021b --- .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb index b4e4f83ca06..7c58b58e5fd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb @@ -122,6 +122,12 @@ excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. 'distributed/test_distributed_spawn', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', ] } From 39ebe1c6a21d141327a4da894e2192a0da1e689e Mon Sep 17 00:00:00 2001 From: ll4strw Date: Tue, 11 Apr 2023 09:40:34 +0200 Subject: [PATCH 7110/9987] Added build dependency for hierarchical module naming scheme --- easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb index 0f78f6e8ed9..86ae2b180e9 100644 --- a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb +++ b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb @@ -14,6 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['3fdf5b100206953f674c94d40599bdb3ea255244dcc42fab0d75855ee3645581'] builddependencies = [ + ('GCCcore', '11.2.0'), # required for hierarchical module naming scheme ('binutils', '2.37', '', ('GCCcore', '11.2.0')), ('CMake', '3.22.1', '', ('GCCcore', '11.2.0')), ('ZeroMQ', '4.3.4', '', ('GCCcore', '11.2.0')), From b7c176b29210e5b0c9945b826320a916de41b05a Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 11 Apr 2023 10:17:25 +0200 Subject: [PATCH 7111/9987] Add CUDA versionsuffix to OpenMM --- .../a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb | 2 +- ...0.0-foss-2022a.eb => OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb} | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/o/OpenMM/{OpenMM-8.0.0-foss-2022a.eb => OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb} (98%) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb index 6818ca92607..c3d268ba085 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('UCX-CUDA', '1.12.1', versionsuffix), ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), ('NCCL', '2.12.12', versionsuffix), - ('OpenMM', '8.0.0'), + ('OpenMM', '8.0.0', versionsuffix), ] # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb similarity index 98% rename from easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb rename to easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb index 4d937a03a22..3e75fe7bcb3 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb @@ -9,6 +9,7 @@ easyblock = 'CMakeMake' name = 'OpenMM' version = '8.0.0' +versionsuffix= '-CUDA-%(cudaver)s' homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." From 8af41430f7254629f502ca114493bd263e72390c Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 11 Apr 2023 10:59:14 +0200 Subject: [PATCH 7112/9987] Fix style --- .../easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb index 3e75fe7bcb3..4215d0a143f 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb @@ -9,7 +9,7 @@ easyblock = 'CMakeMake' name = 'OpenMM' version = '8.0.0' -versionsuffix= '-CUDA-%(cudaver)s' +versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://openmm.org' description = "OpenMM is a toolkit for molecular simulation." From 736af1fdd8f6825551905c9eba999066f31b940f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Apr 2023 16:17:12 +0200 Subject: [PATCH 7113/9987] stick to matplotlib 3.4.3 as dependency for SignalP 6.0g with foss/2021b --- easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb index 6f37af3df3e..b2f900f3c4a 100644 --- a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb @@ -33,7 +33,7 @@ dependencies = [ ('SciPy-bundle', '2021.10'), # numpy > 1.19.2 ('tqdm', '4.62.3'), # tqdm > 4.46.1 ('PyTorch', '1.12.1'), # torch > 1.7.0 - ('matplotlib', '3.5.2'), # matplotlib > 3.3.2 + ('matplotlib', '3.4.3'), # matplotlib > 3.3.2 ] use_pip = True From ed3a7f58c94366ca08537b3cdf52494dab967d71 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Apr 2023 17:42:14 +0200 Subject: [PATCH 7114/9987] {bio}[GCC/11.3.0] biobambam2 v2.0.87, libmaus2 v2.0.499 --- .../biobambam2-2.0.87-GCC-11.3.0.eb | 27 +++++++++++++++++++ .../l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb | 22 +++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb new file mode 100644 index 00000000000..26c750c21c9 --- /dev/null +++ b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'biobambam2' +version = '2.0.87' + +homepage = 'https://github.com/gt1/biobambam2' +description = "Tools for processing BAM files" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/gt1/biobambam2/archive/'] +sources = ['%(version)s-release-20180301132713.tar.gz'] +checksums = ['a90500e547465d8d0455bda7936e0b660c0fd3f1b243083ec0739527f802dcf4'] + +dependencies = [ + ('libmaus2', '2.0.499'), +] + +configopts = "--with-libmaus2=$EBROOTLIBMAUS2" + +sanity_check_paths = { + 'files': ['bin/bamcollate2', 'bin/bammarkduplicates', 'bin/bammaskflags', 'bin/bamrecompress', + 'bin/bamsormadup', 'bin/bamsort', 'bin/bamtofastq'], + 'dirs': ['share/man'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb new file mode 100644 index 00000000000..5aa65b14cf1 --- /dev/null +++ b/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libmaus2' +version = '2.0.499' + +homepage = 'https://github.com/gt1/libmaus2' +description = "libmaus2 is a collection of data structures and algorithms." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/gt1/libmaus2/archive/'] +sources = ['%(version)s-release-20180606122508.tar.gz'] +checksums = ['5e3643bb14a3342b76b68592252f248e5e97725caffe6a6a3274563a0433338a'] + +sanity_check_paths = { + 'files': ['lib/libmaus2.a', 'lib/libmaus2.%s' % SHLIB_EXT, + 'lib/libmaus2_simd_align_128.a', 'lib/libmaus2_simd_align_128.%s' % SHLIB_EXT, + 'lib/libmaus2_simd_align_256.a', 'lib/libmaus2_simd_align_256.%s' % SHLIB_EXT], + 'dirs': ['include/libmaus2'], +} + +moduleclass = 'lib' From 109c7f83949cdd5040fd54fc4c01ceca2273862c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Apr 2023 17:48:07 +0200 Subject: [PATCH 7115/9987] add sanity check commands for biobambam2 --- .../b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb index 26c750c21c9..62dfa0f74a1 100644 --- a/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb @@ -18,10 +18,14 @@ dependencies = [ configopts = "--with-libmaus2=$EBROOTLIBMAUS2" +local_binaries = ['bamcollate2', 'bammarkduplicates', 'bammaskflags', 'bamrecompress', + 'bamsormadup', 'bamsort', 'bamtofastq'] + sanity_check_paths = { - 'files': ['bin/bamcollate2', 'bin/bammarkduplicates', 'bin/bammaskflags', 'bin/bamrecompress', - 'bin/bamsormadup', 'bin/bamsort', 'bin/bamtofastq'], + 'files': ['bin/%s' % x for x in local_binaries], 'dirs': ['share/man'], } +sanity_check_commands = ["%s --help" % x for x in local_binaries] + moduleclass = 'bio' From a7a807fdff5fa4b4c8dcdd304f8101c225b84546 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Apr 2023 18:35:46 +0200 Subject: [PATCH 7116/9987] add PMA/unikn/ppcor extensions to R 4.2.x easyconfigs --- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 9 +++++++++ easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 9 +++++++++ easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 9 +++++++++ 3 files changed, 27 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 6175f90d834..7f0e053f59b 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -3360,6 +3360,15 @@ exts_list = [ ('geeM', '0.10.1', { 'checksums': ['fe76a32981b55835095041e777d1cf2e9ce43edb8d9488db56279f7cb6f43fe5'], }), + ('PMA', '1.2.1', { + 'checksums': ['3a155b89e380273dfd4ab301c422184a3f6d4679dc9e3d1bb65939392af511e6'], + }), + ('unikn', '0.8.0', { + 'checksums': ['77954418cf5475e57ccd5d28edefd97f82c49cd8e148b55b1b74f55b8c1c620f'], + }), + ('ppcor', '1.1', { + 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 7829620a4a2..2efbf9482f0 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3469,6 +3469,15 @@ exts_list = [ ('dlm', '1.1-6', { 'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'], }), + ('PMA', '1.2.1', { + 'checksums': ['3a155b89e380273dfd4ab301c422184a3f6d4679dc9e3d1bb65939392af511e6'], + }), + ('unikn', '0.8.0', { + 'checksums': ['77954418cf5475e57ccd5d28edefd97f82c49cd8e148b55b1b74f55b8c1c620f'], + }), + ('ppcor', '1.1', { + 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index ae739c4baf5..f89a16e5c6d 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3540,6 +3540,15 @@ exts_list = [ ('dlm', '1.1-6', { 'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'], }), + ('PMA', '1.2.1', { + 'checksums': ['3a155b89e380273dfd4ab301c422184a3f6d4679dc9e3d1bb65939392af511e6'], + }), + ('unikn', '0.8.0', { + 'checksums': ['77954418cf5475e57ccd5d28edefd97f82c49cd8e148b55b1b74f55b8c1c620f'], + }), + ('ppcor', '1.1', { + 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], + }), ] moduleclass = 'lang' From b0ca99edf8d2fc9a168cb9b51614366fd13f9de0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Apr 2023 18:36:33 +0200 Subject: [PATCH 7117/9987] adding easyconfigs: DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb --- ...IALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb diff --git a/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb new file mode 100644 index 00000000000..b2a1f818c5d --- /dev/null +++ b/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'DIALOGUE' +local_commit = '7109f6a' +# see DESCRIPTION to determine version, +# but add date stamp of commit since version is not always bumped +version = '1.0-20230228' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/livnatje/DIALOGUE' +description = """DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to + identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/livnatje/DIALOGUE/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['28a57c61c6854ca4c54114a3067437de6cee0eb1090c46ea45619457affdfb08'] + +dependencies = [ + ('R', '4.2.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From c6c4bb149603e666625392e4ad9f64a940abc24e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 11 Apr 2023 19:42:09 +0200 Subject: [PATCH 7118/9987] fix homepage in ELPA easyconfigs (due to switch to new domain) --- .../e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb | 2 +- easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb index 6d9cb0dca9b..fe138398a7a 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb @@ -10,7 +10,7 @@ name = 'ELPA' version = '2022.05.001' versionsuffix = '-CUDA-%(cudaver)s' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications.""" toolchain = {'name': 'foss', 'version': '2022a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb index 54a1ab0f515..09d5330ca5b 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2022.05.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications.""" toolchain = {'name': 'foss', 'version': '2022a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb index 6af27dad529..2da3666b859 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2022.05.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications.""" toolchain = {'name': 'intel', 'version': '2022a'} From 2addb7b2d3111454b424a57af7992f4f4dc0adb3 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 11 Apr 2023 19:44:26 +0200 Subject: [PATCH 7119/9987] adding easyconfigs: ELPA-2022.05.001-foss-2022b.eb, ELPA-2022.05.001-intel-2022b.eb, ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb --- ...ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb | 48 +++++++++++++++++++ .../e/ELPA/ELPA-2022.05.001-foss-2022b.eb | 43 +++++++++++++++++ .../e/ELPA/ELPA-2022.05.001-intel-2022b.eb | 47 ++++++++++++++++++ 3 files changed, 138 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022b.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb new file mode 100644 index 00000000000..0bf44c8db66 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2022.05.001' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, + {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': + '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +dependencies = [ + ('CUDA', '12.0.0', '', SYSTEM) +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b.eb new file mode 100644 index 00000000000..c9bf9efef08 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2022.05.001' + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, + {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': + '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022b.eb new file mode 100644 index 00000000000..473b2dce033 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022b.eb @@ -0,0 +1,47 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2022.05.001' + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, + {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': + '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' +# If the build is running in a batch job, make sure Intel libmpi does +# not try to use Slurm to run the MPI_THREAD test code that ELPA's +# configure is running without "mpirun". +preconfigopts += 'unset SLURM_JOBID && unset SLURM_NODELIST && unset I_MPI_PMI_LIBRARY && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' From 7694d11ca53bcabe3338de86f1ac248eabe68d37 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Apr 2023 21:38:19 +0200 Subject: [PATCH 7120/9987] remove PGPLOT with GCCcore/10.3.0, since we have no need for it (as dependency) --- .../p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb | 59 ------------------- 1 file changed, 59 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb deleted file mode 100644 index e71115ce833..00000000000 --- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-10.3.0.eb +++ /dev/null @@ -1,59 +0,0 @@ -# Contribution from Imperial College London (UK) -# Uploaded by J. Sassmannshausen - -easyblock = 'CmdCp' - -name = 'PGPLOT' -version = '5.2.2' - -homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/' -description = """The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, -device-independent graphics package for making simple scientific graphs. It is intended -for making graphical images of publication quality with minimum effort on the part of -the user. For most applications, the program can be device-independent, and the output -can be directed to the appropriate device at run time.""" - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/'] -sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')] -patches = ['pgplot-compiler-pgplot522.patch'] - -checksums = [ - 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4', # pgplot522.tar.gz - 'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec', # pgplot-compiler-pgplot522.patch -] - -builddependencies = [ - ('binutils', '2.36.1'), -] - -dependencies = [ - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), - ('X11', '20210518'), -] - -cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')] - -files_to_copy = [ - (['pgdemo*'], 'bin'), - (['libpgplot.*', 'libcpgplot.*'], 'lib'), - (['grfont.dat'], 'share'), - (['cpgplot.h'], 'include'), -] - -postinstallcmds = [ - # create symlinks - "cd %(installdir)s/lib && ln -s libcpgplot.so.5.2.2 libcpgplot.so.5 ; ln -s libcpgplot.so.5.2.2 libcpgplot.so && " - " ln -s libpgplot.so.5.2.2 libpgplot.so.5 ; ln -s libpgplot.so.5.2.2 libpgplot.so" -] - -sanity_check_paths = { - 'files': ['lib/libpgplot.a', 'lib/libcpgplot.a', 'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT], - 'dirs': [] -} - -modextravars = {'PGPLOT_FONT': '%(installdir)s/share/grfont.dat'} - -moduleclass = 'vis' From c074f0bb3110c27d9969c3d0b19dde3eca868bd4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Apr 2023 21:42:51 +0200 Subject: [PATCH 7121/9987] rename patch for PGPLOT 5.2.2 + clean up postinstallcmds + enhance sanity check --- .../p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb | 20 ++++++++++--------- ...=> PGPLOT-5.2.2_gfortran-deps-fixes.patch} | 0 2 files changed, 11 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/p/PGPLOT/{pgplot-compiler-pgplot522.patch => PGPLOT-5.2.2_gfortran-deps-fixes.patch} (100%) diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb index 3ffb0eb70e6..4033ffc1c52 100644 --- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb @@ -17,11 +17,10 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/'] sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')] -patches = ['pgplot-compiler-pgplot522.patch'] - +patches = ['PGPLOT-5.2.2_gfortran-deps-fixes.patch'] checksums = [ - 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4', # pgplot522.tar.gz - 'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec', # pgplot-compiler-pgplot522.patch + {'pgplot522.tar.gz': 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4'}, + {'PGPLOT-5.2.2_gfortran-deps-fixes.patch': 'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec'}, ] builddependencies = [ @@ -43,15 +42,18 @@ files_to_copy = [ (['cpgplot.h'], 'include'), ] +# create .so symlinks for shared libraries postinstallcmds = [ - # create symlinks - "cd %(installdir)s/lib && ln -s libcpgplot.so.5.2.2 libcpgplot.so.5 ; ln -s libcpgplot.so.5.2.2 libcpgplot.so && " - " ln -s libpgplot.so.5.2.2 libpgplot.so.5 ; ln -s libpgplot.so.5.2.2 libpgplot.so" + "cd %%(installdir)s/lib && ln -s libcpgplot.%s.5.2.2 libcpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libcpgplot.%s.5.2.2 libcpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libpgplot.%s.5.2.2 libpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libpgplot.%s.5.2.2 libpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), ] sanity_check_paths = { - 'files': ['lib/libpgplot.a', 'lib/libcpgplot.a', 'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT], - 'dirs': [] + 'files': ['include/cpgplot.h', 'lib/libpgplot.a', 'lib/libcpgplot.a', + 'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT], + 'dirs': ['bin'], } modextravars = {'PGPLOT_FONT': '%(installdir)s/share/grfont.dat'} diff --git a/easybuild/easyconfigs/p/PGPLOT/pgplot-compiler-pgplot522.patch b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2_gfortran-deps-fixes.patch similarity index 100% rename from easybuild/easyconfigs/p/PGPLOT/pgplot-compiler-pgplot522.patch rename to easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2_gfortran-deps-fixes.patch From 259b0c94df31f5ff6ef1dc5ed39d54c4594ff8a5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Apr 2023 22:25:28 +0200 Subject: [PATCH 7122/9987] add sanity check command for WCSLIB --- easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb index 782f085864d..68d5f0a82df 100644 --- a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb @@ -38,4 +38,6 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = ["wcsgrid --help 2>&1 | grep '^Usage: wcsgrid'"] + moduleclass = 'geo' From 70e7c9b1291bfdb87be5cc4eb81d0371faafb119 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 11 Apr 2023 22:44:23 +0200 Subject: [PATCH 7123/9987] adding easyconfigs: DBG2OLC-20200724-GCC-11.3.0.eb --- .../d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb new file mode 100644 index 00000000000..0c8e9e7176c --- /dev/null +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CmdCp' + +name = 'DBG2OLC' +version = '20200724' +local_commit = '9514828' + +homepage = 'https://github.com/yechengxi/DBG2OLC' +description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation + Sequencing Technologies""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['52a05518a377a2bd784265a8dc05c49009f858d4c1c893b4dddbb12106bc0f99'] + +cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +sanity_check_commands = ["DBG2OLC 2>&1 | grep 'For third-gen sequencing: DBG2OLC'"] + +moduleclass = 'bio' From 8834ee40a30093f464e4c2b66c29e560f054255c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 12 Apr 2023 01:10:04 +0200 Subject: [PATCH 7124/9987] adding easyconfigs: jax-0.3.25-foss-2022a-CUDA-11.7.0.eb, jax-0.3.25-foss-2022a.eb and patches: jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch, jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch --- .../jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb | 124 ++++++++++++++++++ .../j/jax/jax-0.3.25-foss-2022a.eb | 114 ++++++++++++++++ ...p-qdwh-test-rank-deficient-deficient.patch | 14 ++ ..._skip-test-bcoo-dot-general-cusparse.patch | 14 ++ 4 files changed, 266 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a.eb create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..8c8935d85b4 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,124 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.25' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.36.0', '-nodocs'), + ('matplotlib', '3.5.2'), # required for tests/lobpcg_test.py +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), + ('NCCL', '2.12.12', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in WORKSPACE +local_tf_commit = 'f0fe8d4c04fab1f157854a1aa3c136377901cdef' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.3.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['463c38a08d2e4cef6c498b76ba5bd4858e4c6ef51da1a5a1f27139a022e20248'], + }), + ('jaxlib', version, { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.3.25.tar.gz + '73ebc7868631cd9d520385557bbd7f08762d748a5a6a1bebef0f3b8d7ba748ef', + # tensorflow-f0fe8d4c04fab1f157854a1aa3c136377901cdef.tar.gz + '9ebba3031e8a81993682e4b9e43891ebb8480b6287e635df8e7efaa45ab5ede7', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': [ + 'jax-0.3.23_relax-testPoly5-tolerance.patch', + 'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch', + 'jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch', + 'jax-0.4.4_cusparse.patch', + ], + 'checksums': [ + {'jax-v0.3.25.tar.gz': '49e8ce88ddd7dd0de86116c9d75d98a577a9061377ec423493fbac5ea29f79f0'}, + {'jax-0.3.23_relax-testPoly5-tolerance.patch': + 'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'}, + {'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch': + '70f16f2dba03ab162ce6e13ea61774524b485e9630209bbd4bec81fd16c8812f'}, + {'jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch': + '335a8e206d14338176bf4136a131afe5d7b75999ac2c67f0ae79031322e25936'}, + {'jax-0.4.4_cusparse.patch': '7414115533cce9f37c60850c09c69563a0ed6477c73f03c4132b9c2ae75ae60f'}, + ], + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + + "JAX_ENABLE_X64=true pytest -vv tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a.eb new file mode 100644 index 00000000000..fb821e58e1d --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a.eb @@ -0,0 +1,114 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.25' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.36.0', '-nodocs'), + ('matplotlib', '3.5.2'), # required for tests/lobpcg_test.py +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in WORKSPACE +local_tf_commit = 'f0fe8d4c04fab1f157854a1aa3c136377901cdef' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.3.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['463c38a08d2e4cef6c498b76ba5bd4858e4c6ef51da1a5a1f27139a022e20248'], + }), + ('jaxlib', version, { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.3.25.tar.gz + '73ebc7868631cd9d520385557bbd7f08762d748a5a6a1bebef0f3b8d7ba748ef', + # tensorflow-f0fe8d4c04fab1f157854a1aa3c136377901cdef.tar.gz + '9ebba3031e8a81993682e4b9e43891ebb8480b6287e635df8e7efaa45ab5ede7', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': [ + 'jax-0.3.23_relax-testPoly5-tolerance.patch', + 'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch', + ], + 'checksums': [ + {'jax-v0.3.25.tar.gz': '49e8ce88ddd7dd0de86116c9d75d98a577a9061377ec423493fbac5ea29f79f0'}, + {'jax-0.3.23_relax-testPoly5-tolerance.patch': + 'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'}, + {'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch': + '70f16f2dba03ab162ce6e13ea61774524b485e9630209bbd4bec81fd16c8812f'}, + ], + 'runtest': "pytest -n %(parallel)s tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch new file mode 100644 index 00000000000..50eef092964 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch @@ -0,0 +1,14 @@ +This test is known to fail on certain CPU arquitectures +see https://github.com/google/jax/issues/14793 +author: Alex Domingo (Vrije Universiteit Brussel) +--- tests/qdwh_test.py.orig 2023-04-06 10:38:07.838718000 +0200 ++++ tests/qdwh_test.py 2023-04-06 10:38:24.168026081 +0200 +@@ -168,7 +168,7 @@ + [dict(m=m, n=n) for m, n in [(10, 10), (8, 8)]], + log_cond=np.linspace(1, 4, 4), + ) +- def testQdwhWithOnRankDeficientInput(self, m, n, log_cond): ++ def disabled_testQdwhWithOnRankDeficientInput(self, m, n, log_cond): + """Tests qdwh with rank-deficient input.""" + a = jnp.triu(jnp.ones((m, n))).astype(_QDWH_TEST_DTYPE) + diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch new file mode 100644 index 00000000000..8a70ed941cf --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch @@ -0,0 +1,14 @@ +Skip flaky tests with cuSPARSE as its API is quite variable, +might solve itself in future versions of CUDA or jax +see https://github.com/google/jax/issues/14663 +author: Alex Domingo (Vrije Universiteit Brussel) +--- tests/sparse_test.py.orig 2023-04-06 23:41:58.192895000 +0200 ++++ tests/sparse_test.py 2023-04-06 23:59:56.319161821 +0200 +@@ -1173,6 +1173,7 @@ + ], + dtype=jtu.dtypes.floating + jtu.dtypes.complex, + ) ++ @unittest.skip("CUSPARSE_OPERATION_NON_TRANSPOSE is not supported with CUSPARSE_SPMM_COO_ALG2 on CUDA 11.7.0") + def test_bcoo_dot_general_cusparse( + self, lhs_shape, rhs_shape, dtype, lhs_contracting, rhs_contracting): + rng = jtu.rand_small(self.rng()) From 9cc30bbda3abf060b24d763a46c63423ec1e9eaf Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 12 Apr 2023 13:13:48 +0800 Subject: [PATCH 7125/9987] enable building VASP in parallel --- easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb b/easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb index 435a614ebf3..ea2a9c6c20c 100644 --- a/easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb +++ b/easybuild/easyconfigs/v/VASP/VASP-6.3.2-nvofbf-2022.07.eb @@ -26,6 +26,7 @@ local_targets = ['std', 'gam', 'ncl'] buildopts = '%s ' % ' '.join(local_targets) buildopts += 'FFTW_ROOT="${EBROOTFFTW}" ' +buildopts += 'DEPS=1 ' # required for VASP parallel builds # https://www.vasp.at/wiki/index.php/Validation_tests @@ -52,8 +53,6 @@ local_test_skip += "SiC_HSE06_ALGO=A_RPR SiC_HSE06_ALGO=D SiC_HSE06_ALGO=D_RPR" pretestopts += 'export VASP_TESTSUITE_SKIP_TESTS="%s" && ' % local_test_skip runtest = 'test' -parallel = 1 - files_to_copy = [(['bin/vasp_' + x for x in local_targets], 'bin')] sanity_check_paths = { From b0cad395b794c9bcd352bffca9e31899ca31cebb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 12 Apr 2023 11:07:24 +0200 Subject: [PATCH 7126/9987] improve sanity_check_paths for casacore 3.4.0 --- .../easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb index 8c95efa1c75..aab5e755fdf 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb @@ -40,8 +40,9 @@ configopts = ' -DBUILD_PYTHON3=ON -DBUILD_PYTHON=OFF -Wno-dev -DDATA_DIR=%(insta configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON ' sanity_check_paths = { - 'files': [('lib/libcasa_casa.%s', 'lib/libcasa_mirlib.%s' % SHLIB_EXT, 'lib64/libcasa_ms.%s' % SHLIB_EXT)], - 'dirs': ['include/casacore'], + 'files': ['lib/libcasa_casa.%s' % SHLIB_EXT, 'lib/libcasa_mirlib.%s' % SHLIB_EXT, + 'lib/libcasa_ms.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/casacore'], } moduleclass = 'lib' From 4ca05dc7cc6ab887447f82f7f8639cbfa7a41189 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 12 Apr 2023 19:01:01 +0200 Subject: [PATCH 7127/9987] adding easyconfigs: spglib-2.0.2-GCCcore-11.3.0.eb, ShengBTE-1.5.0-foss-2022a.eb, thirdorder-1.1.1-foss-2022a.eb --- .../s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb | 43 +++++++++++++++++++ .../s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb | 31 +++++++++++++ .../thirdorder/thirdorder-1.1.1-foss-2022a.eb | 40 +++++++++++++++++ 3 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/thirdorder/thirdorder-1.1.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb new file mode 100644 index 00000000000..494b3757f7b --- /dev/null +++ b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb @@ -0,0 +1,43 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'ShengBTE' +version = '1.5.0' + +homepage = 'https://bitbucket.org/sousaw/shengbte' +description = "A solver for the Boltzmann transport equation for phonons." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +bitbucket_account = 'sousaw' +source_urls = [BITBUCKET_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['fc1299921aa5f8046473d0c73114b826f803650b9a44e94338eaeb13e9c67381'] + +dependencies = [ + ('spglib', '2.0.2'), +] + +start_dir = 'Src' + +# strip "include arch.make" -- not needed as we already set necessary env vars +prebuildopts = "sed -i 's/^include arch.make//' Makefile && " +# -fallow-argument-mismatch needed for GCC 10+ +buildopts = '-j 1 LIBS="$LIBBLAS -lsymspg" FFLAGS="$FFLAGS -fallow-argument-mismatch"' + +local_tests = ["Test-%s" % x for x in ['QE', 'RTA', 'VASP']] + +files_to_copy = [([name], 'bin'), (['LICENSE', 'README.md'], 'share')] + local_tests + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] + local_tests, +} + +sanity_check_commands = [ + "cd %%(builddir)s/*%%(namelower)s*/%s && %%(mpi_cmd_prefix)s %%(name)s" % x for x in local_tests +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..256f29f77b5 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'spglib' +version = '2.0.2' + +homepage = 'https://spglib.github.io/spglib/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/spglib/spglib/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['10e44a35099a0a5d0fc6ee0cdb39d472c23cb98b1f5167c0e2b08f6069f3db1e'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +postinstallcmds = ["cd %(installdir)s/include && mkdir spglib && ln -s ../spglib.h spglib/"] + +sanity_check_paths = { + 'files': [ + 'include/spglib.h', + 'lib/libsymspg.a', + 'lib/libsymspg.%s' % SHLIB_EXT + ], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/thirdorder/thirdorder-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/t/thirdorder/thirdorder-1.1.1-foss-2022a.eb new file mode 100644 index 00000000000..9ef61b93414 --- /dev/null +++ b/easybuild/easyconfigs/t/thirdorder/thirdorder-1.1.1-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' +name = 'thirdorder' +version = '1.1.1' + +homepage = 'https://bitbucket.org/sousaw/thirdorder/' +description = """A Python script to help create input files for computing anhamonic +interatomic force constants, harnessing the symmetries of the system to minimize the +number of required DFT calculations. A second mode of operation allows the user to +build the third-order IFC matrix from the results of those runs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('spglib', '2.0.2'), +] + +source_urls = ['https://bitbucket.org/sousaw/thirdorder/get/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f95e6371d78231d68028ec4e28d1d45ce60b1093e64f87e4b0cdb259375cd0d4'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# Thirdorder need to be built using Cython and it needs to have a version in setup.py +preinstallopts = r'sed -i -e "s/^USE_CYTHON.*/USE_CYTHON=True/" ' +preinstallopts += r'-e "s/^\(setup(.*\))$/\1, version=\"%(version)s\")/" setup.py && ' + +options = {'modulename': 'thirdorder_core'} + +postinstallcmds = ["mkdir %(installdir)s/bin && cp thirdorder_*.py %(installdir)s/bin/"] + +sanity_check_paths = { + 'files': ['bin/thirdorder_%s.py' % x for x in ["castep", "espresso", "vasp"]], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'chem' From 60d597de08ed03222259bf1be6d2dce002387c43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 12 Apr 2023 19:16:27 +0200 Subject: [PATCH 7128/9987] adding easyconfigs: buildenv-default-foss-2022b-CUDA-12.0.0.eb, buildenv-default-foss-2022b.eb, buildenv-default-intel-2022b.eb --- ...buildenv-default-foss-2022b-CUDA-12.0.0.eb | 20 +++++++++++++++++++ .../b/buildenv/buildenv-default-foss-2022b.eb | 13 ++++++++++++ .../buildenv/buildenv-default-intel-2022b.eb | 13 ++++++++++++ 3 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b-CUDA-12.0.0.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022b.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b-CUDA-12.0.0.eb new file mode 100644 index 00000000000..c3821707135 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b-CUDA-12.0.0.eb @@ -0,0 +1,20 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('CUDA', '12.0.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', versionsuffix), + ('UCC-CUDA', '1.1.0', versionsuffix), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b.eb new file mode 100644 index 00000000000..1638fdb195d --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022b.eb new file mode 100644 index 00000000000..47b7eb84b22 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2022b'} + +moduleclass = 'devel' From f3a08eca112a5aab06cecd51bbb82303b4933c44 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 12 Apr 2023 19:39:27 +0200 Subject: [PATCH 7129/9987] adding easyconfigs: libxc-6.1.0-GCC-12.2.0.eb, libxc-6.1.0-intel-compilers-2022.2.1.eb --- .../l/libxc/libxc-6.1.0-GCC-12.2.0.eb | 45 +++++++++++++++++++ .../libxc-6.1.0-intel-compilers-2022.2.1.eb | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..14cd0a84781 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.1.0' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a3aa16915942543031a5d9c4a92c439ce54249bdcda8c91c4e69e65329dc9a54'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Perl', '5.36.0'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..0675ab1e243 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.1.0' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a3aa16915942543031a5d9c4a92c439ce54249bdcda8c91c4e69e65329dc9a54'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Perl', '5.36.0'), +] + +separate_build_dir = True + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], +} + +moduleclass = 'chem' From 72ec416a8469379c9cbbd667b82fba69b47c61c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 12 Apr 2023 20:14:52 +0200 Subject: [PATCH 7130/9987] Fix sanity check to use lib/cmake/ dir --- easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb index 14cd0a84781..8177e558c29 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb @@ -39,7 +39,7 @@ runtest = 'test' sanity_check_paths = { 'files': ['bin/xc-info'] + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], } moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb index 0675ab1e243..7b8ab41914b 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb @@ -39,7 +39,7 @@ runtest = 'test' sanity_check_paths = { 'files': ['bin/xc-info'] + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], - 'dirs': ['include', 'lib/pkgconfig', 'share/cmake/Libxc'], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], } moduleclass = 'chem' From e86deaef7f1ca24b1ae078668628e157c59dc0d7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 12 Apr 2023 23:11:19 +0200 Subject: [PATCH 7131/9987] add comment explaining runtest command to jax v0.3.25 with CUDA Co-authored-by: Kenneth Hoste --- .../easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb index 8c8935d85b4..4ddfd6746ec 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb @@ -114,6 +114,12 @@ exts_list = [ '335a8e206d14338176bf4136a131afe5d7b75999ac2c67f0ae79031322e25936'}, {'jax-0.4.4_cusparse.patch': '7414115533cce9f37c60850c09c69563a0ed6477c73f03c4132b9c2ae75ae60f'}, ], + # deliberately not testing in parallel, as that results in (additional) failing tests; + # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, + # see https://github.com/google/jax/issues/7323 and + # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; + # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; + # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + "JAX_ENABLE_X64=true pytest -vv tests", }), From 4af5a6c9fc62aeb32331674d22ab694d8934eed9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 13 Apr 2023 02:22:05 +0200 Subject: [PATCH 7132/9987] Add sanity check command --- easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb | 4 ++-- .../l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb index 8177e558c29..4549d2c41b2 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb @@ -18,8 +18,6 @@ builddependencies = [ ('Perl', '5.36.0'), ] -separate_build_dir = True - local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" # perform iterative build to get both static and shared libraries @@ -42,4 +40,6 @@ sanity_check_paths = { 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], } +sanity_check_commands = ['xc-info 1'] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb index 7b8ab41914b..8973869bc36 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb @@ -18,8 +18,6 @@ builddependencies = [ ('Perl', '5.36.0'), ] -separate_build_dir = True - local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" # perform iterative build to get both static and shared libraries @@ -42,4 +40,6 @@ sanity_check_paths = { 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], } +sanity_check_commands = ['xc-info 1'] + moduleclass = 'chem' From 422394fcb4377acb67577363778747a980d5db95 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 13 Apr 2023 02:49:44 +0200 Subject: [PATCH 7133/9987] adding easyconfigs: QuantumESPRESSO-7.2-foss-2022b.eb, QuantumESPRESSO-7.2-intel-2022b.eb --- .../QuantumESPRESSO-7.2-foss-2022b.eb | 51 +++++++++++++++++++ .../QuantumESPRESSO-7.2-intel-2022b.eb | 51 +++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb new file mode 100644 index 00000000000..6ec9f2f0d9d --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb @@ -0,0 +1,51 @@ +name = 'QuantumESPRESSO' +version = '7.2' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', +] +sources = [ + { + 'filename': 'q-e-qe-%(version)s.tar.gz', + 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + }, + { + 'filename': 'qe-gipaw-%(version)s.tar.gz', + 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/'] + }, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, +] +checksums = [ + {'q-e-qe-7.2.tar.gz': 'b348a4a7348b66a73545d9ca317a2645755c98d343c1cfe8def475ad030808c0'}, + {'qe-gipaw-7.2.tar.gz': '2c202f1c94c1800c663622b0b7d685d4472b6e5fb150bdb3854f39caab7f39ce'}, + {'wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [('M4', '1.4.19')] + +dependencies = [ + ('HDF5', '1.14.0'), + ('ELPA', '2022.05.001'), + ('libxc', '6.1.0'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb new file mode 100644 index 00000000000..5fbb08073cd --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb @@ -0,0 +1,51 @@ +name = 'QuantumESPRESSO' +version = '7.2' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = [ + 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', +] +sources = [ + { + 'filename': 'q-e-qe-%(version)s.tar.gz', + 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + }, + { + 'filename': 'qe-gipaw-%(version)s.tar.gz', + 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/'] + }, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, +] +checksums = [ + {'q-e-qe-7.2.tar.gz': 'b348a4a7348b66a73545d9ca317a2645755c98d343c1cfe8def475ad030808c0'}, + {'qe-gipaw-7.2.tar.gz': '2c202f1c94c1800c663622b0b7d685d4472b6e5fb150bdb3854f39caab7f39ce'}, + {'wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [('M4', '1.4.19')] + +dependencies = [ + ('HDF5', '1.14.0'), + ('ELPA', '2022.05.001'), + ('libxc', '6.1.0'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = 'all gwl xspectra couple epw gipaw w90' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' From a1f307ad2f143c353d0dcb33699c7a4d6b07797f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Apr 2023 10:42:25 +0200 Subject: [PATCH 7134/9987] update jax dependency of AlphaFold 2.3.1 to 0.3.25 --- .../a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb index c3d268ba085..6dc2fe0aa60 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('HH-suite', '3.3.0'), ('HMMER', '3.3.2'), ('Kalign', '3.3.5'), - ('jax', '0.3.14', versionsuffix), # also provides absl-py + ('jax', '0.3.25', versionsuffix), # also provides absl-py ('UCX-CUDA', '1.12.1', versionsuffix), ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), ('NCCL', '2.12.12', versionsuffix), From a4ac0ff20bbfb20957e1f1e8b8e05028ae243e39 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Thu, 13 Apr 2023 11:21:21 +0200 Subject: [PATCH 7135/9987] Update easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../libWallModelledLES-0.6.1-foss-2021b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb index 0efcf31e2cf..fdb85787dae 100644 --- a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb @@ -35,7 +35,10 @@ install_cmd += "export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && " install_cmd += "pwd && ls && ./Allwmake -j %(parallel)s " install_cmd += " && cp -av tests %(installdir)s " -sanity_check_paths = {"dirs": ["lib", "tests"], "files": ["lib/libWallModelledLES.so"]} +sanity_check_paths = { + "files": ["lib/libWallModelledLES.%s" % SHLIB_EXT], + "dirs": ["tests"], +} sanity_check_commands = [ "source $FOAM_BASH && cd %(installdir)s/tests/testCases/channel_flow && pimpleFoam" ] From 5da2c31ad6cffa86d8bc444b251874236ae914cb Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 13 Apr 2023 10:29:15 +0100 Subject: [PATCH 7136/9987] Update easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb --- .../l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb index fdb85787dae..41c152957ce 100644 --- a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb +++ b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb @@ -15,7 +15,7 @@ toolchain = {"name": "foss", "version": "2021b"} toolchainopts = {"cstd": "c++11", "vectorize": False} source_urls = ["https://bitbucket.org/lesituu/libwallmodelledles/get/"] -sources = ["af3c659d16d54238364e8812ae8fbe3e46f5e656.tar.gz"] +sources = ["v%(version)s.tar.gz"] checksums = ["06b2c06ef76b5247c0a0c0260ea1e4a58bed8e930d0a0add9fe60e626c4bc0f8"] dependencies = [ From c38d6d03b26616dda738eed6a897aa9e6dbc0ddf Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 13 Apr 2023 13:24:34 +0200 Subject: [PATCH 7137/9987] Revised package list --- .../LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb index bc52a152c36..c2d6932e11c 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb @@ -36,11 +36,11 @@ dependencies = [ ('zlib', '1.2.12'), ('gzip', '1.12'), ('cURL', '7.83.0'), - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('tbb', '2021.5.0'), ('PCRE', '8.45'), ('libxml2', '2.9.13'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.4.2'), ('Voro++', '0.4.6'), ('kim-api', '2.3.0'), ('Eigen', '3.4.0'), @@ -67,6 +67,7 @@ dependencies = [ # include the following extra packages into the build general_packages = [ + 'AMOEBA', 'ASPHERE', 'ATC', 'AWPMD', @@ -75,7 +76,7 @@ general_packages = [ 'BPM', 'BROWNIAN', 'CG-DNA', - 'CG-SDK', + 'CG-SPICA', 'CLASS2', 'COLLOID', 'COLVARS', @@ -97,21 +98,27 @@ general_packages = [ 'EXTRA-MOLECULE', 'EXTRA-PAIR', 'FEP', + 'GPU', 'GRANULAR', 'H5MD', + 'INTEL', 'INTERLAYER', 'KIM', + 'KOKKOS', 'KSPACE', 'LATBOLTZ', - 'MANIFOLD', + 'LEPTON', 'MACHDYN', + 'MANIFOLD', 'MANYBODY', 'MC', + 'MDI', 'MEAM', 'MGPT', 'MISC', 'ML-IAP', 'ML-PACE', + 'ML-POD', 'ML-RANN', 'ML-SNAP', 'MOFFF', @@ -120,6 +127,7 @@ general_packages = [ 'MPIIO', 'NETCDF', 'OPENMP', + 'OPT', 'ORIENT', 'PERI', 'PHONON', From 1fd4e449a6060076ce56b101a56d55207eb7c319 Mon Sep 17 00:00:00 2001 From: Maxim Date: Thu, 13 Apr 2023 14:17:29 +0200 Subject: [PATCH 7138/9987] Update LAMMPS-23Jun2022-foss-2022a-kokkos.eb Remove general packages that are handled by the easyblock --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb index c2d6932e11c..71f3ac87550 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb @@ -63,7 +63,8 @@ dependencies = [ # packages auto-enabled by easyblock # 'GPU' - if cuda package is present and kokkos is disabled # 'KOKKOS' - if kokkos is enabled (by default) - +# 'INTEL' - if builing on Intel CPU +# 'OPENMP' - if OpenMP swithed on in 'toolchainopts' # include the following extra packages into the build general_packages = [ @@ -98,13 +99,10 @@ general_packages = [ 'EXTRA-MOLECULE', 'EXTRA-PAIR', 'FEP', - 'GPU', 'GRANULAR', 'H5MD', - 'INTEL', 'INTERLAYER', 'KIM', - 'KOKKOS', 'KSPACE', 'LATBOLTZ', 'LEPTON', @@ -126,7 +124,6 @@ general_packages = [ 'MOLFILE', 'MPIIO', 'NETCDF', - 'OPENMP', 'OPT', 'ORIENT', 'PERI', From 7ce1cff20ecb550368806057a36f672248b75a12 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 13 Apr 2023 14:38:44 +0200 Subject: [PATCH 7139/9987] Add ESPResSo and deps for 2021a --- .../Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb | 29 ++++++++++++++ .../c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb | 38 +++++++++++++++++++ .../ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb | 38 +++++++++++++++++++ .../p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb | 25 ++++++++++++ 4 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb create mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb new file mode 100644 index 00000000000..9a5bff9bd31 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.76.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['7bd7ddceec1a1dfdcbdb3e609b60d01739c38390a5f956385a12f3122049f0ca'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('zstd', '1.4.9'), + ('ICU', '69.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..faff04ca575 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '0.29.34' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1909688f5d7b521a60c396d20bba9e47a1b2d2784bfb085401e1e1e7d29a29a8'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cython --version', +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..4cdcffd3901 --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'ESPResSo' +version = '4.2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://espressomd.org/wordpress' +description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" + +source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e6e17fafa9ba80b46f542dc86e07677a8d641cfd0102ebc4db2f7ee47d5fb6f1'] + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', SYSTEM), + ('SciPy-bundle', '2021.05'), + ('Boost.MPI', '1.76.0'), + ('Cython', '0.29.34'), + ('HDF5', '1.10.7'), + ('Mesa', '21.1.1'), + ('GSL', '2.7'), + ('IPython', '7.25.0'), + ('Pint', '0.20.1'), +] + +configopts = ' -DCMAKE_SKIP_RPATH=OFF ' + +separate_build_dir = True + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..36db893fe73 --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Pint' +version = '0.20.1' + +homepage = 'https://github.com/hgrecco/pint' +description = """Pint is a Python package to define, operate and +manipulate physical quantities: the product of a numerical value and a +unit of measurement. It allows arithmetic operations between them and +conversions from and to different units.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'numlib' From e4090a57702f4c1e6126c6174f80d0526ea5130d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 13 Apr 2023 15:18:03 +0200 Subject: [PATCH 7140/9987] Update easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb --- .../d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb index b2a1f818c5d..9b146a684ba 100644 --- a/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'RPackage' name = 'DIALOGUE' local_commit = '7109f6a' -# see DESCRIPTION to determine version, +# see DESCRIPTION file in source to determine version, # but add date stamp of commit since version is not always bumped version = '1.0-20230228' versionsuffix = '-R-%(rver)s' From a8ca4a2ecbb3a958cc4a56e9418b45dd28e16a34 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 13 Apr 2023 15:20:58 +0200 Subject: [PATCH 7141/9987] use recommended Java dependency 11 - also SYSTEM instead of True --- ...re-uftp-1.4.2-Java-1.8.eb => unicore-uftp-1.4.2-Java-11.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/u/unicore-uftp/{unicore-uftp-1.4.2-Java-1.8.eb => unicore-uftp-1.4.2-Java-11.eb} (84%) diff --git a/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb b/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-11.eb similarity index 84% rename from easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb rename to easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-11.eb index cc641945cc6..920e80869a6 100644 --- a/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-1.8.eb +++ b/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-11.eb @@ -13,8 +13,7 @@ source_urls = ['https://downloads.sourceforge.net/project/unicore/Clients/UFTP-C sources = ['uftp-client-%(version)s-all.zip'] checksums = ['49670714416077274a0dfdc261e5552bcabbdd5cc4454181a794158491524c54'] -# specify dependency on Java/1.8 "wrapper", rather than a specific Java version -dependencies = [('Java', '1.8', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] postinstallcmds = ["chmod +x %(installdir)s/bin/uftp"] From 675e1e2f6f6233384f8099133152c79c8f95575c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 13 Apr 2023 14:37:33 +0100 Subject: [PATCH 7142/9987] adding easyconfigs: PICI-LIGGGHTS-3.8.1-foss-2022a.eb --- .../PICI-LIGGGHTS-3.8.1-foss-2022a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb b/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb new file mode 100644 index 00000000000..4c7f30339f9 --- /dev/null +++ b/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb @@ -0,0 +1,48 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' + +name = 'PICI-LIGGGHTS' +version = '3.8.1' + +homepage = 'https://github.com/uob-positron-imaging-centre/PICI-LIGGGHTS' +description = """UoB Postron Imaging Centre's Improved LIGGGHTS distribution with + an emphasis on the Python interface.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/uob-positron-imaging-centre/PICI-LIGGGHTS/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['49df8c0379b00ebb57eac7c8ec25755976c2459c0a9f569090b55a0aafee628f'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('libjpeg-turbo', '2.1.3'), + ('VTK', '9.2.2'), +] + +configopts = '-DVTK_DIR=$EBROOTVTK' + +_pydir = "%(installdir)s/lib/python%(pyshortver)s/site-packages" +postinstallcmds = [ + "mkdir -p %s" % _pydir, + "cd %%(builddir)s/%%(name)s*/python && python install.py %%(installdir)s/lib %s" % _pydir, + "cp -r %(builddir)s/%(name)s*/examples %(installdir)s/", +] +start_dir = 'src' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/liggghts', 'lib/libliggghts.a', 'lib/libliggghts.%s' % SHLIB_EXT], + 'dirs': ['examples/LIGGGHTS/Tutorials_public', 'include'], +} + +sanity_check_commands = ['python -c "import liggghts"'] + +moduleclass = 'cae' From 399a01583ddfd34e189f46de83b83733c74ba4eb Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 13 Apr 2023 15:38:10 +0200 Subject: [PATCH 7143/9987] Add sanity check --- .../ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb index 4cdcffd3901..3dac9d9fef5 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb @@ -35,4 +35,20 @@ separate_build_dir = True modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} +_binaries = ['ipypresso', 'pypresso'] +_libs = [ + 'Espresso_config.so', 'Espresso_core.so', 'Espresso_script_interface.so', 'Espresso_shapes.so', + '_init.so', 'analyze.so', 'code_info.so', 'cuda_init.so', 'electrokinetics.so', 'galilei.so', + 'integrate.so', 'interactions.so', 'lb.so', 'particle_data.so', 'polymer.so', 'profiler.so', + 'script_interface.so', 'system.so', 'thermostat.so', 'utils.so', 'version.so', +] + +_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + [_lib_path + '/%s' % x for x in _libs], + 'dirs': ['bin', 'lib'] +} + moduleclass = 'chem' From 8ee2b1cfbdec034a73190879ef4d1eaeec3d3dda Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 13 Apr 2023 17:21:27 +0200 Subject: [PATCH 7144/9987] Change filename --- ...-CUDA-11.7.0.eb => ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb} | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/e/ESPResSo/{ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb => ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb} (93%) diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb similarity index 93% rename from easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb rename to easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb index 3dac9d9fef5..f89a0dddce5 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb @@ -29,7 +29,9 @@ dependencies = [ ('Pint', '0.20.1'), ] -configopts = ' -DCMAKE_SKIP_RPATH=OFF ' +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON' + +buildopts = ' && make check_unit_tests && make check_python ' separate_build_dir = True From 674c3e0fa341f483bcc389270ab813f75dec39cb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 13 Apr 2023 15:47:14 +0000 Subject: [PATCH 7145/9987] adding easyconfigs: ruffus-2.8.4-GCCcore-11.3.0.eb --- .../r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d0606a41e97 --- /dev/null +++ b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'ruffus' +version = '2.8.4' + +homepage = 'http://www.ruffus.org.uk/' +description = """Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, + and widely used in science and bioinformatics.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'] + +dependencies = [ + ('Python', '3.10.4'), + ('Graphviz', '5.0.0'), +] + +download_dep_fail = True + +use_pip = True +sanity_pip_check = True + + +sanity_check_commands = ["python -c 'import ruffus.graph'"] + +moduleclass = 'lib' From 8cd3bc9ac7304dc26e85afeaf1f2c35026bafa3c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Apr 2023 18:06:58 +0200 Subject: [PATCH 7146/9987] skip test_native_mha for PyTorch 1.13.1, which fails on Broadwell systems --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index 8a737d028c0..5f15c785eb3 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -100,6 +100,9 @@ excluded_tests = { 'distributions/test_constraints', # no xdoctest 'doctests', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'test_native_mha', ] } From f113a552daba71c4196a8e62ba3030b4008cd916 Mon Sep 17 00:00:00 2001 From: Maxim Date: Thu, 13 Apr 2023 18:28:48 +0200 Subject: [PATCH 7147/9987] Update ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb --- .../e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb index f89a0dddce5..51fa7dc8424 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb @@ -31,8 +31,6 @@ dependencies = [ configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON' -buildopts = ' && make check_unit_tests && make check_python ' - separate_build_dir = True modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} From bdca62103b6e42bfff2449a7a64e636e0a0b5e4a Mon Sep 17 00:00:00 2001 From: Maxim Date: Thu, 13 Apr 2023 18:29:58 +0200 Subject: [PATCH 7148/9987] Rename ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb to ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb --- ...1a-CUDA-11.3.1.eb => ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/e/ESPResSo/{ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb => ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb} (100%) diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb similarity index 100% rename from easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb rename to easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb From c802939db634b4e661dac25665b4b13f40ce5ab1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 13 Apr 2023 18:35:34 +0200 Subject: [PATCH 7149/9987] add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test (fixes #17693) --- .../SciPy-bundle-2023.02-gfbf-2022b.eb | 2 + .../scipy-1.10.1_fix-lobpcg-test.patch | 185 ++++++++++++++++++ 2 files changed, 187 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb index f6d9d0f8045..171798e25d4 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb @@ -51,12 +51,14 @@ exts_list = [ 'patches': [ 'scipy-1.10.1_disable-tests.patch', 'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch', + 'scipy-1.10.1_fix-lobpcg-test.patch', ], 'checksums': [ {'scipy-1.10.1.tar.gz': '2cf9dfb80a7b4589ba4c40ce7588986d6d5cebc5457cad2c2880f6bc2d42f3a5'}, {'scipy-1.10.1_disable-tests.patch': '5d36d416fb7ea9297514c3988d9f506793e39dc4c0daedccf6733c3dd7e3dcc0'}, {'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch': '48177d6af51cf3e3d46aed8425807f0a65a498f7558f475032e0ad846559a23e'}, + {'scipy-1.10.1_fix-lobpcg-test.patch': '45d6c9e0241b9e5d035474033d0caacec705c58ad89e22419c62bef2b17ae8aa'}, ], 'enable_slow_tests': True, 'ignore_test_result': False, diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch new file mode 100644 index 00000000000..f05389c915c --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch @@ -0,0 +1,185 @@ +see https://github.com/scipy/scipy/issues/17954 + https://github.com/scipy/scipy/pull/17975 +From: Andrew Knyazev +Date: Tue, 14 Feb 2023 17:09:13 -0500 +Subject: [PATCH 1/6] Update test_lobpcg.py + +test +--- + scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 7 +++---- + 1 file changed, 3 insertions(+), 4 deletions(-) + +diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +index afd7a106ea0..8e6de348a34 100644 +--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py ++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +@@ -255,17 +255,16 @@ def test_fiedler_large_12(): + _check_fiedler(12, 2) + + +-@pytest.mark.skipif(platform.machine() == 'aarch64', +- reason="issue #15935") ++@pytest.mark.filterwarnings("ignore:Failed at iteration") + def test_failure_to_run_iterations(): + """Check that the code exists gracefully without breaking. Issue #10974. ++ The code may or not issue a warning, filtered out. Issue #15935, #17954. + """ + rnd = np.random.RandomState(0) + X = rnd.standard_normal((100, 10)) + A = X @ X.T + Q = rnd.standard_normal((X.shape[0], 4)) +- with pytest.warns(UserWarning, match="Failed at iteration"): +- eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) ++ eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) + assert np.max(eigenvalues) > 0 + + + +From ad2054168d1eb522cc9b71eebc9ea32aa0fbd4e3 Mon Sep 17 00:00:00 2001 +From: Andrew Knyazev +Date: Tue, 14 Feb 2023 18:14:37 -0500 +Subject: [PATCH 2/6] Update test_lobpcg.py + +"Exited at iteration" also needs filtering out +--- + scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +index 8e6de348a34..aa3a0c29842 100644 +--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py ++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +@@ -256,6 +256,7 @@ def test_fiedler_large_12(): + + + @pytest.mark.filterwarnings("ignore:Failed at iteration") ++@pytest.mark.filterwarnings("ignore:Exited at iteration") + def test_failure_to_run_iterations(): + """Check that the code exists gracefully without breaking. Issue #10974. + The code may or not issue a warning, filtered out. Issue #15935, #17954. + +From 5357bcbd970cdc6ef88be5e58ff3a46d34fde61e Mon Sep 17 00:00:00 2001 +From: Andrew Knyazev +Date: Tue, 14 Feb 2023 18:34:51 -0500 +Subject: [PATCH 3/6] Update test_lobpcg.py + +added one more filter +@pytest.mark.filterwarnings("ignore:Exited postprocessing") +--- + scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +index aa3a0c29842..87f3756c37d 100644 +--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py ++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +@@ -257,6 +257,7 @@ def test_fiedler_large_12(): + + @pytest.mark.filterwarnings("ignore:Failed at iteration") + @pytest.mark.filterwarnings("ignore:Exited at iteration") ++@pytest.mark.filterwarnings("ignore:Exited postprocessing") + def test_failure_to_run_iterations(): + """Check that the code exists gracefully without breaking. Issue #10974. + The code may or not issue a warning, filtered out. Issue #15935, #17954. + +From bcad369ce894320f310c761e0136816c0a1410fb Mon Sep 17 00:00:00 2001 +From: Andrew Knyazev +Date: Wed, 15 Feb 2023 07:59:37 -0500 +Subject: [PATCH 4/6] Update test_lobpcg.py + +as proposed by reviewer +--- + scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 7 +++---- + 1 file changed, 3 insertions(+), 4 deletions(-) + +diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +index 87f3756c37d..936cc6f8db7 100644 +--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py ++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +@@ -255,9 +255,6 @@ def test_fiedler_large_12(): + _check_fiedler(12, 2) + + +-@pytest.mark.filterwarnings("ignore:Failed at iteration") +-@pytest.mark.filterwarnings("ignore:Exited at iteration") +-@pytest.mark.filterwarnings("ignore:Exited postprocessing") + def test_failure_to_run_iterations(): + """Check that the code exists gracefully without breaking. Issue #10974. + The code may or not issue a warning, filtered out. Issue #15935, #17954. +@@ -266,7 +263,9 @@ def test_failure_to_run_iterations(): + X = rnd.standard_normal((100, 10)) + A = X @ X.T + Q = rnd.standard_normal((X.shape[0], 4)) +- eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) ++ with warnings.catch_warnings(): ++ warnings.simplefilter("ignore") ++ eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) + assert np.max(eigenvalues) > 0 + + + +From bf8f497984c2056819068d8da5231c1e430659b3 Mon Sep 17 00:00:00 2001 +From: Andrew Knyazev +Date: Wed, 15 Feb 2023 10:25:29 -0500 +Subject: [PATCH 5/6] Update test_lobpcg.py + +import warnings added +--- + scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +index 936cc6f8db7..db87940e6a8 100644 +--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py ++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +@@ -4,6 +4,7 @@ + import itertools + import platform + import sys ++import warnings + import pytest + import numpy as np + from numpy import ones, r_, diag + +From 77b9f45041bcfcb8e531b4d44c0399f103850e4d Mon Sep 17 00:00:00 2001 +From: Andrew Knyazev +Date: Wed, 15 Feb 2023 11:51:01 -0500 +Subject: [PATCH 6/6] Update test_lobpcg.py + +fall back to what has passed +--- + scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +index db87940e6a8..87f3756c37d 100644 +--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py ++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +@@ -4,7 +4,6 @@ + import itertools + import platform + import sys +-import warnings + import pytest + import numpy as np + from numpy import ones, r_, diag +@@ -256,6 +255,9 @@ def test_fiedler_large_12(): + _check_fiedler(12, 2) + + ++@pytest.mark.filterwarnings("ignore:Failed at iteration") ++@pytest.mark.filterwarnings("ignore:Exited at iteration") ++@pytest.mark.filterwarnings("ignore:Exited postprocessing") + def test_failure_to_run_iterations(): + """Check that the code exists gracefully without breaking. Issue #10974. + The code may or not issue a warning, filtered out. Issue #15935, #17954. +@@ -264,9 +266,7 @@ def test_failure_to_run_iterations(): + X = rnd.standard_normal((100, 10)) + A = X @ X.T + Q = rnd.standard_normal((X.shape[0], 4)) +- with warnings.catch_warnings(): +- warnings.simplefilter("ignore") +- eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) ++ eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) + assert np.max(eigenvalues) > 0 + + From 157c9349492d346f662ca453d6e648124c758619 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 13 Apr 2023 18:25:45 +0100 Subject: [PATCH 7150/9987] generate patch that applies --- .../SciPy-bundle-2023.02-gfbf-2022b.eb | 2 +- .../scipy-1.10.1_fix-lobpcg-test.patch | 170 +----------------- 2 files changed, 8 insertions(+), 164 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb index 171798e25d4..ec4572d24d0 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb @@ -58,7 +58,7 @@ exts_list = [ {'scipy-1.10.1_disable-tests.patch': '5d36d416fb7ea9297514c3988d9f506793e39dc4c0daedccf6733c3dd7e3dcc0'}, {'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch': '48177d6af51cf3e3d46aed8425807f0a65a498f7558f475032e0ad846559a23e'}, - {'scipy-1.10.1_fix-lobpcg-test.patch': '45d6c9e0241b9e5d035474033d0caacec705c58ad89e22419c62bef2b17ae8aa'}, + {'scipy-1.10.1_fix-lobpcg-test.patch': '4940d3856d66f88af4b242dcd3b83f83a9b30da36ead73776f8d72cc17c56f12'}, ], 'enable_slow_tests': True, 'ignore_test_result': False, diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch index f05389c915c..e1a3fda99ec 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch @@ -1,24 +1,18 @@ +change test for a warning to filterwarnings since the code may or not issue a warning depending on an arch see https://github.com/scipy/scipy/issues/17954 + https://github.com/scipy/scipy/pull/17975 -From: Andrew Knyazev -Date: Tue, 14 Feb 2023 17:09:13 -0500 -Subject: [PATCH 1/6] Update test_lobpcg.py - -test ---- - scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 7 +++---- - 1 file changed, 3 insertions(+), 4 deletions(-) - diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -index afd7a106ea0..8e6de348a34 100644 +index afd7a106ea0..87f3756c37d 100644 --- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -@@ -255,17 +255,16 @@ def test_fiedler_large_12(): +@@ -255,17 +255,18 @@ _check_fiedler(12, 2) -@pytest.mark.skipif(platform.machine() == 'aarch64', - reason="issue #15935") -+@pytest.mark.filterwarnings("ignore:Failed at iteration") +++@pytest.mark.filterwarnings("ignore:Failed at iteration") +++@pytest.mark.filterwarnings("ignore:Exited at iteration") +++@pytest.mark.filterwarnings("ignore:Exited postprocessing") def test_failure_to_run_iterations(): """Check that the code exists gracefully without breaking. Issue #10974. + The code may or not issue a warning, filtered out. Issue #15935, #17954. @@ -30,156 +24,6 @@ index afd7a106ea0..8e6de348a34 100644 - with pytest.warns(UserWarning, match="Failed at iteration"): - eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) + eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) - assert np.max(eigenvalues) > 0 - - - -From ad2054168d1eb522cc9b71eebc9ea32aa0fbd4e3 Mon Sep 17 00:00:00 2001 -From: Andrew Knyazev -Date: Tue, 14 Feb 2023 18:14:37 -0500 -Subject: [PATCH 2/6] Update test_lobpcg.py - -"Exited at iteration" also needs filtering out ---- - scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -index 8e6de348a34..aa3a0c29842 100644 ---- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -+++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -@@ -256,6 +256,7 @@ def test_fiedler_large_12(): - - - @pytest.mark.filterwarnings("ignore:Failed at iteration") -+@pytest.mark.filterwarnings("ignore:Exited at iteration") - def test_failure_to_run_iterations(): - """Check that the code exists gracefully without breaking. Issue #10974. - The code may or not issue a warning, filtered out. Issue #15935, #17954. - -From 5357bcbd970cdc6ef88be5e58ff3a46d34fde61e Mon Sep 17 00:00:00 2001 -From: Andrew Knyazev -Date: Tue, 14 Feb 2023 18:34:51 -0500 -Subject: [PATCH 3/6] Update test_lobpcg.py - -added one more filter -@pytest.mark.filterwarnings("ignore:Exited postprocessing") ---- - scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -index aa3a0c29842..87f3756c37d 100644 ---- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -+++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -@@ -257,6 +257,7 @@ def test_fiedler_large_12(): - - @pytest.mark.filterwarnings("ignore:Failed at iteration") - @pytest.mark.filterwarnings("ignore:Exited at iteration") -+@pytest.mark.filterwarnings("ignore:Exited postprocessing") - def test_failure_to_run_iterations(): - """Check that the code exists gracefully without breaking. Issue #10974. - The code may or not issue a warning, filtered out. Issue #15935, #17954. - -From bcad369ce894320f310c761e0136816c0a1410fb Mon Sep 17 00:00:00 2001 -From: Andrew Knyazev -Date: Wed, 15 Feb 2023 07:59:37 -0500 -Subject: [PATCH 4/6] Update test_lobpcg.py - -as proposed by reviewer ---- - scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 7 +++---- - 1 file changed, 3 insertions(+), 4 deletions(-) - -diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -index 87f3756c37d..936cc6f8db7 100644 ---- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -+++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -@@ -255,9 +255,6 @@ def test_fiedler_large_12(): - _check_fiedler(12, 2) - - --@pytest.mark.filterwarnings("ignore:Failed at iteration") --@pytest.mark.filterwarnings("ignore:Exited at iteration") --@pytest.mark.filterwarnings("ignore:Exited postprocessing") - def test_failure_to_run_iterations(): - """Check that the code exists gracefully without breaking. Issue #10974. - The code may or not issue a warning, filtered out. Issue #15935, #17954. -@@ -266,7 +263,9 @@ def test_failure_to_run_iterations(): - X = rnd.standard_normal((100, 10)) - A = X @ X.T - Q = rnd.standard_normal((X.shape[0], 4)) -- eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) -+ with warnings.catch_warnings(): -+ warnings.simplefilter("ignore") -+ eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) - assert np.max(eigenvalues) > 0 - - - -From bf8f497984c2056819068d8da5231c1e430659b3 Mon Sep 17 00:00:00 2001 -From: Andrew Knyazev -Date: Wed, 15 Feb 2023 10:25:29 -0500 -Subject: [PATCH 5/6] Update test_lobpcg.py - -import warnings added ---- - scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -index 936cc6f8db7..db87940e6a8 100644 ---- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -+++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -@@ -4,6 +4,7 @@ - import itertools - import platform - import sys -+import warnings - import pytest - import numpy as np - from numpy import ones, r_, diag - -From 77b9f45041bcfcb8e531b4d44c0399f103850e4d Mon Sep 17 00:00:00 2001 -From: Andrew Knyazev -Date: Wed, 15 Feb 2023 11:51:01 -0500 -Subject: [PATCH 6/6] Update test_lobpcg.py - -fall back to what has passed ---- - scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | 8 ++++---- - 1 file changed, 4 insertions(+), 4 deletions(-) - -diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -index db87940e6a8..87f3756c37d 100644 ---- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -+++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py -@@ -4,7 +4,6 @@ - import itertools - import platform - import sys --import warnings - import pytest - import numpy as np - from numpy import ones, r_, diag -@@ -256,6 +255,9 @@ def test_fiedler_large_12(): - _check_fiedler(12, 2) - - -+@pytest.mark.filterwarnings("ignore:Failed at iteration") -+@pytest.mark.filterwarnings("ignore:Exited at iteration") -+@pytest.mark.filterwarnings("ignore:Exited postprocessing") - def test_failure_to_run_iterations(): - """Check that the code exists gracefully without breaking. Issue #10974. - The code may or not issue a warning, filtered out. Issue #15935, #17954. -@@ -264,9 +266,7 @@ def test_failure_to_run_iterations(): - X = rnd.standard_normal((100, 10)) - A = X @ X.T - Q = rnd.standard_normal((X.shape[0], 4)) -- with warnings.catch_warnings(): -- warnings.simplefilter("ignore") -- eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) -+ eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) - assert np.max(eigenvalues) > 0 + assert(np.max(eigenvalues) > 0) From 95080c97c4c5d47aacca3a156a70b3d8bd748371 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 13 Apr 2023 18:32:00 +0100 Subject: [PATCH 7151/9987] remove extra + --- .../s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb | 2 +- .../s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb index ec4572d24d0..9f60a08cff4 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb @@ -58,7 +58,7 @@ exts_list = [ {'scipy-1.10.1_disable-tests.patch': '5d36d416fb7ea9297514c3988d9f506793e39dc4c0daedccf6733c3dd7e3dcc0'}, {'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch': '48177d6af51cf3e3d46aed8425807f0a65a498f7558f475032e0ad846559a23e'}, - {'scipy-1.10.1_fix-lobpcg-test.patch': '4940d3856d66f88af4b242dcd3b83f83a9b30da36ead73776f8d72cc17c56f12'}, + {'scipy-1.10.1_fix-lobpcg-test.patch': 'eb4c576959108df0b1749705e64fe42e79edcf5aa8f6b4d7908f9b136d0d6648'}, ], 'enable_slow_tests': True, 'ignore_test_result': False, diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch index e1a3fda99ec..45668de46ae 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch @@ -10,9 +10,9 @@ index afd7a106ea0..87f3756c37d 100644 -@pytest.mark.skipif(platform.machine() == 'aarch64', - reason="issue #15935") -++@pytest.mark.filterwarnings("ignore:Failed at iteration") -++@pytest.mark.filterwarnings("ignore:Exited at iteration") -++@pytest.mark.filterwarnings("ignore:Exited postprocessing") ++@pytest.mark.filterwarnings("ignore:Failed at iteration") ++@pytest.mark.filterwarnings("ignore:Exited at iteration") ++@pytest.mark.filterwarnings("ignore:Exited postprocessing") def test_failure_to_run_iterations(): """Check that the code exists gracefully without breaking. Issue #10974. + The code may or not issue a warning, filtered out. Issue #15935, #17954. From 3b22c01c46bb91ce2d39a0f8f7c5df8a6b1a7def Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 13 Apr 2023 13:37:00 -0400 Subject: [PATCH 7152/9987] adding easyconfigs: phyx-1.3-foss-2022a.eb, Armadillo-11.4.3-foss-2022a.eb and patches: phyx-1.3_link_flexiblas.patch --- .../Armadillo/Armadillo-11.4.3-foss-2022a.eb | 22 ++++++++ .../easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb | 51 +++++++++++++++++++ .../p/phyx/phyx-1.3_link_flexiblas.patch | 14 +++++ 3 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb new file mode 100644 index 00000000000..261ecca60bb --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb @@ -0,0 +1,22 @@ +name = 'Armadillo' +version = '11.4.3' + +homepage = 'https://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['87603263664988af41da2ca4f36205e36ea47a9281fa6cfd463115f3797a1da2'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Boost', '1.79.0'), + ('arpack-ng', '3.8.0'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb new file mode 100644 index 00000000000..1418ab60d05 --- /dev/null +++ b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'phyx' +version = '1.3' + +homepage = 'https://github.com/FePhyFoFum/%(name)s' +description = "phyx performs phylogenetics analyses on trees and sequences." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +github_account = 'FePhyFoFum' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_link_flexiblas.patch'] +checksums = [ + {'v1.3.tar.gz': 'b09677f98f997838b39cd2724463be06d0627ddc90a7e659dc90d4e02db624eb'}, + {'phyx-1.3_link_flexiblas.patch': 'e9dc98da0f3c5df8e5b8ac3e64c2b0f77358f61fc60a4aadce5ad790b636ebdd'}, +] + +builddependencies = [ + ('Autotools', '20220317', '', ('GCCcore', '11.3.0')), +] + +dependencies = [ + ('Armadillo', '11.4.3'), + ('NLopt', '2.7.1'), +] + +start_dir = 'src' + +#preconfigopts = 'autoconf && ' +preconfigopts = "autoreconf -f -i && " + + +preinstallopts = 'mkdir %(installdir)s/bin && ' + +sanity_check_paths = { + 'files': ['bin/' + _exec for _exec in ["pxaa2cdn", "pxbdfit", "pxbdsim", + "pxboot", "pxbp", "pxcat", "pxclsq", "pxcltr", "pxcolt", "pxconsq", + "pxcontrates", "pxfqfilt", "pxlog", "pxlssq", "pxlstr", "pxmrca", + "pxmrcacut", "pxmrcaname", "pxnw", "pxrecode", "pxrevcomp", + "pxrls", "pxrlt", "pxrmk", "pxrms", "pxrmt", "pxrr", "pxs2fa", "pxs2nex", + "pxs2phy", "pxseqgen", "pxssort", "pxsstat", "pxstrec", "pxsw", "pxt2new", + "pxt2nex", "pxtcol", "pxtcomb", "pxtlate", "pxtrt", "pxtscale", + "pxvcf2fa"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch b/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch new file mode 100644 index 00000000000..1b541919cf8 --- /dev/null +++ b/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch @@ -0,0 +1,14 @@ +replace linking with lapack and blas by flexiblas +autor: Graham Derryberry +diff -Naur phyx-1.3.orig/src/Makefile.in phyx-1.3/src/Makefile.in +--- phyx-1.3.orig/src/Makefile.in 2023-04-12 22:44:14.000000000 -0400 ++++ phyx-1.3/src/Makefile.in 2023-04-13 09:57:34.000000000 -0400 +@@ -17,7 +17,7 @@ + HARM := @HARM@ + HOMP := @HOMP@ + +-CPP_LIBS = -llapack -lblas -lpthread -lm ++CPP_LIBS = -lflexiblas -lpthread -lm + ifeq "$(HNLOPT)" "Y" + CPP_LIBS += -lnlopt + endif From ad4a7024987d2c486de9e4edbbea0962b11df1d9 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 13 Apr 2023 14:07:37 -0400 Subject: [PATCH 7153/9987] Fixing style error by removing commented out dead code --- easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb index 1418ab60d05..8eb989c720d 100644 --- a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb +++ b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb @@ -30,10 +30,8 @@ dependencies = [ start_dir = 'src' -#preconfigopts = 'autoconf && ' preconfigopts = "autoreconf -f -i && " - preinstallopts = 'mkdir %(installdir)s/bin && ' sanity_check_paths = { From 942ab161e81b9de042c8cc0f79589936f42a5165 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Apr 2023 09:13:07 +0200 Subject: [PATCH 7154/9987] adding easyconfigs: RevBayes-1.2.1-gompi-2022a.eb --- .../r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb new file mode 100644 index 00000000000..525ec2e7c03 --- /dev/null +++ b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb @@ -0,0 +1,40 @@ +# easybuild easyconfig +# +# John Dey +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +easyblock = 'CmdCp' + +name = 'RevBayes' +version = '1.2.1' + +homepage = 'https://revbayes.github.io' +description = """RevBayes provides an interactive environment for statistical computation in + phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in + evolutionary biology, particularly phylogenetics.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/revbayes/revbayes/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['58c320ee7251a7a244aba57b471a6e695f3db8196ea4c9381bb2bc1076bcedfa'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Boost', '1.79.0'), +] + +start_dir = 'projects/cmake' +local_cmd = './build.sh -mpi true -DCMAKE_CXX_FLAGS="-pthread" -DBoost_NO_BOOST_CMAKE=ON' +cmds_map = [('', local_cmd)] + +files_to_copy = [(['projects/cmake/rb-mpi'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/rb-mpi'], + 'dirs': [], +} + +moduleclass = 'bio' From 42aed9962f7c0bb46bea6e6b5d6811d7582bb555 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Apr 2023 09:28:35 +0200 Subject: [PATCH 7155/9987] use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0 --- .../AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb | 2 +- ...1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb | 66 +++++++++++++++++++ 2 files changed, 67 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb index 348e3a6aaed..b37b644450f 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb @@ -29,7 +29,7 @@ dependencies = [ ('UCX-CUDA', '1.11.2', versionsuffix), ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), - ('OpenMM', '7.5.1', '-DeepMind-patch'), + ('OpenMM', '7.5.1', '%(versionsuffix)s-DeepMind-patch'), ] # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb new file mode 100644 index 00000000000..335b9a7e2da --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.1' +versionsuffix = '-CUDA-%(cudaver)s-DeepMind-patch' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + ('OpenMM-%(version)s_DeepMind.patch', 'wrappers/python'), + 'OpenMM-7.5.0_fix_path_to_nvcc.patch', + 'OpenMM-8.0.0_add_no_tree_vectorize.patch', +] +checksums = [ + {'7.5.1.tar.gz': 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7'}, + {'OpenMM-7.5.1_DeepMind.patch': '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6'}, + {'OpenMM-7.5.0_fix_path_to_nvcc.patch': '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c'}, + {'OpenMM-8.0.0_add_no_tree_vectorize.patch': '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd'}, +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('CUDA', '11.4.1', '', SYSTEM), + ('SWIG', '4.0.2'), +] + +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 52cbf0e64ab4be9e4aa7baf54080e2656f0c2697 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 14 Apr 2023 08:54:06 +0100 Subject: [PATCH 7156/9987] skip distributed/rpc/test_tensorpipe_agent --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index 5f15c785eb3..af5f58752a4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -103,6 +103,9 @@ excluded_tests = { # failing on broadwell # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 'test_native_mha', + # intermittent failures on various systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'distributed/rpc/test_tensorpipe_agent', ] } From ecaf64829b6ee050d01edfc8ea36d6db6133c1b1 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 14 Apr 2023 10:28:32 +0000 Subject: [PATCH 7157/9987] Add missing binutils builddep --- easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb index d0606a41e97..0354e336f08 100644 --- a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} sources = [SOURCE_TAR_GZ] checksums = ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'] +builddependencies = [('binutils', '2.38')] + dependencies = [ ('Python', '3.10.4'), ('Graphviz', '5.0.0'), @@ -22,7 +24,6 @@ download_dep_fail = True use_pip = True sanity_pip_check = True - sanity_check_commands = ["python -c 'import ruffus.graph'"] moduleclass = 'lib' From 56d2abd327d418a81977d5720ef5f5ba7ed2cbbd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 14 Apr 2023 13:38:08 +0200 Subject: [PATCH 7158/9987] adding easyconfigs: Structure-2.3.4-GCC-12.2.0.eb --- .../s/Structure/Structure-2.3.4-GCC-12.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-12.2.0.eb b/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-12.2.0.eb new file mode 100644 index 00000000000..94412d6b87a --- /dev/null +++ b/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-12.2.0.eb @@ -0,0 +1,41 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'Structure' +version = '2.3.4' + +homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html' +description = """The program structure is a free software package for using multi-locus genotype data to investigate + population structure.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/'] +sources = [{'download_filename': 'structure_kernel_source.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f2b72b9189a514f53e921bbdc1aa3dbaca7ac34a8467af1f972c7e4fc9c0bb37'] + +# Add -fcommon to fix "multiple definition" errors +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' +buildopts = 'all CC="$CC" OPT="$CFLAGS"' + +files_to_copy = [(['structure'], 'bin')] + +sanity_check_commands = [ + 'structure | grep "Version %(version)s"' +] + +sanity_check_paths = { + 'files': ['bin/structure'], + 'dirs': [], +} + +moduleclass = 'bio' From 38820779269cb4a22508388e425357726befb0cb Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 14 Apr 2023 12:40:02 +0100 Subject: [PATCH 7159/9987] fix typo Co-authored-by: Adam Huffman --- .../p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb b/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb index 4c7f30339f9..f0929b054cd 100644 --- a/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb @@ -5,7 +5,7 @@ name = 'PICI-LIGGGHTS' version = '3.8.1' homepage = 'https://github.com/uob-positron-imaging-centre/PICI-LIGGGHTS' -description = """UoB Postron Imaging Centre's Improved LIGGGHTS distribution with +description = """UoB Positron Imaging Centre's Improved LIGGGHTS distribution with an emphasis on the Python interface.""" toolchain = {'name': 'foss', 'version': '2022a'} From c1f46a78b297a1a37fc81164c1ccde8e27a7de5c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 14 Apr 2023 14:30:13 +0200 Subject: [PATCH 7160/9987] install shared libraries for tesseract --- .../easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb index fed7c2635a0..2c7b0dfdd73 100644 --- a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb @@ -45,6 +45,8 @@ dependencies = [ separate_build_dir = True +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + postinstallcmds = [ 'rm %(builddir)s/tessdata_best-4.1.0/configs', 'rm -rf %(builddir)s/tessdata_best-4.1.0/tessconfigs', @@ -56,7 +58,7 @@ modextrapaths = { } sanity_check_paths = { - 'files': ['bin/tesseract'], + 'files': ['bin/tesseract', 'lib/libtesseract.a', 'lib/libtesseract.%s' % SHLIB_EXT], 'dirs': ['share/tessdata', 'include/tesseract'] } From 64c6649fcd73c7a1ca8acbe8ce2902698fa89cbe Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 14 Apr 2023 14:31:50 +0200 Subject: [PATCH 7161/9987] adding easyconfigs: R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb --- .../R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..367d0c8c5f7 --- /dev/null +++ b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'R-tesseract' +version = '5.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/package=tesseract' +description = "The R extension for using tesseract" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [('pkgconf', '1.8.0')] + +dependencies = [ + ('R', '4.2.1'), + ('poppler', '22.12.0'), + ('tesseract', '5.3.0'), +] + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('askpass', '1.1', { + 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], + }), + ('qpdf', '1.3.2', { + 'checksums': ['d9c905a4879274d72de0c638f2e14737ec0a59895cbba9814e05c62b43e8e976'], + }), + ('pdftools', '3.3.3', { + 'checksums': ['ffc0dfa5205ac3c26ee22713289784cb6b9aada6c21417d79bfd4d7f5bd5909c'], + }), + ('rappdirs', '0.3.3', { + 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], + }), + ('tesseract', version, { + 'preinstallopts': 'INCLUDE_DIR="$EBROOTTESSERACT/include/tesseract -I$EBROOTLEPTONICA/include/leptonica"' + + ' LIB_DIR=$EBROOTTESSERACT/lib', + 'checksums': ['6dae7cbc1d4cf6decabb2d1c56d95b5eb6a0a4a1cbc9f9a1c274ba558b31cdfa'], + }), +] + +sanity_check_paths = { + 'files': ['tesseract/libs/tesseract.%s' % SHLIB_EXT, 'tesseract/R/tesseract'], + 'dirs': ['askpass', 'qpdf', 'pdftools', 'rappdirs'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'vis' From 79a6d8a8b0c987c945010443ba4843c4dca77b16 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 14 Apr 2023 14:35:08 +0200 Subject: [PATCH 7162/9987] remove unneeded separate_build_dir --- .../easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb index 2c7b0dfdd73..9bf893a4d12 100644 --- a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb @@ -43,8 +43,6 @@ dependencies = [ ('Pango', '1.50.7'), ] -separate_build_dir = True - configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] postinstallcmds = [ From 1674aed7cfd2f191f096dd6990ae162ea3f4069a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 14 Apr 2023 15:16:51 +0200 Subject: [PATCH 7163/9987] adding easyconfigs: prokka-1.14.5-gompi-2022a.eb, Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb --- .../Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb | 28 +++++++++++ .../p/prokka/prokka-1.14.5-gompi-2022a.eb | 50 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..840b2a8d6fa --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.34.1'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb new file mode 100644 index 00000000000..c1a3cfa1cd2 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.13.0'), + ('Java', '11', '', SYSTEM), + ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20220722'), + ('tbl2asn', '20220427', '-linux64', SYSTEM), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' From 585880c569c0dc03ea1d6206cf2cfbb83d015f2c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 14 Apr 2023 15:36:26 +0200 Subject: [PATCH 7164/9987] adding easyconfigs: Subread-2.0.4-GCC-11.3.0.eb --- .../s/Subread/Subread-2.0.4-GCC-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/Subread/Subread-2.0.4-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.4-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.4-GCC-11.3.0.eb new file mode 100644 index 00000000000..27bc601b2e9 --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.4-GCC-11.3.0.eb @@ -0,0 +1,39 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'MakeCp' + +name = 'Subread' +version = '2.0.4' + +homepage = 'https://subread.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +checksums = ['c54b37ed83b34318d8f119b5c02fb9d0a65c811195bcc9e1745df6daf74ca2db'] + +start_dir = 'src' + +prebuildopts = "sed -i 's/-mtune=core2//g' Makefile.Linux && " +prebuildopts += "sed -i 's/-mtune=core2//g' longread-one/Makefile && " + +buildopts = " -f Makefile.Linux" + +files_to_copy = ['bin'] + +local_binaries_list = [ + 'exactSNP', 'featureCounts', 'subindel', 'subjunc', 'sublong', '%(namelower)s-align', '%(namelower)s-buildindex', +] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_binaries_list], + 'dirs': ['bin/utilities'], +} + +sanity_check_commands = [ + 'cd %(builddir)s/%(namelower)s-%(version)s-source/test && bash test_all.sh' +] + +moduleclass = 'bio' From 84c717f657e2047dddb11fc6ae212a09b4f663c7 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Fri, 14 Apr 2023 14:38:49 +0100 Subject: [PATCH 7165/9987] let EasyBuild map toolchains automatically --- .../p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb index 8666c0f0dc9..6bb64936f1e 100644 --- a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb +++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb @@ -7,8 +7,6 @@ homepage = 'https://easybuild.io/' description = """Python distribution with a number of widely used extensions incl. NumPy, SciPy, Matplotlib, JupyterLab, MPI4PY, ... """ -local_gccver = '11.3.0' - toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True, 'lowopt': True} @@ -16,7 +14,7 @@ dependencies = [ ('Python', version), ('SciPy-bundle', '2022.05'), ('matplotlib', '3.5.2'), - ('JupyterLab', '3.5.0', '', ('GCCcore', local_gccver)), + ('JupyterLab', '3.5.0'), ] sanity_check_paths = { From 5c29f147dbef75ac8e6af824c91ed75667698972 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Fri, 14 Apr 2023 14:39:23 +0100 Subject: [PATCH 7166/9987] remove sanity check, and add moduleclass --- .../p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb index 6bb64936f1e..0d2db0765c9 100644 --- a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb +++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb @@ -17,7 +17,4 @@ dependencies = [ ('JupyterLab', '3.5.0'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ["easybuild/"], -} +moduleclass = 'lang' From 315b36740f23596f2439ea7eb8a0784a9781773c Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Fri, 14 Apr 2023 14:41:53 +0100 Subject: [PATCH 7167/9987] add Python-bundle to bundles_whitelist in test_pr_sanity_check_paths --- test/easyconfigs/easyconfigs.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9e2523ae1b9..40c597ba675 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1130,8 +1130,9 @@ def test_pr_sanity_check_paths(self): 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, - # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co - bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm'] + # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co, + # Python-bundle: Python + SciPy-bundle + matplotlib + JupyterLab + bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'Python-bundle', 'ROCm'] failing_checks = [] From 7fdbaa70628e4428ca99f75a2b1406dddd3cb090 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 14 Apr 2023 15:55:12 +0200 Subject: [PATCH 7168/9987] adding easyconfigs: Kraken2-2.1.2-gompi-2022a.eb --- .../k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb new file mode 100644 index 00000000000..78064ba7f3e --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb @@ -0,0 +1,62 @@ +easyblock = 'PackedBinary' + +name = 'Kraken2' +version = '2.1.2' + +homepage = 'https://github.com/DerrickWood/kraken2/wiki' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# part is compiled with $CXX, the rest is in Perl +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-2.1.1_fix_installation_for_easybuild.patch', + '%(name)s-%(version)s_fix_ncbi_https_server.patch', +] +checksums = [ + 'e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3', # v2.1.2.tar.gz + # Kraken2-2.1.1_fix_installation_for_easybuild.patch + '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11', + '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116', # Kraken2-2.1.2_fix_ncbi_https_server.patch +] + +dependencies = [ + ('Perl', '5.34.1'), + ('BLAST+', '2.13.0'), + ('wget', '1.21.3'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken2.sh %(installdir)s/bin' + +# Kraken2 databases can be downloaded from https://benlangmead.github.io/aws-indexes/k2 +# or built as described in https://github.com/DerrickWood/kraken2/wiki/Manual#kraken-2-databases +# The following commands will build and install the standard databases (100GB) in local_db_path +# local_db_path = '%(installdir)s/db' +# postinstallcmds = [ +# 'mkdir %s' % local_db_path, +# 'cd %%(installdir)s/bin && ./kraken2-build --standard --threads %%(parallel)s --db %s' % local_db_path, +# ] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + '16S_gg_installation.sh', '16S_rdp_installation.sh', '16S_silva_installation.sh', 'add_to_library.sh', + 'build_db', 'build_gg_taxonomy.pl', 'build_kraken2_db.sh', 'build_rdp_taxonomy.pl', 'build_silva_taxonomy.pl', + 'classify', 'clean_db.sh', 'cp_into_tempfile.pl', 'download_genomic_library.sh', 'download_taxonomy.sh', + 'dump_table', 'estimate_capacity', 'kraken2', 'kraken2-build', 'kraken2-inspect', 'kraken2lib.pm', + 'lookup_accession_numbers.pl', 'make_seqid2taxid_map.pl', 'mask_low_complexity.sh', 'rsync_from_ncbi.pl', + 'scan_fasta_file.pl']], + 'dirs': [], +} + +moduleclass = 'bio' From db2cfd72de79fe98b62ea75d5740d864607b2ac4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 14 Apr 2023 16:03:10 +0200 Subject: [PATCH 7169/9987] add a few sanity check commands --- .../easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb index 78064ba7f3e..9ed7324537c 100644 --- a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb @@ -59,4 +59,12 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'kraken2 --help', + 'kraken2-build --help', + 'kraken2-inspect --help', + 'build_db -h', + 'classify -h', +] + moduleclass = 'bio' From d129d03285cc090a2d55f061146aee6fe65c72b5 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 14 Apr 2023 16:30:18 +0200 Subject: [PATCH 7170/9987] PyTorch-1.12.1-foss-2022a-CUDA-11.7.0 fix flaky test optim test --- .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 3 + ....1_use-predefined-data-in-test-optim.patch | 132 ++++++++++++++++++ 2 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index 528fb671557..a62ed5dddbe 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -44,6 +44,7 @@ patches = [ 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -99,6 +100,8 @@ checksums = [ '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch # PyTorch-1.12.1_skip-test_round_robin.patch '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349', + # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch + 'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch new file mode 100644 index 00000000000..5dc393c17fd --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch @@ -0,0 +1,132 @@ +The test test_optim.test_nadam has high error rate, this let's the test use +predefined data instead to be more stable. See +https://github.com/pytorch/pytorch/issues/98414 + +Viktor Rehnberg +diff --git a/test/test_optim.py b/test/test_optim.py +index 6d587b4b352..c8ec9db87e1 100644 +--- a/test/test_optim.py ++++ b/test/test_optim.py +@@ -244,8 +244,14 @@ class TestOptim(TestCase): + return set(k for k in obj.__dict__ if not k.startswith('_')) + self.assertEqual(getPublicAttr(optimizer), getPublicAttr(deepcopy(optimizer))) + +- def _test_basic_cases(self, constructor, scheduler_constructors=None, +- ignore_multidevice=False, constructor_accepts_maximize=False): ++ def _test_basic_cases( ++ self, ++ constructor, ++ scheduler_constructors=None, ++ ignore_multidevice=False, ++ constructor_accepts_maximize=False, ++ use_predefined_data=False, ++ ): + if scheduler_constructors is None: + scheduler_constructors = [] + +@@ -254,26 +260,60 @@ class TestOptim(TestCase): + return lambda weight, bias: constructor(weight, bias, maximize) + return constructor + ++ def make_weight_tensor(): ++ if use_predefined_data: ++ return torch.Tensor([ ++ [ 0.6390, -0.5524, -0.1877, -1.1132, 0.3412], ++ [-0.6489, -0.6220, -1.2537, -0.0966, 0.5481], ++ [-0.6923, 0.5768, -0.9141, 1.9410, 1.0036], ++ [ 0.5842, 1.1618, -0.1871, 1.0344, 0.5668], ++ [ 0.2123, 2.3076, 0.7522, -0.7059, 1.3849], ++ [-0.1537, 0.5159, -1.2004, 0.2017, -0.0903], ++ [ 0.9434, -0.7030, 0.0618, -1.2951, 1.7721], ++ [ 0.5890, -1.0763, -1.2541, -0.8403, -0.4343], ++ [-0.2065, -0.6883, 0.8464, -0.7792, 0.6750], ++ [-1.6577, 0.4532, 0.0791, 0.2243, 0.1148], ++ ]) ++ else: ++ return torch.randn(10, 5) ++ ++ def make_bias_tensor(): ++ if use_predefined_data: ++ return torch.Tensor([ ++ -2.4031, -0.9295, -1.0762, 0.4600, -1.8620, -0.6234, 0.1999, -0.0612, 0.8319, -1.6673, ++ ]) ++ else: ++ return torch.randn(10) ++ ++ def make_input_tensor(): ++ if use_predefined_data: ++ return torch.Tensor([1.1119, -0.4309, -0.7759, -0.0659, 0.4746]) ++ else: ++ return torch.randn(5) ++ ++ def make_non_contiguous(tensor): ++ return torch.stack([tensor, tensor]).view(*tensor.size(), 2)[..., 0] ++ + for maximize in (True, False): + self._test_state_dict( +- torch.randn(10, 5), +- torch.randn(10), +- torch.randn(5), ++ make_weight_tensor(), ++ make_bias_tensor(), ++ make_input_tensor(), + make_two_arg_constructor(constructor, maximize), + ) + self._test_basic_cases_template( +- torch.randn(10, 5), +- torch.randn(10), +- torch.randn(5), ++ make_weight_tensor(), ++ make_bias_tensor(), ++ make_input_tensor(), + constructor, + scheduler_constructors, + constructor_accepts_maximize, + ) + # non-contiguous parameters + self._test_basic_cases_template( +- torch.randn(10, 5, 2)[..., 0], +- torch.randn(10, 2)[..., 0], +- torch.randn(5), ++ make_non_contiguous(make_weight_tensor()), ++ make_non_contiguous(make_bias_tensor()), ++ make_input_tensor(), + constructor, + scheduler_constructors, + constructor_accepts_maximize, +@@ -282,9 +322,9 @@ class TestOptim(TestCase): + if not torch.cuda.is_available(): + return + self._test_basic_cases_template( +- torch.randn(10, 5).cuda(), +- torch.randn(10).cuda(), +- torch.randn(5).cuda(), ++ make_weight_tensor().cuda(), ++ make_bias_tensor().cuda(), ++ make_input_tensor().cuda(), + constructor, + scheduler_constructors, + constructor_accepts_maximize, +@@ -293,9 +333,9 @@ class TestOptim(TestCase): + if not torch.cuda.device_count() > 1 or ignore_multidevice: + return + self._test_basic_cases_template( +- torch.randn(10, 5).cuda(0), +- torch.randn(10).cuda(1), +- torch.randn(5).cuda(0), ++ make_weight_tensor().cuda(0), ++ make_bias_tensor().cuda(1), ++ make_input_tensor().cuda(0), + constructor, + scheduler_constructors, + constructor_accepts_maximize, +@@ -668,7 +708,8 @@ class TestOptim(TestCase): + self._test_basic_cases( + lambda weight, bias: optimizer( + self._build_params_dict(weight, bias, lr=1e-2), +- lr=1e-3) ++ lr=1e-3), ++ use_predefined_data=True, + ) + self._test_basic_cases( + lambda weight, bias: optimizer([weight, bias], lr=1e-3, weight_decay=0.1, momentum_decay=6e-3) From 374c6c78ff7dc530070bb818947289c5ed56492a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 14 Apr 2023 18:18:13 +0200 Subject: [PATCH 7171/9987] adding easyconfigs: MATLAB-2023a.eb --- .../easyconfigs/m/MATLAB/MATLAB-2023a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2023a.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2023a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2023a.eb new file mode 100644 index 00000000000..052dc0ace6e --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2023a.eb @@ -0,0 +1,27 @@ +name = 'MATLAB' +version = '2023a' + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +download_instructions = 'Download R%(version)s_Linux.iso from mathworks.com' +sources = ['R%(version)s_Linux.iso'] +checksums = ['f18225237c2a5ff1294f19ed0c9945cfe691c3a3a62a6a8d324473d73ec92913'] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server_port = 'XXXXX' + +moduleclass = 'math' From 1404041f71da1741c3c657ddd4325f289870d746 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 14 Apr 2023 18:48:35 +0200 Subject: [PATCH 7172/9987] add tvem extension to R 4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 2efbf9482f0..67f669fec01 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3478,6 +3478,9 @@ exts_list = [ ('ppcor', '1.1', { 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], }), + ('tvem', '1.3.1', { + 'checksums': ['931085e210891744df64288ce174dface7a68bdb6b21a5883a9d83bb66a132c3'], + }), ] moduleclass = 'lang' From 92b4203a7392059ecbc156ec966e19171bda0047 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 14 Apr 2023 19:52:36 +0200 Subject: [PATCH 7173/9987] Update easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb --- easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb index 8eb989c720d..ba5ddd69573 100644 --- a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb +++ b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb @@ -20,7 +20,7 @@ checksums = [ ] builddependencies = [ - ('Autotools', '20220317', '', ('GCCcore', '11.3.0')), + ('Autotools', '20220317'), ] dependencies = [ From ddf44bbe195f35283d9147847609643957566a2d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 15 Apr 2023 12:59:43 +0100 Subject: [PATCH 7174/9987] fix flaky test optim test PyTorch 1.12.1 foss/2022a --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb index c31da630572..415463c968a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -41,6 +41,7 @@ patches = [ 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', + 'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -92,6 +93,8 @@ checksums = [ '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', + # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch + 'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054', ] osdependencies = [OS_PKG_IBVERBS_DEV] From 1ea0fea83eb69d1c838ce6b570c0dff055362266 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 15 Apr 2023 13:00:16 +0100 Subject: [PATCH 7175/9987] fix flaky test optim test PyTorch 1.12.1 foss/2021b --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb index 7c58b58e5fd..45b84bdea56 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb @@ -41,6 +41,7 @@ patches = [ 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -92,6 +93,8 @@ checksums = [ '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch # PyTorch-1.12.1_skip-test_round_robin.patch '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349', + # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch + 'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054', ] osdependencies = [OS_PKG_IBVERBS_DEV] From 5fe4aa37d3eb9b6fbd5802f0a8b567abd2f5974a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Apr 2023 15:49:57 +0200 Subject: [PATCH 7176/9987] adding easyconfigs: Casanovo-3.3.0-foss-2022a.eb --- .../c/Casanovo/Casanovo-3.3.0-foss-2022a.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a.eb b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a.eb new file mode 100644 index 00000000000..8318aafc346 --- /dev/null +++ b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'Casanovo' +version = '3.3.0' + +homepage = 'https://casanovo.readthedocs.io' +description = "De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('h5py', '3.7.0'), + ('lxml', '4.9.1'), + ('einops', '0.4.1'), + ('PyTorch', '1.12.0'), + ('PyTorch-Lightning', '1.8.4'), + ('scikit-learn', '1.1.2'), + ('numba', '0.56.4'), + ('tensorboard', '2.10.0'), +] + +exts_list = [ + ('pyteomics', '4.5.6', { + 'checksums': ['8c6e79068f18d853218967a312c22861422df69fdcf62499a258526f687b126f'], + }), + ('depthcharge-ms', '0.1.0', { + 'checksums': ['237f8e70fd237fdc945882e981170321ac7da2638ba24b52f72dad9ff2262096'], + 'modulename': 'depthcharge', + }), + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + ('PyGithub', '1.58.1', { + 'checksums': ['7d528b4ad92bc13122129fafd444ce3d04c47d2d801f6446b6e6ee2d410235b3'], + 'modulename': 'github', + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('fastobo', '0.12.2', { + 'checksums': ['2f2779f70ac54874329dddc74cabd86fea88abe56c544c2238076c1d27fe045e'], + }), + ('lark', '1.1.5', { + 'checksums': ['4b534eae1f9af5b4ea000bea95776350befe1981658eea3820a01c37e504bb4d'], + }), + ('spectrum-utils', '0.4.1', { + 'sources': ['spectrum_utils-%(version)s.tar.gz'], + 'checksums': ['c4f1c80de8144fb8d6fc276968ef4d5e896dad03bb8a9316f69c73ee82affd85'], + }), + ('casanovo', version, { + 'checksums': ['d9358c64a549d00f0568ebef65d5500ad63041e9ea2ebd348a7e650c8177ff81'], + }), +] + +sanity_check_paths = { + 'files': ['bin/casanovo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["casanovo --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 11630a829321c17b4d84d9c04648a15b51c7e6be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 15 Apr 2023 15:50:21 +0200 Subject: [PATCH 7177/9987] adding easyconfigs: Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb --- .../Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..13264c0021f --- /dev/null +++ b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'Casanovo' +version = '3.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://casanovo.readthedocs.io' +description = "De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('h5py', '3.7.0'), + ('lxml', '4.9.1'), + ('einops', '0.4.1'), + ('PyTorch', '1.12.0', versionsuffix), + ('PyTorch-Lightning', '1.8.4', versionsuffix), + ('scikit-learn', '1.1.2'), + ('numba', '0.56.4', versionsuffix), + ('tensorboard', '2.10.0'), +] + +exts_list = [ + ('pyteomics', '4.5.6', { + 'checksums': ['8c6e79068f18d853218967a312c22861422df69fdcf62499a258526f687b126f'], + }), + ('depthcharge-ms', '0.1.0', { + 'checksums': ['237f8e70fd237fdc945882e981170321ac7da2638ba24b52f72dad9ff2262096'], + 'modulename': 'depthcharge', + }), + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + ('PyGithub', '1.58.1', { + 'checksums': ['7d528b4ad92bc13122129fafd444ce3d04c47d2d801f6446b6e6ee2d410235b3'], + 'modulename': 'github', + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('fastobo', '0.12.2', { + 'checksums': ['2f2779f70ac54874329dddc74cabd86fea88abe56c544c2238076c1d27fe045e'], + }), + ('lark', '1.1.5', { + 'checksums': ['4b534eae1f9af5b4ea000bea95776350befe1981658eea3820a01c37e504bb4d'], + }), + ('spectrum-utils', '0.4.1', { + 'sources': ['spectrum_utils-%(version)s.tar.gz'], + 'checksums': ['c4f1c80de8144fb8d6fc276968ef4d5e896dad03bb8a9316f69c73ee82affd85'], + }), + ('casanovo', version, { + 'checksums': ['d9358c64a549d00f0568ebef65d5500ad63041e9ea2ebd348a7e650c8177ff81'], + }), +] + +sanity_check_paths = { + 'files': ['bin/casanovo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["casanovo --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 7164894a61c46ae3b159e7f9873c314625b7c9b1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 15 Apr 2023 18:05:11 +0100 Subject: [PATCH 7178/9987] revert use predefined data in test option for PyTorch 1.12.1 --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb | 3 --- .../p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 3 --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 3 --- 3 files changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb index 45b84bdea56..7c58b58e5fd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb @@ -41,7 +41,6 @@ patches = [ 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', - 'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -93,8 +92,6 @@ checksums = [ '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch # PyTorch-1.12.1_skip-test_round_robin.patch '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349', - # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch - 'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index a62ed5dddbe..528fb671557 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -44,7 +44,6 @@ patches = [ 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', - 'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -100,8 +99,6 @@ checksums = [ '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch # PyTorch-1.12.1_skip-test_round_robin.patch '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349', - # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch - 'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb index 415463c968a..c31da630572 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -41,7 +41,6 @@ patches = [ 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', - 'PyTorch-1.12.1_use-predefined-data-in-test-optim.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -93,8 +92,6 @@ checksums = [ '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', - # PyTorch-1.12.1_use-predefined-data-in-test-optim.patch - 'a55f5465f5324cddae44416d67ef7506acb3513df7c4efb47db2f19eaa169054', ] osdependencies = [OS_PKG_IBVERBS_DEV] From 85ec3bf10f46489ced77fbf73aa07d6c32b8eaae Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 16 Apr 2023 17:15:21 +0200 Subject: [PATCH 7179/9987] update recent R easyconfigs with additional R packages --- .../easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 53 ++++++++++++++++--- .../easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 42 +++++++++++++++ 2 files changed, 88 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 67f669fec01..34241cc8cdc 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -1798,8 +1798,8 @@ exts_list = [ ('HWxtest', '1.1.9', { 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], 'checksums': [ - 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz - '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch + {'HWxtest_1.1.9.tar.gz': 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6'}, + {'HWxtest-1.1.9_add-fcommon.patch': '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451'}, ], }), ('diveRsity', '1.9.90', { @@ -2322,9 +2322,9 @@ exts_list = [ # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ - '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz - # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch - '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, + {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch': + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'}, ], }), ('oddsratio', '2.0.1', { @@ -3478,8 +3478,47 @@ exts_list = [ ('ppcor', '1.1', { 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], }), - ('tvem', '1.3.1', { - 'checksums': ['931085e210891744df64288ce174dface7a68bdb6b21a5883a9d83bb66a132c3'], + ('berryFunctions', '1.22.0', { + 'checksums': ['8d8578d746e8e4f7a1deb0b1d49ff8603c5e51504d5fe549bcba54f20fe9d498'], + }), + ('cld2', '1.2.4', { + 'checksums': ['79e04de836812a980406a540c0f022926ba71c2bf5294ad5eaa437a9c33e615b'], + }), + ('crfsuite', '0.4.1', { + 'checksums': ['be4f8e7773caa2e3ceac7e35d47ef323f6b121d2b2da1e3b90b4e3b4fc7da46e'], + }), + ('doc2vec', '0.2.0', { + 'checksums': ['db3853685072554402434ea699d703e01ac7818044cf47a2ee7d0e1040858908'], + }), + ('fastDummies', '1.6.3', { + 'checksums': ['bd3934fe19d7dff2723438bbb7b89334118143f8ce151d98477ae964ee5d81df'], + }), + ('quanteda', '3.2.3', { + 'checksums': ['f34b0e89ad7795eed0d624fb57a9fb924175a03df0c23fc1f71eefe6a14d93ae'], + }), + ('rlist', '0.4.6.2', { + 'checksums': ['ebde658d897c8a27a90ebb892b9e2bad15e2ad75557a7352fb08cbb5604e0997'], + }), + ('ISOweek', '0.6-2', { + 'checksums': ['b58a37b61ee772ea2704d510e9fce69dea4dd641b45124d566242825df4530b8'], + }), + ('sentometrics', '1.0.0', { + 'checksums': ['b5c238bb72f36331cb1ed63b581a9a2a73cefc96f80bf770b0e064a89fe31b1b'], + }), + ('tau', '0.0-24', { + 'checksums': ['f08d9fc92ed11ec01f7da12ccf98862e36ef8bb69d5e42584a08b46cea6917e1'], + }), + ('textcat', '1.0-8', { + 'checksums': ['cb650147576bae9c78381524831c9fcc85c76177274672098aac1860aa39749e'], + }), + ('textplot', '0.2.2', { + 'checksums': ['6e99a204b4be2ccd317978eda900b923e0e0a0f34217405777a0eb5fcc80e2a9'], + }), + ('udpipe', '0.8.11', { + 'checksums': ['522900de24d1f0f4f15e6b26df5521ac6efaf63c5fcfc35171a78275b3633233'], + }), + ('word2vec', '0.3.4', { + 'checksums': ['53db1d8c8d6af8ace8636adec1e254b0b61fbdba77ba7a295afc7da3eb4e4362'], }), ] diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index f89a16e5c6d..e8a09bc8b64 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3549,6 +3549,48 @@ exts_list = [ ('ppcor', '1.1', { 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], }), + ('berryFunctions', '1.22.0', { + 'checksums': ['8d8578d746e8e4f7a1deb0b1d49ff8603c5e51504d5fe549bcba54f20fe9d498'], + }), + ('cld2', '1.2.4', { + 'checksums': ['79e04de836812a980406a540c0f022926ba71c2bf5294ad5eaa437a9c33e615b'], + }), + ('crfsuite', '0.4.1', { + 'checksums': ['be4f8e7773caa2e3ceac7e35d47ef323f6b121d2b2da1e3b90b4e3b4fc7da46e'], + }), + ('doc2vec', '0.2.0', { + 'checksums': ['db3853685072554402434ea699d703e01ac7818044cf47a2ee7d0e1040858908'], + }), + ('fastDummies', '1.6.3', { + 'checksums': ['bd3934fe19d7dff2723438bbb7b89334118143f8ce151d98477ae964ee5d81df'], + }), + ('quanteda', '3.3.0', { + 'checksums': ['03256faf63455d16d643349a34b068d0bf69506a0e952b99ab2391e6423663a5'], + }), + ('rlist', '0.4.6.2', { + 'checksums': ['ebde658d897c8a27a90ebb892b9e2bad15e2ad75557a7352fb08cbb5604e0997'], + }), + ('ISOweek', '0.6-2', { + 'checksums': ['b58a37b61ee772ea2704d510e9fce69dea4dd641b45124d566242825df4530b8'], + }), + ('sentometrics', '1.0.0', { + 'checksums': ['b5c238bb72f36331cb1ed63b581a9a2a73cefc96f80bf770b0e064a89fe31b1b'], + }), + ('tau', '0.0-24', { + 'checksums': ['f08d9fc92ed11ec01f7da12ccf98862e36ef8bb69d5e42584a08b46cea6917e1'], + }), + ('textcat', '1.0-8', { + 'checksums': ['cb650147576bae9c78381524831c9fcc85c76177274672098aac1860aa39749e'], + }), + ('textplot', '0.2.2', { + 'checksums': ['6e99a204b4be2ccd317978eda900b923e0e0a0f34217405777a0eb5fcc80e2a9'], + }), + ('udpipe', '0.8.11', { + 'checksums': ['522900de24d1f0f4f15e6b26df5521ac6efaf63c5fcfc35171a78275b3633233'], + }), + ('word2vec', '0.3.4', { + 'checksums': ['53db1d8c8d6af8ace8636adec1e254b0b61fbdba77ba7a295afc7da3eb4e4362'], + }), ] moduleclass = 'lang' From 2a918696a3f5eb48a02e923699df0dbe5bdd6242 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 16 Apr 2023 17:26:34 +0200 Subject: [PATCH 7180/9987] re-add tvem --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 34241cc8cdc..c0a40a9552d 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3478,6 +3478,9 @@ exts_list = [ ('ppcor', '1.1', { 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], }), + ('tvem', '1.3.1', { + 'checksums': ['931085e210891744df64288ce174dface7a68bdb6b21a5883a9d83bb66a132c3'], + }), ('berryFunctions', '1.22.0', { 'checksums': ['8d8578d746e8e4f7a1deb0b1d49ff8603c5e51504d5fe549bcba54f20fe9d498'], }), From ddfc056fb45612e645daab725be78b92b75073e2 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 16 Apr 2023 17:51:32 +0200 Subject: [PATCH 7181/9987] adding easyconfigs: RPostgreSQL-0.7-5-foss-2022a.eb --- .../RPostgreSQL-0.7-5-foss-2022a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/r/RPostgreSQL/RPostgreSQL-0.7-5-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/RPostgreSQL/RPostgreSQL-0.7-5-foss-2022a.eb b/easybuild/easyconfigs/r/RPostgreSQL/RPostgreSQL-0.7-5-foss-2022a.eb new file mode 100644 index 00000000000..88f4b40198b --- /dev/null +++ b/easybuild/easyconfigs/r/RPostgreSQL/RPostgreSQL-0.7-5-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'RPostgreSQL' +version = '0.7-5' + +homepage = 'https://cran.r-project.org/package=tesseract' +description = """ +Database interface and 'PostgreSQL' driver for 'R'. This package provides a +Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL' +database systems.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('R', '4.2.1'), + ('PostgreSQL', '14.4'), +] + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + (name, version, { + 'checksums': ['6b5401ee55bd948ae7bc84520d789ceb422533a7d5e5bd6e10e3b54447f29fa1'], + }), +] + +sanity_check_paths = { + 'files': ['RPostgreSQL/libs/RPostgreSQL.%s' % SHLIB_EXT, 'RPostgreSQL/R/RPostgreSQL'], + 'dirs': [], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'data' From 9b5e8a17067589c8d224cc286beba3a390bc3280 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Apr 2023 09:27:05 +0200 Subject: [PATCH 7182/9987] adding easyconfigs: AlphaFold-2.3.1-foss-2022a.eb, OpenMM-8.0.0-foss-2022a.eb --- .../a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb | 159 ++++++++++++++++++ .../o/OpenMM/OpenMM-8.0.0-foss-2022a.eb | 60 +++++++ 2 files changed, 219 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb new file mode 100644 index 00000000000..77990ac93a2 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb @@ -0,0 +1,159 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.3.1' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '5.1.1'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('TensorFlow', '2.11.0'), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.5'), + ('jax', '0.3.25'), # also provides absl-py + ('OpenMM', '8.0.0'), +] + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.3.0_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.3.1_use_openmm_7.7.0.patch', + ], + 'checksums': [ + '1161b2609fa896b16399b900ec2b813e5a0b363fe4e2b26bd826953ba234736a', # v2.3.1.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '5cff3fc7104e020ef546d23cb4fb1b8d6517562783f055cc55fc65fe2b0248d0', # AlphaFold-2.3.0_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + # AlphaFold-2.3.1_use_openmm_7.7.0.patch + 'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec', + + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.8.1', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.6', { + 'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('dm-tree', '0.1.8', { + 'modulename': 'tree', + 'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('docker', '6.0.1', { + 'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'], + }), + ('immutabledict', '2.2.3', { + 'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold*.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m openmm.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextravars = { + 'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-%(version)s', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb new file mode 100644 index 00000000000..47d3bdbfaf5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.0.0' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SWIG', '4.0.2'), +] + +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 6cf20bad67d360d2c60fea43a7e1b3a06b0e8116 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Apr 2023 09:49:12 +0200 Subject: [PATCH 7183/9987] comment out ALPHAFOLD_DATA_DIR in AlphaFold-2.3.1-foss-2022a.eb --- easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb index 77990ac93a2..565504238bb 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb @@ -153,7 +153,7 @@ sanity_check_commands = [ sanity_pip_check = True modextravars = { - 'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-%(version)s', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt } moduleclass = 'bio' From 8d95a7d96fd1ed37c1752c5830ee327c1a9ed95d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Apr 2023 09:59:09 +0200 Subject: [PATCH 7184/9987] upgrade dependency on Libint to v2.7.2 and PLUMED to v2.8.1 of CP2K v9.1 and v2022.1 --- .../c/CP2K/CP2K-2022.1-foss-2022a.eb | 4 +- .../easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb | 4 +- .../Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb | 52 ---------------- .../p/PLUMED/PLUMED-2.8.0-foss-2022a.eb | 60 ------------------- 4 files changed, 4 insertions(+), 116 deletions(-) delete mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb delete mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb index 3521d55a090..a979cbf28d2 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb @@ -19,11 +19,11 @@ checksums = ['2c34f1a7972973c62d471cd35856f444f11ab22f2ff930f6ead20f3454fd228b'] # https://github.com/cp2k/cp2k/releases/download/v2022.1/cp2k-2022.1.tar.bz2 dependencies = [ - ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('Libint', '2.7.2', '-lmax-6-cp2k'), ('libxc', '5.2.3'), ('libxsmm', '1.17'), ('FFTW', '3.3.10'), - ('PLUMED', '2.8.0'), + ('PLUMED', '2.8.1'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb index b2e72836ed6..67b7353f347 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb @@ -18,11 +18,11 @@ sources = [SOURCELOWER_TAR_BZ2] checksums = ['fedb4c684a98ad857cd49b69a3ae51a73f85a9c36e9cb63e3b02320c74454ce6'] dependencies = [ - ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('Libint', '2.7.2', '-lmax-6-cp2k'), ('libxc', '5.2.3'), ('libxsmm', '1.17'), ('FFTW', '3.3.10'), - ('PLUMED', '2.8.0'), + ('PLUMED', '2.8.1'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb deleted file mode 100644 index a992dd7921d..00000000000 --- a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-GCC-11.3.0-lmax-6-cp2k.eb +++ /dev/null @@ -1,52 +0,0 @@ -## -# Author: Robert Mijakovic -## -name = 'Libint' -version = '2.6.0' -local_lmax = 6 -# custom configuration, to be used as dependency for CP2K -versionsuffix = '-lmax-%s-cp2k' % local_lmax - -homepage = 'https://github.com/evaleev/libint' -description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body - matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" - -toolchain = {'name': 'GCC', 'version': '11.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} - -source_urls = ['https://github.com/evaleev/libint/archive'] -sources = ['v%(version)s.tar.gz'] -patches = [ - 'Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch', - 'Libint-2.6.0_remove-test-eri.patch', -] -checksums = [ - '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz - # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch - 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', - # Libint-2.6.0_remove-test-eri.patch - 'e47868901250078adeb35b80ab866ba8063ad9756881d1b557cb925334df653b', -] - -builddependencies = [ - ('Autotools', '20220317'), - ('GMP', '6.2.1'), - ('Boost', '1.79.0'), - ('Eigen', '3.4.0'), - ('Python', '3.10.4'), -] - -# configure options as required by CP2K, -# see Jenkinsfile in https://github.com/cp2k/libint-cp2k -local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) -local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) - -libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax -libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am -libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am -libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am -libint_compiler_configopts += '--enable-generic-code --disable-unrolling' - -with_fortran = True - -moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb deleted file mode 100644 index 8775e1beada..00000000000 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2022a.eb +++ /dev/null @@ -1,60 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PLUMED' -version = '2.8.0' - -homepage = 'https://www.plumed.org' -description = """PLUMED is an open source library for free energy calculations in molecular systems which - works together with some of the most popular molecular dynamics engines. Free energy calculations can be - performed as a function of many order parameters with a particular focus on biological problems, using - state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. - The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. -""" - -toolchain = {'name': 'foss', 'version': '2022a'} -toolchainopts = {'usempi': 'True'} - -source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] -sources = [SOURCE_TGZ] -checksums = ['24b243c531fa83752be5e54f5f0b677164855da539bc2b2c5b00dcc9f192aa82'] - -builddependencies = [ - ('xxd', '8.2.4220'), -] - -dependencies = [ - ('zlib', '1.2.12'), - ('GSL', '2.7'), - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('Boost', '1.79.0'), -] - -preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' -configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' -configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' -prebuildopts = 'source sourceme.sh && ' - -# make sure that ld.gold linker is used -# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" -# (problem with intel build but maintain consistency between easyconfigs) -buildopts = 'LD_RO="ld.gold -r -o"' - -# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed -preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' - -sanity_check_paths = { - 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], - 'dirs': [], -} - -sanity_check_commands = ["python -c 'import plumed'"] - -modextrapaths = { - 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, - 'PLUMED_ROOT': 'lib/plumed', - 'PYTHONPATH': 'lib/plumed/python', -} - -moduleclass = 'chem' From 92f4183e5e24c377ef53100b0cbc461bfcc7b4eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 17 Apr 2023 11:09:26 +0200 Subject: [PATCH 7185/9987] adding easyconfigs: GL2PS-1.4.2-GCCcore-11.3.0.eb, GL2PS-1.4.2-GCCcore-12.2.0.eb, freeglut-3.4.0-GCCcore-12.2.0.eb --- .../freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb | 39 +++++++++++++++++++ .../g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb | 34 ++++++++++++++++ .../g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb | 34 ++++++++++++++++ 3 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/f/freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0f9d2c52215 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.4.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3c0bcb915d9b180a97edaebd011b7a1de54583a838644dcd42bb0ea0c6f3eaec'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.%s" ' % SHLIB_EXT +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..46eedfaa2df --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.2' + +homepage = 'https://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] +checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.38'), +] + +dependencies = [ + ('X11', '20220504'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('freeglut', '3.2.2'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..6bd5ffab398 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.2' + +homepage = 'https://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] +checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), + ('freeglut', '3.4.0'), + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From bdef0d696b58bcdefe0dd4669f79f3db75d9f90f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 17 Apr 2023 15:23:44 +0200 Subject: [PATCH 7186/9987] adding easyconfigs: BoltzTraP2-22.12.1-foss-2022a.eb, pyFFTW-0.13.1-foss-2022a.eb and patches: BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch --- .../BoltzTraP2-22.12.1-foss-2022a.eb | 44 ++++++++++++++++ ...ltzTraP2-22.12.1_use_EB_spglib+eigen.patch | 51 +++++++++++++++++++ .../p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb | 24 +++++++++ 3 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch create mode 100755 easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb new file mode 100644 index 00000000000..8f1717a32bb --- /dev/null +++ b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'BoltzTraP2' +version = '22.12.1' + +homepage = 'https://www.boltztrap.org' +description = """BoltzTraP2 provides a numerically stable and efficient +method for obtaining analytic representations of electronic bands based +on density-functional-theory results for relatively sparse grids. It +achieves this goal by using smoothed Fourier interpolation.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('pyFFTW', '0.13.1'), + ('spglib', '2.0.2'), + ('Eigen', '3.4.0'), + ('matplotlib', '3.5.2'), + ('ASE', '3.22.1'), + ('netcdf4-python', '1.6.1'), + ('VTK', '9.2.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'BoltzTraP2', + 'patches': ['BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch'], + 'checksums': [ + {'BoltzTraP2-22.12.1.tar.gz': '8338d600c509705e40c834b5431ee8a556d87b06aa1a09853031960a1ff65b3e'}, + {'BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch': + '63791c73ffcb36c0615111377ac5666abfce48872800d3bcc8c93113e37c9030'}, + ], + }), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch new file mode 100644 index 00000000000..ccf7129bb7b --- /dev/null +++ b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch @@ -0,0 +1,51 @@ +Use spglib and Eigen from EB install + +Åke Sandgren, 2023-04-17 +diff -ru BoltzTraP2-22.12.1.orig/setup.py BoltzTraP2-22.12.1/setup.py +--- BoltzTraP2-22.12.1.orig/setup.py 2022-12-19 19:38:59.000000000 +0100 ++++ BoltzTraP2-22.12.1/setup.py 2023-04-17 12:32:46.654682662 +0200 +@@ -187,7 +187,8 @@ + + def run(self): + """Run build_spglib and then delegate on the normal build_ext.""" +- self.run_command("build_spglib") ++ # Use spglib from EB installation ++ # self.run_command("build_spglib") + DefaultBuildExtCommand.run(self) + + +@@ -213,12 +214,6 @@ + else: + extension = "cpp" + +-eigen_dir = os.path.abspath( +- os.path.join( +- os.path.dirname(__file__), "external", "eigen-eigen-3215c06819b9" +- ) +-) +- + extensions = [ + Extension( + "BoltzTraP2.sphere.frontend", +@@ -228,10 +223,10 @@ + ], + language="c++", + include_dirs=INCLUDE_DIRS +- + [np.get_include(), BuildSPGlibCommand.header_dir, eigen_dir], ++ + [np.get_include()], + library_dirs=LIBRARY_DIRS, + runtime_library_dirs=LIBRARY_DIRS, +- extra_objects=[BuildSPGlibCommand.static_library], ++ libraries = ['symspg'], + ) + ] + +@@ -282,8 +277,6 @@ + ext_modules=extensions, + cmdclass={ + "build_ext": BuildExtCommand, +- "build_spglib": BuildSPGlibCommand, +- "clean_spglib": CleanSPGlibCommand, + }, + install_requires=[ + "spglib", diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb new file mode 100755 index 00000000000..fa32aafe1c2 --- /dev/null +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pyFFTW' +version = '0.13.1' + +homepage = 'https://github.com/pyFFTW/pyFFTW' +description = """A pythonic wrapper around FFTW, the FFT library, presenting a unified interface + for all the supported transforms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['09155e90a0c6d0c1f2d1f3668180a7de95fb9f83fef5137a112fb05978e87320'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From bdc3b270faec9d34aa239feb792014061d370197 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 17 Apr 2023 15:27:01 +0200 Subject: [PATCH 7187/9987] Include Viktors fixes --- ...ch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb | 45 +++++++++++++------ 1 file changed, 31 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb index 62ab4bc5ff8..de2c1894efa 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -10,48 +10,65 @@ description = """PyTorch with compatible versions of official Torch extensions." toolchain = {'name': 'foss', 'version': '2022a'} builddependencies = [ + ('CMake', '3.23.1'), ('RE2', '2022-06-01'), # for torchtext ] dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), ('PyTorch', version, versionsuffix), ('Pillow-SIMD', '9.2.0'), # for torchvision ('SentencePiece', '0.1.97'), # for torchtext ('tqdm', '4.64.0'), # for torchtext ('double-conversion', '3.2.0'), # for torchtext + ('utf8proc', '2.7.0'), # for torchtext + ('tensorboard', '2.10.0'), # for torch-tb-profiler ] use_pip = True exts_list = [ - ('torchvision', '0.14.1', { - 'source_urls': ['https://github.com/pytorch/vision/archive'], + ('portalocker', '2.7.0', { + 'checksums': ['032e81d534a88ec1736d03f780ba073f047a06c478b06e2937486f334e955c51'], + }), + ('torchdata', '0.4.1', { + 'preinstallopts': "USE_SYSTEM_LIBS=1 ", + 'source_urls': ['https://github.com/pytorch/data/archive'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['ced67e1cf1f97e168cdf271851a4d0b6d382ab7936e7bcbb39aaa87239c324b6'], + 'checksums': ['71c0aa3aca3b04a986a2cd4cc2e0be114984ca836dc4def2c700bf1bd1ff087e'], }), - ('torchtext', '0.14.1', { - # Disable bundled libraries to use those from EB: RE2, SentencePiece - 'preinstallopts': "sed -i '/third_party/d;/BuildExtension/d' setup.py &&", + ('torchtext', '0.13.1', { 'source_urls': ['https://github.com/pytorch/text/archive'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'], + 'patches': [ + 'torchtext-0.13.1_use-system-libs.patch', + 'torchtext-0.13.1_deps-fix.patch', + ], + 'checksums': [ + {'torchtext-0.13.1.tar.gz': '1f7de1fd8c6303ea13ef2aed48a6df67df5f92d1c4a6918253be7decd93753be'}, + {'torchtext-0.13.1_use-system-libs.patch': + 'fa899453bd826141ea98f2736a67d255b3a8941c6ca2a236fc352850364efdcc'}, + {'torchtext-0.13.1_deps-fix.patch': '6e7a9bb854d68eecc70567b92cfbc26f6547aea3f65d4b5cf79cbb19ea43a192'}, + ], }), - ('torchaudio', '0.13.1', { - 'source_urls': ['https://github.com/pytorch/audio/archive'], + ('torchvision', '0.13.1', { + 'source_urls': ['https://github.com/pytorch/vision/archive'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['3a5c108a9ea31d0e6533a2cd6cbaf133efaefe4bdcb4b689183a33b991c95d12'], + 'checksums': ['c32fab734e62c7744dadeb82f7510ff58cc3bca1189d17b16aa99b08afc42249'], }), ('pytorch-ignite', '0.4.11', { + 'modulename': 'ignite', 'source_urls': ['https://github.com/pytorch/ignite/archive'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['33e7485cea3cac08d7a49a3a01d3013e1156128867602bff0a8e32b2c5ebd4e9'], }), - ('torchdata', '0.5.1', { - 'source_urls': ['https://github.com/pytorch/data/archive'], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['69d80bd33ce8f08e7cfeeb71cefddfc29cede25a85881e33dbae47576b96ed29'], + ('torch-tb-profiler', '0.4.1', { + 'modulename': 'torch.profiler', + 'sources': ['torch_tb_profiler-%(version)s.tar.gz'], + 'checksums': ['f2c7fb27d420be443ffde50ada655c19f76a245d21e7772de753196fd0967685'], }), + # torchaudio-0.12.1 needs more work before it can be added ] sanity_pip_check = True From dfcc41ce59d6c5a87b2adcaf4c7348440b00bc6b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 17 Apr 2023 15:44:53 +0200 Subject: [PATCH 7188/9987] Fix patch descriptions --- ...ch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb | 6 +- .../torchtext-0.13.1_cxx_17.patch | 19 ++++++ .../torchtext-0.13.1_use-system-libs.patch | 67 +++++++++++++++++++ 3 files changed, 89 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_cxx_17.patch create mode 100644 easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_use-system-libs.patch diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb index de2c1894efa..17069b4ee78 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -43,13 +43,13 @@ exts_list = [ 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'patches': [ 'torchtext-0.13.1_use-system-libs.patch', - 'torchtext-0.13.1_deps-fix.patch', + 'torchtext-0.13.1_cxx_17.patch', ], 'checksums': [ {'torchtext-0.13.1.tar.gz': '1f7de1fd8c6303ea13ef2aed48a6df67df5f92d1c4a6918253be7decd93753be'}, {'torchtext-0.13.1_use-system-libs.patch': - 'fa899453bd826141ea98f2736a67d255b3a8941c6ca2a236fc352850364efdcc'}, - {'torchtext-0.13.1_deps-fix.patch': '6e7a9bb854d68eecc70567b92cfbc26f6547aea3f65d4b5cf79cbb19ea43a192'}, + '3e2f170a2870ac274f452b53862f65e5e94f6da1c3af488aeb3001e0500cb0e5'}, + {'torchtext-0.13.1_cxx_17.patch': 'fd242c139baa27352d1065cece4658a3ede76f46ffec08ac04a554301e547f22'}, ], }), ('torchvision', '0.13.1', { diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_cxx_17.patch b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_cxx_17.patch new file mode 100644 index 00000000000..c980e7c2ebf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_cxx_17.patch @@ -0,0 +1,19 @@ +The error "string_view has not been declared in std" appears when not using C++17 +Split from "deps_fix" patch from torchtext +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 1ead15d46..879118c60 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -24,10 +24,10 @@ string(FIND "${CMAKE_CXX_FLAGS}" "-std=c++" env_cxx_standard) + if(env_cxx_standard GREATER -1) + message( + WARNING "C++ standard version definition detected in environment variable." +- "PyTorch requires -std=c++14. Please remove -std=c++ settings in your environment.") ++ "PyTorch requires -std=c++17. Please remove -std=c++ settings in your environment.") + endif() + +-set(CMAKE_CXX_STANDARD 14) ++set(CMAKE_CXX_STANDARD 17) + set(CMAKE_C_STANDARD 11) + + set(CMAKE_EXPORT_COMPILE_COMMANDS ON) diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_use-system-libs.patch b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_use-system-libs.patch new file mode 100644 index 00000000000..d0902da8c9e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_use-system-libs.patch @@ -0,0 +1,67 @@ +Use external deps for third party libraries +Split from "deps_fix" patch from torchtext +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 1ead15d46..21f85e555 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -63,5 +63,9 @@ endif() + # TORCH_CXX_FLAGS contains the same -D_GLIBCXX_USE_CXX11_ABI value as PyTorch + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall ${TORCH_CXX_FLAGS}") + +-add_subdirectory(third_party) ++find_package(double-conversion) ++find_package(re2) ++find_library(SENTENCEPIECE_LIBRARY sentencepiece PATHS $ENV{EBROOTSENTENCEPIECE}/lib64) ++find_library(SENTENCEPIECE_TRAIN_LIBRARY sentencepiece_train PATHS $ENV{EBROOTSENTENCEPIECE}/lib64) ++find_library(UTF8PROC_LIBRARY utf8proc PATHS $ENV{UTF8PROC}/lib64) + add_subdirectory(torchtext/csrc) +diff --git a/packaging/build_wheel.sh b/packaging/build_wheel.sh +index 9882cb1b2..43e2a05d8 100755 +--- a/packaging/build_wheel.sh ++++ b/packaging/build_wheel.sh +@@ -10,7 +10,6 @@ setup_env + setup_wheel_python + pip_install numpy future cmake>=3.18.0 ninja + setup_pip_pytorch_version +-git submodule update --init --recursive + python setup.py clean + if [[ "$OSTYPE" == "msys" ]]; then + "$script_dir/vc_env_helper.bat" python setup.py bdist_wheel +diff --git a/setup.py b/setup.py +index 080415f7e..bd84405be 100644 +--- a/setup.py ++++ b/setup.py +@@ -68,7 +68,6 @@ class clean(distutils.command.clean.clean): + # Remove build directory + build_dirs = [ + ROOT_DIR / "build", +- ROOT_DIR / "third_party" / "build", + ] + for path in build_dirs: + if path.exists(): +diff --git a/torchtext/csrc/CMakeLists.txt b/torchtext/csrc/CMakeLists.txt +index 037f814dc..658b90342 100644 +--- a/torchtext/csrc/CMakeLists.txt ++++ b/torchtext/csrc/CMakeLists.txt +@@ -24,10 +24,6 @@ set( + set( + LIBTORCHTEXT_INCLUDE_DIRS + ${PROJECT_SOURCE_DIR} +- ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src +- $ +- $ +- $ + ${TORCH_INSTALL_PREFIX}/include + ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include + ) +@@ -123,10 +119,6 @@ if (BUILD_TORCHTEXT_PYTHON_EXTENSION) + set( + EXTENSION_INCLUDE_DIRS + ${PROJECT_SOURCE_DIR} +- ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src +- $ +- $ +- $ + ${TORCH_INSTALL_PREFIX}/include + ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include + ) From f7469fa2e8743cdbaebf99be38bd5d30f2ba4f02 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 17 Apr 2023 15:49:16 +0200 Subject: [PATCH 7189/9987] adding easyconfigs: ROOT-6.26.10-foss-2022b.eb --- .../r/ROOT/ROOT-6.26.10-foss-2022b.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb new file mode 100644 index 00000000000..4acf0146bc4 --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb @@ -0,0 +1,55 @@ +name = 'ROOT' +version = '6.26.10' + +homepage = 'https://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['https://root.cern.ch/download/'] +sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +checksums = ['8e56bec397104017aa54f9eb554de7a1a134474fe0b3bb0f43a70fc4fabd625f'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('GSL', '2.7'), + ('libxml2', '2.10.3'), + ('PCRE', '8.45'), + ('CFITSIO', '4.2.0'), + ('freetype', '2.12.1'), + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('zlib', '1.2.12'), + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), + ('GL2PS', '1.4.2'), + ('FFTW', '3.3.10'), + ('SQLite', '3.39.4'), + ('XZ', '5.2.7'), + ('libpng', '1.6.38'), +] + +# NOTE: Ensure that each configopts string begins with a blank +# disable some components +configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" + +# make sure some components are enabled +configopts += " -Dpcre=ON -Dzlib=ON -Dpyroot=ON" +configopts += " -Dunuran=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " + +# Add component-specific settings based on dependencies +configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' + +# Set C++ standard to C++17 for better stability +configopts += ' -DCMAKE_CXX_STANDARD=17' + +configopts += " -Dgallium-drivers=swrast" + +moduleclass = 'data' From 145138485cedb77a8cbee01bdc05274a27790174 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 17 Apr 2023 16:00:04 +0200 Subject: [PATCH 7190/9987] Drop CMake since it is not really needed and fix extra space. --- .../b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb index 8f1717a32bb..663a6d225c6 100644 --- a/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb @@ -11,10 +11,6 @@ achieves this goal by using smoothed Fourier interpolation.""" toolchain = {'name': 'foss', 'version': '2022a'} -builddependencies = [ - ('CMake', '3.23.1'), -] - dependencies = [ ('Python', '3.10.4'), ('pyFFTW', '0.13.1'), @@ -41,4 +37,4 @@ exts_list = [ }), ] -moduleclass = 'phys' +moduleclass = 'phys' From 58d65f2cc237434c3f789c1bfa6e400ba5b27cf2 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 17 Apr 2023 15:15:19 +0100 Subject: [PATCH 7191/9987] exclude test_optim --- .../p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 3 +++ easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 3 +++ .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb | 5 ++++- easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb | 3 +++ .../p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 3 +++ easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 3 +++ 6 files changed, 19 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 9778d40af76..dba21cb3e1e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -122,6 +122,9 @@ excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', ] } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index 4417c0cacee..5a1a052ef23 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -111,6 +111,9 @@ excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. 'distributed/test_distributed_spawn', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', ] } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb index 7d0cc431687..4bbdb824152 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb @@ -146,7 +146,10 @@ excluded_tests = { 'distributed/fsdp/test_fsdp_core', # failing on broadwell # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 - 'test_native_mha' + 'test_native_mha', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', ] } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb index 7c58b58e5fd..9f564b7abe1 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb @@ -128,6 +128,9 @@ excluded_tests = { # flaky test which fails on some systems, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 'distributed/elastic/multiprocessing/api_test', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', ] } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index 528fb671557..e10e5221763 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -140,6 +140,9 @@ excluded_tests = { # Those 2 abort on some machines. Skip for now 'distributed/fsdp/test_fsdp_input', 'distributed/fsdp/test_fsdp_mixed_precision', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', ] } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb index c31da630572..6768a396213 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -123,6 +123,9 @@ excluded_tests = { 'distributed/test_distributed_spawn', # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 'distributions/test_constraints', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', ] } From 40c0644024f645fcf2848def93d18cddddd99a7c Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 17 Apr 2023 15:26:50 +0100 Subject: [PATCH 7192/9987] add test excludes documented in 17615 to all 1.12.1 easyconfigs --- .../p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 9 +++++++++ .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 9 +++++++++ .../p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb | 3 +++ .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb | 3 +++ .../p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 9 +++++++++ .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 9 +++++++++ 6 files changed, 42 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index dba21cb3e1e..df2f07b6db3 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -122,6 +122,15 @@ excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. 'distributed/test_distributed_spawn', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 'test_optim', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index 5a1a052ef23..550c24d748b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -111,6 +111,15 @@ excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. 'distributed/test_distributed_spawn', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 'test_optim', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb index 4bbdb824152..3ce09263594 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb @@ -147,6 +147,9 @@ excluded_tests = { # failing on broadwell # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 'test_optim', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb index 9f564b7abe1..b4ca5e1483a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb @@ -122,6 +122,9 @@ excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. 'distributed/test_distributed_spawn', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', # failing on broadwell # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 'test_native_mha', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index e10e5221763..8cc442f469d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -140,6 +140,15 @@ excluded_tests = { # Those 2 abort on some machines. Skip for now 'distributed/fsdp/test_fsdp_input', 'distributed/fsdp/test_fsdp_mixed_precision', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 'test_optim', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb index 6768a396213..3f02df492ba 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -123,6 +123,15 @@ excluded_tests = { 'distributed/test_distributed_spawn', # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 'distributions/test_constraints', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 'test_optim', From ca7f8e07bd86b8bcb279134f15857ee83b9fcadc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 17 Apr 2023 17:50:00 +0200 Subject: [PATCH 7193/9987] adding easyconfigs: PYTHIA-8.309-foss-2022b.eb --- .../p/PYTHIA/PYTHIA-8.309-foss-2022b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.309-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.309-foss-2022b.eb b/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.309-foss-2022b.eb new file mode 100644 index 00000000000..e664b716b74 --- /dev/null +++ b/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.309-foss-2022b.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'PYTHIA' +version = '8.309' + +homepage = 'https://www.pythia.org' +description = """PYTHIA is a program for the generation of high-energy physics collision events, i.e. for the +description of collisions at high energies between electrons, protons, photons and heavy nuclei. It contains theory +and models for a number of physics aspects, including hard and soft interactions, parton distributions, initial- and +final-state parton showers, multiparton interactions, fragmentation and decay. It is largely based on original +research, but also borrows many formulae and other knowledge from the literature. As such it is categorized as a +general purpose Monte Carlo event generator.""" + + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.pythia.org/download/pythia83/'] +sources = ['pythia%(version_major)s%(version_minor)s.tgz'] +checksums = ['5bdafd9f2c4a1c47fd8a4e82fb9f0d8fcfba4de1003b8e14be4e0347436d6c33'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Python', '3.10.8'), + ('ROOT', '6.26.10'), + ('HDF5', '1.14.0'), +] + +configopts = '--cxx="$CXX" --cxx-common="$CXXFLAGS" ' +configopts += '--with-openmp --with-mpich --with-gzip --with-root --with-hdf5 ' +configopts += '--with-python --with-python-include=$EBROOTPYTHON/include/python*/ ' + +sanity_check_paths = { + 'files': ['bin/pythia%(version_major)s-config', 'lib/libpythia%(version_major)s.a', + 'lib/libpythia%%(version_major)s.%s' % SHLIB_EXT, 'lib/pythia8.%s' % SHLIB_EXT], + 'dirs': ['include/Pythia%(version_major)s', 'include/Pythia%(version_major)sPlugins', 'share'], +} +sanity_check_commands = ["python -c 'import pythia%(version_major)s'"] + +modextrapaths = {'PYTHONPATH': 'lib'} + +moduleclass = 'phys' From 2cdfef6c096493e071f7c00ecb2ce98cbd8d3210 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 18 Apr 2023 00:52:56 +0200 Subject: [PATCH 7194/9987] Add espresso 4.2.1 --- ... ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb} | 0 .../ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb | 53 +++++++++++++++++++ 2 files changed, 53 insertions(+) rename easybuild/easyconfigs/e/ESPResSo/{ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb => ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb} (100%) create mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb similarity index 100% rename from easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2-foss-2021a-CUDA-11.3.1.eb rename to easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..3924a2baf37 --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'ESPResSo' +version = '4.2.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://espressomd.org/wordpress' +description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" + +source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f7264d78fe1fd7774b89972fe10d5b15d2e9d620d406158dab90df5df0b9f255'] + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', SYSTEM), + ('SciPy-bundle', '2021.05'), + ('Boost.MPI', '1.76.0'), + ('HDF5', '1.10.7'), + ('Mesa', '21.1.1'), + ('GSL', '2.7'), + ('IPython', '7.25.0'), + ('Pint', '0.20.1'), +] + +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON' + +runtest = 'check_unit_tests && make check_python' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +_binaries = ['ipypresso', 'pypresso'] +_libs = [ + 'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes', + '_init', 'analyze', 'code_info', 'cuda_init', 'electrokinetics', 'galilei', + 'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler', + 'script_interface', 'system', 'thermostat', 'utils', 'version', +] + +_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + [_lib_path + f'/%s.{SHLIB_EXT}' % x for x in _libs], + 'dirs': ['bin', 'lib'] +} + +moduleclass = 'chem' From 0b7899aa0af4f289934fb7cebffa8dcaba3e178a Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 18 Apr 2023 00:54:20 +0200 Subject: [PATCH 7195/9987] Remove v4.2.0 --- .../ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb | 54 ------------------- 1 file changed, 54 deletions(-) delete mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb deleted file mode 100644 index 51fa7dc8424..00000000000 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.0-foss-2021a-CUDA-11.3.1.eb +++ /dev/null @@ -1,54 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'ESPResSo' -version = '4.2.0' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://espressomd.org/wordpress' -description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" - -source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/'] -sources = ['%(version)s.tar.gz'] -checksums = ['e6e17fafa9ba80b46f542dc86e07677a8d641cfd0102ebc4db2f7ee47d5fb6f1'] - -toolchain = {'name': 'foss', 'version': '2021a'} -toolchainopts = {'usempi': True, 'pic': True} - -builddependencies = [('CMake', '3.20.1')] - -dependencies = [ - ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', SYSTEM), - ('SciPy-bundle', '2021.05'), - ('Boost.MPI', '1.76.0'), - ('Cython', '0.29.34'), - ('HDF5', '1.10.7'), - ('Mesa', '21.1.1'), - ('GSL', '2.7'), - ('IPython', '7.25.0'), - ('Pint', '0.20.1'), -] - -configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON' - -separate_build_dir = True - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - -_binaries = ['ipypresso', 'pypresso'] -_libs = [ - 'Espresso_config.so', 'Espresso_core.so', 'Espresso_script_interface.so', 'Espresso_shapes.so', - '_init.so', 'analyze.so', 'code_info.so', 'cuda_init.so', 'electrokinetics.so', 'galilei.so', - 'integrate.so', 'interactions.so', 'lb.so', 'particle_data.so', 'polymer.so', 'profiler.so', - 'script_interface.so', 'system.so', 'thermostat.so', 'utils.so', 'version.so', -] - -_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in _binaries] + - [_lib_path + '/%s' % x for x in _libs], - 'dirs': ['bin', 'lib'] -} - -moduleclass = 'chem' From 2e438593742a1a64f5121e59d9da1a02b02e505f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 18 Apr 2023 00:55:50 +0200 Subject: [PATCH 7196/9987] Remove Cython --- .../c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb deleted file mode 100644 index faff04ca575..00000000000 --- a/easybuild/easyconfigs/c/Cython/Cython-0.29.34-GCCcore-10.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Cython' -version = '0.29.34' - -homepage = 'https://cython.org/' -description = """ -Cython is an optimising static compiler for both the Python programming -language and the extended Cython programming language (based on Pyrex). -""" -docurls = [ - 'https://cython.org/#documentation', - 'https://github.com/cython/cython', -] - -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['1909688f5d7b521a60c396d20bba9e47a1b2d2784bfb085401e1e1e7d29a29a8'] - -builddependencies = [('binutils', '2.36.1')] - -dependencies = [('Python', '3.9.5')] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - 'cython --version', -] - -moduleclass = 'lang' From fef63e850bb980fd82af9d3e39368d6b8f8aabd5 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 18 Apr 2023 00:59:13 +0200 Subject: [PATCH 7197/9987] Add sanity check cmds --- .../e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb index 3924a2baf37..8bf837144e0 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb @@ -50,4 +50,6 @@ sanity_check_paths = { 'dirs': ['bin', 'lib'] } +sanity_check_commands = ['pypresso -h', 'ipypresso -h'] + moduleclass = 'chem' From 1f5ab2097618bfe8abf21cc25db4e014d513e834 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Tue, 18 Apr 2023 09:05:45 +0200 Subject: [PATCH 7198/9987] adding easyconfigs: make-4.4.1-GCCcore-12.2.0.eb --- .../m/make/make-4.4.1-GCCcore-12.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a4107e59ee5 --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.4.1' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['dd16fb1d67bfab79a72f5e8390735c49e3e8e70b4945a15ab1f81ddb78658fb3'] + +builddependencies = [('binutils', '2.39')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' From d998e393444848e1bd7aa76836b73eb460d04aea Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 18 Apr 2023 11:01:57 +0200 Subject: [PATCH 7199/9987] Adapt for python-2 --- .../e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb index 8bf837144e0..a8901cbb3d1 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb @@ -46,7 +46,7 @@ _lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' sanity_check_paths = { 'files': ['bin/%s' % x for x in _binaries] + - [_lib_path + f'/%s.{SHLIB_EXT}' % x for x in _libs], + [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs], 'dirs': ['bin', 'lib'] } From b6a44a2cc67045a5289a018cebe1399fe0220e17 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 18 Apr 2023 10:33:22 +0100 Subject: [PATCH 7200/9987] adding easyconfigs: GenMap-1.3.0-GCCcore-11.2.0.eb --- .../g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100755 easybuild/easyconfigs/g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb new file mode 100755 index 00000000000..2a1f332ae41 --- /dev/null +++ b/easybuild/easyconfigs/g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'GenMap' +version = '1.3.0' + +homepage = 'https://github.com/cpockrandt/genmap' + +description = """GenMap - Fast and Exact Computation of Genome Mappability""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/cpockrandt/genmap/archive/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['d237b284bb26d000039078e7be81bbebae21ee65d614ce89bd47a45f99fafb64'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('SeqAn', '2.4.0'), +] + +configopts = "-DSeqAn_DIR=$EBROOTSEQAN/util/cmake" + +sanity_check_paths = { + 'files': ["bin/genmap"], + 'dirs': [], +} + +sanity_check_commands = ["genmap %s --help" % x for x in ["", "index", "map"]] + +moduleclass = 'bio' From 558c33249b51a6a925563f630ac36c441235b21f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 18 Apr 2023 12:29:21 +0100 Subject: [PATCH 7201/9987] adding easyconfigs: pyslim-1.0.1-foss-2022a.eb --- .../p/pyslim/pyslim-1.0.1-foss-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2022a.eb new file mode 100644 index 00000000000..da7c91bba12 --- /dev/null +++ b/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'pyslim' +version = '1.0.1' + +homepage = 'https://tskit.dev/pyslim/docs/stable/introduction.html' +description = """A Python API for reading and modifying tskit tree +sequence files produced by SLiM, or modifying files produced by other +programs (e.g., msprime, fwdpy11, and tsinfer) for use in SLiM.""" + + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for numpy + ('msprime', '1.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['d65923658df9303962997f8911449245d33cf7f56aada8df4573ad301a9934c6'], + }), +] + +moduleclass = 'bio' From de2d32348deff7fda8fd2ed7326bb1b5e3cef6df Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 18 Apr 2023 12:30:56 +0100 Subject: [PATCH 7202/9987] adding easyconfigs: msprime-1.2.0-foss-2022a.eb --- .../m/msprime/msprime-1.2.0-foss-2022a.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb new file mode 100644 index 00000000000..b5ea22facf2 --- /dev/null +++ b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'msprime' +version = '1.2.0' + +homepage = 'https://msprime.readthedocs.io' +description = "msprime is a coalescent simulator and library for processing tree-based genetic data." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for numpy + ('GSL', '2.7'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('svgwrite', '1.4.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['a8fbdfd4443302a6619a7f76bc937fc683daf2628d9b737c891ec08b8ce524c3'], + }), + ('tskit', '0.5.4', { + 'checksums': ['be1a6381c72a95f0011bea26ca317e1b4503b8d2dcd87096c68aa16c8946c6fe'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('ruamel.yaml', '0.17.21', { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('demes', '0.2.2', { + 'checksums': ['8eebe4b236b2d19e057228892f5b5f53f3e0d127ca9128efead1728a65115dac'], + }), + ('newick', '1.9.0', { + 'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'], + }), + (name, version, { + 'checksums': ['60025ad9fd30d827a72ae6e760b6cff07a1d0e169b2c1da1024cb0fc23e4a7aa'], + }), +] + +sanity_check_paths = { + 'files': ['bin/msp', 'bin/mspms', 'bin/tskit', 'bin/demes'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'demes --help', + 'tskit --help', + 'msp --help', + 'mspms --help', +] + +moduleclass = 'bio' From 2597a1f4a3833e1050c63049a38ed8bd279a922f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 18 Apr 2023 12:33:01 +0100 Subject: [PATCH 7203/9987] adding easyconfigs: SLiM-4.0.1-GCC-11.3.0.eb and patches: SLiM-4.0.1_use_external_zlib_gsl.patch --- .../s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb | 48 ++++++ .../SLiM-4.0.1_use_external_zlib_gsl.patch | 161 ++++++++++++++++++ 2 files changed, 209 insertions(+) create mode 100644 easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..4d9a4c39ed5 --- /dev/null +++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'SLiM' +version = '4.0.1' + +homepage = 'https://messerlab.org/slim' +description = """SLiM is an evolutionary simulation framework that combines a powerful engine for population + genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/MesserLab/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_external_zlib_gsl.patch', +] +checksums = [ + {'v4.0.1.tar.gz': 'a44564023db372cd438b4e6c729a4ba59200d1217a63b3694ca7903436886cc2'}, + {'SLiM-4.0.1_use_external_zlib_gsl.patch': '7290f24ec9e04edc696aa85e3b4186cfcffa76b3c9b08bdf379ea00eac578755'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('GSL', '2.7'), + ('Mesa', '22.0.3'), + ('libglvnd', '1.4.0'), + ('Qt5', '5.15.5'), +] + +configopts = '-DBUILD_SLIMGUI=ON ' + +sanity_check_paths = { + 'files': ['bin/eidos', 'bin/slim'], + 'dirs': [], +} + +sanity_check_commands = [ + "eidos -usage", + "eidos -testEidos", + "slim -usage", + "slim -testSLiM", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch new file mode 100644 index 00000000000..894f69dd4f3 --- /dev/null +++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch @@ -0,0 +1,161 @@ +commit 2ba4892b9327e5d21fdd712e178447d2ecd3665a +Author: Ake Sandgren +Date: Wed Aug 24 08:15:39 2022 +0200 + + Use external Zlib and GSL instead of internal ones. + And use correctly names zlib functions. + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 487c7bcd..0aae03ea 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -157,18 +157,20 @@ endif() + #endif() + + # GSL +-set(TARGET_NAME gsl) +-file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c) +-set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg) +-add_library(${TARGET_NAME} STATIC ${GSL_SOURCES}) +-target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES}) ++# Use external GSL instead ++#set(TARGET_NAME gsl) ++#file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c) ++#set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg) ++#add_library(${TARGET_NAME} STATIC ${GSL_SOURCES}) ++#target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES}) + + # ZLIB +-set(TARGET_NAME eidos_zlib) +-file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c) +-set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib) +-add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES}) +-target_include_directories(${TARGET_NAME} PUBLIC) ++# Use external Zlib instead ++#set(TARGET_NAME eidos_zlib) ++#file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c) ++#set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib) ++#add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES}) ++#target_include_directories(${TARGET_NAME} PUBLIC) + + # KASTORE + set(TARGET_NAME kastore) +@@ -198,7 +200,7 @@ list(APPEND SLIM_SOURCES "${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp" ${PROJECT_SOU + + add_executable(${TARGET_NAME} ${SLIM_SOURCES}) + target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/eidos") +-target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables) ++target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables) + if(WIN32) + set_source_files_properties(${SLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") + set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") +@@ -211,7 +213,7 @@ set(TARGET_NAME eidos) + file(GLOB_RECURSE EIDOS_SOURCES ${PROJECT_SOURCE_DIR}/eidos/*.cpp ${PROJECT_SOURCE_DIR}/eidostool/*.cpp) + add_executable(${TARGET_NAME} ${EIDOS_SOURCES}) + target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/eidos") +-target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables) ++target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables) + if(WIN32) + set_source_files_properties(${EIDOS_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") + set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") +@@ -244,15 +246,15 @@ set_target_properties( ${TARGET_NAME} PROPERTIES LINKER_LANGUAGE CXX) + target_compile_definitions( ${TARGET_NAME} PRIVATE EIDOSGUI=1 SLIMGUI=1) + target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/QtSLiM" "${PROJECT_SOURCE_DIR}/eidos" "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/treerec" "${PROJECT_SOURCE_DIR}/treerec/tskit/kastore") + if(APPLE) +- target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib /usr/lib/libobjc.A.dylib ) ++ target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z /usr/lib/libobjc.A.dylib ) + else() + if(WIN32) + set_source_files_properties(${QTSLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") + set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos SLiMgui PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") + target_include_directories(${TARGET_NAME} BEFORE PUBLIC ${GNU_DIR}) +- target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib gnu ) ++ target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z gnu ) + else() +- target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib ) ++ target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z ) + endif() + endif() + install(TARGETS ${TARGET_NAME} DESTINATION bin) +diff --git a/eidos/eidos_functions.cpp b/eidos/eidos_functions.cpp +index 4f52c763..ac9de199 100644 +--- a/eidos/eidos_functions.cpp ++++ b/eidos/eidos_functions.cpp +@@ -55,11 +55,11 @@ + + #include "string.h" + +-#include "gsl_linalg.h" +-#include "gsl_errno.h" +-#include "gsl_cdf.h" ++#include ++#include ++#include + +-#include "../eidos_zlib/zlib.h" ++#include + + #include "eidos_globals.h" + #if EIDOS_ROBIN_HOOD_HASHING +@@ -11475,7 +11475,7 @@ EidosValue_SP Eidos_ExecuteFunction_writeTempFile(const std::vector + + // for Eidos_calc_sha_256() + #include + + // for _Eidos_FlushZipBuffer() +-#include "../eidos_zlib/zlib.h" ++#include + + // for Eidos_ColorPaletteLookup() + #include "eidos_tinycolormap.h" +@@ -1570,7 +1570,7 @@ bool _Eidos_FlushZipBuffer(const std::string &file_path, const std::string &outs + { + //std::cout << "_Eidos_FlushZipBuffer() called for " << file_path << std::endl; + +- gzFile gzf = z_gzopen(file_path.c_str(), "ab"); ++ gzFile gzf = gzopen(file_path.c_str(), "ab"); + + if (!gzf) + return false; +@@ -1678,7 +1678,7 @@ void Eidos_WriteToFile(const std::string &p_file_path, std::vector ++#include + + #include + #include From 1f2330e2fb7bc7a4e7c79c9f41f4feff70ecb333 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 18 Apr 2023 13:44:47 +0200 Subject: [PATCH 7204/9987] adding easyconfigs: Check-0.15.2-GCCcore-11.3.0.eb --- .../c/Check/Check-0.15.2-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f1ca4ac1035 --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Check' +version = '0.15.2' + +homepage = 'https://libcheck.github.io/check/' +description = """ +Check is a unit testing framework for C. It features a simple interface for +defining unit tests, putting little in the way of the developer. Tests are +run in a separate address space, so both assertion failures and code errors +that cause segmentation faults or other signals can be caught. Test results +are reportable in the following: Subunit, TAP, XML, and a generic logging +format.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'libcheck' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['998d355294bb94072f40584272cf4424571c396c631620ce463f6ea97aa67d2e'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-build-docs" + +sanity_check_paths = { + 'files': ['bin/checkmk', 'lib/libcheck.a', 'lib/libcheck.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' From 4512e49ababe85f69dd7c104a91b2a83309c4607 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Apr 2023 14:52:48 +0200 Subject: [PATCH 7205/9987] adding easyconfigs: ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb, ColabFold-1.5.2-foss-2022a.eb, AlphaFold-2.3.4-foss-2022a-ColabFold.eb, AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb and patches: AlphaFold-ColabFold-2.3.4_data-dep-paths.patch, AlphaFold-ColabFold-2.3.4_fix-scp-path.patch --- ...-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb | 178 ++++++++++++++++++ .../AlphaFold-2.3.4-foss-2022a-ColabFold.eb | 167 ++++++++++++++++ ...aFold-ColabFold-2.3.4_data-dep-paths.patch | 134 +++++++++++++ ...phaFold-ColabFold-2.3.4_fix-scp-path.patch | 14 ++ .../ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb | 58 ++++++ .../c/ColabFold/ColabFold-1.5.2-foss-2022a.eb | 56 ++++++ 6 files changed, 607 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_data-dep-paths.patch create mode 100644 easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_fix-scp-path.patch create mode 100644 easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb new file mode 100644 index 00000000000..51dbe4220f7 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb @@ -0,0 +1,178 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.3.4' +_colab_suffix = '-ColabFold' +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = _cuda_suffix + _colab_suffix +_commit = '41807ea2c75706cf03f790f06ca191dc04331e41' + +homepage = 'https://github.com/sokrypton/alphafold' +description = """ +AlphaFold can predict protein structures with atomic accuracy even where no +similar structure is known. +This package of AlphaFold contains patches for ColabFold.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '5.1.1'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('TensorFlow', '2.11.0', _cuda_suffix), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.5'), + ('jax', '0.3.25', _cuda_suffix), # also provides absl-py + ('UCX-CUDA', '1.12.1', _cuda_suffix), + ('cuDNN', '8.4.1.50', _cuda_suffix, SYSTEM), + ('NCCL', '2.12.12', _cuda_suffix), + ('OpenMM', '8.0.0', _cuda_suffix), +] + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/sokrypton/alphafold/archive/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': '%s.tar.gz' % _commit, + 'filename': '%s-%s.tar.gz' % (name.lower() + _colab_suffix.lower(), version) + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-ColabFold-2.3.4_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-ColabFold-2.3.4_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.3.1_use_openmm_7.7.0.patch', + ], + 'checksums': [ + 'be6778333fc110b8662b0e262798d6fc1663a14d9341469c6558b2d7771b8024', # alphafold-colabfold-2.3.4.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + # AlphaFold-ColabFold-2.3.4_data-dep-paths.patch + '3826e357c35a58b2c8c0fab41ac8ae1b4d4c135162fe47ded577a13dade0c6f3', + # AlphaFold-2.0.0_n-cpu.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', + # AlphaFold-ColabFold-2.3.4_fix-scp-path.patch + '07bf81f987bc1ab67b7d71121396449289d3ffb499cddb62a135574f2ca7115a', + # AlphaFold-2.0.1_setup_rm_tfcpu.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', + # AlphaFold-2.3.1_use_openmm_7.7.0.patch + 'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec', + ], + 'start_dir': 'alphafold-%s' % _commit, + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.8.1', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.6', { + 'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('dm-tree', '0.1.8', { + 'modulename': 'tree', + 'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('docker', '6.0.1', { + 'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'], + }), + ('immutabledict', '2.2.3', { + 'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +_alphafold_buildir = '%%(builddir)s/%%(namelower)s-%s' % _commit + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %s/run_alphafold.py >> %%(installdir)s/bin/run_alphafold.py" % _alphafold_buildir, + "chmod a+x %(installdir)s/bin/run_alphafold*.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %s/scripts %%(installdir)s/" % _alphafold_buildir, + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:$PYTHONPATH " + "python %s/run_alphafold_test.py" % _alphafold_buildir, +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m openmm.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '3', + 'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-2.3.1', + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb new file mode 100644 index 00000000000..9297ff62b97 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb @@ -0,0 +1,167 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.3.4' +versionsuffix = '-ColabFold' +_commit = '41807ea2c75706cf03f790f06ca191dc04331e41' + +homepage = 'https://github.com/sokrypton/alphafold' +description = """ +AlphaFold can predict protein structures with atomic accuracy even where no +similar structure is known. +This package of AlphaFold contains patches for ColabFold.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '5.1.1'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('TensorFlow', '2.11.0'), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.5'), + ('jax', '0.3.25'), # also provides absl-py + ('OpenMM', '8.0.0'), +] + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/sokrypton/alphafold/archive/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': '%s.tar.gz' % _commit, + 'filename': '%s-%s.tar.gz' % (name.lower() + versionsuffix.lower(), version) + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-ColabFold-2.3.4_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-ColabFold-2.3.4_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.3.1_use_openmm_7.7.0.patch', + ], + 'checksums': [ + 'be6778333fc110b8662b0e262798d6fc1663a14d9341469c6558b2d7771b8024', # alphafold-colabfold-2.3.4.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + # AlphaFold-ColabFold-2.3.4_data-dep-paths.patch + '3826e357c35a58b2c8c0fab41ac8ae1b4d4c135162fe47ded577a13dade0c6f3', + # AlphaFold-2.0.0_n-cpu.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', + # AlphaFold-ColabFold-2.3.4_fix-scp-path.patch + '07bf81f987bc1ab67b7d71121396449289d3ffb499cddb62a135574f2ca7115a', + # AlphaFold-2.0.1_setup_rm_tfcpu.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', + # AlphaFold-2.3.1_use_openmm_7.7.0.patch + 'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec', + ], + 'start_dir': 'alphafold-%s' % _commit, + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.8.1', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.6', { + 'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('dm-tree', '0.1.8', { + 'modulename': 'tree', + 'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('docker', '6.0.1', { + 'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'], + }), + ('immutabledict', '2.2.3', { + 'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +_alphafold_buildir = '%%(builddir)s/%%(namelower)s-%s' % _commit + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %s/run_alphafold.py >> %%(installdir)s/bin/run_alphafold.py" % _alphafold_buildir, + "chmod a+x %(installdir)s/bin/run_alphafold*.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %s/scripts %%(installdir)s/" % _alphafold_buildir, + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:$PYTHONPATH " + "python %s/run_alphafold_test.py" % _alphafold_buildir, +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m openmm.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextravars = { + 'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-2.3.1', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_data-dep-paths.patch new file mode 100644 index 00000000000..388d7aa02d2 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_data-dep-paths.patch @@ -0,0 +1,134 @@ +pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data +(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py); +pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) +--- run_alphafold.py.orig 2023-02-18 15:59:05.000000000 +0100 ++++ run_alphafold.py 2023-04-17 13:54:08.910029182 +0200 +@@ -42,6 +42,46 @@ + import numpy as np + + # Internal import (7716). ++use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:]) ++use_monomer_preset = not any("--model_preset=multimer" in s for s in sys.argv[1:]) ++ ++data_dir = os.getenv('ALPHAFOLD_DATA_DIR') ++use_gpu_relax = os.getenv('OPENMM_RELAX')=='CUDA' ++ ++if data_dir: ++ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters_2022_05.fa') ++ uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') ++ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') ++ obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') ++ if use_monomer_preset: ++ pdb_seqres_database_path = None ++ uniprot_database_path = None ++ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') ++ else: ++ pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt') ++ uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.fasta') ++ pdb70_database_path = None ++ if use_reduced_dbs: ++ small_bfd_database_path = os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta') ++ uniref30_database_path = None ++ bfd_database_path = None ++ else: ++ small_bfd_database_path = None ++ bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') ++ uniref30_database_path = os.path.join(data_dir, 'uniref30', 'UniRef30_2021_03') ++else: ++ sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!") ++ uniref90_database_path = None ++ mgnify_database_path = None ++ bfd_database_path = None ++ uniref30_database_path = None ++ pdb70_database_path = None ++ template_mmcif_dir = None ++ obsolete_pdbs_path = None ++ small_bfd_database_path = None ++ uniprot_database_path = None ++ pdb_seqres_database_path = None ++ use_gpu_relax = None + + logging.set_verbosity(logging.INFO) + +@@ -59,7 +99,7 @@ + 'separated by commas. All FASTA paths must have a unique basename as the ' + 'basename is used to name the output directories for each prediction.') + +-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') ++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') + flags.DEFINE_string('output_dir', None, 'Path to a directory that will ' + 'store the results.') + flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'), +@@ -74,27 +114,27 @@ + 'Path to the hmmbuild executable.') + flags.DEFINE_string('kalign_binary_path', shutil.which('kalign'), + 'Path to the Kalign executable.') +-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 ' ++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify ' ++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD ' ++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD ' + 'database for use by HHblits.') +-flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small ' ++flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small ' + 'version of BFD used with the "reduced_dbs" preset.') +-flags.DEFINE_string('uniref30_database_path', None, 'Path to the UniRef30 ' ++flags.DEFINE_string('uniref30_database_path', uniref30_database_path, 'Path to the UniRef30 ' + 'database for use by HHblits.') +-flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot ' ++flags.DEFINE_string('uniprot_database_path', uniprot_database_path, 'Path to the Uniprot ' + 'database for use by JackHMMer.') +-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 ' ++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 ' + 'database for use by HHsearch.') +-flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB ' ++flags.DEFINE_string('pdb_seqres_database_path', pdb_seqres_database_path, 'Path to the PDB ' + 'seqres database for use by hmmsearch.') +-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with ' ++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with ' + 'template mmCIF structures, each named .cif') + flags.DEFINE_string('max_template_date', None, 'Maximum template release date ' + 'to consider. Important if folding historical test sets.') +-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a ' ++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a ' + 'mapping from obsolete PDB IDs to the PDB IDs of their ' + 'replacements.') + flags.DEFINE_enum('db_preset', 'full_dbs', +@@ -137,7 +177,7 @@ + 'distracting stereochemical violations but might help ' + 'in case you are having issues with the relaxation ' + 'stage.') +-flags.DEFINE_boolean('use_gpu_relax', None, 'Whether to relax on GPU. ' ++flags.DEFINE_boolean('use_gpu_relax', use_gpu_relax, 'Whether to relax on GPU. ' + 'Relax on GPU can be much faster than CPU, so it is ' + 'recommended to enable if possible. GPUs must be available' + ' if this setting is enabled.') +@@ -334,6 +374,10 @@ + 'sure it is installed on your system.') + + use_small_bfd = FLAGS.db_preset == 'reduced_dbs' ++ if use_small_bfd and data_dir: ++ bfd_database_path = None ++ uniref30_database_path = None ++ + _check_flag('small_bfd_database_path', 'db_preset', + should_be_set=use_small_bfd) + _check_flag('bfd_database_path', 'db_preset', +@@ -456,13 +500,7 @@ + flags.mark_flags_as_required([ + 'fasta_paths', + 'output_dir', +- 'data_dir', +- 'uniref90_database_path', +- 'mgnify_database_path', +- 'template_mmcif_dir', + 'max_template_date', +- 'obsolete_pdbs_path', +- 'use_gpu_relax', + ]) + + app.run(main) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_fix-scp-path.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_fix-scp-path.patch new file mode 100644 index 00000000000..0714243785e --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_fix-scp-path.patch @@ -0,0 +1,14 @@ +fix path to stereo_chemical_props.txt when AlphaFold is installed with EasyBuild +author: Kenneth Hoste (HPC-UGent) +update 2.0.0 -> 2.1.0: Thomas Hoffmann (EMBL Heidelberg) +--- alphafold/common/residue_constants.py.orig 2023-04-17 13:59:57.535153646 +0200 ++++ alphafold/common/residue_constants.py 2023-04-17 14:02:33.555747657 +0200 +@@ -25,7 +25,7 @@ + # Internal import (35fd). + + from . import __file__ +-stereo_chemical_props_path = os.path.join(os.path.dirname(__file__), f'stereo_chemical_props.txt') ++stereo_chemical_props_path = os.path.join(os.getenv('EBROOTALPHAFOLD', 'alphafold/common'), 'stereo_chemical_props.txt') + + # Distance from one CA to next CA [trans configuration: omega = 180]. + ca_ca = 3.80209737096 diff --git a/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..8d8017276a6 --- /dev/null +++ b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'ColabFold' +version = '1.5.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/sokrypton/ColabFold' +description = """Making protein folding accessible to all. Predict proteins structures both in +google colab and on your machine.""" +github_account = 'sokrypton' + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('AlphaFold', '2.3.4', versionsuffix + '-%(name)s'), + ('matplotlib', '3.5.2'), + ('tqdm', '4.64.0'), + ('py3Dmol', '2.0.1.post1'), +] + +use_pip = True + +exts_list = [ + ('colabfold', version, { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['b3b82e831e241a6ab40f2b0c6d560ac5328c6a0b505a0186c75e397ca1a16477'], + # fix requirement on Python 3.10.x revisions and TensorFlow + 'preinstallopts': r"sed -i 's/^\(python =.*\)<=3.10\"$/\1<3.11\"/;s/flow-cpu/flow/' pyproject.toml &&", + 'use_pip_extras': 'alphafold', + }), +] + +postinstallcmds = [ + # Copy notebooks to installation directory + "mkdir %(installdir)s/notebooks", + "cp AlphaFold2.ipynb ESMFold.ipynb RoseTTAFold.ipynb %(installdir)s/notebooks/", +] + +sanity_check_paths = { + 'files': ['bin/colabfold_batch', 'bin/colabfold_search', 'bin/colabfold_split_msas'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'notebooks'], +} + +sanity_check_commands = [ + "colabfold_batch --help", +] + +sanity_pip_check = True + +modloadmsg = """ +%(name)s notebooks are located in $EBROOTCOLABFOLD/notebooks +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb new file mode 100644 index 00000000000..c8ebee84c19 --- /dev/null +++ b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'ColabFold' +version = '1.5.2' + +homepage = 'https://github.com/sokrypton/ColabFold' +description = """Making protein folding accessible to all. Predict proteins structures both in +google colab and on your machine.""" +github_account = 'sokrypton' + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('AlphaFold', '2.3.4', '-%(name)s'), + ('matplotlib', '3.5.2'), + ('tqdm', '4.64.0'), + ('py3Dmol', '2.0.1.post1'), +] + +use_pip = True + +exts_list = [ + ('colabfold', version, { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['b3b82e831e241a6ab40f2b0c6d560ac5328c6a0b505a0186c75e397ca1a16477'], + # fix requirement on Python 3.10.x revisions and TensorFlow + 'preinstallopts': r"sed -i 's/^\(python =.*\)<=3.10\"$/\1<3.11\"/;s/flow-cpu/flow/' pyproject.toml &&", + 'use_pip_extras': 'alphafold', + }), +] + +postinstallcmds = [ + # Copy notebooks to installation directory + "mkdir %(installdir)s/notebooks", + "cp AlphaFold2.ipynb ESMFold.ipynb RoseTTAFold.ipynb %(installdir)s/notebooks/", +] + +sanity_check_paths = { + 'files': ['bin/colabfold_batch', 'bin/colabfold_search', 'bin/colabfold_split_msas'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'notebooks'], +} + +sanity_check_commands = [ + "colabfold_batch --help", +] + +sanity_pip_check = True + +modloadmsg = """ +%(name)s notebooks are located in $EBROOTCOLABFOLD/notebooks +""" + +moduleclass = 'bio' From 67ba82f1331e1305932cdfcabeb686b3dca43a18 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Apr 2023 14:58:22 +0200 Subject: [PATCH 7206/9987] comment out ALPHAFOLD_DATA_DIR in AlphaFold-ColabFold v2.3.4 --- .../AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb | 2 +- .../a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb index 51dbe4220f7..0842216c4e9 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb @@ -171,7 +171,7 @@ sanity_pip_check = True modextravars = { 'TF_FORCE_UNIFIED_MEMORY': '1', 'XLA_PYTHON_CLIENT_MEM_FRACTION': '3', - 'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-2.3.1', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt, 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 } diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb index 9297ff62b97..614a7fe1e6e 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb @@ -161,7 +161,7 @@ sanity_check_commands = [ sanity_pip_check = True modextravars = { - 'ALPHAFOLD_DATA_DIR': '/databases/bio/%(namelower)s-2.3.1', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt } moduleclass = 'bio' From fca88c0dcd2143012c584ada7377ddbd5c65d248 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Apr 2023 15:30:07 +0200 Subject: [PATCH 7207/9987] adding easyconfigs: py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb --- .../py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..de2808866ae --- /dev/null +++ b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'py3Dmol' +version = '2.0.1.post1' + +homepage = 'https://github.com/3dmol/3Dmol.js/tree/master/py3Dmol' +description = "A simple IPython/Jupyter widget to embed an interactive 3Dmol.js viewer in a notebook." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': '%(name)s', + 'checksums': ['add70ecf8f647970925eb8c1043c5c1343813fa49e613b77f0628e522c4148ac'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From db5a46bb9e693aa6597107dbb800b2109fc1a7aa Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 18 Apr 2023 15:49:37 +0200 Subject: [PATCH 7208/9987] add build dependency on binutils to py3Dmol v2.0.1.post1 --- .../p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb index de2808866ae..9e22b8a26a6 100644 --- a/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb @@ -8,6 +8,10 @@ description = "A simple IPython/Jupyter widget to embed an interactive 3Dmol.js toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +builddependencies = [ + ('binutils', '2.38'), +] + dependencies = [ ('Python', '3.10.4'), ('IPython', '8.5.0'), From f945c4323074659aa89562981551d39f0538bce3 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 18 Apr 2023 16:38:22 +0100 Subject: [PATCH 7209/9987] adding easyconfigs: FUSE-3.14.1-foss-2022a.eb --- .../f/FUSE/FUSE-3.14.1-foss-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb new file mode 100644 index 00000000000..8f0af720ccd --- /dev/null +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'MesonNinja' + +name = 'FUSE' +version = '3.14.1' + +homepage = 'https://github.com/libfuse/libfuse' +description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/libfuse/libfuse/releases/download/fuse-%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20'] + +builddependencies = [ + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), +] + +# -Dutils=True only works as root +configopts = '-Dutils=False' + +sanity_check_paths = { + 'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT, + 'lib64/pkgconfig/fuse%(version_major)s.pc'], + 'dirs': ['include/fuse%(version_major)s'], +} + +moduleclass = 'lib' From f36809d220cdfbcade30e5618e80acf886bf40c2 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 18 Apr 2023 16:41:58 +0100 Subject: [PATCH 7210/9987] adding easyconfigs: dxpy-0.345.0-foss-2022a.eb --- .../d/dxpy/dxpy-0.345.0-foss-2022a.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb new file mode 100644 index 00000000000..e9f96f64f44 --- /dev/null +++ b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'dxpy' +version = '0.345.0' + +homepage = 'http://autodoc.dnanexus.com/' +description = "DNAnexus Platform API bindings for Python" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('FUSE', '3.14.1'), +] + +use_pip = True + +exts_list = [ + ('xattr', '0.10.1', { + 'checksums': ['c12e7d81ffaa0605b3ac8c22c2994a8e18a9cf1c59287a1b7722a2289c952ec5'], + }), + ('fusepy', '3.0.1', { + 'modulename': 'fuse', + 'checksums': ['72ff783ec2f43de3ab394e3f7457605bf04c8cf288a2f4068b4cde141d4ee6bd'], + }), + ('backports.ssl_match_hostname', '3.7.0.1', { + 'checksums': ['bb82e60f9fbf4c080eabd957c39f0641f0fc247d9a16e31e26d594d8f42b9fd2'], + }), + ('psutil', '5.9.5', { + 'checksums': ['5410638e4df39c54d957fc51ce03048acd8e6d60abc0f5107af51e5fb566eb3c'], + }), + ('trove-classifiers', '2023.4.18', { + 'checksums': ['9f892a83ccbdf9e669861a947c6b03d5b91a87f449aefef1d76fc4169f78ddba'], + }), + # The Python pathspec is too old for hatchling, version >= 0.10.0 is required + ('pathspec', '0.11.1', { + 'checksums': ['2798de800fa92780e33acca925945e9a19a133b715067cf165b8866c15a31687'], + }), + ('hatchling', '1.14.0', { + 'checksums': ['462ea91df03ff5d52813b5613fec1313a1a2059d2e37343e572b3f979867c5da'], + }), + ('beautifulsoup4', '4.12.2', { + 'modulename': 'bs4', + 'checksums': ['492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da'], + }), + ('python-magic', '0.4.27', { + 'modulename': 'magic', + 'checksums': ['c1ba14b08e4a5f5c31a302b7721239695b2f0f058d125bd5ce1ee36b9d9d3c3b'], + }), + ('websocket_client', '1.5.1', { + 'modulename': 'websocket', + 'sources': 'websocket-client-%(version)s.tar.gz', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + ('cffi', '1.15.1', { + 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], + }), + (name, version, { + 'checksums': ['cf5b47e83866a9c87a4fc59262eac500e860f6a890e6a897a577eff68e28cff2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 3337b7f9875711c31e0947f4dba08877c3500967 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 18 Apr 2023 17:13:32 +0100 Subject: [PATCH 7211/9987] Missing required libfuse.patch added --- .../d/dxpy/dxpy-0.345.0-foss-2022a.eb | 6 +++++- .../d/dxpy/fusepy-3.0.1_fix-libfuse.patch | 17 +++++++++++++++++ 2 files changed, 22 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/d/dxpy/fusepy-3.0.1_fix-libfuse.patch diff --git a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb index e9f96f64f44..0fcb809500a 100644 --- a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb @@ -21,7 +21,11 @@ exts_list = [ }), ('fusepy', '3.0.1', { 'modulename': 'fuse', - 'checksums': ['72ff783ec2f43de3ab394e3f7457605bf04c8cf288a2f4068b4cde141d4ee6bd'], + 'patches': ['fusepy-3.0.1_fix-libfuse.patch'], + 'checksums': [ + '72ff783ec2f43de3ab394e3f7457605bf04c8cf288a2f4068b4cde141d4ee6bd', # fusepy-3.0.1.tar.gz + '7650c5f922c24b820f2b33e0b5b1af8923c1a5c4ff397701cd970ea33c757fbe', # fusepy-3.0.1_fix-libfuse.patch + ], }), ('backports.ssl_match_hostname', '3.7.0.1', { 'checksums': ['bb82e60f9fbf4c080eabd957c39f0641f0fc247d9a16e31e26d594d8f42b9fd2'], diff --git a/easybuild/easyconfigs/d/dxpy/fusepy-3.0.1_fix-libfuse.patch b/easybuild/easyconfigs/d/dxpy/fusepy-3.0.1_fix-libfuse.patch new file mode 100644 index 00000000000..52eb7ae9be9 --- /dev/null +++ b/easybuild/easyconfigs/d/dxpy/fusepy-3.0.1_fix-libfuse.patch @@ -0,0 +1,17 @@ +fix name of FUSE library to search for (libfuse3.so for FUSE 3.x) +author: Kenneth Hoste (HPC-UGent) +updated to 3.0.1 +author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/fusepy-3.0.1.orig/fuse.py b/fusepy-3.0.1/fuse.py +index 7c2ddc4..f95730f 100644 +--- a/fusepy-3.0.1.orig/fuse.py ++++ b/fusepy-3.0.1/fuse.py +@@ -109,7 +109,7 @@ if not _libfuse_path: + if _libfuse_path: + _libfuse_path += r"bin\winfsp-%s.dll" % ("x64" if sys.maxsize > 0xffffffff else "x86") + else: +- _libfuse_path = find_library('fuse') ++ _libfuse_path = find_library('fuse3') + + if not _libfuse_path: + raise EnvironmentError('Unable to find libfuse') From c27be343ee6fbdaeb5999c7f1a8211d2591d858e Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 18 Apr 2023 11:41:34 -0700 Subject: [PATCH 7212/9987] {bio}[SYSTEM] IgBlast 1.21.0 update --- .../i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb diff --git a/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb b/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb new file mode 100644 index 00000000000..8d3bf7d2572 --- /dev/null +++ b/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb @@ -0,0 +1,30 @@ +# Easybuild Easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Center - Seattle Washington +easyblock = "Tarball" + +name = 'IgBLAST' +version = '1.21.0' +versionsuffix = '-x64-linux' + +homepage = 'https://ncbi.github.io/igblast' +description = """IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.""" + +toolchain = SYSTEM + +source_urls = ['ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/%(version)s'] +sources = ['ncbi-%(namelower)s-%(version)s-x64-linux.tar.gz'] +checksums = ['737d19aed8f3d8d717fcd8a2fa22e93b0830dd9cced729f41a67df95c8aef136'] + +sanity_check_paths = { + 'files': ["bin/igblastn", 'bin/igblastp'], + 'dirs': ['bin'] +} + +sanity_check_commands = ['%(namelower)sn -h'] + +modextravars = {'IGDATA': '%(installdir)s/internal_data'} + +moduleclass = 'bio' From d12b3630f3503af1dbad8679dc14ef956464fc9f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 18 Apr 2023 21:48:51 +0100 Subject: [PATCH 7213/9987] Patchfile from PR #16110 used as identical --- .../s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb | 4 +- .../SLiM-4.0.1_use_external_zlib_gsl.patch | 161 ------------------ 2 files changed, 2 insertions(+), 163 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb index 4d9a4c39ed5..496b738e7b5 100644 --- a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb @@ -12,11 +12,11 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/MesserLab/%(name)s/archive'] sources = ['v%(version)s.tar.gz'] patches = [ - '%(name)s-%(version)s_use_external_zlib_gsl.patch', + '%(name)s-4.0_use_external_zlib_gsl.patch', ] checksums = [ {'v4.0.1.tar.gz': 'a44564023db372cd438b4e6c729a4ba59200d1217a63b3694ca7903436886cc2'}, - {'SLiM-4.0.1_use_external_zlib_gsl.patch': '7290f24ec9e04edc696aa85e3b4186cfcffa76b3c9b08bdf379ea00eac578755'}, + {'SLiM-4.0_use_external_zlib_gsl.patch': '7290f24ec9e04edc696aa85e3b4186cfcffa76b3c9b08bdf379ea00eac578755'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch deleted file mode 100644 index 894f69dd4f3..00000000000 --- a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1_use_external_zlib_gsl.patch +++ /dev/null @@ -1,161 +0,0 @@ -commit 2ba4892b9327e5d21fdd712e178447d2ecd3665a -Author: Ake Sandgren -Date: Wed Aug 24 08:15:39 2022 +0200 - - Use external Zlib and GSL instead of internal ones. - And use correctly names zlib functions. - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 487c7bcd..0aae03ea 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -157,18 +157,20 @@ endif() - #endif() - - # GSL --set(TARGET_NAME gsl) --file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c) --set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg) --add_library(${TARGET_NAME} STATIC ${GSL_SOURCES}) --target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES}) -+# Use external GSL instead -+#set(TARGET_NAME gsl) -+#file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c) -+#set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg) -+#add_library(${TARGET_NAME} STATIC ${GSL_SOURCES}) -+#target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES}) - - # ZLIB --set(TARGET_NAME eidos_zlib) --file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c) --set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib) --add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES}) --target_include_directories(${TARGET_NAME} PUBLIC) -+# Use external Zlib instead -+#set(TARGET_NAME eidos_zlib) -+#file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c) -+#set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib) -+#add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES}) -+#target_include_directories(${TARGET_NAME} PUBLIC) - - # KASTORE - set(TARGET_NAME kastore) -@@ -198,7 +200,7 @@ list(APPEND SLIM_SOURCES "${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp" ${PROJECT_SOU - - add_executable(${TARGET_NAME} ${SLIM_SOURCES}) - target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/eidos") --target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables) -+target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables) - if(WIN32) - set_source_files_properties(${SLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") - set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") -@@ -211,7 +213,7 @@ set(TARGET_NAME eidos) - file(GLOB_RECURSE EIDOS_SOURCES ${PROJECT_SOURCE_DIR}/eidos/*.cpp ${PROJECT_SOURCE_DIR}/eidostool/*.cpp) - add_executable(${TARGET_NAME} ${EIDOS_SOURCES}) - target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/eidos") --target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables) -+target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables) - if(WIN32) - set_source_files_properties(${EIDOS_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") - set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") -@@ -244,15 +246,15 @@ set_target_properties( ${TARGET_NAME} PROPERTIES LINKER_LANGUAGE CXX) - target_compile_definitions( ${TARGET_NAME} PRIVATE EIDOSGUI=1 SLIMGUI=1) - target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/QtSLiM" "${PROJECT_SOURCE_DIR}/eidos" "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/treerec" "${PROJECT_SOURCE_DIR}/treerec/tskit/kastore") - if(APPLE) -- target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib /usr/lib/libobjc.A.dylib ) -+ target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z /usr/lib/libobjc.A.dylib ) - else() - if(WIN32) - set_source_files_properties(${QTSLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") - set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos SLiMgui PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") - target_include_directories(${TARGET_NAME} BEFORE PUBLIC ${GNU_DIR}) -- target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib gnu ) -+ target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z gnu ) - else() -- target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib ) -+ target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z ) - endif() - endif() - install(TARGETS ${TARGET_NAME} DESTINATION bin) -diff --git a/eidos/eidos_functions.cpp b/eidos/eidos_functions.cpp -index 4f52c763..ac9de199 100644 ---- a/eidos/eidos_functions.cpp -+++ b/eidos/eidos_functions.cpp -@@ -55,11 +55,11 @@ - - #include "string.h" - --#include "gsl_linalg.h" --#include "gsl_errno.h" --#include "gsl_cdf.h" -+#include -+#include -+#include - --#include "../eidos_zlib/zlib.h" -+#include - - #include "eidos_globals.h" - #if EIDOS_ROBIN_HOOD_HASHING -@@ -11475,7 +11475,7 @@ EidosValue_SP Eidos_ExecuteFunction_writeTempFile(const std::vector - - // for Eidos_calc_sha_256() - #include - - // for _Eidos_FlushZipBuffer() --#include "../eidos_zlib/zlib.h" -+#include - - // for Eidos_ColorPaletteLookup() - #include "eidos_tinycolormap.h" -@@ -1570,7 +1570,7 @@ bool _Eidos_FlushZipBuffer(const std::string &file_path, const std::string &outs - { - //std::cout << "_Eidos_FlushZipBuffer() called for " << file_path << std::endl; - -- gzFile gzf = z_gzopen(file_path.c_str(), "ab"); -+ gzFile gzf = gzopen(file_path.c_str(), "ab"); - - if (!gzf) - return false; -@@ -1678,7 +1678,7 @@ void Eidos_WriteToFile(const std::string &p_file_path, std::vector -+#include - - #include - #include From 4d9c00a0af0c524be471111001d4de8025027095 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 18 Apr 2023 22:09:02 +0100 Subject: [PATCH 7214/9987] Missing sanity_pip_check added, style corrected --- easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb index 0fcb809500a..c3e66f3e3cd 100644 --- a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb @@ -14,6 +14,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_list = [ ('xattr', '0.10.1', { @@ -53,7 +54,7 @@ exts_list = [ }), ('websocket_client', '1.5.1', { 'modulename': 'websocket', - 'sources': 'websocket-client-%(version)s.tar.gz', + 'sources': ['websocket-client-%(version)s.tar.gz'], 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], }), ('pycparser', '2.21', { From 8c6dac0ebc9e9b9ed275d6867cf7dc9d4e00f2bd Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 19 Apr 2023 14:45:32 +0100 Subject: [PATCH 7215/9987] adding easyconfigs: FUSE-3.14.1-foss-2022b.eb --- .../f/FUSE/FUSE-3.14.1-foss-2022b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb new file mode 100644 index 00000000000..54ea701e95e --- /dev/null +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb @@ -0,0 +1,29 @@ +easyblock = 'MesonNinja' + +name = 'FUSE' +version = '3.14.1' + +homepage = 'https://github.com/libfuse/libfuse' +description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/libfuse/libfuse/releases/download/fuse-%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20'] + +builddependencies = [ + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] + +# -Dutils=True only works as root +configopts = '-Dutils=False' + +sanity_check_paths = { + 'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT, + 'lib64/pkgconfig/fuse%(version_major)s.pc'], + 'dirs': ['include/fuse%(version_major)s'], +} + +moduleclass = 'lib' From 213cb0ba7beb248426b29ec928dccec4e42a716d Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 19 Apr 2023 16:49:44 +0200 Subject: [PATCH 7216/9987] adding easyconfigs: GCC-13.0.1.eb, GCCcore-13.0.1.eb, binutils-2.40.eb, binutils-2.40-GCCcore-13.0.1.eb, Bison-3.8.2-GCCcore-13.0.1.eb, flex-2.6.4-GCCcore-13.0.1.eb, help2man-1.49.3-GCCcore-13.0.1.eb, M4-1.4.19-GCCcore-13.0.1.eb, zlib-1.2.13.eb, zlib-1.2.13-GCCcore-13.0.1.eb --- .../b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb | 28 ++++++++ .../binutils/binutils-2.40-GCCcore-13.0.1.eb | 31 +++++++++ .../easyconfigs/b/binutils/binutils-2.40.eb | 26 +++++++ .../f/flex/flex-2.6.4-GCCcore-13.0.1.eb | 34 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb | 22 ++++++ .../easyconfigs/g/GCCcore/GCCcore-13.0.1.eb | 67 +++++++++++++++++++ .../help2man-1.49.3-GCCcore-13.0.1.eb | 25 +++++++ .../m/M4/M4-1.4.19-GCCcore-13.0.1.eb | 29 ++++++++ .../z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb | 30 +++++++++ easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb | 32 +++++++++ 10 files changed, 324 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.40.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb new file mode 100644 index 00000000000..45f87974dc5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '13.0.1'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.39', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb new file mode 100644 index 00000000000..36234b61ea1 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.40' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '13.0.1'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d7f82c4047decf43a6f769ac32456a92ddb6932409a585c633cdd4e9df23d956'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', SYSTEM) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.13'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40.eb new file mode 100644 index 00000000000..a04b02ae921 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.40.eb @@ -0,0 +1,26 @@ +name = 'binutils' +version = '2.40' + +homepage = 'https://directory.fsf.org/project/binutils/' + +description = "binutils: GNU binary utilities" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d7f82c4047decf43a6f769ac32456a92ddb6932409a585c633cdd4e9df23d956'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.13'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb new file mode 100644 index 00000000000..e4b6d071111 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.0.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.39', '', SYSTEM), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb b/easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb new file mode 100644 index 00000000000..b9c224ad66e --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '13.0.1' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.40', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb new file mode 100644 index 00000000000..0b8d30d3782 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb @@ -0,0 +1,67 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '13.0.1' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + { + 'source_urls': ['https://gcc.gnu.org/pub/gcc/snapshots/13.1.0-RC2-20230419/'], + 'filename': 'gcc-13.1.0-RC2-20230419.tar.gz', + }, + # 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.1.0.tar.bz2', + 'mpc-1.2.1.tar.gz', + 'isl-0.24.tar.bz2', + 'newlib-4.1.0.tar.gz', + {'download_filename': '93e0090.tar.gz', 'filename': 'nvptx-tools-20230122.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + {'gcc-13.1.0-RC2-20230419.tar.gz': '31188ab89af2b52fc5e3a2ef77c52d4b762e18320b3d741fa947e3d0dd306134'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.40'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb new file mode 100644 index 00000000000..92adccec4f1 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '13.0.1'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.40', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb new file mode 100644 index 00000000000..6a458ba47b3 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '13.0.1'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.39', '', SYSTEM)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb new file mode 100644 index 00000000000..32d9c8ca56c --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.13' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.0.1'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = [ + 'b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30', # zlib-1.2.12.tar.gz + # 'f35eb05334a4f8d7b40b6c5610a6369f654863b5fa1a19c2507888f918025238', # zlib-1.2.12_fix-CC-logic-in-configure.patch +] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.40', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb new file mode 100644 index 00000000000..397dbe63b57 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.13' + +homepage = 'https://www.zlib.net/' + +description = """ + zlib is designed to be a free, general-purpose, legally unencumbered -- that + is, not covered by any patents -- lossless data-compression library for use + on virtually any computer hardware and operating system. +""" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30'] + +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid +# compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', + 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 57b4586f94402bbc4bb400a26aba12417c5c013d Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 19 Apr 2023 16:12:59 +0100 Subject: [PATCH 7217/9987] Toolchain bumped to foss-2022b to deal with hatchling dependencies --- ...ss-2022a.eb => dxpy-0.345.0-foss-2022b.eb} | 32 +++++++++++-------- 1 file changed, 18 insertions(+), 14 deletions(-) rename easybuild/easyconfigs/d/dxpy/{dxpy-0.345.0-foss-2022a.eb => dxpy-0.345.0-foss-2022b.eb} (70%) diff --git a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022b.eb similarity index 70% rename from easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb rename to easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022b.eb index c3e66f3e3cd..e689c573156 100644 --- a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022b.eb @@ -1,3 +1,6 @@ +# Updated to latest version +# Author: J. Sassmannshausen (Imperial College London/UK) + easyblock = 'PythonBundle' name = 'dxpy' @@ -6,10 +9,10 @@ version = '0.345.0' homepage = 'http://autodoc.dnanexus.com/' description = "DNAnexus Platform API bindings for Python" -toolchain = {'name': 'foss', 'version': '2022a'} +toolchain = {'name': 'foss', 'version': '2022b'} dependencies = [ - ('Python', '3.10.4'), + ('Python', '3.10.8'), ('FUSE', '3.14.1'), ] @@ -17,6 +20,9 @@ use_pip = True sanity_pip_check = True exts_list = [ + ('argcomplete', '3.0.5', { + 'checksums': ['fe3ce77125f434a0dd1bffe5f4643e64126d5731ce8d173d36f62fa43d6eb6f7'], + }), ('xattr', '0.10.1', { 'checksums': ['c12e7d81ffaa0605b3ac8c22c2994a8e18a9cf1c59287a1b7722a2289c952ec5'], }), @@ -34,15 +40,8 @@ exts_list = [ ('psutil', '5.9.5', { 'checksums': ['5410638e4df39c54d957fc51ce03048acd8e6d60abc0f5107af51e5fb566eb3c'], }), - ('trove-classifiers', '2023.4.18', { - 'checksums': ['9f892a83ccbdf9e669861a947c6b03d5b91a87f449aefef1d76fc4169f78ddba'], - }), - # The Python pathspec is too old for hatchling, version >= 0.10.0 is required - ('pathspec', '0.11.1', { - 'checksums': ['2798de800fa92780e33acca925945e9a19a133b715067cf165b8866c15a31687'], - }), - ('hatchling', '1.14.0', { - 'checksums': ['462ea91df03ff5d52813b5613fec1313a1a2059d2e37343e572b3f979867c5da'], + ('soupsieve', '2.4.1', { + 'checksums': ['89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea'], }), ('beautifulsoup4', '4.12.2', { 'modulename': 'bs4', @@ -52,10 +51,9 @@ exts_list = [ 'modulename': 'magic', 'checksums': ['c1ba14b08e4a5f5c31a302b7721239695b2f0f058d125bd5ce1ee36b9d9d3c3b'], }), - ('websocket_client', '1.5.1', { + ('websocket_client', '0.54.0', { 'modulename': 'websocket', - 'sources': ['websocket-client-%(version)s.tar.gz'], - 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + 'checksums': ['e51562c91ddb8148e791f0155fdb01325d99bb52c4cdbb291aee7a3563fd0849'], }), ('pycparser', '2.21', { 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], @@ -63,6 +61,12 @@ exts_list = [ ('cffi', '1.15.1', { 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], }), + ('charset-normalizer', '2.0.12', { + 'checksums': ['2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597'], + }), + ('requests', '2.27.1', { + 'checksums': ['68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61'], + }), (name, version, { 'checksums': ['cf5b47e83866a9c87a4fc59262eac500e860f6a890e6a897a577eff68e28cff2'], }), From d50486411c5bda609b36e944587ea4058e90343d Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 19 Apr 2023 17:40:21 +0100 Subject: [PATCH 7218/9987] Demoted to GCCcore --- ...{FUSE-3.14.1-foss-2022b.eb => FUSE-3.14.1-GCCcore-12.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/f/FUSE/{FUSE-3.14.1-foss-2022b.eb => FUSE-3.14.1-GCCcore-12.2.0.eb} (93%) diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb similarity index 93% rename from easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb rename to easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb index 54ea701e95e..a71b0002a5c 100644 --- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022b.eb +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb @@ -6,7 +6,7 @@ version = '3.14.1' homepage = 'https://github.com/libfuse/libfuse' description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface" -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://github.com/libfuse/libfuse/releases/download/fuse-%(version)s/'] sources = [SOURCELOWER_TAR_XZ] From c98853bc01ae507eecf03939a74a4cd968808409 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Wed, 19 Apr 2023 20:09:04 +0100 Subject: [PATCH 7219/9987] Update FUSE-3.14.1-GCCcore-12.2.0.eb Binutils added --- easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb index a71b0002a5c..1be42749206 100644 --- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb @@ -15,6 +15,7 @@ checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20'] builddependencies = [ ('Meson', '0.64.0'), ('Ninja', '1.11.1'), + ('binutils', '2.39') ] # -Dutils=True only works as root From 32183c4fcf8090d6a762e4e2c4f64df53fc5cd09 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 19 Apr 2023 21:14:05 +0100 Subject: [PATCH 7220/9987] Demoted from foss to GCCcore, as done in PR #17759 --- ...FUSE-3.14.1-foss-2022a.eb => FUSE-3.14.1-GCCcore-11.3.0.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/f/FUSE/{FUSE-3.14.1-foss-2022a.eb => FUSE-3.14.1-GCCcore-11.3.0.eb} (90%) diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb similarity index 90% rename from easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb rename to easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb index 8f0af720ccd..e917f49a009 100644 --- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-foss-2022a.eb +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb @@ -6,7 +6,7 @@ version = '3.14.1' homepage = 'https://github.com/libfuse/libfuse' description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface" -toolchain = {'name': 'foss', 'version': '2022a'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/libfuse/libfuse/releases/download/fuse-%(version)s/'] sources = [SOURCELOWER_TAR_XZ] @@ -15,6 +15,7 @@ checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20'] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), + ('binutils','2.38'), ] # -Dutils=True only works as root From bf6ea38cb1f914021e7bede65b05ddec0a6da6c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Wed, 19 Apr 2023 22:02:10 +0100 Subject: [PATCH 7221/9987] Whitespace corrected --- easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb index e917f49a009..856159422b1 100644 --- a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb @@ -15,7 +15,7 @@ checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20'] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), - ('binutils','2.38'), + ('binutils', '2.38'), ] # -Dutils=True only works as root From 88a819d1d5696443caffd6f1f158a3a9f4fd49d8 Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Thu, 20 Apr 2023 18:50:46 +0800 Subject: [PATCH 7222/9987] add pcre dependency for interproscan --- .../i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb index d4535511479..aa12f6d8bf5 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb @@ -27,6 +27,7 @@ dependencies = [ ('Perl', '5.32.1'), ('libgd', '2.3.1'), ('Python', '3.9.5'), + ('PCRE', '8.44'), ] # NOTE some analyses done by InterProScan require extra tools not included in the interproscan # distribution because of license issues. From 5f6a9eb9ccf4ab32dcdb28324b406c1a19ce37e3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 20 Apr 2023 15:13:28 +0200 Subject: [PATCH 7223/9987] Fix source urls so that incorrect sources aren't downloaded --- .../QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb | 10 +++++----- .../QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb index 6ec9f2f0d9d..fa5e68e2a05 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb @@ -11,20 +11,20 @@ It is based on density-functional theory, plane waves, and pseudopotentials toolchain = {'name': 'foss', 'version': '2022b'} toolchainopts = {'usempi': True, 'openmp': True} -source_urls = [ - 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', -] sources = [ { 'filename': 'q-e-qe-%(version)s.tar.gz', 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'], }, { 'filename': 'qe-gipaw-%(version)s.tar.gz', 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/'] }, - {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', - 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, + { + 'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'] + }, ] checksums = [ {'q-e-qe-7.2.tar.gz': 'b348a4a7348b66a73545d9ca317a2645755c98d343c1cfe8def475ad030808c0'}, diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb index 5fbb08073cd..0039b43162f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb @@ -11,20 +11,20 @@ It is based on density-functional theory, plane waves, and pseudopotentials toolchain = {'name': 'intel', 'version': '2022b'} toolchainopts = {'usempi': True, 'openmp': True} -source_urls = [ - 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', -] sources = [ { 'filename': 'q-e-qe-%(version)s.tar.gz', 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'], }, { 'filename': 'qe-gipaw-%(version)s.tar.gz', 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/'] }, - {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', - 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, + { + 'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'] + }, ] checksums = [ {'q-e-qe-7.2.tar.gz': 'b348a4a7348b66a73545d9ca317a2645755c98d343c1cfe8def475ad030808c0'}, From 30d858247cfbd826f70617a5e84e01545636d67c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Apr 2023 15:57:15 +0200 Subject: [PATCH 7224/9987] correct the python building of DGL, requires static libs --- .../easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb index 9aa9bdcd151..71615bf8576 100644 --- a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb @@ -103,7 +103,10 @@ _copts = [ ] configopts = ' '.join(_copts) -build_shared_libs = True +# Must not build shared libs, DGL uses internal versions of, among others, METIS +# but it doesn't install these internal libraries and simply assumes that everything is +# statically linked. +build_shared_libs = False runtest = 'test' @@ -118,10 +121,9 @@ exts_default_options = { exts_list = [ ('dgl', version, { - 'modulename': False, 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', 'start_dir': 'python', - 'use_pip': False, + 'installopts': '--use-feature=in-tree-build ', 'checksums': ['8d26ebb7ed976665bbf5bbd1792d8e6efb13a8fa16e5eb1efed75e07fb982e04'], }), ] From d7773dfecde0650884d84ed38deeb63a0a3b8cbc Mon Sep 17 00:00:00 2001 From: "A.H. Kole" Date: Thu, 20 Apr 2023 16:17:57 +0200 Subject: [PATCH 7225/9987] adding easyconfigs: xmlf90-1.5.6-GCC-11.3.0.eb --- .../x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb new file mode 100644 index 00000000000..8ec08d98951 --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'xmlf90' +version = '1.5.6' + +homepage = 'https://gitlab.com/siesta-project/libraries/xmlf90' +description = """A fast XML parser and generator in Fortran""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/xmlf90/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c4492596c911b668b94fee40a53453f06aef3bc41014b9e2f4b51e640ad20528'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libxmlf90.a'], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/xmlf90'], +} + +runtest = 'test' + +moduleclass = 'data' From 641a99f6111a378a5417db192dc32601f9c24c42 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 20 Apr 2023 16:59:14 +0200 Subject: [PATCH 7226/9987] Only use QE gitlab source url for QE itself --- .../QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb | 10 +++++----- .../QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb index 9257514652d..87066c6ae6d 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb @@ -11,20 +11,20 @@ It is based on density-functional theory, plane waves, and pseudopotentials toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'usempi': True, 'openmp': True} -source_urls = [ - 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', -] sources = [ { 'filename': 'q-e-qe-%(version)s.tar.gz', 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'], }, { 'filename': 'qe-gipaw-%(version)s.tar.gz', 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/'] }, - {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', - 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, + { + 'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'] + }, ] checksums = [ 'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6', # q-e-qe-7.1.tar.gz diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb index e9f90039005..a81be226c25 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb @@ -11,20 +11,20 @@ It is based on density-functional theory, plane waves, and pseudopotentials toolchain = {'name': 'intel', 'version': '2022a'} toolchainopts = {'usempi': True, 'openmp': True} -source_urls = [ - 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', -] sources = [ { 'filename': 'q-e-qe-%(version)s.tar.gz', 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'], }, { 'filename': 'qe-gipaw-%(version)s.tar.gz', 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/'] }, - {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', - 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, + { + 'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'] + }, ] checksums = [ 'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6', # q-e-qe-7.1.tar.gz From bbd111dbc103b6000641acd774e60835778f5dec Mon Sep 17 00:00:00 2001 From: "A.H. Kole" Date: Thu, 20 Apr 2023 17:01:40 +0200 Subject: [PATCH 7227/9987] adding easyconfigs: libPSML-1.1.12-GCC-11.3.0.eb --- .../l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb new file mode 100644 index 00000000000..6dba042d193 --- /dev/null +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libPSML' +version = '1.1.12' + +homepage = 'https://gitlab.com/siesta-project/libraries/libpsml' +description = """A library to handle pseudopotentials in PSML format""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libpsml/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c61503d5a5de119f970f1bf27aa0ac8059b87e81d1a8013bef1bb7993df44c56'] + +dependencies = [ + ('xmlf90', '1.5.6'), +] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libpsml.a'], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libpsml'], +} + +runtest = 'test' + +moduleclass = 'data' From 562e6b2fd247e5ad8aef0ff6ec15cbf1c8fbc7d7 Mon Sep 17 00:00:00 2001 From: "A.H. Kole" Date: Thu, 20 Apr 2023 17:40:06 +0200 Subject: [PATCH 7228/9987] adding easyconfigs: libGridXC-1.1.0-gompi-2022a.eb --- .../libGridXC/libGridXC-1.1.0-gompi-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb new file mode 100644 index 00000000000..e44041efa6c --- /dev/null +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'libGridXC' +version = '1.1.0' + +homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' +description = """A library to compute the exchange and correlation energy + and potential in spherical (i.e. atoms) or periodic systems.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e7883e57a4db2438ee59437740291c06e0cfe1c8ae1901e4001f32312307e46a'] + +configopts = "-DWITH_MPI=ON -DWITH_LIBXC=ON" + +dependencies = [('libxc', '5.2.3')] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libgridxc.a'], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libgridxc'], +} + +runtest = 'test' + +moduleclass = 'phys' From ab83b6fbfda8d338033c28d39e97419fcb7ed23a Mon Sep 17 00:00:00 2001 From: Arnold Kole <35299166+ahkole@users.noreply.github.com> Date: Thu, 20 Apr 2023 21:15:30 +0200 Subject: [PATCH 7229/9987] Remove explicit setting of default option MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb index 8ec08d98951..262cfb87e36 100644 --- a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb @@ -16,8 +16,6 @@ builddependencies = [ ('CMake', '3.23.1'), ] -separate_build_dir = True - sanity_check_paths = { 'files': ['lib/libxmlf90.a'], 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/xmlf90'], From 357a14ec8805990e2494a755c5cd4d0adad3babd Mon Sep 17 00:00:00 2001 From: Arnold Kole <35299166+ahkole@users.noreply.github.com> Date: Thu, 20 Apr 2023 21:16:28 +0200 Subject: [PATCH 7230/9987] Remove explicit setting of default option MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb index e44041efa6c..1b2f864e5f2 100644 --- a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb @@ -22,8 +22,6 @@ builddependencies = [ ('CMake', '3.23.1'), ] -separate_build_dir = True - sanity_check_paths = { 'files': ['lib/libgridxc.a'], 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libgridxc'], From 916e30e2c51aabb143d66075bd865b80b0292ec8 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 20 Apr 2023 15:50:28 -0400 Subject: [PATCH 7231/9987] adding easyconfigs: BWA-0.7.17-GCCcore-12.2.0.eb --- .../b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ec08bbe74b1 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' + +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Perl', '5.36.0'), + ('zlib', '1.2.12'), +] + +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " + +moduleclass = 'bio' From 5f3a339458779b17acae12408219e79587c34141 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 20 Apr 2023 15:54:41 -0400 Subject: [PATCH 7232/9987] adding easyconfigs: picard-3.0.0-Java-17.eb --- .../p/picard/picard-3.0.0-Java-17.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb diff --git a/easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb b/easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb new file mode 100644 index 00000000000..b9cd29fae76 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb @@ -0,0 +1,60 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.10.1: +# Adam Huffman +# The Francis Crick Institute +# 2.18.11: +# Jonas Demeulemeester +# The Francis Crick Institute +# 2.21.1 +# Pavel Grochal (INUITS) +# 2.25.1 +# J. Sassmannshausen (GSTT) +# 2.25.5 +# Erica Bianco (HPCNow!) +# 2.26.10 +# Christoph Siegert (Leipzig University) +# 3.0.0 +# Graham Derryberry (UTK) +## + +easyblock = 'JAR' + +name = 'picard' +version = '3.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = [{ + 'filename': '%(name)s-%(version)s.jar', + 'download_filename': '%(name)s.jar', +}] +checksums = ['0d5e28ab301fad3b02030d01923888129ba82c5f722ac5ccb2d418ab76ac5499'] + +postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] + +dependencies = [('Java', '17')] + +sanity_check_commands = ['java -jar $EBROOTPICARD/picard.jar 2>&1 | grep USAGE'] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' From 41df7683c2463dd409555cb966b31ca132af7b1e Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 20 Apr 2023 15:59:22 -0400 Subject: [PATCH 7233/9987] adding easyconfigs: BEDTools-2.30.0-GCC-12.2.0.eb, BamTools-2.5.2-GCC-12.2.0.eb --- .../b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb | 45 +++++++++++++++++++ .../b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb | 19 ++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..e85979fa033 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb @@ -0,0 +1,45 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.30.0' + +homepage = "https://bedtools.readthedocs.io/" +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8'] + +builddependencies = [('Python', '3.10.8')] + +dependencies = [ + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +sanity_check_commands = ['bedtools --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb new file mode 100644 index 00000000000..324af5c529f --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb @@ -0,0 +1,19 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +name = 'BamTools' +version = '2.5.2' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8'] + +builddependencies = [('CMake', '3.24.3')] + +moduleclass = 'bio' From 91b2f308a868a53f24f6fa2576ac588121b7abfa Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 20 Apr 2023 16:10:20 -0400 Subject: [PATCH 7234/9987] adding easyconfigs: VCFtools-0.1.16-GCC-12.2.0.eb --- .../v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb new file mode 100644 index 00000000000..0ff539325ea --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +builddependencies = [ + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('Perl', '5.36.0'), + ('HTSlib', '1.17'), + ('zlib', '1.2.12'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' From 419dd75458e298d013b5f5e34a44fe27fdeff718 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 20 Apr 2023 17:10:57 -0400 Subject: [PATCH 7235/9987] adding easyconfigs: Trimmomatic-0.39-Java-17.eb --- .../t/Trimmomatic/Trimmomatic-0.39-Java-17.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb new file mode 100644 index 00000000000..5f9d39b5c69 --- /dev/null +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'Tarball' + +name = 'Trimmomatic' +version = '0.39' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.usadellab.org/cms/?page=trimmomatic' +description = """Trimmomatic performs a variety of useful trimming tasks for illumina + paired-end and single ended data.The selection of trimming steps and their associated + parameters are supplied on the command line. """ + +toolchain = SYSTEM + +source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/'] +sources = [SOURCE_ZIP] +checksums = ['2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca'] + +dependencies = [('Java', '17')] + +modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar\n""" + +sanity_check_paths = { + 'files': ["trimmomatic-%(version)s.jar"], + 'dirs': [""], +} + +moduleclass = 'bio' From 745949002f31740ed546b2d586f1d6d0a8f9f4fb Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 20 Apr 2023 23:36:31 +0200 Subject: [PATCH 7236/9987] adding easyconfigs: AlphaPulldown-0.30.4-foss-2020b.eb, cctbx-base-2022.8-foss-2020b.eb, Kalign-2.0.4-GCCcore-11.2.0.eb and patches: AlphaPulldown-0.30.4_fix-deps.patch --- .../AlphaPulldown-0.30.4-foss-2020b.eb | 93 +++++++++++++++++++ .../AlphaPulldown-0.30.4_fix-deps.patch | 34 +++++++ .../cctbx-base-2022.8-foss-2020b.eb | 74 +++++++++++++++ .../k/Kalign/Kalign-2.0.4-GCCcore-11.2.0.eb | 28 ++++++ 4 files changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch create mode 100644 easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb create mode 100644 easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb new file mode 100644 index 00000000000..e0c1549fb9e --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -0,0 +1,93 @@ +# created by Denis Kristak (Inuits) +easyblock = "PythonBundle" + +name = "AlphaPulldown" +version = "0.30.4" + +homepage = "https://github.com/KosinskiLab/AlphaPulldown" +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '3.7.2'), +] + +dependencies = [ + ('Python', '3.8.6'), + ("OpenMM", "7.5.0"), + ("Kalign", "3.3.1"), + ('PyYAML', '5.3.1'), + ("cctbx-base", "2022.8"), + ('jax', '0.2.19'), # also provides absl-py + ('Biopython', '1.78'), + ('h5py', '3.1.0'), + ('IPython', '7.18.1'), + ('JupyterLab', '2.2.8'), + ('matplotlib', '3.3.3'), + ('TensorFlow', '2.4.1'), + ('tqdm', '4.56.2'), +] + +use_pip = True + +exts_list = [ + ('py3Dmol', '2.0.1.post1', { + 'modulename': 'py3Dmol', + 'checksums': ['add70ecf8f647970925eb8c1043c5c1343813fa49e613b77f0628e522c4148ac'], + }), + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('dm-tree', '0.1.6', { + 'modulename': 'tree', + 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], + }), + ('importlib-resources', '5.12.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('tabulate', '0.8.9', { + 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_fix-deps.patch'], + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': [ + {'alphapulldown-0.30.4.tar.gz': '7797500abaee2e92d28034dc97844bca8c8d7281817e29dc110220824e9d1b5b'}, + {'AlphaPulldown-0.30.4_fix-deps.patch': 'c31cd3fcb6688f77a9277ccb779e54bb862c84e1cac485b03a9f00d10eb9ffe6'}, + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + "files": ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + "dirs": ["lib/python%(pyshortver)s/site-packages/alphapulldown"], +} + +sanity_check_commands = [('python -c "import alphapulldown"')] + +moduleclass = "data" diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch new file mode 100644 index 00000000000..adcad416081 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch @@ -0,0 +1,34 @@ +# making AlphaPulldown's dependencies less strict +diff -ruN alphapulldown-0.30.4_orig/setup.cfg alphapulldown-0.30.4/setup.cfg +--- alphapulldown-0.30.4_orig/setup.cfg 2023-04-05 13:59:25.000000000 +0100 ++++ alphapulldown-0.30.4/setup.cfg 2023-04-06 14:10:45.424577468 +0100 +@@ -17,19 +17,19 @@ + include_package_data = True + python_requires = ==3.8.* + install_requires = +- absl-py >= 0.13.0 +- dm-haiku==0.0.9 ++ absl-py >= 0.10.0 ++ dm-haiku==0.0.4 + dm-tree==0.1.6 +- h5py==3.1.0 ++ h5py==2.10.0 + matplotlib==3.3.3 +- ml-collections==0.1.0 +- numpy==1.21.6 +- pandas==1.3.4 +- tensorflow==2.9.0 +- importlib-resources==5.8.0 ++ ml-collections==0.1.1 ++ numpy==1.19.4 ++ pandas==1.1.4 ++ tensorflow==2.4.1 ++ importlib-resources==5.12.0 + biopython==1.78 +- nbformat==5.4.0 +- py3Dmol==2.0.1 ++ nbformat==5.0.7 ++ py3Dmol==2.0.1.post1 + ipython + tqdm + appdirs diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb new file mode 100644 index 00000000000..acb8e7ba159 --- /dev/null +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb @@ -0,0 +1,74 @@ +# author: Denis Kristak (Inuits) +easyblock = "PythonBundle" + +name = "cctbx-base" +version = "2022.8" + +homepage = "https://github.com/cctbx/cctbx_project" +description = """ +The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix +project. The goal of the Phenix project is to advance automation of macromolecular structure determination. +Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable +library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific +applications. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Boost', '1.74.0'), + ('HDF5', '1.10.7'), + ('libGLU', '9.0.1'), + ('LIBSVM', '3.25'), + ('LibTIFF', '4.1.0'), + ('matplotlib', '3.3.3'), + ('mrcfile', '1.3.0'), +] + +local_metadata_folder = "%(installdir)s/lib/python3.8/site-packages/cctbx_base-2020.8.dist-info/METADATA" + +local_metadata_content = """ +Metadata-Version: 2.1 +Name: cctbx_base +Version: 2020.8 +License: BSD-3-Clause-LBNL AND BSD-3-Clause AND BSL-1.0 AND LGPL-2.0-only AND LGPL-2.1-only AND LGPL-3.0-only AND MIT AND LGPL-2.0-or-later WITH WxWindows-exception-3.1 +Summary: The Computational Crystallography Toolbox +Home-page: https://github.com/cctbx/cctbx_project +Project-URL: Documentation, https://cctbx.github.io/ +Project-URL: Development, https://github.com/cctbx/cctbx_project + +The Computational Crystallography Toolbox (cctbx) is being developed +as the open source component of the Phenix system. The goal of the +Phenix project is to advance automation of macromolecular structure +determination. Phenix depends on the cctbx, but not vice versa. This +hierarchical approach enforces a clean design as a reusable library. +The cctbx is therefore also useful for small-molecule crystallography +and even general scientific applications. +""" + +exts_list = [ + ('reportlab', '3.5.66', { + 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], + }), + (name, version, { + 'modulename': 'cctbx', + # remove deps (they fail during sanity check, even though they are installed) + 'postinstallcmds': ["echo '' > %(installdir)s/lib/python3.8/site-packages/cctbx_base-2020.8.dist-info/METADATA"], + 'sources': [{'download_filename': 'cctbx_base-2020.8-0_py38h167b89d-cp38-cp38m-manylinux2010_x86_64.whl', 'filename': 'cctbx_base-2020.8-cp38-cp38-manylinux2010_x86_64.whl'}], + 'checksums': ['5c7ac0710d9011072c678771876aa57ca3735986ed321d403f51989a7444e592'], + }), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + "files": ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], + "dirs": ['lib/python3.8/site-packages/cctbx_website'], +} + +sanity_check_commands = [('python -c "import cctbx"')] + +moduleclass = "lib" diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..53da691c60e --- /dev/null +++ b/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-11.2.0.eb @@ -0,0 +1,28 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# updated by Denis Kristak (Inuits) + +easyblock = "ConfigureMake" + +name = "Kalign" +version = "2.0.4" + +homepage = "https://msa.sbc.su.se/cgi-bin/msa.cgi" +description = ( + "Kalign is a fast multiple sequence alignment program for biological sequences." +) + +toolchain = {"name": "GCCcore", "version": "11.2.0"} + +source_urls = ["http://msa.sbc.su.se/downloads/kalign/"] +sources = [{"filename": SOURCELOWER_TAR_GZ, "download_filename": "current.tar.gz"}] +checksums = ['8cf20ac4e1807dc642e7ffba8f42a117313beccaee4f87c5555d53a2eeac4cbb'] + +install_cmd = "mkdir %(installdir)s/bin && cp kalign %(installdir)s/bin" + +sanity_check_paths = { + "files": ["bin/kalign"], + "dirs": [], +} + +moduleclass = "bio" From afed07fbda53155b087899b35a1446f21edda585 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 21 Apr 2023 00:01:36 +0200 Subject: [PATCH 7237/9987] code style checks --- .../cctbx-base-2022.8-foss-2020b.eb | 25 +++---------------- 1 file changed, 4 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb index acb8e7ba159..dc2fd189965 100644 --- a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb @@ -28,25 +28,6 @@ dependencies = [ local_metadata_folder = "%(installdir)s/lib/python3.8/site-packages/cctbx_base-2020.8.dist-info/METADATA" -local_metadata_content = """ -Metadata-Version: 2.1 -Name: cctbx_base -Version: 2020.8 -License: BSD-3-Clause-LBNL AND BSD-3-Clause AND BSL-1.0 AND LGPL-2.0-only AND LGPL-2.1-only AND LGPL-3.0-only AND MIT AND LGPL-2.0-or-later WITH WxWindows-exception-3.1 -Summary: The Computational Crystallography Toolbox -Home-page: https://github.com/cctbx/cctbx_project -Project-URL: Documentation, https://cctbx.github.io/ -Project-URL: Development, https://github.com/cctbx/cctbx_project - -The Computational Crystallography Toolbox (cctbx) is being developed -as the open source component of the Phenix system. The goal of the -Phenix project is to advance automation of macromolecular structure -determination. Phenix depends on the cctbx, but not vice versa. This -hierarchical approach enforces a clean design as a reusable library. -The cctbx is therefore also useful for small-molecule crystallography -and even general scientific applications. -""" - exts_list = [ ('reportlab', '3.5.66', { 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], @@ -55,13 +36,15 @@ exts_list = [ 'modulename': 'cctbx', # remove deps (they fail during sanity check, even though they are installed) 'postinstallcmds': ["echo '' > %(installdir)s/lib/python3.8/site-packages/cctbx_base-2020.8.dist-info/METADATA"], - 'sources': [{'download_filename': 'cctbx_base-2020.8-0_py38h167b89d-cp38-cp38m-manylinux2010_x86_64.whl', 'filename': 'cctbx_base-2020.8-cp38-cp38-manylinux2010_x86_64.whl'}], + 'sources': [{ + 'download_filename': 'cctbx_base-2020.8-0_py38h167b89d-cp38-cp38m-manylinux2010_x86_64.whl', + 'filename': 'cctbx_base-2020.8-cp38-cp38-manylinux2010_x86_64.whl' + }], 'checksums': ['5c7ac0710d9011072c678771876aa57ca3735986ed321d403f51989a7444e592'], }), ] use_pip = True -download_dep_fail = True sanity_pip_check = True sanity_check_paths = { From 93b611fb04dc319f31a1bb9e483a0d62ee9fe6ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 21 Apr 2023 00:18:53 +0200 Subject: [PATCH 7238/9987] Version bump Java to latest builds that include ppc --- easybuild/easyconfigs/j/Java/Java-11.0.18.eb | 30 +++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-11.eb | 2 +- easybuild/easyconfigs/j/Java/Java-17.0.6.eb | 30 +++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-17.eb | 2 +- easybuild/easyconfigs/j/Java/Java-8.362.eb | 31 ++++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-8.eb | 2 +- 6 files changed, 94 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/j/Java/Java-11.0.18.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-17.0.6.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-8.362.eb diff --git a/easybuild/easyconfigs/j/Java/Java-11.0.18.eb b/easybuild/easyconfigs/j/Java/Java-11.0.18.eb new file mode 100644 index 00000000000..c41c7c582f9 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-11.0.18.eb @@ -0,0 +1,30 @@ +name = 'Java' +version = '11.0.18' +local_build = '10' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + '4a29efda1d702b8ff38e554cf932051f40ec70006caed5c4857a8cbc7a0b7db7', + local_tarball_tmpl % ('aarch64', local_build): + '04d5eeff6a6449bcdca0f52cd97bafd43ce09d40ef1e73fa0e1add63bea4a9c8', + local_tarball_tmpl % ('ppc64le', local_build): + '459148d489b08ceec2d901e950ac36722b4c55e907e979291ddfc954ebdcea47', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-11.eb b/easybuild/easyconfigs/j/Java/Java-11.eb index d53c0b9b2f5..77086a3e1b8 100644 --- a/easybuild/easyconfigs/j/Java/Java-11.eb +++ b/easybuild/easyconfigs/j/Java/Java-11.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.0.16')] +dependencies = [('Java', '%(version)s.0.18')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.6.eb b/easybuild/easyconfigs/j/Java/Java-17.0.6.eb new file mode 100644 index 00000000000..71d89858ea4 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-17.0.6.eb @@ -0,0 +1,30 @@ +name = 'Java' +version = '17.0.6' +local_build = '10' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + 'a0b1b9dd809d51a438f5fa08918f9aca7b2135721097f0858cf29f77a35d4289', + local_tarball_tmpl % ('aarch64', local_build): + '9e0e88bbd9fa662567d0c1e22d469268c68ac078e9e5fe5a7244f56fec71f55f', + local_tarball_tmpl % ('ppc64le', local_build): + 'cb772c3fdf3f9fed56f23a37472acf2b80de20a7113fe09933891c6ef0ecde95', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-17.eb b/easybuild/easyconfigs/j/Java/Java-17.eb index b5936b5a154..1efea31e843 100644 --- a/easybuild/easyconfigs/j/Java/Java-17.eb +++ b/easybuild/easyconfigs/j/Java/Java-17.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.0.4')] +dependencies = [('Java', '%(version)s.0.6')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-8.362.eb b/easybuild/easyconfigs/j/Java/Java-8.362.eb new file mode 100644 index 00000000000..f8c6b809aa0 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-8.362.eb @@ -0,0 +1,31 @@ +name = 'Java' +version = '8.362' +local_build = 'b09' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK8U-jdk_%s_linux_hotspot_%%(version_major)su%%(version_minor)s%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin8-binaries/releases/download/' + 'jdk%%(version_major)su%%(version_minor)s-%s/' % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + '1486a792fb224611ce0cd0e83d4aacd3503b56698549f8e9a9f0a6ebb83bdba1', + local_tarball_tmpl % ('aarch64', local_build): + '9290a8beefd7a94f0eb030f62d402411a852100482b9c5b63714bacc57002c2a', + local_tarball_tmpl % ('ppc64le', local_build): + '69658dd316c6a160915655971573179766e19c6610ea03880c1e578a0e518f74', + + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-8.eb b/easybuild/easyconfigs/j/Java/Java-8.eb index 8c9091f83dd..854eccb56cb 100644 --- a/easybuild/easyconfigs/j/Java/Java-8.eb +++ b/easybuild/easyconfigs/j/Java/Java-8.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.345')] +dependencies = [('Java', '%(version)s.362')] moduleclass = 'lang' From 5ab3f23585ade0e16822ce16fc09c01d5a565c21 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 21 Apr 2023 13:45:14 +0200 Subject: [PATCH 7239/9987] adding easyconfigs: pod5-file-format-0.1.8-foss-2022a.eb and patches: pod5-file-format-0.1.8_dep_fix.patch --- .../pod5-file-format-0.1.8-foss-2022a.eb | 81 +++++++++++++++++++ .../pod5-file-format-0.1.8_dep_fix.patch | 22 +++++ 2 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb new file mode 100644 index 00000000000..b924d3aef43 --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb @@ -0,0 +1,81 @@ +easyblock = 'CMakeMake' + +name = 'pod5-file-format' +version = '0.1.8' + +homepage = 'https://github.com/nanoporetech/pod5-file-format' +description = """POD5 is a file format for storing nanopore dna data in an easily accessible way. + The format is able to be written in a streaming manner which allows a sequencing + instrument to directly write the format.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/nanoporetech/%(name)s/archive/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['pod5-file-format-0.1.8_dep_fix.patch'] +checksums = [ + {'pod5-file-format-0.1.8.tar.gz': '262b85a44b2e5e93be55bfc2d55a49c07a012b04b59aa24e1d59fd981ac58b5c'}, + {'pod5-file-format-0.1.8_dep_fix.patch': 'd05e52467387c67bc87551eccbf5a6c3253ad1c4019eaf21ad861895e9a086c6'}, +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Arrow', '8.0.0'), + ('SciPy-bundle', '2022.05'), + ('zstd', '1.5.2'), + ('flatbuffers', '2.0.0'), + ('pybind11', '2.9.2'), + ('Boost', '1.79.0'), + ('build', '0.10.0'), + ('pkg-config', '0.29.2'), + ('HDF5', '1.12.2'), + ('h5py', '3.7.0'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'installopts': '', +} + +exts_list = [ + ('pkgconfig', '1.5.5', { + 'checksums': ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'], + }), + ('attrs', '22.2.0', { + 'checksums': ['c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99'], + }), + ('vbz_h5py_plugin', '1.0.1', { + 'checksums': ['c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341'], + }), + ('iso8601', '1.1.0', { + 'checksums': ['32811e7b81deee2063ea6d2e94f8819a86d1f3811e49d23623a41fa832bef03f'], + }), + ('pod5', version, { + 'source_urls': source_urls, + 'sources': sources, + 'start_dir': 'python/pod5', + 'checksums': ['262b85a44b2e5e93be55bfc2d55a49c07a012b04b59aa24e1d59fd981ac58b5c'], + }), +] + +configopts = ' -DBUILD_PYTHON_WHEEL=ON -DZSTD_LIB="$EBROOTZSTD/lib/libzstd.a" ' + +installopts = ' && export XDG_CACHE_HOME=%(builddir)s && cd %(installdir)s' +installopts += ' && pip install --no-deps --ignore-installed --prefix %(installdir)s lib_pod5-%(version)s-*.whl' + +postinstallcmds = ['rm %(installdir)s/lib_pod5-%(version)s-*.whl'] + +sanity_check_commands = ['pod5 subset --help'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch new file mode 100644 index 00000000000..2782bdeb102 --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch @@ -0,0 +1,22 @@ +diff -u pod5-file-format-0.1.8/c++/CMakeLists.txt.orig pod5-file-format-0.1.8/c++/CMakeLists.txt +--- pod5-file-format-0.1.8/c++/CMakeLists.txt.orig 2023-01-20 12:22:05.000000000 +0100 ++++ pod5-file-format-0.1.8/c++/CMakeLists.txt 2023-01-23 10:11:12.097686513 +0100 +@@ -21,6 +21,7 @@ + endif() + + find_package(Threads REQUIRED) ++find_package(pybind11 REQUIRED) + + find_program( + FLATBUFFERS_FLATC_EXECUTABLE +diff -u pod5-file-format-0.1.8/CMakeLists.txt.orig pod5-file-format-0.1.8/CMakeLists.txt +--- pod5-file-format-0.1.8/CMakeLists.txt.orig 2023-01-20 12:22:05.000000000 +0100 ++++ pod5-file-format-0.1.8/CMakeLists.txt 2023-01-23 10:34:44.860294168 +0100 +@@ -92,7 +91,6 @@ + + if (BUILD_PYTHON_WHEEL) + find_package (Python ${PYTHON_VERSION} EXACT COMPONENTS Interpreter Development) +- add_subdirectory(third_party/pybind11) + endif() + + add_subdirectory(c++) From 7094086458de57a7c32002f30a61021a0ac29d72 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 21 Apr 2023 13:49:55 +0200 Subject: [PATCH 7240/9987] add missing dependency --- .../build-0.10.0-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb new file mode 100644 index 00000000000..ce8f9a50a22 --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'build' +version = '0.10.0' + +homepage = 'https://github.com/pypa/build' +description = """A simple, correct Python build frontend.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyparsing', '3.0.9', { + 'checksums': ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'], + }), + ('packaging', '20.4', { + 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + (name, version, { + 'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'], + }), +] + +sanity_check_commands = [ + "python3 -m build -V", +] + +moduleclass = 'devel' From 71b1f09fb6ac48e3be5e92ba92cdb1e7bd4c1b7c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 21 Apr 2023 14:00:35 +0200 Subject: [PATCH 7241/9987] adding easyconfigs: OptaDOS-1.2.380-GCC-11.3.0.eb --- .../o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb new file mode 100644 index 00000000000..99a1e6a6a88 --- /dev/null +++ b/easybuild/easyconfigs/o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'OptaDOS' +version = '1.2.380' + +homepage = 'http://www.optados.org/' +description = """OptaDOS is a program for calculating core-electron and low-loss electron energy +loss spectra (EELS) and optical spectra along with total-, projected- and +joint-density of electronic states (DOS) from single-particle eigenenergies and +dipole transition coefficients.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'optados-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['606d3db28dba791f62b05ef638ed0b1e42474763db65e04abd63a30501bb2eac'] + +buildopts = "SYSTEM=gfortran COMMS_ARCH=serial PREFIX=%(installdir)s " +buildopts += 'FFLAGS="$FFLAGS -fconvert=big-endian -ffree-line-length-150"' + +files_to_copy = [ + (['src/%(namelower)s.gfortran.*'], 'bin'), + 'documents', + 'examples', + 'tools', +] + +postinstallcmds = [ + "cd %(installdir)s/bin && ln -s %(namelower)s.gfortran.* %(namelower)s", +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['documents', 'examples', 'tools'] +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'phys' From 96f79baf307404cdeb0c1041d5be7119875876ea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 21 Apr 2023 14:31:00 +0200 Subject: [PATCH 7242/9987] add sanity check paths --- .../p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb index b924d3aef43..15436f8c712 100644 --- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb @@ -74,6 +74,11 @@ installopts += ' && pip install --no-deps --ignore-installed --prefix %(installd postinstallcmds = ['rm %(installdir)s/lib_pod5-%(version)s-*.whl'] +sanity_check_paths = { + 'files': ['bin/pod5', 'lib/libpod5_format.a'], + 'dirs': ['include/pod5_format', 'lib/python%(pyshortver)s/site-packages'], +} + sanity_check_commands = ['pod5 subset --help'] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From fbd9fa617cd0291cca3baa2476f608bd82efa189 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 21 Apr 2023 15:22:44 +0200 Subject: [PATCH 7243/9987] Add egg file to OpenCV 4.6.0 python package for pip --- .../OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb | 8 ++++++++ .../o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 8 ++++++++ .../easyconfigs/o/OpenCV/opencv-contrib-python.egg-info | 5 +++++ 3 files changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb index 70276c87526..2e67ca665c5 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb @@ -32,6 +32,7 @@ sources = [ 'extract_cmd': 'cp %s %(builddir)s' }, ] +patches = [('opencv-contrib-python.egg-info', '..')] checksums = [ '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip @@ -82,6 +83,13 @@ configopts = " ".join([ "-DCUDA_NVCC_FLAGS=--std=c++14", ]) +# Install a egg-info file so it is more python friendly +local_egg_info_src = '%(builddir)s/opencv-contrib-python.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv-contrib-python-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + enhance_sanity_check = True local_contrib_libs = [ diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index b957c01b7d4..c764ad56a61 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -31,6 +31,7 @@ sources = [ 'extract_cmd': 'cp %s %(builddir)s' }, ] +patches = [('opencv-contrib-python.egg-info', '..')] checksums = [ '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip @@ -78,6 +79,13 @@ configopts = " ".join([ "-DBUILD_opencv_python2=OFF", ]) +# Install a egg-info file so it is more python friendly +local_egg_info_src = '%(builddir)s/opencv-contrib-python.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv-contrib-python-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + enhance_sanity_check = True local_contrib_libs = [ diff --git a/easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info b/easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info new file mode 100644 index 00000000000..073e127f34d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info @@ -0,0 +1,5 @@ +Metadata-Version: 2.1 +Name: opencv-contrib-python +Version: #OPENCV_VERSION# +Summary: Wrapper package for OpenCV python bindings. +Platform: UNKNOWN From 88bd6ba8e0092fce9c63b0ec5a0450bc361b8e07 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 21 Apr 2023 15:24:09 +0200 Subject: [PATCH 7244/9987] adding easyconfigs: RepeatMasker-4.1.5-foss-2022a.eb --- .../RepeatMasker-4.1.5-foss-2022a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2022a.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2022a.eb new file mode 100644 index 00000000000..d7e8df4c81d --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2022a.eb @@ -0,0 +1,57 @@ +easyblock = 'Tarball' + +name = 'RepeatMasker' +version = '4.1.5' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://www.repeatmasker.org/%(name)s'] +sources = [ + SOURCE_TAR_GZ, + # optional but recommended: RepBase RepeatMasker Edition + # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php + # { + # 'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz', + # 'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1", + # }, +] +checksums = ['16e07f9efd99adf15f4492b0e334df5ad4ea6ca38ddf62bdd180d257f2f4753f'] + +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('TRF', '4.09.1'), + ('h5py', '3.7.0'), + # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match + ('HMMER', '3.3.2'), + ('RMBlast', '2.13.0'), +] + +local_default_search_engine = 'RMBlast' + +local_config_command = 'cd %(installdir)s &&' +local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() + +postinstallcmds = [local_config_command] + +fix_perl_shebang_for = ['RepeatMasker'] + +sanity_check_paths = { + 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], + 'dirs': ['Libraries', 'util'], +} + +sanity_check_commands = ['RepeatMasker -help'] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} + +moduleclass = 'bio' From e04695b0a53f6d4fd861e0aacbe37b6e8714ae8b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 21 Apr 2023 16:34:11 +0200 Subject: [PATCH 7245/9987] Fix checksums --- .../OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb | 8 +++++--- .../o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 8 +++++--- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb index 2e67ca665c5..0edcf1239a6 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb @@ -34,9 +34,11 @@ sources = [ ] patches = [('opencv-contrib-python.egg-info', '..')] checksums = [ - '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip - '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip - '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz + {'opencv-4.6.0.zip': '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359'}, + {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'}, + {'ippicv_2020_lnx_intel64_20191018_general.tgz': + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246'}, + {'opencv-contrib-python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index c764ad56a61..6373a8db53e 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -33,9 +33,11 @@ sources = [ ] patches = [('opencv-contrib-python.egg-info', '..')] checksums = [ - '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip - '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip - '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz + {'opencv-4.6.0.zip': '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359'}, + {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'}, + {'ippicv_2020_lnx_intel64_20191018_general.tgz': + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246'}, + {'opencv-contrib-python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'}, ] builddependencies = [ From d25f27151ae72d8e102221218158f36427da4c56 Mon Sep 17 00:00:00 2001 From: sam Date: Fri, 21 Apr 2023 17:01:34 +0200 Subject: [PATCH 7246/9987] adding easyconfigs: ReaxFF-2.0-GCC-11.3.0.eb --- .../r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb b/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..a3082257b1f --- /dev/null +++ b/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'ReaxFF' +version = '2.0' + +homepage = 'https://www.engr.psu.edu/adri/ReaxffManual.aspx' + +description = """ +REAXFF Reactive force field program +""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a62829d25b6eb5c311206a89a892e1de6fd3ee33cae40489901bb9f50d53f4d2'] + +download_instructions = """ +Register at https://www.engr.psu.edu/adri/Home.aspx and follow instructions +""" + +buildopts = 'SUFFIX="-c -O3 -std=legacy"' + +files_to_copy = [ + (['reac'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/reac'], + 'dirs': [], +} + +moduleclass = 'chem' From 2c713d31877460663643e3298a5ee98238540ff0 Mon Sep 17 00:00:00 2001 From: Arnold Kole <35299166+ahkole@users.noreply.github.com> Date: Sat, 22 Apr 2023 01:14:01 +0200 Subject: [PATCH 7247/9987] Remove explicit setting of default option --- easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb index 6dba042d193..3b6c72c06b5 100644 --- a/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb @@ -20,8 +20,6 @@ builddependencies = [ ('CMake', '3.23.1'), ] -separate_build_dir = True - sanity_check_paths = { 'files': ['lib/libpsml.a'], 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libpsml'], From f324ff1f8ea8f06067e5ee00bb009dbd577acd82 Mon Sep 17 00:00:00 2001 From: Arnold Kole <35299166+ahkole@users.noreply.github.com> Date: Sat, 22 Apr 2023 01:15:24 +0200 Subject: [PATCH 7248/9987] Restrict to serial compilation to fix build error --- .../easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb index 1b2f864e5f2..7373a16da20 100644 --- a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb @@ -22,6 +22,8 @@ builddependencies = [ ('CMake', '3.23.1'), ] +parallel = 1 + sanity_check_paths = { 'files': ['lib/libgridxc.a'], 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libgridxc'], From a228a0c137b93ef5b2eaef61481a2e52988cb3ef Mon Sep 17 00:00:00 2001 From: Arnold Kole <35299166+ahkole@users.noreply.github.com> Date: Sat, 22 Apr 2023 12:31:39 +0200 Subject: [PATCH 7249/9987] Fixed failed build to the pkg-config dependency --- .../easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb index 7373a16da20..474990ff216 100644 --- a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb @@ -16,10 +16,13 @@ checksums = ['e7883e57a4db2438ee59437740291c06e0cfe1c8ae1901e4001f32312307e46a'] configopts = "-DWITH_MPI=ON -DWITH_LIBXC=ON" +preconfigopts = 'CPATH= ' # gfortran ignores CPATH, but pkgconf also excludes dirs from CPATH + dependencies = [('libxc', '5.2.3')] builddependencies = [ ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), ] parallel = 1 From a0086d5881e7c7bbd7e7c7999638fb3f59a68933 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 22 Apr 2023 22:42:31 +0200 Subject: [PATCH 7250/9987] adding easyconfigs: CLIP-20230220-foss-2022a-CUDA-11.7.0.eb --- .../CLIP-20230220-foss-2022a-CUDA-11.7.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..cacf9b91d85 --- /dev/null +++ b/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'CLIP' +version = '20230220' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = 'a9b1bf5' + +homepage = 'https://github.com/openai/CLIP' +description = """ +CLIP (Contrastive Language-Image Pre-Training) is a neural network trained on a +variety of (image, text) pairs. It can be instructed in natural language to +predict the most relevant text snippet, given an image, without directly +optimizing for the task, similarly to the zero-shot capabilities of GPT-2 and +3.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('torchvision', '0.13.1', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('ftfy', '6.1.1', { + 'checksums': ['bfc2019f84fcd851419152320a6375604a0f1459c281b5b199b2cd0d2e727f8f'], + }), + (name, version, { + 'source_urls': ['https://github.com/openai/CLIP/archive'], + 'sources': [{'download_filename': 'a9b1bf5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['9cbe833d1a8c1d5ea6db87c290119fda4d35a3fe2f7a94d6a88779de502a98e3'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 774535448b8662609c69af7e8e8ebc118577d8be Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 23 Apr 2023 12:51:41 +0200 Subject: [PATCH 7251/9987] adding easyconfigs: Meep-1.26.0-foss-2020b.eb, Guile-3.0.9-GCCcore-10.2.0.eb, libGDSII-0.21-GCCcore-10.2.0.eb, libctl-4.5.1-GCCcore-10.2.0.eb, Harminv-1.4.2-foss-2020b.eb, MPB-1.11.1-foss-2020b.eb --- .../g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb | 46 ++++++++++++++++ .../h/Harminv/Harminv-1.4.2-foss-2020b.eb | 28 ++++++++++ .../libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb | 26 +++++++++ .../l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb | 31 +++++++++++ .../m/MPB/MPB-1.11.1-foss-2020b.eb | 48 +++++++++++++++++ .../m/Meep/Meep-1.26.0-foss-2020b.eb | 53 +++++++++++++++++++ 6 files changed, 232 insertions(+) create mode 100644 easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb create mode 100644 easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb create mode 100644 easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..cd161186dfc --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '3.0.9' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['18525079ad29a0d46d15c76581b5d91c8702301bfd821666d2e1d13726162811'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('gc', '8.2.2'), + ('GMP', '6.2.0'), + ('libffi', '3.3'), + ('libunistring', '1.1'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb new file mode 100644 index 00000000000..7065f827a27 --- /dev/null +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Harminv' +version = '1.4.2' + +homepage = 'https://github.com/stevengj/harminv' +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'cstd': 'c99'} + +source_urls = ['https://github.com/stevengj/harminv/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5a9a1bf710972442f065d0d62c62d0c4ec3da4a3696d7160a35602c9470bc7a2'] + +builddependencies = [('pkg-config', '0.29.2')] + +configopts = "--with-pic --with-blas=openblas --with-lapack=openblas --enable-shared" + +sanity_check_paths = { + 'files': ['bin/harminv', 'lib/libharminv.a', 'lib/libharminv.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..5ebb3d807a4 --- /dev/null +++ b/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libGDSII' +version = '0.21' + +homepage = 'https://github.com/HomerReid/libGDSII' +description = """libGDSII is a C++ library for working with GDSII binary data files, + intended primarily for use with the computational electromagnetism codes + scuff-em and meep but sufficiently general-purpose to allow other uses as well.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/HomerReid/libGDSII/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['31c90a4fb699746d051c0c597ef0543889c9f17b2a711fed398756ac4f1b1f4c'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/GDSIIConvert', 'include/libGDSII.h', 'lib/libGDSII.a', 'lib/libGDSII.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..3dfc9fe295b --- /dev/null +++ b/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libctl' +version = '4.5.1' + +homepage = 'https://libctl.readthedocs.io/en/latest/' +description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/NanoComp/libctl/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['fcfeb2f13dda05b560f0ec6872757d9318fdfe8f4bc587eb2053a29ba328ae25'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), # required for libtool +] + +dependencies = [('Guile', '3.0.9')] + +configopts = '--with-pic --enable-shared' + +sanity_check_paths = { + 'files': ['bin/gen-ctl-io', 'lib/libctl.a', 'lib/libctlgeom.a', + 'lib/libctlgeom.%s' % SHLIB_EXT, 'lib/libctl.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb b/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb new file mode 100644 index 00000000000..bff6686a320 --- /dev/null +++ b/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'MPB' +version = '1.11.1' + +homepage = 'https://mpb.readthedocs.io/en/latest/' +description = """MPB is a free and open-source software package for computing + the band structures, or dispersion relations, and electromagnetic + modes of periodic dielectric structures, on both serial + and parallel computers. MPB is an acronym for MIT Photonic Bands.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://github.com/NanoComp/mpb/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dc55b081c56079727dac92d309f8e4ea84ca6eea9122ec24b7955f8c258608e1'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('HDF5', '1.10.7'), + ('libctl', '4.5.1'), + ('Guile', '3.0.9'), + ('libreadline', '8.0'), +] + +local_common_configopts = "--with-pic --with-blas=openblas --with-lapack=openblas " +local_common_configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " + +configopts = [ + local_common_configopts + " ", + local_common_configopts + " --with-inv-symmetry", + local_common_configopts + " --with-mpi ", + local_common_configopts + " --with-mpi --with-inv-symmetry", +] + +sanity_check_paths = { + 'files': ['bin/mpb%s' % x for x in ['', '-data', 'i', 'i-data', 'i-mpi', 'i-split', '-mpi', '-split']] + + ['lib/libmpb.a', 'lib/libmpbi_mpi.a', 'lib/libmpbi.a', 'lib/libmpb_mpi.a', 'lib/libmpb.%s' % SHLIB_EXT, + 'lib/libmpbi_mpi.%s' % SHLIB_EXT, 'lib/libmpbi.%s' % SHLIB_EXT, 'lib/libmpb_mpi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb new file mode 100644 index 00000000000..d7c07a5167e --- /dev/null +++ b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'Meep' +version = '1.26.0' + +homepage = 'https://meep.readthedocs.io/en/latest/' +description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package + developed at MIT to model electromagnetic systems.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['https://github.com/NanoComp/meep/releases/download/v%(version)s/'] +sources = ['meep-%(version)s.tar.gz'] +checksums = ['3f89f1bd781e46b938aa02e315a4526a4ae9896687db75c187b4f17febcbc301'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), + ('SWIG', '4.0.2') +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('MPB', '1.11.1'), + ('Harminv', '1.4.2'), + ('HDF5', '1.10.7'), + ('libctl', '4.5.1'), + ('libGDSII', '0.21'), + ('GSL', '2.6'), + ('Guile', '3.0.9'), +] + +configopts = "--with-pic --with-mpi --with-blas=openblas --with-lapack=openblas --without-gcc-arch " +configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " +configopts += "LDFLAGS=$LDFLAGS+' -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl -lmpi_mpifh'" + +sanity_check_paths = { + 'files': ['bin/meep', 'include/meep.hpp', 'lib/libmeep.a', 'lib/libpympb.a', + 'lib/libmeep.%s' % SHLIB_EXT, 'lib/libpympb.%s' % SHLIB_EXT], + 'dirs': ['include/meep', 'lib/python%(pyshortver)s/site-packages/meep', 'share/meep'], +} + +sanity_check_commands = [ + "meep --help", + "python -c 'import meep'", +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'phys' From 5c8b0fef7eab2f9bd10d6f6bdaf1f646f4503339 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 24 Apr 2023 01:46:43 +0200 Subject: [PATCH 7252/9987] adding easyconfigs: SOCI-4.0.3-GCC-12.2.0.eb --- .../s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb new file mode 100644 index 00000000000..2b1ee760c82 --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.3' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Boost', '1.81.0'), + ('SQLite', '3.39.4'), + ('PostgreSQL', '15.2'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' From 237961a9f21e32ce3c15f9f8bb1034e2877d239a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 24 Apr 2023 02:24:44 +0200 Subject: [PATCH 7253/9987] adding easyconfigs: yaml-cpp-0.7.0-GCCcore-12.2.0.eb --- .../yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e09fb068964 --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' +name = 'yaml-cpp' +version = '0.7.0' + +homepage = "https://github.com/jbeder/yaml-cpp" +description = """yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/jbeder/%(name)s/archive/'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-cmake-export.patch'] +checksums = [ + '43e6a9fcb146ad871515f0d0873947e5d497a1c9c60c58cb102a97b47208b7c3', + 'c562a575bbb161af478795e43bfd9073e3f874bea07134a321c1063cd7098c1c', # yaml-cpp-0.7.0_fix-cmake-export.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3') +] + +sanity_check_paths = { + 'files': ['lib/libyaml-cpp.a', 'include/yaml-cpp/yaml.h'], + 'dirs': ['lib', 'include'], +} + +moduleclass = 'tools' From 82b53e7248db4480428658ea85f9b8074e66295e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 24 Apr 2023 10:10:10 +0200 Subject: [PATCH 7254/9987] use commit var --- .../easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb index cacf9b91d85..e7b38dfeff1 100644 --- a/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb @@ -31,7 +31,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://github.com/openai/CLIP/archive'], - 'sources': [{'download_filename': 'a9b1bf5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': _commit + '.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['9cbe833d1a8c1d5ea6db87c290119fda4d35a3fe2f7a94d6a88779de502a98e3'], }), ] From 290b86485824863e2920e52219cfd5c1066aebb0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 24 Apr 2023 10:23:44 +0200 Subject: [PATCH 7255/9987] adding easyconfigs: timm-0.6.13-foss-2022a-CUDA-11.7.0.eb --- .../timm-0.6.13-foss-2022a-CUDA-11.7.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..7cc34b4454a --- /dev/null +++ b/easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'timm' +version = '0.6.13' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/timm' +description = """ +timm is a library containing SOTA computer vision models, layers, utilities, +optimizers, schedulers, data-loaders, augmentations, and training/evaluation +scripts. It comes packaged with >700 pretrained models, and is designed to be +flexible and easy to use. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.0', versionsuffix), + ('PyYAML', '6.0'), + ('tqdm', '4.64.0'), + ('torchvision', '0.13.1', versionsuffix), +] + +builddependencies = [ + ('Rust', '1.65.0'), # for safetensors +] + +use_pip = True + +exts_list = [ + ('huggingface_hub', '0.13.4', { + 'checksums': ['db83d9c2f76aed8cf49893ffadd6be24e82074da2f64b1d36b8ba40eb255e115'], + }), + ('safetensors', '0.3.0', { + 'checksums': ['5be8b2fccdc6aec84c9d6732180575fe1ba3afc559cbe96e2301eacc45c5b9a6'], + }), + (name, version, { + 'checksums': ['745c54f7b7985a18e08bd66c997b018c1c3fef99bbb8c018879a6f85571782f5'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 036204609a0617c9df77ab705e352db5d717fa44 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 24 Apr 2023 11:42:29 +0200 Subject: [PATCH 7256/9987] gc v8.0.4, libunistring v1.1 and update to Meep v1.26.0 --- .../g/gc/gc-8.2.2-GCCcore-10.2.0.eb | 42 +++++++++++++++++++ .../libunistring-1.1-GCCcore-10.2.0.eb | 31 ++++++++++++++ .../m/Meep/Meep-1.26.0-foss-2020b.eb | 1 - 3 files changed, 73 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..5061399f2ff --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.2.2' +local_libatomic_version = '7.8.0' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a + garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + {'gc-8.2.2.tar.gz': 'f30107bcb062e0920a790ffffa56d9512348546859364c23a14be264b38836a0'}, + {'libatomic_ops-7.8.0.tar.gz': '15676e7674e11bda5a7e50a73f4d9e7d60452271b8acf6fd39a71fefdf89fa31'}, +] + +builddependencies = [ + ('binutils', '2.35'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..f93fd922791 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.1' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['827c1eb9cb6e7c738b171745dac0888aa58c5924df2e59239318383de0729b98'] + +builddependencies = [ + ('binutils', '2.35'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb index d7c07a5167e..0b54a760099 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb @@ -35,7 +35,6 @@ dependencies = [ configopts = "--with-pic --with-mpi --with-blas=openblas --with-lapack=openblas --without-gcc-arch " configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " -configopts += "LDFLAGS=$LDFLAGS+' -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl -lmpi_mpifh'" sanity_check_paths = { 'files': ['bin/meep', 'include/meep.hpp', 'lib/libmeep.a', 'lib/libpympb.a', From bda2ad3b2ff00c3ad2197e75fb9ebeea4e7321d2 Mon Sep 17 00:00:00 2001 From: Arnold Kole <35299166+ahkole@users.noreply.github.com> Date: Mon, 24 Apr 2023 12:33:09 +0200 Subject: [PATCH 7257/9987] Removed forcing of serial compilation --- .../easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb index 474990ff216..acb27067217 100644 --- a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb @@ -25,8 +25,6 @@ builddependencies = [ ('pkgconf', '1.8.0'), ] -parallel = 1 - sanity_check_paths = { 'files': ['lib/libgridxc.a'], 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libgridxc'], From 688b26ab483b194bfadc14d8d47ce67d82c4a03c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 24 Apr 2023 16:34:23 +0200 Subject: [PATCH 7258/9987] correctly disable some specific tests that cause problems on A40s --- .../c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb index ddafffc0fed..12a85d600f5 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb @@ -35,13 +35,17 @@ _skip_tests = [ 'tests/cupyx_tests/tools_tests', 'tests/example_tests', 'tests/cupy_tests/testing_tests/test_parameterized.py', - 'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_', 'tests/cupy_tests/fft_tests/test_fft.py', +] +_ignore_list = ' --ignore='.join(_skip_tests) + +_deselect_tests = [ + 'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_', # float16 has too low precision for these tests as they are written # See https://github.com/easybuilders/easybuild-easyconfigs/pull/17526#issuecomment-1470843170 for details. 'tests/cupy_tests/linalg_tests/test_product.py::TestProduct', ] -_ignore_list = ' --ignore='.join(_skip_tests) +_deselect_list = ' --deselect='.join(_deselect_tests) exts_list = [ ('fastrlock', '0.5', { @@ -50,8 +54,8 @@ exts_list = [ ('cupy', version, { # Must run tests here since the required version of pytest is a builddep # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory. - 'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && pytest --ignore=%s tests' % - _ignore_list, + 'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && ' + 'pytest --ignore=%s --deselect=%s tests' % (_ignore_list, _deselect_list), 'testinstall': True, 'checksums': ['03d52b2626e02a3a2b46d714c1cd03e702c8fe33915fcca6ed8de5c539964f49'], }), From b672bcf5fe754f10acee17692750dbb02d10d7c3 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Mon, 24 Apr 2023 16:58:35 +0200 Subject: [PATCH 7259/9987] adding easyconfigs: IsoSeq-3.8.2-linux-x86_64.eb --- .../i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb diff --git a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb new file mode 100644 index 00000000000..7a7e2856fef --- /dev/null +++ b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb @@ -0,0 +1,25 @@ +easyblock = 'Binary' + +name = 'IsoSeq' +version = '3.8.2' +versionsuffix = '-linux-x86_64' + +homepage = 'https://github.com/PacificBiosciences/ioseq3' +description = """IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added.""" + +toolchain = SYSTEM + +source_urls = ["https://github.com/PacificBiosciences/%(namelower)s"] +sources = ["releases/download/v%(version)s/%(namelower)s3"] +checksums = ['3d012810dc4cb54f89a7c80b26fc5f27da26c11f7ad6062cab462a6c691678f7'] + +extract_sources = False + +postinstallcmds = ["cp %(builddir)s/releases/download/v%(version)s/%(namelower)s* %(installdir)s"] + +sanity_check_paths = { + 'files': ['isoseq3',], + 'dirs': [''], +} + +moduleclass = 'bio' \ No newline at end of file From b3c7596709b471eb0c38314b0305fa4bd6d27dc7 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Mon, 24 Apr 2023 17:51:43 +0200 Subject: [PATCH 7260/9987] adding easyconfigs: GLI-4.5.31-GCCcore-10.2.0.eb, GLI-4.5.31-GCCcore-12.2.0.eb --- .../g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb | 51 +++++++++++++++++++ .../g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb | 51 +++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..7820338ddff --- /dev/null +++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb @@ -0,0 +1,51 @@ +easyblock = "ConfigureMake" + +name = "GLI" +version = "4.5.31" + +homepage = "https://pgi-jcns.fz-juelich.de/portal/pages/gli.html" +description = "Graphics Language Interpreter" + +toolchain = {"name": "GCCcore", "version": "10.2.0"} +toolchainopts = {"pic": True} + +source_urls = ["http://iffwww.iff.kfa-juelich.de/gli/"] +sources = [SOURCELOWER_TAR_GZ] +checksums = ["13b7def217672ab4fa01e39977af26f3fbbe0f7bbe7e7c42c2c4aa0ea5fc8c05"] + +builddependencies = [("binutils", "2.35")] + +dependencies = [ + ('X11', '20201008'), + ('zlib', '1.2.11'), + ('Tk', '8.6.10'), + ('Tcl', '8.6.10'), + ('libtirpc', '1.3.1') +] + +preconfigopts = 'cd src && ' +configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc ' +configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib' + +prebuildopts = 'cd src &&' + +preinstallopts = 'cd src &&' + +parallel = 1 + +modextravars = { + "GLI_WSTYPE": "217", + "GLI_HOME": "%(installdir)s" +} + +modextrapaths = { + "PATH": "", + "LD_LIBRARY_PATH": "", +} + +sanity_check_paths = { + "files": ["libgks.a", "libgks.%s" % SHLIB_EXT, "libgli.a", "libgus.%s" % SHLIB_EXT], + "dirs": ["demo", "tcl/lib"], +} + +moduleclass = "vis" diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..68de3e62b7c --- /dev/null +++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb @@ -0,0 +1,51 @@ +easyblock = "ConfigureMake" + +name = "GLI" +version = "4.5.31" + +homepage = "https://pgi-jcns.fz-juelich.de/portal/pages/gli.html" +description = "Graphics Language Interpreter" + +toolchain = {"name": "GCCcore", "version": "12.2.0"} +toolchainopts = {"pic": True} + +source_urls = ["http://iffwww.iff.kfa-juelich.de/gli/"] +sources = [SOURCELOWER_TAR_GZ] +checksums = ["13b7def217672ab4fa01e39977af26f3fbbe0f7bbe7e7c42c2c4aa0ea5fc8c05"] + +builddependencies = [("binutils", "2.39")] + +dependencies = [ + ('X11', '20221110'), + ('zlib', '1.2.12'), + ('Tk', '8.6.12'), + ('Tcl', '8.6.12'), + ('libtirpc', '1.3.3') +] + +preconfigopts = 'cd src && ' +configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc ' +configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib' + +prebuildopts = 'cd src &&' + +preinstallopts = 'cd src &&' + +parallel = 1 + +modextravars = { + "GLI_WSTYPE": "217", + "GLI_HOME": "%(installdir)s" +} + +modextrapaths = { + "PATH": "", + "LD_LIBRARY_PATH": "", +} + +sanity_check_paths = { + "files": ["libgks.a", "libgks.%s" % SHLIB_EXT, "libgli.a", "libgus.%s" % SHLIB_EXT], + "dirs": ["demo", "tcl/lib"], +} + +moduleclass = "vis" From 4ca82898f696db37ee6c512355a16e8d92b47374 Mon Sep 17 00:00:00 2001 From: Kim Serradell Date: Tue, 25 Apr 2023 12:04:05 +0200 Subject: [PATCH 7261/9987] Replacing AOCC broken link --- easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb index aca9ebc5b59..b2b557cf891 100644 --- a/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb @@ -8,7 +8,7 @@ description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0 # already specified as the toolchain. toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -source_urls = ['http://developer.amd.com/wordpress/media/files/'] +source_urls = ['https://download.amd.com/developer/eula/aocc-compiler/'] sources = ['aocc-compiler-%(version)s.tar'] checksums = ['2729ec524cbc927618e479994330eeb72df5947e90cfcc49434009eee29bf7d4'] From 966a84ec6cd037be5aac904806dd904370a7dc95 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 25 Apr 2023 14:18:08 +0200 Subject: [PATCH 7262/9987] fix flatbuffers version --- .../pod5-file-format-0.1.8-foss-2022a.eb | 4 ++-- .../pod5-file-format-0.1.8_dep_fix.patch | 16 +++++++++++----- 2 files changed, 13 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb index 15436f8c712..5804c85e8ec 100644 --- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb @@ -15,7 +15,7 @@ sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ patches = ['pod5-file-format-0.1.8_dep_fix.patch'] checksums = [ {'pod5-file-format-0.1.8.tar.gz': '262b85a44b2e5e93be55bfc2d55a49c07a012b04b59aa24e1d59fd981ac58b5c'}, - {'pod5-file-format-0.1.8_dep_fix.patch': 'd05e52467387c67bc87551eccbf5a6c3253ad1c4019eaf21ad861895e9a086c6'}, + {'pod5-file-format-0.1.8_dep_fix.patch': 'd24fab7477d735ba7bb4a286c7a64d6138bf6a82a5a021b257eeeb5dfa06d82e'}, ] builddependencies = [ @@ -28,7 +28,7 @@ dependencies = [ ('Arrow', '8.0.0'), ('SciPy-bundle', '2022.05'), ('zstd', '1.5.2'), - ('flatbuffers', '2.0.0'), + ('flatbuffers', '2.0.7'), ('pybind11', '2.9.2'), ('Boost', '1.79.0'), ('build', '0.10.0'), diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch index 2782bdeb102..f9430ef0310 100644 --- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch @@ -1,12 +1,18 @@ diff -u pod5-file-format-0.1.8/c++/CMakeLists.txt.orig pod5-file-format-0.1.8/c++/CMakeLists.txt ---- pod5-file-format-0.1.8/c++/CMakeLists.txt.orig 2023-01-20 12:22:05.000000000 +0100 -+++ pod5-file-format-0.1.8/c++/CMakeLists.txt 2023-01-23 10:11:12.097686513 +0100 -@@ -21,6 +21,7 @@ +--- pod5-file-format-0.1.8/c++/CMakeLists.txt.orig 2023-02-23 19:17:13.000000000 +0100 ++++ pod5-file-format-0.1.8/c++/CMakeLists.txt 2023-04-25 14:07:28.174884834 +0200 +@@ -16,11 +16,12 @@ + COMPONENTS + headers + ) +- find_package(Flatbuffers REQUIRED) ++ find_package(FlatBuffers REQUIRED) + find_package(zstd REQUIRED) endif() - + find_package(Threads REQUIRED) +find_package(pybind11 REQUIRED) - + find_program( FLATBUFFERS_FLATC_EXECUTABLE diff -u pod5-file-format-0.1.8/CMakeLists.txt.orig pod5-file-format-0.1.8/CMakeLists.txt From 12f781a6bcfc4e6d9530ac4e931a06db3e9f71de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 25 Apr 2023 14:36:39 +0200 Subject: [PATCH 7263/9987] add build easyconfig --- .../b/build/build-0.10.0-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb new file mode 100644 index 00000000000..ce8f9a50a22 --- /dev/null +++ b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'build' +version = '0.10.0' + +homepage = 'https://github.com/pypa/build' +description = """A simple, correct Python build frontend.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyparsing', '3.0.9', { + 'checksums': ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'], + }), + ('packaging', '20.4', { + 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + (name, version, { + 'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'], + }), +] + +sanity_check_commands = [ + "python3 -m build -V", +] + +moduleclass = 'devel' From b0adb1c2ac2811c2dda57b95d87353753ded5dc4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 25 Apr 2023 14:38:33 +0200 Subject: [PATCH 7264/9987] remove unwanted file --- .../build-0.10.0-foss-2022a.eb | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb deleted file mode 100644 index ce8f9a50a22..00000000000 --- a/easybuild/easyconfigs/p/pod5-file-format/build-0.10.0-foss-2022a.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'build' -version = '0.10.0' - -homepage = 'https://github.com/pypa/build' -description = """A simple, correct Python build frontend.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -dependencies = [ - ('Python', '3.10.4'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('pyparsing', '3.0.9', { - 'checksums': ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'], - }), - ('packaging', '20.4', { - 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], - }), - ('tomli', '2.0.1', { - 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], - }), - ('pyproject_hooks', '1.0.0', { - 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], - }), - (name, version, { - 'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'], - }), -] - -sanity_check_commands = [ - "python3 -m build -V", -] - -moduleclass = 'devel' From c20dade423b7e1d9c88a79cbe24188b0c7308be8 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Tue, 25 Apr 2023 15:18:20 +0200 Subject: [PATCH 7265/9987] adding easyconfigs: libRmath-4.2.1-GCCcore-11.3.0.eb --- .../libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..bd707d8a2e1 --- /dev/null +++ b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# Updated: Denis Kristak (INUITS) +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'libRmath' +version = '4.2.1' + +homepage = 'https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library' +description = """The routines supporting the distribution and special functions in R and a few others are declared + in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = ['R-%(version)s.tar.gz'] +checksums = ['4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('cURL', '7.83.0'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.12'), + ('PCRE2', '10.40'), +] + +preconfigopts = "cd %(builddir)s/R-%(version)s && " +configopts = "--with-readline=no --with-recommended-packages=no --with-x=no" + +parallel = 1 + +postinstallcmds = ['cp -r %(builddir)s/R-%(version)s/src/include/R_ext %(installdir)s/include/'] +runtest = 'check' +start_dir = 'src/nmath/standalone' + +sanity_check_paths = { + 'files': ['lib/libRmaths.%s' % SHLIB_EXT, 'lib/%(name)s.a', 'lib/pkgconfig/%(name)s.pc', 'include/Rmath.h'], + 'dirs': [], +} + +moduleclass = 'lib' From 7ef647b926d6c82bece5f2cdf1f2cd6915f7fb7b Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 25 Apr 2023 15:38:21 +0100 Subject: [PATCH 7266/9987] adding easyconfigs: Infernal-1.1.4-foss-2022b.eb --- .../i/Infernal/Infernal-1.1.4-foss-2022b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb new file mode 100644 index 00000000000..1f071f3e656 --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.4" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' From f8b8db8d9b9a1249cf6ac8570d5a5a2e89399373 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Tue, 25 Apr 2023 16:47:11 +0200 Subject: [PATCH 7267/9987] adding easyconfigs: rgdal-1.6-6-foss-2022a-R-4.2.1.eb --- .../r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..168c2f06bc2 --- /dev/null +++ b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb @@ -0,0 +1,33 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'RPackage' + +name = 'rgdal' +version = '1.6-6' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://rgdal.r-forge.r-project.org/' +description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and + access to projection/transformation operations from the 'PROJ.4' library.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['d742d7aadfc004771e61cac28a1faffeb4dbda981dea19115be11c541087399a'] + +dependencies = [ + ('R', '4.2.1'), + ('GDAL', '3.5.0'), +] + + +sanity_check_paths = { + 'files': ['%(name)s/R/%(name)s'], + 'dirs': [], +} + +moduleclass = 'geo' From 2c8afe8b366004a39a8d286b1d33f9de6d459521 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Tue, 25 Apr 2023 18:18:47 +0200 Subject: [PATCH 7268/9987] Remove pointless version suffix, remove empty line. --- .../r/rgdal/rgdal-1.6-6-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a.eb b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a.eb new file mode 100644 index 00000000000..9f53672f0cb --- /dev/null +++ b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a.eb @@ -0,0 +1,31 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'RPackage' + +name = 'rgdal' +version = '1.6-6' + +homepage = 'https://rgdal.r-forge.r-project.org/' +description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and + access to projection/transformation operations from the 'PROJ.4' library.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['d742d7aadfc004771e61cac28a1faffeb4dbda981dea19115be11c541087399a'] + +dependencies = [ + ('R', '4.2.1'), + ('GDAL', '3.5.0'), +] + +sanity_check_paths = { + 'files': ['%(name)s/R/%(name)s'], + 'dirs': [], +} + +moduleclass = 'geo' From 7e156451bef9c4133b47cd37a47285b8c611cc18 Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 25 Apr 2023 17:23:02 +0100 Subject: [PATCH 7269/9987] Copied in attribution and licence comments from previous versions, as per request of @verdurin. --- .../i/Infernal/Infernal-1.1.4-foss-2022b.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb index 1f071f3e656..57d29e7b2b7 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb @@ -1,3 +1,16 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# Updated:: Denis Kristak (INUITS) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + easyblock = 'ConfigureMake' name = 'Infernal' From 32ab02196e1f89f01506a31810e817bcfdf1944f Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Tue, 25 Apr 2023 18:26:04 +0200 Subject: [PATCH 7270/9987] Rename easyconfig, remove R version suffix. --- .../r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb deleted file mode 100644 index 168c2f06bc2..00000000000 --- a/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a-R-4.2.1.eb +++ /dev/null @@ -1,33 +0,0 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. -easyblock = 'RPackage' - -name = 'rgdal' -version = '1.6-6' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://rgdal.r-forge.r-project.org/' -description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and - access to projection/transformation operations from the 'PROJ.4' library.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] -sources = ['%(name)s_%(version)s.tar.gz'] -checksums = ['d742d7aadfc004771e61cac28a1faffeb4dbda981dea19115be11c541087399a'] - -dependencies = [ - ('R', '4.2.1'), - ('GDAL', '3.5.0'), -] - - -sanity_check_paths = { - 'files': ['%(name)s/R/%(name)s'], - 'dirs': [], -} - -moduleclass = 'geo' From 795a2807237a5e982d88ad01a8c23b5ac37529fb Mon Sep 17 00:00:00 2001 From: Ghepardo Date: Tue, 25 Apr 2023 18:25:21 +0100 Subject: [PATCH 7271/9987] adding easyconfigs: tRNAscan-SE-2.0.12-foss-2022b.eb --- .../tRNAscan-SE-2.0.12-foss-2022b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb new file mode 100644 index 00000000000..f65eb9761f8 --- /dev/null +++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'tRNAscan-SE' +version = '2.0.12' + +homepage = 'http://trna.ucsc.edu/tRNAscan-SE/' +description = """tRNAscan-SE is the most widely employed tool for identifying + and annotating tRNA genes in genomes.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['http://trna.ucsc.edu/software/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96fa4af507cd918c1c623763d9260bd6ed055d091662b44314426f6bbf447251'] + +dependencies = [ + ('Autoconf', '2.69', '', SYSTEM), + ('Infernal', '1.1.4'), +] + +sanity_check_paths = { + 'files': [ + 'bin/tRNAscan-SE', + 'lib/tRNAscan-SE/tRNAscanSE/tRNA.pm', + ], + 'dirs': [ + 'bin', + 'include', + 'lib', + ], +} + +# tRNAscan-SE.conf sets the Infernal bin directory to be ours. +postinstallcmds = [ + "for b in $(ls $EBROOTINFERNAL/bin); do ln -s $EBROOTINFERNAL/bin/$b %(installdir)s/bin; done", +] + +moduleclass = 'bio' From 9821440595d05123d0c8e28a80d32b2df2deaf64 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Tue, 25 Apr 2023 22:25:45 +0200 Subject: [PATCH 7272/9987] adding easyconfigs: muParser-2.3.4-GCCcore-11.3.0.eb --- .../muParser/muParser-2.3.4-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a5938bb05c3 --- /dev/null +++ b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'muParser' +version = '2.3.4' + +homepage = 'https://beltoforion.de/article.php?a=muparser' +description = """ + muParser is an extensible high performance math expression parser library + written in C++. It works by transforming a mathematical expression into + bytecode and precalculating constant parts of the expression. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/beltoforion/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0c3fa54a3ebf36dda0ed3e7cd5451c964afbb15102bdbcba08aafb359a290121'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +configopts = "-DENABLE_SAMPLES=OFF -DBUILD_SHARED_LIBS=ON" + + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/libmuparser.%s' % SHLIB_EXT ], + 'dirs': [], +} + +moduleclass = 'math' From 789f22e9811d1290f1b9ccc98ef252085f425aa8 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 26 Apr 2023 08:28:20 +0200 Subject: [PATCH 7273/9987] Fix whitespace before square bracket. --- .../easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb index a5938bb05c3..f20ab6b457e 100644 --- a/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb @@ -26,7 +26,7 @@ configopts = "-DENABLE_SAMPLES=OFF -DBUILD_SHARED_LIBS=ON" sanity_check_paths = { - 'files': ['include/%(name)s.h', 'lib/libmuparser.%s' % SHLIB_EXT ], + 'files': ['include/%(name)s.h', 'lib/libmuparser.%s' % SHLIB_EXT], 'dirs': [], } From b9bb9ef65899c8dcb33865555544dd2f172f5f26 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Wed, 26 Apr 2023 08:34:33 +0200 Subject: [PATCH 7274/9987] Fix sanity check after breaking it. --- .../easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb index bd707d8a2e1..b8e5a2762f5 100644 --- a/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb @@ -41,7 +41,7 @@ runtest = 'check' start_dir = 'src/nmath/standalone' sanity_check_paths = { - 'files': ['lib/libRmaths.%s' % SHLIB_EXT, 'lib/%(name)s.a', 'lib/pkgconfig/%(name)s.pc', 'include/Rmath.h'], + 'files': ['lib/libRmath.%s' % SHLIB_EXT, 'lib/%(name)s.a', 'lib/pkgconfig/%(name)s.pc', 'include/Rmath.h'], 'dirs': [], } From dd0ee03b00d45729994216f4064966d08226f781 Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Wed, 26 Apr 2023 10:27:36 +0200 Subject: [PATCH 7275/9987] adding easyconfigs: rocm-smi-5.4.4-GCCcore-11.3.0.eb --- .../rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..adb4b6dc91d --- /dev/null +++ b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'rocm-smi' +version = '5.4.4' + +homepage = 'https://github.com/RadeonOpenCompute/rocm_smi_lib' +description = """The ROCm System Management Interface Library, or ROCm SMI +library, is part of the Radeon Open Compute ROCm software stack. It is a C +library for Linux that provides a user space interface for applications to +monitor and control GPU applications.""" +docurls = ['https://rocmdocs.amd.com'] + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ["https://github.com/RadeonOpenCompute/rocm_smi_lib/archive/"] +sources = ["rocm-%(version)s.tar.gz"] +checksums = ['27a6d851a493a3ab11ca3af079b4a0509579aa7bab2b2891af3bdf816a456ff0'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['bin/rocm-smi'], + 'dirs': [''], +} + +sanity_check_commands = ['rocm-smi --help'] + +moduleclass = 'tools' From 2e996c9468e76e8aaf8d06d0d2c7bf4dca7a371b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 26 Apr 2023 11:16:37 +0200 Subject: [PATCH 7276/9987] update to use final GCC 13.1.0 release --- ...GCCcore-13.0.1.eb => Bison-3.8.2-GCCcore-13.1.0.eb} | 4 ++-- ...Ccore-13.0.1.eb => binutils-2.40-GCCcore-13.1.0.eb} | 2 +- ...-GCCcore-13.0.1.eb => flex-2.6.4-GCCcore-13.1.0.eb} | 6 +++--- .../easyconfigs/g/GCC/{GCC-13.0.1.eb => GCC-13.1.0.eb} | 2 +- .../g/GCCcore/{GCCcore-13.0.1.eb => GCCcore-13.1.0.eb} | 10 +++------- ...ore-13.0.1.eb => help2man-1.49.3-GCCcore-13.1.0.eb} | 2 +- ...9-GCCcore-13.0.1.eb => M4-1.4.19-GCCcore-13.1.0.eb} | 2 +- ...GCCcore-13.0.1.eb => zlib-1.2.13-GCCcore-13.1.0.eb} | 7 ++----- 8 files changed, 14 insertions(+), 21 deletions(-) rename easybuild/easyconfigs/b/Bison/{Bison-3.8.2-GCCcore-13.0.1.eb => Bison-3.8.2-GCCcore-13.1.0.eb} (88%) rename easybuild/easyconfigs/b/binutils/{binutils-2.40-GCCcore-13.0.1.eb => binutils-2.40-GCCcore-13.1.0.eb} (94%) rename easybuild/easyconfigs/f/flex/{flex-2.6.4-GCCcore-13.0.1.eb => flex-2.6.4-GCCcore-13.1.0.eb} (86%) rename easybuild/easyconfigs/g/GCC/{GCC-13.0.1.eb => GCC-13.1.0.eb} (97%) rename easybuild/easyconfigs/g/GCCcore/{GCCcore-13.0.1.eb => GCCcore-13.1.0.eb} (88%) rename easybuild/easyconfigs/h/help2man/{help2man-1.49.3-GCCcore-13.0.1.eb => help2man-1.49.3-GCCcore-13.1.0.eb} (91%) rename easybuild/easyconfigs/m/M4/{M4-1.4.19-GCCcore-13.0.1.eb => M4-1.4.19-GCCcore-13.1.0.eb} (94%) rename easybuild/easyconfigs/z/zlib/{zlib-1.2.13-GCCcore-13.0.1.eb => zlib-1.2.13-GCCcore-13.1.0.eb} (73%) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.1.0.eb similarity index 88% rename from easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb rename to easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.1.0.eb index 45f87974dc5..859d6c75e5a 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.0.1.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.1.0.eb @@ -7,7 +7,7 @@ homepage = 'https://www.gnu.org/software/bison' description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" -toolchain = {'name': 'GCCcore', 'version': '13.0.1'} +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] @@ -16,7 +16,7 @@ checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] builddependencies = [ ('M4', '1.4.19'), # use same binutils version that was used when building GCCcore toolchain - ('binutils', '2.39', '', SYSTEM), + ('binutils', '2.40', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.1.0.eb similarity index 94% rename from easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb rename to easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.1.0.eb index 36234b61ea1..10be685a805 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.0.1.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.1.0.eb @@ -4,7 +4,7 @@ version = '2.40' homepage = 'https://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" -toolchain = {'name': 'GCCcore', 'version': '13.0.1'} +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.1.0.eb similarity index 86% rename from easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb rename to easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.1.0.eb index e4b6d071111..6d11a9f3e06 100644 --- a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.0.1.eb +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.1.0.eb @@ -1,7 +1,7 @@ name = 'flex' version = '2.6.4' -homepage = 'http://flex.sourceforge.net/' +homepage = 'https://github.com/westes/flex' description = """ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, @@ -9,7 +9,7 @@ description = """ in text. """ -toolchain = {'name': 'GCCcore', 'version': '13.0.1'} +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] @@ -20,7 +20,7 @@ builddependencies = [ ('Bison', '3.8.2'), ('help2man', '1.49.3'), # use same binutils version that was used when building GCC toolchain - ('binutils', '2.39', '', SYSTEM), + ('binutils', '2.40', '', SYSTEM), ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb b/easybuild/easyconfigs/g/GCC/GCC-13.1.0.eb similarity index 97% rename from easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb rename to easybuild/easyconfigs/g/GCC/GCC-13.1.0.eb index b9c224ad66e..8bf33a423ce 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-13.0.1.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-13.1.0.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'GCC' -version = '13.0.1' +version = '13.1.0' homepage = 'https://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb similarity index 88% rename from easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb rename to easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb index 0b8d30d3782..3493e06b275 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.0.1.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb @@ -1,7 +1,7 @@ easyblock = 'EB_GCC' name = 'GCCcore' -version = '13.0.1' +version = '13.1.0' homepage = 'https://gcc.gnu.org/' description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, @@ -22,11 +22,7 @@ source_urls = [ 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools ] sources = [ - { - 'source_urls': ['https://gcc.gnu.org/pub/gcc/snapshots/13.1.0-RC2-20230419/'], - 'filename': 'gcc-13.1.0-RC2-20230419.tar.gz', - }, - # 'gcc-%(version)s.tar.gz', + 'gcc-%(version)s.tar.gz', 'gmp-6.2.1.tar.bz2', 'mpfr-4.1.0.tar.bz2', 'mpc-1.2.1.tar.gz', @@ -39,7 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', ] checksums = [ - {'gcc-13.1.0-RC2-20230419.tar.gz': '31188ab89af2b52fc5e3a2ef77c52d4b762e18320b3d741fa947e3d0dd306134'}, + {'gcc-13.1.0.tar.gz': 'bacd4c614d8bd5983404585e53478d467a254249e0f1bb747c8bc6d787bd4fa2'}, {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.1.0.eb similarity index 91% rename from easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb rename to easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.1.0.eb index 92adccec4f1..7cf3afc6f6c 100644 --- a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.0.1.eb +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.1.0.eb @@ -6,7 +6,7 @@ version = '1.49.3' homepage = 'https://www.gnu.org/software/help2man/' description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" -toolchain = {'name': 'GCCcore', 'version': '13.0.1'} +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_XZ] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb similarity index 94% rename from easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb rename to easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb index 6a458ba47b3..88a7a87c4dc 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.0.1.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb @@ -8,7 +8,7 @@ description = """GNU M4 is an implementation of the traditional Unix macro proce although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" -toolchain = {'name': 'GCCcore', 'version': '13.0.1'} +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.1.0.eb similarity index 73% rename from easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb rename to easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.1.0.eb index 32d9c8ca56c..082092433d1 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.0.1.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.1.0.eb @@ -8,16 +8,13 @@ description = """zlib is designed to be a free, general-purpose, legally unencum not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.""" -toolchain = {'name': 'GCCcore', 'version': '13.0.1'} +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} toolchainopts = {'pic': True} source_urls = ['https://zlib.net/fossils'] sources = [SOURCELOWER_TAR_GZ] # patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] -checksums = [ - 'b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30', # zlib-1.2.12.tar.gz - # 'f35eb05334a4f8d7b40b6c5610a6369f654863b5fa1a19c2507888f918025238', # zlib-1.2.12_fix-CC-logic-in-configure.patch -] +checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30'] # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.40', '', SYSTEM)] From cb81b83c1ce952633b84b9131faae943c4b8cbef Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 26 Apr 2023 11:24:25 +0200 Subject: [PATCH 7277/9987] use correct binutils version --- easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb index 88a7a87c4dc..5f8b9df7e74 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb @@ -15,7 +15,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] # use same binutils version that was used when building GCC toolchain -builddependencies = [('binutils', '2.39', '', SYSTEM)] +builddependencies = [('binutils', '2.40', '', SYSTEM)] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, # see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 From 3d53a0d73f9966d7fbf14768a0e60525173f2598 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Wed, 26 Apr 2023 12:26:51 +0200 Subject: [PATCH 7278/9987] blacked to solve formatting issues --- .../i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb | 24 +++++++++++-------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb index 7a7e2856fef..0acc15a6486 100644 --- a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb @@ -1,25 +1,29 @@ -easyblock = 'Binary' +easyblock = "Binary" -name = 'IsoSeq' -version = '3.8.2' -versionsuffix = '-linux-x86_64' +name = "IsoSeq" +version = "3.8.2" +versionsuffix = "-linux-x86_64" -homepage = 'https://github.com/PacificBiosciences/ioseq3' +homepage = "https://github.com/PacificBiosciences/ioseq3" description = """IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added.""" toolchain = SYSTEM source_urls = ["https://github.com/PacificBiosciences/%(namelower)s"] sources = ["releases/download/v%(version)s/%(namelower)s3"] -checksums = ['3d012810dc4cb54f89a7c80b26fc5f27da26c11f7ad6062cab462a6c691678f7'] +checksums = ["3d012810dc4cb54f89a7c80b26fc5f27da26c11f7ad6062cab462a6c691678f7"] extract_sources = False -postinstallcmds = ["cp %(builddir)s/releases/download/v%(version)s/%(namelower)s* %(installdir)s"] +postinstallcmds = [ + "cp %(builddir)s/releases/download/v%(version)s/%(namelower)s* %(installdir)s" +] sanity_check_paths = { - 'files': ['isoseq3',], - 'dirs': [''], + "files": [ + "isoseq3", + ], + "dirs": [""], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = "bio" From 2ec32b7cbeefdb44171e3f0715e7e9eef80c9392 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 26 Apr 2023 13:42:32 +0200 Subject: [PATCH 7279/9987] adding easyconfigs: GitPython-3.1.31-GCCcore-12.2.0.eb --- .../GitPython-3.1.31-GCCcore-12.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-3.1.31-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.31-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.31-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..84adb82aa2e --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.31-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.31' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('git', '2.38.1', '-nodocs'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('smmap', '5.0.0', { + 'checksums': ['c840e62059cd3be204b0c9c9f74be2c09d5648eddd4580d9314c3ecde0b30936'], + }), + ('gitdb', '4.0.10', { + 'checksums': ['6eb990b69df4e15bad899ea868dc46572c3f75339735663b81de79b06f17eb9a'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['8ce3bcf69adfdf7c7d503e78fd3b1c492af782d58893b650adb2ac8912ddd573'], + }), +] + +moduleclass = 'lib' From 70c578d60b721112a90734d205720ae6083c6d40 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 26 Apr 2023 14:03:57 +0200 Subject: [PATCH 7280/9987] adding easyconfigs: Autotools-20220317-GCCcore-13.1.0.eb, Autoconf-2.71-GCCcore-13.1.0.eb, Automake-1.16.5-GCCcore-13.1.0.eb, libtool-2.4.7-GCCcore-13.1.0.eb, Perl-5.36.1-GCCcore-13.1.0.eb --- .../Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb | 48 +++++++++++++++++++ .../Automake-1.16.5-GCCcore-13.1.0.eb | 39 +++++++++++++++ .../Autotools-20220317-GCCcore-13.1.0.eb | 24 ++++++++++ .../l/libtool/libtool-2.4.7-GCCcore-13.1.0.eb | 32 +++++++++++++ .../p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb | 25 ++++++++++ 5 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..de56240d150 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.1.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.71' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('M4', '1.4.19'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.36.1'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +sanity_check_commands = [ + "autoconf --help", + "autom4te --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.1.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..93493ff6472 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.1.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.5' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Autoconf', '2.71'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.36.1'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ['bin/aclocal', 'bin/automake'], + 'dirs': [] +} + +sanity_check_commands = [ + "aclocal --help", + "automake --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-13.1.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..37eed5a53f3 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-13.1.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20220317' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +dependencies = [ + ('Autoconf', '2.71'), # 20210128 + ('Automake', '1.16.5'), # 20211003 + ('libtool', '2.4.7'), # 20220317 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-13.1.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..cdad138698d --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-13.1.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.7' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..7abb8010a4b --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb @@ -0,0 +1,25 @@ +name = 'Perl' +version = '5.36.1' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +This is a minimal build without any modules. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +moduleclass = 'lang' From dfe0c0fb516dd92c90144673cdc8f56b0fae3a3f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 26 Apr 2023 14:18:01 +0200 Subject: [PATCH 7281/9987] adding easyconfigs: ncurses-6.4-GCCcore-13.1.0.eb, bzip2-1.0.8-GCCcore-13.1.0.eb, cURL-8.0.1-GCCcore-13.1.0.eb, XZ-5.4.2-GCCcore-13.1.0.eb, libarchive-3.6.2-GCCcore-13.1.0.eb, CMake-3.26.3-GCCcore-13.1.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb | 27 +++++++++++ .../c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb | 30 ++++++++++++ .../c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb | 43 +++++++++++++++++ .../libarchive-3.6.2-GCCcore-13.1.0.eb | 33 +++++++++++++ .../n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb | 47 +++++++++++++++++++ .../x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb | 34 ++++++++++++++ 6 files changed, 214 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..e719f5aa433 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb @@ -0,0 +1,27 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.40'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..ce03c3694cd --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.26.3' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bbd8d39217509d163cb544a40d6428ac666ddc83e22905d3e52c925781f0f659'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('cURL', '8.0.1'), + ('libarchive', '3.6.2'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..10cd7fbe3f2 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '8.0.1' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fd29000a4089934f121eff456101f0a5d09e2a3e89da1d714adf06c4be887cb'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..f0260cb95ae --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.6.2' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ba6d02f15ba04aba9c23fd5f236bb234eab9d5209e95d1c4df85c44d5f19b9b3'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('XZ', '5.4.2'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..edca9ab5954 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.4' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6931283d9ac87c5073f30b6290c4c75f21632bb4fc3603ac8100812bed248159'] + +builddependencies = [('binutils', '2.40')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts, + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..ffee85b04a3 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.4.2' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['aa49909cbd9028c4666a35fa4975f9a6203ed98154fbb8223ee43ef9ceee97c3'] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.21.1', '', SYSTEM), + ('binutils', '2.40'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' From eddba5189bb751e5c319fce339ab217e12d9bcb4 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 26 Apr 2023 14:23:29 +0200 Subject: [PATCH 7282/9987] adding easyconfigs: pyperf-2.6.0-GCCcore-12.2.0.eb --- .../p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2cc5f691e4a --- /dev/null +++ b/easybuild/easyconfigs/p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'pyperf' +version = '2.6.0' + +homepage = 'https://github.com/psf/pyperf' +description = "The Python pyperf module is a toolkit to write, run and analyze benchmarks" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d7e367a1ec7035d7a2b25f55a5925596c00cb15851f28cffd85b05b7307232af'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/pyperf'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyperf --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From d3b605a96402cf4befb5436f3046c9376d32ca1e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 26 Apr 2023 14:36:49 +0200 Subject: [PATCH 7283/9987] adding easyconfigs: pkgconf-1.9.4-GCCcore-13.1.0.eb --- .../p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..6e817cde0bd --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '1.9.4' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d6b844ab6bf8ca685e9ef8103dee64fb39b2484c7a18da64ae5ba269514c9f78'] + +builddependencies = [('binutils', '2.40')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' From 121a231fd0e180ab01412f27b9c756e72d84e388 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 26 Apr 2023 14:54:02 +0200 Subject: [PATCH 7284/9987] adding easyconfigs: VTK-9.2.6-foss-2022b.eb, meshio-5.3.4-foss-2022b.eb --- .../m/meshio/meshio-5.3.4-foss-2022b.eb | 37 ++++++++ .../easyconfigs/v/VTK/VTK-9.2.6-foss-2022b.eb | 90 +++++++++++++++++++ 2 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2022b.eb diff --git a/easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb b/easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb new file mode 100644 index 00000000000..25e3148d6ef --- /dev/null +++ b/easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'meshio' +version = '5.3.4' + +homepage = 'https://github.com/nschloe/meshio' +description = "meshio is a tool for reading/writing various mesh formats representing unstructured meshes" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), # includes numpy + ('h5py', '3.8.0'), + ('VTK', '9.2.6'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pipdate', '0.5.6', { + 'checksums': ['1b6b7ec2c5468fb7036ec9d6b2ced7a8a538db55aaca03f30199216d3bbd264b'], + }), + (name, version, { + 'checksums': ['e240692d7ff279c12b13c6e5d7b403629a86ad2b44e9230958b3f00c1ec369f0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/meshio', 'bin/pipdate'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2022b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2022b.eb new file mode 100644 index 00000000000..771c7802cbc --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2022b.eb @@ -0,0 +1,90 @@ +## +# Authors:: +# * Fotis Georgatos +# * Robert Mijakovic +## + +easyblock = 'CMakeNinja' + +name = 'VTK' +version = '9.2.6' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + {'VTK-9.2.2.tar.gz': '1c5b0a2be71fac96ff4831af69e350f7a0ea3168981f790c000709dcf9121075'}, + {'VTKData-9.2.2.tar.gz': '4b0ac438c77773ff741fd02c0e3b0dc1406b4c51e6cbe4e8304306fa125f27bf'}, + {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('XZ', '5.2.7'), + ('libGLU', '9.0.2'), + ('X11', '20221110'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + +moduleclass = 'vis' From 40f28d899009ae3cc95b3887d1e3d3841b3f47a5 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Wed, 26 Apr 2023 15:16:28 +0200 Subject: [PATCH 7285/9987] blacked to solve formatting issues - once more --- .../easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb index 0acc15a6486..7a5b7acf67a 100644 --- a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb @@ -5,7 +5,16 @@ version = "3.8.2" versionsuffix = "-linux-x86_64" homepage = "https://github.com/PacificBiosciences/ioseq3" -description = """IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique, allows to process the ever-increasing yield of PacBio machines with similar performance to IsoSeq versions 1 and 2. Starting with version 3.4, support for UMI and cell barcode based deduplication has been added.""" +description = """IsoSeq v3 contains the newest tools to identify transcripts + in PacBio single-molecule sequencing data. Starting in SMRT + Link v6.0.0, those tools power the IsoSeq GUI-based analysis + application. A composable workflow of existing tools and + algorithms, combined with a new clustering technique, allows + to process the ever-increasing yield of PacBio machines with + similar performance to IsoSeq versions 1 and 2. Starting with + version 3.4, support for UMI and cell barcode based + deduplication has been added. + """ toolchain = SYSTEM From 9ef8c8599cf564bd5a9d1f0de0f6e64237993b90 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 26 Apr 2023 18:53:28 +0200 Subject: [PATCH 7286/9987] adding easyconfigs: Tcl-8.6.13-GCCcore-13.1.0.eb, UnZip-6.0-GCCcore-13.1.0.eb, libreadline-8.2-GCCcore-13.1.0.eb, SQLite-3.41.2-GCCcore-13.1.0.eb, libffi-3.4.4-GCCcore-13.1.0.eb --- .../l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb | 29 +++++++++ .../libreadline-8.2-GCCcore-13.1.0.eb | 41 +++++++++++++ .../s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb | 39 ++++++++++++ .../t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb | 41 +++++++++++++ .../u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb | 59 +++++++++++++++++++ 5 files changed, 209 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..d64748fec2e --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.4' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d66c56ad259a82cf2a9dfc408b32bf5da52371500b84745f7fb8b645712df676'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..2c0323f20bf --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.1.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.2' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['3feb7171f16a84ee82ca18a36d7b9be109a52c04f492a053331d7d1095007c35'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('ncurses', '6.4'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..4ea12e5cf78 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.41.2' +local_filename_version = '3410200' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2023/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['e98c100dd1da4e30fa460761dab7c0b91a50b785e167f8c57acc46514fae9499'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('libreadline', '8.2'), + ('Tcl', '8.6.13'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..f8906b46e22 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.13' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('zlib', '1.2.13'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb new file mode 100644 index 00000000000..bfb9b30c73c --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT' + '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD', + '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT'] + +buildopts = ' '.join([ + "-f unix/Makefile", + 'CC="$CC"', + 'D_USE_BZ2=-DUSE_BZIP2', + 'L_BZ2=-lbz2', + 'LF2="$LDFLAGS"', + 'CF="%s"' % ' '.join(local_cf), + 'unzips', +]) + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From 7cdf4ef12498bdbc30c9ebb0f96da5d02efa89fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 26 Apr 2023 19:02:02 +0200 Subject: [PATCH 7287/9987] Fix checksum for tcl --- easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb index f8906b46e22..172e6387099 100644 --- a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.1.0'} source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] sources = ['%(namelower)s%(version)s-src.tar.gz'] -checksums = ['e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855'] +checksums = ['43a1fae7412f61ff11de2cfd05d28cfc3a73762f354a417c62370a54e2caf066'] builddependencies = [ ('binutils', '2.40'), From 5fa1cea38525a007bc67eec28fd19812d09a90b7 Mon Sep 17 00:00:00 2001 From: Christian Meesters Date: Thu, 27 Apr 2023 10:59:38 +0200 Subject: [PATCH 7288/9987] Update easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb Co-authored-by: Adam Huffman --- easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb index 7a5b7acf67a..5e8f0c47b88 100644 --- a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb @@ -35,4 +35,6 @@ sanity_check_paths = { "dirs": [""], } +sanity_check_commands = ['isoseq3 --version'] + moduleclass = "bio" From 7020045b2d3691c05c46098dfb441893ec460071 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 27 Apr 2023 14:34:58 +0200 Subject: [PATCH 7289/9987] meshio/5.3.4 remove download_dep_fail --- easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb b/easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb index 25e3148d6ef..b301aa32cb5 100644 --- a/easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb +++ b/easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb @@ -14,7 +14,6 @@ dependencies = [ ('VTK', '9.2.6'), ] -download_dep_fail = True use_pip = True exts_list = [ From 75aa600d869fd262c2d4315a61abf5d7a7ebb2c5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 27 Apr 2023 15:01:28 +0200 Subject: [PATCH 7290/9987] adding easyconfigs: xarray-2023.4.2-foss-2022b.eb --- .../x/xarray/xarray-2023.4.2-foss-2022b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2023.4.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-2023.4.2-foss-2022b.eb b/easybuild/easyconfigs/x/xarray/xarray-2023.4.2-foss-2022b.eb new file mode 100644 index 00000000000..5d8e95b6d72 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2023.4.2-foss-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'xarray' +version = '2023.4.2' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['958ec588220352343b910cbc05e54e7ab54d4e8c1c3a7783d6bfe7549d0bd0d2'], + }), +] + +moduleclass = 'data' From 0bf969f0db1548097e5b283d23f3f458f8c918a1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 27 Apr 2023 15:15:43 +0200 Subject: [PATCH 7291/9987] adding easyconfigs: coverage-7.2.3-GCCcore-12.2.0.eb --- .../coverage/coverage-7.2.3-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..724f8c3da15 --- /dev/null +++ b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'coverage' +version = '7.2.3' + +homepage = 'https://coverage.readthedocs.io' +description = """ Coverage.py is a tool for measuring code coverage of Python programs. + It monitors your program, noting which parts of the code have been executed, + then analyzes the source to identify code that could have been executed but was not. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d298c2815fa4891edd9abe5ad6e6cb4207104c7dd9fd13aea3fdebf6f9b91259'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'tools' From c7e9fcd8c17a1a3e23eebd9ec442a291863155bc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 27 Apr 2023 15:23:11 +0200 Subject: [PATCH 7292/9987] adding easyconfigs: PyTables-3.8.0-foss-2022b.eb --- .../p/PyTables/PyTables-3.8.0-foss-2022b.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022b.eb new file mode 100644 index 00000000000..82fda5ef075 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022b.eb @@ -0,0 +1,74 @@ +# http://www.pytables.org/usersguide/installation.html +# updated: Denis Kristak (INUITS) + +easyblock = 'PythonBundle' + +name = 'PyTables' +version = '3.8.0' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing, + processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and + disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions + such as relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('scikit-build', '0.17.2'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # provides numexpr + ('HDF5', '1.14.0'), + ('LZO', '2.10'), + ('Blosc', '1.21.3'), + ('Blosc2', '2.8.0'), + ('py-cpuinfo', '9.0.0'), +] + +use_pip = True + +exts_list = [ + ('blosc2', '2.0.0', { + 'patches': ['blosc2-2.0.0_use-Blosc2-dep.patch'], + 'checksums': [ + {'blosc2-2.0.0.tar.gz': 'f19b0b3674f6c825b490f00d8264b0c540c2cdc11ec7e81178d38b83c57790a1'}, + {'blosc2-2.0.0_use-Blosc2-dep.patch': '6a9443f378472ada3c8fe8a8a346fe16f22b01bab7d9e60c23b64b546178054b'}, + ], + }), + ('tables', version, { + 'patches': [ + 'PyTables-%(version)s_fix-libs.patch', + 'PyTables-3.8.0_fix-find-blosc2-library-path.patch', + ], + 'checksums': [ + {'tables-3.8.0.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'}, + {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'}, + {'PyTables-3.8.0_fix-find-blosc2-library-path.patch': + 'dcf6c3a16a138454296161e99cf6470620755d4c26303186a744f09a11e6013b'}, + ], + }), +] + +local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +sanity_pip_check = True + +moduleclass = 'data' From 2cf5df89b02c953abc4328dec43bfd1b13a9d7e5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 27 Apr 2023 15:28:34 +0200 Subject: [PATCH 7293/9987] adding easyconfigs: PyGEOS-0.14-gfbf-2022b.eb --- .../p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb new file mode 100644 index 00000000000..28d542d1710 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'PyGEOS' +version = '0.14' + +homepage = "https://pygeos.readthedocs.io" +description = """PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in + the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance + improvement when operating on arrays of geometries.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['30fbc17f64844200b85133b885fcfb65541b8779531f6ef4f8fe467d3fba7623'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('GEOS', '3.11.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'geo' From e4dc506ee19265c7eb71da6da57d6a7fda4517eb Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 27 Apr 2023 15:29:36 +0200 Subject: [PATCH 7294/9987] adding easyconfigs: netcdf4-python-1.6.3-foss-2022b.eb --- .../netcdf4-python-1.6.3-foss-2022b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.3-foss-2022b.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.3-foss-2022b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.3-foss-2022b.eb new file mode 100644 index 00000000000..ef656081b80 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.3-foss-2022b.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.3' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('netCDF', '4.9.0'), + ('cURL', '7.86.0'), + ('mpi4py', '3.1.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + (name, version, { + 'patches': [ + 'netcdf4-python-1.1.8-avoid-diskless-test.patch', + 'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch', + ], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + {'netCDF4-1.6.3.tar.gz': '8c98a3a8cda06920ee8bd24a71226ddf0328c22bd838b0afca9cb45fb4580d99'}, + {'netcdf4-python-1.1.8-avoid-diskless-test.patch': + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72'}, + {'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch': + '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166'}, + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' From 17604bd08f25e6dddeb8f114df24b81da94e2310 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 27 Apr 2023 15:30:42 +0200 Subject: [PATCH 7295/9987] adding easyconfigs: lxml-4.9.2-GCCcore-12.2.0.eb --- .../l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..20323870198 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '4.9.2' + +homepage = 'https://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2455cfaeb7ac70338b3257f41e21f0724f4b5b0c0e7702da67ee6c3640835b67'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('libxml2', '2.10.3'), + ('libxslt', '1.1.37'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 6c4b000fad66898b1e2206661929d19c8ad0cb70 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 27 Apr 2023 15:43:03 +0200 Subject: [PATCH 7296/9987] meshio v5.3.4: enable sanity_pip_check --- easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb b/easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb index b301aa32cb5..d9bcd5c7380 100644 --- a/easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb +++ b/easybuild/easyconfigs/m/meshio/meshio-5.3.4-foss-2022b.eb @@ -15,6 +15,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_list = [ ('appdirs', '1.4.4', { From c9462d49d8e13362aa927a0ae35787c41c409a66 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 27 Apr 2023 15:47:13 +0200 Subject: [PATCH 7297/9987] scikit-build/0.17.2, Blosc/1.21.3, Blosc2/2.8.0, py-cpuinfo/9.0.0 for GCCcore/12.2.0 --- .../b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb | 28 +++++++++++++ .../b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb | 31 +++++++++++++++ .../py-cpuinfo-9.0.0-GCCcore-12.2.0.eb | 39 +++++++++++++++++++ .../scikit-build-0.17.2-GCCcore-12.2.0.eb | 33 ++++++++++++++++ 4 files changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a3e524a900f --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.21.3' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['941016c4564bca662080bb01aea74f06630bd665e598c6f6967fd91b2e2e0bb6'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8eb833b9f41 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.8.0' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['be608cdf68deb02e0d3ee62e183942a0fe5d5d3185375b9b6566e2ae35a9bdbd'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a36d83f17ab --- /dev/null +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'py-cpuinfo' +version = '9.0.0' + +homepage = 'https://github.com/workhorsy/py-cpuinfo' +description = "py-cpuinfo gets CPU info with pure Python." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/cpuinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cpuinfo", + "python -m cpuinfo", +] + +options = {'modulename': 'cpuinfo'} + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ed4f8e89aff --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.2-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.17.2' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('scikit_build', version, { + 'modulename': 'skbuild', + 'checksums': ['348cfd2137c68cbf9fa589ed74fd07b0340a65a1888e2481cfc63356485188a6'], + }), +] + +moduleclass = 'lib' From 884ac473ecdaffa13d244287d9da3781c027cd81 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 28 Apr 2023 10:15:42 +0200 Subject: [PATCH 7298/9987] adding easyconfigs: cutadapt-2.10-GCCcore-10.2.0.eb --- .../cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b8f8f0dc947 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-2.10-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modufied by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Tom Strempel +# Helmholtz-Centre for Environmental Research - UFZ + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '2.10' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '0.8.4', { + 'checksums': ['dcd8f5ef5da5564f514a990573a48a0c347ee1fdbb9b6374d31592819868f7ba'], + }), + ('dnaio', '0.4.2', { + 'checksums': ['fa55a45bfd5d9272409b714158fb3a7de5dceac1034a0af84502c7f503ee84f8'], + }), + (name, version, { + 'checksums': ['936b88374b5b393a954852a0fe317a85b798dd4faf5ec52cf3ef4f3c062c242a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 93e913272139930011a83e8724c2d4e9d747852a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 28 Apr 2023 11:27:24 +0200 Subject: [PATCH 7299/9987] adding easyconfigs: bcbio-gff-0.7.0-foss-2020b.eb --- .../b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb new file mode 100644 index 00000000000..66fc839020b --- /dev/null +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb @@ -0,0 +1,42 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v0.6.7 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'bcbio-gff' +version = '0.7.0' + +homepage = 'https://github.com/chapmanb/bcbb/tree/master/gff' + +description = """ +Read and write Generic Feature Format (GFF) with Biopython integration. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['f7b3922ee274106f8716703f41f05a1795aa9d73e903f4e481995ed8f5f65d2d'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +local_bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' +local_targets = ['GFFOutput.py', 'GFFParser.py'] + +sanity_check_paths = { + 'files': [local_bcbiogffroot + '/BCBio/GFF/%s' % x for x in local_targets], + 'dirs': [local_bcbiogffroot], +} + +options = {'modulename': 'BCBio.GFF'} + +moduleclass = 'bio' From 67de0c2e182236bd2723a1e331c300e96bd22051 Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Fri, 28 Apr 2023 13:12:09 +0200 Subject: [PATCH 7300/9987] adding easyconfigs: BAMM-2.5.0-foss-2022a.eb --- .../b/BAMM/BAMM-2.5.0-foss-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb new file mode 100644 index 00000000000..023f4d53608 --- /dev/null +++ b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'BAMM' +version = '2.5.0' + +homepage = 'http://bamm-project.org/' +description = """ BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. +It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of +lineage diversification and trait evolution. """ + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +# https://github.com/macroevolution/bamm +github_account = 'macroevolution' +# source_urls = ['https://github.com/macroevolution/bamm/archive'] +source_urls = ['GITHUB_LOWER_SOURCE'] +sources = ['v%(version)s.tar.gz'] +checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4'] + +builddependencies = [('CMake', '3.23.1')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["%(namelower)s"] + +moduleclass = 'bio' From 618489ae9eb03eb44ba84a92d1e6d082aab890aa Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 28 Apr 2023 14:28:12 +0000 Subject: [PATCH 7301/9987] adding easyconfigs: ont-guppy-6.4.8-CUDA-11.7.0.eb --- .../ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb new file mode 100644 index 00000000000..65649652d4d --- /dev/null +++ b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Tarball' + +name = 'ont-guppy' +version = '6.4.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://community.nanoporetech.com/protocols/Guppy-protocol' +description = """ +Guppy is a bioinformatics toolkit that enables real-time basecalling and several + post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms. + + For Research Use Only +""" + +toolchain = SYSTEM + +source_urls = ['https://mirror.oxfordnanoportal.com/software/analysis'] +sources = ['%(name)s_%(version)s_linux64.tar.gz'] +checksums = ['d58aba66b1b29180946ecacf3f7b423a6933db5d12aeda783485b1ee82fd110b'] + +dependencies = [ + ('CUDA', '11.7.0'), +] + +_bins = ['guppy_%s' % x for x in ['aligner', 'barcoder', 'basecall_client', 'basecaller', 'basecaller_duplex', + 'basecaller_supervisor', 'basecall_server']] +_libs = ['lib/libvbz_hdf_plugin.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins] + _libs, + 'dirs': ['data'], +} + +# requires libcuda.so to be present, else it exits with code 127 +# sanity_check_commands = ['%s --help' % x for x in _bins] + +moduleclass = 'bio' From ad2d8a50d44b7eb248fb628febdf45efe86d10c5 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Fri, 28 Apr 2023 16:55:35 +0200 Subject: [PATCH 7302/9987] Fix ZLIB linking --- easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb | 2 ++ easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb index 7820338ddff..ca2a334a1af 100644 --- a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb @@ -24,7 +24,9 @@ dependencies = [ ] preconfigopts = 'cd src && ' +preconfigopts += 'sed -i -e "/ac_cv_c_zlib=.*with_zlib/s,},}/libz.so," configure && ' configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc ' +configopts += '--with-zlib=$EBROOTZLIB/lib --with-zlibinclude=$EBROOTZLIB/include ' configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib' prebuildopts = 'cd src &&' diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb index 68de3e62b7c..5f8d5037d42 100644 --- a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb @@ -24,7 +24,9 @@ dependencies = [ ] preconfigopts = 'cd src && ' +preconfigopts += 'sed -i -e "/ac_cv_c_zlib=.*with_zlib/s,},}/libz.so," configure && ' configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc ' +configopts += '--with-zlib=$EBROOTZLIB/lib --with-zlibinclude=$EBROOTZLIB/include ' configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib' prebuildopts = 'cd src &&' From 6426027275789c39f47c54c31f991af5f478881d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 28 Apr 2023 16:13:10 +0100 Subject: [PATCH 7303/9987] specify source_urls inside exts_default_options to ensure correct name expansion for the archivedd packages --- .../Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb | 18 ++++++++---------- .../Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb | 17 ++++++++--------- .../Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb | 15 ++++++++------- .../Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb | 15 ++++++++------- .../Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb | 15 ++++++++------- 5 files changed, 40 insertions(+), 40 deletions(-) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb index be3f28cdb22..0489f0e3fcf 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb @@ -9,37 +9,35 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] - dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', versionsuffix), ] exts_defaultclass = 'RPackage' -exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} exts_list = [ ('spatstat.utils', '2.1-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.utils'], 'checksums': ['ed3569fea295b62396c49cdcfe476414b0b0f3e52044175532f316a402d3f8a1'], }), ('spatstat.data', '2.1-0', { 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], }), ('spatstat.geom', '2.0-1', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'], 'checksums': ['70ebfe115e733b2e6778baf6e2935861472154c0dd21f15a84ec2a61e0a3f6e4'], }), ('spatstat.sparse', '2.0-0', { 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], }), ('spatstat.core', '2.0-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'], 'checksums': ['fde9a91bd32b7a3c8b25e802a16d470dcc919c24da5715149e1d91eeec119ba7'], }), (name, version, { diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb index d71472a2d5e..b8a228157b7 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb @@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] - dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', versionsuffix), ] exts_defaultclass = 'RPackage' -exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} exts_list = [ ('spatstat.utils', '2.2-0', { @@ -31,14 +32,12 @@ exts_list = [ 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], }), ('spatstat.geom', '2.2-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'], 'checksums': ['70b063a7f317f531b2afb3afaedb047fce81b39ee481a4067962529d6069634c'], }), ('spatstat.sparse', '2.0-0', { 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], }), ('spatstat.core', '2.2-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'], 'checksums': ['0ecbc1ae688c8d4f41db3efa6253ac8db5c432ef714240d01a2b195950d65253'], }), ('Matrix', '1.3-4', { diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb index af03c570285..19cfccaecdc 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb @@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'foss', 'version': '2022a'} -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] - dependencies = [ ('R', '4.2.1'), ('R-bundle-Bioconductor', '3.15', versionsuffix), ] exts_defaultclass = 'RPackage' -exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} exts_list = [ ('Matrix', '1.5-1', { diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb index b98250be5b3..fe25468c3f6 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb @@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'foss', 'version': '2021b'} -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] - dependencies = [ ('R', '4.1.2'), ('R-bundle-Bioconductor', '3.14', versionsuffix), ] exts_defaultclass = 'RPackage' -exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} exts_list = [ ('Matrix', '1.5-3', { diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb index 3529ca55994..032d6c672cd 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb @@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'foss', 'version': '2022a'} -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] - dependencies = [ ('R', '4.2.1'), ('R-bundle-Bioconductor', '3.15', versionsuffix), ] exts_defaultclass = 'RPackage' -exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} exts_list = [ ('Matrix', '1.5-4', { From 04b54c5cfec69df6ae9e3ee70d69683cb9f5c36c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 1 May 2023 01:06:27 +0200 Subject: [PATCH 7304/9987] adding easyconfigs: Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb --- ...-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb | 456 ++++++++++++++++++ 1 file changed, 456 insertions(+) create mode 100644 easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb diff --git a/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb b/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb new file mode 100644 index 00000000000..b3535b944b2 --- /dev/null +++ b/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb @@ -0,0 +1,456 @@ +easyblock = 'Cargo' + +name = 'Evcxr-REPL' +version = '0.14.2' +local_rustver = '1.65.0' +versionsuffix = '-Rust-' + local_rustver + +homepage = 'https://github.com/evcxr' +description = "A Rust REPL (Read-Eval-Print loop) built using the evcxr evaluation context." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +crates = [ + ('evcxr_repl', version), + ('evcxr', version), + ('addr2line', '0.19.0'), + ('adler', '1.0.2'), + ('always-assert', '0.1.2'), + ('ansi_term', '0.12.1'), + ('anyhow', '1.0.68'), + ('anymap', '1.0.0-beta.2'), + ('ariadne', '0.1.5'), + ('arrayvec', '0.7.2'), + ('atty', '0.2.14'), + ('autocfg', '1.1.0'), + ('backtrace', '0.3.67'), + ('bitflags', '1.3.2'), + ('camino', '1.1.1'), + ('cargo-platform', '0.1.2'), + ('cargo_metadata', '0.15.2'), + ('cc', '1.0.78'), + ('cfg-if', '1.0.0'), + ('chalk-derive', '0.88.0'), + ('chalk-ir', '0.88.0'), + ('chalk-recursive', '0.88.0'), + ('chalk-solve', '0.88.0'), + ('clap', '2.34.0'), + ('clipboard-win', '4.4.2'), + ('colored', '2.0.0'), + ('countme', '3.0.1'), + ('cov-mark', '2.0.0-pre.1'), + ('crossbeam-channel', '0.5.6'), + ('crossbeam-deque', '0.8.2'), + ('crossbeam-epoch', '0.9.13'), + ('crossbeam-utils', '0.8.14'), + ('ctrlc', '3.2.4'), + ('dashmap', '5.4.0'), + ('dirs', '4.0.0'), + ('dirs-next', '2.0.0'), + ('dirs-sys', '0.3.7'), + ('dirs-sys-next', '0.1.2'), + ('dissimilar', '1.0.5'), + ('dot', '0.1.4'), + ('drop_bomb', '0.1.5'), + ('either', '1.8.0'), + ('ena', '0.14.0'), + ('endian-type', '0.1.2'), + ('errno', '0.2.8'), + ('errno-dragonfly', '0.1.2'), + ('error-code', '2.3.1'), + ('evcxr_input', '1.0.0'), + ('fastrand', '1.8.0'), + ('fd-lock', '3.0.8'), + ('filetime', '0.2.19'), + ('fixedbitset', '0.2.0'), + ('form_urlencoded', '1.1.0'), + ('fsevent-sys', '4.1.0'), + ('fst', '0.4.7'), + ('getrandom', '0.2.8'), + ('gimli', '0.27.0'), + ('hashbrown', '0.12.3'), + ('heck', '0.3.3'), + ('hermit-abi', '0.1.19'), + ('hermit-abi', '0.2.6'), + ('hkalbasi-rustc-ap-rustc_abi', '0.0.20221221'), + ('hkalbasi-rustc-ap-rustc_index', '0.0.20221221'), + ('home', '0.5.4'), + ('idna', '0.3.0'), + ('indexmap', '1.9.2'), + ('inotify', '0.9.6'), + ('inotify-sys', '0.1.5'), + ('instant', '0.1.12'), + ('io-lifetimes', '1.0.3'), + ('itertools', '0.10.5'), + ('itoa', '1.0.5'), + ('jod-thread', '0.1.2'), + ('json', '0.12.4'), + ('kqueue', '1.0.7'), + ('kqueue-sys', '1.0.3'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.139'), + ('libloading', '0.7.4'), + ('libmimalloc-sys', '0.1.28'), + ('linux-raw-sys', '0.1.4'), + ('lock_api', '0.4.9'), + ('log', '0.4.17'), + ('memchr', '2.5.0'), + ('memoffset', '0.6.5'), + ('memoffset', '0.7.1'), + ('mimalloc', '0.1.32'), + ('miniz_oxide', '0.6.2'), + ('mio', '0.8.5'), + ('miow', '0.5.0'), + ('nibble_vec', '0.1.0'), + ('nix', '0.24.3'), + ('nix', '0.26.1'), + ('notify', '5.0.0'), + ('num_cpus', '1.15.0'), + ('object', '0.30.0'), + ('once_cell', '1.17.0'), + ('oorandom', '11.1.3'), + ('parking_lot', '0.11.2'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.8.6'), + ('parking_lot_core', '0.9.5'), + ('percent-encoding', '2.2.0'), + ('perf-event', '0.4.8'), + ('perf-event-open-sys', '4.0.0'), + ('petgraph', '0.5.1'), + ('pin-project-lite', '0.2.9'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '1.0.49'), + ('pulldown-cmark', '0.9.2'), + ('pulldown-cmark-to-cmark', '10.0.4'), + ('quote', '1.0.23'), + ('ra_ap_base_db', '0.0.145'), + ('ra_ap_cfg', '0.0.145'), + ('ra_ap_hir', '0.0.145'), + ('ra_ap_hir_def', '0.0.145'), + ('ra_ap_hir_expand', '0.0.145'), + ('ra_ap_hir_ty', '0.0.145'), + ('ra_ap_ide', '0.0.145'), + ('ra_ap_ide_assists', '0.0.145'), + ('ra_ap_ide_completion', '0.0.145'), + ('ra_ap_ide_db', '0.0.145'), + ('ra_ap_ide_diagnostics', '0.0.145'), + ('ra_ap_ide_ssr', '0.0.145'), + ('ra_ap_la-arena', '0.0.145'), + ('ra_ap_limit', '0.0.145'), + ('ra_ap_mbe', '0.0.145'), + ('ra_ap_parser', '0.0.145'), + ('ra_ap_paths', '0.0.145'), + ('ra_ap_profile', '0.0.145'), + ('ra_ap_project_model', '0.0.145'), + ('ra_ap_stdx', '0.0.145'), + 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{'winapi-util-0.1.5.tar.gz': '70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.42.0.tar.gz': '5a3e1820f08b8513f676f7ab6c1f99ff312fb97b553d30ff4dd86f9f15728aa7'}, + {'windows_aarch64_gnullvm-0.42.0.tar.gz': '41d2aa71f6f0cbe00ae5167d90ef3cfe66527d6f613ca78ac8024c3ccab9a19e'}, + {'windows_aarch64_msvc-0.42.0.tar.gz': 'dd0f252f5a35cac83d6311b2e795981f5ee6e67eb1f9a7f64eb4500fbc4dcdb4'}, + {'windows_i686_gnu-0.42.0.tar.gz': 'fbeae19f6716841636c28d695375df17562ca208b2b7d0dc47635a50ae6c5de7'}, + {'windows_i686_msvc-0.42.0.tar.gz': '84c12f65daa39dd2babe6e442988fc329d6243fdce47d7d2d155b8d874862246'}, + {'windows_x86_64_gnu-0.42.0.tar.gz': 'bf7b1b21b5362cbc318f686150e5bcea75ecedc74dd157d874d754a2ca44b0ed'}, + {'windows_x86_64_gnullvm-0.42.0.tar.gz': '09d525d2ba30eeb3297665bd434a54297e4170c7f1a44cad4ef58095b4cd2028'}, + {'windows_x86_64_msvc-0.42.0.tar.gz': 'f40009d85759725a34da6d89a94e63d7bdc50a862acf0dbc7c8e488f1edcb6f5'}, + {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'}, +] + +dependencies = [ + ('Rust', local_rustver), +] + +sanity_check_paths = { + 'files': ['bin/evcxr'], + 'dirs': [], +} + +sanity_check_commands = ["evcxr --help"] + +moduleclass = 'tools' From a6fbc1bae854038b0c740e84a9775681ec1da6dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 1 May 2023 01:17:22 +0200 Subject: [PATCH 7305/9987] Change Perl description --- easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb index 7abb8010a4b..8afe00dcf4d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb @@ -4,7 +4,7 @@ version = '5.36.1' homepage = 'https://www.perl.org/' description = """Larry Wall's Practical Extraction and Report Language -This is a minimal build without any modules. Should only be used for build dependencies. +This is a minimal build without any extra modules. """ toolchain = {'name': 'GCCcore', 'version': '13.1.0'} From b29995e8200602e5895b165c6bbcd5dcd502e0bb Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Mon, 1 May 2023 09:40:18 +0200 Subject: [PATCH 7306/9987] remove single quotes --- easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb index 023f4d53608..9fe5174b287 100644 --- a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb @@ -13,8 +13,7 @@ toolchainopts = {'usempi': True} # https://github.com/macroevolution/bamm github_account = 'macroevolution' -# source_urls = ['https://github.com/macroevolution/bamm/archive'] -source_urls = ['GITHUB_LOWER_SOURCE'] +source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4'] From 7e7a359704a4608043f2bea2170ed9e520d38e43 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 2 May 2023 11:23:39 +0200 Subject: [PATCH 7307/9987] adding easyconfigs: EZC3D-1.5.2-foss-2022a.eb --- .../e/EZC3D/EZC3D-1.5.2-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/e/EZC3D/EZC3D-1.5.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/EZC3D/EZC3D-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EZC3D/EZC3D-1.5.2-foss-2022a.eb new file mode 100644 index 00000000000..e7880604adc --- /dev/null +++ b/easybuild/easyconfigs/e/EZC3D/EZC3D-1.5.2-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = "CMakePythonPackage" + +name = 'EZC3D' +version = '1.5.2' + +homepage = 'https://pyomeca.github.io/Documentation/ezc3d/index.html' +description = """EZC3D is an easy to use reader, modifier and writer for C3D format files. It is +written en C++ with proper binders for Python and MATLAB/Octave scripting +langages.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'pyomeca' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['Release_%(version)s.tar.gz'] +checksums = ['469c2089c0f885c9dd994bb02d70939da1ec2ddd37ea353964aafa8a5b2d7165'] + +builddependencies = { + ('binutils', '2.38'), + ('CMake', '3.24.3'), + ('SWIG', '4.0.2'), +} + +dependencies = { + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +} + +# enable Python bindings +_py_install_dir = "%(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s" +configopts = "-DBINDER_PYTHON3=ON " +configopts += "-DPYTHON_INSTALL_PREFIX=%s" % _py_install_dir + +sanity_check_paths = { + 'files': ['lib/libezc3d.%s' % SHLIB_EXT], + 'dirs': ['include/ezc3d', _py_install_dir], +} + +moduleclass = 'lib' From 8c6ba56161e0fd0abf7ce99a9a32bda775b6a8e9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 2 May 2023 09:28:49 +0000 Subject: [PATCH 7308/9987] adding easyconfigs: MRPRESSO-1.0-20230502-foss-2022a.eb --- .../MRPRESSO-1.0-20230502-foss-2022a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb b/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb new file mode 100644 index 00000000000..710f1feccad --- /dev/null +++ b/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'MRPRESSO' +# In spite of the repo name, everything else refers to MRPRESSO +local_commit = 'cece763' +# see DESCRIPTION to determine version, +# but also take date of last commit into account (since version isn't always bumped) +version = '1.0-20230502' + +homepage = 'https://github.com/rondolab/MR-PRESSO' +description = "Performs the Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO) method.." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/rondolab/MR-PRESSO/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['f6c464f239eaf6341ac19bde272b3b1c0700013c32bcf480c1a2f18d177b630f'] + +dependencies = [ + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 45e2023300aa74f4173ce91ba122441e13ef8934 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 2 May 2023 11:29:04 +0200 Subject: [PATCH 7309/9987] adding easyconfigs: h5netcdf-1.1.0-foss-2021b.eb --- .../h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb new file mode 100644 index 00000000000..7efee9efd0a --- /dev/null +++ b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'h5netcdf' +version = '1.1.0' + +homepage = 'https://h5netcdf.org/' +description = """A Python interface for the netCDF4 file-format that reads and writes local or +remote HDF5 files directly via h5py or h5pyd, without relying on the Unidata +netCDF library.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('h5py', '3.6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['932c3b573bed7370ebfc9e802cd60f1a4da5236efb11b36eeff897324d76bf56'], + }), +] + +moduleclass = 'data' From c7ae9b1d4b12e700e5eaaa3694d9525c790dbbd5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 2 May 2023 11:25:32 +0200 Subject: [PATCH 7310/9987] adding easyconfigs: batchgenerators-0.25-foss-2021a.eb, HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb, HD-BET-20220318-foss-2021a.eb --- .../batchgenerators-0.25-foss-2021a.eb | 30 ++++++++++++++++ .../HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb | 34 +++++++++++++++++++ .../h/HD-BET/HD-BET-20220318-foss-2021a.eb | 32 +++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb create mode 100644 easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a.eb diff --git a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb new file mode 100644 index 00000000000..8fc66740160 --- /dev/null +++ b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'batchgenerators' +version = '0.25' + +homepage = 'https://github.com/MIC-DKFZ/batchgenerators' +description = """Data augmentation toolkit developed at the Division of Medical +Image Computing at the German Cancer Research Center (DKFZ) to suit all our +deep learning data augmentation needs.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['38a67413e847ff367e64abac36331fcb065494202d526ae96f7644de3a0e5495'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-image', '0.18.3'), + ('scikit-learn', '0.24.2'), +] + +# remove requirement on Pillow and unittest2, which are not actually used +preinstallopts = "sed -i '13d;19d' setup.py &&" + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..0b7aef32343 --- /dev/null +++ b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'HD-BET' +version = '20220318' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = '56c7fb8e6509563aa6377cdb0f2dd4e7ad359252' + +homepage = 'https://github.com/MIC-DKFZ/HD-BET' +description = "Tool for brain extraction." + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'MIC-DKFZ' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%s.tar.gz' % _commit] +checksums = ['744eb7b084feefb4243855529537a47fa4d1c1d93b6b967969c2ede8b9b8b46a'] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyTorch', '1.10.0', versionsuffix), + ('scikit-image', '0.18.3'), + ('SimpleITK', '2.1.1'), + ('batchgenerators', '0.25'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'HD_BET'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a.eb b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a.eb new file mode 100644 index 00000000000..e671387837e --- /dev/null +++ b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'HD-BET' +version = '20220318' +_commit = '56c7fb8e6509563aa6377cdb0f2dd4e7ad359252' + +homepage = 'https://github.com/MIC-DKFZ/HD-BET' +description = "Tool for brain extraction." + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'MIC-DKFZ' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%s.tar.gz' % _commit] +checksums = ['744eb7b084feefb4243855529537a47fa4d1c1d93b6b967969c2ede8b9b8b46a'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyTorch', '1.10.0'), + ('scikit-image', '0.18.3'), + ('SimpleITK', '2.1.1'), + ('batchgenerators', '0.25'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'HD_BET'} + +moduleclass = 'bio' From 44666e9328860d34494adc722c98be3f1f05504c Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 2 May 2023 13:30:18 +0200 Subject: [PATCH 7311/9987] Delete Kalign-2.0.4-GCCcore-11.2.0.eb removed unnecessary Kalign --- .../k/Kalign/Kalign-2.0.4-GCCcore-11.2.0.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-11.2.0.eb deleted file mode 100644 index 53da691c60e..00000000000 --- a/easybuild/easyconfigs/k/Kalign/Kalign-2.0.4-GCCcore-11.2.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -# Contribution from the NIHR Biomedical Research Centre -# Guy's and St Thomas' NHS Foundation Trust and King's College London -# updated by Denis Kristak (Inuits) - -easyblock = "ConfigureMake" - -name = "Kalign" -version = "2.0.4" - -homepage = "https://msa.sbc.su.se/cgi-bin/msa.cgi" -description = ( - "Kalign is a fast multiple sequence alignment program for biological sequences." -) - -toolchain = {"name": "GCCcore", "version": "11.2.0"} - -source_urls = ["http://msa.sbc.su.se/downloads/kalign/"] -sources = [{"filename": SOURCELOWER_TAR_GZ, "download_filename": "current.tar.gz"}] -checksums = ['8cf20ac4e1807dc642e7ffba8f42a117313beccaee4f87c5555d53a2eeac4cbb'] - -install_cmd = "mkdir %(installdir)s/bin && cp kalign %(installdir)s/bin" - -sanity_check_paths = { - "files": ["bin/kalign"], - "dirs": [], -} - -moduleclass = "bio" From a0ea025a9c06474f005cd3a0e63fd699b1d701a9 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 2 May 2023 13:43:51 +0200 Subject: [PATCH 7312/9987] adding easyconfigs: python-docx-0.8.11-GCCcore-12.2.0.eb --- .../python-docx-0.8.11-GCCcore-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4dc389d5dc9 --- /dev/null +++ b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'python-docx' +version = '0.8.11' + +homepage = 'https://python-docx.readthedocs.io/en/latest/' +description = 'python-docx is a Python library for creating and updating Microsoft Word (.docx) files' + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1105d233a0956dd8dd1e710d20b159e2d72ac3c301041b95f4d4ceb3e0ebebc4'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('lxml', '4.9.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'docx'} + +moduleclass = 'tools' From 4b031244095230c28cc9b4ce2a128605502e13ec Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 2 May 2023 13:49:09 +0200 Subject: [PATCH 7313/9987] adding easyconfigs: trimesh-3.21.5-gfbf-2022b.eb --- .../t/trimesh/trimesh-3.21.5-gfbf-2022b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/trimesh/trimesh-3.21.5-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-3.21.5-gfbf-2022b.eb b/easybuild/easyconfigs/t/trimesh/trimesh-3.21.5-gfbf-2022b.eb new file mode 100644 index 00000000000..b0321430d59 --- /dev/null +++ b/easybuild/easyconfigs/t/trimesh/trimesh-3.21.5-gfbf-2022b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'trimesh' +version = '3.21.5' + +homepage = 'https://trimsh.org/' +description = """Trimesh is a Python (2.7- 3.3+) library for loading and using triangular meshes with an emphasis on +watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy +manipulation and analysis, in the style of the excellent Polygon object in the Shapely library.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['74741bc7f9fcb94b98951db8dc8ec8364a2ef52ac2ca0761c7ba06182ef329be'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # numpy required +] + +moduleclass = 'lib' From 69dc5916aec10b0cc5748fb2f77cc94e0185731c Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 2 May 2023 13:50:45 +0200 Subject: [PATCH 7314/9987] style improvements --- .../easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb index dc2fd189965..a9e23e124d4 100644 --- a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb @@ -35,7 +35,7 @@ exts_list = [ (name, version, { 'modulename': 'cctbx', # remove deps (they fail during sanity check, even though they are installed) - 'postinstallcmds': ["echo '' > %(installdir)s/lib/python3.8/site-packages/cctbx_base-2020.8.dist-info/METADATA"], + 'postinstallcmds': ["echo '' > %s" % local_metadata_folder], 'sources': [{ 'download_filename': 'cctbx_base-2020.8-0_py38h167b89d-cp38-cp38m-manylinux2010_x86_64.whl', 'filename': 'cctbx_base-2020.8-cp38-cp38-manylinux2010_x86_64.whl' From 509d547095a608e4de580fa96bac037abf6ac21d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 2 May 2023 13:15:41 +0100 Subject: [PATCH 7315/9987] add Doxygen build dependency to X11 --- easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb | 1 + easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb | 1 + easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb | 1 + easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb | 1 + easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb | 1 + easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb | 1 + easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb | 1 + 7 files changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb index 21b4362d798..44897b5de17 100644 --- a/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb @@ -31,6 +31,7 @@ builddependencies = [ ('gettext', '0.20.1'), ('pkg-config', '0.29.2'), ('intltool', '0.51.0'), + ('Doxygen', '1.8.16'), ] default_easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb index 0c4398adb92..ae81bf67362 100644 --- a/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.55.1', '-Python-3.8.2'), ('Ninja', '1.10.0'), + ('Doxygen', '1.8.17'), ] dependencies = [ ('bzip2', '1.0.8'), diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb index d1a9f51ec07..c5a69cfdb84 100644 --- a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.55.3'), ('Ninja', '1.10.1'), + ('Doxygen', '1.8.20'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb index b2104033854..e277989781e 100644 --- a/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.58.0'), ('Ninja', '1.10.2'), + ('Doxygen', '1.9.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb index 259c0017c55..adc8a9e814b 100644 --- a/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.58.2'), ('Ninja', '1.10.2'), + ('Doxygen', '1.9.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb index d417d954c4b..0b3c1e7407b 100644 --- a/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.62.1'), ('Ninja', '1.10.2'), + ('Doxygen', '1.9.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb index ea22050d122..f98e6b15dbc 100644 --- a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.64.0'), ('Ninja', '1.11.1'), + ('Doxygen', '1.9.5'), ] dependencies = [ From c21337d03bda7d5be2098ecd774bb5ec3c97c732 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 2 May 2023 13:31:32 +0200 Subject: [PATCH 7316/9987] adding easyconfigs: Rtree-1.0.1-GCCcore-12.2.0.eb, libspatialindex-1.9.3-GCCcore-12.2.0.eb --- .../libspatialindex-1.9.3-GCCcore-12.2.0.eb | 25 +++++++++++++++++ .../r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb | 28 +++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0535f0e96f8 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'libspatialindex' +version = '1.9.3' + +homepage = 'https://libspatialindex.org' +description = """C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/libspatialindex/libspatialindex/releases/download/%(version)s/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['47d8779e32477b330e46b62fb7e62cb812caee5d8e684c35cb635a42a749f3fc'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['lib/libspatialindex.%s' % SHLIB_EXT], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5650717ef68 --- /dev/null +++ b/easybuild/easyconfigs/r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Rtree' +version = '1.0.1' + +homepage = 'https://toblerity.org/rtree/' +description = """Rtree is a ctypes Python wrapper of libspatialindex that provides a number of advanced spatial + indexing features for the spatially curious Python user.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['222121699c303a64065d849bf7038b1ecabc37b65c7fa340bedb38ef0e805429'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('libspatialindex', '1.9.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'data' From cb4bd2fd96026b32434cd910050025413c5527e8 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 2 May 2023 14:49:08 +0200 Subject: [PATCH 7317/9987] adding easyconfigs: xxHash-0.8.1-GCCcore-12.2.0.eb, python-xxhash-3.2.0-GCCcore-12.2.0.eb --- .../python-xxhash-3.2.0-GCCcore-12.2.0.eb | 29 +++++++++++++++++ .../x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.2.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.2.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..54e733c36c8 --- /dev/null +++ b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.2.0-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'python-xxhash' +version = '3.2.0' + +homepage = 'https://github.com/ifduyue/python-xxhash' +description = 'xxhash is a Python binding for the xxHash library by Yann Collet.' + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('xxHash', '0.8.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xxhash', version, { + 'checksums': ['1afd47af8955c5db730f630ad53ae798cf7fae0acb64cebb3cf94d35c47dd088'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..1cb665e6061 --- /dev/null +++ b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'xxHash' +version = '0.8.1' + +homepage = 'https://cyan4973.github.io/xxHash' +description = "xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/Cyan4973/xxHash/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3bb6b7d6f30c591dd65aaaff1c8b7a5b94d81687998ca9400082c739a690436c'] + +builddependencies = [ + ('binutils', '2.39'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/xxhsum', 'include/xxh3.h', 'include/xxhash.h', + 'lib/libxxhash.a', 'lib/libxxhash.%s' % SHLIB_EXT, 'lib/pkgconfig/libxxhash.pc'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["xxhsum --help"] + +moduleclass = 'tools' From 79b0363bd7b281997d672d23dbf9503312dbc9ee Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 2 May 2023 17:25:20 +0200 Subject: [PATCH 7318/9987] adding easyconfigs: Pandoc-3.1.2.eb --- .../easyconfigs/p/Pandoc/Pandoc-3.1.2.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pandoc/Pandoc-3.1.2.eb diff --git a/easybuild/easyconfigs/p/Pandoc/Pandoc-3.1.2.eb b/easybuild/easyconfigs/p/Pandoc/Pandoc-3.1.2.eb new file mode 100644 index 00000000000..5916797cde8 --- /dev/null +++ b/easybuild/easyconfigs/p/Pandoc/Pandoc-3.1.2.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'Tarball' + +name = 'Pandoc' +version = '3.1.2' + +homepage = 'https://pandoc.org' +description = "If you need to convert files from one markup format into another, pandoc is your swiss-army knife" + +toolchain = SYSTEM + +_archs = {'x86_64': 'amd64', 'aarch64': 'arm64'} + +source_urls = ['https://github.com/jgm/pandoc/releases/download/%(version)s/'] +sources = ['%%(namelower)s-%%(version)s-linux-%s.tar.gz' % _archs[ARCH]] +checksums = ['4e1c607f7e4e9243fa1e1f5b208cd4f1d3f6fd055d5d8c39ba0cdc38644e1c35'] + +sanity_check_paths = { + 'files': ['bin/pandoc'], + 'dirs': ['share'], +} + +sanity_check_commands = ['pandoc --help'] + +moduleclass = 'tools' From 8b13fe7ee04c69580d05155624951306d3846845 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 2 May 2023 18:01:20 +0200 Subject: [PATCH 7319/9987] Include core CPAN packages for autotools --- .../p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb | 63 ++++++++++++++++++- 1 file changed, 62 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb index 8afe00dcf4d..687af7133ae 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb @@ -4,7 +4,7 @@ version = '5.36.1' homepage = 'https://www.perl.org/' description = """Larry Wall's Practical Extraction and Report Language -This is a minimal build without any extra modules. +Includes a small selection of extra CPAN packages for core functionality. """ toolchain = {'name': 'GCCcore', 'version': '13.1.0'} @@ -22,4 +22,65 @@ dependencies = [ ('zlib', '1.2.13'), ] +# !! order of extensions is important !! +# extensions updated on 2023-05-02 +# includes all dependencies for Autotools +exts_list = [ + ('threads', '2.21', { + 'source_tmpl': 'threads-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['28394c98a2bcae6f20ffb8a3d965a1c194b764c650169e2050ee38dbaa10f110'], + }), + ('constant', '1.33', { + 'source_tmpl': 'constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], + }), + ('Getopt::Long', '2.54', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + 'checksums': ['584ba3c99bb2d6b341375212f9b874613f706cfb01cee21b8a2676a98ab985fe'], + }), + ('File::Path', '2.18', { + 'source_tmpl': 'File-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN/'], + 'checksums': ['980f0a17edb353df46e9cd7b357f9f5929cde0f80c45fd7a06cf7e0e8bd6addd'], + }), + ('File::Spec', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('IO::File', '1.51', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'], + 'checksums': ['5493ea55998728cd2b7ecb8234c58fb5d5df27098d0f07addca22444d7616ce0'], + }), + ('Thread::Queue', '3.13', { + 'source_tmpl': 'Thread-Queue-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['6ba3dacddd2fbb66822b4aa1d11a0a5273cd04c825cb3ff31c20d7037cbfdce8'], + }), + ('Carp', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('Exporter', '5.77', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['3892ee5c6ae6e482068d53b61e25cae4fc71ddc79cc47446e385df0a669bb8ed'], + }), + ('Text::ParseWords', '3.31', { + 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], + 'checksums': ['3892ee5c6ae6e482068d53b61e25cae4fc71ddc79cc47446e385df0a669bb8ed'], + }), + ('Data::Dumper', '2.183', { + 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], + 'checksums': ['3892ee5c6ae6e482068d53b61e25cae4fc71ddc79cc47446e385df0a669bb8ed'], + }), +] + moduleclass = 'lang' From e7da521e0c7ab286d8539b17ac418f6ab994498d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 2 May 2023 18:13:48 +0200 Subject: [PATCH 7320/9987] Fix checksums --- easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb index 687af7133ae..929a2807a02 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb @@ -74,12 +74,12 @@ exts_list = [ ('Text::ParseWords', '3.31', { 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], - 'checksums': ['3892ee5c6ae6e482068d53b61e25cae4fc71ddc79cc47446e385df0a669bb8ed'], + 'checksums': ['2ae555ba084d75b2b8feeeb8d1a00911276815ada86bccb1452236964d5a2fc7'], }), ('Data::Dumper', '2.183', { 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], - 'checksums': ['3892ee5c6ae6e482068d53b61e25cae4fc71ddc79cc47446e385df0a669bb8ed'], + 'checksums': ['e42736890b7dae1b37818d9c5efa1f1fdc52dec04f446a33a4819bf1d4ab5ad3'], }), ] From fe2f067953c44d6272a1fbde82a4bef7f238d535 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 3 May 2023 02:40:01 +0200 Subject: [PATCH 7321/9987] Make download instructions more general --- easybuild/easyconfigs/m/MATLAB/MATLAB-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2023a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2023a.eb index 052dc0ace6e..296a007e994 100644 --- a/easybuild/easyconfigs/m/MATLAB/MATLAB-2023a.eb +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2023a.eb @@ -8,9 +8,9 @@ description = """MATLAB is a high-level language and interactive environment toolchain = SYSTEM -download_instructions = 'Download R%(version)s_Linux.iso from mathworks.com' sources = ['R%(version)s_Linux.iso'] checksums = ['f18225237c2a5ff1294f19ed0c9945cfe691c3a3a62a6a8d324473d73ec92913'] +download_instructions = 'Download %s from mathworks.com' % sources[0] java_options = '-Xmx2048m' From c5dd2aab92a81d29afbafa87dcde688e240e210a Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 May 2023 12:01:44 +0100 Subject: [PATCH 7322/9987] adding easyconfigs: Gurobi-10.0.1-GCCcore-12.2.0.eb --- .../g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7f8752b1f3f --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +name = 'Gurobi' +version = '10.0.1' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +patches = ['%(name)s-9.0.1_use-eb-python-gurobi-shell.patch'] +checksums = [ + {'gurobi10.0.1_linux64.tar.gz': 'a0b551156df2c94107b3428cae278716a0a6c913f63ac132573852b9725b6c59'}, + {'Gurobi-9.0.1_use-eb-python-gurobi-shell.patch': + 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01'}, +] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license is mandatory for installation +license_file = "HOME" + '/licenses/%(name)s.lic' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' From 9f297980819762b7a4fd5671b811b94986ba6777 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 3 May 2023 13:42:15 +0200 Subject: [PATCH 7323/9987] adding easyconfigs: CPC2-0.1-foss-2022a.eb and patches: CPC2-0.1_fix_libsvm_path_and_python2.patch --- .../easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb | 40 +++++++++ ...CPC2-0.1_fix_libsvm_path_and_python2.patch | 82 +++++++++++++++++++ 2 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb new file mode 100644 index 00000000000..59ab7d33d1f --- /dev/null +++ b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb @@ -0,0 +1,40 @@ +# Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +# Updated: Denis Kristak (Inuits) +# Update to a Python3 version +easyblock = 'PackedBinary' + +name = 'CPC2' +version = '0.1' +local_commit = '813487e' + +homepage = 'http://cpc2.cbi.pku.edu.cn' +description = """ a fast and accurate coding potential calculator based on sequence intrinsic features """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +# original sources at http://cpc2.cbi.pku.edu.cn/download.php are currently not available +# download from github mirror +source_urls = ['https://github.com/lucventurini/CPC2/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = ['%(name)s-%(version)s_fix_libsvm_path_and_python2.patch'] +checksums = [ + {'CPC2-0.1.tar.gz': '6fd4f3fb05b179073709c033481ae082085eabc7c5281cd743c9419d3ec6de67'}, + {'CPC2-0.1_fix_libsvm_path_and_python2.patch': '657f552ebfad925e8c051a19426cd5bb1b8ad7da8cdcc3e701e1220673330842'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('LIBSVM', '3.30'), + ('Biopython', '1.79'), +] + +install_cmd = 'cp -a CPC2*/{bin,data} %(installdir)s/' + +sanity_check_paths = { + 'files': ['bin/CPC2.py'], + 'dirs': [], +} + +sanity_check_commands = ['CPC2.py -i %(installdir)s/data/example.fa -o example.out'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch b/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch new file mode 100644 index 00000000000..38190f1c201 --- /dev/null +++ b/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch @@ -0,0 +1,82 @@ +Use libsvm from the environment instead of the one provided with CPC2 +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +Update: Fix incompatible syntax with Python 3 +Updated by: Denis Kristak (Inuits) +diff -ruN cpc2_orig/bin/compress.py cpc2/bin/compress.py +--- cpc2_orig/bin/compress.py 2018-10-22 17:58:22.000000000 +0200 ++++ cpc2/bin/compress.py 2023-05-03 12:37:36.240001307 +0200 +@@ -11,7 +11,7 @@ + fq_fp = gzip.open(fq_file,mode+"b",level) + else: + sys.stderr.write("[INFO] read file '%s'\n"%fq_file) +- fq_fp = file(fq_file,mode) ++ fq_fp = open(fq_file,mode) + except: + sys.stderr.write("Error: Fail to IO file: %s\n"%(fq_file)) + sys.exit(1) +diff -ruN cpc2_orig/bin/CPC2.py cpc2/bin/CPC2.py +--- cpc2_orig/bin/CPC2.py 2023-05-02 16:41:34.222887000 +0200 ++++ cpc2/bin/CPC2.py 2023-05-03 12:40:15.817915000 +0200 +@@ -78,7 +78,7 @@ + ''' + while True: + try: +- codon,index = triplet_got.next() ++ codon,index = next(triplet_got) + except StopIteration: + break + if codon in starts and codon not in stops: +@@ -89,7 +89,7 @@ + end_extension = False + while True: + try: +- codon,index = triplet_got.next() ++ codon,index = next(triplet_got) + except StopIteration: + end_extension = True + integrity = -1 +@@ -245,9 +245,9 @@ + ''' + strinfoAmbiguous = re.compile("X|B|Z|J|U",re.I) + ptU = re.compile("U",re.I) +- ftmp_feat = file(outfile + ".feat","w") +- ftmp_svm = file(outfile + ".tmp.1","w") +- ftmp_result = file(outfile,"w") ++ ftmp_feat = open(outfile + ".feat","w") ++ ftmp_svm = open(outfile + ".tmp.1","w") ++ ftmp_result = open(outfile,"w") + ftmp_result.write("\t".join(map(str,["#ID","transcript_length","peptide_length","Fickett_score","pI","ORF_integrity","coding_probability","label"]))+"\n") + ftmp_result.close() + fickett_obj = Fickett() +@@ -288,16 +288,16 @@ + script_dir,filename = os.path.split(os.path.abspath(sys.argv[0])) + data_dir = script_dir + "/../data/" + lib_dir = script_dir + "/../libs/" +- app_svm_scale = lib_dir + "libsvm/libsvm-3.18/svm-scale" +- app_svm_predict = lib_dir + "libsvm/libsvm-3.18/svm-predict" +- os.system('test -x '+ app_svm_scale + ' || echo \"[ERROR] No excutable svm-scale on CPC2 path!\" > /dev/stderr') +- os.system('test -x '+ app_svm_predict + ' || echo \"[ERROR] No excutable svm-predict on CPC2 path!\" > /dev/stderr') ++ app_svm_scale = 'svm-scale' ++ app_svm_predict = 'svm-predict' ++ os.system('which ' + app_svm_scale + ' || echo \"[ERROR] No excutable svm-scale on CPC2 path!\" > /dev/stderr') ++ os.system('which ' + app_svm_predict + ' || echo \"[ERROR] No excutable svm-predict on CPC2 path!\" > /dev/stderr') + + cmd = app_svm_scale + ' -r ' + data_dir + 'cpc2.range ' + outfile + '.tmp.1 > ' + outfile + '.tmp.2 &&' + cmd = cmd + app_svm_predict + ' -b 1 -q ' + outfile + '.tmp.2 ' + data_dir + 'cpc2.model ' + outfile + '.tmp.1 &&' + cmd = cmd + 'awk -vOFS="\\t" \'{if ($1 == 1){print $2,"coding"} else if ($1 == 0){print $2,"noncoding"}}\' ' + outfile + '.tmp.1 > ' + outfile + '.tmp.2 &&' + cmd = cmd + 'paste ' + outfile + '.feat ' + outfile + '.tmp.2 >>' + outfile +- command = suprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) ++ command = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + (outtext, errtext) = command.communicate() + exitstatus = command.returncode + os.system('rm -f ' + outfile + '.tmp.1 ' + outfile + '.tmp.2') +@@ -306,7 +306,8 @@ + # pass + if exitstatus == 0: + rm_cmd = "rm -f " + outfile + '.feat' +- subprocess.call(rm_cmd) ++ print(rm_cmd) ++ subprocess.run(rm_cmd, shell=True) + sys.stderr.write("[INFO] Running Done!\n") + return 0 + else: From 7d9fcc0bd7a218ce8e41aa29db6f93287c6756b5 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 3 May 2023 13:57:42 +0200 Subject: [PATCH 7324/9987] code style --- easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb index 59ab7d33d1f..043d64d9573 100644 --- a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb @@ -22,7 +22,7 @@ checksums = [ {'CPC2-0.1_fix_libsvm_path_and_python2.patch': '657f552ebfad925e8c051a19426cd5bb1b8ad7da8cdcc3e701e1220673330842'}, ] -dependencies = [ +dependencies = [ ('Python', '3.10.4'), ('LIBSVM', '3.30'), ('Biopython', '1.79'), @@ -30,7 +30,7 @@ dependencies = [ install_cmd = 'cp -a CPC2*/{bin,data} %(installdir)s/' -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/CPC2.py'], 'dirs': [], } From 602e7cf7cc55bad3ff70b11544290dee5fbe81a1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 3 May 2023 14:39:14 +0200 Subject: [PATCH 7325/9987] adding easyconfigs: SoupX-1.6.2-foss-2022a-R-4.2.1.eb --- .../s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..3354780d23e --- /dev/null +++ b/easybuild/easyconfigs/s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'SoupX' +version = '1.6.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/constantAmateur/SoupX' +description = """" +Quantify, profile and remove ambient mRNA contamination (the "soup") from +droplet based single cell RNA-seq experiments. Implements the method described +in Young et al. (2018) .""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://cran.r-project.org/src/contrib/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['9b6226cd7c0691498a874d5c029f8ff81fd2060295c298985397521c1f7ee3a5'] + +dependencies = [ + ('R', '4.2.1'), + ('Seurat', '4.3.0', versionsuffix) +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 7877a55877e5c9ad47d9ff3fd6df6cdeda7e31a1 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Wed, 3 May 2023 14:17:05 +0100 Subject: [PATCH 7326/9987] Add exts epitools to R-4.2.1 & deepSNV to R-bundle-Bioconductor --- ...bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 15 +++++++++++---- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++ 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 72d0887ac92..c6c39172ea7 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -11,7 +11,8 @@ description = """Bioconductor provides tools for the analysis and coprehension toolchain = {'name': 'foss', 'version': '2022a'} # lpsymphony fails to build with pkgconf, so stick to pkg-config -# error in: https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286 +# error in: +# https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286 builddependencies = [('pkg-config', '0.29.2')] dependencies = [ @@ -28,9 +29,11 @@ exts_default_options = { 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s', 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/', 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + # package archive + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + # mirror alternative for current packages + 'https://cran.freestatistics.org/src/contrib', ], 'source_tmpl': '%(name)s_%(version)s.tar.gz' } @@ -41,7 +44,8 @@ exts_defaultclass = 'RPackage' # (some versions in this bundle may be newer than the ones provided by R) local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" -exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) +exts_filter = ("R -q --no-save", "%s { %s }" % + (local_ext_version_check, local_stop_msg)) # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! @@ -1206,6 +1210,9 @@ exts_list = [ ('SpatialExperiment', '1.6.1', { 'checksums': ['31e516e14e827e4b9fe853bc136066863dd762053012631c569ec3c00c6cbab5'], }), + ('deepSNV', '1.42.1', { + 'checksums': ['f64d43645d696af7b375c66f7dccf877d099482f8470dd18c4aba8b1f30bf22d'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index c0a40a9552d..313583b74ab 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3523,6 +3523,9 @@ exts_list = [ ('word2vec', '0.3.4', { 'checksums': ['53db1d8c8d6af8ace8636adec1e254b0b61fbdba77ba7a295afc7da3eb4e4362'], }), + ('epitools', '0.5-10.1', { + 'checksums': ['b418854de1fcedd126f3bf19dc27e8a71ee6efae5371098ab64a53a2d51d164b'], + }), ] moduleclass = 'lang' From 412b0d96c4b77b6531a71f5188c9e4ccd91037ee Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Wed, 3 May 2023 14:24:47 +0100 Subject: [PATCH 7327/9987] Formatting --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index c6c39172ea7..d19d5c0d3c5 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -11,8 +11,7 @@ description = """Bioconductor provides tools for the analysis and coprehension toolchain = {'name': 'foss', 'version': '2022a'} # lpsymphony fails to build with pkgconf, so stick to pkg-config -# error in: -# https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286 +# error in: https://github.com/easybuilders/easybuild-easyconfigs/pull/15829#issuecomment-1178655286 builddependencies = [('pkg-config', '0.29.2')] dependencies = [ @@ -28,12 +27,10 @@ exts_default_options = { 'https://bioconductor.org/packages/3.15/bioc/src/contrib/', 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s', 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/', - 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/', - # package archive + 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/', # package archive 'https://cran.r-project.org/src/contrib/Archive/%(name)s', 'https://cran.r-project.org/src/contrib/', # current version of packages - # mirror alternative for current packages - 'https://cran.freestatistics.org/src/contrib', + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ], 'source_tmpl': '%(name)s_%(version)s.tar.gz' } @@ -44,8 +41,7 @@ exts_defaultclass = 'RPackage' # (some versions in this bundle may be newer than the ones provided by R) local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" -exts_filter = ("R -q --no-save", "%s { %s }" % - (local_ext_version_check, local_stop_msg)) +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) # CRAN packages on which these Bioconductor packages depend are available in R module on which this depends # !! order of packages is important !! From 880eba1cfb0cbc2806ac121abd21dea4e6862d93 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 May 2023 14:25:10 +0100 Subject: [PATCH 7328/9987] adding easyconfigs: Pyomo-6.5.0-foss-2022b.eb --- .../p/Pyomo/Pyomo-6.5.0-foss-2022b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb new file mode 100644 index 00000000000..8e787b4623c --- /dev/null +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Pyomo' +version = '6.5.0' + +homepage = 'https://www.pyomo.org/' +description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization + capabilities for formulating and analyzing optimization models. """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [('Python', '3.10.8')] + +exts_list = [ + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('PyUtilib', '6.0.0', { + 'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'], + 'preinstallopts': """sed -i "s/'nose',//g" setup.py && """, + }), + (name, version, { + 'checksums': ['5a23e775bba9fdbad22698fa1a841e662482edc979f2dea41cc6c54b1bb4b968'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['pyomo -h'] + +moduleclass = 'math' From 2224e67bbeb0c4ef66bcb8f64d67be0b980d2048 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Wed, 3 May 2023 14:27:31 +0100 Subject: [PATCH 7329/9987] Replace comment --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index d19d5c0d3c5..1ccecc5efcd 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -27,8 +27,8 @@ exts_default_options = { 'https://bioconductor.org/packages/3.15/bioc/src/contrib/', 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s', 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/', - 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/', # package archive - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'https://cran.r-project.org/src/contrib/', # current version of packages 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ], From 3b3790756bc2dc37b65444bb3f8eb98cde0ba268 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 May 2023 16:18:12 +0100 Subject: [PATCH 7330/9987] Missing mpi4py added --- easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb index 8e787b4623c..c924968a115 100644 --- a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb @@ -9,7 +9,10 @@ description = """ Pyomo is a Python-based open-source software package that supp toolchain = {'name': 'foss', 'version': '2022b'} -dependencies = [('Python', '3.10.8')] +dependencies = [ + ('Python', '3.10.8'), + ('mpi4py', '3.1.4'), +] exts_list = [ ('ply', '3.11', { From 28b35d2903b221d915a5bf7fbca40f982474bbd0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 May 2023 11:53:12 +0200 Subject: [PATCH 7331/9987] also check for 'data' in sanity check for CPC2 --- easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb index 043d64d9573..9bcd7cf4116 100644 --- a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb @@ -32,7 +32,7 @@ install_cmd = 'cp -a CPC2*/{bin,data} %(installdir)s/' sanity_check_paths = { 'files': ['bin/CPC2.py'], - 'dirs': [], + 'dirs': ['data'], } sanity_check_commands = ['CPC2.py -i %(installdir)s/data/example.fa -o example.out'] From c4417f1ea2591a2811b2ff00b96330295e15dc8a Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 4 May 2023 13:19:09 +0200 Subject: [PATCH 7332/9987] Update release to v4 --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb index c2d6932e11c..19786fd6656 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb @@ -19,8 +19,8 @@ toolchainopts = {'openmp': True, 'usempi': True} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] -sources = ['stable_%(version)s_update1.tar.gz'] -checksums = ['58e3b2b984f8935bb0db5631e143be2826c45ffd48844f7c394f36624a3e17a2'] +sources = ['stable_%(version)s_update4.tar.gz'] +checksums = ['42541b4dbd0d339d16ddb377e76d192bc3d1d5712fdf9e2cdc838fc980d0a0cf'] builddependencies = [ ('CMake', '3.23.1'), From a3bcf2047353256ac1d3048762e8d9d1fb33b850 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 4 May 2023 13:53:24 +0200 Subject: [PATCH 7333/9987] adding easyconfigs: CellChat-1.5.0-foss-2022a-R-4.2.1.eb --- .../CellChat-1.5.0-foss-2022a-R-4.2.1.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..97b28ca1651 --- /dev/null +++ b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,57 @@ +easyblock = 'Bundle' + +name = 'CellChat' +version = '1.5.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/sqjin/CellChat' +description = """" +R toolkit for inference, visualization and analysis of cell-cell communication +from single-cell data""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('umap-learn', '0.5.3'), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} + +exts_list = [ + ('ggalluvial', '0.12.5', { + 'checksums': ['90044c880e70096137a733d601b11e558fe55e4e7d3aaacac6f08d7847415d71'], + }), + ('systemfonts', '1.0.4', { + 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], + }), + ('svglite', '2.1.1', { + 'checksums': ['48700169eec1b05dbee9e2bae000aa84c544617b018cb3ac431a128cfd8dac56'], + }), + (name, version, { + 'preinstallopts': "rm src/*.o src/*.so && ", + 'source_urls': ['https://github.com/sqjin/CellChat/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c9e31327cbbcf1fec5e6d8a0dfe011ded8e543557107e93dd4a417c4c137d1c6'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From da0aa7473ac373116529cb5d228cb121fccf904d Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 4 May 2023 15:12:55 +0200 Subject: [PATCH 7334/9987] Change PLUMED version --- .../easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb index 09de0962691..9b19d8f2a32 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb @@ -44,7 +44,7 @@ dependencies = [ ('Voro++', '0.4.6'), ('kim-api', '2.3.0'), ('Eigen', '3.4.0'), - ('PLUMED', '2.8.0'), + ('PLUMED', '2.8.1'), ('ScaFaCoS', '1.0.4'), ('SciPy-bundle', '2022.05'), # VTK package is auto-disabled if this dep is not available From e18a0cc06d871e622a373946a5ec22b51c2d0f5b Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 4 May 2023 14:18:08 +0100 Subject: [PATCH 7335/9987] comment license --- .../easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb index 7f8752b1f3f..4eeb0dae621 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb @@ -30,7 +30,9 @@ dependencies = [ postinstallcmds = ['rm %(installdir)s/bin/python*'] # license is mandatory for installation -license_file = "HOME" + '/licenses/%(name)s.lic' +# use EB_GUROBI_LICENSE_FILE environment variable, or +# uncomment and modify the following variable: +# license_file = '/path/to/my-license-file' modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' From 66a226666a0d9c3f7a285732e87b8741916f071b Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 4 May 2023 15:34:18 +0200 Subject: [PATCH 7336/9987] Change VTK version --- .../easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb index 9b19d8f2a32..74e899cdc1e 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb @@ -48,7 +48,7 @@ dependencies = [ ('ScaFaCoS', '1.0.4'), ('SciPy-bundle', '2022.05'), # VTK package is auto-disabled if this dep is not available - ('VTK', '9.2.0.rc2'), + ('VTK', '9.2.2'), ] # To use additional custom configuration options, use the 'configopts' easyconfig parameter From 6e32e71b8b50058388165704a3088ab5325249cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 4 May 2023 17:09:33 +0200 Subject: [PATCH 7337/9987] adding easyconfigs: rustworkx-0.12.1-foss-2022a.eb --- .../rustworkx/rustworkx-0.12.1-foss-2022a.eb | 169 ++++++++++++++++++ 1 file changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2022a.eb new file mode 100644 index 00000000000..73bcca7c937 --- /dev/null +++ b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2022a.eb @@ -0,0 +1,169 @@ +easyblock = "CargoPythonPackage" + +name = 'rustworkx' +version = '0.12.1' + +homepage = 'https://github.com/Qiskit/rustworkx' +description = """rustworkx (previously retworkx) is a general purpose graph library for Python written in Rust to take +advantage of the performance and safety that Rust provides. It is designed to provide a high performance general +purpose graph library for any Python application.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Rust', '1.65.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +crates = [ + ('ahash', '0.7.6'), + ('autocfg', '1.1.0'), + ('bitflags', '1.3.2'), + ('cfg-if', '1.0.0'), + ('crossbeam-channel', '0.5.4'), + ('crossbeam-deque', '0.8.1'), + ('crossbeam-epoch', '0.9.8'), + ('crossbeam-utils', '0.8.8'), + ('either', '1.6.1'), + ('fixedbitset', '0.4.2'), + ('getrandom', '0.2.6'), + ('hashbrown', '0.11.2'), + ('hermit-abi', '0.1.19'), + ('indexmap', '1.7.0'), + ('indoc', '1.0.6'), + ('instant', '0.1.12'), + ('itoa', '1.0.2'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.126'), + ('lock_api', '0.4.7'), + ('matrixmultiply', '0.2.4'), + ('memchr', '2.5.0'), + ('memoffset', '0.6.5'), + ('ndarray', '0.13.1'), + ('num-bigint', '0.4.3'), + ('num-complex', '0.2.4'), + ('num-complex', '0.4.1'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.15'), + ('num_cpus', '1.13.1'), + ('numpy', '0.17.2'), + ('once_cell', '1.12.0'), + ('parking_lot', '0.11.2'), + ('parking_lot_core', '0.8.5'), + ('petgraph', '0.6.2'), + ('ppv-lite86', '0.2.16'), + ('priority-queue', '1.2.0'), + ('proc-macro2', '1.0.39'), + ('pyo3', '0.17.3'), + ('pyo3-build-config', '0.17.3'), + ('pyo3-ffi', '0.17.3'), + ('pyo3-macros', '0.17.3'), + ('pyo3-macros-backend', '0.17.3'), + ('quick-xml', '0.22.0'), + ('quote', '1.0.18'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.3'), + ('rand_pcg', '0.3.1'), + ('rawpointer', '0.2.1'), + ('rayon', '1.5.3'), + ('rayon-core', '1.9.3'), + ('redox_syscall', '0.2.13'), + ('ryu', '1.0.10'), + ('scopeguard', '1.1.0'), + ('serde', '1.0.145'), + ('serde_derive', '1.0.145'), + ('serde_json', '1.0.89'), + ('smallvec', '1.8.0'), + ('syn', '1.0.96'), + ('target-lexicon', '0.12.4'), + ('unicode-ident', '1.0.0'), + ('unindent', '0.1.9'), + ('version_check', '0.9.4'), + ('wasi', '0.10.2+wasi-snapshot-preview1'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + {'rustworkx-0.12.1.tar.gz': '13a19a2f64dff086b3bffffb294c4630100ecbc13634b4995d9d36a481ae130e'}, + {'ahash-0.7.6.tar.gz': 'fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'crossbeam-channel-0.5.4.tar.gz': '5aaa7bd5fb665c6864b5f963dd9097905c54125909c7aa94c9e18507cdbe6c53'}, + {'crossbeam-deque-0.8.1.tar.gz': '6455c0ca19f0d2fbf751b908d5c55c1f5cbc65e03c4225427254b46890bdde1e'}, + {'crossbeam-epoch-0.9.8.tar.gz': '1145cf131a2c6ba0615079ab6a638f7e1973ac9c2634fcbeaaad6114246efe8c'}, + {'crossbeam-utils-0.8.8.tar.gz': '0bf124c720b7686e3c2663cf54062ab0f68a88af2fb6a030e87e30bf721fcb38'}, + {'either-1.6.1.tar.gz': 'e78d4f1cc4ae33bbfc157ed5d5a5ef3bc29227303d595861deb238fcec4e9457'}, + {'fixedbitset-0.4.2.tar.gz': '0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80'}, + {'getrandom-0.2.6.tar.gz': '9be70c98951c83b8d2f8f60d7065fa6d5146873094452a1008da8c2f1e4205ad'}, + {'hashbrown-0.11.2.tar.gz': 'ab5ef0d4909ef3724cc8cce6ccc8572c5c817592e9285f5464f8e86f8bd3726e'}, + {'hermit-abi-0.1.19.tar.gz': '62b467343b94ba476dcb2500d242dadbb39557df889310ac77c5d99100aaac33'}, + {'indexmap-1.7.0.tar.gz': 'bc633605454125dec4b66843673f01c7df2b89479b32e0ed634e43a91cff62a5'}, + {'indoc-1.0.6.tar.gz': '05a0bd019339e5d968b37855180087b7b9d512c5046fbd244cf8c95687927d6e'}, + {'instant-0.1.12.tar.gz': '7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c'}, + {'itoa-1.0.2.tar.gz': '112c678d4050afce233f4f2852bb2eb519230b3cf12f33585275537d7e41578d'}, + {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'}, + {'libc-0.2.126.tar.gz': '349d5a591cd28b49e1d1037471617a32ddcda5731b99419008085f72d5a53836'}, + {'lock_api-0.4.7.tar.gz': '327fa5b6a6940e4699ec49a9beae1ea4845c6bab9314e4f84ac68742139d8c53'}, + {'matrixmultiply-0.2.4.tar.gz': '916806ba0031cd542105d916a97c8572e1fa6dd79c9c51e7eb43a09ec2dd84c1'}, + {'memchr-2.5.0.tar.gz': '2dffe52ecf27772e601905b7522cb4ef790d2cc203488bbd0e2fe85fcb74566d'}, + {'memoffset-0.6.5.tar.gz': '5aa361d4faea93603064a027415f07bd8e1d5c88c9fbf68bf56a285428fd79ce'}, + {'ndarray-0.13.1.tar.gz': 'ac06db03ec2f46ee0ecdca1a1c34a99c0d188a0d83439b84bf0cb4b386e4ab09'}, + {'num-bigint-0.4.3.tar.gz': 'f93ab6289c7b344a8a9f60f88d80aa20032336fe78da341afc91c8a2341fc75f'}, + {'num-complex-0.2.4.tar.gz': 'b6b19411a9719e753aff12e5187b74d60d3dc449ec3f4dc21e3989c3f554bc95'}, + {'num-complex-0.4.1.tar.gz': '97fbc387afefefd5e9e39493299f3069e14a140dd34dc19b4c1c1a8fddb6a790'}, + {'num-integer-0.1.45.tar.gz': '225d3389fb3509a24c93f5c29eb6bde2586b98d9f016636dff58d7c6f7569cd9'}, + {'num-traits-0.2.15.tar.gz': '578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd'}, + {'num_cpus-1.13.1.tar.gz': '19e64526ebdee182341572e50e9ad03965aa510cd94427a4549448f285e957a1'}, + {'numpy-0.17.2.tar.gz': 'a462c1af5ba1fddec1488c4646993a23ae7931f9e170ccba23e9c7c834277797'}, + {'once_cell-1.12.0.tar.gz': '7709cef83f0c1f58f666e746a08b21e0085f7440fa6a29cc194d68aac97a4225'}, + {'parking_lot-0.11.2.tar.gz': '7d17b78036a60663b797adeaee46f5c9dfebb86948d1255007a1d6be0271ff99'}, + {'parking_lot_core-0.8.5.tar.gz': 'd76e8e1493bcac0d2766c42737f34458f1c8c50c0d23bcb24ea953affb273216'}, + {'petgraph-0.6.2.tar.gz': 'e6d5014253a1331579ce62aa67443b4a658c5e7dd03d4bc6d302b94474888143'}, + {'ppv-lite86-0.2.16.tar.gz': 'eb9f9e6e233e5c4a35559a617bf40a4ec447db2e84c20b55a6f83167b7e57872'}, + {'priority-queue-1.2.0.tar.gz': 'cf40e51ccefb72d42720609e1d3c518de8b5800d723a09358d4a6d6245e1f8ca'}, + {'proc-macro2-1.0.39.tar.gz': 'c54b25569025b7fc9651de43004ae593a75ad88543b17178aa5e1b9c4f15f56f'}, + {'pyo3-0.17.3.tar.gz': '268be0c73583c183f2b14052337465768c07726936a260f480f0857cb95ba543'}, + {'pyo3-build-config-0.17.3.tar.gz': '28fcd1e73f06ec85bf3280c48c67e731d8290ad3d730f8be9dc07946923005c8'}, + {'pyo3-ffi-0.17.3.tar.gz': '0f6cb136e222e49115b3c51c32792886defbfb0adead26a688142b346a0b9ffc'}, + {'pyo3-macros-0.17.3.tar.gz': '94144a1266e236b1c932682136dc35a9dee8d3589728f68130c7c3861ef96b28'}, + {'pyo3-macros-backend-0.17.3.tar.gz': 'c8df9be978a2d2f0cdebabb03206ed73b11314701a5bfe71b0d753b81997777f'}, + {'quick-xml-0.22.0.tar.gz': '8533f14c8382aaad0d592c812ac3b826162128b65662331e1127b45c3d18536b'}, + {'quote-1.0.18.tar.gz': 'a1feb54ed693b93a84e14094943b84b7c4eae204c512b7ccb95ab0c66d278ad1'}, + {'rand-0.8.5.tar.gz': '34af8d1a0e25924bc5b7c43c079c942339d8f0a8b57c39049bef581b46327404'}, + {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'}, + {'rand_core-0.6.3.tar.gz': 'd34f1408f55294453790c48b2f1ebbb1c5b4b7563eb1f418bcfcfdbb06ebb4e7'}, + {'rand_pcg-0.3.1.tar.gz': '59cad018caf63deb318e5a4586d99a24424a364f40f1e5778c29aca23f4fc73e'}, + {'rawpointer-0.2.1.tar.gz': '60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3'}, + {'rayon-1.5.3.tar.gz': 'bd99e5772ead8baa5215278c9b15bf92087709e9c1b2d1f97cdb5a183c933a7d'}, + {'rayon-core-1.9.3.tar.gz': '258bcdb5ac6dad48491bb2992db6b7cf74878b0384908af124823d118c99683f'}, + {'redox_syscall-0.2.13.tar.gz': '62f25bc4c7e55e0b0b7a1d43fb893f4fa1361d0abe38b9ce4f323c2adfe6ef42'}, + {'ryu-1.0.10.tar.gz': 'f3f6f92acf49d1b98f7a81226834412ada05458b7364277387724a237f062695'}, + {'scopeguard-1.1.0.tar.gz': 'd29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd'}, + {'serde-1.0.145.tar.gz': '728eb6351430bccb993660dfffc5a72f91ccc1295abaa8ce19b27ebe4f75568b'}, + {'serde_derive-1.0.145.tar.gz': '81fa1584d3d1bcacd84c277a0dfe21f5b0f6accf4a23d04d4c6d61f1af522b4c'}, + {'serde_json-1.0.89.tar.gz': '020ff22c755c2ed3f8cf162dbb41a7268d934702f3ed3631656ea597e08fc3db'}, + {'smallvec-1.8.0.tar.gz': 'f2dd574626839106c320a323308629dcb1acfc96e32a8cba364ddc61ac23ee83'}, + {'syn-1.0.96.tar.gz': '0748dd251e24453cb8717f0354206b91557e4ec8703673a4b30208f2abaf1ebf'}, + {'target-lexicon-0.12.4.tar.gz': 'c02424087780c9b71cc96799eaeddff35af2bc513278cda5c99fc1f5d026d3c1'}, + {'unicode-ident-1.0.0.tar.gz': 'd22af068fba1eb5edcb4aea19d382b2a3deb4c8f9d475c589b6ada9e0fd493ee'}, + {'unindent-0.1.9.tar.gz': '52fee519a3e570f7df377a06a1a7775cdbfb7aa460be7e08de2b1f0e69973a44'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'wasi-0.10.2+wasi-snapshot-preview1.tar.gz': 'fd6fbd9a79829dd1ad0cc20627bf1ed606756a7f77edff7b66b7064f9cb327c6'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' From 4730edaa631fe8db8d00c5a0fc1d5bd5dabea3d9 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 4 May 2023 18:29:36 +0200 Subject: [PATCH 7338/9987] adding easyconfigs: Zip-3.0-GCCcore-12.2.0.eb --- .../z/Zip/Zip-3.0-GCCcore-12.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..84708515be8 --- /dev/null +++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Zip' +version = '3.0' + +homepage = 'http://www.info-zip.org/Zip.html' +description = """Zip is a compression and file packaging/archive utility. +Although highly compatible both with PKWARE's PKZIP and PKUNZIP +utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives +have been portability and other-than-MSDOS functionality""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' +buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' +buildopts += 'generic_gcc' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["zip --version"] + +moduleclass = 'tools' From d8abe94bcc09f3b35095c61e423f0f5ae04940ce Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Thu, 4 May 2023 18:36:15 +0200 Subject: [PATCH 7339/9987] adding easyconfigs: Abseil-20230125.2-GCCcore-12.2.0.eb --- .../Abseil-20230125.2-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ac3526452ed --- /dev/null +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Abseil' +version = '20230125.2' + +homepage = 'https://abseil.io/' +description = """Abseil is an open-source collection of C++ library code designed to augment the +C++ standard library. The Abseil library code is collected from Google's own +C++ code base, has been extensively tested and used in production, and is the +same code we depend on in our daily coding lives.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++17'} + +source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['9a2b5752d7bfade0bdeee2701de17c9480620f8b237e1964c1b9967c75374906'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], + 'dirs': ['include/absl'], +} + +moduleclass = 'lib' From 8050e2bdaacd19ae00b5f1ad6cc529ecda39bd49 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 5 May 2023 00:48:43 +0200 Subject: [PATCH 7340/9987] Update easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb --- .../easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb index adb4b6dc91d..a94e4236997 100644 --- a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.4.4-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ sanity_check_paths = { 'files': ['bin/rocm-smi'], - 'dirs': [''], + 'dirs': [], } sanity_check_commands = ['rocm-smi --help'] From 558a424a3f3ee742693ce587573a308faac448ca Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 5 May 2023 09:14:03 +0200 Subject: [PATCH 7341/9987] remove versionsuffix --- .../c/CellChat/CellChat-1.5.0-foss-2022a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a.eb new file mode 100644 index 00000000000..8b0c66ef249 --- /dev/null +++ b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'CellChat' +version = '1.5.0' + +homepage = 'https://github.com/sqjin/CellChat' +description = """" +R toolkit for inference, visualization and analysis of cell-cell communication +from single-cell data""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', '-R-%(rver)s'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('umap-learn', '0.5.3'), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} + +exts_list = [ + ('ggalluvial', '0.12.5', { + 'checksums': ['90044c880e70096137a733d601b11e558fe55e4e7d3aaacac6f08d7847415d71'], + }), + ('systemfonts', '1.0.4', { + 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], + }), + ('svglite', '2.1.1', { + 'checksums': ['48700169eec1b05dbee9e2bae000aa84c544617b018cb3ac431a128cfd8dac56'], + }), + (name, version, { + 'preinstallopts': "rm src/*.o src/*.so && ", + 'source_urls': ['https://github.com/sqjin/CellChat/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c9e31327cbbcf1fec5e6d8a0dfe011ded8e543557107e93dd4a417c4c137d1c6'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From ca79d6add74b5338e0e5ee2d885d3c4a9c190485 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 5 May 2023 09:15:22 +0200 Subject: [PATCH 7342/9987] remove versionsuffix --- .../CellChat-1.5.0-foss-2022a-R-4.2.1.eb | 57 ------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb deleted file mode 100644 index 97b28ca1651..00000000000 --- a/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a-R-4.2.1.eb +++ /dev/null @@ -1,57 +0,0 @@ -easyblock = 'Bundle' - -name = 'CellChat' -version = '1.5.0' -versionsuffix = '-R-%(rver)s' - -homepage = 'https://github.com/sqjin/CellChat' -description = """" -R toolkit for inference, visualization and analysis of cell-cell communication -from single-cell data""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -dependencies = [ - ('R', '4.2.1'), - ('R-bundle-Bioconductor', '3.15', versionsuffix), - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('umap-learn', '0.5.3'), -] - -exts_defaultclass = 'RPackage' -exts_default_options = { - 'sources': ['%(name)s_%(version)s.tar.gz'], - 'source_urls': [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages - ], -} - -exts_list = [ - ('ggalluvial', '0.12.5', { - 'checksums': ['90044c880e70096137a733d601b11e558fe55e4e7d3aaacac6f08d7847415d71'], - }), - ('systemfonts', '1.0.4', { - 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], - }), - ('svglite', '2.1.1', { - 'checksums': ['48700169eec1b05dbee9e2bae000aa84c544617b018cb3ac431a128cfd8dac56'], - }), - (name, version, { - 'preinstallopts': "rm src/*.o src/*.so && ", - 'source_urls': ['https://github.com/sqjin/CellChat/archive/'], - 'sources': ['v%(version)s.tar.gz'], - 'checksums': ['c9e31327cbbcf1fec5e6d8a0dfe011ded8e543557107e93dd4a417c4c137d1c6'], - }), -] - -sanity_check_paths = { - 'files': [], - 'dirs': [name], -} - -modextrapaths = {'R_LIBS_SITE': ''} - -moduleclass = 'bio' From 5c4debc9532d6f1f1ffc3fa4133f932b235683cb Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 5 May 2023 10:06:17 +0200 Subject: [PATCH 7343/9987] adding easyconfigs: AGeNT-3.0.6.eb --- easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb | 69 ++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb diff --git a/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb b/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb new file mode 100644 index 00000000000..545544653f1 --- /dev/null +++ b/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb @@ -0,0 +1,69 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +# JAR files are in a subdirectory with other stuff, so use Binary +easyblock = 'Binary' + +name = 'AGeNT' +version = '3.0.6' + +homepage = 'https://www.agilent.com/en/product/next-generation-sequencing/' +homepage += 'hybridization-based-next-generation-sequencing-ngs/ngs-software/agent-232879' +description = """The Agilent Genomics NextGen Toolkit (AGeNT) is a Java-based software +module that processes the read sequences from targeted high-throughput sequencing data +generated by sequencing Agilent SureSelect and HaloPlex libraries. + +The Trimmer utility of the AGeNT module processes the read sequences to identify and +remove the adaptor sequences and extracts dual molecular barcodes (for SureSelect XT HS2). + +The LocatIt utility of the AGeNT module processes the Molecular Barcode (MBC) information +from HaloPlex HS, SureSelect XT HS, and SureSelect XT HS2 Illumina sequencing runs with +options to either mark or merge duplicate reads and output in BAM file format. The Illumina +InterOp libraries are a set of common routines used for reading InterOp metric files +produced by Illumina sequencers including NextSeq 1k/2k. These libraries are backwards +compatible and capable of supporting prior releases of the software, with one exception: +GA systems have been excluded.""" + +software_license = 'LicenseVeryRestrictive' +# For Research Use Only. Not for use in diagnostic procedures. + +toolchain = SYSTEM + +builddependencies = [ + ('UnZip', '6.0', '', ('GCCcore', '10.3.0')), +] +dependencies = [ + ('Java', '11'), +] + +# Fill the form at https://explore.agilent.com/AGeNT-Software-Download-Form +# to get the zip file. +sources = ['AGeNT_%(version)s.zip'] +checksums = ['746e4445567ee41b7ced5cab3cd252d27d8f6f9eab56766e5d7ca74894e3db73'] + +extract_sources = False + +install_cmd = 'unzip ' + sources[0] + ' && ' +install_cmd += 'cp -ar *.html *.md agent/* %(installdir)s/ && ' +install_cmd += 'find %(installdir)s/ -type f -name \*.txt -exec chmod -x {} \; && ' +install_cmd += 'find %(installdir)s/ -type f -name \*.md -exec chmod -x {} \; && ' +install_cmd += 'find %(installdir)s/ -type f -name \*.cmd -exec rm -f {} \; && ' +install_cmd += 'find %(installdir)s/ -type f -name \*.html -exec rm -f {} \; && ' +install_cmd += 'mkdir %(installdir)s/bin && ' +install_cmd += 'mv %(installdir)s/*.sh %(installdir)s/bin/ && ' +install_cmd += 'ln -s ../lib %(installdir)s/bin/lib && ' +install_cmd += 'sed -i "s@ lib/@ ../lib/@" %(installdir)s/bin/*.sh' + +sanity_check_paths = { + 'files': ['bin/agent.sh'], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ["agent.sh"] + +moduleclass = 'bio' From cefd6e365f5e22518dd84822841abf907a44a73b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 5 May 2023 10:36:53 +0200 Subject: [PATCH 7344/9987] Fix Static Analysis issues --- easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb b/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb index 545544653f1..c176dbde77c 100644 --- a/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb +++ b/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb @@ -50,10 +50,10 @@ extract_sources = False install_cmd = 'unzip ' + sources[0] + ' && ' install_cmd += 'cp -ar *.html *.md agent/* %(installdir)s/ && ' -install_cmd += 'find %(installdir)s/ -type f -name \*.txt -exec chmod -x {} \; && ' -install_cmd += 'find %(installdir)s/ -type f -name \*.md -exec chmod -x {} \; && ' -install_cmd += 'find %(installdir)s/ -type f -name \*.cmd -exec rm -f {} \; && ' -install_cmd += 'find %(installdir)s/ -type f -name \*.html -exec rm -f {} \; && ' +install_cmd += 'chmod -x %(installdir)s/*.txt && ' +install_cmd += 'chmod -x %(installdir)s/*.md && ' +install_cmd += 'rm -f %(installdir)s/*.cmd && ' +install_cmd += 'rm -f %(installdir)s/*.html && ' install_cmd += 'mkdir %(installdir)s/bin && ' install_cmd += 'mv %(installdir)s/*.sh %(installdir)s/bin/ && ' install_cmd += 'ln -s ../lib %(installdir)s/bin/lib && ' From bc8a6f0eff3a9328b1c80f629f8c6741d22d791e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 5 May 2023 10:41:01 +0100 Subject: [PATCH 7345/9987] adding easyconfigs: Triplexator-1.3.3-GCC-11.2.0.eb and patches: Triplexator-1.3.3_support-modern-compilers.patch --- .../Triplexator-1.3.3-GCC-11.2.0.eb | 43 +++++++ ...xator-1.3.3_support-modern-compilers.patch | 113 ++++++++++++++++++ 2 files changed, 156 insertions(+) create mode 100755 easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3-GCC-11.2.0.eb create mode 100755 easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3_support-modern-compilers.patch diff --git a/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3-GCC-11.2.0.eb b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3-GCC-11.2.0.eb new file mode 100755 index 00000000000..4a007546c50 --- /dev/null +++ b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3-GCC-11.2.0.eb @@ -0,0 +1,43 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' + +name = 'Triplexator' +version = '1.3.3' + +homepage = "https://github.com/Gurado/triplexator" +description = """Triplexator is a tool for detecting nucleic acid triple helices and triplex features in nucleotide + sequences using the canonical triplex-formation rules.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'Gurado' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['Triplexator-1.3.3_support-modern-compilers.patch'] +checksums = [ + {'v1.3.3.tar.gz': '24b862062ea36bef67beaa9fcade7860450f98c14dcfa499fca666e2b8c570b2'}, + {'Triplexator-1.3.3_support-modern-compilers.patch': + '1c2bee4aab6693c1f5836eb1688a4345b1ff5fa22333bf3252eb749f15995e64'}, +] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +dependencies = [ + ('Boost', '1.79.0'), +] + +# The above patch makes the code buildable with CMAKE_CXX_STANDARD 11, so set that here +configopts = '-DCMAKE_CXX_STANDARD=11' + +sanity_check_commands = [ + "cd %(builddir)s/%(namelower)s-%(version)s && ./demos/smoketest_triplexator.sh %(installdir)s/bin/%(namelower)s" +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3_support-modern-compilers.patch b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3_support-modern-compilers.patch new file mode 100755 index 00000000000..3a10a3a2639 --- /dev/null +++ b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3_support-modern-compilers.patch @@ -0,0 +1,113 @@ +From e1f86e7df06dd53f0af242858db3909eaa35dac6 Mon Sep 17 00:00:00 2001 +From: amatria +Date: Thu, 8 Sep 2022 12:41:02 +0200 +Subject: [PATCH] compile with a modern c++ compiler + +--- + src/seqan/file/file_format.h | 32 +++++++++---------- + .../parallel/parallel_generated_forwards.h | 2 +- + src/seqan/parallel/parallel_splitting.h | 6 ++-- + src/triplexator.cpp | 4 +-- + 4 files changed, 23 insertions(+), 21 deletions(-) + +diff --git a/src/seqan/file/file_format.h b/src/seqan/file/file_format.h +index da64632..d6df116 100644 +--- a/src/seqan/file/file_format.h ++++ b/src/seqan/file/file_format.h +@@ -205,27 +205,27 @@ struct FileFormat + ~FileFormat() {} + FileFormat const & operator =(FileFormat const &) { return *this; } + +- virtual void * +- formatID_() const = 0; ++ void * ++ formatID_(); + +- virtual void +- read_(TFile & file, TData & data) const = 0; +- virtual void +- read_(TFile & file, TData & data, TSize limit) const = 0; ++ void ++ read_(TFile & file, TData & data); ++ void ++ read_(TFile & file, TData & data, TSize limit); + +- virtual void +- readMeta_(TFile & file, TMeta & meta) const = 0; ++ void ++ readMeta_(TFile & file, TMeta & meta); + +- virtual void +- goNext_(TFile & file) const = 0; ++ void ++ goNext_(TFile & file); + +- virtual TSize +- length_(TFile & file) const = 0; ++ TSize ++ length_(TFile & file); + +- virtual void +- write_(TFile & file, TData & data) const = 0; +- virtual void +- write_(TFile & file, TData & data, TMeta & meta) const = 0; ++ void ++ write_(TFile & file, TData & data); ++ void ++ write_(TFile & file, TData & data, TMeta & meta); + + }; + +diff --git a/src/seqan/parallel/parallel_generated_forwards.h b/src/seqan/parallel/parallel_generated_forwards.h +index 78e9e3e..682bd45 100644 +--- a/src/seqan/parallel/parallel_generated_forwards.h ++++ b/src/seqan/parallel/parallel_generated_forwards.h +@@ -57,7 +57,7 @@ namespace seqan { + //____________________________________________________________________________ + // computeSplitters + +-template void computeSplitters(String & splitters, TSize size, TCount count); // "/Users/fabianbuske/Documents/research/triplex/seqan/core/include/seqan/parallel/parallel_splitting.h"(64) ++template void computeSplitters(TPosString & splitters, TSize size, TCount count); // "/Users/fabianbuske/Documents/research/triplex/seqan/core/include/seqan/parallel/parallel_splitting.h"(64) + + } //namespace seqan + +diff --git a/src/seqan/parallel/parallel_splitting.h b/src/seqan/parallel/parallel_splitting.h +index f8d862f..1ed786d 100755 +--- a/src/seqan/parallel/parallel_splitting.h ++++ b/src/seqan/parallel/parallel_splitting.h +@@ -59,9 +59,11 @@ computeSplitters(splitters, 10, 5); + ..include:seqan/parallel.h + */ + +-template +-void computeSplitters(String & splitters, TSize size, TCount count) ++template ++void computeSplitters(TPosString & splitters, TSize size, TCount count) + { ++ typedef typename Value::Type TPos; ++ + resize(splitters, count + 1); + splitters[0] = 0; + TSize blockLength = size / count; +diff --git a/src/triplexator.cpp b/src/triplexator.cpp +index a3738cb..d6d8e7f 100644 +--- a/src/triplexator.cpp ++++ b/src/triplexator.cpp +@@ -917,7 +917,7 @@ namespace SEQAN_NAMESPACE_MAIN + appendValue(duplexNames, id, Generous()); + + read(file, duplexString, Fasta()); // read Fasta sequence +- ttsnoToFileMap.insert(::std::make_pair >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile))); ++ ttsnoToFileMap.insert(::std::make_pair >(::std::move(seqNo),::std::make_pair< ::std::string,unsigned>(::std::move(filename),::std::move(seqNoWithinFile)))); + + if (options._debugLevel > 1 ) + options.logFileHandle << _getTimeStamp() << " ... Finished reading next duplex sequence" << ::std::endl; +@@ -1040,7 +1040,7 @@ namespace SEQAN_NAMESPACE_MAIN + readShortID(file, id, Fasta()); // read Fasta id up to first whitespace + appendValue(duplexNames, id, Generous()); + read(file, duplexString, Fasta()); // read Fasta sequence +- ttsnoToFileMap.insert(::std::make_pair >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile))); ++ ttsnoToFileMap.insert(::std::make_pair >(::std::move(seqNo),::std::make_pair< ::std::string,unsigned>(::std::move(filename),::std::move(seqNoWithinFile)))); + appendValue(duplexSet, duplexString); + + if (options._debugLevel > 1 ) From 91e9b05b34f79dd8989a446205ea4086b1fab32e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 5 May 2023 14:45:28 +0200 Subject: [PATCH 7346/9987] remove unnecessary deps --- .../easyconfigs/b/build/build-0.10.0-foss-2022a.eb | 9 --------- .../pod5-file-format-0.1.8-foss-2022a.eb | 12 ++++++------ .../pod5-file-format-0.1.8_dep_fix.patch | 3 +++ 3 files changed, 9 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb index ce8f9a50a22..4c80ab3d18f 100644 --- a/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb +++ b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb @@ -16,15 +16,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('pyparsing', '3.0.9', { - 'checksums': ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'], - }), - ('packaging', '20.4', { - 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], - }), - ('tomli', '2.0.1', { - 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], - }), ('pyproject_hooks', '1.0.0', { 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], }), diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb index 5804c85e8ec..e1c12919d47 100644 --- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb @@ -15,12 +15,13 @@ sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ patches = ['pod5-file-format-0.1.8_dep_fix.patch'] checksums = [ {'pod5-file-format-0.1.8.tar.gz': '262b85a44b2e5e93be55bfc2d55a49c07a012b04b59aa24e1d59fd981ac58b5c'}, - {'pod5-file-format-0.1.8_dep_fix.patch': 'd24fab7477d735ba7bb4a286c7a64d6138bf6a82a5a021b257eeeb5dfa06d82e'}, + {'pod5-file-format-0.1.8_dep_fix.patch': '9c7fe8e8aa79c8fff9e43ea3ae1754c5ef0d3023c47f7e4a157d12b34be378a4'}, ] builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), + ('pkgconfig', '1.5.5', '-python'), ] dependencies = [ @@ -32,7 +33,6 @@ dependencies = [ ('pybind11', '2.9.2'), ('Boost', '1.79.0'), ('build', '0.10.0'), - ('pkg-config', '0.29.2'), ('HDF5', '1.12.2'), ('h5py', '3.7.0'), ] @@ -47,9 +47,6 @@ exts_default_options = { } exts_list = [ - ('pkgconfig', '1.5.5', { - 'checksums': ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'], - }), ('attrs', '22.2.0', { 'checksums': ['c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99'], }), @@ -79,7 +76,10 @@ sanity_check_paths = { 'dirs': ['include/pod5_format', 'lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ['pod5 subset --help'] +sanity_check_commands = [ + "pod5 subset --help", + "python -c 'import lib_pod5'", +] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch index f9430ef0310..3015c600bb5 100644 --- a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch @@ -1,3 +1,6 @@ +Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake' +We want to use our pybind11 instead of the one in git submodules +Author: Petr Král (INUITS) diff -u pod5-file-format-0.1.8/c++/CMakeLists.txt.orig pod5-file-format-0.1.8/c++/CMakeLists.txt --- pod5-file-format-0.1.8/c++/CMakeLists.txt.orig 2023-02-23 19:17:13.000000000 +0100 +++ pod5-file-format-0.1.8/c++/CMakeLists.txt 2023-04-25 14:07:28.174884834 +0200 From 84fc5207c2af70c20ea2f8fe931ba04d28473b0b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 5 May 2023 15:37:17 +0200 Subject: [PATCH 7347/9987] Move FLINT to gfbf/foss level. --- .../f/FLINT/FLINT-2.8.4-foss-2021b.eb | 46 +++++++++++++++++++ .../f/FLINT/FLINT-2.8.4_find_flexiblas.patch | 23 ++++++++++ .../f/FLINT/FLINT-2.9.0-gfbf-2022a.eb | 42 +++++++++++++++++ .../n/NTL/NTL-11.5.1-GCC-11.2.0.eb | 44 ++++++++++++++++++ .../n/NTL/NTL-11.5.1-GCC-11.3.0.eb | 44 ++++++++++++++++++ 5 files changed, 199 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.8.4_find_flexiblas.patch create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022a.eb create mode 100644 easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-foss-2021b.eb new file mode 100644 index 00000000000..493b0f97e4f --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-foss-2021b.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'FLINT' +version = '2.8.4' + +homepage = 'https://www.flintlib.org/' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.flintlib.org'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_find_flexiblas.patch', +] +checksums = [ + {'flint-2.8.4.tar.gz': '61df92ea8c8e9dc692d46c71d7f50aaa09a33d4ba08d02a1784730a445e5e4be'}, + {'FLINT-2.8.4_find_flexiblas.patch': '35a3db14646daf584449f2b9c6880b66e7b082a665eba56234230610bab77c6e'}, +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('NTL', '11.5.1'), +] + +configopts = '-DWITH_NTL=on -DBUILD_TESTING=yes' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4_find_flexiblas.patch b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4_find_flexiblas.patch new file mode 100644 index 00000000000..54412d05b23 --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4_find_flexiblas.patch @@ -0,0 +1,23 @@ +Use FlexiBLAS when available + +Åke Sandgren, 2023-05-03 +diff -ru flint-2.8.4.orig/CMake/FindCBLAS.cmake flint-2.8.4/CMake/FindCBLAS.cmake +--- flint-2.8.4.orig/CMake/FindCBLAS.cmake 2021-11-17 18:43:50.000000000 +0100 ++++ flint-2.8.4/CMake/FindCBLAS.cmake 2023-05-03 09:29:36.599062848 +0200 +@@ -11,13 +11,13 @@ + find_path(CBLAS_INCLUDE_DIRS NAMES cblas.h + HINTS CBLAS_ROOT ENV CBLAS_ROOT + PATHS ${INCLUDE_INSTALL_DIR} ${CMAKE_INSTALL_PREFIX}/include +- PATH_SUFFIXES openblas cblas blis ++ PATH_SUFFIXES flexiblas openblas cblas blis + ) + +-find_library(CBLAS_LIBRARIES NAMES accelerate openblas cblas blas blis ++find_library(CBLAS_LIBRARIES NAMES accelerate flexiblas openblas cblas blas blis + HINTS CBLAS_ROOT ENV CBLAS_ROOT + PATHS ${LIB_INSTALL_DIR} ${CMAKE_INSTALL_PREFIX}/lib +- PATH_SUFFIXES openblas cblas blis ++ PATH_SUFFIXES flexiblas openblas cblas blis + ) + + include(FindPackageHandleStandardArgs) diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022a.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022a.eb new file mode 100644 index 00000000000..8d6bb6cc6fb --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'FLINT' +version = '2.9.0' + +homepage = 'https://www.flintlib.org/' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.flintlib.org'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-2.8.4_find_flexiblas.patch', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Python', '3.10.4'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('NTL', '11.5.1'), +] + +configopts = '-DWITH_NTL=on -DBUILD_TESTING=yes' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.2.0.eb b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.2.0.eb new file mode 100644 index 00000000000..cbeb836cd91 --- /dev/null +++ b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.2.0.eb @@ -0,0 +1,44 @@ +# contributed by Guilherme Peretti-Pezzi (CSCS) +# updated by Alex Domingo (Vrije Universiteit Brussel) +# updated by Åke Sandgren(Umeå University) + +easyblock = 'ConfigureMake' + +name = 'NTL' +version = '11.5.1' + +homepage = 'https://shoup.net/ntl/' + +description = """NTL is a high-performance, portable C++ library providing data structures and +algorithms for manipulating signed, arbitrary length integers, and for vectors, +matrices, and polynomials over the integers and over finite fields.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'libntl' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ef578fa8b6c0c64edd1183c4c303b534468b58dd3eb8df8c9a5633f984888de5'] + +builddependencies = [ + ('Perl', '5.34.0'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +start_dir = 'src' + +prefix_opt = 'PREFIX=' +configopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" GMP_PREFIX="$EBROOTGMP" SHARED=on' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libntl.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/NTL', 'share/doc'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.3.0.eb b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..89c7288994f --- /dev/null +++ b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.3.0.eb @@ -0,0 +1,44 @@ +# contributed by Guilherme Peretti-Pezzi (CSCS) +# updated by Alex Domingo (Vrije Universiteit Brussel) +# updated by Åke Sandgren(Umeå University) + +easyblock = 'ConfigureMake' + +name = 'NTL' +version = '11.5.1' + +homepage = 'https://shoup.net/ntl/' + +description = """NTL is a high-performance, portable C++ library providing data structures and +algorithms for manipulating signed, arbitrary length integers, and for vectors, +matrices, and polynomials over the integers and over finite fields.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'libntl' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ef578fa8b6c0c64edd1183c4c303b534468b58dd3eb8df8c9a5633f984888de5'] + +builddependencies = [ + ('Perl', '5.34.1'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +start_dir = 'src' + +prefix_opt = 'PREFIX=' +configopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" GMP_PREFIX="$EBROOTGMP" SHARED=on' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libntl.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/NTL', 'share/doc'], +} + +moduleclass = 'math' From 4304c1a1e067884325dcb5aba7e0347f19852687 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 5 May 2023 15:42:06 +0200 Subject: [PATCH 7348/9987] FLINT: Drop GCC level easyconfigs for GCC 11.2.0/11.3.0 They should be at gfbf/foss level depending on toolchain version due to BLAS being a depedency. --- .../f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb | 34 ------------------- .../f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb | 34 ------------------- 2 files changed, 68 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb delete mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb deleted file mode 100644 index 8b3d55e165d..00000000000 --- a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'FLINT' -version = '2.8.4' - -homepage = 'https://www.flintlib.org/' - -description = """FLINT (Fast Library for Number Theory) is a C library in support of computations - in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, - factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides - various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" - -toolchain = {'name': 'GCC', 'version': '11.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.flintlib.org'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['61df92ea8c8e9dc692d46c71d7f50aaa09a33d4ba08d02a1784730a445e5e4be'] - -builddependencies = [ - ('CMake', '3.22.1'), -] - -dependencies = [ - ('GMP', '6.2.1'), - ('MPFR', '4.1.0'), -] - -sanity_check_paths = { - 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb deleted file mode 100644 index 90131d5e4c4..00000000000 --- a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'FLINT' -version = '2.9.0' - -homepage = 'https://www.flintlib.org/' - -description = """FLINT (Fast Library for Number Theory) is a C library in support of computations - in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, - factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides - various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" - -toolchain = {'name': 'GCC', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.flintlib.org'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['2fc090d51033c93208e6c10d406397a53c983ae5343b958eb25f72a57a4ce76a'] - -builddependencies = [ - ('CMake', '3.23.1'), -] - -dependencies = [ - ('GMP', '6.2.1'), - ('MPFR', '4.1.0'), -] - -sanity_check_paths = { - 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'math' From c3d1da0b78ef4590d3151335d02200d802242c50 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 5 May 2023 16:16:50 +0200 Subject: [PATCH 7349/9987] Move Arb and polymake to gfbf/foss level. --- .../a/Arb/Arb-2.22.1-foss-2021b.eb | 35 ++++++++++++++++++ .../a/Arb/Arb-2.23.0-gfbf-2022a.eb | 35 ++++++++++++++++++ .../p/polymake/polymake-4.8-foss-2021b.eb | 37 +++++++++++++++++++ .../p/polymake/polymake-4.8-gfbf-2022a.eb | 37 +++++++++++++++++++ .../easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb | 26 +++++++++++++ 5 files changed, 170 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arb/Arb-2.22.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/a/Arb/Arb-2.23.0-gfbf-2022a.eb create mode 100644 easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2021b.eb create mode 100644 easybuild/easyconfigs/p/polymake/polymake-4.8-gfbf-2022a.eb create mode 100644 easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.22.1-foss-2021b.eb b/easybuild/easyconfigs/a/Arb/Arb-2.22.1-foss-2021b.eb new file mode 100644 index 00000000000..6aede555b93 --- /dev/null +++ b/easybuild/easyconfigs/a/Arb/Arb-2.22.1-foss-2021b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Arb' +version = '2.22.1' + +homepage = 'https://arblib.org/' + +description = """Arb is a C library for arbitrary-precision interval arithmetic. + It has full support for both real and complex numbers. The library is thread-safe, + portable, and extensively tested.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +github_account = 'fredrik-johansson' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['1ef85518eee04885e8a90196498bc75e4e2410621d4184f2bc01d46b7080a243'] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('FLINT', '2.8.4'), +] + +configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.23.0-gfbf-2022a.eb b/easybuild/easyconfigs/a/Arb/Arb-2.23.0-gfbf-2022a.eb new file mode 100644 index 00000000000..06c0fa3ab76 --- /dev/null +++ b/easybuild/easyconfigs/a/Arb/Arb-2.23.0-gfbf-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Arb' +version = '2.23.0' + +homepage = 'https://arblib.org/' + +description = """Arb is a C library for arbitrary-precision interval arithmetic. + It has full support for both real and complex numbers. The library is thread-safe, + portable, and extensively tested.""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} +toolchainopts = {'pic': True} + +github_account = 'fredrik-johansson' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['977d41bde46f5442511d5165c705cec32c03e852c84d7d1836135d412ce702bb'] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('FLINT', '2.9.0'), +] + +configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2021b.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2021b.eb new file mode 100644 index 00000000000..a15d42eeece --- /dev/null +++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2021b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'polymake' +version = '4.8' + +homepage = 'https://polymake.org' +description = """polymake is open source software for research in polyhedral geometry. +It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, +graphs, tropical hypersurfaces, and other objects.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://polymake.org/lib/exe/fetch.php/download/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['3f7bd19d6ac1372ae32368e57134ff37a11fbe9eb1f6abe8195b34c5eec29b11'] + +dependencies = [ + ('Ninja', '1.10.2'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('libreadline', '8.1'), + ('Perl', '5.34.0'), + ('SVG', '2.87'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('Boost', '1.77.0'), + ('FLINT', '2.8.4'), + ('Java', '11', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT, + 'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT], + 'dirs': ['include/polymake', 'lib/polymake', 'share/polymake'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-gfbf-2022a.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-gfbf-2022a.eb new file mode 100644 index 00000000000..5eff12ad133 --- /dev/null +++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-gfbf-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'polymake' +version = '4.8' + +homepage = 'https://polymake.org' +description = """polymake is open source software for research in polyhedral geometry. +It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, +graphs, tropical hypersurfaces, and other objects.""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} + +source_urls = ['https://polymake.org/lib/exe/fetch.php/download/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['3f7bd19d6ac1372ae32368e57134ff37a11fbe9eb1f6abe8195b34c5eec29b11'] + +dependencies = [ + ('Ninja', '1.10.2'), + ('libxml2', '2.9.13'), + ('libxslt', '1.1.34'), + ('libreadline', '8.1.2'), + ('Perl', '5.34.1'), + ('SVG', '2.87'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('Boost', '1.79.0'), + ('FLINT', '2.9.0'), + ('Java', '11', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT, + 'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT], + 'dirs': ['include/polymake', 'lib/polymake', 'share/polymake'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb new file mode 100644 index 00000000000..1eaefad2e9d --- /dev/null +++ b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PerlModule' + +name = 'SVG' +version = '2.87' + +homepage = 'https://metacpan.org/pod/SVG' +description = "Perl binding for SVG" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b3fa58c1c59942b4ebef003da97c3e01e531480ca29e8efbe327ff0589c0bd3c'] + +dependencies = [ + ('Perl', '5.34.0'), +] + +options = {'modulename': 'SVG'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/SVG.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/SVG'], +} + +moduleclass = 'data' From 580a723e3e361f3a5988dfc34da0be2488d35adc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 5 May 2023 16:21:29 +0200 Subject: [PATCH 7350/9987] Drop Arb and polymake at GCC level since FLINT is now at gfbf/foss New Arb and polymake versions in PR #17869 --- .../a/Arb/Arb-2.22.1-GCC-11.2.0.eb | 35 ------------------ .../p/polymake/polymake-4.8-GCC-11.3.0.eb | 37 ------------------- 2 files changed, 72 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb delete mode 100644 easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb deleted file mode 100644 index f729c96081d..00000000000 --- a/easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Arb' -version = '2.22.1' - -homepage = 'https://arblib.org/' - -description = """Arb is a C library for arbitrary-precision interval arithmetic. - It has full support for both real and complex numbers. The library is thread-safe, - portable, and extensively tested.""" - -toolchain = {'name': 'GCC', 'version': '11.2.0'} -toolchainopts = {'pic': True} - -github_account = 'fredrik-johansson' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['1ef85518eee04885e8a90196498bc75e4e2410621d4184f2bc01d46b7080a243'] - -dependencies = [ - ('FLINT', '2.8.4'), - ('GMP', '6.2.1'), - ('MPFR', '4.1.0'), -] - -configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], - 'dirs': ['include'], -} - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb deleted file mode 100644 index bb766d01955..00000000000 --- a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'polymake' -version = '4.8' - -homepage = 'https://polymake.org' -description = """polymake is open source software for research in polyhedral geometry. -It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, -graphs, tropical hypersurfaces, and other objects.""" - -toolchain = {'name': 'GCC', 'version': '11.3.0'} - -source_urls = ['https://polymake.org/lib/exe/fetch.php/download/'] -sources = [SOURCE_TAR_BZ2] -checksums = ['3f7bd19d6ac1372ae32368e57134ff37a11fbe9eb1f6abe8195b34c5eec29b11'] - -dependencies = [ - ('Ninja', '1.10.2'), - ('libxml2', '2.9.13'), - ('libxslt', '1.1.34'), - ('libreadline', '8.1.2'), - ('Perl', '5.34.1'), - ('SVG', '2.87'), - ('GMP', '6.2.1'), - ('MPFR', '4.1.0'), - ('Boost', '1.79.0'), - ('FLINT', '2.9.0'), - ('Java', '11', '', SYSTEM), -] - -sanity_check_paths = { - 'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT, - 'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT], - 'dirs': ['include/polymake', 'lib/polymake', 'share/polymake'], -} - -moduleclass = 'math' From 7eebeef97c90c71ac8c75cf5ca71a47f97978a1a Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 5 May 2023 17:28:41 +0200 Subject: [PATCH 7351/9987] adding easyconfigs: HDF5-1.10.6-iompi-2020a.eb --- .../h/HDF5/HDF5-1.10.6-iompi-2020a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb new file mode 100644 index 00000000000..6c000f1179e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.6' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iompi', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' + From cbb0bcd11f34117536dd4d5c8552c84571670e1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 5 May 2023 18:26:01 +0200 Subject: [PATCH 7352/9987] Update easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb --- easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb index 6c000f1179e..ddde88aa068 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb @@ -19,4 +19,3 @@ dependencies = [ ] moduleclass = 'data' - From 6ccedd91662bf0f304d5d13e556002841c66bc98 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 5 May 2023 19:57:21 +0200 Subject: [PATCH 7353/9987] review updates --- .../AlphaPulldown-0.30.4-foss-2020b.eb | 20 +++--- .../AlphaPulldown-0.30.4_fix-deps.patch | 11 ++- .../dm-haiku-0.0.4_fix-deps.patch | 8 +++ .../cctbx-base-2020.8-foss-2020b.eb | 69 +++++++++++++++++++ 4 files changed, 90 insertions(+), 18 deletions(-) create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/dm-haiku-0.0.4_fix-deps.patch create mode 100644 easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb index e0c1549fb9e..c9fa9aa9728 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} builddependencies = [ # required for installing dm-tree - ('Bazel', '3.7.2'), + # ('Bazel', '3.7.2'), ] dependencies = [ @@ -29,6 +29,7 @@ dependencies = [ ('matplotlib', '3.3.3'), ('TensorFlow', '2.4.1'), ('tqdm', '4.56.2'), + ('dm-tree', '0.1.5'), ] use_pip = True @@ -45,17 +46,17 @@ exts_list = [ }), ('dm-haiku', '0.0.4', { 'modulename': 'haiku', + 'patches': ['%(name)s-%(version)s_fix-deps.patch'], 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'], + 'checksums': [ + {'dm-haiku-0.0.4.tar.gz': 'e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'}, + {'dm-haiku-0.0.4_fix-deps.patch': '66400ed767d25e63c0c3b6a631bc6ea2496aaac6346563669199d9874cd1c549'}, + ], }), ('toolz', '0.11.1', { 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], }), - ('dm-tree', '0.1.6', { - 'modulename': 'tree', - 'checksums': ['6776404b23b4522c01012ffb314632aba092c9541577004ab153321e87da439a'], - }), ('importlib-resources', '5.12.0', { 'modulename': 'importlib_resources', 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', @@ -68,15 +69,12 @@ exts_list = [ 'sources': ['ml_collections-%(version)s.tar.gz'], 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], }), - ('tabulate', '0.8.9', { - 'checksums': ['eb1d13f25760052e8931f2ef80aaf6045a6cceb47514db8beab24cded16f13a7'], - }), (name, version, { 'patches': ['%(name)s-%(version)s_fix-deps.patch'], 'sources': ['%(namelower)s-%(version)s.tar.gz'], 'checksums': [ {'alphapulldown-0.30.4.tar.gz': '7797500abaee2e92d28034dc97844bca8c8d7281817e29dc110220824e9d1b5b'}, - {'AlphaPulldown-0.30.4_fix-deps.patch': 'c31cd3fcb6688f77a9277ccb779e54bb862c84e1cac485b03a9f00d10eb9ffe6'}, + {'AlphaPulldown-0.30.4_fix-deps.patch': 'ddadf42da3ca95423004f6bb7db6ce85e6a338e993411286f3bdf859e72e860f'}, ], }), ] @@ -88,6 +86,4 @@ sanity_check_paths = { "dirs": ["lib/python%(pyshortver)s/site-packages/alphapulldown"], } -sanity_check_commands = [('python -c "import alphapulldown"')] - moduleclass = "data" diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch index adcad416081..4a1dc05563b 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch @@ -1,17 +1,16 @@ -# making AlphaPulldown's dependencies less strict -diff -ruN alphapulldown-0.30.4_orig/setup.cfg alphapulldown-0.30.4/setup.cfg ---- alphapulldown-0.30.4_orig/setup.cfg 2023-04-05 13:59:25.000000000 +0100 -+++ alphapulldown-0.30.4/setup.cfg 2023-04-06 14:10:45.424577468 +0100 +--- setup.cfg_orig 2023-05-05 15:41:50.159415210 +0200 ++++ setup.cfg 2023-05-05 15:41:28.563066879 +0200 @@ -17,19 +17,19 @@ include_package_data = True python_requires = ==3.8.* install_requires = - absl-py >= 0.13.0 - dm-haiku==0.0.9 +- dm-tree==0.1.6 +- h5py==3.1.0 + absl-py >= 0.10.0 + dm-haiku==0.0.4 - dm-tree==0.1.6 -- h5py==3.1.0 ++ dm-tree==0.1.5 + h5py==2.10.0 matplotlib==3.3.3 - ml-collections==0.1.0 diff --git a/easybuild/easyconfigs/a/AlphaPulldown/dm-haiku-0.0.4_fix-deps.patch b/easybuild/easyconfigs/a/AlphaPulldown/dm-haiku-0.0.4_fix-deps.patch new file mode 100644 index 00000000000..0605624756c --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/dm-haiku-0.0.4_fix-deps.patch @@ -0,0 +1,8 @@ +--- requirements_orig.txt 2021-04-12 10:32:51.000000000 +0100 ++++ requirements.txt 2023-05-05 18:13:43.278174328 +0100 +@@ -1,4 +1,4 @@ + absl-py>=0.7.1 + numpy>=1.18.0 +-tabulate>=0.8.9 ++tabulate>=0.8.7 + typing_extensions; python_version<"3.8" \ No newline at end of file diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb new file mode 100644 index 00000000000..b01de853ba2 --- /dev/null +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb @@ -0,0 +1,69 @@ +# author: Denis Kristak (Inuits) +easyblock = "PythonBundle" + +name = "cctbx-base" +version = "2020.8" +local_pyver = "3.8.6" + +# local_pyver_special is used to create the wheel filename +# it contains the first two digits of the python version (with no delimiter) +local_tmp = local_pyver.split('.') +local_tmp.pop() +# compose a string +local_pyver_special = ''.join(local_tmp) +local_tmp = None # cleanup + +homepage = "https://github.com/cctbx/cctbx_project" +description = """ +The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix +project. The goal of the Phenix project is to advance automation of macromolecular structure determination. +Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable +library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific +applications. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', local_pyver), + ('Boost', '1.74.0'), + ('HDF5', '1.10.7'), + ('libGLU', '9.0.1'), + ('LIBSVM', '3.25'), + ('LibTIFF', '4.1.0'), + ('matplotlib', '3.3.3'), + ('mrcfile', '1.3.0'), +] + +local_metadata = "%(installdir)s/lib/python%(pyshortver)s/site-packages/cctbx_base-%(version)s.dist-info/METADATA" + + +exts_list = [ + ('reportlab', '3.5.66', { + 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], + }), + (name, version, { + 'modulename': 'cctbx', + # remove deps (they fail during sanity check, even though they are installed) + 'postinstallcmds': ["echo '' > %s" % local_metadata], + 'sources': [{ + 'download_filename': 'cctbx_base-%s-0_py%sh167b89d-cp%s-cp%sm-manylinux2010_x86_64.whl' % ( + version, local_pyver_special, local_pyver_special, local_pyver_special + ), + 'filename': 'cctbx_base-%s-cp%s-cp%s-manylinux2010_x86_64.whl' % ( + version, local_pyver_special, local_pyver_special + ), + }], + 'checksums': ['5c7ac0710d9011072c678771876aa57ca3735986ed321d403f51989a7444e592'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + "files": ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], + "dirs": ['lib/python%(pyshortver)s/site-packages/cctbx_website'], +} + +moduleclass = "lib" From ff378769003dbad30a3f7d341941c32c46dee266 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 5 May 2023 20:04:37 +0200 Subject: [PATCH 7354/9987] review updates --- .../a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb index c9fa9aa9728..4bcbb49ca81 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -10,11 +10,6 @@ interaction screens and high-throughput modelling of higher-order oligomers usin toolchain = {'name': 'foss', 'version': '2020b'} -builddependencies = [ - # required for installing dm-tree - # ('Bazel', '3.7.2'), -] - dependencies = [ ('Python', '3.8.6'), ("OpenMM", "7.5.0"), From 02112bea481f97bd43e30e14040a7faaab39acd3 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 5 May 2023 20:05:39 +0200 Subject: [PATCH 7355/9987] Delete cctbx-base-2022.8-foss-2020b.eb messed up version, removing this one as it uses the wrong version --- .../cctbx-base-2022.8-foss-2020b.eb | 57 ------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb deleted file mode 100644 index a9e23e124d4..00000000000 --- a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2022.8-foss-2020b.eb +++ /dev/null @@ -1,57 +0,0 @@ -# author: Denis Kristak (Inuits) -easyblock = "PythonBundle" - -name = "cctbx-base" -version = "2022.8" - -homepage = "https://github.com/cctbx/cctbx_project" -description = """ -The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix -project. The goal of the Phenix project is to advance automation of macromolecular structure determination. -Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable -library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific -applications. -""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -dependencies = [ - ('Python', '3.8.6'), - ('Boost', '1.74.0'), - ('HDF5', '1.10.7'), - ('libGLU', '9.0.1'), - ('LIBSVM', '3.25'), - ('LibTIFF', '4.1.0'), - ('matplotlib', '3.3.3'), - ('mrcfile', '1.3.0'), -] - -local_metadata_folder = "%(installdir)s/lib/python3.8/site-packages/cctbx_base-2020.8.dist-info/METADATA" - -exts_list = [ - ('reportlab', '3.5.66', { - 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], - }), - (name, version, { - 'modulename': 'cctbx', - # remove deps (they fail during sanity check, even though they are installed) - 'postinstallcmds': ["echo '' > %s" % local_metadata_folder], - 'sources': [{ - 'download_filename': 'cctbx_base-2020.8-0_py38h167b89d-cp38-cp38m-manylinux2010_x86_64.whl', - 'filename': 'cctbx_base-2020.8-cp38-cp38-manylinux2010_x86_64.whl' - }], - 'checksums': ['5c7ac0710d9011072c678771876aa57ca3735986ed321d403f51989a7444e592'], - }), -] - -use_pip = True -sanity_pip_check = True - -sanity_check_paths = { - "files": ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], - "dirs": ['lib/python3.8/site-packages/cctbx_website'], -} - -sanity_check_commands = [('python -c "import cctbx"')] - -moduleclass = "lib" From 76f17ddf6214ef04c05b1dc31960f2d66351c827 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 5 May 2023 20:29:25 +0200 Subject: [PATCH 7356/9987] fixing gh errors --- .../a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb | 6 +++--- .../a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch | 2 ++ .../a/AlphaPulldown/dm-haiku-0.0.4_fix-deps.patch | 2 ++ .../c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb | 1 - 4 files changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb index 4bcbb49ca81..1354c1e2a67 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -15,7 +15,7 @@ dependencies = [ ("OpenMM", "7.5.0"), ("Kalign", "3.3.1"), ('PyYAML', '5.3.1'), - ("cctbx-base", "2022.8"), + ("cctbx-base", "2020.8"), ('jax', '0.2.19'), # also provides absl-py ('Biopython', '1.78'), ('h5py', '3.1.0'), @@ -46,7 +46,7 @@ exts_list = [ 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': [ {'dm-haiku-0.0.4.tar.gz': 'e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'}, - {'dm-haiku-0.0.4_fix-deps.patch': '66400ed767d25e63c0c3b6a631bc6ea2496aaac6346563669199d9874cd1c549'}, + {'dm-haiku-0.0.4_fix-deps.patch': 'c509e0aa049401f340234b0a5eba59c9e8af8eff94b9e92f0693aeadfa4c5aa8'}, ], }), ('toolz', '0.11.1', { @@ -69,7 +69,7 @@ exts_list = [ 'sources': ['%(namelower)s-%(version)s.tar.gz'], 'checksums': [ {'alphapulldown-0.30.4.tar.gz': '7797500abaee2e92d28034dc97844bca8c8d7281817e29dc110220824e9d1b5b'}, - {'AlphaPulldown-0.30.4_fix-deps.patch': 'ddadf42da3ca95423004f6bb7db6ce85e6a338e993411286f3bdf859e72e860f'}, + {'AlphaPulldown-0.30.4_fix-deps.patch': 'fc5bf395cb36d02efa6d538df49749e722b2d2c257197e3dac83a81c9405c0c9'}, ], }), ] diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch index 4a1dc05563b..37773ee4bbd 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4_fix-deps.patch @@ -1,3 +1,5 @@ +making dependencies less strict +author: Denis Kristak (Inuits) --- setup.cfg_orig 2023-05-05 15:41:50.159415210 +0200 +++ setup.cfg 2023-05-05 15:41:28.563066879 +0200 @@ -17,19 +17,19 @@ diff --git a/easybuild/easyconfigs/a/AlphaPulldown/dm-haiku-0.0.4_fix-deps.patch b/easybuild/easyconfigs/a/AlphaPulldown/dm-haiku-0.0.4_fix-deps.patch index 0605624756c..4fe3da29116 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/dm-haiku-0.0.4_fix-deps.patch +++ b/easybuild/easyconfigs/a/AlphaPulldown/dm-haiku-0.0.4_fix-deps.patch @@ -1,3 +1,5 @@ +make dependencies less strict +Author: Denis Kristak (Inuits) --- requirements_orig.txt 2021-04-12 10:32:51.000000000 +0100 +++ requirements.txt 2023-05-05 18:13:43.278174328 +0100 @@ -1,4 +1,4 @@ diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb index b01de853ba2..edb2dd60460 100644 --- a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb @@ -11,7 +11,6 @@ local_tmp = local_pyver.split('.') local_tmp.pop() # compose a string local_pyver_special = ''.join(local_tmp) -local_tmp = None # cleanup homepage = "https://github.com/cctbx/cctbx_project" description = """ From 69e3e594c1f82e93e1c5ec803c67ad8905ce1795 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Sat, 6 May 2023 14:29:41 +0200 Subject: [PATCH 7357/9987] Update easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit thanks, didnt notice Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb index 9bcd7cf4116..e2ffcd2d854 100644 --- a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb @@ -7,7 +7,7 @@ name = 'CPC2' version = '0.1' local_commit = '813487e' -homepage = 'http://cpc2.cbi.pku.edu.cn' +homepage = 'http://cpc2.gao-lab.org/' description = """ a fast and accurate coding potential calculator based on sequence intrinsic features """ toolchain = {'name': 'foss', 'version': '2022a'} From 9f1c0513aebfc0458cd2863d34c820580d1e4123 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 6 May 2023 21:23:16 +0200 Subject: [PATCH 7358/9987] adding easyconfigs: gpustat-1.1-GCCcore-11.3.0.eb --- .../g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a581373ba1e --- /dev/null +++ b/easybuild/easyconfigs/g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'gpustat' +version = '1.1' + +homepage = 'https://github.com/wookayin/gpustat' +description = "A simple command-line utility for querying and monitoring GPU status" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +# This software works directly against the nvidia drivers and doesn't require CUDA. +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_list = [ + ('blessed', '1.20.0', { + 'checksums': ['2cdd67f8746e048f00df47a2880f4d6acbcdb399031b604e34ba8f71d5787680'], + }), + ('nvidia-ml-py', '11.525.112', { + 'modulename': 'pynvml', + 'checksums': ['c64e473953b65ec0ccc76cf3601c3130a0ac8060bbcaea912cc00fa8e4c9868d'], + }), + (name, version, { + 'checksums': ['c8fc105404aac11884f70ed2fa06cfd210d3cd389ccae4a9bc38579c72460cee'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gpustat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gpustat --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From 2f66aedb8f2f1628790bdf0c36b67865c5bbcd31 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 8 May 2023 08:23:38 +0200 Subject: [PATCH 7359/9987] adding easyconfigs: ReFrame-4.2.0.eb --- .../easyconfigs/r/ReFrame/ReFrame-4.2.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb new file mode 100644 index 00000000000..dc290fcc04d --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb @@ -0,0 +1,63 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.2.0' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + ('reframe', version, { + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['f1d38133023b37d01fdee46b2bf472f8fd36bf410d1c909db043b9f9d7df6122'], + }), +] + +postinstallcmds = [ + "cp -a hpctestlib tools tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'hpctestlib', 'lib', 'tools', 'tutorials'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 24883f825dd505761b42ab6c53faefbeba0b278f Mon Sep 17 00:00:00 2001 From: lukelabrie Date: Mon, 8 May 2023 12:14:57 +0200 Subject: [PATCH 7360/9987] fix broken tarball links for ispc 1.6, 1.10 and 1.12 easyconfigs --- easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb | 6 +++--- easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb | 6 +++--- easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb | 3 ++- 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb index c83e203d15d..5c8c24efaf6 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb @@ -13,9 +13,9 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high- toolchain = SYSTEM -sources = ['ispc-v%(version)s-linux.tar.gz'] -source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] -checksums = ['453211ade91c33826f4facb1336114831adbd35196d016e09d589a6ad8699aa3'] +source_urls = ['https://github.com/ispc/ispc/releases/download/v%(version)s/'] +sources = ['ispc-v%(version)sb-linux.tar.gz'] +checksums = ['7fbcf27be161d80a28ab258b3beef3f137a72ac4edc9aa92b1cca044521ff6ca'] sanity_check_paths = { 'files': ["bin/ispc"], diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb index 450f335d81a..cb286e82948 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb @@ -13,9 +13,9 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high- toolchain = SYSTEM -source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] -sources = ['ispc-v%(version)s-linux.tar.gz'] -checksums = ['79decaef42bc5433ab30f5879eb91af14473a42e8b51ec727a97f61ee918497e'] +source_urls = ['https://github.com/ispc/ispc/releases/download/v%(version)s/'] +sources = ['ispc-v%(version)sb-linux.tar.gz'] +checksums = ['7a2bdd5fff5c1882639cfbd66bca31dbb68c7177f3013e80b0813a37fe0fdc23'] sanity_check_paths = { 'files': ["bin/ispc"], diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb index b266d99faac..0b7e085e0e3 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb @@ -13,8 +13,9 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high- toolchain = SYSTEM +source_urls = ['https://github.com/ispc/ispc/releases/download/v%(version)s/'] sources = ['ispc-v%(version)s-linux.tar.gz'] -source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] +checksums = ['67abd92645ead651ced74c4e358313414f5786f0275d975ef4888f168ca342d1'] sanity_check_paths = { 'files': ["ispc"], From c799b96a5d1ae72f15bd6ac1a83deedd93930a45 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Mon, 8 May 2023 14:18:19 +0200 Subject: [PATCH 7361/9987] adding easyconfigs: libharu-2.3.0-GCCcore-11.3.0.eb, pftoolsV3-3.2.12-GCCcore-11.3.0.eb --- .../l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb | 33 ++++++++++ .../pftoolsV3-3.2.12-GCCcore-11.3.0.eb | 60 +++++++++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7b7f71ea537 --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'https://github.com/libharu/libharu/' +description = """libHaru is a free, cross platform, open source library for generating PDF files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GITHUB_SOURCE] # https://github.com/libharu/libharu/archive/ +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [('libpng', '1.6.37')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': [ + 'if', + 'include', + 'lib', + ] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..51c1ebbe912 --- /dev/null +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'CMakeMake' + +name = 'pftoolsV3' +version = '3.2.12' + +homepage = 'https://github.com/sib-swiss/pftools3' +description = """A suite of tools to build and search generalized profiles (protein and DNA).""" +software_license = 'LicenseGPLv2' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/'] +checksums = ['1de33d6444015942afa690d54a103ad5a3d68f416fad63f247c12fa3f71a550c'] # pftools3-3.2.12.tar.gz + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('make', '4.3'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('libgd', '2.3.3'), + ('libharu', '2.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('PCRE2', '10.40'), + ('Perl', '5.34.1'), + ('zlib', '1.2.12'), +] + +configopts = '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON -DUSE_AFFINITY=OFF' # Disable affinity for some old architectures + +runtest = 'test' + +sanity_check_paths = { + 'files': [ + 'bin/2ft', + 'bin/6ft', + 'bin/htop', + 'bin/pfdump', + 'bin/pfscan', + 'bin/pfscanV3', + 'bin/pfsearch', + 'bin/pfsearchV3', + 'bin/ptof', + ], + 'dirs': [ + 'share/doc', + 'share/man' + ], +} + +sanity_check_commands = [ + 'pfscanV3 --help', + 'pfsearchV3 --help', +] + +moduleclass = 'bio' From b46ce7927c8f02d8cd44388e1364d2504307bc29 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 8 May 2023 18:14:54 +0200 Subject: [PATCH 7362/9987] adding easyconfigs: GCC-12.3.0.eb, GCCcore-12.3.0.eb, binutils-2.40-GCCcore-12.3.0.eb, Bison-3.8.2-GCCcore-12.3.0.eb, flex-2.6.4-GCCcore-12.3.0.eb, help2man-1.49.3-GCCcore-12.3.0.eb, M4-1.4.19-GCCcore-12.3.0.eb, zlib-1.2.13-GCCcore-12.3.0.eb --- .../b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb | 28 +++++++++ .../binutils/binutils-2.40-GCCcore-12.3.0.eb | 31 +++++++++ .../f/flex/flex-2.6.4-GCCcore-12.3.0.eb | 34 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb | 22 +++++++ .../easyconfigs/g/GCCcore/GCCcore-12.3.0.eb | 63 +++++++++++++++++++ .../help2man-1.49.3-GCCcore-12.3.0.eb | 25 ++++++++ .../m/M4/M4-1.4.19-GCCcore-12.3.0.eb | 29 +++++++++ .../z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb | 27 ++++++++ 8 files changed, 259 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..36f8bac232a --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.40', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..db717c869d8 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.40' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d7f82c4047decf43a6f769ac32456a92ddb6932409a585c633cdd4e9df23d956'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', SYSTEM) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.13'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a1d5afb9dbd --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'https://github.com/westes/flex' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.40', '', SYSTEM), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb new file mode 100644 index 00000000000..e2701264c4c --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '12.3.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.40', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c7e0b2a3d08 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb @@ -0,0 +1,63 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '12.3.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.1.0.tar.bz2', + 'mpc-1.2.1.tar.gz', + 'isl-0.24.tar.bz2', + 'newlib-4.1.0.tar.gz', + {'download_filename': '93e0090.tar.gz', 'filename': 'nvptx-tools-20230122.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + {'gcc-12.3.0.tar.gz': '11275aa7bb34cd8ab101d01b341015499f8d9466342a2574ece93f954d92273b'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.40'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d3579d82fd8 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.40', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9bed7ee958f --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.40', '', SYSTEM)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b139a83d3cd --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.13' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.40', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 29e0658671e1cb6747a0160dd1ec2574b92c81f7 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 8 May 2023 18:27:12 +0200 Subject: [PATCH 7363/9987] GCCcore 12.3.0: update sources --- .../easyconfigs/g/GCCcore/GCCcore-12.3.0.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb index c7e0b2a3d08..45270c7b7f8 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb @@ -24,10 +24,10 @@ source_urls = [ sources = [ 'gcc-%(version)s.tar.gz', 'gmp-6.2.1.tar.bz2', - 'mpfr-4.1.0.tar.bz2', - 'mpc-1.2.1.tar.gz', - 'isl-0.24.tar.bz2', - 'newlib-4.1.0.tar.gz', + 'mpfr-4.2.0.tar.bz2', + 'mpc-1.3.1.tar.gz', + 'isl-0.26.tar.bz2', + 'newlib-4.3.0.20230120.tar.gz', {'download_filename': '93e0090.tar.gz', 'filename': 'nvptx-tools-20230122.tar.gz'}, ] patches = [ @@ -37,10 +37,10 @@ patches = [ checksums = [ {'gcc-12.3.0.tar.gz': '11275aa7bb34cd8ab101d01b341015499f8d9466342a2574ece93f954d92273b'}, {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, - {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, - {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, - {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, - {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'mpfr-4.2.0.tar.bz2': '691db39178e36fc460c046591e4b0f2a52c8f2b3ee6d750cc2eab25f1eaa999d'}, + {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'}, + {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'}, + {'newlib-4.3.0.20230120.tar.gz': '83a62a99af59e38eb9b0c58ed092ee24d700fff43a22c03e433955113ef35150'}, {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, From 055b6ddef4faad423db1531d833f2a6c491844eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 8 May 2023 20:05:13 +0200 Subject: [PATCH 7364/9987] adding easyconfigs: bzip2-1.0.8-GCCcore-12.3.0.eb, CMake-3.26.3-GCCcore-12.3.0.eb, cURL-8.0.1-GCCcore-12.3.0.eb, libarchive-3.6.2-GCCcore-12.3.0.eb, ncurses-6.4-GCCcore-12.3.0.eb, XZ-5.4.2-GCCcore-12.3.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb | 27 +++++++++++ .../c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb | 30 ++++++++++++ .../c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb | 43 +++++++++++++++++ .../libarchive-3.6.2-GCCcore-12.3.0.eb | 33 +++++++++++++ .../n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb | 47 +++++++++++++++++++ .../x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb | 34 ++++++++++++++ 6 files changed, 214 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..cb5b2748e2b --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.40'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d9b8ac7afaa --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.26.3' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bbd8d39217509d163cb544a40d6428ac666ddc83e22905d3e52c925781f0f659'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('cURL', '8.0.1'), + ('libarchive', '3.6.2'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..18bf937586b --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '8.0.1' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fd29000a4089934f121eff456101f0a5d09e2a3e89da1d714adf06c4be887cb'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3126faae1c5 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.6.2' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ba6d02f15ba04aba9c23fd5f236bb234eab9d5209e95d1c4df85c44d5f19b9b3'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('XZ', '5.4.2'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b1731393710 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.4' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6931283d9ac87c5073f30b6290c4c75f21632bb4fc3603ac8100812bed248159'] + +builddependencies = [('binutils', '2.40')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts, + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ade6916dd58 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.4.2' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['aa49909cbd9028c4666a35fa4975f9a6203ed98154fbb8223ee43ef9ceee97c3'] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.21.1', '', SYSTEM), + ('binutils', '2.40'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' From 1baef1234c448b2a0fccebc3c2ef5682074b6ae1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 9 May 2023 00:10:18 +0200 Subject: [PATCH 7365/9987] adding easyconfigs: dask-labextension-6.0.0-foss-2022a.eb --- .../dask-labextension-6.0.0-foss-2022a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb new file mode 100644 index 00000000000..584ac781fbc --- /dev/null +++ b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'dask-labextension' +version = '6.0.0' + +homepage = 'https://github.com/dask/dask-labextension' +description = """This package provides a JupyterLab extension to manage Dask clusters, as well +as embed Dask's dashboard plots directly into JupyterLab panes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('binutils', '2.38'), + ('nodejs', '16.15.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('JupyterLab', '3.5.0'), + ('jupyter-server-proxy', '3.2.2'), + ('dask', '2022.10.0'), +] + +use_pip = True + +exts_list = [ + ('dask_labextension', version, { + 'checksums': ['516d1faccd0b172d07f794250a5c3427b082d70954ebe8d3f9c92dc08cb79f7e'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/dask_labextension', 'etc/jupyter', 'share/jupyter'], +} + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'tools' From 4db0c8d618eeece87cf6e2e9d19b6f7f867977df Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 9 May 2023 10:30:24 +0200 Subject: [PATCH 7366/9987] Also update MPFR & co in GCCcore 13.1.0 --- .../easyconfigs/g/GCCcore/GCCcore-13.1.0.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb index 3493e06b275..5805f7d8a96 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb @@ -24,10 +24,10 @@ source_urls = [ sources = [ 'gcc-%(version)s.tar.gz', 'gmp-6.2.1.tar.bz2', - 'mpfr-4.1.0.tar.bz2', - 'mpc-1.2.1.tar.gz', - 'isl-0.24.tar.bz2', - 'newlib-4.1.0.tar.gz', + 'mpfr-4.2.0.tar.bz2', + 'mpc-1.3.1.tar.gz', + 'isl-0.26.tar.bz2', + 'newlib-4.3.0.20230120.tar.gz', {'download_filename': '93e0090.tar.gz', 'filename': 'nvptx-tools-20230122.tar.gz'}, ] patches = [ @@ -37,10 +37,10 @@ patches = [ checksums = [ {'gcc-13.1.0.tar.gz': 'bacd4c614d8bd5983404585e53478d467a254249e0f1bb747c8bc6d787bd4fa2'}, {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, - {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, - {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, - {'isl-0.24.tar.bz2': 'fcf78dd9656c10eb8cf9fbd5f59a0b6b01386205fe1934b3b287a0a1898145c0'}, - {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'mpfr-4.2.0.tar.bz2': '691db39178e36fc460c046591e4b0f2a52c8f2b3ee6d750cc2eab25f1eaa999d'}, + {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'}, + {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'}, + {'newlib-4.3.0.20230120.tar.gz': '83a62a99af59e38eb9b0c58ed092ee24d700fff43a22c03e433955113ef35150'}, {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, From ce274e8179ed3fbd4fdb8fb1bb964471fd6bd9bc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 9 May 2023 13:52:38 +0000 Subject: [PATCH 7367/9987] adding easyconfigs: BayesPrism-2.0-foss-2022a-R-4.2.1.eb --- .../BayesPrism-2.0-foss-2022a-R-4.2.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/BayesPrism/BayesPrism-2.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/b/BayesPrism/BayesPrism-2.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/b/BayesPrism/BayesPrism-2.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..a95446be4a1 --- /dev/null +++ b/easybuild/easyconfigs/b/BayesPrism/BayesPrism-2.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,33 @@ +easyblock = 'RPackage' + +name = 'BayesPrism' +version = '2.0' +# Still have versionsuffix because we need Bioconductor, which also still has it +versionsuffix = '-R-%(rver)s' +github_account = 'Danko-Lab' +local_commit = '1ad3e82' + +homepage = 'https://github.com/Danko-Lab/BayesPrism' +description = """Bayesian cell Proportion Reconstruction Inferred using Statistical Marginalization + (BayesPrism): A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression + """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +source_urls = ['https://github.com/%(github_account)s/%(name)s/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['bfbddbb6853422ddc327166ef5c9c581d3a7baa21d8734af95c55f02e5cf66bd'] + +start_dir = 'BayesPrism' + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s'], +} + +moduleclass = 'bio' From 3ee5447b983bcde19c15c1fc1abc18adebfa9e22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 9 May 2023 18:47:06 +0200 Subject: [PATCH 7368/9987] Rename opencv egg info, also add pkg info file generation --- .../o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb | 3 ++- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 5 +++-- ...ontrib-python.egg-info => opencv_contrib_python.egg-info} | 0 3 files changed, 5 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/o/OpenCV/{opencv-contrib-python.egg-info => opencv_contrib_python.egg-info} (100%) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb index 0edcf1239a6..31c84ed6b6e 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb @@ -38,7 +38,7 @@ checksums = [ {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'}, {'ippicv_2020_lnx_intel64_20191018_general.tgz': '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246'}, - {'opencv-contrib-python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'}, + {'opencv_contrib_python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'}, ] builddependencies = [ @@ -71,6 +71,7 @@ dependencies = [ # ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 configopts = " ".join([ "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DOPENCV_GENERATE_PKGCONFIG=ON", "-DFREETYPE_FOUND=ON", "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 6373a8db53e..62d6005f265 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -37,7 +37,7 @@ checksums = [ {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'}, {'ippicv_2020_lnx_intel64_20191018_general.tgz': '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246'}, - {'opencv-contrib-python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'}, + {'opencv_contrib_python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'}, ] builddependencies = [ @@ -68,6 +68,7 @@ dependencies = [ # ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 configopts = " ".join([ "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DOPENCV_GENERATE_PKGCONFIG=ON", "-DFREETYPE_FOUND=ON", "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", @@ -98,7 +99,7 @@ local_contrib_libs = [ ] sanity_check_paths = { - 'files': ['lib64/libopencv_%s.%s' % (s, SHLIB_EXT) for s in local_contrib_libs], + 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], 'dirs': [], } diff --git a/easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info b/easybuild/easyconfigs/o/OpenCV/opencv_contrib_python.egg-info similarity index 100% rename from easybuild/easyconfigs/o/OpenCV/opencv-contrib-python.egg-info rename to easybuild/easyconfigs/o/OpenCV/opencv_contrib_python.egg-info From 7aa8e3dae5396387b4ef113b61e9014a0c60be26 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 9 May 2023 19:33:46 +0200 Subject: [PATCH 7369/9987] Fix patch filename --- .../o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb | 2 +- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb index 31c84ed6b6e..bb75837b40e 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb @@ -32,7 +32,7 @@ sources = [ 'extract_cmd': 'cp %s %(builddir)s' }, ] -patches = [('opencv-contrib-python.egg-info', '..')] +patches = [('opencv_contrib_python.egg-info', '..')] checksums = [ {'opencv-4.6.0.zip': '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359'}, {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'}, diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index 62d6005f265..b2fd1d672bc 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -31,7 +31,7 @@ sources = [ 'extract_cmd': 'cp %s %(builddir)s' }, ] -patches = [('opencv-contrib-python.egg-info', '..')] +patches = [('opencv_contrib_python.egg-info', '..')] checksums = [ {'opencv-4.6.0.zip': '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359'}, {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'}, From c2d40724a619e995e0d65675681bbe4ae23e5354 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 9 May 2023 11:38:10 -0700 Subject: [PATCH 7370/9987] update version, add ABSL replace PR #17862 --- .../protobuf/protobuf-22.4-GCCcore-12.2.0.eb | 39 +++++++++++++++++++ .../protobuf-22.4_linking-error.patch | 37 ++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..3c78b97f75d --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '22.4' + +homepage = 'https://github.com/protocolbuffers/protobuf' +description = """Protocol Buffers (a.k.a., protobuf) are Google's +language-neutral, platform-neutral, extensible mechanism for +serializing structured data.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['protobuf-22.4_linking-error.patch'] +checksums = [ + 'def8683aafc1ebaddbc777da252dfdc8e324a197757e3bfcd8b4de90d4b8cf6a', # v22.4.tar.gz + '6c514ee1854fe40855a2db4a1cd197f9a30ec5be6d7c50932d4eb061788a151c', # protobuf-22.4_linking-error.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +srcdir = 'cmake' + +configopts = "-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER='package'" + +dependencies = [ + ('Abseil', '20230125.2'), +] + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch b/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch new file mode 100644 index 00000000000..0e83d971c78 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch @@ -0,0 +1,37 @@ +# https://github.com/protocolbuffers/protobuf/pull/11032 +diff -ruN protobuf-22.4.orig/src/libprotobuf-lite.map protobuf-22.4/src/libprotobuf-lite.map +--- protobuf-22.4.orig/src/libprotobuf-lite.map 2023-05-03 10:23:58.000000000 -0700 ++++ protobuf-22.4/src/libprotobuf-lite.map 2023-05-09 10:53:18.018860000 -0700 +@@ -3,6 +3,8 @@ + extern "C++" { + *google*; + }; ++ scc_info_*; ++ descriptor_table_*; + + local: + *; +diff -ruN protobuf-22.4.orig/src/libprotobuf.map protobuf-22.4/src/libprotobuf.map +--- protobuf-22.4.orig/src/libprotobuf.map 2023-05-03 10:23:58.000000000 -0700 ++++ protobuf-22.4/src/libprotobuf.map 2023-05-09 10:53:56.908337000 -0700 +@@ -3,6 +3,8 @@ + extern "C++" { + *google*; + }; ++ scc_info_*; ++ descriptor_table_*; + + local: + *; +diff -ruN protobuf-22.4.orig/src/libprotoc.map protobuf-22.4/src/libprotoc.map +--- protobuf-22.4.orig/src/libprotoc.map 2023-05-03 10:23:58.000000000 -0700 ++++ protobuf-22.4/src/libprotoc.map 2023-05-09 10:54:46.728401000 -0700 +@@ -3,6 +3,8 @@ + extern "C++" { + *google*; + }; ++ scc_info_*; ++ descriptor_table_*; + + local: + *; From 2523a40b4847bba44dddf635dbd4d7a1bb9298d0 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 9 May 2023 12:01:25 -0700 Subject: [PATCH 7371/9987] more protobuf --- .../protobuf-python-4.23.0-GCCcore-12.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..957af949a32 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '4.23.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = ['protobuf-%(version)s.tar.gz'] +checksums = ['5f1eba1da2a2f3f7df469fccddef3cc060b8a16cfe3cc65961ad36b4dbcf59c5'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('protobuf', '22.4') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' From 29245ce43891922da478f9269442dc0ea2ef2061 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 9 May 2023 21:35:37 +0200 Subject: [PATCH 7372/9987] install dask-labextension v6.0.0 from wheel --- .../dask-labextension-6.0.0-foss-2022a.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb index 584ac781fbc..54f6a5881f7 100644 --- a/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb @@ -9,11 +9,6 @@ as embed Dask's dashboard plots directly into JupyterLab panes.""" toolchain = {'name': 'foss', 'version': '2022a'} -builddependencies = [ - ('binutils', '2.38'), - ('nodejs', '16.15.1'), -] - dependencies = [ ('Python', '3.10.4'), ('JupyterLab', '3.5.0'), @@ -25,7 +20,8 @@ use_pip = True exts_list = [ ('dask_labextension', version, { - 'checksums': ['516d1faccd0b172d07f794250a5c3427b082d70954ebe8d3f9c92dc08cb79f7e'], + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['6b9e6a66fec891d6533314b03a57e121eb9822aaf98c94139c913e7c30212002'], }), ] From 6ff2c1f432760095ee24c964a3b5818e499a73a3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 9 May 2023 22:38:37 +0200 Subject: [PATCH 7373/9987] add dependency on PycURL to JupyterHub-3.0.0-GCCcore-11.3.0.eb --- .../JupyterHub-3.0.0-GCCcore-11.3.0.eb | 3 +- .../p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb index 9f427a4cb20..4addecfb2d6 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb @@ -19,7 +19,8 @@ dependencies = [ ('Mako', '1.2.0'), ('configurable-http-proxy', '4.5.3'), ('OpenSSL', '1.1', '', SYSTEM), - ('jupyter-server-proxy', '3.2.2') # This is optional, but commonly used together + ('jupyter-server-proxy', '3.2.2'), # optional, but commonly used together + ('PycURL', '7.45.2'), # optional, recommended with large number of users ] use_pip = True diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..721db47c2b2 --- /dev/null +++ b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'PycURL' +version = '7.45.2' + +homepage = "http://pycurl.io/" +description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL + from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of + features.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('cURL', '7.83.0'), +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5730590be0271364a5bddd9e245c9cc0fb710c4cbacbdd95264a3122d23224ca'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From 4035b4ee11cb1dc9e2c6398ce837bd52d5fa3dba Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 9 May 2023 22:42:51 +0200 Subject: [PATCH 7374/9987] adding easyconfigs: jupyterlmod-4.0.3-GCCcore-11.3.0.eb --- .../jupyterlmod-4.0.3-GCCcore-11.3.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..741b452e01a --- /dev/null +++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'jupyterlmod' +version = '4.0.3' + +# This easyconfig installs the notebook and lab extension of Jupyter Lmod + +homepage = 'https://github.com/cmd-ntrf/jupyter-lmod' +description = """Jupyter interactive notebook server extension that allows user to interact with +environment modules before launching kernels. The extension use Lmod's Python +interface to accomplish module related task like loading, unloading, saving +collection, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('jupyter-server', '1.21.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['9939bd7927c2c347f9884247bac58018ca44d56184c5f29e9d704a9b3a09a299'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'share/jupyter'], +} + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'tools' From 945ee02a75df9b36649d0e658e4333d65b80ad88 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 9 May 2023 17:49:27 -0700 Subject: [PATCH 7375/9987] bump version --- .../protobuf-python-4.23.0-GCCcore-12.2.0.eb | 2 +- .../protobuf/protobuf-22.4-GCCcore-12.2.0.eb | 39 ------------------- .../protobuf-22.4_linking-error.patch | 37 ------------------ 3 files changed, 1 insertion(+), 77 deletions(-) delete mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb delete mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb index 957af949a32..5a00b1b6fdd 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb @@ -16,7 +16,7 @@ builddependencies = [('binutils', '2.39')] dependencies = [ ('Python', '3.10.8'), - ('protobuf', '22.4') + ('protobuf', '23.0') ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb deleted file mode 100644 index 3c78b97f75d..00000000000 --- a/easybuild/easyconfigs/p/protobuf/protobuf-22.4-GCCcore-12.2.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'protobuf' -version = '22.4' - -homepage = 'https://github.com/protocolbuffers/protobuf' -description = """Protocol Buffers (a.k.a., protobuf) are Google's -language-neutral, platform-neutral, extensible mechanism for -serializing structured data.""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/'] -sources = ['v%(version)s.tar.gz'] -patches = ['protobuf-22.4_linking-error.patch'] -checksums = [ - 'def8683aafc1ebaddbc777da252dfdc8e324a197757e3bfcd8b4de90d4b8cf6a', # v22.4.tar.gz - '6c514ee1854fe40855a2db4a1cd197f9a30ec5be6d7c50932d4eb061788a151c', # protobuf-22.4_linking-error.patch -] - -builddependencies = [ - ('binutils', '2.39'), - ('CMake', '3.24.3'), -] - -srcdir = 'cmake' - -configopts = "-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER='package'" - -dependencies = [ - ('Abseil', '20230125.2'), -] - -sanity_check_paths = { - 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch b/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch deleted file mode 100644 index 0e83d971c78..00000000000 --- a/easybuild/easyconfigs/p/protobuf/protobuf-22.4_linking-error.patch +++ /dev/null @@ -1,37 +0,0 @@ -# https://github.com/protocolbuffers/protobuf/pull/11032 -diff -ruN protobuf-22.4.orig/src/libprotobuf-lite.map protobuf-22.4/src/libprotobuf-lite.map ---- protobuf-22.4.orig/src/libprotobuf-lite.map 2023-05-03 10:23:58.000000000 -0700 -+++ protobuf-22.4/src/libprotobuf-lite.map 2023-05-09 10:53:18.018860000 -0700 -@@ -3,6 +3,8 @@ - extern "C++" { - *google*; - }; -+ scc_info_*; -+ descriptor_table_*; - - local: - *; -diff -ruN protobuf-22.4.orig/src/libprotobuf.map protobuf-22.4/src/libprotobuf.map ---- protobuf-22.4.orig/src/libprotobuf.map 2023-05-03 10:23:58.000000000 -0700 -+++ protobuf-22.4/src/libprotobuf.map 2023-05-09 10:53:56.908337000 -0700 -@@ -3,6 +3,8 @@ - extern "C++" { - *google*; - }; -+ scc_info_*; -+ descriptor_table_*; - - local: - *; -diff -ruN protobuf-22.4.orig/src/libprotoc.map protobuf-22.4/src/libprotoc.map ---- protobuf-22.4.orig/src/libprotoc.map 2023-05-03 10:23:58.000000000 -0700 -+++ protobuf-22.4/src/libprotoc.map 2023-05-09 10:54:46.728401000 -0700 -@@ -3,6 +3,8 @@ - extern "C++" { - *google*; - }; -+ scc_info_*; -+ descriptor_table_*; - - local: - *; From 8b26880d863a8aacefd390e40994b76553748d86 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 9 May 2023 17:50:47 -0700 Subject: [PATCH 7376/9987] bump version --- .../protobuf/protobuf-23.0-GCCcore-12.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-23.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-23.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-23.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..962f6810124 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-23.0-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '23.0' + +homepage = 'https://github.com/protocolbuffers/protobuf' +description = """Protocol Buffers (a.k.a., protobuf) are Google's +language-neutral, platform-neutral, extensible mechanism for +serializing structured data.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b8faf8487cc364e5c2b47a9abd77512bc79a6389ea45392ca938ba7617eae877'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +srcdir = '.' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER="package" ' + +dependencies = [ + ('Abseil', '20230125.2'), +] + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From a1d2ff4ef82f032f247a152716b7beeeec128be1 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 10 May 2023 09:22:16 +0100 Subject: [PATCH 7377/9987] Update jupyterlmod-4.0.3-GCCcore-11.3.0.eb Minor grammar fixes to description --- .../j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb index 741b452e01a..552befac655 100644 --- a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb @@ -6,10 +6,10 @@ version = '4.0.3' # This easyconfig installs the notebook and lab extension of Jupyter Lmod homepage = 'https://github.com/cmd-ntrf/jupyter-lmod' -description = """Jupyter interactive notebook server extension that allows user to interact with -environment modules before launching kernels. The extension use Lmod's Python -interface to accomplish module related task like loading, unloading, saving -collection, etc.""" +description = """Jupyter interactive notebook server extension that allows users to interact with +environment modules before launching kernels. The extension uses Lmod's Python +interface to accomplish module-related tasks like loading, unloading, saving +collections, etc.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} From 0f4e75499e8fbd0eec4b665c5c5a4928aa5ec09e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 10 May 2023 10:49:54 +0200 Subject: [PATCH 7378/9987] Fix another incorrect filename path --- .../o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb | 4 ++-- .../easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb index bb75837b40e..4ca1c26a38c 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb @@ -87,8 +87,8 @@ configopts = " ".join([ ]) # Install a egg-info file so it is more python friendly -local_egg_info_src = '%(builddir)s/opencv-contrib-python.egg-info' -local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv-contrib-python-%(version)s.egg-info' +local_egg_info_src = '%(builddir)s/opencv_contrib_python.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv_contrib_python-%(version)s.egg-info' postinstallcmds = [ 'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), ] diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index b2fd1d672bc..f71431e0f08 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -83,8 +83,8 @@ configopts = " ".join([ ]) # Install a egg-info file so it is more python friendly -local_egg_info_src = '%(builddir)s/opencv-contrib-python.egg-info' -local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv-contrib-python-%(version)s.egg-info' +local_egg_info_src = '%(builddir)s/opencv_contrib_python.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv_contrib_python-%(version)s.egg-info' postinstallcmds = [ 'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), ] From 2251af9b2a4c8a4d80afee1ab80589dd03b0fbf5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2023 11:19:50 +0200 Subject: [PATCH 7379/9987] adding easyconfigs: L_RNA_scaffolder-20190530-GCC-11.3.0.eb --- .../L_RNA_scaffolder-20190530-GCC-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb new file mode 100644 index 00000000000..59d93ffd865 --- /dev/null +++ b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'L_RNA_scaffolder' +local_commit = '98f19e3' +version = '20190530' + +homepage = 'https://github.com/CAFS-bioinformatics/L_RNA_scaffolder' +description = "L_RNA_scaffolder is a genome scaffolding tool with long trancriptome reads" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/CAFS-bioinformatics/L_RNA_scaffolder/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['ef4c5bf3511e9947bdb33201bdcaf1ff779ca315a2139f73bb549fb6bfc05f5a'] + +dependencies = [ + ('BioPerl', '1.7.8'), +] + +fix_perl_shebang_for = ['*.pl'] + +postinstallcmds = ["chmod a+x %(installdir)s/L_RNA_scaffolder.sh"] + +sanity_check_paths = { + 'files': ['calculate-lc', 'calculate-pid', 'convert', 'convert_linker', 'count_connection_frequency', + 'delete_block', 'delete_linker', 'delete_same_fragment', 'filter_scaffold.pl', + 'find_end_node', 'find_reliable_connection', 'find_start_node', 'form_block', + 'form_path.pl', 'generate_scaffold.pl', 'generate_unscaffold.pl', 'L_RNA_scaffolder.sh', 'link_block', + 'order', 'overlap', 'route.pl', 'search_guider', 'select_nodes'], + 'dirs': [], +} + +sanity_check_commands = ["L_RNA_scaffolder.sh -? | grep '^Usage: sh L_RNA_scaffolder.sh'"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From cf9584cf02e01f29ac0dc5fee1e5586c82a5df45 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2023 13:37:47 +0200 Subject: [PATCH 7380/9987] adding easyconfigs: HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb --- .../HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..a27f94eeae3 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'HPL' +local_patch_version = '15' +version = '2.0.%s' % local_patch_version +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +# download via https://developer.nvidia.com/computeworks-developer-exclusive-downloads +sources = ['hpl-%%(version_major_minor)s_FERMI_v%s.tgz' % local_patch_version] +patches = ['HPL_parallel-make.patch'] +checksums = [ + {'hpl-2.0_FERMI_v15.tgz': '16dd21af22fced613923a6cb09805d63952fc9c9f278cb7582061a43fe39a408'}, + {'HPL_parallel-make.patch': '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6'}, +] + +# fix Make dependencies, so parallel build also works +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), +] + +buildopts = "TOPdir=${PWD}" + +files_to_copy = [(['bin/CUDA/HPL.dat', 'bin/CUDA/xhpl'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/HPL.dat', 'bin/xhpl'], + 'dirs': [], +} + +moduleclass = 'tools' From 3a834b09f72196bf10d55e0d0aa6eb89fdcb8ffd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 May 2023 14:58:19 +0200 Subject: [PATCH 7381/9987] remoe extra space in HPL easyconfig --- .../easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb index a27f94eeae3..4ab35a334cf 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb @@ -30,7 +30,7 @@ buildopts = "TOPdir=${PWD}" files_to_copy = [(['bin/CUDA/HPL.dat', 'bin/CUDA/xhpl'], 'bin')] -sanity_check_paths = { +sanity_check_paths = { 'files': ['bin/HPL.dat', 'bin/xhpl'], 'dirs': [], } From bd7583cea7d004676c98fd340a862f2d0f241704 Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Wed, 10 May 2023 16:45:57 +0200 Subject: [PATCH 7382/9987] texlive: add historical repo paths to install cmd * see discussion in https://github.com/easybuilders/easybuild-easyconfigs/issues/17871 --- .../t/texlive/texlive-20200406-GCCcore-8.3.0.eb | 7 ++++++- .../easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb | 6 ++++-- .../easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb | 6 ++++-- .../easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb | 2 ++ 4 files changed, 16 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb index 7c74e626642..4e8bf18c2f4 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb @@ -4,6 +4,7 @@ easyblock = 'Tarball' name = 'texlive' version = '20200406' +local_version_year = version[:4] homepage = 'https://tug.org' description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript @@ -13,7 +14,10 @@ description = """TeX is a typesetting language. Instead of visually formatting y toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['ftp://tug.org/texlive/historic/2020/'] +source_urls = [ + 'ftp://tug.org/texlive/historic/%s/' % local_version_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year, +] sources = [ { 'download_filename': 'install-tl-unx.tar.gz', @@ -41,6 +45,7 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' + ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb index 9809666eaa4..86aa9943d93 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb @@ -4,6 +4,7 @@ easyblock = 'Tarball' name = 'texlive' version = '20210324' +local_version_year = version[:4] homepage = 'https://tug.org' description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript @@ -14,8 +15,8 @@ description = """TeX is a typesetting language. Instead of visually formatting y toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = [ - 'ftp://tug.org/texlive/historic/2021/', - 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/', + 'ftp://tug.org/texlive/historic/%s/' % local_version_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year, ] sources = [ { @@ -44,6 +45,7 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' + ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb index b00d0026d53..7f55d4478f9 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb @@ -4,6 +4,7 @@ easyblock = 'Tarball' name = 'texlive' version = '20210324' +local_version_year = version[:4] homepage = 'https://tug.org' description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript @@ -14,8 +15,8 @@ description = """TeX is a typesetting language. Instead of visually formatting y toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = [ - 'ftp://tug.org/texlive/historic/2021/', - 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/', + 'ftp://tug.org/texlive/historic/%s/' % local_version_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year, ] sources = [ { @@ -44,6 +45,7 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' + ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { diff --git a/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb index d249ac772bf..014f57053c8 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb @@ -4,6 +4,7 @@ easyblock = 'Tarball' name = 'texlive' version = '20220321' +local_version_year = version[:4] homepage = 'https://tug.org' description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript @@ -44,6 +45,7 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' + ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { From 15554c337c2f2f13666b32bd7bf77b3dcdbbf30f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 10 May 2023 17:04:04 +0200 Subject: [PATCH 7383/9987] adding easyconfigs: Ultralytics-8.0.92-foss-2022a-CUDA-11.7.0.eb --- ...tralytics-8.0.92-foss-2022a-CUDA-11.7.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/u/Ultralytics/Ultralytics-8.0.92-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/u/Ultralytics/Ultralytics-8.0.92-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/Ultralytics/Ultralytics-8.0.92-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..ad0a8d41096 --- /dev/null +++ b/easybuild/easyconfigs/u/Ultralytics/Ultralytics-8.0.92-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'Ultralytics' +version = '8.0.92' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/ultralytics/ultralytics' +description = """Ultralytics YOLOv8 is a cutting-edge, state-of-the-art (SOTA) model that builds upon the success of +previous YOLO versions and introduces new features and improvements to further boost performance and flexibility. +YOLOv8 is designed to be fast, accurate, and easy to use, making it an excellent choice for a wide range of object +detection and tracking, instance segmentation, image classification and pose estimation tasks.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.1', versionsuffix), + ('PyTorch-bundle', '1.12.1', versionsuffix), # torchvision + ('Pillow-SIMD', '9.2.0'), + ('matplotlib', '3.5.2'), + ('OpenCV', '4.6.0', '-contrib'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), + ('Seaborn', '0.12.1'), + ('psutil', '5.9.3'), +] + +use_pip = True + +exts_list = [ + ('thop', '0.1.1.post2209072238', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['01473c225231927d2ad718351f78ebf7cffe6af3bed464c4f1ba1ef0f7cdda27'], + }), + ('ultralytics', version, { + 'preinstallopts': 'sed -i "s/opencv-python/opencv-contrib-python/" requirements.txt &&', + 'checksums': ['f4285476621e5fba40a78a117930ea1073e358e8dd410171a45c1a357b735109'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 809c2b68617dec8974cb56394b8f6ed6f28aed99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 10 May 2023 18:30:35 +0200 Subject: [PATCH 7384/9987] Remove dup checksum --- .../easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb index d24ee4f3b3c..c11baed2797 100644 --- a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb @@ -164,7 +164,6 @@ crates = [ source_urls = ['https://github.com/pjedge/longshot/archive'] sources = ['v%(version)s.tar.gz'] checksums = [ - {'v0.4.5.tar.gz': '7c9f570e17012b2fee386892ae64daf5f104d59adeb59dc7e710b876c1a11cad'}, {'v0.4.5.tar.gz': '7c9f570e17012b2fee386892ae64daf5f104d59adeb59dc7e710b876c1a11cad'}, {'addr2line-0.19.0.tar.gz': 'a76fd60b23679b7d19bd066031410fb7e458ccc5e958eb5c325888ce4baedc97'}, {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, From 10412a687581c2fb22697570155851c2e764378e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 10 May 2023 18:34:30 +0200 Subject: [PATCH 7385/9987] Add checksums for all crates --- .../bamtofastq-1.4.0-GCCcore-10.3.0.eb | 170 +++++++++++++++++- 1 file changed, 169 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb index 2daaefe9ffe..f882fbbd838 100644 --- a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb @@ -178,7 +178,175 @@ crates = [ ] source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags'] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['b51d32e8aee3b9ace08c54397fddb590209571f47f4051077bcb22b98ca3a5ed'] +checksums = [ + {'bamtofastq-1.4.0.tar.gz': 'b51d32e8aee3b9ace08c54397fddb590209571f47f4051077bcb22b98ca3a5ed'}, + {'anyhow-1.0.44.tar.gz': '61604a8f862e1d5c3229fdd78f8b02c68dcf73a4c4b05fd636d12240aaa242c1'}, + {'backtrace-0.3.61.tar.gz': 'e7a905d892734eea339e896738c14b9afce22b5318f64b951e70bf3844419b01'}, + {'addr2line-0.16.0.tar.gz': '3e61f2b7f93d2c7d2b08263acaa4a363b3e276806c68af6134c44f523bf1aacd'}, + {'gimli-0.25.0.tar.gz': 'f0a01e0497841a3b2db4f8afa483cce65f7e96a3498bd6c541734792aeac8fe7'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'}, + {'miniz_oxide-0.4.4.tar.gz': 'a92518e98c078586bc6c934028adcca4c92a53d6a958196de835170a01d84e4b'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'autocfg-1.0.1.tar.gz': 'cdb031dd78e28731d87d56cc8ffef4a8f36ca26c38fe2de700543e627f8a464a'}, + {'object-0.26.2.tar.gz': 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{'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'crossbeam-utils-0.8.5.tar.gz': 'd82cfc11ce7f2c3faef78d8a684447b40d503d9681acebed6cb728d45940c4db'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'}, + {'log-0.4.14.tar.gz': '51b9bbe6c47d51fc3e1a9b945965946b4c44142ab8792c50835a980d362c2710'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'lz4-1.23.2.tar.gz': 'aac20ed6991e01bf6a2e68cc73df2b389707403662a8ba89f68511fb340f724c'}, + {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'}, + {'lz4-sys-1.9.2.tar.gz': 'dca79aa95d8b3226213ad454d328369853be3a1382d89532a854f4d69640acae'}, + {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'}, + {'cc-1.0.71.tar.gz': '79c2681d6594606957bbb8631c4b90a7fcaaa72cdb714743a437b156d6a7eedd'}, + {'min-max-heap-1.3.0.tar.gz': '2687e6cf9c00f48e9284cf9fd15f2ef341d03cc7743abf9df4c5f07fdee50b18'}, + {'serde-1.0.130.tar.gz': 'f12d06de37cf59146fbdecab66aa99f9fe4f78722e3607577a5375d66bd0c913'}, + {'tempfile-3.2.0.tar.gz': 'dac1c663cfc93810f88aed9b8941d48cabf856a1b111c29a40439018d870eb22'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'}, + {'rand-0.8.4.tar.gz': '2e7573632e6454cf6b99d7aac4ccca54be06da05aca2ef7423d22d27d4d4bcd8'}, + {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'}, + {'rand_chacha-0.3.1.tar.gz': 'e6c10a63a0fa32252be49d21e7709d4d4baf8d231c2dbce1eaa8141b9b127d88'}, + {'ppv-lite86-0.2.10.tar.gz': 'ac74c624d6b2d21f425f752262f42188365d7b8ff1aff74c82e45136510a4857'}, + {'rand_core-0.6.3.tar.gz': 'd34f1408f55294453790c48b2f1ebbb1c5b4b7563eb1f418bcfcfdbb06ebb4e7'}, + {'getrandom-0.2.3.tar.gz': '7fcd999463524c52659517fe2cea98493cfe485d10565e7b0fb07dbba7ad2753'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'libc-0.2.103.tar.gz': 'dd8f7255a17a627354f321ef0055d63b898c6fb27eff628af4d1b66b7331edf6'}, + {'rand_core-0.6.3.tar.gz': 'd34f1408f55294453790c48b2f1ebbb1c5b4b7563eb1f418bcfcfdbb06ebb4e7'}, + {'remove_dir_all-0.5.3.tar.gz': '3acd125665422973a33ac9d3dd2df85edad0f4ae9b00dafb1a05e43a9f5ef8e7'}, + {'redox_syscall-0.2.10.tar.gz': '8383f39639269cde97d255a32bdb68c047337295414940c68bdd30c2e13203ff'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'curl-sys-0.4.49+curl-7.79.1.tar.gz': 'e0f44960aea24a786a46907b8824ebc0e66ca06bf4e4978408c7499620343483'}, + {'openssl-sys-0.9.67.tar.gz': '69df2d8dfc6ce3aaf44b40dec6f487d5a886516cf6879c49e98e0710f310a058'}, + {'rand_hc-0.3.1.tar.gz': 'd51e9f596de227fda2ea6c84607f5558e196eeaf43c986b724ba4fb8fdf497e7'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'openssl-src-111.16.0+1.1.1l.tar.gz': '7ab2173f69416cf3ec12debb5823d244127d23a9b127d5a5189aa97c5fa2859f'}, + {'wasi-0.10.2+wasi-snapshot-preview1.tar.gz': 'fd6fbd9a79829dd1ad0cc20627bf1ed606756a7f77edff7b66b7064f9cb327c6'}, +] builddependencies = [ ('binutils', '2.36.1'), From f2684acbfff6f367aa1b9b7d1d7f89902cd999c4 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 10 May 2023 18:36:30 +0200 Subject: [PATCH 7386/9987] add missing FastTreeMP binary for FastTree --- .../easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb | 5 +++++ .../easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb | 5 +++++ .../easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb | 5 +++++ .../easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb | 5 +++++ 4 files changed, 20 insertions(+) diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb index 11318dc50bb..2d4bc28f2bd 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb @@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s - files_to_copy = [(['FastTree'], 'bin')] +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + sanity_check_paths = { 'files': ['bin/FastTree'], 'dirs': [], diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb index ad1c23f20f5..fdcb06c67f3 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb @@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s - files_to_copy = [(['FastTree'], 'bin')] +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + sanity_check_paths = { 'files': ['bin/FastTree'], 'dirs': [], diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb index 51f3e343ef9..9bbfa3f435b 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb @@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s - files_to_copy = [(['FastTree'], 'bin')] +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + sanity_check_paths = { 'files': ['bin/FastTree'], 'dirs': [], diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb index a79c7a054da..c1bb41ac734 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb @@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s - files_to_copy = [(['FastTree'], 'bin')] +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + sanity_check_paths = { 'files': ['bin/FastTree'], 'dirs': [], From 3757fc78506ade7f14b39c01851978e0ce104256 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 11 May 2023 10:37:53 +0200 Subject: [PATCH 7387/9987] adding easyconfigs: pytesseract-0.3.10-GCCcore-11.3.0.eb and patches: pytesseract-0.3.10_relax-packaging-version-requirements.patch --- .../pytesseract-0.3.10-GCCcore-11.3.0.eb | 38 +++++++++++++++++++ ...relax-packaging-version-requirements.patch | 14 +++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10_relax-packaging-version-requirements.patch diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f7fbc2c5f56 --- /dev/null +++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'pytesseract' +version = '0.3.10' + +homepage = "https://github.com/madmaze/pytesseract" +description = """Python-tesseract is an optical character recognition (OCR) +tool for python. That is, it will recognize and "read" the text embedded in +images. + +Python-tesseract is a wrapper for Google's Tesseract-OCR Engine. It is also +useful as a stand-alone invocation script to tesseract, as it can read all +image types supported by the Pillow and Leptonica imaging libraries, including +jpeg, png, gif, bmp, tiff, and others. Additionally, if used as a script, +Python-tesseract will print the recognized text instead of writing it to a +file.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +patches = ['pytesseract-0.3.10_relax-packaging-version-requirements.patch'] +checksums = [{ + SOURCELOWER_TAR_GZ: 'f1c3a8b0f07fd01a1085d451f5b8315be6eec1d5577a6796d46dc7a62bd4120f', + 'pytesseract-0.3.10_relax-packaging-version-requirements.patch': \ + '17bcf10055dd421572654b8da3a7899115c0eb50ec32bb6ab58371d16530f8c6', +}] + +dependencies = [ + ('tesseract', '5.3.0'), + ('Python', '3.10.4'), + ('Pillow', '9.1.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10_relax-packaging-version-requirements.patch b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10_relax-packaging-version-requirements.patch new file mode 100644 index 00000000000..90471c98279 --- /dev/null +++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10_relax-packaging-version-requirements.patch @@ -0,0 +1,14 @@ +Packaging is used with Version, parse and InvalidVersion that does not strictly +need the versions specified in setup.cfg +Author: Viktor Rehnberg +--- ./setup.cfg.orig 2023-05-11 10:30:41.231633193 +0200 ++++ ./setup.cfg 2023-05-11 10:33:01.127272708 +0200 +@@ -27,7 +27,7 @@ + packages = find: + include_package_data = True + install_requires = +- packaging>=21.3 ++ packaging>=20.9 + Pillow>=8.0.0 + python_requires = >=3.7 + From 0e14d223649e44c3270ca261c9a27b0a351a12ed Mon Sep 17 00:00:00 2001 From: Thomas Hayward-Schneider Date: Thu, 11 May 2023 10:40:30 +0200 Subject: [PATCH 7388/9987] Switch ftp to http for texlive repos --- .../t/texlive/texlive-20200406-GCCcore-8.3.0.eb | 8 ++++---- .../easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb | 2 +- .../easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb | 2 +- .../easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb | 6 +++--- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb index 4e8bf18c2f4..27046de748b 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb @@ -45,11 +45,11 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' - ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year + ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { - 'PATH': 'bin/x86_64-linux', + 'PATH': 'bin/%(arch)s-linux', 'INFOPATH': 'texmf-dist/doc/info', 'MANPATH': 'texmf-dist/doc/man', } @@ -58,8 +58,8 @@ modextravars = { } sanity_check_paths = { - 'files': ['bin/x86_64-linux/tex', 'bin/x86_64-linux/latex'], - 'dirs': ['bin/x86_64-linux', 'texmf-dist'], + 'files': ['bin/%(arch)s-linux/tex', 'bin/%(arch)s-linux/latex'], + 'dirs': ['bin/%(arch)s-linux', 'texmf-dist'], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb index 86aa9943d93..97dde3d44ad 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb @@ -45,7 +45,7 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' - ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year + ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb index 7f55d4478f9..dc4af0f23ae 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb @@ -45,7 +45,7 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' - ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year + ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { diff --git a/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb index 014f57053c8..46445148922 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb @@ -15,8 +15,8 @@ description = """TeX is a typesetting language. Instead of visually formatting y toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = [ - 'ftp://tug.org/texlive/historic/2022/', - 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2022/', + 'ftp://tug.org/texlive/historic/%s/' % local_version_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year, ] sources = [ { @@ -45,7 +45,7 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' - ' -repository ' + 'ftp://tug.org/historic/systems/texlive/%s/tlnet-final' % local_version_year + ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { From 80eb4272c099061c46f78da4180ce513f8457137 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 11 May 2023 10:42:15 +0200 Subject: [PATCH 7389/9987] Fix style --- .../p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb index f7fbc2c5f56..2dc6d2f4d67 100644 --- a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb @@ -21,7 +21,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = ['pytesseract-0.3.10_relax-packaging-version-requirements.patch'] checksums = [{ SOURCELOWER_TAR_GZ: 'f1c3a8b0f07fd01a1085d451f5b8315be6eec1d5577a6796d46dc7a62bd4120f', - 'pytesseract-0.3.10_relax-packaging-version-requirements.patch': \ + 'pytesseract-0.3.10_relax-packaging-version-requirements.patch': '17bcf10055dd421572654b8da3a7899115c0eb50ec32bb6ab58371d16530f8c6', }] From 65b4c8c12f1de71f6b3c9303653e6bfcbc607a44 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 11 May 2023 11:19:24 +0200 Subject: [PATCH 7390/9987] Fix checksum list semantics --- .../p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb index 2dc6d2f4d67..454b392c46c 100644 --- a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb @@ -19,11 +19,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} sources = [SOURCELOWER_TAR_GZ] patches = ['pytesseract-0.3.10_relax-packaging-version-requirements.patch'] -checksums = [{ - SOURCELOWER_TAR_GZ: 'f1c3a8b0f07fd01a1085d451f5b8315be6eec1d5577a6796d46dc7a62bd4120f', - 'pytesseract-0.3.10_relax-packaging-version-requirements.patch': - '17bcf10055dd421572654b8da3a7899115c0eb50ec32bb6ab58371d16530f8c6', -}] +checksums = [ + {SOURCELOWER_TAR_GZ: 'f1c3a8b0f07fd01a1085d451f5b8315be6eec1d5577a6796d46dc7a62bd4120f'}, + {'pytesseract-0.3.10_relax-packaging-version-requirements.patch': + '17bcf10055dd421572654b8da3a7899115c0eb50ec32bb6ab58371d16530f8c6'}, +] dependencies = [ ('tesseract', '5.3.0'), From 11524e1bf7894b5eb26211cd6fc74acccc00a677 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 11 May 2023 13:37:36 +0200 Subject: [PATCH 7391/9987] Add missing extensions --- .../Ultralytics-8.0.92-foss-2022a-CUDA-11.7.0.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/Ultralytics/Ultralytics-8.0.92-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/Ultralytics/Ultralytics-8.0.92-foss-2022a-CUDA-11.7.0.eb index ad0a8d41096..8f0fe0bc655 100644 --- a/easybuild/easyconfigs/u/Ultralytics/Ultralytics-8.0.92-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/u/Ultralytics/Ultralytics-8.0.92-foss-2022a-CUDA-11.7.0.eb @@ -19,7 +19,7 @@ dependencies = [ ('PyTorch-bundle', '1.12.1', versionsuffix), # torchvision ('Pillow-SIMD', '9.2.0'), ('matplotlib', '3.5.2'), - ('OpenCV', '4.6.0', '-contrib'), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), ('SciPy-bundle', '2022.05'), ('tqdm', '4.64.0'), ('Seaborn', '0.12.1'), @@ -33,6 +33,12 @@ exts_list = [ 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['01473c225231927d2ad718351f78ebf7cffe6af3bed464c4f1ba1ef0f7cdda27'], }), + ('urllib3', '1.26.11', { + 'checksums': ['ea6e8fb210b19d950fab93b60c9009226c63a28808bc8386e05301e25883ac0a'], + }), + ('sentry-sdk', '1.22.2', { + 'checksums': ['5932c092c6e6035584eb74d77064e4bce3b7935dfc4a331349719a40db265840'], + }), ('ultralytics', version, { 'preinstallopts': 'sed -i "s/opencv-python/opencv-contrib-python/" requirements.txt &&', 'checksums': ['f4285476621e5fba40a78a117930ea1073e358e8dd410171a45c1a357b735109'], From 91543aa6f57e9b3c121e3a5d4fc8dcfe58e79f35 Mon Sep 17 00:00:00 2001 From: x0139045 Date: Thu, 11 May 2023 14:25:49 +0200 Subject: [PATCH 7392/9987] adding easyconfigs: FFTW-3.3.10-iimpi-2022b.eb --- .../f/FFTW/FFTW-3.3.10-iimpi-2022b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022b.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022b.eb new file mode 100644 index 00000000000..441ffa2eca8 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-iimpi-2022b.eb @@ -0,0 +1,27 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +# no quad precision, requires GCC v4.6 or higher +# see also +# https://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html +with_quad_prec = False + +# compilation fails on AMD systems when configuring with --enable-avx-128-fma, +# because Intel compilers do not support FMA4 instructions +use_fma4 = False + + +runtest = 'check' + +moduleclass = 'numlib' From 3317a0dc9a51478c39f692b6422c468b60392d54 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 11 May 2023 14:40:26 +0200 Subject: [PATCH 7393/9987] Fix MKL related test failures --- ...TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb | 3 + .../TensorFlow/TensorFlow-2.9.1-foss-2022a.eb | 3 + .../TensorFlow-2.9.1_fix-check-for-MKL.patch | 197 ++++++++++++++++++ 3 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_fix-check-for-MKL.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb index 7d8fc26cca1..75d2c976761 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb @@ -176,6 +176,7 @@ exts_list = [ 'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch', 'TensorFlow-2.8.4_fix-PPC-JIT.patch', 'TensorFlow-2.8.4_resolve-gcc-symlinks.patch', + 'TensorFlow-2.9.1_fix-check-for-MKL.patch', 'TensorFlow-2.9.1_fix-PPC-Eigen-build.patch', 'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch', 'TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch', @@ -204,6 +205,8 @@ exts_list = [ '27d28293105b4dd0a25f58346c68b672f57215756f14a97c442d0e3317e93a2b'}, {'TensorFlow-2.8.4_resolve-gcc-symlinks.patch': '43ce9acc6bffff68a31d2263d0064d272999b2e0a2c6546690287cd1c9c90f04'}, + {'TensorFlow-2.9.1_fix-check-for-MKL.patch': + '3b9d20b43391def093a30dbc45b7502a48916efedf7314700f78cc7b2cc1b645'}, {'TensorFlow-2.9.1_fix-PPC-Eigen-build.patch': '5f559a6eade65df665c7c69bc2e5d5d4214b85ea836e966f5dba73211307b972'}, {'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch': diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb index 434de47a58b..0a382edbaef 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb @@ -172,6 +172,7 @@ exts_list = [ 'TensorFlow-2.8.4_exclude-xnnpack-on-ppc.patch', 'TensorFlow-2.8.4_fix-PPC-JIT.patch', 'TensorFlow-2.8.4_resolve-gcc-symlinks.patch', + 'TensorFlow-2.9.1_fix-check-for-MKL.patch', 'TensorFlow-2.9.1_fix-PPC-Eigen-build.patch', 'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch', 'TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch', @@ -200,6 +201,8 @@ exts_list = [ '27d28293105b4dd0a25f58346c68b672f57215756f14a97c442d0e3317e93a2b'}, {'TensorFlow-2.8.4_resolve-gcc-symlinks.patch': '43ce9acc6bffff68a31d2263d0064d272999b2e0a2c6546690287cd1c9c90f04'}, + {'TensorFlow-2.9.1_fix-check-for-MKL.patch': + '3b9d20b43391def093a30dbc45b7502a48916efedf7314700f78cc7b2cc1b645'}, {'TensorFlow-2.9.1_fix-PPC-Eigen-build.patch': '5f559a6eade65df665c7c69bc2e5d5d4214b85ea836e966f5dba73211307b972'}, {'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch': diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_fix-check-for-MKL.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_fix-check-for-MKL.patch new file mode 100644 index 00000000000..a9c1da7bc9a --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_fix-check-for-MKL.patch @@ -0,0 +1,197 @@ +Tests are incorrectly not skipped causing failures related to MKL. +See https://github.com/tensorflow/tensorflow/issues/59252 + +Use a patch from TF 2.11: https://github.com/tensorflow/tensorflow/commit/5ec3d2e626589540bcfbeb7dac40255034e587df + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/core/util/BUILD b/tensorflow/core/util/BUILD +index 8881f6fd5e9..25882152abf 100644 +--- a/tensorflow/core/util/BUILD ++++ b/tensorflow/core/util/BUILD +@@ -491,6 +491,11 @@ cc_library( + "//tensorflow/python:__pkg__", + "//tensorflow/python/util:__pkg__", + ], ++ deps = [ ++ "//tensorflow/core/platform:platform_port", ++ "//tensorflow/core/util:env_var", ++ "@com_google_absl//absl/base", ++ ], + alwayslink = 1, + ) + +diff --git a/tensorflow/core/util/port.cc b/tensorflow/core/util/port.cc +index 358b39bfb00..0aa3cfa708e 100644 +--- a/tensorflow/core/util/port.cc ++++ b/tensorflow/core/util/port.cc +@@ -15,6 +15,9 @@ limitations under the License. + + #include "tensorflow/core/util/port.h" + ++#include "absl/base/call_once.h" ++#include "tensorflow/core/platform/cpu_info.h" ++#include "tensorflow/core/util/env_var.h" + + namespace tensorflow { + +@@ -60,10 +63,57 @@ bool GpuSupportsHalfMatMulAndConv() { + } + + bool IsMklEnabled() { +-#if defined(INTEL_MKL) && defined(ENABLE_MKL) +- return true; +-#else ++#ifndef INTEL_MKL + return false; +-#endif // INTEL_MKL && ENABLE_MKL ++#endif ++ static absl::once_flag once; // NOLINT(clang-diagnostic-unreachable-code) ++#ifdef ENABLE_MKL ++ // Keeping TF_DISABLE_MKL env variable for legacy reasons. ++ static bool oneDNN_disabled = false; ++ absl::call_once(once, [&] { ++ TF_CHECK_OK(ReadBoolFromEnvVar("TF_DISABLE_MKL", false, &oneDNN_disabled)); ++ if (oneDNN_disabled) VLOG(2) << "TF-MKL: Disabling oneDNN"; ++ }); ++ return (!oneDNN_disabled); ++#else ++ // Linux: Turn oneDNN on by default for CPUs with neural network features. ++ // Windows: oneDNN is off by default. ++ // No need to guard for other platforms here because INTEL_MKL is only defined ++ // for non-mobile Linux or Windows. ++ static bool oneDNN_enabled = ++#ifdef __linux__ ++ port::TestCPUFeature(port::CPUFeature::AVX512_VNNI) || ++ port::TestCPUFeature(port::CPUFeature::AVX512_BF16) || ++ port::TestCPUFeature(port::CPUFeature::AVX_VNNI) || ++ port::TestCPUFeature(port::CPUFeature::AMX_TILE) || ++ port::TestCPUFeature(port::CPUFeature::AMX_INT8) || ++ port::TestCPUFeature(port::CPUFeature::AMX_BF16); ++#else ++ false; ++#endif // __linux__ ++ absl::call_once(once, [&] { ++ auto status = ReadBoolFromEnvVar("TF_ENABLE_ONEDNN_OPTS", oneDNN_enabled, ++ &oneDNN_enabled); ++ if (!status.ok()) { ++ LOG(WARNING) << "TF_ENABLE_ONEDNN_OPTS is not set to either '0', 'false'," ++ << " '1', or 'true'. Using the default setting: " ++ << oneDNN_enabled; ++ } ++ if (oneDNN_enabled) { ++#ifndef DNNL_AARCH64_USE_ACL ++ LOG(INFO) << "oneDNN custom operations are on. " ++ << "You may see slightly different numerical results due to " ++ << "floating-point round-off errors from different computation " ++ << "orders. To turn them off, set the environment variable " ++ << "`TF_ENABLE_ONEDNN_OPTS=0`."; ++#else ++ LOG(INFO) << "Experimental oneDNN custom operations are on. " ++ << "If you experience issues, please turn them off by setting " ++ << "the environment variable `TF_ENABLE_ONEDNN_OPTS=0`."; ++#endif // !DNNL_AARCH64_USE_ACL ++ } ++ }); ++ return oneDNN_enabled; ++#endif // ENABLE_MKL + } + } // end namespace tensorflow +diff --git a/tensorflow/core/util/util.cc b/tensorflow/core/util/util.cc +index eef2618de91..1c12f552d7d 100644 +--- a/tensorflow/core/util/util.cc ++++ b/tensorflow/core/util/util.cc +@@ -15,16 +15,10 @@ limitations under the License. + + #include "tensorflow/core/util/util.h" + +-#include +-#include +- +-#include "absl/base/call_once.h" +-#include "tensorflow/core/framework/device_factory.h" + #include "tensorflow/core/lib/gtl/inlined_vector.h" + #include "tensorflow/core/lib/strings/strcat.h" +-#include "tensorflow/core/platform/cpu_info.h" + #include "tensorflow/core/platform/logging.h" +-#include "tensorflow/core/util/env_var.h" ++#include "tensorflow/core/util/port.h" + + namespace tensorflow { + +@@ -127,59 +121,7 @@ string SliceDebugString(const TensorShape& shape, const int64_t flat) { + return result; + } + +-bool IsMKLEnabled() { +-#ifndef INTEL_MKL +- return false; +-#endif // !INTEL_MKL +- static absl::once_flag once; +-#ifdef ENABLE_MKL +- // Keeping TF_DISABLE_MKL env variable for legacy reasons. +- static bool oneDNN_disabled = false; +- absl::call_once(once, [&] { +- TF_CHECK_OK(ReadBoolFromEnvVar("TF_DISABLE_MKL", false, &oneDNN_disabled)); +- if (oneDNN_disabled) VLOG(2) << "TF-MKL: Disabling oneDNN"; +- }); +- return (!oneDNN_disabled); +-#else +- // Linux: Turn oneDNN on by default for CPUs with neural network features. +- // Windows: oneDNN is off by default. +- // No need to guard for other platforms here because INTEL_MKL is only defined +- // for non-mobile Linux or Windows. +- static bool oneDNN_enabled = +-#ifdef __linux__ +- port::TestCPUFeature(port::CPUFeature::AVX512_VNNI) || +- port::TestCPUFeature(port::CPUFeature::AVX512_BF16) || +- port::TestCPUFeature(port::CPUFeature::AVX_VNNI) || +- port::TestCPUFeature(port::CPUFeature::AMX_TILE) || +- port::TestCPUFeature(port::CPUFeature::AMX_INT8) || +- port::TestCPUFeature(port::CPUFeature::AMX_BF16); +-#else +- false; +-#endif // __linux__ +- absl::call_once(once, [&] { +- auto status = ReadBoolFromEnvVar("TF_ENABLE_ONEDNN_OPTS", oneDNN_enabled, +- &oneDNN_enabled); +- if (!status.ok()) { +- LOG(WARNING) << "TF_ENABLE_ONEDNN_OPTS is not set to either '0', 'false'," +- << " '1', or 'true'. Using the default setting: " +- << oneDNN_enabled; +- } +- if (oneDNN_enabled) { +-#ifndef DNNL_AARCH64_USE_ACL +- LOG(INFO) << "oneDNN custom operations are on. " +- << "You may see slightly different numerical results due to " +- << "floating-point round-off errors from different computation " +- << "orders. To turn them off, set the environment variable " +- << "`TF_ENABLE_ONEDNN_OPTS=0`."; +-#else +- LOG(INFO) << "Experimental oneDNN custom operations are on. " +- << "If you experience issues, please turn them off by setting " +- << "the environment variable `TF_ENABLE_ONEDNN_OPTS=0`."; +-#endif // !DNNL_AARCH64_USE_ACL +- } +- }); +- return oneDNN_enabled; +-#endif // ENABLE_MKL +-} ++// TODO(penporn): Remove this function from util.cc ++bool IsMKLEnabled() { return IsMklEnabled(); } + + } // namespace tensorflow +diff --git a/tensorflow/python/framework/test_util.py b/tensorflow/python/framework/test_util.py +index 02149d89b2f..e859ec47a1e 100644 +--- a/tensorflow/python/framework/test_util.py ++++ b/tensorflow/python/framework/test_util.py +@@ -359,8 +359,7 @@ def GpuSupportsHalfMatMulAndConv(): + + + def IsMklEnabled(): +- return (_pywrap_util_port.IsMklEnabled() or +- os.getenv("TF_ENABLE_ONEDNN_OPTS", "False").lower() in ["true", "1"]) ++ return _pywrap_util_port.IsMklEnabled() + + + def InstallStackTraceHandler(): From e08cac308df6d0f9709f8fb5c560f7cdfb81725e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 11 May 2023 15:13:20 +0200 Subject: [PATCH 7394/9987] adding easyconfigs: Go-1.20.4.eb --- easybuild/easyconfigs/g/Go/Go-1.20.4.eb | 31 +++++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.20.4.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.20.4.eb b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb new file mode 100644 index 00000000000..082ea644519 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb @@ -0,0 +1,31 @@ +# Update to 1.20.4 +# Jordi Camps / CNAG +# Sebastien Moretti / SIB + +easyblock = 'Tarball' + +name = 'Go' +version = "1.20.4" + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] + +local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} +sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] +checksums = ['698ef3243972a51ddb4028e4a1ac63dc6d60821bf18e59a807e051fee0a385bd'] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +sanity_check_commands = ["go help"] + +modextravars = {'GOROOT': '%(installdir)s'} + +moduleclass = 'compiler' From 57d83da9b7059eceab16126a2ddb27b138536624 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 11 May 2023 15:27:37 +0200 Subject: [PATCH 7395/9987] Add binutils as builddependency --- .../p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb index 454b392c46c..3f3e9090b61 100644 --- a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb @@ -25,6 +25,10 @@ checksums = [ '17bcf10055dd421572654b8da3a7899115c0eb50ec32bb6ab58371d16530f8c6'}, ] +builddependencies = [ + ('binutils', '2.38'), +] + dependencies = [ ('tesseract', '5.3.0'), ('Python', '3.10.4'), From e6d90aeea63a7ce698c3ac589de5f5e767870d61 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 11 May 2023 16:10:11 +0200 Subject: [PATCH 7396/9987] copy required libdgemm.so* for CUDA-aware HPL --- .../h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb index 4ab35a334cf..ea1db37a03d 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb @@ -28,10 +28,13 @@ dependencies = [ buildopts = "TOPdir=${PWD}" -files_to_copy = [(['bin/CUDA/HPL.dat', 'bin/CUDA/xhpl'], 'bin')] +files_to_copy = [ + (['bin/CUDA/HPL.dat', 'bin/CUDA/xhpl'], 'bin'), + (['src/cuda/libdgemm.so*'], 'lib'), +] sanity_check_paths = { - 'files': ['bin/HPL.dat', 'bin/xhpl'], + 'files': ['bin/HPL.dat', 'bin/xhpl', 'lib/libdgemm.so'], 'dirs': [], } From f178a5ac4ff4270845680f66e614624b06133307 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 11 May 2023 16:34:45 +0200 Subject: [PATCH 7397/9987] Add the checksum for the other arch --- easybuild/easyconfigs/g/Go/Go-1.20.4.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Go/Go-1.20.4.eb b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb index 082ea644519..2291970e9da 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.20.4.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb @@ -17,7 +17,10 @@ source_urls = ['https://storage.googleapis.com/golang/'] local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] -checksums = ['698ef3243972a51ddb4028e4a1ac63dc6d60821bf18e59a807e051fee0a385bd'] +checksums = [ + '698ef3243972a51ddb4028e4a1ac63dc6d60821bf18e59a807e051fee0a385bd', # amd64 + '105889992ee4b1d40c7c108555222ca70ae43fccb42e20fbf1eebb822f5e72c6', # arm64 +] sanity_check_paths = { 'files': ['bin/go', 'bin/gofmt'], From 7a40ad6caeacf67a89f6511f512ac85fa1ad3a47 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 11 May 2023 19:01:50 +0200 Subject: [PATCH 7398/9987] Update flatbuffers dependency --- .../t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb | 2 +- .../easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb index 75d2c976761..c89dc40d70f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb @@ -28,7 +28,7 @@ dependencies = [ ('cURL', '7.83.0'), ('dill', '0.3.6'), ('double-conversion', '3.2.0'), - ('flatbuffers', '2.0.0'), + ('flatbuffers', '2.0.7'), ('giflib', '5.2.1'), ('hwloc', '2.7.1'), ('ICU', '71.1'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb index 0a382edbaef..33b24bfe7b2 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb @@ -24,7 +24,7 @@ dependencies = [ ('cURL', '7.83.0'), ('dill', '0.3.6'), ('double-conversion', '3.2.0'), - ('flatbuffers', '2.0.0'), + ('flatbuffers', '2.0.7'), ('giflib', '5.2.1'), ('hwloc', '2.7.1'), ('ICU', '71.1'), From 0b40e04972bbacd929ca56fb2f58396dbbd86bce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 12 May 2023 10:32:08 +0200 Subject: [PATCH 7399/9987] Fix broken multi arch checksums for Go 1.18.3 --- easybuild/easyconfigs/g/Go/Go-1.18.3.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Go/Go-1.18.3.eb b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb index cb532faf480..fc45e80f1eb 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.18.3.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb @@ -16,7 +16,10 @@ source_urls = ['https://storage.googleapis.com/golang/'] local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] -checksums = ['956f8507b302ab0bb747613695cdae10af99bbd39a90cae522b7c0302cc27245'] +checksums = [{ + 'go%(version)s.linux-amd64.tar.gz': '956f8507b302ab0bb747613695cdae10af99bbd39a90cae522b7c0302cc27245', + 'go%(version)s.linux-arm64.tar.gz': 'beacbe1441bee4d7978b900136d1d6a71d150f0a9bb77e9d50c822065623a35a', +}] sanity_check_paths = { 'files': ['bin/go', 'bin/gofmt'], From 23029fe33fa68e8d1ced9322ecf88edf8c7dbe1e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 12 May 2023 11:04:57 +0200 Subject: [PATCH 7400/9987] Fix broken multi arch checksums --- easybuild/easyconfigs/g/Go/Go-1.20.4.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/Go/Go-1.20.4.eb b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb index 2291970e9da..a294c0de68f 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.20.4.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb @@ -17,10 +17,10 @@ source_urls = ['https://storage.googleapis.com/golang/'] local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] -checksums = [ - '698ef3243972a51ddb4028e4a1ac63dc6d60821bf18e59a807e051fee0a385bd', # amd64 - '105889992ee4b1d40c7c108555222ca70ae43fccb42e20fbf1eebb822f5e72c6', # arm64 -] +checksums = [{ + 'go%(version)s.linux-amd64.tar.gz': '698ef3243972a51ddb4028e4a1ac63dc6d60821bf18e59a807e051fee0a385bd', + 'go%(version)s.linux-arm64.tar.gz': '105889992ee4b1d40c7c108555222ca70ae43fccb42e20fbf1eebb822f5e72c6', +}] sanity_check_paths = { 'files': ['bin/go', 'bin/gofmt'], From 95a91891cc23c4b9d12537e0d1dfa7de8f20c9da Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 12 May 2023 13:51:37 +0200 Subject: [PATCH 7401/9987] Add patch for updated flatbuffers --- ...TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb | 3 + .../TensorFlow/TensorFlow-2.9.1-foss-2022a.eb | 3 + ...Flow-2.9.1_support_flatbuffers_2.0.6.patch | 4901 +++++++++++++++++ 3 files changed, 4907 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_support_flatbuffers_2.0.6.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb index c89dc40d70f..5c6801151e2 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb @@ -181,6 +181,7 @@ exts_list = [ 'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch', 'TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch', 'TensorFlow-2.9.1_support_flatbuffers_2.0.patch', + 'TensorFlow-2.9.1_support_flatbuffers_2.0.6.patch', ], 'checksums': [ {'v2.9.1.tar.gz': '6eaf86ead73e23988fe192da1db68f4d3828bcdd0f3a9dc195935e339c95dbdc'}, @@ -215,6 +216,8 @@ exts_list = [ '13a987ce8e20957d9a618493f6a0e8f67e0f9c8b11596f27bcd7322a8e62113d'}, {'TensorFlow-2.9.1_support_flatbuffers_2.0.patch': 'aaf0e0f86ad26f98a2bbb230dc2bbc2fb5f04886ab340049b5eaf3c70ae18f39'}, + {'TensorFlow-2.9.1_support_flatbuffers_2.0.6.patch': + 'b6203d42d68fe42a637499b78e423b66e1310dbc34ef3d1d2d804f8c665997ae'}, ], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb index 33b24bfe7b2..d75ff3264c5 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a.eb @@ -177,6 +177,7 @@ exts_list = [ 'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch', 'TensorFlow-2.9.1_remove-libclang-and-io-gcs-deps.patch', 'TensorFlow-2.9.1_support_flatbuffers_2.0.patch', + 'TensorFlow-2.9.1_support_flatbuffers_2.0.6.patch', ], 'checksums': [ {'v2.9.1.tar.gz': '6eaf86ead73e23988fe192da1db68f4d3828bcdd0f3a9dc195935e339c95dbdc'}, @@ -211,6 +212,8 @@ exts_list = [ '13a987ce8e20957d9a618493f6a0e8f67e0f9c8b11596f27bcd7322a8e62113d'}, {'TensorFlow-2.9.1_support_flatbuffers_2.0.patch': 'aaf0e0f86ad26f98a2bbb230dc2bbc2fb5f04886ab340049b5eaf3c70ae18f39'}, + {'TensorFlow-2.9.1_support_flatbuffers_2.0.6.patch': + 'b6203d42d68fe42a637499b78e423b66e1310dbc34ef3d1d2d804f8c665997ae'}, ], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_support_flatbuffers_2.0.6.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_support_flatbuffers_2.0.6.patch new file mode 100644 index 00000000000..9612f06140a --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1_support_flatbuffers_2.0.6.patch @@ -0,0 +1,4901 @@ +Add support for flatbuffers 2.0.6 on top of 2.0 +Taken from https://github.com/tensorflow/tensorflow/commit/3ef396642bb88580b527077cf2d6dc12325085be + +Backported to 2.9.1 by +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/lite/CMakeLists.txt b/tensorflow/lite/CMakeLists.txt +index 40f9485b5d6..5ac317b9c13 100644 +--- a/tensorflow/lite/CMakeLists.txt ++++ b/tensorflow/lite/CMakeLists.txt +@@ -306,6 +306,11 @@ if(TFLITE_ENABLE_GPU) + ${TFLITE_SOURCE_DIR}/tools/versioning/gpu_compatibility.cc + ${TFLITE_SOURCE_DIR}/tools/versioning/op_signature.cc + ) ++ include_directories( ++ AFTER ++ ${TFLITE_SOURCE_DIR}/delegates/gpu/common ++ ${TFLITE_SOURCE_DIR}/delegates/gpu/common/task ++ ) + if(TFLITE_ENABLE_METAL AND "${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin") + # + # libmetal_delegate library +diff --git a/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h b/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h +index 8a12bf2a9db..ec0f176b45a 100644 +--- a/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h ++++ b/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h +@@ -26,10 +26,13 @@ namespace cl { + namespace data { + + struct Program; ++struct ProgramBuilder; + + struct CompiledCache; ++struct CompiledCacheBuilder; + + struct Program FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { ++ typedef ProgramBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FINGERPRINT = 4, + VT_BINARY = 6 +@@ -42,7 +45,7 @@ struct Program FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FINGERPRINT) && ++ VerifyField(verifier, VT_FINGERPRINT, 8) && + VerifyOffset(verifier, VT_BINARY) && + verifier.VerifyVector(binary()) && + verifier.EndTable(); +@@ -50,6 +53,7 @@ struct Program FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ProgramBuilder { ++ typedef Program Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_fingerprint(uint64_t fingerprint) { +@@ -62,7 +66,6 @@ struct ProgramBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ProgramBuilder &operator=(const ProgramBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -92,6 +95,7 @@ inline flatbuffers::Offset CreateProgramDirect( + } + + struct CompiledCache FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { ++ typedef CompiledCacheBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_DRIVER_VERSION = 4, + VT_PROGRAMS = 6 +@@ -99,8 +103,8 @@ struct CompiledCache FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + const flatbuffers::String *driver_version() const { + return GetPointer(VT_DRIVER_VERSION); + } +- const flatbuffers::Vector> *programs() const { +- return GetPointer> *>(VT_PROGRAMS); ++ const flatbuffers::Vector> *programs() const { ++ return GetPointer> *>(VT_PROGRAMS); + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +@@ -114,19 +118,19 @@ struct CompiledCache FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct CompiledCacheBuilder { ++ typedef CompiledCache Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_driver_version(flatbuffers::Offset driver_version) { + fbb_.AddOffset(CompiledCache::VT_DRIVER_VERSION, driver_version); + } +- void add_programs(flatbuffers::Offset>> programs) { ++ void add_programs(flatbuffers::Offset>> programs) { + fbb_.AddOffset(CompiledCache::VT_PROGRAMS, programs); + } + explicit CompiledCacheBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- CompiledCacheBuilder &operator=(const CompiledCacheBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -137,7 +141,7 @@ struct CompiledCacheBuilder { + inline flatbuffers::Offset CreateCompiledCache( + flatbuffers::FlatBufferBuilder &_fbb, + flatbuffers::Offset driver_version = 0, +- flatbuffers::Offset>> programs = 0) { ++ flatbuffers::Offset>> programs = 0) { + CompiledCacheBuilder builder_(_fbb); + builder_.add_programs(programs); + builder_.add_driver_version(driver_version); +@@ -147,9 +151,9 @@ inline flatbuffers::Offset CreateCompiledCache( + inline flatbuffers::Offset CreateCompiledCacheDirect( + flatbuffers::FlatBufferBuilder &_fbb, + const char *driver_version = nullptr, +- const std::vector> *programs = nullptr) { ++ const std::vector> *programs = nullptr) { + auto driver_version__ = driver_version ? _fbb.CreateString(driver_version) : 0; +- auto programs__ = programs ? _fbb.CreateVector>(*programs) : 0; ++ auto programs__ = programs ? _fbb.CreateVector>(*programs) : 0; + return tflite::gpu::cl::data::CreateCompiledCache( + _fbb, + driver_version__, +@@ -173,6 +177,11 @@ inline bool CompiledCacheBufferHasIdentifier(const void *buf) { + buf, CompiledCacheIdentifier()); + } + ++inline bool SizePrefixedCompiledCacheBufferHasIdentifier(const void *buf) { ++ return flatbuffers::BufferHasIdentifier( ++ buf, CompiledCacheIdentifier(), true); ++} ++ + inline bool VerifyCompiledCacheBuffer( + flatbuffers::Verifier &verifier) { + return verifier.VerifyBuffer(CompiledCacheIdentifier()); +diff --git a/tensorflow/lite/delegates/gpu/cl/serialization_generated.h b/tensorflow/lite/delegates/gpu/cl/serialization_generated.h +index 26691adb44a..aa4affb7ed4 100644 +--- a/tensorflow/lite/delegates/gpu/cl/serialization_generated.h ++++ b/tensorflow/lite/delegates/gpu/cl/serialization_generated.h +@@ -19,8 +19,9 @@ limitations under the License. + #define FLATBUFFERS_GENERATED_SERIALIZATION_TFLITE_GPU_CL_DATA_H_ + + #include "flatbuffers/flatbuffers.h" +-#include "tensorflow/lite/delegates/gpu/common/gpu_model_generated.h" +-#include "tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h" ++ ++#include "serialization_base_generated.h" ++#include "gpu_model_generated.h" + + namespace tflite { + namespace gpu { +@@ -39,15 +40,18 @@ struct BinaryProgram FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + VT_FINGERPRINT = 4, + VT_BINARY = 6 + }; +- uint64_t fingerprint() const { return GetField(VT_FINGERPRINT, 0); } ++ uint64_t fingerprint() const { ++ return GetField(VT_FINGERPRINT, 0); ++ } + const flatbuffers::Vector *binary() const { + return GetPointer *>(VT_BINARY); + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FINGERPRINT) && ++ VerifyField(verifier, VT_FINGERPRINT, 8) && + VerifyOffset(verifier, VT_BINARY) && +- verifier.VerifyVector(binary()) && verifier.EndTable(); ++ verifier.VerifyVector(binary()) && ++ verifier.EndTable(); + } + }; + +@@ -62,7 +66,7 @@ struct BinaryProgramBuilder { + fbb_.AddOffset(BinaryProgram::VT_BINARY, binary); + } + explicit BinaryProgramBuilder(flatbuffers::FlatBufferBuilder &_fbb) +- : fbb_(_fbb) { ++ : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } + flatbuffers::Offset Finish() { +@@ -73,7 +77,8 @@ struct BinaryProgramBuilder { + }; + + inline flatbuffers::Offset CreateBinaryProgram( +- flatbuffers::FlatBufferBuilder &_fbb, uint64_t fingerprint = 0, ++ flatbuffers::FlatBufferBuilder &_fbb, ++ uint64_t fingerprint = 0, + flatbuffers::Offset> binary = 0) { + BinaryProgramBuilder builder_(_fbb); + builder_.add_fingerprint(fingerprint); +@@ -82,11 +87,14 @@ inline flatbuffers::Offset CreateBinaryProgram( + } + + inline flatbuffers::Offset CreateBinaryProgramDirect( +- flatbuffers::FlatBufferBuilder &_fbb, uint64_t fingerprint = 0, ++ flatbuffers::FlatBufferBuilder &_fbb, ++ uint64_t fingerprint = 0, + const std::vector *binary = nullptr) { + auto binary__ = binary ? _fbb.CreateVector(*binary) : 0; +- return tflite::gpu::cl::data::CreateBinaryProgram(_fbb, fingerprint, +- binary__); ++ return tflite::gpu::cl::data::CreateBinaryProgram( ++ _fbb, ++ fingerprint, ++ binary__); + } + + struct InferenceContext FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { +@@ -104,25 +112,18 @@ struct InferenceContext FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + const flatbuffers::String *driver_version() const { + return GetPointer(VT_DRIVER_VERSION); + } +- const flatbuffers::Vector< +- flatbuffers::Offset> +- *binary_programs() const { +- return GetPointer> *>( +- VT_BINARY_PROGRAMS); ++ const flatbuffers::Vector> *binary_programs() const { ++ return GetPointer> *>(VT_BINARY_PROGRAMS); + } +- const flatbuffers::Vector> +- *tuned_work_group_sizes_per_node() const { +- return GetPointer> *>( +- VT_TUNED_WORK_GROUP_SIZES_PER_NODE); ++ const flatbuffers::Vector> *tuned_work_group_sizes_per_node() const { ++ return GetPointer> *>(VT_TUNED_WORK_GROUP_SIZES_PER_NODE); + } + const flatbuffers::Vector *fingerprints_per_node() const { +- return GetPointer *>( +- VT_FINGERPRINTS_PER_NODE); ++ return GetPointer *>(VT_FINGERPRINTS_PER_NODE); + } + bool Verify(flatbuffers::Verifier &verifier) const { +- return VerifyTableStart(verifier) && VerifyOffset(verifier, VT_GPU_MODEL) && ++ return VerifyTableStart(verifier) && ++ VerifyOffset(verifier, VT_GPU_MODEL) && + verifier.VerifyTable(gpu_model()) && + VerifyOffset(verifier, VT_DRIVER_VERSION) && + verifier.VerifyString(driver_version()) && +@@ -142,32 +143,20 @@ struct InferenceContextBuilder { + typedef InferenceContext Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; +- void add_gpu_model( +- flatbuffers::Offset gpu_model) { ++ void add_gpu_model(flatbuffers::Offset gpu_model) { + fbb_.AddOffset(InferenceContext::VT_GPU_MODEL, gpu_model); + } +- void add_driver_version( +- flatbuffers::Offset driver_version) { ++ void add_driver_version(flatbuffers::Offset driver_version) { + fbb_.AddOffset(InferenceContext::VT_DRIVER_VERSION, driver_version); + } +- void add_binary_programs( +- flatbuffers::Offset>> +- binary_programs) { ++ void add_binary_programs(flatbuffers::Offset>> binary_programs) { + fbb_.AddOffset(InferenceContext::VT_BINARY_PROGRAMS, binary_programs); + } +- void add_tuned_work_group_sizes_per_node( +- flatbuffers::Offset< +- flatbuffers::Vector>> +- tuned_work_group_sizes_per_node) { +- fbb_.AddOffset(InferenceContext::VT_TUNED_WORK_GROUP_SIZES_PER_NODE, +- tuned_work_group_sizes_per_node); ++ void add_tuned_work_group_sizes_per_node(flatbuffers::Offset>> tuned_work_group_sizes_per_node) { ++ fbb_.AddOffset(InferenceContext::VT_TUNED_WORK_GROUP_SIZES_PER_NODE, tuned_work_group_sizes_per_node); + } +- void add_fingerprints_per_node( +- flatbuffers::Offset> +- fingerprints_per_node) { +- fbb_.AddOffset(InferenceContext::VT_FINGERPRINTS_PER_NODE, +- fingerprints_per_node); ++ void add_fingerprints_per_node(flatbuffers::Offset> fingerprints_per_node) { ++ fbb_.AddOffset(InferenceContext::VT_FINGERPRINTS_PER_NODE, fingerprints_per_node); + } + explicit InferenceContextBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { +@@ -184,14 +173,9 @@ inline flatbuffers::Offset CreateInferenceContext( + flatbuffers::FlatBufferBuilder &_fbb, + flatbuffers::Offset gpu_model = 0, + flatbuffers::Offset driver_version = 0, +- flatbuffers::Offset>> +- binary_programs = 0, +- flatbuffers::Offset< +- flatbuffers::Vector>> +- tuned_work_group_sizes_per_node = 0, +- flatbuffers::Offset> fingerprints_per_node = +- 0) { ++ flatbuffers::Offset>> binary_programs = 0, ++ flatbuffers::Offset>> tuned_work_group_sizes_per_node = 0, ++ flatbuffers::Offset> fingerprints_per_node = 0) { + InferenceContextBuilder builder_(_fbb); + builder_.add_fingerprints_per_node(fingerprints_per_node); + builder_.add_tuned_work_group_sizes_per_node(tuned_work_group_sizes_per_node); +@@ -205,31 +189,20 @@ inline flatbuffers::Offset CreateInferenceContextDirect( + flatbuffers::FlatBufferBuilder &_fbb, + flatbuffers::Offset gpu_model = 0, + const char *driver_version = nullptr, +- const std::vector> +- *binary_programs = nullptr, +- const std::vector> +- *tuned_work_group_sizes_per_node = nullptr, ++ const std::vector> *binary_programs = nullptr, ++ const std::vector> *tuned_work_group_sizes_per_node = nullptr, + const std::vector *fingerprints_per_node = nullptr) { +- auto driver_version__ = +- driver_version ? _fbb.CreateString(driver_version) : 0; +- auto binary_programs__ = +- binary_programs +- ? _fbb.CreateVector< +- flatbuffers::Offset>( +- *binary_programs) +- : 0; +- auto tuned_work_group_sizes_per_node__ = +- tuned_work_group_sizes_per_node +- ? _fbb.CreateVector>( +- *tuned_work_group_sizes_per_node) +- : 0; +- auto fingerprints_per_node__ = +- fingerprints_per_node +- ? _fbb.CreateVector(*fingerprints_per_node) +- : 0; ++ auto driver_version__ = driver_version ? _fbb.CreateString(driver_version) : 0; ++ auto binary_programs__ = binary_programs ? _fbb.CreateVector>(*binary_programs) : 0; ++ auto tuned_work_group_sizes_per_node__ = tuned_work_group_sizes_per_node ? _fbb.CreateVector>(*tuned_work_group_sizes_per_node) : 0; ++ auto fingerprints_per_node__ = fingerprints_per_node ? _fbb.CreateVector(*fingerprints_per_node) : 0; + return tflite::gpu::cl::data::CreateInferenceContext( +- _fbb, gpu_model, driver_version__, binary_programs__, +- tuned_work_group_sizes_per_node__, fingerprints_per_node__); ++ _fbb, ++ gpu_model, ++ driver_version__, ++ binary_programs__, ++ tuned_work_group_sizes_per_node__, ++ fingerprints_per_node__); + } + + inline const tflite::gpu::cl::data::InferenceContext *GetInferenceContext(const void *buf) { +diff --git a/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h b/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h +index 0f0873b1e44..8cc0d6c75c9 100644 +--- a/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h ++++ b/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h +@@ -18,7 +18,8 @@ limitations under the License. + #define FLATBUFFERS_GENERATED_GPUMODEL_TFLITE_GPU_DATA_H_ + + #include "flatbuffers/flatbuffers.h" +-#include "tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h" ++ ++#include "serialization_base_generated.h" + + namespace tflite { + namespace gpu { +@@ -45,11 +46,15 @@ struct TensorDescWithId FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + const tflite::gpu::data::TensorDescriptor *desc() const { + return GetPointer(VT_DESC); + } +- int32_t id() const { return GetField(VT_ID, 0); } ++ int32_t id() const { ++ return GetField(VT_ID, 0); ++ } + bool Verify(flatbuffers::Verifier &verifier) const { +- return VerifyTableStart(verifier) && VerifyOffset(verifier, VT_DESC) && ++ return VerifyTableStart(verifier) && ++ VerifyOffset(verifier, VT_DESC) && + verifier.VerifyTable(desc()) && +- VerifyField(verifier, VT_ID) && verifier.EndTable(); ++ VerifyField(verifier, VT_ID, 4) && ++ verifier.EndTable(); + } + }; + +@@ -64,7 +69,7 @@ struct TensorDescWithIdBuilder { + fbb_.AddElement(TensorDescWithId::VT_ID, id, 0); + } + explicit TensorDescWithIdBuilder(flatbuffers::FlatBufferBuilder &_fbb) +- : fbb_(_fbb) { ++ : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } + flatbuffers::Offset Finish() { +@@ -90,12 +95,17 @@ struct PairOfValueIds FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + VT_FIRST = 4, + VT_SECOND = 6 + }; +- int32_t first() const { return GetField(VT_FIRST, 0); } +- int32_t second() const { return GetField(VT_SECOND, 0); } ++ int32_t first() const { ++ return GetField(VT_FIRST, 0); ++ } ++ int32_t second() const { ++ return GetField(VT_SECOND, 0); ++ } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FIRST) && +- VerifyField(verifier, VT_SECOND) && verifier.EndTable(); ++ VerifyField(verifier, VT_FIRST, 4) && ++ VerifyField(verifier, VT_SECOND, 4) && ++ verifier.EndTable(); + } + }; + +@@ -110,7 +120,7 @@ struct PairOfValueIdsBuilder { + fbb_.AddElement(PairOfValueIds::VT_SECOND, second, 0); + } + explicit PairOfValueIdsBuilder(flatbuffers::FlatBufferBuilder &_fbb) +- : fbb_(_fbb) { ++ : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } + flatbuffers::Offset Finish() { +@@ -121,7 +131,8 @@ struct PairOfValueIdsBuilder { + }; + + inline flatbuffers::Offset CreatePairOfValueIds( +- flatbuffers::FlatBufferBuilder &_fbb, int32_t first = 0, ++ flatbuffers::FlatBufferBuilder &_fbb, ++ int32_t first = 0, + int32_t second = 0) { + PairOfValueIdsBuilder builder_(_fbb); + builder_.add_second(second); +@@ -150,13 +161,15 @@ struct GpuNode FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return GetPointer(VT_NAME); + } + bool Verify(flatbuffers::Verifier &verifier) const { +- return VerifyTableStart(verifier) && VerifyOffset(verifier, VT_GPU_OP) && ++ return VerifyTableStart(verifier) && ++ VerifyOffset(verifier, VT_GPU_OP) && + verifier.VerifyTable(gpu_op()) && + VerifyOffset(verifier, VT_INPUT_IDS) && + verifier.VerifyVector(input_ids()) && + VerifyOffset(verifier, VT_OUTPUT_IDS) && + verifier.VerifyVector(output_ids()) && +- VerifyOffset(verifier, VT_NAME) && verifier.VerifyString(name()) && ++ VerifyOffset(verifier, VT_NAME) && ++ verifier.VerifyString(name()) && + verifier.EndTable(); + } + }; +@@ -168,18 +181,17 @@ struct GpuNodeBuilder { + void add_gpu_op(flatbuffers::Offset gpu_op) { + fbb_.AddOffset(GpuNode::VT_GPU_OP, gpu_op); + } +- void add_input_ids( +- flatbuffers::Offset> input_ids) { ++ void add_input_ids(flatbuffers::Offset> input_ids) { + fbb_.AddOffset(GpuNode::VT_INPUT_IDS, input_ids); + } +- void add_output_ids( +- flatbuffers::Offset> output_ids) { ++ void add_output_ids(flatbuffers::Offset> output_ids) { + fbb_.AddOffset(GpuNode::VT_OUTPUT_IDS, output_ids); + } + void add_name(flatbuffers::Offset name) { + fbb_.AddOffset(GpuNode::VT_NAME, name); + } +- explicit GpuNodeBuilder(flatbuffers::FlatBufferBuilder &_fbb) : fbb_(_fbb) { ++ explicit GpuNodeBuilder(flatbuffers::FlatBufferBuilder &_fbb) ++ : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } + flatbuffers::Offset Finish() { +@@ -212,8 +224,12 @@ inline flatbuffers::Offset CreateGpuNodeDirect( + auto input_ids__ = input_ids ? _fbb.CreateVector(*input_ids) : 0; + auto output_ids__ = output_ids ? _fbb.CreateVector(*output_ids) : 0; + auto name__ = name ? _fbb.CreateString(name) : 0; +- return tflite::gpu::data::CreateGpuNode(_fbb, gpu_op, input_ids__, +- output_ids__, name__); ++ return tflite::gpu::data::CreateGpuNode( ++ _fbb, ++ gpu_op, ++ input_ids__, ++ output_ids__, ++ name__); + } + + struct GpuModel FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { +@@ -228,24 +244,14 @@ struct GpuModel FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + VT_OUTPUT_REFS = 16, + VT_VARIABLE_IDS_AND_REFS = 18 + }; +- const flatbuffers::Vector> +- *nodes() const { +- return GetPointer> *>(VT_NODES); +- } +- const flatbuffers::Vector< +- flatbuffers::Offset> +- *tensors() const { +- return GetPointer> *>( +- VT_TENSORS); +- } +- const flatbuffers::Vector< +- flatbuffers::Offset> +- *const_tensors() const { +- return GetPointer> *>( +- VT_CONST_TENSORS); ++ const flatbuffers::Vector> *nodes() const { ++ return GetPointer> *>(VT_NODES); ++ } ++ const flatbuffers::Vector> *tensors() const { ++ return GetPointer> *>(VT_TENSORS); ++ } ++ const flatbuffers::Vector> *const_tensors() const { ++ return GetPointer> *>(VT_CONST_TENSORS); + } + const flatbuffers::Vector *input_ids() const { + return GetPointer *>(VT_INPUT_IDS); +@@ -259,15 +265,12 @@ struct GpuModel FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + const flatbuffers::Vector *output_refs() const { + return GetPointer *>(VT_OUTPUT_REFS); + } +- const flatbuffers::Vector< +- flatbuffers::Offset> +- *variable_ids_and_refs() const { +- return GetPointer> *>( +- VT_VARIABLE_IDS_AND_REFS); ++ const flatbuffers::Vector> *variable_ids_and_refs() const { ++ return GetPointer> *>(VT_VARIABLE_IDS_AND_REFS); + } + bool Verify(flatbuffers::Verifier &verifier) const { +- return VerifyTableStart(verifier) && VerifyOffset(verifier, VT_NODES) && ++ return VerifyTableStart(verifier) && ++ VerifyOffset(verifier, VT_NODES) && + verifier.VerifyVector(nodes()) && + verifier.VerifyVectorOfTables(nodes()) && + VerifyOffset(verifier, VT_TENSORS) && +@@ -295,47 +298,32 @@ struct GpuModelBuilder { + typedef GpuModel Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; +- void add_nodes( +- flatbuffers::Offset< +- flatbuffers::Vector>> +- nodes) { ++ void add_nodes(flatbuffers::Offset>> nodes) { + fbb_.AddOffset(GpuModel::VT_NODES, nodes); + } +- void add_tensors( +- flatbuffers::Offset>> +- tensors) { ++ void add_tensors(flatbuffers::Offset>> tensors) { + fbb_.AddOffset(GpuModel::VT_TENSORS, tensors); + } +- void add_const_tensors( +- flatbuffers::Offset>> +- const_tensors) { ++ void add_const_tensors(flatbuffers::Offset>> const_tensors) { + fbb_.AddOffset(GpuModel::VT_CONST_TENSORS, const_tensors); + } +- void add_input_ids( +- flatbuffers::Offset> input_ids) { ++ void add_input_ids(flatbuffers::Offset> input_ids) { + fbb_.AddOffset(GpuModel::VT_INPUT_IDS, input_ids); + } +- void add_output_ids( +- flatbuffers::Offset> output_ids) { ++ void add_output_ids(flatbuffers::Offset> output_ids) { + fbb_.AddOffset(GpuModel::VT_OUTPUT_IDS, output_ids); + } +- void add_input_refs( +- flatbuffers::Offset> input_refs) { ++ void add_input_refs(flatbuffers::Offset> input_refs) { + fbb_.AddOffset(GpuModel::VT_INPUT_REFS, input_refs); + } +- void add_output_refs( +- flatbuffers::Offset> output_refs) { ++ void add_output_refs(flatbuffers::Offset> output_refs) { + fbb_.AddOffset(GpuModel::VT_OUTPUT_REFS, output_refs); + } +- void add_variable_ids_and_refs( +- flatbuffers::Offset>> +- variable_ids_and_refs) { ++ void add_variable_ids_and_refs(flatbuffers::Offset>> variable_ids_and_refs) { + fbb_.AddOffset(GpuModel::VT_VARIABLE_IDS_AND_REFS, variable_ids_and_refs); + } +- explicit GpuModelBuilder(flatbuffers::FlatBufferBuilder &_fbb) : fbb_(_fbb) { ++ explicit GpuModelBuilder(flatbuffers::FlatBufferBuilder &_fbb) ++ : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } + flatbuffers::Offset Finish() { +@@ -347,22 +335,14 @@ struct GpuModelBuilder { + + inline flatbuffers::Offset CreateGpuModel( + flatbuffers::FlatBufferBuilder &_fbb, +- flatbuffers::Offset< +- flatbuffers::Vector>> +- nodes = 0, +- flatbuffers::Offset>> +- tensors = 0, +- flatbuffers::Offset>> +- const_tensors = 0, ++ flatbuffers::Offset>> nodes = 0, ++ flatbuffers::Offset>> tensors = 0, ++ flatbuffers::Offset>> const_tensors = 0, + flatbuffers::Offset> input_ids = 0, + flatbuffers::Offset> output_ids = 0, + flatbuffers::Offset> input_refs = 0, + flatbuffers::Offset> output_refs = 0, +- flatbuffers::Offset>> +- variable_ids_and_refs = 0) { ++ flatbuffers::Offset>> variable_ids_and_refs = 0) { + GpuModelBuilder builder_(_fbb); + builder_.add_variable_ids_and_refs(variable_ids_and_refs); + builder_.add_output_refs(output_refs); +@@ -377,48 +357,32 @@ inline flatbuffers::Offset CreateGpuModel( + + inline flatbuffers::Offset CreateGpuModelDirect( + flatbuffers::FlatBufferBuilder &_fbb, +- const std::vector> *nodes = +- nullptr, +- const std::vector> +- *tensors = nullptr, +- const std::vector> +- *const_tensors = nullptr, ++ const std::vector> *nodes = nullptr, ++ const std::vector> *tensors = nullptr, ++ const std::vector> *const_tensors = nullptr, + const std::vector *input_ids = nullptr, + const std::vector *output_ids = nullptr, + const std::vector *input_refs = nullptr, + const std::vector *output_refs = nullptr, +- const std::vector> +- *variable_ids_and_refs = nullptr) { +- auto nodes__ = +- nodes +- ? _fbb.CreateVector>( +- *nodes) +- : 0; +- auto tensors__ = +- tensors ? _fbb.CreateVector< +- flatbuffers::Offset>( +- *tensors) +- : 0; +- auto const_tensors__ = +- const_tensors +- ? _fbb.CreateVector< +- flatbuffers::Offset>( +- *const_tensors) +- : 0; ++ const std::vector> *variable_ids_and_refs = nullptr) { ++ auto nodes__ = nodes ? _fbb.CreateVector>(*nodes) : 0; ++ auto tensors__ = tensors ? _fbb.CreateVector>(*tensors) : 0; ++ auto const_tensors__ = const_tensors ? _fbb.CreateVector>(*const_tensors) : 0; + auto input_ids__ = input_ids ? _fbb.CreateVector(*input_ids) : 0; + auto output_ids__ = output_ids ? _fbb.CreateVector(*output_ids) : 0; + auto input_refs__ = input_refs ? _fbb.CreateVector(*input_refs) : 0; +- auto output_refs__ = +- output_refs ? _fbb.CreateVector(*output_refs) : 0; +- auto variable_ids_and_refs__ = +- variable_ids_and_refs +- ? _fbb.CreateVector< +- flatbuffers::Offset>( +- *variable_ids_and_refs) +- : 0; ++ auto output_refs__ = output_refs ? _fbb.CreateVector(*output_refs) : 0; ++ auto variable_ids_and_refs__ = variable_ids_and_refs ? _fbb.CreateVector>(*variable_ids_and_refs) : 0; + return tflite::gpu::data::CreateGpuModel( +- _fbb, nodes__, tensors__, const_tensors__, input_ids__, output_ids__, +- input_refs__, output_refs__, variable_ids_and_refs__); ++ _fbb, ++ nodes__, ++ tensors__, ++ const_tensors__, ++ input_ids__, ++ output_ids__, ++ input_refs__, ++ output_refs__, ++ variable_ids_and_refs__); + } + + } // namespace data +diff --git a/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h b/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h +index a8f7b714e80..c2bd14c3c1a 100644 +--- a/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h ++++ b/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h +@@ -139,17 +139,38 @@ enum class DataType : int8_t { + + inline const DataType (&EnumValuesDataType())[12] { + static const DataType values[] = { +- DataType::UNKNOWN, DataType::FLOAT16, DataType::FLOAT32, +- DataType::FLOAT64, DataType::UINT8, DataType::INT8, +- DataType::UINT16, DataType::INT16, DataType::UINT32, +- DataType::INT32, DataType::UINT64, DataType::INT64}; ++ DataType::UNKNOWN, ++ DataType::FLOAT16, ++ DataType::FLOAT32, ++ DataType::FLOAT64, ++ DataType::UINT8, ++ DataType::INT8, ++ DataType::UINT16, ++ DataType::INT16, ++ DataType::UINT32, ++ DataType::INT32, ++ DataType::UINT64, ++ DataType::INT64 ++ }; + return values; + } + + inline const char * const *EnumNamesDataType() { +- static const char *const names[13] = { +- "UNKNOWN", "FLOAT16", "FLOAT32", "FLOAT64", "UINT8", "INT8", "UINT16", +- "INT16", "UINT32", "INT32", "UINT64", "INT64", nullptr}; ++ static const char * const names[13] = { ++ "UNKNOWN", ++ "FLOAT16", ++ "FLOAT32", ++ "FLOAT64", ++ "UINT8", ++ "INT8", ++ "UINT16", ++ "INT16", ++ "UINT32", ++ "INT32", ++ "UINT64", ++ "INT64", ++ nullptr ++ }; + return names; + } + +@@ -315,21 +336,26 @@ enum class CalculationsPrecision : int8_t { + }; + + inline const CalculationsPrecision (&EnumValuesCalculationsPrecision())[3] { +- static const CalculationsPrecision values[] = {CalculationsPrecision::F32, +- CalculationsPrecision::F32_F16, +- CalculationsPrecision::F16}; ++ static const CalculationsPrecision values[] = { ++ CalculationsPrecision::F32, ++ CalculationsPrecision::F32_F16, ++ CalculationsPrecision::F16 ++ }; + return values; + } + +-inline const char *const *EnumNamesCalculationsPrecision() { +- static const char *const names[4] = {"F32", "F32_F16", "F16", nullptr}; ++inline const char * const *EnumNamesCalculationsPrecision() { ++ static const char * const names[4] = { ++ "F32", ++ "F32_F16", ++ "F16", ++ nullptr ++ }; + return names; + } + + inline const char *EnumNameCalculationsPrecision(CalculationsPrecision e) { +- if (flatbuffers::IsOutRange(e, CalculationsPrecision::F32, +- CalculationsPrecision::F16)) +- return ""; ++ if (flatbuffers::IsOutRange(e, CalculationsPrecision::F32, CalculationsPrecision::F16)) return ""; + const size_t index = static_cast(e); + return EnumNamesCalculationsPrecision()[index]; + } +@@ -346,26 +372,29 @@ enum class TensorToGrid : int8_t { + + inline const TensorToGrid (&EnumValuesTensorToGrid())[5] { + static const TensorToGrid values[] = { +- TensorToGrid::CUSTOM, TensorToGrid::WB_TO_X_HD_TO_Y_S_TO_Z, +- TensorToGrid::WB_TO_X_HD_TO_Y_Z_IS_1, TensorToGrid::WB_TO_X_H_TO_Y_D_TO_Z, +- TensorToGrid::B_TO_X_Y_IS_1_Z_IS_1}; ++ TensorToGrid::CUSTOM, ++ TensorToGrid::WB_TO_X_HD_TO_Y_S_TO_Z, ++ TensorToGrid::WB_TO_X_HD_TO_Y_Z_IS_1, ++ TensorToGrid::WB_TO_X_H_TO_Y_D_TO_Z, ++ TensorToGrid::B_TO_X_Y_IS_1_Z_IS_1 ++ }; + return values; + } + +-inline const char *const *EnumNamesTensorToGrid() { +- static const char *const names[6] = {"CUSTOM", +- "WB_TO_X_HD_TO_Y_S_TO_Z", +- "WB_TO_X_HD_TO_Y_Z_IS_1", +- "WB_TO_X_H_TO_Y_D_TO_Z", +- "B_TO_X_Y_IS_1_Z_IS_1", +- nullptr}; ++inline const char * const *EnumNamesTensorToGrid() { ++ static const char * const names[6] = { ++ "CUSTOM", ++ "WB_TO_X_HD_TO_Y_S_TO_Z", ++ "WB_TO_X_HD_TO_Y_Z_IS_1", ++ "WB_TO_X_H_TO_Y_D_TO_Z", ++ "B_TO_X_Y_IS_1_Z_IS_1", ++ nullptr ++ }; + return names; + } + + inline const char *EnumNameTensorToGrid(TensorToGrid e) { +- if (flatbuffers::IsOutRange(e, TensorToGrid::CUSTOM, +- TensorToGrid::B_TO_X_Y_IS_1_Z_IS_1)) +- return ""; ++ if (flatbuffers::IsOutRange(e, TensorToGrid::CUSTOM, TensorToGrid::B_TO_X_Y_IS_1_Z_IS_1)) return ""; + const size_t index = static_cast(e); + return EnumNamesTensorToGrid()[index]; + } +@@ -383,30 +412,31 @@ enum class CompilerOptions : int8_t { + + inline const CompilerOptions (&EnumValuesCompilerOptions())[6] { + static const CompilerOptions values[] = { +- CompilerOptions::ADRENO_FULL_SIMD_LINE, +- CompilerOptions::ADRENO_MORE_WAVES, +- CompilerOptions::CL_FAST_RELAXED_MATH, +- CompilerOptions::CL_OPT_DISABLE, +- CompilerOptions::CL_2_0, +- CompilerOptions::CL_3_0}; ++ CompilerOptions::ADRENO_FULL_SIMD_LINE, ++ CompilerOptions::ADRENO_MORE_WAVES, ++ CompilerOptions::CL_FAST_RELAXED_MATH, ++ CompilerOptions::CL_OPT_DISABLE, ++ CompilerOptions::CL_2_0, ++ CompilerOptions::CL_3_0 ++ }; + return values; + } + +-inline const char *const *EnumNamesCompilerOptions() { +- static const char *const names[7] = {"ADRENO_FULL_SIMD_LINE", +- "ADRENO_MORE_WAVES", +- "CL_FAST_RELAXED_MATH", +- "CL_OPT_DISABLE", +- "CL_2_0", +- "CL_3_0", +- nullptr}; ++inline const char * const *EnumNamesCompilerOptions() { ++ static const char * const names[7] = { ++ "ADRENO_FULL_SIMD_LINE", ++ "ADRENO_MORE_WAVES", ++ "CL_FAST_RELAXED_MATH", ++ "CL_OPT_DISABLE", ++ "CL_2_0", ++ "CL_3_0", ++ nullptr ++ }; + return names; + } + + inline const char *EnumNameCompilerOptions(CompilerOptions e) { +- if (flatbuffers::IsOutRange(e, CompilerOptions::ADRENO_FULL_SIMD_LINE, +- CompilerOptions::CL_3_0)) +- return ""; ++ if (flatbuffers::IsOutRange(e, CompilerOptions::ADRENO_FULL_SIMD_LINE, CompilerOptions::CL_3_0)) return ""; + const size_t index = static_cast(e); + return EnumNamesCompilerOptions()[index]; + } +@@ -433,10 +463,10 @@ struct Int4 FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_X) && +- VerifyField(verifier, VT_Y) && +- VerifyField(verifier, VT_Z) && +- VerifyField(verifier, VT_W) && ++ VerifyField(verifier, VT_X, 4) && ++ VerifyField(verifier, VT_Y, 4) && ++ VerifyField(verifier, VT_Z, 4) && ++ VerifyField(verifier, VT_W, 4) && + verifier.EndTable(); + } + }; +@@ -500,9 +530,9 @@ struct Int3 FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_X) && +- VerifyField(verifier, VT_Y) && +- VerifyField(verifier, VT_Z) && ++ VerifyField(verifier, VT_X, 4) && ++ VerifyField(verifier, VT_Y, 4) && ++ VerifyField(verifier, VT_Z, 4) && + verifier.EndTable(); + } + }; +@@ -557,8 +587,8 @@ struct Int2 FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_X) && +- VerifyField(verifier, VT_Y) && ++ VerifyField(verifier, VT_X, 4) && ++ VerifyField(verifier, VT_Y, 4) && + verifier.EndTable(); + } + }; +@@ -676,7 +706,7 @@ struct GPUObjectDescriptor FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + VerifyOffset(verifier, VT_STATE_VARS) && + verifier.VerifyVector(state_vars()) && + verifier.VerifyVectorOfTables(state_vars()) && +- VerifyField(verifier, VT_ACCESS_TYPE) && ++ VerifyField(verifier, VT_ACCESS_TYPE, 1) && + verifier.EndTable(); + } + }; +@@ -743,8 +773,8 @@ struct IntValue FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_NAME) && + verifier.VerifyString(name()) && +- VerifyField(verifier, VT_VALUE) && +- VerifyField(verifier, VT_ACTIVE) && ++ VerifyField(verifier, VT_VALUE, 4) && ++ VerifyField(verifier, VT_ACTIVE, 1) && + verifier.EndTable(); + } + }; +@@ -818,8 +848,8 @@ struct FloatValue FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_NAME) && + verifier.VerifyString(name()) && +- VerifyField(verifier, VT_VALUE) && +- VerifyField(verifier, VT_ACTIVE) && ++ VerifyField(verifier, VT_VALUE, 4) && ++ VerifyField(verifier, VT_ACTIVE, 1) && + verifier.EndTable(); + } + }; +@@ -893,8 +923,8 @@ struct HalfValue FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_NAME) && + verifier.VerifyString(name()) && +- VerifyField(verifier, VT_VALUE) && +- VerifyField(verifier, VT_ACTIVE) && ++ VerifyField(verifier, VT_VALUE, 4) && ++ VerifyField(verifier, VT_ACTIVE, 1) && + verifier.EndTable(); + } + }; +@@ -984,13 +1014,13 @@ struct BufferDescriptor FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_BASE_OBJ) && + verifier.VerifyTable(base_obj()) && +- VerifyField(verifier, VT_ELEMENT_TYPE) && +- VerifyField(verifier, VT_ELEMENT_SIZE) && +- VerifyField(verifier, VT_MEMORY_TYPE) && ++ VerifyField(verifier, VT_ELEMENT_TYPE, 1) && ++ VerifyField(verifier, VT_ELEMENT_SIZE, 4) && ++ VerifyField(verifier, VT_MEMORY_TYPE, 1) && + VerifyOffset(verifier, VT_ATTRIBUTES) && + verifier.VerifyVector(attributes()) && + verifier.VerifyVectorOfStrings(attributes()) && +- VerifyField(verifier, VT_SIZE) && ++ VerifyField(verifier, VT_SIZE, 4) && + VerifyOffset(verifier, VT_DATA) && + verifier.VerifyVector(data()) && + verifier.EndTable(); +@@ -1107,9 +1137,9 @@ struct Texture2DDescriptor FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_BASE_OBJ) && + verifier.VerifyTable(base_obj()) && +- VerifyField(verifier, VT_ELEMENT_TYPE) && +- VerifyField(verifier, VT_NORMALIZED) && +- VerifyField(verifier, VT_NORMALIZED_TYPE) && ++ VerifyField(verifier, VT_ELEMENT_TYPE, 1) && ++ VerifyField(verifier, VT_NORMALIZED, 1) && ++ VerifyField(verifier, VT_NORMALIZED_TYPE, 1) && + VerifyOffset(verifier, VT_SIZE) && + verifier.VerifyTable(size()) && + VerifyOffset(verifier, VT_DATA) && +@@ -1220,10 +1250,10 @@ struct TensorLinearDescriptor FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tab + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_BASE_OBJ) && + verifier.VerifyTable(base_obj()) && +- VerifyField(verifier, VT_STORAGE_TYPE) && +- VerifyField(verifier, VT_ELEMENT_TYPE) && +- VerifyField(verifier, VT_MEMORY_TYPE) && +- VerifyField(verifier, VT_SIZE) && ++ VerifyField(verifier, VT_STORAGE_TYPE, 1) && ++ VerifyField(verifier, VT_ELEMENT_TYPE, 1) && ++ VerifyField(verifier, VT_MEMORY_TYPE, 1) && ++ VerifyField(verifier, VT_SIZE, 4) && + VerifyOffset(verifier, VT_DATA) && + verifier.VerifyVector(data()) && + verifier.EndTable(); +@@ -1326,11 +1356,11 @@ struct BHWDC FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_B) && +- VerifyField(verifier, VT_H) && +- VerifyField(verifier, VT_W) && +- VerifyField(verifier, VT_D) && +- VerifyField(verifier, VT_C) && ++ VerifyField(verifier, VT_B, 4) && ++ VerifyField(verifier, VT_H, 4) && ++ VerifyField(verifier, VT_W, 4) && ++ VerifyField(verifier, VT_D, 4) && ++ VerifyField(verifier, VT_C, 4) && + verifier.EndTable(); + } + }; +@@ -1418,17 +1448,18 @@ struct TensorDescriptor FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return GetField(VT_USE_BUFFER_FOR_WRITE_ONLY_IMAGE_BUFFER, 0) != 0; + } + bool Verify(flatbuffers::Verifier &verifier) const { +- return VerifyTableStart(verifier) && VerifyOffset(verifier, VT_BASE_OBJ) && ++ return VerifyTableStart(verifier) && ++ VerifyOffset(verifier, VT_BASE_OBJ) && + verifier.VerifyTable(base_obj()) && +- VerifyField(verifier, VT_DATA_TYPE) && +- VerifyField(verifier, VT_STORAGE_TYPE) && +- VerifyField(verifier, VT_LAYOUT) && +- VerifyOffset(verifier, VT_SHAPE) && verifier.VerifyTable(shape()) && +- VerifyOffset(verifier, VT_DATA) && verifier.VerifyVector(data()) && +- VerifyField(verifier, +- VT_USE_BUFFER_FOR_WRITE_ONLY_2D_TEXTURE) && +- VerifyField(verifier, +- VT_USE_BUFFER_FOR_WRITE_ONLY_IMAGE_BUFFER) && ++ VerifyField(verifier, VT_DATA_TYPE, 1) && ++ VerifyField(verifier, VT_STORAGE_TYPE, 1) && ++ VerifyField(verifier, VT_LAYOUT, 1) && ++ VerifyOffset(verifier, VT_SHAPE) && ++ verifier.VerifyTable(shape()) && ++ VerifyOffset(verifier, VT_DATA) && ++ verifier.VerifyVector(data()) && ++ VerifyField(verifier, VT_USE_BUFFER_FOR_WRITE_ONLY_2D_TEXTURE, 1) && ++ VerifyField(verifier, VT_USE_BUFFER_FOR_WRITE_ONLY_IMAGE_BUFFER, 1) && + verifier.EndTable(); + } + }; +@@ -1455,17 +1486,11 @@ struct TensorDescriptorBuilder { + void add_data(flatbuffers::Offset> data) { + fbb_.AddOffset(TensorDescriptor::VT_DATA, data); + } +- void add_use_buffer_for_write_only_2d_texture( +- bool use_buffer_for_write_only_2d_texture) { +- fbb_.AddElement( +- TensorDescriptor::VT_USE_BUFFER_FOR_WRITE_ONLY_2D_TEXTURE, +- static_cast(use_buffer_for_write_only_2d_texture), 0); ++ void add_use_buffer_for_write_only_2d_texture(bool use_buffer_for_write_only_2d_texture) { ++ fbb_.AddElement(TensorDescriptor::VT_USE_BUFFER_FOR_WRITE_ONLY_2D_TEXTURE, static_cast(use_buffer_for_write_only_2d_texture), 0); + } +- void add_use_buffer_for_write_only_image_buffer( +- bool use_buffer_for_write_only_image_buffer) { +- fbb_.AddElement( +- TensorDescriptor::VT_USE_BUFFER_FOR_WRITE_ONLY_IMAGE_BUFFER, +- static_cast(use_buffer_for_write_only_image_buffer), 0); ++ void add_use_buffer_for_write_only_image_buffer(bool use_buffer_for_write_only_image_buffer) { ++ fbb_.AddElement(TensorDescriptor::VT_USE_BUFFER_FOR_WRITE_ONLY_IMAGE_BUFFER, static_cast(use_buffer_for_write_only_image_buffer), 0); + } + explicit TensorDescriptorBuilder(flatbuffers::FlatBufferBuilder &_fbb) + : fbb_(_fbb) { +@@ -1481,10 +1506,8 @@ struct TensorDescriptorBuilder { + inline flatbuffers::Offset CreateTensorDescriptor( + flatbuffers::FlatBufferBuilder &_fbb, + flatbuffers::Offset base_obj = 0, +- tflite::gpu::data::DataType data_type = +- tflite::gpu::data::DataType::UNKNOWN, +- tflite::gpu::data::TensorStorageType storage_type = +- tflite::gpu::data::TensorStorageType::UNKNOWN, ++ tflite::gpu::data::DataType data_type = tflite::gpu::data::DataType::UNKNOWN, ++ tflite::gpu::data::TensorStorageType storage_type = tflite::gpu::data::TensorStorageType::UNKNOWN, + tflite::gpu::data::Layout layout = tflite::gpu::data::Layout::UNKNOWN, + flatbuffers::Offset shape = 0, + flatbuffers::Offset> data = 0, +@@ -1494,10 +1517,8 @@ inline flatbuffers::Offset CreateTensorDescriptor( + builder_.add_data(data); + builder_.add_shape(shape); + builder_.add_base_obj(base_obj); +- builder_.add_use_buffer_for_write_only_image_buffer( +- use_buffer_for_write_only_image_buffer); +- builder_.add_use_buffer_for_write_only_2d_texture( +- use_buffer_for_write_only_2d_texture); ++ builder_.add_use_buffer_for_write_only_image_buffer(use_buffer_for_write_only_image_buffer); ++ builder_.add_use_buffer_for_write_only_2d_texture(use_buffer_for_write_only_2d_texture); + builder_.add_layout(layout); + builder_.add_storage_type(storage_type); + builder_.add_data_type(data_type); +@@ -1507,10 +1528,8 @@ inline flatbuffers::Offset CreateTensorDescriptor( + inline flatbuffers::Offset CreateTensorDescriptorDirect( + flatbuffers::FlatBufferBuilder &_fbb, + flatbuffers::Offset base_obj = 0, +- tflite::gpu::data::DataType data_type = +- tflite::gpu::data::DataType::UNKNOWN, +- tflite::gpu::data::TensorStorageType storage_type = +- tflite::gpu::data::TensorStorageType::UNKNOWN, ++ tflite::gpu::data::DataType data_type = tflite::gpu::data::DataType::UNKNOWN, ++ tflite::gpu::data::TensorStorageType storage_type = tflite::gpu::data::TensorStorageType::UNKNOWN, + tflite::gpu::data::Layout layout = tflite::gpu::data::Layout::UNKNOWN, + flatbuffers::Offset shape = 0, + const std::vector *data = nullptr, +@@ -1518,7 +1537,13 @@ inline flatbuffers::Offset CreateTensorDescriptorDirect( + bool use_buffer_for_write_only_image_buffer = false) { + auto data__ = data ? _fbb.CreateVector(*data) : 0; + return tflite::gpu::data::CreateTensorDescriptor( +- _fbb, base_obj, data_type, storage_type, layout, shape, data__, ++ _fbb, ++ base_obj, ++ data_type, ++ storage_type, ++ layout, ++ shape, ++ data__, + use_buffer_for_write_only_2d_texture, + use_buffer_for_write_only_image_buffer); + } +@@ -1989,32 +2014,24 @@ struct OperationDef FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + VT_DST_TENSORS = 8 + }; + tflite::gpu::data::CalculationsPrecision precision() const { +- return static_cast( +- GetField(VT_PRECISION, 0)); +- } +- const flatbuffers::Vector< +- flatbuffers::Offset> +- *src_tensors() const { +- return GetPointer> *>( +- VT_SRC_TENSORS); +- } +- const flatbuffers::Vector< +- flatbuffers::Offset> +- *dst_tensors() const { +- return GetPointer> *>( +- VT_DST_TENSORS); ++ return static_cast(GetField(VT_PRECISION, 0)); ++ } ++ const flatbuffers::Vector> *src_tensors() const { ++ return GetPointer> *>(VT_SRC_TENSORS); ++ } ++ const flatbuffers::Vector> *dst_tensors() const { ++ return GetPointer> *>(VT_DST_TENSORS); + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_PRECISION) && ++ VerifyField(verifier, VT_PRECISION, 1) && + VerifyOffset(verifier, VT_SRC_TENSORS) && + verifier.VerifyVector(src_tensors()) && + verifier.VerifyVectorOfTables(src_tensors()) && + VerifyOffset(verifier, VT_DST_TENSORS) && + verifier.VerifyVector(dst_tensors()) && +- verifier.VerifyVectorOfTables(dst_tensors()) && verifier.EndTable(); ++ verifier.VerifyVectorOfTables(dst_tensors()) && ++ verifier.EndTable(); + } + }; + +@@ -2023,23 +2040,16 @@ struct OperationDefBuilder { + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_precision(tflite::gpu::data::CalculationsPrecision precision) { +- fbb_.AddElement(OperationDef::VT_PRECISION, +- static_cast(precision), 0); ++ fbb_.AddElement(OperationDef::VT_PRECISION, static_cast(precision), 0); + } +- void add_src_tensors( +- flatbuffers::Offset>> +- src_tensors) { ++ void add_src_tensors(flatbuffers::Offset>> src_tensors) { + fbb_.AddOffset(OperationDef::VT_SRC_TENSORS, src_tensors); + } +- void add_dst_tensors( +- flatbuffers::Offset>> +- dst_tensors) { ++ void add_dst_tensors(flatbuffers::Offset>> dst_tensors) { + fbb_.AddOffset(OperationDef::VT_DST_TENSORS, dst_tensors); + } + explicit OperationDefBuilder(flatbuffers::FlatBufferBuilder &_fbb) +- : fbb_(_fbb) { ++ : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } + flatbuffers::Offset Finish() { +@@ -2051,14 +2061,9 @@ struct OperationDefBuilder { + + inline flatbuffers::Offset CreateOperationDef( + flatbuffers::FlatBufferBuilder &_fbb, +- tflite::gpu::data::CalculationsPrecision precision = +- tflite::gpu::data::CalculationsPrecision::F32, +- flatbuffers::Offset>> +- src_tensors = 0, +- flatbuffers::Offset>> +- dst_tensors = 0) { ++ tflite::gpu::data::CalculationsPrecision precision = tflite::gpu::data::CalculationsPrecision::F32, ++ flatbuffers::Offset>> src_tensors = 0, ++ flatbuffers::Offset>> dst_tensors = 0) { + OperationDefBuilder builder_(_fbb); + builder_.add_dst_tensors(dst_tensors); + builder_.add_src_tensors(src_tensors); +@@ -2068,26 +2073,16 @@ inline flatbuffers::Offset CreateOperationDef( + + inline flatbuffers::Offset CreateOperationDefDirect( + flatbuffers::FlatBufferBuilder &_fbb, +- tflite::gpu::data::CalculationsPrecision precision = +- tflite::gpu::data::CalculationsPrecision::F32, +- const std::vector> +- *src_tensors = nullptr, +- const std::vector> +- *dst_tensors = nullptr) { +- auto src_tensors__ = +- src_tensors +- ? _fbb.CreateVector< +- flatbuffers::Offset>( +- *src_tensors) +- : 0; +- auto dst_tensors__ = +- dst_tensors +- ? _fbb.CreateVector< +- flatbuffers::Offset>( +- *dst_tensors) +- : 0; +- return tflite::gpu::data::CreateOperationDef(_fbb, precision, src_tensors__, +- dst_tensors__); ++ tflite::gpu::data::CalculationsPrecision precision = tflite::gpu::data::CalculationsPrecision::F32, ++ const std::vector> *src_tensors = nullptr, ++ const std::vector> *dst_tensors = nullptr) { ++ auto src_tensors__ = src_tensors ? _fbb.CreateVector>(*src_tensors) : 0; ++ auto dst_tensors__ = dst_tensors ? _fbb.CreateVector>(*dst_tensors) : 0; ++ return tflite::gpu::data::CreateOperationDef( ++ _fbb, ++ precision, ++ src_tensors__, ++ dst_tensors__); + } + + struct CompilerOption FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { +@@ -2096,12 +2091,12 @@ struct CompilerOption FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + VT_OPTION = 4 + }; + tflite::gpu::data::CompilerOptions option() const { +- return static_cast( +- GetField(VT_OPTION, 0)); ++ return static_cast(GetField(VT_OPTION, 0)); + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_OPTION) && verifier.EndTable(); ++ VerifyField(verifier, VT_OPTION, 1) && ++ verifier.EndTable(); + } + }; + +@@ -2110,11 +2105,10 @@ struct CompilerOptionBuilder { + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_option(tflite::gpu::data::CompilerOptions option) { +- fbb_.AddElement(CompilerOption::VT_OPTION, +- static_cast(option), 0); ++ fbb_.AddElement(CompilerOption::VT_OPTION, static_cast(option), 0); + } + explicit CompilerOptionBuilder(flatbuffers::FlatBufferBuilder &_fbb) +- : fbb_(_fbb) { ++ : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } + flatbuffers::Offset Finish() { +@@ -2126,8 +2120,7 @@ struct CompilerOptionBuilder { + + inline flatbuffers::Offset CreateCompilerOption( + flatbuffers::FlatBufferBuilder &_fbb, +- tflite::gpu::data::CompilerOptions option = +- tflite::gpu::data::CompilerOptions::ADRENO_FULL_SIMD_LINE) { ++ tflite::gpu::data::CompilerOptions option = tflite::gpu::data::CompilerOptions::ADRENO_FULL_SIMD_LINE) { + CompilerOptionBuilder builder_(_fbb); + builder_.add_option(option); + return builder_.Finish(); +@@ -2164,23 +2157,24 @@ struct GPUOperation FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + const tflite::gpu::data::Int3 *work_group_size() const { + return GetPointer(VT_WORK_GROUP_SIZE); + } +- const flatbuffers::Vector< +- flatbuffers::Offset> +- *compiler_options() const { +- return GetPointer> *>( +- VT_COMPILER_OPTIONS); ++ const flatbuffers::Vector> *compiler_options() const { ++ return GetPointer> *>(VT_COMPILER_OPTIONS); + } + tflite::gpu::data::TensorToGrid tensor_to_grid() const { +- return static_cast( +- GetField(VT_TENSOR_TO_GRID, 0)); ++ return static_cast(GetField(VT_TENSOR_TO_GRID, 0)); ++ } ++ bool elementwise() const { ++ return GetField(VT_ELEMENTWISE, 0) != 0; ++ } ++ bool linkable() const { ++ return GetField(VT_LINKABLE, 0) != 0; + } +- bool elementwise() const { return GetField(VT_ELEMENTWISE, 0) != 0; } +- bool linkable() const { return GetField(VT_LINKABLE, 0) != 0; } + bool check_src_channels_size() const { + return GetField(VT_CHECK_SRC_CHANNELS_SIZE, 0) != 0; + } +- uint64_t flops() const { return GetField(VT_FLOPS, 0); } ++ uint64_t flops() const { ++ return GetField(VT_FLOPS, 0); ++ } + const tflite::gpu::data::OperationDef *definition() const { + return GetPointer(VT_DEFINITION); + } +@@ -2188,23 +2182,16 @@ struct GPUOperation FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return GetField(VT_GRID_DIMENSION, 0); + } + const tflite::gpu::data::Int3 *work_group_launch_order() const { +- return GetPointer( +- VT_WORK_GROUP_LAUNCH_ORDER); ++ return GetPointer(VT_WORK_GROUP_LAUNCH_ORDER); + } + const tflite::gpu::data::Int3 *grid_size() const { + return GetPointer(VT_GRID_SIZE); + } +- const flatbuffers::Vector> +- *src_tensors_names() const { +- return GetPointer< +- const flatbuffers::Vector> *>( +- VT_SRC_TENSORS_NAMES); ++ const flatbuffers::Vector> *src_tensors_names() const { ++ return GetPointer> *>(VT_SRC_TENSORS_NAMES); + } +- const flatbuffers::Vector> +- *dst_tensors_names() const { +- return GetPointer< +- const flatbuffers::Vector> *>( +- VT_DST_TENSORS_NAMES); ++ const flatbuffers::Vector> *dst_tensors_names() const { ++ return GetPointer> *>(VT_DST_TENSORS_NAMES); + } + const tflite::gpu::data::Int3 *work_groups_count() const { + return GetPointer(VT_WORK_GROUPS_COUNT); +@@ -2216,22 +2203,24 @@ struct GPUOperation FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return GetPointer(VT_ELEMENTWISE_CODE); + } + bool Verify(flatbuffers::Verifier &verifier) const { +- return VerifyTableStart(verifier) && VerifyOffset(verifier, VT_ARGUMENTS) && ++ return VerifyTableStart(verifier) && ++ VerifyOffset(verifier, VT_ARGUMENTS) && + verifier.VerifyTable(arguments()) && +- VerifyOffset(verifier, VT_CODE) && verifier.VerifyString(code()) && ++ VerifyOffset(verifier, VT_CODE) && ++ verifier.VerifyString(code()) && + VerifyOffset(verifier, VT_WORK_GROUP_SIZE) && + verifier.VerifyTable(work_group_size()) && + VerifyOffset(verifier, VT_COMPILER_OPTIONS) && + verifier.VerifyVector(compiler_options()) && + verifier.VerifyVectorOfTables(compiler_options()) && +- VerifyField(verifier, VT_TENSOR_TO_GRID) && +- VerifyField(verifier, VT_ELEMENTWISE) && +- VerifyField(verifier, VT_LINKABLE) && +- VerifyField(verifier, VT_CHECK_SRC_CHANNELS_SIZE) && +- VerifyField(verifier, VT_FLOPS) && ++ VerifyField(verifier, VT_TENSOR_TO_GRID, 1) && ++ VerifyField(verifier, VT_ELEMENTWISE, 1) && ++ VerifyField(verifier, VT_LINKABLE, 1) && ++ VerifyField(verifier, VT_CHECK_SRC_CHANNELS_SIZE, 1) && ++ VerifyField(verifier, VT_FLOPS, 8) && + VerifyOffset(verifier, VT_DEFINITION) && + verifier.VerifyTable(definition()) && +- VerifyField(verifier, VT_GRID_DIMENSION) && ++ VerifyField(verifier, VT_GRID_DIMENSION, 4) && + VerifyOffset(verifier, VT_WORK_GROUP_LAUNCH_ORDER) && + verifier.VerifyTable(work_group_launch_order()) && + VerifyOffset(verifier, VT_GRID_SIZE) && +@@ -2244,9 +2233,10 @@ struct GPUOperation FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + verifier.VerifyVectorOfStrings(dst_tensors_names()) && + VerifyOffset(verifier, VT_WORK_GROUPS_COUNT) && + verifier.VerifyTable(work_groups_count()) && +- VerifyField(verifier, VT_LINKABLE_COUNT) && ++ VerifyField(verifier, VT_LINKABLE_COUNT, 4) && + VerifyOffset(verifier, VT_ELEMENTWISE_CODE) && +- verifier.VerifyString(elementwise_code()) && verifier.EndTable(); ++ verifier.VerifyString(elementwise_code()) && ++ verifier.EndTable(); + } + }; + +@@ -2254,84 +2244,62 @@ struct GPUOperationBuilder { + typedef GPUOperation Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; +- void add_arguments( +- flatbuffers::Offset arguments) { ++ void add_arguments(flatbuffers::Offset arguments) { + fbb_.AddOffset(GPUOperation::VT_ARGUMENTS, arguments); + } + void add_code(flatbuffers::Offset code) { + fbb_.AddOffset(GPUOperation::VT_CODE, code); + } +- void add_work_group_size( +- flatbuffers::Offset work_group_size) { ++ void add_work_group_size(flatbuffers::Offset work_group_size) { + fbb_.AddOffset(GPUOperation::VT_WORK_GROUP_SIZE, work_group_size); + } +- void add_compiler_options( +- flatbuffers::Offset>> +- compiler_options) { ++ void add_compiler_options(flatbuffers::Offset>> compiler_options) { + fbb_.AddOffset(GPUOperation::VT_COMPILER_OPTIONS, compiler_options); + } + void add_tensor_to_grid(tflite::gpu::data::TensorToGrid tensor_to_grid) { +- fbb_.AddElement(GPUOperation::VT_TENSOR_TO_GRID, +- static_cast(tensor_to_grid), 0); ++ fbb_.AddElement(GPUOperation::VT_TENSOR_TO_GRID, static_cast(tensor_to_grid), 0); + } + void add_elementwise(bool elementwise) { +- fbb_.AddElement(GPUOperation::VT_ELEMENTWISE, +- static_cast(elementwise), 0); ++ fbb_.AddElement(GPUOperation::VT_ELEMENTWISE, static_cast(elementwise), 0); + } + void add_linkable(bool linkable) { +- fbb_.AddElement(GPUOperation::VT_LINKABLE, +- static_cast(linkable), 0); ++ fbb_.AddElement(GPUOperation::VT_LINKABLE, static_cast(linkable), 0); + } + void add_check_src_channels_size(bool check_src_channels_size) { +- fbb_.AddElement(GPUOperation::VT_CHECK_SRC_CHANNELS_SIZE, +- static_cast(check_src_channels_size), 0); ++ fbb_.AddElement(GPUOperation::VT_CHECK_SRC_CHANNELS_SIZE, static_cast(check_src_channels_size), 0); + } + void add_flops(uint64_t flops) { + fbb_.AddElement(GPUOperation::VT_FLOPS, flops, 0); + } +- void add_definition( +- flatbuffers::Offset definition) { ++ void add_definition(flatbuffers::Offset definition) { + fbb_.AddOffset(GPUOperation::VT_DEFINITION, definition); + } + void add_grid_dimension(int32_t grid_dimension) { +- fbb_.AddElement(GPUOperation::VT_GRID_DIMENSION, grid_dimension, +- 0); ++ fbb_.AddElement(GPUOperation::VT_GRID_DIMENSION, grid_dimension, 0); + } +- void add_work_group_launch_order( +- flatbuffers::Offset work_group_launch_order) { +- fbb_.AddOffset(GPUOperation::VT_WORK_GROUP_LAUNCH_ORDER, +- work_group_launch_order); ++ void add_work_group_launch_order(flatbuffers::Offset work_group_launch_order) { ++ fbb_.AddOffset(GPUOperation::VT_WORK_GROUP_LAUNCH_ORDER, work_group_launch_order); + } + void add_grid_size(flatbuffers::Offset grid_size) { + fbb_.AddOffset(GPUOperation::VT_GRID_SIZE, grid_size); + } +- void add_src_tensors_names( +- flatbuffers::Offset< +- flatbuffers::Vector>> +- src_tensors_names) { ++ void add_src_tensors_names(flatbuffers::Offset>> src_tensors_names) { + fbb_.AddOffset(GPUOperation::VT_SRC_TENSORS_NAMES, src_tensors_names); + } +- void add_dst_tensors_names( +- flatbuffers::Offset< +- flatbuffers::Vector>> +- dst_tensors_names) { ++ void add_dst_tensors_names(flatbuffers::Offset>> dst_tensors_names) { + fbb_.AddOffset(GPUOperation::VT_DST_TENSORS_NAMES, dst_tensors_names); + } +- void add_work_groups_count( +- flatbuffers::Offset work_groups_count) { ++ void add_work_groups_count(flatbuffers::Offset work_groups_count) { + fbb_.AddOffset(GPUOperation::VT_WORK_GROUPS_COUNT, work_groups_count); + } + void add_linkable_count(int32_t linkable_count) { +- fbb_.AddElement(GPUOperation::VT_LINKABLE_COUNT, linkable_count, +- 0); ++ fbb_.AddElement(GPUOperation::VT_LINKABLE_COUNT, linkable_count, 0); + } +- void add_elementwise_code( +- flatbuffers::Offset elementwise_code) { ++ void add_elementwise_code(flatbuffers::Offset elementwise_code) { + fbb_.AddOffset(GPUOperation::VT_ELEMENTWISE_CODE, elementwise_code); + } + explicit GPUOperationBuilder(flatbuffers::FlatBufferBuilder &_fbb) +- : fbb_(_fbb) { ++ : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } + flatbuffers::Offset Finish() { +@@ -2346,23 +2314,18 @@ inline flatbuffers::Offset CreateGPUOperation( + flatbuffers::Offset arguments = 0, + flatbuffers::Offset code = 0, + flatbuffers::Offset work_group_size = 0, +- flatbuffers::Offset>> +- compiler_options = 0, +- tflite::gpu::data::TensorToGrid tensor_to_grid = +- tflite::gpu::data::TensorToGrid::CUSTOM, +- bool elementwise = false, bool linkable = false, +- bool check_src_channels_size = false, uint64_t flops = 0, ++ flatbuffers::Offset>> compiler_options = 0, ++ tflite::gpu::data::TensorToGrid tensor_to_grid = tflite::gpu::data::TensorToGrid::CUSTOM, ++ bool elementwise = false, ++ bool linkable = false, ++ bool check_src_channels_size = false, ++ uint64_t flops = 0, + flatbuffers::Offset definition = 0, + int32_t grid_dimension = 0, + flatbuffers::Offset work_group_launch_order = 0, + flatbuffers::Offset grid_size = 0, +- flatbuffers::Offset< +- flatbuffers::Vector>> +- src_tensors_names = 0, +- flatbuffers::Offset< +- flatbuffers::Vector>> +- dst_tensors_names = 0, ++ flatbuffers::Offset>> src_tensors_names = 0, ++ flatbuffers::Offset>> dst_tensors_names = 0, + flatbuffers::Offset work_groups_count = 0, + int32_t linkable_count = 0, + flatbuffers::Offset elementwise_code = 0) { +@@ -2393,47 +2356,46 @@ inline flatbuffers::Offset CreateGPUOperationDirect( + flatbuffers::Offset arguments = 0, + const char *code = nullptr, + flatbuffers::Offset work_group_size = 0, +- const std::vector> +- *compiler_options = nullptr, +- tflite::gpu::data::TensorToGrid tensor_to_grid = +- tflite::gpu::data::TensorToGrid::CUSTOM, +- bool elementwise = false, bool linkable = false, +- bool check_src_channels_size = false, uint64_t flops = 0, ++ const std::vector> *compiler_options = nullptr, ++ tflite::gpu::data::TensorToGrid tensor_to_grid = tflite::gpu::data::TensorToGrid::CUSTOM, ++ bool elementwise = false, ++ bool linkable = false, ++ bool check_src_channels_size = false, ++ uint64_t flops = 0, + flatbuffers::Offset definition = 0, + int32_t grid_dimension = 0, + flatbuffers::Offset work_group_launch_order = 0, + flatbuffers::Offset grid_size = 0, +- const std::vector> +- *src_tensors_names = nullptr, +- const std::vector> +- *dst_tensors_names = nullptr, ++ const std::vector> *src_tensors_names = nullptr, ++ const std::vector> *dst_tensors_names = nullptr, + flatbuffers::Offset work_groups_count = 0, +- int32_t linkable_count = 0, const char *elementwise_code = nullptr) { ++ int32_t linkable_count = 0, ++ const char *elementwise_code = nullptr) { + auto code__ = code ? _fbb.CreateString(code) : 0; +- auto compiler_options__ = +- compiler_options +- ? _fbb.CreateVector< +- flatbuffers::Offset>( +- *compiler_options) +- : 0; +- auto src_tensors_names__ = +- src_tensors_names +- ? _fbb.CreateVector>( +- *src_tensors_names) +- : 0; +- auto dst_tensors_names__ = +- dst_tensors_names +- ? _fbb.CreateVector>( +- *dst_tensors_names) +- : 0; +- auto elementwise_code__ = +- elementwise_code ? _fbb.CreateString(elementwise_code) : 0; ++ auto compiler_options__ = compiler_options ? _fbb.CreateVector>(*compiler_options) : 0; ++ auto src_tensors_names__ = src_tensors_names ? _fbb.CreateVector>(*src_tensors_names) : 0; ++ auto dst_tensors_names__ = dst_tensors_names ? _fbb.CreateVector>(*dst_tensors_names) : 0; ++ auto elementwise_code__ = elementwise_code ? _fbb.CreateString(elementwise_code) : 0; + return tflite::gpu::data::CreateGPUOperation( +- _fbb, arguments, code__, work_group_size, compiler_options__, +- tensor_to_grid, elementwise, linkable, check_src_channels_size, flops, +- definition, grid_dimension, work_group_launch_order, grid_size, +- src_tensors_names__, dst_tensors_names__, work_groups_count, +- linkable_count, elementwise_code__); ++ _fbb, ++ arguments, ++ code__, ++ work_group_size, ++ compiler_options__, ++ tensor_to_grid, ++ elementwise, ++ linkable, ++ check_src_channels_size, ++ flops, ++ definition, ++ grid_dimension, ++ work_group_launch_order, ++ grid_size, ++ src_tensors_names__, ++ dst_tensors_names__, ++ work_groups_count, ++ linkable_count, ++ elementwise_code__); + } + + } // namespace data +diff --git a/tensorflow/lite/experimental/acceleration/configuration/BUILD b/tensorflow/lite/experimental/acceleration/configuration/BUILD +index 4aa77261555..54fa181e5c2 100644 +--- a/tensorflow/lite/experimental/acceleration/configuration/BUILD ++++ b/tensorflow/lite/experimental/acceleration/configuration/BUILD +@@ -83,31 +83,11 @@ tf_proto_library_py( + ) + # copybara:comment_end + +-# TODO(b/191428000): The automatic generation is temporarily disabled until +-# https://github.com/google/flatbuffers/pull/6486 is landed and tensorflow +-# flatbuffer version updated. +-# Until that time you need to build configuration_for_generation_generated.h +-# and copy the result to configuration_generated.h. +-genrule( +- name = "copy_configuration_fbs", +- srcs = ["configuration.fbs"], +- outs = ["configuration_for_generation.fbs"], +- cmd = "cp $(<) $(@)", +-) +- + flatbuffer_cc_library( +- name = "configuration_fbs_for_generation", +- srcs = [":configuration_for_generation.fbs"], +- flatc_args = DEFAULT_FLATC_ARGS + ["--gen-compare"], +- visibility = ["//visibility:private"], +-) +- +-cc_library( + name = "configuration_fbs", +- hdrs = ["configuration_generated.h"], ++ srcs = [":configuration.fbs"], + compatible_with = get_compatible_with_portable(), +- linkstatic = True, +- deps = ["@flatbuffers//:runtime_cc"], ++ flatc_args = DEFAULT_FLATC_ARGS + ["--gen-compare"], + ) + + flatbuffer_java_library( +diff --git a/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h b/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h +old mode 100644 +new mode 100755 +index 40b0f0322bc..1491cb9ff83 +--- a/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h ++++ b/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h +@@ -12,86 +12,109 @@ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + ==============================================================================*/ +-// clang-format off + // automatically generated by the FlatBuffers compiler, do not modify + +-#ifndef FLATBUFFERS_GENERATED_CONFIGURATIONFORGENERATION_TFLITE_H_ +-#define FLATBUFFERS_GENERATED_CONFIGURATIONFORGENERATION_TFLITE_H_ ++#ifndef FLATBUFFERS_GENERATED_CONFIGURATION_TFLITE_H_ ++#define FLATBUFFERS_GENERATED_CONFIGURATION_TFLITE_H_ + + #include "flatbuffers/flatbuffers.h" + + namespace tflite { + + struct ComputeSettings; ++struct ComputeSettingsBuilder; + struct ComputeSettingsT; + + struct NNAPISettings; ++struct NNAPISettingsBuilder; + struct NNAPISettingsT; + + struct GPUSettings; ++struct GPUSettingsBuilder; + struct GPUSettingsT; + + struct HexagonSettings; ++struct HexagonSettingsBuilder; + struct HexagonSettingsT; + + struct XNNPackSettings; ++struct XNNPackSettingsBuilder; + struct XNNPackSettingsT; + + struct CoreMLSettings; ++struct CoreMLSettingsBuilder; + struct CoreMLSettingsT; + + struct EdgeTpuDeviceSpec; ++struct EdgeTpuDeviceSpecBuilder; + struct EdgeTpuDeviceSpecT; + + struct EdgeTpuInactivePowerConfig; ++struct EdgeTpuInactivePowerConfigBuilder; + struct EdgeTpuInactivePowerConfigT; + + struct EdgeTpuSettings; ++struct EdgeTpuSettingsBuilder; + struct EdgeTpuSettingsT; + + struct CoralSettings; ++struct CoralSettingsBuilder; + struct CoralSettingsT; + + struct CPUSettings; ++struct CPUSettingsBuilder; + struct CPUSettingsT; + + struct TFLiteSettings; ++struct TFLiteSettingsBuilder; + struct TFLiteSettingsT; + + struct FallbackSettings; ++struct FallbackSettingsBuilder; + struct FallbackSettingsT; + + struct BenchmarkMetric; ++struct BenchmarkMetricBuilder; + struct BenchmarkMetricT; + + struct BenchmarkResult; ++struct BenchmarkResultBuilder; + struct BenchmarkResultT; + + struct ErrorCode; ++struct ErrorCodeBuilder; + struct ErrorCodeT; + + struct BenchmarkError; ++struct BenchmarkErrorBuilder; + struct BenchmarkErrorT; + + struct BenchmarkEvent; ++struct BenchmarkEventBuilder; + struct BenchmarkEventT; + + struct BestAccelerationDecision; ++struct BestAccelerationDecisionBuilder; + struct BestAccelerationDecisionT; + + struct BenchmarkInitializationFailure; ++struct BenchmarkInitializationFailureBuilder; + struct BenchmarkInitializationFailureT; + + struct MiniBenchmarkEvent; ++struct MiniBenchmarkEventBuilder; + struct MiniBenchmarkEventT; + + struct ModelFile; ++struct ModelFileBuilder; + struct ModelFileT; + + struct BenchmarkStoragePaths; ++struct BenchmarkStoragePathsBuilder; + struct BenchmarkStoragePathsT; + + struct MinibenchmarkSettings; ++struct MinibenchmarkSettingsBuilder; + struct MinibenchmarkSettingsT; + + bool operator==(const ComputeSettingsT &lhs, const ComputeSettingsT &rhs); +@@ -143,7 +166,7 @@ bool operator!=(const BenchmarkStoragePathsT &lhs, const BenchmarkStoragePathsT + bool operator==(const MinibenchmarkSettingsT &lhs, const MinibenchmarkSettingsT &rhs); + bool operator!=(const MinibenchmarkSettingsT &lhs, const MinibenchmarkSettingsT &rhs); + +-enum ExecutionPreference { ++enum ExecutionPreference : int32_t { + ExecutionPreference_ANY = 0, + ExecutionPreference_LOW_LATENCY = 1, + ExecutionPreference_LOW_POWER = 2, +@@ -179,7 +202,7 @@ inline const char *EnumNameExecutionPreference(ExecutionPreference e) { + return EnumNamesExecutionPreference()[index]; + } + +-enum Delegate { ++enum Delegate : int32_t { + Delegate_NONE = 0, + Delegate_NNAPI = 1, + Delegate_GPU = 2, +@@ -227,7 +250,7 @@ inline const char *EnumNameDelegate(Delegate e) { + return EnumNamesDelegate()[index]; + } + +-enum NNAPIExecutionPreference { ++enum NNAPIExecutionPreference : int32_t { + NNAPIExecutionPreference_UNDEFINED = 0, + NNAPIExecutionPreference_NNAPI_LOW_POWER = 1, + NNAPIExecutionPreference_NNAPI_FAST_SINGLE_ANSWER = 2, +@@ -263,7 +286,7 @@ inline const char *EnumNameNNAPIExecutionPreference(NNAPIExecutionPreference e) + return EnumNamesNNAPIExecutionPreference()[index]; + } + +-enum NNAPIExecutionPriority { ++enum NNAPIExecutionPriority : int32_t { + NNAPIExecutionPriority_NNAPI_PRIORITY_UNDEFINED = 0, + NNAPIExecutionPriority_NNAPI_PRIORITY_LOW = 1, + NNAPIExecutionPriority_NNAPI_PRIORITY_MEDIUM = 2, +@@ -299,7 +322,7 @@ inline const char *EnumNameNNAPIExecutionPriority(NNAPIExecutionPriority e) { + return EnumNamesNNAPIExecutionPriority()[index]; + } + +-enum GPUBackend { ++enum GPUBackend : int32_t { + GPUBackend_UNSET = 0, + GPUBackend_OPENCL = 1, + GPUBackend_OPENGL = 2, +@@ -332,7 +355,7 @@ inline const char *EnumNameGPUBackend(GPUBackend e) { + return EnumNamesGPUBackend()[index]; + } + +-enum GPUInferencePriority { ++enum GPUInferencePriority : int32_t { + GPUInferencePriority_GPU_PRIORITY_AUTO = 0, + GPUInferencePriority_GPU_PRIORITY_MAX_PRECISION = 1, + GPUInferencePriority_GPU_PRIORITY_MIN_LATENCY = 2, +@@ -368,7 +391,7 @@ inline const char *EnumNameGPUInferencePriority(GPUInferencePriority e) { + return EnumNamesGPUInferencePriority()[index]; + } + +-enum GPUInferenceUsage { ++enum GPUInferenceUsage : int32_t { + GPUInferenceUsage_GPU_INFERENCE_PREFERENCE_FAST_SINGLE_ANSWER = 0, + GPUInferenceUsage_GPU_INFERENCE_PREFERENCE_SUSTAINED_SPEED = 1, + GPUInferenceUsage_MIN = GPUInferenceUsage_GPU_INFERENCE_PREFERENCE_FAST_SINGLE_ANSWER, +@@ -400,7 +423,7 @@ inline const char *EnumNameGPUInferenceUsage(GPUInferenceUsage e) { + + namespace CoreMLSettings_ { + +-enum EnabledDevices { ++enum EnabledDevices : int32_t { + EnabledDevices_DEVICES_ALL = 0, + EnabledDevices_DEVICES_WITH_NEURAL_ENGINE = 1, + EnabledDevices_MIN = EnabledDevices_DEVICES_ALL, +@@ -434,7 +457,7 @@ inline const char *EnumNameEnabledDevices(EnabledDevices e) { + + namespace EdgeTpuDeviceSpec_ { + +-enum PlatformType { ++enum PlatformType : int32_t { + PlatformType_MMIO = 0, + PlatformType_REFERENCE = 1, + PlatformType_SIMULATOR = 2, +@@ -472,7 +495,7 @@ inline const char *EnumNamePlatformType(PlatformType e) { + + } // namespace EdgeTpuDeviceSpec_ + +-enum EdgeTpuPowerState { ++enum EdgeTpuPowerState : int32_t { + EdgeTpuPowerState_UNDEFINED_POWERSTATE = 0, + EdgeTpuPowerState_TPU_CORE_OFF = 1, + EdgeTpuPowerState_READY = 2, +@@ -522,7 +545,7 @@ inline const char *EnumNameEdgeTpuPowerState(EdgeTpuPowerState e) { + + namespace EdgeTpuSettings_ { + +-enum FloatTruncationType { ++enum FloatTruncationType : int32_t { + FloatTruncationType_UNSPECIFIED = 0, + FloatTruncationType_NO_TRUNCATION = 1, + FloatTruncationType_BFLOAT16 = 2, +@@ -558,7 +581,7 @@ inline const char *EnumNameFloatTruncationType(FloatTruncationType e) { + return EnumNamesFloatTruncationType()[index]; + } + +-enum QosClass { ++enum QosClass : int32_t { + QosClass_QOS_UNDEFINED = 0, + QosClass_BEST_EFFORT = 1, + QosClass_REALTIME = 2, +@@ -595,7 +618,7 @@ inline const char *EnumNameQosClass(QosClass e) { + + namespace CoralSettings_ { + +-enum Performance { ++enum Performance : int32_t { + Performance_UNDEFINED = 0, + Performance_MAXIMUM = 1, + Performance_HIGH = 2, +@@ -636,7 +659,7 @@ inline const char *EnumNamePerformance(Performance e) { + + } // namespace CoralSettings_ + +-enum BenchmarkEventType { ++enum BenchmarkEventType : int32_t { + BenchmarkEventType_UNDEFINED_BENCHMARK_EVENT_TYPE = 0, + BenchmarkEventType_START = 1, + BenchmarkEventType_END = 2, +@@ -678,7 +701,7 @@ inline const char *EnumNameBenchmarkEventType(BenchmarkEventType e) { + return EnumNamesBenchmarkEventType()[index]; + } + +-enum BenchmarkStage { ++enum BenchmarkStage : int32_t { + BenchmarkStage_UNKNOWN = 0, + BenchmarkStage_INITIALIZATION = 1, + BenchmarkStage_INFERENCE = 2, +@@ -713,18 +736,20 @@ inline const char *EnumNameBenchmarkStage(BenchmarkStage e) { + + struct ComputeSettingsT : public flatbuffers::NativeTable { + typedef ComputeSettings TableType; +- tflite::ExecutionPreference preference; +- std::unique_ptr tflite_settings; +- std::string model_namespace_for_statistics; +- std::string model_identifier_for_statistics; +- std::unique_ptr settings_to_test_locally; +- ComputeSettingsT() +- : preference(tflite::ExecutionPreference_ANY) { +- } ++ tflite::ExecutionPreference preference = tflite::ExecutionPreference_ANY; ++ std::unique_ptr tflite_settings{}; ++ std::string model_namespace_for_statistics{}; ++ std::string model_identifier_for_statistics{}; ++ std::unique_ptr settings_to_test_locally{}; ++ ComputeSettingsT() = default; ++ ComputeSettingsT(const ComputeSettingsT &o); ++ ComputeSettingsT(ComputeSettingsT&&) FLATBUFFERS_NOEXCEPT = default; ++ ComputeSettingsT &operator=(ComputeSettingsT o) FLATBUFFERS_NOEXCEPT; + }; + + struct ComputeSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ComputeSettingsT NativeTableType; ++ typedef ComputeSettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_PREFERENCE = 4, + VT_TFLITE_SETTINGS = 6, +@@ -749,7 +774,7 @@ struct ComputeSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_PREFERENCE) && ++ VerifyField(verifier, VT_PREFERENCE, 4) && + VerifyOffset(verifier, VT_TFLITE_SETTINGS) && + verifier.VerifyTable(tflite_settings()) && + VerifyOffset(verifier, VT_MODEL_NAMESPACE_FOR_STATISTICS) && +@@ -766,6 +791,7 @@ struct ComputeSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ComputeSettingsBuilder { ++ typedef ComputeSettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_preference(tflite::ExecutionPreference preference) { +@@ -787,7 +813,6 @@ struct ComputeSettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ComputeSettingsBuilder &operator=(const ComputeSettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -833,32 +858,27 @@ flatbuffers::Offset CreateComputeSettings(flatbuffers::FlatBuff + + struct NNAPISettingsT : public flatbuffers::NativeTable { + typedef NNAPISettings TableType; +- std::string accelerator_name; +- std::string cache_directory; +- std::string model_token; +- tflite::NNAPIExecutionPreference execution_preference; +- int32_t no_of_nnapi_instances_to_cache; +- std::unique_ptr fallback_settings; +- bool allow_nnapi_cpu_on_android_10_plus; +- tflite::NNAPIExecutionPriority execution_priority; +- bool allow_dynamic_dimensions; +- bool allow_fp16_precision_for_fp32; +- bool use_burst_computation; +- int64_t support_library_handle; +- NNAPISettingsT() +- : execution_preference(tflite::NNAPIExecutionPreference_UNDEFINED), +- no_of_nnapi_instances_to_cache(0), +- allow_nnapi_cpu_on_android_10_plus(false), +- execution_priority(tflite::NNAPIExecutionPriority_NNAPI_PRIORITY_UNDEFINED), +- allow_dynamic_dimensions(false), +- allow_fp16_precision_for_fp32(false), +- use_burst_computation(false), +- support_library_handle(0) { +- } ++ std::string accelerator_name{}; ++ std::string cache_directory{}; ++ std::string model_token{}; ++ tflite::NNAPIExecutionPreference execution_preference = tflite::NNAPIExecutionPreference_UNDEFINED; ++ int32_t no_of_nnapi_instances_to_cache = 0; ++ std::unique_ptr fallback_settings{}; ++ bool allow_nnapi_cpu_on_android_10_plus = false; ++ tflite::NNAPIExecutionPriority execution_priority = tflite::NNAPIExecutionPriority_NNAPI_PRIORITY_UNDEFINED; ++ bool allow_dynamic_dimensions = false; ++ bool allow_fp16_precision_for_fp32 = false; ++ bool use_burst_computation = false; ++ int64_t support_library_handle = 0; ++ NNAPISettingsT() = default; ++ NNAPISettingsT(const NNAPISettingsT &o); ++ NNAPISettingsT(NNAPISettingsT&&) FLATBUFFERS_NOEXCEPT = default; ++ NNAPISettingsT &operator=(NNAPISettingsT o) FLATBUFFERS_NOEXCEPT; + }; + + struct NNAPISettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef NNAPISettingsT NativeTableType; ++ typedef NNAPISettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_ACCELERATOR_NAME = 4, + VT_CACHE_DIRECTORY = 6, +@@ -917,16 +937,16 @@ struct NNAPISettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + verifier.VerifyString(cache_directory()) && + VerifyOffset(verifier, VT_MODEL_TOKEN) && + verifier.VerifyString(model_token()) && +- VerifyField(verifier, VT_EXECUTION_PREFERENCE) && +- VerifyField(verifier, VT_NO_OF_NNAPI_INSTANCES_TO_CACHE) && ++ VerifyField(verifier, VT_EXECUTION_PREFERENCE, 4) && ++ VerifyField(verifier, VT_NO_OF_NNAPI_INSTANCES_TO_CACHE, 4) && + VerifyOffset(verifier, VT_FALLBACK_SETTINGS) && + verifier.VerifyTable(fallback_settings()) && +- VerifyField(verifier, VT_ALLOW_NNAPI_CPU_ON_ANDROID_10_PLUS) && +- VerifyField(verifier, VT_EXECUTION_PRIORITY) && +- VerifyField(verifier, VT_ALLOW_DYNAMIC_DIMENSIONS) && +- VerifyField(verifier, VT_ALLOW_FP16_PRECISION_FOR_FP32) && +- VerifyField(verifier, VT_USE_BURST_COMPUTATION) && +- VerifyField(verifier, VT_SUPPORT_LIBRARY_HANDLE) && ++ VerifyField(verifier, VT_ALLOW_NNAPI_CPU_ON_ANDROID_10_PLUS, 1) && ++ VerifyField(verifier, VT_EXECUTION_PRIORITY, 4) && ++ VerifyField(verifier, VT_ALLOW_DYNAMIC_DIMENSIONS, 1) && ++ VerifyField(verifier, VT_ALLOW_FP16_PRECISION_FOR_FP32, 1) && ++ VerifyField(verifier, VT_USE_BURST_COMPUTATION, 1) && ++ VerifyField(verifier, VT_SUPPORT_LIBRARY_HANDLE, 8) && + verifier.EndTable(); + } + NNAPISettingsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -935,6 +955,7 @@ struct NNAPISettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct NNAPISettingsBuilder { ++ typedef NNAPISettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_accelerator_name(flatbuffers::Offset accelerator_name) { +@@ -977,7 +998,6 @@ struct NNAPISettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- NNAPISettingsBuilder &operator=(const NNAPISettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -1052,28 +1072,20 @@ flatbuffers::Offset CreateNNAPISettings(flatbuffers::FlatBufferBu + + struct GPUSettingsT : public flatbuffers::NativeTable { + typedef GPUSettings TableType; +- bool is_precision_loss_allowed; +- bool enable_quantized_inference; +- tflite::GPUBackend force_backend; +- tflite::GPUInferencePriority inference_priority1; +- tflite::GPUInferencePriority inference_priority2; +- tflite::GPUInferencePriority inference_priority3; +- tflite::GPUInferenceUsage inference_preference; +- std::string cache_directory; +- std::string model_token; +- GPUSettingsT() +- : is_precision_loss_allowed(false), +- enable_quantized_inference(true), +- force_backend(tflite::GPUBackend_UNSET), +- inference_priority1(tflite::GPUInferencePriority_GPU_PRIORITY_AUTO), +- inference_priority2(tflite::GPUInferencePriority_GPU_PRIORITY_AUTO), +- inference_priority3(tflite::GPUInferencePriority_GPU_PRIORITY_AUTO), +- inference_preference(tflite::GPUInferenceUsage_GPU_INFERENCE_PREFERENCE_FAST_SINGLE_ANSWER) { +- } ++ bool is_precision_loss_allowed = false; ++ bool enable_quantized_inference = true; ++ tflite::GPUBackend force_backend = tflite::GPUBackend_UNSET; ++ tflite::GPUInferencePriority inference_priority1 = tflite::GPUInferencePriority_GPU_PRIORITY_AUTO; ++ tflite::GPUInferencePriority inference_priority2 = tflite::GPUInferencePriority_GPU_PRIORITY_AUTO; ++ tflite::GPUInferencePriority inference_priority3 = tflite::GPUInferencePriority_GPU_PRIORITY_AUTO; ++ tflite::GPUInferenceUsage inference_preference = tflite::GPUInferenceUsage_GPU_INFERENCE_PREFERENCE_FAST_SINGLE_ANSWER; ++ std::string cache_directory{}; ++ std::string model_token{}; + }; + + struct GPUSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef GPUSettingsT NativeTableType; ++ typedef GPUSettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_IS_PRECISION_LOSS_ALLOWED = 4, + VT_ENABLE_QUANTIZED_INFERENCE = 6, +@@ -1114,13 +1126,13 @@ struct GPUSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_IS_PRECISION_LOSS_ALLOWED) && +- VerifyField(verifier, VT_ENABLE_QUANTIZED_INFERENCE) && +- VerifyField(verifier, VT_FORCE_BACKEND) && +- VerifyField(verifier, VT_INFERENCE_PRIORITY1) && +- VerifyField(verifier, VT_INFERENCE_PRIORITY2) && +- VerifyField(verifier, VT_INFERENCE_PRIORITY3) && +- VerifyField(verifier, VT_INFERENCE_PREFERENCE) && ++ VerifyField(verifier, VT_IS_PRECISION_LOSS_ALLOWED, 1) && ++ VerifyField(verifier, VT_ENABLE_QUANTIZED_INFERENCE, 1) && ++ VerifyField(verifier, VT_FORCE_BACKEND, 4) && ++ VerifyField(verifier, VT_INFERENCE_PRIORITY1, 4) && ++ VerifyField(verifier, VT_INFERENCE_PRIORITY2, 4) && ++ VerifyField(verifier, VT_INFERENCE_PRIORITY3, 4) && ++ VerifyField(verifier, VT_INFERENCE_PREFERENCE, 4) && + VerifyOffset(verifier, VT_CACHE_DIRECTORY) && + verifier.VerifyString(cache_directory()) && + VerifyOffset(verifier, VT_MODEL_TOKEN) && +@@ -1133,6 +1145,7 @@ struct GPUSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct GPUSettingsBuilder { ++ typedef GPUSettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_is_precision_loss_allowed(bool is_precision_loss_allowed) { +@@ -1166,7 +1179,6 @@ struct GPUSettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- GPUSettingsBuilder &operator=(const GPUSettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -1228,20 +1240,15 @@ flatbuffers::Offset CreateGPUSettings(flatbuffers::FlatBufferBuilde + + struct HexagonSettingsT : public flatbuffers::NativeTable { + typedef HexagonSettings TableType; +- int32_t debug_level; +- int32_t powersave_level; +- bool print_graph_profile; +- bool print_graph_debug; +- HexagonSettingsT() +- : debug_level(0), +- powersave_level(0), +- print_graph_profile(false), +- print_graph_debug(false) { +- } ++ int32_t debug_level = 0; ++ int32_t powersave_level = 0; ++ bool print_graph_profile = false; ++ bool print_graph_debug = false; + }; + + struct HexagonSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef HexagonSettingsT NativeTableType; ++ typedef HexagonSettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_DEBUG_LEVEL = 4, + VT_POWERSAVE_LEVEL = 6, +@@ -1262,10 +1269,10 @@ struct HexagonSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_DEBUG_LEVEL) && +- VerifyField(verifier, VT_POWERSAVE_LEVEL) && +- VerifyField(verifier, VT_PRINT_GRAPH_PROFILE) && +- VerifyField(verifier, VT_PRINT_GRAPH_DEBUG) && ++ VerifyField(verifier, VT_DEBUG_LEVEL, 4) && ++ VerifyField(verifier, VT_POWERSAVE_LEVEL, 4) && ++ VerifyField(verifier, VT_PRINT_GRAPH_PROFILE, 1) && ++ VerifyField(verifier, VT_PRINT_GRAPH_DEBUG, 1) && + verifier.EndTable(); + } + HexagonSettingsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -1274,6 +1281,7 @@ struct HexagonSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct HexagonSettingsBuilder { ++ typedef HexagonSettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_debug_level(int32_t debug_level) { +@@ -1292,7 +1300,6 @@ struct HexagonSettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- HexagonSettingsBuilder &operator=(const HexagonSettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -1318,14 +1325,12 @@ flatbuffers::Offset CreateHexagonSettings(flatbuffers::FlatBuff + + struct XNNPackSettingsT : public flatbuffers::NativeTable { + typedef XNNPackSettings TableType; +- int32_t num_threads; +- XNNPackSettingsT() +- : num_threads(0) { +- } ++ int32_t num_threads = 0; + }; + + struct XNNPackSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef XNNPackSettingsT NativeTableType; ++ typedef XNNPackSettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NUM_THREADS = 4 + }; +@@ -1334,7 +1339,7 @@ struct XNNPackSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_NUM_THREADS) && ++ VerifyField(verifier, VT_NUM_THREADS, 4) && + verifier.EndTable(); + } + XNNPackSettingsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -1343,6 +1348,7 @@ struct XNNPackSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct XNNPackSettingsBuilder { ++ typedef XNNPackSettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_num_threads(int32_t num_threads) { +@@ -1352,7 +1358,6 @@ struct XNNPackSettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- XNNPackSettingsBuilder &operator=(const XNNPackSettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -1372,20 +1377,15 @@ flatbuffers::Offset CreateXNNPackSettings(flatbuffers::FlatBuff + + struct CoreMLSettingsT : public flatbuffers::NativeTable { + typedef CoreMLSettings TableType; +- tflite::CoreMLSettings_::EnabledDevices enabled_devices; +- int32_t coreml_version; +- int32_t max_delegated_partitions; +- int32_t min_nodes_per_partition; +- CoreMLSettingsT() +- : enabled_devices(tflite::CoreMLSettings_::EnabledDevices_DEVICES_ALL), +- coreml_version(0), +- max_delegated_partitions(0), +- min_nodes_per_partition(2) { +- } ++ tflite::CoreMLSettings_::EnabledDevices enabled_devices = tflite::CoreMLSettings_::EnabledDevices_DEVICES_ALL; ++ int32_t coreml_version = 0; ++ int32_t max_delegated_partitions = 0; ++ int32_t min_nodes_per_partition = 2; + }; + + struct CoreMLSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef CoreMLSettingsT NativeTableType; ++ typedef CoreMLSettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_ENABLED_DEVICES = 4, + VT_COREML_VERSION = 6, +@@ -1406,10 +1406,10 @@ struct CoreMLSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_ENABLED_DEVICES) && +- VerifyField(verifier, VT_COREML_VERSION) && +- VerifyField(verifier, VT_MAX_DELEGATED_PARTITIONS) && +- VerifyField(verifier, VT_MIN_NODES_PER_PARTITION) && ++ VerifyField(verifier, VT_ENABLED_DEVICES, 4) && ++ VerifyField(verifier, VT_COREML_VERSION, 4) && ++ VerifyField(verifier, VT_MAX_DELEGATED_PARTITIONS, 4) && ++ VerifyField(verifier, VT_MIN_NODES_PER_PARTITION, 4) && + verifier.EndTable(); + } + CoreMLSettingsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -1418,6 +1418,7 @@ struct CoreMLSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct CoreMLSettingsBuilder { ++ typedef CoreMLSettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_enabled_devices(tflite::CoreMLSettings_::EnabledDevices enabled_devices) { +@@ -1436,7 +1437,6 @@ struct CoreMLSettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- CoreMLSettingsBuilder &operator=(const CoreMLSettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -1462,19 +1462,15 @@ flatbuffers::Offset CreateCoreMLSettings(flatbuffers::FlatBuffer + + struct EdgeTpuDeviceSpecT : public flatbuffers::NativeTable { + typedef EdgeTpuDeviceSpec TableType; +- tflite::EdgeTpuDeviceSpec_::PlatformType platform_type; +- int32_t num_chips; +- std::vector device_paths; +- int32_t chip_family; +- EdgeTpuDeviceSpecT() +- : platform_type(tflite::EdgeTpuDeviceSpec_::PlatformType_MMIO), +- num_chips(0), +- chip_family(0) { +- } ++ tflite::EdgeTpuDeviceSpec_::PlatformType platform_type = tflite::EdgeTpuDeviceSpec_::PlatformType_MMIO; ++ int32_t num_chips = 0; ++ std::vector device_paths{}; ++ int32_t chip_family = 0; + }; + + struct EdgeTpuDeviceSpec FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef EdgeTpuDeviceSpecT NativeTableType; ++ typedef EdgeTpuDeviceSpecBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_PLATFORM_TYPE = 4, + VT_NUM_CHIPS = 6, +@@ -1495,12 +1491,12 @@ struct EdgeTpuDeviceSpec FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_PLATFORM_TYPE) && +- VerifyField(verifier, VT_NUM_CHIPS) && ++ VerifyField(verifier, VT_PLATFORM_TYPE, 4) && ++ VerifyField(verifier, VT_NUM_CHIPS, 4) && + VerifyOffset(verifier, VT_DEVICE_PATHS) && + verifier.VerifyVector(device_paths()) && + verifier.VerifyVectorOfStrings(device_paths()) && +- VerifyField(verifier, VT_CHIP_FAMILY) && ++ VerifyField(verifier, VT_CHIP_FAMILY, 4) && + verifier.EndTable(); + } + EdgeTpuDeviceSpecT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -1509,6 +1505,7 @@ struct EdgeTpuDeviceSpec FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct EdgeTpuDeviceSpecBuilder { ++ typedef EdgeTpuDeviceSpec Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_platform_type(tflite::EdgeTpuDeviceSpec_::PlatformType platform_type) { +@@ -1527,7 +1524,6 @@ struct EdgeTpuDeviceSpecBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- EdgeTpuDeviceSpecBuilder &operator=(const EdgeTpuDeviceSpecBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -1568,16 +1564,13 @@ flatbuffers::Offset CreateEdgeTpuDeviceSpec(flatbuffers::Flat + + struct EdgeTpuInactivePowerConfigT : public flatbuffers::NativeTable { + typedef EdgeTpuInactivePowerConfig TableType; +- tflite::EdgeTpuPowerState inactive_power_state; +- int64_t inactive_timeout_us; +- EdgeTpuInactivePowerConfigT() +- : inactive_power_state(tflite::EdgeTpuPowerState_UNDEFINED_POWERSTATE), +- inactive_timeout_us(0) { +- } ++ tflite::EdgeTpuPowerState inactive_power_state = tflite::EdgeTpuPowerState_UNDEFINED_POWERSTATE; ++ int64_t inactive_timeout_us = 0; + }; + + struct EdgeTpuInactivePowerConfig FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef EdgeTpuInactivePowerConfigT NativeTableType; ++ typedef EdgeTpuInactivePowerConfigBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_INACTIVE_POWER_STATE = 4, + VT_INACTIVE_TIMEOUT_US = 6 +@@ -1590,8 +1583,8 @@ struct EdgeTpuInactivePowerConfig FLATBUFFERS_FINAL_CLASS : private flatbuffers: + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_INACTIVE_POWER_STATE) && +- VerifyField(verifier, VT_INACTIVE_TIMEOUT_US) && ++ VerifyField(verifier, VT_INACTIVE_POWER_STATE, 4) && ++ VerifyField(verifier, VT_INACTIVE_TIMEOUT_US, 8) && + verifier.EndTable(); + } + EdgeTpuInactivePowerConfigT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -1600,6 +1593,7 @@ struct EdgeTpuInactivePowerConfig FLATBUFFERS_FINAL_CLASS : private flatbuffers: + }; + + struct EdgeTpuInactivePowerConfigBuilder { ++ typedef EdgeTpuInactivePowerConfig Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_inactive_power_state(tflite::EdgeTpuPowerState inactive_power_state) { +@@ -1612,7 +1606,6 @@ struct EdgeTpuInactivePowerConfigBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- EdgeTpuInactivePowerConfigBuilder &operator=(const EdgeTpuInactivePowerConfigBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -1634,23 +1627,22 @@ flatbuffers::Offset CreateEdgeTpuInactivePowerConfig + + struct EdgeTpuSettingsT : public flatbuffers::NativeTable { + typedef EdgeTpuSettings TableType; +- tflite::EdgeTpuPowerState inference_power_state; +- std::vector> inactive_power_configs; +- int32_t inference_priority; +- std::unique_ptr edgetpu_device_spec; +- std::string model_token; +- tflite::EdgeTpuSettings_::FloatTruncationType float_truncation_type; +- tflite::EdgeTpuSettings_::QosClass qos_class; +- EdgeTpuSettingsT() +- : inference_power_state(tflite::EdgeTpuPowerState_UNDEFINED_POWERSTATE), +- inference_priority(-1), +- float_truncation_type(tflite::EdgeTpuSettings_::FloatTruncationType_UNSPECIFIED), +- qos_class(tflite::EdgeTpuSettings_::QosClass_QOS_UNDEFINED) { +- } ++ tflite::EdgeTpuPowerState inference_power_state = tflite::EdgeTpuPowerState_UNDEFINED_POWERSTATE; ++ std::vector> inactive_power_configs{}; ++ int32_t inference_priority = -1; ++ std::unique_ptr edgetpu_device_spec{}; ++ std::string model_token{}; ++ tflite::EdgeTpuSettings_::FloatTruncationType float_truncation_type = tflite::EdgeTpuSettings_::FloatTruncationType_UNSPECIFIED; ++ tflite::EdgeTpuSettings_::QosClass qos_class = tflite::EdgeTpuSettings_::QosClass_QOS_UNDEFINED; ++ EdgeTpuSettingsT() = default; ++ EdgeTpuSettingsT(const EdgeTpuSettingsT &o); ++ EdgeTpuSettingsT(EdgeTpuSettingsT&&) FLATBUFFERS_NOEXCEPT = default; ++ EdgeTpuSettingsT &operator=(EdgeTpuSettingsT o) FLATBUFFERS_NOEXCEPT; + }; + + struct EdgeTpuSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef EdgeTpuSettingsT NativeTableType; ++ typedef EdgeTpuSettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_INFERENCE_POWER_STATE = 4, + VT_INACTIVE_POWER_CONFIGS = 6, +@@ -1683,17 +1675,17 @@ struct EdgeTpuSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_INFERENCE_POWER_STATE) && ++ VerifyField(verifier, VT_INFERENCE_POWER_STATE, 4) && + VerifyOffset(verifier, VT_INACTIVE_POWER_CONFIGS) && + verifier.VerifyVector(inactive_power_configs()) && + verifier.VerifyVectorOfTables(inactive_power_configs()) && +- VerifyField(verifier, VT_INFERENCE_PRIORITY) && ++ VerifyField(verifier, VT_INFERENCE_PRIORITY, 4) && + VerifyOffset(verifier, VT_EDGETPU_DEVICE_SPEC) && + verifier.VerifyTable(edgetpu_device_spec()) && + VerifyOffset(verifier, VT_MODEL_TOKEN) && + verifier.VerifyString(model_token()) && +- VerifyField(verifier, VT_FLOAT_TRUNCATION_TYPE) && +- VerifyField(verifier, VT_QOS_CLASS) && ++ VerifyField(verifier, VT_FLOAT_TRUNCATION_TYPE, 4) && ++ VerifyField(verifier, VT_QOS_CLASS, 4) && + verifier.EndTable(); + } + EdgeTpuSettingsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -1702,6 +1694,7 @@ struct EdgeTpuSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct EdgeTpuSettingsBuilder { ++ typedef EdgeTpuSettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_inference_power_state(tflite::EdgeTpuPowerState inference_power_state) { +@@ -1729,7 +1722,6 @@ struct EdgeTpuSettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- EdgeTpuSettingsBuilder &operator=(const EdgeTpuSettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -1783,19 +1775,15 @@ flatbuffers::Offset CreateEdgeTpuSettings(flatbuffers::FlatBuff + + struct CoralSettingsT : public flatbuffers::NativeTable { + typedef CoralSettings TableType; +- std::string device; +- tflite::CoralSettings_::Performance performance; +- bool usb_always_dfu; +- int32_t usb_max_bulk_in_queue_length; +- CoralSettingsT() +- : performance(tflite::CoralSettings_::Performance_UNDEFINED), +- usb_always_dfu(false), +- usb_max_bulk_in_queue_length(0) { +- } ++ std::string device{}; ++ tflite::CoralSettings_::Performance performance = tflite::CoralSettings_::Performance_UNDEFINED; ++ bool usb_always_dfu = false; ++ int32_t usb_max_bulk_in_queue_length = 0; + }; + + struct CoralSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef CoralSettingsT NativeTableType; ++ typedef CoralSettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_DEVICE = 4, + VT_PERFORMANCE = 6, +@@ -1818,9 +1806,9 @@ struct CoralSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_DEVICE) && + verifier.VerifyString(device()) && +- VerifyField(verifier, VT_PERFORMANCE) && +- VerifyField(verifier, VT_USB_ALWAYS_DFU) && +- VerifyField(verifier, VT_USB_MAX_BULK_IN_QUEUE_LENGTH) && ++ VerifyField(verifier, VT_PERFORMANCE, 4) && ++ VerifyField(verifier, VT_USB_ALWAYS_DFU, 1) && ++ VerifyField(verifier, VT_USB_MAX_BULK_IN_QUEUE_LENGTH, 4) && + verifier.EndTable(); + } + CoralSettingsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -1829,6 +1817,7 @@ struct CoralSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct CoralSettingsBuilder { ++ typedef CoralSettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_device(flatbuffers::Offset device) { +@@ -1847,7 +1836,6 @@ struct CoralSettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- CoralSettingsBuilder &operator=(const CoralSettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -1888,14 +1876,12 @@ flatbuffers::Offset CreateCoralSettings(flatbuffers::FlatBufferBu + + struct CPUSettingsT : public flatbuffers::NativeTable { + typedef CPUSettings TableType; +- int32_t num_threads; +- CPUSettingsT() +- : num_threads(-1) { +- } ++ int32_t num_threads = -1; + }; + + struct CPUSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef CPUSettingsT NativeTableType; ++ typedef CPUSettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NUM_THREADS = 4 + }; +@@ -1904,7 +1890,7 @@ struct CPUSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_NUM_THREADS) && ++ VerifyField(verifier, VT_NUM_THREADS, 4) && + verifier.EndTable(); + } + CPUSettingsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -1913,6 +1899,7 @@ struct CPUSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct CPUSettingsBuilder { ++ typedef CPUSettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_num_threads(int32_t num_threads) { +@@ -1922,7 +1909,6 @@ struct CPUSettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- CPUSettingsBuilder &operator=(const CPUSettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -1942,25 +1928,26 @@ flatbuffers::Offset CreateCPUSettings(flatbuffers::FlatBufferBuilde + + struct TFLiteSettingsT : public flatbuffers::NativeTable { + typedef TFLiteSettings TableType; +- tflite::Delegate delegate; +- std::unique_ptr nnapi_settings; +- std::unique_ptr gpu_settings; +- std::unique_ptr hexagon_settings; +- std::unique_ptr xnnpack_settings; +- std::unique_ptr coreml_settings; +- std::unique_ptr cpu_settings; +- int32_t max_delegated_partitions; +- std::unique_ptr edgetpu_settings; +- std::unique_ptr coral_settings; +- std::unique_ptr fallback_settings; +- TFLiteSettingsT() +- : delegate(tflite::Delegate_NONE), +- max_delegated_partitions(0) { +- } ++ tflite::Delegate delegate = tflite::Delegate_NONE; ++ std::unique_ptr nnapi_settings{}; ++ std::unique_ptr gpu_settings{}; ++ std::unique_ptr hexagon_settings{}; ++ std::unique_ptr xnnpack_settings{}; ++ std::unique_ptr coreml_settings{}; ++ std::unique_ptr cpu_settings{}; ++ int32_t max_delegated_partitions = 0; ++ std::unique_ptr edgetpu_settings{}; ++ std::unique_ptr coral_settings{}; ++ std::unique_ptr fallback_settings{}; ++ TFLiteSettingsT() = default; ++ TFLiteSettingsT(const TFLiteSettingsT &o); ++ TFLiteSettingsT(TFLiteSettingsT&&) FLATBUFFERS_NOEXCEPT = default; ++ TFLiteSettingsT &operator=(TFLiteSettingsT o) FLATBUFFERS_NOEXCEPT; + }; + + struct TFLiteSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef TFLiteSettingsT NativeTableType; ++ typedef TFLiteSettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_DELEGATE = 4, + VT_NNAPI_SETTINGS = 6, +@@ -2009,7 +1996,7 @@ struct TFLiteSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_DELEGATE) && ++ VerifyField(verifier, VT_DELEGATE, 4) && + VerifyOffset(verifier, VT_NNAPI_SETTINGS) && + verifier.VerifyTable(nnapi_settings()) && + VerifyOffset(verifier, VT_GPU_SETTINGS) && +@@ -2022,7 +2009,7 @@ struct TFLiteSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + verifier.VerifyTable(coreml_settings()) && + VerifyOffset(verifier, VT_CPU_SETTINGS) && + verifier.VerifyTable(cpu_settings()) && +- VerifyField(verifier, VT_MAX_DELEGATED_PARTITIONS) && ++ VerifyField(verifier, VT_MAX_DELEGATED_PARTITIONS, 4) && + VerifyOffset(verifier, VT_EDGETPU_SETTINGS) && + verifier.VerifyTable(edgetpu_settings()) && + VerifyOffset(verifier, VT_CORAL_SETTINGS) && +@@ -2037,6 +2024,7 @@ struct TFLiteSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct TFLiteSettingsBuilder { ++ typedef TFLiteSettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_delegate(tflite::Delegate delegate) { +@@ -2076,7 +2064,6 @@ struct TFLiteSettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- TFLiteSettingsBuilder &operator=(const TFLiteSettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -2116,16 +2103,13 @@ flatbuffers::Offset CreateTFLiteSettings(flatbuffers::FlatBuffer + + struct FallbackSettingsT : public flatbuffers::NativeTable { + typedef FallbackSettings TableType; +- bool allow_automatic_fallback_on_compilation_error; +- bool allow_automatic_fallback_on_execution_error; +- FallbackSettingsT() +- : allow_automatic_fallback_on_compilation_error(false), +- allow_automatic_fallback_on_execution_error(false) { +- } ++ bool allow_automatic_fallback_on_compilation_error = false; ++ bool allow_automatic_fallback_on_execution_error = false; + }; + + struct FallbackSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef FallbackSettingsT NativeTableType; ++ typedef FallbackSettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_ALLOW_AUTOMATIC_FALLBACK_ON_COMPILATION_ERROR = 4, + VT_ALLOW_AUTOMATIC_FALLBACK_ON_EXECUTION_ERROR = 6 +@@ -2138,8 +2122,8 @@ struct FallbackSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_ALLOW_AUTOMATIC_FALLBACK_ON_COMPILATION_ERROR) && +- VerifyField(verifier, VT_ALLOW_AUTOMATIC_FALLBACK_ON_EXECUTION_ERROR) && ++ VerifyField(verifier, VT_ALLOW_AUTOMATIC_FALLBACK_ON_COMPILATION_ERROR, 1) && ++ VerifyField(verifier, VT_ALLOW_AUTOMATIC_FALLBACK_ON_EXECUTION_ERROR, 1) && + verifier.EndTable(); + } + FallbackSettingsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -2148,6 +2132,7 @@ struct FallbackSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct FallbackSettingsBuilder { ++ typedef FallbackSettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_allow_automatic_fallback_on_compilation_error(bool allow_automatic_fallback_on_compilation_error) { +@@ -2160,7 +2145,6 @@ struct FallbackSettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- FallbackSettingsBuilder &operator=(const FallbackSettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -2182,14 +2166,13 @@ flatbuffers::Offset CreateFallbackSettings(flatbuffers::FlatBu + + struct BenchmarkMetricT : public flatbuffers::NativeTable { + typedef BenchmarkMetric TableType; +- std::string name; +- std::vector values; +- BenchmarkMetricT() { +- } ++ std::string name{}; ++ std::vector values{}; + }; + + struct BenchmarkMetric FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BenchmarkMetricT NativeTableType; ++ typedef BenchmarkMetricBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NAME = 4, + VT_VALUES = 6 +@@ -2214,6 +2197,7 @@ struct BenchmarkMetric FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct BenchmarkMetricBuilder { ++ typedef BenchmarkMetric Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_name(flatbuffers::Offset name) { +@@ -2226,7 +2210,6 @@ struct BenchmarkMetricBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BenchmarkMetricBuilder &operator=(const BenchmarkMetricBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -2260,19 +2243,20 @@ flatbuffers::Offset CreateBenchmarkMetric(flatbuffers::FlatBuff + + struct BenchmarkResultT : public flatbuffers::NativeTable { + typedef BenchmarkResult TableType; +- std::vector initialization_time_us; +- std::vector inference_time_us; +- int32_t max_memory_kb; +- bool ok; +- std::vector> metrics; +- BenchmarkResultT() +- : max_memory_kb(0), +- ok(false) { +- } ++ std::vector initialization_time_us{}; ++ std::vector inference_time_us{}; ++ int32_t max_memory_kb = 0; ++ bool ok = false; ++ std::vector> metrics{}; ++ BenchmarkResultT() = default; ++ BenchmarkResultT(const BenchmarkResultT &o); ++ BenchmarkResultT(BenchmarkResultT&&) FLATBUFFERS_NOEXCEPT = default; ++ BenchmarkResultT &operator=(BenchmarkResultT o) FLATBUFFERS_NOEXCEPT; + }; + + struct BenchmarkResult FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BenchmarkResultT NativeTableType; ++ typedef BenchmarkResultBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_INITIALIZATION_TIME_US = 4, + VT_INFERENCE_TIME_US = 6, +@@ -2301,8 +2285,8 @@ struct BenchmarkResult FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + verifier.VerifyVector(initialization_time_us()) && + VerifyOffset(verifier, VT_INFERENCE_TIME_US) && + verifier.VerifyVector(inference_time_us()) && +- VerifyField(verifier, VT_MAX_MEMORY_KB) && +- VerifyField(verifier, VT_OK) && ++ VerifyField(verifier, VT_MAX_MEMORY_KB, 4) && ++ VerifyField(verifier, VT_OK, 1) && + VerifyOffset(verifier, VT_METRICS) && + verifier.VerifyVector(metrics()) && + verifier.VerifyVectorOfTables(metrics()) && +@@ -2314,6 +2298,7 @@ struct BenchmarkResult FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct BenchmarkResultBuilder { ++ typedef BenchmarkResult Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_initialization_time_us(flatbuffers::Offset> initialization_time_us) { +@@ -2335,7 +2320,6 @@ struct BenchmarkResultBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BenchmarkResultBuilder &operator=(const BenchmarkResultBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -2382,18 +2366,14 @@ flatbuffers::Offset CreateBenchmarkResult(flatbuffers::FlatBuff + + struct ErrorCodeT : public flatbuffers::NativeTable { + typedef ErrorCode TableType; +- tflite::Delegate source; +- int32_t tflite_error; +- int64_t underlying_api_error; +- ErrorCodeT() +- : source(tflite::Delegate_NONE), +- tflite_error(0), +- underlying_api_error(0) { +- } ++ tflite::Delegate source = tflite::Delegate_NONE; ++ int32_t tflite_error = 0; ++ int64_t underlying_api_error = 0; + }; + + struct ErrorCode FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ErrorCodeT NativeTableType; ++ typedef ErrorCodeBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_SOURCE = 4, + VT_TFLITE_ERROR = 6, +@@ -2410,9 +2390,9 @@ struct ErrorCode FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_SOURCE) && +- VerifyField(verifier, VT_TFLITE_ERROR) && +- VerifyField(verifier, VT_UNDERLYING_API_ERROR) && ++ VerifyField(verifier, VT_SOURCE, 4) && ++ VerifyField(verifier, VT_TFLITE_ERROR, 4) && ++ VerifyField(verifier, VT_UNDERLYING_API_ERROR, 8) && + verifier.EndTable(); + } + ErrorCodeT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -2421,6 +2401,7 @@ struct ErrorCode FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ErrorCodeBuilder { ++ typedef ErrorCode Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_source(tflite::Delegate source) { +@@ -2436,7 +2417,6 @@ struct ErrorCodeBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ErrorCodeBuilder &operator=(const ErrorCodeBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -2460,21 +2440,20 @@ flatbuffers::Offset CreateErrorCode(flatbuffers::FlatBufferBuilder &_ + + struct BenchmarkErrorT : public flatbuffers::NativeTable { + typedef BenchmarkError TableType; +- tflite::BenchmarkStage stage; +- int32_t exit_code; +- int32_t signal; +- std::vector> error_code; +- int32_t mini_benchmark_error_code; +- BenchmarkErrorT() +- : stage(tflite::BenchmarkStage_UNKNOWN), +- exit_code(0), +- signal(0), +- mini_benchmark_error_code(0) { +- } ++ tflite::BenchmarkStage stage = tflite::BenchmarkStage_UNKNOWN; ++ int32_t exit_code = 0; ++ int32_t signal = 0; ++ std::vector> error_code{}; ++ int32_t mini_benchmark_error_code = 0; ++ BenchmarkErrorT() = default; ++ BenchmarkErrorT(const BenchmarkErrorT &o); ++ BenchmarkErrorT(BenchmarkErrorT&&) FLATBUFFERS_NOEXCEPT = default; ++ BenchmarkErrorT &operator=(BenchmarkErrorT o) FLATBUFFERS_NOEXCEPT; + }; + + struct BenchmarkError FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BenchmarkErrorT NativeTableType; ++ typedef BenchmarkErrorBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_STAGE = 4, + VT_EXIT_CODE = 6, +@@ -2499,13 +2478,13 @@ struct BenchmarkError FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_STAGE) && +- VerifyField(verifier, VT_EXIT_CODE) && +- VerifyField(verifier, VT_SIGNAL) && ++ VerifyField(verifier, VT_STAGE, 4) && ++ VerifyField(verifier, VT_EXIT_CODE, 4) && ++ VerifyField(verifier, VT_SIGNAL, 4) && + VerifyOffset(verifier, VT_ERROR_CODE) && + verifier.VerifyVector(error_code()) && + verifier.VerifyVectorOfTables(error_code()) && +- VerifyField(verifier, VT_MINI_BENCHMARK_ERROR_CODE) && ++ VerifyField(verifier, VT_MINI_BENCHMARK_ERROR_CODE, 4) && + verifier.EndTable(); + } + BenchmarkErrorT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -2514,6 +2493,7 @@ struct BenchmarkError FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct BenchmarkErrorBuilder { ++ typedef BenchmarkError Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_stage(tflite::BenchmarkStage stage) { +@@ -2535,7 +2515,6 @@ struct BenchmarkErrorBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BenchmarkErrorBuilder &operator=(const BenchmarkErrorBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -2580,21 +2559,21 @@ flatbuffers::Offset CreateBenchmarkError(flatbuffers::FlatBuffer + + struct BenchmarkEventT : public flatbuffers::NativeTable { + typedef BenchmarkEvent TableType; +- std::unique_ptr tflite_settings; +- tflite::BenchmarkEventType event_type; +- std::unique_ptr result; +- std::unique_ptr error; +- int64_t boottime_us; +- int64_t wallclock_us; +- BenchmarkEventT() +- : event_type(tflite::BenchmarkEventType_UNDEFINED_BENCHMARK_EVENT_TYPE), +- boottime_us(0), +- wallclock_us(0) { +- } ++ std::unique_ptr tflite_settings{}; ++ tflite::BenchmarkEventType event_type = tflite::BenchmarkEventType_UNDEFINED_BENCHMARK_EVENT_TYPE; ++ std::unique_ptr result{}; ++ std::unique_ptr error{}; ++ int64_t boottime_us = 0; ++ int64_t wallclock_us = 0; ++ BenchmarkEventT() = default; ++ BenchmarkEventT(const BenchmarkEventT &o); ++ BenchmarkEventT(BenchmarkEventT&&) FLATBUFFERS_NOEXCEPT = default; ++ BenchmarkEventT &operator=(BenchmarkEventT o) FLATBUFFERS_NOEXCEPT; + }; + + struct BenchmarkEvent FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BenchmarkEventT NativeTableType; ++ typedef BenchmarkEventBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_TFLITE_SETTINGS = 4, + VT_EVENT_TYPE = 6, +@@ -2625,13 +2604,13 @@ struct BenchmarkEvent FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_TFLITE_SETTINGS) && + verifier.VerifyTable(tflite_settings()) && +- VerifyField(verifier, VT_EVENT_TYPE) && ++ VerifyField(verifier, VT_EVENT_TYPE, 4) && + VerifyOffset(verifier, VT_RESULT) && + verifier.VerifyTable(result()) && + VerifyOffset(verifier, VT_ERROR) && + verifier.VerifyTable(error()) && +- VerifyField(verifier, VT_BOOTTIME_US) && +- VerifyField(verifier, VT_WALLCLOCK_US) && ++ VerifyField(verifier, VT_BOOTTIME_US, 8) && ++ VerifyField(verifier, VT_WALLCLOCK_US, 8) && + verifier.EndTable(); + } + BenchmarkEventT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -2640,6 +2619,7 @@ struct BenchmarkEvent FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct BenchmarkEventBuilder { ++ typedef BenchmarkEvent Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_tflite_settings(flatbuffers::Offset tflite_settings) { +@@ -2664,7 +2644,6 @@ struct BenchmarkEventBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BenchmarkEventBuilder &operator=(const BenchmarkEventBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -2694,17 +2673,18 @@ flatbuffers::Offset CreateBenchmarkEvent(flatbuffers::FlatBuffer + + struct BestAccelerationDecisionT : public flatbuffers::NativeTable { + typedef BestAccelerationDecision TableType; +- int32_t number_of_source_events; +- std::unique_ptr min_latency_event; +- int64_t min_inference_time_us; +- BestAccelerationDecisionT() +- : number_of_source_events(0), +- min_inference_time_us(0) { +- } ++ int32_t number_of_source_events = 0; ++ std::unique_ptr min_latency_event{}; ++ int64_t min_inference_time_us = 0; ++ BestAccelerationDecisionT() = default; ++ BestAccelerationDecisionT(const BestAccelerationDecisionT &o); ++ BestAccelerationDecisionT(BestAccelerationDecisionT&&) FLATBUFFERS_NOEXCEPT = default; ++ BestAccelerationDecisionT &operator=(BestAccelerationDecisionT o) FLATBUFFERS_NOEXCEPT; + }; + + struct BestAccelerationDecision FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BestAccelerationDecisionT NativeTableType; ++ typedef BestAccelerationDecisionBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_NUMBER_OF_SOURCE_EVENTS = 4, + VT_MIN_LATENCY_EVENT = 6, +@@ -2721,10 +2701,10 @@ struct BestAccelerationDecision FLATBUFFERS_FINAL_CLASS : private flatbuffers::T + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_NUMBER_OF_SOURCE_EVENTS) && ++ VerifyField(verifier, VT_NUMBER_OF_SOURCE_EVENTS, 4) && + VerifyOffset(verifier, VT_MIN_LATENCY_EVENT) && + verifier.VerifyTable(min_latency_event()) && +- VerifyField(verifier, VT_MIN_INFERENCE_TIME_US) && ++ VerifyField(verifier, VT_MIN_INFERENCE_TIME_US, 8) && + verifier.EndTable(); + } + BestAccelerationDecisionT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -2733,6 +2713,7 @@ struct BestAccelerationDecision FLATBUFFERS_FINAL_CLASS : private flatbuffers::T + }; + + struct BestAccelerationDecisionBuilder { ++ typedef BestAccelerationDecision Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_number_of_source_events(int32_t number_of_source_events) { +@@ -2748,7 +2729,6 @@ struct BestAccelerationDecisionBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BestAccelerationDecisionBuilder &operator=(const BestAccelerationDecisionBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -2772,14 +2752,12 @@ flatbuffers::Offset CreateBestAccelerationDecision(fla + + struct BenchmarkInitializationFailureT : public flatbuffers::NativeTable { + typedef BenchmarkInitializationFailure TableType; +- int32_t initialization_status; +- BenchmarkInitializationFailureT() +- : initialization_status(0) { +- } ++ int32_t initialization_status = 0; + }; + + struct BenchmarkInitializationFailure FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BenchmarkInitializationFailureT NativeTableType; ++ typedef BenchmarkInitializationFailureBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_INITIALIZATION_STATUS = 4 + }; +@@ -2788,7 +2766,7 @@ struct BenchmarkInitializationFailure FLATBUFFERS_FINAL_CLASS : private flatbuff + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_INITIALIZATION_STATUS) && ++ VerifyField(verifier, VT_INITIALIZATION_STATUS, 4) && + verifier.EndTable(); + } + BenchmarkInitializationFailureT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -2797,6 +2775,7 @@ struct BenchmarkInitializationFailure FLATBUFFERS_FINAL_CLASS : private flatbuff + }; + + struct BenchmarkInitializationFailureBuilder { ++ typedef BenchmarkInitializationFailure Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_initialization_status(int32_t initialization_status) { +@@ -2806,7 +2785,6 @@ struct BenchmarkInitializationFailureBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BenchmarkInitializationFailureBuilder &operator=(const BenchmarkInitializationFailureBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -2826,17 +2804,19 @@ flatbuffers::Offset CreateBenchmarkInitializatio + + struct MiniBenchmarkEventT : public flatbuffers::NativeTable { + typedef MiniBenchmarkEvent TableType; +- bool is_log_flushing_event; +- std::unique_ptr best_acceleration_decision; +- std::unique_ptr initialization_failure; +- std::unique_ptr benchmark_event; +- MiniBenchmarkEventT() +- : is_log_flushing_event(false) { +- } ++ bool is_log_flushing_event = false; ++ std::unique_ptr best_acceleration_decision{}; ++ std::unique_ptr initialization_failure{}; ++ std::unique_ptr benchmark_event{}; ++ MiniBenchmarkEventT() = default; ++ MiniBenchmarkEventT(const MiniBenchmarkEventT &o); ++ MiniBenchmarkEventT(MiniBenchmarkEventT&&) FLATBUFFERS_NOEXCEPT = default; ++ MiniBenchmarkEventT &operator=(MiniBenchmarkEventT o) FLATBUFFERS_NOEXCEPT; + }; + + struct MiniBenchmarkEvent FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef MiniBenchmarkEventT NativeTableType; ++ typedef MiniBenchmarkEventBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_IS_LOG_FLUSHING_EVENT = 4, + VT_BEST_ACCELERATION_DECISION = 6, +@@ -2857,7 +2837,7 @@ struct MiniBenchmarkEvent FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_IS_LOG_FLUSHING_EVENT) && ++ VerifyField(verifier, VT_IS_LOG_FLUSHING_EVENT, 1) && + VerifyOffset(verifier, VT_BEST_ACCELERATION_DECISION) && + verifier.VerifyTable(best_acceleration_decision()) && + VerifyOffset(verifier, VT_INITIALIZATION_FAILURE) && +@@ -2872,6 +2852,7 @@ struct MiniBenchmarkEvent FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct MiniBenchmarkEventBuilder { ++ typedef MiniBenchmarkEvent Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_is_log_flushing_event(bool is_log_flushing_event) { +@@ -2890,7 +2871,6 @@ struct MiniBenchmarkEventBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- MiniBenchmarkEventBuilder &operator=(const MiniBenchmarkEventBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -2916,19 +2896,15 @@ flatbuffers::Offset CreateMiniBenchmarkEvent(flatbuffers::Fl + + struct ModelFileT : public flatbuffers::NativeTable { + typedef ModelFile TableType; +- std::string filename; +- int64_t fd; +- int64_t offset; +- int64_t length; +- ModelFileT() +- : fd(0), +- offset(0), +- length(0) { +- } ++ std::string filename{}; ++ int64_t fd = 0; ++ int64_t offset = 0; ++ int64_t length = 0; + }; + + struct ModelFile FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef ModelFileT NativeTableType; ++ typedef ModelFileBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_FILENAME = 4, + VT_FD = 6, +@@ -2951,9 +2927,9 @@ struct ModelFile FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_FILENAME) && + verifier.VerifyString(filename()) && +- VerifyField(verifier, VT_FD) && +- VerifyField(verifier, VT_OFFSET) && +- VerifyField(verifier, VT_LENGTH) && ++ VerifyField(verifier, VT_FD, 8) && ++ VerifyField(verifier, VT_OFFSET, 8) && ++ VerifyField(verifier, VT_LENGTH, 8) && + verifier.EndTable(); + } + ModelFileT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -2962,6 +2938,7 @@ struct ModelFile FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + }; + + struct ModelFileBuilder { ++ typedef ModelFile Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_filename(flatbuffers::Offset filename) { +@@ -2980,7 +2957,6 @@ struct ModelFileBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- ModelFileBuilder &operator=(const ModelFileBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -3021,14 +2997,13 @@ flatbuffers::Offset CreateModelFile(flatbuffers::FlatBufferBuilder &_ + + struct BenchmarkStoragePathsT : public flatbuffers::NativeTable { + typedef BenchmarkStoragePaths TableType; +- std::string storage_file_path; +- std::string data_directory_path; +- BenchmarkStoragePathsT() { +- } ++ std::string storage_file_path{}; ++ std::string data_directory_path{}; + }; + + struct BenchmarkStoragePaths FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef BenchmarkStoragePathsT NativeTableType; ++ typedef BenchmarkStoragePathsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_STORAGE_FILE_PATH = 4, + VT_DATA_DIRECTORY_PATH = 6 +@@ -3053,6 +3028,7 @@ struct BenchmarkStoragePaths FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tabl + }; + + struct BenchmarkStoragePathsBuilder { ++ typedef BenchmarkStoragePaths Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_storage_file_path(flatbuffers::Offset storage_file_path) { +@@ -3065,7 +3041,6 @@ struct BenchmarkStoragePathsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- BenchmarkStoragePathsBuilder &operator=(const BenchmarkStoragePathsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -3099,15 +3074,18 @@ flatbuffers::Offset CreateBenchmarkStoragePaths(flatbuffe + + struct MinibenchmarkSettingsT : public flatbuffers::NativeTable { + typedef MinibenchmarkSettings TableType; +- std::vector> settings_to_test; +- std::unique_ptr model_file; +- std::unique_ptr storage_paths; +- MinibenchmarkSettingsT() { +- } ++ std::vector> settings_to_test{}; ++ std::unique_ptr model_file{}; ++ std::unique_ptr storage_paths{}; ++ MinibenchmarkSettingsT() = default; ++ MinibenchmarkSettingsT(const MinibenchmarkSettingsT &o); ++ MinibenchmarkSettingsT(MinibenchmarkSettingsT&&) FLATBUFFERS_NOEXCEPT = default; ++ MinibenchmarkSettingsT &operator=(MinibenchmarkSettingsT o) FLATBUFFERS_NOEXCEPT; + }; + + struct MinibenchmarkSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + typedef MinibenchmarkSettingsT NativeTableType; ++ typedef MinibenchmarkSettingsBuilder Builder; + enum FlatBuffersVTableOffset FLATBUFFERS_VTABLE_UNDERLYING_TYPE { + VT_SETTINGS_TO_TEST = 4, + VT_MODEL_FILE = 6, +@@ -3139,6 +3117,7 @@ struct MinibenchmarkSettings FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tabl + }; + + struct MinibenchmarkSettingsBuilder { ++ typedef MinibenchmarkSettings Table; + flatbuffers::FlatBufferBuilder &fbb_; + flatbuffers::uoffset_t start_; + void add_settings_to_test(flatbuffers::Offset>> settings_to_test) { +@@ -3154,7 +3133,6 @@ struct MinibenchmarkSettingsBuilder { + : fbb_(_fbb) { + start_ = fbb_.StartTable(); + } +- MinibenchmarkSettingsBuilder &operator=(const MinibenchmarkSettingsBuilder &); + flatbuffers::Offset Finish() { + const auto end = fbb_.EndTable(start_); + auto o = flatbuffers::Offset(end); +@@ -3204,20 +3182,37 @@ inline bool operator!=(const ComputeSettingsT &lhs, const ComputeSettingsT &rhs) + } + + ++inline ComputeSettingsT::ComputeSettingsT(const ComputeSettingsT &o) ++ : preference(o.preference), ++ tflite_settings((o.tflite_settings) ? new tflite::TFLiteSettingsT(*o.tflite_settings) : nullptr), ++ model_namespace_for_statistics(o.model_namespace_for_statistics), ++ model_identifier_for_statistics(o.model_identifier_for_statistics), ++ settings_to_test_locally((o.settings_to_test_locally) ? new tflite::MinibenchmarkSettingsT(*o.settings_to_test_locally) : nullptr) { ++} ++ ++inline ComputeSettingsT &ComputeSettingsT::operator=(ComputeSettingsT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(preference, o.preference); ++ std::swap(tflite_settings, o.tflite_settings); ++ std::swap(model_namespace_for_statistics, o.model_namespace_for_statistics); ++ std::swap(model_identifier_for_statistics, o.model_identifier_for_statistics); ++ std::swap(settings_to_test_locally, o.settings_to_test_locally); ++ return *this; ++} ++ + inline ComputeSettingsT *ComputeSettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ComputeSettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ComputeSettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ComputeSettings::UnPackTo(ComputeSettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; + { auto _e = preference(); _o->preference = _e; } +- { auto _e = tflite_settings(); if (_e) _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = tflite_settings(); if (_e) { if(_o->tflite_settings) { _e->UnPackTo(_o->tflite_settings.get(), _resolver); } else { _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = model_namespace_for_statistics(); if (_e) _o->model_namespace_for_statistics = _e->str(); } + { auto _e = model_identifier_for_statistics(); if (_e) _o->model_identifier_for_statistics = _e->str(); } +- { auto _e = settings_to_test_locally(); if (_e) _o->settings_to_test_locally = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = settings_to_test_locally(); if (_e) { if(_o->settings_to_test_locally) { _e->UnPackTo(_o->settings_to_test_locally.get(), _resolver); } else { _o->settings_to_test_locally = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline flatbuffers::Offset ComputeSettings::Pack(flatbuffers::FlatBufferBuilder &_fbb, const ComputeSettingsT* _o, const flatbuffers::rehasher_function_t *_rehasher) { +@@ -3264,10 +3259,41 @@ inline bool operator!=(const NNAPISettingsT &lhs, const NNAPISettingsT &rhs) { + } + + ++inline NNAPISettingsT::NNAPISettingsT(const NNAPISettingsT &o) ++ : accelerator_name(o.accelerator_name), ++ cache_directory(o.cache_directory), ++ model_token(o.model_token), ++ execution_preference(o.execution_preference), ++ no_of_nnapi_instances_to_cache(o.no_of_nnapi_instances_to_cache), ++ fallback_settings((o.fallback_settings) ? new tflite::FallbackSettingsT(*o.fallback_settings) : nullptr), ++ allow_nnapi_cpu_on_android_10_plus(o.allow_nnapi_cpu_on_android_10_plus), ++ execution_priority(o.execution_priority), ++ allow_dynamic_dimensions(o.allow_dynamic_dimensions), ++ allow_fp16_precision_for_fp32(o.allow_fp16_precision_for_fp32), ++ use_burst_computation(o.use_burst_computation), ++ support_library_handle(o.support_library_handle) { ++} ++ ++inline NNAPISettingsT &NNAPISettingsT::operator=(NNAPISettingsT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(accelerator_name, o.accelerator_name); ++ std::swap(cache_directory, o.cache_directory); ++ std::swap(model_token, o.model_token); ++ std::swap(execution_preference, o.execution_preference); ++ std::swap(no_of_nnapi_instances_to_cache, o.no_of_nnapi_instances_to_cache); ++ std::swap(fallback_settings, o.fallback_settings); ++ std::swap(allow_nnapi_cpu_on_android_10_plus, o.allow_nnapi_cpu_on_android_10_plus); ++ std::swap(execution_priority, o.execution_priority); ++ std::swap(allow_dynamic_dimensions, o.allow_dynamic_dimensions); ++ std::swap(allow_fp16_precision_for_fp32, o.allow_fp16_precision_for_fp32); ++ std::swap(use_burst_computation, o.use_burst_computation); ++ std::swap(support_library_handle, o.support_library_handle); ++ return *this; ++} ++ + inline NNAPISettingsT *NNAPISettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new NNAPISettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new NNAPISettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void NNAPISettings::UnPackTo(NNAPISettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3278,7 +3304,7 @@ inline void NNAPISettings::UnPackTo(NNAPISettingsT *_o, const flatbuffers::resol + { auto _e = model_token(); if (_e) _o->model_token = _e->str(); } + { auto _e = execution_preference(); _o->execution_preference = _e; } + { auto _e = no_of_nnapi_instances_to_cache(); _o->no_of_nnapi_instances_to_cache = _e; } +- { auto _e = fallback_settings(); if (_e) _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = fallback_settings(); if (_e) { if(_o->fallback_settings) { _e->UnPackTo(_o->fallback_settings.get(), _resolver); } else { _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = allow_nnapi_cpu_on_android_10_plus(); _o->allow_nnapi_cpu_on_android_10_plus = _e; } + { auto _e = execution_priority(); _o->execution_priority = _e; } + { auto _e = allow_dynamic_dimensions(); _o->allow_dynamic_dimensions = _e; } +@@ -3343,9 +3369,9 @@ inline bool operator!=(const GPUSettingsT &lhs, const GPUSettingsT &rhs) { + + + inline GPUSettingsT *GPUSettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new GPUSettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new GPUSettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void GPUSettings::UnPackTo(GPUSettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3407,9 +3433,9 @@ inline bool operator!=(const HexagonSettingsT &lhs, const HexagonSettingsT &rhs) + + + inline HexagonSettingsT *HexagonSettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new HexagonSettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new HexagonSettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void HexagonSettings::UnPackTo(HexagonSettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3453,9 +3479,9 @@ inline bool operator!=(const XNNPackSettingsT &lhs, const XNNPackSettingsT &rhs) + + + inline XNNPackSettingsT *XNNPackSettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new XNNPackSettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new XNNPackSettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void XNNPackSettings::UnPackTo(XNNPackSettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3493,9 +3519,9 @@ inline bool operator!=(const CoreMLSettingsT &lhs, const CoreMLSettingsT &rhs) { + + + inline CoreMLSettingsT *CoreMLSettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new CoreMLSettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new CoreMLSettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void CoreMLSettings::UnPackTo(CoreMLSettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3542,9 +3568,9 @@ inline bool operator!=(const EdgeTpuDeviceSpecT &lhs, const EdgeTpuDeviceSpecT & + + + inline EdgeTpuDeviceSpecT *EdgeTpuDeviceSpec::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new EdgeTpuDeviceSpecT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new EdgeTpuDeviceSpecT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void EdgeTpuDeviceSpec::UnPackTo(EdgeTpuDeviceSpecT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3589,9 +3615,9 @@ inline bool operator!=(const EdgeTpuInactivePowerConfigT &lhs, const EdgeTpuInac + + + inline EdgeTpuInactivePowerConfigT *EdgeTpuInactivePowerConfig::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new EdgeTpuInactivePowerConfigT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new EdgeTpuInactivePowerConfigT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void EdgeTpuInactivePowerConfig::UnPackTo(EdgeTpuInactivePowerConfigT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3634,19 +3660,41 @@ inline bool operator!=(const EdgeTpuSettingsT &lhs, const EdgeTpuSettingsT &rhs) + } + + ++inline EdgeTpuSettingsT::EdgeTpuSettingsT(const EdgeTpuSettingsT &o) ++ : inference_power_state(o.inference_power_state), ++ inference_priority(o.inference_priority), ++ edgetpu_device_spec((o.edgetpu_device_spec) ? new tflite::EdgeTpuDeviceSpecT(*o.edgetpu_device_spec) : nullptr), ++ model_token(o.model_token), ++ float_truncation_type(o.float_truncation_type), ++ qos_class(o.qos_class) { ++ inactive_power_configs.reserve(o.inactive_power_configs.size()); ++ for (const auto &v : o.inactive_power_configs) { inactive_power_configs.emplace_back((v) ? new tflite::EdgeTpuInactivePowerConfigT(*v) : nullptr); } ++} ++ ++inline EdgeTpuSettingsT &EdgeTpuSettingsT::operator=(EdgeTpuSettingsT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(inference_power_state, o.inference_power_state); ++ std::swap(inactive_power_configs, o.inactive_power_configs); ++ std::swap(inference_priority, o.inference_priority); ++ std::swap(edgetpu_device_spec, o.edgetpu_device_spec); ++ std::swap(model_token, o.model_token); ++ std::swap(float_truncation_type, o.float_truncation_type); ++ std::swap(qos_class, o.qos_class); ++ return *this; ++} ++ + inline EdgeTpuSettingsT *EdgeTpuSettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new EdgeTpuSettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new EdgeTpuSettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void EdgeTpuSettings::UnPackTo(EdgeTpuSettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; + { auto _e = inference_power_state(); _o->inference_power_state = _e; } +- { auto _e = inactive_power_configs(); if (_e) { _o->inactive_power_configs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inactive_power_configs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } ++ { auto _e = inactive_power_configs(); if (_e) { _o->inactive_power_configs.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->inactive_power_configs[_i]) { _e->Get(_i)->UnPackTo(_o->inactive_power_configs[_i].get(), _resolver); } else { _o->inactive_power_configs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = inference_priority(); _o->inference_priority = _e; } +- { auto _e = edgetpu_device_spec(); if (_e) _o->edgetpu_device_spec = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = edgetpu_device_spec(); if (_e) { if(_o->edgetpu_device_spec) { _e->UnPackTo(_o->edgetpu_device_spec.get(), _resolver); } else { _o->edgetpu_device_spec = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = model_token(); if (_e) _o->model_token = _e->str(); } + { auto _e = float_truncation_type(); _o->float_truncation_type = _e; } + { auto _e = qos_class(); _o->qos_class = _e; } +@@ -3693,9 +3741,9 @@ inline bool operator!=(const CoralSettingsT &lhs, const CoralSettingsT &rhs) { + + + inline CoralSettingsT *CoralSettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new CoralSettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new CoralSettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void CoralSettings::UnPackTo(CoralSettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3739,9 +3787,9 @@ inline bool operator!=(const CPUSettingsT &lhs, const CPUSettingsT &rhs) { + + + inline CPUSettingsT *CPUSettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new CPUSettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new CPUSettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void CPUSettings::UnPackTo(CPUSettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3785,26 +3833,55 @@ inline bool operator!=(const TFLiteSettingsT &lhs, const TFLiteSettingsT &rhs) { + } + + ++inline TFLiteSettingsT::TFLiteSettingsT(const TFLiteSettingsT &o) ++ : delegate(o.delegate), ++ nnapi_settings((o.nnapi_settings) ? new tflite::NNAPISettingsT(*o.nnapi_settings) : nullptr), ++ gpu_settings((o.gpu_settings) ? new tflite::GPUSettingsT(*o.gpu_settings) : nullptr), ++ hexagon_settings((o.hexagon_settings) ? new tflite::HexagonSettingsT(*o.hexagon_settings) : nullptr), ++ xnnpack_settings((o.xnnpack_settings) ? new tflite::XNNPackSettingsT(*o.xnnpack_settings) : nullptr), ++ coreml_settings((o.coreml_settings) ? new tflite::CoreMLSettingsT(*o.coreml_settings) : nullptr), ++ cpu_settings((o.cpu_settings) ? new tflite::CPUSettingsT(*o.cpu_settings) : nullptr), ++ max_delegated_partitions(o.max_delegated_partitions), ++ edgetpu_settings((o.edgetpu_settings) ? new tflite::EdgeTpuSettingsT(*o.edgetpu_settings) : nullptr), ++ coral_settings((o.coral_settings) ? new tflite::CoralSettingsT(*o.coral_settings) : nullptr), ++ fallback_settings((o.fallback_settings) ? new tflite::FallbackSettingsT(*o.fallback_settings) : nullptr) { ++} ++ ++inline TFLiteSettingsT &TFLiteSettingsT::operator=(TFLiteSettingsT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(delegate, o.delegate); ++ std::swap(nnapi_settings, o.nnapi_settings); ++ std::swap(gpu_settings, o.gpu_settings); ++ std::swap(hexagon_settings, o.hexagon_settings); ++ std::swap(xnnpack_settings, o.xnnpack_settings); ++ std::swap(coreml_settings, o.coreml_settings); ++ std::swap(cpu_settings, o.cpu_settings); ++ std::swap(max_delegated_partitions, o.max_delegated_partitions); ++ std::swap(edgetpu_settings, o.edgetpu_settings); ++ std::swap(coral_settings, o.coral_settings); ++ std::swap(fallback_settings, o.fallback_settings); ++ return *this; ++} ++ + inline TFLiteSettingsT *TFLiteSettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new TFLiteSettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new TFLiteSettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void TFLiteSettings::UnPackTo(TFLiteSettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; + { auto _e = delegate(); _o->delegate = _e; } +- { auto _e = nnapi_settings(); if (_e) _o->nnapi_settings = std::unique_ptr(_e->UnPack(_resolver)); } +- { auto _e = gpu_settings(); if (_e) _o->gpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } +- { auto _e = hexagon_settings(); if (_e) _o->hexagon_settings = std::unique_ptr(_e->UnPack(_resolver)); } +- { auto _e = xnnpack_settings(); if (_e) _o->xnnpack_settings = std::unique_ptr(_e->UnPack(_resolver)); } +- { auto _e = coreml_settings(); if (_e) _o->coreml_settings = std::unique_ptr(_e->UnPack(_resolver)); } +- { auto _e = cpu_settings(); if (_e) _o->cpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = nnapi_settings(); if (_e) { if(_o->nnapi_settings) { _e->UnPackTo(_o->nnapi_settings.get(), _resolver); } else { _o->nnapi_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = gpu_settings(); if (_e) { if(_o->gpu_settings) { _e->UnPackTo(_o->gpu_settings.get(), _resolver); } else { _o->gpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = hexagon_settings(); if (_e) { if(_o->hexagon_settings) { _e->UnPackTo(_o->hexagon_settings.get(), _resolver); } else { _o->hexagon_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = xnnpack_settings(); if (_e) { if(_o->xnnpack_settings) { _e->UnPackTo(_o->xnnpack_settings.get(), _resolver); } else { _o->xnnpack_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = coreml_settings(); if (_e) { if(_o->coreml_settings) { _e->UnPackTo(_o->coreml_settings.get(), _resolver); } else { _o->coreml_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = cpu_settings(); if (_e) { if(_o->cpu_settings) { _e->UnPackTo(_o->cpu_settings.get(), _resolver); } else { _o->cpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = max_delegated_partitions(); _o->max_delegated_partitions = _e; } +- { auto _e = edgetpu_settings(); if (_e) _o->edgetpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } +- { auto _e = coral_settings(); if (_e) _o->coral_settings = std::unique_ptr(_e->UnPack(_resolver)); } +- { auto _e = fallback_settings(); if (_e) _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = edgetpu_settings(); if (_e) { if(_o->edgetpu_settings) { _e->UnPackTo(_o->edgetpu_settings.get(), _resolver); } else { _o->edgetpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = coral_settings(); if (_e) { if(_o->coral_settings) { _e->UnPackTo(_o->coral_settings.get(), _resolver); } else { _o->coral_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = fallback_settings(); if (_e) { if(_o->fallback_settings) { _e->UnPackTo(_o->fallback_settings.get(), _resolver); } else { _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline flatbuffers::Offset TFLiteSettings::Pack(flatbuffers::FlatBufferBuilder &_fbb, const TFLiteSettingsT* _o, const flatbuffers::rehasher_function_t *_rehasher) { +@@ -3854,9 +3931,9 @@ inline bool operator!=(const FallbackSettingsT &lhs, const FallbackSettingsT &rh + + + inline FallbackSettingsT *FallbackSettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new FallbackSettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new FallbackSettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void FallbackSettings::UnPackTo(FallbackSettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3895,9 +3972,9 @@ inline bool operator!=(const BenchmarkMetricT &lhs, const BenchmarkMetricT &rhs) + + + inline BenchmarkMetricT *BenchmarkMetric::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BenchmarkMetricT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BenchmarkMetricT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BenchmarkMetric::UnPackTo(BenchmarkMetricT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3938,10 +4015,28 @@ inline bool operator!=(const BenchmarkResultT &lhs, const BenchmarkResultT &rhs) + } + + ++inline BenchmarkResultT::BenchmarkResultT(const BenchmarkResultT &o) ++ : initialization_time_us(o.initialization_time_us), ++ inference_time_us(o.inference_time_us), ++ max_memory_kb(o.max_memory_kb), ++ ok(o.ok) { ++ metrics.reserve(o.metrics.size()); ++ for (const auto &v : o.metrics) { metrics.emplace_back((v) ? new tflite::BenchmarkMetricT(*v) : nullptr); } ++} ++ ++inline BenchmarkResultT &BenchmarkResultT::operator=(BenchmarkResultT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(initialization_time_us, o.initialization_time_us); ++ std::swap(inference_time_us, o.inference_time_us); ++ std::swap(max_memory_kb, o.max_memory_kb); ++ std::swap(ok, o.ok); ++ std::swap(metrics, o.metrics); ++ return *this; ++} ++ + inline BenchmarkResultT *BenchmarkResult::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BenchmarkResultT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BenchmarkResultT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BenchmarkResult::UnPackTo(BenchmarkResultT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -3951,7 +4046,7 @@ inline void BenchmarkResult::UnPackTo(BenchmarkResultT *_o, const flatbuffers::r + { auto _e = inference_time_us(); if (_e) { _o->inference_time_us.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inference_time_us[_i] = _e->Get(_i); } } } + { auto _e = max_memory_kb(); _o->max_memory_kb = _e; } + { auto _e = ok(); _o->ok = _e; } +- { auto _e = metrics(); if (_e) { _o->metrics.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->metrics[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } ++ { auto _e = metrics(); if (_e) { _o->metrics.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->metrics[_i]) { _e->Get(_i)->UnPackTo(_o->metrics[_i].get(), _resolver); } else { _o->metrics[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline flatbuffers::Offset BenchmarkResult::Pack(flatbuffers::FlatBufferBuilder &_fbb, const BenchmarkResultT* _o, const flatbuffers::rehasher_function_t *_rehasher) { +@@ -3990,9 +4085,9 @@ inline bool operator!=(const ErrorCodeT &lhs, const ErrorCodeT &rhs) { + + + inline ErrorCodeT *ErrorCode::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ErrorCodeT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ErrorCodeT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ErrorCode::UnPackTo(ErrorCodeT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -4036,10 +4131,28 @@ inline bool operator!=(const BenchmarkErrorT &lhs, const BenchmarkErrorT &rhs) { + } + + ++inline BenchmarkErrorT::BenchmarkErrorT(const BenchmarkErrorT &o) ++ : stage(o.stage), ++ exit_code(o.exit_code), ++ signal(o.signal), ++ mini_benchmark_error_code(o.mini_benchmark_error_code) { ++ error_code.reserve(o.error_code.size()); ++ for (const auto &v : o.error_code) { error_code.emplace_back((v) ? new tflite::ErrorCodeT(*v) : nullptr); } ++} ++ ++inline BenchmarkErrorT &BenchmarkErrorT::operator=(BenchmarkErrorT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(stage, o.stage); ++ std::swap(exit_code, o.exit_code); ++ std::swap(signal, o.signal); ++ std::swap(error_code, o.error_code); ++ std::swap(mini_benchmark_error_code, o.mini_benchmark_error_code); ++ return *this; ++} ++ + inline BenchmarkErrorT *BenchmarkError::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BenchmarkErrorT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BenchmarkErrorT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BenchmarkError::UnPackTo(BenchmarkErrorT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -4048,7 +4161,7 @@ inline void BenchmarkError::UnPackTo(BenchmarkErrorT *_o, const flatbuffers::res + { auto _e = stage(); _o->stage = _e; } + { auto _e = exit_code(); _o->exit_code = _e; } + { auto _e = signal(); _o->signal = _e; } +- { auto _e = error_code(); if (_e) { _o->error_code.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->error_code[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } ++ { auto _e = error_code(); if (_e) { _o->error_code.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->error_code[_i]) { _e->Get(_i)->UnPackTo(_o->error_code[_i].get(), _resolver); } else { _o->error_code[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = mini_benchmark_error_code(); _o->mini_benchmark_error_code = _e; } + } + +@@ -4090,19 +4203,38 @@ inline bool operator!=(const BenchmarkEventT &lhs, const BenchmarkEventT &rhs) { + } + + ++inline BenchmarkEventT::BenchmarkEventT(const BenchmarkEventT &o) ++ : tflite_settings((o.tflite_settings) ? new tflite::TFLiteSettingsT(*o.tflite_settings) : nullptr), ++ event_type(o.event_type), ++ result((o.result) ? new tflite::BenchmarkResultT(*o.result) : nullptr), ++ error((o.error) ? new tflite::BenchmarkErrorT(*o.error) : nullptr), ++ boottime_us(o.boottime_us), ++ wallclock_us(o.wallclock_us) { ++} ++ ++inline BenchmarkEventT &BenchmarkEventT::operator=(BenchmarkEventT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(tflite_settings, o.tflite_settings); ++ std::swap(event_type, o.event_type); ++ std::swap(result, o.result); ++ std::swap(error, o.error); ++ std::swap(boottime_us, o.boottime_us); ++ std::swap(wallclock_us, o.wallclock_us); ++ return *this; ++} ++ + inline BenchmarkEventT *BenchmarkEvent::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BenchmarkEventT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BenchmarkEventT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BenchmarkEvent::UnPackTo(BenchmarkEventT *_o, const flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = tflite_settings(); if (_e) _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = tflite_settings(); if (_e) { if(_o->tflite_settings) { _e->UnPackTo(_o->tflite_settings.get(), _resolver); } else { _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = event_type(); _o->event_type = _e; } +- { auto _e = result(); if (_e) _o->result = std::unique_ptr(_e->UnPack(_resolver)); } +- { auto _e = error(); if (_e) _o->error = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = result(); if (_e) { if(_o->result) { _e->UnPackTo(_o->result.get(), _resolver); } else { _o->result = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = error(); if (_e) { if(_o->error) { _e->UnPackTo(_o->error.get(), _resolver); } else { _o->error = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = boottime_us(); _o->boottime_us = _e; } + { auto _e = wallclock_us(); _o->wallclock_us = _e; } + } +@@ -4144,17 +4276,30 @@ inline bool operator!=(const BestAccelerationDecisionT &lhs, const BestAccelerat + } + + ++inline BestAccelerationDecisionT::BestAccelerationDecisionT(const BestAccelerationDecisionT &o) ++ : number_of_source_events(o.number_of_source_events), ++ min_latency_event((o.min_latency_event) ? new tflite::BenchmarkEventT(*o.min_latency_event) : nullptr), ++ min_inference_time_us(o.min_inference_time_us) { ++} ++ ++inline BestAccelerationDecisionT &BestAccelerationDecisionT::operator=(BestAccelerationDecisionT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(number_of_source_events, o.number_of_source_events); ++ std::swap(min_latency_event, o.min_latency_event); ++ std::swap(min_inference_time_us, o.min_inference_time_us); ++ return *this; ++} ++ + inline BestAccelerationDecisionT *BestAccelerationDecision::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BestAccelerationDecisionT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BestAccelerationDecisionT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BestAccelerationDecision::UnPackTo(BestAccelerationDecisionT *_o, const flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; + { auto _e = number_of_source_events(); _o->number_of_source_events = _e; } +- { auto _e = min_latency_event(); if (_e) _o->min_latency_event = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = min_latency_event(); if (_e) { if(_o->min_latency_event) { _e->UnPackTo(_o->min_latency_event.get(), _resolver); } else { _o->min_latency_event = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = min_inference_time_us(); _o->min_inference_time_us = _e; } + } + +@@ -4188,9 +4333,9 @@ inline bool operator!=(const BenchmarkInitializationFailureT &lhs, const Benchma + + + inline BenchmarkInitializationFailureT *BenchmarkInitializationFailure::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BenchmarkInitializationFailureT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BenchmarkInitializationFailureT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BenchmarkInitializationFailure::UnPackTo(BenchmarkInitializationFailureT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -4227,19 +4372,34 @@ inline bool operator!=(const MiniBenchmarkEventT &lhs, const MiniBenchmarkEventT + } + + ++inline MiniBenchmarkEventT::MiniBenchmarkEventT(const MiniBenchmarkEventT &o) ++ : is_log_flushing_event(o.is_log_flushing_event), ++ best_acceleration_decision((o.best_acceleration_decision) ? new tflite::BestAccelerationDecisionT(*o.best_acceleration_decision) : nullptr), ++ initialization_failure((o.initialization_failure) ? new tflite::BenchmarkInitializationFailureT(*o.initialization_failure) : nullptr), ++ benchmark_event((o.benchmark_event) ? new tflite::BenchmarkEventT(*o.benchmark_event) : nullptr) { ++} ++ ++inline MiniBenchmarkEventT &MiniBenchmarkEventT::operator=(MiniBenchmarkEventT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(is_log_flushing_event, o.is_log_flushing_event); ++ std::swap(best_acceleration_decision, o.best_acceleration_decision); ++ std::swap(initialization_failure, o.initialization_failure); ++ std::swap(benchmark_event, o.benchmark_event); ++ return *this; ++} ++ + inline MiniBenchmarkEventT *MiniBenchmarkEvent::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new MiniBenchmarkEventT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new MiniBenchmarkEventT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void MiniBenchmarkEvent::UnPackTo(MiniBenchmarkEventT *_o, const flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; + { auto _e = is_log_flushing_event(); _o->is_log_flushing_event = _e; } +- { auto _e = best_acceleration_decision(); if (_e) _o->best_acceleration_decision = std::unique_ptr(_e->UnPack(_resolver)); } +- { auto _e = initialization_failure(); if (_e) _o->initialization_failure = std::unique_ptr(_e->UnPack(_resolver)); } +- { auto _e = benchmark_event(); if (_e) _o->benchmark_event = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = best_acceleration_decision(); if (_e) { if(_o->best_acceleration_decision) { _e->UnPackTo(_o->best_acceleration_decision.get(), _resolver); } else { _o->best_acceleration_decision = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = initialization_failure(); if (_e) { if(_o->initialization_failure) { _e->UnPackTo(_o->initialization_failure.get(), _resolver); } else { _o->initialization_failure = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = benchmark_event(); if (_e) { if(_o->benchmark_event) { _e->UnPackTo(_o->benchmark_event.get(), _resolver); } else { _o->benchmark_event = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline flatbuffers::Offset MiniBenchmarkEvent::Pack(flatbuffers::FlatBufferBuilder &_fbb, const MiniBenchmarkEventT* _o, const flatbuffers::rehasher_function_t *_rehasher) { +@@ -4277,9 +4437,9 @@ inline bool operator!=(const ModelFileT &lhs, const ModelFileT &rhs) { + + + inline ModelFileT *ModelFile::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new ModelFileT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new ModelFileT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void ModelFile::UnPackTo(ModelFileT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -4324,9 +4484,9 @@ inline bool operator!=(const BenchmarkStoragePathsT &lhs, const BenchmarkStorage + + + inline BenchmarkStoragePathsT *BenchmarkStoragePaths::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new BenchmarkStoragePathsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new BenchmarkStoragePathsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void BenchmarkStoragePaths::UnPackTo(BenchmarkStoragePathsT *_o, const flatbuffers::resolver_function_t *_resolver) const { +@@ -4365,18 +4525,32 @@ inline bool operator!=(const MinibenchmarkSettingsT &lhs, const MinibenchmarkSet + } + + ++inline MinibenchmarkSettingsT::MinibenchmarkSettingsT(const MinibenchmarkSettingsT &o) ++ : model_file((o.model_file) ? new tflite::ModelFileT(*o.model_file) : nullptr), ++ storage_paths((o.storage_paths) ? new tflite::BenchmarkStoragePathsT(*o.storage_paths) : nullptr) { ++ settings_to_test.reserve(o.settings_to_test.size()); ++ for (const auto &v : o.settings_to_test) { settings_to_test.emplace_back((v) ? new tflite::TFLiteSettingsT(*v) : nullptr); } ++} ++ ++inline MinibenchmarkSettingsT &MinibenchmarkSettingsT::operator=(MinibenchmarkSettingsT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(settings_to_test, o.settings_to_test); ++ std::swap(model_file, o.model_file); ++ std::swap(storage_paths, o.storage_paths); ++ return *this; ++} ++ + inline MinibenchmarkSettingsT *MinibenchmarkSettings::UnPack(const flatbuffers::resolver_function_t *_resolver) const { +- auto _o = new MinibenchmarkSettingsT(); +- UnPackTo(_o, _resolver); +- return _o; ++ auto _o = std::unique_ptr(new MinibenchmarkSettingsT()); ++ UnPackTo(_o.get(), _resolver); ++ return _o.release(); + } + + inline void MinibenchmarkSettings::UnPackTo(MinibenchmarkSettingsT *_o, const flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = settings_to_test(); if (_e) { _o->settings_to_test.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->settings_to_test[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); } } } +- { auto _e = model_file(); if (_e) _o->model_file = std::unique_ptr(_e->UnPack(_resolver)); } +- { auto _e = storage_paths(); if (_e) _o->storage_paths = std::unique_ptr(_e->UnPack(_resolver)); } ++ { auto _e = settings_to_test(); if (_e) { _o->settings_to_test.resize(_e->size()); for (flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->settings_to_test[_i]) { _e->Get(_i)->UnPackTo(_o->settings_to_test[_i].get(), _resolver); } else { _o->settings_to_test[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = model_file(); if (_e) { if(_o->model_file) { _e->UnPackTo(_o->model_file.get(), _resolver); } else { _o->model_file = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = storage_paths(); if (_e) { if(_o->storage_paths) { _e->UnPackTo(_o->storage_paths.get(), _resolver); } else { _o->storage_paths = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline flatbuffers::Offset MinibenchmarkSettings::Pack(flatbuffers::FlatBufferBuilder &_fbb, const MinibenchmarkSettingsT* _o, const flatbuffers::rehasher_function_t *_rehasher) { +@@ -4399,4 +4573,4 @@ inline flatbuffers::Offset CreateMinibenchmarkSettings(fl + + } // namespace tflite + +-#endif // FLATBUFFERS_GENERATED_CONFIGURATIONFORGENERATION_TFLITE_H_ ++#endif // FLATBUFFERS_GENERATED_CONFIGURATION_TFLITE_H_ +diff --git a/tensorflow/lite/schema/schema_generated.h b/tensorflow/lite/schema/schema_generated.h +index 0de55f064ef..886eddaeaac 100755 +--- a/tensorflow/lite/schema/schema_generated.h ++++ b/tensorflow/lite/schema/schema_generated.h +@@ -4023,10 +4023,10 @@ struct QuantizationParameters FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tab + verifier.VerifyVector(scale()) && + VerifyOffset(verifier, VT_ZERO_POINT) && + verifier.VerifyVector(zero_point()) && +- VerifyField(verifier, VT_DETAILS_TYPE) && ++ VerifyField(verifier, VT_DETAILS_TYPE, 1) && + VerifyOffset(verifier, VT_DETAILS) && + VerifyQuantizationDetails(verifier, details(), details_type()) && +- VerifyField(verifier, VT_QUANTIZED_DIMENSION) && ++ VerifyField(verifier, VT_QUANTIZED_DIMENSION, 4) && + verifier.EndTable(); + } + QuantizationParametersT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -4367,12 +4367,12 @@ struct DimensionMetadata FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FORMAT) && +- VerifyField(verifier, VT_DENSE_SIZE) && +- VerifyField(verifier, VT_ARRAY_SEGMENTS_TYPE) && ++ VerifyField(verifier, VT_FORMAT, 1) && ++ VerifyField(verifier, VT_DENSE_SIZE, 4) && ++ VerifyField(verifier, VT_ARRAY_SEGMENTS_TYPE, 1) && + VerifyOffset(verifier, VT_ARRAY_SEGMENTS) && + VerifySparseIndexVector(verifier, array_segments(), array_segments_type()) && +- VerifyField(verifier, VT_ARRAY_INDICES_TYPE) && ++ VerifyField(verifier, VT_ARRAY_INDICES_TYPE, 1) && + VerifyOffset(verifier, VT_ARRAY_INDICES) && + VerifySparseIndexVector(verifier, array_indices(), array_indices_type()) && + verifier.EndTable(); +@@ -4464,6 +4464,10 @@ struct SparsityParametersT : public flatbuffers::NativeTable { + std::vector traversal_order{}; + std::vector block_map{}; + std::vector> dim_metadata{}; ++ SparsityParametersT() = default; ++ SparsityParametersT(const SparsityParametersT &o); ++ SparsityParametersT(SparsityParametersT&&) FLATBUFFERS_NOEXCEPT = default; ++ SparsityParametersT &operator=(SparsityParametersT o) FLATBUFFERS_NOEXCEPT; + }; + + struct SparsityParameters FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { +@@ -4562,6 +4566,10 @@ struct TensorT : public flatbuffers::NativeTable { + bool is_variable = false; + std::unique_ptr sparsity{}; + std::vector shape_signature{}; ++ TensorT() = default; ++ TensorT(const TensorT &o); ++ TensorT(TensorT&&) FLATBUFFERS_NOEXCEPT = default; ++ TensorT &operator=(TensorT o) FLATBUFFERS_NOEXCEPT; + }; + + struct Tensor FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { +@@ -4605,13 +4613,13 @@ struct Tensor FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_SHAPE) && + verifier.VerifyVector(shape()) && +- VerifyField(verifier, VT_TYPE) && +- VerifyField(verifier, VT_BUFFER) && ++ VerifyField(verifier, VT_TYPE, 1) && ++ VerifyField(verifier, VT_BUFFER, 4) && + VerifyOffset(verifier, VT_NAME) && + verifier.VerifyString(name()) && + VerifyOffset(verifier, VT_QUANTIZATION) && + verifier.VerifyTable(quantization()) && +- VerifyField(verifier, VT_IS_VARIABLE) && ++ VerifyField(verifier, VT_IS_VARIABLE, 1) && + VerifyOffset(verifier, VT_SPARSITY) && + verifier.VerifyTable(sparsity()) && + VerifyOffset(verifier, VT_SHAPE_SIGNATURE) && +@@ -4752,12 +4760,12 @@ struct Conv2DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_PADDING) && +- VerifyField(verifier, VT_STRIDE_W) && +- VerifyField(verifier, VT_STRIDE_H) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_DILATION_W_FACTOR) && +- VerifyField(verifier, VT_DILATION_H_FACTOR) && ++ VerifyField(verifier, VT_PADDING, 1) && ++ VerifyField(verifier, VT_STRIDE_W, 4) && ++ VerifyField(verifier, VT_STRIDE_H, 4) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_DILATION_W_FACTOR, 4) && ++ VerifyField(verifier, VT_DILATION_H_FACTOR, 4) && + verifier.EndTable(); + } + Conv2DOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -4869,14 +4877,14 @@ struct Conv3DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_PADDING) && +- VerifyField(verifier, VT_STRIDE_D) && +- VerifyField(verifier, VT_STRIDE_W) && +- VerifyField(verifier, VT_STRIDE_H) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_DILATION_D_FACTOR) && +- VerifyField(verifier, VT_DILATION_W_FACTOR) && +- VerifyField(verifier, VT_DILATION_H_FACTOR) && ++ VerifyField(verifier, VT_PADDING, 1) && ++ VerifyField(verifier, VT_STRIDE_D, 4) && ++ VerifyField(verifier, VT_STRIDE_W, 4) && ++ VerifyField(verifier, VT_STRIDE_H, 4) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_DILATION_D_FACTOR, 4) && ++ VerifyField(verifier, VT_DILATION_W_FACTOR, 4) && ++ VerifyField(verifier, VT_DILATION_H_FACTOR, 4) && + verifier.EndTable(); + } + Conv3DOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -4988,12 +4996,12 @@ struct Pool2DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_PADDING) && +- VerifyField(verifier, VT_STRIDE_W) && +- VerifyField(verifier, VT_STRIDE_H) && +- VerifyField(verifier, VT_FILTER_WIDTH) && +- VerifyField(verifier, VT_FILTER_HEIGHT) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && ++ VerifyField(verifier, VT_PADDING, 1) && ++ VerifyField(verifier, VT_STRIDE_W, 4) && ++ VerifyField(verifier, VT_STRIDE_H, 4) && ++ VerifyField(verifier, VT_FILTER_WIDTH, 4) && ++ VerifyField(verifier, VT_FILTER_HEIGHT, 4) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && + verifier.EndTable(); + } + Pool2DOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5100,13 +5108,13 @@ struct DepthwiseConv2DOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tab + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_PADDING) && +- VerifyField(verifier, VT_STRIDE_W) && +- VerifyField(verifier, VT_STRIDE_H) && +- VerifyField(verifier, VT_DEPTH_MULTIPLIER) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_DILATION_W_FACTOR) && +- VerifyField(verifier, VT_DILATION_H_FACTOR) && ++ VerifyField(verifier, VT_PADDING, 1) && ++ VerifyField(verifier, VT_STRIDE_W, 4) && ++ VerifyField(verifier, VT_STRIDE_H, 4) && ++ VerifyField(verifier, VT_DEPTH_MULTIPLIER, 4) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_DILATION_W_FACTOR, 4) && ++ VerifyField(verifier, VT_DILATION_H_FACTOR, 4) && + verifier.EndTable(); + } + DepthwiseConv2DOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5198,7 +5206,7 @@ struct ConcatEmbeddingsOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Ta + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_NUM_CHANNELS) && ++ VerifyField(verifier, VT_NUM_CHANNELS, 4) && + VerifyOffset(verifier, VT_NUM_COLUMNS_PER_CHANNEL) && + verifier.VerifyVector(num_columns_per_channel()) && + VerifyOffset(verifier, VT_EMBEDDING_DIM_PER_CHANNEL) && +@@ -5278,7 +5286,7 @@ struct LSHProjectionOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_TYPE) && ++ VerifyField(verifier, VT_TYPE, 1) && + verifier.EndTable(); + } + LSHProjectionOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5340,9 +5348,9 @@ struct SVDFOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_RANK) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS) && ++ VerifyField(verifier, VT_RANK, 4) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS, 1) && + verifier.EndTable(); + } + SVDFOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5409,8 +5417,8 @@ struct RNNOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS, 1) && + verifier.EndTable(); + } + RNNOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5477,9 +5485,9 @@ struct SequenceRNNOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_TIME_MAJOR) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS) && ++ VerifyField(verifier, VT_TIME_MAJOR, 1) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS, 1) && + verifier.EndTable(); + } + SequenceRNNOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5556,10 +5564,10 @@ struct BidirectionalSequenceRNNOptions FLATBUFFERS_FINAL_CLASS : private flatbuf + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_TIME_MAJOR) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_MERGE_OUTPUTS) && +- VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS) && ++ VerifyField(verifier, VT_TIME_MAJOR, 1) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_MERGE_OUTPUTS, 1) && ++ VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS, 1) && + verifier.EndTable(); + } + BidirectionalSequenceRNNOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5641,10 +5649,10 @@ struct FullyConnectedOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tabl + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_WEIGHTS_FORMAT) && +- VerifyField(verifier, VT_KEEP_NUM_DIMS) && +- VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_WEIGHTS_FORMAT, 1) && ++ VerifyField(verifier, VT_KEEP_NUM_DIMS, 1) && ++ VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS, 1) && + verifier.EndTable(); + } + FullyConnectedOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5711,7 +5719,7 @@ struct SoftmaxOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_BETA) && ++ VerifyField(verifier, VT_BETA, 4) && + verifier.EndTable(); + } + SoftmaxOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5768,8 +5776,8 @@ struct ConcatenationOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_AXIS) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && ++ VerifyField(verifier, VT_AXIS, 4) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && + verifier.EndTable(); + } + ConcatenationOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5831,8 +5839,8 @@ struct AddOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_POT_SCALE_INT16) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_POT_SCALE_INT16, 1) && + verifier.EndTable(); + } + AddOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5889,7 +5897,7 @@ struct MulOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && + verifier.EndTable(); + } + MulOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -5941,7 +5949,7 @@ struct L2NormOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && + verifier.EndTable(); + } + L2NormOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -6008,10 +6016,10 @@ struct LocalResponseNormalizationOptions FLATBUFFERS_FINAL_CLASS : private flatb + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_RADIUS) && +- VerifyField(verifier, VT_BIAS) && +- VerifyField(verifier, VT_ALPHA) && +- VerifyField(verifier, VT_BETA) && ++ VerifyField(verifier, VT_RADIUS, 4) && ++ VerifyField(verifier, VT_BIAS, 4) && ++ VerifyField(verifier, VT_ALPHA, 4) && ++ VerifyField(verifier, VT_BETA, 4) && + verifier.EndTable(); + } + LocalResponseNormalizationOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -6098,11 +6106,11 @@ struct LSTMOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_CELL_CLIP) && +- VerifyField(verifier, VT_PROJ_CLIP) && +- VerifyField(verifier, VT_KERNEL_TYPE) && +- VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_CELL_CLIP, 4) && ++ VerifyField(verifier, VT_PROJ_CLIP, 4) && ++ VerifyField(verifier, VT_KERNEL_TYPE, 1) && ++ VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS, 1) && + verifier.EndTable(); + } + LSTMOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -6194,11 +6202,11 @@ struct UnidirectionalSequenceLSTMOptions FLATBUFFERS_FINAL_CLASS : private flatb + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_CELL_CLIP) && +- VerifyField(verifier, VT_PROJ_CLIP) && +- VerifyField(verifier, VT_TIME_MAJOR) && +- VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_CELL_CLIP, 4) && ++ VerifyField(verifier, VT_PROJ_CLIP, 4) && ++ VerifyField(verifier, VT_TIME_MAJOR, 1) && ++ VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS, 1) && + verifier.EndTable(); + } + UnidirectionalSequenceLSTMOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -6295,12 +6303,12 @@ struct BidirectionalSequenceLSTMOptions FLATBUFFERS_FINAL_CLASS : private flatbu + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_CELL_CLIP) && +- VerifyField(verifier, VT_PROJ_CLIP) && +- VerifyField(verifier, VT_MERGE_OUTPUTS) && +- VerifyField(verifier, VT_TIME_MAJOR) && +- VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_CELL_CLIP, 4) && ++ VerifyField(verifier, VT_PROJ_CLIP, 4) && ++ VerifyField(verifier, VT_MERGE_OUTPUTS, 1) && ++ VerifyField(verifier, VT_TIME_MAJOR, 1) && ++ VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS, 1) && + verifier.EndTable(); + } + BidirectionalSequenceLSTMOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -6382,8 +6390,8 @@ struct ResizeBilinearOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tabl + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_ALIGN_CORNERS) && +- VerifyField(verifier, VT_HALF_PIXEL_CENTERS) && ++ VerifyField(verifier, VT_ALIGN_CORNERS, 1) && ++ VerifyField(verifier, VT_HALF_PIXEL_CENTERS, 1) && + verifier.EndTable(); + } + ResizeBilinearOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -6445,8 +6453,8 @@ struct ResizeNearestNeighborOptions FLATBUFFERS_FINAL_CLASS : private flatbuffer + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_ALIGN_CORNERS) && +- VerifyField(verifier, VT_HALF_PIXEL_CENTERS) && ++ VerifyField(verifier, VT_ALIGN_CORNERS, 1) && ++ VerifyField(verifier, VT_HALF_PIXEL_CENTERS, 1) && + verifier.EndTable(); + } + ResizeNearestNeighborOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -6503,7 +6511,7 @@ struct CallOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_SUBGRAPH) && ++ VerifyField(verifier, VT_SUBGRAPH, 4) && + verifier.EndTable(); + } + CallOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -6783,9 +6791,9 @@ struct SkipGramOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_NGRAM_SIZE) && +- VerifyField(verifier, VT_MAX_SKIP_SIZE) && +- VerifyField(verifier, VT_INCLUDE_ALL_NGRAMS) && ++ VerifyField(verifier, VT_NGRAM_SIZE, 4) && ++ VerifyField(verifier, VT_MAX_SKIP_SIZE, 4) && ++ VerifyField(verifier, VT_INCLUDE_ALL_NGRAMS, 1) && + verifier.EndTable(); + } + SkipGramOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -6847,7 +6855,7 @@ struct SpaceToDepthOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_BLOCK_SIZE) && ++ VerifyField(verifier, VT_BLOCK_SIZE, 4) && + verifier.EndTable(); + } + SpaceToDepthOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -6899,7 +6907,7 @@ struct DepthToSpaceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_BLOCK_SIZE) && ++ VerifyField(verifier, VT_BLOCK_SIZE, 4) && + verifier.EndTable(); + } + DepthToSpaceOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -6956,8 +6964,8 @@ struct SubOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && +- VerifyField(verifier, VT_POT_SCALE_INT16) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && ++ VerifyField(verifier, VT_POT_SCALE_INT16, 1) && + verifier.EndTable(); + } + SubOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -7014,7 +7022,7 @@ struct DivOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION) && ++ VerifyField(verifier, VT_FUSED_ACTIVATION_FUNCTION, 1) && + verifier.EndTable(); + } + DivOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -7105,7 +7113,7 @@ struct EmbeddingLookupSparseOptions FLATBUFFERS_FINAL_CLASS : private flatbuffer + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_COMBINER) && ++ VerifyField(verifier, VT_COMBINER, 1) && + verifier.EndTable(); + } + EmbeddingLookupSparseOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -7162,8 +7170,8 @@ struct GatherOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_AXIS) && +- VerifyField(verifier, VT_BATCH_DIMS) && ++ VerifyField(verifier, VT_AXIS, 4) && ++ VerifyField(verifier, VT_BATCH_DIMS, 4) && + verifier.EndTable(); + } + GatherOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -7337,7 +7345,7 @@ struct ReducerOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_KEEP_DIMS) && ++ VerifyField(verifier, VT_KEEP_DIMS, 1) && + verifier.EndTable(); + } + ReducerOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -7451,7 +7459,7 @@ struct SplitOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_NUM_SPLITS) && ++ VerifyField(verifier, VT_NUM_SPLITS, 4) && + verifier.EndTable(); + } + SplitOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -7503,7 +7511,7 @@ struct SplitVOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_NUM_SPLITS) && ++ VerifyField(verifier, VT_NUM_SPLITS, 4) && + verifier.EndTable(); + } + SplitVOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -7575,11 +7583,11 @@ struct StridedSliceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_BEGIN_MASK) && +- VerifyField(verifier, VT_END_MASK) && +- VerifyField(verifier, VT_ELLIPSIS_MASK) && +- VerifyField(verifier, VT_NEW_AXIS_MASK) && +- VerifyField(verifier, VT_SHRINK_AXIS_MASK) && ++ VerifyField(verifier, VT_BEGIN_MASK, 4) && ++ VerifyField(verifier, VT_END_MASK, 4) && ++ VerifyField(verifier, VT_ELLIPSIS_MASK, 4) && ++ VerifyField(verifier, VT_NEW_AXIS_MASK, 4) && ++ VerifyField(verifier, VT_SHRINK_AXIS_MASK, 4) && + verifier.EndTable(); + } + StridedSliceOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -7695,8 +7703,8 @@ struct CastOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_IN_DATA_TYPE) && +- VerifyField(verifier, VT_OUT_DATA_TYPE) && ++ VerifyField(verifier, VT_IN_DATA_TYPE, 1) && ++ VerifyField(verifier, VT_OUT_DATA_TYPE, 1) && + verifier.EndTable(); + } + CastOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -7870,7 +7878,7 @@ struct ArgMaxOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_OUTPUT_TYPE) && ++ VerifyField(verifier, VT_OUTPUT_TYPE, 1) && + verifier.EndTable(); + } + ArgMaxOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -7922,7 +7930,7 @@ struct ArgMinOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_OUTPUT_TYPE) && ++ VerifyField(verifier, VT_OUTPUT_TYPE, 1) && + verifier.EndTable(); + } + ArgMinOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -8257,9 +8265,9 @@ struct TransposeConvOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_PADDING) && +- VerifyField(verifier, VT_STRIDE_W) && +- VerifyField(verifier, VT_STRIDE_H) && ++ VerifyField(verifier, VT_PADDING, 1) && ++ VerifyField(verifier, VT_STRIDE_W, 4) && ++ VerifyField(verifier, VT_STRIDE_H, 4) && + verifier.EndTable(); + } + TransposeConvOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -8360,7 +8368,7 @@ struct SparseToDenseOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_VALIDATE_INDICES) && ++ VerifyField(verifier, VT_VALIDATE_INDICES, 1) && + verifier.EndTable(); + } + SparseToDenseOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -8490,7 +8498,7 @@ struct ShapeOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_OUT_TYPE) && ++ VerifyField(verifier, VT_OUT_TYPE, 1) && + verifier.EndTable(); + } + ShapeOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -8635,10 +8643,10 @@ struct FakeQuantOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_MIN) && +- VerifyField(verifier, VT_MAX) && +- VerifyField(verifier, VT_NUM_BITS) && +- VerifyField(verifier, VT_NARROW_RANGE) && ++ VerifyField(verifier, VT_MIN, 4) && ++ VerifyField(verifier, VT_MAX, 4) && ++ VerifyField(verifier, VT_NUM_BITS, 4) && ++ VerifyField(verifier, VT_NARROW_RANGE, 1) && + verifier.EndTable(); + } + FakeQuantOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -8710,8 +8718,8 @@ struct PackOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_VALUES_COUNT) && +- VerifyField(verifier, VT_AXIS) && ++ VerifyField(verifier, VT_VALUES_COUNT, 4) && ++ VerifyField(verifier, VT_AXIS, 4) && + verifier.EndTable(); + } + PackOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -8807,7 +8815,7 @@ struct OneHotOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_AXIS) && ++ VerifyField(verifier, VT_AXIS, 4) && + verifier.EndTable(); + } + OneHotOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -9020,8 +9028,8 @@ struct UnpackOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_NUM) && +- VerifyField(verifier, VT_AXIS) && ++ VerifyField(verifier, VT_NUM, 4) && ++ VerifyField(verifier, VT_AXIS, 4) && + verifier.EndTable(); + } + UnpackOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -9312,7 +9320,7 @@ struct LeakyReluOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_ALPHA) && ++ VerifyField(verifier, VT_ALPHA, 4) && + verifier.EndTable(); + } + LeakyReluOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -9403,7 +9411,7 @@ struct MirrorPadOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_MODE) && ++ VerifyField(verifier, VT_MODE, 1) && + verifier.EndTable(); + } + MirrorPadOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -9455,7 +9463,7 @@ struct UniqueOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_IDX_OUT_TYPE) && ++ VerifyField(verifier, VT_IDX_OUT_TYPE, 1) && + verifier.EndTable(); + } + UniqueOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -9668,8 +9676,8 @@ struct ReverseSequenceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Tab + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_SEQ_DIM) && +- VerifyField(verifier, VT_BATCH_DIM) && ++ VerifyField(verifier, VT_SEQ_DIM, 4) && ++ VerifyField(verifier, VT_BATCH_DIM, 4) && + verifier.EndTable(); + } + ReverseSequenceOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -9848,8 +9856,8 @@ struct IfOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_THEN_SUBGRAPH_INDEX) && +- VerifyField(verifier, VT_ELSE_SUBGRAPH_INDEX) && ++ VerifyField(verifier, VT_THEN_SUBGRAPH_INDEX, 4) && ++ VerifyField(verifier, VT_ELSE_SUBGRAPH_INDEX, 4) && + verifier.EndTable(); + } + IfOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -9906,7 +9914,7 @@ struct CallOnceOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_INIT_SUBGRAPH_INDEX) && ++ VerifyField(verifier, VT_INIT_SUBGRAPH_INDEX, 4) && + verifier.EndTable(); + } + CallOnceOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -9963,8 +9971,8 @@ struct WhileOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_COND_SUBGRAPH_INDEX) && +- VerifyField(verifier, VT_BODY_SUBGRAPH_INDEX) && ++ VerifyField(verifier, VT_COND_SUBGRAPH_INDEX, 4) && ++ VerifyField(verifier, VT_BODY_SUBGRAPH_INDEX, 4) && + verifier.EndTable(); + } + WhileOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -10265,9 +10273,9 @@ struct BatchMatMulOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_ADJ_X) && +- VerifyField(verifier, VT_ADJ_Y) && +- VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS) && ++ VerifyField(verifier, VT_ADJ_X, 1) && ++ VerifyField(verifier, VT_ADJ_Y, 1) && ++ VerifyField(verifier, VT_ASYMMETRIC_QUANTIZE_INPUTS, 1) && + verifier.EndTable(); + } + BatchMatMulOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -10334,8 +10342,8 @@ struct CumsumOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_EXCLUSIVE) && +- VerifyField(verifier, VT_REVERSE) && ++ VerifyField(verifier, VT_EXCLUSIVE, 1) && ++ VerifyField(verifier, VT_REVERSE, 1) && + verifier.EndTable(); + } + CumsumOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -10480,9 +10488,9 @@ struct HashtableOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_TABLE_ID) && +- VerifyField(verifier, VT_KEY_DTYPE) && +- VerifyField(verifier, VT_VALUE_DTYPE) && ++ VerifyField(verifier, VT_TABLE_ID, 4) && ++ VerifyField(verifier, VT_KEY_DTYPE, 1) && ++ VerifyField(verifier, VT_VALUE_DTYPE, 1) && + verifier.EndTable(); + } + HashtableOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -10821,8 +10829,8 @@ struct RandomOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_SEED) && +- VerifyField(verifier, VT_SEED2) && ++ VerifyField(verifier, VT_SEED, 8) && ++ VerifyField(verifier, VT_SEED2, 8) && + verifier.EndTable(); + } + RandomOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -10941,7 +10949,7 @@ struct GeluOptions FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_APPROXIMATE) && ++ VerifyField(verifier, VT_APPROXIMATE, 1) && + verifier.EndTable(); + } + GeluOptionsT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -11047,11 +11055,11 @@ struct OperatorCode FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_DEPRECATED_BUILTIN_CODE) && ++ VerifyField(verifier, VT_DEPRECATED_BUILTIN_CODE, 1) && + VerifyOffset(verifier, VT_CUSTOM_CODE) && + verifier.VerifyString(custom_code()) && +- VerifyField(verifier, VT_VERSION) && +- VerifyField(verifier, VT_BUILTIN_CODE) && ++ VerifyField(verifier, VT_VERSION, 4) && ++ VerifyField(verifier, VT_BUILTIN_CODE, 4) && + verifier.EndTable(); + } + OperatorCodeT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -11524,17 +11532,17 @@ struct Operator FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_OPCODE_INDEX) && ++ VerifyField(verifier, VT_OPCODE_INDEX, 4) && + VerifyOffset(verifier, VT_INPUTS) && + verifier.VerifyVector(inputs()) && + VerifyOffset(verifier, VT_OUTPUTS) && + verifier.VerifyVector(outputs()) && +- VerifyField(verifier, VT_BUILTIN_OPTIONS_TYPE) && ++ VerifyField(verifier, VT_BUILTIN_OPTIONS_TYPE, 1) && + VerifyOffset(verifier, VT_BUILTIN_OPTIONS) && + VerifyBuiltinOptions(verifier, builtin_options(), builtin_options_type()) && + VerifyOffset(verifier, VT_CUSTOM_OPTIONS) && + verifier.VerifyVector(custom_options()) && +- VerifyField(verifier, VT_CUSTOM_OPTIONS_FORMAT) && ++ VerifyField(verifier, VT_CUSTOM_OPTIONS_FORMAT, 1) && + VerifyOffset(verifier, VT_MUTATING_VARIABLE_INPUTS) && + verifier.VerifyVector(mutating_variable_inputs()) && + VerifyOffset(verifier, VT_INTERMEDIATES) && +@@ -12118,6 +12126,10 @@ struct SubGraphT : public flatbuffers::NativeTable { + std::vector outputs{}; + std::vector> operators{}; + std::string name{}; ++ SubGraphT() = default; ++ SubGraphT(const SubGraphT &o); ++ SubGraphT(SubGraphT&&) FLATBUFFERS_NOEXCEPT = default; ++ SubGraphT &operator=(SubGraphT o) FLATBUFFERS_NOEXCEPT; + }; + + struct SubGraph FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { +@@ -12321,7 +12333,7 @@ struct Metadata FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_NAME) && + verifier.VerifyString(name()) && +- VerifyField(verifier, VT_BUFFER) && ++ VerifyField(verifier, VT_BUFFER, 4) && + verifier.EndTable(); + } + MetadataT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -12396,7 +12408,7 @@ struct TensorMap FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_NAME) && + verifier.VerifyString(name()) && +- VerifyField(verifier, VT_TENSOR_INDEX) && ++ VerifyField(verifier, VT_TENSOR_INDEX, 4) && + verifier.EndTable(); + } + TensorMapT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -12454,6 +12466,10 @@ struct SignatureDefT : public flatbuffers::NativeTable { + std::vector> outputs{}; + std::string signature_key{}; + uint32_t subgraph_index = 0; ++ SignatureDefT() = default; ++ SignatureDefT(const SignatureDefT &o); ++ SignatureDefT(SignatureDefT&&) FLATBUFFERS_NOEXCEPT = default; ++ SignatureDefT &operator=(SignatureDefT o) FLATBUFFERS_NOEXCEPT; + }; + + struct SignatureDef FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { +@@ -12487,7 +12503,7 @@ struct SignatureDef FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + verifier.VerifyVectorOfTables(outputs()) && + VerifyOffset(verifier, VT_SIGNATURE_KEY) && + verifier.VerifyString(signature_key()) && +- VerifyField(verifier, VT_SUBGRAPH_INDEX) && ++ VerifyField(verifier, VT_SUBGRAPH_INDEX, 4) && + verifier.EndTable(); + } + SignatureDefT *UnPack(const flatbuffers::resolver_function_t *_resolver = nullptr) const; +@@ -12565,6 +12581,10 @@ struct ModelT : public flatbuffers::NativeTable { + std::vector metadata_buffer{}; + std::vector> metadata{}; + std::vector> signature_defs{}; ++ ModelT() = default; ++ ModelT(const ModelT &o); ++ ModelT(ModelT&&) FLATBUFFERS_NOEXCEPT = default; ++ ModelT &operator=(ModelT o) FLATBUFFERS_NOEXCEPT; + }; + + struct Model FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { +@@ -12606,7 +12626,7 @@ struct Model FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_VERSION) && ++ VerifyField(verifier, VT_VERSION, 4) && + VerifyOffset(verifier, VT_OPERATOR_CODES) && + verifier.VerifyVector(operator_codes()) && + verifier.VerifyVectorOfTables(operator_codes()) && +@@ -12917,6 +12937,20 @@ inline flatbuffers::Offset CreateDimensionMetadata(flatbuffer + _array_indices); + } + ++inline SparsityParametersT::SparsityParametersT(const SparsityParametersT &o) ++ : traversal_order(o.traversal_order), ++ block_map(o.block_map) { ++ dim_metadata.reserve(o.dim_metadata.size()); ++ for (const auto &v : o.dim_metadata) { dim_metadata.emplace_back((v) ? new tflite::DimensionMetadataT(*v) : nullptr); } ++} ++ ++inline SparsityParametersT &SparsityParametersT::operator=(SparsityParametersT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(traversal_order, o.traversal_order); ++ std::swap(block_map, o.block_map); ++ std::swap(dim_metadata, o.dim_metadata); ++ return *this; ++} ++ + inline SparsityParametersT *SparsityParameters::UnPack(const flatbuffers::resolver_function_t *_resolver) const { + auto _o = std::unique_ptr(new SparsityParametersT()); + UnPackTo(_o.get(), _resolver); +@@ -12949,6 +12983,29 @@ inline flatbuffers::Offset CreateSparsityParameters(flatbuff + _dim_metadata); + } + ++inline TensorT::TensorT(const TensorT &o) ++ : shape(o.shape), ++ type(o.type), ++ buffer(o.buffer), ++ name(o.name), ++ quantization((o.quantization) ? new tflite::QuantizationParametersT(*o.quantization) : nullptr), ++ is_variable(o.is_variable), ++ sparsity((o.sparsity) ? new tflite::SparsityParametersT(*o.sparsity) : nullptr), ++ shape_signature(o.shape_signature) { ++} ++ ++inline TensorT &TensorT::operator=(TensorT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(shape, o.shape); ++ std::swap(type, o.type); ++ std::swap(buffer, o.buffer); ++ std::swap(name, o.name); ++ std::swap(quantization, o.quantization); ++ std::swap(is_variable, o.is_variable); ++ std::swap(sparsity, o.sparsity); ++ std::swap(shape_signature, o.shape_signature); ++ return *this; ++} ++ + inline TensorT *Tensor::UnPack(const flatbuffers::resolver_function_t *_resolver) const { + auto _o = std::unique_ptr(new TensorT()); + UnPackTo(_o.get(), _resolver); +@@ -16198,6 +16255,25 @@ inline flatbuffers::Offset CreateOperator(flatbuffers::FlatBufferBuild + _intermediates); + } + ++inline SubGraphT::SubGraphT(const SubGraphT &o) ++ : inputs(o.inputs), ++ outputs(o.outputs), ++ name(o.name) { ++ tensors.reserve(o.tensors.size()); ++ for (const auto &v : o.tensors) { tensors.emplace_back((v) ? new tflite::TensorT(*v) : nullptr); } ++ operators.reserve(o.operators.size()); ++ for (const auto &v : o.operators) { operators.emplace_back((v) ? new tflite::OperatorT(*v) : nullptr); } ++} ++ ++inline SubGraphT &SubGraphT::operator=(SubGraphT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(tensors, o.tensors); ++ std::swap(inputs, o.inputs); ++ std::swap(outputs, o.outputs); ++ std::swap(operators, o.operators); ++ std::swap(name, o.name); ++ return *this; ++} ++ + inline SubGraphT *SubGraph::UnPack(const flatbuffers::resolver_function_t *_resolver) const { + auto _o = std::unique_ptr(new SubGraphT()); + UnPackTo(_o.get(), _resolver); +@@ -16321,6 +16397,23 @@ inline flatbuffers::Offset CreateTensorMap(flatbuffers::FlatBufferBui + _tensor_index); + } + ++inline SignatureDefT::SignatureDefT(const SignatureDefT &o) ++ : signature_key(o.signature_key), ++ subgraph_index(o.subgraph_index) { ++ inputs.reserve(o.inputs.size()); ++ for (const auto &v : o.inputs) { inputs.emplace_back((v) ? new tflite::TensorMapT(*v) : nullptr); } ++ outputs.reserve(o.outputs.size()); ++ for (const auto &v : o.outputs) { outputs.emplace_back((v) ? new tflite::TensorMapT(*v) : nullptr); } ++} ++ ++inline SignatureDefT &SignatureDefT::operator=(SignatureDefT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(inputs, o.inputs); ++ std::swap(outputs, o.outputs); ++ std::swap(signature_key, o.signature_key); ++ std::swap(subgraph_index, o.subgraph_index); ++ return *this; ++} ++ + inline SignatureDefT *SignatureDef::UnPack(const flatbuffers::resolver_function_t *_resolver) const { + auto _o = std::unique_ptr(new SignatureDefT()); + UnPackTo(_o.get(), _resolver); +@@ -16356,6 +16449,34 @@ inline flatbuffers::Offset CreateSignatureDef(flatbuffers::FlatBuf + _subgraph_index); + } + ++inline ModelT::ModelT(const ModelT &o) ++ : version(o.version), ++ description(o.description), ++ metadata_buffer(o.metadata_buffer) { ++ operator_codes.reserve(o.operator_codes.size()); ++ for (const auto &v : o.operator_codes) { operator_codes.emplace_back((v) ? new tflite::OperatorCodeT(*v) : nullptr); } ++ subgraphs.reserve(o.subgraphs.size()); ++ for (const auto &v : o.subgraphs) { subgraphs.emplace_back((v) ? new tflite::SubGraphT(*v) : nullptr); } ++ buffers.reserve(o.buffers.size()); ++ for (const auto &v : o.buffers) { buffers.emplace_back((v) ? new tflite::BufferT(*v) : nullptr); } ++ metadata.reserve(o.metadata.size()); ++ for (const auto &v : o.metadata) { metadata.emplace_back((v) ? new tflite::MetadataT(*v) : nullptr); } ++ signature_defs.reserve(o.signature_defs.size()); ++ for (const auto &v : o.signature_defs) { signature_defs.emplace_back((v) ? new tflite::SignatureDefT(*v) : nullptr); } ++} ++ ++inline ModelT &ModelT::operator=(ModelT o) FLATBUFFERS_NOEXCEPT { ++ std::swap(version, o.version); ++ std::swap(operator_codes, o.operator_codes); ++ std::swap(subgraphs, o.subgraphs); ++ std::swap(description, o.description); ++ std::swap(buffers, o.buffers); ++ std::swap(metadata_buffer, o.metadata_buffer); ++ std::swap(metadata, o.metadata); ++ std::swap(signature_defs, o.signature_defs); ++ return *this; ++} ++ + inline ModelT *Model::UnPack(const flatbuffers::resolver_function_t *_resolver) const { + auto _o = std::unique_ptr(new ModelT()); + UnPackTo(_o.get(), _resolver); +@@ -19111,6 +19232,11 @@ inline bool ModelBufferHasIdentifier(const void *buf) { + buf, ModelIdentifier()); + } + ++inline bool SizePrefixedModelBufferHasIdentifier(const void *buf) { ++ return flatbuffers::BufferHasIdentifier( ++ buf, ModelIdentifier(), true); ++} ++ + inline bool VerifyModelBuffer( + flatbuffers::Verifier &verifier) { + return verifier.VerifyBuffer(ModelIdentifier()); +diff --git a/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake b/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake +index ac91a03a48a..d1d06d09505 100644 +--- a/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake ++++ b/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake +@@ -23,7 +23,7 @@ OverridableFetchContent_Declare( + flatbuffers + GIT_REPOSITORY https://github.com/google/flatbuffers + # Sync with tensorflow/third_party/flatbuffers/workspace.bzl +- GIT_TAG v2.0.5 ++ GIT_TAG v2.0.6 + GIT_SHALLOW TRUE + GIT_PROGRESS TRUE + SOURCE_DIR "${CMAKE_BINARY_DIR}/flatbuffers" +diff --git a/tensorflow/opensource_only.files b/tensorflow/opensource_only.files +index 8cf130f5509..8ccaae2b9c6 100644 +--- a/tensorflow/opensource_only.files ++++ b/tensorflow/opensource_only.files +@@ -61,6 +61,7 @@ tensorflow/lite/delegates/gpu/cl/serialization_generated.h: + tensorflow/lite/delegates/gpu/common/gpu_model_generated.h: + tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h: + tensorflow/lite/delegates/hexagon/hexagon_nn/BUILD: ++tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h: + tensorflow/lite/experimental/acceleration/mini_benchmark/libjpeg.h: + tensorflow/lite/experimental/acceleration/mini_benchmark/special_rules.bzl: + tensorflow/lite/ios/BUILD: +diff --git a/third_party/flatbuffers/workspace.bzl b/third_party/flatbuffers/workspace.bzl +index 84aae9dc51f..ceb8a2720da 100644 +--- a/third_party/flatbuffers/workspace.bzl ++++ b/third_party/flatbuffers/workspace.bzl +@@ -5,9 +5,9 @@ load("//third_party:repo.bzl", "tf_http_archive", "tf_mirror_urls") + def repo(): + tf_http_archive( + name = "flatbuffers", +- strip_prefix = "flatbuffers-2.0.5", +- sha256 = "b01e97c988c429e164c5c7df9e87c80007ca87f593c0d73733ba536ddcbc8f98", +- urls = tf_mirror_urls("https://github.com/google/flatbuffers/archive/v2.0.5.tar.gz"), ++ strip_prefix = "flatbuffers-2.0.6", ++ sha256 = "e2dc24985a85b278dd06313481a9ca051d048f9474e0f199e372fea3ea4248c9", ++ urls = tf_mirror_urls("https://github.com/google/flatbuffers/archive/v2.0.6.tar.gz"), + build_file = "//third_party/flatbuffers:flatbuffers.BUILD", + system_build_file = "//third_party/flatbuffers:BUILD.system", + link_files = { From 7f62900e873efd9a1c30e6dab59077fcad9a947b Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 15 May 2023 16:23:00 +0200 Subject: [PATCH 7402/9987] using cpc2 made for python3 --- .../c/CPC2/CPC2-1.0.1-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb new file mode 100644 index 00000000000..f03104d04f7 --- /dev/null +++ b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'PackedBinary' + +name = 'CPC2' +version = '1.0.1' + +homepage = 'http://cpc2.cbi.pku.edu.cn' +description = """ a fast and accurate coding potential calculator based on sequence intrinsic features """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +# original sources at http://cpc2.cbi.pku.edu.cn/download.php are currently not available +# download from github mirror +source_urls = ['https://github.com/gao-lab/CPC2_standalone/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['31f3d1e2466aea25f03ffcb5abd4556cd17862ef65ed3a1e42f3d99665529d08'] + +local_svm_orig = "lib_dir + \"libsvm/libsvm-3.18/" + +postinstallcmds = [ + "sed -i 's|" + local_svm_orig + "svm-scale\"|\"$EBROOTLIBSVM/bin/svm-scale\"|g' %(installdir)s/bin/CPC2.py", + "sed -i 's|" + local_svm_orig + "svm-predict\"|\"$EBROOTLIBSVM/bin/svm-predict\"|g' %(installdir)s/bin/CPC2.py", +] + +dependencies = [ + ('Python', '3.10.4'), + ('LIBSVM', '3.30'), + ('Biopython', '1.79'), +] + +install_cmd = 'cp -a CPC2*/{bin,data} %(installdir)s/' + +sanity_check_paths = { + 'files': ['bin/CPC2.py'], + 'dirs': [], +} + +sanity_check_commands = ['CPC2.py -i %(installdir)s/data/example.fa -o example.out'] + +moduleclass = 'lib' From 8a93adc8b8693cebc5af0d48df582e5fb9ce3831 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 15 May 2023 16:25:01 +0200 Subject: [PATCH 7403/9987] Delete CPC2-0.1_fix_libsvm_path_and_python2.patch unnecessary, as source files for python3 were found --- ...CPC2-0.1_fix_libsvm_path_and_python2.patch | 82 ------------------- 1 file changed, 82 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch b/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch deleted file mode 100644 index 38190f1c201..00000000000 --- a/easybuild/easyconfigs/c/CPC2/CPC2-0.1_fix_libsvm_path_and_python2.patch +++ /dev/null @@ -1,82 +0,0 @@ -Use libsvm from the environment instead of the one provided with CPC2 -Author: Samuel Moors, Vrije Universiteit Brussel (VUB) -Update: Fix incompatible syntax with Python 3 -Updated by: Denis Kristak (Inuits) -diff -ruN cpc2_orig/bin/compress.py cpc2/bin/compress.py ---- cpc2_orig/bin/compress.py 2018-10-22 17:58:22.000000000 +0200 -+++ cpc2/bin/compress.py 2023-05-03 12:37:36.240001307 +0200 -@@ -11,7 +11,7 @@ - fq_fp = gzip.open(fq_file,mode+"b",level) - else: - sys.stderr.write("[INFO] read file '%s'\n"%fq_file) -- fq_fp = file(fq_file,mode) -+ fq_fp = open(fq_file,mode) - except: - sys.stderr.write("Error: Fail to IO file: %s\n"%(fq_file)) - sys.exit(1) -diff -ruN cpc2_orig/bin/CPC2.py cpc2/bin/CPC2.py ---- cpc2_orig/bin/CPC2.py 2023-05-02 16:41:34.222887000 +0200 -+++ cpc2/bin/CPC2.py 2023-05-03 12:40:15.817915000 +0200 -@@ -78,7 +78,7 @@ - ''' - while True: - try: -- codon,index = triplet_got.next() -+ codon,index = next(triplet_got) - except StopIteration: - break - if codon in starts and codon not in stops: -@@ -89,7 +89,7 @@ - end_extension = False - while True: - try: -- codon,index = triplet_got.next() -+ codon,index = next(triplet_got) - except StopIteration: - end_extension = True - integrity = -1 -@@ -245,9 +245,9 @@ - ''' - strinfoAmbiguous = re.compile("X|B|Z|J|U",re.I) - ptU = re.compile("U",re.I) -- ftmp_feat = file(outfile + ".feat","w") -- ftmp_svm = file(outfile + ".tmp.1","w") -- ftmp_result = file(outfile,"w") -+ ftmp_feat = open(outfile + ".feat","w") -+ ftmp_svm = open(outfile + ".tmp.1","w") -+ ftmp_result = open(outfile,"w") - ftmp_result.write("\t".join(map(str,["#ID","transcript_length","peptide_length","Fickett_score","pI","ORF_integrity","coding_probability","label"]))+"\n") - ftmp_result.close() - fickett_obj = Fickett() -@@ -288,16 +288,16 @@ - script_dir,filename = os.path.split(os.path.abspath(sys.argv[0])) - data_dir = script_dir + "/../data/" - lib_dir = script_dir + "/../libs/" -- app_svm_scale = lib_dir + "libsvm/libsvm-3.18/svm-scale" -- app_svm_predict = lib_dir + "libsvm/libsvm-3.18/svm-predict" -- os.system('test -x '+ app_svm_scale + ' || echo \"[ERROR] No excutable svm-scale on CPC2 path!\" > /dev/stderr') -- os.system('test -x '+ app_svm_predict + ' || echo \"[ERROR] No excutable svm-predict on CPC2 path!\" > /dev/stderr') -+ app_svm_scale = 'svm-scale' -+ app_svm_predict = 'svm-predict' -+ os.system('which ' + app_svm_scale + ' || echo \"[ERROR] No excutable svm-scale on CPC2 path!\" > /dev/stderr') -+ os.system('which ' + app_svm_predict + ' || echo \"[ERROR] No excutable svm-predict on CPC2 path!\" > /dev/stderr') - - cmd = app_svm_scale + ' -r ' + data_dir + 'cpc2.range ' + outfile + '.tmp.1 > ' + outfile + '.tmp.2 &&' - cmd = cmd + app_svm_predict + ' -b 1 -q ' + outfile + '.tmp.2 ' + data_dir + 'cpc2.model ' + outfile + '.tmp.1 &&' - cmd = cmd + 'awk -vOFS="\\t" \'{if ($1 == 1){print $2,"coding"} else if ($1 == 0){print $2,"noncoding"}}\' ' + outfile + '.tmp.1 > ' + outfile + '.tmp.2 &&' - cmd = cmd + 'paste ' + outfile + '.feat ' + outfile + '.tmp.2 >>' + outfile -- command = suprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) -+ command = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) - (outtext, errtext) = command.communicate() - exitstatus = command.returncode - os.system('rm -f ' + outfile + '.tmp.1 ' + outfile + '.tmp.2') -@@ -306,7 +306,8 @@ - # pass - if exitstatus == 0: - rm_cmd = "rm -f " + outfile + '.feat' -- subprocess.call(rm_cmd) -+ print(rm_cmd) -+ subprocess.run(rm_cmd, shell=True) - sys.stderr.write("[INFO] Running Done!\n") - return 0 - else: From 9b71436e2705f060e827578a2aca0c92486bc534 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Mon, 15 May 2023 16:25:37 +0200 Subject: [PATCH 7404/9987] Delete CPC2-0.1-foss-2022a.eb removing, as src files for py3 were found (and version change was necessary, renaming the file) --- .../easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb | 40 ------------------- 1 file changed, 40 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb deleted file mode 100644 index e2ffcd2d854..00000000000 --- a/easybuild/easyconfigs/c/CPC2/CPC2-0.1-foss-2022a.eb +++ /dev/null @@ -1,40 +0,0 @@ -# Author: Samuel Moors, Vrije Universiteit Brussel (VUB) -# Updated: Denis Kristak (Inuits) -# Update to a Python3 version -easyblock = 'PackedBinary' - -name = 'CPC2' -version = '0.1' -local_commit = '813487e' - -homepage = 'http://cpc2.gao-lab.org/' -description = """ a fast and accurate coding potential calculator based on sequence intrinsic features """ - -toolchain = {'name': 'foss', 'version': '2022a'} - -# original sources at http://cpc2.cbi.pku.edu.cn/download.php are currently not available -# download from github mirror -source_urls = ['https://github.com/lucventurini/CPC2/archive/'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = ['%(name)s-%(version)s_fix_libsvm_path_and_python2.patch'] -checksums = [ - {'CPC2-0.1.tar.gz': '6fd4f3fb05b179073709c033481ae082085eabc7c5281cd743c9419d3ec6de67'}, - {'CPC2-0.1_fix_libsvm_path_and_python2.patch': '657f552ebfad925e8c051a19426cd5bb1b8ad7da8cdcc3e701e1220673330842'}, -] - -dependencies = [ - ('Python', '3.10.4'), - ('LIBSVM', '3.30'), - ('Biopython', '1.79'), -] - -install_cmd = 'cp -a CPC2*/{bin,data} %(installdir)s/' - -sanity_check_paths = { - 'files': ['bin/CPC2.py'], - 'dirs': ['data'], -} - -sanity_check_commands = ['CPC2.py -i %(installdir)s/data/example.fa -o example.out'] - -moduleclass = 'lib' From 7f48b5ecd0c076ff6e01a45d507292910ea8d53d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 May 2023 17:41:38 +0200 Subject: [PATCH 7405/9987] adding easyconfigs: vsc-mympirun-5.3.1.eb --- .../v/vsc-mympirun/vsc-mympirun-5.3.1.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.1.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.1.eb new file mode 100644 index 00000000000..944357dedd6 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.1.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'vsc-mympirun' +version = '5.3.1' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """mympirun is a tool to make it easier for users of HPC clusters to +run MPI programs with good performance.""" + +# we build this to work with every python version +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +use_pip = False + +exts_list = [ + ('setuptools', '41.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6afa61b391dcd16cb8890ec9f66cc4015a8a31a6e1c2b4e0c464514be1a3d722'], + }), + ('future', '0.18.3', { + 'checksums': ['34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307'], + }), + ('pbr', '5.11.1', { + 'checksums': ['aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '5.0.2', { + 'checksums': ['06f18d7d65b44428202b145a9a36e99c2ee00d1eb992df0caf881d4664377891'], + }), + ('IPy', '1.01', { + 'modulename': 'IPy', + 'checksums': ['edeca741dea2d54aca568fa23740288c3fe86c0f3ea700344571e9ef14a7cc1a'], + }), + ('vsc-install', '0.18.5', { + 'modulename': 'vsc.install', + 'checksums': ['90e00ddde9d394fdb5426f6f4d466425c69acded3fdf25ce73a0b345f6afc036'], + }), + ('vsc-base', '3.5.3', { + 'modulename': 'vsc.utils', + 'checksums': ['7c4df43fc0508d6857acf8127deb1088b899cd364a14c688dac2d61617579ba9'], + }), + (name, version, { + 'modulename': False, + 'checksums': ['67fb89855044678e595fef39415aafdd26a1a9a4c89b3f89a4d34a1824df7bcf'], + }), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mypmirun', 'bin/mympisanity', 'bin/mytasks'], + 'dirs': ['bin/fake'], +} +sanity_check_commands = ["mympirun --help"] + +# can't enable 'pip check' since pip may not be installed in OS +sanity_pip_check = False + +moduleclass = 'tools' From ae4f9c64fd60825b43976258007742b8dd2a58af Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 15 May 2023 20:10:22 +0200 Subject: [PATCH 7406/9987] Annocript + small change to BioPerl --- .../Annocript-2.0-foss-2022a-Python-3.10.4.eb | 77 +++++++++++++++++++ .../a/Annocript/annocript_fix_paths.patch | 36 +++++++++ .../a/Annocript/annocript_no_background.patch | 23 ++++++ .../b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb | 7 +- 4 files changed, 142 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb create mode 100644 easybuild/easyconfigs/a/Annocript/annocript_fix_paths.patch create mode 100644 easybuild/easyconfigs/a/Annocript/annocript_no_background.patch diff --git a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb new file mode 100644 index 00000000000..4c30feb8389 --- /dev/null +++ b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb @@ -0,0 +1,77 @@ +easyblock = 'PackedBinary' + +name = 'Annocript' +version = '2.0' +local_commit = '84fd67b' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/frankMusacchia/Annocript' +description = """ Annocript is a pipeline for the annotation of de-novo generated transcriptomes. + It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division + adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways. + Annocript also gives information about the longest ORF and the non-coding potential using external software. + Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology + and sequence features. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/frankMusacchia/Annocript/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = [ + 'annocript_fix_paths.patch', + 'annocript_no_background.patch', +] +checksums = [ + {'Annocript-2.0.tar.gz': '151dec3a390826fd2bcc7d794a9565535702dfc9c4672842e825a9fcf21406d9'}, + {'annocript_fix_paths.patch': '95359e335a6a992f5f269e8f199c9df92d765f7ff41890298acead12d562685c'}, + {'annocript_no_background.patch': 'ca02c2b02b7574c25128c9a4ce2b69a13a0bb2b409efd2ea63562053bf2e2c57'}, +] + +dependencies = [ + ('Compress-Raw-Zlib', '2.202'), + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('BioPerl', '1.7.8'), + ('R', '4.2.1'), + ('CPC2', '1.0.1'), + ('BLAST+', '2.13.0'), + ('LIBSVM', '3.30'), + ('MariaDB', '10.9.3'), + ('DBD-mysql', '4.050'), +] + +postinstallcmds = [ + # Extract dna2pep to annocript's bin folder, set permissions. + # It is just a series Python scripts and I'm not building it as a standalone dependency, as sources for this SW + # are not available elsewhere than in the Annocript repository anyway. + "mkdir %(installdir)s/bin ", + "cp %(builddir)s/Annocript-*/DL_PROGRAMS/dna2pep-1.1.tar.gz %(installdir)s/bin ", + "cd %(installdir)s/bin && tar -zxvf dna2pep-1.1.tar.gz ", + "rm %(installdir)s/bin/dna2pep-1.1.tar.gz && chmod 755 %(installdir)s/bin/dna2pep-1.1/dna2pep.py ", + # extract annocript itself + 'mv %(installdir)s/annocript.pl %(installdir)s/bin/', + 'sed -i -e "1s|#!.*$|#!/usr/bin/env perl|g" %(installdir)s/bin/annocript.pl', + 'chmod a+rx %(installdir)s/bin/annocript.pl', +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('CGI', '4.43', { + 'source_tmpl': 'CGI-4.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + 'checksums': ['14b94f9df6e48fc26ebc4fa1e01a7b534cbc1611028a49028f9ac9d8ca27b734'], + }), +] + +modextrapaths = {'PERL5LIB': ['', 'lib/perl5/site_perl/%(perlver)s/']} + +sanity_check_paths = { + 'files': ['bin/annocript.pl'], + 'dirs': [], +} + +sanity_check_commands = ['annocript.pl --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/Annocript/annocript_fix_paths.patch b/easybuild/easyconfigs/a/Annocript/annocript_fix_paths.patch new file mode 100644 index 00000000000..c863a8425a1 --- /dev/null +++ b/easybuild/easyconfigs/a/Annocript/annocript_fix_paths.patch @@ -0,0 +1,36 @@ +Do not use full paths for executables in the config file: they should be in the PATH +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ruN Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/CONFIGURATION/config_user.txt Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/CONFIGURATION/config_user.txt +--- Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/CONFIGURATION/config_user.txt 2023-05-15 18:02:35.946010508 +0200 ++++ Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/CONFIGURATION/config_user.txt 2023-05-15 18:04:08.262818993 +0200 +@@ -114,7 +114,7 @@ + + #Programs Paths + diamondPath = +-blastPath = /home/francesco/bin/ncbi-blast-2.7.1+/bin/ +-lncRNAPredProgPath = /home/francesco/bin/CPC2-beta/bin/CPC2.py +-dna2pepPath = /home/francesco/bin/dna2pep-1.1/dna2pep.py ++blastPath = ++lncRNAPredProgPath = CPC2.py ++dna2pepPath = dna2pep.py + ############################## +diff -ruN Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/LIB/annocript_management.pm Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/LIB/annocript_management.pm +--- Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/LIB/annocript_management.pm 2023-05-15 18:02:36.477018945 +0200 ++++ Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/LIB/annocript_management.pm 2023-05-15 18:05:42.646383000 +0200 +@@ -748,9 +748,15 @@ + + #Here we collect the path to the programs using an array initialized in the beginning of the page + # with all the programs used by Annocript ++ # first expand executables to full path ++ use File::Which; + foreach my $program (@$blastProgramsInUse){ + my $var= $program.'Path'; +- $configHash->{$var} = $configHash->{'blastPath'}.$program; ++ $configHash->{$var} = which($program) or die "error: blast executable $program not found\n"; ++ } ++ foreach my $mypath ('lncRNAPredProgPath', 'dna2pepPath', 'makeblastdbPath'){ ++ my $myexec = $configHash->{$mypath}; ++ $configHash->{$mypath} = which($myexec) or die "error: executable $myexec not found\n"; + } + + #CONTROLS THE PATH TO THE PROGRAMS diff --git a/easybuild/easyconfigs/a/Annocript/annocript_no_background.patch b/easybuild/easyconfigs/a/Annocript/annocript_no_background.patch new file mode 100644 index 00000000000..cf3b8ef36e3 --- /dev/null +++ b/easybuild/easyconfigs/a/Annocript/annocript_no_background.patch @@ -0,0 +1,23 @@ +Do not start perl script in background +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ruN Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/annocript.pl Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/annocript.pl +--- Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/annocript.pl 2023-05-15 18:02:36.827824452 +0200 ++++ Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/annocript.pl 2023-05-15 18:13:45.525029000 +0200 +@@ -301,7 +301,7 @@ + ."\n\nPlease let us know if any problem occurs during the computation or you don't get from Annocript the expected result.\n" + ."You may want to use the forum at: https://groups.google.com/forum/#!forum/annocript.\n",$log_file);#DEBUGCODE + +- nice_printing("STARTING ANNOCRIPT IN BACKGROUND! BYE!",$log_file); ++ nice_printing("STARTING ANNOCRIPT IN FOREGROUND! BYE!",$log_file); + + close ( $logFHandle ); + +@@ -325,7 +325,7 @@ + chdir $program_folder; + + #This perl script will be run in background +- my $runAnnocriptCmd = "nohup perl ".$configHash->{'ProgExecFolder'} ."/annocript_executor.pl $user_config $program_config $timesFile $configHashPath >> $log_file &"; ++ my $runAnnocriptCmd = "perl ".$configHash->{'ProgExecFolder'} ."/annocript_executor.pl $user_config $program_config $timesFile $configHashPath >> $log_file"; + ( system($runAnnocriptCmd) ) == 0 + or die("Unable to start annocript_executor!\n"); + } diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb index 5b7057ffa26..72311a255bb 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb @@ -36,7 +36,12 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], }), - ('BioPerl', version, { + ('Bio::DB::SeqFeature', '1.7.4', { + 'source_tmpl': 'Bio-DB-SeqFeature-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['f2304f95fb77a12732b1883817525609e54fa70b2638ed2de0696d503407fe91'], + }), + (name, version, { 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], }), From 848e40a4447ad3dcccb4a5be364572e79c5c1b2a Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 15 May 2023 20:14:55 +0200 Subject: [PATCH 7407/9987] updated moduleclass --- .../a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb index 4c30feb8389..aa1f8921915 100644 --- a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb +++ b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb @@ -74,4 +74,4 @@ sanity_check_paths = { sanity_check_commands = ['annocript.pl --help'] -moduleclass = 'lib' +moduleclass = 'bio' From c3a6165d8998d5970807ea7ca0f8502d2771ac8e Mon Sep 17 00:00:00 2001 From: p251204 Date: Tue, 16 May 2023 09:50:12 +0200 Subject: [PATCH 7408/9987] adding easyconfigs: breseq-0.38.1-foss-2022a.eb --- .../b/breseq/breseq-0.38.1-foss-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/breseq/breseq-0.38.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/breseq/breseq-0.38.1-foss-2022a.eb b/easybuild/easyconfigs/b/breseq/breseq-0.38.1-foss-2022a.eb new file mode 100644 index 00000000000..7d1f5285c68 --- /dev/null +++ b/easybuild/easyconfigs/b/breseq/breseq-0.38.1-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'breseq' +version = '0.38.1' + +homepage = 'https://barricklab.org/breseq' +description = "breseq is a computational pipeline for the analysis of short-read re-sequencing data" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/barricklab/breseq/releases/download/v%(version)s/'] +sources = ['breseq-%(version)s-Source.tar.gz'] +checksums = ['92af34f7248f7c8cf65951e1b86ffc0d6f7446dbe9d3323aa43c577ea1ff48b3'] + +dependencies = [ + ('R', '4.2.1'), + ('Bowtie2', '2.4.5'), + ('zlib', '1.2.12'), + ('ncurses', '6.3'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/breseq', 'bin/gdtools'], + 'dirs': [], +} + +# breseq --help exists with non-zero exit code, so use grep +sanity_check_commands = ["breseq --help | grep 'Usage: breseq'"] + +moduleclass = 'bio' From 9e87e7a00b605d3e16de58e2bf40c256bfc3dc5e Mon Sep 17 00:00:00 2001 From: p251204 Date: Tue, 16 May 2023 10:31:43 +0200 Subject: [PATCH 7409/9987] adding easyconfigs: PALEOMIX-1.3.7-foss-2022a.eb, seqtk-1.3-GCC-11.3.0.eb, mapDamage-2.2.1-foss-2022a.eb --- .../m/mapDamage/mapDamage-2.2.1-foss-2022a.eb | 36 ++++++++++++++ .../p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb | 48 +++++++++++++++++++ .../s/seqtk/seqtk-1.3-GCC-11.3.0.eb | 33 +++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2022a.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2022a.eb new file mode 100644 index 00000000000..500f6c287a4 --- /dev/null +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'mapDamage' +version = '2.2.1' + +github_account = 'ginolhac' + +homepage = 'https://ginolhac.github.io/mapDamage/' +description = """mapDamage2 is a computational framework written in Python and + R, which tracks and quantifies DNA damage patterns among ancient DNA + sequencing reads generated by Next-Generation Sequencing platforms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-2.2.1_use-external-seqtk.patch'] +checksums = [ + 'f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c', # 2.2.1.tar.gz + 'f01a90c29123460f8cb6ba2fe0f42e9ec66b0febff430d4ec4f0ab1197c552e7', # mapDamage-2.2.1_use-external-seqtk.patch +] + +dependencies = [ + ('Python', '3.10.4'), + ('seqtk', '1.3'), + ('Pysam', '0.19.1'), + ('R', '4.2.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_commands = ['mapDamage --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb new file mode 100644 index 00000000000..c9b7f7186e6 --- /dev/null +++ b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'PALEOMIX' +version = '1.3.7' + +homepage = 'https://github.com/MikkelSchubert/paleomix' +description = """The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing + of High-Throughput Sequencing (HTS) data.""" + +toolchain = {'name' : 'foss', 'version' : '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SAMtools', '1.16.1'), + ('AdapterRemoval', '2.3.3'), + ('picard', '3.0.0', '-Java-17', SYSTEM), + ('Bowtie2', '2.4.5'), + ('mapDamage', '2.2.1'), + ('Pysam', '0.19.1'), + ('ruamel.yaml', '0.17.21'), +] + +use_pip = True + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('ConfigArgParse', '1.5.3', { + 'checksums': ['1b0b3cbf664ab59dada57123c81eff3d9737e0d11d8cf79e3d6eb10823f1739f'], + }), + ('setproctitle', '1.3.2', { + 'checksums': ['b9fb97907c830d260fa0658ed58afd48a86b2b88aac521135c352ff7fd3477fd'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['effc402cd4207916ee062edf68b18b21b6c1adc596eea30d58805a75c8652767'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ['paleomix --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.3.0.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.3.0.eb new file mode 100644 index 00000000000..165375a4e10 --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'seqtk' +version = '1.3' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563'] + +dependencies = [('zlib', '1.2.12')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BINDIR=%(installdir)s/bin/' + +sanity_check_paths = { + 'files': ['bin/seqtk'], + 'dirs': [], +} + +sanity_check_commands = ["seqtk 2>&1 | grep 'Usage:[ ]*seqtk'"] + +moduleclass = 'bio' From 950678994ec0c5d5819d148bb2f8f53a217ade08 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 16 May 2023 10:54:51 +0200 Subject: [PATCH 7410/9987] use picard 2.25.1 --- easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb index c9b7f7186e6..e2b4d2246f8 100644 --- a/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb @@ -13,7 +13,7 @@ dependencies = [ ('Python', '3.10.4'), ('SAMtools', '1.16.1'), ('AdapterRemoval', '2.3.3'), - ('picard', '3.0.0', '-Java-17', SYSTEM), + ('picard', '2.25.1', '-Java-11', SYSTEM), ('Bowtie2', '2.4.5'), ('mapDamage', '2.2.1'), ('Pysam', '0.19.1'), From f8c4e498e408d4bf3053bc2d3e7f8874ea16aa80 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 16 May 2023 11:17:13 +0200 Subject: [PATCH 7411/9987] remove whitespaces --- easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb index e2b4d2246f8..b145680d1ec 100644 --- a/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/MikkelSchubert/paleomix' description = """The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data.""" -toolchain = {'name' : 'foss', 'version' : '2022a'} +toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), From ff933f3dce0eb97275459f6cbe433f4159b3f840 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 16 May 2023 11:55:40 +0200 Subject: [PATCH 7412/9987] adding easyconfigs: Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb, Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb --- ...7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb | 37 +++++++++++++++++++ ...aindecode-0.7-foss-2021a-PyTorch-1.10.2.eb | 36 ++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb new file mode 100644 index 00000000000..6e6c6ca13e1 --- /dev/null +++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'Braindecode' +version = '0.7' +versionsuffix = '-PyTorch-1.10.2-CUDA-%(cudaver)s' + +homepage = 'https://braindecode.org/' +description = """Braindecode is an open-source Python toolbox for decoding raw +electrophysiological brain data with deep learning models. It includes dataset +fetchers, data preprocessing and visualization tools, as well as +implementations of several deep learning architectures and data augmentations +for analysis of EEG, ECoG and MEG.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), + ('matplotlib', '3.4.2'), + ('MNE-Python', '0.24.1'), + ('MOABB', '0.4.6'), + ('skorch', '0.11.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['e2bca3d096b70b041d7b30ca2dfeaffae79ea722a4578cee04c9864ec07effce'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb new file mode 100644 index 00000000000..c503d33df9c --- /dev/null +++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Braindecode' +version = '0.7' +versionsuffix = '-PyTorch-1.10.2' + +homepage = 'https://braindecode.org/' +description = """Braindecode is an open-source Python toolbox for decoding raw +electrophysiological brain data with deep learning models. It includes dataset +fetchers, data preprocessing and visualization tools, as well as +implementations of several deep learning architectures and data augmentations +for analysis of EEG, ECoG and MEG.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), + ('matplotlib', '3.4.2'), + ('MNE-Python', '0.24.1'), + ('MOABB', '0.4.6'), + ('skorch', '0.11.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['e2bca3d096b70b041d7b30ca2dfeaffae79ea722a4578cee04c9864ec07effce'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From a41289da5b0bc16fafe031f8d149598c9645464f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 16 May 2023 12:14:41 +0200 Subject: [PATCH 7413/9987] adding easyconfigs: CREST-2.11.2-intel-2021a.eb --- .../c/CREST/CREST-2.11.2-intel-2021a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CREST/CREST-2.11.2-intel-2021a.eb diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.11.2-intel-2021a.eb b/easybuild/easyconfigs/c/CREST/CREST-2.11.2-intel-2021a.eb new file mode 100644 index 00000000000..4746716d31d --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.11.2-intel-2021a.eb @@ -0,0 +1,32 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'CMakeMake' + +name = 'CREST' +version = '2.11.2' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f17da872064eb64502ac24c19e431467940d98dcb1bd391f7267f412a0a79dab'] + +builddependencies = [('CMake', '3.20.1')] + +sanity_check_paths = { + 'files': ['bin/%s' % name.lower()], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' From ff15d5374978cd446b9d8b299b140ac257ecc810 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Tue, 16 May 2023 12:15:52 +0200 Subject: [PATCH 7414/9987] removed python version suffix --- .../a/Annocript/Annocript-2.0-foss-2022a.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a.eb b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a.eb new file mode 100644 index 00000000000..7efa2268907 --- /dev/null +++ b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a.eb @@ -0,0 +1,76 @@ +easyblock = 'PackedBinary' + +name = 'Annocript' +version = '2.0' +local_commit = '84fd67b' + +homepage = 'https://github.com/frankMusacchia/Annocript' +description = """ Annocript is a pipeline for the annotation of de-novo generated transcriptomes. + It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division + adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways. + Annocript also gives information about the longest ORF and the non-coding potential using external software. + Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology + and sequence features. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/frankMusacchia/Annocript/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = [ + 'annocript_fix_paths.patch', + 'annocript_no_background.patch', +] +checksums = [ + {'Annocript-2.0.tar.gz': '151dec3a390826fd2bcc7d794a9565535702dfc9c4672842e825a9fcf21406d9'}, + {'annocript_fix_paths.patch': '95359e335a6a992f5f269e8f199c9df92d765f7ff41890298acead12d562685c'}, + {'annocript_no_background.patch': 'ca02c2b02b7574c25128c9a4ce2b69a13a0bb2b409efd2ea63562053bf2e2c57'}, +] + +dependencies = [ + ('Compress-Raw-Zlib', '2.202'), + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('BioPerl', '1.7.8'), + ('R', '4.2.1'), + ('CPC2', '1.0.1'), + ('BLAST+', '2.13.0'), + ('LIBSVM', '3.30'), + ('MariaDB', '10.9.3'), + ('DBD-mysql', '4.050'), +] + +postinstallcmds = [ + # Extract dna2pep to annocript's bin folder, set permissions. + # It is just a series Python scripts and I'm not building it as a standalone dependency, as sources for this SW + # are not available elsewhere than in the Annocript repository anyway. + "mkdir %(installdir)s/bin ", + "cp %(builddir)s/Annocript-*/DL_PROGRAMS/dna2pep-1.1.tar.gz %(installdir)s/bin ", + "cd %(installdir)s/bin && tar -zxvf dna2pep-1.1.tar.gz ", + "rm %(installdir)s/bin/dna2pep-1.1.tar.gz && chmod 755 %(installdir)s/bin/dna2pep-1.1/dna2pep.py ", + # extract annocript itself + 'mv %(installdir)s/annocript.pl %(installdir)s/bin/', + 'sed -i -e "1s|#!.*$|#!/usr/bin/env perl|g" %(installdir)s/bin/annocript.pl', + 'chmod a+rx %(installdir)s/bin/annocript.pl', +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('CGI', '4.43', { + 'source_tmpl': 'CGI-4.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + 'checksums': ['14b94f9df6e48fc26ebc4fa1e01a7b534cbc1611028a49028f9ac9d8ca27b734'], + }), +] + +modextrapaths = {'PERL5LIB': ['', 'lib/perl5/site_perl/%(perlver)s/']} + +sanity_check_paths = { + 'files': ['bin/annocript.pl'], + 'dirs': [], +} + +sanity_check_commands = ['annocript.pl --help'] + +moduleclass = 'bio' From d455e4779699305d261f54c6a5bb2b446291eac5 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 16 May 2023 12:16:39 +0200 Subject: [PATCH 7415/9987] Update easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb index f03104d04f7..27e523b16f2 100644 --- a/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb @@ -8,8 +8,6 @@ description = """ a fast and accurate coding potential calculator based on seque toolchain = {'name': 'foss', 'version': '2022a'} -# original sources at http://cpc2.cbi.pku.edu.cn/download.php are currently not available -# download from github mirror source_urls = ['https://github.com/gao-lab/CPC2_standalone/archive/'] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] checksums = ['31f3d1e2466aea25f03ffcb5abd4556cd17862ef65ed3a1e42f3d99665529d08'] From 7d1ab2487f5957a877701a135087c9e2105e3396 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Tue, 16 May 2023 12:16:57 +0200 Subject: [PATCH 7416/9987] Update easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb index 27e523b16f2..008b9e1c179 100644 --- a/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'PackedBinary' name = 'CPC2' version = '1.0.1' -homepage = 'http://cpc2.cbi.pku.edu.cn' +homepage = 'http://cpc2.gao-lab.org/' description = """ a fast and accurate coding potential calculator based on sequence intrinsic features """ toolchain = {'name': 'foss', 'version': '2022a'} From 904ef5ad87539dc1f0da1cab9d5c5d47d995de36 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 16 May 2023 13:51:09 +0200 Subject: [PATCH 7417/9987] Rebuild with compiled Go code --- .../EDirect-19.0.20230216-foss-2021a.eb | 86 ------------------- .../EDirect-19.5.20230508-GCCcore-10.3.0.eb | 64 ++++++++++++++ 2 files changed, 64 insertions(+), 86 deletions(-) delete mode 100644 easybuild/easyconfigs/e/EDirect/EDirect-19.0.20230216-foss-2021a.eb create mode 100644 easybuild/easyconfigs/e/EDirect/EDirect-19.5.20230508-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/e/EDirect/EDirect-19.0.20230216-foss-2021a.eb b/easybuild/easyconfigs/e/EDirect/EDirect-19.0.20230216-foss-2021a.eb deleted file mode 100644 index 258e192f57d..00000000000 --- a/easybuild/easyconfigs/e/EDirect/EDirect-19.0.20230216-foss-2021a.eb +++ /dev/null @@ -1,86 +0,0 @@ -## -# This is a contribution from SIB Swiss Institute of Bioinformatics -# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it -# -# Authors:: Sebastien Moretti -# -## -easyblock = 'Binary' - -name = 'EDirect' -version = '19.0.20230216' - -homepage = 'https://www.ncbi.nlm.nih.gov/books/NBK25501/' -# See also https://dataguide.nlm.nih.gov/edirect/install.html -description = """Entrez Direct (EDirect) provides access to the NCBI's suite of -interconnected databases from a Unix terminal window. Search terms are entered -as command-line arguments. Individual operations are connected with Unix pipes -to construct multi-step queries. Selected records can then be retrieved in a -variety of formats.""" -# software_license = 'Public Domain' - -toolchain = {'name': 'foss', 'version': '2021a'} - -source_urls = ['https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/%(version)s/'] -# Only get Linux x86_64 and ARM binaries -sources = [ - {'download_filename': 'edirect-%(version)s.tar.gz', - 'filename': 'edirect-%s.tar.gz' % version, - }, - {'download_filename': 'rchive.ARM.gz', - 'filename': 'rchive-%s.ARM.gz' % version, - }, - {'download_filename': 'rchive.Linux.gz', - 'filename': 'rchive-%s.Linux.gz' % version, - }, - {'download_filename': 'transmute.ARM.gz', - 'filename': 'transmute-%s.ARM.gz' % version, - }, - {'download_filename': 'transmute.Linux.gz', - 'filename': 'transmute-%s.Linux.gz' % version, - }, - {'download_filename': 'xtract.ARM.gz', - 'filename': 'xtract-%s.ARM.gz' % version, - }, - {'download_filename': 'xtract.Linux.gz', - 'filename': 'xtract-%s.Linux.gz' % version, - }, -] -checksums = [ - 'a571af35b8debef31eab3f79246a2c419c8802dc8948141a130c6b3bdd0e4394', # edirect-19.0.20230216.tar.gz - 'eba2c7485f1bd2fd66c81493e06573cea006d001ad4ee79934d1412802a57aaa', # rchive-19.0.20230216.ARM.gz - 'dbc1c1050bd8d9144a3e00c1a21efb43b9ac263a1d7366cdbe89db3afcb93901', # rchive-19.0.20230216.Linux.gz - '1ac989fdad9314e10be912c29363cd4675d3d6181bfac281b230b2217c053298', # transmute-19.0.20230216.ARM.gz - '1c6824a4c17cbeb63462afee8e3c1c1fe82fe9b0af720a5b984c47822163bc54', # transmute-19.0.20230216.Linux.gz - '6450b5bab81c85403c136a45a4426c464d191951fd956d6ceff12e2bb3553a79', # xtract-19.0.20230216.ARM.gz - '857b1d9efae55b87f86b52c2a8925c29eb35b5fd5afb006762a3bb492cb98662', # xtract-19.0.20230216.Linux.gz -] - -dependencies = [ - ('Python', '3.9.5'), - ('Perl', '5.32.1'), -] - -extract_sources = True - -postinstallcmds = [ - "mkdir %(installdir)s/bin && cd %(installdir)s/ && " - "install %(builddir)s/*.ARM %(builddir)s/*.Linux . && " - "for arm in *.ARM; do ln -s $arm ${arm/-*.ARM/.ARM}; done && " - "for lin in *.Linux; do ln -s $lin ${lin/-*.Linux/.Linux}; done && " - "cd bin/ && ln -s ../* . && rm -f easybuild README readme.pdf bin" -] - -sanity_check_paths = { - 'files': ['einfo', 'README'], - 'dirs': ['bin', 'cmd', 'eutils', 'help'], -} - -sanity_check_commands = [ - "esearch -version && " - "xtract -version && " - "esearch -db pubmed -query 'Babalobi OO[au] AND 2008[pdat]' | efetch -format xml | " - "xtract -pattern Author -if Affiliation -contains Medicine -element Initials" -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EDirect/EDirect-19.5.20230508-GCCcore-10.3.0.eb b/easybuild/easyconfigs/e/EDirect/EDirect-19.5.20230508-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..b3fd36f0616 --- /dev/null +++ b/easybuild/easyconfigs/e/EDirect/EDirect-19.5.20230508-GCCcore-10.3.0.eb @@ -0,0 +1,64 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## +easyblock = 'Binary' + +name = 'EDirect' +version = '19.5.20230508' + +homepage = 'https://www.ncbi.nlm.nih.gov/books/NBK25501/' +# See also https://dataguide.nlm.nih.gov/edirect/install.html +description = """Entrez Direct (EDirect) provides access to the NCBI's suite of +interconnected databases from a Unix terminal window. Search terms are entered +as command-line arguments. Individual operations are connected with Unix pipes +to construct multi-step queries. Selected records can then be retrieved in a +variety of formats.""" +# software_license = 'Public Domain' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/%(version)s/'] +sources = [ + {'download_filename': 'edirect-%(version)s.tar.gz', + 'filename': 'edirect-%s.tar.gz' % version, + }, +] +checksums = [ + '1a73f832a464f150e41c9330e3d8f8f8775f7c39c9352639480289d588fa4889', # edirect-19.5.20230508.tar.gz +] + +builddependencies = [ + ('Go', '1.20.4', '', SYSTEM), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), +] + +extract_sources = True + +postinstallcmds = [ + "mkdir %(installdir)s/bin && cd %(installdir)s/cmd/ && " + "sed -i 's@target=\"\\$HOME/Misc/scripts/\"@target=\"\\$PWD/../\"@' build.sh && " + "./build.sh install && cd ../ && rm -rf cmd/ eutils/ && " + "cd bin/ && ln -s ../* . && rm -f easybuild README readme.pdf bin" +] + +sanity_check_paths = { + 'files': ['einfo', 'README'], + 'dirs': ['bin', 'help'], +} + +sanity_check_commands = [ + "esearch -version && " + "xtract -version && " + "esearch -db pubmed -query 'Babalobi OO[au] AND 2008[pdat]' | efetch -format xml | " + "xtract -pattern Author -if Affiliation -contains Medicine -element Initials" +] + +moduleclass = 'bio' From 6bc7da1abf066dae4852d72d30985ba4d55ae72f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 16 May 2023 14:27:53 +0200 Subject: [PATCH 7418/9987] adding easyconfigs: T-Coffee-13.45.61.3c310a9.eb --- .../t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb diff --git a/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb b/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb new file mode 100644 index 00000000000..006a187b85b --- /dev/null +++ b/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb @@ -0,0 +1,40 @@ +easyblock = "Tarball" + +name = 'T-Coffee' +version = '13.45.61.3c310a9' + +homepage = 'https://www.tcoffee.org/' +description = """A collection of tools for Computing, Evaluating and Manipulating Multiple +Alignments of DNA, RNA, Protein Sequences and Structures""" + +toolchain = SYSTEM + +source_urls = ['https://s3.eu-central-1.amazonaws.com/tcoffee-packages/Archives/'] +sources = ['T-COFFEE_installer_Version_%(version)s_linux_x64.tar.gz'] +checksums = ['8bc60336f5c203d4a20cc8c9e0ba10c5f4275a11ccfd15a0dd26a03510314513'] + +sanity_check_paths = { + 'files': ['bin/t_coffee'], + 'dirs': ['mcoffee', 'perl', 'plugins', 'src'], +} + +sanity_check_commands = ["t_coffee --help"] + +modextrapaths = { + 'PATH': 'perl/bin', + 'PERL5LIB': 'perl/lib/perl5', +} + +# optionally set extra variables +# default DIR_4_TCOFFEE is $HOME/.t_coffee +# see https://tcoffee.readthedocs.io/en/latest/tcoffee_technical_documentation.html#setting-up-the-variables +_tcoffee_dir = '/tmp/.t_coffee' +modextravars = { + 'DIR_4_TCOFFEE': _tcoffee_dir, + 'TMP_4_TCOFFEE': _tcoffee_dir + '/tmp', + 'CACHE_4_TCOFFEE': _tcoffee_dir + '/cache', + 'PLUGINS_4_TCOFFEE': _tcoffee_dir + '/plugins', + # 'PDB_DIR': , +} + +moduleclass = 'bio' From b3d89091a65d21961fe37910d718e475cadec68f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 16 May 2023 14:38:54 +0200 Subject: [PATCH 7419/9987] adding easyconfigs: turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb --- ...inesFoam-20220516-foss-2020a-OpenFOAM-8.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb diff --git a/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb b/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb new file mode 100644 index 00000000000..890702f6e8a --- /dev/null +++ b/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb @@ -0,0 +1,35 @@ +easyblock = 'CmdCp' + +name = 'turbinesFoam' +version = '20220516' +_openfoamver = '8' +_commit = '480eeef' +versionsuffix = '-OpenFOAM-%s' % _openfoamver + +homepage = 'https://github.com/turbinesFoam/turbinesFoam' +description = """ +turbinesFoam is a library for simulating wind and marine hydrokinetic turbines +in OpenFOAM using the actuator line method. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +github_account = 'turbinesFoam' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['2e13faec8b2489e91108ea3fc8eb31b1b32bb1478e608853c9cfa9b78a3206d1'] + +dependencies = [ + ('OpenFOAM', _openfoamver), +] + +cmds_map = [('.*', 'source "$FOAM_BASH" && FOAM_USER_LIBBIN="$PWD/lib" ./Allwmake')] + +files_to_copy = ['lib'] + +sanity_check_paths = { + 'files': ['lib/libturbinesFoam.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From b37c3d85a8fb3e1eb84929c3c82fd3c2e91d5de5 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 16 May 2023 15:23:56 +0200 Subject: [PATCH 7420/9987] adding easyconfigs: Yambo-5.2-intel-2021b.eb --- .../y/Yambo/Yambo-5.2-intel-2021b.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb new file mode 100644 index 00000000000..5af8ef7cf8b --- /dev/null +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb @@ -0,0 +1,77 @@ +easyblock = 'MakeCp' + +name = 'Yambo' +version = '5.2' +local_commit = '21109ae' + +homepage = 'http://www.yambo-code.org' +description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. + Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = { + 'usempi': True, + 'openmp': True, +} + +local_copy_cmd_pattern = 'cp %s yambo-%(version)s/lib/archive/' + +source_urls = ['https://github.com/yambo-code/yambo/archive/'] +sources = [ + { 'filename': '%s.tar.gz' % local_commit, + 'download_filename': 'yambo-%(version)s.tar.gz', + 'extract_cmd': 'mkdir yambo-%(version)s && tar --strip-components=1 -xzf %s -C yambo-%(version)s' + }, # Yambo + { + 'source_urls': ['https://github.com/yambo-code/yambo-libraries/archive/'], + 'filename': '1.0.tar.gz', + 'extract_cmd': 'mkdir yambo-%(version)s/lib/yambo/ && tar --strip-components=1 -xzf %s -C yambo-%(version)s/lib/yambo/', + }, + { + 'source_urls': ['https://github.com/yambo-code/yambo/files/962173/'], + 'filename': 'iotk-y1.2.2.tar.gz', + 'extract_cmd': local_copy_cmd_pattern, + }, +] + +dependencies = [ + ('HDF5', '1.12.1'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('PETSc', '3.18.4'), + ('SLEPc', '3.18.2'), + ('libxc', '5.1.6'), +] + +with_configure = True + +configopts = 'FC=mpiifort CC=mpiicc ' +configopts += '--prefix=%(builddir)s/%(namelower)s-%(version)s/ ' +configopts += '--enable-open-mp --enable-hdf5-par-io ' +configopts += '--with-blas-libs="$LIBBLAS" ' +configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs=mkl ' +configopts += '--with-scalapack-libs=mkl ' +configopts += '--with-fft-libs="-mkl" --with-fft-includedir="$FFT_INC_DIR" ' +configopts += '--with-netcdf-lib=$EBROOTNETCDF/lib --with-netcdf-include="$EBROOTNETCDF\include" ' +configopts += '--with-netcdff-path="$EBROOTNETCDFMINFORTRAN" ' +configopts += '--with-hdf5-path="$EBROOTHDF5" --with-petsc-path="$EBROOTPETSC" ' +configopts += '--with-slepc-path="$EBROOTSLEPC" --with-libxc-path="$EBROOTLIBXC" ' +configopts += '--enable-par-linalg --enable-slepc-linalg ' + +prebuildopts = "export FPATH=$EBROOTPETSC/include:$EBROOTSLEPC/include:$FPATH && " +buildopts = 'all' + +files_to_copy = [ + (['bin/*'], 'bin'), + (['%(builddir)s/%(namelower)s-%(version)s/lib/external/intel/mpiifort/bin/*'], 'bin') +] + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['a2y', 'p2y', 'yambo', 'yambo_ph', 'ypp', 'ypp_ph', + 'iotk', 'iotk.x']], + 'dirs': [] +} + +sanity_check_commands = ["yambo -h"] + +moduleclass = 'phys' From 77e292bb65c1582c3e2b57d78b4f1b5642213b90 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 16 May 2023 15:31:48 +0200 Subject: [PATCH 7421/9987] Fixed typo - used backslash instead of slash + added checksums --- easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb index 5af8ef7cf8b..7f08d457d9d 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb @@ -33,6 +33,11 @@ sources = [ 'extract_cmd': local_copy_cmd_pattern, }, ] +checksums = [ + {'21109ae.tar.gz': '19b909da970c70438d0a741a54008a2207abf1fca54b83c31529cec84d9b3ac7'}, + {'1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'}, + {'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'}, +] dependencies = [ ('HDF5', '1.12.1'), @@ -52,7 +57,7 @@ configopts += '--with-blas-libs="$LIBBLAS" ' configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs=mkl ' configopts += '--with-scalapack-libs=mkl ' configopts += '--with-fft-libs="-mkl" --with-fft-includedir="$FFT_INC_DIR" ' -configopts += '--with-netcdf-lib=$EBROOTNETCDF/lib --with-netcdf-include="$EBROOTNETCDF\include" ' +configopts += '--with-netcdf-lib=$EBROOTNETCDF/lib --with-netcdf-include="$EBROOTNETCDF/include" ' configopts += '--with-netcdff-path="$EBROOTNETCDFMINFORTRAN" ' configopts += '--with-hdf5-path="$EBROOTHDF5" --with-petsc-path="$EBROOTPETSC" ' configopts += '--with-slepc-path="$EBROOTSLEPC" --with-libxc-path="$EBROOTLIBXC" ' From bbdf095e5bf2c746b65918f69204685ca3249a85 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 16 May 2023 17:57:20 +0200 Subject: [PATCH 7422/9987] Added requested changes --- ... => Yambo-5.2.dev-20230512-intel-2021b.eb} | 31 +++++++++---------- 1 file changed, 14 insertions(+), 17 deletions(-) rename easybuild/easyconfigs/y/Yambo/{Yambo-5.2-intel-2021b.eb => Yambo-5.2.dev-20230512-intel-2021b.eb} (71%) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb similarity index 71% rename from easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb rename to easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb index 7f08d457d9d..121760399be 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-5.2-intel-2021b.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb @@ -1,43 +1,40 @@ easyblock = 'MakeCp' name = 'Yambo' -version = '5.2' -local_commit = '21109ae' +version = '5.2.dev-20230512' +local_yambo_libs_ver = '1.0' +local_commit = 'dfa2752' homepage = 'http://www.yambo-code.org' description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" toolchain = {'name': 'intel', 'version': '2021b'} -toolchainopts = { - 'usempi': True, - 'openmp': True, -} +toolchainopts = {'usempi': True, 'openmp': True} -local_copy_cmd_pattern = 'cp %s yambo-%(version)s/lib/archive/' +local_yambo_ext_cmd = 'mkdir yambo-%(version)s && ' +local_yambo_ext_cmd += 'tar --strip-components=1 -xzf %s -C yambo-%(version)s' +local_yambo_lib_ext_cmd = 'mkdir yambo-%(version)s/lib/yambo/ && ' +local_yambo_lib_ext_cmd += 'tar --strip-components=1 -xzf %s -C yambo-%(version)s/lib/yambo/' source_urls = ['https://github.com/yambo-code/yambo/archive/'] sources = [ - { 'filename': '%s.tar.gz' % local_commit, - 'download_filename': 'yambo-%(version)s.tar.gz', - 'extract_cmd': 'mkdir yambo-%(version)s && tar --strip-components=1 -xzf %s -C yambo-%(version)s' + { + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': 'yambo-%(version)s.tar.gz', + 'extract_cmd': local_yambo_ext_cmd, }, # Yambo { 'source_urls': ['https://github.com/yambo-code/yambo-libraries/archive/'], 'filename': '1.0.tar.gz', - 'extract_cmd': 'mkdir yambo-%(version)s/lib/yambo/ && tar --strip-components=1 -xzf %s -C yambo-%(version)s/lib/yambo/', + 'extract_cmd': local_yambo_lib_ext_cmd, }, { 'source_urls': ['https://github.com/yambo-code/yambo/files/962173/'], 'filename': 'iotk-y1.2.2.tar.gz', - 'extract_cmd': local_copy_cmd_pattern, + 'extract_cmd': 'cp %s yambo-%(version)s/lib/archive/', }, ] -checksums = [ - {'21109ae.tar.gz': '19b909da970c70438d0a741a54008a2207abf1fca54b83c31529cec84d9b3ac7'}, - {'1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'}, - {'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'}, -] dependencies = [ ('HDF5', '1.12.1'), From 9fd424eb21423236585b680df5833107f6a85450 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 16 May 2023 18:23:23 +0200 Subject: [PATCH 7423/9987] Added correct checksums --- .../y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb index 121760399be..355974ff289 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb @@ -35,6 +35,11 @@ sources = [ 'extract_cmd': 'cp %s yambo-%(version)s/lib/archive/', }, ] +checksums = [ + {'yambo-5.2.dev-20230512.tar.gz': '4a993b86543fec7c5fa79838ab699a9f4432a215f63eca537c0819335ab9981c'}, + {'1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'}, + {'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'}, +] dependencies = [ ('HDF5', '1.12.1'), From 69ba59461cad53ae229742f69cf0ab3502273d4b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 16 May 2023 21:05:02 +0200 Subject: [PATCH 7424/9987] {chem}[iomkl/2021a] OpenMolcas v21.06 --- .../GlobalArrays-5.8-iomkl-2021a.eb | 24 ++++++++++ .../h/HDF5/HDF5-1.10.7-iompi-2021a.eb | 22 +++++++++ .../OpenMolcas-21.06-iomkl-2021a.eb | 46 +++++++++++++++++++ 3 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-iomkl-2021a.eb diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb new file mode 100644 index 00000000000..6f35fb227fb --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.8' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'iomkl', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(name)s/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['64df7d1ea4053d24d84ca361e67a6f51c7b17ed7d626cb18a9fbc759f4a078ac'] + +configopts = ' --with-mpi --enable-i8 --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64" --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl" --with-mpi-ts' + + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb new file mode 100644 index 00000000000..2f1d4b6ddb6 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.7' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iompi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-iomkl-2021a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-iomkl-2021a.eb new file mode 100644 index 00000000000..2de233814bf --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-iomkl-2021a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'OpenMolcas' +version = '21.06' + +homepage = 'https://gitlab.com/Molcas/OpenMolcas' +description = "OpenMolcas is a quantum chemistry software package" + +toolchain = {'name': 'iomkl', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/Molcas/%(name)s/-/archive/v%(version)s/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = ['%(name)s-21.06_mcpdft_deps.patch'] +checksums = [ + '54cf989c1e0fcb7e8927f0c64fe356b300bf3537e4868356eea47105a8a06e3a', # %(name)s-v21.06.tar.gz + '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a', # %(name)s-21.06_mcpdft_deps.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), +] +dependencies = [ + ('GlobalArrays', '5.8'), + ('HDF5', '1.10.7'), + ('Python', '3.9.5'), +] + +preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' +configopts = "-DLINALG=MKL -DMKLROOT=$MKLROOT -DMPI=ON -DOPENMP=ON -DGA=ON -DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON" + + +sanity_check_paths = { + 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.so', 'sbin/help_basis', 'pymolcas'], + 'dirs': ['data/', 'basis_library/'], +} + +modextrapaths = {'PATH': ''} + +modextravars = { + 'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', +} + +moduleclass = 'chem' From 93abeea1a6a862309775c83d83d4f4808afd3fec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2023 21:25:57 +0200 Subject: [PATCH 7425/9987] shorten source URL in HDF5 easyconfig by using 'hdf5' instead of '%(namelower)s' --- easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb index 2f1d4b6ddb6..8e71c233455 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb @@ -9,7 +9,7 @@ description = """HDF5 is a data model, library, and file format for storing and toolchain = {'name': 'iompi', 'version': '2021a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] From 51a4637435ab2437ea105ca5163486f78ef33de9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 16 May 2023 21:31:46 +0200 Subject: [PATCH 7426/9987] fix line lengths --- .../g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb | 10 ++++++++-- .../easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb | 4 ++-- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb index 6f35fb227fb..e462c994af7 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb @@ -13,11 +13,17 @@ source_urls = ['https://github.com/%(name)s/ga/releases/download/'] sources = ['v%(version)s/ga-%(version)s.tar.gz'] checksums = ['64df7d1ea4053d24d84ca361e67a6f51c7b17ed7d626cb18a9fbc759f4a078ac'] -configopts = ' --with-mpi --enable-i8 --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64" --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl" --with-mpi-ts' +configopts = ' --with-mpi --enable-i8 ' +configopts += '--with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64" ' +configopts += '--with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' sanity_check_paths = { - 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libcomex.a', 'lib/libga.a'], + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', + 'lib/libcomex.a', 'lib/libga.a'], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb index 2f1d4b6ddb6..2d9b79ce8c6 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb @@ -9,10 +9,10 @@ description = """HDF5 is a data model, library, and file format for storing and toolchain = {'name': 'iompi', 'version': '2021a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s' + '-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] - dependencies = [ ('zlib', '1.2.11'), ('Szip', '2.1.1'), From 24daaf14698edbd3b92e46a0c7802b6c86bedff9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 16 May 2023 21:36:42 +0200 Subject: [PATCH 7427/9987] fix line lengths2 --- easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb index 2d9b79ce8c6..31678f0dd6d 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb @@ -9,8 +9,7 @@ description = """HDF5 is a data model, library, and file format for storing and toolchain = {'name': 'iompi', 'version': '2021a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s' - '-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF/releases/hdf-%(version_major_minor)s/hdf-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] dependencies = [ From a74f24b47fde8350ae6a8ed33ad5486f877e73bc Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 16 May 2023 21:39:36 +0200 Subject: [PATCH 7428/9987] fix line lengths3 --- easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb index 31678f0dd6d..2b0187340e2 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb @@ -9,7 +9,7 @@ description = """HDF5 is a data model, library, and file format for storing and toolchain = {'name': 'iompi', 'version': '2021a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['https://support.hdfgroup.org/ftp/HDF/releases/hdf-%(version_major_minor)s/hdf-%(version)s/src'] +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] sources = [SOURCELOWER_TAR_GZ] checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] dependencies = [ From 7ae58b8b24f94f0a56b491a5c3fe2e8ca16a27e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2023 21:39:57 +0200 Subject: [PATCH 7429/9987] adding easyconfigs: GapFiller-2.1.2-GCC-11.3.0.eb --- .../g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..8e6de771d67 --- /dev/null +++ b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GapFiller' +version = '2.1.2' + +homepage = 'https://sourceforge.net/projects/gapfiller' +description = """GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. + It can be used for both DNA and RNA and it has been tested on Illumina data.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'cstd': 'c++11', 'extra_cxxflags': '-fpermissive'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4c5235b1ee17e277d08cc945dbfa05af084559e546a2b7f15c9c1b703f4b237'] + +dependencies = [ + ('Boost', '1.79.0'), + ('zlib', '1.2.12'), +] + +buildopts = 'bin_PROGRAMS=GapFiller ' +buildopts += 'GapFiller_CFLAGS="$CFLAGS $LDFLAGS -lz" GapFiller_CXXFLAGS="$CXXFLAGS $LDFLAGS -lz"' +installopts = 'bin_PROGRAMS=GapFiller ' + +postinstallcmds = ["cp -a README %(installdir)s"] + +sanity_check_paths = { + 'files': ['bin/GapFiller', 'README'], + 'dirs': [], +} + +sanity_check_commands = ["GapFiller --help"] + +moduleclass = 'bio' From 97c16ab9c608cf7399c887d6169b187c3431e910 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 May 2023 21:44:33 +0200 Subject: [PATCH 7430/9987] minor code cleanup in easyconfigs for cctbx-base and AlphaPullDown --- .../AlphaPulldown-0.30.4-foss-2020b.eb | 20 ++++++------- .../cctbx-base-2020.8-foss-2020b.eb | 28 ++++++++----------- 2 files changed, 22 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb index 1354c1e2a67..05ab7469fa0 100644 --- a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-foss-2020b.eb @@ -1,10 +1,10 @@ # created by Denis Kristak (Inuits) -easyblock = "PythonBundle" +easyblock = 'PythonBundle' -name = "AlphaPulldown" -version = "0.30.4" +name = 'AlphaPulldown' +version = '0.30.4' -homepage = "https://github.com/KosinskiLab/AlphaPulldown" +homepage = 'https://github.com/KosinskiLab/AlphaPulldown' description = """AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" @@ -12,10 +12,10 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), - ("OpenMM", "7.5.0"), - ("Kalign", "3.3.1"), + ('OpenMM', '7.5.0'), + ('Kalign', '3.3.1'), ('PyYAML', '5.3.1'), - ("cctbx-base", "2020.8"), + ('cctbx-base', '2020.8'), ('jax', '0.2.19'), # also provides absl-py ('Biopython', '1.78'), ('h5py', '3.1.0'), @@ -77,8 +77,8 @@ exts_list = [ sanity_pip_check = True sanity_check_paths = { - "files": ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], - "dirs": ["lib/python%(pyshortver)s/site-packages/alphapulldown"], + 'files': ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/alphapulldown'], } -moduleclass = "data" +moduleclass = 'data' diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb index edb2dd60460..afe41e8b972 100644 --- a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-foss-2020b.eb @@ -1,18 +1,15 @@ # author: Denis Kristak (Inuits) -easyblock = "PythonBundle" +easyblock = 'PythonBundle' -name = "cctbx-base" -version = "2020.8" -local_pyver = "3.8.6" +name = 'cctbx-base' +version = '2020.8' # local_pyver_special is used to create the wheel filename # it contains the first two digits of the python version (with no delimiter) -local_tmp = local_pyver.split('.') -local_tmp.pop() -# compose a string -local_pyver_special = ''.join(local_tmp) +local_pyver = '3.8.6' +local_pyver_special = ''.join(local_pyver.split('.')[:2]) -homepage = "https://github.com/cctbx/cctbx_project" +homepage = 'https://github.com/cctbx/cctbx_project' description = """ The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix project. The goal of the Phenix project is to advance automation of macromolecular structure determination. @@ -36,15 +33,11 @@ dependencies = [ local_metadata = "%(installdir)s/lib/python%(pyshortver)s/site-packages/cctbx_base-%(version)s.dist-info/METADATA" - exts_list = [ ('reportlab', '3.5.66', { 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], }), (name, version, { - 'modulename': 'cctbx', - # remove deps (they fail during sanity check, even though they are installed) - 'postinstallcmds': ["echo '' > %s" % local_metadata], 'sources': [{ 'download_filename': 'cctbx_base-%s-0_py%sh167b89d-cp%s-cp%sm-manylinux2010_x86_64.whl' % ( version, local_pyver_special, local_pyver_special, local_pyver_special @@ -54,6 +47,9 @@ exts_list = [ ), }], 'checksums': ['5c7ac0710d9011072c678771876aa57ca3735986ed321d403f51989a7444e592'], + # remove deps (they fail during sanity check, even though they are installed) + 'postinstallcmds': ["echo '' > %s" % local_metadata], + 'modulename': 'cctbx', }), ] @@ -61,8 +57,8 @@ use_pip = True sanity_pip_check = True sanity_check_paths = { - "files": ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], - "dirs": ['lib/python%(pyshortver)s/site-packages/cctbx_website'], + 'files': ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cctbx_website'], } -moduleclass = "lib" +moduleclass = 'lib' From 4d46fdb6fe8c711fd847cae518183ba552699a1c Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Wed, 17 May 2023 16:06:31 +0200 Subject: [PATCH 7431/9987] Add Clang 16.0.4 and deps --- .../c/Clang/Clang-16.0.4-GCCcore-12.2.0.eb | 59 +++++++++++++++++++ .../z/Z3/Z3-4.12.2-GCCcore-12.2.0.eb | 35 +++++++++++ 2 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-16.0.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-16.0.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-16.0.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e1885d3b52f --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-16.0.4-GCCcore-12.2.0.eb @@ -0,0 +1,59 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '16.0.4' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-project-%(version)s.src.tar.xz', +] +checksums = [ + {'llvm-project-16.0.4.src.tar.xz': 'cf3c2a1152ed7a99866bd7f12c24528ada6d9f6336afb7a08416938762004c9f'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Perl', '5.36.0'), + # Including Python bindings would require this as a runtime dep + ('Python', '3.10.8'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.39'), + ('hwloc', '2.8.0'), + ('libxml2', '2.10.3'), + ('ncurses', '6.3'), + ('GMP', '6.2.1'), + ('Z3', '4.12.2'), +] + +# enabling RTTI makes the flang compiler need to link to libc++ so instead of +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 +# you would need +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++ +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9582be51172 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'Z3' +version = '4.12.2' + +homepage = 'https://github.com/Z3Prover/z3' +description = """ + Z3 is a theorem prover from Microsoft Research. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/Z3Prover/z3/archive/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + {'z3-4.12.2.tar.gz': '9f58f3710bd2094085951a75791550f547903d75fe7e2fcb373c5f03fc761b8f'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = '-DZ3_USE_LIB_GMP=ON -DZ3_LINK_TIME_OPTIMIZATION=ON ' + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From a3f9162b81ad9084a23acc052bcacb3a273d8b0a Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 17 May 2023 20:10:43 +0200 Subject: [PATCH 7432/9987] Added the rest of requested changes + edited the format of checksums --- .../y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb index 355974ff289..756ed0906fc 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb @@ -26,7 +26,8 @@ sources = [ }, # Yambo { 'source_urls': ['https://github.com/yambo-code/yambo-libraries/archive/'], - 'filename': '1.0.tar.gz', + 'download_filename': '%s.tar.gz' % local_yambo_libs_ver, + 'filename': 'yambo-libraries-%s.tar.gz' % local_yambo_libs_ver, 'extract_cmd': local_yambo_lib_ext_cmd, }, { @@ -36,9 +37,9 @@ sources = [ }, ] checksums = [ - {'yambo-5.2.dev-20230512.tar.gz': '4a993b86543fec7c5fa79838ab699a9f4432a215f63eca537c0819335ab9981c'}, - {'1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'}, - {'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'}, + ('4a993b86543fec7c5fa79838ab699a9f4432a215f63eca537c0819335ab9981c', + 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492', + 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543') ] dependencies = [ From 28ba52b7b25cd4dc91db332f18419f20775af5d8 Mon Sep 17 00:00:00 2001 From: Victor Lopez Date: Mon, 15 May 2023 16:28:51 +0200 Subject: [PATCH 7433/9987] Add dlb v3.3.1 --- .../d/dlb/dlb-3.3.1-gompi-2022a.eb | 35 +++++++++++++++++++ .../d/dlb/dlb-3.3.1-iimpi-2022a.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/d/dlb/dlb-3.3.1-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/d/dlb/dlb-3.3.1-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.3.1-gompi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-gompi-2022a.eb new file mode 100644 index 00000000000..2f86924aff4 --- /dev/null +++ b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-gompi-2022a.eb @@ -0,0 +1,35 @@ +# vim: set syntax=python: +easyblock = 'ConfigureMake' + +name = 'dlb' +version = '3.3.1' + +description = """ +DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., +two levels of parallelism) by improving the load balance of the outer level of +parallelism (e.g., MPI) by dynamically redistributing the computational +resources at the inner level of parallelism (e.g., OpenMP). at run time. +""" +homepage = 'https://pm.bsc.es/dlb/' +docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] + +toolchain = {'name': 'gompi', 'version': '2022a'} +builddependencies = [('Python', '3.10.4', '-bare')] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] + +checksums = ['1b245acad80b03eb83e815fd59dcfc598cfddd899de4504cf6a9572fe5359f40'] + +configopts = '--with-mpi' + +sanity_check_paths = { + 'files': [ + 'bin/dlb', + 'lib/libdlb.a', 'lib/libdlb.%s' % SHLIB_EXT, + 'lib64/libdlb.%s' % SHLIB_EXT + ], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.3.1-iimpi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-iimpi-2022a.eb new file mode 100644 index 00000000000..7d1205a8d95 --- /dev/null +++ b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-iimpi-2022a.eb @@ -0,0 +1,35 @@ +# vim: set syntax=python: +easyblock = 'ConfigureMake' + +name = 'dlb' +version = '3.3.1' + +description = """ +DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., +two levels of parallelism) by improving the load balance of the outer level of +parallelism (e.g., MPI) by dynamically redistributing the computational +resources at the inner level of parallelism (e.g., OpenMP). at run time. +""" +homepage = 'https://pm.bsc.es/dlb/' +docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] + +toolchain = {'name': 'iimpi', 'version': '2022a'} +builddependencies = [('Python', '3.10.4', '-bare')] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] + +checksums = ['1b245acad80b03eb83e815fd59dcfc598cfddd899de4504cf6a9572fe5359f40'] + +configopts = '--with-mpi' + +sanity_check_paths = { + 'files': [ + 'bin/dlb', + 'lib/libdlb.a', 'lib/libdlb.%s' % SHLIB_EXT, + 'lib64/libdlb.%s' % SHLIB_EXT + ], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 2555a34d17f3a93f8cc14115e9f5aa519cb1813b Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Thu, 18 May 2023 14:25:42 +0100 Subject: [PATCH 7434/9987] Fixed checksums --- .../y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb index 756ed0906fc..f6c67300dc0 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb @@ -37,9 +37,9 @@ sources = [ }, ] checksums = [ - ('4a993b86543fec7c5fa79838ab699a9f4432a215f63eca537c0819335ab9981c', - 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492', - 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543') + {'yambo-5.2.dev-20230512.tar.gz': '4a993b86543fec7c5fa79838ab699a9f4432a215f63eca537c0819335ab9981c'}, + {'yambo-libraries-1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'}, + {'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'}, ] dependencies = [ From f9de626dc68fdb364dd3058c894352ded6009f02 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 18 May 2023 15:55:18 +0200 Subject: [PATCH 7435/9987] removing version suffix --- .../a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb index aa1f8921915..7efa2268907 100644 --- a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb +++ b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb @@ -3,7 +3,6 @@ easyblock = 'PackedBinary' name = 'Annocript' version = '2.0' local_commit = '84fd67b' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/frankMusacchia/Annocript' description = """ Annocript is a pipeline for the annotation of de-novo generated transcriptomes. From cbb7198078f2b773b244683b049fa9f8b3e2fb05 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 18 May 2023 16:08:32 +0200 Subject: [PATCH 7436/9987] Delete Annocript-2.0-foss-2022a-Python-3.10.4.eb removed easyconfig with versionsuffix --- .../Annocript-2.0-foss-2022a-Python-3.10.4.eb | 76 ------------------- 1 file changed, 76 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb diff --git a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb deleted file mode 100644 index 7efa2268907..00000000000 --- a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a-Python-3.10.4.eb +++ /dev/null @@ -1,76 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'Annocript' -version = '2.0' -local_commit = '84fd67b' - -homepage = 'https://github.com/frankMusacchia/Annocript' -description = """ Annocript is a pipeline for the annotation of de-novo generated transcriptomes. - It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division - adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways. - Annocript also gives information about the longest ORF and the non-coding potential using external software. - Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology - and sequence features. """ - -toolchain = {'name': 'foss', 'version': '2022a'} - -source_urls = ['https://github.com/frankMusacchia/Annocript/archive'] -sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] -patches = [ - 'annocript_fix_paths.patch', - 'annocript_no_background.patch', -] -checksums = [ - {'Annocript-2.0.tar.gz': '151dec3a390826fd2bcc7d794a9565535702dfc9c4672842e825a9fcf21406d9'}, - {'annocript_fix_paths.patch': '95359e335a6a992f5f269e8f199c9df92d765f7ff41890298acead12d562685c'}, - {'annocript_no_background.patch': 'ca02c2b02b7574c25128c9a4ce2b69a13a0bb2b409efd2ea63562053bf2e2c57'}, -] - -dependencies = [ - ('Compress-Raw-Zlib', '2.202'), - ('Python', '3.10.4'), - ('Perl', '5.34.1'), - ('BioPerl', '1.7.8'), - ('R', '4.2.1'), - ('CPC2', '1.0.1'), - ('BLAST+', '2.13.0'), - ('LIBSVM', '3.30'), - ('MariaDB', '10.9.3'), - ('DBD-mysql', '4.050'), -] - -postinstallcmds = [ - # Extract dna2pep to annocript's bin folder, set permissions. - # It is just a series Python scripts and I'm not building it as a standalone dependency, as sources for this SW - # are not available elsewhere than in the Annocript repository anyway. - "mkdir %(installdir)s/bin ", - "cp %(builddir)s/Annocript-*/DL_PROGRAMS/dna2pep-1.1.tar.gz %(installdir)s/bin ", - "cd %(installdir)s/bin && tar -zxvf dna2pep-1.1.tar.gz ", - "rm %(installdir)s/bin/dna2pep-1.1.tar.gz && chmod 755 %(installdir)s/bin/dna2pep-1.1/dna2pep.py ", - # extract annocript itself - 'mv %(installdir)s/annocript.pl %(installdir)s/bin/', - 'sed -i -e "1s|#!.*$|#!/usr/bin/env perl|g" %(installdir)s/bin/annocript.pl', - 'chmod a+rx %(installdir)s/bin/annocript.pl', -] - -exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") - -exts_list = [ - ('CGI', '4.43', { - 'source_tmpl': 'CGI-4.43.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], - 'checksums': ['14b94f9df6e48fc26ebc4fa1e01a7b534cbc1611028a49028f9ac9d8ca27b734'], - }), -] - -modextrapaths = {'PERL5LIB': ['', 'lib/perl5/site_perl/%(perlver)s/']} - -sanity_check_paths = { - 'files': ['bin/annocript.pl'], - 'dirs': [], -} - -sanity_check_commands = ['annocript.pl --help'] - -moduleclass = 'bio' From 4349ee0e2181575f2f92d189772b2e6fefd39cc4 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 18 May 2023 20:58:35 +0200 Subject: [PATCH 7437/9987] adding easyconfigs: alleleCount-4.2.1-GCC-11.3.0.eb, ASCAT-3.1.2-foss-2022a-R-4.2.1.eb, alleleIntegrator-0.8.8-foss-2022a-R-4.2.1.eb --- .../a/ASCAT/ASCAT-3.1.2-foss-2022a-R-4.2.1.eb | 30 +++++++++++ .../alleleCount-4.2.1-GCC-11.3.0.eb | 50 +++++++++++++++++ ...leleIntegrator-0.8.8-foss-2022a-R-4.2.1.eb | 53 +++++++++++++++++++ 3 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASCAT/ASCAT-3.1.2-foss-2022a-R-4.2.1.eb create mode 100644 easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/a/alleleIntegrator/alleleIntegrator-0.8.8-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/a/ASCAT/ASCAT-3.1.2-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/a/ASCAT/ASCAT-3.1.2-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..41567de2406 --- /dev/null +++ b/easybuild/easyconfigs/a/ASCAT/ASCAT-3.1.2-foss-2022a-R-4.2.1.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'ASCAT' +version = '3.1.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/VanLoo-lab/ascat' +description = """ASCAT is a method to derive copy number profiles of tumor cells, + accounting for normal cell admixture and tumor aneuploidy.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/VanLoo-lab/ascat/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5d65aef417ad12ea0e638b4179def5a9b8f25e1ccd757e41a6509534fe20eb17'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('alleleCount', '4.2.1'), +] + +start_dir = '%(name)s' + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..1365367075e --- /dev/null +++ b/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb @@ -0,0 +1,50 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Institute, London, UK +## + +easyblock = 'CmdCp' + +name = 'alleleCount' +version = '4.2.1' + +homepage = 'http://cancerit.github.io/alleleCount/' +description = """ The alleleCount package primarily exists to prevent code duplication +between some other projects, specifically AscatNGS and Battenberg. As of v4 the perl +code wraps the C implementation of allele counting code for BAM/CRAM processing. """ + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/cancerit/%(name)s/archive/v%(version)s'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dbec2d47fb4fad8ead72f55c4b6e3c02b216cbed285c05617b62e9a38c32e400'] + +cmds_map = [('.*', "./setup.sh . ${EBROOTPERL}/lib/perl5")] + +# HTSlib 1.7 is built, used and removed again in the provided setup script +dependencies = [ + ('Perl', '5.34.1'), + ('HTSlib', '1.15.1'), + ('libdeflate', '1.10'), +] + +files_to_copy = [ + "bin", + "lib", + "man", + "example", + "testData" +] + +sanity_check_paths = { + 'files': ["bin/alleleCounter", "bin/alleleCounter.pl", "lib/perl5/LWP.pm"], + 'dirs': ["lib/perl5"], +} + +sanity_check_commands = ["alleleCounter --help"] + +modextrapaths = {'PERL5LIB': 'lib/perl5'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/alleleIntegrator/alleleIntegrator-0.8.8-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/a/alleleIntegrator/alleleIntegrator-0.8.8-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..103d3b10eeb --- /dev/null +++ b/easybuild/easyconfigs/a/alleleIntegrator/alleleIntegrator-0.8.8-foss-2022a-R-4.2.1.eb @@ -0,0 +1,53 @@ +easyblock = 'Bundle' + +name = 'alleleIntegrator' +version = '0.8.8' +# There is only one release in the repo called "PublishedVersion.tar.gz" +local_commit = '7bf7970' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/constantAmateur/alleleIntegrator' +description = 'R package to generate allele specific counts for scRNA data and use it to identify cancer cells' + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('alleleCount', '4.2.1'), + ('BCFtools', '1.15.1'), + ('parallel', '20220722'), + ('ASCAT', '3.1.2', versionsuffix) +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} + +exts_list = [ + ('grr', '0.9.5', { + 'checksums': ['292606de2983ac5840c90d3e0977441b482c9e73c1674b662f8b4fb8f3632b2b'], + }), + ('Matrix.utils', '0.9.8', { + 'checksums': ['ebc59d3ef751775515586ff1f2396e429a1e9d91a10099d804134fcf74c0ae28'], + }), + (name, version, { + 'source_urls': ['https://github.com/constantAmateur/alleleIntegrator/archive/'], + 'sources': [{'download_filename': '7bf7970.tar.gz', 'filename': '%(namelower)s-%(version)s.tar.gz'}], + 'checksums': ['9e852c37485548c27c8ce29b90d163818c394410874d459e4fd92f184e4ff004'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 682dba8893da014588029b97179fca8078818b0f Mon Sep 17 00:00:00 2001 From: Richard Top Date: Fri, 19 May 2023 06:49:23 +0000 Subject: [PATCH 7438/9987] Adding make 4.3 as build-dependency for OpenBLAS-0.3.15-GCC-10.3.0 --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb index 3b8d83f4116..f3bb9483823 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb @@ -28,7 +28,7 @@ checksums = [ # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] - +builddependencies = [('make', '4.3')] # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' From e096c0fec8037599cd1e88cc006b0d881dac8bf5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 May 2023 11:27:12 +0200 Subject: [PATCH 7439/9987] consistently use make 4.3 as build dependency for recent OpenBLAS versions --- .../m/make/make-4.3-GCCcore-12.2.0.eb | 29 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb | 4 +++ .../o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb | 6 +++- .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb | 4 +++ .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 1 + .../o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 1 + .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 1 + .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 1 + .../OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb | 4 +++ .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 1 + .../o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb | 4 +++ 11 files changed, 55 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/make/make-4.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/make/make-4.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2d7194c6354 --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.3' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e05fdde47c5f7ca45cb697e973894ff4f5d79e13b750ed57d7b66d8defc78e19'] + +builddependencies = [('binutils', '2.39')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index c98d769985e..48333ab642d 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -31,6 +31,10 @@ checksums = [ '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', ] +builddependencies = [ + ('make', '4.3'), +] + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb index f3bb9483823..13b731bc6d1 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb @@ -28,7 +28,11 @@ checksums = [ # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] -builddependencies = [('make', '4.3')] + +builddependencies = [ + ('make', '4.3'), +] + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb index ae8fd51485e..a7984cac146 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb @@ -25,6 +25,10 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] +builddependencies = [ + ('make', '4.3'), +] + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index c4b29c67422..1df506125c2 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -39,6 +39,7 @@ checksums = [ ] builddependencies = [ + ('make', '4.3'), # required by LAPACK test suite ('Python', '3.9.6', '-bare'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 762a9558bfb..e00c62b1089 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -36,6 +36,7 @@ checksums = [ ] builddependencies = [ + ('make', '4.3'), # required by LAPACK test suite ('Python', '3.9.6', '-bare'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index 98f44c83e7c..ad53aa70e6b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -34,6 +34,7 @@ checksums = [ ] builddependencies = [ + ('make', '4.3'), # required by LAPACK test suite ('Python', '3.9.6', '-bare'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 4496c0bc5b3..c00bedf7a63 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -34,6 +34,7 @@ checksums = [ ] builddependencies = [ + ('make', '4.3'), # required by LAPACK test suite ('Python', '3.10.4', '-bare'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb index 39645058d21..7b49821c348 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb @@ -33,6 +33,10 @@ checksums = [ {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] +builddependencies = [ + ('make', '4.3'), +] + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb index b0244cb98ce..274aeeec351 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -34,6 +34,7 @@ checksums = [ ] builddependencies = [ + ('make', '4.3'), # required by LAPACK test suite ('Python', '3.10.8', '-bare'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb index c390c260b68..0e4b7e6439e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb @@ -36,6 +36,10 @@ checksums = [ '9210a94ae418b4ce6d9f7fab4e00dd3155451f5ef3769536a4d954a2149ca733', # OpenBLAS-0.3.9_fix-lapack_h.patch ] +builddependencies = [ + ('make', '4.3'), +] + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' From bf7999b6dc64d25045d9dfcfac2369a0748d4389 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 19 May 2023 15:04:33 +0200 Subject: [PATCH 7440/9987] fix moduleclass --- .../turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb b/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb index 890702f6e8a..0fa522cb25d 100644 --- a/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb +++ b/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb @@ -32,4 +32,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'bio' +moduleclass = 'cae' From 5304e84215f8e70751c41955f95d6136b5b7f9ad Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 May 2023 15:20:09 +0000 Subject: [PATCH 7441/9987] adding easyconfigs: MRPRESSO-1.0-20230502-foss-2022a.eb --- .../MRPRESSO-1.0-20230502-foss-2022a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb b/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb new file mode 100644 index 00000000000..710f1feccad --- /dev/null +++ b/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'MRPRESSO' +# In spite of the repo name, everything else refers to MRPRESSO +local_commit = 'cece763' +# see DESCRIPTION to determine version, +# but also take date of last commit into account (since version isn't always bumped) +version = '1.0-20230502' + +homepage = 'https://github.com/rondolab/MR-PRESSO' +description = "Performs the Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO) method.." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/rondolab/MR-PRESSO/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['f6c464f239eaf6341ac19bde272b3b1c0700013c32bcf480c1a2f18d177b630f'] + +dependencies = [ + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 19f6f48cb13ba989baead6c764bb793721f87c02 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 18:21:44 +0200 Subject: [PATCH 7442/9987] adding easyconfigs: pkgconf-1.9.5-GCCcore-12.3.0.eb --- .../p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..716412bd025 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '1.9.5' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6466efd2e38c4c0ac5de4e345f0dc6dad57e689efb08c31f2a71547683d20dc7'] + +builddependencies = [('binutils', '2.40')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' From 7fb2e4076754e77b825ab4fb2879c9f55ab823ff Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 18:24:41 +0200 Subject: [PATCH 7443/9987] adding easyconfigs: libtool-2.4.7-GCCcore-12.3.0.eb --- .../l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d3c279ea343 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.7' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' From 36c9729c22bbe435eeb5cfad59ea5a2a51c53d4e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 19 May 2023 16:38:51 +0000 Subject: [PATCH 7444/9987] adding easyconfigs: LIANA-0.1.11-foss-2022a-R-4.2.1.eb --- .../LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/l/LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/l/LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..2584ae7e67f --- /dev/null +++ b/easybuild/easyconfigs/l/LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'LIANA' +version = '0.1.11' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://saezlab.github.io/liana/' +description = """LIANA: a LIgand-receptor ANalysis frAmework. LIANA enables the use of any + combination of ligand-receptor methods and resources, and their consensus.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + 'https://bioconductor.org/packages/release/bioc/src/contrib/' # contrib for Bioconductor packages +] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': source_urls, +} + +exts_list = [ + ('rlang', '1.0.4', { + 'checksums': ['1fb789d46c6a855ce37eba63c353b85aa600c4a2a7ca6075f2632540b42a8696'], + }), + ('tidyselect', '1.2.0', { + 'checksums': ['538d26b727e37d618e2efd3b00836048f103112a03e6994bf07a02392e269e3b'], + }), + ('OmnipathR', '3.8.0', { + 'checksums': ['0e12ea562e135a8c670b5b4ec4000463c9ee12bd6d957bfcc2db36b5ecd85664'], + }), + (name, version, { + 'source_urls': ['https://github.com/saezlab/liana/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['fd866f4b66ee3d98c63f43d5437527c541ce624fe303a2ee2fdb729770afa91e'], + 'modulename': 'liana' + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['liana'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From a535e134c2c0fb39c4481853bc4ef2af35c7bf97 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 19:00:43 +0200 Subject: [PATCH 7445/9987] adding easyconfigs: libxml2-2.11.4-GCCcore-12.3.0.eb, gettext-0.21.1-GCCcore-12.3.0.eb --- .../gettext/gettext-0.21.1-GCCcore-12.3.0.eb | 37 +++++++++++++++++++ .../libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb | 27 ++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d3c0439ba9c --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21.1' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e8c3650e1d8cee875c4f355642382c1df83058bd5a11ee8555c0cf276d646d45'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('libxml2', '2.11.4'), + ('ncurses', '6.4'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..13845741e03 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.11.4' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['737e1d7f8ab3f139729ca13a2494fd17bf30ddb4b7a427cf336252cab57f57f7'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), +] + +moduleclass = 'lib' From ce52564c3c53585b977851c30a5e85defffb25d0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 19:03:29 +0200 Subject: [PATCH 7446/9987] adding easyconfigs: libpng-1.6.39-GCCcore-12.3.0.eb --- .../l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1bd630a9c13 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.39' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['af4fb7f260f839919e5958e5ab01a275d4fe436d45442a36ee62f73e5beb75ba'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +local_majminver = '%(version_major)s%(version_minor)s' + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' From c6fa45e029b3060ea23dbd06a3a007fb4f1506fa Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 19:12:28 +0200 Subject: [PATCH 7447/9987] adding easyconfigs: zstd-1.5.5-GCCcore-12.3.0.eb, gzip-1.12-GCCcore-12.3.0.eb, lz4-1.9.4-GCCcore-12.3.0.eb --- .../g/gzip/gzip-1.12-GCCcore-12.3.0.eb | 29 +++++++++++++ .../l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb | 30 ++++++++++++++ .../z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb | 41 +++++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..917a7468794 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.12' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['gzip-1.12_fix-gnulib-strndup-redeclaration.patch'] +checksums = [ + '5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085', # gzip-1.12.tar.gz + # gzip-1.12_fix-gnulib-strndup-redeclaration.patch + '9c67e3e88848f7ff1f19f29d87f286bac1cc8f027f7eea9bcaf53883b95032e4', +] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1386e6dc615 --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.4' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b0e3aa07c8c063ddf40b082bdf7e37a1562bda40a0ff5272957f3e987e0e54b'] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..dda0d74b174 --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.5.5' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['98e9c3d949d1b924e28e01eccb7deed865eefebf25c2f21c702e5cd5b63b85e1'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('gzip', '1.12'), + ('XZ', '5.4.2'), + ('lz4', '1.9.4'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From b78b8c46ec1b290b3f5bac4bfe8a4d3c8d35c726 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 19:21:39 +0200 Subject: [PATCH 7448/9987] adding easyconfigs: libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb, NASM-2.16.01-GCCcore-12.3.0.eb --- .../libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb | 42 +++++++++++++++++++ .../n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb | 25 +++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..db21ae7cbeb --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.1.5.1' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2fdc3feb6e9deb17adec9bafa3321419aa19f8f4e5dea7bf8486844ca22207bf'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('NASM', '2.16.01'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5c1bbfafd36 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.16.01' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['35b6ad2ee048d41c4779f073f3efca7762a822b7d2d4ef4e8df24cf65747bb2e'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' From 51cfc490643aa93ead80de5defef6b76cffd4c53 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 20:18:31 +0200 Subject: [PATCH 7449/9987] adding easyconfigs: double-conversion-3.3.0-GCCcore-12.3.0.eb --- .../double-conversion-3.3.0-GCCcore-12.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..66e54112889 --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.3.0' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['04ec44461850abbf33824da84978043b22554896b552c5fd11a9c5ae4b4d296e'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +separate_build_dir = True + +build_type = 'Release' + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a', + '-DBUILD_SHARED_LIBS=ON' +] + +sanity_check_paths = { + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 46e712d814a7dd6e26ad1fad7c4436c3dcb97889 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 20:26:48 +0200 Subject: [PATCH 7450/9987] adding easyconfigs: mold-1.11.0-GCCcore-12.3.0.eb --- .../m/mold/mold-1.11.0-GCCcore-12.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/mold/mold-1.11.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/mold/mold-1.11.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mold/mold-1.11.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..256cc29ec4c --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-1.11.0-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'mold' +version = '1.11.0' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['99318eced81b09a77e4c657011076cc8ec3d4b6867bd324b8677974545bc4d6f'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' From 82073c29e1ad9b149862c41915b3af592c395003 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 20:55:32 +0200 Subject: [PATCH 7451/9987] adding easyconfigs: NSS-3.89.1-GCCcore-12.3.0.eb, NSPR-4.35-GCCcore-12.3.0.eb --- .../n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb | 30 +++++++++ .../n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb | 61 +++++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a5ee868d241 --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.35' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7ea3297ea5969b5d25a5dd8d47f2443cda88e9ee746301f6e1e1426f8a6abc8f'] + +builddependencies = [('binutils', '2.40')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +sanity_check_commands = ["nspr-config --version"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7b9beb5c086 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.89.1' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%s_RTM/src/' % version.replace('.', '_')] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', + 'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', +] +checksums = [ + {'nss-3.89.1.tar.gz': '3adaedb9e70c3c5f40603bf60a01e336190a6dbe01929d395f16b01fe84a0156'}, + {'NSS-3.39_pkgconfig.patch': '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774'}, + {'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch': + '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'}, +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('NSPR', '4.35'), + ('zlib', '1.2.13'), +] + +# building in parallel fails +parallel = 1 + +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " +# fix for not being able to find header files +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], +} + +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' From 5c4de2bbe909eb60840c61e072fd3c6bb831e41d Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 22:26:59 +0200 Subject: [PATCH 7452/9987] adding easyconfigs: DBus-1.15.4-GCCcore-12.3.0.eb, expat-2.5.0-GCCcore-12.3.0.eb --- .../d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb | 44 +++++++++++++++++++ .../e/expat/expat-2.5.0-GCCcore-12.3.0.eb | 31 +++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..686c369b6a7 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.15.4' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['bfe53d9e54a4977ec344928521b031af2e97cf78aea58f5d8e2b85ea0a80028b'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('expat', '2.5.0'), +] + +configopts = '--with-systemdsystemunitdir=no ' +# disable documentation +configopts += '--disable-xml-docs --disable-doxygen-docs --disable-ducktype-docs' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5cca3ac204e --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.5.0' + +homepage = 'https://libexpat.github.io' + +description = """Expat is an XML parser library written in C. It is a stream-oriented parser +in which an application registers handlers for things the parser might find +in the XML document (like start tags).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_TAR_BZ2] +checksums = ['6f0e6e01f7b30025fa05c85fdad1e5d0ec7fd35d9f61b22f34998de11969ff67'] + +builddependencies = [('binutils', '2.40')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From e9c6e7366182578377f1bd35d79bd13912d26d9b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 22:37:27 +0200 Subject: [PATCH 7453/9987] adding easyconfigs: snappy-1.1.10-GCCcore-12.3.0.eb --- .../s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..52a0f6777b8 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.10' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-1.1.9_use-default-rtti.patch', +] +checksums = [{ + '1.1.10.tar.gz': '49d831bffcc5f3d01482340fe5af59852ca2fe76c3e05df0e67203ebbe0f1d90', + 'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d', +}] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [] +} + +moduleclass = 'lib' From a73725f77e872fbec77fed54979b6cd6e06522a6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 22:39:59 +0200 Subject: [PATCH 7454/9987] adding easyconfigs: graphite2-1.3.14-GCCcore-12.3.0.eb --- .../graphite2-1.3.14-GCCcore-12.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0c6ebe10a4c --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' From 6fcdebd415e78f64918bf0ab9d3317c2463677f6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 22:51:29 +0200 Subject: [PATCH 7455/9987] adding easyconfigs: Doxygen-1.9.7-GCCcore-12.3.0.eb, libiconv-1.17-GCCcore-12.3.0.eb --- .../d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ .../libiconv/libiconv-1.17-GCCcore-12.3.0.eb | 23 ++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..26007e7a823 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +name = 'Doxygen' +version = '1.9.7' + +homepage = 'https://www.doxygen.org' +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['87007641c38e2c392c8596f36711eb97633b984c8430f389e7bcf6323a098d94'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('libiconv', '1.17'), +] + +configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2f013448152 --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.17' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8f74213b56238c85a50a5329f77e06198771e70dd9a739779f4c02f65d971313'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' From ba2fef107abce8c2f7f3b94aa0bccdfcfd554bf6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 23:08:18 +0200 Subject: [PATCH 7456/9987] update snappy-1.1.10-GCCcore-12.3.0.eb: use correct checksums --- .../easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb index 52a0f6777b8..a221f9f9ea5 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb @@ -15,10 +15,10 @@ sources = ['%(version)s.tar.gz'] patches = [ '%(name)s-1.1.9_use-default-rtti.patch', ] -checksums = [{ - '1.1.10.tar.gz': '49d831bffcc5f3d01482340fe5af59852ca2fe76c3e05df0e67203ebbe0f1d90', - 'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d', -}] +checksums = [ + {'1.1.10.tar.gz': '49d831bffcc5f3d01482340fe5af59852ca2fe76c3e05df0e67203ebbe0f1d90'}, + {'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d'}, +] builddependencies = [ ('binutils', '2.40'), From 3e40883aef575be4b612aa5d1cc25623e9d16680 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 19 May 2023 23:16:06 +0200 Subject: [PATCH 7457/9987] adding easyconfigs: JasPer-4.0.0-GCCcore-12.3.0.eb --- .../j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1568d4b64e4 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '4.0.0' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['977c4c2e4210f4e37313cd2232d99e73d57ab561917b3c060bcdd5e83a0a13f1'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' From 0f83fa5bc9ddb1bd1e2a60288a10c4694768336e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 21 May 2023 13:28:56 +0200 Subject: [PATCH 7458/9987] adding easyconfigs: make-4.4.1-GCCcore-12.3.0.eb --- .../m/make/make-4.4.1-GCCcore-12.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..283fa0f57f8 --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.4.1' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['dd16fb1d67bfab79a72f5e8390735c49e3e8e70b4945a15ab1f81ddb78658fb3'] + +builddependencies = [('binutils', '2.40')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' From b5c1188c9c895757fdf842563ce302eeff2b8a00 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 21 May 2023 13:37:54 +0200 Subject: [PATCH 7459/9987] adding easyconfigs: PCRE2-10.42-GCCcore-12.3.0.eb, PCRE-8.45-GCCcore-12.3.0.eb --- .../p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb | 45 +++++++++++++++++++ .../p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb | 28 ++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b0f34719345 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.45' + +homepage = 'https://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.pcre.org/pub/pcre/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4e6ce03e0336e8b4a3d6c2b70b1c5e18590a5673a98186da90d4f33c23defc09'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +configopts = ' '.join([ + '--enable-utf', + '--enable-unicode-properties', + '--enable-pcre16', + '--enable-pcre32', +]) + +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..01813f20f0b --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.42' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c33b418e3b936ee3153de2c61cc638e7e4fe3156022a5c77d0711bcbb9d64f1f'] + +builddependencies = [('binutils', '2.40')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' From df8d01fc9828b77cf5b033cdec0064a7239b1c5b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 21 May 2023 14:03:58 +0200 Subject: [PATCH 7460/9987] adding easyconfigs: SQLite-3.42.0-GCCcore-12.3.0.eb, Tcl-8.6.13-GCCcore-12.3.0.eb, UnZip-6.0-GCCcore-12.3.0.eb, libffi-3.4.4-GCCcore-12.3.0.eb, libreadline-8.2-GCCcore-12.3.0.eb --- .../l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb | 29 +++++++++ .../libreadline-8.2-GCCcore-12.3.0.eb | 41 +++++++++++++ .../s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb | 39 ++++++++++++ .../t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb | 41 +++++++++++++ .../u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb | 59 +++++++++++++++++++ 5 files changed, 209 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..416e3945706 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.4' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d66c56ad259a82cf2a9dfc408b32bf5da52371500b84745f7fb8b645712df676'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ade8ec67a13 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.2' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['3feb7171f16a84ee82ca18a36d7b9be109a52c04f492a053331d7d1095007c35'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('ncurses', '6.4'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f3ebb9f775e --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.42.0' +local_filename_version = '3420000' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2023/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['7abcfd161c6e2742ca5c6c0895d1f853c940f203304a0b49da4e1eca5d088ca6'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('libreadline', '8.2'), + ('Tcl', '8.6.13'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a85651a4106 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.13' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['43a1fae7412f61ff11de2cfd05d28cfc3a73762f354a417c62370a54e2caf066'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('zlib', '1.2.13'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7baea9a00a2 --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT' + '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD', + '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT'] + +buildopts = ' '.join([ + "-f unix/Makefile", + 'CC="$CC"', + 'D_USE_BZ2=-DUSE_BZIP2', + 'L_BZ2=-lbz2', + 'LF2="$LDFLAGS"', + 'CF="%s"' % ' '.join(local_cf), + 'unzips', +]) + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From a136a8c96418f20e4f1f37c4a5fab6ca978dac46 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 18:04:32 +0200 Subject: [PATCH 7461/9987] adding easyconfigs: Perl-5.36.1-GCCcore-12.3.0.eb --- .../p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0d05c82ee82 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb @@ -0,0 +1,86 @@ +name = 'Perl' +version = '5.36.1' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +Includes a small selection of extra CPAN packages for core functionality. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +# !! order of extensions is important !! +# extensions updated on 2023-05-02 +# includes all dependencies for Autotools +exts_list = [ + ('threads', '2.21', { + 'source_tmpl': 'threads-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['28394c98a2bcae6f20ffb8a3d965a1c194b764c650169e2050ee38dbaa10f110'], + }), + ('constant', '1.33', { + 'source_tmpl': 'constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], + }), + ('Getopt::Long', '2.54', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + 'checksums': ['584ba3c99bb2d6b341375212f9b874613f706cfb01cee21b8a2676a98ab985fe'], + }), + ('File::Path', '2.18', { + 'source_tmpl': 'File-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN/'], + 'checksums': ['980f0a17edb353df46e9cd7b357f9f5929cde0f80c45fd7a06cf7e0e8bd6addd'], + }), + ('File::Spec', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('IO::File', '1.51', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'], + 'checksums': ['5493ea55998728cd2b7ecb8234c58fb5d5df27098d0f07addca22444d7616ce0'], + }), + ('Thread::Queue', '3.13', { + 'source_tmpl': 'Thread-Queue-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['6ba3dacddd2fbb66822b4aa1d11a0a5273cd04c825cb3ff31c20d7037cbfdce8'], + }), + ('Carp', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('Exporter', '5.77', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['3892ee5c6ae6e482068d53b61e25cae4fc71ddc79cc47446e385df0a669bb8ed'], + }), + ('Text::ParseWords', '3.31', { + 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], + 'checksums': ['2ae555ba084d75b2b8feeeb8d1a00911276815ada86bccb1452236964d5a2fc7'], + }), + ('Data::Dumper', '2.183', { + 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], + 'checksums': ['e42736890b7dae1b37818d9c5efa1f1fdc52dec04f446a33a4819bf1d4ab5ad3'], + }), +] + +moduleclass = 'lang' From 55792ec8404c91f3256a03474c6490dba9b59a86 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 21:21:26 +0200 Subject: [PATCH 7462/9987] adding easyconfigs: numactl-2.0.16-GCCcore-12.3.0.eb --- .../numactl/numactl-2.0.16-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..68237d4c0cc --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.16' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1b242f893af977a1d31af6ce9d6b8dafdd2d8ec3dc9207f7c2dc0d3446e7c7c8'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' From 7b3f7392c48bb36a9adcfeb41dc182561b5da2e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 21:58:56 +0200 Subject: [PATCH 7463/9987] adding easyconfigs: googletest-1.13.0-GCCcore-12.3.0.eb --- .../googletest-1.13.0-GCCcore-12.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d54ca5d0453 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.13.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/googletest/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ad7fdba11ea011c1d925b3289cf4af2c66a352e18d4c7264392fead75e919363'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' From 19c6e6559fd80fb29b0bf9bd4e4369a598ec9dcb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 22:06:58 +0200 Subject: [PATCH 7464/9987] adding easyconfigs: Eigen-3.4.0-GCCcore-12.3.0.eb --- .../e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..dfd909ce779 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.4.0' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.40'), # to make CMake compiler health check pass on old systems + ('CMake', '3.26.3'), +] + +moduleclass = 'math' From d82c81ac80fa462d4b66e2dd9c86c853522dd6ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 22:11:04 +0200 Subject: [PATCH 7465/9987] adding easyconfigs: LZO-2.10-GCCcore-12.3.0.eb, Brotli-1.0.9-GCCcore-12.3.0.eb, Szip-2.1.1-GCCcore-12.3.0.eb, Zip-3.0-GCCcore-12.3.0.eb, libdeflate-1.18-GCCcore-12.3.0.eb --- .../b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb | 36 +++++++++++++++++ .../l/LZO/LZO-2.10-GCCcore-12.3.0.eb | 27 +++++++++++++ .../libdeflate-1.18-GCCcore-12.3.0.eb | 37 +++++++++++++++++ .../s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb | 29 ++++++++++++++ .../z/Zip/Zip-3.0-GCCcore-12.3.0.eb | 40 +++++++++++++++++++ 5 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.18-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..36c52aae8f7 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Brotli' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brotli-%(version)s_pc_link_flags.patch'] +checksums = [ + 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz + '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'dirs': [], +} + +sanity_check_commands = ["brotli --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..38c850b17e8 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.40')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.18-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.18-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3e44ca69301 --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.18-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'libdeflate' +version = '1.18' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['225d982bcaf553221c76726358d2ea139bb34913180b20823c782cede060affd'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e0a01221b9d --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ff3257294a7 --- /dev/null +++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Zip' +version = '3.0' + +homepage = 'http://www.info-zip.org/Zip.html' +description = """Zip is a compression and file packaging/archive utility. +Although highly compatible both with PKWARE's PKZIP and PKUNZIP +utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives +have been portability and other-than-MSDOS functionality""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' +buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' +buildopts += 'generic_gcc' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["zip --version"] + +moduleclass = 'tools' From a4fa006233165c82c3f2065432db0c16e3f37a4c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 22:31:01 +0200 Subject: [PATCH 7466/9987] adding easyconfigs: FLAC-1.4.2-GCCcore-12.3.0.eb, libvorbis-1.3.7-GCCcore-12.3.0.eb, libogg-1.3.5-GCCcore-12.3.0.eb, libopus-1.4-GCCcore-12.3.0.eb --- .../f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb | 30 +++++++++++++++++++ .../l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb | 25 ++++++++++++++++ .../l/libopus/libopus-1.4-GCCcore-12.3.0.eb | 30 +++++++++++++++++++ .../libvorbis-1.3.7-GCCcore-12.3.0.eb | 30 +++++++++++++++++++ 4 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libopus/libopus-1.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..6b89c621af0 --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.4.2' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e322d58a1f48d23d9dd38f432672865f6f79e73a6f9cc5a5f57fcaa83eb5a8e4'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +sanity_check_commands = ["flac --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8d57716f577 --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.5' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705'] + +builddependencies = [('binutils', '2.40')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..576b4556eec --- /dev/null +++ b/easybuild/easyconfigs/l/libopus/libopus-1.4-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libopus' +version = '1.4' + +homepage = 'https://www.opus-codec.org/' +description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive + speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is + standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s + SILK codec and Xiph.Org’s CELT codec.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://downloads.xiph.org/releases/opus/'] +sources = ['opus-%(version)s.tar.gz'] +checksums = ['c9b32b4253be5ae63d1ff16eea06b94b5f0f2951b7a02aceef58e3a3ce49c51f'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT], + 'dirs': ['include/opus'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..40c5f137808 --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' From cdd9bee3ea98f1310ca6d5bac5753bc77236e6b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 22:39:21 +0200 Subject: [PATCH 7467/9987] adding easyconfigs: jbigkit-2.1-GCCcore-12.3.0.eb, LibTIFF-4.5.0-GCCcore-12.3.0.eb, OpenJPEG-2.5.0-GCCcore-12.3.0.eb --- .../j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb | 45 +++++++++++++++++++ .../l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb | 35 +++++++++++++++ .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb | 42 +++++++++++++++++ 3 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b6086a98262 --- /dev/null +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'jbigkit' +version = '2.1' + +homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' +description = """JBIG-KIT is a software implementation of the JBIG1 data + compression standard (ITU-T T.82), which was designed for bi-level image + data, such as scanned documents.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_libpath.patch', + '%(name)s-%(version)s_shlib.patch', +] +checksums = [ + {'jbigkit-2.1.tar.gz': 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932'}, + {'jbigkit-2.1_libpath.patch': '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce'}, + {'jbigkit-2.1_shlib.patch': '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +files_to_copy = [ + (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), + (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libjbig85.a', 'lib/libjbig.a', + 'bin/pbmtojbg', 'bin/jbgtopbm', + 'include/jbig.h', 'include/jbig_ar.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..706cc20c7dc --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.5.0' + +homepage = 'https://libtiff.gitlab.io/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['c7a1d9296649233979fa3eacffef3fa024d73d05d589cb622727b5b08c423464'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('zlib', '1.2.13'), + ('libjpeg-turbo', '2.1.5.1'), + ('XZ', '5.4.2'), + ('jbigkit', '2.1'), + ('zstd', '1.5.5'), + ('libdeflate', '1.18'), +] + +configopts = "--enable-ld-version-script " +configopts += '--disable-webp' + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e930df38233 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.0' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.13'), + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' From c76c26d0faa8b6041d713b307fc1f480b1551f78 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 22:47:18 +0200 Subject: [PATCH 7468/9987] adding easyconfigs: OpenEXR-3.1.7-GCCcore-12.3.0.eb, Imath-3.1.7-GCCcore-12.3.0.eb --- .../i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb | 28 ++++++++++++++ .../o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb | 38 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b6497fabaeb --- /dev/null +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Imath' +version = '3.1.7' + +homepage = 'https://imath.readthedocs.io/en/latest/' +description = """ +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bff1fa140f4af0e7f02c6cb78d41b9a7d5508e6bcdfda3a583e35460eb6d4b47'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libImath.%s' % SHLIB_EXT], + 'dirs': ['include/Imath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f66f45d25c3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.7' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['78dbca39115a1c526e6728588753955ee75fa7f5bb1a6e238bed5b6d66f91fd7'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Imath', '3.1.7'), + ('zlib', '1.2.13') +] + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' From 84191cff1aa331e25e687099524739f0475ab2fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 22:54:19 +0200 Subject: [PATCH 7469/9987] adding easyconfigs: spdlog-1.11.0-GCCcore-12.3.0.eb, libunwind-1.6.2-GCCcore-12.3.0.eb, utf8proc-2.8.0-GCCcore-12.3.0.eb --- .../libunwind-1.6.2-GCCcore-12.3.0.eb | 32 +++++++++++++++++++ .../s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb | 24 ++++++++++++++ .../utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb | 30 +++++++++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9ca69508042 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.6.2' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4a6aec666991fb45d0889c44aede8ad6eb108071c3554fcdff671f9c94794976'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('XZ', '5.4.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fno-common" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..72f5f9a9923 --- /dev/null +++ b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'spdlog' +version = '1.11.0' + +homepage = 'https://github.com/gabime/spdlog' +description = 'Very fast, header-only/compiled, C++ logging library.' +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/gabime/spdlog/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ca5cae8d6cac15dae0ec63b21d6ad3530070650f68076f3a4a862ca293a858bb'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['include/spdlog/spdlog.h'], + 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..74f889da933 --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.8.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a0a60a79fe6f6d54e7d411facbfcc867a6e198608f2cd992490e46f04b1bcecc'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 0145adc5d707cd2ce27a2d6c6a458d213381f872 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 23:16:31 +0200 Subject: [PATCH 7470/9987] adding easyconfigs: Python-3.11.3-GCCcore-12.3.0.eb --- .../p/Python/Python-3.11.3-GCCcore-12.3.0.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..01c46749a29 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb @@ -0,0 +1,73 @@ +name = 'Python' +version = '3.11.3' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['1a79f3df32265d9e6625f1a0b31c28eb1594df911403d11f3320ee1da1b3e048'] + +builddependencies = [ + ('UnZip', '6.0'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('binutils', '2.40'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.13'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('SQLite', '3.42.0'), + ('XZ', '5.4.2'), + ('libffi', '3.4.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 2023-05-17 +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('wheel', '0.40.0', { + 'checksums': ['cd1196f3faee2b31968d626e1731c94f99cbdb67cf5a46e4f5656cbee7738873'], + }), + ('setuptools', '67.7.2', { + 'checksums': ['f104fa03692a2602fa0fec6c6a9e63b6c8a968de13e17c026957dd1f53d80990'], + }), + ('pip', '23.1.2', { + 'checksums': ['0e7c86f486935893c708287b30bd050a36ac827ec7fe5e43fe7cb198dd835fba'], + }), + ('distlib', '0.3.6', { + 'checksums': ['14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46'], + }), + ('filelock', '3.12.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ad98852315c2ab702aeb628412cbf7e95b7ce8c3bf9565670b4eaecf1db370a9'], + }), + ('platformdirs', '3.5.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e2378146f1964972c03c085bb5662ae80b2b8c06226c54b2ff4aa9483e8a13a5'], + }), + ('virtualenv', '20.23.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['6abec7670e5802a528357fdc75b26b9f57d5d92f29c5462ba0fbe45feacc685e'], + }), +] + +moduleclass = 'lang' From 4ad0284e7ea35c1e17c439b8b8b9d6518377cf93 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 23:20:11 +0200 Subject: [PATCH 7471/9987] adding easyconfigs: Highway-1.0.4-GCCcore-12.3.0.eb, Brunsli-0.1-GCCcore-12.3.0.eb, fmt-10.0.0-GCCcore-12.3.0.eb, UDUNITS-2.2.28-GCCcore-12.3.0.eb, DB-18.1.40-GCCcore-12.3.0.eb, libevent-2.1.12-GCCcore-12.3.0.eb, elfutils-0.189-GCCcore-12.3.0.eb --- .../b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb | 50 +++++++++++++++++++ .../d/DB/DB-18.1.40-GCCcore-12.3.0.eb | 33 ++++++++++++ .../elfutils/elfutils-0.189-GCCcore-12.3.0.eb | 41 +++++++++++++++ .../f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb | 26 ++++++++++ .../h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb | 32 ++++++++++++ .../libevent-2.1.12-GCCcore-12.3.0.eb | 38 ++++++++++++++ .../UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb | 44 ++++++++++++++++ 7 files changed, 264 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e9d6adbb76f --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '1.0.4'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib*/", + "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5d02753039b --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d1d7854b68d --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.189' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['39bd8f1a338e2b7cd4abc3ff11a0eddc6e690f69578a57478d8179b4148708c8'] + +builddependencies = [ + ('M4', '1.4.19'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('binutils', '2.40'), + ('bzip2', '1.0.8'), + ('libarchive', '3.6.2'), + ('XZ', '5.4.2'), + ('zstd', '1.5.5'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f4b60c8afb7 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '10.0.0' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['cceb4cb9366e18a5742128cb3524ce5f50e88b476f1e54737a47ffdf4df4c996'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a05239847d3 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Highway' +version = '1.0.4' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('googletest', '1.13.0'), +] + +configopts = "-DHWY_SYSTEM_GTEST=ON" + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..61bf17145f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..67b179fd479 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.28' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/%(version)s/', + 'https://sources.easybuild.io/u/UDUNITS/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['590baec83161a3fd62c00efa66f6113cec8a7c461e3f61a5182167e0cc5d579e'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('expat', '2.5.0')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From f749b7a72fa99c110c5977d04d0bc71494c261d1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 23:26:57 +0200 Subject: [PATCH 7472/9987] Fix checksum --- easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb index f4b60c8afb7..ad80d0891f9 100644 --- a/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb @@ -11,7 +11,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] sources = ['fmt-%(version)s.zip'] -checksums = ['cceb4cb9366e18a5742128cb3524ce5f50e88b476f1e54737a47ffdf4df4c996'] +checksums = ['4943cb165f3f587f26da834d3056ee8733c397e024145ca7d2a8a96bb71ac281'] builddependencies = [ ('binutils', '2.40'), From b40f6191343e1b87973aaedb879ca3546d0b2d99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 21 May 2023 23:56:04 +0200 Subject: [PATCH 7473/9987] Add autotools --- .../Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb | 48 +++++++++++++++++++ .../Automake-1.16.5-GCCcore-12.3.0.eb | 39 +++++++++++++++ .../Autotools-20220317-GCCcore-12.3.0.eb | 24 ++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0b47b6d9a77 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-12.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.71' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('M4', '1.4.19'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.36.1'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +sanity_check_commands = [ + "autoconf --help", + "autom4te --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..86496ab7d32 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.5' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Autoconf', '2.71'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.36.1'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ['bin/aclocal', 'bin/automake'], + 'dirs': [] +} + +sanity_check_commands = [ + "aclocal --help", + "automake --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..57d84ce4906 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20220317' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +dependencies = [ + ('Autoconf', '2.71'), # 20210128 + ('Automake', '1.16.5'), # 20211003 + ('libtool', '2.4.7'), # 20220317 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' From 3fcda9852e1fad91992d19873e3151e6fe7ac8f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 22 May 2023 00:27:07 +0200 Subject: [PATCH 7474/9987] adding easyconfigs: Abseil-20230125.3-GCCcore-12.3.0.eb, Blitz++-1.0.2-GCCcore-12.3.0.eb, groff-1.22.4-GCCcore-12.3.0.eb, json-c-0.16-GCCcore-12.3.0.eb, METIS-5.1.0-GCCcore-12.3.0.eb, libtirpc-1.3.3-GCCcore-12.3.0.eb, libxslt-1.1.38-GCCcore-12.3.0.eb, libyaml-0.2.5-GCCcore-12.3.0.eb, libgeotiff-1.7.1-GCCcore-12.3.0.eb, PROJ-9.2.0-GCCcore-12.3.0.eb, nlohmann_json-3.11.2-GCCcore-12.3.0.eb --- .../Abseil-20230125.3-GCCcore-12.3.0.eb | 31 ++++++++++++ .../b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb | 36 ++++++++++++++ .../g/groff/groff-1.22.4-GCCcore-12.3.0.eb | 27 ++++++++++ .../j/json-c/json-c-0.16-GCCcore-12.3.0.eb | 32 ++++++++++++ .../libgeotiff-1.7.1-GCCcore-12.3.0.eb | 36 ++++++++++++++ .../libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb | 28 +++++++++++ .../libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb | 34 +++++++++++++ .../l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb | 25 ++++++++++ .../m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb | 36 ++++++++++++++ .../nlohmann_json-3.11.2-GCCcore-12.3.0.eb | 25 ++++++++++ .../p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb | 49 +++++++++++++++++++ 11 files changed, 359 insertions(+) create mode 100644 easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b76e53de45b --- /dev/null +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Abseil' +version = '20230125.3' + +homepage = 'https://abseil.io/' +description = """Abseil is an open-source collection of C++ library code designed to augment the +C++ standard library. The Abseil library code is collected from Google's own +C++ code base, has been extensively tested and used in production, and is the +same code we depend on in our daily coding lives.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++17'} + +source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['5366d7e7fa7ba0d915014d387b66d0d002c03236448e1ba9ef98122c13b35c36'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], + 'dirs': ['include/absl'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..eb9097baf3e --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Blitz++' +version = '1.0.2' + +homepage = 'https://github.com/blitzpp/blitz' + +description = """ + Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation + in C++ with a speed comparable to Fortran implementations, while preserving an + object-oriented interface +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [('https://github.com/blitzpp/blitz/archive/')] +sources = ['%(version)s.tar.gz'] +patches = ['blitz-%(version)s_pkgconfig.patch'] +checksums = [ + {'1.0.2.tar.gz': '500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'}, + {'blitz-1.0.2_pkgconfig.patch': 'd15fb397e75eb009809ecacdd7f2f154ff05e6586895f3b0511d0b53a6e3b9fe'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3') +] + +sanity_check_paths = { + 'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT], + 'dirs': ['include/blitz/array', 'include/blitz/meta', + 'include/random', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..957f3fbd53c --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.22.4' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = '--with-doc=no' + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..50a777efb87 --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.16' +local_suff = '-20220414' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['3ecaeedffd99a60b1262819f9e60d7d983844073abc74e495cb822b251904185'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f11da8ce849 --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.7.1' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['05ab1347aaa471fc97347d8d4269ff0c00f30fa666d956baba37948ec87e55d6'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('PROJ', '9.2.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('zlib', '1.2.13'), + ('SQLite', '3.42.0'), + ('LibTIFF', '4.5.0'), + ('cURL', '8.0.1'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..409cc8bc2a0 --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.3' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['6474e98851d9f6f33871957ddee9714fdcd9d8a5ee9abb5a98d63ea2e60e12f3'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.40') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..171353e0fac --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.38' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['1f32450425819a09acaff2ab7a5a7f8a2ec7956e505d7beeb45e843d0e1ecab1'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libxml2', '2.11.4'), +] + +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..76fee75bd36 --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.5' + +homepage = 'https://pyyaml.org/wiki/LibYAML' +description = "LibYAML is a YAML parser and emitter written in C." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pyyaml.org/download/%(name)s/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['c642ae9b75fee120b2d96c712538bd2cf283228d2337df2cf2988e3c02678ef4'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2a363ae76ca --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s-use-doubles.patch'] +checksums = [ + {'metis-5.1.0.tar.gz': '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2'}, + {'METIS-5.1.0-use-doubles.patch': '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67'}, +] + +# We use 32bit for indices and 64bit for content +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1ad7b6c1af6 --- /dev/null +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'nlohmann_json' +version = '3.11.2' + +homepage = 'https://github.com/nlohmann/json' +description = """JSON for Modern C++""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d69f9deb6a75e2580465c6c4c5111b89c4dc2fa94e3a85fcd2ffcd9a143d9273'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['include/nlohmann/json.hpp'], + 'dirs': ['share/cmake', 'share/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..deb26d4ed5d --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'CMakeMake' + +name = 'PROJ' +version = '9.2.0' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dea816f5aa732ae6b2ee3977b9bdb28b1d848cf56a1aad8faf6708b89f0ed50e'] + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('googletest', '1.13.0'), +] + +dependencies = [ + ('SQLite', '3.42.0'), + ('LibTIFF', '4.5.0'), + ('cURL', '8.0.1'), + ('XZ', '5.4.2'), + ('nlohmann_json', '3.11.2'), +] + +# build twice, once for static, once for shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 62162245805637fc813294cdcc38fd4a933a3935 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 22 May 2023 11:03:37 +0200 Subject: [PATCH 7475/9987] adding easyconfigs: ripunzip-0.4.0.eb --- .../easyconfigs/r/ripunzip/ripunzip-0.4.0.eb | 484 ++++++++++++++++++ 1 file changed, 484 insertions(+) create mode 100644 easybuild/easyconfigs/r/ripunzip/ripunzip-0.4.0.eb diff --git a/easybuild/easyconfigs/r/ripunzip/ripunzip-0.4.0.eb b/easybuild/easyconfigs/r/ripunzip/ripunzip-0.4.0.eb new file mode 100644 index 00000000000..ef9b2d15dd9 --- /dev/null +++ b/easybuild/easyconfigs/r/ripunzip/ripunzip-0.4.0.eb @@ -0,0 +1,484 @@ +easyblock = 'Cargo' + +name = 'ripunzip' +version = '0.4.0' + +homepage = 'https://github.com/google/ripunzip' +description = "A tool to unzip files in parallel." + +toolchain = SYSTEM + +crates = [ + ('adler', '1.0.2'), + ('aes', '0.7.5'), + ('aho-corasick', '0.7.20'), + ('anyhow', '1.0.66'), + ('arbitrary', '1.2.0'), + ('arrayvec', '0.5.2'), + ('atty', '0.2.14'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64ct', '1.5.3'), + ('bitflags', '1.3.2'), + ('block-buffer', '0.10.3'), + ('bstr', '0.2.17'), + ('bumpalo', '3.11.1'), + ('byteorder', '1.4.3'), + ('bytes', '1.3.0'), + ('bzip2', '0.4.3'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cast', '0.3.0'), + ('cc', '1.0.77'), + ('cfg-if', '1.0.0'), + ('cipher', '0.3.0'), + ('clap', '2.34.0'), + ('clap', '4.0.29'), + ('clap_derive', '4.0.21'), + ('clap_lex', '0.3.0'), + ('console', '0.15.2'), + ('constant_time_eq', '0.1.5'), + ('core-foundation', '0.9.3'), + ('core-foundation-sys', '0.8.3'), + ('cpufeatures', '0.2.5'), + ('crc32fast', '1.3.2'), + ('criterion', '0.3.6'), + ('criterion-plot', '0.4.5'), + ('crossbeam-channel', '0.5.6'), + ('crossbeam-deque', '0.8.2'), + ('crossbeam-epoch', '0.9.13'), + ('crossbeam-utils', '0.8.14'), + ('crypto-common', '0.1.6'), + ('csv', '1.1.6'), + ('csv-core', '0.1.10'), + ('derive_arbitrary', '1.2.1'), + ('digest', '0.10.6'), + ('either', '1.8.0'), + ('encode_unicode', '0.3.6'), + ('encoding_rs', '0.8.31'), + ('env_logger', '0.10.0'), + ('errno', '0.2.8'), + ('errno-dragonfly', '0.1.2'), + ('fastrand', '1.8.0'), + ('flate2', '1.0.25'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.1.0'), + ('futures', '0.3.25'), + ('futures-channel', '0.3.25'), + ('futures-core', '0.3.25'), + ('futures-io', '0.3.25'), + ('futures-macro', '0.3.25'), + ('futures-sink', '0.3.25'), + ('futures-task', '0.3.25'), + ('futures-util', '0.3.25'), + ('generic-array', '0.14.6'), + ('getrandom', '0.2.8'), + ('h2', '0.3.15'), + ('half', '1.8.2'), + ('hashbrown', '0.12.3'), + ('heck', '0.4.0'), + ('hermit-abi', '0.1.19'), + ('hermit-abi', '0.2.6'), + ('hexdump', '0.1.1'), + ('hmac', '0.12.1'), + ('http', '0.2.8'), + ('http-body', '0.4.5'), + ('httparse', '1.8.0'), + ('httpdate', '1.0.2'), + ('httptest', '0.15.4'), + ('humantime', '2.1.0'), + ('hyper', '0.14.23'), + ('hyper-tls', '0.5.0'), + ('idna', '0.3.0'), + ('indexmap', '1.9.2'), + ('indicatif', '0.17.2'), + ('instant', '0.1.12'), + ('io-lifetimes', '1.0.3'), + ('ipnet', '2.5.1'), + ('is-terminal', '0.4.1'), + ('itertools', '0.4.19'), + ('itertools', '0.10.5'), + ('itoa', '0.4.8'), + ('itoa', '1.0.4'), + ('jobserver', '0.1.25'), + ('js-sys', '0.3.60'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.138'), + ('linux-raw-sys', '0.1.3'), + ('lipsum', '0.8.2'), + ('log', '0.4.17'), + ('memchr', '2.5.0'), + ('memoffset', '0.7.1'), + ('mime', '0.3.16'), + ('miniz_oxide', '0.6.2'), + ('mio', '0.8.5'), + ('monitor', '0.1.0'), + ('native-tls', '0.2.11'), + ('num-traits', '0.2.15'), + ('num_cpus', '1.14.0'), + ('number_prefix', '0.4.0'), + ('once_cell', '1.16.0'), + ('oorandom', '11.1.3'), + ('opaque-debug', '0.3.0'), + ('openssl', '0.10.44'), + ('openssl-macros', '0.1.0'), + ('openssl-probe', '0.1.5'), + ('openssl-sys', '0.9.79'), + ('os_str_bytes', '6.4.1'), + ('password-hash', '0.4.2'), + ('pbkdf2', '0.11.0'), + ('percent-encoding', '2.2.0'), + ('pin-project-lite', '0.2.9'), + ('pin-utils', '0.1.0'), + ('pkg-config', '0.3.26'), + ('plotters', '0.3.4'), + ('plotters-backend', '0.3.4'), + ('plotters-svg', '0.3.3'), + ('portable-atomic', '0.3.15'), + ('ppv-lite86', '0.2.17'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '1.0.47'), + ('progress-streams', '1.1.0'), + ('quote', '1.0.21'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rayon', '1.6.0'), + ('rayon-core', '1.10.1'), + ('redox_syscall', '0.2.16'), + ('regex', '1.7.0'), + ('regex-automata', '0.1.10'), + ('regex-syntax', '0.6.28'), + ('remove_dir_all', '0.5.3'), + ('reqwest', '0.11.13'), + ('rustix', '0.36.5'), + ('rustversion', '1.0.11'), + ('ryu', '1.0.11'), + ('same-file', '1.0.6'), + ('schannel', '0.1.20'), + ('scopeguard', '1.1.0'), + ('security-framework', '2.7.0'), + ('security-framework-sys', '2.6.1'), + ('serde', '1.0.149'), + ('serde_cbor', '0.11.2'), + ('serde_derive', '1.0.151'), + ('serde_json', '1.0.89'), + ('serde_urlencoded', '0.7.1'), + ('sha1', '0.10.5'), + ('sha2', '0.10.6'), + ('slab', '0.4.7'), + ('socket2', '0.4.7'), + ('strsim', '0.10.0'), + ('strum', '0.24.1'), + ('strum_macros', '0.24.3'), + ('subtle', '2.4.1'), + ('syn', '1.0.105'), + ('tempfile', '3.3.0'), + ('termcolor', '1.1.3'), + ('terminal_size', '0.1.17'), + ('test-log', '0.2.11'), + ('textwrap', '0.11.0'), + ('thiserror', '1.0.37'), + ('thiserror-impl', '1.0.37'), + ('time', '0.3.17'), + ('time-core', 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('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.36.1'), + ('windows-sys', '0.42.0'), + ('windows_aarch64_gnullvm', '0.42.0'), + ('windows_aarch64_msvc', '0.36.1'), + ('windows_aarch64_msvc', '0.42.0'), + ('windows_i686_gnu', '0.36.1'), + ('windows_i686_gnu', '0.42.0'), + ('windows_i686_msvc', '0.36.1'), + ('windows_i686_msvc', '0.42.0'), + ('windows_x86_64_gnu', '0.36.1'), + ('windows_x86_64_gnu', '0.42.0'), + ('windows_x86_64_gnullvm', '0.42.0'), + ('windows_x86_64_msvc', '0.36.1'), + ('windows_x86_64_msvc', '0.42.0'), + ('winreg', '0.10.1'), + ('zip', '0.6.3'), + ('zstd', '0.11.2+zstd.1.5.2'), + ('zstd-safe', '5.0.2+zstd.1.5.2'), + ('zstd-sys', '2.0.4+zstd.1.5.2'), +] +source_urls = ['https://github.com/google/ripunzip/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.4.0.tar.gz': 'ea8aaeb319dc72a4b2407fde8dafb310b0dfd9ced0c1602e2f3bcb068f9ee29b'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, 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{'unicode-normalization-0.1.22.tar.gz': '5c5713f0fc4b5db668a2ac63cdb7bb4469d8c9fed047b1d0292cc7b0ce2ba921'}, + {'unicode-width-0.1.10.tar.gz': 'c0edd1e5b14653f783770bce4a4dabb4a5108a5370a5f5d8cfe8710c361f6c8b'}, + {'url-2.3.1.tar.gz': '0d68c799ae75762b8c3fe375feb6600ef5602c883c5d21eb51c09f22b83c4643'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'walkdir-2.3.2.tar.gz': '808cf2735cd4b6866113f648b791c6adc5714537bc222d9347bb203386ffda56'}, + {'want-0.3.0.tar.gz': '1ce8a968cb1cd110d136ff8b819a556d6fb6d919363c61534f6860c7eb172ba0'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'wasm-bindgen-0.2.83.tar.gz': 'eaf9f5aceeec8be17c128b2e93e031fb8a4d469bb9c4ae2d7dc1888b26887268'}, + {'wasm-bindgen-backend-0.2.83.tar.gz': '4c8ffb332579b0557b52d268b91feab8df3615f265d5270fec2a8c95b17c1142'}, + {'wasm-bindgen-futures-0.4.33.tar.gz': '23639446165ca5a5de86ae1d8896b737ae80319560fbaa4c2887b7da6e7ebd7d'}, + {'wasm-bindgen-macro-0.2.83.tar.gz': '052be0f94026e6cbc75cdefc9bae13fd6052cdcaf532fa6c45e7ae33a1e6c810'}, + {'wasm-bindgen-macro-support-0.2.83.tar.gz': '07bc0c051dc5f23e307b13285f9d75df86bfdf816c5721e573dec1f9b8aa193c'}, + {'wasm-bindgen-shared-0.2.83.tar.gz': '1c38c045535d93ec4f0b4defec448e4291638ee608530863b1e2ba115d4fff7f'}, + {'web-sys-0.3.60.tar.gz': 'bcda906d8be16e728fd5adc5b729afad4e444e106ab28cd1c7256e54fa61510f'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.5.tar.gz': '70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.36.1.tar.gz': 'ea04155a16a59f9eab786fe12a4a450e75cdb175f9e0d80da1e17db09f55b8d2'}, + {'windows-sys-0.42.0.tar.gz': '5a3e1820f08b8513f676f7ab6c1f99ff312fb97b553d30ff4dd86f9f15728aa7'}, + {'windows_aarch64_gnullvm-0.42.0.tar.gz': '41d2aa71f6f0cbe00ae5167d90ef3cfe66527d6f613ca78ac8024c3ccab9a19e'}, + {'windows_aarch64_msvc-0.36.1.tar.gz': '9bb8c3fd39ade2d67e9874ac4f3db21f0d710bee00fe7cab16949ec184eeaa47'}, + {'windows_aarch64_msvc-0.42.0.tar.gz': 'dd0f252f5a35cac83d6311b2e795981f5ee6e67eb1f9a7f64eb4500fbc4dcdb4'}, + {'windows_i686_gnu-0.36.1.tar.gz': '180e6ccf01daf4c426b846dfc66db1fc518f074baa793aa7d9b9aaeffad6a3b6'}, + {'windows_i686_gnu-0.42.0.tar.gz': 'fbeae19f6716841636c28d695375df17562ca208b2b7d0dc47635a50ae6c5de7'}, + {'windows_i686_msvc-0.36.1.tar.gz': 'e2e7917148b2812d1eeafaeb22a97e4813dfa60a3f8f78ebe204bcc88f12f024'}, + {'windows_i686_msvc-0.42.0.tar.gz': '84c12f65daa39dd2babe6e442988fc329d6243fdce47d7d2d155b8d874862246'}, + {'windows_x86_64_gnu-0.36.1.tar.gz': '4dcd171b8776c41b97521e5da127a2d86ad280114807d0b2ab1e462bc764d9e1'}, + {'windows_x86_64_gnu-0.42.0.tar.gz': 'bf7b1b21b5362cbc318f686150e5bcea75ecedc74dd157d874d754a2ca44b0ed'}, + {'windows_x86_64_gnullvm-0.42.0.tar.gz': '09d525d2ba30eeb3297665bd434a54297e4170c7f1a44cad4ef58095b4cd2028'}, + {'windows_x86_64_msvc-0.36.1.tar.gz': 'c811ca4a8c853ef420abd8592ba53ddbbac90410fab6903b3e79972a631f7680'}, + {'windows_x86_64_msvc-0.42.0.tar.gz': 'f40009d85759725a34da6d89a94e63d7bdc50a862acf0dbc7c8e488f1edcb6f5'}, + {'winreg-0.10.1.tar.gz': '80d0f4e272c85def139476380b12f9ac60926689dd2e01d4923222f40580869d'}, + {'zip-0.6.3.tar.gz': '537ce7411d25e54e8ae21a7ce0b15840e7bfcff15b51d697ec3266cc76bdf080'}, + {'zstd-0.11.2+zstd.1.5.2.tar.gz': '20cc960326ece64f010d2d2107537f26dc589a6573a316bd5b1dba685fa5fde4'}, + {'zstd-safe-5.0.2+zstd.1.5.2.tar.gz': '1d2a5585e04f9eea4b2a3d1eca508c4dee9592a89ef6f450c11719da0726f4db'}, + {'zstd-sys-2.0.4+zstd.1.5.2.tar.gz': '4fa202f2ef00074143e219d15b62ffc317d17cc33909feac471c044087cad7b0'}, +] + +builddependencies = [ + ('Rust', '1.65.0', '', ('GCCcore', '12.2.0')), +] + +sanity_check_paths = { + 'files': ['bin/ripunzip'], + 'dirs': [], +} + +sanity_check_commands = ["ripunzip --help"] + +moduleclass = 'tools' From a70763dd99846e9ba31ebb5ba6c962db1f9a4d0a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 22 May 2023 14:10:58 +0200 Subject: [PATCH 7476/9987] fix dependency of Braindecode v0.7 on PyTorch --- ...=> Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb} | 2 +- ...h-1.10.2.eb => Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/b/Braindecode/{Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb => Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb} (94%) rename easybuild/easyconfigs/b/Braindecode/{Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb => Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb} (96%) diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb similarity index 94% rename from easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb rename to easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb index 6e6c6ca13e1..10e39d0b33e 100644 --- a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb @@ -2,7 +2,7 @@ easyblock = 'PythonBundle' name = 'Braindecode' version = '0.7' -versionsuffix = '-PyTorch-1.10.2-CUDA-%(cudaver)s' +versionsuffix = '-PyTorch-1.10.0-CUDA-%(cudaver)s' homepage = 'https://braindecode.org/' description = """Braindecode is an open-source Python toolbox for decoding raw diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb similarity index 96% rename from easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb rename to easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb index c503d33df9c..9780e1b0bc1 100644 --- a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.2.eb +++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb @@ -2,7 +2,7 @@ easyblock = 'PythonBundle' name = 'Braindecode' version = '0.7' -versionsuffix = '-PyTorch-1.10.2' +versionsuffix = '-PyTorch-1.10.0' homepage = 'https://braindecode.org/' description = """Braindecode is an open-source Python toolbox for decoding raw From f8e14f9ba0fae82f216cbd8860238ad496414dda Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 22 May 2023 14:11:21 +0200 Subject: [PATCH 7477/9987] adding easyconfigs: MOABB-0.4.6-foss-2021a.eb --- .../m/MOABB/MOABB-0.4.6-foss-2021a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/m/MOABB/MOABB-0.4.6-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MOABB/MOABB-0.4.6-foss-2021a.eb b/easybuild/easyconfigs/m/MOABB/MOABB-0.4.6-foss-2021a.eb new file mode 100644 index 00000000000..dffd885177d --- /dev/null +++ b/easybuild/easyconfigs/m/MOABB/MOABB-0.4.6-foss-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'MOABB' +version = '0.4.6' + +homepage = 'https://neurotechx.github.io/moabb/' +description = """Build a comprehensive benchmark of popular Brain-Computer Interface (BCI) +algorithms applied on an extensive list of freely available EEG datasets.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('MNE-Python', '0.24.1'), + ('h5py', '3.2.1'), + ('scikit-learn', '0.24.2'), + ('matplotlib', '3.4.2'), + ('Seaborn', '0.11.2'), + ('PyYAML', '5.4.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +# relax requirements of unmatchable dependencies (requirements seem quite arbitrary) +_relax_req = ';'.join(['s/^%s.*/%s = "*"/' % (d, d) for d in ['scikit-learn', 'tqdm']]) + +exts_list = [ + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + ('coverage', '5.5', { + 'checksums': ['ebe78fe9a0e874362175b02371bdfbee64d8edc42a044253ddf4ee7d3c15212c'], + }), + ('pyriemann', '0.2.7', { + 'checksums': ['1feed8f72d94414bdc9ca4485333711a3f91f9742ae8794874a7399f4166758a'], + }), + ('moabb', version, { + 'preinstallopts': "sed -i '%s' pyproject.toml &&" % _relax_req, + 'checksums': ['4278be10aa721ba3ced0b03037901cccfeaeca6d04f7a157f1cf42f60395757d'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 8357b48c2f784b23a7b4d414c648d78ec83f5edf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 22 May 2023 14:21:10 +0200 Subject: [PATCH 7478/9987] add exisiting author contributions to mstore --- easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb index 8ddbf0c4fc0..a8015f4cc5f 100644 --- a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb @@ -1,3 +1,5 @@ +# J. Sassmannshausen (Imperial College London/UK) + easyblock = 'CMakeMake' name = 'mstore' From a44e30ce8513cf5ff02978fb426c5f970c16ac73 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 22 May 2023 14:22:48 +0200 Subject: [PATCH 7479/9987] explain runtest command in Simple-DFTD3-0.7.0-foss-2022a.eb --- .../easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb index 4d92d2d0cde..f2575df8691 100644 --- a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb +++ b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb @@ -34,6 +34,7 @@ build_shared_libs = True configopts = '-DWITH_BLAS=1 -DWITH_OpenMP=1' +# run suite of tests with ctest test_cmd = 'ctest' runtest = '' From 845b7e951a8011a7d8950b42173869275dc6a639 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 22 May 2023 14:58:46 +0200 Subject: [PATCH 7480/9987] adding easyconfigs: skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb --- ...0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb new file mode 100644 index 00000000000..6e5bfbf74c3 --- /dev/null +++ b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'skorch' +version = '0.11.0' +local_pt_version = '1.10.0' +versionsuffix = '-PyTorch-%s-CUDA-%%(cudaver)s' % local_pt_version + +homepage = 'https://skorch.readthedocs.io/' +description = "A scikit-learn compatible neural network library that wraps PyTorch." + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b35cb4e50045742f0ffcfad33044af691d5d36b50212573753a804483a947ca9'] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-learn', '0.24.2'), + ('tqdm', '4.61.2'), + ('PyTorch', local_pt_version, '-CUDA-%(cudaver)s'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From cff99850291fdbe4acb114364b3835209dbffe72 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 15 May 2023 17:25:26 +0200 Subject: [PATCH 7481/9987] fix test_quantization in PyTorch 1.12.1 --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 3 +++ .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 3 +++ .../PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb | 3 +++ .../p/PyTorch/PyTorch-1.12.1-foss-2021b.eb | 3 +++ .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 3 +++ .../p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 3 +++ ...ch-1.12.1_add-hypothesis-suppression.patch | 20 +++++++++++++++++++ 7 files changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_add-hypothesis-suppression.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index df2f07b6db3..855d6a9bfdd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -63,6 +64,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.11.1_skip-test_init_from_local_shards.patch '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index 550c24d748b..b8fd4fe4a0b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -23,6 +23,7 @@ patches = [ 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -59,6 +60,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb index 3ce09263594..b8bf2014778 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', @@ -68,6 +69,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.11.1_skip-test_init_from_local_shards.patch '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch 'd97cd6b0570a167ecc3e631dc4ea884d95ace285cc38aa980566f4fec2c0d089', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb index b4ca5e1483a..a6e1886d545 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb @@ -23,6 +23,7 @@ patches = [ 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -63,6 +64,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index 8cc442f469d..f7cf757ee24 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', @@ -68,6 +69,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.11.1_skip-test_init_from_local_shards.patch '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch 'd97cd6b0570a167ecc3e631dc4ea884d95ace285cc38aa980566f4fec2c0d089', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb index 3f02df492ba..2d70b6c97a8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -23,6 +23,7 @@ patches = [ 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -63,6 +64,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_add-hypothesis-suppression.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_add-hypothesis-suppression.patch new file mode 100644 index 00000000000..43a08b24044 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_add-hypothesis-suppression.patch @@ -0,0 +1,20 @@ +The @settings decorator overwrites `suppress_health_check` accidentally removing the `too_slow` filter +inherited by the profile. +Add it explicitely. +See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615#issuecomment-1504930435 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/quantization/core/test_quantized_op.py b/test/quantization/core/test_quantized_op.py +index 41e90bc6ec7..c19324cf86a 100644 +--- a/test/quantization/core/test_quantized_op.py ++++ b/test/quantization/core/test_quantized_op.py +@@ -5569,7 +5569,7 @@ class TestQNNPackOps(TestCase): + msg="QNNPACK Sigmoid failed (FBGEMM ref)!") + + """Tests the correctness of the quantized::add (qnnpack) op.""" +- @settings(suppress_health_check=(HealthCheck.filter_too_much,)) ++ @settings(suppress_health_check=(HealthCheck.filter_too_much, HealthCheck.too_slow)) + @given(A=hu.tensor(shapes=hu.array_shapes(1, 5, 1, 5), + qparams=hu.qparams(dtypes=[torch.quint8, torch.qint8])), + zero_point=st.sampled_from([0, 2, 5, 15, 127]), From 59cd469428389ab445f20098982d9420b61c3a67 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 23 May 2023 14:59:43 +0200 Subject: [PATCH 7482/9987] Avoided using the setup.sh script --- .../alleleCount-4.2.1-GCC-11.3.0.eb | 50 +++++++++++++++---- 1 file changed, 41 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb index 1365367075e..e5c8cb0195e 100644 --- a/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb @@ -5,7 +5,7 @@ # The Francis Crick Institute, London, UK ## -easyblock = 'CmdCp' +easyblock = 'ConfigureMake' name = 'alleleCount' version = '4.2.1' @@ -21,7 +21,11 @@ source_urls = ['https://github.com/cancerit/%(name)s/archive/v%(version)s'] sources = ['v%(version)s.tar.gz'] checksums = ['dbec2d47fb4fad8ead72f55c4b6e3c02b216cbed285c05617b62e9a38c32e400'] -cmds_map = [('.*', "./setup.sh . ${EBROOTPERL}/lib/perl5")] +skipsteps = ['configure'] + +buildopts = "-C c && cd perl && perl Makefile.PL INSTALL_BASE=%(installdir)s " +preinstallopts = "cd perl && " +installopts = " && cd .. && cp -a c/bin/alleleCounter %(installdir)s/bin/" # HTSlib 1.7 is built, used and removed again in the provided setup script dependencies = [ @@ -30,16 +34,44 @@ dependencies = [ ('libdeflate', '1.10'), ] -files_to_copy = [ - "bin", - "lib", - "man", - "example", - "testData" +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') +exts_default_options = { + 'buildopts': '', + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('Const::Fast', '0.014', { + 'source_tmpl': 'Const-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + 'checksums': ['f805953a08c57846a16a4d85d7b766398afaf7c36c1465fcb1dea09e5fa394db'], + }), + ('Devel::Cover', '1.40', { + 'source_tmpl': 'Devel-Cover-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PJ/PJCJ/'], + 'checksums': ['26e2f431fbcf7bff3851f352f83b84067c09ff206f40ab975cad8d2bafe711a8'], + }), + ('Pod::Coverage', '0.23', { + 'source_tmpl': 'Pod-Coverage-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], + 'checksums': ['30b7a0b0c942f44a7552c0d34e9b1f2e0ba0b67955c61e3b1589ec369074b107'], + }), + ('Pod::Parser', '1.66', { + 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + 'checksums': ['22928a7bffe61b452c05bbbb8f5216d4b9cf9fe2a849b776c25500d24d20df7c'], + }), + ('Devel::Symdump', '2.18', { + 'source_tmpl': 'Devel-Symdump-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDK/'], + 'checksums': ['826f81a107f5592a2516766ed43beb47e10cc83edc9ea48090b02a36040776c0'], + }), ] sanity_check_paths = { - 'files': ["bin/alleleCounter", "bin/alleleCounter.pl", "lib/perl5/LWP.pm"], + 'files': ["bin/alleleCounter", "bin/alleleCounter.pl"], 'dirs': ["lib/perl5"], } From d24faf90b2afe419f74ad7f16b5e2be67dea9bfb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 23 May 2023 15:42:47 +0200 Subject: [PATCH 7483/9987] {chem}[gomkl/2021a] ASE 3.22.1 --- .../a/ASE/ASE-3.22.1-gomkl-2021a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-gomkl-2021a.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gomkl-2021a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gomkl-2021a.eb new file mode 100644 index 00000000000..cefd29a8957 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gomkl-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Flask', '1.1.4'), + ('matplotlib', '3.4.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.1'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' From 9790218cd6faed35a4d03d754db7d44da8c0f66a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 23 May 2023 18:29:16 +0200 Subject: [PATCH 7484/9987] adding easyconfigs: awscli-2.11.21-GCCcore-11.3.0.eb --- .../a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..080aebf9855 --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'awscli' +version = '2.11.21' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), # required for awscrt +] + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('ruamel.yaml', '0.17.21'), +] + +use_pip = True + +exts_list = [ + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('botocore', '1.29.138', { + 'checksums': ['31edc237088c104f7a05887646bbec31d7459dd2e108fd90cbffa315902817e2'], + }), + ('s3transfer', '0.6.1', { + 'checksums': ['640bb492711f4c0c0905e1f62b6aaeb771881935ad27884852411f8e9cacbca9'], + }), + ('prompt-toolkit', '3.0.38', { + 'sources': ['prompt_toolkit-%(version)s.tar.gz'], + 'checksums': ['23ac5d50538a9a38c8bde05fecb47d0b403ecd0662857a86f886f798563d5b9b'], + }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('awscrt', '0.16.16', { + 'checksums': ['13075df2c1d7942fe22327b6483274517ee0f6ae765c4e6b6ae9ef5b4c43a827'], + # cfr. https://github.com/awslabs/aws-crt-python/tree/main#openssl-and-libcrypto-unix-only + 'preinstallopts': "export AWS_CRT_BUILD_USE_SYSTEM_LIBCRYPTO=1 && ", + }), + (name, version, { + 'source_urls': ['https://github.com/aws/aws-cli/archive/'], + 'source_tmpl': '%(version)s.tar.gz', + 'checksums': ['74b6f7b1d773eafdefbb0972ea8db68be6814d382d7406707e94a25a0e6c1ebf'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/aws'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["aws help"] + +moduleclass = 'tools' From 1d9d14e9abfb39fa653b8aac8e285fb13f3718d4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 24 May 2023 09:31:19 +0100 Subject: [PATCH 7485/9987] adding easyconfigs: pytest-cpp-2.3.0-GCCcore-11.3.0.eb, pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb --- .../pytest-cpp-2.3.0-GCCcore-11.3.0.eb | 21 +++++++++++++++++++ ...pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb | 21 +++++++++++++++++++ 2 files changed, 42 insertions(+) create mode 100755 easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb create mode 100755 easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb new file mode 100755 index 00000000000..f5d720e5b7a --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'pytest-cpp' +version = '2.3.0' + +homepage = 'http://github.com/pytest-dev/pytest-cpp' +description = """Use pytest runner to discover and execute C++ tests.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] + +use_pip = True +sanity_pip_check = True +download_dep_fail = False + +sources = [SOURCE_TAR_GZ] +checksums = ['37abfa693697940aed2e7c034698188dee3616183ad9b3f764f3b06aeb75ed4a'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb new file mode 100755 index 00000000000..af5753f1645 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'pytest-flakefinder' +version = '1.1.0' + +homepage = 'https://github.com/dropbox/pytest-flakefinder' +description = """Runs tests multiple times to expose flakiness.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] + +use_pip = True +sanity_pip_check = True +download_dep_fail = False + +sources = [SOURCE_TAR_GZ] +checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e'] + +moduleclass = 'tools' From bbe7cdff7b5266c36303b17cab854110eaf97c33 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 May 2023 13:25:00 +0200 Subject: [PATCH 7486/9987] fix download of R-transport by adding archive source URL --- .../r/R-transport/R-transport-0.13-0-foss-2021b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb b/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb index a025135e559..fbc8b3c32f9 100644 --- a/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb @@ -9,7 +9,10 @@ description = "transport: Computation of Optimal Transport Plans and Wasserstein toolchain = {'name': 'foss', 'version': '2021b'} -source_urls = ['https://cran.r-project.org/src/contrib/'] +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/transport/', + 'https://cran.r-project.org/src/contrib/', +] sources = ['%s_%%(version)s.tar.gz' % local_rpkg] checksums = ['c55efbdd93e36e92ef39e4b9529ee64c3c7ecb965d77ec9c469a7c56c93f5f57'] From 2878c4273d73b9c6ce0702ea3c0593b68c8473f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 May 2023 17:51:21 +0200 Subject: [PATCH 7487/9987] add binutils build dependency in Evcxr-REPL easyconfig --- .../Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb b/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb index b3535b944b2..90325d9c67c 100644 --- a/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb +++ b/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb @@ -442,6 +442,10 @@ checksums = [ {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'}, ] +builddependencies = [ + ('binutils', '2.39'), +] + dependencies = [ ('Rust', local_rustver), ] From 7bfaeaa8d48294bfc98cbf4245329ca50b80b9fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 May 2023 18:06:58 +0200 Subject: [PATCH 7488/9987] don't require custom sanity_check_paths when using CargoPythonPackage, since it inherits a decent sanity_check_paths from PythonPackage --- test/easyconfigs/easyconfigs.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 40c597ba675..4e9b5508fd7 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1124,10 +1124,10 @@ def test_pr_sanity_check_paths(self): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # some generic easyblocks already have a decent customised sanity_check_paths, - # including CMakePythonPackage, GoPackage, JuliaBundle, PythonBundle & PythonPackage; + # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle, PythonBundle & PythonPackage; # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. - whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'ModuleRC', - 'PythonBundle', 'PythonPackage', 'Toolchain'] + whitelist = ['BuildEnv', 'CargoPythonPackage', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', + 'JuliaBundle', 'ModuleRC', 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co, From c62d883883267d0cb25fda5feb1abfd8883c8c76 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 24 May 2023 18:07:40 +0200 Subject: [PATCH 7489/9987] adding easyconfigs: Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb --- .../Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 1885 +++++++++++++++++ 1 file changed, 1885 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..222b05dded1 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -0,0 +1,1885 @@ +easyblock = 'Bundle' + +name = 'Perl-bundle-CPAN' +version = '5.36.1' + +homepage = 'https://www.perl.org/' +description = """A set of common packages from CPAN""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('groff', '1.22.4'), +] + +dependencies = [ + ('Perl', version), + ('zlib', '1.2.13'), # for Net::SSLeay + ('expat', '2.5.0'), # for XML::Parser + ('ncurses', '6.4'), # for Term::ReadLine::Gnu + ('libreadline', '8.2'), # for Term::ReadLine::Gnu + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +# !! order of extensions is important !! +# extensions updated on 2023-05-23 +exts_list = [ + ('Config::General', '2.65', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['4d6d5754be3a9f30906836f0cc10e554c8832e14e7a1341efb15b05d706fc58f'], + }), + ('File::Listing', '6.15', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['46c4fb9f9eb9635805e26b7ea55b54455e47302758a10ed2a0b92f392713770c'], + }), + ('ExtUtils::InstallPaths', '0.012', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], + }), + ('Test::Harness', '3.44', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['7eb591ea6b499ece6745ff3e80e60cee669f0037f9ccbc4e4511425f593e5297'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], + }), + ('Module::Build::Tiny', '0.045', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['d20692eee246d0b329b7f7659f36286b14ae0696fe91078a64b7078f8876d300'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Test::Fatal', '0.017', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['37dfffdafb84b762efe96b02fb2aa41f37026c73e6b83590db76229697f3c4a6'], + }), + ('Test::Warnings', '0.031', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['1e542909fef305e45563e9878ea1c3b0c7cef1b28bb7ae07eba2e1efabec477b'], + }), + ('File::ShareDir', '1.118', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], + }), + ('File::ShareDir::Install', '0.14', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'], + }), + ('IPC::System::Simple', '1.30', { + 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], + }), + ('Importer', '0.026', { + 'source_tmpl': 'Importer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], + }), + ('Term::Table', '0.016', { + 'source_tmpl': 'Term-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], + }), + ('Scope::Guard', '0.21', { + 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], + 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], + }), + ('Sub::Info', '0.002', { + 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], + }), + ('Test2::Require::Module', '0.000155', { + 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['c78e6bc4d69bc097836976863382b52b9e0c31ee185066ce60c54bd74baad53d'], + }), + ('Test2::Plugin::NoWarnings', '0.09', { + 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], + }), + ('Class::Tiny', '1.008', { + 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], + }), + ('Test::File::ShareDir::Dist', '1.001002', { + 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], + }), + ('DateTime::Locale', '1.38', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['dd7f6d358279d1df0ea7d78b9127690435246cdf46867500e9888016f9d4c867'], + }), + ('DateTime::TimeZone', '2.60', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['f0460d379323905b579bed44e141237a337dc25dd26b6ab0c60ac2b80629323d'], + }), + ('Test::Requires', '0.11', { + 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + 'checksums': ['4b88de549597eecddf7c3c38a4d0204a16f59ad804577b671896ac04e24e040f'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], + }), + ('Module::Build', '0.4234', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['66aeac6127418be5e471ead3744648c766bd01482825c5b66652675f2bc86a8f'], + }), + ('Module::Runtime', '0.016', { + 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + 'checksums': ['68302ec646833547d410be28e09676db75006f4aa58a11f3bdb44ffe99f0f024'], + }), + ('Try::Tiny', '0.31', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['3300d31d8a4075b26d8f46ce864a1d913e0e8467ceeba6655d5d2b2e206c11be'], + }), + ('Params::Validate', '1.31', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['1bf2518ef2c4869f91590e219f545c8ef12ed53cf313e0eb5704adf7f1b2961e'], + }), + ('List::MoreUtils', '0.430', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['63b1f7842cd42d9b538d1e34e0330de5ff1559e4c2737342506418276f646527'], + }), + ('Exporter::Tiny', '1.006002', { + 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': ['6f295e2cbffb1dbc15bdb9dadc341671c1e0cd2bdf2d312b17526273c322638d'], + }), + ('Class::Singleton', '1.6', { + 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['27ba13f0d9512929166bbd8c9ef95d90d630fc80f0c9a1b7458891055e9282a4'], + }), + ('CPAN::Meta::Check', '0.017', { + 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['0454ab93f12780b1d579df15b5f939e09702e954be82028fadd40e8bc9b0f091'], + }), + ('Test::Without::Module', '0.21', { + 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['3cdeafadac4853ebeafe689346d555da5dfa3cfa9d4c84e3e5e7bfee50beec46'], + }), + ('DateTime', '1.59', { + 'source_tmpl': 'DateTime-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['de3e9a63ce15470b4db4adad4ba6ac8ec297d88c0c6c6b354b081883b0a67695'], + }), + ('File::Find::Rule::Perl', '1.16', { + 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ae1886050d9ca21223c073e2870abdc80dc30e3f55289a11c37da3820a8321ff'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + 'checksums': ['4b23542491af010d44a5c7c861244738acc74ababae6b8838d354dfb19462b5e'], + }), + ('Git', '0.42', { + 'source_tmpl': 'Git-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + 'checksums': ['9469a9f398f3a2bf2b0500566ee41d3ff6fae460412a137185767a1cc4783a6d'], + }), + ('Tree::DAG_Node', '1.32', { + 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['22d9de3d6e6f4afd89e6d825c664f9482878bd49e29cb81342a707af40542d3d'], + }), + ('Template', '3.101', { + 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': ['d2a32dd6c21e4b37c6a93df8087ca9e880cfae613a3e5efaea307b0bdcaedb58'], + }), + ('DBI', '1.643', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'], + }), + ('DBD::SQLite', '1.72', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['5ca41e61eb52b52bd862a3088b912a75fe70910ac789b9a9983e0a449e94f551'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': ['11a815fc45fdf0efabb1822ab77faad8b9eea162572c5f0940c8ed7d56e6b8b8'], + }), + ('Archive::Extract', '0.88', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['cffcf135cd0622287d3b02154f7d6716495449fcaed03966621948e25ea5f742'], + }), + ('DBIx::Simple', '1.37', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + 'checksums': ['46d311aa2ce08907401c56119658426dbb044c5a40de73d9a7b79bf50390cae3'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + 'checksums': ['f7dbebf65261ed0e5abd0f57052b64d665a1a830bab4c8bbc220f235bd39caf5'], + }), + ('Test::Simple', '1.302195', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['b390bb23592e0b946c95adbb3c30b11bc634a286b2847be611ad929c57e39a6c'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + 'checksums': ['a3dc1526f3dde72d3c64ea00007b86ce608cdcd93567cf6e6e42dc10fdc4511d'], + }), + ('IO::Stringy', '2.113', { + 'source_tmpl': 'IO-Stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['51220fcaf9f66a639b69d251d7b0757bf4202f4f9debd45bdd341a6aca62fe4e'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1'], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0'], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': ['47e995859f8dd0413aa3f22d350c4a62da652e854267aa0586ae544ae2bae5ef'], + }), + ('XML::SAX', '1.02', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['4506c387043aa6a77b455f00f57409f3720aa7e553495ab2535263b4ed1ea12a'], + }), + ('Test::LeakTrace', '0.17', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': ['777d64d2938f5ea586300eef97ef03eacb43d4c1853c9c3b1091eb3311467970'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['156b13f07764f766d8b45a43728f2439af81a3512625438deab783b7883eb533'], + }), + ('Text::Aligner', '0.16', { + 'source_tmpl': 'Text-Aligner-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['5c857dbce586f57fa3d7c4ebd320023ab3b2963b2049428ae01bd3bc4f215725'], + }), + ('Text::Table', '1.135', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['fca3c16e83127f7c44dde3d3f7e3c73ea50d109a1054445de8082fea794ca5d2'], + }), + ('MIME::Types', '2.24', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['629e361f22b220be50c2da7354e23c0451757709a03c25a22f3160edb94cb65f'], + }), + ('File::Copy::Recursive', '0.45', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['d3971cf78a8345e38042b208bb7b39cb695080386af629f4a04ffd6549df1157'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + 'checksums': ['7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77'], + }), + ('Capture::Tiny', '0.48', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['6c23113e87bad393308c90a207013e505f659274736638d8c79bac9c67cc3e19'], + }), + ('File::Copy::Recursive::Reduced', '0.006', { + 'source_tmpl': 'File-Copy-Recursive-Reduced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['e618f993a69f4355205c58fffff6982609f28b47f646ec6e244e41b5c6707e2c'], + }), + ('Module::Build::XSUtil', '0.19', { + 'source_tmpl': 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['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'], + 'checksums': ['1bb7a6e0c0d251f23d6e60bf84c9adefc5b74eec58475bfee4d39107e60870f0'], + }), + ('Unicode::LineBreak', '2019.001', { + 'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'], + 'checksums': ['486762e4cacddcc77b13989f979a029f84630b8175e7fef17989e157d4b6318a'], + }), + ('String::Print', '0.94', { + 'source_tmpl': 'String-Print-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'], + }), + ('Log::Report', '1.34', { + 'source_tmpl': 'Log-Report-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['1faeb18993ab8796dce4cccda2ec912f8f565aa0258026f88197aa0fe3004a78'], + }), + ('Log::Report::Optional', '1.07', { + 'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], + }), + ('Sys::Info::Driver::Unknown', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Sys::Info::Driver::Linux', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), + ('Devel::Size', '0.83', { + 'source_tmpl': 'Devel-Size-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['757a67e0aa59ae103ea5ca092cbecc025644ebdc326731688ffab6f8823ef4b3'], + }), + ('Math::Utils', '1.14', { + 'source_tmpl': 'Math-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE'], + 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], + }), +] + +moduleclass = 'lang' From 149da1af9a004118262147075f9b6db3d8211948 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 May 2023 09:05:42 +0200 Subject: [PATCH 7490/9987] adding easyconfigs: mpifileutils-0.11.1-gompi-2022a.eb --- .../a/attr/attr-2.5.1-GCCcore-11.3.0.eb | 26 +++++++++++++ .../d/dtcmp/dtcmp-1.1.4-gompi-2022a.eb | 39 +++++++++++++++++++ .../l/libcircle/libcircle-0.3-gompi-2022a.eb | 38 ++++++++++++++++++ .../l/lwgrp/lwgrp-1.0.5-gompi-2022a.eb | 36 +++++++++++++++++ .../mpifileutils-0.11.1-gompi-2022a.eb | 37 ++++++++++++++++++ 5 files changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.4-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.5-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ca867bfaae6 --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.5.1' + +homepage = 'https://savannah.nongnu.org/projects/attr' + +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['bae1c6949b258a0d68001367ce0c741cebdacdd3b62965d17e5eb23cd78adaf8'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', + 'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h', + 'include/%(name)s/libattr.h', 'lib/libattr.a', + 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.4-gompi-2022a.eb b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.4-gompi-2022a.eb new file mode 100644 index 00000000000..2d17d7a2344 --- /dev/null +++ b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.4-gompi-2022a.eb @@ -0,0 +1,39 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'dtcmp' +version = '1.1.4' + +homepage = 'https://github.com/LLNL/dtcmp' +description = """The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined +comparison operations to compare the values of two items which can be arbitrary MPI datatypes. +Using these comparison operations, the library provides various routines for manipulating data, +which may be distributed over the processes of an MPI communicator.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5015b7b330b35e1871a6b5e53cf7045cfb0a29e61f9a678d1919f3bf14a85437'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('lwgrp', '1.0.5'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-lwgrp=$EBROOTLWGRP' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT, 'share/%(name)s/README.md'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2022a.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2022a.eb new file mode 100644 index 00000000000..0b622840791 --- /dev/null +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2022a.eb @@ -0,0 +1,38 @@ +## +# Authors: +# * Petar Forai +# * Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'libcircle' +version = '0.3' + +homepage = 'https://github.com/hpc/libcircle/' + +description = """ + An API to provide an efficient distributed queue on a cluster. libcircle is an + API for distributing embarrassingly parallel workloads using self-stabilization. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.5-gompi-2022a.eb b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.5-gompi-2022a.eb new file mode 100644 index 00000000000..c288e0a47a1 --- /dev/null +++ b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.5-gompi-2022a.eb @@ -0,0 +1,36 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'lwgrp' +version = '1.0.5' + +homepage = 'https://github.com/LLNL/lwgrp' +description = """The light-weight group library defines data structures and collective operations to +group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators +when the overhead of communicator creation is too costly. For example, certain sorting algorithms +recursively divide processes into subgroups as the sort algorithm progresses. These groups may be +different with each invocation, so that it is inefficient to create and destroy communicators during +the sort routine.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['1fac5fad3aed9f0a83026c19f438a33f9807d69990284e452b646b44a95fe72b'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['share/%(name)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2022a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2022a.eb new file mode 100644 index 00000000000..417593512aa --- /dev/null +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'mpifileutils' +version = "0.11.1" + +homepage = 'https://hpc.github.io/mpifileutils/' + +description = """ + MPI-Based File Utilities For Distributed Systems +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e2cba53309b5b3ee581b6ff82e4e66f54628370cce694c34224ed947fece32d4'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('attr', '2.5.1'), + ('bzip2', '1.0.8'), + ('lwgrp', '1.0.5'), + ('dtcmp', '1.1.4'), + ('libarchive', '3.6.1'), + ('libcircle', '0.3'), +] + +sanity_check_paths = { + 'files': ['bin/dsync', 'include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'tools' From 582b95580d3155a3e4b68100b1cf78d37ca7a4f5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 May 2023 10:30:35 +0200 Subject: [PATCH 7491/9987] add --disable-sphinx for LibTIFF 4.5.0 to avoid trouble when Sphinx is available in OS + enhance sanity check --- .../easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb index 706cc20c7dc..9d9e6c1971c 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb @@ -25,11 +25,14 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += '--disable-webp' +configopts += "--disable-webp --disable-sphinx " sanity_check_paths = { - 'files': ['bin/tiffinfo'], + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], 'dirs': [], } +sanity_check_commands = ["tiffinfo -h"] + moduleclass = 'lib' From 1f657304a5d87f45868a06df6b5f0a05b2c05552 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 May 2023 11:21:06 +0200 Subject: [PATCH 7492/9987] enhance sanity check for recent LibTIFF easyconfigs --- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 7 +++++-- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb | 7 +++++-- .../easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb | 7 +++++-- .../easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb | 7 +++++-- .../easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb | 7 +++++-- .../easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.3.0.eb | 7 +++++-- .../easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb | 7 +++++-- 7 files changed, 35 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb index c2e41230be6..30ebb82f4de 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -37,11 +37,14 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += '--disable-webp --disable-libdeflate ' +configopts += "--disable-webp --disable-libdeflate " sanity_check_paths = { - 'files': ['bin/tiffinfo'], + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], 'dirs': [], } +sanity_check_commands = ["tiffinfo -h"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb index 43672697339..e87e43c6521 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb @@ -37,11 +37,14 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += '--disable-webp --disable-libdeflate ' +configopts += "--disable-webp --disable-libdeflate " sanity_check_paths = { - 'files': ['bin/tiffinfo'], + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], 'dirs': [], } +sanity_check_commands = ["tiffinfo -h"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb index 69ec3684019..a7672a0b44e 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb @@ -37,11 +37,14 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += '--disable-webp --disable-libdeflate ' +configopts += "--disable-webp --disable-libdeflate " sanity_check_paths = { - 'files': ['bin/tiffinfo'], + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], 'dirs': [], } +sanity_check_commands = ["tiffinfo -h"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb index bf4e3e54c68..06ba435fef8 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.2.0-GCCcore-10.3.0.eb @@ -26,11 +26,14 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += '--disable-webp --disable-libdeflate ' +configopts += "--disable-webp --disable-libdeflate " sanity_check_paths = { - 'files': ['bin/tiffinfo'], + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], 'dirs': [], } +sanity_check_commands = ["tiffinfo -h"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb index 7d9585aa7b5..aff028c58ab 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.2.0.eb @@ -26,11 +26,14 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += '--disable-webp --disable-libdeflate ' +configopts += "--disable-webp --disable-libdeflate " sanity_check_paths = { - 'files': ['bin/tiffinfo'], + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], 'dirs': [], } +sanity_check_commands = ["tiffinfo -h"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.3.0.eb index a35ee9ee659..7e67eb521f7 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.3.0-GCCcore-11.3.0.eb @@ -27,11 +27,14 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += '--disable-webp' +configopts += "--disable-webp " sanity_check_paths = { - 'files': ['bin/tiffinfo'], + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], 'dirs': [], } +sanity_check_commands = ["tiffinfo -h"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb index b2fb13f5ec3..d9ac3eaca8f 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb @@ -25,11 +25,14 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += '--disable-webp' +configopts += "--disable-webp " sanity_check_paths = { - 'files': ['bin/tiffinfo'], + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], 'dirs': [], } +sanity_check_commands = ["tiffinfo -h"] + moduleclass = 'lib' From b427b48f53c51b16c13034bafb112adaa51f9ad1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 25 May 2023 16:36:36 +0200 Subject: [PATCH 7493/9987] set user depot ~/.julia as top entry in JULIA_DEPOT_PATH --- .../easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb | 11 ++++++----- .../easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb | 11 ++++++----- .../easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb | 11 ++++++----- .../easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb | 11 ++++++----- .../easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb | 11 ++++++----- .../easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb | 11 ++++++----- .../easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb | 11 ++++++----- .../easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb | 11 ++++++----- .../easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb | 11 ++++++----- .../easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb | 11 ++++++----- 10 files changed, 60 insertions(+), 50 deletions(-) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb index 2d06511dc08..b3c98820f76 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb @@ -29,16 +29,17 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] _depot_paths = ':'.join([ - # default shared directory in install dir - '%(installdir)s/share/julia', - # allow users to add their own packages to Julia + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', ]) modextravars = { 'JULIA_DEPOT_PATH': _depot_paths, - # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) - # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', } diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb index aed8623dde7..f6493a94ce4 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb @@ -29,16 +29,17 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] _depot_paths = ':'.join([ - # default shared directory in install dir - '%(installdir)s/share/julia', - # allow users to add their own packages to Julia + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', ]) modextravars = { 'JULIA_DEPOT_PATH': _depot_paths, - # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) - # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', } diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb index 3101c0d69fb..9bbe7e50e31 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb @@ -29,16 +29,17 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] _depot_paths = ':'.join([ - # default shared directory in install dir - '%(installdir)s/share/julia', - # allow users to add their own packages to Julia + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', ]) modextravars = { 'JULIA_DEPOT_PATH': _depot_paths, - # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) - # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', } diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb index 8d0d71e88c9..7c1e51bc5cd 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb @@ -29,16 +29,17 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] _depot_paths = ':'.join([ - # default shared directory in install dir - '%(installdir)s/share/julia', - # allow users to add their own packages to Julia + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', ]) modextravars = { 'JULIA_DEPOT_PATH': _depot_paths, - # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) - # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', } diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb index acf27d328de..5fc2b605f10 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb @@ -29,16 +29,17 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] _depot_paths = ':'.join([ - # default shared directory in install dir - '%(installdir)s/share/julia', - # allow users to add their own packages to Julia + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', ]) modextravars = { 'JULIA_DEPOT_PATH': _depot_paths, - # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) - # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', } diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb index 6ba496e97b2..a7da9095153 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb @@ -29,16 +29,17 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] _depot_paths = ':'.join([ - # default shared directory in install dir - '%(installdir)s/share/julia', - # allow users to add their own packages to Julia + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', ]) modextravars = { 'JULIA_DEPOT_PATH': _depot_paths, - # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) - # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', } diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb index 9f61082c329..5e0aa491de1 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb @@ -29,16 +29,17 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] _depot_paths = ':'.join([ - # default shared directory in install dir - '%(installdir)s/share/julia', - # allow users to add their own packages to Julia + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', ]) modextravars = { 'JULIA_DEPOT_PATH': _depot_paths, - # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) - # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', } diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb index 149083b00cc..9876377c1b3 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb @@ -29,16 +29,17 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] _depot_paths = ':'.join([ - # default shared directory in install dir - '%(installdir)s/share/julia', - # allow users to add their own packages to Julia + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', ]) modextravars = { 'JULIA_DEPOT_PATH': _depot_paths, - # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) - # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', } diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb index 152b7ec1d72..c09419b4f04 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb @@ -29,16 +29,17 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] _depot_paths = ':'.join([ - # default shared directory in install dir - '%(installdir)s/share/julia', - # allow users to add their own packages to Julia + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', ]) modextravars = { 'JULIA_DEPOT_PATH': _depot_paths, - # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) - # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', } diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb index f0b02f1ec3c..3ef9341cc06 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb @@ -29,16 +29,17 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] _depot_paths = ':'.join([ - # default shared directory in install dir - '%(installdir)s/share/julia', - # allow users to add their own packages to Julia + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', ]) modextravars = { 'JULIA_DEPOT_PATH': _depot_paths, - # 'set JULIA_HISTORY to user's DEPOT_PATH (~/.julia) - # by default it will point to the DEPOT_PATH (install dir) of the last module loaded + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', } From 141408ffd04031629301c8be22c0e801c26ed345 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 25 May 2023 16:51:43 +0200 Subject: [PATCH 7494/9987] adding easyconfigs: Julia-1.9.0-linux-x86_64.eb --- .../j/Julia/Julia-1.9.0-linux-x86_64.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb new file mode 100644 index 00000000000..cd119189826 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.9.0' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['00c614466ef9809c2eb23480e38d196a2c577fff2730c4f83d135b913d473359'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +_depot_paths = ':'.join([ + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ + '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + +moduleclass = 'lang' From a3935c7f557e8ab08558e5f5e7666c36469089e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 May 2023 21:36:02 +0200 Subject: [PATCH 7495/9987] adding easyconfigs: PyWBGT-1.0.0-foss-2022a.eb --- .../p/PyWBGT/PyWBGT-1.0.0-foss-2022a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2022a.eb new file mode 100644 index 00000000000..ded9345b19e --- /dev/null +++ b/easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'PyWBGT' +version = '1.0.0' + +homepage = 'https://github.com/QINQINKONG/PyWBGT' +description = """Cython source code for estimating wet bulb globe temperature (WBGT) from datasets of standard +meterological measurements using models developed by Liljegren et al (2008)""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('xarray', '2022.9.0'), +] + +use_pip = True + +# strip out extra compiler flags -qopenmp and -Ofast, which cause trouble (GCC doesn't know about -qopenmp) +local_common_preinstallopts = r"""sed -i "s/'-qopenmp'//g" setup.py && sed -i "s/,'-Ofast'//g" setup.py && """ + +# inject correct version into setup.py to avoid 0.0.0 version in installation +local_common_preinstallopts += r"""sed -i "s/name=/version='%(version)s', name=/g" setup.py && """ + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + ('WBGT', version, { + 'source_urls': ['https://github.com/QINQINKONG/PyWBGT/archive/'], + 'sources': [{ + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'PyWBGT-%(version)s.tar.gz', + }], + 'checksums': ['476d18a65a1bce9bdd1e82076ecdbdeda199fd2fe3a2fbe0cc013d11d7b1b6e8'], + 'start_dir': 'src', + 'preinstallopts': "rm *.so && ln -s setupWBGT.py setup.py && " + local_common_preinstallopts, + 'modulename': 'WBGT', + }), + ('coszenith', version, { + 'source_urls': ['https://github.com/QINQINKONG/PyWBGT/archive/'], + 'sources': [{ + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'PyWBGT-%(version)s.tar.gz', + }], + 'checksums': ['476d18a65a1bce9bdd1e82076ecdbdeda199fd2fe3a2fbe0cc013d11d7b1b6e8'], + 'start_dir': 'src', + 'preinstallopts': "rm *.so && ln -s setupcoszenith.py setup.py && " + local_common_preinstallopts, + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From a9a410b87498881fe786966793104f4a9efd3c4f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 May 2023 21:57:27 +0200 Subject: [PATCH 7496/9987] stick to xarray 2022.6.0 as dependency for PyWBGT --- easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2022a.eb index ded9345b19e..112c19e53fa 100644 --- a/easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2022a.eb @@ -13,7 +13,7 @@ toolchainopts = {'openmp': True} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('xarray', '2022.9.0'), + ('xarray', '2022.6.0'), ] use_pip = True From 50c253af6ebc0e13f37b86871bd1cdcd3d47d96a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 May 2023 22:46:30 +0200 Subject: [PATCH 7497/9987] adding easyconfigs: PyWBGT-1.0.0-foss-2021b.eb --- .../p/PyWBGT/PyWBGT-1.0.0-foss-2021b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2021b.eb b/easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2021b.eb new file mode 100644 index 00000000000..c4f7abef078 --- /dev/null +++ b/easybuild/easyconfigs/p/PyWBGT/PyWBGT-1.0.0-foss-2021b.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'PyWBGT' +version = '1.0.0' + +homepage = 'https://github.com/QINQINKONG/PyWBGT' +description = """Cython source code for estimating wet bulb globe temperature (WBGT) from datasets of standard +meterological measurements using models developed by Liljegren et al (2008)""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('xarray', '0.20.1'), +] + +use_pip = True + +# strip out extra compiler flags -qopenmp and -Ofast, which cause trouble (GCC doesn't know about -qopenmp) +local_common_preinstallopts = r"""sed -i "s/'-qopenmp'//g" setup.py && sed -i "s/,'-Ofast'//g" setup.py && """ + +# inject correct version into setup.py to avoid 0.0.0 version in installation +local_common_preinstallopts += r"""sed -i "s/name=/version='%(version)s', name=/g" setup.py && """ + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + ('WBGT', version, { + 'source_urls': ['https://github.com/QINQINKONG/PyWBGT/archive/'], + 'sources': [{ + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'PyWBGT-%(version)s.tar.gz', + }], + 'checksums': ['476d18a65a1bce9bdd1e82076ecdbdeda199fd2fe3a2fbe0cc013d11d7b1b6e8'], + 'start_dir': 'src', + 'preinstallopts': "rm *.so && ln -s setupWBGT.py setup.py && " + local_common_preinstallopts, + 'modulename': 'WBGT', + }), + ('coszenith', version, { + 'source_urls': ['https://github.com/QINQINKONG/PyWBGT/archive/'], + 'sources': [{ + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'PyWBGT-%(version)s.tar.gz', + }], + 'checksums': ['476d18a65a1bce9bdd1e82076ecdbdeda199fd2fe3a2fbe0cc013d11d7b1b6e8'], + 'start_dir': 'src', + 'preinstallopts': "rm *.so && ln -s setupcoszenith.py setup.py && " + local_common_preinstallopts, + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 3350dea24b7475976ffbd795daaa81b7771cb0c6 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 26 May 2023 12:01:02 +0200 Subject: [PATCH 7498/9987] update JupyterLab v3.5.0 to set JUPYTERLAB_SETTINGS_DIR and JUPYTERLAB_WORKSPACES_DIR on module load --- .../j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb index 1ce74b3d8a8..45e53c31094 100644 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb @@ -53,4 +53,9 @@ modextravars = { 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', } +modluafooter = """ +setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) +setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) +""" + moduleclass = 'tools' From 92ffc4492e83bc8afb88c25f3dd06b90ff82dfc7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 26 May 2023 13:34:42 +0200 Subject: [PATCH 7499/9987] add comment about modluafooter settings in JupyterLab 3.5.0 --- .../easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb index 45e53c31094..1e72adbb6f5 100644 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb @@ -53,6 +53,7 @@ modextravars = { 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', } +# allow users to keep their own configuration for the lab modluafooter = """ setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) From 291deba625e76de62d778248e9076b73f23a131e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 27 May 2023 11:18:58 +0200 Subject: [PATCH 7500/9987] prepare release notes for EasyBuild v4.7.2 + bump version to 4.7.2 --- RELEASE_NOTES | 94 ++++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 94 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index f4454f0b91e..26d8721fa48 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,102 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 16,628 easyconfig files, for 2,995 different software packages, +The latest version of easybuild-easyconfig provides 17,098 easyconfig files, for 3,085 different software packages, incl. 39 different (compiler) toolchains. +v4.7.2 (27 May 2023) +-------------------- + +update/bugfix release + +- added easyconfigs for intel/2023.03 (#17676) +- added example easyconfig files for 89 new software packages: + - AGeNT (#17864), anndata (#17677), Annocript (#17910), avro-cpp (#17527), batchgenerators (#17833), + BoltzTraP2 (#17742), Braindecode (#17913), build (#17776), casacore (#15499), Casanovo (#17735, #17736), + CASPR (#17606), CellChat (#17856), CellOracle (#17507), CLIP (#17782), CodingQuarry (#17682), ColabFold (#17751), + CopyKAT (#17646), CPC2 (#17849), cppzmq (#17601), dask-labextension (#17882), DIALOGUE (#17696), DiCE-ML (#17591), + ESPResSo (#17709), Evcxr-REPL (#17831), EZC3D (#17832), funannotate (#17588), FunGAP (#17652), GATB-Core (#17635), + GenMap (#17746), GimmeMotifs (#17507), GLI (#17793), GOBNILP (#17639), h5netcdf (#17835), HD-BET (#17833), + HTSplotter (#17369, #17586), ipympl (#17613), IsoSeq (#17791), KrakenUniq (#17569), LIANA (#17928), + libWallModelledLES (#17480), LoRDEC (#17635), M3GNet (#17555), mandrake (#17394), mctc-lib (#16760), MOABB (#17913), + MRPRESSO (#17925), ont-guppy (#17477, #17828), OptaDOS (#17777), PALEOMIX (#17912), PGPLOT (#15496), + PICI-LIGGGHTS (#17710), pod5-file-format (#17776), powerlaw (#17647), pp-sketchlib (#17397), + py3Dmol (#17752), pytesseract (#17898), pytest-cpp (#17966), pytest-flakefinder (#17966), Python-bundle (#17626), + python-xxhash (#17844), PyTorch-bundle (#17540), qnorm (#17507), R-MXM (#17667), R-transport (#17642, #17968), + Raven (#15833), ReaxFF (#17780), ripunzip (#17959), RPostgreSQL (#17739), rustworkx (#17857), Scalene (#16472), + sceasy (#17677), SCIP (#17639), Simple-DFTD3 (#16760), SMAP (#17672), SoPlex (#17639), SoupX (#17851), + spektral (#15551), synthcity (#17623), sysbench (#17643), tantan (#17681), thirdorder (#17703), TOPAS (#17553), + Triplexator (#17866), tRNAscan-SE (#17680, #17800), turbinesFoam (#17917), unicore-uftp (#17665), vispr (#17606), + WCSLIB (#15497), ZIMPL (#17639) +- added additional easyconfigs for various supported software packages, including: + - Abseil v20230125.2, AlphaFold v2.3.1 + v2.3.4, Arrow v11.0.0, arrow-R v11.0.0.3, astropy v5.2.2, awscli v2.11.21, + Bismark v0.24.0, biom-format v2.1.14, Blender v3.5.0, Blosc2 v2.8.0, Bottleneck v1.3.7, breseq v0.38.1, + bwa-meth v0.2.6, buildenv default for foss/2022b + CUDA 12.0.0, Cantera v2.6.0, CapnProto v0.10.3, CASTEP v22.11, + Clang v15.0.5, CLHEP v2.4.6.4, CMake v3.26.3, CMSeq v1.0.4, coverage v7.2.3, CP2K v9.1 + v2022.1, CPLEX v22.1.1, + CREST v2.11.2, cURL v8.0.1, CuPy v11.4.0, DBus v1.15.4, DBG2OLC v20200724, dlb v3.3.1, double-conversion v3.3.0, + Doxygen v1.9.7, expat v2.5.0, FASTA v36.3.8i, FHI-aims v221103, fio v3.34, Fiona v1.9.2, Flask v2.2.3, fmt v10.0.0, + freeglut v3.4.0, FUSE v3.14.1, GapFiller v2.1.2, GCC 12.3.0 + 13.1.0, GDCM v3.0.21, GitPython v3.1.31, Go v1.20.4, + googletest v1.13.0, gpustat v1.1, Guile v3.0.9, Gurobi v10.0.1, Harminv v1.4.2, Highway v1.0.4, IgBlast v1.21.0, + Imath v3.1.7, infercnvpy v0.4.2, IQ-TREE v2.2.2.3, jax v0.3.25, jupyterlmod v4.0.3, Kalign v3.3.5, + L_RNA_scaffolder v20190530, libaio v0.3.113, libarchive v3.6.2, libctl v4.5.1, libdeflate v1.8, libgcrypt v1.10.1, + libGridXC v1.1.0, libjpeg-turbo v2.1.5.1, libmaus2 v2.0.499, libopus v1.4, libpng v1.6.39, libPSML v1.1.12, + libRmath v4.2.1, libsigc++ v3.4.0, LibTIFF v4.5.0, libunistring v1.1, libxc v6.1.0, libxml2 v2.11.4, + libxslt v1.1.38, lifelines v0.27.4, lxml v4.9.2, make v4.4.1, MariaDB v10.11.2, Meep v1.26.0, MetaPhlAn v4.0.6, + mold v1.11.0, MPB v1.11.1, muParser v2.3.4, NAG v7.1, NAGfor v7.1, nano v7.2, NASM v2.16.01, ncurses v6.4, + netcdf4-python v1.6.3, networkx v2.8.8, NSS v3.89.1, numexpr v2.8.4, nvtop v3.0.1, OpenEXR v3.1.7, OpenMM v8.0.0, + Pandoc v3.1.2, ParaView v5.11.0, PCRE2 v10.42, PhyloPhlAn v3.0.3, phyx v1.3, picard v3.0.0, Pint v0.20.1, + pkgconf v1.9.5, PostgreSQL v15.2, PROJ v9.2.0, Proteinortho v6.2.3, protobuf v23.0, protobuf-python v4.23.0, + pydantic v1.10.4, pyFFTW v0.13.1, PyGEOS v0.14, Pyomo v6.5.0, pyparsing v3.0.9, pyperf v2.6.0, pyproj v3.5.0, + pytest v7.2.2, PYTHIA v8.309, Qtconsole v5.4.0, R-bundle-Bioconductor v3.16, R-tesseract v5.1.0, RE2 v2023-03-01, + ReFrame v4.2.0, RepeatMasker v4.1.5, RevBayes v1.2.1, rgdal v1.6-6, rioxarray v0.14.0, rocm-smi v5.4.4, + ROOT v6.26.10, Rtree v1.0.1, scib v1.1.3, scikit-build v0.17.2, Seaborn v0.12.2, SHAP v0.41.0, Shapely v2.0.1, + ShengBTE v1.5.0, SLiM v4.0.1, snappy v1.1.10, spdlog v1.11.0, spglib v2.0.2, spglib-python v2.0.2, SQLite v3.42.0, + Subread v2.0.4, Tcl v8.6.13, tcsh v6.24.05, torchtext v0.14.1, trimesh v3.21.5, UCC-CUDA v1.1.0, utf8proc v2.8.0, + Vim v9.0.1434, vsc-mympirun v5.3.1, WRF v4.4.1, xmlf90 v1.5.6, xxHash v0.8.1, XZ v5.4.2, zsh v5.9, zstd v1.5.5 +- minor enhancements, including: + - add local::lib extension to Perl 5.34.0 (#17679) + - install shared libraries for tesseract (#17721) + - add additional extensions to recent R easyconfigs: word2vec, tau, quanteda, ... (#17738) + - add extensions to R-bundle-Bioconductor 3.15: deepSNV (#17852) + - add extensions to R 4.2.x: dlm (#17640), PMA + unikn + ppcor (#17695), tvem (#17729), epitools (#17852) +- various bug fixes, including: + - add patch for UCC 1.1.0 for multiple component paths (#17255) + - fix configure step for ELSI 2.5.0+ (#17288) + - switch bamtofastq to Cargo easyblock (#17595) + - add missing OpenJPEG dependency for recent GDAL versions (#17599) + - fix CodAn bin/* executable permissions for all users #(#17607) + - upgrade traitlets, ipywidgets, and widgetsnbextension + downgrade jupyterlab_widgets extensions in IPython v8.5.0 to fix known issues (#17612) + - add patch for GPAW-22.8.0 with 2022a toolchain to make test tolerance a bit less strict (#17618) + - add alternative checksum for MONAI 1.0.1 (#17628) + - fix paths to Perl modules in MAKER v3.01.04 (#17629) + - add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6 (#17631) + - explicitely disable mpi/python in Boost (intel-compilers/2021.4.0) (#17638) + - remove LLVM build dependency from TensorFlow easyconfigs (#17641) + - update easyconfig for Longshot 0.4.5 to use Cargo easyblock (#17666) + - fix homepage in ELPA easyconfigs (due to switch to new domain) (#17697) + - add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test (#17713) + - use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0 (#17717) + - exclude flaky test_optim for PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent (#17726, #17730, #17731, #17737) + - add missing PCRE dependency for InterProScan 5.55-88.0 (#17762) + - fix building Python bindings of DGL, requires static libs (#17764) + - only use QEF gitlab source url for QuantumESPRESSO itself (#17766) + - add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file (#17779) + - fix broken source URL for AOCC 4.0.0 (#17794) + - specify source_urls inside exts_default_options in Seurat easyconfigs to ensure correct name expansion for the archived packages (#17830) + - add Doxygen build dependency to X11 (#17842) + - FLINT needs BLAS so move it up from GCC level (#17868) + - fix broken tarball links for ispc 1.6, 1.10, and 1.12 easyconfigs (#17875) + - add dependency on PycURL to JupyterHub-3.0.0-GCCcore-11.3.0.eb (#17887) + - add historical repo paths to install cmd for old versions of texlive (#17893) + - add missing FastTreeMP binary for FastTree (#17897) + - add checksum for arm64 source tarball for Go 1.18.3 (#17903) + - add patch to fix test_quantization in PyTorch 1.12.1 (#17908) + - add make 4.3 as build dependency for recent OpenBLAS versions (#17924) +- other changes: + - bump versions in Java wrappers to latest builds that include ppc64le: Java/8.362, Java/11.0.8, Java/17.0.6 (#17775) + - move Arb and polymake to gfbf/foss since FLINT is now at gfbf/foss (#17869) + v4.7.1 (March 20th 2023) ------------------------ diff --git a/setup.py b/setup.py index 1e5caaddac1..70004ce1b12 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.7.2.dev0' +VERSION = '4.7.2' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From ba1d5cb59e5fa41f4ee058c77b62d5f095e64531 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 28 May 2023 00:40:24 +0200 Subject: [PATCH 7501/9987] adding easyconfigs: EasyBuild-4.7.2.eb --- .../e/EasyBuild/EasyBuild-4.7.2.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.2.eb new file mode 100644 index 00000000000..8153a7f1f36 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.2.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.7.2' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/07/e1/c9bb4ddce9e02dccbff5afb41a25e0d61274ba8db8def11aed4b7f4bb8aa/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/83/0c/c4953eadf14c7fd5af42873b97a02498a32cb6827213b5549ffab8730e52/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/80/86/791f7470292f1d6b26eb84e08a53ceb37c3d75e45d02ae48d8b51a3d4075/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + {'easybuild-framework-4.7.2.tar.gz': '508ed5ffbb450aa1212bd451b51b2555109b94964c6bbd2818a150eb47fb3662'}, + {'easybuild-easyblocks-4.7.2.tar.gz': '6347aac95c56a5172688db98fd2cad3e348df206dd2a9c0389adab3208046699'}, + {'easybuild-easyconfigs-4.7.2.tar.gz': 'd678c541bd1f0d3d2ccd2a203fb0eaa8f958d77c910138c3d2518f61047bc17e'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From af6cee96656e1a07da1f13f31b9c7ff79af0b1a3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 30 May 2023 13:24:10 +0200 Subject: [PATCH 7502/9987] replicate module footer for tcl in JupyterLab v3.5.0 --- .../j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb index 1e72adbb6f5..f74d9b48ea3 100644 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb @@ -53,10 +53,15 @@ modextravars = { 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', } -# allow users to keep their own configuration for the lab +# keep user's configuration in their home directory +# note: '~' is not expanded by JupyterLab modluafooter = """ setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) """ +modtclfooter = """ +setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" +setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" +""" moduleclass = 'tools' From 3e9a9e1e81e8c5dbf42c79641e51c58a2d54f630 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 30 May 2023 14:05:20 +0200 Subject: [PATCH 7503/9987] adding easyconfigs: DaliLite-4.1-gompi-2021a.eb and patches: DaliLite-4.1_fix-labels-without-statements.patch --- .../d/DaliLite/DaliLite-4.1-gompi-2021a.eb | 60 +++++++++++++++++++ ...te-4.1_fix-labels-without-statements.patch | 31 ++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/d/DaliLite/DaliLite-4.1-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/d/DaliLite/DaliLite-4.1_fix-labels-without-statements.patch diff --git a/easybuild/easyconfigs/d/DaliLite/DaliLite-4.1-gompi-2021a.eb b/easybuild/easyconfigs/d/DaliLite/DaliLite-4.1-gompi-2021a.eb new file mode 100644 index 00000000000..89757de6ef6 --- /dev/null +++ b/easybuild/easyconfigs/d/DaliLite/DaliLite-4.1-gompi-2021a.eb @@ -0,0 +1,60 @@ +easyblock = 'MakeCp' + +name = 'DaliLite' +version = '4.1' + +homepage = 'http://ekhidna2.biocenter.helsinki.fi/dali/' +description = """DaliLite is a light version of the software run by the Dali server. The web +server has search and data visualization options which are not included in this +package. DaliLite supports data import (import.pl) to convert PDB entries to +Dali's internal data format and pairwise comparison (dali.pl) to structurally +align a list of query structures to a list of target structures.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['http://ekhidna2.biocenter.helsinki.fi/dali'] +sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': '%(name)s.v%(version_major)s.tar.gz'}] +patches = ['DaliLite-4.1_fix-labels-without-statements.patch'] +checksums = [ + '6267acefd2a477dd3720f9bbb5b911bbcfc97a9c0de58ebde651f48b4e0cb5cb', # DaliLite-4.1.tar.gz + # DaliLite-4.1_fix-labels-without-statements.patch + 'fb719f2d5ce33e5e47e565f4bb82d9e5d33cf4be341cd773daa0a33fcd65fe10', +] + +dependencies = [ + ('Perl', '5.32.1'), +] + +# Build +_make_home = "HOME=%(builddir)s/%(name)s.v%(version)s" + +prebuildopts = "make clean %s &&" % _make_home +buildopts = 'FC=${FC} FC_MPI=${MPIF90} CFLAGS="${FCFLAGS} -fallow-argument-mismatch" ' +buildopts += 'CC="${CC} ${CFLAGS}" CC_MPI=${MPICC} ' + _make_home + +# Installation +_bin_files = ['dsspcmbi', 'filter95fitz', 'fssp', 'mpicompare', 'pipe', 'pipedccp', 'puu', 'puutos', + 'selfdccp', 'serialcompare'] +_perl_scripts = ['dali.pl', 'dccp2dalicon.pl', 'fsspfilter.pl', 'fsspselect.pl', 'htmljs.pl', 'import.pl', + 'pairwise.pl', 'pipe96-free.pl', 'pipe96.pl', 'sortdccp.pl'] +_perl_mods = ['mpidali.pm', 'upgma.pm'] + +files_to_copy = [ + (['bin/%s' % x for x in _bin_files + _perl_scripts], 'bin'), + (['bin/%s' % x for x in _perl_mods], 'lib/perl5/site_perl/%(perlver)s/'), +] + +# Fix perl scritps +fix_perl_shebang_for = ['bin/%s' % x for x in _perl_scripts] +postinstallcmds = ["chmod 755 %(installdir)s/bin/*.pl"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bin_files + _perl_scripts], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/'], +} + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DaliLite/DaliLite-4.1_fix-labels-without-statements.patch b/easybuild/easyconfigs/d/DaliLite/DaliLite-4.1_fix-labels-without-statements.patch new file mode 100644 index 00000000000..7770b0b962d --- /dev/null +++ b/easybuild/easyconfigs/d/DaliLite/DaliLite-4.1_fix-labels-without-statements.patch @@ -0,0 +1,31 @@ +Remove statement labels from those lines without any statement +author: Alex Domingo (Vrije Universiteit Brussel) +diff --git a/src/pipe.f.orig b/src/pipe.f +index d127f2e..e8096cb 100644 +--- a/src/pipe.f.orig ++++ b/src/pipe.f +@@ -36,12 +36,12 @@ c + !filnam=constructfilnam(cd1,dalidatpath_1,'.dat') + !open(91,file=filnam,status='old',err=11) + !goto 12 +-11 !filnam=constructfilnam(cd1,dalidatpath_2,'.dat') ++ !filnam=constructfilnam(cd1,dalidatpath_2,'.dat') + !open(11,file=filnam,status='old',err=10) +-12 !continue ++ !continue + ! try second dalidatpath + ! i=0 +-200 ! read(91,530,end=219) line ++ ! read(91,530,end=219) line + ! if(line(1:4).ne.'>>>>') goto 200 + ! read(line,551) ndom + ! i=i+1 +@@ -50,7 +50,7 @@ c + ! read(91,710,end=219) j,domns(j), + ! $ ((domseglist(i,k,j),k=1,2),i=1,domns(j)) + ! end do +-219 ! close(91) ++ ! close(91) + !close(91) + c + c output From 61da4a3f8433fce4eaec708e234a7cf9ab37b1bc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 30 May 2023 14:08:50 +0200 Subject: [PATCH 7504/9987] adding easyconfigs: Demystify-0.0.17-foss-2020b.eb --- .../Demystify/Demystify-0.0.17-foss-2020b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb new file mode 100644 index 00000000000..7e1167c2acd --- /dev/null +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Demystify' +version = '0.0.17' + +homepage = 'https://github.com/stacs-cp/demystify' +description = """ +Demystify is a tool which allows puzzles to be expressed in a high-level +constraint programming language and uses MUSes to automatically produce +descriptions of steps in the puzzle solving.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93779a131aa78f7de0dffdbe8e89124836b5eb6d0e9b4bc385821845a4628f52'] + +dependencies = [ + ('Python', '3.8.6'), + ('PySAT', '0.1.7.dev1'), + ('SciPy-bundle', '2020.11'), + ('Z3', '4.8.10', '-Python-%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From 43b52ac6fa6b5c9bb7778bbd429eb5f56d133aea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 May 2023 16:55:27 +0200 Subject: [PATCH 7505/9987] bump version to 4.7.3dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 70004ce1b12..cf3a30f7d86 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.7.2' +VERSION = '4.7.3.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 79e0fafa48edd489571bdf27672c48b5a7c21c57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 May 2023 21:41:12 +0200 Subject: [PATCH 7506/9987] {toolchain} GCC 11.4.0 --- .../b/Bison/Bison-3.8.2-GCCcore-11.4.0.eb | 27 ++++++++ .../binutils/binutils-2.40-GCCcore-11.4.0.eb | 31 +++++++++ .../f/flex/flex-2.6.4-GCCcore-11.4.0.eb | 34 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-11.4.0.eb | 22 ++++++ .../easyconfigs/g/GCCcore/GCCcore-11.4.0.eb | 68 +++++++++++++++++++ .../help2man-1.49.3-GCCcore-11.4.0.eb | 25 +++++++ .../m/M4/M4-1.4.19-GCCcore-11.4.0.eb | 29 ++++++++ .../z/zlib/zlib-1.2.13-GCCcore-11.4.0.eb | 27 ++++++++ 8 files changed, 263 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.4.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-11.4.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.4.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-11.4.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-11.4.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-11.4.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.4.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-11.4.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.4.0.eb new file mode 100644 index 00000000000..527f9ab53d1 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-11.4.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '11.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.40', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-11.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-11.4.0.eb new file mode 100644 index 00000000000..f8fd00a923f --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-11.4.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.40' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '11.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d7f82c4047decf43a6f769ac32456a92ddb6932409a585c633cdd4e9df23d956'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', SYSTEM) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.13'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.4.0.eb new file mode 100644 index 00000000000..cab31c1aaf1 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-11.4.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'http://flex.sourceforge.net/' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.40', '', SYSTEM), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-11.4.0.eb b/easybuild/easyconfigs/g/GCC/GCC-11.4.0.eb new file mode 100644 index 00000000000..b72e811f68d --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-11.4.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '11.4.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.40', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.4.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.4.0.eb new file mode 100644 index 00000000000..e7a933e69e9 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.4.0.eb @@ -0,0 +1,68 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '11.4.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.2.0.tar.bz2', + 'mpc-1.3.1.tar.gz', + 'isl-0.26.tar.bz2', + 'newlib-4.3.0.20230120.tar.gz', + {'download_filename': '93e0090.tar.gz', 'filename': 'nvptx-tools-20230122.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCCcore-11.3.0_fuse-ld-mold.patch', +] +checksums = [ + {'gcc-11.4.0.tar.gz': 'af828619dd1970734dda3cfb792ea3f2cba61b5a00170ba8bce4910749d73c07'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.2.0.tar.bz2': '691db39178e36fc460c046591e4b0f2a52c8f2b3ee6d750cc2eab25f1eaa999d'}, + {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'}, + {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'}, + {'newlib-4.3.0.20230120.tar.gz': '83a62a99af59e38eb9b0c58ed092ee24d700fff43a22c03e433955113ef35150'}, + {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCCcore-11.3.0_fuse-ld-mold.patch': 'bba64714f8b84ad58b3b43c0d21b4ffc298274ae699f514ed2934f002146d840'}, +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.40'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-11.4.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-11.4.0.eb new file mode 100644 index 00000000000..701913a5ae0 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-11.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '11.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.40', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.4.0.eb new file mode 100644 index 00000000000..cdfad17f02c --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-11.4.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '11.4.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.40', '', SYSTEM)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-11.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-11.4.0.eb new file mode 100644 index 00000000000..6c16569826e --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-11.4.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.13' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '11.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.40', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 06af1c76fb94fe4b38d12398642c431e32fd0f0f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 31 May 2023 11:07:57 +0200 Subject: [PATCH 7507/9987] adding easyconfigs: json-fortran-8.3.0-GCCcore-10.2.0.eb, json-fortran-8.3.0-GCCcore-12.2.0.eb --- .../json-fortran-8.3.0-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ .../json-fortran-8.3.0-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..30199cec525 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.20.1'), +] + +configopts = [ + '-DUSE_GNU_INSTALL_CONVENTION=TRUE', +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..c2755034346 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = [ + '-DUSE_GNU_INSTALL_CONVENTION=TRUE', +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 28a2f14bec51c67657ead6f098e936fa621113e1 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 31 May 2023 14:56:08 +0200 Subject: [PATCH 7508/9987] contribute lib with foss/2022b compiler --- .../expecttest-0.1.3-GCCcore-12.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8a91ea0f1eb --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.3-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.1.3' + +homepage = 'https://github.com/ezyang/expecttest' +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['83057695811d94128aed13ed094a070db90e0a92ea40071f8ee073cbab57149a'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From 5755b8482bee6ce14eef61fd5d2ddb68c579e9b7 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 31 May 2023 14:35:01 +0100 Subject: [PATCH 7509/9987] adding easyconfigs: GEM-1.5.1-foss-2022a.eb, GEM-1.5.1-foss-2022b.eb and patches: GEM-1.5.1-makefile-thirdparty.patch --- .../easyconfigs/g/GEM/GEM-1.5.1-foss-2022a.eb | 50 ++++++++++++++ .../easyconfigs/g/GEM/GEM-1.5.1-foss-2022b.eb | 50 ++++++++++++++ .../g/GEM/GEM-1.5.1-makefile-thirdparty.patch | 67 +++++++++++++++++++ 3 files changed, 167 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEM/GEM-1.5.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GEM/GEM-1.5.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/g/GEM/GEM-1.5.1-makefile-thirdparty.patch diff --git a/easybuild/easyconfigs/g/GEM/GEM-1.5.1-foss-2022a.eb b/easybuild/easyconfigs/g/GEM/GEM-1.5.1-foss-2022a.eb new file mode 100644 index 00000000000..6ab102385f2 --- /dev/null +++ b/easybuild/easyconfigs/g/GEM/GEM-1.5.1-foss-2022a.eb @@ -0,0 +1,50 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'GEM' +version = '1.5.1' + +homepage = 'https://github.com/large-scale-gxe-methods/GEM' + +description = """ +GEM (Gene-Environment interaction analysis for Millions of samples) is a +software program for large-scale gene-environment interaction testing in +samples from unrelated individuals. It enables genome-wide association +studies in up to millions of samples while allowing for multiple exposures, +control for genotype-covariate interactions, and robust inference. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/large-scale-gxe-methods/GEM/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-makefile-thirdparty.patch'] +checksums = [ + {'v1.5.1.tar.gz': 'fcac26c43f362b18e568f06345c660bc8921f6aa4956bccd8b33317b60a94d18'}, + {'GEM-1.5.1-makefile-thirdparty.patch': '155a9bebae55a98291927aa04bda5f2dd261755d757681d59457968169f37143'}, +] + +builddependencies = [ + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('Armadillo', '11.4.3'), + ('libdeflate', '1.10'), + ('zstd', '1.5.2'), +] + +start_dir = 'src' + +files_to_copy = [(['GEM'], 'bin'), 'example', 'README.md'] + +sanity_check_paths = { + 'files': ['bin/GEM'], + 'dirs': [], +} + +# Using --version or --help results in a return value of 1 +sanity_check_commands = ["GEM --version | grep v1.5.1"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GEM/GEM-1.5.1-foss-2022b.eb b/easybuild/easyconfigs/g/GEM/GEM-1.5.1-foss-2022b.eb new file mode 100644 index 00000000000..f0223b7f410 --- /dev/null +++ b/easybuild/easyconfigs/g/GEM/GEM-1.5.1-foss-2022b.eb @@ -0,0 +1,50 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'GEM' +version = '1.5.1' + +homepage = 'https://github.com/large-scale-gxe-methods/GEM' + +description = """ +GEM (Gene-Environment interaction analysis for Millions of samples) is a +software program for large-scale gene-environment interaction testing in +samples from unrelated individuals. It enables genome-wide association +studies in up to millions of samples while allowing for multiple exposures, +control for genotype-covariate interactions, and robust inference. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/large-scale-gxe-methods/GEM/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s-makefile-thirdparty.patch'] +checksums = [ + {'v1.5.1.tar.gz': 'fcac26c43f362b18e568f06345c660bc8921f6aa4956bccd8b33317b60a94d18'}, + {'GEM-1.5.1-makefile-thirdparty.patch': '155a9bebae55a98291927aa04bda5f2dd261755d757681d59457968169f37143'}, +] + +builddependencies = [ + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('Armadillo', '11.4.3'), + ('libdeflate', '1.15'), + ('zstd', '1.5.2'), +] + +start_dir = 'src' + +files_to_copy = [(['GEM'], 'bin'), 'example', 'README.md'] + +sanity_check_paths = { + 'files': ['bin/GEM'], + 'dirs': [], +} + +# Using --version or --help results in a return value of 1 +sanity_check_commands = ["GEM --version | grep v1.5.1"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GEM/GEM-1.5.1-makefile-thirdparty.patch b/easybuild/easyconfigs/g/GEM/GEM-1.5.1-makefile-thirdparty.patch new file mode 100644 index 00000000000..70078684fd8 --- /dev/null +++ b/easybuild/easyconfigs/g/GEM/GEM-1.5.1-makefile-thirdparty.patch @@ -0,0 +1,67 @@ +Patch for makefile, and ReadBGEN.cpp to use EasyBuild provided +third party software. Does not change the original DOS format to UNIX! +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/GEM-1.5.1.orig/src/ReadBGEN.cpp b/GEM-1.5.1/src/ReadBGEN.cpp +index ecbc243..7162579 100755 +--- a/GEM-1.5.1.orig/src/ReadBGEN.cpp ++++ b/GEM-1.5.1/src/ReadBGEN.cpp +@@ -2,8 +2,8 @@ + #include "declars.h" + #include "ReadBGEN.h" + #include "ReadParameters.h" +-#include "../thirdparty/zstd-1.5.5/lib/zstd.h" +-#include "../thirdparty/libdeflate-1.18/libdeflate.h" ++#include "zstd.h" ++#include "libdeflate.h" + + /************************************** + This function is revised based on the Parse function in BOLT-LMM v2.3 source code +diff --git a/GEM-1.5.1.orig/src/makefile b/GEM-1.5.1/src/makefile +index 969daae..3b968b2 100644 +--- a/GEM-1.5.1.orig/src/makefile ++++ b/GEM-1.5.1/src/makefile +@@ -1,12 +1,10 @@ + CC=gcc # Do not change this for libdeflate package. + CXX=g++ +-CXXFLAGS = -std=c++11 -O2 -g ++CXXFLAGS = -std=c++11 -O2 + +-BOOST_INC=../boost +-Eigen_INC=../eigen + BOOST_LIB=-lboost_thread -lboost_program_options -lboost_system -lboost_filesystem + +-DYN_LIBS=-lmkl_gf_lp64 -lmkl_sequential -lmkl_core -ldl -lpthread -lm -larmadillo ++DYN_LIBS=-lflexiblas -lzstd -ldeflate -ldl -lpthread -lm -larmadillo + + + # Uncomment line below for LAPACK/BLAS only and comment other lines beginning with LIBS. +@@ -14,18 +12,16 @@ DYN_LIBS=-lmkl_gf_lp64 -lmkl_sequential -lmkl_core -ldl -lpthread -lm -larmadill + + #LIBS= -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -ldl -lpthread -lm -lboost_program_options -lboost_thread -lboost_system -lboost_filesystem + +-C_SOURCES= $(wildcard ../thirdparty/zstd-1.5.5/lib/common/*.c) $(wildcard ../thirdparty/zstd-1.5.5/lib/compress/*.c) $(wildcard ../thirdparty/zstd-1.5.5/lib/decompress/*.c) $(wildcard ../thirdparty/libdeflate-1.18/lib/*.c) $(wildcard ../thirdparty/libdeflate-1.18/lib/x86/*.c) $(wildcard ../thirdparty/libdeflate-1.18/lib/arm/*.c) + CXX_SOURCES= MatrixUtils.cpp ReadParameters.cpp TimeUtils.cpp BinaryEUtils.cpp ReadBGEN.cpp ReadPGEN.cpp ReadBed.cpp GEM.cpp + CC_SOURCES=$(wildcard ../thirdparty/plink-2.0/*.cc) + CXX_OBJECTS= $(CXX_SOURCES:.cpp=.o) +-C_OBJECTS= $(C_SOURCES:.c=.o) + CC_OBJ= $(CC_SOURCES:.cc=.o) +-OBJS= $(CXX_OBJECTS) $(C_OBJECTS) $(CC_OBJ) ++OBJS= $(CXX_OBJECTS) $(CC_OBJ) + + #targets + all: GEM + +-GEM: $(CXX_OBJECTS) $(C_OBJECTS) $(CC_OBJ) ++GEM: $(CXX_OBJECTS) $(CC_OBJ) + $(CXX) $^ $(CXXFLAGS) $(BOOST_LIB_TD) $(BOOST_LIB) -o $@ $(DYN_LIBS) + + %.o: %.c +@@ -35,7 +31,7 @@ GEM: $(CXX_OBJECTS) $(C_OBJECTS) $(CC_OBJ) + $(CXX) $(CXXFLAGS) -c $< -o $@ + + %.o: %.cpp +- $(CXX) $(CXXFLAGS) -c $< -o $@ -I$(BOOST_INC) -I$(Eigen_INC) ++ $(CXX) $(CXXFLAGS) -I${EBROOTZSTD}/include -I${EBROOTLIBDEFLATE}/include -I${EBROOTEIGEN}/include -c $< -o $@ + + .PHONY: clean + clean: From 39a3e9e57af3671d72160f6cb57f2f13144b81d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 May 2023 17:17:52 +0200 Subject: [PATCH 7510/9987] stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2 --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb index b009ef44f7f..99d84d40bcd 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ dependencies = [ ('LAME', '3.100'), ('libmad', '0.15.1b'), ('libvorbis', '1.3.7'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.4.2'), ] sanity_check_paths = { From 1f14182c7472532dd157d53b857b2a293dd35856 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 31 May 2023 15:32:04 +0000 Subject: [PATCH 7511/9987] adding easyconfigs: WhatsHap-1.7-foss-2022a.eb --- .../w/WhatsHap/WhatsHap-1.7-foss-2022a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.7-foss-2022a.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.7-foss-2022a.eb new file mode 100644 index 00000000000..7733024d32a --- /dev/null +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.7-foss-2022a.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'WhatsHap' +version = '1.7' + +homepage = 'https://whatshap.readthedocs.io' +description = """WhatsHap is a software for phasing genomic variants using DNA +sequencing reads, also called read-based phasing or haplotype assembly. It is +especially suitable for long reads, but works also well with short reads.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Pysam', '0.20.0'), + ('networkx', '2.8.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('Yasm', '1.3.0'), + ('pyfaidx', '0.7.1'), + ('python-isal', '1.1.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('xopen', '1.5.0', { + 'checksums': ['822b926afd39b6904e5d2fdee6e0944d342023f2a42339103c1507b0da48c693'], + }), + ('pulp', '2.7.0', { + 'source_tmpl': 'PuLP-%(version)s.tar.gz', + 'checksums': ['e73ee6b32d639c9b8cf4b4aded334ba158be5f8313544e056f796ace0a10ae63'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['abd90551a4e19426ceb3a84ed1c8e23f609869956a7f16609f6950aedc930a2c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' From a7101b3ed99c66a9896517b72de203bc4fe86403 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 1 Jun 2023 08:10:21 +0000 Subject: [PATCH 7512/9987] Use 2022a version of Pysam dep --- easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.7-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.7-foss-2022a.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.7-foss-2022a.eb index 7733024d32a..f99182d699d 100644 --- a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.7-foss-2022a.eb +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-1.7-foss-2022a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), - ('Pysam', '0.20.0'), + ('Pysam', '0.19.1'), ('networkx', '2.8.4'), ('SciPy-bundle', '2022.05'), ('Biopython', '1.79'), From 8cf56ee3830559e3841209ba5433c197c394f783 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 1 Jun 2023 14:44:27 +0200 Subject: [PATCH 7513/9987] adding easyconfigs: libheif-1.12.0-GCC-11.3.0.eb, libde265-1.0.11-GCC-11.3.0.eb, libjxl-0.5-foss-2022a.eb, Highway-0.12.2-GCCcore-11.3.0.eb, Zopfli-1.0.3-GCCcore-11.3.0.eb, zlib-ng-2.0.7-GCCcore-11.3.0.eb and patches: libjxl-0.3.7_external_lcms2.patch, libjxl-0.5_remove-broken-test.patch --- .../Highway/Highway-0.12.2-GCCcore-11.3.0.eb | 34 ++++++++++ .../l/libde265/libde265-1.0.11-GCC-11.3.0.eb | 31 +++++++++ .../l/libheif/libheif-1.12.0-GCC-11.3.0.eb | 42 ++++++++++++ .../l/libjxl/libjxl-0.5-foss-2022a.eb | 64 +++++++++++++++++++ .../z/Zopfli/Zopfli-1.0.3-GCCcore-11.3.0.eb | 37 +++++++++++ .../z/zlib-ng/zlib-ng-2.0.7-GCCcore-11.3.0.eb | 30 +++++++++ 6 files changed, 238 insertions(+) create mode 100644 easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.5-foss-2022a.eb create mode 100644 easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.7-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7af1f6c6911 --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'Highway' +version = '0.12.2' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e1d47ce510429fdcf31f41697ca74fb0dcd59d933196e531a86d51751a56f4cc'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('googletest', '1.13.0'), +] + +configopts = "-DHWY_SYSTEM_GTEST=ON" + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb new file mode 100644 index 00000000000..a553f85b55f --- /dev/null +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libde265' +version = '1.0.11' + +homepage = 'https://github.com/strukturag/libde265' +description = "libde265 is an open source implementation of the h.265 video codec" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2f8f12cabbdb15e53532b7c1eb964d4e15d444db1be802505e6ac97a25035bab'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['bin/dec265', 'lib/libde265.%s' % SHLIB_EXT], + 'dirs': ['include/libde265', 'lib/cmake/libde265'], +} + +sanity_check_commands = [ + "dec265 --help", + # "enc265 --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..8528903bbae --- /dev/null +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.3.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libheif' +version = '1.12.0' + +homepage = 'https://github.com/strukturag/libheif' +description = "libheif is an HEIF and AVIF file format decoder and encoder" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('libde265', '1.0.8'), + ('x265', '3.5'), + ('Gdk-Pixbuf', '2.42.8'), +] + +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +sanity_check_paths = { + 'files': ['bin/heif-info', 'lib/libheif.a', 'lib/libheif.%s' % SHLIB_EXT, 'lib/pkgconfig/libheif.pc'], + 'dirs': ['include/libheif'], +} + +sanity_check_commands = ["heif-info --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.5-foss-2022a.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.5-foss-2022a.eb new file mode 100644 index 00000000000..ae493f049f6 --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.5-foss-2022a.eb @@ -0,0 +1,64 @@ +easyblock = 'CMakeMake' + +name = 'libjxl' +version = '0.5' +local_lodepng_version = "48e5364" + +homepage = 'https://github.com/libjxl/libjxl' +description = "JPEG XL image format reference implementation" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'optarch': False} # optarch causes some test failures + +github_account = 'libjxl' +source_urls = [GITHUB_SOURCE] +sources = [ + 'v%(version)s.tar.gz', + {'filename': 'lodepng-%s.tar.gz' % local_lodepng_version, + 'download_filename': local_lodepng_version, + 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], + 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, +] +patches = [ + 'libjxl-0.3.7_external_lcms2.patch', + 'libjxl-%(version)s_remove-broken-test.patch', +] +checksums = [ + '911cb4b50eb621131ca22382166f40d4914a4ff4453dd299ade1e3292f311f89', # v0.5.tar.gz + 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz + '9e6decaf6be74eeccfd5728df175930b4be33de6cbdf9e1816f68cb4b718fa1b', # libjxl-0.3.7_external_lcms2.patch + '5b62751da5b3b3c4aad58a841d49cc506bc330425bbd0df7f19f99aa98c52c26', # libjxl-0.5_remove-broken-test.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('googletest', '1.13.0'), + ('pkg-config', '0.29.2'), + ('Highway', '0.12.2'), # Highway only has a static library +] + +dependencies = [ + ('LittleCMS', '2.13.1'), + ('Brotli', '1.0.9'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('giflib', '5.2.1'), + ('libwebp', '1.2.4'), + ('OpenEXR', '3.1.5'), + ('gperftools', '2.10'), +] + +configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' +# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) +configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4892a6729ab --- /dev/null +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits) +easyblock = 'CMakeMake' + +name = 'Zopfli' +version = '1.0.3' + +homepage = 'https://github.com/google/zopfli' +description = """Zopfli Compression Algorithm is a compression library programmed in C to perform +very good, but slow, deflate or zlib compression.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF', +] + +sanity_check_paths = { + 'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["zopfli --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2f4e46a256d --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.7-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak (Inuits) +# Updated: Thomas Hoffmann (EMBL), Denis Kristak (Inuits) +easyblock = 'CMakeMake' + +name = 'zlib-ng' +version = '2.0.7' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6c0853bb27738b811f2b4d4af095323c3d5ce36ceed6b50e5f773204fb8f7200'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +configopts = ' -DZLIB_ENABLE_TESTS=True ' + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From 978f4fab31f3b96304bdc8a1dede73235bd28a21 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 1 Jun 2023 14:46:07 +0200 Subject: [PATCH 7514/9987] adding easyconfigs: jxrlib-1.1-GCCcore-11.3.0.eb, imagecodecs-2022.9.26-foss-2022a.eb, LERC-4.0.0-GCCcore-11.3.0.eb, libavif-0.11.1-foss-2022a.eb, LibLZF-3.6-GCCcore-11.3.0.eb, zfp-1.0.0-GCCcore-11.3.0.eb --- .../imagecodecs-2022.9.26-foss-2022a.eb | 72 +++++++++++++++++++ .../j/jxrlib/jxrlib-1.1-GCCcore-11.3.0.eb | 39 ++++++++++ .../l/LERC/LERC-4.0.0-GCCcore-11.3.0.eb | 39 ++++++++++ .../l/LibLZF/LibLZF-3.6-GCCcore-11.3.0.eb | 31 ++++++++ .../l/libavif/libavif-0.11.1-foss-2022a.eb | 36 ++++++++++ .../z/zfp/zfp-1.0.0-GCCcore-11.3.0.eb | 40 +++++++++++ 6 files changed, 257 insertions(+) create mode 100644 easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb create mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb new file mode 100644 index 00000000000..50e2daa8082 --- /dev/null +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb @@ -0,0 +1,72 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL), Denis Kristak (Inuits) +easyblock = 'PythonBundle' + +name = 'imagecodecs' +version = '2022.9.26' # opting for older version because of compatibility issues with LibTIFF + +homepage = 'https://github.com/cgohlke/imagecodecs' +description = """Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, +compression, and decompression functions for use in the tifffile, czifile, zarr, and other +scientific image input/output modules.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +local_openjpeg_maj_min = '2.5' +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('Brotli', '1.0.9'), + ('bzip2', '1.0.8'), + ('Blosc', '1.21.3'), + ('Blosc2', '2.4.3'), + ('CFITSIO', '4.2.0'), + ('CharLS', '2.4.1'), + ('giflib', '5.2.1'), + ('jxrlib', '1.1'), + ('LittleCMS', '2.13.1'), + ('LERC', '4.0.0'), + ('libaec', '1.0.6'), + ('libavif', '0.11.1'), + ('libdeflate', '1.10'), + ('libjpeg-turbo', '2.1.3'), + ('libjxl', '0.5'), + ('LibLZF', '3.6'), + ('libpng', '1.6.37'), + ('XZ', '5.2.5'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.4'), + ('lz4', '1.9.3'), + ('OpenJPEG', local_openjpeg_maj_min + '.0'), + ('snappy', '1.1.9'), + ('zlib', '1.2.12'), + ('zlib-ng', '2.0.7'), + ('Zopfli', '1.0.3'), + ('zfp', '1.0.0'), + ('zstd', '1.5.2'), + ('Brunsli', '0.1'), + ('HDF5', '1.12.2'), + ('h5py', '3.7.0'), + ('libheif', '1.12.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bitshuffle', '0.3.5', { + 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['c3f4461d8013e3d9db0d58defec77b143164652de505a1fba3df088eaa19be2f'], + }), + (name, version, { + 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", + 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.5/:$CPATH && ", + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['04d5757d8fd7819844b0f8d9eed05025dca4962f280d0010b42c7c9c993fe371'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..db73ae8495a --- /dev/null +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +# Update: Thomas Hoffmann (EMBL) +## + +easyblock = 'CMakeMake' + +name = 'jxrlib' +version = '1.1' + +homepage = 'https://github.com/4creators/jxrlib' +description = """Open source implementation of jpegxr""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] +sources = ['%(name)s_%(version)s.orig.tar.gz'] +patches = [('jxrlib-%(version)s_cmake.patch', 1)] +checksums = [ + {'jxrlib_1.1.orig.tar.gz': 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303'}, + {'jxrlib-1.1_cmake.patch': 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74'}, +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] + +modextrapaths = {'CPATH': 'include/jxrlib'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fa7d3b7baa5 --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'LERC' +version = '4.0.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/Esri/lerc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91431c2b16d0e3de6cbaea188603359f87caed08259a645fd5a3805784ee30a0'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +postinstallcmds = [ + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/test.c", +] + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cd %(builddir)s && g++ %(installdir)s/test.c -o lerctest -lLerc && ./lerctest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f278878029d --- /dev/null +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL), Denis Kristak +easyblock = 'ConfigureMake' + +name = 'LibLZF' +version = '3.6' + +homepage = 'http://oldhome.schmorp.de/marc/liblzf.html' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] +sources = ['liblzf-%(version)s.tar.gz'] +checksums = ['9c5de01f7b9ccae40c3f619d26a7abec9986c06c36d260c179cedd04b89fb46a'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_commands = ['lzf -h'] + +sanity_check_paths = { + 'files': ['bin/lzf', 'lib/liblzf.a'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2022a.eb b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2022a.eb new file mode 100644 index 00000000000..b34d2a8449b --- /dev/null +++ b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2022a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak (Inuits) +# Update: Thomas Hoffmann (EMBL), Denis Kristak (Inuits) +easyblock = 'CMakeMake' + +name = 'libavif' +version = '0.11.1' + +homepage = 'https://github.com/AOMediaCodec/libavif' +description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format, +as described here: https://aomediacodec.github.io/av1-avif/ +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0eb49965562a0e5e5de58389650d434cff32af84c34185b6c9b7b2fccae06d4e'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('NASM', '2.15.05'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('Rust', '1.60.0'), +] + +sanity_check_paths = { + 'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c08bb6e10da --- /dev/null +++ b/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'MakeCp' + +name = 'zfp' +version = '1.0.0' + +homepage = 'https://github.com/LLNL/zfp' +description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. +zfp provides compressed-array classes that support high throughput read and write random access to individual array +elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications +that read and write large data sets to and from disk.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/zfp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['fe13b03141ee9b571692aed42ff76cf37c9dcda40f9a43a808870dca3558a57c'] + +builddependencies = [ + ('binutils', '2.38'), +] + +prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && " +buildopts = 'ZFP_WITH_OPENMP=1' + +runtest = 'test' + +files_to_copy = ['bin', 'include', 'lib'] + +sanity_check_paths = { + 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], + 'dirs': ['include/zfp'], +} + +sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] + +moduleclass = 'lib' From a2e254d40ec491b05d75b23d862f7fad177703d4 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 1 Jun 2023 14:46:47 +0200 Subject: [PATCH 7515/9987] adding easyconfigs: PyQtGraph-0.13.3-foss-2022a.eb --- .../PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb new file mode 100644 index 00000000000..cfd1663a6f4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb @@ -0,0 +1,29 @@ +# updated: Denis Kristak +easyblock = 'PythonPackage' +name = 'PyQtGraph' +version = '0.13.3' + +homepage = 'http://www.pyqtgraph.org/' +description = """PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +github_account = 'pyqtgraph' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2dd03b68543fba85aea04e3c07311bfe7d5fd87f40ad6954e83b261d23f92de1'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyQt5', '5.15.5'), + ('PyOpenGL', '3.1.6'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'vis' From 99bd1a036a58bed224eae2648c02401c3fdf1ad4 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 1 Jun 2023 14:48:14 +0200 Subject: [PATCH 7516/9987] adding the main thing - cellpose - to the PR --- .../c/cellpose/cellpose-2.2.2-foss-2022a.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb b/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb new file mode 100644 index 00000000000..0fbccf1d9dd --- /dev/null +++ b/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'cellpose' +version = '2.2.2' + +homepage = '' +description = "" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('OpenCV', '4.6.0', '-contrib'), + ('SciPy-bundle', '2022.05'), + ('PyQt5', '5.15.5'), + ('PyTorch', '1.12.0'), + ('PyQtGraph', '0.13.3'), + ('numba', '0.56.4'), + ('tqdm', '4.64.0'), + ('imagecodecs', '2022.9.26'), + ('scikit-build', '0.15.0'), +] + +# preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && " + +use_pip = True + +exts_list = [ + ('tifffile', '2023.4.12', { + 'checksums': ['2fa99f9890caab919d932a0acaa9d0f5843dc2ef3594e212963932e20713badd'], + }), + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + ('fastremap', '1.13.5', { + 'preinstallopts': "export PBR_VERSION=1.2.3 && ", + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/seung-lab/fastremap/archive/'], + 'checksums': ['ee0e9e798e9f331b7c46e98768735a42bb6e287b3aa56c31c322ba585f4036b7'], + }), + ('roifile', '2023.5.12', { + 'checksums': ['32eeba0d9ad52cc249d6a234b737c1808a6c5d7d9baae6453709eb74222b3433'], + }), + (name, version, { + 'preinstallopts': "sed -i 's/opencv-python-headless//g' setup.py && ", + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'use_pip_extras': 'gui', + 'checksums': ['f21773d364d117eb6fd84c3fb27375845ef373793139ef1668c15491294a3b47'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From fb6472ba6b77e578f65b54e5b8aeadb04ecb7326 Mon Sep 17 00:00:00 2001 From: x0139045 Date: Thu, 1 Jun 2023 16:20:38 +0200 Subject: [PATCH 7517/9987] adding easyconfigs: BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb and patches: BGC-Bayesian-genomic-clines-1.03_Makefile.patch --- ...ayesian-genomic-clines-1.03-gompi-2021a.eb | 34 +++++++++++++++++++ ...ayesian-genomic-clines-1.03_Makefile.patch | 20 +++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03_Makefile.patch diff --git a/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb b/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb new file mode 100644 index 00000000000..a5402652bea --- /dev/null +++ b/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'BGC-Bayesian-genomic-clines' +version = '1.03' +local_commit = '9c8c8cb' + +homepage = 'https://github.com/zgompert/BGC-Bayesian-genomic-clines' +description = """Collection of code for Bayesian genomic cline analyses.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +github_account = 'zgompert' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = [('%(name)s-%(version)s_Makefile.patch', 1)] +checksums = [ + {'9c8c8cb.tar.gz': '105cd1f545c5d9cd55d965436e8e31934fc77a5981399aa6373acd6e42f73cf1'}, + {'BGC-Bayesian-genomic-clines-1.03_Makefile.patch': + 'c32853077658731dba2ac7f4916a67f43c9f7679916d602750a8c70d60d810de'}, +] + +dependencies = [('GSL', '2.7'), + ('HDF5', '1.12.1')] + +files_to_copy = [ + (['bgc', 'estpost'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/bgc', 'bin/estpost'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03_Makefile.patch b/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03_Makefile.patch new file mode 100644 index 00000000000..a2e7e14105c --- /dev/null +++ b/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03_Makefile.patch @@ -0,0 +1,20 @@ +# Add a Makefile to compile according to instructions +# in https://github.com/zgompert/BGC-Bayesian-genomic-clines/blob/main/bgc_manual.pdf +# Added by steven.vandenbrande@kuleuven.be +--- /dev/null 1970-01-01 01:00:00.000000000 +0100 ++++ BGC-Bayesian-genomic-clines/Makefile 2023-05-25 19:16:20.145112000 +0200 +@@ -0,0 +1,14 @@ ++CXX = h5c++ ++CXXFLAGS = -Wall -O3 ++LIBS = -lgsl -lgslcblas ++ ++all: bgc estpost ++ ++bgc: ++ $(CXX) $(CXXFLAGS) -o $@ bgc_main_v1.03.C bgc_func_hdf5_v1.03.C \ ++ bgc_func_linkage_v1.03.C bgc_func_ngs_v1.03.C bgc_func_write_v1.03.C \ ++ bgc_func_initialize_v1.03.C bgc_func_mcmc_v1.03.C bgc_func_readdata_v1.03.C \ ++ mvrandist_v1.03.c $(LIBS) ++ ++estpost: ++ $(CXX) $(CXXFLAGS) -o $@ estpost_h5_v1.03.c $(LIBS) From 9c732d150aa81cbcf3762828b871e54a1580facc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Jun 2023 19:20:29 +0200 Subject: [PATCH 7518/9987] stop running easyconfig unit tests with Python 2.7 (and test with Python 3.11 instead) --- .github/workflows/unit_tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index d71a03ca5b9..f4967ef237c 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -13,10 +13,10 @@ jobs: runs-on: ubuntu-20.04 strategy: matrix: - python: [2.7, 3.6] + python: [3.6, '3.11'] modules_tool: [Lmod-7.8.22, Lmod-8.6.8] module_syntax: [Lua, Tcl] - # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 2.7 & 3.6 + # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 3.6 exclude: - modules_tool: Lmod-7.8.22 module_syntax: Tcl @@ -159,7 +159,7 @@ jobs: runs-on: ubuntu-20.04 strategy: matrix: - python: [2.7, 3.6, 3.7] + python: [3.6, '3.11'] steps: - uses: actions/checkout@v2 From 3c35a7c956db60b61d84c9263dfb899ae3536f3b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Jun 2023 19:23:29 +0200 Subject: [PATCH 7519/9987] use v4 of actions/setup-python --- .github/workflows/unit_tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index f4967ef237c..70fa5933661 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -34,7 +34,7 @@ jobs: key: eb-sourcepath - name: set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: ${{matrix.python}} architecture: x64 @@ -164,7 +164,7 @@ jobs: - uses: actions/checkout@v2 - name: set up Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v4 with: python-version: ${{matrix.python}} From e7176b18a297e8fd6e19102dc8327196323b74fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Jun 2023 19:45:41 +0200 Subject: [PATCH 7520/9987] only run easyconfigs test suite with Python 3.6 for now, since 'python setup.py sdist' doesn't fully work with Python 3.11 (probably due to a recent setuptools version) --- .github/workflows/unit_tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 70fa5933661..d36d0a6398e 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-20.04 strategy: matrix: - python: [3.6, '3.11'] + python: [3.6] modules_tool: [Lmod-7.8.22, Lmod-8.6.8] module_syntax: [Lua, Tcl] # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 3.6 @@ -159,7 +159,7 @@ jobs: runs-on: ubuntu-20.04 strategy: matrix: - python: [3.6, '3.11'] + python: [3.6] steps: - uses: actions/checkout@v2 From 7f0c63f735b5eec901fae66213f0ebe372203d54 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 1 Jun 2023 11:39:11 -0700 Subject: [PATCH 7521/9987] Add pkgconfig to fix error: Could not load pkg-config data for "icu-i18n" --- easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb index 2ea5d3c974f..d43ceead246 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb @@ -19,6 +19,7 @@ checksums = ['ba8174dda00d5b90943f37c6a180a1d37c861d91e04a4cb38dc1c0c74981c186'] builddependencies = [ ('binutils', '2.39'), ('Python', '3.10.8', '-bare'), + ('pkgconfig', '1.5.5', '-python'), ] dependencies = [ From 7eb69e3dea5acb09d91986864442c2d973c51d95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 2 Jun 2023 09:13:40 +0200 Subject: [PATCH 7522/9987] also run easyconfigs test suite with Python 3.11 --- .github/workflows/unit_tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index d36d0a6398e..70fa5933661 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-20.04 strategy: matrix: - python: [3.6] + python: [3.6, '3.11'] modules_tool: [Lmod-7.8.22, Lmod-8.6.8] module_syntax: [Lua, Tcl] # exclude some configurations: only test Tcl module syntax with Lmod 8.x and Python 3.6 @@ -159,7 +159,7 @@ jobs: runs-on: ubuntu-20.04 strategy: matrix: - python: [3.6] + python: [3.6, '3.11'] steps: - uses: actions/checkout@v2 From 97f9b5349a1708faa62361327b4ab466787a9235 Mon Sep 17 00:00:00 2001 From: x0139045 Date: Fri, 2 Jun 2023 09:27:43 +0200 Subject: [PATCH 7523/9987] Update HDF5 dependency version --- .../BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb b/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb index a5402652bea..0ffd3aa510e 100644 --- a/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb +++ b/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb @@ -20,7 +20,7 @@ checksums = [ ] dependencies = [('GSL', '2.7'), - ('HDF5', '1.12.1')] + ('HDF5', '1.10.7')] files_to_copy = [ (['bgc', 'estpost'], 'bin'), From ae982b6ac84f44dfade9a88c127609829000425e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 2 Jun 2023 10:39:31 +0200 Subject: [PATCH 7524/9987] adding CUDA toolchains --- .../AlphaPulldown-0.30.4-fosscuda-2020b.eb | 84 +++++++++++++++++++ .../cctbx-base-2020.8-fosscuda-2020b.eb | 68 +++++++++++++++ 2 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb create mode 100644 easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb new file mode 100644 index 00000000000..fe9b5468284 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaPulldown/AlphaPulldown-0.30.4-fosscuda-2020b.eb @@ -0,0 +1,84 @@ +# created by Denis Kristak (Inuits) +easyblock = "PythonBundle" + +name = "AlphaPulldown" +version = "0.30.4" + +homepage = "https://github.com/KosinskiLab/AlphaPulldown" +description = """AlphaPulldown is a Python package that streamlines protein-protein +interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ("OpenMM", "7.5.0"), + ("Kalign", "3.3.1"), + ('PyYAML', '5.3.1'), + ("cctbx-base", "2020.8"), + ('jax', '0.2.19'), # also provides absl-py + ('Biopython', '1.78'), + ('h5py', '3.1.0'), + ('IPython', '7.18.1'), + ('JupyterLab', '2.2.8'), + ('matplotlib', '3.3.3'), + ('TensorFlow', '2.4.1'), + ('tqdm', '4.56.2'), + ('dm-tree', '0.1.5'), +] + +use_pip = True + +exts_list = [ + ('py3Dmol', '2.0.1.post1', { + 'modulename': 'py3Dmol', + 'checksums': ['add70ecf8f647970925eb8c1043c5c1343813fa49e613b77f0628e522c4148ac'], + }), + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('dm-haiku', '0.0.4', { + 'modulename': 'haiku', + 'patches': ['%(name)s-%(version)s_fix-deps.patch'], + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': [ + {'dm-haiku-0.0.4.tar.gz': 'e9896d161938b53f869fde207f3f6fca496d09b2a47d21dd9b6b65e897ad6aab'}, + {'dm-haiku-0.0.4_fix-deps.patch': 'c509e0aa049401f340234b0a5eba59c9e8af8eff94b9e92f0693aeadfa4c5aa8'}, + ], + }), + ('toolz', '0.11.1', { + 'checksums': ['c7a47921f07822fe534fb1c01c9931ab335a4390c782bd28c6bcc7c2f71f3fbf'], + }), + ('importlib-resources', '5.12.0', { + 'modulename': 'importlib_resources', + 'source_tmpl': 'importlib_resources-%(version)s.tar.gz', + 'checksums': ['4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml-collections', '0.1.1', { + 'sources': ['ml_collections-%(version)s.tar.gz'], + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_fix-deps.patch'], + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': [ + {'alphapulldown-0.30.4.tar.gz': '7797500abaee2e92d28034dc97844bca8c8d7281817e29dc110220824e9d1b5b'}, + {'AlphaPulldown-0.30.4_fix-deps.patch': 'fc5bf395cb36d02efa6d538df49749e722b2d2c257197e3dac83a81c9405c0c9'}, + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + "files": ['bin/run_multimer_jobs.py', 'bin/rename_colab_search_a3m.py'], + "dirs": ["lib/python%(pyshortver)s/site-packages/alphapulldown"], +} + +moduleclass = "data" diff --git a/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb new file mode 100644 index 00000000000..b695ed8ce23 --- /dev/null +++ b/easybuild/easyconfigs/c/cctbx-base/cctbx-base-2020.8-fosscuda-2020b.eb @@ -0,0 +1,68 @@ +# author: Denis Kristak (Inuits) +easyblock = "PythonBundle" + +name = "cctbx-base" +version = "2020.8" +local_pyver = "3.8.6" + +# local_pyver_special is used to create the wheel filename +# it contains the first two digits of the python version (with no delimiter) +local_tmp = local_pyver.split('.') +local_tmp.pop() +# compose a string +local_pyver_special = ''.join(local_tmp) + +homepage = "https://github.com/cctbx/cctbx_project" +description = """ +The Computational Crystallography Toolbox (cctbx) is being developed as the open source component of the Phenix +project. The goal of the Phenix project is to advance automation of macromolecular structure determination. +Phenix depends on the cctbx, but not vice versa. This hierarchical approach enforces a clean design as a reusable +library. The cctbx is therefore also useful for small-molecule crystallography and even general scientific +applications. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', local_pyver), + ('Boost', '1.74.0'), + ('HDF5', '1.10.7'), + ('libGLU', '9.0.1'), + ('LIBSVM', '3.25'), + ('LibTIFF', '4.1.0'), + ('matplotlib', '3.3.3'), + ('mrcfile', '1.3.0'), +] + +local_metadata = "%(installdir)s/lib/python%(pyshortver)s/site-packages/cctbx_base-%(version)s.dist-info/METADATA" + + +exts_list = [ + ('reportlab', '3.5.66', { + 'checksums': ['63fba51babad0047def4ffaa41d0065248ca39d680e98dc9e3010de5425539b4'], + }), + (name, version, { + 'modulename': 'cctbx', + # remove deps (they fail during sanity check, even though they are installed) + 'postinstallcmds': ["echo '' > %s" % local_metadata], + 'sources': [{ + 'download_filename': 'cctbx_base-%s-0_py%sh167b89d-cp%s-cp%sm-manylinux2010_x86_64.whl' % ( + version, local_pyver_special, local_pyver_special, local_pyver_special + ), + 'filename': 'cctbx_base-%s-cp%s-cp%s-manylinux2010_x86_64.whl' % ( + version, local_pyver_special, local_pyver_special + ), + }], + 'checksums': ['5c7ac0710d9011072c678771876aa57ca3735986ed321d403f51989a7444e592'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + "files": ['bin/smtbx.python', 'bin/cctbx.brehm_diederichs'], + "dirs": ['lib/python%(pyshortver)s/site-packages/cctbx_website'], +} + +moduleclass = "lib" From e694f87c46bf90adfb02c6bc615bb2aca2641018 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 2 Jun 2023 11:58:22 +0200 Subject: [PATCH 7525/9987] fixing errors --- .../Highway/Highway-0.12.2-GCCcore-11.3.0.eb | 2 +- .../l/libde265/libde265-1.0.8-GCC-11.3.0.eb | 31 +++++++++++++++++++ .../l/libjxl/libjxl-0.5-foss-2022a.eb | 2 +- 3 files changed, 33 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-11.3.0.eb index 7af1f6c6911..7e8539c6ad3 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-11.3.0.eb @@ -19,7 +19,7 @@ checksums = ['e1d47ce510429fdcf31f41697ca74fb0dcd59d933196e531a86d51751a56f4cc'] builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), - ('googletest', '1.13.0'), + ('googletest', '1.11.0'), ] configopts = "-DHWY_SYSTEM_GTEST=ON" diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.3.0.eb new file mode 100644 index 00000000000..3fc2cdd07f7 --- /dev/null +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libde265' +version = '1.0.8' + +homepage = 'https://github.com/strukturag/libde265' +description = "libde265 is an open source implementation of the h.265 video codec" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2f8f12cabbdb15e53532b7c1eb964d4e15d444db1be802505e6ac97a25035bab'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['bin/dec265', 'lib/libde265.%s' % SHLIB_EXT], + 'dirs': ['include/libde265', 'lib/cmake/libde265'], +} + +sanity_check_commands = [ + "dec265 --help", + # "enc265 --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.5-foss-2022a.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.5-foss-2022a.eb index ae493f049f6..d826e4fd828 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.5-foss-2022a.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.5-foss-2022a.eb @@ -33,7 +33,7 @@ checksums = [ builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), - ('googletest', '1.13.0'), + ('googletest', '1.11.0'), ('pkg-config', '0.29.2'), ('Highway', '0.12.2'), # Highway only has a static library ] From e66aa4f616115eb7632cebec8b58bdfda3936958 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 2 Jun 2023 12:20:06 +0100 Subject: [PATCH 7526/9987] adding easyconfigs: Dalton-2020.1-foss-2022b.eb --- .../d/Dalton/Dalton-2020.1-foss-2022b.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2020.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2020.1-foss-2022b.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2020.1-foss-2022b.eb new file mode 100644 index 00000000000..770eba258c5 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2020.1-foss-2022b.eb @@ -0,0 +1,68 @@ +# Updated to version 2020.1 using the original 2020.0 EasyConfig +# As the patches created by Åke Sandgren for the 2020.0 version work as well, +# we fix the version here as it has been done for the 2016 patch +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'Dalton' +version = '2020.1' + +homepage = 'https://daltonprogram.org/' +description = """The Dalton code is a powerful tool for a wide range of molecular properties + at different levels of theory. + Any published work arising from use of one of the Dalton2016 programs + must acknowledge that by a proper reference, + https://www.daltonprogram.org/www/citation.html.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://gitlab.com/dalton', + 'repo_name': 'dalton', + 'tag': '2020.1', + 'recursive': True, + }, +}] +patches = [ + '%(name)s-2016-fix-cmake-install.patch', + '%(name)s-2020.0_use-EB-install-for-dalton-script.patch', + '%(name)s-2020.0_fix-uninits.patch', + '%(name)s-2016-fix-bad-includepath-add.patch', + '%(name)s-2020.0_use_flexiblas.patch', + '%(name)s-2020.0_disable_failing_tests.patch', +] + +checksums = [ + None, # Dalton-2020.0.tar.gz + '3159b03a488d6f5ee23d468be02ea62eacd08cbdf68cd64ef4e5a0d469a6718b', # Dalton-2016-fix-cmake-install.patch + # Dalton-2020.0_use-EB-install-for-dalton-script.patch + 'f38b434d2af609b667b341192d8f0d7e37ee1e0461cc68c780b049c7027bfcf5', + 'bc446cd1a9fb63836d1d621eb92be65fcd3a46095a0ba4ecb5b7f292dccbb609', # Dalton-2020.0_fix-uninits.patch + '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch + 'c1ac29f4ebfcf42b2b3858008cbd25ffbe7035675b9d954b63a5851183f72abb', # Dalton-2020.0_use_flexiblas.patch + '296f550d4a4429a546c45304881a6091d482bc098c33d18b5aa123b516d8ae4b', # Dalton-2020.0_disable_failing_tests.patch +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Python', '3.10.8', '-bare'), +] + +configopts = '-DENABLE_MPI=ON ' +configopts += '-DENABLE_OMP=ON ' + +pretestopts = 'env EBROOTDALTON=%(builddir)s/easybuild_obj DALTON_TMPDIR=%(builddir)s ' +# Just run the essential tests +testopts = 'ARGS="-L essential" ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/dalton', 'bin/dalton.x'], + 'dirs': ['basis'], +} + +moduleclass = 'chem' From 43e7042341dc8f47df50f6ecfd2431e9893230b3 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 2 Jun 2023 13:51:04 +0200 Subject: [PATCH 7527/9987] adding easyconfigs: AutoDock-GPU-1.5.3-GCC-11.3.0-CUDA-11.7.0.eb --- ...toDock-GPU-1.5.3-GCC-11.3.0-CUDA-11.7.0.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-11.3.0-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..d2feffd75b6 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock-GPU/AutoDock-GPU-1.5.3-GCC-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,60 @@ +easyblock = 'MakeCp' + +name = 'AutoDock-GPU' +version = '1.5.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/ccsb-scripps/AutoDock-GPU' +description = """OpenCL and Cuda accelerated version of AutoDock. It leverages its embarrasingly +parallelizable LGA by processing ligand-receptor poses in parallel over +multiple compute units. +AutoDock is a suite of automated docking tools. It is designed to predict how +small molecules, such as substrates or drug candidates, bind to a receptor of +known 3D structure.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'cstd': 'c++11'} + +github_account = 'ccsb-scripps' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6557df95eed99323befddcef6b8da8b67eba22476efccd1e69a87ffdf075e5f4'] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), +] + +parallel = 1 + +# Default CUDA compute capabilities (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.2', '6.0', '6.1', '7.0'] +# put CUDA compute capabilities in a shell variable to strip dots in make command +prebuildopts = 'CUDA_CC_TARGETS="%(cuda_cc_space_sep)s"; ' + +# Use complation flags from EB +prebuildopts += "sed -i 's/^LFLAGS=.*/LFLAGS=$(LDFLAGS)/;s/^CFLAGS=.*/CFLAGS+=$(IFLAGS) $(LFLAGS)/' Makefile.Cuda && " + +prebuildopts += 'GPU_INCLUDE_PATH=$EBROOTCUDA/include ' +prebuildopts += 'GPU_LIBRARY_PATH=$EBROOTCUDA/lib ' + +# build for CUDA with defined CUDA compute capabilities +buildopts = 'DEVICE=CUDA TARGETS="${CUDA_CC_TARGETS//./}"' + +files_to_copy = [ + (['bin/*'], 'bin'), + (['doc', 'examples', 'LICENSE', 'LICENSE_LGPL', 'README.md'], 'share'), + (['input'], 'share/examples'), +] + +postinstallcmds = [ + "cd %(installdir)s/bin && ln -s autodock_gpu_64wi autodock_gpu", +] + +sanity_check_paths = { + 'files': ['bin/autodock_gpu', 'bin/autodock_gpu_64wi', 'bin/adgpu_analysis'], + 'dirs': ['share'], +} + +sanity_check_commands = [('autodock_gpu', '--help')] + +moduleclass = 'tools' From 3531c1a38259acff9674f8d0ce2130bea07ea076 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 2 Jun 2023 12:48:26 +0000 Subject: [PATCH 7528/9987] adding easyconfigs: OpenBLAS-0.3.23-GCC-12.3.0.eb --- .../o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb new file mode 100644 index 00000000000..f55e447fa3b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb @@ -0,0 +1,45 @@ +name = 'OpenBLAS' +version = '0.3.23' + +homepage = 'http://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.23_fix-parallel-build.patch', +] +checksums = [ + {'v0.3.23.tar.gz': '5d9491d07168a5d00116cdc068a40022c3455bf9293c7cb86a65b1054d7e5114'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.23_fix-parallel-build.patch': 'abe10ba3b0ca54772dbf235596e35325a5159018f6a60cfc88824c2c220d99d9'}, +] + +builddependencies = [ + ('make', '4.4.1'), + # required by LAPACK test suite + ('Python', '3.11.3'), +] + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From b5d42f9a3625237169ea68b4c08b6847a3d1edc5 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 2 Jun 2023 12:55:02 +0000 Subject: [PATCH 7529/9987] Add parallel build patch for OpenBLAS 0.3.23 --- .../OpenBLAS-0.3.23_fix-parallel-build.patch | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-parallel-build.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-parallel-build.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-parallel-build.patch new file mode 100644 index 00000000000..97e9344271f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-parallel-build.patch @@ -0,0 +1,69 @@ +From https://github.com/xianyi/OpenBLAS/pull/3983 + +From 281e834566a06f1c756d262dc31e809faaf8933f Mon Sep 17 00:00:00 2001 +From: Guillaume Horel +Date: Thu, 30 Mar 2023 15:15:25 -0400 +Subject: [PATCH 1/2] do not pass -j flag to the MAKE variable + +--- + getarch.c | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/getarch.c b/getarch.c +index 937a8db68c..87384c0840 100644 +--- a/getarch.c ++++ b/getarch.c +@@ -1930,15 +1930,15 @@ printf("ELF_VERSION=2\n"); + + #ifdef MAKE_NB_JOBS + #if MAKE_NB_JOBS > 0 +- printf("MAKE += -j %d\n", MAKE_NB_JOBS); ++ printf("MAKEFLAGS += -j %d\n", MAKE_NB_JOBS); + #else + // Let make use parent -j argument or -j1 if there + // is no make parent + #endif + #elif NO_PARALLEL_MAKE==1 +- printf("MAKE += -j 1\n"); ++ printf("MAKEFLAGS += -j 1\n"); + #else +- printf("MAKE += -j %d\n", get_num_cores()); ++ printf("MAKEFLAGS += -j %d\n", get_num_cores()); + #endif + + break; + +From 397108fba299c87ce17957452d57469af914f516 Mon Sep 17 00:00:00 2001 +From: Guillaume Horel +Date: Fri, 31 Mar 2023 09:22:40 -0400 +Subject: [PATCH 2/2] serialize shared prerequisites + +--- + Makefile | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile b/Makefile +index 144b3400db..3c4b8948af 100644 +--- a/Makefile ++++ b/Makefile +@@ -40,9 +40,9 @@ LAPACK_NOOPT := $(filter-out -O0 -O1 -O2 -O3 -Ofast -O -Og -Os,$(LAPACK_FFLAGS)) + SUBDIRS_ALL = $(SUBDIRS) test ctest utest exports benchmark ../laswp ../bench cpp_thread_test + + .PHONY : all libs netlib $(RELA) test ctest shared install +-.NOTPARALLEL : all libs $(RELA) prof lapack-test install blas-test ++.NOTPARALLEL : shared + +-all :: libs netlib $(RELA) tests shared ++all :: tests + @echo + @echo " OpenBLAS build complete. ($(LIB_COMPONENTS))" + @echo +@@ -150,7 +150,7 @@ ifeq ($(OSNAME), CYGWIN_NT) + endif + endif + +-tests : libs netlib $(RELA) shared ++tests : shared + ifeq ($(NOFORTRAN), $(filter 0,$(NOFORTRAN))) + touch $(LIBNAME) + ifndef NO_FBLAS From fa67c19c43845a95869665f97e4d394bf7fbacbd Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 2 Jun 2023 15:07:51 +0200 Subject: [PATCH 7530/9987] Compile directly in the buildir + Don't create a useless bin dir + Update version --- ...0.eb => EDirect-19.7.20230531-GCCcore-10.3.0.eb} | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/e/EDirect/{EDirect-19.5.20230508-GCCcore-10.3.0.eb => EDirect-19.7.20230531-GCCcore-10.3.0.eb} (78%) diff --git a/easybuild/easyconfigs/e/EDirect/EDirect-19.5.20230508-GCCcore-10.3.0.eb b/easybuild/easyconfigs/e/EDirect/EDirect-19.7.20230531-GCCcore-10.3.0.eb similarity index 78% rename from easybuild/easyconfigs/e/EDirect/EDirect-19.5.20230508-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/e/EDirect/EDirect-19.7.20230531-GCCcore-10.3.0.eb index b3fd36f0616..8e19e535ef4 100644 --- a/easybuild/easyconfigs/e/EDirect/EDirect-19.5.20230508-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/e/EDirect/EDirect-19.7.20230531-GCCcore-10.3.0.eb @@ -8,7 +8,7 @@ easyblock = 'Binary' name = 'EDirect' -version = '19.5.20230508' +version = '19.7.20230531' homepage = 'https://www.ncbi.nlm.nih.gov/books/NBK25501/' # See also https://dataguide.nlm.nih.gov/edirect/install.html @@ -28,7 +28,7 @@ sources = [ }, ] checksums = [ - '1a73f832a464f150e41c9330e3d8f8f8775f7c39c9352639480289d588fa4889', # edirect-19.5.20230508.tar.gz + 'c25d2818a75fbfce4a81907f30a6c80ff13df6ada8b2f67d67d705fc887500d1', # edirect-19.7.20230531.tar.gz ] builddependencies = [ @@ -43,15 +43,14 @@ dependencies = [ extract_sources = True postinstallcmds = [ - "mkdir %(installdir)s/bin && cd %(installdir)s/cmd/ && " - "sed -i 's@target=\"\\$HOME/Misc/scripts/\"@target=\"\\$PWD/../\"@' build.sh && " - "./build.sh install && cd ../ && rm -rf cmd/ eutils/ && " - "cd bin/ && ln -s ../* . && rm -f easybuild README readme.pdf bin" + "cd cmd/ && " + "sed -i 's@target=\"\\$HOME/Misc/scripts/\"@target=\"%(installdir)s/\"@' build.sh && " + "./build.sh install && cd %(installdir)s/ && rm -rf cmd/ eutils/" ] sanity_check_paths = { 'files': ['einfo', 'README'], - 'dirs': ['bin', 'help'], + 'dirs': ['help'], } sanity_check_commands = [ From 4d07f3eec82f7695f0548757a103eef03b338b4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 2 Jun 2023 17:53:39 +0200 Subject: [PATCH 7531/9987] adding easyconfigs: dm-haiku-0.0.9-foss-2021a-CUDA-11.3.1.eb --- .../dm-haiku-0.0.9-foss-2021a-CUDA-11.3.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000000..65c6e384b88 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'dm-haiku' +version = '0.0.9' +versionsuffix = '-CUDA-11.3.1' + +homepage = 'https://github.com/deepmind/dm-haiku' +description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural +network library for TensorFlow.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('jax', '0.2.24', versionsuffix), # required by jmp, also provides absl-py +] + +use_pip = True + +exts_list = [ + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + (name, version, { + 'modulename': 'haiku', + 'checksums': ['97752b32cdbe5a3e2d1c60ea884d33eb4b36e7d410000f0d61b571417c925435'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From a5de02e3a32e7a2bad38490f87af3d892093fc29 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 2 Jun 2023 19:27:49 +0200 Subject: [PATCH 7532/9987] Update easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb Co-authored-by: Kenneth Hoste --- .../p/Python/Python-3.11.3-GCCcore-12.3.0.eb | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb index 01c46749a29..2bea26aa47d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb @@ -53,21 +53,6 @@ exts_list = [ ('pip', '23.1.2', { 'checksums': ['0e7c86f486935893c708287b30bd050a36ac827ec7fe5e43fe7cb198dd835fba'], }), - ('distlib', '0.3.6', { - 'checksums': ['14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46'], - }), - ('filelock', '3.12.0', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['ad98852315c2ab702aeb628412cbf7e95b7ce8c3bf9565670b4eaecf1db370a9'], - }), - ('platformdirs', '3.5.1', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['e2378146f1964972c03c085bb5662ae80b2b8c06226c54b2ff4aa9483e8a13a5'], - }), - ('virtualenv', '20.23.0', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['6abec7670e5802a528357fdc75b26b9f57d5d92f29c5462ba0fbe45feacc685e'], - }), ] moduleclass = 'lang' From 824ac13d892347d364e9380b9630dd34b1ac1c51 Mon Sep 17 00:00:00 2001 From: p251204 Date: Fri, 2 Jun 2023 19:29:11 +0200 Subject: [PATCH 7533/9987] adding easyconfigs: GetOrganelle-1.7.7.0-foss-2022a.eb, Bandage-0.9.0-GCCcore-11.3.0.eb --- .../b/Bandage/Bandage-0.9.0-GCCcore-11.3.0.eb | 30 +++++++++++++ .../GetOrganelle-1.7.7.0-foss-2022a.eb | 43 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..264152f103d --- /dev/null +++ b/easybuild/easyconfigs/b/Bandage/Bandage-0.9.0-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'Bandage' +version = '0.9.0' + +homepage = 'http://rrwick.github.io/Bandage' +description = "Bandage is a program for visualising de novo assembly graphs" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/rrwick/Bandage/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['04de8152d8bf5e5aa32b41a63cf1c23e1fee7b67ccd9f1407db8dc2824ca4e30'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Qt5', '5.15.5')] + +prebuildopts = "qmake Bandage.pro && " + +files_to_copy = [(['Bandage'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/Bandage'], + 'dirs': [], +} + +sanity_check_commands = ["Bandage --help && ldd $(which Bandage)"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.0-foss-2022a.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.0-foss-2022a.eb new file mode 100644 index 00000000000..ac60b7bd6f4 --- /dev/null +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.0-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'GetOrganelle' +version = '1.7.7.0' + +homepage = 'https://github.com/Kinggerm/GetOrganelle' +description = """This toolkit assemblies organelle genome from genomic skimming data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/Kinggerm/GetOrganelle/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dd351b5cd33688adfcd8bff9794ae0cc0ce01a572dac2bcf6c9d7db77b3e4883'] + +dependencies = [ + ('Python', '3.10.4'), + ('Bandage', '0.9.0'), + ('SciPy-bundle', '2022.05'), + ('sympy', '1.11.1'), + ('SPAdes', '3.15.5'), + ('Bowtie2', '2.4.5'), + ('BLAST+', '2.13.0'), + ('Perl', '5.34.1'), + ('matplotlib', '3.5.2') +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': False} + +fix_python_shebang_for = ['bin/*.py'] + +sanity_pip_check = True + +sanity_check_commands = ["get_organelle_from_reads.py -h"] + +sanity_check_paths = { + 'files': ['bin/check_annotations.py', 'bin/get_organelle_from_reads.py', 'bin/slim_graph.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 3b5785ccfb24cbdf226ee491bfde9d7c0b06fbe1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 2 Jun 2023 19:44:46 +0200 Subject: [PATCH 7534/9987] use sympy 1.10.1, which is the default for this toolchain --- .../g/GetOrganelle/GetOrganelle-1.7.7.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.0-foss-2022a.eb b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.0-foss-2022a.eb index ac60b7bd6f4..1dee0e28933 100644 --- a/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GetOrganelle/GetOrganelle-1.7.7.0-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.10.4'), ('Bandage', '0.9.0'), ('SciPy-bundle', '2022.05'), - ('sympy', '1.11.1'), + ('sympy', '1.10.1'), ('SPAdes', '3.15.5'), ('Bowtie2', '2.4.5'), ('BLAST+', '2.13.0'), From 9486264cc84572ae401d4c648be4b8e9bedb2600 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 2 Jun 2023 20:05:57 +0000 Subject: [PATCH 7535/9987] adding easyconfigs: BLIS-0.9.0-GCC-12.3.0.eb --- .../b/BLIS/BLIS-0.9.0-GCC-12.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..af82905aa57 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.9.0' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_disable_power9_kernels.patch', + '%(name)s-%(version)s_enable_ppc_autodetect.patch', +] +checksums = [ + '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz + # BLIS-0.9.0_disable_power9_kernels.patch + 'ed7a326bc5c5c21c42faefbec2fd7be609d1c7236981b466475edace39307279', + # BLIS-0.9.0_enable_ppc_autodetect.patch + 'f373fb252c0d14036fb631f048091976cceb02abb3e570a97fbaeac2fbb12328', +] +builddependencies = [ + ('Python', '3.11.3'), + ('Perl', '5.36.0'), +] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' From c89addae34d18bf91af38344e0cd888f7e80da79 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 2 Jun 2023 23:29:10 +0200 Subject: [PATCH 7536/9987] Changed easyblock to JuliaBundle --- .../Circuitscape-5.12.3-Julia-1.7.2.eb | 18 +----------------- 1 file changed, 1 insertion(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb index af5d027ce73..c7d7bc3c47c 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'JuliaBundle' name = 'Circuitscape' version = '5.12.3' @@ -14,13 +14,6 @@ dependencies = [ ('Julia', _julia_ver, '-linux-%s' % ARCH, True), ] -exts_defaultclass = 'JuliaPackage' -exts_filter = ("LD_LIBRARY_PATH="" julia -e 'using %(ext_name)s'", "") -exts_default_options = { - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], -} - - exts_list = [ ('Preferences', '1.3.0', { 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], @@ -406,15 +399,6 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['packages'], -} - sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"Circuitscape\")'"] -modextrapaths = { - 'JULIA_DEPOT_PATH': '', -} - moduleclass = 'lib' From eadef8f729d5a36fa8bf0dcb5058558b1118653a Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 2 Jun 2023 23:52:42 +0000 Subject: [PATCH 7537/9987] Use correct Perl dependency --- easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.3.0.eb index af82905aa57..c481e2a27c4 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.3.0.eb @@ -24,7 +24,7 @@ checksums = [ ] builddependencies = [ ('Python', '3.11.3'), - ('Perl', '5.36.0'), + ('Perl', '5.36.1'), ] configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' From d881c08c18574dfe2441d21cc56b4c76bb78daff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 3 Jun 2023 14:27:57 +0200 Subject: [PATCH 7538/9987] adding easyconfigs: Rust-1.70.0-GCCcore-12.3.0.eb --- .../r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ef47c353d2c --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.70.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.60_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.70.0-src.tar.gz': 'b2bfae000b7a5040e4ec4bbc50a09f21548190cb7570b0ed77358368413bd27c'}, + {'Rust-1.60_sysroot-fix-interpreter.patch': 'b59ed4c2591fc9098277299be21dd6752654f6f193d8652b7d21cb0fa0dd8716'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' From f4379c226595484f6d4e3c7d2470deab08f212f2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 3 Jun 2023 15:05:23 +0200 Subject: [PATCH 7539/9987] Update patch --- .../r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb | 4 +- .../Rust-1.70_sysroot-fix-interpreter.patch | 42 +++++++++++++++++++ 2 files changed, 44 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.70_sysroot-fix-interpreter.patch diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb index ef47c353d2c..5993705b657 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb @@ -11,10 +11,10 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] -patches = ['Rust-1.60_sysroot-fix-interpreter.patch'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] checksums = [ {'rustc-1.70.0-src.tar.gz': 'b2bfae000b7a5040e4ec4bbc50a09f21548190cb7570b0ed77358368413bd27c'}, - {'Rust-1.60_sysroot-fix-interpreter.patch': 'b59ed4c2591fc9098277299be21dd6752654f6f193d8652b7d21cb0fa0dd8716'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '72bffa54837d1a2a117ad63c16deb4078a56a3d9d4f4cbc7430d68dd4cb3effc'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.70_sysroot-fix-interpreter.patch b/easybuild/easyconfigs/r/Rust/Rust-1.70_sysroot-fix-interpreter.patch new file mode 100644 index 00000000000..1abd9d01d6d --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.70_sysroot-fix-interpreter.patch @@ -0,0 +1,42 @@ +Use patchelf to fix interpreter of binaries that are used during Rust bootstrap procedure +when EasyBuild is configured to build in an alternate sysroot + +This fixes problems like due to a clash with the interpreter from the host, and a more recent libc.so.6 that's picked up +from the alternate sysroot: +error: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (required by /tmp/easybuild/build/Rust/1.52.1/GCCcore-10.3.0/rustc-1.52.1-src/build/bootstrap/debug/deps/libproc_macro_error_attr-fbfef320d848b049.so) + +author: Kenneth Hoste (HPC-UGent) +updated by: micketeer@gmail.com + +--- src/bootstrap/bootstrap.py.orig 2023-06-03 14:29:59.905599698 +0200 ++++ src/bootstrap/bootstrap.py 2023-06-03 14:51:45.781307274 +0200 +@@ -481,6 +481,10 @@ + if self._should_fix_bins_and_dylibs is not None: + return self._should_fix_bins_and_dylibs + ++ if os.getenv("EASYBUILD_SYSROOT"): ++ self._should_fix_bins_and_dylibs = True ++ return True ++ + def get_answer(): + default_encoding = sys.getdefaultencoding() + try: +@@ -531,6 +535,18 @@ + assert self._should_fix_bins_and_dylibs is True + print("attempting to patch", fname) + ++ sysroot = os.getenv("EASYBUILD_SYSROOT") ++ if sysroot and not fname.endswith(".so"): ++ # determine patch to interpreter in host via output produced by 'file -b /bin/bash' ++ readelf_out = subprocess.check_output(['readelf', '-l', '/bin/bash']).decode('ascii', 'ignore').strip() ++ regex = re.compile('.*program interpreter: ([^\]]+)', re.M) ++ res = regex.search(readelf_out) ++ interpreter_path = os.path.join(sysroot, res.group(1).lstrip('/')) ++ if not os.path.exists(interpreter_path): ++ raise Exception("Derived path to interpreter does not exist: %s" % interpreter_path) ++ cmd = ["patchelf", "--set-interpreter", interpreter_path, fname] ++ run(cmd, verbose=True) ++ + # Only build `.nix-deps` once. + nix_deps_dir = self.nix_deps_dir + if not nix_deps_dir: From 1b15de766b1eeec81d20699f8f2183501d5896dc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 4 Jun 2023 09:33:08 +0100 Subject: [PATCH 7540/9987] adding easyconfigs: Ninja-1.11.1-GCCcore-12.3.0.eb --- .../n/Ninja/Ninja-1.11.1-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..66ca5673279 --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.11.1' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['31747ae633213f1eda3842686f83c2aa1412e0f5691d1c14dbbcc67fe7400cea'] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.3'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +sanity_check_commands = ["ninja --version"] + +moduleclass = 'tools' From 167ab81e6ff56cf1cc13af707b6b30b1da3100e6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 4 Jun 2023 10:37:07 +0100 Subject: [PATCH 7541/9987] adding easyconfigs: FFTW-3.3.10-GCC-12.3.0.eb --- .../f/FFTW/FFTW-3.3.10-GCC-12.3.0.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.3.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.3.0.eb new file mode 100644 index 00000000000..4cc48a4800b --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.3.0.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +runtest = 'check' + +moduleclass = 'numlib' From 9f7c38987d0774700ff3062829a1dfe21168d3dc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 13:11:34 +0200 Subject: [PATCH 7542/9987] Use ninja --- easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb index 5993705b657..62f7310864c 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb @@ -13,7 +13,7 @@ source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] checksums = [ - {'rustc-1.70.0-src.tar.gz': 'b2bfae000b7a5040e4ec4bbc50a09f21548190cb7570b0ed77358368413bd27c'}, + {'rustc-%(version)s-src.tar.gz': 'b2bfae000b7a5040e4ec4bbc50a09f21548190cb7570b0ed77358368413bd27c'}, {'Rust-1.70_sysroot-fix-interpreter.patch': '72bffa54837d1a2a117ad63c16deb4078a56a3d9d4f4cbc7430d68dd4cb3effc'}, ] @@ -21,6 +21,7 @@ builddependencies = [ ('binutils', '2.40'), ('CMake', '3.26.3'), ('Python', '3.11.3'), + ('Ninja', '1.11.1'), ('pkgconf', '1.9.5'), ] @@ -30,10 +31,6 @@ dependencies = [ configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " -# avoid build dependency on Ninja, which requires Python, -# since Rust is a build dependency for cryptography that is included with Python -configopts += "--set=llvm.ninja=false " - # Use ./x.py to bootstrap so that options like -j N are correctly passed through # see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy # (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) From d96917da958c3a9b1fcc739675cc3cfe91338846 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 4 Jun 2023 14:24:32 +0200 Subject: [PATCH 7543/9987] fix sysroot patch for Rust 1.70.0 --- .../r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb | 4 +-- .../Rust-1.70_sysroot-fix-interpreter.patch | 30 ++++++++++--------- 2 files changed, 18 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb index 62f7310864c..2d73f5a4efa 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb @@ -13,8 +13,8 @@ source_urls = ['https://static.rust-lang.org/dist/'] sources = ['rustc-%(version)s-src.tar.gz'] patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] checksums = [ - {'rustc-%(version)s-src.tar.gz': 'b2bfae000b7a5040e4ec4bbc50a09f21548190cb7570b0ed77358368413bd27c'}, - {'Rust-1.70_sysroot-fix-interpreter.patch': '72bffa54837d1a2a117ad63c16deb4078a56a3d9d4f4cbc7430d68dd4cb3effc'}, + {'rustc-1.70.0-src.tar.gz': 'b2bfae000b7a5040e4ec4bbc50a09f21548190cb7570b0ed77358368413bd27c'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.70_sysroot-fix-interpreter.patch b/easybuild/easyconfigs/r/Rust/Rust-1.70_sysroot-fix-interpreter.patch index 1abd9d01d6d..a5e3d50eb2b 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.70_sysroot-fix-interpreter.patch +++ b/easybuild/easyconfigs/r/Rust/Rust-1.70_sysroot-fix-interpreter.patch @@ -8,8 +8,8 @@ error: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (required author: Kenneth Hoste (HPC-UGent) updated by: micketeer@gmail.com ---- src/bootstrap/bootstrap.py.orig 2023-06-03 14:29:59.905599698 +0200 -+++ src/bootstrap/bootstrap.py 2023-06-03 14:51:45.781307274 +0200 +--- rustc-1.70.0-src.orig/src/bootstrap/bootstrap.py 2023-05-31 21:28:10.000000000 +0200 ++++ rustc-1.70.0-src/src/bootstrap/bootstrap.py 2023-06-04 14:15:39.784929373 +0200 @@ -481,6 +481,10 @@ if self._should_fix_bins_and_dylibs is not None: return self._should_fix_bins_and_dylibs @@ -21,21 +21,23 @@ updated by: micketeer@gmail.com def get_answer(): default_encoding = sys.getdefaultencoding() try: -@@ -531,6 +535,18 @@ +@@ -531,6 +535,20 @@ assert self._should_fix_bins_and_dylibs is True print("attempting to patch", fname) -+ sysroot = os.getenv("EASYBUILD_SYSROOT") -+ if sysroot and not fname.endswith(".so"): -+ # determine patch to interpreter in host via output produced by 'file -b /bin/bash' -+ readelf_out = subprocess.check_output(['readelf', '-l', '/bin/bash']).decode('ascii', 'ignore').strip() -+ regex = re.compile('.*program interpreter: ([^\]]+)', re.M) -+ res = regex.search(readelf_out) -+ interpreter_path = os.path.join(sysroot, res.group(1).lstrip('/')) -+ if not os.path.exists(interpreter_path): -+ raise Exception("Derived path to interpreter does not exist: %s" % interpreter_path) -+ cmd = ["patchelf", "--set-interpreter", interpreter_path, fname] -+ run(cmd, verbose=True) ++ easybuild_sysroot = os.getenv("EASYBUILD_SYSROOT") ++ if easybuild_sysroot: ++ if not fname.endswith(".so"): ++ # determine patch to interpreter in host via output produced by 'readelf -l /bin/bash' ++ readelf_out = subprocess.check_output(['readelf', '-l', '/bin/bash']).decode('ascii', 'ignore').strip() ++ regex = re.compile('.*program interpreter: ([^\]]+)', re.M) ++ res = regex.search(readelf_out) ++ interpreter_path = os.path.join(easybuild_sysroot, res.group(1).lstrip('/')) ++ if not os.path.exists(interpreter_path): ++ raise Exception("Derived path to interpreter does not exist: %s" % interpreter_path) ++ cmd = ["patchelf", "--set-interpreter", interpreter_path, fname] ++ run(cmd, verbose=True) ++ return + # Only build `.nix-deps` once. nix_deps_dir = self.nix_deps_dir From 09867c54131a0eb4340fa12d939fbb977b909c8f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 14:45:32 +0200 Subject: [PATCH 7544/9987] adding easyconfigs: GMP-6.2.1-GCCcore-12.3.0.eb, GSL-2.7-GCCcore-12.3.0.eb, MPFR-4.2.0-GCCcore-12.3.0.eb --- .../g/GMP/GMP-6.2.1-GCCcore-12.3.0.eb | 40 +++++++++++++++++++ .../g/GSL/GSL-2.7-GCCcore-12.3.0.eb | 29 ++++++++++++++ .../m/MPFR/MPFR-4.2.0-GCCcore-12.3.0.eb | 39 ++++++++++++++++++ 3 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-4.2.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..15f01302836 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.2.1' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +# copy libgmp.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9f94ed4cf46 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.7' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.2.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4016fc31b80 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.2.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '4.2.0' + +homepage = 'https://www.mpfr.org' + +description = """ + The MPFR library is a C library for multiple-precision floating-point + computations with correct rounding. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['691db39178e36fc460c046591e4b0f2a52c8f2b3ee6d750cc2eab25f1eaa999d'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +runtest = 'check' + +# copy libmpfr.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a src/.libs/libmpfr.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' From 9227337b4f0bd8765865416405f726e8c1e43460 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 14:49:51 +0200 Subject: [PATCH 7545/9987] adding easyconfigs: Meson-1.1.1-GCCcore-12.3.0.eb, xorg-macros-1.20.0-GCCcore-12.3.0.eb --- .../m/Meson/Meson-1.1.1-GCCcore-12.3.0.eb | 36 +++++++++++++++++++ .../xorg-macros-1.20.0-GCCcore-12.3.0.eb | 27 ++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-1.1.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-1.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Meson/Meson-1.1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8f653ab16a1 --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-1.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '1.1.1' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d04b541f97ca439fb82fab7d0d480988be4bd4e62563a5ca35fadb5400727b1c'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), # includes required 'wheel' package + ('Ninja', '1.11.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["meson --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3750322b9f2 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.20.0' + +homepage = 'https://gitlab.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['8205d210a580da0938f5ce4392a96b60cf1d9a5f792eaa1474fa4c1977aef4d0'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From 2f8ecfa8d57557cd33b80672fb473bb5ddd50910 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 14:52:06 +0200 Subject: [PATCH 7546/9987] Fix checksum in xorg-macros --- .../x/xorg-macros/xorg-macros-1.20.0-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-12.3.0.eb index 3750322b9f2..0354254573f 100644 --- a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-12.3.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] sources = ['macros-util-macros-%(version)s.tar.gz'] -checksums = ['8205d210a580da0938f5ce4392a96b60cf1d9a5f792eaa1474fa4c1977aef4d0'] +checksums = ['efd8eefab568981e47dd64d3e9b5ee2b7165a30d4feca105770f249f9b59979c'] builddependencies = [ ('binutils', '2.40'), From 157f0f8110974502fb4f9aae9fb8989ecd1dc33a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 15:22:15 +0200 Subject: [PATCH 7547/9987] adding easyconfigs: hwloc-2.9.1-GCCcore-12.3.0.eb, libpciaccess-0.17-GCCcore-12.3.0.eb --- .../h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb | 45 +++++++++++++++++++ .../libpciaccess-0.17-GCCcore-12.3.0.eb | 26 +++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0d8d703db3b --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.9.1' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['20b2bd4df436827d8e50f7afeafb6f967259f2fb374ce7330244f8d0ed2dde6f'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('numactl', '2.0.16'), + ('libxml2', '2.11.4'), + ('libpciaccess', '0.17'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fd12768ece2 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.17' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bf6985a77d2ecb00e2c79da3edfb26b909178ffca3f2e9d14ed0620259ab733b'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('xorg-macros', '1.20.0'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' From 2c1347589d6399c53e7559dc6a69b526aa28eb82 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 15:26:49 +0200 Subject: [PATCH 7548/9987] Fix hwloc checksum --- easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb index 0d8d703db3b..f3d054d78d2 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb @@ -20,7 +20,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] sources = [SOURCE_TAR_GZ] -checksums = ['20b2bd4df436827d8e50f7afeafb6f967259f2fb374ce7330244f8d0ed2dde6f'] +checksums = ['a440e2299f7451dc10a57ddbfa3f116c2a6c4be1bb97c663edd3b9c7b3b3b4cf'] builddependencies = [ ('binutils', '2.40'), From d8afdd5ad49af3fe551e40b474feb6b7faf722b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 15:28:46 +0200 Subject: [PATCH 7549/9987] adding easyconfigs: util-linux-2.39-GCCcore-12.3.0.eb --- .../util-linux-2.39-GCCcore-12.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..65988d47494 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.39' + +homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b1f597ad172a2ee17b0a7ae4be7ab7e1b1a6f9394ddbd3d8ec90ae4ed7333579'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), +] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' From eedc385de499ca4a71d81f341161ce4bd39ce9d1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 4 Jun 2023 15:43:07 +0200 Subject: [PATCH 7550/9987] Update json-fortran toolchains to reflect creation of fortran modules --- ....0.eb => json-fortran-8.3.0-GCC-10.2.0.eb} | 5 +-- ....0.eb => json-fortran-8.3.0-GCC-12.2.0.eb} | 5 +-- .../json-fortran-8.3.0-iccifort-2020.4.304.eb | 34 +++++++++++++++++++ ...-fortran-8.3.0-intel-compilers-2022.2.1.eb | 34 +++++++++++++++++++ 4 files changed, 74 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/j/json-fortran/{json-fortran-8.3.0-GCCcore-10.2.0.eb => json-fortran-8.3.0-GCC-10.2.0.eb} (84%) rename easybuild/easyconfigs/j/json-fortran/{json-fortran-8.3.0-GCCcore-12.2.0.eb => json-fortran-8.3.0-GCC-12.2.0.eb} (84%) create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-10.2.0.eb similarity index 84% rename from easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb rename to easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-10.2.0.eb index 30199cec525..fdd554d13d3 100644 --- a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-10.2.0.eb @@ -8,7 +8,7 @@ version = '8.3.0' homepage = 'https://github.com/jacobwilliams/json-fortran' description = "JSON-Fortran: A Modern Fortran JSON API" -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] sources = ['%(version)s.tar.gz'] @@ -26,7 +26,8 @@ configopts = [ runtest = 'check' sanity_check_paths = { - 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-12.2.0.eb similarity index 84% rename from easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-12.2.0.eb index c2755034346..6ce6846cfe3 100644 --- a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCC-12.2.0.eb @@ -8,7 +8,7 @@ version = '8.3.0' homepage = 'https://github.com/jacobwilliams/json-fortran' description = "JSON-Fortran: A Modern Fortran JSON API" -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchain = {'name': 'GCC', 'version': '12.2.0'} source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] sources = ['%(version)s.tar.gz'] @@ -26,7 +26,8 @@ configopts = [ runtest = 'check' sanity_check_paths = { - 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb new file mode 100644 index 00000000000..074e64ca5ca --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-iccifort-2020.4.304.eb @@ -0,0 +1,34 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'iccifort', 'version': '2020.4.304'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.20.1'), +] + +configopts = [ + '-DUSE_GNU_INSTALL_CONVENTION=TRUE', +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..36775cb2724 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.2.1.eb @@ -0,0 +1,34 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = [ + '-DUSE_GNU_INSTALL_CONVENTION=TRUE', +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 3ab6b2b383a9b60ce2b7980943038cb30ee1a1a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 15:43:30 +0200 Subject: [PATCH 7551/9987] adding easyconfigs: Yasm-1.3.0-GCCcore-12.3.0.eb, yaml-cpp-0.7.0-GCCcore-12.3.0.eb, Xerces-C++-3.2.4-GCCcore-12.3.0.eb, lxml-4.9.2-GCCcore-12.3.0.eb, PyYAML-6.0-GCCcore-12.3.0.eb --- .../l/lxml/lxml-4.9.2-GCCcore-12.3.0.eb | 26 +++++++++++++ .../p/PyYAML/PyYAML-6.0-GCCcore-12.3.0.eb | 27 +++++++++++++ .../Xerces-C++-3.2.4-GCCcore-12.3.0.eb | 39 +++++++++++++++++++ .../y/Yasm/Yasm-1.3.0-GCCcore-12.3.0.eb | 24 ++++++++++++ .../yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.3.0.eb | 30 ++++++++++++++ 5 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8584189eb55 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '4.9.2' + +homepage = 'https://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2455cfaeb7ac70338b3257f41e21f0724f4b5b0c0e7702da67ee6c3640835b67'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('libxml2', '2.11.4'), + ('libxslt', '1.1.38'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a1f8e4ff4f6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '6.0' + +homepage = 'https://github.com/yaml/pyyaml' +description = "PyYAML is a YAML parser and emitter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('libyaml', '0.2.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'yaml'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8953e54f312 --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Xerces-C++' +version = '3.2.4' + +homepage = 'https://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['3d8ec1c7f94e38fee0e4ca5ad1e1d9db23cbf3a10bba626f6b4afa2dedafe5ab'] + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('cURL', '8.0.1'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/XInclude', + 'include/xercesc/xinclude/XIncludeUtils.hpp', + 'lib/libxerces-c-3.2.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7dcaaf0ef67 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'https://www.tortall.net/projects/yasm/' +description = "Yasm: Complete rewrite of the NASM assembler with BSD license" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..45bef4248fe --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' +name = 'yaml-cpp' +version = '0.7.0' + +homepage = "https://github.com/jbeder/yaml-cpp" +description = """yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/jbeder/%(name)s/archive/'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-cmake-export.patch'] +checksums = [ + '43e6a9fcb146ad871515f0d0873947e5d497a1c9c60c58cb102a97b47208b7c3', + 'c562a575bbb161af478795e43bfd9073e3f874bea07134a321c1063cd7098c1c', # yaml-cpp-0.7.0_fix-cmake-export.patch +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3') +] + +sanity_check_paths = { + 'files': ['lib/libyaml-cpp.a', 'include/yaml-cpp/yaml.h'], + 'dirs': ['lib', 'include'], +} + +moduleclass = 'tools' From b72af34c0cb6fefea61ff9cdef489fd9ebde1f78 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 15:45:28 +0200 Subject: [PATCH 7552/9987] adding easyconfigs: libfabric-1.18.0-GCCcore-12.3.0.eb --- .../libfabric-1.18.0-GCCcore-12.3.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ebd850639eb --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.18.0' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +# The psm3 provider (enabled by default) requires an AVX capable system to run +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ofiwg/libfabric/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +patches = [ + '%(name)s-1.12.1_disable-psm3-avx-config.patch', +] +checksums = [ + {'libfabric-1.18.0.tar.bz2': '912fb7c7b3cf2a91140520962b004a1c5d2f39184adbbd98ae5919b0178afd43'}, + {'libfabric-1.12.1_disable-psm3-avx-config.patch': + '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('numactl', '2.0.16'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# Regenerate build files to pick up psm3-axv-config patch +preconfigopts = "./autogen.sh &&" + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) +configopts += "--disable-usnic " + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' From f6b9608fc7016da8937697142ccdec73f53a0234 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 15:55:08 +0200 Subject: [PATCH 7553/9987] Include waitpid fix --- .../util-linux-2.39-GCCcore-12.3.0.eb | 6 ++- .../util-linux-2.39_fix_waitpid.patch | 43 +++++++++++++++++++ 2 files changed, 48 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.39_fix_waitpid.patch diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb index 65988d47494..5deb9258ddc 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb @@ -12,7 +12,11 @@ toolchainopts = {'pic': True} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -checksums = ['b1f597ad172a2ee17b0a7ae4be7ab7e1b1a6f9394ddbd3d8ec90ae4ed7333579'] +patches = ['util-linux-%(version)s_fix_waitpid.patch'] +checksums = [ + {'util-linux-2.39.tar.gz': 'b1f597ad172a2ee17b0a7ae4be7ab7e1b1a6f9394ddbd3d8ec90ae4ed7333579'}, + {'util-linux-2.39_fix_waitpid.patch': '99cbd4ee8293f3ffad4467e9f245d0da4e10a98b6599f5e5f9d4cb99c7eebbd2'}, +] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.39_fix_waitpid.patch b/easybuild/easyconfigs/u/util-linux/util-linux-2.39_fix_waitpid.patch new file mode 100644 index 00000000000..8b423607226 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.39_fix_waitpid.patch @@ -0,0 +1,43 @@ +From ffdd75cceedafac3ba7a80b86e1b103c383b260e Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Thomas=20Wei=C3=9Fschuh?= +Date: Mon, 22 May 2023 18:24:47 +0200 +Subject: [PATCH] waitpid: only build when pidfd_open is available +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +Fixes #2256 + +[kzak@redhat.com: - fix UL_BUILD_INIT() use] + +Signed-off-by: Thomas Weißschuh +Signed-off-by: Karel Zak +--- + configure.ac | 1 + + meson.build | 1 + + 2 files changed, 2 insertions(+) + +diff --git a/configure.ac b/configure.ac +index dfdcdbdce8..1f6158e7f7 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -1856,6 +1856,7 @@ AC_ARG_ENABLE([waitpid], + ) + UL_BUILD_INIT([waitpid]) + UL_REQUIRES_LINUX([waitpid]) ++UL_REQUIRES_SYSCALL_CHECK([waitpid], [UL_CHECK_SYSCALL([pidfd_open])], [pidfd_open]) + AM_CONDITIONAL([BUILD_WAITPID], [test "x$build_waitpid" = xyes]) + + UL_BUILD_INIT([enosys], [check]) +diff --git a/meson.build b/meson.build +index 3783a5be98..029f93cf49 100644 +--- a/meson.build ++++ b/meson.build +@@ -2848,6 +2848,7 @@ if not is_disabler(exe) + bashcompletions += ['fadvise'] + endif + ++# XXX: HAVE_PIDFD_OPEN + exe = executable( + 'waitpid', + waitpid_sources, From d6be64dc99bc4fa00d5fe817a88ba889064aad00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 16:05:36 +0200 Subject: [PATCH 7554/9987] Update patch for 1.18.0 --- .../libfabric-1.18.0-GCCcore-12.3.0.eb | 6 +- ...abric-1.18.0_disable-psm3-avx-config.patch | 90 +++++++++++++++++++ 2 files changed, 93 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.18.0_disable-psm3-avx-config.patch diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb index ebd850639eb..a0acd145b4c 100644 --- a/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0-GCCcore-12.3.0.eb @@ -18,12 +18,12 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/ofiwg/libfabric/releases/download/v%(version)s'] sources = [SOURCE_TAR_BZ2] patches = [ - '%(name)s-1.12.1_disable-psm3-avx-config.patch', + '%(name)s-%(version)s_disable-psm3-avx-config.patch', ] checksums = [ {'libfabric-1.18.0.tar.bz2': '912fb7c7b3cf2a91140520962b004a1c5d2f39184adbbd98ae5919b0178afd43'}, - {'libfabric-1.12.1_disable-psm3-avx-config.patch': - '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a'}, + {'libfabric-1.18.0_disable-psm3-avx-config.patch': + '79db0bfe759d65ef68301701e0842f1e8dcd4ace8bfc5bca8f7c8846501a67cb'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0_disable-psm3-avx-config.patch b/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0_disable-psm3-avx-config.patch new file mode 100644 index 00000000000..a9492c6f059 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.18.0_disable-psm3-avx-config.patch @@ -0,0 +1,90 @@ +The AVX/AVX2 detection seems to be based on compiler instead of CPU capabilities +which can lead to broken binaries as result of the build (eg AVX2 binaries in Intel IvyBridge) +Completetly disable this detection as it is already set by EasyBuild +author: Alex Domingo (Vrije Universiteit Brussel) +--- prov/psm3/configure.m4.orig 2023-06-04 15:45:48.900664549 +0200 ++++ prov/psm3/configure.m4 2023-06-04 16:00:11.300135166 +0200 +@@ -134,45 +134,45 @@ + ]) + CFLAGS=$save_CFLAGS + +- AC_MSG_CHECKING([for -mavx support]) +- save_CFLAGS=$CFLAGS +- CFLAGS="$PSM3_STRIP_OPTFLAGS -mavx -O0" +- AC_LINK_IFELSE( +- [AC_LANG_PROGRAM( +- [[#include ]], +- [[unsigned long long _a[4] = {1ULL,2ULL,3ULL,4ULL}; +- __m256i vA = _mm256_loadu_si256((__m256i *)_a); +- __m256i vB; +- _mm256_store_si256(&vB, vA); +- return 0;]]) +- ],[ +- AC_MSG_RESULT([yes]) +- PSM3_ARCH_CFLAGS="-mavx" +- ],[ +- psm3_happy=0 +- AC_MSG_RESULT([no]) +- AC_MSG_NOTICE([psm3 requires minimum of avx instruction set to build]) +- ]) +- CFLAGS=$save_CFLAGS ++dnl AC_MSG_CHECKING([for -mavx support]) ++dnl save_CFLAGS=$CFLAGS ++dnl CFLAGS="$PSM3_STRIP_OPTFLAGS -mavx -O0" ++dnl AC_LINK_IFELSE( ++dnl [AC_LANG_PROGRAM( ++dnl [[#include ]], ++dnl [[unsigned long long _a[4] = {1ULL,2ULL,3ULL,4ULL}; ++dnl __m256i vA = _mm256_loadu_si256((__m256i *)_a); ++dnl __m256i vB; ++dnl _mm256_store_si256(&vB, vA); ++dnl return 0;]]) ++dnl ],[ ++dnl AC_MSG_RESULT([yes]) ++dnl PSM3_ARCH_CFLAGS="-mavx" ++dnl ],[ ++dnl psm3_happy=0 ++dnl AC_MSG_RESULT([no]) ++dnl AC_MSG_NOTICE([psm3 requires minimum of avx instruction set to build]) ++dnl ]) ++dnl CFLAGS=$save_CFLAGS + +- AC_MSG_CHECKING([for -mavx2 support]) +- save_CFLAGS=$CFLAGS +- CFLAGS="$PSM3_STRIP_OPTFLAGS -mavx2 -O0" +- AC_LINK_IFELSE( +- [AC_LANG_PROGRAM( +- [[#include ]], +- [[unsigned long long _a[4] = {1ULL,2ULL,3ULL,4ULL}; +- __m256i vA = _mm256_loadu_si256((__m256i *)_a); +- __m256i vB = _mm256_add_epi64(vA, vA); +- (void)vB; +- return 0;]]) +- ],[ +- AC_MSG_RESULT([yes]) +- PSM3_ARCH_CFLAGS="-mavx2" +- ],[ +- AC_MSG_RESULT([no]) +- ]) +- CFLAGS=$save_CFLAGS ++dnl AC_MSG_CHECKING([for -mavx2 support]) ++dnl save_CFLAGS=$CFLAGS ++dnl CFLAGS="$PSM3_STRIP_OPTFLAGS -mavx2 -O0" ++dnl AC_LINK_IFELSE( ++dnl [AC_LANG_PROGRAM( ++dnl [[#include ]], ++dnl [[unsigned long long _a[4] = {1ULL,2ULL,3ULL,4ULL}; ++dnl __m256i vA = _mm256_loadu_si256((__m256i *)_a); ++dnl __m256i vB = _mm256_add_epi64(vA, vA); ++dnl (void)vB; ++dnl return 0;]]) ++dnl ],[ ++dnl AC_MSG_RESULT([yes]) ++dnl PSM3_ARCH_CFLAGS="-mavx2" ++dnl ],[ ++dnl AC_MSG_RESULT([no]) ++dnl ]) ++dnl CFLAGS=$save_CFLAGS + + AC_PROG_GREP() + From 09adfaf5c21e9ec33417faf24cbe7a0c2a3c7b59 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 16:08:04 +0200 Subject: [PATCH 7555/9987] adding easyconfigs: UCX-1.14.1-GCCcore-12.3.0.eb --- .../u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0b912f993c8 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.14.1' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', + 'UCX-1.13.1_fix-undeclared-PTR.patch', +] +checksums = [ + {'ucx-1.14.1.tar.gz': 'baa0634cafb269a3112f626eb226bcd2ca8c9fcf0fec3b8e2a3553baad5f77aa'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, + {'UCX-1.13.1_fix-undeclared-PTR.patch': 'ef22c29604552ad3223f2a6bac352f30023cc5cf68f786abfdc4ad7c04189a76'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.5'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.13'), + ('numactl', '2.0.16'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From effb09733c7267a0abaabd77f16747c50ebf43fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 16:13:36 +0200 Subject: [PATCH 7556/9987] Include autotools for patch --- .../u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb index 5deb9258ddc..d3da3633cd4 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb @@ -18,7 +18,10 @@ checksums = [ {'util-linux-2.39_fix_waitpid.patch': '99cbd4ee8293f3ffad4467e9f245d0da4e10a98b6599f5e5f9d4cb99c7eebbd2'}, ] -builddependencies = [('binutils', '2.40')] +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), # for fix_waitpid patch +] dependencies = [ ('ncurses', '6.4'), From 94aacedc0bb0b7b5e15fe2d0233ca4885f61ee6f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 16:21:02 +0200 Subject: [PATCH 7557/9987] Drop fixed patch --- easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb index 0b912f993c8..0d862216f7a 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb @@ -16,12 +16,10 @@ source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.gz'] patches = [ 'UCX-1.13.1-dynamic_modules.patch', - 'UCX-1.13.1_fix-undeclared-PTR.patch', ] checksums = [ {'ucx-1.14.1.tar.gz': 'baa0634cafb269a3112f626eb226bcd2ca8c9fcf0fec3b8e2a3553baad5f77aa'}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, - {'UCX-1.13.1_fix-undeclared-PTR.patch': 'ef22c29604552ad3223f2a6bac352f30023cc5cf68f786abfdc4ad7c04189a76'}, ] builddependencies = [ From 1d6b2ef51b27823d7656847f92da42532d10d50f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 16:21:55 +0200 Subject: [PATCH 7558/9987] Also include pkgconf for patch --- .../easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb index d3da3633cd4..f3bc453a771 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb @@ -21,6 +21,7 @@ checksums = [ builddependencies = [ ('binutils', '2.40'), ('Autotools', '20220317'), # for fix_waitpid patch + ('pkgconf', '1.9.5'), # for fix_waitpid patch ] dependencies = [ From 232035baa594ff00bfabe839eccf6f4b9a551579 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 17:45:44 +0200 Subject: [PATCH 7559/9987] adding easyconfigs: X11-20221110-GCCcore-12.3.0.eb, gperf-3.1-GCCcore-12.3.0.eb, intltool-0.51.0-GCCcore-12.3.0.eb, freetype-2.13.0-GCCcore-12.3.0.eb, fontconfig-2.14.2-GCCcore-12.3.0.eb --- .../fontconfig-2.14.2-GCCcore-12.3.0.eb | 40 ++++ .../freetype-2.13.0-GCCcore-12.3.0.eb | 43 ++++ .../g/gperf/gperf-3.1-GCCcore-12.3.0.eb | 32 +++ .../intltool-0.51.0-GCCcore-12.3.0.eb | 37 +++ .../x/X11/X11-20221110-GCCcore-12.3.0.eb | 214 ++++++++++++++++++ 5 files changed, 366 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.13.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8e0aff02c97 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.2-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.14.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3ba2dd92158718acec5caaf1a716043b5aa055c27b081d914af3ccb40dce8a55'] + +builddependencies = [ + ('binutils', '2.40'), + ('gperf', '3.1'), + ('pkgconf', '1.9.5'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('expat', '2.5.0'), + ('freetype', '2.13.0'), + ('util-linux', '2.39'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.13.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.13.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7dc1c7cfa62 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.13.0-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +name = 'freetype' +version = '2.13.0' + +homepage = 'https://www.freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + GNU_SAVANNAH_SOURCE, + SOURCEFORGE_SOURCE, +] +sources = [SOURCE_TAR_GZ] +checksums = ['a7aca0e532a276ea8d85bd31149f0a74c33d19c8d287116ef8f5f8357b4f1f80'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('Brotli', '1.0.9'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +sanity_check_commands = ["freetype-config --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..72563a3b1cd --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'https://www.gnu.org/software/gperf/' +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [], +} + +sanity_check_commands = ["gperf --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4e0a8b32b26 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Perl-bundle-CPAN', '5.36.1'), +] + +fix_perl_shebang_for = ['bin/intltool-*'] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +sanity_check_commands = ["intltool-merge --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0b789d1f854 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.3.0.eb @@ -0,0 +1,214 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20221110' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('Bison', '3.8.2'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.5'), + ('intltool', '0.51.0'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.14.2'), + ('freetype', '2.13.0'), + ('zlib', '1.2.13'), + ('xorg-macros', '1.20.0'), + ('libpciaccess', '0.17'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libpthread-stubs', '0.4', { # 2017-03-14 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('xorgproto', '2022.2', { # 2022-08-11 + 'checksums': ['da351a403d07a7006d7bdc8dcfc14ddc1b588b38fb81adab9989a8eef605757b'], + }), + ('libXau', '1.0.11', { # 2022-12-08 + 'checksums': ['51a54da42475d4572a0b59979ec107c27dacf6c687c2b7b04e5cf989a7c7e60c'], + }), + ('libXdmcp', '1.1.4', { # 2022-11-19 + 'checksums': ['2ef9653d32e09d1bf1b837d0e0311024979653fe755ad3aaada8db1aa6ea180c'], + }), + ('xcb-proto', '1.15.2', { # 2022-06-17 + 'checksums': ['6b1ed9cd7cf35e37913eeecca37e5b85b14903002942b3e332f321335c27a8eb'], + }), + ('libxcb', '1.15', { # 2022-05-03 + 'checksums': ['1cb65df8543a69ec0555ac696123ee386321dfac1964a3da39976c9a05ad724d'], + }), + ('xtrans', '1.5.0', { # 2023-06-03 + 'checksums': ['48ed850ce772fef1b44ca23639b0a57e38884045ed2cbb18ab137ef33ec713f9'], + }), + ('libxkbcommon', '1.5.0', { # 2023-01-02 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['943c07a1e2198026d8102b17270a1f406e4d3d6bbc4ae105b9e1b82d7d136b39'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.8.5', { # 2023-06-01 + 'checksums': ['f1bc56187bee0f830e1179ac5068ac93b78c51ace94eb27702ffb2efd116587b'], + }), + ('libXext', '1.3.5', { # 2022-10-29 + 'checksums': ['1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'], + }), + ('libFS', '1.0.9', { # 2022-08-26 + 'checksums': ['8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'], + }), + ('libICE', '1.1.1', { # 2022-12-08 + 'checksums': ['1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d'], + }), + ('libSM', '1.2.4', { # 2022-12-20 + 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], + }), + ('libXScrnSaver', '1.2.4', { # 2022-12-05 + 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], + }), + ('libXt', '1.3.0', { # 2023-05-09 + 'checksums': ['6da1bfa9dd0ed87430a5ce95b129485086394df308998ebe34d98e378e3dfb33'], + }), + ('libXmu', '1.1.4', { # 2022-10-17 + 'checksums': ['3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'], + }), + ('libXpm', '3.5.16', { # 2023-04-17 + 'checksums': ['e3dfb0fb8c1f127432f2a498c7856b37ce78a61e8da73f1aab165a73dd97ad00'], + }), + ('libXaw', '1.0.15', { # 2023-03-16 + 'checksums': ['59cfed2712cc80bbfe62dd1aacf24f58d74a76dd08329a922077b134a8d8048f'], + }), + ('libXfixes', '6.0.1', { # 2023-04-09 + 'checksums': ['82045da5625350838390c9440598b90d69c882c324ca92f73af9f0e992cb57c7'], + }), + ('libXcomposite', '0.4.6', { # 2022-12-04 + 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], + }), + ('libXrender', '0.9.11', { # 2022-10-22 + 'checksums': ['6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'], + }), + ('libXcursor', '1.2.1', { # 2022-04-03 + 'checksums': ['77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'], + }), + ('libXdamage', '1.1.6', { # 2022-12-04 + 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], + }), + ('libfontenc', '1.1.7', { # 2022-12-08 + 'checksums': ['c103543a47ce5c0200fb1867f32df5e754a7c3ef575bf1fe72187117eac22a53'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.6', { # 2022-08-26 + 'checksums': ['a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'], + }), + ('libXft', '2.3.8', { # 2023-04-17 + 'checksums': ['b7e59f69e0bbabe9438088775f7e5a7c16a572e58b11f9722519385d38192df5'], + }), + ('libXi', '1.8.1', { # 2023-05-04 + 'checksums': ['c80fd200a1190e4406bb4cc6958839d9651638cb47fa546a595d4bebcd3b9e2d'], + }), + ('libXinerama', '1.1.5', { # 2022-10-29 + 'checksums': ['2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'], + }), + ('libXrandr', '1.5.3', { # 2022-11-20 + 'checksums': ['3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e'], + }), + ('libXres', '1.2.2', { # 2022-12-05 + 'checksums': ['918fb33c3897b389a1fbb51571c5c04c6b297058df286d8b48faa5af85e88bcc'], + }), + ('libXtst', '1.2.4', { # 2022-09-27 + 'checksums': ['01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'], + }), + ('libXv', '1.0.12', { # 2022-12-05 + 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], + }), + ('libXvMC', '1.0.13', { # 2022-03-22 + 'checksums': ['e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'], + }), + ('libXxf86dga', '1.1.6', { # 2022-12-05 + 'checksums': ['715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69'], + }), + ('libXxf86vm', '1.1.5', { # 2022-09-27 + 'checksums': ['f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'], + }), + ('libdmx', '1.1.5', { # 2023-06-03 + 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], + }), + ('libxkbfile', '1.1.2', { # 2022-12-08 + 'checksums': ['87faee6d4873c5631e8bb53e85134084b862185da682de8617f08ca18d82e216'], + }), + ('libxshmfence', '1.3.2', { # 2022-12-08 + 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], + }), + ('xcb-util', '0.4.0', { # 2014-10-15 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.1', { # 2022-10-18 + 'checksums': ['0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'], + }), + ('xcb-util-keysyms', '0.4.1', { # 2022-10-19 + 'checksums': ['1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'], + }), + ('xcb-util-renderutil', '0.3.10', { # 2022-10-19 + 'checksums': ['e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'], + }), + ('xcb-util-wm', '0.4.2', { # 2022-10-19 + 'checksums': ['dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'], + }), + ('xcb-util-cursor', '0.1.4', { # 2022-10-18 + 'checksums': ['cc8608ebb695742b6cf84712be29b2b66aa5f6768039528794fca0fa283022bf'], + }), + ('xkeyboard-config', '2.38', { # 2022-02-04 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['eb1383a5ac4b6210d7c7302b9d6fab052abdf51c5d2c9b55f1f779997ba68c6c'], + # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing + 'preconfigopts': '', + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.4', { # 2022-09-12 + 'checksums': ['05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'], + }), + ('xbitmaps', '1.1.3', { # 2023-02-23 + 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' From 1912a59ba71f4da2136737f109a4fb30d3476dd6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Jun 2023 17:48:34 +0200 Subject: [PATCH 7560/9987] Fix version string in X11 --- ...0221110-GCCcore-12.3.0.eb => X11-20230603-GCCcore-12.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/x/X11/{X11-20221110-GCCcore-12.3.0.eb => X11-20230603-GCCcore-12.3.0.eb} (99%) diff --git a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20230603-GCCcore-12.3.0.eb similarity index 99% rename from easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/x/X11/X11-20230603-GCCcore-12.3.0.eb index 0b789d1f854..dac22500934 100644 --- a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20230603-GCCcore-12.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'X11' -version = '20221110' +version = '20230603' homepage = 'https://www.x.org' description = "The X Window System (X11) is a windowing system for bitmap displays" From db912e9e1828ead9c02a84e2a3eb5ef7051cbb19 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 08:45:33 +0200 Subject: [PATCH 7561/9987] adding easyconfigs: GLIMPSE-2.0.0-GCC-11.3.0.eb --- .../g/GLIMPSE/GLIMPSE-2.0.0-GCC-11.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..dffbd942f4f --- /dev/null +++ b/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-11.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'MakeCp' + +name = 'GLIMPSE' +version = '2.0.0' + +homepage = 'https://github.com/odelaneau/GLIMPSE' +description = "GLIMPSE2 is a set of tools for phasing and imputation for low-coverage sequencing datasets" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/odelaneau/GLIMPSE/archive/'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/odelaneau/', + 'repo_name': 'GLIMPSE', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, +}] +checksums = [None] + +builddependencies = [ + ('git', '2.36.0', '-nodocs'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('bzip2', '1.0.8'), + ('cURL', '7.83.0'), + ('HTSlib', '1.15.1'), + ('XZ', '5.2.5'), + ('zlib', '1.2.12'), +] + +prebuildopts = 'ls */makefile | xargs sed -i "s/^CXXFLAG=.*/CXXFLAG=${CXXFLAGS}/g" && ' +prebuildopts += 'ls */makefile | xargs sed -i "s/^LDFLAG=.*/LDFLAG=${CXXFLAGS}/g" && ' +buildopts = 'CXX="$CXX" HTSSRC=${EBROOTHTSLIB} HTSLIB_LIB="-lhts -lcurl" BOOST_INC=$EBROOTBOOST/include ' +buildopts += 'BOOST_LIB_IO="-lboost_iostreams" BOOST_LIB_PO="-lboost_program_options" ' +buildopts += 'BOOST_LIB_SE="-lboost_serialization" ' + +files_to_copy = [(['*/bin/*'], 'bin')] + +local_binaries = ['GLIMPSE2_chunk', 'GLIMPSE2_concordance', 'GLIMPSE2_ligate', + 'GLIMPSE2_phase', 'GLIMPSE2_split_reference'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ["%s --help" % x for x in local_binaries] + +moduleclass = 'bio' From e4262ebbd647d14f822bf87a73a7ab917e6d99a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 09:55:56 +0200 Subject: [PATCH 7562/9987] add RBesT extension to R 4.2.1 + 4.2.2 (+ missing epitools extension for R 4.2.2) --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++ easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 6 ++++++ 2 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 313583b74ab..daf90905c51 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3526,6 +3526,9 @@ exts_list = [ ('epitools', '0.5-10.1', { 'checksums': ['b418854de1fcedd126f3bf19dc27e8a71ee6efae5371098ab64a53a2d51d164b'], }), + ('RBesT', '1.6-6', { + 'checksums': ['0301ee95f9b46722b9e1bacd668b570eee14badaa8ca0a7d0ccd8d3d9068d485'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index e8a09bc8b64..b0b5f3b307f 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3591,6 +3591,12 @@ exts_list = [ ('word2vec', '0.3.4', { 'checksums': ['53db1d8c8d6af8ace8636adec1e254b0b61fbdba77ba7a295afc7da3eb4e4362'], }), + ('epitools', '0.5-10.1', { + 'checksums': ['b418854de1fcedd126f3bf19dc27e8a71ee6efae5371098ab64a53a2d51d164b'], + }), + ('RBesT', '1.6-6', { + 'checksums': ['0301ee95f9b46722b9e1bacd668b570eee14badaa8ca0a7d0ccd8d3d9068d485'], + }), ] moduleclass = 'lang' From 664ed45c16b82c7097bda2f943be029a363b25a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 10:05:36 +0200 Subject: [PATCH 7563/9987] fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530 --- .../l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb index 59d93ffd865..778fc080c64 100644 --- a/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb @@ -19,7 +19,8 @@ dependencies = [ fix_perl_shebang_for = ['*.pl'] -postinstallcmds = ["chmod a+x %(installdir)s/L_RNA_scaffolder.sh"] +# make sure exec permissions are set for all binaries and scripts (everything except README.md and easybuild subdir) +postinstallcmds = ["ls -d %(installdir)s/* | egrep -v '/README.md|/easybuild$' | xargs chmod a+x"] sanity_check_paths = { 'files': ['calculate-lc', 'calculate-pid', 'convert', 'convert_linker', 'count_connection_frequency', From ac7bbf9fe617c581450c7eca4ac4ec23bfe3893f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 11:23:49 +0200 Subject: [PATCH 7564/9987] use libde265 1.0.11 as dependency for libheif 1.12.0 --- .../l/libde265/libde265-1.0.8-GCC-11.3.0.eb | 31 ------------------- .../l/libheif/libheif-1.12.0-GCC-11.3.0.eb | 2 +- 2 files changed, 1 insertion(+), 32 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.3.0.eb deleted file mode 100644 index 3fc2cdd07f7..00000000000 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'libde265' -version = '1.0.8' - -homepage = 'https://github.com/strukturag/libde265' -description = "libde265 is an open source implementation of the h.265 video codec" - -toolchain = {'name': 'GCC', 'version': '11.3.0'} - -source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] -sources = [SOURCE_TAR_GZ] -checksums = ['2f8f12cabbdb15e53532b7c1eb964d4e15d444db1be802505e6ac97a25035bab'] - -builddependencies = [ - ('CMake', '3.23.1'), -] - -sanity_check_paths = { - 'files': ['bin/dec265', 'lib/libde265.%s' % SHLIB_EXT], - 'dirs': ['include/libde265', 'lib/cmake/libde265'], -} - -sanity_check_commands = [ - "dec265 --help", - # "enc265 --help", -] - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.3.0.eb index 8528903bbae..64bd5dd7b7f 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.3.0.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('libpng', '1.6.37'), ('libjpeg-turbo', '2.1.3'), - ('libde265', '1.0.8'), + ('libde265', '1.0.11'), ('x265', '3.5'), ('Gdk-Pixbuf', '2.42.8'), ] From 199132de2303fa6ae186cb9a297102a717408997 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 11:24:32 +0200 Subject: [PATCH 7565/9987] enanble both decoder and encoder support in easyconfig for libde265 1.0.11 --- .../easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb index a553f85b55f..7640cb6a545 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb @@ -18,14 +18,16 @@ builddependencies = [ ('CMake', '3.23.1'), ] +configopts = "-DENABLE_DECODER=ON -DENABLE_ENCODER=ON" + sanity_check_paths = { - 'files': ['bin/dec265', 'lib/libde265.%s' % SHLIB_EXT], + 'files': ['bin/dec265', 'bin/enc265', 'lib/libde265.%s' % SHLIB_EXT, 'lib/pkgconfig/libde265.pc'], 'dirs': ['include/libde265', 'lib/cmake/libde265'], } sanity_check_commands = [ "dec265 --help", - # "enc265 --help", + "enc265 --help", ] moduleclass = 'tools' From dcf0eb075bda2cfb668a5cc79232b38960c8dac4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 5 Jun 2023 11:46:40 +0200 Subject: [PATCH 7566/9987] Switch to PerlBundle easyblock --- .../Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index 222b05dded1..49e03fe60b2 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PerlBundle' name = 'Perl-bundle-CPAN' version = '5.36.1' @@ -23,9 +23,6 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] -exts_defaultclass = 'PerlModule' -exts_filter = ("perldoc -lm %(ext_name)s ", "") - # !! order of extensions is important !! # extensions updated on 2023-05-23 exts_list = [ @@ -34,6 +31,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], 'checksums': ['4d6d5754be3a9f30906836f0cc10e554c8832e14e7a1341efb15b05d706fc58f'], }), + ('HTTP::Date', '6.05', { + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS/'], + }), ('File::Listing', '6.15', { 'source_tmpl': 'File-Listing-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], From da6af317cdc8e3e9de9dd9ca8f91c094b567a718 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 5 Jun 2023 11:47:49 +0200 Subject: [PATCH 7567/9987] Add Extrae-4.0.4 --- .../Extrae-4.0.4-change_libdwarf_path.patch | 62 +++++++++++++++++++ .../e/Extrae/Extrae-4.0.4-gompi-2022a.eb | 45 ++++++++++++++ 2 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-change_libdwarf_path.patch create mode 100644 easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-change_libdwarf_path.patch b/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-change_libdwarf_path.patch new file mode 100644 index 00000000000..68b82db0cad --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-change_libdwarf_path.patch @@ -0,0 +1,62 @@ +# Change path to the libdwarf headers and adjust the aclocal version, since we change the *.m4 file too +# Author: maxim-masterov + +diff -Nru extrae-4.0.4.orig/config/macros.m4 extrae-4.0.4/config/macros.m4 +--- extrae-4.0.4.orig/config/macros.m4 2023-06-05 11:16:01.296643000 +0200 ++++ extrae-4.0.4/config/macros.m4 2023-06-05 11:21:10.535531000 +0200 +@@ -1666,8 +1666,8 @@ + if test -f "${DWARF_HOME}/include/libdwarf.h" -a \ + -f "${DWARF_HOME}/include/dwarf.h" ; then + libdwarf_found="yes" +- elif test -f "${DWARF_HOME}/include/libdwarf/libdwarf.h" -a \ +- -f "${DWARF_HOME}/include/libdwarf/dwarf.h" ; then ++ elif test -f "${DWARF_HOME}/include/libdwarf-0/libdwarf.h" -a \ ++ -f "${DWARF_HOME}/include/libdwarf-0/dwarf.h" ; then + libdwarf_found="yes" + else + AC_MSG_ERROR([Cannot find DWARF header files in ${dwarf_paths}/include]) +@@ -1678,8 +1678,8 @@ + -f "${DWARF_HOME}/include/dwarf.h" ; then + libdwarf_found="yes" + DWARF_LIBSDIR="${DWARF_LIBSDIR_MULTIARCH}" +- elif test -f "${DWARF_HOME}/include/libdwarf/libdwarf.h" -a \ +- -f "${DWARF_HOME}/include/libdwarf/dwarf.h" ; then ++ elif test -f "${DWARF_HOME}/include/libdwarf-0/libdwarf.h" -a \ ++ -f "${DWARF_HOME}/include/libdwarf-0/dwarf.h" ; then + libdwarf_found="yes" + DWARF_LIBSDIR="${DWARF_LIBSDIR_MULTIARCH}" + else +diff -Nru extrae-4.0.4.orig/configure extrae-4.0.4/configure +--- extrae-4.0.4.orig/configure 2023-06-05 11:16:01.298502695 +0200 ++++ extrae-4.0.4/configure 2023-06-05 11:32:55.962736435 +0200 +@@ -4683,7 +4683,7 @@ + fi + + # Initialize automake +-am__api_version='1.13' ++am__api_version='1.16' + + # Find a good install program. We prefer a C program (faster), + # so one script is as good as another. But avoid the broken or +@@ -30469,8 +30469,8 @@ + if test -f "${DWARF_HOME}/include/libdwarf.h" -a \ + -f "${DWARF_HOME}/include/dwarf.h" ; then + libdwarf_found="yes" +- elif test -f "${DWARF_HOME}/include/libdwarf/libdwarf.h" -a \ +- -f "${DWARF_HOME}/include/libdwarf/dwarf.h" ; then ++ elif test -f "${DWARF_HOME}/include/libdwarf-0/libdwarf.h" -a \ ++ -f "${DWARF_HOME}/include/libdwarf-0/dwarf.h" ; then + libdwarf_found="yes" + else + as_fn_error $? "Cannot find DWARF header files in ${dwarf_paths}/include" "$LINENO" 5 +@@ -30481,8 +30481,8 @@ + -f "${DWARF_HOME}/include/dwarf.h" ; then + libdwarf_found="yes" + DWARF_LIBSDIR="${DWARF_LIBSDIR_MULTIARCH}" +- elif test -f "${DWARF_HOME}/include/libdwarf/libdwarf.h" -a \ +- -f "${DWARF_HOME}/include/libdwarf/dwarf.h" ; then ++ elif test -f "${DWARF_HOME}/include/libdwarf-0/libdwarf.h" -a \ ++ -f "${DWARF_HOME}/include/libdwarf-0/dwarf.h" ; then + libdwarf_found="yes" + DWARF_LIBSDIR="${DWARF_LIBSDIR_MULTIARCH}" + else diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb new file mode 100644 index 00000000000..8875b56177b --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb @@ -0,0 +1,45 @@ +name = 'Extrae' +version = '4.0.4' + +homepage = 'https://www.bsc.es/computer-sciences/performance-tools' +description = """Extrae is the core instrumentation package developed by +the Performance Tools group at BSC. Extrae is capable of instrumenting +applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 +using different instrumentation approaches. The information gathered by +Extrae typically includes timestamped events of runtime calls, +performance counters and source code references. Besides, Extrae +provides its own API to allow the user to manually instrument his or her +application.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] +# source_urls = ['https://github.com/bsc-performance-tools/extrae/archive/refs/tags'] +sources = ['%(namelower)s-%(version)s-src.tar.bz2'] +# sources = ['%(version)s.tar.gz'] +#patches = ['extrae_dbg.patch'] +patches = ['test.patch'] +checksums = [ + '003bede870de6d88b705c1a13eabe63b6beb928d8f389f5dd70ca5db8450a1f9', + 'ef93fc365b1b8abdecfb7f1c3a72e1f5fdc2cef220b9d37e10a58839c4419964', # test.patch + # 'e6765eb087be3f3c162e08d65f425de5f26912811392527d56ecd75d4fb6b99d', +# '768f18d7537277b5d1baa8122ec05c1f684afa4d6351fd2cce53ce97f9a7b94e', +# '003bede870de6d88b705c1a13eabe63b6beb928d8f389f5dd70ca5db8450a1f9', +# '2a8524b666ba9a1b051206b35b42dcdef19f491586d47eda617921addf2618d9', # extrae_dbg.patch +] + +builddependencies = [ + ('Automake', '1.16.5'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('Boost', '1.79.0'), + ('libunwind', '1.6.2'), + ('libxml2', '2.9.13'), + ('libdwarf', '0.4.1'), + ('PAPI', '7.0.0'), +] + +moduleclass = 'perf' From e4a8aaca988ea8f84dcf733a9fff8427f465cb85 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 5 Jun 2023 11:52:10 +0200 Subject: [PATCH 7568/9987] Cleaning --- .../e/Extrae/Extrae-4.0.4-gompi-2022a.eb | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb index 8875b56177b..666f0ba1682 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb @@ -15,18 +15,11 @@ toolchain = {'name': 'gompi', 'version': '2022a'} toolchainopts = {'usempi': True} source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] -# source_urls = ['https://github.com/bsc-performance-tools/extrae/archive/refs/tags'] sources = ['%(namelower)s-%(version)s-src.tar.bz2'] -# sources = ['%(version)s.tar.gz'] -#patches = ['extrae_dbg.patch'] -patches = ['test.patch'] +patches = ['Extrae-4.0.4-change_libdwarf_path.patch'] checksums = [ - '003bede870de6d88b705c1a13eabe63b6beb928d8f389f5dd70ca5db8450a1f9', - 'ef93fc365b1b8abdecfb7f1c3a72e1f5fdc2cef220b9d37e10a58839c4419964', # test.patch - # 'e6765eb087be3f3c162e08d65f425de5f26912811392527d56ecd75d4fb6b99d', -# '768f18d7537277b5d1baa8122ec05c1f684afa4d6351fd2cce53ce97f9a7b94e', -# '003bede870de6d88b705c1a13eabe63b6beb928d8f389f5dd70ca5db8450a1f9', -# '2a8524b666ba9a1b051206b35b42dcdef19f491586d47eda617921addf2618d9', # extrae_dbg.patch + '003bede870de6d88b705c1a13eabe63b6beb928d8f389f5dd70ca5db8450a1f9', # extrae-4.0.4-src.tar.bz2 + '74759b956246671a323acc3b267f9943bc2e190bb231259ad0c62784ec233a52', # Extrae-4.0.4-change_libdwarf_path.patch ] builddependencies = [ From 26ba23ded3c0748bf7155019c63ba5ee99525435 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 5 Jun 2023 12:09:57 +0200 Subject: [PATCH 7569/9987] Add Paraver --- .../p/Paraver/Paraver-4.11.1-foss-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/p/Paraver/Paraver-4.11.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.1-foss-2022a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.1-foss-2022a.eb new file mode 100644 index 00000000000..849185d175c --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.1-foss-2022a.eb @@ -0,0 +1,21 @@ +name = 'Paraver' +version = '4.11.1' + +homepage = 'https://tools.bsc.es/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://ftp.tools.bsc.es/wxparaver/'] +sources = ['wxparaver-%(version)s-src.tar.bz2'] +checksums = ['b1c1cc8ce69adb095b9f8a4500250c0baa50668be60825f75d75fddca9a88f77'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Boost', '1.79.0'), + ('wxWidgets', '3.2.1'), +] + +moduleclass = 'perf' From c6ffb8dc5f08ad119924cf730ecbaccb35f55963 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Jun 2023 11:12:20 +0100 Subject: [PATCH 7570/9987] adding easyconfigs: subset-bam-1.1.0-GCCcore-10.3.0.eb --- .../subset-bam-1.1.0-GCCcore-10.3.0.eb | 305 ++++++++++++++++++ 1 file changed, 305 insertions(+) create mode 100644 easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..167671ca189 --- /dev/null +++ b/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,305 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'Cargo' + +name = 'subset-bam' +version = '1.1.0' + +homepage = 'https://github.com/10XGenomics/subset-bam' +description = """subset-bam is a tool to subset a 10x Genomics BAM file based on a tag, +most commonly the cell barcode tag.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +crates = [ + ('addr2line', '0.12.1'), + ('adler32', '1.1.0'), + ('aho-corasick', '0.6.10'), + ('aho-corasick', '0.7.10'), + ('ansi_term', '0.11.0'), + ('arrayref', '0.3.6'), + ('arrayvec', '0.5.1'), + ('atty', '0.2.14'), + ('autocfg', '1.0.0'), + ('backtrace', '0.3.49'), + ('base64', '0.11.0'), + ('bindgen', '0.36.1'), + ('bitflags', '0.9.1'), + ('bitflags', '1.2.1'), + ('blake2b_simd', '0.5.10'), + ('bstr', '0.2.13'), + ('byteorder', '1.3.4'), + ('cc', '1.0.54'), + ('cexpr', '0.2.3'), + ('cfg-if', '0.1.10'), + ('chrono', '0.4.11'), + ('clang-sys', '0.22.0'), + ('clap', '2.33.1'), + ('constant_time_eq', '0.1.5'), + ('crossbeam-deque', '0.7.3'), + ('crossbeam-epoch', '0.8.2'), + ('crossbeam-queue', '0.2.3'), + ('crossbeam-utils', '0.7.2'), + ('csv', '1.1.3'), + ('csv-core', '0.1.10'), + ('custom_derive', '0.1.7'), + ('data-encoding', '2.2.1'), + ('dirs', '1.0.5'), + ('either', '1.5.3'), + ('env_logger', '0.5.13'), + ('faccess', '0.2.3'), + ('failure', '0.1.8'), + ('failure_derive', '0.1.8'), + ('fs-utils', '1.1.4'), + ('getrandom', '0.1.14'), + ('gimli', '0.21.0'), + ('glob', '0.2.11'), + ('hermit-abi', '0.1.14'), + ('human-panic', '1.0.3'), + ('humantime', '1.3.0'), + ('idna', '0.1.5'), + ('ieee754', '0.2.6'), + ('itertools', '0.6.5'), + ('itoa', '0.4.6'), + ('lazy_static', '0.2.11'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.71'), + ('libloading', '0.5.2'), + ('linear-map', '1.2.0'), + ('log', '0.4.8'), + ('matches', '0.1.8'), + ('maybe-uninit', '2.0.0'), + ('memchr', '1.0.2'), + ('memchr', '2.3.3'), + ('memoffset', '0.5.4'), + ('miniz_oxide', '0.3.7'), + ('newtype_derive', '0.1.6'), + ('nom', '3.2.1'), + ('num-integer', '0.1.43'), + ('num-traits', '0.2.12'), + ('num_cpus', '1.13.0'), + ('object', '0.20.0'), + ('os_type', '2.2.0'), + ('peeking_take_while', '0.1.2'), + ('percent-encoding', '1.0.1'), + ('ppv-lite86', '0.2.8'), + ('proc-macro2', '0.3.5'), + ('proc-macro2', '1.0.18'), + ('quick-error', '1.2.3'), + ('quote', '0.5.2'), + ('quote', '1.0.7'), + ('rand', '0.7.3'), + ('rand_chacha', '0.2.2'), + ('rand_core', '0.5.1'), + ('rand_hc', '0.2.0'), + ('rayon', '1.3.1'), + ('rayon-core', '1.7.1'), + ('redox_syscall', '0.1.56'), + ('redox_users', '0.3.4'), + ('regex', '0.2.11'), + ('regex', '1.3.9'), + ('regex-automata', '0.1.9'), + ('regex-syntax', '0.5.6'), + ('regex-syntax', '0.6.18'), + ('remove_dir_all', '0.5.3'), + ('ring', '0.14.6'), + ('rust-argon2', '0.7.0'), + ('rust-htslib', '0.20.0'), + ('rustc-demangle', '0.1.16'), + ('rustc_version', '0.1.7'), + ('ryu', '1.0.5'), + ('scopeguard', '1.1.0'), + ('semver', '0.1.20'), + ('serde', '1.0.113'), + ('serde_derive', '1.0.113'), + ('simplelog', '0.5.3'), + ('spin', '0.5.2'), + ('strsim', '0.8.0'), + ('syn', '1.0.31'), + ('synstructure', '0.12.4'), + ('tempfile', '3.1.0'), + ('term', '0.5.2'), + ('termcolor', '1.1.0'), + ('terminal_size', '0.1.12'), + ('textwrap', '0.11.0'), + ('thread_local', '0.3.6'), + ('thread_local', '1.0.1'), + ('time', '0.1.43'), + ('tinyvec', '0.3.3'), + ('toml', '0.5.6'), + ('ucd-util', '0.1.8'), + ('unicode-bidi', '0.3.4'), + ('unicode-normalization', '0.1.13'), + ('unicode-width', '0.1.7'), + ('unicode-xid', '0.1.0'), + ('unicode-xid', '0.2.0'), + ('untrusted', '0.6.2'), + ('url', '1.7.2'), + ('utf8-ranges', '1.0.4'), + ('uuid', '0.8.1'), + ('vec_map', '0.8.2'), + ('wasi', '0.9.0+wasi-snapshot-preview1'), + ('which', '1.0.5'), + ('winapi', '0.3.8'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.5'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), +] + +source_urls = ['https://github.com/10XGenomics/subset-bam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ 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'3acd125665422973a33ac9d3dd2df85edad0f4ae9b00dafb1a05e43a9f5ef8e7'}, + {'ring-0.14.6.tar.gz': '426bc186e3e95cac1e4a4be125a4aca7e84c2d616ffc02244eef36e2a60a093c'}, + {'rust-argon2-0.7.0.tar.gz': '2bc8af4bda8e1ff4932523b94d3dd20ee30a87232323eda55903ffd71d2fb017'}, + {'rust-htslib-0.20.0.tar.gz': 'f702eebd89609dd27605999d981b67b3380861cc2d4318a2e827709c884006c4'}, + {'rustc-demangle-0.1.16.tar.gz': '4c691c0e608126e00913e33f0ccf3727d5fc84573623b8d65b2df340b5201783'}, + {'rustc_version-0.1.7.tar.gz': 'c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084'}, + {'ryu-1.0.5.tar.gz': '71d301d4193d031abdd79ff7e3dd721168a9572ef3fe51a1517aba235bd8f86e'}, + {'scopeguard-1.1.0.tar.gz': 'd29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd'}, + {'semver-0.1.20.tar.gz': 'd4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac'}, + {'serde-1.0.113.tar.gz': '6135c78461981c79497158ef777264c51d9d0f4f3fc3a4d22b915900e42dac6a'}, + {'serde_derive-1.0.113.tar.gz': '93c5eaa17d0954cb481cdcfffe9d84fcfa7a1a9f2349271e678677be4c26ae31'}, + {'simplelog-0.5.3.tar.gz': '2e95345f185d5adeb8ec93459d2dc99654e294cc6ccf5b75414d8ea262de9a13'}, + {'spin-0.5.2.tar.gz': '6e63cff320ae2c57904679ba7cb63280a3dc4613885beafb148ee7bf9aa9042d'}, + {'strsim-0.8.0.tar.gz': '8ea5119cdb4c55b55d432abb513a0429384878c15dde60cc77b1c99de1a95a6a'}, + {'syn-1.0.31.tar.gz': 'b5304cfdf27365b7585c25d4af91b35016ed21ef88f17ced89c7093b43dba8b6'}, + {'synstructure-0.12.4.tar.gz': 'b834f2d66f734cb897113e34aaff2f1ab4719ca946f9a7358dba8f8064148701'}, + {'tempfile-3.1.0.tar.gz': '7a6e24d9338a0a5be79593e2fa15a648add6138caa803e2d5bc782c371732ca9'}, + {'term-0.5.2.tar.gz': 'edd106a334b7657c10b7c540a0106114feadeb4dc314513e97df481d5d966f42'}, + {'termcolor-1.1.0.tar.gz': 'bb6bfa289a4d7c5766392812c0a1f4c1ba45afa1ad47803c11e1f407d846d75f'}, + {'terminal_size-0.1.12.tar.gz': '8038f95fc7a6f351163f4b964af631bd26c9e828f7db085f2a84aca56f70d13b'}, + {'textwrap-0.11.0.tar.gz': 'd326610f408c7a4eb6f51c37c330e496b08506c9457c9d34287ecc38809fb060'}, + {'thread_local-0.3.6.tar.gz': 'c6b53e329000edc2b34dbe8545fd20e55a333362d0a321909685a19bd28c3f1b'}, + {'thread_local-1.0.1.tar.gz': 'd40c6d1b69745a6ec6fb1ca717914848da4b44ae29d9b3080cbee91d72a69b14'}, + {'time-0.1.43.tar.gz': 'ca8a50ef2360fbd1eeb0ecd46795a87a19024eb4b53c5dc916ca1fd95fe62438'}, + {'tinyvec-0.3.3.tar.gz': '53953d2d3a5ad81d9f844a32f14ebb121f50b650cd59d0ee2a07cf13c617efed'}, + {'toml-0.5.6.tar.gz': 'ffc92d160b1eef40665be3a05630d003936a3bc7da7421277846c2613e92c71a'}, + {'ucd-util-0.1.8.tar.gz': 'c85f514e095d348c279b1e5cd76795082cf15bd59b93207832abe0b1d8fed236'}, + {'unicode-bidi-0.3.4.tar.gz': '49f2bd0c6468a8230e1db229cff8029217cf623c767ea5d60bfbd42729ea54d5'}, + {'unicode-normalization-0.1.13.tar.gz': '6fb19cf769fa8c6a80a162df694621ebeb4dafb606470b2b2fce0be40a98a977'}, + {'unicode-width-0.1.7.tar.gz': 'caaa9d531767d1ff2150b9332433f32a24622147e5ebb1f26409d5da67afd479'}, + {'unicode-xid-0.1.0.tar.gz': 'fc72304796d0818e357ead4e000d19c9c174ab23dc11093ac919054d20a6a7fc'}, + {'unicode-xid-0.2.0.tar.gz': '826e7639553986605ec5979c7dd957c7895e93eabed50ab2ffa7f6128a75097c'}, + {'untrusted-0.6.2.tar.gz': '55cd1f4b4e96b46aeb8d4855db4a7a9bd96eeeb5c6a1ab54593328761642ce2f'}, + {'url-1.7.2.tar.gz': 'dd4e7c0d531266369519a4aa4f399d748bd37043b00bde1e4ff1f60a120b355a'}, + {'utf8-ranges-1.0.4.tar.gz': 'b4ae116fef2b7fea257ed6440d3cfcff7f190865f170cdad00bb6465bf18ecba'}, + {'uuid-0.8.1.tar.gz': '9fde2f6a4bea1d6e007c4ad38c6839fa71cbb63b6dbf5b595aa38dc9b1093c11'}, + {'vec_map-0.8.2.tar.gz': 'f1bddf1187be692e79c5ffeab891132dfb0f236ed36a43c7ed39f1165ee20191'}, + {'wasi-0.9.0+wasi-snapshot-preview1.tar.gz': 'cccddf32554fecc6acb585f82a32a72e28b48f8c4c1883ddfeeeaa96f7d8e519'}, + {'which-1.0.5.tar.gz': 'e84a603e7e0b1ce1aa1ee2b109c7be00155ce52df5081590d1ffb93f4f515cb2'}, + {'winapi-0.3.8.tar.gz': '8093091eeb260906a183e6ae1abdba2ef5ef2257a21801128899c3fc699229c6'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.5.tar.gz': '70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Rust', '1.52.1'), + ('Clang', '12.0.1'), +] + +# It looks like we need to specify this as else it will not work. +buildopts = '-Z unstable-options ' +testopts = '-Z unstable-options ' +installopts = '-Z unstable-options ' + +sanity_check_paths = { + 'files': ['bin/subset-bam'], + 'dirs': [], +} + +sanity_check_commands = ["subset-bam --help"] + +moduleclass = 'bio' From fd2ba670519f307d118b5acece01f3a77a6dcfdc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 5 Jun 2023 10:48:01 +0000 Subject: [PATCH 7571/9987] adding easyconfigs: samblaster-0.1.26-GCC-11.3.0.eb --- .../samblaster-0.1.26-GCC-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-11.3.0.eb b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-11.3.0.eb new file mode 100644 index 00000000000..e0c9cf711e6 --- /dev/null +++ b/easybuild/easyconfigs/s/samblaster/samblaster-0.1.26-GCC-11.3.0.eb @@ -0,0 +1,37 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org fizwit@github.com +easyblock = 'MakeCp' + +name = 'samblaster' +version = '0.1.26' + +description = """samblaster is a fast and flexible program for marking + duplicates in read-id grouped1 paired-end SAM files.""" + +homepage = 'https://github.com/GregoryFaust/samblaster' + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/GregoryFaust/samblaster/archive/'] +sources = [{ + 'download_filename': 'v.%(version)s.zip', + 'filename': SOURCE_ZIP +}] +checksums = ['79ff6f8306482e73e04678424bf14b840d80561660bb59deac1b75ada2f330cf'] + +files_to_copy = [ + (["samblaster"], "bin/"), + 'README.md', + 'SAMBLASTER_Supplemental.pdf', + 'LICENSE.txt', +] + +sanity_check_paths = { + 'files': ['bin/samblaster', 'README.md'], + 'dirs': [] +} + +sanity_check_commands = ["samblaster --help"] + +moduleclass = 'bio' From 1e5dea60563f7d2ea4e385476c05f4dab2e44bbd Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 5 Jun 2023 12:52:39 +0000 Subject: [PATCH 7572/9987] Add LAPACK test fix patch --- .../o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb | 2 ++ .../OpenBLAS-0.3.23_fix-lapack-test.patch | 15 +++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-lapack-test.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb index f55e447fa3b..f63af09621e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb @@ -18,6 +18,7 @@ patches = [ 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.23_fix-parallel-build.patch', + 'OpenBLAS-0.3.23_fix-lapack-test.patch', ] checksums = [ {'v0.3.23.tar.gz': '5d9491d07168a5d00116cdc068a40022c3455bf9293c7cb86a65b1054d7e5114'}, @@ -28,6 +29,7 @@ checksums = [ {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_fix-parallel-build.patch': 'abe10ba3b0ca54772dbf235596e35325a5159018f6a60cfc88824c2c220d99d9'}, + {'OpenBLAS-0.3.23_fix-lapack-test.patch': '22a087b5194f0767ebc94ddb0c44390a7646b966408cabc4b88aef9f02b707da'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-lapack-test.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-lapack-test.patch new file mode 100644 index 00000000000..bb7aa1cd1f1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-lapack-test.patch @@ -0,0 +1,15 @@ +Avoid a nearly singular matrix in lapack testing, which can trigger an error depending +on FMA. Swapping matrix dimensions is sufficient here since the matrices are generated +using a random number generator, and we were just unlucky here. + +Author: Bart Oldeman +--- OpenBLAS-0.3.23/lapack-netlib/TESTING/dgd.in.orig 2023-06-05 12:12:08.222632285 +0000 ++++ OpenBLAS-0.3.23/lapack-netlib/TESTING/dgd.in 2023-06-05 12:12:19.323715597 +0000 +@@ -1,6 +1,6 @@ + DGS Data for the Real Nonsymmetric Schur Form Driver + 5 Number of matrix dimensions +-2 6 10 12 20 30 Matrix dimensions ++6 2 10 12 20 30 Matrix dimensions + 1 1 1 2 1 Parameters NB, NBMIN, NXOVER, NS, NBCOL + 10 Threshold for test ratios + .TRUE. Put T to test the error exits From 55a2a4f74e27cb66791355475f26846c803ac8a7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 16:37:45 +0200 Subject: [PATCH 7573/9987] update Highway to v1.0.4, update libjxl to v0.8.1, update libheif to v1.16.2 --- ...3.0.eb => Highway-1.0.4-GCCcore-11.3.0.eb} | 4 +-- ...11.3.0.eb => libheif-1.16.2-GCC-11.3.0.eb} | 4 +-- ...ss-2022a.eb => libjxl-0.8.1-foss-2022a.eb} | 35 +++++++------------ 3 files changed, 16 insertions(+), 27 deletions(-) rename easybuild/easyconfigs/h/Highway/{Highway-0.12.2-GCCcore-11.3.0.eb => Highway-1.0.4-GCCcore-11.3.0.eb} (88%) rename easybuild/easyconfigs/l/libheif/{libheif-1.12.0-GCC-11.3.0.eb => libheif-1.16.2-GCC-11.3.0.eb} (90%) rename easybuild/easyconfigs/l/libjxl/{libjxl-0.5-foss-2022a.eb => libjxl-0.8.1-foss-2022a.eb} (50%) diff --git a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-11.3.0.eb similarity index 88% rename from easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-11.3.0.eb index 7e8539c6ad3..6b5785ddb81 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-0.12.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'Highway' -version = '0.12.2' +version = '1.0.4' homepage = 'https://github.com/google/highway' @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/google/highway/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -checksums = ['e1d47ce510429fdcf31f41697ca74fb0dcd59d933196e531a86d51751a56f4cc'] +checksums = ['faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb similarity index 90% rename from easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.3.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb index 64bd5dd7b7f..9d966d5571b 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libheif' -version = '1.12.0' +version = '1.16.2' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" @@ -12,7 +12,7 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] +checksums = ['7f97e4205c0bd9f9b8560536c8bd2e841d1c9a6d610401eb3eb87ed9cdfe78ea'] builddependencies = [ ('CMake', '3.23.1'), diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.5-foss-2022a.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.8.1-foss-2022a.eb similarity index 50% rename from easybuild/easyconfigs/l/libjxl/libjxl-0.5-foss-2022a.eb rename to easybuild/easyconfigs/l/libjxl/libjxl-0.8.1-foss-2022a.eb index d826e4fd828..c9c368990b3 100644 --- a/easybuild/easyconfigs/l/libjxl/libjxl-0.5-foss-2022a.eb +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.8.1-foss-2022a.eb @@ -1,8 +1,7 @@ easyblock = 'CMakeMake' name = 'libjxl' -version = '0.5' -local_lodepng_version = "48e5364" +version = '0.8.1' homepage = 'https://github.com/libjxl/libjxl' description = "JPEG XL image format reference implementation" @@ -12,30 +11,15 @@ toolchainopts = {'optarch': False} # optarch causes some test failures github_account = 'libjxl' source_urls = [GITHUB_SOURCE] -sources = [ - 'v%(version)s.tar.gz', - {'filename': 'lodepng-%s.tar.gz' % local_lodepng_version, - 'download_filename': local_lodepng_version, - 'source_urls': ['https://github.com/lvandeve/lodepng/tarball/'], - 'extract_cmd': 'tar -C libjxl-%(version)s/third_party/lodepng --strip-components=1 -xf %s'}, -] -patches = [ - 'libjxl-0.3.7_external_lcms2.patch', - 'libjxl-%(version)s_remove-broken-test.patch', -] -checksums = [ - '911cb4b50eb621131ca22382166f40d4914a4ff4453dd299ade1e3292f311f89', # v0.5.tar.gz - 'f38176fc103fe1f6d23ba6addd5b14e6a54d546dfaa64663306acfe7b6d912ea', # lodepng-48e5364.tar.gz - '9e6decaf6be74eeccfd5728df175930b4be33de6cbdf9e1816f68cb4b718fa1b', # libjxl-0.3.7_external_lcms2.patch - '5b62751da5b3b3c4aad58a841d49cc506bc330425bbd0df7f19f99aa98c52c26', # libjxl-0.5_remove-broken-test.patch -] +sources = ['v%(version)s.tar.gz'] +checksums = ['60f43921ad3209c9e180563025eda0c0f9b1afac51a2927b9ff59fff3950dc56'] builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), ('googletest', '1.11.0'), ('pkg-config', '0.29.2'), - ('Highway', '0.12.2'), # Highway only has a static library + ('Highway', '1.0.4'), # Highway only has a static library ] dependencies = [ @@ -52,13 +36,18 @@ dependencies = [ configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' # building man pages requires/uses asciidoc (which may be installed in OS, and may fail) -configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF' - -runtest = "test" +configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF ' +configopts += '-DJPEGXL_FORCE_SYSTEM_BROTLI=ON -DJPEGXL_FORCE_SYSTEM_HWY=ON ' +configopts += '-DJPEGXL_FORCE_SYSTEM_GTEST=ON -DJPEGXL_FORCE_SYSTEM_LCMS2=ON ' sanity_check_paths = { 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], 'dirs': ['include'], } +sanity_check_commands = [ + "cjxl --help", + "djxl --help", +] + moduleclass = 'lib' From e7aeb48e152b411a2a2afff9121e3c93d1386119 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 16:46:17 +0200 Subject: [PATCH 7574/9987] use Java/11 as dependency for 3d-dna 180922 --- .../0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb index e3fbb217c74..f64e48e7645 100644 --- a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb @@ -17,7 +17,7 @@ checksums = ['348c3e019ea29e47382eb2d85228a56bc11b316c130afabae016ad8e7d7640ca'] dependencies = [ ('Python', '2.7.15'), ('LASTZ', '1.02.00'), - ('Java', '1.8', '', True), + ('Java', '11', '', True), ('parallel', '20190622'), ] From 5adb980e815f5cce716076554351dc7dbbc81762 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 16:47:52 +0200 Subject: [PATCH 7575/9987] remove easyconfig for 3d-dna 180922 using foss/2019a toolchain --- .../3d-dna-180922-foss-2019a-Python-2.7.15.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb diff --git a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb deleted file mode 100644 index f64e48e7645..00000000000 --- a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-foss-2019a-Python-2.7.15.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'Tarball' - -name = '3d-dna' -version = '180922' -versionsuffix = '-Python-%(pyver)s' -local_githash = '529ccf46599825b3047e58a69091d599e9858a19' - -homepage = 'https://github.com/theaidenlab/3d-dna' -description = """3D de novo assembly (3D DNA) pipeline""" - -toolchain = {'name': 'foss', 'version': '2019a'} - -source_urls = ['https://github.com/theaidenlab/%(name)s/archive'] -sources = ['%s.zip' % local_githash] -checksums = ['348c3e019ea29e47382eb2d85228a56bc11b316c130afabae016ad8e7d7640ca'] - -dependencies = [ - ('Python', '2.7.15'), - ('LASTZ', '1.02.00'), - ('Java', '11', '', True), - ('parallel', '20190622'), -] - -modextrapaths = {'PATH': '.'} - -postinstallcmds = ['chmod 755 %(installdir)s/*.sh'] - -sanity_check_paths = { - 'files': ['run-asm-pipeline.sh', 'run-asm-pipeline-post-review.sh'], - 'dirs': [], -} - -moduleclass = 'bio' From 247549fab3ef49d43a5fcd417dd3a093a1823a4e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 16:48:49 +0200 Subject: [PATCH 7576/9987] fix Java/11 dependency in easyconfig for 3d-dna 180922 --- .../0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb index 56b6f12cab2..0974dbf387f 100644 --- a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb +++ b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb @@ -17,7 +17,7 @@ checksums = ['348c3e019ea29e47382eb2d85228a56bc11b316c130afabae016ad8e7d7640ca'] dependencies = [ ('Python', '2.7.15'), ('LASTZ', '1.02.00'), - ('Java', '1.11', '', True), + ('Java', '11', '', True), ('parallel', '20190622'), ] From 1d48cae5b73bddcb70cb21c9458a1e65804915be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 16:49:43 +0200 Subject: [PATCH 7577/9987] use SYSTEM rather than True in Java dependency for 3d-dna --- .../0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb index 0974dbf387f..ae362d8f697 100644 --- a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb +++ b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb @@ -17,7 +17,7 @@ checksums = ['348c3e019ea29e47382eb2d85228a56bc11b316c130afabae016ad8e7d7640ca'] dependencies = [ ('Python', '2.7.15'), ('LASTZ', '1.02.00'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('parallel', '20190622'), ] From 9fd3908a95640ea4241d62c16f685ce83d84f99f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 17:11:06 +0200 Subject: [PATCH 7578/9987] stick to Java/1.8 for 3d-dna using GCCcore/8.2.0 --- .../0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb index ae362d8f697..cf14ae0d7a3 100644 --- a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb +++ b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb @@ -17,7 +17,7 @@ checksums = ['348c3e019ea29e47382eb2d85228a56bc11b316c130afabae016ad8e7d7640ca'] dependencies = [ ('Python', '2.7.15'), ('LASTZ', '1.02.00'), - ('Java', '11', '', SYSTEM), + ('Java', '1.8', '', SYSTEM), ('parallel', '20190622'), ] From 497e9298a2babe688006a86421b2e62521e10207 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Jun 2023 16:11:28 +0100 Subject: [PATCH 7579/9987] Missing bzip2 added --- .../s/subset-bam/subset-bam-1.1.0-GCCcore-10.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0-GCCcore-10.3.0.eb index 167671ca189..1f424531e42 100644 --- a/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0-GCCcore-10.3.0.eb @@ -290,6 +290,10 @@ builddependencies = [ ('Clang', '12.0.1'), ] +dependencies = [ + ('bzip2', '1.0.8'), +] + # It looks like we need to specify this as else it will not work. buildopts = '-Z unstable-options ' testopts = '-Z unstable-options ' From d4dd50a25a420ce404a6b9bc80915b72efb9e58e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 17:24:05 +0200 Subject: [PATCH 7580/9987] adding easyconfigs: Anaconda3-2023.03-1.eb --- .../a/Anaconda3/Anaconda3-2023.03-1.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.03-1.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.03-1.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.03-1.eb new file mode 100644 index 00000000000..db18ed4f421 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.03-1.eb @@ -0,0 +1,31 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, +# 2019.10, 2020.2, 2020.11, 2022.05, +# 2022.10 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2023.03-1' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH) +sources = ['%%(name)s-%%(version)s-Linux-%s.sh' % local_arch] +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': '95102d7c732411f1458a20bdf47e4c1b0b6c8a21a2edfe4052ca370aaae57bab', + '%(name)s-%(version)s-Linux-ppc64le.sh': 'a31f2d6da83534cff7c994403cc11fa634b31fcd10eb4153d00233345ee084b2', + '%(name)s-%(version)s-Linux-aarch64.sh': '54e600faa2af63a25717af30ecaddf1ee428cdfebd3721a70f41462e232e8153', + } +] + +moduleclass = 'lang' From cc4adda1f7c7939ef524ee1412792a71b548aa8b Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 5 Jun 2023 17:20:07 +0100 Subject: [PATCH 7581/9987] adding easyconfigs: FreeSurfer-7.4.0-centos8_x86_64.eb, FreeSurfer-7.4.0-ubuntu20_amd64.eb, FreeSurfer-7.4.0-ubuntu22_amd64.eb --- .../FreeSurfer-7.4.0-centos8_x86_64.eb | 33 +++++++++++++++++++ .../FreeSurfer-7.4.0-ubuntu20_amd64.eb | 33 +++++++++++++++++++ .../FreeSurfer-7.4.0-ubuntu22_amd64.eb | 33 +++++++++++++++++++ 3 files changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-centos8_x86_64.eb create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu20_amd64.eb create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu22_amd64.eb diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-centos8_x86_64.eb new file mode 100644 index 00000000000..5f72e9c0cde --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-centos8_x86_64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.4.0' +versionsuffix = '-centos8_x86_64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + {'freesurfer-linux-centos8_x86_64-7.4.0.tar.gz': + 'a2eb8ca6d12c9133c4af90167d6b9fa532f7ace98cc0e1bc97c8a6135b53c237'}, + {'runtime2014bLinux.tar.gz': '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648'}, +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu20_amd64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu20_amd64.eb new file mode 100644 index 00000000000..42b6fc18c68 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu20_amd64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.4.0' +versionsuffix = '-ubuntu20_amd64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + {'freesurfer-linux-ubuntu20_amd64-7.4.0.tar.gz': + '2149e0d54220abf81b0caa5736b648b56f409b1e6578d921d0f7e4d62d586ca5'}, + {'runtime2014bLinux.tar.gz': '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648'}, +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu22_amd64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu22_amd64.eb new file mode 100644 index 00000000000..cd51ff885bd --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu22_amd64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.4.0' +versionsuffix = '-ubuntu22_amd64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + {'freesurfer-linux-ubuntu22_amd64-7.4.0.tar.gz': + 'acd7f8b9a75cf41fab837caa95f2c9017079c15ca4446df2c47c88c321264f82'}, + {'runtime2014bLinux.tar.gz': '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648'}, +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' From b91bda503adfaa09f53f6f148f9adbb6bf1aa2a8 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 5 Jun 2023 18:22:04 +0200 Subject: [PATCH 7582/9987] adding easyconfigs: PyQtGraph-0.13.3-foss-2022a.eb --- .../PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb new file mode 100644 index 00000000000..287fdcba532 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb @@ -0,0 +1,31 @@ +# updated: Denis Kristak +easyblock = 'PythonPackage' +# TH77EMBL adapted from PyQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb +name = 'PyQtGraph' +version = '0.13.3' + +homepage = 'http://www.pyqtgraph.org/' +description = """PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +github_account = 'pyqtgraph' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2dd03b68543fba85aea04e3c07311bfe7d5fd87f40ad6954e83b261d23f92de1'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyQt5', '5.15.5'), + ('PyOpenGL', '3.1.6'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'vis' + From 793d2ecdaad4aff911ade711a38dfdef487389fb Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 5 Jun 2023 18:24:12 +0200 Subject: [PATCH 7583/9987] adding easyconfigs: psycopg2-2.9.6-GCCcore-11.3.0.eb --- .../psycopg2/psycopg2-2.9.6-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.6-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..25a24c12236 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.6-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'psycopg2' +version = '2.9.6' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f15158418fd826831b28585e2ab48ed8df2d0d98f502a2b4fe619e7d5ca29011'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('PostgreSQL', '14.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'lib' From 9adb23e3463de2acb933d18c49bfd49e76c123ae Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 5 Jun 2023 18:25:49 +0200 Subject: [PATCH 7584/9987] adding easyconfigs: ParaView-5.11.1-foss-2022a-mpi.eb --- .../ParaView-5.11.1-foss-2022a-mpi.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi.eb new file mode 100644 index 00000000000..986c2b0cc0f --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi.eb @@ -0,0 +1,61 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.11.1' +versionsuffix = '-mpi' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +checksums = [ + 'de32f3e576b5f639ffc6903aa9e4cd46ac30c753185edc4366a7f305a6951b16', # ParaView-v5.11.1.tar.gz +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('XZ', '5.2.5'), + ('HDF5', '1.12.2'), + ('netCDF', '4.9.0'), + ('libGLU', '9.0.2'), + ('X11', '20220504'), + ('Mesa', '22.0.3'), + ('Qt5', '5.15.5'), + ('zlib', '1.2.12'), + ('FFmpeg', '4.4.2'), + ('Szip', '2.1.1'), +] + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' + From 403b3c6faf37cbe6fc23276e3dce94761ea6ad02 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 5 Jun 2023 18:27:25 +0200 Subject: [PATCH 7585/9987] adding easyconfigs: SUNDIALS-6.5.1-foss-2022a.eb --- .../s/SUNDIALS/SUNDIALS-6.5.1-foss-2022a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.5.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.5.1-foss-2022a.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.5.1-foss-2022a.eb new file mode 100644 index 00000000000..df08784684d --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.5.1-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '6.5.1' + +homepage = 'https://computation.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4252303805171e4dbdd19a01e52c1dcfe0dafc599c3cfedb0a5c2ffb045a8a75'] + +builddependencies = [('CMake', '3.23.1')] + +separate_build_dir = True + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' From 86c598f788a540d2166f6bce26d986b0ac19a427 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 18:28:36 +0200 Subject: [PATCH 7586/9987] add sanity check command + rename source file after download in 3d-dna easyconfig --- .../0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb index cf14ae0d7a3..5dec8adc921 100644 --- a/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb +++ b/easybuild/easyconfigs/0/3d-dna/3d-dna-180922-GCCcore-8.2.0-Python-2.7.15.eb @@ -11,7 +11,7 @@ description = """3D de novo assembly (3D DNA) pipeline""" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['https://github.com/theaidenlab/%(name)s/archive'] -sources = ['%s.zip' % local_githash] +sources = [{'download_filename': '%s.zip' % local_githash, 'filename': SOURCE_ZIP}] checksums = ['348c3e019ea29e47382eb2d85228a56bc11b316c130afabae016ad8e7d7640ca'] dependencies = [ @@ -21,8 +21,6 @@ dependencies = [ ('parallel', '20190622'), ] -modextrapaths = {'PATH': '.'} - postinstallcmds = ['chmod 755 %(installdir)s/*.sh'] sanity_check_paths = { @@ -30,4 +28,8 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["run-asm-pipeline.sh --help"] + +modextrapaths = {'PATH': ''} + moduleclass = 'bio' From fc2c1ad011c18a304fdb28d110ee510c4f69083e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 18:31:52 +0200 Subject: [PATCH 7587/9987] bump libjxl + libheif dependencies and bitshuffle extension in easyconfig for imagecodecs 2022.9.26 with foss/2022a --- .../i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb index 50e2daa8082..697a0ce3317 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb @@ -32,7 +32,7 @@ dependencies = [ ('libavif', '0.11.1'), ('libdeflate', '1.10'), ('libjpeg-turbo', '2.1.3'), - ('libjxl', '0.5'), + ('libjxl', '0.8.1'), ('LibLZF', '3.6'), ('libpng', '1.6.37'), ('XZ', '5.2.5'), @@ -49,17 +49,15 @@ dependencies = [ ('Brunsli', '0.1'), ('HDF5', '1.12.2'), ('h5py', '3.7.0'), - ('libheif', '1.12.0'), + ('libheif', '1.16.2'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('bitshuffle', '0.3.5', { - 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'], - 'sources': ['%(version)s.tar.gz'], - 'checksums': ['c3f4461d8013e3d9db0d58defec77b143164652de505a1fba3df088eaa19be2f'], + ('bitshuffle', '0.5.1', { + 'checksums': ['988f224739aa6858475a4c59172968c7b51cc657d2249580c8f96848708fbae3'], }), (name, version, { 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", From c81e0f78288f904372d406f55ac9f1ecb6d4e7a8 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 5 Jun 2023 18:33:11 +0200 Subject: [PATCH 7588/9987] CVodes from SUNDIALS 6.3.0 was bugged --- .../easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb index 2b8fbc5a70c..0692807beaf 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb @@ -15,9 +15,13 @@ checksums = ['7273622ea76a53373cee820f939613b15eea3dd83db6e1b127c5ed043f77dc5b'] dependencies = [ ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('pygraphviz', '1.10'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('PyQt5', '5.15.5'), ('Boost', '1.79.0'), - ('SUNDIALS', '6.3.0'), + ('SUNDIALS', '6.5.1'), ('yaml-cpp', '0.7.0'), ('ruamel.yaml', '0.17.21'), ] From 75d03ea09eeb5c038b7d421f3516effd176be4a5 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 5 Jun 2023 18:42:41 +0200 Subject: [PATCH 7589/9987] Update PyQtGraph-0.13.3-foss-2022a.eb removed empty lines at the end of the file --- easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb index 287fdcba532..fb3b71bfa6b 100644 --- a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.13.3-foss-2022a.eb @@ -28,4 +28,3 @@ download_dep_fail = True sanity_pip_check = True moduleclass = 'vis' - From 99c768cf0848de27c7cb7f9a296e51ce085b20e3 Mon Sep 17 00:00:00 2001 From: iotaka Date: Mon, 5 Jun 2023 18:43:44 +0200 Subject: [PATCH 7590/9987] Update ParaView-5.11.1-foss-2022a-mpi.eb removed empty lines at the end of the file --- .../easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi.eb index 986c2b0cc0f..479b6c9ee20 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi.eb @@ -58,4 +58,3 @@ sanity_check_commands = ['python -c "import paraview"'] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} moduleclass = 'vis' - From c9b38a46c1e2cdea9e1cdf02102ea0f8e8cdfcc9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Jun 2023 19:20:49 +0200 Subject: [PATCH 7591/9987] bump Blosc2 dependency to v2.6.1 in easyconfig for imagecodecs 2022.9.26 with foss/2022a --- .../i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb index 697a0ce3317..f33ff8c46b9 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2022a.eb @@ -21,7 +21,7 @@ dependencies = [ ('Brotli', '1.0.9'), ('bzip2', '1.0.8'), ('Blosc', '1.21.3'), - ('Blosc2', '2.4.3'), + ('Blosc2', '2.6.1'), ('CFITSIO', '4.2.0'), ('CharLS', '2.4.1'), ('giflib', '5.2.1'), From 2a7ab5cd4ad5560618c9c971d0cb76538057b358 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Jun 2023 09:48:30 +0200 Subject: [PATCH 7592/9987] fix homepage + description in cellpose 2.2.2 easyconfig --- easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb b/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb index 0fbccf1d9dd..ad0df673250 100644 --- a/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb +++ b/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb @@ -5,8 +5,8 @@ easyblock = 'PythonBundle' name = 'cellpose' version = '2.2.2' -homepage = '' -description = "" +homepage = 'https://cellpose.readthedocs.io' +description = "cellpose is an anatomical segmentation algorithm" toolchain = {'name': 'foss', 'version': '2022a'} From a453c8746b6c21e84e4da5d432bfc148b2cb8b0e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Jun 2023 09:48:48 +0200 Subject: [PATCH 7593/9987] remove commented out preinstallopts in cellpose 2.2.2 easyconfig --- easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb b/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb index ad0df673250..fd469c4c5da 100644 --- a/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb +++ b/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb @@ -27,8 +27,6 @@ dependencies = [ ('scikit-build', '0.15.0'), ] -# preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && " - use_pip = True exts_list = [ From 049919e35603d12e2485ec46f996e47694058ed3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Jun 2023 09:57:10 +0200 Subject: [PATCH 7594/9987] tweak setup.py to use opencv-contrib-python requirement, which is provided by OpenCV dependency of cellpose 2.2.2 --- easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb b/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb index fd469c4c5da..d3c7a6ebd25 100644 --- a/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb +++ b/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb @@ -46,7 +46,8 @@ exts_list = [ 'checksums': ['32eeba0d9ad52cc249d6a234b737c1808a6c5d7d9baae6453709eb74222b3433'], }), (name, version, { - 'preinstallopts': "sed -i 's/opencv-python-headless//g' setup.py && ", + # OpenCV dependency provides opencv-contrib-python (equivalent to opencv-python-headless) + 'preinstallopts': "sed -i 's/opencv-python-headless/opencv-contrib-python/g' setup.py && ", 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', 'use_pip_extras': 'gui', 'checksums': ['f21773d364d117eb6fd84c3fb27375845ef373793139ef1668c15491294a3b47'], From 9b3851a6ea70933e6ff9f0bc16cd5c7c2035e6dc Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 6 Jun 2023 11:16:53 +0200 Subject: [PATCH 7595/9987] adding easyconfigs: mannkendall-1.1.1-foss-2022a.eb --- .../mannkendall-1.1.1-foss-2022a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/mannkendall/mannkendall-1.1.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/mannkendall/mannkendall-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/m/mannkendall/mannkendall-1.1.1-foss-2022a.eb new file mode 100644 index 00000000000..ff16aa1859f --- /dev/null +++ b/easybuild/easyconfigs/m/mannkendall/mannkendall-1.1.1-foss-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'mannkendall' +version = '1.1.1' + +homepage = 'https://github.com/mmhs013/pymannkendall' +description = """A python package for non parametric Mann Kendall family of trend tests.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('statsmodels', '0.13.1'), +] + +exts_list = [ + (name, version, { + 'checksums': ['66993f53b78327b3e556511ccddd5929fbba38f4a8fbcb23754e37729d5d60fa'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From 1f1b0d08f8d8f20246080e08dbc2d1c478dec450 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 6 Jun 2023 11:18:37 +0200 Subject: [PATCH 7596/9987] adding easyconfigs: pyMannKendall-1.4.3-foss-2022a.eb --- .../pyMannKendall-1.4.3-foss-2022a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyMannKendall/pyMannKendall-1.4.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pyMannKendall/pyMannKendall-1.4.3-foss-2022a.eb b/easybuild/easyconfigs/p/pyMannKendall/pyMannKendall-1.4.3-foss-2022a.eb new file mode 100644 index 00000000000..a49ad264275 --- /dev/null +++ b/easybuild/easyconfigs/p/pyMannKendall/pyMannKendall-1.4.3-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonBundle' + +name = 'pyMannKendall' +version = '1.4.3' + +homepage = 'https://github.com/mmhs013/pymannkendall' +description = """A python package for non parametric Mann Kendall family of trend tests.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +exts_list = [ + ('pymannkendall', version, { + 'checksums': ['f9e3bbbb583b5285d15082aa0007825e5bea4dde9858d2e7ca81ee6f1e378e82'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From be804f789a19ead0941e35ba6ef79d7cc426753a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Jun 2023 11:13:20 +0200 Subject: [PATCH 7597/9987] adding easyconfigs: MAGeCK-0.5.9.5-foss-2022b.eb --- .../m/MAGeCK/MAGeCK-0.5.9.5-foss-2022b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.5-foss-2022b.eb diff --git a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.5-foss-2022b.eb b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.5-foss-2022b.eb new file mode 100644 index 00000000000..5082d969dbe --- /dev/null +++ b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.5-foss-2022b.eb @@ -0,0 +1,43 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +# Updated: Denis Kristak (Inuits) +easyblock = 'PythonPackage' + +name = 'MAGeCK' +version = '0.5.9.5' + +homepage = "https://sourceforge.net/p/mageck/wiki/Home/" +description = """Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify + important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed + by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute, and is being actively updated + by Wei Li lab from Children's National Medical Center.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b06a18036da63959cd7751911a46727aefe2fb1d8dd79d95043c3e3bdaf1d93a'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +postinstallcmds = ["cp -a demo %(installdir)s"] + +sanity_check_paths = { + 'files': ['bin/mageck', 'bin/mageckGSEA', 'bin/RRA'], + 'dirs': ['demo', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + # copy demo to build directory, after making sure it exists, so --sanity-check-only works; + # enable write permissions, since installation directory may be read-only + "mkdir -p %(builddir)s && cp -a %(installdir)s/demo %(builddir)s/ && chmod -R u+w %(builddir)s/demo", + "cd %(builddir)s/demo/demo1 && ./run.sh", +] + ["%s -h" % x for x in ['mageck', 'mageckGSEA']] + +moduleclass = 'bio' From 97839f11a447f0c6102f7914a83819887bf3f686 Mon Sep 17 00:00:00 2001 From: benjamic Date: Tue, 6 Jun 2023 12:44:09 +0200 Subject: [PATCH 7598/9987] adding easyconfigs: pypmt-1.1.0-foss-2022a.eb --- .../p/pypmt/pypmt-1.1.0-foss-2022a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2022a.eb b/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2022a.eb new file mode 100644 index 00000000000..e3b25e5c4ff --- /dev/null +++ b/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'pypmt' +version = '1.1.0' + +homepage = 'https://git.astron.nl/RD/pmt' +description = """PMT is a high-level software library capable of + collecting power consumption measurements on various hardware.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +sources = [{ + 'filename': 'pmt-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://git.astron.nl/RD', + 'repo_name': 'pmt', + 'tag': '%(version)s' + }, +}] + +checksums = ['d6332ce193dfdbc8073ba1fb600d1cebbd0a17c00f650003fab044aa721faf70'] + +configopts = '-DBUILD_PYTHON_PMT=1' + +sanity_check_paths = { + 'files': ["bin/Rapl-test"], + 'dirs': [ + "lib", + "lib/python", + "include"], +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python'] +} + +moduleclass = 'lib' From 215b256b95b43f15b552599b662b703967872371 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Jun 2023 13:27:30 +0200 Subject: [PATCH 7599/9987] fix --sanity-check-only for MAGeCK v0.5.9.4 --- .../m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb | 15 +++++++++++++-- .../m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb | 15 +++++++++++++-- 2 files changed, 26 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb index ea581cdd09d..fa80cdacb44 100644 --- a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb @@ -29,7 +29,18 @@ download_dep_fail = True sanity_pip_check = True use_pip = True -sanity_check_commands = ["cd %(builddir)s/%(namelower)s-%(version)s/demo/demo1 && ./run.sh"] + [ - "%s -h" % x for x in ['mageck', 'mageckGSEA']] +postinstallcmds = ["cp -a demo %(installdir)s"] + +sanity_check_paths = { + 'files': ['bin/mageck', 'bin/mageckGSEA', 'bin/RRA'], + 'dirs': ['demo', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + # copy demo to build directory, after making sure it exists, so --sanity-check-only works; + # enable write permissions, since installation directory may be read-only + "mkdir -p %(builddir)s && cp -a %(installdir)s/demo %(builddir)s/ && chmod -R u+w %(builddir)s/demo", + "cd %(builddir)s/demo/demo1 && ./run.sh", +] + ["%s -h" % x for x in ['mageck', 'mageckGSEA']] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb index cc54713c3c6..dcc58ecf8bf 100644 --- a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb @@ -30,7 +30,18 @@ download_dep_fail = True sanity_pip_check = True use_pip = True -sanity_check_commands = ["cd %(builddir)s/%(namelower)s-%(version)s/demo/demo1 && ./run.sh"] + [ - "%s -h" % x for x in ['mageck', 'mageckGSEA']] +postinstallcmds = ["cp -a demo %(installdir)s"] + +sanity_check_paths = { + 'files': ['bin/mageck', 'bin/mageckGSEA', 'bin/RRA'], + 'dirs': ['demo', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + # copy demo to build directory, after making sure it exists, so --sanity-check-only works; + # enable write permissions, since installation directory may be read-only + "mkdir -p %(builddir)s && cp -a %(installdir)s/demo %(builddir)s/ && chmod -R u+w %(builddir)s/demo", + "cd %(builddir)s/demo/demo1 && ./run.sh", +] + ["%s -h" % x for x in ['mageck', 'mageckGSEA']] moduleclass = 'bio' From cc52adda113a778be495f64caaa9e4ee9120877f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Jun 2023 13:38:10 +0200 Subject: [PATCH 7600/9987] use gfbf/2022b as toolchain for MAGeCK 0.5.9.5 --- ...AGeCK-0.5.9.5-foss-2022b.eb => MAGeCK-0.5.9.5-gfbf-2022b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/MAGeCK/{MAGeCK-0.5.9.5-foss-2022b.eb => MAGeCK-0.5.9.5-gfbf-2022b.eb} (96%) diff --git a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.5-foss-2022b.eb b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.5-gfbf-2022b.eb similarity index 96% rename from easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.5-foss-2022b.eb rename to easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.5-gfbf-2022b.eb index 5082d969dbe..b623b1b15ef 100644 --- a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.5-foss-2022b.eb +++ b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.5-gfbf-2022b.eb @@ -11,7 +11,7 @@ description = """Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeC by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute, and is being actively updated by Wei Li lab from Children's National Medical Center.""" -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'gfbf', 'version': '2022b'} dependencies = [ ('Python', '3.10.8'), From 76a0bf56a47baa2cafb2f37372e8f7aa94678d84 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 6 Jun 2023 14:20:48 +0200 Subject: [PATCH 7601/9987] adding easyconfigs: Sniffles-2.0.7-foss-2022a.eb --- .../s/Sniffles/Sniffles-2.0.7-foss-2022a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb new file mode 100644 index 00000000000..419acb4c4f6 --- /dev/null +++ b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'Sniffles' +version = '2.0.7' + +homepage = 'https://github.com/fritzsedlazeck/Sniffles' +description = """A fast structural variant caller for long-read sequencing, + Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Pysam', '0.20.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': '%(namelower)s', + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['bf532eb0b3aaeaee840100a3bb3339f1d5175ba98adfe3cf19685b0abb0885a1'], + }), +] + +sanity_check_commands = [ + "python -c 'from sniffles import sv'", + "sniffles --help", +] + +moduleclass = 'tools' From be7758e28a8f0562b3c840b57f64f523cfd19745 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 6 Jun 2023 14:40:49 +0200 Subject: [PATCH 7602/9987] dep version fix --- easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb index 419acb4c4f6..52a15c05c4c 100644 --- a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb +++ b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), - ('Pysam', '0.20.0'), + ('Pysam', '0.19.1'), ] use_pip = True From 157dcd87e1fca4bb5133db9aba2714254ff2e833 Mon Sep 17 00:00:00 2001 From: benjamic Date: Tue, 6 Jun 2023 14:40:56 +0200 Subject: [PATCH 7603/9987] Updating sanity check command and checksum issue --- .../easyconfigs/p/pypmt/pypmt-1.1.0-foss-2022a.eb | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2022a.eb b/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2022a.eb index e3b25e5c4ff..b52a9b4b673 100644 --- a/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2022a.eb @@ -15,16 +15,9 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ] -sources = [{ - 'filename': 'pmt-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://git.astron.nl/RD', - 'repo_name': 'pmt', - 'tag': '%(version)s' - }, -}] - -checksums = ['d6332ce193dfdbc8073ba1fb600d1cebbd0a17c00f650003fab044aa721faf70'] +source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] +sources = ['pmt-%(version)s.tar.gz'] +checksums = ['ab342ec33992c1ad4c42e0e66031710fe6320f73a1ca2a6e34cb1d4739da781f'] configopts = '-DBUILD_PYTHON_PMT=1' @@ -35,6 +28,7 @@ sanity_check_paths = { "lib/python", "include"], } +sanity_check_commands = [('python', "-c 'import pmt'")] modextrapaths = { 'PYTHONPATH': ['lib/python'] From a7b4633e90c08568620cbca5202f2678acce6d89 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 6 Jun 2023 14:53:45 +0200 Subject: [PATCH 7604/9987] sanity check fixes --- .../easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb index 52a15c05c4c..0567ecc4c20 100644 --- a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb +++ b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb @@ -19,15 +19,19 @@ sanity_pip_check = True exts_list = [ (name, version, { - 'modulename': '%(namelower)s', 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['bf532eb0b3aaeaee840100a3bb3339f1d5175ba98adfe3cf19685b0abb0885a1'], }), ] +sanity_check_paths = { + 'files': ['bin/sniffles'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + sanity_check_commands = [ "python -c 'from sniffles import sv'", "sniffles --help", ] -moduleclass = 'tools' +moduleclass = 'bio' From 1282c2882134b91ed4a0e3e7e139a6bcfaea9b8b Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 6 Jun 2023 16:15:19 +0200 Subject: [PATCH 7605/9987] adding easyconfigs: affinity-20230524-foss-2022a.eb, affinity-20230524-intel-2022a.eb --- .../affinity/affinity-20230524-foss-2022a.eb | 29 +++++++++++++++++++ .../affinity/affinity-20230524-intel-2022a.eb | 29 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/a/affinity/affinity-20230524-foss-2022a.eb create mode 100644 easybuild/easyconfigs/a/affinity/affinity-20230524-intel-2022a.eb diff --git a/easybuild/easyconfigs/a/affinity/affinity-20230524-foss-2022a.eb b/easybuild/easyconfigs/a/affinity/affinity-20230524-foss-2022a.eb new file mode 100644 index 00000000000..418c6686a6f --- /dev/null +++ b/easybuild/easyconfigs/a/affinity/affinity-20230524-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'affinity' +version = '20230524' +local_commit = '7d4d426' + +homepage = 'https://github.com/vkarak/affinity' +description = """A small C++ wrapper for managing Linux CPU sets and CPU affinity. +It also includes a tool to report binding, which is useful for testing different binding options""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/vkarak/affinity/archive/'] +sources = ['%s.tar.gz' % local_commit] + +buildopts = r'CXX="$MPICXX" OPENMP=1 MPI=1 ' +buildopts += '&& mkdir -p bin && mv affinity bin/' +buildopts +='&& rm Makefile && rm README.md && rm -r src && rm -r tests' + +files_to_copy = ['*'] + +sanity_check_commands = ['mpirun -np 1 affinity'] + +sanity_check_paths = { + 'files': ['bin/affinity'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/affinity/affinity-20230524-intel-2022a.eb b/easybuild/easyconfigs/a/affinity/affinity-20230524-intel-2022a.eb new file mode 100644 index 00000000000..6525be240dd --- /dev/null +++ b/easybuild/easyconfigs/a/affinity/affinity-20230524-intel-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'affinity' +version = '20230524' +local_commit = '7d4d426' + +homepage = 'https://github.com/vkarak/affinity' +description = """A small C++ wrapper for managing Linux CPU sets and CPU affinity. +It also includes a tool to report binding, which is useful for testing different binding options""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://github.com/vkarak/affinity/archive/'] +sources = ['%s.tar.gz' % local_commit] + +buildopts = r'CXX="$MPICXX" OPENMP=1 MPI=1 ' +buildopts += '&& mkdir -p bin && mv affinity bin/' +buildopts +='&& rm Makefile && rm README.md && rm -r src && rm -r tests' + +files_to_copy = ['*'] + +sanity_check_commands = ['mpirun -np 1 affinity'] + +sanity_check_paths = { + 'files': ['bin/affinity'], + 'dirs': [], +} + +moduleclass = 'tools' From 0220b16c328c9e285ac45f788ddda88ca6764b09 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 6 Jun 2023 16:35:11 +0200 Subject: [PATCH 7606/9987] Update Cantera-2.6.0-foss-2022a.eb --- easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb index 0692807beaf..c5e1ed193ac 100644 --- a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb @@ -19,7 +19,6 @@ dependencies = [ ('pygraphviz', '1.10'), ('JupyterLab', '3.5.0'), ('matplotlib', '3.5.2'), - ('PyQt5', '5.15.5'), ('Boost', '1.79.0'), ('SUNDIALS', '6.5.1'), ('yaml-cpp', '0.7.0'), From 0b637dae9a7e19cb84e79ebe330081024ea22662 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 6 Jun 2023 16:36:53 +0200 Subject: [PATCH 7607/9987] Updated checksums, fixed style issue --- .../easyconfigs/a/affinity/affinity-20230524-foss-2022a.eb | 3 ++- .../easyconfigs/a/affinity/affinity-20230524-intel-2022a.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/affinity/affinity-20230524-foss-2022a.eb b/easybuild/easyconfigs/a/affinity/affinity-20230524-foss-2022a.eb index 418c6686a6f..ca44c02246d 100644 --- a/easybuild/easyconfigs/a/affinity/affinity-20230524-foss-2022a.eb +++ b/easybuild/easyconfigs/a/affinity/affinity-20230524-foss-2022a.eb @@ -12,10 +12,11 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://github.com/vkarak/affinity/archive/'] sources = ['%s.tar.gz' % local_commit] +checksums = ['d4d245deca0ac46c870773f6c5f43d4a5d4d2a13cefdf4d912f3588ee2d41072'] buildopts = r'CXX="$MPICXX" OPENMP=1 MPI=1 ' buildopts += '&& mkdir -p bin && mv affinity bin/' -buildopts +='&& rm Makefile && rm README.md && rm -r src && rm -r tests' +buildopts += '&& rm Makefile && rm README.md && rm -r src && rm -r tests' files_to_copy = ['*'] diff --git a/easybuild/easyconfigs/a/affinity/affinity-20230524-intel-2022a.eb b/easybuild/easyconfigs/a/affinity/affinity-20230524-intel-2022a.eb index 6525be240dd..03af1139e3a 100644 --- a/easybuild/easyconfigs/a/affinity/affinity-20230524-intel-2022a.eb +++ b/easybuild/easyconfigs/a/affinity/affinity-20230524-intel-2022a.eb @@ -12,10 +12,11 @@ toolchain = {'name': 'intel', 'version': '2022a'} source_urls = ['https://github.com/vkarak/affinity/archive/'] sources = ['%s.tar.gz' % local_commit] +checksums = ['d4d245deca0ac46c870773f6c5f43d4a5d4d2a13cefdf4d912f3588ee2d41072'] buildopts = r'CXX="$MPICXX" OPENMP=1 MPI=1 ' buildopts += '&& mkdir -p bin && mv affinity bin/' -buildopts +='&& rm Makefile && rm README.md && rm -r src && rm -r tests' +buildopts += '&& rm Makefile && rm README.md && rm -r src && rm -r tests' files_to_copy = ['*'] From 2ff125a381584f57b1301c1076fedeaf69de092e Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 6 Jun 2023 17:02:35 +0200 Subject: [PATCH 7608/9987] Added workaround for jsc-zen2 --- .../easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb index e5c8cb0195e..dd4080b2086 100644 --- a/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb @@ -77,6 +77,6 @@ sanity_check_paths = { sanity_check_commands = ["alleleCounter --help"] -modextrapaths = {'PERL5LIB': 'lib/perl5'} +modextrapaths = {'PERL5LIB': ['lib/perl5', 'lib/perl5/site_perl/%(perlver)s']} moduleclass = 'bio' From 93b1ab481889b4bd9085ef6c4153e7344c61133e Mon Sep 17 00:00:00 2001 From: benjamic Date: Tue, 6 Jun 2023 17:27:36 +0200 Subject: [PATCH 7609/9987] adding easyconfigs: pmt-1.1.0-GCCcore-11.3.0.eb --- .../p/pmt/pmt-1.1.0-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/pmt/pmt-1.1.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pmt/pmt-1.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b2eda8583d9 --- /dev/null +++ b/easybuild/easyconfigs/p/pmt/pmt-1.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'pmt' +version = '1.1.0' + +homepage = 'https://git.astron.nl/RD/pmt' +description = """PMT is a high-level software library capable of + collecting power consumption measurements on various hardware.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38') +] + +source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] +sources = ['pmt-%(version)s.tar.gz'] +checksums = ['ab342ec33992c1ad4c42e0e66031710fe6320f73a1ca2a6e34cb1d4739da781f'] + +sanity_check_paths = { + 'files': ["bin/Rapl-test"], + 'dirs': ["lib", "include"], +} + +moduleclass = 'lib' From b96deac15dd16def11e2513aac12dd9c810a9dac Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 6 Jun 2023 22:41:46 +0000 Subject: [PATCH 7610/9987] adding easyconfigs: PMIx-4.2.3-GCCcore-12.3.0.eb, UCC-1.1.0-GCCcore-12.3.0.eb, OpenMPI-4.1.5-GCC-12.3.0.eb --- .../o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb | 62 +++++++++++++++++++ .../p/PMIx/PMIx-4.2.3-GCCcore-12.3.0.eb | 45 ++++++++++++++ .../u/UCC/UCC-1.1.0-GCCcore-12.3.0.eb | 41 ++++++++++++ 3 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.2.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb new file mode 100644 index 00000000000..14ad304b8bb --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb @@ -0,0 +1,62 @@ +name = 'OpenMPI' +version = '4.1.5' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', +] +checksums = [ + {'openmpi-4.1.5.tar.bz2': 'a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3'}, + {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, + {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, +] + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('Perl', '5.36.1'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('hwloc', '2.9.1'), + ('libevent', '2.1.12'), + ('UCX', '1.14.1'), + ('libfabric', '1.18.0'), + ('PMIx', '4.2.3'), + ('UCC', '1.1.0'), +] + +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' + +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0495a0ed3ed --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.3-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '4.2.3' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['c3d9d6885ae39c15627a86dc4718e050baf604acda71b8b9e2ee3b12ad5c2d2a'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.2.13'), + ('hwloc', '2.9.1'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fee0812efd6 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'UCC' +version = '1.1.0' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = ['UCC-%(version)s-multiple_component_paths.patch'] +checksums = [ + {'v1.1.0.tar.gz': '74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'}, + {'UCC-1.1.0-multiple_component_paths.patch': '3081d0f694331daa4a88a0fa3fb54b9a918015248ae5eb7b3157b924abd31bee'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCX', '1.14.1'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/ucc_info'], + 'dirs': ['include', 'lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +moduleclass = 'lib' From 0a838b38e5c2f10d9c1b4a15f5f8918e597d72d9 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 7 Jun 2023 14:05:18 +0000 Subject: [PATCH 7611/9987] Update LAPACK test fix patch to include single prec for aarch64 --- .../o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.3.23_fix-lapack-test.patch | 10 ++++++++++ 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb index f63af09621e..2368237262b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb @@ -29,7 +29,7 @@ checksums = [ {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_fix-parallel-build.patch': 'abe10ba3b0ca54772dbf235596e35325a5159018f6a60cfc88824c2c220d99d9'}, - {'OpenBLAS-0.3.23_fix-lapack-test.patch': '22a087b5194f0767ebc94ddb0c44390a7646b966408cabc4b88aef9f02b707da'}, + {'OpenBLAS-0.3.23_fix-lapack-test.patch': 'f6b3d81061f136e34aaf5359bb80fb9d2bba28825cc1dd26179b8dd01a9a0054'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-lapack-test.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-lapack-test.patch index bb7aa1cd1f1..dfb16cced30 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-lapack-test.patch +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-lapack-test.patch @@ -13,3 +13,13 @@ Author: Bart Oldeman 1 1 1 2 1 Parameters NB, NBMIN, NXOVER, NS, NBCOL 10 Threshold for test ratios .TRUE. Put T to test the error exits +--- OpenBLAS-0.3.23/lapack-netlib/TESTING/sgd.in.orig 2023-06-06 11:01:50.512947527 +0000 ++++ OpenBLAS-0.3.23/lapack-netlib/TESTING/sgd.in 2023-06-06 11:02:05.318078733 +0000 +@@ -1,6 +1,6 @@ + SGS Data for the Real Nonsymmetric Schur Form Driver + 5 Number of matrix dimensions +-2 6 10 12 20 30 Matrix dimensions ++6 2 10 12 20 30 Matrix dimensions + 1 1 1 2 1 Parameters NB, NBMIN, NXOVER, NS, NBCOL + 10 Threshold for test ratios + .TRUE. Put T to test the error exits From 7d6f730a1e8144511f7000811b960360926eb3c7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 7 Jun 2023 17:00:33 +0200 Subject: [PATCH 7612/9987] adding easyconfigs: CASA-6.5.5-21-py3.8.eb --- .../easyconfigs/c/CASA/CASA-6.5.5-21-py3.8.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/CASA/CASA-6.5.5-21-py3.8.eb diff --git a/easybuild/easyconfigs/c/CASA/CASA-6.5.5-21-py3.8.eb b/easybuild/easyconfigs/c/CASA/CASA-6.5.5-21-py3.8.eb new file mode 100644 index 00000000000..96b5132b10a --- /dev/null +++ b/easybuild/easyconfigs/c/CASA/CASA-6.5.5-21-py3.8.eb @@ -0,0 +1,27 @@ +easyblock = "Tarball" + +name = 'CASA' +version = '6.5.5-21' +versionsuffix = '-py3.8' + +homepage = 'https://casa.nrao.edu/' +description = """ +CASA, the Common Astronomy Software Applications package, is the primary data processing software for the Atacama Large +Millimeter/submillimeter Array (ALMA) and NSF's Karl G. Jansky Very Large Array (VLA), and is frequently used also for +other radio telescopes. The CASA software can process data from both single-dish and aperture-synthesis telescopes, and +one of its core functionalities is to support the data reduction and imaging pipelines for ALMA, VLA and the VLA Sky +Survey (VLASS). +""" + +toolchain = SYSTEM + +source_urls = ['https://casa.nrao.edu/download/distro/casa/release/rhel/'] +sources = ['casa-%%(version)s%s.tar.xz' % versionsuffix] +checksums = ['f1bbd088a1aa0130984a684ade03702f2ff93627af14b038dce01d8253f58c15'] + +sanity_check_paths = { + 'files': ['bin/casaviewer', 'bin/casa'], + 'dirs': [] +} + +moduleclass = 'astro' From 42ea9cc986546e7d6d95a69698f06734c83c0af5 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 7 Jun 2023 20:35:43 +0000 Subject: [PATCH 7613/9987] adding easyconfigs: FlexiBLAS-3.3.1-GCC-12.3.0.eb --- .../f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-12.3.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..b1ada954f80 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-12.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'FlexiBLAS' +version = '3.3.1' + +homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' +description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation +used by a program without recompiling or relinking it.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" +toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), # required for running the tests + ('BLIS', '0.9.0'), +] + +dependencies = [ + ('OpenBLAS', '0.3.23'), +] + +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +local_backends = ['OpenBLAS', 'BLIS'] + +# imkl supplies its backend via the imkl module, not as a dependency +if ARCH == 'x86_64': + local_backends.append('imkl') + +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://gitlab.mpi-magdeburg.mpg.de/api/v4/projects/386/packages/generic/flexiblas-source/v3.3.1/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['bbeebf5e5a006924558fec43f49affbe1aaa4cbacfc472a9ff6066ffda142e18'], + 'backends': local_backends, + }), + ('LAPACK', '3.11.0', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['4b9ba79bfd4921ca820e83979db76ab3363155709444a787979e81c22285ffa9'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + +moduleclass = 'lib' From e29c61509fd28263bc0689f3638faa5da0255381 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 7 Jun 2023 21:32:56 +0000 Subject: [PATCH 7614/9987] Avoid overlong line --- .../easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-12.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-12.3.0.eb index b1ada954f80..9ea54c6b1e5 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-12.3.0.eb @@ -35,7 +35,8 @@ sanity_check_all_components = True # Also build and install LAPACKE, which FlexiBLAS does not support yet components = [ (name, version, { - 'source_urls': ['https://gitlab.mpi-magdeburg.mpg.de/api/v4/projects/386/packages/generic/flexiblas-source/v3.3.1/'], + 'source_urls': + ['https://gitlab.mpi-magdeburg.mpg.de/api/v4/projects/386/packages/generic/flexiblas-source/v3.3.1/'], 'sources': [SOURCELOWER_TAR_GZ], 'checksums': ['bbeebf5e5a006924558fec43f49affbe1aaa4cbacfc472a9ff6066ffda142e18'], 'backends': local_backends, From 9328e740ca14b08eada4253ebb65db6f9f510157 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 8 Jun 2023 01:47:32 +0000 Subject: [PATCH 7615/9987] adding easyconfigs: gompi-2023.05.eb, OSU-Micro-Benchmarks-7.1-1-gompi-2023.05.eb, FFTW.MPI-3.3.10-gompi-2023.05.eb --- .../FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023.05.eb | 19 ++++++++++++++ .../easyconfigs/g/gompi/gompi-2023.05.eb | 20 ++++++++++++++ ...SU-Micro-Benchmarks-7.1-1-gompi-2023.05.eb | 26 +++++++++++++++++++ 3 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023.05.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2023.05.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-gompi-2023.05.eb diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023.05.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023.05.eb new file mode 100644 index 00000000000..f62882baa61 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023.05.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2023.05'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2023.05.eb b/easybuild/easyconfigs/g/gompi/gompi-2023.05.eb new file mode 100644 index 00000000000..c04bdc52a3a --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2023.05.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2023.05' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '12.3.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.1.5', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-gompi-2023.05.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-gompi-2023.05.eb new file mode 100644 index 00000000000..5701c50be05 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-gompi-2023.05.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.1-1' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2023.05'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['85f4dd8be1df31255e232852769ae5b82e87a5fb14be2f8eba1ae9de8ffe391a'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 6bbbc4fab60906daff5beb4c4e581fa3981a5936 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Jun 2023 09:35:23 +0200 Subject: [PATCH 7616/9987] toolchain fix --- .../s/Sniffles/Sniffles-2.0.7-GCC-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-GCC-11.3.0.eb new file mode 100644 index 00000000000..48aa053395e --- /dev/null +++ b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-GCC-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'Sniffles' +version = '2.0.7' + +homepage = 'https://github.com/fritzsedlazeck/Sniffles' +description = """A fast structural variant caller for long-read sequencing, + Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('Pysam', '0.19.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['bf532eb0b3aaeaee840100a3bb3339f1d5175ba98adfe3cf19685b0abb0885a1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/sniffles'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'from sniffles import sv'", + "sniffles --help", +] + +moduleclass = 'bio' From 5771a83de9f19c5c6c748892db790a6d6b0924ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Jun 2023 09:46:46 +0200 Subject: [PATCH 7617/9987] remove duplicate --- .../s/Sniffles/Sniffles-2.0.7-foss-2022a.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb deleted file mode 100644 index 0567ecc4c20..00000000000 --- a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.0.7-foss-2022a.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Sniffles' -version = '2.0.7' - -homepage = 'https://github.com/fritzsedlazeck/Sniffles' -description = """A fast structural variant caller for long-read sequencing, - Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -dependencies = [ - ('Python', '3.10.4'), - ('Pysam', '0.19.1'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - (name, version, { - 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['bf532eb0b3aaeaee840100a3bb3339f1d5175ba98adfe3cf19685b0abb0885a1'], - }), -] - -sanity_check_paths = { - 'files': ['bin/sniffles'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "python -c 'from sniffles import sv'", - "sniffles --help", -] - -moduleclass = 'bio' From 1cbf39de3c422271da8a81fc3b1abddd52763de0 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Thu, 8 Jun 2023 14:41:10 +0200 Subject: [PATCH 7618/9987] Fix toolchain for networkx-3.0 foss-2022b -> gfbf-2022b --- .../{networkx-3.0-foss-2022b.eb => networkx-3.0-gfbf-2022b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/n/networkx/{networkx-3.0-foss-2022b.eb => networkx-3.0-gfbf-2022b.eb} (92%) diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.0-foss-2022b.eb b/easybuild/easyconfigs/n/networkx/networkx-3.0-gfbf-2022b.eb similarity index 92% rename from easybuild/easyconfigs/n/networkx/networkx-3.0-foss-2022b.eb rename to easybuild/easyconfigs/n/networkx/networkx-3.0-gfbf-2022b.eb index 5825b79f6d4..72e1e9f112e 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-3.0-foss-2022b.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-3.0-gfbf-2022b.eb @@ -7,7 +7,7 @@ homepage = 'https://pypi.python.org/pypi/networkx' description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.""" -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'gfbf', 'version': '2022b'} sources = [SOURCE_TAR_GZ] checksums = ['9a9992345353618ae98339c2b63d8201c381c2944f38a2ab49cb45a4c667e412'] From 4cedf283763ac62caccea0f144babc1e14e2c630 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 8 Jun 2023 14:51:31 +0200 Subject: [PATCH 7619/9987] Remove unused PyTorch-1.12.1_use-predefined-data-in-test-optim.patch The usage of this patch was removed in #17737 so this patch is no longer required to be kept. --- ....1_use-predefined-data-in-test-optim.patch | 132 ------------------ 1 file changed, 132 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch deleted file mode 100644 index 5dc393c17fd..00000000000 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch +++ /dev/null @@ -1,132 +0,0 @@ -The test test_optim.test_nadam has high error rate, this let's the test use -predefined data instead to be more stable. See -https://github.com/pytorch/pytorch/issues/98414 - -Viktor Rehnberg -diff --git a/test/test_optim.py b/test/test_optim.py -index 6d587b4b352..c8ec9db87e1 100644 ---- a/test/test_optim.py -+++ b/test/test_optim.py -@@ -244,8 +244,14 @@ class TestOptim(TestCase): - return set(k for k in obj.__dict__ if not k.startswith('_')) - self.assertEqual(getPublicAttr(optimizer), getPublicAttr(deepcopy(optimizer))) - -- def _test_basic_cases(self, constructor, scheduler_constructors=None, -- ignore_multidevice=False, constructor_accepts_maximize=False): -+ def _test_basic_cases( -+ self, -+ constructor, -+ scheduler_constructors=None, -+ ignore_multidevice=False, -+ constructor_accepts_maximize=False, -+ use_predefined_data=False, -+ ): - if scheduler_constructors is None: - scheduler_constructors = [] - -@@ -254,26 +260,60 @@ class TestOptim(TestCase): - return lambda weight, bias: constructor(weight, bias, maximize) - return constructor - -+ def make_weight_tensor(): -+ if use_predefined_data: -+ return torch.Tensor([ -+ [ 0.6390, -0.5524, -0.1877, -1.1132, 0.3412], -+ [-0.6489, -0.6220, -1.2537, -0.0966, 0.5481], -+ [-0.6923, 0.5768, -0.9141, 1.9410, 1.0036], -+ [ 0.5842, 1.1618, -0.1871, 1.0344, 0.5668], -+ [ 0.2123, 2.3076, 0.7522, -0.7059, 1.3849], -+ [-0.1537, 0.5159, -1.2004, 0.2017, -0.0903], -+ [ 0.9434, -0.7030, 0.0618, -1.2951, 1.7721], -+ [ 0.5890, -1.0763, -1.2541, -0.8403, -0.4343], -+ [-0.2065, -0.6883, 0.8464, -0.7792, 0.6750], -+ [-1.6577, 0.4532, 0.0791, 0.2243, 0.1148], -+ ]) -+ else: -+ return torch.randn(10, 5) -+ -+ def make_bias_tensor(): -+ if use_predefined_data: -+ return torch.Tensor([ -+ -2.4031, -0.9295, -1.0762, 0.4600, -1.8620, -0.6234, 0.1999, -0.0612, 0.8319, -1.6673, -+ ]) -+ else: -+ return torch.randn(10) -+ -+ def make_input_tensor(): -+ if use_predefined_data: -+ return torch.Tensor([1.1119, -0.4309, -0.7759, -0.0659, 0.4746]) -+ else: -+ return torch.randn(5) -+ -+ def make_non_contiguous(tensor): -+ return torch.stack([tensor, tensor]).view(*tensor.size(), 2)[..., 0] -+ - for maximize in (True, False): - self._test_state_dict( -- torch.randn(10, 5), -- torch.randn(10), -- torch.randn(5), -+ make_weight_tensor(), -+ make_bias_tensor(), -+ make_input_tensor(), - make_two_arg_constructor(constructor, maximize), - ) - self._test_basic_cases_template( -- torch.randn(10, 5), -- torch.randn(10), -- torch.randn(5), -+ make_weight_tensor(), -+ make_bias_tensor(), -+ make_input_tensor(), - constructor, - scheduler_constructors, - constructor_accepts_maximize, - ) - # non-contiguous parameters - self._test_basic_cases_template( -- torch.randn(10, 5, 2)[..., 0], -- torch.randn(10, 2)[..., 0], -- torch.randn(5), -+ make_non_contiguous(make_weight_tensor()), -+ make_non_contiguous(make_bias_tensor()), -+ make_input_tensor(), - constructor, - scheduler_constructors, - constructor_accepts_maximize, -@@ -282,9 +322,9 @@ class TestOptim(TestCase): - if not torch.cuda.is_available(): - return - self._test_basic_cases_template( -- torch.randn(10, 5).cuda(), -- torch.randn(10).cuda(), -- torch.randn(5).cuda(), -+ make_weight_tensor().cuda(), -+ make_bias_tensor().cuda(), -+ make_input_tensor().cuda(), - constructor, - scheduler_constructors, - constructor_accepts_maximize, -@@ -293,9 +333,9 @@ class TestOptim(TestCase): - if not torch.cuda.device_count() > 1 or ignore_multidevice: - return - self._test_basic_cases_template( -- torch.randn(10, 5).cuda(0), -- torch.randn(10).cuda(1), -- torch.randn(5).cuda(0), -+ make_weight_tensor().cuda(0), -+ make_bias_tensor().cuda(1), -+ make_input_tensor().cuda(0), - constructor, - scheduler_constructors, - constructor_accepts_maximize, -@@ -668,7 +708,8 @@ class TestOptim(TestCase): - self._test_basic_cases( - lambda weight, bias: optimizer( - self._build_params_dict(weight, bias, lr=1e-2), -- lr=1e-3) -+ lr=1e-3), -+ use_predefined_data=True, - ) - self._test_basic_cases( - lambda weight, bias: optimizer([weight, bias], lr=1e-3, weight_decay=0.1, momentum_decay=6e-3) From 0068213362daefe1f920f457725cb86f28782197 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Jun 2023 22:01:15 +0200 Subject: [PATCH 7620/9987] add svglite extension to R 4.2.1 + 4.2.2 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 6 ++++++ easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 3 +++ 2 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index daf90905c51..45606708fe8 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3529,6 +3529,12 @@ exts_list = [ ('RBesT', '1.6-6', { 'checksums': ['0301ee95f9b46722b9e1bacd668b570eee14badaa8ca0a7d0ccd8d3d9068d485'], }), + ('systemfonts', '1.0.4', { + 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], + }), + ('svglite', '2.1.1', { + 'checksums': ['48700169eec1b05dbee9e2bae000aa84c544617b018cb3ac431a128cfd8dac56'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index b0b5f3b307f..2eb8dcd4e1e 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3597,6 +3597,9 @@ exts_list = [ ('RBesT', '1.6-6', { 'checksums': ['0301ee95f9b46722b9e1bacd668b570eee14badaa8ca0a7d0ccd8d3d9068d485'], }), + ('svglite', '2.1.1', { + 'checksums': ['48700169eec1b05dbee9e2bae000aa84c544617b018cb3ac431a128cfd8dac56'], + }), ] moduleclass = 'lang' From 0c1c1a8148521303a7899db5d7d6d5d2a7b23816 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 9 Jun 2023 09:01:35 +0100 Subject: [PATCH 7621/9987] enable building static libs^Cnd check for libexslt.* in libxslt --- .../easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb | 6 ++++-- .../easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb index 2b58bca7a16..f35fce8e6e9 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb @@ -24,10 +24,12 @@ dependencies = [ ] # Make sure it doesn't pick up OS installed libgcrypt or Python -configopts = '--with-crypto=no --with-python=no ' +# enable building static libs +configopts = '--with-crypto=no --with-python=no --enable-static=yes ' sanity_check_paths = { - 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a', + 'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a',], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb index 171353e0fac..ba5d4ea4226 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb @@ -24,10 +24,12 @@ dependencies = [ ] # Make sure it doesn't pick up OS installed libgcrypt or Python -configopts = '--with-crypto=no --with-python=no ' +# enable building static libs +configopts = '--with-crypto=no --with-python=no --enable-static=yes ' sanity_check_paths = { - 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a', + 'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a',], 'dirs': [], } From 0890be1e6ad0c41c0d34a150c18ec04b107e045a Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 9 Jun 2023 09:19:32 +0100 Subject: [PATCH 7622/9987] add include folder sanity check and fix for CI --- .../easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb | 4 ++-- .../easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb index f35fce8e6e9..4ca890df973 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.37-GCCcore-12.2.0.eb @@ -29,8 +29,8 @@ configopts = '--with-crypto=no --with-python=no --enable-static=yes ' sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a', - 'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a',], - 'dirs': [], + 'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a'], + 'dirs': ['include/libxslt', 'include/libexslt'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb index ba5d4ea4226..3e21064eaf4 100644 --- a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb @@ -29,8 +29,8 @@ configopts = '--with-crypto=no --with-python=no --enable-static=yes ' sanity_check_paths = { 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a', - 'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a',], - 'dirs': [], + 'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a'], + 'dirs': ['include/libxslt', 'include/libexslt'], } moduleclass = 'lib' From 94efe4157d5743333015db371b99d864b9f2d93b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 9 Jun 2023 10:27:12 +0200 Subject: [PATCH 7623/9987] adding easyconfigs: SRA-Toolkit-3.0.5-gompi-2021a.eb, ncbi-vdb-3.0.5-gompi-2021a.eb --- .../n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2021a.eb | 38 ++++++++++ .../SRA-Toolkit-3.0.5-gompi-2021a.eb | 69 +++++++++++++++++++ 2 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2021a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2021a.eb new file mode 100644 index 00000000000..73172c451c9 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'ncbi-vdb' +version = '3.0.5' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['a32672d7f76507a77ceb29f023855eaf5bf4d150ddd21b55c013b499f3b83735'] + +builddependencies = [ + ('Perl', '5.32.1', '-minimal'), + ('Python', '3.9.5', '-bare'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('libxml2', '2.9.10'), + ('bzip2', '1.0.8'), +] + +configopts = "-DHDF5_INCDIR=$EBROOTHDF5/include -DHDF5_LIBDIR=$EBROOTHDF5/lib " +configopts += "-DXML2_INCDIR=$EBROOTLIBXML2/include -DXML2_LIBDIR=$EBROOTLIBXML2/lib " + +sanity_check_paths = { + 'files': ['include/ncbi/ncbi.h', 'include/ncbi/vdb-blast.h'] + + [('lib/libncbi-%s.%s' % (k, e)) for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb new file mode 100644 index 00000000000..8e6ec5a05e4 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb @@ -0,0 +1,69 @@ +# updated: Denis Kristak (INUITS) +# updated: Sebastien Moretti (SIB - Vital-IT) +easyblock = 'CMakeMake' + +name = 'SRA-Toolkit' +version = '3.0.5' + +homepage = 'https://github.com/ncbi/sra-tools' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" +github_account = 'ncbi' + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'extra_cflags': '-DH5_USE_110_API'} + +source_urls = ['https://github.com/ncbi/sra-tools/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = [ + {'SRA-Toolkit-3.0.5.tar.gz': '6dca9889ca9cfa83e9ce1c39bf7ae5654576fc79c4f608e902272a49573a05e0'}, +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('Perl', '5.32.1', '-minimal'), + ('Python', '3.9.5', '-bare'), +] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('ncbi-vdb', '3.0.5'), + ('bzip2', '1.0.8'), + ('file', '5.40'), + ('HDF5', '1.10.7'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), +] + +configopts = '-DVDB_INCDIR="$EBROOTNCBIMINVDB/include" -DVDB_LIBDIR="$EBROOTNCBIMINVDB/lib" ' +configopts += '-DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON' + +_sra_bin = [ + 'abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', 'fastq-dump', + 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'latf-load', 'pacbio-load', + 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', + 'sratools', 'srf-load', 'test-sra', 'vdb-config', 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-lock', + 'vdb-unlock', 'vdb-validate', +] + +_ngs_libs = ['libncbi-ngs.a', 'libncbi-ngs-c++.a', 'libncbi-ngs.%s' % SHLIB_EXT, + 'libngs-c++.a', 'libngs-c++.%s' % SHLIB_EXT] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _sra_bin] + ['lib/%s' % l for l in _ngs_libs], + 'dirs': ['jar', 'include/ncbi-vdb', 'include/ngs'] +} + +sanity_check_commands = [ + "abi-dump --help", + "kar --help", + "sra-sort --help", +] + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' From 356877f9ba1cc6779fee5e226fda17a571d6788f Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 9 Jun 2023 13:09:05 +0000 Subject: [PATCH 7624/9987] adding easyconfigs: ScaLAPACK-2.2.0-gompi-2023.05-fb.eb, foss-2023.05.eb, HPL-2.3-foss-2023.05.eb --- easybuild/easyconfigs/f/foss/foss-2023.05.eb | 28 ++++++++++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2023.05.eb | 21 +++++++++ .../ScaLAPACK-2.2.0-gompi-2023.05-fb.eb | 43 +++++++++++++++++++ 3 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/f/foss/foss-2023.05.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023.05.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023.05-fb.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2023.05.eb b/easybuild/easyconfigs/f/foss/foss-2023.05.eb new file mode 100644 index 00000000000..5fffa227468 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2023.05.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2023.05' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '12.3.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.1.5', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023.05.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023.05.eb new file mode 100644 index 00000000000..646e1fac7b3 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023.05.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2023.05'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023.05-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023.05-fb.eb new file mode 100644 index 00000000000..62bf4aa61dc --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023.05-fb.eb @@ -0,0 +1,43 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2023.05'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.3.1'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From 872d1a917ceaffd81d0ab148b2f3a3aa1b603d22 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Fri, 9 Jun 2023 14:59:15 +0100 Subject: [PATCH 7625/9987] adding easyconfigs: PSI4-1.7-foss-2021b-Python-3.9.6.eb, psutil-5.9.4-GCCcore-11.2.0.eb and patches: PSI4-1.7_fix_cmake_release.patch, PSI4-1.7_fix_snsmp2_version.patch --- .../PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb | 90 +++++++++++++++ .../p/PSI4/PSI4-1.7_fix_cmake_release.patch | 109 ++++++++++++++++++ .../p/PSI4/PSI4-1.7_fix_snsmp2_version.patch | 15 +++ .../p/psutil/psutil-5.9.4-GCCcore-11.2.0.eb | 26 +++++ 4 files changed, 240 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb create mode 100644 easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_cmake_release.patch create mode 100644 easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_snsmp2_version.patch create mode 100644 easybuild/easyconfigs/p/psutil/psutil-5.9.4-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb new file mode 100644 index 00000000000..61bb68bc783 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb @@ -0,0 +1,90 @@ +easyblock = 'EB_PSI' + +name = 'PSI4' +version = '1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for +efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform +computations with more than 2500 basis functions running serially or in parallel. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/psi4/psi4/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'PSI4-%(version)s_fix_cmake_release.patch', + 'PSI4-%(version)s_fix_snsmp2_version.patch', +] +checksums = [ + '85a2772a148d57423a909fd91f3f9b068ae393b161510e78e7a824fbe3997366', # v1.7.tar.gz + '130fefba44d7856e3f4359b3f75be11b5e1f1a4b8b4a9115933d2b4a742aea68', # PSI4-1.3.1_fix_cmake_release.patch + '064dcf60e74e0c449f77bb6e4dcf4b3338edad7d9a046089ecc2979aed1a00f9', # PSI4-1.7_fix_snsmp2_version.patch +] + +dependencies = [ + ('Python', '3.9.6'), + ('libxc', '5.1.6'), + ('CheMPS2', '1.8.11'), + ('networkx', '2.6.3'), + ('psutil', '5.9.4'), + ('pytest', '7.1.3'), + ('Boost', '1.79.0'), +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Eigen', '3.4.0'), +] + +configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF ' +# Install python module to the standard location instead of lib +configopts += '-DPYMOD_INSTALL_LIBDIR=/python%(pyshortver)s/site-packages ' +# Add bundled (downloaded) packages +# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore +configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON ' +# allow PSI4 to download and build a forked version of PCMSolver otherwise tests fail +configopts += '-DENABLE_PCMSolver=ON ' + +# runtest uses ctest, and some of the tests have to be manually compared +# to the reference output (those tests are marked failed) +# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework) +# runtest = '-L smoke' +runtest = False + +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('typing_extensions', '4.5.0', { + 'checksums': ['5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb'], + }), + ('pydantic', '1.10.5', { + 'checksums': ['9e337ac83686645a46db0e825acceea8e02fca4062483f40e9ae178e8bd1103a'], + }), + ('Pint', '0.20.1', { + 'checksums': ['387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067'], + }), + ('msgpack-python', '0.5.6', { + 'modulename': 'msgpack', + 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], + }), + ('py-cpuinfo', '9.0.0', { + 'modulename': 'cpuinfo', + 'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'], + }) +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_commands = ["python -c 'import psi4'"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_cmake_release.patch b/easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_cmake_release.patch new file mode 100644 index 00000000000..b860b707aee --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_cmake_release.patch @@ -0,0 +1,109 @@ +remove CMAKE_BUILD_TYPE check (beacuse it is set to EasyBuildRelease to avoid -O3 optimization flag) +original patch by B. Hajgato - (Free University Brussels - VUB) +ported to PSI4 1.3.1 by Kenneth Hoste (HPC-UGent) +ported to PSI4 1.7 by Neil Douglas (neil.douglas@york.ac.uk) +diff -ru psi4-1.7.orig/cmake/autocmake_safeguards.cmake psi4-1.7/cmake/autocmake_safeguards.cmake +--- psi4-1.7.orig/cmake/autocmake_safeguards.cmake 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.7/cmake/autocmake_safeguards.cmake 2019-05-17 19:51:47.000000000 +0200 +@@ -19,8 +19,8 @@ + string(TOLOWER "${CMAKE_BUILD_TYPE}" cmake_build_type_tolower) + string(TOUPPER "${CMAKE_BUILD_TYPE}" cmake_build_type_toupper) + +-if(NOT cmake_build_type_tolower STREQUAL "debug" AND +- NOT cmake_build_type_tolower STREQUAL "release" AND +- NOT cmake_build_type_tolower STREQUAL "relwithdebinfo") +- message(FATAL_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo (case-insensitive).") +-endif() ++#if(NOT cmake_build_type_tolower STREQUAL "debug" AND ++# NOT cmake_build_type_tolower STREQUAL "release" AND ++# NOT cmake_build_type_tolower STREQUAL "relwithdebinfo") ++# message(FATAL_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo (case-insensitive).") ++#endif() +diff -ru psi4-1.7.orig/external/upstream/dkh/CMakeLists.txt psi4-1.7/external/upstream/dkh/CMakeLists.txt +--- psi4-1.7.orig/external/upstream/dkh/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.7/external/upstream/dkh/CMakeLists.txt 2019-05-17 19:55:10.000000000 +0200 +@@ -16,6 +16,7 @@ + GIT_REPOSITORY https://github.com/psi4/dkh + GIT_TAG v1.2 + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.7/external/upstream/dkh: CMakeLists.txt.orig +Only in psi4-1.7/external/upstream/dkh: CMakeLists.txt.rej +diff -ru psi4-1.7.orig/external/upstream/gau2grid/CMakeLists.txt psi4-1.7/external/upstream/gau2grid/CMakeLists.txt +--- psi4-1.7.orig/external/upstream/gau2grid/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.7/external/upstream/gau2grid/CMakeLists.txt 2019-05-17 19:53:08.000000000 +0200 +@@ -16,6 +16,7 @@ + GIT_REPOSITORY https://github.com/dgasmith/gau2grid + GIT_TAG v1.3.1 + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.7/external/upstream/gau2grid: CMakeLists.txt.orig +Only in psi4-1.7/external/upstream/gau2grid: CMakeLists.txt.rej +diff -ru psi4-1.7.orig/external/upstream/gdma/CMakeLists.txt psi4-1.7/external/upstream/gdma/CMakeLists.txt +--- psi4-1.7.orig/external/upstream/gdma/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.7/external/upstream/gdma/CMakeLists.txt 2019-05-17 19:55:48.000000000 +0200 +@@ -16,6 +16,7 @@ + GIT_REPOSITORY https://github.com/psi4/gdma + GIT_TAG 9d607d7 # v2.2.6-2-g9d607d7 + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.7/external/upstream/gdma: CMakeLists.txt.orig +Only in psi4-1.7/external/upstream/gdma: CMakeLists.txt.rej +diff -ru psi4-1.7.orig/external/upstream/libefp/CMakeLists.txt psi4-1.7/external/upstream/libefp/CMakeLists.txt +--- psi4-1.7.orig/external/upstream/libefp/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.7/external/upstream/libefp/CMakeLists.txt 2019-05-17 19:55:38.000000000 +0200 +@@ -17,6 +17,7 @@ + GIT_REPOSITORY https://github.com/ilyak/libefp + GIT_TAG 15cd7ce # v1.5.0 + 10 (docs and a cmake lapack patch) + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.7/external/upstream/libefp: CMakeLists.txt.orig +Only in psi4-1.7/external/upstream/libefp: CMakeLists.txt.rej +diff -ru psi4-1.7.orig/external/upstream/libint/CMakeLists.txt psi4-1.7/external/upstream/libint/CMakeLists.txt +--- psi4-1.7.orig/external/upstream/libint/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.7/external/upstream/libint/CMakeLists.txt 2019-05-17 19:54:22.000000000 +0200 +@@ -14,6 +14,7 @@ + ExternalProject_Add(libint_external + # "git checkout" fails on Windows, because of "*" in filenames (e.g. basis set files) + URL https://github.com/loriab/libint/archive/libint_t.tar.gz ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.7/external/upstream/libint: CMakeLists.txt.orig +Only in psi4-1.7/external/upstream/libint: CMakeLists.txt.rej +diff -ru psi4-1.7.orig/external/upstream/libxc/CMakeLists.txt psi4-1.7/external/upstream/libxc/CMakeLists.txt +--- psi4-1.7.orig/external/upstream/libxc/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.7/external/upstream/libxc/CMakeLists.txt 2019-05-17 19:56:11.000000000 +0200 +@@ -15,6 +15,7 @@ + #GIT_REPOSITORY https://gitlab.com/libxc/libxc.git + #GIT_TAG 5.1.5 + #UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.7/external/upstream/libxc: CMakeLists.txt.orig +Only in psi4-1.7/external/upstream/libxc: CMakeLists.txt.rej +--- psi4-1.7.orig/external/upstream/pcmsolver/CMakeLists.txt 2023-02-27 14:33:58.771017491 +0000 ++++ psi4-1.7/external/upstream/pcmsolver/CMakeLists.txt 2023-02-27 14:35:00.507500122 +0000 +@@ -24,6 +24,7 @@ + ExternalProject_Add(pcmsolver_external + #URL https://github.com/PCMSolver/pcmsolver/archive/v1.3.1.tar.gz + URL https://github.com/loriab/pcmsolver/archive/v1211.tar.gz ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/downloaded/autocmake_safeguards.cmake + UPDATE_COMMAND "" + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_snsmp2_version.patch b/easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_snsmp2_version.patch new file mode 100644 index 00000000000..dd63fa064d7 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_snsmp2_version.patch @@ -0,0 +1,15 @@ +Fixes build error 'Versioning for this project requires either an sdist tarball, or access to an upstream git repository' +--- psi4-1.7/external/downstream/snsmp2/CMakeLists.txt 2023-02-22 14:56:49.000000000 +0000 ++++ psi4-1.7/external/downstream/snsmp2/CMakeLists.txt 2023-02-22 15:00:11.000000000 +0000 +@@ -22,7 +22,7 @@ + URL https://github.com/DEShawResearch/sns-mp2/archive/12462c6.tar.gz # v1.0 + 26 + CONFIGURE_COMMAND "" + UPDATE_COMMAND "" +- BUILD_COMMAND ${Python_EXECUTABLE} setup.py build ++ BUILD_COMMAND PBR_VERSION=1.0 ${Python_EXECUTABLE} setup.py build + BUILD_IN_SOURCE 1 +- INSTALL_COMMAND ${Python_EXECUTABLE} setup.py install ++ INSTALL_COMMAND PBR_VERSION=1.0 ${Python_EXECUTABLE} setup.py install + --record=record.txt + --single-version-externally-managed + --install-lib=${STAGED_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}${PYMOD_INSTALL_LIBDIR}) diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.4-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..be9c08d05c6 --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.4-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '5.9.4' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['3d7f9739eb435d4b1338944abe23f49584bde5395f27487d2ee25ad9a8774a62'], + }), +] + +moduleclass = 'lib' From ca6edbd908aad68cc5c345be15ac82bca38dc834 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Fri, 9 Jun 2023 15:26:27 +0100 Subject: [PATCH 7626/9987] rename file to remove Python --- .../PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb | 90 ------------------- 1 file changed, 90 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb deleted file mode 100644 index 61bb68bc783..00000000000 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb +++ /dev/null @@ -1,90 +0,0 @@ -easyblock = 'EB_PSI' - -name = 'PSI4' -version = '1.7' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.psicode.org/' -description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for -efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform -computations with more than 2500 basis functions running serially or in parallel. -""" - -toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/psi4/psi4/archive'] -sources = ['v%(version)s.tar.gz'] -patches = [ - 'PSI4-%(version)s_fix_cmake_release.patch', - 'PSI4-%(version)s_fix_snsmp2_version.patch', -] -checksums = [ - '85a2772a148d57423a909fd91f3f9b068ae393b161510e78e7a824fbe3997366', # v1.7.tar.gz - '130fefba44d7856e3f4359b3f75be11b5e1f1a4b8b4a9115933d2b4a742aea68', # PSI4-1.3.1_fix_cmake_release.patch - '064dcf60e74e0c449f77bb6e4dcf4b3338edad7d9a046089ecc2979aed1a00f9', # PSI4-1.7_fix_snsmp2_version.patch -] - -dependencies = [ - ('Python', '3.9.6'), - ('libxc', '5.1.6'), - ('CheMPS2', '1.8.11'), - ('networkx', '2.6.3'), - ('psutil', '5.9.4'), - ('pytest', '7.1.3'), - ('Boost', '1.79.0'), -] - -builddependencies = [ - ('CMake', '3.22.1'), - ('Eigen', '3.4.0'), -] - -configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF ' -# Install python module to the standard location instead of lib -configopts += '-DPYMOD_INSTALL_LIBDIR=/python%(pyshortver)s/site-packages ' -# Add bundled (downloaded) packages -# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore -configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON ' -# allow PSI4 to download and build a forked version of PCMSolver otherwise tests fail -configopts += '-DENABLE_PCMSolver=ON ' - -# runtest uses ctest, and some of the tests have to be manually compared -# to the reference output (those tests are marked failed) -# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework) -# runtest = '-L smoke' -runtest = False - -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'download_dep_fail': True, - 'use_pip': True, -} - -exts_list = [ - ('typing_extensions', '4.5.0', { - 'checksums': ['5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb'], - }), - ('pydantic', '1.10.5', { - 'checksums': ['9e337ac83686645a46db0e825acceea8e02fca4062483f40e9ae178e8bd1103a'], - }), - ('Pint', '0.20.1', { - 'checksums': ['387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067'], - }), - ('msgpack-python', '0.5.6', { - 'modulename': 'msgpack', - 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], - }), - ('py-cpuinfo', '9.0.0', { - 'modulename': 'cpuinfo', - 'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'], - }) -] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -sanity_check_commands = ["python -c 'import psi4'"] - -moduleclass = 'chem' From c34b2a6b5033dfd96176076167ea112104d89fc9 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Fri, 9 Jun 2023 15:28:13 +0100 Subject: [PATCH 7627/9987] add with new filename --- .../PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb | 90 +++++++++++++++++++ 1 file changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb new file mode 100644 index 00000000000..61bb68bc783 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb @@ -0,0 +1,90 @@ +easyblock = 'EB_PSI' + +name = 'PSI4' +version = '1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for +efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform +computations with more than 2500 basis functions running serially or in parallel. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/psi4/psi4/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'PSI4-%(version)s_fix_cmake_release.patch', + 'PSI4-%(version)s_fix_snsmp2_version.patch', +] +checksums = [ + '85a2772a148d57423a909fd91f3f9b068ae393b161510e78e7a824fbe3997366', # v1.7.tar.gz + '130fefba44d7856e3f4359b3f75be11b5e1f1a4b8b4a9115933d2b4a742aea68', # PSI4-1.3.1_fix_cmake_release.patch + '064dcf60e74e0c449f77bb6e4dcf4b3338edad7d9a046089ecc2979aed1a00f9', # PSI4-1.7_fix_snsmp2_version.patch +] + +dependencies = [ + ('Python', '3.9.6'), + ('libxc', '5.1.6'), + ('CheMPS2', '1.8.11'), + ('networkx', '2.6.3'), + ('psutil', '5.9.4'), + ('pytest', '7.1.3'), + ('Boost', '1.79.0'), +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Eigen', '3.4.0'), +] + +configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF ' +# Install python module to the standard location instead of lib +configopts += '-DPYMOD_INSTALL_LIBDIR=/python%(pyshortver)s/site-packages ' +# Add bundled (downloaded) packages +# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore +configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON ' +# allow PSI4 to download and build a forked version of PCMSolver otherwise tests fail +configopts += '-DENABLE_PCMSolver=ON ' + +# runtest uses ctest, and some of the tests have to be manually compared +# to the reference output (those tests are marked failed) +# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework) +# runtest = '-L smoke' +runtest = False + +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('typing_extensions', '4.5.0', { + 'checksums': ['5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb'], + }), + ('pydantic', '1.10.5', { + 'checksums': ['9e337ac83686645a46db0e825acceea8e02fca4062483f40e9ae178e8bd1103a'], + }), + ('Pint', '0.20.1', { + 'checksums': ['387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067'], + }), + ('msgpack-python', '0.5.6', { + 'modulename': 'msgpack', + 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], + }), + ('py-cpuinfo', '9.0.0', { + 'modulename': 'cpuinfo', + 'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'], + }) +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_commands = ["python -c 'import psi4'"] + +moduleclass = 'chem' From 59c632061f8aef69eaee7283712afb43317d97fb Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Fri, 9 Jun 2023 15:36:54 +0100 Subject: [PATCH 7628/9987] remove versionsuffix --- .../easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb | 89 +++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb new file mode 100644 index 00000000000..a5957981624 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb @@ -0,0 +1,89 @@ +easyblock = 'EB_PSI' + +name = 'PSI4' +version = '1.7' + +homepage = 'https://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for +efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform +computations with more than 2500 basis functions running serially or in parallel. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/psi4/psi4/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'PSI4-%(version)s_fix_cmake_release.patch', + 'PSI4-%(version)s_fix_snsmp2_version.patch', +] +checksums = [ + '85a2772a148d57423a909fd91f3f9b068ae393b161510e78e7a824fbe3997366', # v1.7.tar.gz + '130fefba44d7856e3f4359b3f75be11b5e1f1a4b8b4a9115933d2b4a742aea68', # PSI4-1.3.1_fix_cmake_release.patch + '064dcf60e74e0c449f77bb6e4dcf4b3338edad7d9a046089ecc2979aed1a00f9', # PSI4-1.7_fix_snsmp2_version.patch +] + +dependencies = [ + ('Python', '3.9.6'), + ('libxc', '5.1.6'), + ('CheMPS2', '1.8.11'), + ('networkx', '2.6.3'), + ('psutil', '5.9.4'), + ('pytest', '7.1.3'), + ('Boost', '1.79.0'), +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Eigen', '3.4.0'), +] + +configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF ' +# Install python module to the standard location instead of lib +configopts += '-DPYMOD_INSTALL_LIBDIR=/python%(pyshortver)s/site-packages ' +# Add bundled (downloaded) packages +# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore +configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON ' +# allow PSI4 to download and build a forked version of PCMSolver otherwise tests fail +configopts += '-DENABLE_PCMSolver=ON ' + +# runtest uses ctest, and some of the tests have to be manually compared +# to the reference output (those tests are marked failed) +# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework) +# runtest = '-L smoke' +runtest = False + +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('typing_extensions', '4.5.0', { + 'checksums': ['5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb'], + }), + ('pydantic', '1.10.5', { + 'checksums': ['9e337ac83686645a46db0e825acceea8e02fca4062483f40e9ae178e8bd1103a'], + }), + ('Pint', '0.20.1', { + 'checksums': ['387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067'], + }), + ('msgpack-python', '0.5.6', { + 'modulename': 'msgpack', + 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], + }), + ('py-cpuinfo', '9.0.0', { + 'modulename': 'cpuinfo', + 'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'], + }) +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_commands = ["python -c 'import psi4'"] + +moduleclass = 'chem' From 2e60b52bee29f637730cea8d578eda17ed9dc13c Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Fri, 9 Jun 2023 15:37:53 +0100 Subject: [PATCH 7629/9987] remove old file --- .../PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb | 90 ------------------- 1 file changed, 90 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb deleted file mode 100644 index 61bb68bc783..00000000000 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b-Python-3.9.6.eb +++ /dev/null @@ -1,90 +0,0 @@ -easyblock = 'EB_PSI' - -name = 'PSI4' -version = '1.7' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://www.psicode.org/' -description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for -efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform -computations with more than 2500 basis functions running serially or in parallel. -""" - -toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/psi4/psi4/archive'] -sources = ['v%(version)s.tar.gz'] -patches = [ - 'PSI4-%(version)s_fix_cmake_release.patch', - 'PSI4-%(version)s_fix_snsmp2_version.patch', -] -checksums = [ - '85a2772a148d57423a909fd91f3f9b068ae393b161510e78e7a824fbe3997366', # v1.7.tar.gz - '130fefba44d7856e3f4359b3f75be11b5e1f1a4b8b4a9115933d2b4a742aea68', # PSI4-1.3.1_fix_cmake_release.patch - '064dcf60e74e0c449f77bb6e4dcf4b3338edad7d9a046089ecc2979aed1a00f9', # PSI4-1.7_fix_snsmp2_version.patch -] - -dependencies = [ - ('Python', '3.9.6'), - ('libxc', '5.1.6'), - ('CheMPS2', '1.8.11'), - ('networkx', '2.6.3'), - ('psutil', '5.9.4'), - ('pytest', '7.1.3'), - ('Boost', '1.79.0'), -] - -builddependencies = [ - ('CMake', '3.22.1'), - ('Eigen', '3.4.0'), -] - -configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF ' -# Install python module to the standard location instead of lib -configopts += '-DPYMOD_INSTALL_LIBDIR=/python%(pyshortver)s/site-packages ' -# Add bundled (downloaded) packages -# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore -configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON ' -# allow PSI4 to download and build a forked version of PCMSolver otherwise tests fail -configopts += '-DENABLE_PCMSolver=ON ' - -# runtest uses ctest, and some of the tests have to be manually compared -# to the reference output (those tests are marked failed) -# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework) -# runtest = '-L smoke' -runtest = False - -exts_defaultclass = 'PythonPackage' -exts_filter = ("python -c 'import %(ext_name)s'", '') -exts_default_options = { - 'source_urls': [PYPI_SOURCE], - 'download_dep_fail': True, - 'use_pip': True, -} - -exts_list = [ - ('typing_extensions', '4.5.0', { - 'checksums': ['5cb5f4a79139d699607b3ef622a1dedafa84e115ab0024e0d9c044a9479ca7cb'], - }), - ('pydantic', '1.10.5', { - 'checksums': ['9e337ac83686645a46db0e825acceea8e02fca4062483f40e9ae178e8bd1103a'], - }), - ('Pint', '0.20.1', { - 'checksums': ['387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067'], - }), - ('msgpack-python', '0.5.6', { - 'modulename': 'msgpack', - 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], - }), - ('py-cpuinfo', '9.0.0', { - 'modulename': 'cpuinfo', - 'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'], - }) -] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -sanity_check_commands = ["python -c 'import psi4'"] - -moduleclass = 'chem' From efc04deffe5f7e52eaa852f445197aef1a39372e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 9 Jun 2023 16:46:13 +0200 Subject: [PATCH 7630/9987] adding easyconfigs: LuaJIT-2.1.0-beta3_20230602-GCC-11.3.0.eb --- .../LuaJIT-2.1.0-beta3_20230602-GCC-11.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/LuaJIT/LuaJIT-2.1.0-beta3_20230602-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LuaJIT/LuaJIT-2.1.0-beta3_20230602-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LuaJIT/LuaJIT-2.1.0-beta3_20230602-GCC-11.3.0.eb new file mode 100644 index 00000000000..65bed514c7e --- /dev/null +++ b/easybuild/easyconfigs/l/LuaJIT/LuaJIT-2.1.0-beta3_20230602-GCC-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'LuaJIT' +_ver = '2.1.0-beta3' +version = _ver + '_20230602' +_commit = '51fb2f2' + +homepage = "https://luajit.org/" +description = """LuaJIT is a Just-In-Time Compiler (JIT) for the Lua +programming language. Lua is a powerful, dynamic and light-weight programming +language. It may be embedded or used as a general-purpose, stand-alone +language. """ + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +# Releases are only made occasionally. You're strongly encouraged to follow the git branches. +sources = [{ + 'source_urls': ['https://github.com/LuaJIT/LuaJIT/archive'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['d081eaa1a5bca419763712397f4696e0dd10db8d9b2e091e15c71d9fc50c24c9'] + +dependencies = [('ncurses', '6.3')] + +skipsteps = ['configure'] +installopts = 'PREFIX=%(installdir)s' + +postinstallcmds = ['cd %%(installdir)s/bin && ln -s luajit-%s luajit' % _ver] + +sanity_check_paths = { + 'files': ["bin/luajit"], + 'dirs': [], +} + +sanity_check_commands = ['luajit -v'] + +moduleclass = "lang" From bfabea1f9acbb000117edcd62c46bd0c5a292535 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 9 Jun 2023 15:00:03 +0000 Subject: [PATCH 7631/9987] adding easyconfigs: SpaceRanger-2.1.0-GCC-11.3.0.eb, SpaceRanger-2.1.0-GCC-12.2.0.eb, bcl2fastq2-2.20.0-GCC-12.2.0.eb --- .../bcl2fastq2-2.20.0-GCC-12.2.0.eb | 65 +++++++++++++++++++ .../SpaceRanger-2.1.0-GCC-11.3.0.eb | 37 +++++++++++ .../SpaceRanger-2.1.0-GCC-12.2.0.eb | 37 +++++++++++ 3 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.1.0-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.1.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..ed8b4174d37 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-12.2.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMake' + +name = 'bcl2fastq2' +version = '2.20.0' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html' +description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by + Illumina sequencing systems to standard FASTQ file formats for downstream analysis.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/'] +sources = [{ + 'filename': '%s-v%s-tar.zip' % (name, version.replace('.', '-')), + 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz +}] +patches = [ + '%(name)s-%(version)s-fix-cmake-target-libs.patch', + # bcl2fastq2 v2.20.0 is not compatible with recent Boost versions, use bundled Boost + '%(name)s-%(version)s-find-boost.patch', +] +checksums = [ + {'bcl2fastq2-v2-20-0-tar.zip': '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3'}, + {'bcl2fastq2-2.20.0-fix-cmake-target-libs.patch': + '3f2736a8335b533646e25093f02bbbcf1aa629c68a0433b9bb5d66fadaa28edb'}, + {'bcl2fastq2-2.20.0-find-boost.patch': '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('libxml2', '2.10.3'), + ('libxslt', '1.1.37'), + ('zlib', '1.2.12'), +] + +start_dir = 'src' + +# check versions of libxml2 and libxslt from EB +local_cmakelists = '%(builddir)s/bcl2fastq/src/CMakeLists.txt' +local_sed_libver = r'sed -i "s/%(l)s_VERSION [0-9\.]*/%(l)s_VERSION $EBVERSION%(l)s/g" %(f)s && ' +preconfigopts = local_sed_libver % {'l': 'LIBXML2', 'f': local_cmakelists} +preconfigopts += local_sed_libver % {'l': 'LIBXSLT', 'f': local_cmakelists} + +# remove hardcoded compilation flags +local_cmakecxx = '%(builddir)s/bcl2fastq/src/cmake/cxxConfigure.cmake' +preconfigopts += r'sed -i "s/-std=[a-z0-9\+]* //g;s/-O. //g" %s && ' % local_cmakecxx + +configopts = '-DBCL2FASTQ_VERSION:STRING=%(version)s ' +configopts += '-DBCL2FASTQ_PREFIX:STRING=%(installdir)s ' +configopts += '-DBCL2FASTQ_SOURCE_DIR:STRING=%(builddir)s/bcl2fastq/src ' +# Make sure CMake doesn't use any system installed Boost versions cmake-config files. +configopts += '-DBoost_NO_BOOST_CMAKE=ON ' + +sanity_check_paths = { + 'files': ['bin/bcl2fastq'], + 'dirs': ['lib'], +} + +sanity_check_commands = ["bcl2fastq --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.1.0-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.1.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..ecd20c84183 --- /dev/null +++ b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.1.0-GCC-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'SpaceRanger' +version = '2.1.0' + +homepage = 'https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger' +description = """ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output +and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, +perform clustering and gene expression analysis, and place spots in spatial context on the slide image. """ + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +download_instructions = """ +Download sources from homepage, registration no longer required, but link is dynamic +https://www.10xgenomics.com/support/software/space-ranger/downloads +""" + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4486c0164e47810d06dc2ba4d3d45bd638fdcc30ee826debc5745f9307e3d227'] + +dependencies = [ + ('bcl2fastq2', '2.20.0'), + ('libxslt', '1.1.34'), +] + +allow_prepend_abs_path = True +# prepend reference databases GRCh38 and mm10 to PATH +# modextrapaths = {'PATH': '/path/to/databases/%(namelower)s-%(version)s'} + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['external', 'lib', 'mro'], +} + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.1.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..0b0e94b0a1a --- /dev/null +++ b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.1.0-GCC-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'SpaceRanger' +version = '2.1.0' + +homepage = 'https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger' +description = """ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output +and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, +perform clustering and gene expression analysis, and place spots in spatial context on the slide image. """ + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +download_instructions = """ +Download sources from homepage, registration no longer required, but link is dynamic +https://www.10xgenomics.com/support/software/space-ranger/downloads +""" + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4486c0164e47810d06dc2ba4d3d45bd638fdcc30ee826debc5745f9307e3d227'] + +dependencies = [ + ('bcl2fastq2', '2.20.0'), + ('libxslt', '1.1.37'), +] + +allow_prepend_abs_path = True +# prepend reference databases GRCh38 and mm10 to PATH +# modextrapaths = {'PATH': '/path/to/databases/%(namelower)s-%(version)s'} + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['external', 'lib', 'mro'], +} + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From 41ffcb03ba7b6f6eb18a2b0e427f2b9209dc23d8 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Fri, 9 Jun 2023 16:42:54 +0100 Subject: [PATCH 7632/9987] update Boost version --- easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb index a5957981624..e55370d1275 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb @@ -31,7 +31,7 @@ dependencies = [ ('networkx', '2.6.3'), ('psutil', '5.9.4'), ('pytest', '7.1.3'), - ('Boost', '1.79.0'), + ('Boost', '1.77.0'), ] builddependencies = [ From 807006da60b5f78d8ee3916dace9a51e46f6e87c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 9 Jun 2023 21:49:23 +0200 Subject: [PATCH 7633/9987] adding easyconfigs: SVIM-2.0.0-foss-2022a.eb, pyspoa-0.0.9-GCC-11.3.0.eb, spoa-4.0.7-GCC-11.3.0.eb and patches: pyspoa-0.0.9_use-spoa-dep.patch --- .../p/pyspoa/pyspoa-0.0.9-GCC-11.3.0.eb | 53 +++++++++++++++++++ .../p/pyspoa/pyspoa-0.0.9_use-spoa-dep.patch | 25 +++++++++ .../s/SVIM/SVIM-2.0.0-foss-2022a.eb | 43 +++++++++++++++ .../s/spoa/spoa-4.0.7-GCC-11.3.0.eb | 29 ++++++++++ 4 files changed, 150 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9_use-spoa-dep.patch create mode 100644 easybuild/easyconfigs/s/SVIM/SVIM-2.0.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9-GCC-11.3.0.eb new file mode 100644 index 00000000000..01299533940 --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9-GCC-11.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonPackage' + +name = 'pyspoa' +version = '0.0.9' + +local_cereal_version = '1.3.2' + +homepage = 'https://github.com/nanoporetech/pyspoa' +description = "Python bindings to spoa." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +sources = [ + { + 'source_urls': ['https://github.com/nanoporetech/pyspoa/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'pyspoa-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/USCiLab/cereal/archive/'], + 'download_filename': 'v%s.tar.gz' % local_cereal_version, + 'filename': 'cereal-%s.tar.gz' % local_cereal_version, + }, +] +patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] + +checksums = [ + {'pyspoa-0.0.9.tar.gz': '30b883b8dfc2355a6062f9f848e825f7ffac169657190d797cf17b4314d588fe'}, + {'cereal-%s.tar.gz' % local_cereal_version: '16a7ad9b31ba5880dac55d62b5d6f243c3ebc8d46a3514149e56b5e7ea81f85f'}, + {'pyspoa-0.0.9_use-spoa-dep.patch': 'fdd11ecc22f65e5c06491fb60f59aab3427d264903d678d59095029ab1e65da7'}, +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('pybind11', '2.9.2'), + ('spoa', '4.0.7'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " +# strip out cmake requirements, since we provide that as proper dependency +preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " + +options = {'modulename': 'spoa'} + +sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9_use-spoa-dep.patch b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9_use-spoa-dep.patch new file mode 100644 index 00000000000..969e77f0ffa --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9_use-spoa-dep.patch @@ -0,0 +1,25 @@ +use spoa dependency provided through EasyBuild + +author: Kenneth Hoste (HPC-UGent) +updated by: Petr Král (Inuits) +diff --git a/pyspoa-0.0.9/setup.py.orig b/pyspoa-0.0.9/setup.py +index 53338a5..6aaff2b 100644 +--- a/pyspoa-0.0.9/setup.py.orig ++++ b/pyspoa-0.0.9/setup.py +@@ -106,14 +106,14 @@ ext_modules = [ + 'spoa', + ['pyspoa.cpp'], + include_dirs=[ +- 'src/include/spoa', ++ os.path.join(os.getenv('EBROOTSPOA'), 'include/spoa'), + 'src/vendor/cereal/include', + get_pybind_include(), + get_pybind_include(user=True), + ], + language='c++', + extra_objects=[ +- 'src/build/lib/libspoa.a' ++ os.path.join(os.getenv('EBROOTSPOA'), 'lib64/libspoa.a'), + ], + + ), diff --git a/easybuild/easyconfigs/s/SVIM/SVIM-2.0.0-foss-2022a.eb b/easybuild/easyconfigs/s/SVIM/SVIM-2.0.0-foss-2022a.eb new file mode 100644 index 00000000000..9b31271e9ce --- /dev/null +++ b/easybuild/easyconfigs/s/SVIM/SVIM-2.0.0-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'SVIM' +version = '2.0.0' + +homepage = 'https://github.com/eldariont/svim' +description = """SVIM (pronounced swim) is a structural variant caller for third-generation sequencing reads. + It is able to detect and classify the following six classes of structural variation: deletions, insertions, + inversions, tandem duplications, interspersed duplications and translocations.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Pysam', '0.19.1'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('edlib', '1.3.9'), + ('pyspoa', '0.0.9'), + ('py-cpuinfo', '9.0.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['1be9cfb84e420858b9e08fc3664b8d16d76bd2f241e6a87d876d9292d66ea1a3'], + }), +] + +sanity_check_paths = { + 'files': ['bin/svim'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'from svim.SVSignature import SignatureDeletion'", + "svim alignment --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-11.3.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-11.3.0.eb new file mode 100644 index 00000000000..658c26ac530 --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '4.0.7' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] +sources = ['spoa-v%(version)s.tar.gz'] +checksums = ['f7a8cd039e4aabea1481e123387fedaa8f87e55418a3649408a615f5c6b1b9a4'] + +builddependencies = [('CMake', '3.23.1')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a', 'lib/pkgconfig/spoa-1.pc'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +moduleclass = 'bio' From d0c688047579348edeb769a2088f945d403a3c23 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 10 Jun 2023 10:25:16 +0200 Subject: [PATCH 7634/9987] add -pthread flag for dorado --- .../d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb index fd5b9dab93d..1c2ca1b3f4b 100644 --- a/easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/d/dorado/dorado-0.1.1-foss-2022a-CUDA-11.7.0.eb @@ -48,6 +48,9 @@ preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLi configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib -DHTSLIB_LIBRARIES=hts " +# add -pthread flag (in addition to -lpthread) to avoid linking error: +# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' +configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" ' sanity_check_paths = { 'files': ['bin/dorado'], From c11a946cb20c113688bbd620c0eeeb9fb4ad2342 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 10 Jun 2023 10:29:59 +0200 Subject: [PATCH 7635/9987] adding easyconfigs: LuaRocks-3.9.2-GCCcore-11.3.0.eb --- .../LuaRocks/LuaRocks-3.9.2-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/l/LuaRocks/LuaRocks-3.9.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LuaRocks/LuaRocks-3.9.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LuaRocks/LuaRocks-3.9.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1f334665619 --- /dev/null +++ b/easybuild/easyconfigs/l/LuaRocks/LuaRocks-3.9.2-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'LuaRocks' +version = '3.9.2' + +homepage = 'https://luarocks.org' +description = """ +LuaRocks is the package manager for Lua modules. It allows you to create and +install Lua modules as self-contained packages called rocks. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://luarocks.github.io/luarocks/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bca6e4ecc02c203e070acdb5f586045d45c078896f6236eb46aa33ccd9b94edb'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Lua', '5.4.4'), +] + +configopts = '--with-lua=$EBROOTLUA' + +sanity_check_paths = { + 'files': ['bin/luarocks', 'bin/luarocks-admin'], + 'dirs': ['etc/luarocks', 'share/lua'] +} + +sanity_check_commands = ['luarocks --help'] + +moduleclass = 'lib' From 8dfd5d93cdac3dd7a487f93af61091a9afdce38a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 10 Jun 2023 10:41:18 +0200 Subject: [PATCH 7636/9987] update moduleclass --- .../easyconfigs/l/LuaRocks/LuaRocks-3.9.2-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LuaRocks/LuaRocks-3.9.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LuaRocks/LuaRocks-3.9.2-GCCcore-11.3.0.eb index 1f334665619..055a45cf5ca 100644 --- a/easybuild/easyconfigs/l/LuaRocks/LuaRocks-3.9.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LuaRocks/LuaRocks-3.9.2-GCCcore-11.3.0.eb @@ -32,4 +32,4 @@ sanity_check_paths = { sanity_check_commands = ['luarocks --help'] -moduleclass = 'lib' +moduleclass = 'tools' From d98d475088e051f851bc23c4397ec1c9e358aebb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 11 Jun 2023 15:57:35 +0200 Subject: [PATCH 7637/9987] Add a ton of missing test deps --- .../Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 1075 ++++++++++------- 1 file changed, 654 insertions(+), 421 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index 49e03fe60b2..d0f5960b2d1 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -33,13 +33,19 @@ exts_list = [ }), ('HTTP::Date', '6.05', { 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['365d6294dfbd37ebc51def8b65b81eb79b3934ecbc95a2ec2d4d827efe6a922b'], }), ('File::Listing', '6.15', { 'source_tmpl': 'File-Listing-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], 'checksums': ['46c4fb9f9eb9635805e26b7ea55b54455e47302758a10ed2a0b92f392713770c'], }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], + }), ('ExtUtils::InstallPaths', '0.012', { 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], @@ -55,11 +61,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], 'checksums': ['7eb591ea6b499ece6745ff3e80e60cee669f0037f9ccbc4e4511425f593e5297'], }), - ('ExtUtils::Config', '0.008', { - 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], - }), ('Module::Build::Tiny', '0.045', { 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], @@ -80,6 +81,16 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59'], + }), ('GO::Utils', '0.15', { 'source_tmpl': 'go-perl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], @@ -90,6 +101,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], }), + ('Try::Tiny', '0.31', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + 'checksums': ['3300d31d8a4075b26d8f46ce864a1d913e0e8467ceeba6655d5d2b2e206c11be'], + }), ('Test::Fatal', '0.017', { 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], @@ -100,16 +116,21 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': ['1e542909fef305e45563e9878ea1c3b0c7cef1b28bb7ae07eba2e1efabec477b'], }), - ('File::ShareDir', '1.118', { - 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], - 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], + ('Class::Inspector', '1.36', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['cc295d23a472687c24489d58226ead23b9fdc2588e522f0b5f0747741700694e'], }), ('File::ShareDir::Install', '0.14', { 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'], }), + ('File::ShareDir', '1.118', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], + }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], @@ -150,81 +171,201 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], }), - ('Test::File::ShareDir::Dist', '1.001002', { - 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], - 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], + ('Path::Tiny', '0.144', { + 'source_tmpl': 'Path-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['f6ea094ece845c952a02c2789332579354de8d410a707f9b7045bd241206487d'], }), - ('DateTime::Locale', '1.38', { - 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['dd7f6d358279d1df0ea7d78b9127690435246cdf46867500e9888016f9d4c867'], + ('Test::Deep', '1.204', { + 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['b6591f6ccdd853c7efc9ff3c5756370403211cffe46047f082b1cd1611a84e5f'], }), - ('DateTime::TimeZone', '2.60', { - 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['f0460d379323905b579bed44e141237a337dc25dd26b6ab0c60ac2b80629323d'], + ('Test::File', '1.993', { + 'source_tmpl': 'Test-File-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['ef2ffe1aaec7b42d874ad411ec647547b9b9bc2f5fb93e49e3399488456afc7a'], + }), + ('Test::Needs', '0.002010', { + 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['923ffdc78fcba96609753e4bae26b0ba0186893de4a63cd5236e012c7c90e208'], }), ('Test::Requires', '0.11', { 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], 'checksums': ['4b88de549597eecddf7c3c38a4d0204a16f59ad804577b671896ac04e24e040f'], }), - ('Module::Implementation', '0.09', { - 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], + ('File::Copy::Recursive', '0.45', { + 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['d3971cf78a8345e38042b208bb7b39cb695080386af629f4a04ffd6549df1157'], }), - ('Module::Build', '0.4234', { - 'source_tmpl': 'Module-Build-%(version)s.tar.gz', + ('Test::File::ShareDir::Dist', '1.001002', { + 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], + }), + ('CPAN::Meta::Check', '0.017', { + 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['66aeac6127418be5e471ead3744648c766bd01482825c5b66652675f2bc86a8f'], + 'checksums': ['0454ab93f12780b1d579df15b5f939e09702e954be82028fadd40e8bc9b0f091'], + }), + ('Sub::Exporter::Progressive', '0.001013', { + 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + 'checksums': ['d535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056'], }), ('Module::Runtime', '0.016', { 'source_tmpl': 'Module-Runtime-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], 'checksums': ['68302ec646833547d410be28e09676db75006f4aa58a11f3bdb44ffe99f0f024'], }), - ('Try::Tiny', '0.31', { - 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['c15f1a12f0c2130c9efff3c2e1afe5887b08ccd033bd132186d1e7d5087fd66d'], + }), + ('B::Hooks::EndOfScope', '0.26', { + 'source_tmpl': 'B-Hooks-EndOfScope-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['3300d31d8a4075b26d8f46ce864a1d913e0e8467ceeba6655d5d2b2e206c11be'], + 'checksums': ['39df2f8c007a754672075f95b90797baebe97ada6d944b197a6352709cb30671'], }), - ('Params::Validate', '1.31', { - 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['1bf2518ef2c4869f91590e219f545c8ef12ed53cf313e0eb5704adf7f1b2961e'], + ('Package::Stash', '0.40', { + 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['5a9722c6d9cb29ee133e5f7b08a5362762a0b5633ff5170642a5b0686e95e066'], }), - ('List::MoreUtils', '0.430', { - 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], - 'checksums': ['63b1f7842cd42d9b538d1e34e0330de5ff1559e4c2737342506418276f646527'], + ('namespace::clean', '0.27', { + 'source_tmpl': 'namespace-clean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + 'checksums': ['8a10a83c3e183dc78f9e7b7aa4d09b47c11fb4e7d3a33b9a12912fd22e31af9d'], + }), + ('Sub::Identify', '0.14', { + 'source_tmpl': 'Sub-Identify-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RG/RGARCIA'], + 'checksums': ['068d272086514dd1e842b6a40b1bedbafee63900e5b08890ef6700039defad6f'], + }), + ('namespace::autoclean', '0.29', { + 'source_tmpl': 'namespace-autoclean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['45ebd8e64a54a86f88d8e01ae55212967c8aa8fed57e814085def7608ac65804'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': ['ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad'], }), ('Exporter::Tiny', '1.006002', { 'source_tmpl': 'Exporter-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], 'checksums': ['6f295e2cbffb1dbc15bdb9dadc341671c1e0cd2bdf2d312b17526273c322638d'], }), + ('Type::Tiny', '2.004000', { + 'source_tmpl': 'Type-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + 'checksums': ['697e7f775edfc85f4cf07792d04fd19b09c25285f98f5938e8efc4f74507a128'], + }), + ('Class::Data::Inheritable', '0.09', { + 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSHERER'], + 'checksums': ['44088d6e90712e187b8a5b050ca5b1c70efe2baa32ae123e9bd8f59f29f06e4d'], + }), + ('Devel::StackTrace', '2.04', { + 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['cd3c03ed547d3d42c61fa5814c98296139392e7971c092e09a431f2c9f5d6855'], + }), + ('Exception::Class', '1.45', { + 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['5482a77ef027ca1f9f39e1f48c558356e954936fc8fbbdee6c811c512701b249'], + }), + ('Role::Tiny', '2.002004', { + 'source_tmpl': 'Role-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['d7bdee9e138a4f83aa52d0a981625644bda87ff16642dfa845dcb44d9a242b45'], + }), + ('MRO::Compat', '0.15', { + 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['0d4535f88e43babd84ab604866215fc4d04398bd4db7b21852d4a31b1c15ef61'], + }), + ('Sub::Quote', '2.006008', { + 'source_tmpl': 'Sub-Quote-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['94bebd500af55762e83ea2f2bc594d87af828072370c7110c60c238a800d15b2'], + }), + ('Specio', '0.48', { + 'source_tmpl': 'Specio-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['0c85793580f1274ef08173079131d101f77b22accea7afa8255202f0811682b2'], + }), + ('Test::Without::Module', '0.21', { + 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['3cdeafadac4853ebeafe689346d555da5dfa3cfa9d4c84e3e5e7bfee50beec46'], + }), + ('Params::ValidationCompiler', '0.31', { + 'source_tmpl': 'Params-ValidationCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['7b6497173f1b6adb29f5d51d8cf9ec36d2f1219412b4b2410e9d77a901e84a6d'], + }), + ('DateTime::Locale', '1.38', { + 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['dd7f6d358279d1df0ea7d78b9127690435246cdf46867500e9888016f9d4c867'], + }), ('Class::Singleton', '1.6', { 'source_tmpl': 'Class-Singleton-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], 'checksums': ['27ba13f0d9512929166bbd8c9ef95d90d630fc80f0c9a1b7458891055e9282a4'], }), - ('CPAN::Meta::Check', '0.017', { - 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', + ('DateTime::TimeZone', '2.60', { + 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['f0460d379323905b579bed44e141237a337dc25dd26b6ab0c60ac2b80629323d'], + }), + ('Module::Build', '0.4234', { + 'source_tmpl': 'Module-Build-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['0454ab93f12780b1d579df15b5f939e09702e954be82028fadd40e8bc9b0f091'], + 'checksums': ['66aeac6127418be5e471ead3744648c766bd01482825c5b66652675f2bc86a8f'], }), - ('Test::Without::Module', '0.21', { - 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], - 'checksums': ['3cdeafadac4853ebeafe689346d555da5dfa3cfa9d4c84e3e5e7bfee50beec46'], + ('Params::Validate', '1.31', { + 'source_tmpl': 'Params-Validate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['1bf2518ef2c4869f91590e219f545c8ef12ed53cf313e0eb5704adf7f1b2961e'], + }), + ('List::MoreUtils::XS', '0.430', { + 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], + }), + ('List::MoreUtils', '0.430', { + 'source_tmpl': 'List-MoreUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['63b1f7842cd42d9b538d1e34e0330de5ff1559e4c2737342506418276f646527'], }), ('DateTime', '1.59', { 'source_tmpl': 'DateTime-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['de3e9a63ce15470b4db4adad4ba6ac8ec297d88c0c6c6b354b081883b0a67695'], }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['83293737e803b43112830443fb5208ec5208a2e6ea512ed54ef8e4dd2b880827'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['7e6f16cc33eb1f29ff25bee51d513f4b8a84947bbfa18edb2d3cc40a2d64cafe'], + }), + ('Params::Util', '1.102', { + 'source_tmpl': 'Params-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['499bb1b482db24fda277a51525596ad092c2bd51dd508fa8fec2e9f849097402'], + }), ('File::Find::Rule::Perl', '1.16', { 'source_tmpl': 'File-Find-Rule-Perl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], @@ -240,6 +381,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], 'checksums': ['9469a9f398f3a2bf2b0500566ee41d3ff6fae460412a137185767a1cc4783a6d'], }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['452995beeabf0e923e65fdc627a725dbb12c9e10c00d8018c16d10ba62757f1e'], + }), ('Tree::DAG_Node', '1.32', { 'source_tmpl': 'Tree-DAG_Node-%(version)s.tgz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], @@ -320,6 +466,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], 'checksums': ['777d64d2938f5ea586300eef97ef03eacb43d4c1853c9c3b1091eb3311467970'], }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293'], + }), ('Test::Exception', '0.43', { 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], @@ -340,11 +491,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], 'checksums': ['629e361f22b220be50c2da7354e23c0451757709a03c25a22f3160edb94cb65f'], }), - ('File::Copy::Recursive', '0.45', { - 'source_tmpl': 'File-Copy-Recursive-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], - 'checksums': ['d3971cf78a8345e38042b208bb7b39cb695080386af629f4a04ffd6549df1157'], - }), ('Cwd::Guard', '0.05', { 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], @@ -370,11 +516,51 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], 'checksums': ['0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117'], }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + 'checksums': ['82d659cb16461764fd44d11a9ce9e6a4f5e8767dc1069eb03467c6e55de257f3'], + }), ('Template::Plugin::Number::Format', '1.06', { 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], 'checksums': ['0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843'], }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['adb17dac9e36cd011f5243881c9739417fd102fce760f8de4e9be4c7131108e2'], + }), + ('URI', '5.19', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMBABQUE'], + 'checksums': ['8fed5f819905c8a8e18f4447034322d042c3536b43c13ac1f09ba92e1a50a394'], + }), + ('B::COW', '0.007', { + 'source_tmpl': 'B-COW-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['1290daf227e8b09889a31cf182e29106f1cf9f1a4e9bf7752f9de92ed1158b44'], + }), + ('Clone', '0.46', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': ['aadeed5e4c8bd6bbdf68c0dd0066cb513e16ab9e5b4382dc4a0aafd55890697b'], + }), + ('IO::HTML', '1.004', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + 'checksums': ['c87b2df59463bbf2c39596773dfb5c03bde0f7e1051af339f963f58c1cbd8bf5'], + }), + ('LWP::MediaTypes', '6.04', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['8f1bca12dab16a1c2a7c03a49c5e58cce41a6fec9519f0aadfba8dad997919d9'], + }), + ('HTTP::Message', '6.44', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['398b647bf45aa972f432ec0111f6617742ba32fc773c6612d21f64ab4eacbca1'], + }), ('HTML::Parser', '3.81', { 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], @@ -385,15 +571,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], 'checksums': ['c36fd2b68d48c2e17417bf2873c78820f3ae02460fdf5976b8eeab887d59e16c'], }), - ('Params::Util', '1.102', { - 'source_tmpl': 'Params-Util-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], - 'checksums': ['499bb1b482db24fda277a51525596ad092c2bd51dd508fa8fec2e9f849097402'], - }), - ('IO::HTML', '1.004', { - 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], - 'checksums': ['c87b2df59463bbf2c39596773dfb5c03bde0f7e1051af339f963f58c1cbd8bf5'], + ('XML::Parser', '2.46', { + 'source_tmpl': 'XML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['d331332491c51cccfb4cb94ffc44f9cd73378e618498d4a37df9e043661c515d'], }), ('Data::Grove', '0.08', { 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', @@ -405,10 +586,10 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], 'checksums': ['8816f34e9a38e849a10df756030dccf9fe061a196c11ac3faafd7113c929b964'], }), - ('URI', '5.19', { - 'source_tmpl': 'URI-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMBABQUE'], - 'checksums': ['8fed5f819905c8a8e18f4447034322d042c3536b43c13ac1f09ba92e1a50a394'], + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': ['85e2f805bfc81cd738c294316b27a515397036f397a0ff1c6c8d754c38530306'], }), ('Ima::DBI', '0.35', { 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', @@ -420,16 +601,47 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], 'checksums': ['fabb0b8c97e67c9b34b6cc18ed66f6c5e01c55b257dcf007555e0b027d4caf56'], }), + ('Parse::RecDescent', '1.967015', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + 'checksums': ['1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37'], + }), ('GO', '0.04', { + 'runtest': False, # Problem with indirect dependency DBD::Pg 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], 'checksums': ['8eb73d591ad767e7cf26def40cffd84833875f1ad51e456960b9ed73dc23641b'], }), + ('Class::Trigger', '0.15', { + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['b7a878d44dea67d64df2ca18020d9d868a95596debd16f1a264874209332b07f'], + }), + ('Class::Accessor', '0.51', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['bf12a3e5de5a2c6e8a447b364f4f5a050bf74624c56e315022ae7992ff2f411c'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['94ce27a546cd57cb52e080a8f2533a7cc2350028388582485bd1039a37871f9c'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': ['541354fe361c56850cb11261f6ca089a14573fa764792447444ff736ae626206'], + }), ('Class::DBI::SQLite', '0.11', { 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], 'checksums': ['c4661b00afb7e53c97ac36e13f34dde43c1a93540a2f4ff97e6182b0c731e4e7'], }), + ('File::Slurper', '0.014', { + 'source_tmpl': 'File-Slurper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['d5a36487339888c3cd758e648160ee1d70eb4153cacbaff57846dbcefb344b0c'], + }), ('Pod::POM', '2.01', { 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], @@ -440,11 +652,21 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], 'checksums': ['73a7329a86e54a5c29a440382e5803095b58f33129e61a1df0093b4824de9327'], }), + ('Algorithm::Diff', '1.201', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0022da5982645d9ef0207f3eb9ef63e70e9713ed2340ed7b3850779b0d842a7d'], + }), ('Text::Diff', '1.45', { 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], 'checksums': ['e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04'], }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['bd697dd62aaf26d118e9f0a0813429deb1c544e4501559879b61fcbdfe99fe46'], + }), ('Log::Message::Simple', '0.10', { 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], @@ -466,35 +688,140 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['dce28e3932762c2ff92aa52d90405c06e898e81cb7b164ccae8966ae77f1dcab'], }), - ('Sub::Uplevel', '0.2800', { - 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], - 'checksums': ['b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293'], - }), ('Meta::Builder', '0.004', { 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['acb499aa7206eb9db21eb85357a74521bfe3bdae4a6416d50a7c75b939cf56fe'], }), - ('Exporter::Declare', '0.114', { - 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], - 'checksums': ['4bd70d6ca76f6f6ba7e4c618d4ac93b8593a58f1233ccbe18b10f5f204f1d4e4'], + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['4bd70d6ca76f6f6ba7e4c618d4ac93b8593a58f1233ccbe18b10f5f204f1d4e4'], + }), + ('Mouse', 'v2.5.10', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SK/SKAJI'], + 'checksums': ['ce8dc23946153a467ff09765167ee2590f5c502120f48a2d9441733f39aa32ee'], + }), + ('Test::Version', '2.09', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['9ce1dd2897a5f30e1b7f8966ec66f57d8d8f280f605f28c7ca221fa79aca38e0'], + }), + ('Class::Method::Modifiers', '2.15', { + 'source_tmpl': 'Class-Method-Modifiers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['65cd85bfe475d066e9186f7a8cc636070985b30b0ebb1cde8681cf062c2e15fc'], + }), + ('Moo', '2.005005', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['fb5a2952649faed07373f220b78004a9c6aba387739133740c1770e9b1f4b108'], + }), + ('Data::Dumper::Concise', '2.023', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['a6c22f113caf31137590def1b7028a7e718eface3228272d0672c25e035d5853'], + }), + ('DBIx::Admin::CreateTable', '2.11', { + 'source_tmpl': 'DBIx-Admin-CreateTable-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['07b1427fbc15455657ca57217749004162a50c04abb243022a5b479e4b2a5912'], + }), + ('Config::Tiny', '2.29', { + 'source_tmpl': 'Config-Tiny-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['3de79b0ea03a8d6a93e9d9128fe845fb556222b14699a4f6f0d5ca057ae3333b'], + }), + ('File::Slurp', '9999.32', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['4c3c21992a9d42be3a79dd74a3c83d27d38057269d65509a2f555ea0fb2bc5b0'], + }), + ('DBIx::Admin::DSNManager', '2.02', { + 'source_tmpl': 'DBIx-Admin-DSNManager-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['c25511f42328ccb606a0cd78413a74181c87fb37a382d38aa3fad106b540adcb'], + }), + ('Lingua::EN::PluralToSingular', '0.21', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + 'checksums': ['f8a8b7de28c25c96190d7f48c90b5ad9b9bf517f3835c77641f0e8fa546c0d1d'], + }), + ('Test::Warn', '0.37', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + 'checksums': ['98ca32e7f2f5ea89b8bfb9a0609977f3d153e242e2e51705126cb954f1a06b57'], + }), + ('Test::Differences', '0.69', { + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': ['18f644fdd4a1fef93ef3f7f67df8e95b593d811899f34bcbbaba4d717222f58f'], + }), + ('Test::Most', '0.38', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + 'checksums': ['089eb894f7bace4c37c6334e0e290eb20338ee10223af0c82cbe7281c78382df'], + }), + ('Const::Fast', '0.014', { + 'source_tmpl': 'Const-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['f805953a08c57846a16a4d85d7b766398afaf7c36c1465fcb1dea09e5fa394db'], + }), + ('Ref::Util', '0.204', { + 'source_tmpl': 'Ref-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARC'], + 'checksums': ['415fa73dbacf44f3d5d79c14888cc994562720ab468e6f71f91cd1f769f105e1'], + }), + ('Class::XSAccessor', '1.19', { + 'source_tmpl': 'Class-XSAccessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['99c56b395f1239af19901f2feeb125d9ecb4e351a0d80daa9529211a4700a6f2'], + }), + ('Hash::Objectify', '0.008', { + 'source_tmpl': 'Hash-Objectify-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['236d5829cdebf3ba648d34e1295cd9099a20506d8d0284668e617e0058cebeed'], + }), + ('Const::Exporter', '1.2.2', { + 'source_tmpl': 'Const-Exporter-v%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRWO'], + 'checksums': ['ae7560499fa3b8d211e7b8b3de926fb56bed3c28b1e7a5a7a5fad12f20c132ed'], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c'], + }), + ('List::SomeUtils', '0.59', { + 'source_tmpl': 'List-SomeUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['fab30372e4c67bf5a46062da38d1d0c8756279feada866eb439fa29571a2dc7b'], + }), + ('List::UtilsBy', '0.12', { + 'source_tmpl': 'List-UtilsBy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['fff1281fd469fe982b1a58044becfd970f313bff3a26e1c7b2b3f4c0a5ed71e0'], + }), + ('List::AllUtils', '0.19', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['30a8146ab21a7787b8c56d5829cf9a7f2b15276d3b3fca07336ac38d3002ffbc'], }), - ('Log::Message', '0.08', { - 'source_tmpl': 'Log-Message-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], - 'checksums': ['bd697dd62aaf26d118e9f0a0813429deb1c544e4501559879b61fcbdfe99fe46'], + ('Unicode::EastAsianWidth', '12.0', { + 'source_tmpl': 'Unicode-EastAsianWidth-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AU/AUDREYT'], + 'checksums': ['2a5bfd926c4fe5f77e6137da2c31ac2545282ae5fec6e9af0fdd403555a90ff4'], }), - ('Mouse', 'v2.5.10', { - 'source_tmpl': 'Mouse-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SK/SKAJI'], - 'checksums': ['ce8dc23946153a467ff09765167ee2590f5c502120f48a2d9441733f39aa32ee'], + ('String::TtyLength', '0.03', { + 'source_tmpl': 'String-TtyLength-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['4fedaf72028511d80eb6afba523993e9aaa245d7af558345d5d4ed46e2e82ce1'], }), - ('Test::Version', '2.09', { - 'source_tmpl': 'Test-Version-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], - 'checksums': ['9ce1dd2897a5f30e1b7f8966ec66f57d8d8f280f605f28c7ca221fa79aca38e0'], + ('Text::Table::Manifold', '1.03', { + 'source_tmpl': 'Text-Table-Manifold-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['e680713169557b0768952fa6932f25576a61dccfb96bd9036dcf6fcefb35e09e'], }), ('DBIx::Admin::TableInfo', '3.04', { 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', @@ -506,26 +833,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], 'checksums': ['62faf9a5b84235443fe18f780e69cecf057dea3de271d7d8a0ba72724458a1a2'], }), - ('Test::Deep', '1.204', { - 'source_tmpl': 'Test-Deep-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['b6591f6ccdd853c7efc9ff3c5756370403211cffe46047f082b1cd1611a84e5f'], - }), - ('Test::Warn', '0.37', { - 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], - 'checksums': ['98ca32e7f2f5ea89b8bfb9a0609977f3d153e242e2e51705126cb954f1a06b57'], - }), - ('MRO::Compat', '0.15', { - 'source_tmpl': 'MRO-Compat-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], - 'checksums': ['0d4535f88e43babd84ab604866215fc4d04398bd4db7b21852d4a31b1c15ef61'], - }), - ('Moo', '2.005005', { - 'source_tmpl': 'Moo-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], - 'checksums': ['fb5a2952649faed07373f220b78004a9c6aba387739133740c1770e9b1f4b108'], - }), ('Clone::Choose', '0.010', { 'source_tmpl': 'Clone-Choose-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'], @@ -546,21 +853,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMBABQUE'], 'checksums': ['43bfaa7087393487d2d51261a1aa7f6f81a97b1d8fef7a48fcf6ef32b16d6454'], }), - ('Number::Compare', '0.03', { - 'source_tmpl': 'Number-Compare-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], - 'checksums': ['83293737e803b43112830443fb5208ec5208a2e6ea512ed54ef8e4dd2b880827'], - }), ('IPC::Run', '20220807.0', { 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], 'checksums': ['277d781dbbc98af18e979c7ef36f222513d7361742c52507c3348b265f6f5e69'], }), - ('HTML::Entities::Interpolate', '1.10', { - 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], - 'checksums': ['f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c'], - }), ('File::Remove', '1.61', { 'source_tmpl': 'File-Remove-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], @@ -576,36 +873,21 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': ['fbf91007f30565f3920e106055fd0d4287981d5e7dad8b35323ce4b733f15a7b'], }), - ('Config::Tiny', '2.29', { - 'source_tmpl': 'Config-Tiny-%(version)s.tgz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], - 'checksums': ['3de79b0ea03a8d6a93e9d9128fe845fb556222b14699a4f6f0d5ca057ae3333b'], - }), ('Test::ClassAPI', '1.07', { 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': ['30e9dbfc5e0cc2ee14eae8f3465a908a710daecbd0a3ebdb2888fc4504fa18aa'], }), - ('Test::Most', '0.38', { - 'source_tmpl': 'Test-Most-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], - 'checksums': ['089eb894f7bace4c37c6334e0e290eb20338ee10223af0c82cbe7281c78382df'], - }), - ('Class::Accessor', '0.51', { - 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], - 'checksums': ['bf12a3e5de5a2c6e8a447b364f4f5a050bf74624c56e315022ae7992ff2f411c'], - }), - ('Test::Differences', '0.69', { - 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], - 'checksums': ['18f644fdd4a1fef93ef3f7f67df8e95b593d811899f34bcbbaba4d717222f58f'], - }), ('HTTP::Tiny', '0.082', { 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['54e9e4a559a92cbb90e3f19c8a88ff067ec2f68fbe39bbb694ee70828cd5f4b8'], }), + ('Sub::Install', '0.929', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['80b1e281d8cd3b2b31dac711f5c8a1657a87cd80bbe69af3924bcbeb4e5db077'], + }), ('Package::DeprecationManager', '0.18', { 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], @@ -656,6 +938,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], 'checksums': ['1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016'], }), + ('Email::Date::Format', '1.008', { + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['432b7c83ff88749af128003f5257c573aec1a463418db90ed22843cbbc258b4f'], + }), ('MIME::Lite', '3.033', { 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], @@ -667,6 +954,7 @@ exts_list = [ 'checksums': ['6540085e3804b82a6f0752c1122cf78cadd221990136dd6fd4c097d056c84d40'], }), ('B::Lint', '1.20', { + 'runtest': False, # One failing subtest 'source_tmpl': 'B-Lint-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['dc49408964fd8b7963859c92e013f0b9f92f74be5a7c2a78e3996279827c10b3'], @@ -711,11 +999,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], 'checksums': ['ce39fcb53e0fe9f1cbcd86ddf152e1db48566266b70ec0769ef364eeabdd8941'], }), - ('HTML::Tagset', '3.20', { - 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], - 'checksums': ['adb17dac9e36cd011f5243881c9739417fd102fce760f8de4e9be4c7131108e2'], - }), ('HTML::Tree', '5.07', { 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], @@ -731,6 +1014,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], 'checksums': ['46b502e7a288d559429891eeb5d979461dd3ecc6a5c491ead85d165b6e03a51e'], }), + ('IO::Tty', '1.17', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['a5f1a83020bc5b5dd6c1b570f48c7546e0a8f7fac10a068740b03925ad9e14e8'], + }), ('Expect', '1.35', { 'source_tmpl': 'Expect-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], @@ -761,11 +1049,36 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], 'checksums': ['b04edeea26bfed435aa6029956798c281f7f52d4545f3f45b2ad44954e96f939'], }), + ('Data::OptList', '0.114', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9fd1093b917a21fb79ae1607db53d113b4e0ad8fe0ae776cb077a7e50044fdf3'], + }), ('Class::Load', '0.25', { 'source_tmpl': 'Class-Load-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': ['2a48fa779b5297e56156380e8b32637c6c58decb4f4a7f3c7350523e11275f8f'], }), + ('HTTP::Daemon', '6.16', { + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['b38d092725e6fa4e0c4dc2a47e157070491bafa0dbe16c78a358e806aa7e173d'], + }), + ('Test::RequiresInternet', '0.05', { + 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN'], + 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], + }), + ('HTTP::Cookies', '6.10', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['e36f36633c5ce6b5e4b876ffcf74787cc5efe0736dd7f487bdd73c14f0bd7007'], + }), + ('HTTP::CookieJar', '0.014', { + 'source_tmpl': 'HTTP-CookieJar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['7094ea5c91f536d263b85e83ab4e9a963e11c4408ce08ecae553fa9c0cc47e73'], + }), ('LWP::Simple', '6.70', { 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMBABQUE'], @@ -781,6 +1094,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': ['26bad65c1959c57379b3e139dc776fbec5f702906617ef27cdc293ddf1239231'], }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': ['b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7'], + }), ('Set::Array', '0.30', { 'source_tmpl': 'Set-Array-%(version)s.tgz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], @@ -791,16 +1109,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], 'checksums': ['95c088085c3e83bf680fe6ce16d8264ec26310490f7d1680e416ea7a118f156a'], }), - ('Number::Format', '1.75', { - 'source_tmpl': 'Number-Format-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], - 'checksums': ['82d659cb16461764fd44d11a9ce9e6a4f5e8767dc1069eb03467c6e55de257f3'], - }), - ('Data::Stag', '0.14', { - 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], - 'checksums': ['4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59'], - }), ('Test::NoWarnings', '1.06', { 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], @@ -811,21 +1119,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], 'checksums': ['2db1ebb5837b4cb20051c0ee5b733b4453e3137df0a92306034c867621edd7e7'], }), - ('Class::Inspector', '1.36', { - 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], - 'checksums': ['cc295d23a472687c24489d58226ead23b9fdc2588e522f0b5f0747741700694e'], - }), - ('Parse::RecDescent', '1.967015', { - 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], - 'checksums': ['1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37'], - }), - ('XML::Parser', '2.46', { - 'source_tmpl': 'XML-Parser-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], - 'checksums': ['d331332491c51cccfb4cb94ffc44f9cd73378e618498d4a37df9e043661c515d'], - }), ('XML::XPath', '1.48', { 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], @@ -846,41 +1139,21 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': ['5bc22cf536ebfd2564c5bdaf42f0d8a4cee3d1930fc8b44b7d4a42038622add1'], }), + ('Data::Types', '0.17', { + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['860751feb79b7dfc1af71c4b7fe920220ec6d31c4ab9402b8f178f7f4b8293c1'], + }), ('Set::IntSpan::Fast', '1.15', { 'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], 'checksums': ['cfb1768c24f55208e87405b17f537f0f303fa141891d0b22d509a941aa57e24e'], }), - ('Sub::Exporter::Progressive', '0.001013', { - 'source_tmpl': 'Sub-Exporter-Progressive-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], - 'checksums': ['d535b7954d64da1ac1305b1fadf98202769e3599376854b2ced90c382beac056'], - }), - ('Data::Dumper::Concise', '2.023', { - 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['a6c22f113caf31137590def1b7028a7e718eface3228272d0672c25e035d5853'], - }), - ('File::Slurp::Tiny', '0.004', { - 'source_tmpl': 'File-Slurp-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['452995beeabf0e923e65fdc627a725dbb12c9e10c00d8018c16d10ba62757f1e'], - }), - ('Algorithm::Diff', '1.201', { - 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['0022da5982645d9ef0207f3eb9ef63e70e9713ed2340ed7b3850779b0d842a7d'], - }), ('Text::Iconv', '1.7', { 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], 'checksums': ['5b80b7d5e709d34393bcba88971864a17b44a5bf0f9e4bcee383d029e7d2d5c3'], }), - ('Class::Data::Inheritable', '0.09', { - 'source_tmpl': 'Class-Data-Inheritable-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSHERER'], - 'checksums': ['44088d6e90712e187b8a5b050ca5b1c70efe2baa32ae123e9bd8f59f29f06e4d'], - }), ('Text::Balanced', '2.06', { 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], @@ -901,11 +1174,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], 'checksums': ['3201f1a60e3f16484082e6045c896842261fc345de9fb2e620fd2a2c7af3a93a'], }), - ('Email::Date::Format', '1.008', { - 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['432b7c83ff88749af128003f5257c573aec1a463418db90ed22843cbbc258b4f'], - }), ('Error', '0.17029', { 'source_tmpl': 'Error-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], @@ -926,36 +1194,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], 'checksums': ['f6a8482740b075fad22aaf4d987d38ef927c6d2b452d4ae0d0bd8f779830556e'], }), - ('Class::DBI', 'v3.0.17', { - 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], - 'checksums': ['541354fe361c56850cb11261f6ca089a14573fa764792447444ff736ae626206'], - }), - ('List::SomeUtils', '0.59', { - 'source_tmpl': 'List-SomeUtils-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['fab30372e4c67bf5a46062da38d1d0c8756279feada866eb439fa29571a2dc7b'], - }), - ('List::UtilsBy', '0.12', { - 'source_tmpl': 'List-UtilsBy-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], - 'checksums': ['fff1281fd469fe982b1a58044becfd970f313bff3a26e1c7b2b3f4c0a5ed71e0'], - }), - ('List::AllUtils', '0.19', { - 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['30a8146ab21a7787b8c56d5829cf9a7f2b15276d3b3fca07336ac38d3002ffbc'], - }), - ('UNIVERSAL::moniker', '0.08', { - 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], - 'checksums': ['94ce27a546cd57cb52e080a8f2533a7cc2350028388582485bd1039a37871f9c'], - }), - ('Exception::Class', '1.45', { - 'source_tmpl': 'Exception-Class-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['5482a77ef027ca1f9f39e1f48c558356e954936fc8fbbdee6c811c512701b249'], - }), ('File::CheckTree', '4.42', { 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], @@ -966,107 +1204,53 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), + ('Pod::Parser', '1.66', { + 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], + 'checksums': ['22928a7bffe61b452c05bbbb8f5216d4b9cf9fe2a849b776c25500d24d20df7c'], + }), ('Pod::LaTeX', '0.61', { 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], 'checksums': ['15a840ea1c8a76cd3c865fbbf2fec33b03615c0daa50f9c800c54e0cf0659d46'], }), - ('Eval::Closure', '0.14', { - 'source_tmpl': 'Eval-Closure-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], - 'checksums': ['ea0944f2f5ec98d895bef6d503e6e4a376fea6383a6bc64c7670d46ff2218cad'], - }), - ('HTTP::Request', '6.44', { - 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['398b647bf45aa972f432ec0111f6617742ba32fc773c6612d21f64ab4eacbca1'], - }), ('XML::Twig', '3.52', { 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], 'checksums': ['fef75826c24f2b877d0a0d2645212fc4fb9756ed4d2711614ac15c497e8680ad'], }), - ('IO::String', '1.08', { - 'source_tmpl': 'IO-String-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], - 'checksums': ['2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0'], - }), ('XML::Simple', '2.25', { 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], 'checksums': ['531fddaebea2416743eb5c4fdfab028f502123d9a220405a4100e68fc480dbf8'], }), - ('Sub::Install', '0.929', { - 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['80b1e281d8cd3b2b31dac711f5c8a1657a87cd80bbe69af3924bcbeb4e5db077'], - }), - ('HTTP::Cookies', '6.10', { - 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['e36f36633c5ce6b5e4b876ffcf74787cc5efe0736dd7f487bdd73c14f0bd7007'], - }), ('Pod::Plainer', '1.04', { 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], 'checksums': ['1bbfbf7d1d4871e5a83bab2137e22d089078206815190eb1d5c1260a3499456f'], }), - ('LWP::MediaTypes', '6.04', { - 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['8f1bca12dab16a1c2a7c03a49c5e58cce41a6fec9519f0aadfba8dad997919d9'], - }), ('Data::Section::Simple', '0.07', { 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], - 'checksums': ['0b3035ffdb909aa1f7ded6b608fa9d894421c82c097d51e7171170d67579a9cb'], - }), - ('Class::Trigger', '0.15', { - 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], - 'checksums': ['b7a878d44dea67d64df2ca18020d9d868a95596debd16f1a264874209332b07f'], - }), - ('Test::Needs', '0.002010', { - 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], - 'checksums': ['923ffdc78fcba96609753e4bae26b0ba0186893de4a63cd5236e012c7c90e208'], - }), - ('HTTP::Daemon', '6.16', { - 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['b38d092725e6fa4e0c4dc2a47e157070491bafa0dbe16c78a358e806aa7e173d'], + 'checksums': ['0b3035ffdb909aa1f7ded6b608fa9d894421c82c097d51e7171170d67579a9cb'], }), ('File::HomeDir', '1.006', { 'source_tmpl': 'File-HomeDir-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], 'checksums': ['593737c62df0f6dab5d4122e0b4476417945bb6262c33eedc009665ef1548852'], }), - ('HTTP::Date', '6.05', { - 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], - 'checksums': ['365d6294dfbd37ebc51def8b65b81eb79b3934ecbc95a2ec2d4d827efe6a922b'], - }), ('Authen::SASL', '2.16', { 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], 'checksums': ['6614fa7518f094f853741b63c73f3627168c5d3aca89b1d02b1016dc32854e09'], }), - ('Clone', '0.46', { - 'source_tmpl': 'Clone-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], - 'checksums': ['aadeed5e4c8bd6bbdf68c0dd0066cb513e16ab9e5b4382dc4a0aafd55890697b'], - }), - ('Data::Types', '0.17', { - 'source_tmpl': 'Data-Types-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], - 'checksums': ['860751feb79b7dfc1af71c4b7fe920220ec6d31c4ab9402b8f178f7f4b8293c1'], - }), ('Import::Into', '1.002005', { 'source_tmpl': 'Import-Into-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], 'checksums': ['bd9e77a3fb662b40b43b18d3280cd352edf9fad8d94283e518181cc1ce9f0567'], }), ('DateTime::Tiny', '1.07', { + 'runtest': False, # One subset fails due to locale 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['83568a22838cb518fbeb9e060460ec7f59d5a0b0a1cc06562954c3674d7cf7e4'], @@ -1086,16 +1270,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], 'checksums': ['3a5c80e7128454770f83acab8cbd3e70e5ec3d59a61dc32792a178f0b31bf74d'], }), - ('DBIx::ContextualFetch', '1.03', { - 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], - 'checksums': ['85e2f805bfc81cd738c294316b27a515397036f397a0ff1c6c8d754c38530306'], - }), - ('Devel::StackTrace', '2.04', { - 'source_tmpl': 'Devel-StackTrace-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['cd3c03ed547d3d42c61fa5814c98296139392e7971c092e09a431f2c9f5d6855'], - }), ('Term::ReadKey', '2.38', { 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], @@ -1111,11 +1285,21 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], }), + ('File::pushd', '1.016', { + 'source_tmpl': 'File-pushd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['d73a7f09442983b098260df3df7a832a5f660773a313ca273fa8b56665f97cdc'], + }), ('Test::CleanNamespaces', '0.24', { 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], }), + ('Devel::OverloadInfo', '0.007', { + 'source_tmpl': 'Devel-OverloadInfo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + 'checksums': ['21a184163b90f91f06ffc7f5de0b968356546ae9b400a9d75c573c958c246222'], + }), ('Moose', '2.2203', { 'source_tmpl': 'Moose-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], @@ -1136,31 +1320,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['3d81c3cc1b5cff69cca9361e2c6e38df0352251ae7b41e2ff3febc850e463565'], }), - ('File::Find::Rule', '0.34', { - 'source_tmpl': 'File-Find-Rule-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], - 'checksums': ['7e6f16cc33eb1f29ff25bee51d513f4b8a84947bbfa18edb2d3cc40a2d64cafe'], - }), ('SQL::Statement', '1.414', { 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], 'checksums': ['dde8bdcfa6a136eedda06519ba0f3efaec085c39db0df9c472dc0ec6cd781a49'], }), - ('File::Slurp', '9999.32', { - 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], - 'checksums': ['4c3c21992a9d42be3a79dd74a3c83d27d38057269d65509a2f555ea0fb2bc5b0'], - }), - ('Package::Stash', '0.40', { - 'source_tmpl': 'Package-Stash-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['5a9722c6d9cb29ee133e5f7b08a5362762a0b5633ff5170642a5b0686e95e066'], - }), - ('Data::OptList', '0.114', { - 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['9fd1093b917a21fb79ae1607db53d113b4e0ad8fe0ae776cb077a7e50044fdf3'], - }), ('Package::Constants', '0.06', { 'source_tmpl': 'Package-Constants-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], @@ -1181,16 +1345,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['f6dd55b4280b25dea978221839864382560074e1d6933395faee2510c2db60ed'], }), - ('Lingua::EN::PluralToSingular', '0.21', { - 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], - 'checksums': ['f8a8b7de28c25c96190d7f48c90b5ad9b9bf517f3835c77641f0e8fa546c0d1d'], - }), - ('Want', '0.29', { - 'source_tmpl': 'Want-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], - 'checksums': ['b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7'], - }), ('Mail::Util', '2.21', { 'source_tmpl': 'MailTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], @@ -1261,11 +1415,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MN/MNEYLON'], 'checksums': ['462e15274eb6278521407ea302d9eea7252cd44cab2382871f7de833d5f85632'], }), - ('File::Slurper', '0.014', { - 'source_tmpl': 'File-Slurper-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], - 'checksums': ['d5a36487339888c3cd758e648160ee1d70eb4153cacbaff57846dbcefb344b0c'], - }), ('File::Temp', '0.2311', { 'source_tmpl': 'File-Temp-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], @@ -1286,6 +1435,16 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], 'checksums': ['7a60c7746da3f2da43f4acea703be2ad8fa24b26a623a0745876020e6ecd970e'], }), + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + ('Parse::Yapp', '1.21', { + 'source_tmpl': 'Parse-Yapp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WB/WBRASWELL'], + 'checksums': ['3810e998308fba2e0f4f26043035032b027ce51ce5c8a52a8b8e340ca65f13e5'], + }), ('Graph::ReadWrite', '2.10', { 'source_tmpl': 'Graph-ReadWrite-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], @@ -1296,16 +1455,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], 'checksums': ['bcd2848b72df290b5e984fae8b1a6ca96f6d072003cf222389a8c9e8e1c570cd'], }), - ('Devel::OverloadInfo', '0.007', { - 'source_tmpl': 'Devel-OverloadInfo-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], - 'checksums': ['21a184163b90f91f06ffc7f5de0b968356546ae9b400a9d75c573c958c246222'], - }), - ('Sub::Identify', '0.14', { - 'source_tmpl': 'Sub-Identify-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RG/RGARCIA'], - 'checksums': ['068d272086514dd1e842b6a40b1bedbafee63900e5b08890ef6700039defad6f'], - }), ('Digest::MD5::File', '0.08', { 'source_tmpl': 'Digest-MD5-File-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], @@ -1321,16 +1470,16 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['9b8d15fcaf18fdd740246b438f0e7eb914b831c51d9d708c099eca776622076d'], }), + ('IO::TieCombine', '1.005', { + 'source_tmpl': 'IO-TieCombine-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['402d4db8300b3d271632f4995e0ade329d89280a7e47f2badf8b38af6e5569af'], + }), ('App::Cmd', '0.335', { 'source_tmpl': 'App-Cmd-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['f95517fc4df348d9e7ea01467aabd9725f0715662ee483b54b81d3f0b38c9874'], }), - ('Path::Tiny', '0.144', { - 'source_tmpl': 'Path-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], - 'checksums': ['f6ea094ece845c952a02c2789332579354de8d410a707f9b7045bd241206487d'], - }), ('Carp::Clan', '6.08', { 'source_tmpl': 'Carp-Clan-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], @@ -1351,66 +1500,56 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT'], 'checksums': ['ba4083b2c31ff2694f2371333d554c826aaf24b4d98d03e48b5b4a43a2a0e679'], }), - ('B::Hooks::EndOfScope', '0.26', { - 'source_tmpl': 'B-Hooks-EndOfScope-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['39df2f8c007a754672075f95b90797baebe97ada6d944b197a6352709cb30671'], - }), - ('namespace::clean', '0.27', { - 'source_tmpl': 'namespace-clean-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], - 'checksums': ['8a10a83c3e183dc78f9e7b7aa4d09b47c11fb4e7d3a33b9a12912fd22e31af9d'], - }), - ('namespace::autoclean', '0.29', { - 'source_tmpl': 'namespace-autoclean-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['45ebd8e64a54a86f88d8e01ae55212967c8aa8fed57e814085def7608ac65804'], - }), - ('File::pushd', '1.016', { - 'source_tmpl': 'File-pushd-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], - 'checksums': ['d73a7f09442983b098260df3df7a832a5f660773a313ca273fa8b56665f97cdc'], - }), ('MooseX::Types::Perl', '0.101344', { 'source_tmpl': 'MooseX-Types-Perl-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['87644354f74fa65235cb2bfca44277930a7eabe51acc5f81fb631530a8355e24'], }), - ('Role::Tiny', '2.002004', { - 'source_tmpl': 'Role-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], - 'checksums': ['d7bdee9e138a4f83aa52d0a981625644bda87ff16642dfa845dcb44d9a242b45'], - }), - ('Specio', '0.48', { - 'source_tmpl': 'Specio-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['0c85793580f1274ef08173079131d101f77b22accea7afa8255202f0811682b2'], - }), - ('Params::ValidationCompiler', '0.31', { - 'source_tmpl': 'Params-ValidationCompiler-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['7b6497173f1b6adb29f5d51d8cf9ec36d2f1219412b4b2410e9d77a901e84a6d'], - }), ('Log::Dispatch', '2.71', { 'source_tmpl': 'Log-Dispatch-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['9d60d9648c35ce2754731eb4deb7f05809ece1bd633b74d74795aed9ec732570'], }), + ('JSON::MaybeXS', '1.004005', { + 'source_tmpl': 'JSON-MaybeXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['f5b6bc19f579e66b7299f8748b8ac3e171936dc4e7fcb72a8a257a9bd482a331'], + }), ('String::Flogger', '1.101246', { 'source_tmpl': 'String-Flogger-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['15f8491e07818bb3cfa9f6bd3aabf6430ba9b4e309f18114358be3d81bff3a0f'], }), + ('Log::Dispatch::Array', '1.005', { + 'source_tmpl': 'Log-Dispatch-Array-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['311640b7a967f8dd7c9bb41a227073565636d70df4fcc1d44fed8a8223b347ca'], + }), + ('Sub::Exporter::GlobExporter', '0.006', { + 'source_tmpl': 'Sub-Exporter-GlobExporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['de743f08026701c2a6a222a8b41c4cdc254b1a4afe7ef98987cd3aba4ce52696'], + }), ('Log::Dispatchouli', '3.002', { 'source_tmpl': 'Log-Dispatchouli-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['86a739f970c8d8e7fcfe52cd75f0844a7cb96e1d9c151f1ba8cba26b541f34ee'], }), + ('Test::FailWarnings', '0.008', { + 'source_tmpl': 'Test-FailWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['da34ef9029f6849d6026201d49127d054ee6ac4b979c82210315f5721964a96f'], + }), ('Data::Section', '0.200008', { 'source_tmpl': 'Data-Section-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['83acc7a55d3dd7ed36e9d78d350af3138c69cfa178a44765822712ff433b990e'], }), + ('Test::CheckDeps', '0.010', { + 'source_tmpl': 'Test-CheckDeps-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['66fccca6c6f330e7ecc898bd6a51846e2145b3e02d78c4997ba6b7de23b551ee'], + }), ('Software::License', '0.104003', { 'source_tmpl': 'Software-License-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], @@ -1426,46 +1565,51 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], 'checksums': ['95ba9687d735d25a3cbe64508d7894f009c7fa2a1726c3e786e9e21da2251d0b'], }), - ('Config::MVP', '2.200013', { - 'source_tmpl': 'Config-MVP-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['018d161623ee3a67f860d9e680e22e61b79eae6018f0e7c3b525fc934f5b7d45'], - }), ('Throwable', '1.001', { 'source_tmpl': 'Throwable-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['d0cb5e9d7d06d70f2cc56eecf857a83a45eaca43850dcdda91d3feb4ddde4c51'], }), - ('Sub::Quote', '2.006008', { - 'source_tmpl': 'Sub-Quote-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], - 'checksums': ['94bebd500af55762e83ea2f2bc594d87af828072370c7110c60c238a800d15b2'], - }), ('Role::Identifiable::HasIdent', '0.009', { 'source_tmpl': 'Role-Identifiable-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['5a735e9f7177f9ebae047eb7bae29b7ec29ec020ae37637aea5350d30c087b76'], }), - ('Role::HasMessage', '0.007', { - 'source_tmpl': 'Role-HasMessage-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], - 'checksums': ['5e267a4d7620b368481204c88ea2044b8b2a58ff8b05577f2717b2754c0414ce'], + ('MooseX::Role::Parameterized', '1.11', { + 'source_tmpl': 'MooseX-Role-Parameterized-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['1cfe766c5d7f0ecab57f733dcca430a2a2acd6b995757141b940ade3692bec9e'], }), ('MooseX::OneArgNew', '0.007', { 'source_tmpl': 'MooseX-OneArgNew-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['84282435f1169cf09d7513fa9387e2091791635cf35a078b500b829aeea06138'], }), - ('MooseX::Role::Parameterized', '1.11', { - 'source_tmpl': 'MooseX-Role-Parameterized-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['1cfe766c5d7f0ecab57f733dcca430a2a2acd6b995757141b940ade3692bec9e'], - }), ('MooseX::LazyRequire', '0.11', { 'source_tmpl': 'MooseX-LazyRequire-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], 'checksums': ['ef620c1e019daf9cf3f23a943d25a94c91e93ab312bcd63be2e9740ec0b94288'], }), + ('String::Formatter', '1.235', { + 'source_tmpl': 'String-Formatter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['08236a913b911ce652cf08598e7c07d2df3f369fc47bf401a485a504a1660783'], + }), + ('String::Errf', '0.009', { + 'source_tmpl': 'String-Errf-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['e1fedbf9b4fd64b64ea81038ddb76a4c6cd85f5db15bc21f10656a298349dc1f'], + }), + ('Role::HasMessage', '0.007', { + 'source_tmpl': 'Role-HasMessage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5e267a4d7620b368481204c88ea2044b8b2a58ff8b05577f2717b2754c0414ce'], + }), + ('Config::MVP', '2.200013', { + 'source_tmpl': 'Config-MVP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['018d161623ee3a67f860d9e680e22e61b79eae6018f0e7c3b525fc934f5b7d45'], + }), ('Mixin::Linewise::Readers', '0.111', { 'source_tmpl': 'Mixin-Linewise-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], @@ -1491,11 +1635,56 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['750c3a79d8e1824758a6ef7d2dd077dcddca503542b8c34eccd5acbb779dc423'], }), + ('Test::Object', '0.08', { + 'source_tmpl': 'Test-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['65278964147837313f4108e55b59676e8a364d6edf01b3dc198aee894ab1d0bb'], + }), + ('Hook::LexWrap', '0.26', { + 'source_tmpl': 'Hook-LexWrap-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b60bdc5f98f94f9294b06adef82b1d996da192d5f183f9f434b610fd1137ec2d'], + }), + ('Test::SubCalls', '1.10', { + 'source_tmpl': 'Test-SubCalls-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['cbc1e9b35a05e71febc13e5ef547a31c8249899bb6011dbdc9d9ff366ddab6c2'], + }), + ('PPI', '1.276', { + 'source_tmpl': 'PPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['657655470e78b7c5b7660f7dec82893489c2e2d880e449135613da3b37500f01'], + }), + ('Config::MVP::Reader::INI', '2.101465', { + 'source_tmpl': 'Config-MVP-Reader-INI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['13c7aa27c1df98cd33ada399e59ff38fabfa9d65513e42af02f72c2d3f636247'], + }), ('Pod::Weaver', '4.019', { 'source_tmpl': 'Pod-Weaver-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], 'checksums': ['6946ad1f04eaf9aa11f24cc54494e1d57962f58e05912f364b74f9593e7de7f7'], }), + ('CPAN::Uploader', '0.103018', { + 'source_tmpl': 'CPAN-Uploader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['c4ffe4ede9db79b396e3bfc5e7cdf0e2e9821e1f1e087f523bcfa74c9fc9e248'], + }), + ('Devel::FindPerl', '0.016', { + 'source_tmpl': 'Devel-FindPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['43a2bf2f787a3f1b881179063162b2aa3e7cb044f6e5e76ec6466ae90a861138'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), + ('Perl::PrereqScanner', '1.100', { + 'source_tmpl': 'Perl-PrereqScanner-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['01181d38a2e7aff838d262122563c50636ba4b3652ee5d1d4f8ef5ba3f5b186b'], + }), ('Dist::Zilla', '6.030', { 'source_tmpl': 'Dist-Zilla-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], @@ -1531,6 +1720,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/Y/YA/YANICK'], 'checksums': ['c1b2970a8bb666c3de7caac4a8f4dbcc043ab819bbc337692ec7bf27adae4404'], }), + ('Object::InsideOut', '4.05', { + 'source_tmpl': 'Object-InsideOut-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], + }), ('Logger::Simple', '2.0', { 'source_tmpl': 'Logger-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TS/TSTANLEY'], @@ -1541,6 +1735,21 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], 'checksums': ['d7501b6d410703db5b1c1942fbfc41af8964a35525d7f766058acf5ca2cc4440'], }), + ('Spiffy', '0.46', { + 'source_tmpl': 'Spiffy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['8f58620a8420255c49b6c43c5ff5802bd25e4f09240c51e5bf2b022833d41da3'], + }), + ('Test::Base', '0.89', { + 'source_tmpl': 'Test-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['2794a1aaaeb1d3a287dd2c7286258663796562f7db9ccc6b424bc4f1de8ad014'], + }), + ('Test::YAML', '1.07', { + 'source_tmpl': 'Test-YAML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TINITA'], + 'checksums': ['1f300d034f46298cb92960912cc04bac33fb27f05b8852d8f051e110b9cd995f'], + }), ('YAML', '1.30', { 'source_tmpl': 'YAML-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TINITA'], @@ -1557,6 +1766,7 @@ exts_list = [ 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], }), ('Term::ReadLine::Gnu', '1.45', { + 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['9f4f7abbc69ea58ab7f24992d47f7391bb4aed6fb701fedaeb1a9f1cdc7fab8a'], @@ -1607,6 +1817,7 @@ exts_list = [ 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], }), ('if', '0.0608', { + 'modulename': False, 'source_tmpl': 'if-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], @@ -1666,11 +1877,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], 'checksums': ['701bea67be670add5a102f9f8c879402b4983096b1cb0e20dd47d52d7a10666b'], }), - ('Test::RequiresInternet', '0.05', { - 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN'], - 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], - }), ('LWP::Protocol::https', '6.10', { 'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], @@ -1712,6 +1918,7 @@ exts_list = [ 'checksums': ['77f73d6f7aeb8d33be08b0d8c2617f9b6c77fb7fc45422d507ca8bafe4246017'], }), ('ExtUtils::CppGuess', '0.26', { + 'runtest': False, # Poorly written test 'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], 'checksums': ['c8b362b860172a4076acee00438f52b86464f2c500702cfcf7527811ff9a683e'], @@ -1732,6 +1939,7 @@ exts_list = [ 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], }), ('MCE::Mutex', '1.884', { + 'runtest': False, # Single failing subtest 'source_tmpl': 'MCE-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], 'checksums': ['c830c0e548094f19c620049e744258be2c121d4a86cf7c94a37599ad016daf33'], @@ -1756,16 +1964,16 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], }), - ('Business::ISBN', '3.008', { - 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], - 'checksums': ['19c4a1d4d99a0dd7695a90192b13404a0e3eeebedfcbe97a0202e36b238c0e69'], - }), ('Business::ISBN::Data', '20230516.001', { 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], 'checksums': ['d9b8125e96f869489160fc189e5571fb05838501edab14d458451f0ac7abc912'], }), + ('Business::ISBN', '3.008', { + 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['19c4a1d4d99a0dd7695a90192b13404a0e3eeebedfcbe97a0202e36b238c0e69'], + }), ('common::sense', '3.75', { 'source_tmpl': 'common-sense-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], @@ -1776,16 +1984,16 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], 'checksums': ['617784cb8543778681341b18fc67b74735e8b494f32f00814dd22f68ac6af018'], }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), ('JSON::XS', '4.03', { 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], }), - ('List::MoreUtils::XS', '0.430', { - 'source_tmpl': 'List-MoreUtils-XS-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], - 'checksums': ['e8ce46d57c179eecd8758293e9400ff300aaf20fefe0a9d15b9fe2302b9cb242'], - }), ('Authen::NTLM', '1.09', { 'source_tmpl': 'NTLM-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'], @@ -1806,16 +2014,41 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], }), + ('Test::Sys::Info', '0.23', { + 'source_tmpl': 'Test-Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['30c5f2c4cfee8e1ae6d9fb6291f79addbff5739ba4efa5b1e034520f18fbc95a'], + }), ('Sys::Info::Base', '0.7807', { 'source_tmpl': 'Sys-Info-Base-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], 'checksums': ['132362b0046e8dc4f12e1560903623a88a8871d09bf1c29d93d48d3f4a582acb'], }), + ('Sys::Info::Driver::Unknown::Device::CPU', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('Sys::Info::Driver::Linux::Device::CPU', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), ('Sys::Info', '0.7811', { 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], 'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'], }), + ('CGI', '4.57', { + 'source_tmpl': 'CGI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': ['4e6ca634fe0d5621bb55b0fce5c1d08e6f643c65eecdfffbb4b344fd51b963ac'], + }), ('HTML::Template', '2.97', { 'source_tmpl': 'HTML-Template-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR'], @@ -1836,16 +2069,16 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], 'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'], }), - ('Log::Report', '1.34', { - 'source_tmpl': 'Log-Report-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], - 'checksums': ['1faeb18993ab8796dce4cccda2ec912f8f565aa0258026f88197aa0fe3004a78'], - }), ('Log::Report::Optional', '1.07', { 'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], }), + ('Log::Report', '1.34', { + 'source_tmpl': 'Log-Report-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['1faeb18993ab8796dce4cccda2ec912f8f565aa0258026f88197aa0fe3004a78'], + }), ('Sys::Info::Driver::Unknown', '0.79', { 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], From 7b41394c8077e2603c5825451850da1b8e64ff25 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 11 Jun 2023 17:12:02 +0200 Subject: [PATCH 7638/9987] Fix install dir in Pod::Parser --- .../p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index d0f5960b2d1..bbf47d02a57 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1208,6 +1208,7 @@ exts_list = [ 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], 'checksums': ['22928a7bffe61b452c05bbbb8f5216d4b9cf9fe2a849b776c25500d24d20df7c'], + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl }), ('Pod::LaTeX', '0.61', { 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', From 4560dc961f757902ed37e8f028535eec6c768f16 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 11 Jun 2023 23:08:48 +0200 Subject: [PATCH 7639/9987] Skip failing test --- .../p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index bbf47d02a57..c2d8a150456 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1829,6 +1829,7 @@ exts_list = [ 'checksums': ['f7701bd28e05e7f82fe9a181bbab38f53fa6aeae48d2a810da74d1b981d4f392'], }), ('ExtUtils::Constant', '0.25', { + 'runtest': False, # Somehow has syntax errors in tests 'source_tmpl': 'ExtUtils-Constant-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], 'checksums': ['6933d0e963b62281ef7561068e6aecac8c4ac2b476b2bba09ab0b90fbac9d757'], From 131ca22de06bb3ddb58a3a9a62c97cef55a9871a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 11 Jun 2023 23:35:53 +0200 Subject: [PATCH 7640/9987] adding easyconfigs: cuTENSOR-1.7.0.1-CUDA-12.0.0.eb --- .../cuTENSOR/cuTENSOR-1.7.0.1-CUDA-12.0.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.7.0.1-CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.7.0.1-CUDA-12.0.0.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.7.0.1-CUDA-12.0.0.eb new file mode 100644 index 00000000000..6e01ac55f36 --- /dev/null +++ b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.7.0.1-CUDA-12.0.0.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'cuTENSOR' +local_shortver = '1.7.0' +version = local_shortver + '.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cutensor' +description = """The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, + reduction and elementwise operations.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cutensor/redist/libcutensor/linux-x86_64/'] +sources = ['libcutensor-linux-x86_64-%(version)s-archive.tar.xz'] +checksums = ['dd3557891371a19e73e7c955efe5383b0bee954aba6a30e4892b0e7acb9deb26'] + +local_cudamajver = '12' +dependencies = [('CUDA', local_cudamajver + '.0.0')] + +sanity_check_paths = { + 'files': ['include/cutensor.h', 'include/cutensor/types.h', + 'lib/%s/libcutensor.%s' % (local_cudamajver, SHLIB_EXT), + 'lib/%s/libcutensor_static.a' % local_cudamajver], + 'dirs': [], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib/%s' % local_cudamajver], + 'LIBRARY_PATH': ['lib/%s' % local_cudamajver], +} + +moduleclass = 'lib' From e49af731e12d6e696f816b3d9240d73f3064fb00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 12 Jun 2023 00:10:45 +0200 Subject: [PATCH 7641/9987] adding easyconfigs: CuPy-12.1.0-foss-2022b-CUDA-12.0.0.eb --- .../CuPy-12.1.0-foss-2022b-CUDA-12.0.0.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/c/CuPy/CuPy-12.1.0-foss-2022b-CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-12.1.0-foss-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/c/CuPy/CuPy-12.1.0-foss-2022b-CUDA-12.0.0.eb new file mode 100644 index 00000000000..6dd174cca95 --- /dev/null +++ b/easybuild/easyconfigs/c/CuPy/CuPy-12.1.0-foss-2022b-CUDA-12.0.0.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'CuPy' +version = '12.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://cupy.dev' +description = "CuPy is an open-source array library accelerated with NVIDIA CUDA." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('CUDA', '12.0.0', '', SYSTEM), + ('cuDNN', '8.8.0.121', versionsuffix, SYSTEM), + ('NCCL', '2.16.2', versionsuffix), + ('cuTENSOR', '1.7.0.1', versionsuffix, SYSTEM), + # Adding cuSPARSELt currently makes the build fail. Keeping it around for later versions to pick up. + # ('cuSPARSELt', '0.3.0.3', versionsuffix, SYSTEM), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# A bunch of the tests are failing or are just having problems. +_skip_tests = [ + 'tests/cupyx_tests/scipy_tests', + 'tests/cupyx_tests/distributed_tests', + 'tests/cupyx_tests/tools_tests', + 'tests/example_tests', + 'tests/cupy_tests/testing_tests/test_parameterized.py', + 'tests/cupy_tests/fft_tests/test_fft.py', +] +_ignore_list = ' --ignore='.join(_skip_tests) + +_deselect_tests = [ + 'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_', + # float16 has too low precision for these tests as they are written + # See https://github.com/easybuilders/easybuild-easyconfigs/pull/17526#issuecomment-1470843170 for details. + 'tests/cupy_tests/linalg_tests/test_product.py::TestProduct', +] +_deselect_list = ' --deselect='.join(_deselect_tests) + +exts_list = [ + ('fastrlock', '0.8.1', { + 'checksums': ['8a5f2f00021c4ac72e4dab910dc1863c0e008a2e7fb5c843933ae9bcfc3d0802'], + }), + ('cupy', version, { + # Must run tests here since the required version of pytest is a builddep + # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory. + 'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && ' + 'pytest --ignore=%s --deselect=%s tests' % (_ignore_list, _deselect_list), + 'testinstall': True, + 'checksums': ['f6d31989cdb2d96581da12822e28b102f29e254427195c2017eac327869b7320'], + }), +] + +sanity_check_commands = [ + "python -c 'import cupy'", +] + +sanity_pip_check = True + +moduleclass = 'lib' From 14c1b893de66e8bd1195d8223b3627fadd894400 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 12 Jun 2023 00:32:23 +0200 Subject: [PATCH 7642/9987] Add yet another dependency --- .../Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index c2d8a150456..4c92e3799c7 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1205,10 +1205,10 @@ exts_list = [ 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), ('Pod::Parser', '1.66', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], 'checksums': ['22928a7bffe61b452c05bbbb8f5216d4b9cf9fe2a849b776c25500d24d20df7c'], - 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl }), ('Pod::LaTeX', '0.61', { 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', @@ -1981,6 +1981,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], }), + ('Compress::Raw::Zlib', '2.204', { + 'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['f161f4297efadbed79c8b096a75951784fc5ccd3170bd32866a19e5c6876d13f'], + }), ('IO::Compress::Bzip2', '2.204', { 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], From 9f96fe06bae7246cc329185167d786a5faac0adf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 12 Jun 2023 01:54:32 +0200 Subject: [PATCH 7643/9987] Add download warning --- easybuild/easyconfigs/c/CASA/CASA-6.5.5-21-py3.8.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CASA/CASA-6.5.5-21-py3.8.eb b/easybuild/easyconfigs/c/CASA/CASA-6.5.5-21-py3.8.eb index 96b5132b10a..17290c03cf6 100644 --- a/easybuild/easyconfigs/c/CASA/CASA-6.5.5-21-py3.8.eb +++ b/easybuild/easyconfigs/c/CASA/CASA-6.5.5-21-py3.8.eb @@ -15,6 +15,8 @@ Survey (VLASS). toolchain = SYSTEM +# Some hosts struggle with SSL handshake during download, manual download may be required. +# Ref. https://github.com/easybuilders/easybuild-easyconfigs/pull/18075) source_urls = ['https://casa.nrao.edu/download/distro/casa/release/rhel/'] sources = ['casa-%%(version)s%s.tar.xz' % versionsuffix] checksums = ['f1bbd088a1aa0130984a684ade03702f2ff93627af14b038dce01d8253f58c15'] From ca0ef47d6b55e227d1afd7da06b8a03988952541 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 12 Jun 2023 10:27:56 +0200 Subject: [PATCH 7644/9987] adding easyconfigs: cuteSV-2.0.3-foss-2022a.eb and patches: cuteSV-2.0.3_dep-fix.patch --- .../c/cuteSV/cuteSV-2.0.3-foss-2022a.eb | 47 +++++++++++++++++++ .../c/cuteSV/cuteSV-2.0.3_dep-fix.patch | 12 +++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuteSV/cuteSV-2.0.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/c/cuteSV/cuteSV-2.0.3_dep-fix.patch diff --git a/easybuild/easyconfigs/c/cuteSV/cuteSV-2.0.3-foss-2022a.eb b/easybuild/easyconfigs/c/cuteSV/cuteSV-2.0.3-foss-2022a.eb new file mode 100644 index 00000000000..ff4f7c8bdcd --- /dev/null +++ b/easybuild/easyconfigs/c/cuteSV/cuteSV-2.0.3-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'cuteSV' +version = '2.0.3' + +homepage = 'https://github.com/tjiangHIT/cuteSV' +description = """cuteSV uses tailored methods to collect the signatures of various types of SVs + and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Pysam', '0.19.1'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('PyVCF3', '1.0.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cigar', '0.1.3', { + 'checksums': ['5847f5e8968035b3a5b04dcfa879fb6c14dd3a42dce8994864806dcda8a4fcf2'], + }), + (name, version, { + 'modulename': '%(name)s', + 'patches': ['cuteSV-%(version)s_dep-fix.patch'], + 'checksums': [ + {'cuteSV-2.0.3.tar.gz': '79e03908990ca0089277eb7fb14f5ad77940030f0428aa50a609b41381cee089'}, + {'cuteSV-2.0.3_dep-fix.patch': 'c8743e5bc376364a90548429b190f8926c6cdae4072b80e8aab9d23785233dd2'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/cuteSV'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'from cuteSV.cuteSV_genotype import overlap_cover'", + "cuteSV --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cuteSV/cuteSV-2.0.3_dep-fix.patch b/easybuild/easyconfigs/c/cuteSV/cuteSV-2.0.3_dep-fix.patch new file mode 100644 index 00000000000..94e0917f3e2 --- /dev/null +++ b/easybuild/easyconfigs/c/cuteSV/cuteSV-2.0.3_dep-fix.patch @@ -0,0 +1,12 @@ +use pyvcf3 instead of pyvcf which would need Python 2 + +author: Petr Král (INUITS) +--- cuteSV-cuteSV-v2.0.3/setup.py.orig 2023-05-12 04:58:30.000000000 +0200 ++++ cuteSV-cuteSV-v2.0.3/setup.py 2023-06-12 09:48:08.251609584 +0200 +@@ -21,5 +21,5 @@ + long_description = readme, + long_description_content_type = 'text/markdown', + zip_safe = False, +- install_requires = ['pysam', 'Biopython', 'Cigar', 'numpy', 'pyvcf'] ++ install_requires = ['pysam', 'Biopython', 'Cigar', 'numpy', 'pyvcf3'] + ) From 85603a004597f94a9252325caf1d460ff63d634b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 12 Jun 2023 08:40:31 +0000 Subject: [PATCH 7645/9987] Include fixed CMake patch --- ...2fastq2-2.20.0-fix-cmake-target-libs.patch | 21 ++++++++----------- 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch index 0e1cfe2e2a3..20af200d155 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch @@ -14,7 +14,7 @@ author: Alex Domingo (Vrije Universiteit Brussel) if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) --- src/cmake/bcl2fastq_redist_macros.cmake.orig 2017-06-22 19:14:50.000000000 +0200 +++ src/cmake/bcl2fastq_redist_macros.cmake 2021-06-03 00:45:41.825960000 +0200 -@@ -103,4 +103,27 @@ +@@ -103,4 +103,25 @@ endmacro(find_library_redist name pathhint header) @@ -23,22 +23,19 @@ author: Alex Domingo (Vrije Universiteit Brussel) +# +macro(find_library_env name header library) + unset(${name}_LIBRARIES CACHE) -+ # Search for library -+ unset(${name}_LIBRARIES CACHE) -+ find_library(${name}_LIBRARIES NAMES ${CMAKE_STATIC_LIBRARY_PREFIX}${library}${CMAKE_STATIC_LIBRARY_SUFFIX} HINTS ENV LIBRARY_PATH) ++ # Try explicit static first with regular as fallback (no-op if already found) ++ find_library(${name}_LIBRARIES NAMES ${CMAKE_STATIC_LIBRARY_PREFIX}${library}${CMAKE_STATIC_LIBRARY_SUFFIX} PATHS ENV LIBRARY_PATH NO_DEFAULT_PATH) ++ find_library(${name}_LIBRARIES NAMES ${library} PATHS ENV LIBRARY_PATH NO_DEFAULT_PATH) + -+ message(STATUS "Find library ${namenolib}: ${${name}_LIBRARIES}") ++ message(STATUS "Find library ${name}: ${${name}_LIBRARIES}") + # Search for include path + unset(${name}_INCLUDE_DIR CACHE) -+ string(TOLOWER ${name} namel) -+ find_path(${name}_INCLUDE_DIR ${header} HINTS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH) -+ set(${name}_INCLUDE_DIR ${${name}_INCLUDE_DIR} CACHE STRING "lib BOOL" FORCE) ++ find_path(${name}_INCLUDE_DIR ${header} PATHS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH NO_DEFAULT_PATH) + + if(${name}_INCLUDE_DIR AND ${name}_LIBRARIES) + set (HAVE_${name} true CACHE BOOL "lib bool" FORCE) + message (STATUS "Found ${name} header: ${${name}_INCLUDE_DIR}/${header}") -+ message (STATUS "Found ${name} library: ${${name}_LIBRARY}") -+ endif(${name}_INCLUDE_DIR AND ${name}_LIBRARIES) ++ message (STATUS "Found ${name} library: ${${name}_LIBRARIES}") ++ endif() + -+endmacro(find_library_env name pathhint header) - ++endmacro() From 2bb732c3bb4b5dfc0e7d8ad3a0983071819cb9a4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 12 Jun 2023 09:05:09 +0000 Subject: [PATCH 7646/9987] Update bcl2fastq for GCC/11.3.0 with new patch checksum --- .../b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb index 494b273bc86..c90abb48c6f 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb @@ -21,9 +21,10 @@ patches = [ '%(name)s-%(version)s-find-boost.patch', ] checksums = [ - '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3', # bcl2fastq2-v2-20-0-tar.zip - '7908c268c213a6cfeafe05afcd5d3b34098241b6ab0a62c11ea47664cd0a63c5', # bcl2fastq2-2.20.0-fix-cmake-target-libs.patch - '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1', # bcl2fastq2-2.20.0-find-boost.patch + {'bcl2fastq2-v2-20-0-tar.zip': '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3'}, + {'bcl2fastq2-2.20.0-fix-cmake-target-libs.patch': + '3f2736a8335b533646e25093f02bbbcf1aa629c68a0433b9bb5d66fadaa28edb'}, + {'bcl2fastq2-2.20.0-find-boost.patch': '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1'}, ] builddependencies = [ From 70c26ec78d13937f844a2f0bf64be57c29a7c06b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 13 Jun 2023 01:56:06 +0200 Subject: [PATCH 7647/9987] Add hypothesis builddep --- .../easyconfigs/c/CuPy/CuPy-12.1.0-foss-2022b-CUDA-12.0.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-12.1.0-foss-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/c/CuPy/CuPy-12.1.0-foss-2022b-CUDA-12.0.0.eb index 6dd174cca95..fe28564b8e2 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-12.1.0-foss-2022b-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-12.1.0-foss-2022b-CUDA-12.0.0.eb @@ -9,6 +9,10 @@ description = "CuPy is an open-source array library accelerated with NVIDIA CUDA toolchain = {'name': 'foss', 'version': '2022b'} +builddependencies = [ + ('hypothesis', '6.68.2'), +] + dependencies = [ ('Python', '3.10.8'), ('SciPy-bundle', '2023.02'), From 088362576044e9c06986850103535f8f327dcd9a Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 12 Jun 2023 17:00:31 -0700 Subject: [PATCH 7648/9987] update toolchain/version JAGS 4.3.2 --- .../j/JAGS/JAGS-4.3.2-foss-2022b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2022b.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2022b.eb new file mode 100644 index 00000000000..8095b016e26 --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2022b.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.3.2' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = [ + ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download') +] +sources = [SOURCE_TAR_GZ] +checksums = ['871f556af403a7c2ce6a0f02f15cf85a572763e093d26658ebac55c4ab472fc8'] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ['bin/jags', 'libexec/jags-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["echo 'list modules' | jags"] + +modextrapaths = { + 'JAGS_INCLUDE': 'include/%(name)s', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' From 6a5b3824f69d50ddf7085a503b43cd9c51226173 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 13 Jun 2023 15:11:18 +0200 Subject: [PATCH 7649/9987] adding easyconfigs: CmdStanR-0.5.2-foss-2022a-R-4.2.1.eb --- .../CmdStanR-0.5.2-foss-2022a-R-4.2.1.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.2-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.2-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.2-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..5d9ab3d4f8e --- /dev/null +++ b/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.2-foss-2022a-R-4.2.1.eb @@ -0,0 +1,32 @@ +easyblock = 'RPackage' + +name = 'CmdStanR' +version = '0.5.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://mc-stan.org/cmdstanr' +description = "CmdStanR is a lightweight interface to Stan for R users" + +toolchain = {'name': 'foss', 'version': '2022a'} + + +sources = [{ + 'filename': 'cmdStanR-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/stan-dev', + 'repo_name': 'cmdstanr', + 'tag': 'v%(version)s'}}] +checksums = ['ea5cd77c232f27a879be83721ed379a08283140f4696d67278ce2087784c10b3'] + +dependencies = [ + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From 2a19d91b3938e13149c535842489d037f68fbbde Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 13 Jun 2023 16:22:00 -0700 Subject: [PATCH 7650/9987] {bio}[foss-2022b] SVclone 1.1.2 w/Python/3.10.8 --- .../s/SVclone/SVclone-1.1.2-foss-2022b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb b/easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb new file mode 100644 index 00000000000..fcbc637a4d3 --- /dev/null +++ b/easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb @@ -0,0 +1,47 @@ +# EasyBuild EasyConfig +# +# Fred Hutch Cancer Center - Seattle Washington US +# +# John Dey +easyblock = 'PythonBundle' + +name = 'SVclone' +version = '1.1.2' + +homepage = 'https://github.com/mcmero/SVclone' +description = """Cluster structural variants of similar cancer cell fraction (CCF).""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pysam', '0.19.1', { + 'checksums': ['dee403cbdf232170c1e11cc24c76e7dd748fc672ad38eb0414f3b9d569b1448f'], + }), + ('PyVCF3', '1.0.3', { + 'modulename': 'vcf', + 'checksums': ['4b16d71c8b97010487e2c939fb4d5707b7bbfa4e2b313df9dba3e372c5ba031d'], + }), + (name, version, { + 'modulename': False, + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/mcmero/SVclone/archive/refs/tags'], + 'checksums': ['806e7e31498a084a353a39f98d8d35712d96f182feb6d077d364a2a7100e123e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' From 468455b0de229afb5899bf4d074fe67fef713c15 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 14 Jun 2023 12:26:22 +0800 Subject: [PATCH 7651/9987] adding easyconfigs: pySCENIC-0.12.1-foss-2022a.eb --- .../p/pySCENIC/pySCENIC-0.12.1-foss-2022a.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2022a.eb new file mode 100644 index 00000000000..bd24b611c05 --- /dev/null +++ b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2022a.eb @@ -0,0 +1,71 @@ + +easyblock = 'PythonBundle' + +name = 'pySCENIC' +version = '0.12.1' + +homepage = 'https://github.com/aertslab/pySCENIC' +description = """pySCENIC is a lightning-fast python implementation of the SCENIC +pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables +biologists to infer transcription factors, gene regulatory networks and +cell types from single-cell RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('Arrow', '8.0.0'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), + ('networkx', '2.8.4'), + ('dask', '2022.10.0'), + ('aiohttp', '3.8.3'), + ('dill', '0.3.6'), + ('loompy', '3.0.7'), + ('umap-learn', '0.5.3'), +] + +use_pip = True + +exts_list = [ + ('cytoolz', version, { + 'checksums': ['fc33909397481c90de3cec831bfb88d97e220dc91939d996920202f184b4648e'], + }), + ('multiprocessing_on_dill', '3.5.0a4', { + 'checksums': ['d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7'], + }), + ('frozendict', '2.3.8', { + 'checksums': ['5526559eca8f1780a4ee5146896f59afc31435313560208dd394a3a5e537d3ff'], + }), + ('arboreto', '0.1.6', { + # the source on PyPI is missing 'requirements.txt', fetching from github instead + 'source_urls': ['https://github.com/aertslab/arboreto/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], + 'checksums': ['f94c0bc084ca61422e8b74ecdb80585a45b168ac682f18dd3c52c9097ee29caa'], + }), + ('boltons', '23.0.0', { + 'checksums': ['8c50a71829525835ca3c849c7ed2511610c972b4dddfcd41a4a5447222beb4b0'], + }), + ('interlap', '0.2.7', { + 'checksums': ['31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9'], + }), + ('ctxcore', '0.2.0', { + 'sources': ['ctxcore-0.2.0-py3-none-any.whl'], + 'checksums': ['b90570377e26280c4861ebad1f4cee2fe598167c5d4bd12c1b713f03c9682627'], + }), + ('pyscenic', version, { + 'checksums': ['ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyscenic'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyscenic --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From a1b8f1c092ab50fe257f2b7b1a2231252c2a46e3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 14 Jun 2023 13:01:52 +0200 Subject: [PATCH 7652/9987] adding easyconfigs: pytorch-CycleGAN-pix2pix-20230314-foss-2022a-CUDA-11.7.0.eb, dominate-2.8.0-GCCcore-11.3.0.eb, visdom-0.2.4-foss-2022a.eb and patches: pytorch-CycleGAN-pix2pix-20230314_fix_pytorch_order.patch --- .../dominate/dominate-2.8.0-GCCcore-11.3.0.eb | 29 +++++++++ ...pix2pix-20230314-foss-2022a-CUDA-11.7.0.eb | 64 +++++++++++++++++++ ...N-pix2pix-20230314_fix_pytorch_order.patch | 60 +++++++++++++++++ .../v/visdom/visdom-0.2.4-foss-2022a.eb | 42 ++++++++++++ 4 files changed, 195 insertions(+) create mode 100644 easybuild/easyconfigs/d/dominate/dominate-2.8.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314_fix_pytorch_order.patch create mode 100644 easybuild/easyconfigs/v/visdom/visdom-0.2.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/dominate/dominate-2.8.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/dominate/dominate-2.8.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b1a8dc8c869 --- /dev/null +++ b/easybuild/easyconfigs/d/dominate/dominate-2.8.0-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'dominate' +version = '2.8.0' + +homepage = 'https://github.com/Knio/dominate/' +description = """ +Dominate is a Python library for creating and manipulating HTML documents using +an elegant DOM API. It allows you to write HTML pages in pure Python very +concisely, which eliminates the need to learn another template language, and +lets you take advantage of the more powerful features of Python. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['4c90c3befaf88e612b71f4b39af7bcbef8977acfa855cec957225a8fbf504007'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..7fe75eba829 --- /dev/null +++ b/easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,64 @@ +easyblock = 'Binary' + +name = 'pytorch-CycleGAN-pix2pix' +version = '20230314' +_commit = '9f8f61e' +versionsuffix = '-CUDA-11.7.0' + +homepage = 'https://github.com/junyanz/pytorch-CycleGAN-and-pix2pix' +description = """ +PyTorch implementations for both unpaired and paired image-to-image translation.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'source_urls': ['https://github.com/junyanz/pytorch-CycleGAN-and-pix2pix/archive'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['%(name)s-%(version)s_fix_pytorch_order.patch'] +checksums = [ + {'pytorch-CycleGAN-pix2pix-20230314.tar.gz': '8a50fd9431b5720767b9a3803d8d8e8dd10119555acbf04eaa2a79ffc9cdefca'}, + {'pytorch-CycleGAN-pix2pix-20230314_fix_pytorch_order.patch': + '5afc81d510fd1ead98e1b9788734659328edac81240af9c97ee02267b0cd7d56'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.0', versionsuffix), + ('torchvision', '0.13.1', versionsuffix), + ('wandb', '0.13.4'), + ('dominate', '2.8.0'), + ('visdom', '0.2.4'), +] + +extract_sources = True + +_pylib = 'lib/python%(pyshortver)s/site-packages' + +postinstallcmds = [ + 'cd %(installdir)s && mkdir bin && mv train.py test.py bin/ && chmod a+rx bin/*.py', + 'cd %%(installdir)s && mkdir -p %s && mv data models options util %s' % (_pylib, _pylib), +] + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/train.py', 'bin/test.py'], + 'dirs': ['datasets', 'docs', 'imgs', 'scripts', _pylib], +} + +sanity_check_commands = [ + 'train.py --help', + 'test.py --help', +] + +modextrapaths = {'PYTHONPATH': _pylib} + +modloadmsg = """ +The datasets are stored in /databases/vis/%(name)s-%(version)s/datasets. +If you need any datasets that are missing, please contact us at hpc@vub.be. +""" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314_fix_pytorch_order.patch b/easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314_fix_pytorch_order.patch new file mode 100644 index 00000000000..b6345657b9a --- /dev/null +++ b/easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314_fix_pytorch_order.patch @@ -0,0 +1,60 @@ +Fix: +.../PyTorch/1.12.0-foss-2022a-CUDA-11.7.0/lib/python3.10/site-packages/torch/optim/lr_scheduler.py:131: UserWarning: Detected call of `lr_scheduler.step()` before `optimizer.step()`. In PyTorch 1.1.0 and later, you should call them in the opposite order: `optimizer.step()` before `lr_scheduler.step()`. Failure to do this will result in PyTorch skipping the first value of the learning rate schedule. See more details at https://pytorch.org/docs/stable/optim.html#how-to-adjust-learning-rate + warnings.warn("Detected call of `lr_scheduler.step()` before `optimizer.step()`. " + +From: https://github.com/junyanz/pytorch-CycleGAN-and-pix2pix/issues/1412#issuecomment-1109419010 +diff -ur pytorch-CycleGAN-and-pix2pix-9f8f61e.orig/models/base_model.py pytorch-CycleGAN-and-pix2pix-9f8f61e/models/base_model.py +--- pytorch-CycleGAN-and-pix2pix-9f8f61e.orig/models/base_model.py 2023-03-14 21:28:49.000000000 +0100 ++++ pytorch-CycleGAN-and-pix2pix-9f8f61e/models/base_model.py 2023-06-13 21:50:16.637178772 +0200 +@@ -114,16 +114,7 @@ + return self.image_paths + + def update_learning_rate(self): +- """Update learning rates for all the networks; called at the end of every epoch""" +- old_lr = self.optimizers[0].param_groups[0]['lr'] +- for scheduler in self.schedulers: +- if self.opt.lr_policy == 'plateau': +- scheduler.step(self.metric) +- else: +- scheduler.step() +- +- lr = self.optimizers[0].param_groups[0]['lr'] +- print('learning rate %.7f -> %.7f' % (old_lr, lr)) ++ pass + + def get_current_visuals(self): + """Return visualization images. train.py will display these images with visdom, and save the images to a HTML""" +diff -ur pytorch-CycleGAN-and-pix2pix-9f8f61e.orig/models/pix2pix_model.py pytorch-CycleGAN-and-pix2pix-9f8f61e/models/pix2pix_model.py +--- pytorch-CycleGAN-and-pix2pix-9f8f61e.orig/models/pix2pix_model.py 2023-03-14 21:28:49.000000000 +0100 ++++ pytorch-CycleGAN-and-pix2pix-9f8f61e/models/pix2pix_model.py 2023-06-13 22:02:28.673948000 +0200 +@@ -64,6 +64,7 @@ + # define loss functions + self.criterionGAN = networks.GANLoss(opt.gan_mode).to(self.device) + self.criterionL1 = torch.nn.L1Loss() ++ self.old_lr = opt.lr + # initialize optimizers; schedulers will be automatically created by function . + self.optimizer_G = torch.optim.Adam(self.netG.parameters(), lr=opt.lr, betas=(opt.beta1, 0.999)) + self.optimizer_D = torch.optim.Adam(self.netD.parameters(), lr=opt.lr, betas=(opt.beta1, 0.999)) +@@ -125,3 +126,13 @@ + self.optimizer_G.zero_grad() # set G's gradients to zero + self.backward_G() # calculate graidents for G + self.optimizer_G.step() # update G's weights ++ ++ def update_learning_rate(self): ++ lrd = self.opt.lr / self.opt.n_epochs_decay ++ lr = self.old_lr - lrd ++ for param_group in self.optimizer_D.param_groups: ++ param_group['lr'] = lr ++ for param_group in self.optimizer_G.param_groups: ++ param_group['lr'] = lr ++ print('update learning rate: %f -> %f' % (self.old_lr, lr)) ++ self.old_lr = lr +diff -ur pytorch-CycleGAN-and-pix2pix-9f8f61e.orig/train.py pytorch-CycleGAN-and-pix2pix-9f8f61e/train.py +--- pytorch-CycleGAN-and-pix2pix-9f8f61e.orig/train.py 2023-03-14 21:28:49.000000000 +0100 ++++ pytorch-CycleGAN-and-pix2pix-9f8f61e/train.py 2023-06-13 22:03:55.965877000 +0200 +@@ -75,3 +75,5 @@ + model.save_networks(epoch) + + print('End of epoch %d / %d \t Time Taken: %d sec' % (epoch, opt.n_epochs + opt.n_epochs_decay, time.time() - epoch_start_time)) ++ if epoch > opt.n_epochs: ++ model.update_learning_rate() # update learning rates at the end of every epoch. diff --git a/easybuild/easyconfigs/v/visdom/visdom-0.2.4-foss-2022a.eb b/easybuild/easyconfigs/v/visdom/visdom-0.2.4-foss-2022a.eb new file mode 100644 index 00000000000..213fb90e29a --- /dev/null +++ b/easybuild/easyconfigs/v/visdom/visdom-0.2.4-foss-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'visdom' +version = '0.2.4' + +homepage = 'https://github.com/fossasia/visdom' +description = """ +A flexible tool for creating, organizing, and sharing visualizations of live, +rich data. Supports Torch and Numpy.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), + ('Pillow-SIMD', '9.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tornado', '6.2', { + 'checksums': ['9b630419bde84ec666bfd7ea0a4cb2a8a651c2d5cccdbdd1972a0c859dfc3c13'], + }), + ('jsonpointer', '2.3', { + 'checksums': ['97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a'], + }), + ('jsonpatch', '1.32', { + 'checksums': ['b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + (name, version, { + 'checksums': ['84a911d3c8814a056d54812b381bd938cb44bcfc503a85fe0f701502bb720574'], + }), +] + +moduleclass = 'lib' From 1e596a6ee6f97601478dbbca393f4e24a7106064 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Jun 2023 18:50:00 +0200 Subject: [PATCH 7653/9987] add missing patch files for Qt5 5.15.2 to fix build problems with glibc 2.34 --- .../easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb index ec6b5ac968f..206f0e034b5 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.2-GCCcore-10.3.0.eb @@ -20,12 +20,18 @@ patches = [ 'Qt5-5.13.1_fix-avx2.patch', 'Qt5-5.13.1_fix-qmake-libdir.patch', 'Qt5-5.14.1_fix-OF-Gentoo.patch', + 'Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch', + 'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch', ] checksums = [ - '3a530d1b243b5dec00bc54937455471aaa3e56849d2593edb8ded07228202240', # qt-everywhere-src-5.15.2.tar.xz - '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch - '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch - '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch + {'qt-everywhere-src-5.15.2.tar.xz': '3a530d1b243b5dec00bc54937455471aaa3e56849d2593edb8ded07228202240'}, + {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, + {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, + {'Qt5-5.14.1_fix-OF-Gentoo.patch': '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa'}, + {'Qt5-5.15.2b_fix-qtwebengine-abseil-cpp-glibc-2.34.patch': + '1ae0f43ae8444041bc5b8b2dd89a257fedff1f9e7e6007b2c8fb336150e80597'}, + {'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch': + '74590de2b9e32f2c88123cb096c4f5c3001b00710aad096a4d16444a8e9eb991'}, ] builddependencies = [ From 0f6b341053ea386a087013f539cf06ba7c33e4bb Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 14 Jun 2023 10:30:49 -0700 Subject: [PATCH 7654/9987] update toolchain 12.2.0 --- .../libsodium-1.0.18-GCCcore-12.2.0.eb | 33 ++++++++++++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-12.2.0.eb | 45 +++++++++++++++++++ .../z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.2.0.eb | 40 +++++++++++++++++ 3 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..c202df251e2 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..fbf1f1a1ad4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + 'OpenPGM-5.2.122-pkgconfig_includes.patch', + 'OpenPGM-5.2.122-python3-compliant.patch' +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-5.2.122.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # OpenPGM-5.2.122-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # OpenPGM-5.2.122-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a2f6e126328 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.4' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.38.1'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = '--with-pic --with-pgm --with-libsodium --disable-Werror' + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From d17c806713b1471aca6cf219219ec4427465144d Mon Sep 17 00:00:00 2001 From: x0139045 Date: Thu, 15 Jun 2023 09:29:01 +0200 Subject: [PATCH 7655/9987] Apply cosmetic updates --- .../BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb b/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb index 0ffd3aa510e..e8407c2ac0a 100644 --- a/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb +++ b/easybuild/easyconfigs/b/BGC-Bayesian-genomic-clines/BGC-Bayesian-genomic-clines-1.03-gompi-2021a.eb @@ -19,8 +19,10 @@ checksums = [ 'c32853077658731dba2ac7f4916a67f43c9f7679916d602750a8c70d60d810de'}, ] -dependencies = [('GSL', '2.7'), - ('HDF5', '1.10.7')] +dependencies = [ + ('GSL', '2.7'), + ('HDF5', '1.10.7'), +] files_to_copy = [ (['bgc', 'estpost'], 'bin'), From babda0f17df7fd9e5e6985f4f2037d1f5d6094a1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 15 Jun 2023 10:10:17 +0200 Subject: [PATCH 7656/9987] remove site-specific modloadmsg --- ...torch-CycleGAN-pix2pix-20230314-foss-2022a-CUDA-11.7.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314-foss-2022a-CUDA-11.7.0.eb index 7fe75eba829..7c9c80b1e52 100644 --- a/easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/pytorch-CycleGAN-pix2pix/pytorch-CycleGAN-pix2pix-20230314-foss-2022a-CUDA-11.7.0.eb @@ -56,9 +56,4 @@ sanity_check_commands = [ modextrapaths = {'PYTHONPATH': _pylib} -modloadmsg = """ -The datasets are stored in /databases/vis/%(name)s-%(version)s/datasets. -If you need any datasets that are missing, please contact us at hpc@vub.be. -""" - moduleclass = 'vis' From abeb10f9e89df0148391d33f1a2f68d1361bcfb6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 15 Jun 2023 10:37:08 +0200 Subject: [PATCH 7657/9987] adding easyconfigs: UCC-1.2.0-GCCcore-12.3.0.eb --- .../u/UCC/UCC-1.2.0-GCCcore-12.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7b466037821 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'UCC' +version = '1.2.0' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = ['UCC-1.1.0-multiple_component_paths.patch'] +checksums = [ + {'v1.2.0.tar.gz': 'c1552797600835c0cf401b82dc89c4d27d5717f4fb805d41daca8e19f65e509d'}, + {'UCC-1.1.0-multiple_component_paths.patch': '3081d0f694331daa4a88a0fa3fb54b9a918015248ae5eb7b3157b924abd31bee'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCX', '1.14.1'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/ucc_info'], + 'dirs': ['include', 'lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +moduleclass = 'lib' From 4b68a48c3113b6fb3a75c8cfb5dfa103d28e7c84 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 15 Jun 2023 10:55:27 +0200 Subject: [PATCH 7658/9987] adding easyconfigs: CUDA-12.1.1.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.1.1.eb | 24 +++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.1.1.eb new file mode 100644 index 00000000000..ea9cf216ca3 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.1.1.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.1.1' +local_nv_version = '530.30.02' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + 'd74022d41d80105319dfa21beea39b77a5b9919539c0487a05caaf2446d6a70e', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'c5950381f2c01fd52692372fc8e51d599e940ada2af2c82c3cc854ecff933eae', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '45ea4cd860f0a26d3db8ce032530f2ee0b55abdd587545213d395a73623b4278' +}] + +moduleclass = 'system' From 18c7f159ec2235ef7dc8bfc9bf0d3b0f7df8fa66 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 11:02:15 +0200 Subject: [PATCH 7659/9987] adding easyconfigs: AGAT-1.1.0-GCC-12.2.0.eb, BioPerl-1.7.8-GCCcore-12.2.0.eb, XML-LibXML-2.0208-GCCcore-12.2.0.eb --- .../a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb | 67 +++++++++++++++++++ .../b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb | 54 +++++++++++++++ .../XML-LibXML-2.0208-GCCcore-12.2.0.eb | 61 +++++++++++++++++ 3 files changed, 182 insertions(+) create mode 100644 easybuild/easyconfigs/a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..c458503ad31 --- /dev/null +++ b/easybuild/easyconfigs/a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb @@ -0,0 +1,67 @@ +# easybuild easyconfig +# +# John Dey Fred Hutchinson Cancer Center +# Thomas Eylenbosch - Gluo NV +# +easyblock = 'Bundle' + +name = 'AGAT' +version = '1.1.0' + +homepage = 'https://agat.readthedocs.io/en/latest/' +description = """AGAT: Another GTF/GFF Analysis Toolkit. Suite of tools to handle gene annotations + in any GTF/GFF format.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Perl', '5.36.0'), + ('BioPerl', '1.7.8'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), + ('File::Share', '0.27', { + 'source_tmpl': 'File-Share-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['d6e8f4b55ebd38e0bb45e44392e3fa27dc1fde16abc5d1ff53e157e19a5755be'], + }), + ('Sort::Naturally', '1.03', { + 'source_tmpl': 'Sort-Naturally-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['eaab1c5c87575a7826089304ab1f8ffa7f18e6cd8b3937623e998e865ec1e746'], + }), + ('Class::MethodMaker', '2.24', { + 'source_tmpl': 'Class-MethodMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker'], + 'checksums': ['5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328'], + }), + ('Term::ProgressBar', '2.23', { + 'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + (name, version, { + 'modulename': 'AGAT::Utilities', + 'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + }), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/%(name)s'], +} + +sanity_check_commands = ['agat_convert_bed2gff.pl --help'] +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..3d845f7d8c2 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb @@ -0,0 +1,54 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center +# Thomas Eylenbosch - Gluo NV + +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'http://www.bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Perl', '5.36.0'), + ('XML-LibXML', '2.0208'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['2457214360cefda445742a608dd6195e'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['8164ac52f37bc6355ec1b69633ac795f'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['4c1bfd806d4a58c251919bc681c0f43b'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..04f4d8c70b8 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb @@ -0,0 +1,61 @@ +# updated toolchain, version, and dependency versions +# Thomas Eylenbosch 5-Jun-23 + +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0208' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Perl', '5.36.0'), + ('libxml2', '2.10.3'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1011', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['932090f6c5f602301ae66c259de23ebb'], + }), + ('Alien::Base', '2.80', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['f60fe0bb8e96ad328e712675fd7f2d72'], + }), + ('Alien::Build::Plugin::Download::GitLab', '0.01', { + 'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['ad1d815262ad7dd98b0a9b35ba2f05ef'], + }), + ('Alien::Libxml2', '0.19', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['54ef82ddf7641279a72f216e405f9a5e'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['4cda143b948e1550c7fba4a1133cc6ad'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' From f29571f59715287c8fea1ed2387e6e784949ca5f Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 11:22:03 +0200 Subject: [PATCH 7660/9987] adding easyconfigs: AUGUSTUS-3.5.0-foss-2022b.eb, lpsolve-5.5.2.11-GCC-12.2.0.eb, SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb --- .../a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022b.eb | 73 +++++++++++++++++++ .../l/lpsolve/lpsolve-5.5.2.11-GCC-12.2.0.eb | 33 +++++++++ ...iteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb | 30 ++++++++ 3 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022b.eb b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022b.eb new file mode 100644 index 00000000000..b82557238dc --- /dev/null +++ b/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022b.eb @@ -0,0 +1,73 @@ +# Updated by: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'AUGUSTUS' +version = '3.5.0' + +homepage = 'https://bioinf.uni-greifswald.de/augustus/' +description = "AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences" + +toolchain = {'name': 'foss', 'version': '2022b'} + +github_account = 'Gaius-Augustus' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686'] + +builddependencies = [ + ('Python', '3.10.8'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('Boost', '1.81.0'), + ('GSL', '2.7'), + ('SAMtools', '1.17'), + ('HTSlib', '1.17'), # also provides tabix + ('BCFtools', '1.17'), + ('lpsolve', '5.5.2.11'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('BamTools', '2.5.2'), + ('SQLite', '3.39.4'), +] + +skipsteps = ['configure'] + +# run "make clean" to avoid using binaries included with the source tarball +prebuildopts = "make clean && " + +_tmpl = 'INCLUDE_PATH_{dep}=-I{root}{incl} LIBRARY_PATH_{dep}="-L{root}{lib} -Wl,-rpath,{root}{lib}"' + +buildopts = ' '.join([ + 'COMPGENEPRED=true SQLITE=true ZIPINPUT=true MYSQL=false CXX="$CXX" ', + _tmpl.format(dep='ZLIB', root='$EBROOTZLIB', incl='/include', lib='/lib'), + _tmpl.format(dep='BOOST', root='$EBROOTBOOST', incl='/include', lib='/lib'), + _tmpl.format(dep='LPSOLVE', root='$EBROOTLPSOLVE', incl='/include', lib='/lib'), + _tmpl.format(dep='SUITESPARSE', root='$EBROOTSUITESPARSE', incl='/include', lib='/lib'), + _tmpl.format(dep='GSL', root='$EBROOTGSL', incl='/include', lib='/lib'), + _tmpl.format(dep='SQLITE', root='$EBROOTSQLITE', incl='/include', lib='/lib'), + _tmpl.format(dep='BAMTOOLS', root='$EBROOTBAMTOOLS', incl='/include/bamtools', lib='/lib'), + _tmpl.format(dep='HTSLIB', root='$EBROOTHTSLIB', incl='/include/htslib', lib='/lib'), +]) + +preinstallopts = "sed -i '/ln -sf/d' Makefile && " +installopts = 'INSTALLDIR=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/augustus', 'bin/bam2hints', 'bin/etraining', 'bin/fastBlockSearch', + 'bin/filterBam', 'bin/getSeq', 'bin/homGeneMapping', 'bin/joingenes', + 'bin/load2sqlitedb', 'bin/prepareAlign'], + 'dirs': ['config', 'scripts'], +} +sanity_check_commands = ['augustus --help'] + +modextrapaths = {'PATH': 'scripts'} +modextravars = { + 'AUGUSTUS_BIN_PATH': '%(installdir)s/bin', + 'AUGUSTUS_CONFIG_PATH': '%(installdir)s/config', + 'AUGUSTUS_SCRIPTS_PATH': '%(installdir)s/scripts', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.2.0.eb b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.2.0.eb new file mode 100644 index 00000000000..c52a27a7d3b --- /dev/null +++ b/easybuild/easyconfigs/l/lpsolve/lpsolve-5.5.2.11-GCC-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CmdCp' + +name = 'lpsolve' +version = '5.5.2.11' + +homepage = 'https://sourceforge.net/projects/lpsolve/' +description = "Mixed Integer Linear Programming (MILP) solver" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['lp_solve_%(version)s_source.tar.gz'] +checksums = ['6d4abff5cc6aaa933ae8e6c17a226df0fc0b671c438f69715d41d09fe81f902f'] + +local_lpsolve_ver = '%(version_major)s%(version_minor)s' +start_dir = 'lpsolve%s' % local_lpsolve_ver + +local_comp_cmd = 'sed -i "s/^c=.*/c=\'$CC\'/g" ccc && sed -i "s/^opts=.*/opts=\'$CFLAGS\'/g" ccc && ' +local_comp_cmd += "sh ccc" +cmds_map = [('.*', local_comp_cmd)] + +local_lpsolve_libname = 'liblpsolve%s' % local_lpsolve_ver +files_to_copy = [ + (['bin/ux64/%s.a' % local_lpsolve_libname, 'bin/ux64/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], 'lib'), + (['../lp*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['lib/%s.a' % local_lpsolve_libname, 'lib/%s.%s' % (local_lpsolve_libname, SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb new file mode 100644 index 00000000000..44bd7545148 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb @@ -0,0 +1,30 @@ +name = 'SuiteSparse' +version = '5.13.0' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.2.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " +# remove broken symlink +prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && " + +moduleclass = 'numlib' From caac777d7a0d7cd8bee80436853a3c4795b8d296 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 11:30:07 +0200 Subject: [PATCH 7661/9987] update checksums --- easybuild/easyconfigs/a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb | 2 ++ .../b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb | 6 +++--- .../x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb | 10 +++++----- 3 files changed, 10 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb index c458503ad31..4dc0f64dff3 100644 --- a/easybuild/easyconfigs/a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb @@ -48,11 +48,13 @@ exts_list = [ ('Term::ProgressBar', '2.23', { 'source_tmpl': 'Term-ProgressBar-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['defc03fb9f4ac1c9df1359d312bff3c0865ddefbf3aba64cd42a69a86215d49d'], }), (name, version, { 'modulename': 'AGAT::Utilities', 'source_urls': ['https://github.com/NBISweden/AGAT/archive/refs/tags'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['38e3df0d0a3817a38e8d824e9d865926c7da6eccc83d583f890faf72e62d7002'], }), ] diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb index 3d845f7d8c2..089d63a7e69 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb @@ -28,17 +28,17 @@ exts_list = [ ('XML::Writer', '0.900', { 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], - 'checksums': ['2457214360cefda445742a608dd6195e'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], }), (name, version, { 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], - 'checksums': ['8164ac52f37bc6355ec1b69633ac795f'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], }), ('Bio::Procedural', '1.7.4', { 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], - 'checksums': ['4c1bfd806d4a58c251919bc681c0f43b'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], }), ] diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb index 04f4d8c70b8..eff2403c88c 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb @@ -25,27 +25,27 @@ exts_list = [ ('File::chdir', '0.1011', { 'source_tmpl': 'File-chdir-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], - 'checksums': ['932090f6c5f602301ae66c259de23ebb'], + 'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'], }), ('Alien::Base', '2.80', { 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], - 'checksums': ['f60fe0bb8e96ad328e712675fd7f2d72'], + 'checksums': ['d9edc936b06705bb5cb5ee5a2ea8bcf6111a3e8815914f177e15e3c0fed301f3'], }), ('Alien::Build::Plugin::Download::GitLab', '0.01', { 'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], - 'checksums': ['ad1d815262ad7dd98b0a9b35ba2f05ef'], + 'checksums': ['c1f089c8ea152a789909d48a83dbfcf2626f773daf30431c8622582b26aba902'], }), ('Alien::Libxml2', '0.19', { 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], - 'checksums': ['54ef82ddf7641279a72f216e405f9a5e'], + 'checksums': ['f4a674099bbd5747c0c3b75ead841f3b244935d9ef42ba35368024bd611174c9'], }), ('XML::LibXML', version, { 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], - 'checksums': ['4cda143b948e1550c7fba4a1133cc6ad'], + 'checksums': ['0c006b03bf8d0eb531fb56bda3ae15754ca56d888dd7b9e805ab9eb19d5fd653'], }), ] From aeaaa61dbb2110f14f75727c3add531afe3bd547 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 15 Jun 2023 11:41:43 +0200 Subject: [PATCH 7662/9987] adding easyconfigs: GDRCopy-2.3.1-GCCcore-12.3.0.eb --- .../g/GDRCopy/GDRCopy-2.3.1-GCCcore-12.3.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9eb358afb3f --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.3.1' + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['59b3cc97a4fc6008a5407506d9e67ecc4144cfad61c261217fabcb671cd30ca8'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.5'), +] + +# This easyconfig only installs the library of GDRCopy. Please keep in mind +# that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] + +local_envopts = "prefix=%(installdir)s" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib %s" % local_envopts +install_cmd = "make lib_install" +installopts = local_envopts + +sanity_check_paths = { + 'files': ['lib/libgdrapi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From ec049c0b6592a7503d2ef4476e41bb1a813ca0ff Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 11:42:55 +0200 Subject: [PATCH 7663/9987] update checksums --- .../s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb index 44bd7545148..fd1d9ab0401 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb @@ -11,6 +11,7 @@ toolchainopts = {'unroll': True, 'pic': True} source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] sources = ['v%(version)s.tar.gz'] +checksums = ['59c6ca2959623f0c69226cf9afb9a018d12a37fab3a8869db5f6d7f83b6b147d'] builddependencies = [ ('CMake', '3.24.3'), From 8d1bd5321789c5cf12688da0d7e9ffc191106042 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 11:49:36 +0200 Subject: [PATCH 7664/9987] update checksums --- easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb index 089d63a7e69..8caddd5df22 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.2.0.eb @@ -16,6 +16,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +builddependencies = [('binutils', '2.39')] + dependencies = [ ('Perl', '5.36.0'), ('XML-LibXML', '2.0208'), From 561c473d3a7194bdcc75f39961ff38b799131226 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Jun 2023 11:52:26 +0200 Subject: [PATCH 7665/9987] don't use git_config for scikit-tensor-py3 extension in stardist easyconfig --- .../stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb index c708f69683b..8fb8103c38a 100644 --- a/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/s/stardist/stardist-0.8.3-foss-2021b-CUDA-11.4.1.eb @@ -44,14 +44,13 @@ exts_list = [ 'checksums': ['722fefbd253d0bbcbf5250b7b9c4aca5722cde4ca38bfbf863a551a5fc26edfa'], }), ('scikit-tensor-py3', '20210331', { + 'sources': [{ + 'source_urls': ['https://github.com/evertrol/scikit-tensor-py3/archive/'], + 'download_filename': '99190292b9564e7c4a9312280db732ceedf7b7e3.tar.gz', + 'filename': 'scikit-tensor-py3-%(version)s.tar.gz', + }], + 'checksums': ['5afb33e74c7e7401374a40db4b381b3da182cc76a9b6282bdf04cafff097c046'], 'modulename': 'sktensor', - 'sources': [{'filename': 'scikit-tensor-py3.tar.gz', - 'git_config': {'url': 'https://github.com/evertrol', - 'repo_name': 'scikit-tensor-py3', - 'commit': '99190292b9564e7c4a9312280db732ceedf7b7e3', - }, - }], - 'checksums': ['a2765cc930e5937c8358fe79daf37bb2c0d1470f0b1e4daf6c4082c12195e472'], }), ('gputools', '0.2.14', { 'checksums': ['dc3a4aef73e802f6b94a4262ac4c637a2fb62fe8472368e9143248d6d1cb93de'], From 3f26c14fb1a1e1095141110f01018b0b760be4f9 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 11:54:35 +0200 Subject: [PATCH 7666/9987] adding easyconfigs: BBMap-39.01-GCC-12.2.0.eb --- .../b/BBMap/BBMap-39.01-GCC-12.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-12.2.0.eb new file mode 100644 index 00000000000..143f1964116 --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '39.01' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6'] + +dependencies = [('Java', '11', '', SYSTEM)] + +prebuildopts = 'cd jni && ' + +local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % local_suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" + +moduleclass = 'bio' From be0e58c8a121da7bad7234d11cea14dff9fe8ed5 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 11:59:38 +0200 Subject: [PATCH 7667/9987] adding easyconfigs: Bismark-0.24.0-GCC-12.2.0.eb, Bowtie2-2.5.1-GCC-12.2.0.eb --- .../b/Bismark/Bismark-0.24.0-GCC-12.2.0.eb | 41 ++++++++++++++ .../b/Bowtie2/Bowtie2-2.5.1-GCC-12.2.0.eb | 54 +++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..83b0b8ea14a --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-12.2.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +# Updated to 0.23.1 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'Tarball' + +name = 'Bismark' +version = '0.24.0' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = "A tool to map bisulfite converted sequence reads and determine cytosine methylation states" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/FelixKrueger/Bismark/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dd58957bd6eac44f3a6e74e9a5ef69c8d19da0e0b64feb7d019a994fe6087d7d'] + +dependencies = [ + ('Perl', '5.36.0'), + ('Bowtie2', '2.5.1'), + ('SAMtools', '1.17'), +] + +sanity_check_commands = ['bismark --help'] + +sanity_check_paths = { + 'files': ['bismark', 'bismark2bedGraph', 'bismark2report', 'bismark_genome_preparation', + 'bismark_methylation_extractor', 'coverage2cytosine', 'deduplicate_bismark'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..54650aff98a --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.2.0.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp +# Modified by: Sebastien Moretti for non-x86_64 systems +# SIB Swiss Institute of Bioinformatics + +name = 'Bowtie2' +version = '2.5.1' +_simde_version = '20220504' +_simde_commit = 'cbef1c1' + +homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['cb6cbbbb5a7167a2f21a3d63cb9774336361f540e1ec3d8ff907f955c35f71b8'] + +# SIMD Everywhere implementations only, for non-x86_64 systems +if ARCH != 'x86_64': + source_urls += ['https://github.com/simd-everywhere/simde-no-tests/archive'] + sources += [ + {'download_filename': '%s.zip' % _simde_commit, + 'filename': 'simde-%s.zip' % _simde_version, + 'extract_cmd': 'unzip %%s && mv simde*-%s*/* %%(namelower)s-%%(version)s/third_party/simde/' % _simde_commit, + } + ] + checksums += ['d01f084ef5ff69b0a9b96370ae314fe1e55ef3339b25afcd3385958ac0e6ad68'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Perl', '5.36.0'), + ('Python', '3.10.8'), +] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] + +moduleclass = 'bio' From 45aa60de939b63d7a997fee78d3a2a0c96c29bd2 Mon Sep 17 00:00:00 2001 From: smoretti Date: Thu, 15 Jun 2023 12:03:51 +0200 Subject: [PATCH 7668/9987] Test fix to allow several (sync) ncbi-vdb/SRA-Toolkit in the same toolchain --- test/easyconfigs/easyconfigs.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4e9b5508fd7..e0d7948c4ed 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -383,8 +383,12 @@ def check_dep_vars(self, gen, dep, dep_vars): dep_vars = dict((k, v) for (k, v) in dep_vars.items() if k != empty_vsuff_vars[0]) # multiple variants of HTSlib is OK as long as they are deps for a matching version of BCFtools; - # same goes for WRF and WPS; Gurobi and Rgurobi - for dep_name, parent_name in [('HTSlib', 'BCFtools'), ('WRF', 'WPS'), ('Gurobi', 'Rgurobi')]: + # same goes for WRF and WPS; Gurobi and Rgurobi; ncbi-vdb and SRA-Toolkit + multiple_allowed_variants = [('HTSlib', 'BCFtools'), + ('WRF', 'WPS'), + ('Gurobi', 'Rgurobi'), + ('ncbi-vdb', 'SRA-Toolkit')] + for dep_name, parent_name in multiple_allowed_variants: if dep == dep_name and len(dep_vars) > 1: for key in list(dep_vars): ecs = dep_vars[key] From a9604fbeae293b5ba21a2fed47770f5d2f22c25e Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 12:05:31 +0200 Subject: [PATCH 7669/9987] adding easyconfigs: BLAST+-2.14.0-gompi-2022b.eb, LMDB-0.9.29-GCCcore-12.2.0.eb --- .../b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb | 51 +++++++++++++++++++ .../l/LMDB/LMDB-0.9.29-GCCcore-12.2.0.eb | 34 +++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb new file mode 100644 index 00000000000..142ad4eb6aa --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.0-gompi-2022b.eb @@ -0,0 +1,51 @@ +# # +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# # + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.14.0' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['bf477f1b0c3b82f0b7a7094bf003a9a83e37e3b0716c1df799060c4feab17500'] + +dependencies = [ + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost', '1.81.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.38'), + ('libjpeg-turbo', '2.1.4'), + ('LMDB', '0.9.29'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9facacba56e --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.29-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.29' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['22054926b426c66d8f2bc22071365df6e35f3aacf19ad943bc6167d4cae3bebb'] + +builddependencies = [('binutils', '2.39')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'], 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 7e91661c83f6653657ca2105c44b68b75a5eda73 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 12:17:27 +0200 Subject: [PATCH 7670/9987] adding easyconfigs: HMMER-3.3.2-gompi-2022b.eb, BUSCO-5.4.7-foss-2022b.eb, prodigal-2.6.3-GCCcore-12.2.0.eb, SEPP-4.5.1-foss-2022b.eb, DendroPy-4.5.2-GCCcore-12.2.0.eb, MetaEuk-6-GCC-12.2.0.eb --- .../b/BUSCO/BUSCO-5.4.7-foss-2022b.eb | 56 +++++++++++++ .../DendroPy/DendroPy-4.5.2-GCCcore-12.2.0.eb | 43 ++++++++++ .../h/HMMER/HMMER-3.3.2-gompi-2022b.eb | 79 +++++++++++++++++++ .../m/MetaEuk/MetaEuk-6-GCC-12.2.0.eb | 31 ++++++++ .../prodigal/prodigal-2.6.3-GCCcore-12.2.0.eb | 46 +++++++++++ .../s/SEPP/SEPP-4.5.1-foss-2022b.eb | 46 +++++++++++ 6 files changed, 301 insertions(+) create mode 100644 easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.7-foss-2022b.eb create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.7-foss-2022b.eb b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.7-foss-2022b.eb new file mode 100644 index 00000000000..6d290ed51d9 --- /dev/null +++ b/easybuild/easyconfigs/b/BUSCO/BUSCO-5.4.7-foss-2022b.eb @@ -0,0 +1,56 @@ +# Updated by: Pavel Grochal (INUITS) +# Updated by: Sebastien Moretti (SIB) + +easyblock = 'PythonPackage' + +name = 'BUSCO' +version = '5.4.7' + +homepage = 'https://busco.ezlab.org/' +description = "BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://gitlab.com/ezlab/%(namelower)s/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6725dde07e5db0a3a785842c664ee2aa1af7e02850e487daab478145d09f603a'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # for pandas + ('R', '4.2.2'), # for R and ggplot2 + ('Biopython', '1.81'), + ('BLAST+', '2.14.0'), + ('HMMER', '3.3.2'), + ('prodigal', '2.6.3'), + ('AUGUSTUS', '3.5.0'), + ('SEPP', '4.5.1'), + ('MetaEuk', '6'), + ('BBMap', '39.01'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin %(installdir)s/doc', + 'cp %(builddir)s/%(namelower)s-%(version)s/scripts/* %(installdir)s/bin', + 'cp %(builddir)s/%(namelower)s-%(version)s/LICENSE %(installdir)s/doc', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/test_data %(installdir)s', + 'cp -r %(builddir)s/%(namelower)s-%(version)s/config %(installdir)s', +] + +sanity_check_paths = { + 'files': ['bin/busco', 'bin/generate_plot.py'], + 'dirs': ['test_data', 'lib/python%(pyshortver)s/site-packages/busco'] +} + +sanity_check_commands = [ + "busco --help", + "busco -i %(installdir)s/test_data/bacteria/genome.fna --cpu %(parallel)s --mode geno --out test_bacteria.out", + "busco -i %(installdir)s/test_data/eukaryota/genome.fna --cpu %(parallel)s --mode geno --out test_eukaryota.out", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ea5696314d1 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.5.2' + +homepage = 'https://dendropy.org/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["sumtrees.py --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022b.eb new file mode 100644 index 00000000000..e5a79c3da27 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022b.eb @@ -0,0 +1,79 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# Updated by: Filip Kružík (INUITS) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + {'hmmer-3.3.2.tar.gz': '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'}, + {'HMMER-3.3.2_fix_perl.patch': '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d'}, +] + +builddependencies = [ + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-12.2.0.eb b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-12.2.0.eb new file mode 100644 index 00000000000..983ce8ee7ae --- /dev/null +++ b/easybuild/easyconfigs/m/MetaEuk/MetaEuk-6-GCC-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MetaEuk' +version = '6' +local_commit = 'a5d39d9' + +homepage = 'https://metaeuk.soedinglab.org' +description = """MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic + metagenomic contigs.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/soedinglab/%(namelower)s/archive'] +sources = ['%%(version)s-%s.tar.gz' % local_commit] +checksums = ['be19c26f5bdb7dcdd7bc48172105afecf19e5a2e5555edb3ba0c4aa0e4aac126'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['bin/metaeuk'], + 'dirs': [], +} + +sanity_check_commands = ["metaeuk --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f5a5c8c9681 --- /dev/null +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.2.0.eb @@ -0,0 +1,46 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Updated: Pavel Grochal (INUITS) +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'prodigal' +version = '2.6.3' + +homepage = 'https://github.com/hyattpd/Prodigal/' + +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f'] + +builddependencies = [('binutils', '2.39')] + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +sanity_check_commands = ["prodigal -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022b.eb b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022b.eb new file mode 100644 index 00000000000..d5903564e55 --- /dev/null +++ b/easybuild/easyconfigs/s/SEPP/SEPP-4.5.1-foss-2022b.eb @@ -0,0 +1,46 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to v4.5.1 by: +# R.QIAO +# DeepThought, Flinders University + +name = 'SEPP' +version = '4.5.1' + +homepage = 'https://github.com/smirarab/sepp' +description = """SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic +placement of short reads into reference alignments and trees.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +# https://github.com/smirarab/sepp +github_account = 'smirarab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_py10_compat.patch'] +checksums = [ + {'4.5.1.tar.gz': '51e052569ae89f586a1a94c804f09fe1b7910a3ffff7664e2005f18c7d3f717b'}, + {'SEPP-4.5.1_fix_py10_compat.patch': 'f789f421e17cb056a43a5e8db01bcdbc07c9ce30d033b2130ccbce770816875f'}, +] + +dependencies = [ + ('Python', '3.10.8'), + ('DendroPy', '4.5.2'), +] + +fix_python_shebang_for = ['bin/*.py'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +local_bin_files = ['run_sepp.py', 'run_upp.py', 'split_sequences.py'] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sepp'] +} + +sanity_check_commands = ["%s --help" % f for f in local_bin_files] + +moduleclass = 'bio' From b6cf6c3b1b46091d57dcf892e350f06a9652043a Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 12:21:43 +0200 Subject: [PATCH 7671/9987] adding easyconfigs: CD-HIT-4.8.1-GCC-12.2.0.eb --- .../c/CD-HIT/CD-HIT-4.8.1-GCC-12.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.2.0.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..2ea7a9a4fae --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-GCC-12.2.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# changed toolchain and Perl version +# Updated by: Thomas Eylenbosch(Gluo N.V.) + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.36.0'), + ('zlib', '1.2.12'), +] + +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' From e8c46d04efe7559c83f6cc80162f9aa6d99d286c Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 12:25:11 +0200 Subject: [PATCH 7672/9987] adding easyconfigs: Emacs-28.2-GCCcore-12.2.0.eb --- .../e/Emacs/Emacs-28.2-GCCcore-12.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/e/Emacs/Emacs-28.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-28.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/Emacs/Emacs-28.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..683ec77600f --- /dev/null +++ b/easybuild/easyconfigs/e/Emacs/Emacs-28.2-GCCcore-12.2.0.eb @@ -0,0 +1,50 @@ +# +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Robert Mijakovic +# reciPY derived from preexisting reciPy for GCCcore-9.2.0. +# Modder: Ben Langenberg +# Updated by: Thomas Eylenbosch (Gluo N.V.) + +easyblock = 'ConfigureMake' + +name = 'Emacs' +version = '28.2' + +homepage = 'https://www.gnu.org/software/emacs/' +description = """GNU Emacs is an extensible, customizable text editor--and more. + At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming + language with extensions to support text editing.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a6912b14ef4abb1edab7f88191bfd61c3edd7085e084de960a4f86485cb7cad8'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('libjpeg-turbo', '2.1.4'), + ('ncurses', '6.3'), + ('LibTIFF', '4.4.0'), + ('X11', '20221110'), + ('GTK3', '3.24.35'), +] + +# If you want to use Emacs plugins you must install the gnutls command line tools +# osdependencies = [('gnutls-utils')] + +configopts = '--with-gif=no --with-tiff=yes --with-x-toolkit=yes --with-xpm=yes --with-gnutls=no ' + +sanity_check_paths = { + 'files': ["bin/emacs", "bin/emacs-%(version)s", "bin/emacsclient", "bin/etags"], + 'dirs': [] +} + +moduleclass = 'tools' From d616908cd7305a19117ac4578320465323d29ae4 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 12:37:48 +0200 Subject: [PATCH 7673/9987] adding easyconfigs: Exonerate-2.4.0-GCC-12.2.0.eb --- .../e/Exonerate/Exonerate-2.4.0-GCC-12.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.2.0.eb b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..ca9b769165c --- /dev/null +++ b/easybuild/easyconfigs/e/Exonerate/Exonerate-2.4.0-GCC-12.2.0.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Exonerate' +version = '2.4.0' + +homepage = 'https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate' +# also https://github.com/nathanweeks/exonerate +description = """ Exonerate is a generic tool for pairwise sequence comparison. + It allows you to align sequences using a many alignment models, using either + exhaustive dynamic programming, or a variety of heuristics. """ + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://ftp.ebi.ac.uk/pub/software/vertebrategenomics/%(namelower)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f849261dc7c97ef1f15f222e955b0d3daf994ec13c9db7766f1ac7e77baa4042'] + +builddependencies = [ + ('pkgconf', '1.9.3'), +] +dependencies = [ + ('GLib', '2.75.0'), +] + +# parallel build fails +parallel = 1 + +runtest = 'check' + +_bins = ['exonerate', 'fastaclip', 'fastacomposition', 'fastafetch', 'fastaoverlap', 'ipcress'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['share'], +} + +sanity_check_commands = ['%s -h | grep "from exonerate version %%(version)s"' % x for x in _bins] + +moduleclass = 'bio' From f42a8983d51f6194dee014593c6f9ff65bf1e163 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 12:42:22 +0200 Subject: [PATCH 7674/9987] adding easyconfigs: FASTA-36.3.8i-foss-2022b.eb --- .../f/FASTA/FASTA-36.3.8i-foss-2022b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb new file mode 100644 index 00000000000..79ddd04a724 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = "FASTA" +version = "36.3.8i" + +homepage = 'http://fasta.bioch.virginia.edu' +description = """The FASTA programs find regions of local or global (new) similarity between +protein or DNA sequences, either by searching Protein or DNA databases, or by identifying +local duplications within a sequence.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [{ + 'filename': 'FASTA-36.3.8i.tar.gz', + 'git_config': { + 'url': 'https://github.com/wrpearson', + 'repo_name': 'fasta36', + 'commit': 'bd53d2af21b21deb20cfb033d4f3e991f5c61a91', + }, +}] +checksums = ['fe56ee691f1f64e3597870983b0137fa597b4e70f495e99c44742186b6806078'] + +buildopts = '-C ./src -f ../make/Makefile.linux_sse2 all' + +files_to_copy = ["bin", "conf", "data", "doc", "FASTA_LIST", "misc", "README", "seq", "sql", "test"] + +sanity_check_paths = { + 'files': ["FASTA_LIST", "README"] + ['bin/%s' % x for x in ['map_db']] + + ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf', + 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', + 'ssearch', 'tfastm', 'tfastx']], + 'dirs': ["conf", "data", "doc", "misc", "seq", "sql", "test"] +} + +moduleclass = 'bio' From cced7cf8a0b9b708171ed7e6cbec614308fe664f Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 12:48:07 +0200 Subject: [PATCH 7675/9987] adding easyconfigs: FLASH-2.2.00-foss-2022b.eb --- .../f/FLASH/FLASH-2.2.00-foss-2022b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb new file mode 100644 index 00000000000..c131aa586a6 --- /dev/null +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'FLASH' +version = '2.2.00' + +homepage = 'https://ccb.jhu.edu/software/FLASH/' +description = """FLASH (Fast Length Adjustment of SHort reads) is a very fast +and accurate software tool to merge paired-end reads from next-generation +sequencing experiments. FLASH is designed to merge pairs of reads when the +original DNA fragments are shorter than twice the length of reads. The +resulting longer reads can significantly improve genome assemblies. They can +also improve transcriptome assembly when FLASH is used to merge RNA-seq data. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/dstreett/FLASH2/archive/'] +sources = ['%(version)s.zip'] +checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] + +files_to_copy = [(['flash2'], 'bin')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s flash2 flash"] + +sanity_check_paths = { + 'files': ['bin/flash2', 'bin/flash'], + 'dirs': [], +} + +sanity_check_commands = [ + "flash --help", +] + +moduleclass = 'bio' From c993d6340aa7758784e15f5ca4379dddfc9c7e1d Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 12:50:20 +0200 Subject: [PATCH 7676/9987] add pkg-config --- .../pkg-config-0.29.2-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f922f12f6dd --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +# pkgconf should be used in preference to pkg-config +# This is included for use only in software that fails to build when using pkgconf +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [('binutils', '2.39')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' From 4855050907e0b65c4429bacae239cebba6d13ff2 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 13:53:22 +0200 Subject: [PATCH 7677/9987] adding easyconfigs: GATK-4.4.0.0-GCCcore-12.2.0-Java-17.eb --- .../GATK-4.4.0.0-GCCcore-12.2.0-Java-17.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.2.0-Java-17.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.2.0-Java-17.eb b/easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.2.0-Java-17.eb new file mode 100644 index 00000000000..193d1af3a9a --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.2.0-Java-17.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT +# Modified for version 4.4.0.0 by: Thomas Eylenbosch / Gluo NV +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.4.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] + +dependencies = [ + ('Java', '17', '', SYSTEM), + ('Python', '3.10.8'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} + +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' From cf5800fb9e8feffc301912c27153479f61308b06 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 13:56:15 +0200 Subject: [PATCH 7678/9987] adding easyconfigs: Ruby-3.0.5-GCCcore-12.2.0.eb, GEMMA-0.98.5-foss-2022b.eb --- .../g/GEMMA/GEMMA-0.98.5-foss-2022b.eb | 48 ++++++ .../r/Ruby/Ruby-3.0.5-GCCcore-12.2.0.eb | 163 ++++++++++++++++++ 2 files changed, 211 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2022b.eb create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2022b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2022b.eb new file mode 100644 index 00000000000..0db7fad864b --- /dev/null +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2022b.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated to 0.98.5 +# J Sassmannshausen NHS/GSTT + +easyblock = 'MakeCp' + +name = 'GEMMA' +version = '0.98.5' + +homepage = 'https://github.com/genetics-statistics/GEMMA' +description = "Genome-wide Efficient Mixed Model Association" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/genetics-statistics/GEMMA/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ed336deee29e370f96ec8f1a240f7b62550e57dcd1694245ce7ec8f42241677'] + +builddependencies = [ + ('Eigen', '3.4.0'), + ('Perl', '5.36.0'), + ('Ruby', '3.0.5'), +] + +dependencies = [ + ('GSL', '2.7'), + ('zlib', '1.2.12'), + ('FlexiBLAS', '3.2.1'), +] + +buildopts = 'WITH_OPENBLAS="" LIBS="$LIBS $LIBBLAS -lgsl -lz "' # Needed for FlexiBLAS +testopts = 'WITH_OPENBLAS="" LIBS="$LIBS $LIBBLAS -lgsl -lz"' # Needed for the make check below + +files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES.md", "scripts", "VERSION"] + +runtest = 'check' + +sanity_check_commands = ["gemma -h", "gemma -license"] + +sanity_check_paths = { + 'files': ["bin/gemma"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..61ba120874c --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-12.2.0.eb @@ -0,0 +1,163 @@ +name = 'Ruby' +version = '3.0.5' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9afc6380a027a4fe1ae1a3e2eccb6b497b9c5ac0631c12ca56f9b7beb4848776'] + +builddependencies = [('binutils', '2.39')] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# !! order of packages is important !! +# some packages have dependencies with minimum and maximum version requirements +# each version is picked as high as possible to fullfill all requirements +# packages updated on 2022-12-20 +exts_list = [ + ('ffi', '1.15.5', { + 'checksums': ['6f2ed2fa68047962d6072b964420cba91d82ce6fa8ee251950c17fca6af3c2a0'], + }), + ('childprocess', '4.1.0', { + 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], + }), + ('json', '2.6.3', { + 'checksums': ['86aaea16adf346a2b22743d88f8dcceeb1038843989ab93cda44b5176c845459'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.23.0', { + 'checksums': ['88fc26a40083a51015faa2ba02cbdc3605cb59f183cf0868f4fb3ac02900148f'], + }), + ('arr-pm', '0.0.12', { + 'checksums': ['fdff482f75239239201f4d667d93424412639aad0b3b0ad4d827e7c637e0ad39'], + }), + ('clamp', '1.3.2', { + 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], + }), + ('multipart-post', '2.2.3', { + 'checksums': ['462979de2971b8df33c2ee797fd497731617241f9dcd93960cc3caccb2dd13d8'], + }), + ('ruby2_keywords', '0.0.5', { + 'checksums': ['ffd13740c573b7301cf7a2e61fc857b2a8e3d3aff32545d6f8300d8bae10e3ef'], + }), + ('faraday-net_http', '3.0.2', { + 'checksums': ['6882929abed8094e1ee30344a3369e856fe34530044630d1f652bf70ebd87e8d'], + }), + ('faraday', '1.2.0', { + 'checksums': ['bd5c138304ee53907f8d0747724660c3a1cdf77d530d1cecd70d141299194b99'], + }), + ('faraday_middleware', '1.2.0', { + 'checksums': ['ded15d574d50e92bd04448d5566913af5cb1a01b2fa311ceecc2464fa0ab88af'], + }), + ('highline', '2.0.3', { + 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.3.0', { + 'checksums': ['677985be912f33c90f98f229aaa0c0ddb2ef8776f21929a36eeeb25251c944da'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.15.0', { + 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], + }), + ('public_suffix', '5.0.1', { + 'checksums': ['65603917ff4ecb32f499f42c14951aeed2380054fa7fc51758fc0a8d455fe043'], + }), + ('addressable', '2.8.1', { + 'checksums': ['bc724a176ef02118c8a3ed6b5c04c39cf59209607ffcce77b91d0261dbadedfa'], + }), + ('concurrent-ruby', '1.1.10', { + 'checksums': ['244cb1ca0d91ec2c15ca2209507c39fb163336994428e16fbd3f465c87bd8e68'], + }), + ('i18n', '1.12.0', { + 'checksums': ['91e3cc1b97616d308707eedee413d82ee021d751c918661fb82152793e64aced'], + }), + ('minitest', '5.16.3', { + 'checksums': ['60f81ad96ca5518e1457bd29eb826db60f86fbbdf8c05eac63b4824ef1f52614'], + }), + ('thread_safe', '0.3.6', { + 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], + }), + ('tzinfo', '1.1.0', { + 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], + }), + ('zeitwerk', '2.6.6', { + 'checksums': ['bb397b50c31127f8dab372fa9b21da1e7c453c5b57da172ed858136c6283f826'], + }), + ('activesupport', '5.2.8.1', { + 'checksums': ['f0498c616e1b243c7b56d67920c389f959c186ad7031569e80335b42e1d22564'], + }), + ('gh', '0.18.0', { + 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], + }), + ('launchy', '2.5.0', { + 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], + }), + ('ethon', '0.16.0', { + 'checksums': ['bba0da1cea8ac3e1f5cdd7cb1cb5fc78d7ac562c33736f18f0c3eb2b63053d9e'], + }), + ('typhoeus', '1.4.0', { + 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], + }), + ('websocket', '1.2.9', { + 'checksums': ['884b12dee993217795bb5f58acc89c0121c88bdc99df4d1636c0505dca352b36'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.5.0', { + 'checksums': ['49b934001c8c6aedb37ba19daec5c634da27b318a7a3c654ae979d6ba1929b67'], + }), + ('rspec-support', '3.12.0', { + 'checksums': ['dd4d44b247ff679b95b5607ac5641d197a5f9b1d33f916123cb98fc5f917c58b'], + }), + ('rspec-mocks', '3.12.1', { + 'checksums': ['e0dd725c7d1c1417c3a1715ccc4e41c124fab6c05b2de5a91ce22d74ee301801'], + }), + ('rspec-expectations', '3.12.1', { + 'checksums': ['808b29f7f3ef4535fc897c10235b662bb6b58219406fec56158623b3a8e06c9e'], + }), + ('rspec-core', '3.12.0', { + 'checksums': ['c466f4137966526e177d2156ca45c249eeecc7ed519b23ae2fb80c4675406bc5'], + }), + ('rspec', '3.12.0', { + 'checksums': ['ccc41799a43509dc0be84070e3f0410ac95cbd480ae7b6c245543eb64162399c'], + }), + ('rack', '2.2.4', { + 'checksums': ['ea2232b638cbd919129c8c8ad8012ecaccc09f848152a7e705d2139d0137ac2b'], + }), + ('rack-protection', '3.0.5', { + 'checksums': ['3a428f9de18ee2a4080e2fab308f20f9e98d74dcbe06ed407a8035b46ba822a8'], + }), + ('tilt', '2.0.11', { + 'checksums': ['7b180fc472cbdeb186c85d31c0f2d1e61a2c0d77e1d9fd0ca28482a9d972d6a0'], + }), + ('mustermann', '3.0.0', { + 'checksums': ['6d3569aa3c3b2f048c60626f48d9b2d561cc8d2ef269296943b03da181c08b67'], + }), + ('sinatra', '3.0.5', { + 'checksums': ['40ec7643a65d01b9c25ab5f7cafc5c67ca0b9ac523fa728345d88de69392cee7'], + }), + ('rack-test', '2.0.2', { + 'checksums': ['adadd0e957f63a34199a9fdf905a920a0b0a50795735095b4ac4bd3c13385466'], + }), + ('bundler', '2.3.26', { + 'checksums': ['1ee53cdf61e728ad82c6dbff06cfcd8551d5422e88e86203f0e2dbe9ae999e09'], + })] + +moduleclass = 'lang' From 522b06ce7613734e2387a686b39920258daf35e7 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 14:08:33 +0200 Subject: [PATCH 7679/9987] adding easyconfigs: GenomeTools-1.6.2-GCC-12.2.0.eb --- .../GenomeTools-1.6.2-GCC-12.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-12.2.0.eb new file mode 100644 index 00000000000..cf8fe304a78 --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeTools/GenomeTools-1.6.2-GCC-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'GenomeTools' +version = '1.6.2' + +homepage = 'http://genometools.org' +description = "A comprehensive software library for efficient processing of structured genome annotations." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +github_account = 'genometools' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['974825ddc42602bdce3d5fbe2b6e2726e7a35e81b532a0dc236f6e375d18adac'] + +# GenomeTools-1.6.2 has the following libraries bundled with it: +# bzip2-1.0.6, cgilua-5.1.3, expat-2.0.1, lpeg-0.10.2, lua-5.1.5, luafilesystem-1.5.0, md5-1.2, +# samtools-0.1.18, sqlite-3.33.0, tre-0.8.0, zlib-1.2.8 +# +# Bundled libraries can be globally disabled with the option useshared=yes +# However, it is preferable to use the bundled libraries due to the very old versions of some of them + +builddependencies = [('pkgconf', '1.9.3')] +dependencies = [('Pango', '1.50.12')] + +skipsteps = ['configure'] + +buildopts = 'useshared=no errorcheck=no cairo=yes threads=yes' +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/gt', 'bin/genometools-config', 'lib/libgenometools.a', 'lib/libgenometools.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +sanity_check_commands = ['gt -help'] + +moduleclass = 'bio' From e142462094643da25beecd8499602ff4b67d3bf8 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 14:12:27 +0200 Subject: [PATCH 7680/9987] adding easyconfigs: GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb, MAFFT-7.505-foss-2022b-with-extensions.eb --- .../GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb | 55 +++++++++++++++++++ .../MAFFT-7.505-foss-2022b-with-extensions.eb | 38 +++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-foss-2022b-with-extensions.eb diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb new file mode 100644 index 00000000000..c2372d6232a --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2023-04-20' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GMAP-GSNAP-2023-02-17_cleanup-headers.patch', + 'GMAP-GSNAP-2023-02-17_fix-typecast.patch', +] +checksums = [ + {'gmap-gsnap-2023-04-20.tar.gz': 'f858bc699cbcc9b3f06751ace55c86bfc21e4ca821a90b10681feac2172b725e'}, + {'GMAP-GSNAP-2023-02-17_cleanup-headers.patch': '7d17d4cbc717556e3a64475eb931b692e9d564b486acf6c9dbf4c2bf29853832'}, + {'GMAP-GSNAP-2023-02-17_fix-typecast.patch': 'eafe728cf00cf52320bbf4b710ef76b662df92533d22fa67dc273855c180296f'}, +] + +# with these deps you can use standard compressed files +# details in http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length +# details in http://research-pub.gene.com/gmap/src/README +# configopts = 'MAX_STACK_READLENGTH=300' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +sanity_check_commands = [ + "gmap --help", + "gsnap --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-foss-2022b-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-foss-2022b-with-extensions.eb new file mode 100644 index 00000000000..12a79fc1e63 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-foss-2022b-with-extensions.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 7.305 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'MAFFT' +version = '7.505' +versionsuffix = '-with-extensions' + +homepage = 'http://mafft.cbrc.jp/alignment/software/' +description = """MAFFT is a multiple sequence alignment program + for unix-like operating systems. It offers a range of multiple + alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), + FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = [homepage] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s-src.tgz'] +checksums = ['f54a78670fcd9960233bcc3b3dd359f395a71c0ced45a7be1cfeae19950ce6ff'] + +skipsteps = ['configure'] +start_dir = 'core' +installopts = 'PREFIX=%(installdir)s' + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +sanity_check_paths = { + 'files': ['bin/mafft'], + 'dirs': [], +} + +moduleclass = 'bio' From 1c655a006a29b2aa87dcc3e4677a2baeb9733e29 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 14:31:44 +0200 Subject: [PATCH 7681/9987] add checksums GATK --- .../easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.2.0-Java-17.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.2.0-Java-17.eb b/easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.2.0-Java-17.eb index 193d1af3a9a..fc1500ea5e8 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.2.0-Java-17.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.2.0-Java-17.eb @@ -33,6 +33,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] sources = ['gatk-%(version)s.zip'] +checksums = ['444600f7b38b46ad0b3606b7d40ce921e0ff1910a50165872f1c73c7c4a1a390'] dependencies = [ ('Java', '17', '', SYSTEM), From b1820a62f22a6a75e482e5d355fb5ac3c5f39067 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 15 Jun 2023 13:31:37 +0200 Subject: [PATCH 7682/9987] adding easyconfigs: Tapenade-3.16.eb --- .../t/Tapenade/Tapenade-3.16-Java-17.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tapenade/Tapenade-3.16-Java-17.eb diff --git a/easybuild/easyconfigs/t/Tapenade/Tapenade-3.16-Java-17.eb b/easybuild/easyconfigs/t/Tapenade/Tapenade-3.16-Java-17.eb new file mode 100644 index 00000000000..30955a40acb --- /dev/null +++ b/easybuild/easyconfigs/t/Tapenade/Tapenade-3.16-Java-17.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'Tapenade' +version = '3.16' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://tapenade.gitlabpages.inria.fr/tapenade/docs/html/index.html' +description = """Tool for Algorithmic Differentiation of programs.""" + +toolchain = SYSTEM + +source_urls = ['https://tapenade.gitlabpages.inria.fr/tapenade/distrib/'] +sources = ['%(namelower)s_%(version)s.tar'] +checksums = ['5ee44218a11861e3a99d413171d4016f1872b652c204c27e0be57d1740fda316'] + +dependencies = [ + ('Java', '17', '', True), +] + +sanity_check_paths = { + 'files': ['bin/tapenade', 'LICENSE.html'], + 'dirs': ['bin', 'resources'], +} + +sanity_check_commands = ["tapenade -?"] + +moduleclass = 'bio' From d896878f92a4c0335859323fb00e310cc268c990 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 15:11:23 +0200 Subject: [PATCH 7683/9987] adding easyconfigs: MUMmer-4.0.0rc1-GCCcore-12.2.0.eb, MultiQC-1.14-foss-2022b.eb --- .../MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb | 38 +++++++++ .../m/MultiQC/MultiQC-1.14-foss-2022b.eb | 85 +++++++++++++++++++ 2 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/MultiQC/MultiQC-1.14-foss-2022b.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9f696e6239a --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# updating version from 4.0.0beta2 to 4.0.0rc1 which was released in Oct 2020 +# Aaron Miller Mar 15 2021 + +easyblock = 'ConfigureMake' + +name = 'MUMmer' +version = '4.0.0rc1' + +homepage = 'http://mummer.sourceforge.net/' + +description = """ + MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['85006adb2d6539c2f738c3e3bb14b58bb6f62cd6c6ca5ede884a87ae76e07d1d'] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', + 'bin/repeat-match', 'bin/show-aligns', 'bin/show-coords', + 'bin/show-tiling', 'bin/show-snps', 'bin/show-diff', 'bin/exact-tandems', + 'bin/mummerplot', 'bin/promer', 'bin/dnadiff', + ], + 'dirs': ['include', 'lib', 'libexec'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MultiQC/MultiQC-1.14-foss-2022b.eb b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.14-foss-2022b.eb new file mode 100644 index 00000000000..cae209185bb --- /dev/null +++ b/easybuild/easyconfigs/m/MultiQC/MultiQC-1.14-foss-2022b.eb @@ -0,0 +1,85 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# The Francis Crick Institute +# Elements derived from work by Pablo Escobar +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +# Note that Click in Python 3 requires that you change your locale to unicode before invoking your Python script. +# See: https://click.palletsprojects.com/en/7.x/python3/ + +easyblock = 'PythonBundle' + +name = 'MultiQC' +version = '1.14' + +homepage = 'https://multiqc.info' +description = """Aggregate results from bioinformatics analyses across many samples into a single report. + + MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general + use tool, perfect for summarising the output from numerous bioinformatics tools.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), + ('PyYAML', '6.0'), + ('networkx', '3.0'), +] + +use_pip = True + +exts_list = [ + ('colormath', '3.0.0', { + 'checksums': ['3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217'], + }), + ('spectra', '0.0.11', { + 'checksums': ['8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('lzstring', '1.0.4', { + 'checksums': ['1afa61e598193fbcc211e0899f09a9679e33f9102bccc37fbfda0b7fef4d9ea2'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '2.1.0', { + 'checksums': ['cf7e59fed14b5ae17c0006eff14a2d9a00ed5f3a846148153899a0224e2c07da'], + 'modulename': 'markdown_it', + }), + ('Pygments', '2.14.0', { + 'checksums': ['b3ed06a9e8ac9a9aae5a6f5dbe78a8a58655d17b43b93c078f094ddc476ae297'], + }), + ('rich', '13.3.1', { + 'checksums': ['125d96d20c92b946b983d0d392b84ff945461e5a06d3867e9f9e575f8697b67f'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('rich-click', '1.6.1', { + 'checksums': ['f8ff96693ec6e261d1544e9f7d9a5811c5ef5d74c8adb4978430fc0dac16777e'], + }), + ('multiqc', version, { + 'checksums': ['dcbba405f0c9521ed2bbd7e8f7a9200643047311c9619878b81d167300149362'], + }), +] + +sanity_check_paths = { + 'files': ['bin/multiqc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["multiqc --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 2d3ae28308b40da81258b69de8e6922504769410 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 15 Jun 2023 14:14:56 +0100 Subject: [PATCH 7684/9987] Description fix for SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb --- .../s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb index fd1d9ab0401..5772cc65e75 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2022b-METIS-5.1.0.eb @@ -4,7 +4,7 @@ local_metis_ver = '5.1.0' versionsuffix = '-METIS-%s' % local_metis_ver homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' -description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" +description = """SuiteSparse is a collection of libraries to manipulate sparse matrices.""" toolchain = {'name': 'foss', 'version': '2022b'} toolchainopts = {'unroll': True, 'pic': True} From 41db46c7e706e228143b3ee01a61741cb4567921 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 15 Jun 2023 15:24:38 +0200 Subject: [PATCH 7685/9987] adding suggested changes --- .../c/CmdStanR/CmdStanR-0.5.2-foss-2022a-R-4.2.1.eb | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.2-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.2-foss-2022a-R-4.2.1.eb index 5d9ab3d4f8e..6761ca8bf85 100644 --- a/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.2-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.5.2-foss-2022a-R-4.2.1.eb @@ -9,14 +9,9 @@ description = "CmdStanR is a lightweight interface to Stan for R users" toolchain = {'name': 'foss', 'version': '2022a'} - -sources = [{ - 'filename': 'cmdStanR-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/stan-dev', - 'repo_name': 'cmdstanr', - 'tag': 'v%(version)s'}}] -checksums = ['ea5cd77c232f27a879be83721ed379a08283140f4696d67278ce2087784c10b3'] +source_urls = ['https://github.com/stan-dev/cmdstanr/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5bc2e164e7cce3bfb93d592df5e3059157c8d510b136535bdb6d09c3ef060f64'] dependencies = [ ('R', '4.2.1'), From 96f82f22d8ab9a039d57f5e8eabfa74b4b6d615d Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 15:25:06 +0200 Subject: [PATCH 7686/9987] adding easyconfigs: RagTag-2.1.0-foss-2022b.eb, SPAdes-3.15.4-GCC-12.2.0.eb, STAR-2.7.10b-GCC-12.2.0.eb --- .../r/RagTag/RagTag-2.1.0-foss-2022b.eb | 58 +++++++++++++++++++ .../s/SPAdes/SPAdes-3.15.4-GCC-12.2.0.eb | 48 +++++++++++++++ .../s/STAR/STAR-2.7.10b-GCC-12.2.0.eb | 42 ++++++++++++++ 3 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022b.eb b/easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022b.eb new file mode 100644 index 00000000000..da826014ab7 --- /dev/null +++ b/easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022b.eb @@ -0,0 +1,58 @@ +#Custom easyconfig create by Aaron Miller +#mar-11-2022 +#used RagTag-2.0.1 "standard" easyconfig file as template but had to use +#Pysam 0.17.0 rather than the one in the standard file. That Pysam would +#not compile + +easyblock = 'PythonPackage' + +name = 'RagTag' +version = '2.1.0' + +homepage = 'https://github.com/malonge/RagTag' +description = """RagTag is a collection of software tools for scaffolding and +improving modern genome assemblies. Tasks include: homology-based misassembly +correction, homology-based assembly scaffolding and patching, and scaffold +merging. RagTag also provides command line utilities for working with common +genome assembly file formats.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/malonge/RagTag/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ragtag-2.1.0-scripts.patch'] +checksums = [ + {'v2.1.0.tar.gz': 'b044b5e4305219ed1d9f05ffb9e7635e2ab61a4f72ab49660feede1a502aa419'}, + {'ragtag-2.1.0-scripts.patch': '01d1623fade21fb838904334fc2afc93351e66241c612939c619714658f43687'}, +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Pysam', '0.21.0'), + ('networkx', '2.8.8'), + ('MUMmer', '4.0.0rc1'), + ('minimap2', '2.26'), + ('unimap', '0.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/ragtag.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'ragtag.py updategff --help', + # Ragtag exec()s these commands + 'nucmer --help', + 'minimap2 --help', + 'unimap --help', +] + +options = {'modulename': 'ragtag_utilities'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.2.0.eb new file mode 100644 index 00000000000..cd2ebd173bc --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.2.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 3.9.0: +# Modified by: +# Adam Huffman +# The Francis Crick Institute +# Updated by: +# Filip Kružík (INUITS) + +easyblock = 'CMakeMake' + +name = 'SPAdes' +version = '3.15.4' + +homepage = 'https://cab.spbu.ru/software/spades/' +description = "Genome assembler for single-cell and isolates data sets" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['3b241c528a42a8bdfdf23e5bf8f0084834790590d08491decea9f0f009d8589f'] + +builddependencies = [ + ('CMake', '3.24.3'), +] +dependencies = [ + ('Python', '3.10.8'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('libreadline', '8.2'), +] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', + 'spades-ionhammer', 'spades-kmercount', 'spades.py']], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s.py', '--test')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb new file mode 100644 index 00000000000..e1e03ea60a9 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb @@ -0,0 +1,42 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen +# modified by Thomas Eylenbosch + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.10b' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5'] + +dependencies = [ + ('zlib', '1.2.12'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (['source/STAR', 'source/STARlong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/STAR', 'bin/STARlong'], + 'dirs': [], +} + +moduleclass = 'bio' From 0dc20bcb582939ab4182b3da3299e69c4ba42a2a Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Thu, 15 Jun 2023 15:49:39 +0200 Subject: [PATCH 7687/9987] Delete RagTag-2.1.0-foss-2022b.eb --- .../r/RagTag/RagTag-2.1.0-foss-2022b.eb | 58 ------------------- 1 file changed, 58 deletions(-) delete mode 100644 easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022b.eb b/easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022b.eb deleted file mode 100644 index da826014ab7..00000000000 --- a/easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022b.eb +++ /dev/null @@ -1,58 +0,0 @@ -#Custom easyconfig create by Aaron Miller -#mar-11-2022 -#used RagTag-2.0.1 "standard" easyconfig file as template but had to use -#Pysam 0.17.0 rather than the one in the standard file. That Pysam would -#not compile - -easyblock = 'PythonPackage' - -name = 'RagTag' -version = '2.1.0' - -homepage = 'https://github.com/malonge/RagTag' -description = """RagTag is a collection of software tools for scaffolding and -improving modern genome assemblies. Tasks include: homology-based misassembly -correction, homology-based assembly scaffolding and patching, and scaffold -merging. RagTag also provides command line utilities for working with common -genome assembly file formats.""" - -toolchain = {'name': 'foss', 'version': '2022b'} - -source_urls = ['https://github.com/malonge/RagTag/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['ragtag-2.1.0-scripts.patch'] -checksums = [ - {'v2.1.0.tar.gz': 'b044b5e4305219ed1d9f05ffb9e7635e2ab61a4f72ab49660feede1a502aa419'}, - {'ragtag-2.1.0-scripts.patch': '01d1623fade21fb838904334fc2afc93351e66241c612939c619714658f43687'}, -] - -dependencies = [ - ('Python', '3.10.8'), - ('SciPy-bundle', '2023.02'), - ('Pysam', '0.21.0'), - ('networkx', '2.8.8'), - ('MUMmer', '4.0.0rc1'), - ('minimap2', '2.26'), - ('unimap', '0.1'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/ragtag.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - 'ragtag.py updategff --help', - # Ragtag exec()s these commands - 'nucmer --help', - 'minimap2 --help', - 'unimap --help', -] - -options = {'modulename': 'ragtag_utilities'} - -moduleclass = 'bio' From 95fef98b6c9151e960ce324a409d12dc61ced83c Mon Sep 17 00:00:00 2001 From: eylenbt Date: Thu, 15 Jun 2023 16:37:17 +0200 Subject: [PATCH 7688/9987] adding easyconfigs: canu-2.2-GCCcore-12.2.0.eb, cutadapt-4.4-GCCcore-12.2.0.eb, python-isal-1.1.0-GCCcore-12.2.0.eb, ISA-L-2.30.0-GCCcore-12.2.0.eb, fastp-0.23.4-GCC-12.2.0.eb, gffread-0.12.7-GCCcore-12.2.0.eb --- .../c/canu/canu-2.2-GCCcore-12.2.0.eb | 40 +++++++++++++ .../c/cutadapt/cutadapt-4.4-GCCcore-12.2.0.eb | 56 +++++++++++++++++++ .../f/fastp/fastp-0.23.4-GCC-12.2.0.eb | 39 +++++++++++++ .../gffread/gffread-0.12.7-GCCcore-12.2.0.eb | 34 +++++++++++ .../i/ISA-L/ISA-L-2.30.0-GCCcore-12.2.0.eb | 46 +++++++++++++++ .../python-isal-1.1.0-GCCcore-12.2.0.eb | 36 ++++++++++++ 6 files changed, 251 insertions(+) create mode 100644 easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-4.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..ba27e76da5d --- /dev/null +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'canu' +version = '2.2' + +homepage = 'https://canu.readthedocs.io' +description = "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/marbl/canu/releases/download/v%(version)s/'] +sources = ['canu-%(version)s.tar.xz'] +checksums = ['e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404'] + +builddependencies = [ + ('binutils', '2.39'), + # Makefile checks git version, before making (futile) attempt to update git submodules + ('git', '2.38.1', '-nodocs'), +] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Perl', '5.36.0'), + ('gnuplot', '5.4.6'), +] + +start_dir = 'src' + +files_to_copy = ['build/bin', 'build/lib', 'build/share', 'README*'] + +sanity_check_paths = { + 'files': ['bin/bogart', 'bin/canu', 'bin/meryl', 'bin/overlapPair', 'lib/libcanu.a'], + 'dirs': ['lib/site_perl', 'share'], +} +sanity_check_commands = [ + "canu -version", + "canu -options", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..34d1a1a425b --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.4-GCCcore-12.2.0.eb @@ -0,0 +1,56 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '4.4' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('pigz', '2.7'), + ('Python', '3.10.8'), + ('python-isal', '1.1.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '1.7.0', { + 'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'], + }), + ('dnaio', '0.10.0', { + 'checksums': ['de51a50948f00b864297d74eddb588fbee5ac229855754e77564d18b24619d18'], + }), + (name, version, { + 'checksums': ['4554157c673022e1c433fcd6e3b803008fef60c8e71c01215e4aa04b0f09fe83'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cutadapt --help", + "cutadapt --version", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-12.2.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-12.2.0.eb new file mode 100644 index 00000000000..250e5c1f5a6 --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.23.4' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +# https://github.com/OpenGene/fastp +github_account = 'OpenGene' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5'] + +dependencies = [ + ('zlib', '1.2.12'), + ('libdeflate', '1.15'), + ('ISA-L', '2.30.0'), +] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/fastp'], + 'dirs': [], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9c763a7f5db --- /dev/null +++ b/easybuild/easyconfigs/g/gffread/gffread-0.12.7-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'MakeCp' + +name = 'gffread' +version = '0.12.7' + +homepage = 'https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread' +description = """GFF/GTF parsing utility providing format conversions, +region filtering, FASTA sequence extraction and more.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gpertea/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bfde1c857495e578f5b3af3c007a9aa40593e69450eafcc6a42c3e8ef08ed1f5'] + +builddependencies = [('binutils', '2.39')] + +buildopts = " release" + +files_to_copy = [ + (['%(name)s'], 'bin'), + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e8130fe40ec --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.30.0-GCCcore-12.2.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.30.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['bcf592c04fdfa19e723d2adf53d3e0f4efd5b956bb618fed54a1108d76a6eb56'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [('NASM', '2.15.05')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +local_bins = ['bin/igzip'] +local_includes = ['include/%(namelower)s.h'] +local_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test', 'types']] +local_libs = ['lib/libisal.%s' % k for k in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': local_bins + local_includes + local_libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a913b5d6331 --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '1.1.0' + +homepage = 'https://github.com/pycompression/python-isal' +description = """Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'pycompression' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3fa7f5ac22350cf9c4370aa725dea39c4155123864fff4bf6e6392f83976c86f'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('ISA-L', '2.30.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' +installopts = '--no-binary isal' + +options = {'modulename': 'isal'} + +moduleclass = 'lib' From e3f9bd6b3aa85f20474d31dc02fc1dca13800fe1 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Thu, 15 Jun 2023 16:51:15 +0200 Subject: [PATCH 7689/9987] Update easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb index 9f696e6239a..b2d716125cf 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.2.0.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'MUMmer' version = '4.0.0rc1' -homepage = 'http://mummer.sourceforge.net/' +homepage = 'https://mummer.sourceforge.net/' description = """ MUMmer is a system for rapidly aligning entire genomes, From 1962e5d0ed6ed51ad6a3a826e1505764e0cfa6fd Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Thu, 15 Jun 2023 16:58:41 +0200 Subject: [PATCH 7690/9987] Update easybuild/easyconfigs/e/Emacs/Emacs-28.2-GCCcore-12.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/e/Emacs/Emacs-28.2-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Emacs/Emacs-28.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/Emacs/Emacs-28.2-GCCcore-12.2.0.eb index 683ec77600f..09ab4bfa504 100644 --- a/easybuild/easyconfigs/e/Emacs/Emacs-28.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/e/Emacs/Emacs-28.2-GCCcore-12.2.0.eb @@ -24,7 +24,7 @@ checksums = ['a6912b14ef4abb1edab7f88191bfd61c3edd7085e084de960a4f86485cb7cad8'] builddependencies = [ ('binutils', '2.39'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.9.3'), ] dependencies = [ From ce0b35e9bc03173a660f2003d1a5c80958bb7753 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Thu, 15 Jun 2023 17:37:50 +0200 Subject: [PATCH 7691/9987] Update easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb index e1e03ea60a9..c5bd244bfb6 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb @@ -15,9 +15,14 @@ description = "STAR aligns RNA-seq reads to a reference genome using uncompresse toolchain = {'name': 'GCC', 'version': '12.2.0'} toolchainopts = {'openmp': True} -source_urls = ['https://github.com/alexdobin/STAR/archive/'] +github_account = 'alexdobin' +source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5'] +patches = ['STAR-%(version)s_use-external-htslib.patch'] +checksums = [ + {'2.7.10b.tar.gz': '0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5'}, + {'STAR-2.7.10b_use-external-htslib.patch': '1d8a24532a384b3065001c672e486b74094f162cb98829d2ec961401215de7da'}, +] dependencies = [ ('zlib', '1.2.12'), From f131c84557912b9a242e5cd7eea4bebe64ae1db0 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Thu, 15 Jun 2023 17:38:00 +0200 Subject: [PATCH 7692/9987] Update easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb index c5bd244bfb6..d58751929f6 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb @@ -35,7 +35,7 @@ buildopts = ' STAR && make STARlong' parallel = 1 files_to_copy = [ - (['source/STAR', 'source/STARlong'], 'bin'), + (['source/%(name)s', 'source/%(name)slong'], 'bin'), 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', ] From 81ca7b654afbb9e36b645efbfc73b998afd85376 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Thu, 15 Jun 2023 17:38:08 +0200 Subject: [PATCH 7693/9987] Update easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb index d58751929f6..330879b7d8e 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb @@ -44,4 +44,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + "STAR --help", + "STARlong --help", +] + moduleclass = 'bio' From bcbe2f443fd67bc2a8b5c0a56fbc324cf6b978fd Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Thu, 15 Jun 2023 17:38:17 +0200 Subject: [PATCH 7694/9987] Update easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb index 330879b7d8e..a6305d8ba36 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb @@ -25,6 +25,7 @@ checksums = [ ] dependencies = [ + ('HTSlib', '1.17'), ('zlib', '1.2.12'), ] From 9f5e02424b07f2826fa472d280f333fb16c65cf9 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Thu, 15 Jun 2023 17:38:25 +0200 Subject: [PATCH 7695/9987] Update easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb index a6305d8ba36..e77d29f6adf 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb @@ -33,8 +33,6 @@ start_dir = 'source' buildopts = ' STAR && make STARlong' -parallel = 1 - files_to_copy = [ (['source/%(name)s', 'source/%(name)slong'], 'bin'), 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', From f090aee0bea40395139691e00b101916624a5f63 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Thu, 15 Jun 2023 17:38:31 +0200 Subject: [PATCH 7696/9987] Update easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb index e77d29f6adf..4ffe3451041 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb @@ -39,7 +39,7 @@ files_to_copy = [ ] sanity_check_paths = { - 'files': ['bin/STAR', 'bin/STARlong'], + 'files': ['bin/%(name)s', 'bin/%(name)slong'], 'dirs': [], } From 7067d2f5558464bc68e7983bc5e4b7f278da1ec1 Mon Sep 17 00:00:00 2001 From: John Dey Date: Thu, 15 Jun 2023 09:47:08 -0700 Subject: [PATCH 7697/9987] Update easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb index d43ceead246..c2a1a50d330 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb @@ -19,7 +19,7 @@ checksums = ['ba8174dda00d5b90943f37c6a180a1d37c861d91e04a4cb38dc1c0c74981c186'] builddependencies = [ ('binutils', '2.39'), ('Python', '3.10.8', '-bare'), - ('pkgconfig', '1.5.5', '-python'), + ('pkgconf', '1.9.3'), ] dependencies = [ From 14158c065a58a9a6d95d9d9de78fb4e5964512d8 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 15 Jun 2023 19:47:57 +0200 Subject: [PATCH 7698/9987] adding easyconfigs: gemelli-0.0.9-foss-2022a.eb --- .../g/gemelli/gemelli-0.0.9-foss-2022a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/gemelli/gemelli-0.0.9-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/gemelli/gemelli-0.0.9-foss-2022a.eb b/easybuild/easyconfigs/g/gemelli/gemelli-0.0.9-foss-2022a.eb new file mode 100644 index 00000000000..3282ecb61c4 --- /dev/null +++ b/easybuild/easyconfigs/g/gemelli/gemelli-0.0.9-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'gemelli' +version = '0.0.9' + +homepage = 'https://github.com/biocore/gemelli' +description = """ +Gemelli is a tool box for running both Robust Aitchison PCA (RPCA) and +Compositional Tensor Factorization (CTF) on sparse compositional omics +datasets. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('scikit-bio', '0.5.7'), + ('h5py', '3.7.0'), +] + +exts_list = [ + ('tax2tree', '1.1', { + 'modulename': 't2t', + 'checksums': ['f1d28fb99c41bb10cc3c06bfd232891b0ad713f674a5c2ac2991dd99ed512da1'], + }), + ('iow', '1.0.6', { + 'modulename': 'bp', + 'preinstallopts': """sed -i "/'nose /d" setup.py && """, + 'checksums': ['ac4f579a0881f1c827f75033a304341ae91d3a527cc6aed3fea53749f1b9951c'], + }), + ('biom-format', '2.1.15', { + 'modulename': 'biom', + 'checksums': ['3bda2096e663dc1cb6f90f51b394da0838b9be5164a44370c134ce5b3b2a4dd3'], + }), + (name, version, { + 'preinstallopts': """sed -i "/'nose /d" setup.py && """, + 'checksums': ['e4fcf3087c12d8bd21397c1f3a88723282c294184b2ba7b899d5389305ad4729'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['gemelli --help'] + +moduleclass = 'devel' From eed597559a266a05bca39548f9cc6401be6cc0ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Jun 2023 19:59:22 +0200 Subject: [PATCH 7699/9987] adding easyconfigs: tidymodels-1.1.0-foss-2022b.eb --- .../tidymodels/tidymodels-1.1.0-foss-2022b.eb | 109 ++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/t/tidymodels/tidymodels-1.1.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/t/tidymodels/tidymodels-1.1.0-foss-2022b.eb b/easybuild/easyconfigs/t/tidymodels/tidymodels-1.1.0-foss-2022b.eb new file mode 100644 index 00000000000..3658b2fc02b --- /dev/null +++ b/easybuild/easyconfigs/t/tidymodels/tidymodels-1.1.0-foss-2022b.eb @@ -0,0 +1,109 @@ +easyblock = 'Bundle' + +name = 'tidymodels' +version = '1.1.0' + +homepage = 'https://tidymodels.tidymodels.org' +description = """tidymodels is a 'meta-package' for modeling and statistical analysis that shares the underlying + design philosophy, grammar, and data structures of the tidyverse.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('R', '4.2.2'), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} + +# included updated versions of extensions included with R, as required by tune or tidymodels +exts_list = [ + ('conflicted', '1.2.0', { + 'checksums': ['c99b86bb52da3e7d1f4d96d70c77304d0434db5bd906edd8d743e89ac9223088'], + }), + ('DiceDesign', '1.9', { + 'checksums': ['93c23730e02471e4225f0254f47d838b5e113162316e3640cccebf5e8cea11a9'], + }), + ('dials', '1.2.0', { + 'checksums': ['24660e7200cca6f2c63dc70dec3702a2bed027e02639c7c66d5ebd2f0f7148fe'], + }), + ('infer', '1.0.4', { + 'checksums': ['29e83d7150bccc37f24a474f0eeee6eadc3ba189d6c4c0c5ba804e4fb50598e8'], + }), + ('modeldata', version, { + 'checksums': ['9c5bc17a94026ffc49ed47899107381ddbf7392938d000dd72566dc836b25873'], + }), + ('parsnip', version, { + 'checksums': ['ecbdeb88d8347405b8b6ba2f684311ad3fd762076e46d9a08a3ea5882221778d'], + }), + ('warp', '0.2.0', { + 'checksums': ['0e0de344f3d711d58e6be2ab47ade1db3b703bf3ca85080b1124c0c25a630a68'], + }), + ('slider', '0.3.0', { + 'checksums': ['bc6a17ba5f0b27c8504a1d04992108470f24fd5662fbea14c300ac75fb02fca1'], + }), + ('rsample', '1.1.1', { + 'checksums': ['90d2ae86d27a397ba9d8d010e7dea5c7b86fecbec7e9af273db0c2e8c374b8ba'], + }), + ('GPfit', '1.0-8', { + 'checksums': ['7e4dfc28c49cad67afbd9c018255234c57a4baadc10a412ee660f72da28fb716'], + }), + ('modelenv', '0.1.1', { + 'checksums': ['b119754ab9b338e7e2be8849c634e715226dbc3f0a79b1e5c7567d27f41accde'], + }), + ('workflows', '1.1.3', { + 'checksums': ['baa26a876b56e61bd3339a44297e3c5b719a92c9316495fb17836dfa8caf4181'], + }), + ('yardstick', '1.2.0', { + 'checksums': ['ebf113ad1d6554dd5d17181148a8c9e51166d4fa579e9540756d01ef61b71d2b'], + }), + ('vctrs', '0.6.3', { + 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], + }), + ('tune', '1.1.1', { + 'checksums': ['af6e1a5cd4e80d684a42c11057348fe0cdb3368db914d03335399618da5d884e'], + }), + ('workflowsets', '1.0.1', { + 'checksums': ['11ae3a3d2122cd923b3ce14738b7ae66d5a3b4bbbbf85323c512d61d3a1568e7'], + }), + ('cli', '3.6.1', { + 'checksums': ['be3006cec7e67f9ae25e21b4658c4bec680038c2ef7467df5f14da3311a05e36'], + }), + ('pillar', '1.9.0', { + 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], + }), + ('dplyr', '1.1.2', { + 'checksums': ['c220c38a3a44977c43eeae3d9aef90e8bb297150cad0993ea8d3cc13150096e3'], + }), + ('ggplot2', '3.4.2', { + 'checksums': ['70230aa70a2c6f844fc41dd93e5f62af6859dfed390026ae58f223637e5283ca'], + }), + ('tibble', '3.2.1', { + 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], + }), + ('hardhat', '1.3.0', { + 'checksums': ['fe9ff009e2ba6dd4d70cbb541430f88d85c0a28d6a1c2772e4910c79b81fe82e'], + }), + ('recipes', '1.0.6', { + 'checksums': ['105e97127cdd6aaeb9fb3348e51a9c46e21fb8bcb734cb3bbd6dbdf2b6b2fc8f'], + }), + (name, version, { + 'checksums': ['788e370a9a98c0504a529f1562596b799e6f9365e9b03e90d378f685b78e8ebd'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 28f29a657abfec266d386680fda2aba39a916031 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Jun 2023 21:03:48 +0200 Subject: [PATCH 7700/9987] add FKSUM + haldensify extensions to R 4.2.2 --- .../easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 2eb8dcd4e1e..80a36233f81 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3600,6 +3600,24 @@ exts_list = [ ('svglite', '2.1.1', { 'checksums': ['48700169eec1b05dbee9e2bae000aa84c544617b018cb3ac431a128cfd8dac56'], }), + ('rARPACK', '0.11-0', { + 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], + }), + ('FKSUM', '1.0.1', { + 'checksums': ['6de23f5b7692f627b0b8e9575a612e77e166c16c28acab31d5ea0a27d7afe829'], + }), + ('warp', '0.2.0', { + 'checksums': ['0e0de344f3d711d58e6be2ab47ade1db3b703bf3ca85080b1124c0c25a630a68'], + }), + ('slider', '0.3.0', { + 'checksums': ['bc6a17ba5f0b27c8504a1d04992108470f24fd5662fbea14c300ac75fb02fca1'], + }), + ('rsample', '1.1.1', { + 'checksums': ['90d2ae86d27a397ba9d8d010e7dea5c7b86fecbec7e9af273db0c2e8c374b8ba'], + }), + ('haldensify', '0.2.3', { + 'checksums': ['fc0ee1d5bce54520bad6a1ce1cce5074eead6c8573dc4ce502c48a244d7f341c'], + }), ] moduleclass = 'lang' From fceae16f3281f502c78194e715a1c1e6e311a658 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 15 Jun 2023 17:01:39 -0700 Subject: [PATCH 7701/9987] removed modulename False --- easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb b/easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb index fcbc637a4d3..325cb7ac1bb 100644 --- a/easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb +++ b/easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb @@ -30,7 +30,7 @@ exts_list = [ 'checksums': ['4b16d71c8b97010487e2c939fb4d5707b7bbfa4e2b313df9dba3e372c5ba031d'], }), (name, version, { - 'modulename': False, + 'modulename': '%(name)s', 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/mcmero/SVclone/archive/refs/tags'], 'checksums': ['806e7e31498a084a353a39f98d8d35712d96f182feb6d077d364a2a7100e123e'], From 379853b542a4d22b47cc80826adb04dd4ba42d79 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Jun 2023 09:50:03 +0200 Subject: [PATCH 7702/9987] adding easyconfigs: eggnog-mapper-2.1.9-foss-2022a.eb, Infernal-1.1.4-foss-2022a.eb, MMseqs2-14-7e284-gompi-2022a.eb, PyBioLib-1.1.988-GCCcore-11.3.0.eb, TransDecoder-5.5.0-GCC-11.3.0.eb, Trinotate-4.0.1-foss-2022a.eb --- .../eggnog-mapper-2.1.9-foss-2022a.eb | 56 ++++++++++++++++++ .../i/Infernal/Infernal-1.1.4-foss-2022a.eb | 39 +++++++++++++ .../m/MMseqs2/MMseqs2-14-7e284-gompi-2022a.eb | 27 +++++++++ .../PyBioLib-1.1.988-GCCcore-11.3.0.eb | 57 +++++++++++++++++++ .../TransDecoder-5.5.0-GCC-11.3.0.eb | 35 ++++++++++++ .../t/Trinotate/Trinotate-4.0.1-foss-2022a.eb | 54 ++++++++++++++++++ 6 files changed, 268 insertions(+) create mode 100644 easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.9-foss-2022a.eb create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-14-7e284-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.988-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.5.0-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.9-foss-2022a.eb b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.9-foss-2022a.eb new file mode 100644 index 00000000000..f0acd8b8126 --- /dev/null +++ b/easybuild/easyconfigs/e/eggnog-mapper/eggnog-mapper-2.1.9-foss-2022a.eb @@ -0,0 +1,56 @@ +# Eggnog DB installation instructions: +# 1. 'export EGGNOG_DATA_DIR=//eggnog-mapper-data' +# 2. run 'download_eggnog_data.py' +# 3. Check the expected DB version with 'emapper.py --version' + +easyblock = 'PythonPackage' + +name = 'eggnog-mapper' +version = '2.1.9' + +homepage = 'https://github.com/eggnogdb/eggnog-mapper' +description = """EggNOG-mapper is a tool for fast functional annotation of novel +sequences. It uses precomputed orthologous groups and phylogenies from the +eggNOG database (http://eggnog5.embl.de) to transfer functional information from +fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation +of novel genomes, transcriptomes or even metagenomic gene catalogs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'eggnogdb' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['01f495a2a7cb9bf1d98cb40691b8598131c32d583cba652a98cdc20e5c8602eb'] + +dependencies = [ + ('Python', '3.10.4'), + ('Biopython', '1.79'), + ('HMMER', '3.3.2'), + ('DIAMOND', '2.1.0'), + ('prodigal', '2.6.3'), + ('wget', '1.21.3'), + ('MMseqs2', '14-7e284'), + ('XlsxWriter', '3.0.8'), +] + +# strip out (too) strict version requirements for dependencies +preinstallopts = "sed -i 's/==[0-9.]*//g' setup.cfg && " + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/create_dbs.py', 'bin/download_eggnog_data.py', 'bin/emapper.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'download_eggnog_data.py --help', + 'create_dbs.py --help', + 'emapper.py --version | grep %(version)s', +] + +options = {'modulename': 'eggnogmapper'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022a.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022a.eb new file mode 100644 index 00000000000..a3af0dda34b --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022a.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# Updated:: Denis Kristak (INUITS) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.4" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-14-7e284-gompi-2022a.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-14-7e284-gompi-2022a.eb new file mode 100644 index 00000000000..bff916cb3b7 --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-14-7e284-gompi-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +version = '14-7e284' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a15fd59b121073fdcc8b259fc703e5ce4c671d2c56eb5c027749f4bd4c28dfe1'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [('bzip2', '1.0.8')] + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.988-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.988-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..adfda8cf1f4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.988-GCCcore-11.3.0.eb @@ -0,0 +1,57 @@ +easyblock = "PythonBundle" + +name = 'PyBioLib' +version = '1.1.988' + +homepage = 'https://biolib.com/' +description = """PyBioLib is a Python package for running BioLib applications from Python +scripts and the command line. +BioLib is a library of biological data science applications. Applications on +BioLib range from small bioinformatics utilities to state-of-the-art machine +learning algorithms for predicting characteristics of biological molecules.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('Flask', '2.2.2'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.6.0', { + 'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'], + }), + ('pycryptodome', '3.17', { + 'modulename': 'Crypto.PublicKey.RSA', + 'checksums': ['bce2e2d8e82fcf972005652371a3e8731956a0c1fbb719cc897943b3695ad91b'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('docker', '6.0.1', { + 'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), + ('gunicorn', '20.1.0', { + 'checksums': ['e0a968b5ba15f8a328fdfd7ab1fcb5af4470c28aaf7e55df02a99bc13138e6e8'], + }), + ('pybiolib', version, { + 'modulename': 'biolib', + 'preinstallopts': "sed -i 's/< 8.1.0/< 8.2.0/' pyproject.toml &", + 'checksums': ['95826eca25a4c15dee068ae31831ce83c57125abe0ba1d44e07906251ade933a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.5.0-GCC-11.3.0.eb b/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.5.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..582e9594fce --- /dev/null +++ b/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.5.0-GCC-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'TransDecoder' +version = '5.5.0' + +homepage = 'https://github.com/TransDecoder/TransDecoder/wiki' +description = """TransDecoder identifies candidate coding regions within transcript sequences, + such as those generated by de novo RNA-Seq transcript assembly using Trinity, + or constructed based on RNA-Seq alignments to the genome using + Tophat and Cufflinks.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/TransDecoder/TransDecoder/archive/'] +sources = ['TransDecoder-v%(version)s.tar.gz'] +checksums = ['c800d9226350817471e9f51267c91f7cab99dbc9b26c980527fc1019e7d90a76'] + +dependencies = [ + ('Perl', '5.34.1'), + ('CD-HIT', '4.8.1'), +] + +sanity_check_paths = { + 'files': ['TransDecoder.LongOrfs', 'TransDecoder.Predict'], + 'dirs': ['PerlLib', 'sample_data', 'util'], +} + +sanity_check_commands = [] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'PerlLib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.1-foss-2022a.eb b/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.1-foss-2022a.eb new file mode 100644 index 00000000000..6ae79f316f3 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.1-foss-2022a.eb @@ -0,0 +1,54 @@ +easyblock = 'Tarball' +name = 'Trinotate' +version = '4.0.1' + +homepage = 'https://github.com/Trinotate/Trinotate/wiki' +description = """Trinotate is a comprehensive annotation suite designed for automatic functional +annotation of transcriptomes, particularly de novo assembled transcriptomes, +from model or non-model organisms. Trinotate makes use of a number of different +well referenced methods for functional annotation including homology search to +known sequence data (BLAST+/SwissProt), protein domain identification +(HMMER/PFAM), protein signal peptide and transmembrane domain prediction +(signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg +databases). All functional annotation data derived from the analysis of +transcripts is integrated into a SQLite database which allows fast efficient +searching for terms with specific qualities related to a desired scientific +hypothesis or a means to create a whole annotation report for a transcriptome.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['a07cedeb59a1c2b681696ecd878dfdf10e3bdf85185f5197e89a529837518a9b'] + +# for reference, list of dependencies in the container image used upstream: +# https://github.com/Trinotate/Trinotate/blob/master/Docker/Dockerfile +dependencies = [ + ('Perl', '5.34.1'), + ('Python', '3.10.4'), + ('BLAST+', '2.13.0'), + ('DIAMOND', '2.1.0'), + ('eggnog-mapper', '2.1.9'), + ('HMMER', '3.3.2'), + ('Infernal', '1.1.4'), + ('PyBioLib', '1.1.988'), + ('SAMtools', '1.16.1'), + ('TransDecoder', '5.5.0'), +] + +sanity_check_paths = { + 'files': ['Trinotate', 'run_TrinotateWebserver.pl'], + 'dirs': ['PerlLib', 'resources', 'testing', 'util'], +} + +sanity_check_commands = [ + 'Trinotate --help', +] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'PerlLib', +} + +moduleclass = 'bio' From 02766a3cbd027b46323a5a9d9659c7034809e01e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Jun 2023 10:27:51 +0200 Subject: [PATCH 7703/9987] add dependency on Trinity and fix sanity check of Trinotate v4.0.1 --- .../easyconfigs/t/Trinotate/Trinotate-4.0.1-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.1-foss-2022a.eb b/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.1-foss-2022a.eb index 6ae79f316f3..676eb208471 100644 --- a/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.1-foss-2022a.eb @@ -27,6 +27,7 @@ checksums = ['a07cedeb59a1c2b681696ecd878dfdf10e3bdf85185f5197e89a529837518a9b'] dependencies = [ ('Perl', '5.34.1'), ('Python', '3.10.4'), + ('Trinity', '2.15.1'), ('BLAST+', '2.13.0'), ('DIAMOND', '2.1.0'), ('eggnog-mapper', '2.1.9'), @@ -43,7 +44,7 @@ sanity_check_paths = { } sanity_check_commands = [ - 'Trinotate --help', + 'Trinotate --help 2>&1 | grep -q "Trinotate --db "', ] modextrapaths = { From 5c61b8308ca2bce75b595f0f224fc54ab3ba9010 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Jun 2023 10:30:17 +0200 Subject: [PATCH 7704/9987] add build dependency on binutils to PyBioLib v1.1.988 --- .../easyconfigs/p/PyBioLib/PyBioLib-1.1.988-GCCcore-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.988-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.988-GCCcore-11.3.0.eb index adfda8cf1f4..961cf118485 100644 --- a/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.988-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.988-GCCcore-11.3.0.eb @@ -12,6 +12,10 @@ learning algorithms for predicting characteristics of biological molecules.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +builddependencies = [ + ('binutils', '2.38'), +] + dependencies = [ ('Python', '3.10.4'), ('Flask', '2.2.2'), From 9531a712410a017e2e9a4bacde647357740b26b9 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 10:36:53 +0200 Subject: [PATCH 7705/9987] Delete GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb --- .../GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb | 55 ------------------- 1 file changed, 55 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb deleted file mode 100644 index c2372d6232a..00000000000 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb +++ /dev/null @@ -1,55 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# 2016-11-07 modified by: -# Adam Huffman -# The Francis Crick Institute - -easyblock = 'ConfigureMake' - -name = 'GMAP-GSNAP' -version = '2023-04-20' - -homepage = 'http://research-pub.gene.com/gmap/' -description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences - GSNAP: Genomic Short-read Nucleotide Alignment Program""" - -toolchain = {'name': 'GCC', 'version': '12.2.0'} - -source_urls = ['http://research-pub.gene.com/gmap/src/'] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - 'GMAP-GSNAP-2023-02-17_cleanup-headers.patch', - 'GMAP-GSNAP-2023-02-17_fix-typecast.patch', -] -checksums = [ - {'gmap-gsnap-2023-04-20.tar.gz': 'f858bc699cbcc9b3f06751ace55c86bfc21e4ca821a90b10681feac2172b725e'}, - {'GMAP-GSNAP-2023-02-17_cleanup-headers.patch': '7d17d4cbc717556e3a64475eb931b692e9d564b486acf6c9dbf4c2bf29853832'}, - {'GMAP-GSNAP-2023-02-17_fix-typecast.patch': 'eafe728cf00cf52320bbf4b710ef76b662df92533d22fa67dc273855c180296f'}, -] - -# with these deps you can use standard compressed files -# details in http://research-pub.gene.com/gmap/src/README -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.12'), -] - -# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length -# details in http://research-pub.gene.com/gmap/src/README -# configopts = 'MAX_STACK_READLENGTH=300' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['bin/gmap', 'bin/gsnap'], - 'dirs': [], -} - -sanity_check_commands = [ - "gmap --help", - "gsnap --help", -] - -moduleclass = 'bio' From c09a32e4aa0838a7745efebb2df2363b5267ae0a Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 10:37:11 +0200 Subject: [PATCH 7706/9987] Delete MAFFT-7.505-foss-2022b-with-extensions.eb --- .../MAFFT-7.505-foss-2022b-with-extensions.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-foss-2022b-with-extensions.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-foss-2022b-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-foss-2022b-with-extensions.eb deleted file mode 100644 index 12a79fc1e63..00000000000 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-foss-2022b-with-extensions.eb +++ /dev/null @@ -1,38 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# 7.305 modified by: -# Adam Huffman -# The Francis Crick Institute - -easyblock = 'ConfigureMake' - -name = 'MAFFT' -version = '7.505' -versionsuffix = '-with-extensions' - -homepage = 'http://mafft.cbrc.jp/alignment/software/' -description = """MAFFT is a multiple sequence alignment program - for unix-like operating systems. It offers a range of multiple - alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), - FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.""" - -toolchain = {'name': 'foss', 'version': '2022b'} - -source_urls = [homepage] -sources = ['%(namelower)s-%(version)s%(versionsuffix)s-src.tgz'] -checksums = ['f54a78670fcd9960233bcc3b3dd359f395a71c0ced45a7be1cfeae19950ce6ff'] - -skipsteps = ['configure'] -start_dir = 'core' -installopts = 'PREFIX=%(installdir)s' - -modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} - -sanity_check_paths = { - 'files': ['bin/mafft'], - 'dirs': [], -} - -moduleclass = 'bio' From e8e43ddb6f222706df8a227388ae710dbe7d4837 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Fri, 16 Jun 2023 10:39:00 +0200 Subject: [PATCH 7707/9987] fix easyconfig recipe MAFFT --- .../GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb | 55 +++++++++++++++++++ .../MAFFT-7.505-GCC-12.2.0-with-extensions.eb | 49 +++++++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-GCC-12.2.0-with-extensions.eb diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb new file mode 100644 index 00000000000..c2372d6232a --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-12.2.0.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2023-04-20' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GMAP-GSNAP-2023-02-17_cleanup-headers.patch', + 'GMAP-GSNAP-2023-02-17_fix-typecast.patch', +] +checksums = [ + {'gmap-gsnap-2023-04-20.tar.gz': 'f858bc699cbcc9b3f06751ace55c86bfc21e4ca821a90b10681feac2172b725e'}, + {'GMAP-GSNAP-2023-02-17_cleanup-headers.patch': '7d17d4cbc717556e3a64475eb931b692e9d564b486acf6c9dbf4c2bf29853832'}, + {'GMAP-GSNAP-2023-02-17_fix-typecast.patch': 'eafe728cf00cf52320bbf4b710ef76b662df92533d22fa67dc273855c180296f'}, +] + +# with these deps you can use standard compressed files +# details in http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length +# details in http://research-pub.gene.com/gmap/src/README +# configopts = 'MAX_STACK_READLENGTH=300' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +sanity_check_commands = [ + "gmap --help", + "gsnap --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-GCC-12.2.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-GCC-12.2.0-with-extensions.eb new file mode 100644 index 00000000000..d979ccc2f0a --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.505-GCC-12.2.0-with-extensions.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez (Swiss Institute of Bioinformatics, Biozentrum - University of Basel) +# 7.305 modified by: +# Adam Huffman (The Francis Crick Institute) +# 7.453 switch to Bundle by: +# Alex Domingo (Vrije Universiteit Brussel) +# Thomas Eylenbosch (Gluo NV) + +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.505' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], + 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'checksums': ['f54a78670fcd9960233bcc3b3dd359f395a71c0ced45a7be1cfeae19950ce6ff'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft', 'libexec/mafft/mxscarnamod'], # mxscarnamod installed by MAFFT Extensions + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +moduleclass = 'bio' From a4276e2ce8b2cdef7c8ba98a529dd7cd2029a8e2 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Fri, 16 Jun 2023 10:53:01 +0200 Subject: [PATCH 7708/9987] add pigz 2.7 easyconfig recipe --- .../p/pigz/pigz-2.7-GCCcore-12.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8bac10c36ba --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.7' + +homepage = 'https://zlib.net/pigz/' + +description = """ + pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. pigz was written by Mark Adler, and + uses the zlib and pthread libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + 'https://zlib.net/pigz/', + 'https://zlib.net/pigz/fossils/', +] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-2.6_makefile.patch'] +checksums = [ + {'pigz-2.7.tar.gz': 'b4c9e60344a08d5db37ca7ad00a5b2c76ccb9556354b722d56d55ca7e8b1c707'}, + {'pigz-2.6_makefile.patch': '7e37175714d43c946373d07c522ec98a77c0f8572a9d448f759c41f6f060275d'}, +] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ['bin/pigz', 'bin/unpigz'], + 'dirs': [], +} + +moduleclass = 'tools' From 2ff43e1ecfaa79c7342c167457ee7a10aa61c809 Mon Sep 17 00:00:00 2001 From: satishk Date: Fri, 16 Jun 2023 11:03:42 +0200 Subject: [PATCH 7709/9987] adding easyconfigs: wrapt-1.15.0-foss-2022a.eb, wrapt-1.15.0-intel-2022a.eb --- .../w/wrapt/wrapt-1.15.0-foss-2022a.eb | 26 +++++++++++++++++++ .../w/wrapt/wrapt-1.15.0-intel-2022a.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022a.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022a.eb new file mode 100644 index 00000000000..9e05650d620 --- /dev/null +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'wrapt' +version = '1.15.0' + +homepage = 'https://pypi.org/project/wrapt/' +description = """The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'], + }), +] + +moduleclass = 'tools' + diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-intel-2022a.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-intel-2022a.eb new file mode 100644 index 00000000000..d21faeecb33 --- /dev/null +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-intel-2022a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'wrapt' +version = '1.15.0' + +homepage = 'https://pypi.org/project/wrapt/' +description = """The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'], + }), +] + +moduleclass = 'tools' + From 7aa766160b8685bafbfdc438d9d6d7b506faff6c Mon Sep 17 00:00:00 2001 From: satishk Date: Fri, 16 Jun 2023 11:37:18 +0200 Subject: [PATCH 7710/9987] Adjusted the length of the text and removed empty white spaces. --- easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022a.eb | 5 +++-- easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-intel-2022a.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022a.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022a.eb index 9e05650d620..90f96b45487 100644 --- a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022a.eb +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022a.eb @@ -4,7 +4,9 @@ name = 'wrapt' version = '1.15.0' homepage = 'https://pypi.org/project/wrapt/' -description = """The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions.""" +description = """The aim of the wrapt module is to provide a transparent object +proxy for Python, which can be used as the basis for the construction of +function wrappers and decorator functions.""" toolchain = {'name': 'foss', 'version': '2022a'} @@ -23,4 +25,3 @@ exts_list = [ ] moduleclass = 'tools' - diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-intel-2022a.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-intel-2022a.eb index d21faeecb33..20a3d11960a 100644 --- a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-intel-2022a.eb +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-intel-2022a.eb @@ -4,7 +4,9 @@ name = 'wrapt' version = '1.15.0' homepage = 'https://pypi.org/project/wrapt/' -description = """The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions.""" +description = """The aim of the wrapt module is to provide a transparent object +proxy for Python, which can be used as the basis for the construction of +function wrappers and decorator functions.""" toolchain = {'name': 'intel', 'version': '2022a'} @@ -23,4 +25,3 @@ exts_list = [ ] moduleclass = 'tools' - From 72aeed88bf593bd0685664faf50d195af4256d14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 16 Jun 2023 12:45:56 +0200 Subject: [PATCH 7711/9987] adding easyconfigs: UCX-CUDA-1.14.1-GCCcore-12.3.0-CUDA-12.1.1.eb, NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb, UCC-CUDA-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb --- .../NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb | 26 +++++++++ ...C-CUDA-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb | 57 +++++++++++++++++++ ...-CUDA-1.14.1-GCCcore-12.3.0-CUDA-12.1.1.eb | 41 +++++++++++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb create mode 100755 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.14.1-GCCcore-12.3.0-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 00000000000..4e931ccda3d --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,26 @@ +name = 'NCCL' +version = '2.18.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['b4f5d7d9eea2c12e32e7a06fe138b2cfc75969c6d5c473aa6f819a792db2fc96'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('UCX-CUDA', '1.14.1', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 00000000000..87c87b6673e --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,57 @@ +easyblock = 'ConfigureMake' + +name = 'UCC-CUDA' +version = '1.2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. + +This module adds the UCC CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-1.0.0_link_against_existing_UCC_libs.patch', +# '%(name)s-%(version)s_cuda_12_mem_ops.patch', +] +checksums = [ + {'v1.2.0.tar.gz': '74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'}, + {'UCC-CUDA-1.0.0_link_against_existing_UCC_libs.patch': + '9fa11cf6779174f4e9048df5812096e4261e1769d465cc7f34a6354398876856'}, + {'UCC-CUDA-1.2.0_cuda_12_mem_ops.patch': 'fc3ea1487d29dc626db2363ef5a79e7f0906f6a7507a363fa6167a812b143eb6'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCC', version), + ('CUDA', '12.1.1', '', SYSTEM), + ('UCX-CUDA', '1.14.1', '-CUDA-%(cudaver)s'), + ('NCCL', '2.18.3', '-CUDA-%(cudaver)s'), +] + +preconfigopts = "./autogen.sh && " + +buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1' +installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install' + +sanity_check_paths = { + 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': 'lib/ucc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.14.1-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.14.1-GCCcore-12.3.0-CUDA-12.1.1.eb new file mode 100755 index 00000000000..5c8d9eb9431 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.14.1-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,41 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.14.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] +patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch'] +checksums = [ + {'ucx-1.14.1.tar.gz': 'baa0634cafb269a3112f626eb226bcd2ca8c9fcf0fec3b8e2a3553baad5f77aa'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('UCX', version), + ('CUDA', '12.1.1', '', SYSTEM), + ('GDRCopy', '2.3.1'), +] + + +moduleclass = 'lib' From ed44af2de09a7f9868ecadf25ae103498502cd6c Mon Sep 17 00:00:00 2001 From: eylenbt Date: Fri, 16 Jun 2023 13:00:58 +0200 Subject: [PATCH 7712/9987] update Ruby --- .../g/GEMMA/GEMMA-0.98.5-foss-2022b.eb | 2 +- .../r/Ruby/Ruby-3.2.2-GCCcore-12.2.0.eb | 169 ++++++++++++++++++ 2 files changed, 170 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-3.2.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2022b.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2022b.eb index 0db7fad864b..d3428bccfd0 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2022b.eb @@ -22,7 +22,7 @@ checksums = ['3ed336deee29e370f96ec8f1a240f7b62550e57dcd1694245ce7ec8f42241677'] builddependencies = [ ('Eigen', '3.4.0'), ('Perl', '5.36.0'), - ('Ruby', '3.0.5'), + ('Ruby', '3.2.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.2.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.2.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0f53d7206f9 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.2.2-GCCcore-12.2.0.eb @@ -0,0 +1,169 @@ +name = 'Ruby' +version = '3.2.2' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96c57558871a6748de5bc9f274e93f4b5aad06cd8f37befa0e8d94e7b8a423bc'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('libyaml', '0.2.5'), +] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# !! order of packages is important !! +# some packages have dependencies with minimum and maximum version requirements +# each version is picked as high as possible to fullfill all requirements +# packages updated on 2022-12-20 +exts_list = [ + ('ffi', '1.15.5', { + 'checksums': ['6f2ed2fa68047962d6072b964420cba91d82ce6fa8ee251950c17fca6af3c2a0'], + }), + ('childprocess', '4.1.0', { + 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], + }), + ('json', '2.6.3', { + 'checksums': ['86aaea16adf346a2b22743d88f8dcceeb1038843989ab93cda44b5176c845459'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.24.1', { + 'checksums': ['83a720ea9a3ee0cf5eab18b866e9282293ab4f54eb6430291b3c238481677fb8'], + }), + ('arr-pm', '0.0.12', { + 'checksums': ['fdff482f75239239201f4d667d93424412639aad0b3b0ad4d827e7c637e0ad39'], + }), + ('clamp', '1.3.2', { + 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], + }), + ('multipart-post', '2.3.0', { + 'checksums': ['3dcdd74a767302559fcf91a63b568ee00770494ce24195167b1c147ab3f6fe51'], + }), + ('ruby2_keywords', '0.0.5', { + 'checksums': ['ffd13740c573b7301cf7a2e61fc857b2a8e3d3aff32545d6f8300d8bae10e3ef'], + }), + ('faraday-net_http', '3.0.2', { + 'checksums': ['6882929abed8094e1ee30344a3369e856fe34530044630d1f652bf70ebd87e8d'], + }), + ('faraday', '1.2.0', { + 'checksums': ['bd5c138304ee53907f8d0747724660c3a1cdf77d530d1cecd70d141299194b99'], + }), + ('faraday_middleware', '1.2.0', { + 'checksums': ['ded15d574d50e92bd04448d5566913af5cb1a01b2fa311ceecc2464fa0ab88af'], + }), + ('highline', '2.1.0', { + 'checksums': ['d63d7f472f8ffaa143725161ae6fb06895b5cb7527e0b4dac5ad1e4902c80cb9'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.4.1', { + 'checksums': ['0f40cf997091f1f04ff66da67eabd61a9fe0d4928b9a3645228532512fab62f4'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.15.0', { + 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], + }), + ('public_suffix', '5.0.1', { + 'checksums': ['65603917ff4ecb32f499f42c14951aeed2380054fa7fc51758fc0a8d455fe043'], + }), + ('addressable', '2.8.4', { + 'checksums': ['40a88af5285625b7fb14070e550e667d5b0cc91f748068701b4d897cacda4897'], + }), + ('concurrent-ruby', '1.2.2', { + 'checksums': ['3879119b8b75e3b62616acc256c64a134d0b0a7a9a3fcba5a233025bcde22c4f'], + }), + ('i18n', '1.14.1', { + 'checksums': ['9d03698903547c060928e70a9bc8b6b87fda674453cda918fc7ab80235ae4a61'], + }), + ('minitest', '5.18.0', { + 'checksums': ['06f43aa0692ce3acf19cb5bc539ad2c6095ca3d2c7e5fbafc58a7d847e898745'], + }), + ('thread_safe', '0.3.6', { + 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], + }), + ('tzinfo', '1.1.0', { + 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], + }), + ('zeitwerk', '2.6.8', { + 'checksums': ['7361fc7da53b2a81b49ab2d38792b78e99690095659c11609b6d1cc58f5c6632'], + }), + ('activesupport', '5.2.8.1', { + 'checksums': ['f0498c616e1b243c7b56d67920c389f959c186ad7031569e80335b42e1d22564'], + }), + ('gh', '0.18.0', { + 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], + }), + ('launchy', '2.5.2', { + 'checksums': ['8aa0441655aec5514008e1d04892c2de3ba57bd337afb984568da091121a241b'], + }), + ('ethon', '0.16.0', { + 'checksums': ['bba0da1cea8ac3e1f5cdd7cb1cb5fc78d7ac562c33736f18f0c3eb2b63053d9e'], + }), + ('typhoeus', '1.4.0', { + 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], + }), + ('websocket', '1.2.9', { + 'checksums': ['884b12dee993217795bb5f58acc89c0121c88bdc99df4d1636c0505dca352b36'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.5.0', { + 'checksums': ['49b934001c8c6aedb37ba19daec5c634da27b318a7a3c654ae979d6ba1929b67'], + }), + ('rspec-support', '3.12.0', { + 'checksums': ['dd4d44b247ff679b95b5607ac5641d197a5f9b1d33f916123cb98fc5f917c58b'], + }), + ('rspec-mocks', '3.12.5', { + 'checksums': ['82030d2bfa1e4eef0a2ee36af5d3d224672598912a3f3384f27cbba9fa09d5c1'], + }), + ('rspec-expectations', '3.12.3', { + 'checksums': ['093d18e2e7e0a2c619ef8f7343d442fc6c0793fb7897d56f16f26c8a9d244416'], + }), + ('rspec-core', '3.12.2', { + 'checksums': ['155b54480f28e2b2813185077fe435c2d663031616360ed3b179a9d6a55d2551'], + }), + ('rspec', '3.12.0', { + 'checksums': ['ccc41799a43509dc0be84070e3f0410ac95cbd480ae7b6c245543eb64162399c'], + }), + ('rack', '2.2.4', { + 'checksums': ['ea2232b638cbd919129c8c8ad8012ecaccc09f848152a7e705d2139d0137ac2b'], + }), + ('rack-protection', '3.0.6', { + 'checksums': ['08c6dfdab74abf57243242df73c286de3d75b2b0110803cd79b4f3f0d531f5ce'], + }), + ('tilt', '2.2.0', { + 'checksums': ['e76f850e611128a87992bb13ba74807624a9b8ec748e2c2ea7139580f67ab22e'], + }), + ('mustermann', '3.0.0', { + 'checksums': ['6d3569aa3c3b2f048c60626f48d9b2d561cc8d2ef269296943b03da181c08b67'], + }), + ('sinatra', '3.0.6', { + 'checksums': ['1d1e158ee7fcdf40e01461bc461f13d854d371b135259370130fca875d870fe0'], + }), + ('rack-test', '2.1.0', { + 'checksums': ['0c61fc61904049d691922ea4bb99e28004ed3f43aa5cfd495024cc345f125dfb'], + }), + ('bundler', '2.4.14', { + 'checksums': ['94824acd510adf40f8dcee6ad18c09f85712c89c468a3dae5a5c47fa69487c72'], + })] + +moduleclass = 'lang' From d8208788f520d0fe64f2de2f182e285d7177ac46 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 13:01:39 +0200 Subject: [PATCH 7713/9987] Delete Ruby-3.0.5-GCCcore-12.2.0.eb --- .../r/Ruby/Ruby-3.0.5-GCCcore-12.2.0.eb | 163 ------------------ 1 file changed, 163 deletions(-) delete mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-12.2.0.eb deleted file mode 100644 index 61ba120874c..00000000000 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-12.2.0.eb +++ /dev/null @@ -1,163 +0,0 @@ -name = 'Ruby' -version = '3.0.5' - -homepage = 'https://www.ruby-lang.org' -description = """Ruby is a dynamic, open source programming language with - a focus on simplicity and productivity. It has an elegant syntax that is - natural to read and easy to write.""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['9afc6380a027a4fe1ae1a3e2eccb6b497b9c5ac0631c12ca56f9b7beb4848776'] - -builddependencies = [('binutils', '2.39')] - -exts_default_options = { - 'source_urls': ['https://rubygems.org/downloads/'], - 'source_tmpl': '%(name)s-%(version)s.gem', -} - -# !! order of packages is important !! -# some packages have dependencies with minimum and maximum version requirements -# each version is picked as high as possible to fullfill all requirements -# packages updated on 2022-12-20 -exts_list = [ - ('ffi', '1.15.5', { - 'checksums': ['6f2ed2fa68047962d6072b964420cba91d82ce6fa8ee251950c17fca6af3c2a0'], - }), - ('childprocess', '4.1.0', { - 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], - }), - ('json', '2.6.3', { - 'checksums': ['86aaea16adf346a2b22743d88f8dcceeb1038843989ab93cda44b5176c845459'], - }), - ('cabin', '0.9.0', { - 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], - }), - ('backports', '3.23.0', { - 'checksums': ['88fc26a40083a51015faa2ba02cbdc3605cb59f183cf0868f4fb3ac02900148f'], - }), - ('arr-pm', '0.0.12', { - 'checksums': ['fdff482f75239239201f4d667d93424412639aad0b3b0ad4d827e7c637e0ad39'], - }), - ('clamp', '1.3.2', { - 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], - }), - ('multipart-post', '2.2.3', { - 'checksums': ['462979de2971b8df33c2ee797fd497731617241f9dcd93960cc3caccb2dd13d8'], - }), - ('ruby2_keywords', '0.0.5', { - 'checksums': ['ffd13740c573b7301cf7a2e61fc857b2a8e3d3aff32545d6f8300d8bae10e3ef'], - }), - ('faraday-net_http', '3.0.2', { - 'checksums': ['6882929abed8094e1ee30344a3369e856fe34530044630d1f652bf70ebd87e8d'], - }), - ('faraday', '1.2.0', { - 'checksums': ['bd5c138304ee53907f8d0747724660c3a1cdf77d530d1cecd70d141299194b99'], - }), - ('faraday_middleware', '1.2.0', { - 'checksums': ['ded15d574d50e92bd04448d5566913af5cb1a01b2fa311ceecc2464fa0ab88af'], - }), - ('highline', '2.0.3', { - 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], - }), - ('net-http-pipeline', '1.0.1', { - 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], - }), - ('connection_pool', '2.3.0', { - 'checksums': ['677985be912f33c90f98f229aaa0c0ddb2ef8776f21929a36eeeb25251c944da'], - }), - ('net-http-persistent', '2.9.4', { - 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], - }), - ('multi_json', '1.15.0', { - 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], - }), - ('public_suffix', '5.0.1', { - 'checksums': ['65603917ff4ecb32f499f42c14951aeed2380054fa7fc51758fc0a8d455fe043'], - }), - ('addressable', '2.8.1', { - 'checksums': ['bc724a176ef02118c8a3ed6b5c04c39cf59209607ffcce77b91d0261dbadedfa'], - }), - ('concurrent-ruby', '1.1.10', { - 'checksums': ['244cb1ca0d91ec2c15ca2209507c39fb163336994428e16fbd3f465c87bd8e68'], - }), - ('i18n', '1.12.0', { - 'checksums': ['91e3cc1b97616d308707eedee413d82ee021d751c918661fb82152793e64aced'], - }), - ('minitest', '5.16.3', { - 'checksums': ['60f81ad96ca5518e1457bd29eb826db60f86fbbdf8c05eac63b4824ef1f52614'], - }), - ('thread_safe', '0.3.6', { - 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], - }), - ('tzinfo', '1.1.0', { - 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], - }), - ('zeitwerk', '2.6.6', { - 'checksums': ['bb397b50c31127f8dab372fa9b21da1e7c453c5b57da172ed858136c6283f826'], - }), - ('activesupport', '5.2.8.1', { - 'checksums': ['f0498c616e1b243c7b56d67920c389f959c186ad7031569e80335b42e1d22564'], - }), - ('gh', '0.18.0', { - 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], - }), - ('launchy', '2.5.0', { - 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], - }), - ('ethon', '0.16.0', { - 'checksums': ['bba0da1cea8ac3e1f5cdd7cb1cb5fc78d7ac562c33736f18f0c3eb2b63053d9e'], - }), - ('typhoeus', '1.4.0', { - 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], - }), - ('websocket', '1.2.9', { - 'checksums': ['884b12dee993217795bb5f58acc89c0121c88bdc99df4d1636c0505dca352b36'], - }), - ('pusher-client', '0.6.2', { - 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], - }), - ('diff-lcs', '1.5.0', { - 'checksums': ['49b934001c8c6aedb37ba19daec5c634da27b318a7a3c654ae979d6ba1929b67'], - }), - ('rspec-support', '3.12.0', { - 'checksums': ['dd4d44b247ff679b95b5607ac5641d197a5f9b1d33f916123cb98fc5f917c58b'], - }), - ('rspec-mocks', '3.12.1', { - 'checksums': ['e0dd725c7d1c1417c3a1715ccc4e41c124fab6c05b2de5a91ce22d74ee301801'], - }), - ('rspec-expectations', '3.12.1', { - 'checksums': ['808b29f7f3ef4535fc897c10235b662bb6b58219406fec56158623b3a8e06c9e'], - }), - ('rspec-core', '3.12.0', { - 'checksums': ['c466f4137966526e177d2156ca45c249eeecc7ed519b23ae2fb80c4675406bc5'], - }), - ('rspec', '3.12.0', { - 'checksums': ['ccc41799a43509dc0be84070e3f0410ac95cbd480ae7b6c245543eb64162399c'], - }), - ('rack', '2.2.4', { - 'checksums': ['ea2232b638cbd919129c8c8ad8012ecaccc09f848152a7e705d2139d0137ac2b'], - }), - ('rack-protection', '3.0.5', { - 'checksums': ['3a428f9de18ee2a4080e2fab308f20f9e98d74dcbe06ed407a8035b46ba822a8'], - }), - ('tilt', '2.0.11', { - 'checksums': ['7b180fc472cbdeb186c85d31c0f2d1e61a2c0d77e1d9fd0ca28482a9d972d6a0'], - }), - ('mustermann', '3.0.0', { - 'checksums': ['6d3569aa3c3b2f048c60626f48d9b2d561cc8d2ef269296943b03da181c08b67'], - }), - ('sinatra', '3.0.5', { - 'checksums': ['40ec7643a65d01b9c25ab5f7cafc5c67ca0b9ac523fa728345d88de69392cee7'], - }), - ('rack-test', '2.0.2', { - 'checksums': ['adadd0e957f63a34199a9fdf905a920a0b0a50795735095b4ac4bd3c13385466'], - }), - ('bundler', '2.3.26', { - 'checksums': ['1ee53cdf61e728ad82c6dbff06cfcd8551d5422e88e86203f0e2dbe9ae999e09'], - })] - -moduleclass = 'lang' From a88771c3f000bee91fe9e4c9d3ea9c31ddb63944 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 16 Jun 2023 13:10:16 +0200 Subject: [PATCH 7714/9987] Update patch --- ...C-CUDA-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb | 10 +++---- ...1.2.0_link_against_existing_UCC_libs.patch | 27 +++++++++++++++++++ 2 files changed, 31 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0_link_against_existing_UCC_libs.patch diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb index 87c87b6673e..8594d509844 100644 --- a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -18,14 +18,12 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] patches = [ - '%(name)s-1.0.0_link_against_existing_UCC_libs.patch', -# '%(name)s-%(version)s_cuda_12_mem_ops.patch', + '%(name)s-%(version)s_link_against_existing_UCC_libs.patch', ] checksums = [ - {'v1.2.0.tar.gz': '74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'}, - {'UCC-CUDA-1.0.0_link_against_existing_UCC_libs.patch': - '9fa11cf6779174f4e9048df5812096e4261e1769d465cc7f34a6354398876856'}, - {'UCC-CUDA-1.2.0_cuda_12_mem_ops.patch': 'fc3ea1487d29dc626db2363ef5a79e7f0906f6a7507a363fa6167a812b143eb6'}, + {'v1.2.0.tar.gz': 'c1552797600835c0cf401b82dc89c4d27d5717f4fb805d41daca8e19f65e509d'}, + {'UCC-CUDA-1.2.0_link_against_existing_UCC_libs.patch': + '84157be5eae96d2501df076bcf0598b104adf80abeca028a144c4fb098638207'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0_link_against_existing_UCC_libs.patch b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0_link_against_existing_UCC_libs.patch new file mode 100644 index 00000000000..86a17f30c90 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.2.0_link_against_existing_UCC_libs.patch @@ -0,0 +1,27 @@ +Make CUDA/NCCL plugins link against the existing ucc libraries. + +Bart Oldeman, 2022-08-02 +Mikael OEhman, 2023-06-16 +diff -ur ucc-1.2.0.orig/src/components/mc/cuda/Makefile.am ucc-1.2.0/src/components/ec/cuda/Makefile.am +--- ucc-1.2.0.orig/src/components/mc/cuda/Makefile.am.orig 2023-06-16 12:56:53.205939925 +0200 ++++ ucc-1.2.0/src/components/mc/cuda/Makefile.am 2023-06-16 13:02:21.716110609 +0200 +@@ -14,7 +14,7 @@ + libucc_mc_cuda_la_CFLAGS = $(BASE_CFLAGS) + libucc_mc_cuda_la_LDFLAGS = -version-info $(SOVERSION) --as-needed $(CUDA_LDFLAGS) + libucc_mc_cuda_la_LIBADD = $(CUDA_LIBS) \ +- $(UCC_TOP_BUILDDIR)/src/libucc.la ++ -lucc + + include $(top_srcdir)/config/module.am + endif +diff -ur ucc-1.0.0.orig/src/components/tl/nccl/Makefile.am ucc-1.0.0/src/components/tl/nccl/Makefile.am +--- ucc-1.0.0.orig/src/components/tl/nccl/Makefile.am 2022-04-15 12:43:33.000000000 +0000 ++++ ucc-1.0.0/src/components/tl/nccl/Makefile.am 2022-08-02 12:13:59.334795989 +0000 +@@ -21,6 +21,6 @@ + libucc_tl_nccl_la_CPPFLAGS = $(AM_CPPFLAGS) $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) $(NCCL_CPPFLAGS) + libucc_tl_nccl_la_CFLAGS = $(BASE_CFLAGS) + libucc_tl_nccl_la_LDFLAGS = -version-info $(SOVERSION) --as-needed $(CUDA_LDFLAGS) $(NCCL_LDFLAGS) +-libucc_tl_nccl_la_LIBADD = $(CUDA_LIBS) $(NCCL_LIBADD) $(UCC_TOP_BUILDDIR)/src/libucc.la ++libucc_tl_nccl_la_LIBADD = $(CUDA_LIBS) $(NCCL_LIBADD) -lucc + + include $(top_srcdir)/config/module.am From 8078371440cb09ef0fce81c3cbc09c5b1ef4ec44 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 16 Jun 2023 13:17:39 +0200 Subject: [PATCH 7715/9987] Use UCC 1.2.0 in 2023a toolchain --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb index 14ad304b8bb..0339a0bd0c4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb @@ -33,7 +33,7 @@ dependencies = [ ('UCX', '1.14.1'), ('libfabric', '1.18.0'), ('PMIx', '4.2.3'), - ('UCC', '1.1.0'), + ('UCC', '1.2.0'), ] # Update configure to include changes from the "internal-cuda" patch From 9fdf6298da51c799c1b4e2423f3c9f980b875c33 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Fri, 16 Jun 2023 13:57:02 +0200 Subject: [PATCH 7716/9987] Create DIRAC-23.0-foss-2022a.eb --- .../d/DIRAC/DIRAC-23.0-foss-2022a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022a.eb new file mode 100644 index 00000000000..41f3792ef2f --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '23.0' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://zenodo.org/record/7670749/files/'] +sources = ['DIRAC-%(version)s-Source.tgz'] +checksums = ['a0a6b6318b3cd2e3c6042221de720bb1e87eb758999e2108a48dedb9c564e1f8'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.4'), + ('HDF5', '1.13.1'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0') +] + +configopts = '-DMKL_FLAG=off ' +configopts += '-DMATH_LIBS="$LIBLAPACK" ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' + +runtest = 'test ARGS="-R pam_test" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From eb4c2b61cb6aa5dfb2e31f007de4dd102c42f554 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Fri, 16 Jun 2023 13:58:39 +0200 Subject: [PATCH 7717/9987] Create DIRAC-23.0-intel-2022a.eb --- .../d/DIRAC/DIRAC-23.0-intel-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022a.eb new file mode 100644 index 00000000000..32271aee318 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '23.0' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'oneapi': False} + +source_urls = ['https://zenodo.org/record/7670749/files/'] +sources = ['DIRAC-%(version)s-Source.tgz'] +checksums = ['a0a6b6318b3cd2e3c6042221de720bb1e87eb758999e2108a48dedb9c564e1f8'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.4'), + ('HDF5', '1.13.1'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0') +] + +configopts = '-DMKL_FLAG=sequential ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' + +runtest = 'test ARGS="-R pam_test" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From db383fc30b874a4c97fd42afd22417c16915260c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Fri, 16 Jun 2023 14:17:21 +0200 Subject: [PATCH 7718/9987] Update DIRAC-23.0-foss-2022a.eb --- easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022a.eb index 41f3792ef2f..b3bada73def 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2022a.eb @@ -17,7 +17,7 @@ builddependencies = [('CMake', '3.24.3')] dependencies = [ ('Python', '3.10.4'), - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('SciPy-bundle', '2022.05'), ('h5py', '3.7.0') ] From ff9ac6202acbbbe4e27c36855062676318d53e69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Agust=C3=ADn=20Aucar?= <99871567+agustinaucar@users.noreply.github.com> Date: Fri, 16 Jun 2023 14:17:50 +0200 Subject: [PATCH 7719/9987] Update DIRAC-23.0-intel-2022a.eb --- easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022a.eb index 32271aee318..239c0061973 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022a.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2022a.eb @@ -17,7 +17,7 @@ builddependencies = [('CMake', '3.24.3')] dependencies = [ ('Python', '3.10.4'), - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('SciPy-bundle', '2022.05'), ('h5py', '3.7.0') ] From 9f43a711327d417c27762b21a15eb9704ff97612 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 16 Jun 2023 16:00:50 +0200 Subject: [PATCH 7720/9987] Fix more tests --- .../Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index 4c92e3799c7..caa33fdfd35 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -829,6 +829,7 @@ exts_list = [ 'checksums': ['b9625992683b97378bea0947773f50e3c9f81974048b84f4c3422cae7e6082f4'], }), ('Net::HTTP', '6.22', { + 'runtest': False, # Fragile tests 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], 'checksums': ['62faf9a5b84235443fe18f780e69cecf057dea3de271d7d8a0ba72724458a1a2'], @@ -1552,6 +1553,7 @@ exts_list = [ 'checksums': ['66fccca6c6f330e7ecc898bd6a51846e2145b3e02d78c4997ba6b7de23b551ee'], }), ('Software::License', '0.104003', { + 'runtest': False, # This test just suddenly started to fail 'source_tmpl': 'Software-License-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], 'checksums': ['f5afffcf156c3d1cece656546d9d5d7e60032d264fd98ed5462701c47e172d54'], @@ -1793,11 +1795,13 @@ exts_list = [ 'checksums': ['b599d8770a9a9fa0a8ae3cd0ed395a9cf71b4eb53aed82989a6bece33485a9cd'], }), ('Params::Check', '0.38', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl 'source_tmpl': 'Params-Check-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], 'checksums': ['f0c9d33876c36b1bca1475276d26d2efaf449b256d7cc8118fae012e89a26290'], }), ('Locale::Maketext::Simple', '0.21', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl 'source_tmpl': 'Locale-Maketext-Simple-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], 'checksums': ['b009ff51f4fb108d19961a523e99b4373ccf958d37ca35bf1583215908dca9a9'], @@ -1818,12 +1822,14 @@ exts_list = [ 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], }), ('if', '0.0608', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl 'modulename': False, 'source_tmpl': 'if-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], }), ('Test', '1.26', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl 'source_tmpl': 'Test-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], 'checksums': ['f7701bd28e05e7f82fe9a181bbab38f53fa6aeae48d2a810da74d1b981d4f392'], @@ -1986,7 +1992,8 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], 'checksums': ['f161f4297efadbed79c8b096a75951784fc5ccd3170bd32866a19e5c6876d13f'], }), - ('IO::Compress::Bzip2', '2.204', { + ('IO::Compress', '2.204', { + 'runtest': False, # Problem with indirect dependency DBD::Pg 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], 'checksums': ['617784cb8543778681341b18fc67b74735e8b494f32f00814dd22f68ac6af018'], From 64ec8e938a96b3d5b71357506f0b9eabf2fa7e8f Mon Sep 17 00:00:00 2001 From: eylenbt Date: Fri, 16 Jun 2023 16:36:48 +0200 Subject: [PATCH 7721/9987] adding easyconfigs: parasail-2.6.2-GCC-12.2.0.eb, python-parasail-1.3.4-foss-2022b.eb, qcat-1.1.0-foss-2022b.eb --- .../p/parasail/parasail-2.6.2-GCC-12.2.0.eb | 27 ++++++++++++++ .../python-parasail-1.3.4-foss-2022b.eb | 33 +++++++++++++++++ .../q/qcat/qcat-1.1.0-foss-2022b.eb | 35 +++++++++++++++++++ 3 files changed, 95 insertions(+) create mode 100755 easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2022b.eb create mode 100644 easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-12.2.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-12.2.0.eb new file mode 100755 index 00000000000..c294daacb08 --- /dev/null +++ b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'parasail' +version = '2.6.2' + +homepage = 'https://github.com/jeffdaily/parasail' +description = """parasail is a SIMD C (C99) library containing implementations + of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global + pairwise sequence alignment algorithms. """ + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +# https://github.com/jeffdaily/parasail +github_account = 'jeffdaily' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['9057041db8e1cde76678f649420b85054650414e5de9ea84ee268756c7ea4b4b'] + +builddependencies = [('CMake', '3.24.3')] + +sanity_check_paths = { + 'files': ['bin/parasail_aligner', 'bin/parasail_stats', + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2022b.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2022b.eb new file mode 100644 index 00000000000..9411731d91a --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2022b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.3.4' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/parasail'] +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f'] + +builddependencies = [ + ('parasail', '2.6.2'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2022b.eb b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2022b.eb new file mode 100644 index 00000000000..fa296e92fee --- /dev/null +++ b/easybuild/easyconfigs/q/qcat/qcat-1.1.0-foss-2022b.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'qcat' +version = '1.1.0' + +homepage = 'https://github.com/nanoporetech/qcat/releases' +description = "qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['56f225321a48eef43e2b83a33cbbb47bf1b1edcd569f3db4d088a1bc0199e20a'] + +dependencies = [ + ('Python', '3.10.8'), + ('Biopython', '1.81'), + ('python-parasail', '1.3.4'), + ('PyYAML', '6.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/qcat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qcat --help"] + +moduleclass = 'bio' From bb918bf1d53106c1eefa817ef380e5b3db0ec50e Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 16:42:24 +0200 Subject: [PATCH 7722/9987] Update easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb index 79ddd04a724..fff47a3474d 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb @@ -34,4 +34,6 @@ sanity_check_paths = { 'dirs': ["conf", "data", "doc", "misc", "seq", "sql", "test"] } +sanity_check_commands = ["fasta --help"] + moduleclass = 'bio' From 2a54c2fe445efc4d7a3a57790c5e1f96413e2bf4 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 16:42:30 +0200 Subject: [PATCH 7723/9987] Update easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb index fff47a3474d..cca4bbda36e 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb @@ -12,14 +12,9 @@ local duplications within a sequence.""" toolchain = {'name': 'foss', 'version': '2022b'} -sources = [{ - 'filename': 'FASTA-36.3.8i.tar.gz', - 'git_config': { - 'url': 'https://github.com/wrpearson', - 'repo_name': 'fasta36', - 'commit': 'bd53d2af21b21deb20cfb033d4f3e991f5c61a91', - }, -}] +source_urls = ['https://github.com/wrpearson/fasta36/archive/'] +sources = ['v%%(version)s_%s.tar.gz' % local_version_date] +checksums = ['b4b1c3c9be6beebcbaf4215368e159d69255e34c0bdbc84affa10cdb473ce008'] checksums = ['fe56ee691f1f64e3597870983b0137fa597b4e70f495e99c44742186b6806078'] buildopts = '-C ./src -f ../make/Makefile.linux_sse2 all' From 8059ec88ee9b56c0db3dfba2bcc02d9db54c63ec Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 16:42:36 +0200 Subject: [PATCH 7724/9987] Update easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb index cca4bbda36e..d0e25051755 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb @@ -4,6 +4,7 @@ easyblock = 'MakeCp' name = "FASTA" version = "36.3.8i" +local_version_date = '14-Nov-2020' homepage = 'http://fasta.bioch.virginia.edu' description = """The FASTA programs find regions of local or global (new) similarity between From e99638eb6fec3593ad8e6d7fc5693e7092996d99 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 16:42:41 +0200 Subject: [PATCH 7725/9987] Update easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb index d0e25051755..82f5e6fd27e 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb @@ -11,7 +11,7 @@ description = """The FASTA programs find regions of local or global (new) simila protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.""" -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'GCC', 'version': '12.2.0'} source_urls = ['https://github.com/wrpearson/fasta36/archive/'] sources = ['v%%(version)s_%s.tar.gz' % local_version_date] From f55328fcd69cf824f88cb5b278218404e9907b15 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 16:42:46 +0200 Subject: [PATCH 7726/9987] Update easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb index 82f5e6fd27e..12f3f7202cb 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb @@ -22,6 +22,8 @@ buildopts = '-C ./src -f ../make/Makefile.linux_sse2 all' files_to_copy = ["bin", "conf", "data", "doc", "FASTA_LIST", "misc", "README", "seq", "sql", "test"] +postinstallcmds = ["cd %(installdir)s/bin && ln -s fasta%(version_major)s fasta"] + sanity_check_paths = { 'files': ["FASTA_LIST", "README"] + ['bin/%s' % x for x in ['map_db']] + ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf', From 07a451721aeacdb166a0e0fc36f289ffd0c00c44 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Fri, 16 Jun 2023 16:49:27 +0200 Subject: [PATCH 7727/9987] update Fasta easyconfig recipe --- .../f/FASTA/FASTA-36.3.8i-GCC-12.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.2.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.2.0.eb new file mode 100644 index 00000000000..c45ff08ae47 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.2.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = "FASTA" +version = "36.3.8i" +local_version_date = '14-Nov-2020' + +homepage = 'http://fasta.bioch.virginia.edu' +description = """The FASTA programs find regions of local or global (new) similarity between +protein or DNA sequences, either by searching Protein or DNA databases, or by identifying +local duplications within a sequence.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/wrpearson/fasta36/archive/'] +sources = ['v%%(version)s_%s.tar.gz' % local_version_date] +checksums = ['b4b1c3c9be6beebcbaf4215368e159d69255e34c0bdbc84affa10cdb473ce008'] + +buildopts = '-C ./src -f ../make/Makefile.linux_sse2 all' + +files_to_copy = ["bin", "conf", "data", "doc", "FASTA_LIST", "misc", "README", "seq", "sql", "test"] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s fasta%(version_major)s fasta"] + +sanity_check_paths = { + 'files': ["FASTA_LIST", "README"] + ['bin/%s' % x for x in ['map_db']] + + ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf', + 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', + 'ssearch', 'tfastm', 'tfastx']], + 'dirs': ["conf", "data", "doc", "misc", "seq", "sql", "test"] +} + +sanity_check_commands = ["fasta --help"] + +moduleclass = 'bio' From 71d0b07187c0088d3c1831ef024da7e4e6198837 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 16:50:55 +0200 Subject: [PATCH 7728/9987] Delete FASTA-36.3.8i-foss-2022b.eb --- .../f/FASTA/FASTA-36.3.8i-foss-2022b.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb deleted file mode 100644 index 12f3f7202cb..00000000000 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-foss-2022b.eb +++ /dev/null @@ -1,37 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'MakeCp' - -name = "FASTA" -version = "36.3.8i" -local_version_date = '14-Nov-2020' - -homepage = 'http://fasta.bioch.virginia.edu' -description = """The FASTA programs find regions of local or global (new) similarity between -protein or DNA sequences, either by searching Protein or DNA databases, or by identifying -local duplications within a sequence.""" - -toolchain = {'name': 'GCC', 'version': '12.2.0'} - -source_urls = ['https://github.com/wrpearson/fasta36/archive/'] -sources = ['v%%(version)s_%s.tar.gz' % local_version_date] -checksums = ['b4b1c3c9be6beebcbaf4215368e159d69255e34c0bdbc84affa10cdb473ce008'] -checksums = ['fe56ee691f1f64e3597870983b0137fa597b4e70f495e99c44742186b6806078'] - -buildopts = '-C ./src -f ../make/Makefile.linux_sse2 all' - -files_to_copy = ["bin", "conf", "data", "doc", "FASTA_LIST", "misc", "README", "seq", "sql", "test"] - -postinstallcmds = ["cd %(installdir)s/bin && ln -s fasta%(version_major)s fasta"] - -sanity_check_paths = { - 'files': ["FASTA_LIST", "README"] + ['bin/%s' % x for x in ['map_db']] + - ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf', - 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', - 'ssearch', 'tfastm', 'tfastx']], - 'dirs': ["conf", "data", "doc", "misc", "seq", "sql", "test"] -} - -sanity_check_commands = ["fasta --help"] - -moduleclass = 'bio' From 853958eadb1dea969450ff5d97938343650fabaa Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 16:53:27 +0200 Subject: [PATCH 7729/9987] Update easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb index c131aa586a6..49c98760505 100644 --- a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb @@ -18,6 +18,10 @@ source_urls = ['https://github.com/dstreett/FLASH2/archive/'] sources = ['%(version)s.zip'] checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] +builddependencies = [('binutils', '2.39')] + +dependencies = [('zlib', '1.2.12')] + files_to_copy = [(['flash2'], 'bin')] postinstallcmds = ["cd %(installdir)s/bin && ln -s flash2 flash"] From 0af1701ecb67a134435cb9b8dcbf6b557f6bd414 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 16:53:32 +0200 Subject: [PATCH 7730/9987] Update easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb index 49c98760505..022f8adffbe 100644 --- a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb @@ -12,7 +12,7 @@ resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. """ -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://github.com/dstreett/FLASH2/archive/'] sources = ['%(version)s.zip'] From 5d4a4744238ed35adabb392ff2e34efc2bd4223b Mon Sep 17 00:00:00 2001 From: eylenbt Date: Fri, 16 Jun 2023 16:57:44 +0200 Subject: [PATCH 7731/9987] update FLASH easyconfig recipe --- .../f/FLASH/FLASH-2.2.00-GCCcore-12.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..022f8adffbe --- /dev/null +++ b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'FLASH' +version = '2.2.00' + +homepage = 'https://ccb.jhu.edu/software/FLASH/' +description = """FLASH (Fast Length Adjustment of SHort reads) is a very fast +and accurate software tool to merge paired-end reads from next-generation +sequencing experiments. FLASH is designed to merge pairs of reads when the +original DNA fragments are shorter than twice the length of reads. The +resulting longer reads can significantly improve genome assemblies. They can +also improve transcriptome assembly when FLASH is used to merge RNA-seq data. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/dstreett/FLASH2/archive/'] +sources = ['%(version)s.zip'] +checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('zlib', '1.2.12')] + +files_to_copy = [(['flash2'], 'bin')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s flash2 flash"] + +sanity_check_paths = { + 'files': ['bin/flash2', 'bin/flash'], + 'dirs': [], +} + +sanity_check_commands = [ + "flash --help", +] + +moduleclass = 'bio' From 29f42b7b1552ed1f2f9717c7e69f87abcf097c88 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 16 Jun 2023 16:58:11 +0200 Subject: [PATCH 7732/9987] Delete FLASH-2.2.00-foss-2022b.eb --- .../f/FLASH/FLASH-2.2.00-foss-2022b.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb diff --git a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb b/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb deleted file mode 100644 index 022f8adffbe..00000000000 --- a/easybuild/easyconfigs/f/FLASH/FLASH-2.2.00-foss-2022b.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'MakeCp' - -name = 'FLASH' -version = '2.2.00' - -homepage = 'https://ccb.jhu.edu/software/FLASH/' -description = """FLASH (Fast Length Adjustment of SHort reads) is a very fast -and accurate software tool to merge paired-end reads from next-generation -sequencing experiments. FLASH is designed to merge pairs of reads when the -original DNA fragments are shorter than twice the length of reads. The -resulting longer reads can significantly improve genome assemblies. They can -also improve transcriptome assembly when FLASH is used to merge RNA-seq data. -""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -source_urls = ['https://github.com/dstreett/FLASH2/archive/'] -sources = ['%(version)s.zip'] -checksums = ['1e54b2dd7d21ca3e0595a3ffdd27ef3098f88c4de5b9302ec5ea074b49b79960'] - -builddependencies = [('binutils', '2.39')] - -dependencies = [('zlib', '1.2.12')] - -files_to_copy = [(['flash2'], 'bin')] - -postinstallcmds = ["cd %(installdir)s/bin && ln -s flash2 flash"] - -sanity_check_paths = { - 'files': ['bin/flash2', 'bin/flash'], - 'dirs': [], -} - -sanity_check_commands = [ - "flash --help", -] - -moduleclass = 'bio' From dd01feadfd624e116e6c25f748a87fa18ab6eb94 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Fri, 16 Jun 2023 17:17:40 +0200 Subject: [PATCH 7733/9987] adding easyconfigs: seqtk-1.4-GCC-12.2.0.eb --- .../s/seqtk/seqtk-1.4-GCC-12.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-1.4-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.4-GCC-12.2.0.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.4-GCC-12.2.0.eb new file mode 100644 index 00000000000..d0845fed4d2 --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.4-GCC-12.2.0.eb @@ -0,0 +1,35 @@ +## +# created by Thomas Eylenbosch +## + +easyblock = 'ConfigureMake' + +name = 'seqtk' +version = '1.4' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d124604ec24f29ed14ce127426ab90e0f3a2c0280c80d1a3ff8b1c09feede19c'] + +dependencies = [('zlib', '1.2.12')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BINDIR=%(installdir)s/bin/' + +sanity_check_paths = { + 'files': ['bin/seqtk'], + 'dirs': [], +} + +moduleclass = 'bio' From 1fa00999204ab0473f622b916cdb7f06c06ff5a1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 16 Jun 2023 18:15:25 +0200 Subject: [PATCH 7734/9987] adding easyconfigs: cuDNN-8.9.2.26-CUDA-12.1.1.eb --- .../c/cuDNN/cuDNN-8.9.2.26-CUDA-12.1.1.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.1.1.eb new file mode 100644 index 00000000000..8fba5b522d0 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.1.1.eb @@ -0,0 +1,40 @@ +name = 'cuDNN' +version = '8.9.2.26' +versionsuffix = '-CUDA-%(cudaver)s' +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN is tied to specific to CUDA versions, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +local_cuda_major = '12' + +source_urls = [ + 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%(cudnnarch)s/' +] +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = [{ + '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '4f5e5bd01570c4805b93fb199f8bb6f8475d016948c55abf48fed9ffe89d13e5', + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '898d00c82f9ad8797bd6f6c639327b320a38fa4aeebfb2b3fbb2db0d38f7e1b0', + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'ccafd7d15c2bf26187d52d79d9ccf95104f4199980f5075a7c1ee3347948ce32', +}] + +dependencies = [('CUDA', '12.1.1')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From a4a7cb611ac83df9b0a30e51f399f34185f81eae Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 16 Jun 2023 18:15:13 +0100 Subject: [PATCH 7735/9987] Patch description typo fix --- easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_cmake_release.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_cmake_release.patch b/easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_cmake_release.patch index b860b707aee..7c57b511a1b 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_cmake_release.patch +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.7_fix_cmake_release.patch @@ -1,4 +1,4 @@ -remove CMAKE_BUILD_TYPE check (beacuse it is set to EasyBuildRelease to avoid -O3 optimization flag) +remove CMAKE_BUILD_TYPE check (because it is set to EasyBuildRelease to avoid -O3 optimization flag) original patch by B. Hajgato - (Free University Brussels - VUB) ported to PSI4 1.3.1 by Kenneth Hoste (HPC-UGent) ported to PSI4 1.7 by Neil Douglas (neil.douglas@york.ac.uk) From 12a7e6438f3c4009c04cf95d179d6d567093dbf7 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 16 Jun 2023 12:42:18 -0700 Subject: [PATCH 7736/9987] plinkliftover --- .../plinkliftover-0.3.0-foss-2022b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/plinkliftover/plinkliftover-0.3.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/plinkliftover/plinkliftover-0.3.0-foss-2022b.eb b/easybuild/easyconfigs/p/plinkliftover/plinkliftover-0.3.0-foss-2022b.eb new file mode 100644 index 00000000000..5d149fa5722 --- /dev/null +++ b/easybuild/easyconfigs/p/plinkliftover/plinkliftover-0.3.0-foss-2022b.eb @@ -0,0 +1,47 @@ +# EasyBuild EasyConfig +# +# Fred Hutch Cancer Center - Seattle Washington US +# +# John Dey +easyblock = 'PythonBundle' + +name = 'plinkliftover' +version = '0.3.0' + +homepage = 'https://github.com/milescsmith/plinkliftover' +description = """PLINKLiftOver is a utility enabling liftOver to work on genomics files from PLINK, + allowing one to update the coordinates from one genome reference version to another.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('typer', '0.4.1', { + 'checksums': ['5646aef0d936b2c761a10393f0384ee6b5c7fe0bb3e5cd710b17134ca1d99cff'], + }), + ('rich', '10.16.2', { + 'checksums': ['720974689960e06c2efdb54327f8bf0cdbdf4eae4ad73b6c94213cad405c371b'], + }), + (name, version, { + 'checksums': ['fa38546f0c92def1ecf454c34a1044597f3b7025d3142a9e2dcc1c0976aa16ae'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' From 7638a9d9fce0399ee5c08670fddc607bfa64d896 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Mon, 19 Jun 2023 08:53:51 +0100 Subject: [PATCH 7737/9987] fix checksum --- easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb index e55370d1275..a45e9eb8eb6 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb @@ -20,7 +20,7 @@ patches = [ ] checksums = [ '85a2772a148d57423a909fd91f3f9b068ae393b161510e78e7a824fbe3997366', # v1.7.tar.gz - '130fefba44d7856e3f4359b3f75be11b5e1f1a4b8b4a9115933d2b4a742aea68', # PSI4-1.3.1_fix_cmake_release.patch + 'a8af68947fb4d632d16adb3341b90990d9129d3fe9a28dee733b67bcd2aeff08', # PSI4-1.3.1_fix_cmake_release.patch '064dcf60e74e0c449f77bb6e4dcf4b3338edad7d9a046089ecc2979aed1a00f9', # PSI4-1.7_fix_snsmp2_version.patch ] From 7dcc8b66d0ad65beceac36f93d93f3892db1bf59 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 19 Jun 2023 08:30:37 +0000 Subject: [PATCH 7738/9987] adding easyconfigs: Pysam-0.21.0-GCC-12.2.0.eb --- .../p/Pysam/Pysam-0.21.0-GCC-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100755 easybuild/easyconfigs/p/Pysam/Pysam-0.21.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.21.0-GCC-12.2.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.21.0-GCC-12.2.0.eb new file mode 100755 index 00000000000..abaae145a96 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.21.0-GCC-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.21.0' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8b0c0d1d621892a0acea3d3dbf27564353b088d5bf6ee68852b1b8f3a408ccdf'] + +dependencies = [ + ('Python', '3.10.8'), + ('ncurses', '6.3'), + ('cURL', '7.86.0'), + ('XZ', '5.2.7'), +] + +# https://github.com/pysam-developers/pysam/issues/1146#issuecomment-1309421979 +preinstallopts = """export CFLAGS="-fPIC $CFLAGS" && """ +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' From 7c1ed506d3e4aaf7f1deac953595771adefcb971 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 19 Jun 2023 08:34:30 +0000 Subject: [PATCH 7739/9987] adding easyconfigs: pyfaidx-0.7.2.1-GCCcore-12.2.0.eb --- .../pyfaidx/pyfaidx-0.7.2.1-GCCcore-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.2.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.2.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a236fced155 --- /dev/null +++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.7.2.1-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pyfaidx' +version = '0.7.2.1' + +homepage = 'https://pypi.python.org/pypi/pyfaidx' +description = "pyfaidx: efficient pythonic random access to fasta subsequences" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['30f0d20a9e3d53353fb20eb69b7e22e6f01a53ed4f21b3e17dd408f0be5051a0'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/faidx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["faidx --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From a75dca8328a1e0dbebcdbfdb8899808a30deb5cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 19 Jun 2023 10:45:15 +0200 Subject: [PATCH 7740/9987] adding easyconfigs: torchaudio-0.12.0-foss-2022a-PyTorch-1.12.0.eb --- ...haudio-0.12.0-foss-2022a-PyTorch-1.12.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchaudio/torchaudio-0.12.0-foss-2022a-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/t/torchaudio/torchaudio-0.12.0-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.12.0-foss-2022a-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..07889b645b2 --- /dev/null +++ b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.12.0-foss-2022a-PyTorch-1.12.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'torchaudio' +version = '0.12.0' +local_pytorch_version = '1.12.0' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/audio' +description = """ Data manipulation and transformation for audio signal +processing, powered by PyTorch """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'audio', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] + +checksums = [None] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', local_pytorch_version), + ('SoX', '14.4.2'), + ('FFmpeg', '4.4.2'), +] + +preinstallopts = 'USE_FFMPEG=1' +installopts = '--no-use-pep517' + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From b7f92d85ea82cdf1c76c705716699b19ad470b42 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Jun 2023 11:48:40 +0200 Subject: [PATCH 7741/9987] fix version string of Z3 in Demystify v0.0.17 --- .../easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb index 7e1167c2acd..ee305c91e29 100644 --- a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -19,7 +19,7 @@ dependencies = [ ('Python', '3.8.6'), ('PySAT', '0.1.7.dev1'), ('SciPy-bundle', '2020.11'), - ('Z3', '4.8.10', '-Python-%(pyver)s'), + ('Z3', '4.8.10'), ] use_pip = True From 076a39e19c67475177c5cd3ae0b441df2c574c4a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Jun 2023 11:49:29 +0200 Subject: [PATCH 7742/9987] set download_dep_fail in Demystify v0.0.17 --- easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb index ee305c91e29..356c7a33d87 100644 --- a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -23,6 +23,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True moduleclass = 'math' From a5eb091480afd8f37c46aa480ebb1bab85a6a8fd Mon Sep 17 00:00:00 2001 From: eylenbt Date: Mon, 19 Jun 2023 11:50:05 +0200 Subject: [PATCH 7743/9987] adding easyconfigs: edlib-1.3.9-GCC-12.2.0.eb, pyspoa-0.0.9-GCC-12.2.0.eb, spoa-4.0.7-GCC-12.2.0.eb --- .../e/edlib/edlib-1.3.9-GCC-12.2.0.eb | 22 ++++++++ .../p/pyspoa/pyspoa-0.0.9-GCC-12.2.0.eb | 52 +++++++++++++++++++ .../s/spoa/spoa-4.0.7-GCC-12.2.0.eb | 29 +++++++++++ 3 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-12.2.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-12.2.0.eb new file mode 100644 index 00000000000..0be9e7fb15e --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-12.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'edlib' +version = '1.3.9' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766'] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9-GCC-12.2.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9-GCC-12.2.0.eb new file mode 100644 index 00000000000..ff7e7b177e9 --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.9-GCC-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonPackage' + +name = 'pyspoa' +version = '0.0.9' + +homepage = 'https://github.com/nanoporetech/pyspoa' +description = "Python bindings to spoa." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +sources = [ + { + 'source_urls': ['https://github.com/nanoporetech/pyspoa/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'pyspoa-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/USCiLab/cereal/archive/'], + 'download_filename': '3e4d1b8.tar.gz', + 'filename': 'cereal-20200423.tar.gz', + }, +] +patches = ['pyspoa-0.0.8_use-spoa-dep.patch'] +checksums = [ + {'pyspoa-0.0.9.tar.gz': '30b883b8dfc2355a6062f9f848e825f7ffac169657190d797cf17b4314d588fe'}, + {'cereal-20200423.tar.gz': '284cd14c1e60b36c966bcc8ce650d0b798b8a836d6c379e021e0da0dbe6ddf38'}, + {'pyspoa-0.0.8_use-spoa-dep.patch': 'a98c82ae8346b48952b171675f9df7ab1c95ea5421afcf5bcd778c01c5ee5a52'}, +] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.8'), + ('pybind11', '2.10.3'), + ('spoa', '4.0.7'), +] + +download_dep_fail = True + +preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " +# strip out cmake requirements, since we provide that as proper dependency +preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " + +use_pip = True + +options = {'modulename': 'spoa'} + +sanity_pip_check = True + +sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-12.2.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-12.2.0.eb new file mode 100644 index 00000000000..abf4a21b04e --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-4.0.7-GCC-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '4.0.7' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] +sources = ['spoa-v%(version)s.tar.gz'] +checksums = ['f7a8cd039e4aabea1481e123387fedaa8f87e55418a3649408a615f5c6b1b9a4'] + +builddependencies = [('CMake', '3.24.3')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a', 'lib/pkgconfig/spoa-1.pc'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +moduleclass = 'bio' From 3886f8fc729a8d1e9469739a88d3aa0d21377cd9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Jun 2023 12:20:25 +0200 Subject: [PATCH 7744/9987] use legacy fortran standard in DaliLite v4.1 --- easybuild/easyconfigs/d/DaliLite/DaliLite-4.1-gompi-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DaliLite/DaliLite-4.1-gompi-2021a.eb b/easybuild/easyconfigs/d/DaliLite/DaliLite-4.1-gompi-2021a.eb index 89757de6ef6..4c7cd1ce6a2 100644 --- a/easybuild/easyconfigs/d/DaliLite/DaliLite-4.1-gompi-2021a.eb +++ b/easybuild/easyconfigs/d/DaliLite/DaliLite-4.1-gompi-2021a.eb @@ -29,7 +29,7 @@ dependencies = [ _make_home = "HOME=%(builddir)s/%(name)s.v%(version)s" prebuildopts = "make clean %s &&" % _make_home -buildopts = 'FC=${FC} FC_MPI=${MPIF90} CFLAGS="${FCFLAGS} -fallow-argument-mismatch" ' +buildopts = 'FC=${FC} FC_MPI=${MPIF90} CFLAGS="${FCFLAGS} -std=legacy -fallow-argument-mismatch" ' buildopts += 'CC="${CC} ${CFLAGS}" CC_MPI=${MPICC} ' + _make_home # Installation From 865a15432b9c253f5709f4adc4aac98b773d1459 Mon Sep 17 00:00:00 2001 From: vsc10054 Date: Mon, 19 Jun 2023 14:34:38 +0200 Subject: [PATCH 7745/9987] adding easyconfigs: pygmo-2.18.0-foss-2022a.eb, pagmo-2.18.0-foss-2022a.eb --- .../p/pagmo/pagmo-2.18.0-foss-2022a.eb | 36 ++++++++++++ .../p/pygmo/pygmo-2.18.0-foss-2022a.eb | 56 +++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2022a.eb b/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2022a.eb new file mode 100644 index 00000000000..8b32a6f297f --- /dev/null +++ b/easybuild/easyconfigs/p/pagmo/pagmo-2.18.0-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'pagmo' +version = '2.18.0' + +homepage = 'https://esa.github.io/pagmo2' +description = "pagmo is a C++ scientific library for massively parallel optimization." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/esa/pagmo2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5ad40bf3aa91857a808d6b632d9e1020341a33f1a4115d7a2b78b78fd063ae31'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('tbb', '2021.5.0'), + ('Eigen', '3.4.0'), + ('NLopt', '2.7.1'), +] + +configopts = "-DPAGMO_WITH_EIGEN3=ON -DPAGMO_WITH_NLOPT=ON -DPAGMO_BUILD_TESTS=ON" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libpagmo.%s' % SHLIB_EXT], + 'dirs': ['include/pagmo', 'lib/cmake/pagmo'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2022a.eb b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2022a.eb new file mode 100644 index 00000000000..235eb433fa9 --- /dev/null +++ b/easybuild/easyconfigs/p/pygmo/pygmo-2.18.0-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakePythonPackage' + +name = 'pygmo' +version = '2.18.0' + +homepage = 'https://esa.github.io/pygmo2' +description = "pygmo is a scientific Python library for massively parallel optimization." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/esa/pygmo2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9f081cc973297894af09f713f889870ac452bfb32b471f9f7ba08a5e0bb9a125'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pybind11', '2.9.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), + ('pagmo', '2.18.0'), + ('matplotlib', '3.5.2'), + ('networkx', '2.8.4'), + ('dill', '0.3.6'), +] + +# make sure that all files are installed in the correct location (-DCMAKE_INSTALL_PREFIX is not enough)... +configopts = "-DPYGMO_INSTALL_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" + +runtest = False + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/pygmo'], +} + +sanity_pip_check = True + +moduleclass = 'lib' From 02a73f09affb53f5aae9bf6f6270c8d311f635ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 19 Jun 2023 16:12:59 +0200 Subject: [PATCH 7746/9987] add CUDA version --- ...0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchaudio/torchaudio-0.12.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/t/torchaudio/torchaudio-0.12.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.12.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..32638151e0a --- /dev/null +++ b/easybuild/easyconfigs/t/torchaudio/torchaudio-0.12.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonPackage' + +name = 'torchaudio' +version = '0.12.0' +local_pytorch_version = '1.12.0' +versionsuffix = '-PyTorch-' + local_pytorch_version + '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pytorch/audio' +description = """ Data manipulation and transformation for audio signal +processing, powered by PyTorch """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/pytorch', + 'repo_name': 'audio', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] + +checksums = [None] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), + ('SoX', '14.4.2'), + ('FFmpeg', '4.4.2'), +] + +preinstallopts = 'USE_FFMPEG=1' +installopts = '--no-use-pep517' + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From e56b158e3aeb7ef97741dfd5e89aafe56315675a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 19 Jun 2023 17:35:21 +0200 Subject: [PATCH 7747/9987] Update easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb Co-authored-by: SebastianAchilles --- .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb index fa5e68e2a05..376073c6808 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2022b.eb @@ -28,7 +28,7 @@ sources = [ ] checksums = [ {'q-e-qe-7.2.tar.gz': 'b348a4a7348b66a73545d9ca317a2645755c98d343c1cfe8def475ad030808c0'}, - {'qe-gipaw-7.2.tar.gz': '2c202f1c94c1800c663622b0b7d685d4472b6e5fb150bdb3854f39caab7f39ce'}, + {'qe-gipaw-7.2.tar.gz': '3375e6e8242b9d0a1ebf9ff9ac1111f4cc5c95d3f654bc2534c396b3b4e59a2f'}, {'wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, ] From b301c0c90b5b572a884e4131e4d24f72d01c9c06 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 19 Jun 2023 17:35:26 +0200 Subject: [PATCH 7748/9987] Update easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb Co-authored-by: SebastianAchilles --- .../q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb index 0039b43162f..8b78a44b1f6 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-intel-2022b.eb @@ -28,7 +28,7 @@ sources = [ ] checksums = [ {'q-e-qe-7.2.tar.gz': 'b348a4a7348b66a73545d9ca317a2645755c98d343c1cfe8def475ad030808c0'}, - {'qe-gipaw-7.2.tar.gz': '2c202f1c94c1800c663622b0b7d685d4472b6e5fb150bdb3854f39caab7f39ce'}, + {'qe-gipaw-7.2.tar.gz': '3375e6e8242b9d0a1ebf9ff9ac1111f4cc5c95d3f654bc2534c396b3b4e59a2f'}, {'wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, ] From 61b4ff10210966afc0ee349c32f490990337bde9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 19 Jun 2023 16:43:33 +0000 Subject: [PATCH 7749/9987] adding easyconfigs: CNVkit-0.9.10-foss-2022b-R-4.2.2.eb --- .../CNVkit-0.9.10-foss-2022b-R-4.2.2.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.10-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.10-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.10-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..66c165e9b21 --- /dev/null +++ b/easybuild/easyconfigs/c/CNVkit/CNVkit-0.9.10-foss-2022b-R-4.2.2.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'CNVkit' +version = '0.9.10' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/etal/cnvkit' +description = """A command-line toolkit and Python library for detecting copy + number variants and alterations genome-wide from high-throughput sequencing.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('scikit-learn', '1.2.1'), + ('Biopython', '1.81'), + ('matplotlib', '3.7.0'), + ('networkx', '3.0'), + ('Pillow', '9.4.0'), + ('Pysam', '0.21.0'), + ('PyYAML', '6.0'), + ('pyfaidx', '0.7.2.1'), + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), +] + +exts_list = [ + ('reportlab', '3.6.8', { + 'checksums': ['dc7657fcb0bc3e485c3c869a44dddb52d711356a01a456664b7bef827222c982'], + }), + ('pomegranate', '0.14.8', { + 'checksums': ['2296651290482dd53204ffaaaea267ceee057ce1b3ef1f9d9793febe66d6693d'], + }), + (name, version, { + 'modulename': 'cnvlib', + # workflow test disabled for now during build - directory available for later running + # 'postinstallcmds': ['cd test/ && make'], + 'postinstallcmds': ['cp -a test %(installdir)s'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/etal/cnvkit/archive/'], + 'checksums': ['56739496f1f59511661107e662d81e5fd8af413571e853b0a1b34d882a19349a'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cnvkit.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cnvkit.py --help', +] + +moduleclass = 'bio' From dd15bf482861c4d7f26e43e672247361c8e4b2b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 19 Jun 2023 20:58:30 +0200 Subject: [PATCH 7750/9987] rename cellpose to Cellpose + fix homepage/description --- .../Cellpose-2.2.2-foss-2022a.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/c/{cellpose/cellpose-2.2.2-foss-2022a.eb => Cellpose/Cellpose-2.2.2-foss-2022a.eb} (93%) diff --git a/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb b/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a.eb similarity index 93% rename from easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb rename to easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a.eb index d3c7a6ebd25..ccb478c890b 100644 --- a/easybuild/easyconfigs/c/cellpose/cellpose-2.2.2-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a.eb @@ -2,11 +2,11 @@ # Author: Denis Kristak easyblock = 'PythonBundle' -name = 'cellpose' +name = 'Cellpose' version = '2.2.2' -homepage = 'https://cellpose.readthedocs.io' -description = "cellpose is an anatomical segmentation algorithm" +homepage = 'https://www.cellpose.org' +description = """a generalist algorithm for cellular segmentation""" toolchain = {'name': 'foss', 'version': '2022a'} From ae170262d421cef65ec18cc042d360a83e47bb56 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 19 Jun 2023 19:01:47 +0000 Subject: [PATCH 7751/9987] Use PMIx 4.2.4 in 2023a toolchain --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb | 2 +- ...x-4.2.3-GCCcore-12.3.0.eb => PMIx-4.2.4-GCCcore-12.3.0.eb} | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/PMIx/{PMIx-4.2.3-GCCcore-12.3.0.eb => PMIx-4.2.4-GCCcore-12.3.0.eb} (93%) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb index 0339a0bd0c4..f54e9e48c72 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb @@ -32,7 +32,7 @@ dependencies = [ ('libevent', '2.1.12'), ('UCX', '1.14.1'), ('libfabric', '1.18.0'), - ('PMIx', '4.2.3'), + ('PMIx', '4.2.4'), ('UCC', '1.2.0'), ] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.4-GCCcore-12.3.0.eb similarity index 93% rename from easybuild/easyconfigs/p/PMIx/PMIx-4.2.3-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/p/PMIx/PMIx-4.2.4-GCCcore-12.3.0.eb index 0495a0ed3ed..611c34c2b5f 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.4-GCCcore-12.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'PMIx' -version = '4.2.3' +version = '4.2.4' homepage = 'https://pmix.org/' description = """Process Management for Exascale Environments @@ -21,7 +21,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['c3d9d6885ae39c15627a86dc4718e050baf604acda71b8b9e2ee3b12ad5c2d2a'] +checksums = ['c4699543f2278d3a78bdac72b4b2da9cd92d11d18478d66522b8991764b021c8'] builddependencies = [('binutils', '2.40')] From 3ec503648bcdad515611f78bc63c3d976929456f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 20 Jun 2023 01:23:59 +0200 Subject: [PATCH 7752/9987] Tweak perl-bundle yet more --- .../Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index caa33fdfd35..350f4e317e9 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1992,7 +1992,7 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], 'checksums': ['f161f4297efadbed79c8b096a75951784fc5ccd3170bd32866a19e5c6876d13f'], }), - ('IO::Compress', '2.204', { + ('IO::Compress::Zip', '2.204', { 'runtest': False, # Problem with indirect dependency DBD::Pg 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], From 68587ed86eab816c2f1d76aa01ebf6db117fce87 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 20 Jun 2023 01:26:40 +0200 Subject: [PATCH 7753/9987] Remove old UCC from GCCcore 12.3.0 --- .../u/UCC/UCC-1.1.0-GCCcore-12.3.0.eb | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.3.0.eb deleted file mode 100644 index fee0812efd6..00000000000 --- a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'UCC' -version = '1.1.0' - -homepage = 'https://www.openucx.org/' -description = """UCC (Unified Collective Communication) is a collective -communication operations API and library that is flexible, complete, and -feature-rich for current and emerging programming models and runtimes. -""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -patches = ['UCC-%(version)s-multiple_component_paths.patch'] -checksums = [ - {'v1.1.0.tar.gz': '74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'}, - {'UCC-1.1.0-multiple_component_paths.patch': '3081d0f694331daa4a88a0fa3fb54b9a918015248ae5eb7b3157b924abd31bee'}, -] - -builddependencies = [ - ('binutils', '2.40'), - ('Autotools', '20220317'), -] - -dependencies = [ - ('UCX', '1.14.1'), -] - -preconfigopts = "./autogen.sh && " - -sanity_check_paths = { - 'files': ['bin/ucc_info'], - 'dirs': ['include', 'lib'] -} - -sanity_check_commands = ["ucc_info -c"] - -moduleclass = 'lib' From 94b2a3c1d3f5773b8dab13c5878a920e138f8645 Mon Sep 17 00:00:00 2001 From: satishk Date: Tue, 20 Jun 2023 10:11:17 +0200 Subject: [PATCH 7754/9987] adding easyconfigs: Gurobi-10.0.1-GCCcore-11.3.0.eb --- .../g/Gurobi/Gurobi-10.0.1-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..16411d9bf00 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +name = 'Gurobi' +version = '10.0.1' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +patches = ['%(name)s-9.0.1_use-eb-python-gurobi-shell.patch'] +checksums = [ + {'gurobi10.0.1_linux64.tar.gz': 'a0b551156df2c94107b3428cae278716a0a6c913f63ac132573852b9725b6c59'}, + {'Gurobi-9.0.1_use-eb-python-gurobi-shell.patch': + 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01'}, +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license is mandatory for installation +# use EB_GUROBI_LICENSE_FILE environment variable, or +# uncomment and modify the following variable: +# license_file = '/path/to/my-license-file' +license_file = HOME + '/licenses/%(name)s.lic' + + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' From 65da748cfe2916210d80083cc6b1c41058d049f9 Mon Sep 17 00:00:00 2001 From: eylenbt Date: Tue, 20 Jun 2023 10:55:04 +0200 Subject: [PATCH 7755/9987] adding easyconfigs: ncbi-vdb-3.0.5-gompi-2022b.eb --- .../n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2022b.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2022b.eb diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2022b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2022b.eb new file mode 100644 index 00000000000..05f1f30ef7d --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2022b.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'ncbi-vdb' +version = '3.0.5' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['a32672d7f76507a77ceb29f023855eaf5bf4d150ddd21b55c013b499f3b83735'] + +builddependencies = [ + ('Perl', '5.36.0', '-minimal'), + ('Python', '3.10.8', '-bare'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('HDF5', '1.14.0'), + ('libxml2', '2.10.3'), + ('bzip2', '1.0.8'), +] + +configopts = "-DHDF5_INCDIR=$EBROOTHDF5/include -DHDF5_LIBDIR=$EBROOTHDF5/lib " +configopts += "-DXML2_INCDIR=$EBROOTLIBXML2/include -DXML2_LIBDIR=$EBROOTLIBXML2/lib " + +sanity_check_paths = { + 'files': ['include/ncbi/ncbi.h', 'include/ncbi/vdb-blast.h'] + + [('lib/libncbi-%s.%s' % (k, e)) for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' From 93b41ea9632a9968f9f0c5a37070c50939275864 Mon Sep 17 00:00:00 2001 From: "Lasse R. Mark" Date: Tue, 20 Jun 2023 12:37:46 +0200 Subject: [PATCH 7756/9987] Added config for Nextflow 23.04.2 --- .../n/Nextflow/Nextflow-23.04.2.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb new file mode 100644 index 00000000000..4ab073f1904 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb @@ -0,0 +1,33 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '23.04.2' + +homepage = 'https://www.%(namelower)s.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-all'] +checksums = ['d7a6c3eacc400648da85c0a56866ce39d240b3aab4c88ee470180f4dcf1847b4'] + +dependencies = [('Java', '11')] + +install_cmd = "mkdir -p %(installdir)s/bin &&" +install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" +install_cmd += "cd %(installdir)s/bin && ln -s %(namelower)s-%(version)s-all %(namelower)s &&" +install_cmd += "chmod +x %(installdir)s/bin/%(namelower)s-%(version)s-all" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-%(version)s-all', 'bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' \ No newline at end of file From d171b2132ff821a3224c476e02471bac3142da2c Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 20 Jun 2023 12:24:26 +0100 Subject: [PATCH 7757/9987] adding easyconfigs: GCTA-1.94.1-gfbf-2022a.eb --- .../g/GCTA/GCTA-1.94.1-gfbf-2022a.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCTA/GCTA-1.94.1-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.1-gfbf-2022a.eb b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.1-gfbf-2022a.eb new file mode 100644 index 00000000000..3579318b3ca --- /dev/null +++ b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.1-gfbf-2022a.eb @@ -0,0 +1,70 @@ +# Author: Jasper Grimm (UoY) +# Updated to 1.94.1. J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMakeCp' + +name = 'GCTA' +version = '1.94.1' +_plink_commit = '3744540' + +homepage = 'https://yanglab.westlake.edu.cn/software/gcta/' +description = """ +GCTA (Genome-wide Complex Trait Analysis) is a software package, which was + initially developed to estimate the proportion of phenotypic variance explained + by all genome-wide SNPs for a complex trait but has been extensively extended + for many other analyses of data from genome-wide association studies (GWASs). +""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/jianyangqt/gcta/archive'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/zhilizheng/plink-ng/archive'], + 'download_filename': '%s.tar.gz' % _plink_commit, + 'filename': 'plink-ng-%s.tar.gz' % _plink_commit, + 'extract_cmd': "tar xzvf %%s --strip-components 1 -C gcta-%s/submods/plink-ng" % version, + }, +] +patches = [ + 'GCTA-1.94.0beta_allow-BLAS-selection.patch', + 'GCTA-1.94.0beta_lapack-compatibility.patch', +] +checksums = [ + {'GCTA-1.94.1.tar.gz': 'd38841587bef016d7885cc1b3287d7ed0373bd370674130e814e2c5e6a90bfbf'}, + {'plink-ng-3744540.tar.gz': 'a7c70c237d49d64fc1668ced373036c09b41d7c61d0b8b24b47e2fb76474455d'}, + {'GCTA-1.94.0beta_allow-BLAS-selection.patch': '320a5d82d12cf453f1396b228723ac18dc98e32bc459394dd4d712fc16b24747'}, + {'GCTA-1.94.0beta_lapack-compatibility.patch': '643282a2e2c02fc683431b673a4623a498129870431481d33d33e19a509026ce'}, +] + +builddependencies = [ + ('CMake', '3.23.1'), + # Eigen and SpectrA are header-only C++ libraries + ('Eigen', '3.4.0'), + ('SpectrA', '1.0.1'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('SQLite', '3.38.3'), + ('zstd', '1.5.2'), + ('GSL', '2.7'), +] + +preconfigopts = 'EIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include SPECTRA_LIB=$EBROOTSPECTRA/include' +preconfigopts += ' BOOST_LIB=$EBROOTBOOST/include ' + +files_to_copy = [(['gcta64'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/gcta64'], + 'dirs': [], +} + +sanity_check_commands = ["gcta64 | grep -e 'Analysis started'"] + +moduleclass = 'bio' From d7d68bf05342f15d555145b96a2ab76aeeecdec9 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 20 Jun 2023 12:34:19 +0100 Subject: [PATCH 7758/9987] adding easyconfigs: gengetopt-2.23-GCCcore-11.3.0.eb --- .../gengetopt-2.23-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..09ec20b23bb --- /dev/null +++ b/easybuild/easyconfigs/g/gengetopt/gengetopt-2.23-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'gengetopt' +version = '2.23' + +homepage = 'https://www.gnu.org/software/gengetopt/gengetopt.html' +description = "Gengetopt is a tool to write command line option parsing code for C programs." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['b941aec9011864978dd7fdeb052b1943535824169d2aa2b0e7eae9ab807584ac'] + +builddependencies = [ + ('binutils', '2.38'), + ('makeinfo', '6.8'), +] + +sanity_check_paths = { + 'files': ['bin/gengetopt'], + 'dirs': ['share'], +} + +sanity_check_commands = ["gengetopt --help"] + +moduleclass = 'tools' From 16bfa20bf2cfe259f75f3e1cd74671cf3ff150db Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Jun 2023 15:02:26 +0200 Subject: [PATCH 7759/9987] {bio}[foss/2022a] Cellpose v2.2.2 w/ Python 3.10.4 + CUDA 11.7.0 --- .../Cellpose-2.2.2-foss-2022a-CUDA-11.7.0.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..d0f93dfe418 --- /dev/null +++ b/easybuild/easyconfigs/c/Cellpose/Cellpose-2.2.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,61 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Cellpose' +version = '2.2.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.cellpose.org' +description = """a generalist algorithm for cellular segmentation""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), + ('SciPy-bundle', '2022.05'), + ('PyQt5', '5.15.5'), + ('PyTorch', '1.12.0', versionsuffix), + ('PyQtGraph', '0.13.3'), + ('numba', '0.56.4', versionsuffix), + ('tqdm', '4.64.0'), + ('imagecodecs', '2022.9.26'), + ('scikit-build', '0.15.0'), +] + +use_pip = True + +exts_list = [ + ('tifffile', '2023.4.12', { + 'checksums': ['2fa99f9890caab919d932a0acaa9d0f5843dc2ef3594e212963932e20713badd'], + }), + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + ('fastremap', '1.13.5', { + 'preinstallopts': "export PBR_VERSION=1.2.3 && ", + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/seung-lab/fastremap/archive/'], + 'checksums': ['ee0e9e798e9f331b7c46e98768735a42bb6e287b3aa56c31c322ba585f4036b7'], + }), + ('roifile', '2023.5.12', { + 'checksums': ['32eeba0d9ad52cc249d6a234b737c1808a6c5d7d9baae6453709eb74222b3433'], + }), + (name, version, { + # OpenCV dependency provides opencv-contrib-python (equivalent to opencv-python-headless) + 'preinstallopts': "sed -i 's/opencv-python-headless/opencv-contrib-python/g' setup.py && ", + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'use_pip_extras': 'gui', + 'checksums': ['f21773d364d117eb6fd84c3fb27375845ef373793139ef1668c15491294a3b47'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 74fb07b0c385bec63109d891a2cf28bb49e2ad3b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 20 Jun 2023 13:57:29 +0000 Subject: [PATCH 7760/9987] adding easyconfigs: GLIMPSE-2.0.0-GCC-12.2.0.eb --- .../g/GLIMPSE/GLIMPSE-2.0.0-GCC-12.2.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..57eca82043d --- /dev/null +++ b/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-12.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'MakeCp' + +name = 'GLIMPSE' +version = '2.0.0' + +homepage = 'https://github.com/odelaneau/GLIMPSE' +description = "GLIMPSE2 is a set of tools for phasing and imputation for low-coverage sequencing datasets" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/odelaneau/GLIMPSE/archive/'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/odelaneau/', + 'repo_name': 'GLIMPSE', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, +}] +checksums = [None] + +builddependencies = [ + ('git', '2.38.1', '-nodocs'), +] + +dependencies = [ + ('Boost', '1.81.0'), + ('bzip2', '1.0.8'), + ('cURL', '7.86.0'), + ('HTSlib', '1.17'), + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), +] + +prebuildopts = 'ls */makefile | xargs sed -i "s/^CXXFLAG=.*/CXXFLAG=${CXXFLAGS}/g" && ' +prebuildopts += 'ls */makefile | xargs sed -i "s/^LDFLAG=.*/LDFLAG=${CXXFLAGS}/g" && ' +buildopts = 'CXX="$CXX" HTSSRC=${EBROOTHTSLIB} HTSLIB_LIB="-lhts -lcurl" BOOST_INC=$EBROOTBOOST/include ' +buildopts += 'BOOST_LIB_IO="-lboost_iostreams" BOOST_LIB_PO="-lboost_program_options" ' +buildopts += 'BOOST_LIB_SE="-lboost_serialization" ' + +files_to_copy = [(['*/bin/*'], 'bin')] + +local_binaries = ['GLIMPSE2_chunk', 'GLIMPSE2_concordance', 'GLIMPSE2_ligate', + 'GLIMPSE2_phase', 'GLIMPSE2_split_reference'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ["%s --help" % x for x in local_binaries] + +moduleclass = 'bio' From 745cf9a34c728a4c40dca93a8b867f51f2c4eb91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 20 Jun 2023 16:38:10 +0200 Subject: [PATCH 7761/9987] adding easyconfigs: duplex-tools-0.3.3-foss-2022a.eb --- .../duplex-tools-0.3.3-foss-2022a.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2022a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2022a.eb new file mode 100644 index 00000000000..3696742010d --- /dev/null +++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2022a.eb @@ -0,0 +1,74 @@ +# Author: Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) +easyblock = 'PythonBundle' + +name = 'duplex-tools' +version = '0.3.3' + +homepage = 'https://github.com/nanoporetech/duplex-tools' +description = """ +Duplex Tools contains a set of utilities for dealing with Duplex sequencing data. Tools are provided + to identify and prepare duplex pairs for basecalling by Dorado (recommended) and Guppy, and for + recovering simplex basecalls from incorrectly concatenated pairs. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +_minimap2_ver = '2.24' +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('edlib', '1.3.9'), + ('minimap2', _minimap2_ver), + ('python-parasail', '1.3.3'), + ('Pysam', '0.20.0'), + ('tqdm', '4.64.0'), + ('Arrow', '8.0.0'), + ('h5py', '3.7.0'), + ('pod5-file-format', '0.1.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mappy', _minimap2_ver, { + 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('iso8601', '1.1.0', { + 'checksums': ['32811e7b81deee2063ea6d2e94f8819a86d1f3811e49d23623a41fa832bef03f'], + }), + ('vbz-h5py-plugin', '1.0.1', { + 'source_tmpl': 'vbz_h5py_plugin-%(version)s.tar.gz', + 'checksums': ['c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341'], + }), + ('pyfastx', '1.1.0', { + # PYPI source tarball is incomplete, causes ImportErrors + # see https://github.com/lmdu/pyfastx/issues/60 + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/lmdu/%(name)s/archive'], + 'checksums': ['b9974b21d21067350694ea37d33f99647255546b90eee8addeb74c8d18d824e8'], + }), + (name, version, { + 'source_tmpl': 'duplex_tools-%(version)s.tar.gz', + 'checksums': ['883e0a6610d14328a640b6a31eaef90592d2967cda68db0547a4d99924281300'], + }), +] + +_bins = ['dorado_stereo.sh', 'duplex_tools', 'minimap2.py', 'natsort', 'pyfastx'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'dorado_stereo.sh -h', + 'duplex_tools --help', + 'pyfastx --help', +] + +moduleclass = 'bio' From c11b7673198c45ea3530bc3fc2529095653b8c19 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Jun 2023 19:16:18 +0200 Subject: [PATCH 7762/9987] adding easyconfigs: dorado-0.3.0-foss-2022a-CUDA-11.7.0.eb --- .../dorado-0.3.0-foss-2022a-CUDA-11.7.0.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.3.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/dorado/dorado-0.3.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..6c8bfc91292 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.3.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,67 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), + ('HDF5', '1.12.2'), + ('zstd', '1.5.2'), + ('HTSlib', '1.15.1'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " + +configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " +configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " +configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib -DHTSLIB_LIBRARIES=hts " +# add -pthread flag (in addition to -lpthread) to avoid linking error: +# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' +configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" ' + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' From dcb64ecec55d4a57fe7204b33edcf2c4c175d513 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 20 Jun 2023 16:12:06 -0700 Subject: [PATCH 7763/9987] {bio}[GCC-12.2.0] easel 0.48 --- .../e/easel/easel-0.48-GCC-12.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb b/easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb new file mode 100644 index 00000000000..03d88e42cb3 --- /dev/null +++ b/easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb @@ -0,0 +1,38 @@ +# easybuild easyconfig +# +# Fred Hutchinson Cancer Center +# John Dey +# +easyblock = 'ConfigureMake' + +name = 'easel' +version = '0.48' + +homepage = 'https://www.wxwidgets.org' +description = """Easel supports computational analysis of biological sequences using probabilistic models.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +github_name = 'EddyRivasLab' +source_urls = ['https://github.com/EddyRivasLab/easel/archive/refs/tags'] +sources = [SOURCE_TAR_GZ] +checksums = ['c5d055acbe88fa834e81424a15fc5fa54ac787e35f2ea72d4ffd9ea2c1aa29cf'] + +builddependencies = [ + ('Autoconf', '2.71'), +] + +dependencies = [ +] + +preconfigopts = 'autoconf && ' +buildopts = '&& make check' + +sanity_check_paths = { + 'files': ['bin/easel'], + 'dirs': [] +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' From 5715ab217a2bc006dae78e282cb3f02db6e323ba Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 20 Jun 2023 16:21:19 -0700 Subject: [PATCH 7764/9987] fix homepage --- easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb b/easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb index 03d88e42cb3..0a8134009c9 100644 --- a/easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb @@ -8,7 +8,7 @@ easyblock = 'ConfigureMake' name = 'easel' version = '0.48' -homepage = 'https://www.wxwidgets.org' +homepage = 'https://bioeasel.org/' description = """Easel supports computational analysis of biological sequences using probabilistic models.""" toolchain = {'name': 'GCC', 'version': '12.2.0'} From f9a0fd920b19a1d32edc221765344485e45c2bb9 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 20 Jun 2023 18:48:36 -0700 Subject: [PATCH 7765/9987] HMMER update for gompi-2022b --- .../h/HMMER/HMMER-3.3.2-gompi-2022b.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022b.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022b.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022b.eb new file mode 100644 index 00000000000..e5a79c3da27 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.2-gompi-2022b.eb @@ -0,0 +1,79 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# Updated by: Filip Kružík (INUITS) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.2' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_perl.patch'] +checksums = [ + {'hmmer-3.3.2.tar.gz': '92fee9b5efe37a5276352d3502775e7c46e9f7a0ee45a331eacb2a0cac713c69'}, + {'HMMER-3.3.2_fix_perl.patch': '9f04123ca33118549b94adf6a07df9ab1cb7b680dd706d7b76ee0794f2def22d'}, +] + +builddependencies = [ + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From eb8c913a79059caf6510989421ef2fd47f89dd97 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 20 Jun 2023 18:52:26 -0700 Subject: [PATCH 7766/9987] checksums! --- easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb b/easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb index 0a8134009c9..3191b688777 100644 --- a/easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/e/easel/easel-0.48-GCC-12.2.0.eb @@ -13,8 +13,8 @@ description = """Easel supports computational analysis of biological sequences u toolchain = {'name': 'GCC', 'version': '12.2.0'} -github_name = 'EddyRivasLab' -source_urls = ['https://github.com/EddyRivasLab/easel/archive/refs/tags'] +github_account = 'EddyRivasLab' +source_urls = ['https://github.com/%(github_account)s/easel/archive/refs/tags'] sources = [SOURCE_TAR_GZ] checksums = ['c5d055acbe88fa834e81424a15fc5fa54ac787e35f2ea72d4ffd9ea2c1aa29cf'] From ebaadb0625afbce49f9b769b7eb1b6aed8326fe7 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 20 Jun 2023 19:19:42 -0700 Subject: [PATCH 7767/9987] Issue #4282 --- .../x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb index eff2403c88c..23fbad63969 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb @@ -11,7 +11,10 @@ description = "Perl binding for libxml2" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -builddependencies = [('binutils', '2.39')] +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] dependencies = [ ('Perl', '5.36.0'), From 77a516e945af444247f35341e879abfa67411bee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 21 Jun 2023 08:06:10 +0200 Subject: [PATCH 7768/9987] adding easyconfigs: MaxQuant-2.4.2.0.eb --- .../m/MaxQuant/MaxQuant-2.4.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb diff --git a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb new file mode 100644 index 00000000000..adf1b1c001e --- /dev/null +++ b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'Tarball' + +name = 'MaxQuant' +version = '2.4.2.0' + +homepage = 'https://maxquant.org/maxquant' +description = """MaxQuant is a quantitative proteomics software package designed for analyzing large + mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling + techniques as well as label-free quantification are supported.""" + +toolchain = SYSTEM + +# requires registration at https://www.maxquant.org/download_asset/maxquant/latest +sources = ['%(name)s_%(version)s.zip'] +checksums = ['03d8acc28ff8d71772d72d3da493e508553bd30f52f09c979bb9fcdb090e7799'] + +dependencies = [('dotNET-SDK', '3.1.300', '-linux-x64')] + +sanity_check_paths = { + 'files': ['%(name)s.exe', 'bin/%(name)sCmd.exe', 'bin/%(name)sGui.exe'], + 'dirs': [], +} + +sanity_check_commands = [ + ("dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.exe --version 2>&1 | grep -q 2.4.1.0", ''), # reports wrong version + ("dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.exe --help 2>&1 | grep -q USAGE", '')] + +modaliases = { + 'maxquantcmd': 'dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.exe', + 'maxquantgui': 'dotnet $EBROOTMAXQUANT/bin/%(name)sGui.exe', +} + +modloadmsg = """ +To run MaxQuant in command-line mode: maxquantcmd + in GUI mode: maxquantgui +""" + +moduleclass = 'bio' From 19644ee6a7f0dfc48a82f8130f0d5699574a59e6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 21 Jun 2023 08:26:00 +0200 Subject: [PATCH 7769/9987] Fix formatting --- easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb index adf1b1c001e..d8c25cbdce3 100644 --- a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb +++ b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb @@ -22,8 +22,9 @@ sanity_check_paths = { } sanity_check_commands = [ - ("dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.exe --version 2>&1 | grep -q 2.4.1.0", ''), # reports wrong version - ("dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.exe --help 2>&1 | grep -q USAGE", '')] + ("dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.exe --version 2>&1 | grep -q 2.4.1.0", ''), # reports wrong version + ("dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.exe --help 2>&1 | grep -q USAGE", '') +] modaliases = { 'maxquantcmd': 'dotnet $EBROOTMAXQUANT/bin/%(name)sCmd.exe', From de84fd5f27628b7c0f0485ae1723459e057edac8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 21 Jun 2023 09:39:24 +0200 Subject: [PATCH 7770/9987] Better sync version between ncbi-vdb and SRA-Toolkit --- .../easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb index 8e6ec5a05e4..eea86dfb250 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb @@ -31,7 +31,7 @@ builddependencies = [ dependencies = [ ('Java', '11', '', SYSTEM), ('OpenSSL', '1.1', '', SYSTEM), - ('ncbi-vdb', '3.0.5'), + ('ncbi-vdb', version), ('bzip2', '1.0.8'), ('file', '5.40'), ('HDF5', '1.10.7'), From c3318ca9685a5ba6c6f903f50bf1ab3dc3d6a1a5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 09:43:10 +0200 Subject: [PATCH 7771/9987] strip out excess spaces in (build)dependencies in SRA-Toolkit + ncbi-vdb 3.0.5 easyconfigs --- .../n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2021a.eb | 8 +++---- .../SRA-Toolkit-3.0.5-gompi-2021a.eb | 22 +++++++++---------- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2021a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2021a.eb index 73172c451c9..e1590e7094e 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2021a.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.5-gompi-2021a.eb @@ -15,15 +15,15 @@ sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ checksums = ['a32672d7f76507a77ceb29f023855eaf5bf4d150ddd21b55c013b499f3b83735'] builddependencies = [ - ('Perl', '5.32.1', '-minimal'), + ('Perl', '5.32.1', '-minimal'), ('Python', '3.9.5', '-bare'), - ('CMake', '3.20.1'), + ('CMake', '3.20.1'), ] dependencies = [ - ('HDF5', '1.10.7'), + ('HDF5', '1.10.7'), ('libxml2', '2.9.10'), - ('bzip2', '1.0.8'), + ('bzip2', '1.0.8'), ] configopts = "-DHDF5_INCDIR=$EBROOTHDF5/include -DHDF5_LIBDIR=$EBROOTHDF5/lib " diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb index eea86dfb250..e38914e188e 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb @@ -21,22 +21,22 @@ checksums = [ ] builddependencies = [ - ('CMake', '3.20.1'), - ('flex', '2.6.4'), - ('Bison', '3.7.6'), - ('Perl', '5.32.1', '-minimal'), + ('CMake', '3.20.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('Perl', '5.32.1', '-minimal'), ('Python', '3.9.5', '-bare'), ] dependencies = [ - ('Java', '11', '', SYSTEM), - ('OpenSSL', '1.1', '', SYSTEM), + ('Java', '11', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), ('ncbi-vdb', version), - ('bzip2', '1.0.8'), - ('file', '5.40'), - ('HDF5', '1.10.7'), - ('libxml2', '2.9.10'), - ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('file', '5.40'), + ('HDF5', '1.10.7'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), ] configopts = '-DVDB_INCDIR="$EBROOTNCBIMINVDB/include" -DVDB_LIBDIR="$EBROOTNCBIMINVDB/lib" ' From cc92d11a6f23aaa8be4b14e90947ff2d178fc7e8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 21 Jun 2023 09:49:40 +0200 Subject: [PATCH 7772/9987] Strip out excess spaces --- .../s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb index e38914e188e..9759bd16641 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.5-gompi-2021a.eb @@ -25,11 +25,11 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.7.6'), ('Perl', '5.32.1', '-minimal'), - ('Python', '3.9.5', '-bare'), + ('Python', '3.9.5', '-bare'), ] dependencies = [ - ('Java', '11', '', SYSTEM), + ('Java', '11', '', SYSTEM), ('OpenSSL', '1.1', '', SYSTEM), ('ncbi-vdb', version), ('bzip2', '1.0.8'), From bb903f7952f95493facedd3d9d794bc068f19316 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 09:58:13 +0200 Subject: [PATCH 7773/9987] add missing libglvnd dependency for OpenMM 7.4.1 with fosscuda/2019b --- .../o/OpenMM/OpenMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb index be94dc54b60..a0837a8fe3a 100644 --- a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.4.1-fosscuda-2019b-Python-3.7.4.eb @@ -34,6 +34,7 @@ dependencies = [ ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), ('SWIG', '4.0.1'), + ('libglvnd', '1.2.0'), ] configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" From 16d73f2dfcadce78c2e55396c0ae5538e4cb5bd0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 21 Jun 2023 10:05:07 +0200 Subject: [PATCH 7774/9987] add newline character at end of file --- easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb index 4ab073f1904..aab831581f7 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb @@ -30,4 +30,4 @@ sanity_check_commands = [ "%(namelower)s help", ] -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' From 7a3ac30fbe2e1bd33c4b3005959e2419c10fe879 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 21 Jun 2023 10:38:18 +0200 Subject: [PATCH 7775/9987] adding easyconfigs: FragPipe-20.0-Java-11.eb --- .../f/FragPipe/FragPipe-20.0-Java-11.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragPipe/FragPipe-20.0-Java-11.eb diff --git a/easybuild/easyconfigs/f/FragPipe/FragPipe-20.0-Java-11.eb b/easybuild/easyconfigs/f/FragPipe/FragPipe-20.0-Java-11.eb new file mode 100644 index 00000000000..f8ecd6e78dd --- /dev/null +++ b/easybuild/easyconfigs/f/FragPipe/FragPipe-20.0-Java-11.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'FragPipe' +version = '20.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://fragpipe.nesvilab.org' +description = """FragPipe is a Java Graphical User Interface (GUI) for a suite of computational + tools enabling comprehensive analysis of mass spectrometry-based proteomics data.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/Nesvilab/%(name)s/releases/download/%(version)s/'] +sources = ['%(name)s-%(version)s.zip'] +checksums = ['0d77db85ae26c190a915823e1c68238f3a19533810734b008564b2a8d85d1bd6'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'lib/%(namelower)s-%(version)s.jar'], + 'dirs': [], +} + +sanity_check_commands = [("%(namelower)s -h | grep -q v%(version)s")] + +moduleclass = 'bio' From 1d31e0fa1f30f4f77e265b149c0328fbd1f7040c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 21 Jun 2023 09:03:42 +0000 Subject: [PATCH 7776/9987] adding easyconfigs: IQ-TREE-2.2.2.6-gompi-2022a.eb, LSD2-2.4.1-GCCcore-12.2.0.eb, IQ-TREE-2.2.2.6-gompi-2022b.eb --- .../i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb | 57 +++++++++++++++++++ .../i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb | 57 +++++++++++++++++++ .../l/LSD2/LSD2-2.4.1-GCCcore-12.2.0.eb | 38 +++++++++++++ 3 files changed, 152 insertions(+) create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb new file mode 100644 index 00000000000..16b1ef14e9f --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb @@ -0,0 +1,57 @@ +# Updated to v2.1.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.2.2.6' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'IQ-TREE-2.1.2_use_EB_LSD2.patch', + 'IQ-TREE-2.2.1_fix-mpi.patch', +] +checksums = [ + {'v2.2.2.6.tar.gz': 'f5d10c033f2ed1c81bb473f572c7a9fe72a275a48e2e93ad74e5f1c3d32fa8b9'}, + {'IQ-TREE-2.1.2_use_EB_LSD2.patch': 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816'}, + {'IQ-TREE-2.2.1_fix-mpi.patch': '9ead6808efd11d4c01dd265cca6094cffd6377746d3b2fc84b43d2faeee0777c'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('Boost', '1.79.0'), + ('LSD2', '2.3'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = [ + "iqtree2 --help", + "mkdir -p $TMPDIR/{test-omp,test-mpi}", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy", + "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb new file mode 100644 index 00000000000..3605d94c4f9 --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb @@ -0,0 +1,57 @@ +# Updated to v2.1.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.2.2.6' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'IQ-TREE-2.1.2_use_EB_LSD2.patch', + 'IQ-TREE-2.2.1_fix-mpi.patch', +] +checksums = [ + {'v2.2.2.6.tar.gz': 'f5d10c033f2ed1c81bb473f572c7a9fe72a275a48e2e93ad74e5f1c3d32fa8b9'}, + {'IQ-TREE-2.1.2_use_EB_LSD2.patch': 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816'}, + {'IQ-TREE-2.2.1_fix-mpi.patch': '9ead6808efd11d4c01dd265cca6094cffd6377746d3b2fc84b43d2faeee0777c'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('Boost', '1.81.0'), + ('LSD2', '2.4.1'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = [ + "iqtree2 --help", + "mkdir -p $TMPDIR/{test-omp,test-mpi}", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy", + "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2626f47769c --- /dev/null +++ b/easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +# Updated to v2.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'LSD2' +version = '2.4.1' + +homepage = 'https://github.com/tothuhien/lsd2' +description = "Least-squares methods to estimate rates and dates from phylogenies" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'tothuhien' + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v.%(version)s.tar.gz'] +patches = ['%(name)s-1.9.7_fix_cmake_to_build_lib_and_binary.patch'] +checksums = [ + {'v.2.4.1.tar.gz': '3d0921c96edb8f30498dc8a27878a76d785516043fbede4a72eefd84b5955458'}, + {'LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch': + '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From e2ed24e19151d6d288991d673242fbfbb8f1ba9d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 21 Jun 2023 09:10:50 +0000 Subject: [PATCH 7777/9987] adding easyconfigs: GLIMPSE-2.0.0-GCC-10.3.0.eb --- .../g/GLIMPSE/GLIMPSE-2.0.0-GCC-10.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-10.3.0.eb new file mode 100644 index 00000000000..8ae4197452c --- /dev/null +++ b/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-10.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'MakeCp' + +name = 'GLIMPSE' +version = '2.0.0' + +homepage = 'https://github.com/odelaneau/GLIMPSE' +description = "GLIMPSE2 is a set of tools for phasing and imputation for low-coverage sequencing datasets" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/odelaneau/GLIMPSE/archive/'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/odelaneau/', + 'repo_name': 'GLIMPSE', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, +}] +checksums = [None] + +builddependencies = [ + ('git', '2.32.0', '-nodocs'), +] + +dependencies = [ + ('Boost', '1.76.0'), + ('bzip2', '1.0.8'), + ('cURL', '7.76.0'), + ('HTSlib', '1.12'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), +] + +prebuildopts = 'ls */makefile | xargs sed -i "s/^CXXFLAG=.*/CXXFLAG=${CXXFLAGS}/g" && ' +prebuildopts += 'ls */makefile | xargs sed -i "s/^LDFLAG=.*/LDFLAG=${CXXFLAGS}/g" && ' +buildopts = 'CXX="$CXX" HTSSRC=${EBROOTHTSLIB} HTSLIB_LIB="-lhts -lcurl" BOOST_INC=$EBROOTBOOST/include ' +buildopts += 'BOOST_LIB_IO="-lboost_iostreams" BOOST_LIB_PO="-lboost_program_options" ' +buildopts += 'BOOST_LIB_SE="-lboost_serialization" ' + +files_to_copy = [(['*/bin/*'], 'bin')] + +local_binaries = ['GLIMPSE2_chunk', 'GLIMPSE2_concordance', 'GLIMPSE2_ligate', + 'GLIMPSE2_phase', 'GLIMPSE2_split_reference'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ["%s --help" % x for x in local_binaries] + +moduleclass = 'bio' From 0f2364934aa26a3e929420669651468dc803cccd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 21 Jun 2023 11:13:48 +0200 Subject: [PATCH 7778/9987] stick to older Pysam --- .../easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2022a.eb b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2022a.eb index 3696742010d..bed3911b036 100644 --- a/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2022a.eb +++ b/easybuild/easyconfigs/d/duplex-tools/duplex-tools-0.3.3-foss-2022a.eb @@ -22,7 +22,7 @@ dependencies = [ ('edlib', '1.3.9'), ('minimap2', _minimap2_ver), ('python-parasail', '1.3.3'), - ('Pysam', '0.20.0'), + ('Pysam', '0.19.1'), ('tqdm', '4.64.0'), ('Arrow', '8.0.0'), ('h5py', '3.7.0'), From bd77e4c64122f012021bf3e1e94dacd9b626f76d Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 21 Jun 2023 10:50:37 +0100 Subject: [PATCH 7779/9987] Unify AutoDock, AutoGrid easyconfigs into AutoDockSuite --- .../AutoDockSuite-4.2.6-GCCcore-8.3.0.eb} | 19 +++++++----- .../AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb | 30 ------------------- 2 files changed, 11 insertions(+), 38 deletions(-) rename easybuild/easyconfigs/a/{AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb => AutoDockSuite/AutoDockSuite-4.2.6-GCCcore-8.3.0.eb} (53%) delete mode 100644 easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/AutoDockSuite/AutoDockSuite-4.2.6-GCCcore-8.3.0.eb similarity index 53% rename from easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb rename to easybuild/easyconfigs/a/AutoDockSuite/AutoDockSuite-4.2.6-GCCcore-8.3.0.eb index efaf7902dcb..c1f2898ba56 100644 --- a/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.6-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/AutoDockSuite/AutoDockSuite-4.2.6-GCCcore-8.3.0.eb @@ -1,30 +1,33 @@ -# Currently there is not an EasyBlock to unify AutoDock and AutoGrid so this is a happy medium until then easyblock = 'ConfigureMake' -name = 'AutoDock' +name = 'AutoDockSuite' version = '4.2.6' homepage = 'https://autodock.scripps.edu/' description = """ - AutoDock is a suite of automated docking tools. It is designed to - predict how small molecules, such as substrates or drug candidates, bind to + AutoDock is a suite of automated docking tools. It is designed to + predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['https://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/'] -sources = ['%(namelower)ssuite-%(version)s-src.tar.gz'] +source_urls = ['https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10'] +sources = ['%(namelower)s-%(version)s-src.tar.gz'] checksums = ['4b24ce4baf216a5e1a6a79bb664eeed684aed17cede64ff0061aa1bcc17874c4'] builddependencies = [('binutils', '2.32')] -start_dir = 'autodock' +preconfigopts = ['cd %s &&' % x for x in ['autodock', 'autogrid']] +prebuildopts = preconfigopts +preinstallopts = preconfigopts sanity_check_paths = { - 'files': ["bin/autodock4"], + 'files': ["bin/autodock4", "bin/autogrid4"], 'dirs': [] } +sanity_check_commands = ['%s %s' % (x, y) for x in ['autodock4', 'autogrid4'] for y in ['--help', '--version']] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb deleted file mode 100644 index 73f2a7a7985..00000000000 --- a/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.6-GCCcore-8.3.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -# Currently there is not an EasyBlock to unify AutoDock and AutoGrid so this is a happy medium until then -easyblock = 'ConfigureMake' - -name = 'AutoGrid' -version = '4.2.6' - -homepage = 'https://autodock.scripps.edu/' - -description = """ - AutoDock is a suite of automated docking tools. It is designed to - predict how small molecules, such as substrates or drug candidates, bind to - a receptor of known 3D structure. -""" - -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} - -source_urls = ['https://autodock.scripps.edu/downloads/autodock-registration/tars/dist426/'] -sources = ['autodocksuite-%(version)s-src.tar.gz'] -checksums = ['4b24ce4baf216a5e1a6a79bb664eeed684aed17cede64ff0061aa1bcc17874c4'] - -builddependencies = [('binutils', '2.32')] - -start_dir = 'autogrid' - -sanity_check_paths = { - 'files': ["bin/autogrid4"], - 'dirs': [] -} - -moduleclass = 'tools' From 114df41a1e7a97c3084d050d406fd203a0f348f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 13:41:28 +0200 Subject: [PATCH 7780/9987] don't require custom sanity_check_paths in easyconfigs using PerlBundle --- test/easyconfigs/easyconfigs.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4e9b5508fd7..54e38e4faa8 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1124,10 +1124,11 @@ def test_pr_sanity_check_paths(self): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # some generic easyblocks already have a decent customised sanity_check_paths, - # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle, PythonBundle & PythonPackage; + # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle, PerlBundle, + # PythonBundle & PythonPackage; # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. whitelist = ['BuildEnv', 'CargoPythonPackage', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', - 'JuliaBundle', 'ModuleRC', 'PythonBundle', 'PythonPackage', 'Toolchain'] + 'JuliaBundle', 'ModuleRC', 'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co, From 17a2671e22613e1359fe755e6aa2edf36c1333e9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 21 Jun 2023 14:20:48 +0200 Subject: [PATCH 7781/9987] fix homepage --- easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.2.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.2.0.eb index c45ff08ae47..cac48a1006e 100644 --- a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-12.2.0.eb @@ -6,7 +6,7 @@ name = "FASTA" version = "36.3.8i" local_version_date = '14-Nov-2020' -homepage = 'http://fasta.bioch.virginia.edu' +homepage = 'https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml' description = """The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.""" From b2681489b8addcf57a53b8bdc5c07e43f6446746 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 21 Jun 2023 14:21:44 +0200 Subject: [PATCH 7782/9987] Add download_instructions --- easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb index d8c25cbdce3..edf1480c621 100644 --- a/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb +++ b/easybuild/easyconfigs/m/MaxQuant/MaxQuant-2.4.2.0.eb @@ -10,7 +10,12 @@ description = """MaxQuant is a quantitative proteomics software package designed toolchain = SYSTEM -# requires registration at https://www.maxquant.org/download_asset/maxquant/latest +download_instructions = """ +To download the MaxQuant source tarball, register at: + https://www.maxquant.org/download_asset/maxquant/latest +You should receive a unique download URL via email. +""" + sources = ['%(name)s_%(version)s.zip'] checksums = ['03d8acc28ff8d71772d72d3da493e508553bd30f52f09c979bb9fcdb090e7799'] From 3f462c0f1a2b8d8a05e487f355dbd3f53876d706 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 21 Jun 2023 14:56:48 +0200 Subject: [PATCH 7783/9987] Revert faulty sanity check command --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 2 -- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb | 2 -- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb | 2 -- 3 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb index 30ebb82f4de..f5661b09387 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -45,6 +45,4 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["tiffinfo -h"] - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb index e87e43c6521..433c867d0d7 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb @@ -45,6 +45,4 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["tiffinfo -h"] - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb index a7672a0b44e..e6481f975cf 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb @@ -45,6 +45,4 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["tiffinfo -h"] - moduleclass = 'lib' From ebcee4e782302ef36346f99c5a94851b4a6e2ff6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 21 Jun 2023 13:04:11 +0000 Subject: [PATCH 7784/9987] Move to GCC --- .../s/SortMeRNA/SortMeRNA-2.1-GCC-9.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-GCC-9.3.0.eb b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-GCC-9.3.0.eb new file mode 100644 index 00000000000..710019073e2 --- /dev/null +++ b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-GCC-9.3.0.eb @@ -0,0 +1,37 @@ +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# # +easyblock = 'ConfigureMake' + +name = 'SortMeRNA' +version = '2.1' + +homepage = 'https://bioinfo.lifl.fr/RNA/sortmerna/' +description = "SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads." + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/biocore/%(namelower)s/archive/'] +sources = ['%(version)s.tar.gz'] +# Patch for double includes of header files in Makefile.in +patches = ['%(name)s-%(version)s_Makefile.in.patch'] +checksums = [ + '44a3b29570e339da235acc00a35cde18f4fff03b7087b0fa8100f6c3826385d5', # 2.1.tar.gz + '0137ee3d4c583f3c4a4b18aadd1029e8a9cf0ff1748d364d993b82482777d4d5', # SortMeRNA-2.1_Makefile.in.patch +] + +sanity_check_paths = { + 'files': ['bin/indexdb_rna', 'bin/%(namelower)s'], + 'dirs': ['include', '%(namelower)s'], +} + +moduleclass = 'bio' From 2cbf83c124fbebc00f79e3d5c09ddc697915f6c7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 21 Jun 2023 13:09:52 +0000 Subject: [PATCH 7785/9987] Remove obsolete download_dep_fail --- easybuild/easyconfigs/p/pastml/pastml-1.9.34-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pastml/pastml-1.9.34-foss-2021a.eb b/easybuild/easyconfigs/p/pastml/pastml-1.9.34-foss-2021a.eb index 017de129f45..8f83b335609 100644 --- a/easybuild/easyconfigs/p/pastml/pastml-1.9.34-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pastml/pastml-1.9.34-foss-2021a.eb @@ -16,7 +16,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From c6c52aa405a1d1e8c780916a0f1d4b4e26ee24b5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 21 Jun 2023 14:34:47 +0100 Subject: [PATCH 7786/9987] delete foss version --- .../s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb diff --git a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb deleted file mode 100644 index 3aac61c0081..00000000000 --- a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2020a.eb +++ /dev/null @@ -1,37 +0,0 @@ -# # -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Cedric Laczny , Fotis Georgatos -# License:: MIT/GPL -# $Id$ -# -# This work implements a part of the HPCBIOS project and is a component of the policy: -# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html -# # -easyblock = 'ConfigureMake' - -name = 'SortMeRNA' -version = '2.1' - -homepage = 'https://bioinfo.lifl.fr/RNA/sortmerna/' -description = "SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads." - -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = ['https://github.com/biocore/%(namelower)s/archive/'] -sources = ['%(version)s.tar.gz'] -# Patch for double includes of header files in Makefile.in -patches = ['%(name)s-%(version)s_Makefile.in.patch'] -checksums = [ - '44a3b29570e339da235acc00a35cde18f4fff03b7087b0fa8100f6c3826385d5', # 2.1.tar.gz - '0137ee3d4c583f3c4a4b18aadd1029e8a9cf0ff1748d364d993b82482777d4d5', # SortMeRNA-2.1_Makefile.in.patch -] - -sanity_check_paths = { - 'files': ['bin/indexdb_rna', 'bin/%(namelower)s'], - 'dirs': ['include', '%(namelower)s'], -} - -moduleclass = 'bio' From 02ebe40c8d9bcb61f404b9e37cb51e11c01addb8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 21 Jun 2023 15:47:43 +0200 Subject: [PATCH 7787/9987] adding easyconfigs: Geant4-11.1.2-GCC-11.3.0.eb and patches: Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch --- .../c/CLHEP/CLHEP-2.4.6.2-GCC-11.3.0.eb | 28 ++++++++++ .../g/Geant4-data/Geant4-data-11.1.eb | 55 +++++++++++++++++++ .../g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb | 42 ++++++++++++++ ...ata_env_vars_from_Geant4-data_module.patch | 24 ++++++++ 4 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.1.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/Geant4/Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.2-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..d185341cba2 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.2-GCC-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.6.2' + +homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] +sources = [SOURCELOWER_TGZ] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.1.eb b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.1.eb new file mode 100644 index 00000000000..887025db76b --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.1.eb @@ -0,0 +1,55 @@ +easyblock = 'Tarball' +name = 'Geant4-data' +version = '11.1' # version should somewhat match the Geant4 version it should be used in + +homepage = 'https://geant4.web.cern.ch/' +description = """Datasets for Geant4.""" + +toolchain = SYSTEM + +# Pick up the correct sets and versions from cmake/Modules/G4DatasetDefinitions.cmake +# in the Geant source +local_datasets = [ + ('G4NDL', '4.7', 'G4NDL', 'G4NEUTRONHPDATA'), # NDL + ('G4EMLOW', '8.2', 'G4EMLOW', 'G4LEDATA'), # Low energy electromagnetics + ('PhotonEvaporation', '5.7', 'G4PhotonEvaporation', 'G4LEVELGAMMADATA'), # Photon evaporation + ('RadioactiveDecay', '5.6', 'G4RadioactiveDecay', 'G4RADIOACTIVEDATA'), # Radioisotopes + ('G4SAIDDATA', '2.0', 'G4SAIDDATA', 'G4SAIDXSDATA'), # SAID + ('G4PARTICLEXS', '4.0', 'G4PARTICLEXS', 'G4PARTICLEXSDATA'), # Particle XS - replaces Neutron XS + ('G4PII', '1.3', 'G4PII', 'G4PIIDATA'), # PII + ('RealSurface', '2.2', 'G4RealSurface', 'G4REALSURFACEDATA'), # Optical Surfaces + ('G4SAIDDATA', '2.0', 'G4SAIDDATA', 'G4SAIDXSDATA'), # SAID + ('G4ABLA', '3.1', 'G4ABLA', 'G4ABLADATA'), # ABLA + ('G4INCL', '1.0', 'G4INCL', 'G4INCLDATA'), # INCL + ('G4ENSDFSTATE', '2.3', 'G4ENSDFSTATE', 'G4ENSDFSTATEDATA'), # ENSDFSTATE + ('G4TENDL', '1.4', 'G4TENDL', 'G4PARTICLEHPDATA'), # TENDL +] + +source_urls = ['https://cern.ch/geant4-data/datasets'] +sources = ['%s.%s.tar.gz' % (x[2], x[1]) for x in local_datasets] +checksums = [ + {'G4NDL.4.7.tar.gz': '7e7d3d2621102dc614f753ad928730a290d19660eed96304a9d24b453d670309'}, + {'G4EMLOW.8.2.tar.gz': '3d7768264ff5a53bcb96087604bbe11c60b7fea90aaac8f7d1252183e1a8e427'}, + {'G4PhotonEvaporation.5.7.tar.gz': '761e42e56ffdde3d9839f9f9d8102607c6b4c0329151ee518206f4ee9e77e7e5'}, + {'G4RadioactiveDecay.5.6.tar.gz': '3886077c9c8e5a98783e6718e1c32567899eeb2dbb33e402d4476bc2fe4f0df1'}, + {'G4SAIDDATA.2.0.tar.gz': '1d26a8e79baa71e44d5759b9f55a67e8b7ede31751316a9e9037d80090c72e91'}, + {'G4PARTICLEXS.4.0.tar.gz': '9381039703c3f2b0fd36ab4999362a2c8b4ff9080c322f90b4e319281133ca95'}, + {'G4PII.1.3.tar.gz': '6225ad902675f4381c98c6ba25fc5a06ce87549aa979634d3d03491d6616e926'}, + {'G4RealSurface.2.2.tar.gz': '9954dee0012f5331267f783690e912e72db5bf52ea9babecd12ea22282176820'}, + {'G4SAIDDATA.2.0.tar.gz': '1d26a8e79baa71e44d5759b9f55a67e8b7ede31751316a9e9037d80090c72e91'}, + {'G4ABLA.3.1.tar.gz': '7698b052b58bf1b9886beacdbd6af607adc1e099fc730ab6b21cf7f090c027ed'}, + {'G4INCL.1.0.tar.gz': '716161821ae9f3d0565fbf3c2cf34f4e02e3e519eb419a82236eef22c2c4367d'}, + {'G4ENSDFSTATE.2.3.tar.gz': '9444c5e0820791abd3ccaace105b0e47790fadce286e11149834e79c4a8e9203'}, + {'G4TENDL.1.4.tar.gz': '4b7274020cc8b4ed569b892ef18c2e088edcdb6b66f39d25585ccee25d9721e0'}, +] + +start_dir = '..' + +modextrapaths = {x[3]: x[0] + x[1] for x in local_datasets} + +sanity_check_paths = { + 'files': [], + 'dirs': [x[0] + x[1] for x in local_datasets], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..ed2d9ab7572 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb @@ -0,0 +1,42 @@ +name = 'Geant4' +version = '11.1.2' + +homepage = 'https://geant4.web.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'Geant4' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = [ + 'Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch', +] +checksums = [ + {'geant4-11.1.2.tar.gz': 'b0d0ca79188f85e5a6a178cf8e5ebde16cfeb30959f8862517daab60e0ae2691'}, + {'Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch': + '3c6a91fc38cf88f0aa09c2410b7c7c4dd1b41b5504cf3a8f3ab8217183ac5ec5'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('expat', '2.4.8'), + # recommended CLHEP version, see https://geant4.web.cern.ch/download/release-notes/notes-v11.1.0.html + ('CLHEP', '2.4.6.2'), + ('Geant4-data', '11.1', '', SYSTEM), +] + +_copts = [ + "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so", + "-DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include", + "-DCLHEP_ROOT_DIR=$EBROOTCLHEP", + "-DGEANT4_INSTALL_DATA=OFF", +] +configopts = ' '.join(_copts) + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch b/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch new file mode 100644 index 00000000000..0dcfcf32a9f --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch @@ -0,0 +1,24 @@ +Make geant4make.sh pick up the data dirs from the Geant4-data module + +Åke Sandgren, 2023-06-21 +diff -ru geant4-11.1.2.orig/cmake/Modules/G4ConfigureGNUMakeHelpers.cmake geant4-11.1.2/cmake/Modules/G4ConfigureGNUMakeHelpers.cmake +--- geant4-11.1.2.orig/cmake/Modules/G4ConfigureGNUMakeHelpers.cmake 2023-06-19 17:14:55.000000000 +0200 ++++ geant4-11.1.2/cmake/Modules/G4ConfigureGNUMakeHelpers.cmake 2023-06-21 13:15:18.015596299 +0200 +@@ -499,11 +499,12 @@ + endif() + + # - Resource file paths +- set(GEANT4_TC_DATASETS ) +- foreach(_ds ${GEANT4_EXPORTED_DATASETS}) +- _g4tc_setenv_command(_dssetenvcmd ${SHELL_FAMILY} ${${_ds}_ENVVAR} ${${_ds}_PATH}) +- set(GEANT4_TC_DATASETS "${GEANT4_TC_DATASETS}${_dssetenvcmd}\n") +- endforeach() ++# Take the env vars from the EB Geant4-data module ++# set(GEANT4_TC_DATASETS ) ++# foreach(_ds ${GEANT4_EXPORTED_DATASETS}) ++# _g4tc_setenv_command(_dssetenvcmd ${SHELL_FAMILY} ${${_ds}_ENVVAR} ${${_ds}_PATH}) ++# set(GEANT4_TC_DATASETS "${GEANT4_TC_DATASETS}${_dssetenvcmd}\n") ++# endforeach() + + set(GEANT4_TC_TOOLS_FONT_PATH "# FREETYPE SUPPORT NOT AVAILABLE") + if(GEANT4_USE_FREETYPE) From 12c43704c95d8de9c272e6d8143ff1d5adef9af9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 21 Jun 2023 16:23:46 +0200 Subject: [PATCH 7788/9987] fix generation of geant4.sh to pick up data dirs from Geant4-data module too. --- .../g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb | 2 +- ...ata_env_vars_from_Geant4-data_module.patch | 30 +++++++++++++++++-- 2 files changed, 29 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb index ed2d9ab7572..afb73b7a296 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb @@ -17,7 +17,7 @@ patches = [ checksums = [ {'geant4-11.1.2.tar.gz': 'b0d0ca79188f85e5a6a178cf8e5ebde16cfeb30959f8862517daab60e0ae2691'}, {'Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch': - '3c6a91fc38cf88f0aa09c2410b7c7c4dd1b41b5504cf3a8f3ab8217183ac5ec5'}, + '822265b7cbcaacdffd28b1094786a3c94122aff63338e514d5d3810cdf9218a6'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch b/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch index 0dcfcf32a9f..ce997291c17 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2_use_data_env_vars_from_Geant4-data_module.patch @@ -1,9 +1,9 @@ -Make geant4make.sh pick up the data dirs from the Geant4-data module +Make geant4make.sh and geant4.sh pick up the data dirs from the Geant4-data module Åke Sandgren, 2023-06-21 diff -ru geant4-11.1.2.orig/cmake/Modules/G4ConfigureGNUMakeHelpers.cmake geant4-11.1.2/cmake/Modules/G4ConfigureGNUMakeHelpers.cmake --- geant4-11.1.2.orig/cmake/Modules/G4ConfigureGNUMakeHelpers.cmake 2023-06-19 17:14:55.000000000 +0200 -+++ geant4-11.1.2/cmake/Modules/G4ConfigureGNUMakeHelpers.cmake 2023-06-21 13:15:18.015596299 +0200 ++++ geant4-11.1.2/cmake/Modules/G4ConfigureGNUMakeHelpers.cmake 2023-06-21 16:07:17.147729642 +0200 @@ -499,11 +499,12 @@ endif() @@ -22,3 +22,29 @@ diff -ru geant4-11.1.2.orig/cmake/Modules/G4ConfigureGNUMakeHelpers.cmake geant4 set(GEANT4_TC_TOOLS_FONT_PATH "# FREETYPE SUPPORT NOT AVAILABLE") if(GEANT4_USE_FREETYPE) +@@ -987,8 +988,8 @@ + + # - Set data paths + set(GEANT4_ENV_DATASETS ) +- _g4tc_setenv_command(_dssetenvcmd ${_shell} GEANT4_DATA_DIR ${GEANT4_DATA_DIR}) +- set(GEANT4_ENV_DATASETS "${GEANT4_ENV_DATASETS}${_dssetenvcmd}\n") ++# _g4tc_setenv_command(_dssetenvcmd ${_shell} GEANT4_DATA_DIR ${GEANT4_DATA_DIR}) ++# set(GEANT4_ENV_DATASETS "${GEANT4_ENV_DATASETS}${_dssetenvcmd}\n") + set(_dssetenvcmd " + # - Variables for individual datasets + # Uncomment the line and edit the path to the dataset if installed in not standard location.") +@@ -1072,10 +1073,10 @@ + + # - Set data paths + set(GEANT4_ENV_DATASETS ) +- _g4tc_setenv_command(_dssetenvcmd ${_shell} GEANT4_DATA_DIR ${GEANT4_DATA_DIRW}) +- set(GEANT4_ENV_DATASETS "${GEANT4_ENV_DATASETS}${_dssetenvcmd}\n") +- set(_dssetenvcmd "FOR /F %%i IN ( \"%GEANT4_DATA_DIR%\" ) DO set \"GEANT4_DATA_DIR=%%~fi\"") +- set(GEANT4_ENV_DATASETS "${GEANT4_ENV_DATASETS}${_dssetenvcmd}\n\n") ++# _g4tc_setenv_command(_dssetenvcmd ${_shell} GEANT4_DATA_DIR ${GEANT4_DATA_DIRW}) ++# set(GEANT4_ENV_DATASETS "${GEANT4_ENV_DATASETS}${_dssetenvcmd}\n") ++# set(_dssetenvcmd "FOR /F %%i IN ( \"%GEANT4_DATA_DIR%\" ) DO set \"GEANT4_DATA_DIR=%%~fi\"") ++# set(GEANT4_ENV_DATASETS "${GEANT4_ENV_DATASETS}${_dssetenvcmd}\n\n") + set(_dssetenvcmd " + rem - Variables for individual datasets + rem Uncomment the line and edit the path to the dataset if installed in not standard location.") From e062959bd1bead29050f32a07e759f19f63fe5d0 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 21 Jun 2023 16:24:02 +0200 Subject: [PATCH 7789/9987] update easyconfig: QuantumESPRESSO-6.6-intel-2020a.eb --- .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb index e121b620371..62fb6813075 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb @@ -18,12 +18,12 @@ source_urls = [ ] sources = [ 'qe-%(version)s-ReleasePack.tgz', - # to be uncommented once qe-gipaw-6.6 is released - # {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}, + {'filename': 'qe-gipaw-%(version)s.tar.gz', 'download_filename': '%(version)s.tar.gz'}, {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz'}, ] checksums = [ 'de6996b9f1bf480bcd0166d24e918f5ff3c8fdb710f59f781bc9d33819280eb5', # qe-6.6-ReleasePack.tgz + '277fbe3bd10cb8f64e0f351a0c2fff1f68fb3ccdeb18107900803f4566661459', # qe-gipaw-6.6.tar.gz '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz ] @@ -35,7 +35,7 @@ dependencies = [ # The third party packages should be installed separately and added as # dependencies. The exception is w90, which is force built -buildopts = 'all gwl xspectra couple epw w90' # gipaw +buildopts = 'all gwl xspectra couple epw gipaw w90' # parallel build tends to fail parallel = 1 From 5c06b15518f97f7ebc08145838bad6d73c4460e5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 16:20:40 +0200 Subject: [PATCH 7790/9987] fix perl shebang for alleleCounter.pl + add extra sanity check command in alleleCount easyconfig --- .../alleleCount-4.2.1-GCC-11.3.0.eb | 25 ++++++++++++------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb index dd4080b2086..69fc3d7f616 100644 --- a/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/a/alleleCount/alleleCount-4.2.1-GCC-11.3.0.eb @@ -21,12 +21,6 @@ source_urls = ['https://github.com/cancerit/%(name)s/archive/v%(version)s'] sources = ['v%(version)s.tar.gz'] checksums = ['dbec2d47fb4fad8ead72f55c4b6e3c02b216cbed285c05617b62e9a38c32e400'] -skipsteps = ['configure'] - -buildopts = "-C c && cd perl && perl Makefile.PL INSTALL_BASE=%(installdir)s " -preinstallopts = "cd perl && " -installopts = " && cd .. && cp -a c/bin/alleleCounter %(installdir)s/bin/" - # HTSlib 1.7 is built, used and removed again in the provided setup script dependencies = [ ('Perl', '5.34.1'), @@ -34,6 +28,12 @@ dependencies = [ ('libdeflate', '1.10'), ] +skipsteps = ['configure'] + +buildopts = "-C c && cd perl && perl Makefile.PL INSTALL_BASE=%(installdir)s " +preinstallopts = "cd perl && " +installopts = " && cd .. && cp -a c/bin/alleleCounter %(installdir)s/bin/" + exts_defaultclass = 'PerlModule' exts_filter = ("perl -e 'require %(ext_name)s'", '') exts_default_options = { @@ -70,12 +70,19 @@ exts_list = [ }), ] +postinstallcmds = ["chmod u+w %(installdir)s/bin/alleleCounter.pl"] + +fix_perl_shebang_for = ['bin/alleleCounter.pl'] + sanity_check_paths = { - 'files': ["bin/alleleCounter", "bin/alleleCounter.pl"], - 'dirs': ["lib/perl5"], + 'files': ['bin/alleleCounter', 'bin/alleleCounter.pl'], + 'dirs': ['lib/perl5'], } -sanity_check_commands = ["alleleCounter --help"] +sanity_check_commands = [ + "alleleCounter --help", + "alleleCounter.pl --help", +] modextrapaths = {'PERL5LIB': ['lib/perl5', 'lib/perl5/site_perl/%(perlver)s']} From c88592f0c6233c66f33034d29d84db7ffffa1765 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 21 Jun 2023 16:41:31 +0200 Subject: [PATCH 7791/9987] Update checksums --- .../x/X11/X11-20230603-GCCcore-12.3.0.eb | 261 ++++++++---------- 1 file changed, 109 insertions(+), 152 deletions(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20230603-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20230603-GCCcore-12.3.0.eb index dac22500934..5b749a4e98d 100644 --- a/easybuild/easyconfigs/x/X11/X11-20230603-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20230603-GCCcore-12.3.0.eb @@ -8,15 +8,6 @@ description = "The X Window System (X11) is a windowing system for bitmap displa toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -source_urls = [ - XORG_LIB_SOURCE, - XORG_PROTO_SOURCE, - 'https://xcb.freedesktop.org/dist/', - 'https://xkbcommon.org/download/', - XORG_DATA_SOURCE + '/xkeyboard-config', - XORG_DATA_SOURCE, -] - builddependencies = [ ('binutils', '2.40'), ('Autotools', '20220317'), @@ -38,6 +29,15 @@ dependencies = [ ('libpciaccess', '0.17'), ] +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + default_easyblock = 'ConfigureMake' default_component_specs = { @@ -46,163 +46,120 @@ default_component_specs = { } components = [ - ('libpthread-stubs', '0.4', { # 2017-03-14 - 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], - }), - ('xorgproto', '2022.2', { # 2022-08-11 - 'checksums': ['da351a403d07a7006d7bdc8dcfc14ddc1b588b38fb81adab9989a8eef605757b'], - }), - ('libXau', '1.0.11', { # 2022-12-08 - 'checksums': ['51a54da42475d4572a0b59979ec107c27dacf6c687c2b7b04e5cf989a7c7e60c'], - }), - ('libXdmcp', '1.1.4', { # 2022-11-19 - 'checksums': ['2ef9653d32e09d1bf1b837d0e0311024979653fe755ad3aaada8db1aa6ea180c'], - }), - ('xcb-proto', '1.15.2', { # 2022-06-17 - 'checksums': ['6b1ed9cd7cf35e37913eeecca37e5b85b14903002942b3e332f321335c27a8eb'], - }), - ('libxcb', '1.15', { # 2022-05-03 - 'checksums': ['1cb65df8543a69ec0555ac696123ee386321dfac1964a3da39976c9a05ad724d'], - }), - ('xtrans', '1.5.0', { # 2023-06-03 - 'checksums': ['48ed850ce772fef1b44ca23639b0a57e38884045ed2cbb18ab137ef33ec713f9'], - }), + ('libpthread-stubs', '0.4'), # 2017-03-14 + ('xorgproto', '2022.2'), # 2022-08-11 + ('libXau', '1.0.11'), # 2022-12-08 + ('libXdmcp', '1.1.4'), # 2022-11-19 + ('xcb-proto', '1.15.2'), # 2022-06-17 + ('libxcb', '1.15'), # 2022-05-03 + ('xtrans', '1.5.0'), # 2023-06-03 ('libxkbcommon', '1.5.0', { # 2023-01-02 'easyblock': 'MesonNinja', 'sources': [SOURCE_TAR_XZ], - 'checksums': ['943c07a1e2198026d8102b17270a1f406e4d3d6bbc4ae105b9e1b82d7d136b39'], 'preconfigopts': '', 'configopts': '-Denable-wayland=false -Denable-docs=false ', }), - ('libX11', '1.8.5', { # 2023-06-01 - 'checksums': ['f1bc56187bee0f830e1179ac5068ac93b78c51ace94eb27702ffb2efd116587b'], - }), - ('libXext', '1.3.5', { # 2022-10-29 - 'checksums': ['1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'], - }), - ('libFS', '1.0.9', { # 2022-08-26 - 'checksums': ['8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'], - }), - ('libICE', '1.1.1', { # 2022-12-08 - 'checksums': ['1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d'], - }), - ('libSM', '1.2.4', { # 2022-12-20 - 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], - }), - ('libXScrnSaver', '1.2.4', { # 2022-12-05 - 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], - }), - ('libXt', '1.3.0', { # 2023-05-09 - 'checksums': ['6da1bfa9dd0ed87430a5ce95b129485086394df308998ebe34d98e378e3dfb33'], - }), - ('libXmu', '1.1.4', { # 2022-10-17 - 'checksums': ['3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'], - }), - ('libXpm', '3.5.16', { # 2023-04-17 - 'checksums': ['e3dfb0fb8c1f127432f2a498c7856b37ce78a61e8da73f1aab165a73dd97ad00'], - }), - ('libXaw', '1.0.15', { # 2023-03-16 - 'checksums': ['59cfed2712cc80bbfe62dd1aacf24f58d74a76dd08329a922077b134a8d8048f'], - }), - ('libXfixes', '6.0.1', { # 2023-04-09 - 'checksums': ['82045da5625350838390c9440598b90d69c882c324ca92f73af9f0e992cb57c7'], - }), - ('libXcomposite', '0.4.6', { # 2022-12-04 - 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], - }), - ('libXrender', '0.9.11', { # 2022-10-22 - 'checksums': ['6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'], - }), - ('libXcursor', '1.2.1', { # 2022-04-03 - 'checksums': ['77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'], - }), - ('libXdamage', '1.1.6', { # 2022-12-04 - 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], - }), - ('libfontenc', '1.1.7', { # 2022-12-08 - 'checksums': ['c103543a47ce5c0200fb1867f32df5e754a7c3ef575bf1fe72187117eac22a53'], - }), - ('libXfont', '1.5.4', { # 2017-11-28 - 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], - }), - ('libXfont2', '2.0.6', { # 2022-08-26 - 'checksums': ['a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'], - }), - ('libXft', '2.3.8', { # 2023-04-17 - 'checksums': ['b7e59f69e0bbabe9438088775f7e5a7c16a572e58b11f9722519385d38192df5'], - }), - ('libXi', '1.8.1', { # 2023-05-04 - 'checksums': ['c80fd200a1190e4406bb4cc6958839d9651638cb47fa546a595d4bebcd3b9e2d'], - }), - ('libXinerama', '1.1.5', { # 2022-10-29 - 'checksums': ['2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'], - }), - ('libXrandr', '1.5.3', { # 2022-11-20 - 'checksums': ['3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e'], - }), - ('libXres', '1.2.2', { # 2022-12-05 - 'checksums': ['918fb33c3897b389a1fbb51571c5c04c6b297058df286d8b48faa5af85e88bcc'], - }), - ('libXtst', '1.2.4', { # 2022-09-27 - 'checksums': ['01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'], - }), - ('libXv', '1.0.12', { # 2022-12-05 - 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], - }), - ('libXvMC', '1.0.13', { # 2022-03-22 - 'checksums': ['e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'], - }), - ('libXxf86dga', '1.1.6', { # 2022-12-05 - 'checksums': ['715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69'], - }), - ('libXxf86vm', '1.1.5', { # 2022-09-27 - 'checksums': ['f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'], - }), - ('libdmx', '1.1.5', { # 2023-06-03 - 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], - }), - ('libxkbfile', '1.1.2', { # 2022-12-08 - 'checksums': ['87faee6d4873c5631e8bb53e85134084b862185da682de8617f08ca18d82e216'], - }), - ('libxshmfence', '1.3.2', { # 2022-12-08 - 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], - }), - ('xcb-util', '0.4.0', { # 2014-10-15 - 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], - }), - ('xcb-util-image', '0.4.1', { # 2022-10-18 - 'checksums': ['0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'], - }), - ('xcb-util-keysyms', '0.4.1', { # 2022-10-19 - 'checksums': ['1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'], - }), - ('xcb-util-renderutil', '0.3.10', { # 2022-10-19 - 'checksums': ['e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'], - }), - ('xcb-util-wm', '0.4.2', { # 2022-10-19 - 'checksums': ['dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'], - }), - ('xcb-util-cursor', '0.1.4', { # 2022-10-18 - 'checksums': ['cc8608ebb695742b6cf84712be29b2b66aa5f6768039528794fca0fa283022bf'], - }), + ('libX11', '1.8.5'), # 2023-06-01 + ('libXext', '1.3.5'), # 2022-10-29 + ('libFS', '1.0.9'), # 2022-08-26 + ('libICE', '1.1.1'), # 2022-12-08 + ('libSM', '1.2.4'), # 2022-12-20 + ('libXScrnSaver', '1.2.4'), # 2022-12-05 + ('libXt', '1.3.0'), # 2023-05-09 + ('libXmu', '1.1.4'), # 2022-10-17 + ('libXpm', '3.5.16'), # 2023-04-17 + ('libXaw', '1.0.15'), # 2023-03-16 + ('libXfixes', '6.0.1'), # 2023-04-09 + ('libXcomposite', '0.4.6'), # 2022-12-04 + ('libXrender', '0.9.11'), # 2022-10-22 + ('libXcursor', '1.2.1'), # 2022-04-03 + ('libXdamage', '1.1.6'), # 2022-12-04 + ('libfontenc', '1.1.7'), # 2022-12-08 + ('libXfont', '1.5.4'), # 2017-11-28 + ('libXfont2', '2.0.6'), # 2022-08-26 + ('libXft', '2.3.8'), # 2023-04-17 + ('libXi', '1.8.1'), # 2023-05-04 + ('libXinerama', '1.1.5'), # 2022-10-29 + ('libXrandr', '1.5.3'), # 2022-11-20 + ('libXres', '1.2.2'), # 2022-12-05 + ('libXtst', '1.2.4'), # 2022-09-27 + ('libXv', '1.0.12'), # 2022-12-05 + ('libXvMC', '1.0.13'), # 2022-03-22 + ('libXxf86dga', '1.1.6'), # 2022-12-05 + ('libXxf86vm', '1.1.5'), # 2022-09-27 + ('libdmx', '1.1.5'), # 2023-06-03 + ('libxkbfile', '1.1.2'), # 2022-12-08 + ('libxshmfence', '1.3.2'), # 2022-12-08 + ('xcb-util', '0.4.0'), # 2014-10-15 + ('xcb-util-image', '0.4.1'), # 2022-10-18 + ('xcb-util-keysyms', '0.4.1'), # 2022-10-19 + ('xcb-util-renderutil', '0.3.10'), # 2022-10-19 + ('xcb-util-wm', '0.4.2'), # 2022-10-19 + ('xcb-util-cursor', '0.1.4'), # 2022-10-18 ('xkeyboard-config', '2.38', { # 2022-02-04 'easyblock': 'MesonNinja', 'sources': [SOURCE_TAR_XZ], - 'checksums': ['eb1383a5ac4b6210d7c7302b9d6fab052abdf51c5d2c9b55f1f779997ba68c6c'], # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing 'preconfigopts': '', }), - ('printproto', '1.0.5', { # 2011-01-06 - 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], - }), - ('libXp', '1.0.4', { # 2022-09-12 - 'checksums': ['05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'], - }), - ('xbitmaps', '1.1.3', { # 2023-02-23 - 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], - }), + ('printproto', '1.0.5'), # 2011-01-06 + ('libXp', '1.0.4'), # 2022-09-12 + ('xbitmaps', '1.1.3'), # 2023-02-23 +] + +checksums = [ + {'libpthread-stubs-0.4.tar.gz': '50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'}, + {'xorgproto-2022.2.tar.gz': 'da351a403d07a7006d7bdc8dcfc14ddc1b588b38fb81adab9989a8eef605757b'}, + {'libXau-1.0.11.tar.gz': '3a321aaceb803577a4776a5efe78836eb095a9e44bbc7a465d29463e1a14f189'}, + {'libXdmcp-1.1.4.tar.gz': '55041a8ff8992ab02777478c4b19c249c0f8399f05a752cb4a1a868a9a0ccb9a'}, + {'xcb-proto-1.15.2.tar.gz': '6b1ed9cd7cf35e37913eeecca37e5b85b14903002942b3e332f321335c27a8eb'}, + {'libxcb-1.15.tar.gz': '1cb65df8543a69ec0555ac696123ee386321dfac1964a3da39976c9a05ad724d'}, + {'xtrans-1.5.0.tar.gz': 'a806f8a92f879dcd0146f3f1153fdffe845f2fc0df9b1a26c19312b7b0a29c86'}, + {'libxkbcommon-1.5.0.tar.xz': '560f11c4bbbca10f495f3ef7d3a6aa4ca62b4f8fb0b52e7d459d18a26e46e017'}, + {'libX11-1.8.5.tar.gz': 'd84a35c324d5a1724692eafc1ed76f1689c833021e0062933773ec437f91a56b'}, + {'libXext-1.3.5.tar.gz': '1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'}, + {'libFS-1.0.9.tar.gz': '8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'}, + {'libICE-1.1.1.tar.gz': '04fbd34a11ba08b9df2e3cdb2055c2e3c1c51b3257f683d7fcf42dabcf8e1210'}, + {'libSM-1.2.4.tar.gz': '51464ce1abce323d5b6707ceecf8468617106e1a8a98522f8342db06fd024c15'}, + {'libXScrnSaver-1.2.4.tar.gz': '0656b2630475104d6df75d91ebb8e0153e61d14e9871ef1f403bcda4a62a838a'}, + {'libXt-1.3.0.tar.gz': 'de4a80c4cc7785b9620e572de71026805f68e85a2bf16c386009ef0e50be3f77'}, + {'libXmu-1.1.4.tar.gz': '3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'}, + {'libXpm-3.5.16.tar.gz': '43a70e6f9b67215fb223ca270d83bdcb868c513948441d5b781ea0765df6bfb4'}, + {'libXaw-1.0.15.tar.gz': 'ca8a613884c922985202075b3cc8ee8821bfa83a5eb066189ae3cca131e63972'}, + {'libXfixes-6.0.1.tar.gz': 'e69eaa321173c748ba6e2f15c7cf8da87f911d3ea1b6af4b547974aef6366bec'}, + {'libXcomposite-0.4.6.tar.gz': '3599dfcd96cd48d45e6aeb08578aa27636fa903f480f880c863622c2b352d076'}, + {'libXrender-0.9.11.tar.gz': '6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'}, + {'libXcursor-1.2.1.tar.gz': '77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'}, + {'libXdamage-1.1.6.tar.gz': '2afcc139eb6eb926ffe344494b1fc023da25def42874496e6e6d3aa8acef8595'}, + {'libfontenc-1.1.7.tar.gz': '5e5f210329823f08f97bfe9fd5b4105070c789bc5aef88ce01d86d8203d4aa9f'}, + {'libXfont-1.5.4.tar.gz': '59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'}, + {'libXfont2-2.0.6.tar.gz': 'a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'}, + {'libXft-2.3.8.tar.gz': '32e48fe2d844422e64809e4e99b9d8aed26c1b541a5acf837c5037b8d9f278a8'}, + {'libXi-1.8.1.tar.gz': '3b5f47c223e4b63d7f7fe758886b8bf665b20a7edb6962c423892fd150e326ea'}, + {'libXinerama-1.1.5.tar.gz': '2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'}, + {'libXrandr-1.5.3.tar.gz': '3ad316c1781fe2fe22574b819e81f0eff087a8560377f521ba932238b41b251f'}, + {'libXres-1.2.2.tar.gz': '8abce597ced4a7ab89032aee91f6f784d9960adc772b2b59f17e515cd4127950'}, + {'libXtst-1.2.4.tar.gz': '01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'}, + {'libXv-1.0.12.tar.gz': 'ce706619a970a580a0e35e9b5c98bdd2af243ac6494c65f44608a89a86100126'}, + {'libXvMC-1.0.13.tar.gz': 'e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'}, + {'libXxf86dga-1.1.6.tar.gz': '87c7482b1e29b4eeb415815641c4f69c00545a8138e1b73ff1f361f7d9c22ac4'}, + {'libXxf86vm-1.1.5.tar.gz': 'f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'}, + {'libdmx-1.1.5.tar.gz': '070e82cc1daa1b21ee1339aef56a909eab04cbe7d430fabfbb01ecd21b2dd9f3'}, + {'libxkbfile-1.1.2.tar.gz': 'd1a7e659bc7ae1aa1fc1ecced261c734df5ad5d86af1ef7a946be0e2d841e51d'}, + {'libxshmfence-1.3.2.tar.gz': 'e93a85099604beb244ee756dcaf70e18b08701c1ca84c4de0126cd71bd6c8181'}, + {'xcb-util-0.4.0.tar.gz': '0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'}, + {'xcb-util-image-0.4.1.tar.gz': '0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'}, + {'xcb-util-keysyms-0.4.1.tar.gz': '1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'}, + {'xcb-util-renderutil-0.3.10.tar.gz': 'e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'}, + {'xcb-util-wm-0.4.2.tar.gz': 'dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'}, + {'xcb-util-cursor-0.1.4.tar.gz': 'cc8608ebb695742b6cf84712be29b2b66aa5f6768039528794fca0fa283022bf'}, + {'xkeyboard-config-2.38.tar.xz': '0690a91bab86b18868f3eee6d41e9ec4ce6894f655443d490a2184bfac56c872'}, + {'printproto-1.0.5.tar.gz': 'e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'}, + {'libXp-1.0.4.tar.gz': '05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'}, + {'xbitmaps-1.1.3.tar.gz': '93b433b7ff223c4685fdba583b4bd30f2706be2413a670021084422d85b0269d'}, ] + preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " sanity_check_paths = { From df62b7b018466ef7f229e9eae8ee500c2a0a874c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 21 Jun 2023 17:01:51 +0200 Subject: [PATCH 7792/9987] add missing checksum --- easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.2-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.2-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.2-GCC-11.3.0.eb index d185341cba2..f557d9b7075 100644 --- a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.2-GCC-11.3.0.eb @@ -13,6 +13,7 @@ toolchainopts = {'pic': True} source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] sources = [SOURCELOWER_TGZ] +checksums = ['aded73e49bac85a5b4e86f64a0ee3d6f3cfe5551b0f7731c78b6d8f9dac6e8dc'] builddependencies = [ ('CMake', '3.24.3'), From 5222c223d0c701012a30175f545ab80fe9b47506 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 21 Jun 2023 17:10:35 +0200 Subject: [PATCH 7793/9987] update QuantumESPRESSO-6.6-intel-2020a.eb use same 'ELPA' dependency in easyconfigs using '2020a' toolchain generation --- .../q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb index 62fb6813075..9f590db57c1 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-6.6-intel-2020a.eb @@ -29,7 +29,7 @@ checksums = [ dependencies = [ ('HDF5', '1.10.6'), - ('ELPA', '2020.05.001'), + ('ELPA', '2019.11.001'), ('libxc', '4.3.4'), ] From 8cf54d37b52e440896d6efa53d90a6cdbd4bf856 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 17:35:26 +0200 Subject: [PATCH 7794/9987] use custom easyblock for Rust 1.70.0 --- .../r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb | 25 ------------------- 1 file changed, 25 deletions(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb index 2d73f5a4efa..9755389b4bd 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'Rust' version = '1.70.0' @@ -29,27 +27,4 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] -configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " - -# Use ./x.py to bootstrap so that options like -j N are correctly passed through -# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy -# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) -build_cmd = "./x.py build" -install_cmd = "./x.py install -j %(parallel)s" - -# avoid failure when home directory is an NFS mount, -# see https://github.com/rust-lang/cargo/issues/6652 -prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " -preinstallopts = prebuildopts - -sanity_check_paths = { - 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], - 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], -} - -sanity_check_commands = [ - "cargo --version", - "rustc --version", -] - moduleclass = 'lang' From d145eaa7508a3d65143c09a7306926680a48aa9a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 21:15:41 +0200 Subject: [PATCH 7795/9987] strip out useless (...) in sanity check command for FragPipe --- easybuild/easyconfigs/f/FragPipe/FragPipe-20.0-Java-11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FragPipe/FragPipe-20.0-Java-11.eb b/easybuild/easyconfigs/f/FragPipe/FragPipe-20.0-Java-11.eb index f8ecd6e78dd..1a87ec68749 100644 --- a/easybuild/easyconfigs/f/FragPipe/FragPipe-20.0-Java-11.eb +++ b/easybuild/easyconfigs/f/FragPipe/FragPipe-20.0-Java-11.eb @@ -21,6 +21,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = [("%(namelower)s -h | grep -q v%(version)s")] +sanity_check_commands = ["%(namelower)s -h | grep -q v%(version)s"] moduleclass = 'bio' From c9b1de08a8c0d59bd15189ff4bd09727e14db453 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 21:49:56 +0200 Subject: [PATCH 7796/9987] fix homepage + source URL for popt v1.16 --- easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb index 5d58b1b1a3c..b455329798a 100644 --- a/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/p/popt/popt-1.16-GCC-10.2.0.eb @@ -1,19 +1,18 @@ easyblock = 'ConfigureMake' name = 'popt' -version = "1.16" +version = '1.16' -homepage = "http://freecode.com/projects/popt" +homepage = 'https://github.com/rpm-software-management/popt' description = """Popt is a C library for parsing command line parameters.""" toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'optarch': False} -source_urls = ['https://src.fedoraproject.org/repo/pkgs/popt/popt-1.16.tar.gz/3743beefa3dd6247a73f8f7a32c14c33/'] +source_urls = ['https://ftp.osuosl.org/pub/rpm/popt/releases/historical/'] sources = [SOURCE_TAR_GZ] - checksums = ['e728ed296fe9f069a0e005003c3d6b2dde3d9cad453422a10d6558616d304cc8'] -toolchainopts = {'optarch': False} sanity_check_paths = { 'files': ['include/popt.h', ('lib/libpopt.a', 'lib64/libpopt.a'), From 0ee4a6ce200394ebad4dcee2ffd1f82d84e1ffa7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 21:51:31 +0200 Subject: [PATCH 7797/9987] sync EIGENSOFT 7.2.1 using foss/2020b with more recent EIGENSOFT easyconfigs --- .../e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb | 22 +++++++++++-------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb index 6199519bcc9..09a11071180 100644 --- a/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-7.2.1-foss-2020b.eb @@ -1,7 +1,7 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # Author: Pablo Escobar Lopez # sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics +# SIB Swiss Institute of Bioinformatics # 6.1.4 modified by: # Adam Huffman # The Francis Crick Institute @@ -15,21 +15,25 @@ name = 'EIGENSOFT' version = '7.2.1' homepage = 'https://www.hsph.harvard.edu/alkes-price/software/' -description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. -2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal -components analysis to explicitly model ancestry differences between cases and controls along continuous axes of -variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral -populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT +description = """The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. +2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal +components analysis to explicitly model ancestry differences between cases and controls along continuous axes of +variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral +populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.""" toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/DReichLab/EIG/archive'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_Fix_makefile_openblas.patch'] +patches = [ + '%(name)s-%(version)s_Fix_makefile_openblas.patch', + ('%(name)s-%(version)s_restore-ploteig.patch', 0), +] checksums = [ 'f09a46ec4b83c5062ec71eaca48a78f2373f1666fe23cbf17757150a679c8650', # v7.2.1.tar.gz 'e49e3754f2326210114fe5a731a77c7ffd240c8a9134eb8e8e1517bfe06c71e1', # EIGENSOFT-7.2.1_Fix_makefile_openblas.patch + '8a7a0273ae4d0d3ec0c9927facd41a1a43b8540725af3bd06e007cd86afaf9e0', # EIGENSOFT-7.2.1_restore-ploteig.patch ] dependencies = [ @@ -44,10 +48,10 @@ buildopts = ' && make install' files_to_copy = ['bin', 'CONVERTF', 'EIGENSTRAT', 'POPGEN', 'README'] -fix_perl_shebang_for = ['bin/*.perl'] +fix_perl_shebang_for = ['bin/*.perl', 'bin/ploteig'] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL"]], + 'files': ['bin/%s' % x for x in ["baseprog", "convertf", "eigenstrat", "eigenstratQTL", "ploteig"]], 'dirs': [] } From 9ee7082460b3a69bdf86df2339bb98a67166db4d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 22:05:01 +0200 Subject: [PATCH 7798/9987] fix sources + source URL for BayesTraits v3.0.2 --- .../easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb index 7a9fa738f6c..081776b01e7 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb @@ -20,9 +20,8 @@ description = """ BayesTraits is a computer package for performing analyses of t toolchain = SYSTEM -source_urls = ['https://github.com/AndrewPMeade/BayesTraits-Public/blob/main'] -sources = ['%(name)sV%(version)s/%(name)sV%(version)s%(versionsuffix)s.tar.gz'] - +source_urls = ['https://github.com/AndrewPMeade/BayesTraits-Public/blob/main/%(name)sV%(version)s'] +sources = ['%(name)sV%(version)s%(versionsuffix)s.tar.gz'] checksums = ['8b4dbd48583f970d3a4e363685940a9c99d412be1b2e96eb682294f751b4fa51'] sanity_check_paths = { From 6d28bf4ab5d46011416427c0baf9851cf879ef4c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 22:06:31 +0200 Subject: [PATCH 7799/9987] explicitely specify -DPython3_INCLUDE_DIRS and -DPython3_LIBRARIES in ecFlow configure command Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 25947a6df2c..ad372170aa9 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -33,6 +33,8 @@ dependencies = [ configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DPython3_INCLUDE_DIRS=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPython3_LIBRARIES=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 4b94ae25d0260496f8994dd5d4d5c9a6c0a328e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 22:06:52 +0200 Subject: [PATCH 7800/9987] avoid hardcoding Python version, use %(pyshortver)s template instead Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index ad372170aa9..877a0a096e6 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -42,7 +42,7 @@ modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_commands = ['ecflow_client --help'] sanity_check_paths = { 'files': ['bin/ecflow_client', 'bin/ecflow_server'], - 'dirs': ['lib/python3.8/site-packages/ecflow', 'share/ecflow/etc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/ecflow', 'share/ecflow/etc'], } moduleclass = "vis" From 295e82e694c34ddc38fcc4a3a2d9c92f9f43fd6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Jun 2023 22:10:16 +0200 Subject: [PATCH 7801/9987] really fix sources + source URL for BayesTraits v3.0.2 --- .../easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb index 081776b01e7..9f4b79cae32 100644 --- a/easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb +++ b/easybuild/easyconfigs/b/BayesTraits/BayesTraits-3.0.2-Linux.eb @@ -20,8 +20,8 @@ description = """ BayesTraits is a computer package for performing analyses of t toolchain = SYSTEM -source_urls = ['https://github.com/AndrewPMeade/BayesTraits-Public/blob/main/%(name)sV%(version)s'] -sources = ['%(name)sV%(version)s%(versionsuffix)s.tar.gz'] +source_urls = ['https://github.com/AndrewPMeade/BayesTraits-Public/raw/main/BayesTraitsV%(version)s/'] +sources = ['BayesTraitsV%(version)s%(versionsuffix)s.tar.gz'] checksums = ['8b4dbd48583f970d3a4e363685940a9c99d412be1b2e96eb682294f751b4fa51'] sanity_check_paths = { From be93d3ec128f27a9c121e91145ebbe59f16e4d9d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 08:54:11 +0200 Subject: [PATCH 7802/9987] adding easyconfigs: patchelf-0.18.0-GCCcore-12.3.0.eb --- .../patchelf-0.18.0-GCCcore-12.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b87a53d6bda --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.18.0' + +homepage = 'https://github.com/NixOS/patchelf' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +sanity_check_commands = ["patchelf --help"] + +moduleclass = 'tools' From e1aa6c6e7102578e8ff4456d2a089b9cc122c3f3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 22 Jun 2023 08:57:36 +0200 Subject: [PATCH 7803/9987] use name directly --- easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb b/easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb index 325cb7ac1bb..68a0b328c71 100644 --- a/easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb +++ b/easybuild/easyconfigs/s/SVclone/SVclone-1.1.2-foss-2022b.eb @@ -30,7 +30,7 @@ exts_list = [ 'checksums': ['4b16d71c8b97010487e2c939fb4d5707b7bbfa4e2b313df9dba3e372c5ba031d'], }), (name, version, { - 'modulename': '%(name)s', + 'modulename': name, 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/mcmero/SVclone/archive/refs/tags'], 'checksums': ['806e7e31498a084a353a39f98d8d35712d96f182feb6d077d364a2a7100e123e'], From 3fab952556a2834590de5d27bd9ac8b794912605 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Thu, 22 Jun 2023 09:13:23 +0200 Subject: [PATCH 7804/9987] remove 'source_urls' in exts_default_options since using the default value --- .../p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb index 84124a4b951..7e7975cedd3 100644 --- a/easybuild/easyconfigs/p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/pyiron/pyiron-0.3.0-intel-2020a-Python-3.8.2.eb @@ -32,8 +32,6 @@ dependencies = [ check_ldshared = True use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('h5io', '0.1.2', { 'checksums': ['6400543224c489f1cf487be551f892310fa7060fcd4935b84e515efdc1e1fa43'], From f92f0d5012053b36a97c35e154ab3c23ff9e9ca0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 09:29:07 +0200 Subject: [PATCH 7805/9987] use SHLIB_EXT constant in libSBML easyconfig --- easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb index ea2d22663c1..bbf22c8faf6 100644 --- a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.0-GCC-10.2.0.eb @@ -43,7 +43,6 @@ checksums = [ '52b3274ce1fdfb329bc53feb67b9862833a1240539eca2f137fcdca00800e34e', # libsbml-fix_perl_auto_case.patch ] - builddependencies = [ ('CMake', '3.18.4'), ('make', '4.3'), @@ -66,11 +65,10 @@ configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF ' configure_cmd += '-DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER,GROUPS,MULTI,DISTRIB}=ON ' configure_cmd += '../libSBML-%(version)s-Source/' - runtest = 'check' sanity_check_paths = { - 'files': ['lib64/libsbml.so', 'lib64/perl5/vendor_perl/LibSBML.pm'], + 'files': ['lib64/libsbml.%s' % SHLIB_EXT, 'lib64/perl5/vendor_perl/LibSBML.pm'], 'dirs': ['lib64', 'include', 'share'] } @@ -78,5 +76,4 @@ modextrapaths = { 'PERL5LIB': 'lib64/perl5/vendor_perl/', } - moduleclass = 'bio' From f38a32f24e1c8a051392873905fcf69bd71bc93a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 22 Jun 2023 10:46:20 +0200 Subject: [PATCH 7806/9987] adding easyconfigs: GRIDSS-2.13.2-foss-2021b-Java-11.eb --- .../GRIDSS-2.13.2-foss-2021b-Java-11.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/g/GRIDSS/GRIDSS-2.13.2-foss-2021b-Java-11.eb diff --git a/easybuild/easyconfigs/g/GRIDSS/GRIDSS-2.13.2-foss-2021b-Java-11.eb b/easybuild/easyconfigs/g/GRIDSS/GRIDSS-2.13.2-foss-2021b-Java-11.eb new file mode 100644 index 00000000000..68924b5d99d --- /dev/null +++ b/easybuild/easyconfigs/g/GRIDSS/GRIDSS-2.13.2-foss-2021b-Java-11.eb @@ -0,0 +1,48 @@ +# # +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Jordi Blasco +# License:: GPL-v3.0 +# Author: Åke Sandgren (HPC2N) +# # + +easyblock = 'BinariesTarball' + +name = 'GRIDSS' +version = '2.13.2' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation' +description = """GRIDSS is a module software suite containing tools useful for +the detection of genomic rearrangements. GRIDSS includes a genome-wide +break-end assembler, as well as a structural variation caller for Illumina +sequencing data. GRIDSS calls variants based on alignment-guided positional de +Bruijn graph genome-wide break-end assembly, split read, and read pair +evidence.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'PapenfussLab' +source_urls = [GITHUB_LOWER_RELEASE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4d5651b1fc27928c0f76f1e8e7b90a74e6feae0c1cb9abea17fa2bd359f1d704'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('picard', '2.25.1', versionsuffix, SYSTEM), + ('R', '4.1.2'), + ('SAMtools', '1.14'), + ('BWA', '0.7.17'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gridss-%(version)s-gridss-jar-with-dependencies.jar', 'gridss.config.R', + 'gridss_somatic_filter', 'libgridss.R', 'gridss']], + 'dirs': [], +} + +modextrapaths = { + 'GRIDSS_JAR': ['bin'], +} + +moduleclass = 'bio' From b564c6702cb97e49407be671fbd5896d91d0dfd4 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 22 Jun 2023 09:48:33 +0100 Subject: [PATCH 7807/9987] Update easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 877a0a096e6..2238d742735 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -33,6 +33,7 @@ dependencies = [ configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " configopts += "-DPython3_INCLUDE_DIRS=$EBROOTPYTHON/include/python%(pyshortver)s " configopts += "-DPython3_LIBRARIES=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' From 1856fb0432f285212337ec00c901f44720eed2fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 12:02:53 +0200 Subject: [PATCH 7808/9987] add sanity check command for jq 1.5 --- easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb index 139e674e29e..926327a17f6 100644 --- a/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/jq/jq-1.5-GCCcore-10.2.0.eb @@ -23,4 +23,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["jq --help"] + moduleclass = 'tools' From 509c21c4280479bc117c2b93a32ac9129dd26dce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 12:06:14 +0200 Subject: [PATCH 7809/9987] add sanity check commands for Mesquite 2.3.0 --- .../easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb index 5121180a915..d28f9928eea 100644 --- a/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mesquite/Mesquite-2.3.0-GCCcore-10.2.0.eb @@ -23,4 +23,9 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = [ + "msqquality -h", + "msqshape -h", +] + moduleclass = 'math' From b6d31018bab5f116d7cc752d7f09eca64b215819 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 22 Jun 2023 13:18:40 +0200 Subject: [PATCH 7810/9987] adding easyconfigs: GROMACS-2023.1-foss-2022a.eb, GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb and patches: GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch, GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch --- .../GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb | 87 +++++++++++++++++++ .../g/GROMACS/GROMACS-2023.1-foss-2022a.eb | 85 ++++++++++++++++++ ...023.1_drop_mpiexec_from_mpi_starters.patch | 15 ++++ ...S-2023.1_fix_threads_gpu_Gmxapitests.patch | 59 +++++++++++++ 4 files changed, 246 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..24d230f0232 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,87 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-%(version)s_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-%(version)s_drop_mpiexec_from_mpi_starters.patch', +] +checksums = [ + {'gromacs-2023.1.tar.gz': 'eef2bb4a6cb6314cf9da47f26df2a0d27af4bf7b3099723d43601073ab0a42f4'}, + {'GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch': + 'ba781f706a1f2604206480c8582a9ade22e3236fb609a09ba1acd82a0e35e7d9'}, + {'GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch': + 'c013247a2145be406f60bb1c052298eb329548c7020abda0b6d623a6854114a4'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('scikit-build', '0.15.0'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), +] + +runtest = False + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['7fd58e6a4b1391043379e8ba55555ebeba255c5b394f5df9d676e6a5571d7eba'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb new file mode 100644 index 00000000000..43933480930 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb @@ -0,0 +1,85 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.1' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-%(version)s_fix_threads_gpu_Gmxapitests.patch', + 'GROMACS-%(version)s_drop_mpiexec_from_mpi_starters.patch', +] +checksums = [ + {'gromacs-2023.1.tar.gz': 'eef2bb4a6cb6314cf9da47f26df2a0d27af4bf7b3099723d43601073ab0a42f4'}, + {'GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch': + 'ba781f706a1f2604206480c8582a9ade22e3236fb609a09ba1acd82a0e35e7d9'}, + {'GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch': + 'c013247a2145be406f60bb1c052298eb329548c7020abda0b6d623a6854114a4'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('scikit-build', '0.15.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), +] + +runtest = False + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.0', { + 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", + 'checksums': ['7fd58e6a4b1391043379e8ba55555ebeba255c5b394f5df9d676e6a5571d7eba'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch new file mode 100644 index 00000000000..358c7198046 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch @@ -0,0 +1,15 @@ +Drop mpiexec from MPI starter programs, it often clashes with OpenMPI + +Åke Sandgren, 2023-06-22 +diff -ru gromacs-2023.1.orig/cmake/gmxManageMPI.cmake gromacs-2023.1/cmake/gmxManageMPI.cmake +--- gromacs-2023.1.orig/cmake/gmxManageMPI.cmake 2023-04-21 15:12:07.000000000 +0200 ++++ gromacs-2023.1/cmake/gmxManageMPI.cmake 2023-06-22 11:38:57.210310320 +0200 +@@ -148,7 +148,7 @@ + # need to find the full MPI library build system support. + if (NOT MPIEXEC_EXECUTABLE) + find_program(MPIEXEC +- NAMES mpiexec mpirun lamexec srun aprun poe ++ NAMES mpirun lamexec srun aprun poe + HINTS ${MPI_HOME} $ENV{MPI_HOME} + PATH_SUFFIXES bin + DOC "Executable for running MPI programs.") diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch new file mode 100644 index 00000000000..eaaa248cfed --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch @@ -0,0 +1,59 @@ +Handle GMX_THREAD_MPI builds in gmxapi testing. + +Åke Sandgren, 2023-06-21 +diff -ru gromacs-2023.1.orig/python_packaging/gmxapi/test/CMakeLists.txt gromacs-2023.1/python_packaging/gmxapi/test/CMakeLists.txt +--- gromacs-2023.1.orig/python_packaging/gmxapi/test/CMakeLists.txt 2023-04-21 15:12:07.000000000 +0200 ++++ gromacs-2023.1/python_packaging/gmxapi/test/CMakeLists.txt 2023-06-22 11:33:54.200663820 +0200 +@@ -60,11 +60,20 @@ + set(GMXAPI_PYTEST_FOUND TRUE CACHE INTERNAL "Suppress checking for Python pytest module.") + endif() + +-add_custom_target(gmxapi_pytest ++if (NOT GMX_THREAD_MPI) ++ add_custom_target(gmxapi_pytest + COMMAND ${PYTHON_EXECUTABLE} -m pytest + -rA -l --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} + DEPENDS _gmxapi + WORKING_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}) ++else() ++ add_custom_target(gmxapi_pytest ++ COMMAND ${CMAKE_COMMAND} -E env --unset=OMP_NUM_THREADS ${PYTHON_EXECUTABLE} -m pytest ++ -rA -l --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} ++ DEPENDS _gmxapi ++ WORKING_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}) ++endif() ++ + # The current test fixtures require the `gmx` tool-wrapper executable. + add_dependencies(gmxapi_pytest gmx) + +diff -ru gromacs-2023.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt gromacs-2023.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt +--- gromacs-2023.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2023-04-21 15:12:07.000000000 +0200 ++++ gromacs-2023.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2023-06-22 11:30:46.282100539 +0200 +@@ -19,12 +19,24 @@ + + get_target_property(GMXAPI_PYTHON_STAGING_DIR _gmxapi staging_dir) + get_target_property(PLUGINPATH gmxapi_extension LIBRARY_OUTPUT_DIRECTORY) +-add_custom_target(gmxapi_extension_pytest ++if (NOT GMX_THREAD_MPI) ++ add_custom_target(gmxapi_extension_pytest + COMMAND ${CMAKE_COMMAND} +- -E env PYTHONPATH=${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} ++ -E env PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} + ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR + ${CMAKE_CURRENT_SOURCE_DIR} +- DEPENDS gmxapi_extension _gmxapi) ++ DEPENDS gmxapi_extension _gmxapi ++ WORKING_DIRECTORY ${PLUGINPATH}) ++else() ++ add_custom_target(gmxapi_extension_pytest ++ COMMAND ${CMAKE_COMMAND} ++ -E env --unset=OMP_NUM_THREADS PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} ++ ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR ++ ${CMAKE_CURRENT_SOURCE_DIR} ++ DEPENDS gmxapi_extension _gmxapi ++ WORKING_DIRECTORY ${PLUGINPATH}) ++endif() ++ + # The current test fixtures require the `gmx` tool-wrapper executable. + add_dependencies(gmxapi_extension_pytest gmx) + From b71e432125cfa569e4faa1dd9bce793f48deb3d6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 14:48:10 +0200 Subject: [PATCH 7811/9987] add patchelf build dependency for Rust 1.70.0 --- easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb index 9755389b4bd..6b3271c7a20 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.70.0-GCCcore-12.3.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('Python', '3.11.3'), ('Ninja', '1.11.1'), ('pkgconf', '1.9.5'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled ] dependencies = [ From 3895a99e70768dc3b2b59593b0eae389beb6fac9 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Thu, 22 Jun 2023 14:53:33 +0200 Subject: [PATCH 7812/9987] fix typo in segemehl-0.3.4-iccifort-2020.4.304.eb Co-authored-by: Alexander Grund --- .../s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb index 7a0308a476a..1dba3da2387 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb @@ -7,7 +7,7 @@ homepage = 'https://www.bioinf.uni-leipzig.de/Software/segemehl/' description = """segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able - to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching + to map primer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.""" From a894fd17138f02a1fca94cd7192598d5de1baed1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 17:27:26 +0200 Subject: [PATCH 7813/9987] retain useful comment regarding disabling 'vectorize' toolchain option --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb index 38e19f85b0b..c39a721d0c6 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2020b.eb @@ -13,6 +13,9 @@ description = """OpenFOAM is a free, open source CFD software package. to solid dynamics and electromagnetics.""" toolchain = {'name': 'foss', 'version': '2020b'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. toolchainopts = {'cstd': 'c++14', 'vectorize': False} source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] From afc25928282f1aeab76cf095ebbc490924bf8d11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 18:46:19 +0200 Subject: [PATCH 7814/9987] update easyconfig for Nextflow 23.04.2 to use `install_cmds` --- easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb index aab831581f7..88a839637ea 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-23.04.2.eb @@ -15,10 +15,12 @@ checksums = ['d7a6c3eacc400648da85c0a56866ce39d240b3aab4c88ee470180f4dcf1847b4'] dependencies = [('Java', '11')] -install_cmd = "mkdir -p %(installdir)s/bin &&" -install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" -install_cmd += "cd %(installdir)s/bin && ln -s %(namelower)s-%(version)s-all %(namelower)s &&" -install_cmd += "chmod +x %(installdir)s/bin/%(namelower)s-%(version)s-all" +install_cmds = [ + "mkdir -p %(installdir)s/bin", + "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin", + "cd %(installdir)s/bin && ln -s %(namelower)s-%(version)s-all %(namelower)s", + "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/%(namelower)s-%(version)s-all", +] sanity_check_paths = { 'files': ['bin/%(namelower)s-%(version)s-all', 'bin/%(namelower)s'], From 55656a80c7c06a33f1a04c54b6ec9d315b6213f0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Jun 2023 18:53:31 +0200 Subject: [PATCH 7815/9987] use custom easyblock for Rust 1.65.0 --- .../r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb index 757f1d6d4bf..31a461e1867 100644 --- a/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'Rust' version = '1.65.0' @@ -28,31 +26,4 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] -configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " - -# avoid build dependency on Ninja, which requires Python, -# since Rust is a build dependency for cryptography that is included with Python -configopts += "--set=llvm.ninja=false " - -# Use ./x.py to bootstrap so that options like -j N are correctly passed through -# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy -# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) -build_cmd = "./x.py build" -install_cmd = "./x.py install -j %(parallel)s" - -# avoid failure when home directory is an NFS mount, -# see https://github.com/rust-lang/cargo/issues/6652 -prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " -preinstallopts = prebuildopts - -sanity_check_paths = { - 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], - 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], -} - -sanity_check_commands = [ - "cargo --version", - "rustc --version", -] - moduleclass = 'lang' From 119f988106d55310d340057d8af448b42f21f7ac Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 23 Jun 2023 11:14:18 +0800 Subject: [PATCH 7816/9987] adding easyconfigs: oxDNA-3.5.2-foss-2022a-CUDA-11.7.0.eb --- .../oxDNA-3.5.2-foss-2022a-CUDA-11.7.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..0d41088be5f --- /dev/null +++ b/easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'oxDNA' +version = '3.5.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/lorenzo-rovigatti/oxDNA' +description = """oxDNA is a simulation code that was initially conceived as an implementation + of the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. + It has been since reworked and it is now an extensible simulation+analysis framework. + It natively supports DNA, RNA, Lennard-Jones and patchy particle simulations of different kinds + on both single CPU cores and NVIDIA GPUs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'lorenzo-rovigatti' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d76351b572334421aedb7774bb095db6f8f0a9c851e0242f0b665887d9d754bb'] + +builddependencies = [ + ('CMake', '3.23.1') +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +configopts = "-DCUDA=1 -DCUDA_COMMON_ARCH=ON -DPython=ON -DOxpySystemInstall=ON " +# configopts += "-DMPI=ON " # still "unsupported feature that should be used by developers only"? + +postinstallcmds = [ + "mkdir %(installdir)s/lib", + "mv %(builddir)s/easybuild_obj/bin %(installdir)s/bin", + "mv %(builddir)s/easybuild_obj/oxpy/lib_oxpy_lib.a %(installdir)s/lib/", + "mv %%(builddir)s/easybuild_obj/src/liboxdna_common.%s %%(installdir)s/lib/" % SHLIB_EXT, + "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages", + "mv %(builddir)s/easybuild_obj/oxpy/python/oxpy %(installdir)s/lib/python%(pyshortver)s/site-packages/", +] + +sanity_check_paths = { + 'files': ['bin/confGenerator', 'bin/DNAnalysis', 'bin/oxDNA', + 'lib/liboxdna_common.%s' % SHLIB_EXT, 'lib/lib_oxpy_lib.a'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/oxpy'], +} + +sanity_check_commands = ["python -c 'import oxpy'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' From e6e0bca3d771352316df69aaddbde5013ad34984 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Fri, 23 Jun 2023 16:06:42 +1000 Subject: [PATCH 7817/9987] Create datamash-1.8-GCCcore-11.3.0.eb New version, new toolchain, new binutils. --- .../d/datamash/datamash-1.8-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/d/datamash/datamash-1.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/datamash/datamash-1.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/datamash/datamash-1.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f3364d92c73 --- /dev/null +++ b/easybuild/easyconfigs/d/datamash/datamash-1.8-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'datamash' +version = '1.8' + +homepage = 'https://www.gnu.org/software/datamash/' +description = "GNU datamash performs basic numeric, textual and statistical operations on input data files" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['7ad97e8c7ef616dd03aa5bd67ae24c488272db3e7d1f5774161c18b75f29f6fd'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['bin/datamash'], + 'dirs': ['share/man'] +} + +moduleclass = 'data' From 74cd002e2f11927dd44e0b0882c7c63d2c9ce438 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Fri, 23 Jun 2023 16:09:36 +1000 Subject: [PATCH 7818/9987] Create barrnap-0.9-gompi-2022a.eb New toolchain, new dependencies --- .../b/barrnap/barrnap-0.9-gompi-2022a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2022a.eb diff --git a/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2022a.eb b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2022a.eb new file mode 100644 index 00000000000..a857af10dc5 --- /dev/null +++ b/easybuild/easyconfigs/b/barrnap/barrnap-0.9-gompi-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'barrnap' +version = '0.9' + +homepage = 'https://github.com/tseemann/barrnap' +description = "Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes." + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/tseemann/barrnap/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['36c27cd4350531d98b3b2fb7d294a2d35c15b7365771476456d7873ba33cce15'] + +dependencies = [ + ('Perl', '5.34.1'), + ('HMMER', '3.3.2'), + ('BEDTools', '2.30.0'), +] + +sanity_check_paths = { + 'files': ['bin/barrnap'], + 'dirs': [], +} + +sanity_check_commands = ["barrnap --help"] + +moduleclass = 'bio' From 6515eef348eeeb39110b586ff63f816519706e66 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 23 Jun 2023 09:14:22 +0200 Subject: [PATCH 7819/9987] adding easyconfigs: AMS-2023.101-iimpi-2022a-intelmpi.eb --- .../AMS/AMS-2023.101-iimpi-2022a-intelmpi.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMS/AMS-2023.101-iimpi-2022a-intelmpi.eb diff --git a/easybuild/easyconfigs/a/AMS/AMS-2023.101-iimpi-2022a-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2023.101-iimpi-2022a-intelmpi.eb new file mode 100644 index 00000000000..9a285b8b7a4 --- /dev/null +++ b/easybuild/easyconfigs/a/AMS/AMS-2023.101-iimpi-2022a-intelmpi.eb @@ -0,0 +1,47 @@ +easyblock = 'Tarball' + +name = 'AMS' +version = '2023.101' +versionsuffix = '-intelmpi' + +homepage = 'https://www.scm.com/amsterdam-modeling-suite/' +description = """ +The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for +computational chemistry and materials science, from quantum mechanics to fluid +thermodynamics. +""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} + +sources = ['ams%(version)s.pc64_linux.intelmpi.bin.tgz'] +checksums = ['0060933e85cfe1795280cba88e5b2329cfcf83061e7e9b18321e49dd77dd4d46'] + +dependencies = [('libGLU', '9.0.2')] + +keepsymlinks = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +# check if license file is installed +# sanity_check_commands = ['dirac check'] + +modextrapaths = { + 'AMSHOME': '', + 'AMSBIN': 'bin', + 'AMSRESOURCES': 'atomicdata', +} + +modextravars = { + # use Intel MPI from EasyBuild + 'SCM_USE_LOCAL_IMPI': '1', +} + +modloadmsg = """These environment variables need to be defined before using AMS: + * $SCMLICENSE: path to AMS license file + * $SCM_TMPDIR: path to user scratch directory +""" + +moduleclass = 'chem' From 60c1404af7f60ef3c6aad74c40dc5e361e8ea9c0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 23 Jun 2023 09:37:44 +0200 Subject: [PATCH 7820/9987] adding easyconfigs: ASF-SearchAPI-6.5.0-foss-2022a.eb --- .../ASF-SearchAPI-6.5.0-foss-2022a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASF-SearchAPI/ASF-SearchAPI-6.5.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/ASF-SearchAPI/ASF-SearchAPI-6.5.0-foss-2022a.eb b/easybuild/easyconfigs/a/ASF-SearchAPI/ASF-SearchAPI-6.5.0-foss-2022a.eb new file mode 100644 index 00000000000..0ee44c7ec65 --- /dev/null +++ b/easybuild/easyconfigs/a/ASF-SearchAPI/ASF-SearchAPI-6.5.0-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = "PythonBundle" + +name = 'ASF-SearchAPI' +version = '6.5.0' + +homepage = 'https://docs.asf.alaska.edu/' +description = """asf_search is a Python module for performing searches of the ASF catalog. In +addition, it offers baseline functionality and download support.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Shapely', '1.8.2'), +] + +use_pip = True + +exts_list = [ + ('remotezip', '0.12.1', { + 'checksums': ['ce65b7910c5c25d8950ed402023592967f5791ac14987141c050016ffad18dec'], + }), + ('tzdata', '2022.7', { + 'checksums': ['fe5f866eddd8b96e9fcba978f8e503c909b19ea7efda11e52e39494bad3a7bfa'], + }), + ('pytz-deprecation-shim', '0.1.0.post0', { + 'sources': ['pytz_deprecation_shim-%(version)s.tar.gz'], + 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], + }), + ('tzlocal', '4.2', { + 'checksums': ['ee5842fa3a795f023514ac2d801c4a81d1743bbe642e3940143326b3a00addd7'], + }), + ('dateparser', '1.1.8', { + 'checksums': ['86b8b7517efcc558f085a142cdb7620f0921543fcabdb538c8a4c4001d8178e3'], + }), + ('tenacity', '8.2.2', { + 'checksums': ['43af037822bd0029025877f3b2d97cc4d7bb0c2991000a3d59d71517c5c969e0'], + }), + ('asf_search', version, { + 'checksums': ['fda492742fa47737c451c33590d93d226e2b1ddee51d430fe5c853f74f03e5f3'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From ac4010af5140fb0f7253583657d0034f96d4620b Mon Sep 17 00:00:00 2001 From: eylenbt Date: Fri, 23 Jun 2023 10:29:15 +0200 Subject: [PATCH 7821/9987] update checksum EMBOSS --- .../b/Bismark/Bismark-0.24.1-GCC-12.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bismark/Bismark-0.24.1-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.24.1-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.24.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..324c2f74ac2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.24.1-GCC-12.2.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +# Updated to 0.23.1 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'Tarball' + +name = 'Bismark' +version = '0.24.1' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = "A tool to map bisulfite converted sequence reads and determine cytosine methylation states" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/FelixKrueger/Bismark/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c5409f5fa470ea5ac07327ced28c60b793f5ef88c5a7bc75b71dde0f52f39894'] + +dependencies = [ + ('Perl', '5.36.0'), + ('Bowtie2', '2.5.1'), + ('SAMtools', '1.17'), +] + +sanity_check_commands = ['bismark --help'] + +sanity_check_paths = { + 'files': ['bismark', 'bismark2bedGraph', 'bismark2report', 'bismark_genome_preparation', + 'bismark_methylation_extractor', 'coverage2cytosine', 'deduplicate_bismark'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 457bbb6764da140cdc8154837a8a81abfd82b581 Mon Sep 17 00:00:00 2001 From: Thomas Eylenbosch Date: Fri, 23 Jun 2023 10:30:00 +0200 Subject: [PATCH 7822/9987] Delete Bismark-0.24.0-GCC-12.2.0.eb --- .../b/Bismark/Bismark-0.24.0-GCC-12.2.0.eb | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-12.2.0.eb deleted file mode 100644 index 83b0b8ea14a..00000000000 --- a/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-12.2.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2013-2014 The Cyprus Institute -# Authors:: Thekla Loizou -# License:: MIT/GPL -# -# Updated to 0.23.1 -# J. Sassmannshausen NHS/GSTT - -easyblock = 'Tarball' - -name = 'Bismark' -version = '0.24.0' - -homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/bismark/' -description = "A tool to map bisulfite converted sequence reads and determine cytosine methylation states" - -toolchain = {'name': 'GCC', 'version': '12.2.0'} - -source_urls = ['https://github.com/FelixKrueger/Bismark/archive/refs/tags/'] -sources = ['%(version)s.tar.gz'] -checksums = ['dd58957bd6eac44f3a6e74e9a5ef69c8d19da0e0b64feb7d019a994fe6087d7d'] - -dependencies = [ - ('Perl', '5.36.0'), - ('Bowtie2', '2.5.1'), - ('SAMtools', '1.17'), -] - -sanity_check_commands = ['bismark --help'] - -sanity_check_paths = { - 'files': ['bismark', 'bismark2bedGraph', 'bismark2report', 'bismark_genome_preparation', - 'bismark_methylation_extractor', 'coverage2cytosine', 'deduplicate_bismark'], - 'dirs': [], -} - -modextrapaths = {'PATH': ''} - -moduleclass = 'bio' From 005a4d75b0c25835f86113f77b1022c496144751 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 23 Jun 2023 09:59:26 +0000 Subject: [PATCH 7823/9987] Add sanity check command for LSD2 --- easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.2.0.eb index 2626f47769c..9e53a5268c9 100644 --- a/easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.2.0.eb @@ -35,4 +35,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['lsd2 -h'] + moduleclass = 'bio' From a4c3bfe0a42e1ddb34be129a5f21a89a743c00fb Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 23 Jun 2023 11:16:17 +0100 Subject: [PATCH 7824/9987] add sanity check commands Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 2238d742735..eea4370632f 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -40,10 +40,14 @@ prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} -sanity_check_commands = ['ecflow_client --help'] sanity_check_paths = { 'files': ['bin/ecflow_client', 'bin/ecflow_server'], 'dirs': ['lib/python%(pyshortver)s/site-packages/ecflow', 'share/ecflow/etc'], } +sanity_check_commands = [ + "ecflow_client --help", + "python -c 'import ecflow'", +] + moduleclass = "vis" From c82d39afded1f9545ca75e0ae852cd58419151d7 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 23 Jun 2023 11:34:23 +0100 Subject: [PATCH 7825/9987] update homepage --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index eea4370632f..9d74ea2b9e1 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -5,7 +5,7 @@ easyblock = "CMakeMake" name = 'ecFlow' version = '5.7.0' -homepage = "https://confluence.ecmwf.int/display/ECFLOW/ecflow+home" +homepage = "https://ecflow.readthedocs.io/en/latest/index.html" description = """ecFlow is a client/server workflow package that enables users to run a large number of programs (with dependencies on each other and on time) in a controlled environment. It provides reasonable tolerance for hardware and From 528d4c697545cbf069ceedbd2532842e3e2c0cd8 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 23 Jun 2023 10:42:28 +0000 Subject: [PATCH 7826/9987] Add missing sanity check syntax fix for 2022a --- easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb index 16b1ef14e9f..b3314fe82c3 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb @@ -51,7 +51,7 @@ sanity_check_commands = [ "iqtree2 --help", "mkdir -p $TMPDIR/{test-omp,test-mpi}", "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy", - "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy", + "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo", ] moduleclass = 'bio' From 9bf5d855313d8082af8ad556ce09d616e512466a Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 23 Jun 2023 12:09:25 +0100 Subject: [PATCH 7827/9987] fix boost linking --- .../e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 9d74ea2b9e1..66a241be8a0 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -31,11 +31,15 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] -configopts = "-DBOOST_ROOT=$EBROOTBOOST -DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib " -configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " -configopts += "-DPython3_INCLUDE_DIRS=$EBROOTPYTHON/include/python%(pyshortver)s " -configopts += "-DPython3_LIBRARIES=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts = " ".join([ + "-DBOOST_ROOT=$EBROOTBOOST", + "-DENABLE_STATIC_BOOST_LIBS=OFF", + "-DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib/libboost_python38.so", + "-DPython3_ROOT_DIR=$EBROOTPYTHON", + "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python", + "-DPython3_INCLUDE_DIRS=$EBROOTPYTHON/include/python%(pyshortver)s", + "-DPython3_LIBRARIES=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s" % SHLIB_EXT, +]) prebuildopts = 'export LDFLAGS="$LDFLAGS -lssl" && ' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From a0587e425953d1c822af30507547b7c8edcb4676 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Jun 2023 13:27:04 +0200 Subject: [PATCH 7828/9987] remove excess trailing whitespace --- easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb index 66a241be8a0..d4ce0c41bf7 100644 --- a/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/e/ecFlow/ecFlow-5.7.0-GCC-10.2.0.eb @@ -31,7 +31,7 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] -configopts = " ".join([ +configopts = " ".join([ "-DBOOST_ROOT=$EBROOTBOOST", "-DENABLE_STATIC_BOOST_LIBS=OFF", "-DBoost_PYTHON38_LIBRARY_RELEASE=$EBROOTBOOSTPYTHON/lib/libboost_python38.so", From 697e9a436b64b73f405c28ed7d944bc549484a30 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 23 Jun 2023 14:59:34 +0200 Subject: [PATCH 7829/9987] adding easyconfigs: MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0.eb, MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb, pydicom-seg-0.4.1-foss-2022a.eb, requests-2.31.0-foss-2022a.eb and patches: MONAI-Label-0.5.2_dep-fix.patch, pydicom-seg-0.4.1_dep-fix.patch --- ...2-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb | 161 ++++++++++++++++++ ...I-Label-0.5.2-foss-2022a-PyTorch-1.12.0.eb | 160 +++++++++++++++++ .../MONAI-Label-0.5.2_dep-fix.patch | 47 +++++ .../pydicom-seg-0.4.1-foss-2022a.eb | 31 ++++ .../pydicom-seg-0.4.1_dep-fix.patch | 38 +++++ .../r/requests/requests-2.31.0-foss-2022a.eb | 23 +++ 6 files changed, 460 insertions(+) create mode 100644 easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0.eb create mode 100644 easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2_dep-fix.patch create mode 100644 easybuild/easyconfigs/p/pydicom-seg/pydicom-seg-0.4.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pydicom-seg/pydicom-seg-0.4.1_dep-fix.patch create mode 100644 easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..6c273769a54 --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb @@ -0,0 +1,161 @@ +easyblock = 'PythonBundle' + +name = 'MONAI-Label' +version = '0.5.2' + +local_pytorch_version = '1.12.0' +versionsuffix = '-PyTorch-' + local_pytorch_version + '-CUDA-%(cudaver)s' + +homepage = 'https://docs.monai.io/projects/label/en/latest/' +description = """MONAI Label is an intelligent open source image labeling and learning tool + that enables users to create annotated datasets and build AI annotation models for clinical evaluation. + MONAI Label enables application developers to build labeling apps in a serverless way, + where custom labeling apps are exposed as a service through the MONAI Label Server.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), + ('torchvision', '0.13.1', '-CUDA-%(cudaver)s'), + ('torchaudio', '0.12.0', '-PyTorch-' + local_pytorch_version + '-CUDA-%(cudaver)s'), + ('requests', '2.31.0'), + ('einops', '0.4.1'), + ('MONAI', '1.0.1', '-CUDA-%(cudaver)s'), + ('OpenCV', '4.6.0', '-CUDA-%(cudaver)s' + '-contrib'), + ('pydantic', '1.10.4'), + ('pydicom', '2.3.0'), + ('pydicom-seg', '0.4.1'), + ('GEOS', '3.10.3'), + ('SimpleITK', '2.1.1.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('asgiref', '3.7.2', { + 'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'], + }), + ('h11', '0.12.0', { + 'checksums': ['47222cb6067e4a307d535814917cd98fd0a57b6788ce715755fa2b6c28b56042'], + }), + ('httpcore', '0.15.0', { + 'checksums': ['18b68ab86a3ccf3e7dc0f43598eaddcf472b602aba29f9aa6ab85fe2ada3980b'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('diskcache', '5.6.1', { + 'checksums': ['e4c978532feff5814c4cc00fe1e11e40501985946643d73220d41ee7737c72c3'], + }), + ('starlette', '0.19.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['5a60c5c2d051f3a8eb546136aa0c9399773a689595e099e0877704d5888279bf'], + }), + ('retrying', '1.3.4', { + 'checksums': ['345da8c5765bd982b1d1915deb9102fd3d1f7ad16bd84a9700b85f64d24e8f3e'], + }), + ('anyio', '3.7.0', { + 'checksums': ['275d9973793619a5374e1c89a4f4ad3f4b0a5510a2b5b939444bee8f4c4d37ce'], + }), + ('exceptiongroup', '1.1.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['232c37c63e4f682982c8b6459f33a8981039e5fb8756b2074364e5055c498c9e'], + }), + ('dicomweb-client', '0.56.2', { + 'checksums': ['8e7782e3958dcb1db8912b5f1d689a4b9cc92e56e0684b98898c7b8c7b47beb1'], + }), + ('expiring-dict', '1.1.0', { + 'checksums': ['3c404adb1e4369468cb7e51bfbc9c470d7e2e863efe2a1c75d4ed706d0dce1a6'], + }), + ('expiringdict', '1.2.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['09a5d20bc361163e6432a874edd3179676e935eb81b925eccef48d409a8a45e8'], + }), + ('fastapi', '0.78.0', { + 'checksums': ['3233d4a789ba018578658e2af1a4bb5e38bdd122ff722b313666a9b2c6786a83'], + }), + ('girder-client', '3.1.14', { + 'checksums': ['30e874d50c32316df70bbb55ae66968639bcd19c22261f35439f0796c5cf8de1'], + }), + ('httpx', '0.23.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['42974f577483e1e932c3cdc3cd2303e883cbfba17fe228b0f63589764d7b9c4b'], + }), + ('ninja', '1.10.2.3', { + 'checksums': ['e1b86ad50d4e681a7dbdff05fc23bb52cb773edb90bc428efba33fa027738408'], + }), + ('numpymaxflow', '0.0.2', { + 'checksums': ['28e906b7e1c275cf559acab3fad5553511ec25b84f538bece5d2c4f293862a79'], + }), + ('passlib', '1.7.4', { + 'checksums': ['defd50f72b65c5402ab2c573830a6978e5f202ad0d984793c8dde2c4152ebe04'], + }), + ('pynetdicom', '2.0.2', { + 'checksums': ['231212e9b9c5e0debf2af4f17d8afa14ecd1b262a11cdb891b2b2b15f7ab5939'], + }), + ('pynrrd', '0.4.3', { + 'modulename': 'nrrd', + 'checksums': ['e8b8a0e65b7c899201bf9dc42190cdd054478bfa967e3d34b8834652590c1e2b'], + }), + ('python-dotenv', '0.20.0', { + 'modulename': 'dotenv', + 'checksums': ['b7e3b04a59693c42c36f9ab1cc2acc46fa5df8c78e178fc33a8d4cd05c8d498f'], + }), + ('python-jose', '3.3.0', { + 'modulename': 'jose', + 'checksums': ['55779b5e6ad599c6336191246e95eb2293a9ddebd555f796a65f838f07e5d78a'], + }), + ('python-multipart', '0.0.5', { + 'modulename': 'multipart', + 'checksums': ['f7bb5f611fc600d15fa47b3974c8aa16e93724513b49b5f95c81e6624c83fa43'], + }), + ('schedule', '1.1.0', { + 'checksums': ['e6ca13585e62c810e13a08682e0a6a8ad245372e376ba2b8679294f377dfc8e4'], + }), + ('Shapely', '1.8.2', { + 'checksums': ['572af9d5006fd5e3213e37ee548912b0341fb26724d6dc8a4e3950c10197ebb6'], + }), + ('timeloop', '1.0.2', { + 'checksums': ['4e716c67fe6bcadcee7ddb91e2520792426818a70f27e630cfbbbd9becc48a13'], + }), + ('uvicorn', '0.17.6', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['19e2a0e96c9ac5581c01eb1a79a7d2f72bb479691acd2b8921fce48ed5b961a6'], + }), + ('watchdog', '2.1.8', { + 'checksums': ['6d03149126864abd32715d4e9267d2754cede25a69052901399356ad3bc5ecff'], + }), + ('filelock', '3.7.1', { + 'checksums': ['3a0fd85166ad9dbab54c9aec96737b744106dc5f15c0b09a6744a445299fcf04'], + }), + ('monailabel', version, { + 'source_urls': ['https://github.com/Project-MONAI/MONAILabel/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'patches': ['MONAI-Label-0.5.2_dep-fix.patch'], + 'checksums': [ + '9c4b14812f3db72fdccadfed36ecab1c8d18df3aa82c97ef16af18b5f4649a50', # MONAILabel-0.5.2.tar.gz + 'd920362ad31a903c8263334ed7791723026fbba22b082e9c4ec2a2ea69ec69fa', # MONAI-Label-0.5.2_dep-fix.patch + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/monailabel'], + 'dirs': [], +} + +sanity_check_commands = ["monailabel --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..f80125213a7 --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0.eb @@ -0,0 +1,160 @@ +easyblock = 'PythonBundle' + +name = 'MONAI-Label' +version = '0.5.2' + +local_pytorch_version = '1.12.0' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://docs.monai.io/projects/label/en/latest/' +description = """MONAI Label is an intelligent open source image labeling and learning tool + that enables users to create annotated datasets and build AI annotation models for clinical evaluation. + MONAI Label enables application developers to build labeling apps in a serverless way, + where custom labeling apps are exposed as a service through the MONAI Label Server.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', local_pytorch_version), + ('torchvision', '0.13.1'), # CUDA + ('torchaudio', '0.12.0', '-PyTorch-%s' % local_pytorch_version), + ('requests', '2.31.0'), + ('einops', '0.4.1'), + ('MONAI', '1.0.1'), + ('OpenCV', '4.6.0', '-contrib'), + ('pydantic', '1.10.4'), + ('pydicom', '2.3.0'), + ('pydicom-seg', '0.4.1'), + ('GEOS', '3.10.3'), + ('SimpleITK', '2.1.1.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('asgiref', '3.7.2', { + 'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'], + }), + ('h11', '0.12.0', { + 'checksums': ['47222cb6067e4a307d535814917cd98fd0a57b6788ce715755fa2b6c28b56042'], + }), + ('httpcore', '0.15.0', { + 'checksums': ['18b68ab86a3ccf3e7dc0f43598eaddcf472b602aba29f9aa6ab85fe2ada3980b'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('diskcache', '5.6.1', { + 'checksums': ['e4c978532feff5814c4cc00fe1e11e40501985946643d73220d41ee7737c72c3'], + }), + ('starlette', '0.19.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['5a60c5c2d051f3a8eb546136aa0c9399773a689595e099e0877704d5888279bf'], + }), + ('retrying', '1.3.4', { + 'checksums': ['345da8c5765bd982b1d1915deb9102fd3d1f7ad16bd84a9700b85f64d24e8f3e'], + }), + ('anyio', '3.7.0', { + 'checksums': ['275d9973793619a5374e1c89a4f4ad3f4b0a5510a2b5b939444bee8f4c4d37ce'], + }), + ('exceptiongroup', '1.1.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['232c37c63e4f682982c8b6459f33a8981039e5fb8756b2074364e5055c498c9e'], + }), + ('dicomweb-client', '0.56.2', { + 'checksums': ['8e7782e3958dcb1db8912b5f1d689a4b9cc92e56e0684b98898c7b8c7b47beb1'], + }), + ('expiring-dict', '1.1.0', { + 'checksums': ['3c404adb1e4369468cb7e51bfbc9c470d7e2e863efe2a1c75d4ed706d0dce1a6'], + }), + ('expiringdict', '1.2.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['09a5d20bc361163e6432a874edd3179676e935eb81b925eccef48d409a8a45e8'], + }), + ('fastapi', '0.78.0', { + 'checksums': ['3233d4a789ba018578658e2af1a4bb5e38bdd122ff722b313666a9b2c6786a83'], + }), + ('girder-client', '3.1.14', { + 'checksums': ['30e874d50c32316df70bbb55ae66968639bcd19c22261f35439f0796c5cf8de1'], + }), + ('httpx', '0.23.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['42974f577483e1e932c3cdc3cd2303e883cbfba17fe228b0f63589764d7b9c4b'], + }), + ('ninja', '1.10.2.3', { + 'checksums': ['e1b86ad50d4e681a7dbdff05fc23bb52cb773edb90bc428efba33fa027738408'], + }), + ('numpymaxflow', '0.0.2', { + 'checksums': ['28e906b7e1c275cf559acab3fad5553511ec25b84f538bece5d2c4f293862a79'], + }), + ('passlib', '1.7.4', { + 'checksums': ['defd50f72b65c5402ab2c573830a6978e5f202ad0d984793c8dde2c4152ebe04'], + }), + ('pynetdicom', '2.0.2', { + 'checksums': ['231212e9b9c5e0debf2af4f17d8afa14ecd1b262a11cdb891b2b2b15f7ab5939'], + }), + ('pynrrd', '0.4.3', { + 'modulename': 'nrrd', + 'checksums': ['e8b8a0e65b7c899201bf9dc42190cdd054478bfa967e3d34b8834652590c1e2b'], + }), + ('python-dotenv', '0.20.0', { + 'modulename': 'dotenv', + 'checksums': ['b7e3b04a59693c42c36f9ab1cc2acc46fa5df8c78e178fc33a8d4cd05c8d498f'], + }), + ('python-jose', '3.3.0', { + 'modulename': 'jose', + 'checksums': ['55779b5e6ad599c6336191246e95eb2293a9ddebd555f796a65f838f07e5d78a'], + }), + ('python-multipart', '0.0.5', { + 'modulename': 'multipart', + 'checksums': ['f7bb5f611fc600d15fa47b3974c8aa16e93724513b49b5f95c81e6624c83fa43'], + }), + ('schedule', '1.1.0', { + 'checksums': ['e6ca13585e62c810e13a08682e0a6a8ad245372e376ba2b8679294f377dfc8e4'], + }), + ('Shapely', '1.8.2', { + 'checksums': ['572af9d5006fd5e3213e37ee548912b0341fb26724d6dc8a4e3950c10197ebb6'], + }), + ('timeloop', '1.0.2', { + 'checksums': ['4e716c67fe6bcadcee7ddb91e2520792426818a70f27e630cfbbbd9becc48a13'], + }), + ('uvicorn', '0.17.6', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['19e2a0e96c9ac5581c01eb1a79a7d2f72bb479691acd2b8921fce48ed5b961a6'], + }), + ('watchdog', '2.1.8', { + 'checksums': ['6d03149126864abd32715d4e9267d2754cede25a69052901399356ad3bc5ecff'], + }), + ('filelock', '3.7.1', { + 'checksums': ['3a0fd85166ad9dbab54c9aec96737b744106dc5f15c0b09a6744a445299fcf04'], + }), + ('monailabel', version, { + 'source_urls': ['https://github.com/Project-MONAI/MONAILabel/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'patches': ['MONAI-Label-0.5.2_dep-fix.patch'], + 'checksums': [ + '9c4b14812f3db72fdccadfed36ecab1c8d18df3aa82c97ef16af18b5f4649a50', # MONAILabel-0.5.2.tar.gz + 'd920362ad31a903c8263334ed7791723026fbba22b082e9c4ec2a2ea69ec69fa', # MONAI-Label-0.5.2_dep-fix.patch + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/monailabel'], + 'dirs': [], +} + +sanity_check_commands = ["monailabel --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2_dep-fix.patch b/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2_dep-fix.patch new file mode 100644 index 00000000000..a274659352b --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2_dep-fix.patch @@ -0,0 +1,47 @@ +Some requirements are unnecessarily strict. +Use opencv-contrib-python (installed with OpenCV 4.6.0) instead of opencv-python-headless +Author: Petr Král (INUITS) +diff -u MONAILabel-0.5.2/requirements.txt.orig MONAILabel-0.5.2/requirements.txt +--- MONAILabel-0.5.2/requirements.txt.orig 2022-10-24 22:48:45.000000000 +0200 ++++ MONAILabel-0.5.2/requirements.txt 2023-06-23 13:11:07.961592853 +0200 +@@ -21,15 +21,15 @@ + schedule==1.1.0 + dicomweb-client==0.56.2 + timeloop==1.0.2 +-expiringdict==1.2.1 ++expiringdict>=1.2.1 + expiring_dict==1.1.0 + cachetools==5.2.0 + watchdog==2.1.8 + pydicom==2.3.0 +-pydicom-seg==0.4.0 ++pydicom-seg>=0.4.0 + pynetdicom==2.0.2 + pynrrd==0.4.3 +-opencv-python-headless==4.5.5.64 ++opencv-contrib-python>=4.6.0 + numpymaxflow==0.0.2 + girder-client==3.1.14 + ninja==1.10.2.3 +diff -u MONAILabel-0.5.2/setup.cfg.orig MONAILabel-0.5.2/setup.cfg +--- MONAILabel-0.5.2/setup.cfg.orig 2023-06-23 09:54:07.723287930 +0200 ++++ MONAILabel-0.5.2/setup.cfg 2023-06-23 13:11:24.785087729 +0200 +@@ -47,15 +47,15 @@ + schedule==1.1.0 + dicomweb-client==0.56.2 + timeloop==1.0.2 +- expiringdict==1.2.1 ++ expiringdict>=1.2.1 + expiring_dict==1.1.0 + cachetools==5.2.0 + watchdog==2.1.8 + pydicom==2.3.0 +- pydicom-seg==0.4.0 ++ pydicom-seg>=0.4.0 + pynetdicom==2.0.2 + pynrrd==0.4.3 +- opencv-python-headless==4.5.5.64 ++ opencv-contrib-python>=4.6.0 + numpymaxflow==0.0.2 + girder-client==3.1.14 + ninja==1.10.2.3 diff --git a/easybuild/easyconfigs/p/pydicom-seg/pydicom-seg-0.4.1-foss-2022a.eb b/easybuild/easyconfigs/p/pydicom-seg/pydicom-seg-0.4.1-foss-2022a.eb new file mode 100644 index 00000000000..6d9a6cd4b45 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom-seg/pydicom-seg-0.4.1-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'pydicom-seg' +version = '0.4.1' + +homepage = 'https://github.com/razorx89/pydicom-seg' +description = """Reading and writing of DICOM-SEG medical image segmentation storage files + using pydicom as DICOM serialization/deserialization library.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SimpleITK', '2.1.1.2'), + ('pydicom', '2.3.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'patches': ['pydicom-seg-0.4.1_dep-fix.patch'], + 'checksums': [ + 'ec6bbd961d44b2fb347a9aa313d6b66c5aa8db9d002d28a58fa549ff48a431fb', # pydicom-seg-0.4.1.tar.gz + '71d312e66894e9f7eebca690bfa129bfcd9cfb9ddac974657fafbe34a08d4524', # pydicom-seg-0.4.1_dep-fix.patch + ], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pydicom-seg/pydicom-seg-0.4.1_dep-fix.patch b/easybuild/easyconfigs/p/pydicom-seg/pydicom-seg-0.4.1_dep-fix.patch new file mode 100644 index 00000000000..3e793f96d7c --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom-seg/pydicom-seg-0.4.1_dep-fix.patch @@ -0,0 +1,38 @@ +Python 3.10.4 for GCCcore-11.3.0 uses jsonschema 4.4.0 +Author: Petr Král (INUITS) +diff -u pydicom-seg-0.4.1/pyproject.toml.orig pydicom-seg-0.4.1/pyproject.toml +--- pydicom-seg-0.4.1/pyproject.toml.orig 2023-02-16 11:32:28.351423500 +0100 ++++ pydicom-seg-0.4.1/pyproject.toml 2023-06-23 12:08:00.072754917 +0200 +@@ -18,7 +18,7 @@ + pydicom = ">=1.4.2" + SimpleITK = ">1.2.4" + numpy = "^1.18.0" +-jsonschema = "^3.2.0" ++jsonschema = ">=3.2.0" + + [tool.poetry.dev-dependencies] + pytest = "^5.3.2" +diff -u pydicom-seg-0.4.1/setup.py.orig pydicom-seg-0.4.1/setup.py +--- pydicom-seg-0.4.1/setup.py.orig 2023-02-16 11:34:18.241670100 +0100 ++++ pydicom-seg-0.4.1/setup.py 2023-06-23 12:08:22.012960453 +0200 +@@ -9,7 +9,7 @@ + + install_requires = \ + ['SimpleITK>1.2.4', +- 'jsonschema>=3.2.0,<4.0.0', ++ 'jsonschema>=3.2.0', + 'numpy>=1.18.0,<2.0.0', + 'pydicom>=1.4.2'] + +diff -u pydicom-seg-0.4.1/PKG-INFO.orig pydicom-seg-0.4.1/PKG-INFO +--- pydicom-seg-0.4.1/PKG-INFO.orig 2023-02-16 11:34:18.242097400 +0100 ++++ pydicom-seg-0.4.1/PKG-INFO 2023-06-23 12:08:38.909784959 +0200 +@@ -14,7 +14,7 @@ + Classifier: Programming Language :: Python :: 3.8 + Classifier: Programming Language :: Python :: 3.9 + Requires-Dist: SimpleITK (>1.2.4) +-Requires-Dist: jsonschema (>=3.2.0,<4.0.0) ++Requires-Dist: jsonschema (>=3.2.0) + Requires-Dist: numpy (>=1.18.0,<2.0.0) + Requires-Dist: pydicom (>=1.4.2) + Description-Content-Type: text/markdown diff --git a/easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb b/easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb new file mode 100644 index 00000000000..08788da5098 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.31.0' + +homepage = 'https://pypi.python.org/pypi/requests/%(version)s' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.10.4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/requests-%(version)s-py%(pyshortver)s.egg'] +} + +moduleclass = 'devel' From 1d93d9d6d4b74af003d543ca87664582136d7e58 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 23 Jun 2023 15:08:25 +0200 Subject: [PATCH 7830/9987] adding easyconfigs: DEICODE-0.2.4-foss-2022a.eb --- .../d/DEICODE/DEICODE-0.2.4-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/d/DEICODE/DEICODE-0.2.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/DEICODE/DEICODE-0.2.4-foss-2022a.eb b/easybuild/easyconfigs/d/DEICODE/DEICODE-0.2.4-foss-2022a.eb new file mode 100644 index 00000000000..f81e65cc515 --- /dev/null +++ b/easybuild/easyconfigs/d/DEICODE/DEICODE-0.2.4-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'DEICODE' +version = '0.2.4' + +homepage = 'https://library.qiime2.org/plugins/deicode/19/' +description = """ +DEICODE is a form of Aitchison Distance that is robust to high levels of +sparsity. DEICODE utilizes a natural solution to the zero problem formulated in +recommendation systems called matrix completion. A simple way to interpret the +method is, as a robust compositional PCA (via SVD) where zero values do not +influence the resulting ordination. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-bio', '0.5.7'), + ('h5py', '3.7.0'), +] + +exts_list = [ + ('biom-format', '2.1.15', { + 'modulename': 'biom', + 'checksums': ['3bda2096e663dc1cb6f90f51b394da0838b9be5164a44370c134ce5b3b2a4dd3'], + }), + ('deicode', version, { + 'preinstallopts': """sed -i "/'nose /d" setup.py && """, + 'checksums': ['29472dc1f2d7c0cefeab3517d957a2476b5fb981861d1f3deeb75dfa291b34e4'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['deicode --help'] + +moduleclass = 'math' From 356a6d24011ac86e76d4b6e914ba102c6bc5f3fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 23 Jun 2023 15:42:33 +0200 Subject: [PATCH 7831/9987] add missing checksums --- .../r/requests/requests-2.31.0-foss-2022a.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb b/easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb index 08788da5098..bf8932f86b5 100644 --- a/easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb +++ b/easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb @@ -8,16 +8,16 @@ description = """Python http for humans""" toolchain = {'name': 'foss', 'version': '2022a'} -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] +sources = [SOURCE_TAR_GZ] + +checksums = ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'] dependencies = [ ('Python', '3.10.4'), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/requests-%(version)s-py%(pyshortver)s.egg'] -} +sanity_pip_check = True +use_pip = True +download_dep_fail = True moduleclass = 'devel' From c33a68abdd4b0134f042e8d3b3ad08c1d50332fb Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 23 Jun 2023 14:07:09 +0000 Subject: [PATCH 7832/9987] Always use -redo option for tests --- easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb | 2 +- easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb index b3314fe82c3..9f8e8abad12 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022a.eb @@ -50,7 +50,7 @@ sanity_check_paths = { sanity_check_commands = [ "iqtree2 --help", "mkdir -p $TMPDIR/{test-omp,test-mpi}", - "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy -redo", "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo", ] diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb index 3605d94c4f9..bc6834e8e80 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.6-gompi-2022b.eb @@ -50,7 +50,7 @@ sanity_check_paths = { sanity_check_commands = [ "iqtree2 --help", "mkdir -p $TMPDIR/{test-omp,test-mpi}", - "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy -redo", "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo", ] From 59098f9876f43d1105e6b1084b17e4e9d45cbad4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 23 Jun 2023 16:07:46 +0200 Subject: [PATCH 7833/9987] adding easyconfigs: build-0.10.0-foss-2022b.eb --- .../b/build/build-0.10.0-foss-2022b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/build/build-0.10.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022b.eb b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022b.eb new file mode 100644 index 00000000000..784b28f5fb3 --- /dev/null +++ b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'build' +version = '0.10.0' + +homepage = 'https://github.com/pypa/build' +description = """A simple, correct Python build frontend.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + (name, version, { + 'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'], + }), +] + +sanity_check_commands = [ + "python3 -m build -V", +] + +moduleclass = 'devel' From 1403db23750e1fcf632684e41233e7f91da427f0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 23 Jun 2023 16:08:18 +0200 Subject: [PATCH 7834/9987] adding easyconfigs: minimap2-2.26-GCCcore-12.2.0.eb --- .../minimap2/minimap2-2.26-GCCcore-12.2.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.26-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.26-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.26-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..34d616d1e19 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.26-GCCcore-12.2.0.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# DeepThought, Flinders University +# Updated to 2.22 +# R.QIAO + +# Update Petr Král (INUITS) +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.26' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['6a588efbd273bff4f4808d5190957c50272833d2daeb4407ccf4c1b78143624c'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('zlib', '1.2.12')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' From 2539c4a5a94b41a67e8abbd1e762babcfa1285fe Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 23 Jun 2023 15:52:50 +0100 Subject: [PATCH 7835/9987] update homepage for NWChem 7.x --- .../n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb | 2 +- .../n/NWChem/NWChem-7.0.2-intel-2019b-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb | 2 +- easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb index 791e0dc8351..79f6cbbc42f 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.0-intel-2019b-Python-3.7.4.eb @@ -4,7 +4,7 @@ versionsuffix = '-Python-%(pyver)s' local_verdate = '2020-02-26' local_revision = '2c9a1c7c' -homepage = 'http://www.nwchem-sw.org' +homepage = 'https://nwchemgit.github.io/' description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2019b-Python-3.7.4.eb index e176204adb4..098a37fd47c 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2019b-Python-3.7.4.eb @@ -4,7 +4,7 @@ versionsuffix = '-Python-%(pyver)s' local_verdate = '2020-10-12' local_revision = 'b9985dfa' -homepage = 'https://www.nwchem-sw.org' +homepage = 'https://nwchemgit.github.io/' description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb index b613590b4a3..ebc87eaa333 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2021a.eb @@ -3,7 +3,7 @@ version = '7.0.2' local_verdate = '2020-10-12' local_revision = 'b9985dfa' -homepage = 'https://www.nwchem-sw.org' +homepage = 'https://nwchemgit.github.io/' description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb index 25d9440384b..53768c81107 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb @@ -3,7 +3,7 @@ version = '7.0.2' local_verdate = '2020-10-12' local_revision = 'b9985dfa' -homepage = 'https://www.nwchem-sw.org' +homepage = 'https://nwchemgit.github.io/' description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. From 18bb8c592e8870b6360025028935a13d690a913a Mon Sep 17 00:00:00 2001 From: vsc10800 Date: Fri, 23 Jun 2023 17:07:18 +0200 Subject: [PATCH 7836/9987] adding easyconfigs: Transformers-4.29.2-foss-2022a.eb --- .../Transformers-4.29.2-foss-2022a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/t/Transformers/Transformers-4.29.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.29.2-foss-2022a.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.29.2-foss-2022a.eb new file mode 100644 index 00000000000..632079f4a9d --- /dev/null +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.29.2-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'Transformers' +version = '4.29.2' + +homepage = 'https://github.com/huggingface/transformers' +description = """ +State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('Rust', '1.60.0'), # required for setuptools-rust, which is needed for tokenizers +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('regex', '2022.10.31', { + 'checksums': ['a3a98921da9a1bf8457aeee6a551948a83601689e5ecdd736894ea9bbec77e83'], + }), + ('tokenizers', '0.13.2', { + 'checksums': ['f9525375582fd1912ac3caa2f727d36c86ff8c0c6de45ae1aaff90f87f33b907'], + }), + ('huggingface-hub', '0.15.1', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['a61b7d1a7769fe10119e730277c72ab99d95c48d86a3d6da3e9f3d0f632a4081'], + }), + ('transformers', version, { + 'checksums': ['ed9467661f459f1ce49461d83f18f3b36b6a37f306182dc2ba272935f3b93ebb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From ec53a235de0d41f6a59a4f643b334f5158906deb Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 23 Jun 2023 16:40:47 +0100 Subject: [PATCH 7837/9987] remove default sanity_check_paths Co-authored-by: Alex Domingo --- .../p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb index 6912c2271d7..9bd7a58dcbe 100644 --- a/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb @@ -42,11 +42,6 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_pip_check = True moduleclass = 'bio' From 5bb88efddb8c96bdc5fc2d616f540e4982f10026 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 23 Jun 2023 16:43:54 +0100 Subject: [PATCH 7838/9987] remove default exts_default_options --- .../p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb index 9bd7a58dcbe..d70d646ec66 100644 --- a/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb @@ -20,8 +20,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('edlib', '1.3.8.post1', { 'checksums': ['81bc688e8fc69d657a6b5067e104a0924b0217b7ab54547155278935d09346e0'], From c363809cb98f4af7939c4168cb322f83cac4006b Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 23 Jun 2023 16:58:15 +0100 Subject: [PATCH 7839/9987] Use existing python-parasail and tqdm deps. --- .../Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb index d70d646ec66..02d9af193c6 100644 --- a/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/Pychopper/Pychopper-2.3.1-intel-2019b-Python-3.7.4.eb @@ -15,7 +15,9 @@ dependencies = [ ('matplotlib', '3.1.1', versionsuffix), ('Biopython', '1.75', versionsuffix), ('parasail', '2.4.1'), + ('python-parasail', '1.2', versionsuffix), ('Seaborn', '0.10.0', versionsuffix), + ('tqdm', '4.41.1'), ] use_pip = True @@ -24,15 +26,9 @@ exts_list = [ ('edlib', '1.3.8.post1', { 'checksums': ['81bc688e8fc69d657a6b5067e104a0924b0217b7ab54547155278935d09346e0'], }), - ('parasail', '1.2', { - 'checksums': ['6ceef978e7d06293c38c9824f76557f3d7e137cb05487be31bf89286f7a8201e'], - }), ('sphinx_rtd_theme', '0.4.3', { 'checksums': ['728607e34d60456d736cc7991fd236afb828b21b82f956c5ea75f94c8414040a'], }), - ('tqdm', '4.45.0', { - 'checksums': ['00339634a22c10a7a22476ee946bbde2dbe48d042ded784e4d88e0236eca5d81'], - }), (name, version, { 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/nanoporetech/pychopper/archive'], From 6101f784d9a6bd142018c7996bd59a2673363d8e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 23 Jun 2023 20:00:58 +0200 Subject: [PATCH 7840/9987] add python builddependencies, also run tests_v1 test and use intel toolchain --- .../easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb | 9 +++++---- ....1-iimpi-2019b.eb => ABINIT-9.2.1-intel-2019b.eb} | 12 ++++++------ 2 files changed, 11 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/a/ABINIT/{ABINIT-9.2.1-iimpi-2019b.eb => ABINIT-9.2.1-intel-2019b.eb} (83%) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb index 38ed401f349..e5246fc8c99 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-foss-2019b.eb @@ -17,6 +17,9 @@ source_urls = ['https://www.abinit.org/sites/default/files/packages/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0'] +builddependencies = [ + ('Python', '3.7.4'), +] dependencies = [ ('libxc', '4.3.4'), ('netCDF', '4.7.1'), @@ -45,10 +48,8 @@ configopts += '--with-hdf5="${EBROOTHDF5}" ' configopts += 'FCFLAGS="${FCFLAGS} --free-line-length-none" ' # `make check` is just executing some basic unit tests. -# In principle, one should run `make tests_v1`` to have some basic validation -# but it seems it's not possible to execute abinit at the end of the build -# due to missing dynamic libs (e.g. libxc) -runtest = "check" +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb similarity index 83% rename from easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb rename to easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb index 4a255ae464f..846d9837a95 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-iimpi-2019b.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2019b.eb @@ -10,15 +10,17 @@ description = """ABINIT is a package whose main program allows one to find the t and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" -toolchain = {'name': 'iimpi', 'version': '2019b'} +toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'usempi': True, 'pic': True} source_urls = ['https://www.abinit.org/sites/default/files/packages/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0'] +builddependencies = [ + ('Python', '3.7.4'), +] dependencies = [ - ("imkl", "2019.5.281"), ('libxc', '4.3.4'), ('netCDF', '4.7.1'), ('netCDF-Fortran', '4.5.2'), @@ -44,10 +46,8 @@ configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' configopts += '--with-hdf5="${EBROOTHDF5}" ' # `make check` is just executing some basic unit tests. -# In principle, one should run `make tests_v1`` to have some basic validation -# but it seems it's not possible to execute abinit at the end of the build -# due to missing dynamic libs (e.g. libxc) -runtest = 'check' +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], From 3684bfaf78d43a15835b891ca7d163e9a4e4a910 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 23 Jun 2023 19:27:57 +0100 Subject: [PATCH 7841/9987] Apply suggestions from code review Co-authored-by: Alex Domingo --- .../f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb b/easybuild/easyconfigs/f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb index a29e2ae4bff..529db9c4abd 100644 --- a/easybuild/easyconfigs/f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/f/fastp/fastp-0.20.1-iccifort-2020.1.217.eb @@ -9,10 +9,16 @@ description = """A tool designed to provide fast all-in-one preprocessing for Fa toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -source_urls = ['https://github.com/OpenGene/fastp/archive/'] +# https://github.com/OpenGene/fastp +github_account = 'OpenGene' +source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['e1b663717850bed7cb560c0c540e9a05dd9448ec76978faaf853a6959fd5b1b3'] +dependencies = [ + ('zlib', '1.2.11'), +] + skipsteps = ['configure'] buildopts = ' CXX=${CXX}' @@ -22,8 +28,8 @@ preinstallopts = 'mkdir -p %(installdir)s/bin && ' installopts = 'PREFIX=%(installdir)s' sanity_check_paths = { - 'dirs': [], 'files': ['bin/fastp'], + 'dirs': [], } sanity_check_commands = [('fastp', '--help')] From df0c21d3c67ca52f27b2bfce157a80040aa538b3 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 23 Jun 2023 20:51:50 +0100 Subject: [PATCH 7842/9987] remove out of date comment --- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb | 3 --- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb | 3 --- 2 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb index 794ce9c8257..2d5442b1329 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-foss-2020b.eb @@ -14,9 +14,6 @@ source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/ sources = [SOURCELOWER_TAR_GZ] checksums = ['195d5593772fc483f63f08794d79e4bab30c2ec58e6ce4b0fb6bcc0e0c48f31d'] -# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, -# other for new source tarball downloaded from GitHub - builddependencies = [('CMake', '3.18.4')] separate_build_dir = True diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb index 332c5869a4b..1637aac0c64 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.2.0-intel-2020b.eb @@ -14,9 +14,6 @@ source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/ sources = [SOURCELOWER_TAR_GZ] checksums = ['195d5593772fc483f63f08794d79e4bab30c2ec58e6ce4b0fb6bcc0e0c48f31d'] -# two valid checksums: one for original source tarball downloaded from computation.llnl.gov, -# other for new source tarball downloaded from GitHub - builddependencies = [('CMake', '3.18.4')] separate_build_dir = True From 1dc0da2ceb3a19fb1bce120692b612996751af96 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 23 Jun 2023 20:56:25 +0100 Subject: [PATCH 7843/9987] update homepage for SUNDIALS 5.x and 6.x --- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-foss-2019b.eb | 2 +- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb | 2 +- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb | 2 +- .../easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb | 2 +- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb | 2 +- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2022a.eb | 2 +- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.5.1-foss-2022a.eb | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-foss-2019b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-foss-2019b.eb index 7c93955f97a..262e01cdaf4 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-foss-2019b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-foss-2019b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SUNDIALS' version = '5.1.0' -homepage = 'https://computation.llnl.gov/projects/sundials' +homepage = 'https://computing.llnl.gov/projects/sundials' description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb index e1d296dc51e..37c34c0232f 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.1.0-intel-2019b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SUNDIALS' version = '5.1.0' -homepage = 'https://computation.llnl.gov/projects/sundials' +homepage = 'https://computing.llnl.gov/projects/sundials' description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb index 51543acdb79..29b35cb8304 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-foss-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SUNDIALS' version = '5.7.0' -homepage = 'https://computation.llnl.gov/projects/sundials' +homepage = 'https://computing.llnl.gov/projects/sundials' description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb index ccf4e479638..52675e145f0 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-fosscuda-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SUNDIALS' version = '5.7.0' -homepage = 'https://computation.llnl.gov/projects/sundials' +homepage = 'https://computing.llnl.gov/projects/sundials' description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb index 5c283e4de39..76e6c5a3a94 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-5.7.0-intel-2020b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SUNDIALS' version = '5.7.0' -homepage = 'https://computation.llnl.gov/projects/sundials' +homepage = 'https://computing.llnl.gov/projects/sundials' description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2021b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2021b.eb index 59ea1cd22a1..12e9f082554 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2021b.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SUNDIALS' version = '6.3.0' -homepage = 'https://computation.llnl.gov/projects/sundials' +homepage = 'https://computing.llnl.gov/projects/sundials' description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2022a.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2022a.eb index efe9f2b54de..3ab52d26040 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.3.0-foss-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SUNDIALS' version = '6.3.0' -homepage = 'https://computation.llnl.gov/projects/sundials' +homepage = 'https://computing.llnl.gov/projects/sundials' description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.5.1-foss-2022a.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.5.1-foss-2022a.eb index df08784684d..04e91b5411a 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.5.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.5.1-foss-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'SUNDIALS' version = '6.5.1' -homepage = 'https://computation.llnl.gov/projects/sundials' +homepage = 'https://computing.llnl.gov/projects/sundials' description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" From c6bfb5dd8713cd0c7f5bb535bee4559b0522fd28 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 24 Jun 2023 08:15:22 +0100 Subject: [PATCH 7844/9987] remove unneded preinstallopts --- .../TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb index f9603ef4d94..98bc920ae4a 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Graphics/TensorFlow-Graphics-2021.12.3-foss-2021b-CUDA-11.4.1.eb @@ -43,7 +43,6 @@ exts_list = [ ('OpenEXR', '1.3.9', { 'modulename': 'Imath', 'patches': ['TensorFlow-Graphics-2021.12.3_openexr-setup.patch'], - 'preinstallopts': "env | grep '^EB' && cat setup.py && ", 'checksums': [ {'OpenEXR-1.3.9.tar.gz': 'cffcd13906291ef1a81b369c1c0e907648ecd24363668873691f44866704ab21'}, {'TensorFlow-Graphics-2021.12.3_openexr-setup.patch': From 7efdc28fb7848bca80a02e9b963e2f26748349ed Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 24 Jun 2023 09:35:05 +0100 Subject: [PATCH 7845/9987] clarify info in comment --- easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb b/easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb index 9fc25a873aa..0bbf278870b 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-5.0.6-intel-2019b.eb @@ -8,6 +8,7 @@ description = """manipulates and analyzes data stored in netCDF-accessible forma toolchain = {'name': 'intel', 'version': '2019b'} # compile with -O1 to work around Intel compiler crash (Segmentation violation signal raised) +# which happens on some processors (such as skylake, cascadelake) toolchainopts = {'lowopt': True} source_urls = ['https://github.com/nco/nco/archive/'] From f93c07868b3b5f397a6108b291dc46a5ec5a588f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 24 Jun 2023 13:30:39 +0200 Subject: [PATCH 7846/9987] adding easyconfigs: gfbf-2023.05.eb --- easybuild/easyconfigs/g/gfbf/gfbf-2023.05.eb | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2023.05.eb diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2023.05.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2023.05.eb new file mode 100644 index 00000000000..f77e8efd7d8 --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2023.05.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2023.05' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '12.3.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' From 262774e263bf14d2656572828266afd62a2e26aa Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 24 Jun 2023 17:33:38 +0200 Subject: [PATCH 7847/9987] Update easybuild/easyconfigs/t/Tapenade/Tapenade-3.16-Java-17.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/t/Tapenade/Tapenade-3.16-Java-17.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Tapenade/Tapenade-3.16-Java-17.eb b/easybuild/easyconfigs/t/Tapenade/Tapenade-3.16-Java-17.eb index 30955a40acb..f474d6f883d 100644 --- a/easybuild/easyconfigs/t/Tapenade/Tapenade-3.16-Java-17.eb +++ b/easybuild/easyconfigs/t/Tapenade/Tapenade-3.16-Java-17.eb @@ -14,7 +14,7 @@ sources = ['%(namelower)s_%(version)s.tar'] checksums = ['5ee44218a11861e3a99d413171d4016f1872b652c204c27e0be57d1740fda316'] dependencies = [ - ('Java', '17', '', True), + ('Java', '17'), ] sanity_check_paths = { From 9819445f3815fb97da80faf3f904162c74ffd855 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 24 Jun 2023 18:21:36 +0200 Subject: [PATCH 7848/9987] xarray/2023.4.2: foss/2022b -> gfbf/2022b --- ...ray-2023.4.2-foss-2022b.eb => xarray-2023.4.2-gfbf-2022b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/x/xarray/{xarray-2023.4.2-foss-2022b.eb => xarray-2023.4.2-gfbf-2022b.eb} (92%) diff --git a/easybuild/easyconfigs/x/xarray/xarray-2023.4.2-foss-2022b.eb b/easybuild/easyconfigs/x/xarray/xarray-2023.4.2-gfbf-2022b.eb similarity index 92% rename from easybuild/easyconfigs/x/xarray/xarray-2023.4.2-foss-2022b.eb rename to easybuild/easyconfigs/x/xarray/xarray-2023.4.2-gfbf-2022b.eb index 5d8e95b6d72..a8020c97ff4 100644 --- a/easybuild/easyconfigs/x/xarray/xarray-2023.4.2-foss-2022b.eb +++ b/easybuild/easyconfigs/x/xarray/xarray-2023.4.2-gfbf-2022b.eb @@ -8,7 +8,7 @@ description = """xarray (formerly xray) is an open source project and Python pac the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures.""" -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'gfbf', 'version': '2022b'} dependencies = [ ('Python', '3.10.8'), From 792795efd459e6a0a4492cad4ed889f5a9342ede Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sat, 24 Jun 2023 18:25:02 +0200 Subject: [PATCH 7849/9987] Correct checksums in VTK/9.2.6 for foss/2022b --- easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2022b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2022b.eb index 771c7802cbc..8182cdf8c40 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2022b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.2.6-foss-2022b.eb @@ -26,8 +26,8 @@ sources = [ ] patches = [('vtk-version.egg-info', '.')] checksums = [ - {'VTK-9.2.2.tar.gz': '1c5b0a2be71fac96ff4831af69e350f7a0ea3168981f790c000709dcf9121075'}, - {'VTKData-9.2.2.tar.gz': '4b0ac438c77773ff741fd02c0e3b0dc1406b4c51e6cbe4e8304306fa125f27bf'}, + {'VTK-9.2.6.tar.gz': '06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12'}, + {'VTKData-9.2.6.tar.gz': '032c4b827173f859c898403d25360dc99409a4674559ad58f48828f23a6258b8'}, {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'}, ] From 70ee6b0b1f7b640cf4b3e9bcfe37fd00f2fac5e8 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 24 Jun 2023 22:34:29 +0200 Subject: [PATCH 7850/9987] bump OpenSSL 1.1 wrapper fallback to 1.1.1u --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb index ee1e94ca6bb..001713087da 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb @@ -27,11 +27,11 @@ builddependencies = [('pkgconf', '1.8.0')] # component list, which will be build and installed as usual. components = [ - (name, '1.1.1t', { + (name, '1.1.1u', { 'easyblock': 'EB_OpenSSL', 'source_urls': ['https://www.openssl.org/source/'], 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['8dee9b24bdb1dcbf0c3d1e9b02fb8f6bf22165e807f45adeb7c9677536859d3b'], + 'checksums': ['e2f8d84b523eecd06c7be7626830370300fbcc15386bf5142d72758f6963ebc6'], 'start_dir': '%(namelower)s-%(version)s', }), ] From 6d6131febaffaf4dd501dbdd487edd6712026fba Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 25 Jun 2023 09:57:08 +0100 Subject: [PATCH 7851/9987] Apply suggestions from code review --- .../PheWeb-1.1.20-foss-2019b-Python-3.7.4.eb | 20 ++----------------- 1 file changed, 2 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/p/PheWeb/PheWeb-1.1.20-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PheWeb/PheWeb-1.1.20-foss-2019b-Python-3.7.4.eb index 32260ebf77c..50017dfb45d 100644 --- a/easybuild/easyconfigs/p/PheWeb/PheWeb-1.1.20-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PheWeb/PheWeb-1.1.20-foss-2019b-Python-3.7.4.eb @@ -4,26 +4,22 @@ name = 'PheWeb' version = '1.1.20' versionsuffix = '-Python-%(pyver)s' - homepage = 'https://github.com/statgen/pheweb' description = """A tool for building PheWAS websites from association files""" toolchain = {'name': 'foss', 'version': '2019b'} - dependencies = [ ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), ('Pysam', '0.15.3'), - ('openpyxl', '3.0.3', versionsuffix, ('GCCcore', '8.3.0')), - ('Flask', '1.1.2', versionsuffix, ('GCCcore', '8.3.0')), + ('openpyxl', '3.0.3', versionsuffix), + ('Flask', '1.1.2', versionsuffix), ('tqdm', '4.41.1'), ] use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('Brotli', '1.0.7', { 'source_tmpl': '%(name)s-%(version)s.zip', @@ -41,24 +37,12 @@ exts_list = [ ('marisa-trie', '0.7.5', { 'checksums': ['c73bc25d868e8c4ea7aa7f1e19892db07bba2463351269b05340ccfa06eb2baf'], }), - ('sortedcontainers', '2.2.2', { - 'checksums': ['4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba'], - }), - ('intervaltree', '3.0.2', { - 'checksums': ['cb4f61c81dcb4fea6c09903f3599015a83c9bdad1f0bbd232495e6681e19e273'], - }), - ('requests', '2.24.0', { - 'checksums': ['b3559a131db72c33ee969480840fff4bb6dd111de7dd27c8ee1f820f4f00231b'], - }), ('gunicorn', '20.0.4', { 'checksums': ['1904bb2b8a43658807108d59c3f3d56c2b6121a701161de0ddf9ad140073c626'], }), ('boltons', '19.1.0', { 'checksums': ['c32b2d121331a9bc7c220050d4273f3aa359b7569cb4794188e71524603113dc'], }), - ('blist', '1.3.6', { - 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], - }), ('wget', '3.2', { 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['35e630eca2aa50ce998b9b1a127bb26b30dfee573702782aa982f875e3f16061'], From 7252efcd41c8b43fb8a670348d3fafb83eb79933 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 25 Jun 2023 13:02:13 +0200 Subject: [PATCH 7852/9987] adding easyconfigs: tmux-3.3a.eb, tmux-3.3a-GCCcore-12.2.0.eb, tmux-3.3a-GCCcore-12.3.0.eb --- .../t/tmux/tmux-3.3a-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ .../t/tmux/tmux-3.3a-GCCcore-12.3.0.eb | 36 +++++++++++++++++++ easybuild/easyconfigs/t/tmux/tmux-3.3a.eb | 30 ++++++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/tmux/tmux-3.3a.eb diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9a8359f7887 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.3a' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e4fd347843bd0772c4f48d6dde625b0b109b7a380ff15db21e97c11a4dcdf93f'] + +builddependencies = [ + ('binutils', '2.39'), + ('Bison', '3.8.2'), + ('make', '4.4.1'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.3'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ac1145d1c84 --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.3a' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e4fd347843bd0772c4f48d6dde625b0b109b7a380ff15db21e97c11a4dcdf93f'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('make', '4.4.1'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.4'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.3a.eb b/easybuild/easyconfigs/t/tmux/tmux-3.3a.eb new file mode 100644 index 00000000000..0868cabd26d --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.3a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.3a' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e4fd347843bd0772c4f48d6dde625b0b109b7a380ff15db21e97c11a4dcdf93f'] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.4'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +sanity_check_commands = ["tmux --help 2>&1 | grep 'usage: tmux'"] + +moduleclass = 'tools' From 16c6a3d21acb3fcd9323c540ca878c25d52ae53e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 25 Jun 2023 13:04:40 +0200 Subject: [PATCH 7853/9987] adding easyconfigs: ncurses-6.4.eb --- .../easyconfigs/n/ncurses/ncurses-6.4.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.4.eb diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.4.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.4.eb new file mode 100644 index 00000000000..7edecb90d1b --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.4.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.4' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6931283d9ac87c5073f30b6290c4c75f21632bb4fc3603ac8100812bed248159'] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts, + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' From f60d60c4b42b66114fb9e985d78aae8f1d8fd96e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 25 Jun 2023 21:48:03 +0200 Subject: [PATCH 7854/9987] adding easyconfigs: git-2.41.0-GCCcore-12.3.0-nodocs.eb --- .../g/git/git-2.41.0-GCCcore-12.3.0-nodocs.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.41.0-GCCcore-12.3.0-nodocs.eb diff --git a/easybuild/easyconfigs/g/git/git-2.41.0-GCCcore-12.3.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.41.0-GCCcore-12.3.0-nodocs.eb new file mode 100644 index 00000000000..c327d507709 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.41.0-GCCcore-12.3.0-nodocs.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.41.0' +versionsuffix = '-nodocs' + +homepage = 'https://git-scm.com' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4f0b74bbde2800b00d3a50a7f389bcf1d59f1265b6986c00048d8ba4892ab01a'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('cURL', '8.0.1'), + ('expat', '2.5.0'), + ('gettext', '0.21.1'), + ('Perl', '5.36.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +postinstallcmds = ['cd contrib/subtree; make install'] + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['libexec/git-core', 'share'], +} + +moduleclass = 'tools' From 79a4d64e629bcf34c2f44b422fc18ea5cf9de301 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Mon, 26 Jun 2023 13:39:05 +1000 Subject: [PATCH 7855/9987] Create deepTools-3.5.2-foss-2022a.eb New version, new toolchain, new dependencies --- .../d/deepTools/deepTools-3.5.2-foss-2022a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/d/deepTools/deepTools-3.5.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.2-foss-2022a.eb b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.2-foss-2022a.eb new file mode 100644 index 00000000000..fb636a9cec8 --- /dev/null +++ b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.2-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'deepTools' +version = '3.5.2' + +homepage = 'https://deeptools.readthedocs.io/' +description = """deepTools is a suite of python tools particularly developed for the efficient analysis of + high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('plotly.py', '5.12.0'), + ('Pysam', '0.19.1'), + ('pyBigWig', '0.3.18'), +] + +use_pip = True + +exts_list = [ + ('py2bit', '0.3.0', { + 'checksums': ['450555c40cba66957ac8c9a4b6afb625fb34c4bb41638de78c87661ff8b682ef'], + }), + ('deeptoolsintervals', '0.1.9', { + 'checksums': ['7d94c36fd2b6f10d8b99e536d2672e8228971f1fc810497d33527bba2c40d4f6'], + }), + ('numpydoc', '1.5.0', { + 'checksums': ['b0db7b75a32367a0e25c23b397842c65e344a1206524d16c8069f0a1c91b5f4c'], + }), + (name, version, { + 'checksums': ['9367f9037b1822b7d69d5abaf47ca25bf0e5dc4cb8be85bd55b6f63c90781941'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bamCompare', 'bin/bamCoverage', 'bin/bamPEFragmentSize', 'bin/computeGCBias', 'bin/computeMatrix', + 'bin/correctGCBias', 'bin/multiBamSummary', 'bin/plotCorrelation', 'bin/plotCoverage', + 'bin/plotHeatmap', 'bin/plotProfile'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From ef21e56fe3a29c3abf16f231a30902b31bfcfbff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2023 09:21:16 +0200 Subject: [PATCH 7856/9987] adding easyconfigs: openpyxl-3.1.2-GCCcore-12.2.0.eb --- .../openpyxl/openpyxl-3.1.2-GCCcore-12.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d705d5cf4ab --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.1.2' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('lxml', '4.9.2'), + ('Pillow', '9.4.0'), +] + +use_pip = True + +exts_list = [ + ('et_xmlfile', '1.1.0', { + 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['a6f5977418eff3b2d5500d54d9db50c8277a368436f4e4f8ddb1be3422870184'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From c737b204cbee63fe6a429b6ad54d760f2bf6159f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 26 Jun 2023 10:05:51 +0200 Subject: [PATCH 7857/9987] build Geant4 with QT and GDML, add necessary deps, simplify config options. --- .../g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb | 12 ++++-- .../Xerces-C++-3.2.4-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ 2 files changed, 48 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb index afb73b7a296..d535658d41f 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-11.1.2-GCC-11.3.0.eb @@ -28,14 +28,20 @@ dependencies = [ ('expat', '2.4.8'), # recommended CLHEP version, see https://geant4.web.cern.ch/download/release-notes/notes-v11.1.0.html ('CLHEP', '2.4.6.2'), + ('Xerces-C++', '3.2.4'), + ('Qt5', '5.15.5'), ('Geant4-data', '11.1', '', SYSTEM), ] _copts = [ - "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so", - "-DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include", - "-DCLHEP_ROOT_DIR=$EBROOTCLHEP", "-DGEANT4_INSTALL_DATA=OFF", + "-DGEANT4_USE_SYSTEM_ZLIB=ON", + "-DGEANT4_USE_SYSTEM_EXPAT=ON", + "-DGEANT4_USE_SYSTEM_CLHEP=ON", + "-DGEANT4_USE_QT=ON", + "-DGEANT4_USE_GDML=ON", + "-DGEANT4_USE_OPENGL_X11=ON", + "-DGEANT4_USE_RAYTRACER_X11=ON", ] configopts = ' '.join(_copts) diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..a35a5c214fe --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.4-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Xerces-C++' +version = '3.2.4' + +homepage = 'https://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['3d8ec1c7f94e38fee0e4ca5ad1e1d9db23cbf3a10bba626f6b4afa2dedafe5ab'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('cURL', '7.83.0'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/XInclude', + 'include/xercesc/xinclude/XIncludeUtils.hpp', + 'lib/libxerces-c-3.2.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' From 96b0ca50a02bd68e6ea6b6b850081d33921d9f20 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 26 Jun 2023 13:51:54 +0200 Subject: [PATCH 7858/9987] adding easyconfigs: LISFLOOD-FP-8.1-gompi-2022a.eb --- .../LISFLOOD-FP-8.1-gompi-2022a.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb new file mode 100644 index 00000000000..830048feaab --- /dev/null +++ b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'LISFLOOD-FP' +version = '8.1' + +homepage = 'https://www.seamlesswave.com/LISFLOOD8.0.html' +description = """The LISFLOOD-FP is a raster-based hydrodynamic model originally developed by +the University of Bristol. It has undergone extensive development since +conception and includes a collection of numerical schemes implemented to solve +a variety of mathematical approximations of the 2D shallow water equations of +different complexity. +The local inertia solver, known as the ACC solver, is widely used to simulate +floods with gradually-varying, subcritical flow over sufficiently rough +surfaces with Manning’s coefficient of at least 0.03. It has a version with +CPU-specific optimisations and enhanced with a subgrid channel model. +LISFLOOD-FP also includes second-order discontinuous Galerkin (DG2) and +first-order finite volume (FV1) solvers of the full shallow water equations for +modelling a wide range of flows, including rapidly-propagating, supercritical +flows, shock waves, or flows over very smooth surfaces. The DG2/FV1 solvers are +parallelised for the multi-core CPU architecture, but do not integrate with the +subgrid channel model nor with the CPU-specific optimisations. +""" + +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://zenodo.org/record/6912932/files/'] +sources = [{'download_filename': '%(name)s%20v%(version)s.zip', 'filename': SOURCE_ZIP}] +checksums = ['57df4ff38f8a47e6907bc4a98466bca6eecb540862a89b9db7e1c4fbe9259d95'] + +builddependencies = [ + ('CMake', '3.23.1') +] + +dependencies = [ + ('netCDF', '4.9.0') +] + +_lisflood_bins = ['DG2downscale', 'generateDG2DEM', 'generateDG2start', 'lisflood'] + +# It doesn't have a working make install, emulate in post-install step +skipsteps = ['install'] +postinstallcmds = ["mkdir %(installdir)s/bin"] +postinstallcmds += ["cp %s %%(installdir)s/bin/" % x for x in _lisflood_bins] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _lisflood_bins], + 'dirs': [], +} + +moduleclass = 'phys' From 9152837619dcd403f1992a4df26be860d294857d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2023 14:28:08 +0200 Subject: [PATCH 7859/9987] add Polychrome, shinycssloaders, princurve extensions to R 4.2.2 --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 80a36233f81..b0a37ef3a79 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3618,6 +3618,15 @@ exts_list = [ ('haldensify', '0.2.3', { 'checksums': ['fc0ee1d5bce54520bad6a1ce1cce5074eead6c8573dc4ce502c48a244d7f341c'], }), + ('Polychrome', '1.5.1', { + 'checksums': ['6fe7da62459d7b94b1a8516a4626971cf35b76331f46e36798b05d29aa00d143'], + }), + ('shinycssloaders', '1.0.0', { + 'checksums': ['744641836a4cede2bb47caff1b600bff2c3e450dfccd2af4fab0413a8ea87d64'], + }), + ('princurve', '2.1.6', { + 'checksums': ['0216332390eb27013b6ba62232782156dfc99ca640087fcaff53d2be9218f373'], + }), ] moduleclass = 'lang' From 01ff838af2538eaa5b5cb1862bd3a353a1cfc106 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2023 14:29:56 +0200 Subject: [PATCH 7860/9987] add TrajectoryUtils + slingshot extensions to R-bundle-Bioconductor 3.16 --- .../R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index 1b5f6973977..05cf1957834 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -1220,6 +1220,12 @@ exts_list = [ ('SpatialExperiment', '1.8.1', { 'checksums': ['0fdfc5642dde227b73d81812b6641f2d10223de66892b9d61ac80664cd6cbacd'], }), + ('TrajectoryUtils', '1.6.0', { + 'checksums': ['03f0ef8643c0a8be48e042efe5b17ce1840719dd70f16151216fe6aaef261c8c'], + }), + ('slingshot', '2.6.0', { + 'checksums': ['6348ecd10a1572593de1d329318f03d8b1352dc041290a092d25a72f5a8c0902'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From f21d2fda11c8a5e292940aa26e329853181b30b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2023 14:42:29 +0200 Subject: [PATCH 7861/9987] adding easyconfigs: KerasTuner-1.3.5-foss-2022a.eb --- .../KerasTuner/KerasTuner-1.3.5-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/k/KerasTuner/KerasTuner-1.3.5-foss-2022a.eb diff --git a/easybuild/easyconfigs/k/KerasTuner/KerasTuner-1.3.5-foss-2022a.eb b/easybuild/easyconfigs/k/KerasTuner/KerasTuner-1.3.5-foss-2022a.eb new file mode 100644 index 00000000000..83d26febf7b --- /dev/null +++ b/easybuild/easyconfigs/k/KerasTuner/KerasTuner-1.3.5-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'KerasTuner' +version = '1.3.5' + +homepage = 'https://keras.io/keras_tuner' +description = """KerasTuner is an easy-to-use, scalable hyperparameter optimization framework that solves the pain +points of hyperparameter search.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('TensorFlow', '2.11.0'), + ('scikit-learn', '1.1.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('kt-legacy', '1.0.5', { + 'checksums': ['dbbade58f12c6a6da6062f4b045a6395a8d4195815e3e064bc3e609b69c8a26c'], + 'modulename': 'kerastuner', + }), + ('keras-tuner', version, { + 'checksums': ['5f65fbf932e17883290b40cf4b95987129947cf607972594b453e3c26e5314b7'], + }), +] + +moduleclass = 'phys' From 01015060b045cf6bacf098c7eb0c43305715f233 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2023 14:51:37 +0200 Subject: [PATCH 7862/9987] add sanity check commands for deepTools 3.5.2 --- .../easyconfigs/d/deepTools/deepTools-3.5.2-foss-2022a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.2-foss-2022a.eb b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.2-foss-2022a.eb index fb636a9cec8..e52c04711ec 100644 --- a/easybuild/easyconfigs/d/deepTools/deepTools-3.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/d/deepTools/deepTools-3.5.2-foss-2022a.eb @@ -42,6 +42,12 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = [ + "bamCompare --help", + "multiBamSummary --help", + "plotHeatmap --help", +] + sanity_pip_check = True moduleclass = 'bio' From 87a8aace9efa13c022bb2644174af0d9e7f12cef Mon Sep 17 00:00:00 2001 From: ec-buzh Date: Mon, 26 Jun 2023 15:02:03 +0200 Subject: [PATCH 7863/9987] adding easyconfigs: MView-1.67-foss-2022a-Perl-5.34.1.eb --- .../MView-1.67-foss-2022a-Perl-5.34.1.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb diff --git a/easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb b/easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb new file mode 100644 index 00000000000..39229057947 --- /dev/null +++ b/easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb @@ -0,0 +1,25 @@ +easyblock = "Tarball" + +name = 'MView' +version = "1.67" +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://sourceforge.net/projects/bio-mview/' +description = """ MView reformats the results of a sequence database search or a + multiple alignment, optionally adding HTML markup.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Perl', '5.34.1')] + +sanity_check_paths = { + 'files': ["bin/mview"], + 'dirs': ["lib"], +} + +modextrapaths = {'PERL5LIB': 'lib'} + +moduleclass = 'bio' From 95bb0d65a716410b46ce6cf358f56145ed8c0f11 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 26 Jun 2023 15:02:25 +0200 Subject: [PATCH 7864/9987] add a sanity check command to LISFLOOD-FP v8.1 --- .../easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb index 830048feaab..ed8d404fced 100644 --- a/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb @@ -41,7 +41,7 @@ _lisflood_bins = ['DG2downscale', 'generateDG2DEM', 'generateDG2start', 'lisfloo # It doesn't have a working make install, emulate in post-install step skipsteps = ['install'] -postinstallcmds = ["mkdir %(installdir)s/bin"] +postinstallcmds = ["mkdir -p %(installdir)s/bin"] postinstallcmds += ["cp %s %%(installdir)s/bin/" % x for x in _lisflood_bins] sanity_check_paths = { @@ -49,4 +49,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["lisflood -version"] + moduleclass = 'phys' From 80436ac9ecb46236322a451c5f15f424a76b24e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 26 Jun 2023 15:10:01 +0200 Subject: [PATCH 7865/9987] adding easyconfigs: NanoStat-1.6.0-foss-2021a.eb --- .../n/NanoStat/NanoStat-1.6.0-foss-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2021a.eb b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2021a.eb new file mode 100644 index 00000000000..21aa0707fab --- /dev/null +++ b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'NanoStat' +version = '1.6.0' + + +homepage = 'https://github.com/wdecoster/nanostat' +description = """Calculate various statistics from a long read sequencing dataset in fastq, + bam or albacore sequencing summary format.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('nanoget', '1.18.1'), + ('nanomath', '1.2.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['e45fa8d1ab49bdaed17596c26c0af148b44e4af46238391a8bb7a1b4cc940079'], + }), +] + +sanity_check_paths = { + 'files': ['bin/NanoStat'], + 'dirs': [], +} + +sanity_check_commands = ["NanoStat --help"] + +moduleclass = 'tools' From b7654dabc3f920e164fe973254ad389102ad3223 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Jun 2023 15:16:00 +0200 Subject: [PATCH 7866/9987] remove duplicate empty line --- easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2021a.eb b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2021a.eb index 21aa0707fab..ae38968c030 100644 --- a/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2021a.eb +++ b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2021a.eb @@ -3,7 +3,6 @@ easyblock = 'PythonBundle' name = 'NanoStat' version = '1.6.0' - homepage = 'https://github.com/wdecoster/nanostat' description = """Calculate various statistics from a long read sequencing dataset in fastq, bam or albacore sequencing summary format.""" From ce268d9e3d4faa2d81c8cf838b6ea837bd906c65 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 26 Jun 2023 17:52:53 +0200 Subject: [PATCH 7867/9987] adding easyconfigs: Transformers-4.30.2-foss-2022b.eb, tokenizers-0.13.3-GCCcore-12.2.0.eb --- .../Transformers-4.30.2-foss-2022b.eb | 47 +++++++++++++++++++ .../tokenizers-0.13.3-GCCcore-12.2.0.eb | 27 +++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/t/Transformers/Transformers-4.30.2-foss-2022b.eb create mode 100644 easybuild/easyconfigs/t/tokenizers/tokenizers-0.13.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.30.2-foss-2022b.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.30.2-foss-2022b.eb new file mode 100644 index 00000000000..43cd50eb927 --- /dev/null +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.30.2-foss-2022b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'Transformers' +version = '4.30.2' + +homepage = 'https://github.com/huggingface/transformers' +description = """State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('Rust', '1.65.0'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('PyYAML', '6.0'), + ('tqdm', '4.64.1'), + ('tokenizers', '0.13.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('safetensors', '0.3.1', { + 'checksums': ['571da56ff8d0bec8ae54923b621cda98d36dcef10feb36fd492c4d0c2cd0e869'], + }), + ('regex', '2023.6.3', { + 'checksums': ['72d1a25bf36d2050ceb35b517afe13864865268dfb45910e2e17a84be6cbfeb0'], + }), + ('huggingface-hub', '0.15.1', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['a61b7d1a7769fe10119e730277c72ab99d95c48d86a3d6da3e9f3d0f632a4081'], + }), + ('%(namelower)s', version, { + 'checksums': ['f4a8aac4e1baffab4033f4a345b0d7dc7957d12a4f1ba969afea08205a513045'], + }), +] + +sanity_check_commands = [ + "python -c 'from transformers import AutoTokenizer'", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tokenizers/tokenizers-0.13.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.13.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a1a6dc421fc --- /dev/null +++ b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.13.3-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'tokenizers' +version = '0.13.3' + +homepage = 'https://github.com/huggingface/tokenizers' +description = "Fast State-of-the-Art Tokenizers optimized for Research and Production" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2e546dbb68b623008a5442353137fbb0123d311a6d7ba52f2667c8862a75af2e'] + +builddependencies = [ + ('binutils', '2.39'), + ('Rust', '1.65.0'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'lib' From c8afe3a6c21a26059dd2c1f8972c1daf0c2075f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 26 Jun 2023 19:01:01 +0200 Subject: [PATCH 7868/9987] adding easyconfigs: NanoStat-1.6.0-foss-2022a.eb, nanoget-1.18.1-foss-2022a.eb, nanomath-1.3.0-foss-2022a.eb --- .../n/NanoStat/NanoStat-1.6.0-foss-2022a.eb | 34 +++++++++++++++++++ .../n/nanoget/nanoget-1.18.1-foss-2022a.eb | 30 ++++++++++++++++ .../n/nanomath/nanomath-1.3.0-foss-2022a.eb | 33 ++++++++++++++++++ 3 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/n/nanomath/nanomath-1.3.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2022a.eb b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2022a.eb new file mode 100644 index 00000000000..40c1f10d183 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoStat/NanoStat-1.6.0-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'NanoStat' +version = '1.6.0' + +homepage = 'https://github.com/wdecoster/nanostat' +description = """Calculate various statistics from a long read sequencing dataset in fastq, + bam or albacore sequencing summary format.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('nanoget', '1.18.1'), + ('nanomath', '1.3.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['e45fa8d1ab49bdaed17596c26c0af148b44e4af46238391a8bb7a1b4cc940079'], + }), +] + +sanity_check_paths = { + 'files': ['bin/NanoStat'], + 'dirs': [], +} + +sanity_check_commands = ["NanoStat --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2022a.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2022a.eb new file mode 100644 index 00000000000..7c915c25e40 --- /dev/null +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2022a.eb @@ -0,0 +1,30 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'nanoget' +version = '1.18.1' + +homepage = 'https://github.com/wdecoster/nanoget' +description = "Functions to extract information from Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e4fa37ab1bccc3287947f5792acad3c96fd1c02cb9c0a1f5d218d26bcdbe1632'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('Pysam', '0.19.1'), + ('nanomath', '1.3.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-1.3.0-foss-2022a.eb b/easybuild/easyconfigs/n/nanomath/nanomath-1.3.0-foss-2022a.eb new file mode 100644 index 00000000000..769d14a481e --- /dev/null +++ b/easybuild/easyconfigs/n/nanomath/nanomath-1.3.0-foss-2022a.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Update: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'nanomath' +version = '1.3.0' + +homepage = 'https://github.com/wdecoster/nanomath' +description = "A few simple math function for other Oxford Nanopore processing scripts" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Python-Deprecated', '1.1.0', { + 'modulename': 'deprecated', + 'checksums': ['a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f'], + }), + (name, version, { + 'checksums': ['c35a024b10b34dd8f539cefed1fd69e0a46d18037ca48bed63c7941c67ae028e'], + }), +] + +moduleclass = 'math' From ee8006f728e58870ab6571e3d6cc9c382ee13c89 Mon Sep 17 00:00:00 2001 From: Andreas Skau Date: Mon, 26 Jun 2023 20:44:00 +0200 Subject: [PATCH 7869/9987] Update easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb b/easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb index 39229057947..d78e0908016 100644 --- a/easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb +++ b/easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb @@ -2,7 +2,6 @@ easyblock = "Tarball" name = 'MView' version = "1.67" -versionsuffix = '-Perl-%(perlver)s' homepage = 'http://sourceforge.net/projects/bio-mview/' description = """ MView reformats the results of a sequence database search or a From a09ba7211aa7fd39f35534ade53c224fe530358a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 26 Jun 2023 23:59:53 +0200 Subject: [PATCH 7870/9987] add files_to_copy to LISFLOOD-FP v8.1 Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb index ed8d404fced..ac13d09132c 100644 --- a/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb @@ -39,10 +39,7 @@ dependencies = [ _lisflood_bins = ['DG2downscale', 'generateDG2DEM', 'generateDG2start', 'lisflood'] -# It doesn't have a working make install, emulate in post-install step -skipsteps = ['install'] -postinstallcmds = ["mkdir -p %(installdir)s/bin"] -postinstallcmds += ["cp %s %%(installdir)s/bin/" % x for x in _lisflood_bins] +files_to_copy = [(_lisflood_bins, 'bin')] sanity_check_paths = { 'files': ['bin/%s' % x for x in _lisflood_bins], From e0a3884615c7a8edde0ab66a2a2cf9a5b6629268 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 27 Jun 2023 00:00:17 +0200 Subject: [PATCH 7871/9987] switch LISFLOOD-FP v8.1 to CMakeMakeCp easyblock Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb index ac13d09132c..1fd6f10d2bf 100644 --- a/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb @@ -1,4 +1,4 @@ -easyblock = 'CMakeMake' +easyblock = 'CMakeMakeCp' name = 'LISFLOOD-FP' version = '8.1' From 12df7243a16927ec2e25061c0182dbe34279cbca Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 27 Jun 2023 00:20:32 +0200 Subject: [PATCH 7872/9987] upgrade build dependency on CMake to v3.24.3 in LISFLOOD-FP v8.1 --- .../easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb index 1fd6f10d2bf..0922eeff5ef 100644 --- a/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a.eb @@ -30,7 +30,7 @@ sources = [{'download_filename': '%(name)s%20v%(version)s.zip', 'filename': SOUR checksums = ['57df4ff38f8a47e6907bc4a98466bca6eecb540862a89b9db7e1c4fbe9259d95'] builddependencies = [ - ('CMake', '3.23.1') + ('CMake', '3.24.3') ] dependencies = [ From f785c32ddb589afa680cf14baea7017d82e400d2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 27 Jun 2023 00:22:04 +0200 Subject: [PATCH 7873/9987] adding easyconfigs: LISFLOOD-FP-8.1-gompi-2022a-CUDA-11.7.0.eb --- ...LISFLOOD-FP-8.1-gompi-2022a-CUDA-11.7.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..423df27aa0a --- /dev/null +++ b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1-gompi-2022a-CUDA-11.7.0.eb @@ -0,0 +1,65 @@ +easyblock = 'CMakeMakeCp' + +name = 'LISFLOOD-FP' +version = '8.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.seamlesswave.com/LISFLOOD8.0.html' +description = """The LISFLOOD-FP is a raster-based hydrodynamic model originally developed by +the University of Bristol. It has undergone extensive development since +conception and includes a collection of numerical schemes implemented to solve +a variety of mathematical approximations of the 2D shallow water equations of +different complexity. +The local inertia solver, known as the ACC solver, is widely used to simulate +floods with gradually-varying, subcritical flow over sufficiently rough +surfaces with Manning’s coefficient of at least 0.03. It has a version with +CPU-specific optimisations and enhanced with a subgrid channel model. +LISFLOOD-FP also includes second-order discontinuous Galerkin (DG2) and +first-order finite volume (FV1) solvers of the full shallow water equations for +modelling a wide range of flows, including rapidly-propagating, supercritical +flows, shock waves, or flows over very smooth surfaces. The DG2/FV1 solvers are +parallelised for the multi-core CPU architecture, but do not integrate with the +subgrid channel model nor with the CPU-specific optimisations. +""" + +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://zenodo.org/record/6912932/files/'] +sources = [{'download_filename': '%(name)s%20v%(version)s.zip', 'filename': SOURCE_ZIP}] +patches = ['LISFLOOD-FP-%(version)s_thrust_cub_check.patch'] +checksums = [ + {'LISFLOOD-FP-8.1.zip': '57df4ff38f8a47e6907bc4a98466bca6eecb540862a89b9db7e1c4fbe9259d95'}, + {'LISFLOOD-FP-8.1_thrust_cub_check.patch': 'de2c031d76d517ebe8dc21405bde8eafdc12c64924b9b4fae330bd0d5c58ae93'}, +] + +builddependencies = [ + ('CMake', '3.24.3') +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('netCDF', '4.9.0') +] + +# CUB bundled in LISFLOOD is not compatible with our CUDA Toolkit +# remove in favour of CUB provided in CUDA Toolkit +preconfigopts = "rm -rf %(builddir)s/%(name)s-trunk/cuda/cub &" + +# Default CUDA compute capabilities (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] +configopts = '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s"' + +_lisflood_bins = ['DG2downscale', 'generateDG2DEM', 'generateDG2start', 'lisflood'] + +files_to_copy = [(_lisflood_bins, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _lisflood_bins], + 'dirs': [], +} + +sanity_check_commands = ["lisflood -version"] + +moduleclass = 'phys' From 8baff77dda65366026f4827715b4493f1e127710 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 27 Jun 2023 00:24:10 +0200 Subject: [PATCH 7874/9987] adding patch: LISFLOOD-FP-8.1_thrust_cub_check.patch --- .../LISFLOOD-FP-8.1_thrust_cub_check.patch | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1_thrust_cub_check.patch diff --git a/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1_thrust_cub_check.patch b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1_thrust_cub_check.patch new file mode 100644 index 00000000000..44fda459635 --- /dev/null +++ b/easybuild/easyconfigs/l/LISFLOOD-FP/LISFLOOD-FP-8.1_thrust_cub_check.patch @@ -0,0 +1,16 @@ +Check the compatibility between Thrust in CUDA Toolkit and any bundled CUB. +Ignoring this check is just a bad idea, the build will fail anyway if those +are not compatible. +author: Alex Domingo (Vrije Universiteit Brussel) +diff --git a/CMakeLists.txt.orig b/CMakeLists.txt +index 4038ffd..a23571d 100644 +--- a/CMakeLists.txt.orig ++++ b/CMakeLists.txt +@@ -74,7 +74,6 @@ if (CMAKE_CUDA_COMPILER) + enable_language(CUDA) + set_property(TARGET lisflood PROPERTY CUDA_SEPARABLE_COMPILATION ON) + +- add_compile_definitions(CUDA THRUST_IGNORE_CUB_VERSION_CHECK) + target_sources(lisflood PRIVATE + cuda/cuda_boundary.cu + cuda/cuda_dem.cu From 6246a09fae232263d8bc7f27a61920f14b844342 Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Tue, 27 Jun 2023 16:45:15 +1000 Subject: [PATCH 7875/9987] Create RASPA2-2.0.47-foss-2022a.eb New minor version, new toolchain --- .../r/RASPA2/RASPA2-2.0.47-foss-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.47-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.47-foss-2022a.eb b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.47-foss-2022a.eb new file mode 100644 index 00000000000..feb01d4ea06 --- /dev/null +++ b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.47-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'RASPA2' +version = '2.0.47' + +homepage = 'https://iraspa.org/raspa/' +description = """RASPA is a software package for simulating adsorption and diffusion of +molecules in flexible nanoporous materials.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/iRASPA/RASPA2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1a14524f95ab86e7a2910b53641262ec98ec23f794f1c3665982c32efc1997ed'] + +builddependencies = [ + ('Autotools', '20220317') +] + +preconfigopts = 'rm -rf autom4te.cache && ' +preconfigopts += 'mkdir m4 && ' +preconfigopts += 'aclocal && ' +preconfigopts += 'autoreconf -i && ' +preconfigopts += 'automake --add-missing && ' +preconfigopts += 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/simulate'], + 'dirs': [] +} + +sanity_check_commands = ['simulate -h'] + +moduleclass = 'phys' From aad8110a6297605626c0446cfad561d3289ee95b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Jun 2023 08:48:22 +0200 Subject: [PATCH 7876/9987] adding easyconfigs: DALI-2.1.2-foss-2022b-R-4.2.2.eb --- .../d/DALI/DALI-2.1.2-foss-2022b-R-4.2.2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/d/DALI/DALI-2.1.2-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/d/DALI/DALI-2.1.2-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/d/DALI/DALI-2.1.2-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..fde6e6c1e27 --- /dev/null +++ b/easybuild/easyconfigs/d/DALI/DALI-2.1.2-foss-2022b-R-4.2.2.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'DALI' +version = '2.1.2' +versionsuffix = '-R-%(rver)s' +local_biocver = '3.16' + +homepage = 'https://github.com/vibscc/DALI' +description = "R-package for the analysis of single-cell TCR/BCR data in the Seurat ecosystem" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), +] + +source_urls = ['https://github.com/vibscc/DALI/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8162b52e8d9f836012e127dd4243cec0374d1165468180fa6f7c5f3793a811d6'] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 2eac841645da1ae508e15b7964a32093ec165f9d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 27 Jun 2023 09:23:56 +0200 Subject: [PATCH 7877/9987] Update patches to be smaller and more correct. The fix_env_for_subprocesses.patch is taken from PR #17906. Enable testing for both builds. --- .../GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb | 20 +- .../g/GROMACS/GROMACS-2023.1-foss-2022a.eb | 20 +- ...MACS-2023.1_fix_env_for_subprocesses.patch | 206 ++++++++++++++++++ ...-2023.1_fix_tests_for_gmx_thread_mpi.patch | 68 ++++++ ..._omp_num_threads_env_for_ntomp_tests.patch | 14 ++ 5 files changed, 302 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_env_for_subprocesses.patch create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb index 24d230f0232..f72e6e7a1dd 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb @@ -38,15 +38,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'GROMACS-%(version)s_fix_threads_gpu_Gmxapitests.patch', - 'GROMACS-%(version)s_drop_mpiexec_from_mpi_starters.patch', -] -checksums = [ - {'gromacs-2023.1.tar.gz': 'eef2bb4a6cb6314cf9da47f26df2a0d27af4bf7b3099723d43601073ab0a42f4'}, - {'GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch': - 'ba781f706a1f2604206480c8582a9ade22e3236fb609a09ba1acd82a0e35e7d9'}, - {'GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch': - 'c013247a2145be406f60bb1c052298eb329548c7020abda0b6d623a6854114a4'}, + 'GROMACS-%(version)s_fix_env_for_subprocesses.patch', + 'GROMACS-%(version)s_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-%(version)s_fix_tests_for_gmx_thread_mpi.patch', ] builddependencies = [ @@ -62,8 +56,6 @@ dependencies = [ ('networkx', '2.8.4'), ] -runtest = False - exts_defaultclass = 'PythonPackage' exts_default_options = { @@ -75,8 +67,10 @@ exts_default_options = { exts_list = [ ('gmxapi', '0.4.0', { - 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", - 'checksums': ['7fd58e6a4b1391043379e8ba55555ebeba255c5b394f5df9d676e6a5571d7eba'], + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.1.tar.gz', + 'start_dir': 'python_packaging/gmxapi', }), ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb index 43933480930..7905006e385 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb @@ -38,15 +38,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'GROMACS-%(version)s_fix_threads_gpu_Gmxapitests.patch', - 'GROMACS-%(version)s_drop_mpiexec_from_mpi_starters.patch', -] -checksums = [ - {'gromacs-2023.1.tar.gz': 'eef2bb4a6cb6314cf9da47f26df2a0d27af4bf7b3099723d43601073ab0a42f4'}, - {'GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch': - 'ba781f706a1f2604206480c8582a9ade22e3236fb609a09ba1acd82a0e35e7d9'}, - {'GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch': - 'c013247a2145be406f60bb1c052298eb329548c7020abda0b6d623a6854114a4'}, + 'GROMACS-%(version)s_fix_env_for_subprocesses.patch', + 'GROMACS-%(version)s_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-%(version)s_fix_tests_for_gmx_thread_mpi.patch', ] builddependencies = [ @@ -60,8 +54,6 @@ dependencies = [ ('networkx', '2.8.4'), ] -runtest = False - exts_defaultclass = 'PythonPackage' exts_default_options = { @@ -73,8 +65,10 @@ exts_default_options = { exts_list = [ ('gmxapi', '0.4.0', { - 'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ", - 'checksums': ['7fd58e6a4b1391043379e8ba55555ebeba255c5b394f5df9d676e6a5571d7eba'], + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.1.tar.gz', + 'start_dir': 'python_packaging/gmxapi', }), ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_env_for_subprocesses.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_env_for_subprocesses.patch new file mode 100644 index 00000000000..b9f3bb536bd --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_env_for_subprocesses.patch @@ -0,0 +1,206 @@ +Fix for providing a more carefully filtered environment for subprocesses, based on GROMACS PR #3574: +https://gitlab.com/gromacs/gromacs/-/merge_requests/3574 + +Author: Bob Dröge, University of Groningen + +diff -ru gromacs-2023.1-orig/python_packaging/gmxapi/src/gmxapi/commandline.py gromacs-2023.1/python_packaging/gmxapi/src/gmxapi/commandline.py +--- gromacs-2023.1-orig/python_packaging/gmxapi/src/gmxapi/commandline.py 2023-04-21 15:12:07.000000000 +0200 ++++ gromacs-2023.1/python_packaging/gmxapi/src/gmxapi/commandline.py 2023-05-09 10:42:28.800802318 +0200 +@@ -507,16 +507,9 @@ + shell = gmx.make_constant(False) + + if env is None: +- +- @gmx.function_wrapper( +- # allow_duplicate=True +- ) +- def _env() -> dict: +- import os +- +- return dict(os.environ) +- +- env = _env().output.data ++ env = gmx.function_wrapper(allow_duplicate=True)( ++ gmxapi.runtime.filtered_mpi_environ ++ )().output.data + cli_args = {"command": command, "shell": shell, "env": env} + cli_args.update(**kwargs) + if stdin is not None: +diff -ru gromacs-2023.1-orig/python_packaging/gmxapi/src/gmxapi/runtime.py gromacs-2023.1/python_packaging/gmxapi/src/gmxapi/runtime.py +--- gromacs-2023.1-orig/python_packaging/gmxapi/src/gmxapi/runtime.py 2023-04-21 15:12:07.000000000 +0200 ++++ gromacs-2023.1/python_packaging/gmxapi/src/gmxapi/runtime.py 2023-05-09 10:44:50.869215242 +0200 +@@ -67,6 +67,8 @@ + """ + + __all__ = ( ++ "filtered_mpi_environ", ++ "filtered_prefixes", + "scoped_resources", + "ResourceAllocation", + "ResourceAssignment", +@@ -75,12 +77,11 @@ + + import dataclasses + import functools ++import os + import threading + import typing + import warnings + import weakref +-from typing import TYPE_CHECKING +-from _weakref import ReferenceType + from contextlib import contextmanager + + import gmxapi.utility +@@ -100,9 +101,9 @@ + logger.info("Importing {}".format(__name__)) + + +-if TYPE_CHECKING: ++if typing.TYPE_CHECKING: + try: +- import Comm as Communicator ++ import mpi4py.MPI.Comm as Communicator + except ImportError: + Communicator = None + +@@ -760,3 +761,43 @@ + yield resources + finally: + resources.close() ++ ++ ++filtered_prefixes = ( ++ "DCMF_", # IBM ++ "MPICH_", ++ "MPIEXEC_", ++ "MPIO_", # IBM ++ "MV2_", # MVAPICH2 and some forks ++ "MVAPICH_", ++ "HYDRA_", # MPICH ++ "OMPI_", # OpenMPI ++ "PMI_", # Process Management Interface ++ "PMIX_", # Newer PMI and batch systems ++ "I_MPI_", # Intel MPI ++) ++"""MPI-related environment variable prefixes. ++ ++Environment variable prefixes known to be associated with MPI implementations, ++which may affect MPI context detection, and which should not matter outside of ++MPI contexts. ++ ++References: ++ * :issue:`4423` ++ * :issue:`4736` ++ ++""" ++ ++ ++def filtered_mpi_environ() -> dict: ++ """Return a filtered environment variables map with MPI-related entries removed. ++ ++ See Also: ++ :py:data:`filtered_prefixes` ++ ++ """ ++ return { ++ key: value ++ for key, value in os.environ.items() ++ if not any(key.startswith(prefix) for prefix in filtered_prefixes) ++ } +diff -ru gromacs-2023.1-orig/python_packaging/gmxapi/test/conftest.py gromacs-2023.1/python_packaging/gmxapi/test/conftest.py +--- gromacs-2023.1-orig/python_packaging/gmxapi/test/conftest.py 2023-04-21 15:12:07.000000000 +0200 ++++ gromacs-2023.1/python_packaging/gmxapi/test/conftest.py 2023-05-09 10:46:49.399228381 +0200 +@@ -73,7 +73,8 @@ + Prepare the MD input in a freshly created working directory. + Solvate a 5nm cubic box with spc water. Return a dictionary of the artifacts produced. + """ +- import gmxapi as gmx ++ import gmxapi ++ import gmxapi.runtime + from gmxapi.testsupport import scoped_chdir + + # TODO: (#2896) Fetch MD input from package / library data. +@@ -108,7 +109,7 @@ + fh.write("\n") + + assert os.path.exists(topfile) +- solvate = gmx.commandline_operation( ++ solvate = gmxapi.commandline_operation( + gmxcli, + arguments=["solvate", "-box", "5", "5", "5"], + # We use the default solvent instead of specifying one. +@@ -117,7 +118,6 @@ + "-p": topfile, + "-o": structurefile, + }, +- env={"PATH": os.getenv("PATH")}, + ) + assert os.path.exists(topfile) + +@@ -154,7 +154,7 @@ + # it will be created in the current working directory. + mdout_mdp = os.path.join(tempdir, "mdout.mdp") + +- grompp = gmx.commandline_operation( ++ grompp = gmxapi.commandline_operation( + gmxcli, + "grompp", + input_files={ +@@ -164,7 +164,6 @@ + "-po": mdout_mdp, + }, + output_files={"-o": tprfile}, +- env={"PATH": os.getenv("PATH")}, + ) + tprfilename = grompp.output.file["-o"].result() + if grompp.output.returncode.result() != 0: +diff -ru gromacs-2023.1-orig/python_packaging/sample_restraint/tests/conftest.py gromacs-2023.1/python_packaging/sample_restraint/tests/conftest.py +--- gromacs-2023.1-orig/python_packaging/sample_restraint/tests/conftest.py 2023-04-21 15:12:07.000000000 +0200 ++++ gromacs-2023.1/python_packaging/sample_restraint/tests/conftest.py 2023-05-09 10:48:39.500098358 +0200 +@@ -48,7 +48,8 @@ + + Prepare the MD input in a freshly created working directory. + """ +- import gmxapi as gmx ++ import gmxapi ++ import gmxapi.runtime + from gmxapi.testsupport import scoped_chdir + + # TODO: (#2896) Fetch MD input from package / library data. +@@ -83,8 +84,8 @@ + fh.write("\n") + + assert os.path.exists(topfile) +- assert gmx.version.api_is_at_least(0, 3, 1) +- solvate = gmx.commandline_operation( ++ assert gmxapi.version.api_is_at_least(0, 3, 1) ++ solvate = gmxapi.commandline_operation( + gmxcli, + arguments=["solvate", "-box", "5", "5", "5"], + # We use the default solvent instead of specifying one. +@@ -93,7 +94,6 @@ + "-p": topfile, + "-o": structurefile, + }, +- env={"PATH": os.getenv("PATH")}, + ) + assert os.path.exists(topfile) + +@@ -128,7 +128,7 @@ + # it will be created in the current working directory. + mdout_mdp = os.path.join(tempdir, "mdout.mdp") + +- grompp = gmx.commandline_operation( ++ grompp = gmxapi.commandline_operation( + gmxcli, + "grompp", + input_files={ +@@ -138,7 +138,6 @@ + "-po": mdout_mdp, + }, + output_files={"-o": tprfile}, +- env={"PATH": os.getenv("PATH")}, + ) + tprfilename = grompp.output.file["-o"].result() + if grompp.output.returncode.result() != 0: diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch new file mode 100644 index 00000000000..8860ace45e0 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch @@ -0,0 +1,68 @@ +Make testing of GMX_THREAD_MPI work. +Don't drop relevant PYTHONPATH and LD_LIBRARY_PATH settings. +Make sure OMP_NUM_THREADS is not set so it doesn't fail when -ntomp is set. +Don't use mpiexec for GMX_THREAD_MPI runs. + +Åke Sandgren, 2023-06-27 +diff -ru gromacs-2023.1.orig/python_packaging/gmxapi/test/CMakeLists.txt gromacs-2023.1/python_packaging/gmxapi/test/CMakeLists.txt +--- gromacs-2023.1.orig/python_packaging/gmxapi/test/CMakeLists.txt 2023-04-21 15:12:07.000000000 +0200 ++++ gromacs-2023.1/python_packaging/gmxapi/test/CMakeLists.txt 2023-06-27 08:08:49.967184214 +0200 +@@ -61,7 +61,7 @@ + endif() + + add_custom_target(gmxapi_pytest +- COMMAND ${PYTHON_EXECUTABLE} -m pytest ++ COMMAND ${CMAKE_COMMAND} -E env --unset=OMP_NUM_THREADS ${PYTHON_EXECUTABLE} -m pytest + -rA -l --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} + DEPENDS _gmxapi + WORKING_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}) +@@ -70,6 +70,7 @@ + + add_dependencies(check gmxapi_pytest) + ++if (GMX_MPI) + if(MPIEXEC_EXECUTABLE) + if(NOT GMXAPI_MPI4PY_FOUND) + if (MPI_C_COMPILER) +@@ -107,3 +108,4 @@ + + add_dependencies(check gmxapi_pytest_mpi) + endif() ++endif() +diff -ru gromacs-2023.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt gromacs-2023.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt +--- gromacs-2023.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2023-04-21 15:12:07.000000000 +0200 ++++ gromacs-2023.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2023-06-27 09:10:31.134866196 +0200 +@@ -21,15 +21,18 @@ + get_target_property(PLUGINPATH gmxapi_extension LIBRARY_OUTPUT_DIRECTORY) + add_custom_target(gmxapi_extension_pytest + COMMAND ${CMAKE_COMMAND} +- -E env PYTHONPATH=${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} ++ -E env --unset=OMP_NUM_THREADS LD_LIBRARY_PATH=$ENV{LD_LIBRARY_PATH} PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} + ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR + ${CMAKE_CURRENT_SOURCE_DIR} +- DEPENDS gmxapi_extension _gmxapi) ++ DEPENDS gmxapi_extension _gmxapi ++ WORKING_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}) ++ + # The current test fixtures require the `gmx` tool-wrapper executable. + add_dependencies(gmxapi_extension_pytest gmx) + + add_dependencies(check gmxapi_extension_pytest) + ++if (GMX_MPI) + if(MPIEXEC_EXECUTABLE) + if(NOT GMXAPI_MPI4PY_FOUND) + if (MPI_C_COMPILER) +@@ -58,10 +61,11 @@ + # (https://www.open-mpi.org/doc/v3.0/man1/mpiexec.1.php) + add_custom_target( + gmxapi_extension_pytest_mpi +- COMMAND ${MPIEXEC_EXECUTABLE} -n 4 -x PYTHONPATH=${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} ++ COMMAND ${MPIEXEC_EXECUTABLE} -n 4 -x PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} + ${PYTHON_EXECUTABLE} -m mpi4py -m pytest -x --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} + DEPENDS gmxapi_extension _gmxapi gmx + ) + + add_dependencies(check gmxapi_extension_pytest_mpi) + endif() ++endif() diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch new file mode 100644 index 00000000000..ae22b6c7828 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch @@ -0,0 +1,14 @@ +Make sure env OMP_NUM_THREADS matches -ntomp argument during testing. + +Åke Sandgren, 2023-06-22 +diff -ru gromacs-2023.1.orig/src/testutils/TestMacros.cmake gromacs-2023.1/src/testutils/TestMacros.cmake +--- gromacs-2023.1.orig/src/testutils/TestMacros.cmake 2023-04-21 15:12:08.000000000 +0200 ++++ gromacs-2023.1/src/testutils/TestMacros.cmake 2023-06-22 16:29:28.338270785 +0200 +@@ -288,6 +288,7 @@ + endif () + set(_cmd ${_prefix_cmd} $) + if (ARG_OPENMP_THREADS) ++ set(_cmd "env" "OMP_NUM_THREADS=${ARG_OPENMP_THREADS}" ${_cmd}) + if (GMX_OPENMP) + list(APPEND _cmd -ntomp ${ARG_OPENMP_THREADS}) + endif() From be90715f4bcaa98b23208fabcac27d97aea11d67 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 27 Jun 2023 09:27:03 +0200 Subject: [PATCH 7878/9987] Drop no longer used patches --- ...023.1_drop_mpiexec_from_mpi_starters.patch | 15 ----- ...S-2023.1_fix_threads_gpu_Gmxapitests.patch | 59 ------------------- 2 files changed, 74 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch delete mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch deleted file mode 100644 index 358c7198046..00000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_drop_mpiexec_from_mpi_starters.patch +++ /dev/null @@ -1,15 +0,0 @@ -Drop mpiexec from MPI starter programs, it often clashes with OpenMPI - -Åke Sandgren, 2023-06-22 -diff -ru gromacs-2023.1.orig/cmake/gmxManageMPI.cmake gromacs-2023.1/cmake/gmxManageMPI.cmake ---- gromacs-2023.1.orig/cmake/gmxManageMPI.cmake 2023-04-21 15:12:07.000000000 +0200 -+++ gromacs-2023.1/cmake/gmxManageMPI.cmake 2023-06-22 11:38:57.210310320 +0200 -@@ -148,7 +148,7 @@ - # need to find the full MPI library build system support. - if (NOT MPIEXEC_EXECUTABLE) - find_program(MPIEXEC -- NAMES mpiexec mpirun lamexec srun aprun poe -+ NAMES mpirun lamexec srun aprun poe - HINTS ${MPI_HOME} $ENV{MPI_HOME} - PATH_SUFFIXES bin - DOC "Executable for running MPI programs.") diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch deleted file mode 100644 index eaaa248cfed..00000000000 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1_fix_threads_gpu_Gmxapitests.patch +++ /dev/null @@ -1,59 +0,0 @@ -Handle GMX_THREAD_MPI builds in gmxapi testing. - -Åke Sandgren, 2023-06-21 -diff -ru gromacs-2023.1.orig/python_packaging/gmxapi/test/CMakeLists.txt gromacs-2023.1/python_packaging/gmxapi/test/CMakeLists.txt ---- gromacs-2023.1.orig/python_packaging/gmxapi/test/CMakeLists.txt 2023-04-21 15:12:07.000000000 +0200 -+++ gromacs-2023.1/python_packaging/gmxapi/test/CMakeLists.txt 2023-06-22 11:33:54.200663820 +0200 -@@ -60,11 +60,20 @@ - set(GMXAPI_PYTEST_FOUND TRUE CACHE INTERNAL "Suppress checking for Python pytest module.") - endif() - --add_custom_target(gmxapi_pytest -+if (NOT GMX_THREAD_MPI) -+ add_custom_target(gmxapi_pytest - COMMAND ${PYTHON_EXECUTABLE} -m pytest - -rA -l --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} - DEPENDS _gmxapi - WORKING_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}) -+else() -+ add_custom_target(gmxapi_pytest -+ COMMAND ${CMAKE_COMMAND} -E env --unset=OMP_NUM_THREADS ${PYTHON_EXECUTABLE} -m pytest -+ -rA -l --log-cli-level ERROR ${CMAKE_CURRENT_SOURCE_DIR} -+ DEPENDS _gmxapi -+ WORKING_DIRECTORY ${GMXAPI_PYTHON_STAGING_DIR}) -+endif() -+ - # The current test fixtures require the `gmx` tool-wrapper executable. - add_dependencies(gmxapi_pytest gmx) - -diff -ru gromacs-2023.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt gromacs-2023.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt ---- gromacs-2023.1.orig/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2023-04-21 15:12:07.000000000 +0200 -+++ gromacs-2023.1/python_packaging/sample_restraint/tests/CMakeGROMACS.txt 2023-06-22 11:30:46.282100539 +0200 -@@ -19,12 +19,24 @@ - - get_target_property(GMXAPI_PYTHON_STAGING_DIR _gmxapi staging_dir) - get_target_property(PLUGINPATH gmxapi_extension LIBRARY_OUTPUT_DIRECTORY) --add_custom_target(gmxapi_extension_pytest -+if (NOT GMX_THREAD_MPI) -+ add_custom_target(gmxapi_extension_pytest - COMMAND ${CMAKE_COMMAND} -- -E env PYTHONPATH=${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} -+ -E env PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} - ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR - ${CMAKE_CURRENT_SOURCE_DIR} -- DEPENDS gmxapi_extension _gmxapi) -+ DEPENDS gmxapi_extension _gmxapi -+ WORKING_DIRECTORY ${PLUGINPATH}) -+else() -+ add_custom_target(gmxapi_extension_pytest -+ COMMAND ${CMAKE_COMMAND} -+ -E env --unset=OMP_NUM_THREADS PYTHONPATH=$ENV{PYTHONPATH}:${GMXAPI_PYTHON_STAGING_DIR}:${PLUGINPATH} -+ ${PYTHON_EXECUTABLE} -m pytest --log-cli-level ERROR -+ ${CMAKE_CURRENT_SOURCE_DIR} -+ DEPENDS gmxapi_extension _gmxapi -+ WORKING_DIRECTORY ${PLUGINPATH}) -+endif() -+ - # The current test fixtures require the `gmx` tool-wrapper executable. - add_dependencies(gmxapi_extension_pytest gmx) - From 6d49a73d9bf3ca537385459e9118a398a0631770 Mon Sep 17 00:00:00 2001 From: ec-buzh Date: Tue, 27 Jun 2023 09:58:50 +0200 Subject: [PATCH 7879/9987] Switched to GCC only toolchain, added sanity check command --- .../m/MView/MView-1.67-GCC-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MView/MView-1.67-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/m/MView/MView-1.67-GCC-11.3.0.eb b/easybuild/easyconfigs/m/MView/MView-1.67-GCC-11.3.0.eb new file mode 100644 index 00000000000..b0545bbb584 --- /dev/null +++ b/easybuild/easyconfigs/m/MView/MView-1.67-GCC-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = "Tarball" + +name = 'MView' +version = "1.67" + +homepage = 'https://desmid.github.io/mview/' +description = """ MView reformats the results of a sequence database search or a + multiple alignment, optionally adding HTML markup.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Perl', '5.34.1')] + +sanity_check_paths = { + 'files': ["bin/mview"], + 'dirs': ["lib"], +} + +sanity_check_commands = [('mview', '--help')] + +modextrapaths = {'PERL5LIB': 'lib'} + +moduleclass = 'bio' From ac2321877a1a0d4df67dd6bc23d778bdaf62df91 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 27 Jun 2023 10:19:35 +0200 Subject: [PATCH 7880/9987] Add missing checksums --- .../GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb | 13 +++++++++++-- .../g/GROMACS/GROMACS-2023.1-foss-2022a.eb | 13 +++++++++++-- 2 files changed, 22 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb index f72e6e7a1dd..73cee4bb718 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb @@ -42,6 +42,15 @@ patches = [ 'GROMACS-%(version)s_set_omp_num_threads_env_for_ntomp_tests.patch', 'GROMACS-%(version)s_fix_tests_for_gmx_thread_mpi.patch', ] +checksums = [ + {'gromacs-2023.1.tar.gz': 'eef2bb4a6cb6314cf9da47f26df2a0d27af4bf7b3099723d43601073ab0a42f4'}, + {'GROMACS-2023.1_fix_env_for_subprocesses.patch': + '39ba066c936cddc190bab13c47d6af1575f5d7737d5c0719fe46211a13cd3539'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] builddependencies = [ ('CMake', '3.24.3'), @@ -67,10 +76,10 @@ exts_default_options = { exts_list = [ ('gmxapi', '0.4.0', { - 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + - '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', 'source_tmpl': 'gromacs-2023.1.tar.gz', 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['eef2bb4a6cb6314cf9da47f26df2a0d27af4bf7b3099723d43601073ab0a42f4'], }), ] diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb index 7905006e385..537036abad2 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb @@ -42,6 +42,15 @@ patches = [ 'GROMACS-%(version)s_set_omp_num_threads_env_for_ntomp_tests.patch', 'GROMACS-%(version)s_fix_tests_for_gmx_thread_mpi.patch', ] +checksums = [ + {'gromacs-2023.1.tar.gz': 'eef2bb4a6cb6314cf9da47f26df2a0d27af4bf7b3099723d43601073ab0a42f4'}, + {'GROMACS-2023.1_fix_env_for_subprocesses.patch': + '39ba066c936cddc190bab13c47d6af1575f5d7737d5c0719fe46211a13cd3539'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] builddependencies = [ ('CMake', '3.24.3'), @@ -65,10 +74,10 @@ exts_default_options = { exts_list = [ ('gmxapi', '0.4.0', { - 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + - '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', 'source_tmpl': 'gromacs-2023.1.tar.gz', 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['eef2bb4a6cb6314cf9da47f26df2a0d27af4bf7b3099723d43601073ab0a42f4'], }), ] From a3fb35552032d3cfa54bee9ffa5bf4f33c3d797e Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 27 Jun 2023 09:37:27 +0100 Subject: [PATCH 7881/9987] remove foss version --- .../MView-1.67-foss-2022a-Perl-5.34.1.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb diff --git a/easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb b/easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb deleted file mode 100644 index d78e0908016..00000000000 --- a/easybuild/easyconfigs/m/MView/MView-1.67-foss-2022a-Perl-5.34.1.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = "Tarball" - -name = 'MView' -version = "1.67" - -homepage = 'http://sourceforge.net/projects/bio-mview/' -description = """ MView reformats the results of a sequence database search or a - multiple alignment, optionally adding HTML markup.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] -sources = [SOURCELOWER_TAR_GZ] - -dependencies = [('Perl', '5.34.1')] - -sanity_check_paths = { - 'files': ["bin/mview"], - 'dirs': ["lib"], -} - -modextrapaths = {'PERL5LIB': 'lib'} - -moduleclass = 'bio' From 22e5fdff9195c8413b607ae64d2a640bb98c1b78 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85ke=20Sandgren?= Date: Tue, 27 Jun 2023 13:36:41 +0200 Subject: [PATCH 7882/9987] Update easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb Re-split line that got unsplit by injecting checksums Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb index 73cee4bb718..fdefe9a299b 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a-CUDA-11.7.0.eb @@ -76,7 +76,8 @@ exts_default_options = { exts_list = [ ('gmxapi', '0.4.0', { - 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', 'source_tmpl': 'gromacs-2023.1.tar.gz', 'start_dir': 'python_packaging/gmxapi', 'checksums': ['eef2bb4a6cb6314cf9da47f26df2a0d27af4bf7b3099723d43601073ab0a42f4'], From 8ca72854f8709c9b27c69ad952bed91508cc24b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85ke=20Sandgren?= Date: Tue, 27 Jun 2023 13:36:50 +0200 Subject: [PATCH 7883/9987] Update easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb Re-split line that got unsplit by injecting checksums Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb index 537036abad2..23dfc2084f5 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.1-foss-2022a.eb @@ -74,7 +74,8 @@ exts_default_options = { exts_list = [ ('gmxapi', '0.4.0', { - 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', 'source_tmpl': 'gromacs-2023.1.tar.gz', 'start_dir': 'python_packaging/gmxapi', 'checksums': ['eef2bb4a6cb6314cf9da47f26df2a0d27af4bf7b3099723d43601073ab0a42f4'], From ddf6847ed136a69cfd0a258fd57ccf32cdb69297 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 27 Jun 2023 17:05:13 +0200 Subject: [PATCH 7884/9987] adding easyconfigs: Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb, hatchling-1.18.0-GCCcore-12.3.0.eb, virtualenv-20.23.1-GCCcore-12.3.0.eb, poetry-1.5.1-GCCcore-12.3.0.eb and patches: Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch, Python-3.10-bist-1.3.6-compatibility.patch, Python-3.11-bist-1.3.6-compatibility.patch --- .../hatchling-1.18.0-GCCcore-12.3.0.eb | 61 ++ ...Python-3.10-bist-1.3.6-compatibility.patch | 182 ++++++ ...Python-3.11-bist-1.3.6-compatibility.patch | 56 ++ ...efined_symbol_PyObject_GC_IS_TRACKED.patch | 238 ++++++++ ...thon-bundle-PyPI-2023.06-GCCcore-12.3.0.eb | 549 ++++++++++++++++++ .../p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb | 205 +++++++ .../virtualenv-20.23.1-GCCcore-12.3.0.eb | 46 ++ 7 files changed, 1337 insertions(+) create mode 100644 easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3.10-bist-1.3.6-compatibility.patch create mode 100644 easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3.11-bist-1.3.6-compatibility.patch create mode 100644 easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch create mode 100644 easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb create mode 100755 easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c7971ec5172 --- /dev/null +++ b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'hatchling' +version = '1.18.0' + +homepage = 'https://python-poetry.org' +description = """Python packaging and dependency management made easy. Poetry helps you declare, manage and install + dependencies of Python projects, ensuring you have the right stack everywhere.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + ('setuptools_scm', '7.1.0', { + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('typing_extensions', '4.6.3', { + 'checksums': ['d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5'], + }), + ('pathspec', '0.11.1', { + 'checksums': ['2798de800fa92780e33acca925945e9a19a133b715067cf165b8866c15a31687'], + }), + ('pluggy', '1.2.0', { + 'checksums': ['d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3'], + }), + ('editables', '0.3', { + 'checksums': ['167524e377358ed1f1374e61c268f0d7a4bf7dbd046c656f7b410cde16161b1a'], + }), + ('trove_classifiers', '2023.5.24', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d9d7ae14fb90bf3d50bef99c3941b176b5326509e6e9037e622562d6352629d0'], + }), + (name, version, { + 'checksums': ['50e99c3110ce0afc3f7bdbadff1c71c17758e476731c27607940cfa6686489ca'], + }), + ('hatch_vcs', '0.3.0', { + 'checksums': ['cec5107cfce482c67f8bc96f18bbc320c9aa0d068180e14ad317bbee5a153fee'], + }), + ('hatch_fancy_pypi_readme', '23.1.0', { + 'checksums': ['b1df44063094af1e8248ceacd47a92c9cf313d6b9823bf66af8a927c3960287d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3.10-bist-1.3.6-compatibility.patch b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3.10-bist-1.3.6-compatibility.patch new file mode 100644 index 00000000000..a19979e4909 --- /dev/null +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3.10-bist-1.3.6-compatibility.patch @@ -0,0 +1,182 @@ +From 4b88010f208080173d0976d271d4c3100bfbef17 Mon Sep 17 00:00:00 2001 +From: Steve Langasek +Date: Thu, 18 Nov 2021 13:42:17 -0400 +Subject: [PATCH 1/2] Python 3.10 support: use Py_SET_REFCNT() + +Py_REFCNT() is no longer an lvalue; use Py_SET_REFCNT() instead. +--- + blist/_blist.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/blist/_blist.c b/blist/_blist.c +index f7fcb60..cacd6f2 100644 +--- a/blist/_blist.c ++++ b/blist/_blist.c +@@ -6589,7 +6589,7 @@ py_blist_sort(PyBListRoot *self, PyObject *args, PyObject *kwds) + memcpy(&saved.BLIST_FIRST_FIELD, &self->BLIST_FIRST_FIELD, + sizeof(*self) - offsetof(PyBListRoot, BLIST_FIRST_FIELD)); + Py_TYPE(&saved) = &PyRootBList_Type; +- Py_REFCNT(&saved) = 1; ++ Py_SET_REFCNT(&saved, 1); + + if (extra_list != NULL) { + self->children = extra_list; + +From fddb7837e2094560789a09790360feb75f06ed86 Mon Sep 17 00:00:00 2001 +From: Steve Langasek +Date: Thu, 18 Nov 2021 13:42:42 -0400 +Subject: [PATCH 2/2] Python 3.10 support: use collections.abc.MutableSet + +collections.MutableSet is obsolete, replaced by +collections.abc.MutableSet. +--- + blist/__init__.py | 2 +- + blist/_btuple.py | 2 +- + blist/_sorteddict.py | 8 ++++---- + blist/_sortedlist.py | 24 ++++++++++++------------ + blist/test/sortedlist_tests.py | 4 ++-- + 5 files changed, 20 insertions(+), 20 deletions(-) + +diff --git a/blist/__init__.py b/blist/__init__.py +index 931aaac..38c01a9 100644 +--- a/blist/__init__.py ++++ b/blist/__init__.py +@@ -1,6 +1,6 @@ + __version__ = '1.3.6' + from blist._blist import * +-import collections ++import collections.abc as collections + if hasattr(collections, 'MutableSet'): # Only supported in Python 2.6+ + from blist._sortedlist import sortedlist, sortedset, weaksortedlist, weaksortedset + from blist._sorteddict import sorteddict +diff --git a/blist/_btuple.py b/blist/_btuple.py +index 1e409cd..3a17972 100644 +--- a/blist/_btuple.py ++++ b/blist/_btuple.py +@@ -1,7 +1,7 @@ + from blist._blist import blist + from ctypes import c_int + import collections +-class btuple(collections.Sequence): ++class btuple(collections.abc.Sequence): + def __init__(self, seq=None): + if isinstance(seq, btuple): + self._blist = seq._blist +diff --git a/blist/_sorteddict.py b/blist/_sorteddict.py +index fcdf7e4..daa132c 100644 +--- a/blist/_sorteddict.py ++++ b/blist/_sorteddict.py +@@ -6,7 +6,7 @@ class missingdict(dict): + def __missing__(self, key): + return self._missing(key) + +-class KeysView(collections.KeysView, collections.Sequence): ++class KeysView(collections.abc.KeysView, collections.abc.Sequence): + def __getitem__(self, index): + return self._mapping._sortedkeys[index] + def __reversed__(self): +@@ -23,7 +23,7 @@ def bisect_right(self, key): + return self._mapping._sortedkeys.bisect_right(key) + bisect = bisect_right + +-class ItemsView(collections.ItemsView, collections.Sequence): ++class ItemsView(collections.abc.ItemsView, collections.abc.Sequence): + def __getitem__(self, index): + if isinstance(index, slice): + keys = self._mapping._sortedkeys[index] +@@ -46,7 +46,7 @@ def _from_iterable(self, it): + else: + return sortedset(it, key=lambda item: keyfunc(item[0])) + +-class ValuesView(collections.ValuesView, collections.Sequence): ++class ValuesView(collections.abc.ValuesView, collections.abc.Sequence): + def __getitem__(self, index): + if isinstance(index, slice): + keys = self._mapping._sortedkeys[index] +@@ -54,7 +54,7 @@ def __getitem__(self, index): + key = self._mapping._sortedkeys[index] + return self._mapping[key] + +-class sorteddict(collections.MutableMapping): ++class sorteddict(collections.abc.MutableMapping): + def __init__(self, *args, **kw): + if hasattr(self, '__missing__'): + self._map = missingdict() +diff --git a/blist/_sortedlist.py b/blist/_sortedlist.py +index b34f69e..7b8a2f3 100644 +--- a/blist/_sortedlist.py ++++ b/blist/_sortedlist.py +@@ -25,7 +25,7 @@ def __exit__(self, exc_type, exc_val, exc_tb): + del self.local.repr_count[self.ob_id] + return False + +-class _sortedbase(collections.Sequence): ++class _sortedbase(collections.abc.Sequence): + def __init__(self, iterable=(), key=None): + self._key = key + if key is not None and not hasattr(key, '__call__'): +@@ -428,23 +428,23 @@ def __iter__(self): + + def safe_cmp(f): + def g(self, other): +- if not isinstance(other, collections.Set): ++ if not isinstance(other, collections.abc.Set): + raise TypeError("can only compare to a set") + return f(self, other) + return g + +-class _setmixin2(collections.MutableSet): +- "methods that override or supplement the collections.MutableSet methods" ++class _setmixin2(collections.abc.MutableSet): ++ "methods that override or supplement the collections.abc.MutableSet methods" + +- __ror__ = collections.MutableSet.__or__ +- __rand__ = collections.MutableSet.__and__ +- __rxor__ = collections.MutableSet.__xor__ ++ __ror__ = collections.abc.MutableSet.__or__ ++ __rand__ = collections.abc.MutableSet.__and__ ++ __rxor__ = collections.abc.MutableSet.__xor__ + + if sys.version_info[0] < 3: # pragma: no cover +- __lt__ = safe_cmp(collections.MutableSet.__lt__) +- __gt__ = safe_cmp(collections.MutableSet.__gt__) +- __le__ = safe_cmp(collections.MutableSet.__le__) +- __ge__ = safe_cmp(collections.MutableSet.__ge__) ++ __lt__ = safe_cmp(collections.abc.MutableSet.__lt__) ++ __gt__ = safe_cmp(collections.abc.MutableSet.__gt__) ++ __le__ = safe_cmp(collections.abc.MutableSet.__le__) ++ __ge__ = safe_cmp(collections.abc.MutableSet.__ge__) + + def __ior__(self, it): + if self is it: +@@ -476,7 +476,7 @@ def __rsub__(self, other): + return self._from_iterable(other) - self + + def _make_set(self, iterable): +- if isinstance(iterable, collections.Set): ++ if isinstance(iterable, collections.abc.Set): + return iterable + return self._from_iterable(iterable) + +diff --git a/blist/test/sortedlist_tests.py b/blist/test/sortedlist_tests.py +index 1cff8b9..ad392e9 100644 +--- a/blist/test/sortedlist_tests.py ++++ b/blist/test/sortedlist_tests.py +@@ -29,7 +29,7 @@ def test_empty_repr(self): + repr(self.type2test())) + + def validate_comparison(self, instance): +- if sys.version_info[0] < 3 and isinstance(instance, collections.Set): ++ if sys.version_info[0] < 3 and isinstance(instance, collections.abc.Set): + ops = ['ne', 'or', 'and', 'xor', 'sub'] + else: + ops = ['lt', 'gt', 'le', 'ge', 'ne', 'or', 'and', 'xor', 'sub'] +@@ -185,7 +185,7 @@ def __cmp__(self, other): # pragma: no cover + def test_order(self): + stuff = [self.build_item(random.randrange(1000000)) + for i in range(1000)] +- if issubclass(self.type2test, collections.Set): ++ if issubclass(self.type2test, collections.abc.Set): + stuff = set(stuff) + sorted_stuff = list(sorted(stuff)) + u = self.type2test diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3.11-bist-1.3.6-compatibility.patch b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3.11-bist-1.3.6-compatibility.patch new file mode 100644 index 00000000000..b77df275ef6 --- /dev/null +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3.11-bist-1.3.6-compatibility.patch @@ -0,0 +1,56 @@ +From: Stefano Rivera +Date: Tue, 15 Nov 2022 20:43:01 +0200 +Subject: Python 3.11 support + +Since Py_TYPE() is changed to a inline static function, Py_TYPE(obj) = new_type +must be replaced with Py_SET_TYPE(obj, new_type): see the Py_SET_TYPE() function +(available since Python 3.9) + +See: bpo-39573 +Forwarded: https://github.com/DanielStutzbach/blist/pull/101 +Bug-Debian: https://bugs.debian.org/1023905 +--- + blist/_blist.c | 16 +++++++++++----- + 1 file changed, 11 insertions(+), 5 deletions(-) + +diff --git a/blist/_blist.c b/blist/_blist.c +index 71321e3..1ae7f5e 100644 +--- a/blist/_blist.c ++++ b/blist/_blist.c +@@ -130,6 +130,12 @@ + + #endif + ++#if PY_VERSION_HEX < 0x030900A4 && !defined(Py_SET_TYPE) ++static inline void _Py_SET_TYPE(PyObject *ob, PyTypeObject *type) ++{ ob->ob_type = type; } ++#define Py_SET_TYPE(ob, type) _Py_SET_TYPE((PyObject*)(ob), type) ++#endif ++ + #ifndef BLIST_IN_PYTHON + #include "blist.h" + #endif +@@ -6594,7 +6600,7 @@ py_blist_sort(PyBListRoot *self, PyObject *args, PyObject *kwds) + memset(&saved, 0, offsetof(PyBListRoot, BLIST_FIRST_FIELD)); + memcpy(&saved.BLIST_FIRST_FIELD, &self->BLIST_FIRST_FIELD, + sizeof(*self) - offsetof(PyBListRoot, BLIST_FIRST_FIELD)); +- Py_TYPE(&saved) = &PyRootBList_Type; ++ Py_SET_TYPE(&saved, &PyRootBList_Type); + Py_SET_REFCNT(&saved, 1); + + if (extra_list != NULL) { +@@ -7381,10 +7387,10 @@ init_blist_types1(void) + decref_init(); + highest_set_bit_init(); + +- Py_TYPE(&PyBList_Type) = &PyType_Type; +- Py_TYPE(&PyRootBList_Type) = &PyType_Type; +- Py_TYPE(&PyBListIter_Type) = &PyType_Type; +- Py_TYPE(&PyBListReverseIter_Type) = &PyType_Type; ++ Py_SET_TYPE(&PyBList_Type, &PyType_Type); ++ Py_SET_TYPE(&PyRootBList_Type, &PyType_Type); ++ Py_SET_TYPE(&PyBListIter_Type, &PyType_Type); ++ Py_SET_TYPE(&PyBListReverseIter_Type, &PyType_Type); + + Py_INCREF(&PyBList_Type); + Py_INCREF(&PyRootBList_Type); diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch new file mode 100644 index 00000000000..41967a2a390 --- /dev/null +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch @@ -0,0 +1,238 @@ +From d816f8c30cc15b1a7cdc9fa855ff919359069fb3 Mon Sep 17 00:00:00 2001 +From: "H. Vetinari" +Date: Tue, 13 Oct 2020 16:34:17 +0200 +Subject: [PATCH 4/4] compatibility with PEP 620 + +--- + blist/_blist.c | 8 +- + blist/pythoncapi_compat.h | 192 ++++++++++++++++++++++++++++++++++++++ + 2 files changed, 199 insertions(+), 1 deletion(-) + create mode 100644 blist/pythoncapi_compat.h + +diff --git a/blist/_blist.c b/blist/_blist.c +index fee7b1a..9fdf178 100644 +--- a/blist/_blist.c ++++ b/blist/_blist.c +@@ -98,7 +98,7 @@ + #endif + #endif + +-/* This macro is defined in Python 3. We need it since calling ++/* This macro is defined in Python<3.9. We need it since calling + * PyObject_GC_UnTrack twice is unsafe. */ + /* True if the object is currently tracked by the GC. */ + #define _PyObject_GC_IS_TRACKED(o) \ +@@ -122,6 +122,12 @@ + #define PyInt_AsLong PyLong_AsLong + #define PyInt_AsSsize_t PyLong_AsSsize_t + #define PyInt_FromLong PyLong_FromLong ++#if PY_MINOR_VERSION > 8 ++/* _PyObject_GC_IS_TRACKED was removed from Python 3.9, re-add it; ++ * see PEP 620 and https://github.com/pythoncapi/pythoncapi_compat */ ++#include "pythoncapi_compat.h" ++#define _PyObject_GC_IS_TRACKED(o) PyObject_GC_IsTracked((PyObject*)(o)) ++#endif + #endif + + #ifndef BLIST_IN_PYTHON +diff --git a/blist/pythoncapi_compat.h b/blist/pythoncapi_compat.h +new file mode 100644 +index 0000000..a255b3a +--- /dev/null ++++ b/blist/pythoncapi_compat.h +@@ -0,0 +1,192 @@ ++/* Header file providing new functions of the Python C API ++ for old Python versions. ++ ++ File distributed under the MIT license. ++ Homepage: https://github.com/pythoncapi/pythoncapi_compat. ++*/ ++ ++#ifndef PYTHONCAPI_COMPAT ++#define PYTHONCAPI_COMPAT ++ ++#ifdef __cplusplus ++extern "C" { ++#endif ++ ++#include ++#include "frameobject.h" // PyFrameObject ++ ++ ++// bpo-39573: Py_TYPE(), Py_REFCNT() and Py_SIZE() can no longer be used ++// as l-value in Python 3.10. ++#if PY_VERSION_HEX < 0x030900A4 ++static inline void _Py_SET_REFCNT(PyObject *ob, Py_ssize_t refcnt) ++{ ++ ob->ob_refcnt = refcnt; ++} ++#define Py_SET_REFCNT(ob, refcnt) _Py_SET_REFCNT((PyObject*)(ob), refcnt) ++ ++ ++static inline void ++_Py_SET_TYPE(PyObject *ob, PyTypeObject *type) ++{ ++ ob->ob_type = type; ++} ++#define Py_SET_TYPE(ob, type) _Py_SET_TYPE((PyObject*)(ob), type) ++ ++static inline void ++_Py_SET_SIZE(PyVarObject *ob, Py_ssize_t size) ++{ ++ ob->ob_size = size; ++} ++#define Py_SET_SIZE(ob, size) _Py_SET_SIZE((PyVarObject*)(ob), size) ++ ++#endif // PY_VERSION_HEX < 0x030900A4 ++ ++ ++#if PY_VERSION_HEX < 0x030900B1 ++static inline PyCodeObject* ++PyFrame_GetCode(PyFrameObject *frame) ++{ ++ assert(frame != NULL); ++ PyCodeObject *code = frame->f_code; ++ assert(code != NULL); ++ Py_INCREF(code); ++ return code; ++} ++#endif ++ ++ ++#if PY_VERSION_HEX < 0x030900B1 ++static inline PyFrameObject* ++PyFrame_GetBack(PyFrameObject *frame) ++{ ++ assert(frame != NULL); ++ PyFrameObject *back = frame->f_back; ++ Py_XINCREF(back); ++ return back; ++} ++#endif ++ ++ ++#if PY_VERSION_HEX < 0x030900A5 ++static inline PyInterpreterState * ++PyThreadState_GetInterpreter(PyThreadState *tstate) ++{ ++ assert(tstate != NULL); ++ return tstate->interp; ++} ++#endif ++ ++ ++#if PY_VERSION_HEX < 0x030900B1 ++static inline PyFrameObject* ++PyThreadState_GetFrame(PyThreadState *tstate) ++{ ++ assert(tstate != NULL); ++ PyFrameObject *frame = tstate->frame; ++ Py_XINCREF(frame); ++ return frame; ++} ++#endif ++ ++ ++#if PY_VERSION_HEX < 0x030900A5 ++static inline PyInterpreterState * ++PyInterpreterState_Get(void) ++{ ++ PyThreadState *tstate = PyThreadState_GET(); ++ if (tstate == NULL) { ++ Py_FatalError("GIL released (tstate is NULL)"); ++ } ++ PyInterpreterState *interp = tstate->interp; ++ if (interp == NULL) { ++ Py_FatalError("no current interpreter"); ++ } ++ return interp; ++} ++#endif ++ ++ ++#if 0x030700A1 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x030900A6 ++static inline uint64_t ++PyThreadState_GetID(PyThreadState *tstate) ++{ ++ assert(tstate != NULL); ++ return tstate->id; ++} ++#endif ++ ++ ++#if PY_VERSION_HEX < 0x030900A1 ++static inline PyObject* ++PyObject_CallNoArgs(PyObject *func) ++{ ++ return PyObject_CallFunctionObjArgs(func, NULL); ++} ++#endif ++ ++ ++#if PY_VERSION_HEX < 0x030900A4 ++static inline PyObject* ++PyObject_CallOneArg(PyObject *func, PyObject *arg) ++{ ++ return PyObject_CallFunctionObjArgs(func, arg, NULL); ++} ++#endif ++ ++ ++#if PY_VERSION_HEX < 0x030900A5 ++static inline int ++PyModule_AddType(PyObject *module, PyTypeObject *type) ++{ ++ if (PyType_Ready(type) < 0) { ++ return -1; ++ } ++ ++ // inline _PyType_Name() ++ const char *name = type->tp_name; ++ assert(name != NULL); ++ const char *dot = strrchr(name, '.'); ++ if (dot != NULL) { ++ name = dot + 1; ++ } ++ ++ Py_INCREF(type); ++ if (PyModule_AddObject(module, name, (PyObject *)type) < 0) { ++ Py_DECREF(type); ++ return -1; ++ } ++ ++ return 0; ++} ++#endif ++ ++ ++#if PY_VERSION_HEX < 0x030900A6 ++static inline int ++PyObject_GC_IsTracked(PyObject* obj) ++{ ++ return (PyObject_IS_GC(obj) && _PyObject_GC_IS_TRACKED(obj)); ++} ++ ++static inline int ++PyObject_GC_IsFinalized(PyObject *obj) ++{ ++ return (PyObject_IS_GC(obj) && _PyGCHead_FINALIZED((PyGC_Head *)(obj)-1)); ++} ++#endif // PY_VERSION_HEX < 0x030900A6 ++ ++ ++#if PY_VERSION_HEX < 0x030900A4 ++static inline int ++_Py_IS_TYPE(const PyObject *ob, const PyTypeObject *type) { ++ return ob->ob_type == type; ++} ++#define Py_IS_TYPE(ob, type) _Py_IS_TYPE((const PyObject*)(ob), type) ++#endif ++ ++ ++#ifdef __cplusplus ++} ++#endif ++#endif // PYTHONCAPI_COMPAT +-- +2.26.2.windows.1 + diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a2382fe6f52 --- /dev/null +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb @@ -0,0 +1,549 @@ +easyblock = 'PythonBundle' + +name = 'Python-bundle-PyPI' +version = '2023.06' + +homepage = 'https://python.org/' +description = "Bundle of Python packages from PyPI" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('UnZip', '6.0'), + ('Rust', '1.70.0'), # required for setuptools-rust, which is needed for cryptography and bcrypt + ('pkgconf', '1.9.5'), + ('git', '2.41.0', '-nodocs'), # required for pbr + ('hatchling', '1.18.0'), + ('virtualenv', '20.23.1'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('binutils', '2.40'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.13'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('SQLite', '3.42.0'), + ('XZ', '5.4.2'), + ('GMP', '6.2.1'), # required for pycrypto + ('libffi', '3.4.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +# order is important! +# package versions updated 2023-06-26 +exts_list = [ + ('blist', '1.3.6', { + 'patches': [ + 'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch', + 'Python-3.10-bist-1.3.6-compatibility.patch', + 'Python-3.11-bist-1.3.6-compatibility.patch', + ], + 'checksums': [ + {'blist-1.3.6.tar.gz': '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'}, + {'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch': + '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0'}, + {'Python-3.10-bist-1.3.6-compatibility.patch': + '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741'}, + {'Python-3.11-bist-1.3.6-compatibility.patch': + 'da283300bc5f0524b9982c9d9de4670908711634667849d3d81ccd87fc82c4ee'}, + ], + }), + ('pbr', '5.11.1', { + 'checksums': ['aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3'], + }), + ('Cython', '0.29.35', { + 'checksums': ['6e381fa0bf08b3c26ec2f616b19ae852c06f5750f4290118bf986b6f85c8c527'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + # ('tomli', '2.0.1', { + # 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + # }), + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + # ('setuptools_scm', '7.1.0', { + # 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + # }), + ('python-dateutil', '2.8.2', { + 'modulename': 'dateutil', + 'checksums': ['0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycryptodome', '3.18.0', { + 'modulename': 'Crypto.PublicKey.RSA', + 'checksums': ['c9adee653fc882d98956e33ca2c1fb582e23a8af7ac82fee75bd6113c55a0413'], + }), + ('ecdsa', '0.18.0', { + 'checksums': ['190348041559e21b22a1d65cee485282ca11a6f81d503fddb84d5017e9ed1e49'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.5.1', { + 'checksums': ['13ae38502be632115abf8a24cbe5f4da52e3b5231990aff31123c805306ccb9c'], + }), + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + ('cffi', '1.15.1', { + 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], + }), + ('semantic_version', '2.10.0', { + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + ('typing_extensions', '4.6.3', { + 'checksums': ['d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5'], + }), + # ('setuptools-rust', '1.6.0', { + # 'checksums': ['c86e734deac330597998bfbc08da45187e6b27837e23bd91eadb320732392262'], + # }), + ('cryptography', '41.0.1', { + # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, + # see https://github.com/rust-lang/cargo/issues/6652 + 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", + 'checksums': ['d34579085401d3f49762d2f7d6634d6b6c2ae1242202e860f4d26b046e3a1006'], + }), + ('pyasn1', '0.5.0', { + 'checksums': ['97b7290ca68e62a832558ec3976f15cbf911bf5d7c7039d8b861c2a0ece69fde'], + }), + ('PyNaCl', '1.5.0', { + 'modulename': 'nacl', + 'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'], + }), + ('bcrypt', '4.0.1', { + 'checksums': ['27d375903ac8261cfe4047f6709d16f7d18d39b1ec92aaf72af989552a650ebd'], + }), + ('paramiko', '3.2.0', { + 'checksums': ['93cdce625a8a1dc12204439d45033f3261bdb2c201648cfcdc06f9fd0f94ec29'], + }), + ('pyparsing', '3.1.0', { + 'checksums': ['edb662d6fe322d6e990b1594b5feaeadf806803359e3d4d42f11e295e588f0ea'], + }), + ('netifaces', '0.11.0', { + 'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'], + }), + ('netaddr', '0.8.0', { + 'checksums': ['d6cc57c7a07b1d9d2e917aa8b36ae8ce61c35ba3fcd1b83ca31c5a0ee2b5a243'], + }), + ('mock', '5.0.2', { + 'checksums': ['06f18d7d65b44428202b145a9a36e99c2ee00d1eb992df0caf881d4664377891'], + }), + ('pytz', '2023.3', { + 'checksums': ['1d8ce29db189191fb55338ee6d0387d82ab59f3d00eac103412d64e0ebd0c588'], + }), + ('bitstring', '4.0.2', { + 'checksums': ['a391db8828ac4485dd5ce72c80b27ebac3e7b989631359959e310cd9729723b2'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + # ('distlib', '0.3.6', { + # 'checksums': ['14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46'], + # }), + ('zipp', '3.15.0', { + 'checksums': ['112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b'], + }), + ('importlib_metadata', '6.7.0', { + 'checksums': ['1aaf550d4f73e5d6783e7acb77aec43d49da8017410afae93822cc9cca98c4d4'], + }), + ('backports.entry-points-selectable', '1.2.0', { + 'sources': ['backports.entry_points_selectable-%(version)s.tar.gz'], + 'checksums': ['4706f59179657ca7c1d325a543ee1370f8f46331f432bcac62fab242fdf0afa5'], + }), + # ('pathspec', '0.11.1', { + # 'checksums': ['2798de800fa92780e33acca925945e9a19a133b715067cf165b8866c15a31687'], + # }), + ('pluggy', '1.2.0', { + 'checksums': ['d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3'], + }), + # ('editables', '0.3', { + # 'checksums': ['167524e377358ed1f1374e61c268f0d7a4bf7dbd046c656f7b410cde16161b1a'], + # }), + # ('trove_classifiers', '2023.5.24', { + # 'source_tmpl': SOURCE_PY3_WHL, + # 'checksums': ['d9d7ae14fb90bf3d50bef99c3941b176b5326509e6e9037e622562d6352629d0'], + # }), + # ('hatchling', '1.18.0', { + # 'checksums': ['50e99c3110ce0afc3f7bdbadff1c71c17758e476731c27607940cfa6686489ca'], + # }), + # ('hatch_vcs', '0.3.0', { + # 'checksums': ['cec5107cfce482c67f8bc96f18bbc320c9aa0d068180e14ad317bbee5a153fee'], + # }), + # ('filelock', '3.12.2', { + # 'checksums': ['002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81'], + # }), + ('platformdirs', '3.8.0', { + 'checksums': ['b0cabcb11063d21a0b261d557acb0a9d2126350e63b70cdf7db6347baea456dc'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.7.post1', { + 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], + }), + ('importlib_resources', '5.12.0', { + 'checksums': ['4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6'], + }), + # ('virtualenv', '20.23.1', { + # 'checksums': ['8ff19a38c1021c742148edc4f81cb43d7f8c6816d2ede2ab72af5b84c749ade1'], + # }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '1.2.0', { + 'checksums': ['e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018'], + }), + ('chardet', '5.1.0', { + 'checksums': ['0d62712b956bc154f85fb0a266e2a3c5913c2967e00348701b32411d6def31e5'], + }), + ('certifi', '2023.5.7', { + 'checksums': ['0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7'], + }), + # poetry 1.5.1 has requirement urllib3<2.0.0,>=1.26.0 + ('urllib3', '1.26.16', { + 'checksums': ['8f135f6502756bde6b2a9b28989df5fbe87c9970cecaa69041edcce7f0589b14'], + }), + ('charset-normalizer', '3.1.0', { + 'checksums': ['34e0a2f9c370eb95597aae63bf85eb5e96826d81e3dcf88b8886012906f509b5'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('py_expression_eval', '0.3.14', { + 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('ujson', '5.8.0', { + 'checksums': ['78e318def4ade898a461b3d92a79f9441e7e0e4d2ad5419abed4336d702c7425'], + }), + ('atomicwrites', '1.4.1', { + 'checksums': ['81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11'], + }), + ('py', '1.11.0', { + 'checksums': ['51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719'], + }), + ('more-itertools', '9.1.0', { + 'checksums': ['cabaa341ad0389ea83c17a94566a53ae4c9d07349861ecb14dc6d0345cf9ac5d'], + }), + # ('hatch_fancy_pypi_readme', '23.1.0', { + # 'checksums': ['b1df44063094af1e8248ceacd47a92c9cf313d6b9823bf66af8a927c3960287d'], + # }), + ('attrs', '23.1.0', { + 'modulename': 'attr', + 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], + }), + ('backports.functools_lru_cache', '1.6.5', { + 'checksums': ['e7efcdd8cf92279bcb09fdb9b31e984ffdc96fc9f21e22ff20538884cb99b97d'], + }), + ('wcwidth', '0.2.6', { + 'checksums': ['a5220780a404dbe3353789870978e472cfe477761f06ee55077256e509b156d0'], + }), + ('iniconfig', '2.0.0', { + 'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'], + }), + ('colorama', '0.4.6', { + 'checksums': ['08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44'], + }), + # ('flit_scm', '1.7.0', { + # 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + # }), + ('exceptiongroup', '1.1.1', { + 'checksums': ['d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785'], + }), + ('pytest', '7.4.0', { + 'checksums': ['b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a'], + }), + ('MarkupSafe', '2.1.3', { + 'checksums': ['af598ed32d6ae86f1b747b82783958b1a4ab8f617b06fe68795c7f026abbdcad'], + }), + ('Jinja2', '3.1.2', { + 'checksums': ['31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852'], + }), + ('sphinxcontrib-serializinghtml', '1.1.5', { + 'modulename': 'sphinxcontrib.serializinghtml', + 'checksums': ['aa5f6de5dfdf809ef505c4895e51ef5c9eac17d0f287933eb49ec495280b6952'], + }), + ('sphinxcontrib-websupport', '1.2.4', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['4edf0223a0685a7c485ae5a156b6f529ba1ee481a1417817935b20bde1956232'], + }), + ('Pygments', '2.15.1', { + 'checksums': ['8ace4d3c1dd481894b2005f560ead0f9f19ee64fe983366be1a21e171d12775c'], + }), + ('imagesize', '1.4.1', { + 'checksums': ['69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a'], + }), + ('docutils', '0.20.1', { + 'checksums': ['f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b'], + }), + ('snowballstemmer', '2.2.0', { + 'checksums': ['09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1'], + }), + ('alabaster', '0.7.13', { + 'checksums': ['a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2'], + }), + ('sphinxcontrib-applehelp', '1.0.4', { + 'modulename': 'sphinxcontrib.applehelp', + 'checksums': ['828f867945bbe39817c210a1abfd1bc4895c8b73fcaade56d45357a348a07d7e'], + }), + ('sphinxcontrib-devhelp', '1.0.2', { + 'modulename': 'sphinxcontrib.devhelp', + 'checksums': ['ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4'], + }), + ('sphinxcontrib-htmlhelp', '2.0.1', { + 'modulename': 'sphinxcontrib.htmlhelp', + 'checksums': ['0cbdd302815330058422b98a113195c9249825d681e18f11e8b1f78a2f11efff'], + }), + ('sphinxcontrib-jsmath', '1.0.1', { + 'modulename': 'sphinxcontrib.jsmath', + 'checksums': ['a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8'], + }), + ('sphinxcontrib-qthelp', '1.0.3', { + 'modulename': 'sphinxcontrib.qthelp', + 'checksums': ['4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72'], + }), + ('Babel', '2.12.1', { + 'checksums': ['cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455'], + }), + ('Sphinx', '7.0.1', { + 'checksums': ['61e025f788c5977d9412587e733733a289e2b9fdc2fef8868ddfbfc4ccfe881d'], + }), + ('sphinx-bootstrap-theme', '0.8.1', { + 'checksums': ['683e3b735448dadd0149f76edecf95ff4bd9157787e9e77e0d048ca6f1d680df'], + }), + ('click', '8.1.3', { + 'checksums': ['7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e'], + }), + ('psutil', '5.9.5', { + 'checksums': ['5410638e4df39c54d957fc51ce03048acd8e6d60abc0f5107af51e5fb566eb3c'], + }), + ('future', '0.18.3', { + 'checksums': ['34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('zipfile36', '0.1.3', { + 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], + }), + # ('tomli_w', '1.0.0', { + # 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + # }), + # ('flit', '3.9.0', { + # 'checksums': ['d75edf5eb324da20d53570a6a6f87f51e606eee8384925cd66a90611140844c7'], + # }), + ('regex', '2023.6.3', { + 'checksums': ['72d1a25bf36d2050ceb35b517afe13864865268dfb45910e2e17a84be6cbfeb0'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('pylev', '1.4.0', { + 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], + }), + ('pastel', '0.2.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], + }), + ('crashtest', '0.4.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'], + }), + # clikit 0.6.2 has requirement crashtest<0.4.0,>=0.3.0 + # but poetry 1.5.1 has requirement crashtest>=0.4.1 + # and cleo 2.0.1 has requirement crashtest>=0.4.1 + # ('clikit', '0.6.2', { + # 'source_tmpl': SOURCE_WHL, + # 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], + # }), + ('jeepney', '0.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], + }), + ('SecretStorage', '3.3.3', { + 'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'], + }), + # poetry 1.5.1 has requirement keyring<24.0.0,>=23.9.0 + ('keyring', '23.13.1', { + 'modulename': False, + 'checksums': ['ba2e15a9b35e21908d0aaf4e0a47acc52d6ae33444df0da2b49d41a46ef6d678'], + }), + ('jaraco.classes', '3.2.3', { + 'checksums': ['89559fa5c1d3c34eff6f631ad80bb21f378dbcbb35dd161fd2c6b93f5be2f98a'], + }), + ('keyrings.alt', '4.2.0', { + 'modulename': False, + 'checksums': ['2ba3d56441ba0637f5f9c096068f67010ac0453f9d0b626de2aa3019353b6431'], + }), + # ('tomlkit', '0.11.8', { + # 'source_tmpl': SOURCE_PY3_WHL, + # 'checksums': ['8c726c4c202bdb148667835f68d68780b9a003a9ec34167b6c673b38eff2a171'], + # }), + # ('shellingham', '1.5.0.post1', { + # 'checksums': ['823bc5fb5c34d60f285b624e7264f4dda254bc803a3774a147bf99c0e3004a28'], + # }), + # ('requests-toolbelt', '1.0.0', { + # 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], + # }), + ('pyrsistent', '0.19.3', { + 'checksums': ['1a2994773706bbb4995c31a97bc94f1418314923bd1048c6d964837040376440'], + }), + # ('pkginfo', '1.9.6', { + # 'checksums': ['8fd5896e8718a4372f0ea9cc9d96f6417c9b986e23a4d116dda26b62cc29d046'], + # }), + # ('ptyprocess', '0.7.0', { + # 'source_tmpl': SOURCE_WHL, + # 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + # }), + # ('pexpect', '4.8.0', { + # 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + # }), + ('jsonschema', '4.17.3', { + 'checksums': ['0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d'], + }), + ('simplejson', '3.19.1', { + 'checksums': ['6277f60848a7d8319d27d2be767a7546bc965535b28070e310b3a9af90604a4c'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + # ('distro', '1.8.0', { + # 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + # }), + # ('scikit_build', '0.17.6', { + # 'modulename': 'skbuild', + # 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], + # }), + ('rapidfuzz', '2.15.1', { + 'checksums': ['d62137c2ca37aea90a11003ad7dc109c8f1739bfbe5a9a217f3cdb07d7ac00f6'], + }), + ('cleo', '2.0.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['6eb133670a3ed1f3b052d53789017b6e50fca66d1287e6e6696285f4cb8ea448'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.5', { + 'checksums': ['c075544284eadc5cddc70f4757331d99dcbc16b2bbd4849d15f8aae4cf36d31c'], + }), + ('CacheControl', '0.12.14', { + 'checksums': ['d1087f45781c0e00616479bfd282c78504371ca71da017b49df9f5365a95feba'], + }), + # ('lockfile', '0.12.2', { + # 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + # }), + # ('poetry_core', '1.6.1', { + # 'modulename': 'poetry.core', + # 'checksums': ['0f9b0de39665f36d6594657e7d57b6f463cc10f30c28e6d1c3b9ff54c26c9ac3'], + # }), + ('glob2', '0.7', { + 'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'], + }), + # ('dulwich', '0.21.5', { + # 'checksums': ['70955e4e249ddda6e34a4636b90f74e931e558f993b17c52570fa6144b993103'], + # }), + # ('poetry_plugin_export', '1.4.0', { + # 'checksums': ['f16974cd9f222d4ef640fa97a8d661b04d4fb339e51da93973f1bc9d578e183f'], + # }), + # ('build', '0.10.0', { + # 'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'], + # }), + # ('installer', '0.7.0', { + # 'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631'], + # }), + # ('pyproject_hooks', '1.0.0', { + # 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + # }), + # ('poetry', '1.5.1', { + # 'checksums': ['cc7ea4524d1a11558006224bfe8ba8ed071417d4eb5ef6c89decc6a37d437eeb'], + # }), + ('fsspec', '2023.6.0', { + 'checksums': ['d0b2f935446169753e7a5c5c55681c54ea91996cc67be93c39a154fb3a2742af'], + }), + ('threadpoolctl', '3.1.0', { + 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('pooch', '1.7.0', { + 'checksums': ['f174a1041b6447f0eef8860f76d17f60ed2f857dc0efa387a7f08228af05d998'], + }), + ('doit', '0.36.0', { + 'checksums': ['71d07ccc9514cb22fe59d98999577665eaab57e16f644d04336ae0b4bae234bc'], + }), + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('pydevtool', '0.3.0', { + 'checksums': ['25e3ba4f3d33ccac33ee2b9775995848d49e9b318b7a146477fb5d52f786fc8a'], + }), + ('Pygments', '2.15.1', { + 'checksums': ['8ace4d3c1dd481894b2005f560ead0f9f19ee64fe983366be1a21e171d12775c'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '3.0.0', { + 'modulename': 'markdown_it', + 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], + }), + ('rich', '13.4.2', { + 'checksums': ['d653d6bccede5844304c605d5aac802c7cf9621efd700b46c7ec2b51ea914898'], + }), + ('rich-click', '1.6.1', { + 'checksums': ['f8ff96693ec6e261d1544e9f7d9a5811c5ef5d74c8adb4978430fc0dac16777e'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('execnet', '1.9.0', { + 'checksums': ['8f694f3ba9cc92cab508b152dcfe322153975c29bda272e2fd7f3f00f36e47c5'], + }), + ('pytest-xdist', '3.3.1', { + 'modulename': 'xdist', + 'checksums': ['d5ee0520eb1b7bcca50a60a518ab7a7707992812c578198f8b44fdfac78e8c93'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb new file mode 100755 index 00000000000..9d5fe570b3e --- /dev/null +++ b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb @@ -0,0 +1,205 @@ +easyblock = 'PythonBundle' + +name = 'poetry' +version = '1.5.1' + +homepage = 'https://python-poetry.org' +description = """Python packaging and dependency management made easy. Poetry helps you declare, manage and install + dependencies of Python projects, ensuring you have the right stack everywhere.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.70.0'), # required for setuptools-rust, which is needed for cryptography +] + +dependencies = [ + ('Python', '3.11.3'), + ('hatchling', '1.18.0'), + ('virtualenv', '20.23.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + ('setuptools_scm', '7.1.0', { + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('certifi', '2023.5.7', { + 'checksums': ['0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7'], + }), + # poetry 1.5.1 has requirement urllib3<2.0.0,>=1.26.0 + ('urllib3', '1.26.16', { + 'checksums': ['8f135f6502756bde6b2a9b28989df5fbe87c9970cecaa69041edcce7f0589b14'], + }), + ('charset-normalizer', '3.1.0', { + 'checksums': ['34e0a2f9c370eb95597aae63bf85eb5e96826d81e3dcf88b8886012906f509b5'], + }), + ('flit_scm', '1.7.0', { + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('dulwich', '0.21.5', { + 'checksums': ['70955e4e249ddda6e34a4636b90f74e931e558f993b17c52570fa6144b993103'], + }), + ('docutils', '0.20.1', { + 'checksums': ['f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b'], + }), + ('tomli_w', '1.0.0', { + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), + ('flit', '3.9.0', { + 'checksums': ['d75edf5eb324da20d53570a6a6f87f51e606eee8384925cd66a90611140844c7'], + }), + ('crashtest', '0.4.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'], + }), + ('zipp', '3.15.0', { + 'checksums': ['112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b'], + }), + ('importlib_metadata', '6.7.0', { + 'checksums': ['1aaf550d4f73e5d6783e7acb77aec43d49da8017410afae93822cc9cca98c4d4'], + }), + ('jeepney', '0.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], + }), + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + ('cffi', '1.15.1', { + 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], + }), + ('semantic_version', '2.10.0', { + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + ('setuptools-rust', '1.6.0', { + 'checksums': ['c86e734deac330597998bfbc08da45187e6b27837e23bd91eadb320732392262'], + }), + ('cryptography', '41.0.1', { + # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, + # see https://github.com/rust-lang/cargo/issues/6652 + 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", + 'checksums': ['d34579085401d3f49762d2f7d6634d6b6c2ae1242202e860f4d26b046e3a1006'], + }), + ('pyasn1', '0.5.0', { + 'checksums': ['97b7290ca68e62a832558ec3976f15cbf911bf5d7c7039d8b861c2a0ece69fde'], + }), + ('SecretStorage', '3.3.3', { + 'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'], + }), + ('more-itertools', '9.1.0', { + 'checksums': ['cabaa341ad0389ea83c17a94566a53ae4c9d07349861ecb14dc6d0345cf9ac5d'], + }), + ('jaraco.classes', '3.2.3', { + 'checksums': ['89559fa5c1d3c34eff6f631ad80bb21f378dbcbb35dd161fd2c6b93f5be2f98a'], + }), + # poetry 1.5.1 has requirement keyring<24.0.0,>=23.9.0 + ('keyring', '23.13.1', { + 'modulename': False, + 'checksums': ['ba2e15a9b35e21908d0aaf4e0a47acc52d6ae33444df0da2b49d41a46ef6d678'], + }), + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + ('build', '0.10.0', { + 'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'], + }), + ('installer', '0.7.0', { + 'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('scikit_build', '0.17.6', { + 'modulename': 'skbuild', + 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], + }), + ('rapidfuzz', '2.15.1', { + 'checksums': ['d62137c2ca37aea90a11003ad7dc109c8f1739bfbe5a9a217f3cdb07d7ac00f6'], + }), + ('cleo', '2.0.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['6eb133670a3ed1f3b052d53789017b6e50fca66d1287e6e6696285f4cb8ea448'], + }), + ('attrs', '23.1.0', { + 'modulename': 'attr', + 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], + }), + ('pyrsistent', '0.19.3', { + 'checksums': ['1a2994773706bbb4995c31a97bc94f1418314923bd1048c6d964837040376440'], + }), + ('requests-toolbelt', '1.0.0', { + 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], + }), + ('pkginfo', '1.9.6', { + 'checksums': ['8fd5896e8718a4372f0ea9cc9d96f6417c9b986e23a4d116dda26b62cc29d046'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('jsonschema', '4.17.3', { + 'checksums': ['0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d'], + }), + ('platformdirs', '3.8.0', { + 'checksums': ['b0cabcb11063d21a0b261d557acb0a9d2126350e63b70cdf7db6347baea456dc'], + }), + ('shellingham', '1.5.0', { + 'checksums': ['72fb7f5c63103ca2cb91b23dee0c71fe8ad6fbfd46418ef17dbe40db51592dad'], + }), + ('tomlkit', '0.11.8', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8c726c4c202bdb148667835f68d68780b9a003a9ec34167b6c673b38eff2a171'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('msgpack', '1.0.5', { + 'checksums': ['c075544284eadc5cddc70f4757331d99dcbc16b2bbd4849d15f8aae4cf36d31c'], + }), + ('CacheControl', '0.12.14', { + 'checksums': ['d1087f45781c0e00616479bfd282c78504371ca71da017b49df9f5365a95feba'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry_core', '1.6.1', { + 'modulename': 'poetry.core', + 'checksums': ['0f9b0de39665f36d6594657e7d57b6f463cc10f30c28e6d1c3b9ff54c26c9ac3'], + }), + ('poetry_plugin_export', '1.4.0', { + 'checksums': ['f16974cd9f222d4ef640fa97a8d661b04d4fb339e51da93973f1bc9d578e183f'], + }), + (name, version, { + 'checksums': ['cc7ea4524d1a11558006224bfe8ba8ed071417d4eb5ef6c89decc6a37d437eeb'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1313eef14d5 --- /dev/null +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'virtualenv' +version = '20.23.1' + +homepage = 'https://python.org/' +description = "A tool for creating isolated virtual python environments." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('distlib', '0.3.6', { + 'checksums': ['14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46'], + }), + ('filelock', '3.12.2', { + 'checksums': ['002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81'], + }), + ('platformdirs', '3.8.0', { + 'checksums': ['b0cabcb11063d21a0b261d557acb0a9d2126350e63b70cdf7db6347baea456dc'], + }), + (name, version, { + 'checksums': ['8ff19a38c1021c742148edc4f81cb43d7f8c6816d2ede2ab72af5b84c749ade1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' From 6d49b8d59f59f577b2ef15158ee01a3be2fff571 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 27 Jun 2023 17:19:23 +0200 Subject: [PATCH 7885/9987] add pkgconf builddependency to poetry-1.5.1-GCCcore-12.3.0.eb --- easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb index 9d5fe570b3e..87953f0ae2a 100755 --- a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), + ('pkgconf', '1.9.5'), ('Rust', '1.70.0'), # required for setuptools-rust, which is needed for cryptography ] From e54f7094ebcc91263ea5793370a195a7acb60a31 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 27 Jun 2023 18:25:44 +0200 Subject: [PATCH 7886/9987] add binutils builddependency to virtualenv-20.23.1-GCCcore-12.3.0.eb and hatchling-1.18.0-GCCcore-12.3.0.eb --- .../h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb | 4 ++++ .../v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb | 1 + 2 files changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb index c7971ec5172..9d2ea5e7d3f 100644 --- a/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb @@ -9,6 +9,10 @@ description = """Python packaging and dependency management made easy. Poetry he toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [ + ('binutils', '2.40'), +] + dependencies = [ ('Python', '3.11.3'), ] diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb index 1313eef14d5..93fdd5fa2d3 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} builddependencies = [ + ('binutils', '2.40'), ('hatchling', '1.18.0'), ] From 0a19d818cd21e576eb696cfbdea9ecb7bdbf79ad Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 28 Jun 2023 08:36:45 +0200 Subject: [PATCH 7887/9987] remove requests dep --- ...2-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb | 1 - ...I-Label-0.5.2-foss-2022a-PyTorch-1.12.0.eb | 3 +-- .../r/requests/requests-2.31.0-foss-2022a.eb | 23 ------------------- 3 files changed, 1 insertion(+), 26 deletions(-) delete mode 100644 easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb index 6c273769a54..01c4c751e7b 100644 --- a/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb @@ -26,7 +26,6 @@ dependencies = [ ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), ('torchvision', '0.13.1', '-CUDA-%(cudaver)s'), ('torchaudio', '0.12.0', '-PyTorch-' + local_pytorch_version + '-CUDA-%(cudaver)s'), - ('requests', '2.31.0'), ('einops', '0.4.1'), ('MONAI', '1.0.1', '-CUDA-%(cudaver)s'), ('OpenCV', '4.6.0', '-CUDA-%(cudaver)s' + '-contrib'), diff --git a/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0.eb index f80125213a7..3d0905eca1f 100644 --- a/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0.eb +++ b/easybuild/easyconfigs/m/MONAI-Label/MONAI-Label-0.5.2-foss-2022a-PyTorch-1.12.0.eb @@ -23,9 +23,8 @@ builddependencies = [ dependencies = [ ('Python', '3.10.4'), ('PyTorch', local_pytorch_version), - ('torchvision', '0.13.1'), # CUDA + ('torchvision', '0.13.1'), ('torchaudio', '0.12.0', '-PyTorch-%s' % local_pytorch_version), - ('requests', '2.31.0'), ('einops', '0.4.1'), ('MONAI', '1.0.1'), ('OpenCV', '4.6.0', '-contrib'), diff --git a/easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb b/easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb deleted file mode 100644 index bf8932f86b5..00000000000 --- a/easybuild/easyconfigs/r/requests/requests-2.31.0-foss-2022a.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'requests' -version = '2.31.0' - -homepage = 'https://pypi.python.org/pypi/requests/%(version)s' -description = """Python http for humans""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -sources = [SOURCE_TAR_GZ] - -checksums = ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'] - -dependencies = [ - ('Python', '3.10.4'), -] - -sanity_pip_check = True -use_pip = True -download_dep_fail = True - -moduleclass = 'devel' From 0384bf970bc9559c419616502bdf181d86df3e64 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 28 Jun 2023 10:21:10 +0200 Subject: [PATCH 7888/9987] add missing source_urls for SimpleITK --- .../easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb index 9a0f8d8c8e2..ee1cda90622 100644 --- a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb @@ -9,6 +9,7 @@ description = """SimpleITK is a simplified programming interface to the algorith toolchain = {'name': 'foss', 'version': '2022a'} +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['%(name)s-%(version)s_allow-lua54-for-code-generation.patch'] checksums = [ From 86d1f16e247fda8a955e3d851345064dc9a892f0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 28 Jun 2023 11:23:01 +0200 Subject: [PATCH 7889/9987] include all extensions except the ones that are clearly only needed for building python packages --- ...thon-bundle-PyPI-2023.06-GCCcore-12.3.0.eb | 94 +++++++++---------- 1 file changed, 47 insertions(+), 47 deletions(-) diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb index a2382fe6f52..ac498be08d8 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb @@ -70,9 +70,9 @@ exts_list = [ ('toml', '0.10.2', { 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], }), - # ('tomli', '2.0.1', { - # 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], - # }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), ('packaging', '23.1', { 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], }), @@ -161,9 +161,9 @@ exts_list = [ ('appdirs', '1.4.4', { 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], }), - # ('distlib', '0.3.6', { - # 'checksums': ['14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46'], - # }), + ('distlib', '0.3.6', { + 'checksums': ['14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46'], + }), ('zipp', '3.15.0', { 'checksums': ['112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b'], }), @@ -174,15 +174,15 @@ exts_list = [ 'sources': ['backports.entry_points_selectable-%(version)s.tar.gz'], 'checksums': ['4706f59179657ca7c1d325a543ee1370f8f46331f432bcac62fab242fdf0afa5'], }), - # ('pathspec', '0.11.1', { - # 'checksums': ['2798de800fa92780e33acca925945e9a19a133b715067cf165b8866c15a31687'], - # }), + ('pathspec', '0.11.1', { + 'checksums': ['2798de800fa92780e33acca925945e9a19a133b715067cf165b8866c15a31687'], + }), ('pluggy', '1.2.0', { 'checksums': ['d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3'], }), - # ('editables', '0.3', { - # 'checksums': ['167524e377358ed1f1374e61c268f0d7a4bf7dbd046c656f7b410cde16161b1a'], - # }), + ('editables', '0.3', { + 'checksums': ['167524e377358ed1f1374e61c268f0d7a4bf7dbd046c656f7b410cde16161b1a'], + }), # ('trove_classifiers', '2023.5.24', { # 'source_tmpl': SOURCE_PY3_WHL, # 'checksums': ['d9d7ae14fb90bf3d50bef99c3941b176b5326509e6e9037e622562d6352629d0'], @@ -193,9 +193,9 @@ exts_list = [ # ('hatch_vcs', '0.3.0', { # 'checksums': ['cec5107cfce482c67f8bc96f18bbc320c9aa0d068180e14ad317bbee5a153fee'], # }), - # ('filelock', '3.12.2', { - # 'checksums': ['002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81'], - # }), + ('filelock', '3.12.2', { + 'checksums': ['002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81'], + }), ('platformdirs', '3.8.0', { 'checksums': ['b0cabcb11063d21a0b261d557acb0a9d2126350e63b70cdf7db6347baea456dc'], }), @@ -361,9 +361,9 @@ exts_list = [ ('zipfile36', '0.1.3', { 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], }), - # ('tomli_w', '1.0.0', { - # 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], - # }), + ('tomli_w', '1.0.0', { + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), # ('flit', '3.9.0', { # 'checksums': ['d75edf5eb324da20d53570a6a6f87f51e606eee8384925cd66a90611140844c7'], # }), @@ -410,29 +410,29 @@ exts_list = [ 'modulename': False, 'checksums': ['2ba3d56441ba0637f5f9c096068f67010ac0453f9d0b626de2aa3019353b6431'], }), - # ('tomlkit', '0.11.8', { - # 'source_tmpl': SOURCE_PY3_WHL, - # 'checksums': ['8c726c4c202bdb148667835f68d68780b9a003a9ec34167b6c673b38eff2a171'], - # }), - # ('shellingham', '1.5.0.post1', { - # 'checksums': ['823bc5fb5c34d60f285b624e7264f4dda254bc803a3774a147bf99c0e3004a28'], - # }), - # ('requests-toolbelt', '1.0.0', { - # 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], - # }), + ('tomlkit', '0.11.8', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8c726c4c202bdb148667835f68d68780b9a003a9ec34167b6c673b38eff2a171'], + }), + ('shellingham', '1.5.0.post1', { + 'checksums': ['823bc5fb5c34d60f285b624e7264f4dda254bc803a3774a147bf99c0e3004a28'], + }), + ('requests-toolbelt', '1.0.0', { + 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], + }), ('pyrsistent', '0.19.3', { 'checksums': ['1a2994773706bbb4995c31a97bc94f1418314923bd1048c6d964837040376440'], }), - # ('pkginfo', '1.9.6', { - # 'checksums': ['8fd5896e8718a4372f0ea9cc9d96f6417c9b986e23a4d116dda26b62cc29d046'], - # }), - # ('ptyprocess', '0.7.0', { - # 'source_tmpl': SOURCE_WHL, - # 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], - # }), - # ('pexpect', '4.8.0', { - # 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], - # }), + ('pkginfo', '1.9.6', { + 'checksums': ['8fd5896e8718a4372f0ea9cc9d96f6417c9b986e23a4d116dda26b62cc29d046'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), ('jsonschema', '4.17.3', { 'checksums': ['0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d'], }), @@ -445,9 +445,9 @@ exts_list = [ ('html5lib', '1.1', { 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), - # ('distro', '1.8.0', { - # 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], - # }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), # ('scikit_build', '0.17.6', { # 'modulename': 'skbuild', # 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], @@ -468,9 +468,9 @@ exts_list = [ ('CacheControl', '0.12.14', { 'checksums': ['d1087f45781c0e00616479bfd282c78504371ca71da017b49df9f5365a95feba'], }), - # ('lockfile', '0.12.2', { - # 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], - # }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), # ('poetry_core', '1.6.1', { # 'modulename': 'poetry.core', # 'checksums': ['0f9b0de39665f36d6594657e7d57b6f463cc10f30c28e6d1c3b9ff54c26c9ac3'], @@ -478,9 +478,9 @@ exts_list = [ ('glob2', '0.7', { 'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'], }), - # ('dulwich', '0.21.5', { - # 'checksums': ['70955e4e249ddda6e34a4636b90f74e931e558f993b17c52570fa6144b993103'], - # }), + ('dulwich', '0.21.5', { + 'checksums': ['70955e4e249ddda6e34a4636b90f74e931e558f993b17c52570fa6144b993103'], + }), # ('poetry_plugin_export', '1.4.0', { # 'checksums': ['f16974cd9f222d4ef640fa97a8d661b04d4fb339e51da93973f1bc9d578e183f'], # }), From ea0810a27d007865bad9a0fa841912fabc7e9f11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Jun 2023 11:54:31 +0200 Subject: [PATCH 7890/9987] add sanity check command for ATAC 3.36 --- easybuild/easyconfigs/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb index cc6fecdbffa..5b29bd248a6 100644 --- a/easybuild/easyconfigs/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/a/ATAT/ATAT-3.36-GCCcore-9.3.0.eb @@ -63,6 +63,10 @@ sanity_check_paths = { 'dirs': local_to_copy[:-1] } +sanity_check_commands = [ + "maps --help 2>&1 | grep '^MIT Ab initio Phase Stability (MAPS) code %(version)s'" +] + modloadmsg = "First-time users please run:\necho set atatdir=$EBROOTATAT > $HOME/.atat.rc\n" moduleclass = 'chem' From d974bfbfe225d9f5ea608d35c9fd6b04999d5ccd Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 28 Jun 2023 18:46:22 +0800 Subject: [PATCH 7891/9987] patch oxDNA/oxpy to use correct pip install prefix --- .../oxDNA-3.5.2-foss-2022a-CUDA-11.7.0.eb | 26 ++++++++++++------- .../o/oxDNA/oxDNA-3.5.2_pip_install.patch | 13 ++++++++++ 2 files changed, 30 insertions(+), 9 deletions(-) create mode 100644 easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2_pip_install.patch diff --git a/easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2-foss-2022a-CUDA-11.7.0.eb index 0d41088be5f..23f38d6955d 100644 --- a/easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2-foss-2022a-CUDA-11.7.0.eb @@ -16,7 +16,11 @@ toolchain = {'name': 'foss', 'version': '2022a'} github_account = 'lorenzo-rovigatti' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['d76351b572334421aedb7774bb095db6f8f0a9c851e0242f0b665887d9d754bb'] +patches = ['oxDNA-3.5.2_pip_install.patch'] +checksums = [ + {'v3.5.2.tar.gz': 'd76351b572334421aedb7774bb095db6f8f0a9c851e0242f0b665887d9d754bb'}, + {'oxDNA-3.5.2_pip_install.patch': '50cf60d4c65c7a953ec6f28ba1ce464e493565fb98221c5ffc429ba26c08d939'}, +] builddependencies = [ ('CMake', '3.23.1') @@ -26,27 +30,31 @@ dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('matplotlib', '3.5.2'), ] -configopts = "-DCUDA=1 -DCUDA_COMMON_ARCH=ON -DPython=ON -DOxpySystemInstall=ON " +configopts = "-DCUDA=1 -DCUDA_COMMON_ARCH=ON -DPython=ON " # configopts += "-DMPI=ON " # still "unsupported feature that should be used by developers only"? postinstallcmds = [ - "mkdir %(installdir)s/lib", - "mv %(builddir)s/easybuild_obj/bin %(installdir)s/bin", + "mv %(builddir)s/easybuild_obj/bin/* %(installdir)s/bin/", "mv %(builddir)s/easybuild_obj/oxpy/lib_oxpy_lib.a %(installdir)s/lib/", "mv %%(builddir)s/easybuild_obj/src/liboxdna_common.%s %%(installdir)s/lib/" % SHLIB_EXT, - "mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages", - "mv %(builddir)s/easybuild_obj/oxpy/python/oxpy %(installdir)s/lib/python%(pyshortver)s/site-packages/", ] sanity_check_paths = { - 'files': ['bin/confGenerator', 'bin/DNAnalysis', 'bin/oxDNA', + 'files': ['bin/confGenerator', 'bin/DNAnalysis', 'bin/oxDNA', 'bin/oat', 'lib/liboxdna_common.%s' % SHLIB_EXT, 'lib/lib_oxpy_lib.a'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/oxpy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/oxpy', + 'lib/python%(pyshortver)s/site-packages/oxDNA_analysis_tools'], } -sanity_check_commands = ["python -c 'import oxpy'"] +sanity_check_commands = [ + "oxDNA 2>&1 | grep Usage", + "python -c 'import oxpy'", + "python -c 'import oxDNA_analysis_tools'", +] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2_pip_install.patch b/easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2_pip_install.patch new file mode 100644 index 00000000000..30876d0b804 --- /dev/null +++ b/easybuild/easyconfigs/o/oxDNA/oxDNA-3.5.2_pip_install.patch @@ -0,0 +1,13 @@ +install oxpy into the oxDNA installation directory instead of the user or Python installation directory +author: Miguel Dias Costa (National University of Singapore) +--- oxDNA-3.5.2/oxpy/CMakeLists.txt.orig 2023-06-28 15:22:31.870578035 +0800 ++++ oxDNA-3.5.2/oxpy/CMakeLists.txt 2023-06-28 18:05:27.313737196 +0800 +@@ -62,7 +62,7 @@ + if(OxpySystemInstall) + INSTALL(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} -m pip install ${OXPY_OUTPUT_DIR})") + else() +- INSTALL(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} -m pip install --user ${OXPY_OUTPUT_DIR})") ++ INSTALL(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} -m pip install --prefix=${CMAKE_INSTALL_PREFIX} ${OXPY_OUTPUT_DIR})") + endif() + + ENDIF(Python) From 1703da2ec7a0e92cd7a8eea42108498b813db322 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Jun 2023 13:56:09 +0200 Subject: [PATCH 7892/9987] use OpenSSL/1.1 as dependency + tweak sanity check for axel --- .../easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb | 13 +++++++++---- .../easyconfigs/a/axel/axel-2.17.9-GCCcore-9.3.0.eb | 13 +++++++++---- 2 files changed, 18 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb index 28b86b3e619..3b8baf41014 100644 --- a/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-8.3.0.eb @@ -20,13 +20,18 @@ builddependencies = [ ('gettext', '0.20.1'), ] -dependencies = [('OpenSSL', '1.1.1d')] +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] sanity_check_paths = { - 'files': ["bin/axel"], - 'dirs': [""], + 'files': ['bin/axel'], + 'dirs': [], } -sanity_check_commands = [True, ('%(name)s', '--version')] +sanity_check_commands = [ + "axel -h", + "axel --version", +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-9.3.0.eb index dbbbd372428..de813fa81e5 100644 --- a/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/a/axel/axel-2.17.9-GCCcore-9.3.0.eb @@ -20,13 +20,18 @@ builddependencies = [ ('gettext', '0.20.1'), ] -dependencies = [('OpenSSL', '1.1.1e')] +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] sanity_check_paths = { - 'files': ["bin/axel"], - 'dirs': [""], + 'files': ['bin/axel'], + 'dirs': [], } -sanity_check_commands = [True, ('%(name)s', '--version')] +sanity_check_commands = [ + "axel -h", + "axel --version", +] moduleclass = 'tools' From 6bc5efbb554f9cca1194b1a8300c80d36cd9b1e0 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 28 Jun 2023 14:34:03 +0200 Subject: [PATCH 7893/9987] adding easyconfigs: MUSCLE-5.1.0-GCCcore-10.3.0.eb --- .../m/MUSCLE/MUSCLE-5.1.0-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..f41e38c73c2 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '5.1.0' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +github_account = 'rcedgar' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +start_dir = 'src' + +# Use build environment defined by EasyBuild +prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&" +buildopts = "CPP=${CXX} CC=${CC}" + +files_to_copy = [(['Linux/muscle'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/muscle'], + 'dirs': [], +} + +sanity_check_commands = ["muscle -h"] + +moduleclass = 'bio' From e048e1f768324de99b8f513eb0c96667abcaf4b8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 28 Jun 2023 15:18:40 +0200 Subject: [PATCH 7894/9987] adding easyconfigs: RMBlast-2.14.0-gompi-2021a.eb, RepeatMasker-4.1.5-foss-2021a.eb --- .../r/RMBlast/RMBlast-2.14.0-gompi-2021a.eb | 63 +++++++++++++++++++ .../RepeatMasker-4.1.5-foss-2021a.eb | 57 +++++++++++++++++ 2 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.0-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2021a.eb diff --git a/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.0-gompi-2021a.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.0-gompi-2021a.eb new file mode 100644 index 00000000000..0a3059df10a --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.14.0-gompi-2021a.eb @@ -0,0 +1,63 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'RMBlast' +version = '2.14.0' + +homepage = 'https://www.repeatmasker.org/rmblast/' +description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary + difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' + for use with RepeatMasker and RepeatModeler.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'usempi': True} + +# RMBlast is distributed as a patch that applies on top of BLAST+ +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [('https://www.repeatmasker.org/%(namelower)s/isb-%(version)s+-%(namelower)s.patch.gz', 2)] +checksums = [ + {'ncbi-blast-2.14.0+-src.tar.gz': 'bf477f1b0c3b82f0b7a7094bf003a9a83e37e3b0716c1df799060c4feab17500'}, + {'isb-2.14.0+-rmblast.patch.gz': '9de0e67467a4cffdde0c5f67e3658fb52ed313e4550f9a36a251bddb2ba33f49'}, +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('PCRE', '8.44'), + ('Boost.MPI', '1.76.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.28'), +] + +# Disable auto-vectorization for the API on CPUs with AVX512 (Intel Skylake and onwards) +# Compilation fails on src/algo/blast/api/prelim_stage.cpp +local_apimake = 'src/algo/blast/api/Makefile.xblast.lib' +preconfigopts = "sed -i 's/FAST_CXXFLAGS)/FAST_CXXFLAGS) -fno-tree-vectorize/g' %s &&" % local_apimake + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +prebuildopts = "sed -i 's/LIBS =/LIBS = $(BLAST_THIRD_PARTY_LIBS)/' src/app/rmblastn/Makefile.rmblastn.app && " + +sanity_check_paths = { + 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2021a.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2021a.eb new file mode 100644 index 00000000000..85b04e1a138 --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2021a.eb @@ -0,0 +1,57 @@ +easyblock = 'Tarball' + +name = 'RepeatMasker' +version = '4.1.5' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://www.repeatmasker.org/%(name)s'] +sources = [ + SOURCE_TAR_GZ, + # optional but recommended: RepBase RepeatMasker Edition + # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php + # { + # 'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz', + # 'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1", + # }, +] +checksums = ['16e07f9efd99adf15f4492b0e334df5ad4ea6ca38ddf62bdd180d257f2f4753f'] + +dependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), + ('TRF', '4.09.1'), + ('h5py', '3.2.1'), + # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match + ('HMMER', '3.3.2'), + ('RMBlast', '2.14.0'), +] + +local_default_search_engine = 'RMBlast' + +local_config_command = 'cd %(installdir)s &&' +local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() + +postinstallcmds = [local_config_command] + +fix_perl_shebang_for = ['RepeatMasker'] + +sanity_check_paths = { + 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], + 'dirs': ['Libraries', 'util'], +} + +sanity_check_commands = ['RepeatMasker -help'] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} + +moduleclass = 'bio' From c234ddf4cf204e95144ff105f1b1a07976c5ba92 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Wed, 28 Jun 2023 15:59:38 +0200 Subject: [PATCH 7895/9987] adding easyconfigs: fastparquet-2023.4.0-gfbf-2022b.eb, patchelf-0.17.2-GCCcore-12.2.0.eb --- .../fastparquet-2023.4.0-gfbf-2022b.eb | 41 +++++++++++++++++++ .../patchelf-0.17.2-GCCcore-12.2.0.eb | 27 ++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.17.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb new file mode 100644 index 00000000000..dd2b4d8f045 --- /dev/null +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'fastparquet' +version = '2023.4.0' + +homepage = "https://fastparquet.readthedocs.io/" +description = """fastparquet is a python implementation of the parquet format, aiming to integrate +into python-based big data work-flows. It is used implicitly by the projects +Dask, Pandas and intake-parquet.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +builddependencies = [ + ('patchelf', '0.17.2'), + ('Rust', '1.65.0'), # needed by maturin +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('maturin', '1.1.0', { + 'checksums': ['4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'], + }), + ('thrift', '0.16.0', { + 'checksums': ['2b5b6488fcded21f9d312aa23c9ff6a0195d0f6ae26ddbd5ad9e3e25dfc14408'], + }), + ('cramjam', '2.6.2', { + 'checksums': ['1ffdc8d1381b5fee57b33b537e38fa7fd29e8d8f3b544dbab1d71dbfaaec3bef'], + }), + (name, version, { + 'checksums': ['917e6d288ea07e10b28b5fa4b4c0b70f60b14971ece3ba5bf30690320a53aa70'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.17.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.17.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..01967b9be37 --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.17.2-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.17.2' + +homepage = 'https://github.com/NixOS/patchelf' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['039f755bd3533f92cc07b8034419117c763d8a97a909aefbef6a6ecf86e679fc'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +moduleclass = 'tools' From 8cf40a8cbc1fcb5abfaf2c3f8e0c2a61d10970ec Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 28 Jun 2023 16:04:17 +0200 Subject: [PATCH 7896/9987] adding easyconfigs: HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb --- ...HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..fc983ab5255 --- /dev/null +++ b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'HOOMD-blue' +version = "4.0.1" +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://bitbucket.org/glotzer/hoomd-blue" +description = """HOOMD-blue is a general-purpose particle simulation +toolkit, implementing molecular dynamics and hard particle Monte Carlo +optimized for fast execution on both GPUs and CPUs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +github_account = 'glotzerlab' +source_urls = [GITHUB_LOWER_RELEASE] +sources = ['hoomd-%(version)s.tar.gz'] +checksums = ['b63dd8debb96f9c530983bd54ecbafa8fd07e017ded3ea64604cfb1f41a644b8'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pybind11', '2.9.2'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tbb', '2021.5.0'), + ('Eigen', '3.4.0'), + ('Cereal', '1.3.2', '', SYSTEM), +] + +_copts = [ + '-DENABLE_GPU=ON', + '-DHOOMD_GPU_PLATFORM=CUDA', + '-DENABLE_MPI=ON', + '-DBUILD_MD=ON', + '-DBUILD_METAL=ON', + '-DENABLE_TBB=ON', + '-DBUILD_TESTING=ON', +] +configopts = ' '.join(_copts) + +postinstallcmds = [ + 'ln -s hoomd/include %(installdir)s/include', +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['hoomd/__init__.py', 'hoomd/include/hoomd/Compute.h'], + 'dirs': ['lib/cmake'], +} + +sanity_check_commands = [ + "python -c 'import hoomd'", +] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'phys' From 5305816d200a14f80f31abee6c845068d6bd760a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 28 Jun 2023 16:15:42 +0200 Subject: [PATCH 7897/9987] adding easyconfigs: Structure_threader-1.3.10-foss-2022b.eb --- .../Structure_threader-1.3.10-foss-2022b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/Structure_threader/Structure_threader-1.3.10-foss-2022b.eb diff --git a/easybuild/easyconfigs/s/Structure_threader/Structure_threader-1.3.10-foss-2022b.eb b/easybuild/easyconfigs/s/Structure_threader/Structure_threader-1.3.10-foss-2022b.eb new file mode 100644 index 00000000000..0b9a2c3c537 --- /dev/null +++ b/easybuild/easyconfigs/s/Structure_threader/Structure_threader-1.3.10-foss-2022b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'Structure_threader' +version = '1.3.10' + + +homepage = 'https://github.com/StuntsPT/Structure_threader' +description = """A program to parallelize the runs of Structure, + fastStructure, MavericK and ALStructure software.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('plotly.py', '5.13.1'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('colorlover', '0.3.0', { + 'checksums': ['b8fb7246ab46e1f5e6715649453c1762e245a515de5ff2d2b4aab7a6e67fa4e2'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['b4d7258e5be370a001f6715599cb60a07583e32b7a8c385b0c87874a669c38b8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/structure_threader'], + 'dirs': [], +} + +sanity_check_commands = ["structure_threader --help"] + +moduleclass = 'tools' From 6db99c9931607c936b0d073ba6c8ab7b7bd131f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 28 Jun 2023 17:03:24 +0200 Subject: [PATCH 7898/9987] remove empty line --- .../s/Structure_threader/Structure_threader-1.3.10-foss-2022b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Structure_threader/Structure_threader-1.3.10-foss-2022b.eb b/easybuild/easyconfigs/s/Structure_threader/Structure_threader-1.3.10-foss-2022b.eb index 0b9a2c3c537..bdec08d7d4d 100644 --- a/easybuild/easyconfigs/s/Structure_threader/Structure_threader-1.3.10-foss-2022b.eb +++ b/easybuild/easyconfigs/s/Structure_threader/Structure_threader-1.3.10-foss-2022b.eb @@ -3,7 +3,6 @@ easyblock = 'PythonBundle' name = 'Structure_threader' version = '1.3.10' - homepage = 'https://github.com/StuntsPT/Structure_threader' description = """A program to parallelize the runs of Structure, fastStructure, MavericK and ALStructure software.""" From d143ca6cac9d1c6ff6d22158f1cc22dae994ae89 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 28 Jun 2023 17:49:55 +0200 Subject: [PATCH 7899/9987] adding easyconfigs: Safetensors-0.3.1-foss-2022a-CUDA-11.7.0.eb, Safetensors-0.3.1-foss-2022a.eb, PyTorch-Image-Models-0.9.2-foss-2022a-CUDA-11.7.0.eb, PyTorch-Image-Models-0.9.2-foss-2022a.eb, pycocotools-2.0.6-foss-2022a.eb, LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb, LayoutParser-0.3.4-foss-2022a.eb --- ...youtParser-0.3.4-foss-2022a-CUDA-11.7.0.eb | 99 +++++++++++++++++++ .../LayoutParser-0.3.4-foss-2022a.eb | 97 ++++++++++++++++++ ...age-Models-0.9.2-foss-2022a-CUDA-11.7.0.eb | 38 +++++++ .../PyTorch-Image-Models-0.9.2-foss-2022a.eb | 36 +++++++ .../pycocotools-2.0.6-foss-2022a.eb | 25 +++++ ...afetensors-0.3.1-foss-2022a-CUDA-11.7.0.eb | 37 +++++++ .../Safetensors-0.3.1-foss-2022a.eb | 35 +++++++ 7 files changed, 367 insertions(+) create mode 100644 easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-Image-Models/PyTorch-Image-Models-0.9.2-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-Image-Models/PyTorch-Image-Models-0.9.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.6-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/Safetensors/Safetensors-0.3.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/s/Safetensors/Safetensors-0.3.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..1c513a4b596 --- /dev/null +++ b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,99 @@ +easyblock = "PythonBundle" + +name = 'LayoutParser' +version = '0.3.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://layout-parser.github.io/' +description = "A Unified Toolkit for Deep Learning Based Document Image Analysis" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), + ('Pillow', '9.1.1'), + ('PyYAML', '6.0'), + ('ImageMagick', '7.1.0-37'), # needed by Wand + ('poppler', '22.12.0'), # needed by pdf2image + ('protobuf-python', '3.19.4'), # needed by google-api-core + ('pycocotools', '2.0.6'), # needed by effdet + ('PyTorch-Image-Models', '0.9.2', versionsuffix), # needed by effdet + ('tqdm', '4.64.0'), # needed by iopath + ('torchvision', '0.13.1', versionsuffix), # layoutmodels extra +] + +use_pip = True + +# remove opencv-python from requirements: since pip is not aware of cv2 in OpenCV from EB +_del_opencv_req = "sed -i '/opencv-python/d' setup.py &&" +# relax dependency on PyTorch of pytesseract +_relax_torch_req = "sed -i 's/torch >= 1\.12\.1/torch >= 1.12.0/' setup.py &&" + +exts_list = [ + ('portalocker', '2.7.0', { + 'checksums': ['032e81d534a88ec1736d03f780ba073f047a06c478b06e2937486f334e955c51'], + }), + ('iopath', '0.1.10', { + 'checksums': ['3311c16a4d9137223e20f141655759933e1eda24f8bff166af834af3c645ef01'], + }), + ('Wand', '0.6.11', { + 'checksums': ['b661700da9f8f1e931e52726e4fc643a565b9514f5883d41b773e3c37c9fa995'], + }), + ('pdfminer.six', '20221105', { + 'modulename': 'pdfminer', + 'checksums': ['8448ab7b939d18b64820478ecac5394f482d7a79f5f7eaa7703c6c959c175e1d'], + 'use_pip_extras': 'image', + }), + ('pdfplumber', '0.9.0', { + 'checksums': ['a43a213e125ed72b2358c0d3428f9b72f83939109ec33b77ef9325eeab9846f0'], + }), + ('pdf2image', '1.16.3', { + 'checksums': ['74208810c2cef4d9e347769b8e62a52303982ddb4f2dfd744c7ab4b940ae287e'], + }), + ('antlr4-python3-runtime', '4.9.3', { + 'modulename': 'antlr4', + 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], + }), + ('omegaconf', '2.3.0', { + 'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'], + }), + ('cachetools', '4.2.4', { + 'checksums': ['89ea6f1b638d5a73a4f9226be57ac5e4f399d22770b92355f92dcb0f7f001693'], + }), + ('google-auth', '1.35.0', { + 'modulename': 'google.auth', + 'checksums': ['b7033be9028c188ee30200b204ea00ed82ea1162e8ac1df4aa6ded19a191d88e'], + }), + ('googleapis-common-protos', '1.56.4', { + 'modulename': 'google.api', + 'checksums': ['c25873c47279387cfdcbdafa36149887901d36202cb645a0e4f29686bf6e4417'], + }), + ('google-api-core', '1.32.0', { + 'modulename': 'google.api_core', + 'checksums': ['101c3c4cf8e7d53badd1dbca7071464353a04b17319a3dbb3a94eaa893da091c'], + 'use_pip_extras': 'grpc', + }), + ('google-cloud-vision', '1.0.2', { + 'modulename': 'google.cloud.vision', + 'checksums': ['0c349f771ee49027781e05df2efa6fc1a8b4f7d1d74ab57675f9151a04b01d6f'], + }), + ('pytesseract', '0.3.8', { + 'checksums': ['6148a01e4375760862e8f56ea718e22b5d13b281454df46ea8dac9807793fc5a'], + }), + ('effdet', '0.4.1', { + 'checksums': ['ac5589fd304a5650c201986b2ef5f8e10c111093a71b1c49fa6b8817710812b5'], + 'preinstallopts': _relax_torch_req, + }), + ('layoutparser', version, { + 'checksums': ['0dfb2194c36a5ad1075b8310f3cbc280c00306d1758cef127d20283f7ce085ea'], + 'preinstallopts': _del_opencv_req, + 'use_pip_extras': 'ocr,gcv,tesseract,layoutmodels,effdet', + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb new file mode 100644 index 00000000000..f6289d05d9f --- /dev/null +++ b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb @@ -0,0 +1,97 @@ +easyblock = "PythonBundle" + +name = 'LayoutParser' +version = '0.3.4' + +homepage = 'https://layout-parser.github.io/' +description = "A Unified Toolkit for Deep Learning Based Document Image Analysis" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('OpenCV', '4.6.0', '-contrib'), + ('Pillow', '9.1.1'), + ('PyYAML', '6.0'), + ('ImageMagick', '7.1.0-37'), # needed by Wand + ('poppler', '22.12.0'), # needed by pdf2image + ('protobuf-python', '3.19.4'), # needed by google-api-core + ('pycocotools', '2.0.6'), # needed by effdet + ('PyTorch-Image-Models', '0.9.2'), # needed by effdet + ('tqdm', '4.64.0'), # needed by iopath + ('torchvision', '0.13.1'), # layoutmodels extra +] + +use_pip = True + +# remove opencv-python from requirements: since pip is not aware of cv2 in OpenCV from EB +_del_opencv_req = "sed -i '/opencv-python/d' setup.py &&" +# relax dependency on PyTorch of pytesseract +_relax_torch_req = "sed -i 's/torch >= 1\.12\.1/torch >= 1.12.0/' setup.py &&" + +exts_list = [ + ('portalocker', '2.7.0', { + 'checksums': ['032e81d534a88ec1736d03f780ba073f047a06c478b06e2937486f334e955c51'], + }), + ('iopath', '0.1.10', { + 'checksums': ['3311c16a4d9137223e20f141655759933e1eda24f8bff166af834af3c645ef01'], + }), + ('Wand', '0.6.11', { + 'checksums': ['b661700da9f8f1e931e52726e4fc643a565b9514f5883d41b773e3c37c9fa995'], + }), + ('pdfminer.six', '20221105', { + 'modulename': 'pdfminer', + 'checksums': ['8448ab7b939d18b64820478ecac5394f482d7a79f5f7eaa7703c6c959c175e1d'], + 'use_pip_extras': 'image', + }), + ('pdfplumber', '0.9.0', { + 'checksums': ['a43a213e125ed72b2358c0d3428f9b72f83939109ec33b77ef9325eeab9846f0'], + }), + ('pdf2image', '1.16.3', { + 'checksums': ['74208810c2cef4d9e347769b8e62a52303982ddb4f2dfd744c7ab4b940ae287e'], + }), + ('antlr4-python3-runtime', '4.9.3', { + 'modulename': 'antlr4', + 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], + }), + ('omegaconf', '2.3.0', { + 'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'], + }), + ('cachetools', '4.2.4', { + 'checksums': ['89ea6f1b638d5a73a4f9226be57ac5e4f399d22770b92355f92dcb0f7f001693'], + }), + ('google-auth', '1.35.0', { + 'modulename': 'google.auth', + 'checksums': ['b7033be9028c188ee30200b204ea00ed82ea1162e8ac1df4aa6ded19a191d88e'], + }), + ('googleapis-common-protos', '1.56.4', { + 'modulename': 'google.api', + 'checksums': ['c25873c47279387cfdcbdafa36149887901d36202cb645a0e4f29686bf6e4417'], + }), + ('google-api-core', '1.32.0', { + 'modulename': 'google.api_core', + 'checksums': ['101c3c4cf8e7d53badd1dbca7071464353a04b17319a3dbb3a94eaa893da091c'], + 'use_pip_extras': 'grpc', + }), + ('google-cloud-vision', '1.0.2', { + 'modulename': 'google.cloud.vision', + 'checksums': ['0c349f771ee49027781e05df2efa6fc1a8b4f7d1d74ab57675f9151a04b01d6f'], + }), + ('pytesseract', '0.3.8', { + 'checksums': ['6148a01e4375760862e8f56ea718e22b5d13b281454df46ea8dac9807793fc5a'], + }), + ('effdet', '0.4.1', { + 'checksums': ['ac5589fd304a5650c201986b2ef5f8e10c111093a71b1c49fa6b8817710812b5'], + 'preinstallopts': _relax_torch_req, + }), + ('layoutparser', version, { + 'checksums': ['0dfb2194c36a5ad1075b8310f3cbc280c00306d1758cef127d20283f7ce085ea'], + 'preinstallopts': _del_opencv_req, + 'use_pip_extras': 'ocr,gcv,tesseract,layoutmodels,effdet', + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyTorch-Image-Models/PyTorch-Image-Models-0.9.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Image-Models/PyTorch-Image-Models-0.9.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..bcc6dac2001 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Image-Models/PyTorch-Image-Models-0.9.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,38 @@ +easyblock = "PythonBundle" + +name = 'PyTorch-Image-Models' +version = '0.9.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/timm' +description = """PyTorch Image Models (timm) is a collection of image models, layers, utilities, +optimizers, schedulers, data-loaders / augmentations, and reference training / +validation scripts that aim to pull together a wide variety of SOTA models with +ability to reproduce ImageNet training results.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('torchvision', '0.13.1', versionsuffix), + ('Safetensors', '0.3.1', versionsuffix), + ('tqdm', '4.64.0'), # needed by huggingface-hub +] + +use_pip = True + +exts_list = [ + ('huggingface-hub', '0.15.1', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['a61b7d1a7769fe10119e730277c72ab99d95c48d86a3d6da3e9f3d0f632a4081'], + }), + ('timm', version, { + 'checksums': ['d0977cc5e02c69bda979fca8b52aa315a5f2cb64ebf8ad2c4631b1e452762c14'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch-Image-Models/PyTorch-Image-Models-0.9.2-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch-Image-Models/PyTorch-Image-Models-0.9.2-foss-2022a.eb new file mode 100644 index 00000000000..385912e3d65 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Image-Models/PyTorch-Image-Models-0.9.2-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = "PythonBundle" + +name = 'PyTorch-Image-Models' +version = '0.9.2' + +homepage = 'https://huggingface.co/docs/timm' +description = """PyTorch Image Models (timm) is a collection of image models, layers, utilities, +optimizers, schedulers, data-loaders / augmentations, and reference training / +validation scripts that aim to pull together a wide variety of SOTA models with +ability to reproduce ImageNet training results.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('torchvision', '0.13.1'), + ('Safetensors', '0.3.1'), + ('tqdm', '4.64.0'), # needed by huggingface-hub +] + +use_pip = True + +exts_list = [ + ('huggingface-hub', '0.15.1', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['a61b7d1a7769fe10119e730277c72ab99d95c48d86a3d6da3e9f3d0f632a4081'], + }), + ('timm', version, { + 'checksums': ['d0977cc5e02c69bda979fca8b52aa315a5f2cb64ebf8ad2c4631b1e452762c14'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.6-foss-2022a.eb b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.6-foss-2022a.eb new file mode 100644 index 00000000000..6791855a959 --- /dev/null +++ b/easybuild/easyconfigs/p/pycocotools/pycocotools-2.0.6-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'pycocotools' +version = '2.0.6' + +homepage = 'https://pypi.org/project/pycocotools' +description = "Official APIs for the MS-COCO dataset" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7fe089b05cc18e806dcf3bd764708d86dab922a100f3734eb77fb77a70a1d18c'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.3.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..c437db1f3a6 --- /dev/null +++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.3.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,37 @@ +easyblock = "PythonBundle" + +name = 'Safetensors' +version = '0.3.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/safetensors' +description = """Safetensors is a new simple format for storing tensors safely (as opposed to +pickle) and that is still fast (zero-copy). Safetensors is really fast.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Rust', '1.60.0'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('jax', '0.3.25', versionsuffix), + ('PyTorch', '1.12.0', versionsuffix), + ('TensorFlow', '2.11.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('safetensors', version, { + 'use_pip_extras': 'jax,numpy,tensorflow,torch', + 'checksums': ['571da56ff8d0bec8ae54923b621cda98d36dcef10feb36fd492c4d0c2cd0e869'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.3.1-foss-2022a.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.3.1-foss-2022a.eb new file mode 100644 index 00000000000..b0307d32f5d --- /dev/null +++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.3.1-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = "PythonBundle" + +name = 'Safetensors' +version = '0.3.1' + +homepage = 'https://huggingface.co/docs/safetensors' +description = """Safetensors is a new simple format for storing tensors safely (as opposed to +pickle) and that is still fast (zero-copy). Safetensors is really fast.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Rust', '1.60.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('jax', '0.3.25'), + ('PyTorch', '1.12.0'), + ('TensorFlow', '2.11.0'), +] + +use_pip = True + +exts_list = [ + ('safetensors', version, { + 'use_pip_extras': 'jax,numpy,tensorflow,torch', + 'checksums': ['571da56ff8d0bec8ae54923b621cda98d36dcef10feb36fd492c4d0c2cd0e869'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 08f6ad2e948b1a4fecdb1cb4045f4d31941f2b10 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 28 Jun 2023 17:57:39 +0200 Subject: [PATCH 7900/9987] remove invalid escape sequences from LayoutParser v0.3.4 --- .../l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb | 2 +- .../easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb index 1c513a4b596..5d6d21f334f 100644 --- a/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb @@ -30,7 +30,7 @@ use_pip = True # remove opencv-python from requirements: since pip is not aware of cv2 in OpenCV from EB _del_opencv_req = "sed -i '/opencv-python/d' setup.py &&" # relax dependency on PyTorch of pytesseract -_relax_torch_req = "sed -i 's/torch >= 1\.12\.1/torch >= 1.12.0/' setup.py &&" +_relax_torch_req = "sed -i 's/torch >= 1.12.1/torch >= 1.12.0/' setup.py &&" exts_list = [ ('portalocker', '2.7.0', { diff --git a/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb index f6289d05d9f..8475d56b88d 100644 --- a/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb +++ b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb @@ -28,7 +28,7 @@ use_pip = True # remove opencv-python from requirements: since pip is not aware of cv2 in OpenCV from EB _del_opencv_req = "sed -i '/opencv-python/d' setup.py &&" # relax dependency on PyTorch of pytesseract -_relax_torch_req = "sed -i 's/torch >= 1\.12\.1/torch >= 1.12.0/' setup.py &&" +_relax_torch_req = "sed -i 's/torch >= 1.12.1/torch >= 1.12.0/' setup.py &&" exts_list = [ ('portalocker', '2.7.0', { From 4671752c9789ed46e5b0ffd88eb4bc92bf0e6367 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 28 Jun 2023 18:05:13 +0200 Subject: [PATCH 7901/9987] correct comment in LayoutParser v0.3.4 --- .../l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb | 2 +- .../easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb index 5d6d21f334f..b6dd4bfcb8b 100644 --- a/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a-CUDA-11.7.0.eb @@ -29,7 +29,7 @@ use_pip = True # remove opencv-python from requirements: since pip is not aware of cv2 in OpenCV from EB _del_opencv_req = "sed -i '/opencv-python/d' setup.py &&" -# relax dependency on PyTorch of pytesseract +# relax dependency on PyTorch of effdet _relax_torch_req = "sed -i 's/torch >= 1.12.1/torch >= 1.12.0/' setup.py &&" exts_list = [ diff --git a/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb index 8475d56b88d..792b0550540 100644 --- a/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb +++ b/easybuild/easyconfigs/l/LayoutParser/LayoutParser-0.3.4-foss-2022a.eb @@ -27,7 +27,7 @@ use_pip = True # remove opencv-python from requirements: since pip is not aware of cv2 in OpenCV from EB _del_opencv_req = "sed -i '/opencv-python/d' setup.py &&" -# relax dependency on PyTorch of pytesseract +# relax dependency on PyTorch of effdet _relax_torch_req = "sed -i 's/torch >= 1.12.1/torch >= 1.12.0/' setup.py &&" exts_list = [ From 08b30e97dd25c6eac2ca56665d6713a24aa82f74 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 28 Jun 2023 16:16:30 +0000 Subject: [PATCH 7902/9987] adding easyconfigs: R-4.3.1-gfbf-2022b.eb --- .../easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb | 374 ++++++++++++++++++ 1 file changed, 374 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb new file mode 100644 index 00000000000..772ec5bf8b3 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb @@ -0,0 +1,374 @@ +name = 'R' +version = '4.3.1' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['8dd0bf24f1023c6f618c3b317383d291b4a494f40d73b983ac22ffea99e4ba99'] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('Xvfb', '21.1.6'), + ('Autotools', '20220317'), +] +dependencies = [ + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), + ('cairo', '1.17.4'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), + ('SQLite', '3.39.4'), + ('PCRE2', '10.40'), + ('libpng', '1.6.38'), # for plotting in R + ('libjpeg-turbo', '2.1.4'), # for plottting in R + ('LibTIFF', '4.4.0'), + ('Java', '11', '', SYSTEM), + ('libgit2', '1.5.0'), + ('OpenSSL', '1.1', '', SYSTEM), + ('cURL', '7.86.0'), + ('Tk', '8.6.12'), # for tcltk + ('libxml2', '2.10.3'), # for XML + ('HarfBuzz', '5.3.1'), # for textshaping + ('FriBidi', '1.0.12'), # for textshaping + +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 22nd June 2023 +exts_list = [ + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('rlang', '1.1.1', { + 'checksums': ['5e5ec9a7796977216c39d94b1e342e08f0681746657067ba30de11b8fa8ada99'], + }), + ('Rcpp', '1.0.10', { + 'checksums': ['1e65e24a9981251ab5fc4f9fd65fe4eab4ba0255be3400a8c5abe20b62b5d546'], + }), + ('R6', '2.5.1', { + 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], + }), + ('cli', '3.6.1', { + 'checksums': ['be3006cec7e67f9ae25e21b4658c4bec680038c2ef7467df5f14da3311a05e36'], + }), + ('vctrs', '0.6.3', { + 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], + }), + ('base64enc', '0.1-3', { + 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], + }), + ('rprojroot', '2.0.3', { + 'checksums': ['50604247470e910cecfe9b76df754bf96a0d701f81b732f7aa9c90a20d30f897'], + }), + ('xfun', '0.39', { + 'checksums': ['d0ecaabb243dd3496da6029932fcdd4772914843de7ffd0b78a172efde1356c9'], + }), + ('commonmark', '1.9.0', { + 'checksums': ['6dd01a5a26c8d436486abf69c2f6ad0f8dd1c811f575c31983aeb4dbd376548f'], + }), + ('highr', '0.10', { + 'checksums': ['ec55bc1ff66390ed66806dc2a7b6c17dbfd089b3d73fe2e369017f8cb4bc347b'], + }), + ('digest', '0.6.31', { + 'checksums': ['5a284f490eaca6750f695f00a584cfca3f180ca1046ac1107202141149d431b9'], + }), + ('desc', '1.4.2', { + 'checksums': ['758acf14be478c09ba7e84ade3a7ce512becf35d44e5e6a997b932065f2a227c'], + }), + ('ellipsis', '0.3.2', { + 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], + }), + ('prettyunits', '1.1.1', { + 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], + }), + ('crayon', '1.5.2', { + 'checksums': ['70a9a505b5b3c0ee6682ad8b965e28b7e24d9f942160d0a2bad18eec22b45a7a'], + }), + ('stringi', '1.7.12', { + 'checksums': ['efe8ac2900001f986a75db5641fbb24587a6d23de274a6a85c39dfa58921e009'], + }), + ('magrittr', '2.0.3', { + 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], + }), + ('stringr', '1.5.0', { + 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], + }), + ('evaluate', '0.21', { + 'checksums': ['3178c99cee8917d7d128806d064d4fecce7845ed07f42e759dcc0adda89c22b9'], + }), + ('ps', '1.7.5', { + 'checksums': ['1abc3ae3c55797b994973f7e43bf5c7bbb4da649a0dcfad36675e196dba4cb4e'], + }), + ('processx', '3.8.1', { + 'checksums': ['e008472b81d4ca1a37a4ba7dd58e5e944f96ab2e44c8ccc8840d43e9fe99e93c'], + }), + ('callr', '3.7.3', { + 'checksums': ['567bfedf073a1d4c5785f0553341608a214938110567b9a6495ff20ebb2fd04e'], + }), + ('pkgbuild', '1.4.1', { + 'checksums': ['cdb0ace14444f362be9725bd84e9752dab92f4771296504b63b9b8084f5e8a6b'], + }), + ('fs', '1.6.2', { + 'checksums': ['548b7c0ed5ab26dc4fbd88707ae12987bcaef834dbc6de4e17d453846dc436b2'], + }), + ('utf8', '1.2.3', { + 'checksums': ['c0a88686591f4ad43b52917d0964e9df4c62d8858fe25135a1bf357dfcbd6347'], + }), + ('fansi', '1.0.4', { + 'checksums': ['3163214e6c40922bbb495229259ed8ce1bebd98b77098a6936d234e43da9c49f'], + }), + ('pillar', '1.9.0', { + 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], + }), + ('pkgconfig', '2.0.3', { + 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], + }), + ('tibble', '3.2.1', { + 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], + }), + ('withr', '2.5.0', { + 'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'], + }), + ('glue', '1.6.2', { + 'checksums': ['9da518f12be584c90e75fe8e07f711ee3f6fc0d03d817f72c25dc0f66499fdbf'], + }), + ('rstudioapi', '0.14', { + 'checksums': ['469d0987b1ad728a96c363a422fba712a5cebc8b11a5f7e953b4a671044dafc4'], + }), + ('pkgload', '1.3.2', { + 'checksums': ['35d19a032bfeeefcab92d76a768b4a420c2ede0920badaf48cca878592b46b2f'], + }), + ('htmltools', '0.5.5', { + 'checksums': ['c8b23fab855a89c6ed0f6d6c7cad0ff9c5ae329c0bdb479940443ee752f26659'], + }), + ('yaml', '2.3.7', { + 'checksums': ['d20cb219e0f9c48aba02f132f81cfa9ecda5e22c925e36726840218ed56680ab'], + }), + ('knitr', '1.43', { + 'checksums': ['3d29baea8c349aaa9310879ceb9a9d51bcaec39827ad46d422c3793c8a4ed53c'], + }), + ('mime', '0.12', { + 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], + }), + ('praise', '1.0.0', { + 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], + }), + ('brio', '1.1.3', { + 'checksums': ['eaa89041856189bee545bf1c42c7920a0bb0f1f70bb477487c467ee3e8fedcc6'], + }), + ('jsonlite', '1.8.5', { + 'checksums': ['dc3cca4bdca1b6d6836c412760ea9656140683126c54cb89c3e42219dec4a3ad'], + }), + ('lifecycle', '1.0.3', { + 'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'], + }), + ('diffobj', '0.3.5', { + 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], + }), + ('rematch2', '2.1.2', { + 'checksums': ['fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb'], + }), + ('waldo', '0.5.1', { + 'checksums': ['45bf076cff449e3c506c95857734bb73fdf30040333709b8845d09a12c6fdf46'], + }), + ('testthat', '3.1.9', { + 'checksums': ['4da1f992549c9b8db211f205059ec4c5d91a45d5971d60ebae21058268448375'], + }), + ('xml2', '1.3.4', { + 'checksums': ['340bb1a18e643a5008c0b4e92d71c3b0abacb44f1742e3a77d0cb33cb73b3030'], + }), + ('curl', '5.0.1', { + 'checksums': ['b7058f9cc7fa8f649505583584b61383fc08dccf746faa5381ba3d0b8bdf93a6'], + }), + ('sys', '3.4.2', { + 'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'], + }), + ('askpass', '1.1', { + 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], + }), + ('openssl', '2.0.6', { + 'checksums': ['77f3032a16270f0d1734f269b8d348eedc75b277812854386091143082c1b3f3'], + }), + ('httr', '1.4.6', { + 'checksums': ['8d6d86cbef23738d2b4390490f7486d8cf7674f0a59c19f515f61cad35ec37b2'], + }), + ('jquerylib', '0.1.4', { + 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], + }), + ('rappdirs', '0.3.3', { + 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], + }), + ('sass', '0.4.6', { + 'checksums': ['2ee82ce709b7fdee78f7e2364d04f369f58fc2cda4bb5a235bd53c49d311c019'], + }), + ('purrr', '1.0.1', { + 'checksums': ['0a7911be3539355a4c40d136f2602befcaaad5a3f7222078500bfb969a6f2ba2'], + }), + ('fastmap', '1.1.1', { + 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], + }), + ('cachem', '1.0.8', { + 'checksums': ['ea9ca919fe615dce8770758ecc2fc88ac99074f66ff1cde3a0b95d40007f45c2'], + }), + ('memoise', '2.0.1', { + 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], + }), + ('bslib', '0.5.0', { + 'checksums': ['a2c6fbc62242806e10bb58c5d1ba04a6d3bf4e546bc53d7acf1b8eb1160bd115'], + }), + ('fontawesome', '0.5.0', { + 'checksums': ['4117b417a33e82d626881d7059eb54e7534cba202e75dae7e27021cb3796e90b'], + }), + ('tinytex', '0.45', { + 'checksums': ['0c2fbbd09e80af80ca6b685bf0653f070da97b85413d39af966aba28f376e92c'], + }), + ('rmarkdown', '2.22', { + 'checksums': ['c6635519503e0fcdd518696d3ac96d8d28d9d4ecd9db0532c53426002f6387b8'], + }), + ('downlit', '0.4.2', { + 'checksums': ['33dff66909104d1a5ba8e57b1288986e82b61fd5e91dce0cd358d53724b37e3c'], + }), + ('cpp11', '0.4.3', { + 'checksums': ['f1a60e4971a86dbbcf6a16bbd739b59bb66d9c45d93cfd8dedc2a87e302598f1'], + }), + ('systemfonts', '1.0.4', { + 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], + }), + ('textshaping', '0.3.6', { + 'checksums': ['80e2c087962f55ce2811fbc798b09f5638c06c6b28c10cd3cb3827005b902ada'], + }), + ('ragg', '1.2.5', { + 'checksums': ['936f4d75e0e01cdeefb9f57d121cdd7812d0de5a9e1a3a8315f92ce1c84da8f9'], + }), + ('whisker', '0.4.1', { + 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], + }), + ('pkgdown', '2.0.7', { + 'checksums': ['f33872869dfa8319182d87e90eab3245ff69293b3b791471bf9538afb81b356a'], + }), + ('htmlwidgets', '1.6.2', { + 'checksums': ['7fda1672a4c0fbc203c790677b6ee7c40d2c2d72be4f6772f75288fc712b10bc'], + }), + ('profvis', '0.3.8', { + 'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'], + }), + ('urlchecker', '1.0.1', { + 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], + }), + ('later', '1.3.1', { + 'checksums': ['23eed681f0b9eacebbc3c6a5ba14ee0b676a4bf6e69af194c5a36edfe11464ac'], + }), + ('promises', '1.2.0.1', { + 'checksums': ['8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7'], + }), + ('xtable', '1.8-4', { + 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], + }), + ('httpuv', '1.6.11', { + 'checksums': ['8ba79e0a8351274daf2dc566c71f88e891127cdedca62ad77a4b27a8103eeef5'], + }), + ('sourcetools', '0.1.7-1', { + 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], + }), + ('shiny', '1.7.4', { + 'checksums': ['bbfcdd7375013b8f59248b3f3f4e752acd445feb25179f3f7f65cd69614da4b5'], + }), + ('miniUI', '0.1.1.1', { + 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], + }), + ('brew', '1.0-8', { + 'checksums': ['11652d5a7042d645cc5be5f9f97ff4d46083cea7d3ad2dd6ad1570b52c097826'], + }), + ('roxygen2', '7.2.3', { + 'checksums': ['d844fab977d2575ab942fa1309ac7ff67f35f099a75d8b41c79efe6ea10416da'], + }), + ('rversions', '2.1.2', { + 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], + }), + ('sessioninfo', '1.2.2', { + 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], + }), + ('xopen', '1.0.0', { + 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], + }), + ('rcmdcheck', '1.4.0', { + 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], + }), + ('remotes', '2.4.2', { + 'checksums': ['f2ef875f24a485bf4f55a8c830f87cdd5db868f9a8cdb624dc452d0bf66ba516'], + }), + ('clipr', '0.8.0', { + 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.2', { + 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], + }), + ('httr2', '0.2.3', { + 'checksums': ['352032029512f28f6f440ace0078e859ad3945d6b20841963b372523b6974b3d'], + }), + ('gh', '1.4.0', { + 'checksums': ['68c69fcd18429b378e639a09652465a4e92b7b5b5704804d0c5b1ca2b9b58b71'], + }), + ('credentials', '1.3.2', { + 'checksums': ['2ffa7c11bedbfa034adf553d0a2f2e4f6a496b858af753a09a89219cff9028b8'], + }), + ('zip', '2.3.0', { + 'checksums': ['33eba844922af9981732ee6ec1582d46cf04c562344f09a0f0f14a22c6f74543'], + }), + ('gert', '1.9.2', { + 'checksums': ['42ca1b4bcafb1fdbbc7f54df0ee4476ecd19e9e7d563b53fe7064e0086ab665e'], + }), + ('usethis', '2.2.0', { + 'checksums': ['2ccebe690aadebff96451cc9c226dc1a1e9ca5ac6ec83310e12a1312cb163b4f'], + }), + ('devtools', '2.4.5', { + 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], + }), +] + +moduleclass = 'lang' From f12111e9f77a7ece53533b07eaf713417efb885f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 28 Jun 2023 19:35:01 +0100 Subject: [PATCH 7903/9987] remove default separate_build_dir = True and build_type = 'Release' from double-conversion --- .../double-conversion-3.2.0-GCCcore-11.3.0.eb | 4 ---- .../double-conversion-3.2.1-GCCcore-12.2.0.eb | 4 ---- .../double-conversion-3.3.0-GCCcore-12.3.0.eb | 4 ---- 3 files changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.0-GCCcore-11.3.0.eb index 177cc580c99..922d510f660 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.0-GCCcore-11.3.0.eb @@ -17,10 +17,6 @@ builddependencies = [ ('CMake', '3.23.1'), ] -separate_build_dir = True - -build_type = 'Release' - # Build static lib, static lib with -fPIC and shared lib configopts = [ '', diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb index d3221353d9f..159f1a025a6 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb @@ -17,10 +17,6 @@ builddependencies = [ ('CMake', '3.24.3'), ] -separate_build_dir = True - -build_type = 'Release' - # Build static lib, static lib with -fPIC and shared lib configopts = [ '', diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb index 66e54112889..e0e20e455b5 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb @@ -17,10 +17,6 @@ builddependencies = [ ('CMake', '3.26.3'), ] -separate_build_dir = True - -build_type = 'Release' - # Build static lib, static lib with -fPIC and shared lib configopts = [ '', From 0ebbc8507d45d887f4dd5ba9d24acd657b2edaab Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 28 Jun 2023 19:38:27 +0100 Subject: [PATCH 7904/9987] remove default separate_build_dir = True and build_type = 'Release' from MariaDB --- .../easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb | 5 +---- easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb | 5 +---- easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb | 5 +---- 3 files changed, 3 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb index 37fce889bdc..c82bd9ecd86 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb @@ -40,10 +40,7 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest ] -separate_build_dir = True - -configopts = "-DCMAKE_BUILD_TYPE=Release " -configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. configopts += "-DWITH_ZLIB=system " diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb index aefe88e5390..afc9476839f 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0.eb @@ -40,10 +40,7 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest ] -separate_build_dir = True - -configopts = "-DCMAKE_BUILD_TYPE=Release " -configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. configopts += "-DWITH_ZLIB=system " diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb index d090e5a8ce7..b08debd8ac0 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.9.3-GCC-11.3.0.eb @@ -40,10 +40,7 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest ] -separate_build_dir = True - -configopts = "-DCMAKE_BUILD_TYPE=Release " -configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. configopts += "-DWITH_ZLIB=system " From f82cade8f64bb3c83757092fa647dbe3fced555b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85ke=20Sandgren?= Date: Thu, 29 Jun 2023 07:23:44 +0200 Subject: [PATCH 7905/9987] Update easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb index fc983ab5255..3ddba230d4b 100644 --- a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb @@ -4,7 +4,7 @@ name = 'HOOMD-blue' version = "4.0.1" versionsuffix = '-CUDA-%(cudaver)s' -homepage = "https://bitbucket.org/glotzer/hoomd-blue" +homepage = "https://glotzerlab.engin.umich.edu/hoomd-blue/" description = """HOOMD-blue is a general-purpose particle simulation toolkit, implementing molecular dynamics and hard particle Monte Carlo optimized for fast execution on both GPUs and CPUs.""" From f78ae8f97202def313c14607766a424ec124efaa Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 29 Jun 2023 08:09:26 +0200 Subject: [PATCH 7906/9987] adding easyconfigs: HOOMD-blue-4.0.1-foss-2022a.eb --- .../HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb new file mode 100644 index 00000000000..f476a2ced04 --- /dev/null +++ b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb @@ -0,0 +1,59 @@ +easyblock = 'CMakeMake' + +name = 'HOOMD-blue' +version = "4.0.1" + +homepage = "https://bitbucket.org/glotzer/hoomd-blue" +description = """HOOMD-blue is a general-purpose particle simulation +toolkit, implementing molecular dynamics and hard particle Monte Carlo +optimized for fast execution on both GPUs and CPUs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +github_account = 'glotzerlab' +source_urls = [GITHUB_LOWER_RELEASE] +sources = ['hoomd-%(version)s.tar.gz'] +checksums = ['b63dd8debb96f9c530983bd54ecbafa8fd07e017ded3ea64604cfb1f41a644b8'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pybind11', '2.9.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tbb', '2021.5.0'), + ('Eigen', '3.4.0'), + ('Cereal', '1.3.2', '', SYSTEM), +] + +_copts = [ + '-DENABLE_GPU=OFF', + '-DENABLE_MPI=ON', + '-DBUILD_MD=ON', + '-DBUILD_METAL=ON', + '-DENABLE_TBB=ON', + '-DBUILD_TESTING=ON', +] +configopts = ' '.join(_copts) + +postinstallcmds = [ + 'ln -s hoomd/include %(installdir)s/include', +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['hoomd/__init__.py', 'hoomd/include/hoomd/Compute.h'], + 'dirs': ['lib/cmake'], +} + +sanity_check_commands = [ + "python -c 'import hoomd'", +] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'phys' From e25a4cb661ead0406dc485d5c371c643ac44e78b Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Jun 2023 08:16:17 +0000 Subject: [PATCH 7907/9987] Fix comment formatting --- easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb index 772ec5bf8b3..1109fa7bb52 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb @@ -37,8 +37,8 @@ dependencies = [ ('cURL', '7.86.0'), ('Tk', '8.6.12'), # for tcltk ('libxml2', '2.10.3'), # for XML - ('HarfBuzz', '5.3.1'), # for textshaping - ('FriBidi', '1.0.12'), # for textshaping + ('HarfBuzz', '5.3.1'), # for textshaping + ('FriBidi', '1.0.12'), # for textshaping ] From a6d44b07ad0ae84b101621be0b948cc942be1875 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 29 Jun 2023 10:25:26 +0200 Subject: [PATCH 7908/9987] Update easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb b/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb index 92c08277777..1bce2a99d52 100644 --- a/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb +++ b/easybuild/easyconfigs/a/AIMAll/AIMAll-19.10.12-intel-2020b-linux_64bit.eb @@ -12,8 +12,8 @@ data.""" toolchain = {'name': 'intel', 'version': '2020b'} -# download sources from http://aim.tkgristmill.com/download/download.html (requires login) -# to run in professional mode, add required license files to the main AIMAll directory +download_instructions = """Download sources from http://aim.tkgristmill.com/download/download.html (requires login). +To run in professional mode, add required license files to the main AIMAll directory.""" sources = [ {'filename': 'aimall_%s_linux_64bit.tar.gz' % version.replace('.', '_'), 'extract_cmd': 'tar -xzf %s --strip-components=1'}, From 13565b1d5d2489a02a00b42b193c62bbd5f2ec6f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2023 10:33:15 +0200 Subject: [PATCH 7909/9987] adding easyconfigs: ont-fast5-api-4.1.1-foss-2022b.eb --- .../ont-fast5-api-4.1.1-foss-2022b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.1-foss-2022b.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.1-foss-2022b.eb new file mode 100644 index 00000000000..c33603ff16c --- /dev/null +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.1-foss-2022b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '4.1.1' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('h5py', '3.8.0'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + (name, version, { + 'checksums': ['71ea44087f310a2792d1a6c2ffbf5bc194367e769ce96a15961787f90ec7707b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/compress_fast5', 'bin/fast5_subset', 'bin/multi_to_single_fast5', 'bin/single_to_multi_fast5'], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From d0c76a685dc825c16d53fced905d0d7e7e663741 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 29 Jun 2023 10:51:59 +0200 Subject: [PATCH 7910/9987] adding easyconfigs: hifiasm-0.19.5-GCCcore-11.2.0.eb --- .../hifiasm/hifiasm-0.19.5-GCCcore-11.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/hifiasm/hifiasm-0.19.5-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/h/hifiasm/hifiasm-0.19.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.19.5-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..8d271908c78 --- /dev/null +++ b/easybuild/easyconfigs/h/hifiasm/hifiasm-0.19.5-GCCcore-11.2.0.eb @@ -0,0 +1,42 @@ +# Author: Jasper Grimm (UoY) +# Update: Sebastien Moretti (SIB) + +easyblock = 'MakeCp' + +name = 'hifiasm' +version = '0.19.5' + +homepage = 'https://github.com/chhylp123/hifiasm' +description = """Hifiasm: a haplotype-resolved assembler for accurate Hifi reads.""" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'chhylp123' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['18ed6889972e38d0088ccbdafee90756158977d6b1e1b6e56f522b870d71c072'] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +buildopts = 'CC="$CC" CXX="$CXX" CPPFLAGS="$CPPFLAGS"' + +files_to_copy = [ + ([name], 'bin'), + (['*.h'], 'include/hifiasm'), + 'LICENSE', 'README.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} +sanity_check_commands = ["%(name)s -h"] + +moduleclass = 'bio' From c6249c95d4f290cae2f21ba5d7641d631f4fe293 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2023 11:02:25 +0200 Subject: [PATCH 7911/9987] adding easyconfigs: InterProScan-5.62-94.0-foss-2022b.eb --- .../InterProScan-5.62-94.0-foss-2022b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/i/InterProScan/InterProScan-5.62-94.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.62-94.0-foss-2022b.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.62-94.0-foss-2022b.eb new file mode 100644 index 00000000000..fb71e8845fa --- /dev/null +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.62-94.0-foss-2022b.eb @@ -0,0 +1,53 @@ +easyblock = 'Binary' + +name = 'InterProScan' +version = '5.62-94.0' + +homepage = 'https://www.ebi.ac.uk/interpro/' +# also https://github.com/ebi-pf-team/interproscan +description = """InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines + different protein signature recognition methods into one resource [code only: libraries and external binaries + but no data].""" +# software_license = 'LicenseApachev2' + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://ftp.ebi.ac.uk/pub/software/unix/iprscan/%(version_major)s/%(version)s/alt/'] +sources = ['interproscan-core-%(version)s.tar.gz'] +checksums = ['98caccaea4d47dbbb0975e7a09a4253b7e7b2796163567d2763f39d0a822c2a9'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Perl', '5.36.0'), + ('libgd', '2.3.3'), + ('Python', '3.10.8'), + ('PCRE', '8.45'), +] +# NOTE some analyses done by InterProScan require extra tools not included in the interproscan +# distribution because of license issues. +# Those tools are SignalP, TMHMM and Phobius. +# To allow InterProScan to use them you have to copy or symlink their executable in the +# corresponding %(installdir)s/bin/TOOL/VERSION/ folder. + +extract_sources = False + +# NOTE The data can be added manually afterwards with for example a symlink called *data* +# in %(installdir)s/ +# But simpler to use the InterProScan_data-*.eb file. The regular InterProScan data package +# does not contain the lookup_service data way too large! +install_cmd = 'tar xfz %(namelower)s-core-%(version)s.tar.gz && ' +install_cmd += 'cd %(namelower)s-%(version)s/ && ' +install_cmd += 'find . -type d -name bin32 | xargs rm -Rf && ' +install_cmd += 'rm -f test* && rm -Rf src/ && ' +install_cmd += 'chmod -x *.jar && ' +install_cmd += 'cp -r * %(installdir)s/ && cd .. && ' +install_cmd += 'rm -Rf %(namelower)s-%(version)s/' + +sanity_check_paths = { + 'files': ['interproscan-%(version_major)s.jar', 'interproscan.sh', 'interproscan.properties'], + 'dirs': ['bin', 'lib'], +} + +sanity_check_commands = ["interproscan.sh 2>&1 | grep 'Welcome to InterProScan-%(version)s'"] + +moduleclass = 'bio' From 02983275292138fb4ce09c9ae5121f60018b6119 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2023 11:26:44 +0200 Subject: [PATCH 7912/9987] adding easyconfigs: PyCalib-20230531-gfbf-2022b.eb, statsmodels-0.14.0-gfbf-2022b.eb --- .../p/PyCalib/PyCalib-20230531-gfbf-2022b.eb | 28 ++++++++++++++++++ .../statsmodels-0.14.0-gfbf-2022b.eb | 29 +++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyCalib/PyCalib-20230531-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.0-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/p/PyCalib/PyCalib-20230531-gfbf-2022b.eb b/easybuild/easyconfigs/p/PyCalib/PyCalib-20230531-gfbf-2022b.eb new file mode 100644 index 00000000000..61154630966 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCalib/PyCalib-20230531-gfbf-2022b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyCalib' +version = '20230531' +local_commit = '70cfbcb' + +homepage = 'https://github.com/classifier-calibration/PyCalib' +description = "Python library for classifier calibration" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://github.com/classifier-calibration/PyCalib/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCELOWER_TAR_GZ}] +checksums = ['00728de1e7afd27a85050f505f6e21cca509d423a0785f8c586054a1bb79d30a'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), + ('scikit-learn', '1.2.1'), + ('statsmodels', '0.14.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.0-gfbf-2022b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.0-gfbf-2022b.eb new file mode 100644 index 00000000000..11abb6318f6 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.0-gfbf-2022b.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.14.0' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.3', { + 'checksums': ['bdc18001875e319bc91c812c1eb6a10be4bb13cb81eb763f466179dca3b67277'], + }), + (name, version, { + 'checksums': ['6875c7d689e966d948f15eb816ab5616f4928706b180cf470fd5907ab6f647a4'], + }), +] + +moduleclass = 'math' From d69ec0bd343f9d257c25c92e4c0fc0c205a8acd1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 29 Jun 2023 11:28:56 +0200 Subject: [PATCH 7913/9987] adding easyconfigs: pbipa-1.8.0-foss-2021b.eb --- .../p/pbipa/pbipa-1.8.0-foss-2021b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/pbipa/pbipa-1.8.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/p/pbipa/pbipa-1.8.0-foss-2021b.eb b/easybuild/easyconfigs/p/pbipa/pbipa-1.8.0-foss-2021b.eb new file mode 100644 index 00000000000..2ad7859af59 --- /dev/null +++ b/easybuild/easyconfigs/p/pbipa/pbipa-1.8.0-foss-2021b.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'pbipa' +version = '1.8.0' + +homepage = 'https://github.com/PacificBiosciences/pbipa' +description = """Improved Phased Assembler (IPA) is the official PacBio +software for HiFi genome assembly. IPA was designed to utilize the +accuracy of PacBio HiFi reads to produce high-quality phased genome +assemblies. IPA is an end-to-end solution, starting with input reads and +resulting in a polished assembly. IPA is fast, providing an easy to use +local run mode or a distributed pipeline for a cluster.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'PacificBiosciences' +source_urls = [GITHUB_RELEASE] +sources = [{'download_filename': '%(name)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['8c08fc53a17dfc6e773c10a3e565ea7224595829e0b48adcd76556418544388a'] + +dependencies = [ + ('Python', '3.9.6'), + ('snakemake', '6.10.0'), +] + +sanity_check_paths = { + 'files': ['bin/ipa', 'etc/ipa.snakefile'], + 'dirs': [], +} + +sanity_check_commands = [ + 'ipa --version', +] + +moduleclass = 'bio' From ae01739d0551330ef949d2cb39b4bfac5d393ca6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Jun 2023 10:20:58 +0000 Subject: [PATCH 7914/9987] Fix dependency ordering for vctrs --- easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb index 1109fa7bb52..57028db3fbd 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb @@ -93,9 +93,6 @@ exts_list = [ ('cli', '3.6.1', { 'checksums': ['be3006cec7e67f9ae25e21b4658c4bec680038c2ef7467df5f14da3311a05e36'], }), - ('vctrs', '0.6.3', { - 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], - }), ('base64enc', '0.1-3', { 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], }), @@ -204,6 +201,9 @@ exts_list = [ ('lifecycle', '1.0.3', { 'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'], }), + ('vctrs', '0.6.3', { + 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], + }), ('diffobj', '0.3.5', { 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], }), From 84e96c26020f81174961209722d5af8377239d2b Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Thu, 29 Jun 2023 13:02:28 +0200 Subject: [PATCH 7915/9987] Update QT5-5.17.7-GCCcore-12.20.0 for SIGSTKSZ? --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb index 592deb7c5f5..afb1406fa10 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb @@ -20,6 +20,8 @@ patches = [ 'Qt5-5.13.1_fix-avx2.patch', 'Qt5-5.13.1_fix-qmake-libdir.patch', 'Qt5-5.14.1_fix-OF-Gentoo.patch', + 'Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch', + 'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch', 'Qt5-5.15.7_GCC-12.patch', ] checksums = [ @@ -27,6 +29,8 @@ checksums = [ {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, {'Qt5-5.14.1_fix-OF-Gentoo.patch': '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa'}, + {'Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch': 'f39506495b70cc0968fb7a5f4c9028b0f0a180c552906ff4e58e0bcae83cf187'}, + {'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch': '74590de2b9e32f2c88123cb096c4f5c3001b00710aad096a4d16444a8e9eb991'}, {'Qt5-5.15.7_GCC-12.patch': '9a5bde91b223a3e2e90d3d6bec107af69a1a0f18d789593738a953080473fa68'}, ] From 44fe97e6adb2163f6d588a30e2c9271f2a75a86c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 29 Jun 2023 13:20:17 +0200 Subject: [PATCH 7916/9987] Adjust incorrect version for GMAP-GSNAP 2021-12-17 The original tarfile was named gmap-gsnap-2021-21-17.tar.gz but has later been corrected for the typo. Also adjust the version in rnaQUAST-2.2.2-foss-2021b.eb which is the only place it is used. --- ...-21-17-GCC-11.2.0.eb => GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb} | 2 +- easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/GMAP-GSNAP/{GMAP-GSNAP-2021-21-17-GCC-11.2.0.eb => GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb} (98%) diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-21-17-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb similarity index 98% rename from easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-21-17-GCC-11.2.0.eb rename to easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb index 8ec3299dc96..de879542abf 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-21-17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb @@ -9,7 +9,7 @@ easyblock = 'ConfigureMake' name = 'GMAP-GSNAP' -version = '2021-21-17' +version = '2021-12-17' homepage = 'http://research-pub.gene.com/gmap/' description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences diff --git a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb index 06463e95584..20225e8951c 100644 --- a/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/rnaQUAST/rnaQUAST-2.2.2-foss-2021b.eb @@ -16,7 +16,7 @@ checksums = ['941aeb9a296aa0135f8973c0cffa76e05d7451cc698f0f56c23c5627ae163c8f'] dependencies = [ ('Python', '3.9.6'), - ('GMAP-GSNAP', '2021-21-17'), + ('GMAP-GSNAP', '2021-12-17'), ('Biopython', '1.79'), ('matplotlib', '3.4.3'), ('BLAST+', '2.12.0'), From de8bf5617d1c8af79f2ecfaf1df5afc2a0c59123 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Jun 2023 11:30:14 +0000 Subject: [PATCH 7917/9987] adding easyconfigs: dx-toolkit-0.350.1-foss-2022b.eb --- .../dx-toolkit-0.350.1-foss-2022b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-foss-2022b.eb b/easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-foss-2022b.eb new file mode 100644 index 00000000000..d6c5f67c61e --- /dev/null +++ b/easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-foss-2022b.eb @@ -0,0 +1,46 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'dx-toolkit' +version = '0.350.1' + +homepage = 'https://documentation.dnanexus.com/downloads#dnanexus-platform-sdk' +description = """The DNAnexus Platform SDK - also called dx-toolkit - includes the dx command-line client; + tools for building and debugging apps; utilities for working with DNA data on the DNAnexus Platform; + and Python, Java, C++ and R bindings for working on the DNAnexus Platform. + """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('argcomplete', '3.1.1', { + 'checksums': ['6c4c563f14f01440aaffa3eae13441c5db2357b5eec639abe7c0b15334627dff'], + }), + ('websocket-client', '0.54.0', { + 'source_tmpl': 'websocket_client-%(version)s.tar.gz', + 'checksums': ['e51562c91ddb8148e791f0155fdb01325d99bb52c4cdbb291aee7a3563fd0849'], + 'modulename': 'websocket', + }), + ('dxpy', version, { + 'checksums': ['3378a233454beaefb8d291ed4a4450a784917347e3056812e4fd709be09aace4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dx', 'bin/wsdump.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'dx --help', +] + +moduleclass = 'tools' From 52a336163bad8349ad22f6e8ee46e4ade34c35e4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 29 Jun 2023 13:33:00 +0200 Subject: [PATCH 7918/9987] GMAP-GSNAP: utilities depends on Perl --- .../easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb index de879542abf..6228f5c0e86 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb @@ -26,6 +26,7 @@ checksums = ['9e8368bc997d79292f84a3553bc1a09c1d5ea5337d252dadc0f6ed85b4bb6dae'] dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), + ('Perl','5.34.0'), ] # GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length From 43f7ebaedf6905ebe3f46bd3119124c202a36505 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Jun 2023 11:33:55 +0000 Subject: [PATCH 7919/9987] Use GCCcore instead of foss --- .../dx-toolkit-0.350.1-GCCcore-12.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2b1396e8f5d --- /dev/null +++ b/easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-GCCcore-12.2.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'dx-toolkit' +version = '0.350.1' + +homepage = 'https://documentation.dnanexus.com/downloads#dnanexus-platform-sdk' +description = """The DNAnexus Platform SDK - also called dx-toolkit - includes the dx command-line client; + tools for building and debugging apps; utilities for working with DNA data on the DNAnexus Platform; + and Python, Java, C++ and R bindings for working on the DNAnexus Platform. + """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('argcomplete', '3.1.1', { + 'checksums': ['6c4c563f14f01440aaffa3eae13441c5db2357b5eec639abe7c0b15334627dff'], + }), + ('websocket-client', '0.54.0', { + 'source_tmpl': 'websocket_client-%(version)s.tar.gz', + 'checksums': ['e51562c91ddb8148e791f0155fdb01325d99bb52c4cdbb291aee7a3563fd0849'], + 'modulename': 'websocket', + }), + ('dxpy', version, { + 'checksums': ['3378a233454beaefb8d291ed4a4450a784917347e3056812e4fd709be09aace4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dx', 'bin/wsdump.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'dx --help', +] + +moduleclass = 'tools' From 439fca934ac35edce2c518d2e730b102c41c56d7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Jun 2023 12:34:14 +0100 Subject: [PATCH 7920/9987] Delete dx-toolkit-0.350.1-foss-2022b.eb --- .../dx-toolkit-0.350.1-foss-2022b.eb | 46 ------------------- 1 file changed, 46 deletions(-) delete mode 100644 easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-foss-2022b.eb b/easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-foss-2022b.eb deleted file mode 100644 index d6c5f67c61e..00000000000 --- a/easybuild/easyconfigs/d/dx-toolkit/dx-toolkit-0.350.1-foss-2022b.eb +++ /dev/null @@ -1,46 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild - -easyblock = 'PythonBundle' - -name = 'dx-toolkit' -version = '0.350.1' - -homepage = 'https://documentation.dnanexus.com/downloads#dnanexus-platform-sdk' -description = """The DNAnexus Platform SDK - also called dx-toolkit - includes the dx command-line client; - tools for building and debugging apps; utilities for working with DNA data on the DNAnexus Platform; - and Python, Java, C++ and R bindings for working on the DNAnexus Platform. - """ - -toolchain = {'name': 'foss', 'version': '2022b'} - -dependencies = [ - ('Python', '3.10.8'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('argcomplete', '3.1.1', { - 'checksums': ['6c4c563f14f01440aaffa3eae13441c5db2357b5eec639abe7c0b15334627dff'], - }), - ('websocket-client', '0.54.0', { - 'source_tmpl': 'websocket_client-%(version)s.tar.gz', - 'checksums': ['e51562c91ddb8148e791f0155fdb01325d99bb52c4cdbb291aee7a3563fd0849'], - 'modulename': 'websocket', - }), - ('dxpy', version, { - 'checksums': ['3378a233454beaefb8d291ed4a4450a784917347e3056812e4fd709be09aace4'], - }), -] - -sanity_check_paths = { - 'files': ['bin/dx', 'bin/wsdump.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - 'dx --help', -] - -moduleclass = 'tools' From 2aeefd63feec37ca3504f9aa2b535a2f12dc145d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 29 Jun 2023 13:36:38 +0200 Subject: [PATCH 7921/9987] adding easyconfigs: POT-0.9.0-foss-2022a.eb, CVXOPT-1.3.1-foss-2022a.eb --- .../c/CVXOPT/CVXOPT-1.3.1-foss-2022a.eb | 42 +++++++++++++++++++ .../easyconfigs/p/POT/POT-0.9.0-foss-2022a.eb | 40 ++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/POT/POT-0.9.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1-foss-2022a.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1-foss-2022a.eb new file mode 100644 index 00000000000..9bac0454227 --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1-foss-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'CVXOPT' +version = '1.3.1' + +homepage = 'https://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['CVXOPT-1.3.1_fix-setup-py.patch'] + +checksums = [ + '8d567981cbfa2a4ba1667b3e6f73cb941cf1c6992bf1438911035963294aa498', # cvxopt-1.3.1.tar.gz + '350904c0427d4652fc73b95b7e0d78a17c917cb94ed6c356dbbbfb07f2173849', # CVXOPT-1.3.1_fix-setup-py.patch +] + +dependencies = [ + ('Python', '3.10.4'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('GSL', '2.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = 'CVXOPT_BUILD_FFTW=1 CVXOPT_BUILD_GSL=1 CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBLAPACK" ' +preinstallopts += 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT" CVXOPT_SUITESPARSE_SRC_DIR=$EBROOTSUITESPARSE' + +installopts = ' --no-binary cvxopt' + +sanity_check_commands = ['cd %(builddir)s/%(namelower)s-%(version)s && python -m unittest discover -s tests'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/POT/POT-0.9.0-foss-2022a.eb b/easybuild/easyconfigs/p/POT/POT-0.9.0-foss-2022a.eb new file mode 100644 index 00000000000..716388b4c20 --- /dev/null +++ b/easybuild/easyconfigs/p/POT/POT-0.9.0-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'POT' +version = '0.9.0' + +homepage = 'https://github.com/rflamary/POT' +description = """POT (Python Optimal Transport) is a Python library provide several solvers for optimization problems + related to Optimal Transport for signal, image processing and machine learning.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('scikit-learn', '1.1.2'), + ('PyTorch', '1.12.0'), + ('jax', '0.3.25'), + ('CVXOPT', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('autograd', '1.6.2', { + 'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'], + }), + ('versioneer', '0.28', { + 'checksums': ['7175ca8e7bb4dd0e3c9779dd2745e5b4a6036304af3f5e50bd896f10196586d6'], + }), + ('pymanopt', '2.1.1', { + 'checksums': ['07f6996b944eb43a15ce762841e01f7f7aa2d29005253eb7087db3926fdd8aa6'], + }), + (name, version, { + 'modulename': 'ot', + 'checksums': ['300864ae2b469a7b66155fc610a134961d9d46f1ecde0d85e484d14acd06b215'], + }), +] + +moduleclass = 'lib' From 760a13bf7e0b50b4b606b10f6be05fa5942a3026 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 29 Jun 2023 13:40:00 +0200 Subject: [PATCH 7922/9987] adding easyconfigs: nose3-1.3.8-GCCcore-11.3.0.eb, coverage-7.2.7-GCCcore-11.3.0.eb --- .../coverage/coverage-7.2.7-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ .../n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb | 33 +++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/c/coverage/coverage-7.2.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/coverage/coverage-7.2.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/coverage/coverage-7.2.7-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..75b1ec28581 --- /dev/null +++ b/easybuild/easyconfigs/c/coverage/coverage-7.2.7-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'coverage' +version = '7.2.7' + +homepage = 'https://coverage.readthedocs.io' +description = """ Coverage.py is a tool for measuring code coverage of Python programs. + It monitors your program, noting which parts of the code have been executed, + then analyzes the source to identify code that could have been executed but was not. """ + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['924d94291ca674905fe9481f12294eb11f2d3d3fd1adb20314ba89e94f44ed59'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ["coverage --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c71f875bc79 --- /dev/null +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'nose3' +version = '1.3.8' + +homepage = 'https://nose.readthedocs.io/' +description = """Nose extends unittest to make testing easier.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] + +checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'], + +options = {'modulename': 'nose'} + +dependencies = [ + ('Python', '3.10.4'), + ('coverage', '7.2.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/nosetests'], + 'dirs': [], +} + +sanity_check_commands = ["nosetests --help"] + +moduleclass = 'devel' From 77fd4d1b84077012ce4da22758fc4d4ed4b7037e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 29 Jun 2023 13:49:57 +0200 Subject: [PATCH 7923/9987] GMAP-GSNAP: Fix missing space. --- .../g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb index 6228f5c0e86..b184438655e 100644 --- a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2021-12-17-GCC-11.2.0.eb @@ -26,7 +26,7 @@ checksums = ['9e8368bc997d79292f84a3553bc1a09c1d5ea5337d252dadc0f6ed85b4bb6dae'] dependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.11'), - ('Perl','5.34.0'), + ('Perl', '5.34.0'), ] # GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length From 71f3bb86962fef29d5c3728aba7c5310e14ef807 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 29 Jun 2023 13:55:19 +0200 Subject: [PATCH 7924/9987] forgotten patch file --- .../c/CVXOPT/CVXOPT-1.3.1_fix-setup-py.patch | 130 ++++++++++++++++++ 1 file changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1_fix-setup-py.patch diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1_fix-setup-py.patch b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1_fix-setup-py.patch new file mode 100644 index 00000000000..4788469ac8f --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.1_fix-setup-py.patch @@ -0,0 +1,130 @@ +# Patches the setup.py to use EB settings for BLAS/LAPACK, FFTW, etc +# original by wpoely86@gmail.com, ported to v1.2.1 by Kenneth Hoste (HPC-UGent) +# Update: Petr Král (INUITS) +diff -u cvxopt-1.3.1/setup.py.orig cvxopt-1.3.1/setup.py +--- cvxopt-1.3.1/setup.py.orig 2023-05-10 13:52:37.000000000 +0200 ++++ cvxopt-1.3.1/setup.py 2023-06-28 10:58:21.228590970 +0200 +@@ -90,9 +90,11 @@ + LAPACK_LIB = os.environ.get("CVXOPT_LAPACK_LIB",LAPACK_LIB) + BLAS_LIB_DIR = os.environ.get("CVXOPT_BLAS_LIB_DIR",BLAS_LIB_DIR) + BLAS_EXTRA_LINK_ARGS = os.environ.get("CVXOPT_BLAS_EXTRA_LINK_ARGS",BLAS_EXTRA_LINK_ARGS) ++FFTW_EXTRA_LINK_ARGS = os.environ.get("CVXOPT_FFTW_EXTRA_LINK_ARGS",'') + if type(BLAS_LIB) is str: BLAS_LIB = BLAS_LIB.strip().split(';') + if type(LAPACK_LIB) is str: LAPACK_LIB = LAPACK_LIB.strip().split(';') +-if type(BLAS_EXTRA_LINK_ARGS) is str: BLAS_EXTRA_LINK_ARGS = BLAS_EXTRA_LINK_ARGS.strip().split(';') ++if type(BLAS_EXTRA_LINK_ARGS) is str: BLAS_EXTRA_LINK_ARGS = BLAS_EXTRA_LINK_ARGS.strip().split(' ') ++if type(FFTW_EXTRA_LINK_ARGS) is str: FFTW_EXTRA_LINK_ARGS = FFTW_EXTRA_LINK_ARGS.strip().split(' ') + BUILD_GSL = int(os.environ.get("CVXOPT_BUILD_GSL",BUILD_GSL)) + GSL_LIB_DIR = os.environ.get("CVXOPT_GSL_LIB_DIR",GSL_LIB_DIR) + GSL_INC_DIR = os.environ.get("CVXOPT_GSL_INC_DIR",GSL_INC_DIR) +@@ -128,7 +130,7 @@ + # optional modules + + if BUILD_GSL: +- gsl = Extension('gsl', libraries = M_LIB + ['gsl'] + BLAS_LIB, ++ gsl = Extension('gsl', libraries = M_LIB + ['gsl'], + include_dirs = [ GSL_INC_DIR ], + library_dirs = [ GSL_LIB_DIR, BLAS_LIB_DIR ], + define_macros = GSL_MACROS, +@@ -137,11 +139,11 @@ + extmods += [gsl]; + + if BUILD_FFTW: +- fftw = Extension('fftw', libraries = ['fftw3'] + BLAS_LIB, ++ fftw = Extension('fftw', + include_dirs = [ FFTW_INC_DIR ], + library_dirs = [ FFTW_LIB_DIR, BLAS_LIB_DIR ], + define_macros = FFTW_MACROS, +- extra_link_args = BLAS_EXTRA_LINK_ARGS, ++ extra_link_args = BLAS_EXTRA_LINK_ARGS + FFTW_EXTRA_LINK_ARGS, + sources = ['src/C/fftw.c'] ) + extmods += [fftw]; + +@@ -153,7 +155,7 @@ + extmods += [glpk]; + + if BUILD_DSDP: +- dsdp = Extension('dsdp', libraries = ['dsdp'] + LAPACK_LIB + BLAS_LIB, ++ dsdp = Extension('dsdp', libraries = ['dsdp'], + include_dirs = [ DSDP_INC_DIR ], + library_dirs = [ DSDP_LIB_DIR, BLAS_LIB_DIR ], + extra_link_args = BLAS_EXTRA_LINK_ARGS, +@@ -162,19 +164,19 @@ + + # Required modules + +-base = Extension('base', libraries = M_LIB + LAPACK_LIB + BLAS_LIB, ++base = Extension('base', + library_dirs = [ BLAS_LIB_DIR ], + define_macros = MACROS, + extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = ['src/C/base.c','src/C/dense.c','src/C/sparse.c']) + +-blas = Extension('blas', libraries = BLAS_LIB, ++blas = Extension('blas', + library_dirs = [ BLAS_LIB_DIR ], + define_macros = MACROS, + extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = ['src/C/blas.c'] ) + +-lapack = Extension('lapack', libraries = LAPACK_LIB + BLAS_LIB, ++lapack = Extension('lapack', + library_dirs = [ BLAS_LIB_DIR ], + define_macros = MACROS, + extra_link_args = BLAS_EXTRA_LINK_ARGS, +@@ -182,9 +184,10 @@ + + if not SUITESPARSE_SRC_DIR: + umfpack = Extension('umfpack', +- libraries = ['umfpack','cholmod','amd','colamd','suitesparseconfig'] + LAPACK_LIB + BLAS_LIB + RT_LIB, ++ libraries = ['umfpack','cholmod','amd','colamd','suitesparseconfig'] + RT_LIB, + include_dirs = [SUITESPARSE_INC_DIR], + library_dirs = [SUITESPARSE_LIB_DIR, BLAS_LIB_DIR], ++ extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = ['src/C/umfpack.c']) + else: + umfpack = Extension('umfpack', +@@ -195,7 +198,6 @@ + SUITESPARSE_SRC_DIR + '/SuiteSparse_config' ], + library_dirs = [ BLAS_LIB_DIR ], + define_macros = MACROS + [('NTIMER', '1'), ('NCHOLMOD', '1')], +- libraries = LAPACK_LIB + BLAS_LIB, + extra_compile_args = UMFPACK_EXTRA_COMPILE_ARGS, + extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = [ 'src/C/umfpack.c', +@@ -208,14 +210,13 @@ + + if not SUITESPARSE_SRC_DIR: + cholmod = Extension('cholmod', +- libraries = ['cholmod','colamd','amd','suitesparseconfig'] + LAPACK_LIB + BLAS_LIB + RT_LIB, ++ libraries = ['cholmod','colamd','amd','suitesparseconfig'] + RT_LIB, + include_dirs = [SUITESPARSE_INC_DIR], + library_dirs = [SUITESPARSE_LIB_DIR, BLAS_LIB_DIR], + sources = [ 'src/C/cholmod.c' ]) + else: + cholmod = Extension('cholmod', + library_dirs = [ BLAS_LIB_DIR ], +- libraries = LAPACK_LIB + BLAS_LIB, + include_dirs = [ SUITESPARSE_SRC_DIR + '/CHOLMOD/Include', + SUITESPARSE_SRC_DIR + '/COLAMD', + SUITESPARSE_SRC_DIR + '/AMD/Include', +@@ -237,17 +238,18 @@ + libraries = ['amd','suitesparseconfig'] + RT_LIB, + include_dirs = [SUITESPARSE_INC_DIR], + library_dirs = [SUITESPARSE_LIB_DIR], ++ extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = ['src/C/amd.c']) + else: + amd = Extension('amd', + include_dirs = [SUITESPARSE_SRC_DIR + '/AMD/Include', + SUITESPARSE_SRC_DIR + '/SuiteSparse_config' ], + define_macros = MACROS + [('NTIMER', '1')], ++ extra_link_args = BLAS_EXTRA_LINK_ARGS, + sources = [ 'src/C/amd.c', SUITESPARSE_SRC_DIR + '/SuiteSparse_config/SuiteSparse_config.c'] + + glob(SUITESPARSE_SRC_DIR + '/AMD/Source/*.c') ) + + misc_solvers = Extension('misc_solvers', +- libraries = LAPACK_LIB + BLAS_LIB, + library_dirs = [ BLAS_LIB_DIR ], + define_macros = MACROS, + extra_link_args = BLAS_EXTRA_LINK_ARGS, From a05bd5fb7a2f569526768741255472e1327a4e8d Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Thu, 29 Jun 2023 13:55:20 +0200 Subject: [PATCH 7925/9987] Update Qt5-5.15.7-GCCcore-12.2.0.eb fix of stylistic issues --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb index afb1406fa10..fedde0639fa 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb @@ -29,8 +29,10 @@ checksums = [ {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, {'Qt5-5.14.1_fix-OF-Gentoo.patch': '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa'}, - {'Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch': 'f39506495b70cc0968fb7a5f4c9028b0f0a180c552906ff4e58e0bcae83cf187'}, - {'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch': '74590de2b9e32f2c88123cb096c4f5c3001b00710aad096a4d16444a8e9eb991'}, + {'Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch': + 'f39506495b70cc0968fb7a5f4c9028b0f0a180c552906ff4e58e0bcae83cf187'}, + {'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch': + '74590de2b9e32f2c88123cb096c4f5c3001b00710aad096a4d16444a8e9eb991'}, {'Qt5-5.15.7_GCC-12.patch': '9a5bde91b223a3e2e90d3d6bec107af69a1a0f18d789593738a953080473fa68'}, ] From 6336345ed2793836dd252e126e04f4edd61f16b4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 29 Jun 2023 12:02:36 +0000 Subject: [PATCH 7926/9987] More dep order fixes --- .../easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb index 57028db3fbd..4d71b6f0525 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb @@ -129,9 +129,6 @@ exts_list = [ ('magrittr', '2.0.3', { 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], }), - ('stringr', '1.5.0', { - 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], - }), ('evaluate', '0.21', { 'checksums': ['3178c99cee8917d7d128806d064d4fecce7845ed07f42e759dcc0adda89c22b9'], }), @@ -156,15 +153,9 @@ exts_list = [ ('fansi', '1.0.4', { 'checksums': ['3163214e6c40922bbb495229259ed8ce1bebd98b77098a6936d234e43da9c49f'], }), - ('pillar', '1.9.0', { - 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], - }), ('pkgconfig', '2.0.3', { 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], }), - ('tibble', '3.2.1', { - 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], - }), ('withr', '2.5.0', { 'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'], }), @@ -177,6 +168,9 @@ exts_list = [ ('pkgload', '1.3.2', { 'checksums': ['35d19a032bfeeefcab92d76a768b4a420c2ede0920badaf48cca878592b46b2f'], }), + ('fastmap', '1.1.1', { + 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], + }), ('htmltools', '0.5.5', { 'checksums': ['c8b23fab855a89c6ed0f6d6c7cad0ff9c5ae329c0bdb479940443ee752f26659'], }), @@ -204,6 +198,15 @@ exts_list = [ ('vctrs', '0.6.3', { 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], }), + ('stringr', '1.5.0', { + 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], + }), + ('pillar', '1.9.0', { + 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], + }), + ('tibble', '3.2.1', { + 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], + }), ('diffobj', '0.3.5', { 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], }), @@ -246,9 +249,6 @@ exts_list = [ ('purrr', '1.0.1', { 'checksums': ['0a7911be3539355a4c40d136f2602befcaaad5a3f7222078500bfb969a6f2ba2'], }), - ('fastmap', '1.1.1', { - 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], - }), ('cachem', '1.0.8', { 'checksums': ['ea9ca919fe615dce8770758ecc2fc88ac99074f66ff1cde3a0b95d40007f45c2'], }), From 868a92124231a289e0a76a35046598cfe8a26add Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Jun 2023 15:51:33 +0200 Subject: [PATCH 7927/9987] Fix CUDA build of TensorFlow when using compiler symlinks Add the TensorFlow-2.1.0_fix-cuda-build.patch to the TensorFlow-CUDA ECs to fix failure when compilers are on symlinked paths and e.g. ccache or rpath wrappers are used. Fixes #17892 --- .../t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb | 3 +++ .../t/TensorFlow/TensorFlow-2.8.4-foss-2021b-CUDA-11.4.1.eb | 3 +++ .../t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb index dc20d8bac90..2251d882c55 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.11.0-foss-2022a-CUDA-11.7.0.eb @@ -159,6 +159,7 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', '%(name)s-2.4.0_dont-use-var-lock.patch', '%(name)s-2.5.0-fix-alias-violation-in-absl.patch', '%(name)s-2.5.0_fix-crash-on-shutdown.patch', @@ -173,6 +174,8 @@ exts_list = [ ], 'checksums': [ {'v2.11.0.tar.gz': '99c732b92b1b37fc243a559e02f9aef5671771e272758aa4aec7f34dc92dac48'}, + {'TensorFlow-2.1.0_fix-cuda-build.patch': + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a'}, {'TensorFlow-2.4.0_dont-use-var-lock.patch': 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, {'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch': diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b-CUDA-11.4.1.eb index 7af33a9479b..969be86e142 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b-CUDA-11.4.1.eb @@ -152,6 +152,7 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', 'TensorFlow-2.4.0_add-ldl.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', @@ -168,6 +169,8 @@ exts_list = [ ], 'checksums': [ {'v2.8.4.tar.gz': 'c08a222792bdbff9da299c7885561ee27b95d414d1111c426efac4ccdce92cde'}, + {'TensorFlow-2.1.0_fix-cuda-build.patch': + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a'}, {'TensorFlow-2.4.0_add-ldl.patch': '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3'}, {'TensorFlow-2.4.0_dont-use-var-lock.patch': 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb index 5c6801151e2..5dc7c5b4535 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.9.1-foss-2022a-CUDA-11.7.0.eb @@ -165,6 +165,7 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', 'TensorFlow-2.4.0_add-ldl.patch', 'TensorFlow-2.4.0_dont-use-var-lock.patch', 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', @@ -185,6 +186,8 @@ exts_list = [ ], 'checksums': [ {'v2.9.1.tar.gz': '6eaf86ead73e23988fe192da1db68f4d3828bcdd0f3a9dc195935e339c95dbdc'}, + {'TensorFlow-2.1.0_fix-cuda-build.patch': + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a'}, {'TensorFlow-2.4.0_add-ldl.patch': '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3'}, {'TensorFlow-2.4.0_dont-use-var-lock.patch': 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, From 68702305cc6ab6e409f8232aefc70313c4050258 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 29 Jun 2023 16:02:57 +0200 Subject: [PATCH 7928/9987] fix incorrect version for GMAP-GSNAP dependency of Trinity 2.15.1 --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb index 2f7ce8144b5..bfed544edbd 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb @@ -45,7 +45,7 @@ dependencies = [ ('BLAT', '3.7'), ('Bowtie', '1.3.1'), ('Bowtie2', '2.4.4'), - ('GMAP-GSNAP', '2021-21-17'), + ('GMAP-GSNAP', '2021-12-17'), ('HISAT2', '2.2.1'), ('HTSlib', '1.14'), ('Jellyfish', '2.3.0'), From c396a6d2a279c8e794f901273062c9267f724774 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2023 17:44:26 +0200 Subject: [PATCH 7929/9987] stick to GATK 4.2.3.0 as dependency for Trinity 2.15.1 --- easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb index bfed544edbd..d904f619a21 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.15.1-foss-2021b.eb @@ -37,7 +37,7 @@ dependencies = [ ('Java', '11', '', SYSTEM), ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), ('picard', '2.25.1', '-Java-%(javaver)s', SYSTEM), - ('GATK', '4.2.6.1', '-Java-%(javaver)s'), + ('GATK', '4.2.3.0', '-Java-%(javaver)s'), ('Perl', '5.34.0'), ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), From 847cf3402e7cfc867a36d1c2ce1f0239d7f00a64 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2023 17:57:59 +0200 Subject: [PATCH 7930/9987] allow ncbi-vdb v2.x as indrect dependency of RSEM + Trinity --- test/easyconfigs/easyconfigs.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3a958a4bb45..23b69a221b8 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -509,10 +509,11 @@ def check_dep_vars(self, gen, dep, dep_vars): r'QGIS-3\.28\.1']), ], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], - # ncbi-vdb v2.x requires HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) + # ncbi-vdb v2.x requires HDF5 v1.10.x; + # HISAT2, RSEM, shovill, SKESA, Trinity (indirectly) depend on ncbi-vdb 'HDF5': [ - (r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', - r'shovill-1\.1\.']), + (r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'RSEM-1\.3\.3', + r'SKESA-2\.4\.', r'shovill-1\.1\.', r'Trinity-2\.15\.1']), ], # VMTK 1.4.x requires ITK 4.13.x 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], From b11c428d0a9ce6f37922453cfae9e5eb0a6c0ccd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2023 18:20:01 +0200 Subject: [PATCH 7931/9987] use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 --- .../easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb index 8b443db27f1..6b0d196e674 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb @@ -15,6 +15,7 @@ sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ patches = [ 'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch', 'ncbi-vdb-cstdlib.patch', + 'ncbi-vdb-3.0.0_hdf5_api.patch', ] checksums = [ '647efea2762d63dee6d3e462b1fed2ae6d0f2cf1adb0da583ac95f3ee073abdf', # ncbi-vdb-2.11.2.tar.gz @@ -31,7 +32,7 @@ builddependencies = [ dependencies = [ ('NGS', '2.11.2'), ('file', '5.41'), # provides libmagic - ('HDF5', '1.10.8'), # version 1.12.x has changes to API and is not compatible + ('HDF5', '1.12.1'), ('libxml2', '2.9.10'), ('bzip2', '1.0.8'), ] From b5427eafb2a2c4bb363a82bf63f0d147545c530b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2023 18:21:01 +0200 Subject: [PATCH 7932/9987] remove exception for HDF5 1.10.x dependency variant via ncbi-vdb 2.11.2 from check for single dependency variant per easyconfig generation --- test/easyconfigs/easyconfigs.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3a958a4bb45..9e3825b80a1 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -509,11 +509,6 @@ def check_dep_vars(self, gen, dep, dep_vars): r'QGIS-3\.28\.1']), ], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], - # ncbi-vdb v2.x requires HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) - 'HDF5': [ - (r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', - r'shovill-1\.1\.']), - ], # VMTK 1.4.x requires ITK 4.13.x 'ITK': [(r'4\.13\.', [r'VMTK-1\.4\.'])], # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) From 6f3fe40b04542f5d2c0ccdd71028b232fa20d86a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2023 18:44:53 +0200 Subject: [PATCH 7933/9987] add checksum for ncbi-vdb-3.0.0_hdf5_api.patch in easyconfig for ncbi-vdb 2.11.2 --- .../easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb index 6b0d196e674..e35c9eed526 100644 --- a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.11.2-gompi-2021b.eb @@ -18,9 +18,10 @@ patches = [ 'ncbi-vdb-3.0.0_hdf5_api.patch', ] checksums = [ - '647efea2762d63dee6d3e462b1fed2ae6d0f2cf1adb0da583ac95f3ee073abdf', # ncbi-vdb-2.11.2.tar.gz - 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch - 'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655', # ncbi-vdb-cstdlib.patch + {'ncbi-vdb-2.11.2.tar.gz': '647efea2762d63dee6d3e462b1fed2ae6d0f2cf1adb0da583ac95f3ee073abdf'}, + {'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch': 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133'}, + {'ncbi-vdb-cstdlib.patch': 'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655'}, + {'ncbi-vdb-3.0.0_hdf5_api.patch': '34bdad822248118a011b5106fe5b5efaa068c19b66ed10f949a9c0b07a79de8b'}, ] builddependencies = [ From 73518dfc1e21d553d4893dcd989c7a547e2351da Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 29 Jun 2023 18:09:29 +0100 Subject: [PATCH 7934/9987] upate source_urls for Velvet --- .../v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb index e59516e0cbd..8fcd1cc53f8 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb @@ -15,15 +15,16 @@ name = 'Velvet' version = '1.2.10' versionsuffix = '-mt-kmer_191' -homepage = 'https://www.ebi.ac.uk/~zerbino/velvet/' +homepage = 'https://github.com/dzerbino/velvet/' description = """Sequence assembler for very short reads""" toolchain = {'name': 'GCC', 'version': '11.2.0'} toolchainopts = {'openmp': True, 'pic': True} -source_urls = ['https://www.ebi.ac.uk/~zerbino/velvet'] -sources = ['%(namelower)s_%(version)s.tgz'] -checksums = ['884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640'] +github_account = 'dzerbino' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4615e52dc2e8a05f1009daf2c0978c218860be364afa044f73677cd298f10c7b'] dependencies = [('zlib', '1.2.11')] From 7c226ca3f715ddc244bd0e32bb04c35d8d1fd9bd Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 29 Jun 2023 18:13:24 +0100 Subject: [PATCH 7935/9987] and the other Velvet easyconfigs --- .../v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb | 1 - .../v/Velvet/Velvet-1.2.10-GCC-8.3.0-mt-kmer_191.eb | 9 +++++---- .../v/Velvet/Velvet-1.2.10-foss-2018a-mt-kmer_191.eb | 9 +++++---- .../v/Velvet/Velvet-1.2.10-foss-2018b-mt-kmer_191.eb | 9 +++++---- .../v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb | 8 +++++--- 5 files changed, 20 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb index 8fcd1cc53f8..d8364622efb 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb @@ -24,7 +24,6 @@ toolchainopts = {'openmp': True, 'pic': True} github_account = 'dzerbino' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['4615e52dc2e8a05f1009daf2c0978c218860be364afa044f73677cd298f10c7b'] dependencies = [('zlib', '1.2.11')] diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-8.3.0-mt-kmer_191.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-8.3.0-mt-kmer_191.eb index ea774fc7287..cb47999342a 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-8.3.0-mt-kmer_191.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-8.3.0-mt-kmer_191.eb @@ -15,15 +15,16 @@ name = 'Velvet' version = '1.2.10' versionsuffix = '-mt-kmer_191' -homepage = 'https://www.ebi.ac.uk/~zerbino/velvet/' +homepage = 'https://github.com/dzerbino/velvet/' description = """Sequence assembler for very short reads""" toolchain = {'name': 'GCC', 'version': '8.3.0'} toolchainopts = {'openmp': True, 'pic': True} -source_urls = ['https://www.ebi.ac.uk/~zerbino/velvet'] -sources = ['%(namelower)s_%(version)s.tgz'] -checksums = ['884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640'] +github_account = 'dzerbino' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4615e52dc2e8a05f1009daf2c0978c218860be364afa044f73677cd298f10c7b'] dependencies = [('zlib', '1.2.11')] diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2018a-mt-kmer_191.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2018a-mt-kmer_191.eb index 34910dc01cd..ee42af90210 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2018a-mt-kmer_191.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2018a-mt-kmer_191.eb @@ -15,15 +15,16 @@ name = 'Velvet' version = '1.2.10' versionsuffix = '-mt-kmer_191' -homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' +homepage = 'https://github.com/dzerbino/velvet/' description = """Sequence assembler for very short reads""" toolchain = {'name': 'foss', 'version': '2018a'} toolchainopts = {'openmp': True, 'pic': True} -source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] -sources = ['%(namelower)s_%(version)s.tgz'] -checksums = ['884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640'] +github_account = 'dzerbino' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4615e52dc2e8a05f1009daf2c0978c218860be364afa044f73677cd298f10c7b'] dependencies = [('zlib', '1.2.11')] diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2018b-mt-kmer_191.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2018b-mt-kmer_191.eb index f5c9e5e44d7..4a23a439630 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2018b-mt-kmer_191.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2018b-mt-kmer_191.eb @@ -15,15 +15,16 @@ name = 'Velvet' version = '1.2.10' versionsuffix = '-mt-kmer_191' -homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' +homepage = 'https://github.com/dzerbino/velvet/' description = """Sequence assembler for very short reads""" toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'openmp': True, 'pic': True} -source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] -sources = ['%(namelower)s_%(version)s.tgz'] -checksums = ['884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640'] +github_account = 'dzerbino' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4615e52dc2e8a05f1009daf2c0978c218860be364afa044f73677cd298f10c7b'] dependencies = [('zlib', '1.2.11')] diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb index 8e2cfba9b55..7291b701408 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-intel-2017a-mt-kmer_37.eb @@ -15,14 +15,16 @@ name = 'Velvet' version = '1.2.10' versionsuffix = '-mt-kmer_37' -homepage = 'http://www.ebi.ac.uk/~zerbino/velvet/' +homepage = 'https://github.com/dzerbino/velvet/' description = """Sequence assembler for very short reads""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'openmp': True, 'pic': True} -sources = ['%(namelower)s_%(version)s.tgz'] -source_urls = ['http://www.ebi.ac.uk/~zerbino/%(namelower)s'] +github_account = 'dzerbino' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4615e52dc2e8a05f1009daf2c0978c218860be364afa044f73677cd298f10c7b'] buildopts = "OPENMP=1 MAXKMERLENGTH=%s LONGSEQUENCES=1" % versionsuffix.split('_')[1] From ef69e5b5423a6c6ae9b28d3ed84f705731ae773b Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 29 Jun 2023 18:16:03 +0100 Subject: [PATCH 7936/9987] restore accidentally deleted checksum --- .../easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb index d8364622efb..8fcd1cc53f8 100644 --- a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-GCC-11.2.0-mt-kmer_191.eb @@ -24,6 +24,7 @@ toolchainopts = {'openmp': True, 'pic': True} github_account = 'dzerbino' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] +checksums = ['4615e52dc2e8a05f1009daf2c0978c218860be364afa044f73677cd298f10c7b'] dependencies = [('zlib', '1.2.11')] From 78c234796066ca0d80b5a2d8dfdbd47c87797224 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2023 21:22:50 +0200 Subject: [PATCH 7937/9987] adding easyconfigs: regionmask-0.10.0-foss-2022b.eb --- .../b/boto3/boto3-1.26.163-GCCcore-12.2.0.eb | 39 ++++++++++++++ .../r/rasterio/rasterio-1.3.8-foss-2022b.eb | 54 +++++++++++++++++++ .../regionmask-0.10.0-foss-2022b.eb | 31 +++++++++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.26.163-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/r/rasterio/rasterio-1.3.8-foss-2022b.eb create mode 100644 easybuild/easyconfigs/r/regionmask/regionmask-0.10.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.26.163-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.26.163-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..8a9debf1c2c --- /dev/null +++ b/easybuild/easyconfigs/b/boto3/boto3-1.26.163-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'boto3' +version = '1.26.163' + +homepage = 'https://github.com/boto/boto3' +description = """Boto3 is the Amazon Web Services (AWS) Software Development Kit +(SDK) for Python, which allows Python developers to write software that makes +use of services like Amazon S3 and Amazon EC2.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +exts_list = [ + ('botocore', '1.29.163', { + 'checksums': ['f374bea656bf9025ad685f47e7b8ff9e20b1a2584823855ba1c4c58957768612'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.6.1', { + 'checksums': ['640bb492711f4c0c0905e1f62b6aaeb771881935ad27884852411f8e9cacbca9'], + }), + (name, version, { + 'checksums': ['341ad62c53f9717cfe5fb2ae33e34f2dd3ee930abaa0fc864a10c018c0c78783'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/rasterio/rasterio-1.3.8-foss-2022b.eb b/easybuild/easyconfigs/r/rasterio/rasterio-1.3.8-foss-2022b.eb new file mode 100644 index 00000000000..58109f4cb4d --- /dev/null +++ b/easybuild/easyconfigs/r/rasterio/rasterio-1.3.8-foss-2022b.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'rasterio' +version = '1.3.8' + +homepage = 'https://github.com/mapbox/rasterio' +description = "Rasterio reads and writes geospatial raster data." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('GDAL', '3.6.2'), + ('matplotlib', '3.7.0'), # plot extra + ('boto3', '1.26.163'), # s3 extra +] + +use_pip = True + +exts_list = [ + ('affine', '2.4.0', { + 'checksums': ['a24d818d6a836c131976d22f8c27b8d3ca32d0af64c1d8d29deb7bafa4da1eea'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('snuggs', '1.4.7', { + 'checksums': ['501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b'], + }), + (name, version, { + 'use_pip_extras': 'plot,s3', + 'checksums': ['ffdd18e78efdf8ad5861065fd812a66dd34264293317ff6540a078ea891cdef8'], + }), +] + +fix_python_shebang_for = ['bin/jp.py', 'bin/rio'] + +sanity_check_paths = { + 'files': ['bin/rio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "jp.py --help", + "rio --help", +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/regionmask/regionmask-0.10.0-foss-2022b.eb b/easybuild/easyconfigs/r/regionmask/regionmask-0.10.0-foss-2022b.eb new file mode 100644 index 00000000000..dec0c537305 --- /dev/null +++ b/easybuild/easyconfigs/r/regionmask/regionmask-0.10.0-foss-2022b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'regionmask' +version = '0.10.0' + +homepage = 'https://regionmask.readthedocs.io' +description = """regionmask creates masks of geographical regions. It determines to which +geographic region each grid point belongs.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('geopandas', '0.12.2'), + ('rasterio', '1.3.8'), + ('Shapely', '2.0.1'), + ('xarray', '2023.4.2'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['6e951ad3513234d1fbd9ed2bfe71b4fd8b088d3fd270606251692854976a3a6b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 495c8605f58579e04eca29ddf825188c2cf1a81b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 29 Jun 2023 22:39:46 +0200 Subject: [PATCH 7938/9987] update CFITSIO dep for ROOT 6.26.06 to v4.2.0 --- .../c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb | 50 ------------------- .../r/ROOT/ROOT-6.26.06-foss-2022a.eb | 2 +- 2 files changed, 1 insertion(+), 51 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb deleted file mode 100644 index 21756d0af91..00000000000 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.1.0-GCCcore-11.3.0.eb +++ /dev/null @@ -1,50 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -easyblock = 'CMakeMake' - -name = 'CFITSIO' -version = '4.1.0' - -homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' -description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in -FITS (Flexible Image Transport System) data format.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] -sources = ['%%(namelower)s-%s.tar.gz' % version] -patches = ['CFITSIO-3.48_install_test_data.patch'] -checksums = [ - 'b367c695d2831958e7166921c3b356d5dfa51b1ecee505b97416ba39d1b6c17a', # cfitsio-4.1.0.tar.gz - 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch -] - -builddependencies = [ - ('binutils', '2.38'), - ('CMake', '3.23.1'), -] - -dependencies = [ - # curl for HTTPS support - ('cURL', '7.83.0'), - ('zlib', '1.2.12'), -] - -# make would create just static libcfitsio.a. -# Let's create dynamic lib and testprog too. -# buildopts = '&& make shared && make testprog' - -configopts = [ - "-DBUILD_SHARED_LIBS=OFF -DTESTS=ON", - "-DBUILD_SHARED_LIBS=ON -DTESTS=ON", -] - -buildopts = " && ./TestProg" - -sanity_check_paths = { - 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb index 60338bda758..1579d8dda22 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb @@ -21,7 +21,7 @@ dependencies = [ ('GSL', '2.7'), ('libxml2', '2.9.13'), ('PCRE', '8.45'), - ('CFITSIO', '4.1.0'), + ('CFITSIO', '4.2.0'), ('freetype', '2.12.1'), ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), From 96e8d23a40f3d40433d8352335ede6bb52071c5e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 30 Jun 2023 08:58:53 +0200 Subject: [PATCH 7939/9987] adding easyconfigs: DIAMOND-2.1.8-GCC-10.3.0.eb --- .../d/DIAMOND/DIAMOND-2.1.8-GCC-10.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-10.3.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-10.3.0.eb new file mode 100644 index 00000000000..9d3344fae45 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.1.8' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'bbuchfink' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b6088259f2bc92d1f9dc4add44590cff68321bcbf91eefbc295a3525118b9415'] + +builddependencies = [('CMake', '3.20.1')] +dependencies = [('zlib', '1.2.11')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["%(namelower)s help"] + +moduleclass = 'bio' From 90c3d731c2c4b9d87e9dc40644badf555e180a91 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 30 Jun 2023 09:33:06 +0200 Subject: [PATCH 7940/9987] adding easyconfigs: corner-2.2.2-foss-2021b.eb --- .../c/corner/corner-2.2.2-foss-2021b.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/corner/corner-2.2.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/corner/corner-2.2.2-foss-2021b.eb b/easybuild/easyconfigs/c/corner/corner-2.2.2-foss-2021b.eb new file mode 100644 index 00000000000..3d8b3503eef --- /dev/null +++ b/easybuild/easyconfigs/c/corner/corner-2.2.2-foss-2021b.eb @@ -0,0 +1,24 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'corner' +version = '2.2.2' + +homepage = 'https://corner.readthedocs.io/en/latest/' +description = """Make some beautiful corner plots.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4bc79f3b6778c270103f0926e64ef2606c48c3b6f92daf5382fc4babf5d608d1'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), +] + +use_pip = True +download_dep_fail = True + +moduleclass = 'vis' From 8562554cbfb8419386cf37c8e7c0a0443090424a Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 30 Jun 2023 09:33:44 +0200 Subject: [PATCH 7941/9987] adding easyconfigs: LMfit-1.2.1-foss-2021b.eb --- .../l/LMfit/LMfit-1.2.1-foss-2021b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMfit/LMfit-1.2.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/l/LMfit/LMfit-1.2.1-foss-2021b.eb b/easybuild/easyconfigs/l/LMfit/LMfit-1.2.1-foss-2021b.eb new file mode 100644 index 00000000000..f56e1afc397 --- /dev/null +++ b/easybuild/easyconfigs/l/LMfit/LMfit-1.2.1-foss-2021b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'LMfit' +version = '1.2.1' + +homepage = 'https://lmfit.github.io/lmfit-py' +description = """Lmfit provides a high-level interface to non-linear optimization +and curve fitting problems for Python""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asteval', '0.9.30', { + 'checksums': ['a3021215568186eb866bec4dce2730f0fda3863eef9ff79e2f7b6cc4a84c26df'], + }), + ('uncertainties', '3.1.7', { + 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['00cef5bd145bf81b73630b78926af24b24f1805421e6211ca585588aa7cc415b'], + }), +] + +moduleclass = 'math' From 1edec82d5026f6c9d43034d45e98c38a206760d2 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 30 Jun 2023 09:36:56 +0200 Subject: [PATCH 7942/9987] adding easyconfigs: emcee-3.1.4-foss-2021b.eb --- .../e/emcee/emcee-3.1.4-foss-2021b.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb diff --git a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb b/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb new file mode 100644 index 00000000000..39671f3d000 --- /dev/null +++ b/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'emcee' +version = '3.1.4' + +homepage = 'https://dfm.io/emcee' +description = """Emcee is an extensible, pure-Python implementation of +Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. +It's designed for Bayesian parameter estimation and it's really sweet! """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8e0e19dc8bcef9c6d02f860bef8ddc6c876b8878a6ce666943e2c5cfd9317fed'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'], +} + +sanity_check_commands = [('pytest')] + +moduleclass = 'astro' From bcac14113789e5e8a73d58ee3ca13719a437c87b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 30 Jun 2023 10:53:45 +0200 Subject: [PATCH 7943/9987] add extra packages to recent R easyconfigs --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 12 ++++++++++++ easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 12 ++++++++++++ 2 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 45606708fe8..0d3b45c12b3 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3535,6 +3535,18 @@ exts_list = [ ('svglite', '2.1.1', { 'checksums': ['48700169eec1b05dbee9e2bae000aa84c544617b018cb3ac431a128cfd8dac56'], }), + ('ECOSolveR', '0.5.5', { + 'checksums': ['2594ed1602b2fe159cc9aff3475e9cba7c1927b496c3daeabc1c0d227943ecc7'], + }), + ('scs', '3.2.4', { + 'checksums': ['c3f39874bf4532fa8c2f2e2c41533ba4fe20b61cf6dfc6314407dc981621298f'], + }), + ('osqp', '0.6.0.8', { + 'checksums': ['14034045ae4ae5ec4eae4944653d41d94282fa85a0cd53614ac86f34fd02ed97'], + }), + ('CVXR', '1.0-11', { + 'checksums': ['e92a9638f35f4909e2a29c3b7106081e3dae7ff88b14bb6466b87fbdc80b972a'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index b0a37ef3a79..010f787f26f 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3627,6 +3627,18 @@ exts_list = [ ('princurve', '2.1.6', { 'checksums': ['0216332390eb27013b6ba62232782156dfc99ca640087fcaff53d2be9218f373'], }), + ('ECOSolveR', '0.5.5', { + 'checksums': ['2594ed1602b2fe159cc9aff3475e9cba7c1927b496c3daeabc1c0d227943ecc7'], + }), + ('scs', '3.2.4', { + 'checksums': ['c3f39874bf4532fa8c2f2e2c41533ba4fe20b61cf6dfc6314407dc981621298f'], + }), + ('osqp', '0.6.0.8', { + 'checksums': ['14034045ae4ae5ec4eae4944653d41d94282fa85a0cd53614ac86f34fd02ed97'], + }), + ('CVXR', '1.0-11', { + 'checksums': ['e92a9638f35f4909e2a29c3b7106081e3dae7ff88b14bb6466b87fbdc80b972a'], + }), ] moduleclass = 'lang' From 64f1dd03b7860f9f1050a447f45c8555d0cd5f01 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 30 Jun 2023 11:03:29 +0200 Subject: [PATCH 7944/9987] add extra packages to recent R-bundle-Bioconductor easyconfigs --- ...dle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 18 ++++++++++++++++++ ...dle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 1ccecc5efcd..7cdf078b8bb 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1209,6 +1209,24 @@ exts_list = [ ('deepSNV', '1.42.1', { 'checksums': ['f64d43645d696af7b375c66f7dccf877d099482f8470dd18c4aba8b1f30bf22d'], }), + ('dada2', '1.24.0', { + 'checksums': ['9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b'], + }), + ('TreeSummarizedExperiment', '2.4.0', { + 'checksums': ['a7339e41cb1ed74bb633b6c4ae6e762f25eeeae2c396da6fa676b29550b7182f'], + }), + ('decontam', '1.16.0', { + 'checksums': ['09a3e41b012678e3c9a3aa8bd577b59f33fbfd05dc270382f8065feb986330bd'], + }), + ('DECIPHER', '2.24.0', { + 'checksums': ['059fbb6df17a7e5dc0e6bd4b95677c44cd4babcd30ef9f3dfc3ee0f7dd12b810'], + }), + ('mia', '1.4.0', { + 'checksums': ['b332f5bc9a2955fd4fff40b98c06696a816fcf15224c0799ea00afa40d4eea96'], + }), + ('ANCOMBC', '1.6.4', { + 'checksums': ['ff5e80929cdbf6beb1073a6f5e008e2d2d8bdaccf5f65635b7fccf6d96b9710b'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index 05cf1957834..f47caf3b5d0 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -1226,6 +1226,24 @@ exts_list = [ ('slingshot', '2.6.0', { 'checksums': ['6348ecd10a1572593de1d329318f03d8b1352dc041290a092d25a72f5a8c0902'], }), + ('dada2', '1.26.0', { + 'checksums': ['6c9ee66abfa2e21096b8a3669346a445ee051308d9773f2d9e6e4ea230c1aeb1'], + }), + ('TreeSummarizedExperiment', '2.6.0', { + 'checksums': ['82aa3d7ec6935f5bd8fde3d1be38f9827c6bf2bd2a1af98889a9001aec7ddf8c'], + }), + ('decontam', '1.18.0', { + 'checksums': ['02b95f72c76af5abbc5d2febbb2f51b88fab76ebc355b45252bc5bea848a672e'], + }), + ('DECIPHER', '2.26.0', { + 'checksums': ['c10e55204abbfb691a697f40a5527d8e1d645710f43459fad553ece24aeb1f06'], + }), + ('mia', '1.6.0', { + 'checksums': ['ccfaca9cc948778e10bc6157fa95f69db0157c7abcc7cf1b63b934b3df43e87b'], + }), + ('ANCOMBC', '2.0.2', { + 'checksums': ['e577ffe62a86090de9ea3743c84a4f3b34c3d645dcedff3c8af675b8c9b69136'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 844f5d0c6dff6fc9d8450772d4a85bd2acdec326 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 30 Jun 2023 11:48:59 +0200 Subject: [PATCH 7945/9987] remove duplicate dada2 package --- .../R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index f47caf3b5d0..a117c707b50 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -1226,9 +1226,6 @@ exts_list = [ ('slingshot', '2.6.0', { 'checksums': ['6348ecd10a1572593de1d329318f03d8b1352dc041290a092d25a72f5a8c0902'], }), - ('dada2', '1.26.0', { - 'checksums': ['6c9ee66abfa2e21096b8a3669346a445ee051308d9773f2d9e6e4ea230c1aeb1'], - }), ('TreeSummarizedExperiment', '2.6.0', { 'checksums': ['82aa3d7ec6935f5bd8fde3d1be38f9827c6bf2bd2a1af98889a9001aec7ddf8c'], }), From ea03725d014f7c281af2fe52e9b76183aa6c331a Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 30 Jun 2023 12:41:15 +0200 Subject: [PATCH 7946/9987] Add sanity_pip_check --- easybuild/easyconfigs/c/corner/corner-2.2.2-foss-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/corner/corner-2.2.2-foss-2021b.eb b/easybuild/easyconfigs/c/corner/corner-2.2.2-foss-2021b.eb index 3d8b3503eef..dbd2c511b8b 100644 --- a/easybuild/easyconfigs/c/corner/corner-2.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/c/corner/corner-2.2.2-foss-2021b.eb @@ -20,5 +20,6 @@ dependencies = [ use_pip = True download_dep_fail = True +sanity_pip_check = True moduleclass = 'vis' From 4e40733a54b3e528bcbf51e99731092a44d58c2a Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 30 Jun 2023 12:41:46 +0200 Subject: [PATCH 7947/9987] Add sanity_pip_check --- easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb b/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb index 39671f3d000..1980b4da714 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb @@ -20,6 +20,7 @@ dependencies = [ use_pip = True download_dep_fail = True +sanity_pip_check = True sanity_check_paths = { 'files': [], From 862b67a5227ef44e4792604fb9e946bce9a2e1c7 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Fri, 30 Jun 2023 12:37:59 +0100 Subject: [PATCH 7948/9987] adding easyconfigs: xtb-6.6.0-foss-2022a.eb and patches: xtb-6.6.0-foss-2022a_fix-custom-libraries.patch --- .../easyconfigs/x/xtb/xtb-6.6.0-foss-2022a.eb | 49 +++++++++++++++++++ ....6.0-foss-2022a_fix-custom-libraries.patch | 26 ++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.6.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/x/xtb/xtb-6.6.0-foss-2022a_fix-custom-libraries.patch diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.6.0-foss-2022a.eb b/easybuild/easyconfigs/x/xtb/xtb-6.6.0-foss-2022a.eb new file mode 100644 index 00000000000..9fad4ae5452 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.6.0-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = 'MesonNinja' + +name = 'xtb' +version = '6.6.0' + +homepage = 'https://xtb-docs.readthedocs.io' +description = """ xtb - An extended tight-binding semi-empirical program package. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] + +patches = ['xtb-6.6.0-foss-2022a_fix-custom-libraries.patch'] + +checksums = [ + '1845a9ba71c7bdb414e14ef3dad676728c31a2a94b26303551da57704c78a3e3', # v6.6.0.tar.gz + # xtb-6.6.0-foss-2022a_fix-custom-libraries.patch + '4e2e21b13a8d71b6b5d29c586fb28423a0f9a9ad518ebdca18cf0fa0cf27bc6e', +] + +builddependencies = [ + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +configopts = "-Dlapack='custom' " +configopts += "-Dcustom_libraries='flexiblas' " +configopts += "--buildtype release " + + +runtest = 'meson' +testopts = 'test -C %(builddir)s/easybuild_obj -t 60' # Ensure test don't timeout + +sanity_check_paths = { + 'files': ['bin/xtb', 'include/xtb.h'] + ['lib/libxtb.%s' % e for e in ('a', SHLIB_EXT)], + 'dirs': ['share'], +} + +sanity_check_commands = ["xtb --help"] + +modextravars = { + 'XTBHOME': '%(installdir)s', + 'XTBPATH': '%(installdir)s', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.6.0-foss-2022a_fix-custom-libraries.patch b/easybuild/easyconfigs/x/xtb/xtb-6.6.0-foss-2022a_fix-custom-libraries.patch new file mode 100644 index 00000000000..f2e22bd99f6 --- /dev/null +++ b/easybuild/easyconfigs/x/xtb/xtb-6.6.0-foss-2022a_fix-custom-libraries.patch @@ -0,0 +1,26 @@ +From 2d82c0d639e77c12408244d1d0308dc322058b9c Mon Sep 17 00:00:00 2001 +From: Susi Lehtola +Date: Sat, 15 Apr 2023 19:10:19 +0300 +Subject: [PATCH] Restore support for custom lapack backend (#785) + +Signed-off-by: Susi Lehtola +--- + meson/meson.build | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/meson/meson.build b/meson/meson.build +index 16bba9983..7c3192780 100644 +--- a/meson/meson.build ++++ b/meson/meson.build +@@ -146,6 +146,11 @@ elif lapack_vendor == 'openblas' + lib_deps += lapack_dep + endif + ++elif lapack_vendor == 'custom' ++ foreach lib: get_option('custom_libraries') ++ lib_deps += fc.find_library(lib) ++ endforeach ++ + else + lapack_dep = dependency('lapack', required: false) + if not lapack_dep.found() From c61b0df270dabf9dc85926fede2aa7b51b3af6de Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 30 Jun 2023 13:33:19 +0100 Subject: [PATCH 7949/9987] use upstream patch for symmbol compatibility in XZ 5.2.5 --- .../x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb | 8 +- .../x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 8 +- .../x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb | 8 +- .../x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb | 8 +- .../x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb | 8 +- .../x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb | 8 +- .../x/XZ/XZ-5.2.5_compat-libs.patch | 35 - .../x/XZ/xz-5.2.5_fix-symbols.patch | 681 ++++++++++++++++++ 8 files changed, 705 insertions(+), 59 deletions(-) delete mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch create mode 100755 easybuild/easyconfigs/x/XZ/xz-5.2.5_fix-symbols.patch diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb index c7d8e9fe1d7..c521a59409b 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb @@ -21,13 +21,13 @@ toolchain = {'name': 'GCCcore', 'version': '10.1.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5_fix-symbols.patch', 'xz-5.2.5-cve-2022-1271.patch', ] checksums = [ - '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch - '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch + {'xz-5.2.5.tar.bz2': '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df'}, + {'xz-5.2.5_fix-symbols.patch': 'ce80545e7bd88466fd9561a8abb9da87e62ebc71a1531c909a492fa2844da6d0'}, + {'xz-5.2.5-cve-2022-1271.patch': '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb index 2ba344e0acb..a76867949b4 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -21,13 +21,13 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5_fix-symbols.patch', 'xz-5.2.5-cve-2022-1271.patch', ] checksums = [ - '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch - '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch + {'xz-5.2.5.tar.bz2': '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df'}, + {'xz-5.2.5_fix-symbols.patch': 'ce80545e7bd88466fd9561a8abb9da87e62ebc71a1531c909a492fa2844da6d0'}, + {'xz-5.2.5-cve-2022-1271.patch': '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb index 2f9102b6d69..388eada116a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb @@ -14,13 +14,13 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5_fix-symbols.patch', 'xz-5.2.5-cve-2022-1271.patch', ] checksums = [ - '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch - '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch + {'xz-5.2.5.tar.bz2': '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df'}, + {'xz-5.2.5_fix-symbols.patch': 'ce80545e7bd88466fd9561a8abb9da87e62ebc71a1531c909a492fa2844da6d0'}, + {'xz-5.2.5-cve-2022-1271.patch': '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb index a482f548042..3a16d8aa2f2 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb @@ -14,13 +14,13 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5_fix-symbols.patch', 'xz-5.2.5-cve-2022-1271.patch', ] checksums = [ - '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch - '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch + {'xz-5.2.5.tar.bz2': '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df'}, + {'xz-5.2.5_fix-symbols.patch': 'ce80545e7bd88466fd9561a8abb9da87e62ebc71a1531c909a492fa2844da6d0'}, + {'xz-5.2.5-cve-2022-1271.patch': '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb index c965c1e1efa..5104d57b39b 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb @@ -14,13 +14,13 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5_fix-symbols.patch', 'xz-5.2.5-cve-2022-1271.patch', ] checksums = [ - '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch - '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch + {'xz-5.2.5.tar.bz2': '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df'}, + {'xz-5.2.5_fix-symbols.patch': 'ce80545e7bd88466fd9561a8abb9da87e62ebc71a1531c909a492fa2844da6d0'}, + {'xz-5.2.5-cve-2022-1271.patch': '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb index 73a74e9e92a..aa3ab0b60c1 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb @@ -11,13 +11,13 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = ['https://tukaani.org/xz/'] sources = [SOURCELOWER_TAR_BZ2] patches = [ - 'XZ-5.2.5_compat-libs.patch', + 'xz-5.2.5_fix-symbols.patch', 'xz-5.2.5-cve-2022-1271.patch', ] checksums = [ - '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 - '9747c8fdf0b3c9501ac5479a807151d75b99bea7816a59565edea267230da195', # XZ-5.2.5_compat-libs.patch - '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec', # xz-5.2.5-cve-2022-1271.patch + {'xz-5.2.5.tar.bz2': '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df'}, + {'xz-5.2.5_fix-symbols.patch': 'ce80545e7bd88466fd9561a8abb9da87e62ebc71a1531c909a492fa2844da6d0'}, + {'xz-5.2.5-cve-2022-1271.patch': '98c6cb1042284fe704ec30083f3fc87364ce9ed2ea51f62bbb0ee9d3448717ec'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch b/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch deleted file mode 100644 index 275f9dbe01d..00000000000 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5_compat-libs.patch +++ /dev/null @@ -1,35 +0,0 @@ -Based on https://git.centos.org/rpms/xz/blob/c7/f/SOURCES/xz-5.2.2-compat-libs.patch -(which is a CentOS7-only patch) -but includes the XZ_5.2 symbols as the lack of these is causing problems in -other scenarios -(see https://github.com/easybuilders/easybuild-easyconfigs/issues/14991) - -diff -rupN xz-5.2.5/src/liblzma/liblzma.map xz-5.2.5_updated/src/liblzma/liblzma.map ---- xz-5.2.5/src/liblzma/liblzma.map 2020-03-17 14:28:54.000000000 +0000 -+++ xz-5.2.5_updated/src/liblzma/liblzma.map 2022-07-13 18:54:15.280407061 +0000 -@@ -95,14 +95,21 @@ global: - lzma_vli_size; - }; - --XZ_5.2 { -+XZ_5.1.2alpha { -+global: -+ lzma_stream_encoder_mt; -+ lzma_stream_encoder_mt_memusage; -+} XZ_5.0; -+ -+XZ_5.2.2 { - global: - lzma_block_uncomp_encode; - lzma_cputhreads; - lzma_get_progress; -- lzma_stream_encoder_mt; -- lzma_stream_encoder_mt_memusage; - - local: - *; --} XZ_5.0; -+} XZ_5.1.2alpha; -+ -+XZ_5.2 { -+} XZ_5.2.2; diff --git a/easybuild/easyconfigs/x/XZ/xz-5.2.5_fix-symbols.patch b/easybuild/easyconfigs/x/XZ/xz-5.2.5_fix-symbols.patch new file mode 100755 index 00000000000..fb5ac8f063d --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/xz-5.2.5_fix-symbols.patch @@ -0,0 +1,681 @@ +From 31d80c6b261b24220776dfaeb8a04f80f80e0a24 Mon Sep 17 00:00:00 2001 +From: Lasse Collin +Date: Sun, 4 Sep 2022 23:23:00 +0300 +Subject: [PATCH] liblzma: Vaccinate against an ill patch from RHEL/CentOS 7. + +RHEL/CentOS 7 shipped with 5.1.2alpha, including the threaded +encoder that is behind #ifdef LZMA_UNSTABLE in the API headers. +In 5.1.2alpha these symbols are under XZ_5.1.2alpha in liblzma.map. +API/ABI compatibility tracking isn't done between development +releases so newer releases didn't have XZ_5.1.2alpha anymore. + +Later RHEL/CentOS 7 updated xz to 5.2.2 but they wanted to keep +the exported symbols compatible with 5.1.2alpha. After checking +the ABI changes it turned out that >= 5.2.0 ABI is backward +compatible with the threaded encoder functions from 5.1.2alpha +(but not vice versa as fixes and extensions to these functions +were made between 5.1.2alpha and 5.2.0). + +In RHEL/CentOS 7, XZ Utils 5.2.2 was patched with +xz-5.2.2-compat-libs.patch to modify liblzma.map: + + - XZ_5.1.2alpha was added with lzma_stream_encoder_mt and + lzma_stream_encoder_mt_memusage. This matched XZ Utils 5.1.2alpha. + + - XZ_5.2 was replaced with XZ_5.2.2. It is clear that this was + an error; the intention was to keep using XZ_5.2 (XZ_5.2.2 + has never been used in XZ Utils). So XZ_5.2.2 lists all + symbols that were listed under XZ_5.2 before the patch. + lzma_stream_encoder_mt and _mt_memusage are included too so + they are listed both here and under XZ_5.1.2alpha. + +The patch didn't add any __asm__(".symver ...") lines to the .c +files. Thus the resulting liblzma.so exports the threaded encoder +functions under XZ_5.1.2alpha only. Listing the two functions +also under XZ_5.2.2 in liblzma.map has no effect without +matching .symver lines. + +The lack of XZ_5.2 in RHEL/CentOS 7 means that binaries linked +against unpatched XZ Utils 5.2.x won't run on RHEL/CentOS 7. +This is unfortunate but this alone isn't too bad as the problem +is contained within RHEL/CentOS 7 and doesn't affect users +of other distributions. It could also be fixed internally in +RHEL/CentOS 7. + +The second problem is more serious: In XZ Utils 5.2.2 the API +headers don't have #ifdef LZMA_UNSTABLE for obvious reasons. +This is true in RHEL/CentOS 7 version too. Thus now programs +using new APIs can be compiled without an extra #define. However, +the programs end up depending on symbol version XZ_5.1.2alpha +(and possibly also XZ_5.2.2) instead of XZ_5.2 as they would +with an unpatched XZ Utils 5.2.2. This means that such binaries +won't run on other distributions shipping XZ Utils >= 5.2.0 as +they don't provide XZ_5.1.2alpha or XZ_5.2.2; they only provide +XZ_5.2 (and XZ_5.0). (This includes RHEL/CentOS 8 as the patch +luckily isn't included there anymore with XZ Utils 5.2.4.) + +Binaries built by RHEL/CentOS 7 users get distributed and then +people wonder why they don't run on some other distribution. +Seems that people have found out about the patch and been copying +it to some build scripts, seemingly curing the symptoms but +actually spreading the illness further and outside RHEL/CentOS 7. + +The ill patch seems to be from late 2016 (RHEL 7.3) and in 2017 it +had spread at least to EasyBuild. I heard about the events only +recently. :-( + +This commit splits liblzma.map into two versions: one for +GNU/Linux and another for other OSes that can use symbol versioning +(FreeBSD, Solaris, maybe others). The Linux-specific file and the +matching additions to .c files add full compatibility with binaries +that have been built against a RHEL/CentOS-patched liblzma. Builds +for OSes other than GNU/Linux won't get the vaccine as they should +be immune to the problem (I really hope that no build script uses +the RHEL/CentOS 7 patch outside GNU/Linux). + +The RHEL/CentOS compatibility symbols XZ_5.1.2alpha and XZ_5.2.2 +are intentionally put *after* XZ_5.2 in liblzma_linux.map. This way +if one forgets to #define HAVE_SYMBOL_VERSIONS_LINUX when building, +the resulting liblzma.so.5 will have lzma_stream_encoder_mt@@XZ_5.2 +since XZ_5.2 {...} is the first one that lists that function. +Without HAVE_SYMBOL_VERSIONS_LINUX @XZ_5.1.2alpha and @XZ_5.2.2 +will be missing but that's still a minor problem compared to +only having lzma_stream_encoder_mt@@XZ_5.1.2alpha! + +The "local: *;" line was moved to XZ_5.0 so that it doesn't need +to be moved around. It doesn't matter where it is put. + +Having two similar liblzma_*.map files is a bit silly as it is, +at least for now, easily possible to generate the generic one +from the Linux-specific file. But that adds extra steps and +increases the risk of mistakes when supporting more than one +build system. So I rather maintain two files in parallel and let +validate_map.sh check that they are in sync when "make mydist" +is run. + +This adds .symver lines for lzma_stream_encoder_mt@XZ_5.2.2 and +lzma_stream_encoder_mt_memusage@XZ_5.2.2 even though these +weren't exported by RHEL/CentOS 7 (only @@XZ_5.1.2alpha was +for these two). I added these anyway because someone might +misunderstand the RHEL/CentOS 7 patch and think that @XZ_5.2.2 +(@@XZ_5.2.2) versions were exported too. + +At glance one could suggest using __typeof__ to copy the function +prototypes when making aliases. However, this doesn't work trivially +because __typeof__ won't copy attributes (lzma_nothrow, lzma_pure) +and it won't change symbol visibility from hidden to default (done +by LZMA_API()). Attributes could be copied with __copy__ attribute +but that needs GCC 9 and a fallback method would be needed anyway. + +This uses __symver__ attribute with GCC >= 10 and +__asm__(".symver ...") with everything else. The attribute method +is required for LTO (-flto) support with GCC. Using -flto with +GCC older than 10 is now broken on GNU/Linux and will not be fixed +(can silently result in a broken liblzma build that has dangerously +incorrect symbol versions). LTO builds with Clang seem to work +with the traditional __asm__(".symver ...") method. + +Thanks to Boud Roukema for reporting the problem and discussing +the details and testing the fix. +--- + configure.ac | 23 +++- + src/liblzma/Makefile.am | 10 +- + src/liblzma/common/block_buffer_encoder.c | 18 +++ + src/liblzma/common/common.c | 14 ++ + src/liblzma/common/common.h | 28 ++++ + src/liblzma/common/hardware_cputhreads.c | 12 ++ + src/liblzma/common/stream_encoder_mt.c | 42 ++++++ + .../{liblzma.map => liblzma_generic.map} | 6 +- + src/liblzma/liblzma_linux.map | 123 ++++++++++++++++++ + src/liblzma/validate_map.sh | 113 ++++++++++++++-- + 10 files changed, 374 insertions(+), 15 deletions(-) + rename src/liblzma/{liblzma.map => liblzma_generic.map} (100%) + create mode 100644 src/liblzma/liblzma_linux.map + +diff --git a/configure.ac b/configure.ac +index 7945934..0167c09 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -493,7 +493,28 @@ if test "x$enable_symbol_versions" = xauto; then + esac + fi + AC_MSG_RESULT([$enable_symbol_versions]) +-AM_CONDITIONAL([COND_SYMVERS], [test "x$enable_symbol_versions" = xyes]) ++ ++# There are two variants for symbol versioning. ++# See src/liblzma/validate_map.sh for details. ++if test "x$enable_symbol_versions" = xyes; then ++ case $host_os in ++ linux*) ++ enable_symbol_versions=linux ++ AC_DEFINE([HAVE_SYMBOL_VERSIONS_LINUX], [1], ++ [Define to 1 to if GNU/Linux-specific details ++ are wanted for symbol versioning. This must ++ be used together with liblzma_linux.map.]) ++ ;; ++ *) ++ enable_symbol_versions=generic ++ ;; ++ esac ++fi ++ ++AM_CONDITIONAL([COND_SYMVERS_LINUX], ++ [test "x$enable_symbol_versions" = xlinux]) ++AM_CONDITIONAL([COND_SYMVERS_GENERIC], ++ [test "x$enable_symbol_versions" = xgeneric]) + + + ############## +diff --git a/src/liblzma/Makefile.am b/src/liblzma/Makefile.am +index ae8967c..cf2144d 100644 +--- a/src/liblzma/Makefile.am ++++ b/src/liblzma/Makefile.am +@@ -26,10 +26,14 @@ liblzma_la_CPPFLAGS = \ + -DTUKLIB_SYMBOL_PREFIX=lzma_ + liblzma_la_LDFLAGS = -no-undefined -version-info 7:6:2 + +-EXTRA_DIST += liblzma.map validate_map.sh +-if COND_SYMVERS ++EXTRA_DIST += liblzma_generic.map liblzma_linux.map validate_map.sh ++if COND_SYMVERS_GENERIC + liblzma_la_LDFLAGS += \ +- -Wl,--version-script=$(top_srcdir)/src/liblzma/liblzma.map ++ -Wl,--version-script=$(top_srcdir)/src/liblzma/liblzma_generic.map ++endif ++if COND_SYMVERS_LINUX ++liblzma_la_LDFLAGS += \ ++ -Wl,--version-script=$(top_srcdir)/src/liblzma/liblzma_linux.map + endif + + liblzma_la_SOURCES += ../common/tuklib_physmem.c +diff --git a/src/liblzma/common/block_buffer_encoder.c b/src/liblzma/common/block_buffer_encoder.c +index 39e263a..a47342e 100644 +--- a/src/liblzma/common/block_buffer_encoder.c ++++ b/src/liblzma/common/block_buffer_encoder.c +@@ -325,6 +325,24 @@ lzma_block_buffer_encode(lzma_block *block, const lzma_allocator *allocator, + } + + ++#ifdef HAVE_SYMBOL_VERSIONS_LINUX ++// This is for compatibility with binaries linked against liblzma that ++// has been patched with xz-5.2.2-compat-libs.patch from RHEL/CentOS 7. ++LZMA_SYMVER_API("lzma_block_uncomp_encode@XZ_5.2.2", ++ lzma_ret, lzma_block_uncomp_encode_522)(lzma_block *block, ++ const uint8_t *in, size_t in_size, ++ uint8_t *out, size_t *out_pos, size_t out_size) ++ lzma_nothrow lzma_attr_warn_unused_result ++ __attribute__((__alias__("lzma_block_uncomp_encode_52"))); ++ ++LZMA_SYMVER_API("lzma_block_uncomp_encode@@XZ_5.2", ++ lzma_ret, lzma_block_uncomp_encode_52)(lzma_block *block, ++ const uint8_t *in, size_t in_size, ++ uint8_t *out, size_t *out_pos, size_t out_size) ++ lzma_nothrow lzma_attr_warn_unused_result; ++ ++#define lzma_block_uncomp_encode lzma_block_uncomp_encode_52 ++#endif + extern LZMA_API(lzma_ret) + lzma_block_uncomp_encode(lzma_block *block, + const uint8_t *in, size_t in_size, +diff --git a/src/liblzma/common/common.c b/src/liblzma/common/common.c +index cf714e5..10fc884 100644 +--- a/src/liblzma/common/common.c ++++ b/src/liblzma/common/common.c +@@ -366,6 +366,20 @@ lzma_end(lzma_stream *strm) + } + + ++#ifdef HAVE_SYMBOL_VERSIONS_LINUX ++// This is for compatibility with binaries linked against liblzma that ++// has been patched with xz-5.2.2-compat-libs.patch from RHEL/CentOS 7. ++LZMA_SYMVER_API("lzma_get_progress@XZ_5.2.2", ++ void, lzma_get_progress_522)(lzma_stream *strm, ++ uint64_t *progress_in, uint64_t *progress_out) lzma_nothrow ++ __attribute__((__alias__("lzma_get_progress_52"))); ++ ++LZMA_SYMVER_API("lzma_get_progress@@XZ_5.2", ++ void, lzma_get_progress_52)(lzma_stream *strm, ++ uint64_t *progress_in, uint64_t *progress_out) lzma_nothrow; ++ ++#define lzma_get_progress lzma_get_progress_52 ++#endif + extern LZMA_API(void) + lzma_get_progress(lzma_stream *strm, + uint64_t *progress_in, uint64_t *progress_out) +diff --git a/src/liblzma/common/common.h b/src/liblzma/common/common.h +index b3d3b7a..6b659c6 100644 +--- a/src/liblzma/common/common.h ++++ b/src/liblzma/common/common.h +@@ -34,6 +34,34 @@ + + #include "lzma.h" + ++#ifdef HAVE_SYMBOL_VERSIONS_LINUX ++// To keep link-time optimization (LTO, -flto) working with GCC, ++// the __symver__ attribute must be used instead of __asm__(".symver ..."). ++// Otherwise the symbol versions may be lost, resulting in broken liblzma ++// that has wrong default versions in the exported symbol list! ++// The attribute was added in GCC 10; LTO with older GCC is not supported. ++// ++// To keep -Wmissing-prototypes happy, use LZMA_SYMVER_API only with function ++// declarations (including those with __alias__ attribute) and LZMA_API with ++// the function definitions. This means a little bit of silly copy-and-paste ++// between declarations and definitions though. ++// ++// As of GCC 12.2, the __symver__ attribute supports only @ and @@ but the ++// very convenient @@@ isn't supported (it's supported by GNU assembler ++// since 2000). When using @@ instead of @@@, the internal name must not be ++// the same as the external name to avoid problems in some situations. This ++// is why "#define foo_52 foo" is needed for the default symbol versions. ++# if TUKLIB_GNUC_REQ(10, 0) ++# define LZMA_SYMVER_API(extnamever, type, intname) \ ++ extern __attribute__((__symver__(extnamever))) \ ++ LZMA_API(type) intname ++# else ++# define LZMA_SYMVER_API(extnamever, type, intname) \ ++ __asm__(".symver " #intname "," extnamever); \ ++ extern LZMA_API(type) intname ++# endif ++#endif ++ + // These allow helping the compiler in some often-executed branches, whose + // result is almost always the same. + #ifdef __GNUC__ +diff --git a/src/liblzma/common/hardware_cputhreads.c b/src/liblzma/common/hardware_cputhreads.c +index f468366..5d246d2 100644 +--- a/src/liblzma/common/hardware_cputhreads.c ++++ b/src/liblzma/common/hardware_cputhreads.c +@@ -15,6 +15,18 @@ + #include "tuklib_cpucores.h" + + ++#ifdef HAVE_SYMBOL_VERSIONS_LINUX ++// This is for compatibility with binaries linked against liblzma that ++// has been patched with xz-5.2.2-compat-libs.patch from RHEL/CentOS 7. ++LZMA_SYMVER_API("lzma_cputhreads@XZ_5.2.2", ++ uint32_t, lzma_cputhreads_522)(void) lzma_nothrow ++ __attribute__((__alias__("lzma_cputhreads_52"))); ++ ++LZMA_SYMVER_API("lzma_cputhreads@@XZ_5.2", ++ uint32_t, lzma_cputhreads_52)(void) lzma_nothrow; ++ ++#define lzma_cputhreads lzma_cputhreads_52 ++#endif + extern LZMA_API(uint32_t) + lzma_cputhreads(void) + { +diff --git a/src/liblzma/common/stream_encoder_mt.c b/src/liblzma/common/stream_encoder_mt.c +index 2ab4d04..819b227 100644 +--- a/src/liblzma/common/stream_encoder_mt.c ++++ b/src/liblzma/common/stream_encoder_mt.c +@@ -1078,6 +1078,31 @@ stream_encoder_mt_init(lzma_next_coder *next, const lzma_allocator *allocator, + } + + ++#ifdef HAVE_SYMBOL_VERSIONS_LINUX ++// These are for compatibility with binaries linked against liblzma that ++// has been patched with xz-5.2.2-compat-libs.patch from RHEL/CentOS 7. ++// Actually that patch didn't create lzma_stream_encoder_mt@XZ_5.2.2 ++// but it has been added here anyway since someone might misread the ++// RHEL patch and think both @XZ_5.1.2alpha and @XZ_5.2.2 exist. ++LZMA_SYMVER_API("lzma_stream_encoder_mt@XZ_5.1.2alpha", ++ lzma_ret, lzma_stream_encoder_mt_512a)( ++ lzma_stream *strm, const lzma_mt *options) ++ lzma_nothrow lzma_attr_warn_unused_result ++ __attribute__((__alias__("lzma_stream_encoder_mt_52"))); ++ ++LZMA_SYMVER_API("lzma_stream_encoder_mt@XZ_5.2.2", ++ lzma_ret, lzma_stream_encoder_mt_522)( ++ lzma_stream *strm, const lzma_mt *options) ++ lzma_nothrow lzma_attr_warn_unused_result ++ __attribute__((__alias__("lzma_stream_encoder_mt_52"))); ++ ++LZMA_SYMVER_API("lzma_stream_encoder_mt@@XZ_5.2", ++ lzma_ret, lzma_stream_encoder_mt_52)( ++ lzma_stream *strm, const lzma_mt *options) ++ lzma_nothrow lzma_attr_warn_unused_result; ++ ++#define lzma_stream_encoder_mt lzma_stream_encoder_mt_52 ++#endif + extern LZMA_API(lzma_ret) + lzma_stream_encoder_mt(lzma_stream *strm, const lzma_mt *options) + { +@@ -1093,6 +1118,23 @@ lzma_stream_encoder_mt(lzma_stream *strm, const lzma_mt *options) + } + + ++#ifdef HAVE_SYMBOL_VERSIONS_LINUX ++LZMA_SYMVER_API("lzma_stream_encoder_mt_memusage@XZ_5.1.2alpha", ++ uint64_t, lzma_stream_encoder_mt_memusage_512a)( ++ const lzma_mt *options) lzma_nothrow lzma_attr_pure ++ __attribute__((__alias__("lzma_stream_encoder_mt_memusage_52"))); ++ ++LZMA_SYMVER_API("lzma_stream_encoder_mt_memusage@XZ_5.2.2", ++ uint64_t, lzma_stream_encoder_mt_memusage_522)( ++ const lzma_mt *options) lzma_nothrow lzma_attr_pure ++ __attribute__((__alias__("lzma_stream_encoder_mt_memusage_52"))); ++ ++LZMA_SYMVER_API("lzma_stream_encoder_mt_memusage@@XZ_5.2", ++ uint64_t, lzma_stream_encoder_mt_memusage_52)( ++ const lzma_mt *options) lzma_nothrow lzma_attr_pure; ++ ++#define lzma_stream_encoder_mt_memusage lzma_stream_encoder_mt_memusage_52 ++#endif + // This function name is a monster but it's consistent with the older + // monster names. :-( 31 chars is the max that C99 requires so in that + // sense it's not too long. ;-) +diff --git a/src/liblzma/liblzma.map b/src/liblzma/liblzma_generic.map +similarity index 100% +rename from src/liblzma/liblzma.map +rename to src/liblzma/liblzma_generic.map +index f53a4ea..8cca05b 100644 +--- a/src/liblzma/liblzma.map ++++ b/src/liblzma/liblzma_generic.map +@@ -93,6 +93,9 @@ global: + lzma_vli_decode; + lzma_vli_encode; + lzma_vli_size; ++ ++local: ++ *; + }; + + XZ_5.2 { +@@ -102,7 +105,4 @@ global: + lzma_get_progress; + lzma_stream_encoder_mt; + lzma_stream_encoder_mt_memusage; +- +-local: +- *; + } XZ_5.0; +diff --git a/src/liblzma/liblzma_linux.map b/src/liblzma/liblzma_linux.map +new file mode 100644 +index 0000000..4be882c +--- /dev/null ++++ b/src/liblzma/liblzma_linux.map +@@ -0,0 +1,123 @@ ++XZ_5.0 { ++global: ++ lzma_alone_decoder; ++ lzma_alone_encoder; ++ lzma_auto_decoder; ++ lzma_block_buffer_bound; ++ lzma_block_buffer_decode; ++ lzma_block_buffer_encode; ++ lzma_block_compressed_size; ++ lzma_block_decoder; ++ lzma_block_encoder; ++ lzma_block_header_decode; ++ lzma_block_header_encode; ++ lzma_block_header_size; ++ lzma_block_total_size; ++ lzma_block_unpadded_size; ++ lzma_check_is_supported; ++ lzma_check_size; ++ lzma_code; ++ lzma_crc32; ++ lzma_crc64; ++ lzma_easy_buffer_encode; ++ lzma_easy_decoder_memusage; ++ lzma_easy_encoder; ++ lzma_easy_encoder_memusage; ++ lzma_end; ++ lzma_filter_decoder_is_supported; ++ lzma_filter_encoder_is_supported; ++ lzma_filter_flags_decode; ++ lzma_filter_flags_encode; ++ lzma_filter_flags_size; ++ lzma_filters_copy; ++ lzma_filters_update; ++ lzma_get_check; ++ lzma_index_append; ++ lzma_index_block_count; ++ lzma_index_buffer_decode; ++ lzma_index_buffer_encode; ++ lzma_index_cat; ++ lzma_index_checks; ++ lzma_index_decoder; ++ lzma_index_dup; ++ lzma_index_encoder; ++ lzma_index_end; ++ lzma_index_file_size; ++ lzma_index_hash_append; ++ lzma_index_hash_decode; ++ lzma_index_hash_end; ++ lzma_index_hash_init; ++ lzma_index_hash_size; ++ lzma_index_init; ++ lzma_index_iter_init; ++ lzma_index_iter_locate; ++ lzma_index_iter_next; ++ lzma_index_iter_rewind; ++ lzma_index_memusage; ++ lzma_index_memused; ++ lzma_index_size; ++ lzma_index_stream_count; ++ lzma_index_stream_flags; ++ lzma_index_stream_padding; ++ lzma_index_stream_size; ++ lzma_index_total_size; ++ lzma_index_uncompressed_size; ++ lzma_lzma_preset; ++ lzma_memlimit_get; ++ lzma_memlimit_set; ++ lzma_memusage; ++ lzma_mf_is_supported; ++ lzma_mode_is_supported; ++ lzma_physmem; ++ lzma_properties_decode; ++ lzma_properties_encode; ++ lzma_properties_size; ++ lzma_raw_buffer_decode; ++ lzma_raw_buffer_encode; ++ lzma_raw_decoder; ++ lzma_raw_decoder_memusage; ++ lzma_raw_encoder; ++ lzma_raw_encoder_memusage; ++ lzma_stream_buffer_bound; ++ lzma_stream_buffer_decode; ++ lzma_stream_buffer_encode; ++ lzma_stream_decoder; ++ lzma_stream_encoder; ++ lzma_stream_flags_compare; ++ lzma_stream_footer_decode; ++ lzma_stream_footer_encode; ++ lzma_stream_header_decode; ++ lzma_stream_header_encode; ++ lzma_version_number; ++ lzma_version_string; ++ lzma_vli_decode; ++ lzma_vli_encode; ++ lzma_vli_size; ++ ++local: ++ *; ++}; ++ ++XZ_5.2 { ++global: ++ lzma_block_uncomp_encode; ++ lzma_cputhreads; ++ lzma_get_progress; ++ lzma_stream_encoder_mt; ++ lzma_stream_encoder_mt_memusage; ++} XZ_5.0; ++ ++XZ_5.1.2alpha { ++global: ++ lzma_stream_encoder_mt; ++ lzma_stream_encoder_mt_memusage; ++} XZ_5.0; ++ ++XZ_5.2.2 { ++global: ++ lzma_block_uncomp_encode; ++ lzma_cputhreads; ++ lzma_get_progress; ++ lzma_stream_encoder_mt; ++ lzma_stream_encoder_mt_memusage; ++} XZ_5.1.2alpha; +diff --git a/src/liblzma/validate_map.sh b/src/liblzma/validate_map.sh +index 3aee466..2bf6f8b 100644 +--- a/src/liblzma/validate_map.sh ++++ b/src/liblzma/validate_map.sh +@@ -2,7 +2,79 @@ + + ############################################################################### + # +-# Check liblzma.map for certain types of errors ++# Check liblzma_*.map for certain types of errors. ++# ++# liblzma_generic.map is for FreeBSD and Solaris and possibly others ++# except GNU/Linux. ++# ++# liblzma_linux.map is for GNU/Linux only. This and the matching extra code ++# in the .c files make liblzma >= 5.2.7 compatible with binaries that were ++# linked against ill-patched liblzma in RHEL/CentOS 7. By providing the ++# compatibility in official XZ Utils release will hopefully prevent people ++# from further copying the broken patch to other places when they want ++# compatibility with binaries linked on RHEL/CentOS 7. The long version ++# of the story: ++# ++# RHEL/CentOS 7 shipped with 5.1.2alpha, including the threaded ++# encoder that is behind #ifdef LZMA_UNSTABLE in the API headers. ++# In 5.1.2alpha these symbols are under XZ_5.1.2alpha in liblzma.map. ++# API/ABI compatibility tracking isn't done between development ++# releases so newer releases didn't have XZ_5.1.2alpha anymore. ++# ++# Later RHEL/CentOS 7 updated xz to 5.2.2 but they wanted to keep ++# the exported symbols compatible with 5.1.2alpha. After checking ++# the ABI changes it turned out that >= 5.2.0 ABI is backward ++# compatible with the threaded encoder functions from 5.1.2alpha ++# (but not vice versa as fixes and extensions to these functions ++# were made between 5.1.2alpha and 5.2.0). ++# ++# In RHEL/CentOS 7, XZ Utils 5.2.2 was patched with ++# xz-5.2.2-compat-libs.patch to modify liblzma.map: ++# ++# - XZ_5.1.2alpha was added with lzma_stream_encoder_mt and ++# lzma_stream_encoder_mt_memusage. This matched XZ Utils 5.1.2alpha. ++# ++# - XZ_5.2 was replaced with XZ_5.2.2. It is clear that this was ++# an error; the intention was to keep using XZ_5.2 (XZ_5.2.2 ++# has never been used in XZ Utils). So XZ_5.2.2 lists all ++# symbols that were listed under XZ_5.2 before the patch. ++# lzma_stream_encoder_mt and _mt_memusage are included too so ++# they are listed both here and under XZ_5.1.2alpha. ++# ++# The patch didn't add any __asm__(".symver ...") lines to the .c ++# files. Thus the resulting liblzma.so exports the threaded encoder ++# functions under XZ_5.1.2alpha only. Listing the two functions ++# also under XZ_5.2.2 in liblzma.map has no effect without ++# matching .symver lines. ++# ++# The lack of XZ_5.2 in RHEL/CentOS 7 means that binaries linked ++# against unpatched XZ Utils 5.2.x won't run on RHEL/CentOS 7. ++# This is unfortunate but this alone isn't too bad as the problem ++# is contained within RHEL/CentOS 7 and doesn't affect users ++# of other distributions. It could also be fixed internally in ++# RHEL/CentOS 7. ++# ++# The second problem is more serious: In XZ Utils 5.2.2 the API ++# headers don't have #ifdef LZMA_UNSTABLE for obvious reasons. ++# This is true in RHEL/CentOS 7 version too. Thus now programs ++# using new APIs can be compiled without an extra #define. However, ++# the programs end up depending on symbol version XZ_5.1.2alpha ++# (and possibly also XZ_5.2.2) instead of XZ_5.2 as they would ++# with an unpatched XZ Utils 5.2.2. This means that such binaries ++# won't run on other distributions shipping XZ Utils >= 5.2.0 as ++# they don't provide XZ_5.1.2alpha or XZ_5.2.2; they only provide ++# XZ_5.2 (and XZ_5.0). (This includes RHEL/CentOS 8 as the patch ++# luckily isn't included there anymore with XZ Utils 5.2.4.) ++# ++# Binaries built by RHEL/CentOS 7 users get distributed and then ++# people wonder why they don't run on some other distribution. ++# Seems that people have found out about the patch and been copying ++# it to some build scripts, seemingly curing the symptoms but ++# actually spreading the illness further and outside RHEL/CentOS 7. ++# Adding compatibility in an official XZ Utils release should work ++# as a vaccine against this ill patch and stop it from spreading. ++# The vaccine is kept GNU/Linux-only as other OSes should be immune ++# (hopefully it hasn't spread via some build script to other OSes). + # + # Author: Lasse Collin + # +@@ -18,11 +90,11 @@ STATUS=0 + + cd "$(dirname "$0")" + +-# Get the list of symbols that aren't defined in liblzma.map. ++# Get the list of symbols that aren't defined in liblzma_generic.map. + SYMS=$(sed -n 's/^extern LZMA_API([^)]*) \([a-z0-9_]*\)(.*$/\1;/p' \ + api/lzma/*.h \ + | sort \ +- | grep -Fve "$(sed '/[{}:*]/d;/^$/d;s/^ //' liblzma.map)") ++ | grep -Fve "$(sed '/[{}:*]/d;/^$/d;s/^ //' liblzma_generic.map)") + + # Check that there are no old alpha or beta versions listed. + VER=$(cd ../.. && sh build-aux/version.sh) +@@ -30,21 +102,41 @@ NAMES= + case $VER in + *alpha | *beta) + NAMES=$(sed -n 's/^.*XZ_\([^ ]*\)\(alpha\|beta\) .*$/\1\2/p' \ +- liblzma.map | grep -Fv "$VER") ++ liblzma_generic.map | grep -Fv "$VER") + ;; + esac + + # Check for duplicate lines. It can catch missing dependencies. +-DUPS=$(sort liblzma.map | sed '/^$/d;/^global:$/d' | uniq -d) ++DUPS=$(sort liblzma_generic.map | sed '/^$/d;/^global:$/d' | uniq -d) ++ ++# Check that liblzma_linux.map is in sync with liblzma_generic.map. ++# The RHEL/CentOS 7 compatibility symbols are in a fixed location ++# so it makes it easy to remove them for comparison with liblzma_generic.map. ++# ++# NOTE: Putting XZ_5.2 before the compatibility symbols XZ_5.1.2alpha ++# and XZ_5.2.2 in liblzma_linux.map is important: If liblzma_linux.map is ++# incorrectly used without #define HAVE_SYMBOL_VERSIONS_LINUX, only the first ++# occurrence of each function name will be used from liblzma_linux.map; ++# the rest are ignored by the linker. Thus having XZ_5.2 before the ++# compatibility symbols means that @@XZ_5.2 will be used for the symbols ++# listed under XZ_5.2 {...} and the same function names later in ++# the file under XZ_5.1.2alpha {...} and XZ_5.2.2 {...} will be ++# ignored (@XZ_5.1.2alpha or @XZ_5.2.2 won't be added at all when ++# the #define HAVE_SYMBOL_VERSIONS_LINUX isn't used). ++IN_SYNC= ++if ! sed '109,123d' liblzma_linux.map \ ++ | cmp -s - liblzma_generic.map; then ++ IN_SYNC=no ++fi + + # Print error messages if needed. +-if test -n "$SYMS$NAMES$DUPS"; then ++if test -n "$SYMS$NAMES$DUPS$IN_SYNC"; then + echo +- echo 'validate_map.sh found problems from liblzma.map:' ++ echo 'validate_map.sh found problems from liblzma_*.map:' + echo + + if test -n "$SYMS"; then +- echo 'liblzma.map lacks the following symbols:' ++ echo 'liblzma_generic.map lacks the following symbols:' + echo "$SYMS" + echo + fi +@@ -61,6 +153,11 @@ if test -n "$SYMS$NAMES$DUPS"; then + echo + fi + ++ if test -n "$IN_SYNC"; then ++ echo "liblzma_generic.map and liblzma_linux.map aren't in sync" ++ echo ++ fi ++ + STATUS=1 + fi + +-- +2.20.1 + From 0186e6844fd30b57432697a1c2313616311d6855 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 30 Jun 2023 15:00:17 +0200 Subject: [PATCH 7950/9987] remove duplicated G4SAIDDATA --- easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.1.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.1.eb b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.1.eb index 887025db76b..5f9812478e6 100644 --- a/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.1.eb +++ b/easybuild/easyconfigs/g/Geant4-data/Geant4-data-11.1.eb @@ -18,7 +18,6 @@ local_datasets = [ ('G4PARTICLEXS', '4.0', 'G4PARTICLEXS', 'G4PARTICLEXSDATA'), # Particle XS - replaces Neutron XS ('G4PII', '1.3', 'G4PII', 'G4PIIDATA'), # PII ('RealSurface', '2.2', 'G4RealSurface', 'G4REALSURFACEDATA'), # Optical Surfaces - ('G4SAIDDATA', '2.0', 'G4SAIDDATA', 'G4SAIDXSDATA'), # SAID ('G4ABLA', '3.1', 'G4ABLA', 'G4ABLADATA'), # ABLA ('G4INCL', '1.0', 'G4INCL', 'G4INCLDATA'), # INCL ('G4ENSDFSTATE', '2.3', 'G4ENSDFSTATE', 'G4ENSDFSTATEDATA'), # ENSDFSTATE @@ -36,7 +35,6 @@ checksums = [ {'G4PARTICLEXS.4.0.tar.gz': '9381039703c3f2b0fd36ab4999362a2c8b4ff9080c322f90b4e319281133ca95'}, {'G4PII.1.3.tar.gz': '6225ad902675f4381c98c6ba25fc5a06ce87549aa979634d3d03491d6616e926'}, {'G4RealSurface.2.2.tar.gz': '9954dee0012f5331267f783690e912e72db5bf52ea9babecd12ea22282176820'}, - {'G4SAIDDATA.2.0.tar.gz': '1d26a8e79baa71e44d5759b9f55a67e8b7ede31751316a9e9037d80090c72e91'}, {'G4ABLA.3.1.tar.gz': '7698b052b58bf1b9886beacdbd6af607adc1e099fc730ab6b21cf7f090c027ed'}, {'G4INCL.1.0.tar.gz': '716161821ae9f3d0565fbf3c2cf34f4e02e3e519eb419a82236eef22c2c4367d'}, {'G4ENSDFSTATE.2.3.tar.gz': '9444c5e0820791abd3ccaace105b0e47790fadce286e11149834e79c4a8e9203'}, From b2dd1fad205ac325d48fd64aebb04787afc25c28 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 30 Jun 2023 14:11:49 +0100 Subject: [PATCH 7951/9987] add system Autotools as a builddependency --- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb | 2 ++ easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 2 ++ easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb | 2 ++ easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb | 2 ++ easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb | 2 ++ easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb | 2 ++ 6 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb index c521a59409b..3723116173d 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb @@ -33,6 +33,8 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.20.1', '', SYSTEM), + # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency + ('Autotools','20220317', '', SYSTEM), ('binutils', '2.34'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb index a76867949b4..ab86b893cc5 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -33,6 +33,8 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.21', '', SYSTEM), + # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency + ('Autotools','20220317', '', SYSTEM), ('binutils', '2.35'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb index 388eada116a..e6dc69d5c40 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb @@ -26,6 +26,8 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.21', '', SYSTEM), + # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency + ('Autotools','20220317', '', SYSTEM), ('binutils', '2.36.1'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb index 3a16d8aa2f2..4539c721d68 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb @@ -26,6 +26,8 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.21', '', SYSTEM), + # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency + ('Autotools','20220317', '', SYSTEM), ('binutils', '2.37'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb index 5104d57b39b..a3f0568ffab 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb @@ -26,6 +26,8 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.21', '', SYSTEM), + # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency + ('Autotools','20220317', '', SYSTEM), ('binutils', '2.38'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb index aa3ab0b60c1..e4e28af276f 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb @@ -23,6 +23,8 @@ checksums = [ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.20.1', '', SYSTEM), + # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency + ('Autotools','20220317', '', SYSTEM), ('binutils', '2.34'), ] From 31f74044e78b05cbec7304463abb9b28ac3ea50d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 30 Jun 2023 14:33:48 +0100 Subject: [PATCH 7952/9987] add missing space --- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb index 3723116173d..29468c0afac 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.1.0.eb @@ -34,7 +34,7 @@ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.20.1', '', SYSTEM), # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency - ('Autotools','20220317', '', SYSTEM), + ('Autotools', '20220317', '', SYSTEM), ('binutils', '2.34'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb index ab86b893cc5..633fc22773e 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -34,7 +34,7 @@ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.21', '', SYSTEM), # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency - ('Autotools','20220317', '', SYSTEM), + ('Autotools', '20220317', '', SYSTEM), ('binutils', '2.35'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb index e6dc69d5c40..ed72f2ac7c8 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.3.0.eb @@ -27,7 +27,7 @@ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.21', '', SYSTEM), # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency - ('Autotools','20220317', '', SYSTEM), + ('Autotools', '20220317', '', SYSTEM), ('binutils', '2.36.1'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb index 4539c721d68..56ff0db94f9 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.2.0.eb @@ -27,7 +27,7 @@ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.21', '', SYSTEM), # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency - ('Autotools','20220317', '', SYSTEM), + ('Autotools', '20220317', '', SYSTEM), ('binutils', '2.37'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb index a3f0568ffab..c24a57a45c3 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-11.3.0.eb @@ -27,7 +27,7 @@ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.21', '', SYSTEM), # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency - ('Autotools','20220317', '', SYSTEM), + ('Autotools', '20220317', '', SYSTEM), ('binutils', '2.38'), ] diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb index e4e28af276f..f797b8b490a 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-9.3.0.eb @@ -24,7 +24,7 @@ builddependencies = [ # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) ('gettext', '0.20.1', '', SYSTEM), # use Autotools built with system toolchain as build dep to avoid conflicting ncurses dependency - ('Autotools','20220317', '', SYSTEM), + ('Autotools', '20220317', '', SYSTEM), ('binutils', '2.34'), ] From 50b231913a3812526e4247a4a167eb901aae9540 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 30 Jun 2023 16:49:04 +0200 Subject: [PATCH 7953/9987] adding easyconfigs: MXNet-1.9.1-foss-2022a.eb and patches: mxnet-fix_blas.patch --- .../m/MXNet/MXNet-1.9.1-foss-2022a.eb | 67 +++++++++++++++++++ .../easyconfigs/m/MXNet/mxnet-fix_blas.patch | 34 ++++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/m/MXNet/mxnet-fix_blas.patch diff --git a/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb new file mode 100644 index 00000000000..ac79b1bfdc9 --- /dev/null +++ b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb @@ -0,0 +1,67 @@ +name = 'MXNet' +version = '1.9.1' + +homepage = 'https://mxnet.io/' +description = """Flexible and Efficient Library for Deep Learning""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'cstd': 'c++14', 'opt': True, 'pic': True, 'openmp': True, 'extra_cflags': '-lflexiblas'} + +source_urls = [ + 'https://github.com/apache/mxnet/archive', + 'https://github.com/oneapi-src/oneDNN/archive/', +] +sources = [ + 'v%(version)s.tar.gz', # MXNet + 'https://github.com/dmlc/ps-lite/archive/34fd45cae457d59850fdcb2066467778d0673f21.tar.gz', # ps-lite + 'https://github.com/apache/tvm/archive/efdac9439506d1de5eec91ecc795982c78e41909.tar.gz', # tvm + 'https://github.com/dmlc/dmlc-core/archive/5df8305fe699d3b503d10c60a231ab0223142407.tar.gz', # dmlc-core + 'https://github.com/dmlc/dlpack/archive/3efc489b55385936531a06ff83425b719387ec63.tar.gz', # dlpack + 'https://github.com/google/googletest/archive/eb9225ce361affe561592e0912320b9db84985d0.tar.gz', # googletest + 'https://github.com/kpu/intgemm/archive/8f28282c3bd854922da638024d2659be52e892e9.tar.gz', # intgemm + 'https://github.com/NVlabs/cub/archive/0158fa19f28619886232defd412433974af89611.tar.gz', # cub + 'https://github.com/onnx/onnx-tensorrt/archive/2eb74d933f89e1590fdbfc64971a36e5f72df720.tar.gz', # onnx-tensorrt + # oneDNN: + { + 'download_filename': '5818c40f07bdb6307f9bc64e929836fe036da644.tar.gz', + 'filename': 'mkldnn.tar.gz' + } +] +patches = [ + 'mxnet-fix_blas.patch', +] +checksums = [ + {'v1.9.1.tar.gz': '9927f986b2c2c8315f2ba675e050ce1f4e24e84c4692e5f0a96248876784a8a7'}, + {'34fd45cae457d59850fdcb2066467778d0673f21.tar.gz': + 'ec5d5baab8bbf0c3983ad5f18d7f963f15ae7cd4d154ec204b03c1dceccf209b'}, + {'efdac9439506d1de5eec91ecc795982c78e41909.tar.gz': + '656c38d66baeab885b0212602148bb55ad3cf7d22f52ded8ece53f88e103a2f5'}, + {'5df8305fe699d3b503d10c60a231ab0223142407.tar.gz': + 'a8046f752f36005564d2924b4b6f73e1aea3cce7ff10f9e19d99ad6a22a045b2'}, + {'3efc489b55385936531a06ff83425b719387ec63.tar.gz': + 'b59586ce69bcf3efdbf3cf4803fadfeaae4948044e2b8d89cf912194cf28f233'}, + {'eb9225ce361affe561592e0912320b9db84985d0.tar.gz': + 'a4cb4b0c3ebb191b798594aca674ad47eee255dcb4c26885cf7f49777703484f'}, + {'8f28282c3bd854922da638024d2659be52e892e9.tar.gz': + 'bc8bd8015613a13747eb769876385ec53e8c1ea7ae3f8414521dc53b8fcdfc65'}, + {'0158fa19f28619886232defd412433974af89611.tar.gz': + '43424c4c17a997d1d730c89ec14688671245de7941e02b388d7d3df6ea53777a'}, + {'2eb74d933f89e1590fdbfc64971a36e5f72df720.tar.gz': + 'df99819727445c247fb5c21c2fd825ded3269376867457ae84fa6d6f1c0ae331'}, + {'mkldnn.tar.gz': 'aeb8e65bb13d1a3171673ab749d41e8c3a6538371d922a7fa881afef277128ba'}, + {'mxnet-fix_blas.patch': '274d683f70ae60a65c981eac8a9b27e4a13c4f6f7386ac0f3eb0a462377860f0'}, +] + +# MXNet pulls in a bunch of submodules which don't have releases. +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('graphviz-python', '0.20.1'), + ('OpenCV', '4.6.0', '-contrib'), + ('R', '4.2.1'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MXNet/mxnet-fix_blas.patch b/easybuild/easyconfigs/m/MXNet/mxnet-fix_blas.patch new file mode 100644 index 00000000000..16de2009609 --- /dev/null +++ b/easybuild/easyconfigs/m/MXNet/mxnet-fix_blas.patch @@ -0,0 +1,34 @@ +source: https://github.com/apache/mxnet/pull/21093 +diff -ruN mxnet-1.9.1_orig/cmake/ChooseBlas.cmake mxnet-1.9.1/cmake/ChooseBlas.cmake +--- mxnet-1.9.1_orig/cmake/ChooseBlas.cmake 2022-04-22 00:45:57.000000000 +0200 ++++ mxnet-1.9.1/cmake/ChooseBlas.cmake 2023-06-21 13:23:41.986229000 +0200 +@@ -16,10 +16,11 @@ + # under the License. + + set(BLAS "Open" CACHE STRING "Selected BLAS library") +-set_property(CACHE BLAS PROPERTY STRINGS "Atlas;Open;MKL") ++set_property(CACHE BLAS PROPERTY STRINGS "Atlas;Open;MKL;FlexiBLAS") + + if(DEFINED USE_BLAS) + set(BLAS "${USE_BLAS}") ++ message(STATUS "BLAS is set to ${USE_BLAS}") + else() + if(USE_MKL_IF_AVAILABLE) + if(NOT MKL_FOUND) +@@ -31,7 +32,15 @@ + endif() + endif() + +-if(BLAS STREQUAL "Atlas" OR BLAS STREQUAL "atlas") ++if(BLAS STREQUAL "FlexiBLAS" OR BLAS STREQUAL "flexiblas") ++ set(BLA_VENDOR FlexiBLAS) ++ find_package(BLAS REQUIRED) ++ include_directories(SYSTEM ${BLAS_INCLUDE_DIR}) ++ list(APPEND mshadow_LINKER_LIBS ${BLAS_LIBRARIES}) ++ add_definitions(-DMSHADOW_USE_CBLAS=1) ++ add_definitions(-DMSHADOW_USE_MKL=0) ++ add_definitions(-DMXNET_USE_LAPACK=1) ++elseif(BLAS STREQUAL "Atlas" OR BLAS STREQUAL "atlas") + find_package(Atlas REQUIRED) + include_directories(SYSTEM ${Atlas_INCLUDE_DIR}) + list(APPEND mshadow_LINKER_LIBS ${Atlas_LIBRARIES}) From 3dccb97b32848a5ed0d60f6a5b56702db8d84e0c Mon Sep 17 00:00:00 2001 From: vsc10800 Date: Fri, 30 Jun 2023 17:04:33 +0200 Subject: [PATCH 7954/9987] adding easyconfigs: PortMidi-2.0.4-GCCcore-11.3.0.eb, SDL2_image-2.6.3-GCCcore-11.3.0.eb, SDL2_mixer-2.6.3-GCCcore-11.3.0.eb, SDL2_ttf-2.20.2-GCCcore-11.3.0.eb, pygame-2.1.0-GCCcore-11.3.0.eb --- .../PortMidi/PortMidi-2.0.4-GCCcore-11.3.0.eb | 35 ++++++++++++++ .../p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb | 46 +++++++++++++++++++ .../SDL2_image-2.6.3-GCCcore-11.3.0.eb | 39 ++++++++++++++++ .../SDL2_mixer-2.6.3-GCCcore-11.3.0.eb | 37 +++++++++++++++ .../SDL2_ttf-2.20.2-GCCcore-11.3.0.eb | 36 +++++++++++++++ 5 files changed, 193 insertions(+) create mode 100644 easybuild/easyconfigs/p/PortMidi/PortMidi-2.0.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.6.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SDL2_mixer/SDL2_mixer-2.6.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SDL2_ttf/SDL2_ttf-2.20.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PortMidi/PortMidi-2.0.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PortMidi/PortMidi-2.0.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5cab8eed7b8 --- /dev/null +++ b/easybuild/easyconfigs/p/PortMidi/PortMidi-2.0.4-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'PortMidi' +version = '2.0.4' + +homepage = 'https://github.com/PortMidi/portmidi' +description = """ +PortMidi is a library for software developers. It supports real-time input and +output of MIDI data using a system-independent interface. PortMidi runs on +Windows (using MME), Macintosh (using CoreMIDI), and Linux (using ALSA). +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PortMidi/portmidi/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['64893e823ae146cabd3ad7f9a9a9c5332746abe7847c557b99b2577afa8a607c'] + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('alsa-lib', '1.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libportmidi.%s' % SHLIB_EXT, 'include/portmidi.h', 'include/porttime.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5f88ef0af90 --- /dev/null +++ b/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'pygame' +version = '2.1.0' + +homepage = 'https://www.pygame.org' +description = """ +Pygame is a set of Python modules designed for writing video games. Pygame adds +functionality on top of the excellent SDL library. This allows you to create +fully featured games and multimedia programs in the python language. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SDL2_image', '2.6.3'), + ('SDL2_mixer', '2.6.3'), + ('SDL2_ttf', '2.20.2'), + ('PortMidi', '2.0.4'), +] + +use_pip = True + +_pygame_extra_base = ':'.join([ + '$EBROOTSDL2_IMAGE', + '$EBROOTSDL2_MIXER', + '$EBROOTSDL2_TTF', + '$EBROOTLIBJPEGMINTURBO', + '$EBROOTPORTMIDI', +]) + +exts_list = [ + ('pygame', '2.1.0', { + 'preinstallopts': 'PYGAME_EXTRA_BASE="%s"' % _pygame_extra_base, + 'checksums': ['232e51104db0e573221660d172af8e6fc2c0fda183c5dbf2aa52170f29aa9ec9'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.6.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4e44d5c5e43 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.6.3-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'SDL2_image' +version = '2.6.3' + +homepage = 'https://github.com/libsdl-org/SDL_image' +description = """ +This is a simple library to load images of various formats as SDL surfaces. It +can load BMP, GIF, JPEG, LBM, PCX, PNG, PNM (PPM/PGM/PBM), QOI, TGA, XCF, XPM, +and simple SVG format images. It can also load AVIF, JPEG-XL, TIFF, and WebP +images, depending on build options (see the note below for details.) +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/libsdl-org/SDL_image/archive/refs/tags/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['e3fb5136e1c0e0e118051fbd96cddaf988715ed9fec9296b4861e21823c75b75'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('SDL2', '2.0.22'), +] + +sanity_check_paths = { + 'files': ['include/SDL2/SDL_image.h', 'lib/libSDL2_image.%s' % SHLIB_EXT, + 'lib/pkgconfig/SDL2_image.pc'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SDL2_mixer/SDL2_mixer-2.6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SDL2_mixer/SDL2_mixer-2.6.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d58dba77b9f --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2_mixer/SDL2_mixer-2.6.3-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'SDL2_mixer' +version = '2.6.3' + +homepage = 'https://github.com/libsdl-org/SDL_mixer' +description = """ +Due to popular demand, here is a simple multi-channel audio mixer. It supports +8 channels of 16 bit stereo audio, plus a single channel of music. It can load +FLAC, MP3, Ogg, VOC, and WAV format audio. It can also load MIDI, MOD, and Opus +audio, depending on build options (see the note below for details.) +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/libsdl-org/SDL_mixer/archive/refs/tags/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['91dd065e9e63f499e5317350b110184b0ba96bc5f63c39b3a9939a136c40c035'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('SDL2', '2.0.22'), + ('FFmpeg', '4.4.2'), +] + +sanity_check_paths = { + 'files': ['include/SDL2/SDL_mixer.h', 'lib/libSDL2_mixer.%s' % SHLIB_EXT, + 'lib/pkgconfig/SDL2_mixer.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SDL2_ttf/SDL2_ttf-2.20.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SDL2_ttf/SDL2_ttf-2.20.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1e431529e09 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2_ttf/SDL2_ttf-2.20.2-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2_ttf' +version = '2.20.2' + +homepage = 'https://github.com/libsdl-org/SDL_ttf' +description = """ +This library is a wrapper around the FreeType and Harfbuzz libraries, allowing +you to use TrueType fonts to render text in SDL applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/libsdl-org/SDL_ttf/archive/refs/tags/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['0fe9d587cdc4e6754b647536d0803bea8ca6ac77146c4209e0bed22391cf8241'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('SDL2', '2.0.22'), + ('freetype', '2.12.1'), +] + +configopts = '--disable-harfbuzz --disable-freetype-builtin' + +sanity_check_paths = { + 'files': ['include/SDL2/SDL_ttf.h', 'lib/libSDL2_ttf.%s' % SHLIB_EXT, + 'lib/pkgconfig/SDL2_ttf.pc'], + 'dirs': [], +} + +moduleclass = 'lib' From 35e5885ea5afa52873851aecbae87d682a5f11ba Mon Sep 17 00:00:00 2001 From: vsc10800 Date: Fri, 30 Jun 2023 17:23:52 +0200 Subject: [PATCH 7955/9987] adding easyconfigs: python-mujoco-2.2.2-foss-2022a.eb, MuJoCo-2.2.2-GCCcore-11.3.0.eb, glew-2.2.0-GCCcore-11.3.0-osmesa.eb, Abseil-20230125.2-GCCcore-11.3.0.eb, pybind11-2.10.4-GCCcore-11.3.0.eb and patches: python-mujoco-2.2.2_use_eb_deps.patch --- .../Abseil-20230125.2-GCCcore-11.3.0.eb | 31 +++++++++++ .../glew/glew-2.2.0-GCCcore-11.3.0-osmesa.eb | 43 +++++++++++++++ .../m/MuJoCo/MuJoCo-2.2.2-GCCcore-11.3.0.eb | 48 +++++++++++++++++ .../pybind11-2.10.4-GCCcore-11.3.0.eb | 23 ++++++++ .../python-mujoco-2.2.2-foss-2022a.eb | 54 +++++++++++++++++++ .../python-mujoco-2.2.2_use_eb_deps.patch | 32 +++++++++++ 6 files changed, 231 insertions(+) create mode 100644 easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-osmesa.eb create mode 100644 easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.2.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.10.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2_use_eb_deps.patch diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ae09e8b085b --- /dev/null +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Abseil' +version = '20230125.2' + +homepage = 'https://abseil.io/' +description = """Abseil is an open-source collection of C++ library code designed to augment the +C++ standard library. The Abseil library code is collected from Google's own +C++ code base, has been extensively tested and used in production, and is the +same code we depend on in our daily coding lives.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++17'} + +source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['9a2b5752d7bfade0bdeee2701de17c9480620f8b237e1964c1b9967c75374906'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], + 'dirs': ['include/absl'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-osmesa.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-osmesa.eb new file mode 100644 index 00000000000..11e014811b7 --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-osmesa.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' +versionsuffix = '-osmesa' +# available: -glx, -osmesa, -egl +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# offscreen), and OSMESA (offscreen software only). + +name = 'glew' +version = '2.2.0' + +homepage = 'https://github.com/nigels-com/glew' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Mesa', '22.0.3'), + ('X11', '20220504'), +] + +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all ' + local_system + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.2.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..01b0b71bbb2 --- /dev/null +++ b/easybuild/easyconfigs/m/MuJoCo/MuJoCo-2.2.2-GCCcore-11.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PackedBinary' + +name = 'MuJoCo' +version = '2.2.2' + +homepage = 'https://mujoco.org/' +description = """MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose +physics engine that aims to facilitate research and development in robotics, +biomechanics, graphics and animation, machine learning, and other areas which +demand fast and accurate simulation of articulated structures interacting with +their environment.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/deepmind/mujoco/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-linux-%(arch)s.tar.gz'] +checksums = ['c887a4c315201ce47cf654e0115a55c29648567450d44cd8afe8e3a09d34ea1e'] + +builddependencies = [ + ('binutils', '2.38'), +] + +# MuJoCo bundles 3 variants of glew using non-standard sonames: +# - libglew with GLX +# - libglewegl with EGL +# - libglewosmesa with OSMESA +# - Software depending on MuJoCo expect these non-standard sonames, so they should not be removed +# - libglew and libglewegl seem to work with Mesa and X11 for toolchain GCCcore/11.2.0 +# - libglewosmesa has to be replaced as it links to an old libOSMesa + +dependencies = [ + ('glew', '2.2.0', '-osmesa'), +] + +postinstallcmds = [ + # replace bundled libglewosmesa.so with glew libs from EB + "ln -sf $EBROOTGLEW/lib64/libGLEW.so %(installdir)s/lib/libglewosmesa.so", +] + +sanity_check_paths = { + 'files': ['bin/basic', 'bin/derivative', 'bin/record', 'bin/simulate', + 'lib/libmujoco.%s' % SHLIB_EXT], + 'dirs': ['include', 'model', 'sample'], +} + +sanity_check_commands = ['basic'] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..839821133b6 --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.4-GCCcore-11.3.0.eb @@ -0,0 +1,23 @@ +name = 'pybind11' +version = '2.10.4' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['832e2f309c57da9c1e6d4542dedd34b24e4192ecb4d62f6f4866a737454c9970'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), + ('Eigen', '3.4.0'), +] +dependencies = [('Python', '3.10.4')] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2-foss-2022a.eb b/easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2-foss-2022a.eb new file mode 100644 index 00000000000..daba1df3716 --- /dev/null +++ b/easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2-foss-2022a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'python-mujoco' +version = '2.2.2' + +homepage = 'https://www.mujoco.org' +description = """ +This package is the canonical Python bindings for the MuJoCo physics engine. +The mujoco package provides direct access to raw MuJoCo C API functions, structs, +constants, and enumerations. Structs are provided as Python classes, with +Pythonic initialization and deletion semantics. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.24.3'), + ('Eigen', '3.4.0'), + ('pybind11', '2.9.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Abseil', '20230125.2'), + ('MuJoCo', '2.2.2'), + ('GLFW', '3.3.8'), + ('PyOpenGL', '3.1.6'), +] + +use_pip = True + +exts_list = [ + ('mujoco', version, { + 'patches': ['python-mujoco-2.2.2_use_eb_deps.patch'], + 'preinstallopts': 'MUJOCO_PATH="$EBROOTMUJOCO"', + 'checksums': [ + {'mujoco-2.2.2.tar.gz': 'b1ca70b21ef01d0e56952d03a387bdae9c6b141c042379226596410a3ac82085'}, + {'python-mujoco-2.2.2_use_eb_deps.patch': + 'dc05de6a86abbc12e23becdcec4c04715c8dcb9abf3dfcdd6baf0113e22273c9'}, + ], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('glfw', '2.6.1', { + 'checksums': ['e15c21f06e74cc9740bf36c3c618b5f0d015ef09fb4e216d138967d8ee532567'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2_use_eb_deps.patch b/easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2_use_eb_deps.patch new file mode 100644 index 00000000000..4142c9277fc --- /dev/null +++ b/easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2_use_eb_deps.patch @@ -0,0 +1,32 @@ +Use EasyBuild provided dependencies +Author: Cintia Willemyns (Vrije Universiteit Brussel) +diff -ur mujoco-2.2.2.orig/mujoco/CMakeLists.txt mujoco-2.2.2/mujoco/CMakeLists.txt +--- mujoco-2.2.2.orig/mujoco/CMakeLists.txt 2022-09-06 20:39:39.000000000 +0200 ++++ mujoco-2.2.2/mujoco/CMakeLists.txt 2023-06-28 11:50:43.850376703 +0200 +@@ -119,7 +119,7 @@ + set(MUJOCO_PYTHON_ABSL_TARGETS absl::core_headers absl::flat_hash_map absl::span) + findorfetch( + USE_SYSTEM_PACKAGE +- OFF ++ ON + PACKAGE_NAME + absl + LIBRARY_NAME +@@ -152,7 +152,7 @@ + add_compile_definitions(EIGEN_MPL2_ONLY) + findorfetch( + USE_SYSTEM_PACKAGE +- OFF ++ ON + PACKAGE_NAME + Eigen3 + LIBRARY_NAME +@@ -169,7 +169,7 @@ + # ==================== PYBIND11 ================================================ + findorfetch( + USE_SYSTEM_PACKAGE +- OFF ++ ON + PACKAGE_NAME + pybind11 + LIBRARY_NAME From 4f9a87c0748f8459f54002b7299b43fb28cf8954 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 30 Jun 2023 17:45:39 +0200 Subject: [PATCH 7956/9987] also for the 2022a version --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 7cdf078b8bb..70a2e6684d3 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1209,9 +1209,6 @@ exts_list = [ ('deepSNV', '1.42.1', { 'checksums': ['f64d43645d696af7b375c66f7dccf877d099482f8470dd18c4aba8b1f30bf22d'], }), - ('dada2', '1.24.0', { - 'checksums': ['9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b'], - }), ('TreeSummarizedExperiment', '2.4.0', { 'checksums': ['a7339e41cb1ed74bb633b6c4ae6e762f25eeeae2c396da6fa676b29550b7182f'], }), From a8776afb11ed008bba85cf051ee175517beec261 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 30 Jun 2023 17:59:36 +0200 Subject: [PATCH 7957/9987] add CMake builddep --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 0d3b45c12b3..9d7060cf52e 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -15,6 +15,7 @@ builddependencies = [ ('pkgconf', '1.8.0'), ('Xvfb', '21.1.3'), ('Autotools', '20220317'), + ('CMake', '3.24.3'), ] dependencies = [ ('X11', '20220504'), From d85c8de694166ecaf36f54620a8c4bbf1c81838b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 30 Jun 2023 18:04:18 +0200 Subject: [PATCH 7958/9987] add CMake builddep also for 2022b --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 010f787f26f..a497c759bcb 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -15,6 +15,7 @@ builddependencies = [ ('pkgconf', '1.9.3'), ('Xvfb', '21.1.6'), ('Autotools', '20220317'), + ('CMake', '3.24.3'), ] dependencies = [ ('X11', '20221110'), From 96dfcf7cf4ee18bc6aec62fa3888bd2611ca7aa6 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 1 Jul 2023 09:22:55 +0100 Subject: [PATCH 7959/9987] update homepage --- easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb b/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb index 1980b4da714..9d9e5ec1c4d 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2021b.eb @@ -3,7 +3,7 @@ easyblock = 'PythonPackage' name = 'emcee' version = '3.1.4' -homepage = 'https://dfm.io/emcee' +homepage = 'https://emcee.readthedocs.io/' description = """Emcee is an extensible, pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. It's designed for Bayesian parameter estimation and it's really sweet! """ From a2968cbf0221b972ee1fb82a47384d4e3d22b12e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 1 Jul 2023 14:51:10 +0200 Subject: [PATCH 7960/9987] adding easyconfigs: dorado-0.3.1-foss-2022a-CUDA-11.7.0.eb --- .../dorado-0.3.1-foss-2022a-CUDA-11.7.0.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.3.1-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/dorado/dorado-0.3.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..d1b1e7a7376 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.3.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,67 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.3.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), + ('HDF5', '1.12.2'), + ('zstd', '1.5.2'), + ('HTSlib', '1.15.1'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " + +configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " +configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " +configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib -DHTSLIB_LIBRARIES=hts " +# add -pthread flag (in addition to -lpthread) to avoid linking error: +# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' +configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" ' + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' From f36540f4c175acf29dc8df1b1ddd0678a36402a4 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 1 Jul 2023 16:36:25 +0100 Subject: [PATCH 7961/9987] Apply suggestions from code review --- .../Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb index dc0b6545e61..3fd76cfa7b5 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb @@ -8,7 +8,7 @@ versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version homepage = 'https://github.com/uber/horovod' description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. -This build only have PyTorch enabled.""" +This build only has PyTorch enabled.""" toolchain = {'name': 'foss', 'version': '2021a'} @@ -19,7 +19,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), ('PyYAML', '5.4.1'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('NCCL', '2.10.3', local_cuda_suffix), ('PyTorch', local_pt_version, local_cuda_suffix), ] From 0ad724e359ed8b17935b385a605b76c7ac8ee95a Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 1 Jul 2023 16:59:39 +0100 Subject: [PATCH 7962/9987] use existing utf8proc --- .../s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb index d7aacc65f36..a72ba66c7e4 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb @@ -32,7 +32,7 @@ dependencies = [ ('SQLite', '3.38.3'), ('zlib', '1.2.12'), ('lz4', '1.9.3'), - ('utf8proc', '2.8.0'), + ('utf8proc', '2.7.0'), ('Serf', '1.3.9'), ] From ea9bff1eea3db6e9a62d92b49cd72d12a97a2299 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 1 Jul 2023 17:06:02 +0100 Subject: [PATCH 7963/9987] Add util_linux to provide libuuid --- .../easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb index a72ba66c7e4..3ef09d2ffa2 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.2-GCCcore-11.3.0.eb @@ -34,6 +34,7 @@ dependencies = [ ('lz4', '1.9.3'), ('utf8proc', '2.7.0'), ('Serf', '1.3.9'), + ('util-linux', '2.38'), ] preconfigopts = './autogen.sh && ' From 57b8cdd4bf8ec4671bc1da6c83ce082dd9fe3088 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 1 Jul 2023 18:48:53 +0100 Subject: [PATCH 7964/9987] point cmake at the EB Python --- .../easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb index f476a2ced04..f58d1244c04 100644 --- a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb @@ -36,6 +36,7 @@ _copts = [ '-DBUILD_METAL=ON', '-DENABLE_TBB=ON', '-DBUILD_TESTING=ON', + '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python', ] configopts = ' '.join(_copts) From 602659fc433426cff39ecf6978b699a1063b2827 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 1 Jul 2023 18:48:58 +0100 Subject: [PATCH 7965/9987] point cmake at the EB Python --- .../h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb index 3ddba230d4b..ab46959e6c7 100644 --- a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a-CUDA-11.7.0.eb @@ -40,6 +40,7 @@ _copts = [ '-DBUILD_METAL=ON', '-DENABLE_TBB=ON', '-DBUILD_TESTING=ON', + '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python', ] configopts = ' '.join(_copts) From a4534400a5ce8c25198f38410656c1f781821bf9 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 2 Jul 2023 10:43:41 +0100 Subject: [PATCH 7966/9987] Apply suggestions from code review --- easybuild/easyconfigs/m/MView/MView-1.67-GCC-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MView/MView-1.67-GCC-11.3.0.eb b/easybuild/easyconfigs/m/MView/MView-1.67-GCC-11.3.0.eb index b0545bbb584..cd81e9c65a3 100644 --- a/easybuild/easyconfigs/m/MView/MView-1.67-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/m/MView/MView-1.67-GCC-11.3.0.eb @@ -4,13 +4,14 @@ name = 'MView' version = "1.67" homepage = 'https://desmid.github.io/mview/' -description = """ MView reformats the results of a sequence database search or a +description = """MView reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup.""" toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] sources = [SOURCELOWER_TAR_GZ] +checksums = ['e5bac78960f8f6c091b2f7ea8a3c6075e9bea5a062391fd3e1e44fca14025e46'] dependencies = [('Perl', '5.34.1')] From 9173f3c31ae3403a068186278c3de3bf8395682d Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 2 Jul 2023 10:49:07 +0100 Subject: [PATCH 7967/9987] fix typo --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 5780787ba3f..914a2262747 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1160,7 +1160,7 @@ def test_pr_CMAKE_BUILD_TYPE(self): failing_checks.append("Found -DCMAKE_BUILD_TYPE in configopts. Use build_type instead: %s" % ec_fn) if build_type == 'Release': failing_checks.append("build_type was set to the default of 'Release'. " - "Ommit this to base it on toolchain_opts.debug: %s" % ec_fn) + "Omit this to base it on toolchain_opts.debug: %s" % ec_fn) if failing_checks: self.fail('\n'.join(failing_checks)) From c137831a4ae62766f9abcf1b747e5534c3ffc942 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 2 Jul 2023 11:44:23 +0100 Subject: [PATCH 7968/9987] allow OpenMPI oversubscription --- .../easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb index f58d1244c04..f576061ecc4 100644 --- a/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/h/HOOMD-blue/HOOMD-blue-4.0.1-foss-2022a.eb @@ -44,6 +44,7 @@ postinstallcmds = [ 'ln -s hoomd/include %(installdir)s/include', ] +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " runtest = 'test' sanity_check_paths = { From fdbca2fb0b5c1d43e1e3fa2fb8b6c48c1af6e08c Mon Sep 17 00:00:00 2001 From: Lev Lafayette Date: Mon, 3 Jul 2023 18:49:08 +1000 Subject: [PATCH 7969/9987] Create DMTCP-3.0.0-GCCcore-11.3.0.eb New major release, new toolchain. --- .../d/DMTCP/DMTCP-3.0.0-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..09d769732a5 --- /dev/null +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-3.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '3.0.0' + +homepage = 'http://dmtcp.sourceforge.net/index.html' +description = """DMTCP is a tool to transparently checkpoint the state of multiple +simultaneous applications, including multi-threaded and distributed applications. +It operates directly on the user binary executable, without any Linux kernel modules +or other kernel modifications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2c7e95e1dbc55db33433bfee48a65f274298e98f246a36ab6dad1e0694750d37'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' From 2939e5199bb864f7cf22a5ac80a2fb9e7ec9be12 Mon Sep 17 00:00:00 2001 From: vsc10800 Date: Mon, 3 Jul 2023 12:00:50 +0200 Subject: [PATCH 7970/9987] adding easyconfigs: Arcade-Learning-Environment-0.8.1-foss-2022a.eb, OpenAI-Gym-0.26.2-foss-2022a.eb and patches: ale-py-0.8.1_fix_version.patch --- ...e-Learning-Environment-0.8.1-foss-2022a.eb | 63 +++++++++++++++++++ .../ale-py-0.8.1_fix_version.patch | 14 +++++ .../OpenAI-Gym-0.26.2-foss-2022a.eb | 53 ++++++++++++++++ 3 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/a/Arcade-Learning-Environment/ale-py-0.8.1_fix_version.patch create mode 100644 easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2022a.eb b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2022a.eb new file mode 100644 index 00000000000..649548201c6 --- /dev/null +++ b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2022a.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'Arcade-Learning-Environment' +version = '0.8.1' + +homepage = 'https://github.com/mgbellemare/Arcade-Learning-Environment' +description = """The Arcade Learning Environment (ALE) is a simple framework that allows +researchers and hobbyists to develop AI agents for Atari 2600 games. It is +built on top of the Atari 2600 emulator Stella and separates the details of +emulation from agent design. This video depicts over 50 games currently +supported in the ALE.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'mgbellemare' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['28960616cd89c18925ced7bbdeec01ab0b2ebd2d8ce5b7c88930e97381b4c3b5'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('SDL2', '2.0.22'), + ('zlib', '1.2.12'), +] + +# main build of C++ libraries +configopts = "-DBUILD_PYTHON_LIB=OFF" + +# install Python bindings and its dependencies +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('ale-py', version, { + 'patches': ['%(name)s-%(version)s_fix_version.patch'], + 'preinstallopts': 'ALE_BUILD_VERSION=%(version)s', + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': [ + {'v0.8.1.tar.gz': '28960616cd89c18925ced7bbdeec01ab0b2ebd2d8ce5b7c88930e97381b4c3b5'}, + {'ale-py-0.8.1_fix_version.patch': 'b582fe15875b733c25a7902e96197589df3eea05bc2d0641f4927730788721c2'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/ale-import-roms', 'lib64/libale.a'], + 'dirs': ['include/ale', 'lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["ale-import-roms --help"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Arcade-Learning-Environment/ale-py-0.8.1_fix_version.patch b/easybuild/easyconfigs/a/Arcade-Learning-Environment/ale-py-0.8.1_fix_version.patch new file mode 100644 index 00000000000..cb483a4d74b --- /dev/null +++ b/easybuild/easyconfigs/a/Arcade-Learning-Environment/ale-py-0.8.1_fix_version.patch @@ -0,0 +1,14 @@ +Avoid git repo requirement for determining the version +Author: Cintia Willemyns (Vrije Universiteit Brussel) +diff -ur Arcade-Learning-Environment-0.8.1.orig/setup.py Arcade-Learning-Environment-0.8.1/setup.py +--- Arcade-Learning-Environment-0.8.1.orig/setup.py 2023-02-17 06:52:26.000000000 +0100 ++++ Arcade-Learning-Environment-0.8.1/setup.py 2023-06-23 10:22:16.662443000 +0200 +@@ -120,6 +120,9 @@ + raises AssertionError: If `${GITHUB_REF#/v/*/}` doesn't start with + the version specified in `version_file`. + """ ++ if os.getenv('ALE_BUILD_VERSION'): ++ return os.getenv('ALE_BUILD_VERSION') ++ + semver_regex = r"(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)\.(?P0|[1-9]\d*)(?:-(?P(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+(?P[0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?" + semver_prog = re.compile(semver_regex) diff --git a/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2022a.eb b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2022a.eb new file mode 100644 index 00000000000..666ddb08942 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenAI-Gym/OpenAI-Gym-0.26.2-foss-2022a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'OpenAI-Gym' +version = '0.26.2' + +homepage = 'https://gym.openai.com' +description = "A toolkit for developing and comparing reinforcement learning algorithms." + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.24.3'), + ('SWIG', '4.0.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Arcade-Learning-Environment', '0.8.1'), + ('OpenCV', '4.6.0', '-contrib'), + ('lz4', '1.9.3'), + ('pygame', '2.1.0'), + ('python-mujoco', '2.2.2'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('gym-notices', '0.0.8', { + 'checksums': ['ad25e200487cafa369728625fe064e88ada1346618526102659b4640f2b4b911'], + }), + ('box2d-py', '2.3.5', { + 'modulename': 'Box2D', + 'checksums': ['b37dc38844bcd7def48a97111d2b082e4f81cca3cece7460feb3eacda0da2207'], + }), + ('lz4', '3.1.10', { + 'checksums': ['439e575ecfa9ecffcbd63cfed99baefbe422ab9645b1e82278024d8a21d9720b'], + }), + ('gym', version, { + 'use_pip_extras': 'all', + 'checksums': ['e0d882f4b54f0c65f203104c24ab8a38b039f1289986803c7d02cdbe214fbcc4'], + }), +] + +local_envs = ['box2d', 'classic_control', 'mujoco', 'toy_text'] +sanity_check_commands = ["python -c 'import gym.envs.%s'" % e for e in local_envs] + +sanity_pip_check = True + +moduleclass = 'tools' From ae0880a0ed2dbe4e46d701e15c69638cf4535575 Mon Sep 17 00:00:00 2001 From: vsc10800 Date: Mon, 3 Jul 2023 14:03:56 +0200 Subject: [PATCH 7971/9987] patch checksum fixed --- .../Arcade-Learning-Environment-0.8.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2022a.eb b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2022a.eb index 649548201c6..766053c3dcf 100644 --- a/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/Arcade-Learning-Environment/Arcade-Learning-Environment-0.8.1-foss-2022a.eb @@ -46,7 +46,7 @@ exts_list = [ 'source_tmpl': 'v%(version)s.tar.gz', 'checksums': [ {'v0.8.1.tar.gz': '28960616cd89c18925ced7bbdeec01ab0b2ebd2d8ce5b7c88930e97381b4c3b5'}, - {'ale-py-0.8.1_fix_version.patch': 'b582fe15875b733c25a7902e96197589df3eea05bc2d0641f4927730788721c2'}, + {'ale-py-0.8.1_fix_version.patch': '3ad39a05eb82c3aacf34a6de562ad2d76c254a906963bdef6a810f0b5ce0d22f'}, ], }), ] From 607eb13e1d11952a030c5a0978c424be62992043 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jul 2023 11:01:36 +0200 Subject: [PATCH 7972/9987] adding easyconfigs: XlsxWriter-3.1.2-GCCcore-12.2.0.eb --- .../XlsxWriter-3.1.2-GCCcore-12.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0a2285a563d --- /dev/null +++ b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.2-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'XlsxWriter' +version = '3.1.2' + +homepage = 'https://xlsxwriter.readthedocs.io/' +description = "A Python module for creating Excel XLSX files" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['78751099a770273f1c98b8d6643351f68f98ae8e6acf9d09d37dc6798f8cd3de'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/vba_extract.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['vba_extract.py --help'] + +sanity_pip_check = True + +moduleclass = 'tools' From df2ef0a86d6f2674cb10bf6df74b1e3ec89f46db Mon Sep 17 00:00:00 2001 From: vsc10800 Date: Tue, 4 Jul 2023 16:05:03 +0200 Subject: [PATCH 7973/9987] deleting pybind11-2.10.4, updated version not needed (using v2.9.2) --- .../pybind11-2.10.4-GCCcore-11.3.0.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.10.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.4-GCCcore-11.3.0.eb deleted file mode 100644 index 839821133b6..00000000000 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.4-GCCcore-11.3.0.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'pybind11' -version = '2.10.4' - -homepage = 'https://pybind11.readthedocs.io' -description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, - mainly to create Python bindings of existing C++ code.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://github.com/pybind/pybind11/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['832e2f309c57da9c1e6d4542dedd34b24e4192ecb4d62f6f4866a737454c9970'] - -builddependencies = [ - ('binutils', '2.38'), - ('CMake', '3.24.3'), - ('Eigen', '3.4.0'), -] -dependencies = [('Python', '3.10.4')] - -configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" - -moduleclass = 'lib' From 58363c7ab46327773f1a442dfa0c0f7082092939 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jul 2023 17:46:13 +0200 Subject: [PATCH 7974/9987] remove useless '-Dgallium-drivers=swrast' from configure options for ROOT 6.26.06 --- easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb index 1579d8dda22..e3109d99f7d 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.06-foss-2022a.eb @@ -50,6 +50,4 @@ configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' # Set C++ standard to C++17 for better stability configopts += ' -DCMAKE_CXX_STANDARD=17' -configopts += " -Dgallium-drivers=swrast" - moduleclass = 'data' From b10932d4e7cac249120345d5e7b932940aa1ee7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jul 2023 20:01:26 +0200 Subject: [PATCH 7975/9987] remove incorrect '-Dgallium-drivers=swrast' configure option in ROOT easyconfigs --- easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb | 2 -- easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb | 2 -- easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb | 2 -- 3 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb index 020ed48f660..ab70796cf4a 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.22.08-foss-2020b.eb @@ -50,6 +50,4 @@ configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' # Set C++ standard to C++17 for better stability configopts += ' -DCMAKE_CXX_STANDARD=17' -configopts += " -Dgallium-drivers=swrast" - moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb index 0ab4dcba930..91350423753 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.24.06-foss-2021b.eb @@ -50,6 +50,4 @@ configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' # Set C++ standard to C++17 for better stability configopts += ' -DCMAKE_CXX_STANDARD=17' -configopts += " -Dgallium-drivers=swrast" - moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb index 4acf0146bc4..6e41414b19b 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb @@ -50,6 +50,4 @@ configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' # Set C++ standard to C++17 for better stability configopts += ' -DCMAKE_CXX_STANDARD=17' -configopts += " -Dgallium-drivers=swrast" - moduleclass = 'data' From c68b4aa025bc45cedc57cca79e8b85fd9238169d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Jul 2023 20:40:07 +0200 Subject: [PATCH 7976/9987] specify checksums for X11 20230603 in 'components' --- .../x/X11/X11-20230603-GCCcore-12.3.0.eb | 243 +++++++++++------- 1 file changed, 143 insertions(+), 100 deletions(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20230603-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20230603-GCCcore-12.3.0.eb index 5b749a4e98d..62b97f725fb 100644 --- a/easybuild/easyconfigs/x/X11/X11-20230603-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20230603-GCCcore-12.3.0.eb @@ -46,120 +46,163 @@ default_component_specs = { } components = [ - ('libpthread-stubs', '0.4'), # 2017-03-14 - ('xorgproto', '2022.2'), # 2022-08-11 - ('libXau', '1.0.11'), # 2022-12-08 - ('libXdmcp', '1.1.4'), # 2022-11-19 - ('xcb-proto', '1.15.2'), # 2022-06-17 - ('libxcb', '1.15'), # 2022-05-03 - ('xtrans', '1.5.0'), # 2023-06-03 + ('libpthread-stubs', '0.4', { # 2017-03-14 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('xorgproto', '2022.2', { # 2022-08-11 + 'checksums': ['da351a403d07a7006d7bdc8dcfc14ddc1b588b38fb81adab9989a8eef605757b'], + }), + ('libXau', '1.0.11', { # 2022-12-08 + 'checksums': ['3a321aaceb803577a4776a5efe78836eb095a9e44bbc7a465d29463e1a14f189'], + }), + ('libXdmcp', '1.1.4', { # 2022-11-19 + 'checksums': ['55041a8ff8992ab02777478c4b19c249c0f8399f05a752cb4a1a868a9a0ccb9a'], + }), + ('xcb-proto', '1.15.2', { # 2022-06-17 + 'checksums': ['6b1ed9cd7cf35e37913eeecca37e5b85b14903002942b3e332f321335c27a8eb'], + }), + ('libxcb', '1.15', { # 2022-05-03 + 'checksums': ['1cb65df8543a69ec0555ac696123ee386321dfac1964a3da39976c9a05ad724d'], + }), + ('xtrans', '1.5.0', { # 2023-06-03 + 'checksums': ['a806f8a92f879dcd0146f3f1153fdffe845f2fc0df9b1a26c19312b7b0a29c86'], + }), ('libxkbcommon', '1.5.0', { # 2023-01-02 'easyblock': 'MesonNinja', 'sources': [SOURCE_TAR_XZ], + 'checksums': ['560f11c4bbbca10f495f3ef7d3a6aa4ca62b4f8fb0b52e7d459d18a26e46e017'], 'preconfigopts': '', 'configopts': '-Denable-wayland=false -Denable-docs=false ', }), - ('libX11', '1.8.5'), # 2023-06-01 - ('libXext', '1.3.5'), # 2022-10-29 - ('libFS', '1.0.9'), # 2022-08-26 - ('libICE', '1.1.1'), # 2022-12-08 - ('libSM', '1.2.4'), # 2022-12-20 - ('libXScrnSaver', '1.2.4'), # 2022-12-05 - ('libXt', '1.3.0'), # 2023-05-09 - ('libXmu', '1.1.4'), # 2022-10-17 - ('libXpm', '3.5.16'), # 2023-04-17 - ('libXaw', '1.0.15'), # 2023-03-16 - ('libXfixes', '6.0.1'), # 2023-04-09 - ('libXcomposite', '0.4.6'), # 2022-12-04 - ('libXrender', '0.9.11'), # 2022-10-22 - ('libXcursor', '1.2.1'), # 2022-04-03 - ('libXdamage', '1.1.6'), # 2022-12-04 - ('libfontenc', '1.1.7'), # 2022-12-08 - ('libXfont', '1.5.4'), # 2017-11-28 - ('libXfont2', '2.0.6'), # 2022-08-26 - ('libXft', '2.3.8'), # 2023-04-17 - ('libXi', '1.8.1'), # 2023-05-04 - ('libXinerama', '1.1.5'), # 2022-10-29 - ('libXrandr', '1.5.3'), # 2022-11-20 - ('libXres', '1.2.2'), # 2022-12-05 - ('libXtst', '1.2.4'), # 2022-09-27 - ('libXv', '1.0.12'), # 2022-12-05 - ('libXvMC', '1.0.13'), # 2022-03-22 - ('libXxf86dga', '1.1.6'), # 2022-12-05 - ('libXxf86vm', '1.1.5'), # 2022-09-27 - ('libdmx', '1.1.5'), # 2023-06-03 - ('libxkbfile', '1.1.2'), # 2022-12-08 - ('libxshmfence', '1.3.2'), # 2022-12-08 - ('xcb-util', '0.4.0'), # 2014-10-15 - ('xcb-util-image', '0.4.1'), # 2022-10-18 - ('xcb-util-keysyms', '0.4.1'), # 2022-10-19 - ('xcb-util-renderutil', '0.3.10'), # 2022-10-19 - ('xcb-util-wm', '0.4.2'), # 2022-10-19 - ('xcb-util-cursor', '0.1.4'), # 2022-10-18 + ('libX11', '1.8.5', { # 2023-06-01 + 'checksums': ['d84a35c324d5a1724692eafc1ed76f1689c833021e0062933773ec437f91a56b'], + }), + ('libXext', '1.3.5', { # 2022-10-29 + 'checksums': ['1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'], + }), + ('libFS', '1.0.9', { # 2022-08-26 + 'checksums': ['8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'], + }), + ('libICE', '1.1.1', { # 2022-12-08 + 'checksums': ['04fbd34a11ba08b9df2e3cdb2055c2e3c1c51b3257f683d7fcf42dabcf8e1210'], + }), + ('libSM', '1.2.4', { # 2022-12-20 + 'checksums': ['51464ce1abce323d5b6707ceecf8468617106e1a8a98522f8342db06fd024c15'], + }), + ('libXScrnSaver', '1.2.4', { # 2022-12-05 + 'checksums': ['0656b2630475104d6df75d91ebb8e0153e61d14e9871ef1f403bcda4a62a838a'], + }), + ('libXt', '1.3.0', { # 2023-05-09 + 'checksums': ['de4a80c4cc7785b9620e572de71026805f68e85a2bf16c386009ef0e50be3f77'], + }), + ('libXmu', '1.1.4', { # 2022-10-17 + 'checksums': ['3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'], + }), + ('libXpm', '3.5.16', { # 2023-04-17 + 'checksums': ['43a70e6f9b67215fb223ca270d83bdcb868c513948441d5b781ea0765df6bfb4'], + }), + ('libXaw', '1.0.15', { # 2023-03-16 + 'checksums': ['ca8a613884c922985202075b3cc8ee8821bfa83a5eb066189ae3cca131e63972'], + }), + ('libXfixes', '6.0.1', { # 2023-04-09 + 'checksums': ['e69eaa321173c748ba6e2f15c7cf8da87f911d3ea1b6af4b547974aef6366bec'], + }), + ('libXcomposite', '0.4.6', { # 2022-12-04 + 'checksums': ['3599dfcd96cd48d45e6aeb08578aa27636fa903f480f880c863622c2b352d076'], + }), + ('libXrender', '0.9.11', { # 2022-10-22 + 'checksums': ['6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'], + }), + ('libXcursor', '1.2.1', { # 2022-04-03 + 'checksums': ['77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'], + }), + ('libXdamage', '1.1.6', { # 2022-12-04 + 'checksums': ['2afcc139eb6eb926ffe344494b1fc023da25def42874496e6e6d3aa8acef8595'], + }), + ('libfontenc', '1.1.7', { # 2022-12-08 + 'checksums': ['5e5f210329823f08f97bfe9fd5b4105070c789bc5aef88ce01d86d8203d4aa9f'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.6', { # 2022-08-26 + 'checksums': ['a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'], + }), + ('libXft', '2.3.8', { # 2023-04-17 + 'checksums': ['32e48fe2d844422e64809e4e99b9d8aed26c1b541a5acf837c5037b8d9f278a8'], + }), + ('libXi', '1.8.1', { # 2023-05-04 + 'checksums': ['3b5f47c223e4b63d7f7fe758886b8bf665b20a7edb6962c423892fd150e326ea'], + }), + ('libXinerama', '1.1.5', { # 2022-10-29 + 'checksums': ['2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'], + }), + ('libXrandr', '1.5.3', { # 2022-11-20 + 'checksums': ['3ad316c1781fe2fe22574b819e81f0eff087a8560377f521ba932238b41b251f'], + }), + ('libXres', '1.2.2', { # 2022-12-05 + 'checksums': ['8abce597ced4a7ab89032aee91f6f784d9960adc772b2b59f17e515cd4127950'], + }), + ('libXtst', '1.2.4', { # 2022-09-27 + 'checksums': ['01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'], + }), + ('libXv', '1.0.12', { # 2022-12-05 + 'checksums': ['ce706619a970a580a0e35e9b5c98bdd2af243ac6494c65f44608a89a86100126'], + }), + ('libXvMC', '1.0.13', { # 2022-03-22 + 'checksums': ['e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'], + }), + ('libXxf86dga', '1.1.6', { # 2022-12-05 + 'checksums': ['87c7482b1e29b4eeb415815641c4f69c00545a8138e1b73ff1f361f7d9c22ac4'], + }), + ('libXxf86vm', '1.1.5', { # 2022-09-27 + 'checksums': ['f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'], + }), + ('libdmx', '1.1.5', { # 2023-06-03 + 'checksums': ['070e82cc1daa1b21ee1339aef56a909eab04cbe7d430fabfbb01ecd21b2dd9f3'], + }), + ('libxkbfile', '1.1.2', { # 2022-12-08 + 'checksums': ['d1a7e659bc7ae1aa1fc1ecced261c734df5ad5d86af1ef7a946be0e2d841e51d'], + }), + ('libxshmfence', '1.3.2', { # 2022-12-08 + 'checksums': ['e93a85099604beb244ee756dcaf70e18b08701c1ca84c4de0126cd71bd6c8181'], + }), + ('xcb-util', '0.4.0', { # 2014-10-15 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.1', { # 2022-10-18 + 'checksums': ['0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'], + }), + ('xcb-util-keysyms', '0.4.1', { # 2022-10-19 + 'checksums': ['1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'], + }), + ('xcb-util-renderutil', '0.3.10', { # 2022-10-19 + 'checksums': ['e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'], + }), + ('xcb-util-wm', '0.4.2', { # 2022-10-19 + 'checksums': ['dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'], + }), + ('xcb-util-cursor', '0.1.4', { # 2022-10-18 + 'checksums': ['cc8608ebb695742b6cf84712be29b2b66aa5f6768039528794fca0fa283022bf'], + }), ('xkeyboard-config', '2.38', { # 2022-02-04 'easyblock': 'MesonNinja', 'sources': [SOURCE_TAR_XZ], + 'checksums': ['0690a91bab86b18868f3eee6d41e9ec4ce6894f655443d490a2184bfac56c872'], # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing 'preconfigopts': '', }), - ('printproto', '1.0.5'), # 2011-01-06 - ('libXp', '1.0.4'), # 2022-09-12 - ('xbitmaps', '1.1.3'), # 2023-02-23 -] - -checksums = [ - {'libpthread-stubs-0.4.tar.gz': '50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'}, - {'xorgproto-2022.2.tar.gz': 'da351a403d07a7006d7bdc8dcfc14ddc1b588b38fb81adab9989a8eef605757b'}, - {'libXau-1.0.11.tar.gz': '3a321aaceb803577a4776a5efe78836eb095a9e44bbc7a465d29463e1a14f189'}, - {'libXdmcp-1.1.4.tar.gz': '55041a8ff8992ab02777478c4b19c249c0f8399f05a752cb4a1a868a9a0ccb9a'}, - {'xcb-proto-1.15.2.tar.gz': '6b1ed9cd7cf35e37913eeecca37e5b85b14903002942b3e332f321335c27a8eb'}, - {'libxcb-1.15.tar.gz': '1cb65df8543a69ec0555ac696123ee386321dfac1964a3da39976c9a05ad724d'}, - {'xtrans-1.5.0.tar.gz': 'a806f8a92f879dcd0146f3f1153fdffe845f2fc0df9b1a26c19312b7b0a29c86'}, - {'libxkbcommon-1.5.0.tar.xz': '560f11c4bbbca10f495f3ef7d3a6aa4ca62b4f8fb0b52e7d459d18a26e46e017'}, - {'libX11-1.8.5.tar.gz': 'd84a35c324d5a1724692eafc1ed76f1689c833021e0062933773ec437f91a56b'}, - {'libXext-1.3.5.tar.gz': '1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'}, - {'libFS-1.0.9.tar.gz': '8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'}, - {'libICE-1.1.1.tar.gz': '04fbd34a11ba08b9df2e3cdb2055c2e3c1c51b3257f683d7fcf42dabcf8e1210'}, - {'libSM-1.2.4.tar.gz': '51464ce1abce323d5b6707ceecf8468617106e1a8a98522f8342db06fd024c15'}, - {'libXScrnSaver-1.2.4.tar.gz': '0656b2630475104d6df75d91ebb8e0153e61d14e9871ef1f403bcda4a62a838a'}, - {'libXt-1.3.0.tar.gz': 'de4a80c4cc7785b9620e572de71026805f68e85a2bf16c386009ef0e50be3f77'}, - {'libXmu-1.1.4.tar.gz': '3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'}, - {'libXpm-3.5.16.tar.gz': '43a70e6f9b67215fb223ca270d83bdcb868c513948441d5b781ea0765df6bfb4'}, - {'libXaw-1.0.15.tar.gz': 'ca8a613884c922985202075b3cc8ee8821bfa83a5eb066189ae3cca131e63972'}, - {'libXfixes-6.0.1.tar.gz': 'e69eaa321173c748ba6e2f15c7cf8da87f911d3ea1b6af4b547974aef6366bec'}, - {'libXcomposite-0.4.6.tar.gz': '3599dfcd96cd48d45e6aeb08578aa27636fa903f480f880c863622c2b352d076'}, - {'libXrender-0.9.11.tar.gz': '6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'}, - {'libXcursor-1.2.1.tar.gz': '77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'}, - {'libXdamage-1.1.6.tar.gz': '2afcc139eb6eb926ffe344494b1fc023da25def42874496e6e6d3aa8acef8595'}, - {'libfontenc-1.1.7.tar.gz': '5e5f210329823f08f97bfe9fd5b4105070c789bc5aef88ce01d86d8203d4aa9f'}, - {'libXfont-1.5.4.tar.gz': '59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'}, - {'libXfont2-2.0.6.tar.gz': 'a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'}, - {'libXft-2.3.8.tar.gz': '32e48fe2d844422e64809e4e99b9d8aed26c1b541a5acf837c5037b8d9f278a8'}, - {'libXi-1.8.1.tar.gz': '3b5f47c223e4b63d7f7fe758886b8bf665b20a7edb6962c423892fd150e326ea'}, - {'libXinerama-1.1.5.tar.gz': '2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'}, - {'libXrandr-1.5.3.tar.gz': '3ad316c1781fe2fe22574b819e81f0eff087a8560377f521ba932238b41b251f'}, - {'libXres-1.2.2.tar.gz': '8abce597ced4a7ab89032aee91f6f784d9960adc772b2b59f17e515cd4127950'}, - {'libXtst-1.2.4.tar.gz': '01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'}, - {'libXv-1.0.12.tar.gz': 'ce706619a970a580a0e35e9b5c98bdd2af243ac6494c65f44608a89a86100126'}, - {'libXvMC-1.0.13.tar.gz': 'e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'}, - {'libXxf86dga-1.1.6.tar.gz': '87c7482b1e29b4eeb415815641c4f69c00545a8138e1b73ff1f361f7d9c22ac4'}, - {'libXxf86vm-1.1.5.tar.gz': 'f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'}, - {'libdmx-1.1.5.tar.gz': '070e82cc1daa1b21ee1339aef56a909eab04cbe7d430fabfbb01ecd21b2dd9f3'}, - {'libxkbfile-1.1.2.tar.gz': 'd1a7e659bc7ae1aa1fc1ecced261c734df5ad5d86af1ef7a946be0e2d841e51d'}, - {'libxshmfence-1.3.2.tar.gz': 'e93a85099604beb244ee756dcaf70e18b08701c1ca84c4de0126cd71bd6c8181'}, - {'xcb-util-0.4.0.tar.gz': '0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'}, - {'xcb-util-image-0.4.1.tar.gz': '0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'}, - {'xcb-util-keysyms-0.4.1.tar.gz': '1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'}, - {'xcb-util-renderutil-0.3.10.tar.gz': 'e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'}, - {'xcb-util-wm-0.4.2.tar.gz': 'dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'}, - {'xcb-util-cursor-0.1.4.tar.gz': 'cc8608ebb695742b6cf84712be29b2b66aa5f6768039528794fca0fa283022bf'}, - {'xkeyboard-config-2.38.tar.xz': '0690a91bab86b18868f3eee6d41e9ec4ce6894f655443d490a2184bfac56c872'}, - {'printproto-1.0.5.tar.gz': 'e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'}, - {'libXp-1.0.4.tar.gz': '05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'}, - {'xbitmaps-1.1.3.tar.gz': '93b433b7ff223c4685fdba583b4bd30f2706be2413a670021084422d85b0269d'}, + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.4', { # 2022-09-12 + 'checksums': ['05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'], + }), + ('xbitmaps', '1.1.3', { # 2023-02-23 + 'checksums': ['93b433b7ff223c4685fdba583b4bd30f2706be2413a670021084422d85b0269d'], + }), ] - preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " sanity_check_paths = { From 1d98ee49c5a30013a95242dfe583438f7ef52d85 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 4 Jul 2023 21:26:48 +0200 Subject: [PATCH 7977/9987] add --enable-mpers=check to strace-5.14-GCCcore-11.2.0.eb --- easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb index 4eba20db189..ef709f5fd5a 100644 --- a/easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/s/strace/strace-5.14-GCCcore-11.2.0.eb @@ -20,6 +20,8 @@ builddependencies = [ ('binutils', '2.37'), ] +configopts = "--enable-mpers=check" + sanity_check_paths = { 'files': ['bin/strace-log-merge', 'bin/strace'], 'dirs': ['share'] From a4febc6ce11bf48d17146399c3032e7f3f96471b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Jul 2023 10:09:38 +0200 Subject: [PATCH 7978/9987] adding easyconfigs: popscle-0.1-beta-20210505-GCC-11.3.0.eb and patches: popscle-0.1-beta-20210505_fix-limits.patch --- .../popscle-0.1-beta-20210505-GCC-11.3.0.eb | 49 +++++++++++++++++++ ...popscle-0.1-beta-20210505_fix-limits.patch | 12 +++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/p/popscle/popscle-0.1-beta-20210505-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/popscle/popscle-0.1-beta-20210505_fix-limits.patch diff --git a/easybuild/easyconfigs/p/popscle/popscle-0.1-beta-20210505-GCC-11.3.0.eb b/easybuild/easyconfigs/p/popscle/popscle-0.1-beta-20210505-GCC-11.3.0.eb new file mode 100644 index 00000000000..00fd99b414b --- /dev/null +++ b/easybuild/easyconfigs/p/popscle/popscle-0.1-beta-20210505-GCC-11.3.0.eb @@ -0,0 +1,49 @@ +# Author: Arne Soete +# VIB-UGent Center for Inflammation Research +# updated by Kenneth Hoste (HPC-UGent) +easyblock = 'CMakeMake' + +name = 'popscle' +version = '0.1-beta-20210505' +local_commit = 'da70fc7' + +homepage = 'https://github.com/statgen/popscle' +description = """A suite of +population scale analysis tools for single-cell genomics data including +implementation of Demuxlet / Freemuxlet methods and auxilary tools """ + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++14'} + +source_urls = ['https://github.com/statgen/popscle/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = ['popscle-0.1-beta-20210505_fix-limits.patch'] +checksums = [ + {'popscle-0.1-beta-20210505.tar.gz': 'f4723a8f098f88262e04ecd4d3e62b7d6884e2a3d4eb0b08196aab1651a95d6c'}, + {'popscle-0.1-beta-20210505_fix-limits.patch': 'c476b9f1b8a340bbb8873bff8a831261ade03e48f4b354b2d956bd0204278071'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('HTSlib', '1.15.1'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), +] + +configopts = "-DHTS_INCLUDE_DIRS=$EBROOTHTSLIB/include -DHTS_LIBRARIES=$EBROOTHTSLIB/lib/libhts.a " +configopts += "-DBZIP2_INCLUDE_DIRS=$EBROOTBZIP2/include -DBZIP2_LIBRARIES=$EBROOTBZIP2/lib/libbz2.a " +configopts += "-DLZMA_INCLUDE_DIRS=$EBROOTXZ/include -DLZMA_LIBRARIES=$EBROOTXZ/lib/liblzma.a " + +install_cmd = "mkdir %(installdir)s/bin && install %(builddir)s/%(name)s-*/bin/popscle %(installdir)s/bin/" + +sanity_check_paths = { + 'files': ['bin/popscle'], + 'dirs': [], +} + +sanity_check_commands = ["popscle --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/popscle/popscle-0.1-beta-20210505_fix-limits.patch b/easybuild/easyconfigs/p/popscle/popscle-0.1-beta-20210505_fix-limits.patch new file mode 100644 index 00000000000..75e3257d83c --- /dev/null +++ b/easybuild/easyconfigs/p/popscle/popscle-0.1-beta-20210505_fix-limits.patch @@ -0,0 +1,12 @@ +fix for: error: 'numeric_limits' is not a member of 'std' +author: Kenneth Hoste (HPC-UGent) +--- popscle-da70fc78da385ef049e0e890342acfd62842cae0/gtf_interval_tree.h.orig 2021-05-05 06:49:20.000000000 +0200 ++++ popscle-da70fc78da385ef049e0e890342acfd62842cae0/gtf_interval_tree.h 2023-07-05 09:13:54.273004779 +0200 +@@ -29,6 +29,7 @@ + #include + #include + #include ++#include + + template + class gtfInterval { From ed42247a48b716ed04f0831c3fb0021216c18b03 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 Jul 2023 11:00:14 +0200 Subject: [PATCH 7979/9987] Remove superflous dependencies from Horovod --- .../h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb | 1 - .../h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb | 1 - .../Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb | 1 - .../Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb | 1 - .../Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb | 3 --- 5 files changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb index 7335bc5ac23..5a3037fc26a 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.21.3-fosscuda-2020b-PyTorch-1.7.1.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ ('CMake', '3.18.4'), - ('flatbuffers', '1.12.0'), ] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb index 450a4626c5f..838513f4e84 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.0-fosscuda-2020b-PyTorch-1.8.1.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ ('CMake', '3.18.4'), - ('flatbuffers', '1.12.0'), ] dependencies = [ ('Python', '3.8.6'), diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb index 6933ece700e..eb686e3e46a 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb @@ -17,7 +17,6 @@ builddependencies = [ ] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), - ('UCX-CUDA', '1.10.0', local_cuda_suffix), ('NCCL', '2.10.3', local_cuda_suffix), ('Python', '3.9.5'), ('PyYAML', '5.4.1'), diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb index ff4cb82b3f6..f2cc41c3079 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb @@ -13,7 +13,6 @@ toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ ('CMake', '3.20.1'), - ('flatbuffers', '2.0.0'), ] dependencies = [ ('Python', '3.9.5'), diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb index 3fd76cfa7b5..c383032bf6d 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb @@ -14,7 +14,6 @@ toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ ('CMake', '3.20.1'), - ('flatbuffers', '2.0.0'), ] dependencies = [ ('Python', '3.9.5'), @@ -30,8 +29,6 @@ sanity_pip_check = True preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' -parallel = 1 # Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend - exts_list = [ ('cloudpickle', '2.1.0', { 'checksums': ['bb233e876a58491d9590a676f93c7a5473a08f747d5ab9df7f9ce564b3e7938e'], From 6e5d21b822470c67f50621692c69e32fd4951bff Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Wed, 5 Jul 2023 11:26:48 +0200 Subject: [PATCH 7980/9987] Switching python-mujoco's moduleclass to 'phys' MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../p/python-mujoco/python-mujoco-2.2.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2-foss-2022a.eb b/easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2-foss-2022a.eb index daba1df3716..1ee171c4091 100644 --- a/easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2-foss-2022a.eb +++ b/easybuild/easyconfigs/p/python-mujoco/python-mujoco-2.2.2-foss-2022a.eb @@ -51,4 +51,4 @@ exts_list = [ sanity_pip_check = True -moduleclass = 'lib' +moduleclass = 'phys' From a18e8467cb8db19dedc34e79d9d4294b231de099 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Jul 2023 12:14:45 +0200 Subject: [PATCH 7981/9987] change base for intel/2023.03 to GCCcore/12.3.0 --- .../i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb | 2 +- .../easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb | 4 ++-- easybuild/easyconfigs/i/intel/intel-2023.03.eb | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb index 6e886d07ac1..f890b966ec3 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb @@ -11,6 +11,6 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/718d sources = ['l_mpi_oneapi_p_%(version)s.43482_offline.sh'] checksums = ['5c170cdf26901311408809ced28498b630a494428703685203ceef6e62735ef8'] -dependencies = [('UCX', '1.14.0')] +dependencies = [('UCX', '1.14.1')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb index 91d2ec40b6e..58579245be7 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb @@ -28,10 +28,10 @@ checksums = [ '7639af4b6c928e9e3ba92297a054f78a55f4f4d0db9db0d144cc6653004e4f24'}, ] -local_gccver = '12.2.0' +local_gccver = '12.3.0' dependencies = [ ('GCCcore', local_gccver), - ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('binutils', '2.40', '', ('GCCcore', local_gccver)), ] moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2023.03.eb b/easybuild/easyconfigs/i/intel/intel-2023.03.eb index 9c71d4bc13e..a57e1ebc96e 100644 --- a/easybuild/easyconfigs/i/intel/intel-2023.03.eb +++ b/easybuild/easyconfigs/i/intel/intel-2023.03.eb @@ -9,10 +9,10 @@ description = "Compiler toolchain including Intel compilers, Intel MPI and Intel toolchain = SYSTEM local_comp_ver = '2023.1.0' -local_gccver = '12.2.0' +local_gccver = '12.3.0' dependencies = [ ('GCCcore', local_gccver), - ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('binutils', '2.40', '', ('GCCcore', local_gccver)), ('intel-compilers', local_comp_ver), ('impi', '2021.9.0', '', ('intel-compilers', local_comp_ver)), ('imkl', local_comp_ver, '', SYSTEM), From c04c93c350cc715245278c3fd8e38139045d4137 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 Jul 2023 13:30:28 +0200 Subject: [PATCH 7982/9987] adding easyconfigs: Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.5.3.eb, Horovod-0.28.1-foss-2021b-CUDA-11.4.1-TensorFlow-2.7.1.eb, Horovod-0.28.1-foss-2021b-CUDA-11.4.1-TensorFlow-2.8.4.eb, Horovod-0.28.1-foss-2022a-CUDA-11.7.0-TensorFlow-2.11.0.eb, Horovod-0.28.1-foss-2022a-CUDA-11.7.0-TensorFlow-2.9.1.eb and patches: Horovod-0.28.1_support_flatbuffers_2.0.6.patch --- ...foss-2021a-CUDA-11.3.1-TensorFlow-2.5.3.eb | 48 ++++++++ ...foss-2021b-CUDA-11.4.1-TensorFlow-2.7.1.eb | 45 +++++++ ...foss-2021b-CUDA-11.4.1-TensorFlow-2.8.4.eb | 45 +++++++ ...oss-2022a-CUDA-11.7.0-TensorFlow-2.11.0.eb | 49 ++++++++ ...foss-2022a-CUDA-11.7.0-TensorFlow-2.9.1.eb | 49 ++++++++ ...vod-0.28.1_support_flatbuffers_2.0.6.patch | 110 ++++++++++++++++++ 6 files changed, 346 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.5.3.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.4.1-TensorFlow-2.7.1.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.4.1-TensorFlow-2.8.4.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-TensorFlow-2.11.0.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-TensorFlow-2.9.1.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1_support_flatbuffers_2.0.6.patch diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.5.3.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.5.3.eb new file mode 100644 index 00000000000..fbf6e95ce61 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.5.3.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.22.1' +local_tf_version = '2.5.3' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-TensorFlow-%s' % local_tf_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('CMake', '3.20.1'), +] +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('NCCL', '2.10.3', local_cuda_suffix), + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('TensorFlow', local_tf_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +# Bug in CMake causes a race condition on horovod_cuda_kernels_generated_cuda_kernels.cu.o.NVCC-depend +maxparallel = 1 + +exts_list = [ + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('horovod', version, { + 'checksums': ['c45bfcb9bd96852d79c62976eda12e9320b58b64f55bee3772877b3fc6243f2a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.4.1-TensorFlow-2.7.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.4.1-TensorFlow-2.7.1.eb new file mode 100644 index 00000000000..055e911b986 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.4.1-TensorFlow-2.7.1.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_tf_version = '2.7.1' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-TensorFlow-%s' % local_tf_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('CMake', '3.21.1'), +] +dependencies = [ + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), + ('CUDA', '11.4.1', '', SYSTEM), + ('NCCL', '2.10.3', local_cuda_suffix), + ('TensorFlow', local_tf_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.4.1-TensorFlow-2.8.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.4.1-TensorFlow-2.8.4.eb new file mode 100644 index 00000000000..36db415d50f --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.4.1-TensorFlow-2.8.4.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_tf_version = '2.8.4' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-TensorFlow-%s' % local_tf_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('CMake', '3.21.1'), +] +dependencies = [ + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), + ('CUDA', '11.4.1', '', SYSTEM), + ('NCCL', '2.10.3', local_cuda_suffix), + ('TensorFlow', local_tf_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-TensorFlow-2.11.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-TensorFlow-2.11.0.eb new file mode 100644 index 00000000000..32fac5e88fe --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-TensorFlow-2.11.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_tf_version = '2.11.0' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-TensorFlow-%s' % local_tf_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('CUDA', '11.7.0', '', SYSTEM), + ('NCCL', '2.12.12', local_cuda_suffix), + ('TensorFlow', local_tf_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'patches': ['Horovod-0.28.1_support_flatbuffers_2.0.6.patch'], + 'checksums': [ + '92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0', + '9696ffb3b2bad1d6dd5a9f37bc58078ca7c585f933bcbec037036ad9fc0b297d', + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-TensorFlow-2.9.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-TensorFlow-2.9.1.eb new file mode 100644 index 00000000000..b27e65b21c4 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-TensorFlow-2.9.1.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_tf_version = '2.9.1' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-TensorFlow-%s' % local_tf_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('CUDA', '11.7.0', '', SYSTEM), + ('NCCL', '2.12.12', local_cuda_suffix), + ('TensorFlow', local_tf_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'patches': ['Horovod-0.28.1_support_flatbuffers_2.0.6.patch'], + 'checksums': [ + '92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0', + '9696ffb3b2bad1d6dd5a9f37bc58078ca7c585f933bcbec037036ad9fc0b297d', + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1_support_flatbuffers_2.0.6.patch b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1_support_flatbuffers_2.0.6.patch new file mode 100644 index 00000000000..e2284062b1f --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1_support_flatbuffers_2.0.6.patch @@ -0,0 +1,110 @@ +TF 2.10+ (for us: 2.9+) use flatbuffers 2.0.6 which horovod isn't yet compatible with, +see https://github.com/horovod/horovod/issues/3956 + +Manually update the calls +Author: Alexander Grund (TU Dresden) + +diff --git a/horovod/common/wire/message_generated.h b/horovod/common/wire/message_generated.h +index 33d46e2..9a7f856 100644 +--- a/horovod/common/wire/message_generated.h ++++ b/horovod/common/wire/message_generated.h +@@ -279,18 +279,18 @@ struct Request FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_REQUEST_RANK) && +- VerifyField(verifier, VT_REQUEST_TYPE) && +- VerifyField(verifier, VT_TENSOR_TYPE) && ++ VerifyField(verifier, VT_REQUEST_RANK, 4) && ++ VerifyField(verifier, VT_REQUEST_TYPE, 1) && ++ VerifyField(verifier, VT_TENSOR_TYPE, 1) && + VerifyOffset(verifier, VT_TENSOR_NAME) && + verifier.VerifyString(tensor_name()) && +- VerifyField(verifier, VT_ROOT_RANK) && +- VerifyField(verifier, VT_DEVICE) && ++ VerifyField(verifier, VT_ROOT_RANK, 4) && ++ VerifyField(verifier, VT_DEVICE, 4) && + VerifyOffset(verifier, VT_TENSOR_SHAPE) && + verifier.VerifyVector(tensor_shape()) && +- VerifyField(verifier, VT_PRESCALE_FACTOR) && +- VerifyField(verifier, VT_POSTSCALE_FACTOR) && +- VerifyField(verifier, VT_REDUCE_OP) && ++ VerifyField(verifier, VT_PRESCALE_FACTOR, 8) && ++ VerifyField(verifier, VT_POSTSCALE_FACTOR, 8) && ++ VerifyField(verifier, VT_REDUCE_OP, 1) && + verifier.EndTable(); + } + }; +@@ -411,7 +411,7 @@ struct RequestList FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + VerifyOffset(verifier, VT_REQUESTS) && + verifier.VerifyVector(requests()) && + verifier.VerifyVectorOfTables(requests()) && +- VerifyField(verifier, VT_SHUTDOWN) && ++ VerifyField(verifier, VT_SHUTDOWN, 1) && + verifier.EndTable(); + } + }; +@@ -504,7 +504,7 @@ struct Response FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + } + bool Verify(flatbuffers::Verifier &verifier) const { + return VerifyTableStart(verifier) && +- VerifyField(verifier, VT_RESPONSE_TYPE) && ++ VerifyField(verifier, VT_RESPONSE_TYPE, 1) && + VerifyOffset(verifier, VT_TENSOR_NAMES) && + verifier.VerifyVector(tensor_names()) && + verifier.VerifyVectorOfStrings(tensor_names()) && +@@ -514,11 +514,11 @@ struct Response FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + verifier.VerifyVector(devices()) && + VerifyOffset(verifier, VT_TENSOR_SIZES) && + verifier.VerifyVector(tensor_sizes()) && +- VerifyField(verifier, VT_TENSOR_TYPE) && +- VerifyField(verifier, VT_PRESCALE_FACTOR) && +- VerifyField(verifier, VT_POSTSCALE_FACTOR) && +- VerifyField(verifier, VT_LAST_JOINED_RANK) && +- VerifyField(verifier, VT_REDUCE_OP) && ++ VerifyField(verifier, VT_TENSOR_TYPE, 1) && ++ VerifyField(verifier, VT_PRESCALE_FACTOR, 8) && ++ VerifyField(verifier, VT_POSTSCALE_FACTOR, 8) && ++ VerifyField(verifier, VT_LAST_JOINED_RANK, 4) && ++ VerifyField(verifier, VT_REDUCE_OP, 1) && + verifier.EndTable(); + } + }; +@@ -641,7 +641,7 @@ struct ResponseList FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + VerifyOffset(verifier, VT_RESPONSES) && + verifier.VerifyVector(responses()) && + verifier.VerifyVectorOfTables(responses()) && +- VerifyField(verifier, VT_SHUTDOWN) && ++ VerifyField(verifier, VT_SHUTDOWN, 1) && + verifier.EndTable(); + } + }; +diff --git a/horovod/tensorflow/custom_call_config_generated.h b/horovod/tensorflow/custom_call_config_generated.h +index 1406a2f..0e2543a 100644 +--- a/horovod/tensorflow/custom_call_config_generated.h ++++ b/horovod/tensorflow/custom_call_config_generated.h +@@ -109,18 +109,18 @@ struct CustomCallConfig FLATBUFFERS_FINAL_CLASS : private flatbuffers::Table { + return VerifyTableStart(verifier) && + VerifyOffset(verifier, VT_TENSOR_NAME) && + verifier.VerifyString(tensor_name()) && +- VerifyField(verifier, VT_TENSOR_TYPE) && ++ VerifyField(verifier, VT_TENSOR_TYPE, 1) && + VerifyOffset(verifier, VT_INPUT_SHAPES) && + verifier.VerifyVector(input_shapes()) && + verifier.VerifyVectorOfTables(input_shapes()) && + VerifyOffset(verifier, VT_OUTPUT_SHAPES) && + verifier.VerifyVector(output_shapes()) && + verifier.VerifyVectorOfTables(output_shapes()) && +- VerifyField(verifier, VT_PRESCALE_FACTOR) && +- VerifyField(verifier, VT_POSTSCALE_FACTOR) && +- VerifyField(verifier, VT_ROOT_RANK) && +- VerifyField(verifier, VT_REDUCE_OP) && +- VerifyField(verifier, VT_PROCESS_SET_ID) && ++ VerifyField(verifier, VT_PRESCALE_FACTOR, 4) && ++ VerifyField(verifier, VT_POSTSCALE_FACTOR, 4) && ++ VerifyField(verifier, VT_ROOT_RANK, 4) && ++ VerifyField(verifier, VT_REDUCE_OP, 4) && ++ VerifyField(verifier, VT_PROCESS_SET_ID, 4) && + verifier.EndTable(); + } + }; From d6d26e07001438eb98ebbf38438c3d4e5de8c034 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 Jul 2023 13:31:32 +0200 Subject: [PATCH 7983/9987] adding easyconfigs: Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.11.0.eb, Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.12.1.eb, Horovod-0.28.1-foss-2021b-CUDA-11.5.2-PyTorch-1.12.1.eb, Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb, Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.1.eb, Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb, Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb --- ...1-foss-2021a-CUDA-11.3.1-PyTorch-1.11.0.eb | 48 +++++++++++++++++++ ...1-foss-2021a-CUDA-11.3.1-PyTorch-1.12.1.eb | 48 +++++++++++++++++++ ...1-foss-2021b-CUDA-11.5.2-PyTorch-1.12.1.eb | 48 +++++++++++++++++++ ...1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 48 +++++++++++++++++++ ...1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.1.eb | 48 +++++++++++++++++++ ...1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb | 48 +++++++++++++++++++ ...vod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb | 43 +++++++++++++++++ 7 files changed, 331 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.11.0.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.12.1.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.5.2-PyTorch-1.12.1.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.1.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.11.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.11.0.eb new file mode 100644 index 00000000000..c5bb81abe26 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.11.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_pt_version = '1.11.0' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. +This build only has PyTorch enabled.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('CMake', '3.20.1'), +] +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('CUDA', '11.3.1', '', SYSTEM), + ('NCCL', '2.10.3', local_cuda_suffix), + ('PyTorch', local_pt_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["horovodrun --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.12.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.12.1.eb new file mode 100644 index 00000000000..6768a32d62e --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.12.1.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_pt_version = '1.12.1' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. +This build only has PyTorch enabled.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('CMake', '3.20.1'), +] +dependencies = [ + ('Python', '3.9.5'), + ('PyYAML', '5.4.1'), + ('CUDA', '11.3.1', '', SYSTEM), + ('NCCL', '2.10.3', local_cuda_suffix), + ('PyTorch', local_pt_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["horovodrun --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.5.2-PyTorch-1.12.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.5.2-PyTorch-1.12.1.eb new file mode 100644 index 00000000000..3d12f136c42 --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2021b-CUDA-11.5.2-PyTorch-1.12.1.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_pt_version = '1.12.1' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. +This build only has PyTorch enabled.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('CMake', '3.21.1'), +] +dependencies = [ + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), + ('CUDA', '11.5.2', '', SYSTEM), + ('NCCL', '2.10.3', local_cuda_suffix), + ('PyTorch', local_pt_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["horovodrun --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..d2c40bc50ae --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_pt_version = '1.12.0' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. +This build only has PyTorch enabled.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('CUDA', '11.7.0', '', SYSTEM), + ('NCCL', '2.12.12', local_cuda_suffix), + ('PyTorch', local_pt_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["horovodrun --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.1.eb new file mode 100644 index 00000000000..d385ae1932e --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.12.1.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_pt_version = '1.12.1' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. +This build only has PyTorch enabled.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('CUDA', '11.7.0', '', SYSTEM), + ('NCCL', '2.12.12', local_cuda_suffix), + ('PyTorch', local_pt_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["horovodrun --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb new file mode 100644 index 00000000000..4473bc2e53c --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_pt_version = '1.13.1' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. +This build only has PyTorch enabled.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('CUDA', '11.7.0', '', SYSTEM), + ('NCCL', '2.12.12', local_cuda_suffix), + ('PyTorch', local_pt_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["horovodrun --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb new file mode 100644 index 00000000000..3d2eb91b26c --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-fosscuda-2020b-PyTorch-1.9.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_pt_version = '1.9.0' +versionsuffix = '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +builddependencies = [ + ('CMake', '3.18.4'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1'), + ('NCCL', '2.8.3', '-CUDA-%(cudaver)s'), + ('PyTorch', local_pt_version), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From d56668895b1caffbe1444fead2df7a23cfee4ede Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 5 Jul 2023 14:19:51 +0200 Subject: [PATCH 7984/9987] Remove wrong EC --- ...1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb | 48 ------------------- 1 file changed, 48 deletions(-) delete mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb deleted file mode 100644 index 4473bc2e53c..00000000000 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb +++ /dev/null @@ -1,48 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Horovod' -version = '0.28.1' -local_pt_version = '1.13.1' -local_cuda_suffix = '-CUDA-%(cudaver)s' -versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version - -homepage = 'https://github.com/uber/horovod' -description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. -This build only has PyTorch enabled.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -builddependencies = [ - ('CMake', '3.23.1'), -] -dependencies = [ - ('Python', '3.10.4'), - ('PyYAML', '6.0'), - ('CUDA', '11.7.0', '', SYSTEM), - ('NCCL', '2.12.12', local_cuda_suffix), - ('PyTorch', local_pt_version, local_cuda_suffix), -] - -use_pip = True -sanity_pip_check = True - -preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' -preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' - -exts_list = [ - ('cloudpickle', '2.2.1', { - 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], - }), - ('horovod', version, { - 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], - }), -] - -sanity_check_paths = { - 'files': ['bin/horovodrun'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["horovodrun --help"] - -moduleclass = 'tools' From b2995874de46cecb3207ae255c0b6ebcb89e067b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Jul 2023 12:18:32 +0200 Subject: [PATCH 7985/9987] promote foss/2023.05 to foss/2023a --- ...I-3.3.10-gompi-2023.05.eb => FFTW.MPI-3.3.10-gompi-2023a.eb} | 2 +- easybuild/easyconfigs/f/foss/{foss-2023.05.eb => foss-2023a.eb} | 2 +- easybuild/easyconfigs/g/gfbf/{gfbf-2023.05.eb => gfbf-2023a.eb} | 2 +- .../easyconfigs/g/gompi/{gompi-2023.05.eb => gompi-2023a.eb} | 2 +- .../h/HPL/{HPL-2.3-foss-2023.05.eb => HPL-2.3-foss-2023a.eb} | 2 +- ...mpi-2023.05.eb => OSU-Micro-Benchmarks-7.1-1-gompi-2023a.eb} | 2 +- ....0-gompi-2023.05-fb.eb => ScaLAPACK-2.2.0-gompi-2023a-fb.eb} | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/f/FFTW.MPI/{FFTW.MPI-3.3.10-gompi-2023.05.eb => FFTW.MPI-3.3.10-gompi-2023a.eb} (90%) rename easybuild/easyconfigs/f/foss/{foss-2023.05.eb => foss-2023a.eb} (97%) rename easybuild/easyconfigs/g/gfbf/{gfbf-2023.05.eb => gfbf-2023a.eb} (95%) rename easybuild/easyconfigs/g/gompi/{gompi-2023.05.eb => gompi-2023a.eb} (95%) rename easybuild/easyconfigs/h/HPL/{HPL-2.3-foss-2023.05.eb => HPL-2.3-foss-2023a.eb} (94%) rename easybuild/easyconfigs/o/OSU-Micro-Benchmarks/{OSU-Micro-Benchmarks-7.1-1-gompi-2023.05.eb => OSU-Micro-Benchmarks-7.1-1-gompi-2023a.eb} (92%) rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.2.0-gompi-2023.05-fb.eb => ScaLAPACK-2.2.0-gompi-2023a-fb.eb} (96%) diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023.05.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023a.eb similarity index 90% rename from easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023.05.eb rename to easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023a.eb index f62882baa61..e7c6416b64e 100644 --- a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023.05.eb +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023a.eb @@ -5,7 +5,7 @@ homepage = 'https://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.""" -toolchain = {'name': 'gompi', 'version': '2023.05'} +toolchain = {'name': 'gompi', 'version': '2023a'} toolchainopts = {'pic': True} source_urls = [homepage] diff --git a/easybuild/easyconfigs/f/foss/foss-2023.05.eb b/easybuild/easyconfigs/f/foss/foss-2023a.eb similarity index 97% rename from easybuild/easyconfigs/f/foss/foss-2023.05.eb rename to easybuild/easyconfigs/f/foss/foss-2023a.eb index 5fffa227468..d1f0461c876 100644 --- a/easybuild/easyconfigs/f/foss/foss-2023.05.eb +++ b/easybuild/easyconfigs/f/foss/foss-2023a.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'foss' -version = '2023.05' +version = '2023a' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' description = """GNU Compiler Collection (GCC) based compiler toolchain, including diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2023.05.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2023a.eb similarity index 95% rename from easybuild/easyconfigs/g/gfbf/gfbf-2023.05.eb rename to easybuild/easyconfigs/g/gfbf/gfbf-2023a.eb index f77e8efd7d8..e36028da349 100644 --- a/easybuild/easyconfigs/g/gfbf/gfbf-2023.05.eb +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2023a.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'gfbf' -version = '2023.05' +version = '2023a' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including diff --git a/easybuild/easyconfigs/g/gompi/gompi-2023.05.eb b/easybuild/easyconfigs/g/gompi/gompi-2023a.eb similarity index 95% rename from easybuild/easyconfigs/g/gompi/gompi-2023.05.eb rename to easybuild/easyconfigs/g/gompi/gompi-2023a.eb index c04bdc52a3a..142e0492f73 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2023.05.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2023a.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'gompi' -version = '2023.05' +version = '2023a' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023.05.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023a.eb similarity index 94% rename from easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023.05.eb rename to easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023a.eb index 646e1fac7b3..c43eaacea0d 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023.05.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023a.eb @@ -6,7 +6,7 @@ description = """HPL is a software package that solves a (random) dense linear s arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark.""" -toolchain = {'name': 'foss', 'version': '2023.05'} +toolchain = {'name': 'foss', 'version': '2023a'} toolchainopts = {'usempi': True} source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-gompi-2023.05.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-gompi-2023a.eb similarity index 92% rename from easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-gompi-2023.05.eb rename to easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-gompi-2023a.eb index 5701c50be05..97bc224f423 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-gompi-2023.05.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-gompi-2023a.eb @@ -6,7 +6,7 @@ version = '7.1-1' homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' description = """OSU Micro-Benchmarks""" -toolchain = {'name': 'gompi', 'version': '2023.05'} +toolchain = {'name': 'gompi', 'version': '2023a'} toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023.05-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023a-fb.eb similarity index 96% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023.05-fb.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023a-fb.eb index 62bf4aa61dc..8653a36db29 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023.05-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023a-fb.eb @@ -6,7 +6,7 @@ homepage = 'https://www.netlib.org/scalapack/' description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.""" -toolchain = {'name': 'gompi', 'version': '2023.05'} +toolchain = {'name': 'gompi', 'version': '2023a'} toolchainopts = {'pic': True} source_urls = [homepage] From 233902d1a348f633adf1e0ccee709b7c2bd31de6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Jul 2023 19:17:20 +0200 Subject: [PATCH 7986/9987] add extra patch files for PyTorch 1.13.1 to fix failing tests --- .../p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index af5f58752a4..b6a1e3ca5b2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -14,6 +14,7 @@ patches = [ 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', @@ -21,7 +22,7 @@ patches = [ 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_fix-vsx-loadu.patch', - 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', 'PyTorch-1.13.1_fix-pytest-args.patch', 'PyTorch-1.13.1_fix-test-ops-conf.patch', 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', @@ -38,6 +39,8 @@ checksums = [ {'PyTorch-1.11.0_fix-fsdp-fp16-test.patch': 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13'}, {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.1_add-hypothesis-suppression.patch': + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, @@ -48,10 +51,8 @@ checksums = [ '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d'}, {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, - {'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch': - '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d'}, - {'PyTorch-1.13.1_fix-pytest-args.patch': - 'd3e3c841cf8d73683750f29326f2be56ee0bb5df7ff522baf7d7c3f301a91ec2'}, + {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-pytest-args.patch': 'd3e3c841cf8d73683750f29326f2be56ee0bb5df7ff522baf7d7c3f301a91ec2'}, {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '4c636059850fc9d1ecb27ce275f8aad5d5b6fdc19e35aff0c25b86cb3201352a'}, {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': @@ -62,8 +63,7 @@ checksums = [ 'd53e98bf0da7788b68042dcc31bc5708dae962fde3f110cc827eb807a5d08e49'}, {'PyTorch-1.13.1_install-vsx-vec-headers.patch': '7b678f54bb947afd4767f5877ac424b4b94ce5db609ea20f5a869ccf4027035f'}, - {'PyTorch-1.13.1_skip-failing-grad-test.patch': - '6681200f9509893cb9231b5c93ac9bc5e6d9d9ae4febefca52e7cbc843ba8f51'} + {'PyTorch-1.13.1_skip-failing-grad-test.patch': '6681200f9509893cb9231b5c93ac9bc5e6d9d9ae4febefca52e7cbc843ba8f51'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] From 9b233a36e5d89df8f305650f075eaeea465ddd89 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 5 Jul 2023 19:41:36 +0200 Subject: [PATCH 7987/9987] adding easyconfigs: CUDA-12.2.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.2.0.eb | 24 +++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.2.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.2.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.2.0.eb new file mode 100644 index 00000000000..d6ea95abd16 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.2.0.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.2.0' +local_nv_version = '535.54.03' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + 'ecf3d2afadcbac029f0f4505785810d52d006e4b87ba79ff3f984336a2bbf518', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'f7b5fde5f727b51c380c6199200d0525e8585475944ff8ad2791d06734f54230', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '9c90d79bb63952cd30f1f57f9f8fe11e7a8967bba6f824df45d3464b5d37e5d8' +}] + +moduleclass = 'system' From c22960b8c087380a555929b7311132c2175b93fb Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 6 Jul 2023 09:11:57 +0100 Subject: [PATCH 7988/9987] update source url for pkgconf --- easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb | 2 +- easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb | 2 +- easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb | 2 +- easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb index 072e68192e4..0d6dab08f33 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.2.0.eb @@ -10,7 +10,7 @@ description = """pkgconf is a program which helps to configure compiler and link toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d7b6fdb522d81c11f5a0e0a0629a9f5480809ec90e595058674c1517822dfb8c'] diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb index 2acde1a41bd..cffdf67d1da 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-11.3.0.eb @@ -10,7 +10,7 @@ description = """pkgconf is a program which helps to configure compiler and link toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d7b6fdb522d81c11f5a0e0a0629a9f5480809ec90e595058674c1517822dfb8c'] diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb index 8dfe1dd56e7..710f2739928 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0.eb @@ -10,7 +10,7 @@ description = """pkgconf is a program which helps to configure compiler and link toolchain = SYSTEM -source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d7b6fdb522d81c11f5a0e0a0629a9f5480809ec90e595058674c1517822dfb8c'] diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb index bd5895c7aa0..2d47decfa86 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.3-GCCcore-12.2.0.eb @@ -10,7 +10,7 @@ description = """pkgconf is a program which helps to configure compiler and link toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['6d73ac21a9410f5cc636acf730f3a5bf46b28d1e18a239c89efc4b2c5548792f'] diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb index 6e817cde0bd..c80ab34d708 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb @@ -10,7 +10,7 @@ description = """pkgconf is a program which helps to configure compiler and link toolchain = {'name': 'GCCcore', 'version': '13.1.0'} -source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['d6b844ab6bf8ca685e9ef8103dee64fb39b2484c7a18da64ae5ba269514c9f78'] diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb index 716412bd025..1896354cb61 100644 --- a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb @@ -10,7 +10,7 @@ description = """pkgconf is a program which helps to configure compiler and link toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['6466efd2e38c4c0ac5de4e345f0dc6dad57e689efb08c31f2a71547683d20dc7'] From a4d4ad9ca0f633f899f204bc9364667dcf5be946 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Jul 2023 13:20:17 +0200 Subject: [PATCH 7989/9987] adding easyconfigs: CppHeaderParser-2.7.4-GCCcore-11.3.0.eb --- .../CppHeaderParser-2.7.4-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/CppHeaderParser/CppHeaderParser-2.7.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CppHeaderParser/CppHeaderParser-2.7.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CppHeaderParser/CppHeaderParser-2.7.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..1f46c06f3b6 --- /dev/null +++ b/easybuild/easyconfigs/c/CppHeaderParser/CppHeaderParser-2.7.4-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'CppHeaderParser' +version = '2.7.4' + +homepage = 'https://senexcanis.com/open-source/cppheaderparser' +description = """CppHeaderParser is a pure python module that will parse C++ +header files and generate a data structure representing the class.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + (name, version, { + 'modulename': False, + 'checksums': ['382b30416d95b0a5e8502b214810dcac2a56432917e2651447d3abe253e3cc42'], + }), +] + +fix_python_shebang_for = [ + 'lib/python%(pyshortver)s/site-packages/CppHeaderParser/*.py', + 'lib/python%(pyshortver)s/site-packages/CppHeaderParser/examples/*.py', +] + +moduleclass = 'lib' From 5f56482973ac5e93d7fdfde9fd29e0709805e074 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 6 Jul 2023 14:05:22 +0200 Subject: [PATCH 7990/9987] adding easyconfigs: centerline-1.0.1-foss-2022a.eb --- .../centerline/centerline-1.0.1-foss-2022a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/centerline/centerline-1.0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/centerline/centerline-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/c/centerline/centerline-1.0.1-foss-2022a.eb new file mode 100644 index 00000000000..c5a191ca98d --- /dev/null +++ b/easybuild/easyconfigs/c/centerline/centerline-1.0.1-foss-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'centerline' +version = '1.0.1' + +homepage = 'https://github.com/fitodic/centerline' +description = """ +Roads, rivers and similar linear structures are often represented by long and complex polygons. +Since one of the most important attributes of a linear structure is its length, extracting that +attribute from a polygon can prove to be more or less difficult. +This library tries to solve this problem by creating the the polygon's centerline using the +Voronoi diagram. For more info on how to use this package, see the official documentation. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Fiona', '1.8.21'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['f5d44ea81bece7338146286a9ad4bb080c27055aa6177907f49e51d624d8e12b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 7f7b7e3a16f3fab34600f93537be13117043edf7 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 6 Jul 2023 12:16:28 +0000 Subject: [PATCH 7991/9987] Rename patch for newer toolchains to avoid checksum errors on older toolchains --- .../bcl2fastq2-2.20.0-GCC-11.3.0.eb | 4 +- .../bcl2fastq2-2.20.0-GCC-12.2.0.eb | 4 +- ...-fix-cmake-target-libs-GCC-11.3-plus.patch | 41 +++++++++++++++++++ 3 files changed, 45 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs-GCC-11.3-plus.patch diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb index c90abb48c6f..36126288a90 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-11.3.0.eb @@ -16,13 +16,13 @@ sources = [{ 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz }] patches = [ - '%(name)s-%(version)s-fix-cmake-target-libs.patch', + '%(name)s-%(version)s-fix-cmake-target-libs-GCC-11.3-plus.patch', # bcl2fastq2 v2.20.0 is not compatible with recent Boost versions, use bundled Boost '%(name)s-%(version)s-find-boost.patch', ] checksums = [ {'bcl2fastq2-v2-20-0-tar.zip': '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3'}, - {'bcl2fastq2-2.20.0-fix-cmake-target-libs.patch': + {'bcl2fastq2-2.20.0-fix-cmake-target-libs-GCC-11.3-plus.patch': '3f2736a8335b533646e25093f02bbbcf1aa629c68a0433b9bb5d66fadaa28edb'}, {'bcl2fastq2-2.20.0-find-boost.patch': '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1'}, ] diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-12.2.0.eb index ed8b4174d37..d857a5fb37a 100644 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-GCC-12.2.0.eb @@ -16,13 +16,13 @@ sources = [{ 'extract_cmd': 'unzip -p %s | tar -xzvf -', # source file is a .zip that contains a .tar.gz }] patches = [ - '%(name)s-%(version)s-fix-cmake-target-libs.patch', + '%(name)s-%(version)s-fix-cmake-target-libs-GCC-11.3-plus.patch', # bcl2fastq2 v2.20.0 is not compatible with recent Boost versions, use bundled Boost '%(name)s-%(version)s-find-boost.patch', ] checksums = [ {'bcl2fastq2-v2-20-0-tar.zip': '8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3'}, - {'bcl2fastq2-2.20.0-fix-cmake-target-libs.patch': + {'bcl2fastq2-2.20.0-fix-cmake-target-libs-GCC-11.3-plus.patch': '3f2736a8335b533646e25093f02bbbcf1aa629c68a0433b9bb5d66fadaa28edb'}, {'bcl2fastq2-2.20.0-find-boost.patch': '8ca9ab8843fd21976781185b0d560f97fa83c26ab7962c339c2206b164d845c1'}, ] diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs-GCC-11.3-plus.patch b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs-GCC-11.3-plus.patch new file mode 100644 index 00000000000..20af200d155 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs-GCC-11.3-plus.patch @@ -0,0 +1,41 @@ +find and set appropriate targets for libxml2 and libxslt libraries found in the system +author: Alex Domingo (Vrije Universiteit Brussel) +--- src/cmake/cxxConfigure.cmake.orig 2017-06-22 19:14:50.000000000 +0200 ++++ src/cmake/cxxConfigure.cmake 2021-06-03 00:46:03.509256295 +0200 +@@ -101,6 +101,9 @@ + if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) + find_package_version(LibXml2 ${BCL2FASTQ_LIBXML2_VERSION}) + find_package_version(LibXslt ${BCL2FASTQ_LIBXSLT_VERSION}) ++ find_library_env(LIBXML2 libxml/xpath.h xml2) ++ find_library_env(LIBEXSLT libexslt/exslt.h exslt) ++ find_library_env(LIBXSLT libxslt/xsltconfig.h xslt) + endif((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) + + if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) +--- src/cmake/bcl2fastq_redist_macros.cmake.orig 2017-06-22 19:14:50.000000000 +0200 ++++ src/cmake/bcl2fastq_redist_macros.cmake 2021-06-03 00:45:41.825960000 +0200 +@@ -103,4 +103,25 @@ + + endmacro(find_library_redist name pathhint header) + ++# ++# Find a library in environment, assume version will be correct ++# ++macro(find_library_env name header library) ++ unset(${name}_LIBRARIES CACHE) ++ # Try explicit static first with regular as fallback (no-op if already found) ++ find_library(${name}_LIBRARIES NAMES ${CMAKE_STATIC_LIBRARY_PREFIX}${library}${CMAKE_STATIC_LIBRARY_SUFFIX} PATHS ENV LIBRARY_PATH NO_DEFAULT_PATH) ++ find_library(${name}_LIBRARIES NAMES ${library} PATHS ENV LIBRARY_PATH NO_DEFAULT_PATH) ++ ++ message(STATUS "Find library ${name}: ${${name}_LIBRARIES}") ++ # Search for include path ++ unset(${name}_INCLUDE_DIR CACHE) ++ find_path(${name}_INCLUDE_DIR ${header} PATHS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH NO_DEFAULT_PATH) ++ ++ if(${name}_INCLUDE_DIR AND ${name}_LIBRARIES) ++ set (HAVE_${name} true CACHE BOOL "lib bool" FORCE) ++ message (STATUS "Found ${name} header: ${${name}_INCLUDE_DIR}/${header}") ++ message (STATUS "Found ${name} library: ${${name}_LIBRARIES}") ++ endif() ++ ++endmacro() From 4df3dcc4c6ef33af48863bae4907078528688550 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 6 Jul 2023 13:38:30 +0100 Subject: [PATCH 7992/9987] Delete bcl2fastq2-2.20.0-fix-cmake-target-libs.patch --- ...2fastq2-2.20.0-fix-cmake-target-libs.patch | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch deleted file mode 100644 index 20af200d155..00000000000 --- a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch +++ /dev/null @@ -1,41 +0,0 @@ -find and set appropriate targets for libxml2 and libxslt libraries found in the system -author: Alex Domingo (Vrije Universiteit Brussel) ---- src/cmake/cxxConfigure.cmake.orig 2017-06-22 19:14:50.000000000 +0200 -+++ src/cmake/cxxConfigure.cmake 2021-06-03 00:46:03.509256295 +0200 -@@ -101,6 +101,9 @@ - if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) - find_package_version(LibXml2 ${BCL2FASTQ_LIBXML2_VERSION}) - find_package_version(LibXslt ${BCL2FASTQ_LIBXSLT_VERSION}) -+ find_library_env(LIBXML2 libxml/xpath.h xml2) -+ find_library_env(LIBEXSLT libexslt/exslt.h exslt) -+ find_library_env(LIBXSLT libxslt/xsltconfig.h xslt) - endif((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) - - if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) ---- src/cmake/bcl2fastq_redist_macros.cmake.orig 2017-06-22 19:14:50.000000000 +0200 -+++ src/cmake/bcl2fastq_redist_macros.cmake 2021-06-03 00:45:41.825960000 +0200 -@@ -103,4 +103,25 @@ - - endmacro(find_library_redist name pathhint header) - -+# -+# Find a library in environment, assume version will be correct -+# -+macro(find_library_env name header library) -+ unset(${name}_LIBRARIES CACHE) -+ # Try explicit static first with regular as fallback (no-op if already found) -+ find_library(${name}_LIBRARIES NAMES ${CMAKE_STATIC_LIBRARY_PREFIX}${library}${CMAKE_STATIC_LIBRARY_SUFFIX} PATHS ENV LIBRARY_PATH NO_DEFAULT_PATH) -+ find_library(${name}_LIBRARIES NAMES ${library} PATHS ENV LIBRARY_PATH NO_DEFAULT_PATH) -+ -+ message(STATUS "Find library ${name}: ${${name}_LIBRARIES}") -+ # Search for include path -+ unset(${name}_INCLUDE_DIR CACHE) -+ find_path(${name}_INCLUDE_DIR ${header} PATHS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH NO_DEFAULT_PATH) -+ -+ if(${name}_INCLUDE_DIR AND ${name}_LIBRARIES) -+ set (HAVE_${name} true CACHE BOOL "lib bool" FORCE) -+ message (STATUS "Found ${name} header: ${${name}_INCLUDE_DIR}/${header}") -+ message (STATUS "Found ${name} library: ${${name}_LIBRARIES}") -+ endif() -+ -+endmacro() From 4894e4dd34e5a4995f48e655abd68cd51624d34e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 6 Jul 2023 14:41:06 +0200 Subject: [PATCH 7993/9987] add missing dep on binutils --- .../c/CppHeaderParser/CppHeaderParser-2.7.4-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CppHeaderParser/CppHeaderParser-2.7.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CppHeaderParser/CppHeaderParser-2.7.4-GCCcore-11.3.0.eb index 1f46c06f3b6..97be8af13e4 100644 --- a/easybuild/easyconfigs/c/CppHeaderParser/CppHeaderParser-2.7.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CppHeaderParser/CppHeaderParser-2.7.4-GCCcore-11.3.0.eb @@ -10,6 +10,7 @@ header files and generate a data structure representing the class.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} dependencies = [ + ('binutils', '2.38'), ('Python', '3.10.4'), ] From 73330f60c0faef8c825b25c00f4d4c5025ccf701 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 6 Jul 2023 13:38:26 +0000 Subject: [PATCH 7994/9987] Reinstate original patch for older toolchains --- ...2fastq2-2.20.0-fix-cmake-target-libs.patch | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch diff --git a/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch new file mode 100644 index 00000000000..0e1cfe2e2a3 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl2fastq2/bcl2fastq2-2.20.0-fix-cmake-target-libs.patch @@ -0,0 +1,44 @@ +find and set appropriate targets for libxml2 and libxslt libraries found in the system +author: Alex Domingo (Vrije Universiteit Brussel) +--- src/cmake/cxxConfigure.cmake.orig 2017-06-22 19:14:50.000000000 +0200 ++++ src/cmake/cxxConfigure.cmake 2021-06-03 00:46:03.509256295 +0200 +@@ -101,6 +101,9 @@ + if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) + find_package_version(LibXml2 ${BCL2FASTQ_LIBXML2_VERSION}) + find_package_version(LibXslt ${BCL2FASTQ_LIBXSLT_VERSION}) ++ find_library_env(LIBXML2 libxml/xpath.h xml2) ++ find_library_env(LIBEXSLT libexslt/exslt.h exslt) ++ find_library_env(LIBXSLT libxslt/xsltconfig.h xslt) + endif((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) + + if((NOT HAVE_LIBXML2) OR (NOT HAVE_LIBXSLT)) +--- src/cmake/bcl2fastq_redist_macros.cmake.orig 2017-06-22 19:14:50.000000000 +0200 ++++ src/cmake/bcl2fastq_redist_macros.cmake 2021-06-03 00:45:41.825960000 +0200 +@@ -103,4 +103,27 @@ + + endmacro(find_library_redist name pathhint header) + ++# ++# Find a library in environment, assume version will be correct ++# ++macro(find_library_env name header library) ++ unset(${name}_LIBRARIES CACHE) ++ # Search for library ++ unset(${name}_LIBRARIES CACHE) ++ find_library(${name}_LIBRARIES NAMES ${CMAKE_STATIC_LIBRARY_PREFIX}${library}${CMAKE_STATIC_LIBRARY_SUFFIX} HINTS ENV LIBRARY_PATH) ++ ++ message(STATUS "Find library ${namenolib}: ${${name}_LIBRARIES}") ++ # Search for include path ++ unset(${name}_INCLUDE_DIR CACHE) ++ string(TOLOWER ${name} namel) ++ find_path(${name}_INCLUDE_DIR ${header} HINTS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH) ++ set(${name}_INCLUDE_DIR ${${name}_INCLUDE_DIR} CACHE STRING "lib BOOL" FORCE) ++ ++ if(${name}_INCLUDE_DIR AND ${name}_LIBRARIES) ++ set (HAVE_${name} true CACHE BOOL "lib bool" FORCE) ++ message (STATUS "Found ${name} header: ${${name}_INCLUDE_DIR}/${header}") ++ message (STATUS "Found ${name} library: ${${name}_LIBRARY}") ++ endif(${name}_INCLUDE_DIR AND ${name}_LIBRARIES) ++ ++endmacro(find_library_env name pathhint header) + From 4243465bb5db665c032117df7bdeb2881542c371 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Jul 2023 19:14:49 +0200 Subject: [PATCH 7995/9987] {toolchain} intel/2023a --- .../easyconfigs/h/HPL/HPL-2.3-intel-2023a.eb | 21 ++++++++++++++++++ easybuild/easyconfigs/i/iimpi/iimpi-2023a.eb | 18 +++++++++++++++ .../imkl-FFTW-2023.1.0-iimpi-2023a.eb | 11 ++++++++++ easybuild/easyconfigs/i/intel/intel-2023a.eb | 22 +++++++++++++++++++ 4 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023a.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2023a.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023a.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2023a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023a.eb new file mode 100644 index 00000000000..2d3af45a7c4 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2023a.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2023a.eb new file mode 100644 index 00000000000..c9de798ba2f --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2023a.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2023a' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2023.1.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.9.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023a.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023a.eb new file mode 100644 index 00000000000..8dc2ddc903a --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023a.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2023.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2023a'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/intel/intel-2023a.eb b/easybuild/easyconfigs/i/intel/intel-2023a.eb new file mode 100644 index 00000000000..2b3f1b90ddc --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2023a.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2023a' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2023.1.0' +local_gccver = '12.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.40', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.9.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From 93efb2b88c4dc2f39b5313e859f3f59c34ca0e32 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 7 Jul 2023 09:57:45 +0800 Subject: [PATCH 7996/9987] prepare release notes for EasyBuild v4.8.0 + bump version to 4.8.0 --- RELEASE_NOTES | 77 ++++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 77 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 26d8721fa48..e26937b2606 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,84 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 17,098 easyconfig files, for 3,085 different software packages, +The latest version of easybuild-easyconfig provides 17,511 easyconfig files, for 3,161 different software packages, incl. 39 different (compiler) toolchains. +v4.8.0 (7 Jul 2023) +-------------------- + +feature release + +- added easyconfigs for foss/2023a (#18264) and intel/2023a (#18275) common toolchains +- added example easyconfig files for 76 new software packages: + - 3d-dna (#9258), affinity (#18051), AIMAll (#13153), alleleIntegrator (#17923), AlphaPulldown (#17774), + ASCAT (#17923), ASF-SearchAPI (#18179), ATAT (#18213), AutoDockSuite (#9678), axel (#10961), BayesPrism (#17885), + BGC-Bayesian-genomic-clines (#18005), CalculiX-CrunchiX (#16805), CASA (#18055), cctbx-base (#17774), + Circuitscape (#16720), CppHeaderParser (#18272), CuCLARK (#9482), cuteSV (#18077), DALI (#18204), DaliLite (#17989), + DEICODE (#18181), dm-haiku (#18013), dominate (#18086), dx-toolkit (#18232), easel (#18156), ecFlow (#15719), + EDirect (#17479), FragPipe (#18161), GEM (#18120), gemelli (#18120), GLIMPSE (#18163), GRIDSS (#18170), + HOOMD-blue (#18224), KerasTuner (#18197), LayoutParser (#18220), LISFLOOD-FP (#18194), LuaRocks (#18073), + mannkendall (#18043), MOB-suite (#16798), molecularGSM (#13150), MONAI-Label (#18180), MView (#18198), + NanoStat (#18201), oxDNA (#18214), pastml (#15336), pbipa (#18229), Perl-bundle-CPAN (#17970), PheWeb (#10951), + plinkliftover (#18136), pmt (#18052), PyBioLib (#18124), Pychopper (#10344), pydicom-seg (#18180), pyMannKendall (#18044), + pypmt (#18045), python-mujoco (#18253), pytorch-CycleGAN-pix2pix (#18086), PyTorch-Image-Models (#18220), PyWBGT (#17980), + Safetensors (#18220), Sniffles (#18048), strace (#14381), Structure_threader (#18219), subset-bam (#18032), SVclone (#18084), + SVIM (#18071), Tapenade (#18109), TensorFlow-Graphics (#17465), timm (#17787), Trinotate (#18124), Ultralytics (#17894), + visdom (#18086), wrapt (#18125), xclip (#17055), xdotool (#17055) +- added additional easyconfigs for various supported software packages, including: + - 3d dna, ABINIT 9.2.1, ABINIT 9.2.1, Abseil 20230125.2, affinity 20230524, affinity 20230524, AGAT 1.1.0, AIMAll 19.10.12, alleleCount 4.2.1, alleleIntegrator 0.8.8, AlphaPulldown 0.30.4, AlphaPulldown 0.30.4, AMS 2023.101, Anaconda3 2023.03, ANSYS 2023R1.eb, ASCAT 3.1.2, ASF SearchAPI, ATAT 3.36, attr 2.5.1, AUGUSTUS 3.5.0, Autoconf 2.71, Autoconf 2.71, AutoDock GPU, AutoDockSuite 4.2.6, Automake 1.16.5, Automake 1.16.5, Autotools 20220317, Autotools 20220317, axel 2.17.9, axel 2.17.9, Bandage 0.9.0, barrnap 0.9, BayesPrism 2.0, BayesTraits 3.0.2, BBMap 39.01, BGC Bayesian, binutils 2.40, BioPerl 1.7.8, Bismark 0.24.1, Bison 3.8.2, BLAST+ 2.14.0, BLAT 3.7, BLIS 0.9.0, boto3 1.26.163, Bowtie2 2.5.1, build 0.10.0, BUSCO 5.4.7, CalculiX CrunchiX, canu 2.2, CASA 6.5.5, ccache 4.6.3, cctbx base, cctbx base, CD HIT, Cellpose 2.2.2, Cellpose 2.2.2, CHERAB 1.4.0, CHERAB 1.4.0, Circuitscape 5.12.3, CLHEP 2.4.5.3, CLHEP 2.4.6.2, CmdStanR 0.5.2, CNVkit 0.9.10, corner 2.2.2, CppHeaderParser 2.7.4, CuCLARK 1.1, CUDA 12.1.1.eb, CUDA 12.2.0.eb, cuDNN 8.9.2.26, cutadapt 2.10, cutadapt 4.4, cuTENSOR 1.7.0.1, cuteSV 2.0.3, CVXOPT 1.3.1, DALI 2.1.2, DaliLite 4.1, Dalton 2020.1, datamash 1.8, deepTools 3.5.2, DEICODE 0.2.4, DendroPy 4.5.2, DIAMOND 2.1.8, dicom2nifti 2.3.0, DIRAC 23.0, DIRAC 23.0, dm haiku, DMTCP 3.0.0, dominate 2.8.0, dorado 0.3.0, dorado 0.3.1, dtcmp 1.1.4, duplex tools, dx toolkit, easel 0.48, EasyBuild 4.7.2.eb, ecFlow 5.7.0, EDirect 19.7.20230531, edlib 1.3.9, eggnog mapper, EIGENSOFT 7.2.1, elastix 5.0.0, ELPA 2021.11.001, Emacs 28.2, emcee 3.1.4, ETE 3.1.2, Exonerate 2.4.0, Extrae 4.0.4, FASTA 36.3.8i, fastp 0.20.1, fastp 0.23.4, FFTW 3.3.10, FFTW 3.3.10, FFTW.MPI 3.3.10, FLASH 2.2.00, flex 2.6.4, FlexiBLAS 3.3.1, FLUENT 2019R3.eb, fontconfig 2.14.2, foss 2023a.eb, FragPipe 20.0, FreeSurfer 7.4.0, FreeSurfer 7.4.0, FreeSurfer 7.4.0, freetype 2.13.0, GATE 9.2, GATK 4.4.0.0, GBprocesS 4.0.0.post1, GCC 11.4.0.eb, GCCcore 11.4.0.eb, GCTA 1.94.1, GDRCopy 2.3.1, Geant4 11.0.2, Geant4 11.1.2, Geant4 data, GEM 1.5.1, GEM 1.5.1, gemelli 0.0.9, GEMMA 0.98.5, gengetopt 2.23, GenomeTools 1.6.2, GetOrganelle 1.7.7.0, gfbf 2023a.eb, gffread 0.12.7, git 2.41.0, glew 2.2.0, GLIMPSE 2.0.0, GLIMPSE 2.0.0, GLIMPSE 2.0.0, GMAP GSNAP, GMAP GSNAP, GMP 6.2.1, gompi 2023a.eb, gperf 3.1, graphite2 1.3.14, GRIDSS 2.13.2, GROMACS 2019.4, GROMACS 2019.4, GROMACS 2019.4, GROMACS 2023.1, GROMACS 2023.1, GSL 2.7, Gurobi 10.0.1, HDF5 1.12.2, HDF5 1.12.2, help2man 1.49.3, hifiasm 0.19.5, Highway 1.0.4, HMMER 3.3.2, HOOMD blue, Horovod 0.25.0, HPL 2.3, HPL 2.3, hwloc 2.9.1, iimpi 2023a.eb, imagecodecs 2022.9.26, imkl FFTW, Infernal 1.1.4, intel 2023a.eb, InterProScan 5.62, intltool 0.51.0, IQ TREE, IQ TREE, ISA L, ITK 5.2.1, ITSTool 2.0.7, JAGS 4.3.2, jq 1.5, Julia 1.9.0, jxrlib 1.1, KerasTuner 1.3.5, kim api, LAMMPS 23Jun2022, LASTZ 1.02.00, LayoutParser 0.3.4, LayoutParser 0.3.4, LERC 4.0.0, libavif 0.11.1, libcircle 0.3, libde265 1.0.11, libevent 2.1.8, libfabric 1.18.0, libheif 1.16.2, libjxl 0.8.1, LibLZF 3.6, libpciaccess 0.17, libpspio 0.2.4, libpspio 0.2.4, libpspio 0.2.4, libSBML 5.19.0, libsodium 1.0.18, libtool 2.4.7, LISFLOOD FP, LISFLOOD FP, LMDB 0.9.29, LMfit 1.2.1, lpsolve 5.5.2.11, LSD2 2.4.1, LuaJIT 2.1.0, LuaRocks 3.9.2, lwgrp 1.0.5, lxml 4.9.2, M4 1.4.19, MAFFT 7.505, MAGeCK 0.5.9.5, mannkendall 1.1.1, MATLAB 2023a.eb, MaxQuant 2.4.2.0.eb, MCR R2022a.5.eb, MedPy 0.4.0, meshio 5.3.4, Meson 1.1.1, Mesquite 2.3.0, MetaEuk 6, minimap2 2.26, MITObim 1.9.1, MMseqs2 14, MOB suite, molecularGSM 20190826, MONAI Label, MONAI Label, MPFR 4.2.0, mpifileutils 0.11.1, MuJoCo 2.2.2, MultiQC 1.14, MUMmer 4.0.0rc1, MUSCLE 5.1.0, MUST 1.7.1, MView 1.67, NAMD 2.14, nanoget 1.18.1, nanomath 1.3.0, NanoStat 1.6.0, NanoStat 1.6.0, ncbi vdb, ncbi vdb, NCCL 2.18.3, NCO 5.0.6, ncurses 6.4.eb, netCDF 4.7.4, networkx 3.0, Nextflow 23.04.2.eb, ngspice 39, Ninja 1.11.1, nnU Net, ont fast5, OpenBLAS 0.3.23, OpenFOAM v2112, OpenMM 7.4.1, OpenMPI 4.1.5, OpenPGM 5.2.122, openpyxl 3.1.2, OSU Micro, oxDNA 3.5.2, pagmo 2.18.0, parasail 2.6.2, Paraver 4.11.1, ParaView 5.11.1, pastml 1.9.34, patchelf 0.18.0, pbipa 1.8.0, PEAR 0.9.11, Perl 5.36.1, Perl 5.36.1, Perl bundle, PheWeb 1.1.20, pigz 2.7, pkg config, plinkliftover 0.3.0, PLUMED 2.5.4, PLUMED 2.5.4, PMIx 4.2.4, pmt 1.1.0, popscle 0.1, popt 1.16, POT 0.9.0, prodigal 2.6.3, PSI4 1.7, psutil 5.9.4, psycopg2 2.9.6, PyBioLib 1.1.988, PyCalib 20230531, Pychopper 2.3.1, pycocotools 2.0.6, pydicom seg, pyfaidx 0.7.2.1, pygmo 2.18.0, pyiron 0.3.0, pyMannKendall 1.4.3, PyOpenCL 2021.2.13, pypmt 1.1.0, PyQtGraph 0.13.3, Pysam 0.21.0, pySCENIC 0.12.1, pyspoa 0.0.9, pyspoa 0.0.9, Python 3.11.3, python isal, python mujoco, python parasail, PyTorch 1.13.1, pytorch CycleGAN, PyTorch Image, PyTorch Image, PyWBGT 1.0.0, PyWBGT 1.0.0, PyYAML 6.0, qcat 1.1.0, QuantumESPRESSO 6.6, rasterio 1.3.8, regionmask 0.10.0, RNA SeQC, ROOT 6.26.06, RSEM 1.3.3, Ruby 3.2.2, Rust 1.70.0, Safetensors 0.3.1, Safetensors 0.3.1, samblaster 0.1.26, ScaFaCoS 1.0.4, ScaLAPACK 2.2.0, scArches 0.5.6, segemehl 0.3.4, SEPP 4.5.1, seqtk 1.4, SimpleITK 2.1.0, Sniffles 2.0.7, SortMeRNA 2.1, SPAdes 3.15.4, spoa 4.0.7, spoa 4.0.7, SRA Toolkit, STAR 2.7.10b, stardist 0.8.3, statsmodels 0.14.0, strace 5.14, Structure_threader 1.3.10, subset bam, Subversion 1.14.2, SuiteSparse 5.13.0, SUNDIALS 6.2.0, SUNDIALS 6.2.0, SUNDIALS 6.5.1, SVclone 1.1.2, SVIM 2.0.0, Tapenade 3.16, TensorFlow 2.8.4, TensorFlow 2.9.1, TensorFlow 2.9.1, TensorFlow Graphics, tidymodels 1.1.0, timm 0.6.13, tmux 3.3a, tmux 3.3a, tmux 3.3a.eb, tokenizers 0.13.3, TopHat 2.1.2, TopHat 2.1.2, torchaudio 0.12.0, torchaudio 0.12.0, TransDecoder 5.5.0, Transformers 4.29.2, Transformers 4.30.2, Triangle 1.6, Trinity 2.15.1, Trinotate 4.0.1, UCC 1.2.0, UCC CUDA, UCX 1.14.1, UCX CUDA, Ultralytics 8.0.92, util linux, VASP 6.3.2, visdom 0.2.4, Voro++ 0.4.6, VTK 9.0.1, VTK 9.2.6, WhatsHap 1.7, wrapt 1.15.0, wrapt 1.15.0, X11 20230603, xarray 2023.4.2, xclip 0.13, xdotool 3.20211022.1, Xerces C++, Xerces C++, XlsxWriter 3.1.2, XML LibXML, xorg macros, yaml cpp, Yasm 1.3.0, ZeroMQ 4.3.4, zfp 1.0.0, zlib 1.2.13, zlib ng, Zopfli 1.0.3 +- minor enhancements, including: + - add CI check for -DCMAKE_BUILD_TYPE, should use build_type instead (#14008) + - enhance sanity check for recent LibTIFF easyconfigs (#17975) + - update JupyterLab v3.5.0 to set JUPYTERLAB_SETTINGS_DIR and JUPYTERLAB_WORKSPACES_DIR on module load (#17982) + - add RBesT extension to R 4.2.1 + 4.2.2 (+ missing epitools extension for R 4.2.2) (#18029) + - add svglite extension to R 4.2.1 + 4.2.2 (#18063) + - add FKSUM + haldensify extensions to R 4.2.2 (#18122) + - use custom easyblock for Rust 1.65.0 (#18174) and Rust 1.70.0 (#18167) + - update easyconfig for Nextflow 23.04.2 to use `install_cmds` (#18173) + - add Polychrome, shinycssloaders, princurve extensions to R 4.2.2 (#18195) + - add TrajectoryUtils + slingshot extensions to R-bundle-Bioconductor 3.16 (#18196) + - add extra packages to recent R easyconfigs (#18245) + - add extra packages to recent R-bundle-Bioconductor easyconfigs (#18246) +- various bug fixes, including: + - add patches to fix TensorFlow 2.7.1 on POWER (#16795) + - fix TensorFlow-2.8.4-foss-2021b.eb (#17058) + - stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2 (#17998) + - add pkgconfig as build dependency for nodejs , required for finding ICU dependency (#18007) + - fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530 (#18030) + - update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add missing dependencies (#18041) + - fix --sanity-check-only for MAGeCK v0.5.9.4 (#18047) + - enable building static libs and check for libexslt.* in libxslt (#18064) + - add -pthread flag for dorado (#18072) + - add missing patch files for Qt5 5.15.2 to fix build problems with glibc 2.34 (#18087) + - add missing pkgconf build dependency for XML-LibXML v2.0208 (#18159) + - update homepage for NWChem 7.x (#18184) + - update homepage for SUNDIALS 5.x and 6.x (#18186) + - add missing source_urls for SimpleITK (#18212) + - patch oxDNA/oxpy to use correct pip install prefix (#18214) + - patch files for QT5-5.17.7-GCCcore-12.20.0.eb for SIGSTKSZ in glibc 2.34 (#18230) + - fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17) (#18231) + - fix CUDA build of recent TensorFlow easyconfigs when using compiler symlinks (#18235) + - use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 (#18236) + - update source_urls for Velvet 1.2.10 (#18237) + - use upstream patch for symbol compatibility in XZ 5.2.5 (#18250) + - update source url for pkgconf (#18271) +- other changes: + - stop running easyconfig unit tests with Python 2.7 (#18006) + - fix toolchain for networkx-3.0 foss-2022b -> gfbf-2022b (#18061) + - remove unused PyTorch patch (#18062) + - allow multiply dependency variants of ncbi-vdb for SRA-TOolkit per easyconfigs generation, as long as versions match (#18098) + - use UCC 1.2.0 as dependency for OpenMPI 4.1.5 (component for foss/2023a toolchain) (#18127) + - use PMIx 4.2.4 as dependency for OpenMPI 4.1.5 (component for foss/2023a toolchain) (#18144) + - remove old UCC (1.1.0) from GCCcore 12.3.0 (#18145) + - bump OpenSSL 1.1 wrapper fallback to 1.1.1u (#18188) + - remove default `separate_build_dir = True` and `build_type = 'Release'` from double-conversion (#18222) + - remove default `separate_build_dir = True` and `CMAKE_BUILD_TYPE=Release` from MariaDB (#18223) + - remove incorrect '-Dgallium-drivers=swrast' configure option in ROOT easyconfigs (#18260) + - change base for intel/2023.03 to GCCcore/12.3.0 (#18263) + + v4.7.2 (27 May 2023) -------------------- @@ -99,6 +173,7 @@ update/bugfix release - bump versions in Java wrappers to latest builds that include ppc64le: Java/8.362, Java/11.0.8, Java/17.0.6 (#17775) - move Arb and polymake to gfbf/foss since FLINT is now at gfbf/foss (#17869) + v4.7.1 (March 20th 2023) ------------------------ diff --git a/setup.py b/setup.py index cf3a30f7d86..9a351bf2919 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.7.3.dev0' +VERSION = '4.8.0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 21b41ce6dcce8204847a3037df1f4462daf2a4df Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Fri, 7 Jul 2023 09:26:56 +0200 Subject: [PATCH 7997/9987] Adding sanity check command Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/c/centerline/centerline-1.0.1-foss-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/centerline/centerline-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/c/centerline/centerline-1.0.1-foss-2022a.eb index c5a191ca98d..6c73ce42def 100644 --- a/easybuild/easyconfigs/c/centerline/centerline-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/centerline/centerline-1.0.1-foss-2022a.eb @@ -30,4 +30,6 @@ exts_list = [ sanity_pip_check = True +sanity_check_commands = ["create_centerlines --help"] + moduleclass = 'lib' From 0e2c2cf8232c1c5bc7963c67559a9b2322bd2086 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 7 Jul 2023 11:33:31 +0200 Subject: [PATCH 7998/9987] adding missing dependency libpng to pygame-2.1.0 --- easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb index 5f88ef0af90..22e0595ea3a 100644 --- a/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb @@ -22,6 +22,7 @@ dependencies = [ ('SDL2_mixer', '2.6.3'), ('SDL2_ttf', '2.20.2'), ('PortMidi', '2.0.4'), + ('libpng', '1.6.37'), ] use_pip = True From 93fb7a21a6106b7072c2d749db1abf73fc212cae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jul 2023 18:46:12 +0200 Subject: [PATCH 7999/9987] minor tweaks to release notes for EasyBuild v4.8.0 --- RELEASE_NOTES | 59 ++++++++++++++++++++++++++++++--------------------- 1 file changed, 35 insertions(+), 24 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index e26937b2606..f3ce7640d11 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -22,30 +22,45 @@ feature release EDirect (#17479), FragPipe (#18161), GEM (#18120), gemelli (#18120), GLIMPSE (#18163), GRIDSS (#18170), HOOMD-blue (#18224), KerasTuner (#18197), LayoutParser (#18220), LISFLOOD-FP (#18194), LuaRocks (#18073), mannkendall (#18043), MOB-suite (#16798), molecularGSM (#13150), MONAI-Label (#18180), MView (#18198), - NanoStat (#18201), oxDNA (#18214), pastml (#15336), pbipa (#18229), Perl-bundle-CPAN (#17970), PheWeb (#10951), - plinkliftover (#18136), pmt (#18052), PyBioLib (#18124), Pychopper (#10344), pydicom-seg (#18180), pyMannKendall (#18044), - pypmt (#18045), python-mujoco (#18253), pytorch-CycleGAN-pix2pix (#18086), PyTorch-Image-Models (#18220), PyWBGT (#17980), - Safetensors (#18220), Sniffles (#18048), strace (#14381), Structure_threader (#18219), subset-bam (#18032), SVclone (#18084), - SVIM (#18071), Tapenade (#18109), TensorFlow-Graphics (#17465), timm (#17787), Trinotate (#18124), Ultralytics (#17894), - visdom (#18086), wrapt (#18125), xclip (#17055), xdotool (#17055) + NanoStat (#18201), oxDNA (#18175 + #18214), pastml (#15336), pbipa (#18229), Perl-bundle-CPAN (#17970), PheWeb (#10951), + plinkliftover (#18136), pmt (#18052), PyBioLib (#18124), Pychopper (#10344), pydicom-seg (#18180), + pyMannKendall (#18044), pypmt (#18045), python-mujoco (#18253), pytorch-CycleGAN-pix2pix (#18086), + PyTorch-Image-Models (#18220), PyWBGT (#17980), Safetensors (#18220), Sniffles (#18048), strace (#14381), + Structure_threader (#18219), subset-bam (#18032), SVclone (#18084), SVIM (#18071), Tapenade (#18109), + TensorFlow-Graphics (#17465), timm (#17787), Trinotate (#18124), Ultralytics (#17894), visdom (#18086), + wrapt (#18125), xclip (#17055), xdotool (#17055) - added additional easyconfigs for various supported software packages, including: - - 3d dna, ABINIT 9.2.1, ABINIT 9.2.1, Abseil 20230125.2, affinity 20230524, affinity 20230524, AGAT 1.1.0, AIMAll 19.10.12, alleleCount 4.2.1, alleleIntegrator 0.8.8, AlphaPulldown 0.30.4, AlphaPulldown 0.30.4, AMS 2023.101, Anaconda3 2023.03, ANSYS 2023R1.eb, ASCAT 3.1.2, ASF SearchAPI, ATAT 3.36, attr 2.5.1, AUGUSTUS 3.5.0, Autoconf 2.71, Autoconf 2.71, AutoDock GPU, AutoDockSuite 4.2.6, Automake 1.16.5, Automake 1.16.5, Autotools 20220317, Autotools 20220317, axel 2.17.9, axel 2.17.9, Bandage 0.9.0, barrnap 0.9, BayesPrism 2.0, BayesTraits 3.0.2, BBMap 39.01, BGC Bayesian, binutils 2.40, BioPerl 1.7.8, Bismark 0.24.1, Bison 3.8.2, BLAST+ 2.14.0, BLAT 3.7, BLIS 0.9.0, boto3 1.26.163, Bowtie2 2.5.1, build 0.10.0, BUSCO 5.4.7, CalculiX CrunchiX, canu 2.2, CASA 6.5.5, ccache 4.6.3, cctbx base, cctbx base, CD HIT, Cellpose 2.2.2, Cellpose 2.2.2, CHERAB 1.4.0, CHERAB 1.4.0, Circuitscape 5.12.3, CLHEP 2.4.5.3, CLHEP 2.4.6.2, CmdStanR 0.5.2, CNVkit 0.9.10, corner 2.2.2, CppHeaderParser 2.7.4, CuCLARK 1.1, CUDA 12.1.1.eb, CUDA 12.2.0.eb, cuDNN 8.9.2.26, cutadapt 2.10, cutadapt 4.4, cuTENSOR 1.7.0.1, cuteSV 2.0.3, CVXOPT 1.3.1, DALI 2.1.2, DaliLite 4.1, Dalton 2020.1, datamash 1.8, deepTools 3.5.2, DEICODE 0.2.4, DendroPy 4.5.2, DIAMOND 2.1.8, dicom2nifti 2.3.0, DIRAC 23.0, DIRAC 23.0, dm haiku, DMTCP 3.0.0, dominate 2.8.0, dorado 0.3.0, dorado 0.3.1, dtcmp 1.1.4, duplex tools, dx toolkit, easel 0.48, EasyBuild 4.7.2.eb, ecFlow 5.7.0, EDirect 19.7.20230531, edlib 1.3.9, eggnog mapper, EIGENSOFT 7.2.1, elastix 5.0.0, ELPA 2021.11.001, Emacs 28.2, emcee 3.1.4, ETE 3.1.2, Exonerate 2.4.0, Extrae 4.0.4, FASTA 36.3.8i, fastp 0.20.1, fastp 0.23.4, FFTW 3.3.10, FFTW 3.3.10, FFTW.MPI 3.3.10, FLASH 2.2.00, flex 2.6.4, FlexiBLAS 3.3.1, FLUENT 2019R3.eb, fontconfig 2.14.2, foss 2023a.eb, FragPipe 20.0, FreeSurfer 7.4.0, FreeSurfer 7.4.0, FreeSurfer 7.4.0, freetype 2.13.0, GATE 9.2, GATK 4.4.0.0, GBprocesS 4.0.0.post1, GCC 11.4.0.eb, GCCcore 11.4.0.eb, GCTA 1.94.1, GDRCopy 2.3.1, Geant4 11.0.2, Geant4 11.1.2, Geant4 data, GEM 1.5.1, GEM 1.5.1, gemelli 0.0.9, GEMMA 0.98.5, gengetopt 2.23, GenomeTools 1.6.2, GetOrganelle 1.7.7.0, gfbf 2023a.eb, gffread 0.12.7, git 2.41.0, glew 2.2.0, GLIMPSE 2.0.0, GLIMPSE 2.0.0, GLIMPSE 2.0.0, GMAP GSNAP, GMAP GSNAP, GMP 6.2.1, gompi 2023a.eb, gperf 3.1, graphite2 1.3.14, GRIDSS 2.13.2, GROMACS 2019.4, GROMACS 2019.4, GROMACS 2019.4, GROMACS 2023.1, GROMACS 2023.1, GSL 2.7, Gurobi 10.0.1, HDF5 1.12.2, HDF5 1.12.2, help2man 1.49.3, hifiasm 0.19.5, Highway 1.0.4, HMMER 3.3.2, HOOMD blue, Horovod 0.25.0, HPL 2.3, HPL 2.3, hwloc 2.9.1, iimpi 2023a.eb, imagecodecs 2022.9.26, imkl FFTW, Infernal 1.1.4, intel 2023a.eb, InterProScan 5.62, intltool 0.51.0, IQ TREE, IQ TREE, ISA L, ITK 5.2.1, ITSTool 2.0.7, JAGS 4.3.2, jq 1.5, Julia 1.9.0, jxrlib 1.1, KerasTuner 1.3.5, kim api, LAMMPS 23Jun2022, LASTZ 1.02.00, LayoutParser 0.3.4, LayoutParser 0.3.4, LERC 4.0.0, libavif 0.11.1, libcircle 0.3, libde265 1.0.11, libevent 2.1.8, libfabric 1.18.0, libheif 1.16.2, libjxl 0.8.1, LibLZF 3.6, libpciaccess 0.17, libpspio 0.2.4, libpspio 0.2.4, libpspio 0.2.4, libSBML 5.19.0, libsodium 1.0.18, libtool 2.4.7, LISFLOOD FP, LISFLOOD FP, LMDB 0.9.29, LMfit 1.2.1, lpsolve 5.5.2.11, LSD2 2.4.1, LuaJIT 2.1.0, LuaRocks 3.9.2, lwgrp 1.0.5, lxml 4.9.2, M4 1.4.19, MAFFT 7.505, MAGeCK 0.5.9.5, mannkendall 1.1.1, MATLAB 2023a.eb, MaxQuant 2.4.2.0.eb, MCR R2022a.5.eb, MedPy 0.4.0, meshio 5.3.4, Meson 1.1.1, Mesquite 2.3.0, MetaEuk 6, minimap2 2.26, MITObim 1.9.1, MMseqs2 14, MOB suite, molecularGSM 20190826, MONAI Label, MONAI Label, MPFR 4.2.0, mpifileutils 0.11.1, MuJoCo 2.2.2, MultiQC 1.14, MUMmer 4.0.0rc1, MUSCLE 5.1.0, MUST 1.7.1, MView 1.67, NAMD 2.14, nanoget 1.18.1, nanomath 1.3.0, NanoStat 1.6.0, NanoStat 1.6.0, ncbi vdb, ncbi vdb, NCCL 2.18.3, NCO 5.0.6, ncurses 6.4.eb, netCDF 4.7.4, networkx 3.0, Nextflow 23.04.2.eb, ngspice 39, Ninja 1.11.1, nnU Net, ont fast5, OpenBLAS 0.3.23, OpenFOAM v2112, OpenMM 7.4.1, OpenMPI 4.1.5, OpenPGM 5.2.122, openpyxl 3.1.2, OSU Micro, oxDNA 3.5.2, pagmo 2.18.0, parasail 2.6.2, Paraver 4.11.1, ParaView 5.11.1, pastml 1.9.34, patchelf 0.18.0, pbipa 1.8.0, PEAR 0.9.11, Perl 5.36.1, Perl 5.36.1, Perl bundle, PheWeb 1.1.20, pigz 2.7, pkg config, plinkliftover 0.3.0, PLUMED 2.5.4, PLUMED 2.5.4, PMIx 4.2.4, pmt 1.1.0, popscle 0.1, popt 1.16, POT 0.9.0, prodigal 2.6.3, PSI4 1.7, psutil 5.9.4, psycopg2 2.9.6, PyBioLib 1.1.988, PyCalib 20230531, Pychopper 2.3.1, pycocotools 2.0.6, pydicom seg, pyfaidx 0.7.2.1, pygmo 2.18.0, pyiron 0.3.0, pyMannKendall 1.4.3, PyOpenCL 2021.2.13, pypmt 1.1.0, PyQtGraph 0.13.3, Pysam 0.21.0, pySCENIC 0.12.1, pyspoa 0.0.9, pyspoa 0.0.9, Python 3.11.3, python isal, python mujoco, python parasail, PyTorch 1.13.1, pytorch CycleGAN, PyTorch Image, PyTorch Image, PyWBGT 1.0.0, PyWBGT 1.0.0, PyYAML 6.0, qcat 1.1.0, QuantumESPRESSO 6.6, rasterio 1.3.8, regionmask 0.10.0, RNA SeQC, ROOT 6.26.06, RSEM 1.3.3, Ruby 3.2.2, Rust 1.70.0, Safetensors 0.3.1, Safetensors 0.3.1, samblaster 0.1.26, ScaFaCoS 1.0.4, ScaLAPACK 2.2.0, scArches 0.5.6, segemehl 0.3.4, SEPP 4.5.1, seqtk 1.4, SimpleITK 2.1.0, Sniffles 2.0.7, SortMeRNA 2.1, SPAdes 3.15.4, spoa 4.0.7, spoa 4.0.7, SRA Toolkit, STAR 2.7.10b, stardist 0.8.3, statsmodels 0.14.0, strace 5.14, Structure_threader 1.3.10, subset bam, Subversion 1.14.2, SuiteSparse 5.13.0, SUNDIALS 6.2.0, SUNDIALS 6.2.0, SUNDIALS 6.5.1, SVclone 1.1.2, SVIM 2.0.0, Tapenade 3.16, TensorFlow 2.8.4, TensorFlow 2.9.1, TensorFlow 2.9.1, TensorFlow Graphics, tidymodels 1.1.0, timm 0.6.13, tmux 3.3a, tmux 3.3a, tmux 3.3a.eb, tokenizers 0.13.3, TopHat 2.1.2, TopHat 2.1.2, torchaudio 0.12.0, torchaudio 0.12.0, TransDecoder 5.5.0, Transformers 4.29.2, Transformers 4.30.2, Triangle 1.6, Trinity 2.15.1, Trinotate 4.0.1, UCC 1.2.0, UCC CUDA, UCX 1.14.1, UCX CUDA, Ultralytics 8.0.92, util linux, VASP 6.3.2, visdom 0.2.4, Voro++ 0.4.6, VTK 9.0.1, VTK 9.2.6, WhatsHap 1.7, wrapt 1.15.0, wrapt 1.15.0, X11 20230603, xarray 2023.4.2, xclip 0.13, xdotool 3.20211022.1, Xerces C++, Xerces C++, XlsxWriter 3.1.2, XML LibXML, xorg macros, yaml cpp, Yasm 1.3.0, ZeroMQ 4.3.4, zfp 1.0.0, zlib 1.2.13, zlib ng, Zopfli 1.0.3 + - AGAT 1.1.0, alleleCount 4.2.1, AMS 2023.101, ANSYS 2023R1, BayesTraits 3.0.2, Bismark 0.24.1, BLAST+ 2.14.0, + boto3 1.26.163, Bowtie2 2.5.1, BUSCO 5.4.7, Cellpose 2.2.2, CHERAB 1.4.0, CmdStanR 0.5.2, CNVkit 0.9.10, + corner 2.2.2, CUDA 12.1.1 + 12.2.0, cuDNN 8.9.2.26, cutadapt 4.4, cuTENSOR 1.7.0.1, CVXOPT 1.3.1, Dalton 2020.1, + datamash 1.8, deepTools 3.5.2, DIAMOND 2.1.8, DMTCP 3.0.0, dorado 0.3.0 + 0.3.1, dtcmp 1.1.4, duplex-tools 0.3.3, + elastix 5.0.0, Emacs 28.2, emcee 3.1.4, Extrae 4.0.4, fastp 0.23.4, FlexiBLAS 3.3.1, fontconfig 2.14.2, + FreeSurfer 7.4.0, freetype 2.13.0, GATK 4.4.0.0, GBprocesS 4.0.0.post1, GCC 11.4.0, GCTA 1.94.1, GDRCopy 2.3.1, + Geant4 11.1.2, Geant4-data 11.1, GetOrganelle 1.7.7.0, git 2.41.0, GMAP-GSNAP 2023-04-20, GROMACS 2023.1, + hifiasm 0.19.5, Horovod 0.25.0, hwloc 2.9.1, InterProScan 5.62, IQ-TREE 2.2.2.3, ITSTool 2.0.7, JAGS 4.3.2, + Julia 1.9.0, libfabric 1.18.0, libheif 1.16.2, libjxl 0.8.1, LibLZF 3.6, LMfit 1.2.1, LSD2 2.4.1, LuaJIT 2.1.0, + lwgrp 1.0.5, MAGeCK 0.5.9.5, MATLAB 2023a, MaxQuant 2.4.2.0.eb, MCR R2022a.5, meshio 5.3.4, Meson 1.1.1, + minimap2 2.26, MMseqs2 14-7e284, mpifileutils 0.11.1, MuJoCo 2.2.2, nanomath 1.3.0, ncbi-vdb 3.0.5, NCCL 2.18.3, + Nextflow 23.04.2, ngspice 39, ont-fast5-api 4.1.1, OpenBLAS 0.3.23, OpenMPI 4.1.5, openpyxl 3.1.2, + OSU-Micro-Benchmarks 7.1-1, parasail 2.6.2, Paraver 4.11.1, ParaView 5.11.1, patchelf 0.18.0, Perl 5.36.1, + PMIx 4.2.4, POT 0.9.0, PSI4 1.7, psutil 5.9.4, psycopg2 2.9.6, PyCalib 20230531, pycocotools 2.0.6, + pyfaidx 0.7.2.1, pyiron 0.3.0, PyQtGraph 0.13.3, Pysam 0.21.0, pySCENIC 0.12.1, pyspoa 0.0.9, Python 3.11.3, + python-parasail 1.3.4, PyTorch 1.13.1, rasterio 1.3.8, regionmask 0.10.0, Ruby 3.2.2, Rust 1.70.0, ScaFaCoS 1.0.4, + seqtk 1.4, SRA-Toolkit 3.0.5, statsmodels 0.14.0, strace 5.14, Subversion 1.14.2, SUNDIALS 6.5.1, tidymodels 1.1.0, + tokenizers 0.13.3, torchaudio 0.12.0, TransDecoder 5.5.0, Transformers 4.29.2 + 4.30.2, UCC 1.2.0, UCC-CUDA 1.2.0, + UCX 1.14.1, UCX-CUDA 1.14.1, util-linux 2.39, VASP 6.3.2, VTK 9.2.6, WhatsHap 1.7, X11 20230603, xarray 2023.4.2, + XlsxWriter 3.1.2, XML-LibXML 2.0208, xorg-macros 1.20.0, zlib-ng 2.0.7 - minor enhancements, including: - add CI check for -DCMAKE_BUILD_TYPE, should use build_type instead (#14008) - enhance sanity check for recent LibTIFF easyconfigs (#17975) - - update JupyterLab v3.5.0 to set JUPYTERLAB_SETTINGS_DIR and JUPYTERLAB_WORKSPACES_DIR on module load (#17982) - - add RBesT extension to R 4.2.1 + 4.2.2 (+ missing epitools extension for R 4.2.2) (#18029) - - add svglite extension to R 4.2.1 + 4.2.2 (#18063) - - add FKSUM + haldensify extensions to R 4.2.2 (#18122) + - update JupyterLab v3.5.0 to set `$JUPYTERLAB_SETTINGS_DIR` and `$JUPYTERLAB_WORKSPACES_DIR` on loading of module (#17982) - use custom easyblock for Rust 1.65.0 (#18174) and Rust 1.70.0 (#18167) - update easyconfig for Nextflow 23.04.2 to use `install_cmds` (#18173) - - add Polychrome, shinycssloaders, princurve extensions to R 4.2.2 (#18195) - - add TrajectoryUtils + slingshot extensions to R-bundle-Bioconductor 3.16 (#18196) - - add extra packages to recent R easyconfigs (#18245) - - add extra packages to recent R-bundle-Bioconductor easyconfigs (#18246) + - add extra packages to recent R easyconfigs (#18029, #18063, #18122, #18195, #18245) + - add extra packages to recent R-bundle-Bioconductor easyconfigs (#18196, #18246) - various bug fixes, including: - add patches to fix TensorFlow 2.7.1 on POWER (#16795) - - fix TensorFlow-2.8.4-foss-2021b.eb (#17058) + - fix patches + extensions in easyconfig for TensorFlow 2.8.4 w/ foss/2021b (#17058) - stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2 (#17998) - add pkgconfig as build dependency for nodejs , required for finding ICU dependency (#18007) - fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530 (#18030) @@ -58,8 +73,7 @@ feature release - update homepage for NWChem 7.x (#18184) - update homepage for SUNDIALS 5.x and 6.x (#18186) - add missing source_urls for SimpleITK (#18212) - - patch oxDNA/oxpy to use correct pip install prefix (#18214) - - patch files for QT5-5.17.7-GCCcore-12.20.0.eb for SIGSTKSZ in glibc 2.34 (#18230) + - use patch files for Qt5 v5.17.7 to fix compatiblity with glibc 2.34 (#18230) - fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17) (#18231) - fix CUDA build of recent TensorFlow easyconfigs when using compiler symlinks (#18235) - use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 (#18236) @@ -68,17 +82,14 @@ feature release - update source url for pkgconf (#18271) - other changes: - stop running easyconfig unit tests with Python 2.7 (#18006) - - fix toolchain for networkx-3.0 foss-2022b -> gfbf-2022b (#18061) + - fix toolchain for networkx-3.0 (foss/2022b -> gfbf/2022b) (#18061) - remove unused PyTorch patch (#18062) - - allow multiply dependency variants of ncbi-vdb for SRA-TOolkit per easyconfigs generation, as long as versions match (#18098) - - use UCC 1.2.0 as dependency for OpenMPI 4.1.5 (component for foss/2023a toolchain) (#18127) - - use PMIx 4.2.4 as dependency for OpenMPI 4.1.5 (component for foss/2023a toolchain) (#18144) - - remove old UCC (1.1.0) from GCCcore 12.3.0 (#18145) + - allow multiple dependency variants of ncbi-vdb for SRA-TOolkit per easyconfigs generation, as long as versions match (#18098) - bump OpenSSL 1.1 wrapper fallback to 1.1.1u (#18188) - remove default `separate_build_dir = True` and `build_type = 'Release'` from double-conversion (#18222) - remove default `separate_build_dir = True` and `CMAKE_BUILD_TYPE=Release` from MariaDB (#18223) - remove incorrect '-Dgallium-drivers=swrast' configure option in ROOT easyconfigs (#18260) - - change base for intel/2023.03 to GCCcore/12.3.0 (#18263) + - change base compiler for intel/2023.03 to GCCcore/12.3.0 (required to use it as intel/2023a) (#18263) v4.7.2 (27 May 2023) From 3693353a06997caefecc7ca0164badab38542221 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jul 2023 21:39:36 +0200 Subject: [PATCH 8000/9987] add UCell extension to R-bundle-Bioconductor 3.16 --- .../R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index a117c707b50..cf9d68930ab 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -1241,6 +1241,9 @@ exts_list = [ ('ANCOMBC', '2.0.2', { 'checksums': ['e577ffe62a86090de9ea3743c84a4f3b34c3d645dcedff3c8af675b8c9b69136'], }), + ('UCell', '2.2.0', { + 'checksums': ['e3ca2b2d77a780a9450853e869bc10654c47485777d39a703203dc44d97df4bc'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From fe28fb0204a1586fe4f3e0e111b0ba6d4cf98591 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jul 2023 22:29:21 +0200 Subject: [PATCH 8001/9987] adding easyconfigs: EasyBuild-4.8.0.eb --- .../e/EasyBuild/EasyBuild-4.8.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.0.eb new file mode 100644 index 00000000000..8aa03116c7b --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.0.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.8.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/c5/99/f1debe9cd43817f3a71a7e27760668a824b6f679cacb69e6c4cc7b7833f5/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/be/07/f78fbbb52e635b24e74e8aab2177c6e39732ebd8c6904594d97f87942832/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/d4/c8/d2750fe1f56ca3fac2cf3453c9a0be1951cca4036b7285ee06941e5f7d72/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + {'easybuild-framework-4.8.0.tar.gz': '3ce1b0af247e3465b71829fadb8df92b6299224dc50053078bfb1d5672b7ae0f'}, + {'easybuild-easyblocks-4.8.0.tar.gz': '982ddca8ca6d0a43970484330f34127c2cffcf49833a2599fb30c8b2a0b06ab5'}, + {'easybuild-easyconfigs-4.8.0.tar.gz': '92334a53d28e7b75a1566446dba9e1cbd6ce5d039d104ae7c3ff4cf8c0385700'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 55321452bde12dd8f93e0806b90c39beff0ce91d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 7 Jul 2023 22:40:10 +0200 Subject: [PATCH 8002/9987] bump version to 4.8.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 9a351bf2919..a8bebcc31f8 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.8.0' +VERSION = '4.8.1.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 0a3fd15a41a538e25ddc619a3073ec7bec3596a7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 7 Jul 2023 23:35:01 +0200 Subject: [PATCH 8003/9987] adding easyconfigs: Z3-4.10.2-GCCcore-11.3.0-Python-3.10.4.eb, Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb, Z3-4.8.11-GCCcore-10.3.0-Python-3.9.5.eb, Z3-4.8.12-GCCcore-11.2.0-Python-3.9.6.eb, Z3-4.8.16-GCCcore-11.3.0-Python-3.10.4.eb, Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb --- .../Z3-4.10.2-GCCcore-11.3.0-Python-3.10.4.eb | 54 +++++++++++++++++++ .../Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb | 53 ++++++++++++++++++ .../Z3-4.8.11-GCCcore-10.3.0-Python-3.9.5.eb | 54 +++++++++++++++++++ .../Z3-4.8.12-GCCcore-11.2.0-Python-3.9.6.eb | 54 +++++++++++++++++++ .../Z3-4.8.16-GCCcore-11.3.0-Python-3.10.4.eb | 54 +++++++++++++++++++ .../Z3/Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb | 46 ++++++++++++++++ 6 files changed, 315 insertions(+) create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.10.2-GCCcore-11.3.0-Python-3.10.4.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.8.11-GCCcore-10.3.0-Python-3.9.5.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.8.12-GCCcore-11.2.0-Python-3.9.6.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.8.16-GCCcore-11.3.0-Python-3.10.4.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.10.2-GCCcore-11.3.0-Python-3.10.4.eb b/easybuild/easyconfigs/z/Z3/Z3-4.10.2-GCCcore-11.3.0-Python-3.10.4.eb new file mode 100644 index 00000000000..4a9bcec963d --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.10.2-GCCcore-11.3.0-Python-3.10.4.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.10.2' +versionsuffix = '-Python-%(pyver)s' +_z3_solver_version = '%s.0' % version + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3_solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('GMP', '6.2.1'), +] + +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py &&""" +_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py &&""" + +exts_list = [ + ('z3-solver', _z3_solver_version, { + 'modulename': 'z3', + 'checksums': ['a861081c8f5710996f3f545f12c1137ab38ba4b5b02f0f15d59ba52f6f81d237'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + "cd %%(installdir)s && ln -s %s/include include" % _z3_site_path, + "cd %%(installdir)s/lib && ln -s ../%s/lib/libz3.so libz3.so" % _z3_site_path, +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb new file mode 100644 index 00000000000..ab0584e8a8d --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.8.10-GCCcore-10.2.0-Python-3.8.6.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.8.10' +versionsuffix = '-Python-%(pyver)s' +_z3_solver_version = '%s.0' % version + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3_solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('GMP', '6.2.0'), +] + +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py &&""" +_enable_gmp = "sed -i 's/^GMP=.*/GMP=True/' core/scripts/mk_util.py &&" + +exts_list = [ + ('z3-solver', _z3_solver_version, { + 'modulename': 'z3', + 'checksums': ['cd022a66524685bdd8b265027bd22f24c35f8db29a4287d005e0005757ffdc21'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + "cd %%(installdir)s && ln -s %s/include include" % _z3_site_path, + "cd %%(installdir)s/lib && ln -s ../%s/lib/libz3.so libz3.so" % _z3_site_path, +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.11-GCCcore-10.3.0-Python-3.9.5.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.11-GCCcore-10.3.0-Python-3.9.5.eb new file mode 100644 index 00000000000..316ed3ebf17 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.8.11-GCCcore-10.3.0-Python-3.9.5.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.8.11' +versionsuffix = '-Python-%(pyver)s' +_z3_solver_version = '%s.0' % version + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3_solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('GMP', '6.2.1'), +] + +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py &&""" +_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py &&""" + +exts_list = [ + ('z3-solver', _z3_solver_version, { + 'modulename': 'z3', + 'checksums': ['3621f464baf48aabbf74bcb85cd97ef46e928af3ca3a28e27d6816601e3b7290'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + "cd %%(installdir)s && ln -s %s/include include" % _z3_site_path, + "cd %%(installdir)s/lib && ln -s ../%s/lib/libz3.so libz3.so" % _z3_site_path, +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.12-GCCcore-11.2.0-Python-3.9.6.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.12-GCCcore-11.2.0-Python-3.9.6.eb new file mode 100644 index 00000000000..a6e219907a5 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.8.12-GCCcore-11.2.0-Python-3.9.6.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.8.12' +versionsuffix = '-Python-%(pyver)s' +_z3_solver_version = '%s.0' % version + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3_solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('GMP', '6.2.1'), +] + +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py &&""" +_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py &&""" + +exts_list = [ + ('z3-solver', _z3_solver_version, { + 'modulename': 'z3', + 'checksums': ['48f66e52d5b267e6df6fab9fccdefdf7e09a846d9e309bc2dccff983c27da612'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + "cd %%(installdir)s && ln -s %s/include include" % _z3_site_path, + "cd %%(installdir)s/lib && ln -s ../%s/lib/libz3.so libz3.so" % _z3_site_path, +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.16-GCCcore-11.3.0-Python-3.10.4.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.16-GCCcore-11.3.0-Python-3.10.4.eb new file mode 100644 index 00000000000..37b6fb4f819 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.8.16-GCCcore-11.3.0-Python-3.10.4.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.8.16' +versionsuffix = '-Python-%(pyver)s' +_z3_solver_version = '%s.0' % version + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3_solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('GMP', '6.2.1'), +] + +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py &&""" +_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py &&""" + +exts_list = [ + ('z3-solver', _z3_solver_version, { + 'modulename': 'z3', + 'checksums': ['a84ade2852d4c3ca2ae32a3ddc554b8f3da6d5d69efd474b5627ab6db509e787'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + "cd %%(installdir)s && ln -s %s/include include" % _z3_site_path, + "cd %%(installdir)s/lib && ln -s ../%s/lib/libz3.so libz3.so" % _z3_site_path, +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..0780f885152 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakePythonPackage' + +name = 'Z3' +version = '4.8.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Z3Prover/z3' +description = "Z3 is a theorem prover from Microsoft Research." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +github_account = 'Z3Prover' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c9fd04b9b33be74fffaac3ec2bc2c320d1a4cc32e395203c55126b12a14ff3f4'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('GMP', '6.2.0'), +] + +local_py_srcdir = '%(builddir)s/z3-z3-%(version)s/src/api/python' +local_py_installdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +configopts = "-DZ3_USE_LIB_GMP=ON -DZ3_LINK_TIME_OPTIMIZATION=ON " +configopts += "-DZ3_BUILD_PYTHON_BINDINGS:BOOL=ON -DZ3_INSTALL_PYTHON_BINDINGS:BOOL=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR:PATH=lib " +configopts += "-DCMAKE_INSTALL_PYTHON_PKG_DIR:PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages " + +postinstallcmds = [ + # install egg-info of the python bindings to make pip aware of them + "cd %s && python setup.py install_egg_info -d %s" % (local_py_srcdir, local_py_installdir) +] + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'numlib' From 69048bef663ab5eeaf66739c575c41fb30ff1c18 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 7 Jul 2023 23:36:38 +0200 Subject: [PATCH 8004/9987] deleting easyconfig Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb --- .../Z3/Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb | 46 ------------------- 1 file changed, 46 deletions(-) delete mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/z/Z3/Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb deleted file mode 100644 index 0780f885152..00000000000 --- a/easybuild/easyconfigs/z/Z3/Z3-4.8.9-GCCcore-9.3.0-Python-3.8.2.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'CMakePythonPackage' - -name = 'Z3' -version = '4.8.9' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Z3Prover/z3' -description = "Z3 is a theorem prover from Microsoft Research." - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -toolchainopts = {'pic': True} - -github_account = 'Z3Prover' -source_urls = [GITHUB_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['c9fd04b9b33be74fffaac3ec2bc2c320d1a4cc32e395203c55126b12a14ff3f4'] - -builddependencies = [ - ('binutils', '2.34'), - ('CMake', '3.16.4'), -] - -dependencies = [ - ('Python', '3.8.2'), - ('GMP', '6.2.0'), -] - -local_py_srcdir = '%(builddir)s/z3-z3-%(version)s/src/api/python' -local_py_installdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' - -configopts = "-DZ3_USE_LIB_GMP=ON -DZ3_LINK_TIME_OPTIMIZATION=ON " -configopts += "-DZ3_BUILD_PYTHON_BINDINGS:BOOL=ON -DZ3_INSTALL_PYTHON_BINDINGS:BOOL=ON " -configopts += "-DCMAKE_INSTALL_LIBDIR:PATH=lib " -configopts += "-DCMAKE_INSTALL_PYTHON_PKG_DIR:PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages " - -postinstallcmds = [ - # install egg-info of the python bindings to make pip aware of them - "cd %s && python setup.py install_egg_info -d %s" % (local_py_srcdir, local_py_installdir) -] - -sanity_check_paths = { - 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], - 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'numlib' From 10db66bc709b33588fe6e20f53c7e4aebb2b395e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 8 Jul 2023 00:33:14 +0200 Subject: [PATCH 8005/9987] add Z3 as exception to Python verionsuffix test --- test/easyconfigs/easyconfigs.py | 41 ++++++++++++++++++--------------- 1 file changed, 22 insertions(+), 19 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 0025555b060..ad11f8d3f46 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1054,33 +1054,36 @@ def test_pr_python_packages(self): if exts_default_options.get(key) is None: failing_checks.append("'%s' should be set in exts_default_options in %s" % (key, ec_fn)) - # if Python is a dependency, that should be reflected in the versionsuffix + # if Python is a dependency, that should be reflected in the versionsuffix since v3.8.6 + has_recent_python3_dep = any(LooseVersion(dep['version']) >= LooseVersion('3.8.6') + for dep in ec['dependencies'] if dep['name'] == 'Python') + has_old_python_dep = any(LooseVersion(dep['version']) < LooseVersion('3.8.6') + for dep in ec['dependencies'] if dep['name'] == 'Python') # Tkinter is an exception, since its version always matches the Python version anyway - # Python 3.8.6 and later are also excluded, as we consider python 3 the default python - # Also whitelist some updated versions of Amber + # Z3 is an exception, since it has easyconfigs with and without Python bindings + exception_python_suffix = ['Tkinter', 'Z3'] + # Also whitelist some specific easyconfigs from this check + # TODO: clean whitelist in EB 5.0 whitelist_python_suffix = [ 'Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb', 'R-keras-2.1.6-foss-2018a-R-3.4.4.eb', ] whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix) - has_python_dep = any(LooseVersion(dep['version']) < LooseVersion('3.8.6') - for dep in ec['dependencies'] if dep['name'] == 'Python') - if has_python_dep and ec.name != 'Tkinter' and not whitelisted: - if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): - msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn - # This is only a failure for newly added ECs, not for existing ECS - # As that would probably break many ECs - if ec_fn in self.added_ecs_filenames: - failing_checks.append(msg) - else: - print('\nNote: Failed non-critical check: ' + msg) - else: - has_recent_python3_dep = any(LooseVersion(dep['version']) >= LooseVersion('3.8.6') - for dep in ec['dependencies'] if dep['name'] == 'Python') - if has_recent_python3_dep and re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): - msg = "'-Python-%%(pyver)s' should no longer be included in versionsuffix in %s" % ec_fn + + if ec.name in exception_python_suffix or whitelisted: + continue + elif has_old_python_dep and not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): + msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn + # This is only a failure for newly added ECs, not for existing ECS + # As that would probably break many ECs + if ec_fn in self.added_ecs_filenames: failing_checks.append(msg) + else: + print('\nNote: Failed non-critical check: ' + msg) + elif has_recent_python3_dep and re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): + msg = "'-Python-%%(pyver)s' should no longer be included in versionsuffix in %s" % ec_fn + failing_checks.append(msg) # require that running of "pip check" during sanity check is enabled via sanity_pip_check if easyblock in ['PythonBundle', 'PythonPackage']: From 149cdfd10bd6d5d904153af5ff447d44c1cb2151 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 8 Jul 2023 01:07:18 +0200 Subject: [PATCH 8006/9987] set JULIA_DEPOT_PATH with default value --- .../j/Julia/Julia-1.6.5-linux-x86_64.eb | 17 ++------- .../j/Julia/Julia-1.6.6-linux-x86_64.eb | 17 ++------- .../j/Julia/Julia-1.6.7-linux-x86_64.eb | 17 ++------- .../j/Julia/Julia-1.7.0-linux-x86_64.eb | 17 ++------- .../j/Julia/Julia-1.7.1-linux-x86_64.eb | 17 ++------- .../j/Julia/Julia-1.7.2-linux-x86_64.eb | 17 ++------- .../j/Julia/Julia-1.7.3-linux-x86_64.eb | 17 ++------- .../j/Julia/Julia-1.8.0-linux-x86_64.eb | 17 ++------- .../j/Julia/Julia-1.8.2-linux-x86_64.eb | 17 ++------- .../j/Julia/Julia-1.8.5-linux-x86_64.eb | 17 ++------- .../j/Julia/Julia-1.9.0-linux-x86_64.eb | 38 +++++++++++++++++++ 11 files changed, 78 insertions(+), 130 deletions(-) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb index b3c98820f76..45b365aa65d 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.5-linux-x86_64.eb @@ -28,20 +28,11 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] -_depot_paths = ':'.join([ - # first entry must be the user depot - # see https://pkgdocs.julialang.org/v1/glossary/ - '~/.julia', - # base installation of Julia - '%(installdir)s/share/julia', -]) - modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # by default JULIA_HISTORY points to top path in DEPOT_PATH - # set JULIA_HISTORY to always use the user depot (~/.julia) - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb index f6493a94ce4..48c2259422e 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.6-linux-x86_64.eb @@ -28,20 +28,11 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] -_depot_paths = ':'.join([ - # first entry must be the user depot - # see https://pkgdocs.julialang.org/v1/glossary/ - '~/.julia', - # base installation of Julia - '%(installdir)s/share/julia', -]) - modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # by default JULIA_HISTORY points to top path in DEPOT_PATH - # set JULIA_HISTORY to always use the user depot (~/.julia) - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb index 9bbe7e50e31..f5d1446913f 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.7-linux-x86_64.eb @@ -28,20 +28,11 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] -_depot_paths = ':'.join([ - # first entry must be the user depot - # see https://pkgdocs.julialang.org/v1/glossary/ - '~/.julia', - # base installation of Julia - '%(installdir)s/share/julia', -]) - modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # by default JULIA_HISTORY points to top path in DEPOT_PATH - # set JULIA_HISTORY to always use the user depot (~/.julia) - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb index 7c1e51bc5cd..ecc3020f4c0 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.0-linux-x86_64.eb @@ -28,20 +28,11 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] -_depot_paths = ':'.join([ - # first entry must be the user depot - # see https://pkgdocs.julialang.org/v1/glossary/ - '~/.julia', - # base installation of Julia - '%(installdir)s/share/julia', -]) - modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # by default JULIA_HISTORY points to top path in DEPOT_PATH - # set JULIA_HISTORY to always use the user depot (~/.julia) - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb index 5fc2b605f10..b8b0a744c04 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.1-linux-x86_64.eb @@ -28,20 +28,11 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] -_depot_paths = ':'.join([ - # first entry must be the user depot - # see https://pkgdocs.julialang.org/v1/glossary/ - '~/.julia', - # base installation of Julia - '%(installdir)s/share/julia', -]) - modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # by default JULIA_HISTORY points to top path in DEPOT_PATH - # set JULIA_HISTORY to always use the user depot (~/.julia) - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb index a7da9095153..e88e509e098 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.2-linux-x86_64.eb @@ -28,20 +28,11 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] -_depot_paths = ':'.join([ - # first entry must be the user depot - # see https://pkgdocs.julialang.org/v1/glossary/ - '~/.julia', - # base installation of Julia - '%(installdir)s/share/julia', -]) - modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # by default JULIA_HISTORY points to top path in DEPOT_PATH - # set JULIA_HISTORY to always use the user depot (~/.julia) - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb index 5e0aa491de1..dac9088825a 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.7.3-linux-x86_64.eb @@ -28,20 +28,11 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] -_depot_paths = ':'.join([ - # first entry must be the user depot - # see https://pkgdocs.julialang.org/v1/glossary/ - '~/.julia', - # base installation of Julia - '%(installdir)s/share/julia', -]) - modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # by default JULIA_HISTORY points to top path in DEPOT_PATH - # set JULIA_HISTORY to always use the user depot (~/.julia) - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb index 9876377c1b3..c7f6214e4a8 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.0-linux-x86_64.eb @@ -28,20 +28,11 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] -_depot_paths = ':'.join([ - # first entry must be the user depot - # see https://pkgdocs.julialang.org/v1/glossary/ - '~/.julia', - # base installation of Julia - '%(installdir)s/share/julia', -]) - modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # by default JULIA_HISTORY points to top path in DEPOT_PATH - # set JULIA_HISTORY to always use the user depot (~/.julia) - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb index c09419b4f04..37b817f557e 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.2-linux-x86_64.eb @@ -28,20 +28,11 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] -_depot_paths = ':'.join([ - # first entry must be the user depot - # see https://pkgdocs.julialang.org/v1/glossary/ - '~/.julia', - # base installation of Julia - '%(installdir)s/share/julia', -]) - modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # by default JULIA_HISTORY points to top path in DEPOT_PATH - # set JULIA_HISTORY to always use the user depot (~/.julia) - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb index 3ef9341cc06..1d5fa47c96c 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.8.5-linux-x86_64.eb @@ -28,20 +28,11 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] -_depot_paths = ':'.join([ - # first entry must be the user depot - # see https://pkgdocs.julialang.org/v1/glossary/ - '~/.julia', - # base installation of Julia - '%(installdir)s/share/julia', -]) - modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # by default JULIA_HISTORY points to top path in DEPOT_PATH - # set JULIA_HISTORY to always use the user depot (~/.julia) - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', } moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb new file mode 100644 index 00000000000..2ee4230cbb9 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.0-linux-x86_64.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.9.0' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['00c614466ef9809c2eb23480e38d196a2c577fff2730c4f83d135b913d473359'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +modextravars = { + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', +} + +moduleclass = 'lang' From 999274867ac568e5c01a8c4996053df7f10503db Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 7 Jul 2023 17:43:04 -0700 Subject: [PATCH 8007/9987] update Cluster-Buster --- .../Cluster-Buster-0.0-GCC-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-0.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-0.0-GCC-12.2.0.eb b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-0.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..20b44c5118a --- /dev/null +++ b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-0.0-GCC-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'Cluster-Buster' +version = '0.0' + +homepage = 'https://github.com/weng-lab/cluster-buster' +description = """Cluster-Buster is a program for finding interesting functional regions, + such as transcriptional enhancers, in DNA sequences.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +sources = [{ + 'git_config': { + 'url': 'https://github.com/weng-lab', + 'repo_name': '%(namelower)s', + 'commit': 'ac1d33cffff0c276216450ebced471595cf01488', + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['1654f16b0da0203268a2c785d13abeac24aa6e4dfacb4351a8e79905c585c277'] + +files_to_copy = [(['cbust'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cbust'], + 'dirs': [], +} + +sanity_check_commands = ['cbust -h'] + +moduleclass = 'bio' From 1a6c1785aff9d1a89e7961c3794b6fe0fd8a39fb Mon Sep 17 00:00:00 2001 From: fizwit Date: Sat, 8 Jul 2023 08:42:24 -0700 Subject: [PATCH 8008/9987] fix version --- .../Cluster-Buster-20200507-GCC-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20200507-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20200507-GCC-12.2.0.eb b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20200507-GCC-12.2.0.eb new file mode 100644 index 00000000000..0636ef933ae --- /dev/null +++ b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20200507-GCC-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'Cluster-Buster' +version = '20200507' + +homepage = 'https://github.com/weng-lab/cluster-buster' +description = """Cluster-Buster is a program for finding interesting functional regions, + such as transcriptional enhancers, in DNA sequences.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +sources = [{ + 'git_config': { + 'url': 'https://github.com/weng-lab', + 'repo_name': '%(namelower)s', + 'commit': 'ac1d33cffff0c276216450ebced471595cf01488', + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +files_to_copy = [(['cbust'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cbust'], + 'dirs': [], +} + +sanity_check_commands = ['cbust -h'] + +moduleclass = 'bio' From 16cde5b9fb09bd4189701acae25379c672e9b2fe Mon Sep 17 00:00:00 2001 From: John Dey Date: Sat, 8 Jul 2023 08:47:21 -0700 Subject: [PATCH 8009/9987] Delete Cluster-Buster-0.0-GCC-12.2.0.eb changed module version --- .../Cluster-Buster-0.0-GCC-12.2.0.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-0.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-0.0-GCC-12.2.0.eb b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-0.0-GCC-12.2.0.eb deleted file mode 100644 index 20b44c5118a..00000000000 --- a/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-0.0-GCC-12.2.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'MakeCp' - -name = 'Cluster-Buster' -version = '0.0' - -homepage = 'https://github.com/weng-lab/cluster-buster' -description = """Cluster-Buster is a program for finding interesting functional regions, - such as transcriptional enhancers, in DNA sequences.""" - -toolchain = {'name': 'GCC', 'version': '12.2.0'} - -sources = [{ - 'git_config': { - 'url': 'https://github.com/weng-lab', - 'repo_name': '%(namelower)s', - 'commit': 'ac1d33cffff0c276216450ebced471595cf01488', - }, - 'filename': SOURCE_TAR_GZ, -}] -checksums = ['1654f16b0da0203268a2c785d13abeac24aa6e4dfacb4351a8e79905c585c277'] - -files_to_copy = [(['cbust'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/cbust'], - 'dirs': [], -} - -sanity_check_commands = ['cbust -h'] - -moduleclass = 'bio' From ad6d23387a8fad1f013fcb7990ffaccecfaa04c5 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 10 Jul 2023 11:52:13 +0200 Subject: [PATCH 8010/9987] adding easyconfigs: kb-python-0.27.3-foss-2022a.eb --- .../kb-python/kb-python-0.27.3-foss-2022a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2022a.eb b/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2022a.eb new file mode 100644 index 00000000000..4d094874eeb --- /dev/null +++ b/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'kb-python' +version = '0.27.3' + +homepage = 'https://www.kallistobus.tools/' +description = """kallisto | bustools is a workflow for pre-processing single-cell RNA-seq data. + Pre-processing single-cell RNA-seq involves: (1) association of reads with their cells of origin, + (2) collapsing of reads according to unique molecular identifiers (UMIs), and (3) generation of + gene or feature counts from the reads to generate a cell x gene matrix.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('h5py', '3.7.0'), + ('IPython', '8.5.0'), + ('loompy', '3.0.7'), + ('Pysam', '0.19.1'), + ('Python', '3.10.4'), + ('scanpy', '1.9.1'), + ('scikit-learn', '1.1.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('shortuuid', '1.0.11', { + 'checksums': ['fc75f2615914815a8e4cb1501b3a513745cb66ef0fd5fc6fb9f8c3fa3481f789'], + }), + ('ngs-tools', '1.8.3', { + 'checksums': ['c50e36105654cdea14b4c7971994a3e710157663aaf0fd72c4d83a486f12cdb0'], + }), + ('tenacity', '8.1.0', { + 'checksums': ['e48c437fdf9340f5666b92cd7990e96bc5fc955e1298baf4a907e3972067a445'], + }), + ('plotly', '5.13.0', { + 'checksums': ['81a3aae4021d5ab91790fc71c3433791f41bfc71586e857f7777f429a955039a'], + }), + (name, version, { + 'sources': ['kb_python-%(version)s.tar.gz'], + 'checksums': ['dc98f6ceb4402d666b7e0d19be17c63d33e8b710a35cdc33de7c0f457122f43f'], + }), +] + +sanity_check_commands = ['kb info | grep "kb_python %(version)s"'] + +moduleclass = 'bio' From 0e8695b3a86280222a51f09485b2002c06dad1f1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 10 Jul 2023 12:03:49 +0200 Subject: [PATCH 8011/9987] adding easyconfigs: MUSCLE3-0.7.0-gfbf-2022b.eb, QCG-PilotJob-0.13.1-gfbf-2022b.eb, Kaleido-0.2.1-GCCcore-12.2.0.eb, msgpack-c-6.0.0-GCCcore-12.2.0.eb, PyZMQ-25.1.0-GCCcore-12.2.0.eb --- .../k/Kaleido/Kaleido-0.2.1-GCCcore-12.2.0.eb | 23 ++++ .../m/MUSCLE3/MUSCLE3-0.7.0-gfbf-2022b.eb | 103 ++++++++++++++++++ .../msgpack-c-6.0.0-GCCcore-12.2.0.eb | 34 ++++++ .../p/PyZMQ/PyZMQ-25.1.0-GCCcore-12.2.0.eb | 28 +++++ .../QCG-PilotJob-0.13.1-gfbf-2022b.eb | 57 ++++++++++ 5 files changed, 245 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/m/msgpack-c/msgpack-c-6.0.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a8ba636a58d --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Kaleido' +version = '0.2.1' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = ['kaleido-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl'] +checksums = ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [('Python', '3.10.8')] + +download_dep_fail = True +use_pip = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-gfbf-2022b.eb b/easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-gfbf-2022b.eb new file mode 100644 index 00000000000..c6e983d5c35 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-gfbf-2022b.eb @@ -0,0 +1,103 @@ +easyblock = 'ConfigureMakePythonPackage' + +name = 'MUSCLE3' +version = '0.7.0' + +homepage = 'https://muscle3.readthedocs.io/en/latest/index.html' + +description = """MUSCLE3 allows connecting multiple simulation models + together into a multiscale simulation. Simulation models can be as + simple as a single Python file, or as complex as a combination of + multiple separate simulation codes written in C++ or Fortran, and + running on an HPC machine.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://github.com/multiscale/%(namelower)s/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['e2ab6f0d219845c7bcdf9ebade9572b647d5dc464179b4714211db68fd9cb062'] + +builddependencies = [ + ('googletest', '1.12.1'), +] + +dependencies = [ + ('msgpack-c', '6.0.0'), + ('zlib', '1.2.12'), + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('QCG-PilotJob', '0.13.1'), + ('ruamel.yaml', '0.17.21'), + ('matplotlib', '3.7.0'), +] + +skipsteps = ['configure'] + +prebuildopts = 'msgpack_ROOT=$EBROOTMSGPACKMINC ' +preinstallopts = 'PREFIX=%(installdir)s ' +testopts = 'googletest_ROOT=$EBROOTGOOGLETEST' + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('typing_extensions', '4.7.1', { + 'checksums': ['b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2'], + }), + ('msgpack', '1.0.5', { + 'checksums': ['c075544284eadc5cddc70f4757331d99dcbc16b2bbd4849d15f8aae4cf36d31c'], + }), + ('click', '8.1.4', { + 'checksums': ['b97d0c74955da062a7d4ef92fadb583806a585b2ea81958a81bd72726cbb8e37'], + }), + ('yatiml', '0.10.0', { + 'checksums': ['4d23bfd7bbf45ae603c08fcb70d0c86404934a0cef24fb77b532705ff195fc92'], + }), + ('ymmsl', '0.13.0', { + 'checksums': ['861c8b728d2808b8e8eb31592af42c5c4317b441fbd83d050ccf91fa24a9212e'], + }), + ('netifaces', '0.11.0', { + 'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'], + }), + ('muscle3', version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/multiscale/muscle3/archive/refs/tags/'], + 'checksums': ['e2ab6f0d219845c7bcdf9ebade9572b647d5dc464179b4714211db68fd9cb062'], + }), +] + +modextrapaths = { + 'MUSCLE3_HOME': '', +} + +sanity_check_paths = { + 'files': ['include/libmuscle.f90', + 'include/libmuscle.mod', + 'include/libmuscle/libmuscle.hpp', + 'include/ymmsl/ymmsl.hpp', + 'lib/libmuscle.a', + 'lib/libmuscle.%s' % SHLIB_EXT, + 'lib/libmuscle_fortran.a', + 'lib/libmuscle_fortran.%s' % SHLIB_EXT, + 'lib/libymmsl.a', + 'lib/libymmsl.%s' % SHLIB_EXT, + 'lib/libymmsl_fortran.a', + 'lib/libymmsl_fortran.%s' % SHLIB_EXT, + 'lib/pkgconfig/libmuscle.pc', + 'lib/pkgconfig/libmuscle_fortran.pc', + 'lib/pkgconfig/ymmsl.pc', + 'lib/pkgconfig/ymmsl_fortran.pc'], + 'dirs': ['bin', + 'include/libmuscle/mcp', + 'include/ymmsl', + 'lib/pkgconfig', + 'lib64'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/msgpack-c/msgpack-c-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/msgpack-c/msgpack-c-6.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..cb567b6c10e --- /dev/null +++ b/easybuild/easyconfigs/m/msgpack-c/msgpack-c-6.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04 +easyblock = 'CMakeMake' + +name = 'msgpack-c' +version = '6.0.0' + +homepage = 'http://msgpack.org/' +description = """MessagePack is an efficient binary serialization format, which lets you exchange +data among multiple languages like JSON, except that it's faster and smaller. +Small integers are encoded into a single byte while typical short strings +require only one extra byte in addition to the strings themselves.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/msgpack/msgpack-c/releases/download/c-%(version)s'] +sources = ['msgpack-c-%(version)s.tar.gz'] +checksums = ['3654f5e2c652dc52e0a993e270bb57d5702b262703f03771c152bba51602aeba'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), + ('Boost', '1.81.0'), + ('googletest', '1.12.1'), +] + +sanity_check_paths = { + 'files': [ + ['lib/libmsgpack-c.%s' % x for x in ['a', '%s' % SHLIB_EXT]], + ['include/msgpack.%s' % x for x in ['h']] + ], + 'dirs': ['lib/pkgconfig', 'include/msgpack'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e3ee288bac1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '25.1.0' + +homepage = 'https://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['80c41023465d36280e801564a69cbfce8ae85ff79b080e1913f6e90481fb8957'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('ZeroMQ', '4.3.4'), +] + +options = {'modulename': 'zmq'} + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb new file mode 100644 index 00000000000..b775a3a725d --- /dev/null +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'QCG-PilotJob' +version = '0.13.1' + +homepage = 'https://qcg-pilotjob.readthedocs.org' +description = """A python service for easy execution of many tasks inside a single allocation.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('PyZMQ', '25.1.0'), + ('Kaleido', '0.2.1'), + ('statsmodels', '0.14.0'), + ('plotly.py', '5.13.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.3', { + 'checksums': ['bdc18001875e319bc91c812c1eb6a10be4bb13cb81eb763f466179dca3b67277'], + }), + ('plotly_express', '0.4.1', { + 'checksums': ['ff73a41ce02fb43d1d8e8fa131ef3e6589857349ca216b941b8f3f862bce0278'], + }), + ('prompt_toolkit', '3.0.39', { + 'checksums': ['04505ade687dc26dc4284b1ad19a83be2f2afe83e7a828ace0c72f3a1df72aac'], + }), + ('termcolor', '2.3.0', { + 'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'], + }), + ('qcg-pilotjob', version, { + 'modulename': 'qcg.pilotjob', + 'patches': ['QCG-PilotJob-0.12.3_rename_zmq.patch'], + 'checksums': [ + {'qcg-pilotjob-0.13.1.tar.gz': '6aff74436edde78e8f584066a732298731e8ce1190f7fe69edfaab64a3ecc29d'}, + {'QCG-PilotJob-0.12.3_rename_zmq.patch': + '51cba1bfe1dcd33180dffe65941acdfa70823d6cae4b81182fd16a7debf907cd'}, + ], + }), + ('qcg-pilotjob-cmds', version, { + 'modulename': 'qcg.pilotjob.cmds', + 'checksums': ['dc7d4a30b65f2194cf68ec876401581647f683d766215a4fef32b438ec4cbffe'], + }), + ('qcg-pilotjob-executor-api', version, { + 'modulename': 'qcg.pilotjob.api', + 'checksums': ['9d7303199bcce1de35d480f96bc2da93b5259a5cac31476c486f790ccbdeebdf'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 6dc69db821d278443d1b8b8383c2ad65e494afe2 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Mon, 10 Jul 2023 13:28:50 +0200 Subject: [PATCH 8012/9987] removing unnecessities from the patch + fixing the style of easyconfig --- .../m/MXNet/MXNet-1.9.1-foss-2022a.eb | 40 ++++++++++--------- .../m/MXNet/mxnet-1.9.1-add_flexiblas.patch | 33 +++++++++++++++ 2 files changed, 55 insertions(+), 18 deletions(-) create mode 100644 easybuild/easyconfigs/m/MXNet/mxnet-1.9.1-add_flexiblas.patch diff --git a/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb index ac79b1bfdc9..be89769cc90 100644 --- a/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb @@ -7,28 +7,33 @@ description = """Flexible and Efficient Library for Deep Learning""" toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'cstd': 'c++14', 'opt': True, 'pic': True, 'openmp': True, 'extra_cflags': '-lflexiblas'} +# MXNet pulls in a bunch of submodules with specific commits source_urls = [ 'https://github.com/apache/mxnet/archive', + 'https://github.com/dmlc/ps-lite/archive/', + 'https://github.com/apache/tvm/archive/', + 'https://github.com/dmlc/dmlc-core/archive/', + 'https://github.com/dmlc/dlpack/archive/', + 'https://github.com/google/googletest/archive/', + 'https://github.com/kpu/intgemm/archive/', + 'https://github.com/NVlabs/cub/archive/', + 'https://github.com/onnx/onnx-tensorrt/archive/', 'https://github.com/oneapi-src/oneDNN/archive/', ] sources = [ 'v%(version)s.tar.gz', # MXNet - 'https://github.com/dmlc/ps-lite/archive/34fd45cae457d59850fdcb2066467778d0673f21.tar.gz', # ps-lite - 'https://github.com/apache/tvm/archive/efdac9439506d1de5eec91ecc795982c78e41909.tar.gz', # tvm - 'https://github.com/dmlc/dmlc-core/archive/5df8305fe699d3b503d10c60a231ab0223142407.tar.gz', # dmlc-core - 'https://github.com/dmlc/dlpack/archive/3efc489b55385936531a06ff83425b719387ec63.tar.gz', # dlpack - 'https://github.com/google/googletest/archive/eb9225ce361affe561592e0912320b9db84985d0.tar.gz', # googletest - 'https://github.com/kpu/intgemm/archive/8f28282c3bd854922da638024d2659be52e892e9.tar.gz', # intgemm - 'https://github.com/NVlabs/cub/archive/0158fa19f28619886232defd412433974af89611.tar.gz', # cub - 'https://github.com/onnx/onnx-tensorrt/archive/2eb74d933f89e1590fdbfc64971a36e5f72df720.tar.gz', # onnx-tensorrt - # oneDNN: - { - 'download_filename': '5818c40f07bdb6307f9bc64e929836fe036da644.tar.gz', - 'filename': 'mkldnn.tar.gz' - } + '34fd45cae457d59850fdcb2066467778d0673f21.tar.gz', # ps-lite + 'efdac9439506d1de5eec91ecc795982c78e41909.tar.gz', # tvm + '5df8305fe699d3b503d10c60a231ab0223142407.tar.gz', # dmlc-core + '3efc489b55385936531a06ff83425b719387ec63.tar.gz', # dlpack + 'eb9225ce361affe561592e0912320b9db84985d0.tar.gz', # googletest + '8f28282c3bd854922da638024d2659be52e892e9.tar.gz', # intgemm + '0158fa19f28619886232defd412433974af89611.tar.gz', # cub + '2eb74d933f89e1590fdbfc64971a36e5f72df720.tar.gz', # onnx-tensorrt + '5818c40f07bdb6307f9bc64e929836fe036da644.tar.gz', # oneDNN ] patches = [ - 'mxnet-fix_blas.patch', + 'mxnet-1.9.1-add_flexiblas.patch', ] checksums = [ {'v1.9.1.tar.gz': '9927f986b2c2c8315f2ba675e050ce1f4e24e84c4692e5f0a96248876784a8a7'}, @@ -48,11 +53,11 @@ checksums = [ '43424c4c17a997d1d730c89ec14688671245de7941e02b388d7d3df6ea53777a'}, {'2eb74d933f89e1590fdbfc64971a36e5f72df720.tar.gz': 'df99819727445c247fb5c21c2fd825ded3269376867457ae84fa6d6f1c0ae331'}, - {'mkldnn.tar.gz': 'aeb8e65bb13d1a3171673ab749d41e8c3a6538371d922a7fa881afef277128ba'}, - {'mxnet-fix_blas.patch': '274d683f70ae60a65c981eac8a9b27e4a13c4f6f7386ac0f3eb0a462377860f0'}, + {'5818c40f07bdb6307f9bc64e929836fe036da644.tar.gz': + 'aeb8e65bb13d1a3171673ab749d41e8c3a6538371d922a7fa881afef277128ba'}, + {'mxnet-1.9.1-add_flexiblas.patch': '92b3a9b9ffd87c3be30efe1b400b4d152ba3fe4e105970bc6c63906dfcb59084'}, ] -# MXNet pulls in a bunch of submodules which don't have releases. builddependencies = [ ('CMake', '3.23.1'), ] @@ -61,7 +66,6 @@ dependencies = [ ('Python', '3.10.4'), ('graphviz-python', '0.20.1'), ('OpenCV', '4.6.0', '-contrib'), - ('R', '4.2.1'), ] moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MXNet/mxnet-1.9.1-add_flexiblas.patch b/easybuild/easyconfigs/m/MXNet/mxnet-1.9.1-add_flexiblas.patch new file mode 100644 index 00000000000..d1bbfb1dc5b --- /dev/null +++ b/easybuild/easyconfigs/m/MXNet/mxnet-1.9.1-add_flexiblas.patch @@ -0,0 +1,33 @@ +source: https://github.com/apache/mxnet/pull/21093 +diff -ruN mxnet-1.9.1_orig/cmake/ChooseBlas.cmake mxnet-1.9.1/cmake/ChooseBlas.cmake +--- mxnet-1.9.1_orig/cmake/ChooseBlas.cmake 2022-04-22 00:45:57.000000000 +0200 ++++ mxnet-1.9.1/cmake/ChooseBlas.cmake 2023-07-10 12:13:14.448174000 +0200 +@@ -16,10 +16,11 @@ + # under the License. + + set(BLAS "Open" CACHE STRING "Selected BLAS library") +-set_property(CACHE BLAS PROPERTY STRINGS "Atlas;Open;MKL") ++set_property(CACHE BLAS PROPERTY STRINGS "Atlas;Open;MKL;FlexiBLAS") + + if(DEFINED USE_BLAS) + set(BLAS "${USE_BLAS}") ++ message(STATUS "BLAS is set to ${USE_BLAS}") + else() + if(USE_MKL_IF_AVAILABLE) + if(NOT MKL_FOUND) +@@ -31,7 +32,14 @@ + endif() + endif() + +-if(BLAS STREQUAL "Atlas" OR BLAS STREQUAL "atlas") ++if(BLAS STREQUAL "FlexiBLAS" OR BLAS STREQUAL "flexiblas") ++ set(BLA_VENDOR FlexiBLAS) ++ find_package(BLAS REQUIRED) ++ include_directories(SYSTEM ${BLAS_INCLUDE_DIR}) ++ add_definitions(-DMSHADOW_USE_CBLAS=1) ++ add_definitions(-DMSHADOW_USE_MKL=0) ++ add_definitions(-DMXNET_USE_LAPACK=1) ++elseif(BLAS STREQUAL "Atlas" OR BLAS STREQUAL "atlas") + find_package(Atlas REQUIRED) + include_directories(SYSTEM ${Atlas_INCLUDE_DIR}) + list(APPEND mshadow_LINKER_LIBS ${Atlas_LIBRARIES}) From dc83b0e84b6689927585945afb9b562a9139e59d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 10 Jul 2023 13:44:50 +0200 Subject: [PATCH 8013/9987] Updates to Kaleido/0.2.1 and Boost/1.81.0 for GCCcore/12.2.0 --- .../b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb | 32 +++++++++++++++++++ .../k/Kaleido/Kaleido-0.2.1-GCCcore-12.2.0.eb | 1 + 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e04dbec9ab0 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +name = 'Boost' +version = '1.81.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['205666dea9f6a7cfed87c7a6dfbeb52a2c1b9de55712c9c1a87735d7181452b6'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('XZ', '5.2.7'), + ('zstd', '1.5.2'), + ('ICU', '72.1'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.2.0.eb index a8ba636a58d..9858859ed7a 100644 --- a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-12.2.0.eb @@ -19,5 +19,6 @@ dependencies = [('Python', '3.10.8')] download_dep_fail = True use_pip = True +sanity_pip_check = True moduleclass = 'vis' From 96f7034156737cc04af5df7d9576fc79f4702ff7 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 10 Jul 2023 11:31:18 -0700 Subject: [PATCH 8014/9987] fix pkgconfig version --- .../easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb index 2d6a713e053..54de0646472 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb @@ -19,7 +19,7 @@ checksums = ['d8be783efd5cd4ae534cee4132338e3f40f182c3205d23b200094ec85faaaef8'] builddependencies = [('binutils', '2.37')] dependencies = [ - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ('libtasn1', '4.18.0'), ('libffi', '3.4.2'), ] From 3a5e76333a32bb97e89e0f92c049a0afcdeb34bf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 11 Jul 2023 17:19:15 +0200 Subject: [PATCH 8015/9987] use Z3 with Python bindings in Demystify v0.0.17 --- .../easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb index 356c7a33d87..3a7d86ba8dc 100644 --- a/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb +++ b/easybuild/easyconfigs/d/Demystify/Demystify-0.0.17-foss-2020b.eb @@ -19,7 +19,7 @@ dependencies = [ ('Python', '3.8.6'), ('PySAT', '0.1.7.dev1'), ('SciPy-bundle', '2020.11'), - ('Z3', '4.8.10'), + ('Z3', '4.8.10', '-Python-%(pyver)s'), ] use_pip = True From ddc65c5b1b18e13a0123a0c77f7de27503ff0868 Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 11 Jul 2023 21:02:48 +0200 Subject: [PATCH 8016/9987] adding easyconfigs: connected-components-3d-3.12.1-foss-2022b.eb --- ...nnected-components-3d-3.12.1-foss-2022b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb new file mode 100644 index 00000000000..3d1c6d438f4 --- /dev/null +++ b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb @@ -0,0 +1,28 @@ +# connected-components-3d-3.12.1 + +easyblock = 'PythonPackage' + +name = 'connected-components-3d' +version = '3.12.1' +options = {'modulename': 'cc3d'} + + +homepage = 'https://github.com/seung-lab/connected-components-3d/' +description = """cc3d is an implementation of connected components in three dimensions using a 26, 18, + or 6-connected neighborhood in 3D or 4 and 8-connected in 2D.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e40445bccbea51bb8ba256411f9e8fc7e43226502af5a913f090ec81181daf1f'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + + +use_pip = True + +sanity_pip_check = True +moduleclass = 'data' From 62a7374945e79b06b12df67e54638d4dc0e1084a Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 11 Jul 2023 21:27:17 +0200 Subject: [PATCH 8017/9987] =add download_dep_fail option --- .../connected-components-3d-3.12.1-foss-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb index 3d1c6d438f4..08eaf31cc7a 100644 --- a/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb +++ b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb @@ -21,6 +21,7 @@ dependencies = [ ('SciPy-bundle', '2023.02'), ] +download_dep_fail = True use_pip = True From e857e6fe036a0d7e21c2547b4df291e3b375d0c3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 12 Jul 2023 06:49:30 +0800 Subject: [PATCH 8018/9987] adding easyconfigs: segment-anything-1.0-foss-2022a.eb --- .../segment-anything-1.0-foss-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2022a.eb b/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2022a.eb new file mode 100644 index 00000000000..124012ea1d4 --- /dev/null +++ b/easybuild/easyconfigs/s/segment-anything/segment-anything-1.0-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'segment-anything' +version = '1.0' + +homepage = 'https://github.com/facebookresearch/segment-anything' +description = """The Segment Anything Model (SAM) produces high quality object masks from input prompts + such as points or boxes, and it can be used to generate masks for all objects in an image. + It has been trained on a dataset of 11 million images and 1.1 billion masks, and has strong zero-shot + performance on a variety of segmentation tasks.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = ['segment_anything-%(version)s.tar.gz'] +checksums = ['ed0c9f6fb07bbef9c6238a7028a13c8272f1ba6b6305ca73e3e064266503736b'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('torchvision', '0.13.1'), + ('OpenCV', '4.6.0', '-contrib'), + ('pycocotools', '2.0.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'ai' From 000bfca095e00311099a8e1aa359bb883970b4f7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 12 Jul 2023 11:18:12 +0800 Subject: [PATCH 8019/9987] adding easyconfigs: Rhodium-1.2.0-foss-2022a.eb, Platypus-Opt-1.1.0-foss-2022a.eb --- .../Platypus-Opt-1.1.0-foss-2022a.eb | 27 ++++++++++ .../r/Rhodium/Rhodium-1.2.0-foss-2022a.eb | 52 +++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.1.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/Rhodium/Rhodium-1.2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.1.0-foss-2022a.eb b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.1.0-foss-2022a.eb new file mode 100644 index 00000000000..e817b3051b1 --- /dev/null +++ b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.1.0-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Platypus-Opt' +version = '1.1.0' + +homepage = 'https://github.com/Project-Platypus/Platypus' +description = """Platypus is a framework for evolutionary computing in Python with a focus on + multiobjective evolutionary algorithms (MOEAs).""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['19610123c204e2dfc10741c69403b57a649589d9494de0fce0fc27579e586bbd'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'platypus'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/Rhodium/Rhodium-1.2.0-foss-2022a.eb b/easybuild/easyconfigs/r/Rhodium/Rhodium-1.2.0-foss-2022a.eb new file mode 100644 index 00000000000..962c9b8aab0 --- /dev/null +++ b/easybuild/easyconfigs/r/Rhodium/Rhodium-1.2.0-foss-2022a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'Rhodium' +version = '1.2.0' + +homepage = 'https://github.com/Project-Platypus/Rhodium' +description = """Rhodium is an open source Python library for robust decision making (RDM) and + multiobjective robust decision making (MORDM), and exploratory modelling (EM).""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('poetry', '1.2.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('graphviz-python', '0.20.1'), + ('Platypus-Opt', '1.1.0'), + ('pydot', '1.4.2'), + ('scikit-learn', '1.1.2'), + ('Seaborn', '0.12.1'), +] + +use_pip = True + +exts_list = [ + ('mplcursors', '0.5.2', { + 'checksums': ['78febb32adf2d9040e2f6fc84b5e4cfb8f96b4ede4916fc418e5fffbcfdc0957'], + }), + ('PRIM', '0.5.0', { + 'checksums': ['22cebf7ce677f9eab80e4236ee34cd10e115a82b7eee436f6c7b21dddba302e4'], + }), + ('dill', '0.3.6', { + 'checksums': ['e5db55f3687856d8fbdab002ed78544e1c4559a130302693d839dfe8f93f2373'], + }), + ('multiprocess', '0.70.14', { + 'checksums': ['3eddafc12f2260d27ae03fe6069b12570ab4764ab59a75e81624fac453fbf46a'], + }), + ('salib', '1.4.7', { + 'modulename': 'SALib', + 'checksums': ['2e6cb19ec772d6cb7368feceae0f61e51f2d6afdbc4f8986a780b87d657b38cc'], + }), + (name, version, { + 'checksums': ['557b5914a4dce4ccb085bfa183ae083812161821bcb2aea743578e34b7c7405f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From e2a08c521e51ce120b00d6c7cec50c6b53c8304c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 12 Jul 2023 11:36:46 +0800 Subject: [PATCH 8020/9987] remove source_urls with default PyPi value --- .../easyconfigs/p/Platypus-Opt/Platypus-Opt-1.1.0-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.1.0-foss-2022a.eb b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.1.0-foss-2022a.eb index e817b3051b1..a9f982ab9f2 100644 --- a/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/Platypus-Opt/Platypus-Opt-1.1.0-foss-2022a.eb @@ -9,7 +9,6 @@ description = """Platypus is a framework for evolutionary computing in Python wi toolchain = {'name': 'foss', 'version': '2022a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['19610123c204e2dfc10741c69403b57a649589d9494de0fce0fc27579e586bbd'] From 31b54a931c7e4b818e489f1924421174f629ff1a Mon Sep 17 00:00:00 2001 From: alberta Date: Wed, 12 Jul 2023 10:35:18 +0200 Subject: [PATCH 8021/9987] adding easyconfigs: libnsl-2.0.0-GCCcore-12.2.0.eb --- .../l/libnsl/libnsl-2.0.0-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libnsl/libnsl-2.0.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..af937a9f274 --- /dev/null +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libnsl' +version = '2.0.0' + +homepage = 'https://github.com/thkukuk/libnsl' +description = """The libnsl package contains the public client interface for NIS(YP).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['2da075ef1893ebdfc5f074f83ac811873dc06fd5c62bc9a4729fd2e27a40341a'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('libtirpc', '1.3.3'), +] + +# Provide a symlink for libnsl.so.1, which used to be part of glibc. +# This new version of libnsl should be backwards compatible. +postinstallcmds = ['ln -s libnsl.so %(installdir)s/lib/libnsl.so.1'] + +sanity_check_paths = { + 'files': ['include/rpcsvc/yp.h', 'lib/libnsl.a', + 'lib/libnsl.%s' % SHLIB_EXT, 'lib/libnsl.%s.1' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' From a1bf195ba2a75c799e0bda6a6fdd87ff59e9e87e Mon Sep 17 00:00:00 2001 From: adam Date: Wed, 12 Jul 2023 10:06:56 +0100 Subject: [PATCH 8022/9987] adding easyconfigs: kma-1.4.12a-foss-2022b.eb --- .../k/kma/kma-1.4.12a-foss-2022b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/k/kma/kma-1.4.12a-foss-2022b.eb diff --git a/easybuild/easyconfigs/k/kma/kma-1.4.12a-foss-2022b.eb b/easybuild/easyconfigs/k/kma/kma-1.4.12a-foss-2022b.eb new file mode 100644 index 00000000000..87958151305 --- /dev/null +++ b/easybuild/easyconfigs/k/kma/kma-1.4.12a-foss-2022b.eb @@ -0,0 +1,36 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# 1.4.2 - updated by Adam Huffman, University of Oxford + +easyblock = 'MakeCp' + +name = 'kma' +version = '1.4.12a' + +homepage = 'https://bitbucket.org/genomicepidemiology/kma' +description = """KMA is a mapping method designed to map raw reads directly against redundant databases, +in an ultra-fast manner using seed and extend.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +# https://bitbucket.org/genomicepidemiology/kma +bitbucket_account = 'genomicepidemiology' +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] +checksums = ['e19758106647a15f7809ce47b9dbefd27a76b8527cd0368259d631fb13a6b996'] + +dependencies = [ + ('zlib', '1.2.12'), +] + +local_bin_list = ['kma', 'kma_index', 'kma_shm', 'kma_update'] + +files_to_copy = [(local_bin_list, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_list], + 'dirs': [] +} +sanity_check_commands = ['%s -h' % f for f in local_bin_list] + +moduleclass = 'bio' From f0065c5ceff81fa77550880b0156a141b29289c2 Mon Sep 17 00:00:00 2001 From: adam Date: Wed, 12 Jul 2023 10:08:37 +0100 Subject: [PATCH 8023/9987] adding easyconfigs: Delly-1.1.6-GCC-12.2.0.eb --- .../d/Delly/Delly-1.1.6-GCC-12.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/d/Delly/Delly-1.1.6-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/d/Delly/Delly-1.1.6-GCC-12.2.0.eb b/easybuild/easyconfigs/d/Delly/Delly-1.1.6-GCC-12.2.0.eb new file mode 100644 index 00000000000..4d86e151a7c --- /dev/null +++ b/easybuild/easyconfigs/d/Delly/Delly-1.1.6-GCC-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'Delly' +version = '1.1.6' + +homepage = 'https://github.com/dellytools/delly/' +description = """Delly is an integrated structural variant (SV) prediction +method that can discover, genotype and visualize deletions, tandem duplications, +inversions and translocations at single-nucleotide resolution in short-read +massively parallel sequencing data. It uses paired-ends, split-reads and +read-depth to sensitively and accurately delineate genomic rearrangements +throughout the genome.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'dellytools' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['08961e9c81431eb486476fa71eea94941ad24ec1970b71e5a7720623a39bfd2a'] + +dependencies = [ + ('HTSlib', '1.17'), + ('Boost', '1.81.0'), +] + +build_cmd = 'make PARALLEL=1 -B src/delly' + +files_to_copy = [ + (['src/delly'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/delly'], + 'dirs': ['bin'] +} + +sanity_check_commands = ['delly'] + +moduleclass = 'bio' From e03f9d1c9459755d7db92cb66f0f0953d52a7624 Mon Sep 17 00:00:00 2001 From: adam Date: Wed, 12 Jul 2023 12:11:43 +0100 Subject: [PATCH 8024/9987] Move to GCC/12.2.0 --- .../k/kma/kma-1.4.12a-GCC-12.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/k/kma/kma-1.4.12a-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/k/kma/kma-1.4.12a-GCC-12.2.0.eb b/easybuild/easyconfigs/k/kma/kma-1.4.12a-GCC-12.2.0.eb new file mode 100644 index 00000000000..350f33cd863 --- /dev/null +++ b/easybuild/easyconfigs/k/kma/kma-1.4.12a-GCC-12.2.0.eb @@ -0,0 +1,36 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# 1.4.2 - updated by Adam Huffman, University of Oxford + +easyblock = 'MakeCp' + +name = 'kma' +version = '1.4.12a' + +homepage = 'https://bitbucket.org/genomicepidemiology/kma' +description = """KMA is a mapping method designed to map raw reads directly against redundant databases, +in an ultra-fast manner using seed and extend.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +# https://bitbucket.org/genomicepidemiology/kma +bitbucket_account = 'genomicepidemiology' +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] +checksums = ['e19758106647a15f7809ce47b9dbefd27a76b8527cd0368259d631fb13a6b996'] + +dependencies = [ + ('zlib', '1.2.12'), +] + +local_bin_list = ['kma', 'kma_index', 'kma_shm', 'kma_update'] + +files_to_copy = [(local_bin_list, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_list], + 'dirs': [] +} +sanity_check_commands = ['%s -h' % f for f in local_bin_list] + +moduleclass = 'bio' From 021ce0b019661fdd3800b3174381fc6c51a37c90 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 12 Jul 2023 12:12:08 +0100 Subject: [PATCH 8025/9987] Delete kma-1.4.12a-foss-2022b.eb --- .../k/kma/kma-1.4.12a-foss-2022b.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/k/kma/kma-1.4.12a-foss-2022b.eb diff --git a/easybuild/easyconfigs/k/kma/kma-1.4.12a-foss-2022b.eb b/easybuild/easyconfigs/k/kma/kma-1.4.12a-foss-2022b.eb deleted file mode 100644 index 87958151305..00000000000 --- a/easybuild/easyconfigs/k/kma/kma-1.4.12a-foss-2022b.eb +++ /dev/null @@ -1,36 +0,0 @@ -# Author: Pavel Grochal (INUITS) -# License: GPLv2 -# 1.4.2 - updated by Adam Huffman, University of Oxford - -easyblock = 'MakeCp' - -name = 'kma' -version = '1.4.12a' - -homepage = 'https://bitbucket.org/genomicepidemiology/kma' -description = """KMA is a mapping method designed to map raw reads directly against redundant databases, -in an ultra-fast manner using seed and extend.""" - -toolchain = {'name': 'foss', 'version': '2022b'} - -# https://bitbucket.org/genomicepidemiology/kma -bitbucket_account = 'genomicepidemiology' -source_urls = [BITBUCKET_SOURCE] -sources = ['%(version)s.tar.bz2'] -checksums = ['e19758106647a15f7809ce47b9dbefd27a76b8527cd0368259d631fb13a6b996'] - -dependencies = [ - ('zlib', '1.2.12'), -] - -local_bin_list = ['kma', 'kma_index', 'kma_shm', 'kma_update'] - -files_to_copy = [(local_bin_list, 'bin')] - -sanity_check_paths = { - 'files': ['bin/%s' % f for f in local_bin_list], - 'dirs': [] -} -sanity_check_commands = ['%s -h' % f for f in local_bin_list] - -moduleclass = 'bio' From 42656a585ce49a3d928ea640b02314bc94307f21 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 12 Jul 2023 12:14:19 +0100 Subject: [PATCH 8026/9987] Update Boost-1.81.0-GCCcore-12.2.0.eb Remove trailing whitespace --- easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb index e04dbec9ab0..5fc718928fd 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb @@ -13,7 +13,7 @@ checksums = ['205666dea9f6a7cfed87c7a6dfbeb52a2c1b9de55712c9c1a87735d7181452b6'] builddependencies = [ ('binutils', '2.39'), -] +] dependencies = [ ('bzip2', '1.0.8'), From 4b18fec7768c859ed54be262ab77b20b172f6162 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 12 Jul 2023 14:09:32 +0200 Subject: [PATCH 8027/9987] update exts_list --- .../k/kb-python/kb-python-0.27.3-foss-2022a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2022a.eb b/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2022a.eb index 4d094874eeb..8633efb7165 100644 --- a/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2022a.eb +++ b/easybuild/easyconfigs/k/kb-python/kb-python-0.27.3-foss-2022a.eb @@ -31,11 +31,11 @@ exts_list = [ ('ngs-tools', '1.8.3', { 'checksums': ['c50e36105654cdea14b4c7971994a3e710157663aaf0fd72c4d83a486f12cdb0'], }), - ('tenacity', '8.1.0', { - 'checksums': ['e48c437fdf9340f5666b92cd7990e96bc5fc955e1298baf4a907e3972067a445'], + ('tenacity', '8.2.2', { + 'checksums': ['43af037822bd0029025877f3b2d97cc4d7bb0c2991000a3d59d71517c5c969e0'], }), - ('plotly', '5.13.0', { - 'checksums': ['81a3aae4021d5ab91790fc71c3433791f41bfc71586e857f7777f429a955039a'], + ('plotly', '5.15.0', { + 'checksums': ['822eabe53997d5ebf23c77e1d1fcbf3bb6aa745eb05d532afd4b6f9a2e2ab02f'], }), (name, version, { 'sources': ['kb_python-%(version)s.tar.gz'], From 049e1db2ec38e21631a58a10991b53c49e283586 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 12 Jul 2023 14:34:55 +0200 Subject: [PATCH 8028/9987] adding easyconfigs: h5netcdf-1.2.0-foss-2022a.eb --- .../h/h5netcdf/h5netcdf-1.2.0-foss-2022a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2022a.eb b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2022a.eb new file mode 100644 index 00000000000..f9de3cf3b26 --- /dev/null +++ b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'h5netcdf' +version = '1.2.0' + +homepage = 'https://h5netcdf.org/' +description = """A Python interface for the netCDF4 file-format that reads and writes local or +remote HDF5 files directly via h5py or h5pyd, without relying on the Unidata +netCDF library.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('h5py', '3.7.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['7f6b2733bde06ea2575b79a6450d9bd5c38918ff4cb2a355bf22bbe8c86c6bcf'], + }), +] + +moduleclass = 'data' From d47a14bb07d1252653ff83cf7d3a18054996f54b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 12 Jul 2023 14:41:52 +0200 Subject: [PATCH 8029/9987] Style changes --- .../q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb index b775a3a725d..c589e9bb12a 100644 --- a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb @@ -52,6 +52,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'tools' From 55a826b6030730fc552123909f9f5d3cd425a71a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 12 Jul 2023 15:17:57 +0200 Subject: [PATCH 8030/9987] adding easyconfigs: h4toh5-2.2.5-gompi-2022a.eb, HDF-EOS2-3.0-GCCcore-11.3.0.eb --- .../h/HDF-EOS2/HDF-EOS2-3.0-GCCcore-11.3.0.eb | 38 +++++++++++++++++++ .../h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb | 29 ++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF-EOS2/HDF-EOS2-3.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb diff --git a/easybuild/easyconfigs/h/HDF-EOS2/HDF-EOS2-3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HDF-EOS2/HDF-EOS2-3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..6faf7065a64 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF-EOS2/HDF-EOS2-3.0-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'HDF-EOS2' +version = '3.0' + +homepage = 'https://hdfeos.org/' +description = """HDF-EOS libraries are software libraries built on HDF libraries. + It supports three data structures for remote sensing data: Grid, Point and Swath.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://git.earthdata.nasa.gov/projects/DAS/repos/hdfeos/raw/'] +sources = [ + {'download_filename': '%(namelower)s-%(version)s-src.tar.gz?at=3128a738021501c821549955f6c78348e5f33850', + 'filename': SOURCE_TAR_GZ} +] +checksums = ['3a5564b4d69b541139ff7dfdad948696cf31d9d1a6ea8af290c91a4c0ee37188'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('HDF', '4.2.15'), + ('Szip', '2.1.1'), +] + +preconfigopts = 'export CC="$EBROOTHDF/bin/h4cc -Df2cFortran" && ' + +configopts = "--with-szlib=$EBROOTSZIP --enable-install-include" + +sanity_check_paths = { + 'files': ['include/HdfEosDef.h', 'lib/libGctp.a', 'lib/libhdfeos.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb new file mode 100644 index 00000000000..1a825bc8ed8 --- /dev/null +++ b/easybuild/easyconfigs/h/h4toh5/h4toh5-2.2.5-gompi-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'h4toh5' +version = '2.2.5' + +homepage = 'http://www.hdfgroup.org/h4toh5/' +description = """The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, + as well as a conversion library for converting between individual HDF4 and HDF5 objects.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/%(name)s/%(name)s-%(version)s/src/'] +sources = ['h4h5tools-%(version)s.tar.gz'] +checksums = ['79f6505c1df3ad0c2cc1a19b9b433b5d955dfd7d2dffefc080d89fdde01fd6f2'] + +dependencies = [ + ('HDF', '4.2.15'), + ('HDF5', '1.12.2'), + ('HDF-EOS2', '3.0'), +] + +configopts = "CC=$EBROOTHDF/bin/h4cc --with-hdf5=$EBROOTHDF5 --with-hdfeos2=$EBROOTHDFMINEOS" + +sanity_check_paths = { + 'files': ['bin/h4toh5', 'bin/h5toh4', 'include/h4toh5.h', 'lib/libh4toh5.a'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'data' From 55cd0adf252c495603388598a21ac6c9747235f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 12 Jul 2023 17:26:40 +0200 Subject: [PATCH 8031/9987] adding easyconfigs: inferCNV-1.16.0-foss-2022a-R-4.2.1.eb --- .../inferCNV-1.16.0-foss-2022a-R-4.2.1.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..187ae5ad65d --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,53 @@ +easyblock = 'Bundle' + +name = 'inferCNV' +version = '1.16.0' +versionsuffix = '-R-%(rver)s' +local_biocver = '3.15' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('R', '4.2.1'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-13', '-R-%(rver)s'), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_biocver, + 'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_biocver, + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_list = [ + ('phyclust', '0.1-33', { + 'checksums': ['38786608193bcad6aeb5517f2d5f836c9773bdd09fc484b4bd40b06a71f5a413'], + }), + ('infercnv', version, { + 'checksums': ['af7c53de0bc78d5a030fa695d35531f8bac6c8ea83a4b7097437490eff25d3a5'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +moduleclass = 'bio' From 5cf79511b7e4929b6bc7ff863dadcdade8a614ee Mon Sep 17 00:00:00 2001 From: garadar Date: Wed, 12 Jul 2023 21:10:36 +0200 Subject: [PATCH 8032/9987] Update easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../connected-components-3d-3.12.1-foss-2022b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb index 08eaf31cc7a..36561dd4ff9 100644 --- a/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb +++ b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb @@ -1,5 +1,3 @@ -# connected-components-3d-3.12.1 - easyblock = 'PythonPackage' name = 'connected-components-3d' From c65bbfe7d105800e9a37c66ba9ff84c0f6b3d218 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 13 Jul 2023 09:48:58 +0200 Subject: [PATCH 8033/9987] add source --- .../easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb index 187ae5ad65d..1333467e390 100644 --- a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb @@ -21,6 +21,7 @@ dependencies = [ exts_default_options = { 'source_urls': [ + 'https://bioconductor.org/packages/release/bioc/src/contrib/', # current version of packages 'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_biocver, 'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_biocver, 'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_biocver, From bf73f8b5750931dd4748ad7373e20505ac523587 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 13 Jul 2023 10:50:22 +0200 Subject: [PATCH 8034/9987] disable documentation --- .../easyconfigs/l/libsigc++/libsigc++-2.10.0-GCCcore-6.4.0.eb | 2 ++ .../easyconfigs/l/libsigc++/libsigc++-2.10.1-GCCcore-7.3.0.eb | 2 ++ .../easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.2.0.eb | 2 ++ .../easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.3.0.eb | 2 ++ .../easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb | 1 + 5 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-GCCcore-6.4.0.eb index 5fd469f7efa..a50f90446c9 100644 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-GCCcore-6.4.0.eb @@ -18,6 +18,8 @@ builddependencies = [ ('Autotools', '20170619'), ] +configopts = "--disable-documentation" + sanity_check_paths = { 'files': ['lib/libsigc-2.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.1-GCCcore-7.3.0.eb index 43b545404e2..3d9d2127eb2 100644 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.1-GCCcore-7.3.0.eb @@ -18,6 +18,8 @@ builddependencies = [ ('Autotools', '20180311'), ] +configopts = "--disable-documentation" + sanity_check_paths = { 'files': ['lib/libsigc-2.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.2.0.eb index 83f9164c81c..487644433f6 100644 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.2.0.eb @@ -18,6 +18,8 @@ builddependencies = [ ('Autotools', '20180311'), ] +configopts = "--disable-documentation" + sanity_check_paths = { 'files': ['lib/libsigc-2.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.3.0.eb index 3bd7a43f5b0..a17fae753ce 100644 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.2-GCCcore-8.3.0.eb @@ -18,6 +18,8 @@ builddependencies = [ ('Autotools', '20180311'), ] +configopts = "--disable-documentation" + sanity_check_paths = { 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb index 95ef05bda6a..301e4e20e77 100644 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.8-GCCcore-10.3.0.eb @@ -23,6 +23,7 @@ builddependencies = [ ] preconfigopts = "./autogen.sh && " +configopts = "--disable-documentation" sanity_check_paths = { 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], From 4607e19318a2e679cb9718a78908525daed0b25b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 13 Jul 2023 11:03:26 +0200 Subject: [PATCH 8035/9987] undo the configopts change for 2.10.0 --- .../easyconfigs/l/libsigc++/libsigc++-2.10.0-GCCcore-6.4.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-GCCcore-6.4.0.eb index a50f90446c9..5fd469f7efa 100644 --- a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.10.0-GCCcore-6.4.0.eb @@ -18,8 +18,6 @@ builddependencies = [ ('Autotools', '20170619'), ] -configopts = "--disable-documentation" - sanity_check_paths = { 'files': ['lib/libsigc-2.0.%s' % SHLIB_EXT], 'dirs': [], From 74a4839129210bb25dec0c147dd84191d23863bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 13 Jul 2023 11:19:06 +0200 Subject: [PATCH 8036/9987] lower version --- ...2022a-R-4.2.1.eb => inferCNV-1.12.0-foss-2022a-R-4.2.1.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/i/inferCNV/{inferCNV-1.16.0-foss-2022a-R-4.2.1.eb => inferCNV-1.12.0-foss-2022a-R-4.2.1.eb} (94%) diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.12.0-foss-2022a-R-4.2.1.eb similarity index 94% rename from easybuild/easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb rename to easybuild/easyconfigs/i/inferCNV/inferCNV-1.12.0-foss-2022a-R-4.2.1.eb index 1333467e390..71e6a1c5b06 100644 --- a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.16.0-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.12.0-foss-2022a-R-4.2.1.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'inferCNV' -version = '1.16.0' +version = '1.12.0' versionsuffix = '-R-%(rver)s' local_biocver = '3.15' @@ -40,7 +40,7 @@ exts_list = [ 'checksums': ['38786608193bcad6aeb5517f2d5f836c9773bdd09fc484b4bd40b06a71f5a413'], }), ('infercnv', version, { - 'checksums': ['af7c53de0bc78d5a030fa695d35531f8bac6c8ea83a4b7097437490eff25d3a5'], + 'checksums': ['740d5e8c29f76a07b0a5a9175b8babed3cbc6933c4cf3cc64105d4de5c10c005'], }), ] From f164003b61a44054218f466396c069bb73b6ca20 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 13 Jul 2023 14:10:37 +0200 Subject: [PATCH 8037/9987] separate easyconfig for cryptography using CargoPythonPackage, separate easyconfig for setuptools-rust, virtualenv, pycparser, cffi and scikit-build --- .../c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb | 27 ++++ .../cryptography-41.0.1-GCCcore-12.3.0.eb | 142 ++++++++++++++++++ ...thon-bundle-PyPI-2023.06-GCCcore-12.3.0.eb | 61 +------- .../p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb | 42 +++--- .../pycparser-2.21-GCCcore-12.3.0.eb | 24 +++ .../scikit-build-0.17.6-GCCcore-12.3.0.eb | 37 +++++ .../setuptools-rust-1.6.0-GCCcore-12.3.0.eb | 39 +++++ 7 files changed, 291 insertions(+), 81 deletions(-) create mode 100644 easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8de7f750994 --- /dev/null +++ b/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = "PythonPackage" + +name = 'cffi' +version = '1.15.1' + +homepage = 'https://cffi.readthedocs.io/en/latest/' +description = """C Foreign Function Interface for Python. Interact with almost any C code from +Python, based on C-like declarations that you can often copy-paste from header +files or documentation. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'] + +dependencies = [ + ('Python', '3.11.3'), + ('pycparser', '2.21'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2a262b5cd23 --- /dev/null +++ b/easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb @@ -0,0 +1,142 @@ +easyblock = 'CargoPythonPackage' + +name = 'cryptography' +version = '41.0.1' + +homepage = 'https://github.com/pyca/cryptography' +description = "cryptography is a package designed to expose cryptographic primitives and recipes to Python developers." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.70.0'), # required for cryptography + ('hatchling', '1.18.0'), + ('setuptools-rust', '1.6.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('pycparser', '2.21'), + ('cffi', '1.15.1'), +] + +crates = [ + ('Inflector', '0.11.4'), + ('aliasable', '0.1.3'), + ('asn1', '0.15.2'), + ('asn1_derive', '0.15.2'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('bitflags', '1.3.2'), + ('cc', '1.0.79'), + ('cfg-if', '1.0.0'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('indoc', '1.0.9'), + ('libc', '0.2.144'), + ('lock_api', '0.4.9'), + ('memoffset', '0.8.0'), + ('once_cell', '1.17.2'), + ('openssl', '0.10.54'), + ('openssl-macros', '0.1.1'), + ('openssl-sys', '0.9.88'), + ('ouroboros', '0.15.6'), + ('ouroboros_macro', '0.15.6'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.7'), + ('pem', '1.1.1'), + ('pkg-config', '0.3.27'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '1.0.59'), + ('pyo3', '0.18.3'), + ('pyo3-build-config', '0.18.3'), + ('pyo3-ffi', '0.18.3'), + ('pyo3-macros', '0.18.3'), + ('pyo3-macros-backend', '0.18.3'), + ('quote', '1.0.28'), + ('redox_syscall', '0.2.16'), + ('scopeguard', '1.1.0'), + ('smallvec', '1.10.0'), + ('syn', '1.0.109'), + ('syn', '2.0.18'), + ('target-lexicon', '0.12.7'), + ('unicode-ident', '1.0.9'), + ('unindent', '0.1.11'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('windows-sys', '0.45.0'), + ('windows-targets', '0.42.2'), + ('windows_aarch64_gnullvm', '0.42.2'), + ('windows_aarch64_msvc', '0.42.2'), + ('windows_i686_gnu', '0.42.2'), + ('windows_i686_msvc', '0.42.2'), + ('windows_x86_64_gnu', '0.42.2'), + ('windows_x86_64_gnullvm', '0.42.2'), + ('windows_x86_64_msvc', '0.42.2'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'cryptography-41.0.1.tar.gz': 'd34579085401d3f49762d2f7d6634d6b6c2ae1242202e860f4d26b046e3a1006'}, + {'Inflector-0.11.4.tar.gz': 'fe438c63458706e03479442743baae6c88256498e6431708f6dfc520a26515d3'}, + {'aliasable-0.1.3.tar.gz': '250f629c0161ad8107cf89319e990051fae62832fd343083bea452d93e2205fd'}, + {'asn1-0.15.2.tar.gz': '28c19b9324de5b815b6487e0f8098312791b09de0dbf3d5c2db1fe2d95bab973'}, + {'asn1_derive-0.15.2.tar.gz': 'a045c3ccad89f244a86bd1e6cf1a7bf645296e7692698b056399b6efd4639407'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'base64-0.13.1.tar.gz': '9e1b586273c5702936fe7b7d6896644d8be71e6314cfe09d3167c95f712589e8'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'cc-1.0.79.tar.gz': '50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'foreign-types-0.3.2.tar.gz': 'f6f339eb8adc052cd2ca78910fda869aefa38d22d5cb648e6485e4d3fc06f3b1'}, + {'foreign-types-shared-0.1.1.tar.gz': '00b0228411908ca8685dba7fc2cdd70ec9990a6e753e89b6ac91a84c40fbaf4b'}, + {'indoc-1.0.9.tar.gz': 'bfa799dd5ed20a7e349f3b4639aa80d74549c81716d9ec4f994c9b5815598306'}, + {'libc-0.2.144.tar.gz': '2b00cc1c228a6782d0f076e7b232802e0c5689d41bb5df366f2a6b6621cfdfe1'}, + {'lock_api-0.4.9.tar.gz': '435011366fe56583b16cf956f9df0095b405b82d76425bc8981c0e22e60ec4df'}, + {'memoffset-0.8.0.tar.gz': 'd61c719bcfbcf5d62b3a09efa6088de8c54bc0bfcd3ea7ae39fcc186108b8de1'}, + {'once_cell-1.17.2.tar.gz': '9670a07f94779e00908f3e686eab508878ebb390ba6e604d3a284c00e8d0487b'}, + {'openssl-0.10.54.tar.gz': '69b3f656a17a6cbc115b5c7a40c616947d213ba182135b014d6051b73ab6f019'}, + {'openssl-macros-0.1.1.tar.gz': 'a948666b637a0f465e8564c73e89d4dde00d72d4d473cc972f390fc3dcee7d9c'}, + {'openssl-sys-0.9.88.tar.gz': 'c2ce0f250f34a308dcfdbb351f511359857d4ed2134ba715a4eadd46e1ffd617'}, + {'ouroboros-0.15.6.tar.gz': 'e1358bd1558bd2a083fed428ffeda486fbfb323e698cdda7794259d592ca72db'}, + {'ouroboros_macro-0.15.6.tar.gz': '5f7d21ccd03305a674437ee1248f3ab5d4b1db095cf1caf49f1713ddf61956b7'}, + {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'}, + {'parking_lot_core-0.9.7.tar.gz': '9069cbb9f99e3a5083476ccb29ceb1de18b9118cafa53e90c9551235de2b9521'}, + {'pem-1.1.1.tar.gz': 'a8835c273a76a90455d7344889b0964598e3316e2a79ede8e36f16bdcf2228b8'}, + {'pkg-config-0.3.27.tar.gz': '26072860ba924cbfa98ea39c8c19b4dd6a4a25423dbdf219c1eca91aa0cf6964'}, + {'proc-macro-error-1.0.4.tar.gz': 'da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c'}, + {'proc-macro-error-attr-1.0.4.tar.gz': 'a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869'}, + {'proc-macro2-1.0.59.tar.gz': '6aeca18b86b413c660b781aa319e4e2648a3e6f9eadc9b47e9038e6fe9f3451b'}, + {'pyo3-0.18.3.tar.gz': 'e3b1ac5b3731ba34fdaa9785f8d74d17448cd18f30cf19e0c7e7b1fdb5272109'}, + {'pyo3-build-config-0.18.3.tar.gz': '9cb946f5ac61bb61a5014924910d936ebd2b23b705f7a4a3c40b05c720b079a3'}, + {'pyo3-ffi-0.18.3.tar.gz': 'fd4d7c5337821916ea2a1d21d1092e8443cf34879e53a0ac653fbb98f44ff65c'}, + {'pyo3-macros-0.18.3.tar.gz': 'a9d39c55dab3fc5a4b25bbd1ac10a2da452c4aca13bb450f22818a002e29648d'}, + {'pyo3-macros-backend-0.18.3.tar.gz': '97daff08a4c48320587b5224cc98d609e3c27b6d437315bd40b605c98eeb5918'}, + {'quote-1.0.28.tar.gz': '1b9ab9c7eadfd8df19006f1cf1a4aed13540ed5cbc047010ece5826e10825488'}, + {'redox_syscall-0.2.16.tar.gz': 'fb5a58c1855b4b6819d59012155603f0b22ad30cad752600aadfcb695265519a'}, + {'scopeguard-1.1.0.tar.gz': 'd29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd'}, + {'smallvec-1.10.0.tar.gz': 'a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0'}, + {'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'}, + {'syn-2.0.18.tar.gz': '32d41677bcbe24c20c52e7c70b0d8db04134c5d1066bf98662e2871ad200ea3e'}, + {'target-lexicon-0.12.7.tar.gz': 'fd1ba337640d60c3e96bc6f0638a939b9c9a7f2c316a1598c279828b3d1dc8c5'}, + {'unicode-ident-1.0.9.tar.gz': 'b15811caf2415fb889178633e7724bad2509101cde276048e013b9def5e51fa0'}, + {'unindent-0.1.11.tar.gz': 'e1766d682d402817b5ac4490b3c3002d91dfa0d22812f341609f97b08757359c'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'windows-sys-0.45.0.tar.gz': '75283be5efb2831d37ea142365f009c02ec203cd29a3ebecbc093d52315b66d0'}, + {'windows-targets-0.42.2.tar.gz': '8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071'}, + {'windows_aarch64_gnullvm-0.42.2.tar.gz': '597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8'}, + {'windows_aarch64_msvc-0.42.2.tar.gz': 'e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43'}, + {'windows_i686_gnu-0.42.2.tar.gz': 'c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f'}, + {'windows_i686_msvc-0.42.2.tar.gz': '44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060'}, + {'windows_x86_64_gnu-0.42.2.tar.gz': '8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36'}, + {'windows_x86_64_gnullvm-0.42.2.tar.gz': '26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3'}, + {'windows_x86_64_msvc-0.42.2.tar.gz': '9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0'}, +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb index ac498be08d8..f55e94daf8e 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb @@ -14,9 +14,10 @@ builddependencies = [ ('Rust', '1.70.0'), # required for setuptools-rust, which is needed for cryptography and bcrypt ('pkgconf', '1.9.5'), ('git', '2.41.0', '-nodocs'), # required for pbr + ('setuptools-rust', '1.6.0'), # required for cryptography and bcrypt ('hatchling', '1.18.0'), - ('virtualenv', '20.23.1'), ('poetry', '1.5.1'), + ('scikit-build', '0.17.6'), ] dependencies = [ @@ -31,6 +32,7 @@ dependencies = [ ('GMP', '6.2.1'), # required for pycrypto ('libffi', '3.4.4'), ('OpenSSL', '1.1', '', SYSTEM), + ('cryptography', '41.0.1'), ] exts_default_options = { @@ -76,9 +78,6 @@ exts_list = [ ('packaging', '23.1', { 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], }), - # ('setuptools_scm', '7.1.0', { - # 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], - # }), ('python-dateutil', '2.8.2', { 'modulename': 'dateutil', 'checksums': ['0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86'], @@ -118,15 +117,6 @@ exts_list = [ ('typing_extensions', '4.6.3', { 'checksums': ['d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5'], }), - # ('setuptools-rust', '1.6.0', { - # 'checksums': ['c86e734deac330597998bfbc08da45187e6b27837e23bd91eadb320732392262'], - # }), - ('cryptography', '41.0.1', { - # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, - # see https://github.com/rust-lang/cargo/issues/6652 - 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", - 'checksums': ['d34579085401d3f49762d2f7d6634d6b6c2ae1242202e860f4d26b046e3a1006'], - }), ('pyasn1', '0.5.0', { 'checksums': ['97b7290ca68e62a832558ec3976f15cbf911bf5d7c7039d8b861c2a0ece69fde'], }), @@ -183,16 +173,6 @@ exts_list = [ ('editables', '0.3', { 'checksums': ['167524e377358ed1f1374e61c268f0d7a4bf7dbd046c656f7b410cde16161b1a'], }), - # ('trove_classifiers', '2023.5.24', { - # 'source_tmpl': SOURCE_PY3_WHL, - # 'checksums': ['d9d7ae14fb90bf3d50bef99c3941b176b5326509e6e9037e622562d6352629d0'], - # }), - # ('hatchling', '1.18.0', { - # 'checksums': ['50e99c3110ce0afc3f7bdbadff1c71c17758e476731c27607940cfa6686489ca'], - # }), - # ('hatch_vcs', '0.3.0', { - # 'checksums': ['cec5107cfce482c67f8bc96f18bbc320c9aa0d068180e14ad317bbee5a153fee'], - # }), ('filelock', '3.12.2', { 'checksums': ['002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81'], }), @@ -208,9 +188,6 @@ exts_list = [ ('importlib_resources', '5.12.0', { 'checksums': ['4be82589bf5c1d7999aedf2a45159d10cb3ca4f19b2271f8792bc8e6da7b22f6'], }), - # ('virtualenv', '20.23.1', { - # 'checksums': ['8ff19a38c1021c742148edc4f81cb43d7f8c6816d2ede2ab72af5b84c749ade1'], - # }), ('docopt', '0.6.2', { 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], }), @@ -254,9 +231,6 @@ exts_list = [ ('more-itertools', '9.1.0', { 'checksums': ['cabaa341ad0389ea83c17a94566a53ae4c9d07349861ecb14dc6d0345cf9ac5d'], }), - # ('hatch_fancy_pypi_readme', '23.1.0', { - # 'checksums': ['b1df44063094af1e8248ceacd47a92c9cf313d6b9823bf66af8a927c3960287d'], - # }), ('attrs', '23.1.0', { 'modulename': 'attr', 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], @@ -273,9 +247,6 @@ exts_list = [ ('colorama', '0.4.6', { 'checksums': ['08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44'], }), - # ('flit_scm', '1.7.0', { - # 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], - # }), ('exceptiongroup', '1.1.1', { 'checksums': ['d484c3090ba2889ae2928419117447a14daf3c1231d5e30d0aae34f354f01785'], }), @@ -364,9 +335,6 @@ exts_list = [ ('tomli_w', '1.0.0', { 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], }), - # ('flit', '3.9.0', { - # 'checksums': ['d75edf5eb324da20d53570a6a6f87f51e606eee8384925cd66a90611140844c7'], - # }), ('regex', '2023.6.3', { 'checksums': ['72d1a25bf36d2050ceb35b517afe13864865268dfb45910e2e17a84be6cbfeb0'], }), @@ -448,10 +416,6 @@ exts_list = [ ('distro', '1.8.0', { 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], }), - # ('scikit_build', '0.17.6', { - # 'modulename': 'skbuild', - # 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], - # }), ('rapidfuzz', '2.15.1', { 'checksums': ['d62137c2ca37aea90a11003ad7dc109c8f1739bfbe5a9a217f3cdb07d7ac00f6'], }), @@ -471,31 +435,12 @@ exts_list = [ ('lockfile', '0.12.2', { 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), - # ('poetry_core', '1.6.1', { - # 'modulename': 'poetry.core', - # 'checksums': ['0f9b0de39665f36d6594657e7d57b6f463cc10f30c28e6d1c3b9ff54c26c9ac3'], - # }), ('glob2', '0.7', { 'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'], }), ('dulwich', '0.21.5', { 'checksums': ['70955e4e249ddda6e34a4636b90f74e931e558f993b17c52570fa6144b993103'], }), - # ('poetry_plugin_export', '1.4.0', { - # 'checksums': ['f16974cd9f222d4ef640fa97a8d661b04d4fb339e51da93973f1bc9d578e183f'], - # }), - # ('build', '0.10.0', { - # 'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'], - # }), - # ('installer', '0.7.0', { - # 'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631'], - # }), - # ('pyproject_hooks', '1.0.0', { - # 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], - # }), - # ('poetry', '1.5.1', { - # 'checksums': ['cc7ea4524d1a11558006224bfe8ba8ed071417d4eb5ef6c89decc6a37d437eeb'], - # }), ('fsspec', '2023.6.0', { 'checksums': ['d0b2f935446169753e7a5c5c55681c54ea91996cc67be93c39a154fb3a2742af'], }), diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb index 87953f0ae2a..ebec73898ee 100755 --- a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb @@ -13,13 +13,15 @@ builddependencies = [ ('binutils', '2.40'), ('pkgconf', '1.9.5'), ('Rust', '1.70.0'), # required for setuptools-rust, which is needed for cryptography + ('setuptools-rust', '1.6.0'), + ('scikit-build', '0.17.6'), ] dependencies = [ ('Python', '3.11.3'), ('hatchling', '1.18.0'), - ('virtualenv', '20.23.1'), ('OpenSSL', '1.1', '', SYSTEM), + ('cryptography', '41.0.1'), ] use_pip = True @@ -77,24 +79,9 @@ exts_list = [ 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], }), - ('pycparser', '2.21', { - 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], - }), - ('cffi', '1.15.1', { - 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], - }), ('semantic_version', '2.10.0', { 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], }), - ('setuptools-rust', '1.6.0', { - 'checksums': ['c86e734deac330597998bfbc08da45187e6b27837e23bd91eadb320732392262'], - }), - ('cryptography', '41.0.1', { - # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, - # see https://github.com/rust-lang/cargo/issues/6652 - 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", - 'checksums': ['d34579085401d3f49762d2f7d6634d6b6c2ae1242202e860f4d26b046e3a1006'], - }), ('pyasn1', '0.5.0', { 'checksums': ['97b7290ca68e62a832558ec3976f15cbf911bf5d7c7039d8b861c2a0ece69fde'], }), @@ -127,13 +114,13 @@ exts_list = [ ('html5lib', '1.1', { 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), - ('distro', '1.8.0', { - 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], - }), - ('scikit_build', '0.17.6', { - 'modulename': 'skbuild', - 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], - }), + # ('distro', '1.8.0', { + # 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + # }), + # ('scikit_build', '0.17.6', { + # 'modulename': 'skbuild', + # 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], + # }), ('rapidfuzz', '2.15.1', { 'checksums': ['d62137c2ca37aea90a11003ad7dc109c8f1739bfbe5a9a217f3cdb07d7ac00f6'], }), @@ -193,6 +180,15 @@ exts_list = [ ('poetry_plugin_export', '1.4.0', { 'checksums': ['f16974cd9f222d4ef640fa97a8d661b04d4fb339e51da93973f1bc9d578e183f'], }), + ('distlib', '0.3.6', { + 'checksums': ['14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46'], + }), + ('filelock', '3.12.2', { + 'checksums': ['002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81'], + }), + ('virtualenv', '20.23.1', { + 'checksums': ['8ff19a38c1021c742148edc4f81cb43d7f8c6816d2ede2ab72af5b84c749ade1'], + }), (name, version, { 'checksums': ['cc7ea4524d1a11558006224bfe8ba8ed071417d4eb5ef6c89decc6a37d437eeb'], }), diff --git a/easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..46d0e1cf5ff --- /dev/null +++ b/easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'pycparser' +version = '2.21' + +homepage = 'https://github.com/eliben/pycparser' +description = """pycparser is a parser for the C language, written in pure Python. It is a +module designed to be easily integrated into applications that need to parse C source code.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'] + +dependencies = [ + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..624754a216d --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.17.6' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('scikit_build', version, { + 'modulename': 'skbuild', + 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..10b275d3966 --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'setuptools-rust' +version = '1.6.0' + +homepage = 'https://python.org/' +description = "A tool for creating isolated virtual python environments." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.70.0'), # required for setuptools-rust +] + +dependencies = [ + ('Python', '3.11.3'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('typing_extensions', '4.6.3', { + 'checksums': ['d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5'], + }), + ('semantic_version', '2.10.0', { + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + (name, version, { + 'checksums': ['c86e734deac330597998bfbc08da45187e6b27837e23bd91eadb320732392262'], + }), +] + +moduleclass = 'tools' From 82069cc881d2009a74b9476298e9e45bc5284d44 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 13 Jul 2023 14:18:32 +0200 Subject: [PATCH 8038/9987] add pkgconf builddependency to cryptography easyconfig --- .../c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb index 2a262b5cd23..eca6ec79d06 100644 --- a/easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb @@ -11,6 +11,7 @@ toolchainopts = {'pic': True} builddependencies = [ ('binutils', '2.40'), + ('pkgconf', '1.9.5'), ('Rust', '1.70.0'), # required for cryptography ('hatchling', '1.18.0'), ('setuptools-rust', '1.6.0'), From b4699b7b0b0cfde019352438da1bcde655cf17bd Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 13 Jul 2023 13:19:14 +0100 Subject: [PATCH 8039/9987] use MCR dependency in FreeSurfer 7.3.2 and 7.4.0 --- .../FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb | 15 +++++---------- .../FreeSurfer/FreeSurfer-7.3.2-centos8_x86_64.eb | 15 +++++---------- .../FreeSurfer/FreeSurfer-7.4.0-centos8_x86_64.eb | 15 +++++---------- .../FreeSurfer/FreeSurfer-7.4.0-ubuntu20_amd64.eb | 15 +++++---------- .../FreeSurfer/FreeSurfer-7.4.0-ubuntu22_amd64.eb | 15 +++++---------- 5 files changed, 25 insertions(+), 50 deletions(-) diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb index 56892c77fd0..b748541a3a9 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb @@ -10,21 +10,16 @@ longitudinal data.""" toolchain = SYSTEM -source_urls = [ - 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', - 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' -] -sources = [ - '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', - 'runtime2014bLinux.tar.gz' -] +source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/'] +sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz'] checksums = [ {'freesurfer-linux-centos7_x86_64-7.3.2.tar.gz': '58518d3ee5abd2e05109208aed2eef145c4e3b994164df8c4e0033c1343b9e56'}, - {'runtime2014bLinux.tar.gz': '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648'}, ] -postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] +dependencies = [('MCR', 'R2019b.8')] + +postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"] license_text = """email@example.com 00000 diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos8_x86_64.eb index ed3474f3130..1fc9fd09b84 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos8_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos8_x86_64.eb @@ -10,21 +10,16 @@ longitudinal data.""" toolchain = SYSTEM -source_urls = [ - 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', - 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' -] -sources = [ - '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', - 'runtime2014bLinux.tar.gz' -] +source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/'] +sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz'] checksums = [ # freesurfer-linux-centos8_x86_64-7.3.2.tar.gz '1448e64000b02a06aaad81548a4c8f92faf575f8320e67bdcd15a430ad10879b', - '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648', # runtime2014bLinux.tar.gz ] -postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] +dependencies = [('MCR', 'R2019b.8')] + +postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"] license_text = """email@example.com 00000 diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-centos8_x86_64.eb index 5f72e9c0cde..d50470775f8 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-centos8_x86_64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-centos8_x86_64.eb @@ -10,21 +10,16 @@ longitudinal data.""" toolchain = SYSTEM -source_urls = [ - 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', - 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' -] -sources = [ - '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', - 'runtime2014bLinux.tar.gz' -] +source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/'] +sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz'] checksums = [ {'freesurfer-linux-centos8_x86_64-7.4.0.tar.gz': 'a2eb8ca6d12c9133c4af90167d6b9fa532f7ace98cc0e1bc97c8a6135b53c237'}, - {'runtime2014bLinux.tar.gz': '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648'}, ] -postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] +dependencies = [('MCR', 'R2019b.8')] + +postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"] license_text = """email@example.com 00000 diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu20_amd64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu20_amd64.eb index 42b6fc18c68..68ca847668d 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu20_amd64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu20_amd64.eb @@ -10,21 +10,16 @@ longitudinal data.""" toolchain = SYSTEM -source_urls = [ - 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', - 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' -] -sources = [ - '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', - 'runtime2014bLinux.tar.gz' -] +source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/'] +sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz'] checksums = [ {'freesurfer-linux-ubuntu20_amd64-7.4.0.tar.gz': '2149e0d54220abf81b0caa5736b648b56f409b1e6578d921d0f7e4d62d586ca5'}, - {'runtime2014bLinux.tar.gz': '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648'}, ] -postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] +dependencies = [('MCR', 'R2019b.8')] + +postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"] license_text = """email@example.com 00000 diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu22_amd64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu22_amd64.eb index cd51ff885bd..0ae8d331302 100644 --- a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu22_amd64.eb +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.0-ubuntu22_amd64.eb @@ -10,21 +10,16 @@ longitudinal data.""" toolchain = SYSTEM -source_urls = [ - 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', - 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' -] -sources = [ - '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', - 'runtime2014bLinux.tar.gz' -] +source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/'] +sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz'] checksums = [ {'freesurfer-linux-ubuntu22_amd64-7.4.0.tar.gz': 'acd7f8b9a75cf41fab837caa95f2c9017079c15ca4446df2c47c88c321264f82'}, - {'runtime2014bLinux.tar.gz': '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648'}, ] -postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] +dependencies = [('MCR', 'R2019b.8')] + +postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"] license_text = """email@example.com 00000 From 4ce7219ab64fa337a6cfcd4301441f13376b6570 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Thu, 13 Jul 2023 14:25:35 +0200 Subject: [PATCH 8040/9987] Adding environment variable for libpng MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb index 22e0595ea3a..d07fe2730ad 100644 --- a/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb @@ -32,6 +32,7 @@ _pygame_extra_base = ':'.join([ '$EBROOTSDL2_MIXER', '$EBROOTSDL2_TTF', '$EBROOTLIBJPEGMINTURBO', + '$EBROOTLIBPNG', '$EBROOTPORTMIDI', ]) From 34e58127c8d4e1ae1ea0c7f5828a9f5a0e7a30f3 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 13 Jul 2023 14:36:04 +0200 Subject: [PATCH 8041/9987] add binutils builddependency to pycparser and cffi easyconfig --- easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb | 4 ++++ .../easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb index 8de7f750994..289c0b41712 100644 --- a/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb @@ -15,6 +15,10 @@ toolchainopts = {'pic': True} sources = [SOURCE_TAR_GZ] checksums = ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'] +builddependencies = [ + ('binutils', '2.40'), +] + dependencies = [ ('Python', '3.11.3'), ('pycparser', '2.21'), diff --git a/easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb index 46d0e1cf5ff..b03acaf84d9 100644 --- a/easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb @@ -13,6 +13,10 @@ toolchainopts = {'pic': True} sources = [SOURCE_TAR_GZ] checksums = ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'] +builddependencies = [ + ('binutils', '2.40'), +] + dependencies = [ ('Python', '3.11.3'), ] From 02e8f5cbd077dbd2a99b937e9aa843bfcf713647 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 13 Jul 2023 14:45:55 +0200 Subject: [PATCH 8042/9987] update virtualenv to depend on Python-bundle-PyPI --- .../v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb index 93fdd5fa2d3..48030df472c 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb @@ -16,6 +16,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), ] exts_default_options = { @@ -25,15 +26,6 @@ exts_default_options = { } exts_list = [ - ('distlib', '0.3.6', { - 'checksums': ['14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46'], - }), - ('filelock', '3.12.2', { - 'checksums': ['002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81'], - }), - ('platformdirs', '3.8.0', { - 'checksums': ['b0cabcb11063d21a0b261d557acb0a9d2126350e63b70cdf7db6347baea456dc'], - }), (name, version, { 'checksums': ['8ff19a38c1021c742148edc4f81cb43d7f8c6816d2ede2ab72af5b84c749ade1'], }), From 734cba051b0767d71d3345c9b41b5ea6ecc0f279 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 13 Jul 2023 17:18:07 +0200 Subject: [PATCH 8043/9987] adding easyconfigs: RFdiffusion-1.1.0-foss-2022a.eb, e3nn-0.3.3-foss-2022a.eb, Hydra-1.3.2-GCCcore-11.3.0.eb and patches: RFdiffusion-1.1.0_fix-find-packages.patch --- .../e/e3nn/e3nn-0.3.3-foss-2022a.eb | 37 ++++++++++++ .../h/Hydra/Hydra-1.3.2-GCCcore-11.3.0.eb | 47 ++++++++++++++++ .../RFdiffusion-1.1.0-foss-2022a.eb | 56 +++++++++++++++++++ .../RFdiffusion-1.1.0_fix-find-packages.patch | 20 +++++++ 4 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0_fix-find-packages.patch diff --git a/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a.eb b/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a.eb new file mode 100644 index 00000000000..b15c5d16a2d --- /dev/null +++ b/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'e3nn' +version = '0.3.3' + +homepage = 'https://e3nn.org/' +description = """ +Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant +neural networks for the group O(3). +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.0'), + ('sympy', '1.11.1'), +] + +use_pip = True + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('opt_einsum_fx', '0.1.4', { + 'checksums': ['7eeb7f91ecb70be65e6179c106ea7f64fc1db6319e3d1289a4518b384f81e74f'], + }), + (name, version, { + 'checksums': ['532b34a5644153659253c59943fe4224cd9c3c46ce8a79f1dc7c00afccb44ecb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..ef233b53ed6 --- /dev/null +++ b/easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'Hydra' +version = '1.3.2' + +homepage = "https://hydra.cc/" +description = """ +Hydra is an open-source Python framework that simplifies the development of +research and other complex applications. The key feature is the ability to +dynamically create a hierarchical configuration by composition and override it +through config files and the command line. The name Hydra comes from its +ability to run multiple similar jobs - much like a Hydra with multiple heads. +""" + +github_account = 'facebookresearch' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('Java', '17', '', SYSTEM), # needed by ANTLR runtime +] + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), # needed by omegaconf +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('antlr4-python3-runtime', '4.9', { + 'modulename': 'antlr4', + 'checksums': ['02d9afb720c13c52b336234286966cdf5aff704f230a513e635adb0d94de97ae'], + }), + ('omegaconf', '2.3.0', { + 'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'], + }), + ('hydra', version, { + 'source_urls': ['https://github.com/%(github_account)s/%(namelower)s/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['3f0f14305e9c6ae4b1dbcba344fe09dd0fc79c0a0656470c249f4f7ca46bf471'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a.eb b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a.eb new file mode 100644 index 00000000000..c0d318b938d --- /dev/null +++ b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'RFdiffusion' +version = '1.1.0' + +homepage = 'https://github.com/RosettaCommons/RFdiffusion' +description = """ +RFdiffusion is an open source method for structure generation, with or without conditional information +(a motif, target etc). It can perform a whole range of protein design challenges as we have outlined +in the RFdiffusion paper. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('e3nn', '0.3.3'), + ('wandb', '0.13.4'), +] + +use_pip = True + +exts_list = [ + ('pynvml', '11.0.0', { + 'checksums': ['d5fc4a22d355b40c341d6ba0aa888a2d4d2253177d243900f8401b7e6cacb1bb'], + }), + ('dllogger', '1.0.0', { + 'source_urls': ['https://github.com/NVIDIA/dllogger/archive/refs/tags'], + 'sources': ['v%(version)s.zip'], + 'checksums': ['07d0cd9b9b56f454f0c186a0889137e9f94e1979fca3d35911967c874c93c191'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('se3-transformer', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/RosettaCommons/RFdiffusion/archive/refs/tags'], + 'start_dir': 'env/SE3Transformer', + 'checksums': ['57d82f0d43540c2912eda3f1d34ad90b13db14966ee069c427e217fe78f0297f'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_fix-find-packages.patch'], + 'source_urls': ['https://github.com/RosettaCommons/RFdiffusion/archive/refs/tags'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': [ + {'v1.1.0.tar.gz': '57d82f0d43540c2912eda3f1d34ad90b13db14966ee069c427e217fe78f0297f'}, + {'RFdiffusion-1.1.0_fix-find-packages.patch': + '0e92f970a48e29dfb2d0354341f18f05ba4d79e864d5e4970b5c8d78a6f1bdb0'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0_fix-find-packages.patch b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0_fix-find-packages.patch new file mode 100644 index 00000000000..c2870df522c --- /dev/null +++ b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0_fix-find-packages.patch @@ -0,0 +1,20 @@ +diff --git a/setup.py b/setup.py +index 2761c12..6eb62b6 100644 +--- a/setup.py ++++ b/setup.py +@@ -1,10 +1,10 @@ +-from distutils.core import setup ++from setuptools import setup, find_packages + + setup(name='rfdiffusion', +- version='1.0.0', ++ version='1.1.0', + description='RFdiffusion is an open source method for protein structure generation.', + author='Rosetta Commons', + url='https://github.com/RosettaCommons/RFdiffusion', + scripts=["scripts/run_inference.py"], +- packages=["rfdiffusion"], +- install_requires=['torch', 'se3-transformer']) +\ No newline at end of file ++ packages=find_packages(), ++ install_requires=['torch', 'se3-transformer']) From dc35036d8c770caa8d756251b3ac6c70486a9d22 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 13 Jul 2023 18:09:53 +0200 Subject: [PATCH 8044/9987] adding easyconfigs: ruptures-1.1.8-foss-2022a.eb and patches: ruptures-1.1.8_fix-scipy-version.patch --- .../r/ruptures/ruptures-1.1.8-foss-2022a.eb | 38 +++++++++++++++++++ .../ruptures-1.1.8_fix-scipy-version.patch | 14 +++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/r/ruptures/ruptures-1.1.8-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/ruptures/ruptures-1.1.8_fix-scipy-version.patch diff --git a/easybuild/easyconfigs/r/ruptures/ruptures-1.1.8-foss-2022a.eb b/easybuild/easyconfigs/r/ruptures/ruptures-1.1.8-foss-2022a.eb new file mode 100644 index 00000000000..58dc52ba0ee --- /dev/null +++ b/easybuild/easyconfigs/r/ruptures/ruptures-1.1.8-foss-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'ruptures' +version = '1.1.8' + +homepage = 'https://github.com/deepcharles/ruptures/' +description = """ +ruptures is a Python library for off-line change point detection. This package provides +methods for the analysis and segmentation of non-stationary signals. Implemented +algorithms include exact and approximate detection for various parametric and +non-parametric models. ruptures focuses on ease of use by providing a well-documented and +consistent interface. In addition, thanks to its modular structure, different algorithms +and models can be connected and extended within this package. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'patches': ['%(name)s-%(version)s_fix-scipy-version.patch'], + 'checksums': [ + {'ruptures-1.1.8.tar.gz': '75e1814851b706218c47a733d3d1c94acdcc690f35c69c08d48f0df9d3672cb6'}, + {'ruptures-1.1.8_fix-scipy-version.patch': + '6e0d1286e5b9db7372d13cb01d8f8cb0cf0e722b08950a2cf074d3082ba57c43'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ruptures/ruptures-1.1.8_fix-scipy-version.patch b/easybuild/easyconfigs/r/ruptures/ruptures-1.1.8_fix-scipy-version.patch new file mode 100644 index 00000000000..e4395507856 --- /dev/null +++ b/easybuild/easyconfigs/r/ruptures/ruptures-1.1.8_fix-scipy-version.patch @@ -0,0 +1,14 @@ +Avoid scipy and numpy version requirement +Author: Cintia Willemyns (Vrije Universiteit Brussel) +--- a/pyproject.toml 2023-07-13 16:11:09.662444000 +0200 ++++ b/pyproject.toml 2023-07-13 16:12:18.320284000 +0200 +@@ -5,8 +5,8 @@ + "wheel", + "Cython>=0.28.5", + "setuptools_scm[toml]>=3.4", # https://scikit-hep.org/developer/packaging#git-tags-official-pypa-method +- "oldest-supported-numpy", # https://github.com/scipy/oldest-supported-numpy +- "scipy>=0.19.1", ++ "numpy", ++ "scipy", + ] + build-backend = "setuptools.build_meta" From 50b07b636e46fa6daa28bb8c464dbb24958547e2 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Thu, 13 Jul 2023 16:10:58 -0700 Subject: [PATCH 8045/9987] Use CargoPythonPackage with maturin MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb index dd2b4d8f045..edfd1ab8d11 100644 --- a/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb @@ -25,6 +25,8 @@ sanity_pip_check = True exts_list = [ ('maturin', '1.1.0', { + 'easyblock': 'CargoPythonPackage', + 'offline': False, 'checksums': ['4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'], }), ('thrift', '0.16.0', { From 8322ce927768dc59d9e10eab71c00cdf88326fba Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 14 Jul 2023 09:43:00 +0200 Subject: [PATCH 8046/9987] update poetry to use scikit-build builddependecy --- .../easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb index ebec73898ee..34166a0b0b4 100755 --- a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb @@ -114,13 +114,6 @@ exts_list = [ ('html5lib', '1.1', { 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), - # ('distro', '1.8.0', { - # 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], - # }), - # ('scikit_build', '0.17.6', { - # 'modulename': 'skbuild', - # 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], - # }), ('rapidfuzz', '2.15.1', { 'checksums': ['d62137c2ca37aea90a11003ad7dc109c8f1739bfbe5a9a217f3cdb07d7ac00f6'], }), From 8c2b214df8f6b6f3038c902075aa61b8a025f0b7 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 14 Jul 2023 11:09:44 +0200 Subject: [PATCH 8047/9987] changing sympy version to version in 2022a toolchain generation (version: 1.10.1) --- easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a.eb b/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a.eb index b15c5d16a2d..acfcfad4838 100644 --- a/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a.eb +++ b/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a.eb @@ -15,7 +15,7 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('PyTorch', '1.12.0'), - ('sympy', '1.11.1'), + ('sympy', '1.10.1'), ] use_pip = True From 354cf60bc6ded379b2ee50abadd2d93e3571ddf9 Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 14 Jul 2023 10:04:31 +0000 Subject: [PATCH 8048/9987] adding easyconfigs: Seurat-4.1.0-foss-2021a-R-4.1.0.eb --- .../Seurat/Seurat-4.1.0-foss-2021a-R-4.1.0.eb | 75 +++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.1.0-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.1.0-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.1.0-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..acea76329ab --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.1.0-foss-2021a-R-4.1.0.eb @@ -0,0 +1,75 @@ +# # +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Arturo Gimeno , Pau Ruiz +# License:: GPL-v3.0 +# # + +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('R', '4.1.0'), + ('R-bundle-Bioconductor', '3.13', versionsuffix), +] + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('Matrix', '1.5-1', { + 'checksums': ['557dba0358172d67dc63eb5db90841915bb5ce1528f941a8005ae808d635575d'], + }), + ('scattermore', '0.7', { + 'checksums': ['f36280197b8476314d6ce81a51c4ae737180b180204043d2937bc25bf3a5dfa2'], + }), + ('rlang', '0.4.10', { + 'checksums': ['07530270c4c199f2b7efc5d57a476d99babd9d0c3388a02bb7d57fe312da3576'], + }), + ('RcppAnnoy', '0.0.18', { + 'checksums': ['e4e7ddf071109b47b4fdf285db6d2155618ed73da829c30d8e64fc778e63c858'], + }), + ('Rcpp', '1.0.7', { + 'checksums': ['15e5a4732216daed16263c79fb37017c2ada84a2d4e785e3b76445d0eba3dc1d'], + }), + ('rgeos', '0.6-3', { + 'checksums': ['1ebc5a99fdcf7d293811ce26379ba1525a2b9f23b11f1fb4a9c582bf27fc2b3c'], + }), + ('SeuratObject', version, { + 'checksums': ['9ca406cb3bd95c588e1a81c5383e3173a446cc0667142b139ca32685b4b20a05'], + }), + ('sctransform', '0.3.5', { + 'checksums': ['c08e56df05d64ed04ee53eb9e1d4d321da8aff945e36d56db1d5ceb1cd7e6e0b'], + }), + ('uwot', '0.1.10', { + 'checksums': ['6ee1b6027bce679cd5a35f647f516a5b327632234bcf323c7f3d5b5e10807d23'], + }), + (name, version, { + 'checksums': ['2505829a2763e449684dd1b107ee6982e019ee9fecb093adca7b283cad1b315d'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name, 'scattermore', 'rlang', 'RcppAnnoy', 'Rcpp', 'SeuratObject', 'sctransform', 'uwot'], +} + +moduleclass = 'bio' From 0bdf60817e4530d9551f4e7000f2c4eba717222d Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 14 Jul 2023 14:08:44 +0200 Subject: [PATCH 8049/9987] adding easyconfigs: Mercurial-6.4.5-GCCcore-12.3.0.eb --- .../Mercurial-6.4.5-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mercurial/Mercurial-6.4.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-6.4.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.4.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4544ab05627 --- /dev/null +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-6.4.5-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +## +# Author: Robert Mijakovic +## +easyblock = "PythonPackage" + +name = 'Mercurial' +version = '6.4.5' + +homepage = 'https://www.mercurial-scm.org' +description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects +of any size and offers an easy and intuitive interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.mercurial-scm.org/release/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b0b4b00b8b2639c8be387394796f0425beb339314df7e72937f8ddd2a41b1b8a'] + +dependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.3') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_commands = ["hg --help"] + +moduleclass = 'tools' From 3581e4bccb1323b489ccaff755f0444c6aead2ae Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 14 Jul 2023 15:11:56 +0200 Subject: [PATCH 8050/9987] adding easyconfigs: Lua-5.4.6-GCCcore-12.3.0.eb --- .../l/Lua/Lua-5.4.6-GCCcore-12.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.4.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.4.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.4.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3886e8a463e --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.4.6-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +name = 'Lua' +version = '5.4.6' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7d5ea1b9cb6aa0b59ca3dde1c6adcb57ef83a1ba8e5432c0ecd06bf439b3ad88'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('libreadline', '8.2'), +] + +moduleclass = 'lang' From 9a23aa4aa2678b5f731c44b89f4b8ea5f2dc765c Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 14 Jul 2023 15:26:42 +0200 Subject: [PATCH 8051/9987] adding easyconfigs: Julia-1.9.2-linux-x86_64.eb --- .../j/Julia/Julia-1.9.2-linux-x86_64.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb new file mode 100644 index 00000000000..160f52e7e4d --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.9.2' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['4c2d799f442d7fe718827b19da2bacb72ea041b9ce55f24eee7b1313f57c4383'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +_depot_paths = ':'.join([ + # first entry must be the user depot + # see https://pkgdocs.julialang.org/v1/glossary/ + '~/.julia', + # base installation of Julia + '%(installdir)s/share/julia', +]) + +modextravars = { + 'JULIA_DEPOT_PATH': _depot_paths, + # by default JULIA_HISTORY points to top path in DEPOT_PATH + # set JULIA_HISTORY to always use the user depot (~/.julia) + # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY + 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', +} + +moduleclass = 'lang' From 981d50f15f09794d623a8836c72889332d76b6da Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 14 Jul 2023 16:03:24 +0200 Subject: [PATCH 8052/9987] Add Guile and dependencies --- .../g/Guile/Guile-3.0.9-GCCcore-12.3.0.eb | 46 +++++++++++++++++++ .../g/gc/gc-8.2.2-GCCcore-12.3.0.eb | 42 +++++++++++++++++ .../libunistring-1.1-GCCcore-12.3.0.eb | 31 +++++++++++++ 3 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1e338e06f27 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '3.0.9' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['18525079ad29a0d46d15c76581b5d91c8702301bfd821666d2e1d13726162811'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('gc', '8.2.2'), + ('GMP', '6.2.1'), + ('libffi', '3.4.4'), + ('libunistring', '1.1'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9675538152d --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.2.2' +local_libatomic_version = '7.6.14' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a +garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + 'f30107bcb062e0920a790ffffa56d9512348546859364c23a14be264b38836a0', # gc-8.2.2.tar.gz + '390f244d424714735b7050d056567615b3b8f29008a663c262fb548f1802d292', # libatomic_ops-7.6.14.tar.gz +] + +builddependencies = [ + ('binutils', '2.40'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..26999b04bd7 --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.1' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['827c1eb9cb6e7c738b171745dac0888aa58c5924df2e59239318383de0729b98'] + +builddependencies = [ + ('binutils', '2.40'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' From 0b46ffd9ee2324ed9acfcb26d0ef68a44414c637 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Fri, 14 Jul 2023 17:32:59 +0200 Subject: [PATCH 8053/9987] set PORTMIDI_INC_PORTTIME in pygame MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb index d07fe2730ad..8289fdb8c6b 100644 --- a/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pygame/pygame-2.1.0-GCCcore-11.3.0.eb @@ -38,7 +38,7 @@ _pygame_extra_base = ':'.join([ exts_list = [ ('pygame', '2.1.0', { - 'preinstallopts': 'PYGAME_EXTRA_BASE="%s"' % _pygame_extra_base, + 'preinstallopts': 'PORTMIDI_INC_PORTTIME=1 PYGAME_EXTRA_BASE="%s"' % _pygame_extra_base, 'checksums': ['232e51104db0e573221660d172af8e6fc2c0fda183c5dbf2aa52170f29aa9ec9'], }), ] From 97627121f9aa183bcf28d5ddb9584873a4d24bd4 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 15 Jul 2023 09:16:50 +0100 Subject: [PATCH 8054/9987] reorder easyconfig --- .../connected-components-3d-3.12.1-foss-2022b.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb index 36561dd4ff9..c1828ecce9e 100644 --- a/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb +++ b/easybuild/easyconfigs/c/connected-components-3d/connected-components-3d-3.12.1-foss-2022b.eb @@ -2,8 +2,6 @@ easyblock = 'PythonPackage' name = 'connected-components-3d' version = '3.12.1' -options = {'modulename': 'cc3d'} - homepage = 'https://github.com/seung-lab/connected-components-3d/' description = """cc3d is an implementation of connected components in three dimensions using a 26, 18, @@ -20,8 +18,9 @@ dependencies = [ ] download_dep_fail = True - use_pip = True - sanity_pip_check = True + +options = {'modulename': 'cc3d'} + moduleclass = 'data' From f305574473e74108f08bb36a4b3e763891678ec0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Jul 2023 10:42:48 +0200 Subject: [PATCH 8055/9987] set MAX_N_PID_4_TCOFFEE in T-Coffee v13.45.61.3c310a9 --- easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb b/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb index 006a187b85b..3c11b060d6b 100644 --- a/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb +++ b/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb @@ -34,6 +34,7 @@ modextravars = { 'TMP_4_TCOFFEE': _tcoffee_dir + '/tmp', 'CACHE_4_TCOFFEE': _tcoffee_dir + '/cache', 'PLUGINS_4_TCOFFEE': _tcoffee_dir + '/plugins', + 'MAX_N_PID_4_TCOFFEE': '786432', # see issue https://github.com/cbcrg/tcoffee/issues/27 # 'PDB_DIR': , } From 978d81dd90f2b691c283d36be737070092d8f630 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 17 Jul 2023 10:53:40 +0200 Subject: [PATCH 8056/9987] Add patch description and author information --- .../easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a.eb | 2 +- .../r/RFdiffusion/RFdiffusion-1.1.0_fix-find-packages.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a.eb b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a.eb index c0d318b938d..04ca8f30e95 100644 --- a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a.eb @@ -46,7 +46,7 @@ exts_list = [ 'checksums': [ {'v1.1.0.tar.gz': '57d82f0d43540c2912eda3f1d34ad90b13db14966ee069c427e217fe78f0297f'}, {'RFdiffusion-1.1.0_fix-find-packages.patch': - '0e92f970a48e29dfb2d0354341f18f05ba4d79e864d5e4970b5c8d78a6f1bdb0'}, + 'e25da7f476acacb6af58bd84f40aca712538900b0b48532b22f9a133d6886da2'}, ], }), ] diff --git a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0_fix-find-packages.patch b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0_fix-find-packages.patch index c2870df522c..3dbe92b07f4 100644 --- a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0_fix-find-packages.patch +++ b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0_fix-find-packages.patch @@ -1,3 +1,5 @@ +Fix version and switch setup.py from distutils to setuptools to fix find packages +Author: Cintia Willemyns (Vrije Universiteit Brussel) diff --git a/setup.py b/setup.py index 2761c12..6eb62b6 100644 --- a/setup.py From 3d563bef5ebe710b3f881a79b4f87500fa2df0c2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Jul 2023 10:53:59 +0200 Subject: [PATCH 8057/9987] increase MAX_N_PID to 4M in T-Coffee v13.45.61.3c310a9 --- easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb b/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb index 3c11b060d6b..1392a37d6ea 100644 --- a/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb +++ b/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.45.61.3c310a9.eb @@ -34,7 +34,7 @@ modextravars = { 'TMP_4_TCOFFEE': _tcoffee_dir + '/tmp', 'CACHE_4_TCOFFEE': _tcoffee_dir + '/cache', 'PLUGINS_4_TCOFFEE': _tcoffee_dir + '/plugins', - 'MAX_N_PID_4_TCOFFEE': '786432', # see issue https://github.com/cbcrg/tcoffee/issues/27 + 'MAX_N_PID_4_TCOFFEE': '4194304', # see issue https://github.com/cbcrg/tcoffee/issues/27 # 'PDB_DIR': , } From 7bc0dd3d9c1463ed78498cd63b850e130bf6310a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Jul 2023 11:32:41 +0200 Subject: [PATCH 8058/9987] adding easyconfigs: T-Coffee-13.46.0.919e8c6b.eb --- .../t/T-Coffee/T-Coffee-13.46.0.919e8c6b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.46.0.919e8c6b.eb diff --git a/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.46.0.919e8c6b.eb b/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.46.0.919e8c6b.eb new file mode 100644 index 00000000000..4301a85f744 --- /dev/null +++ b/easybuild/easyconfigs/t/T-Coffee/T-Coffee-13.46.0.919e8c6b.eb @@ -0,0 +1,41 @@ +easyblock = "Tarball" + +name = 'T-Coffee' +version = '13.46.0.919e8c6b' + +homepage = 'https://www.tcoffee.org/' +description = """A collection of tools for Computing, Evaluating and Manipulating Multiple +Alignments of DNA, RNA, Protein Sequences and Structures""" + +toolchain = SYSTEM + +source_urls = ['https://s3.eu-central-1.amazonaws.com/tcoffee-packages/Archives/'] +sources = ['T-COFFEE_installer_Version_%(version)s_linux_x64.tar.gz'] +checksums = ['53b63a470fbed5023128be037a3700ac69d8ee3b962550c69a510bada500c0e6'] + +sanity_check_paths = { + 'files': ['bin/t_coffee'], + 'dirs': ['mcoffee', 'perl', 'plugins', 'src'], +} + +sanity_check_commands = ["t_coffee --help"] + +modextrapaths = { + 'PATH': 'perl/bin', + 'PERL5LIB': 'perl/lib/perl5', +} + +# optionally set extra variables +# default DIR_4_TCOFFEE is $HOME/.t_coffee +# see https://tcoffee.readthedocs.io/en/latest/tcoffee_technical_documentation.html#setting-up-the-variables +_tcoffee_dir = '/tmp/.t_coffee' +modextravars = { + 'DIR_4_TCOFFEE': _tcoffee_dir, + 'TMP_4_TCOFFEE': _tcoffee_dir + '/tmp', + 'CACHE_4_TCOFFEE': _tcoffee_dir + '/cache', + 'PLUGINS_4_TCOFFEE': _tcoffee_dir + '/plugins', + 'MAX_N_PID_4_TCOFFEE': '4194304', # see issue https://github.com/cbcrg/tcoffee/issues/27 + # 'PDB_DIR': , +} + +moduleclass = 'bio' From d62aa5ebd35f55af09a36f24e4e2904df05580d0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 17 Jul 2023 10:32:52 +0100 Subject: [PATCH 8059/9987] adding easyconfigs: HPL-2.3-intel-2022a.eb --- .../easyconfigs/h/HPL/HPL-2.3-intel-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022a.eb new file mode 100644 index 00000000000..c890efd86c2 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' From 59176b1f9e82018732b25e1ba49541523c06b234 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 17 Jul 2023 11:39:03 +0200 Subject: [PATCH 8060/9987] set JULIA_DEPOT_PATH with default value in Julia v1.9.2 --- .../j/Julia/Julia-1.9.2-linux-x86_64.eb | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb index 160f52e7e4d..a0d92b7aacb 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.2-linux-x86_64.eb @@ -28,20 +28,11 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] -_depot_paths = ':'.join([ - # first entry must be the user depot - # see https://pkgdocs.julialang.org/v1/glossary/ - '~/.julia', - # base installation of Julia - '%(installdir)s/share/julia', -]) - modextravars = { - 'JULIA_DEPOT_PATH': _depot_paths, - # by default JULIA_HISTORY points to top path in DEPOT_PATH - # set JULIA_HISTORY to always use the user depot (~/.julia) - # https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_HISTORY - 'JULIA_HISTORY': '~/.julia/logs/repl_history.jl', + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', } moduleclass = 'lang' From b6c32270b579794ba0a3b3496db2b644a87b61e7 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 17 Jul 2023 12:31:01 +0200 Subject: [PATCH 8061/9987] Change gc version --- ...8.2.2-GCCcore-12.3.0.eb => gc-8.2.4-GCCcore-12.3.0.eb} | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/g/gc/{gc-8.2.2-GCCcore-12.3.0.eb => gc-8.2.4-GCCcore-12.3.0.eb} (81%) diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.4-GCCcore-12.3.0.eb similarity index 81% rename from easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/g/gc/gc-8.2.4-GCCcore-12.3.0.eb index 9675538152d..fbd0f278c0a 100644 --- a/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/gc/gc-8.2.4-GCCcore-12.3.0.eb @@ -1,8 +1,8 @@ easyblock = 'ConfigureMake' name = 'gc' -version = '8.2.2' -local_libatomic_version = '7.6.14' +version = '8.2.4' +local_libatomic_version = '7.8.0' homepage = 'https://hboehm.info/gc/' description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a @@ -21,8 +21,8 @@ sources = [ 'libatomic_ops-%s.tar.gz' % local_libatomic_version, ] checksums = [ - 'f30107bcb062e0920a790ffffa56d9512348546859364c23a14be264b38836a0', # gc-8.2.2.tar.gz - '390f244d424714735b7050d056567615b3b8f29008a663c262fb548f1802d292', # libatomic_ops-7.6.14.tar.gz + '3d0d3cdbe077403d3106bb40f0cbb563413d6efdbb2a7e1cd6886595dec48fc2', # gc-8.2.4.tar.gz + '15676e7674e11bda5a7e50a73f4d9e7d60452271b8acf6fd39a71fefdf89fa31', # libatomic_ops-7.8.0.tar.gz ] builddependencies = [ From 0962729d6896b5126850ecda8a086b281890a594 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 17 Jul 2023 11:43:43 +0100 Subject: [PATCH 8062/9987] update gc version used in Guile --- easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-12.3.0.eb index 1e338e06f27..5cc6d1882f6 100644 --- a/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-12.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ ] dependencies = [ - ('gc', '8.2.2'), + ('gc', '8.2.4'), ('GMP', '6.2.1'), ('libffi', '3.4.4'), ('libunistring', '1.1'), From af4065cb5201dc571b97c1d9e1bd624adca3eb99 Mon Sep 17 00:00:00 2001 From: Satish Kamath Date: Mon, 17 Jul 2023 17:50:37 +0200 Subject: [PATCH 8063/9987] Adding hpctestlib to the PYTHONPATH. --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb index dc290fcc04d..4ff8a0f466d 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb @@ -58,6 +58,8 @@ sanity_pip_check = True modextrapaths = { # bootstrap script installs required dependencies to 'external' subdirectory 'PYTHONPATH': 'external', + # hpctestlib should be a part of the PYTHONPATH + 'PYTHONPATH': 'hpctestlib', } moduleclass = 'devel' From a7d8c4005132263f9ab2a0bf45bb6faa80e4f626 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 17 Jul 2023 18:22:56 +0200 Subject: [PATCH 8064/9987] remove dependencies and extensions in poetry that are no longer needed --- .../easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb | 8 -------- 1 file changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb index 34166a0b0b4..282e6a93965 100755 --- a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb @@ -12,8 +12,6 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), ('pkgconf', '1.9.5'), - ('Rust', '1.70.0'), # required for setuptools-rust, which is needed for cryptography - ('setuptools-rust', '1.6.0'), ('scikit-build', '0.17.6'), ] @@ -31,12 +29,6 @@ exts_list = [ ('six', '1.16.0', { 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], }), - ('packaging', '23.1', { - 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], - }), - ('setuptools_scm', '7.1.0', { - 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], - }), ('idna', '3.4', { 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], }), From 88cd8a20fe954414d07d59276597bf4c32adcac3 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 17 Jul 2023 18:23:57 +0200 Subject: [PATCH 8065/9987] remove unneeded Rust dependency in setupttools-rust --- .../s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb index 10b275d3966..ada0621cf43 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb @@ -11,7 +11,6 @@ toolchainopts = {'pic': True} builddependencies = [ ('binutils', '2.40'), - ('Rust', '1.70.0'), # required for setuptools-rust ] dependencies = [ From 11fad45ae9abd466f5532f8e629e016a24359e63 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 17 Jul 2023 18:25:16 +0200 Subject: [PATCH 8066/9987] remove unneeded pycparser dependency in cryptography --- .../c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb index eca6ec79d06..1a55594e9a4 100644 --- a/easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/cryptography/cryptography-41.0.1-GCCcore-12.3.0.eb @@ -19,7 +19,6 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), - ('pycparser', '2.21'), ('cffi', '1.15.1'), ] From a160ed6f88d57b1e4898d5fb436e311096f85091 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 17 Jul 2023 18:27:31 +0200 Subject: [PATCH 8067/9987] update virtualenv to only depend on distlib, filelock and platformdirs --- .../v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb index 48030df472c..93fdd5fa2d3 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb @@ -16,7 +16,6 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), ] exts_default_options = { @@ -26,6 +25,15 @@ exts_default_options = { } exts_list = [ + ('distlib', '0.3.6', { + 'checksums': ['14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46'], + }), + ('filelock', '3.12.2', { + 'checksums': ['002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81'], + }), + ('platformdirs', '3.8.0', { + 'checksums': ['b0cabcb11063d21a0b261d557acb0a9d2126350e63b70cdf7db6347baea456dc'], + }), (name, version, { 'checksums': ['8ff19a38c1021c742148edc4f81cb43d7f8c6816d2ede2ab72af5b84c749ade1'], }), From ff899417ddb7ae3a81e7a8d91cec0bdcf1513865 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 17 Jul 2023 18:35:48 +0200 Subject: [PATCH 8068/9987] remove unneeded dependencies in Python-bundle-PyPI and separate bcrypt and paramiko extensions --- ...ython-bundle-PyPI-2023.06-GCCcore-12.3.0.eb | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb index f55e94daf8e..51f1f70f5a1 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb @@ -11,10 +11,8 @@ toolchainopts = {'pic': True} builddependencies = [ ('UnZip', '6.0'), - ('Rust', '1.70.0'), # required for setuptools-rust, which is needed for cryptography and bcrypt ('pkgconf', '1.9.5'), ('git', '2.41.0', '-nodocs'), # required for pbr - ('setuptools-rust', '1.6.0'), # required for cryptography and bcrypt ('hatchling', '1.18.0'), ('poetry', '1.5.1'), ('scikit-build', '0.17.6'), @@ -22,16 +20,6 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), - ('binutils', '2.40'), - ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib - ('zlib', '1.2.13'), - ('libreadline', '8.2'), - ('ncurses', '6.4'), - ('SQLite', '3.42.0'), - ('XZ', '5.4.2'), - ('GMP', '6.2.1'), # required for pycrypto - ('libffi', '3.4.4'), - ('OpenSSL', '1.1', '', SYSTEM), ('cryptography', '41.0.1'), ] @@ -124,12 +112,6 @@ exts_list = [ 'modulename': 'nacl', 'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'], }), - ('bcrypt', '4.0.1', { - 'checksums': ['27d375903ac8261cfe4047f6709d16f7d18d39b1ec92aaf72af989552a650ebd'], - }), - ('paramiko', '3.2.0', { - 'checksums': ['93cdce625a8a1dc12204439d45033f3261bdb2c201648cfcdc06f9fd0f94ec29'], - }), ('pyparsing', '3.1.0', { 'checksums': ['edb662d6fe322d6e990b1594b5feaeadf806803359e3d4d42f11e295e588f0ea'], }), From 00d1fc4ec8440337420d66ee2afcbda8f287db9b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 17 Jul 2023 18:36:44 +0200 Subject: [PATCH 8069/9987] adding easyconfigs: bcrypt-4.0.1-GCCcore-12.3.0.eb, paramiko-3.2.0-GCCcore-12.3.0.eb --- .../b/bcrypt/bcrypt-4.0.1-GCCcore-12.3.0.eb | 134 ++++++++++++++++++ .../paramiko/paramiko-3.2.0-GCCcore-12.3.0.eb | 34 +++++ 2 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcrypt/bcrypt-4.0.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/paramiko/paramiko-3.2.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/bcrypt/bcrypt-4.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/bcrypt/bcrypt-4.0.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a24eee7c987 --- /dev/null +++ b/easybuild/easyconfigs/b/bcrypt/bcrypt-4.0.1-GCCcore-12.3.0.eb @@ -0,0 +1,134 @@ +easyblock = 'CargoPythonPackage' + +name = 'bcrypt' +version = '4.0.1' + +homepage = 'https://github.com/pyca/bcrypt/' +description = """Acceptable password hashing for your software and your servers (but you should +really use argon2id or scrypt) +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.70.0'), + ('setuptools-rust', '1.6.0'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +crates = [ + ('autocfg', '1.1.0'), + ('base64', '0.13.0'), + ('bcrypt', '0.13.0'), + ('bcrypt-pbkdf', '0.8.1'), + ('bitflags', '1.3.2'), + ('block-buffer', '0.10.3'), + ('blowfish', '0.9.1'), + ('byteorder', '1.4.3'), + ('cfg-if', '1.0.0'), + ('cipher', '0.4.3'), + ('cpufeatures', '0.2.5'), + ('crypto-common', '0.1.6'), + ('digest', '0.10.5'), + ('generic-array', '0.14.6'), + ('getrandom', '0.2.7'), + ('indoc', '0.3.6'), + ('indoc-impl', '0.3.6'), + ('inout', '0.1.3'), + ('instant', '0.1.12'), + ('libc', '0.2.134'), + ('lock_api', '0.4.9'), + ('once_cell', '1.15.0'), + ('parking_lot', '0.11.2'), + ('parking_lot_core', '0.8.5'), + ('paste', '0.1.18'), + ('paste-impl', '0.1.18'), + ('pbkdf2', '0.10.1'), + ('proc-macro-hack', '0.5.19'), + ('proc-macro2', '1.0.46'), + ('pyo3', '0.15.2'), + ('pyo3-build-config', '0.15.2'), + ('pyo3-macros', '0.15.2'), + ('pyo3-macros-backend', '0.15.2'), + ('quote', '1.0.21'), + ('redox_syscall', '0.2.16'), + ('scopeguard', '1.1.0'), + ('sha2', '0.10.6'), + ('smallvec', '1.10.0'), + ('subtle', '2.4.1'), + ('syn', '1.0.102'), + ('typenum', '1.15.0'), + ('unicode-ident', '1.0.4'), + ('unindent', '0.1.10'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('zeroize', '1.5.7'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'bcrypt-4.0.1.tar.gz': '27d375903ac8261cfe4047f6709d16f7d18d39b1ec92aaf72af989552a650ebd'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'base64-0.13.0.tar.gz': '904dfeac50f3cdaba28fc6f57fdcddb75f49ed61346676a78c4ffe55877802fd'}, + {'bcrypt-0.13.0.tar.gz': 'a7e7c93a3fb23b2fdde989b2c9ec4dd153063ec81f408507f84c090cd91c6641'}, + {'bcrypt-pbkdf-0.8.1.tar.gz': 'f4ef233ffa9cb9c7820b2b0e9efd0821ed180e866c9120ec9f45518659742074'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'block-buffer-0.10.3.tar.gz': '69cce20737498f97b993470a6e536b8523f0af7892a4f928cceb1ac5e52ebe7e'}, + {'blowfish-0.9.1.tar.gz': 'e412e2cd0f2b2d93e02543ceae7917b3c70331573df19ee046bcbc35e45e87d7'}, + {'byteorder-1.4.3.tar.gz': '14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'cipher-0.4.3.tar.gz': 'd1873270f8f7942c191139cb8a40fd228da6c3fd2fc376d7e92d47aa14aeb59e'}, + {'cpufeatures-0.2.5.tar.gz': '28d997bd5e24a5928dd43e46dc529867e207907fe0b239c3477d924f7f2ca320'}, + {'crypto-common-0.1.6.tar.gz': '1bfb12502f3fc46cca1bb51ac28df9d618d813cdc3d2f25b9fe775a34af26bb3'}, + {'digest-0.10.5.tar.gz': 'adfbc57365a37acbd2ebf2b64d7e69bb766e2fea813521ed536f5d0520dcf86c'}, + {'generic-array-0.14.6.tar.gz': 'bff49e947297f3312447abdca79f45f4738097cc82b06e72054d2223f601f1b9'}, + {'getrandom-0.2.7.tar.gz': '4eb1a864a501629691edf6c15a593b7a51eebaa1e8468e9ddc623de7c9b58ec6'}, + {'indoc-0.3.6.tar.gz': '47741a8bc60fb26eb8d6e0238bbb26d8575ff623fdc97b1a2c00c050b9684ed8'}, + {'indoc-impl-0.3.6.tar.gz': 'ce046d161f000fffde5f432a0d034d0341dc152643b2598ed5bfce44c4f3a8f0'}, + {'inout-0.1.3.tar.gz': 'a0c10553d664a4d0bcff9f4215d0aac67a639cc68ef660840afe309b807bc9f5'}, + {'instant-0.1.12.tar.gz': '7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c'}, + {'libc-0.2.134.tar.gz': '329c933548736bc49fd575ee68c89e8be4d260064184389a5b77517cddd99ffb'}, + {'lock_api-0.4.9.tar.gz': '435011366fe56583b16cf956f9df0095b405b82d76425bc8981c0e22e60ec4df'}, + {'once_cell-1.15.0.tar.gz': 'e82dad04139b71a90c080c8463fe0dc7902db5192d939bd0950f074d014339e1'}, + {'parking_lot-0.11.2.tar.gz': '7d17b78036a60663b797adeaee46f5c9dfebb86948d1255007a1d6be0271ff99'}, + {'parking_lot_core-0.8.5.tar.gz': 'd76e8e1493bcac0d2766c42737f34458f1c8c50c0d23bcb24ea953affb273216'}, + {'paste-0.1.18.tar.gz': '45ca20c77d80be666aef2b45486da86238fabe33e38306bd3118fe4af33fa880'}, + {'paste-impl-0.1.18.tar.gz': 'd95a7db200b97ef370c8e6de0088252f7e0dfff7d047a28528e47456c0fc98b6'}, + {'pbkdf2-0.10.1.tar.gz': '271779f35b581956db91a3e55737327a03aa051e90b1c47aeb189508533adfd7'}, + {'proc-macro-hack-0.5.19.tar.gz': 'dbf0c48bc1d91375ae5c3cd81e3722dff1abcf81a30960240640d223f59fe0e5'}, + {'proc-macro2-1.0.46.tar.gz': '94e2ef8dbfc347b10c094890f778ee2e36ca9bb4262e86dc99cd217e35f3470b'}, + {'pyo3-0.15.2.tar.gz': 'd41d50a7271e08c7c8a54cd24af5d62f73ee3a6f6a314215281ebdec421d5752'}, + {'pyo3-build-config-0.15.2.tar.gz': '779239fc40b8e18bc8416d3a37d280ca9b9fb04bda54b98037bb6748595c2410'}, + {'pyo3-macros-0.15.2.tar.gz': '00b247e8c664be87998d8628e86f282c25066165f1f8dda66100c48202fdb93a'}, + {'pyo3-macros-backend-0.15.2.tar.gz': '5a8c2812c412e00e641d99eeb79dd478317d981d938aa60325dfa7157b607095'}, + {'quote-1.0.21.tar.gz': 'bbe448f377a7d6961e30f5955f9b8d106c3f5e449d493ee1b125c1d43c2b5179'}, + {'redox_syscall-0.2.16.tar.gz': 'fb5a58c1855b4b6819d59012155603f0b22ad30cad752600aadfcb695265519a'}, + {'scopeguard-1.1.0.tar.gz': 'd29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd'}, + {'sha2-0.10.6.tar.gz': '82e6b795fe2e3b1e845bafcb27aa35405c4d47cdfc92af5fc8d3002f76cebdc0'}, + {'smallvec-1.10.0.tar.gz': 'a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0'}, + {'subtle-2.4.1.tar.gz': '6bdef32e8150c2a081110b42772ffe7d7c9032b606bc226c8260fd97e0976601'}, + {'syn-1.0.102.tar.gz': '3fcd952facd492f9be3ef0d0b7032a6e442ee9b361d4acc2b1d0c4aaa5f613a1'}, + {'typenum-1.15.0.tar.gz': 'dcf81ac59edc17cc8697ff311e8f5ef2d99fcbd9817b34cec66f90b6c3dfd987'}, + {'unicode-ident-1.0.4.tar.gz': 'dcc811dc4066ac62f84f11307873c4850cb653bfa9b1719cee2bd2204a4bc5dd'}, + {'unindent-0.1.10.tar.gz': '58ee9362deb4a96cef4d437d1ad49cffc9b9e92d202b6995674e928ce684f112'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'zeroize-1.5.7.tar.gz': 'c394b5bd0c6f669e7275d9c20aa90ae064cb22e75a1cad54e1b34088034b149f'}, +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/paramiko/paramiko-3.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/paramiko/paramiko-3.2.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..572ebb6e242 --- /dev/null +++ b/easybuild/easyconfigs/p/paramiko/paramiko-3.2.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'paramiko' +version = '3.2.0' + +homepage = 'https://paramiko.org' +description = """Paramiko is a pure-Python (3.6+) implementation of the SSHv2 protocol, +providing both client and server functionality. It provides the foundation +for the high-level SSH library Fabric, which is what we recommend you use for +common client use-cases such as running remote shell commands or transferring +files. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['93cdce625a8a1dc12204439d45033f3261bdb2c201648cfcdc06f9fd0f94ec29'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('bcrypt', '4.0.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From dba95f61eb9ef145989e5a0ff80dd4b3b09cc98c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 17 Jul 2023 19:48:38 +0200 Subject: [PATCH 8070/9987] add binutils builddependency to Python-bundle-PyPI --- .../Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb index 51f1f70f5a1..9c3b9912fc9 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} builddependencies = [ + ('binutils', '2.40'), ('UnZip', '6.0'), ('pkgconf', '1.9.5'), ('git', '2.41.0', '-nodocs'), # required for pbr From d708e18c03f80599ff4353d10151d1aaaa164f20 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 18 Jul 2023 09:24:59 +0200 Subject: [PATCH 8071/9987] update dependencies in paramiko easyconfig --- .../paramiko/paramiko-3.2.0-GCCcore-12.3.0.eb | 26 +++++++++++++------ 1 file changed, 18 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/paramiko/paramiko-3.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/paramiko/paramiko-3.2.0-GCCcore-12.3.0.eb index 572ebb6e242..42a419cb9a6 100644 --- a/easybuild/easyconfigs/p/paramiko/paramiko-3.2.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/paramiko/paramiko-3.2.0-GCCcore-12.3.0.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = "PythonBundle" name = 'paramiko' version = '3.2.0' @@ -14,21 +14,31 @@ files. toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -sources = [SOURCE_TAR_GZ] -checksums = ['93cdce625a8a1dc12204439d45033f3261bdb2c201648cfcdc06f9fd0f94ec29'] - builddependencies = [ ('binutils', '2.40'), ] dependencies = [ ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), ('bcrypt', '4.0.1'), + ('cffi', '1.15.1'), + ('cryptography', '41.0.1'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('PyNaCl', '1.5.0', { + 'modulename': 'nacl', + 'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'], + }), + (name, version, { + 'checksums': ['93cdce625a8a1dc12204439d45033f3261bdb2c201648cfcdc06f9fd0f94ec29'], + }), +] moduleclass = 'tools' From bed7749626338724e9209b90d16ace4d06d751ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 18 Jul 2023 16:15:04 +0200 Subject: [PATCH 8072/9987] adding easyconfigs: CalculiX-CrunchiX-2.20-foss-2022b.eb, SPOOLES-2.2-gompi-2022b.eb and patches: CalculiX-CrunchiX-2.20_improve-makefile.patch --- .../CalculiX-CrunchiX-2.20-foss-2022b.eb | 50 ++++++++++++++++++ .../s/SPOOLES/SPOOLES-2.2-gompi-2022b.eb | 51 +++++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2022b.eb create mode 100644 easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2022b.eb diff --git a/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2022b.eb b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2022b.eb new file mode 100644 index 00000000000..0e5ed433555 --- /dev/null +++ b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2022b.eb @@ -0,0 +1,50 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MakeCp' + +name = 'CalculiX-CrunchiX' +version = '2.20' + +homepage = 'http://www.calculix.de' +description = 'A Free Software Three-Dimensional Structural Finite Element Program' + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['http://www.dhondt.de'] +sources = ['ccx_%(version)s.src.tar.bz2'] +patches = ['CalculiX-CrunchiX-2.20_improve-makefile.patch'] +checksums = [ + {'ccx_2.20.src.tar.bz2': '63bf6ea09e7edcae93e0145b1bb0579ea7ae82e046f6075a27c8145b72761bcf'}, + {'CalculiX-CrunchiX-2.20_improve-makefile.patch': + 'ada15598029d231f804f61d959ce91e2bb3a58749fe5955398f42fbe87dc970c'}, +] + +builddependencies = [ + ('Perl', '5.36.0', '-minimal'), +] + +dependencies = [ + ('arpack-ng', '3.8.0'), + ('SPOOLES', '2.2'), +] + +start_dir = 'CalculiX/ccx_%(version)s/src' + +prebuildopts = 'CFLAGS="$CFLAGS $CPPFLAGS" FFLAGS="$FFLAGS -fallow-argument-mismatch"' +buildopts = 'SPOOLES_INC_DIR="$EBROOTSPOOLES/include/spooles"' + +files_to_copy = [(['ccx_%(version)s'], 'bin')] + +postinstallcmds = ['cd %(installdir)s/bin && ln -sf ccx_%(version)s ccx'] + +sanity_check_paths = { + 'files': ['bin/ccx'], + 'dirs': [], +} + +sanity_check_commands = [ + # ccx {,-v} exit with code 201 + "ccx | grep 'Usage: CalculiX.exe -i jobname'", + "ccx -v | grep 'Version %(version)s'", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2022b.eb b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2022b.eb new file mode 100644 index 00000000000..7208c8569af --- /dev/null +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2022b.eb @@ -0,0 +1,51 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MakeCp' + +name = 'SPOOLES' +version = '2.2' + +homepage = 'https://netlib.org/linalg/spooles/spooles.2.2.html' +description = """SPOOLES is a library for solving sparse real and complex linear + systems of equations, written in the C language using object oriented design. +""" + +toolchain = {'name': 'gompi', 'version': '2022b'} + +source_urls = ['https://netlib.org/linalg/spooles'] +sources = ['%(namelower)s.%(version)s.tgz'] +patches = [ + '%(name)s-2.2_build-mpi-mt.patch', + '%(name)s-2.2_shared-libs.patch', +] +checksums = [ + {'spooles.2.2.tgz': 'a84559a0e987a1e423055ef4fdf3035d55b65bbe4bf915efaa1a35bef7f8c5dd'}, + {'SPOOLES-2.2_build-mpi-mt.patch': 'c983c7f37eb0904959cd2f6dff0b1fdb6a36440ca2a044fb2d324fd301e3dd7c'}, + {'SPOOLES-2.2_shared-libs.patch': 'bca50e13e3c552240f7494c4d9f69be8725054c9f79ebc82dbe6b7531588d09e'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('Perl', '5.36.0', '-minimal'), +] + +build_cmd_targets = 'lib' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" MPI_LIB_PATH="-L$MPI_LIB_DIR" MPI_INCLUDE_DIR="-I$MPI_INC_DIR"' + +files_to_copy = [ + (['libspooles*'], 'lib'), +] + +# install header files, keeping relative subdirectories +_install_headers = " ".join([ + "cd %(builddir)s && mkdir -p %(installdir)s/include/spooles &&", + r"find . -name '*.h' -print -exec install -D {} %(installdir)s/include/spooles/{} \;" +]) + +postinstallcmds = [_install_headers] + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/spooles'], +} + +moduleclass = 'math' From 12e8ebbbbfffc4aa40b3ea6bb62f4e01d4b6fbc0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 18 Jul 2023 17:02:14 +0200 Subject: [PATCH 8073/9987] Build dependency on Perl-minimal replaced by Perl in order to avoid dependency conflict --- .../c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2022b.eb | 2 +- easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2022b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2022b.eb b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2022b.eb index 0e5ed433555..a79e07f059f 100644 --- a/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2022b.eb +++ b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2022b.eb @@ -19,7 +19,7 @@ checksums = [ ] builddependencies = [ - ('Perl', '5.36.0', '-minimal'), + ('Perl', '5.36.0'), ] dependencies = [ diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2022b.eb b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2022b.eb index 7208c8569af..9d3ae4f917b 100644 --- a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2022b.eb +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2022b.eb @@ -25,7 +25,7 @@ checksums = [ builddependencies = [ ('Autotools', '20220317'), - ('Perl', '5.36.0', '-minimal'), + ('Perl', '5.36.0'), ] build_cmd_targets = 'lib' From 0785c0b65dcb1e8dd91d59a1bbf55b4306616edd Mon Sep 17 00:00:00 2001 From: satishskamath <41335185+satishskamath@users.noreply.github.com> Date: Tue, 18 Jul 2023 17:30:39 +0200 Subject: [PATCH 8074/9987] Update easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb index 4ff8a0f466d..bb27d3d5fb2 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb @@ -57,9 +57,8 @@ sanity_pip_check = True modextrapaths = { # bootstrap script installs required dependencies to 'external' subdirectory - 'PYTHONPATH': 'external', # hpctestlib should be a part of the PYTHONPATH - 'PYTHONPATH': 'hpctestlib', + 'PYTHONPATH': ['external', 'hpctestlib'], } moduleclass = 'devel' From 718620da79b32b8b42112095c0a195ebeaba96e0 Mon Sep 17 00:00:00 2001 From: Satish Kamath Date: Tue, 18 Jul 2023 19:03:42 +0200 Subject: [PATCH 8075/9987] Now hpctestlib is copied to external which is included in the PYTHONPATH. --- easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb index bb27d3d5fb2..b00fc07a257 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb @@ -38,7 +38,10 @@ exts_list = [ ] postinstallcmds = [ - "cp -a hpctestlib tools tutorials %(installdir)s", + "cp -a tools tutorials %(installdir)s", + # Adding hpctestlib separately to the external directory so that it can be + # imported and is in the PYTHONPATH + "cp -a hpctestlib %(installdir)s/external", "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", ] @@ -48,7 +51,7 @@ sanity_check_paths = { 'share/completions/reframe.bash', 'share/completions/reframe.fish', 'share/completions/reframe.tcsh'], - 'dirs': ['external', 'hpctestlib', 'lib', 'tools', 'tutorials'] + 'dirs': ['external', 'lib', 'tools', 'tutorials'] } sanity_check_commands = ['reframe -V'] @@ -57,8 +60,7 @@ sanity_pip_check = True modextrapaths = { # bootstrap script installs required dependencies to 'external' subdirectory - # hpctestlib should be a part of the PYTHONPATH - 'PYTHONPATH': ['external', 'hpctestlib'], + 'PYTHONPATH': 'external', } moduleclass = 'devel' From 51fbca8faaa489301bc52fbbdd602becb1e290df Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Tue, 18 Jul 2023 20:04:03 +0200 Subject: [PATCH 8076/9987] update description in setuptools-rust Co-authored-by: Alex Domingo --- .../setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb index ada0621cf43..8cbf2db9fe7 100644 --- a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.6.0-GCCcore-12.3.0.eb @@ -3,8 +3,9 @@ easyblock = 'PythonBundle' name = 'setuptools-rust' version = '1.6.0' -homepage = 'https://python.org/' -description = "A tool for creating isolated virtual python environments." +homepage = 'https://github.com/PyO3/setuptools-rust' +description = """setuptools-rust is a plugin for setuptools to build Rust Python extensions +implemented with PyO3 or rust-cpython.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} From 2470f0f4ed0a7ddc15f06054de10d6776fbb881d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 18 Jul 2023 20:04:16 +0200 Subject: [PATCH 8077/9987] adding easyconfigs: SuperLU_DIST-8.1.2-foss-2022b.eb --- .../SuperLU_DIST-8.1.2-foss-2022b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb new file mode 100644 index 00000000000..44b3702b12b --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb @@ -0,0 +1,40 @@ +easyblock = "EB_SuperLU" + +name = 'SuperLU_DIST' +version = '8.1.2' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['7b16c442bb01ea8b298c0aab9a2584aa4615d09786aac968cb2f3118c058206b'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('ParMETIS', '4.0.3'), +] + +configopts = '-DTPL_PARMETIS_INCLUDE_DIRS="${EBROOTPARMETIS}/include" ' +configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${EBROOTPARMETIS}/lib/libmetis.a" ' + +# Some tests run longer than default 1500s timeout on fairly big machine (36 cores). +# Include only first four tests, which should be fairly small to run +pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && ' + +postinstallcmds = [ + "rm %(installdir)s/lib64/libsuperlu.a", # remove broken symlink to libsuperlu.a +] + +sanity_check_paths = { + 'files': ['lib64/libsuperlu_dist.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' From 233bd7574d9d42de7488b6f381d41541c8db3a2d Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Tue, 18 Jul 2023 20:04:43 +0200 Subject: [PATCH 8078/9987] update homepage in virtualenv Co-authored-by: Alex Domingo --- .../v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb index 93fdd5fa2d3..122f3d8d6c8 100644 --- a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.23.1-GCCcore-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'virtualenv' version = '20.23.1' -homepage = 'https://python.org/' +homepage = 'https://github.com/pypa/virtualenv' description = "A tool for creating isolated virtual python environments." toolchain = {'name': 'GCCcore', 'version': '12.3.0'} From 7afcc7e4eaa2b47d298620554dd0733780fb4528 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Tue, 18 Jul 2023 20:05:26 +0200 Subject: [PATCH 8079/9987] update description in hatchling Co-authored-by: Alex Domingo --- .../h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb index 9d2ea5e7d3f..85919d3f2b7 100644 --- a/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb @@ -3,9 +3,9 @@ easyblock = 'PythonBundle' name = 'hatchling' version = '1.18.0' -homepage = 'https://python-poetry.org' -description = """Python packaging and dependency management made easy. Poetry helps you declare, manage and install - dependencies of Python projects, ensuring you have the right stack everywhere.""" +homepage = 'https://hatch.pypa.io' +description = """Extensible, standards compliant build backend used by Hatch, +a modern, extensible Python project manager.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} From 56593ee3d2b2a9dcca826a8b8568b57ce8fc2ad4 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Tue, 18 Jul 2023 20:06:24 +0200 Subject: [PATCH 8080/9987] update dependencies in poetry Co-authored-by: Alex Domingo --- easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb index 282e6a93965..8e4abdcd412 100755 --- a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb @@ -18,7 +18,6 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), ('hatchling', '1.18.0'), - ('OpenSSL', '1.1', '', SYSTEM), ('cryptography', '41.0.1'), ] From 65ea6041da6dd66a1c79092c298a33af7f47ae95 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 19 Jul 2023 11:36:41 +0200 Subject: [PATCH 8081/9987] IsoQuant 3.3.0 --- .../g/gffutils/gffutils-0.12-foss-2022b.eb | 44 +++++++++++++++++ .../i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb | 47 +++++++++++++++++++ .../pybedtools/pybedtools-0.9.0-GCC-12.2.0.eb | 26 ++++++++++ .../s/STAR/STAR-2.7.10b-GCC-12.2.0.eb | 18 +++---- 4 files changed, 123 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/g/gffutils/gffutils-0.12-foss-2022b.eb create mode 100644 easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/g/gffutils/gffutils-0.12-foss-2022b.eb b/easybuild/easyconfigs/g/gffutils/gffutils-0.12-foss-2022b.eb new file mode 100644 index 00000000000..dce3bfc54fd --- /dev/null +++ b/easybuild/easyconfigs/g/gffutils/gffutils-0.12-foss-2022b.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'gffutils' +version = '0.12' + +homepage = 'https://github.com/daler/gffutils' +description = """Gffutils is a Python package for working with and manipulating + the GFF and GTF format files typically used for genomic annotations.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('pyfaidx', '0.7.2.1'), + ('Biopython', '1.81'), + ('pybedtools', '0.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('argh', '0.28.1', { + 'checksums': ['b2093086f0e809a3ecc24b64a2145309ee8f56d034936cd59e57c558a357329d'], + }), + ('argcomplete', '3.1.1', { + 'checksums': ['6c4c563f14f01440aaffa3eae13441c5db2357b5eec639abe7c0b15334627dff'], + }), + ('simplejson', '3.19.1', { + 'checksums': ['6277f60848a7d8319d27d2be767a7546bc965535b28070e310b3a9af90604a4c'], + }), + (name, version, { + 'checksums': ['b31e261db5bd8737cb712c361c129eb2c373ef62f03b62770320589f10da1983'], + }), +] + +sanity_check_commands = [ + "python -c 'from gffutils import helpers'" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb new file mode 100644 index 00000000000..bb16126eb22 --- /dev/null +++ b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb @@ -0,0 +1,47 @@ +easyblock = 'Tarball' + +name = 'IsoQuant' +version = '3.3.0' + +homepage = 'https://github.com/ablab/IsoQuant' +description = """IsoQuant is a tool for the genome-based analysis of long RNA reads, + such as PacBio or Oxford Nanopores. IsoQuant allows to reconstruct and quantify + transcript models with high precision and decent recall. If the reference annotation is given, + IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. + IsoQuant further performs annotated gene, isoform, exon and intron quantification. + If reads are grouped (e.g. according to cell type), counts are reported according to the provided grouping.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/ablab/%(name)s/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] + +checksums = ['5c0e793a33f1b39b9f4888f7bade7f827f68bfb113535e08099906f7ad4689ce'] + +dependencies = [ + ('Python', '3.10.8'), + ('gffutils', '0.12'), + ('Biopython', '1.81'), + ('SciPy-bundle', '2023.02'), + ('pybedtools', '0.9.0'), + ('Pysam', '0.21.0'), + ('pyfaidx', '0.7.2.1'), + ('minimap2', '2.26'), + ('SAMtools', '1.17'), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +files_to_copy = [(['isoquant.py'], 'bin')] + +sanity_check_paths = { + 'files': ['isoquant.py'], + 'dirs': [], +} + +sanity_check_commands = ["isoquant.py --test"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-12.2.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..d7062b3aade --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'pybedtools' +version = '0.9.0' + +homepage = 'https://daler.github.io/pybedtools' +description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +dependencies = [ + ('Python', '3.10.8'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.21.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['9267c92cd764173449d9c31baedac0659b4eccc3d7c05e22ec378f86c0fc30a3'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb index 4ffe3451041..e8b10e708e8 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb @@ -2,7 +2,7 @@ # Guy's and St Thomas' NHS Foundation Trust and King's College London # Based on STAR-2.7.7a-GCC-10.2.0.eb # uploaded by J. Sassmannshausen -# modified by Thomas Eylenbosch +# Updated: Petr Král (INUITS) easyblock = 'MakeCp' @@ -18,20 +18,17 @@ toolchainopts = {'openmp': True} github_account = 'alexdobin' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -patches = ['STAR-%(version)s_use-external-htslib.patch'] -checksums = [ - {'2.7.10b.tar.gz': '0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5'}, - {'STAR-2.7.10b_use-external-htslib.patch': '1d8a24532a384b3065001c672e486b74094f162cb98829d2ec961401215de7da'}, -] +checksums = ['0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5'] dependencies = [ - ('HTSlib', '1.17'), ('zlib', '1.2.12'), ] start_dir = 'source' -buildopts = ' STAR && make STARlong' +buildopts = ' %(name)s && make %(name)slong' + +parallel = 1 files_to_copy = [ (['source/%(name)s', 'source/%(name)slong'], 'bin'), @@ -43,9 +40,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = [ - "STAR --help", - "STARlong --help", -] +sanity_check_commands = ["STAR --help"] moduleclass = 'bio' From 57cbed34f17e9201f550a4084a6b57e7f1c50ef2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 19 Jul 2023 11:53:55 +0200 Subject: [PATCH 8082/9987] fix typo --- easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb index bb16126eb22..8496bf20113 100644 --- a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb +++ b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb @@ -35,8 +35,6 @@ modextrapaths = { 'PYTHONPATH': '', } -files_to_copy = [(['isoquant.py'], 'bin')] - sanity_check_paths = { 'files': ['isoquant.py'], 'dirs': [], From 6ba5425293501d803c85fc8b27786de8e13afece Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 19 Jul 2023 13:04:28 +0200 Subject: [PATCH 8083/9987] Use CargoPythonBundle for timm --- .../timm-0.6.13-foss-2022a-CUDA-11.7.0.eb | 44 ++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb index 7cc34b4454a..736f977f3d7 100644 --- a/easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/timm/timm-0.6.13-foss-2022a-CUDA-11.7.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'CargoPythonBundle' name = 'timm' version = '0.6.13' @@ -27,6 +27,48 @@ builddependencies = [ ('Rust', '1.65.0'), # for safetensors ] +crates = [ + ('autocfg', '1.1.0'), + ('bitflags', '1.3.2'), + ('cfg-if', '1.0.0'), + ('indoc', '1.0.9'), + ('itoa', '1.0.9'), + ('libc', '0.2.147'), + ('lock_api', '0.4.10'), + ('memmap2', '0.5.10'), + ('memoffset', '0.8.0'), + ('once_cell', '1.18.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('proc-macro2', '1.0.66'), + ('pyo3', '0.18.3'), + ('pyo3-build-config', '0.18.3'), + ('pyo3-ffi', '0.18.3'), + ('pyo3-macros', '0.18.3'), + ('pyo3-macros-backend', '0.18.3'), + ('quote', '1.0.31'), + ('redox_syscall', '0.3.5'), + ('ryu', '1.0.15'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.171'), + ('serde_derive', '1.0.171'), + ('serde_json', '1.0.103'), + ('smallvec', '1.11.0'), + ('syn', '1.0.109'), + ('syn', '2.0.26'), + ('target-lexicon', '0.12.10'), + ('unicode-ident', '1.0.11'), + ('unindent', '0.1.11'), + ('windows-targets', '0.48.1'), + ('windows_aarch64_gnullvm', '0.48.0'), + ('windows_aarch64_msvc', '0.48.0'), + ('windows_i686_gnu', '0.48.0'), + ('windows_i686_msvc', '0.48.0'), + ('windows_x86_64_gnu', '0.48.0'), + ('windows_x86_64_gnullvm', '0.48.0'), + ('windows_x86_64_msvc', '0.48.0'), +] + use_pip = True exts_list = [ From e1ef7cdc8b3a54ee81550d72d630e87ac84efded Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 19 Jul 2023 13:14:14 +0200 Subject: [PATCH 8084/9987] adding easyconfigs: PICRUSt2-2.5.2-foss-2022b.eb, biom-format-2.1.15-foss-2022b.eb --- .../biom-format-2.1.15-foss-2022b.eb | 48 +++++++++++++++++++ .../p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb | 39 +++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/b/biom-format/biom-format-2.1.15-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.15-foss-2022b.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.15-foss-2022b.eb new file mode 100644 index 00000000000..eef21fa64ce --- /dev/null +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.15-foss-2022b.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Revised BSD +# +# Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b +## +# Updated: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'biom-format' +version = '2.1.15' + +homepage = 'https://biom-format.org' +description = """ +The BIOM file format (canonically pronounced biome) is designed to be + a general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth Microbiome + Project and is a Genomics Standards Consortium supported project. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['3bda2096e663dc1cb6f90f51b394da0838b9be5164a44370c134ce5b3b2a4dd3'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('h5py', '3.8.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/biom'], + 'dirs': ['lib'], +} + +options = {'modulename': 'biom'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb new file mode 100644 index 00000000000..785152f32e1 --- /dev/null +++ b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'PICRUSt2' +version = '2.5.2' + +homepage = 'https://github.com/picrust/picrust2' +description = """PICRUSt2 (Phylogenetic Investigation of Communities by + Reconstruction of Unobserved States) is a software for predicting + functional abundances based only on marker gene sequences. .""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('h5py', '3.8.0'), + ('biom-format', '2.1.15'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('joblib', '1.3.1', { + 'checksums': ['1f937906df65329ba98013dc9692fe22a4c5e4a648112de500508b18a21b41e3'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_urls': ['https://github.com/picrust/%(namelower)s/archive'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['a8c3832bf759233b52b41c56a0ffef72491e431fee347a7c05695596c76a1a4c'], + }), +] + +sanity_check_commands = [ + "python -c 'from picrust2.default import default_tables'" +] + +moduleclass = 'bio' From 501a6a30185b5f6e4d886fcaece2fa103bc28993 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 19 Jul 2023 14:19:14 +0200 Subject: [PATCH 8085/9987] fix typo --- easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb index 785152f32e1..cf6e747f07e 100644 --- a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb @@ -6,7 +6,7 @@ version = '2.5.2' homepage = 'https://github.com/picrust/picrust2' description = """PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting - functional abundances based only on marker gene sequences. .""" + functional abundances based only on marker gene sequences.""" toolchain = {'name': 'foss', 'version': '2022b'} From 96bf63372dcd4211431cf02f4af23a85b2b4350a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 19 Jul 2023 14:25:18 +0200 Subject: [PATCH 8086/9987] adding easyconfigs: pyodbc-4.0.39-foss-2022b.eb, unixODBC-2.3.11-foss-2022b.eb --- .../p/pyodbc/pyodbc-4.0.39-foss-2022b.eb | 27 +++++++++++++++++++ .../u/unixODBC/unixODBC-2.3.11-foss-2022b.eb | 21 +++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyodbc/pyodbc-4.0.39-foss-2022b.eb create mode 100644 easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.11-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/pyodbc/pyodbc-4.0.39-foss-2022b.eb b/easybuild/easyconfigs/p/pyodbc/pyodbc-4.0.39-foss-2022b.eb new file mode 100644 index 00000000000..026e13f54fb --- /dev/null +++ b/easybuild/easyconfigs/p/pyodbc/pyodbc-4.0.39-foss-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'pyodbc' +version = '4.0.39' + +homepage = 'https://github.com/mkleehammer/pyodbc' +description = """pyodbc is an open source Python module that makes + accessing ODBC databases simple. It implements the DB API 2.0 + specification but is packed with even more Pythonic convenience.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('unixODBC', '2.3.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['e528bb70dd6d6299ee429868925df0866e3e919c772b9eff79c8e17920d8f116'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.11-foss-2022b.eb b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.11-foss-2022b.eb new file mode 100644 index 00000000000..147df25f2d5 --- /dev/null +++ b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.11-foss-2022b.eb @@ -0,0 +1,21 @@ +# Easyconfig for unixODBC +# Author: Lykle Voort +# SURFsara, Amsterdam, The Netherlands +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'unixODBC' +version = '2.3.11' + +homepage = "https://www.unixodbc.org" +description = """unixODBC provides a uniform interface between +application and database driver""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://www.unixodbc.org/'] +checksums = ['d9e55c8e7118347e3c66c87338856dad1516b490fb7c756c1562a2c267c73b5c'] + +moduleclass = 'data' From 4a23229b475d8abbac80afce76853d2c71bd8d55 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 19 Jul 2023 15:10:49 +0200 Subject: [PATCH 8087/9987] fix typo --- easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb index c71f875bc79..62140b372d3 100644 --- a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} sources = [SOURCE_TAR_GZ] -checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'], +checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'] options = {'modulename': 'nose'} From e345ace6bce8bec843f1f8d8c98cea97a23d7ef1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 19 Jul 2023 15:21:28 +0200 Subject: [PATCH 8088/9987] adding easyconfigs: Sabre-2013-09-28-GCC-12.2.0.eb --- .../s/Sabre/Sabre-2013-09-28-GCC-12.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sabre/Sabre-2013-09-28-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/s/Sabre/Sabre-2013-09-28-GCC-12.2.0.eb b/easybuild/easyconfigs/s/Sabre/Sabre-2013-09-28-GCC-12.2.0.eb new file mode 100644 index 00000000000..2c74245cd7a --- /dev/null +++ b/easybuild/easyconfigs/s/Sabre/Sabre-2013-09-28-GCC-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'Sabre' +local_commit = '039a55e' +version = '2013-09-28' + +homepage = 'https://github.com/najoshi/sabre' +description = """A utility tool to filter alignments from bam files, + using identity percent, low complexity and read coverage.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/najoshi/sabre/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['8101eda078eded6c755d607a83ad5c659023dad9f0f2dadc11445c0ca305bf02'] + +dependencies = [ + ('zlib', '1.2.12'), +] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['sabre'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/sabre'], + 'dirs': [] +} + +sanity_check_commands = ['sabre --help'] + +moduleclass = 'bio' From b92dcf7cfd16b20cd2b34b4b346d9856e278313c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 19 Jul 2023 15:33:06 +0200 Subject: [PATCH 8089/9987] fix description --- .../easyconfigs/s/Sabre/Sabre-2013-09-28-GCC-12.2.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Sabre/Sabre-2013-09-28-GCC-12.2.0.eb b/easybuild/easyconfigs/s/Sabre/Sabre-2013-09-28-GCC-12.2.0.eb index 2c74245cd7a..184fad23944 100644 --- a/easybuild/easyconfigs/s/Sabre/Sabre-2013-09-28-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/Sabre/Sabre-2013-09-28-GCC-12.2.0.eb @@ -5,8 +5,12 @@ local_commit = '039a55e' version = '2013-09-28' homepage = 'https://github.com/najoshi/sabre' -description = """A utility tool to filter alignments from bam files, - using identity percent, low complexity and read coverage.""" +description = """Sabre is a tool that will demultiplex barcoded reads + into separate files. It will work on both single-end and paired-end + data in fastq format. It simply compares the provided barcodes with + each read and separates the read into its appropriate barcode file, + after stripping the barcode from the read (and also stripping + the quality values of the barcode bases).""" toolchain = {'name': 'GCC', 'version': '12.2.0'} From f960835729c273b9ec4709076f43db98dd850e60 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 19 Jul 2023 15:25:45 +0100 Subject: [PATCH 8090/9987] add --no-build-isolation to Arrow easyconfigs --- easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb | 3 ++- easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb | 3 ++- easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb | 3 ++- easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb | 3 ++- easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb | 3 ++- 5 files changed, 10 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb index d35cad0f1b3..a4fd6056b3a 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb @@ -53,7 +53,8 @@ local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && expo local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT -local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb index 638d160140b..36370e7bb59 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb @@ -48,7 +48,8 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " -local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb index 8e67baea105..b371e7adc4c 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb @@ -49,7 +49,8 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb index 6b7ebcc3c0f..4bfc742e061 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb @@ -48,7 +48,8 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " -local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb index 19aac4c1a50..10cf539670d 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb @@ -50,7 +50,8 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 5ab22988dcf4ee435bd6d4b5961ac9cc72e82886 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 19 Jul 2023 19:20:10 +0200 Subject: [PATCH 8091/9987] adding easyconfigs: CGAL-5.5.2-GCCcore-12.2.0.eb --- .../c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..1c3becd7fc4 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb @@ -0,0 +1,20 @@ +name = 'CGAL' +version = '5.5.2' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b2b05d5616ecc69facdc24417cce0b04fb4321491d107db45103add520e3d8c3'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +moduleclass = 'numlib' From d639692cb754fb1f7af3df45943e52ea128b2d87 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 19 Jul 2023 19:23:52 +0200 Subject: [PATCH 8092/9987] Use CMakeMake easyblock --- easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb index 1c3becd7fc4..57269cd1743 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb @@ -1,3 +1,4 @@ +easyblock = 'CMakeMake' name = 'CGAL' version = '5.5.2' From 542beb865884dec205bb1bb894b8ced9bd3fedad Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 19 Jul 2023 19:55:24 +0200 Subject: [PATCH 8093/9987] update extensions in poetry-1.5.1-GCCcore-12.3.0.eb Co-authored-by: Alex Domingo --- .../p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb index 8e4abdcd412..d97c76dbe4c 100755 --- a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb @@ -41,21 +41,9 @@ exts_list = [ ('charset-normalizer', '3.1.0', { 'checksums': ['34e0a2f9c370eb95597aae63bf85eb5e96826d81e3dcf88b8886012906f509b5'], }), - ('flit_scm', '1.7.0', { - 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], - }), ('dulwich', '0.21.5', { 'checksums': ['70955e4e249ddda6e34a4636b90f74e931e558f993b17c52570fa6144b993103'], }), - ('docutils', '0.20.1', { - 'checksums': ['f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b'], - }), - ('tomli_w', '1.0.0', { - 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], - }), - ('flit', '3.9.0', { - 'checksums': ['d75edf5eb324da20d53570a6a6f87f51e606eee8384925cd66a90611140844c7'], - }), ('crashtest', '0.4.1', { 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'], @@ -70,12 +58,6 @@ exts_list = [ 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], }), - ('semantic_version', '2.10.0', { - 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], - }), - ('pyasn1', '0.5.0', { - 'checksums': ['97b7290ca68e62a832558ec3976f15cbf911bf5d7c7039d8b861c2a0ece69fde'], - }), ('SecretStorage', '3.3.3', { 'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'], }), From ae8a78f824fa86d53df4b82198a186cf7d0b6278 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 19 Jul 2023 20:13:29 +0200 Subject: [PATCH 8094/9987] add virtualenv dependency in poetry-1.5.1-GCCcore-12.3.0.eb --- easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb index d97c76dbe4c..81f9eaa6351 100755 --- a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb @@ -19,6 +19,7 @@ dependencies = [ ('Python', '3.11.3'), ('hatchling', '1.18.0'), ('cryptography', '41.0.1'), + ('virtualenv', '20.23.1'), ] use_pip = True @@ -152,9 +153,6 @@ exts_list = [ ('filelock', '3.12.2', { 'checksums': ['002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81'], }), - ('virtualenv', '20.23.1', { - 'checksums': ['8ff19a38c1021c742148edc4f81cb43d7f8c6816d2ede2ab72af5b84c749ade1'], - }), (name, version, { 'checksums': ['cc7ea4524d1a11558006224bfe8ba8ed071417d4eb5ef6c89decc6a37d437eeb'], }), From 0c6111c1859380b3c06fec000fcd8e6ac74d567e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 19 Jul 2023 22:07:58 +0200 Subject: [PATCH 8095/9987] bundle pycparser with cffi in cffi-1.15.1-GCCcore-12.3.0.eb --- .../c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb | 23 +++++++++------ .../pycparser-2.21-GCCcore-12.3.0.eb | 28 ------------------- 2 files changed, 15 insertions(+), 36 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb index 289c0b41712..b511d571cbe 100644 --- a/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-12.3.0.eb @@ -1,4 +1,4 @@ -easyblock = "PythonPackage" +easyblock = "PythonBundle" name = 'cffi' version = '1.15.1' @@ -12,20 +12,27 @@ files or documentation. toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -sources = [SOURCE_TAR_GZ] -checksums = ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'] - builddependencies = [ ('binutils', '2.40'), ] dependencies = [ ('Python', '3.11.3'), - ('pycparser', '2.21'), ] -download_dep_fail = True -use_pip = True -sanity_pip_check = True +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + (name, version, { + 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], + }), +] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb deleted file mode 100644 index b03acaf84d9..00000000000 --- a/easybuild/easyconfigs/p/pycparser/pycparser-2.21-GCCcore-12.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = "PythonPackage" - -name = 'pycparser' -version = '2.21' - -homepage = 'https://github.com/eliben/pycparser' -description = """pycparser is a parser for the C language, written in pure Python. It is a -module designed to be easily integrated into applications that need to parse C source code.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True} - -sources = [SOURCE_TAR_GZ] -checksums = ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'] - -builddependencies = [ - ('binutils', '2.40'), -] - -dependencies = [ - ('Python', '3.11.3'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -moduleclass = 'tools' From 30cf48a8b7373fa831579e1526c083a66bf7463f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 19 Jul 2023 22:10:07 +0200 Subject: [PATCH 8096/9987] adding easyconfigs: flit-3.9.0-GCCcore-12.3.0.eb --- .../f/flit/flit-3.9.0-GCCcore-12.3.0.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..15b9ad83d78 --- /dev/null +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'flit' +version = '3.9.0' + +homepage = 'https://github.com/pypa/flit' +description = "A simple packaging tool for simple packages." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('certifi', '2023.5.7', { + 'checksums': ['0f0d56dc5a6ad56fd4ba36484d6cc34451e1c6548c61daad8c320169f91eddc7'], + }), + ('urllib3', '1.26.16', { + 'checksums': ['8f135f6502756bde6b2a9b28989df5fbe87c9970cecaa69041edcce7f0589b14'], + }), + ('charset-normalizer', '3.1.0', { + 'checksums': ['34e0a2f9c370eb95597aae63bf85eb5e96826d81e3dcf88b8886012906f509b5'], + }), + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + ('setuptools_scm', '7.1.0', { + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('typing_extensions', '4.6.3', { + 'checksums': ['d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5'], + }), + ('flit_scm', '1.7.0', { + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('docutils', '0.20.1', { + 'checksums': ['f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b'], + }), + ('tomli_w', '1.0.0', { + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), + (name, version, { + 'checksums': ['d75edf5eb324da20d53570a6a6f87f51e606eee8384925cd66a90611140844c7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' From 03a3b99f165ecc8ac26cb1f190da38563dd8b417 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 19 Jul 2023 22:11:36 +0200 Subject: [PATCH 8097/9987] add flit build dependency and virtualenv dependency to Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb --- .../Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb index 9c3b9912fc9..642b6fed379 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb @@ -17,11 +17,13 @@ builddependencies = [ ('hatchling', '1.18.0'), ('poetry', '1.5.1'), ('scikit-build', '0.17.6'), + ('flit', '3.9.0'), ] dependencies = [ ('Python', '3.11.3'), ('cryptography', '41.0.1'), + ('virtualenv', '20.23.1'), ] exts_default_options = { From b6884392a64b0fd9ac5a8281639b3b56ec0816d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 19 Jul 2023 22:59:32 +0200 Subject: [PATCH 8098/9987] Add sanity check --- easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb index 57269cd1743..d3b3328cd05 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.5.2-GCCcore-12.2.0.eb @@ -18,4 +18,9 @@ builddependencies = [ ('binutils', '2.39'), ] +sanity_check_paths = { + 'files': ['include/CGAL/Simple_cartesian.h'], + 'dirs': ['include/CGAL', 'lib/cmake/CGAL'], +} + moduleclass = 'numlib' From c160a7f851d0e2a079030e0b92ae9cb3e5b9d810 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 19 Jul 2023 15:18:02 -0700 Subject: [PATCH 8099/9987] MACS3 new to EB! --- .../m/MACS3/MACS3-3.0.0b2-foss-2021b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2021b.eb b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2021b.eb new file mode 100644 index 00000000000..ba7e3d8b54f --- /dev/null +++ b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2021b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'MACS3' +version = '3.0.0b2' + +homepage = 'https://macs3-project.github.io/MACS/' +description = """Model Based Analysis for ChIP-Seq data""" + +toolchain = {'name': 'foss', 'version': '2021b'} + + +builddependencies = [ + ('pybind11', '2.7.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('scikit-learn', '1.0.1'), + ('matplotlib', '3.4.3'), +] + +use_pip = True + +exts_list = [ + ('cykhash', '2.0.1', { + 'checksums': ['b4794bc9f549114d8cf1d856d9f64e08ff5f246bf043cf369fdb414e9ceb97f7'], + }), + ('hmmlearn', '0.2.6', { + 'checksums': ['2a289cf28b31be59fa8ba5d3253d4a2a992401d45a8cdc221ae484fbf390c0d7'], + }), + (name, version, { + 'modulename': 'MACS3', + 'checksums': ['9b13fed49b93623ddde4b2d5106fc92a796111fa92148cafe7d8bd9a2e8aa43f'], + }), +] + +sanity_check_commands = [('%(namelower)s --help')] + +moduleclass = 'bio' From cd8848da094111991d3e8fc2dfdf9bd7f1164b13 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 20 Jul 2023 15:16:32 +0200 Subject: [PATCH 8100/9987] remove extensions provided by virtualenv from poetry v1.5.1 --- .../easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb index 81f9eaa6351..f88ebb3614b 100755 --- a/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.5.1-GCCcore-12.3.0.eb @@ -147,12 +147,6 @@ exts_list = [ ('poetry_plugin_export', '1.4.0', { 'checksums': ['f16974cd9f222d4ef640fa97a8d661b04d4fb339e51da93973f1bc9d578e183f'], }), - ('distlib', '0.3.6', { - 'checksums': ['14bad2d9b04d3a36127ac97f30b12a19268f211063d8f8ee4f47108896e11b46'], - }), - ('filelock', '3.12.2', { - 'checksums': ['002740518d8aa59a26b0c76e10fb8c6e15eae825d34b6fdf670333fd7b938d81'], - }), (name, version, { 'checksums': ['cc7ea4524d1a11558006224bfe8ba8ed071417d4eb5ef6c89decc6a37d437eeb'], }), From 4a562af404f53eac1a5d8f185c87e21be4616927 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 21 Jul 2023 13:07:45 +0200 Subject: [PATCH 8101/9987] adding easyconfigs: Chemaxon-Marvin-23.9.eb --- .../c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb diff --git a/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb new file mode 100644 index 00000000000..b88324a00dc --- /dev/null +++ b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb @@ -0,0 +1,71 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +# Cannot use *easyblock = 'Rpm'* because the RPM misses some fields: +# Summary and License fields must be present in package: (main package) +easyblock = 'Binary' + +name = 'Chemaxon-Marvin' +version = '23.9' + +homepage = 'https://chemaxon.com/products/marvin' +description = """Marvin suite is a chemically intelligent desktop toolkit built +to help you draw, edit, publish, render, import and export your chemical structures +and as well as allowing you to convert between various chemical and graphical file +formats. It is free for individual, academic and non-commercial use.""" + +# NOTE not in the license list of EB +# software_license = 'Proprietary: Personal, Commercial or Academic' +software_license_urls = ['https://www.chemaxon.com/marvin/license.html'] +docurls = [ + 'https://docs.chemaxon.com/display/docs/marvinsketch-user-s-guide.md', + 'https://docs.chemaxon.com/display/docs/marvinview-user-s-guide.md', + 'https://docs.chemaxon.com/display/docs/file-formats.md', +] + +toolchain = SYSTEM + +# Download and license at https://chemaxon.com/products/marvin +# Once logged in download files can be found here: +# https://chemaxon.com/products/marvin/download#download +sources = ['marvin_linux_%(version)s_openjdk11.rpm'] +checksums = ['21a3bcd75d41d614fb9768949e713bfbb299e5c782a7166eaad0cd13654b140f'] + +osdependencies = [('rpm', 'cpio')] # for extracting rpm-files + +dependencies = [ + ('Java', '11'), +] + +extract_sources = False + +install_cmd = 'rpm2cpio ' + sources[0] + ' | cpio -idmv && ' +install_cmd += 'cd opt/chemaxon/marvinsuite/ && ' +install_cmd += 'chmod -x bin/*.bat && ' +install_cmd += 'cp -ar . %(installdir)s/' + +# plugins directory is empty +sanity_check_paths = { + 'files': ["bin/cxcalc", "bin/cxtrain", "bin/evaluate", "bin/molconvert", + "bin/msketch", "bin/mview", "EULA.html"], + 'dirs': ['lib'] +} + +sanity_check_commands = ["molconvert"] + +# You need a key/license file to fully activate Chemaxon Marvin +# +# COMMERCIAL +# For commercial use please contact sales@chemaxon.com +# NON-COMMERCIAL +# For personal use get a key to be renewed every 2 months at https://chemaxon.com/products/marvin/download +# For academic use get a key for research or educational purposes at https://chemaxon.com/academic-license +# +# The license file "license.cxl" has to be placed in $HOME/.chemaxon/ + +moduleclass = 'chem' From e1c4d0e44fe0e7e2ee3f4f27119d281e79f6513f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 21 Jul 2023 16:41:29 +0200 Subject: [PATCH 8102/9987] adding easyconfigs: OpenFOAM-v2306-foss-2022b.eb --- .../o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb new file mode 100644 index 00000000000..74cc6908afa --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -0,0 +1,47 @@ +name = 'OpenFOAM' +version = 'v2306' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {'usempi': True, 'cstd': 'c++11', 'vectorize': False} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2206-cleanup.patch', 1), + 'OpenFOAM-v1906-wmake-ompi.patch', +] +checksums = [ + {'OpenFOAM-v2306.tgz': 'd7fba773658c0f06ad17f90199565f32e9bf502b7bb03077503642064e1f5344'}, + {'OpenFOAM-v2206-cleanup.patch': '25333124581acae57c173587de4ebd6e143b894b1a26e4f0326db8b7e0cb1972'}, + {'OpenFOAM-v1906-wmake-ompi.patch': '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.24.3'), + ('flex', '2.6.4'), + ('CGAL', '5.5.2'), # header only +] + +dependencies = [ + ('libreadline', '8.2'), + ('ncurses', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('KaHIP', '3.14'), + ('Boost', '1.81.0'), + ('ParaView', '5.11.0', '-mpi'), + ('gnuplot', '5.4.6'), +] + +moduleclass = 'cae' From 076fbb4ec2ded3be0202e78feacc7870e24cb9cd Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 21 Jul 2023 15:00:51 -0700 Subject: [PATCH 8103/9987] newer toolchain --- ...oss-2021b.eb => MACS3-3.0.0b2-foss-2022b.eb} | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/m/MACS3/{MACS3-3.0.0b2-foss-2021b.eb => MACS3-3.0.0b2-foss-2022b.eb} (64%) diff --git a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2021b.eb b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb similarity index 64% rename from easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2021b.eb rename to easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb index ba7e3d8b54f..6c4cc540d89 100644 --- a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb @@ -6,28 +6,29 @@ version = '3.0.0b2' homepage = 'https://macs3-project.github.io/MACS/' description = """Model Based Analysis for ChIP-Seq data""" -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {'name': 'foss', 'version': '2022b'} builddependencies = [ - ('pybind11', '2.7.1'), + ('pybind11', '2.10.3'), ] dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('scikit-learn', '1.0.1'), - ('matplotlib', '3.4.3'), + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('scikit-learn', '1.2.1'), + ('matplotlib', '3.7.0'), ] use_pip = True +sanity_pip_check = True exts_list = [ ('cykhash', '2.0.1', { 'checksums': ['b4794bc9f549114d8cf1d856d9f64e08ff5f246bf043cf369fdb414e9ceb97f7'], }), - ('hmmlearn', '0.2.6', { - 'checksums': ['2a289cf28b31be59fa8ba5d3253d4a2a992401d45a8cdc221ae484fbf390c0d7'], + ('hmmlearn', '0.3.0', { + 'checksums': ['d13a91ea3695df881465e3d36132d7eef4e84d483f4ba538a4b46e24b5ea100f'], }), (name, version, { 'modulename': 'MACS3', From 1ed3b56715911671478798e637d38ed854952da8 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 21 Jul 2023 16:22:41 -0700 Subject: [PATCH 8104/9987] GCCcore 11.2.0 was skipped --- .../s/spdlog/spdlog-1.10.0-GCCcore-11.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/spdlog/spdlog-1.10.0-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/s/spdlog/spdlog-1.10.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/spdlog/spdlog-1.10.0-GCCcore-11.2.0.eb new file mode 100644 index 00000000000..abc8066853a --- /dev/null +++ b/easybuild/easyconfigs/s/spdlog/spdlog-1.10.0-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'spdlog' +version = '1.10.0' + +homepage = 'https://github.com/gabime/spdlog' +description = 'Very fast, header-only/compiled, C++ logging library.' +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/gabime/spdlog/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['697f91700237dbae2326b90469be32b876b2b44888302afbc7aceb68bcfe8224'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), +] + +sanity_check_paths = { + 'files': ['include/spdlog/spdlog.h'], + 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 2f61086d6940032fb50331fea8dee7c5a70c01bf Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 22 Jul 2023 13:19:24 +0100 Subject: [PATCH 8105/9987] python -m pip install --- easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb | 2 +- easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb | 2 +- easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb | 2 +- easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb | 2 +- easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb index a4fd6056b3a..05a7cb4386e 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb @@ -54,7 +54,7 @@ local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " -local_install_pyarrow_cmds += "pip install --prefix %(installdir)s --no-build-isolation ." +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb index 36370e7bb59..313f50a90b1 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb @@ -49,7 +49,7 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " -local_install_pyarrow_cmds += "pip install --prefix %(installdir)s --no-build-isolation ." +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb index b371e7adc4c..49eabfce7af 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb @@ -50,7 +50,7 @@ local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && expo local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " -local_install_pyarrow_cmds += "pip install --prefix %(installdir)s --no-build-isolation ." +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb index 4bfc742e061..c1522dd1d30 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb @@ -49,7 +49,7 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " -local_install_pyarrow_cmds += "pip install --prefix %(installdir)s --no-build-isolation ." +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb index 10cf539670d..63f8267f34f 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb @@ -51,7 +51,7 @@ local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && expo local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " -local_install_pyarrow_cmds += "pip install --prefix %(installdir)s --no-build-isolation ." +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 92f278cf43409ae5d54ee3cafba412fa4cc3593d Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 24 Jul 2023 11:04:31 +0200 Subject: [PATCH 8106/9987] adding easyconfigs: Pylint-2.17.4-GCCcore-12.2.0.eb --- .../p/Pylint/Pylint-2.17.4-GCCcore-12.2.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pylint/Pylint-2.17.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/Pylint/Pylint-2.17.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pylint/Pylint-2.17.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..3fe567849fd --- /dev/null +++ b/easybuild/easyconfigs/p/Pylint/Pylint-2.17.4-GCCcore-12.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'Pylint' +version = '2.17.4' + +homepage = 'https://www.pylint.org/' +description = """Pylint is a tool that checks for errors in Python code, tries to enforce + a coding standard and looks for code smells. It can also look for certain type errors, + it can recommend suggestions about how particular blocks can be refactored and + can offer you details about the code's complexity.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True + +exts_list = [ + ('dill', '0.3.7', { + 'checksums': ['cc1c8b182eb3013e24bd475ff2e9295af86c1a38eb1aff128dac8962a9ce3c03'], + }), + ('lazy-object-proxy', '1.9.0', { + 'checksums': ['659fb5809fa4629b8a1ac5106f669cfc7bef26fbb389dda53b3e010d1ac4ebae'], + }), + ('wrapt', '1.15.0', { + 'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'], + }), + ('astroid', '2.15.6', { + 'checksums': ['903f024859b7c7687d7a7f3a3f73b17301f8e42dfd9cc9df9d4418172d3e2dbd'], + }), + ('isort', '5.12.0', { + 'checksums': ['8bef7dde241278824a6d83f44a544709b065191b95b6e50894bdc722fcba0504'], + }), + ('mccabe', '0.7.0', { + 'checksums': ['348e0240c33b60bbdf4e523192ef919f28cb2c3d7d5c7794f74009290f236325'], + }), + ('pylint', version, { + 'checksums': ['5dcf1d9e19f41f38e4e85d10f511e5b9c35e1aa74251bf95cdd8cb23584e2db1'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/pylint'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From af83f54c90398c81f34f88979d92c5cc05dfefbd Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 24 Jul 2023 13:26:49 +0200 Subject: [PATCH 8107/9987] adding easyconfigs: sentinelsat-1.2.1-GCCcore-11.3.0.eb --- .../sentinelsat-1.2.1-GCCcore-11.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7e417e7da77 --- /dev/null +++ b/easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'sentinelsat' +version = '1.2.1' + +homepage = 'https://github.com/sentinelsat/sentinelsat' +description = """ +Sentinelsat makes searching, downloading and retrieving the metadata of Sentinel +satellite images from the Copernicus Open Access Hub easy. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('html2text', '2020.1.16', { + 'checksums': ['e296318e16b059ddb97f7a8a1d6a5c1d7af4544049a01e261731d2d5cc277bbb'], + }), + ('geojson', '3.0.1', { + 'checksums': ['ff3d75acab60b1e66504a11f7ea12c104bad32ff3c410a807788663b966dee4a'], + }), + ('geomet', '1.0.0', { + 'checksums': ['0020a4426469934fb58f541cdc23f27c0c0fbbb3d003ee2cb76bb7ffa96a7506'], + }), + (name, version, { + 'checksums': ['d38de0ae1e167d7311426973b0207380e9fa1c4a6f5353dc58bd83bf88b5db4d'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 3764bfa2660034724ec944692e82b8b21bbcc3c4 Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Mon, 24 Jul 2023 14:36:07 +0200 Subject: [PATCH 8108/9987] adding easyconfigs: MACS2-2.2.7.1-foss-2021a.eb --- .../m/MACS2/MACS2-2.2.7.1-foss-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021a.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021a.eb new file mode 100644 index 00000000000..ce729591c95 --- /dev/null +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021a.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonPackage' + +name = 'MACS2' +version = '2.2.7.1' + +homepage = 'https://github.com/taoliu/MACS' +description = "Model Based Analysis for ChIP-Seq data" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ad2ca69bdd02a8942a68aae23133289b5c16ba382bcbe20c39fabf3948929de5'] + +dependencies = [ + ('Python', '3.9.5'), + ('Boost', '1.76.0'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/macs2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('%(namelower)s --version')] + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' From 2a5f1f476097e2709c9ed822c1474df56abb59ee Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 24 Jul 2023 15:03:45 +0200 Subject: [PATCH 8109/9987] Add bintuils 2.38 as build dependency --- .../s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb index 7e417e7da77..4d37dd7e284 100644 --- a/easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb @@ -11,6 +11,8 @@ satellite images from the Copernicus Open Access Hub easy. toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +builddependencies = [('binutils', '2.38')] + dependencies = [ ('Python', '3.10.4'), ('tqdm', '4.64.0'), From 90153d66e3abd2475e286dabb9caa495e0c653f7 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 24 Jul 2023 15:08:30 +0200 Subject: [PATCH 8110/9987] Moved version to 5.1.2 + added a patchfix for Yambo pre-5.2 SLEPc bug --- ...el-2021b.eb => Yambo-5.1.2-intel-2021b.eb} | 35 ++-- .../easyconfigs/y/Yambo/yambo_slepc_fix.patch | 169 ++++++++++++++++++ 2 files changed, 191 insertions(+), 13 deletions(-) rename easybuild/easyconfigs/y/Yambo/{Yambo-5.2.dev-20230512-intel-2021b.eb => Yambo-5.1.2-intel-2021b.eb} (63%) create mode 100644 easybuild/easyconfigs/y/Yambo/yambo_slepc_fix.patch diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb similarity index 63% rename from easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb rename to easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb index f6c67300dc0..66f0b200671 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-5.2.dev-20230512-intel-2021b.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb @@ -1,29 +1,29 @@ easyblock = 'MakeCp' name = 'Yambo' -version = '5.2.dev-20230512' +# see https://github.com/yambo-code/yambo/wiki/Releases-%28tar.gz-format%29 +version = '5.1.2' local_yambo_libs_ver = '1.0' -local_commit = 'dfa2752' homepage = 'http://www.yambo-code.org' description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" toolchain = {'name': 'intel', 'version': '2021b'} -toolchainopts = {'usempi': True, 'openmp': True} +toolchainopts = {'usempi': True} local_yambo_ext_cmd = 'mkdir yambo-%(version)s && ' local_yambo_ext_cmd += 'tar --strip-components=1 -xzf %s -C yambo-%(version)s' -local_yambo_lib_ext_cmd = 'mkdir yambo-%(version)s/lib/yambo/ && ' +local_yambo_lib_ext_cmd = 'mkdir -p yambo-%(version)s/lib/yambo/ && ' local_yambo_lib_ext_cmd += 'tar --strip-components=1 -xzf %s -C yambo-%(version)s/lib/yambo/' source_urls = ['https://github.com/yambo-code/yambo/archive/'] sources = [ { - 'download_filename': '%s.tar.gz' % local_commit, + 'download_filename': '%(version)s.tar.gz', 'filename': 'yambo-%(version)s.tar.gz', 'extract_cmd': local_yambo_ext_cmd, - }, # Yambo + }, { 'source_urls': ['https://github.com/yambo-code/yambo-libraries/archive/'], 'download_filename': '%s.tar.gz' % local_yambo_libs_ver, @@ -31,15 +31,18 @@ sources = [ 'extract_cmd': local_yambo_lib_ext_cmd, }, { + # see https://github.com/yambo-code/yambo/wiki/Libraries#external-libraries 'source_urls': ['https://github.com/yambo-code/yambo/files/962173/'], 'filename': 'iotk-y1.2.2.tar.gz', 'extract_cmd': 'cp %s yambo-%(version)s/lib/archive/', }, ] +patches = ['yambo_slepc_fix.patch'] checksums = [ - {'yambo-5.2.dev-20230512.tar.gz': '4a993b86543fec7c5fa79838ab699a9f4432a215f63eca537c0819335ab9981c'}, + {'yambo-5.1.2.tar.gz': '9625d8a96bd9a3ff3713ebe53228d5ac9be0a98adecbe2a2bad67234c0e26a2e'}, {'yambo-libraries-1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'}, {'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'}, + {'yambo_slepc_fix.patch': '2653aeecb887c3919204da575d65e9d985b0b23608d5780dc8aa1bba02dc12c5'}, ] dependencies = [ @@ -53,20 +56,26 @@ dependencies = [ with_configure = True -configopts = 'FC=mpiifort CC=mpiicc ' +configopts = 'FC=mpiifort CC=mpiicc --enable-msgs-comps ' configopts += '--prefix=%(builddir)s/%(namelower)s-%(version)s/ ' configopts += '--enable-open-mp --enable-hdf5-par-io ' -configopts += '--with-blas-libs="$LIBBLAS" ' -configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs=mkl ' -configopts += '--with-scalapack-libs=mkl ' -configopts += '--with-fft-libs="-mkl" --with-fft-includedir="$FFT_INC_DIR" ' -configopts += '--with-netcdf-lib=$EBROOTNETCDF/lib --with-netcdf-include="$EBROOTNETCDF/include" ' +configopts += '--with-blas-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" ' +configopts += '--with-lapack-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" --with-blacs-libs=mkl ' +configopts += '--with-scalapack-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" ' +configopts += '--with-fft-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" --with-fft-includedir="${MKLROOT}/include" ' +configopts += '--with-netcdf-path=$EBROOTNETCDF ' configopts += '--with-netcdff-path="$EBROOTNETCDFMINFORTRAN" ' configopts += '--with-hdf5-path="$EBROOTHDF5" --with-petsc-path="$EBROOTPETSC" ' configopts += '--with-slepc-path="$EBROOTSLEPC" --with-libxc-path="$EBROOTLIBXC" ' configopts += '--enable-par-linalg --enable-slepc-linalg ' prebuildopts = "export FPATH=$EBROOTPETSC/include:$EBROOTSLEPC/include:$FPATH && " + +prebuildopts = "export SHELL='sh -x' && " buildopts = 'all' files_to_copy = [ diff --git a/easybuild/easyconfigs/y/Yambo/yambo_slepc_fix.patch b/easybuild/easyconfigs/y/Yambo/yambo_slepc_fix.patch new file mode 100644 index 00000000000..6b305af1a41 --- /dev/null +++ b/easybuild/easyconfigs/y/Yambo/yambo_slepc_fix.patch @@ -0,0 +1,169 @@ +diff -ruN yambo-5.1.2.orig/src/bse/K_multiply_by_V_slepc.F yambo-5.1.2/src/bse/K_multiply_by_V_slepc.F +--- yambo-5.1.2.orig/src/bse/K_multiply_by_V_slepc.F 2023-07-24 14:31:48.203323300 +0200 ++++ yambo-5.1.2/src/bse/K_multiply_by_V_slepc.F 2023-07-24 14:35:13.933323300 +0200 +@@ -1,5 +1,5 @@ + ! +-! Copyright (C) 2000-2023 the YAMBO team ++! Copyright (C) 2000-2022 the YAMBO team + ! http://www.yambo-code.org + ! + ! Authors (see AUTHORS file for details): HM DS IMA +@@ -26,7 +26,7 @@ + ! Interface with the K_multiply_by_V from the Haydock method + ! This function has to take the same arguments as MatMult from PETSC + ! +- use pars, ONLY : SP ++ use pars, ONLY : SP,cI + use BS_solvers, ONLY : Slepc_v,BSS_Slepc_double_grp + use BS, ONLY : BS_T_grp,BS_nT_grps,BS_K_dim + use parallel_m, ONLY : PAR_IND_T_Haydock +@@ -45,7 +45,7 @@ + ! + implicit none + ! +- PetscScalar :: tmp_value(1) ++ PetscScalar :: tmp_value(1),tmp_value_star(1) + PetscInt :: H_pos(1), pet_one + PetscErrorCode :: ierr + ! +@@ -108,12 +108,13 @@ + do i_c=1,BS_T_grp(i_g)%size + H_pos=start_index+i_c + tmp_value=cmplx(Slepc_v%Vo(i_g)%fragment(i_c,1)) ++ tmp_value_star=real(Slepc_v%Vo(i_g)%fragment(i_c,1))-cI*aimag(Slepc_v%Vo(i_g)%fragment(i_c,1)) + !SLEPC funcitons expect C indexes both in Fortran and C + call VecSetValues( vo, pet_one, H_pos, tmp_value, INSERT_VALUES, ierr ) + if(BSS_slepc_double_grp) then + ! Expand vo to anti-resonant block + H_pos=start_index_dg+i_c +- call VecSetValues( vo, pet_one, H_pos, fac*conjg(tmp_value), INSERT_VALUES, ierr ) ++ call VecSetValues( vo, pet_one, H_pos, fac*tmp_value_star, INSERT_VALUES, ierr ) + endif + enddo + enddo +diff -ruN yambo-5.1.2.orig/src/bse/K_multiply_by_V_transpose_slepc.F yambo-5.1.2/src/bse/K_multiply_by_V_transpose_slepc.F +--- yambo-5.1.2.orig/src/bse/K_multiply_by_V_transpose_slepc.F 2023-07-24 14:31:48.203323300 +0200 ++++ yambo-5.1.2/src/bse/K_multiply_by_V_transpose_slepc.F 2023-07-24 14:34:40.413323300 +0200 +@@ -1,5 +1,5 @@ + ! +-! Copyright (C) 2000-2023 the YAMBO team ++! Copyright (C) 2000-2022 the YAMBO team + ! http://www.yambo-code.org + ! + ! Authors (see AUTHORS file for details): HM DS IMA +@@ -26,7 +26,7 @@ + ! Interface with the K_multiply_by_V from the Haydock method + ! This function has to take the same arguments as MatMult from PETSC + ! +- use pars, ONLY : SP ++ use pars, ONLY : SP,cI + use BS_solvers, ONLY : Slepc_v,BSS_Slepc_double_grp + use BS, ONLY : BS_T_grp,BS_nT_grps,BS_K_dim + use parallel_m, ONLY : PAR_IND_T_Haydock +@@ -45,7 +45,7 @@ + ! + implicit none + ! +- PetscScalar :: tmp_value(1) ++ PetscScalar :: tmp_value(1),tmp_value_star(1) + PetscInt :: H_pos(1), pet_one + PetscErrorCode :: ierr + ! +@@ -109,12 +109,13 @@ + do i_c=1,BS_T_grp(i_g)%size + H_pos=start_index+i_c + tmp_value=cmplx(Slepc_v%Vo(i_g)%fragment(i_c,1)) ++ tmp_value_star=real(Slepc_v%Vo(i_g)%fragment(i_c,1))-cI*aimag(Slepc_v%Vo(i_g)%fragment(i_c,1)) + !SLEPC funcitons expect C indexes both in Fortran and C + call VecSetValues( vo, pet_one, H_pos, tmp_value, INSERT_VALUES, ierr ) + if(BSS_slepc_double_grp) then + ! Expand vo to anti-resonant block + H_pos=start_index_dg+i_c +- call VecSetValues( vo, pet_one, H_pos, fac*conjg(tmp_value), INSERT_VALUES, ierr ) ++ call VecSetValues( vo, pet_one, H_pos, fac*tmp_value_star, INSERT_VALUES, ierr ) + endif + enddo + enddo +diff -ruN yambo-5.1.2.orig/src/bse/K_stored_in_a_slepc_matrix.F yambo-5.1.2/src/bse/K_stored_in_a_slepc_matrix.F +--- yambo-5.1.2.orig/src/bse/K_stored_in_a_slepc_matrix.F 2023-07-24 14:31:48.203323300 +0200 ++++ yambo-5.1.2/src/bse/K_stored_in_a_slepc_matrix.F 2023-07-24 14:35:46.923323300 +0200 +@@ -1,5 +1,5 @@ + ! +-! Copyright (C) 2000-2023 the YAMBO team ++! Copyright (C) 2000-2022 the YAMBO team + ! http://www.yambo-code.org + ! + ! Authors (see AUTHORS file for details): HM DS +@@ -53,7 +53,7 @@ + Mat, intent(out) :: slepc_mat + ! + integer :: i_c,i_r,i_Tk,i_Tp,i_B,H_shift(2) +- PetscScalar :: Mij ++ PetscScalar :: Mij,Mij_star + PetscInt :: H_pos(2),SL_K_dim(2),SL_H_dim + PetscErrorCode :: ierr + ! +@@ -95,14 +95,17 @@ + if (H_pos(1)+H_shift(1)>H_pos(2)+H_shift(2)) cycle + if (l_BS_ares_from_res.and.H_pos(1)>H_pos(2)) cycle + ! +- Mij=BS_blk(i_B)%mat(i_r,i_c) ++ Mij = BS_blk(i_B)%mat(i_r,i_c) ++ Mij_star= real(BS_blk(i_B)%mat(i_r,i_c))-cI*aimag(BS_blk(i_B)%mat(i_r,i_c)) + ! + ! Add energies to the diagonal + ! + if(H_pos(1)+H_shift(1)==H_pos(2)+H_shift(2)) then +- Mij=real(Mij)+BSS_eh_E(H_pos(1)+H_shift(1)+1)*cONE ++ Mij =real(Mij) +BSS_eh_E(H_pos(1)+H_shift(1)+1)*cONE ++ Mij_star=real(Mij_star)+BSS_eh_E(H_pos(1)+H_shift(1)+1)*cONE + if (allocated(BSS_eh_W).and..not.BSS_perturbative_width) then +- Mij=Mij+cI*BSS_eh_W(H_pos(1)+H_shift(1)+1) ++ Mij =Mij +cI*BSS_eh_W(H_pos(1)+H_shift(1)+1) ++ Mij_star=Mij_star -cI*BSS_eh_W(H_pos(1)+H_shift(1)+1) + endif + endif + ! +@@ -110,35 +113,35 @@ + case("R") + call MatSetValue( slepc_mat, H_pos(1), H_pos(2), Mij , INSERT_VALUES, ierr ) + ! The resonant block is hermitial +- call MatSetValue( slepc_mat, H_pos(2), H_pos(1), conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2), H_pos(1), Mij_star, INSERT_VALUES, ierr ) + if (l_BS_ares_from_res.and.BS_K_coupling) then + ! The anti-resonant block is A=-R* +- call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2)+SL_K_dim(1),-conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2)+SL_K_dim(1), -Mij_star, INSERT_VALUES, ierr ) + ! The anti-resonant block is hermitian + call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1)+SL_K_dim(1), -Mij, INSERT_VALUES, ierr ) + endif + case("C") + call MatSetValue( slepc_mat, H_pos(1), H_pos(2)+SL_K_dim(1), Mij , INSERT_VALUES, ierr ) + ! Anti-coupling from coupling: the whole BSE matrix is Pseudo-HErmitian +- call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1),-conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1), -Mij_star , INSERT_VALUES, ierr ) + if (l_BS_ares_from_res) then + ! The coupling block and the anti-coupling block are symmetric + call MatSetValue( slepc_mat, H_pos(2), H_pos(1)+SL_K_dim(1), Mij , INSERT_VALUES, ierr ) +- call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2),-conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2), -Mij_star , INSERT_VALUES, ierr ) + endif + case("A") + ! The anti-resonant block is hermitial + if(BS_res_ares_n_mat==1) then + call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2)+SL_K_dim(1), Mij , INSERT_VALUES, ierr ) +- call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1)+SL_K_dim(1), conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1)+SL_K_dim(1), Mij_star , INSERT_VALUES, ierr ) + else + call MatSetValue( slepc_mat, H_pos(1), H_pos(2), Mij , INSERT_VALUES, ierr ) +- call MatSetValue( slepc_mat, H_pos(2), H_pos(1), conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2), H_pos(1), Mij_star , INSERT_VALUES, ierr ) + endif + case("Q") + call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2), Mij , INSERT_VALUES, ierr ) + ! Coupling from anti-coupling: the whole BSE matrix is Pseudo-HErmitian +- call MatSetValue( slepc_mat, H_pos(2), H_pos(1)+SL_K_dim(1),-conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2), H_pos(1)+SL_K_dim(1), -Mij_star , INSERT_VALUES, ierr ) + end select + ! + enddo From 5ec33fc1c226274af4b38d823d9f903fbaa5e28b Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 24 Jul 2023 15:20:09 +0200 Subject: [PATCH 8111/9987] Added patch description --- easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb | 2 +- easybuild/easyconfigs/y/Yambo/yambo_slepc_fix.patch | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb index 66f0b200671..e1c46a2245e 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb @@ -42,7 +42,7 @@ checksums = [ {'yambo-5.1.2.tar.gz': '9625d8a96bd9a3ff3713ebe53228d5ac9be0a98adecbe2a2bad67234c0e26a2e'}, {'yambo-libraries-1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'}, {'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'}, - {'yambo_slepc_fix.patch': '2653aeecb887c3919204da575d65e9d985b0b23608d5780dc8aa1bba02dc12c5'}, + {'yambo_slepc_fix.patch': 'e44a0f85ec5eb55da7c7d42937b4c452bde2ed2c6d2f98fffca15696c82b7df6'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/y/Yambo/yambo_slepc_fix.patch b/easybuild/easyconfigs/y/Yambo/yambo_slepc_fix.patch index 6b305af1a41..8f2810b4b80 100644 --- a/easybuild/easyconfigs/y/Yambo/yambo_slepc_fix.patch +++ b/easybuild/easyconfigs/y/Yambo/yambo_slepc_fix.patch @@ -1,3 +1,6 @@ +Fixes a bug with some parts of Yambo that use SLEPc +Applies most of this commit to this version +https://github.com/yambo-code/yambo/commit/1846c85fdd08ec80ecf90082821cf957a0c93747 diff -ruN yambo-5.1.2.orig/src/bse/K_multiply_by_V_slepc.F yambo-5.1.2/src/bse/K_multiply_by_V_slepc.F --- yambo-5.1.2.orig/src/bse/K_multiply_by_V_slepc.F 2023-07-24 14:31:48.203323300 +0200 +++ yambo-5.1.2/src/bse/K_multiply_by_V_slepc.F 2023-07-24 14:35:13.933323300 +0200 From 825bd116a3aa4a0dfbe251daf087fd110c710ede Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 24 Jul 2023 13:52:32 +0000 Subject: [PATCH 8112/9987] adding R_LIBS_SITE in modextrapaths --- .../easyconfigs/s/Seurat/Seurat-4.1.0-foss-2021a-R-4.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.1.0-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.1.0-foss-2021a-R-4.1.0.eb index acea76329ab..e978b2577d0 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.1.0-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.1.0-foss-2021a-R-4.1.0.eb @@ -65,7 +65,7 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS': ''} +modextrapaths = {'R_LIBS_SITE': ''} sanity_check_paths = { 'files': [], From 6b094ed0de0598eee1030b11a3d2a780d68960ea Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 24 Jul 2023 16:43:52 +0200 Subject: [PATCH 8113/9987] Fix patches for PyTorch 1.13.1 --- .../p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 8 +-- ...skip-ao-sparsity-test-without-fbgemm.patch | 26 ------- ...rch-1.13.1_skip-tests-without-fbgemm.patch | 68 +++++++++++++++++++ 3 files changed, 72 insertions(+), 30 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index b6a1e3ca5b2..9f4fc4b3fd5 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -27,7 +27,7 @@ patches = [ 'PyTorch-1.13.1_fix-test-ops-conf.patch', 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', - 'PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', 'PyTorch-1.13.1_increase-tolerance-test_ops.patch', 'PyTorch-1.13.1_install-vsx-vec-headers.patch', 'PyTorch-1.13.1_skip-failing-grad-test.patch', @@ -57,10 +57,10 @@ checksums = [ {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '4c636059850fc9d1ecb27ce275f8aad5d5b6fdc19e35aff0c25b86cb3201352a'}, {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': 'be83ff61fe2dedab6d49c232936d5622df81ab49154264490021c6c828e53315'}, - {'PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch': - '92cd48ef6d01aa7e07ccce1dcaf40bc3fb0f220c4aa4fea15f3e05fb42e37909'}, + {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': + '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, {'PyTorch-1.13.1_increase-tolerance-test_ops.patch': - 'd53e98bf0da7788b68042dcc31bc5708dae962fde3f110cc827eb807a5d08e49'}, + 'c909fdfc2b12df457e1eb5514265ffec3eab653994949416f3f048668421e223'}, {'PyTorch-1.13.1_install-vsx-vec-headers.patch': '7b678f54bb947afd4767f5877ac424b4b94ce5db609ea20f5a869ccf4027035f'}, {'PyTorch-1.13.1_skip-failing-grad-test.patch': '6681200f9509893cb9231b5c93ac9bc5e6d9d9ae4febefca52e7cbc843ba8f51'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch deleted file mode 100644 index 481b013de21..00000000000 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-ao-sparsity-test-without-fbgemm.patch +++ /dev/null @@ -1,26 +0,0 @@ -Those tests (from test_ao_sparsity) require FBGEMM which may not be available. -So add the skip decorator. -See https://github.com/pytorch/pytorch/issues/87364 - -Author: Alexander Grund (TU Dresden) - -diff --git a/test/ao/sparsity/test_composability.py b/test/ao/sparsity/test_composability.py -index 6a1b6067a4c..b2eed72e3e3 100644 ---- a/test/ao/sparsity/test_composability.py -+++ b/test/ao/sparsity/test_composability.py -@@ -9,6 +9,7 @@ import torch.ao.quantization as tq - from torch import nn - from torch.ao import sparsity - from torch.testing._internal.common_utils import TestCase -+from torch.testing._internal.common_quantization import skipIfNoFBGEMM - from torch.ao.quantization.quantize_fx import prepare_fx, convert_fx, convert_to_reference_fx, prepare_qat_fx - from torch.ao.sparsity import fqn_to_module - -@@ -62,6 +63,7 @@ def _calculate_sparsity(tensor): - # This series of tests are to check the composability goals for sparsity and quantization. Namely - # that performing quantization and sparsity model manipulations in various orderings - # does not cause problems -+@skipIfNoFBGEMM - class TestComposability(TestCase): - # This test checks whether performing quantization prepare before sparse prepare - # causes any issues and verifies that the correct observers are inserted and that diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch new file mode 100644 index 00000000000..77dde5f3110 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch @@ -0,0 +1,68 @@ +Those tests (from test_ao_sparsity & test_quantization) require FBGEMM which may not be available. +So add the skip decorator. +See https://github.com/pytorch/pytorch/issues/87364 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/ao/sparsity/test_composability.py b/test/ao/sparsity/test_composability.py +index 6a1b6067a4c..0c43f585af2 100644 +--- a/test/ao/sparsity/test_composability.py ++++ b/test/ao/sparsity/test_composability.py +@@ -9,6 +9,7 @@ import torch.ao.quantization as tq + from torch import nn + from torch.ao import sparsity + from torch.testing._internal.common_utils import TestCase ++from torch.testing._internal.common_quantization import skipIfNoFBGEMM + from torch.ao.quantization.quantize_fx import prepare_fx, convert_fx, convert_to_reference_fx, prepare_qat_fx + from torch.ao.sparsity import fqn_to_module + +@@ -62,6 +63,7 @@ def _calculate_sparsity(tensor): + # This series of tests are to check the composability goals for sparsity and quantization. Namely + # that performing quantization and sparsity model manipulations in various orderings + # does not cause problems ++@skipIfNoFBGEMM + class TestComposability(TestCase): + # This test checks whether performing quantization prepare before sparse prepare + # causes any issues and verifies that the correct observers are inserted and that +@@ -326,6 +328,7 @@ class TestFxComposability(TestCase): + r"""This series of tests checks that various steps of the quantization and sparsity flow + compose cleanly despite variation in sequencing. + """ ++ @skipIfNoFBGEMM + def test_q_prep_fx_before_s_prep(self): + r""" + This test checks that the ordering of prepare_fx -> sparse prepare -> convert_fx +@@ -445,6 +448,7 @@ class TestFxComposability(TestCase): + ) + self.assertGreaterAlmostEqual(cur_sparsity, sparse_config[0]["sparsity_level"]) + ++ @skipIfNoFBGEMM + def test_s_prep_before_q_prep_fx(self): + r""" + This test checks that the ordering of sparse prepare -> prepare_fx -> convert_fx +@@ -490,6 +494,7 @@ class TestFxComposability(TestCase): + ) + self.assertGreaterAlmostEqual(cur_sparsity, sparse_config[0]["sparsity_level"]) + ++ @skipIfNoFBGEMM + def test_s_prep_before_qat_prep_fx(self): + r""" + This test checks that the ordering of sparse prepare -> prepare_qat_fx -> convert_fx +diff --git a/test/quantization/core/test_docs.py b/test/quantization/core/test_docs.py +index 27842b46ce7..8e50ffa3166 100644 +--- a/test/quantization/core/test_docs.py ++++ b/test/quantization/core/test_docs.py +@@ -10,11 +10,13 @@ import torch + from torch.testing._internal.common_quantization import ( + QuantizationTestCase, + SingleLayerLinearModel, ++ skipIfNoFBGEMM, + ) + from torch.testing._internal.common_quantized import override_quantized_engine + from torch.testing._internal.common_utils import IS_ARM64 + + ++@skipIfNoFBGEMM + class TestQuantizationDocs(QuantizationTestCase): + r""" + The tests in this section import code from the quantization docs and check that From 05a6ced0d063807d73a0af32d1fe05ade5aca807 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 24 Jul 2023 16:46:10 +0200 Subject: [PATCH 8114/9987] Add updated patch --- ...h-1.13.1_increase-tolerance-test_ops.patch | 32 +++++++++++-------- 1 file changed, 19 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch index fb28aadbefa..b07becd652e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch @@ -4,18 +4,24 @@ > Greatest absolute difference: 1.430511474609375e-05 at index (4, 5) (up to 1e-05 allowed) > Greatest relative difference: 4.65393206065873e-06 at index (4, 5) (up to 1.3e-06 allowed) +See https://github.com/pytorch/pytorch/pull/86365 + Author: Alexander Grund (TU Dresden) -Updated for PyTorch 1.13.1: Simon Branford (University of Birmingham) ---- a/test/test_ops.py -+++ b/test/test_ops.py -@@ -545,6 +545,9 @@ - else list(supported_dtypes)[0] - ) - -+ if dtype is torch.float32: -+ self.precision, self.rel_tol = (1.5e-05, 1e-05) -+ - samples = op.sample_inputs(device, dtype) - for sample in samples: - # calls it normally to get the expected result +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 4b2d0ebabc46b..bab7843a72b74 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -8503,7 +8503,11 @@ op_db: List[OpInfo] = [ + DecorateInfo( + toleranceOverride({torch.float32: tol(atol=1.3e-05, rtol=1.3e-05), + torch.complex64: tol(atol=1e-05, rtol=1.2e-03)}), +- 'TestCommon', 'test_numpy_refs')], ++ 'TestCommon', 'test_numpy_refs'), ++ DecorateInfo( ++ toleranceOverride({torch.float32: tol(atol=1.5e-05, rtol=1e-05)}), ++ 'TestCommon', 'test_out'), ++ ], + skips=( + # NVIDIA only assures that bfloat16 is supported by bmm if SM >= 5.3 + DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes', device_type='cuda', active_if=not SM53OrLater), From 2a2dac6bc0d83a9ec4243bd14ffce23653dd016e Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Jul 2023 15:56:07 +0100 Subject: [PATCH 8115/9987] adding easyconfigs: pFUnit-4.7.3-gompi-2022a.eb --- .../p/pFUnit/pFUnit-4.7.3-gompi-2022a.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/pFUnit/pFUnit-4.7.3-gompi-2022a.eb diff --git a/easybuild/easyconfigs/p/pFUnit/pFUnit-4.7.3-gompi-2022a.eb b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.7.3-gompi-2022a.eb new file mode 100644 index 00000000000..9c37998e90d --- /dev/null +++ b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.7.3-gompi-2022a.eb @@ -0,0 +1,60 @@ +easyblock = 'CMakeMake' + +name = 'pFUnit' +version = '4.7.3' +local_fargparse_major_minor_version = '1.5' +local_gftl_major_minor_version = '1.10' +local_gftl_shared_major_minor_version = '1.6' + +homepage = 'https://github.com/Goddard-Fortran-Ecosystem/pFUnit' +description = """pFUnit is a unit testing framework enabling JUnit-like testing of serial + and MPI-parallel software written in Fortran.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/Goddard-Fortran-Ecosystem/pFUnit/releases/download/v%(version)s'] +sources = ['%(name)s-v%(version)s.tar'] +checksums = ['247239298b55e847417b7830183d7fc62cca93dc92c8ec7c0067784b7ce34544'] + +builddependencies = [('CMake', '3.24.3')] +dependencies = [('Python', '3.10.4')] + +sanity_check_paths = { + 'files': [ + 'PFUNIT-%(version_major_minor)s/bin/funitproc', + 'PFUNIT-%(version_major_minor)s/lib/libpfunit.a' + ], + 'dirs': [ + 'FARGPARSE-%s' % local_fargparse_major_minor_version, + 'GFTL-%s' % local_gftl_major_minor_version, + 'GFTL_SHARED-%s' % local_gftl_shared_major_minor_version, + ], +} + +sanity_check_commands = ["funitproc --help"] + +modextrapaths = { + 'PATH': ['PFUNIT-%(version_major_minor)s/bin'], + 'CPATH': [ + 'FARGPARSE-%s/include' % local_fargparse_major_minor_version, + 'GFTL-%s/include' % local_gftl_major_minor_version, + 'GFTL_SHARED-%s/include' % local_gftl_shared_major_minor_version, + 'PFUNIT-%(version_major_minor)s/include', + ], + 'LD_LIBRARY_PATH': [ + 'FARGPARSE-%s/lib' % local_fargparse_major_minor_version, + 'GFTL-%s/lib' % local_gftl_major_minor_version, + 'GFTL_SHARED-%s/lib' % local_gftl_shared_major_minor_version, + 'PFUNIT-%(version_major_minor)s/lib', + ], + 'CMAKE_PREFIX_PATH': [ + 'FARGPARSE-%s/cmake' % local_fargparse_major_minor_version, + 'GFTL-%s/cmake' % local_gftl_major_minor_version, + 'GFTL_SHARED-%s/cmake' % local_gftl_shared_major_minor_version, + 'PFUNIT-%(version_major_minor)s/cmake', + ], +} + +modextravars = {'PFUNIT': '%(installdir)s'} + +moduleclass = 'tools' From 86a827493205c3e2952ba7fa35ab0b06a665d4e9 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Jul 2023 16:10:46 +0100 Subject: [PATCH 8116/9987] Missing M4 added --- easybuild/easyconfigs/p/pFUnit/pFUnit-4.7.3-gompi-2022a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pFUnit/pFUnit-4.7.3-gompi-2022a.eb b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.7.3-gompi-2022a.eb index 9c37998e90d..b0cf52a8184 100644 --- a/easybuild/easyconfigs/p/pFUnit/pFUnit-4.7.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/p/pFUnit/pFUnit-4.7.3-gompi-2022a.eb @@ -16,7 +16,10 @@ source_urls = ['https://github.com/Goddard-Fortran-Ecosystem/pFUnit/releases/dow sources = ['%(name)s-v%(version)s.tar'] checksums = ['247239298b55e847417b7830183d7fc62cca93dc92c8ec7c0067784b7ce34544'] -builddependencies = [('CMake', '3.24.3')] +builddependencies = [ + ('CMake', '3.24.3'), + ('M4', '1.4.19'), +] dependencies = [('Python', '3.10.4')] sanity_check_paths = { From a2c7d74074cd4028247d0d1822b68b57c20c800a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 24 Jul 2023 17:15:40 +0200 Subject: [PATCH 8117/9987] dep fix --- easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb index 62140b372d3..a3a84995147 100644 --- a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb @@ -9,11 +9,14 @@ description = """Nose extends unittest to make testing easier.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} sources = [SOURCE_TAR_GZ] - checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'] options = {'modulename': 'nose'} +builddependencies = [ + ('binutils', '2.38'), +] + dependencies = [ ('Python', '3.10.4'), ('coverage', '7.2.7'), From 11b28897966e76de1b553593835b1bc36f0e0932 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Jul 2023 16:19:05 +0100 Subject: [PATCH 8118/9987] adding easyconfigs: json-fortran-8.3.0-GCCcore-11.3.0.eb --- .../json-fortran-8.3.0-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..dbe6dd8df7a --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +configopts = [ + '-DUSE_GNU_INSTALL_CONVENTION=TRUE', +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From ca62632d9516954e40aad6e65a9e0e7a4981d63a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 24 Jul 2023 17:49:18 +0200 Subject: [PATCH 8119/9987] don't use my version of STAR --- .../s/STAR/STAR-2.7.10b-GCC-12.2.0.eb | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb index e8b10e708e8..4ffe3451041 100644 --- a/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.10b-GCC-12.2.0.eb @@ -2,7 +2,7 @@ # Guy's and St Thomas' NHS Foundation Trust and King's College London # Based on STAR-2.7.7a-GCC-10.2.0.eb # uploaded by J. Sassmannshausen -# Updated: Petr Král (INUITS) +# modified by Thomas Eylenbosch easyblock = 'MakeCp' @@ -18,17 +18,20 @@ toolchainopts = {'openmp': True} github_account = 'alexdobin' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5'] +patches = ['STAR-%(version)s_use-external-htslib.patch'] +checksums = [ + {'2.7.10b.tar.gz': '0d1b71de6c5be1c5d90b32130d2abcd5785a4fc7c1e9bf19cc391947f2dc46e5'}, + {'STAR-2.7.10b_use-external-htslib.patch': '1d8a24532a384b3065001c672e486b74094f162cb98829d2ec961401215de7da'}, +] dependencies = [ + ('HTSlib', '1.17'), ('zlib', '1.2.12'), ] start_dir = 'source' -buildopts = ' %(name)s && make %(name)slong' - -parallel = 1 +buildopts = ' STAR && make STARlong' files_to_copy = [ (['source/%(name)s', 'source/%(name)slong'], 'bin'), @@ -40,6 +43,9 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["STAR --help"] +sanity_check_commands = [ + "STAR --help", + "STARlong --help", +] moduleclass = 'bio' From c8d8eb720d4e010631a590a1519077688e830988 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 24 Jul 2023 18:59:33 +0200 Subject: [PATCH 8120/9987] Removed unused prebuildopts --- easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb index e1c46a2245e..e29b903deef 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb @@ -73,8 +73,6 @@ configopts += '--with-hdf5-path="$EBROOTHDF5" --with-petsc-path="$EBROOTPETSC" ' configopts += '--with-slepc-path="$EBROOTSLEPC" --with-libxc-path="$EBROOTLIBXC" ' configopts += '--enable-par-linalg --enable-slepc-linalg ' -prebuildopts = "export FPATH=$EBROOTPETSC/include:$EBROOTSLEPC/include:$FPATH && " - prebuildopts = "export SHELL='sh -x' && " buildopts = 'all' From 1d1a6a5d97bc4c5ae2dbfa4af9fec5808017d6de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Mon, 24 Jul 2023 18:15:49 +0100 Subject: [PATCH 8121/9987] Update easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.3.0.eb Habit I guess. :-) Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../j/json-fortran/json-fortran-8.3.0-GCCcore-11.3.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.3.0.eb index dbe6dd8df7a..4570b385ff2 100644 --- a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-11.3.0.eb @@ -19,9 +19,7 @@ builddependencies = [ ('CMake', '3.24.3'), ] -configopts = [ - '-DUSE_GNU_INSTALL_CONVENTION=TRUE', -] +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' runtest = 'check' From e7cf9b2a9f63b210f722622bbd41b5d8ceeca1f1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 24 Jul 2023 18:56:19 +0100 Subject: [PATCH 8122/9987] adding easyconfigs: imageio-2.31.1-foss-2022b.eb --- .../i/imageio/imageio-2.31.1-foss-2022b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100755 easybuild/easyconfigs/i/imageio/imageio-2.31.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.31.1-foss-2022b.eb b/easybuild/easyconfigs/i/imageio/imageio-2.31.1-foss-2022b.eb new file mode 100755 index 00000000000..a06ef30cd77 --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.31.1-foss-2022b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.31.1' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f8436a02af02fd63f272dab50f7d623547a38f0e04a4a73e2b02ae1b8b180f27'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Pillow', '9.4.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 69a50f3a28882dea166396e4d275074fde372b7d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 24 Jul 2023 18:56:48 +0100 Subject: [PATCH 8123/9987] adding easyconfigs: scikit-plot-0.3.7-foss-2022b.eb --- .../scikit-plot-0.3.7-foss-2022b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100755 easybuild/easyconfigs/s/scikit-plot/scikit-plot-0.3.7-foss-2022b.eb diff --git a/easybuild/easyconfigs/s/scikit-plot/scikit-plot-0.3.7-foss-2022b.eb b/easybuild/easyconfigs/s/scikit-plot/scikit-plot-0.3.7-foss-2022b.eb new file mode 100755 index 00000000000..0975080b0b1 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-plot/scikit-plot-0.3.7-foss-2022b.eb @@ -0,0 +1,27 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'scikit-plot' +version = '0.3.7' + +homepage = "https://github.com/reiinakano/scikit-plot" +description = """Scikit-plot is the result of an unartistic data scientist's dreadful realization that *visualization + is one of the most crucial components in the data science process, not just a mere afterthought*.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), + ('scikit-learn', '1.2.1'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['2c7948817fd2dc06879cfe3c1fdde56a8e71fa5ac626ffbe79f043650baa6242'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'scikitplot'} + +moduleclass = 'vis' From c5a53efb3f40c1c88f96fa4fc1f8f1fcd1b19876 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 24 Jul 2023 19:16:04 +0100 Subject: [PATCH 8124/9987] adding easyconfigs: libwebp-1.3.1-GCCcore-12.2.0.eb --- .../l/libwebp/libwebp-1.3.1-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100755 easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.2.0.eb new file mode 100755 index 00000000000..0e456339344 --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.3.1' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b3779627c2dfd31e3d8c4485962c2efe17785ef975e2be5c8c0c9e6cd3c4ef66'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('LibTIFF', '4.4.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + +sanity_check_paths = { + 'files': ( + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ), + 'dirs': ['lib/'] +} + +moduleclass = 'lib' From f931e24cd40310d6effbf37cfd3a94d8b9d937bb Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 24 Jul 2023 20:41:28 +0200 Subject: [PATCH 8125/9987] Attempt on static lib linking --- ...xplorer2-2.3.8-foss-2021b-Python-2.7.18.eb | 6 +-- .../MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb | 23 ++++---- .../TopHat-2.1.2-GCC-11.2.0-Python-2.7.18.eb | 54 +++++++++++++++++++ 3 files changed, 71 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb index 82872607b68..2272a3bde87 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb @@ -2,7 +2,7 @@ easyblock = 'PythonPackage' name = 'CIRCexplorer2' version = '2.3.8' -versionsuffix = '-Python-%(pyver)s' +versionsuffix = "-Python-%(pyver)s" homepage = 'http://circexplorer2.readthedocs.io/' description = "CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset." @@ -15,8 +15,8 @@ checksums = ['8261ee884f6d895131ce681d5eda6554376e973851a9de4dc50e2b3e242ccc80'] dependencies = [ ('Python', '2.7.18'), ('SciPy-bundle', '2021.10', versionsuffix), - # Using version 2.1.0, since there may be problems with newer versions - ('TopHat', '2.1.0', versionsuffix), + # sticking to v2.1.0, since using v2.1.1 has problems, cfr. https://www.biostars.org/p/186979/ + ('TopHat', '2.1.2', versionsuffix), ('Cufflinks', '20190706'), ('BEDTools', '2.30.0'), ('Kent_tools', '422', '-Boost-1.75.0'), diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb index 1eb91a7f0f7..4ca72f2b9cb 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb @@ -10,17 +10,22 @@ Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] -checksums = [ - '75bf9b147a95d38160d01a73b098d50a1960563b46d16a235971fff64d99643c', # mariadb-10.6.4.tar.gz - '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19', # MariaDB-10.1.13-link-rt-for-jemalloc.patch +local_pcre2_ver = '10.37' +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', + 'https://downloads.sourceforge.net/project/pcre/pcre2/%s/' % local_pcre2_ver, +] +sources = [ + SOURCELOWER_TAR_GZ, + {'filename': 'pcre2-%s.zip' % local_pcre2_ver, 'extract_cmd': "cp %s %(builddir)s/"}, ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] builddependencies = [ ('CMake', '3.21.1'), ('libaio', '0.3.112'), + ('Boost', '1.75.0'), # needed by OQGraph ] dependencies = [ @@ -32,13 +37,12 @@ dependencies = [ ('jemalloc', '5.2.1'), # optional ('snappy', '1.1.9'), # needed by RocksDB; optional for InnoDB ('libxml2', '2.9.10'), # needed by Connect XML - ('Boost', '1.75.0'), # needed by OQGraph ('Judy', '1.0.5'), # needed by OQGraph - ('PCRE2', '10.37'), ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest ] -separate_build_dir = True +local_pcre2_path = '%%(builddir)s/pcre2-%s.zip' % local_pcre2_ver +preconfigopts = "sed -i 's@http://.*.zip@file://%s@g' ../mariadb-%%(version)s/cmake/pcre.cmake && " % local_pcre2_path configopts = "-DCMAKE_BUILD_TYPE=Release " configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker @@ -47,6 +51,7 @@ configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we bui configopts += "-DWITH_ZLIB=system " configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc +configopts += "-DBoost_USE_STATIC_LIBS=ON" sanity_check_commands = ["mysql --help", "mysqltest --help"] diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..068f10e7ce3 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.2.0-Python-2.7.18.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' +description = "TopHat is a fast splice junction mapper for RNA-Seq reads." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'cstd': 'gnu++98', 'pic': True, 'static': True} + +github_account = 'infphilo' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(namelower)s-2.0.13-zlib.patch'] +checksums = [ + '15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1', # v2.1.2.tar.gz + 'a33075c2affda995ddbd250933dbcaf94f68768b1eebead58a69705fc40306ef', # tophat-2.0.13-zlib.patch +] + +builddependencies = [ + ('Boost', '1.75.0'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '2.7.18'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-boost=$EBROOTBOOST' +postinstallcmds = [ + "ls %(installdir)s", + "sed -i 's|#!/usr/bin/env python|#!/usr/bin/env python2|g' %(installdir)s/bin/tophat"] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['tophat --version'] + +moduleclass = 'bio' From f9b74db3ab1758f60365942c7b238ff17e8921b7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 24 Jul 2023 22:59:05 +0200 Subject: [PATCH 8126/9987] enable support for libvori in CP2K v9.1 and v2022.1 --- .../c/CP2K/CP2K-2022.1-foss-2022a.eb | 1 + .../easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb | 1 + .../libvori/libvori-220621-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 3 files changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/libvori/libvori-220621-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb index a979cbf28d2..b4edfa41eea 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb @@ -22,6 +22,7 @@ dependencies = [ ('Libint', '2.7.2', '-lmax-6-cp2k'), ('libxc', '5.2.3'), ('libxsmm', '1.17'), + ('libvori', '220621'), ('FFTW', '3.3.10'), ('PLUMED', '2.8.1'), ] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb index 67b7353f347..3b1db6bf105 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb @@ -21,6 +21,7 @@ dependencies = [ ('Libint', '2.7.2', '-lmax-6-cp2k'), ('libxc', '5.2.3'), ('libxsmm', '1.17'), + ('libvori', '220621'), ('FFTW', '3.3.10'), ('PLUMED', '2.8.1'), ] diff --git a/easybuild/easyconfigs/l/libvori/libvori-220621-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libvori/libvori-220621-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..45bda0e4013 --- /dev/null +++ b/easybuild/easyconfigs/l/libvori/libvori-220621-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'libvori' +version = '220621' + +homepage = 'https://brehm-research.de/libvori.php' +description = """C++ library implementing the Voronoi integration as well as the compressed bqb +file format. The present version of libvori is a very early development +version, which is hard-coded to work with the CP2k program package.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://brehm-research.de/files/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1cfa98c564814bddacf1c0e7f11582137d758668f6307e6eb392c72317984c14'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['lib/libvori.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 41c9750e8b8cc47090dbb389749cb6edeac6669b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 24 Jul 2023 22:13:33 +0100 Subject: [PATCH 8127/9987] adding easyconfigs: GTK4-4.11.3-GCC-12.2.0.eb, GST-plugins-bad-1.22.5-GCC-12.2.0.eb, PyCairo-1.24.0-GCCcore-12.2.0.eb, PyGObject-3.44.1-GCCcore-12.2.0.eb, Wayland-1.22.0-GCCcore-12.2.0.eb and patches: GTK4-4.11.3_g_set_str.patch, adwaita-icon-theme-44.0_disable-svg-conversion.patch --- .../GST-plugins-bad-1.22.5-GCC-12.2.0.eb | 44 ++++++++++ .../g/GTK4/GTK4-4.11.3-GCC-12.2.0.eb | 85 +++++++++++++++++++ .../g/GTK4/GTK4-4.11.3_g_set_str.patch | 13 +++ ...on-theme-44.0_disable-svg-conversion.patch | 17 ++++ .../PyCairo/PyCairo-1.24.0-GCCcore-12.2.0.eb | 44 ++++++++++ .../PyGObject-3.44.1-GCCcore-12.2.0.eb | 38 +++++++++ .../Wayland/Wayland-1.22.0-GCCcore-12.2.0.eb | 63 ++++++++++++++ 7 files changed, 304 insertions(+) create mode 100755 easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.2.0.eb create mode 100755 easybuild/easyconfigs/g/GTK4/GTK4-4.11.3-GCC-12.2.0.eb create mode 100755 easybuild/easyconfigs/g/GTK4/GTK4-4.11.3_g_set_str.patch create mode 100755 easybuild/easyconfigs/g/GTK4/adwaita-icon-theme-44.0_disable-svg-conversion.patch create mode 100755 easybuild/easyconfigs/p/PyCairo/PyCairo-1.24.0-GCCcore-12.2.0.eb create mode 100755 easybuild/easyconfigs/p/PyGObject/PyGObject-3.44.1-GCCcore-12.2.0.eb create mode 100755 easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.2.0.eb new file mode 100755 index 00000000000..bc36176bdfb --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-bad' +version = '1.22.5' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-bad'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e64e75cdafd7ff2fc7fc34e855b06b1e3ed227cc06fa378d17bbcd76780c338c'] + +builddependencies = [ + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.74.0'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('GLib', '2.75.0'), + ('GStreamer', '1.22.1'), + ('Gdk-Pixbuf', '2.42.10'), + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('Graphene', '1.10.8'), + ('GST-plugins-base', '1.22.1'), +] + +sanity_check_paths = { + 'files': ['bin/gst-transcoder-1.0', 'bin/playout'] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['adaptivedemux', 'badaudio', 'codecs', 'player']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK4/GTK4-4.11.3-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GTK4/GTK4-4.11.3-GCC-12.2.0.eb new file mode 100755 index 00000000000..0a39ef44d91 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK4/GTK4-4.11.3-GCC-12.2.0.eb @@ -0,0 +1,85 @@ +easyblock = 'Bundle' + +name = 'GTK4' +version = '4.11.3' + +homepage = 'https://docs.gtk.org/gtk4/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('GObject-Introspection', '1.74.0'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), + ('cairo', '1.17.4'), + ('Perl', '5.36.0'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] +dependencies = [ + ('ATK', '2.38.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.10'), + ('Pango', '1.50.12'), + ('libepoxy', '1.5.10'), + ('X11', '20221110'), + ('FriBidi', '1.0.12'), + ('GST-plugins-bad', '1.22.5'), + ('Wayland', '1.22.0'), + ('PyGObject', '3.44.1'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK', version, { + 'easyblock': 'MesonNinja', + 'source_urls': [FTPGNOME_SOURCE], + 'configopts': "-Dintrospection=enabled -Dgtk_doc=false", + 'patches': ['GTK4-4.11.3_g_set_str.patch'], + 'checksums': [ + '22b9b21a13b205d4f430b9d73a0d216f133047cf638a2563fcd9297a4b39eb00', + '96c114de353f2798ce57de9823c6d2eaa6b92175b49c3333d209dd3d3a0b7ce4'], # GTK4-4.11.3_g_set_str.patch + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '44.0', { + 'preconfigopts': 'autoreconf -f -i && ', + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'patches': ['adwaita-icon-theme-44.0_disable-svg-conversion.patch'], + 'checksums': [ + '4889c5601bbfecd25d80ba342209d0a936dcf691ee56bd6eca4cde361f1a664c', + # adwaita-icon-theme-44.0_disable-svg-conversion.patch + 'f70ad3d11d52e3104cf1548eccd161efc9448d41f9521c7ac4670228b19ca2b9' + ], + }), +] + +postinstallcmds = ['gtk4-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk4-demo', 'gtk4-demo-application', 'gtk4-icon-browser', 'gtk4-widget-factory', + 'gtk4-builder-tool', 'gtk4-launch', 'gtk4-query-settings', + 'gtk4-update-icon-cache', 'gtk4-widget-factory']] + + ['lib/libgtk-4.%s' % SHLIB_EXT], + 'dirs': ['include/%s-%%(version_major)s.0/%s' % ('gtk', x) for x in ['gdk', 'gsk', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK4/GTK4-4.11.3_g_set_str.patch b/easybuild/easyconfigs/g/GTK4/GTK4-4.11.3_g_set_str.patch new file mode 100755 index 00000000000..df6cc614987 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK4/GTK4-4.11.3_g_set_str.patch @@ -0,0 +1,13 @@ +Correct GLib version check on g_set_str +Patch by Simon Branford (University of Birmingham) +--- gdk/gdkprivate.h.orig 2023-07-24 20:41:16.096936629 +0100 ++++ gdk/gdkprivate.h 2023-07-24 20:41:24.875062247 +0100 +@@ -22,7 +22,7 @@ + #define I_(string) g_intern_static_string (string) + #endif + +-#if !GLIB_CHECK_VERSION (2, 75, 1) ++#if !GLIB_CHECK_VERSION (2, 75, 0) + static inline gboolean + g_set_str (char **str_pointer, + const char *new_str) diff --git a/easybuild/easyconfigs/g/GTK4/adwaita-icon-theme-44.0_disable-svg-conversion.patch b/easybuild/easyconfigs/g/GTK4/adwaita-icon-theme-44.0_disable-svg-conversion.patch new file mode 100755 index 00000000000..a81806274be --- /dev/null +++ b/easybuild/easyconfigs/g/GTK4/adwaita-icon-theme-44.0_disable-svg-conversion.patch @@ -0,0 +1,17 @@ +As we don't have SVG support we disable the search for the converter. + +Author: Alexander Grund (TU Dresden) +Updated for v44.0 by Simon Branford (University of Birmingham) + +diff -aur a/configure.ac b/configure.ac +--- configure.ac.orig 2023-07-24 21:38:28.066689617 +0100 ++++ configure.ac 2023-07-24 21:38:54.077313220 +0100 +@@ -49,7 +49,7 @@ + AM_CONDITIONAL(ALLOW_RENDERING, test "x$allow_rendering" = "xyes") + + symbolic_encode_sizes="16x16 32x32" +-AC_PATH_PROG([GTK_ENCODE_SYMBOLIC_SVG], [gtk-encode-symbolic-svg], [false]) ++GTK_ENCODE_SYMBOLIC_SVG="false" + if test "x$GTK_ENCODE_SYMBOLIC_SVG" = "xfalse"; then + symbolic_encode_sizes="" + fi diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.24.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.24.0-GCCcore-12.2.0.eb new file mode 100755 index 00000000000..8d5a4b8447a --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.24.0-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonPackage' + +name = 'PyCairo' +version = '1.24.0' + +homepage = 'https://pycairo.readthedocs.io/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1444d52f1bb4cc79a4a0c0fe2ccec4bd78ff885ab01ebe1c0f637d8392bcafb6'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('cairo', '1.17.4'), +] + +# PyGTK needs PyCairo installed by pip +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# remove pyproject.toml, which causes trouble (header files and .pc file are not installed) +preinstallopts = "rm pyproject.toml && " + +# Don't build a wheel or the pkg-cfg file won't be installed +installopts = '--no-binary=%(namelower)s' + +sanity_check_paths = { + 'files': ['%s/py3cairo.%s' % (p, e) for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')]], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +options = {'modulename': 'cairo'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.44.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.44.1-GCCcore-12.2.0.eb new file mode 100755 index 00000000000..d1e9e8a9d1a --- /dev/null +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.44.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'PyGObject' +version = '3.44.1' + +homepage = 'https://pygobject.readthedocs.io/' +description = """PyGObject is a Python package which provides bindings for GObject based +libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['665fbe980c91e8b31ad78ed3f66879946948200864002d193f67eccc1d7d5d83'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('GLib', '2.75.0'), + ('GObject-Introspection', '1.74.0'), + ('PyCairo', '1.24.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['include/pygobject-%(version_major)s.0/pygobject.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'gi'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-12.2.0.eb new file mode 100755 index 00000000000..2c77288b85d --- /dev/null +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-12.2.0.eb @@ -0,0 +1,63 @@ +# Author: Jasper Grimm (UoY) +# URL of Wayland download changed to GitLab due to changes upstream +# Author: J. Sassmannshausen (Imperial College London/UK) +easyblock = 'Bundle' + +name = 'Wayland' +version = '1.22.0' + +homepage = 'https://wayland.freedesktop.org/' +description = """ +Wayland is a project to define a protocol for a compositor to talk to + its clients as well as a library implementation of the protocol. The + compositor can be a standalone display server running on Linux kernel + modesetting and evdev input devices, an X application, or a wayland + client itself. The clients can be traditional applications, X servers + (rootless or fullscreen) or other display servers. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('CMake', '3.24.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('libffi', '3.4.4'), + ('expat', '2.4.9'), + ('libxml2', '2.10.3'), +] + +default_easyblock = 'MesonNinja' +default_component_specs = { + 'source_urls': ['https://wayland.freedesktop.org/releases'], + 'sources': [SOURCE_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('wayland', version, { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/wayland/-/releases/%(version)s/downloads'], + 'configopts': "-Ddocumentation=false", + 'checksums': ['1540af1ea698a471c2d8e9d288332c7e0fd360c8f1d12936ebb7e7cbc2425842'], + }), + ('wayland-protocols', '1.32', { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/wayland-protocols/-/releases/%(version)s/downloads'], + 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH ", + 'checksums': ['7459799d340c8296b695ef857c07ddef24c5a09b09ab6a74f7b92640d2b1ba11'], + }), +] + +_libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']] +sanity_check_paths = { + 'files': ['bin/wayland-scanner'] + _libs, + 'dirs': ['lib'], +} + +sanity_check_commands = ["wayland-scanner --help", "wayland-scanner --version"] + +moduleclass = 'vis' From a1d7ae186068b3f4fe172715b759a1aa229e6016 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 25 Jul 2023 06:39:23 +0100 Subject: [PATCH 8128/9987] adding easyconfigs: OpenCV-4.8.0-foss-2022b-contrib.eb --- .../OpenCV/OpenCV-4.8.0-foss-2022b-contrib.eb | 106 ++++++++++++++++++ 1 file changed, 106 insertions(+) create mode 100755 easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.0-foss-2022b-contrib.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.0-foss-2022b-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.0-foss-2022b-contrib.eb new file mode 100755 index 00000000000..7acf42f7a39 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.0-foss-2022b-contrib.eb @@ -0,0 +1,106 @@ +name = 'OpenCV' +version = '4.8.0' +versionsuffix = '-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = '1224f78da6684df04397ac0f40c961ed37f79ccb' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [ + { + 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': SOURCELOWER_ZIP + }, + { + 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': '%(namelower)s_contrib-%(version)s.zip' + }, + { + 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2021.8_lnx_intel64_20230330_general.tgz', + 'extract_cmd': 'cp %s %(builddir)s' + }, +] +patches = [('opencv_contrib_python.egg-info', '..')] +checksums = [ + {'opencv-4.8.0.zip': '9dc6a9a95edc133e165e9f6db9412dd899e28d4e5e4979f17cb5966f4b7f3fb1'}, + {'opencv_contrib-4.8.0.zip': '14da1d786cbff86bf8fca840e9e83035395be3cccc6835bbdd53e00a30f1cbf7'}, + {'ippicv_2021.8_lnx_intel64_20230330_general.tgz': + '7cfe0fb0e15ea8f3d2d971c19df2d14382469943d4efa85e48bf358930daa85d'}, + {'opencv_contrib_python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), +] +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('zlib', '1.2.12'), + ('FFmpeg', '5.1.2'), + ('freetype', '2.12.1'), + ('HarfBuzz', '5.3.1'), + ('libjpeg-turbo', '2.1.4'), + ('OpenJPEG', '2.5.0'), + ('libpng', '1.6.38'), + ('LibTIFF', '4.4.0'), + ('libwebp', '1.3.1'), + ('OpenEXR', '3.1.5'), + ('JasPer', '4.0.0'), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.12', '-Java-%(javaver)s', SYSTEM), + ('GLib', '2.75.0'), + ('GTK4', '4.11.3'), + ('HDF5', '1.14.0'), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = " ".join([ + "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DOPENCV_GENERATE_PKGCONFIG=ON", + "-DFREETYPE_FOUND=ON", + "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", + "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", + "-DHARFBUZZ_FOUND=ON", + "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", + "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", + "-DBUILD_opencv_python2=OFF", +]) + +# Install a egg-info file so it is more python friendly +local_egg_info_src = '%(builddir)s/opencv_contrib_python.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv_contrib_python-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' From e6b788c5fd3de008ca09d3873f8fd0c1543dcf1d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 25 Jul 2023 09:05:12 +0200 Subject: [PATCH 8129/9987] Add updated patch and sort patches --- .../p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 24 +++++++++---------- .../PyTorch-1.13.1_fix-fsdp-fp16-test.patch | 21 ++++++++++++++++ 2 files changed, 33 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-fp16-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index 9f4fc4b3fd5..645b2fb8883 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -12,7 +12,6 @@ sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', - 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', @@ -20,23 +19,23 @@ patches = [ 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', - 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-fsdp-fp16-test.patch', 'PyTorch-1.13.1_fix-pytest-args.patch', 'PyTorch-1.13.1_fix-test-ops-conf.patch', - 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', - 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', - 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', 'PyTorch-1.13.1_increase-tolerance-test_ops.patch', 'PyTorch-1.13.1_install-vsx-vec-headers.patch', + 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', 'PyTorch-1.13.1_skip-failing-grad-test.patch', + 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', ] checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, {'PyTorch-1.10.0_fix-kineto-crash.patch': 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb'}, - {'PyTorch-1.11.0_fix-fsdp-fp16-test.patch': 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13'}, {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, {'PyTorch-1.12.1_add-hypothesis-suppression.patch': @@ -49,21 +48,22 @@ checksums = [ {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, {'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch': '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d'}, - {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, + {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-fsdp-fp16-test.patch': '8ae68e60d6e1f92f50322b7f0381c7e65251fba32d7606e3a238a36a2f55b5cf'}, {'PyTorch-1.13.1_fix-pytest-args.patch': 'd3e3c841cf8d73683750f29326f2be56ee0bb5df7ff522baf7d7c3f301a91ec2'}, {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, - {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '4c636059850fc9d1ecb27ce275f8aad5d5b6fdc19e35aff0c25b86cb3201352a'}, - {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': - 'be83ff61fe2dedab6d49c232936d5622df81ab49154264490021c6c828e53315'}, - {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': - '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, {'PyTorch-1.13.1_increase-tolerance-test_ops.patch': 'c909fdfc2b12df457e1eb5514265ffec3eab653994949416f3f048668421e223'}, {'PyTorch-1.13.1_install-vsx-vec-headers.patch': '7b678f54bb947afd4767f5877ac424b4b94ce5db609ea20f5a869ccf4027035f'}, + {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '4c636059850fc9d1ecb27ce275f8aad5d5b6fdc19e35aff0c25b86cb3201352a'}, + {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': + 'be83ff61fe2dedab6d49c232936d5622df81ab49154264490021c6c828e53315'}, {'PyTorch-1.13.1_skip-failing-grad-test.patch': '6681200f9509893cb9231b5c93ac9bc5e6d9d9ae4febefca52e7cbc843ba8f51'}, + {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': + '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-fp16-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-fp16-test.patch new file mode 100644 index 00000000000..567103a376b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-fp16-test.patch @@ -0,0 +1,21 @@ +The test fails on a node with more than 5 V100 GPUs or more than 4 A100 GPUs. +Hence limit the world_size to 4 +See https://github.com/pytorch/pytorch/pull/86280 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/fsdp/test_fsdp_pure_fp16.py b/test/distributed/fsdp/test_fsdp_pure_fp16.py +index 1c663f8263354..e0033ef3d4b72 100644 +--- a/test/distributed/fsdp/test_fsdp_pure_fp16.py ++++ b/test/distributed/fsdp/test_fsdp_pure_fp16.py +@@ -34,8 +34,8 @@ + class TestPureFP16(FSDPTest): + @property + def world_size(self): +- # Test fails due to inaccuracies when using more than 5 GPUs +- return min(5, super().world_size) ++ # Test fails due to inaccuracies when using more than 4 GPUs ++ return min(4, super().world_size) + + @skip_if_lt_x_gpu(2) + @parametrize( From b9a5d0ead876b621ddff6685ca324c1e5180930c Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 25 Jul 2023 10:14:54 +0200 Subject: [PATCH 8130/9987] add sanity_check_commands and change moduleclass to 'geo' --- .../s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb index 4d37dd7e284..98ec47283a1 100644 --- a/easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/sentinelsat/sentinelsat-1.2.1-GCCcore-11.3.0.eb @@ -35,6 +35,11 @@ exts_list = [ }), ] +sanity_check_commands = [ + "sentinelsat --version", + "sentinelsat --help", +] + sanity_pip_check = True -moduleclass = 'lib' +moduleclass = 'geo' From c9330fe7d041b6636748720d709a46c979357fb4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Tue, 25 Jul 2023 11:56:49 +0200 Subject: [PATCH 8131/9987] rename ACT to Artemis --- .../easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb | 26 --------------- .../easyconfigs/a/ACT/ACT-18.0.3-Java-11.eb | 33 ------------------- .../a/Artemis/Artemis-18.0.2-Java-11.eb | 31 +++++++++++++++++ .../a/Artemis/Artemis-18.0.3-Java-11.eb | 31 +++++++++++++++++ 4 files changed, 62 insertions(+), 59 deletions(-) delete mode 100644 easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb delete mode 100644 easybuild/easyconfigs/a/ACT/ACT-18.0.3-Java-11.eb create mode 100644 easybuild/easyconfigs/a/Artemis/Artemis-18.0.2-Java-11.eb create mode 100644 easybuild/easyconfigs/a/Artemis/Artemis-18.0.3-Java-11.eb diff --git a/easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb b/easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb deleted file mode 100644 index 0ede9d4bbab..00000000000 --- a/easybuild/easyconfigs/a/ACT/ACT-18.0.2-Java-11.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'ACT' -version = '18.0.2' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'http://sanger-pathogens.github.io/Artemis/ACT/' -description = """ ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. - It can be used to identify and analyse regions of similarity and difference between genomes - and to explore conservation of synteny, in the context of the entire sequences and their annotation. - It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format. """ - -toolchain = SYSTEM - -source_urls = ['https://github.com/sanger-pathogens/Artemis/releases/download/v%(version)s/'] -sources = ['artemis-unix-release-%(version)s.tar.gz'] -checksums = ['1cb9f36af4c96ae3bde4fa849e01e66c830d4b968867e7842abbab9195b57e60'] - -dependencies = [('Java', '11')] - -sanity_check_paths = { - 'files': ['act', 'art'], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ACT/ACT-18.0.3-Java-11.eb b/easybuild/easyconfigs/a/ACT/ACT-18.0.3-Java-11.eb deleted file mode 100644 index ba982a15488..00000000000 --- a/easybuild/easyconfigs/a/ACT/ACT-18.0.3-Java-11.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'ACT' -version = '18.0.3' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://sanger-pathogens.github.io/Artemis/ACT/' -description = """ ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. - It can be used to identify and analyse regions of similarity and difference between genomes - and to explore conservation of synteny, in the context of the entire sequences and their annotation. - It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format. """ - -toolchain = SYSTEM - -source_urls = ['https://github.com/sanger-pathogens/Artemis/releases/download/v%(version)s/'] -sources = ['artemis-unix-release-%(version)s.tar.gz'] -checksums = ['2603e6daf123c866817fcc22d4577244787349913cebc7acecbcc2e059a8e15c'] - -dependencies = [('Java', '11')] - -sanity_check_paths = { - 'files': ['act', 'art'], - 'dirs': [], -} - -# act -help returns exit-code 1, but it is valid working executable. -# Workaround is to grep phrase from help command output -# https://github.com/sanger-pathogens/Artemis/issues/296 -sanity_check_commands = [ - "act -help | grep -q 'EXAMPLES'" -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/Artemis/Artemis-18.0.2-Java-11.eb b/easybuild/easyconfigs/a/Artemis/Artemis-18.0.2-Java-11.eb new file mode 100644 index 00000000000..d851e2aa64b --- /dev/null +++ b/easybuild/easyconfigs/a/Artemis/Artemis-18.0.2-Java-11.eb @@ -0,0 +1,31 @@ +easyblock = 'PackedBinary' + +name = 'Artemis' +version = '18.0.2' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sanger-pathogens.github.io/Artemis/' +description = """The Artemis Software is a set of software tools for genome browsing and annotation. + It includes: Artemis, Artemis Comparison Tool (ACT), BamView and DNAPlotter.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/sanger-pathogens/%(name)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-unix-release-%(version)s.tar.gz'] +checksums = ['1cb9f36af4c96ae3bde4fa849e01e66c830d4b968867e7842abbab9195b57e60'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['act', 'art', 'bamview', 'dnaplotter'], + 'dirs': [], +} + +# act -help returns exit-code 1, but it is valid working executable. +# Workaround is to grep phrase from help command output +# https://github.com/sanger-pathogens/Artemis/issues/296 +sanity_check_commands = [ + "act -help | grep -q 'EXAMPLES'" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/Artemis/Artemis-18.0.3-Java-11.eb b/easybuild/easyconfigs/a/Artemis/Artemis-18.0.3-Java-11.eb new file mode 100644 index 00000000000..58cd4cbcce6 --- /dev/null +++ b/easybuild/easyconfigs/a/Artemis/Artemis-18.0.3-Java-11.eb @@ -0,0 +1,31 @@ +easyblock = 'PackedBinary' + +name = 'Artemis' +version = '18.0.3' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sanger-pathogens.github.io/Artemis/' +description = """The Artemis Software is a set of software tools for genome browsing and annotation. + It includes: Artemis, Artemis Comparison Tool (ACT), BamView and DNAPlotter.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/sanger-pathogens/%(name)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-unix-release-%(version)s.tar.gz'] +checksums = ['2603e6daf123c866817fcc22d4577244787349913cebc7acecbcc2e059a8e15c'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['act', 'art', 'bamview', 'dnaplotter'], + 'dirs': [], +} + +# act -help returns exit-code 1, but it is valid working executable. +# Workaround is to grep phrase from help command output +# https://github.com/sanger-pathogens/Artemis/issues/296 +sanity_check_commands = [ + "act -help | grep -q 'EXAMPLES'" +] + +moduleclass = 'bio' From 0e02662346293cdc38ac81a3b871bcb5e641c946 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 25 Jul 2023 18:05:25 +0200 Subject: [PATCH 8132/9987] When starting Jupyter Notebook Servers using JupyterHub, if jupyter-server is _also_ present, the traditional notebooks interface requires nbclassic to work. See https://jupyter-server.readthedocs.io/en/latest/operators/migrate-from-nbserver.html#running-jupyter-notebook-on-jupyter-server. --- .../jupyter-server-1.21.0-GCCcore-11.3.0.eb | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb index b511014596e..e42c518ff84 100755 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} builddependencies = [ ('binutils', '2.38'), + ('poetry', '1.2.2'), ] dependencies = [ @@ -33,9 +34,19 @@ exts_list = [ 'modulename': 'websocket', 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], }), + ('notebook_shim', '0.1.0', { + 'checksums': ['7897e47a36d92248925a2143e3596f19c60597708f7bef50d81fcd31d7263e85'], + }), + ('nbclassic', '0.4.8', { + 'checksums': ['c74d8a500f8e058d46b576a41e5bc640711e1032cf7541dde5f73ea49497e283'], + }), ('jupyter_server', version, { 'checksums': ['d0adca19913a3763359be7f0b8c2ea8bfde356f4b8edd8e3149d7d0fbfaa248b'], }), ] +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + moduleclass = 'tools' From 012e568aad3b45e3d5f8a8fe477c29e62c7ec679 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 25 Jul 2023 18:10:28 +0200 Subject: [PATCH 8133/9987] removed poetry, it is not needed for this version of notebook_shim --- .../j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb index e42c518ff84..1057a0deaff 100755 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} builddependencies = [ ('binutils', '2.38'), - ('poetry', '1.2.2'), ] dependencies = [ From 5a6726ecfc9721a45fd98c24cd7519246a16ac66 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 25 Jul 2023 18:43:09 +0200 Subject: [PATCH 8134/9987] Fix batchspawner for JupyterHub 3.0 --- .../JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb index 4addecfb2d6..62506bfa2f0 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb @@ -25,6 +25,8 @@ dependencies = [ use_pip = True +local_batchspawner_commit = '2a9eda0' + exts_list = [ ('certipy', '0.1.3', { 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], @@ -66,8 +68,16 @@ exts_list = [ ('jupyterhub', version, { 'checksums': ['05cdfebd800cf3e55566fb5b61110c5f64fed8ca3c56ef0142290baffbc7fb69'], }), - ('batchspawner', '1.2.0', { - 'checksums': ['b1924bb4f3a3f527a1e312ecdaff3dbc5acfd91e6b13cf074a62cd74340a2e21'], + ('batchspawner', '1.2.0-%s' % local_batchspawner_commit, { + 'sources': { + 'filename': 'main.tar.gz', + 'git_config': { + 'url': 'https://github.com/jupyterhub/', + 'repo_name': 'batchspawner', + 'commit': local_batchspawner_commit, + } + }, + 'checksums': [None], }), ('jupyterhub-systemdspawner', '0.16', { 'modulename': 'systemdspawner', From 975debe5708c7b7897ac1b1b9fae38936bc599f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Wed, 26 Jul 2023 09:56:43 +0200 Subject: [PATCH 8135/9987] adding easyconfigs: Artemis-18.2.0-Java-11.eb --- .../a/Artemis/Artemis-18.2.0-Java-11.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/Artemis/Artemis-18.2.0-Java-11.eb diff --git a/easybuild/easyconfigs/a/Artemis/Artemis-18.2.0-Java-11.eb b/easybuild/easyconfigs/a/Artemis/Artemis-18.2.0-Java-11.eb new file mode 100644 index 00000000000..4e8a42fd6f8 --- /dev/null +++ b/easybuild/easyconfigs/a/Artemis/Artemis-18.2.0-Java-11.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'Artemis' +version = '18.2.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sanger-pathogens.github.io/Artemis/' +description = """The Artemis Software is a set of software tools for genome browsing and annotation. + It includes: Artemis, Artemis Comparison Tool (ACT), BamView and DNAPlotter.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/sanger-pathogens/%(name)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-unix-release-%(version)s.tar.gz'] +checksums = ['06441e1abab139cb0a09d5844cb1b84ae727ace53a6c0efdd1eea8d8cfab8382'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['act', 'art', 'bamview', 'dnaplotter'], + 'dirs': [], +} + +sanity_check_commands = [ + "act --help", + "art --help", + "dnaplotter --help", +] + +moduleclass = 'bio' From de9b0ecb48f3bd651c287dabbc3dc5a3cd82f5c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 26 Jul 2023 10:14:23 +0200 Subject: [PATCH 8136/9987] add sanity check paths --- .../easyconfigs/u/unixODBC/unixODBC-2.3.11-foss-2022b.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.11-foss-2022b.eb b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.11-foss-2022b.eb index 147df25f2d5..a6b423ff484 100644 --- a/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.11-foss-2022b.eb +++ b/easybuild/easyconfigs/u/unixODBC/unixODBC-2.3.11-foss-2022b.eb @@ -18,4 +18,9 @@ sources = [SOURCE_TAR_GZ] source_urls = ['https://www.unixodbc.org/'] checksums = ['d9e55c8e7118347e3c66c87338856dad1516b490fb7c756c1562a2c267c73b5c'] +sanity_check_paths = { + 'files': ['lib/libodbc%s.so' % x for x in ['', 'cr', 'inst']], + 'dirs': [] +} + moduleclass = 'data' From 27c49ba5a4e68cab691c4ff22498f58394e6632c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 26 Jul 2023 14:08:57 +0100 Subject: [PATCH 8137/9987] fix flags and options in ScaLAPACK 2.2.0 --- .../s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022a-fb.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023a-fb.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb | 5 +---- 6 files changed, 6 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb index 6b905fb9221..53161cf0021 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.05-fb.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2022.05'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -31,9 +31,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb index 5b5a3e57d38..0ba4a32980e 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2022.10'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -31,9 +31,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022a-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022a-fb.eb index 5d3f67e7f5f..9c9cce7df25 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022a-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022a-fb.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2022a'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -31,9 +31,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb index fc9fc30a11c..5b0acd500ad 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2022b'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -31,9 +31,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023a-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023a-fb.eb index 8653a36db29..4465e702f88 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023a-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023a-fb.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2023a'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -31,9 +31,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb index ebb363f7759..e4f23b0d226 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'nvompi', 'version': '2022.07'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -31,9 +31,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], From 52eb4bb881948def8ccfda654f9de23d3dd16987 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 26 Jul 2023 14:19:21 +0100 Subject: [PATCH 8138/9987] fix flags and options in ScaLAPACK 2.1.0 --- .../s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-fb.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb | 5 +---- .../s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb | 5 +---- 7 files changed, 7 insertions(+), 28 deletions(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb index 1e77e4ee706..6ae7dea8b33 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -28,9 +28,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb index 1a51184125f..adf6c43a9c3 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,9 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb index 2fba79399b6..e39f1c4ac28 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,9 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLAPACK/lib/liblapack.a" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb index 968586fe952..dcac65cb09b 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2021a'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,9 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-fb.eb index 50c13d45b30..9b95e634595 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-fb.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2021a'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -31,9 +31,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb index b9ce6d67148..7e7a009670d 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2021b'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -31,9 +31,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb index 33b69ea09ab..6d01acd1ff4 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'iimpi', 'version': '2020b'} -toolchainopts = {'pic': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,9 +32,6 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' -configopts += '-DCMAKE_C_COMPILER=mpicc ' -configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' -configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], From e21a4d52ebff44def35459fd48d69862729fa6f4 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 26 Jul 2023 14:21:21 +0100 Subject: [PATCH 8139/9987] adding easyconfigs: tensorflow-probability-0.19.0-foss-2022a-CUDA-11.7.0.eb --- ...obability-0.19.0-foss-2022a-CUDA-11.7.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..5a13241dbb4 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,51 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# License:: MIT/GPL +# $Id$ +# +# Updated to 0.19.0 +# Author: J. Sassmannshausen (Imperial College London/UK) +## + +easyblock = 'PythonBundle' + +name = 'tensorflow-probability' +version = '0.19.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/probability' +description = """TensorFlow Probability (TFP) is a library for +probabilistic reasoning and statistical analysis.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('TensorFlow', '2.11.0', '-CUDA-%(cudaver)s'), + ('dm-tree', '0.1.8'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + (name, version, { + 'installopts': '--install-option="--release"', + 'modulename': 'tensorflow_probability', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/probability/archive/'], + 'checksums': ['b32d2ae211ec727df9791b501839619f5389134bd6d4fe951570f500b0e75f55'], + }), +] + +sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] + +sanity_pip_check = True + +moduleclass = 'lib' From 9df79975ed1a29b463802067e84fed3344080767 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 26 Jul 2023 15:32:07 +0200 Subject: [PATCH 8140/9987] Add decoupleR package to R-bundle-Bioconductor easyconfig as extension --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 70a2e6684d3..f6924e214d5 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1224,6 +1224,9 @@ exts_list = [ ('ANCOMBC', '1.6.4', { 'checksums': ['ff5e80929cdbf6beb1073a6f5e008e2d2d8bdaccf5f65635b7fccf6d96b9710b'], }), + ('decoupleR', '2.2.2', { + 'checksums': ['354d165e9c6f0bf5211966242c63a797117ed2a78867f44b54a8f335b8473c60'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From e62bf261f53ece606b48cb9dd648283abfd4b068 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 26 Jul 2023 15:42:32 +0200 Subject: [PATCH 8141/9987] MUSCLE3 v0.7.0: gfbf/2022b --> foss/2022b --- ...{MUSCLE3-0.7.0-gfbf-2022b.eb => MUSCLE3-0.7.0-foss-2022b.eb} | 2 +- .../q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/m/MUSCLE3/{MUSCLE3-0.7.0-gfbf-2022b.eb => MUSCLE3-0.7.0-foss-2022b.eb} (98%) diff --git a/easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-gfbf-2022b.eb b/easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-foss-2022b.eb similarity index 98% rename from easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-gfbf-2022b.eb rename to easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-foss-2022b.eb index c6e983d5c35..25ab35908b1 100644 --- a/easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-gfbf-2022b.eb +++ b/easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-foss-2022b.eb @@ -11,7 +11,7 @@ description = """MUSCLE3 allows connecting multiple simulation models multiple separate simulation codes written in C++ or Fortran, and running on an HPC machine.""" -toolchain = {'name': 'gfbf', 'version': '2022b'} +toolchain = {'name': 'foss', 'version': '2022b'} source_urls = ['https://github.com/multiscale/%(namelower)s/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb index c589e9bb12a..3f0b96debf8 100644 --- a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb @@ -18,7 +18,6 @@ dependencies = [ ] use_pip = True -sanity_pip_check = True exts_list = [ ('patsy', '0.5.3', { From 6bdef03c00a244c235e8732efae7805a3dd62f30 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 26 Jul 2023 14:55:18 +0100 Subject: [PATCH 8142/9987] revert how MPI is configured due to failure --- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb | 4 +++- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb | 4 +++- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb | 4 +++- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb | 4 +++- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-fb.eb | 4 +++- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb | 4 +++- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb | 4 +++- 7 files changed, 21 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb index 6ae7dea8b33..17c53d6a060 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020a-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2020a'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -28,6 +28,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb index adf6c43a9c3..6b0e672b3bc 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2020b'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,6 +32,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb index e39f1c4ac28..e21675f74cb 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2020b-bl.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2020b'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,6 +32,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLAPACK/lib/liblapack.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb index dcac65cb09b..b430ea04c0e 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2021a'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,6 +32,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-fb.eb index 9b95e634595..5de6fb12f1d 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021a-fb.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2021a'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -31,6 +31,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb index 7e7a009670d..656bf80900b 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompi-2021b-fb.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'gompi', 'version': '2021b'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -31,6 +31,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb index 6d01acd1ff4..a0eb663ad60 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'iimpi', 'version': '2020b'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -32,6 +32,8 @@ dependencies = [ configopts = '-DBUILD_SHARED_LIBS=ON ' configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], From 3323b522b6c88726ec3aa0f65cb91f25599f8959 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 26 Jul 2023 15:31:57 +0100 Subject: [PATCH 8143/9987] undo changes to iimpi version --- .../easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb index a0eb663ad60..33b69ea09ab 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-iimpi-2020b-bf.eb @@ -7,7 +7,7 @@ description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of redesigned for distributed memory MIMD parallel computers.""" toolchain = {'name': 'iimpi', 'version': '2020b'} -toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = [homepage] sources = [SOURCELOWER_TGZ] @@ -34,6 +34,7 @@ configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis.a" ' configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" ' configopts += '-DCMAKE_C_COMPILER=mpicc ' configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' sanity_check_paths = { 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], From 3a2e31378fb769ab90e7c534b2acbe838707e5a9 Mon Sep 17 00:00:00 2001 From: nikishe <115556635+nikishe@users.noreply.github.com> Date: Wed, 26 Jul 2023 15:52:55 +0100 Subject: [PATCH 8144/9987] Create rclone-1.63.1-amd64.eb Latest version of rclone (v1.63.1) --- .../r/rclone/rclone-1.63.1-amd64.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.63.1-amd64.eb diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.63.1-amd64.eb b/easybuild/easyconfigs/r/rclone/rclone-1.63.1-amd64.eb new file mode 100644 index 00000000000..ca2d00835c0 --- /dev/null +++ b/easybuild/easyconfigs/r/rclone/rclone-1.63.1-amd64.eb @@ -0,0 +1,37 @@ +# Authors:: Nikishe + +easyblock = 'MakeCp' + +name = 'rclone' +version = '1.63.1' +versionsuffix = '-amd64' + +homepage = 'https://rclone.org/' + +description = """ + Rclone is a command line program to sync files and directories to and from + a variety of online storage services +""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.%(name)s.org/v%(version)s/'] +sources = ['%(name)s-v%(version)s-linux%(versionsuffix)s.zip'] +checksums = ['ca1cb4b1d9a3e45d0704aa77651b0497eacc3e415192936a5be7f7272f2c94c5'] + +skipsteps = ['build'] + +files_to_copy = [ + (['rclone'], 'bin'), + (['rclone.1'], 'share/man/man1'), + (['README.*'], 'share/doc'), +] + +sanity_check_paths = { + 'files': ['bin/rclone', 'share/doc/README.txt', 'share/man/man1/rclone.1'], + 'dirs': [] +} + +sanity_check_commands = ['rclone --version'] + +moduleclass = 'tools' From d5db1fc20aca30e17491618ae86f79a38e51e731 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 26 Jul 2023 17:54:20 +0200 Subject: [PATCH 8145/9987] adding easyconfigs: scGSVA-0.0.14-foss-2022a-R-4.2.1.eb --- .../scGSVA-0.0.14-foss-2022a-R-4.2.1.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/s/scGSVA/scGSVA-0.0.14-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/s/scGSVA/scGSVA-0.0.14-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/scGSVA/scGSVA-0.0.14-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..fac034d935b --- /dev/null +++ b/easybuild/easyconfigs/s/scGSVA/scGSVA-0.0.14-foss-2022a-R-4.2.1.eb @@ -0,0 +1,54 @@ +easyblock = 'Bundle' + +name = 'scGSVA' +version = '0.0.14' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/guokai8/scGSVA' +description = """ +scGSVA provides wrap functions to do GSVA analysis for single cell data. And scGSVA +includes functions to build annotation for almost all species. scGSVA also provides +function to generate figures based on the GSVA results. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', + 'https://cran.r-project.org/src/contrib/', + 'https://cran.freestatistics.org/src/contrib', +] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': source_urls, +} + +exts_list = [ + ('babelgene', '22.3', { + 'checksums': ['0f4a69bd472ce67682cb03e8186238bd3484fb9bbf185c6f291baa2d3481659c'], + }), + ('msigdbr', '7.5.1', { + 'checksums': ['dc30487bdf3594425ae9faec1ca0d7d0cd7278f4f177689133f92880e74acaca'], + }), + (name, version, { + 'source_urls': ['https://github.com/guokai8/scGSVA/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['64a0795cdb6fcc0e8088f3327b2ec178b8610d097c38b16e7ed1efab7c839151'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['scGSVA'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 31ad28a180c79ebef5b53464afb20deb9a7c6116 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 27 Jul 2023 10:25:32 +0200 Subject: [PATCH 8146/9987] Remove embedded JRE --- .../easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb index b88324a00dc..f14a31f4cc2 100644 --- a/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb +++ b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb @@ -47,7 +47,8 @@ extract_sources = False install_cmd = 'rpm2cpio ' + sources[0] + ' | cpio -idmv && ' install_cmd += 'cd opt/chemaxon/marvinsuite/ && ' install_cmd += 'chmod -x bin/*.bat && ' -install_cmd += 'cp -ar . %(installdir)s/' +install_cmd += 'cp -ar . %(installdir)s/ && ' +install_cmd += 'rm -Rf %(installdir)s/jre %(installdir)s/legal' # plugins directory is empty sanity_check_paths = { From 92c2133b8247d66718dc89ae788f7e19a47eccca Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 27 Jul 2023 13:06:21 +0200 Subject: [PATCH 8147/9987] adding easyconfigs: mahotas-1.4.13-foss-2022a.eb, mgen-1.2.1-foss-2022a.eb, ncolor-1.2.1-foss-2022a.eb, peakdetect-1.2-foss-2022a.eb, torchvf-0.1.3-foss-2022a.eb --- .../m/mahotas/mahotas-1.4.13-foss-2022a.eb | 23 +++++++++++ .../m/mgen/mgen-1.2.1-foss-2022a.eb | 24 +++++++++++ .../n/ncolor/ncolor-1.2.1-foss-2022a.eb | 40 +++++++++++++++++++ .../p/peakdetect/peakdetect-1.2-foss-2022a.eb | 25 ++++++++++++ .../t/torchvf/torchvf-0.1.3-foss-2022a.eb | 35 ++++++++++++++++ 5 files changed, 147 insertions(+) create mode 100644 easybuild/easyconfigs/m/mahotas/mahotas-1.4.13-foss-2022a.eb create mode 100644 easybuild/easyconfigs/m/mgen/mgen-1.2.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/n/ncolor/ncolor-1.2.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/peakdetect/peakdetect-1.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/mahotas/mahotas-1.4.13-foss-2022a.eb b/easybuild/easyconfigs/m/mahotas/mahotas-1.4.13-foss-2022a.eb new file mode 100644 index 00000000000..26ee86f494b --- /dev/null +++ b/easybuild/easyconfigs/m/mahotas/mahotas-1.4.13-foss-2022a.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'mahotas' +version = '1.4.13' + +homepage = 'https://mahotas.readthedocs.io/' +description = "Mahotas is a computer vision and image processing library for Python" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a78dfe15045a20a0d9e01538b80f874580cd3525ae3eaa2c83ced51eb455879c'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/mgen/mgen-1.2.1-foss-2022a.eb b/easybuild/easyconfigs/m/mgen/mgen-1.2.1-foss-2022a.eb new file mode 100644 index 00000000000..bb801d138bc --- /dev/null +++ b/easybuild/easyconfigs/m/mgen/mgen-1.2.1-foss-2022a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'mgen' +version = '1.2.1' + +homepage = 'https://github.com/NOhs/mgen/tree/master' +description = "Convenient matrix generation functions" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3caa56fc85ee71250cc55f484832af52d48c0cb84c945e1a32859b458a85ab39'] + +# also requires pbr, which is an extension in Python already +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncolor/ncolor-1.2.1-foss-2022a.eb b/easybuild/easyconfigs/n/ncolor/ncolor-1.2.1-foss-2022a.eb new file mode 100644 index 00000000000..4c3b76cac8b --- /dev/null +++ b/easybuild/easyconfigs/n/ncolor/ncolor-1.2.1-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'ncolor' +version = '1.2.1' + +homepage = 'https://github.com/kevinjohncutler/ncolor' +description = """Fast remapping of instance labels 1,2,3,...,M to +a smaller set of repeating, disjoint labels, 1,2,...,N.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# also requires pbr, which is an extension in Python already +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('numba', '0.56.4'), + ('mahotas', '1.4.13'), + ('scikit-image', '0.19.3'), +] + +exts_list = [ + ('edt', '2.3.1', { + 'checksums': ['3696e1f7de482465af731a734a31b261a8852df8d583118f1b223d61764e063f'], + }), + ('fastremap', '1.13.5', { + 'preinstallopts': "export PBR_VERSION=1.2.3 && ", + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/seung-lab/fastremap/archive/'], + 'checksums': ['ee0e9e798e9f331b7c46e98768735a42bb6e287b3aa56c31c322ba585f4036b7'], + }), + (name, version, { + 'preinstallopts': "sed -i 's/numpy>=1.22.4/numpy>=1.22.3/g' setup.py && ", + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['f05bfc75b8f1ea3ba9ee61c353e13146064bd63503a1655accee00a602ae2797'], + }), +] + +use_pip = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/peakdetect/peakdetect-1.2-foss-2022a.eb b/easybuild/easyconfigs/p/peakdetect/peakdetect-1.2-foss-2022a.eb new file mode 100644 index 00000000000..df1f1e6b33c --- /dev/null +++ b/easybuild/easyconfigs/p/peakdetect/peakdetect-1.2-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'peakdetect' +version = '1.2' + +homepage = 'https://github.com/avhn/peakdetect' +description = "Simple peak detection library for Python based on Billauer's work and this gist." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/avhn/peakdetect/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8f64a1fd6717ecaaec64fca6c16cb15698caa6aa8d6bc83bba3a22090a63e94f'] + +# also requires pbr, which is an extension in Python already +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb b/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb new file mode 100644 index 00000000000..7922d96d72a --- /dev/null +++ b/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'torchvf' +version = '0.1.3' + +homepage = 'https://github.com/ryanirl/torchvf' +description = "TorchVF is a unifying Python library for using vector fields for efficient proposal-free instance segmentation." + +toolchain = {'name': 'foss', 'version': '2022a'} + +# also requires pbr, which is an extension in Python already +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('OpenCV', '4.6.0', '-contrib'), + ('torchvision', '0.13.1'), + ('PyYAML', '6.0'), + ('scikit-learn', '1.1.2'), +] + +use_pip = True + +exts_list = [ + ('edt', '2.3.1', { + 'checksums': ['3696e1f7de482465af731a734a31b261a8852df8d583118f1b223d61764e063f'], + }), + (name, version, { + 'preinstallopts': """sed -i 's/opencv-python-headless = "\*"//g' pyproject.toml && """, + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['b2603ed660009ada68751fa507e02f297119e7180b3549098f4fdfe8242b8699'], + }), +] + +moduleclass = 'ai' From 41bc2f7b6ab8edfe3958e7c331e25bbbbc98ae6a Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 27 Jul 2023 13:10:51 +0200 Subject: [PATCH 8148/9987] adding main thing - omnipose --- .../o/omnipose/omnipose-0.4.4-foss-2022a.eb | 119 ++++++++++++++++++ 1 file changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb b/easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb new file mode 100644 index 00000000000..48ac39350ed --- /dev/null +++ b/easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb @@ -0,0 +1,119 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'omnipose' +version = '0.4.4' + +homepage = 'https://omnipose.readthedocs.io' +description = """ +Omnipose is a general image segmentation tool that builds on Cellpose in a number of ways +described in our paper. It works for both 2D and 3D images and on any imaging modality or +cell shape, so long as you train it on representative images. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyQt5', '5.15.5'), + ('PyTorch', '1.12.0'), + ('PyQtGraph', '0.13.3'), + ('numba', '0.56.4'), + ('scikit-image', '0.19.3'), + ('scikit-learn', '1.1.2'), + ('matplotlib', '3.5.2'), + ('igraph', '0.10.3'), + ('MXNet', '1.9.1'), + ('mgen', '1.2.1'), + ('ncolor', '1.2.1'), + ('mahotas', '1.4.13'), + ('peakdetect', '1.2'), + ('python-igraph', '0.10.3'), + ('torchvf', '0.1.3'), + ('OpenCV', '4.6.0', '-contrib'), + ('tqdm', '4.64.0'), + ('imagecodecs', '2022.9.26'), +] + +use_pip = True + +local_omnipose_preinstallopts = "sed -i 's/numpy>=1.22.4/numpy>=1.22.3/g' setup.py && " + +exts_list = [ + ('edt', '2.3.1', { + 'checksums': ['3696e1f7de482465af731a734a31b261a8852df8d583118f1b223d61764e063f'], + }), + ('tifffile', '2023.4.12', { + 'checksums': ['2fa99f9890caab919d932a0acaa9d0f5843dc2ef3594e212963932e20713badd'], + }), + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + ('fastremap', '1.13.5', { + 'preinstallopts': "export PBR_VERSION=1.2.3 && ", + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/seung-lab/fastremap/archive/'], + 'checksums': ['ee0e9e798e9f331b7c46e98768735a42bb6e287b3aa56c31c322ba585f4036b7'], + }), + ('roifile', '2023.5.12', { + 'checksums': ['32eeba0d9ad52cc249d6a234b737c1808a6c5d7d9baae6453709eb74222b3433'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('googleapis-common-protos', '1.59.1', { + 'modulename': 'google.api', + 'preinstallopts': 'sed -i "s|protobuf>=3.19.5|protobuf>=3.19.4|g" setup.py && ', + 'checksums': ['b35d530fe825fb4227857bc47ad84c33c809ac96f312e13182bdeaa2abe1178a'], + }), + ('cachetools', '5.3.1', { + 'checksums': ['dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b'], + }), + ('google-crc32c', '1.5.0', { + 'modulename': 'google_crc32c', + 'checksums': ['89284716bc6a5a415d4eaa11b1726d2d60a0cd12aadf5439828353662ede9dd7'], + }), + ('google-auth', '2.22.0', { + 'modulename': 'google.auth', + 'checksums': ['164cba9af4e6e4e40c3a4f90a1a6c12ee56f14c0b4868d1ca91b32826ab334ce'], + }), + ('google-cloud-core', '2.3.3', { + 'modulename': 'google.api', + 'checksums': ['37b80273c8d7eee1ae816b3a20ae43585ea50506cb0e60f3cf5be5f87f1373cb'], + }), + ('google-api-core', '2.11.1', { + 'modulename': 'google.api_core', + 'preinstallopts': 'sed -i "s|protobuf>=3.19.5|protobuf>=3.19.4|g" setup.py && ', + 'checksums': ['25d29e05a0058ed5f19c61c0a78b1b53adea4d9364b464d014fbda941f6d1c9a'], + }), + ('google-resumable-media', '2.5.0', { + 'modulename': 'google.resumable_media', + 'checksums': ['218931e8e2b2a73a58eb354a288e03a0fd5fb1c4583261ac6e4c078666468c93'], + }), + ('google-cloud-storage', '2.10.0', { + 'modulename': 'google.cloud.storage', + 'checksums': ['934b31ead5f3994e5360f9ff5750982c5b6b11604dc072bc452c25965e076dc7'], + }), + ('cellpose-omni', '0.9.1', { + 'patches': ['%(name)s-%(version)s_fix_deps_and_scm.patch'], + 'checksums': [ + {'cellpose-omni-0.9.1.tar.gz': '84f3199a751a74ddab643227bd0425ffafedcc2e739a57958f73a6d5f5348b6e'}, + {'cellpose-omni-0.9.1_fix_deps_and_scm.patch': + '9cf3eea507df11825cb492b34508e66d775a9852af7b5c2bd706bbd6e6eab504'}, + ], + }), + (name, version, { + 'preinstallopts': "sed -i 's/numpy>=1.22.4/numpy>=1.22.3/g' setup.py && ", + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['0bf1c333359504b0af511c36cc8db60ba5edba92d22c6aff183d9b858d269fe1'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 14a6bbd2e324b3015eba703be6def40fae0f69d1 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 27 Jul 2023 13:37:08 +0200 Subject: [PATCH 8149/9987] adding cellpose omni patch --- ...cellpose-omni-0.9.1_fix_deps_and_scm.patch | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/o/omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch diff --git a/easybuild/easyconfigs/o/omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch b/easybuild/easyconfigs/o/omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch new file mode 100644 index 00000000000..a1b4e8f7b19 --- /dev/null +++ b/easybuild/easyconfigs/o/omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch @@ -0,0 +1,32 @@ +--- setup_orig.py 2023-07-24 15:21:02.016292082 +0200 ++++ setup.py 2023-07-24 15:45:57.822276166 +0200 +@@ -1,10 +1,10 @@ + import setuptools + from setuptools import setup + +-install_deps = ['numpy>=1.22.4', 'scipy', 'natsort', ++install_deps = ['numpy>=1.22.3', 'scipy', 'natsort', + 'tifffile', 'tqdm', 'numba', + 'torch>=1.6', +- 'opencv-python-headless', # headless not working with pyinstaller ++ 'opencv-contrib-python', # headless not working with pyinstaller + 'fastremap', 'imagecodecs' + ] + +@@ -57,6 +57,7 @@ + + setup( + name="cellpose-omni", ++ version='0.9.1', + license="BSD", + author="Kevin Cutler", + author_email="kevinjohncutler@outlook.com", +@@ -69,7 +70,7 @@ + 'setuptools_scm', + ], + packages=setuptools.find_packages(), +- use_scm_version=True, ++ use_scm_version=False, + install_requires = install_deps, + tests_require=[ + 'pytest' From 49eabaf696c9ddcf45a1fe954ac9827ae2bcfca2 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 27 Jul 2023 13:39:32 +0200 Subject: [PATCH 8150/9987] updated torchvf for tests --- easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb b/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb index 7922d96d72a..0d184b3fb2b 100644 --- a/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb +++ b/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb @@ -4,7 +4,9 @@ name = 'torchvf' version = '0.1.3' homepage = 'https://github.com/ryanirl/torchvf' -description = "TorchVF is a unifying Python library for using vector fields for efficient proposal-free instance segmentation." +description = """ +TorchVF is a unifying Python library for using vector fields for efficient proposal-free instance segmentation. +""" toolchain = {'name': 'foss', 'version': '2022a'} @@ -20,6 +22,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True exts_list = [ ('edt', '2.3.1', { @@ -32,4 +35,5 @@ exts_list = [ }), ] + moduleclass = 'ai' From 4a64d802f89a702125a8e0644131b17170bb25bf Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 27 Jul 2023 14:36:45 +0200 Subject: [PATCH 8151/9987] updated for tests --- easybuild/easyconfigs/n/ncolor/ncolor-1.2.1-foss-2022a.eb | 1 + .../o/omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/ncolor/ncolor-1.2.1-foss-2022a.eb b/easybuild/easyconfigs/n/ncolor/ncolor-1.2.1-foss-2022a.eb index 4c3b76cac8b..86780d544e4 100644 --- a/easybuild/easyconfigs/n/ncolor/ncolor-1.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/n/ncolor/ncolor-1.2.1-foss-2022a.eb @@ -36,5 +36,6 @@ exts_list = [ ] use_pip = True +sanity_pip_check = True moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch b/easybuild/easyconfigs/o/omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch index a1b4e8f7b19..3c9184fc01a 100644 --- a/easybuild/easyconfigs/o/omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch +++ b/easybuild/easyconfigs/o/omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch @@ -1,3 +1,4 @@ +Making dependencies more flexible, adding version, disabling SCM (not working with EasyBuild) --- setup_orig.py 2023-07-24 15:21:02.016292082 +0200 +++ setup.py 2023-07-24 15:45:57.822276166 +0200 @@ -1,10 +1,10 @@ From 69a2e8915597d07b43afca70353c1ae6772e3b54 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 27 Jul 2023 14:43:30 +0200 Subject: [PATCH 8152/9987] Update URLs --- .../easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb index f14a31f4cc2..b33bbef2e31 100644 --- a/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb +++ b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-23.9.eb @@ -13,7 +13,7 @@ easyblock = 'Binary' name = 'Chemaxon-Marvin' version = '23.9' -homepage = 'https://chemaxon.com/products/marvin' +homepage = 'https://chemaxon.com/marvin' description = """Marvin suite is a chemically intelligent desktop toolkit built to help you draw, edit, publish, render, import and export your chemical structures and as well as allowing you to convert between various chemical and graphical file @@ -32,7 +32,7 @@ toolchain = SYSTEM # Download and license at https://chemaxon.com/products/marvin # Once logged in download files can be found here: -# https://chemaxon.com/products/marvin/download#download +# https://download.chemaxon.com/marvin sources = ['marvin_linux_%(version)s_openjdk11.rpm'] checksums = ['21a3bcd75d41d614fb9768949e713bfbb299e5c782a7166eaad0cd13654b140f'] @@ -64,8 +64,8 @@ sanity_check_commands = ["molconvert"] # COMMERCIAL # For commercial use please contact sales@chemaxon.com # NON-COMMERCIAL -# For personal use get a key to be renewed every 2 months at https://chemaxon.com/products/marvin/download -# For academic use get a key for research or educational purposes at https://chemaxon.com/academic-license +# For personal use get a key to be renewed every 2 months at https://download.chemaxon.com/marvin +# For academic use get a key for research or educational purposes at https://chemaxon.com/academic-program # # The license file "license.cxl" has to be placed in $HOME/.chemaxon/ From e9ff5d89ec1a237c2a710bb81e38f7e92c0be04b Mon Sep 17 00:00:00 2001 From: ariel Date: Thu, 27 Jul 2023 17:08:09 +0200 Subject: [PATCH 8153/9987] adding easyconfigs: aiohttp-3.8.5-GCCcore-12.2.0.eb --- .../a/aiohttp/aiohttp-3.8.5-GCCcore-12.2.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..82f3249090f --- /dev/null +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'aiohttp' +version = '3.8.5' + +homepage = 'https://github.com/aio-libs/aiohttp' +description = "Asynchronous HTTP client/server framework for asyncio and Python." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True + +# aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies +exts_list = [ + ('multidict', '6.0.4', { + 'checksums': ['3666906492efb76453c0e7b97f2cf459b0682e7402c0489a95484965dbc1da49'], + }), + ('yarl', '1.9.2', { + 'checksums': ['04ab9d4b9f587c06d801c2abfe9317b77cdf996c65a90d5e84ecc45010823571'], + }), + ('frozenlist', '1.4.0', { + 'checksums': ['09163bdf0b2907454042edb19f887c6d33806adc71fbd54afc14908bfdc22251'], + }), + ('async-timeout', '4.0.2', { + 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + (name, version, { + 'checksums': ['b9552ec52cc147dbf1944ac7ac98af7602e51ea2dcd076ed194ca3c0d1c7d0bc'], + }), + ('aioredis', '2.0.1', { + 'checksums': ['eaa51aaf993f2d71f54b70527c440437ba65340588afeb786cd87c55c89cd98e'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 81c5ece618f9f83c16f23c37d344ae6e357dcf89 Mon Sep 17 00:00:00 2001 From: ariel Date: Thu, 27 Jul 2023 17:09:56 +0200 Subject: [PATCH 8154/9987] adding easyconfigs: maturin-1.1.0-GCCcore-12.2.0.eb --- .../m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4b54d226d79 --- /dev/null +++ b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'maturin' +version = '1.1.0' + +homepage = "https://github.com/pyo3/maturin" +description = """This project is meant as a zero configuration +replacement for setuptools-rust and milksnake. It supports building +wheels for python 3.5+ on windows, linux, mac and freebsd, can upload +them to pypi and has basic pypy and graalpy support.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'] + +dependencies = [ + ('Python', '3.10.8'), + ('Rust', '1.65.0'), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From 39afa958d32fe39c79573746277fd6b8098ad73f Mon Sep 17 00:00:00 2001 From: ariel Date: Thu, 27 Jul 2023 17:30:56 +0200 Subject: [PATCH 8155/9987] adding easyconfigs: PycURL-7.45.2-GCCcore-12.2.0.eb --- .../p/PycURL/PycURL-7.45.2-GCCcore-12.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..77dc8f48bc8 --- /dev/null +++ b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'PycURL' +version = '7.45.2' + +homepage = "http://pycurl.io/" +description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL + from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of + features.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('cURL', '7.86.0'), +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5730590be0271364a5bddd9e245c9cc0fb710c4cbacbdd95264a3122d23224ca'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From eda56c5bbbdeb2854dd25cc38915c8bcdc64e1fe Mon Sep 17 00:00:00 2001 From: ariel Date: Thu, 27 Jul 2023 17:38:20 +0200 Subject: [PATCH 8156/9987] add download_dep_fail option --- easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb index 4b54d226d79..c16559a9133 100644 --- a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb @@ -21,5 +21,6 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True moduleclass = 'tools' From dd243485077c8329c79587e9230e9ea80254d887 Mon Sep 17 00:00:00 2001 From: ariel Date: Thu, 27 Jul 2023 17:39:28 +0200 Subject: [PATCH 8157/9987] add configurable-http-proxy eb --- ...gurable-http-proxy-4.5.5-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.5-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..19c72968045 --- /dev/null +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.5-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'Binary' + +name = 'configurable-http-proxy' +version = '4.5.5' + +homepage = 'https://github.com/jupyterhub/configurable-http-proxy' +description = """HTTP proxy for node.js including a REST API for updating the routing table. + Developed as a part of the Jupyter Hub multi-user server.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = { + ('binutils', '2.39'), +} + +dependencies = [ + ('nodejs', '18.12.1'), +] + +source_urls = ['https://github.com/jupyterhub/configurable-http-proxy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6f2fc05ae9277d76ab5fb4cfe7c98276cd6bd526ba1841dd9af2cea529526b66'] + +install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz' + +sanity_check_paths = { + 'files': ['bin/configurable-http-proxy'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' From f6fc19100fb0c219bf5c84fdd0f4dca12fb88e1a Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 27 Jul 2023 17:42:56 +0200 Subject: [PATCH 8158/9987] fixing omnipose checksums --- easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb b/easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb index 48ac39350ed..02007a72a28 100644 --- a/easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb +++ b/easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb @@ -104,7 +104,7 @@ exts_list = [ 'checksums': [ {'cellpose-omni-0.9.1.tar.gz': '84f3199a751a74ddab643227bd0425ffafedcc2e739a57958f73a6d5f5348b6e'}, {'cellpose-omni-0.9.1_fix_deps_and_scm.patch': - '9cf3eea507df11825cb492b34508e66d775a9852af7b5c2bd706bbd6e6eab504'}, + 'a1c42309d1a39297744a8505b45b9bff2e0f9ef738680349cc4adf8f663c4be0'}, ], }), (name, version, { From 2333cce620a27f3839c0a86b573f005a9fbf434a Mon Sep 17 00:00:00 2001 From: ariel Date: Thu, 27 Jul 2023 18:51:33 +0200 Subject: [PATCH 8159/9987] add required buildep --- .../easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb index c16559a9133..57296d955fe 100644 --- a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb @@ -11,14 +11,16 @@ them to pypi and has basic pypy and graalpy support.""" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -sources = [SOURCE_TAR_GZ] -checksums = ['4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'] +builddependencies = [('binutils', '2.39')] dependencies = [ ('Python', '3.10.8'), ('Rust', '1.65.0'), ] +sources = [SOURCE_TAR_GZ] +checksums = ['4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'] + use_pip = True sanity_pip_check = True download_dep_fail = True From 811d5d3b668cec369896b5529e670a4590f0e775 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 27 Jul 2023 21:12:09 +0200 Subject: [PATCH 8160/9987] adding easyconfigs: QIIME2-2023.5.1-foss-2022a.eb, UniFrac-1.3.2-foss-2022a.eb and patches: QIIME2-2023.5.1_fix.patch, unifrac-1.1.1_fix.patch, UniFrac-1.3.2_fix.patch --- .../q/QIIME2/QIIME2-2023.5.1-foss-2022a.eb | 326 ++++++++++++++++++ .../q/QIIME2/QIIME2-2023.5.1_fix.patch | 17 + .../q/QIIME2/unifrac-1.1.1_fix.patch | 22 ++ .../u/UniFrac/UniFrac-1.3.2-foss-2022a.eb | 52 +++ .../u/UniFrac/UniFrac-1.3.2_fix.patch | 42 +++ 5 files changed, 459 insertions(+) create mode 100644 easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1_fix.patch create mode 100644 easybuild/easyconfigs/q/QIIME2/unifrac-1.1.1_fix.patch create mode 100644 easybuild/easyconfigs/u/UniFrac/UniFrac-1.3.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/u/UniFrac/UniFrac-1.3.2_fix.patch diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1-foss-2022a.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1-foss-2022a.eb new file mode 100644 index 00000000000..4f624d754d5 --- /dev/null +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1-foss-2022a.eb @@ -0,0 +1,326 @@ +easyblock = 'PythonBundle' + +name = 'QIIME2' +version = '2023.5.1' + +homepage = 'https://qiime2.org' +description = """QIIME 2 is a powerful, extensible, and decentralized microbiome bioinformatics platform that is free, +open source, and community developed.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('IPython', '8.5.0'), + ('PyYAML', '6.0'), + ('Java', '11', '', SYSTEM), + ('Perl', '5.34.1'), + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', '-R-%(rver)s'), + ('Parsl', '2023.7.17'), + ('alsa-lib', '1.2.8'), + ('BLAST+', '2.13.0'), + ('bokeh', '2.4.3'), + ('Bowtie2', '2.4.5'), + ('bwidget', '1.9.15'), + ('bzip2', '1.0.8'), + ('cairo', '1.17.4'), + ('cURL', '7.83.0'), + ('cutadapt', '4.2'), + ('DendroPy', '4.5.2'), + ('expat', '2.4.8'), + ('FastTree', '2.1.11'), + ('fontconfig', '2.14.0'), + ('FriBidi', '1.0.12'), + ('giflib', '5.2.1'), + ('GLib', '2.72.1'), + ('GSL', '2.7'), + ('h5py', '3.7.0'), + ('HarfBuzz', '4.2.1'), + ('MAFFT', '7.505', '-with-extensions'), + ('scikit-bio', '0.5.7'), + ('Seaborn', '0.11.2'), + ('statsmodels', '0.13.1'), + ('umap-learn', '0.5.3'), + ('VSEARCH', '2.22.1'), + ('UniFrac', '1.3.2'), + ('attr', '2.5.1'), + ('Brotli-python', '1.0.9'), + ('SAMtools', '1.16.1'), + ('HTSlib', '1.15.1'), + ('HMMER', '3.3.2'), + ('networkx', '2.8.4'), +] + +use_pip = True + +# avoid that hidden (sub)directories like .config/q2cli are created in home directory +preinstallopts = "export HOME=%(builddir)s/home && " + +# avoid hatchling requirement to install altair +# (since installing it introduces conflicting version requirements with poetry included with Python) +# also copy missing vega-lite-schema.json to installdir +_preinstallopts = ' '.join([ + """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g'""", + """-e 's/^requires = .*/requires = ["setuptools"]/g'""", + """-e 's/^license-files = .*//g'""", + r"""-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """, + 'schemadir=%(installdir)s/lib/python%(pyshortver)s/site-packages/altair/vegalite/v5/schema/ && ', + 'mkdir -p $schemadir && cp altair/vegalite/v5/schema/vega-lite-schema.json $schemadir && ', +]) + +# versions of QIIME2 extensions taken from: +# https://github.com/qiime2/package-integration/blob/main/2023.5/staged/core/conda_build_config.yaml +exts_list = [ + ('unifrac', '1.1.1', { + 'patches': ['%(name)s-%(version)s_fix.patch'], + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/biocore/unifrac/archive/refs/tags'], + 'checksums': [ + {'1.1.1.tar.gz': '95aeb107d014ffd614fda5d3c58bfac860c1a6185a63e7cd6eb2462e4d4d4f06'}, + {'unifrac-1.1.1_fix.patch': '4f31e9e1f8c40a166d0a66852f6ae2434a95575664a69e49bb513997891d3806'}, + ], + }), + ('argcomplete', '2.0.0', { + 'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('cached-property', '1.5.2', { + 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], + }), + ('contourpy', '1.0.7', { + 'checksums': ['d8165a088d31798b59e91117d1f5fc3df8168d8b48c4acc10fc0df0d0bdbcc5e'], + }), + ('tzdata', '2022.7', { + 'checksums': ['fe5f866eddd8b96e9fcba978f8e503c909b19ea7efda11e52e39494bad3a7bfa'], + }), + ('pytz-deprecation-shim', '0.1.0.post0', { + 'source_tmpl': 'pytz_deprecation_shim-%(version)s.tar.gz', + 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], + }), + ('tzlocal', '5.0.1', { + 'checksums': ['46eb99ad4bdb71f3f72b7d24f4267753e240944ecfc16f25d2719ba89827a803'], + }), + ('argon2-cffi-bindings', '21.2.0', { + 'modulename': '_argon2_cffi_bindings', + 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], + }), + ('biom-format', '2.1.15', { + 'modulename': 'biom', + 'checksums': ['3bda2096e663dc1cb6f90f51b394da0838b9be5164a44370c134ce5b3b2a4dd3'], + }), + ('pylatexenc', '2.10', { + 'checksums': ['3dd8fd84eb46dc30bee1e23eaab8d8fb5a7f507347b23e5f38ad9675c84f40d3'], + }), + ('bibtexparser', '1.4.0', { + 'checksums': ['ca7ce2bc34e7c48a678dd49416429bb567441f26dbb13b3609082d8cd109ace6'], + }), + ('deblur', '1.1.0', { + 'checksums': ['78ca2c9946ed99c0d49352e92b63083ae10d04734af7682baddb2c31966c1674'], + }), + ('emperor', '1.0.4', { + 'checksums': ['8b57d6ee3709b62b4dfdd8e1f815dd88e5fee3a05947d72fa32191a16ac08854'], + }), + ('fastcluster', '1.2.6', { + 'checksums': ['aab886efa7b6bba7ac124f4498153d053e5a08b822d2254926b7206cdf5a8aa6'], + }), + ('gneiss', '0.4.6', { + 'preinstallopts': "sed -i '/nose/d' setup.py && ", + 'checksums': ['5ebf32148909cf74475e45682042c68224f002c1cbf723a5c96014a30f1cf323'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('ijson', '3.2.3', { + 'checksums': ['10294e9bf89cb713da05bc4790bdff616610432db561964827074898e174f917'], + }), + ('iow', '1.0.6', { + 'modulename': 'bp', + 'preinstallopts': """sed -i "/'nose /d" setup.py && """, + 'checksums': ['ac4f579a0881f1c827f75033a304341ae91d3a527cc6aed3fea53749f1b9951c'], + }), + # using prebuilt wheels for atpublic and flufl.lock because building them requires pdm + ('atpublic', '4.0', { + 'modulename': 'public', + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['80057c55641253b86dcb68b524f82328172371b6547d4c7462a9127fbfbbabfc'], + }), + ('flufl-lock', '8.0.1', { + 'modulename': 'flufl.lock', + 'source_tmpl': 'flufl_lock-%(version)s-py3-none-any.whl', + 'checksums': ['a3df854d76173d59813fdcba91671234b59e2a14db3390793745c77a7bb92d9d'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('interface_meta', '1.3.0', { + 'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('formulaic', '0.4.0', { + 'checksums': ['087950518c53a2491deb52b8ddd66833f953882e517a42e476c007cc8f6892c5'], + }), + ('altair', '5.0.1', { + 'preinstallopts': _preinstallopts, + 'checksums': ['087d7033cb2d6c228493a053e12613058a5d47faf6a36aea3ff60305fd8b4cb0'], + }), + (name, version, { + 'patches': ['QIIME2-2023.5.1_fix.patch'], + 'source_urls': ['https://github.com/qiime2/qiime2/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': [ + {'QIIME2-2023.5.1.tar.gz': '9fe2b29f64204138e575a992970e4333ffb99affd75c132682fdec1c85a95ee8'}, + {'QIIME2-2023.5.1_fix.patch': '6148e5334f478bcdd6f5bf30fbe39426be71c391af1a384a529c49e658ada7a5'}, + ], + }), + ('q2cli', version, { + 'source_urls': ['https://github.com/qiime2/q2cli/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['2ec403e5f701b21a09cf9a68def5c37175577d92f5460d5aa1182dcdf7f29888'], + }), + ('q2-alignment', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-alignment/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['8b492790314d3bf43717668c51c5ce9a4bcd105fca59d7594b2c655a151eb436'], + }), + ('q2-composition', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-composition/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['1fd9ee2bedd049b961a6b0bac3376126cacf6e14c7e4c961853083d3e46d54a1'], + }), + ('q2-cutadapt', version, { + 'source_urls': ['https://github.com/qiime2/q2-cutadapt/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['40cc43f7bc0b063a60d14bcddf5e70da5eacef54e12648eb9e3c2e7baba28087'], + }), + ('q2-dada2', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-dada2/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['091006b59d08540a926acd41429b4bd83859ccac9956fb212759d63fbbff1640'], + }), + ('q2-deblur', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-deblur/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['8997c784dee72f9d9b31920bd33fac283581468ca910769fd2d00f62e7733718'], + }), + ('q2-demux', '2023.5.0', { + 'preinstallopts': "make all && ", + 'source_urls': ['https://github.com/qiime2/q2-demux/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['409a17a02b874ac7804494be7fda6831e4bde3170930705ddd0b5ccf2324c238'], + }), + ('q2-diversity', version, { + 'preinstallopts': "make all && ", + 'source_urls': ['https://github.com/qiime2/q2-diversity/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['21d267613808fdee3b19c51cb3d694932f0a16d80cf6515f6750a6668fd2b8e1'], + }), + ('q2-diversity-lib', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-diversity-lib/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['0971c173611f28e6306db9bdea53ddf7940bae08aa6b01fa543869e111a27f45'], + }), + ('q2-emperor', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-emperor/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['4a877320389001bd4c53b4b4943bc8b50233169cee802fb561d1f90bea6f1c31'], + }), + ('q2-feature-classifier', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-feature-classifier/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['33d59dffa6da2706680d202e8d6da4a5e223d7f8391fe8b975762af3e56e77ec'], + }), + ('q2-feature-table', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-feature-table/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['91a4172d1c82c1571bba9f21080956ab4681a80562491125175e9770a8f7d988'], + }), + ('q2-fragment-insertion', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-fragment-insertion/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6917fdab888388e67e0e7e2e6e90b42e9a90b67cc4fcbcd8f7033aae032d7cd9'], + }), + ('q2-gneiss', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-gneiss/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6bdac2eb4136c0ce181e5daa85fe852a23200e6d5e9aea708d9387c23a47328e'], + }), + ('q2-longitudinal', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-longitudinal/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['ca67146351e7ba8522c8dfa47c26a0e39b66838e0de0d34674fbf0e471f0d98c'], + }), + ('q2-metadata', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-metadata/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f1d0e0604afee936c2f4c58ea0b5b3d4c9796cad3bd86cdf403e038d70d4db52'], + }), + ('q2-phylogeny', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-phylogeny/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['48ef0832e488ed647d68cfa0653632b0afc5dc4ae884898398ca71c3061a5557'], + }), + ('q2-quality-control', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-quality-control/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['595415cbde38e07e025037c88cd576bbfb1b05543db29c3aaa15db0b8c410222'], + }), + ('q2-quality-filter', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-quality-filter/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['aa41f5bc7f26a395ac6ebca5d2308b4d2a8c5b1207ada9375fc37da4fc704820'], + }), + ('q2-sample-classifier', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-sample-classifier/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['50efbbfee0296f9e6214aff8b51a4d2ae1a3c9cfa970c258f1b5b826331da5c4'], + }), + ('q2-taxa', '2023.5.0', { + 'preinstallopts': "make all && ", + 'source_urls': ['https://github.com/qiime2/q2-taxa/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['bf0702721c1ec53f87a0ab1ac7afcaedb0aba3e4b2fba24345672b132a0e35f9'], + }), + ('q2-types', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-types/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['2e583d68e4d6e1be34b2acbbfb3444b9c1eefd71842a85e3848c89579984b4ca'], + }), + ('q2-vsearch', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2-vsearch/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['30e4d7a731d87d595fc2f9903b8def36eedead1ff209b91e5e4d8ed0c8caf694'], + }), + ('q2templates', '2023.5.0', { + 'source_urls': ['https://github.com/qiime2/q2templates/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['08b49f4640bd2f72b4274dd364657ff40a48aabd72fc5650d6460a62f91f6a46'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/biom', 'bin/qiime'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "qiime --help", + "qiime info", + "qiime tools validate " + "%(installdir)s/lib/python%(pyshortver)s/site-packages/q2_sample_classifier/tests/data/vaw.qza", +] + +modextrapaths = {'CONDA_PREFIX': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1_fix.patch b/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1_fix.patch new file mode 100644 index 00000000000..8072243412b --- /dev/null +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1_fix.patch @@ -0,0 +1,17 @@ +Make compatible with `ast` in Python >=3.9 +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur qiime2-2023.5.1.orig/qiime2/core/type/parse.py qiime2-2023.5.1/qiime2/core/type/parse.py +--- qiime2-2023.5.1.orig/qiime2/core/type/parse.py 2023-05-30 19:43:57.000000000 +0200 ++++ qiime2-2023.5.1/qiime2/core/type/parse.py 2023-07-27 11:04:05.167408000 +0200 +@@ -44,7 +44,10 @@ + return _build_predicate(expr.func.id, args, kwargs) + + if node is ast.Subscript: +- field_expr = expr.slice.value ++ if hasattr(expr.slice, "value"): ++ field_expr = expr.slice.value ++ else: ++ field_expr = expr.slice + + if type(field_expr) is ast.Tuple: + field_expr = field_expr.elts diff --git a/easybuild/easyconfigs/q/QIIME2/unifrac-1.1.1_fix.patch b/easybuild/easyconfigs/q/QIIME2/unifrac-1.1.1_fix.patch new file mode 100644 index 00000000000..d1897cae0f6 --- /dev/null +++ b/easybuild/easyconfigs/q/QIIME2/unifrac-1.1.1_fix.patch @@ -0,0 +1,22 @@ +Fix include paths for unifrac +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur unifrac-1.1.1.orig/setup.py unifrac-1.1.1/setup.py +--- unifrac-1.1.1.orig/setup.py 2022-04-13 20:14:51.000000000 +0200 ++++ unifrac-1.1.1/setup.py 2023-07-26 17:12:07.365976000 +0200 +@@ -75,12 +75,15 @@ + + USE_CYTHON = os.environ.get('USE_CYTHON', True) + ext = '.pyx' if USE_CYTHON else '.cpp' ++unifrac_includes = [os.path.join(os.environ['EBROOTUNIFRAC'], 'include', 'unifrac')] + extensions = [Extension("unifrac._api", + sources=["unifrac/_api" + ext], + extra_link_args=LINK_ARGS, + extra_compile_args=COMPILE_ARGS, + include_dirs=([np.get_include()] + +- CONDA_INCLUDES), ++ CONDA_INCLUDES + ++ os.environ['CPATH'].split(':') + ++ unifrac_includes), + libraries=['ssu'])] + + if USE_CYTHON: diff --git a/easybuild/easyconfigs/u/UniFrac/UniFrac-1.3.2-foss-2022a.eb b/easybuild/easyconfigs/u/UniFrac/UniFrac-1.3.2-foss-2022a.eb new file mode 100644 index 00000000000..3fa14b7d585 --- /dev/null +++ b/easybuild/easyconfigs/u/UniFrac/UniFrac-1.3.2-foss-2022a.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UniFrac' +version = '1.3.2' + +homepage = 'https://github.com/biocore/unifrac-binaries' +description = """ +UniFrac is the de facto repository for high-performance phylogenetic diversity +calculations. The methods in this repository are based on an implementation of +the Strided State UniFrac algorithm which is faster, and uses less memory than +Fast UniFrac. Strided State UniFrac supports Unweighted UniFrac, Weighted +UniFrac, Generalized UniFrac, Variance Adjusted UniFrac and meta UniFrac, in +both double and single precision (fp32). This repository also includes Stacked +Faith (manuscript in preparation), a method for calculating Faith's PD that is +faster and uses less memory than the Fast UniFrac-based reference +implementation.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/biocore/unifrac-binaries/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['UniFrac-1.3.2_fix.patch'] +checksums = [ + {'v1.3.2.tar.gz': '3395ce67d967b06a20ffc3cfa24c5cc400b49a7670399333b5daa2e4644627a7'}, + {'UniFrac-1.3.2_fix.patch': '8d4e497c95d7fd1162f3b8228f60493a2411ecae44108a0ceb37704acb14ef24'}, +] + +dependencies = [ + ('HDF5', '1.12.2'), + ('lz4', '1.9.3'), + ('Szip', '2.1.1'), + ('libaec', '1.0.6'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export PREFIX=%(installdir)s && ' +buildopts = 'api && make main' + +pretestopts = prebuildopts +runtest = 'test' + +preinstallopts = prebuildopts + 'mkdir -p %(installdir)s/{lib,bin} && ' + +sanity_check_paths = { + 'files': ['lib/libssu.%s' % SHLIB_EXT, 'bin/ssu'], + 'dirs': ['include/unifrac'], +} + +sanity_check_commands = ['ssu --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/UniFrac/UniFrac-1.3.2_fix.patch b/easybuild/easyconfigs/u/UniFrac/UniFrac-1.3.2_fix.patch new file mode 100644 index 00000000000..32df3db62a4 --- /dev/null +++ b/easybuild/easyconfigs/u/UniFrac/UniFrac-1.3.2_fix.patch @@ -0,0 +1,42 @@ +Fix BLAS and LAPACK headers and libraries +Make sure libccu is found for capi_test +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur unifrac-binaries-1.3.2.orig/src/Makefile unifrac-binaries-1.3.2/src/Makefile +--- unifrac-binaries-1.3.2.orig/src/Makefile 2023-05-09 18:46:16.000000000 +0200 ++++ unifrac-binaries-1.3.2/src/Makefile 2023-07-26 14:28:56.027032000 +0200 +@@ -36,7 +36,7 @@ + PREFIX := $(CONDA_PREFIX) + endif + +-BLASLIB=-llapacke -lcblas ++BLASLIB=-llapacke -lflexiblas + + ifeq ($(PLATFORM),Darwin) + AVX2 := $(shell sysctl -a | grep -c AVX2) +diff -ur unifrac-binaries-1.3.2.orig/src/skbio_alt.cpp unifrac-binaries-1.3.2/src/skbio_alt.cpp +--- unifrac-binaries-1.3.2.orig/src/skbio_alt.cpp 2023-05-09 18:46:16.000000000 +0200 ++++ unifrac-binaries-1.3.2/src/skbio_alt.cpp 2023-07-26 14:07:45.521123760 +0200 +@@ -10,8 +10,9 @@ + #include + + // Not using anything mkl specific, but this is what we get from Conda +-#include +-#include ++#include "cblas.h" ++#include "lapacke.h" ++ + + static std::mt19937 myRandomGenerator; + +diff -ur unifrac-binaries-1.3.2.orig/test/Makefile unifrac-binaries-1.3.2/test/Makefile +--- unifrac-binaries-1.3.2.orig/test/Makefile 2023-05-09 18:46:16.000000000 +0200 ++++ unifrac-binaries-1.3.2/test/Makefile 2023-07-26 15:58:32.421333000 +0200 +@@ -13,7 +13,7 @@ + test_binaries: capi_test + + capi_test: capi_test.c +- $(CC) -std=c99 -O0 -g capi_test.c -I../src -lssu -L${PREFIX}/lib -Wl,-rpath,${PREFIX}/lib -o capi_test ++ $(CC) -std=c99 -O0 -g capi_test.c -I../src -lssu -L../src -Wl,-rpath,../src -o capi_test + + clean: + -rm -f *.o capi_test From c290f9c10976491b37a7e9e788f816035d6993d4 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 28 Jul 2023 08:57:57 +0200 Subject: [PATCH 8161/9987] adding easyconfigs: Parsl-2023.7.17-GCCcore-11.3.0.eb --- .../p/Parsl/Parsl-2023.7.17-GCCcore-11.3.0.eb | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/p/Parsl/Parsl-2023.7.17-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/Parsl/Parsl-2023.7.17-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Parsl/Parsl-2023.7.17-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..9f657370989 --- /dev/null +++ b/easybuild/easyconfigs/p/Parsl/Parsl-2023.7.17-GCCcore-11.3.0.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'Parsl' +version = '2023.7.17' + +homepage = 'https://parsl-project.org/' +description = """ +Parsl extends parallelism in Python beyond a single computer. +You can use Parsl just like Python's parallel executors but across multiple +cores and nodes. However, the real power of Parsl is in expressing multi-step +workflows of functions. Parsl lets you chain functions together and will launch +each function as inputs and computing resources are available. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('PyZMQ', '24.0.1'), + ('dill', '0.3.6'), +] + +use_pip = True + +exts_list = [ + ('types-paramiko', '3.2.0.1', { + 'modulename': False, + 'checksums': ['ecf5781d13c28a1c3513a1f3dffd096682459519c731a56032416f7c7e303e64'], + }), + ('types-urllib3', '1.26.25.14', { + 'modulename': False, + 'checksums': ['229b7f577c951b8c1b92c1bc2b2fdb0b49847bd2af6d1cc2a2e3dd340f3bda8f'], + }), + ('types-requests', '2.31.0.2', { + 'modulename': False, + 'checksums': ['6aa3f7faf0ea52d728bb18c0a0d1522d9bfd8c72d26ff6f61bfc3d06a411cf40'], + }), + ('types-six', '1.16.21.9', { + 'modulename': False, + 'checksums': ['746e6c25b8c48b3c8ab9efe7f68022839111de423d35ba4b206b88b12d75f233'], + }), + ('typeguard', '2.13.3', { + 'checksums': ['00edaa8da3a133674796cf5ea87d9f4b4c367d77476e185e80251cc13dfbb8c4'], + }), + ('typing-extensions', '4.7.1', { + # typing-extensions-4.3.0-GCCcore-11.3.0.eb is too old + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('globus-sdk', '3.25.0', { + 'checksums': ['d9be275d4ec18054db04732f75649c4227800c79b31fbcfb3f4f31eccfa5f4f7'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('setproctitle', '1.3.2', { + 'checksums': ['b9fb97907c830d260fa0658ed58afd48a86b2b88aac521135c352ff7fd3477fd'], + }), + ('parsl', version, { + 'checksums': ['18b1c169e92a73d1f7129bf16c169d5962b39709d5e06c07017a6d3903f50851'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/parsl-perf'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ['parsl-perf --help'] + +moduleclass = 'tools' From 32c2c8f8a1cf2d178fd4c1321baa24e8f8cbfea3 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Fri, 28 Jul 2023 09:43:34 +0200 Subject: [PATCH 8162/9987] Change sanity check path from 'scGSVA' to name. Co-authored-by: Adam Huffman --- .../easyconfigs/s/scGSVA/scGSVA-0.0.14-foss-2022a-R-4.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scGSVA/scGSVA-0.0.14-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/scGSVA/scGSVA-0.0.14-foss-2022a-R-4.2.1.eb index fac034d935b..9815eac64bb 100644 --- a/easybuild/easyconfigs/s/scGSVA/scGSVA-0.0.14-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/s/scGSVA/scGSVA-0.0.14-foss-2022a-R-4.2.1.eb @@ -46,7 +46,7 @@ exts_list = [ sanity_check_paths = { 'files': [], - 'dirs': ['scGSVA'], + 'dirs': [name], } modextrapaths = {'R_LIBS_SITE': ''} From 13a1703b98567434c122ba39728d550815d690d6 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 28 Jul 2023 11:10:34 +0200 Subject: [PATCH 8163/9987] adding easyconfigs: hampel-0.0.5-foss-2022a.eb, py-c3d-0.5.2-foss-2022a.eb --- .../h/hampel/hampel-0.0.5-foss-2022a.eb | 32 +++++++++++++++++++ .../p/py-c3d/py-c3d-0.5.2-foss-2022a.eb | 30 +++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/h/hampel/hampel-0.0.5-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/py-c3d/py-c3d-0.5.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/hampel/hampel-0.0.5-foss-2022a.eb b/easybuild/easyconfigs/h/hampel/hampel-0.0.5-foss-2022a.eb new file mode 100644 index 00000000000..58b53b5774b --- /dev/null +++ b/easybuild/easyconfigs/h/hampel/hampel-0.0.5-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'hampel' +version = '0.0.5' + +homepage = 'https://github.com/MichaelisTrofficus/hampel_filter' +description = """ +The Hampel filter is generally used to detect anomalies in data with a timeseries +structure. It basically consists of a sliding window of a parameterizable size. For each +window, each observation will be compared with the Median Absolute Deviation (MAD). The +observation will be considered an outlier in the case in which it exceeds the MAD by n +times (the parameter n is also parameterizable). +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['c9baa3ea022c76d5cfc1ad8959de8df6c4a232ecdf0dffd599a03609aeae5fdb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/py-c3d/py-c3d-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/p/py-c3d/py-c3d-0.5.2-foss-2022a.eb new file mode 100644 index 00000000000..cfa66a73607 --- /dev/null +++ b/easybuild/easyconfigs/p/py-c3d/py-c3d-0.5.2-foss-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'py-c3d' +version = '0.5.2' + +homepage = 'https://github.com/EmbodiedCognition/py-c3d' +description = """ +This is a small library for reading and writing C3D binary files. C3D files are a standard +format for recording 3-dimensional time sequence data, especially data recorded by a 3D +motion tracking apparatus. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True + +exts_list = [ + ('c3d', version, { + 'checksums': ['b49801237be3b3cede1731a5058f48a96c0bd02339ef25e4e384a4648e23e580'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From a7a72ce5aaadc8d0600773615d7011188b68aeff Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 28 Jul 2023 13:25:50 +0200 Subject: [PATCH 8164/9987] use correct version of Seaborn dep --- easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1-foss-2022a.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1-foss-2022a.eb index 4f624d754d5..74194d08155 100644 --- a/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.5.1-foss-2022a.eb @@ -41,7 +41,7 @@ dependencies = [ ('HarfBuzz', '4.2.1'), ('MAFFT', '7.505', '-with-extensions'), ('scikit-bio', '0.5.7'), - ('Seaborn', '0.11.2'), + ('Seaborn', '0.12.1'), ('statsmodels', '0.13.1'), ('umap-learn', '0.5.3'), ('VSEARCH', '2.22.1'), From b6164f6f8d4643cf580bbebc25ff76bb4463b3f0 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 28 Jul 2023 13:59:06 +0200 Subject: [PATCH 8165/9987] add up2date CUDA enabled Amber for foss/2022a --- ...-foss-2022a-AmberTools-22.5-CUDA-11.7.0.eb | 99 +++++++++++++++++++ 1 file changed, 99 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/Amber/Amber-22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0.eb new file mode 100644 index 00000000000..a60a8c02006 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0.eb @@ -0,0 +1,99 @@ +name = 'Amber' +local_amber_ver = 22 +local_ambertools_ver = 22 +# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php +patchlevels = (5, 4) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s-%%(cudaver)s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'https://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'}, +] +patches = [ + {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_DGESVD_workspace_query.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_dvout_call.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_mexit_calls.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_more_blas_argument_problems.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_multiple_definition.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_potential_use_before_init.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_rism_argument_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_missing_error_check_on_test_run.patch', 'alt_location': 'AmberTools'}, + 'Amber-22_reduce_precision_of_kmmd_test.patch', + 'Amber-22_remove_undeclared_redundant_variable.patch', +] +checksums = [ + '3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16', # Amber22.tar.bz2 + '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools22.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch + # AmberTools-22_fix_missing_error_check_on_test_run.patch + 'a86eee60bd65c16a849469e303cb99dfc207cbadd2ae9e70b9ff580ced785475', + 'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e', # Amber-22_reduce_precision_of_kmmd_test.patch + # Amber-22_remove_undeclared_redundant_variable.patch + 'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # mpi4py required for MMPBSA + ('Perl', '5.34.1'), + ('Boost', '1.79.0'), + ('libreadline', '8.1.2'), + ('matplotlib', '3.5.2'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('PnetCDF', '1.12.3'), + ('Tkinter', '3.10.4'), + ('X11', '20220504'), + ('CUDA', '11.7.0', '', SYSTEM), + ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), + ('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'), +] + +# Some CUDA tests differs from expected results +runtest = False + +static = False + +moduleclass = 'chem' From 8e0b5db92deed273f7a3c65c16b30a80a36d3d96 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 28 Jul 2023 14:10:12 +0200 Subject: [PATCH 8166/9987] [Score-P 8.0] Fix CUDA issue --- .../Score-P-8.0-gompi-2021b-CUDA-11.4.1.eb | 6 +- .../Score-P-8.0-gompi-2022a-CUDA-11.7.0.eb | 6 +- ...Score-P-8.0_fix-race-in-CUDA-adapter.patch | 59 +++++++++++++++++++ 3 files changed, 69 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-race-in-CUDA-adapter.patch diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b-CUDA-11.4.1.eb index 3d4041c3221..b08c8e04f25 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2021b-CUDA-11.4.1.eb @@ -27,7 +27,11 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['4c0f34f20999f92ebe6ca1ff706d0846b8ce6cd537ffbedb49dfaef0faa66311'] +patches = ['Score-P-8.0_fix-race-in-CUDA-adapter.patch'] +checksums = [ + {'scorep-8.0.tar.gz': '4c0f34f20999f92ebe6ca1ff706d0846b8ce6cd537ffbedb49dfaef0faa66311'}, + {'Score-P-8.0_fix-race-in-CUDA-adapter.patch': '6ba0e486fedc9a87b9b1a4657af7ee5f95b6222ee68ddaa5363dcaa99171fa0b'}, +] dependencies = [ ('CUDA', '11.4.1', '', SYSTEM), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a-CUDA-11.7.0.eb index e16a1e6fc6d..c483455077f 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a-CUDA-11.7.0.eb @@ -27,7 +27,11 @@ toolchain = {'name': 'gompi', 'version': '2022a'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['4c0f34f20999f92ebe6ca1ff706d0846b8ce6cd537ffbedb49dfaef0faa66311'] +patches = ['Score-P-8.0_fix-race-in-CUDA-adapter.patch'] +checksums = [ + {'scorep-8.0.tar.gz': '4c0f34f20999f92ebe6ca1ff706d0846b8ce6cd537ffbedb49dfaef0faa66311'}, + {'Score-P-8.0_fix-race-in-CUDA-adapter.patch': '6ba0e486fedc9a87b9b1a4657af7ee5f95b6222ee68ddaa5363dcaa99171fa0b'}, +] dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-race-in-CUDA-adapter.patch b/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-race-in-CUDA-adapter.patch new file mode 100644 index 00000000000..c232c915a2c --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-race-in-CUDA-adapter.patch @@ -0,0 +1,59 @@ +Fix a race condition in the CUDA adapter which leads to +> [Score-P] src/adapters/cuda/scorep_cupti4_activity.c:651: Fatal: Assertion 'free_buffer->valid_size == 0' failed +aborting the application + +Author: Alexander Grund (TU Dresden) +--- + src/adapters/cuda/scorep_cupti4_activity.c | 15 ++++++++++----- + 1 file changed, 10 insertions(+), 5 deletions(-) + +diff --git a/src/adapters/cuda/scorep_cupti4_activity.c b/src/adapters/cuda/scorep_cupti4_activity.c +index 4464b198c2..d47bf6223d 100644 +--- a/src/adapters/cuda/scorep_cupti4_activity.c ++++ b/src/adapters/cuda/scorep_cupti4_activity.c +@@ -553,14 +553,14 @@ mark_complete_buffer( uint8_t* buffer, + return NULL; + } + +- /* mark entry to contain completed, pending records*/ +- buffer_entry->committed = false; ++ buffer_entry->valid_size = validSize; ++ buffer_entry->stream_id = streamId; ++ /* mark entry to contain completed, pending records */ + if ( validSize > 0 ) + { + buffer_entry->pending = true; + } +- buffer_entry->valid_size = validSize; +- buffer_entry->stream_id = streamId; ++ buffer_entry->committed = false; + return result; + } + +@@ -633,6 +633,7 @@ get_free_buffer( scorep_cupti_context* context ) + + free_buffer->buffer = SCOREP_CUPTI_ACTIVITY_ALIGN_BUFFER( free_buffer->buffer ); + free_buffer->pending = false; ++ free_buffer->committed = true; + free_buffer->size = scorep_cupti_activity_buffer_chunk_size; + free_buffer->valid_size = 0; + +@@ -647,10 +648,14 @@ get_free_buffer( scorep_cupti_context* context ) + activity->buffers = free_buffer; + } + } ++ else ++ { ++ free_buffer->committed = true; ++ } ++ + + UTILS_ASSERT( free_buffer->valid_size == 0 ); + +- free_buffer->committed = true; + free_buffer->stream_id = 0; + + return free_buffer; +-- +GitLab + From ca3db9ad837cc1f3dc746c58b206558ef641ff0c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 28 Jul 2023 14:21:35 +0200 Subject: [PATCH 8167/9987] Fix CMake configs of Abseil --- .../easyconfigs/a/Abseil/Abseil-20210324.2-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb | 3 ++- .../easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb | 3 ++- .../easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb | 3 ++- 4 files changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20210324.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20210324.2-GCCcore-11.2.0.eb index 02f2ee7dc25..e68cf117046 100644 --- a/easybuild/easyconfigs/a/Abseil/Abseil-20210324.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20210324.2-GCCcore-11.2.0.eb @@ -21,7 +21,7 @@ builddependencies = [ ('CMake', '3.21.1'), ] -configopts = '-DBUILD_SHARED_LIBS=ON ' +build_shared_libs = True sanity_check_paths = { 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb index ae09e8b085b..48b976f0841 100644 --- a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb @@ -21,7 +21,8 @@ builddependencies = [ ('CMake', '3.24.3'), ] -configopts = '-DBUILD_SHARED_LIBS=ON ' +build_shared_libs = True +configopts = '-DABSL_PROPAGATE_CXX_STD=ON ' sanity_check_paths = { 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb index ac3526452ed..bb35f74269d 100644 --- a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb @@ -21,7 +21,8 @@ builddependencies = [ ('CMake', '3.24.3'), ] -configopts = '-DBUILD_SHARED_LIBS=ON ' +build_shared_libs = True +configopts = '-DABSL_PROPAGATE_CXX_STD=ON ' sanity_check_paths = { 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb index b76e53de45b..c50c396f801 100644 --- a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb @@ -21,7 +21,8 @@ builddependencies = [ ('CMake', '3.26.3'), ] -configopts = '-DBUILD_SHARED_LIBS=ON ' +build_shared_libs = True +configopts = '-DABSL_PROPAGATE_CXX_STD=ON ' sanity_check_paths = { 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], From 4e7f1edf1cba28ee7d91c74b9dff721edad0a9a8 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 28 Jul 2023 14:40:35 +0200 Subject: [PATCH 8168/9987] correct versionsuffix to suite filename --- .../Amber/Amber-22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/Amber/Amber-22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0.eb index a60a8c02006..61dca38c61d 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.4-foss-2022a-AmberTools-22.5-CUDA-11.7.0.eb @@ -4,7 +4,7 @@ local_ambertools_ver = 22 # Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php patchlevels = (5, 4) # (AmberTools, Amber) version = '%s.%s' % (local_amber_ver, patchlevels[1]) -versionsuffix = '-AmberTools-%s.%s-%%(cudaver)s' % (local_ambertools_ver, patchlevels[0]) +versionsuffix = '-AmberTools-%s.%s-CUDA-%%(cudaver)s' % (local_ambertools_ver, patchlevels[0]) homepage = 'https://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing From 19cb4c953d41cf816185cebe7f7ac12c7b0a827a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 28 Jul 2023 17:05:08 +0200 Subject: [PATCH 8169/9987] adding easyconfigs: Hybpiper-2.1.6-foss-2022b.eb, DIAMOND-2.1.8-GCC-12.2.0.eb, parallel-20230722-GCCcore-12.2.0.eb, psutil-5.9.5-GCCcore-12.2.0.eb --- .../d/DIAMOND/DIAMOND-2.1.8-GCC-12.2.0.eb | 25 ++++++++ .../h/Hybpiper/Hybpiper-2.1.6-foss-2022b.eb | 58 +++++++++++++++++++ .../parallel-20230722-GCCcore-12.2.0.eb | 26 +++++++++ .../p/psutil/psutil-5.9.5-GCCcore-12.2.0.eb | 26 +++++++++ 4 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/h/Hybpiper/Hybpiper-2.1.6-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/psutil/psutil-5.9.5-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-12.2.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-12.2.0.eb new file mode 100644 index 00000000000..980b6fffc53 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.1.8' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +github_account = 'bbuchfink' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b6088259f2bc92d1f9dc4add44590cff68321bcbf91eefbc295a3525118b9415'] + +builddependencies = [('CMake', '3.24.3')] +dependencies = [('zlib', '1.2.12')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["%(namelower)s help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/Hybpiper/Hybpiper-2.1.6-foss-2022b.eb b/easybuild/easyconfigs/h/Hybpiper/Hybpiper-2.1.6-foss-2022b.eb new file mode 100644 index 00000000000..c87bbddded1 --- /dev/null +++ b/easybuild/easyconfigs/h/Hybpiper/Hybpiper-2.1.6-foss-2022b.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'Hybpiper' +version = '2.1.6' + +homepage = 'https://github.com/mossmatters/HybPiper' +description = """HybPiper was designed for targeted sequence capture, + in which DNA sequencing libraries are enriched for gene regions of interest, + especially for phylogenetics. HybPiper is a suite of Python scripts/modules + that wrap and connect bioinformatics tools in order to extract target + sequences from high-throughput DNA sequencing reads.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('Seaborn', '0.12.2'), + ('matplotlib', '3.7.0'), + ('SciPy-bundle', '2023.02'), + ('Biopython', '1.81'), + ('psutil', '5.9.5'), + ('Exonerate', '2.4.0'), + ('BLAST+', '2.14.0'), + ('DIAMOND', '2.1.8'), + ('BWA', '0.7.17'), + ('BBMap', '39.01'), + ('SPAdes', '3.15.4'), + ('parallel', '20230722'), + ('SAMtools', '1.17'), + ('MAFFT', '7.505', '-with-extensions'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('Pebble', '5.0.3', { + 'checksums': ['bdcfd9ea7e0aedb895b204177c19e6d6543d9962f4e3402ebab2175004863da8'], + }), + ('progressbar2', '4.2.0', { + 'modulename': 'progressbar', + 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], + }), + ('python-utils', '3.7.0', { + 'checksums': ['1970468fff1c0adbd60b9a751e6a786223a9f0373c954571912d9cf4be49b552'], + }), + (name, version, { + 'source_urls': ['https://github.com/mossmatters/HybPiper/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['ac175b2b02cd9fcc1d195a4edd68dd1e004c6d2e2bb5658f4cce9b2a4339b4c9'], + }), +] + +sanity_check_commands = [ + "hybpiper check_dependencies" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..4d1487aacf5 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20230722' + +homepage = 'https://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['55f991ad195a72f0abfaf1ede8fc1d03dd255cac91bc5eb900f9aa2873d1ff87'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Perl', '5.36.0')] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +sanity_check_commands = ["parallel --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f51a55120b6 --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.5-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '5.9.5' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['5410638e4df39c54d957fc51ce03048acd8e6d60abc0f5107af51e5fb566eb3c'], + }), +] + +moduleclass = 'lib' From d415452bb48e72925f089c57f6b8ccb1a6369aa3 Mon Sep 17 00:00:00 2001 From: ariel Date: Fri, 28 Jul 2023 17:47:00 +0200 Subject: [PATCH 8170/9987] adding easyconfigs: IPython-8.14.0-GCCcore-12.2.0.eb, JupyterHub-4.0.1-GCCcore-12.2.0.eb, JupyterLab-4.0.3-GCCcore-12.2.0.eb, jupyter-server-2.7.0-GCCcore-12.2.0.eb, jupyter-server-proxy-3.2.2-GCCcore-12.2.0.eb --- .../IPython/IPython-8.14.0-GCCcore-12.2.0.eb | 86 ++++++++++ .../JupyterHub-4.0.1-GCCcore-12.2.0.eb | 112 +++++++++++++ .../JupyterLab-4.0.3-GCCcore-12.2.0.eb | 120 ++++++++++++++ ...pyter-server-proxy-3.2.2-GCCcore-12.2.0.eb | 46 ++++++ .../jupyter-server-2.7.0-GCCcore-12.2.0.eb | 154 ++++++++++++++++++ 5 files changed, 518 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..837ae902ebe --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.2.0.eb @@ -0,0 +1,86 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '8.14.0' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('ZeroMQ', '4.3.4'), + ('lxml', '4.9.2'), + ('BeautifulSoup', '4.11.1'), +] + +use_pip = True + +# for the matplotlib-inline required extention we avoid the import sanity check +# as it will fail without matplotlib in the environment, but ipython devs prefer not to make +# matplotlib a required dep (https://github.com/ipython/matplotlib-inline/issues/4) +# we follow the same convention and we not set matplotlib as dependency + +exts_list = [ + ('traitlets', '5.9.0', { + 'checksums': ['f6cde21a9c68cf756af02035f72d5a723bf607e862e7be33ece505abf4a3bad9'], + }), + ('pure_eval', '0.2.2', { + 'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3'], + }), + ('executing', '1.2.0', { + 'checksums': ['19da64c18d2d851112f09c287f8d3dbbdf725ab0e569077efb6cdcbd3497c107'], + }), + ('asttokens', '2.2.1', { + 'checksums': ['4622110b2a6f30b77e1473affaa97e711bc2f07d3f10848420ff1898edbe94f3'], + }), + ('stack_data', '0.6.2', { + 'checksums': ['32d2dd0376772d01b6cb9fc996f3c8b57a357089dec328ed4b6553d037eaf815'], + }), + ('prompt_toolkit', '3.0.39', { + 'checksums': ['04505ade687dc26dc4284b1ad19a83be2f2afe83e7a828ace0c72f3a1df72aac'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('matplotlib-inline', '0.1.6', { + 'modulename': False, # see comment above + 'checksums': ['f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304'], + }), + ('parso', '0.8.3', { + 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], + }), + ('jedi', '0.18.2', { + 'checksums': ['bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['1d197b907b6ba441b692c48cf2a3a2de280dc0ac91a3405b39349a50272ca0a1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/IPython', + ], +} + +sanity_check_commands = [ + "ipython -h", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2fb61674d32 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.1-GCCcore-12.2.0.eb @@ -0,0 +1,112 @@ +easyblock = 'PythonBundle' + +name = 'JupyterHub' +version = '4.0.1' + +homepage = 'https://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed + for centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = { + ('binutils', '2.39'), +} + +dependencies = [ + ('Python', '3.10.8'), + ('IPython', '8.14.0'), + ('Mako', '1.2.4'), + ('configurable-http-proxy', '4.5.5'), + ('OpenSSL', '1.1', '', SYSTEM), + ('jupyter-server-proxy', '3.2.2'), # optional, but commonly used together + ('PycURL', '7.45.2'), # optional, recommended with large number of users +] + +use_pip = True + +exts_list = [ + ('certipy', '0.1.3', { + 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], + }), + ('pamela', '1.1.0', { + 'checksums': ['d4b139fe600e192e176a2a368059207a6bffa0e7879879b13f4fcba0163481be'], + }), + ('greenlet', '2.0.2', { + 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('SQLAlchemy', '2.0.19', { + 'checksums': ['77a14fa20264af73ddcdb1e2b9c5a829b8cc6b8304d0f093271980e36c200a3f'], + }), + ('alembic', '1.11.1', { + 'checksums': ['6a810a6b012c88b33458fceb869aef09ac75d6ace5291915ba7fae44de372c01'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('pyOpenSSL', '23.2.0', { + 'modulename': 'OpenSSL', + 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], + }), + ('ruamel.yaml', '0.17.32', { + 'checksums': ['ec939063761914e14542972a5cba6d33c23b0859ab6342f61cf070cfc600efc2'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('jupyter-telemetry', '0.1.0', { + 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', + 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], + }), + ('jupyterhub', version, { + 'checksums': ['8e283ff59e5c4016712077d2549ed74acd915a32836fe00218678a8781bd7ede'], + }), + ('batchspawner', '1.2.0', { + 'checksums': ['b1924bb4f3a3f527a1e312ecdaff3dbc5acfd91e6b13cf074a62cd74340a2e21'], + }), + ('jupyterhub-systemdspawner', '1.0.1', { + 'modulename': 'systemdspawner', + 'checksums': ['8d614f19d89564321fe55d80ecd134a0e2bf276274d45861495c9bb5a80add28'], + }), + ('jupyterhub-simplespawner', '0.1', { + 'modulename': 'simplespawner', + 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], + }), + ('ldap3', '2.9.1', { + 'checksums': ['f3e7fc4718e3f09dda568b57100095e0ce58633bcabbed8667ce3f8fbaa4229f'], + }), + ('jupyterhub-ldapauthenticator', '1.3.2', { + 'modulename': 'ldapauthenticator', + 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('jupyterhub-jwtauthenticator-v2', '2.0.3', { + 'modulename': 'jwtauthenticator', + 'checksums': ['b94b6dff8246250904c5ee511da3f062680eb657dabe766d75993cbe72747d41'], + }), + ('onetimepass', '1.0.1', { + 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], + }), + ('jupyterhub-nativeauthenticator', '1.2.0', { + 'modulename': 'nativeauthenticator', + 'checksums': ['826228e6e9ca37736361e2e60c5723e245ec72e34fdc42cc218fc54a67f968e1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyterhub'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], +} + +sanity_pip_check = True + +sanity_check_commands = ['jupyterhub --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d068c655cf5 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb @@ -0,0 +1,120 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '4.0.3' + +homepage = "https://jupyter.org/" +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), + ('maturin', '1.1.0'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.0'), +] + +use_pip = True +sanity_pip_check = True + +# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them +# use the versions published in a single release commit instead of blindly pushing to last available version, +# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa + +exts_list = [ + ('trove-classifiers', '2023.7.6', { + 'source_tmpl': 'trove_classifiers-%(version)s-py3-none-any.whl', + 'checksums': ['b420d5aa048ee7c456233a49203f7d58d1736af4a6cde637657d78c13ab7969b'], + }), + ('hatchling', '1.18.0', { + 'checksums': ['50e99c3110ce0afc3f7bdbadff1c71c17758e476731c27607940cfa6686489ca'], + }), + ('attrs', '23.1.0', { + 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], + }), + ('rpds_py', '0.9.2', { + 'modulename': 'rpds', + 'checksums': ['8d70e8f14900f2657c249ea4def963bed86a29b81f81f5b76b5a9215680de945'], + }), + ('referencing', '0.30.0', { + 'checksums': ['47237742e990457f7512c7d27486394a9aadaf876cbfaa4be65b27b4f4d47c6b'], + }), + ('jsonschema_specifications', '2023.7.1', { + 'checksums': ['c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb'], + }), + ('jsonschema', '4.18.4', { + 'checksums': ['fb3642735399fa958c0d2aad7057901554596c63349f4f6b283c493cf692a25d'], + }), + ('notebook_shim', '0.2.3', { + 'checksums': ['f69388ac283ae008cd506dda10d0288b09a017d822d5e8c7129a152cbd3ce7e9'], + }), + ('json5', '0.9.14', { + 'checksums': ['9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02'], + }), + ('jupyterlab_server', '2.23.0', { + 'checksums': ['83c01aa4ad9451cd61b383e634d939ff713850f4640c0056b2cdb2b6211a74c7'], + }), + ('jupyter-lsp', '2.2.0', { + 'checksums': ['8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1'], + }), + ('nest_asyncio', '1.5.6', { + 'checksums': ['d267cc1ff794403f7df692964d1d2a3fa9418ffea2a3f6859a439ff482fef290'], + }), + ('debugpy', '1.6.7', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['53f7a456bc50706a0eaabecf2d3ce44c4d5010e46dfc65b6b81a518b42866267'], + }), + ('comm', '0.1.3', { + 'checksums': ['a61efa9daffcfbe66fd643ba966f846a624e4e6d6767eda9cf6e993aadaab93e'], + }), + ('ipykernel', '6.25.0', { + 'checksums': ['e342ce84712861be4b248c4a73472be4702c1b0dd77448bfd6bcfb3af9d5ddf9'], + }), + ('async-lru', '2.0.3', { + 'checksums': ['b714c9d1415fca4e264da72a9e2abc66880ce7430e03a973341f88ea4c0d4869'], + }), + ('jupyterlab', version, { + 'checksums': ['e14d1ce46a613028111d0d476a1d7d6b094003b7462bac669f5b478317abcb39'], + }), + ('jupyterlab_widgets', '3.0.8', { + 'checksums': ['d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a'], + }), + ('widgetsnbextension', '4.0.8', { + 'checksums': ['9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17'], + }), + ('ipywidgets', '8.0.7', { + 'checksums': ['50ace0a8886e9a0d68b980db82f94c25d55d21ff2340ed36f802dd9365e94acf'], + }), +] + +sanity_check_commands = ["jupyter lab --help"] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} + +# keep user's configuration in their home directory +# note: '~' is not expanded by JupyterLab +modluafooter = """ +setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) +setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) +""" +modtclfooter = """ +setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" +setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" +""" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2b029331d33 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-12.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server-proxy' +version = '3.2.2' + +homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' +description = """Jupyter Server Proxy lets you run arbitrary external processes +(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) +alongside your notebook server and provide authenticated web access to them +using a path like /rstudio next to others like /lab. Alongside the python +package that provides the main functionality, the JupyterLab extension +(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window +to get to RStudio for example.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.0'), + ('OpenSSL', '1.1', '', SYSTEM), + ('aiohttp', '3.8.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('simpervisor', '0.4', { + 'checksums': ['cec79e13cdbd6edb04a5c98c1ff8d4bd9713e706c069226909a1ef0e89d393c5'], + }), + (name, version, { + 'checksums': ['54690ea9467035d187c930c599e76065017baf16e118e6eebae0d3a008c4d946'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9da8e125687 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb @@ -0,0 +1,154 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = '2.7.0' + +homepage = "https://jupyter.org/" +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST +endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and +Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('IPython', '8.14.0'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('hatch_nodejs_version', '0.3.1', { + 'checksums': ['0e55fd713d92c5c1ccfee778efecaa780fd8bcd276d4ca7aff9f6791f6f76d9c'], + }), + ('hatch_jupyter_builder', '0.8.3', { + 'checksums': ['0dbd14a8aef6636764f88a8fd1fcc9a91921e5c50356e6aab251782f264ae960'], + }), + ('websocket-client', '1.6.1', { + 'modulename': 'websocket', + 'checksums': ['c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd'], + }), + ('tornado', '6.3.2', { + 'checksums': ['4b927c4f19b71e627b13f3db2324e4ae660527143f9e1f2e2fb404f3a187e2ba'], + }), + ('terminado', '0.17.1', { + 'checksums': ['6ccbbcd3a4f8a25a5ec04991f39a0b8db52dfcd487ea0e578d977e6752380333'], + }), + ('Send2Trash', '1.8.2', { + 'checksums': ['c132d59fa44b9ca2b1699af5c86f57ce9f4c5eb56629d5d55fbb7a35f84e2312'], + }), + ('pyzmq', '25.1.0', { + 'modulename': 'zmq', + 'checksums': ['80c41023465d36280e801564a69cbfce8ae85ff79b080e1913f6e90481fb8957'], + }), + ('prometheus_client', '0.17.1', { + 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], + }), + ('overrides', '7.3.1', { + 'checksums': ['8b97c6c1e1681b78cbc9424b138d880f0803c2254c5ebaabdde57bb6c62093f2'], + }), + ('jupyter_core', '5.3.1', { + 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], + }), + ('fastjsonschema', '2.17.1', { + 'checksums': ['f4eeb8a77cef54861dbf7424ac8ce71306f12cbb086c45131bcba2c6a4f726e3'], + }), + ('tinycss2', '1.2.1', { + 'checksums': ['8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627'], + }), + ('pandocfilters', '1.5.0', { + 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], + }), + ('mistune', '3.0.1', { + 'checksums': ['e912116c13aa0944f9dc530db38eb88f6a77087ab128f49f84a48f4c05ea163c'], + }), + ('jupyter_packaging', '0.12.3', { + 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], + }), + ('jupyterlab_pygments', '0.2.2', { + 'checksums': ['7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('bleach', '6.0.0', { + 'checksums': ['1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('nbformat', '5.9.1', { + 'checksums': ['3a7f52d040639cbd8a3890218c8b0ffb93211588c57446c90095e32ba5881b5d'], + }), + ('nbclient', '0.8.0', { + 'checksums': ['f9b179cd4b2d7bca965f900a2ebf0db4a12ebff2f36a711cb66861e4ae158e55'], + }), + ('jupyter_client', '8.3.0', { + 'checksums': ['3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f'], + }), + ('nbconvert', '7.7.2', { + 'checksums': ['36d3e7bf32f0c075878176cdeeb645931c994cbed5b747bc7a570ba8cd2321f3'], + }), + ('jupyter_server_terminals', '0.4.4', { + 'checksums': ['57ab779797c25a7ba68e97bcfb5d7740f2b5e8a83b5e8102b10438041a7eac5d'], + }), + ('rfc3986_validator', '0.1.1', { + 'checksums': ['3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055'], + }), + ('rfc3339_validator', '0.1.4', { + 'checksums': ['138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jupyter_events', '0.6.3', { + 'checksums': ['9a6e9995f75d1b7146b436ea24d696ce3a35bfa8bfe45e0c33c334c79464d0b3'], + }), + ('argon2-cffi-bindings', '21.2.0', { + 'modulename': '_argon2_cffi_bindings', + 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], + }), + ('argon2-cffi', '21.3.0', { + 'modulename': 'argon2', + 'checksums': ['d384164d944190a7dd7ef22c6aa3ff197da12962bd04b17f64d4e93d934dba5b'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.7.1', { + 'checksums': ['44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780'], + }), + ('jupyter_server', version, { + 'checksums': ['36da0a266d31a41ac335a366c88933c17dfa5bb817a48f5c02c16d303bc9477f'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +sanity_check_paths = { + 'files': [ + 'bin/jupyter', + ], + 'dirs': [ + 'share/jupyter', + ], +} + +sanity_check_commands = [ + "jupyter --help", +] + +moduleclass = 'tools' From d466a9a487fb568ca6e126f2a9bc444553a25d52 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Jul 2023 17:12:18 +0100 Subject: [PATCH 8171/9987] adding easyconfigs: FreeSurfer-7.4.1-centos7_x86_64.eb, FreeSurfer-7.4.1-centos8_x86_64.eb, FreeSurfer-7.4.1-ubuntu20_amd64.eb, FreeSurfer-7.4.1-ubuntu22_amd64.eb and patches: freesurfer-7.4.1-hardcoded-path.patch --- .../FreeSurfer-7.4.1-centos7_x86_64.eb | 30 +++++++++ .../FreeSurfer-7.4.1-centos8_x86_64.eb | 30 +++++++++ .../FreeSurfer-7.4.1-ubuntu20_amd64.eb | 30 +++++++++ .../FreeSurfer-7.4.1-ubuntu22_amd64.eb | 30 +++++++++ .../freesurfer-7.4.1-hardcoded-path.patch | 64 +++++++++++++++++++ 5 files changed, 184 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-centos7_x86_64.eb create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-centos8_x86_64.eb create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu20_amd64.eb create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu22_amd64.eb create mode 100644 easybuild/easyconfigs/f/FreeSurfer/freesurfer-7.4.1-hardcoded-path.patch diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-centos7_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-centos7_x86_64.eb new file mode 100644 index 00000000000..bb76714227e --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-centos7_x86_64.eb @@ -0,0 +1,30 @@ +name = 'FreeSurfer' +version = '7.4.1' +versionsuffix = '-centos7_x86_64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/'] +sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz'] +patches = ['%(namelower)s-%(version)s-hardcoded-path.patch'] +checksums = [ + {'freesurfer-linux-centos7_x86_64-7.4.1.tar.gz': + '313a96caeb246c5985f483633b5cf43f86ed8f7ccc6d6acfac8eedb638443010'}, + {'freesurfer-7.4.1-hardcoded-path.patch': 'f75d8eeb90086d290b8122c5174b77c210ea5d900bdc3040736aef4d69e65295'}, +] + +dependencies = [('MCR', 'R2019b.8')] + +postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-centos8_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-centos8_x86_64.eb new file mode 100644 index 00000000000..965b5259c75 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-centos8_x86_64.eb @@ -0,0 +1,30 @@ +name = 'FreeSurfer' +version = '7.4.1' +versionsuffix = '-centos8_x86_64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/'] +sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz'] +patches = ['%(namelower)s-%(version)s-hardcoded-path.patch'] +checksums = [ + {'freesurfer-linux-centos8_x86_64-7.4.1.tar.gz': + '302f2745886fcb571f2050bc2e2a7b4ff982e844bcc20c842d0d0b32b514c56a'}, + {'freesurfer-7.4.1-hardcoded-path.patch': 'f75d8eeb90086d290b8122c5174b77c210ea5d900bdc3040736aef4d69e65295'}, +] + +dependencies = [('MCR', 'R2019b.8')] + +postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu20_amd64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu20_amd64.eb new file mode 100644 index 00000000000..984c6cdfbf1 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu20_amd64.eb @@ -0,0 +1,30 @@ +name = 'FreeSurfer' +version = '7.4.1' +versionsuffix = '-ubuntu20_amd64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/'] +sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz'] +patches = ['%(namelower)s-%(version)s-hardcoded-path.patch'] +checksums = [ + {'freesurfer-linux-ubuntu20_amd64-7.4.1.tar.gz': + 'f61ab4bf6594f996e1a664eb00ab60fb731b7642751bacd4f32a915820a1d7c8'}, + {'freesurfer-7.4.1-hardcoded-path.patch': 'f75d8eeb90086d290b8122c5174b77c210ea5d900bdc3040736aef4d69e65295'}, +] + +dependencies = [('MCR', 'R2019b.8')] + +postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu22_amd64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu22_amd64.eb new file mode 100644 index 00000000000..d7d14eab1c5 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.4.1-ubuntu22_amd64.eb @@ -0,0 +1,30 @@ +name = 'FreeSurfer' +version = '7.4.1' +versionsuffix = '-ubuntu22_amd64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = ['https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/'] +sources = ['%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz'] +patches = ['%(namelower)s-%(version)s-hardcoded-path.patch'] +checksums = [ + {'freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz': + '6db470445f3b2e973fcfdc9231c775896e54a4dbfc4ce0d5ef5775bc7dca182d'}, + {'freesurfer-7.4.1-hardcoded-path.patch': 'f75d8eeb90086d290b8122c5174b77c210ea5d900bdc3040736aef4d69e65295'}, +] + +dependencies = [('MCR', 'R2019b.8')] + +postinstallcmds = ["ln -s $EBROOTMCR/v97 %(installdir)s/MCRv97"] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FreeSurfer/freesurfer-7.4.1-hardcoded-path.patch b/easybuild/easyconfigs/f/FreeSurfer/freesurfer-7.4.1-hardcoded-path.patch new file mode 100644 index 00000000000..84e81f19d68 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/freesurfer-7.4.1-hardcoded-path.patch @@ -0,0 +1,64 @@ +A bug was discovered in FreeSurver versions 7.4.0 and 7.4.1 which means the path to freesurver is hard coded. +See: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all-clinical +Thanks to Santiago Lacalle Puig (Imperial College London/UK) for this. +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/freesurfer.orig/bin/recon-all-clinical.sh b/freesurfer/bin/recon-all-clinical.sh +index 7af36a5..f0906d9 100755 +--- a/freesurfer.orig/bin/recon-all-clinical.sh ++++ b/freesurfer/bin/recon-all-clinical.sh +@@ -20,9 +20,9 @@ if( $1 == "--help") then + echo " " + echo "Use this script to process clinical scans of arbitrary orientation, resolution, and " + echo "contrast. It essentially runs a combination of:" +- echo "* SynthSeg: to obtain an aseg.auto_noCCseg.mgz and to compute a Talairach transform" +- echo "* SynthSR: not really needed for volumes / surfaces, but still nice to have a 1mm MPRAGE" +- echo "* SynthSurfaces (or whatever Karthik will name it!): to fit surfaces." ++ echo "* SynthSeg: to obtain a volumetric segmentation and linear registration to Talairach space" ++ echo "* SynthSR: to have a higher resolution 1mm MPRAGE for visualization" ++ echo "* SynthDist: to fit surfaces by predicting the distance maps and reconstructing topologically accurate cortical surfaces" + echo " " + echo "Using this module is very simple: you just provide an input scan, the subject name, the" + echo "number of threads you want to use, and (optionally) the subjects directory:" +@@ -560,7 +560,7 @@ set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsavera + $cmd |& tee -a $LogFile + set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject $SNAME --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface" + $cmd |& tee -a $LogFile +-set cmd="mris_label2annot --s $SNAME --ctab /usr/local/freesurfer/dev/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label" ++set cmd="mris_label2annot --s $SNAME --ctab $FREESURFER_HOME/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label" + $cmd |& tee -a $LogFile + set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject $SNAME --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface" + $cmd |& tee -a $LogFile +@@ -590,9 +590,9 @@ set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsavera + $cmd |& tee -a $LogFile + set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject $SNAME --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface" + $cmd |& tee -a $LogFile +-set cmd="mris_label2annot --s $SNAME --hemi lh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose" ++set cmd="mris_label2annot --s $SNAME --hemi lh --ctab $FREESURFER_HOME/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose" + $cmd |& tee -a $LogFile +-set cmd="mris_label2annot --s $SNAME --hemi lh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose" ++set cmd="mris_label2annot --s $SNAME --hemi lh --ctab $FREESURFER_HOME/average/colortable_BA_thresh.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose" + $cmd |& tee -a $LogFile + set cmd="mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab $SNAME lh white" + $cmd |& tee -a $LogFile +@@ -642,7 +642,7 @@ set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsavera + $cmd |& tee -a $LogFile + set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject $SNAME --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface" + $cmd |& tee -a $LogFile +-set cmd="mris_label2annot --s $SNAME --ctab /usr/local/freesurfer/dev/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label" ++set cmd="mris_label2annot --s $SNAME --ctab $FREESURFER_HOME/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label" + $cmd |& tee -a $LogFile + set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject $SNAME --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface" + $cmd |& tee -a $LogFile +@@ -672,9 +672,9 @@ set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsavera + $cmd |& tee -a $LogFile + set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject $SNAME --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface" + $cmd |& tee -a $LogFile +-set cmd="mris_label2annot --s $SNAME --hemi rh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose" ++set cmd="mris_label2annot --s $SNAME --hemi rh --ctab $FREESURFER_HOME/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose" + $cmd |& tee -a $LogFile +-set cmd="mris_label2annot --s $SNAME --hemi rh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose" ++set cmd="mris_label2annot --s $SNAME --hemi rh --ctab $FREESURFER_HOME/average/colortable_BA_thresh.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose" + $cmd |& tee -a $LogFile + set cmd="mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab $SNAME rh white" + $cmd |& tee -a $LogFile + From c755f9af9bace92ee19793ef947e4ce9c21c5c17 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 30 Jul 2023 12:15:45 +0200 Subject: [PATCH 8172/9987] adding easyconfigs: GCC-13.2.0.eb, GCCcore-13.2.0.eb, binutils-2.40-GCCcore-13.2.0.eb, Bison-3.8.2-GCCcore-13.2.0.eb, flex-2.6.4-GCCcore-13.2.0.eb, help2man-1.49.3-GCCcore-13.2.0.eb, M4-1.4.19-GCCcore-13.2.0.eb, zlib-1.2.13-GCCcore-13.2.0.eb --- .../b/Bison/Bison-3.8.2-GCCcore-13.2.0.eb | 28 +++++++++ .../binutils/binutils-2.40-GCCcore-13.2.0.eb | 31 +++++++++ .../f/flex/flex-2.6.4-GCCcore-13.2.0.eb | 34 ++++++++++ easybuild/easyconfigs/g/GCC/GCC-13.2.0.eb | 22 +++++++ .../easyconfigs/g/GCCcore/GCCcore-13.2.0.eb | 63 +++++++++++++++++++ .../help2man-1.49.3-GCCcore-13.2.0.eb | 25 ++++++++ .../m/M4/M4-1.4.19-GCCcore-13.2.0.eb | 29 +++++++++ .../z/zlib/zlib-1.2.13-GCCcore-13.2.0.eb | 27 ++++++++ 8 files changed, 259 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCC/GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..77e6f24f18e --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.40', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3d83b04688d --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.40' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d7f82c4047decf43a6f769ac32456a92ddb6932409a585c633cdd4e9df23d956'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', SYSTEM) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.13'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a9504117294 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'https://github.com/westes/flex' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.40', '', SYSTEM), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GCC/GCC-13.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-13.2.0.eb new file mode 100644 index 00000000000..174dfc982ce --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-13.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '13.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.40', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c71dc05e7aa --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '13.2.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.2.0.tar.bz2', + 'mpc-1.3.1.tar.gz', + 'isl-0.26.tar.bz2', + 'newlib-4.3.0.20230120.tar.gz', + {'download_filename': '2c6d503.tar.gz', 'filename': 'nvptx-tools-20230725.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + {'gcc-13.2.0.tar.gz': '8cb4be3796651976f94b9356fa08d833524f62420d6292c5033a9a26af315078'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.2.0.tar.bz2': '691db39178e36fc460c046591e4b0f2a52c8f2b3ee6d750cc2eab25f1eaa999d'}, + {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'}, + {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'}, + {'newlib-4.3.0.20230120.tar.gz': '83a62a99af59e38eb9b0c58ed092ee24d700fff43a22c03e433955113ef35150'}, + {'nvptx-tools-20230725.tar.gz': '17ce1f2c64f09c6f1cb709e3af869bb90b0102c412f25da55f338e35bc74b2e2'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.40'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..371d5d25c68 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.40', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ce39b7d1490 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.40', '', SYSTEM)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..329c00a1953 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.13' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.40', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 8cd2d0290b965b661f26b4749996f40df6fd467e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 31 Jul 2023 09:48:39 +0200 Subject: [PATCH 8173/9987] adding easyconfigs: Score-P-8.1-gompi-2022b-CUDA-12.0.0.eb, Score-P-8.1-gompi-2022b.eb, SIONlib-1.7.7-GCCcore-12.2.0-tools.eb, PDT-3.25.1-GCCcore-12.2.0.eb, PAPI-7.0.1-GCCcore-12.2.0.eb, OTF2-3.0.3-GCCcore-12.2.0.eb, OPARI2-2.0.7-GCCcore-12.2.0.eb, CubeLib-4.8.1-GCCcore-12.2.0.eb, CubeWriter-4.8.1-GCCcore-12.2.0.eb and patches: Score-P-8.0_fix-race-in-CUDA-adapter.patch --- .../c/CubeLib/CubeLib-4.8.1-GCCcore-12.2.0.eb | 53 +++++++++++++++ .../CubeWriter-4.8.1-GCCcore-12.2.0.eb | 53 +++++++++++++++ .../o/OPARI2/OPARI2-2.0.7-GCCcore-12.2.0.eb | 44 +++++++++++++ .../o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb | 50 ++++++++++++++ .../p/PAPI/PAPI-7.0.1-GCCcore-12.2.0.eb | 47 +++++++++++++ .../p/PDT/PDT-3.25.1-GCCcore-12.2.0.eb | 37 +++++++++++ .../SIONlib-1.7.7-GCCcore-12.2.0-tools.eb | 51 ++++++++++++++ ...Score-P-8.0_fix-race-in-CUDA-adapter.patch | 59 +++++++++++++++++ .../Score-P-8.1-gompi-2022b-CUDA-12.0.0.eb | 66 +++++++++++++++++++ .../s/Score-P/Score-P-8.1-gompi-2022b.eb | 63 ++++++++++++++++++ 10 files changed, 523 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.0.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-race-in-CUDA-adapter.patch create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2022b-CUDA-12.0.0.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2022b.eb diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d0f2aec8541 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.1-GCCcore-12.2.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.8.1' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e4d974248963edab48c5d0fc5831146d391b0ae4632cccafe840bf5f12cd80a9'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0cfe13dabdc --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.1-GCCcore-12.2.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.8.1' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['42cbd743d87c16e805c8e28e79292ab33de259f2cfba46f2682cb35c1bc032d6'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f81187d76cb --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.7' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e302a4cc265eb2a4aa27c16a90eabd9e1e58cb02a191dd1c4d86f9a0df128715'] + +builddependencies = [ + ('binutils', '2.39'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..54478bf62fa --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.2.0.eb @@ -0,0 +1,50 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '3.0.3' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['18a3905f7917340387e3edc8e5766f31ab1af41f4ecc5665da6c769ca21c4ee8'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.7', '-tools'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..77f6a424cdc --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.1-GCCcore-12.2.0.eb @@ -0,0 +1,47 @@ +## +# Author: Robert Mijakovic +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.0.1' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://icl.utk.edu/projects/papi/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c105da5d8fea7b113b0741a943d467a06c98db959ce71bdd9a50b9f03eecc43e'] + +builddependencies = [ + ('binutils', '2.39'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9fa4c7e9fbd --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25.1' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +checksums = ['0b6f8a6b8769c181b2ae6cae7298f04b8e3e3d68066f598ed24574e19500bc97'] + +builddependencies = [ + ('binutils', '2.39'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb new file mode 100644 index 00000000000..5bf659a141a --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.2.0-tools.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.7' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] + +builddependencies = [ + ('binutils', '2.39'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-race-in-CUDA-adapter.patch b/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-race-in-CUDA-adapter.patch new file mode 100644 index 00000000000..c232c915a2c --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0_fix-race-in-CUDA-adapter.patch @@ -0,0 +1,59 @@ +Fix a race condition in the CUDA adapter which leads to +> [Score-P] src/adapters/cuda/scorep_cupti4_activity.c:651: Fatal: Assertion 'free_buffer->valid_size == 0' failed +aborting the application + +Author: Alexander Grund (TU Dresden) +--- + src/adapters/cuda/scorep_cupti4_activity.c | 15 ++++++++++----- + 1 file changed, 10 insertions(+), 5 deletions(-) + +diff --git a/src/adapters/cuda/scorep_cupti4_activity.c b/src/adapters/cuda/scorep_cupti4_activity.c +index 4464b198c2..d47bf6223d 100644 +--- a/src/adapters/cuda/scorep_cupti4_activity.c ++++ b/src/adapters/cuda/scorep_cupti4_activity.c +@@ -553,14 +553,14 @@ mark_complete_buffer( uint8_t* buffer, + return NULL; + } + +- /* mark entry to contain completed, pending records*/ +- buffer_entry->committed = false; ++ buffer_entry->valid_size = validSize; ++ buffer_entry->stream_id = streamId; ++ /* mark entry to contain completed, pending records */ + if ( validSize > 0 ) + { + buffer_entry->pending = true; + } +- buffer_entry->valid_size = validSize; +- buffer_entry->stream_id = streamId; ++ buffer_entry->committed = false; + return result; + } + +@@ -633,6 +633,7 @@ get_free_buffer( scorep_cupti_context* context ) + + free_buffer->buffer = SCOREP_CUPTI_ACTIVITY_ALIGN_BUFFER( free_buffer->buffer ); + free_buffer->pending = false; ++ free_buffer->committed = true; + free_buffer->size = scorep_cupti_activity_buffer_chunk_size; + free_buffer->valid_size = 0; + +@@ -647,10 +648,14 @@ get_free_buffer( scorep_cupti_context* context ) + activity->buffers = free_buffer; + } + } ++ else ++ { ++ free_buffer->committed = true; ++ } ++ + + UTILS_ASSERT( free_buffer->valid_size == 0 ); + +- free_buffer->committed = true; + free_buffer->stream_id = 0; + + return free_buffer; +-- +GitLab + diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2022b-CUDA-12.0.0.eb new file mode 100644 index 00000000000..e34a7ac1c36 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2022b-CUDA-12.0.0.eb @@ -0,0 +1,66 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2023 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '8.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2022b'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +patches = ['Score-P-8.0_fix-race-in-CUDA-adapter.patch'] +checksums = [ + {'scorep-8.1.tar.gz': '3a40b481fce610871ddf6bdfb88a6d06b9e5eb38c6080faac6d5e44990060a37'}, + {'Score-P-8.0_fix-race-in-CUDA-adapter.patch': '6ba0e486fedc9a87b9b1a4657af7ee5f95b6222ee68ddaa5363dcaa99171fa0b'}, +] + +dependencies = [ + ('CUDA', '12.0.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', versionsuffix), + ('CubeLib', '4.8.1'), + ('CubeWriter', '4.8.1'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'cuda_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2022b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2022b.eb new file mode 100644 index 00000000000..27c79bb3945 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2022b.eb @@ -0,0 +1,63 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2023 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '8.1' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2022b'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +patches = ['Score-P-8.0_fix-race-in-CUDA-adapter.patch'] +checksums = [ + {'scorep-8.1.tar.gz': '3a40b481fce610871ddf6bdfb88a6d06b9e5eb38c6080faac6d5e44990060a37'}, + {'Score-P-8.0_fix-race-in-CUDA-adapter.patch': '6ba0e486fedc9a87b9b1a4657af7ee5f95b6222ee68ddaa5363dcaa99171fa0b'}, +] + +dependencies = [ + ('CubeLib', '4.8.1'), + ('CubeWriter', '4.8.1'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 7dd08c114dbc9ed4beec8f45477012380e5bc42c Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 31 Jul 2023 11:55:52 +0200 Subject: [PATCH 8174/9987] adding easyconfigs: MRtrix-3.0.4-foss-2022b.eb --- .../m/MRtrix/MRtrix-3.0.4-foss-2022b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRtrix/MRtrix-3.0.4-foss-2022b.eb diff --git a/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0.4-foss-2022b.eb b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0.4-foss-2022b.eb new file mode 100644 index 00000000000..abec67d835b --- /dev/null +++ b/easybuild/easyconfigs/m/MRtrix/MRtrix-3.0.4-foss-2022b.eb @@ -0,0 +1,29 @@ +name = 'MRtrix' +version = '3.0.4' + +homepage = 'http://www.brain.org.au/software/index.html#mrtrix' +description = """MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner + robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/MRtrix3/mrtrix3/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f1d1aa289cfc3e46e3a8eca93594b23d061c6d50a0cd03727433a7e2cd14f71a'] + +builddependencies = [ + ('Eigen', '3.4.0'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('Python', '3.10.8'), + ('Mesa', '22.2.4'), + ('Qt5', '5.15.7'), + ('LibTIFF', '4.4.0'), + ('FFTW', '3.3.10'), + ('libpng', '1.6.38'), +] + +moduleclass = 'bio' From 214b3d46f24643a3434c942b9c1e465bb20733c4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 31 Jul 2023 13:39:14 +0200 Subject: [PATCH 8175/9987] adding easyconfigs: PyTorch-1.13.1-foss-2022b.eb and patches: PyTorch-1.13.1_fix-gcc-12-compilation.patch, PyTorch-1.13.1_fix-protobuf-dependency.patch, PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch, PyTorch-1.13.1_increase-tolerance-test_ops.patch, PyTorch-1.13.1_skip-tests-without-fbgemm.patch --- .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 127 ++++++++++++++++++ ...yTorch-1.13.1_fix-gcc-12-compilation.patch | 29 ++++ ...Torch-1.13.1_fix-protobuf-dependency.patch | 35 +++++ ...h-1.13.1_fix-warning-in-test-cpp-api.patch | 29 ++++ ...h-1.13.1_increase-tolerance-test_ops.patch | 32 +++-- ...rch-1.13.1_skip-tests-without-fbgemm.patch | 68 ++++++++++ 6 files changed, 307 insertions(+), 13 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-compilation.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-protobuf-dependency.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb new file mode 100644 index 00000000000..8954512e03a --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -0,0 +1,127 @@ +name = 'PyTorch' +version = '1.13.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +patches = [ + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-gcc-12-compilation.patch', + 'PyTorch-1.13.1_fix-protobuf-dependency.patch', + 'PyTorch-1.13.1_fix-pytest-args.patch', + 'PyTorch-1.13.1_fix-test-ops-conf.patch', + 'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch', + 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', + 'PyTorch-1.13.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.13.1_install-vsx-vec-headers.patch', + 'PyTorch-1.13.1_skip-failing-grad-test.patch', +] +checksums = [ + {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.10.0_fix-kineto-crash.patch': 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb'}, + {'PyTorch-1.11.0_fix-fsdp-fp16-test.patch': 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13'}, + {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.1_add-hypothesis-suppression.patch': + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, + {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, + {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, + {'PyTorch-1.12.1_fix-test_wishart_log_prob.patch': + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45'}, + {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, + {'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch': + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d'}, + {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, + {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, + {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-gcc-12-compilation.patch': + '18df8c61ecaa9fb659346c1e172828bca6b069f0145bb8f6a36b0a23b7bef0a6'}, + {'PyTorch-1.13.1_fix-protobuf-dependency.patch': + '8bd755a0cab7233a243bc65ca57c9630dfccdc9bf8c9792f0de4e07a644fcb00'}, + {'PyTorch-1.13.1_fix-pytest-args.patch': 'd3e3c841cf8d73683750f29326f2be56ee0bb5df7ff522baf7d7c3f301a91ec2'}, + {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, + {'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch': + 'bdde0f2105215c95a54de64ec4b1a4520528510663174fef6d5b900eb1db3937'}, + {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '4c636059850fc9d1ecb27ce275f8aad5d5b6fdc19e35aff0c25b86cb3201352a'}, + {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': + 'be83ff61fe2dedab6d49c232936d5622df81ab49154264490021c6c828e53315'}, + {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': + '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, + {'PyTorch-1.13.1_increase-tolerance-test_ops.patch': + 'c909fdfc2b12df457e1eb5514265ffec3eab653994949416f3f048668421e223'}, + {'PyTorch-1.13.1_install-vsx-vec-headers.patch': + '7b678f54bb947afd4767f5877ac424b4b94ce5db609ea20f5a869ccf4027035f'}, + {'PyTorch-1.13.1_skip-failing-grad-test.patch': '6681200f9509893cb9231b5c93ac9bc5e6d9d9ae4febefca52e7cbc843ba8f51'}, +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.24.3'), + ('hypothesis', '6.68.2'), + # For tests + ('pytest-rerunfailures', '12.0'), + ('pytest-shard', '0.1.2'), +] + +dependencies = [ + ('Ninja', '1.11.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.8'), + ('protobuf', '23.0'), + ('protobuf-python', '4.23.0'), + ('pybind11', '2.10.3'), + ('SciPy-bundle', '2023.02'), + ('PyYAML', '6.0'), + ('MPFR', '4.2.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.16'), + ('FFmpeg', '5.1.2'), + ('Pillow', '9.4.0'), + ('expecttest', '0.1.3'), +] + +custom_opts = ['CMAKE_CXX_STANDARD=17'] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + # no xdoctest + 'doctests', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'test_native_mha', + # intermittent failures on various systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'distributed/rpc/test_tensorpipe_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-compilation.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-compilation.patch new file mode 100644 index 00000000000..a74b69d95f4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-compilation.patch @@ -0,0 +1,29 @@ +Add missing headers that are no longer transitively included in GCC 12 + +Author: Alexander Grund (TU Dresden) + +Submodule third_party/gloo contains modified content +diff --git a/third_party/gloo/gloo/transport/ibverbs/pair.h b/third_party/gloo/gloo/transport/ibverbs/pair.h +index 1ccc050..54dbc7e 100644 +--- a/third_party/gloo/gloo/transport/ibverbs/pair.h ++++ b/third_party/gloo/gloo/transport/ibverbs/pair.h +@@ -8,6 +8,7 @@ + + #pragma once + ++#include + #include + #include + #include +diff --git a/third_party/gloo/gloo/transport/tcp/device.cc b/third_party/gloo/gloo/transport/tcp/device.cc +index 05cf0a4..4408d60 100644 +--- a/third_party/gloo/gloo/transport/tcp/device.cc ++++ b/third_party/gloo/gloo/transport/tcp/device.cc +@@ -8,6 +8,7 @@ + + #include "gloo/transport/tcp/device.h" + ++#include + #include + #include + #include diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-protobuf-dependency.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-protobuf-dependency.patch new file mode 100644 index 00000000000..c92a9d49d02 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-protobuf-dependency.patch @@ -0,0 +1,35 @@ +Add proper dependency in libprotobuf target to get the correct set of flags. +Otherwise the build will fail with e.g.: + undefined reference to `google::protobuf::internal::ThreadSafeArena::thread_cache_' +This is caused by missing the `PROTOBUF_USE_DLLS` define required for libprotobuf as a shared library. +See https://github.com/pytorch/pytorch/issues/106297 + +Author: Alexander Grund (TU Dresden) + +diff --git a/caffe2/proto/CMakeLists.txt b/caffe2/proto/CMakeLists.txt +index ba6b696dde4..5033e228119 100644 +--- a/caffe2/proto/CMakeLists.txt ++++ b/caffe2/proto/CMakeLists.txt +@@ -7,6 +7,7 @@ endif() + caffe2_protobuf_generate_cpp_py(Caffe2_PROTO_SRCS Caffe2_PROTO_HEADERS Caffe2_PROTO_PY ${Caffe2_PROTOBUF_FILES}) + + add_library(Caffe2_PROTO OBJECT ${Caffe2_PROTO_HEADERS} ${Caffe2_PROTO_SRCS}) ++target_link_libraries(Caffe2_PROTO PRIVATE protobuf::libprotobuf) + + if(MSVC) + if(BUILD_SHARED_LIBS) +diff --git a/cmake/ProtoBuf.cmake b/cmake/ProtoBuf.cmake +index 8d7633c4ab0..fb0e9a0c5f7 100644 +--- a/cmake/ProtoBuf.cmake ++++ b/cmake/ProtoBuf.cmake +@@ -122,10 +122,6 @@ if((NOT TARGET protobuf::libprotobuf) AND (NOT TARGET protobuf::libprotobuf-lite + # "Please set the proper paths so that I can find protobuf correctly.") + endif() + +-get_target_property(__tmp protobuf::libprotobuf INTERFACE_INCLUDE_DIRECTORIES) +-message(STATUS "Caffe2 protobuf include directory: " ${__tmp}) +-include_directories(BEFORE SYSTEM ${__tmp}) +- + # If Protobuf_VERSION is known (true in most cases, false if we are building + # local protobuf), then we will add a protobuf version check in + # Caffe2Config.cmake.in. diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch new file mode 100644 index 00000000000..186cfe89dfa --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch @@ -0,0 +1,29 @@ +From 367387bab836c73c23719f97d929572c8b4e0fad Mon Sep 17 00:00:00 2001 +From: Nick Rossenbach +Date: Tue, 18 Apr 2023 23:31:51 +0200 +Subject: [PATCH] Add -Wno-error=nonnull for test/cpp/api/ + +On some platforms the build might fail due to the nonnull error +being triggered by different compiler behavior. + +Fix for #99278. +--- + test/cpp/api/CMakeLists.txt | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/test/cpp/api/CMakeLists.txt b/test/cpp/api/CMakeLists.txt +index 6b801a07318279..181139b01360c3 100644 +--- a/test/cpp/api/CMakeLists.txt ++++ b/test/cpp/api/CMakeLists.txt +@@ -80,6 +80,11 @@ if(NOT MSVC) + target_compile_options_if_supported(test_api "-Wno-maybe-uninitialized") + # gcc gives nonsensical warnings about variadic.h + target_compile_options_if_supported(test_api "-Wno-unused-but-set-parameter") ++ # the nonnull check might trigger for some build configurations, ++ # probably happening due to different code optimization ++ # (see e.g. https://rkoucha.fr/tech_corner/nonnull_gcc_attribute.html) ++ # this happened for a riscv build: https://github.com/pytorch/pytorch/issues/99278 ++ target_compile_options_if_supported(test_api "-Wno-error=nonnull") + endif() + + if(INSTALL_TEST) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch index fb28aadbefa..b07becd652e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch @@ -4,18 +4,24 @@ > Greatest absolute difference: 1.430511474609375e-05 at index (4, 5) (up to 1e-05 allowed) > Greatest relative difference: 4.65393206065873e-06 at index (4, 5) (up to 1.3e-06 allowed) +See https://github.com/pytorch/pytorch/pull/86365 + Author: Alexander Grund (TU Dresden) -Updated for PyTorch 1.13.1: Simon Branford (University of Birmingham) ---- a/test/test_ops.py -+++ b/test/test_ops.py -@@ -545,6 +545,9 @@ - else list(supported_dtypes)[0] - ) - -+ if dtype is torch.float32: -+ self.precision, self.rel_tol = (1.5e-05, 1e-05) -+ - samples = op.sample_inputs(device, dtype) - for sample in samples: - # calls it normally to get the expected result +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 4b2d0ebabc46b..bab7843a72b74 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -8503,7 +8503,11 @@ op_db: List[OpInfo] = [ + DecorateInfo( + toleranceOverride({torch.float32: tol(atol=1.3e-05, rtol=1.3e-05), + torch.complex64: tol(atol=1e-05, rtol=1.2e-03)}), +- 'TestCommon', 'test_numpy_refs')], ++ 'TestCommon', 'test_numpy_refs'), ++ DecorateInfo( ++ toleranceOverride({torch.float32: tol(atol=1.5e-05, rtol=1e-05)}), ++ 'TestCommon', 'test_out'), ++ ], + skips=( + # NVIDIA only assures that bfloat16 is supported by bmm if SM >= 5.3 + DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes', device_type='cuda', active_if=not SM53OrLater), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch new file mode 100644 index 00000000000..77dde5f3110 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch @@ -0,0 +1,68 @@ +Those tests (from test_ao_sparsity & test_quantization) require FBGEMM which may not be available. +So add the skip decorator. +See https://github.com/pytorch/pytorch/issues/87364 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/ao/sparsity/test_composability.py b/test/ao/sparsity/test_composability.py +index 6a1b6067a4c..0c43f585af2 100644 +--- a/test/ao/sparsity/test_composability.py ++++ b/test/ao/sparsity/test_composability.py +@@ -9,6 +9,7 @@ import torch.ao.quantization as tq + from torch import nn + from torch.ao import sparsity + from torch.testing._internal.common_utils import TestCase ++from torch.testing._internal.common_quantization import skipIfNoFBGEMM + from torch.ao.quantization.quantize_fx import prepare_fx, convert_fx, convert_to_reference_fx, prepare_qat_fx + from torch.ao.sparsity import fqn_to_module + +@@ -62,6 +63,7 @@ def _calculate_sparsity(tensor): + # This series of tests are to check the composability goals for sparsity and quantization. Namely + # that performing quantization and sparsity model manipulations in various orderings + # does not cause problems ++@skipIfNoFBGEMM + class TestComposability(TestCase): + # This test checks whether performing quantization prepare before sparse prepare + # causes any issues and verifies that the correct observers are inserted and that +@@ -326,6 +328,7 @@ class TestFxComposability(TestCase): + r"""This series of tests checks that various steps of the quantization and sparsity flow + compose cleanly despite variation in sequencing. + """ ++ @skipIfNoFBGEMM + def test_q_prep_fx_before_s_prep(self): + r""" + This test checks that the ordering of prepare_fx -> sparse prepare -> convert_fx +@@ -445,6 +448,7 @@ class TestFxComposability(TestCase): + ) + self.assertGreaterAlmostEqual(cur_sparsity, sparse_config[0]["sparsity_level"]) + ++ @skipIfNoFBGEMM + def test_s_prep_before_q_prep_fx(self): + r""" + This test checks that the ordering of sparse prepare -> prepare_fx -> convert_fx +@@ -490,6 +494,7 @@ class TestFxComposability(TestCase): + ) + self.assertGreaterAlmostEqual(cur_sparsity, sparse_config[0]["sparsity_level"]) + ++ @skipIfNoFBGEMM + def test_s_prep_before_qat_prep_fx(self): + r""" + This test checks that the ordering of sparse prepare -> prepare_qat_fx -> convert_fx +diff --git a/test/quantization/core/test_docs.py b/test/quantization/core/test_docs.py +index 27842b46ce7..8e50ffa3166 100644 +--- a/test/quantization/core/test_docs.py ++++ b/test/quantization/core/test_docs.py +@@ -10,11 +10,13 @@ import torch + from torch.testing._internal.common_quantization import ( + QuantizationTestCase, + SingleLayerLinearModel, ++ skipIfNoFBGEMM, + ) + from torch.testing._internal.common_quantized import override_quantized_engine + from torch.testing._internal.common_utils import IS_ARM64 + + ++@skipIfNoFBGEMM + class TestQuantizationDocs(QuantizationTestCase): + r""" + The tests in this section import code from the quantization docs and check that From 5e0b81d94c779b5a950c7a31bee7cb890c2ee7c4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 31 Jul 2023 14:07:45 +0200 Subject: [PATCH 8176/9987] Add dependencies --- ...ytest-rerunfailures-12.0-GCCcore-12.2.0.eb | 21 ++++++++++++++ .../pytest-shard-0.1.2-GCCcore-12.2.0.eb | 28 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..eefd52471b1 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.2.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'pytest-rerunfailures' +version = '12.0' + +homepage = 'https://github.com/pytest-dev/pytest-rerunfailures' +description = """pytest plugin to re-run tests to eliminate flaky failures.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] +dependencies = [('Python', '3.10.8')] + +use_pip = True +sanity_pip_check = True +download_dep_fail = False + +sources = [SOURCE_TAR_GZ] +checksums = ['784f462fa87fe9bdf781d0027d856b47a4bfe6c12af108f6bd887057a917b48e'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..bd08dfe54d6 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'pytest-shard' +version = '0.1.2' + +homepage = 'https://github.com/AdamGleave/pytest-shard' +description = """pytest plugin to support parallelism across multiple machines. + +Shards tests based on a hash of their test name enabling easy parallelism across machines, +suitable for a wide variety of continuous integration services. +Tests are split at the finest level of granularity, individual test cases, +enabling parallelism even if all of your tests are in a single file +(or even single parameterized test method). +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] +dependencies = [('Python', '3.10.8')] + +use_pip = True +sanity_pip_check = True +download_dep_fail = False + +sources = [SOURCE_TAR_GZ] +checksums = ['b86a967fbfd1c8e50295095ccda031b7e890862ee06531d5142844f4c1d1cd67'] + +moduleclass = 'tools' From 7d2eb5fa460524afd0e3b509dd51c60e90f1dc21 Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 31 Jul 2023 14:37:33 +0200 Subject: [PATCH 8177/9987] adding easyconfigs: libdwarf-0.7.0-GCCcore-12.3.0.eb --- .../libdwarf/libdwarf-0.7.0-GCCcore-12.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdwarf/libdwarf-0.7.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libdwarf/libdwarf-0.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.7.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7178122d45d --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-0.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libdwarf' +version = '0.7.0' + +homepage = 'https://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/davea42/libdwarf-code/releases/download/v%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['23b71829de875fa5842e49f232c8ee1a5043805749738bc61424d9abc1189f38'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('elfutils', '0.189'), +] + +configopts = "--enable-shared " + +sanity_check_paths = { + 'files': ['bin/dwarfdump', 'lib/libdwarf.a', 'lib/libdwarf.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +sanity_check_commands = ['dwarfdump --help'] + +moduleclass = 'devel' From fda5ac64ad3d95e33c150dc5c65d49e266ceb865 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 31 Jul 2023 15:21:28 +0200 Subject: [PATCH 8178/9987] Add Boost --- .../b/Boost/Boost-1.82.0-GCC-12.3.0.eb | 31 +++++++++++++++++++ .../i/ICU/ICU-73.2-GCCcore-12.3.0.eb | 29 +++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/i/ICU/ICU-73.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..b47082e09df --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.82.0-GCC-12.3.0.eb @@ -0,0 +1,31 @@ +## +# Authors:: Denis Kristak +## +name = 'Boost' +version = '1.82.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['66a469b6e608a51f8347236f4912e27dc5c60c60d7d53ae9bfe4683316c6f04c'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), + ('XZ', '5.4.2'), + ('zstd', '1.5.5'), + ('ICU', '73.2'), +] + +configopts = '--without-libraries=python,mpi' + +# disable MPI, build Boost libraries with tagged layout +boost_mpi = False +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/i/ICU/ICU-73.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/ICU/ICU-73.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b89633b59d8 --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-73.2-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '73.2' + +homepage = 'https://icu.unicode.org' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['818a80712ed3caacd9b652305e01afc7fa167e6f2e94996da44b90c2ab604ce1'] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.3'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' From a2625d3807dadebcebc79585f4aa3808616ade72 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 31 Jul 2023 16:06:14 +0200 Subject: [PATCH 8179/9987] adding easyconfigs: PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb and patches: PyTorch-1.7.0_disable-dev-shm-test.patch, PyTorch-1.10.0_fix-kineto-crash.patch, PyTorch-1.11.1_skip-test_init_from_local_shards.patch, PyTorch-1.12.1_add-hypothesis-suppression.patch, PyTorch-1.12.1_fix-skip-decorators.patch, PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch, PyTorch-1.12.1_fix-test_wishart_log_prob.patch, PyTorch-1.12.1_fix-TestTorch.test_to.patch, PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch, PyTorch-1.12.1_fix-vsx-loadu.patch, PyTorch-1.12.1_fix-vsx-vector-funcs.patch, PyTorch-1.12.1_skip-test_round_robin.patch, PyTorch-1.13.1_fix-fsdp-fp16-test.patch, PyTorch-1.13.1_fix-kineto-crash-on-exit.patch, PyTorch-1.13.1_fix-pytest-args.patch, PyTorch-1.13.1_fix-test-ops-conf.patch, PyTorch-1.13.1_increase-tolerance-test_ops.patch, PyTorch-1.13.1_increase-tolerance-test_optim.patch, PyTorch-1.13.1_install-vsx-vec-headers.patch, PyTorch-1.13.1_no-cuda-stubs-rpath.patch, PyTorch-1.13.1_remove-flaky-test-in-testnn.patch, PyTorch-1.13.1_skip-failing-grad-test.patch, PyTorch-1.13.1_skip-test-requiring-online-access.patch, PyTorch-1.13.1_skip-tests-without-fbgemm.patch --- .../PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb | 140 ++++++++++++++++++ .../PyTorch-1.13.1_fix-fsdp-fp16-test.patch | 21 +++ ...orch-1.13.1_fix-kineto-crash-on-exit.patch | 102 +++++++++++++ ...h-1.13.1_increase-tolerance-test_ops.patch | 32 ++-- ...1.13.1_increase-tolerance-test_optim.patch | 17 +++ ....1_skip-test-requiring-online-access.patch | 25 ++++ ...rch-1.13.1_skip-tests-without-fbgemm.patch | 68 +++++++++ 7 files changed, 392 insertions(+), 13 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-fp16-test.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-kineto-crash-on-exit.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_optim.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-test-requiring-online-access.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..314131b5e65 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,140 @@ +name = 'PyTorch' +version = '1.13.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +patches = [ + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-fsdp-fp16-test.patch', + 'PyTorch-1.13.1_fix-kineto-crash-on-exit.patch', + 'PyTorch-1.13.1_fix-pytest-args.patch', + 'PyTorch-1.13.1_fix-test-ops-conf.patch', + 'PyTorch-1.13.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.13.1_increase-tolerance-test_optim.patch', + 'PyTorch-1.13.1_install-vsx-vec-headers.patch', + 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.13.1_skip-failing-grad-test.patch', + 'PyTorch-1.13.1_skip-test-requiring-online-access.patch', + 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', +] +checksums = [ + {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.10.0_fix-kineto-crash.patch': 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb'}, + {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.1_add-hypothesis-suppression.patch': + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, + {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, + {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, + {'PyTorch-1.12.1_fix-test_wishart_log_prob.patch': + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45'}, + {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, + {'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch': + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d'}, + {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, + {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, + {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-fsdp-fp16-test.patch': '8ae68e60d6e1f92f50322b7f0381c7e65251fba32d7606e3a238a36a2f55b5cf'}, + {'PyTorch-1.13.1_fix-kineto-crash-on-exit.patch': + 'f1e6808ee8d91a2ad76e0caedb4685e5aec3008d5e2e3c3c3e88cbb25cbd71b4'}, + {'PyTorch-1.13.1_fix-pytest-args.patch': 'd3e3c841cf8d73683750f29326f2be56ee0bb5df7ff522baf7d7c3f301a91ec2'}, + {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, + {'PyTorch-1.13.1_increase-tolerance-test_ops.patch': + 'c909fdfc2b12df457e1eb5514265ffec3eab653994949416f3f048668421e223'}, + {'PyTorch-1.13.1_increase-tolerance-test_optim.patch': + 'a079d824085eab89794f5ecfc67792f735ed8cfd3fe7db52e4dea62e583cfe06'}, + {'PyTorch-1.13.1_install-vsx-vec-headers.patch': + '7b678f54bb947afd4767f5877ac424b4b94ce5db609ea20f5a869ccf4027035f'}, + {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '4c636059850fc9d1ecb27ce275f8aad5d5b6fdc19e35aff0c25b86cb3201352a'}, + {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': + 'be83ff61fe2dedab6d49c232936d5622df81ab49154264490021c6c828e53315'}, + {'PyTorch-1.13.1_skip-failing-grad-test.patch': '6681200f9509893cb9231b5c93ac9bc5e6d9d9ae4febefca52e7cbc843ba8f51'}, + {'PyTorch-1.13.1_skip-test-requiring-online-access.patch': + '61c3b7859dc06a9969981b07aa2789630de110d6d1d3633d27364be47af74712'}, + {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': + '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), + # For tests + ('pytest-rerunfailures', '11.1'), + ('pytest-shard', '0.1.2'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.4.2'), + ('Pillow', '9.1.1'), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), + ('magma', '2.6.2', '-CUDA-%(cudaver)s'), + ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + # no xdoctest + 'doctests', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'test_native_mha', + # intermittent failures on various systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'distributed/rpc/test_tensorpipe_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# The readelf sanity check command can be taken out once the TestRPATH test from +# https://github.com/pytorch/pytorch/pull/87593 is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-fp16-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-fp16-test.patch new file mode 100644 index 00000000000..567103a376b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-fp16-test.patch @@ -0,0 +1,21 @@ +The test fails on a node with more than 5 V100 GPUs or more than 4 A100 GPUs. +Hence limit the world_size to 4 +See https://github.com/pytorch/pytorch/pull/86280 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/fsdp/test_fsdp_pure_fp16.py b/test/distributed/fsdp/test_fsdp_pure_fp16.py +index 1c663f8263354..e0033ef3d4b72 100644 +--- a/test/distributed/fsdp/test_fsdp_pure_fp16.py ++++ b/test/distributed/fsdp/test_fsdp_pure_fp16.py +@@ -34,8 +34,8 @@ + class TestPureFP16(FSDPTest): + @property + def world_size(self): +- # Test fails due to inaccuracies when using more than 5 GPUs +- return min(5, super().world_size) ++ # Test fails due to inaccuracies when using more than 4 GPUs ++ return min(4, super().world_size) + + @skip_if_lt_x_gpu(2) + @parametrize( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-kineto-crash-on-exit.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-kineto-crash-on-exit.patch new file mode 100644 index 00000000000..ea4708e3b68 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-kineto-crash-on-exit.patch @@ -0,0 +1,102 @@ +Fix a crash in libkineto on shutdown observed in e.g. test_jit_cuda_fuser.py +Taken from https://github.com/pytorch/kineto/pull/696 +by Dmytro Dzhulgakov + +Backported: Alexander Grund (TU Dresden) + +Submodule third_party/kineto contains modified content +diff --git a/third_party/kineto/libkineto/include/Config.h b/third_party/kineto/libkineto/include/Config.h +index 3e7f2d4..10c80d9 100644 +--- a/third_party/kineto/libkineto/include/Config.h ++++ b/third_party/kineto/libkineto/include/Config.h +@@ -315,6 +315,12 @@ class Config : public AbstractConfig { + + void print(std::ostream& s) const; + ++ // Config relies on some state with global static lifetime. If other ++ // threads are using the config, it's possible that the global state ++ // is destroyed before the threads stop. By hanging onto this handle, ++ // correct destruction order can be ensured. ++ static std::shared_ptr getStaticObjectsLifetimeHandle(); ++ + private: + explicit Config(const Config& other) = default; + +diff --git a/third_party/kineto/libkineto/src/Config.cpp b/third_party/kineto/libkineto/src/Config.cpp +index 2b6e04e..b23abd6 100644 +--- a/third_party/kineto/libkineto/src/Config.cpp ++++ b/third_party/kineto/libkineto/src/Config.cpp +@@ -155,10 +155,8 @@ struct FactoryMap { + + std::shared_ptr configFactories() { + // Ensure this is safe to call during shutdown, even as static +- // destructors are invoked. Once factories destructor has been +- // invoked, weak_ptr.lock() will return nullptr. +- // But calls before that point will have a valid shared_ptr, +- // delaying destruction of the underlying FactoryMap. ++ // destructors are invoked. getStaticObjectLifetimeHandle hangs onto ++ // FactoryMap delaying its destruction. + static auto factories = std::make_shared(); + static std::weak_ptr weak_ptr = factories; + return weak_ptr.lock(); +@@ -210,6 +208,10 @@ Config::Config() + } + } + ++std::shared_ptr Config::getStaticObjectsLifetimeHandle() { ++ return configFactories(); ++} ++ + uint8_t Config::createDeviceMask(const string& val) { + uint8_t res = 0; + for (const auto& d : splitAndTrim(val, ',')) { +diff --git a/third_party/kineto/libkineto/src/ConfigLoader.cpp b/third_party/kineto/libkineto/src/ConfigLoader.cpp +index 4080b67..ca72b32 100644 +--- a/third_party/kineto/libkineto/src/ConfigLoader.cpp ++++ b/third_party/kineto/libkineto/src/ConfigLoader.cpp +@@ -157,7 +157,7 @@ void ConfigLoader::startThread() { + } + } + +-ConfigLoader::~ConfigLoader() { ++void ConfigLoader::stopThread() { + if (updateThread_) { + stopFlag_ = true; + { +@@ -165,7 +165,12 @@ ConfigLoader::~ConfigLoader() { + updateThreadCondVar_.notify_one(); + } + updateThread_->join(); ++ updateThread_ = nullptr; + } ++} ++ ++ConfigLoader::~ConfigLoader() { ++ stopThread(); + #if !USE_GOOGLE_LOG + Logger::clearLoggerObservers(); + #endif // !USE_GOOGLE_LOG +@@ -249,6 +254,11 @@ void ConfigLoader::configureFromDaemon( + } + + void ConfigLoader::updateConfigThread() { ++ // It's important to hang to this reference until the thread stops. ++ // Otherwise, the Config's static members may be destroyed before this ++ // function finishes. ++ auto handle = Config::getStaticObjectsLifetimeHandle(); ++ + auto now = system_clock::now(); + auto next_config_load_time = now; + auto next_on_demand_load_time = now + onDemandConfigUpdateIntervalSecs_; +diff --git a/third_party/kineto/libkineto/src/ConfigLoader.h b/third_party/kineto/libkineto/src/ConfigLoader.h +index 4680816..83a94ac 100644 +--- a/third_party/kineto/libkineto/src/ConfigLoader.h ++++ b/third_party/kineto/libkineto/src/ConfigLoader.h +@@ -108,6 +108,7 @@ class ConfigLoader { + DaemonConfigLoader* daemonConfigLoader(); + + void startThread(); ++ void stopThread(); + void updateConfigThread(); + void updateBaseConfig(); + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch index fb28aadbefa..b07becd652e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_ops.patch @@ -4,18 +4,24 @@ > Greatest absolute difference: 1.430511474609375e-05 at index (4, 5) (up to 1e-05 allowed) > Greatest relative difference: 4.65393206065873e-06 at index (4, 5) (up to 1.3e-06 allowed) +See https://github.com/pytorch/pytorch/pull/86365 + Author: Alexander Grund (TU Dresden) -Updated for PyTorch 1.13.1: Simon Branford (University of Birmingham) ---- a/test/test_ops.py -+++ b/test/test_ops.py -@@ -545,6 +545,9 @@ - else list(supported_dtypes)[0] - ) - -+ if dtype is torch.float32: -+ self.precision, self.rel_tol = (1.5e-05, 1e-05) -+ - samples = op.sample_inputs(device, dtype) - for sample in samples: - # calls it normally to get the expected result +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 4b2d0ebabc46b..bab7843a72b74 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -8503,7 +8503,11 @@ op_db: List[OpInfo] = [ + DecorateInfo( + toleranceOverride({torch.float32: tol(atol=1.3e-05, rtol=1.3e-05), + torch.complex64: tol(atol=1e-05, rtol=1.2e-03)}), +- 'TestCommon', 'test_numpy_refs')], ++ 'TestCommon', 'test_numpy_refs'), ++ DecorateInfo( ++ toleranceOverride({torch.float32: tol(atol=1.5e-05, rtol=1e-05)}), ++ 'TestCommon', 'test_out'), ++ ], + skips=( + # NVIDIA only assures that bfloat16 is supported by bmm if SM >= 5.3 + DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes', device_type='cuda', active_if=not SM53OrLater), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_optim.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_optim.patch new file mode 100644 index 00000000000..566751f4990 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_optim.patch @@ -0,0 +1,17 @@ +Increase tolerance for failing test(s). +See https://github.com/pytorch/pytorch/issues/98414 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_optim.py b/test/test_optim.py +index 2cb27376919..ce7cf2cb160 100644 +--- a/test/test_optim.py ++++ b/test/test_optim.py +@@ -777,6 +777,7 @@ class TestOptim(TestCase): + ) + + def test_nadam(self): ++ self.precision, self.rel_tol = (2e-05, 1e-05) + self._test_basic_cases( + lambda weight, bias, foreach: optim.NAdam([weight, bias], lr=1e-3, foreach=foreach), + constructor_accepts_foreach=True, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-test-requiring-online-access.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-test-requiring-online-access.patch new file mode 100644 index 00000000000..cd50539752f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-test-requiring-online-access.patch @@ -0,0 +1,25 @@ +This tests downloads a Perl file from a Github repo which may fail in: + + File "test/test_cuda.py", line 4632, in test_memory_snapshot + torch.cuda.memory._save_segment_usage(f.name) + File "/torch/cuda/memory.py", line 610, in _save_segment_usage + f.write(_segments(snapshot)) + File "/torch/cuda/_memory_viz.py", line 60, in segments + return format_flamegraph(f.getvalue()) + File "/torch/cuda/_memory_viz.py", line 21, in format_flamegraph + urllib.request.urlretrieve( + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_cuda.py b/test/test_cuda.py +index 50644c22875..64d0eeb2fd4 100644 +--- a/test/test_cuda.py ++++ b/test/test_cuda.py +@@ -4599,6 +4599,7 @@ class TestCudaComm(TestCase): + cat = torch.cat((outputs[0][i].to('cpu'), outputs[1][i].to('cpu'))) + self.assertTrue(torch.equal(x, cat)) + ++ @unittest.skip("Requires internet access") + def test_memory_snapshot(self): + try: + torch.cuda.memory.empty_cache() diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch new file mode 100644 index 00000000000..77dde5f3110 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-tests-without-fbgemm.patch @@ -0,0 +1,68 @@ +Those tests (from test_ao_sparsity & test_quantization) require FBGEMM which may not be available. +So add the skip decorator. +See https://github.com/pytorch/pytorch/issues/87364 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/ao/sparsity/test_composability.py b/test/ao/sparsity/test_composability.py +index 6a1b6067a4c..0c43f585af2 100644 +--- a/test/ao/sparsity/test_composability.py ++++ b/test/ao/sparsity/test_composability.py +@@ -9,6 +9,7 @@ import torch.ao.quantization as tq + from torch import nn + from torch.ao import sparsity + from torch.testing._internal.common_utils import TestCase ++from torch.testing._internal.common_quantization import skipIfNoFBGEMM + from torch.ao.quantization.quantize_fx import prepare_fx, convert_fx, convert_to_reference_fx, prepare_qat_fx + from torch.ao.sparsity import fqn_to_module + +@@ -62,6 +63,7 @@ def _calculate_sparsity(tensor): + # This series of tests are to check the composability goals for sparsity and quantization. Namely + # that performing quantization and sparsity model manipulations in various orderings + # does not cause problems ++@skipIfNoFBGEMM + class TestComposability(TestCase): + # This test checks whether performing quantization prepare before sparse prepare + # causes any issues and verifies that the correct observers are inserted and that +@@ -326,6 +328,7 @@ class TestFxComposability(TestCase): + r"""This series of tests checks that various steps of the quantization and sparsity flow + compose cleanly despite variation in sequencing. + """ ++ @skipIfNoFBGEMM + def test_q_prep_fx_before_s_prep(self): + r""" + This test checks that the ordering of prepare_fx -> sparse prepare -> convert_fx +@@ -445,6 +448,7 @@ class TestFxComposability(TestCase): + ) + self.assertGreaterAlmostEqual(cur_sparsity, sparse_config[0]["sparsity_level"]) + ++ @skipIfNoFBGEMM + def test_s_prep_before_q_prep_fx(self): + r""" + This test checks that the ordering of sparse prepare -> prepare_fx -> convert_fx +@@ -490,6 +494,7 @@ class TestFxComposability(TestCase): + ) + self.assertGreaterAlmostEqual(cur_sparsity, sparse_config[0]["sparsity_level"]) + ++ @skipIfNoFBGEMM + def test_s_prep_before_qat_prep_fx(self): + r""" + This test checks that the ordering of sparse prepare -> prepare_qat_fx -> convert_fx +diff --git a/test/quantization/core/test_docs.py b/test/quantization/core/test_docs.py +index 27842b46ce7..8e50ffa3166 100644 +--- a/test/quantization/core/test_docs.py ++++ b/test/quantization/core/test_docs.py +@@ -10,11 +10,13 @@ import torch + from torch.testing._internal.common_quantization import ( + QuantizationTestCase, + SingleLayerLinearModel, ++ skipIfNoFBGEMM, + ) + from torch.testing._internal.common_quantized import override_quantized_engine + from torch.testing._internal.common_utils import IS_ARM64 + + ++@skipIfNoFBGEMM + class TestQuantizationDocs(QuantizationTestCase): + r""" + The tests in this section import code from the quantization docs and check that From c98b6bd7471bdb1f95f72c9463081ddbdd5fbfa4 Mon Sep 17 00:00:00 2001 From: ariel Date: Mon, 31 Jul 2023 16:24:15 +0200 Subject: [PATCH 8180/9987] remove duplicate ext --- .../easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.2.0.eb index 82f3249090f..9c41cdf1a33 100644 --- a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.2.0.eb @@ -32,9 +32,6 @@ exts_list = [ ('async-timeout', '4.0.2', { 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], }), - ('aiosignal', '1.3.1', { - 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], - }), (name, version, { 'checksums': ['b9552ec52cc147dbf1944ac7ac98af7602e51ea2dcd076ed194ca3c0d1c7d0bc'], }), From 732c1470f90c36b52461356b4c93fbbd13309328 Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 31 Jul 2023 17:25:03 +0200 Subject: [PATCH 8181/9987] adding easyconfigs: AOCC-4.0.0-GCCcore-12.3.0.eb --- .../a/AOCC/AOCC-4.0.0-GCCcore-12.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b48a51d26b2 --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +name = 'AOCC' +version = '4.0.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.amd.com/developer/eula/aocc-compiler/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['2729ec524cbc927618e479994330eeb72df5947e90cfcc49434009eee29bf7d4'] + +clangversion = '14.0.6' + +dependencies = [ + ('binutils', '2.40'), + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('libxml2', '2.11.4'), +] + +moduleclass = 'compiler' From b88745de4a28bfad8c5b5d1d6ce94a3dcd6c9dcb Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 31 Jul 2023 17:37:11 +0200 Subject: [PATCH 8182/9987] {vis}[foss/2022a] wxPython v4.2.1 --- .../attrdict3-2.0.2-GCCcore-11.3.0.eb | 26 ++++++ .../libavif/libavif-0.11.1-GCCcore-11.3.0.eb | 37 ++++++++ .../l/libwpe/libwpe-1.14.1-GCCcore-11.3.0.eb | 43 +++++++++ .../u/unifdef/unifdef-2.12-GCCcore-11.3.0.eb | 34 +++++++ .../WebKitGTK+-2.40.4-GCC-11.3.0.eb | 90 +++++++++++++++++++ .../wpebackend-fdo-1.14.1-GCCcore-11.3.0.eb | 41 +++++++++ .../w/wxPython/wxPython-4.2.1-foss-2022a.eb | 48 ++++++++++ 7 files changed, 319 insertions(+) create mode 100644 easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libavif/libavif-0.11.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libwpe/libwpe-1.14.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/u/unifdef/unifdef-2.12-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.40.4-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.14.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-4.2.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..0fc53c6d0fc --- /dev/null +++ b/easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'attrdict3' +version = '2.0.2' + +homepage = 'https://github.com/pirofti/AttrDict3' +description = """AttrDict is a Python library that provides mapping objects that allow their elements + to be accessed both as keys and as attributes.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'attrdict', + 'checksums': ['004c171ca1120cc1755701db99d7fa4944afb1e68950434efdaa542513335fe8'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.11.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..2d5b1cc7ab9 --- /dev/null +++ b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak (Inuits) +# Update: Thomas Hoffmann (EMBL), Denis Kristak (Inuits) +easyblock = 'CMakeMake' + +name = 'libavif' +version = '0.11.1' + +homepage = 'https://github.com/AOMediaCodec/libavif' +description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format, +as described here: https://aomediacodec.github.io/av1-avif/ +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0eb49965562a0e5e5de58389650d434cff32af84c34185b6c9b7b2fccae06d4e'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), +] + +dependencies = [ + ('NASM', '2.15.05'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('Rust', '1.60.0'), +] + +sanity_check_paths = { + 'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libwpe/libwpe-1.14.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwpe/libwpe-1.14.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..e3cc38a8526 --- /dev/null +++ b/easybuild/easyconfigs/l/libwpe/libwpe-1.14.1-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# update 1.14.1 THEMBL +easyblock = 'CMakeMake' + +name = 'libwpe' +version = '1.14.1' + +homepage = 'https://webkit.org/wpe' +description = """WPE is the reference WebKit port for embedded and +low-consumption computer devices. It has been designed from the +ground-up with performance, small footprint, accelerated content +rendering, and simplicity of deployment in mind, bringing the +excellence of the WebKit engine to countless platforms and target devices.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://wpewebkit.org/releases'] +sources = ['%(name)s-%(version)s.tar.xz'] +patches = ['%(name)s-1.13.3_include-string-before-poison.patch'] +checksums = [ + {'libwpe-1.14.1.tar.xz': 'b1d0cdcf0f8dbb494e65b0f7913e357106da9a0d57f4fbb7b9d1238a6dbe9ade'}, + {'libwpe-1.13.3_include-string-before-poison.patch': + '2d21ed6b2dafa758126cda162e450ab2b3a3c0b622e375ff443523ba32fc5812'}, +] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('CMake', '3.23.1'), + ('Meson', '0.62.1'), +] + +dependencies = [ + ('glew', '2.2.0', '-egl'), +] + +sanity_check_paths = { + 'files': ['lib/libwpe-1.0.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/unifdef/unifdef-2.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/unifdef/unifdef-2.12-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..f653e81c65f --- /dev/null +++ b/easybuild/easyconfigs/u/unifdef/unifdef-2.12-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/07 +easyblock = 'ConfigureMake' + +name = 'unifdef' +version = '2.12' + +homepage = 'https://github.com/fanf2/unifdef' +description = """unifdef - selectively remove C preprocessor conditionals +The unifdef utility selectively processes conditional C preprocessor +and the additional text that they delimit, while otherwise leaving the +file alone.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'fanf2' +source_urls = [GITHUB_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['030369db9ff917acfae7fa4e90bcc1dff8a8dc534d82d1c72c12ef698d2f20e4'] + +preconfigopts = 'echo V=\\"%(name)s-%(version)s\\" > version.sh &&' +preconfigopts += 'echo D=\\"2020-02-14 0:00:00 +0000\\" >> version.sh&&' +configure_cmd = 'sed -i "s/HOME/PREF/g" Makefile #' +preinstallopts = 'export PREF=%(installdir)s &&' + +dependencies = [('binutils', '2.38')] + +sanity_check_commands = ['%(name)s -h'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'share/man'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.40.4-GCC-11.3.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.40.4-GCC-11.3.0.eb new file mode 100644 index 00000000000..c04e23f2150 --- /dev/null +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.40.4-GCC-11.3.0.eb @@ -0,0 +1,90 @@ +# Updated from WebKitGTK+-2.27.4-GCC-8.3.0.eb with more modules added +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'WebKitGTK+' +version = '2.40.4' + +homepage = 'https://webkitgtk.org/' +description = """WebKitGTK+ is a full-featured port of the WebKit +rendering engine, suitable for projects requiring any kind of web +integration, from hybrid HTML/CSS applications to full-fledged web +browsers. It offers WebKit's full functionality and is useful in a wide +range of systems from desktop computers to embedded systems like phones, +tablets, and televisions.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://webkitgtk.org/releases'] +sources = ['webkitgtk-%(version)s.tar.xz'] +checksums = ['8d163379297a2f7f51b455127f99836d9fe1572289f77b630ff3d63a2cb06dac'] + +osdependencies = [ + # Would be better to use the system package due to security reasons + # But we need at least libgcrypt 1.7.0 and Ubuntu 16.04 and RH 7.5 + # are both using a too old version. + # Update: Libcrypt 1.9.3 from EasyBuild added (J.S) + # ('libgcrypt-dev', 'libgcrypt20-dev', 'libgcrypt-devel'), + # libsecret is not actually needed since USE_LIBSECRET option is disabled + # ('libsecret-1-dev', 'libsecret-devel'), +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Python', '3.10.4'), + ('Perl', '5.34.1', '-minimal'), + ('GObject-Introspection', '1.72.0'), + ('pkg-config', '0.29.2'), + ('ccache', '4.6.3'), + ('unifdef', '2.12'), +] +dependencies = [ + ('GLib', '2.72.1'), + ('gperf', '3.1'), + ('cairo', '1.17.4'), + ('GTK3', '3.24.33'), + ('LibSoup', '3.0.8'), + ('ATK', '2.38.0'), + ('libgcrypt', '1.10.1'), + ('wpebackend-fdo', '1.14.1'), + ('libxslt', '1.1.34'), + ('libtasn1', '4.19.0'), + ('GStreamer', '1.20.2'), + ('OpenJPEG', '2.5.0'), + ('Ruby', '3.0.5'), + ('GSL', '2.7'), + ('glew', '2.2.0', '-egl'), + ('pugixml', '1.12.1'), + ('Wayland', '1.21.0'), + ('Waylandpp', '1.0.0'), + ('enchant-2', '2.3.3'), + ('LittleCMS', '2.13.1'), + ('GST-plugins-base', '1.20.2'), + ('libwebp', '1.2.4'), + ('libavif', '0.11.1'), +] + + +# The build takes around 2.5 hours on 24 cores on AMD Rome! +# So be patient! + +# Instead of using a patch file, we are disabling problematic builds in the command line. +# At least this way, if something is not needed it can be turned off, without looking into +# a patch file. +configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON -DPORT=GTK -DCMAKE_FIND_USE_PACKAGE_REGISTRY=FALSE " +configopts += "-DENABLE_GAMEPAD=OFF -DUSE_LIBSECRET=OFF -DUSE_LIBHYPHEN=OFF " +configopts += "-DUSE_WOFF2=OFF -DENABLE_JOURNALD_LOG=OFF -DENABLE_BUBBLEWRAP_SANDBOX=OFF " +configopts += "-DENABLE_INTROSPECTION=OFF -DUSE_LIBNOTIFY=OFF " +configopts += "-DUSE_GSTREAMER_TRANSCODER=OFF " + +prebuildopts = "export CCACHE_DIR=%(builddir)s/ccache && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/WebKitWebDriver', 'lib/libwebkit2gtk-4.1.%s' % SHLIB_EXT, + 'lib/libjavascriptcoregtk-4.1.%s' % SHLIB_EXT], + 'dirs': ['include/webkitgtk-4.1/webkit2', 'libexec/webkit2gtk-4.1'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.14.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.14.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..817421c5bfd --- /dev/null +++ b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.14.1-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) +# update 1.14.1 THEMBL +easyblock = 'MesonNinja' + +name = 'wpebackend-fdo' +version = '1.14.1' + +homepage = 'https://wpewebkit.org/' +description = """WPE WebKit allows embedders to create simple and performant +systems based on Web platform technologies. It is a WebKit port designed with +flexibility and hardware acceleration in mind, leveraging common 3D graphics +APIs for best performance.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://wpewebkit.org/releases'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['01938dd93c62b3a47b18dd13c70d50490a8b8a6caec23c8550a3dbdbcc6bbb50'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('pugixml', '1.12.1'), + ('Waylandpp', '1.0.0'), + ('libepoxy', '1.5.10'), + ('glib-networking', '2.72.1'), + ('libwpe', version), +] + +sanity_check_paths = { + 'files': ['lib/libWPEBackend-fdo-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.2.1-foss-2022a.eb new file mode 100644 index 00000000000..65862ac1a80 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.2.1-foss-2022a.eb @@ -0,0 +1,48 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +name = 'wxPython' +version = '4.2.1' + +homepage = "https://www.wxpython.org/" +description = """Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets +API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel +and requiring very little (if any) platform specific code.""" + + +toolchain = {'name': 'foss', 'version': '2022a'} +sources = ['%(name)s-%(version)s.tar.gz'] +patches = [ + 'wxPython-4.1.1_fix_install_path.patch', + 'wxPython-4.1.1_use_bang_env_python.patch', +] +checksums = [ + {'wxPython-4.2.1.tar.gz': 'e48de211a6606bf072ec3fa778771d6b746c00b7f4b970eb58728ddf56d13d5c'}, + {'wxPython-4.1.1_fix_install_path.patch': 'f13743877deddbf525bbb3f81c8f7a6b0c2dbf1333595926f653f696999e31ce'}, + {'wxPython-4.1.1_use_bang_env_python.patch': 'c355c60a8cce3018fc0c30ffc78623efd2481e9baf33673e22a57863e1a3ac87'}, +] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Pillow', '9.1.1'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('expat', '2.4.8'), + ('GTK3', '3.24.33'), + ('GLib', '2.72.1'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '1.20.2'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('LibSoup', '3.0.8'), + ('wxWidgets', '3.2.1'), # wxPython 4.2 depends on wxWidgets >=3.2 + ('WebKitGTK+', '2.40.4'), + ('attrdict3', '2.0.2'), +] + +moduleclass = 'vis' From 44e275028448d23f3780cd306baf5ef55cd5c632 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 31 Jul 2023 18:12:23 +0200 Subject: [PATCH 8183/9987] add GConf-3.2.6-GCCcore-11.3.0.eb --- .../g/GConf/GConf-3.2.6-GCCcore-11.3.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..29f16349867 --- /dev/null +++ b/easybuild/easyconfigs/g/GConf/GConf-3.2.6-GCCcore-11.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'GConf' +version = '3.2.6' + +# The homeage is no longer reachable! +# homepage = 'https://developer.gnome.org/gconf/' +# The project was depricated with the move to Gnome-3 +# Possible alternative, although 6 years old: +homepage = 'https://gitlab.gnome.org/iainl/gconf' +description = """GConf is a system for storing application preferences. + It is intended for user preferences; not configuration + of something like Apache, or arbitrary data storage.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/GConf/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +patches = [ + '%(name)s-%(version)s_call-dbus_g_thread_init.patch', + '%(name)s-%(version)s_fix_wrong_return_value.patch', + '%(name)s-%(version)s_gconf-path-max-hurd.patch', + '%(name)s-%(version)s_readd_gconf_engine_key_is_writable.patch', +] +checksums = [ + '1912b91803ab09a5eed34d364bf09fe3a2a9c96751fde03a4e0cfa51a04d784c', # GConf-3.2.6.tar.xz + 'ed55bff5bc239115ae27b8520a923ae0d5cab6cb15ca9921a8c23b939306489f', # GConf-3.2.6_call-dbus_g_thread_init.patch + 'f8f7745c3648953098eb56af0f64adc69d8c0b0e78c8db351746a2b4c58e8bb4', # GConf-3.2.6_fix_wrong_return_value.patch + 'ee5524c3cb985088bbe4884531ddc48ba22d2fced2a34865304c77e194a55bde', # GConf-3.2.6_gconf-path-max-hurd.patch + # GConf-3.2.6_readd_gconf_engine_key_is_writable.patch + 'b95dfc2f0474d9162fc686f26cd4d3da5c9b01a9c609dc0a4f2b2bd901d497f3', +] + +builddependencies = [ + ('binutils', '2.38'), + ('GObject-Introspection', '1.72.0'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('GLib', '2.72.1'), + ('dbus-glib', '0.112'), + ('libxml2', '2.9.13'), + ('GTK3', '3.24.33'), + ('intltool', '0.51.0'), +] + +configopts = '--disable-orbit ' + +local_check_filelist = ['bin/gconf%s' % x for x in ['-merge-tree', 'tool-2']] +local_check_filelist += ['bin/gsettings-%s-convert' % x for x in ['data', 'schema']] +local_check_filelist += ['lib/libgconf-2.%s' % x for x in ['a', 'so']] + +sanity_check_paths = { + 'files': local_check_filelist, + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' From b50898214a1fb93d853d62fb43d7ecd5040d84e2 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 31 Jul 2023 20:46:38 +0200 Subject: [PATCH 8184/9987] Use custom EasyBlock --- easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb | 2 -- easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb | 2 -- easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb | 2 -- easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb | 2 -- easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb | 2 -- 5 files changed, 10 deletions(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb index 3799a72d02d..d4edd014076 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'sympy' version = '1.10.1' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb index ef36e3b6591..fae10984feb 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'sympy' version = '1.10.1' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb index 9e54ecf5751..e05bd976573 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'sympy' version = '1.11.1' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb index 38b1a2916d3..dc96b8575d2 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'sympy' version = '1.11.1' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb index 5f50bb21110..c54bb52e04b 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'sympy' version = '1.9' From 67ad89445bdf8bd82774f2a449cbf05e1081ef75 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Mon, 31 Jul 2023 16:22:02 -0400 Subject: [PATCH 8185/9987] {bio}[foss/2020b] PartitionFinder v2.1.1 + PyTables v3.5.2 new source url --- ...onFinder-2.1.1-foss-2020b-Python-2.7.18.eb | 48 +++++++++++++++++++ ...PyTables-3.5.2-foss-2020b-Python-2.7.18.eb | 2 +- 2 files changed, 49 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PartitionFinder/PartitionFinder-2.1.1-foss-2020b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/p/PartitionFinder/PartitionFinder-2.1.1-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/PartitionFinder/PartitionFinder-2.1.1-foss-2020b-Python-2.7.18.eb new file mode 100644 index 00000000000..71d28c2fc13 --- /dev/null +++ b/easybuild/easyconfigs/p/PartitionFinder/PartitionFinder-2.1.1-foss-2020b-Python-2.7.18.eb @@ -0,0 +1,48 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'PartitionFinder' +version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.robertlanfear.com/partitionfinder' +description = """PartitionFinder 2 is a Python program for simultaneously +choosing partitioning schemes and models of molecular evolution for phylogenetic +analyses of DNA, protein, and morphological data. You can PartitionFinder 2 +before running a phylogenetic analysis, in order to decide how to divide up +your sequence data into separate blocks before analysis, and to simultaneously +perform model selection on each of those blocks.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +github_account = 'brettc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ccf3718996ee6ca496909b4b97d2b075028e0543eba3bc47a8c14b689c84e061'] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2020.11', versionsuffix), + ('scikit-learn', '0.20.4', versionsuffix), + ('PyTables', '3.5.2', versionsuffix), +] + +postinstallcmds = ["cd %(installdir)s && chmod a+x PartitionFinder*"] +fix_python_shebang_for = ["*.py"] + +sanity_check_paths = { + 'files': ['%(name)sMorphology.py', '%(name)sProtein.py', '%(name)s.py'], + 'dirs': ['partfinder'], +} + +sanity_check_commands = [ + '%(name)s.py -p %(parallel)s %(installdir)s/examples/nucleotide/test.phy', + '%(name)sProtein.py -p %(parallel)s %(installdir)s/examples/aminoacid/test.phy', + '%(name)sMorphology.py -p %(parallel)s %(installdir)s/examples/morphology/test.phy --raxml', +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb index ce4f3ad63ba..23f3a638cb0 100644 --- a/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.5.2-foss-2020b-Python-2.7.18.eb @@ -17,7 +17,7 @@ description = """PyTables is a package for managing hierarchical datasets and de toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'usempi': True} -source_urls = ['https://github.com/PyTables/PyTables/archive/'] +source_urls = ['https://github.com/PyTables/PyTables/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s-fix-libs.patch'] checksums = [ From 54acef03213165016f23bdb47aeebb37ac59a763 Mon Sep 17 00:00:00 2001 From: ariel Date: Mon, 31 Jul 2023 23:17:26 +0200 Subject: [PATCH 8186/9987] fix comment space --- .../easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.2.0.eb index 837ae902ebe..80cdfe9a129 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.2.0.eb @@ -52,7 +52,7 @@ exts_list = [ 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], }), ('matplotlib-inline', '0.1.6', { - 'modulename': False, # see comment above + 'modulename': False, # see comment above 'checksums': ['f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304'], }), ('parso', '0.8.3', { From de6142a6f8a2187923ceaae9c81a34b52830825b Mon Sep 17 00:00:00 2001 From: ariel Date: Mon, 31 Jul 2023 23:18:53 +0200 Subject: [PATCH 8187/9987] add nbclassic to jupyter-server and reorganize some exts --- .../JupyterLab-4.0.3-GCCcore-12.2.0.eb | 16 -------------- .../jupyter-server-2.7.0-GCCcore-12.2.0.eb | 22 +++++++++++++++++++ 2 files changed, 22 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb index d068c655cf5..a39f3673be6 100644 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb @@ -53,9 +53,6 @@ exts_list = [ ('jsonschema', '4.18.4', { 'checksums': ['fb3642735399fa958c0d2aad7057901554596c63349f4f6b283c493cf692a25d'], }), - ('notebook_shim', '0.2.3', { - 'checksums': ['f69388ac283ae008cd506dda10d0288b09a017d822d5e8c7129a152cbd3ce7e9'], - }), ('json5', '0.9.14', { 'checksums': ['9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02'], }), @@ -65,19 +62,6 @@ exts_list = [ ('jupyter-lsp', '2.2.0', { 'checksums': ['8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1'], }), - ('nest_asyncio', '1.5.6', { - 'checksums': ['d267cc1ff794403f7df692964d1d2a3fa9418ffea2a3f6859a439ff482fef290'], - }), - ('debugpy', '1.6.7', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - 'checksums': ['53f7a456bc50706a0eaabecf2d3ce44c4d5010e46dfc65b6b81a518b42866267'], - }), - ('comm', '0.1.3', { - 'checksums': ['a61efa9daffcfbe66fd643ba966f846a624e4e6d6767eda9cf6e993aadaab93e'], - }), - ('ipykernel', '6.25.0', { - 'checksums': ['e342ce84712861be4b248c4a73472be4702c1b0dd77448bfd6bcfb3af9d5ddf9'], - }), ('async-lru', '2.0.3', { 'checksums': ['b714c9d1415fca4e264da72a9e2abc66880ce7430e03a973341f88ea4c0d4869'], }), diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb index 9da8e125687..86a82490fda 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb @@ -131,6 +131,28 @@ exts_list = [ ('jupyter_server', version, { 'checksums': ['36da0a266d31a41ac335a366c88933c17dfa5bb817a48f5c02c16d303bc9477f'], }), + ('notebook_shim', '0.2.3', { + 'checksums': ['f69388ac283ae008cd506dda10d0288b09a017d822d5e8c7129a152cbd3ce7e9'], + }), + ('nest_asyncio', '1.5.7', { + 'checksums': ['6a80f7b98f24d9083ed24608977c09dd608d83f91cccc24c9d2cba6d10e01c10'], + }), + ('ipykernel', '6.25.0', { + 'checksums': ['e342ce84712861be4b248c4a73472be4702c1b0dd77448bfd6bcfb3af9d5ddf9'], + }), + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('debugpy', '1.6.7', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['53f7a456bc50706a0eaabecf2d3ce44c4d5010e46dfc65b6b81a518b42866267'], + }), + ('comm', '0.1.3', { + 'checksums': ['a61efa9daffcfbe66fd643ba966f846a624e4e6d6767eda9cf6e993aadaab93e'], + }), + ('nbclassic', '1.0.0', { + 'checksums': ['0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'], + }), ] modextrapaths = { From f6246c8d1f56e67267f1f312cb39230a32a1b760 Mon Sep 17 00:00:00 2001 From: ariel Date: Tue, 1 Aug 2023 00:41:21 +0200 Subject: [PATCH 8188/9987] move widgets to jupyter-server eb --- .../j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb | 13 ------------- .../jupyter-server-2.7.0-GCCcore-12.2.0.eb | 13 +++++++++++++ 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb index a39f3673be6..ce74a883802 100644 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb @@ -25,10 +25,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them -# use the versions published in a single release commit instead of blindly pushing to last available version, -# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa - exts_list = [ ('trove-classifiers', '2023.7.6', { 'source_tmpl': 'trove_classifiers-%(version)s-py3-none-any.whl', @@ -68,15 +64,6 @@ exts_list = [ ('jupyterlab', version, { 'checksums': ['e14d1ce46a613028111d0d476a1d7d6b094003b7462bac669f5b478317abcb39'], }), - ('jupyterlab_widgets', '3.0.8', { - 'checksums': ['d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a'], - }), - ('widgetsnbextension', '4.0.8', { - 'checksums': ['9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17'], - }), - ('ipywidgets', '8.0.7', { - 'checksums': ['50ace0a8886e9a0d68b980db82f94c25d55d21ff2340ed36f802dd9365e94acf'], - }), ] sanity_check_commands = ["jupyter lab --help"] diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb index 86a82490fda..371d6d3a26f 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb @@ -23,6 +23,10 @@ dependencies = [ use_pip = True sanity_pip_check = True +# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them +# use the versions published in a single release commit instead of blindly pushing to last available version, +# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa + exts_list = [ ('deprecation', '2.1.0', { 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], @@ -153,6 +157,15 @@ exts_list = [ ('nbclassic', '1.0.0', { 'checksums': ['0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'], }), + ('jupyterlab_widgets', '3.0.8', { + 'checksums': ['d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a'], + }), + ('widgetsnbextension', '4.0.8', { + 'checksums': ['9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17'], + }), + ('ipywidgets', '8.0.7', { + 'checksums': ['50ace0a8886e9a0d68b980db82f94c25d55d21ff2340ed36f802dd9365e94acf'], + }), ] modextrapaths = { From 7ba0d7c02ccae42c371ca63cc4d1fe291e4133ec Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 1 Aug 2023 09:46:15 +0200 Subject: [PATCH 8189/9987] Add missing patches to PyTorch-1.12.0-foss-2022a --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a.eb | 93 +++++++++++++++---- 1 file changed, 77 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb index acaa8d0b12a..bcbc05d3d12 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb @@ -10,30 +10,91 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = [GITHUB_RELEASE] sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ - '%(name)s-1.7.0_avoid-nan-in-test-torch.patch', - '%(name)s-1.7.0_disable-dev-shm-test.patch', - '%(name)s-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - '%(name)s-1.10.0_fix-test-dataloader-fixed-affinity.patch', - '%(name)s-1.10.0_skip_cmake_rpath.patch', - '%(name)s-1.11.0_increase-distributed-test-timeout.patch', - '%(name)s-1.11.0_increase_c10d_gloo_timeout.patch', - '%(name)s-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', ] checksums = [ {'pytorch-v1.12.0.tar.gz': '46eff236370b759c427b03ff535c3597099043e8e467b8f81f9cd4b258a7a321'}, - {'PyTorch-1.7.0_avoid-nan-in-test-torch.patch': 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18'}, + {'PyTorch-1.7.0_avoid-nan-in-test-torch.patch': + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18'}, {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, - {'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch': - 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea'}, + {'PyTorch-1.10.0_fix-kineto-crash.patch': 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb'}, {'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch': '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707'}, - {'PyTorch-1.10.0_skip_cmake_rpath.patch': 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448'}, - {'PyTorch-1.11.0_increase-distributed-test-timeout.patch': - '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f'}, + {'PyTorch-1.10.0_fix-test-model_dump.patch': '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557'}, + {'PyTorch-1.10.0_fix-vsx-vector-functions.patch': + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312'}, + {'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch': + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2'}, + {'PyTorch-1.11.0_fix-fsdp-fp16-test.patch': 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13'}, + {'PyTorch-1.11.0_fix-test_utils.patch': '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861'}, {'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch': '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953'}, - {'PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch': - 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51'}, + {'PyTorch-1.11.0_increase-distributed-test-timeout.patch': + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f'}, + {'PyTorch-1.11.0_install-vsx-vec-headers.patch': + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d'}, + {'PyTorch-1.12.1_add-hypothesis-suppression.patch': + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, + {'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch': + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab'}, + {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, + {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, + {'PyTorch-1.12.1_fix-test_wishart_log_prob.patch': + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45'}, + {'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch': + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2'}, + {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, + {'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch': + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d'}, + {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, + {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, + {'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch': + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695'}, + {'PyTorch-1.12.1_increase-tolerance-test_ops.patch': + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb'}, + {'PyTorch-1.12.1_no-cuda-stubs-rpath.patch': '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6'}, + {'PyTorch-1.12.1_python-3.10-annotation-fix.patch': + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7'}, + {'PyTorch-1.12.1_python-3.10-compat.patch': '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67'}, + {'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch': + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d'}, + {'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch': + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39'}, + {'PyTorch-1.12.1_skip-failing-grad-test.patch': + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc'}, + {'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch': + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d'}, ] builddependencies = [ From 4b2bbebb0e880704b0c30a5aa2f2f1145c032d21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Aug 2023 09:46:59 +0200 Subject: [PATCH 8190/9987] use SYSTEM constant for Eigen build dependency of CGAL --- .../easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb index 834a3fffca6..80118c50358 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb @@ -15,7 +15,7 @@ checksums = ['d4ec2528b88a7c3a07b0b86db96c216822f85b951bf4bc7f9d1f26bf6c369afe'] builddependencies = [ ('CMake', '3.15.3'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ From 0ca69feb66bed3b71e55b92af6aa329f3ed69ad4 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 1 Aug 2023 09:55:10 +0200 Subject: [PATCH 8191/9987] Replacing PR #17467 --- .../gmpy2-2.1.2-intel-compilers-2021.4.0.eb | 25 ++++++++++++ .../s/sympy/sympy-1.9-intel-2021b.eb | 38 +++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb new file mode 100644 index 00000000000..f194fb5a771 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.2' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['da75140bca128ece795895477e53b43773e3748aa90ba6170eae7ca2c74b82d1'] + +dependencies = [ + ('Python', '3.9.6'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('MPC', '1.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb new file mode 100644 index 00000000000..0cf7088a191 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb @@ -0,0 +1,38 @@ +name = 'sympy' +version = '1.9' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('gmpy2', '2.1.2'), +] + +download_dep_fail = True +use_pip = True + +# fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; +# see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 +pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ +runtest = 'python setup.py test' + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/isympy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], +} + +sanity_check_commands = ["isympy --help"] + +moduleclass = 'math' From 8e55af531dde71832c377937592f5bf8a57c2ad4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 1 Aug 2023 09:56:56 +0200 Subject: [PATCH 8192/9987] WebKitGTK+-2.40.4-GCC-11.3.0.eb Wayland 1.21.0 -> 1.20.0 --- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.40.4-GCC-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.40.4-GCC-11.3.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.40.4-GCC-11.3.0.eb index c04e23f2150..16b1ca5e0f5 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.40.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.40.4-GCC-11.3.0.eb @@ -1,5 +1,6 @@ # Updated from WebKitGTK+-2.27.4-GCC-8.3.0.eb with more modules added # Author: J. Sassmannshausen (Imperial College London/UK) +# Update: THEMBL easyblock = 'CMakeMake' @@ -56,7 +57,7 @@ dependencies = [ ('GSL', '2.7'), ('glew', '2.2.0', '-egl'), ('pugixml', '1.12.1'), - ('Wayland', '1.21.0'), + ('Wayland', '1.20.0'), ('Waylandpp', '1.0.0'), ('enchant-2', '2.3.3'), ('LittleCMS', '2.13.1'), From 316c3bb3f841b20882be1ca4fcc4222220c26f72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Aug 2023 10:01:16 +0200 Subject: [PATCH 8193/9987] fix OPENGL_INCLUDE_DIR configure option for CGAL --- .../easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb index 80118c50358..0e40e4e96d2 100644 --- a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.1-foss-2019b-Python-2.7.16.eb @@ -29,7 +29,7 @@ dependencies = [ ('Qt5', '5.13.1'), ] -configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts = '-DOPENGL_INCLUDE_DIR="$EBROOTMESA/include;$EBROOTLIBGLU/include" ' configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " From 7b0520ac12a12fb442e5c091417f075c8ae07394 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 1 Aug 2023 10:09:32 +0200 Subject: [PATCH 8194/9987] Update easyconfigs.py allow variant glew-2.2.0-foss-2022a-egl for wxPython-4.2.0-foss-2022a --- test/easyconfigs/easyconfigs.py | 1 + 1 file changed, 1 insertion(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index ad11f8d3f46..46572103a04 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -499,6 +499,7 @@ def check_dep_vars(self, gen, dep, dep_vars): r'wpebackend-fdo-1\.13\.1-GCCcore-11\.2\.0', r'WebKitGTK\+-2\.37\.1-GCC-11\.2\.0', r'wxPython-4\.2\.0', + r'wxPython-4\.2\.1', r'GRASS-8\.2\.0', r'QGIS-3\.28\.1']), ], From e7fe6db2c98288258a74b6b3fd9780e605879836 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 1 Aug 2023 10:36:09 +0200 Subject: [PATCH 8195/9987] Update Waylandpp-1.0.0-GCCcore-11.3.0.eb adapt Wayland dependency from version 1.21.0 to 1.20.0 --- .../easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb index 84e55e3290e..e467e991a8a 100644 --- a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb @@ -33,7 +33,7 @@ builddependencies = [ dependencies = [ ('pugixml', '1.12.1'), - ('Wayland', '1.21.0'), + ('Wayland', '1.20.0'), ('freeglut', '3.2.2'), ] From 71ca36d7c77f315f54aa155057c122749f4dfccd Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 1 Aug 2023 11:10:07 +0200 Subject: [PATCH 8196/9987] Update easyconfigs.py add glew 2.2.0 egl multi-variant deps: libwpe-1.14.1-GCCcore-11.3.0.eb, wpebackend-fdo-1.14.1-GCCcore-11.3.0.eb --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 46572103a04..d1b0173181f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -496,7 +496,9 @@ def check_dep_vars(self, gen, dep, dep_vars): # egl variant of glew is required by libwpe, wpebackend-fdo + WebKitGTK+ depend on libwpe 'glew': [ ('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0', + r'libwpe-1\.14\.1-GCCcore-11\.3\.0', r'wpebackend-fdo-1\.13\.1-GCCcore-11\.2\.0', + r'wpebackend-fdo-1\.14\.1-GCCcore-11\.3\.0', r'WebKitGTK\+-2\.37\.1-GCC-11\.2\.0', r'wxPython-4\.2\.0', r'wxPython-4\.2\.1', From 8b9f1672daa2bc85034a40c9ddc3228e8d0db653 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Aug 2023 12:09:56 +0200 Subject: [PATCH 8197/9987] fix installation of Python bindings for Arrow 8.0.0 with foss/2022.05 by adding `--no-build-isolation` to `pip install` command --- easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb index 9c2d0b80319..63eb0955dd1 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb @@ -50,7 +50,8 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From efc5ce149395aa00e81a168b9275028cd84e77b9 Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 1 Aug 2023 13:24:41 +0200 Subject: [PATCH 8198/9987] adding easyconfigs: LLVM-16.0.6-GCCcore-12.3.0.eb --- .../l/LLVM/LLVM-16.0.6-GCCcore-12.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-16.0.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-16.0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-16.0.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..124bba69e5e --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-16.0.6-GCCcore-12.3.0.eb @@ -0,0 +1,48 @@ +name = 'LLVM' +version = '16.0.6' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'cstd': 'gnu++11', 'pic': True} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'cmake-%(version)s.src.tar.xz', + 'third-party-%(version)s.src.tar.xz', +] +checksums = [ + {'llvm-%(version)s.src.tar.xz': 'e91db44d1b3bb1c33fcea9a7d1f2423b883eaa9163d3d56ca2aa6d2f0711bc29'}, + {'cmake-%(version)s.src.tar.xz': '39d342a4161095d2f28fb1253e4585978ac50521117da666e2b1f6f28b62f514'}, + {'third-party-%(version)s.src.tar.xz': '15f5b9aeeba938530af977d5f9205612737a091a7f0f6c8075df8723b7713f70'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' From 2aa8ebf4be40d2ce60917d4384c4991a06005229 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 1 Aug 2023 13:30:03 +0200 Subject: [PATCH 8199/9987] Use batchspawner from specific commit, as support for JupyterHub 3.X and 4.X is not in a release yet --- .../JupyterHub/JupyterHub-4.0.1-GCCcore-12.2.0.eb | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.1-GCCcore-12.2.0.eb index 2fb61674d32..103b8b17283 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.1-GCCcore-12.2.0.eb @@ -25,6 +25,8 @@ dependencies = [ use_pip = True +local_batchspawner_commit = '2a9eda0' + exts_list = [ ('certipy', '0.1.3', { 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], @@ -65,8 +67,16 @@ exts_list = [ ('jupyterhub', version, { 'checksums': ['8e283ff59e5c4016712077d2549ed74acd915a32836fe00218678a8781bd7ede'], }), - ('batchspawner', '1.2.0', { - 'checksums': ['b1924bb4f3a3f527a1e312ecdaff3dbc5acfd91e6b13cf074a62cd74340a2e21'], + ('batchspawner', '1.2.0-%s' % local_batchspawner_commit, { + 'sources': { + 'filename': 'main.tar.gz', + 'git_config': { + 'url': 'https://github.com/jupyterhub/', + 'repo_name': 'batchspawner', + 'commit': local_batchspawner_commit, + } + }, + 'checksums': [None], }), ('jupyterhub-systemdspawner', '1.0.1', { 'modulename': 'systemdspawner', From 4dc5b47887c9869fc454d1c31e7aa57a8e258a20 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 1 Aug 2023 14:06:32 +0200 Subject: [PATCH 8200/9987] Add more patches --- .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 13 +- ...-1.13.1_fix-gcc-12-missing-includes.patch} | 0 ...-1.13.1_fix-gcc-12-warning-in-fbgemm.patch | 24 +++ ...yTorch-1.13.1_fix-numpy-deprecations.patch | 102 +++++++++++ ...yTorch-1.13.1_fix-python-3.11-compat.patch | 160 ++++++++++++++++++ 5 files changed, 297 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/PyTorch/{PyTorch-1.13.1_fix-gcc-12-compilation.patch => PyTorch-1.13.1_fix-gcc-12-missing-includes.patch} (100%) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-numpy-deprecations.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-python-3.11-compat.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 8954512e03a..7684662b261 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -23,9 +23,12 @@ patches = [ 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_fix-vsx-loadu.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', - 'PyTorch-1.13.1_fix-gcc-12-compilation.patch', + 'PyTorch-1.13.1_fix-gcc-12-missing-includes.patch', + 'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch', + 'PyTorch-1.13.1_fix-numpy-deprecations.patch', 'PyTorch-1.13.1_fix-protobuf-dependency.patch', 'PyTorch-1.13.1_fix-pytest-args.patch', + 'PyTorch-1.13.1_fix-python-3.11-compat.patch', 'PyTorch-1.13.1_fix-test-ops-conf.patch', 'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch', 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', @@ -55,11 +58,17 @@ checksums = [ {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, - {'PyTorch-1.13.1_fix-gcc-12-compilation.patch': + {'PyTorch-1.13.1_fix-gcc-12-missing-includes.patch': '18df8c61ecaa9fb659346c1e172828bca6b069f0145bb8f6a36b0a23b7bef0a6'}, + {'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch': + '5c7be91a6096083a0b1315efe0001537499c600f1f569953c6a2c7f4cc1d0910'}, + {'PyTorch-1.13.1_fix-numpy-deprecations.patch': + 'f461b570efe0434ddd806bf2fa7020eb213e3ed89d0eb4403e076f4276ba2a46'}, {'PyTorch-1.13.1_fix-protobuf-dependency.patch': '8bd755a0cab7233a243bc65ca57c9630dfccdc9bf8c9792f0de4e07a644fcb00'}, {'PyTorch-1.13.1_fix-pytest-args.patch': 'd3e3c841cf8d73683750f29326f2be56ee0bb5df7ff522baf7d7c3f301a91ec2'}, + {'PyTorch-1.13.1_fix-python-3.11-compat.patch': + 'fa4eb0e27e00a90bb217b77c0023089c4659c03f37d781ab4a681bdcb4f0432f'}, {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, {'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch': 'bdde0f2105215c95a54de64ec4b1a4520528510663174fef6d5b900eb1db3937'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-compilation.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-missing-includes.patch similarity index 100% rename from easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-compilation.patch rename to easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-missing-includes.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch new file mode 100644 index 00000000000..ec1168d3917 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch @@ -0,0 +1,24 @@ +GCC 12 has a regression (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=105593) +leading to warnings/errors during build: https://github.com/pytorch/FBGEMM/issues/1666 +Suppress the affected warning in FBGEMM. + +Author: Alexander Grund (TU Dresden) + +Submodule third_party/fbgemm contains modified content +diff --git a/third_party/fbgemm/CMakeLists.txt b/third_party/fbgemm/CMakeLists.txt +index 58dcb9ae..c888f0f8 100644 +--- a/third_party/fbgemm/CMakeLists.txt ++++ b/third_party/fbgemm/CMakeLists.txt +@@ -147,10 +147,10 @@ else(MSVC) + string(APPEND CMAKE_CXX_FLAGS " -Werror") + string(APPEND CMAKE_CXX_FLAGS " -Wno-deprecated-declarations") + target_compile_options(fbgemm_avx2 PRIVATE +- "-m64" "-mavx2" "-mf16c" "-mfma") ++ "-m64" "-mavx2" "-mf16c" "-mfma" "-Wno-uninitialized") + target_compile_options(fbgemm_avx512 PRIVATE + "-m64" "-mavx2" "-mfma" "-mavx512f" "-mavx512bw" "-mavx512dq" +- "-mavx512vl") ++ "-mavx512vl" "-Wno-uninitialized") + set_source_files_properties( + src/FbgemmFP16UKernelsAvx2.cc + src/FbgemmFP16UKernelsAvx512.cc diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-numpy-deprecations.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-numpy-deprecations.patch new file mode 100644 index 00000000000..e9586796310 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-numpy-deprecations.patch @@ -0,0 +1,102 @@ +Numpy 1.24 removed some types deprecated earlier leading to failures in e.g. test_torch: +> ERROR: test_parsing_intlist (__main__.TestTorch) +> ... +> AttributeError: module 'numpy' has no attribute 'float'. + +Backported from https://github.com/pytorch/pytorch/pull/93997 +Author: Alexander Grund (TU Dresden) + +diff --git a/test/quantization/core/test_quantized_op.py b/test/quantization/core/test_quantized_op.py +index 79297e073f0..827a781df10 100644 +--- a/test/quantization/core/test_quantized_op.py ++++ b/test/quantization/core/test_quantized_op.py +@@ -3010,7 +3010,7 @@ class TestDynamicQuantizedOps(TestCase): + # W_scale = 1.0 + # W_zp = 0 + W_scales = np.ones(output_channels) +- W_zps = np.zeros(output_channels).astype(np.int) ++ W_zps = np.zeros(output_channels).astype(int) + W_value_min = -128 + W_value_max = 127 + W_q0 = np.round( +@@ -3581,9 +3581,9 @@ class TestQuantizedLinear(TestCase): + # xnnpack forces W_zp to 0 when using symmetric quantization + # ONEDNN only supports symmetric quantization of weight + if dtype == torch.qint8 or qengine_is_onednn(): +- W_zps = np.zeros(output_channels).astype(np.int) ++ W_zps = np.zeros(output_channels).astype(int) + else: +- W_zps = np.round(np.random.rand(output_channels) * 100 - 50).astype(np.int) ++ W_zps = np.round(np.random.rand(output_channels) * 100 - 50).astype(int) + # when using symmetric quantization + # special restriction for xnnpack fully connected op weight + # [-127, 127] instead of [-128, 127] +diff --git a/test/test_reductions.py b/test/test_reductions.py +index 0e36906f25f..20fcb6ef9ae 100644 +--- a/test/test_reductions.py ++++ b/test/test_reductions.py +@@ -1323,7 +1323,7 @@ class TestReductions(TestCase): + vals = [[True, True], [True, False], [False, False], []] + for val in vals: + result = torch.prod(torch.tensor(val, device=device), dtype=torch.bool).item() +- expect = np.prod(np.array(val), dtype=np.bool) ++ expect = np.prod(np.array(val), dtype=bool) + self.assertEqual(result, expect) + + result = torch.prod(torch.tensor(val, device=device)).item() +diff --git a/test/test_tensor_creation_ops.py b/test/test_tensor_creation_ops.py +index aab26452496..a71761ce670 100644 +--- a/test/test_tensor_creation_ops.py ++++ b/test/test_tensor_creation_ops.py +@@ -1440,14 +1440,14 @@ class TestTensorCreation(TestCase): + def test_ctor_with_numpy_array(self, device): + correct_dtypes = [ + np.double, +- np.float, ++ float, + np.float16, + np.int64, + np.int32, + np.int16, + np.int8, + np.uint8, +- np.bool, ++ bool, + ] + + incorrect_byteorder = '>' if sys.byteorder == 'little' else '<' +diff --git a/test/test_tensorboard.py b/test/test_tensorboard.py +index e836b0f1ba8..0857873a5fa 100644 +--- a/test/test_tensorboard.py ++++ b/test/test_tensorboard.py +@@ -796,7 +796,7 @@ class TestTensorBoardNumpy(BaseTestCase): + model = ModelHelper(name="mnist") + # how come those inputs don't break the forward pass =.=a + workspace.FeedBlob("data", np.random.randn(1, 3, 64, 64).astype(np.float32)) +- workspace.FeedBlob("label", np.random.randn(1, 1000).astype(np.int)) ++ workspace.FeedBlob("label", np.random.randn(1, 1000).astype(int)) + + with core.NameScope("conv1"): + conv1 = brew.conv(model, "data", 'conv1', dim_in=1, dim_out=20, kernel=5) +@@ -831,7 +831,7 @@ class TestTensorBoardNumpy(BaseTestCase): + def test_caffe2_simple_cnnmodel(self): + model = cnn.CNNModelHelper("NCHW", name="overfeat") + workspace.FeedBlob("data", np.random.randn(1, 3, 64, 64).astype(np.float32)) +- workspace.FeedBlob("label", np.random.randn(1, 1000).astype(np.int)) ++ workspace.FeedBlob("label", np.random.randn(1, 1000).astype(int)) + with core.NameScope("conv1"): + conv1 = model.Conv("data", "conv1", 3, 96, 11, stride=4) + relu1 = model.Relu(conv1, conv1) +diff --git a/test/test_torch.py b/test/test_torch.py +index 8de5b822d00..3121e256b21 100644 +--- a/test/test_torch.py ++++ b/test/test_torch.py +@@ -6182,7 +6182,7 @@ class TestTorch(TestCase): + # fail parse with float variables + self.assertRaises(TypeError, lambda: torch.ones((torch.tensor(3.), torch.tensor(4)))) + # fail parse with numpy floats +- self.assertRaises(TypeError, lambda: torch.ones((np.float(3.), torch.tensor(4)))) ++ self.assertRaises(TypeError, lambda: torch.ones((3., torch.tensor(4)))) + self.assertRaises(TypeError, lambda: torch.ones((np.array(3.), torch.tensor(4)))) + + # fail parse with > 1 element variables diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-python-3.11-compat.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-python-3.11-compat.patch new file mode 100644 index 00000000000..327ff5fba84 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-python-3.11-compat.patch @@ -0,0 +1,160 @@ +Some code isn't compatible with Python 3.11+ +Backport https://github.com/pytorch/pytorch/pull/92895 to fix this. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_fx.py b/test/test_fx.py +index c8da9d3d2cf..6aefb4b9b2c 100644 +--- a/test/test_fx.py ++++ b/test/test_fx.py +@@ -3295,6 +3295,7 @@ class TestFX(JitTestCase): + finally: + del sys.modules["__future__"] + ++ @unittest.skipIf(sys.version_info > (3, 11), "Does not work in 3.11") + def test_annotations_empty_tuple(self): + class Foo(torch.nn.Module): + def forward(self, x: Tuple[()], y: Tuple[str, Tuple[()]]): +@@ -4030,7 +4031,7 @@ class TestFunctionalTracing(JitTestCase): + "max_pool2d": PROXY_ITERATED, + "max_pool3d": PROXY_ITERATED, + +- "group_norm": LEN_ERROR ++ "group_norm": PROXY_ITERATED + } + + @classmethod +@@ -4069,7 +4070,7 @@ class TestFunctionalTracing(JitTestCase): + + def functional_test(self): + if func_name in self.UNTRACEABLE_FUNCTIONALS_PY38 and \ +- sys.version_info >= (3, 8) and sys.version_info < (3, 11): ++ sys.version_info >= (3, 8) and sys.version_info < (3, 12): + exc, err = self.UNTRACEABLE_FUNCTIONALS_PY38[func_name] + with self.assertRaisesRegex(exc, err): + symbolic_trace(fn) +diff --git a/torch/fx/_symbolic_trace.py b/torch/fx/_symbolic_trace.py +index ff9df1161a7..521bb02c846 100644 +--- a/torch/fx/_symbolic_trace.py ++++ b/torch/fx/_symbolic_trace.py +@@ -119,7 +119,29 @@ def _patch_function(fn: FunctionType, nargs: int) -> FunctionType: + co = fn.__code__ + co_flags = co.co_flags & ~HAS_VARSTUFF + co_args: tuple +- if hasattr(co, "co_posonlyargcount"): ++ if hasattr(co, "co_qualname"): ++ # Python-3.11+ code signature ++ co_args = ( ++ nargs, ++ 0, ++ 0, ++ co.co_nlocals, ++ co.co_stacksize, ++ co_flags, ++ co.co_code, ++ co.co_consts, ++ co.co_names, ++ co.co_varnames, ++ co.co_filename, ++ co.co_name, ++ co.co_qualname, # type: ignore[attr-defined] ++ co.co_firstlineno, ++ co.co_lnotab, ++ co.co_exceptiontable, # type: ignore[attr-defined] ++ co.co_freevars, ++ co.co_cellvars, ++ ) ++ elif hasattr(co, "co_posonlyargcount"): + co_args = ( + nargs, + 0, +diff --git a/torch/fx/operator_schemas.py b/torch/fx/operator_schemas.py +index 7ec3bc9a673..7c8971fb3ec 100644 +--- a/torch/fx/operator_schemas.py ++++ b/torch/fx/operator_schemas.py +@@ -61,18 +61,29 @@ def _torchscript_type_to_python_type(ts_type : 'torch._C.JitType') -> Any: + return eval(ts_type.annotation_str, _type_eval_globals) + + def _torchscript_schema_to_signature(ts_schema : torch._C.FunctionSchema) -> inspect.Signature: +- parameters : List[inspect.Parameter] = [] ++ from inspect import Parameter ++ parameters : List[Parameter] = [] + for arg in ts_schema.arguments: + arg_type = _torchscript_type_to_python_type(arg.type) +- default = arg.default_value if arg.has_default_value() else inspect.Parameter.empty ++ default = arg.default_value if arg.has_default_value() else Parameter.empty + # TODO: Figure out if this is safe. It seems like when generating the type signatures for + # PythonArgParser, we emit signatures with `input` instead of `self` as the first tensor + # argument name. Downstream, if someone converts that positional argument to a keyword + # argument, the name mismatch will break things, so here we're going to normalize the + # name to "input" + name = arg.name if arg.name != 'self' else 'input' +- kind = inspect.Parameter.KEYWORD_ONLY if arg.kwarg_only else inspect.Parameter.POSITIONAL_OR_KEYWORD +- parameters.append(inspect.Parameter(name=name, kind=kind, default=default, annotation=arg_type)) ++ kind = Parameter.KEYWORD_ONLY if arg.kwarg_only else Parameter.POSITIONAL_OR_KEYWORD ++ # "from" is a keyword therefore it must be a POSITIONAL_ONLY argument ++ if name == "from": ++ assert kind == Parameter.POSITIONAL_OR_KEYWORD ++ # ParameterKind type is internal implementation detail to inspec package ++ # which makes it hard to do type annoation ++ kind = Parameter.POSITIONAL_ONLY # type: ignore[assignment] ++ # This renders all previous arguments to positional only ++ for idx, p in enumerate(parameters): ++ assert p.kind == Parameter.POSITIONAL_OR_KEYWORD ++ parameters[idx] = Parameter(name=p.name, kind=Parameter.POSITIONAL_ONLY, default=p.default, annotation=p.annotation) ++ parameters.append(Parameter(name=name, kind=kind, default=default, annotation=arg_type)) + return_types = [_torchscript_type_to_python_type(ret.type) for ret in ts_schema.returns] + if len(return_types) == 0: + return_type = None +@@ -392,7 +403,12 @@ def _args_kwargs_to_normalized_args_kwargs(sig : inspect.Signature, args : Tuple + supported_parameter_types = { + inspect.Parameter.POSITIONAL_OR_KEYWORD, inspect.Parameter.KEYWORD_ONLY} + if any(p.kind not in supported_parameter_types for p in sig.parameters.values()): +- return None ++ # Add an exception for one signature, which is common for random/uniform, i.e.: ++ # Tensor(a!) self, float from=0, float to=1, *, Generator? generator=None ++ # `from` is Python keyword and as such functions with that signature should have ++ # positional-only args, but at the same time they could be dispatched as kwargs ++ if list(sig.parameters.keys()) != ['input', 'from', 'to', 'generator']: ++ return None + + bound_args = sig.bind(*args, **kwargs) + bound_args.apply_defaults() +diff --git a/torch/fx/proxy.py b/torch/fx/proxy.py +index 5d65f03e29b..120452dfd71 100644 +--- a/torch/fx/proxy.py ++++ b/torch/fx/proxy.py +@@ -1,4 +1,5 @@ + import dis ++import sys + import torch + import inspect + import operator +@@ -267,7 +268,13 @@ class Proxy: + assert frame is not None + calling_frame = frame.f_back + assert calling_frame is not None +- inst = list(dis.get_instructions(calling_frame.f_code))[calling_frame.f_lasti // 2] ++ inst_list = list(dis.get_instructions(calling_frame.f_code)) ++ if sys.version_info >= (3, 11): ++ from bisect import bisect_left ++ inst_idx = bisect_left(inst_list, calling_frame.f_lasti, key=lambda x: x.offset) ++ else: ++ inst_idx = calling_frame.f_lasti // 2 ++ inst = inst_list[inst_idx] + if inst.opname == 'UNPACK_SEQUENCE': + return (self[i] for i in range(inst.argval)) # type: ignore[index] + +@@ -282,7 +289,11 @@ class Proxy: + calling_frame = frame.f_back + assert calling_frame is not None + insts = list(dis.get_instructions(calling_frame.f_code)) +- cur = calling_frame.f_lasti // 2 ++ if sys.version_info >= (3, 11): ++ from bisect import bisect_left ++ cur = bisect_left(insts, calling_frame.f_lasti, key=lambda x: x.offset) ++ else: ++ cur = calling_frame.f_lasti // 2 + inst = insts[cur] + + if inst.opname == 'POP_JUMP_IF_TRUE': From 7e224d1d7245e653641c9169756c739eed46219f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 1 Aug 2023 14:54:56 +0200 Subject: [PATCH 8201/9987] Fix GCC 12 regression with wrong warnings --- .../easyconfigs/g/GCCcore/GCCcore-12.1.0.eb | 5 + ...Ccore-12.1.0_allow-pragma-wself-init.patch | 451 ++++++++++++++++++ ....0_fix-Wuninitialized-in-AVX-headers.patch | 218 +++++++++ .../easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 5 + 4 files changed, 679 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0_allow-pragma-wself-init.patch create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb index da98d2ef021..015bdcc4c2a 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb @@ -33,6 +33,8 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.1.0_allow-pragma-wself-init.patch', + 'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch', 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ @@ -45,6 +47,9 @@ checksums = [ {'nvptx-tools-20220412.tar.gz': '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.1.0_allow-pragma-wself-init.patch': '464f5faa9b23e805995d10dcdacca83df6321cac70826e9a3bc5bc9cd737f6a1'}, + {'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch': + '0ea675960795e238a43ae7d685a0082b21f0b63cf2fe499f6d55e89e0aaee392'}, {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0_allow-pragma-wself-init.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0_allow-pragma-wself-init.patch new file mode 100644 index 00000000000..1e7f3876bbe --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0_allow-pragma-wself-init.patch @@ -0,0 +1,451 @@ +From aabebf76e9d9a805ea5b443d4ee4f49f13155d87 Mon Sep 17 00:00:00 2001 +From: Marek Polacek +Date: Tue, 26 Jul 2022 13:55:58 -0400 +Subject: [PATCH] c-family: Honor -Wno-init-self for cv-qual vars [PR102633] + +Since r11-5188-g32934a4f45a721, we drop qualifiers during l-to-r +conversion by creating a NOP_EXPR. For e.g. + + const int i = i; + +that means that the DECL_INITIAL is '(int) i' and not 'i' anymore. +Consequently, we don't suppress_warning here: + +711 case DECL_EXPR: +715 if (VAR_P (DECL_EXPR_DECL (*expr_p)) +716 && !DECL_EXTERNAL (DECL_EXPR_DECL (*expr_p)) +717 && !TREE_STATIC (DECL_EXPR_DECL (*expr_p)) +718 && (DECL_INITIAL (DECL_EXPR_DECL (*expr_p)) == DECL_EXPR_DECL (*expr_p)) +719 && !warn_init_self) +720 suppress_warning (DECL_EXPR_DECL (*expr_p), OPT_Winit_self); + +because of the check on line 718 -- (int) i is not i. So -Wno-init-self +doesn't disable the warning as it's supposed to. + +The following patch fixes it by moving the suppress_warning call from +c_gimplify_expr to the front ends, at points where we haven't created +the NOP_EXPR yet. + + PR middle-end/102633 + +gcc/c-family/ChangeLog: + + * c-gimplify.cc (c_gimplify_expr) : Don't call + suppress_warning here. + +gcc/c/ChangeLog: + + * c-parser.cc (c_parser_initializer): Add new tree parameter. Use it. + Call suppress_warning. + (c_parser_declaration_or_fndef): Pass d down to c_parser_initializer. + (c_parser_omp_declare_reduction): Pass omp_priv down to + c_parser_initializer. + +gcc/cp/ChangeLog: + + * decl.cc (cp_finish_decl): Call suppress_warning. + +gcc/testsuite/ChangeLog: + + * c-c++-common/Winit-self1.c: New test. + * c-c++-common/Winit-self2.c: New test. + +(cherry picked from commit 04ce2400b35225302e0d6883bb0817378180f5d7) +--- + gcc/c-family/c-gimplify.cc | 12 --------- + gcc/c/c-parser.cc | 19 ++++++++++++--- + gcc/cp/decl.cc | 8 ++++++ + gcc/testsuite/c-c++-common/Winit-self1.c | 31 ++++++++++++++++++++++++ + gcc/testsuite/c-c++-common/Winit-self2.c | 31 ++++++++++++++++++++++++ + 5 files changed, 85 insertions(+), 16 deletions(-) + create mode 100644 gcc/testsuite/c-c++-common/Winit-self1.c + create mode 100644 gcc/testsuite/c-c++-common/Winit-self2.c + +diff --git a/gcc/c-family/c-gimplify.cc b/gcc/c-family/c-gimplify.cc +index 2b683a399821e..7e55fd73f810d 100644 +--- a/gcc/c-family/c-gimplify.cc ++++ b/gcc/c-family/c-gimplify.cc +@@ -704,18 +704,6 @@ c_gimplify_expr (tree *expr_p, gimple_seq *pre_p ATTRIBUTE_UNUSED, + break; + } + +- case DECL_EXPR: +- /* This is handled mostly by gimplify.cc, but we have to deal with +- not warning about int x = x; as it is a GCC extension to turn off +- this warning but only if warn_init_self is zero. */ +- if (VAR_P (DECL_EXPR_DECL (*expr_p)) +- && !DECL_EXTERNAL (DECL_EXPR_DECL (*expr_p)) +- && !TREE_STATIC (DECL_EXPR_DECL (*expr_p)) +- && (DECL_INITIAL (DECL_EXPR_DECL (*expr_p)) == DECL_EXPR_DECL (*expr_p)) +- && !warn_init_self) +- suppress_warning (DECL_EXPR_DECL (*expr_p), OPT_Winit_self); +- break; +- + case PREINCREMENT_EXPR: + case PREDECREMENT_EXPR: + case POSTINCREMENT_EXPR: +diff --git a/gcc/c/c-parser.cc b/gcc/c/c-parser.cc +index a21449bb83a4c..80f86c177fad3 100644 +--- a/gcc/c/c-parser.cc ++++ b/gcc/c/c-parser.cc +@@ -1513,7 +1513,7 @@ static struct c_arg_info *c_parser_parms_list_declarator (c_parser *, tree, + static struct c_parm *c_parser_parameter_declaration (c_parser *, tree, bool); + static tree c_parser_simple_asm_expr (c_parser *); + static tree c_parser_gnu_attributes (c_parser *); +-static struct c_expr c_parser_initializer (c_parser *); ++static struct c_expr c_parser_initializer (c_parser *, tree); + static struct c_expr c_parser_braced_init (c_parser *, tree, bool, + struct obstack *); + static void c_parser_initelt (c_parser *, struct obstack *); +@@ -2278,7 +2278,7 @@ c_parser_declaration_or_fndef (c_parser *parser, bool fndef_ok, + int flag_sanitize_save = flag_sanitize; + if (TREE_CODE (d) == PARM_DECL) + flag_sanitize = 0; +- init = c_parser_initializer (parser); ++ init = c_parser_initializer (parser, d); + flag_sanitize = flag_sanitize_save; + finish_init (); + } +@@ -5206,11 +5206,13 @@ c_parser_type_name (c_parser *parser, bool alignas_ok) + Any expression without commas is accepted in the syntax for the + constant-expressions, with non-constant expressions rejected later. + ++ DECL is the declaration we're parsing this initializer for. ++ + This function is only used for top-level initializers; for nested + ones, see c_parser_initval. */ + + static struct c_expr +-c_parser_initializer (c_parser *parser) ++c_parser_initializer (c_parser *parser, tree decl) + { + if (c_parser_next_token_is (parser, CPP_OPEN_BRACE)) + return c_parser_braced_init (parser, NULL_TREE, false, NULL); +@@ -5219,6 +5221,15 @@ c_parser_initializer (c_parser *parser) + struct c_expr ret; + location_t loc = c_parser_peek_token (parser)->location; + ret = c_parser_expr_no_commas (parser, NULL); ++ /* This is handled mostly by gimplify.cc, but we have to deal with ++ not warning about int x = x; as it is a GCC extension to turn off ++ this warning but only if warn_init_self is zero. */ ++ if (VAR_P (decl) ++ && !DECL_EXTERNAL (decl) ++ && !TREE_STATIC (decl) ++ && ret.value == decl ++ && !warn_init_self) ++ suppress_warning (decl, OPT_Winit_self); + if (TREE_CODE (ret.value) != STRING_CST + && TREE_CODE (ret.value) != COMPOUND_LITERAL_EXPR) + ret = convert_lvalue_to_rvalue (loc, ret, true, true); +@@ -22393,7 +22404,7 @@ c_parser_omp_declare_reduction (c_parser *parser, enum pragma_context context) + location_t loc = c_parser_peek_token (parser)->location; + rich_location richloc (line_table, loc); + start_init (omp_priv, NULL_TREE, 0, &richloc); +- struct c_expr init = c_parser_initializer (parser); ++ struct c_expr init = c_parser_initializer (parser, omp_priv); + finish_init (); + finish_decl (omp_priv, loc, init.value, + init.original_type, NULL_TREE); +diff --git a/gcc/cp/decl.cc b/gcc/cp/decl.cc +index 64fba7fafac74..7569785988e29 100644 +--- a/gcc/cp/decl.cc ++++ b/gcc/cp/decl.cc +@@ -8240,6 +8240,14 @@ cp_finish_decl (tree decl, tree init, bool init_const_expr_p, + && !TYPE_REF_P (type)) + TREE_CONSTANT (decl) = 1; + } ++ /* This is handled mostly by gimplify.cc, but we have to deal with ++ not warning about int x = x; as it is a GCC extension to turn off ++ this warning but only if warn_init_self is zero. */ ++ if (!DECL_EXTERNAL (decl) ++ && !TREE_STATIC (decl) ++ && decl == tree_strip_any_location_wrapper (init) ++ && !warn_init_self) ++ suppress_warning (decl, OPT_Winit_self); + } + + if (flag_openmp +diff --git a/gcc/testsuite/c-c++-common/Winit-self1.c b/gcc/testsuite/c-c++-common/Winit-self1.c +new file mode 100644 +index 0000000000000..740b83b5e9f3d +--- /dev/null ++++ b/gcc/testsuite/c-c++-common/Winit-self1.c +@@ -0,0 +1,31 @@ ++/* PR middle-end/102633 */ ++/* { dg-do compile } */ ++/* { dg-options "-Wuninitialized -Wno-init-self" } */ ++ ++int ++fn1 (void) ++{ ++ int i = i; ++ return i; ++} ++ ++int ++fn2 () ++{ ++ const int j = j; ++ return j; ++} ++ ++int ++fn3 () ++{ ++ volatile int k = k; ++ return k; ++} ++ ++int ++fn4 () ++{ ++ const volatile int l = l; ++ return l; ++} +diff --git a/gcc/testsuite/c-c++-common/Winit-self2.c b/gcc/testsuite/c-c++-common/Winit-self2.c +new file mode 100644 +index 0000000000000..13aa9efdf2615 +--- /dev/null ++++ b/gcc/testsuite/c-c++-common/Winit-self2.c +@@ -0,0 +1,31 @@ ++/* PR middle-end/102633 */ ++/* { dg-do compile } */ ++/* { dg-options "-Wuninitialized -Winit-self" } */ ++ ++int ++fn1 (void) ++{ ++ int i = i; /* { dg-warning "used uninitialized" } */ ++ return i; ++} ++ ++int ++fn2 () ++{ ++ const int j = j; /* { dg-warning "used uninitialized" } */ ++ return j; ++} ++ ++int ++fn3 () ++{ ++ volatile int k = k; /* { dg-warning "used uninitialized" } */ ++ return k; ++} ++ ++int ++fn4 () ++{ ++ const volatile int l = l; /* { dg-warning "used uninitialized" } */ ++ return l; ++} + +From 732d744e82332e7cc269694197c0df2a3635730f Mon Sep 17 00:00:00 2001 +From: Jakub Jelinek +Date: Mon, 16 Jan 2023 09:40:14 +0100 +Subject: [PATCH] c, c++: Allow ignoring -Winit-self through pragmas [PR105593] + +As mentioned in the PR, various x86 intrinsics need to return +an uninitialized vector. Currently they use self initialization +to avoid -Wuninitialized warnings, which works fine in C, but +doesn't work in C++ where -Winit-self is enabled in -Wall. +We don't have an attribute to mark a variable as knowingly +uninitialized (the uninitialized attribute exists but means +something else, only in the -ftrivial-auto-var-init context), +and trying to suppress either -Wuninitialized or -Winit-self +inside of the _mm_undefined_ps etc. intrinsic definitions +doesn't work, one needs to currently disable through pragmas +-Wuninitialized warning at the point where _mm_undefined_ps etc. +result is actually used, but that goes against the intent of +those intrinsics. + +The -Winit-self warning option actually doesn't do any warning, +all we do is record a suppression for -Winit-self if !warn_init_self +on the decl definition and later look that up in uninit pass. + +The following patch changes those !warn_init_self tests which +are true only based on the command line option setting, not based +on GCC diagnostic pragma overrides to +!warning_enabled_at (DECL_SOURCE_LOCATION (decl), OPT_Winit_self) +such that it takes them into account. + +2023-01-16 Jakub Jelinek + + PR c++/105593 +gcc/c/ + * c-parser.cc (c_parser_initializer): Check warning_enabled_at + at the DECL_SOURCE_LOCATION (decl) for OPT_Winit_self instead + of warn_init_self. +gcc/cp/ + * decl.cc (cp_finish_decl): Check warning_enabled_at + at the DECL_SOURCE_LOCATION (decl) for OPT_Winit_self instead + of warn_init_self. +gcc/testsuite/ + * c-c++-common/Winit-self3.c: New test. + * c-c++-common/Winit-self4.c: New test. + * c-c++-common/Winit-self5.c: New test. + +(cherry picked from commit 98b41fd4045b7856e7b85dd58d67c600bd909379) +--- + gcc/c/c-parser.cc | 2 +- + gcc/cp/decl.cc | 2 +- + gcc/testsuite/c-c++-common/Winit-self3.c | 36 ++++++++++++++++++++++++ + gcc/testsuite/c-c++-common/Winit-self4.c | 36 ++++++++++++++++++++++++ + gcc/testsuite/c-c++-common/Winit-self5.c | 36 ++++++++++++++++++++++++ + 5 files changed, 110 insertions(+), 2 deletions(-) + create mode 100644 gcc/testsuite/c-c++-common/Winit-self3.c + create mode 100644 gcc/testsuite/c-c++-common/Winit-self4.c + create mode 100644 gcc/testsuite/c-c++-common/Winit-self5.c + +diff --git a/gcc/c/c-parser.cc b/gcc/c/c-parser.cc +index 80f86c177fad3..78a313fe31ef2 100644 +--- a/gcc/c/c-parser.cc ++++ b/gcc/c/c-parser.cc +@@ -5228,7 +5228,7 @@ c_parser_initializer (c_parser *parser, tree decl) + && !DECL_EXTERNAL (decl) + && !TREE_STATIC (decl) + && ret.value == decl +- && !warn_init_self) ++ && !warning_enabled_at (DECL_SOURCE_LOCATION (decl), OPT_Winit_self)) + suppress_warning (decl, OPT_Winit_self); + if (TREE_CODE (ret.value) != STRING_CST + && TREE_CODE (ret.value) != COMPOUND_LITERAL_EXPR) +diff --git a/gcc/cp/decl.cc b/gcc/cp/decl.cc +index 7569785988e29..fd1a1cbbf2cb0 100644 +--- a/gcc/cp/decl.cc ++++ b/gcc/cp/decl.cc +@@ -8246,7 +8246,7 @@ cp_finish_decl (tree decl, tree init, bool init_const_expr_p, + if (!DECL_EXTERNAL (decl) + && !TREE_STATIC (decl) + && decl == tree_strip_any_location_wrapper (init) +- && !warn_init_self) ++ && !warning_enabled_at (DECL_SOURCE_LOCATION (decl), OPT_Winit_self)) + suppress_warning (decl, OPT_Winit_self); + } + +diff --git a/gcc/testsuite/c-c++-common/Winit-self3.c b/gcc/testsuite/c-c++-common/Winit-self3.c +new file mode 100644 +index 0000000000000..b83135f193bdd +--- /dev/null ++++ b/gcc/testsuite/c-c++-common/Winit-self3.c +@@ -0,0 +1,36 @@ ++/* PR c++/105593 */ ++/* { dg-do compile } */ ++/* { dg-options "-W -Wall" } */ ++ ++void bar (int); ++ ++static inline int ++baz (void) ++{ ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" ++ int u = u; /* { dg-bogus "'u' is used uninitialized" } */ ++#pragma GCC diagnostic pop ++ return u; ++} ++ ++void ++foo (void) ++{ ++ int u = baz (); ++ bar (u); ++} ++ ++static inline int ++qux (void) ++{ ++ int u = u; /* { dg-warning "'u' is used uninitialized" "" { target c++ } } */ ++ return u; /* { dg-message "'u' was declared here" "" { target c++ } .-1 } */ ++} ++ ++void ++corge (void) ++{ ++ int u = qux (); ++ bar (u); ++} +diff --git a/gcc/testsuite/c-c++-common/Winit-self4.c b/gcc/testsuite/c-c++-common/Winit-self4.c +new file mode 100644 +index 0000000000000..b38b7cc60b578 +--- /dev/null ++++ b/gcc/testsuite/c-c++-common/Winit-self4.c +@@ -0,0 +1,36 @@ ++/* PR c++/105593 */ ++/* { dg-do compile } */ ++/* { dg-options "-W -Wall -Winit-self" } */ ++ ++void bar (int); ++ ++static inline int ++baz (void) ++{ ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" ++ int u = u; /* { dg-bogus "'u' is used uninitialized" } */ ++#pragma GCC diagnostic pop ++ return u; ++} ++ ++void ++foo (void) ++{ ++ int u = baz (); ++ bar (u); ++} ++ ++static inline int ++qux (void) ++{ ++ int u = u; /* { dg-warning "'u' is used uninitialized" } */ ++ return u; /* { dg-message "'u' was declared here" "" { target *-*-* } .-1 } */ ++} ++ ++void ++corge (void) ++{ ++ int u = qux (); ++ bar (u); ++} +diff --git a/gcc/testsuite/c-c++-common/Winit-self5.c b/gcc/testsuite/c-c++-common/Winit-self5.c +new file mode 100644 +index 0000000000000..db2d9a132194c +--- /dev/null ++++ b/gcc/testsuite/c-c++-common/Winit-self5.c +@@ -0,0 +1,36 @@ ++/* PR c++/105593 */ ++/* { dg-do compile } */ ++/* { dg-options "-W -Wall -Wno-init-self" } */ ++ ++void bar (int); ++ ++static inline int ++baz (void) ++{ ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" ++ int u = u; /* { dg-bogus "'u' is used uninitialized" } */ ++#pragma GCC diagnostic pop ++ return u; ++} ++ ++void ++foo (void) ++{ ++ int u = baz (); ++ bar (u); ++} ++ ++static inline int ++qux (void) ++{ ++ int u = u; /* { dg-bogus "'u' is used uninitialized" } */ ++ return u; ++} ++ ++void ++corge (void) ++{ ++ int u = qux (); ++ bar (u); ++} diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch new file mode 100644 index 00000000000..5ab5363a7a4 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch @@ -0,0 +1,218 @@ +From 72af61b122127b112215d496d65c64cfdc56fce8 Mon Sep 17 00:00:00 2001 +From: Jakub Jelinek +Date: Mon, 16 Jan 2023 09:41:38 +0100 +Subject: [PATCH] x86: Avoid -Wuninitialized warnings on _mm*_undefined_* in + C++ [PR105593] + +In https://gcc.gnu.org/pipermail/gcc-patches/2023-January/609844.html +I've posted a patch to allow ignoring -Winit-self using GCC diagnostic +pragmas, such that one can mark self-initialization as intentional +disabling of -Wuninitialized warnings. + +The following incremental patch uses that in the x86 intrinsic +headers. + +2023-01-16 Jakub Jelinek + + PR c++/105593 +gcc/ + * config/i386/xmmintrin.h (_mm_undefined_ps): Temporarily + disable -Winit-self using pragma GCC diagnostic ignored. + * config/i386/emmintrin.h (_mm_undefined_pd, _mm_undefined_si128): + Likewise. + * config/i386/avxintrin.h (_mm256_undefined_pd, _mm256_undefined_ps, + _mm256_undefined_si256): Likewise. + * config/i386/avx512fintrin.h (_mm512_undefined_pd, + _mm512_undefined_ps, _mm512_undefined_epi32): Likewise. + * config/i386/avx512fp16intrin.h (_mm_undefined_ph, + _mm256_undefined_ph, _mm512_undefined_ph): Likewise. +gcc/testsuite/ + * g++.target/i386/pr105593.C: New test. + +(cherry picked from commit 6b0907b4fc455377e5f8109f427d97da02b6aec9) +--- + gcc/config/i386/avx512fintrin.h | 9 +++++++++ + gcc/config/i386/avx512fp16intrin.h | 9 +++++++++ + gcc/config/i386/avxintrin.h | 9 +++++++++ + gcc/config/i386/emmintrin.h | 6 ++++++ + gcc/config/i386/xmmintrin.h | 3 +++ + gcc/testsuite/g++.target/i386/pr105593.C | 20 ++++++++++++++++++++ + 6 files changed, 56 insertions(+) + create mode 100644 gcc/testsuite/g++.target/i386/pr105593.C + +diff --git a/gcc/config/i386/avx512fintrin.h b/gcc/config/i386/avx512fintrin.h +index 77d6249c2bc50..24316c5a49572 100644 +--- a/gcc/config/i386/avx512fintrin.h ++++ b/gcc/config/i386/avx512fintrin.h +@@ -185,7 +185,10 @@ extern __inline __m512 + __attribute__ ((__gnu_inline__, __always_inline__, __artificial__)) + _mm512_undefined_ps (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m512 __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + +@@ -195,7 +198,10 @@ extern __inline __m512d + __attribute__ ((__gnu_inline__, __always_inline__, __artificial__)) + _mm512_undefined_pd (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m512d __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + +@@ -203,7 +209,10 @@ extern __inline __m512i + __attribute__ ((__gnu_inline__, __always_inline__, __artificial__)) + _mm512_undefined_epi32 (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m512i __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + +diff --git a/gcc/config/i386/avx512fp16intrin.h b/gcc/config/i386/avx512fp16intrin.h +index e43acaab12a11..b16ccfcb7f17c 100644 +--- a/gcc/config/i386/avx512fp16intrin.h ++++ b/gcc/config/i386/avx512fp16intrin.h +@@ -204,7 +204,10 @@ extern __inline __m128h + __attribute__ ((__gnu_inline__, __always_inline__, __artificial__)) + _mm_undefined_ph (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m128h __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + +@@ -212,7 +215,10 @@ extern __inline __m256h + __attribute__ ((__gnu_inline__, __always_inline__, __artificial__)) + _mm256_undefined_ph (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m256h __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + +@@ -220,7 +226,10 @@ extern __inline __m512h + __attribute__ ((__gnu_inline__, __always_inline__, __artificial__)) + _mm512_undefined_ph (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m512h __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + +diff --git a/gcc/config/i386/avxintrin.h b/gcc/config/i386/avxintrin.h +index c76d600ee5ce9..d5aff7ddcfa59 100644 +--- a/gcc/config/i386/avxintrin.h ++++ b/gcc/config/i386/avxintrin.h +@@ -1207,21 +1207,30 @@ _mm256_movemask_ps (__m256 __A) + extern __inline __m256d __attribute__((__gnu_inline__, __always_inline__, __artificial__)) + _mm256_undefined_pd (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m256d __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + + extern __inline __m256 __attribute__((__gnu_inline__, __always_inline__, __artificial__)) + _mm256_undefined_ps (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m256 __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + + extern __inline __m256i __attribute__((__gnu_inline__, __always_inline__, __artificial__)) + _mm256_undefined_si256 (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m256i __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + +diff --git a/gcc/config/i386/emmintrin.h b/gcc/config/i386/emmintrin.h +index 654a8e8c9adba..069b1a193a20d 100644 +--- a/gcc/config/i386/emmintrin.h ++++ b/gcc/config/i386/emmintrin.h +@@ -99,7 +99,10 @@ _mm_setr_pd (double __W, double __X) + extern __inline __m128d __attribute__((__gnu_inline__, __always_inline__, __artificial__)) + _mm_undefined_pd (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m128d __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + +@@ -785,7 +788,10 @@ _mm_move_epi64 (__m128i __A) + extern __inline __m128i __attribute__((__gnu_inline__, __always_inline__, __artificial__)) + _mm_undefined_si128 (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m128i __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + +diff --git a/gcc/config/i386/xmmintrin.h b/gcc/config/i386/xmmintrin.h +index 626590806010e..f1c704a2d4325 100644 +--- a/gcc/config/i386/xmmintrin.h ++++ b/gcc/config/i386/xmmintrin.h +@@ -109,7 +109,10 @@ typedef float __v4sf __attribute__ ((__vector_size__ (16))); + extern __inline __m128 __attribute__((__gnu_inline__, __always_inline__, __artificial__)) + _mm_undefined_ps (void) + { ++#pragma GCC diagnostic push ++#pragma GCC diagnostic ignored "-Winit-self" + __m128 __Y = __Y; ++#pragma GCC diagnostic pop + return __Y; + } + +diff --git a/gcc/testsuite/g++.target/i386/pr105593.C b/gcc/testsuite/g++.target/i386/pr105593.C +new file mode 100644 +index 0000000000000..3897f706bb11c +--- /dev/null ++++ b/gcc/testsuite/g++.target/i386/pr105593.C +@@ -0,0 +1,20 @@ ++// PR c++/105593 ++// { dg-do compile { target c++14 } } ++// { dg-options "-mavx512fp16 -W -Wall -O2" } ++ ++#include ++ ++auto f1 () { return _mm_undefined_pd (); } ++auto f2 () { return _mm_undefined_ps (); } ++auto f3 () { return _mm_undefined_si128 (); } ++auto f4 () { return _mm_undefined_ph (); } ++auto f5 () { return _mm256_undefined_pd (); } ++auto f6 () { return _mm256_undefined_ps (); } ++auto f7 () { return _mm256_undefined_si256 (); } ++auto f8 () { return _mm256_undefined_ph (); } ++auto f9 () { return _mm512_undefined_pd (); } ++auto f10 () { return _mm512_undefined_ps (); } ++auto f11 () { return _mm512_undefined_epi32 (); } ++auto f12 () { return _mm512_undefined_ph (); } ++ ++// { dg-bogus "is used uninitialized" "" { target *-*-* } 0 } diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb index 623abd95ffe..c1aee0bbfc9 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -33,6 +33,8 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.1.0_allow-pragma-wself-init.patch', + 'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch', 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ @@ -45,6 +47,9 @@ checksums = [ {'nvptx-tools-20220610.tar.gz': '53e7973af841935490b8a7b9e4d1331f775589b54e21f9921f18589183fb9997'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.1.0_allow-pragma-wself-init.patch': '464f5faa9b23e805995d10dcdacca83df6321cac70826e9a3bc5bc9cd737f6a1'}, + {'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch': + '0ea675960795e238a43ae7d685a0082b21f0b63cf2fe499f6d55e89e0aaee392'}, {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, ] From f7ca543b7eb00234c75f9cf7f0314815426faaf5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 1 Aug 2023 15:10:42 +0200 Subject: [PATCH 8202/9987] Fix new failures --- .../PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb | 6 ++++ ...-1.13.1_fix-fsdp-tp-integration-test.patch | 32 +++++++++++++++++++ ...1.13.1_fix-wrong-check-in-fsdp-tests.patch | 21 ++++++++++++ 3 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-tp-integration-test.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-wrong-check-in-fsdp-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb index 314131b5e65..3f1d7644427 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb @@ -24,9 +24,11 @@ patches = [ 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', 'PyTorch-1.13.1_fix-fsdp-fp16-test.patch', + 'PyTorch-1.13.1_fix-fsdp-tp-integration-test.patch', 'PyTorch-1.13.1_fix-kineto-crash-on-exit.patch', 'PyTorch-1.13.1_fix-pytest-args.patch', 'PyTorch-1.13.1_fix-test-ops-conf.patch', + 'PyTorch-1.13.1_fix-wrong-check-in-fsdp-tests.patch', 'PyTorch-1.13.1_increase-tolerance-test_ops.patch', 'PyTorch-1.13.1_increase-tolerance-test_optim.patch', 'PyTorch-1.13.1_install-vsx-vec-headers.patch', @@ -56,10 +58,14 @@ checksums = [ {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, {'PyTorch-1.13.1_fix-fsdp-fp16-test.patch': '8ae68e60d6e1f92f50322b7f0381c7e65251fba32d7606e3a238a36a2f55b5cf'}, + {'PyTorch-1.13.1_fix-fsdp-tp-integration-test.patch': + '31e2d63b54ae1a8c554575f46db79bf8bbda851b6ca0ffe623c4911207a3c2bc'}, {'PyTorch-1.13.1_fix-kineto-crash-on-exit.patch': 'f1e6808ee8d91a2ad76e0caedb4685e5aec3008d5e2e3c3c3e88cbb25cbd71b4'}, {'PyTorch-1.13.1_fix-pytest-args.patch': 'd3e3c841cf8d73683750f29326f2be56ee0bb5df7ff522baf7d7c3f301a91ec2'}, {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, + {'PyTorch-1.13.1_fix-wrong-check-in-fsdp-tests.patch': + 'cbb5ca9ad668a504a456a2cc02d7254b79ddfd9a971a1648f0508fb103a9fc89'}, {'PyTorch-1.13.1_increase-tolerance-test_ops.patch': 'c909fdfc2b12df457e1eb5514265ffec3eab653994949416f3f048668421e223'}, {'PyTorch-1.13.1_increase-tolerance-test_optim.patch': diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-tp-integration-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-tp-integration-test.patch new file mode 100644 index 00000000000..6f4a52f460f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-fsdp-tp-integration-test.patch @@ -0,0 +1,32 @@ +Similar to the FP16 test this test seems to expect at most 4 GPUs +as indicated by `skip_if_lt_x_gpu(4)` decorators. + +Otherwise: +- test_fsdp_tp_checkpoint_integration fails with + File "/tmp/eb-tmp-2022a-cuda/lib/python3.10/site-packages/torch/distributed/_shard/sharded_tensor/_ops/tensor_ops.py", line 46, in tensor_device + return self_st.local_shards()[0].tensor.device + IndexError: list index out of range +- test_fsdp_tp_integration fails with + AssertionError: Tensor-likes are not close! + + Mismatched elements: 72 / 72 (100.0%) + Greatest absolute difference: 0.958100214600563 at index (0, 2, 7) (up to 1e-05 allowed) + Greatest relative difference: 52.01691657271702 at index (1, 2, 4) (up to 1.3e-06 allowed) + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/fsdp/test_fsdp_tp_integration.py b/test/distributed/fsdp/test_fsdp_tp_integration.py +index e813966ec2f..ec2308c705b 100644 +--- a/test/distributed/fsdp/test_fsdp_tp_integration.py ++++ b/test/distributed/fsdp/test_fsdp_tp_integration.py +@@ -202,6 +202,10 @@ class SimpleModel(torch.nn.Module): + + + class TestTPFSDPIntegration(FSDPTest): ++ @property ++ def world_size(self): ++ return min(4, super().world_size) ++ + def _get_params_and_sharding_info( + self, + model: SimpleModel, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-wrong-check-in-fsdp-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-wrong-check-in-fsdp-tests.patch new file mode 100644 index 00000000000..ec664f7ae32 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-wrong-check-in-fsdp-tests.patch @@ -0,0 +1,21 @@ +A check in the test code was inverted and incomplete. +See https://github.com/pytorch/pytorch/pull/90252 & https://github.com/pytorch/pytorch/pull/90785 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_fsdp.py b/torch/testing/_internal/common_fsdp.py +index eda1b953d95..56a95961371 100644 +--- a/torch/testing/_internal/common_fsdp.py ++++ b/torch/testing/_internal/common_fsdp.py +@@ -1014,7 +1014,10 @@ class FSDPTest(MultiProcessTestCase): + # the DDP parameters are in FP16 (from `half()`) while the FSDP + # parameters are in FP32 (from `summon_full_params()`) and (2) DDP runs + # the optimizer in FP16 while FSDP runs it in FP32 +- if mixed_precision is not None: ++ # TODO: Disable checking the parameters for pure FP16 due to floating ++ # point inaccuracy. Note that this means that the backward pass is not ++ # checked: https://github.com/pytorch/pytorch/issues/90784 ++ if mixed_precision is None and not use_pure_fp16: + self.assertEqual( + ddp_params, + fsdp_unsharded_params, From d95921140d3f998cea13833becf8057e3b9f58c8 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 1 Aug 2023 15:44:08 +0200 Subject: [PATCH 8203/9987] Add Bazel --- .../b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-11.0.20.eb | 30 ++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-11.eb | 2 +- 3 files changed, 62 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-11.0.20.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0d7e0954c6a --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +name = 'Bazel' +version = '6.3.1' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +# patches = [ +# 'Bazel-3.7.1_fix-protobuf-env.patch', +# 'Bazel-3.7.2_fix-GCC-11.patch', +# ] +checksums = [ + '2676319e86c5aeab142dccd42434364a33aa330a091c13562b7de87a10e68775', +] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.3'), + ('Zip', '3.0'), +] + +dependencies = [('Java', '11', '', SYSTEM)] + +runtest = True +testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/Java/Java-11.0.20.eb b/easybuild/easyconfigs/j/Java/Java-11.0.20.eb new file mode 100644 index 00000000000..a66db856ead --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-11.0.20.eb @@ -0,0 +1,30 @@ +name = 'Java' +version = '11.0.20' +local_build = '8' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + '7a99258af2e3ee9047e90f1c0c1775fd6285085759501295358d934d662e01f9', + local_tarball_tmpl % ('aarch64', local_build): + 'eb821c049c2d2f7c3fbf8ddcce2d608d3aa7d488700e76bfbbebabba93021748', + local_tarball_tmpl % ('ppc64le', local_build): + '1125931b3a38e6e305a1932fc6cfd0b023a0fbec2cab10e835a2ee2c50848b42', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-11.eb b/easybuild/easyconfigs/j/Java/Java-11.eb index 77086a3e1b8..199c7cf1cfc 100644 --- a/easybuild/easyconfigs/j/Java/Java-11.eb +++ b/easybuild/easyconfigs/j/Java/Java-11.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.0.18')] +dependencies = [('Java', '%(version)s.0.20')] moduleclass = 'lang' From 7cc7f6dc09669fe74d8e3bbc054f04dbd05e2329 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 1 Aug 2023 15:57:30 +0200 Subject: [PATCH 8204/9987] Fix line length --- easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb | 3 ++- easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb index 015bdcc4c2a..3482f6f3c16 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb @@ -47,7 +47,8 @@ checksums = [ {'nvptx-tools-20220412.tar.gz': '20e3c1eeae7f375c36455b6036c4801de16b854910ff54268bbd3346f3685080'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, - {'GCCcore-12.1.0_allow-pragma-wself-init.patch': '464f5faa9b23e805995d10dcdacca83df6321cac70826e9a3bc5bc9cd737f6a1'}, + {'GCCcore-12.1.0_allow-pragma-wself-init.patch': + '464f5faa9b23e805995d10dcdacca83df6321cac70826e9a3bc5bc9cd737f6a1'}, {'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch': '0ea675960795e238a43ae7d685a0082b21f0b63cf2fe499f6d55e89e0aaee392'}, {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb index c1aee0bbfc9..9a758565b1f 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -47,7 +47,8 @@ checksums = [ {'nvptx-tools-20220610.tar.gz': '53e7973af841935490b8a7b9e4d1331f775589b54e21f9921f18589183fb9997'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, - {'GCCcore-12.1.0_allow-pragma-wself-init.patch': '464f5faa9b23e805995d10dcdacca83df6321cac70826e9a3bc5bc9cd737f6a1'}, + {'GCCcore-12.1.0_allow-pragma-wself-init.patch': + '464f5faa9b23e805995d10dcdacca83df6321cac70826e9a3bc5bc9cd737f6a1'}, {'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch': '0ea675960795e238a43ae7d685a0082b21f0b63cf2fe499f6d55e89e0aaee392'}, {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, From bc1f8ea528b8da955da99d76d967cce234fe94c8 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 1 Aug 2023 16:04:42 +0200 Subject: [PATCH 8205/9987] adding easyconfigs: archspec-0.2.1-GCCcore-12.3.0.eb --- .../archspec/archspec-0.2.1-GCCcore-12.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.2.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7498e082971 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.2.1' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['0974a8a95831d2d43cce906c5b79a35d5fd2bf9be478b0e3b7d83ccc51ac815e'] + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.5.1'), +] + +dependencies = [('Python', '3.11.3')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +moduleclass = 'tools' From b04e323e293153ec517874110acb8c572f381a4d Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 1 Aug 2023 16:05:37 +0200 Subject: [PATCH 8206/9987] adding easyconfigs: APR-1.7.4-GCCcore-12.3.0.eb, APR-util-1.6.3-GCCcore-12.3.0.eb --- .../APR-util/APR-util-1.6.3-GCCcore-12.3.0.eb | 32 +++++++++++++++++++ .../a/APR/APR-1.7.4-GCCcore-12.3.0.eb | 22 +++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..baf013325f7 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.3-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.3' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2b74d8932703826862ca305b094eef2983c27b39d5c9414442e9976a9acf1983'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('APR', '1.7.4'), + ('SQLite', '3.42.0'), + ('expat', '2.5.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a1a41af357a --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.4-GCCcore-12.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.4' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4137dd82a185076fa50ba54232d920a17c6469c30b0876569e1c2a05ff311d9'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' From 7dc87b2d3428ca49dc3f3507f10ea65b14dcae5a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 1 Aug 2023 16:06:34 +0200 Subject: [PATCH 8207/9987] adding easyconfigs: BeautifulSoup-4.12.2-GCCcore-12.3.0.eb --- .../BeautifulSoup-4.12.2-GCCcore-12.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..cc388eeb4ca --- /dev/null +++ b/easybuild/easyconfigs/b/BeautifulSoup/BeautifulSoup-4.12.2-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'BeautifulSoup' +version = '4.12.2' + +homepage = 'https://www.crummy.com/software/BeautifulSoup' +description = "Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40') +] + +dependencies = [ + ('Python', '3.11.3'), + ('hatchling', '1.18.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('soupsieve', '2.4.1', { + 'checksums': ['89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea'], + }), + (name, version, { + 'modulename': 'bs4', + 'source_tmpl': 'beautifulsoup4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/b/beautifulsoup4'], + 'checksums': ['492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da'], + }), +] + +moduleclass = 'data' From 1f4317ed32891e7c5ea60919dfa0a89fb8baf974 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Aug 2023 17:05:05 +0200 Subject: [PATCH 8208/9987] add fallback source URL for LPP in CFDEMcoupling easyconfig --- .../c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2019b.eb | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2019b.eb b/easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2019b.eb index b5a67158ee5..8c7dadce41c 100644 --- a/easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2019b.eb +++ b/easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2019b.eb @@ -19,15 +19,18 @@ sources = [ 'filename': 'LIGGGHTS-%(version)s.tar.gz', }, { - 'source_urls': ['https://github.com/CFDEMproject/LPP/archive/'], + 'source_urls': [ + 'https://github.com/CFDEMproject/LPP/archive/', # no longer exists? + 'https://github.com/alexjwhitehead/LPP/archive', + ], 'download_filename': '633058e.tar.gz', 'filename': 'LPP-20170223.tar.gz', }, ] checksums = [ - '3c90d3178c9667ea84db9507221f65f9efec2aab8d22c51769f8a0c94d813ee4', # CFDEMcoupling-3.8.0.tar.gz - '9cb2e6596f584463ac2f80e3ff7b9588b7e3638c44324635b6329df87b90ab03', # LIGGGHTS-3.8.0.tar.gz - '9b191d89e72fba00bd63b327ee8c79425fb73e4e11aa6c165d464ed8a582627a', # LPP-20170223.tar.gz + {'CFDEMcoupling-3.8.0.tar.gz': '3c90d3178c9667ea84db9507221f65f9efec2aab8d22c51769f8a0c94d813ee4'}, + {'LIGGGHTS-3.8.0.tar.gz': '9cb2e6596f584463ac2f80e3ff7b9588b7e3638c44324635b6329df87b90ab03'}, + {'LPP-20170223.tar.gz': '9b191d89e72fba00bd63b327ee8c79425fb73e4e11aa6c165d464ed8a582627a'}, ] dependencies = [ From 8284e44fe9da5b18bd706566014fe3802268b63a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 1 Aug 2023 18:43:46 +0200 Subject: [PATCH 8209/9987] adding easyconfigs: intel-2023.07.eb, HPL-2.3-intel-2023.07.eb, iimpi-2023.07.eb, imkl-2023.2.0.eb, imkl-FFTW-2023.2.0-iimpi-2023.07.eb, impi-2021.10.0-intel-compilers-2023.2.1.eb, intel-compilers-2023.2.1.eb --- .../h/HPL/HPL-2.3-intel-2023.07.eb | 21 +++++++++++ .../easyconfigs/i/iimpi/iimpi-2023.07.eb | 18 +++++++++ .../imkl-FFTW-2023.2.0-iimpi-2023.07.eb | 11 ++++++ easybuild/easyconfigs/i/imkl/imkl-2023.2.0.eb | 18 +++++++++ ...impi-2021.10.0-intel-compilers-2023.2.1.eb | 16 ++++++++ .../intel-compilers-2023.2.1.eb | 37 +++++++++++++++++++ .../easyconfigs/i/intel/intel-2023.07.eb | 22 +++++++++++ 7 files changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.07.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2023.07.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.2.0-iimpi-2023.07.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2023.2.0.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.2.1.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2023.07.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.07.eb new file mode 100644 index 00000000000..287a40fcf40 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.07.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2023.07'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2023.07.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2023.07.eb new file mode 100644 index 00000000000..7f614dd3c9e --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2023.07.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2023.07' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2023.2.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.10.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.2.0-iimpi-2023.07.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.2.0-iimpi-2023.07.eb new file mode 100644 index 00000000000..4d6319fcee1 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.2.0-iimpi-2023.07.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2023.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2023.07'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.2.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.2.0.eb new file mode 100644 index 00000000000..6768a2ccefd --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.2.0.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2023.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/adb8a02c-4ee7-4882-97d6-a524150da358/'] +sources = ['l_onemkl_p_%(version)s.49497_offline.sh'] +checksums = ['4a0d93da85a94d92e0ad35dc0fc3b3ab7f040bd55ad374c4d5ec81a57a2b872b'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb new file mode 100644 index 00000000000..ffd46a1e59c --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.10.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2023.2.1'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/718d6f8f-2546-4b36-b97b-bc58d5482ebf/'] +sources = ['l_mpi_oneapi_p_%(version)s.49374_offline.sh'] +checksums = ['ab2e97d87b139201a2e7dab9a61ac6e8927b7783b459358c4ad69a1b1c064f40'] + +dependencies = [('UCX', '1.14.1')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.2.1.eb new file mode 100644 index 00000000000..8fcb11f30e5 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.2.1.eb @@ -0,0 +1,37 @@ +name = 'intel-compilers' +version = '2023.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/ebf5d9aa-17a7-46a4-b5df-ace004227c0e/', + ], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.8_offline.sh', + }, + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/0d65c8d4-f245-4756-80c4-6712b43cf835/', + ], + 'filename': 'l_fortran-compiler_p_%(version)s.8_offline.sh', + }, +] +checksums = [ + {'l_dpcpp-cpp-compiler_p_2023.2.1.8_offline.sh': + 'f5656b2f5bb5d904639e6ef1f90a2d2e760d2906e82ebc0dd387709738ca714b'}, + {'l_fortran-compiler_p_2023.2.1.8_offline.sh': + 'd4e36abc014c184698fec318a127f15a696b5333b3b0282aba1968b351207185'}, +] + +local_gccver = '12.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.40', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2023.07.eb b/easybuild/easyconfigs/i/intel/intel-2023.07.eb new file mode 100644 index 00000000000..d301a7461bd --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2023.07.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2023.07' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2023.2.1' +local_gccver = '12.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.40', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.10.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', '2023.2.0', '', SYSTEM), + ('imkl-FFTW', '2023.2.0', '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From c2ec50bb684f8e30ec6fb9182eaf7fbc830591d6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 1 Aug 2023 18:52:34 +0200 Subject: [PATCH 8210/9987] update source_urls --- .../i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb index ffd46a1e59c..3cd8c4a930c 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb @@ -7,7 +7,8 @@ description = "Intel MPI Library, compatible with MPICH ABI" toolchain = {'name': 'intel-compilers', 'version': '2023.2.1'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/718d6f8f-2546-4b36-b97b-bc58d5482ebf/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/4f5871da-0533-4f62-b563-905edfb2e9b7/'] + sources = ['l_mpi_oneapi_p_%(version)s.49374_offline.sh'] checksums = ['ab2e97d87b139201a2e7dab9a61ac6e8927b7783b459358c4ad69a1b1c064f40'] From 7f42e13c862d2b2e8c4f66130047430748d6313c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 1 Aug 2023 18:54:32 +0200 Subject: [PATCH 8211/9987] update source_urls --- .../i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb index 3cd8c4a930c..e1064214201 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb @@ -8,7 +8,6 @@ toolchain = {'name': 'intel-compilers', 'version': '2023.2.1'} # see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/4f5871da-0533-4f62-b563-905edfb2e9b7/'] - sources = ['l_mpi_oneapi_p_%(version)s.49374_offline.sh'] checksums = ['ab2e97d87b139201a2e7dab9a61ac6e8927b7783b459358c4ad69a1b1c064f40'] From a9510955fd77b55aed0fd796ff710f6ad0dfc77d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Aug 2023 21:55:24 +0200 Subject: [PATCH 8212/9987] fix installation of Python bindings for Arrow 0.17.1 by adding `--no-build-isolation` to `pip install` command --- .../a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb | 4 +++- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb | 4 +++- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb | 4 +++- .../a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb | 4 +++- easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb | 4 +++- 5 files changed, 15 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb index 73d913a3791..d0932219b5c 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020a-Python-3.8.2.eb @@ -47,7 +47,8 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -60,6 +61,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb index e348b0044cb..e4a039c7968 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-foss-2020b.eb @@ -44,7 +44,8 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -57,6 +58,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb index 8f577b4f440..941c31686a8 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-fosscuda-2020b.eb @@ -47,7 +47,8 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -60,6 +61,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb index f7866fdbdfc..d2640e626ed 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020a-Python-3.8.2.eb @@ -45,7 +45,8 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -58,6 +59,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb index 101f92aa068..0551ea8b33b 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.17.1-intel-2020b.eb @@ -44,7 +44,8 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -57,6 +58,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] From e49402bf0d79156237c23bccbe27df3fd379a08f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 1 Aug 2023 22:27:23 +0200 Subject: [PATCH 8213/9987] fix installation of Python bindings for Arrow 0.16.0 by adding `--no-build-isolation` to `pip install` command --- .../a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb | 10 +++++++--- .../a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb | 2 +- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb index 8dcb89cd8dc..e7c0d5bd617 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-foss-2019b-Python-3.7.4.eb @@ -43,8 +43,9 @@ prebuildopts += "thrift_ep-prefix/src/thrift_ep-stamp/download-thrift_ep.cmake & local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "export PYARROW_WITH_PARQUET=1 && " -local_install_pyarrow_cmds += " cd %(builddir)s/*arrow-%(version)s/python && " -local_install_pyarrow_cmds += " export XDG_CACHE_HOME=$TMPDIR && pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && " +local_install_pyarrow_cmds += "export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -55,6 +56,9 @@ sanity_check_paths = { 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["python -c 'import pyarrow'"] +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.parquet'", +] moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb index bd28ccba5c3..00220415a2f 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-0.16.0-intel-2019b-Python-3.7.4.eb @@ -48,7 +48,7 @@ prebuildopts += "thrift_ep-prefix/src/thrift_ep-stamp/download-thrift_ep.cmake & local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s --no-build-isolation ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From d8ce80399b0f4a9baf33cd6779a2ee3a60e77332 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 2 Aug 2023 09:52:50 +0200 Subject: [PATCH 8214/9987] adding easyconfigs: SciPy-bundle-2023.07-gfbf-2023a.eb, hypothesis-6.82.0-GCCcore-12.3.0.eb, pybind11-2.11.1-GCCcore-12.3.0.eb and patches: scipy-1.11.1_disable-tests.patch, scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch --- .../hypothesis-6.82.0-GCCcore-12.3.0.eb | 27 ++++++ .../pybind11-2.11.1-GCCcore-12.3.0.eb | 26 ++++++ .../SciPy-bundle-2023.07-gfbf-2023a.eb | 92 +++++++++++++++++++ .../scipy-1.11.1_disable-tests.patch | 26 ++++++ ...xfail-aarch64_test_maxiter_worsening.patch | 15 +++ 5 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-6.82.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_disable-tests.patch create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-6.82.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.82.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3accab32735 --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-6.82.0-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'hypothesis' +version = '6.82.0' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ffece8e40a34329e7112f7408f2c45fe587761978fdbc6f4f91bf0d683a7d4d9'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # required for attrs, sortedcontainers +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b05186f3338 --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +name = 'pybind11' +version = '2.11.1' + +homepage = 'https://pybind11.readthedocs.io' +description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, + mainly to create Python bindings of existing C++ code.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/pybind/pybind11/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d475978da0cdc2d43b73f30910786759d593a9d8ee05b1b6846d1eb16c6d2e0c'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Eigen', '3.4.0'), + ('Python-bundle-PyPI', '2023.06'), # to provide pytest +] +dependencies = [ + ('Python', '3.11.3'), +] + +configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb new file mode 100644 index 00000000000..d634617be9f --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb @@ -0,0 +1,92 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2023.07' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.82.0'), + ('UnZip', '6.0'), + # scipy >= 1.9.0 uses Meson/Ninja + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), # required by scipy +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('pybind11', '2.11.1'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.25.1', { + 'patches': ['numpy-1.22.3_disable-broken-override-test.patch'], + 'checksums': [ + {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.4', { + 'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.13.1', { + 'checksums': ['8aad08162f010e5425a7b254dd68d83311b430bb29f9252dce2eff3ba39497dd'], + }), + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + ('scipy', '1.11.1', { + 'patches': [ + 'scipy-1.11.1_disable-tests.patch', + 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + ], + 'checksums': [ + {'scipy-1.11.1.tar.gz': 'fb5b492fa035334fd249f0973cc79ecad8b09c604b42a127a677b45a9a3d4289'}, + {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, + {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': + '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + ], + 'enable_slow_tests': True, + 'ignore_test_result': False, + }), + ('numexpr', '2.8.4', { + 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], + }), + ('Bottleneck', '1.3.7', { + 'checksums': ['e1467e373ad469da340ed0ff283214d6531cc08bfdca2083361a3aa6470681f8'], + }), + ('tzdata', '2023.3', { + 'checksums': ['11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a'], + }), + ('pandas', '2.0.3', { + 'preinstallopts': "export PANDAS_CI=0 && ", + 'checksums': ['c02f372a88e0d17f36d3093a644c73cfc1788e876a7c4bcb4020a77512e2043c'], + }), + ('mpmath', '1.3.0', { + 'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'], + }), + ('deap', '1.4.0', { + 'checksums': ['ffef2921932a0edbe634fcb6d156189e7a364bf638a2af4ae5d59931a9a4c8cc'], + 'modulename': 'deap.base', + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_disable-tests.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_disable-tests.patch new file mode 100644 index 00000000000..7d59fcb1b2f --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_disable-tests.patch @@ -0,0 +1,26 @@ +disable problematic tests +test_hermitian_modes fails with order of magnitude difference +test_concatenate_int32_overflow fails if not enough memory is available +author: Kenneth Hoste (HPC-UGent) + Simon Branford (University of Birmingham) + Sebastian Achilles (Juelich Supercomputing Centre) +diff -ru scipy-1.11.1.orig/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py scipy-1.11.1/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py +--- scipy-1.11.1.orig/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py 2023-07-28 07:18:00.383649919 +0000 ++++ scipy-1.11.1/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py 2023-07-28 07:19:08.646148457 +0000 +@@ -410,7 +410,7 @@ + None, sigma, mattype, None, mode) + + +-def test_hermitian_modes(): ++def disable_test_hermitian_modes(): + params = SymmetricParams() + k = 2 + symmetric = True +diff -ru scipy-1.11.1.orig/scipy/sparse/tests/test_construct.py scipy-1.11.1/scipy/sparse/tests/test_construct.py --- scipy-1.11.1.orig/scipy/sparse/tests/test_construct.py 2023-07-28 07:18:00.387649832 +0000 ++++ scipy-1.11.1/scipy/sparse/tests/test_construct.py 2023-07-29 17:59:26.471992100 +0000 +@@ -446,7 +446,7 @@ + + @pytest.mark.slow + @pytest.mark.xfail_on_32bit("Can't create large array for test") +- def test_concatenate_int32_overflow(self): ++ def disable_test_concatenate_int32_overflow(self): + """ test for indptr overflow when concatenating matrices """ + check_free_memory(30000) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch new file mode 100644 index 00000000000..fa8b418b4e0 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch @@ -0,0 +1,15 @@ +also xfail test_maxiter_worsening for Python 3.10 on aarch64 +see also https://github.com/scipy/scipy/issues/13019 + https://github.com/scipy/scipy/pull/13022 +author: Kenneth Hoste (HPC-UGent) + Sebastian Achilles (Juelich Supercomputing Centre) +diff -ru scipy-1.11.1.orig/scipy/sparse/linalg/_isolve/tests/test_iterative.py scipy-1.11.1/scipy/sparse/linalg/_isolve/tests/test_iterative.py +--- scipy-1.11.1.orig/scipy/sparse/linalg/_isolve/tests/test_iterative.py 2023-07-28 07:18:00.387649832 +0000 ++++ scipy-1.11.1/scipy/sparse/linalg/_isolve/tests/test_iterative.py 2023-07-29 18:17:22.432356816 +0000 +@@ -465,7 +465,7 @@ + # which they should detect and halt as necessary. + # cf. gh-9100 + if (solver is gmres and platform.machine() == 'aarch64' +- and sys.version_info[1] == 9): ++ and sys.version_info[1] >= 9): + pytest.xfail(reason="gh-13019") + if (solver is lgmres and + platform.machine() not in ['x86_64' 'x86', 'aarch64', 'arm64']): From ff43bea7cdc1a30f8da394027d66018bffe70da1 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 2 Aug 2023 11:58:19 +0200 Subject: [PATCH 8215/9987] Remove redundant comment --- .../easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb index 0d7e0954c6a..b878e18297c 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb @@ -9,13 +9,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] -# patches = [ -# 'Bazel-3.7.1_fix-protobuf-env.patch', -# 'Bazel-3.7.2_fix-GCC-11.patch', -# ] -checksums = [ - '2676319e86c5aeab142dccd42434364a33aa330a091c13562b7de87a10e68775', -] +checksums = ['2676319e86c5aeab142dccd42434364a33aa330a091c13562b7de87a10e68775'] builddependencies = [ ('binutils', '2.40'), From 6b3e74e73f7b432b3b0142889734cbb0099f879b Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 2 Aug 2023 12:23:22 +0200 Subject: [PATCH 8216/9987] Add ELPA --- .../e/ELPA/ELPA-2023.05.001-foss-2023a.eb | 43 +++++++++++++++++ ...-2023.05.001_fix_hardcoded_perl_path.patch | 48 +++++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_hardcoded_perl_path.patch diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb new file mode 100644 index 00000000000..ab85bc7efa1 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2023.05.001' + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + {'elpa-new_release_%(version)s.tar.gz': '7e07ca287ab07c0a73d97df71d5a5431c847b8e4d5c759aae99e12672e6decf3'}, + {'ELPA-%(version)s_fix_hardcoded_perl_path.patch': + '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.11.3'), + ('Perl', '5.36.1'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_hardcoded_perl_path.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_hardcoded_perl_path.patch new file mode 100644 index 00000000000..52bfbaee2dd --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_hardcoded_perl_path.patch @@ -0,0 +1,48 @@ +# Perl scripts in elpa hard-code the location of the perl interpreter +# We replace these so that it picks up on the perl interpreter from the PATH +# (i.e. the one provided as a build dependency by EasyBuild) +diff -Nru elpa-new_release_2023.05.001.orig/fdep/fortran_dependencies.pl elpa-new_release_2023.05.001/fdep/fortran_dependencies.pl +--- elpa-new_release_2023.05.001.orig/fdep/fortran_dependencies.pl 2023-08-01 16:22:09.427685572 +0200 ++++ elpa-new_release_2023.05.001/fdep/fortran_dependencies.pl 2023-08-01 16:23:42.049660819 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + # + # Copyright 2015 Lorenz Hüdepohl + # +diff -Nru elpa-new_release_2023.05.001.orig/test_project_1stage/fdep/fortran_dependencies.pl elpa-new_release_2023.05.001/test_project_1stage/fdep/fortran_dependencies.pl +--- elpa-new_release_2023.05.001.orig/test_project_1stage/fdep/fortran_dependencies.pl 2023-08-01 16:22:09.608936771 +0200 ++++ elpa-new_release_2023.05.001/test_project_1stage/fdep/fortran_dependencies.pl 2023-08-01 16:22:59.982851660 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +diff -Nru elpa-new_release_2023.05.001.orig/test_project_2stage/fdep/fortran_dependencies.pl elpa-new_release_2023.05.001/test_project_2stage/fdep/fortran_dependencies.pl +--- elpa-new_release_2023.05.001.orig/test_project_2stage/fdep/fortran_dependencies.pl 2023-08-01 16:22:09.612651547 +0200 ++++ elpa-new_release_2023.05.001/test_project_2stage/fdep/fortran_dependencies.pl 2023-08-01 16:23:09.349419243 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +diff -Nru elpa-new_release_2023.05.001.orig/test_project_C/fdep/fortran_dependencies.pl elpa-new_release_2023.05.001/test_project_C/fdep/fortran_dependencies.pl +--- elpa-new_release_2023.05.001.orig/test_project_C/fdep/fortran_dependencies.pl 2023-08-01 16:22:09.616368307 +0200 ++++ elpa-new_release_2023.05.001/test_project_C/fdep/fortran_dependencies.pl 2023-08-01 16:23:21.194405678 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + +diff -Nru elpa-new_release_2023.05.001.orig/test_project_C_2stage/fdep/fortran_dependencies.pl elpa-new_release_2023.05.001/test_project_C_2stage/fdep/fortran_dependencies.pl +--- elpa-new_release_2023.05.001.orig/test_project_C_2stage/fdep/fortran_dependencies.pl 2023-08-01 16:22:09.621271936 +0200 ++++ elpa-new_release_2023.05.001/test_project_C_2stage/fdep/fortran_dependencies.pl 2023-08-01 16:23:29.288786729 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/perl -w ++#!/usr/bin/env perl + + use strict; + From dcc283022842956c1c5c80fbba44a053a6de2388 Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 2 Aug 2023 12:38:42 +0200 Subject: [PATCH 8217/9987] adding easyconfigs: SCOTCH-7.0.3-gompi-2023a.eb --- .../s/SCOTCH/SCOTCH-7.0.3-gompi-2023a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2023a.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2023a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2023a.eb new file mode 100644 index 00000000000..645ce6e0e4f --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2023a.eb @@ -0,0 +1,24 @@ +name = 'SCOTCH' +version = '7.0.3' + +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['5b5351f0ffd6fcae9ae7eafeccaa5a25602845b9ffd1afb104db932dd4d4f3c5'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +moduleclass = 'math' From bdaefd15990e2b16a9cd51ae8143cdf9e10452ac Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 2 Aug 2023 13:53:38 +0200 Subject: [PATCH 8218/9987] Add libcerf --- .../l/libcerf/libcerf-2.3-GCCcore-12.3.0.eb | 32 +++++++++++++++++++ .../Perl-5.36.1-GCCcore-12.3.0-minimal.eb | 26 +++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0f3fbf821ba --- /dev/null +++ b/easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'libcerf' +version = '2.3' + +homepage = 'https://jugit.fz-juelich.de/mlz/libcerf' + +description = """ + libcerf is a self-contained numeric library that provides an efficient and + accurate implementation of complex error functions, along with Dawson, + Faddeeva, and Voigt functions. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://jugit.fz-juelich.de/mlz/libcerf/-/archive/v%(version)s/'] +sources = ['libcerf-v%(version)s.tar.gz'] +checksums = ['cceefee46e84ce88d075103390b4f9d04c34e4bc3b96d733292c36836d4f7065'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Perl', '5.36.1', '-minimal'), # required for pod2html +] + +sanity_check_paths = { + 'files': ['lib/libcerf.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb new file mode 100644 index 00000000000..6c5fc8fe267 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb @@ -0,0 +1,26 @@ +name = 'Perl' +version = '5.36.1' +versionsuffix = '-minimal' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +This is a minimal build without any modules. Should only be used for build dependencies. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +moduleclass = 'lang' From c5c34905b881ac38c0fdf34727d550f59c22e8b8 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Wed, 2 Aug 2023 12:22:42 +0000 Subject: [PATCH 8219/9987] BAGEL-1.2.2 using foss2021a --- .../b/BAGEL/BAGEL-1.2.2-foss-2021a.eb | 43 +++++++++++++++++++ .../b/BAGEL/BAGEL-1.2.2_serialization.patch | 11 +++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2_serialization.patch diff --git a/easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2-foss-2021a.eb b/easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2-foss-2021a.eb new file mode 100644 index 00000000000..5098b620045 --- /dev/null +++ b/easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2-foss-2021a.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'BAGEL' +version = '1.2.2' + +homepage = "http://www.nubakery.org" +description = """BAGEL (Brilliantly Advanced General Electronic-structure Library) +is a parallel electronic-structure program.""" + +# Note: A compiler bug(?) in template deduction prevents newer versions of icpc to compile this software. +toolchain = {'name': 'foss', 'version': '2021a'} +patches = [ + '%(name)s-%(version)s_serialization.patch', +] +source_urls = ['https://github.com/nubakery/bagel/archive/'] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + {'v1.2.2.tar.gz': '5dd54b064188771ccf6dd19fe08204da'}, + {'BAGEL-1.2.2_serialization.patch': '25a79715f747b28c01621215456a5f66'}, +] + +builddependencies = [ + ('Autotools', '20210128'), +] + +dependencies = [ + ('Boost', '1.76.0'), + ('libxc', '5.1.5'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'CXXFLAGS="$CXXFLAGS -DNDEBUG " ' +preconfigopts += 'CXXFLAGS="$CXXFLAGS -lflexiblas " ' +configopts = ' --with-boost=$BOOST_ROOT --with-libxc --with-mpi=openmpi ' + +sanity_check_paths = { + 'files': ['bin/BAGEL', 'lib/libbagel.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'phys' + diff --git a/easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2_serialization.patch b/easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2_serialization.patch new file mode 100644 index 00000000000..6b040740443 --- /dev/null +++ b/easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2_serialization.patch @@ -0,0 +1,11 @@ +diff -ruN bagel-1.2.2.org/src/util/serialization.h bagel-1.2.2/src/util/serialization.h +--- bagel-1.2.2.org/src/util/serialization.h 2023-06-29 07:53:18.377601798 +0000 ++++ bagel-1.2.2/src/util/serialization.h 2023-06-29 07:56:21.190019649 +0000 +@@ -33,6 +33,7 @@ + #include + #include + #include ++#include + #include + #include + #include From a1232fd05005772340a797187c21ed3b97028330 Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 2 Aug 2023 14:34:15 +0200 Subject: [PATCH 8220/9987] adding easyconfigs: Hypre-2.29.0-foss-2023a.eb --- .../h/Hypre/Hypre-2.29.0-foss-2023a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hypre/Hypre-2.29.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.29.0-foss-2023a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.29.0-foss-2023a.eb new file mode 100644 index 00000000000..383207b44d0 --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.29.0-foss-2023a.eb @@ -0,0 +1,18 @@ +name = 'Hypre' +version = '2.29.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['98b72115407a0e24dbaac70eccae0da3465f8f999318b2c9241631133f42d511'] + +start_dir = 'src' + +moduleclass = 'numlib' From 807b927c25d78c1338d47c0851334d0b246851cd Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 2 Aug 2023 14:49:55 +0200 Subject: [PATCH 8221/9987] adding easyconfigs: Ax-0.3.3-foss-2022a.eb --- .../easyconfigs/a/Ax/Ax-0.3.3-foss-2022a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/a/Ax/Ax-0.3.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/Ax/Ax-0.3.3-foss-2022a.eb b/easybuild/easyconfigs/a/Ax/Ax-0.3.3-foss-2022a.eb new file mode 100644 index 00000000000..e9e66b25092 --- /dev/null +++ b/easybuild/easyconfigs/a/Ax/Ax-0.3.3-foss-2022a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'Ax' +version = '0.3.3' + +homepage = 'https://ax.dev/' +description = """ +Ax is an accessible, general-purpose platform for understanding, managing, deploying, and +automating adaptive experiments. +Adaptive experimentation is the machine-learning guided process of iteratively exploring +a (possibly infinite) parameter space in order to identify optimal configurations in a +resource-efficient manner. Ax currently supports Bayesian optimization and bandit +optimization as exploration strategies. Bayesian optimization in Ax is powered by +BoTorch, a modern library for Bayesian optimization research built on PyTorch. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.0'), + ('scikit-learn', '1.1.2'), + ('IPython', '8.5.0'), + ('plotly.py', '5.12.0'), + ('Parsl', '2023.7.17'), + ('pyro-ppl', '1.8.4'), +] + +use_pip = True + +exts_list = [ + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('linear_operator', '0.4.0', { + 'checksums': ['7c57c9f8f258c9785c0db4dd7625f4dd03a340313d7314cba0b633644909f5c6'], + }), + ('gpytorch', '1.10', { + 'checksums': ['6dc978ab9fbf220a845a4f1ea13104180fc50e6934081f421b37f6120afb7f18'], + }), + ('botorch', '0.8.5', { + 'checksums': ['8598e3b8a0da26ed7e21a364486c0ae1188de63183d36874652fad39084c5848'], + }), + ('ax-platform', version, { + 'modulename': 'ax', + 'checksums': ['4f067d2b29e8352e826074b9360b5b1ed9f9e17bd49ac01840cf25111c621d1f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 36cf7cadf32e9233f519bb31db180bbfba69a08c Mon Sep 17 00:00:00 2001 From: TopRichard <121792457+TopRichard@users.noreply.github.com> Date: Wed, 2 Aug 2023 15:16:11 +0200 Subject: [PATCH 8222/9987] Update BAGEL-1.2.2-foss-2021a.eb set checksum to sha256 --- .../b/BAGEL/BAGEL-1.2.2-foss-2021a.eb | 21 +++++++++++-------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2-foss-2021a.eb b/easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2-foss-2021a.eb index 5098b620045..0911be96816 100644 --- a/easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2-foss-2021a.eb +++ b/easybuild/easyconfigs/b/BAGEL/BAGEL-1.2.2-foss-2021a.eb @@ -4,22 +4,25 @@ name = 'BAGEL' version = '1.2.2' homepage = "http://www.nubakery.org" -description = """BAGEL (Brilliantly Advanced General Electronic-structure Library) -is a parallel electronic-structure program.""" -# Note: A compiler bug(?) in template deduction prevents newer versions of icpc to compile this software. +description = """ +BAGEL (Brilliantly Advanced General Electronic-structure Library) +is a parallel electronic-structure program. +""" + toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/nubakery/bagel/archive/'] +sources = ['v%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_serialization.patch', ] -source_urls = ['https://github.com/nubakery/bagel/archive/'] -sources = ['v%(version)s.tar.gz'] - checksums = [ - {'v1.2.2.tar.gz': '5dd54b064188771ccf6dd19fe08204da'}, - {'BAGEL-1.2.2_serialization.patch': '25a79715f747b28c01621215456a5f66'}, + {'v1.2.2.tar.gz': 'b9ef9ad5ad9b836b5393badb5a3e5b162d6ff32da497f69d05ef9e4d091b558a'}, + {'BAGEL-1.2.2_serialization.patch': '47fed67e0d0ccea9264b85b5d69e2ec6fffbb37e29631218871943df529d4108'}, ] + builddependencies = [ ('Autotools', '20210128'), ] @@ -32,6 +35,7 @@ dependencies = [ preconfigopts = './autogen.sh && ' preconfigopts += 'CXXFLAGS="$CXXFLAGS -DNDEBUG " ' preconfigopts += 'CXXFLAGS="$CXXFLAGS -lflexiblas " ' + configopts = ' --with-boost=$BOOST_ROOT --with-libxc --with-mpi=openmpi ' sanity_check_paths = { @@ -40,4 +44,3 @@ sanity_check_paths = { } moduleclass = 'phys' - From 62a60f9447468f5765472fe53a7441194bc4ff28 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 2 Aug 2023 15:35:03 +0200 Subject: [PATCH 8223/9987] add missing pyro-ppl dependency --- .../p/pyro-ppl/pyro-ppl-1.8.4-foss-2022a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.4-foss-2022a.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.4-foss-2022a.eb new file mode 100644 index 00000000000..05afed8446b --- /dev/null +++ b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.4-foss-2022a.eb @@ -0,0 +1,44 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'pyro-ppl' +version = '1.8.4' + +homepage = 'https://github.com/pyro-ppl/pyro' +description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + }), + (name, version, { + 'modulename': 'pyro', + 'checksums': ['766fad61e52df48885de96d41213da1f8e8c1b79ecf308ad53189fcd15c1cb41'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'from pyroapi import distributions as dist'", + "python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'", + "python -c 'from pyro import infer, nn, distributions'", +] + +moduleclass = 'tools' From 94828e341797c4bcb70811b7e94b154ddd92185e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Aug 2023 19:27:05 +0200 Subject: [PATCH 8224/9987] {lib}[GCCcore/12.3.0] Mesa v23.1.4, Mako v1.2.4, libdrm v2.4.115, libglvnd v1.6.0 --- .../l/libdrm/libdrm-2.4.115-GCCcore-12.3.0.eb | 32 +++++++++ .../libglvnd/libglvnd-1.6.0-GCCcore-12.3.0.eb | 33 +++++++++ .../m/Mako/Mako-1.2.4-GCCcore-12.3.0.eb | 35 ++++++++++ .../m/Mesa/Mesa-23.1.4-GCCcore-12.3.0.eb | 69 +++++++++++++++++++ 4 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.115-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-23.1.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.115-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.115-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..40663d3baae --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.115-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'libdrm' +version = '2.4.115' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['554cfbfe0542bddb391b4e3e05bfbbfc3e282b955bd56218d21c0616481f65eb'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), +] +dependencies = [('X11', '20230603')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '-Dman-pages=disabled' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7706034bcbf --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'libglvnd' +version = '1.6.0' + +homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] +sources = ['libglvnd-v%(version)s.tar.gz'] +checksums = ['efc756ffd24b24059e1c53677a9d57b4b237b00a01c54a6f1611e1e51661d70c'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), +] + +dependencies = [('X11', '20230603')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b92300cc1d2 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Mako' +version = '1.2.4' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '2.1.3', { + 'checksums': ['af598ed32d6ae86f1b747b82783958b1a4ab8f617b06fe68795c7f026abbdcad'], + }), + (name, version, { + 'checksums': ['d60a3903dc3bb01a18ad6a89cdbe2e4eadc69c0bc8ef1e3773ba53d44c3f7a34'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ["mako-render --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-23.1.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..6cf782f85cd --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.4-GCCcore-12.3.0.eb @@ -0,0 +1,69 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers enabled (swr deprecated as of v22): +# - llvmpipe: uses LLVM for JIT code generation (multi-threaded) +# - softpipe: a reference Gallium driver +# Default renderer is llvmpipe. To use softpipe, set the environment +# variable GALLIUM_DRIVER=softpipe + +name = 'Mesa' +version = '23.1.4' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7261a17fb94867e3dc5a90d8a1f100fa04b0cbbde51d25302c0872b5e9a10959'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '1.9.5'), + ('Mako', '1.2.4'), + ('libxml2', '2.11.4'), + ('expat', '2.5.0'), + ('gettext', '0.21.1'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('zstd', '1.5.5'), + ('libdrm', '2.4.115'), + ('libglvnd', '1.6.0'), + ('libunwind', '1.6.2'), + ('LLVM', '16.0.6'), + ('X11', '20230603'), +] + +configopts = "-Dplatforms=x11 -Dosmesa=true -Dvulkan-drivers='' " +configopts += "-Dllvm=enabled -Dshared-llvm=enabled -Dlibunwind=enabled -Dglvnd=true" + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +# Tells libglvnd where to find EGL libraries +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} + +moduleclass = 'vis' From b9483c20e8d4c56dfed0231ee226f29b2b032022 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 3 Aug 2023 10:25:22 +0200 Subject: [PATCH 8225/9987] adding easyconfigs: arpack-ng-3.9.0-foss-2023a.eb --- .../a/arpack-ng/arpack-ng-3.9.0-foss-2023a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023a.eb new file mode 100644 index 00000000000..bdc9b5aa647 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023a.eb @@ -0,0 +1,35 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.9.0' + +homepage = 'https://github.com/opencollab/arpack-ng' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'opencollab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['24f2a2b259992d3c797d80f626878aa8e2ed5009d549dad57854bbcfb95e1ed0'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.9.5'), + ('Eigen', '3.4.0') +] + +preconfigopts = "sh bootstrap && " +configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ['lib64/libarpack.la', 'lib64/libarpack.%s' % SHLIB_EXT, + 'lib64/libparpack.la', 'lib64/libparpack.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' From 13d0b4711159875123565297e24bba2f9495625d Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 3 Aug 2023 10:27:22 +0200 Subject: [PATCH 8226/9987] adding easyconfigs: GenerativeModels-0.2.1-foss-2022a-CUDA-11.7.0.eb --- ...tiveModels-0.2.1-foss-2022a-CUDA-11.7.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/GenerativeModels/GenerativeModels-0.2.1-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/g/GenerativeModels/GenerativeModels-0.2.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GenerativeModels/GenerativeModels-0.2.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..01f477df11e --- /dev/null +++ b/easybuild/easyconfigs/g/GenerativeModels/GenerativeModels-0.2.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'GenerativeModels' +version = '0.2.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://monai.io/' +description = """ +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'Project-MONAI' + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True + +exts_list = [ + ('monai-weekly', '1.2.dev2304', { + 'modulename': 'monai', + 'checksums': ['3c7458c195871147824cdebfef4a84227756960b4f0ba63b969eeeffdec5f13d'], + }), + (name, version, { + 'modulename': 'generative', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['5ceab1c1e9791f84dde89b06384a0107e0847245f76e07dc2fe18bf3d8bf2a63'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From ed892fab0557a867072c752139605346bd13ccf0 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 3 Aug 2023 10:30:02 +0200 Subject: [PATCH 8227/9987] adding easyconfigs: time-1.9-GCCcore-12.3.0.eb --- .../t/time/time-1.9-GCCcore-12.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..58c010a8245 --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'https://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] + +builddependencies = [('binutils', '2.40')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' From 9c387d6560e36cc67eff66cb15f227a4dedfbc17 Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 3 Aug 2023 10:44:42 +0200 Subject: [PATCH 8228/9987] adding easyconfigs: ncdu-1.18-GCC-12.3.0.eb --- .../n/ncdu/ncdu-1.18-GCC-12.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncdu/ncdu-1.18-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/n/ncdu/ncdu-1.18-GCC-12.3.0.eb b/easybuild/easyconfigs/n/ncdu/ncdu-1.18-GCC-12.3.0.eb new file mode 100644 index 00000000000..27ea3636bc9 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdu/ncdu-1.18-GCC-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ncdu' +version = '1.18' + +homepage = 'https://dev.yorhel.nl/ncdu' +description = """Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a + remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular + desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like + environment with ncurses installed.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://dev.yorhel.nl/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3c37a1a96580c9c5d2cc352dc3c5eef0d909158c05f1cc29db4712544c8b9f95'] + +dependencies = [('ncurses', '6.4')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' From adb5e59c1fcdde2abe3854146d66cdecf85a275f Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Aug 2023 11:49:31 +0200 Subject: [PATCH 8229/9987] fix LIBSVM-3.30-GCCcore-11.3.0.eb: pass CFLAGS/LDFLAGS, add test --- .../l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb | 11 ++++++ .../LIBSVM-3.30_makefile_flags_test.patch | 34 +++++++++++++++++++ 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_makefile_flags_test.patch diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb index d58a61173b8..7e0be3a1e33 100644 --- a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30-GCCcore-11.3.0.eb @@ -8,6 +8,7 @@ description = """LIBSVM is an integrated software for support vector classificat (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'openmp': True, 'pic': True} github_account = 'cjlin1' source_urls = [GITHUB_LOWER_SOURCE] @@ -15,16 +16,20 @@ sources = ['v%s.tar.gz' % version.replace('.', '')] patches = [ 'LIBSVM-3.23_shared_lib.patch', 'LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch', + 'LIBSVM-3.30_makefile_flags_test.patch' ] checksums = [ {'v330.tar.gz': 'e4fe41308c87cc210aec73e4f5f0fb4da14234d90e7a131763fbad3788ca2d80'}, {'LIBSVM-3.23_shared_lib.patch': 'c0ede89365949644f5d7f11382a3f176fd76317c7f5ae5769226ff7c3a801fe6'}, {'LIBSVM-3.30_add_namespace_for_benefit_of_Xmipp.patch': 'f51e4d0b6899041799f43a09aad1e3711a93615a8cc453243042ed8357cabb28'}, + {'LIBSVM-3.30_makefile_flags_test.patch': 'cec86f35714a2bf131d83eaaf4d4bbc53dd93e92d0d5a7b6751774d6d237daba'}, ] dependencies = [('binutils', '2.38')] +runtest = 'test' + local_bins = ['svm-%s' % x for x in ['predict', 'scale', 'train']] files_to_copy = [ @@ -35,6 +40,12 @@ files_to_copy = [ 'tools' ] +sanity_check_commands = [ + 'cd %%(builddir)s/libsvm-%s/ && svm-scale heart_scale' % version.replace('.', ''), + 'cd %%(builddir)s/libsvm-%s/ && svm-train heart_scale' % version.replace('.', ''), + 'cd %%(builddir)s/libsvm-%s/ && echo "1">t && svm-predict t heart_scale.model out' % version.replace('.', '') +] + sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bins] + ['lib/libsvm.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_makefile_flags_test.patch b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_makefile_flags_test.patch new file mode 100644 index 00000000000..570dcbbc978 --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.30_makefile_flags_test.patch @@ -0,0 +1,34 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/08 +# pass CFLAGS and LDFLAGS to make +# add target test +diff -ru libsvm-330/Makefile libsvm-330_flags/Makefile +--- libsvm-330/Makefile 2022-08-10 15:06:45.000000000 +0200 ++++ libsvm-330_flags/Makefile 2023-08-03 10:57:04.906648202 +0200 +@@ -1,5 +1,5 @@ + CXX ?= g++ +-CFLAGS = -Wall -Wconversion -O3 -fPIC ++CFLAGS ?= -Wall -Wconversion -O3 -fPIC + SHVER = 3 + OS = $(shell uname) + +@@ -9,7 +9,7 @@ + if [ "$(OS)" = "Darwin" ]; then \ + SHARED_LIB_FLAG="-dynamiclib -Wl,-install_name,libsvm.so.$(SHVER)"; \ + else \ +- SHARED_LIB_FLAG="-shared -Wl,-soname,libsvm.so.$(SHVER)"; \ ++ SHARED_LIB_FLAG="-shared -Wl,-soname,libsvm.so.$(SHVER) $(LDFLAGS)"; \ + fi; \ + $(CXX) $${SHARED_LIB_FLAG} svm.o -o libsvm.so.$(SHVER) + +@@ -23,3 +23,11 @@ + $(CXX) $(CFLAGS) -c svm.cpp + clean: + rm -f *~ svm.o svm-train svm-predict svm-scale libsvm.so.$(SHVER) ++ ++ ++test: ++ ./svm-scale heart_scale ++ ./svm-train heart_scale ++ echo 1 > t ++ ./svm-predict t heart_scale.model out ++ From 69f5f010eabb1ddfba56d63c92c777a08368ef80 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Aug 2023 12:58:07 +0200 Subject: [PATCH 8230/9987] {lib][foss/2022a] LIBSVM-Python w/ Python 3.10.4 --- .../LIBSVM-Python-3.30-foss-2022a.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/LIBSVM-Python/LIBSVM-Python-3.30-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/LIBSVM-Python/LIBSVM-Python-3.30-foss-2022a.eb b/easybuild/easyconfigs/l/LIBSVM-Python/LIBSVM-Python-3.30-foss-2022a.eb new file mode 100644 index 00000000000..4606d99e571 --- /dev/null +++ b/easybuild/easyconfigs/l/LIBSVM-Python/LIBSVM-Python-3.30-foss-2022a.eb @@ -0,0 +1,52 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/08 +easyblock = 'PythonBundle' + +name = 'LIBSVM-Python' +version = '3.30' + +homepage = 'https://pypi.org/project/libsvm-official/' +description = """This tool provides a simple Python interface to LIBSVM, a library for support +vector machines (http://www.csie.ntu.edu.tw/~cjlin/libsvm). The interface is +very easy to use as the usage is the same as that of LIBSVM. The interface is +developed with the built-in Python library "ctypes".""" + +toolchain = {'name': 'foss', 'version': '2022a'} + + +dependencies = [ + ('Python', '3.10.4'), + ('LIBSVM', version), + ('SciPy-bundle', '2022.05'), +] + +sanity_pip_check = True +use_pip = True +exts_list = [ + (name, version, { + 'modulename': 'libsvm', + 'source_urls': ['https://github.com/cjlin1/libsvm/archive/refs/tags/'], + 'sources': ['v%s.tar.gz' % version.replace('.', '')], + 'start_dir': 'python', + 'checksums': ['e4fe41308c87cc210aec73e4f5f0fb4da14234d90e7a131763fbad3788ca2d80'], + }), +] + +_t = "from libsvm.svm import *; from libsvm.svmutil import *; import numpy as np; import scipy as sc;" +_t += "prob = svm_problem(np.asarray([1, -1]), sc.sparse.csr_matrix(([1, 1, -1, -1], ([0, 0, 1, 1], [0, 2, 0, 2]))));" +_t += "param = svm_parameter('-c 4');" +_t += "m = libsvm.svm_train(prob, param);" +_t += "svm_save_model('%(builddir)s/heart_scale.model', m);" +_t += "x0, max_idx = gen_svm_nodearray((np.asarray([0,2]), np.asarray([1,1])));" +_t += "label = libsvm.svm_predict(m, x0);" +_t += "y, x = svm_read_problem('%%(builddir)s/LIBSVMPython/libsvm-%s/heart_scale');" % version.replace('.', '') +_t += "m = svm_train(y[:200], x[:200], '-c 4');" +_t += "p_label, p_acc, p_val = svm_predict(y[200:], x[200:], m);" + +sanity_check_commands = ['python -c "%s"' % _t] + +sanity_check_paths = { + 'files': [], + 'dirs': ["lib/python%(pyshortver)s/site-packages/libsvm"] +} + +moduleclass = 'lib' From 67b0003138d9c25a6019316d099ab7780331f5db Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 3 Aug 2023 14:56:56 +0200 Subject: [PATCH 8231/9987] adding easyconfigs: qforce-0.6.11-foss-2022a.eb --- .../q/qforce/qforce-0.6.11-foss-2022a.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/q/qforce/qforce-0.6.11-foss-2022a.eb diff --git a/easybuild/easyconfigs/q/qforce/qforce-0.6.11-foss-2022a.eb b/easybuild/easyconfigs/q/qforce/qforce-0.6.11-foss-2022a.eb new file mode 100644 index 00000000000..acb2d84f0a8 --- /dev/null +++ b/easybuild/easyconfigs/q/qforce/qforce-0.6.11-foss-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'qforce' +version = '0.6.11' + +homepage = 'https://github.com/selimsami/qforce' +description = """ +Quantum Mechanically augmented molecular force fields. Q-Force is a software package +for deriving all-atom force fields from quantum mechanical calculations in an automated +manner. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ASE', '3.22.1'), + ('matplotlib', '3.5.2'), + ('Seaborn', '0.11.2'), + ('networkx', '2.8.4'), + ('numba', '0.56.4'), +] + +use_pip = True + +exts_list = [ + ('PuLP', '2.1', { + 'checksums': ['76f9c9f984e6e407959545a556ce10c6cc0fdb0db820d627f0073ecf4f5c5c1b'], + }), + ('pycolt', '0.6.0', { + 'modulename': 'colt', + 'checksums': ['0baf234160e65556477207cad09000bf360694470de1ca2aad4065aa569ef57a'], + }), + (name, version, { + 'checksums': ['8f5e5c8f174f2a4a3468e6d2d973bd56494e9233db9c99a122f8a36ea2f1a01b'], + }), +] + +sanity_check_commands = ["qforce --help"] + +sanity_pip_check = True + +moduleclass = 'chem' From f5bf85548882b9792472e4139af9474debe8f48f Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 3 Aug 2023 15:28:05 +0200 Subject: [PATCH 8232/9987] updatr Seaborn version --- easybuild/easyconfigs/q/qforce/qforce-0.6.11-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/qforce/qforce-0.6.11-foss-2022a.eb b/easybuild/easyconfigs/q/qforce/qforce-0.6.11-foss-2022a.eb index acb2d84f0a8..2152465181b 100644 --- a/easybuild/easyconfigs/q/qforce/qforce-0.6.11-foss-2022a.eb +++ b/easybuild/easyconfigs/q/qforce/qforce-0.6.11-foss-2022a.eb @@ -17,7 +17,7 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('ASE', '3.22.1'), ('matplotlib', '3.5.2'), - ('Seaborn', '0.11.2'), + ('Seaborn', '0.12.1'), ('networkx', '2.8.4'), ('numba', '0.56.4'), ] From aba9a6ce8e659cc32aa773ad47b72d8397a3085d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 3 Aug 2023 16:55:59 +0200 Subject: [PATCH 8233/9987] adding easyconfigs: Valgrind-3.21.0-gompi-2023a.eb --- .../v/Valgrind/Valgrind-3.21.0-gompi-2023a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.21.0-gompi-2023a.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.21.0-gompi-2023a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.21.0-gompi-2023a.eb new file mode 100644 index 00000000000..51070a9bce2 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.21.0-gompi-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.21.0' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'https://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['10ce1618bb3e33fad16eb79552b0a3e1211762448a0d7fce11c8a6243b9ac971'] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] +local_archs = ('amd64', 'arm64', 'ppc64le') + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + [['lib/valgrind/libmpiwrap-%s-linux.%s' % (a, SHLIB_EXT) for a in local_archs]], + 'dirs': [] +} + +moduleclass = 'debugger' From e0518808628705fa4a58bcd012f9aec5d1bd95f0 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 3 Aug 2023 16:56:52 +0200 Subject: [PATCH 8234/9987] adding easyconfigs: Valgrind-3.21.0-gompi-2022b.eb --- .../v/Valgrind/Valgrind-3.21.0-gompi-2022b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.21.0-gompi-2022b.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.21.0-gompi-2022b.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.21.0-gompi-2022b.eb new file mode 100644 index 00000000000..b6cb3470b3f --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.21.0-gompi-2022b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.21.0' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'https://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['10ce1618bb3e33fad16eb79552b0a3e1211762448a0d7fce11c8a6243b9ac971'] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] +local_archs = ('amd64', 'arm64', 'ppc64le') + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + [['lib/valgrind/libmpiwrap-%s-linux.%s' % (a, SHLIB_EXT) for a in local_archs]], + 'dirs': [] +} + +moduleclass = 'debugger' From 166f18ddc1d13d7db1525ac7fba1e0e69adc77d2 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 3 Aug 2023 19:18:35 +0200 Subject: [PATCH 8235/9987] {bio}[foss/2022b] PICRUSt2 v2.5.2, biom-format v2.1.15: resolve error, missing default_files directory --- .../p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb index cf6e747f07e..d56a370e73f 100644 --- a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb @@ -32,8 +32,18 @@ exts_list = [ }), ] +postinstallcmds = [ + 'cp -r %(builddir)s/%(name)s/%(namelower)s-%(version)s/%(namelower)s/default_files ' +\ + '%(installdir)s/lib/python3.10/site-packages/%(namelower)s/', +] + sanity_check_commands = [ "python -c 'from picrust2.default import default_tables'" ] -moduleclass = 'bio' +sanity_check_paths = { + 'files': ['bin/picrust2_pipeline.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/picrust2/default_files', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' \ No newline at end of file From 263dd2fe324589a7b0894c2682bf07d87a222533 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 3 Aug 2023 21:53:25 +0200 Subject: [PATCH 8236/9987] adding easyconfigs: ABINIT-9.10.3-intel-2022a.eb --- .../a/ABINIT/ABINIT-9.10.3-intel-2022a.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.10.3-intel-2022a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.10.3-intel-2022a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.10.3-intel-2022a.eb new file mode 100644 index 00000000000..2a79959bfb9 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.10.3-intel-2022a.eb @@ -0,0 +1,68 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.10.3' + +homepage = 'https://www.abinit.org/' +description = """ +ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of +systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using +pseudopotentials and a planewave or wavelet basis. +""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3f2a9aebbf1fee9855a09dd687f88d2317b8b8e04f97b2628ab96fb898dce49b'] + +builddependencies = [ + ('Python', '3.10.4'), +] +dependencies = [ + ('libxc', '5.2.3'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('HDF5', '1.12.2'), + ('Wannier90', '3.1.0'), +] + +# Ensure MPI with intel wrappers. +configopts = '--with-mpi="yes" ' +configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# Enable OpenMP +configopts += '--enable-openmp="yes" ' + +# BLAS/Lapack from MKL +configopts += '--with-linalg-flavor=mkl ' + +# FFTW from MKL +configopts += '--with-fft-flavor=dfti ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# Enable double precision for GW calculations +configopts += '--enable-gw-dpc ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' From 7bd37d710f4334f885c76e7793b1b39d27283ae3 Mon Sep 17 00:00:00 2001 From: fizwit Date: Thu, 3 Aug 2023 17:01:04 -0700 Subject: [PATCH 8237/9987] bam-readcount update --- .../bam-readcount-1.0.1-GCC-12.2.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/b/bam-readcount/bam-readcount-1.0.1-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-1.0.1-GCC-12.2.0.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-1.0.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..0cecd910147 --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-1.0.1-GCC-12.2.0.eb @@ -0,0 +1,52 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'CMakeMake' + +name = 'bam-readcount' +version = '1.0.1' + +homepage = 'https://github.com/genome/bam-readcount' +description = """Count DNA sequence reads in BAM files""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'genome' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['8ebf84d9efee0f2d3b43f0452dbf16b27337c960e25128f6a7173119e62588b8'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('ncurses', '6.3'), +] + +maxparallel = 1 + +# bam-readcount uses git to insert the version during configuration with CMake +# but in the release archives there is no git information +# local_commit is the git commit hash of the release +local_commit = '944c11f' +local_versionfile = '%(builddir)s/%(name)s*/version/version.h.in' +preconfigopts = "sed -i -e 's/@FULL_VERSION@/%%(version)s/' %s && " % local_versionfile +preconfigopts += "sed -i -e 's/@COMMIT_HASH@/%s/' %s && " % (local_commit, local_versionfile) + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/%(name)s"], + 'dirs': [] +} + +sanity_check_commands = [ + # --help exists with exit code 1, so use grep to check for expected pattern in help output + "%(name)s --help 2>&1 | grep 'Example: bam-readcount -f'", + "%(name)s --version | grep 'version: %(version)s '", +] + +moduleclass = 'bio' From 07a678738dfed38b456cb1d8ba736e9620302144 Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 4 Aug 2023 10:13:28 +0000 Subject: [PATCH 8238/9987] adding easyconfigs: BBMap-38.87-GCC-8.2.0-2.31.1.eb --- .../b/BBMap/BBMap-38.87-GCC-8.2.0-2.31.1.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/b/BBMap/BBMap-38.87-GCC-8.2.0-2.31.1.eb diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.87-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.87-GCC-8.2.0-2.31.1.eb new file mode 100644 index 00000000000..ccceea34743 --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.87-GCC-8.2.0-2.31.1.eb @@ -0,0 +1,41 @@ +# # +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Pau Ruiz +# License:: GPL-v3.0 +# # + +easyblock = 'MakeCp' + +name = 'BBMap' +version = '38.87' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['22ab642b8af88faf208a56763158da895004c5231df572d3163ce52fbfb63240'] + +dependencies = [('Java', '11', '', True)] + +prebuildopts = 'cd jni && ' + +local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % local_suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" + +moduleclass = 'bio' From 22584db210bfbe02cba65a350a3a111095b7f942 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 4 Aug 2023 13:25:33 +0200 Subject: [PATCH 8239/9987] Use new EasyBlock --- easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb index b08af4b4ade..0cf7088a191 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'sympy' version = '1.9' From 106dd4b9caa12b1bef3df941a333111f95a4c80b Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 4 Aug 2023 14:18:02 +0200 Subject: [PATCH 8240/9987] resolving style errors --- .../p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb index d56a370e73f..81aacce8ee7 100644 --- a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb @@ -5,8 +5,8 @@ version = '2.5.2' homepage = 'https://github.com/picrust/picrust2' description = """PICRUSt2 (Phylogenetic Investigation of Communities by - Reconstruction of Unobserved States) is a software for predicting - functional abundances based only on marker gene sequences.""" +Reconstruction of Unobserved States) is a software for predicting +functional abundances based only on marker gene sequences.""" toolchain = {'name': 'foss', 'version': '2022b'} @@ -33,8 +33,7 @@ exts_list = [ ] postinstallcmds = [ - 'cp -r %(builddir)s/%(name)s/%(namelower)s-%(version)s/%(namelower)s/default_files ' +\ - '%(installdir)s/lib/python3.10/site-packages/%(namelower)s/', + "cp -a %(start_dir)s%(name)s/%(namelower)s-%(version)s/%(namelower)s/default_files %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/" ] sanity_check_commands = [ @@ -43,7 +42,8 @@ sanity_check_commands = [ sanity_check_paths = { 'files': ['bin/picrust2_pipeline.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/picrust2/default_files', 'lib/python%(pyshortver)s/site-packages'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/picrust2/default_files'], } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' + From ef2d3d7dc61fb48679904f35b23bb97b652ba328 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 4 Aug 2023 14:38:03 +0200 Subject: [PATCH 8241/9987] resolving style errors --- easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb index 81aacce8ee7..3a761aa547e 100644 --- a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb @@ -5,8 +5,8 @@ version = '2.5.2' homepage = 'https://github.com/picrust/picrust2' description = """PICRUSt2 (Phylogenetic Investigation of Communities by -Reconstruction of Unobserved States) is a software for predicting -functional abundances based only on marker gene sequences.""" + Reconstruction of Unobserved States) is a software for predicting + functional abundances based only on marker gene sequences.""" toolchain = {'name': 'foss', 'version': '2022b'} From 9628ffaf133028d1958cd99e0292ec74c6581a9b Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 4 Aug 2023 14:57:51 +0200 Subject: [PATCH 8242/9987] resolving style errors --- easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb index 3a761aa547e..43d0a9e2fd6 100644 --- a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb @@ -33,7 +33,8 @@ exts_list = [ ] postinstallcmds = [ - "cp -a %(start_dir)s%(name)s/%(namelower)s-%(version)s/%(namelower)s/default_files %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/" + "cp -a %(start_dir)s%(name)s/%(namelower)s-%(version)s/%(namelower)s/default_files" + " %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/" ] sanity_check_commands = [ From c8e5d91e9769fd65b71e8334b2df462745e6c61d Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 4 Aug 2023 13:13:33 +0000 Subject: [PATCH 8243/9987] adding system --- easybuild/easyconfigs/b/BBMap/BBMap-38.87-GCC-8.2.0-2.31.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-38.87-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/b/BBMap/BBMap-38.87-GCC-8.2.0-2.31.1.eb index ccceea34743..8d6da64a6e4 100644 --- a/easybuild/easyconfigs/b/BBMap/BBMap-38.87-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/b/BBMap/BBMap-38.87-GCC-8.2.0-2.31.1.eb @@ -19,7 +19,7 @@ source_urls = [SOURCEFORGE_SOURCE] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['22ab642b8af88faf208a56763158da895004c5231df572d3163ce52fbfb63240'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11', '', SYSTEM)] prebuildopts = 'cd jni && ' From 7430067b6be0cb1f94a6bc72c8c5908b05e578b3 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 4 Aug 2023 15:21:12 +0200 Subject: [PATCH 8244/9987] resolving style errors --- easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb index 43d0a9e2fd6..99189c7d924 100644 --- a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022b.eb @@ -47,4 +47,3 @@ sanity_check_paths = { } moduleclass = 'bio' - From 6bb531ccf7465a98fbd6fd1a9070f7f4275fe9b3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Aug 2023 16:50:06 +0200 Subject: [PATCH 8245/9987] don't add easyconfig for sympy 1.9 with intel/2021b, stick to updating recent existing sympy easyconfig to use custom easyblock --- .../gmpy2-2.1.2-intel-compilers-2021.4.0.eb | 25 ------------ .../s/sympy/sympy-1.9-intel-2021b.eb | 38 ------------------- 2 files changed, 63 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb delete mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb deleted file mode 100644 index f194fb5a771..00000000000 --- a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.2-intel-compilers-2021.4.0.eb +++ /dev/null @@ -1,25 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'gmpy2' -version = '2.1.2' - -homepage = 'https://github.com/aleaxit/gmpy' -description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" - -toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['da75140bca128ece795895477e53b43773e3748aa90ba6170eae7ca2c74b82d1'] - -dependencies = [ - ('Python', '3.9.6'), - ('GMP', '6.2.1'), - ('MPFR', '4.1.0'), - ('MPC', '1.2.1'), -] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb deleted file mode 100644 index 0cf7088a191..00000000000 --- a/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb +++ /dev/null @@ -1,38 +0,0 @@ -name = 'sympy' -version = '1.9' - -homepage = 'https://sympy.org/' -description = """SymPy is a Python library for symbolic mathematics. It aims to - become a full-featured computer algebra system (CAS) while keeping the code as - simple as possible in order to be comprehensible and easily extensible. SymPy - is written entirely in Python and does not require any external libraries.""" - -toolchain = {'name': 'intel', 'version': '2021b'} - -sources = [SOURCE_TAR_GZ] -checksums = ['c7a880e229df96759f955d4f3970d4cabce79f60f5b18830c08b90ce77cd5fdc'] - -dependencies = [ - ('Python', '3.9.6'), - ('SciPy-bundle', '2021.10'), - ('gmpy2', '2.1.2'), -] - -download_dep_fail = True -use_pip = True - -# fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; -# see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 -pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ -runtest = 'python setup.py test' - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/isympy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], -} - -sanity_check_commands = ["isympy --help"] - -moduleclass = 'math' From 0b089969b464b899f90cd153ef4f42e95eb85593 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 4 Aug 2023 16:51:46 +0200 Subject: [PATCH 8246/9987] clean up recent sympy easyconfigs to fully rely on enhanced custom easyblock for sympy that also takes care of sanity check & co --- .../easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb | 13 ------------- .../s/sympy/sympy-1.10.1-intel-2022a.eb | 14 -------------- .../easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb | 14 -------------- .../s/sympy/sympy-1.11.1-intel-2022a.eb | 14 -------------- .../easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb | 13 ------------- 5 files changed, 68 deletions(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb index d4edd014076..57797938135 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-foss-2022a.eb @@ -18,21 +18,8 @@ dependencies = [ ('gmpy2', '2.1.2'), ] -download_dep_fail = True -use_pip = True - # fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; # see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ -runtest = 'python setup.py test' - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/isympy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], -} - -sanity_check_commands = ["isympy --help"] moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb index fae10984feb..19c285f9a68 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.10.1-intel-2022a.eb @@ -18,18 +18,4 @@ dependencies = [ ('gmpy2', '2.1.2'), ] -download_dep_fail = True -use_pip = True - -runtest = 'python setup.py test' - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/isympy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], -} - -sanity_check_commands = ["isympy --help"] - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb index e05bd976573..a0b65156c74 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-foss-2022a.eb @@ -18,18 +18,4 @@ dependencies = [ ('gmpy2', '2.1.2'), ] -download_dep_fail = True -use_pip = True - -runtest = 'python setup.py test' - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/isympy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], -} - -sanity_check_commands = ["isympy --help"] - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb index dc96b8575d2..103ac61a8f4 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.11.1-intel-2022a.eb @@ -18,18 +18,4 @@ dependencies = [ ('gmpy2', '2.1.2'), ] -download_dep_fail = True -use_pip = True - -runtest = 'python setup.py test' - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/isympy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], -} - -sanity_check_commands = ["isympy --help"] - moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb index c54bb52e04b..89e86c0fae4 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.9-foss-2021b.eb @@ -18,21 +18,8 @@ dependencies = [ ('gmpy2', '2.1.2'), ] -download_dep_fail = True -use_pip = True - # fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; # see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ -runtest = 'python setup.py test' - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/isympy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], -} - -sanity_check_commands = ["isympy --help"] moduleclass = 'math' From 77568f314740a3884caa88c9ed8bb13be434be2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 5 Aug 2023 16:51:43 +0200 Subject: [PATCH 8247/9987] don't disable building of third and fourth derivates in libxc 6.1.0 --- easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb | 7 ++++++- .../l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb index 4549d2c41b2..2f6fe0eb5f5 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb @@ -18,7 +18,12 @@ builddependencies = [ ('Perl', '5.36.0'), ] -local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" # perform iterative build to get both static and shared libraries configopts = [ diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb index 8973869bc36..0a6d19415d4 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb @@ -18,7 +18,12 @@ builddependencies = [ ('Perl', '5.36.0'), ] -local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" # perform iterative build to get both static and shared libraries configopts = [ From b57e2d5c3443e104048869a1077de4a862f0953b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 5 Aug 2023 16:58:50 +0200 Subject: [PATCH 8248/9987] =?UTF-8?q?clean=20up=20easyconfig=20for=20sympy?= =?UTF-8?q?=201.9=20w/=20intel/2021b=20to=20fully=20rely=20on=20enhanced?= =?UTF-8?q?=20custom=20ea=E2=80=A6syblock=20for=20sympy=20that=20also=20ta?= =?UTF-8?q?kes=20care=20of=20sanity=20check=20&=20co?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb index 0cf7088a191..de484f459e8 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.9-intel-2021b.eb @@ -18,21 +18,8 @@ dependencies = [ ('gmpy2', '2.1.2'), ] -download_dep_fail = True -use_pip = True - # fix broken test, sympy doesn't actually use gmpy2's Decimal anywhere; # see https://github.com/sympy/sympy/issues/23061#issuecomment-1052424896 pretestopts = """sed -i "s@Decimal('0.6')@'0.6'@g" sympy/external/tests/test_pythonmpq.py && """ -runtest = 'python setup.py test' - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/isympy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/sympy'], -} - -sanity_check_commands = ["isympy --help"] moduleclass = 'math' From 46fe07836a216aa661c86b54311e0b75ce573b62 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 6 Aug 2023 10:57:14 +0200 Subject: [PATCH 8249/9987] add patch for Automake 1.16.5 to fix help2man error --- .../easyconfigs/a/Automake/Automake-1.16.5.eb | 6 +++++- .../Automake-1.16.5_fix-help2man-error.patch | 15 +++++++++++++++ 2 files changed, 20 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.5_fix-help2man-error.patch diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb index 2d7a7d90220..7ad10e93b88 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5.eb @@ -11,7 +11,11 @@ toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] +patches = ['Automake-1.16.5_fix-help2man-error.patch'] +checksums = [ + {'automake-1.16.5.tar.gz': '07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'}, + {'Automake-1.16.5_fix-help2man-error.patch': 'ebcd629aefcf6b7dbb3bc3a8abcdf71d4f7605ecda6c6eae2f93d73271df6930'}, +] dependencies = [ ('Autoconf', '2.71'), diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5_fix-help2man-error.patch b/easybuild/easyconfigs/a/Automake/Automake-1.16.5_fix-help2man-error.patch new file mode 100644 index 00000000000..396cf962b88 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5_fix-help2man-error.patch @@ -0,0 +1,15 @@ +fix for: + help2man: can't get --help info from automake-1.16 + +based on https://github.com/xbmc/xbmc/pull/18584 +--- a/Makefile.in 2020-03-16 19:11:10.000000000 -0700 ++++ b/Makefile.in 2020-10-22 08:06:24.606751367 -0700 +@@ -699,7 +699,7 @@ + update_mans = \ + $(AM_V_GEN): \ + && $(MKDIR_P) doc \ +- && ./pre-inst-env $(PERL) $(srcdir)/doc/help2man --output=$@ ++ && ./pre-inst-env $(PERL) $(srcdir)/doc/help2man --output=$@ --no-discard-stderr + + amhello_sources = \ + doc/amhello/configure.ac \ From 29161d39c310bbc08bd79d193b42bacaed93bb91 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 7 Aug 2023 09:33:50 +0200 Subject: [PATCH 8250/9987] adding easyconfigs: zarr-2.16.0-foss-2022b.eb --- .../z/zarr/zarr-2.16.0-foss-2022b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/z/zarr/zarr-2.16.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.16.0-foss-2022b.eb b/easybuild/easyconfigs/z/zarr/zarr-2.16.0-foss-2022b.eb new file mode 100644 index 00000000000..99c518860cb --- /dev/null +++ b/easybuild/easyconfigs/z/zarr/zarr-2.16.0-foss-2022b.eb @@ -0,0 +1,43 @@ +easyblock = "PythonBundle" + +name = 'zarr' +version = '2.16.0' + +homepage = 'https://zarr.readthedocs.io/en/stable/' +description = """Zarr is a Python package providing an implementation of compressed, +chunked, N-dimensional arrays, designed for use in parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('py-cpuinfo', '9.0.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + ('monotonic', '1.6', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/atdt/monotonic/archive'], + 'checksums': ['9609c249aed584fd714811014870650d08d6f6414402b5a190663c49bf83b221'], + }), + ('numcodecs', '0.11.0', { + 'checksums': ['6c058b321de84a1729299b0eae4d652b2e48ea1ca7f9df0da65cb13470e635eb'], + }), + (name, version, { + 'checksums': ['84e36b695bda0ecea52af9861271984cb22a5c864679907b7b9ba3f79b684f7e'], + }), +] + +moduleclass = 'data' From afd3930b627ae9b454f1b11d08f938814e6a9aa2 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 7 Aug 2023 11:24:37 +0100 Subject: [PATCH 8251/9987] adding easyconfigs: bokeh-3.2.1-foss-2022b.eb, dask-2023.7.1-foss-2022b.eb, scikit-image-0.21.0-foss-2022b.eb, setuptools-64.0.3-GCCcore-12.2.0.eb --- .../b/bokeh/bokeh-3.2.1-foss-2022b.eb | 51 ++++++++++++++ .../d/dask/dask-2023.7.1-foss-2022b.eb | 69 +++++++++++++++++++ .../scikit-image-0.21.0-foss-2022b.eb | 48 +++++++++++++ .../setuptools-64.0.3-GCCcore-12.2.0.eb | 22 ++++++ 4 files changed, 190 insertions(+) create mode 100755 easybuild/easyconfigs/b/bokeh/bokeh-3.2.1-foss-2022b.eb create mode 100755 easybuild/easyconfigs/d/dask/dask-2023.7.1-foss-2022b.eb create mode 100755 easybuild/easyconfigs/s/scikit-image/scikit-image-0.21.0-foss-2022b.eb create mode 100755 easybuild/easyconfigs/s/setuptools/setuptools-64.0.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-3.2.1-foss-2022b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-3.2.1-foss-2022b.eb new file mode 100755 index 00000000000..9429ebf059c --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-3.2.1-foss-2022b.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '3.2.1' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('setuptools', '64.0.3'), + ('meson-python', '0.11.0'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), + ('PyYAML', '6.0'), + ('Pillow', '9.4.0'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True + +exts_list = [ + ('tornado', '6.3.2', { + 'checksums': ['4b927c4f19b71e627b13f3db2324e4ae660527143f9e1f2e2fb404f3a187e2ba'], + }), + ('contourpy', '1.0.7', { # stick to 1.0.7 to avoid need for newer Meson / meson-python + 'checksums': ['d8165a088d31798b59e91117d1f5fc3df8168d8b48c4acc10fc0df0d0bdbcc5e'], + }), + ('xyzservices', '2023.7.0', { + 'checksums': ['0ec928742227d6f5d4367ea7b457fcfed943429f4de2949b5b02a82cdf5569d6'], + }), + (name, version, { + 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """, + 'checksums': ['2371e9a08fd60766879ee8607a4ae54267acfed1e5dee0cc6a20d8348e02e814'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2023.7.1-foss-2022b.eb b/easybuild/easyconfigs/d/dask/dask-2023.7.1-foss-2022b.eb new file mode 100755 index 00000000000..f3760bb1376 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2023.7.1-foss-2022b.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2023.7.1' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2023.02'), + ('bokeh', '3.2.1'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('locket', '1.0.0', { + 'checksums': ['5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632'], + }), + ('partd', '1.4.0', { + 'checksums': ['aa0ff35dbbcc807ae374db56332f4c1b39b46f67bf2975f5151e0b4186aed0d5'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '3.0.0', { + 'checksums': ['e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5'], + }), + ('tblib', '2.0.0', { + 'checksums': ['a6df30f272c08bf8be66e0775fad862005d950a6b8449b94f7c788731d70ecd7'], + }), + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + (name, version, { + 'checksums': ['bec23e3bfed427d86035f3ecfc1cd1ee6ef375ba40bfb1f8a5f03ad3f2fdbbba'], + }), + ('distributed', version, { + 'checksums': ['66442f6af32e03815de6d3a5251f8ad9bbd63bb018c48aa361efca5355e46749'], + }), + ('dask-mpi', '2022.4.0', { + 'checksums': ['0a04f1d7d35a06cdff506593330d4414ea242c9172498ce191f5742eac499e17'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.8.2', { + 'checksums': ['d35407a05a0534347c5d958ae749b9f8535bec529857d013b6e5649cde43914a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.21.0-foss-2022b.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.21.0-foss-2022b.eb new file mode 100755 index 00000000000..75385f5f7b3 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.21.0-foss-2022b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.21.0' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('meson-python', '0.11.0'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), + ('Pillow', '9.4.0'), + ('networkx', '3.0'), + ('dask', '2023.7.1'), + ('imageio', '2.31.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('PyWavelets', '1.4.1', { + 'modulename': 'pywt', + 'checksums': ['6437af3ddf083118c26d8f97ab43b0724b956c9f958e9ea788659f6a2834ba93'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('tifffile', '2023.7.18', { + 'checksums': ['5a5a624b2f7ab7f37e9ec4174ae2df1805b9658f89013f9b4b5550672f65f2a1'], + }), + ('lazy_loader', '0.3', { + 'checksums': ['3b68898e34f5b2a29daaaac172c6555512d0f32074f147e2254e4a6d9d838f37'], + }), + (name, version, { + 'modulename': 'skimage', + 'source_tmpl': 'scikit_image-%(version)s.tar.gz', + 'checksums': ['b33e823c54e6f11873ea390ee49ef832b82b9f70752c8759efd09d5a4e3d87f0'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-64.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/setuptools/setuptools-64.0.3-GCCcore-12.2.0.eb new file mode 100755 index 00000000000..4fadc071b0f --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools/setuptools-64.0.3-GCCcore-12.2.0.eb @@ -0,0 +1,22 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'setuptools' +version = '64.0.3' + +homepage = "https://pypi.org/project/setuptools" +description = """Easily download, build, install, upgrade, and uninstall Python packages""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Python', '3.10.8'), +] + +sources = [SOURCE_TAR_GZ] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'vis' From 9e63c4efa573c082a355b0c3ac37d0ce265e450f Mon Sep 17 00:00:00 2001 From: xina Date: Mon, 7 Aug 2023 13:07:56 +0200 Subject: [PATCH 8252/9987] adding easyconfigs: libxc-6.2.2-GCC-12.3.0.eb --- .../l/libxc/libxc-6.2.2-GCC-12.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..bfa836ef2e4 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.2.2' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Perl', '5.36.1'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' From 599bb2dad18a41de82fb84ae692908ba61aab68b Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Aug 2023 13:20:28 +0200 Subject: [PATCH 8253/9987] Add patch for AVX512 --- .../e/ELPA/ELPA-2023.05.001-foss-2023a.eb | 11 +- .../ELPA-2023.05.001_fix_AVX512_support.patch | 107 ++++++++++++++++++ 2 files changed, 115 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb index ab85bc7efa1..b311ebab552 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb @@ -17,11 +17,16 @@ toolchainopts = {'openmp': True, 'usempi': True} source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] sources = ['elpa-new_release_%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +patches = [ + '%(name)s-%(version)s_fix_hardcoded_perl_path.patch', + '%(name)s-%(version)s_fix_AVX512_support.patch', +] checksums = [ - {'elpa-new_release_%(version)s.tar.gz': '7e07ca287ab07c0a73d97df71d5a5431c847b8e4d5c759aae99e12672e6decf3'}, - {'ELPA-%(version)s_fix_hardcoded_perl_path.patch': + {'%(namelower)s-new_release_%(version)s.tar.gz': '7e07ca287ab07c0a73d97df71d5a5431c847b8e4d5c759aae99e12672e6decf3'}, + {'%(name)s-%(version)s_fix_hardcoded_perl_path.patch': '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, + {'%(name)s-%(version)s_fix_AVX512_support.patch': + '67d73cf119c323203f901f60d36f8101a425d2b21448dba669a16b225c3e551b'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch new file mode 100644 index 00000000000..4b8212c1fe5 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch @@ -0,0 +1,107 @@ +# What: Fixes support for AVX512 on AMD CPUs +# Author: maxim-masterov (SURF) +diff -Nru elpa-new_release_2023.05.001.orig/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c elpa-new_release_2023.05.001/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c +--- elpa-new_release_2023.05.001.orig/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c 2023-08-01 16:22:09.499243000 +0200 ++++ elpa-new_release_2023.05.001/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c 2023-08-07 12:38:56.128823725 +0200 +@@ -2571,12 +2571,12 @@ + #if VEC_SET == AVX_512 + #ifdef HAVE_AVX512_XEON_PHI + #ifdef DOUBLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #ifdef SINGLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #endif + #ifdef HAVE_AVX512_XEON +@@ -4306,12 +4306,12 @@ + #if VEC_SET == AVX_512 + #ifdef HAVE_AVX512_XEON_PHI + #ifdef DOUBLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #ifdef SINGLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #endif + #ifdef HAVE_AVX512_XEON +@@ -5847,12 +5847,12 @@ + #if VEC_SET == AVX_512 + #ifdef HAVE_AVX512_XEON_PHI + #ifdef DOUBLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #ifdef SINGLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #endif + #ifdef HAVE_AVX512_XEON +@@ -7218,12 +7218,12 @@ + #if VEC_SET == AVX_512 + #ifdef HAVE_AVX512_XEON_PHI + #ifdef DOUBLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #ifdef SINGLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #endif + #ifdef HAVE_AVX512_XEON +@@ -8408,12 +8408,12 @@ + #if VEC_SET == AVX_512 + #ifdef HAVE_AVX512_XEON_PHI + #ifdef DOUBLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #ifdef SINGLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #endif + #ifdef HAVE_AVX512_XEON +@@ -9423,12 +9423,12 @@ + #if VEC_SET == AVX_512 + #ifdef HAVE_AVX512_XEON_PHI + #ifdef DOUBLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #ifdef SINGLE_PRECISION_COMPLEX +- h1_real = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_real, (__m512i) sign); +- h1_imag = (__SIMD_DATATYPE) _XOR_EPI((__m512i) h1_imag, (__m512i) sign); ++ h1_real = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_real, (__m512i) sign); ++ h1_imag = (__SIMD_DATATYPE) _SIMD_XOR_EPI((__m512i) h1_imag, (__m512i) sign); + #endif + #endif + #ifdef HAVE_AVX512_XEON From 0e87628a50e200049077d72e9335d4a33331a43a Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Aug 2023 13:50:54 +0200 Subject: [PATCH 8254/9987] Fix style --- easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb index b311ebab552..d1e7b6d8fff 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb @@ -22,7 +22,8 @@ patches = [ '%(name)s-%(version)s_fix_AVX512_support.patch', ] checksums = [ - {'%(namelower)s-new_release_%(version)s.tar.gz': '7e07ca287ab07c0a73d97df71d5a5431c847b8e4d5c759aae99e12672e6decf3'}, + {'%(namelower)s-new_release_%(version)s.tar.gz': + '7e07ca287ab07c0a73d97df71d5a5431c847b8e4d5c759aae99e12672e6decf3'}, {'%(name)s-%(version)s_fix_hardcoded_perl_path.patch': '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, {'%(name)s-%(version)s_fix_AVX512_support.patch': From 84a1b3c5abf9bb85456fdc4cb7b62d3787d5b8cb Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Aug 2023 13:51:30 +0200 Subject: [PATCH 8255/9987] Fix style --- easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb index d1e7b6d8fff..234f2abbe90 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb @@ -22,7 +22,7 @@ patches = [ '%(name)s-%(version)s_fix_AVX512_support.patch', ] checksums = [ - {'%(namelower)s-new_release_%(version)s.tar.gz': + {'%(namelower)s-new_release_%(version)s.tar.gz': '7e07ca287ab07c0a73d97df71d5a5431c847b8e4d5c759aae99e12672e6decf3'}, {'%(name)s-%(version)s_fix_hardcoded_perl_path.patch': '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, From 1fd309d42f7237550b9ee235cc9da325cb53c2a5 Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 7 Aug 2023 15:11:12 +0200 Subject: [PATCH 8256/9987] adding easyconfigs: Miniconda3-23.5.2-0.eb --- .../m/Miniconda3/Miniconda3-23.5.2-0.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.5.2-0.eb diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.5.2-0.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.5.2-0.eb new file mode 100644 index 00000000000..f22db479b4e --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.5.2-0.eb @@ -0,0 +1,17 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda3' +version = '23.5.2-0' + +homepage = 'https://docs.conda.io/en/latest/miniconda.html' +description = """Miniconda is a free minimal installer for conda. It is a small, + bootstrap version of Anaconda that includes only conda, Python, the packages they + depend on, and a small number of other useful packages.""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/miniconda/'] +sources = ['%(name)s-py311_%(version)s-Linux-x86_64.sh'] +checksums = ['634d76df5e489c44ade4085552b97bebc786d49245ed1a830022b0b406de5817'] + +moduleclass = 'lang' From 228f50642eb4ce98232e80ee2db80378d567f74b Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 7 Aug 2023 15:22:39 +0200 Subject: [PATCH 8257/9987] adding easyconfigs: Anaconda3-2023.07-2.eb --- .../a/Anaconda3/Anaconda3-2023.07-2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.07-2.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.07-2.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.07-2.eb new file mode 100644 index 00000000000..517bcc33b13 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.07-2.eb @@ -0,0 +1,31 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, +# 2019.10, 2020.2, 2020.11, 2022.05, +# 2022.10 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2023.07-2' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH) +sources = ['%%(name)s-%%(version)s-Linux-%s.sh' % local_arch] +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': '589fb34fe73bc303379abbceba50f3131254e85ce4e7cd819ba4276ba29cad16', + '%(name)s-%(version)s-Linux-ppc64le.sh': '7a72e301fb3b8e175a96b6457fc84654dd2eb98942528d9988760779b92847e4', + '%(name)s-%(version)s-Linux-aarch64.sh': '75967bc2113d9e336e670e1e557c9198d8b98e59fb9adb82cbe0e71ce5f7c2db', + } +] + +moduleclass = 'lang' From 11af154d58a8fb21f8a0726cd77dde53e0607682 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 7 Aug 2023 14:36:56 +0100 Subject: [PATCH 8258/9987] pipeline --- .../s/setuptools/setuptools-64.0.3-GCCcore-12.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-64.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/setuptools/setuptools-64.0.3-GCCcore-12.2.0.eb index 4fadc071b0f..29349e6b6d4 100755 --- a/easybuild/easyconfigs/s/setuptools/setuptools-64.0.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-64.0.3-GCCcore-12.2.0.eb @@ -9,11 +9,16 @@ description = """Easily download, build, install, upgrade, and uninstall Python toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +builddependencies = [ + ('binutils', '2.39'), +] + dependencies = [ ('Python', '3.10.8'), ] sources = [SOURCE_TAR_GZ] +checksums = ['3bcaf6e27ad3b0f643ba0a48c5ab9eca930c3eb51df0e068f4826ab880c394ea'] download_dep_fail = True sanity_pip_check = True From 764975866e0809de8d580a317e38c50653b2186d Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 7 Aug 2023 15:37:41 +0200 Subject: [PATCH 8259/9987] adding easyconfigs: Mamba-23.1.0-4.eb --- .../easyconfigs/m/Mamba/Mamba-23.1.0-4.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mamba/Mamba-23.1.0-4.eb diff --git a/easybuild/easyconfigs/m/Mamba/Mamba-23.1.0-4.eb b/easybuild/easyconfigs/m/Mamba/Mamba-23.1.0-4.eb new file mode 100644 index 00000000000..c0104840a25 --- /dev/null +++ b/easybuild/easyconfigs/m/Mamba/Mamba-23.1.0-4.eb @@ -0,0 +1,28 @@ +# author: Caspar van Leeuwen +name = 'Mamba' +version = '23.1.0-4' + +homepage = 'https://mamba.readthedocs.io/' +description = """Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux +(ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands. +""" + +toolchain = SYSTEM + +# Note: Using Mambaforge is the recommended way of installing mamba, +# according to https://mamba.readthedocs.io/en/latest/installation.html +local_name = 'Mambaforge' +source_urls = ['https://github.com/conda-forge/miniforge/releases/download/%(version)s'] +sources = ['{local_name}-%(version)s-Linux-%(arch)s.sh'.format(local_name=local_name)] +checksums = [ + { + '{local_name}-%(version)s-Linux-aarch64.sh'.format(local_name=local_name): + '95c354268f62e32d57c84f2e1a0caf9b19f77c894ecc83008db0e5e666ce3d43', + '{local_name}-%(version)s-Linux-ppc64le.sh'.format(local_name=local_name): + '70ed57b9d32457c172c208b16a839937e2dd77e3fa1bff5ef1cb2f1a7da102ba', + '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name=local_name): + '6ca38e02be99c410644c283bac74601f296dd10995ce1c8d345af995a39b5916', + } +] + +moduleclass = 'lang' From ebf7350df4de2fe14b44b54a8b49a0caebce2e97 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 7 Aug 2023 14:38:03 +0100 Subject: [PATCH 8260/9987] adding easyconfigs: OpenFOAM-11-foss-2022a.eb and patches: OpenFOAM-11-ThirdParty.patch --- .../o/OpenFOAM/OpenFOAM-11-ThirdParty.patch | 248 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-11-foss-2022a.eb | 36 +++ 2 files changed, 284 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-ThirdParty.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-ThirdParty.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-ThirdParty.patch new file mode 100644 index 00000000000..a7676590e76 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-ThirdParty.patch @@ -0,0 +1,248 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Aligned hunks by Leon Kos and updated by Simon Branford (University of Birmingham). +# Based on patch for OpenFOAM 5.0 and 4.1 by Kenneth Hoste (HPC-UGent) and Ward Poelmans + +diff -ru OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2022-09-19 11:34:37.930703275 +0200 +@@ -17,8 +17,8 @@ + fi + + # Ensure CMake gets the correct C/C++ compilers +-[ -n "$WM_CC" ] && export CC="$WM_CC" +-[ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++#[ -n "$WM_CC" ] && export CC="$WM_CC" ++#[ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVblockMesh + wmake $targetType vtkPVFoam +diff -ru OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +--- OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt 2022-09-19 11:34:37.932703249 +0200 +@@ -2,6 +2,8 @@ + + PROJECT(PVReaders) + ++FIND_PACKAGE(MPI REQUIRED) ++ + FIND_PACKAGE(ParaView REQUIRED) + + INCLUDE(GNUInstallDirs) +diff -ru OpenFOAM-10-version-10/etc/bashrc OpenFOAM-10/etc/bashrc +--- OpenFOAM-10-version-10/etc/bashrc 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/bashrc 2022-09-19 11:34:37.934703223 +0200 +@@ -43,8 +43,9 @@ + # Please set to the appropriate path if the default is not correct. + # + [ "$BASH" -o "$ZSH_NAME" ] && \ +-export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++#export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \ ++#export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ru OpenFOAM-10-version-10/etc/config.sh/gperftools OpenFOAM-10/etc/config.sh/gperftools +--- OpenFOAM-10-version-10/etc/config.sh/gperftools 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/gperftools 2022-09-19 11:34:37.937703185 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-10-version-10/etc/config.sh/metis OpenFOAM-10/etc/config.sh/metis +--- OpenFOAM-10-version-10/etc/config.sh/metis 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/metis 2022-09-19 11:34:37.938703172 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-10-version-10/etc/config.sh/mpi OpenFOAM-10/etc/config.sh/mpi +--- OpenFOAM-10-version-10/etc/config.sh/mpi 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/mpi 2022-09-19 11:34:37.939703159 +0200 +@@ -254,6 +254,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib/release + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-10-version-10/etc/config.sh/paraview OpenFOAM-10/etc/config.sh/paraview +--- OpenFOAM-10-version-10/etc/config.sh/paraview 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/paraview 2022-09-19 11:34:37.941703134 +0200 +@@ -41,25 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used. Take the most recent. +-unset CMAKE_HOME CMAKE_ROOT +-for cmake in $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/cmake-* +-do +- if [ -d $cmake ] +- then +- if [ -z $CMAKE_HOME ] || \ +- $WM_PROJECT_DIR/bin/tools/foamVersionCompare $CMAKE_HOME lt $cmake +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- fi +- fi +-done +-if [ -n $CMAKE_HOME ] +-then +- export PATH=$cmake/bin:$PATH +-fi +- + #- ParaView version, automatically determine major version + #export ParaView_VERSION=5.6.3 + export ParaView_VERSION=5.10.1 +@@ -62,7 +62,8 @@ + + #- ParaView version, automatically determine major version + #export ParaView_VERSION=5.6.3 +-export ParaView_VERSION=5.10.1 ++#export ParaView_VERSION=5.10.1 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + #export ParaView_GL=system +@@ -109,7 +91,8 @@ + export ParaView_VERSION ParaView_MAJOR + + # Set the binary and source directories +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION ++# export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION ++export ParaView_DIR=$EBROOTPARAVIEW + paraviewSrcDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + + # Set paths if binaries or source are present +@@ -129,8 +112,6 @@ + fi + export ParaView_LIB_DIR=$ParaView_DIR/lib$paraviewArch$paraviewLibSubDir + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -142,18 +123,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi +- + # Alias paraview to launch with mesa if necessary + if [ "$ParaView_GL" = mesa ] + then +diff -ru OpenFOAM-10-version-10/etc/config.sh/scotch OpenFOAM-10/etc/config.sh/scotch +--- OpenFOAM-10-version-10/etc/config.sh/scotch 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/scotch 2022-09-19 11:34:37.942703121 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.9 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-10-version-10/etc/config.sh/settings OpenFOAM-10/etc/config.sh/settings +--- OpenFOAM-10-version-10/etc/config.sh/settings 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/settings 2022-09-19 11:34:37.943703108 +0200 +@@ -61,11 +61,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ru OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/Make/options 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/Make/options 2022-09-19 11:34:37.945703082 +0200 +@@ -4,14 +4,7 @@ + $(PFLAGS) $(PINC) \ + -I$(FOAM_SRC)/Pstream/mpi/lnInclude \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ARCH_PATH)/lib \ +- -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \ +- -lptscotch \ +- -lptscotcherrexit \ +- -lscotch \ +- -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2022-09-19 11:34:37.947703057 +0200 +@@ -31,10 +31,11 @@ + #include "SubField.H" + #include "PstreamGlobals.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-10-version-10/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-10/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-10-version-10/src/parallel/decompose/scotchDecomp/Make/options 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/src/parallel/decompose/scotchDecomp/Make/options 2022-09-19 11:34:37.948703044 +0200 +@@ -6,7 +6,6 @@ + EXE_INC = \ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb new file mode 100644 index 00000000000..4e6d2d638ce --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb @@ -0,0 +1,36 @@ +name = 'OpenFOAM' +version = '11' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-11-ThirdParty.patch'] +checksums = [ + {'version-11.tar.gz': 'ebc0f86ead699abba61290ba8aac5b730aa93256e675d1d93a5d5f116d51e0c0'}, + {'OpenFOAM-11-ThirdParty.patch': '7c526be93a0e241584c849cdcda682c23d1a87f23b1a06eae2fa8372a2cab415'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.1'), + ('CGAL', '4.14.3'), + ('ParaView', '5.10.1', '-mpi'), + ('gnuplot', '5.4.4'), +] + +moduleclass = 'cae' From 71f0a3a1f9dec1af8fec16587954c5c5f3338d42 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Aug 2023 16:37:53 +0200 Subject: [PATCH 8261/9987] Add comment to the patch --- .../easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb | 2 +- .../e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch | 10 +++++++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb index 234f2abbe90..88df11a7604 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb @@ -27,7 +27,7 @@ checksums = [ {'%(name)s-%(version)s_fix_hardcoded_perl_path.patch': '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, {'%(name)s-%(version)s_fix_AVX512_support.patch': - '67d73cf119c323203f901f60d36f8101a425d2b21448dba669a16b225c3e551b'}, + '5e86514aa86c0f88d6f3671717eb019b44357c2ddb25b48ef63f4e5c60c703cf'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch index 4b8212c1fe5..cd9f1ca0e94 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch @@ -1,4 +1,12 @@ -# What: Fixes support for AVX512 on AMD CPUs +# What: +# Fixes support for AVX512 on AMD CPUs. +# Error Msg.: +# "error: cannot convert a value of type 'int' to vector type '__vector(8) double' which has different size". +# Description: +# According to 'configure.ac' one of the 'HAVE_AVX512_XEON' or 'HAVE_AVX512_XEON_PHI' macro should automatically +# be defined if CPU has an AVX512 support. This works on Intel CPUs, however, on AMD CPUs the configure script +# ill-defines `HAVE_AVX512_XEON_PHI` and leaves `HAVE_AVX512_XEON` undefined. This leads to execution of the +# code path guarded by the `#ifdef HAVE_AVX512_XEON_PHI` directive, which calls for an undefined macro `_XOR_EPI`. # Author: maxim-masterov (SURF) diff -Nru elpa-new_release_2023.05.001.orig/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c elpa-new_release_2023.05.001/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c --- elpa-new_release_2023.05.001.orig/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c 2023-08-01 16:22:09.499243000 +0200 From eb54c997b8913741880a17f652106d547335ad01 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 7 Aug 2023 16:43:27 +0200 Subject: [PATCH 8262/9987] Improve description of the patch --- easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb | 2 +- .../e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb index 88df11a7604..dc8e17ac3a3 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb @@ -27,7 +27,7 @@ checksums = [ {'%(name)s-%(version)s_fix_hardcoded_perl_path.patch': '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, {'%(name)s-%(version)s_fix_AVX512_support.patch': - '5e86514aa86c0f88d6f3671717eb019b44357c2ddb25b48ef63f4e5c60c703cf'}, + '7e4bb0b74f8c1229c78b063789ddf32128e19e957466bd651cee6980f804cfaf'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch index cd9f1ca0e94..1da0b07e240 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch @@ -7,6 +7,8 @@ # be defined if CPU has an AVX512 support. This works on Intel CPUs, however, on AMD CPUs the configure script # ill-defines `HAVE_AVX512_XEON_PHI` and leaves `HAVE_AVX512_XEON` undefined. This leads to execution of the # code path guarded by the `#ifdef HAVE_AVX512_XEON_PHI` directive, which calls for an undefined macro `_XOR_EPI`. +# I'm sure that the same error will also appear on Xeon-Phi, so this patch actually fixes a fundamental issue +# in the code. # Author: maxim-masterov (SURF) diff -Nru elpa-new_release_2023.05.001.orig/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c elpa-new_release_2023.05.001/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c --- elpa-new_release_2023.05.001.orig/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c 2023-08-01 16:22:09.499243000 +0200 From 31710bffc18c32fdf58f4d253245496087d756db Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 7 Aug 2023 15:53:11 +0100 Subject: [PATCH 8263/9987] adding easyconfigs: Jblob-3.0.eb --- easybuild/easyconfigs/j/Jblob/Jblob-3.0.eb | 33 ++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jblob/Jblob-3.0.eb diff --git a/easybuild/easyconfigs/j/Jblob/Jblob-3.0.eb b/easybuild/easyconfigs/j/Jblob/Jblob-3.0.eb new file mode 100644 index 00000000000..2e6802c4bb7 --- /dev/null +++ b/easybuild/easyconfigs/j/Jblob/Jblob-3.0.eb @@ -0,0 +1,33 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'Tarball' + +name = 'Jblob' +version = '3.0' + +homepage = "https://www.wdc-climate.de/ui/info?site=jblob" +description = """Jblob - WDC Climate dataset download""" + +toolchain = SYSTEM + +source_urls = ['http://www.wdc-climate.de/jblob/'] +sources = [SOURCELOWER_ZIP] +checksums = ['576b5956358386a8832c6d1d13c410705e54888354a10cfd4f094513458067e4'] + +dependencies = [('Java', '11')] + +# remove hardcoded JBLOB_HOME from launch script +preinstallopts = "sed -i '/^JBLOB_HOME/d' jblob" + +sanity_check_paths = { + 'files': ['jblob'], + 'dirs': [], +} + +modextrapaths = { + 'PATH': '', + 'JBLOB_HOME': '', +} + +sanity_check_commands = ["jblob --help"] + +moduleclass = 'data' From f3abfec65e44bbe208b3d062c9d68822a65cd5d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2023 22:44:12 +0200 Subject: [PATCH 8264/9987] don't set unsupport ENABLE_FORTRAN03 configure option for libxc 6.1.0 Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb index 2f6fe0eb5f5..eed8cc7582a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Perl', '5.36.0'), ] -local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF " +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " # don't disable building of third and fourth derivates, since it's required by some software that depends on libxc # (like ABINIT, which requires "3rd derivatives of energy") diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb index 0a6d19415d4..85b0ffe80f8 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb @@ -18,7 +18,7 @@ builddependencies = [ ('Perl', '5.36.0'), ] -local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF " +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " # don't disable building of third and fourth derivates, since it's required by some software that depends on libxc # (like ABINIT, which requires "3rd derivatives of energy") From 635d00cdc6d48e6ef20b5a72e35773bc6be69b7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Aug 2023 22:45:14 +0200 Subject: [PATCH 8265/9987] don't force sequential build for libxc 6.1.0 --- easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb | 2 -- .../easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb index eed8cc7582a..7dc5e000dd6 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb @@ -31,8 +31,6 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] -parallel = 1 - # make sure that built libraries (libxc*.so*) in build directory are picked when running tests # this is required when RPATH linking is used pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb index 85b0ffe80f8..4e4f288ba98 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb @@ -31,8 +31,6 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] -parallel = 1 - # make sure that built libraries (libxc*.so*) in build directory are picked when running tests # this is required when RPATH linking is used pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " From 33e948bdc570b3c3108bd45fd9d0993845ffb61d Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 8 Aug 2023 09:40:24 +0200 Subject: [PATCH 8266/9987] adding easyconfigs: pdsh-2.34-GCCcore-12.3.0.eb --- .../p/pdsh/pdsh-2.34-GCCcore-12.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..75dde8cd89c --- /dev/null +++ b/easybuild/easyconfigs/p/pdsh/pdsh-2.34-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'pdsh' +version = '2.34' + +homepage = 'https://github.com/chaos/pdsh' +description = "A high performance, parallel remote shell utility" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/chaos/pdsh/releases/download/pdsh-%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b47b3e4662736ef44b6fe86e3d380f95e591863e69163aa0592e9f9f618521e9'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('libreadline', '8.2'), +] + +configopts = "--with-ssh --with-slurm --with-mrsh --with-readline" + +sanity_check_paths = { + 'files': ['bin/dshbak', 'bin/pdcp', 'bin/pdsh', 'bin/rpdcp'], + 'dirs': ['lib/pdsh', 'share/man/man1'], +} + +sanity_check_commands = [ + "dshbak -h", + "pdcp -h 2>&1 | grep '^Usage: pdcp'", + "pdsh -h 2>&1 | grep '^Usage: pdsh'", + "rpdcp -h 2>&1 | grep '^Usage: rpdcp'", +] + +moduleclass = 'tools' From fa9cd76bbc75c1a2132e13c6d1c145dbf9c614ff Mon Sep 17 00:00:00 2001 From: benjamic Date: Tue, 8 Aug 2023 09:55:43 +0200 Subject: [PATCH 8267/9987] adding easyconfigs: htop-3.2.2.eb --- easybuild/easyconfigs/h/htop/htop-3.2.2.eb | 28 ++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/h/htop/htop-3.2.2.eb diff --git a/easybuild/easyconfigs/h/htop/htop-3.2.2.eb b/easybuild/easyconfigs/h/htop/htop-3.2.2.eb new file mode 100644 index 00000000000..b4699ea404c --- /dev/null +++ b/easybuild/easyconfigs/h/htop/htop-3.2.2.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'htop' +version = "3.2.2" + +homepage = 'https://htop.dev' + +description = """An interactive process viewer for Unix""" + +toolchain = SYSTEM + +github_account = 'htop-dev' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['3829c742a835a0426db41bb039d1b976420c21ec65e93b35cd9bfd2d57f44ac8'] + +dependencies = [ + ('ncurses', '6.2'), +] + +preconfigopts = 'LIBS="$LIBS -ltinfo" && ./autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/htop'], + 'dirs': ['share'], +} + +moduleclass = 'tools' From 38601fc04065d1b34c66929b5e2cb43b2afc7561 Mon Sep 17 00:00:00 2001 From: benjamic Date: Tue, 8 Aug 2023 10:21:53 +0200 Subject: [PATCH 8268/9987] adding easyconfigs: parallel-20230722-GCCcore-12.3.0.eb --- .../parallel-20230722-GCCcore-12.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7725cf4990a --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20230722-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20230722' + +homepage = 'https://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['55f991ad195a72f0abfaf1ede8fc1d03dd255cac91bc5eb900f9aa2873d1ff87'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Perl', '5.36.1')] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +sanity_check_commands = ["parallel --help"] + +moduleclass = 'tools' From 875c14042191964bb97c3b607d3048c1f028aa3d Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 8 Aug 2023 09:29:54 +0100 Subject: [PATCH 8269/9987] use version template Co-authored-by: ocaisa --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb index 4e6d2d638ce..9481f562349 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2022a.eb @@ -13,8 +13,8 @@ source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] patches = ['OpenFOAM-11-ThirdParty.patch'] checksums = [ - {'version-11.tar.gz': 'ebc0f86ead699abba61290ba8aac5b730aa93256e675d1d93a5d5f116d51e0c0'}, - {'OpenFOAM-11-ThirdParty.patch': '7c526be93a0e241584c849cdcda682c23d1a87f23b1a06eae2fa8372a2cab415'}, + {'version-%(version)s.tar.gz': 'ebc0f86ead699abba61290ba8aac5b730aa93256e675d1d93a5d5f116d51e0c0'}, + {'OpenFOAM-%(version)s-ThirdParty.patch': '7c526be93a0e241584c849cdcda682c23d1a87f23b1a06eae2fa8372a2cab415'}, ] builddependencies = [ From f1acbec29ecea3cf3341f344b46585c7d6aede0b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 12:35:19 +0200 Subject: [PATCH 8270/9987] Fix spelling of BOOL values in CMake configopts CMake defines options as uppercase: > True if the constant is 1, ON, YES, TRUE, Y, or a non-zero number > False if the constant is 0, OFF, NO, FALSE, N, IGNORE, NOTFOUND, the empty string, or ends in the suffix -NOTFOUND Although it (now?) says "Named boolean constants are case-insensitive." this may not have always been the case. So make all values for `-DBUILD_SHARED_LIBS` ON/OFF to be consistent. --- .../b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb | 2 +- .../c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb | 2 +- easybuild/easyconfigs/g/gflags/gflags-2.2.1-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/g/gflags/gflags-2.2.1-intel-2017a.eb | 2 +- easybuild/easyconfigs/g/gflags/gflags-2.2.1-intel-2017b.eb | 2 +- easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/l/LEMON/LEMON-1.3.1-GCC-8.2.0-2.31.1.eb | 2 +- .../easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb | 2 +- easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb | 2 +- .../easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb | 2 +- .../easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb | 2 +- .../easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/u/utf8proc/utf8proc-2.7.0-GCCcore-11.3.0.eb | 2 +- .../easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb | 2 +- .../easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb | 2 +- 26 files changed, 26 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb b/easybuild/easyconfigs/b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb index d7e13667d5a..1b1e6ebdcf1 100644 --- a/easybuild/easyconfigs/b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/b/BUFRLIB/BUFRLIB-11.3.0.2-iccifort-2020.1.217.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['1023eb590e2112d5bc213c568a212390fc65ff98732ac8d2ccdda5062e6bc8c6'] builddependencies = [('CMake', '3.16.4')] -configopts = " -DBUILD_STATIC_LIBS=1 -DBUILD_SHARED_LIBS=1" +configopts = '-DBUILD_STATIC_LIBS=ON -DBUILD_SHARED_LIBS=ON' sanity_check_paths = { 'files': ['lib/libbufr.a', 'lib/libbufr.so'], diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb index 3a066943a85..c080deabf3c 100644 --- a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.3.0.eb @@ -37,7 +37,7 @@ dependencies = [ # build demo # build static and shared libraries -configopts = ["-DCROSSGUID_TESTS=ON", "-DBUILD_SHARED_LIBS=TRUE"] +configopts = ["-DCROSSGUID_TESTS=ON -DBUILD_SHARED_LIBS=%s" % local_shared for local_shared in ('OFF', 'ON')] # we want to have the crossguid-test postinstallcmds = [ diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb index 5f269fd40d5..a6bfc5573e2 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb @@ -20,7 +20,7 @@ builddependencies = [ ('CMake', '3.4.3'), ] -configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' sanity_check_paths = { 'files': ['bin/gflags_completions.sh'] + diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.1-GCCcore-6.4.0.eb index 957c6fd7d75..f10c4ca4939 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.2.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.1-GCCcore-6.4.0.eb @@ -23,7 +23,7 @@ builddependencies = [ ('CMake', '3.10.2'), ] -configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' sanity_check_paths = { 'files': ['bin/gflags_completions.sh'] + diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.1-intel-2017a.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.1-intel-2017a.eb index 63223f41d74..8220e3b61da 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.2.1-intel-2017a.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.1-intel-2017a.eb @@ -29,7 +29,7 @@ builddependencies = [ ('CMake', '3.9.1') ] -configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' sanity_check_paths = { 'files': ['bin/gflags_completions.sh'] + diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.1-intel-2017b.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.1-intel-2017b.eb index 0dd1faf061f..b00999db0ac 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.2.1-intel-2017b.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.1-intel-2017b.eb @@ -29,7 +29,7 @@ builddependencies = [ ('CMake', '3.9.1') ] -configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' sanity_check_paths = { 'files': ['bin/gflags_completions.sh'] + diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb index 958caa83e61..c4ec8d0dbac 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.2.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('CMake', '3.18.4'), ] -configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' sanity_check_paths = { 'files': ['bin/gflags_completions.sh'] + diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.3.0.eb index 810cfe2af93..42681054385 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-10.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('CMake', '3.20.1'), ] -configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' sanity_check_paths = { 'files': ['bin/gflags_completions.sh'] + diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-11.2.0.eb index c5cf77e7e41..f333c1b70f8 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-11.2.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('CMake', '3.21.1'), ] -configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' sanity_check_paths = { 'files': ['bin/gflags_completions.sh'] + diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.2.0.eb index 0a0d09b9bde..0d147f50672 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.2.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('CMake', '3.13.3'), ] -configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' sanity_check_paths = { 'files': ['bin/gflags_completions.sh'] + diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.3.0.eb index 9d038e815c1..fff3411438a 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-8.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('CMake', '3.15.3'), ] -configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' sanity_check_paths = { 'files': ['bin/gflags_completions.sh'] + diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb index 9433d212418..d3d4062b124 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-9.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('CMake', '3.16.4'), ] -configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' sanity_check_paths = { 'files': ['bin/gflags_completions.sh'] + diff --git a/easybuild/easyconfigs/l/LEMON/LEMON-1.3.1-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/l/LEMON/LEMON-1.3.1-GCC-8.2.0-2.31.1.eb index 5bf9e1fc226..193bd3e93cb 100644 --- a/easybuild/easyconfigs/l/LEMON/LEMON-1.3.1-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/l/LEMON/LEMON-1.3.1-GCC-8.2.0-2.31.1.eb @@ -19,7 +19,7 @@ builddependencies = [('CMake', '3.13.3')] separate_build_dir = True -configopts = ['', '-DBUILD_SHARED_LIBS=TRUE'] +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] runtest = 'check' diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb index 026ff55fa14..f54225c862b 100644 --- a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ ('CMake', '3.23.1'), ] -configopts = '-DBUILD_SHARED_LIBS=1' +configopts = '-DBUILD_SHARED_LIBS=ON' sanity_check_paths = { 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb index a8015f4cc5f..09ee525de2c 100644 --- a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('mctc-lib', '0.3.1'), ] -configopts = '-DBUILD_SHARED_LIBS=1' +configopts = '-DBUILD_SHARED_LIBS=ON' sanity_check_paths = { 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb index 148464f5a74..40c87152392 100644 --- a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-foss-2020b.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(versi sources = [SOURCELOWER_TAR_GZ] checksums = ['5d1abd3dc3286167caf0c326ef14838ac8360aa1e912bd7bd6d212259fbff1ac'] -configopts = ['-DBUILD_SHARED_LIBS=on'] +configopts = '-DBUILD_SHARED_LIBS=ON' builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb index 38ed055e46a..b7e6e5f85e5 100644 --- a/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb +++ b/easybuild/easyconfigs/n/NTPoly/NTPoly-2.5.1-intel-2020b.eb @@ -14,7 +14,7 @@ source_urls = ['https://github.com/william-dawson/NTPoly/archive/ntpoly-v%(versi sources = [SOURCELOWER_TAR_GZ] checksums = ['5d1abd3dc3286167caf0c326ef14838ac8360aa1e912bd7bd6d212259fbff1ac'] -configopts = ['-DBUILD_SHARED_LIBS=on'] +configopts = '-DBUILD_SHARED_LIBS=ON' builddependencies = [('CMake', '3.18.4')] diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb index b04ca54a116..5a713a9019e 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.3.0-GCCcore-8.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ separate_build_dir = True -configopts = ['', '-DBUILD_SHARED_LIBS=true'] +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] sanity_check_paths = { 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb index 28be3ea21de..7b350bf6100 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ separate_build_dir = True -configopts = ['', '-DBUILD_SHARED_LIBS=true'] +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] sanity_check_paths = { 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-8.3.0.eb index ecb83d6d114..e790a4d81cf 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-8.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ separate_build_dir = True -configopts = ['', '-DBUILD_SHARED_LIBS=true'] +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] sanity_check_paths = { 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb index 148e68c23d5..98ebc2555d5 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ separate_build_dir = True -configopts = ['', '-DBUILD_SHARED_LIBS=true'] +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] sanity_check_paths = { 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-10.3.0.eb index 025e8cde284..7eeac43e7e1 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-10.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ separate_build_dir = True -configopts = ['', '-DBUILD_SHARED_LIBS=true'] +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] sanity_check_paths = { 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-11.2.0.eb index b53f6ad6b27..d32efd1f02b 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.6.1-GCCcore-11.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ separate_build_dir = True -configopts = ['', '-DBUILD_SHARED_LIBS=true'] +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] sanity_check_paths = { 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.7.0-GCCcore-11.3.0.eb index be580835593..bc96c93e378 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.7.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.7.0-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ separate_build_dir = True -configopts = ['', '-DBUILD_SHARED_LIBS=true'] +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] sanity_check_paths = { 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb index 33d5c5ec66a..028f01a6164 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb @@ -20,7 +20,7 @@ builddependencies = [ separate_build_dir = True -configopts = ['', '-DBUILD_SHARED_LIBS=true'] +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] sanity_check_paths = { 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb index 74f889da933..ff42c34ef7d 100644 --- a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb @@ -20,7 +20,7 @@ builddependencies = [ separate_build_dir = True -configopts = ['', '-DBUILD_SHARED_LIBS=true'] +configopts = ['-DBUILD_SHARED_LIBS=OFF', '-DBUILD_SHARED_LIBS=ON'] sanity_check_paths = { 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], From 57dcb2f0c862e9af0e8b56f4c7a62f0e165224e9 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 8 Aug 2023 12:42:23 +0200 Subject: [PATCH 8271/9987] Update ESPResSo for 2021a --- .../ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb | 53 +++++++++++++++++++ 2 files changed, 54 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb index a8901cbb3d1..9690edeb0ea 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb @@ -28,7 +28,7 @@ dependencies = [ ('Pint', '0.20.1'), ] -configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON' +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=ON' runtest = 'check_unit_tests && make check_python' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb new file mode 100644 index 00000000000..b18d54ed895 --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'ESPResSo' +version = '4.2.1' + +homepage = 'https://espressomd.org/wordpress' +description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" + +source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f7264d78fe1fd7774b89972fe10d5b15d2e9d620d406158dab90df5df0b9f255'] + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Boost.MPI', '1.76.0'), + ('HDF5', '1.10.7'), + ('Mesa', '21.1.1'), + ('GSL', '2.7'), + ('IPython', '7.25.0'), + ('Pint', '0.20.1'), +] + +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF' + +runtest = 'check_unit_tests && make check_python' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +_binaries = ['ipypresso', 'pypresso'] +_libs = [ + 'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes', + '_init', 'analyze', 'code_info', 'electrokinetics', 'galilei', + 'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler', + 'script_interface', 'system', 'thermostat', 'utils', 'version', +] + +_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ['pypresso -h', 'ipypresso -h'] + +moduleclass = 'chem' From f74edfb969af8e105b626d1df5950e5c3cc8af2e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 8 Aug 2023 12:49:12 +0200 Subject: [PATCH 8272/9987] Add ESPResSo for 2022a --- .../ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb | 55 +++++++++++++++++++ .../e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb | 53 ++++++++++++++++++ .../p/Pint/Pint-0.22-GCCcore-11.3.0.eb | 25 +++++++++ 3 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb create mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb new file mode 100644 index 00000000000..907da191566 --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'ESPResSo' +version = '4.2.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://espressomd.org/wordpress' +description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" + +source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f7264d78fe1fd7774b89972fe10d5b15d2e9d620d406158dab90df5df0b9f255'] + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.8.0', '', SYSTEM), + ('SciPy-bundle', '2022.05'), + ('Boost.MPI', '1.79.0'), + ('HDF5', '1.12.2'), + ('Mesa', '22.0.3'), + ('GSL', '2.7'), + ('IPython', '8.5.0'), + ('Pint', '0.22'), +] + +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=ON' + +runtest = 'check_unit_tests && make check_python' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +_binaries = ['ipypresso', 'pypresso'] +_libs = [ + 'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes', + '_init', 'analyze', 'code_info', 'cuda_init', 'electrokinetics', 'galilei', + 'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler', + 'script_interface', 'system', 'thermostat', 'utils', 'version', +] + +_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ['pypresso -h', 'ipypresso -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb new file mode 100644 index 00000000000..032b259661d --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'ESPResSo' +version = '4.2.1' + +homepage = 'https://espressomd.org/wordpress' +description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" + +source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f7264d78fe1fd7774b89972fe10d5b15d2e9d620d406158dab90df5df0b9f255'] + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost.MPI', '1.79.0'), + ('HDF5', '1.12.2'), + ('Mesa', '22.0.3'), + ('GSL', '2.7'), + ('IPython', '8.5.0'), + ('Pint', '0.22'), +] + +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF' + +runtest = 'check_unit_tests && make check_python' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +_binaries = ['ipypresso', 'pypresso'] +_libs = [ + 'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes', + '_init', 'analyze', 'code_info', 'electrokinetics', 'galilei', + 'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler', + 'script_interface', 'system', 'thermostat', 'utils', 'version', +] + +_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ['pypresso -h', 'ipypresso -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d64c25ab495 --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.22-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Pint' +version = '0.22' + +homepage = 'https://github.com/hgrecco/pint' +description = """Pint is a Python package to define, operate and +manipulate physical quantities: the product of a numerical value and a +unit of measurement. It allows arithmetic operations between them and +conversions from and to different units.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2d139f6abbcf3016cad7d3cec05707fe908ac4f99cf59aedfd6ee667b7a64433'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'numlib' From bf493e0116de25b84ae178d371fe81ab72075d75 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 13:30:02 +0200 Subject: [PATCH 8273/9987] Add checksum --- easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb index a6bfc5573e2..881d2c07ffd 100644 --- a/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb @@ -15,6 +15,7 @@ toolchainopts = {'pic': True} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/gflags/gflags/archive/'] +checksums = ['d8331bd0f7367c8afd5fcb5f5e85e96868a00fd24b7276fa5fcee1e5575c2662'] builddependencies = [ ('CMake', '3.4.3'), From 55d9a17786d09fb8d95d028fe60cac0b2e86c783 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 14:03:37 +0200 Subject: [PATCH 8274/9987] Add patches for PPC --- ...fix-fp16-quantization-without-fbgemm.patch | 25 ++++++++++ ...12.0_fix-EmbeddingBag-without-fbgemm.patch | 48 +++++++++++++++++++ .../PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb | 9 ++++ 3 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 00000000000..b690fc529d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,25 @@ +Fix use-after free leading to random failures in nn/test_embedding +on e.g. POWER platforms where FBGEMM isn't used + +From https://github.com/pytorch/pytorch/pull/84750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 224a66f8abf..f4d018007bf 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -252,9 +252,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row : c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch new file mode 100644 index 00000000000..644c5d87545 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch @@ -0,0 +1,48 @@ +There is a bug in the fallback path for the case where FBGEMM isn't available (e.g. on POWER) +which leads to a race condition: +Data is "copied" for the full buffer while it is processed in chunks by different threads. +This a) duplicates the work and b) might write incomplete/wrong data to the output. + +Found in failing test_embedding_bag_half_cpu_* of nn/test_embedding: +ERROR: test_embedding_bag_half_cpu_int32_int32 (__main__.TestEmbeddingNNDeviceTypeCPU) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/dev/shm/s3248973-EasyBuild/PyTorch/1.13.1/foss-2022a/pytorch-v1.13.1/test/nn/test_embedding.py", line 936, in _test_EmbeddingBag_vs_Embedding + self.assertEqual(output, ref_output, atol=dtype2prec_DONTUSE[wdtype], rtol=0) + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_internal/common_utils.py", line 2470, in assertEqual + assert_equal( + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1093, in assert_equal + raise error_metas[0].to_error(msg) +AssertionError: Tensor-likes are not close! + +Mismatched elements: 1 / 4 (25.0%) +Greatest absolute difference: 1.18359375 at index (1, 1) (up to 0.01 allowed) +Greatest relative difference: 1.0 at index (1, 1) (up to 0 allowed) + + +Introduced by https://github.com/pytorch/pytorch/pull/74844 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/EmbeddingBag.cpp b/aten/src/ATen/native/EmbeddingBag.cpp +index 6d8cea26f52..604ea16bace 100644 +--- a/aten/src/ATen/native/EmbeddingBag.cpp ++++ b/aten/src/ATen/native/EmbeddingBag.cpp +@@ -246,7 +246,7 @@ index_select_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); +@@ -590,7 +590,7 @@ index_select_scale_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb index 3f1d7644427..87f522d6fe6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb @@ -13,7 +13,9 @@ sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -29,6 +31,7 @@ patches = [ 'PyTorch-1.13.1_fix-pytest-args.patch', 'PyTorch-1.13.1_fix-test-ops-conf.patch', 'PyTorch-1.13.1_fix-wrong-check-in-fsdp-tests.patch', + 'PyTorch-1.13.1_increase-tolerance-test_jit.patch', 'PyTorch-1.13.1_increase-tolerance-test_ops.patch', 'PyTorch-1.13.1_increase-tolerance-test_optim.patch', 'PyTorch-1.13.1_install-vsx-vec-headers.patch', @@ -42,8 +45,12 @@ checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, {'PyTorch-1.10.0_fix-kineto-crash.patch': 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb'}, + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': + '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, {'PyTorch-1.12.1_add-hypothesis-suppression.patch': 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, @@ -66,6 +73,8 @@ checksums = [ {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, {'PyTorch-1.13.1_fix-wrong-check-in-fsdp-tests.patch': 'cbb5ca9ad668a504a456a2cc02d7254b79ddfd9a971a1648f0508fb103a9fc89'}, + {'PyTorch-1.13.1_increase-tolerance-test_jit.patch': + 'b97913754a0ae0887b8137db0b0d57caff8c3d7bd96fe555ea27ea01ff14527a'}, {'PyTorch-1.13.1_increase-tolerance-test_ops.patch': 'c909fdfc2b12df457e1eb5514265ffec3eab653994949416f3f048668421e223'}, {'PyTorch-1.13.1_increase-tolerance-test_optim.patch': From 372353d59a2b131c629b0056654d519672c822bb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 14:05:37 +0200 Subject: [PATCH 8275/9987] Add patches for PPC --- ...fix-fp16-quantization-without-fbgemm.patch | 25 ++++++++++ ...12.0_fix-EmbeddingBag-without-fbgemm.patch | 48 +++++++++++++++++++ .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 6 +++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 00000000000..b690fc529d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,25 @@ +Fix use-after free leading to random failures in nn/test_embedding +on e.g. POWER platforms where FBGEMM isn't used + +From https://github.com/pytorch/pytorch/pull/84750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 224a66f8abf..f4d018007bf 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -252,9 +252,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row : c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch new file mode 100644 index 00000000000..644c5d87545 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch @@ -0,0 +1,48 @@ +There is a bug in the fallback path for the case where FBGEMM isn't available (e.g. on POWER) +which leads to a race condition: +Data is "copied" for the full buffer while it is processed in chunks by different threads. +This a) duplicates the work and b) might write incomplete/wrong data to the output. + +Found in failing test_embedding_bag_half_cpu_* of nn/test_embedding: +ERROR: test_embedding_bag_half_cpu_int32_int32 (__main__.TestEmbeddingNNDeviceTypeCPU) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/dev/shm/s3248973-EasyBuild/PyTorch/1.13.1/foss-2022a/pytorch-v1.13.1/test/nn/test_embedding.py", line 936, in _test_EmbeddingBag_vs_Embedding + self.assertEqual(output, ref_output, atol=dtype2prec_DONTUSE[wdtype], rtol=0) + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_internal/common_utils.py", line 2470, in assertEqual + assert_equal( + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1093, in assert_equal + raise error_metas[0].to_error(msg) +AssertionError: Tensor-likes are not close! + +Mismatched elements: 1 / 4 (25.0%) +Greatest absolute difference: 1.18359375 at index (1, 1) (up to 0.01 allowed) +Greatest relative difference: 1.0 at index (1, 1) (up to 0 allowed) + + +Introduced by https://github.com/pytorch/pytorch/pull/74844 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/EmbeddingBag.cpp b/aten/src/ATen/native/EmbeddingBag.cpp +index 6d8cea26f52..604ea16bace 100644 +--- a/aten/src/ATen/native/EmbeddingBag.cpp ++++ b/aten/src/ATen/native/EmbeddingBag.cpp +@@ -246,7 +246,7 @@ index_select_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); +@@ -590,7 +590,7 @@ index_select_scale_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 7684662b261..be935d188b4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -12,8 +12,10 @@ sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -42,9 +44,13 @@ checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, {'PyTorch-1.10.0_fix-kineto-crash.patch': 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb'}, + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, {'PyTorch-1.11.0_fix-fsdp-fp16-test.patch': 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13'}, {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': + '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, {'PyTorch-1.12.1_add-hypothesis-suppression.patch': 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, From 5d870a0b8a980b719c32d15820d4336baa510bfc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 14:07:37 +0200 Subject: [PATCH 8276/9987] Fix quantization failure in PyTorch 1.11.0 on POWER --- .../PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 3 +++ ...fix-fp16-quantization-without-fbgemm.patch | 25 +++++++++++++++++++ 2 files changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index 31f1c76e333..e12ecdc7f98 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -24,6 +24,7 @@ patches = [ 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', 'PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', 'PyTorch-1.11.0_fix-attention_cpp-compilation.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.0_fix_sharded_imports.patch', 'PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch', @@ -59,6 +60,8 @@ checksums = [ 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', # PyTorch-1.11.0_fix-attention_cpp-compilation.patch '84214fcc7e30cf70659a7c3bd70bf11e73d58fd4f7fff2c233e3225619b0e42c', + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '9a04f4285b800dad8a00c3014af0a9713d40d5dd35d10931c7c0da4e89c558e9', # PyTorch-1.11.0_fix_sharded_imports.patch '21fc678febcdfbb9dabd72235be23cd392044e9a954f6580d15b530e1f69dcc1', # PyTorch-1.11.0_fix_skip_jit_cuda_fuser.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 00000000000..b690fc529d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,25 @@ +Fix use-after free leading to random failures in nn/test_embedding +on e.g. POWER platforms where FBGEMM isn't used + +From https://github.com/pytorch/pytorch/pull/84750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 224a66f8abf..f4d018007bf 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -252,9 +252,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row : c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; From 402638a975027b1421ab5c297cbab0e2f73c578d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 14:21:52 +0200 Subject: [PATCH 8277/9987] Fix PyTorch 1.12 (CPU version) on POWER --- ...fix-fp16-quantization-without-fbgemm.patch | 25 ++++++++++ .../p/PyTorch/PyTorch-1.12.0-foss-2022a.eb | 6 +++ ...12.0_fix-EmbeddingBag-without-fbgemm.patch | 48 +++++++++++++++++++ .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 6 +++ .../p/PyTorch/PyTorch-1.12.1-foss-2021b.eb | 6 +++ .../p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 6 +++ 6 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 00000000000..b690fc529d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,25 @@ +Fix use-after free leading to random failures in nn/test_embedding +on e.g. POWER platforms where FBGEMM isn't used + +From https://github.com/pytorch/pytorch/pull/84750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 224a66f8abf..f4d018007bf 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -252,9 +252,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row : c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb index bcbc05d3d12..9d518f41a3d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb @@ -17,11 +17,13 @@ patches = [ 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.0_fix-test_utils.patch', 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', @@ -55,6 +57,8 @@ checksums = [ '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312'}, {'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch': '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2'}, + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, {'PyTorch-1.11.0_fix-fsdp-fp16-test.patch': 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13'}, {'PyTorch-1.11.0_fix-test_utils.patch': '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861'}, {'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch': @@ -63,6 +67,8 @@ checksums = [ '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f'}, {'PyTorch-1.11.0_install-vsx-vec-headers.patch': 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d'}, + {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': + '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, {'PyTorch-1.12.1_add-hypothesis-suppression.patch': 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, {'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch': diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch new file mode 100644 index 00000000000..644c5d87545 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch @@ -0,0 +1,48 @@ +There is a bug in the fallback path for the case where FBGEMM isn't available (e.g. on POWER) +which leads to a race condition: +Data is "copied" for the full buffer while it is processed in chunks by different threads. +This a) duplicates the work and b) might write incomplete/wrong data to the output. + +Found in failing test_embedding_bag_half_cpu_* of nn/test_embedding: +ERROR: test_embedding_bag_half_cpu_int32_int32 (__main__.TestEmbeddingNNDeviceTypeCPU) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/dev/shm/s3248973-EasyBuild/PyTorch/1.13.1/foss-2022a/pytorch-v1.13.1/test/nn/test_embedding.py", line 936, in _test_EmbeddingBag_vs_Embedding + self.assertEqual(output, ref_output, atol=dtype2prec_DONTUSE[wdtype], rtol=0) + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_internal/common_utils.py", line 2470, in assertEqual + assert_equal( + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1093, in assert_equal + raise error_metas[0].to_error(msg) +AssertionError: Tensor-likes are not close! + +Mismatched elements: 1 / 4 (25.0%) +Greatest absolute difference: 1.18359375 at index (1, 1) (up to 0.01 allowed) +Greatest relative difference: 1.0 at index (1, 1) (up to 0 allowed) + + +Introduced by https://github.com/pytorch/pytorch/pull/74844 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/EmbeddingBag.cpp b/aten/src/ATen/native/EmbeddingBag.cpp +index 6d8cea26f52..604ea16bace 100644 +--- a/aten/src/ATen/native/EmbeddingBag.cpp ++++ b/aten/src/ATen/native/EmbeddingBag.cpp +@@ -246,7 +246,7 @@ index_select_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); +@@ -590,7 +590,7 @@ index_select_scale_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index b8fd4fe4a0b..25c318bf603 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -18,11 +18,13 @@ patches = [ 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.0_fix-test_utils.patch', 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', @@ -53,6 +55,8 @@ checksums = [ '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch @@ -60,6 +64,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': + '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, # PyTorch-1.12.1_add-hypothesis-suppression.patch 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb index a6e1886d545..7789981c294 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb @@ -18,11 +18,13 @@ patches = [ 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.0_fix-test_utils.patch', 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', @@ -57,6 +59,8 @@ checksums = [ '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch @@ -64,6 +68,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': + '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, # PyTorch-1.12.1_add-hypothesis-suppression.patch 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb index 2d70b6c97a8..7914c2c0e24 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -18,11 +18,13 @@ patches = [ 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.0_fix-test_utils.patch', 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', @@ -57,6 +59,8 @@ checksums = [ '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch @@ -64,6 +68,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': + '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, # PyTorch-1.12.1_add-hypothesis-suppression.patch 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch From 28c01a54edffca6bd27fff14167bb279b5466796 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 14:26:44 +0200 Subject: [PATCH 8278/9987] Add missing patch for PyTorch 1.12.0-CUDA --- ...fix-fp16-quantization-without-fbgemm.patch | 25 ++++ .../PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 113 ++++++++++++++---- ...12.0_fix-EmbeddingBag-without-fbgemm.patch | 48 ++++++++ 3 files changed, 162 insertions(+), 24 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 00000000000..b690fc529d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,25 @@ +Fix use-after free leading to random failures in nn/test_embedding +on e.g. POWER platforms where FBGEMM isn't used + +From https://github.com/pytorch/pytorch/pull/84750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 224a66f8abf..f4d018007bf 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -252,9 +252,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row : c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index e6bc2880ce8..ea51b1e8d0a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -18,32 +18,97 @@ sources = [{ }, }] patches = [ - '%(name)s-1.7.0_avoid-nan-in-test-torch.patch', - '%(name)s-1.7.0_disable-dev-shm-test.patch', - '%(name)s-1.8.1_dont-use-gpu-ccc-in-test.patch', - '%(name)s-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - '%(name)s-1.10.0_fix-test-dataloader-fixed-affinity.patch', - '%(name)s-1.10.0_skip_cmake_rpath.patch', - '%(name)s-1.11.0_increase-distributed-test-timeout.patch', - '%(name)s-1.11.0_increase_c10d_gloo_timeout.patch', - '%(name)s-1.11.0_disable_failing_jit_cuda_fuser_tests.patch', + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', ] checksums = [ - None, # PyTorch-1.12.0.tar.gz - 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch - '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch - # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch - 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', - 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_cmake_rpath.patch - # PyTorch-1.11.0_increase-distributed-test-timeout.patch - '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', - # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch - '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', - # PyTorch-1.11.0_disable_failing_jit_cuda_fuser_tests.patch - 'e7bfe120a8b3fe2b40dac6839852a5fbab3cb3429fbe44a0fc3a1800adaaee51', + {'pytorch-v1.12.0.tar.gz': '46eff236370b759c427b03ff535c3597099043e8e467b8f81f9cd4b258a7a321'}, + {'PyTorch-1.7.0_avoid-nan-in-test-torch.patch': + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.10.0_fix-kineto-crash.patch': 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb'}, + {'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch': + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707'}, + {'PyTorch-1.10.0_fix-test-model_dump.patch': '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557'}, + {'PyTorch-1.10.0_fix-vsx-vector-functions.patch': + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312'}, + {'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch': + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2'}, + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, + {'PyTorch-1.11.0_fix-fsdp-fp16-test.patch': 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13'}, + {'PyTorch-1.11.0_fix-test_utils.patch': '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861'}, + {'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch': + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953'}, + {'PyTorch-1.11.0_increase-distributed-test-timeout.patch': + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f'}, + {'PyTorch-1.11.0_install-vsx-vec-headers.patch': + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d'}, + {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': + '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, + {'PyTorch-1.12.1_add-hypothesis-suppression.patch': + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, + {'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch': + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab'}, + {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, + {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, + {'PyTorch-1.12.1_fix-test_wishart_log_prob.patch': + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45'}, + {'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch': + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2'}, + {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, + {'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch': + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d'}, + {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, + {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, + {'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch': + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695'}, + {'PyTorch-1.12.1_increase-tolerance-test_ops.patch': + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb'}, + {'PyTorch-1.12.1_no-cuda-stubs-rpath.patch': '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6'}, + {'PyTorch-1.12.1_python-3.10-annotation-fix.patch': + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7'}, + {'PyTorch-1.12.1_python-3.10-compat.patch': '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67'}, + {'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch': + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d'}, + {'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch': + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39'}, + {'PyTorch-1.12.1_skip-failing-grad-test.patch': + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc'}, + {'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch': + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch new file mode 100644 index 00000000000..644c5d87545 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch @@ -0,0 +1,48 @@ +There is a bug in the fallback path for the case where FBGEMM isn't available (e.g. on POWER) +which leads to a race condition: +Data is "copied" for the full buffer while it is processed in chunks by different threads. +This a) duplicates the work and b) might write incomplete/wrong data to the output. + +Found in failing test_embedding_bag_half_cpu_* of nn/test_embedding: +ERROR: test_embedding_bag_half_cpu_int32_int32 (__main__.TestEmbeddingNNDeviceTypeCPU) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/dev/shm/s3248973-EasyBuild/PyTorch/1.13.1/foss-2022a/pytorch-v1.13.1/test/nn/test_embedding.py", line 936, in _test_EmbeddingBag_vs_Embedding + self.assertEqual(output, ref_output, atol=dtype2prec_DONTUSE[wdtype], rtol=0) + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_internal/common_utils.py", line 2470, in assertEqual + assert_equal( + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1093, in assert_equal + raise error_metas[0].to_error(msg) +AssertionError: Tensor-likes are not close! + +Mismatched elements: 1 / 4 (25.0%) +Greatest absolute difference: 1.18359375 at index (1, 1) (up to 0.01 allowed) +Greatest relative difference: 1.0 at index (1, 1) (up to 0 allowed) + + +Introduced by https://github.com/pytorch/pytorch/pull/74844 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/EmbeddingBag.cpp b/aten/src/ATen/native/EmbeddingBag.cpp +index 6d8cea26f52..604ea16bace 100644 +--- a/aten/src/ATen/native/EmbeddingBag.cpp ++++ b/aten/src/ATen/native/EmbeddingBag.cpp +@@ -246,7 +246,7 @@ index_select_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); +@@ -590,7 +590,7 @@ index_select_scale_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); From de229a3a2869e8c251a91e91a5df8686ee5791de Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 14:28:10 +0200 Subject: [PATCH 8279/9987] Add missing patch for JIT test --- ...h-1.13.1_increase-tolerance-test_jit.patch | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_jit.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_jit.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_jit.patch new file mode 100644 index 00000000000..b1d87bd071f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_increase-tolerance-test_jit.patch @@ -0,0 +1,24 @@ +Fix the following failure: + +FAIL: test_freeze_conv_relu_fusion (jit.test_freezing.TestFrozenOptimizations) +---------------------------------------------------------------------- +... +Mismatched elements: 10 / 30 (33.3%) +Greatest absolute difference: 3.057718276977539e-05 at index (2, 3, 0, 0, 0) (up to 1e-05 allowed) +Greatest relative difference: 8.758584417742737e-05 at index (0, 3, 0, 0, 0) (up to 1.3e-06 allowed) + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/jit/test_freezing.py b/test/jit/test_freezing.py +index cdb2187f6bb..900c7dc5f53 100644 +--- a/test/jit/test_freezing.py ++++ b/test/jit/test_freezing.py +@@ -2255,7 +2255,7 @@ class TestFrozenOptimizations(JitTestCase): + else: + FileCheck().check("aten::cudnn_convolution_relu").run(frozen_mod.graph) + +- self.assertEqual(mod_eager(inp), frozen_mod(inp)) ++ self.assertEqual(mod_eager(inp), frozen_mod(inp), atol=5e-5, rtol=1e-4) + + @unittest.skipIf(not (TEST_CUDNN or TEST_WITH_ROCM), "requires CUDNN") + def test_freeze_conv_relu_fusion_not_forward(self): From 0d91a65bf558821c235855ca4a7db8617074b379 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 14:35:56 +0200 Subject: [PATCH 8280/9987] Fix PyTorch-1.12.1-foss-2021a (CUDA) on POWER --- ...fix-fp16-quantization-without-fbgemm.patch | 25 ++++++++++ ...12.0_fix-EmbeddingBag-without-fbgemm.patch | 48 +++++++++++++++++++ .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 6 +++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 00000000000..b690fc529d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,25 @@ +Fix use-after free leading to random failures in nn/test_embedding +on e.g. POWER platforms where FBGEMM isn't used + +From https://github.com/pytorch/pytorch/pull/84750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 224a66f8abf..f4d018007bf 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -252,9 +252,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row : c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch new file mode 100644 index 00000000000..644c5d87545 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch @@ -0,0 +1,48 @@ +There is a bug in the fallback path for the case where FBGEMM isn't available (e.g. on POWER) +which leads to a race condition: +Data is "copied" for the full buffer while it is processed in chunks by different threads. +This a) duplicates the work and b) might write incomplete/wrong data to the output. + +Found in failing test_embedding_bag_half_cpu_* of nn/test_embedding: +ERROR: test_embedding_bag_half_cpu_int32_int32 (__main__.TestEmbeddingNNDeviceTypeCPU) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/dev/shm/s3248973-EasyBuild/PyTorch/1.13.1/foss-2022a/pytorch-v1.13.1/test/nn/test_embedding.py", line 936, in _test_EmbeddingBag_vs_Embedding + self.assertEqual(output, ref_output, atol=dtype2prec_DONTUSE[wdtype], rtol=0) + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_internal/common_utils.py", line 2470, in assertEqual + assert_equal( + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1093, in assert_equal + raise error_metas[0].to_error(msg) +AssertionError: Tensor-likes are not close! + +Mismatched elements: 1 / 4 (25.0%) +Greatest absolute difference: 1.18359375 at index (1, 1) (up to 0.01 allowed) +Greatest relative difference: 1.0 at index (1, 1) (up to 0 allowed) + + +Introduced by https://github.com/pytorch/pytorch/pull/74844 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/EmbeddingBag.cpp b/aten/src/ATen/native/EmbeddingBag.cpp +index 6d8cea26f52..604ea16bace 100644 +--- a/aten/src/ATen/native/EmbeddingBag.cpp ++++ b/aten/src/ATen/native/EmbeddingBag.cpp +@@ -246,7 +246,7 @@ index_select_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); +@@ -590,7 +590,7 @@ index_select_scale_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 855d6a9bfdd..59ced2ffd4f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -19,12 +19,14 @@ patches = [ 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.0_fix-test_utils.patch', 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', @@ -55,6 +57,8 @@ checksums = [ '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch @@ -64,6 +68,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.11.1_skip-test_init_from_local_shards.patch '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': + '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, # PyTorch-1.12.1_add-hypothesis-suppression.patch 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch From ab72a945dcdfa78bccdcdd9e6d8a41443cf69220 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 14:36:19 +0200 Subject: [PATCH 8281/9987] Fix PyTorch-1.12.1-foss-2021b (CUDA) on POWER --- ...fix-fp16-quantization-without-fbgemm.patch | 25 ++++++++++ ...12.0_fix-EmbeddingBag-without-fbgemm.patch | 48 +++++++++++++++++++ .../PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb | 6 +++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 00000000000..b690fc529d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,25 @@ +Fix use-after free leading to random failures in nn/test_embedding +on e.g. POWER platforms where FBGEMM isn't used + +From https://github.com/pytorch/pytorch/pull/84750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 224a66f8abf..f4d018007bf 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -252,9 +252,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row : c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch new file mode 100644 index 00000000000..644c5d87545 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch @@ -0,0 +1,48 @@ +There is a bug in the fallback path for the case where FBGEMM isn't available (e.g. on POWER) +which leads to a race condition: +Data is "copied" for the full buffer while it is processed in chunks by different threads. +This a) duplicates the work and b) might write incomplete/wrong data to the output. + +Found in failing test_embedding_bag_half_cpu_* of nn/test_embedding: +ERROR: test_embedding_bag_half_cpu_int32_int32 (__main__.TestEmbeddingNNDeviceTypeCPU) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/dev/shm/s3248973-EasyBuild/PyTorch/1.13.1/foss-2022a/pytorch-v1.13.1/test/nn/test_embedding.py", line 936, in _test_EmbeddingBag_vs_Embedding + self.assertEqual(output, ref_output, atol=dtype2prec_DONTUSE[wdtype], rtol=0) + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_internal/common_utils.py", line 2470, in assertEqual + assert_equal( + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1093, in assert_equal + raise error_metas[0].to_error(msg) +AssertionError: Tensor-likes are not close! + +Mismatched elements: 1 / 4 (25.0%) +Greatest absolute difference: 1.18359375 at index (1, 1) (up to 0.01 allowed) +Greatest relative difference: 1.0 at index (1, 1) (up to 0 allowed) + + +Introduced by https://github.com/pytorch/pytorch/pull/74844 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/EmbeddingBag.cpp b/aten/src/ATen/native/EmbeddingBag.cpp +index 6d8cea26f52..604ea16bace 100644 +--- a/aten/src/ATen/native/EmbeddingBag.cpp ++++ b/aten/src/ATen/native/EmbeddingBag.cpp +@@ -246,7 +246,7 @@ index_select_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); +@@ -590,7 +590,7 @@ index_select_scale_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb index b8bf2014778..f985f5736c1 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb @@ -19,12 +19,14 @@ patches = [ 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.0_fix-test_utils.patch', 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', @@ -60,6 +62,8 @@ checksums = [ '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch @@ -69,6 +73,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.11.1_skip-test_init_from_local_shards.patch '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': + '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, # PyTorch-1.12.1_add-hypothesis-suppression.patch 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch From 69c9d48893ceaf1118b43c796fa1ca21bf0f413d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 14:36:42 +0200 Subject: [PATCH 8282/9987] Fix PyTorch-1.12.1-foss-2022a (CUDA) on POWER --- ...fix-fp16-quantization-without-fbgemm.patch | 25 ++++++++++ ...12.0_fix-EmbeddingBag-without-fbgemm.patch | 48 +++++++++++++++++++ .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 6 +++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 00000000000..b690fc529d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,25 @@ +Fix use-after free leading to random failures in nn/test_embedding +on e.g. POWER platforms where FBGEMM isn't used + +From https://github.com/pytorch/pytorch/pull/84750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 224a66f8abf..f4d018007bf 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -252,9 +252,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row : c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch new file mode 100644 index 00000000000..644c5d87545 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch @@ -0,0 +1,48 @@ +There is a bug in the fallback path for the case where FBGEMM isn't available (e.g. on POWER) +which leads to a race condition: +Data is "copied" for the full buffer while it is processed in chunks by different threads. +This a) duplicates the work and b) might write incomplete/wrong data to the output. + +Found in failing test_embedding_bag_half_cpu_* of nn/test_embedding: +ERROR: test_embedding_bag_half_cpu_int32_int32 (__main__.TestEmbeddingNNDeviceTypeCPU) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/dev/shm/s3248973-EasyBuild/PyTorch/1.13.1/foss-2022a/pytorch-v1.13.1/test/nn/test_embedding.py", line 936, in _test_EmbeddingBag_vs_Embedding + self.assertEqual(output, ref_output, atol=dtype2prec_DONTUSE[wdtype], rtol=0) + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_internal/common_utils.py", line 2470, in assertEqual + assert_equal( + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1093, in assert_equal + raise error_metas[0].to_error(msg) +AssertionError: Tensor-likes are not close! + +Mismatched elements: 1 / 4 (25.0%) +Greatest absolute difference: 1.18359375 at index (1, 1) (up to 0.01 allowed) +Greatest relative difference: 1.0 at index (1, 1) (up to 0 allowed) + + +Introduced by https://github.com/pytorch/pytorch/pull/74844 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/EmbeddingBag.cpp b/aten/src/ATen/native/EmbeddingBag.cpp +index 6d8cea26f52..604ea16bace 100644 +--- a/aten/src/ATen/native/EmbeddingBag.cpp ++++ b/aten/src/ATen/native/EmbeddingBag.cpp +@@ -246,7 +246,7 @@ index_select_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); +@@ -590,7 +590,7 @@ index_select_scale_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index f7cf757ee24..83c6b9df6c4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -19,12 +19,14 @@ patches = [ 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.0_fix-test_utils.patch', 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', @@ -60,6 +62,8 @@ checksums = [ '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch @@ -69,6 +73,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.11.1_skip-test_init_from_local_shards.patch '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': + '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, # PyTorch-1.12.1_add-hypothesis-suppression.patch 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch From cbdc9332302f917cddc506b821ff90d1195148ee Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 8 Aug 2023 14:42:17 +0200 Subject: [PATCH 8283/9987] adding easyconfigs: GLib-2.77.1-GCCcore-12.3.0.eb --- .../g/GLib/GLib-2.77.1-GCCcore-12.3.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.77.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.77.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.77.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e3f656498ac --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.77.1-GCCcore-12.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.77.1' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['dce8d0c9e916d8c81a64436bd4ee4d6515a52dd3d157c994e1cdb9b3d6300a03'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.11.3'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('libffi', '3.4.4'), + ('gettext', '0.21.1'), + ('libxml2', '2.11.4'), + ('PCRE2', '10.42'), + ('util-linux', '2.39'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + + +moduleclass = 'vis' From e47cab373b720f4fd12e5600df99d0159f6854d7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 15:59:02 +0200 Subject: [PATCH 8284/9987] fix PyTorch-1.13.1-foss-2022a on POWER --- ...fix-fp16-quantization-without-fbgemm.patch | 25 ++++++++++ ...12.0_fix-EmbeddingBag-without-fbgemm.patch | 48 +++++++++++++++++++ .../p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 6 +++ 3 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 00000000000..b690fc529d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,25 @@ +Fix use-after free leading to random failures in nn/test_embedding +on e.g. POWER platforms where FBGEMM isn't used + +From https://github.com/pytorch/pytorch/pull/84750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 224a66f8abf..f4d018007bf 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -252,9 +252,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row : c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch new file mode 100644 index 00000000000..644c5d87545 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch @@ -0,0 +1,48 @@ +There is a bug in the fallback path for the case where FBGEMM isn't available (e.g. on POWER) +which leads to a race condition: +Data is "copied" for the full buffer while it is processed in chunks by different threads. +This a) duplicates the work and b) might write incomplete/wrong data to the output. + +Found in failing test_embedding_bag_half_cpu_* of nn/test_embedding: +ERROR: test_embedding_bag_half_cpu_int32_int32 (__main__.TestEmbeddingNNDeviceTypeCPU) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/dev/shm/s3248973-EasyBuild/PyTorch/1.13.1/foss-2022a/pytorch-v1.13.1/test/nn/test_embedding.py", line 936, in _test_EmbeddingBag_vs_Embedding + self.assertEqual(output, ref_output, atol=dtype2prec_DONTUSE[wdtype], rtol=0) + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_internal/common_utils.py", line 2470, in assertEqual + assert_equal( + File "/tmp/eb-tmp-2022a/lib/python3.10/site-packages/torch/testing/_comparison.py", line 1093, in assert_equal + raise error_metas[0].to_error(msg) +AssertionError: Tensor-likes are not close! + +Mismatched elements: 1 / 4 (25.0%) +Greatest absolute difference: 1.18359375 at index (1, 1) (up to 0.01 allowed) +Greatest relative difference: 1.0 at index (1, 1) (up to 0 allowed) + + +Introduced by https://github.com/pytorch/pytorch/pull/74844 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/EmbeddingBag.cpp b/aten/src/ATen/native/EmbeddingBag.cpp +index 6d8cea26f52..604ea16bace 100644 +--- a/aten/src/ATen/native/EmbeddingBag.cpp ++++ b/aten/src/ATen/native/EmbeddingBag.cpp +@@ -246,7 +246,7 @@ index_select_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); +@@ -590,7 +590,7 @@ index_select_scale_add(const Tensor &select_indices, + /*scale_bias=*/nullptr, + /*normalize_by_lengths=*/false, + /*out=*/output_data_fp32 + start_idx * ddim); +- for (const auto i : c10::irange(output_size)) { ++ for (const auto i : c10::irange(start_idx, end_idx)) { + // Convert FP32 intermediate buffer result back to FP16 for output dtype + for (const auto d : c10::irange(ddim)) { + (output_data + i * ddim)[d] = static_cast((output_data_fp32 + ddim * i)[d]); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index 645b2fb8883..25c524c6b73 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -12,7 +12,9 @@ sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -36,8 +38,12 @@ checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, {'PyTorch-1.10.0_fix-kineto-crash.patch': 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb'}, + {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': + 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': + '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, {'PyTorch-1.12.1_add-hypothesis-suppression.patch': 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, From 58ad3c3296a290e5212369eed19c1a3061c16027 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 8 Aug 2023 15:10:39 +0100 Subject: [PATCH 8285/9987] remove GSL/2.7-GCCcore-12.2.0 as we have GSL/2.7-GCC-12.2.0 --- .../g/GSL/GSL-2.7-GCCcore-12.2.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.2.0.eb deleted file mode 100644 index 04f31f8b603..00000000000 --- a/easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.2.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '2.7' - -homepage = 'https://www.gnu.org/software/gsl/' -description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions - and least-squares fitting.""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] - -builddependencies = [ - ('binutils', '2.39'), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + - ['include/gsl/gsl_types.h'] + - ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], - 'dirs': [], -} - -moduleclass = 'numlib' From 906923b000d1bcf998f7d66bd32f785fdafb9fdd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 16:18:48 +0200 Subject: [PATCH 8286/9987] Try to fix test_jit_legacy failing sometimes --- .../p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 2 ++ .../PyTorch-1.13.1_fix-flaky-jit-test.patch | 21 +++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index 25c524c6b73..c2eb02d4435 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -24,6 +24,7 @@ patches = [ 'PyTorch-1.12.1_fix-vsx-loadu.patch', 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-flaky-jit-test.patch', 'PyTorch-1.13.1_fix-fsdp-fp16-test.patch', 'PyTorch-1.13.1_fix-pytest-args.patch', 'PyTorch-1.13.1_fix-test-ops-conf.patch', @@ -57,6 +58,7 @@ checksums = [ {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-flaky-jit-test.patch': '71efdeb29b5e5b4982c9f5cb2182733654a34d52f85bb5487bc4d7d99b86101b'}, {'PyTorch-1.13.1_fix-fsdp-fp16-test.patch': '8ae68e60d6e1f92f50322b7f0381c7e65251fba32d7606e3a238a36a2f55b5cf'}, {'PyTorch-1.13.1_fix-pytest-args.patch': 'd3e3c841cf8d73683750f29326f2be56ee0bb5df7ff522baf7d7c3f301a91ec2'}, {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch new file mode 100644 index 00000000000..f04de0cc8ed --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch @@ -0,0 +1,21 @@ +Especially `test_jit_legacy` seems to be flaky. +https://github.com/pytorch/pytorch/commit/316ba9e6fc9e2c309c1b3785e35393b4a727b918 +makes the JIT tests run serially avoiding potential races. +So backport that commit. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/run_test.py b/test/run_test.py +index f7c80f3f0a6..9d9b0c553e9 100755 +--- a/test/run_test.py ++++ b/test/run_test.py +@@ -994,7 +994,8 @@ def must_serial(file: str) -> bool: + "distributed" in file or + file in CUSTOM_HANDLERS or + file in RUN_PARALLEL_BLOCKLIST or +- file in CI_SERIAL_LIST ++ file in CI_SERIAL_LIST or ++ file in JIT_EXECUTOR_TESTS + ) + + From 13bb357d2048108eea07262a20d1842436ad58f7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 16:35:04 +0200 Subject: [PATCH 8287/9987] Update patches to sync with 2022a --- .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 26 ++++++++++--------- 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index be935d188b4..b9d649c5002 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -13,7 +13,6 @@ patches = [ 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', - 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', @@ -22,9 +21,11 @@ patches = [ 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', - 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-flaky-jit-test.patch', + 'PyTorch-1.13.1_fix-fsdp-fp16-test.patch', 'PyTorch-1.13.1_fix-gcc-12-missing-includes.patch', 'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch', 'PyTorch-1.13.1_fix-numpy-deprecations.patch', @@ -33,12 +34,12 @@ patches = [ 'PyTorch-1.13.1_fix-python-3.11-compat.patch', 'PyTorch-1.13.1_fix-test-ops-conf.patch', 'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch', - 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', - 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', - 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', 'PyTorch-1.13.1_increase-tolerance-test_ops.patch', 'PyTorch-1.13.1_install-vsx-vec-headers.patch', + 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', 'PyTorch-1.13.1_skip-failing-grad-test.patch', + 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', ] checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, @@ -46,7 +47,6 @@ checksums = [ {'PyTorch-1.10.0_fix-kineto-crash.patch': 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb'}, {'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch': 'cc526130b6446bbbf5f0f7372d3aeee3e7d4c4d6e471524dff028b430b152934'}, - {'PyTorch-1.11.0_fix-fsdp-fp16-test.patch': 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13'}, {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': @@ -61,9 +61,11 @@ checksums = [ {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, {'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch': '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d'}, - {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, + {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-flaky-jit-test.patch': '71efdeb29b5e5b4982c9f5cb2182733654a34d52f85bb5487bc4d7d99b86101b'}, + {'PyTorch-1.13.1_fix-fsdp-fp16-test.patch': '8ae68e60d6e1f92f50322b7f0381c7e65251fba32d7606e3a238a36a2f55b5cf'}, {'PyTorch-1.13.1_fix-gcc-12-missing-includes.patch': '18df8c61ecaa9fb659346c1e172828bca6b069f0145bb8f6a36b0a23b7bef0a6'}, {'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch': @@ -78,16 +80,16 @@ checksums = [ {'PyTorch-1.13.1_fix-test-ops-conf.patch': 'df652eec7753864ebebbfeca546929a53e3fb8f24259d5c9b964266a8551198c'}, {'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch': 'bdde0f2105215c95a54de64ec4b1a4520528510663174fef6d5b900eb1db3937'}, - {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '4c636059850fc9d1ecb27ce275f8aad5d5b6fdc19e35aff0c25b86cb3201352a'}, - {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': - 'be83ff61fe2dedab6d49c232936d5622df81ab49154264490021c6c828e53315'}, - {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': - '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, {'PyTorch-1.13.1_increase-tolerance-test_ops.patch': 'c909fdfc2b12df457e1eb5514265ffec3eab653994949416f3f048668421e223'}, {'PyTorch-1.13.1_install-vsx-vec-headers.patch': '7b678f54bb947afd4767f5877ac424b4b94ce5db609ea20f5a869ccf4027035f'}, + {'PyTorch-1.13.1_no-cuda-stubs-rpath.patch': '4c636059850fc9d1ecb27ce275f8aad5d5b6fdc19e35aff0c25b86cb3201352a'}, + {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': + 'be83ff61fe2dedab6d49c232936d5622df81ab49154264490021c6c828e53315'}, {'PyTorch-1.13.1_skip-failing-grad-test.patch': '6681200f9509893cb9231b5c93ac9bc5e6d9d9ae4febefca52e7cbc843ba8f51'}, + {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': + '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] From 1365387995e2e9ffcd4fd736518b16a2ede0fb9a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 16:36:43 +0200 Subject: [PATCH 8288/9987] Add missing patch --- .../PyTorch-1.13.1_fix-flaky-jit-test.patch | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch new file mode 100644 index 00000000000..f04de0cc8ed --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch @@ -0,0 +1,21 @@ +Especially `test_jit_legacy` seems to be flaky. +https://github.com/pytorch/pytorch/commit/316ba9e6fc9e2c309c1b3785e35393b4a727b918 +makes the JIT tests run serially avoiding potential races. +So backport that commit. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/run_test.py b/test/run_test.py +index f7c80f3f0a6..9d9b0c553e9 100755 +--- a/test/run_test.py ++++ b/test/run_test.py +@@ -994,7 +994,8 @@ def must_serial(file: str) -> bool: + "distributed" in file or + file in CUSTOM_HANDLERS or + file in RUN_PARALLEL_BLOCKLIST or +- file in CI_SERIAL_LIST ++ file in CI_SERIAL_LIST or ++ file in JIT_EXECUTOR_TESTS + ) + + From 753affba90ff16f46e884d8782f988e2d09413e5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 8 Aug 2023 15:37:32 +0100 Subject: [PATCH 8289/9987] move GStreamer to GCC --- ...1.22.1-GCCcore-12.2.0.eb => GStreamer-1.22.1-GCC-12.2.0.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/g/GStreamer/{GStreamer-1.22.1-GCCcore-12.2.0.eb => GStreamer-1.22.1-GCC-12.2.0.eb} (94%) diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.1-GCC-12.2.0.eb similarity index 94% rename from easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.1-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.1-GCC-12.2.0.eb index a66851cc78f..20ecd1c402d 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.1-GCC-12.2.0.eb @@ -9,7 +9,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.""" -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchain = {'name': 'GCC', 'version': '12.2.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] @@ -22,7 +22,6 @@ checksums = [ ] builddependencies = [ - ('binutils', '2.39'), ('Meson', '0.64.0'), ('Ninja', '1.11.1'), ('Perl', '5.36.0'), From 4967c7430e300acab213a315b59e433f74a4241f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 8 Aug 2023 16:40:17 +0200 Subject: [PATCH 8290/9987] Add patch for JIT tests --- .../PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb | 2 ++ .../PyTorch-1.13.1_fix-flaky-jit-test.patch | 21 +++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb index 87f522d6fe6..e2658a4ad2f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.12.1_fix-vsx-loadu.patch', 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-flaky-jit-test.patch', 'PyTorch-1.13.1_fix-fsdp-fp16-test.patch', 'PyTorch-1.13.1_fix-fsdp-tp-integration-test.patch', 'PyTorch-1.13.1_fix-kineto-crash-on-exit.patch', @@ -64,6 +65,7 @@ checksums = [ {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-flaky-jit-test.patch': '71efdeb29b5e5b4982c9f5cb2182733654a34d52f85bb5487bc4d7d99b86101b'}, {'PyTorch-1.13.1_fix-fsdp-fp16-test.patch': '8ae68e60d6e1f92f50322b7f0381c7e65251fba32d7606e3a238a36a2f55b5cf'}, {'PyTorch-1.13.1_fix-fsdp-tp-integration-test.patch': '31e2d63b54ae1a8c554575f46db79bf8bbda851b6ca0ffe623c4911207a3c2bc'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch new file mode 100644 index 00000000000..f04de0cc8ed --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-flaky-jit-test.patch @@ -0,0 +1,21 @@ +Especially `test_jit_legacy` seems to be flaky. +https://github.com/pytorch/pytorch/commit/316ba9e6fc9e2c309c1b3785e35393b4a727b918 +makes the JIT tests run serially avoiding potential races. +So backport that commit. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/run_test.py b/test/run_test.py +index f7c80f3f0a6..9d9b0c553e9 100755 +--- a/test/run_test.py ++++ b/test/run_test.py +@@ -994,7 +994,8 @@ def must_serial(file: str) -> bool: + "distributed" in file or + file in CUSTOM_HANDLERS or + file in RUN_PARALLEL_BLOCKLIST or +- file in CI_SERIAL_LIST ++ file in CI_SERIAL_LIST or ++ file in JIT_EXECUTOR_TESTS + ) + + From 994efd0ddc252bfff868931489b68f75a39fc2bb Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 8 Aug 2023 15:40:46 +0100 Subject: [PATCH 8291/9987] move GST-plugins-base to GCC --- ...GCCcore-12.2.0.eb => GST-plugins-base-1.22.1-GCC-12.2.0.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/g/GST-plugins-base/{GST-plugins-base-1.22.1-GCCcore-12.2.0.eb => GST-plugins-base-1.22.1-GCC-12.2.0.eb} (93%) diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.1-GCC-12.2.0.eb similarity index 93% rename from easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.1-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.1-GCC-12.2.0.eb index e1b10d918d0..739ab50a8d1 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.1-GCC-12.2.0.eb @@ -9,14 +9,13 @@ description = """GStreamer is a library for constructing graphs of media-handlin Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.""" -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchain = {'name': 'GCC', 'version': '12.2.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['59bcaeacc5646b8dbdcfa4ef20ca6e818dd234910efb4cee1bbea441a3801c69'] builddependencies = [ - ('binutils', '2.39'), ('Meson', '0.64.0'), ('Ninja', '1.11.1'), ('GObject-Introspection', '1.74.0'), From 0cdb707a9bdab6790b96bda615c7339fcff3a998 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 8 Aug 2023 15:42:50 +0100 Subject: [PATCH 8292/9987] move wxWidgets to GCC --- ...2.2.1-GCCcore-12.2.0.eb => wxWidgets-3.2.2.1-GCC-12.2.0.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/w/wxWidgets/{wxWidgets-3.2.2.1-GCCcore-12.2.0.eb => wxWidgets-3.2.2.1-GCC-12.2.0.eb} (96%) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCC-12.2.0.eb similarity index 96% rename from easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCC-12.2.0.eb index 763e60230cd..465575b3ec1 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCC-12.2.0.eb @@ -11,7 +11,7 @@ Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI.""" -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchain = {'name': 'GCC', 'version': '12.2.0'} toolchainopts = {'pic': True} github_account = 'wxWidgets' @@ -20,7 +20,6 @@ sources = [SOURCE_TAR_BZ2] checksums = ['dffcb6be71296fff4b7f8840eb1b510178f57aa2eb236b20da41182009242c02'] builddependencies = [ - ('binutils', '2.39'), ('gettext', '0.21.1'), ('pkgconf', '1.9.3'), ('Python', '3.10.8'), From 887742f7d5a91b02bc7c5eecfbf44e6f962e5a22 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 8 Aug 2023 15:46:59 +0100 Subject: [PATCH 8293/9987] move gnuplot and canu to GCC --- .../{canu-2.2-GCCcore-12.2.0.eb => canu-2.2-GCC-12.2.0.eb} | 3 +-- ...lot-5.4.6-GCCcore-12.2.0.eb => gnuplot-5.4.6-GCC-12.2.0.eb} | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/c/canu/{canu-2.2-GCCcore-12.2.0.eb => canu-2.2-GCC-12.2.0.eb} (92%) rename easybuild/easyconfigs/g/gnuplot/{gnuplot-5.4.6-GCCcore-12.2.0.eb => gnuplot-5.4.6-GCC-12.2.0.eb} (92%) diff --git a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/canu/canu-2.2-GCC-12.2.0.eb similarity index 92% rename from easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/c/canu/canu-2.2-GCC-12.2.0.eb index ba27e76da5d..89e36ac8b62 100644 --- a/easybuild/easyconfigs/c/canu/canu-2.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/c/canu/canu-2.2-GCC-12.2.0.eb @@ -6,14 +6,13 @@ version = '2.2' homepage = 'https://canu.readthedocs.io' description = "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing" -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchain = {'name': 'GCC', 'version': '12.2.0'} source_urls = ['https://github.com/marbl/canu/releases/download/v%(version)s/'] sources = ['canu-%(version)s.tar.xz'] checksums = ['e4d0c7b82149114f442ccd39e18f7fe2061c63b28d53700ad896e022b73b7404'] builddependencies = [ - ('binutils', '2.39'), # Makefile checks git version, before making (futile) attempt to update git submodules ('git', '2.38.1', '-nodocs'), ] diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCC-12.2.0.eb similarity index 92% rename from easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCC-12.2.0.eb index d3bd40b6b62..79e961d87ef 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCC-12.2.0.eb @@ -6,14 +6,13 @@ version = '5.4.6' homepage = 'http://gnuplot.sourceforge.net' description = """Portable interactive, function plotting utility""" -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchain = {'name': 'GCC', 'version': '12.2.0'} source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] checksums = ['02fc27918200ed64d8f0c3b84fe81b95b59cd47ad99f270939ae497c19f27419'] builddependencies = [ - ('binutils', '2.39'), ('pkgconf', '1.9.3'), ('Autotools', '20220317'), ] From 85160b795227ccf20e0269012f3ad03c81747b76 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 8 Aug 2023 15:51:03 +0100 Subject: [PATCH 8294/9987] move GSL from GCCcore to GCC for 12.3.0 --- .../{GSL-2.7-GCCcore-12.3.0.eb => GSL-2.7-GCC-12.3.0.eb} | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) rename easybuild/easyconfigs/g/GSL/{GSL-2.7-GCCcore-12.3.0.eb => GSL-2.7-GCC-12.3.0.eb} (88%) diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-12.3.0.eb similarity index 88% rename from easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-12.3.0.eb index 9f94ed4cf46..6b836923e91 100644 --- a/easybuild/easyconfigs/g/GSL/GSL-2.7-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-12.3.0.eb @@ -8,17 +8,13 @@ description = """The GNU Scientific Library (GSL) is a numerical library for C a The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.""" -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchain = {'name': 'GCC', 'version': '12.3.0'} toolchainopts = {'unroll': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] -builddependencies = [ - ('binutils', '2.40'), -] - sanity_check_paths = { 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + ['include/gsl/gsl_types.h'] + From 8e0fc27ec95785b1d93d8b3c9ce1b9f547dcdbd7 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 8 Aug 2023 16:54:29 +0200 Subject: [PATCH 8295/9987] adding easyconfigs: iimkl-2023a.eb --- easybuild/easyconfigs/i/iimkl/iimkl-2023a.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/i/iimkl/iimkl-2023a.eb diff --git a/easybuild/easyconfigs/i/iimkl/iimkl-2023a.eb b/easybuild/easyconfigs/i/iimkl/iimkl-2023a.eb new file mode 100644 index 00000000000..e20470accb9 --- /dev/null +++ b/easybuild/easyconfigs/i/iimkl/iimkl-2023a.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimkl' +version = '2023a' + +homepage = 'https://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel Math Kernel Library (MKL).""" + +toolchain = SYSTEM + +local_comp_ver = '2023.1.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('imkl', local_comp_ver, '', SYSTEM), +] + +moduleclass = 'toolchain' From 37a54a50289ede07c3346785133d0c512570a8c4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 8 Aug 2023 16:40:22 +0100 Subject: [PATCH 8296/9987] adding easyconfigs: Graphviz-8.1.0-GCCcore-12.2.0.eb, GTS-0.7.6-GCCcore-12.2.0.eb, Ghostscript-10.01.2-GCCcore-12.2.0.eb and patches: Graphviz-8.1.0_skip-install-data-hook.patch --- .../g/GTS/GTS-0.7.6-GCCcore-12.2.0.eb | 30 ++++++ .../Ghostscript-10.01.2-GCCcore-12.2.0.eb | 57 +++++++++++ .../Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb | 95 +++++++++++++++++++ ...raphviz-8.1.0_skip-install-data-hook.patch | 88 +++++++++++++++++ 4 files changed, 270 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0_skip-install-data-hook.patch diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..32cd1e37484 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'https://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. +It is an Open Source Free Software Library intended to provide a set of useful +functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('binutils', '2.39'), +] +dependencies = [ + ('GLib', '2.75.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..5a5a5802de1 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb @@ -0,0 +1,57 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '10.01.2' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4cd61a07fec161bee35da0211a5e5cde8ff8a0aaf942fc0176715e499d21661'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('freetype', '2.12.1'), + ('libjpeg-turbo', '2.1.4'), + ('expat', '2.4.9'), + ('GLib', '2.75.0'), + ('cairo', '1.17.4'), + ('LibTIFF', '4.4.0'), + # ('GTK2', '2.24.33'), + ('GTK3', '3.24.35'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic --disable-hidden-visibility" + +postinstallcmds = [ + # build and install shared libs + "make -j %(parallel)s so && make -j %(parallel)s soinstall", + # install header files + "mkdir -p %(installdir)s/include/ghostscript", + "install -v -m644 base/*.h %(installdir)s/include/ghostscript", + "install -v -m644 psi/*.h %(installdir)s/include/ghostscript", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/ghostscript', 'include/ghostscript', 'share/man'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..d206b94f524 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,95 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '8.1.0' +local_pyver_major = '3' + +homepage = 'https://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +# toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_skip-install-data-hook.patch'] +checksums = [ + {'graphviz-8.1.0.tar.gz': '2e4dfee3c24925ad51d1e76a9fb2b19b26a5a0049ef7be6d3e52667aac72eabe'}, + {'Graphviz-8.1.0_skip-install-data-hook.patch': '834666f1b5a8eff35f30899419e322739d71a2936408b27c8ffb4423a99a38e1'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('SWIG', '4.1.1'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Python', '3.10.8'), + ('FriBidi', '1.0.12'), + ('Gdk-Pixbuf', '2.42.10'), + ('Ghostscript', '10.01.2'), + ('GTS', '0.7.6'), + ('libgd', '2.3.3'), + ('Pango', '1.50.12'), + ('Perl', '5.36.0'), + ('Qt5', '5.15.7'), + ('Tcl', '8.6.12'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('libjpeg-turbo', '2.1.4'), + ('expat', '2.4.9'), +] + +preconfigopts = './autogen.sh NOCONFIG && ' + +configopts = '--enable-python%s=yes ' % local_pyver_major +configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' +# Use ltdl from libtool in EB +configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' +configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' +# Override the hardcoded paths to Java libraries +configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' +configopts += '--with-javalibdir=$JAVA_HOME/lib' +configopts += '--with-expatincludedir=$EBROOTEXPAT/include --with-expatlibdir=$EBROOTEXPAT/lib' +configopts += '--with-zincludedir=$EBROOTZLIB/include --with-zlibdir=$EBROOTZLIB/lib' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +postinstallcmds = ['%(installdir)s/bin/dot -c'] # Writes plugin configuration + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acyclic', 'bcomps', 'ccomps', 'cluster', 'diffimg', 'dijkstra', 'dot', + 'dot_builtins', 'edgepaint', 'gc', 'gml2gv', 'graphml2gv', 'gv2gml', + 'gvcolor', 'gvedit', 'gvgen', 'gvmap', 'gvmap.sh', 'gvpack', 'gvpr', 'gxl2gv', + 'neato', 'mm2gv', 'nop', 'prune', 'sccmap', 'tred', 'unflatten', + 'vimdot']] + + ['lib/%s.%s' % (x, SHLIB_EXT) for x in ['libcdt', 'libcgraph', 'libgvc', 'libgvpr', 'liblab_gamut', + 'libpathplan', 'libxdot']], + 'dirs': ['include', 'lib/graphviz', 'lib/graphviz/java', 'lib/graphviz/python%s' % local_pyver_major, + 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), + ('python', '-c "import gv"'), +] + +modextrapaths = { + 'CLASSPATH': 'lib/graphviz/java', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'PYTHONPATH': 'lib/graphviz/python%s' % local_pyver_major, + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0_skip-install-data-hook.patch b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0_skip-install-data-hook.patch new file mode 100644 index 00000000000..b9df6864d38 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0_skip-install-data-hook.patch @@ -0,0 +1,88 @@ +don't create directories and install language bindings in non-owned directories +author: Kenneth Hoste (HPC-UGent) +update version 2.42.2: Alex Domingo (VUB) +update version 5.0.0: Simon Pinches +update version 8.1.0: Simon Branford (University of Birmingham) +diff -Nru graphviz-5.0.0-orig/tclpkg/Makefile.am graphviz-5.0.0/tclpkg/Makefile.am +--- graphviz-5.0.0-orig/tclpkg/Makefile.am 2023-08-08 16:31:24.730129000 +0100 ++++ graphviz-5.0.0/tclpkg/Makefile.am 2023-08-08 16:31:14.040830751 +0100 +@@ -32,78 +32,7 @@ + # ./configure --prefix=$HOME/graphviz; make; make install + # without root privileges. + install-data-hook: +-if WITH_LUA +- -mkdir -p $(DESTDIR)$(LUA_INSTALL_DIR); +- if test -w $(DESTDIR)$(LUA_INSTALL_DIR); then \ +- (cd $(DESTDIR)$(LUA_INSTALL_DIR); \ +- cp -f $(DESTDIR)$(pkgluadir)/libgv_lua.so gv.so;) \ +- else \ +- echo "Warning: $(LUA_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of lua binding."; \ +- fi +-endif +-if WITH_PERL +- -mkdir -p $(DESTDIR)$(PERL_INSTALL_DIR); +- if test -w $(DESTDIR)$(PERL_INSTALL_DIR); then \ +- (cd $(DESTDIR)$(PERL_INSTALL_DIR); \ +- cp -f $(DESTDIR)$(pkgperldir)/libgv_perl.so gv.so; \ +- cp -f $(DESTDIR)$(pkgperldir)/gv.pm gv.pm;) \ +- else \ +- echo "Warning: $(PERL_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of perl binding."; \ +- fi +-endif +-if WITH_PHP +- -mkdir -p $(DESTDIR)$(PHP_INSTALL_DIR); +- if test -w $(DESTDIR)$(PHP_INSTALL_DIR); then \ +- (cd $(DESTDIR)$(PHP_INSTALL_DIR); \ +- cp -f $(DESTDIR)$(pkgphpdir)/libgv_php.so gv.so;) \ +- else \ +- echo "Warning: $(PHP_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of php binding."; \ +- fi +-if WITH_SWIG_PHP_DATA +- -mkdir -p $(DESTDIR)$(PHP_INSTALL_DATADIR); +- if test -w $(DESTDIR)$(PHP_INSTALL_DATADIR); then \ +- (cd $(DESTDIR)$(PHP_INSTALL_DATADIR); \ +- cp -f $(DESTDIR)$(pkgphpdir)/gv.php gv.php;) \ +- else \ +- echo "Warning: $(PHP_INSTALL_DATADIR) is not writable."; \ +- echo "Skipping system installation of php binding."; \ +- fi +-endif +-endif +-if WITH_PYTHON3 +- -mkdir -p $(DESTDIR)$(PYTHON3_INSTALL_DIR); +- if test -w $(DESTDIR)$(PYTHON3_INSTALL_DIR); then \ +- (cd $(DESTDIR)$(PYTHON3_INSTALL_DIR); \ +- cp -f $(DESTDIR)$(pkgpython3dir)/libgv_python3.so _gv.so; \ +- cp -f $(DESTDIR)$(pkgpython3dir)/gv.py gv.py;) \ +- else \ +- echo "Warning: $(PYTHON3_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of python3 binding."; \ +- fi +-endif +-if WITH_RUBY +- -mkdir -p $(DESTDIR)$(RUBY_INSTALL_DIR); +- if test -w $(DESTDIR)$(RUBY_INSTALL_DIR); then \ +- (cd $(DESTDIR)$(RUBY_INSTALL_DIR); \ +- cp -f $(DESTDIR)$(pkgrubydir)/libgv_ruby.so gv.so;) \ +- else \ +- echo "Warning: $(RUBY_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of ruby binding."; \ +- fi +-endif +-if WITH_TCL +- -mkdir -p $(DESTDIR)$(TCL_INSTALL_DIR); +- if test -w $(DESTDIR)$(TCL_INSTALL_DIR)/; then \ +- (cd $(DESTDIR)$(TCL_INSTALL_DIR); \ +- cp -rf $(DESTDIR)$(pkgtcldir) $(PACKAGE_NAME);) \ +- else \ +- echo "Warning: $(TCL_INSTALL_DIR) is not writable."; \ +- echo "Skipping system installation of tcl bindings."; \ +- fi +-endif ++ echo "(installing in non-owned directories has been patched out)" + endif + + # removal of installs into $(xxx_INSTALL_DIR) fail if root From 18c574ab80bd912a897b83393d1b16f9f625e40e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 8 Aug 2023 16:49:05 +0100 Subject: [PATCH 8297/9987] add missing SWIG and remove debug commented out lines --- .../Ghostscript-10.01.2-GCCcore-12.2.0.eb | 1 - .../Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb | 1 - .../s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb | 24 +++++++++++++++++++ 3 files changed, 24 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb index 5a5a5802de1..536267e8ad1 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb @@ -30,7 +30,6 @@ dependencies = [ ('GLib', '2.75.0'), ('cairo', '1.17.4'), ('LibTIFF', '4.4.0'), - # ('GTK2', '2.24.33'), ('GTK3', '3.24.35'), ] diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb index d206b94f524..3cccd2c3485 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb @@ -12,7 +12,6 @@ description = """Graphviz is open source graph visualization software. Graph vis and in visual interfaces for other technical domains.""" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -# toolchainopts = {'cstd': 'c++11'} source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] sources = [SOURCELOWER_TAR_GZ] diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..c55c6368e22 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +name = 'SWIG' +version = '4.1.1' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2af08aced8fcd65cdb5cc62426768914bedc735b1c250325203716f78e39ac9b'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('zlib', '1.2.12'), + ('PCRE', '8.45'), +] + +configopts = '--without-alllang --with-boost=no' + +moduleclass = 'devel' From ad5056e5c95e187ef11892e430bee36a4e8e2075 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 8 Aug 2023 17:08:58 +0100 Subject: [PATCH 8298/9987] use exising Ghostscript --- .../Ghostscript-10.01.2-GCCcore-12.2.0.eb | 56 ------------------- .../Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb | 2 +- 2 files changed, 1 insertion(+), 57 deletions(-) delete mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb deleted file mode 100644 index 536267e8ad1..00000000000 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.2.0.eb +++ /dev/null @@ -1,56 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Ghostscript' -version = '10.01.2' - -homepage = 'https://ghostscript.com' -description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to - different targets. It used to be part of the cups printing stack, but is no longer used for that.""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -toolchainopts = {'pic': True} - -source_urls = [ - 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), -] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['a4cd61a07fec161bee35da0211a5e5cde8ff8a0aaf942fc0176715e499d21661'] - -builddependencies = [ - ('binutils', '2.39'), - ('pkgconf', '1.9.3'), -] - -dependencies = [ - ('zlib', '1.2.12'), - ('libpng', '1.6.38'), - ('freetype', '2.12.1'), - ('libjpeg-turbo', '2.1.4'), - ('expat', '2.4.9'), - ('GLib', '2.75.0'), - ('cairo', '1.17.4'), - ('LibTIFF', '4.4.0'), - ('GTK3', '3.24.35'), -] - -# Do not use local copies of zlib, jpeg, freetype, and png -preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " -preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' - -configopts = "--with-system-libtiff --enable-dynamic --disable-hidden-visibility" - -postinstallcmds = [ - # build and install shared libs - "make -j %(parallel)s so && make -j %(parallel)s soinstall", - # install header files - "mkdir -p %(installdir)s/include/ghostscript", - "install -v -m644 base/*.h %(installdir)s/include/ghostscript", - "install -v -m644 psi/*.h %(installdir)s/include/ghostscript", -] - -sanity_check_paths = { - 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], - 'dirs': ['lib/ghostscript', 'include/ghostscript', 'share/man'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb index 3cccd2c3485..f11b2c6c9b4 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb @@ -35,7 +35,7 @@ dependencies = [ ('Python', '3.10.8'), ('FriBidi', '1.0.12'), ('Gdk-Pixbuf', '2.42.10'), - ('Ghostscript', '10.01.2'), + ('Ghostscript', '10.00.0'), ('GTS', '0.7.6'), ('libgd', '2.3.3'), ('Pango', '1.50.12'), From f0d6febd2da21c39e5b37f1a421ecdb6e10244c2 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Tue, 8 Aug 2023 17:11:41 +0100 Subject: [PATCH 8299/9987] correct version --- .../easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb index f11b2c6c9b4..aa04b6e837c 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb @@ -35,7 +35,7 @@ dependencies = [ ('Python', '3.10.8'), ('FriBidi', '1.0.12'), ('Gdk-Pixbuf', '2.42.10'), - ('Ghostscript', '10.00.0'), + ('Ghostscript', '10.0.0'), ('GTS', '0.7.6'), ('libgd', '2.3.3'), ('Pango', '1.50.12'), From 2d36146fdd2b4599ade66c4b7e41e57941573a1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Aug 2023 21:31:29 +0200 Subject: [PATCH 8300/9987] adding easyconfigs: Boost.Python-NumPy-1.79.0-foss-2022a.eb --- .../Boost.Python-NumPy-1.79.0-foss-2022a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.Python-NumPy/Boost.Python-NumPy-1.79.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/Boost.Python-NumPy/Boost.Python-NumPy-1.79.0-foss-2022a.eb b/easybuild/easyconfigs/b/Boost.Python-NumPy/Boost.Python-NumPy-1.79.0-foss-2022a.eb new file mode 100644 index 00000000000..f9fa7521f37 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python-NumPy/Boost.Python-NumPy-1.79.0-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python-NumPy' +version = '1.79.0' + +homepage = 'https://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c'] + +dependencies = [ + ('Boost', version), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +only_python_bindings = True + +moduleclass = 'lib' From 4bdbb01a378e6293ea17694d1608b0a159a9a5b8 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 8 Aug 2023 14:52:30 -0700 Subject: [PATCH 8301/9987] adding easyconfigs: pyBigWig-0.3.22-foss-2022b.eb --- .../p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb new file mode 100644 index 00000000000..2de7f842c5b --- /dev/null +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'pyBigWig' +version = '0.3.22' + +github_account = 'deeptools' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """A python extension, written in C, for quick access to bigBed + files and access to and creation of bigWig files.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['3b8d62b2bedcee0545a586884466c97a64b64283a309b211300b670f41dd2046'] + +builddependencies = [ + ('setuptools', '64.0.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('cURL', '7.86.0'), + ('NSS', '3.85'), # provides libfreebl3 + ('SciPy-bundle', '2023.02'), # optional, for numpy support +] + +preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ +# do not use setuptools-scm to dectet version +preinstallopts += """sed -i 's/[tool.setuptools_scm]//' pyproject.toml && """ + +use_pip = True +download_dep_fail = True + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' From 3dfc360c946e59fbee8e40665a2e366a7d8cbacc Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 8 Aug 2023 15:56:15 -0700 Subject: [PATCH 8302/9987] update MACS2-2.2.9.1-foss-2022b --- .../m/MACS2/MACS2-2.2.9.1-foss-2022b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MACS2/MACS2-2.2.9.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.2.9.1-foss-2022b.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.9.1-foss-2022b.eb new file mode 100644 index 00000000000..56aa3d1ee7b --- /dev/null +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.9.1-foss-2022b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonPackage' + +name = 'MACS2' +version = '2.2.9.1' + +homepage = 'https://github.com/taoliu/MACS' +description = "Model Based Analysis for ChIP-Seq data" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8d56bc37fb823fc6387d78138ce968405c54a0a8cd9776682705fd0983252d16'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/macs2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('%(namelower)s --version')] + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' From 0394a8bd0cdea88764cd7895d883bbef82b3be54 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 8 Aug 2023 17:41:04 -0700 Subject: [PATCH 8303/9987] remove setuptools --- .../p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb new file mode 100644 index 00000000000..421f65ee50d --- /dev/null +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'pyBigWig' +version = '0.3.22' + +github_account = 'deeptools' +homepage = 'https://github.com/%(github_account)s/%(name)s' +description = """A python extension, written in C, for quick access to bigBed + files and access to and creation of bigWig files.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['3b8d62b2bedcee0545a586884466c97a64b64283a309b211300b670f41dd2046'] + +dependencies = [ + ('Python', '3.10.8'), + ('cURL', '7.86.0'), + ('NSS', '3.85'), # provides libfreebl3 + ('SciPy-bundle', '2023.02'), # optional, for numpy support +] + +# fix version of '0.0.0' issue +preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ +# do not use setuptools-scm to dectet version +preinstallopts += """sed -i 's/[tool.setuptools_scm]//' pyproject.toml && """ + +use_pip = True +download_dep_fail = True + +options = {'modulename': name} + +sanity_pip_check = True + +moduleclass = 'bio' From d0be9099b9c4a5d2104d0217d18132e17c6f96c7 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 8 Aug 2023 17:44:26 -0700 Subject: [PATCH 8304/9987] remove setuptools --- .../easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb index 2de7f842c5b..421f65ee50d 100644 --- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb @@ -14,10 +14,6 @@ source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] checksums = ['3b8d62b2bedcee0545a586884466c97a64b64283a309b211300b670f41dd2046'] -builddependencies = [ - ('setuptools', '64.0.3'), -] - dependencies = [ ('Python', '3.10.8'), ('cURL', '7.86.0'), @@ -25,6 +21,7 @@ dependencies = [ ('SciPy-bundle', '2023.02'), # optional, for numpy support ] +# fix version of '0.0.0' issue preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ # do not use setuptools-scm to dectet version preinstallopts += """sed -i 's/[tool.setuptools_scm]//' pyproject.toml && """ From 20b8181fdb34951c06b1cad1d5f8bf18be5b2135 Mon Sep 17 00:00:00 2001 From: John Dey Date: Tue, 8 Aug 2023 17:44:44 -0700 Subject: [PATCH 8305/9987] Delete pyBigWig-0.3.22-foss-2022b.eb oops --- .../p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb deleted file mode 100644 index 421f65ee50d..00000000000 --- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pyBigWig' -version = '0.3.22' - -github_account = 'deeptools' -homepage = 'https://github.com/%(github_account)s/%(name)s' -description = """A python extension, written in C, for quick access to bigBed - files and access to and creation of bigWig files.""" - -toolchain = {'name': 'foss', 'version': '2022b'} - -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['3b8d62b2bedcee0545a586884466c97a64b64283a309b211300b670f41dd2046'] - -dependencies = [ - ('Python', '3.10.8'), - ('cURL', '7.86.0'), - ('NSS', '3.85'), # provides libfreebl3 - ('SciPy-bundle', '2023.02'), # optional, for numpy support -] - -# fix version of '0.0.0' issue -preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ -# do not use setuptools-scm to dectet version -preinstallopts += """sed -i 's/[tool.setuptools_scm]//' pyproject.toml && """ - -use_pip = True -download_dep_fail = True - -options = {'modulename': name} - -sanity_pip_check = True - -moduleclass = 'bio' From 093886ea0ae86b3991adcf25f731a339d9b66ec9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Aug 2023 07:41:49 +0200 Subject: [PATCH 8306/9987] adding easyconfigs: Clang-16.0.6-GCCcore-12.3.0.eb, Z3-4.12.2-GCCcore-12.3.0.eb --- .../c/Clang/Clang-16.0.6-GCCcore-12.3.0.eb | 57 +++++++++++++++++++ .../z/Z3/Z3-4.12.2-GCCcore-12.3.0.eb | 35 ++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-16.0.6-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-16.0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-16.0.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..cc3f39fb4e3 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-16.0.6-GCCcore-12.3.0.eb @@ -0,0 +1,57 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '16.0.6' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-project-%(version)s.src.tar.xz', +] +checksums = ['ce5e71081d17ce9e86d7cbcfa28c4b04b9300f8fb7e78422b1feb6bc52c3028e'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Perl', '5.36.1'), + # Including Python bindings would require this as a runtime dep + ('Python', '3.11.3'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.40'), + ('hwloc', '2.9.1'), + ('libxml2', '2.11.4'), + ('ncurses', '6.4'), + ('GMP', '6.2.1'), + ('Z3', '4.12.2'), +] + +# enabling RTTI makes the flang compiler need to link to libc++ so instead of +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 +# you would need +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++ +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2d9ade32924 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'Z3' +version = '4.12.2' + +homepage = 'https://github.com/Z3Prover/z3' +description = """ + Z3 is a theorem prover from Microsoft Research. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Z3Prover/z3/archive/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + {'z3-4.12.2.tar.gz': '9f58f3710bd2094085951a75791550f547903d75fe7e2fcb373c5f03fc761b8f'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = '-DZ3_USE_LIB_GMP=ON -DZ3_LINK_TIME_OPTIMIZATION=ON ' + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From 0b1aa9625646ec6a21b266524568d2c918fda296 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 9 Aug 2023 09:18:34 +0200 Subject: [PATCH 8307/9987] Use checksummed release archive --- .../PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 11 ++--------- 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index ea51b1e8d0a..59244119da2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -8,15 +8,8 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2022a'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', From 53fd56543c467da38a2d1c7ba9aa44d2297a7117 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 9 Aug 2023 08:50:48 +0000 Subject: [PATCH 8308/9987] Add tabletools to recent R --- easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb | 5 +++++ easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb | 5 +++++ easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 5 +++++ easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 5 +++++ easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 15 ++++++--------- 5 files changed, 26 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb index f42b0ee31a5..39597e9f6f9 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.0-foss-2021a.eb @@ -3061,6 +3061,11 @@ exts_list = [ ('collapse', '1.6.5', { 'checksums': ['1e232a3a62b5eb5ed5d81e7d92ce1bae34c3d877d593d47d7edbd3f515b95a46'], }), + ('tabletools', '0.1.0', { + 'source_urls': ['https://github.com/JMLuther/%(name)s/archive/'], + 'sources': [{'download_filename': 'cc961c5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['667a4270456d28188734ce31411326130a94e085490ced84096c984789bb174a'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb index e439e147d49..954de88b9cb 100644 --- a/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.1.2-foss-2021b.eb @@ -3327,6 +3327,11 @@ exts_list = [ ('renv', '0.15.5', { 'checksums': ['b4f1a9a7daa82f0c3123ebd4eeba06e98d5485215518e5292b25bc56741d582e'], }), + ('tabletools', '0.1.0', { + 'source_urls': ['https://github.com/JMLuther/%(name)s/archive/'], + 'sources': [{'download_filename': 'cc961c5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['667a4270456d28188734ce31411326130a94e085490ced84096c984789bb174a'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 7f0e053f59b..e1cfa939335 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -3369,6 +3369,11 @@ exts_list = [ ('ppcor', '1.1', { 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], }), + ('tabletools', '0.1.0', { + 'source_urls': ['https://github.com/JMLuther/%(name)s/archive/'], + 'sources': [{'download_filename': 'cc961c5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['667a4270456d28188734ce31411326130a94e085490ced84096c984789bb174a'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 9d7060cf52e..626232ab783 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -3548,6 +3548,11 @@ exts_list = [ ('CVXR', '1.0-11', { 'checksums': ['e92a9638f35f4909e2a29c3b7106081e3dae7ff88b14bb6466b87fbdc80b972a'], }), + ('tabletools', '0.1.0', { + 'source_urls': ['https://github.com/JMLuther/%(name)s/archive/'], + 'sources': [{'download_filename': 'cc961c5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['667a4270456d28188734ce31411326130a94e085490ced84096c984789bb174a'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index a497c759bcb..ab9aacdb9a4 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -78,9 +78,6 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 17th March 2023 exts_list = [ - # include packages that are part of the base installation of R, - # both to make sure they are available (via sanity check), - # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets', @@ -2374,7 +2371,6 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, @@ -2889,12 +2885,8 @@ exts_list = [ 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], }), ('gWidgets2tcltk', '1.0-8', { - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" - 'preinstallopts': "xvfb-run ", - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... 'modulename': False, + 'preinstallopts': "xvfb-run ", 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], }), ('mgsub', '1.7.3', { @@ -3640,6 +3632,11 @@ exts_list = [ ('CVXR', '1.0-11', { 'checksums': ['e92a9638f35f4909e2a29c3b7106081e3dae7ff88b14bb6466b87fbdc80b972a'], }), + ('tabletools', '0.1.0', { + 'source_urls': ['https://github.com/JMLuther/%(name)s/archive/'], + 'sources': [{'download_filename': 'cc961c5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['667a4270456d28188734ce31411326130a94e085490ced84096c984789bb174a'], + }), ] moduleclass = 'lang' From 95d6f469fc6884c9285358b02f82e985fdb8e672 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 9 Aug 2023 11:44:18 +0000 Subject: [PATCH 8309/9987] adding easyconfigs: tornado-6.3.2-GCCcore-12.3.0.eb and patches: tornado-timeouts.patch --- .../t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb | 29 +++++++++++++++++++ .../t/tornado/tornado-timeouts.patch | 15 ++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/tornado/tornado-timeouts.patch diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f63d8f312a9 --- /dev/null +++ b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = "tornado" +version = "6.3.2" + +homepage = "https://github.com/tornadoweb/tornado" +description = "Tornado is a Python web framework and asynchronous networking library." + +toolchain = {"name": "GCCcore", "version": "12.3.0"} + +sources = [SOURCE_TAR_GZ] +patches = ['tornado-timeouts.patch'] +checksums = [ + {'tornado-6.3.2.tar.gz': '4b927c4f19b71e627b13f3db2324e4ae660527143f9e1f2e2fb404f3a187e2ba'}, + {'tornado-timeouts.patch': 'fe0db60604ccdcb5fc111023d1d7bffa0e315465fbe15f2ff512068c649e56f8'}, +] + +builddependencies = [ + ("binutils", "2.40"), +] +dependencies = [ + ("Python", "3.11.3"), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = "lib" diff --git a/easybuild/easyconfigs/t/tornado/tornado-timeouts.patch b/easybuild/easyconfigs/t/tornado/tornado-timeouts.patch new file mode 100644 index 00000000000..02720680265 --- /dev/null +++ b/easybuild/easyconfigs/t/tornado/tornado-timeouts.patch @@ -0,0 +1,15 @@ +diff -Naur tornado.orig/tornado-6.1/tornado/httpclient.py tornado/tornado-6.1/tornado/httpclient.py +--- tornado.orig/tornado-6.1/tornado/httpclient.py 2020-10-30 21:17:45.000000000 +0100 ++++ tornado/tornado-6.1/tornado/httpclient.py 2022-05-01 22:01:50.923741948 +0200 +@@ -345,8 +345,8 @@ + # Merged with the values on the request object by AsyncHTTPClient + # implementations. + _DEFAULTS = dict( +- connect_timeout=20.0, +- request_timeout=20.0, ++ connect_timeout=60.0, ++ request_timeout=1200.0, + follow_redirects=True, + max_redirects=5, + decompress_response=True, + From 28b2e48d7aab7f6c06b0bbd25db761802ca61e06 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 9 Aug 2023 12:02:22 +0000 Subject: [PATCH 8310/9987] adding easyconfigs: Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb, libwebp-1.3.1-GCCcore-12.3.0.eb, giflib-5.2.1-GCCcore-12.3.0.eb --- .../g/giflib/giflib-5.2.1-GCCcore-12.3.0.eb | 28 ++++++++++++ .../l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb | 44 +++++++++++++++++++ .../Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb | 40 +++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a37009e56b8 --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.1' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4ac82164e4b --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.3.1' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b3779627c2dfd31e3d8c4485962c2efe17785ef975e2be5c8c0c9e6cd3c4ef66'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + +sanity_check_paths = { + 'files': ( + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ), + 'dirs': ['lib/'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ed0cd77c949 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '9.5.0' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1a9819343b451b7faf34663156e2abca3ae69ab604f82e445478c8133422e4f0'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('LibTIFF', '4.5.0'), + ('freetype', '2.13.0'), + ('libwebp', '1.3.1'), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From ff4b7a59869804d5d60b3336edf726bd5df20fa0 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 9 Aug 2023 12:20:08 +0000 Subject: [PATCH 8311/9987] adding easyconfigs: ccache-4.7.5.eb, hiredis-1.2.0-GCCcore-12.3.0.eb --- .../easyconfigs/c/ccache/ccache-4.7.5.eb | 54 +++++++++++++++++++ .../h/hiredis/hiredis-1.2.0-GCCcore-12.3.0.eb | 41 ++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.7.5.eb create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.7.5.eb b/easybuild/easyconfigs/c/ccache/ccache-4.7.5.eb new file mode 100644 index 00000000000..8524fcc6905 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.7.5.eb @@ -0,0 +1,54 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.7.5' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['fe304140b0c2e391e6c00fc123e7d202fa0313c569689ca67574686769ac0781'] + +osdependencies = [('glibc-static', 'libc6-dev')] + +local_gccver = '12.3.0' +builddependencies = [ + ('GCC', local_gccver), + ('CMake', '3.26.3', '', ('GCCcore', local_gccver)), + ('Ninja', '1.11.1', '', ('GCCcore', local_gccver)), + ('hiredis', '1.2.0', '', ('GCCcore', local_gccver)), + ('zstd', '1.5.5', '', ('GCCcore', local_gccver)), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + # Link dependencies and binary statically + '-DCMAKE_EXE_LINKER_FLAGS="-static"', + '-DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a"', + '-DHIREDIS_LIBRARY="$EBROOTHIREDIS/lib/libhiredis.a"', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = [ + 'ccache --help', + # Ensure that the binary does not depend on any shared library + 'ldd $(which ccache) | grep -q "not a dynamic executable"', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d02c31b8c22 --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +# Author: Alexander Grund (TU Dresden) +# Based on EC by J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'hiredis' +version = '1.2.0' + +homepage = 'https://github.com/redis/hiredis' +description = """Hiredis is a minimalistic C client library for the Redis database. + +It is minimalistic because it just adds minimal support for the protocol, +but at the same time it uses a high level printf-alike API in order to +make it much higher level than otherwise suggested by its minimal code base +and the lack of explicit bindings for every Redis command.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'redis' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['82ad632d31ee05da13b537c124f819eb88e18851d9cb0c30ae0552084811588c'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = ['', '-DBUILD_SHARED_LIBS=false'] # It builds the shared library by default + +sanity_check_paths = { + 'files': ['lib/libhiredis.a', 'lib/libhiredis.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 0be47a99f14178815edcd00599015e8cca01f204 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 9 Aug 2023 12:41:16 +0000 Subject: [PATCH 8312/9987] adding easyconfigs: dill-0.3.7-GCCcore-12.3.0.eb --- .../d/dill/dill-0.3.7-GCCcore-12.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/d/dill/dill-0.3.7-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1576a8a0291 --- /dev/null +++ b/easybuild/easyconfigs/d/dill/dill-0.3.7-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'dill' +version = '0.3.7' + +homepage = 'https://pypi.org/project/dill/' +description = """dill extends python's pickle module for serializing and de-serializing python objects to the majority + of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse + of which is converting a byte stream back to on python object hierarchy.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['cc1c8b182eb3013e24bd475ff2e9295af86c1a38eb1aff128dac8962a9ce3c03'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From 9042beca4decdeb128c1ff02ac17be48f8bea572 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 9 Aug 2023 13:30:40 +0000 Subject: [PATCH 8313/9987] adding easyconfigs: exiv2-0.28.0-GCCcore-12.3.0.eb, inih-57-GCCcore-12.3.0.eb --- .../e/exiv2/exiv2-0.28.0-GCCcore-12.3.0.eb | 36 +++++++++++++++++++ .../i/inih/inih-57-GCCcore-12.3.0.eb | 30 ++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/e/exiv2/exiv2-0.28.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/i/inih/inih-57-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/e/exiv2/exiv2-0.28.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/exiv2/exiv2-0.28.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..61e00e9b431 --- /dev/null +++ b/easybuild/easyconfigs/e/exiv2/exiv2-0.28.0-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'exiv2' +version = '0.28.0' + +homepage = 'http://www.exiv2.org' +description = """ + Exiv2 is a C++ library and a command line utility to manage image metadata. It provides fast and easy read and write + access to the Exif, IPTC and XMP metadata of digital images in various formats. Exiv2 is available as free software and + with a commercial license, and is used in many projects. +""" + + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Exiv2/exiv2/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-Source.tar.gz'] +checksums = ['89af3b5ef7277753ef7a7b5374ae017c6b9e304db3b688f1948e73e103491f3d'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('expat', '2.5.0'), + ('Brotli', '1.0.9'), + ('inih', '57'), +] + +sanity_check_paths = { + 'files': ['bin/exiv2', 'lib/libexiv2.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/inih/inih-57-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/inih/inih-57-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..901c52d2b33 --- /dev/null +++ b/easybuild/easyconfigs/i/inih/inih-57-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'inih' +version = '57' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/benhoyt/inih/archive/refs/tags/'] +sources = ['r%(version)s.tar.gz'] +checksums = ['f03f98ca35c3adb56b2358573c8d3eda319ccd5287243d691e724b7eafa970b3'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), +] + +# installing manpages requires an extra build dependency (docbook xsl) +# configopts = '-Dman-pages=disabled' + +sanity_check_paths = { + 'files': ['lib/libinih.%s' % SHLIB_EXT, 'include/ini.h'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'lib' From 65d4c9a9d6008dca622808ff645dd11c666dddb8 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 9 Aug 2023 13:50:36 +0000 Subject: [PATCH 8314/9987] adding easyconfigs: expecttest-0.1.5-GCCcore-12.3.0.eb --- .../expecttest-0.1.5-GCCcore-12.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.1.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f7a501bcaa2 --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.5-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.1.5' + +homepage = 'https://github.com/ezyang/expecttest' +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['5b3a6a165250860f5a14199f9c59461752beb3b45d48b93347d9afc7293a611c'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('poetry', '1.5.1'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From a95245bfe86f5a3bd95e13cfa388d7eff5014204 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 9 Aug 2023 16:17:02 +0200 Subject: [PATCH 8315/9987] Add upstream issue to patch description --- easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb | 2 +- .../e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb index dc8e17ac3a3..6561f1917bb 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-foss-2023a.eb @@ -27,7 +27,7 @@ checksums = [ {'%(name)s-%(version)s_fix_hardcoded_perl_path.patch': '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, {'%(name)s-%(version)s_fix_AVX512_support.patch': - '7e4bb0b74f8c1229c78b063789ddf32128e19e957466bd651cee6980f804cfaf'}, + 'ecf08b64fe1da432a218040fa45d4ecfbb3269d58cb018b12da5a2d854bf96be'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch index 1da0b07e240..3a1365ced15 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001_fix_AVX512_support.patch @@ -9,6 +9,8 @@ # code path guarded by the `#ifdef HAVE_AVX512_XEON_PHI` directive, which calls for an undefined macro `_XOR_EPI`. # I'm sure that the same error will also appear on Xeon-Phi, so this patch actually fixes a fundamental issue # in the code. +# Upstream issue: +# https://github.com/marekandreas/elpa/issues/39 # Author: maxim-masterov (SURF) diff -Nru elpa-new_release_2023.05.001.orig/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c elpa-new_release_2023.05.001/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c --- elpa-new_release_2023.05.001.orig/src/elpa2/kernels/complex_128bit_256bit_512bit_BLOCK_template.c 2023-08-01 16:22:09.499243000 +0200 From a1592fac36ebdbad94753b5b967294d2c87cc52d Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 9 Aug 2023 16:45:53 +0100 Subject: [PATCH 8316/9987] add comment on preinstallopts for bokeh --- easybuild/easyconfigs/b/bokeh/bokeh-3.2.1-foss-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-3.2.1-foss-2022b.eb b/easybuild/easyconfigs/b/bokeh/bokeh-3.2.1-foss-2022b.eb index 9429ebf059c..0139ef9c8f8 100755 --- a/easybuild/easyconfigs/b/bokeh/bokeh-3.2.1-foss-2022b.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-3.2.1-foss-2022b.eb @@ -34,6 +34,7 @@ exts_list = [ 'checksums': ['0ec928742227d6f5d4367ea7b457fcfed943429f4de2949b5b02a82cdf5569d6'], }), (name, version, { + # bokeh uses git tags to get version, so we'll instead inject the version into setup.py 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """, 'checksums': ['2371e9a08fd60766879ee8607a4ae54267acfed1e5dee0cc6a20d8348e02e814'], }), From b4e59edcf16144acf7e17aae763bae2f5d354e50 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 9 Aug 2023 15:59:02 +0000 Subject: [PATCH 8317/9987] adding easyconfigs: dcm2niix-1.0.20230411-GCCcore-12.2.0.eb, CharLS-2.4.2-GCCcore-12.2.0.eb --- .../c/CharLS/CharLS-2.4.2-GCCcore-12.2.0.eb | 30 +++++++++++++++ .../dcm2niix-1.0.20230411-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20230411-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..497ee7a3e8b --- /dev/null +++ b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.2-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CharLS' +version = '2.4.2' + +homepage = 'https://github.com/team-charls/charls' +description = """CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image +compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 +compression ratios.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/team-charls/charls/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d1c2c35664976f1e43fec7764d72755e6a50a80f38eca70fcc7553cad4fe19d9'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3') +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libcharls.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20230411-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20230411-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9d52b9a5e66 --- /dev/null +++ b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20230411-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'dcm2niix' +version = '1.0.20230411' + +homepage = 'https://github.com/rordenlab/dcm2niix' +description = """dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rordenlab/dcm2niix/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['990368e627a7d972a607ef965161e4ab0ddc5b0be35d659c1ce387c8ddae8301'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('pigz', '2.7'), + ('OpenJPEG', '2.5.0'), + ('CharLS', '2.4.2'), +] + +configopts = '-DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DOpenJPEG_DIR=$EBROOTOPENJPEG ' + +sanity_check_paths = { + 'files': ['bin/dcm2niix'], + 'dirs': [''], +} + +sanity_check_commands = ['dcm2niix -h'] + +moduleclass = 'bio' From fcdd3328a3638e366e4efc08fc081db708950eb6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Aug 2023 19:06:49 +0200 Subject: [PATCH 8318/9987] adding easyconfigs: pv-1.7.24-GCCcore-12.3.0.eb --- .../p/pv/pv-1.7.24-GCCcore-12.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/pv/pv-1.7.24-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pv/pv-1.7.24-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pv/pv-1.7.24-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..beb37508fe0 --- /dev/null +++ b/easybuild/easyconfigs/p/pv/pv-1.7.24-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'pv' +version = '1.7.24' + +homepage = 'https://www.ivarch.com/programs/pv.shtml' +description = "Pipe Viewer - monitor the progress of data through a pipe" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/a-j-wood/pv/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3bf43c5809c8d50066eaeaea5a115f6503c57a38c151975b710aa2bee857b65e'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/pv'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["pv --help"] + +moduleclass = 'tools' From 8c7dafcb443991f20ef3eaf322a5f756214f2ce2 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 9 Aug 2023 23:04:38 +0200 Subject: [PATCH 8319/9987] adding easyconfigs: HDF5-1.14.0-gompi-2023a.eb, HDF5-1.14.0-iimpi-2023a.eb, netCDF-4.9.2-gompi-2023a.eb, netCDF-4.9.2-iimpi-2023a.eb --- .../h/HDF5/HDF5-1.14.0-gompi-2023a.eb | 26 +++++++++ .../h/HDF5/HDF5-1.14.0-iimpi-2023a.eb | 26 +++++++++ .../n/netCDF/netCDF-4.9.2-gompi-2023a.eb | 57 +++++++++++++++++++ .../n/netCDF/netCDF-4.9.2-iimpi-2023a.eb | 57 +++++++++++++++++++ 4 files changed, 166 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2023a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023a.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2023a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2023a.eb new file mode 100644 index 00000000000..b66881857ec --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-gompi-2023a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.0' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4'] + +# replace src include path with installation dir for $H5BLD_CPPFLAGS +_regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' +postinstallcmds = ['sed -i -r "%s" %%(installdir)s/bin/%s' % (_regex, x) for x in ['h5c++', 'h5pcc']] + +dependencies = [ + ('zlib', '1.2.13'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2023a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2023a.eb new file mode 100644 index 00000000000..0a18df1abcc --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-iimpi-2023a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.0' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4'] + +# replace src include path with installation dir for $H5BLD_CPPFLAGS +_regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' +postinstallcmds = ['sed -i -r "%s" %%(installdir)s/bin/%s' % (_regex, x) for x in ['h5c++', 'h5pcc']] + +dependencies = [ + ('zlib', '1.2.13'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023a.eb new file mode 100644 index 00000000000..963e509508d --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023a.eb @@ -0,0 +1,57 @@ +name = 'netCDF' +version = '4.9.2' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-4.9.0_skip-nasa-test.patch', +] +checksums = [ + {'v4.9.2.tar.gz': 'bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7'}, + {'netCDF-4.9.0_skip-nasa-test.patch': '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('HDF5', '1.14.0'), + ('cURL', '8.0.1'), + ('Szip', '2.1.1'), + ('zstd', '1.5.5'), + ('bzip2', '1.0.8'), + ('libxml2', '2.11.4'), +] + +# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso +# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" + " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") + +# make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023a.eb new file mode 100644 index 00000000000..02ceb912ae5 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023a.eb @@ -0,0 +1,57 @@ +name = 'netCDF' +version = '4.9.2' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-4.9.0_skip-nasa-test.patch', +] +checksums = [ + {'v4.9.2.tar.gz': 'bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7'}, + {'netCDF-4.9.0_skip-nasa-test.patch': '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('HDF5', '1.14.0'), + ('cURL', '8.0.1'), + ('Szip', '2.1.1'), + ('zstd', '1.5.5'), + ('bzip2', '1.0.8'), + ('libxml2', '2.11.4'), +] + +# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso +# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" + " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") + +# make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' From b63935260c25ab6d96a3bc8492740bd124f4a1f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 10 Aug 2023 09:32:26 +0200 Subject: [PATCH 8320/9987] adding easyconfigs: Clp-1.17.8-foss-2022b.eb, MUMPS-5.6.1-foss-2022b-metis.eb, Osi-0.108.8-GCC-12.2.0.eb, CoinUtils-2.11.9-GCC-12.2.0.eb and patches: MUMPS-5.6.1_shared-pord.patch, MUMPS-5.6.1_shared-mumps.patch --- .../c/Clp/Clp-1.17.8-foss-2022b.eb | 61 ++++++++++++++++++ .../CoinUtils/CoinUtils-2.11.9-GCC-12.2.0.eb | 36 +++++++++++ .../m/MUMPS/MUMPS-5.6.1-foss-2022b-metis.eb | 35 +++++++++++ .../m/MUMPS/MUMPS-5.6.1_shared-mumps.patch | 63 +++++++++++++++++++ .../m/MUMPS/MUMPS-5.6.1_shared-pord.patch | 45 +++++++++++++ .../o/Osi/Osi-0.108.8-GCC-12.2.0.eb | 48 ++++++++++++++ 6 files changed, 288 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clp/Clp-1.17.8-foss-2022b.eb create mode 100644 easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.9-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2022b-metis.eb create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1_shared-mumps.patch create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1_shared-pord.patch create mode 100644 easybuild/easyconfigs/o/Osi/Osi-0.108.8-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.8-foss-2022b.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.8-foss-2022b.eb new file mode 100644 index 00000000000..788e70df694 --- /dev/null +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.8-foss-2022b.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'Clp' +version = '1.17.8' + +homepage = "https://github.com/coin-or/Clp" +description = """Clp (Coin-or linear programming) is an open-source linear programming solver. +It is primarily meant to be used as a callable library, but a basic, +stand-alone executable version is also available.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/Clp/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f9931b5ba44f0daf445c6b48fc2c250dc12e667e59ace8ea7b025f158fe31556'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.5'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.6.1', '-metis'), + ('CoinUtils', '2.11.9'), + ('Osi', '0.108.8'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +# Use BLAS/LAPACK from OpenBLAS +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' + +# Use METIS AND MUMPS from EB +# --with-metis-lib is ignored +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh ' +configopts += '-lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr -lscalapack" ' + +# Disable GLPK because Clp requires headers from its sources +configopts += '--without-glpk ' + +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + +# Use Osi from EB +configopts += '--with-osi-lib="-lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Clp', 'ClpSolver', 'OsiClp']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.9-GCC-12.2.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.9-GCC-12.2.0.eb new file mode 100644 index 00000000000..b21da99803c --- /dev/null +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.9-GCC-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CoinUtils' +version = '2.11.9' + +homepage = "https://github.com/coin-or/CoinUtils" +description = """CoinUtils (Coin-OR Utilities) is an open-source collection of classes and +functions that are generally useful to more than one COIN-OR project.""" + +source_urls = ['https://github.com/coin-or/CoinUtils/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['15d572ace4cd3b7c8ce117081b65a2bd5b5a4ebaba54fadc99c7a244160f88b8'] + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.5'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['lib/libCoinUtils.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2022b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2022b-metis.eb new file mode 100644 index 00000000000..6f27fb3e23b --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2022b-metis.eb @@ -0,0 +1,35 @@ +name = 'MUMPS' +version = '5.6.1' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + '1920426d543e34d377604070fde93b8d102aa38ebdf53300cbce9e15f92e2896', # MUMPS_5.6.1.tar.gz + '51d3685208a42581b462592eea977f185d87e871fb65e8e90a54dd2ad18ac715', # MUMPS-5.6.1_shared-pord.patch + '27f788a5f85e8c9a6a7ec1651097b87c1de0ede0be943df7a10fa7c1ff5f494f', # MUMPS-5.6.1_shared-mumps.patch +] + +dependencies = [ + ('SCOTCH', '7.0.3'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1_shared-mumps.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1_shared-mumps.patch new file mode 100644 index 00000000000..6706f332e87 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1_shared-mumps.patch @@ -0,0 +1,63 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared.patch +Author: micketeer@gmail.com +Updatd to version 5.5.0: J. Sassmannshausen/ICL (UK) +Updatd to version 5.5.1: maxim-masterov (SURF) +Updatd to version 5.6.1: Petr Král (INUITS) +diff -u MUMPS_5.6.1/src/Makefile.orig MUMPS_5.6.1/src/Makefile +--- MUMPS_5.6.1/src/Makefile.orig 2023-07-11 09:51:28.000000000 +0200 ++++ MUMPS_5.6.1/src/Makefile 2023-07-26 11:04:16.108637698 +0200 +@@ -15,18 +15,23 @@ + + libcommon: $(incdir)/mumps_int_def.h + $(MAKE) $(libdir)/libmumps_common$(PLAT)$(LIBEXT) ++ $(MAKE) $(libdir)/libmumps_common$(PLAT).so + + s: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=s $(libdir)/libsmumps$(PLAT).so + + d: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=d $(libdir)/libdmumps$(PLAT).so + + c: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=c $(libdir)/libcmumps$(PLAT).so + + z: $(incdir)/mumps_int_def.h libcommon + $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT)$(LIBEXT) ++ $(MAKE) ARITH=z $(libdir)/libzmumps$(PLAT).so + + + # Rules for shared libraries +@@ -223,6 +228,14 @@ + $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT_SHARED): $(OBJS_MOD) $(OBJS_OTHER) $(libdir)/libmumps_common$(PLAT)$(LIBEXT_SHARED) + $(FC) $(OPTL) -shared $(OBJS_MOD) $(OBJS_OTHER) -L$(libdir) $(LORDERINGS) $(LIBS) $(LIBOTHERS) -lmumps_common$(PLAT) -o $@ $(RPATH_OPT) + ++$(libdir)/libmumps_common$(PLAT).so: $(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER) ++ $(FC) -shared $^ -Wl,-soname,libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) $(LORDERINGS) -lpthread $(MUMPS_LIBF77) $(MPIFLIB) $(MPICLIB) $(METISLIB) -o $(libdir)/libmumps_common$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libmumps_common$(PLAT)-$(SONAME_VERSION).so $@ ++ ++$(libdir)/lib$(ARITH)mumps$(PLAT).so: $(OBJS_MOD) $(OBJS_OTHER) ++ $(FC) -shared $^ -Wl,-soname,lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -L$(libdir) -lmumps_common$(PLAT) -lpthread $(MUMPS_LIBF77) $(LORDERINGS) $(MPIFLIB) $(METISLIB) $(SCALAP) -o $(libdir)/lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs lib$(ARITH)mumps$(PLAT)-$(SONAME_VERSION).so $@ ++ + + # Dependencies between modules: + # i) arithmetic-dependent modules: +@@ -447,12 +460,14 @@ + .SUFFIXES: .c .F .o + .F.o: + $(FC) $(OPTF) $(FPIC) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -c $*.F $(OUTF)$*.o ++ $(FC) $(OPTF) -I. -I../include $(INCS) $(IORDERINGSF) $(ORDERINGSF) -fPIC -c $*.F $(OUTF)$*.o + .c.o: + $(CC) $(OPTC) $(FPIC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -c $*.c $(OUTC)$*.o ++ $(CC) $(OPTC) -I../include $(INCS) $(CDEFS) $(IORDERINGSC) $(ORDERINGSC) -fPIC -c $*.c $(OUTC)$*.o + + $(ARITH)mumps_c.o: mumps_c.c + $(CC) $(OPTC) $(FPIC) -I../include $(INCS) $(CDEFS) -DMUMPS_ARITH=MUMPS_ARITH_$(ARITH) \ +- $(IORDERINGSC) $(ORDERINGSC) -c mumps_c.c $(OUTC)$@ ++ $(IORDERINGSC) $(ORDERINGSC) -fPIC -c mumps_c.c $(OUTC)$@ + + clean: + $(RM) *.o *.mod $(incdir)/mumps_int_def.h diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1_shared-pord.patch b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1_shared-pord.patch new file mode 100644 index 00000000000..2819aa26f26 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1_shared-pord.patch @@ -0,0 +1,45 @@ +Heavily inspired from https://src.fedoraproject.org/rpms/MUMPS//blob/rawhide/f/MUMPS-shared.patch +Author: micketeer@gmail.com +Updatd to version 5.5.0: J. Sassmannshausen/ICL (UK) +Updatd to version 5.5.1: maxim-masterov (SURF) +Updatd to version 5.6.1: Petr Král (INUITS) +diff -u MUMPS_5.6.1/Makefile.orig MUMPS_5.6.1/Makefile +--- MUMPS_5.6.1/Makefile.orig 2023-07-11 09:51:28.000000000 +0200 ++++ MUMPS_5.6.1/Makefile 2023-07-26 10:37:43.528871588 +0200 +@@ -65,7 +65,7 @@ + + include Makefile.inc + +-prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) ++prerequisites: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT).so + + prerequisitesshared: Makefile.inc $(LIBSEQNEEDED)sharedlibseq $(libdir)/libpord$(PLAT)$(LIBEXT_SHARED) + +@@ -103,8 +103,11 @@ + cp $(LPORDDIR)/libpord$(LIBEXT_SHARED) $@; \ + fi; + +- +- ++$(libdir)/libpord$(PLAT).so: ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cd $(LPORDDIR); make CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" ARFUNCT= RANLIB="$(RANLIB)" libpord$(PLAT).so; fi; ++ if [ "$(LPORDDIR)" != "" ] ; then \ ++ cp -a $(LPORDDIR)/libpord*.so lib/; fi; + + clean: + (cd src; $(MAKE) clean) +diff -u MUMPS_5.6.1/PORD/lib/Makefile.orig MUMPS_5.6.1/PORD/lib/Makefile +--- MUMPS_5.6.1/PORD/lib/Makefile.orig 2023-07-11 09:51:28.000000000 +0200 ++++ MUMPS_5.6.1/PORD/lib/Makefile 2023-07-26 10:47:36.312139519 +0200 +@@ -31,6 +31,10 @@ + libpord$(PLAT)$(LIBEXT_SHARED):$(OBJS) + $(CC) -shared $(OBJS) -o libpord.so + ++libpord$(PLAT).so: $(OBJS) ++ $(CC) -shared $(OBJS) -Wl,-soname,libpord$(PLAT)-$(SONAME_VERSION).so -o libpord$(PLAT)-$(SONAME_VERSION).so $(OPTL) -Wl,-z,defs ++ ln -fs libpord$(PLAT)-$(SONAME_VERSION).so $@ ++ + clean: + rm -f *.o + diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.8-GCC-12.2.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.8-GCC-12.2.0.eb new file mode 100644 index 00000000000..393ac74ac03 --- /dev/null +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.8-GCC-12.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Osi' +version = '0.108.8' + +homepage = "https://github.com/coin-or/Osi" +description = """Osi (Open Solver Interface) provides an abstract base class to a generic linear +programming (LP) solver, along with derived classes for specific solvers. Many +applications may be able to use the Osi to insulate themselves from a specific +LP solver. That is, programs written to the OSI standard may be linked to any +solver with an OSI interface and should produce correct results. The OSI has +been significantly extended compared to its first incarnation. Currently, the +OSI supports linear programming solvers and has rudimentary support for integer +programming.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/coin-or/Osi/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8b01a49190cb260d4ce95aa7e3948a56c0917b106f138ec0a8544fadca71cf6a'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.5'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CoinUtils', '2.11.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +# Disable GLPK because Osi requires GLPK<=4.48 +configopts = '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + +sanity_check_paths = { + 'files': ['lib/libOsi.%s' % SHLIB_EXT, 'lib/libOsiCommonTests.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" From 79775e052dac0d11e4fc921125174465c48f10b0 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 10 Aug 2023 10:42:40 +0200 Subject: [PATCH 8321/9987] Exclude timed out test --- .../p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb index e12ecdc7f98..a20df9fa1e0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb @@ -120,6 +120,9 @@ excluded_tests = { # Bad tests: https://github.com/pytorch/pytorch/issues/60260 'distributed/elastic/utils/distributed_test', 'distributed/elastic/multiprocessing/api_test', + # This test fails on A10s at the very least, times out forever no matter how long the timeout is. + # Possibly related to NCCL 2.8.3: https://docs.nvidia.com/deeplearning/nccl/release-notes/rel_2-8-3.html + 'distributed/test_distributed_spawn', # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 'test_optim', # These tests appear flaky, possibly related to number of GPUs that are used From b6c5facfd26f956b17f2812af6e2e590bed991dc Mon Sep 17 00:00:00 2001 From: benjamic Date: Thu, 10 Aug 2023 10:51:14 +0200 Subject: [PATCH 8322/9987] Adding Autotools --- easybuild/easyconfigs/h/htop/htop-3.2.2.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/h/htop/htop-3.2.2.eb b/easybuild/easyconfigs/h/htop/htop-3.2.2.eb index b4699ea404c..4056127e091 100644 --- a/easybuild/easyconfigs/h/htop/htop-3.2.2.eb +++ b/easybuild/easyconfigs/h/htop/htop-3.2.2.eb @@ -14,6 +14,10 @@ source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] checksums = ['3829c742a835a0426db41bb039d1b976420c21ec65e93b35cd9bfd2d57f44ac8'] +builddependencies = [ + ('autotools', '20220317'), +] + dependencies = [ ('ncurses', '6.2'), ] From 763c748fef5207f1f5896f2afc5a3f5d91705caa Mon Sep 17 00:00:00 2001 From: benjamic Date: Thu, 10 Aug 2023 10:59:05 +0200 Subject: [PATCH 8323/9987] Fising Typo --- easybuild/easyconfigs/h/htop/htop-3.2.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/htop/htop-3.2.2.eb b/easybuild/easyconfigs/h/htop/htop-3.2.2.eb index 4056127e091..24f2a2a44d4 100644 --- a/easybuild/easyconfigs/h/htop/htop-3.2.2.eb +++ b/easybuild/easyconfigs/h/htop/htop-3.2.2.eb @@ -15,7 +15,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['3829c742a835a0426db41bb039d1b976420c21ec65e93b35cd9bfd2d57f44ac8'] builddependencies = [ - ('autotools', '20220317'), + ('Autotools', '20220317'), ] dependencies = [ From 63869e2c91b7c107d62c77b78424a8db10819550 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 10 Aug 2023 11:12:59 +0200 Subject: [PATCH 8324/9987] added airo-1.17.8-GCCcore-12.3.0.eb pixman-0.42.2-GCCcore-12.3.0.eb --- .../c/cairo/cairo-1.17.8-GCCcore-12.3.0.eb | 52 +++++++++++++++++++ .../p/pixman/pixman-0.42.2-GCCcore-12.3.0.eb | 28 ++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.17.8-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.17.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.17.8-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d34ba91f3ae --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.17.8-GCCcore-12.3.0.eb @@ -0,0 +1,52 @@ +# easyblock = 'ConfigureMake' +easyblock = 'MesonNinja' + + +name = 'cairo' +version = '1.17.8' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [ + 'https://cairographics.org/releases/', + 'https://cairographics.org/snapshots/' +] +sources = [SOURCE_TAR_XZ] +checksums = ['5b10c8892d1b58d70d3f0ba5b47863a061262fa56b9dc7944161f8c8b783bc64'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Ninja', '1.11.1'), + ('Meson', '1.1.1'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), + ('libpng', '1.6.39'), + ('freetype', '2.13.0'), + ('pixman', '0.42.2'), + ('expat', '2.5.0'), + ('GLib', '2.77.1'), + ('X11', '20230603'), +] + +configopts = "--default-library=both" # static and shared library + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8308c32bb59 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.42.2' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ea1480efada2fd948bc75366f7c349e1c96d3297d09a3fe62626e38e234a625e'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 447727e5451da2ffd479851d80f95d2b8e18008d Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 10 Aug 2023 11:14:08 +0200 Subject: [PATCH 8325/9987] removed comment line --- easybuild/easyconfigs/c/cairo/cairo-1.17.8-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.17.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.17.8-GCCcore-12.3.0.eb index d34ba91f3ae..ec0a8d9382d 100644 --- a/easybuild/easyconfigs/c/cairo/cairo-1.17.8-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/cairo/cairo-1.17.8-GCCcore-12.3.0.eb @@ -1,4 +1,3 @@ -# easyblock = 'ConfigureMake' easyblock = 'MesonNinja' From d05cc804cb3808ae57d9248d21ebe3265ee410f8 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 10 Aug 2023 10:18:09 +0100 Subject: [PATCH 8326/9987] switch to PCRE2 --- easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb index c55c6368e22..fa6f80f27fe 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb @@ -16,7 +16,7 @@ builddependencies = [('binutils', '2.39')] dependencies = [ ('zlib', '1.2.12'), - ('PCRE', '8.45'), + ('PCRE2', '10.40'), ] configopts = '--without-alllang --with-boost=no' From f2415c7d5a3f2746ae5b1935c4f02e2871d562d4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 10 Aug 2023 10:21:17 +0100 Subject: [PATCH 8327/9987] add Bison builddep --- easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb index fa6f80f27fe..290050ffb5d 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.2.0.eb @@ -12,7 +12,10 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['2af08aced8fcd65cdb5cc62426768914bedc735b1c250325203716f78e39ac9b'] -builddependencies = [('binutils', '2.39')] +builddependencies = [ + ('binutils', '2.39'), + ('Bison', '3.8.2'), +] dependencies = [ ('zlib', '1.2.12'), From 4038f6d7e27dbecfc67a19ea2f909720b9d8a7d1 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 10 Aug 2023 11:37:15 +0200 Subject: [PATCH 8328/9987] adding easyconfigs: libgd-2.3.3-GCCcore-12.3.0.eb --- .../l/libgd/libgd-2.3.3-GCCcore-12.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4d542a04a10 --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.3' + +homepage = 'https://libgd.github.io' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libgd/libgd/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd3f1f0bb016edcc0b2d082e8229c822ad1d02223511997c80461481759b1ed2'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('fontconfig', '2.14.2'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + +sanity_check_paths = { + 'files': ['lib/libgd.a', 'lib/libgd.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +sanity_check_commands = ['webpng --help'] + +moduleclass = 'lib' From 435596d0796738f7cc4fc49918e5d1dabce6a8c6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 10 Aug 2023 11:26:40 +0100 Subject: [PATCH 8329/9987] Fix typo in comment --- easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb index 421f65ee50d..723a23aefbf 100644 --- a/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb +++ b/easybuild/easyconfigs/p/pyBigWig/pyBigWig-0.3.22-foss-2022b.eb @@ -23,7 +23,7 @@ dependencies = [ # fix version of '0.0.0' issue preinstallopts = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ -# do not use setuptools-scm to dectet version +# do not use setuptools-scm to detect version preinstallopts += """sed -i 's/[tool.setuptools_scm]//' pyproject.toml && """ use_pip = True From 132543a5f94a532e5f15c0fdb3a61ff2ed9b3c34 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 10 Aug 2023 13:06:47 +0200 Subject: [PATCH 8330/9987] added GObject-Introspection-1.76.1-GCCcore-12.3.0.eb --- ...ect-Introspection-1.76.1-GCCcore-12.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.76.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.76.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.76.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5b64d4bc2ab --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.76.1-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.76.1' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['196178bf64345501dcdc4d8469b36aa6fe80489354efe71cb7cb8ab82a3738bf'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('cairo', '1.17.8'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('GLib', '2.77.1'), + ('libffi', '3.4.4'), + ('util-linux', '2.39'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' From cce1b3bb425bb3a11bc1d9e6da2072c11f7c3049 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 10 Aug 2023 13:16:36 +0200 Subject: [PATCH 8331/9987] Update nose3-1.3.8-GCCcore-11.3.0.eb --- easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb index a3a84995147..7244a899c1a 100644 --- a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb @@ -14,7 +14,7 @@ checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'] options = {'modulename': 'nose'} builddependencies = [ - ('binutils', '2.38'), + ('binutils', '2.38'), ] dependencies = [ From 41fa1a55beecba27724ee7bbcaec17fa2cde2136 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 10 Aug 2023 13:29:33 +0200 Subject: [PATCH 8332/9987] adding easyconfigs: PuLP-2.7.0-foss-2022b.eb, Cbc-2.10.5-foss-2022b.eb, Cgl-0.60.7-foss-2022b.eb --- .../c/Cbc/Cbc-2.10.5-foss-2022b.eb | 63 +++++++++++++++++++ .../c/Cgl/Cgl-0.60.7-foss-2022b.eb | 50 +++++++++++++++ .../p/PuLP/PuLP-2.7.0-foss-2022b.eb | 36 +++++++++++ 3 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2022b.eb create mode 100644 easybuild/easyconfigs/c/Cgl/Cgl-0.60.7-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/PuLP/PuLP-2.7.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2022b.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2022b.eb new file mode 100644 index 00000000000..dd56bb68435 --- /dev/null +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.5-foss-2022b.eb @@ -0,0 +1,63 @@ +easyblock = "ConfigureMake" + +name = 'Cbc' +version = '2.10.5' + +homepage = "https://github.com/coin-or/Cbc" +description = """Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming +solver written in C++. It can be used as a callable library or using a +stand-alone executable.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://www.coin-or.org/download/source/%(name)s/'] +sources = [SOURCE_TGZ] +checksums = ['da1a945648679b21ba56b454b81e939451dc7951d9beb3c3e14f18f64dde6972'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.5'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.6.1', '-metis'), + ('CoinUtils', '2.11.9'), + ('Osi', '0.108.8'), + ('Clp', '1.17.8'), + ('Cgl', '0.60.7'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +# Use BLAS/LAPACK from OpenBLAS +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +# Use METIS AND MUMPS from EB +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +# Disable GLPK, dependencies have to be built with it as well +configopts += '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' +# Use Cgl from EB +configopts += '--with-cgl-lib="-lCgl" ' +configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.7-foss-2022b.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.7-foss-2022b.eb new file mode 100644 index 00000000000..f28e99e9fbb --- /dev/null +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.7-foss-2022b.eb @@ -0,0 +1,50 @@ +easyblock = "ConfigureMake" + +name = 'Cgl' +version = '0.60.7' + +homepage = "https://github.com/coin-or/Cgl" +description = """The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that +can be used with other COIN-OR packages that make use of cuts, such as, among +others, the linear solver Clp or the mixed integer linear programming solvers +Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or +communicate with a solver. It does not directly call a solver.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/Cgl/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['93b30a80b5d2880c2e72d5877c64bdeaf4d7c1928b3194ea2f88b1aa4517fb1b'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.5'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CoinUtils', '2.11.9'), + ('Osi', '0.108.8'), + ('Clp', '1.17.8'), +] + +# Use CoinUtils from EB +configopts = '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['lib/libCgl.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.7.0-foss-2022b.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.7.0-foss-2022b.eb new file mode 100644 index 00000000000..d502dceafdf --- /dev/null +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.7.0-foss-2022b.eb @@ -0,0 +1,36 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# Updated: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'PuLP' +version = '2.7.0' + +homepage = 'https://github.com/coin-or/pulp' +description = """ +PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and +call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to +solve linear problems. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e73ee6b32d639c9b8cf4b4aded334ba158be5f8313544e056f796ace0a10ae63'] + +dependencies = [ + ('Python', '3.10.8'), + ('GLPK', '5.0'), + ('Cbc', '2.10.5'), + # Gurobi requires a seperate license + # ('Gurobi', '9.5.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'tools' From 0ac1c9b29bd2b739d546218c66ffc75435d140c8 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 10 Aug 2023 13:38:35 +0200 Subject: [PATCH 8333/9987] add HarfBuzz-5.3.1-GCCcore-12.3.0.eb --- .../HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a97ce9c0a87 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '5.3.1' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['77c8c903f4539b050a6d3a5be79705c7ccf7b1cb66d68152a651486e261edbd2'] + +builddependencies = [ + ('binutils', '2.40'), + ('GObject-Introspection', '1.76.1'), + ('pkgconf', '1.9.5'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('ICU', '73.2'), + ('cairo', '1.17.8'), + ('freetype', '2.13.0'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' From 3f1d063dd9fc9d0c484485a65ce2fc823b131ddf Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 10 Aug 2023 15:17:25 +0200 Subject: [PATCH 8334/9987] adding easyconfigs: NVHPC-23.7-CUDA-12.1.1.eb --- .../n/NVHPC/NVHPC-23.7-CUDA-12.1.1.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.1.1.eb new file mode 100644 index 00000000000..02aab8eea28 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.1.1.eb @@ -0,0 +1,66 @@ +name = 'NVHPC' +version = '23.7' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2023_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = ['fea91d95ff18bca1ce7afde50371caa02001ade8bed6ddfc5ff70862ccbebece'] + +local_gccver = '12.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.40', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.16', '', ('GCCcore', local_gccver)), + ('CUDA', '12.1.1', '', SYSTEM), +] + +module_add_cuda = False + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/$version/cuda/) where $version is the NVHPC version +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '%(cudaver)s' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From a457061facbf4f50f8b9435ec0ae29d5ffd9b161 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 10 Aug 2023 15:48:16 +0200 Subject: [PATCH 8335/9987] FriBidi-1.0.12-GCCcore-12.3.0.eb Pango-1.50.14-GCCcore-12.3.0.eb --- .../FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb | 32 +++++++++++++++ .../p/Pango/Pango-1.50.14-GCCcore-12.3.0.eb | 41 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.50.14-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..df4dacf597f --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.12' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/fribidi/fribidi/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0cd233f97fc8c67bb3ac27ce8440def5d3ffacf516765b91c2cc654498293495'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Autotools', '20220317'), +] + +configopts = '--disable-docs' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.50.14-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.50.14-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a56cf1e8361 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.50.14-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.50.14' + +homepage = 'https://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['1d67f205bfc318c27a29cfdfb6828568df566795df0cb51d2189cde7f2d581e8'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.76.1'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('X11', '20230603'), + ('GLib', '2.77.1'), + ('cairo', '1.17.8'), + ('HarfBuzz', '5.3.1'), + ('FriBidi', '1.0.12'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 5c09992cadde823547c72f9fa7274dffe853a24a Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 10 Aug 2023 15:55:05 +0200 Subject: [PATCH 8336/9987] code review updates --- .../m/MXNet/MXNet-1.9.1-foss-2022a.eb | 98 ++++++++++--------- 1 file changed, 51 insertions(+), 47 deletions(-) diff --git a/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb index be89769cc90..46699c1ee84 100644 --- a/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb @@ -7,55 +7,59 @@ description = """Flexible and Efficient Library for Deep Learning""" toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'cstd': 'c++14', 'opt': True, 'pic': True, 'openmp': True, 'extra_cflags': '-lflexiblas'} + # MXNet pulls in a bunch of submodules with specific commits -source_urls = [ - 'https://github.com/apache/mxnet/archive', - 'https://github.com/dmlc/ps-lite/archive/', - 'https://github.com/apache/tvm/archive/', - 'https://github.com/dmlc/dmlc-core/archive/', - 'https://github.com/dmlc/dlpack/archive/', - 'https://github.com/google/googletest/archive/', - 'https://github.com/kpu/intgemm/archive/', - 'https://github.com/NVlabs/cub/archive/', - 'https://github.com/onnx/onnx-tensorrt/archive/', - 'https://github.com/oneapi-src/oneDNN/archive/', -] sources = [ - 'v%(version)s.tar.gz', # MXNet - '34fd45cae457d59850fdcb2066467778d0673f21.tar.gz', # ps-lite - 'efdac9439506d1de5eec91ecc795982c78e41909.tar.gz', # tvm - '5df8305fe699d3b503d10c60a231ab0223142407.tar.gz', # dmlc-core - '3efc489b55385936531a06ff83425b719387ec63.tar.gz', # dlpack - 'eb9225ce361affe561592e0912320b9db84985d0.tar.gz', # googletest - '8f28282c3bd854922da638024d2659be52e892e9.tar.gz', # intgemm - '0158fa19f28619886232defd412433974af89611.tar.gz', # cub - '2eb74d933f89e1590fdbfc64971a36e5f72df720.tar.gz', # onnx-tensorrt - '5818c40f07bdb6307f9bc64e929836fe036da644.tar.gz', # oneDNN -] -patches = [ - 'mxnet-1.9.1-add_flexiblas.patch', -] -checksums = [ - {'v1.9.1.tar.gz': '9927f986b2c2c8315f2ba675e050ce1f4e24e84c4692e5f0a96248876784a8a7'}, - {'34fd45cae457d59850fdcb2066467778d0673f21.tar.gz': - 'ec5d5baab8bbf0c3983ad5f18d7f963f15ae7cd4d154ec204b03c1dceccf209b'}, - {'efdac9439506d1de5eec91ecc795982c78e41909.tar.gz': - '656c38d66baeab885b0212602148bb55ad3cf7d22f52ded8ece53f88e103a2f5'}, - {'5df8305fe699d3b503d10c60a231ab0223142407.tar.gz': - 'a8046f752f36005564d2924b4b6f73e1aea3cce7ff10f9e19d99ad6a22a045b2'}, - {'3efc489b55385936531a06ff83425b719387ec63.tar.gz': - 'b59586ce69bcf3efdbf3cf4803fadfeaae4948044e2b8d89cf912194cf28f233'}, - {'eb9225ce361affe561592e0912320b9db84985d0.tar.gz': - 'a4cb4b0c3ebb191b798594aca674ad47eee255dcb4c26885cf7f49777703484f'}, - {'8f28282c3bd854922da638024d2659be52e892e9.tar.gz': - 'bc8bd8015613a13747eb769876385ec53e8c1ea7ae3f8414521dc53b8fcdfc65'}, - {'0158fa19f28619886232defd412433974af89611.tar.gz': - '43424c4c17a997d1d730c89ec14688671245de7941e02b388d7d3df6ea53777a'}, - {'2eb74d933f89e1590fdbfc64971a36e5f72df720.tar.gz': - 'df99819727445c247fb5c21c2fd825ded3269376867457ae84fa6d6f1c0ae331'}, - {'5818c40f07bdb6307f9bc64e929836fe036da644.tar.gz': - 'aeb8e65bb13d1a3171673ab749d41e8c3a6538371d922a7fa881afef277128ba'}, - {'mxnet-1.9.1-add_flexiblas.patch': '92b3a9b9ffd87c3be30efe1b400b4d152ba3fe4e105970bc6c63906dfcb59084'}, + { + 'source_urls': ['https://github.com/apache/mxnet/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCELOWER_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/dmlc/ps-lite/archive/'], + 'download_filename': '34fd45cae457d59850fdcb2066467778d0673f21.tar.gz', + 'filename': 'ps-lite-20200229.tar.gz', + }, + { + 'source_urls': ['https://github.com/apache/tvm/archive/'], + 'download_filename': 'efdac9439506d1de5eec91ecc795982c78e41909.tar.gz', + 'filename': 'tvm-20201111.tar.gz', + }, + { + 'source_urls': ['https://github.com/dmlc/dmlc-core/archive/'], + 'download_filename': '5df8305fe699d3b503d10c60a231ab0223142407.tar.gz', + 'filename': 'dmlc-core-20200410.tar.gz', + }, + { + 'source_urls': ['https://github.com/dmlc/dlpack/archive/'], + 'download_filename': '3efc489b55385936531a06ff83425b719387ec63.tar.gz', + 'filename': 'dlpack-20200121.tar.gz', + }, + { + 'source_urls': ['https://github.com/google/googletest/archive/'], + 'download_filename': 'eb9225ce361affe561592e0912320b9db84985d0.tar.gz', + 'filename': 'googletest-20190114.tar.gz', + }, + { + 'source_urls': ['https://github.com/kpu/intgemm/archive/'], + 'download_filename': '8f28282c3bd854922da638024d2659be52e892e9.tar.gz', + 'filename': 'intgemm-20200915.tar.gz', + }, + { + 'source_urls': ['https://github.com/NVlabs/cub/archive/'], + 'download_filename': '0158fa19f28619886232defd412433974af89611.tar.gz', + 'filename': 'cub-20200424.tar.gz', + }, + { + 'source_urls': ['https://github.com/onnx/onnx-tensorrt/archive/'], + 'download_filename': '2eb74d933f89e1590fdbfc64971a36e5f72df720.tar.gz', + 'filename': 'onnx-tensorrt-20200624.tar.gz', + }, + { + 'source_urls': ['https://github.com/oneapi-src/oneDNN/archive/'], + 'download_filename': '5818c40f07bdb6307f9bc64e929836fe036da644.tar.gz', + 'filename': 'oneDNN-20220325.tar.gz', + }, ] builddependencies = [ From 7f58fc82784ca46181a0f2e8792ea0b46401caf4 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 10 Aug 2023 16:07:08 +0200 Subject: [PATCH 8337/9987] added checksums --- .../easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb index 46699c1ee84..463e8940a55 100644 --- a/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb @@ -61,6 +61,18 @@ sources = [ 'filename': 'oneDNN-20220325.tar.gz', }, ] +checksums = [ + {'mxnet-1.9.1.tar.gz': '9927f986b2c2c8315f2ba675e050ce1f4e24e84c4692e5f0a96248876784a8a7'}, + {'ps-lite-20200229.tar.gz': 'ec5d5baab8bbf0c3983ad5f18d7f963f15ae7cd4d154ec204b03c1dceccf209b'}, + {'tvm-20201111.tar.gz': '656c38d66baeab885b0212602148bb55ad3cf7d22f52ded8ece53f88e103a2f5'}, + {'dmlc-core-20200410.tar.gz': 'a8046f752f36005564d2924b4b6f73e1aea3cce7ff10f9e19d99ad6a22a045b2'}, + {'dlpack-20200121.tar.gz': 'b59586ce69bcf3efdbf3cf4803fadfeaae4948044e2b8d89cf912194cf28f233'}, + {'googletest-20190114.tar.gz': 'a4cb4b0c3ebb191b798594aca674ad47eee255dcb4c26885cf7f49777703484f'}, + {'intgemm-20200915.tar.gz': 'bc8bd8015613a13747eb769876385ec53e8c1ea7ae3f8414521dc53b8fcdfc65'}, + {'cub-20200424.tar.gz': '43424c4c17a997d1d730c89ec14688671245de7941e02b388d7d3df6ea53777a'}, + {'onnx-tensorrt-20200624.tar.gz': 'df99819727445c247fb5c21c2fd825ded3269376867457ae84fa6d6f1c0ae331'}, + {'oneDNN-20220325.tar.gz': 'aeb8e65bb13d1a3171673ab749d41e8c3a6538371d922a7fa881afef277128ba'}, +] builddependencies = [ ('CMake', '3.23.1'), From 9267ed479e810f3efe531c7dfa295e21561beeab Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 10 Aug 2023 16:34:58 +0200 Subject: [PATCH 8338/9987] adding easyconfigs: jq-1.6-GCCcore-12.3.0.eb --- .../easyconfigs/j/jq/jq-1.6-GCCcore-12.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..587daad9bbd --- /dev/null +++ b/easybuild/easyconfigs/j/jq/jq-1.6-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'jq' +version = '1.6' + +homepage = 'https://stedolan.github.io/jq/' +description = """jq is a lightweight and flexible command-line JSON processor.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/stedolan/jq/releases/download/jq-%(version)s'] +sources = ['jq-%(version)s.tar.gz'] +checksums = ['5de8c8e29aaa3fb9cc6b47bb27299f271354ebb72514e3accadc7d38b5bbaa72'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -fi && " + +configopts = '--with-oniguruma=builtin' + +sanity_check_paths = { + 'files': ['bin/jq'], + 'dirs': [], +} + +sanity_check_commands = ['jq --help', 'jq --version'] + +moduleclass = 'tools' From df67f6d770ced5183f9924cafbbdf71d24a39113 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 10 Aug 2023 16:40:03 +0200 Subject: [PATCH 8339/9987] Update easybuild/easyconfigs/e/exiv2/exiv2-0.28.0-GCCcore-12.3.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/e/exiv2/exiv2-0.28.0-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/exiv2/exiv2-0.28.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/exiv2/exiv2-0.28.0-GCCcore-12.3.0.eb index 61e00e9b431..0bd2cbba4bc 100644 --- a/easybuild/easyconfigs/e/exiv2/exiv2-0.28.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/e/exiv2/exiv2-0.28.0-GCCcore-12.3.0.eb @@ -33,4 +33,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = ["exiv2 --help"] + moduleclass = 'vis' From ee54d5f91e172e1ae95474c6829aa9188987372b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 10 Aug 2023 17:08:01 +0200 Subject: [PATCH 8340/9987] adding easyconfigs: networkx-3.1-gfbf-2023a.eb --- .../n/networkx/networkx-3.1-gfbf-2023a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb b/easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb new file mode 100644 index 00000000000..2cef5135036 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-3.1-gfbf-2023a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '3.1' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['de346335408f84de0eada6ff9fafafff9bcda11f0a0dfaa931133debb146ab61'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 0b7a52af8a7a3b09af33235316f611a03ac5bb4e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Aug 2023 18:57:00 +0200 Subject: [PATCH 8341/9987] adding easyconfigs: aiohttp-3.8.5-GCCcore-12.3.0.eb --- .../a/aiohttp/aiohttp-3.8.5-GCCcore-12.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3c96a3e7458 --- /dev/null +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.5-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'aiohttp' +version = '3.8.5' + +homepage = 'https://github.com/aio-libs/aiohttp' +description = "Asynchronous HTTP client/server framework for asyncio and Python." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True + +# aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies +exts_list = [ + ('multidict', '6.0.4', { + 'checksums': ['3666906492efb76453c0e7b97f2cf459b0682e7402c0489a95484965dbc1da49'], + }), + ('yarl', '1.9.2', { + 'checksums': ['04ab9d4b9f587c06d801c2abfe9317b77cdf996c65a90d5e84ecc45010823571'], + }), + ('frozenlist', '1.4.0', { + 'checksums': ['09163bdf0b2907454042edb19f887c6d33806adc71fbd54afc14908bfdc22251'], + }), + ('async-timeout', '4.0.2', { + 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], + }), + (name, version, { + 'checksums': ['b9552ec52cc147dbf1944ac7ac98af7602e51ea2dcd076ed194ca3c0d1c7d0bc'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 5a8f174a48a8d7ea752cd80a26b44978cb6c1f72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Aug 2023 18:57:15 +0200 Subject: [PATCH 8342/9987] adding easyconfigs: tqdm-4.66.1-GCCcore-12.3.0.eb --- .../t/tqdm/tqdm-4.66.1-GCCcore-12.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/tqdm/tqdm-4.66.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.66.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1fce3aea1b1 --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.1-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.66.1' + +homepage = "https://github.com/tqdm/tqdm" +description = """A fast, extensible progress bar for Python and CLI""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7'] + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [('Python', '3.11.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' From 28a1635a51e76c6e0512fa45ef9e6c3bd1f4ca28 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 11 Aug 2023 10:59:05 +0200 Subject: [PATCH 8343/9987] adding easyconfigs: libaio-0.3.113-GCCcore-12.3.0.eb --- .../l/libaio/libaio-0.3.113-GCCcore-12.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..19154bc8933 --- /dev/null +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.113' +_libversion = '1.0.2' + +homepage = 'https://pagure.io/libaio' +description = "Asynchronous input/output library that uses the kernels native interface." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['1c561c20670c5c09cc8437a622008c0693c6a7816c1f30332da3796953b2f454'] + +builddependencies = [('binutils', '2.40')] + +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + +files_to_copy = [ + (["src/libaio.a", "src/%s" % _soname], "lib"), + (["src/libaio.h"], "include"), +] + +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] + +sanity_check_paths = { + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' From e3ad26610a27cf22e03115413459660345a2d9b2 Mon Sep 17 00:00:00 2001 From: maximm Date: Fri, 11 Aug 2023 11:57:17 +0200 Subject: [PATCH 8344/9987] adding easyconfigs: re2c-3.1-GCCcore-12.3.0.eb --- .../r/re2c/re2c-3.1-GCCcore-12.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..12c0020bf5f --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '3.1' + +homepage = 'https://re2c.org' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['0ac299ad359e3f512b06a99397d025cfff81d3be34464ded0656f8a96676c029'] + +builddependencies = [('binutils', '2.40')] + +configopts = "--disable-rust" + +sanity_check_paths = { + 'files': ['bin/re2c'], + 'dirs': [], +} + +sanity_check_commands = ["re2c --help"] + +moduleclass = 'tools' From ade8bd0db6b8dbdf55a4674aa7bdb6b0874a2cdb Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 11 Aug 2023 12:01:36 +0200 Subject: [PATCH 8345/9987] nodejs-18.17.1-GCCcore-12.3.0.eb --- .../n/nodejs/nodejs-18.17.1-GCCcore-12.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-18.17.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-18.17.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-18.17.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3490b9455a8 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-18.17.1-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '18.17.1' # LTS on 2023-08-08 +local_libversion = '108' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['1157525a819c395020795ff8c49eee7472b8666cc256b45558b9cbe2e0864c35'] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('ICU', '73.2'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# Use ICU and OpenSSL from EasyBuild +local_common_configopts = "--with-intl=system-icu --shared-openssl " + +configopts = [ + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) + +postinstallcmds = [ + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], + 'dirs': ['lib/node_modules', 'include/node'] +} + +sanity_check_commands = ["node --help"] + +moduleclass = 'lang' From acc2fe1855143b9af8d0efb713e402fcd63171e7 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 11 Aug 2023 13:08:44 +0200 Subject: [PATCH 8346/9987] adding easyconfigs: Python-2.7.18-GCCcore-12.3.0.eb --- .../p/Python/Python-2.7.18-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0ef2a70e6cf --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.18' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +builddependencies = [ + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('binutils', '2.40'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.13'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('SQLite', '3.42.0'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +moduleclass = 'lang' From 3d91fc55b234e9eb16a2b42cab1ad86411bd1e57 Mon Sep 17 00:00:00 2001 From: benjamic Date: Fri, 11 Aug 2023 13:19:01 +0200 Subject: [PATCH 8347/9987] adding easyconfigs: AMD-uProf-4.1.424.eb --- .../a/AMD-uProf/AMD-uProf-4.1.424.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-4.1.424.eb diff --git a/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-4.1.424.eb b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-4.1.424.eb new file mode 100644 index 00000000000..1035c1a8bb8 --- /dev/null +++ b/easybuild/easyconfigs/a/AMD-uProf/AMD-uProf-4.1.424.eb @@ -0,0 +1,37 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Binary' + +name = 'AMD-uProf' +version = '4.1.424' + +homepage = 'https://developer.amd.com/amd-uprof/' +description = """AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD + operating systems. It allows developers to better understand the runtime performance of their application and + to identify ways to improve its performance.""" + +download_instructions = """The sources can be obtained after signing a EULA aggreement + (https://www.amd.com/en/developer/uprof.html#downloads).""" + +toolchain = SYSTEM + +source_urls = ['https://developer.amd.com/wordpress/media/files/'] +sources = ['AMDuProf_Linux_x64_%(version)s.tar.bz2'] +checksums = ['ec8e9eef26f3c8f53e05c4b97e5f292afb14a9ad379c76cb98d2b2419496626c'] + +extract_sources = True + +sanity_check_paths = { + 'files': ['include/AMDTPowerProfileApi.h', 'lib/x64/libAMDProfileController.a', + 'bin/libAMDThreadProfileAPI.%s' % SHLIB_EXT, 'bin/AMDuProf'], + 'dirs': ['Examples'] +} + +sanity_check_commands = ['AMDuProfCLI info --system'] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'bin' +} + +moduleclass = 'perf' From e76cb3515b3368f4fff9fea164a061987e07701c Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Fri, 11 Aug 2023 13:59:55 +0200 Subject: [PATCH 8348/9987] add Python as build dependecy to re2c-3.1-GCCcore-12.3.0.eb --- easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-12.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-12.3.0.eb index 12c0020bf5f..4222b2305c0 100644 --- a/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-12.3.0.eb @@ -15,7 +15,10 @@ source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] sources = ['%(name)s-%(version)s.tar.xz'] checksums = ['0ac299ad359e3f512b06a99397d025cfff81d3be34464ded0656f8a96676c029'] -builddependencies = [('binutils', '2.40')] +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.3') +] configopts = "--disable-rust" From cf4c88e21a71e86fafd8ff2b6e2921b87127fd03 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 11 Aug 2023 14:13:19 +0200 Subject: [PATCH 8349/9987] libGLU-9.0.3-GCCcore-12.3.0.eb --- .../l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c636b6c6a9d --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'MesonNinja' + +name = 'libGLU' +version = '9.0.3' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.xz'] +checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] + +builddependencies = [('binutils', '2.40'), + ('Ninja', '1.11.1'), + ('Meson', '1.1.1')] + +dependencies = [('Mesa', '23.1.4')] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From df80f2077c0d4a307338221c9b7ac72f9aa6ed68 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 11 Aug 2023 15:03:42 +0200 Subject: [PATCH 8350/9987] Add GDB and deps --- .../g/GDB/GDB-13.2-GCCcore-12.3.0.eb | 44 +++++++++++++++++++ .../i/ISL/ISL-0.26-GCCcore-12.3.0.eb | 23 ++++++++++ .../m/MPC/MPC-1.3.1-GCCcore-12.3.0.eb | 35 +++++++++++++++ .../m/makeinfo/makeinfo-7.0-GCCcore-12.3.0.eb | 25 +++++++++++ 4 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-7.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..89cd01d4595 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '13.2' + +homepage = 'https://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['fd5bebb7be1833abdb6e023c2f498a354498281df9d05523d8915babeb893f0a'] + +builddependencies = [ + ('binutils', '2.40'), + ('makeinfo', '7.0'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('expat', '2.5.0'), + ('Python', '3.11.3'), + ('ISL', '0.26'), + ('MPC', '1.3.1'), +] + +preconfigopts = "mkdir obj && cd obj && " +configure_cmd_prefix = '../' +prebuildopts = "cd obj && " +preinstallopts = prebuildopts + +configopts = '--with-system-zlib --with-system-readline --with-expat=$EBROOTEXPAT ' +configopts += '--with-python=$EBROOTPYTHON/bin/python --with-isl=$EBROOTISL --with-mpc=$EBROOTMPC ' +configopts += '--enable-tui --enable-plugins --disable-install-libbfd ' + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..131df5b488a --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-12.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.26' + +homepage = 'https://libisl.sourceforge.io' +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://libisl.sourceforge.io'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('GMP', '6.2.1')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..897bf810ce5 --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.3.1' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-7.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..08c983c1b80 --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-7.0-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '7.0' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['20744b82531ce7a04d8cee34b07143ad59777612c3695d5855f29fba40fbe3e0'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Perl', '5.36.1')] + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' From e0491c688ee5821053d7fec9720e6696c4a2f4dd Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 11 Aug 2023 15:25:16 +0200 Subject: [PATCH 8351/9987] Fix makeinfo version --- easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb | 2 +- ...7.0-GCCcore-12.3.0.eb => makeinfo-7.0.3-GCCcore-12.3.0.eb} | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/m/makeinfo/{makeinfo-7.0-GCCcore-12.3.0.eb => makeinfo-7.0.3-GCCcore-12.3.0.eb} (85%) diff --git a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb index 89cd01d4595..df3bd632ae8 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb @@ -14,7 +14,7 @@ checksums = ['fd5bebb7be1833abdb6e023c2f498a354498281df9d05523d8915babeb893f0a'] builddependencies = [ ('binutils', '2.40'), - ('makeinfo', '7.0'), + ('makeinfo', '7.0.3'), ] dependencies = [ diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-7.0.3-GCCcore-12.3.0.eb similarity index 85% rename from easybuild/easyconfigs/m/makeinfo/makeinfo-7.0-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/m/makeinfo/makeinfo-7.0.3-GCCcore-12.3.0.eb index 08c983c1b80..9b0fa429aa0 100644 --- a/easybuild/easyconfigs/m/makeinfo/makeinfo-7.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-7.0.3-GCCcore-12.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'makeinfo' -version = '7.0' +version = '7.0.3' homepage = 'https://www.gnu.org/software/texinfo/' description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] sources = ['texinfo-%(version)s.tar.xz'] -checksums = ['20744b82531ce7a04d8cee34b07143ad59777612c3695d5855f29fba40fbe3e0'] +checksums = ['74b420d09d7f528e84f97aa330f0dd69a98a6053e7a4e01767eed115038807bf'] builddependencies = [('binutils', '2.40')] dependencies = [('Perl', '5.36.1')] From 2fb203ed98c1fae370a75a28a7adaec9db38bde4 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 11 Aug 2023 17:19:38 +0200 Subject: [PATCH 8352/9987] adding easyconfigs: nettle-3.9.1-GCCcore-12.3.0.eb --- .../n/nettle/nettle-3.9.1-GCCcore-12.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7c06ad87bf4 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.9.1' + +homepage = 'https://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ccfeff981b0ca71bbd6fbcb054f407c60ffb644389a5be80d6716d5b550c6ce3'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = '--disable-openssl ' # openssl is just used for the nettle-openssl example and requires openssl 1.1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' From ac8bde281c7aab451b0c02daaa00bc918854d73e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 11 Aug 2023 17:36:09 +0200 Subject: [PATCH 8353/9987] adding easyconfigs: Xvfb-21.1.6-GCCcore-12.3.0.eb --- .../x/Xvfb/Xvfb-21.1.6-GCCcore-12.3.0.eb | 123 ++++++++++++++++++ 1 file changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f6147301b31 --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.3.0.eb @@ -0,0 +1,123 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '21.1.6' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Python', '3.11.3'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('libxslt', '1.1.38'), + ('gettext', '0.21.1'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('X11', '20230603'), + ('pixman', '0.42.2'), + ('libdrm', '2.4.115'), + ('Mesa', '23.1.4'), + ('nettle', '3.9.1'), + ('libunwind', '1.6.2'), + ('XZ', '5.4.2'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.2', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['4a5af55e670713024639a7f7d10826d905d86faf574cd77e0f5aef2d00e70168'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.3.3', { + 'checksums': ['2094dd4a1ca63a61deb101d2dc618682d6e287cdbe09679502223ac445d277dc'], + }), + ('font-misc-misc', '1.1.2', { + 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], + 'preconfigopts': local_font_misc_preconfigopts, + }), + ('xkbcomp', '1.4.6', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['b216a2c8c0eab83f3dc4a3d5ee2bdf7827b30e49c8907035d0f222138eca0987'], + }), + ('xkeyboard-config', '2.37', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['eb1383a5ac4b6210d7c7302b9d6fab052abdf51c5d2c9b55f1f779997ba68c6c'], + 'configopts': '-Dxorg-rules-symlinks=true', + }), + ('xauth', '1.1.2', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['84d27a1023d8da524c134f424b312e53cb96e08871f96868aa20316bfcbbc054'], + }), + ('libxcvt', '0.1.2', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/lib/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['0561690544796e25cfbd71806ba1b0d797ffe464e9796411123e79450f71db38'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual/xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + '6f9c73ccc50e2731adac17671c8e33687738c8cd556b49ecb9f410ce7217be11', # xorg-server-21.1.3.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' From 5d73ec78f0aba6871347320411d95213df37b2f5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 11 Aug 2023 15:56:40 +0000 Subject: [PATCH 8354/9987] Change to gfbf/2023a and add missing deps --- .../l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb | 27 ++ .../l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb | 34 ++ .../easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb | 374 ++++++++++++++++++ 3 files changed, 435 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..29f37b7fefc --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.3' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.xz'] +checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Mesa', '23.1.4'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..df14e87ef74 --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.7.0' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'libgit2' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['d9d0f84a86bf98b73e68997f5c1543cc5067d0ca9c7a5acaba3e8d117ecefef3'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('PCRE', '8.45'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb new file mode 100644 index 00000000000..24764c1cd82 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb @@ -0,0 +1,374 @@ +name = 'R' +version = '4.3.1' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['8dd0bf24f1023c6f618c3b317383d291b4a494f40d73b983ac22ffea99e4ba99'] + +builddependencies = [ + ('pkgconf', '1.9.5'), + #('Xvfb', '21.1.6'), + ('Autotools', '20220317'), +] +dependencies = [ + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('libGLU', '9.0.3'), + ('cairo', '1.17.8'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('SQLite', '3.42.0'), + ('PCRE2', '10.42'), + ('libpng', '1.6.39'), # for plotting in R + ('libjpeg-turbo', '2.1.5.1'), # for plottting in R + ('LibTIFF', '4.5.0'), + ('Java', '11', '', SYSTEM), + ('libgit2', '1.7.0'), + ('OpenSSL', '1.1', '', SYSTEM), + ('cURL', '8.0.1'), + #('Tk', '8.6.12'), # for tcltk + #('libxml2', '2.10.3'), # for XML + #('HarfBuzz', '5.3.1'), # for textshaping + #('FriBidi', '1.0.12'), # for textshaping + +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 22nd June 2023 +exts_list = [ + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('rlang', '1.1.1', { + 'checksums': ['5e5ec9a7796977216c39d94b1e342e08f0681746657067ba30de11b8fa8ada99'], + }), + ('Rcpp', '1.0.10', { + 'checksums': ['1e65e24a9981251ab5fc4f9fd65fe4eab4ba0255be3400a8c5abe20b62b5d546'], + }), + ('R6', '2.5.1', { + 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], + }), + ('cli', '3.6.1', { + 'checksums': ['be3006cec7e67f9ae25e21b4658c4bec680038c2ef7467df5f14da3311a05e36'], + }), + ('base64enc', '0.1-3', { + 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], + }), + ('rprojroot', '2.0.3', { + 'checksums': ['50604247470e910cecfe9b76df754bf96a0d701f81b732f7aa9c90a20d30f897'], + }), + ('xfun', '0.39', { + 'checksums': ['d0ecaabb243dd3496da6029932fcdd4772914843de7ffd0b78a172efde1356c9'], + }), + ('commonmark', '1.9.0', { + 'checksums': ['6dd01a5a26c8d436486abf69c2f6ad0f8dd1c811f575c31983aeb4dbd376548f'], + }), + ('highr', '0.10', { + 'checksums': ['ec55bc1ff66390ed66806dc2a7b6c17dbfd089b3d73fe2e369017f8cb4bc347b'], + }), + ('digest', '0.6.31', { + 'checksums': ['5a284f490eaca6750f695f00a584cfca3f180ca1046ac1107202141149d431b9'], + }), + ('desc', '1.4.2', { + 'checksums': ['758acf14be478c09ba7e84ade3a7ce512becf35d44e5e6a997b932065f2a227c'], + }), + ('ellipsis', '0.3.2', { + 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], + }), + ('prettyunits', '1.1.1', { + 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], + }), + ('crayon', '1.5.2', { + 'checksums': ['70a9a505b5b3c0ee6682ad8b965e28b7e24d9f942160d0a2bad18eec22b45a7a'], + }), + ('stringi', '1.7.12', { + 'checksums': ['efe8ac2900001f986a75db5641fbb24587a6d23de274a6a85c39dfa58921e009'], + }), + ('magrittr', '2.0.3', { + 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], + }), + ('evaluate', '0.21', { + 'checksums': ['3178c99cee8917d7d128806d064d4fecce7845ed07f42e759dcc0adda89c22b9'], + }), + ('ps', '1.7.5', { + 'checksums': ['1abc3ae3c55797b994973f7e43bf5c7bbb4da649a0dcfad36675e196dba4cb4e'], + }), + ('processx', '3.8.1', { + 'checksums': ['e008472b81d4ca1a37a4ba7dd58e5e944f96ab2e44c8ccc8840d43e9fe99e93c'], + }), + ('callr', '3.7.3', { + 'checksums': ['567bfedf073a1d4c5785f0553341608a214938110567b9a6495ff20ebb2fd04e'], + }), + ('pkgbuild', '1.4.1', { + 'checksums': ['cdb0ace14444f362be9725bd84e9752dab92f4771296504b63b9b8084f5e8a6b'], + }), + ('fs', '1.6.2', { + 'checksums': ['548b7c0ed5ab26dc4fbd88707ae12987bcaef834dbc6de4e17d453846dc436b2'], + }), + ('utf8', '1.2.3', { + 'checksums': ['c0a88686591f4ad43b52917d0964e9df4c62d8858fe25135a1bf357dfcbd6347'], + }), + ('fansi', '1.0.4', { + 'checksums': ['3163214e6c40922bbb495229259ed8ce1bebd98b77098a6936d234e43da9c49f'], + }), + ('pkgconfig', '2.0.3', { + 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], + }), + ('withr', '2.5.0', { + 'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'], + }), + ('glue', '1.6.2', { + 'checksums': ['9da518f12be584c90e75fe8e07f711ee3f6fc0d03d817f72c25dc0f66499fdbf'], + }), + ('rstudioapi', '0.14', { + 'checksums': ['469d0987b1ad728a96c363a422fba712a5cebc8b11a5f7e953b4a671044dafc4'], + }), + ('pkgload', '1.3.2', { + 'checksums': ['35d19a032bfeeefcab92d76a768b4a420c2ede0920badaf48cca878592b46b2f'], + }), + ('fastmap', '1.1.1', { + 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], + }), + ('htmltools', '0.5.5', { + 'checksums': ['c8b23fab855a89c6ed0f6d6c7cad0ff9c5ae329c0bdb479940443ee752f26659'], + }), + ('yaml', '2.3.7', { + 'checksums': ['d20cb219e0f9c48aba02f132f81cfa9ecda5e22c925e36726840218ed56680ab'], + }), + ('knitr', '1.43', { + 'checksums': ['3d29baea8c349aaa9310879ceb9a9d51bcaec39827ad46d422c3793c8a4ed53c'], + }), + ('mime', '0.12', { + 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], + }), + ('praise', '1.0.0', { + 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], + }), + ('brio', '1.1.3', { + 'checksums': ['eaa89041856189bee545bf1c42c7920a0bb0f1f70bb477487c467ee3e8fedcc6'], + }), + ('jsonlite', '1.8.5', { + 'checksums': ['dc3cca4bdca1b6d6836c412760ea9656140683126c54cb89c3e42219dec4a3ad'], + }), + ('lifecycle', '1.0.3', { + 'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'], + }), + ('vctrs', '0.6.3', { + 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], + }), + ('stringr', '1.5.0', { + 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], + }), + ('pillar', '1.9.0', { + 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], + }), + ('tibble', '3.2.1', { + 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], + }), + ('diffobj', '0.3.5', { + 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], + }), + ('rematch2', '2.1.2', { + 'checksums': ['fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb'], + }), + ('waldo', '0.5.1', { + 'checksums': ['45bf076cff449e3c506c95857734bb73fdf30040333709b8845d09a12c6fdf46'], + }), + ('testthat', '3.1.9', { + 'checksums': 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['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], + }), +] + +moduleclass = 'lang' From 1110b11611267d088e3381169bbd56d44c419229 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 11 Aug 2023 16:57:22 +0100 Subject: [PATCH 8355/9987] Delete R-4.3.1-gfbf-2022b.eb --- .../easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb | 374 ------------------ 1 file changed, 374 deletions(-) delete mode 100644 easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb b/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb deleted file mode 100644 index 4d71b6f0525..00000000000 --- a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2022b.eb +++ /dev/null @@ -1,374 +0,0 @@ -name = 'R' -version = '4.3.1' - -homepage = 'https://www.r-project.org/' -description = """R is a free software environment for statistical computing - and graphics.""" - -toolchain = {'name': 'gfbf', 'version': '2022b'} - -source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] -sources = [SOURCE_TAR_GZ] -checksums = ['8dd0bf24f1023c6f618c3b317383d291b4a494f40d73b983ac22ffea99e4ba99'] - -builddependencies = [ - ('pkgconf', '1.9.3'), - ('Xvfb', '21.1.6'), - ('Autotools', '20220317'), -] -dependencies = [ - ('X11', '20221110'), - ('Mesa', '22.2.4'), - ('libGLU', '9.0.2'), - ('cairo', '1.17.4'), - ('libreadline', '8.2'), - ('ncurses', '6.3'), - ('bzip2', '1.0.8'), - ('XZ', '5.2.7'), - ('zlib', '1.2.12'), - ('SQLite', '3.39.4'), - ('PCRE2', '10.40'), - ('libpng', '1.6.38'), # for plotting in R - ('libjpeg-turbo', '2.1.4'), # for plottting in R - ('LibTIFF', '4.4.0'), - ('Java', '11', '', SYSTEM), - ('libgit2', '1.5.0'), - ('OpenSSL', '1.1', '', SYSTEM), - ('cURL', '7.86.0'), - ('Tk', '8.6.12'), # for tcltk - ('libxml2', '2.10.3'), # for XML - ('HarfBuzz', '5.3.1'), # for textshaping - ('FriBidi', '1.0.12'), # for textshaping - -] - -# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. -# Adding it to FLIBS makes sure it is present when needed. -preconfigopts = 'export FLIBS="$FLIBS -lm" && ' - -configopts = "--with-pic --enable-threads --enable-R-shlib" -# some recommended packages may fail in a parallel build (e.g. Matrix), and -# we're installing them anyway below -configopts += " --with-recommended-packages=no" - -# specify that at least EasyBuild v3.5.0 is required, -# since we rely on the updated easyblock for R to configure correctly w.r.t. 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}), - ('sys', '3.4.2', { - 'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'], - }), - ('askpass', '1.1', { - 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], - }), - ('openssl', '2.0.6', { - 'checksums': ['77f3032a16270f0d1734f269b8d348eedc75b277812854386091143082c1b3f3'], - }), - ('httr', '1.4.6', { - 'checksums': ['8d6d86cbef23738d2b4390490f7486d8cf7674f0a59c19f515f61cad35ec37b2'], - }), - ('jquerylib', '0.1.4', { - 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], - }), - ('rappdirs', '0.3.3', { - 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], - }), - ('sass', '0.4.6', { - 'checksums': ['2ee82ce709b7fdee78f7e2364d04f369f58fc2cda4bb5a235bd53c49d311c019'], - }), - ('purrr', '1.0.1', { - 'checksums': ['0a7911be3539355a4c40d136f2602befcaaad5a3f7222078500bfb969a6f2ba2'], - }), - ('cachem', '1.0.8', { - 'checksums': ['ea9ca919fe615dce8770758ecc2fc88ac99074f66ff1cde3a0b95d40007f45c2'], - }), - ('memoise', '2.0.1', { - 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], - }), - ('bslib', '0.5.0', { - 'checksums': ['a2c6fbc62242806e10bb58c5d1ba04a6d3bf4e546bc53d7acf1b8eb1160bd115'], - }), - ('fontawesome', '0.5.0', { - 'checksums': ['4117b417a33e82d626881d7059eb54e7534cba202e75dae7e27021cb3796e90b'], - }), - ('tinytex', '0.45', { - 'checksums': ['0c2fbbd09e80af80ca6b685bf0653f070da97b85413d39af966aba28f376e92c'], - }), - ('rmarkdown', '2.22', { - 'checksums': ['c6635519503e0fcdd518696d3ac96d8d28d9d4ecd9db0532c53426002f6387b8'], - }), - ('downlit', '0.4.2', { - 'checksums': ['33dff66909104d1a5ba8e57b1288986e82b61fd5e91dce0cd358d53724b37e3c'], - }), - ('cpp11', '0.4.3', { - 'checksums': ['f1a60e4971a86dbbcf6a16bbd739b59bb66d9c45d93cfd8dedc2a87e302598f1'], - }), - ('systemfonts', '1.0.4', { - 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], - }), - ('textshaping', '0.3.6', { - 'checksums': ['80e2c087962f55ce2811fbc798b09f5638c06c6b28c10cd3cb3827005b902ada'], - }), - ('ragg', '1.2.5', { - 'checksums': ['936f4d75e0e01cdeefb9f57d121cdd7812d0de5a9e1a3a8315f92ce1c84da8f9'], - }), - ('whisker', '0.4.1', { - 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], - }), - ('pkgdown', '2.0.7', { - 'checksums': ['f33872869dfa8319182d87e90eab3245ff69293b3b791471bf9538afb81b356a'], - }), - ('htmlwidgets', '1.6.2', { - 'checksums': ['7fda1672a4c0fbc203c790677b6ee7c40d2c2d72be4f6772f75288fc712b10bc'], - }), - ('profvis', '0.3.8', { - 'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'], - }), - ('urlchecker', '1.0.1', { - 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], - }), - ('later', '1.3.1', { - 'checksums': ['23eed681f0b9eacebbc3c6a5ba14ee0b676a4bf6e69af194c5a36edfe11464ac'], - }), - ('promises', '1.2.0.1', { - 'checksums': ['8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7'], - }), - ('xtable', '1.8-4', { - 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], - }), - ('httpuv', '1.6.11', { - 'checksums': ['8ba79e0a8351274daf2dc566c71f88e891127cdedca62ad77a4b27a8103eeef5'], - }), - ('sourcetools', '0.1.7-1', { - 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], - }), - ('shiny', '1.7.4', { - 'checksums': ['bbfcdd7375013b8f59248b3f3f4e752acd445feb25179f3f7f65cd69614da4b5'], - }), - ('miniUI', '0.1.1.1', { - 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], - }), - ('brew', '1.0-8', { - 'checksums': ['11652d5a7042d645cc5be5f9f97ff4d46083cea7d3ad2dd6ad1570b52c097826'], - }), - ('roxygen2', '7.2.3', { - 'checksums': ['d844fab977d2575ab942fa1309ac7ff67f35f099a75d8b41c79efe6ea10416da'], - }), - ('rversions', '2.1.2', { - 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], - }), - ('sessioninfo', '1.2.2', { - 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], - }), - ('xopen', '1.0.0', { - 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], - }), - ('rcmdcheck', '1.4.0', { - 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], - }), - ('remotes', '2.4.2', { - 'checksums': ['f2ef875f24a485bf4f55a8c830f87cdd5db868f9a8cdb624dc452d0bf66ba516'], - }), - ('clipr', '0.8.0', { - 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], - }), - ('ini', '0.3.1', { - 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], - }), - ('gitcreds', '0.1.2', { - 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], - }), - ('httr2', '0.2.3', { - 'checksums': ['352032029512f28f6f440ace0078e859ad3945d6b20841963b372523b6974b3d'], - }), - ('gh', '1.4.0', { - 'checksums': ['68c69fcd18429b378e639a09652465a4e92b7b5b5704804d0c5b1ca2b9b58b71'], - }), - ('credentials', '1.3.2', { - 'checksums': ['2ffa7c11bedbfa034adf553d0a2f2e4f6a496b858af753a09a89219cff9028b8'], - }), - ('zip', '2.3.0', { - 'checksums': ['33eba844922af9981732ee6ec1582d46cf04c562344f09a0f0f14a22c6f74543'], - }), - ('gert', '1.9.2', { - 'checksums': ['42ca1b4bcafb1fdbbc7f54df0ee4476ecd19e9e7d563b53fe7064e0086ab665e'], - }), - ('usethis', '2.2.0', { - 'checksums': ['2ccebe690aadebff96451cc9c226dc1a1e9ca5ac6ec83310e12a1312cb163b4f'], - }), - ('devtools', '2.4.5', { - 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], - }), -] - -moduleclass = 'lang' From e2a106985824b0e2fd6a811f0d6caf44027fb617 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 11 Aug 2023 17:07:29 +0100 Subject: [PATCH 8356/9987] libGLU was merged after I triggered the build test... --- .../l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb deleted file mode 100644 index 29f37b7fefc..00000000000 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libGLU' -version = '9.0.3' - -homepage = 'https://mesa.freedesktop.org/archive/glu/' -description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://mesa.freedesktop.org/archive/glu/'] -sources = ['glu-%(version)s.tar.xz'] -checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] - -builddependencies = [('binutils', '2.40')] - -dependencies = [ - ('Mesa', '23.1.4'), -] - -sanity_check_paths = { - 'files': ['lib/libGLU.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' From 3bc371eae8697038bcbbefcfe6e58a461c1a494c Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 11 Aug 2023 18:41:06 +0200 Subject: [PATCH 8357/9987] updated to v21.1.8 and components --- .../x/Xvfb/Xvfb-21.1.8-GCCcore-12.3.0.eb | 123 ++++++++++++++++++ 1 file changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.8-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.8-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5e25aa280fe --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.8-GCCcore-12.3.0.eb @@ -0,0 +1,123 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '21.1.8' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Python', '3.11.3'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('libxslt', '1.1.38'), + ('gettext', '0.21.1'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('X11', '20230603'), + ('pixman', '0.42.2'), + ('libdrm', '2.4.115'), + ('Mesa', '23.1.4'), + ('nettle', '3.9.1'), + ('libunwind', '1.6.2'), + ('XZ', '5.4.2'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.2', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['4a5af55e670713024639a7f7d10826d905d86faf574cd77e0f5aef2d00e70168'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.4.0', { + 'checksums': ['30b90fe52347916be9b08f95f717f17c9c1f58bef8cabb49014d0fdd2b0df643'], + }), + ('font-misc-misc', '1.1.3', { + 'checksums': ['bece4a9482b3cb6f7fad2164fd3b394d22dfe1ad2f96f60030a703bcff30f5a5'], + 'preconfigopts': local_font_misc_preconfigopts, + }), + ('xkbcomp', '1.4.6', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['b216a2c8c0eab83f3dc4a3d5ee2bdf7827b30e49c8907035d0f222138eca0987'], + }), + ('xkeyboard-config', '2.39', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['5ac5f533eff7b0c116805fe254fd79b2c9882700a4f9f2c070f8c4eae5aaa682'], + 'configopts': '-Dxorg-rules-symlinks=true', + }), + ('xauth', '1.1.2', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['84d27a1023d8da524c134f424b312e53cb96e08871f96868aa20316bfcbbc054'], + }), + ('libxcvt', '0.1.2', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/lib/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['0561690544796e25cfbd71806ba1b0d797ffe464e9796411123e79450f71db38'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual/xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + 'd845d1fee2edb33cb94f31b5170f26d98ed31f853ce2da21daca7c60c8ff3aae', # xorg-server-21.1.3.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' From b2cc1896c30b6c6128608de8e622e57586dc93e1 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 11 Aug 2023 18:50:36 +0200 Subject: [PATCH 8358/9987] removed outdated file --- .../x/Xvfb/Xvfb-21.1.6-GCCcore-12.3.0.eb | 123 ------------------ 1 file changed, 123 deletions(-) delete mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.3.0.eb deleted file mode 100644 index f6147301b31..00000000000 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.3.0.eb +++ /dev/null @@ -1,123 +0,0 @@ -easyblock = 'Bundle' - -name = 'Xvfb' -version = '21.1.6' - -homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' -description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. - It emulates a dumb framebuffer using virtual memory.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('pkgconf', '1.9.5'), - ('Python', '3.11.3'), - ('Meson', '1.1.1'), - ('Ninja', '1.11.1'), - ('libxslt', '1.1.38'), - ('gettext', '0.21.1'), - ('Bison', '3.8.2'), -] - -dependencies = [ - ('X11', '20230603'), - ('pixman', '0.42.2'), - ('libdrm', '2.4.115'), - ('Mesa', '23.1.4'), - ('nettle', '3.9.1'), - ('libunwind', '1.6.2'), - ('XZ', '5.4.2'), -] - -default_easyblock = 'ConfigureMake' - -local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " -local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " -local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" - -# use 'make V=1' to see compiler commands -local_xvfb_buildopts = "V=1 " - -# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" -local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' -local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' - -default_component_specs = { - 'source_urls': ['https://www.x.org/archive/individual/font/'], - 'sources': [SOURCE_TAR_GZ], - 'start_dir': '%(name)s-%(version)s', -} - -local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " -local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " - -components = [ - ('mkfontscale', '1.2.2', { - 'source_urls': ['https://www.x.org/archive/individual/app/'], - 'checksums': ['4a5af55e670713024639a7f7d10826d905d86faf574cd77e0f5aef2d00e70168'], - }), - ('mkfontdir', '1.0.7', { - 'source_urls': ['https://www.x.org/archive/individual/app/'], - 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], - }), - ('bdftopcf', '1.1', { - 'source_urls': ['https://www.x.org/archive/individual/app/'], - 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], - }), - ('font-util', '1.3.3', { - 'checksums': ['2094dd4a1ca63a61deb101d2dc618682d6e287cdbe09679502223ac445d277dc'], - }), - ('font-misc-misc', '1.1.2', { - 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], - 'preconfigopts': local_font_misc_preconfigopts, - }), - ('xkbcomp', '1.4.6', { - 'source_urls': ['https://www.x.org/archive/individual/app/'], - 'checksums': ['b216a2c8c0eab83f3dc4a3d5ee2bdf7827b30e49c8907035d0f222138eca0987'], - }), - ('xkeyboard-config', '2.37', { - 'easyblock': 'MesonNinja', - 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], - 'sources': [SOURCE_TAR_XZ], - 'checksums': ['eb1383a5ac4b6210d7c7302b9d6fab052abdf51c5d2c9b55f1f779997ba68c6c'], - 'configopts': '-Dxorg-rules-symlinks=true', - }), - ('xauth', '1.1.2', { - 'source_urls': ['https://www.x.org/releases/individual/app/'], - 'checksums': ['84d27a1023d8da524c134f424b312e53cb96e08871f96868aa20316bfcbbc054'], - }), - ('libxcvt', '0.1.2', { - 'easyblock': 'MesonNinja', - 'source_urls': ['https://www.x.org/archive/individual/lib/'], - 'sources': [SOURCE_TAR_XZ], - 'checksums': ['0561690544796e25cfbd71806ba1b0d797ffe464e9796411123e79450f71db38'], - }), - (name, version, { - 'source_urls': ['https://www.x.org/releases/individual/xserver/'], - 'sources': ['xorg-server-%(version)s.tar.gz'], - 'patches': [('xvfb-run', '.')], - 'checksums': [ - '6f9c73ccc50e2731adac17671c8e33687738c8cd556b49ecb9f410ce7217be11', # xorg-server-21.1.3.tar.gz - 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run - ], - 'start_dir': 'xorg-server-%(version)s', - 'configopts': local_xvfb_configopts, - 'buildopts': local_xvfb_buildopts, - 'installopts': local_xvfb_buildopts, - }), -] - -postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] - -sanity_check_paths = { - 'files': ['bin/Xvfb', 'bin/xvfb-run'], - 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], -} - -sanity_check_commands = [ - "xvfb-run --help", - "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", -] - -moduleclass = 'vis' From 14ff9cbd1fff55c2ae4d7d6f70af3fb6db377b6c Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 11 Aug 2023 10:58:31 -0700 Subject: [PATCH 8359/9987] update igraph, leidenalg igraph --- .../i/igraph/igraph-0.10.6-foss-2022b.eb | 40 +++++++++++++ .../leidenalg/leidenalg-0.10.1-foss-2022b.eb | 45 +++++++++++++++ .../libleidenalg-0.11.1-foss-2022b.eb | 29 ++++++++++ .../python-igraph-0.10.6-foss-2022b.eb | 57 +++++++++++++++++++ 4 files changed, 171 insertions(+) create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.10.6-foss-2022b.eb create mode 100644 easybuild/easyconfigs/l/leidenalg/leidenalg-0.10.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.10.6-foss-2022b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.10.6-foss-2022b.eb new file mode 100644 index 00000000000..5c3e27e113c --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.10.6-foss-2022b.eb @@ -0,0 +1,40 @@ +# Author: Denis Krišťák (INUITS) +# Modified: Jasper Grimm (UoY) + +easyblock = 'CMakeMake' + +name = 'igraph' +version = '0.10.6' + +homepage = 'https://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = [] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('GLPK', '5.0'), + ('libxml2', '2.10.3'), + ('zlib', '1.2.12'), + ('arpack-ng', '3.8.0'), +] + +# Build static and shared libraries +configopts = ["-DBUILD_SHARED_LIBS=OFF", "-DBUILD_SHARED_LIBS=ON"] + +sanity_check_paths = { + 'files': ['include/igraph/igraph.h'] + ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.10.1-foss-2022b.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.10.1-foss-2022b.eb new file mode 100644 index 00000000000..1ea193ccc14 --- /dev/null +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.10.1-foss-2022b.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'leidenalg' +version = '0.10.1' + +homepage = 'https://github.com/vtraag/leidenalg' +description = """Implementation of the Leiden algorithm for various quality +functions to be used with igraph in Python.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('PyYAML', '6.0'), + ('Bison', '3.8.2'), + ('libtool', '2.4.7'), + ('flex', '2.6.4'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('igraph', '0.10.6'), + ('python-igraph', '0.10.6'), + ('libleidenalg', '0.11.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ddt', '1.6.0', { + 'checksums': ['f71b348731b8c78c3100bffbd951a769fbd439088d1fdbb3841eee019af80acd'], + }), + (name, version, { + 'checksums': ['457ad96982a80bd5c657189f42dfeb77eebcd3b744a110e5a2c1618d2eb80b47'], + }), +] + +sanity_check_commands = [ + "python -c 'import leidenalg; import igraph as ig; " + "leidenalg.find_partition(ig.Graph.Erdos_Renyi(100, 0.1), leidenalg.ModularityVertexPartition)'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2022b.eb b/easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2022b.eb new file mode 100644 index 00000000000..58846249a0a --- /dev/null +++ b/easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2022b.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'libleidenalg' +version = '0.11.1' + +homepage = 'https://github.com/vtraag/libleidenalg' +description = """Implements the Leiden algorithm in C++""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/vtraag/libleidenalg/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['7d7392afd214c584e023cc2f0d0ac375f58575c32f2e49ba85062065f1637c7f'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('igraph', '0.10.6'), +] + +sanity_check_paths = { + 'files': ['include/%(name)s/GraphHelper.h', 'include/%(name)s/libleidenalg_export.h', 'lib/lib%(name)s.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb new file mode 100644 index 00000000000..518606828d0 --- /dev/null +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'python-igraph' +version = '0.10.6' + +homepage = 'https://igraph.org/python' +description = """Python interface to the igraph high performance graph library, primarily aimed at complex network + research and analysis.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('igraph', '0.10.6'), + ('Clang', '16.0.4'), + ('libxml2', '2.10.3'), + ('zlib', '1.2.12'), +] + +use_pip = True + +exts_list = [ + ('texttable', '1.6.4', { + 'checksums': ['42ee7b9e15f7b225747c3fa08f43c5d6c83bc899f80ff9bae9319334824076e9'], + }), + ('cairocffi', '1.6.1', { + 'checksums': ['78e6bbe47357640c453d0be929fa49cd05cce2e1286f3d2a1ca9cbda7efdb8b7'], + }), + # Project name 'python-igraph' is depreicated, use pypi package igraph instead. To avoid + # name collision within EB, continue to use the package name 'python-igraph', + # to avoid collision with igraph. + ('igraph', version, { + 'installopts': '--install-option="--use-pkg-config"', + 'modulename': 'igraph', + 'checksums': ['76f7aad294514412f835366a7d9a9c1e7a34c3e6ef0a6c3a1a835234323228e8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/igraph'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# cairo must be available for proper plotting support +sanity_check_commands = [ + "python -c 'from igraph.drawing.cairo.utils import find_cairo; " + "cairo = find_cairo(); cairo.Context'", +] + +sanity_pip_check = True + +moduleclass = 'lib' From 4e14f527bf8220e4df04c775ccbd71cb055ca80e Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 11 Aug 2023 18:05:53 +0000 Subject: [PATCH 8360/9987] Version bumps for gcccore 12.3.0 --- .../f/FFmpeg/FFmpeg-6.0-GCCcore-12.3.0.eb | 45 +++++++++++++++++++ .../f/ffnvcodec/ffnvcodec-12.0.16.0.eb | 32 +++++++++++++ .../l/LAME/LAME-3.100-GCCcore-12.3.0.eb | 36 +++++++++++++++ .../s/SDL2/SDL2-2.28.2-GCCcore-12.3.0.eb | 26 +++++++++++ .../x/x264/x264-20230226-GCCcore-12.3.0.eb | 33 ++++++++++++++ .../x/x265/x265-3.5-GCCcore-12.3.0.eb | 34 ++++++++++++++ 6 files changed, 206 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.0.16.0.eb create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.28.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/x/x264/x264-20230226-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4f5fb4a0bc5 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '6.0' + +homepage = 'https://www.ffmpeg.org/' +description = "A complete, cross-platform solution to record, convert and stream audio and video." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://%(namelower)s.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['47d062731c9f66a78380e35a19aac77cebceccd1c7cc309b9c82343ffc430c3d'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('ffnvcodec', '12.0.16.0', '', SYSTEM), # optional nvenc/dec support +] +dependencies = [ + ('NASM', '2.16.01'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('x264', '20230226'), + ('LAME', '3.100'), + ('x265', '3.5'), + ('X11', '20230603'), + ('freetype', '2.13.0'), + ('fontconfig', '2.14.2'), + ('FriBidi', '1.0.12'), + ('SDL2', '2.28.2'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi --enable-sdl2' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.0.16.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.0.16.0.eb new file mode 100644 index 00000000000..dc51b3036ce --- /dev/null +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.0.16.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ffnvcodec' +version = '12.0.16.0' + +homepage = 'https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git' + +description = """FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present +(picked up dynamically).""" + +toolchain = SYSTEM + +sources = [{ + 'git_config': { + 'url': 'https://git.videolan.org/git/ffmpeg/', + 'repo_name': 'nv-codec-headers', + 'tag': 'n%(version)s', + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +skipsteps = ['configure'] + +preinstallopts = 'sed -i "s|PREFIX =.*|PREFIX ?= %(installdir)s|" Makefile && ' + +sanity_check_paths = { + 'files': ['include/ffnvcodec/nvEncodeAPI.h', 'lib/pkgconfig/ffnvcodec.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4573d76f947 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [('ncurses', '6.4')] + +preconfigopts = "autoconf && " + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.28.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.28.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a362c41ff0b --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.28.2-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.28.2' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['64b1102fa22093515b02ef33dd8739dee1ba57e9dbba6a092942b8bbed1a1c5e'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('X11', '20230603'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/x264/x264-20230226-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/x264/x264-20230226-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..339fbb46631 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20230226-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20230226' + +homepage = 'https://www.videolan.org/developers/x264.html' +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/baee400f/'] +sources = [{'download_filename': '%(name)s-baee400f.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f32bdcd8edaae7686f5aba9d4421d07c1d01e5c3c10c2a87c8f3131bddb59905'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('NASM', '2.16.01'), +] + +configopts = " --enable-shared --enable-static --disable-bashcompletion" + + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x264_config.h', 'include/%(name)s.h', 'lib/libx264.a', 'lib/libx264.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4c754f3021d --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.5' + +homepage = 'https://x265.org/' +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://bitbucket.org/multicoreware/x265_git/downloads/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['e70a3335cacacbba0b3a20ec6fecd6783932288ebc8163ad74bcc9606477cae8'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Yasm', '1.3.0'), +] + +configopts = '-DGIT_ARCHETYPE=1' + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x265_config.h', 'include/%(name)s.h', 'lib/libx265.a', 'lib/libx265.so'], + 'dirs': [], +} + +moduleclass = 'vis' From 5054d9beae47704fad36d09992446672a99048a5 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 11 Aug 2023 22:15:48 +0200 Subject: [PATCH 8361/9987] disable parallel test for netCDF w/ iimpi --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023a.eb index 02ceb912ae5..45bd14d7e4c 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023a.eb @@ -37,7 +37,9 @@ dependencies = [ # disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso # see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 # and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 -preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/18523#issuecomment-1675313158 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 16 ./tst_parallel3|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") From cd9b9e0f218fb943debf43432907bba2020c6e68 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Aug 2023 17:14:45 +0200 Subject: [PATCH 8362/9987] fix sanity check command for IsoQuant when using --read-only-installdir --- easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb index 8496bf20113..d5d7d40f738 100644 --- a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb +++ b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb @@ -40,6 +40,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["isoquant.py --test"] +sanity_check_commands = ["cd %(builddir)s && isoquant.py --test"] moduleclass = 'bio' From 69ee91881c54942cbf99841b2d6d162c6e2325de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Aug 2023 17:27:06 +0200 Subject: [PATCH 8363/9987] make sure build directory exists before changing to it --- easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb index d5d7d40f738..004bb7d155a 100644 --- a/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb +++ b/easybuild/easyconfigs/i/IsoQuant/IsoQuant-3.3.0-foss-2022b.eb @@ -40,6 +40,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["cd %(builddir)s && isoquant.py --test"] +sanity_check_commands = ["mkdir -p %(builddir)s && cd %(builddir)s && isoquant.py --test"] moduleclass = 'bio' From b325213c92a8df7e1cfad822823aa497105490b0 Mon Sep 17 00:00:00 2001 From: fizwit Date: Sun, 13 Aug 2023 14:41:44 -0700 Subject: [PATCH 8364/9987] add checksums --- easybuild/easyconfigs/i/igraph/igraph-0.10.6-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.10.6-foss-2022b.eb b/easybuild/easyconfigs/i/igraph/igraph-0.10.6-foss-2022b.eb index 5c3e27e113c..6945d8d2c8e 100644 --- a/easybuild/easyconfigs/i/igraph/igraph-0.10.6-foss-2022b.eb +++ b/easybuild/easyconfigs/i/igraph/igraph-0.10.6-foss-2022b.eb @@ -16,7 +16,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -checksums = [] +checksums = ['99bf91ee90febeeb9a201f3e0c1d323c09214f0b5f37a4290dc3b63f52839d6d'] builddependencies = [ ('CMake', '3.24.3'), From bd7e08bcebb3c48c2a351a101032a58a32e64665 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Aug 2023 15:17:47 +0200 Subject: [PATCH 8365/9987] add decoupleR extension to R-bundle-Bioconductor v3.16 --- .../R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index cf9d68930ab..392353a7d4b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -1241,6 +1241,9 @@ exts_list = [ ('ANCOMBC', '2.0.2', { 'checksums': ['e577ffe62a86090de9ea3743c84a4f3b34c3d645dcedff3c8af675b8c9b69136'], }), + ('decoupleR', '2.4.0', { + 'checksums': ['b141afd331449b0b1c2dc3dc3097465c2c02b5026129d8f06dd5bfb445bce2a0'], + }), ('UCell', '2.2.0', { 'checksums': ['e3ca2b2d77a780a9450853e869bc10654c47485777d39a703203dc44d97df4bc'], }), From 1d6dcd1cfc831738bdb2ca9313e69ce0e22d5301 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 14 Aug 2023 15:29:08 +0200 Subject: [PATCH 8366/9987] Add Score-P and deps --- .../c/CubeLib/CubeLib-4.8.1-GCCcore-12.3.0.eb | 53 ++++++++++++++++ .../CubeWriter-4.8.1-GCCcore-12.3.0.eb | 53 ++++++++++++++++ .../o/OPARI2/OPARI2-2.0.7-GCCcore-12.3.0.eb | 44 +++++++++++++ .../o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb | 50 +++++++++++++++ .../p/PAPI/PAPI-7.0.1-GCCcore-12.3.0.eb | 47 ++++++++++++++ .../p/PDT/PDT-3.25.1-GCCcore-12.3.0.eb | 37 +++++++++++ .../SIONlib-1.7.7-GCCcore-12.3.0-tools.eb | 51 +++++++++++++++ .../s/Score-P/Score-P-8.1-gompi-2023a.eb | 63 +++++++++++++++++++ 8 files changed, 398 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.0.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2023a.eb diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a0851bdeed2 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.1-GCCcore-12.3.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.8.1' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e4d974248963edab48c5d0fc5831146d391b0ae4632cccafe840bf5f12cd80a9'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1bad3eecd60 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.1-GCCcore-12.3.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.8.1' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['42cbd743d87c16e805c8e28e79292ab33de259f2cfba46f2682cb35c1bc032d6'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d048428c4ea --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.7' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e302a4cc265eb2a4aa27c16a90eabd9e1e58cb02a191dd1c4d86f9a0df128715'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..17595d97acb --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '3.0.3' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['18a3905f7917340387e3edc8e5766f31ab1af41f4ecc5665da6c769ca21c4ee8'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.7', '-tools'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4db6443b5c6 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.1-GCCcore-12.3.0.eb @@ -0,0 +1,47 @@ +## +# Author: Robert Mijakovic +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.0.1' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://icl.utk.edu/projects/papi/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c105da5d8fea7b113b0741a943d467a06c98db959ce71bdd9a50b9f03eecc43e'] + +builddependencies = [ + ('binutils', '2.40'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b1b6694ef76 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25.1' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +checksums = ['0b6f8a6b8769c181b2ae6cae7298f04b8e3e3d68066f598ed24574e19500bc97'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb new file mode 100644 index 00000000000..7cae952e521 --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-12.3.0-tools.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.7' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2023a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2023a.eb new file mode 100644 index 00000000000..18929869269 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.1-gompi-2023a.eb @@ -0,0 +1,63 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2023 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '8.1' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +patches = ['Score-P-8.0_fix-race-in-CUDA-adapter.patch'] +checksums = [ + {'scorep-8.1.tar.gz': '3a40b481fce610871ddf6bdfb88a6d06b9e5eb38c6080faac6d5e44990060a37'}, + {'Score-P-8.0_fix-race-in-CUDA-adapter.patch': '6ba0e486fedc9a87b9b1a4657af7ee5f95b6222ee68ddaa5363dcaa99171fa0b'}, +] + +dependencies = [ + ('CubeLib', '4.8.1'), + ('CubeWriter', '4.8.1'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 85fbae676d4c895e8a01f7b4434aeb7de243b25d Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 14 Aug 2023 15:42:54 +0200 Subject: [PATCH 8367/9987] adding easyconfigs: GLM-0.9.9.8-GCCcore-12.3.0.eb --- .../g/GLM/GLM-0.9.9.8-GCCcore-12.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4333f4a93a0 --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '0.9.9.8' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'GLM-0.9.9.8_fix_missing_install.patch', +] +checksums = [ + '7d508ab72cb5d43227a3711420f06ff99b0a0cb63ee2f93631b162bfe1fe9592', # 0.9.9.8.tar.gz + '1cc199f9d66679b0b5e9a9fbe20bca0d9b15760fa172ca8759dd15bab35802ca', # GLM-0.9.9.8_fix_missing_install.patch +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' From 420f203f67fc7533122d0b87418f3a67cf147dc1 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 14 Aug 2023 16:24:09 +0200 Subject: [PATCH 8368/9987] Add OpenImageIO and deps --- .../i/Imath/Imath-3.1.9-GCCcore-12.3.0.eb | 28 +++++++++++++ .../l/LibTIFF/LibTIFF-4.5.1-GCCcore-12.3.0.eb | 38 ++++++++++++++++++ .../OpenEXR/OpenEXR-3.1.11-GCCcore-12.3.0.eb | 38 ++++++++++++++++++ .../OpenImageIO-2.4.14.0-GCC-12.3.0.eb | 39 +++++++++++++++++++ 4 files changed, 143 insertions(+) create mode 100644 easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.11-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..84aa9eab311 --- /dev/null +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Imath' +version = '3.1.9' + +homepage = 'https://imath.readthedocs.io/en/latest/' +description = """ +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f1d8aacd46afed958babfced3190d2d3c8209b66da451f556abd6da94c165cf3'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libImath.%s' % SHLIB_EXT], + 'dirs': ['include/Imath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..13168f0ae95 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.1-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.5.1' + +homepage = 'https://libtiff.gitlab.io/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['d7f38b6788e4a8f5da7940c5ac9424f494d8a79eba53d555f4a507167dca5e2b'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('zlib', '1.2.13'), + ('libjpeg-turbo', '2.1.5.1'), + ('XZ', '5.4.2'), + ('jbigkit', '2.1'), + ('zstd', '1.5.5'), + ('libdeflate', '1.18'), +] + +configopts = "--enable-ld-version-script " +configopts += "--disable-webp --disable-sphinx " + +sanity_check_paths = { + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], + 'dirs': [], +} + +sanity_check_commands = ["tiffinfo -h"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.11-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..13081d814c9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.11-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.11' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['06b4a20d0791b5ec0f804c855d320a0615ce8445124f293616a086e093f1f1e1'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Imath', '3.1.9'), + ('zlib', '1.2.13') +] + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..6735165af31 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'OpenImageIO' +version = '2.4.14.0' + +homepage = 'https://openimageio.org/' +description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, + and applications.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['92ad4b107394b273397baa1abe90207e1f8ef9fd52ffbfc23b46e3b0005d4439'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('git', '2.41.0', '-nodocs'), +] +dependencies = [ + ('Boost', '1.82.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.1'), + ('OpenEXR', '3.1.11'), + ('freetype', '2.13.0'), + ('zlib', '1.2.13'), +] + +separate_build_dir = True + +configopts = '-DSTOP_ON_WARNING=OFF -DUSE_PYTHON=OFF' + +sanity_check_paths = { + 'files': ['bin/oiiotool', 'lib/libOpenImageIO.%s' % SHLIB_EXT, 'lib/libOpenImageIO_Util.%s' % SHLIB_EXT], + 'dirs': ['include/OpenImageIO', 'share'], +} + +moduleclass = 'lib' From c679ad13875d8d7fa3767e0da6081bc720fb08ed Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 14 Aug 2023 16:41:14 +0200 Subject: [PATCH 8369/9987] Add ATK --- .../a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e975d98ac9c --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.38.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('GObject-Introspection', '1.76.1'), +] + +dependencies = [ + ('GLib', '2.77.1'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 316ef0bae7ccfc50d38db1c10a17212e43cf2a15 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 14 Aug 2023 14:43:31 +0000 Subject: [PATCH 8370/9987] Restore comments removed by checksum injection --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index ab9aacdb9a4..61bd80b3573 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -78,6 +78,9 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 17th March 2023 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets', @@ -2370,6 +2373,7 @@ exts_list = [ 'checksums': ['be50f9fdef0f4bf9676b9c3c2906d0431afc678af55cf48b1119f9fc0adac44f'], }), ('liquidSVM', '1.2.4', { + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ @@ -2885,8 +2889,12 @@ exts_list = [ 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], }), ('gWidgets2tcltk', '1.0-8', { - 'modulename': False, + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], }), ('mgsub', '1.7.3', { From b3b9017813e082c49a4a392b0a6267f8c3d8084c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Aug 2023 16:47:48 +0200 Subject: [PATCH 8371/9987] {chem}[foss/2022b] CP2K v2023.1, PLUMED v2.9.0, Libint v2.7.2, libvori v220621 libxsmm v1.17, xxd 9.0.1696 --- .../c/CP2K/CP2K-2023.1-foss-2022b.eb | 40 +++++++++++++ .../Libint-2.7.2-GCC-12.2.0-lmax-6-cp2k.eb | 52 ++++++++++++++++ .../libvori/libvori-220621-GCCcore-12.2.0.eb | 27 +++++++++ .../l/libxsmm/libxsmm-1.17-GCC-12.2.0.eb | 27 +++++++++ .../p/PLUMED/PLUMED-2.9.0-foss-2022b.eb | 60 +++++++++++++++++++ .../x/xxd/xxd-9.0.1696-GCCcore-12.2.0.eb | 37 ++++++++++++ 6 files changed, 243 insertions(+) create mode 100644 easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-12.2.0-lmax-6-cp2k.eb create mode 100644 easybuild/easyconfigs/l/libvori/libvori-220621-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/x/xxd/xxd-9.0.1696-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2022b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2022b.eb new file mode 100644 index 00000000000..267e5d1b631 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2023.1-foss-2022b.eb @@ -0,0 +1,40 @@ +## +# Author: Robert Mijakovic +## +name = 'CP2K' +version = '2023.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['dff343b4a80c3a79363b805429bdb3320d3e1db48e0ff7d20a3dfd1c946a51ce'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('Libint', '2.7.2', '-lmax-6-cp2k'), + ('libxc', '6.1.0'), + ('libxsmm', '1.17'), + ('libvori', '220621'), + ('FFTW', '3.3.10'), + ('PLUMED', '2.9.0'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-12.2.0-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-12.2.0-lmax-6-cp2k.eb new file mode 100644 index 00000000000..5ce194eec7a --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.7.2-GCC-12.2.0-lmax-6-cp2k.eb @@ -0,0 +1,52 @@ +## +# This easyconfig is based on the easy config written originally by Robert Mijakovic +# Author: Ben Czaja (SURF) +## +name = 'Libint' +version = '2.7.2' +local_lmax = 6 +# custom configuration, to be used as dependency for CP2K +versionsuffix = '-lmax-%s-cp2k' % local_lmax + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/evaleev/libint/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Libint-2.7.2_remove-test-permute.patch', + 'Libint-2.7.2_remove-test-eri.patch', +] +checksums = [ + 'fd0466ce9eb6786b8c5bbe3d510e387ed44b198a163264dfd7e60b337e295fd9', # v2.7.2.tar.gz + 'b019e66a2a3dc7e83ee8a60aa1ae78955a8af4df90ab07b7e57d2ee004ce3677', # Libint-2.7.2_remove-test-permute.patch + '4dd7b2993b6fdebb57e5c14faa9bf46117ae42100c686ace82fe26b7cb0312ab', # Libint-2.7.2_remove-test-eri.patch +] + +builddependencies = [ + ('Autotools', '20220317'), + ('GMP', '6.2.1'), + ('Boost', '1.81.0'), + ('Eigen', '3.4.0'), + ('Python', '3.10.8'), + ('CMake', '3.24.3'), +] + +# configure options as required by CP2K, +# see Jenkinsfile in https://github.com/cp2k/libint-cp2k +local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) +local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) + +libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax +libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am +libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--enable-generic-code --disable-unrolling' + +with_fortran = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libvori/libvori-220621-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libvori/libvori-220621-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a68e263572c --- /dev/null +++ b/easybuild/easyconfigs/l/libvori/libvori-220621-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'libvori' +version = '220621' + +homepage = 'https://brehm-research.de/libvori.php' +description = """C++ library implementing the Voronoi integration as well as the compressed bqb +file format. The present version of libvori is a very early development +version, which is hard-coded to work with the CP2k program package.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://brehm-research.de/files/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1cfa98c564814bddacf1c0e7f11582137d758668f6307e6eb392c72317984c14'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['lib/libvori.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.2.0.eb new file mode 100644 index 00000000000..bd19b03924f --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.17' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb new file mode 100644 index 00000000000..c0b69eef9b1 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb @@ -0,0 +1,60 @@ +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.9.0' + +homepage = 'https://www.plumed.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['534db9ccb9446844f3e99ecdff091ad79c014ce9c4afe212c1536e19f85ab0d1'] + +builddependencies = [ + ('xxd', '9.0.1696'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('GSL', '2.7'), + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Boost', '1.81.0'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' +configopts += '--enable-boost_graph --enable-boost_serialization ' +configopts += '--enable-asmjit ' +prebuildopts = 'source sourceme.sh && ' + +# make sure that ld.gold linker is used +# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564" +# (problem with intel build but maintain consistency between easyconfigs) +buildopts = 'LD_RO="ld.gold -r -o"' + +# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed +preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import plumed'"] + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', + 'PYTHONPATH': 'lib/plumed/python', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/xxd/xxd-9.0.1696-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/xxd/xxd-9.0.1696-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..cec129e0d28 --- /dev/null +++ b/easybuild/easyconfigs/x/xxd/xxd-9.0.1696-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +# Last contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'xxd' +version = '9.0.1696' + +homepage = 'https://www.vim.org' +description = """xxd is part of the VIM package and this will only install xxd, not vim! +xxd converts to/from hexdumps of binary files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/vim/vim/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['43c37b7e491e8ebf186b8459301740186cb1c21ae24c3b277fa26c8d4b64e656'] + +builddependencies = [ + ('binutils', '2.39'), +] + +start_dir = 'src/xxd' + +files_to_copy = [ + (['xxd'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/xxd'], + 'dirs': [], +} + +sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"] + +moduleclass = 'tools' From 3e4ee4124aad6cccbe27adf3ab4267c5b3569b9f Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 15 Aug 2023 10:58:17 +0200 Subject: [PATCH 8372/9987] Qt5-5.15.10 --- .../q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb | 78 ++++++++++++++++++ .../q/Qt5/Qt5-5.15.10_fix-OF-Gentoo.patch | 82 +++++++++++++++++++ ..._fix-qtwebengine-breakpad-glibc-2.34.patch | 11 +++ 3 files changed, 171 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-OF-Gentoo.patch create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0f93f7aa7d7 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb @@ -0,0 +1,78 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.15.10' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] +patches = [ + 'Qt5-5.13.1_fix-avx2.patch', + 'Qt5-5.13.1_fix-qmake-libdir.patch', + 'Qt5-5.15.10_fix-OF-Gentoo.patch', + 'Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch', + 'Qt5-5.15.7_GCC-12.patch', +] +checksums = [ + {'qt-everywhere-opensource-src-5.15.10.tar.xz': 'b545cb83c60934adc9a6bbd27e2af79e5013de77d46f5b9f5bb2a3c762bf55ca'}, + {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, + {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, + {'Qt5-5.15.10_fix-OF-Gentoo.patch': '1c4d3b974422dadb4fd62f79581d48d25ae3d5f5f21489ae8c632e43e2e5286b'}, + {'Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch': + '6890bc538b228ce0f41f09015ea52315471c69fb6ac2f615b9d881e3e8f55fc9'}, + {'Qt5-5.15.7_GCC-12.patch': '9a5bde91b223a3e2e90d3d6bec107af69a1a0f18d789593738a953080473fa68'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + # deps for QtWebEngine + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.11.1'), + ('Python', '3.11.3'), + ('re2c', '3.1'), +] + +dependencies = [ + ('double-conversion', '3.3.0'), + ('GLib', '2.77.1'), + ('PCRE2', '10.42'), + ('libpng', '1.6.39'), + ('HarfBuzz', '5.3.1'), + ('graphite2', '1.3.14'), + # deps for QtWebEngine + ('X11', '20230603'), + ('fontconfig', '2.14.2'), + ('DBus', '1.15.4'), + ('libevent', '2.1.12'), + ('libGLU', '9.0.3'), + ('libjpeg-turbo', '2.1.5.1'), + ('NSS', '3.89.1'), + ('snappy', '1.1.10'), + ('JasPer', '4.0.0'), + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), + ('ICU', '73.2'), + ('nodejs', '18.17.1'), +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +# qtwayland fails to build on (some) Centos 7 systems +configopts = '-skip qtgamepad -skip qtwayland' + +# make sure QtWebEngine component is being built & installed +check_qtwebengine = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-OF-Gentoo.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-OF-Gentoo.patch new file mode 100644 index 00000000000..9ec986bc88f --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-OF-Gentoo.patch @@ -0,0 +1,82 @@ +fix compilation on top of zlib provided by Gentoo, +where OF macro has been renamed to _Z_OF +see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 +since 5.15.10 the file has been moved from qt3d/src/3rdparty/assimp/contrib/unzip/ioapi.h to qt3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h +author: Kenneth Hoste (HPC-UGent) +diff -ru qt-everywhere-src-5.14.1.orig/qt3d/src/3rdparty/assimp/contrib/unzip/ioapi.h qt-everywhere-src-5.14.1/qt3d/src/3rdparty/assimp/contrib/unzip/ioapi.h +--- qt-everywhere-src-5.14.1.orig/qt3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h 2020-01-15 17:09:24.000000000 -0000 ++++ qt-everywhere-src-5.14.1/qt3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h 2020-09-25 18:30:03.146291932 -0000 +@@ -35,6 +35,15 @@ + extern "C" { + #endif + ++// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif ++ + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); + typedef uLong (ZCALLBACK *read_file_func) OF((voidpf opaque, voidpf stream, void* buf, uLong size)); + typedef uLong (ZCALLBACK *write_file_func) OF((voidpf opaque, voidpf stream, const void* buf, uLong size)); +diff -ru qt-everywhere-src-5.14.1.orig/qtquick3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h qt-everywhere-src-5.14.1/qtquick3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h +--- qt-everywhere-src-5.14.1.orig/qtquick3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h 2019-03-10 11:05:27.000000000 -0000 ++++ qt-everywhere-src-5.14.1/qtquick3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h 2020-09-25 18:30:16.136640746 -0000 +@@ -35,6 +35,15 @@ + extern "C" { + #endif + ++// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif ++ + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); + typedef uLong (ZCALLBACK *read_file_func) OF((voidpf opaque, voidpf stream, void* buf, uLong size)); + typedef uLong (ZCALLBACK *write_file_func) OF((voidpf opaque, voidpf stream, const void* buf, uLong size)); +diff -ru qt-everywhere-src-5.14.1.orig/qtquick3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h qt-everywhere-src-5.14.1/qtquick3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h +--- qt-everywhere-src-5.14.1.orig/qtquick3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h 2019-03-10 11:05:27.000000000 -0000 ++++ qt-everywhere-src-5.14.1/qtquick3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h 2020-09-25 18:30:23.096828085 -0000 +@@ -131,6 +131,15 @@ + + + ++// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif ++ + + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); + typedef uLong (ZCALLBACK *read_file_func) OF((voidpf opaque, voidpf stream, void* buf, uLong size)); +diff -ru qt-everywhere-src-5.14.1.orig/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h qt-everywhere-src-5.14.1/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h +--- qt-everywhere-src-5.14.1.orig/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h 2020-01-20 10:37:42.000000000 -0000 ++++ qt-everywhere-src-5.14.1/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h 2020-09-25 18:29:45.635820801 -0000 +@@ -129,8 +129,14 @@ + #endif + #endif + +- +- ++// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif + + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); + typedef uLong (ZCALLBACK *read_file_func) OF((voidpf opaque, voidpf stream, void* buf, uLong size)); diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch new file mode 100644 index 00000000000..160ebbf5a09 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch @@ -0,0 +1,11 @@ +--- a/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc 2023-08-14 14:19:20.751150000 +0200 ++++ b/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc 2023-08-14 16:59:27.366054723 +0200 +@@ -138,7 +138,7 @@ + // SIGSTKSZ may be too small to prevent the signal handlers from overrunning + // the alternative stack. Ensure that the size of the alternative stack is + // large enough. +- static const unsigned kSigStackSize = std::max(16384U, (unsigned)SIGSTKSZ); ++ static const unsigned kSigStackSize = std::max(16384U, (unsigned)SIGSTKSZ); + + // Only set an alternative stack if there isn't already one, or if the current + // one is too small. From 3b8c8828fa120fb2aa223769771df08b2e9b7ec1 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 15 Aug 2023 09:12:34 +0000 Subject: [PATCH 8373/9987] adding easyconfigs: AMRFinderPlus-3.11.18-gompi-2022b.eb, AMRFinderPlus-3.11.18-gompi-2021b.eb --- .../AMRFinderPlus-3.11.18-gompi-2021b.eb | 39 +++++++++++++++++++ .../AMRFinderPlus-3.11.18-gompi-2022b.eb | 39 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2021b.eb create mode 100644 easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2022b.eb diff --git a/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2021b.eb b/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2021b.eb new file mode 100644 index 00000000000..83542dca30f --- /dev/null +++ b/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2021b.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' +name = 'AMRFinderPlus' +version = '3.11.18' + +homepage = 'https://github.com/ncbi/amr' +description = """This software and the accompanying database are designed to find acquired antimicrobial + resistance genes and some point mutations in protein or assembled nucleotide sequences.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +github_account = 'ncbi' +source_urls = ['https://github.com/ncbi/amr/archive/'] +sources = ['amrfinder_v%(version)s.tar.gz'] +checksums = ['fef7740edf1c9548b5581141c4a254d12904e2cc7ed3d5ae4ad2ad645365aaaf'] + +dependencies = [ + ('BLAST+', '2.12.0'), + ('HMMER', '3.3.2'), + ('cURL', '7.78.0') +] + +modextrapaths = {'PATH': ''} + +# a list of binary files that will be produced +local_binaries = ['amr_report', 'amrfinder', 'amrfinder_update', 'dna_mutation', 'fasta2parts', 'fasta_check', + 'fasta_extract', 'gff_check'] + +files_to_copy = local_binaries + +sanity_check_paths = { + 'files': local_binaries, + 'dirs': [], +} + +sanity_check_commands = [ + ('amrfinder', '-h') +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2022b.eb b/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2022b.eb new file mode 100644 index 00000000000..48b14dad8f0 --- /dev/null +++ b/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2022b.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' +name = 'AMRFinderPlus' +version = '3.11.18' + +homepage = 'https://github.com/ncbi/amr' +description = """This software and the accompanying database are designed to find acquired antimicrobial + resistance genes and some point mutations in protein or assembled nucleotide sequences.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} + +github_account = 'ncbi' +source_urls = ['https://github.com/ncbi/amr/archive/'] +sources = ['amrfinder_v%(version)s.tar.gz'] +checksums = ['fef7740edf1c9548b5581141c4a254d12904e2cc7ed3d5ae4ad2ad645365aaaf'] + +dependencies = [ + ('BLAST+', '2.14.0'), + ('HMMER', '3.3.2'), + ('cURL', '7.86.0') +] + +modextrapaths = {'PATH': ''} + +# a list of binary files that will be produced +local_binaries = ['amr_report', 'amrfinder', 'amrfinder_update', 'dna_mutation', 'fasta2parts', 'fasta_check', + 'fasta_extract', 'gff_check'] + +files_to_copy = local_binaries + +sanity_check_paths = { + 'files': local_binaries, + 'dirs': [], +} + +sanity_check_commands = [ + ('amrfinder', '-h') +] + +moduleclass = 'bio' From ee8aa5fd7ec6d9b361b83b00168b66789908442f Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 15 Aug 2023 09:29:50 +0000 Subject: [PATCH 8374/9987] adding easyconfigs: prokka-1.14.5-gompi-2022b.eb, tbl2asn-20230713-linux64.eb, Bio-SearchIO-hmmer-1.7.3-GCC-12.2.0.eb --- .../Bio-SearchIO-hmmer-1.7.3-GCC-12.2.0.eb | 28 +++++++++++ .../p/prokka/prokka-1.14.5-gompi-2022b.eb | 50 +++++++++++++++++++ .../t/tbl2asn/tbl2asn-20230713-linux64.eb | 40 +++++++++++++++ 3 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.2.0.eb new file mode 100644 index 00000000000..d21b8fbf389 --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.36.0'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022b.eb new file mode 100644 index 00000000000..94b4e5939e2 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022b.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2022b'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.14.0'), + ('Java', '11', '', SYSTEM), + ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20230722'), + ('tbl2asn', '20230713', '-linux64', SYSTEM), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb new file mode 100644 index 00000000000..1f682d08a35 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CmdCp' + +name = 'tbl2asn' +version = '20230713' +versionsuffix = '-linux64' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = SYSTEM + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. +source_urls = ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])] +sources = [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:], + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}] +checksums = ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'] + +cmds_map = [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")] + +files_to_copy = [ + (['tbl2asn'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn'], + 'dirs': [], +} + +postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] + +moduleclass = 'bio' From 88545399315fe527ed5eb0c26e5e7be5ce89f7fe Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 15 Aug 2023 12:30:53 +0200 Subject: [PATCH 8375/9987] Skip test_forward_mode_AD_linalg_det_singular_cpu_complex128 and allow 2 failing test (test_quantization may randomly fail) --- .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 8 ++++++ ...13.1_skip-failing-singular-grad-test.patch | 28 +++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-failing-singular-grad-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index b9d649c5002..5eecfa1a3aa 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -39,6 +39,7 @@ patches = [ 'PyTorch-1.13.1_no-cuda-stubs-rpath.patch', 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', 'PyTorch-1.13.1_skip-failing-grad-test.patch', + 'PyTorch-1.13.1_skip-failing-singular-grad-test.patch', 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', ] checksums = [ @@ -88,6 +89,8 @@ checksums = [ {'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch': 'be83ff61fe2dedab6d49c232936d5622df81ab49154264490021c6c828e53315'}, {'PyTorch-1.13.1_skip-failing-grad-test.patch': '6681200f9509893cb9231b5c93ac9bc5e6d9d9ae4febefca52e7cbc843ba8f51'}, + {'PyTorch-1.13.1_skip-failing-singular-grad-test.patch': + '72688a57b2bb617665ad1a1d5e362c5111ae912c10936bb38a089c0204729f48'}, {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, ] @@ -139,6 +142,11 @@ excluded_tests = { runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' +# Especially test_quantization has a few corner cases that are triggered by the random input values, +# those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 +# So allow a low number of tests to fail as the tests "usually" succeed +max_failed_tests = 2 + tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-failing-singular-grad-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-failing-singular-grad-test.patch new file mode 100644 index 00000000000..0933e5a3abc --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_skip-failing-singular-grad-test.patch @@ -0,0 +1,28 @@ +TestGradientsCPU.test_forward_mode_AD_linalg_det_singular_cpu_complex128 sometimes fails with + + raise GradcheckError(_get_notallclose_msg(a, n, j, i, complex_indices, test_imag, is_forward_ad) + jacobians_str) + torch.autograd.gradcheck.GradcheckError: While considering the imaginary part of complex inputs only, Jacobian computed with forward mode mismatch for output 0 with respect to input 0, + numerical:tensor([-0.1722-0.0510j, 0.0925-0.0695j, 0.1424+0.0206j, 0.0174-0.0618j], + dtype=torch.complex128) + analytical:tensor([-0.0000+0.0000j, 0.0925-0.0695j, 0.1424+0.0206j, 0.0174-0.0618j], + dtype=torch.complex128, grad_fn=) + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/opinfo/definitions/linalg.py b/torch/testing/_internal/opinfo/definitions/linalg.py +index 0eb1ca07644..f3e5f9ec6ed 100644 +--- a/torch/testing/_internal/opinfo/definitions/linalg.py ++++ b/torch/testing/_internal/opinfo/definitions/linalg.py +@@ -1341,6 +1341,12 @@ op_db: List[OpInfo] = [ + "test_fn_fwgrad_bwgrad", + dtypes=(torch.complex128,), + ), ++ DecorateInfo( ++ unittest.skip(""), ++ "TestGradients", ++ "test_forward_mode_AD", ++ dtypes=(torch.complex128,), ++ ), + DecorateInfo( + unittest.skip("Skipped, see https://github.com//issues/84192"), + "TestGradients", From e6f86816efc9e0b4a28536f1b2fed11c81e279ec Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 15 Aug 2023 14:02:29 +0200 Subject: [PATCH 8376/9987] Change version of LibTIFF --- .../i/Imath/Imath-3.1.9-GCCcore-12.3.0.eb | 28 -------------- .../l/LibTIFF/LibTIFF-4.5.1-GCCcore-12.3.0.eb | 38 ------------------- .../OpenImageIO-2.4.14.0-GCC-12.3.0.eb | 2 +- 3 files changed, 1 insertion(+), 67 deletions(-) delete mode 100644 easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-12.3.0.eb delete mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-12.3.0.eb deleted file mode 100644 index 84aa9eab311..00000000000 --- a/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-12.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'Imath' -version = '3.1.9' - -homepage = 'https://imath.readthedocs.io/en/latest/' -description = """ -Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics -""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['f1d8aacd46afed958babfced3190d2d3c8209b66da451f556abd6da94c165cf3'] - -builddependencies = [ - ('binutils', '2.40'), - ('CMake', '3.26.3'), -] - -sanity_check_paths = { - 'files': ['lib/libImath.%s' % SHLIB_EXT], - 'dirs': ['include/Imath'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.1-GCCcore-12.3.0.eb deleted file mode 100644 index 13168f0ae95..00000000000 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.1-GCCcore-12.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'LibTIFF' -version = '4.5.1' - -homepage = 'https://libtiff.gitlab.io/libtiff/' -description = "tiff: Library and tools for reading and writing TIFF data files" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://download.osgeo.org/libtiff/'] -sources = ['tiff-%(version)s.tar.gz'] -checksums = ['d7f38b6788e4a8f5da7940c5ac9424f494d8a79eba53d555f4a507167dca5e2b'] - -builddependencies = [('binutils', '2.40')] - -dependencies = [ - ('zlib', '1.2.13'), - ('libjpeg-turbo', '2.1.5.1'), - ('XZ', '5.4.2'), - ('jbigkit', '2.1'), - ('zstd', '1.5.5'), - ('libdeflate', '1.18'), -] - -configopts = "--enable-ld-version-script " -configopts += "--disable-webp --disable-sphinx " - -sanity_check_paths = { - 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, - 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], - 'dirs': [], -} - -sanity_check_commands = ["tiffinfo -h"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb index 6735165af31..6d97dcd1daf 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('Boost', '1.82.0'), ('libjpeg-turbo', '2.1.5.1'), ('libpng', '1.6.39'), - ('LibTIFF', '4.5.1'), + ('LibTIFF', '4.5.0'), ('OpenEXR', '3.1.11'), ('freetype', '2.13.0'), ('zlib', '1.2.13'), From 334e554938b5c8d34f99461e060789c54f3ef5a0 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 15 Aug 2023 14:13:16 +0200 Subject: [PATCH 8377/9987] Downgrade OpenEXR --- .../o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb index 6d97dcd1daf..3ca74380746 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb @@ -22,7 +22,7 @@ dependencies = [ ('libjpeg-turbo', '2.1.5.1'), ('libpng', '1.6.39'), ('LibTIFF', '4.5.0'), - ('OpenEXR', '3.1.11'), + ('OpenEXR', '3.1.7'), ('freetype', '2.13.0'), ('zlib', '1.2.13'), ] From 2f78c23340b94225c453ad1d6c7ca74baa33c3bd Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 15 Aug 2023 14:13:58 +0200 Subject: [PATCH 8378/9987] Remove OpenEXR-3.1.11 --- .../OpenEXR/OpenEXR-3.1.11-GCCcore-12.3.0.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.11-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.11-GCCcore-12.3.0.eb deleted file mode 100644 index 13081d814c9..00000000000 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.11-GCCcore-12.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenEXR' -version = '3.1.11' - -homepage = 'https://www.openexr.com/' -description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic - for use in computer imaging applications""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['06b4a20d0791b5ec0f804c855d320a0615ce8445124f293616a086e093f1f1e1'] - -builddependencies = [ - ('binutils', '2.40'), - ('CMake', '3.26.3'), -] -dependencies = [ - ('Imath', '3.1.9'), - ('zlib', '1.2.13') -] - -local_libs, local_bins = [ - ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], - ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] -] - -sanity_check_paths = { - 'files': ( - ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + - ['bin/exr%s' % b for b in local_bins] - ), - 'dirs': ['include/%(name)s', 'share'], -} - -moduleclass = 'vis' From ed257048f55899d5f9db5e2d188f44c34279a95c Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 15 Aug 2023 14:34:53 +0200 Subject: [PATCH 8379/9987] add description for patch file: Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch --- ....15.10_fix-qtwebengine-breakpad-glibc-2.34.patch | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch index 160ebbf5a09..74d0b4703ad 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch @@ -1,5 +1,14 @@ ---- a/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc 2023-08-14 14:19:20.751150000 +0200 -+++ b/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc 2023-08-14 16:59:27.366054723 +0200 +Fix "no matching function" error. +Patch taken from https://bugs.gentoo.org/811312 + +From a3bc792bdc116806a50e022d9102914c8daf6210 Mon Sep 17 00:00:00 2001 +From: Martin Jansa +Date: Wed, 4 Aug 2021 19:11:06 +0200 +Subject: [PATCH] chromium: breakpad: fix build with glibc-2.34 + +diff -ruN a/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc b/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc +--- a/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc 2022-04-06 15:32:17.000000000 +0200 ++++ b/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/exception_handler.cc 2023-08-15 13:16:53.990656375 +0200 @@ -138,7 +138,7 @@ // SIGSTKSZ may be too small to prevent the signal handlers from overrunning // the alternative stack. Ensure that the size of the alternative stack is From accad0837208380e7135124feb1066eb1500018d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 15 Aug 2023 15:05:24 +0200 Subject: [PATCH 8380/9987] adding easyconfigs: napari-0.4.18-foss-2022a.eb --- .../n/napari/napari-0.4.18-foss-2022a.eb | 136 ++++++++++++++++++ 1 file changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb new file mode 100644 index 00000000000..3a33548c744 --- /dev/null +++ b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb @@ -0,0 +1,136 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2023/08 +easyblock = 'PythonBundle' + +name = 'napari' +version = '0.4.18' + +homepage = 'https://napari.org/' +description = """napari is a fast, interactive, multi-dimensional image viewer for Python. It's +designed for browsing, annotating, and analyzing large multi-dimensional images. +It's built on top of Qt (for the GUI), vispy (for performant GPU-based +rendering), and the scientific Python stack (numpy, scipy).""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyQt5', '5.15.5'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('pydantic', '1.10.2'), + ('dask', '2022.10.0'), + ('PyOpenGL', '3.1.6'), + ('imageio', '2.22.2'), + ('tqdm', '4.64.0'), + ('IPython', '8.5.0'), + ('VisPy', '0.12.2'), # vispy<0.13,>=0.12.1 + ('scikit-image', '0.19.3'), + ('matplotlib', '3.5.2'), + ('Qtconsole', '5.4.0'), + ('Pint', '0.22'), + ('wrapt', '1.15.0'), +] + +use_pip = True +sanity_pip_check = True + + +# avoid hatchling requirement to install (compare genomepy-0.15.0-foss-2022a.eb) +# (since installing it introduces conflicting version requirements with poetry included with Python) +_preinstallopts_no_hatchling = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ +_preinstallopts_no_hatchling += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ +_preinstallopts_no_hatchling += r"""-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ + + +exts_list = [ + # distributed 2022.10.0 (dask) req. tornado <6.2,>=6.0.3; Ipython provides 6.2. + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('in_n_out', '0.1.8', { + 'preinstallopts': _preinstallopts_no_hatchling, + 'checksums': ['8162af8787e682eb4b36d047f914199d80f1124e3a41420cd53de680e7d0a254'], + }), + # stick with app_model=0.1.1, because this version does not require hatchling + ('app-model', '0.1.1', { + 'checksums': ['40830455cb66441001ae25978698842eacf16e6ce1be7d737a0eaaad063de562'], + }), + ('cachey', '0.2.1', { + 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], + }), + ('lazy_loader', '0.3', { + 'checksums': ['3b68898e34f5b2a29daaaac172c6555512d0f32074f147e2254e4a6d9d838f37'], + }), + ('docstring_parser', '0.15', { + 'checksums': ['48ddc093e8b1865899956fcc03b03e66bb7240c310fac5af81814580c55bf682'], + }), + # stick with magicgui=0.6.1,because this version does not require hatchlingdue to hatchling + ('magicgui', '0.6.1', { + 'preinstallopts': _preinstallopts_no_hatchling, + 'checksums': ['319bb789c9d6f047009cf1199b59d9a304017d0447b755b9892d59a0361e5a22'], + }), + ('numpydoc', '1.5.0', { + 'checksums': ['b0db7b75a32367a0e25c23b397842c65e344a1206524d16c8069f0a1c91b5f4c'], + }), + ('psygnal', '0.9.2', { + 'preinstallopts': _preinstallopts_no_hatchling, + 'checksums': ['33010606b4a18ba09e42f622990fb3402baf0683497c3b316660edbd8d5aa2df'], + }), + ('superqt', '0.5.0', { + 'preinstallopts': _preinstallopts_no_hatchling, + 'checksums': ['a88a8671b886e8aa78b6f9978ae65bfc540dceb04f76d045079b753b2d3791b9'], + }), + ('napari-console', '0.0.8', { + 'modulename': 'napari_console', + 'checksums': ['9fa3f665ec0f5f351c364b212e73cdc4004615461dca6cbfaacf028525ec740a'], + }), + ('napari-plugin-engine', '0.2.0', { + 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], + }), + ('napari-svg', '0.1.10', { + 'checksums': ['18e642c888a71e09c9d1097f25bced1e7ef5dde1771469647bcd77975800f77d'], + }), + ('typer', '0.7.0', { + 'checksums': ['ff797846578a9f2a201b53442aedeb543319466870fbe1c701eab66dd7681165'], + }), + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + ('build', '0.10.0', { + 'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '2.1.0', { + 'modulename': 'markdown_it', + 'checksums': ['cf7e59fed14b5ae17c0006eff14a2d9a00ed5f3a846148153899a0224e2c07da'], + }), + # rich >=13.3 req pygments >=2.13, but we have 2.12 + # (MultiQC-1.14-foss-2022a: rich 13.3.1) + ('rich', '13.2.0', { + 'checksums': ['f1a00cdd3eebf999a15d85ec498bfe0b1a77efe9b34f645768a54132ef444ac5'], + }), + ('npe2', '0.7.2', { + 'preinstallopts': _preinstallopts_no_hatchling, + 'checksums': ['33a520f75c22ada5b77ef2fa75ebdee7ff3fed4000f56b3939930a8286b067a1'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + (name, version, { + 'checksums': ['daea9ab94124140fc0f715e945dd1dd6dc3056a1cb2f2cc31fc29b80162943e4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = [ + '%(name)s --help', + 'pyrcc5 -version 2>&1 |grep pyrcc5' # make sure PyQt5 module was not built with --no-tools +] + +moduleclass = 'vis' From f018fa988e0af05b563285eecb673bf592f60465 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 15 Aug 2023 15:10:57 +0200 Subject: [PATCH 8381/9987] add VisPy-0.12.2-foss-2022a.eb and pydantic-1.10.2-GCCcore-11.3.0.eb --- .../pydantic-1.10.2-GCCcore-11.3.0.eb | 27 +++++++++++++ .../v/VisPy/VisPy-0.12.2-foss-2022a.eb | 39 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..89062e0900c --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'pydantic' +version = '1.10.2' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('typing-extensions', '4.3.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-foss-2022a.eb b/easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-foss-2022a.eb new file mode 100644 index 00000000000..adc8e91d926 --- /dev/null +++ b/easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'VisPy' +version = '0.12.2' + +homepage = 'https://vispy.org' +description = """VisPy is a high-performance interactive 2D/3D data visualization library + leveraging the computational power of modern Graphics Processing Units (GPUs) through the + OpenGL library to display very large datasets.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyQt5', '5.15.5'), + ('matplotlib', '3.5.2'), # for kiwisolver + ('freetype', '2.12.1') +] + +use_pip = True + +exts_list = [ + ('freetype_py', '2.4.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-2.4.0.zip'], + 'checksums': ['8ad81195d2f8f339aba61700cebfbd77defad149c51f59b75a2a5e37833ae12e'], + }), + ('hsluv', '5.0.3', { + 'checksums': ['2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377'], + }), + ('vispy', version, { + 'checksums': ['141c2ddccc1158555bc89f09010c4b1d754487e816357333f31e795a7146a024'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From b0c23f5da685ac9d2de875821e0f5332985d12c5 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 15 Aug 2023 15:21:32 +0200 Subject: [PATCH 8382/9987] Add GTS --- .../g/GTS/GTS-0.7.6-GCCcore-12.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1e284e153a1 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. +It is an Open Source Free Software Library intended to provide a set of useful +functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['059c3e13e3e3b796d775ec9f96abdce8f2b3b5144df8514eda0cc12e13e8b81e'] + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), +] +dependencies = [ + ('GLib', '2.77.1'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [], +} + +moduleclass = 'vis' From e04e717a79756e8078b26dcfe820d7f3cc412e25 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 15 Aug 2023 15:35:42 +0200 Subject: [PATCH 8383/9987] Update napari-0.4.18-foss-2022a.eb adapt pydantic dep: 1.10.4 --- easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb index 3a33548c744..261c09a9891 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb @@ -17,7 +17,7 @@ dependencies = [ ('PyQt5', '5.15.5'), ('SciPy-bundle', '2022.05'), ('PyYAML', '6.0'), - ('pydantic', '1.10.2'), + ('pydantic', '1.10.4'), ('dask', '2022.10.0'), ('PyOpenGL', '3.1.6'), ('imageio', '2.22.2'), From 46b29bcbd829a3e8d7612e885035f9a51775fb22 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 15 Aug 2023 15:37:23 +0200 Subject: [PATCH 8384/9987] Delete pydantic-1.10.2-GCCcore-11.3.0.eb adapt pydantic dep: 1.10.4 --- .../pydantic-1.10.2-GCCcore-11.3.0.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.3.0.eb deleted file mode 100644 index 89062e0900c..00000000000 --- a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pydantic' -version = '1.10.2' - -homepage = 'https://github.com/samuelcolvin/pydantic' -description = """Data validation and settings management using Python type hinting.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -builddependencies = [('binutils', '2.38')] - -dependencies = [ - ('Python', '3.10.4'), - ('typing-extensions', '4.3.0'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - (name, version, { - 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], - }), -] - -moduleclass = 'devel' From 279978ef2d049b0fa68810a85e7f5b86094c8664 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 15 Aug 2023 16:21:21 +0200 Subject: [PATCH 8385/9987] Add MUMPS --- .../m/MUMPS/MUMPS-5.6.1-foss-2023a-metis.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023a-metis.eb diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023a-metis.eb new file mode 100644 index 00000000000..09270071de4 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.6.1-foss-2023a-metis.eb @@ -0,0 +1,35 @@ +name = 'MUMPS' +version = '5.6.1' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + '1920426d543e34d377604070fde93b8d102aa38ebdf53300cbce9e15f92e2896', # MUMPS_5.6.1.tar.gz + '51d3685208a42581b462592eea977f185d87e871fb65e8e90a54dd2ad18ac715', # MUMPS-5.6.1_shared-pord.patch + '27f788a5f85e8c9a6a7ec1651097b87c1de0ede0be943df7a10fa7c1ff5f494f', # MUMPS-5.6.1_shared-mumps.patch +] + +dependencies = [ + ('SCOTCH', '7.0.3'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' From 983fe79d6f5bdf5f5aba5792bbd1cddbad7b33fd Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 15 Aug 2023 16:07:16 +0000 Subject: [PATCH 8386/9987] Add comment explaining the need for an extra path --- .../a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2021b.eb | 1 + .../a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2022b.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2021b.eb b/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2021b.eb index 83542dca30f..81971352d4d 100644 --- a/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2021b.eb +++ b/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2021b.eb @@ -19,6 +19,7 @@ dependencies = [ ('cURL', '7.78.0') ] +# Binaries are installed to the root of the installation, so add that root to the PATH: modextrapaths = {'PATH': ''} # a list of binary files that will be produced diff --git a/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2022b.eb b/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2022b.eb index 48b14dad8f0..99076bdbc0f 100644 --- a/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2022b.eb +++ b/easybuild/easyconfigs/a/AMRFinderPlus/AMRFinderPlus-3.11.18-gompi-2022b.eb @@ -19,6 +19,7 @@ dependencies = [ ('cURL', '7.86.0') ] +# Binaries are installed to the root of the installation, so add that root to the PATH: modextrapaths = {'PATH': ''} # a list of binary files that will be produced From 49f691884ffdd7ba395d57c232e02f9ed73c4b01 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 15 Aug 2023 18:16:34 +0200 Subject: [PATCH 8387/9987] Fixed Checksum for qtwebengine-breakpad patch --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb index 0f93f7aa7d7..fddabfc9f0c 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb @@ -29,7 +29,7 @@ checksums = [ {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, {'Qt5-5.15.10_fix-OF-Gentoo.patch': '1c4d3b974422dadb4fd62f79581d48d25ae3d5f5f21489ae8c632e43e2e5286b'}, {'Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch': - '6890bc538b228ce0f41f09015ea52315471c69fb6ac2f615b9d881e3e8f55fc9'}, + '3b536de3b2da9115d96323a00275fc6066bb048f3747f8e6971facd78ed4e2e2'}, {'Qt5-5.15.7_GCC-12.patch': '9a5bde91b223a3e2e90d3d6bec107af69a1a0f18d789593738a953080473fa68'}, ] From 8731ffbb014dd8382e5e1e11f6fcd8c99a31f39a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Aug 2023 18:42:09 +0200 Subject: [PATCH 8388/9987] add alternative checksum for Extrae v4.0.4 --- easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb index 666f0ba1682..f821c5434c0 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb @@ -18,8 +18,9 @@ source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] sources = ['%(namelower)s-%(version)s-src.tar.bz2'] patches = ['Extrae-4.0.4-change_libdwarf_path.patch'] checksums = [ - '003bede870de6d88b705c1a13eabe63b6beb928d8f389f5dd70ca5db8450a1f9', # extrae-4.0.4-src.tar.bz2 - '74759b956246671a323acc3b267f9943bc2e190bb231259ad0c62784ec233a52', # Extrae-4.0.4-change_libdwarf_path.patch + {'extrae-4.0.4-src.tar.bz2': ('003bede870de6d88b705c1a13eabe63b6beb928d8f389f5dd70ca5db8450a1f9', + 'b867d395c344020c04e6630e9bfc10bf126e093df989d5563a2f3a6bc7568224')}, + {'Extrae-4.0.4-change_libdwarf_path.patch': '74759b956246671a323acc3b267f9943bc2e190bb231259ad0c62784ec233a52'}, ] builddependencies = [ From 179e510fa23eaa6af9585deedd6046f57dc88715 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Aug 2023 18:45:42 +0200 Subject: [PATCH 8389/9987] fix checksums spec for Extra v4.0.4 --- easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb index f821c5434c0..a10cfc0d34a 100644 --- a/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb +++ b/easybuild/easyconfigs/e/Extrae/Extrae-4.0.4-gompi-2022a.eb @@ -18,9 +18,10 @@ source_urls = ['https://ftp.tools.bsc.es/%(namelower)s'] sources = ['%(namelower)s-%(version)s-src.tar.bz2'] patches = ['Extrae-4.0.4-change_libdwarf_path.patch'] checksums = [ - {'extrae-4.0.4-src.tar.bz2': ('003bede870de6d88b705c1a13eabe63b6beb928d8f389f5dd70ca5db8450a1f9', - 'b867d395c344020c04e6630e9bfc10bf126e093df989d5563a2f3a6bc7568224')}, - {'Extrae-4.0.4-change_libdwarf_path.patch': '74759b956246671a323acc3b267f9943bc2e190bb231259ad0c62784ec233a52'}, + # extrae-4.0.4-src.tar.bz2 + ('003bede870de6d88b705c1a13eabe63b6beb928d8f389f5dd70ca5db8450a1f9', + 'b867d395c344020c04e6630e9bfc10bf126e093df989d5563a2f3a6bc7568224'), + '74759b956246671a323acc3b267f9943bc2e190bb231259ad0c62784ec233a52', # Extrae-4.0.4-change_libdwarf_path.patch ] builddependencies = [ From 500960df917bdb3eb701c9c29a7d858a90b6dc67 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 15 Aug 2023 21:31:31 +0200 Subject: [PATCH 8390/9987] use Perl instead of Perl minimal as build dependecy for libcerf and remove EasyConfig for Perl minimal --- .../l/libcerf/libcerf-2.3-GCCcore-12.3.0.eb | 2 +- .../Perl-5.36.1-GCCcore-12.3.0-minimal.eb | 26 ------------------- 2 files changed, 1 insertion(+), 27 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb diff --git a/easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.3.0.eb index 0f3fbf821ba..d1f69a956cc 100644 --- a/easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libcerf/libcerf-2.3-GCCcore-12.3.0.eb @@ -21,7 +21,7 @@ checksums = ['cceefee46e84ce88d075103390b4f9d04c34e4bc3b96d733292c36836d4f7065'] builddependencies = [ ('binutils', '2.40'), ('CMake', '3.26.3'), - ('Perl', '5.36.1', '-minimal'), # required for pod2html + ('Perl', '5.36.1'), # required for pod2html ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb deleted file mode 100644 index 6c5fc8fe267..00000000000 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0-minimal.eb +++ /dev/null @@ -1,26 +0,0 @@ -name = 'Perl' -version = '5.36.1' -versionsuffix = '-minimal' - -homepage = 'https://www.perl.org/' -description = """Larry Wall's Practical Extraction and Report Language - -This is a minimal build without any modules. Should only be used for build dependencies. -""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'] - -builddependencies = [ - ('binutils', '2.40'), -] - -dependencies = [ - ('zlib', '1.2.13'), -] - -moduleclass = 'lang' From 9bef1828a880c15d6831a1d61871d655d2462137 Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 15 Aug 2023 15:53:46 -0700 Subject: [PATCH 8391/9987] magma 2.7.0 2022b/CUDA --- .../magma-2.7.0-GCC-12.2.0-CUDA-11.7.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..373c7286881 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-11.7.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'magma' +version = '2.7.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/%(name)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['fda1cbc4607e77cacd8feb1c0f633c5826ba200a018f647f1c5436975b39fd18'] + +#patches = ['%(name)s-%(version_major_minor)s.1_allow-all-sms.patch'] + +builddependencies = [ + ('CMake', '3.24.3'), +] +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.14.1', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +# make sure both static and shared libs are built +configopts = [ + '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') +] + +sanity_check_paths = { + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' From 265e41baf0f69010f9de72555e5ec67ecb8e9fdc Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 15 Aug 2023 16:17:29 -0700 Subject: [PATCH 8392/9987] add SHLIB_EXT, improve comments --- .../l/libleidenalg/libleidenalg-0.11.1-foss-2022b.eb | 6 +++++- .../p/python-igraph/python-igraph-0.10.6-foss-2022b.eb | 5 ++--- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2022b.eb b/easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2022b.eb index 58846249a0a..c6dba27baaf 100644 --- a/easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2022b.eb +++ b/easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2022b.eb @@ -22,7 +22,11 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/%(name)s/GraphHelper.h', 'include/%(name)s/libleidenalg_export.h', 'lib/lib%(name)s.so'], + 'files': [ + 'include/%(name)s/GraphHelper.h', + 'include/%(name)s/libleidenalg_export.h', + 'lib/liblibleidenalg.%s' % SHLIB_EXT, + ], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb index 518606828d0..01e1aa2d9c6 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.10.6-foss-2022b.eb @@ -31,9 +31,8 @@ exts_list = [ ('cairocffi', '1.6.1', { 'checksums': ['78e6bbe47357640c453d0be929fa49cd05cce2e1286f3d2a1ca9cbda7efdb8b7'], }), - # Project name 'python-igraph' is depreicated, use pypi package igraph instead. To avoid - # name collision within EB, continue to use the package name 'python-igraph', - # to avoid collision with igraph. + # The pypi project 'python-igraph' is depreicated, use pypi package igraph instead. To avoid + # collision with the C/C++ build of igraph, continue to use the package name 'python-igraph' ('igraph', version, { 'installopts': '--install-option="--use-pkg-config"', 'modulename': 'igraph', From 32bd21afbd699c6fe5931ac48a691dfd7706d33a Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 16 Aug 2023 09:20:51 +0200 Subject: [PATCH 8393/9987] adding easyconfigs: RegTools-1.0.0-foss-2022b.eb --- .../r/RegTools/RegTools-1.0.0-foss-2022b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/RegTools/RegTools-1.0.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/r/RegTools/RegTools-1.0.0-foss-2022b.eb b/easybuild/easyconfigs/r/RegTools/RegTools-1.0.0-foss-2022b.eb new file mode 100644 index 00000000000..855e142a17c --- /dev/null +++ b/easybuild/easyconfigs/r/RegTools/RegTools-1.0.0-foss-2022b.eb @@ -0,0 +1,41 @@ +# updated: Denis Kristak (INUITS) +# +# updated: Lara Peeters (UGent) +easyblock = 'CMakeMake' + +name = 'RegTools' +version = '1.0.0' + +homepage = 'https://regtools.readthedocs.org' +description = """RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a +regulatory and splicing context.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/griffithlab/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ed2b9db6b71b943924002653caee18511a22ed7cc3c88f428e7e9e0c2e4f431b'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +# required by included scripts +dependencies = [ + ('Python', '3.10.8'), + ('PyYAML', '6.0'), # required by create_IGVsessions.py script + ('R', '4.2.2'), +] + +# 'make install' is not supported... +install_cmd = 'mkdir %(installdir)s/bin && cp -a regtools %(installdir)s/bin/ && ' +install_cmd += 'cp -a %(builddir)s/regtools-%(version)s/scripts %(installdir)s/' + +sanity_check_paths = { + 'files': ['bin/regtools'], + 'dirs': ['scripts'], +} + +sanity_check_commands = ['regtools --help'] + +moduleclass = 'bio' From 15daba0b391a0b538cb46224726f22cdaa0e8c77 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 16 Aug 2023 21:51:55 +0200 Subject: [PATCH 8394/9987] adding easyconfigs: IPython-8.14.0-GCCcore-12.3.0.eb, ZeroMQ-4.3.4-GCCcore-12.3.0.eb, libsodium-1.0.18-GCCcore-12.3.0.eb, OpenPGM-5.2.122-GCCcore-12.3.0.eb --- .../IPython/IPython-8.14.0-GCCcore-12.3.0.eb | 56 +++++++++++++++++++ .../libsodium-1.0.18-GCCcore-12.3.0.eb | 33 +++++++++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-12.3.0.eb | 44 +++++++++++++++ .../z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.3.0.eb | 40 +++++++++++++ 4 files changed, 173 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ca4ee19e75d --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '8.14.0' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('ZeroMQ', '4.3.4'), + ('lxml', '4.9.2'), + ('BeautifulSoup', '4.12.2'), +] + +sanity_pip_check = True +use_pip = True + +# for the matplotlib-inline required extention we avoid the import sanity check +# as it will fail without matplotlib in the environment, but ipython devs prefer not to make +# matplotlib a required dep (https://github.com/ipython/matplotlib-inline/issues/4) +# we follow the same convention and we not set matplotlib as dependency + +exts_list = [ + ('traitlets', '5.9.0', {'checksums': ['f6cde21a9c68cf756af02035f72d5a723bf607e862e7be33ece505abf4a3bad9']}), + ('pure_eval', '0.2.2', {'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3']}), + ('executing', '1.2.0', {'checksums': ['19da64c18d2d851112f09c287f8d3dbbdf725ab0e569077efb6cdcbd3497c107']}), + ('asttokens', '2.2.1', {'checksums': ['4622110b2a6f30b77e1473affaa97e711bc2f07d3f10848420ff1898edbe94f3']}), + ('stack_data', '0.6.2', {'checksums': ['32d2dd0376772d01b6cb9fc996f3c8b57a357089dec328ed4b6553d037eaf815']}), + ('prompt_toolkit', '3.0.39', {'checksums': ['04505ade687dc26dc4284b1ad19a83be2f2afe83e7a828ace0c72f3a1df72aac']}), + ('pickleshare', '0.7.5', {'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca']}), + ('matplotlib-inline', '0.1.6', {'modulename': False, 'checksums': ['f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304']}), + ('parso', '0.8.3', {'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0']}), + ('jedi', '0.18.2', {'checksums': ['bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612']}), + ('backcall', '0.2.0', {'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e']}), + ('ipython', '8.14.0', {'modulename': 'IPython', 'checksums': ['1d197b907b6ba441b692c48cf2a3a2de280dc0ac91a3405b39349a50272ca0a1']}), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..705b6339fd7 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.%(name)s.org/%(name)s/releases/', + 'https://download.%(name)s.org/%(name)s/releases/old/', + 'https://download.%(name)s.org/%(name)s/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/%(name)s.so', 'lib/%(name)s.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..951dbb18955 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/%(namelower)s/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s-pkgconfig_includes.patch', + '%(name)s-%(version)s-python3-compliant.patch', +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-%(version)s.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # %(name)s-%(version)s-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # %(name)s-%(version)s-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.3'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d64409d27db --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.4' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/%(namelower)s/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.39'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = "--with-pic --with-pgm --with-libsodium --disable-Werror" + + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From 890ec70c6f377dd2b7cfcde7c00fe520c5d04439 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 16 Aug 2023 12:58:34 -0700 Subject: [PATCH 8395/9987] fix UCX-CUDA for 12.2.0 --- ...0-CUDA-11.7.0.eb => magma-2.7.0-GCC-12.2.0-CUDA-12.0.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/m/magma/{magma-2.7.0-GCC-12.2.0-CUDA-11.7.0.eb => magma-2.7.0-GCC-12.2.0-CUDA-12.0.0.eb} (93%) diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-12.0.0.eb similarity index 93% rename from easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-11.7.0.eb rename to easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-12.0.0.eb index 373c7286881..0849a2ce18b 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-12.0.0.eb @@ -21,8 +21,8 @@ builddependencies = [ ('CMake', '3.24.3'), ] dependencies = [ - ('CUDA', '11.7.0', '', SYSTEM), - ('UCX-CUDA', '1.14.1', versionsuffix), + ('CUDA', '12.0.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', versionsuffix), ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) From e468630c91ad9f8967994ee47e91f7cdce4d1235 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 17 Aug 2023 09:11:05 +0200 Subject: [PATCH 8396/9987] changed build dep. Python 3 -> 2, see pr 18540 --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb index fddabfc9f0c..7897dbe6736 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb @@ -41,7 +41,7 @@ builddependencies = [ ('flex', '2.6.4'), ('gperf', '3.1'), ('Ninja', '1.11.1'), - ('Python', '3.11.3'), + ('Python', '2.7.18'), ('re2c', '3.1'), ] From dd5c31e3b4f368e9d43d1bf713e333923b442478 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Aug 2023 09:41:41 +0200 Subject: [PATCH 8397/9987] fix trivial code style issues in easyconfig for MXNet 1.9.1 --- .../m/MXNet/MXNet-1.9.1-foss-2022a.eb | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb index 463e8940a55..383e016ef3c 100644 --- a/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb @@ -7,7 +7,6 @@ description = """Flexible and Efficient Library for Deep Learning""" toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'cstd': 'c++14', 'opt': True, 'pic': True, 'openmp': True, 'extra_cflags': '-lflexiblas'} - # MXNet pulls in a bunch of submodules with specific commits sources = [ { @@ -20,42 +19,42 @@ sources = [ 'download_filename': '34fd45cae457d59850fdcb2066467778d0673f21.tar.gz', 'filename': 'ps-lite-20200229.tar.gz', }, - { + { 'source_urls': ['https://github.com/apache/tvm/archive/'], 'download_filename': 'efdac9439506d1de5eec91ecc795982c78e41909.tar.gz', 'filename': 'tvm-20201111.tar.gz', }, - { + { 'source_urls': ['https://github.com/dmlc/dmlc-core/archive/'], 'download_filename': '5df8305fe699d3b503d10c60a231ab0223142407.tar.gz', 'filename': 'dmlc-core-20200410.tar.gz', }, - { + { 'source_urls': ['https://github.com/dmlc/dlpack/archive/'], 'download_filename': '3efc489b55385936531a06ff83425b719387ec63.tar.gz', 'filename': 'dlpack-20200121.tar.gz', }, - { + { 'source_urls': ['https://github.com/google/googletest/archive/'], 'download_filename': 'eb9225ce361affe561592e0912320b9db84985d0.tar.gz', 'filename': 'googletest-20190114.tar.gz', }, - { + { 'source_urls': ['https://github.com/kpu/intgemm/archive/'], 'download_filename': '8f28282c3bd854922da638024d2659be52e892e9.tar.gz', 'filename': 'intgemm-20200915.tar.gz', }, - { + { 'source_urls': ['https://github.com/NVlabs/cub/archive/'], 'download_filename': '0158fa19f28619886232defd412433974af89611.tar.gz', 'filename': 'cub-20200424.tar.gz', }, - { + { 'source_urls': ['https://github.com/onnx/onnx-tensorrt/archive/'], 'download_filename': '2eb74d933f89e1590fdbfc64971a36e5f72df720.tar.gz', 'filename': 'onnx-tensorrt-20200624.tar.gz', }, - { + { 'source_urls': ['https://github.com/oneapi-src/oneDNN/archive/'], 'download_filename': '5818c40f07bdb6307f9bc64e929836fe036da644.tar.gz', 'filename': 'oneDNN-20220325.tar.gz', From 801f0efedcc1080fc790bc8ed67a78c560e2878d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Aug 2023 09:43:27 +0200 Subject: [PATCH 8398/9987] refer to subdirectory of MXNet GitHub repo for source of commits for MXNet sources --- easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb index 383e016ef3c..331f3962a9e 100644 --- a/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MXNet/MXNet-1.9.1-foss-2022a.eb @@ -7,7 +7,8 @@ description = """Flexible and Efficient Library for Deep Learning""" toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'cstd': 'c++14', 'opt': True, 'pic': True, 'openmp': True, 'extra_cflags': '-lflexiblas'} -# MXNet pulls in a bunch of submodules with specific commits +# MXNet pulls in a bunch of submodules with specific commits, +# see https://github.com/apache/mxnet/tree/1.9.1/3rdparty sources = [ { 'source_urls': ['https://github.com/apache/mxnet/archive/'], From 79f535afd970daa56962d08f440c9c16c11cf8fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Aug 2023 09:46:58 +0200 Subject: [PATCH 8399/9987] move down custom modulename in nose3 easyconfig --- easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb index 7244a899c1a..8a9a65a7c28 100644 --- a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-11.3.0.eb @@ -11,8 +11,6 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} sources = [SOURCE_TAR_GZ] checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'] -options = {'modulename': 'nose'} - builddependencies = [ ('binutils', '2.38'), ] @@ -31,6 +29,8 @@ sanity_check_paths = { 'dirs': [], } +options = {'modulename': 'nose'} + sanity_check_commands = ["nosetests --help"] moduleclass = 'devel' From 18582cb47c26127ba6faebf937e81080bfb7c35b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Aug 2023 09:50:59 +0200 Subject: [PATCH 8400/9987] rename patch for Yambo 5.1.2 to fix compilation with SLEPc --- easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb | 4 ++-- .../{yambo_slepc_fix.patch => Yambo-5.1.2_fix-SLEPc.patch} | 0 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/y/Yambo/{yambo_slepc_fix.patch => Yambo-5.1.2_fix-SLEPc.patch} (100%) diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb b/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb index e29b903deef..7f0073ff941 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2-intel-2021b.eb @@ -37,12 +37,12 @@ sources = [ 'extract_cmd': 'cp %s yambo-%(version)s/lib/archive/', }, ] -patches = ['yambo_slepc_fix.patch'] +patches = ['Yambo-5.1.2_fix-SLEPc.patch'] checksums = [ {'yambo-5.1.2.tar.gz': '9625d8a96bd9a3ff3713ebe53228d5ac9be0a98adecbe2a2bad67234c0e26a2e'}, {'yambo-libraries-1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'}, {'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'}, - {'yambo_slepc_fix.patch': 'e44a0f85ec5eb55da7c7d42937b4c452bde2ed2c6d2f98fffca15696c82b7df6'}, + {'Yambo-5.1.2_fix-SLEPc.patch': 'e44a0f85ec5eb55da7c7d42937b4c452bde2ed2c6d2f98fffca15696c82b7df6'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/y/Yambo/yambo_slepc_fix.patch b/easybuild/easyconfigs/y/Yambo/Yambo-5.1.2_fix-SLEPc.patch similarity index 100% rename from easybuild/easyconfigs/y/Yambo/yambo_slepc_fix.patch rename to easybuild/easyconfigs/y/Yambo/Yambo-5.1.2_fix-SLEPc.patch From 3d98ddc20da314b72fb8b6f2dbdb2093ad8bbaf5 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 17 Aug 2023 10:34:46 +0200 Subject: [PATCH 8401/9987] Use Python-bundle-PyPI and update jedi version to 0.19.0 --- .../easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb index ca4ee19e75d..59935a40c5e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ] dependencies = [ ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), ('ZeroMQ', '4.3.4'), ('lxml', '4.9.2'), ('BeautifulSoup', '4.12.2'), @@ -41,9 +42,9 @@ exts_list = [ ('pickleshare', '0.7.5', {'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca']}), ('matplotlib-inline', '0.1.6', {'modulename': False, 'checksums': ['f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304']}), ('parso', '0.8.3', {'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0']}), - ('jedi', '0.18.2', {'checksums': ['bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612']}), + ('jedi', '0.19.0', {'checksums': ['bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612']}), ('backcall', '0.2.0', {'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e']}), - ('ipython', '8.14.0', {'modulename': 'IPython', 'checksums': ['1d197b907b6ba441b692c48cf2a3a2de280dc0ac91a3405b39349a50272ca0a1']}), + ('%(namelower)s', '%(version)s', {'modulename': 'IPython', 'checksums': ['1d197b907b6ba441b692c48cf2a3a2de280dc0ac91a3405b39349a50272ca0a1']}), ] sanity_check_paths = { From a09c31fd3eaa0cd1c484af0236932899577b6cdf Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 17 Aug 2023 10:38:44 +0200 Subject: [PATCH 8402/9987] Update formatting --- .../IPython/IPython-8.14.0-GCCcore-12.3.0.eb | 50 ++++++++++++++----- 1 file changed, 38 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb index 59935a40c5e..978e65a017e 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb @@ -33,18 +33,44 @@ use_pip = True # we follow the same convention and we not set matplotlib as dependency exts_list = [ - ('traitlets', '5.9.0', {'checksums': ['f6cde21a9c68cf756af02035f72d5a723bf607e862e7be33ece505abf4a3bad9']}), - ('pure_eval', '0.2.2', {'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3']}), - ('executing', '1.2.0', {'checksums': ['19da64c18d2d851112f09c287f8d3dbbdf725ab0e569077efb6cdcbd3497c107']}), - ('asttokens', '2.2.1', {'checksums': ['4622110b2a6f30b77e1473affaa97e711bc2f07d3f10848420ff1898edbe94f3']}), - ('stack_data', '0.6.2', {'checksums': ['32d2dd0376772d01b6cb9fc996f3c8b57a357089dec328ed4b6553d037eaf815']}), - ('prompt_toolkit', '3.0.39', {'checksums': ['04505ade687dc26dc4284b1ad19a83be2f2afe83e7a828ace0c72f3a1df72aac']}), - ('pickleshare', '0.7.5', {'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca']}), - ('matplotlib-inline', '0.1.6', {'modulename': False, 'checksums': ['f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304']}), - ('parso', '0.8.3', {'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0']}), - ('jedi', '0.19.0', {'checksums': ['bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612']}), - ('backcall', '0.2.0', {'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e']}), - ('%(namelower)s', '%(version)s', {'modulename': 'IPython', 'checksums': ['1d197b907b6ba441b692c48cf2a3a2de280dc0ac91a3405b39349a50272ca0a1']}), + ('traitlets', '5.9.0', { + 'checksums': ['f6cde21a9c68cf756af02035f72d5a723bf607e862e7be33ece505abf4a3bad9'] + }), + ('pure_eval', '0.2.2', { + 'checksums': ['2b45320af6dfaa1750f543d714b6d1c520a1688dec6fd24d339063ce0aaa9ac3'] + }), + ('executing', '1.2.0', { + 'checksums': ['19da64c18d2d851112f09c287f8d3dbbdf725ab0e569077efb6cdcbd3497c107'] + }), + ('asttokens', '2.2.1', { + 'checksums': ['4622110b2a6f30b77e1473affaa97e711bc2f07d3f10848420ff1898edbe94f3'] + }), + ('stack_data', '0.6.2', { + 'checksums': ['32d2dd0376772d01b6cb9fc996f3c8b57a357089dec328ed4b6553d037eaf815'] + }), + ('prompt_toolkit', '3.0.39', { + 'checksums': ['04505ade687dc26dc4284b1ad19a83be2f2afe83e7a828ace0c72f3a1df72aac'] + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'] + }), + ('matplotlib-inline', '0.1.6', { + 'modulename': False, + 'checksums': ['f887e5f10ba98e8d2b150ddcf4702c1e5f8b3a20005eb0f74bfdbd360ee6f304'] + }), + ('parso', '0.8.3', { + 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'] + }), + ('jedi', '0.19.0', { + 'checksums': ['bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612'] + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'] + }), + ('%(namelower)s', '%(version)s', { + 'modulename': 'IPython', + 'checksums': ['1d197b907b6ba441b692c48cf2a3a2de280dc0ac91a3405b39349a50272ca0a1'] + }), ] sanity_check_paths = { From 90d381bd16cba44af8ed18c9c3fc0ba10c6ed3ee Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 17 Aug 2023 10:59:12 +0200 Subject: [PATCH 8403/9987] added extensions: pip, wheel, setuptools --- .../p/Python/Python-2.7.18-GCCcore-12.3.0.eb | 24 ++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb index 0ef2a70e6cf..8ea8866c3e6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb @@ -28,4 +28,26 @@ dependencies = [ install_pip = True -moduleclass = 'lang' +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 2023-05-17 +# https://pip.pypa.io/en/latest/development/release-process/#python-2-support + +exts_list = [ + ('wheel', '0.37.1', { + 'checksums': ['e9a504e793efbca1b8e0e9cb979a249cf4a0a7b5b8c9e8b65a5e39d49529c1c4'], + }), + ('setuptools', '44.1.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], + }), + ('pip', '20.3.4', { + 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], + }), +] From 2e85e2137d24458ce22436ca04c2f14a880479d7 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 17 Aug 2023 11:10:01 +0200 Subject: [PATCH 8404/9987] Fix checksum --- .../easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb index 978e65a017e..109a9704214 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-8.14.0-GCCcore-12.3.0.eb @@ -62,7 +62,7 @@ exts_list = [ 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'] }), ('jedi', '0.19.0', { - 'checksums': ['bae794c30d07f6d910d32a7048af09b5a39ed740918da923c6b780790ebac612'] + 'checksums': ['bcf9894f1753969cbac8022a8c2eaee06bfa3724e4192470aaffe7eb6272b0c4'] }), ('backcall', '0.2.0', { 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'] From d723902fd4d3ced995f0845e256ee12c88840bfc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Aug 2023 11:41:05 +0200 Subject: [PATCH 8405/9987] use 'Omnipose' rather than 'omnipose' --- .../Omnipose-0.4.4-foss-2022a.eb} | 30 +++++++++---------- ...cellpose-omni-0.9.1_fix_deps_and_scm.patch | 0 2 files changed, 14 insertions(+), 16 deletions(-) rename easybuild/easyconfigs/o/{omnipose/omnipose-0.4.4-foss-2022a.eb => Omnipose/Omnipose-0.4.4-foss-2022a.eb} (96%) rename easybuild/easyconfigs/o/{omnipose => Omnipose}/cellpose-omni-0.9.1_fix_deps_and_scm.patch (100%) diff --git a/easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb b/easybuild/easyconfigs/o/Omnipose/Omnipose-0.4.4-foss-2022a.eb similarity index 96% rename from easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb rename to easybuild/easyconfigs/o/Omnipose/Omnipose-0.4.4-foss-2022a.eb index 02007a72a28..9f96adeaa59 100644 --- a/easybuild/easyconfigs/o/omnipose/omnipose-0.4.4-foss-2022a.eb +++ b/easybuild/easyconfigs/o/Omnipose/Omnipose-0.4.4-foss-2022a.eb @@ -2,7 +2,7 @@ # Author: Denis Kristak easyblock = 'PythonBundle' -name = 'omnipose' +name = 'Omnipose' version = '0.4.4' homepage = 'https://omnipose.readthedocs.io' @@ -39,8 +39,6 @@ dependencies = [ use_pip = True -local_omnipose_preinstallopts = "sed -i 's/numpy>=1.22.4/numpy>=1.22.3/g' setup.py && " - exts_list = [ ('edt', '2.3.1', { 'checksums': ['3696e1f7de482465af731a734a31b261a8852df8d583118f1b223d61764e063f'], @@ -52,10 +50,10 @@ exts_list = [ 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], }), ('fastremap', '1.13.5', { - 'preinstallopts': "export PBR_VERSION=1.2.3 && ", - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/seung-lab/fastremap/archive/'], + 'sources': ['%(version)s.tar.gz'], 'checksums': ['ee0e9e798e9f331b7c46e98768735a42bb6e287b3aa56c31c322ba585f4036b7'], + 'preinstallopts': "export PBR_VERSION=1.2.3 && ", }), ('roifile', '2023.5.12', { 'checksums': ['32eeba0d9ad52cc249d6a234b737c1808a6c5d7d9baae6453709eb74222b3433'], @@ -67,37 +65,37 @@ exts_list = [ 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], }), ('googleapis-common-protos', '1.59.1', { - 'modulename': 'google.api', - 'preinstallopts': 'sed -i "s|protobuf>=3.19.5|protobuf>=3.19.4|g" setup.py && ', 'checksums': ['b35d530fe825fb4227857bc47ad84c33c809ac96f312e13182bdeaa2abe1178a'], + 'preinstallopts': 'sed -i "s|protobuf>=3.19.5|protobuf>=3.19.4|g" setup.py && ', + 'modulename': 'google.api', }), ('cachetools', '5.3.1', { 'checksums': ['dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b'], }), ('google-crc32c', '1.5.0', { - 'modulename': 'google_crc32c', 'checksums': ['89284716bc6a5a415d4eaa11b1726d2d60a0cd12aadf5439828353662ede9dd7'], + 'modulename': 'google_crc32c', }), ('google-auth', '2.22.0', { - 'modulename': 'google.auth', 'checksums': ['164cba9af4e6e4e40c3a4f90a1a6c12ee56f14c0b4868d1ca91b32826ab334ce'], + 'modulename': 'google.auth', }), ('google-cloud-core', '2.3.3', { - 'modulename': 'google.api', 'checksums': ['37b80273c8d7eee1ae816b3a20ae43585ea50506cb0e60f3cf5be5f87f1373cb'], + 'modulename': 'google.api', }), ('google-api-core', '2.11.1', { - 'modulename': 'google.api_core', - 'preinstallopts': 'sed -i "s|protobuf>=3.19.5|protobuf>=3.19.4|g" setup.py && ', 'checksums': ['25d29e05a0058ed5f19c61c0a78b1b53adea4d9364b464d014fbda941f6d1c9a'], + 'preinstallopts': 'sed -i "s|protobuf>=3.19.5|protobuf>=3.19.4|g" setup.py && ', + 'modulename': 'google.api_core', }), ('google-resumable-media', '2.5.0', { - 'modulename': 'google.resumable_media', 'checksums': ['218931e8e2b2a73a58eb354a288e03a0fd5fb1c4583261ac6e4c078666468c93'], + 'modulename': 'google.resumable_media', }), ('google-cloud-storage', '2.10.0', { - 'modulename': 'google.cloud.storage', 'checksums': ['934b31ead5f3994e5360f9ff5750982c5b6b11604dc072bc452c25965e076dc7'], + 'modulename': 'google.cloud.storage', }), ('cellpose-omni', '0.9.1', { 'patches': ['%(name)s-%(version)s_fix_deps_and_scm.patch'], @@ -107,10 +105,10 @@ exts_list = [ 'a1c42309d1a39297744a8505b45b9bff2e0f9ef738680349cc4adf8f663c4be0'}, ], }), - (name, version, { - 'preinstallopts': "sed -i 's/numpy>=1.22.4/numpy>=1.22.3/g' setup.py && ", + ('omnipose', version, { 'sources': ['%(namelower)s-%(version)s.tar.gz'], 'checksums': ['0bf1c333359504b0af511c36cc8db60ba5edba92d22c6aff183d9b858d269fe1'], + 'preinstallopts': "sed -i 's/numpy>=1.22.4/numpy>=1.22.3/g' setup.py && ", }), ] diff --git a/easybuild/easyconfigs/o/omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch b/easybuild/easyconfigs/o/Omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch similarity index 100% rename from easybuild/easyconfigs/o/omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch rename to easybuild/easyconfigs/o/Omnipose/cellpose-omni-0.9.1_fix_deps_and_scm.patch From 7add678f6a46d0a725879cd622275778952d9750 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 17 Aug 2023 13:13:54 +0200 Subject: [PATCH 8406/9987] adding easyconfigs: snakemake-7.32.3-foss-2022b.eb, wrapt-1.15.0-foss-2022b.eb --- .../snakemake/snakemake-7.32.3-foss-2022b.eb | 90 +++++++++++++++++++ .../w/wrapt/wrapt-1.15.0-foss-2022b.eb | 27 ++++++ 2 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-7.32.3-foss-2022b.eb create mode 100644 easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-7.32.3-foss-2022b.eb b/easybuild/easyconfigs/s/snakemake/snakemake-7.32.3-foss-2022b.eb new file mode 100644 index 00000000000..c21728c194d --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-7.32.3-foss-2022b.eb @@ -0,0 +1,90 @@ +easyblock = 'PythonBundle' + +name = 'snakemake' +version = '7.32.3' + +homepage = 'https://snakemake.readthedocs.io' +description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('GitPython', '3.1.31'), + ('IPython', '8.14.0'), + ('PyYAML', '6.0'), + ('wrapt', '1.15.0'), + ('PuLP', '2.7.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ConfigArgParse', '1.7', { + 'checksums': ['e7067471884de5478c58a511e529f0f9bd1c66bfef1dea90935438d6c23306d1'], + }), + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('toposort', '1.10', { + 'checksums': ['bfbb479c53d0a696ea7402601f4e693c97b0367837c8898bc6471adfca37a6bd'], + }), + ('amply', '0.1.6', { + 'checksums': ['61421103ccf8e1066717115fe7917610d831d551c68d31a110876a5b6c78aea4'], + }), + ('smart-open', '6.3.0', { + 'sources': ['smart_open-%(version)s.tar.gz'], + 'checksums': ['d5238825fe9a9340645fac3d75b287c08fbb99fb2b422477de781c9f5f09e019'], + }), + ('connection-pool', '0.0.3', { + 'sources': ['connection_pool-%(version)s.tar.gz'], + 'checksums': ['bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc'], + }), + ('stopit', '1.1.2', { + 'checksums': ['f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d'], + }), + ('reretry', '0.11.8', { + 'checksums': ['f2791fcebe512ea2f1d153a2874778523a8064860b591cd90afc21a8bed432e3'], + }), + ('throttler', '1.2.2', { + 'checksums': ['d54db406d98e1b54d18a9ba2b31ab9f093ac64a0a59d730c1cf7bb1cdfc94a58'], + }), + ('dpath', '2.1.6', { + 'checksums': ['f1e07c72e8605c6a9e80b64bc8f42714de08a789c7de417e49c3f87a19692e47'], + }), + ('plac', '1.3.5', { + 'checksums': ['38bdd864d0450fb748193aa817b9c458a8f5319fbf97b2261151cfc0a5812090'], + }), + ('yte', '1.5.1', { + 'checksums': ['6d0b315b78af83276d78f5f67c107c84238f772a76d74f4fc77905b46f3731f5'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('nbformat', '5.9.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['1c5172d786a41b82bcfd0c23f9e6b6f072e8fb49c39250219e4acfff1efe89e9'], + }), + ('jupyter-core', '5.3.1', { + 'modulename': 'jupyter_core', + 'source_tmpl': 'jupyter_core-%(version)s.tar.gz', + 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], + }), + ('fastjsonschema', '2.18.0', { + 'checksums': ['e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd'], + }), + (name, version, { + 'checksums': ['cbe586fe28349982307f008ca40e839d569cf5d540008b0c91ebfef689b49b18',], + }), +] + +sanity_check_paths = { + 'files': ['bin/snakemake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], +} + +sanity_check_commands = ['snakemake --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022b.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022b.eb new file mode 100644 index 00000000000..d80cc743cca --- /dev/null +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'wrapt' +version = '1.15.0' + +homepage = 'https://pypi.org/project/wrapt/' +description = """The aim of the wrapt module is to provide a transparent object +proxy for Python, which can be used as the basis for the construction of +function wrappers and decorator functions.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'], + }), +] + +moduleclass = 'tools' From 8ba91e09c3e63649ccda61bd65c05b02a34181fb Mon Sep 17 00:00:00 2001 From: benjamic Date: Thu, 17 Aug 2023 13:22:33 +0200 Subject: [PATCH 8407/9987] Updating htop to have toolchain as GCCcore --- .../h/htop/htop-3.2.2-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/h/htop/htop-3.2.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/h/htop/htop-3.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/htop/htop-3.2.2-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..dca9be43903 --- /dev/null +++ b/easybuild/easyconfigs/h/htop/htop-3.2.2-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'htop' +version = "3.2.2" + +homepage = 'https://htop.dev' + +description = """An interactive process viewer for Unix""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'htop-dev' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['3829c742a835a0426db41bb039d1b976420c21ec65e93b35cd9bfd2d57f44ac8'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('ncurses', '6.3'), +] + +preconfigopts = 'LIBS="$LIBS -ltinfo" && ./autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/htop'], + 'dirs': ['share'], +} + +moduleclass = 'tools' From 3975158d9bd5e7d00db52024e130607cc1e53efb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 17 Aug 2023 13:30:32 +0200 Subject: [PATCH 8408/9987] fix typo --- .../easyconfigs/s/snakemake/snakemake-7.32.3-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-7.32.3-foss-2022b.eb b/easybuild/easyconfigs/s/snakemake/snakemake-7.32.3-foss-2022b.eb index c21728c194d..49a41c7b93a 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-7.32.3-foss-2022b.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-7.32.3-foss-2022b.eb @@ -76,7 +76,7 @@ exts_list = [ 'checksums': ['e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd'], }), (name, version, { - 'checksums': ['cbe586fe28349982307f008ca40e839d569cf5d540008b0c91ebfef689b49b18',], + 'checksums': ['cbe586fe28349982307f008ca40e839d569cf5d540008b0c91ebfef689b49b18'], }), ] From 5b8f2bde834d3696606910eff6f9b7532e92864b Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 17 Aug 2023 14:01:22 +0200 Subject: [PATCH 8409/9987] libepoxy-1.5.10-GCCcore-12.3.0 --- .../libepoxy-1.5.10-GCCcore-12.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0138c593d12 --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.10' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a7ced37f4102b745ac86d6a70a9da399cc139ff168ba6b8002b4d8d43c900c15'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('X11', '20230603'), + ('Mesa', '23.1.4'), +] + +configopts = '-Degl=yes --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' From a69d0ac3881ca7d3265ce264dd841b6e1e7dde67 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 17 Aug 2023 14:09:15 +0200 Subject: [PATCH 8410/9987] Add pyproj --- .../p/pyproj/pyproj-3.6.0-GCCcore-12.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.6.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.6.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a9fef51cd71 --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.6.0-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.6.0' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a5b111865b3f0f8b77b3983f2fbe4dd6248fc09d3730295949977c8dcd988062'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('PROJ', '9.2.0'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' From 6e46b9537f3182f4ac6bc4b652831827529238ed Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 17 Aug 2023 14:46:03 +0200 Subject: [PATCH 8411/9987] at-spi2-atk-2.38.0-GCCcore-12.3.0 at-spi2-core-2.49.90-GCCcore-12.3.0 --- .../at-spi2-atk-2.38.0-GCCcore-12.3.0.eb | 37 ++++++++++++++++++ .../at-spi2-core-2.49.90-GCCcore-12.3.0.eb | 39 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5dbd5efc816 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('DBus', '1.15.4'), + ('at-spi2-core', '2.49.90'), + ('libxml2', '2.11.4'), + ('ATK', '2.38.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d6c6af7fbd5 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.49.90' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['1e6612755d71bbe952156dc051b281d1a4326a5696ac3bbc8cfd5ac8fd971f18'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.76.1'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('DBus', '1.15.4'), + ('X11', '20230603'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 25a479c315d2fe8728cdaa5a27da661293cbb32e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 17 Aug 2023 14:56:56 +0200 Subject: [PATCH 8412/9987] Add bedtools --- .../b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb | 53 +++++++++++++++++++ .../b/BamTools/BamTools-2.5.2-GCC-12.3.0.eb | 22 ++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..1889c683f50 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb @@ -0,0 +1,53 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.31.0' + +homepage = 'https://bedtools.readthedocs.io/' +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['183cf9a96aabc50ef4bd557a53fd01557a123c05a0dc87651371878f357439ec'] + +builddependencies = [ + ('Python', '3.11.3'), +] +dependencies = [ + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = [ + 'bin', + 'docs', + 'data', + 'genomes', + 'scripts', + 'test', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': ['bin', 'docs', 'data', 'genomes', 'scripts', 'test'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..96b38f46dda --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.3.0.eb @@ -0,0 +1,22 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +name = 'BamTools' +version = '2.5.2' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' + +moduleclass = 'bio' From e666406ef7688bc2e1b69b3d90214c76c04c05ae Mon Sep 17 00:00:00 2001 From: maximm Date: Thu, 17 Aug 2023 15:09:31 +0200 Subject: [PATCH 8413/9987] adding easyconfigs: HTSlib-1.18-GCC-12.3.0.eb --- .../h/HTSlib/HTSlib-1.18-GCC-12.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.18-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.18-GCC-12.3.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.18-GCC-12.3.0.eb new file mode 100644 index 00000000000..60474232fce --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.18-GCC-12.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Updated to 1.14 +# J. Sassmannshausen /GSTT + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.18' + +homepage = 'https://www.htslib.org/' +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f1ab53a593a2320a1bfadf4ef915dae784006c5b5c922c8a8174d7530a9af18f'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('cURL', '8.0.1'), +] + + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.so'], + 'dirs': [], +} + +moduleclass = 'bio' From 277408fc637cc2665649c95f28036c6cdf957049 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 17 Aug 2023 15:20:33 +0200 Subject: [PATCH 8414/9987] Add samtools and bcftools --- .../b/BCFtools/BCFtools-1.18-GCC-12.3.0.eb | 39 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.18-GCC-12.3.0.eb | 38 ++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.18-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.18-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.18-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.18-GCC-12.3.0.eb new file mode 100644 index 00000000000..5da1f4bca16 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.18-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.18' + +homepage = 'https://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence + variants""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['d9b9d36293e4cc62ab7473aa2539389d4e1de79b1a927d483f6e91f3c3ceac7e'] + +dependencies = [ + ('zlib', '1.2.13'), + ('HTSlib', '1.18'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('GSL', '2.7'), +] + +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/plot-vcfstats', 'bin/vcfutils.pl'], + 'dirs': ['libexec/%(namelower)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.18-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.18-GCC-12.3.0.eb new file mode 100644 index 00000000000..126567600ad --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.18-GCC-12.3.0.eb @@ -0,0 +1,38 @@ +# # +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +# +# Updated to 1.14 and gcc-11.2.0 +# J. Sassmannshausen / GSTT + +name = 'SAMtools' +version = '1.18' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['d686ffa621023ba61822a2a50b70e85d0b18e79371de5adb07828519d3fc06e1'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('cURL', '8.0.1'), +] + + +moduleclass = 'bio' From 07162ef9fcdd603f2fa5feafde7e6668f1b8b327 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 17 Aug 2023 15:49:28 +0200 Subject: [PATCH 8415/9987] Add STAR --- .../s/STAR/STAR-2.7.11a-GCC-12.3.0.eb | 51 ++++++++ .../STAR-2.7.11a_use-external-htslib.patch | 111 ++++++++++++++++++ 2 files changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.11a_use-external-htslib.patch diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb new file mode 100644 index 00000000000..1943af96d5e --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.3.0.eb @@ -0,0 +1,51 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen +# modified by Thomas Eylenbosch + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.11a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +github_account = 'alexdobin' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['STAR-%(version)s_use-external-htslib.patch'] +checksums = [ + {'%(version)s.tar.gz': '542457b1a4fee73f27a581b1776e9f73ad2b4d7e790388b6dc71147bd039f99a'}, + {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, +] + +dependencies = [ + ('HTSlib', '1.18'), + ('zlib', '1.2.13'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +files_to_copy = [ + (['source/%(name)s', 'source/%(name)slong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/%(name)slong'], + 'dirs': [], +} + +sanity_check_commands = [ + "STAR --help", + "STARlong --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a_use-external-htslib.patch b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a_use-external-htslib.patch new file mode 100644 index 00000000000..e0b024fd382 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a_use-external-htslib.patch @@ -0,0 +1,111 @@ +# Use external HTSlib from EasyBuild environment. Based on the similar patch for v2.7.10b. +# See also PR https://github.com/alexdobin/STAR/pull/1586 +# Author: maxim-masterov (SURF) +diff -Nru STAR-2.7.11a.orig/source/BAMfunctions.cpp STAR-2.7.11a/source/BAMfunctions.cpp +--- STAR-2.7.11a.orig/source/BAMfunctions.cpp 2023-08-15 21:21:58.000000000 +0200 ++++ STAR-2.7.11a/source/BAMfunctions.cpp 2023-08-17 15:40:33.432650000 +0200 +@@ -1,5 +1,5 @@ + #include "BAMfunctions.h" +-#include "htslib/htslib/kstring.h" ++#include "htslib/kstring.h" + + + string bam_cigarString (bam1_t *b) {//output CIGAR string +diff -Nru STAR-2.7.11a.orig/source/IncludeDefine.h STAR-2.7.11a/source/IncludeDefine.h +--- STAR-2.7.11a.orig/source/IncludeDefine.h 2023-08-15 21:21:58.000000000 +0200 ++++ STAR-2.7.11a/source/IncludeDefine.h 2023-08-17 15:41:18.348816000 +0200 +@@ -30,8 +30,8 @@ + #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ ) + + //external libs +-#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h" +-#define SAMTOOLS_SAM_H "htslib/htslib/sam.h" ++#define SAMTOOLS_BGZF_H "htslib/bgzf.h" ++#define SAMTOOLS_SAM_H "htslib/sam.h" + + using namespace std; + +diff -Nru STAR-2.7.11a.orig/source/Makefile STAR-2.7.11a/source/Makefile +--- STAR-2.7.11a.orig/source/Makefile 2023-08-15 21:21:58.000000000 +0200 ++++ STAR-2.7.11a/source/Makefile 2023-08-17 15:42:02.606631000 +0200 +@@ -12,8 +12,8 @@ + CXX ?= g++ + + # pre-defined flags +-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz +-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz ++LDFLAGS_shared := -pthread -L$(EBROOTHTSLIB)/lib -Bstatic -lhts -Bdynamic -lz ++LDFLAGS_static := -static -static-libgcc -pthread -L$(EBROOTHTSLIB)/lib -lhts -lz + LDFLAGS_Mac :=-pthread -lz htslib/libhts.a + LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a + LDFLAGS_gdb := $(LDFLAGS_shared) +@@ -131,7 +131,7 @@ + ifneq ($(MAKECMDGOALS),clean_solo) + ifneq ($(MAKECMDGOALS),STARforMac) + ifneq ($(MAKECMDGOALS),STARforMacGDB) +-Depend.list: $(SOURCES) parametersDefault.xxd htslib ++Depend.list: $(SOURCES) parametersDefault.xxd + echo $(SOURCES) + 'rm' -f ./Depend.list + $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list +diff -Nru STAR-2.7.11a.orig/source/STAR.cpp STAR-2.7.11a/source/STAR.cpp +--- STAR-2.7.11a.orig/source/STAR.cpp 2023-08-15 21:21:58.000000000 +0200 ++++ STAR-2.7.11a/source/STAR.cpp 2023-08-17 15:42:41.072327000 +0200 +@@ -30,7 +30,7 @@ + + #include "twoPassRunPass1.h" + +-#include "htslib/htslib/sam.h" ++#include "htslib/sam.h" + #include "parametersDefault.xxd" + + void usage(int usageType) +diff -Nru STAR-2.7.11a.orig/source/bamRemoveDuplicates.cpp STAR-2.7.11a/source/bamRemoveDuplicates.cpp +--- STAR-2.7.11a.orig/source/bamRemoveDuplicates.cpp 2023-08-15 21:21:58.000000000 +0200 ++++ STAR-2.7.11a/source/bamRemoveDuplicates.cpp 2023-08-17 15:40:50.759887000 +0200 +@@ -1,7 +1,7 @@ + #include + #include "bamRemoveDuplicates.h" + #include +-#include "htslib/htslib/sam.h" ++#include "htslib/sam.h" + #include "IncludeDefine.h" + #include SAMTOOLS_BGZF_H + #include "ErrorWarning.h" +diff -Nru STAR-2.7.11a.orig/source/bam_cat.c STAR-2.7.11a/source/bam_cat.c +--- STAR-2.7.11a.orig/source/bam_cat.c 2023-08-15 21:21:58.000000000 +0200 ++++ STAR-2.7.11a/source/bam_cat.c 2023-08-17 15:39:38.314318000 +0200 +@@ -52,8 +52,8 @@ + #include + #include + +-#include "htslib/htslib/bgzf.h" +-#include "htslib/htslib/sam.h" ++#include "htslib/bgzf.h" ++#include "htslib/sam.h" + #include + + #define BUF_SIZE 0x10000 +diff -Nru STAR-2.7.11a.orig/source/bam_cat.h STAR-2.7.11a/source/bam_cat.h +--- STAR-2.7.11a.orig/source/bam_cat.h 2023-08-15 21:21:58.000000000 +0200 ++++ STAR-2.7.11a/source/bam_cat.h 2023-08-17 15:39:59.175559315 +0200 +@@ -1,7 +1,7 @@ + #ifndef CODE_bam_cat + #define CODE_bam_cat + +-#include "htslib/htslib/sam.h" ++#include "htslib/sam.h" + + int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam); + +diff -Nru STAR-2.7.11a.orig/source/signalFromBAM.h STAR-2.7.11a/source/signalFromBAM.h +--- STAR-2.7.11a.orig/source/signalFromBAM.h 2023-08-15 21:21:58.000000000 +0200 ++++ STAR-2.7.11a/source/signalFromBAM.h 2023-08-17 15:42:27.321267434 +0200 +@@ -1,6 +1,6 @@ + #ifndef CODE_signalFromBAM + #define CODE_signalFromBAM +-#include "htslib/htslib/sam.h" ++#include "htslib/sam.h" + #include + #include + #include "Stats.h" From 56872553e4b63c071da6981e1089dbd8e59c885f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 17 Aug 2023 15:51:45 +0200 Subject: [PATCH 8416/9987] cleaning --- .../b/BCFtools/BCFtools-1.18-GCC-12.3.0.eb | 39 ------------------- .../s/SAMtools/SAMtools-1.18-GCC-12.3.0.eb | 38 ------------------ 2 files changed, 77 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.18-GCC-12.3.0.eb delete mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.18-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.18-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.18-GCC-12.3.0.eb deleted file mode 100644 index 5da1f4bca16..00000000000 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.18-GCC-12.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Author: Jonas Demeulemeester -# The Francis Crick Insitute, London, UK - -easyblock = 'ConfigureMake' - -name = 'BCFtools' -version = '1.18' - -homepage = 'https://www.htslib.org/' -description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. - BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence - variants""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['d9b9d36293e4cc62ab7473aa2539389d4e1de79b1a927d483f6e91f3c3ceac7e'] - -dependencies = [ - ('zlib', '1.2.13'), - ('HTSlib', '1.18'), - ('bzip2', '1.0.8'), - ('XZ', '5.4.2'), - ('GSL', '2.7'), -] - -configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" - - -sanity_check_paths = { - 'files': ['bin/%(namelower)s', 'bin/plot-vcfstats', 'bin/vcfutils.pl'], - 'dirs': ['libexec/%(namelower)s'], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.18-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.18-GCC-12.3.0.eb deleted file mode 100644 index 126567600ad..00000000000 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.18-GCC-12.3.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -# # -# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia -# Homepage: https://staff.flinders.edu.au/research/deep-thought -# -# Authors:: Robert Qiao -# License:: MIT -# -# Notes:: -# -# Updated to 1.14 and gcc-11.2.0 -# J. Sassmannshausen / GSTT - -name = 'SAMtools' -version = '1.18' - -homepage = 'https://www.htslib.org/' -description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, - including sorting, merging, indexing and generating alignments in a per-position format.""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/%(version)s'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['d686ffa621023ba61822a2a50b70e85d0b18e79371de5adb07828519d3fc06e1'] - -# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. -# The latter is currently provided by XZ. -dependencies = [ - ('ncurses', '6.4'), - ('zlib', '1.2.13'), - ('bzip2', '1.0.8'), - ('XZ', '5.4.2'), - ('cURL', '8.0.1'), -] - - -moduleclass = 'bio' From 0bfea7170b1e971e879761dea60b72a9b1a279c2 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 17 Aug 2023 23:24:45 +0200 Subject: [PATCH 8417/9987] Update easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb Co-authored-by: SebastianAchilles --- .../easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb index 705b6339fd7..aee38d02eae 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb @@ -26,7 +26,7 @@ builddependencies = [ sanity_check_paths = { - 'files': ['include/sodium.h', 'lib/%(name)s.so', 'lib/%(name)s.a'], + 'files': ['include/sodium.h', 'lib/%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a'], 'dirs': ['include/sodium', 'lib/pkgconfig'], } From 5982aeaab48144b78f46d57bd56b6edec22c9b4d Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 17 Aug 2023 23:24:51 +0200 Subject: [PATCH 8418/9987] Update easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.3.0.eb Co-authored-by: SebastianAchilles --- .../easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.3.0.eb index 951dbb18955..3c19e74c6d0 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-12.3.0.eb @@ -37,7 +37,7 @@ builddependencies = [ start_dir = 'pgm' sanity_check_paths = { - 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], 'dirs': ['include'], } From fcc3d2ef56f76b5d1a5842de0cf441c1107be529 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 17 Aug 2023 23:25:00 +0200 Subject: [PATCH 8419/9987] Update easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.3.0.eb index d64409d27db..87b0fc7b44a 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.4-GCCcore-12.3.0.eb @@ -33,7 +33,7 @@ configopts = "--with-pic --with-pgm --with-libsodium --disable-Werror" sanity_check_paths = { - 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], 'dirs': ['include', 'lib'], } From bcc2e869ba1bb4ec16cbe593988123af8123c2c0 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 17 Aug 2023 23:30:07 +0200 Subject: [PATCH 8420/9987] Delete htop-3.2.2.eb --- easybuild/easyconfigs/h/htop/htop-3.2.2.eb | 32 ---------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/h/htop/htop-3.2.2.eb diff --git a/easybuild/easyconfigs/h/htop/htop-3.2.2.eb b/easybuild/easyconfigs/h/htop/htop-3.2.2.eb deleted file mode 100644 index 24f2a2a44d4..00000000000 --- a/easybuild/easyconfigs/h/htop/htop-3.2.2.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'htop' -version = "3.2.2" - -homepage = 'https://htop.dev' - -description = """An interactive process viewer for Unix""" - -toolchain = SYSTEM - -github_account = 'htop-dev' -source_urls = [GITHUB_SOURCE] -sources = ['%(version)s.tar.gz'] -checksums = ['3829c742a835a0426db41bb039d1b976420c21ec65e93b35cd9bfd2d57f44ac8'] - -builddependencies = [ - ('Autotools', '20220317'), -] - -dependencies = [ - ('ncurses', '6.2'), -] - -preconfigopts = 'LIBS="$LIBS -ltinfo" && ./autogen.sh && ' - -sanity_check_paths = { - 'files': ['bin/htop'], - 'dirs': ['share'], -} - -moduleclass = 'tools' From 8341b0f0b939d54666b606c1fe30c41c494dee39 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 18 Aug 2023 01:54:46 +0200 Subject: [PATCH 8421/9987] adding easyconfigs: assimp-5.2.5-GCCcore-12.3.0.eb --- .../a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ef95ff38d99 --- /dev/null +++ b/easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# Authors:: Richard Lawrence - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'CMakeMake' + +name = 'assimp' +version = '5.2.5' + +homepage = 'https://github.com/assimp/assimp' + +description = """ + Open Asset Import Library (assimp) is a library to import and export various + 3d-model-formats including scene-post-processing to generate missing render data. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b5219e63ae31d895d60d98001ee5bb809fb2c7b2de1e7f78ceeb600063641e1a'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +configopts = '-DBUILD_DOCS=on ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/%(name)s/types.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['share/doc/Assimp'], +} + +moduleclass = 'vis' From d6a7a8e21d376c9ebaa2cd84b3107b77e7a97404 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 18 Aug 2023 02:03:28 +0200 Subject: [PATCH 8422/9987] Fix sanity checks --- easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb index ef95ff38d99..6cf7b191cec 100644 --- a/easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb @@ -27,7 +27,7 @@ builddependencies = [ configopts = '-DBUILD_DOCS=on ' sanity_check_paths = { - 'files': ['bin/%(name)s', 'include/%(name)s/types.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], + 'files': ['include/assimp/types.h', 'lib/libassimp.%s' % SHLIB_EXT], 'dirs': ['share/doc/Assimp'], } From fcec5e1dc13a5067e5e7bd827ae2f2c3d4ec8042 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 18 Aug 2023 02:11:03 +0200 Subject: [PATCH 8423/9987] Drop docs, because all users only read it online anyway --- .../easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb index 6cf7b191cec..6c660d619f1 100644 --- a/easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/assimp/assimp-5.2.5-GCCcore-12.3.0.eb @@ -22,13 +22,12 @@ builddependencies = [ ('binutils', '2.40'), ('CMake', '3.26.3'), ('pkgconf', '1.9.5'), + ('zlib', '1.2.13'), ] -configopts = '-DBUILD_DOCS=on ' - sanity_check_paths = { 'files': ['include/assimp/types.h', 'lib/libassimp.%s' % SHLIB_EXT], - 'dirs': ['share/doc/Assimp'], + 'dirs': [], } moduleclass = 'vis' From d327dab5615b8ed0826a99129eba6ca6d5cf768e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 18 Aug 2023 02:41:29 +0200 Subject: [PATCH 8424/9987] adding easyconfigs: c-ares-1.19.1-GCCcore-12.3.0.eb, protobuf-24.0-GCCcore-12.3.0.eb, RE2-2023-08-01-GCCcore-12.3.0.eb, gRPC-1.57.0-GCCcore-12.3.0.eb --- .../c/c-ares/c-ares-1.19.1-GCCcore-12.3.0.eb | 29 +++++++++++ .../g/gRPC/gRPC-1.57.0-GCCcore-12.3.0.eb | 50 +++++++++++++++++++ .../protobuf/protobuf-24.0-GCCcore-12.3.0.eb | 35 +++++++++++++ .../r/RE2/RE2-2023-08-01-GCCcore-12.3.0.eb | 30 +++++++++++ 4 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/c/c-ares/c-ares-1.19.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/gRPC/gRPC-1.57.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-24.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/RE2/RE2-2023-08-01-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/c-ares/c-ares-1.19.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/c-ares/c-ares-1.19.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..51111d72785 --- /dev/null +++ b/easybuild/easyconfigs/c/c-ares/c-ares-1.19.1-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'c-ares' +version = '1.19.1' + +homepage = 'https://c-ares.org/' +description = "c-ares is a C library for asynchronous DNS requests (including name resolves)" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'c-ares' +source_urls = [GITHUB_SOURCE] +sources = ['%s-%s.tar.gz' % (name.replace('-', ''), version.replace('.', '_'))] +checksums = ['9eadec0b34015941abdf3eb6aead694c8d96a192a792131186a7e0a86f2ad6d9'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': ['lib/libcares.a', 'lib/libcares.%s' % SHLIB_EXT, 'lib/pkgconfig/libcares.pc'], + 'dirs': ['include', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gRPC/gRPC-1.57.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gRPC/gRPC-1.57.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ee16f2e6a35 --- /dev/null +++ b/easybuild/easyconfigs/g/gRPC/gRPC-1.57.0-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'gRPC' +version = '1.57.0' + +homepage = 'https://grpc.io/' +description = """gRPC is a modern, open source, high-performance remote procedure call (RPC) +framework that can run anywhere. gRPC enables client and server applications to +communicate transparently, and simplifies the building of connected systems.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['8c05641b9f91cbc92f51cc4a5b3a226788d7a63f20af4ca7aaca50d92cc94a0d'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), + ('Abseil', '20230125.3'), + ('c-ares', '1.19.1'), + ('protobuf', '24.0'), + ('zlib', '1.2.13'), + ('RE2', '2023-08-01'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += "-DgRPC_ABSL_PROVIDER=package " +configopts += "-DgRPC_CARES_PROVIDER=package " +configopts += "-DgRPC_PROTOBUF_PROVIDER=package " +configopts += "-DgRPC_RE2_PROVIDER=package " +configopts += "-DgRPC_SSL_PROVIDER=package " +configopts += "-DgRPC_ZLIB_PROVIDER=package " + +_grpc_plugins = ['cpp', 'csharp', 'node', 'objective_c', 'php', 'python', 'ruby'] + +sanity_check_paths = { + 'files': ['bin/grpc_%s_plugin' % x for x in _grpc_plugins] + + ['lib/libgrpc.%s' % SHLIB_EXT, 'lib/libgrpc++.%s' % SHLIB_EXT], + 'dirs': ['include/grpc', 'include/grpc++', 'include/grpcpp'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-24.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-24.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..d29fcd6825d --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-24.0-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '24.0' + +homepage = 'https://github.com/protocolbuffers/protobuf' +description = """Protocol Buffers (a.k.a., protobuf) are Google's +language-neutral, platform-neutral, extensible mechanism for +serializing structured data.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['850357336189c470e429e9bdffca92229d8cd5b7f84aa2f3b4c5fdb80ce8351b'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +srcdir = '.' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER="package" ' + +dependencies = [ + ('Abseil', '20230125.3'), +] + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/RE2/RE2-2023-08-01-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2023-08-01-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fbebd652f60 --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2023-08-01-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = "CMakeMake" + +name = 'RE2' +version = '2023-08-01' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['d82d0efe2389949244445e7a6ac9a10fccc3d6a3d267ec4652991a51291647b0'] + +builddependencies = { + ('binutils', '2.40'), + ('CMake', '3.26.3'), +} + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' From 8cfd45eb28875e74a71e1ee9b3927db808256a46 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 18 Aug 2023 02:49:10 +0200 Subject: [PATCH 8425/9987] fix checksum --- easybuild/easyconfigs/g/gRPC/gRPC-1.57.0-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gRPC/gRPC-1.57.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gRPC/gRPC-1.57.0-GCCcore-12.3.0.eb index ee16f2e6a35..b3d6deae4ae 100644 --- a/easybuild/easyconfigs/g/gRPC/gRPC-1.57.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/gRPC/gRPC-1.57.0-GCCcore-12.3.0.eb @@ -14,7 +14,7 @@ toolchainopts = {'pic': True} github_account = 'grpc' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['8c05641b9f91cbc92f51cc4a5b3a226788d7a63f20af4ca7aaca50d92cc94a0d'] +checksums = ['8393767af531b2d0549a4c26cf8ba1f665b16c16fb6c9238a7755e45444881dd'] builddependencies = [ ('binutils', '2.40'), From d746d2bf28232301c882c9a364b4ec7ba00e59fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 18 Aug 2023 02:56:07 +0200 Subject: [PATCH 8426/9987] Fix RE2 deps --- .../easyconfigs/r/RE2/RE2-2023-08-01-GCCcore-12.3.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/RE2/RE2-2023-08-01-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2023-08-01-GCCcore-12.3.0.eb index fbebd652f60..b57a4ad6e9b 100644 --- a/easybuild/easyconfigs/r/RE2/RE2-2023-08-01-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/RE2/RE2-2023-08-01-GCCcore-12.3.0.eb @@ -17,10 +17,14 @@ source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] checksums = ['d82d0efe2389949244445e7a6ac9a10fccc3d6a3d267ec4652991a51291647b0'] -builddependencies = { +builddependencies = [ ('binutils', '2.40'), ('CMake', '3.26.3'), -} +] + +dependencies = [ + ('Abseil', '20230125.3'), +] sanity_check_paths = { 'files': ['lib/libre2.a'], From 6dd8bef33a4b36889bbf253e7028576f95579302 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 18 Aug 2023 03:32:10 +0200 Subject: [PATCH 8427/9987] adding easyconfigs: LittleCMS-2.15-GCCcore-12.3.0.eb --- .../LittleCMS-2.15-GCCcore-12.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..425485c06ca --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.15' + +homepage = 'https://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%s/' % '.'.join(version.split('.')[:2])] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['b20cbcbd0f503433be2a4e81462106fa61050a35074dc24a4e356792d971ab39'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('libjpeg-turbo', '2.1.5.1')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' From 251e755791aae02fb834649f77ee8118c3457849 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Fri, 18 Aug 2023 09:50:47 +0200 Subject: [PATCH 8428/9987] Update easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb Co-authored-by: SebastianAchilles --- .../easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb index aee38d02eae..656602d1719 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-12.3.0.eb @@ -26,7 +26,7 @@ builddependencies = [ sanity_check_paths = { - 'files': ['include/sodium.h', 'lib/%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a'], + 'files': ['include/sodium.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a'], 'dirs': ['include/sodium', 'lib/pkgconfig'], } From c4b4ab7512628c74e4e8fb5e92cd15c81c67c40a Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 18 Aug 2023 10:05:10 +0200 Subject: [PATCH 8429/9987] Update easybuild/easyconfigs/h/HTSlib/HTSlib-1.18-GCC-12.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.18-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.18-GCC-12.3.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.18-GCC-12.3.0.eb index 60474232fce..65824f66485 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.18-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.18-GCC-12.3.0.eb @@ -33,7 +33,7 @@ dependencies = [ sanity_check_paths = { - 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.so'], + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], 'dirs': [], } From 5bf88e96f7c6346713162ed544a9f9387d0b0aec Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 18 Aug 2023 10:06:05 +0200 Subject: [PATCH 8430/9987] Update easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb index 1889c683f50..184e7f7b831 100644 --- a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.31.0-GCC-12.3.0.eb @@ -45,7 +45,7 @@ files_to_copy = [ sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], - 'dirs': ['bin', 'docs', 'data', 'genomes', 'scripts', 'test'], + 'dirs': files_to_copy, } sanity_check_commands = ['%(namelower)s --help'] From 2b1418399a12f6f7443eac6809a44dce8eb12817 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 18 Aug 2023 10:33:50 +0200 Subject: [PATCH 8431/9987] Gdk-Pixbuf-2.42.10 --- .../Gdk-Pixbuf-2.42.10-GCCcore-12.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..4eb2e4a6924 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.10' + +homepage = 'https://docs.gtk.org/gdk-pixbuf/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ee9b6c75d13ba096907a2e3c6b27b61bcd17f5c7ebeab5a5b439d2f2e39fe44b'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('GObject-Introspection', '1.76.1'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.1'), + ('X11', '20230603'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' From 62811703a51b8ea44f42a592c4b7c1337df008b1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 18 Aug 2023 13:58:08 +0200 Subject: [PATCH 8432/9987] adding easyconfigs: fsom-20151117-GCCcore-11.3.0.eb and patches: fsom-20151117_build-libs.patch --- .../f/fsom/fsom-20151117-GCCcore-11.3.0.eb | 43 ++++++++++ .../f/fsom/fsom-20151117_build-libs.patch | 84 +++++++++++++++++++ 2 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/f/fsom/fsom-20151117_build-libs.patch diff --git a/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..abc5225cee2 --- /dev/null +++ b/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-11.3.0.eb @@ -0,0 +1,43 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'fsom' +version = '20151117' +local_commit = '56695e1' + +homepage = 'https://github.com/ekg/fsom' +description = """A tiny C library for managing SOM (Self-Organizing Maps) neural networks.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'ekg' + +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] + +patches = [ + '%(name)s-%(version)s_build-libs.patch', + '%(name)s-20141119_fix-abs-overload.patch' +] + +checksums = [ + '1ba3360985be781bb9f79d974705c86e7bb0719cb83638955e113b5dd83ec8dd', # 56695e1.tar.gz + 'd4e19b2db054cc5d3153ceba88ad2b11e5143e3a3c243103ce1e6994a83c43fe', # fsom-20151117_build-libs.patch + '54dd6ae76033535fe1b0231142d8bd41a815950dc3fd269dc321f698d4973639', # fsom-20141119_fix-abs-overload.patch +] + +builddependencies = [('binutils', '2.38')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfsom.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fsom/fsom-20151117_build-libs.patch b/easybuild/easyconfigs/f/fsom/fsom-20151117_build-libs.patch new file mode 100644 index 00000000000..e4fb74b8f99 --- /dev/null +++ b/easybuild/easyconfigs/f/fsom/fsom-20151117_build-libs.patch @@ -0,0 +1,84 @@ +# Patch to build static and dynamic libraries. Based on PR by outpaddling: +# https://github.com/ekg/fsom/pull/4 +# Updated: Petr Král (INUITS) + +--- fsom-56695e1611d824cda97f08e932d25d08419170cd/Makefile.orig 2015-11-17 13:39:52.000000000 +0100 ++++ fsom-56695e1611d824cda97f08e932d25d08419170cd/Makefile 2023-07-12 13:04:52.141543805 +0200 +@@ -1,22 +1,62 @@ ++# Use ?= to allow overriding from the env or command-line, e.g. ++# ++# make CXXFLAGS="-O3 -fPIC" install ++# ++# Package managers will override many of these variables automatically, so ++# this is aimed at making it easy to create packages (Debian packages, ++# FreeBSD ports, MacPorts, pkgsrc, etc.) + + CXX ?= g++ + CXXFLAGS ?= -w -O3 -pipe -fomit-frame-pointer -ffast-math + +-OBJS = fsom.o split.o main.o ++PREFIX ?= /usr/local ++STRIP ?= strip ++INSTALL ?= install -c ++MKDIR ?= mkdir -p ++AR ?= ar ++ARFLAGS ?= rs ++ ++BIN = fsom ++LIB = libfsom.a ++SOVERSION = 0 ++SLIB = libfsom.so ++OBJS = fsom.o split.o ++MAIN = main.o ++ ++BINDIR = $(DESTDIR)$(PREFIX)/bin ++INCDIR = $(DESTDIR)$(PREFIX)/include/fsom ++LIBDIR = $(DESTDIR)$(PREFIX)/lib ++ ++.SUFFIXES:.c .cpp .o .pico .so ++ ++.c.o .cpp.o: ++ $(CXX) $(CXXFLAGS) -I. -c -o $@ $< ++ ++.c.pico .cpp.pico: ++ $(CXX) $(CXXFLAGS) -I. -fPIC -c -o $@ $< ++ ++all: $(BIN) $(SLIB) $(LIB) ++ ++$(LIB): $(OBJS) ++ $(AR) $(ARFLAGS) $@ $^ ++ ++$(SLIB): $(OBJS:.o=.pico) ++ $(CXX) -shared -Wl,-soname,$(SLIB).$(SOVERSION) $(LDFLAGS) -o $@ $^ $(LIBS) ++ ln -sf $@ $(SLIB).$(SOVERSION) ++ ++$(BIN): $(OBJS) $(MAIN) ++ $(CXX) $(CXXFLAGS) -o $@ $^ $(LIBS) ++ ++install: all ++ $(MKDIR) $(BINDIR) ++ $(MKDIR) $(INCDIR) ++ $(MKDIR) $(LIBDIR) ++ $(INSTALL) $(BIN) $(BINDIR) ++ $(INSTALL) *.h $(INCDIR) ++ $(INSTALL) $(LIB) $(SLIB) $(SLIB).$(SOVERSION) $(LIBDIR) + +-all: fsom +- +-fsom: ${OBJS} +- ${CXX} -o fsom ${OBJS} -lm +- +-fsom.o: fsom.c +- ${CXX} ${CXXFLAGS} -c fsom.c +- +-split.o: split.cpp +- ${CXX} ${CXXFLAGS} -c split.cpp +- +-main.o: main.cpp +- ${CXX} ${CXXFLAGS} -c main.cpp ++install-strip: install ++ $(STRIP) $(BINDIR)/$(BIN) $(LIBDIR)/$(LIB) $(LIBDIR)/$(SLIB) + + clean: +- rm -f *.o fsom ++ rm -rf *.o *.pico $(BIN) $(LIB) $(SLIB) $(DESTDIR) From 0fee75da6bea261dd701685523eddb5c53f483ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 18 Aug 2023 13:59:03 +0200 Subject: [PATCH 8433/9987] adding easyconfigs: tabixpp-1.1.2-GCC-11.3.0.eb and patches: tabixpp-1.1.2_use-external-HTSlib.patch --- .../t/tabixpp/tabixpp-1.1.2-GCC-11.3.0.eb | 41 +++++++ .../tabixpp-1.1.2_use-external-HTSlib.patch | 110 ++++++++++++++++++ 2 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2_use-external-HTSlib.patch diff --git a/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..ae5c8ea0258 --- /dev/null +++ b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-11.3.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'tabixpp' +version = '1.1.2' + +homepage = 'https://github.com/ekg/tabixpp' +description = """C++ wrapper to tabix indexer""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_use-external-HTSlib.patch'] + +checksums = [ + 'c850299c3c495221818a85c9205c60185c8ed9468d5ec2ed034470bb852229dc', # v1.1.2.tar.gz + 'a4684b6c3a69258d0686f601564b635ae3dc098e712783b46d9ca5b7ff996906', # tabixpp-1.1.2_use-external-HTSlib.patch +] + +dependencies = [ + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('HTSlib', '1.15.1'), + ('PCRE', '8.45'), +] + +skipsteps = ['configure'] + +preinstallopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/tabix++', 'lib/libtabixpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2_use-external-HTSlib.patch b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2_use-external-HTSlib.patch new file mode 100644 index 00000000000..e83f26f794f --- /dev/null +++ b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2_use-external-HTSlib.patch @@ -0,0 +1,110 @@ +# Patch to use an existing HTSlib rather than the one shipped with tabixpp, and +# build static and dynamic libaries. Based on the PR by outpaddling: +# https://github.com/ekg/tabixpp/pull/10 +# Updated: Petr Král (INUITS) + +diff -u tabixpp-1.1.2/Makefile.orig tabixpp-1.1.2/Makefile +--- tabixpp-1.1.2/Makefile.orig 2023-01-19 09:01:25.000000000 +0100 ++++ tabixpp-1.1.2/Makefile 2023-07-12 11:55:07.513635497 +0200 +@@ -10,74 +10,57 @@ + CC ?= cc + CXX ?= c++ + CXXFLAGS ?= -g -Wall -O2 #-m64 #-arch ppc +-CXXFLAGS += -fPIC +-INCLUDES ?= -Ihtslib +-HTS_HEADERS ?= htslib/htslib/bgzf.h htslib/htslib/tbx.h +-HTS_LIB ?= htslib/libhts.a +-LIBPATH ?= -L. -Lhtslib ++CPPFLAGS ?= -Ihtslib ++LDLIBS ?= -lhts -llzma -lbz2 -lz -lpthread -lm + +-DESTDIR ?= stage + PREFIX ?= /usr/local + STRIP ?= strip + INSTALL ?= install -c + MKDIR ?= mkdir -p + AR ?= ar ++ARFLAGS ?= rs + + DFLAGS = -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE + BIN = tabix++ +-LIB = libtabix.a ++LIB = libtabixpp.a + SOVERSION = 1 +-SLIB = libtabix.so.$(SOVERSION) ++SLIB = libtabixpp.so + OBJS = tabix.o +-SUBDIRS = . + +-.SUFFIXES:.c .o ++LIBDIR = $(DESTDIR)$(PREFIX)/lib ++BINDIR = $(DESTDIR)$(PREFIX)/bin ++INCDIR = $(DESTDIR)$(PREFIX)/include/tabixpp + +-.c.o: +- $(CC) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@ ++.SUFFIXES:.cpp .o .pico .so + +-all-recur lib-recur clean-recur cleanlocal-recur install-recur: +- @target=`echo $@ | sed s/-recur//`; \ +- wdir=`pwd`; \ +- list='$(SUBDIRS)'; for subdir in $$list; do \ +- cd $$subdir; \ +- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CXXFLAGS="$(CXXFLAGS)" \ +- INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target \ +- || exit 1; \ +- cd $$wdir; \ +- done; ++.cpp.o: ++ $(CXX) $(CXXFLAGS) $(DFLAGS) -I. $(CPPFLAGS) -c -o $@ $< + +-all: $(BIN) $(LIB) $(SLIB) ++.cpp.pico: ++ $(CXX) $(CXXFLAGS) $(DFLAGS) -I. $(CPPFLAGS) -fPIC -c -o $@ $< + +-tabix.o: $(HTS_HEADERS) tabix.cpp tabix.hpp +- $(CXX) $(CXXFLAGS) -c tabix.cpp $(INCLUDES) +- +-htslib/libhts.a: +- cd htslib && $(MAKE) lib-static ++all: $(BIN) $(SLIB) $(LIB) + + $(LIB): $(OBJS) +- $(AR) rs $(LIB) $(OBJS) +- +-$(SLIB): $(OBJS) +- $(CXX) -shared -Wl,-soname,$(SLIB) -o $(SLIB) $(OBJS) ++ $(AR) $(ARFLAGS) $@ $^ + +-tabix++: $(OBJS) main.cpp $(HTS_LIB) +- $(CXX) $(CXXFLAGS) -o $@ main.cpp $(OBJS) $(INCLUDES) $(LIBPATH) \ +- -lhts -lpthread -lm -lz -lcurl -llzma -lbz2 ++$(SLIB): $(OBJS:.o=.pico) ++ $(CXX) -shared -Wl,-soname,$(SLIB).$(SOVERSION) $(LDFLAGS) -o $@ $^ $(LDLIBS) ++ ln -sf $@ $(SLIB).$(SOVERSION) + +-test: all +- ./tabix++ test/vcf_file.vcf.gz ++$(BIN): $(OBJS) main.cpp ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ main.cpp $(OBJS) $(LDLIBS) + + install: all +- $(MKDIR) $(DESTDIR)$(PREFIX)/bin +- $(MKDIR) $(DESTDIR)$(PREFIX)/include +- $(MKDIR) $(DESTDIR)$(PREFIX)/lib +- $(INSTALL) $(BIN) $(DESTDIR)$(PREFIX)/bin +- $(INSTALL) *.hpp $(DESTDIR)$(PREFIX)/include +- $(INSTALL) $(LIB) $(SLIB) $(DESTDIR)$(PREFIX)/lib ++ $(MKDIR) $(BINDIR) ++ $(MKDIR) $(LIBDIR) ++ $(MKDIR) $(INCDIR) ++ $(INSTALL) $(BIN) $(BINDIR) ++ $(INSTALL) *.hpp $(INCDIR) ++ $(INSTALL) $(LIB) $(SLIB) $(SLIB).$(SOVERSION) $(LIBDIR) + + install-strip: install +- $(STRIP) $(DESTDIR)$(PREFIX)/bin/$(BIN) $(DESTDIR)$(PREFIX)/lib/$(SLIB) ++ $(STRIP) $(BINDIR)/$(BIN) $(LIBDIR)/$(LIB) + + cleanlocal: + rm -rf $(BIN) $(LIB) $(SLIB) $(OBJS) $(DESTDIR) From 0ef1406b081d293a3354eb2c39ff95aef8b7e181 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 18 Aug 2023 14:09:31 +0200 Subject: [PATCH 8434/9987] adding matplotlib + its deps for gfbf 2023a --- .../c/cppy/cppy-1.2.1-GCCcore-12.3.0.eb | 32 ++++++++ .../c/cppy/cppy-1.2.1-manual_version.patch | 69 ++++++++++++++++ .../matplotlib-3.7.2-fix_setup.patch | 22 +++++ .../matplotlib/matplotlib-3.7.2-gfbf-2023a.eb | 82 +++++++++++++++++++ .../meson-python-0.13.2-GCCcore-12.3.0.eb | 38 +++++++++ .../p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb | 32 ++++++++ .../q/Qhull/Qhull-2020.2-GCCcore-12.3.0.eb | 40 +++++++++ .../SciPy-bundle-2023.07-gfbf-2023a.eb | 6 +- .../t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb | 38 +++++++++ .../Tkinter/Tkinter-3.11.3-GCCcore-12.3.0.eb | 25 ++++++ 10 files changed, 381 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/cppy/cppy-1.2.1-manual_version.patch create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-fix_setup.patch create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/m/meson-python/meson-python-0.13.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..23edeb73aa1 --- /dev/null +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'cppy' +version = '1.2.1' + +homepage = "https://github.com/nucleic/cppy" +description = """A small C++ header library which makes it easier to write +Python extension modules. The primary feature is a PyObject smart pointer +which automatically handles reference counting and provides convenience +methods for performing common object operations.""" + + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), +] + +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['cppy-1.2.1-manual_version.patch'] +checksums = [ + {'cppy-1.2.1.tar.gz': '83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'}, + {'cppy-1.2.1-manual_version.patch': '048aa0a86fd2e99c6896443b07ec83eaa369724297f639ef74c65c404b8f288f'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-manual_version.patch b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-manual_version.patch new file mode 100644 index 00000000000..b439cd08cc9 --- /dev/null +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-manual_version.patch @@ -0,0 +1,69 @@ +Putting a manually typed version in pyproject.toml, as it wouldnt resolve automatically. +Author: Denis Kristak (Inuits) +diff -ruN cppy-1.2.1_orig/pyproject.toml cppy-1.2.1/pyproject.toml +--- cppy-1.2.1_orig/pyproject.toml 2022-03-30 21:39:41.000000000 +0200 ++++ cppy-1.2.1/pyproject.toml 2023-08-14 14:04:36.664029166 +0200 +@@ -8,6 +8,7 @@ + + [project] + name = "cppy" ++version = "1.2.1" + readme = "README.rst" + requires-python = ">=3.7" + license = {file = "LICENSE"} +@@ -27,8 +28,7 @@ + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: Implementation :: CPython", + ] +-dynamic=["version"] +- ++dynamic=[] + + [project.urls] + homepage = "https://github.com/nucleic/cppy" +@@ -36,42 +36,10 @@ + repository = "https://github.com/nucleic/cppy" + changelog = "https://github.com/nucleic/cppy/blob/main/releasenotes.rst" + +- + [build-system] +-requires = ["setuptools>=61.2", "wheel", "setuptools_scm[toml]>=3.4.3"] ++requires = ["setuptools>=61.2", "wheel"] + build-backend = "setuptools.build_meta" + + [tool.setuptools] + packages = ["cppy"] +-package-data = {cppy = ["include/cppy/*.h"]} +- +-[tool.setuptools_scm] +-write_to = "cppy/version.py" +-write_to_template = """ +-# ----------------------------------------------------------------------------- +-# Copyright (c) 2014-2022, Nucleic Development Team. +-# +-# Distributed under the terms of the Modified BSD License. +-# +-# The full license is in the file LICENSE, distributed with this software. +-# ----------------------------------------------------------------------------- +-# This file is auto-generated by setuptools-scm do NOT edit it. +- +-from collections import namedtuple +- +-#: A namedtuple of the version info for the current release. +-_version_info = namedtuple("_version_info", "major minor micro status") +- +-parts = "{version}".split(".", 3) +-__version_info__ = _version_info( +- int(parts[0]), +- int(parts[1]), +- int(parts[2]), +- parts[3] if len(parts) == 4 else "", +-) +- +-# Remove everything but the 'version_info' from this module. +-del namedtuple, _version_info, parts +- +-__version__ = "{version}" +-""" ++package-data = {cppy = ["include/cppy/*.h"]} +\ No newline at end of file \ No newline at end of file diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-fix_setup.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-fix_setup.patch new file mode 100644 index 00000000000..5d8d2900803 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-fix_setup.patch @@ -0,0 +1,22 @@ +Fixing version (autoresolve fails) and making pyparsing version compatible. +Author: Denis Kristak (Inuits) +diff -ruN matplotlib-3.7.2_orig/setup.py matplotlib-3.7.2/setup.py +--- matplotlib-3.7.2_orig/setup.py 2023-07-05 10:10:26.000000000 +0200 ++++ matplotlib-3.7.2/setup.py 2023-08-15 17:13:13.665147049 +0200 +@@ -270,6 +270,7 @@ + setup( # Finally, pass this all along to setuptools to do the heavy lifting. + name="matplotlib", + description="Python plotting package", ++ version="3.7.2", + author="John D. Hunter, Michael Droettboom", + author_email="matplotlib-users@python.org", + url="https://matplotlib.org", +@@ -325,7 +326,7 @@ + "numpy>=1.20", + "packaging>=20.0", + "pillow>=6.2.0", +- "pyparsing>=2.3.1,<3.1", ++ "pyparsing>=2.3.1,<=3.1", + "python-dateutil>=2.7", + ] + ( + # Installing from a git checkout that is not producing a wheel. \ No newline at end of file diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb new file mode 100644 index 00000000000..85a885405b5 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb @@ -0,0 +1,82 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.7.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('pkgconf', '1.9.5'), # k + ('cppy', '1.2.1'), # k +] + +dependencies = [ + ('Python', '3.11.3'), # k + ('SciPy-bundle', '2023.07'), # k + ('libpng', '1.6.39'), # k + ('freetype', '2.13.0'), # k + ('Tkinter', '%(pyver)s'), # k + ('Pillow', '10.0.0'), # k + ('Qhull', '2020.2'), # k + ('meson-python', '0.13.2'), # k +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.42.0', { + 'modulename': 'fontTools', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/f/fonttools'], + 'checksums': ['614b1283dca88effd20ee48160518e6de275ce9b5456a3134d5f235523fc5065'], + }), + ('Cycler', '0.11.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], + }), + ('kiwisolver', '1.4.4', { + 'patches': ['kiwisolver-1.4.4-fix_version.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': [ + {'kiwisolver-1.4.4.tar.gz': 'd41997519fcba4a1e46eb4a2fe31bc12f0ff957b2b81bac28db24744f333e955'}, + {'kiwisolver-1.4.4-fix_version.patch': '6753afbb3a88856493fcfa0b33989f35742f57bfd41ff3b7f71a98797e1bfbd0'}, + ], + }), + ('contourpy', '1.1.0', { + 'checksums': ['e53046c3863828d21d531cc3b53786e6580eb1ba02477e8681009b6aa0870b21'], + }), + (name, version, { + 'patches': ['matplotlib-3.7.2-fix_setup.patch'], + 'preinstallopts': "sed -e 's/#system_freetype = False/system_freetype = True/g' -e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg && export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': [ + {'matplotlib-3.7.2.tar.gz': 'a8cdb91dddb04436bd2f098b8fdf4b81352e68cf4d2c6756fcc414791076569b'}, + {'matplotlib-3.7.2-fix_setup.patch': '70b38f9fc9f26c67adc38440f5420d7c50d9438353ad08740cbb42a79358fb4f'}, + ], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/meson-python/meson-python-0.13.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/meson-python/meson-python-0.13.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..48c4570903a --- /dev/null +++ b/easybuild/easyconfigs/m/meson-python/meson-python-0.13.2-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'meson-python' +version = '0.13.2' + +homepage = 'https://github.com/mesonbuild/meson-python' +description = "Python build backend (PEP 517) for Meson projects" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Meson', '1.1.1'), +] + +use_pip = True + +exts_list = [ + ('pyproject-metadata', '0.7.1', { + 'checksums': ['0a94f18b108b9b21f3a26a3d541f056c34edcb17dc872a144a15618fed7aef67'], + }), + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + (name, version, { + 'modulename': 'mesonpy', + 'sources': ['meson_python-%(version)s.tar.gz'], + 'checksums': ['80bc9de898acd36eb4b945afaaf7a2b4ca00189c51870d535e329761910cf8ea'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8e3ebcc3888 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '10.0.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9c82b5b3e043c7af0d95792d0d20ccf68f61a1fec6b3530e718b688422727396'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), # k + ('libjpeg-turbo', '2.1.5.1'), # k + ('libpng', '1.6.39'), # k + ('zlib', '1.2.13'), # k + ('LibTIFF', '4.5.0'), # k + ('freetype', '2.13.0') # k +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..818323a0922 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb index d634617be9f..f2e2b3b861a 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb @@ -52,6 +52,8 @@ exts_list = [ 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], }), ('scipy', '1.11.1', { + 'enable_slow_tests': True, + 'ignore_test_result': False, 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', @@ -62,8 +64,6 @@ exts_list = [ {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, ], - 'enable_slow_tests': True, - 'ignore_test_result': False, }), ('numexpr', '2.8.4', { 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], @@ -82,8 +82,8 @@ exts_list = [ 'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'], }), ('deap', '1.4.0', { - 'checksums': ['ffef2921932a0edbe634fcb6d156189e7a364bf638a2af4ae5d59931a9a4c8cc'], 'modulename': 'deap.base', + 'checksums': ['ffef2921932a0edbe634fcb6d156189e7a364bf638a2af4ae5d59931a9a4c8cc'], }), ] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b56f843e9e6 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.13' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['2e65fa069a23365440a3c56c556b8673b5e32a283800d8d9b257e3f584ce0675'] + +# patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Tcl', version), + ('X11', '20230603'), + ('zlib', '1.2.13'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0fbcafae5d2 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.3-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +name = 'Tkinter' +version = '3.11.3' + +homepage = 'https://python.org/' +description = "Tkinter module, built with the Python buildsystem" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['1a79f3df32265d9e6625f1a0b31c28eb1594df911403d11f3320ee1da1b3e048'] + +builddependencies = [ + ('binutils', '2.40'), # k + ('libffi', '3.4.4'), # k +] + +dependencies = [ + ('Python', '3.11.3'), # k + ('Tk', '8.6.13'), # k + ('zlib', '1.2.13'), # k +] + +moduleclass = 'lang' From 2ee93828cf347829baba347829bb4f3c736f4205 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 18 Aug 2023 14:14:12 +0200 Subject: [PATCH 8435/9987] adding graphviz-python and its deps for GCCcore 12.3.0 --- .../a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb | 10 +- .../at-spi2-atk-2.38.0-GCCcore-12.3.0.eb | 18 ++-- .../at-spi2-core-2.49.90-GCCcore-12.3.0.eb | 18 ++-- .../g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb | 70 ++++++++++++++ .../Gdk-Pixbuf-2.42.9-GCCcore-12.3.0.eb | 46 +++++++++ .../Ghostscript-10.01.2-GCCcore-12.3.0.eb | 59 ++++++++++++ .../Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb | 94 +++++++++++++++++++ .../graphviz-python-0.20.1-GCCcore-12.3.0.eb | 30 ++++++ .../Python-2.7.18-GCCcore-12.3.0-bare.eb | 32 +++++++ .../q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb | 77 +++++++++++++++ .../s/SWIG/SWIG-4.1.1-GCCcore-12.3.0.eb | 24 +++++ 11 files changed, 455 insertions(+), 23 deletions(-) create mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.9-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.20.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0-bare.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb index e975d98ac9c..86241944500 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb @@ -17,11 +17,11 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] builddependencies = [ - ('binutils', '2.40'), - ('Meson', '1.1.1'), - ('Ninja', '1.11.1'), - ('pkgconf', '1.9.5'), - ('GObject-Introspection', '1.76.1'), + ('binutils', '2.40'), # k + ('Meson', '1.1.1'), # k + ('Ninja', '1.11.1'), # k + ('pkgconf', '1.9.5'), # k + ('GObject-Introspection', '1.76.1'), # k ] dependencies = [ diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb index 5dbd5efc816..6ff90b0e6ce 100644 --- a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb @@ -13,18 +13,18 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] builddependencies = [ - ('binutils', '2.40'), - ('Meson', '1.1.1'), - ('Ninja', '1.11.1'), - ('pkgconf', '1.9.5'), + ('binutils', '2.40'), # k + ('Meson', '1.1.1'), # k + ('Ninja', '1.11.1'), # k + ('pkgconf', '1.9.5'), # k ] dependencies = [ - ('GLib', '2.77.1'), - ('DBus', '1.15.4'), - ('at-spi2-core', '2.49.90'), - ('libxml2', '2.11.4'), - ('ATK', '2.38.0'), + ('GLib', '2.77.1'), # k + ('DBus', '1.15.4'), # k + ('at-spi2-core', '2.49.90'), # k + ('libxml2', '2.11.4'), # k + ('ATK', '2.38.0'), # k ] configopts = "--libdir lib " diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb index d6c6af7fbd5..cf53f12fd73 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb @@ -15,18 +15,18 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['1e6612755d71bbe952156dc051b281d1a4326a5696ac3bbc8cfd5ac8fd971f18'] builddependencies = [ - ('binutils', '2.40'), - ('Meson', '1.1.1'), - ('Ninja', '1.11.1'), - ('GObject-Introspection', '1.76.1'), - ('gettext', '0.21.1'), - ('pkgconf', '1.9.5'), + ('binutils', '2.40'), # k + ('Meson', '1.1.1'), # k + ('Ninja', '1.11.1'), # k + ('GObject-Introspection', '1.76.1'), # k + ('gettext', '0.21.1'), # k + ('pkgconf', '1.9.5'), # k ] dependencies = [ - ('GLib', '2.77.1'), - ('DBus', '1.15.4'), - ('X11', '20230603'), + ('GLib', '2.77.1'), # k + ('DBus', '1.15.4'), # k + ('X11', '20230603'), # k ] configopts = "--libdir lib " diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bbf842dd48d --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb @@ -0,0 +1,70 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.35' # not updating version, as the latest one doesn't work on configure basis + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), # k + ('Autotools', '20220317'), # k + ('GObject-Introspection', '1.76.1'), # k + ('gettext', '0.21.1'), # k + ('pkgconf', '1.9.5'), # k + ('cairo', '1.17.8'), # k + ('Perl', '5.36.1'), # k +] +dependencies = [ + ('ATK', '2.38.0'), # k + ('at-spi2-atk', '2.38.0'), # k + ('Gdk-Pixbuf', '2.42.9'), # k + ('Pango', '1.50.14'), # k + ('libepoxy', '1.5.10'), # k + ('X11', '20230603'), # k + ('FriBidi', '1.0.12'), # k +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + # fix packaging issue, see https://gitlab.gnome.org/GNOME/gtk/-/issues/5355 + 'preconfigopts': "mv testsuite/gtk/gtkresources.c gtk/ && ", + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + }), + ('adwaita-icon-theme', '42.0', { + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'preconfigopts': 'autoreconf -f -i && ', + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.9-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f4ec4a873ee --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.9-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.9' + +homepage = 'https://docs.gtk.org/gdk-pixbuf/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['28f7958e7bf29a32d4e963556d241d0a41a6786582ff6a5ad11665e0347fc962'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('GObject-Introspection', '1.76.1'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.0'), + ('X11', '20230603'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1aef2844883 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '10.01.2' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4cd61a07fec161bee35da0211a5e5cde8ff8a0aaf942fc0176715e499d21661'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), # k + ('libpng', '1.6.39'), # k + ('freetype', '2.13.0'), # k + ('libjpeg-turbo', '2.1.5.1'), # k + ('expat', '2.5.0'), # k + ('GLib', '2.77.1'), # k + ('cairo', '1.17.8'), # k + ('LibTIFF', '4.5.0'), # k + ('GTK3', '3.24.35'), # k +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic --disable-hidden-visibility" + +# Avoid race condition in build if too much parallelism is used +maxparallel = 4 + +postinstallcmds = [ + # build and install shared libs + "make so && make soinstall", + # install header files + "mkdir -p %(installdir)s/include/ghostscript", + "install -v -m644 base/*.h %(installdir)s/include/ghostscript", + "install -v -m644 psi/*.h %(installdir)s/include/ghostscript", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/ghostscript', 'include/ghostscript', 'share/man'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b79489acb71 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,94 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '8.1.0' +local_pyver_major = '3' + +homepage = 'https://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.com/graphviz/graphviz/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_skip-install-data-hook.patch'] +checksums = [ + {'graphviz-8.1.0.tar.gz': '2e4dfee3c24925ad51d1e76a9fb2b19b26a5a0049ef7be6d3e52667aac72eabe'}, + {'Graphviz-8.1.0_skip-install-data-hook.patch': '834666f1b5a8eff35f30899419e322739d71a2936408b27c8ffb4423a99a38e1'}, +] + +builddependencies = [ + ('Autotools', '20220317'), # k + ('binutils', '2.40'), # k + ('Bison', '3.8.2'), # k + ('flex', '2.6.4'), # k + ('SWIG', '4.1.1'), # k + ('pkgconf', '1.9.5'), # k +] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Python', '3.11.3'), # k + ('FriBidi', '1.0.12'), # k + ('Gdk-Pixbuf', '2.42.9'), # k + ('Ghostscript', '10.01.2'), # k + ('GTS', '0.7.6'), # k + ('libgd', '2.3.3'), # k + ('Pango', '1.50.14'), # k + ('Perl', '5.36.1'), # k + ('Qt5', '5.15.10'), # k + ('Tcl', '8.6.13'), # k + ('zlib', '1.2.13'), # k + ('bzip2', '1.0.8'), # k + ('libjpeg-turbo', '2.1.5.1'), # k + ('expat', '2.5.0'), # k +] + +preconfigopts = './autogen.sh NOCONFIG && ' + +configopts = '--enable-python%s=yes ' % local_pyver_major +configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' +# Use ltdl from libtool in EB +configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' +configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' +# Override the hardcoded paths to Java libraries +configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' +configopts += '--with-javalibdir=$JAVA_HOME/lib' +configopts += '--with-expatincludedir=$EBROOTEXPAT/include --with-expatlibdir=$EBROOTEXPAT/lib' +configopts += '--with-zincludedir=$EBROOTZLIB/include --with-zlibdir=$EBROOTZLIB/lib' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +postinstallcmds = ['%(installdir)s/bin/dot -c'] # Writes plugin configuration + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acyclic', 'bcomps', 'ccomps', 'cluster', 'diffimg', 'dijkstra', 'dot', + 'dot_builtins', 'edgepaint', 'gc', 'gml2gv', 'graphml2gv', 'gv2gml', + 'gvcolor', 'gvedit', 'gvgen', 'gvmap', 'gvmap.sh', 'gvpack', 'gvpr', 'gxl2gv', + 'neato', 'mm2gv', 'nop', 'prune', 'sccmap', 'tred', 'unflatten', + 'vimdot']] + + ['lib/%s.%s' % (x, SHLIB_EXT) for x in ['libcdt', 'libcgraph', 'libgvc', 'libgvpr', 'liblab_gamut', + 'libpathplan', 'libxdot']], + 'dirs': ['include', 'lib/graphviz', 'lib/graphviz/java', 'lib/graphviz/python%s' % local_pyver_major, + 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = [ + ("test ! -d $EBROOTTCL/lib/*/graphviz", ''), + ("test ! -d $EBROOTTCL/lib64/*/graphviz", ''), + ('python', '-c "import gv"'), +] + +modextrapaths = { + 'CLASSPATH': 'lib/graphviz/java', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'PYTHONPATH': 'lib/graphviz/python%s' % local_pyver_major, + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.20.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.20.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7791b18b3dc --- /dev/null +++ b/easybuild/easyconfigs/g/graphviz-python/graphviz-python-0.20.1-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'graphviz-python' +version = '0.20.1' + +homepage = 'https://pypi.python.org/pypi/graphviz' +description = """Simple Python interface for Graphviz""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/g/graphviz'] +sources = ['graphviz-%(version)s.zip'] +checksums = ['8c58f14adaa3b947daf26c19bc1e98c4e0702cdc31cf99153e6f06904d492bf8'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Graphviz', '8.1.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'graphviz'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0-bare.eb new file mode 100644 index 00000000000..b529c6fdaac --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0-bare.eb @@ -0,0 +1,32 @@ +name = 'Python' +version = '2.7.18' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +builddependencies = [ + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('binutils', '2.40'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.13'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('SQLite', '3.42.0'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..53e5d9b8050 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb @@ -0,0 +1,77 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.15.10' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] +patches = [ + 'Qt5-5.13.1_fix-avx2.patch', + 'Qt5-5.13.1_fix-qmake-libdir.patch', + # 'Qt5-5.14.1_fix-OF-Gentoo.patch', + # 'Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch', + # 'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch', + 'Qt5-5.15.7_GCC-12.patch', +] +checksums = [ + {'qt-everywhere-opensource-src-5.15.10.tar.xz': 'b545cb83c60934adc9a6bbd27e2af79e5013de77d46f5b9f5bb2a3c762bf55ca'}, + {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, + {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, + {'Qt5-5.15.7_GCC-12.patch': '9a5bde91b223a3e2e90d3d6bec107af69a1a0f18d789593738a953080473fa68'}, +] + +builddependencies = [ + ('binutils', '2.40'), # k + ('pkgconf', '1.9.5'), # k + # deps for QtWebEngine + ('Bison', '3.8.2'), # k + ('flex', '2.6.4'), # k + ('gperf', '3.1'), # k + ('Ninja', '1.11.1'), # k + # Qt5WebEngine has build dependency on Python 2 + ('Python', '2.7.18', '-bare'), # k + ('re2c', '3.1'), # k +] + +dependencies = [ + ('double-conversion', '3.3.0'), # k + ('GLib', '2.77.1'), # k + ('PCRE2', '10.42'), # k + ('libpng', '1.6.39'), # k + ('HarfBuzz', '5.3.1'), # k + ('graphite2', '1.3.14'), # k + # deps for QtWebEngine + ('X11', '20230603'), # k + ('fontconfig', '2.14.2'), # k + ('DBus', '1.15.4'), # k + ('libevent', '2.1.12'), # k + ('libGLU', '9.0.3'), # k + ('libjpeg-turbo', '2.1.5.1'), # k + ('NSS', '3.89.1'), # k + ('snappy', '1.1.10'), # k + ('JasPer', '4.0.0'), # k + ('bzip2', '1.0.8'), # k + ('OpenSSL', '1.1', '', SYSTEM), # k + ('ICU', '73.2'), # k + ('nodejs', '18.17.1'), # k +] + +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +# qtwayland fails to build on (some) Centos 7 systems +configopts = '-skip qtgamepad -skip qtwayland' + +# make sure QtWebEngine component is being built & installed +check_qtwebengine = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e3e212e0f5e --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +name = 'SWIG' +version = '4.1.1' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2af08aced8fcd65cdb5cc62426768914bedc735b1c250325203716f78e39ac9b'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('zlib', '1.2.13'), + ('PCRE', '8.45'), +] + +configopts = '--without-alllang --with-boost=no' + +moduleclass = 'devel' From 22e74361f7284aa0ca4db12e3828d97cbd5114f9 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:16:20 +0200 Subject: [PATCH 8436/9987] Update ATK-2.38.0-GCCcore-12.3.0.eb removing my debug comments --- .../easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb index 86241944500..e975d98ac9c 100644 --- a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.3.0.eb @@ -17,11 +17,11 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] builddependencies = [ - ('binutils', '2.40'), # k - ('Meson', '1.1.1'), # k - ('Ninja', '1.11.1'), # k - ('pkgconf', '1.9.5'), # k - ('GObject-Introspection', '1.76.1'), # k + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('GObject-Introspection', '1.76.1'), ] dependencies = [ From 11398aa93d132da1f6ca616106ffc95c6a59d305 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:17:04 +0200 Subject: [PATCH 8437/9987] Update at-spi2-atk-2.38.0-GCCcore-12.3.0.eb removing debug comments --- .../at-spi2-atk-2.38.0-GCCcore-12.3.0.eb | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb index 6ff90b0e6ce..5dbd5efc816 100644 --- a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb @@ -13,18 +13,18 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] builddependencies = [ - ('binutils', '2.40'), # k - ('Meson', '1.1.1'), # k - ('Ninja', '1.11.1'), # k - ('pkgconf', '1.9.5'), # k + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), ] dependencies = [ - ('GLib', '2.77.1'), # k - ('DBus', '1.15.4'), # k - ('at-spi2-core', '2.49.90'), # k - ('libxml2', '2.11.4'), # k - ('ATK', '2.38.0'), # k + ('GLib', '2.77.1'), + ('DBus', '1.15.4'), + ('at-spi2-core', '2.49.90'), + ('libxml2', '2.11.4'), + ('ATK', '2.38.0'), ] configopts = "--libdir lib " From 987596b576050ea8c7ae71af4d467f63dd63ac87 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:17:49 +0200 Subject: [PATCH 8438/9987] Update at-spi2-core-2.49.90-GCCcore-12.3.0.eb removing debug comments --- .../at-spi2-core-2.49.90-GCCcore-12.3.0.eb | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb index cf53f12fd73..d6c6af7fbd5 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb @@ -15,18 +15,18 @@ sources = [SOURCELOWER_TAR_XZ] checksums = ['1e6612755d71bbe952156dc051b281d1a4326a5696ac3bbc8cfd5ac8fd971f18'] builddependencies = [ - ('binutils', '2.40'), # k - ('Meson', '1.1.1'), # k - ('Ninja', '1.11.1'), # k - ('GObject-Introspection', '1.76.1'), # k - ('gettext', '0.21.1'), # k - ('pkgconf', '1.9.5'), # k + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.76.1'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.5'), ] dependencies = [ - ('GLib', '2.77.1'), # k - ('DBus', '1.15.4'), # k - ('X11', '20230603'), # k + ('GLib', '2.77.1'), + ('DBus', '1.15.4'), + ('X11', '20230603'), ] configopts = "--libdir lib " From ffe7481a816a36cc05c6bb3334fc8184e89cee3c Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:18:24 +0200 Subject: [PATCH 8439/9987] Update Qt5-5.15.10-GCCcore-12.3.0.eb removing unnecessary patches --- easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb index 53e5d9b8050..ea27cee9e8b 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb @@ -19,9 +19,6 @@ sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] patches = [ 'Qt5-5.13.1_fix-avx2.patch', 'Qt5-5.13.1_fix-qmake-libdir.patch', - # 'Qt5-5.14.1_fix-OF-Gentoo.patch', - # 'Qt5-5.15.2_fix-qtwebengine-abseil-cpp-glibc-2.34.patch', - # 'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch', 'Qt5-5.15.7_GCC-12.patch', ] checksums = [ From 27b2a4a130f9ad7ac6fa94f9bd3ae611f2e526f7 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:19:20 +0200 Subject: [PATCH 8440/9987] Update GTK3-3.24.35-GCCcore-12.3.0.eb removing debug commnets --- .../g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb index bbf842dd48d..5cf20d415fc 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb @@ -14,22 +14,22 @@ description = """GTK+ is the primary library used to construct user interfaces i toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ - ('binutils', '2.40'), # k - ('Autotools', '20220317'), # k - ('GObject-Introspection', '1.76.1'), # k - ('gettext', '0.21.1'), # k - ('pkgconf', '1.9.5'), # k - ('cairo', '1.17.8'), # k - ('Perl', '5.36.1'), # k + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('GObject-Introspection', '1.76.1'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.5'), + ('cairo', '1.17.8'), + ('Perl', '5.36.1'), ] dependencies = [ - ('ATK', '2.38.0'), # k - ('at-spi2-atk', '2.38.0'), # k - ('Gdk-Pixbuf', '2.42.9'), # k - ('Pango', '1.50.14'), # k - ('libepoxy', '1.5.10'), # k - ('X11', '20230603'), # k - ('FriBidi', '1.0.12'), # k + ('ATK', '2.38.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.9'), + ('Pango', '1.50.14'), + ('libepoxy', '1.5.10'), + ('X11', '20230603'), + ('FriBidi', '1.0.12'), ] default_easyblock = 'ConfigureMake' From 5edf46daa7999caad580f4b3f32295fb285f50f5 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:20:09 +0200 Subject: [PATCH 8441/9987] Update Ghostscript-10.01.2-GCCcore-12.3.0.eb removing debug comments --- .../Ghostscript-10.01.2-GCCcore-12.3.0.eb | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb index 1aef2844883..714e8c650f2 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb @@ -22,15 +22,15 @@ builddependencies = [ ] dependencies = [ - ('zlib', '1.2.13'), # k - ('libpng', '1.6.39'), # k - ('freetype', '2.13.0'), # k - ('libjpeg-turbo', '2.1.5.1'), # k - ('expat', '2.5.0'), # k - ('GLib', '2.77.1'), # k - ('cairo', '1.17.8'), # k - ('LibTIFF', '4.5.0'), # k - ('GTK3', '3.24.35'), # k + ('zlib', '1.2.13'), + ('libpng', '1.6.39'), + ('freetype', '2.13.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('expat', '2.5.0'), + ('GLib', '2.77.1'), + ('cairo', '1.17.8'), + ('LibTIFF', '4.5.0'), + ('GTK3', '3.24.35'), ] # Do not use local copies of zlib, jpeg, freetype, and png From ff52b51a6939194db8dbdd9c4e36c7bb191d52b7 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:20:59 +0200 Subject: [PATCH 8442/9987] Update Graphviz-8.1.0-GCCcore-12.3.0.eb removing debug comments --- .../Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb | 40 +++++++++---------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb index b79489acb71..0296c8bf5a4 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb @@ -22,30 +22,30 @@ checksums = [ ] builddependencies = [ - ('Autotools', '20220317'), # k - ('binutils', '2.40'), # k - ('Bison', '3.8.2'), # k - ('flex', '2.6.4'), # k - ('SWIG', '4.1.1'), # k - ('pkgconf', '1.9.5'), # k + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('SWIG', '4.1.1'), + ('pkgconf', '1.9.5'), ] dependencies = [ ('Java', '11', '', SYSTEM), - ('Python', '3.11.3'), # k - ('FriBidi', '1.0.12'), # k - ('Gdk-Pixbuf', '2.42.9'), # k - ('Ghostscript', '10.01.2'), # k - ('GTS', '0.7.6'), # k - ('libgd', '2.3.3'), # k - ('Pango', '1.50.14'), # k - ('Perl', '5.36.1'), # k - ('Qt5', '5.15.10'), # k - ('Tcl', '8.6.13'), # k - ('zlib', '1.2.13'), # k - ('bzip2', '1.0.8'), # k - ('libjpeg-turbo', '2.1.5.1'), # k - ('expat', '2.5.0'), # k + ('Python', '3.11.3'), + ('FriBidi', '1.0.12'), + ('Gdk-Pixbuf', '2.42.9'), + ('Ghostscript', '10.01.2'), + ('GTS', '0.7.6'), + ('libgd', '2.3.3'), + ('Pango', '1.50.14'), + ('Perl', '5.36.1'), + ('Qt5', '5.15.10'), + ('Tcl', '8.6.13'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('libjpeg-turbo', '2.1.5.1'), + ('expat', '2.5.0'), ] preconfigopts = './autogen.sh NOCONFIG && ' From b595e4509a6826e0a43d1800e4fddca2064fc287 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:22:06 +0200 Subject: [PATCH 8443/9987] Update Qt5-5.15.10-GCCcore-12.3.0.eb removing debug comments --- .../q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb | 54 +++++++++---------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb index ea27cee9e8b..3888b70cace 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb @@ -29,39 +29,39 @@ checksums = [ ] builddependencies = [ - ('binutils', '2.40'), # k - ('pkgconf', '1.9.5'), # k + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), # deps for QtWebEngine - ('Bison', '3.8.2'), # k - ('flex', '2.6.4'), # k - ('gperf', '3.1'), # k - ('Ninja', '1.11.1'), # k + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.11.1'), # Qt5WebEngine has build dependency on Python 2 - ('Python', '2.7.18', '-bare'), # k - ('re2c', '3.1'), # k + ('Python', '2.7.18', '-bare'), + ('re2c', '3.1'), ] dependencies = [ - ('double-conversion', '3.3.0'), # k - ('GLib', '2.77.1'), # k - ('PCRE2', '10.42'), # k - ('libpng', '1.6.39'), # k - ('HarfBuzz', '5.3.1'), # k - ('graphite2', '1.3.14'), # k + ('double-conversion', '3.3.0'), + ('GLib', '2.77.1'), + ('PCRE2', '10.42'), + ('libpng', '1.6.39'), + ('HarfBuzz', '5.3.1'), + ('graphite2', '1.3.14'), # deps for QtWebEngine - ('X11', '20230603'), # k - ('fontconfig', '2.14.2'), # k - ('DBus', '1.15.4'), # k - ('libevent', '2.1.12'), # k - ('libGLU', '9.0.3'), # k - ('libjpeg-turbo', '2.1.5.1'), # k - ('NSS', '3.89.1'), # k - ('snappy', '1.1.10'), # k - ('JasPer', '4.0.0'), # k - ('bzip2', '1.0.8'), # k - ('OpenSSL', '1.1', '', SYSTEM), # k - ('ICU', '73.2'), # k - ('nodejs', '18.17.1'), # k + ('X11', '20230603'), + ('fontconfig', '2.14.2'), + ('DBus', '1.15.4'), + ('libevent', '2.1.12'), + ('libGLU', '9.0.3'), + ('libjpeg-turbo', '2.1.5.1'), + ('NSS', '3.89.1'), + ('snappy', '1.1.10'), + ('JasPer', '4.0.0'), + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), + ('ICU', '73.2'), + ('nodejs', '18.17.1'), ] # qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) From d4f0fddd213dbc61b84f67e9b438e67725524430 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 18 Aug 2023 14:23:22 +0200 Subject: [PATCH 8444/9987] adding easyconfigs: CatBoost-1.2-gfbf-2023a.eb, conan-1.60.2-GCCcore-12.3.0.eb, plotly.py-5.16.0-GCCcore-12.3.0.eb and patches: tenacity-8.2.3-fix_version.patch --- .../c/CatBoost/CatBoost-1.2-gfbf-2023a.eb | 44 +++++++++++++ .../c/conan/conan-1.60.2-GCCcore-12.3.0.eb | 64 +++++++++++++++++++ .../plotly.py-5.16.0-GCCcore-12.3.0.eb | 37 +++++++++++ .../tenacity-8.2.3-fix_version.patch | 12 ++++ 4 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/c/conan/conan-1.60.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/plotly.py/plotly.py-5.16.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/plotly.py/tenacity-8.2.3-fix_version.patch diff --git a/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb b/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb new file mode 100644 index 00000000000..2d2eb55b3d5 --- /dev/null +++ b/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'CatBoost' +version = '1.2' + +homepage = 'https://catboost.ai' +description = """CatBoost is a high-performance open source library for gradient boosting on decision trees""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), # k + ('Clang', '16.0.6'), # k + ('SciPy-bundle', '2023.07'), # k + ('matplotlib', '3.7.2'), # k + ('plotly.py', '5.16.0'), # k + ('graphviz-python', '0.20.1'), # k + ('Ninja', '1.11.1'), # k + ('conan', '1.60.2'), # k +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('setuptools', '67.7.2', { + 'checksums': ['f104fa03692a2602fa0fec6c6a9e63b6c8a968de13e17c026957dd1f53d80990'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_disable-widget.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/c/catboost'], + 'sources': ['catboost-%(version)s.tar.gz'], + 'checksums': [ + {'catboost-1.2.tar.gz': '39e53403727ecfbb48156773ef3006b4e71cc35ab49cc9a0cf044b474c34be0c'}, + {'CatBoost-1.2_disable-widget.patch': '468be5b5e9eaf655d407a342b786bb419d4ceaeb9df5c753c256a8bd6d69f9df'}, + ], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/c/conan/conan-1.60.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/conan/conan-1.60.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3c8de0638ed --- /dev/null +++ b/easybuild/easyconfigs/c/conan/conan-1.60.2-GCCcore-12.3.0.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'conan' +version = '1.60.2' # have to stick to an older version because catboost is not compatible with newer one + +homepage = 'https://conan.io' +description = "Decentralized, open-source (MIT), C/C++ package manager." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True + +exts_list = [ + ('bottle', '0.12.25', { + 'checksums': ['e1a9c94970ae6d710b3fb4526294dfeb86f2cb4a81eff3a4b98dc40fb0e5e021'], + }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + ('node-semver', '0.6.1', { + 'modulename': 'semver', + 'checksums': ['4016f7c1071b0493f18db69ea02d3763e98a633606d7c7beca811e53b5ac66b7'], + }), + ('patch-ng', '1.17.4', { + 'checksums': ['627abc5bd723c8b481e96849b9734b10065426224d4d22cd44137004ac0d4ace'], + }), + ('pluginbase', '1.0.1', { + 'checksums': ['ff6c33a98fce232e9c73841d787a643de574937069f0d18147028d70d7dee287'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/conan-io/conan/archive/'], + 'checksums': ['63dc6e92fc7f1d77fe08488bd78cd8a20fdddf454e55e1244107d1aec974377c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/conan'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["conan --help"] + +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.16.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.16.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..1471f01011a --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.16.0-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '5.16.0' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [('Python', '3.11.3')] + +use_pip = True + +exts_list = [ + ('tenacity', '8.2.3', { + 'patches': ['tenacity-8.2.3-fix_version.patch'], + 'checksums': [ + {'tenacity-8.2.3.tar.gz': '5398ef0d78e63f40007c1fb4c0bff96e1911394d2fa8d194f77619c05ff6cc8a'}, + {'tenacity-8.2.3-fix_version.patch': 'eb066e8f70d2dc075fca18e04dbc2a6b0721285815470c602a16c599002b63f7'}, + ], + }), + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + ('plotly', version, { + 'checksums': ['13dc052665dcb4d9eefd89847c0b144984e99aca5c8008f9885d2583b77d8b7d'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/plotly.py/tenacity-8.2.3-fix_version.patch b/easybuild/easyconfigs/p/plotly.py/tenacity-8.2.3-fix_version.patch new file mode 100644 index 00000000000..0bf7c04f34c --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/tenacity-8.2.3-fix_version.patch @@ -0,0 +1,12 @@ +Putting a manually typed version in setup.cfg, as it wouldnt resolve automatically. +Author: Denis Kristak (Inuits)diff -ruN tenacity-8.2.3_orig/setup.cfg tenacity-8.2.3/setup.cfg +--- tenacity-8.2.3_orig/setup.cfg 2023-08-14 15:22:48.000000000 +0200 ++++ tenacity-8.2.3/setup.cfg 2023-08-15 19:47:02.512360441 +0200 +@@ -1,6 +1,7 @@ + [metadata] + name = tenacity + license = Apache 2.0 ++version = 8.2.3 + url = https://github.com/jd/tenacity + summary = Retry code until it succeeds + long_description = Tenacity is a general-purpose retrying library to simplify the task of adding retry behavior to just about anything. From decb69697c252b2e132417a063f18f4496527c8f Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:25:56 +0200 Subject: [PATCH 8445/9987] Update CatBoost-1.2-gfbf-2023a.eb removing debug comments --- .../c/CatBoost/CatBoost-1.2-gfbf-2023a.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb b/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb index 2d2eb55b3d5..b9e7dae7c64 100644 --- a/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb +++ b/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb @@ -13,14 +13,14 @@ builddependencies = [ ] dependencies = [ - ('Python', '3.11.3'), # k - ('Clang', '16.0.6'), # k - ('SciPy-bundle', '2023.07'), # k - ('matplotlib', '3.7.2'), # k - ('plotly.py', '5.16.0'), # k - ('graphviz-python', '0.20.1'), # k - ('Ninja', '1.11.1'), # k - ('conan', '1.60.2'), # k + ('Python', '3.11.3'), + ('Clang', '16.0.6'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('plotly.py', '5.16.0'), + ('graphviz-python', '0.20.1'), + ('Ninja', '1.11.1'), + ('conan', '1.60.2'), ] use_pip = True From c97fa01cb8bb98e3c09bac736ad20fcf13564e1f Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:27:59 +0200 Subject: [PATCH 8446/9987] Update matplotlib-3.7.2-gfbf-2023a.eb removing debug comments --- .../matplotlib/matplotlib-3.7.2-gfbf-2023a.eb | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb index 85a885405b5..384d2c5146b 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb @@ -11,19 +11,19 @@ description = """matplotlib is a python 2D plotting library which produces publi toolchain = {'name': 'gfbf', 'version': '2023a'} builddependencies = [ - ('pkgconf', '1.9.5'), # k - ('cppy', '1.2.1'), # k + ('pkgconf', '1.9.5'), + ('cppy', '1.2.1'), ] dependencies = [ - ('Python', '3.11.3'), # k - ('SciPy-bundle', '2023.07'), # k - ('libpng', '1.6.39'), # k - ('freetype', '2.13.0'), # k - ('Tkinter', '%(pyver)s'), # k - ('Pillow', '10.0.0'), # k - ('Qhull', '2020.2'), # k - ('meson-python', '0.13.2'), # k + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('libpng', '1.6.39'), + ('freetype', '2.13.0'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '10.0.0'), + ('Qhull', '2020.2'), + ('meson-python', '0.13.2'), ] use_pip = True From 443c4888175e8ff3469ab8f374d95464e850e278 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:28:38 +0200 Subject: [PATCH 8447/9987] Update Pillow-10.0.0-GCCcore-12.3.0.eb removing debug comments --- .../p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb index 8e3ebcc3888..85a73b42332 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb @@ -15,12 +15,12 @@ checksums = ['9c82b5b3e043c7af0d95792d0d20ccf68f61a1fec6b3530e718b688422727396'] builddependencies = [('binutils', '2.40')] dependencies = [ - ('Python', '3.11.3'), # k - ('libjpeg-turbo', '2.1.5.1'), # k - ('libpng', '1.6.39'), # k - ('zlib', '1.2.13'), # k - ('LibTIFF', '4.5.0'), # k - ('freetype', '2.13.0') # k + ('Python', '3.11.3'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('LibTIFF', '4.5.0'), + ('freetype', '2.13.0') ] download_dep_fail = True From e50a9d92f1db6356168a5e433167ac87c1e3e547 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 14:29:06 +0200 Subject: [PATCH 8448/9987] Update Tkinter-3.11.3-GCCcore-12.3.0.eb removing debug comments --- .../t/Tkinter/Tkinter-3.11.3-GCCcore-12.3.0.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.3-GCCcore-12.3.0.eb index 0fbcafae5d2..b5350694154 100644 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.3-GCCcore-12.3.0.eb @@ -12,14 +12,14 @@ sources = ['Python-%(version)s.tgz'] checksums = ['1a79f3df32265d9e6625f1a0b31c28eb1594df911403d11f3320ee1da1b3e048'] builddependencies = [ - ('binutils', '2.40'), # k - ('libffi', '3.4.4'), # k + ('binutils', '2.40'), + ('libffi', '3.4.4'), ] dependencies = [ - ('Python', '3.11.3'), # k - ('Tk', '8.6.13'), # k - ('zlib', '1.2.13'), # k + ('Python', '3.11.3'), + ('Tk', '8.6.13'), + ('zlib', '1.2.13'), ] moduleclass = 'lang' From 5aad53e12256cf4e484bcfd4b07af341b5518ac5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 18 Aug 2023 14:56:32 +0200 Subject: [PATCH 8449/9987] adding easyconfigs: smithwaterman-20160702-GCCcore-11.3.0.eb --- .../smithwaterman-20160702-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..09254c6395f --- /dev/null +++ b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'smithwaterman' +version = '20160702' +local_commit = '2610e25' + +homepage = 'https://github.com/ekg/smithwaterman' +description = """smith-waterman-gotoh alignment algorithm.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-%(version)s_build-shared-lib.patch'] +checksums = [ + '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8', # 2610e25.tar.gz + '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582', # smithwaterman-20160702_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.38')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' From 2cd83759e31faff8f257c72330c40f33278bb764 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 18 Aug 2023 14:58:58 +0200 Subject: [PATCH 8450/9987] adding easyconfigs: filevercmp-20191210-GCCcore-11.3.0.eb --- .../filevercmp-20191210-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..678a0fa2178 --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'filevercmp' +version = '20191210' +local_commit = 'df20dcc' + +homepage = 'https://github.com/ekg/filevercmp' +description = """filevercmp function as in sort --version-sort.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-%(version)s_build-libs.patch'] +checksums = [ + '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz + '051438f76dd04219abfb283f61101c04d748407031e180b7ae3841344416ec4f', # filevercmp-20191210_build-libs.patch +] + +builddependencies = [('binutils', '2.38')] + +skipsteps = ['configure'] + +installopts = 'DESTDIR="" PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s abca bcac'] + +moduleclass = 'lib' From 525523fbe98d4feb737bb48c6f0d6fb5edd9a7ec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 18 Aug 2023 15:02:18 +0200 Subject: [PATCH 8451/9987] adding easyconfigs: intervaltree-0.1-GCCcore-11.3.0.eb --- .../intervaltree-0.1-GCCcore-11.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..882c7ce71a2 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'intervaltree' +version = '0.1' + +homepage = 'https://github.com/ekg/intervaltree' +description = """An interval tree can be used to efficiently find a set of numeric intervals + overlapping or containing another interval. This library provides a basic implementation of an + interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-numeric_limits.patch'] +checksums = [ + '7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307', # v0.1.tar.gz + '1d69caf35af86c0a55000e1bde3f9a0f19dd63d1d2b6bd48e4e5fecbb1aaa6b0', # intervaltree-0.1_fix-numeric_limits.patch +] + +builddependencies = [('binutils', '2.38')] + +skipsteps = ['configure'] + +preinstallopts = 'DESTDIR="" PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/interval_tree_test', 'include/intervaltree/IntervalTree.h'], + 'dirs': [], +} +sanity_check_commands = ["interval_tree_test"] + +moduleclass = 'lib' From 53cd7ee52b70d890e33a73fd4556f8329a937be0 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 18 Aug 2023 15:02:29 +0200 Subject: [PATCH 8452/9987] Update CatBoost-1.2-gfbf-2023a.eb removed whitespace --- easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb b/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb index b9e7dae7c64..38b618b1a9d 100644 --- a/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb +++ b/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb @@ -14,7 +14,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), - ('Clang', '16.0.6'), + ('Clang', '16.0.6'), ('SciPy-bundle', '2023.07'), ('matplotlib', '3.7.2'), ('plotly.py', '5.16.0'), From b05b616ab1b78bd939567e7b8a147384e91c395d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 18 Aug 2023 15:04:59 +0200 Subject: [PATCH 8453/9987] adding a patch --- .../c/CatBoost/CatBoost-1.2_disable-widget.patch | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/c/CatBoost/CatBoost-1.2_disable-widget.patch diff --git a/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2_disable-widget.patch b/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2_disable-widget.patch new file mode 100644 index 00000000000..0f60fb8bac5 --- /dev/null +++ b/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2_disable-widget.patch @@ -0,0 +1,14 @@ +Disabling optional widget, as it requires `yarn` +Author: Denis Kristak (Inuits) +diff -ruN catboost-1.2_pypi_orig/setup.py catboost-1.2_pypi/setup.py +--- catboost-1.2_pypi_orig/setup.py 2023-08-08 13:41:49.501481901 +0200 ++++ catboost-1.2_pypi/setup.py 2023-08-08 13:43:39.744105439 +0200 +@@ -245,7 +245,7 @@ + + @staticmethod + def initialize_options(command): +- command.no_widget = False ++ command.no_widget = True + command.prebuilt_widget = False + + @staticmethod From d2742f7d516f3f940a6ff30f6057db32ab16aa90 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 18 Aug 2023 15:07:58 +0200 Subject: [PATCH 8454/9987] adding the missing patch --- .../kiwisolver-1.4.4-fix_version.patch | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/kiwisolver-1.4.4-fix_version.patch diff --git a/easybuild/easyconfigs/m/matplotlib/kiwisolver-1.4.4-fix_version.patch b/easybuild/easyconfigs/m/matplotlib/kiwisolver-1.4.4-fix_version.patch new file mode 100644 index 00000000000..43d02209e4e --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/kiwisolver-1.4.4-fix_version.patch @@ -0,0 +1,21 @@ +Putting a manually typed version in pyproject.toml, as it wouldnt resolve automatically. +Author: Denis Kristak (Inuits) +diff -ruN kiwisolver-1.4.4_orig/pyproject.toml kiwisolver-1.4.4/pyproject.toml +--- kiwisolver-1.4.4_orig/pyproject.toml 2022-07-15 22:13:35.000000000 +0200 ++++ kiwisolver-1.4.4/pyproject.toml 2023-08-15 19:17:41.906636001 +0200 +@@ -9,6 +9,7 @@ + [project] + name = "kiwisolver" + description = "A fast implementation of the Cassowary constraint solver" ++version = "1.4.4" + readme = "README.rst" + requires-python = ">=3.7" + license = {file = "LICENSE"} +@@ -30,7 +31,6 @@ + "Programming Language :: Python :: Implementation :: PyPy", + ] + dependencies = ["typing_extensions;python_version<'3.8'"] +-dynamic=["version"] + + [project.urls] + homepage = "https://github.com/nucleic/kiwi" From 511d786ba80e7d65937117bc2a948ae778968515 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 18 Aug 2023 15:26:00 +0200 Subject: [PATCH 8455/9987] fixing code style err --- .../easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb index 384d2c5146b..e92dd93d593 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb @@ -35,6 +35,10 @@ _fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.t _include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " +local_preinstallopts = "sed -e 's/#system_freetype = False/system_freetype = True/g' -e " +local_preinstallopts += "'s/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg" +local_preinstallopts += "&& export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + exts_list = [ ('fonttools', '4.42.0', { 'modulename': 'fontTools', @@ -61,7 +65,7 @@ exts_list = [ }), (name, version, { 'patches': ['matplotlib-3.7.2-fix_setup.patch'], - 'preinstallopts': "sed -e 's/#system_freetype = False/system_freetype = True/g' -e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg && export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': local_preinstallopts, 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': [ {'matplotlib-3.7.2.tar.gz': 'a8cdb91dddb04436bd2f098b8fdf4b81352e68cf4d2c6756fcc414791076569b'}, From 14c02cbacc0157446b8620e67925080bf2061fc7 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 18 Aug 2023 17:01:45 +0200 Subject: [PATCH 8456/9987] GTK3 --- .../g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb | 82 +++++++++++++++++++ .../Wayland/Wayland-1.22.0-GCCcore-12.3.0.eb | 63 ++++++++++++++ 2 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..516eca3dd0c --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb @@ -0,0 +1,82 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.37' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('GObject-Introspection', '1.76.1'), +# ('binutils', '2.40'), +# ('Autotools', '20220317'), +# ('GObject-Introspection', '1.76.1'), +# ('gettext', '0.21.1'), +# ('pkgconf', '1.9.5'), +# ('Perl', '5.36.1'), +] + +dependencies = [ + ('ATK', '2.38.0'), + # ('at-spi2-atk', '2.38.0'), + ('cairo', '1.17.8'), + ('Gdk-Pixbuf', '2.42.10'), + ('GLib', '2.77.1'), + ('Pango', '1.50.14'), + # ('libepoxy', '1.5.10'), + ('X11', '20230603'), + ('FriBidi', '1.0.12'), + # ('Wayland', '1.22.0'), +] + +default_easyblock = 'MesonNinja' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['6745f0b4c053794151fd0f0e2474b077cccff5f83e9dd1bf3d39fe9fe5fb7f57'], + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '44.0', { + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '4889c5601bbfecd25d80ba342209d0a936dcf691ee56bd6eca4cde361f1a664c', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], + 'preconfigopts': 'autoreconf -f -i && ', + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..78544e0dbfd --- /dev/null +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-12.3.0.eb @@ -0,0 +1,63 @@ +# Author: Jasper Grimm (UoY) +# URL of Wayland download changed to GitLab due to changes upstream +# Author: J. Sassmannshausen (Imperial College London/UK) +easyblock = 'Bundle' + +name = 'Wayland' +version = '1.22.0' + +homepage = 'https://wayland.freedesktop.org/' +description = """ +Wayland is a project to define a protocol for a compositor to talk to + its clients as well as a library implementation of the protocol. The + compositor can be a standalone display server running on Linux kernel + modesetting and evdev input devices, an X application, or a wayland + client itself. The clients can be traditional applications, X servers + (rootless or fullscreen) or other display servers. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), +] + +dependencies = [ + ('libffi', '3.4.4'), + ('expat', '2.5.0'), + ('libxml2', '2.11.4'), +] + +default_easyblock = 'MesonNinja' +default_component_specs = { + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('wayland', version, { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/%(namelower)s/-/releases/%(version)s/downloads'], + 'checksums': ['1540af1ea698a471c2d8e9d288332c7e0fd360c8f1d12936ebb7e7cbc2425842'], + 'sources': [SOURCE_TAR_XZ], + 'configopts': "-Ddocumentation=false", + }), + ('wayland-protocols', '1.32', { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/%(namelower)s/-/releases/%(version)s/downloads'], + 'checksums': ['7459799d340c8296b695ef857c07ddef24c5a09b09ab6a74f7b92640d2b1ba11'], + 'sources': [SOURCE_TAR_XZ], + 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH " + }), +] + +_libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']] +sanity_check_paths = { + 'files': ['bin/wayland-scanner'] + _libs, + 'dirs': ['lib'], +} + +sanity_check_commands = ["wayland-scanner --help", "wayland-scanner --version"] + +moduleclass = 'vis' From eee02a6c3c031052a60a8c723b07d574c327b8ce Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Fri, 18 Aug 2023 17:03:12 +0200 Subject: [PATCH 8457/9987] Update GTK3-3.24.37-GCCcore-12.3.0.eb --- .../g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb index 516eca3dd0c..5170bc41464 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb @@ -19,25 +19,19 @@ builddependencies = [ ('Ninja', '1.11.1'), ('pkgconf', '1.9.5'), ('GObject-Introspection', '1.76.1'), -# ('binutils', '2.40'), -# ('Autotools', '20220317'), -# ('GObject-Introspection', '1.76.1'), -# ('gettext', '0.21.1'), -# ('pkgconf', '1.9.5'), -# ('Perl', '5.36.1'), ] dependencies = [ ('ATK', '2.38.0'), - # ('at-spi2-atk', '2.38.0'), + ('at-spi2-atk', '2.38.0'), ('cairo', '1.17.8'), ('Gdk-Pixbuf', '2.42.10'), ('GLib', '2.77.1'), ('Pango', '1.50.14'), - # ('libepoxy', '1.5.10'), + ('libepoxy', '1.5.10'), ('X11', '20230603'), ('FriBidi', '1.0.12'), - # ('Wayland', '1.22.0'), + ('Wayland', '1.22.0'), ] default_easyblock = 'MesonNinja' From b337eae5a1ecb152755563e4a6644956e8a8cbb9 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 18 Aug 2023 17:41:13 +0200 Subject: [PATCH 8458/9987] GTK3 --- easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb index 5170bc41464..3b25b9bcc74 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb @@ -47,10 +47,12 @@ components = [ 'checksums': ['6745f0b4c053794151fd0f0e2474b077cccff5f83e9dd1bf3d39fe9fe5fb7f57'], }), ('hicolor-icon-theme', '0.17', { + 'easyblock': 'ConfigureMake', 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], }), ('adwaita-icon-theme', '44.0', { + 'easyblock': 'ConfigureMake', 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], 'checksums': [ From 027d8b8562b859509e2d40f1f952d40a2724df7a Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 18 Aug 2023 18:24:23 +0200 Subject: [PATCH 8459/9987] disabled patch --- easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb index 3b25b9bcc74..42db0c38bd4 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb @@ -54,11 +54,8 @@ components = [ ('adwaita-icon-theme', '44.0', { 'easyblock': 'ConfigureMake', 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], - 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], 'checksums': [ '4889c5601bbfecd25d80ba342209d0a936dcf691ee56bd6eca4cde361f1a664c', - # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch - 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', ], 'preconfigopts': 'autoreconf -f -i && ', }), From 3f012bb8daa074c077e4e282e5d011f49aab4374 Mon Sep 17 00:00:00 2001 From: casparl Date: Fri, 18 Aug 2023 18:39:11 +0200 Subject: [PATCH 8460/9987] Add new maturin for GCCcore 12.3.0 and change existing one to use CargoPythonPackage, since it's build with Rust --- .../m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb | 4 ++- .../m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb | 32 +++++++++++++++++++ 2 files changed, 35 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb index 57296d955fe..60cc09db4a3 100644 --- a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'CargoPythonPackage' name = 'maturin' version = '1.1.0' @@ -21,6 +21,8 @@ dependencies = [ sources = [SOURCE_TAR_GZ] checksums = ['4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'] +offline = False + use_pip = True sanity_pip_check = True download_dep_fail = True diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..77459e325e8 --- /dev/null +++ b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CargoPythonPackage' + +name = 'maturin' +version = '1.1.0' + +homepage = 'https://github.com/pyo3/maturin' +description = """This project is meant as a zero configuration +replacement for setuptools-rust and milksnake. It supports building +wheels for python 3.5+ on windows, linux, mac and freebsd, can upload +them to pypi and has basic pypy and graalpy support.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'] + +builddependencies = [ + ('binutils', '2.40'), + ('setuptools-rust', '1.6.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Rust', '1.70.0'), +] + +offline = False + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From 4099ba09ecca968999ddcec51794ab08d4ce03b2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 18 Aug 2023 19:48:11 +0200 Subject: [PATCH 8461/9987] adding easyconfigs: html5lib-1.1-GCCcore-12.3.0.eb --- .../h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..04ead9c7b33 --- /dev/null +++ b/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonBundle' + +name = 'html5lib' +version = '1.1' + +homepage = 'https://github.com/html5lib/html5lib-python' +description = "Standards-compliant library for parsing and serializing HTML documents and fragments in Python" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From df5ee552913527d04d7c1b38cd031b842a16b472 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 19 Aug 2023 01:30:14 +0200 Subject: [PATCH 8462/9987] Add dep --- easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb index 04ead9c7b33..5e387e02309 100644 --- a/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} dependencies = [ ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), ] use_pip = True From 294b8e31d7c712ddbdbd021469a4e098886385c0 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 21 Aug 2023 11:04:07 +0200 Subject: [PATCH 8463/9987] Added crate list --- .../m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb | 292 +++++++++++++++++- .../m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb | 288 ++++++++++++++++- 2 files changed, 577 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb index 60cc09db4a3..22ec28cb817 100644 --- a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb @@ -18,13 +18,301 @@ dependencies = [ ('Rust', '1.65.0'), ] +crates = [ + ('adler', '1.0.2'), + ('ahash', '0.7.6'), + ('aho-corasick', '0.7.20'), + ('anyhow', '1.0.71'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64', '0.21.2'), + ('bitflags', '1.3.2'), + ('block-buffer', '0.10.4'), + ('bstr', '1.5.0'), + ('bumpalo', '3.13.0'), + ('byteorder', '1.4.3'), + ('bytes', '1.4.0'), + ('bytesize', '1.2.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cab', '0.4.1'), + ('camino', '1.1.4'), + ('cargo-config2', '0.1.7'), + ('cargo-options', '0.6.0'), + ('cargo-platform', '0.1.2'), + ('cargo-xwin', '0.14.3'), + ('cargo-zigbuild', '0.16.10'), + ('cargo_metadata', '0.15.4'), + ('cbindgen', '0.24.5'), + ('cc', '1.0.79'), + ('cfb', '0.7.3'), + ('cfg-expr', '0.15.2'), + ('cfg-if', '1.0.0'), + ('charset', '0.1.3'), + ('chumsky', '0.9.2'), + ('clap', '4.1.14'), + ('clap_builder', '4.1.14'), + ('clap_complete', '4.2.3'), + ('clap_complete_command', '0.5.1'), + ('clap_complete_fig', '4.2.0'), + ('clap_complete_nushell', '0.1.11'), + ('clap_derive', '4.1.14'), + ('clap_lex', '0.4.1'), + ('cli-table', '0.4.7'), + ('concolor', '0.0.11'), + ('concolor-query', '0.1.0'), + ('configparser', '3.0.2'), + ('console', '0.15.5'), + ('content_inspector', '0.2.4'), + ('core-foundation', '0.9.3'), + ('core-foundation-sys', '0.8.4'), + ('cpufeatures', '0.2.7'), + ('crc32fast', '1.3.2'), + ('crossbeam-channel', '0.5.8'), + ('crossbeam-deque', '0.8.3'), + ('crossbeam-epoch', '0.9.14'), + ('crossbeam-utils', '0.8.15'), + ('crypto-common', '0.1.6'), + ('ctor', '0.1.26'), + ('data-encoding', '2.4.0'), + ('dialoguer', '0.10.4'), + ('diff', '0.1.13'), + ('digest', '0.10.7'), + ('dirs', '5.0.1'), + ('dirs-sys', '0.4.1'), + ('dunce', '1.0.4'), + ('either', '1.8.1'), + ('encode_unicode', '0.3.6'), + ('encoding_rs', '0.8.32'), + ('errno', '0.3.1'), + ('errno-dragonfly', '0.1.2'), + ('fastrand', '1.9.0'), + ('fat-macho', '0.4.6'), + ('filetime', '0.2.21'), + ('flate2', '1.0.26'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.2.0'), + ('fs-err', '2.9.0'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.10'), + ('glob', '0.3.1'), + ('globset', '0.4.10'), + ('goblin', '0.6.1'), + ('hashbrown', '0.12.3'), + ('heck', '0.4.1'), + ('hermit-abi', '0.2.6'), + ('hermit-abi', '0.3.1'), + ('home', '0.5.4'), + ('humantime', '2.1.0'), + ('humantime-serde', '1.1.1'), + ('idna', '0.4.0'), + ('ignore', '0.4.20'), + ('indexmap', '1.9.3'), + ('indicatif', '0.17.5'), + ('indoc', '2.0.1'), + ('instant', '0.1.12'), + ('io-lifetimes', '1.0.11'), + ('is-terminal', '0.4.7'), + ('itertools', '0.10.5'), + ('itoa', '1.0.6'), + ('js-sys', '0.3.63'), + ('keyring', '2.0.3'), + ('lazy_static', '1.4.0'), + ('lddtree', '0.3.2'), + ('libc', '0.2.146'), + ('linux-keyutils', '0.2.3'), + ('linux-raw-sys', '0.3.8'), + ('lock_api', '0.4.9'), + ('log', '0.4.18'), + ('lzxd', '0.1.4'), + ('mailparse', '0.13.8'), + ('matchers', '0.1.0'), + ('memchr', '2.5.0'), + ('memoffset', '0.8.0'), + ('mime', '0.3.17'), + ('mime_guess', '2.0.4'), + ('minijinja', '0.34.0'), + ('minimal-lexical', '0.2.1'), + ('miniz_oxide', '0.7.1'), + ('msi', '0.5.1'), + ('multipart', '0.18.0'), + ('native-tls', '0.2.11'), + ('nom', '7.1.3'), + ('normalize-line-endings', '0.3.0'), + ('normpath', '1.1.1'), + ('nu-ansi-term', '0.46.0'), + ('num_cpus', '1.15.0'), + ('number_prefix', '0.4.0'), + ('once_cell', '1.18.0'), + ('openssl', '0.10.54'), + ('openssl-macros', '0.1.1'), + ('openssl-probe', '0.1.5'), + ('openssl-src', '111.26.0+1.1.1u'), + ('openssl-sys', '0.9.88'), + ('option-ext', '0.2.0'), + ('os_pipe', '1.1.4'), + ('output_vt100', '0.1.3'), + ('overload', '0.1.1'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.6'), + ('path-slash', '0.2.1'), + ('pep440_rs', '0.3.6'), + ('pep508_rs', '0.2.1'), + ('percent-encoding', '2.3.0'), + ('pin-project-lite', '0.2.9'), + ('pkg-config', '0.3.27'), + ('plain', '0.2.3'), + ('platform-info', '2.0.1'), + ('portable-atomic', '1.3.3'), + ('ppv-lite86', '0.2.17'), + ('pretty_assertions', '1.3.0'), + ('proc-macro2', '1.0.60'), + ('psm', '0.1.21'), + ('pyproject-toml', '0.6.1'), + ('python-pkginfo', '0.5.5'), + ('quote', '1.0.28'), + ('quoted_printable', '0.4.8'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rayon', '1.7.0'), + ('rayon-core', '1.11.0'), + ('redox_syscall', '0.2.16'), + ('redox_syscall', '0.3.5'), + ('redox_users', '0.4.3'), + ('regex', '1.7.3'), + ('regex-automata', '0.1.10'), + ('regex-syntax', '0.6.29'), + ('rfc2047-decoder', '0.2.2'), + ('ring', '0.16.20'), + ('rustc_version', '0.4.0'), + ('rustix', '0.37.19'), + ('rustls', '0.20.8'), + ('rustls-pemfile', '1.0.2'), + ('rustversion', '1.0.12'), + ('ryu', '1.0.13'), + ('same-file', '1.0.6'), + ('schannel', '0.1.21'), + ('scopeguard', '1.1.0'), + ('scroll', '0.11.0'), + ('scroll_derive', '0.11.0'), + ('sct', '0.7.0'), + ('security-framework', '2.9.1'), + ('security-framework-sys', '2.9.0'), + ('semver', '1.0.17'), + ('serde', '1.0.164'), + ('serde_derive', '1.0.164'), + ('serde_json', '1.0.96'), + ('serde_spanned', '0.6.2'), + ('sha2', '0.10.6'), + ('sharded-slab', '0.1.4'), + ('shell-escape', '0.1.5'), + ('shell-words', '1.1.0'), + ('shlex', '1.1.0'), + ('similar', '2.2.1'), + ('smallvec', '1.10.0'), + ('smawk', '0.3.1'), + ('snapbox', '0.4.4'), + ('snapbox-macros', '0.3.4'), + ('socks', '0.3.4'), + ('spin', '0.5.2'), + ('stacker', '0.1.15'), + ('static_assertions', '1.1.0'), + ('strsim', '0.10.0'), + ('syn', '1.0.109'), + ('syn', '2.0.18'), + ('tar', '0.4.38'), + ('target-lexicon', '0.12.7'), + ('tempfile', '3.6.0'), + ('termcolor', '1.2.0'), + ('terminal_size', '0.2.6'), + ('textwrap', '0.16.0'), + ('thiserror', '1.0.40'), + ('thiserror-impl', '1.0.40'), + ('thread_local', '1.1.7'), + ('time', '0.3.20'), + ('time-core', '0.1.0'), + ('time-macros', '0.2.8'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('toml', '0.5.11'), + ('toml', '0.7.4'), + ('toml_datetime', '0.6.2'), + ('toml_edit', '0.19.10'), + ('tracing', '0.1.37'), + ('tracing-attributes', '0.1.24'), + ('tracing-core', '0.1.31'), + ('tracing-log', '0.1.3'), + ('tracing-serde', '0.1.3'), + ('tracing-subscriber', '0.3.17'), + ('trycmd', '0.14.11'), + ('twox-hash', '1.6.3'), + ('typenum', '1.16.0'), + ('unicase', '2.6.0'), + ('unicode-bidi', '0.3.13'), + ('unicode-ident', '1.0.9'), + ('unicode-linebreak', '0.1.4'), + ('unicode-normalization', '0.1.22'), + ('unicode-width', '0.1.10'), + ('untrusted', '0.7.1'), + ('ureq', '2.6.2'), + ('url', '2.4.0'), + ('uuid', '1.3.3'), + ('valuable', '0.1.0'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('versions', '4.1.0'), + ('wait-timeout', '0.2.0'), + ('walkdir', '2.3.3'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.86'), + ('wasm-bindgen-backend', '0.2.86'), + ('wasm-bindgen-macro', '0.2.86'), + ('wasm-bindgen-macro-support', '0.2.86'), + ('wasm-bindgen-shared', '0.2.86'), + ('web-sys', '0.3.63'), + ('webpki', '0.22.0'), + ('webpki-roots', '0.22.6'), + ('which', '4.4.0'), + ('wild', '2.1.0'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.5'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.42.0'), + ('windows-sys', '0.48.0'), + ('windows-targets', '0.48.0'), + ('windows_aarch64_gnullvm', '0.42.2'), + ('windows_aarch64_gnullvm', '0.48.0'), + ('windows_aarch64_msvc', '0.42.2'), + ('windows_aarch64_msvc', '0.48.0'), + ('windows_i686_gnu', '0.42.2'), + ('windows_i686_gnu', '0.48.0'), + ('windows_i686_msvc', '0.42.2'), + ('windows_i686_msvc', '0.48.0'), + ('windows_x86_64_gnu', '0.42.2'), + ('windows_x86_64_gnu', '0.48.0'), + ('windows_x86_64_gnullvm', '0.42.2'), + ('windows_x86_64_gnullvm', '0.48.0'), + ('windows_x86_64_msvc', '0.42.2'), + ('windows_x86_64_msvc', '0.48.0'), + ('winnow', '0.4.6'), + ('xattr', '0.2.3'), + ('xwin', '0.2.12'), + ('yansi', '0.5.1'), + ('zeroize', '1.6.0'), + ('zip', '0.6.6'), +] + sources = [SOURCE_TAR_GZ] checksums = ['4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'] -offline = False - use_pip = True sanity_pip_check = True download_dep_fail = True moduleclass = 'tools' + + diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb index 77459e325e8..f907cc04074 100644 --- a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb @@ -23,7 +23,293 @@ dependencies = [ ('Rust', '1.70.0'), ] -offline = False +crates = [ + ('adler', '1.0.2'), + ('ahash', '0.7.6'), + ('aho-corasick', '0.7.20'), + ('anyhow', '1.0.71'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64', '0.21.2'), + ('bitflags', '1.3.2'), + ('block-buffer', '0.10.4'), + ('bstr', '1.5.0'), + ('bumpalo', '3.13.0'), + ('byteorder', '1.4.3'), + ('bytes', '1.4.0'), + ('bytesize', '1.2.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cab', '0.4.1'), + ('camino', '1.1.4'), + ('cargo-config2', '0.1.7'), + ('cargo-options', '0.6.0'), + ('cargo-platform', '0.1.2'), + ('cargo-xwin', '0.14.3'), + ('cargo-zigbuild', '0.16.10'), + ('cargo_metadata', '0.15.4'), + ('cbindgen', '0.24.5'), + ('cc', '1.0.79'), + ('cfb', '0.7.3'), + ('cfg-expr', '0.15.2'), + ('cfg-if', '1.0.0'), + ('charset', '0.1.3'), + ('chumsky', '0.9.2'), + ('clap', '4.1.14'), + ('clap_builder', '4.1.14'), + ('clap_complete', '4.2.3'), + ('clap_complete_command', '0.5.1'), + ('clap_complete_fig', '4.2.0'), + ('clap_complete_nushell', '0.1.11'), + ('clap_derive', '4.1.14'), + ('clap_lex', '0.4.1'), + ('cli-table', '0.4.7'), + ('concolor', '0.0.11'), + ('concolor-query', '0.1.0'), + ('configparser', '3.0.2'), + ('console', '0.15.5'), + ('content_inspector', '0.2.4'), + ('core-foundation', '0.9.3'), + ('core-foundation-sys', '0.8.4'), + ('cpufeatures', '0.2.7'), + ('crc32fast', '1.3.2'), + ('crossbeam-channel', '0.5.8'), + ('crossbeam-deque', '0.8.3'), + ('crossbeam-epoch', '0.9.14'), + ('crossbeam-utils', '0.8.15'), + ('crypto-common', '0.1.6'), + ('ctor', '0.1.26'), + ('data-encoding', '2.4.0'), + ('dialoguer', '0.10.4'), + ('diff', '0.1.13'), + ('digest', '0.10.7'), + ('dirs', '5.0.1'), + ('dirs-sys', '0.4.1'), + ('dunce', '1.0.4'), + ('either', '1.8.1'), + ('encode_unicode', '0.3.6'), + ('encoding_rs', '0.8.32'), + ('errno', '0.3.1'), + ('errno-dragonfly', '0.1.2'), + ('fastrand', '1.9.0'), + ('fat-macho', '0.4.6'), + ('filetime', '0.2.21'), + ('flate2', '1.0.26'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.2.0'), + ('fs-err', '2.9.0'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.10'), + ('glob', '0.3.1'), + ('globset', '0.4.10'), + ('goblin', '0.6.1'), + ('hashbrown', '0.12.3'), + ('heck', '0.4.1'), + ('hermit-abi', '0.2.6'), + ('hermit-abi', '0.3.1'), + ('home', '0.5.4'), + ('humantime', '2.1.0'), + ('humantime-serde', '1.1.1'), + ('idna', '0.4.0'), + ('ignore', '0.4.20'), + ('indexmap', '1.9.3'), + ('indicatif', '0.17.5'), + ('indoc', '2.0.1'), + ('instant', '0.1.12'), + ('io-lifetimes', '1.0.11'), + ('is-terminal', '0.4.7'), + ('itertools', '0.10.5'), + ('itoa', '1.0.6'), + ('js-sys', '0.3.63'), + ('keyring', '2.0.3'), + ('lazy_static', '1.4.0'), + ('lddtree', '0.3.2'), + ('libc', '0.2.146'), + ('linux-keyutils', '0.2.3'), + ('linux-raw-sys', '0.3.8'), + ('lock_api', '0.4.9'), + ('log', '0.4.18'), + ('lzxd', '0.1.4'), + ('mailparse', '0.13.8'), + ('matchers', '0.1.0'), + ('memchr', '2.5.0'), + ('memoffset', '0.8.0'), + ('mime', '0.3.17'), + ('mime_guess', '2.0.4'), + ('minijinja', '0.34.0'), + ('minimal-lexical', '0.2.1'), + ('miniz_oxide', '0.7.1'), + ('msi', '0.5.1'), + ('multipart', '0.18.0'), + ('native-tls', '0.2.11'), + ('nom', '7.1.3'), + ('normalize-line-endings', '0.3.0'), + ('normpath', '1.1.1'), + ('nu-ansi-term', '0.46.0'), + ('num_cpus', '1.15.0'), + ('number_prefix', '0.4.0'), + ('once_cell', '1.18.0'), + ('openssl', '0.10.54'), + ('openssl-macros', '0.1.1'), + ('openssl-probe', '0.1.5'), + ('openssl-src', '111.26.0+1.1.1u'), + ('openssl-sys', '0.9.88'), + ('option-ext', '0.2.0'), + ('os_pipe', '1.1.4'), + ('output_vt100', '0.1.3'), + ('overload', '0.1.1'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.6'), + ('path-slash', '0.2.1'), + ('pep440_rs', '0.3.6'), + ('pep508_rs', '0.2.1'), + ('percent-encoding', '2.3.0'), + ('pin-project-lite', '0.2.9'), + ('pkg-config', '0.3.27'), + ('plain', '0.2.3'), + ('platform-info', '2.0.1'), + ('portable-atomic', '1.3.3'), + ('ppv-lite86', '0.2.17'), + ('pretty_assertions', '1.3.0'), + ('proc-macro2', '1.0.60'), + ('psm', '0.1.21'), + ('pyproject-toml', '0.6.1'), + ('python-pkginfo', '0.5.5'), + ('quote', '1.0.28'), + ('quoted_printable', '0.4.8'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rayon', '1.7.0'), + ('rayon-core', '1.11.0'), + ('redox_syscall', '0.2.16'), + ('redox_syscall', '0.3.5'), + ('redox_users', '0.4.3'), + ('regex', '1.7.3'), + ('regex-automata', '0.1.10'), + ('regex-syntax', '0.6.29'), + ('rfc2047-decoder', '0.2.2'), + ('ring', '0.16.20'), + ('rustc_version', '0.4.0'), + ('rustix', '0.37.19'), + ('rustls', '0.20.8'), + ('rustls-pemfile', '1.0.2'), + ('rustversion', '1.0.12'), + ('ryu', '1.0.13'), + ('same-file', '1.0.6'), + ('schannel', '0.1.21'), + ('scopeguard', '1.1.0'), + ('scroll', '0.11.0'), + ('scroll_derive', '0.11.0'), + ('sct', '0.7.0'), + ('security-framework', '2.9.1'), + ('security-framework-sys', '2.9.0'), + ('semver', '1.0.17'), + ('serde', '1.0.164'), + ('serde_derive', '1.0.164'), + ('serde_json', '1.0.96'), + ('serde_spanned', '0.6.2'), + ('sha2', '0.10.6'), + ('sharded-slab', '0.1.4'), + ('shell-escape', '0.1.5'), + ('shell-words', '1.1.0'), + ('shlex', '1.1.0'), + ('similar', '2.2.1'), + ('smallvec', '1.10.0'), + ('smawk', '0.3.1'), + ('snapbox', '0.4.4'), + ('snapbox-macros', '0.3.4'), + ('socks', '0.3.4'), + ('spin', '0.5.2'), + ('stacker', '0.1.15'), + ('static_assertions', '1.1.0'), + ('strsim', '0.10.0'), + ('syn', '1.0.109'), + ('syn', '2.0.18'), + ('tar', '0.4.38'), + ('target-lexicon', '0.12.7'), + ('tempfile', '3.6.0'), + ('termcolor', '1.2.0'), + ('terminal_size', '0.2.6'), + ('textwrap', '0.16.0'), + ('thiserror', '1.0.40'), + ('thiserror-impl', '1.0.40'), + ('thread_local', '1.1.7'), + ('time', '0.3.20'), + ('time-core', '0.1.0'), + ('time-macros', '0.2.8'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('toml', '0.5.11'), + ('toml', '0.7.4'), + ('toml_datetime', '0.6.2'), + ('toml_edit', '0.19.10'), + ('tracing', '0.1.37'), + ('tracing-attributes', '0.1.24'), + ('tracing-core', '0.1.31'), + ('tracing-log', '0.1.3'), + ('tracing-serde', '0.1.3'), + ('tracing-subscriber', '0.3.17'), + ('trycmd', '0.14.11'), + ('twox-hash', '1.6.3'), + ('typenum', '1.16.0'), + ('unicase', '2.6.0'), + ('unicode-bidi', '0.3.13'), + ('unicode-ident', '1.0.9'), + ('unicode-linebreak', '0.1.4'), + ('unicode-normalization', '0.1.22'), + ('unicode-width', '0.1.10'), + ('untrusted', '0.7.1'), + ('ureq', '2.6.2'), + ('url', '2.4.0'), + ('uuid', '1.3.3'), + ('valuable', '0.1.0'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('versions', '4.1.0'), + ('wait-timeout', '0.2.0'), + ('walkdir', '2.3.3'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.86'), + ('wasm-bindgen-backend', '0.2.86'), + ('wasm-bindgen-macro', '0.2.86'), + ('wasm-bindgen-macro-support', '0.2.86'), + ('wasm-bindgen-shared', '0.2.86'), + ('web-sys', '0.3.63'), + ('webpki', '0.22.0'), + ('webpki-roots', '0.22.6'), + ('which', '4.4.0'), + ('wild', '2.1.0'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.5'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.42.0'), + ('windows-sys', '0.48.0'), + ('windows-targets', '0.48.0'), + ('windows_aarch64_gnullvm', '0.42.2'), + ('windows_aarch64_gnullvm', '0.48.0'), + ('windows_aarch64_msvc', '0.42.2'), + ('windows_aarch64_msvc', '0.48.0'), + ('windows_i686_gnu', '0.42.2'), + ('windows_i686_gnu', '0.48.0'), + ('windows_i686_msvc', '0.42.2'), + ('windows_i686_msvc', '0.48.0'), + ('windows_x86_64_gnu', '0.42.2'), + ('windows_x86_64_gnu', '0.48.0'), + ('windows_x86_64_gnullvm', '0.42.2'), + ('windows_x86_64_gnullvm', '0.48.0'), + ('windows_x86_64_msvc', '0.42.2'), + ('windows_x86_64_msvc', '0.48.0'), + ('winnow', '0.4.6'), + ('xattr', '0.2.3'), + ('xwin', '0.2.12'), + ('yansi', '0.5.1'), + ('zeroize', '1.6.0'), + ('zip', '0.6.6'), +] download_dep_fail = True sanity_pip_check = True From a4029a9e780eb844a2302b0267c789bc4d7a6789 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 21 Aug 2023 11:23:28 +0200 Subject: [PATCH 8464/9987] Added checksums for crates --- .../m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb | 289 +++++++++++++++++- .../m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb | 289 +++++++++++++++++- 2 files changed, 576 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb index 22ec28cb817..152a693ffa4 100644 --- a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb @@ -307,7 +307,294 @@ crates = [ ] sources = [SOURCE_TAR_GZ] -checksums = ['4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'] +checksums = [ + {'maturin-1.1.0.tar.gz': '4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'ahash-0.7.6.tar.gz': 'fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47'}, + {'aho-corasick-0.7.20.tar.gz': 'cc936419f96fa211c1b9166887b38e5e40b19958e5b895be7c1f93adec7071ac'}, + {'anyhow-1.0.71.tar.gz': '9c7d0618f0e0b7e8ff11427422b64564d5fb0be1940354bfe2e0529b18a9d9b8'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'base64-0.13.1.tar.gz': '9e1b586273c5702936fe7b7d6896644d8be71e6314cfe09d3167c95f712589e8'}, + {'base64-0.21.2.tar.gz': '604178f6c5c21f02dc555784810edfb88d34ac2c73b2eae109655649ee73ce3d'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'block-buffer-0.10.4.tar.gz': '3078c7629b62d3f0439517fa394996acacc5cbc91c5a20d8c658e77abd503a71'}, + {'bstr-1.5.0.tar.gz': 'a246e68bb43f6cd9db24bea052a53e40405417c5fb372e3d1a8a7f770a564ef5'}, + {'bumpalo-3.13.0.tar.gz': 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{'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'}, +] builddependencies = [ ('binutils', '2.40'), From 9b27410398e600cfea3e87d1d841092b16233355 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 21 Aug 2023 11:31:10 +0200 Subject: [PATCH 8465/9987] Add furstj's updated patch --- .../o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch | 12 ++++++++++++ .../o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb | 4 ++-- 2 files changed, 14 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch new file mode 100644 index 00000000000..0cd23ac34f7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch @@ -0,0 +1,12 @@ +# - Add mplibEASYBUILDMPI configuration for wmake (OpenMPI version) +# +# author: Jiri Furst +--- /dev/null 2023-03-06 18:30:28.397302047 +0100 ++++ OpenFOAM-v2212/wmake/rules/General/mplibEASYBUILDMPI 2023-03-10 14:52:38.100740228 +0100 +@@ -0,0 +1,6 @@ ++#------------------------------------------------------------------------------ ++# Use openmpi mpicc to obtain settings - mpicc must be available ++ ++include $(GENERAL_RULES)/mpi-mpicc-openmpi ++ ++#------------------------------------------------------------------------------ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb index 74cc6908afa..4aa214ced62 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -17,12 +17,12 @@ source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] patches = [ ('OpenFOAM-v2206-cleanup.patch', 1), - 'OpenFOAM-v1906-wmake-ompi.patch', + 'OpenFOAM-v2212-wmake-OpenMPI.patch', ] checksums = [ {'OpenFOAM-v2306.tgz': 'd7fba773658c0f06ad17f90199565f32e9bf502b7bb03077503642064e1f5344'}, {'OpenFOAM-v2206-cleanup.patch': '25333124581acae57c173587de4ebd6e143b894b1a26e4f0326db8b7e0cb1972'}, - {'OpenFOAM-v1906-wmake-ompi.patch': '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505'}, + {'OpenFOAM-v2212-wmake-OpenMPI.patch': '4f5110e98df1f057dc4b478a004e4ae2dc5cc763899f0d3ceb6773315c5c8ba9'}, ] builddependencies = [ From 3fb462214d4e9214619ff1a4dd066bd645120ee7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 21 Aug 2023 11:37:14 +0200 Subject: [PATCH 8466/9987] Fix patch level --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb index 4aa214ced62..0b40808465f 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -17,7 +17,7 @@ source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] patches = [ ('OpenFOAM-v2206-cleanup.patch', 1), - 'OpenFOAM-v2212-wmake-OpenMPI.patch', + ('OpenFOAM-v2212-wmake-OpenMPI.patch', 1), ] checksums = [ {'OpenFOAM-v2306.tgz': 'd7fba773658c0f06ad17f90199565f32e9bf502b7bb03077503642064e1f5344'}, From 1b9fbc402ae0dd41a4c243e2e5772bba4ce3444a Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 21 Aug 2023 11:52:45 +0200 Subject: [PATCH 8467/9987] Fix formatting errors --- easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb index 152a693ffa4..83d2b282cc5 100644 --- a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.2.0.eb @@ -601,5 +601,3 @@ sanity_pip_check = True download_dep_fail = True moduleclass = 'tools' - - From ed22fe5c4b5abc94304a3468d276c7e2dc2da329 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Mon, 21 Aug 2023 13:39:43 +0200 Subject: [PATCH 8468/9987] wxWidgets-3.2.2.1-GCCcore-12.3.0 --- .../GST-plugins-base-1.22.5-GCCcore-12.3.0.eb | 44 ++++++++++++ .../GStreamer-1.22.5-GCCcore-12.3.0.eb | 51 +++++++++++++ .../Graphene-1.10.8-GCCcore-12.3.0.eb | 32 +++++++++ .../wxWidgets-3.2.2.1-GCCcore-12.3.0.eb | 72 +++++++++++++++++++ 4 files changed, 199 insertions(+) create mode 100644 easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..229786ea4a0 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.5-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-base' +version = '1.22.5' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['edd4338b45c26a9af28c0d35aab964a024c3884ba6f520d8428df04212c8c93a'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.76.1'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.5'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('GLib', '2.77.1'), + ('GStreamer', '1.22.5'), + ('Gdk-Pixbuf', '2.42.10'), + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('Graphene', '1.10.8'), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play', 'device-monitor']] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['app', 'audio', 'video']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..09d16056f86 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.5-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + +name = 'GStreamer' +version = '1.22.5' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] +sources = [SOURCELOWER_TAR_XZ] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.22.5.tar.xz': '4408d7930f381809e85917acc19712f173261ba85bdf20c5567b2a21b1193b61'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('Perl', '5.36.1'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('GObject-Introspection', '1.76.1'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('zlib', '1.2.13'), + ('GMP', '6.2.1'), + ('GSL', '2.7'), + ('GLib', '2.77.1'), + ('libunwind', '1.6.2'), + ('elfutils', '0.189'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'share', 'libexec'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0d432c32c3a --- /dev/null +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'Graphene' +version = '1.10.8' + +homepage = 'https://ebassi.github.io/graphene/' +description = "Graphene is a thin layer of types for graphic libraries" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'ebassi' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['922dc109d2dc5dc56617a29bd716c79dd84db31721a8493a13a5f79109a4a4ed'] + +builddependencies = [ + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('GObject-Introspection', '1.76.1'), + ('binutils', '2.40'), +] +dependencies = [('GLib', '2.77.1')] + +configopts = "-Dgobject_types=true -Dintrospection=enabled" + +sanity_check_paths = { + 'files': ['lib/libgraphene-1.0.%s' % SHLIB_EXT, 'share/gir-1.0/Graphene-1.0.gir'], + 'dirs': ['include/graphene-1.0', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..00d77af7047 --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,72 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.2.2.1' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'wxWidgets' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_BZ2] +checksums = ['dffcb6be71296fff4b7f8840eb1b510178f57aa2eb236b20da41182009242c02'] + +builddependencies = [ + ('binutils', '2.40'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.5'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('libjpeg-turbo', '2.1.5.1'), + ('XZ', '5.4.2'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.5.1'), + ('expat', '2.5.0'), + ('GTK3', '3.24.37'), + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('libGLU', '9.0.3'), + ('SDL2', '2.28.2'), + ('cairo', '1.17.8'), + ('GST-plugins-base', '1.22.5'), + ('GLib', '2.77.1'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From 5f0edf629cff6bab3c85c1c3fda62c72d44218c1 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Mon, 21 Aug 2023 14:02:58 +0200 Subject: [PATCH 8469/9987] added gnuplot 5.4.8 --- .../g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..cd7f82f9c01 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.4.8' + +homepage = 'http://gnuplot.sourceforge.net' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['931279c7caad1aff7d46cb4766f1ff41c26d9be9daf0bcf0c79deeee3d91f5cf'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('cairo', '1.17.8'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('libgd', '2.3.3'), + ('Pango', '1.50.14'), + ('libcerf', '2.3'), + ('X11', '20230603'), + ('Qt5', '5.15.10'), + ('Lua', '5.4.6'), + ('wxWidgets', '3.2.2.1') +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex ' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' From c644f538d2e492132c123832e6a06b2fe83ea1cf Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 21 Aug 2023 14:58:47 +0200 Subject: [PATCH 8470/9987] {bio][foss/2022a] novaSTA v1.1 /w CUDA v11.7.0 --- .../novaSTA-1.1-foss-2022a-CUDA-11.7.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/novaSTA/novaSTA-1.1-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/novaSTA/novaSTA-1.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/novaSTA/novaSTA-1.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..84a9a699671 --- /dev/null +++ b/easybuild/easyconfigs/n/novaSTA/novaSTA-1.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,48 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/01 +easyblock = 'MakeCp' +name = 'novaSTA' +version = '1.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/turonova/novaSTA' +description = """ C++ version of subtomogram averaging (SA) scripts from TOM/AV3 package +https://doi.org/10.1073/pnas.0409178102. Both CPU and GPU parallelization is +supported although the latter performs significantly worse in terms of +processing time (the code is not well optimized) and is thus not recommended for +larger datasets. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = { + 'cstd': 'c++14', + 'opt': 'True', + 'debug': 'False', + 'usempi': 'True' +} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['db0765eade1b0399929dcd61f2dbeeffd762885902f6ef2811d1fb4f9634a2ac'] + +github_account = 'turonova' +dependencies = [('CUDA', '11.7.0', '', SYSTEM)] + +files_to_copy = [ + (['novaSTA'], 'bin'), + 'parameter_file_example.txt' +] + +# let easybuild set compiler options rather than static statements in makefile +prebuildopts = 'sed -i "s/^CXX/#&/g" ?akefile && ' +# set -s and NDEBUG +prebuildopts += 'export CXXFLAGS="$CXXFLAGS -s -DNDEBUG " && ' + +postinstallcmds = ['strip %(installdir)s/bin/*'] +examples = '%(installdir)s/parameter_file_example.txt' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'parameter_file_example.txt'], + 'dirs': ["."] +} + +moduleclass = 'bio' From 04c05cbca57747e22ada36bce4686e0847ae1796 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Mon, 21 Aug 2023 17:15:04 +0200 Subject: [PATCH 8471/9987] adding easyconfigs: Tk-8.6.13-GCCcore-12.3.0.eb --- .../t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f4a7cfcf052 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.13' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = [ + {'tk8.6.13-src.tar.gz': '2e65fa069a23365440a3c56c556b8673b5e32a283800d8d9b257e3f584ce0675'}, +] + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Tcl', version), + ('X11', '20230603'), + ('zlib', '1.2.13'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' From 2611cd783f53da08e703566a7943b90f86134f08 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Tue, 22 Aug 2023 08:36:05 +0200 Subject: [PATCH 8472/9987] adding easyconfigs: pocl-4.0-GCC-12.3.0.eb, VirtualGL-3.1-GCC-12.3.0.eb --- .../easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0.eb | 47 ++++++++++++++++ .../v/VirtualGL/VirtualGL-3.1-GCC-12.3.0.eb | 54 +++++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..1184e84700c --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0.eb @@ -0,0 +1,47 @@ +# https://github.com/pocl/pocl/issues/1219 +# "PoCL 3.1 supports LLVM only up to 15", so need 4.0 for working with Clang 16 +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '4.0' + +homepage = 'http://portablecl.org' +description = "PoCL is a portable open source (MIT-licensed) implementation of the OpenCL standard (1.2 with some 2.0 features supported)." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [] +checksums = [ + '7f4e8ab608b3191c2b21e3f13c193f1344b40aba7738f78762f7b88f45e8ce03', # v4.0.tar.gz +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Clang', '16.0.6'), + ('hwloc', '2.9.1'), + ('libtool', '2.4.7'), + ('libxml2', '2.11.4'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..751e30d6e04 --- /dev/null +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1-GCC-12.3.0.eb @@ -0,0 +1,54 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# updated by Valentin Plugaru 2019-09-26 +# updated by Paul Melis 2022-10-07, 2023-08-18 + +easyblock = 'CMakeMake' + +name = 'VirtualGL' +version = '3.1' + +homepage = 'https://virtualgl.org/' +description = """VirtualGL is an open source toolkit that gives any Linux or +Unix remote display software the ability to run OpenGL applications with full +hardware acceleration.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['d3d1f721dd9fa7408803b38fcee013483b75ae8bfbbdb84834a72df33ac848c8'] +patches = [ + # In include/X11/XKBlib.h in the X11 sources, function XkbOpenDisplay(), + # the first argument has type `_Xconst char*`, which causes a compile issue + # with server/faker-sym.h, as the latter assumes a non-const `char *`. + # This patch is from the VirtualGL official repo, for post-3.0.1. There, + # it was to fixed compiling against libX11 1.8, but it works here as well +# 'virtualgl-3.0.1-libX11-1.8.patch' +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('libjpeg-turbo', '2.1.5.1'), + ('Mesa', '23.1.4'), + ('libGLU', '9.0.3'), + ('pocl', '4.0'), + ('X11', '20230603'), +] + +local_binaries = [ + 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', + 'vglclient', 'vglconfig', 'vglconnect', 'vglgenkey', 'vgllogin', 'vglrun', + 'vglserver_config' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib64', 'share', 'include'], +} + +moduleclass = 'vis' From 26a383e2c68afc6ab649ba7296efb5761df93703 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 09:11:26 +0200 Subject: [PATCH 8473/9987] adding easyconfigs: NLopt-2.7.1-GCCcore-12.3.0.eb --- .../n/NLopt/NLopt-2.7.1-GCCcore-12.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e7f423ac324 --- /dev/null +++ b/easybuild/easyconfigs/n/NLopt/NLopt-2.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'NLopt' +version = '2.7.1' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/stevengj/nlopt/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['db88232fa5cef0ff6e39943fc63ab6074208831dc0031cf1545f6ecd31ae2a1a'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF' +] + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' From ff86a3a5db5a94c9ccd89eba29f6f7e8f2ec7009 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 09:36:05 +0200 Subject: [PATCH 8474/9987] adding easyconfigs: libgit2-1.7.1-GCCcore-12.3.0.eb --- .../l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b1ce8892a1f --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.7.1' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('PCRE', '8.45'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +github_account = '%(name)s' + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/%(name)s.so', 'lib64/pkgconfig/%(name)s.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From 9658e60fd774c008408afc794d19d9c8ed8b54ec Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 09:43:34 +0200 Subject: [PATCH 8475/9987] added missing checksum --- easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb index b1ce8892a1f..2925136aea6 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = [GITHUB_SOURCE] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['17d2b292f21be3892b704dddff29327b3564f96099a1c53b00edc23160c71327'] builddependencies = [ ('binutils', '2.40'), From 239800338f735964a36b13dcd1e3d5f774504a70 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 09:51:47 +0200 Subject: [PATCH 8476/9987] adding easyconfigs: GLPK-5.0-GCCcore-12.3.0.eb --- .../g/GLPK/GLPK-5.0-GCCcore-12.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..762eea14393 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '5.0' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a1013eebb50f728fc601bdd833b0b2870333c3b3e5a816eeba921d95bec6f15'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = '--with-gmp' + + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/%(namelower)s.h', 'lib/libglpk.so', 'lib/libglpk.a'], + 'dirs': [], +} + +moduleclass = 'tools' From 652006b9cd97d6df7df016277203631bc750b7e2 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 10:25:23 +0200 Subject: [PATCH 8477/9987] adding easyconfigs: Armadillo-12.6.2-foss-2023a.eb --- .../Armadillo/Armadillo-12.6.2-foss-2023a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-12.6.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-12.6.2-foss-2023a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-12.6.2-foss-2023a.eb new file mode 100644 index 00000000000..2ca4adac034 --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-12.6.2-foss-2023a.eb @@ -0,0 +1,24 @@ +name = 'Armadillo' +version = '12.6.2' + +homepage = 'https://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e7efaaf29abda3448447bdf8cba2cceaa19afb802981b62f0c6384c842b01609'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('arpack-ng', '3.9.0'), +] + +moduleclass = 'numlib' From 63cb6621c212829e39d5b97b045e1ddac4b3f891 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Tue, 22 Aug 2023 10:57:58 +0200 Subject: [PATCH 8478/9987] Fix broken indent --- .../easyconfigs/v/VirtualGL/VirtualGL-3.1-GCC-12.3.0.eb | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1-GCC-12.3.0.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1-GCC-12.3.0.eb index 751e30d6e04..76f0487b449 100644 --- a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-3.1-GCC-12.3.0.eb @@ -18,14 +18,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['d3d1f721dd9fa7408803b38fcee013483b75ae8bfbbdb84834a72df33ac848c8'] -patches = [ - # In include/X11/XKBlib.h in the X11 sources, function XkbOpenDisplay(), - # the first argument has type `_Xconst char*`, which causes a compile issue - # with server/faker-sym.h, as the latter assumes a non-const `char *`. - # This patch is from the VirtualGL official repo, for post-3.0.1. There, - # it was to fixed compiling against libX11 1.8, but it works here as well -# 'virtualgl-3.0.1-libX11-1.8.patch' -] +patches = [] builddependencies = [ ('CMake', '3.26.3'), From 204826c8b3d72932a9f1d1f905fc6739ef588114 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Aug 2023 11:01:41 +0200 Subject: [PATCH 8479/9987] revert cosmetic changes to SciPy-bundle-2023.07-gfbf-2023a.eb --- .../s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb index f2e2b3b861a..d634617be9f 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-gfbf-2023a.eb @@ -52,8 +52,6 @@ exts_list = [ 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], }), ('scipy', '1.11.1', { - 'enable_slow_tests': True, - 'ignore_test_result': False, 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', @@ -64,6 +62,8 @@ exts_list = [ {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, ], + 'enable_slow_tests': True, + 'ignore_test_result': False, }), ('numexpr', '2.8.4', { 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], @@ -82,8 +82,8 @@ exts_list = [ 'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'], }), ('deap', '1.4.0', { - 'modulename': 'deap.base', 'checksums': ['ffef2921932a0edbe634fcb6d156189e7a364bf638a2af4ae5d59931a9a4c8cc'], + 'modulename': 'deap.base', }), ] From bf8c352d42ff390ba7387f832896322b467a9f8d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Aug 2023 11:04:54 +0200 Subject: [PATCH 8480/9987] fix trivial code style issue in torchvf easyconfig --- easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb b/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb index 0d184b3fb2b..81a9ed86fa5 100644 --- a/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb +++ b/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a.eb @@ -29,7 +29,7 @@ exts_list = [ 'checksums': ['3696e1f7de482465af731a734a31b261a8852df8d583118f1b223d61764e063f'], }), (name, version, { - 'preinstallopts': """sed -i 's/opencv-python-headless = "\*"//g' pyproject.toml && """, + 'preinstallopts': r"""sed -i 's/opencv-python-headless = "\*"//g' pyproject.toml && """, 'sources': ['%(namelower)s-%(version)s.tar.gz'], 'checksums': ['b2603ed660009ada68751fa507e02f297119e7180b3549098f4fdfe8242b8699'], }), From 9b3c8687120af7e9c655e23298e36cf3b7c58b0b Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Tue, 22 Aug 2023 11:19:22 +0200 Subject: [PATCH 8481/9987] Fix line too long --- easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0.eb index 1184e84700c..64594d3b31f 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0.eb @@ -6,7 +6,8 @@ name = 'pocl' version = '4.0' homepage = 'http://portablecl.org' -description = "PoCL is a portable open source (MIT-licensed) implementation of the OpenCL standard (1.2 with some 2.0 features supported)." +description = """PoCL is a portable open source (MIT-licensed) implementation +of the OpenCL standard (1.2 with some 2.0 features supported).""" toolchain = {'name': 'GCC', 'version': '12.3.0'} From 2dd409767c34bef88d87c7dbcee19de4d3b20546 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 22 Aug 2023 11:52:54 +0200 Subject: [PATCH 8482/9987] adding easyconfigs: Optax-0.1.7-foss-2022a.eb --- .../o/Optax/Optax-0.1.7-foss-2022a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/o/Optax/Optax-0.1.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.1.7-foss-2022a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.1.7-foss-2022a.eb new file mode 100644 index 00000000000..c3d11781d8a --- /dev/null +++ b/easybuild/easyconfigs/o/Optax/Optax-0.1.7-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'Optax' +version = '0.1.7' + +homepage = 'https://github.com/deepmind/optax' +description = """Optax is a gradient processing and optimization library for JAX.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('jax', '0.3.25'), + ('typing-extensions', '4.3.0'), +] + +builddependencies = [ + ('CMake', '3.23.1'), # required for installing dm-tree + ('pytest-xdist', '2.5.0'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('dm-tree', '0.1.8', { + 'modulename': 'tree', + 'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'], + }), + ('chex', '0.1.6', { + 'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'], + }), + ('optax', version, { + 'checksums': ['6a5a848bc5e55e619b187c749fdddc4a5443ea14be85cc769f995779865c110d'], + # ignore equivalence_test.py which imports flax, which depends on optax + 'runtest': 'python -m pytest -n %(parallel)s --pyargs --ignore-glob="**/equivalence_test.py" optax', + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from optax import GradientTransformation'"] + +moduleclass = 'lib' From 457aa6670f2ed5153558c7c866055a3353d0bae5 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 12:28:49 +0200 Subject: [PATCH 8483/9987] adding easyconfigs: netCDF-C++4-4.3.1-gompi-2023a.eb --- .../netCDF-C++4-4.3.1-gompi-2023a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2023a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2023a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2023a.eb new file mode 100644 index 00000000000..a839a82850d --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2023a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.9.2')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' From 090506083f1e3057ba1622f0fad99197aacaa8b1 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 12:39:54 +0200 Subject: [PATCH 8484/9987] adding easyconfigs: netCDF-Fortran-4.6.1-gompi-2023a.eb --- .../netCDF-Fortran-4.6.1-gompi-2023a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2023a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2023a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2023a.eb new file mode 100644 index 00000000000..179a3bfa0d5 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2023a.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['40b534e0c81b853081c67ccde095367bd8a5eead2ee883431331674e7aa9509f'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [ + ('netCDF', '4.9.2'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' From 0fe9ceb0c2d09ec6de33f22bf2032d9c6ea651a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Aug 2023 12:41:33 +0200 Subject: [PATCH 8485/9987] use Python-bundle-PyPI rather than including 'packaging' as extension in easyconfig for meson-python 0.13.2 w/ GCCcore/12.3.0 --- .../m/meson-python/meson-python-0.13.2-GCCcore-12.3.0.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/meson-python/meson-python-0.13.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/meson-python/meson-python-0.13.2-GCCcore-12.3.0.eb index 48c4570903a..75042ffe654 100644 --- a/easybuild/easyconfigs/m/meson-python/meson-python-0.13.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/meson-python/meson-python-0.13.2-GCCcore-12.3.0.eb @@ -14,6 +14,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # provides 'packaging' ('Meson', '1.1.1'), ] @@ -23,13 +24,10 @@ exts_list = [ ('pyproject-metadata', '0.7.1', { 'checksums': ['0a94f18b108b9b21f3a26a3d541f056c34edcb17dc872a144a15618fed7aef67'], }), - ('packaging', '23.1', { - 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], - }), (name, version, { - 'modulename': 'mesonpy', 'sources': ['meson_python-%(version)s.tar.gz'], 'checksums': ['80bc9de898acd36eb4b945afaaf7a2b4ca00189c51870d535e329761910cf8ea'], + 'modulename': 'mesonpy', }), ] From 84b4611475ffd6329920ec48e361a45c4b9160b4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Aug 2023 12:41:54 +0200 Subject: [PATCH 8486/9987] remove unneeded source URLs in easyconfig for matplotlib 3.7.2 --- .../m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb index e92dd93d593..50cd58acdfd 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb @@ -41,20 +41,17 @@ local_preinstallopts += "&& export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/fr exts_list = [ ('fonttools', '4.42.0', { - 'modulename': 'fontTools', 'source_tmpl': '%(name)s-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/f/fonttools'], 'checksums': ['614b1283dca88effd20ee48160518e6de275ce9b5456a3134d5f235523fc5065'], + 'modulename': 'fontTools', }), ('Cycler', '0.11.0', { - 'modulename': 'cycler', 'source_tmpl': 'cycler-%(version)s.tar.gz', - 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], + 'modulename': 'cycler', }), ('kiwisolver', '1.4.4', { 'patches': ['kiwisolver-1.4.4-fix_version.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': [ {'kiwisolver-1.4.4.tar.gz': 'd41997519fcba4a1e46eb4a2fe31bc12f0ff957b2b81bac28db24744f333e955'}, {'kiwisolver-1.4.4-fix_version.patch': '6753afbb3a88856493fcfa0b33989f35742f57bfd41ff3b7f71a98797e1bfbd0'}, @@ -65,12 +62,11 @@ exts_list = [ }), (name, version, { 'patches': ['matplotlib-3.7.2-fix_setup.patch'], - 'preinstallopts': local_preinstallopts, - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], 'checksums': [ {'matplotlib-3.7.2.tar.gz': 'a8cdb91dddb04436bd2f098b8fdf4b81352e68cf4d2c6756fcc414791076569b'}, {'matplotlib-3.7.2-fix_setup.patch': '70b38f9fc9f26c67adc38440f5420d7c50d9438353ad08740cbb42a79358fb4f'}, ], + 'preinstallopts': local_preinstallopts, }), ] From 96fdea7d92ce6f2478053d11803450880cbfc99e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Aug 2023 13:07:07 +0200 Subject: [PATCH 8487/9987] use SHLIB_EXT constant in libgit2 easyconfig --- easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb index 2925136aea6..8453883dbd2 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.1-GCCcore-12.3.0.eb @@ -27,7 +27,7 @@ dependencies = [ github_account = '%(name)s' sanity_check_paths = { - 'files': ['include/git2.h', 'lib64/%(name)s.so', 'lib64/pkgconfig/%(name)s.pc'], + 'files': ['include/git2.h', 'lib64/%%(name)s.%s' % SHLIB_EXT, 'lib64/pkgconfig/%(name)s.pc'], 'dirs': [], } From d6f8002b92acc2810d7a17e8299992ee2306568b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Aug 2023 13:11:06 +0200 Subject: [PATCH 8488/9987] improve sanity check for GLPK 5.0 w/ GCCcore/12.3.0 --- easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.3.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.3.0.eb index 762eea14393..16cc2ff079e 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-12.3.0.eb @@ -27,8 +27,10 @@ configopts = '--with-gmp' sanity_check_paths = { - 'files': ['bin/glpsol', 'include/%(namelower)s.h', 'lib/libglpk.so', 'lib/libglpk.a'], + 'files': ['bin/glpsol', 'include/%(namelower)s.h', 'lib/libglpk.a', 'lib/libglpk.%s' % SHLIB_EXT], 'dirs': [], } +sanity_check_commands = ["glpsol --help"] + moduleclass = 'tools' From 9d4c085aa87f91916054adf8168df25f0c0a22c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 22 Aug 2023 13:18:30 +0200 Subject: [PATCH 8489/9987] adding easyconfigs: Mikado-2.3.4-foss-2022b.eb, Greenlet-2.0.2-foss-2022b.eb, drmaa-python-0.7.9-GCCcore-12.2.0.eb, slurm-drmaa-1.1.3-GCCcore-12.2.0.eb --- .../drmaa-python-0.7.9-GCCcore-12.2.0.eb | 30 +++++++ .../g/Greenlet/Greenlet-2.0.2-foss-2022b.eb | 27 ++++++ .../m/Mikado/Mikado-2.3.4-foss-2022b.eb | 83 +++++++++++++++++++ .../slurm-drmaa-1.1.3-GCCcore-12.2.0.eb | 29 +++++++ 4 files changed, 169 insertions(+) create mode 100644 easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022b.eb create mode 100644 easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb create mode 100644 easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..1d46575521e --- /dev/null +++ b/easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'drmaa-python' +version = '0.7.9' + +homepage = 'https://github.com/pygridtools/drmaa-python' +description = """Distributed Resource Management Application API (DRMAA) bindings for Python.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/drmaa'] +sources = ['drmaa-%(version)s.tar.gz'] +checksums = ['12540cd98afc40d5c0b2f38d7b0e46468d1c45192a2f401f41fc2eda9c9f5542'] + +dependencies = [ + ('Python', '3.10.8'), + ('slurm-drmaa', '1.1.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'drmaa'} + +sanity_check_commands = [ + "python -c 'from drmaa import helpers'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022b.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022b.eb new file mode 100644 index 00000000000..41e17923eb3 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Greenlet' +version = '2.0.2' + +homepage = 'https://github.com/python-greenlet/greenlet' + +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [('Python', '3.10.8')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb b/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb new file mode 100644 index 00000000000..84fc8a169bd --- /dev/null +++ b/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb @@ -0,0 +1,83 @@ +easyblock = 'PythonBundle' + +name = 'Mikado' +version = '2.3.4' + +homepage = 'https://github.com/EI-CoreBioinformatics/mikado' +description = """Mikado is a lightweight Python3 pipeline to identify + the most useful or “best” set of transcripts from multiple transcript + assemblies. Our approach leverages transcript assemblies generated + by multiple methods to define expressed loci, assign a representative + transcript and return a set of gene models that selects against transcripts + that are chimeric, fragmented or with short or disrupted CDS.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('Meson', '0.64.0'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('Biopython', '1.81'), + ('hypothesis', '6.68.2'), + ('networkx', '2.8.8'), + ('SciPy-bundle', '2023.02'), + ('Pysam', '0.21.0'), + ('PyYAML', '6.0'), + ('snakemake', '7.32.3'), + ('pyfaidx', '0.7.2.1'), + ('Greenlet', '2.0.2'), + ('drmaa-python', '0.7.9'), +] + +use_pip = True +sanity_pip_check = True + +local_old_line = 'from scipy._build_utils import numpy_nodepr_api' +local_new_line = """numpy_nodepr_api = dict(define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_9_API_VERSION")])""" + +exts_list = [ + ('SQLAlchemy', '2.0.20', { + 'checksums': ['ca8a5ff2aa7f3ade6c498aaafce25b1eaeabe4e42b73e25519183e4566a16fc6'], + }), + ('SQLAlchemy-Utils', '0.41.1', { + 'checksums': ['a2181bff01eeb84479e38571d2c0718eb52042f9afd8c194d0d02877e84b7d74'], + }), + ('python-rapidjson', '1.10', { + 'modulename': 'rapidjson', + 'checksums': ['acfecbf5edb91ec72a20a125de7f56b8c2f6161eff4c65382c8ee6a2484d3540'], + }), + ('marshmallow', '3.14.1', { + 'checksums': ['4c05c1684e0e97fe779c62b91878f173b937fe097b356cd82f793464f5bc6138'], + }), + ('marshmallow_dataclass', '8.5.3', { + 'checksums': ['c0c5e1ea8d0e557b6fa00343799a9a9e60757b948fb096076beb6aa76bd68d30'], + }), + ('typeguard', '4.1.2', { + 'checksums': ['3be187945f9ef5a9f6d7a926dfe54babb7dfd807085ce05f9a5e8735f2487990'], + }), + ('typing_extensions', '4.7.1', { + 'checksums': ['b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2'], + }), + ('typing_inspect', '0.9.0', { + 'checksums': ['b23fc42ff6f6ef6954e4852c1fb512cdd18dbea03134f91f856a95ccc9461f78'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + (name, version, { + # hardcoded value, used to be imported from scipy._build_utils (which is no longer available since scipy 1.10)' + 'preinstallopts': f"sed -i 's/{local_old_line}/{local_new_line}/g' setup.py && ", + 'modulename': name, + 'checksums': ['6d8844bacacc776214cf35cb148fa638c029b2972751d04fc1f7d0d8f3e961c2'], + }), +] + +sanity_check_commands = [ + "python -c 'import Mikado; Mikado.test()'" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2e172ae8db3 --- /dev/null +++ b/easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'slurm-drmaa' +version = '1.1.3' + +homepage = "https://github.com/natefoo/slurm-drmaa" +description = """DRMAA for Slurm Workload Manager (Slurm) is an implementation + of Open Grid Forum Distributed Resource Management Application API (DRMAA) + version 1 for submission and control of jobs to Slurm. Using DRMAA, + grid applications builders, portal developers and ISVs can use the same + high-level API to link their software with different cluster/resource management systems.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/natefoo/slurm-drmaa/releases/download/%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['145eb1bc3f0f0aac936505eb29ac501dee32228f70781d41df4f032939b9c3ba'] + +sanity_check_paths = { + 'files': [ + 'include/drmaa.h', + 'lib/libdrmaa.a', + 'lib/libdrmaa.so', + 'bin/drmaa-run', + ], + 'dirs': ['etc'] +} + +moduleclass = 'lib' From eeac8d5e36b90eaf0861d7e0a2da73e086fb4fe6 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 22 Aug 2023 13:38:29 +0200 Subject: [PATCH 8490/9987] new easyconfig for leafcutterMD and an update of R-bundle-Bioconductor with depencies for leafcutterMD --- .../leafcutter-0.2.9-foss-2022b-R-4.2.2.eb | 36 +++++++++++++++++++ ...le-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 14 +++++--- 2 files changed, 46 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..0bb4d063692 --- /dev/null +++ b/easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb @@ -0,0 +1,36 @@ +easyblock = 'RPackage' + +name = 'leafcutter' +version = '0.2.9' +# there's no proper 0.2.9 release, so using commit that updated DESCRIPTION file +local_commit = 'd02bc35' +versionsuffix = '-R-%(rver)s' + +homepage = "http://davidaknowles.github.io/leafcutter/index.html" +description = """Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples. The advantages of this approach include: + easy detection of novel introns, modeling of more complex splicing events than exonic PSI, avoiding the challenge of isoform abundance estimation, simple, computationally efficient algorithms scaling to 100s or even 1000s of samples. + For details please see our bioRxiv preprint and corresponding Nature Genetics publication. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/davidaknowles/leafcutter/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['defee98257b330200b86b1a158231b818025a1f30c019c254907c2669efdf9f7'] + +dependencies = [ + ('SAMtools', '1.17'), + ('RegTools', '1.0.0'), + ('Python', '3.10.8'), + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), +] + +start_dir = 'leafcutter' + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index 392353a7d4b..eb0c0c7eebf 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -1241,11 +1241,17 @@ exts_list = [ ('ANCOMBC', '2.0.2', { 'checksums': ['e577ffe62a86090de9ea3743c84a4f3b34c3d645dcedff3c8af675b8c9b69136'], }), - ('decoupleR', '2.4.0', { - 'checksums': ['b141afd331449b0b1c2dc3dc3097465c2c02b5026129d8f06dd5bfb445bce2a0'], + ('intervals', '0.15.4', { + 'checksums': ['50c0e1e3aab3e7b72cc1f0a6559d96caa3a360e969c38538479907e6cbe39f8f'], }), - ('UCell', '2.2.0', { - 'checksums': ['e3ca2b2d77a780a9450853e869bc10654c47485777d39a703203dc44d97df4bc'], + ('oompaBase', '3.2.9', { + 'checksums': ['14ca2b8e713a6a7ce13758f7f5c183dbc4fdfedc4f1244ca31bbdadf8a16bcb2'], + }), + ('oompaData', '3.1.3', { + 'checksums': ['aeb932f75d3de2101d2e1b387fe76677f2d38d4819710320c0e3df07df3ab73d'], + }), + ('TailRank', '3.2.2', { + 'checksums': ['21ed95ea47d21155f08ae2ad7bca9547f89f492000bc1defe1cc5ec172739d09'], }), ] From 555f1c2a5738f58c304648642e7322ae7e7519c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 22 Aug 2023 13:38:50 +0200 Subject: [PATCH 8491/9987] fix deps --- .../d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb | 4 ++++ easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb | 2 +- .../s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb | 4 ++++ 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb index 1d46575521e..8fae0d0fd50 100644 --- a/easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb @@ -12,6 +12,10 @@ source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/drmaa'] sources = ['drmaa-%(version)s.tar.gz'] checksums = ['12540cd98afc40d5c0b2f38d7b0e46468d1c45192a2f401f41fc2eda9c9f5542'] +builddependencies = [ + ('binutils', '2.39'), +] + dependencies = [ ('Python', '3.10.8'), ('slurm-drmaa', '1.1.3'), diff --git a/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb b/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb index 84fc8a169bd..a7bc79e99c8 100644 --- a/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb +++ b/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb @@ -23,7 +23,7 @@ dependencies = [ ('Python', '3.10.8'), ('Biopython', '1.81'), ('hypothesis', '6.68.2'), - ('networkx', '2.8.8'), + ('networkx', '3.0'), ('SciPy-bundle', '2023.02'), ('Pysam', '0.21.0'), ('PyYAML', '6.0'), diff --git a/easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb index 2e172ae8db3..bd4645b7acb 100644 --- a/easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb @@ -16,6 +16,10 @@ source_urls = ['https://github.com/natefoo/slurm-drmaa/releases/download/%(versi sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['145eb1bc3f0f0aac936505eb29ac501dee32228f70781d41df4f032939b9c3ba'] +builddependencies = [ + ('binutils', '2.39'), +] + sanity_check_paths = { 'files': [ 'include/drmaa.h', From bf938606dc6af9b476466f79f645e14d5b9b4703 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 22 Aug 2023 14:36:12 +0200 Subject: [PATCH 8492/9987] cleanup style --- .../l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb index 0bb4d063692..1a11945c089 100644 --- a/easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb @@ -7,8 +7,11 @@ local_commit = 'd02bc35' versionsuffix = '-R-%(rver)s' homepage = "http://davidaknowles.github.io/leafcutter/index.html" -description = """Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples. The advantages of this approach include: - easy detection of novel introns, modeling of more complex splicing events than exonic PSI, avoiding the challenge of isoform abundance estimation, simple, computationally efficient algorithms scaling to 100s or even 1000s of samples. +description = """Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. + The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) + intron usage across samples. The advantages of this approach include: easy detection of novel introns, + modeling of more complex splicing events than exonic PSI, avoiding the challenge of isoform abundance + estimation, simple, computationally efficient algorithms scaling to 100s or even 1000s of samples. For details please see our bioRxiv preprint and corresponding Nature Genetics publication. """ From 413df2c6134d04f9c07f495a875e62d6b38fb038 Mon Sep 17 00:00:00 2001 From: satishk Date: Tue, 22 Aug 2023 14:40:32 +0200 Subject: [PATCH 8493/9987] adding easyconfigs: OSU-Micro-Benchmarks-7.1-1-iimpi-2023a.eb --- .../OSU-Micro-Benchmarks-7.1-1-iimpi-2023a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-iimpi-2023a.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-iimpi-2023a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-iimpi-2023a.eb new file mode 100644 index 00000000000..1173c7c1e12 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.1-1-iimpi-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.1-1' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpi', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['85f4dd8be1df31255e232852769ae5b82e87a5fb14be2f8eba1ae9de8ffe391a'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 17949845b00a602a7029b2748a2da30cd5fb2b4f Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 22 Aug 2023 14:46:14 +0200 Subject: [PATCH 8494/9987] update R-bundle-Bioconductor --- .../R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index eb0c0c7eebf..3a7bb73d953 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -1253,6 +1253,7 @@ exts_list = [ ('TailRank', '3.2.2', { 'checksums': ['21ed95ea47d21155f08ae2ad7bca9547f89f492000bc1defe1cc5ec172739d09'], }), + ] modextrapaths = {'R_LIBS_SITE': ''} From e86134c3aa6d8e5a199087d71b76a28ef4c8000d Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 22 Aug 2023 14:46:37 +0200 Subject: [PATCH 8495/9987] adding easyconfigs: PycURL-7.45.2-GCCcore-12.3.0.eb, PyZMQ-25.1.1-GCCcore-12.3.0.eb, jupyter-server-2.7.2-GCCcore-12.3.0.eb, JupyterHub-4.0.2-GCCcore-12.3.0.eb, JupyterLab-4.0.5-GCCcore-12.3.0.eb, notebook-7.0.2-GCCcore-12.3.0.eb, nbclassic-1.0.0-GCCcore-12.3.0.eb, jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb --- ...gurable-http-proxy-4.5.6-GCCcore-12.3.0.eb | 32 + .../JupyterHub-4.0.2-GCCcore-12.3.0.eb | 122 ++++ .../JupyterLab-4.0.5-GCCcore-12.3.0.eb | 73 +++ ...pyter-server-proxy-4.0.0-GCCcore-12.3.0.eb | 45 ++ .../jupyter-server-2.7.2-GCCcore-12.3.0.eb | 190 ++++++ .../m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb | 605 ++++++++++++++++++ .../nbclassic-1.0.0-GCCcore-12.3.0.eb | 50 ++ .../notebook/notebook-7.0.2-GCCcore-12.3.0.eb | 40 ++ .../p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb | 28 + .../p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb | 29 + .../t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb | 29 + 11 files changed, 1243 insertions(+) create mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fc58c50bc75 --- /dev/null +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'Binary' + +name = 'configurable-http-proxy' +version = '4.5.6' + +homepage = 'https://github.com/jupyterhub/configurable-http-proxy' +description = """HTTP proxy for node.js including a REST API for updating the routing table. + Developed as a part of the Jupyter Hub multi-user server.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/jupyterhub/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4d9d94d0e6e44542ac973963b8a6545f4b40c0a2995e865ae9c80a2279e1e0ab'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('nodejs', '18.17.1'), +] + +install_cmd = "npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz" + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8c8f316a6db --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,122 @@ +easyblock = 'PythonBundle' + +name = 'JupyterHub' +version = '4.0.2' + +homepage = 'https://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed + for centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('setuptools-rust', '1.6.0'), # Needed for bcrypt + ('Rust', '1.70.0'), # Needed for bcrypt +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('Mako', '1.2.4'), + ('configurable-http-proxy', '4.5.6'), + ('OpenSSL', '1.1', '', SYSTEM), + ('jupyter-server-proxy', '4.0.0'), # optional, but commonly used together + ('PycURL', '7.45.2'), # optional, recommended with large number of users +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('certipy', '0.1.3', { + 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], + }), + ('pamela', '1.1.0', { + 'checksums': ['d4b139fe600e192e176a2a368059207a6bffa0e7879879b13f4fcba0163481be'], + }), + ('greenlet', '2.0.2', { + 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('SQLAlchemy', '2.0.20', { + 'checksums': ['ca8a5ff2aa7f3ade6c498aaafce25b1eaeabe4e42b73e25519183e4566a16fc6'], + }), + ('alembic', '1.11.3', { + 'checksums': ['3db4ce81a9072e1b5aa44c2d202add24553182672a12daf21608d6f62a8f9cf9'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('pyOpenSSL', '23.2.0', { + 'modulename': 'OpenSSL', + 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], + }), + ('ruamel.yaml', '0.17.32', { + 'checksums': ['ec939063761914e14542972a5cba6d33c23b0859ab6342f61cf070cfc600efc2'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('jupyter-telemetry', '0.1.0', { + 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', + 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], + }), + ('jupyterhub', version, { + 'checksums': ['d4e450eed8d90dfbcf0eca08f00f2093a0bce74dc51f7cfc0b7057f602341a1d'], + }), + ('batchspawner', '1.2.0-2a9eda0', { + 'sources': { + 'filename': 'main.tar.gz', + 'git_config': { + 'url': 'https://github.com/jupyterhub/', + 'repo_name': 'batchspawner', + 'commit': '2a9eda0'}, # Needs unreleased features to for JupyterHub 4.X compatibility + }, + 'checksums': ['8ecfd2cceb248a5a4da5d5abe65e104086b0d2ff11acf3c6726e12b6a3a4d613'], + }), + ('jupyterhub-systemdspawner', '1.0.1', { + 'modulename': 'systemdspawner', + 'checksums': ['8d614f19d89564321fe55d80ecd134a0e2bf276274d45861495c9bb5a80add28'], + }), + ('jupyterhub-simplespawner', '0.1', { + 'modulename': 'simplespawner', + 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], + }), + ('ldap3', '2.9.1', { + 'checksums': ['f3e7fc4718e3f09dda568b57100095e0ce58633bcabbed8667ce3f8fbaa4229f'], + }), + ('jupyterhub-ldapauthenticator', '1.3.2', { + 'modulename': 'ldapauthenticator', + 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('jupyterhub-jwtauthenticator-v2', '2.0.3', { + 'modulename': 'jwtauthenticator', + 'checksums': ['b94b6dff8246250904c5ee511da3f062680eb657dabe766d75993cbe72747d41'], + }), + ('onetimepass', '1.0.1', { + 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], + }), + ('bcrypt', '4.0.1', { + 'checksums': ['27d375903ac8261cfe4047f6709d16f7d18d39b1ec92aaf72af989552a650ebd'], + }), + ('jupyterhub-nativeauthenticator', '1.2.0', { + 'modulename': 'nativeauthenticator', + 'checksums': ['826228e6e9ca37736361e2e60c5723e245ec72e34fdc42cc218fc54a67f968e1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..19c7e8a6710 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '4.0.5' + +homepage = 'https://jupyter.org/' +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), +] + +# keep user's configuration in their home directory +# note: '~' is not expanded by JupyterLab +modluafooter = """ +setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) +setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) +""" +modtclfooter = """ +setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" +setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" +""" +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('json5', '0.9.14', { + 'checksums': ['9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02'], + }), + ('jupyterlab_server', '2.24.0', { + 'checksums': ['4e6f99e0a5579bbbc32e449c4dbb039561d4f1a7827d5733273ed56738f21f07'], + }), + ('jupyter-lsp', '2.2.0', { + 'checksums': ['8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1'], + }), + ('async-lru', '2.0.4', { + 'checksums': ['b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627'], + }), + ('jupyterlab', version, { + 'checksums': ['de49deb75f9b9aec478ed04754cbefe9c5d22fd796a5783cdc65e212983d3611'], + }), +] + +local_binaries = [ + 'jupyter-lab', + 'jupyter-labextension', + 'jupyter-labhub', +] +sanity_check_paths = { + 'files': [], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter lab --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5c1a64b9090 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server-proxy' +version = '4.0.0' + +homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' +description = """Jupyter Server Proxy lets you run arbitrary external processes +(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) +alongside your notebook server and provide authenticated web access to them +using a path like /rstudio next to others like /lab. Alongside the python +package that provides the main functionality, the JupyterLab extension +(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window +to get to RStudio for example.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), + ('OpenSSL', '1.1', '', SYSTEM), + ('aiohttp', '3.8.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('simpervisor', '1.0.0', { + 'checksums': ['7eb87ca86d5e276976f5bb0290975a05d452c6a7b7f58062daea7d8369c823c1'], + }), + ('jupyter_server_proxy', version, { + 'checksums': ['f5dc12dd204baca71b013df3522c14403692a2d37cb7adcd77851dbab71533b5'], + }), +] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..76b36f7551f --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb @@ -0,0 +1,190 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = "2.7.2" + +homepage = 'https://jupyter.org/' +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST +endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and +Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.1.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('PyYAML', '6.0'), + ('PyZMQ', '25.1.1'), + ('tornado', '6.3.2'), +] + +sanity_pip_check = True +use_pip = True + +# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them +# use the versions published in a single release commit instead of blindly pushing to last available version, +# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa + +exts_list = [ + ('hatch_nodejs_version', '0.3.1', { + 'checksums': ['0e55fd713d92c5c1ccfee778efecaa780fd8bcd276d4ca7aff9f6791f6f76d9c'], + }), + ('hatch_jupyter_builder', '0.8.3', { + 'checksums': ['0dbd14a8aef6636764f88a8fd1fcc9a91921e5c50356e6aab251782f264ae960'], + }), + ('websocket-client', '1.6.1', { + 'modulename': 'websocket', + 'checksums': ['c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd'], + }), + ('terminado', '0.17.1', { + 'checksums': ['6ccbbcd3a4f8a25a5ec04991f39a0b8db52dfcd487ea0e578d977e6752380333'], + }), + ('Send2Trash', '1.8.2', { + 'checksums': ['c132d59fa44b9ca2b1699af5c86f57ce9f4c5eb56629d5d55fbb7a35f84e2312'], + }), + ('prometheus_client', '0.17.1', { + 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], + }), + ('overrides', '7.4.0', { + 'checksums': ['9502a3cca51f4fac40b5feca985b6703a5c1f6ad815588a7ca9e285b9dca6757'], + }), + ('jupyter_core', '5.3.1', { + 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], + }), + ('fastjsonschema', '2.18.0', { + 'checksums': ['e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd'], + }), + ('tinycss2', '1.2.1', { + 'checksums': ['8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627'], + }), + ('pandocfilters', '1.5.0', { + 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], + }), + ('mistune', '3.0.1', { + 'checksums': ['e912116c13aa0944f9dc530db38eb88f6a77087ab128f49f84a48f4c05ea163c'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.3', { + 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], + }), + ('jupyterlab_pygments', '0.2.2', { + 'checksums': ['7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('bleach', '6.0.0', { + 'checksums': ['1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('nbformat', '5.9.2', { + 'checksums': ['5f98b5ba1997dff175e77e0c17d5c10a96eaed2cbd1de3533d1fc35d5e111192'], + }), + ('nbclient', '0.8.0', { + 'checksums': ['f9b179cd4b2d7bca965f900a2ebf0db4a12ebff2f36a711cb66861e4ae158e55'], + }), + ('jupyter_client', '8.3.0', { + 'checksums': ['3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f'], + }), + ('nbconvert', '7.7.4', { + 'checksums': ['1113d039fa3fc3a846ffa5a3b0a019e85aaa94c566a09fa0c400fb7638e46087'], + }), + ('jupyter_server_terminals', '0.4.4', { + 'checksums': ['57ab779797c25a7ba68e97bcfb5d7740f2b5e8a83b5e8102b10438041a7eac5d'], + }), + ('rfc3986_validator', '0.1.1', { + 'checksums': ['3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055'], + }), + ('rfc3339_validator', '0.1.4', { + 'checksums': ['138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b'], + }), + ('rpds_py', '0.9.2', { + 'modulename': 'rpds', + 'checksums': ['8d70e8f14900f2657c249ea4def963bed86a29b81f81f5b76b5a9215680de945'], + }), + ('referencing', '0.30.2', { + 'checksums': ['794ad8003c65938edcdbc027f1933215e0d0ccc0291e3ce20a4d87432b59efc0'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jsonschema_specifications', '2023.7.1', { + 'checksums': ['c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb'], + }), + ('jsonschema', '4.18.0', { + 'checksums': ['8caf5b57a990a98e9b39832ef3cb35c176fe331414252b6e1b26fd5866f891a4'], + }), + ('jupyter_events', '0.7.0', { + 'checksums': ['7be27f54b8388c03eefea123a4f79247c5b9381c49fb1cd48615ee191eb12615'], + }), + ('argon2-cffi-bindings', '21.2.0', { + 'modulename': '_argon2_cffi_bindings', + 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], + }), + ('argon2_cffi', '23.1.0', { + 'modulename': 'argon2', + 'checksums': ['879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.7.1', { + 'checksums': ['44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780'], + }), + ('jupyter_server', version, { + 'checksums': ['d64fb4e593907290e5df916e3c9399c15ab2cd7bdb71cbcd1d36452dbfb30523'], + }), + ('jupyterlab_widgets', '3.0.8', { + 'checksums': ['d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a'], + }), + ('widgetsnbextension', '4.0.8', { + 'checksums': ['9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17'], + }), + ('comm', '0.1.4', { + 'checksums': ['354e40a59c9dd6db50c5cc6b4acc887d82e9603787f83b68c01a80a923984d15'], + }), + ('ipywidgets', '8.1.0', { + 'checksums': ['ce97dd90525b3066fd00094690964e7eac14cf9b7745d35565b5eeac20cce687'], + }), + # The following few extensions are needed for e.g. JupyterLab but also nbclassic. + # Avoid duplication by making it part of this bundle + ('notebook_shim', '0.2.3', { + 'checksums': ['f69388ac283ae008cd506dda10d0288b09a017d822d5e8c7129a152cbd3ce7e9'], + }), + ('nest_asyncio', '1.5.7', { + 'checksums': ['6a80f7b98f24d9083ed24608977c09dd608d83f91cccc24c9d2cba6d10e01c10'], + }), + ('ipykernel', '6.25.1', { + 'checksums': ['050391364c0977e768e354bdb60cbbfbee7cbb943b1af1618382021136ffd42f'], + }), + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('debugpy', '1.6.7.post1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['1093a5c541af079c13ac8c70ab8b24d1d35c8cacb676306cf11e57f699c02926'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter'], + 'dirs': ['share/jupyter', 'etc/jupyter'], +} + +sanity_check_commands = ['jupyter --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..81ebf2ccc9a --- /dev/null +++ b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,605 @@ +easyblock = 'CargoPythonPackage' + +name = 'maturin' +version = '1.1.0' + +homepage = 'https://github.com/pyo3/maturin' +description = """This project is meant as a zero configuration +replacement for setuptools-rust and milksnake. It supports building +wheels for python 3.5+ on windows, linux, mac and freebsd, can upload +them to pypi and has basic pypy and graalpy support.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = [ + {'maturin-1.1.0.tar.gz': '4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'ahash-0.7.6.tar.gz': 'fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47'}, + {'aho-corasick-0.7.20.tar.gz': 'cc936419f96fa211c1b9166887b38e5e40b19958e5b895be7c1f93adec7071ac'}, + {'anyhow-1.0.71.tar.gz': '9c7d0618f0e0b7e8ff11427422b64564d5fb0be1940354bfe2e0529b18a9d9b8'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'base64-0.13.1.tar.gz': '9e1b586273c5702936fe7b7d6896644d8be71e6314cfe09d3167c95f712589e8'}, + {'base64-0.21.2.tar.gz': 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('windows_i686_gnu', '0.48.0'), + ('windows_i686_msvc', '0.42.2'), + ('windows_i686_msvc', '0.48.0'), + ('windows_x86_64_gnu', '0.42.2'), + ('windows_x86_64_gnu', '0.48.0'), + ('windows_x86_64_gnullvm', '0.42.2'), + ('windows_x86_64_gnullvm', '0.48.0'), + ('windows_x86_64_msvc', '0.42.2'), + ('windows_x86_64_msvc', '0.48.0'), + ('winnow', '0.4.6'), + ('xattr', '0.2.3'), + ('xwin', '0.2.12'), + ('yansi', '0.5.1'), + ('zeroize', '1.6.0'), + ('zip', '0.6.6'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..eeea91f55a2 --- /dev/null +++ b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonPackage' + +name = 'nbclassic' +version = "1.0.0" + +homepage = 'https://jupyter.org/' +description = """NbClassic provides a backwards compatible Jupyter Notebook interface + that you can install side-by-side with the latest versions: That way, you can fearlessly + upgrade without worrying about your classic extensions and customizations breaking.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.1.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('jupyter-server', '2.7.2'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['nbclassic-1.0.0_fix_setup_version.patch'] +checksums = [ + {'nbclassic-1.0.0.tar.gz': '0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'}, + {'nbclassic-1.0.0_fix_setup_version.patch': 'c26d91ac1d0cea2b361b2619076acdaf5fcd5ff2363d9e5f5e1bd737b4b50736'}, +] + +sanity_pip_check = True +use_pip = True + +local_binaries = [ + 'jupyter-nbclassic', + 'jupyter-nbclassic-bundlerextension', + 'jupyter-nbclassic-extension', + 'jupyter-nbclassic-serverextension', +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ['jupyter nbclassic --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bd30f0acb08 --- /dev/null +++ b/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'notebook' +version = '7.0.2' + +homepage = 'https://jupyter.org/' +description = """The Jupyter Notebook is the original web application for creating and + sharing computational documents. It offers a simple, streamlined, document-centric experience.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), + ('JupyterLab', '4.0.5'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['d70d6a07418c829bd5f54337ce993b7105261d9026f9d3fe68e9b8aa1a20da9a'] + +sanity_pip_check = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/jupyter-notebook'], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter notebook --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9f4d88872a1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '25.1.1' + +homepage = 'https://www.zeromq.org/bindings:python' +description = "Python bindings for ZeroMQ" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('ZeroMQ', '4.3.4'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'zmq'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2e8cc5dfd61 --- /dev/null +++ b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'PycURL' +version = '7.45.2' + +homepage = 'http://pycurl.io/' +description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL + from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of + features.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5730590be0271364a5bddd9e245c9cc0fb710c4cbacbdd95264a3122d23224ca'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('cURL', '8.0.1'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f63d8f312a9 --- /dev/null +++ b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = "tornado" +version = "6.3.2" + +homepage = "https://github.com/tornadoweb/tornado" +description = "Tornado is a Python web framework and asynchronous networking library." + +toolchain = {"name": "GCCcore", "version": "12.3.0"} + +sources = [SOURCE_TAR_GZ] +patches = ['tornado-timeouts.patch'] +checksums = [ + {'tornado-6.3.2.tar.gz': '4b927c4f19b71e627b13f3db2324e4ae660527143f9e1f2e2fb404f3a187e2ba'}, + {'tornado-timeouts.patch': 'fe0db60604ccdcb5fc111023d1d7bffa0e315465fbe15f2ff512068c649e56f8'}, +] + +builddependencies = [ + ("binutils", "2.40"), +] +dependencies = [ + ("Python", "3.11.3"), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = "lib" From ae7cc5b08f87bd1a5792a98d04649c2cac2a53ba Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Tue, 22 Aug 2023 15:03:08 +0200 Subject: [PATCH 8496/9987] Delete maturin-1.1.0-GCCcore-12.3.0.eb This PR depends on https://github.com/easybuilders/easybuild-easyconfigs/pull/18596 Shouldn't re-add this --- .../m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb | 605 ------------------ 1 file changed, 605 deletions(-) delete mode 100644 easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb deleted file mode 100644 index 81ebf2ccc9a..00000000000 --- a/easybuild/easyconfigs/m/maturin/maturin-1.1.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,605 +0,0 @@ -easyblock = 'CargoPythonPackage' - -name = 'maturin' -version = '1.1.0' - -homepage = 'https://github.com/pyo3/maturin' -description = """This project is meant as a zero configuration -replacement for setuptools-rust and milksnake. It supports building -wheels for python 3.5+ on windows, linux, mac and freebsd, can upload -them to pypi and has basic pypy and graalpy support.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = [ - {'maturin-1.1.0.tar.gz': '4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'}, - {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, - {'ahash-0.7.6.tar.gz': 'fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47'}, - {'aho-corasick-0.7.20.tar.gz': 'cc936419f96fa211c1b9166887b38e5e40b19958e5b895be7c1f93adec7071ac'}, - {'anyhow-1.0.71.tar.gz': '9c7d0618f0e0b7e8ff11427422b64564d5fb0be1940354bfe2e0529b18a9d9b8'}, - {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, - {'base64-0.13.1.tar.gz': '9e1b586273c5702936fe7b7d6896644d8be71e6314cfe09d3167c95f712589e8'}, - {'base64-0.21.2.tar.gz': '604178f6c5c21f02dc555784810edfb88d34ac2c73b2eae109655649ee73ce3d'}, - 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('bzip2-sys', '0.1.11+1.0.8'), - ('cab', '0.4.1'), - ('camino', '1.1.4'), - ('cargo-config2', '0.1.7'), - ('cargo-options', '0.6.0'), - ('cargo-platform', '0.1.2'), - ('cargo-xwin', '0.14.3'), - ('cargo-zigbuild', '0.16.10'), - ('cargo_metadata', '0.15.4'), - ('cbindgen', '0.24.5'), - ('cc', '1.0.79'), - ('cfb', '0.7.3'), - ('cfg-expr', '0.15.2'), - ('cfg-if', '1.0.0'), - ('charset', '0.1.3'), - ('chumsky', '0.9.2'), - ('clap', '4.1.14'), - ('clap_builder', '4.1.14'), - ('clap_complete', '4.2.3'), - ('clap_complete_command', '0.5.1'), - ('clap_complete_fig', '4.2.0'), - ('clap_complete_nushell', '0.1.11'), - ('clap_derive', '4.1.14'), - ('clap_lex', '0.4.1'), - ('cli-table', '0.4.7'), - ('concolor', '0.0.11'), - ('concolor-query', '0.1.0'), - ('configparser', '3.0.2'), - ('console', '0.15.5'), - ('content_inspector', '0.2.4'), - ('core-foundation', '0.9.3'), - ('core-foundation-sys', '0.8.4'), - ('cpufeatures', '0.2.7'), - ('crc32fast', '1.3.2'), - ('crossbeam-channel', '0.5.8'), - ('crossbeam-deque', '0.8.3'), - ('crossbeam-epoch', '0.9.14'), - ('crossbeam-utils', '0.8.15'), - ('crypto-common', '0.1.6'), - ('ctor', '0.1.26'), - ('data-encoding', '2.4.0'), - ('dialoguer', '0.10.4'), - ('diff', '0.1.13'), - ('digest', '0.10.7'), - ('dirs', '5.0.1'), - ('dirs-sys', '0.4.1'), - ('dunce', '1.0.4'), - ('either', '1.8.1'), - ('encode_unicode', '0.3.6'), - ('encoding_rs', '0.8.32'), - ('errno', '0.3.1'), - ('errno-dragonfly', '0.1.2'), - ('fastrand', '1.9.0'), - ('fat-macho', '0.4.6'), - ('filetime', '0.2.21'), - ('flate2', '1.0.26'), - ('fnv', '1.0.7'), - ('foreign-types', '0.3.2'), - ('foreign-types-shared', '0.1.1'), - ('form_urlencoded', '1.2.0'), - ('fs-err', '2.9.0'), - ('generic-array', '0.14.7'), - ('getrandom', '0.2.10'), - ('glob', '0.3.1'), - ('globset', '0.4.10'), - ('goblin', '0.6.1'), - ('hashbrown', '0.12.3'), - ('heck', '0.4.1'), - ('hermit-abi', '0.2.6'), - ('hermit-abi', '0.3.1'), - ('home', '0.5.4'), - ('humantime', '2.1.0'), - ('humantime-serde', '1.1.1'), - ('idna', '0.4.0'), - ('ignore', '0.4.20'), - ('indexmap', '1.9.3'), - ('indicatif', '0.17.5'), - ('indoc', '2.0.1'), - ('instant', '0.1.12'), - ('io-lifetimes', '1.0.11'), - ('is-terminal', '0.4.7'), - ('itertools', '0.10.5'), - ('itoa', '1.0.6'), - ('js-sys', '0.3.63'), - ('keyring', '2.0.3'), - ('lazy_static', '1.4.0'), - ('lddtree', '0.3.2'), - ('libc', '0.2.146'), - ('linux-keyutils', '0.2.3'), - ('linux-raw-sys', '0.3.8'), - ('lock_api', '0.4.9'), - ('log', '0.4.18'), - ('lzxd', '0.1.4'), - ('mailparse', '0.13.8'), - ('matchers', '0.1.0'), - ('memchr', '2.5.0'), - ('memoffset', '0.8.0'), - ('mime', '0.3.17'), - ('mime_guess', '2.0.4'), - ('minijinja', '0.34.0'), - ('minimal-lexical', '0.2.1'), - ('miniz_oxide', '0.7.1'), - ('msi', '0.5.1'), - ('multipart', '0.18.0'), - ('native-tls', '0.2.11'), - ('nom', '7.1.3'), - ('normalize-line-endings', '0.3.0'), - ('normpath', '1.1.1'), - ('nu-ansi-term', '0.46.0'), - ('num_cpus', '1.15.0'), - ('number_prefix', '0.4.0'), - ('once_cell', '1.18.0'), - ('openssl', '0.10.54'), - ('openssl-macros', '0.1.1'), - ('openssl-probe', '0.1.5'), - ('openssl-src', '111.26.0+1.1.1u'), - ('openssl-sys', '0.9.88'), - ('option-ext', '0.2.0'), - ('os_pipe', '1.1.4'), - ('output_vt100', '0.1.3'), - ('overload', '0.1.1'), - ('parking_lot', '0.12.1'), - ('parking_lot_core', '0.9.6'), - ('path-slash', '0.2.1'), - ('pep440_rs', '0.3.6'), - ('pep508_rs', '0.2.1'), - ('percent-encoding', '2.3.0'), - ('pin-project-lite', '0.2.9'), - ('pkg-config', '0.3.27'), - ('plain', '0.2.3'), - ('platform-info', '2.0.1'), - ('portable-atomic', '1.3.3'), - ('ppv-lite86', '0.2.17'), - ('pretty_assertions', '1.3.0'), - ('proc-macro2', '1.0.60'), - ('psm', '0.1.21'), - ('pyproject-toml', '0.6.1'), - ('python-pkginfo', '0.5.5'), - ('quote', '1.0.28'), - ('quoted_printable', '0.4.8'), - ('rand', '0.8.5'), - ('rand_chacha', '0.3.1'), - ('rand_core', '0.6.4'), - ('rayon', '1.7.0'), - ('rayon-core', '1.11.0'), - ('redox_syscall', '0.2.16'), - ('redox_syscall', '0.3.5'), - ('redox_users', '0.4.3'), - ('regex', '1.7.3'), - ('regex-automata', '0.1.10'), - ('regex-syntax', '0.6.29'), - ('rfc2047-decoder', '0.2.2'), - ('ring', '0.16.20'), - ('rustc_version', '0.4.0'), - ('rustix', '0.37.19'), - ('rustls', '0.20.8'), - ('rustls-pemfile', '1.0.2'), - ('rustversion', '1.0.12'), - ('ryu', '1.0.13'), - ('same-file', '1.0.6'), - ('schannel', '0.1.21'), - ('scopeguard', '1.1.0'), - ('scroll', '0.11.0'), - ('scroll_derive', '0.11.0'), - ('sct', '0.7.0'), - ('security-framework', '2.9.1'), - ('security-framework-sys', '2.9.0'), - ('semver', '1.0.17'), - ('serde', '1.0.164'), - ('serde_derive', '1.0.164'), - ('serde_json', '1.0.96'), - ('serde_spanned', '0.6.2'), - ('sha2', '0.10.6'), - ('sharded-slab', '0.1.4'), - ('shell-escape', '0.1.5'), - ('shell-words', '1.1.0'), - ('shlex', '1.1.0'), - ('similar', '2.2.1'), - ('smallvec', '1.10.0'), - ('smawk', '0.3.1'), - ('snapbox', '0.4.4'), - ('snapbox-macros', '0.3.4'), - ('socks', '0.3.4'), - ('spin', '0.5.2'), - ('stacker', '0.1.15'), - ('static_assertions', '1.1.0'), - ('strsim', '0.10.0'), - ('syn', '1.0.109'), - ('syn', '2.0.18'), - ('tar', '0.4.38'), - ('target-lexicon', '0.12.7'), - ('tempfile', '3.6.0'), - ('termcolor', '1.2.0'), - ('terminal_size', '0.2.6'), - ('textwrap', '0.16.0'), - ('thiserror', '1.0.40'), - ('thiserror-impl', '1.0.40'), - ('thread_local', '1.1.7'), - ('time', '0.3.20'), - ('time-core', '0.1.0'), - ('time-macros', '0.2.8'), - ('tinyvec', '1.6.0'), - ('tinyvec_macros', '0.1.1'), - ('toml', '0.5.11'), - ('toml', '0.7.4'), - ('toml_datetime', '0.6.2'), - ('toml_edit', '0.19.10'), - ('tracing', '0.1.37'), - ('tracing-attributes', '0.1.24'), - ('tracing-core', '0.1.31'), - ('tracing-log', '0.1.3'), - ('tracing-serde', '0.1.3'), - ('tracing-subscriber', '0.3.17'), - ('trycmd', '0.14.11'), - ('twox-hash', '1.6.3'), - ('typenum', '1.16.0'), - ('unicase', '2.6.0'), - ('unicode-bidi', '0.3.13'), - ('unicode-ident', '1.0.9'), - ('unicode-linebreak', '0.1.4'), - ('unicode-normalization', '0.1.22'), - ('unicode-width', '0.1.10'), - ('untrusted', '0.7.1'), - ('ureq', '2.6.2'), - ('url', '2.4.0'), - ('uuid', '1.3.3'), - ('valuable', '0.1.0'), - ('vcpkg', '0.2.15'), - ('version_check', '0.9.4'), - ('versions', '4.1.0'), - ('wait-timeout', '0.2.0'), - ('walkdir', '2.3.3'), - ('wasi', '0.11.0+wasi-snapshot-preview1'), - ('wasm-bindgen', '0.2.86'), - ('wasm-bindgen-backend', '0.2.86'), - ('wasm-bindgen-macro', '0.2.86'), - ('wasm-bindgen-macro-support', '0.2.86'), - ('wasm-bindgen-shared', '0.2.86'), - ('web-sys', '0.3.63'), - ('webpki', '0.22.0'), - ('webpki-roots', '0.22.6'), - ('which', '4.4.0'), - ('wild', '2.1.0'), - ('winapi', '0.3.9'), - ('winapi-i686-pc-windows-gnu', '0.4.0'), - ('winapi-util', '0.1.5'), - ('winapi-x86_64-pc-windows-gnu', '0.4.0'), - ('windows-sys', '0.42.0'), - ('windows-sys', '0.48.0'), - ('windows-targets', '0.48.0'), - ('windows_aarch64_gnullvm', '0.42.2'), - ('windows_aarch64_gnullvm', '0.48.0'), - ('windows_aarch64_msvc', '0.42.2'), - ('windows_aarch64_msvc', '0.48.0'), - ('windows_i686_gnu', '0.42.2'), - ('windows_i686_gnu', '0.48.0'), - ('windows_i686_msvc', '0.42.2'), - ('windows_i686_msvc', '0.48.0'), - ('windows_x86_64_gnu', '0.42.2'), - ('windows_x86_64_gnu', '0.48.0'), - ('windows_x86_64_gnullvm', '0.42.2'), - ('windows_x86_64_gnullvm', '0.48.0'), - ('windows_x86_64_msvc', '0.42.2'), - ('windows_x86_64_msvc', '0.48.0'), - ('winnow', '0.4.6'), - ('xattr', '0.2.3'), - ('xwin', '0.2.12'), - ('yansi', '0.5.1'), - ('zeroize', '1.6.0'), - ('zip', '0.6.6'), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -moduleclass = 'tools' From d794d51b65e04fd6f6f8704c31a592b692c083db Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Tue, 22 Aug 2023 15:03:37 +0200 Subject: [PATCH 8497/9987] Delete tornado-6.3.2-GCCcore-12.3.0.eb Depends on https://github.com/easybuilders/easybuild-easyconfigs/pull/18511 , shouldn't re-add this --- .../t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb deleted file mode 100644 index f63d8f312a9..00000000000 --- a/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = "PythonPackage" - -name = "tornado" -version = "6.3.2" - -homepage = "https://github.com/tornadoweb/tornado" -description = "Tornado is a Python web framework and asynchronous networking library." - -toolchain = {"name": "GCCcore", "version": "12.3.0"} - -sources = [SOURCE_TAR_GZ] -patches = ['tornado-timeouts.patch'] -checksums = [ - {'tornado-6.3.2.tar.gz': '4b927c4f19b71e627b13f3db2324e4ae660527143f9e1f2e2fb404f3a187e2ba'}, - {'tornado-timeouts.patch': 'fe0db60604ccdcb5fc111023d1d7bffa0e315465fbe15f2ff512068c649e56f8'}, -] - -builddependencies = [ - ("binutils", "2.40"), -] -dependencies = [ - ("Python", "3.11.3"), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -moduleclass = "lib" From 9e4cea15a6f7647380215ba507853f2c75592ba8 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 22 Aug 2023 15:26:07 +0200 Subject: [PATCH 8498/9987] update style leafcutter.eb --- .../l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb index 1a11945c089..29b15dc2b8c 100644 --- a/easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/l/leafcutter/leafcutter-0.2.9-foss-2022b-R-4.2.2.eb @@ -15,7 +15,7 @@ description = """Leafcutter quantifies RNA splicing variation using short-read R For details please see our bioRxiv preprint and corresponding Nature Genetics publication. """ -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'foss', 'version': '2022b'} source_urls = ['https://github.com/davidaknowles/leafcutter/archive/'] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] From a1f13f86b7ac0293abb8398b8cfe3ebd3eb20dcf Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 22 Aug 2023 15:29:26 +0200 Subject: [PATCH 8499/9987] add missing extentions --- .../R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index 3a7bb73d953..5b7b2d7438c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -1241,6 +1241,12 @@ exts_list = [ ('ANCOMBC', '2.0.2', { 'checksums': ['e577ffe62a86090de9ea3743c84a4f3b34c3d645dcedff3c8af675b8c9b69136'], }), + ('decoupleR', '2.4.0', { + 'checksums': ['b141afd331449b0b1c2dc3dc3097465c2c02b5026129d8f06dd5bfb445bce2a0'], + }), + ('UCell', '2.2.0', { + 'checksums': ['e3ca2b2d77a780a9450853e869bc10654c47485777d39a703203dc44d97df4bc'], + }), ('intervals', '0.15.4', { 'checksums': ['50c0e1e3aab3e7b72cc1f0a6559d96caa3a360e969c38538479907e6cbe39f8f'], }), From 981dba7967b4d12de58fbd1cd087310d37508391 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 15:38:08 +0200 Subject: [PATCH 8500/9987] adding easyconfigs: ncview-2.1.8-gompi-2023a.eb --- .../n/ncview/ncview-2.1.8-gompi-2023a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2023a.eb diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2023a.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2023a.eb new file mode 100644 index 00000000000..95c3aa4bb22 --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.8-gompi-2023a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.8' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e8badc507b9b774801288d1c2d59eb79ab31b004df4858d0674ed0d87dfc91be'] + +# specified compiler is hard checked against (full path to) compiler used for netCDF... +preconfigopts = "CC=$(nc-config --cc) " +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib " +configopts += "--with-nc-config=$EBROOTNETCDF/bin/nc-config" + +dependencies = [ + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('UDUNITS', '2.2.28'), + ('X11', '20230603'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' From a142655e16328dced30c0dea9e9bde8b88cb2280 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 22 Aug 2023 15:44:16 +0200 Subject: [PATCH 8501/9987] Fix style issue JupyterHub. Fix checksums PyZMQ. Fix missing patch nbclassic. Set download_dep_fail in notebook. --- .../JupyterHub-4.0.2-GCCcore-12.3.0.eb | 5 ++-- .../nbclassic-1.0.0_fix_setup_version.patch | 11 +++++++ .../notebook/notebook-7.0.2-GCCcore-12.3.0.eb | 1 + .../p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb | 1 + .../t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb | 29 +++++++++++++++++++ 5 files changed, 45 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0_fix_setup_version.patch create mode 100644 easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb index 8c8f316a6db..37f95412219 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb @@ -73,8 +73,9 @@ exts_list = [ 'git_config': { 'url': 'https://github.com/jupyterhub/', 'repo_name': 'batchspawner', - 'commit': '2a9eda0'}, # Needs unreleased features to for JupyterHub 4.X compatibility - }, + 'commit': '2a9eda0' + }, # Needs unreleased features to for JupyterHub 4.X compatibility + }, 'checksums': ['8ecfd2cceb248a5a4da5d5abe65e104086b0d2ff11acf3c6726e12b6a3a4d613'], }), ('jupyterhub-systemdspawner', '1.0.1', { diff --git a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0_fix_setup_version.patch b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0_fix_setup_version.patch new file mode 100644 index 00000000000..901d376a854 --- /dev/null +++ b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0_fix_setup_version.patch @@ -0,0 +1,11 @@ +diff -Nru nbclassic-1.0.0.orig/setup.cfg nbclassic-1.0.0/setup.cfg +--- nbclassic-1.0.0.orig/setup.cfg 2023-08-18 19:14:00.310355968 +0200 ++++ nbclassic-1.0.0/setup.cfg 2023-08-18 19:14:37.547459988 +0200 +@@ -1,6 +1,6 @@ + [metadata] + name = nbclassic +-version = attr: nbclassic.__version__ ++version = 1.0.0 + description = Jupyter Notebook as a Jupyter Server extension. + long_description = file: README.md + long_description_content_type = text/markdown diff --git a/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb index bd30f0acb08..ca17d12903e 100644 --- a/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb @@ -22,6 +22,7 @@ dependencies = [ sources = [SOURCE_TAR_GZ] checksums = ['d70d6a07418c829bd5f54337ce993b7105261d9026f9d3fe68e9b8aa1a20da9a'] +download_dep_fail = True sanity_pip_check = True use_pip = True diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb index 9f4d88872a1..19a3a61687c 100644 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = [PYPI_LOWER_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['259c22485b71abacdfa8bf79720cd7bcf4b9d128b30ea554f01ae71fdbfdaa23'] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f63d8f312a9 --- /dev/null +++ b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = "tornado" +version = "6.3.2" + +homepage = "https://github.com/tornadoweb/tornado" +description = "Tornado is a Python web framework and asynchronous networking library." + +toolchain = {"name": "GCCcore", "version": "12.3.0"} + +sources = [SOURCE_TAR_GZ] +patches = ['tornado-timeouts.patch'] +checksums = [ + {'tornado-6.3.2.tar.gz': '4b927c4f19b71e627b13f3db2324e4ae660527143f9e1f2e2fb404f3a187e2ba'}, + {'tornado-timeouts.patch': 'fe0db60604ccdcb5fc111023d1d7bffa0e315465fbe15f2ff512068c649e56f8'}, +] + +builddependencies = [ + ("binutils", "2.40"), +] +dependencies = [ + ("Python", "3.11.3"), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = "lib" From bde84bdb1f45787d9ec340740107d9268182f4b9 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 22 Aug 2023 15:59:04 +0200 Subject: [PATCH 8502/9987] Add Shapely and deps --- .../g/GEOS/GEOS-3.12.0-GCC-12.3.0.eb | 26 ++++++++++++++++++ .../s/Shapely/Shapely-2.0.1-foss-2023a.eb | 27 +++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEOS/GEOS-3.12.0-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.12.0-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..92f9459f967 --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.12.0-GCC-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'GEOS' +version = '3.12.0' + +homepage = 'https://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['d96db96011259178a35555a0f6d6e75a739e52a495a6b2aa5efb3d75390fbc39'] + +builddependencies = [('CMake', '3.26.3')] + +# Build static and shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb new file mode 100644 index 00000000000..91366d89edb --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '2.0.1' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['66a6b1a3e72ece97fc85536a281476f9b7794de2e646ca8a4517e2e3c1446893'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('GEOS', '3.12.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' From ef66f77931197c616bd13904e3af4868ac6df4d0 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 22 Aug 2023 16:06:13 +0200 Subject: [PATCH 8503/9987] Set download_dep_fail in nbclassic. --- .../easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb index eeea91f55a2..ba066826463 100644 --- a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb @@ -26,6 +26,7 @@ checksums = [ {'nbclassic-1.0.0_fix_setup_version.patch': 'c26d91ac1d0cea2b361b2619076acdaf5fcd5ff2363d9e5f5e1bd737b4b50736'}, ] +download_dep_fail = True sanity_pip_check = True use_pip = True From 463b628ac3d71b38c8362b9854ceaa51e76f277e Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Tue, 22 Aug 2023 16:06:49 +0200 Subject: [PATCH 8504/9987] Delete tornado-6.3.2-GCCcore-12.3.0.eb Is in dependent PR already --- .../t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb deleted file mode 100644 index f63d8f312a9..00000000000 --- a/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = "PythonPackage" - -name = "tornado" -version = "6.3.2" - -homepage = "https://github.com/tornadoweb/tornado" -description = "Tornado is a Python web framework and asynchronous networking library." - -toolchain = {"name": "GCCcore", "version": "12.3.0"} - -sources = [SOURCE_TAR_GZ] -patches = ['tornado-timeouts.patch'] -checksums = [ - {'tornado-6.3.2.tar.gz': '4b927c4f19b71e627b13f3db2324e4ae660527143f9e1f2e2fb404f3a187e2ba'}, - {'tornado-timeouts.patch': 'fe0db60604ccdcb5fc111023d1d7bffa0e315465fbe15f2ff512068c649e56f8'}, -] - -builddependencies = [ - ("binutils", "2.40"), -] -dependencies = [ - ("Python", "3.11.3"), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -moduleclass = "lib" From fe4f528b4009707603726b4ede8c52c58eb00a85 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 22 Aug 2023 16:53:19 +0200 Subject: [PATCH 8505/9987] Add sympy and deps --- .../g/gmpy2/gmpy2-2.1.5-GCC-12.3.0.eb | 25 +++++++++++++++++++ .../s/sympy/sympy-1.12-foss-2023a.eb | 21 ++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-12.3.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-12.3.0.eb new file mode 100644 index 00000000000..fe7a2d87e48 --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.5' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['bc297f1fd8c377ae67a4f493fc0f926e5d1b157e5c342e30a4d84dc7b9f95d96'] + +dependencies = [ + ('Python', '3.11.3'), + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), + ('MPC', '1.3.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb new file mode 100644 index 00000000000..c10a60b1ad5 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb @@ -0,0 +1,21 @@ +name = 'sympy' +version = '1.12' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ebf595c8dac3e0fdc4152c51878b498396ec7f30e7a914d6071e674d49420fb8'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('gmpy2', '2.1.5'), +] + +moduleclass = 'math' From f49ad16e8d8d0b5654844405d792feb5571cf991 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 22 Aug 2023 17:15:57 +0200 Subject: [PATCH 8506/9987] Add pypmt --- .../p/pypmt/pypmt-1.1.0-foss-2023a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..1de0b1c300c --- /dev/null +++ b/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'pypmt' +version = '1.1.0' + +homepage = 'https://git.astron.nl/RD/pmt' +description = """PMT is a high-level software library capable of + collecting power consumption measurements on various hardware.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] +sources = ['pmt-%(version)s.tar.gz'] +checksums = ['ab342ec33992c1ad4c42e0e66031710fe6320f73a1ca2a6e34cb1d4739da781f'] + +configopts = '-DBUILD_PYTHON_PMT=1' + +sanity_check_paths = { + 'files': ["bin/Rapl-test"], + 'dirs': [ + "lib", + "lib/python", + "include"], +} +sanity_check_commands = [('python', "-c 'import pmt'")] + +modextrapaths = { + 'PYTHONPATH': ['lib/python'] +} + +moduleclass = 'lib' From 6fc53ec3926d0b3af62943e91c6e4f5513616343 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 18:02:50 +0200 Subject: [PATCH 8507/9987] CDO-2.2.2-gompi-2023a.eb --- .../c/CDO/CDO-2.2.2-gompi-2023a.eb | 53 +++++++++++++++++++ .../easyconfigs/e/ecBuild/ecBuild-3.8.0.eb | 35 ++++++++++++ .../e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb | 45 ++++++++++++++++ .../l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb | 33 ++++++++++++ 4 files changed, 166 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.0.eb create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb new file mode 100644 index 00000000000..66de542b2b0 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb @@ -0,0 +1,53 @@ +# updated to version 2.0.6, based on the previous 2.0.5 version +# J. Sassmannshausen (Imperial College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) +# Maxim Masterov (SURF, NL) + +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.2.2' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'cstd': 'c++17', 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/28882/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['419c77315244019af41a296c05066f474cccbf94debfaae9e2106da51bc7c937'] + +builddependencies = [ + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('cURL', '8.0.1'), + ('ecCodes', '2.31.0'), + ('FFTW', '3.3.10'), + ('HDF5', '1.14.0'), + ('libxml2', '2.11.4'), + ('netCDF', '4.9.2'), + ('PROJ', '9.2.0'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.39'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +# sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : %(version)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.0.eb b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.0.eb new file mode 100644 index 00000000000..7ecb3207f49 --- /dev/null +++ b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.8.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'ecBuild' +version = '3.8.0' + +homepage = 'https://ecbuild.readthedocs.io/' + +description = """ +A CMake-based build system, consisting of a collection of CMake macros and +functions that ease the managing of software build systems """ + +toolchain = SYSTEM + +github_account = 'ecmwf' +sources = [ + { + 'source_urls': [GITHUB_SOURCE], + 'filename': '%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s --strip-components=1', + }, +] +checksums = ['6fba30dae40a09ad0f14e16769e5df2b038024df8bbaca55adaddbb7fce49579'] + +buildininstalldir = True + +skipsteps = ['install'] + +sanity_check_paths = { + 'files': ['bin/ecbuild', 'cmake/ecbuild-config.cmake'], + 'dirs': ['bin', 'lib', 'share', 'cmake'], +} + +sanity_check_commands = ['ecbuild --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb new file mode 100644 index 00000000000..71671b8391b --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.31.0' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://github.com/ecmwf/eccodes/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(namelower)s-%(version)s.tar.gz'}] +checksums = ['cb4cd3bab9cebd85a00397e12ce8e4a579b2f0a25aaf6df763436cf37db063e1'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('ecBuild', '3.8.0', '', SYSTEM), +] +dependencies = [ + ('netCDF', '4.9.2'), + ('JasPer', '4.0.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('libaec', '1.0.6'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF -DENABLE_JPG=ON " +configopts += "-DENABLE_JPG_LIBJASPER=ON -DENABLE_ECCODES_THREADS=ON" + + +sanity_check_paths = { + 'files': ['bin/bufr_compare', 'bin/bufr_copy', 'bin/bufr_dump', 'bin/bufr_filter', 'bin/bufr_get', 'bin/bufr_ls', + 'bin/grib_compare', 'bin/grib_copy', 'bin/grib_dump', 'bin/grib_filter', 'bin/grib_get', 'bin/grib_ls', + 'bin/gts_compare', 'bin/gts_copy', 'bin/gts_dump', 'bin/gts_filter', 'bin/gts_get', 'bin/gts_ls', + 'bin/metar_compare', 'bin/metar_copy', 'bin/metar_dump', 'bin/metar_filter', 'bin/metar_get', 'bin/metar_ls', + 'bin/codes_count', 'bin/codes_info', 'bin/codes_split_file', 'lib/libeccodes_f90.so', 'lib/libeccodes.so'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b194a947f0e --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.0.6' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['bin/aec', 'include/%(name)s.h', 'include/szlib.h', 'lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ['aec --help'] + +moduleclass = 'lib' From 81aa486d2763e044458843a621581b580bb2893c Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 18:20:58 +0200 Subject: [PATCH 8508/9987] fixed sanity check --- easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb index 66de542b2b0..658b0ffc5c1 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb @@ -48,6 +48,6 @@ sanity_check_paths = { 'dirs': ['include'], } -# sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : %(version)s'"] +sanity_check_commands = ["cdo --version 2>&1 | grep 'Climate Data Operators version : %(version)s'"] moduleclass = 'data' From 9698f093710d29812f59896110da2072dc94a4a7 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 18:24:28 +0200 Subject: [PATCH 8509/9987] adding easyconfigs: Ghostscript-10.01.2-GCCcore-12.3.0.eb --- .../Ghostscript-10.01.2-GCCcore-12.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bb09de3527b --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '10.01.2' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs10012'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4cd61a07fec161bee35da0211a5e5cde8ff8a0aaf942fc0176715e499d21661'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('zlib', '1.2.13'), + ('libpng', '1.6.39'), + ('freetype', '2.13.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('expat', '2.5.0'), + ('GLib', '2.77.1'), + ('cairo', '1.17.8'), + ('LibTIFF', '4.5.0'), + ('GTK3', '3.24.37'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = 'mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && ' +preconfigopts += 'mv libpng libpng.no && export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' +configopts = "--with-system-libtiff --enable-dynamic --disable-hidden-visibility" + +# Avoid race condition in build if too much parallelism is used +maxparallel = 4 + +postinstallcmds = [ + # build and install shared libs + "make so && make soinstall", + # install header files + "mkdir -p %(installdir)s/include/%(namelower)s", + "install -v -m644 base/*.h %(installdir)s/include/%(namelower)s", + "install -v -m644 psi/*.h %(installdir)s/include/%(namelower)s", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.so'], + 'dirs': ['lib/%(namelower)s', 'include/%(namelower)s', 'share/man'], +} + +moduleclass = 'tools' From ec97b3ad265cb65157e5ebd374970b90deb2438d Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 22 Aug 2023 18:48:15 +0200 Subject: [PATCH 8510/9987] added svg patch --- .../g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb | 3 +++ ...-icon-theme-44.0_disable-svg-conversion.patch | 16 ++++++++++++++++ 2 files changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK3/adwaita-icon-theme-44.0_disable-svg-conversion.patch diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb index 42db0c38bd4..c4a1a99a25b 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb @@ -54,8 +54,11 @@ components = [ ('adwaita-icon-theme', '44.0', { 'easyblock': 'ConfigureMake', 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'patches': ['adwaita-icon-theme-44.0_disable-svg-conversion.patch'], 'checksums': [ '4889c5601bbfecd25d80ba342209d0a936dcf691ee56bd6eca4cde361f1a664c', + # adwaita-icon-theme-44.0_disable-svg-conversion.patch + '9957c8b3d2a1cf8d89d6e943e59c683dbf5c5b37687316265cc82e755208f40b' ], 'preconfigopts': 'autoreconf -f -i && ', }), diff --git a/easybuild/easyconfigs/g/GTK3/adwaita-icon-theme-44.0_disable-svg-conversion.patch b/easybuild/easyconfigs/g/GTK3/adwaita-icon-theme-44.0_disable-svg-conversion.patch new file mode 100644 index 00000000000..b15d0c22404 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/adwaita-icon-theme-44.0_disable-svg-conversion.patch @@ -0,0 +1,16 @@ +diff -aur a/configure.ac b/configure.ac +As we don't have SVG support we disable the search for the converter. +Adopted from: +Author: Alexander Grund (TU Dresden) + +--- a/configure.ac 2023-08-18 17:58:28.032333478 +0200 ++++ b/configure.ac 2023-08-18 17:59:51.554807635 +0200 +@@ -49,7 +49,7 @@ + AM_CONDITIONAL(ALLOW_RENDERING, test "x$allow_rendering" = "xyes") + + symbolic_encode_sizes="16x16 32x32" +-AC_PATH_PROG([GTK_ENCODE_SYMBOLIC_SVG], [gtk-encode-symbolic-svg], [false]) ++GTK_ENCODE_SYMBOLIC_SVG="false" + if test "x$GTK_ENCODE_SYMBOLIC_SVG" = "xfalse"; then + symbolic_encode_sizes="" + fi From 5c5a98accc74ea307d3e1232f276c2e5e9764c61 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 23 Aug 2023 08:26:39 +0200 Subject: [PATCH 8511/9987] adding easyconfigs: fastahack-1.0.0-GCCcore-11.3.0.eb --- .../fastahack-1.0.0-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..95a22a66ce6 --- /dev/null +++ b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'fastahack' +version = '1.0.0' + +homepage = 'https://github.com/ekg/fastahack' +description = """Utilities for indexing and sequence extraction from FASTA files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_build-libs.patch'] +checksums = [ + 'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae', # v1.0.0.tar.gz + '7f804486c6bafd9b1572cb5f86ff28dbebb4d6da551bde1091d6ff8f82748bf4', # fastahack-1.0.0_build-libs.patch +] + +builddependencies = [('binutils', '2.38')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfastahack.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' From 537b109594799957d9023516e08b949e81b3a8f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 23 Aug 2023 08:27:37 +0200 Subject: [PATCH 8512/9987] adding easyconfigs: multichoose-1.0.3-GCCcore-11.3.0.eb --- .../multichoose-1.0.3-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..47eaa5df2bf --- /dev/null +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'multichoose' +version = '1.0.3' + +homepage = 'https://github.com/ekg/multichoose' +description = """generate multiset combinations (n multichoose k).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_improve-build-system.patch'] +checksums = [ + '74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877', # v1.0.3.tar.gz + '96abf6ac1105ee596be078d6e8fb478f870a4ae33fffe70f93e627c0360cfc77', # multichoose-1.0.3_improve-build-system.patch +] + +builddependencies = [('binutils', '2.38')] + +local_bins = [name, 'multipermute'] +files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/%(name)s')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s 1 a'] + +moduleclass = 'bio' From 2436f043ad70b7b0125e44fa1d581a20542ac38f Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 23 Aug 2023 09:53:11 +0200 Subject: [PATCH 8513/9987] Update easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb index 91366d89edb..e4a5f0c0bae 100644 --- a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb @@ -9,7 +9,7 @@ homepage = 'https://github.com/Toblerity/Shapely' description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} sources = [SOURCELOWER_TAR_GZ] checksums = ['66a6b1a3e72ece97fc85536a281476f9b7794de2e646ca8a4517e2e3c1446893'] From fdc11949584347d4027479f946d2c0b898120bc7 Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 23 Aug 2023 09:53:28 +0200 Subject: [PATCH 8514/9987] Update easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb index c10a60b1ad5..6ef48cf5831 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb @@ -7,7 +7,7 @@ description = """SymPy is a Python library for symbolic mathematics. It aims to simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries.""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} sources = [SOURCE_TAR_GZ] checksums = ['ebf595c8dac3e0fdc4152c51878b498396ec7f30e7a914d6071e674d49420fb8'] From f492a3e7781a44cee18192128da71dc65e8e9055 Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 23 Aug 2023 09:53:45 +0200 Subject: [PATCH 8515/9987] Update easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb index 1de0b1c300c..69a0899d6a0 100644 --- a/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb @@ -7,7 +7,7 @@ homepage = 'https://git.astron.nl/RD/pmt' description = """PMT is a high-level software library capable of collecting power consumption measurements on various hardware.""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} builddependencies = [('CMake', '3.26.3')] dependencies = [ From b98aef638eddaa66fe9a5fdb1f68f1ceda2b6a6d Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 23 Aug 2023 10:02:09 +0200 Subject: [PATCH 8516/9987] Rename pypmt-1.1.0-foss-2023a.eb to pypmt-1.1.0-gfbf-2023a.eb --- .../{pypmt-1.1.0-foss-2023a.eb => pypmt-1.1.0-gfbf-2023a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/pypmt/{pypmt-1.1.0-foss-2023a.eb => pypmt-1.1.0-gfbf-2023a.eb} (100%) diff --git a/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-gfbf-2023a.eb similarity index 100% rename from easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-foss-2023a.eb rename to easybuild/easyconfigs/p/pypmt/pypmt-1.1.0-gfbf-2023a.eb From 4365bc002a8d625c76d807503fa529dec97ee967 Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 23 Aug 2023 10:04:19 +0200 Subject: [PATCH 8517/9987] Rename sympy-1.12-foss-2023a.eb to sympy-1.12-gfbf-2023a.eb --- .../sympy/{sympy-1.12-foss-2023a.eb => sympy-1.12-gfbf-2023a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/sympy/{sympy-1.12-foss-2023a.eb => sympy-1.12-gfbf-2023a.eb} (100%) diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb b/easybuild/easyconfigs/s/sympy/sympy-1.12-gfbf-2023a.eb similarity index 100% rename from easybuild/easyconfigs/s/sympy/sympy-1.12-foss-2023a.eb rename to easybuild/easyconfigs/s/sympy/sympy-1.12-gfbf-2023a.eb From 131a1384634af59dfdf5d840ecd9cd98e6f56dc3 Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 23 Aug 2023 10:05:11 +0200 Subject: [PATCH 8518/9987] Rename Shapely-2.0.1-foss-2023a.eb to Shapely-2.0.1-gfbf-2023a.eb --- .../{Shapely-2.0.1-foss-2023a.eb => Shapely-2.0.1-gfbf-2023a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/Shapely/{Shapely-2.0.1-foss-2023a.eb => Shapely-2.0.1-gfbf-2023a.eb} (100%) diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-gfbf-2023a.eb similarity index 100% rename from easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2023a.eb rename to easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-gfbf-2023a.eb From b4782c534634e07e56512f5b2d72dadc535cf1fd Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 23 Aug 2023 11:27:53 +0200 Subject: [PATCH 8519/9987] Update novaSTA-1.1-foss-2022a-CUDA-11.7.0.eb --- .../n/novaSTA/novaSTA-1.1-foss-2022a-CUDA-11.7.0.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/novaSTA/novaSTA-1.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/novaSTA/novaSTA-1.1-foss-2022a-CUDA-11.7.0.eb index 84a9a699671..e69dece43fa 100644 --- a/easybuild/easyconfigs/n/novaSTA/novaSTA-1.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/novaSTA/novaSTA-1.1-foss-2022a-CUDA-11.7.0.eb @@ -16,16 +16,18 @@ toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = { 'cstd': 'c++14', 'opt': 'True', - 'debug': 'False', 'usempi': 'True' } +github_account = 'turonova' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['db0765eade1b0399929dcd61f2dbeeffd762885902f6ef2811d1fb4f9634a2ac'] -github_account = 'turonova' -dependencies = [('CUDA', '11.7.0', '', SYSTEM)] +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), +] files_to_copy = [ (['novaSTA'], 'bin'), @@ -42,7 +44,7 @@ examples = '%(installdir)s/parameter_file_example.txt' sanity_check_paths = { 'files': ['bin/%(name)s', 'parameter_file_example.txt'], - 'dirs': ["."] + 'dirs': [] } moduleclass = 'bio' From 206c9c3d5025a88ed9ae6669b8de4e92bd5f8a1e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 23 Aug 2023 11:32:03 +0200 Subject: [PATCH 8520/9987] use separate easyconfigs for dm-tree and dm-haiku --- .../d/dm-haiku/dm-haiku-0.0.9-foss-2022a.eb | 32 +++++++++++++++++++ .../o/Optax/Optax-0.1.7-foss-2022a.eb | 18 ++--------- 2 files changed, 34 insertions(+), 16 deletions(-) create mode 100644 easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2022a.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2022a.eb new file mode 100644 index 00000000000..a27a9594b4f --- /dev/null +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.9-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'dm-haiku' +version = '0.0.9' + +homepage = 'https://github.com/deepmind/dm-haiku' +description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural +network library for TensorFlow.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('jax', '0.3.25'), # required by jmp, also provides absl-py +] + +use_pip = True + +exts_list = [ + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + (name, version, { + 'modulename': 'haiku', + 'checksums': ['97752b32cdbe5a3e2d1c60ea884d33eb4b36e7d410000f0d61b571417c925435'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/Optax/Optax-0.1.7-foss-2022a.eb b/easybuild/easyconfigs/o/Optax/Optax-0.1.7-foss-2022a.eb index c3d11781d8a..27fa821b7b6 100644 --- a/easybuild/easyconfigs/o/Optax/Optax-0.1.7-foss-2022a.eb +++ b/easybuild/easyconfigs/o/Optax/Optax-0.1.7-foss-2022a.eb @@ -10,13 +10,12 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('jax', '0.3.25'), + ('dm-haiku', '0.0.9'), + ('dm-tree', '0.1.8'), ('typing-extensions', '4.3.0'), ] builddependencies = [ - ('CMake', '3.23.1'), # required for installing dm-tree ('pytest-xdist', '2.5.0'), ] @@ -26,19 +25,6 @@ exts_list = [ ('toolz', '0.12.0', { 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], }), - ('jmp', '0.0.4', { - 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], - }), - ('dm-haiku', '0.0.9', { - 'modulename': 'haiku', - 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], - }), - ('dm-tree', '0.1.8', { - 'modulename': 'tree', - 'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'], - }), ('chex', '0.1.6', { 'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'], }), From 68883b607beaa1e39fec119f690f1f5d918cea9f Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Wed, 23 Aug 2023 17:53:19 +0200 Subject: [PATCH 8521/9987] Remove EGL vendor dir prepend due to move to EasyBlock --- easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb | 3 --- easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb | 3 --- easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb | 3 --- easybuild/easyconfigs/m/Mesa/Mesa-21.1.1-GCCcore-10.3.0.eb | 3 --- easybuild/easyconfigs/m/Mesa/Mesa-21.1.7-GCCcore-11.2.0.eb | 3 --- easybuild/easyconfigs/m/Mesa/Mesa-22.0.3-GCCcore-11.3.0.eb | 3 --- easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb | 3 --- easybuild/easyconfigs/m/Mesa/Mesa-23.1.4-GCCcore-12.3.0.eb | 3 --- 8 files changed, 24 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb index 4038caecb18..4df888ead2c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-19.2.1-GCCcore-8.3.0.eb @@ -72,7 +72,4 @@ configopts += " -Dglvnd=true" # This helps in certain X forwarding situations (e.g. XQuartz) postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] -# Tells libglvnd where to find EGL libraries -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb index 69d8f9a58b9..7fab5b51576 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-20.0.2-GCCcore-9.3.0.eb @@ -67,7 +67,4 @@ configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" # This helps in certain X forwarding situations (e.g. XQuartz) postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] -# Tells libglvnd where to find EGL libraries -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb index a2dbdd6eb60..2c63a42feb3 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb @@ -67,7 +67,4 @@ configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" # This helps in certain X forwarding situations (e.g. XQuartz) postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] -# Tells libglvnd where to find EGL libraries -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-21.1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-21.1.1-GCCcore-10.3.0.eb index fd898dcf82c..b18d10a8a50 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-21.1.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-21.1.1-GCCcore-10.3.0.eb @@ -63,7 +63,4 @@ configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" # This helps in certain X forwarding situations (e.g. XQuartz) postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] -# Tells libglvnd where to find EGL libraries -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-21.1.7-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-21.1.7-GCCcore-11.2.0.eb index 97e9bb87b40..1d789b3cb6c 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-21.1.7-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-21.1.7-GCCcore-11.2.0.eb @@ -63,7 +63,4 @@ configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" # This helps in certain X forwarding situations (e.g. XQuartz) postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] -# Tells libglvnd where to find EGL libraries -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-22.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-22.0.3-GCCcore-11.3.0.eb index 997ab7b2951..34b4b562a8a 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-22.0.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-22.0.3-GCCcore-11.3.0.eb @@ -63,7 +63,4 @@ configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" # This helps in certain X forwarding situations (e.g. XQuartz) postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] -# Tells libglvnd where to find EGL libraries -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb index f59d911be6a..476f46b65db 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb @@ -63,7 +63,4 @@ configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" # This helps in certain X forwarding situations (e.g. XQuartz) postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] -# Tells libglvnd where to find EGL libraries -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-23.1.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.4-GCCcore-12.3.0.eb index 6cf782f85cd..190b07b1d41 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-23.1.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.4-GCCcore-12.3.0.eb @@ -63,7 +63,4 @@ configopts += "-Dllvm=enabled -Dshared-llvm=enabled -Dlibunwind=enabled -Dglvnd= # This helps in certain X forwarding situations (e.g. XQuartz) postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] -# Tells libglvnd where to find EGL libraries -modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} - moduleclass = 'vis' From 2b6c2a464723b180d0f60c83981559bdb227f20a Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Wed, 23 Aug 2023 18:01:02 +0200 Subject: [PATCH 8522/9987] Fat build compatible with hardware rendering, software rendering, headless server mode, as well as interactive mode. --- ...raView-5.11.1-foss-2022a-mpi-egl-osmesa.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb new file mode 100644 index 00000000000..988e8340a0c --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.11.1' +versionsuffix = '-mpi-egl-osmesa' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('XZ', '5.2.5'), + ('HDF5', '1.12.2'), + ('netCDF', '4.9.0'), + ('libGLU', '9.0.2'), + ('libdrm', '2.4.110'), + ('Mesa', '22.0.3'), + ('Qt5', '5.15.5'), + ('zlib', '1.2.12'), + ('FFmpeg', '4.4.2'), + ('Szip', '2.1.1'), +] + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' +configopts += '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include ' +configopts += '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.so ' +configopts += '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.so ' +configopts += '-DVTK_OPENGL_HAS_EGL=ON ' +configopts += '-DVTK_USE_X=ON ' +configopts += '-DVTK_HAS_OSMESA=ON ' + + +sanity_check_paths = { + 'files': ['bin/pvserver', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' From 20fa13e1911dcca8f1eb66b07a1845e13f740eb5 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Wed, 23 Aug 2023 18:02:58 +0200 Subject: [PATCH 8523/9987] Patch to remove spurious GLEW warning. --- .../ParaView-5.11.1-remove_glew_init_warning.patch | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch new file mode 100644 index 00000000000..dc1f05c4d84 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch @@ -0,0 +1,13 @@ +--- VTK/Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx.orig 2023-08-23 16:35:23.418470811 +0200 ++++ VTK/Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx 2023-08-23 16:36:10.830654656 +0200 +@@ -471,8 +471,8 @@ + this->GlewInitValid = (result == GLEW_OK); + if (!this->GlewInitValid) + { +- const char* errorMsg = reinterpret_cast(glewGetErrorString(result)); +- vtkErrorMacro("GLEW could not be initialized: " << errorMsg); ++ //const char* errorMsg = reinterpret_cast(glewGetErrorString(result)); ++ //vtkErrorMacro("GLEW could not be initialized: " << errorMsg); + return; + } + From b5fc93adc1ea3adeb0f780b46665b6d1e2e3cdd6 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 23 Aug 2023 18:03:13 +0200 Subject: [PATCH 8524/9987] Added description to patch after chat on Slack with @Surak --- easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/t/tornado/tornado-timeouts.patch | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb index f63d8f312a9..9fd6757d976 100644 --- a/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/tornado/tornado-6.3.2-GCCcore-12.3.0.eb @@ -12,7 +12,7 @@ sources = [SOURCE_TAR_GZ] patches = ['tornado-timeouts.patch'] checksums = [ {'tornado-6.3.2.tar.gz': '4b927c4f19b71e627b13f3db2324e4ae660527143f9e1f2e2fb404f3a187e2ba'}, - {'tornado-timeouts.patch': 'fe0db60604ccdcb5fc111023d1d7bffa0e315465fbe15f2ff512068c649e56f8'}, + {'tornado-timeouts.patch': 'dd97748cb80506b36570f1274b19c8fc53d81e15f0eb2c5b6d0ba9d80141af34'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/tornado/tornado-timeouts.patch b/easybuild/easyconfigs/t/tornado/tornado-timeouts.patch index 02720680265..635fa6d7143 100644 --- a/easybuild/easyconfigs/t/tornado/tornado-timeouts.patch +++ b/easybuild/easyconfigs/t/tornado/tornado-timeouts.patch @@ -1,3 +1,4 @@ +# Increase timeouts to prevent tornado from killing jupyter on compute nodes diff -Naur tornado.orig/tornado-6.1/tornado/httpclient.py tornado/tornado-6.1/tornado/httpclient.py --- tornado.orig/tornado-6.1/tornado/httpclient.py 2020-10-30 21:17:45.000000000 +0100 +++ tornado/tornado-6.1/tornado/httpclient.py 2022-05-01 22:01:50.923741948 +0200 From e51223cd2722cecd22b992e047c60db1ad5830e4 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Wed, 23 Aug 2023 18:06:05 +0200 Subject: [PATCH 8525/9987] Update sanity check. --- .../p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb index 988e8340a0c..24d94e8f37f 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb @@ -50,7 +50,7 @@ configopts += '-DVTK_HAS_OSMESA=ON ' sanity_check_paths = { - 'files': ['bin/pvserver', 'bin/pvpython'], + 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], } From b23c4b0ad02c34751b9b1e9ccddc20120fde691f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 23 Aug 2023 18:07:29 +0200 Subject: [PATCH 8526/9987] Add binutils dep --- .../easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb index 5e387e02309..456061ea2f0 100644 --- a/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb @@ -8,6 +8,10 @@ description = "Standards-compliant library for parsing and serializing HTML docu toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [ + ('binutils', '2.40'), +] + dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), From 60f85eb6403be2219db4abf34d8cb0185b0d7640 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 23 Aug 2023 19:41:58 +0200 Subject: [PATCH 8527/9987] Remove jupyter-server-proxy as dependency. It _is_ common to use with JupyterHub, but so are JupyterLab, notebook, etc. I'll make a Jupyter-bundle that bundles all these together for convenience in a follow-up PR. It does mean I need to add tornado here as a dependency, previously that was provided through jupyter-server-proxy. --- .../j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb index 37f95412219..16a557654b4 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb @@ -20,7 +20,7 @@ dependencies = [ ('Mako', '1.2.4'), ('configurable-http-proxy', '4.5.6'), ('OpenSSL', '1.1', '', SYSTEM), - ('jupyter-server-proxy', '4.0.0'), # optional, but commonly used together + ('tornado', '6.3.2'), ('PycURL', '7.45.2'), # optional, recommended with large number of users ] @@ -60,10 +60,17 @@ exts_list = [ 'modulename': False, 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), ('jupyter-telemetry', '0.1.0', { 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], }), + ('prometheus_client', '0.17.1', { + 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], + }), ('jupyterhub', version, { 'checksums': ['d4e450eed8d90dfbcf0eca08f00f2093a0bce74dc51f7cfc0b7057f602341a1d'], }), From 586de11102b96c08f40839cb8d38a667ac84d824 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 23 Aug 2023 20:08:16 +0200 Subject: [PATCH 8528/9987] Make sure the batchspawner tarball is downloaded in a way that leads to a reproducible checksum. --- .../JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb index 16a557654b4..17a223e8816 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb @@ -27,6 +27,8 @@ dependencies = [ sanity_pip_check = True use_pip = True +local_batchspawner_commit = '2a9eda060a875a2b65ca9521368fe052a09c3266' + exts_list = [ ('certipy', '0.1.3', { 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], @@ -74,16 +76,13 @@ exts_list = [ ('jupyterhub', version, { 'checksums': ['d4e450eed8d90dfbcf0eca08f00f2093a0bce74dc51f7cfc0b7057f602341a1d'], }), - ('batchspawner', '1.2.0-2a9eda0', { + ('batchspawner', '1.2.0-%s' % local_batchspawner_commit, { + 'source_urls': [GITHUB_SOURCE], 'sources': { - 'filename': 'main.tar.gz', - 'git_config': { - 'url': 'https://github.com/jupyterhub/', - 'repo_name': 'batchspawner', - 'commit': '2a9eda0' - }, # Needs unreleased features to for JupyterHub 4.X compatibility + 'filename': '%(name)s-%(version)s.tar.gz', + 'download_filename': '%s.tar.gz' % local_batchspawner_commit }, - 'checksums': ['8ecfd2cceb248a5a4da5d5abe65e104086b0d2ff11acf3c6726e12b6a3a4d613'], + 'checksums': ['d5cf239ba75522d928ed33971c180532f590131905c42eac1be2651ccad85283'], }), ('jupyterhub-systemdspawner', '1.0.1', { 'modulename': 'systemdspawner', From 64064900d86f1f5b419539272a72458fd38c0773 Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 23 Aug 2023 20:10:40 +0200 Subject: [PATCH 8529/9987] Re-added explaination of why we install batchspawner from a specific commit --- .../easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb index 17a223e8816..db4bc503345 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb @@ -76,6 +76,7 @@ exts_list = [ ('jupyterhub', version, { 'checksums': ['d4e450eed8d90dfbcf0eca08f00f2093a0bce74dc51f7cfc0b7057f602341a1d'], }), + # Needs unreleased features to for JupyterHub 4.X compatibility, hence install from commit ('batchspawner', '1.2.0-%s' % local_batchspawner_commit, { 'source_urls': [GITHUB_SOURCE], 'sources': { From 600f599cd958c90c895409962f3e330440983d8c Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 23 Aug 2023 20:20:06 +0200 Subject: [PATCH 8530/9987] Fix typo --- .../easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb index db4bc503345..6e978bce869 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb @@ -76,7 +76,7 @@ exts_list = [ ('jupyterhub', version, { 'checksums': ['d4e450eed8d90dfbcf0eca08f00f2093a0bce74dc51f7cfc0b7057f602341a1d'], }), - # Needs unreleased features to for JupyterHub 4.X compatibility, hence install from commit + # Needs unreleased features for JupyterHub 4.X compatibility, hence install from commit ('batchspawner', '1.2.0-%s' % local_batchspawner_commit, { 'source_urls': [GITHUB_SOURCE], 'sources': { From c58366a33d9b377780dd039004c05d3750e973d3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 24 Aug 2023 08:35:54 +0200 Subject: [PATCH 8531/9987] remove drmaa from deps --- easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb b/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb index a7bc79e99c8..f4033c48db0 100644 --- a/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb +++ b/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb @@ -30,7 +30,6 @@ dependencies = [ ('snakemake', '7.32.3'), ('pyfaidx', '0.7.2.1'), ('Greenlet', '2.0.2'), - ('drmaa-python', '0.7.9'), ] use_pip = True @@ -38,6 +37,10 @@ sanity_pip_check = True local_old_line = 'from scipy._build_utils import numpy_nodepr_api' local_new_line = """numpy_nodepr_api = dict(define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_9_API_VERSION")])""" +# hardcoded value, used to be imported from scipy._build_utils (which is no longer available since scipy 1.10)' +local_code_patch_cmd = f"sed -i 's/{local_old_line}/{local_new_line}/g' setup.py" +# drmaa-python is not necessary and it would require slurm-drmaa while Slurm is not available on all clusters +local_dep_patch_cmd = "sed -i '/^drmaa$/d' requirements.txt" exts_list = [ ('SQLAlchemy', '2.0.20', { @@ -69,8 +72,7 @@ exts_list = [ 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], }), (name, version, { - # hardcoded value, used to be imported from scipy._build_utils (which is no longer available since scipy 1.10)' - 'preinstallopts': f"sed -i 's/{local_old_line}/{local_new_line}/g' setup.py && ", + 'preinstallopts': f"{local_code_patch_cmd} && {local_dep_patch_cmd} && ", 'modulename': name, 'checksums': ['6d8844bacacc776214cf35cb148fa638c029b2972751d04fc1f7d0d8f3e961c2'], }), From b32587edc20fa287319a1f9530340d870b05c517 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 24 Aug 2023 10:25:50 +0200 Subject: [PATCH 8532/9987] adding easyconfigs: Jupyter-bundle-20230823-GCCcore-12.3.0.eb, jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb, jupyterlmod-4.0.3-GCCcore-12.3.0.eb --- ...gurable-http-proxy-4.5.6-GCCcore-12.3.0.eb | 32 +++ .../Jupyter-bundle-20230823-GCCcore-12.3.0.eb | 24 +++ .../JupyterHub-4.0.2-GCCcore-12.3.0.eb | 130 ++++++++++++ .../JupyterLab-4.0.5-GCCcore-12.3.0.eb | 73 +++++++ ...ter-resource-usage-1.0.0-GCCcore-12.3.0.eb | 37 ++++ ...pyter-server-proxy-4.0.0-GCCcore-12.3.0.eb | 45 +++++ .../jupyter-server-2.7.2-GCCcore-12.3.0.eb | 190 ++++++++++++++++++ .../jupyterlmod-4.0.3-GCCcore-12.3.0.eb | 45 +++++ .../nbclassic-1.0.0-GCCcore-12.3.0.eb | 51 +++++ .../notebook/notebook-7.0.2-GCCcore-12.3.0.eb | 41 ++++ .../p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb | 29 +++ .../p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb | 29 +++ 12 files changed, 726 insertions(+) create mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fc58c50bc75 --- /dev/null +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'Binary' + +name = 'configurable-http-proxy' +version = '4.5.6' + +homepage = 'https://github.com/jupyterhub/configurable-http-proxy' +description = """HTTP proxy for node.js including a REST API for updating the routing table. + Developed as a part of the Jupyter Hub multi-user server.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/jupyterhub/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4d9d94d0e6e44542ac973963b8a6545f4b40c0a2995e865ae9c80a2279e1e0ab'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('nodejs', '18.17.1'), +] + +install_cmd = "npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz" + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..44bade9c3dd --- /dev/null +++ b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Jupyter-bundle' +version = '20230823' + +homepage = "https://jupyter.org/" + +description = """ + This bundle collects a range of Jupyter interfaces (Lab, Notebook and nbclassic), + extensions (Jupyter Server Proxy, Jupyter Resource Monitor, Jupyter Lmod) and + the JupyterHub. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +dependencies = [ + ('JupyterHub', '4.0.2'), + ('JupyterLab', '4.0.5'), + ('notebook', '7.0.2'), + ('nbclassic', '1.0.0'), + ('jupyter-server-proxy', '4.0.0'), + ('jupyterlmod','4.0.3'), + ('jupyter-resource-usage', '1.0.0'), +] diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..6e978bce869 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,130 @@ +easyblock = 'PythonBundle' + +name = 'JupyterHub' +version = '4.0.2' + +homepage = 'https://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed + for centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('setuptools-rust', '1.6.0'), # Needed for bcrypt + ('Rust', '1.70.0'), # Needed for bcrypt +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('Mako', '1.2.4'), + ('configurable-http-proxy', '4.5.6'), + ('OpenSSL', '1.1', '', SYSTEM), + ('tornado', '6.3.2'), + ('PycURL', '7.45.2'), # optional, recommended with large number of users +] + +sanity_pip_check = True +use_pip = True + +local_batchspawner_commit = '2a9eda060a875a2b65ca9521368fe052a09c3266' + +exts_list = [ + ('certipy', '0.1.3', { + 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], + }), + ('pamela', '1.1.0', { + 'checksums': ['d4b139fe600e192e176a2a368059207a6bffa0e7879879b13f4fcba0163481be'], + }), + ('greenlet', '2.0.2', { + 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('SQLAlchemy', '2.0.20', { + 'checksums': ['ca8a5ff2aa7f3ade6c498aaafce25b1eaeabe4e42b73e25519183e4566a16fc6'], + }), + ('alembic', '1.11.3', { + 'checksums': ['3db4ce81a9072e1b5aa44c2d202add24553182672a12daf21608d6f62a8f9cf9'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('pyOpenSSL', '23.2.0', { + 'modulename': 'OpenSSL', + 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], + }), + ('ruamel.yaml', '0.17.32', { + 'checksums': ['ec939063761914e14542972a5cba6d33c23b0859ab6342f61cf070cfc600efc2'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jupyter-telemetry', '0.1.0', { + 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', + 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], + }), + ('prometheus_client', '0.17.1', { + 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], + }), + ('jupyterhub', version, { + 'checksums': ['d4e450eed8d90dfbcf0eca08f00f2093a0bce74dc51f7cfc0b7057f602341a1d'], + }), + # Needs unreleased features for JupyterHub 4.X compatibility, hence install from commit + ('batchspawner', '1.2.0-%s' % local_batchspawner_commit, { + 'source_urls': [GITHUB_SOURCE], + 'sources': { + 'filename': '%(name)s-%(version)s.tar.gz', + 'download_filename': '%s.tar.gz' % local_batchspawner_commit + }, + 'checksums': ['d5cf239ba75522d928ed33971c180532f590131905c42eac1be2651ccad85283'], + }), + ('jupyterhub-systemdspawner', '1.0.1', { + 'modulename': 'systemdspawner', + 'checksums': ['8d614f19d89564321fe55d80ecd134a0e2bf276274d45861495c9bb5a80add28'], + }), + ('jupyterhub-simplespawner', '0.1', { + 'modulename': 'simplespawner', + 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], + }), + ('ldap3', '2.9.1', { + 'checksums': ['f3e7fc4718e3f09dda568b57100095e0ce58633bcabbed8667ce3f8fbaa4229f'], + }), + ('jupyterhub-ldapauthenticator', '1.3.2', { + 'modulename': 'ldapauthenticator', + 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('jupyterhub-jwtauthenticator-v2', '2.0.3', { + 'modulename': 'jwtauthenticator', + 'checksums': ['b94b6dff8246250904c5ee511da3f062680eb657dabe766d75993cbe72747d41'], + }), + ('onetimepass', '1.0.1', { + 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], + }), + ('bcrypt', '4.0.1', { + 'checksums': ['27d375903ac8261cfe4047f6709d16f7d18d39b1ec92aaf72af989552a650ebd'], + }), + ('jupyterhub-nativeauthenticator', '1.2.0', { + 'modulename': 'nativeauthenticator', + 'checksums': ['826228e6e9ca37736361e2e60c5723e245ec72e34fdc42cc218fc54a67f968e1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..19c7e8a6710 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '4.0.5' + +homepage = 'https://jupyter.org/' +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), +] + +# keep user's configuration in their home directory +# note: '~' is not expanded by JupyterLab +modluafooter = """ +setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) +setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) +""" +modtclfooter = """ +setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" +setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" +""" +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('json5', '0.9.14', { + 'checksums': ['9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02'], + }), + ('jupyterlab_server', '2.24.0', { + 'checksums': ['4e6f99e0a5579bbbc32e449c4dbb039561d4f1a7827d5733273ed56738f21f07'], + }), + ('jupyter-lsp', '2.2.0', { + 'checksums': ['8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1'], + }), + ('async-lru', '2.0.4', { + 'checksums': ['b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627'], + }), + ('jupyterlab', version, { + 'checksums': ['de49deb75f9b9aec478ed04754cbefe9c5d22fd796a5783cdc65e212983d3611'], + }), +] + +local_binaries = [ + 'jupyter-lab', + 'jupyter-labextension', + 'jupyter-labhub', +] +sanity_check_paths = { + 'files': [], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter lab --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..104f59c8f5d --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-resource-usage' +version = "1.0.0" + +homepage = 'https://github.com/jupyter-server/jupyter-resource-usage' +description = "Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('jupyter_resource_usage', version, { + 'checksums': ['74b35b5040c6034e06062f72f8bc5b4a473549e009151be488dd3f61866b854b'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyter_resource_usage'], +} + +# Add the notebook extension to the search path for jupyter notebooks +modextrapaths = {'JUPYTER_PATH': 'share/jupyter/'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5c1a64b9090 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server-proxy' +version = '4.0.0' + +homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' +description = """Jupyter Server Proxy lets you run arbitrary external processes +(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) +alongside your notebook server and provide authenticated web access to them +using a path like /rstudio next to others like /lab. Alongside the python +package that provides the main functionality, the JupyterLab extension +(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window +to get to RStudio for example.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), + ('OpenSSL', '1.1', '', SYSTEM), + ('aiohttp', '3.8.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('simpervisor', '1.0.0', { + 'checksums': ['7eb87ca86d5e276976f5bb0290975a05d452c6a7b7f58062daea7d8369c823c1'], + }), + ('jupyter_server_proxy', version, { + 'checksums': ['f5dc12dd204baca71b013df3522c14403692a2d37cb7adcd77851dbab71533b5'], + }), +] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..76b36f7551f --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb @@ -0,0 +1,190 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = "2.7.2" + +homepage = 'https://jupyter.org/' +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST +endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and +Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.1.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('PyYAML', '6.0'), + ('PyZMQ', '25.1.1'), + ('tornado', '6.3.2'), +] + +sanity_pip_check = True +use_pip = True + +# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them +# use the versions published in a single release commit instead of blindly pushing to last available version, +# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa + +exts_list = [ + ('hatch_nodejs_version', '0.3.1', { + 'checksums': ['0e55fd713d92c5c1ccfee778efecaa780fd8bcd276d4ca7aff9f6791f6f76d9c'], + }), + ('hatch_jupyter_builder', '0.8.3', { + 'checksums': ['0dbd14a8aef6636764f88a8fd1fcc9a91921e5c50356e6aab251782f264ae960'], + }), + ('websocket-client', '1.6.1', { + 'modulename': 'websocket', + 'checksums': ['c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd'], + }), + ('terminado', '0.17.1', { + 'checksums': ['6ccbbcd3a4f8a25a5ec04991f39a0b8db52dfcd487ea0e578d977e6752380333'], + }), + ('Send2Trash', '1.8.2', { + 'checksums': ['c132d59fa44b9ca2b1699af5c86f57ce9f4c5eb56629d5d55fbb7a35f84e2312'], + }), + ('prometheus_client', '0.17.1', { + 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], + }), + ('overrides', '7.4.0', { + 'checksums': ['9502a3cca51f4fac40b5feca985b6703a5c1f6ad815588a7ca9e285b9dca6757'], + }), + ('jupyter_core', '5.3.1', { + 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], + }), + ('fastjsonschema', '2.18.0', { + 'checksums': ['e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd'], + }), + ('tinycss2', '1.2.1', { + 'checksums': ['8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627'], + }), + ('pandocfilters', '1.5.0', { + 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], + }), + ('mistune', '3.0.1', { + 'checksums': ['e912116c13aa0944f9dc530db38eb88f6a77087ab128f49f84a48f4c05ea163c'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.3', { + 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], + }), + ('jupyterlab_pygments', '0.2.2', { + 'checksums': ['7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('bleach', '6.0.0', { + 'checksums': ['1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('nbformat', '5.9.2', { + 'checksums': ['5f98b5ba1997dff175e77e0c17d5c10a96eaed2cbd1de3533d1fc35d5e111192'], + }), + ('nbclient', '0.8.0', { + 'checksums': ['f9b179cd4b2d7bca965f900a2ebf0db4a12ebff2f36a711cb66861e4ae158e55'], + }), + ('jupyter_client', '8.3.0', { + 'checksums': ['3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f'], + }), + ('nbconvert', '7.7.4', { + 'checksums': ['1113d039fa3fc3a846ffa5a3b0a019e85aaa94c566a09fa0c400fb7638e46087'], + }), + ('jupyter_server_terminals', '0.4.4', { + 'checksums': ['57ab779797c25a7ba68e97bcfb5d7740f2b5e8a83b5e8102b10438041a7eac5d'], + }), + ('rfc3986_validator', '0.1.1', { + 'checksums': ['3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055'], + }), + ('rfc3339_validator', '0.1.4', { + 'checksums': ['138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b'], + }), + ('rpds_py', '0.9.2', { + 'modulename': 'rpds', + 'checksums': ['8d70e8f14900f2657c249ea4def963bed86a29b81f81f5b76b5a9215680de945'], + }), + ('referencing', '0.30.2', { + 'checksums': ['794ad8003c65938edcdbc027f1933215e0d0ccc0291e3ce20a4d87432b59efc0'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jsonschema_specifications', '2023.7.1', { + 'checksums': ['c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb'], + }), + ('jsonschema', '4.18.0', { + 'checksums': ['8caf5b57a990a98e9b39832ef3cb35c176fe331414252b6e1b26fd5866f891a4'], + }), + ('jupyter_events', '0.7.0', { + 'checksums': ['7be27f54b8388c03eefea123a4f79247c5b9381c49fb1cd48615ee191eb12615'], + }), + ('argon2-cffi-bindings', '21.2.0', { + 'modulename': '_argon2_cffi_bindings', + 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], + }), + ('argon2_cffi', '23.1.0', { + 'modulename': 'argon2', + 'checksums': ['879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.7.1', { + 'checksums': ['44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780'], + }), + ('jupyter_server', version, { + 'checksums': ['d64fb4e593907290e5df916e3c9399c15ab2cd7bdb71cbcd1d36452dbfb30523'], + }), + ('jupyterlab_widgets', '3.0.8', { + 'checksums': ['d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a'], + }), + ('widgetsnbextension', '4.0.8', { + 'checksums': ['9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17'], + }), + ('comm', '0.1.4', { + 'checksums': ['354e40a59c9dd6db50c5cc6b4acc887d82e9603787f83b68c01a80a923984d15'], + }), + ('ipywidgets', '8.1.0', { + 'checksums': ['ce97dd90525b3066fd00094690964e7eac14cf9b7745d35565b5eeac20cce687'], + }), + # The following few extensions are needed for e.g. JupyterLab but also nbclassic. + # Avoid duplication by making it part of this bundle + ('notebook_shim', '0.2.3', { + 'checksums': ['f69388ac283ae008cd506dda10d0288b09a017d822d5e8c7129a152cbd3ce7e9'], + }), + ('nest_asyncio', '1.5.7', { + 'checksums': ['6a80f7b98f24d9083ed24608977c09dd608d83f91cccc24c9d2cba6d10e01c10'], + }), + ('ipykernel', '6.25.1', { + 'checksums': ['050391364c0977e768e354bdb60cbbfbee7cbb943b1af1618382021136ffd42f'], + }), + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('debugpy', '1.6.7.post1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['1093a5c541af079c13ac8c70ab8b24d1d35c8cacb676306cf11e57f699c02926'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter'], + 'dirs': ['share/jupyter', 'etc/jupyter'], +} + +sanity_check_commands = ['jupyter --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f3a22452bde --- /dev/null +++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'jupyterlmod' +version = '4.0.3' + +# This easyconfig installs the notebook and lab extension of Jupyter Lmod + +homepage = 'https://github.com/cmd-ntrf/jupyter-lmod' +description = """Jupyter interactive notebook server extension that allows users to interact with +environment modules before launching kernels. The extension uses Lmod's Python +interface to accomplish module-related tasks like loading, unloading, saving +collections, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('jupyterlmod', '4.0.3', { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['9939bd7927c2c347f9884247bac58018ca44d56184c5f29e9d704a9b3a09a299'] + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'share/jupyter'], +} + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ba066826463 --- /dev/null +++ b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonPackage' + +name = 'nbclassic' +version = "1.0.0" + +homepage = 'https://jupyter.org/' +description = """NbClassic provides a backwards compatible Jupyter Notebook interface + that you can install side-by-side with the latest versions: That way, you can fearlessly + upgrade without worrying about your classic extensions and customizations breaking.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.1.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('jupyter-server', '2.7.2'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['nbclassic-1.0.0_fix_setup_version.patch'] +checksums = [ + {'nbclassic-1.0.0.tar.gz': '0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'}, + {'nbclassic-1.0.0_fix_setup_version.patch': 'c26d91ac1d0cea2b361b2619076acdaf5fcd5ff2363d9e5f5e1bd737b4b50736'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +local_binaries = [ + 'jupyter-nbclassic', + 'jupyter-nbclassic-bundlerextension', + 'jupyter-nbclassic-extension', + 'jupyter-nbclassic-serverextension', +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ['jupyter nbclassic --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ca17d12903e --- /dev/null +++ b/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'notebook' +version = '7.0.2' + +homepage = 'https://jupyter.org/' +description = """The Jupyter Notebook is the original web application for creating and + sharing computational documents. It offers a simple, streamlined, document-centric experience.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), + ('JupyterLab', '4.0.5'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['d70d6a07418c829bd5f54337ce993b7105261d9026f9d3fe68e9b8aa1a20da9a'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/jupyter-notebook'], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter notebook --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..19a3a61687c --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '25.1.1' + +homepage = 'https://www.zeromq.org/bindings:python' +description = "Python bindings for ZeroMQ" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['259c22485b71abacdfa8bf79720cd7bcf4b9d128b30ea554f01ae71fdbfdaa23'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('ZeroMQ', '4.3.4'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'zmq'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2e8cc5dfd61 --- /dev/null +++ b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'PycURL' +version = '7.45.2' + +homepage = 'http://pycurl.io/' +description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL + from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of + features.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5730590be0271364a5bddd9e245c9cc0fb710c4cbacbdd95264a3122d23224ca'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('cURL', '8.0.1'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From 89a9c039c84dd0cd0ae894f81c971ffddcf509b9 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 24 Aug 2023 10:26:34 +0200 Subject: [PATCH 8533/9987] Delete configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb --- ...gurable-http-proxy-4.5.6-GCCcore-12.3.0.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb deleted file mode 100644 index fc58c50bc75..00000000000 --- a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'Binary' - -name = 'configurable-http-proxy' -version = '4.5.6' - -homepage = 'https://github.com/jupyterhub/configurable-http-proxy' -description = """HTTP proxy for node.js including a REST API for updating the routing table. - Developed as a part of the Jupyter Hub multi-user server.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = ['https://github.com/jupyterhub/%(name)s/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['4d9d94d0e6e44542ac973963b8a6545f4b40c0a2995e865ae9c80a2279e1e0ab'] - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('nodejs', '18.17.1'), -] - -install_cmd = "npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz" - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': [], -} - -sanity_check_commands = ['%(name)s --version'] - -moduleclass = 'tools' From 6efaa76f110a1ede07cd0aeda397fd6745a7ffe5 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 24 Aug 2023 10:26:51 +0200 Subject: [PATCH 8534/9987] Delete JupyterHub-4.0.2-GCCcore-12.3.0.eb --- .../JupyterHub-4.0.2-GCCcore-12.3.0.eb | 130 ------------------ 1 file changed, 130 deletions(-) delete mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb deleted file mode 100644 index 6e978bce869..00000000000 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,130 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'JupyterHub' -version = '4.0.2' - -homepage = 'https://jupyter.org' -description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed - for centralized deployments in companies, university classrooms and research labs.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('setuptools-rust', '1.6.0'), # Needed for bcrypt - ('Rust', '1.70.0'), # Needed for bcrypt -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('Mako', '1.2.4'), - ('configurable-http-proxy', '4.5.6'), - ('OpenSSL', '1.1', '', SYSTEM), - ('tornado', '6.3.2'), - ('PycURL', '7.45.2'), # optional, recommended with large number of users -] - -sanity_pip_check = True -use_pip = True - -local_batchspawner_commit = '2a9eda060a875a2b65ca9521368fe052a09c3266' - -exts_list = [ - ('certipy', '0.1.3', { - 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], - }), - ('pamela', '1.1.0', { - 'checksums': ['d4b139fe600e192e176a2a368059207a6bffa0e7879879b13f4fcba0163481be'], - }), - ('greenlet', '2.0.2', { - 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], - }), - ('async_generator', '1.10', { - 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], - }), - ('SQLAlchemy', '2.0.20', { - 'checksums': ['ca8a5ff2aa7f3ade6c498aaafce25b1eaeabe4e42b73e25519183e4566a16fc6'], - }), - ('alembic', '1.11.3', { - 'checksums': ['3db4ce81a9072e1b5aa44c2d202add24553182672a12daf21608d6f62a8f9cf9'], - }), - ('oauthlib', '3.2.2', { - 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], - }), - ('pyOpenSSL', '23.2.0', { - 'modulename': 'OpenSSL', - 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], - }), - ('ruamel.yaml', '0.17.32', { - 'checksums': ['ec939063761914e14542972a5cba6d33c23b0859ab6342f61cf070cfc600efc2'], - }), - ('ruamel.yaml.clib', '0.2.7', { - 'modulename': False, - 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], - }), - ('python-json-logger', '2.0.7', { - 'modulename': 'pythonjsonlogger', - 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], - }), - ('jupyter-telemetry', '0.1.0', { - 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', - 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], - }), - ('prometheus_client', '0.17.1', { - 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], - }), - ('jupyterhub', version, { - 'checksums': ['d4e450eed8d90dfbcf0eca08f00f2093a0bce74dc51f7cfc0b7057f602341a1d'], - }), - # Needs unreleased features for JupyterHub 4.X compatibility, hence install from commit - ('batchspawner', '1.2.0-%s' % local_batchspawner_commit, { - 'source_urls': [GITHUB_SOURCE], - 'sources': { - 'filename': '%(name)s-%(version)s.tar.gz', - 'download_filename': '%s.tar.gz' % local_batchspawner_commit - }, - 'checksums': ['d5cf239ba75522d928ed33971c180532f590131905c42eac1be2651ccad85283'], - }), - ('jupyterhub-systemdspawner', '1.0.1', { - 'modulename': 'systemdspawner', - 'checksums': ['8d614f19d89564321fe55d80ecd134a0e2bf276274d45861495c9bb5a80add28'], - }), - ('jupyterhub-simplespawner', '0.1', { - 'modulename': 'simplespawner', - 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], - }), - ('ldap3', '2.9.1', { - 'checksums': ['f3e7fc4718e3f09dda568b57100095e0ce58633bcabbed8667ce3f8fbaa4229f'], - }), - ('jupyterhub-ldapauthenticator', '1.3.2', { - 'modulename': 'ldapauthenticator', - 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], - }), - ('PyJWT', '2.8.0', { - 'modulename': 'jwt', - 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], - }), - ('jupyterhub-jwtauthenticator-v2', '2.0.3', { - 'modulename': 'jwtauthenticator', - 'checksums': ['b94b6dff8246250904c5ee511da3f062680eb657dabe766d75993cbe72747d41'], - }), - ('onetimepass', '1.0.1', { - 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], - }), - ('bcrypt', '4.0.1', { - 'checksums': ['27d375903ac8261cfe4047f6709d16f7d18d39b1ec92aaf72af989552a650ebd'], - }), - ('jupyterhub-nativeauthenticator', '1.2.0', { - 'modulename': 'nativeauthenticator', - 'checksums': ['826228e6e9ca37736361e2e60c5723e245ec72e34fdc42cc218fc54a67f968e1'], - }), -] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -sanity_check_commands = ['%(namelower)s --help'] - -moduleclass = 'tools' From ee090d5603405033940dd8e6c11f0c786fda7a50 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 24 Aug 2023 10:27:10 +0200 Subject: [PATCH 8535/9987] Delete JupyterLab-4.0.5-GCCcore-12.3.0.eb --- .../JupyterLab-4.0.5-GCCcore-12.3.0.eb | 73 ------------------- 1 file changed, 73 deletions(-) delete mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb deleted file mode 100644 index 19c7e8a6710..00000000000 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb +++ /dev/null @@ -1,73 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'JupyterLab' -version = '4.0.5' - -homepage = 'https://jupyter.org/' -description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar - building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, - etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter - Notebook.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('jupyter-server', '2.7.2'), -] - -# keep user's configuration in their home directory -# note: '~' is not expanded by JupyterLab -modluafooter = """ -setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) -setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) -""" -modtclfooter = """ -setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" -setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" -""" -sanity_pip_check = True -use_pip = True - -exts_list = [ - ('json5', '0.9.14', { - 'checksums': ['9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02'], - }), - ('jupyterlab_server', '2.24.0', { - 'checksums': ['4e6f99e0a5579bbbc32e449c4dbb039561d4f1a7827d5733273ed56738f21f07'], - }), - ('jupyter-lsp', '2.2.0', { - 'checksums': ['8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1'], - }), - ('async-lru', '2.0.4', { - 'checksums': ['b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627'], - }), - ('jupyterlab', version, { - 'checksums': ['de49deb75f9b9aec478ed04754cbefe9c5d22fd796a5783cdc65e212983d3611'], - }), -] - -local_binaries = [ - 'jupyter-lab', - 'jupyter-labextension', - 'jupyter-labhub', -] -sanity_check_paths = { - 'files': [], - 'dirs': ['etc/jupyter', 'share/jupyter'], -} - -sanity_check_commands = ['jupyter lab --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} - -moduleclass = 'tools' From fa613f60f25df51441a30b4618ef4f05aa5edf2e Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 24 Aug 2023 10:29:55 +0200 Subject: [PATCH 8536/9987] Delete jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb --- ...pyter-server-proxy-4.0.0-GCCcore-12.3.0.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb deleted file mode 100644 index 5c1a64b9090..00000000000 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'jupyter-server-proxy' -version = '4.0.0' - -homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' -description = """Jupyter Server Proxy lets you run arbitrary external processes -(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) -alongside your notebook server and provide authenticated web access to them -using a path like /rstudio next to others like /lab. Alongside the python -package that provides the main functionality, the JupyterLab extension -(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window -to get to RStudio for example.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('jupyter-server', '2.7.2'), - ('OpenSSL', '1.1', '', SYSTEM), - ('aiohttp', '3.8.5'), -] - -sanity_pip_check = True -use_pip = True - -exts_list = [ - ('simpervisor', '1.0.0', { - 'checksums': ['7eb87ca86d5e276976f5bb0290975a05d452c6a7b7f58062daea7d8369c823c1'], - }), - ('jupyter_server_proxy', version, { - 'checksums': ['f5dc12dd204baca71b013df3522c14403692a2d37cb7adcd77851dbab71533b5'], - }), -] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From f6a0143d29107017582213effcb7a90d760292f8 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 24 Aug 2023 10:30:14 +0200 Subject: [PATCH 8537/9987] Delete jupyter-server-2.7.2-GCCcore-12.3.0.eb --- .../jupyter-server-2.7.2-GCCcore-12.3.0.eb | 190 ------------------ 1 file changed, 190 deletions(-) delete mode 100644 easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb deleted file mode 100644 index 76b36f7551f..00000000000 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,190 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'jupyter-server' -version = "2.7.2" - -homepage = 'https://jupyter.org/' -description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST -endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and -Voila.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('maturin', '1.1.0'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('PyYAML', '6.0'), - ('PyZMQ', '25.1.1'), - ('tornado', '6.3.2'), -] - -sanity_pip_check = True -use_pip = True - -# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them -# use the versions published in a single release commit instead of blindly pushing to last available version, -# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa - -exts_list = [ - ('hatch_nodejs_version', '0.3.1', { - 'checksums': ['0e55fd713d92c5c1ccfee778efecaa780fd8bcd276d4ca7aff9f6791f6f76d9c'], - }), - ('hatch_jupyter_builder', '0.8.3', { - 'checksums': ['0dbd14a8aef6636764f88a8fd1fcc9a91921e5c50356e6aab251782f264ae960'], - }), - ('websocket-client', '1.6.1', { - 'modulename': 'websocket', - 'checksums': ['c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd'], - }), - ('terminado', '0.17.1', { - 'checksums': ['6ccbbcd3a4f8a25a5ec04991f39a0b8db52dfcd487ea0e578d977e6752380333'], - }), - ('Send2Trash', '1.8.2', { - 'checksums': ['c132d59fa44b9ca2b1699af5c86f57ce9f4c5eb56629d5d55fbb7a35f84e2312'], - }), - ('prometheus_client', '0.17.1', { - 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], - }), - ('overrides', '7.4.0', { - 'checksums': ['9502a3cca51f4fac40b5feca985b6703a5c1f6ad815588a7ca9e285b9dca6757'], - }), - ('jupyter_core', '5.3.1', { - 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], - }), - ('fastjsonschema', '2.18.0', { - 'checksums': ['e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd'], - }), - ('tinycss2', '1.2.1', { - 'checksums': ['8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627'], - }), - ('pandocfilters', '1.5.0', { - 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], - }), - ('mistune', '3.0.1', { - 'checksums': ['e912116c13aa0944f9dc530db38eb88f6a77087ab128f49f84a48f4c05ea163c'], - }), - ('deprecation', '2.1.0', { - 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], - }), - ('jupyter_packaging', '0.12.3', { - 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], - }), - ('jupyterlab_pygments', '0.2.2', { - 'checksums': ['7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d'], - }), - ('defusedxml', '0.7.1', { - 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], - }), - ('bleach', '6.0.0', { - 'checksums': ['1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414'], - }), - ('arrow', '1.2.3', { - 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], - }), - ('nbformat', '5.9.2', { - 'checksums': ['5f98b5ba1997dff175e77e0c17d5c10a96eaed2cbd1de3533d1fc35d5e111192'], - }), - ('nbclient', '0.8.0', { - 'checksums': ['f9b179cd4b2d7bca965f900a2ebf0db4a12ebff2f36a711cb66861e4ae158e55'], - }), - ('jupyter_client', '8.3.0', { - 'checksums': ['3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f'], - }), - ('nbconvert', '7.7.4', { - 'checksums': ['1113d039fa3fc3a846ffa5a3b0a019e85aaa94c566a09fa0c400fb7638e46087'], - }), - ('jupyter_server_terminals', '0.4.4', { - 'checksums': ['57ab779797c25a7ba68e97bcfb5d7740f2b5e8a83b5e8102b10438041a7eac5d'], - }), - ('rfc3986_validator', '0.1.1', { - 'checksums': ['3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055'], - }), - ('rfc3339_validator', '0.1.4', { - 'checksums': ['138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b'], - }), - ('rpds_py', '0.9.2', { - 'modulename': 'rpds', - 'checksums': ['8d70e8f14900f2657c249ea4def963bed86a29b81f81f5b76b5a9215680de945'], - }), - ('referencing', '0.30.2', { - 'checksums': ['794ad8003c65938edcdbc027f1933215e0d0ccc0291e3ce20a4d87432b59efc0'], - }), - ('python-json-logger', '2.0.7', { - 'modulename': 'pythonjsonlogger', - 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], - }), - ('jsonschema_specifications', '2023.7.1', { - 'checksums': ['c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb'], - }), - ('jsonschema', '4.18.0', { - 'checksums': ['8caf5b57a990a98e9b39832ef3cb35c176fe331414252b6e1b26fd5866f891a4'], - }), - ('jupyter_events', '0.7.0', { - 'checksums': ['7be27f54b8388c03eefea123a4f79247c5b9381c49fb1cd48615ee191eb12615'], - }), - ('argon2-cffi-bindings', '21.2.0', { - 'modulename': '_argon2_cffi_bindings', - 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], - }), - ('argon2_cffi', '23.1.0', { - 'modulename': 'argon2', - 'checksums': ['879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08'], - }), - ('sniffio', '1.3.0', { - 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], - }), - ('anyio', '3.7.1', { - 'checksums': ['44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780'], - }), - ('jupyter_server', version, { - 'checksums': ['d64fb4e593907290e5df916e3c9399c15ab2cd7bdb71cbcd1d36452dbfb30523'], - }), - ('jupyterlab_widgets', '3.0.8', { - 'checksums': ['d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a'], - }), - ('widgetsnbextension', '4.0.8', { - 'checksums': ['9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17'], - }), - ('comm', '0.1.4', { - 'checksums': ['354e40a59c9dd6db50c5cc6b4acc887d82e9603787f83b68c01a80a923984d15'], - }), - ('ipywidgets', '8.1.0', { - 'checksums': ['ce97dd90525b3066fd00094690964e7eac14cf9b7745d35565b5eeac20cce687'], - }), - # The following few extensions are needed for e.g. JupyterLab but also nbclassic. - # Avoid duplication by making it part of this bundle - ('notebook_shim', '0.2.3', { - 'checksums': ['f69388ac283ae008cd506dda10d0288b09a017d822d5e8c7129a152cbd3ce7e9'], - }), - ('nest_asyncio', '1.5.7', { - 'checksums': ['6a80f7b98f24d9083ed24608977c09dd608d83f91cccc24c9d2cba6d10e01c10'], - }), - ('ipykernel', '6.25.1', { - 'checksums': ['050391364c0977e768e354bdb60cbbfbee7cbb943b1af1618382021136ffd42f'], - }), - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('debugpy', '1.6.7.post1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - 'checksums': ['1093a5c541af079c13ac8c70ab8b24d1d35c8cacb676306cf11e57f699c02926'], - }), -] - -sanity_check_paths = { - 'files': ['bin/jupyter'], - 'dirs': ['share/jupyter', 'etc/jupyter'], -} - -sanity_check_commands = ['jupyter --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From 1d8f1b2b4a50e50f35f7d44b3ea463aa9b8ac7e8 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 24 Aug 2023 10:30:49 +0200 Subject: [PATCH 8538/9987] Delete nbclassic-1.0.0-GCCcore-12.3.0.eb --- .../nbclassic-1.0.0-GCCcore-12.3.0.eb | 51 ------------------- 1 file changed, 51 deletions(-) delete mode 100644 easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb deleted file mode 100644 index ba066826463..00000000000 --- a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'nbclassic' -version = "1.0.0" - -homepage = 'https://jupyter.org/' -description = """NbClassic provides a backwards compatible Jupyter Notebook interface - that you can install side-by-side with the latest versions: That way, you can fearlessly - upgrade without worrying about your classic extensions and customizations breaking.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('maturin', '1.1.0'), -] -dependencies = [ - ('Python', '3.11.3'), - ('jupyter-server', '2.7.2'), -] - -sources = [SOURCE_TAR_GZ] -patches = ['nbclassic-1.0.0_fix_setup_version.patch'] -checksums = [ - {'nbclassic-1.0.0.tar.gz': '0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'}, - {'nbclassic-1.0.0_fix_setup_version.patch': 'c26d91ac1d0cea2b361b2619076acdaf5fcd5ff2363d9e5f5e1bd737b4b50736'}, -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -local_binaries = [ - 'jupyter-nbclassic', - 'jupyter-nbclassic-bundlerextension', - 'jupyter-nbclassic-extension', - 'jupyter-nbclassic-serverextension', -] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_binaries], - 'dirs': [], -} - -sanity_check_commands = ['jupyter nbclassic --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From 8c2b6c27f9a1ff7114da9efee7401dfa3addcb89 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 24 Aug 2023 10:31:18 +0200 Subject: [PATCH 8539/9987] Delete notebook-7.0.2-GCCcore-12.3.0.eb --- .../notebook/notebook-7.0.2-GCCcore-12.3.0.eb | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb deleted file mode 100644 index ca17d12903e..00000000000 --- a/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'notebook' -version = '7.0.2' - -homepage = 'https://jupyter.org/' -description = """The Jupyter Notebook is the original web application for creating and - sharing computational documents. It offers a simple, streamlined, document-centric experience.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('jupyter-server', '2.7.2'), - ('JupyterLab', '4.0.5'), -] - -sources = [SOURCE_TAR_GZ] -checksums = ['d70d6a07418c829bd5f54337ce993b7105261d9026f9d3fe68e9b8aa1a20da9a'] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -sanity_check_paths = { - 'files': ['bin/jupyter-notebook'], - 'dirs': ['etc/jupyter', 'share/jupyter'], -} - -sanity_check_commands = ['jupyter notebook --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From d2e8e97967b5141bc6838cdc9f64be3b6ddeb763 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 24 Aug 2023 10:31:37 +0200 Subject: [PATCH 8540/9987] Delete PyZMQ-25.1.1-GCCcore-12.3.0.eb --- .../p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb deleted file mode 100644 index 19a3a61687c..00000000000 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyZMQ' -version = '25.1.1' - -homepage = 'https://www.zeromq.org/bindings:python' -description = "Python bindings for ZeroMQ" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['259c22485b71abacdfa8bf79720cd7bcf4b9d128b30ea554f01ae71fdbfdaa23'] - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), - ('ZeroMQ', '4.3.4'), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True -options = {'modulename': 'zmq'} - -moduleclass = 'devel' From 9178035cb91b4afc8c15e80bd5d9cf870a250b7e Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 24 Aug 2023 10:32:00 +0200 Subject: [PATCH 8541/9987] Delete PycURL-7.45.2-GCCcore-12.3.0.eb --- .../p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb deleted file mode 100644 index 2e8cc5dfd61..00000000000 --- a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. -easyblock = 'PythonPackage' - -name = 'PycURL' -version = '7.45.2' - -homepage = 'http://pycurl.io/' -description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL - from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of - features.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['5730590be0271364a5bddd9e245c9cc0fb710c4cbacbdd95264a3122d23224ca'] - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('cURL', '8.0.1'), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -moduleclass = 'tools' From c027b18ebc9d3c9456fb869c287888a9e157263f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2023 10:41:25 +0200 Subject: [PATCH 8542/9987] correct 'dirs' in 'sanity_check_paths' in template easyconfig --- easybuild/easyconfigs/TEMPLATE.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/TEMPLATE.eb b/easybuild/easyconfigs/TEMPLATE.eb index 06218cade8f..ba733e5091d 100644 --- a/easybuild/easyconfigs/TEMPLATE.eb +++ b/easybuild/easyconfigs/TEMPLATE.eb @@ -24,7 +24,7 @@ dependencies = [] # The sanity test MUST be tuned before going production and submitting your contribution to upstream git repositories sanity_check_paths = { 'files': [], - 'dirs': ["."] + 'dirs': [], } # You SHOULD change the following line; Kindly consult other easyconfigs for possible options From fa88c59e7c35c8b7119be1e784b3da3803275970 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 24 Aug 2023 10:53:42 +0200 Subject: [PATCH 8543/9987] adding easyconfigs: vcflib-1.0.9-foss-2022a-R-4.2.1.eb, WFA2-2.3.3-GCCcore-11.3.0.eb --- .../vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb | 78 +++++++++++++++++++ .../w/WFA2/WFA2-2.3.3-GCCcore-11.3.0.eb | 29 +++++++ 2 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb create mode 100644 easybuild/easyconfigs/w/WFA2/WFA2-2.3.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..20f757374a5 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb @@ -0,0 +1,78 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.9' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/vcflib/vcflib' +description = """vcflib provides methods to manipulate and interpret sequence variation as it can be + described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended + to concisely describe reference-indexed genetic variations between individuals.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_dep-fix.patch', +] +checksums = [ + {'v1.0.9.tar.gz': 'd17fcf8a34d65f1dfecf4b4290d058be744422b6baf34ecdef8ea912d59a4569'}, + {'vcflib-1.0.9_dep-fix.patch': '76bce1c9e40dab2ad94b455bb4487dfa24eeafcf50639db0852f5ca7a31331b6'}, +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('R', '4.2.1'), + ('XZ', '5.2.5'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.15.1'), + ('tabixpp', '1.1.2'), + ('intervaltree', '0.1'), + ('fastahack', '1.0.0'), + ('filevercmp', '20191210'), + ('fsom', '20151117'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), + ('WFA2', '2.3.3'), +] + +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f " +preconfigopts += r"-regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" +preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" +preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" +preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" +preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " + +configopts = "-DZIG=OFF -DWFA_GITMODULE=OFF -DWFA_INCLUDE_DIRS=$EBROOTWFA2/include/wfa2lib" + +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = {'PATH': ['scripts']} + +sanity_check_paths = { + 'files': [ + 'bin/vcffilter', + 'bin/vcfcombine', + 'lib/libvcflib.a', + 'lib/pyvcflib.cpython-310-x86_64-linux-gnu.so', + ], + 'dirs': ['scripts', 'include'], +} + +sanity_check_commands = ["vcfwave --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WFA2/WFA2-2.3.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..b096aa173cc --- /dev/null +++ b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.3-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'WFA2' +version = '2.3.3' + +homepage = 'https://github.com/smarco/WFA2-lib' +description = """The wavefront alignment (WFA) algorithm is an exact + gap-affine algorithm that takes advantage of homologous regions + between the sequences to accelerate the alignment process.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/smarco/WFA2-lib/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2569650cdba395f42513a4d2c9175724a736047bb7da99a162c0abdbd651698f'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pkgconf', '1.8.0'), +] + +configopts = "-DOPENMP=ON" + +sanity_check_paths = { + 'files': ['lib/libwfa2.a'], + 'dirs': ['include/wfa2lib'], +} + +moduleclass = 'bio' From 3e3018dde3e0058c6784898fe0a0057a0c18b5c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 24 Aug 2023 11:23:15 +0200 Subject: [PATCH 8544/9987] add forgotten dep and patch --- .../v/vcflib/vcflib-1.0.9_dep-fix.patch | 178 ++++++++++++++++++ .../w/WFA2/WFA2-2.3.3-GCCcore-11.3.0.eb | 1 + 2 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.9_dep-fix.patch diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9_dep-fix.patch b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9_dep-fix.patch new file mode 100644 index 00000000000..19320491c75 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9_dep-fix.patch @@ -0,0 +1,178 @@ +Use our libraries instead of the ones in git submodules +Install libvcflib.a to lib directory instead of bin +Author: Petr Král (INUITS) +diff -u vcflib-1.0.9/CMakeLists.txt.orig vcflib-1.0.9/CMakeLists.txt +--- vcflib-1.0.9/CMakeLists.txt.orig 2023-02-11 17:41:26.000000000 +0100 ++++ vcflib-1.0.9/CMakeLists.txt 2023-08-17 13:59:24.793435374 +0200 +@@ -58,8 +58,8 @@ + find_package(Threads) + set_package_properties(Threads PROPERTIES TYPE REQUIRED) + +-pkg_check_modules(HTSLIB htslib) # Optionally builds from contrib/ +-pkg_check_modules(TABIXPP tabixpp) # Optionally builds from contrib/ ++# pkg_check_modules(HTSLIB htslib) # Optionally builds from contrib/ ++# pkg_check_modules(TABIXPP tabixpp) # Optionally builds from contrib/ + + # ---- Build switches + set(CMAKE_POSITION_INDEPENDENT_CODE ON) +@@ -109,25 +109,25 @@ + # ---- Include files + + include_directories(include) +-include_directories(contrib/fastahack) +-include_directories(contrib/intervaltree) +-include_directories(contrib/smithwaterman) +-include_directories(contrib/multichoose) +-include_directories(contrib/filevercmp) ++# include_directories(contrib/fastahack) ++# include_directories(contrib/intervaltree) ++# include_directories(contrib/smithwaterman) ++# include_directories(contrib/multichoose) ++# include_directories(contrib/filevercmp) + include_directories(contrib/c-progress-bar) + +-if(NOT HTSLIB_FOUND) +- set(HTSLIB_LOCAL contrib/tabixpp/htslib) +- set(TABIX_FOUND OFF) # also build tabixpp if htslib is missing +-endif() +- +-if (NOT TABIX_FOUND) +- set(TABIXPP_LOCAL contrib/tabixpp) +- include_directories(contrib/tabixpp) +- set(tabixpp_SOURCE +- contrib/tabixpp/tabix.cpp +- ) +-endif() ++# if(NOT HTSLIB_FOUND) ++# set(HTSLIB_LOCAL contrib/tabixpp/htslib) ++# set(TABIX_FOUND OFF) # also build tabixpp if htslib is missing ++# endif() ++# ++# if (NOT TABIX_FOUND) ++# set(TABIXPP_LOCAL contrib/tabixpp) ++# include_directories(contrib/tabixpp) ++# set(tabixpp_SOURCE ++# contrib/tabixpp/tabix.cpp ++# ) ++# endif() + + if(WFA_GITMODULE) + set(WFA_LOCAL contrib/WFA2-lib) +@@ -135,12 +135,12 @@ + + file(GLOB INCLUDES + src/*.h* +- contrib/multichoose/*.h* +- contrib/intervaltree/*.h* +- contrib/smithwaterman/*.h* +- contrib/fastahack/*.h* +- contrib/filevercmp/*.h* +- ) ++ # contrib/multichoose/*.h* ++ # contrib/intervaltree/*.h* ++ # contrib/smithwaterman/*.h* ++ # contrib/fastahack/*.h* ++ # contrib/filevercmp/*.h* ++) + + set(vcflib_SOURCE + src/vcf-c-api.cpp +@@ -158,14 +158,14 @@ + src/LeftAlign.cpp + src/cigar.cpp + src/allele.cpp +- contrib/fastahack/Fasta.cpp +- contrib/smithwaterman/SmithWatermanGotoh.cpp +- contrib/smithwaterman/Repeats.cpp +- contrib/smithwaterman/IndelAllele.cpp +- contrib/smithwaterman/disorder.cpp +- contrib/smithwaterman/LeftAlign.cpp +- contrib/fsom/fsom.c +- contrib/filevercmp/filevercmp.c ++ # contrib/fastahack/Fasta.cpp ++ # contrib/smithwaterman/SmithWatermanGotoh.cpp ++ # contrib/smithwaterman/Repeats.cpp ++ # contrib/smithwaterman/IndelAllele.cpp ++ # contrib/smithwaterman/disorder.cpp ++ # contrib/smithwaterman/LeftAlign.cpp ++ # contrib/fsom/fsom.c ++ # contrib/filevercmp/filevercmp.c + contrib/c-progress-bar/progress.c + ) + +@@ -175,7 +175,7 @@ + + add_library(vcflib STATIC + ${vcflib_SOURCE} +- ) ++) + + set(BINS + vcfecho +@@ -302,7 +302,7 @@ + vcfsort + vcf_strip_extra_headers + vcfvarstats +- ) ++) + + # ---- Get version + +@@ -363,7 +363,7 @@ + add_subdirectory(${WFA_LOCAL} EXCLUDE_FROM_ALL) + set(WFALIB wfa2) # pick up the wfa2 lib target from the included CMakeLists.txt + else(WFA_GITMODULE) +- set(WFA_INCLUDE_DIRS ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib) ++ # set(WFA_INCLUDE_DIRS ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib) + find_library(WFALIB wfa2 wfa) # distro search for shared lib + if(NOT WFALIB) + message(STATUS "ERROR: Can not find libfwa! Make sure it is installed or use the git submodule instead") +@@ -403,7 +403,7 @@ + + set(vcflib_DEPS + CURL::libcurl +- ) ++) + + if (ZIG) + list(APPEND vcflib_DEPS ZIG-EXT) +@@ -414,15 +414,18 @@ + endif() + + set(vcflib_LIBS +- ${HTSLIB_LIBRARIES} + ${CURL_LIBRARIES} + ${ZLIB_LIBRARIES} + ${LIBLZMA_LIBRARIES} + ${BZIP2_LIBRARIES} +- ${TABIXPP_LIBRARIES} + ${CMAKE_THREAD_LIBS_INIT} + ${WFA_LINK_LIBRARIES} +- ${HTSLIB_LINK_LIBRARIES} ++ hts ++ tabixpp ++ fastahack ++ sw ++ fsom ++ filevercmp + ) + + if (ZIG) +@@ -510,7 +513,7 @@ + NAME zigvcf + COMMAND zig build test + WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/src/zig +- ) ++ ) + endfunction() + + add_zigtest() +@@ -576,7 +579,7 @@ + + # ---- Install + +-install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR}) ++install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + install(FILES ${INCLUDES} DESTINATION include) + diff --git a/easybuild/easyconfigs/w/WFA2/WFA2-2.3.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.3-GCCcore-11.3.0.eb index b096aa173cc..2b8942ec8b7 100644 --- a/easybuild/easyconfigs/w/WFA2/WFA2-2.3.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.3-GCCcore-11.3.0.eb @@ -15,6 +15,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['2569650cdba395f42513a4d2c9175724a736047bb7da99a162c0abdbd651698f'] builddependencies = [ + ('binutils', '2.38'), ('CMake', '3.24.3'), ('pkgconf', '1.8.0'), ] From cbeef017afb32d757732e536e2be796929a18c30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2023 11:42:14 +0200 Subject: [PATCH 8545/9987] adding easyconfigs: Omnipose-0.4.4-foss-2022a-CUDA-11.7.0.eb, torchvf-0.1.3-foss-2022a-CUDA-11.7.0.eb --- .../Omnipose-0.4.4-foss-2022a-CUDA-11.7.0.eb | 119 ++++++++++++++++++ .../torchvf-0.1.3-foss-2022a-CUDA-11.7.0.eb | 41 ++++++ 2 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/o/Omnipose/Omnipose-0.4.4-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/o/Omnipose/Omnipose-0.4.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/Omnipose/Omnipose-0.4.4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..fc7073d5da7 --- /dev/null +++ b/easybuild/easyconfigs/o/Omnipose/Omnipose-0.4.4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,119 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Omnipose' +version = '0.4.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://omnipose.readthedocs.io' +description = """ +Omnipose is a general image segmentation tool that builds on Cellpose in a number of ways +described in our paper. It works for both 2D and 3D images and on any imaging modality or +cell shape, so long as you train it on representative images. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyQt5', '5.15.5'), + ('PyTorch', '1.12.0', versionsuffix), + ('PyQtGraph', '0.13.3'), + ('numba', '0.56.4'), + ('scikit-image', '0.19.3'), + ('scikit-learn', '1.1.2'), + ('matplotlib', '3.5.2'), + ('igraph', '0.10.3'), + ('MXNet', '1.9.1'), + ('mgen', '1.2.1'), + ('ncolor', '1.2.1'), + ('mahotas', '1.4.13'), + ('peakdetect', '1.2'), + ('python-igraph', '0.10.3'), + ('torchvf', '0.1.3', versionsuffix), + ('OpenCV', '4.6.0', '-contrib'), + ('tqdm', '4.64.0'), + ('imagecodecs', '2022.9.26'), +] + +use_pip = True + +exts_list = [ + ('edt', '2.3.1', { + 'checksums': ['3696e1f7de482465af731a734a31b261a8852df8d583118f1b223d61764e063f'], + }), + ('tifffile', '2023.4.12', { + 'checksums': ['2fa99f9890caab919d932a0acaa9d0f5843dc2ef3594e212963932e20713badd'], + }), + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + ('fastremap', '1.13.5', { + 'source_urls': ['https://github.com/seung-lab/fastremap/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['ee0e9e798e9f331b7c46e98768735a42bb6e287b3aa56c31c322ba585f4036b7'], + 'preinstallopts': "export PBR_VERSION=1.2.3 && ", + }), + ('roifile', '2023.5.12', { + 'checksums': ['32eeba0d9ad52cc249d6a234b737c1808a6c5d7d9baae6453709eb74222b3433'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('googleapis-common-protos', '1.59.1', { + 'checksums': ['b35d530fe825fb4227857bc47ad84c33c809ac96f312e13182bdeaa2abe1178a'], + 'preinstallopts': 'sed -i "s|protobuf>=3.19.5|protobuf>=3.19.4|g" setup.py && ', + 'modulename': 'google.api', + }), + ('cachetools', '5.3.1', { + 'checksums': ['dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b'], + }), + ('google-crc32c', '1.5.0', { + 'checksums': ['89284716bc6a5a415d4eaa11b1726d2d60a0cd12aadf5439828353662ede9dd7'], + 'modulename': 'google_crc32c', + }), + ('google-auth', '2.22.0', { + 'checksums': ['164cba9af4e6e4e40c3a4f90a1a6c12ee56f14c0b4868d1ca91b32826ab334ce'], + 'modulename': 'google.auth', + }), + ('google-cloud-core', '2.3.3', { + 'checksums': ['37b80273c8d7eee1ae816b3a20ae43585ea50506cb0e60f3cf5be5f87f1373cb'], + 'modulename': 'google.api', + }), + ('google-api-core', '2.11.1', { + 'checksums': ['25d29e05a0058ed5f19c61c0a78b1b53adea4d9364b464d014fbda941f6d1c9a'], + 'preinstallopts': 'sed -i "s|protobuf>=3.19.5|protobuf>=3.19.4|g" setup.py && ', + 'modulename': 'google.api_core', + }), + ('google-resumable-media', '2.5.0', { + 'checksums': ['218931e8e2b2a73a58eb354a288e03a0fd5fb1c4583261ac6e4c078666468c93'], + 'modulename': 'google.resumable_media', + }), + ('google-cloud-storage', '2.10.0', { + 'checksums': ['934b31ead5f3994e5360f9ff5750982c5b6b11604dc072bc452c25965e076dc7'], + 'modulename': 'google.cloud.storage', + }), + ('cellpose-omni', '0.9.1', { + 'patches': ['%(name)s-%(version)s_fix_deps_and_scm.patch'], + 'checksums': [ + {'cellpose-omni-0.9.1.tar.gz': '84f3199a751a74ddab643227bd0425ffafedcc2e739a57958f73a6d5f5348b6e'}, + {'cellpose-omni-0.9.1_fix_deps_and_scm.patch': + 'a1c42309d1a39297744a8505b45b9bff2e0f9ef738680349cc4adf8f663c4be0'}, + ], + }), + ('omnipose', version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['0bf1c333359504b0af511c36cc8db60ba5edba92d22c6aff183d9b858d269fe1'], + 'preinstallopts': "sed -i 's/numpy>=1.22.4/numpy>=1.22.3/g' setup.py && ", + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..c09c06e2c52 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvf/torchvf-0.1.3-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'torchvf' +version = '0.1.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/ryanirl/torchvf' +description = """ +TorchVF is a unifying Python library for using vector fields for efficient proposal-free instance segmentation. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# also requires pbr, which is an extension in Python already +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('OpenCV', '4.6.0', '-contrib'), + ('torchvision', '0.13.1', versionsuffix), + ('PyYAML', '6.0'), + ('scikit-learn', '1.1.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('edt', '2.3.1', { + 'checksums': ['3696e1f7de482465af731a734a31b261a8852df8d583118f1b223d61764e063f'], + }), + (name, version, { + 'preinstallopts': r"""sed -i 's/opencv-python-headless = "\*"//g' pyproject.toml && """, + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['b2603ed660009ada68751fa507e02f297119e7180b3549098f4fdfe8242b8699'], + }), +] + + +moduleclass = 'ai' From 9308639ee3ac1635a2ee6c7c06285999b405bef6 Mon Sep 17 00:00:00 2001 From: benjamic Date: Thu, 24 Aug 2023 13:36:22 +0200 Subject: [PATCH 8546/9987] Adding binutils to build dependacy --- easybuild/easyconfigs/h/htop/htop-3.2.2-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/htop/htop-3.2.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/htop/htop-3.2.2-GCCcore-11.3.0.eb index dca9be43903..aefffe2b36a 100644 --- a/easybuild/easyconfigs/h/htop/htop-3.2.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/htop/htop-3.2.2-GCCcore-11.3.0.eb @@ -16,6 +16,7 @@ checksums = ['3829c742a835a0426db41bb039d1b976420c21ec65e93b35cd9bfd2d57f44ac8'] builddependencies = [ ('Autotools', '20220317'), + ('binutils', '2.38') ] dependencies = [ From 7db277a447465d1852f64aa07d9863d44fd20dc1 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 24 Aug 2023 14:22:03 +0200 Subject: [PATCH 8547/9987] Update easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb index 24d94e8f37f..5e15314ffeb 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb @@ -42,8 +42,8 @@ configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' configopts += '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include ' -configopts += '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.so ' -configopts += '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.so ' +configopts += '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s ' % SHLIB_EXT +configopts += '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s ' % SHLIB_EXT configopts += '-DVTK_OPENGL_HAS_EGL=ON ' configopts += '-DVTK_USE_X=ON ' configopts += '-DVTK_HAS_OSMESA=ON ' From ae13432c7f074eb56d4ce2ff46b5de2a28e6bb41 Mon Sep 17 00:00:00 2001 From: Robin Verschoren Date: Thu, 24 Aug 2023 17:08:51 +0200 Subject: [PATCH 8548/9987] adding easyconfigs: intervaltree-python-3.1.0-GCCcore-11.3.0.eb, medaka-1.8.1-foss-2022a.eb, ont-fast5-api-4.1.1-foss-2022a.eb, Racon-1.5.0-GCCcore-11.3.0.eb and patches: medaka-1.8.1-tensorflow_version.patch --- ...ntervaltree-python-3.1.0-GCCcore-11.3.0.eb | 30 ++++++++ .../m/medaka/medaka-1.8.1-foss-2022a.eb | 69 +++++++++++++++++++ .../medaka-1.8.1-tensorflow_version.patch | 12 ++++ .../ont-fast5-api-4.1.1-foss-2022a.eb | 43 ++++++++++++ .../r/Racon/Racon-1.5.0-GCCcore-11.3.0.eb | 29 ++++++++ 5 files changed, 183 insertions(+) create mode 100644 easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.8.1-tensorflow_version.patch create mode 100644 easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..cf74f765780 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'intervaltree-python' +_modname = 'intervaltree' +version = '3.1.0' + +homepage = 'https://github.com/chaimleib/intervaltree' +description = """A mutable, self-balancing interval tree. Queries may be by + point, by range overlap, or by range containment. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/i/%s' % _modname] +sources = ['%s-%s.tar.gz' % (_modname, version)] +checksums = ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': _modname} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb new file mode 100644 index 00000000000..32616caf772 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb @@ -0,0 +1,69 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.8.1' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.24' +dependencies = [ + ('Python', '3.10.4'), # includes cffi + # TensorFlow ~=2.8.0 required by medaka 1.8.1, see requirements.txt + ('TensorFlow', '2.11.0'), + ('Pysam', '0.19.1'), + ('SAMtools', '1.16.1'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.15.1'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.0.9'), + ('python-parasail', '1.3.3'), + ('ont-fast5-api', '4.1.1'), + ('WhatsHap', '1.7'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.15.1'), +] + +use_pip = True + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + }), + (name, version, { + 'checksums': [ + '550b696dd4c84c1b8bf674569217004337b8a5d79a71d8cc892fd0461b05d3df', # medaka-1.8.1.tar.gz + '82bbb03df5144263d4a0c00de7921772207f905b6f9c29f34ec2a4c94c3d15ce', # medaka-1.8.1-tensorflow_version.patch, + ], + 'patches': ['medaka-1.8.1-tensorflow_version.patch'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.8.1-tensorflow_version.patch b/easybuild/easyconfigs/m/medaka/medaka-1.8.1-tensorflow_version.patch new file mode 100644 index 00000000000..d894943352a --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.8.1-tensorflow_version.patch @@ -0,0 +1,12 @@ +diff -ruN medaka-1.8.1/requirements.txt medaka-1.8.1-patched/requirements.txt +--- medaka-1.8.1/requirements.txt 2023-06-08 17:06:54.000000000 +0200 ++++ medaka-1.8.1-patched/requirements.txt 2023-08-04 14:57:18.745020486 +0200 +@@ -5,7 +5,7 @@ + grpcio + h5py + intervaltree +-tensorflow~=2.8.0 ++tensorflow<=2.11.0 + numpy>=1.21.6 + mappy + ont_fast5_api diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.1-foss-2022a.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.1-foss-2022a.eb new file mode 100644 index 00000000000..8398ccc0d84 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.1-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '4.1.1' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + (name, version, { + 'checksums': ['71ea44087f310a2792d1a6c2ffbf5bc194367e769ce96a15961787f90ec7707b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/compress_fast5', 'bin/fast5_subset', 'bin/multi_to_single_fast5', 'bin/single_to_multi_fast5'], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..5150c4f5ea7 --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.5.0' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'lbcb-sci' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['41e362f71cc03b934f17d6e2c0d626e1b2997258261b14551586de006666424a'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.38'), + ('git', '2.36.0', '-nodocs'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' From 0b44bc2eef0811ff24cbf96b92b3e9e47b281f76 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 24 Aug 2023 17:24:48 +0200 Subject: [PATCH 8549/9987] Use C++14 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb index 0b40808465f..ced3f4fa116 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2022b'} # Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. # Disabling vectorize was confirmed to fix the the known issues. # With no test suite, sticking to known working toolchain options until proven otherwise. -toolchainopts = {'usempi': True, 'cstd': 'c++11', 'vectorize': False} +toolchainopts = {'usempi': True, 'cstd': 'c++14', 'vectorize': False} source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] From e26f26f9618aec0e0b7d97bc5b34097a60ed93ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2023 17:42:11 +0200 Subject: [PATCH 8550/9987] set $MUJOCO_PY_FORCE_CPU to avoid that mujoco-py checks for nvidia-smi and aborts installation because /usr/lib/nvidia is not in $LD_LIBRARY_PATH --- .../easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb index a2166416d7b..4e3c01d7bbe 100644 --- a/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb +++ b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb @@ -35,7 +35,7 @@ exts_list = [ 'mujoco-py-%(version)s_fix-builder-lib-paths.patch', 'mujoco-py-%(version)s_fix-builder-lockfile.patch', ], - 'preinstallopts': 'MUJOCO_PY_MUJOCO_PATH=$EBROOTMUJOCO', + 'preinstallopts': 'MUJOCO_PY_MUJOCO_PATH=$EBROOTMUJOCO MUJOCO_PY_FORCE_CPU=1', 'checksums': [ 'eb5b14485acf80a3cf8c15f4b080c6a28a9f79e68869aa696d16cbd51ea7706f', # mujoco-py-2.1.2.14.tar.gz # mujoco-py-2.1.2.14_fix-builder-lib-paths.patch From daf34f4e45c7aae46505925005c3735ab47bdb07 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Aug 2023 17:44:14 +0200 Subject: [PATCH 8551/9987] also add setting of $MUJOCO_PY_FORCE_CPU to mujoco-py module --- .../m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb index a2166416d7b..13fbfe58715 100644 --- a/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb +++ b/easybuild/easyconfigs/m/mujoco-py/mujoco-py-2.1.2.14-foss-2021b.eb @@ -35,7 +35,7 @@ exts_list = [ 'mujoco-py-%(version)s_fix-builder-lib-paths.patch', 'mujoco-py-%(version)s_fix-builder-lockfile.patch', ], - 'preinstallopts': 'MUJOCO_PY_MUJOCO_PATH=$EBROOTMUJOCO', + 'preinstallopts': 'MUJOCO_PY_MUJOCO_PATH=$EBROOTMUJOCO MUJOCO_PY_FORCE_CPU=1', 'checksums': [ 'eb5b14485acf80a3cf8c15f4b080c6a28a9f79e68869aa696d16cbd51ea7706f', # mujoco-py-2.1.2.14.tar.gz # mujoco-py-2.1.2.14_fix-builder-lib-paths.patch @@ -48,6 +48,10 @@ exts_list = [ sanity_pip_check = True +modextravars = { + 'MUJOCO_PY_FORCE_CPU': '1', +} + modluafooter = """ setenv("MUJOCO_PY_MUJOCO_PATH", os.getenv("EBROOTMUJOCO")) """ From 42121f9ac9b98d509126d0acb0044c657940f3b9 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 24 Aug 2023 18:56:12 +0200 Subject: [PATCH 8552/9987] changed LibTIFF dependency 4.5.1 -> 4.5.0, see comments pr #18627 --- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.3.0.eb index 4eb2e4a6924..3d1ffb27864 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.3.0.eb @@ -29,7 +29,7 @@ dependencies = [ ('GLib', '2.77.1'), ('libjpeg-turbo', '2.1.5.1'), ('libpng', '1.6.39'), - ('LibTIFF', '4.5.1'), + ('LibTIFF', '4.5.0'), ('X11', '20230603'), ] From e331c366e197c33bf299fc6b6d272a53974b8f87 Mon Sep 17 00:00:00 2001 From: RVerschoren Date: Fri, 25 Aug 2023 11:34:43 +0200 Subject: [PATCH 8553/9987] Update easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb index 32616caf772..41729e4148e 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb @@ -50,7 +50,8 @@ exts_list = [ '550b696dd4c84c1b8bf674569217004337b8a5d79a71d8cc892fd0461b05d3df', # medaka-1.8.1.tar.gz '82bbb03df5144263d4a0c00de7921772207f905b6f9c29f34ec2a4c94c3d15ce', # medaka-1.8.1-tensorflow_version.patch, ], - 'patches': ['medaka-1.8.1-tensorflow_version.patch'], + # remove TensorFlow version requirement which is too strict + 'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g' requirements.txt && ", }), ] From 72a0e9d9385f495180ed9d1d204aa9fe01395953 Mon Sep 17 00:00:00 2001 From: Robin Verschoren Date: Fri, 25 Aug 2023 11:46:40 +0200 Subject: [PATCH 8554/9987] Updated style, removed patch --- easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb index 41729e4148e..41dd6c3419e 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.8.1-foss-2022a.eb @@ -46,10 +46,7 @@ exts_list = [ 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], }), (name, version, { - 'checksums': [ - '550b696dd4c84c1b8bf674569217004337b8a5d79a71d8cc892fd0461b05d3df', # medaka-1.8.1.tar.gz - '82bbb03df5144263d4a0c00de7921772207f905b6f9c29f34ec2a4c94c3d15ce', # medaka-1.8.1-tensorflow_version.patch, - ], + 'checksums': ['550b696dd4c84c1b8bf674569217004337b8a5d79a71d8cc892fd0461b05d3df'], # remove TensorFlow version requirement which is too strict 'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g' requirements.txt && ", }), From fa14b5c34451badb59e133490252430d21243cb5 Mon Sep 17 00:00:00 2001 From: RVerschoren Date: Fri, 25 Aug 2023 11:48:09 +0200 Subject: [PATCH 8555/9987] Delete medaka-1.8.1-tensorflow_version.patch --- .../m/medaka/medaka-1.8.1-tensorflow_version.patch | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.8.1-tensorflow_version.patch diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.8.1-tensorflow_version.patch b/easybuild/easyconfigs/m/medaka/medaka-1.8.1-tensorflow_version.patch deleted file mode 100644 index d894943352a..00000000000 --- a/easybuild/easyconfigs/m/medaka/medaka-1.8.1-tensorflow_version.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ruN medaka-1.8.1/requirements.txt medaka-1.8.1-patched/requirements.txt ---- medaka-1.8.1/requirements.txt 2023-06-08 17:06:54.000000000 +0200 -+++ medaka-1.8.1-patched/requirements.txt 2023-08-04 14:57:18.745020486 +0200 -@@ -5,7 +5,7 @@ - grpcio - h5py - intervaltree --tensorflow~=2.8.0 -+tensorflow<=2.11.0 - numpy>=1.21.6 - mappy - ont_fast5_api From 09b6e9fb874883ec7d7cda1b55d63798683e695e Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 25 Aug 2023 12:37:56 +0200 Subject: [PATCH 8556/9987] adding easyconfigs: GHC-9.2.2-x86_64.eb --- .../easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb new file mode 100644 index 00000000000..8fd0a77a7bc --- /dev/null +++ b/easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb @@ -0,0 +1,81 @@ +# This is a binary install that requires a './configure' and 'make install' steps for GHC. +# We pull the centos7 binary tarball as is the one built against oldest system libs, +# making it upwards compatible with newer distros. +# +# To get a functional 'ghc' binary on the SYSTEM toolchain we need +# gmp headers and ncurses libtinfo.so.5, to avoid requiring extra OS deps for them +# we include them in this bundle. +# Binaries obtained with ghc do not require them, so it should be possible to use this bundle +# just as builddep among different toolchains. +# +# For details, see the PR discussion: +# https://github.com/easybuilders/easybuild-easyconfigs/pull/11310 + +easyblock = 'Bundle' + +name = 'GHC' +version = '9.2.2' +versionsuffix = '-x86_64' + +homepage = 'https://haskell.org/ghc/' +description = """The Glorious/Glasgow Haskell Compiler""" + +toolchain = SYSTEM + +builddependencies = [ + ('binutils', '2.32'), +] + +default_easyblock = 'ConfigureMake' + +local_distro_tarball = 'centos7' + +default_component_specs = { + 'start_dir': '%(namelower)s-%(version)s', +} +components = [ + ('GMP', '6.2.0', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_BZ2], + 'checksums': ['f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'], + 'configopts': ' --enable-cxx', + }), + ('ncurses', '5.9', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'patches': [ + 'ncurses-%(version)s_configure_darwin.patch', + 'ncurses-%(version)s_fix-missing-const.patch', + ], + 'checksums': [ + '9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b', + '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', + '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', + ], + 'preconfigopts': "export CPPFLAGS='-P' && ", + 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', + }), + (name, version, { + 'source_urls': ['https://downloads.haskell.org/~ghc/%(version)s/'], + 'sources': ['%%(namelower)s-%%(version)s-x86_64-%s-linux.tar.xz' % local_distro_tarball], + 'checksums': ['5100aa7dea87aaf2ed596be83c93165d7199492f6db431d874fcfa07e8ac76ab'], + # ghc-8.6.5-x86_64-centos7-linux.tar.xz + 'skipsteps': ['build'], + 'preinstallopts': 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ', + }), +] + +local_ncurses_libs = ["form", "menu", "ncurses", "panel", "tinfo"] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, y) for x in ['gmp', 'gmpxx'] for y in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'] + + ['lib/lib%s%s.a' % (x, y) for x in local_ncurses_libs for y in ['', '_g']] + + ['lib/lib%s.%s' % (x, y) for x in local_ncurses_libs for y in [SHLIB_EXT]] + + ['bin/ghc', 'bin/ghci', 'bin/ghc-pkg', 'bin/runghc', 'bin/runhaskell'], + 'dirs': ['bin', 'lib', 'share', 'include'], +} + +sanity_check_commands = ['ghc --version'] + +moduleclass = 'compiler' From b7c2e8cb73bd1fd6fa43d4da224ac4855c24d27f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 25 Aug 2023 17:33:20 +0200 Subject: [PATCH 8557/9987] Move gnuplot 5.4.6 back to GCCcore like the rest --- ...-5.4.6-GCC-12.2.0.eb => gnuplot-5.4.6-GCCcore-12.2.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/gnuplot/{gnuplot-5.4.6-GCC-12.2.0.eb => gnuplot-5.4.6-GCCcore-12.2.0.eb} (87%) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCC-12.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb similarity index 87% rename from easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCC-12.2.0.eb rename to easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb index 79e961d87ef..45e7dccbb86 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb @@ -6,13 +6,14 @@ version = '5.4.6' homepage = 'http://gnuplot.sourceforge.net' description = """Portable interactive, function plotting utility""" -toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] checksums = ['02fc27918200ed64d8f0c3b84fe81b95b59cd47ad99f270939ae497c19f27419'] builddependencies = [ + ('binutils', '2.39'), ('pkgconf', '1.9.3'), ('Autotools', '20220317'), ] @@ -28,12 +29,11 @@ dependencies = [ ('X11', '20221110'), ('Qt5', '5.15.7'), ('Lua', '5.4.4'), - ('wxWidgets', '3.2.2.1'), ] preconfigopts = 'autoreconf && ' -configopts = '--with-qt=qt5 --without-latex ' +configopts = '--with-qt=qt5 --without-latex --without-wx' sanity_check_paths = { 'files': ['bin/gnuplot'], From 31efa93210137bc6928dd91f41082f2088d852ce Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 25 Aug 2023 16:35:00 +0100 Subject: [PATCH 8558/9987] adding easyconfigs: MATIO-1.5.23-GCCcore-12.2.0.eb --- .../m/MATIO/MATIO-1.5.23-GCCcore-12.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7cb4ccb60d4 --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'MATIO' +version = '1.5.23' + +homepage = 'https://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] +checksums = ['b3b29fb394e1cfa3f98cd57bac013c0cf7716ae7a085e398f2dfaff8f976f0c5'] + +preconfigopts = 'chmod +x configure && ' + +builddependencies = [('binutils', '2.39')] + +dependencies = [('zlib', '1.2.12')] + +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 4158f839c776d0fbf223d7139fba15946f0610b4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 25 Aug 2023 16:55:39 +0100 Subject: [PATCH 8559/9987] adding easyconfigs: GLM-0.9.9.8-GCCcore-12.2.0.eb --- .../g/GLM/GLM-0.9.9.8-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a2b24730aaf --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '0.9.9.8' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'GLM-0.9.9.8_fix_missing_install.patch', +] +checksums = [ + '7d508ab72cb5d43227a3711420f06ff99b0a0cb63ee2f93631b162bfe1fe9592', # 0.9.9.8.tar.gz + '1cc199f9d66679b0b5e9a9fbe20bca0d9b15760fa172ca8759dd15bab35802ca', # GLM-0.9.9.8_fix_missing_install.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' From f59f161b2870075c92ae403d7fd5ae0e55f5b81a Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 25 Aug 2023 08:55:54 -0700 Subject: [PATCH 8560/9987] bump version magma 2.7.1 --- ...DA-12.0.0.eb => magma-2.7.1-foss-2022b-CUDA-12.0.0.eb} | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/magma/{magma-2.7.0-GCC-12.2.0-CUDA-12.0.0.eb => magma-2.7.1-foss-2022b-CUDA-12.0.0.eb} (83%) diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/m/magma/magma-2.7.1-foss-2022b-CUDA-12.0.0.eb similarity index 83% rename from easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-12.0.0.eb rename to easybuild/easyconfigs/m/magma/magma-2.7.1-foss-2022b-CUDA-12.0.0.eb index 0849a2ce18b..2bb33c46932 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.7.0-GCC-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.7.1-foss-2022b-CUDA-12.0.0.eb @@ -1,21 +1,19 @@ easyblock = 'CMakeMake' name = 'magma' -version = '2.7.0' +version = '2.7.1' versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://icl.cs.utk.edu/magma/' description = """The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" -toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchain = {'name': 'foss', 'version': '2022b'} toolchainopts = {'pic': True, 'openmp': True} source_urls = ['https://icl.cs.utk.edu/projectsfiles/%(name)s/downloads/'] sources = [SOURCE_TAR_GZ] -checksums = ['fda1cbc4607e77cacd8feb1c0f633c5826ba200a018f647f1c5436975b39fd18'] - -#patches = ['%(name)s-%(version_major_minor)s.1_allow-all-sms.patch'] +checksums = ['d9c8711c047a38cae16efde74bee2eb3333217fd2711e1e9b8606cbbb4ae1a50'] builddependencies = [ ('CMake', '3.24.3'), From 067ffa0cadce8023d35c6819493849dec356b9b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Aug 2023 18:05:43 +0200 Subject: [PATCH 8561/9987] adding easyconfigs: medaka-1.9.1-foss-2022a.eb --- .../m/medaka/medaka-1.9.1-foss-2022a.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022a.eb new file mode 100644 index 00000000000..8e769176875 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022a.eb @@ -0,0 +1,67 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.9.1' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.24' +dependencies = [ + ('Python', '3.10.4'), # includes cffi + # TensorFlow ~=2.8.0 required by medaka 1.8.1, see requirements.txt + ('TensorFlow', '2.11.0'), + ('Pysam', '0.19.1'), + ('SAMtools', '1.16.1'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.15.1'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.0.9'), + ('python-parasail', '1.3.3'), + ('ont-fast5-api', '4.1.1'), + ('WhatsHap', '1.7'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.15.1'), +] + +use_pip = True + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + }), + (name, version, { + 'checksums': ['1018c07267d24cb4607ae823ced01a1789939b5f8143d1c240ce243dc1160ef5'], + # remove TensorFlow version requirement which is too strict + 'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g' requirements.txt && ", + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' From 54582ab5d8e88773f33a752cf547bbd0d2f0d8d5 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 04:54:22 +0800 Subject: [PATCH 8562/9987] adding easyconfigs: cicero-1.3.8-foss-2022a-R-4.2.1-Monocle3.eb, Monocle3-1.3.1-foss-2022a-R-4.2.1.eb --- ...icero-1.3.8-foss-2022a-R-4.2.1-Monocle3.eb | 30 +++++ .../Monocle3-1.3.1-foss-2022a-R-4.2.1.eb | 110 ++++++++++++++++++ 2 files changed, 140 insertions(+) create mode 100644 easybuild/easyconfigs/c/cicero/cicero-1.3.8-foss-2022a-R-4.2.1-Monocle3.eb create mode 100644 easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/c/cicero/cicero-1.3.8-foss-2022a-R-4.2.1-Monocle3.eb b/easybuild/easyconfigs/c/cicero/cicero-1.3.8-foss-2022a-R-4.2.1-Monocle3.eb new file mode 100644 index 00000000000..11a64dc05a4 --- /dev/null +++ b/easybuild/easyconfigs/c/cicero/cicero-1.3.8-foss-2022a-R-4.2.1-Monocle3.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'cicero' +# see https://github.com/cole-trapnell-lab/cicero-release/tree/monocle3 +local_commit = '02d1e8d' +version = '1.3.8' +versionsuffix = '-R-%(rver)s-Monocle3' + +homepage = 'https://cole-trapnell-lab.github.io/cicero-release' +description = """Cicero is an R package that provides tools for analyzing single-cell chromatin accessibility + experiments.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/cole-trapnell-lab/cicero-release/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': 'cicero-%(version)s-monocle3.tar.gz'}] +checksums = ['603e4efecfbdd57f38c247d0a3cc389e1f8b006c03af6b348881bcc95894b30f'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', '-R-%(rver)s'), + ('Monocle3', '1.3.1', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..b11ab3798c0 --- /dev/null +++ b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb @@ -0,0 +1,110 @@ +easyblock = 'Bundle' + +name = 'Monocle3' +version = '1.3.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cole-trapnell-lab.github.io/monocle3/' +description = """ An analysis toolkit for single-cell RNA-seq. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('Python', '3.10.4'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('GDAL', '3.5.0'), + ('HarfBuzz', '4.2.1'), # for textshaping + ('FriBidi', '1.0.12'), # for textshaping +] + +github_account = 'cole-trapnell-lab' +exts_defaultclass = 'RPackage' +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('grr', '0.9.5', { + 'checksums': ['292606de2983ac5840c90d3e0977441b482c9e73c1674b662f8b4fb8f3632b2b'], + }), + ('Matrix.utils', '0.9.8', { + 'checksums': ['ebc59d3ef751775515586ff1f2396e429a1e9d91a10099d804134fcf74c0ae28'], + }), + ('pbmcapply', '1.5.1', { + 'checksums': ['7ffc2854a384962f0dd523aa9ef33ce8fc290997206b71b840a49049d87112dd'], + }), + ('furrr', '0.3.1', { + 'checksums': ['0d91735e2e9be759b1ab148d115c2c7429b79740514778828e5dab631dc0e48b'], + }), + ('warp', '0.2.0', { + 'checksums': ['0e0de344f3d711d58e6be2ab47ade1db3b703bf3ca85080b1124c0c25a630a68'], + }), + ('rlang', '1.0.6', { + 'checksums': ['e6973d98a0ea301c0da1eeaa435e9e65d1c3f0b95ed68bdc2d6cb0c610166760'], + }), + ('vctrs', '0.5.2', { + 'checksums': ['76bf10243b9b31e23f56ffdaa1677a01767699e2098487f86bd42cb801d8c047'], + }), + ('slider', '0.3.0', { + 'checksums': ['bc6a17ba5f0b27c8504a1d04992108470f24fd5662fbea14c300ac75fb02fca1'], + }), + ('rsample', '1.1.1', { + 'checksums': ['90d2ae86d27a397ba9d8d010e7dea5c7b86fecbec7e9af273db0c2e8c374b8ba'], + }), + ('RhpcBLASctl', '0.21-247.1', { + 'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'], + }), + ('sf', '1.0-9', { + 'checksums': ['85c0c71a0a64750281e79aa96e36d13e6285927008b2d37d699e52aba7d8013b'], + }), + ('spdep', '1.2-7', { + 'checksums': ['9dac594825bf2d0aa31e845bfec05d8ce206327840fe455391741dbbdf9c9eea'], + }), + ('biglm', '0.9-2.1', { + 'checksums': ['6dcf3c9e7c3f56cdaac94cc0c427f606880467e1e753fe7ea45c10bc44eec947'], + }), + ('speedglm', '0.3-5', { + 'checksums': ['f8663677c10ff324c5639402060ddd2b1a1e917445cb0f8f84e146b85e82bb4b'], + }), + ('uwot', '0.1.14', { + 'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'], + }), + ('systemfonts', '1.0.4', { + 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], + }), + ('textshaping', '0.3.6', { + 'checksums': ['80e2c087962f55ce2811fbc798b09f5638c06c6b28c10cd3cb3827005b902ada'], + }), + ('ragg', '1.2.5', { + 'checksums': ['936f4d75e0e01cdeefb9f57d121cdd7812d0de5a9e1a3a8315f92ce1c84da8f9'], + }), + ('ggrastr', '1.0.1', { + 'checksums': ['82d6e90fa38dec85e829f71018532ed5b709a50a585455fc07cb3bae282f5d1f'], + }), + ('leidenbase', '0.1.9', { + 'source_urls': ['https://github.com/%(github_account)s/leidenbase/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'leidenbase-%(version)s.tar.gz'}], + 'checksums': ['dd893b13b04d4b943243e7ac8d2ef1850b60d0437b2e4d36a9cff57cd4953f54'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_urls': ['https://github.com/%(github_account)s/monocle3/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'Monocle3-%(version)s.tar.gz'}], + 'checksums': ['30e86d5323ea22b302614813ecf102f26774b42710589671a1f1d51ef9ad183d'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['leidenbase', '%(namelower)s'], +} + +moduleclass = 'bio' From bb5a47470c74a84797c69c55441dff4c7645283c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 04:58:42 +0800 Subject: [PATCH 8563/9987] adding easyconfigs: SpiecEasi-1.1.1-foss-2022a-R-4.2.1.eb --- .../SpiecEasi-1.1.1-foss-2022a-R-4.2.1.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-1.1.1-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-1.1.1-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-1.1.1-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..3d5cac629e7 --- /dev/null +++ b/easybuild/easyconfigs/s/SpiecEasi/SpiecEasi-1.1.1-foss-2022a-R-4.2.1.eb @@ -0,0 +1,23 @@ +easyblock = 'RPackage' + +name = 'SpiecEasi' +version = '1.1.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/zdk123/SpiecEasi' +description = "Sparse InversE Covariance estimation for Ecological Association and Statistical Inference" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/zdk123/SpiecEasi/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0f79f5c86a2d28a469116c2f19c29746a7a3495776dcff4d83754137b6158e63'] + +dependencies = [('R', '4.2.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 2574969ac831db1812fe9f16164d75daeabc99a3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 04:59:44 +0800 Subject: [PATCH 8564/9987] adding easyconfigs: SeuratWrappers-20221022-foss-2022a-R-4.2.1.eb --- ...ratWrappers-20221022-foss-2022a-R-4.2.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20221022-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20221022-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20221022-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..b58715ea587 --- /dev/null +++ b/easybuild/easyconfigs/s/SeuratWrappers/SeuratWrappers-20221022-foss-2022a-R-4.2.1.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'SeuratWrappers' +local_commit = 'd28512f' +version = '20221022' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/satijalab/seurat-wrappers' +description = "SeuratWrappers is a collection of community-provided methods and extensions for Seurat" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/satijalab', + 'repo_name': 'seurat-wrappers', + 'commit': local_commit, + }, +}] +checksums = [None] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('Seurat', '4.3.0', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 16d957ee897eb549b37c52139c7508a7e2ec4fea Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 05:12:56 +0800 Subject: [PATCH 8565/9987] adding easyconfigs: RnBeads-2.14.0-foss-2022a-R-4.2.1.eb --- .../RnBeads-2.14.0-foss-2022a-R-4.2.1.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/r/RnBeads/RnBeads-2.14.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/r/RnBeads/RnBeads-2.14.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/RnBeads/RnBeads-2.14.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..2d7ec893ec0 --- /dev/null +++ b/easybuild/easyconfigs/r/RnBeads/RnBeads-2.14.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'RnBeads' +version = '2.14.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://rnbeads.org' +description = """RnBeads is an R package for comprehensive analysis of DNA methylation data obtained with any +experimental protocol that provides single-CpG resolution.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('Ghostscript', '9.56.1'), + ('Zip', '3.0'), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.15/data/experiment/src/contrib/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_list = [ + (name, version, { + 'checksums': ['858c6920745f54cb141e828ba80e366e3a803be2658cafc11d7224049295b6e4'], + }), + ('RnBeads.hg19', '1.28.0', { + 'checksums': ['f017cb82d72bd7d3b9cac2d57cffe441d33c0eb2cc37f531029f6b634dc4728f'], + }), + ('RnBeads.hg38', '1.28.0', { + 'checksums': ['23f7e1cd0bdaf01c915bda9b7d4b2d730867b0472e7139a61ee3179b13aabf71'], + }), + ('RnBeads.mm10', '2.4.1', { + 'checksums': ['449d2d6df80b967482b5d69360567023853464f704d8ab7a5646cd22e2eff181'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 2664e998bcf6f806766f24284aa6510b3dad3490 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 05:43:35 +0800 Subject: [PATCH 8566/9987] adding easyconfigs: bench-1.1.2-foss-2022a-R-4.2.1.eb --- .../b/bench/bench-1.1.2-foss-2022a-R-4.2.1.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/b/bench/bench-1.1.2-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/b/bench/bench-1.1.2-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/b/bench/bench-1.1.2-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..234c3dadbc9 --- /dev/null +++ b/easybuild/easyconfigs/b/bench/bench-1.1.2-foss-2022a-R-4.2.1.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'bench' +version = '1.1.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/bench/index.html' +description = """Tools to accurately benchmark and analyze execution times for R expressions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), +] + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_list = [ + ('profmem', '0.6.0', { + 'checksums': ['745ca9b22a8de3cda4374be6e2454e549742a3b72ff02c8894c972178192e63d'], + }), + (name, version, { + 'checksums': ['af910a768db79fe68597e6e79ff1012b810b8f88fb29c04432cded058ec2439b'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'tools' From 70d3b4c8f7444a44c0f24561aa84da6e6bedba1f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 05:48:39 +0800 Subject: [PATCH 8567/9987] adding easyconfigs: CVglasso-1.0-foss-2022a-R-4.2.1.eb --- .../CVglasso-1.0-foss-2022a-R-4.2.1.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVglasso/CVglasso-1.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/c/CVglasso/CVglasso-1.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/c/CVglasso/CVglasso-1.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..2fce2f9317f --- /dev/null +++ b/easybuild/easyconfigs/c/CVglasso/CVglasso-1.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,25 @@ +easyblock = 'RPackage' + +name = 'CVglasso' +version = '1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/MGallow/CVglasso' +description = """CVglasso is an R package that estimates a lasso-penalized + precision matrix via block-wise coordinate descent – also known as + the graphical lasso (glasso) algorithm.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://cran.r-project.org/src/contrib/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['cd31d042f71cf7c46cca3ed07f15f609b8d1bdda102ae7cbc670290f1a4b00ae'] + +dependencies = [('R', '4.2.1')] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From df390ce0366b373ff45d52991e1f461177eda07c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 05:51:23 +0800 Subject: [PATCH 8568/9987] adding easyconfigs: meboot-1.4-9.2-foss-2022a-R-4.2.1.eb --- .../meboot-1.4-9.2-foss-2022a-R-4.2.1.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/m/meboot/meboot-1.4-9.2-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/m/meboot/meboot-1.4-9.2-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/m/meboot/meboot-1.4-9.2-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..19e0c65d0ca --- /dev/null +++ b/easybuild/easyconfigs/m/meboot/meboot-1.4-9.2-foss-2022a-R-4.2.1.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'meboot' +version = '1.4-9.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/meboot/index.html' +description = """Maximum entropy density based dependent data bootstrap. + An algorithm is provided to create a population of time series (ensemble) without assuming stationarity.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), # provides required hdrcde +] + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_list = [ + ('dynlm', '0.3-6', { + 'checksums': ['f88fd2e8eceebe00199f8b9e36e574f82ebbf6490d6a507519d62753cbd218bd'], + }), + ('tdigest', '0.4.1', { + 'checksums': ['9e34955b2e4e61c2342b2245d7ee66899da8d91cb52f0370f90cf54a03989ebc'], + }), + (name, version, { + 'checksums': ['5c8e8ed2d8be69225f952e04b9ac9fd9c0b3f6aa3c598c5597bcb0d9687d226a'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From 9eac95fbb443e1bb6e882b2c0525630949c3cf43 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 05:59:21 +0800 Subject: [PATCH 8569/9987] adding easyconfigs: gkmSVM-0.82.0-foss-2022a-R-4.2.1.eb --- .../gkmSVM-0.82.0-foss-2022a-R-4.2.1.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/gkmSVM/gkmSVM-0.82.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/g/gkmSVM/gkmSVM-0.82.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/g/gkmSVM/gkmSVM-0.82.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..e57a62d8ca5 --- /dev/null +++ b/easybuild/easyconfigs/g/gkmSVM/gkmSVM-0.82.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,25 @@ +easyblock = 'RPackage' + +name = 'gkmSVM' +version = '0.82.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/gkmSVM/index.html' +description = """Gapped-Kmer Support Vector Machine.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://cran.r-project.org/src/contrib/Archive/%(name)s'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['751d536cde502ebf8a39f6a2b8d57939ec1f045bce954b8054f0650d16c14cd4'] + +dependencies = [ + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From 77ce9351e2169d15580689e3d6f4525122b29029 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 06:03:21 +0800 Subject: [PATCH 8570/9987] adding easyconfigs: tseriesEntropy-0.6-0-foss-2022a-R-4.2.1.eb --- ...tseriesEntropy-0.6-0-foss-2022a-R-4.2.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/t/tseriesEntropy/tseriesEntropy-0.6-0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/t/tseriesEntropy/tseriesEntropy-0.6-0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/t/tseriesEntropy/tseriesEntropy-0.6-0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..aa81737ada1 --- /dev/null +++ b/easybuild/easyconfigs/t/tseriesEntropy/tseriesEntropy-0.6-0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'tseriesEntropy' +version = '0.6-0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/tseriesEntropy/index.html' +description = """Implements an Entropy measure of dependence based on the Bhattacharya-Hellinger-Matusita distance. + Can be used as a (nonlinear) autocorrelation/crosscorrelation function for continuous and categorical time series. + The package includes tests for serial dependence and nonlinearity based on it. + Some routines have a parallel version that can be used in a multicore/cluster environment. + The package makes use of S4 classes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://cran.r-project.org/src/contrib/Archive/%(name)s'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['db8d94d6a6a0f41be010936d5a520b92d2b0893b2c15ccba2db7f838ef749411'] + +dependencies = [ + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From ecd59e87e8e25707341ae8ff865ca1fdc5c2de3c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 06:05:41 +0800 Subject: [PATCH 8571/9987] adding easyconfigs: ChIPseeker-1.32.1-foss-2022a-R-4.2.1.eb --- .../ChIPseeker-1.32.1-foss-2022a-R-4.2.1.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/c/ChIPseeker/ChIPseeker-1.32.1-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/c/ChIPseeker/ChIPseeker-1.32.1-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/c/ChIPseeker/ChIPseeker-1.32.1-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..050adb450ea --- /dev/null +++ b/easybuild/easyconfigs/c/ChIPseeker/ChIPseeker-1.32.1-foss-2022a-R-4.2.1.eb @@ -0,0 +1,53 @@ +easyblock = 'Bundle' + +name = 'ChIPseeker' +version = '1.32.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html' +description = """This package implements functions to retrieve the nearest genes around the peak, + annotate genomic region of the peak, statstical methods for estimate the significance of overlap + among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with + those deposited in database.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_list = [ + ('RVenn', '1.1.0', { + 'checksums': ['c41a96dd4a9b51e7dcc8647cdbaa0faa704ab22d5b0c1d45e593a6b23b00d504'], + }), + ('ggVennDiagram', '1.2.3', { + 'checksums': ['f26c4977d868cef80a3ce80ea418130415ac4106336d4172c5638cd130c87820'], + }), + (name, version, { + 'checksums': ['8eadcd66bbe60d17e72240a4f1c7b95a9cf11a7cd97df9833d1831ba39094550'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 09d2eed22d15aabb9b1f9df3666391d00d41abe6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 06:05:50 +0800 Subject: [PATCH 8572/9987] adding easyconfigs: DiffBind-3.6.5-foss-2022a-R-4.2.1.eb --- .../DiffBind-3.6.5-foss-2022a-R-4.2.1.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/d/DiffBind/DiffBind-3.6.5-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/d/DiffBind/DiffBind-3.6.5-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/d/DiffBind/DiffBind-3.6.5-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..4829c59e0ef --- /dev/null +++ b/easybuild/easyconfigs/d/DiffBind/DiffBind-3.6.5-foss-2022a-R-4.2.1.eb @@ -0,0 +1,69 @@ +easyblock = 'Bundle' + +name = 'DiffBind' +version = '3.6.5' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org/packages/release/bioc/html/DiffBind.html' +description = """Compute differentially bound sites from multiple ChIP-seq experiments using + affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_list = [ + ('amap', '0.8-19', { + 'checksums': ['7349ea684b69eba0fcc48f78b7ac09a838d95d3bc0c6a94b6055605ac0291900'], + }), + ('systemPipeR', '2.2.2', { + 'checksums': ['35a6429a93559f90fcfc443e245dbe85ae350e979e700b6a369bbf249c5bcbfb'], + }), + ('RcppNumerical', '0.5-0', { + 'checksums': ['596127b4d5b5b24f8ab1f61c0e26b5d290b4f1d854f91bf08759eec637020b96'], + }), + ('apeglm', '1.18.0', { + 'checksums': ['7e65e0dc1441fc273cb8d51e9271d6a1a13444a0706ba7f1858674631e99fcde'], + }), + ('invgamma', '1.1', { + 'checksums': ['aaa8de7c2a852fa6df30d8262086f6a3eb2b1fefbbc66dfe2f6c25c68917ea89'], + }), + ('etrunct', '0.1', { + 'checksums': ['19b36c739e382be2f19bdbe4107337935d52a1ab8eb301326612318afdfbca2b'], + }), + ('ashr', '2.2-63', { + 'checksums': ['7fa1957ed3cf0f1f20939b6ebf71fc04ab983ca77616f7b80ce9e9e6fad457c9'], + }), + ('GreyListChIP', '1.28.1', { + 'checksums': ['0f367385fc951724a1d494819618ea3880633d400b90ad570a14672537dfa270'], + }), + (name, version, { + 'checksums': ['fd294fac901efb1a093c948bc6c34b96447c30b820f9f51bf529aab5d8d702b1'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From f6322d324ae15ba1563abad38b5535ae3d9d8251 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 06:05:57 +0800 Subject: [PATCH 8573/9987] adding easyconfigs: IsoformSwitchAnalyzeR-1.18.0-foss-2022a-R-4.2.1.eb --- ...witchAnalyzeR-1.18.0-foss-2022a-R-4.2.1.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/i/IsoformSwitchAnalyzeR/IsoformSwitchAnalyzeR-1.18.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/i/IsoformSwitchAnalyzeR/IsoformSwitchAnalyzeR-1.18.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/i/IsoformSwitchAnalyzeR/IsoformSwitchAnalyzeR-1.18.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..fb68eb66e3a --- /dev/null +++ b/easybuild/easyconfigs/i/IsoformSwitchAnalyzeR/IsoformSwitchAnalyzeR-1.18.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,50 @@ +easyblock = 'Bundle' + +name = 'IsoformSwitchAnalyzeR' +version = '1.18.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org/packages/release/bioc/html/IsoformSwitchAnalyzeR.html' +description = """Analysis of alternative splicing and isoform switches with predicted functional consequences + (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as + Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.15/bioc/src/contrib/Archive/%(name)s', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_list = [ + ('DEXSeq', '1.42.0', { + 'checksums': ['550910c28638c78d74ea57ef8af01ef7d76ba91b36668432cf6c5f54774dfdb7'], + }), + ('tximeta', '1.14.1', { + 'checksums': ['28e7d85a5f840356d54db528439ec9b2944a766e0a217afb50e0c796272db843'], + }), + (name, version, { + 'checksums': ['6d6e3acc1b16a1067fe6fccd20a5b7853871dc1c71f08df5ed35a8fe555a2f58'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 7a028fca871006166d7c05853f84b10d6945882e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 05:56:44 +0800 Subject: [PATCH 8574/9987] adding easyconfigs: geosphere-1.5-18-foss-2022a-R-4.2.1.eb --- .../geosphere-1.5-18-foss-2022a-R-4.2.1.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/geosphere/geosphere-1.5-18-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/g/geosphere/geosphere-1.5-18-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/g/geosphere/geosphere-1.5-18-foss-2022a-R-4.2.1.eb new file mode 100644 index 00000000000..a9a6bf52ae9 --- /dev/null +++ b/easybuild/easyconfigs/g/geosphere/geosphere-1.5-18-foss-2022a-R-4.2.1.eb @@ -0,0 +1,26 @@ +easyblock = 'RPackage' + +name = 'geosphere' +version = '1.5-18' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/geosphere/index.html' +description = """Spherical trigonometry for geographic applications. + That is, compute distances and related measures for angular (longitude/latitude) locations.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://cran.r-project.org/src/contrib/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['99ff6ff050cc8c2d565b6bb1488607fc7950a6d448930f8d9642eccefbc6dac0'] + +dependencies = [ + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'geo' From f56a48687e6fe51595ec15fab5669733fa5aea7e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 26 Aug 2023 07:01:40 +0800 Subject: [PATCH 8575/9987] add pkg-config build dependency --- .../easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb index b11ab3798c0..950ba37bf0b 100644 --- a/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb @@ -9,6 +9,8 @@ description = """ An analysis toolkit for single-cell RNA-seq. """ toolchain = {'name': 'foss', 'version': '2022a'} +builddependencies = [('pkg-config', '0.29.2')] # for textshaping + dependencies = [ ('R', '4.2.1'), ('Python', '3.10.4'), From 941444488649782be955b652ff622fe0b916f32c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 26 Aug 2023 10:36:17 +0100 Subject: [PATCH 8576/9987] adding easyconfigs: TXR-291-GCCcore-12.2.0.eb --- .../t/TXR/TXR-291-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100755 easybuild/easyconfigs/t/TXR/TXR-291-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/t/TXR/TXR-291-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/TXR/TXR-291-GCCcore-12.2.0.eb new file mode 100755 index 00000000000..4fce2a7c5cc --- /dev/null +++ b/easybuild/easyconfigs/t/TXR/TXR-291-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'TXR' +version = '291' + +homepage = "https://www.nongnu.org/txr/" +description = """TXR is a pragmatic, convenient tool ready to take on your daily hacking challenges with its dual + personality: its whole-document pattern matching and extraction language for scraping information from arbitrary text + sources, and its powerful data-processing language to slice through problems like a hot knife through butter. Many + tasks can be accomplished with TXR "one liners" directly from your system prompt.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://www.kylheku.com/cgit/txr/snapshot/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ad79db569cedd48e24b03344597e3fda72637f32724f26be0e90e7f99bdd2582'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [('libffi', '3.4.4')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'tools' From 205eaa747c8773c6ac4077022a94935ba2b030ed Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 26 Aug 2023 10:42:55 +0100 Subject: [PATCH 8577/9987] adding easyconfigs: SUNDIALS-6.6.0-foss-2022b.eb --- .../s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100755 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb new file mode 100755 index 00000000000..043d83c6d48 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '6.6.0' + +homepage = 'https://computing.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f90029b8da846c8faff5530fd1fa4847079188d040554f55c1d5d1e04743d29d'] + +builddependencies = [('CMake', '3.24.3')] + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' From c7e5cfdec1cab1b23b4e8735500972f75cf67766 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 26 Aug 2023 10:59:55 +0100 Subject: [PATCH 8578/9987] adding easyconfigs: FreeImage-3.18.0-GCCcore-12.2.0.eb --- .../FreeImage-3.18.0-GCCcore-12.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100755 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.2.0.eb new file mode 100755 index 00000000000..a06e1d1dbf0 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FreeImage' +version = '3.18.0' + +homepage = 'http://freeimage.sourceforge.net' +description = """FreeImage is an Open Source library project for developers who would like to support popular graphics +image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to +use, fast, multithreading safe.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'cstd': 'c++14'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s3180.zip'] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip + '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # %(name)s-%(version)s-fix-makefile.patch +] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('zlib', '1.2.12')] + +skipsteps = ['configure'] + +buildopts = ['', '-f Makefile.fip'] + +installopts = [ + "INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib", + "-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib", +] + +_incs = ['include/FreeImage%s.h' % x for x in ['', 'Plus']] +_libs = ['lib/libfreeimage%s.%s' % (x, y) for x in ['', 'plus'] for y in ['a', SHLIB_EXT]] + +sanity_check_paths = { + 'files': _incs + _libs, + 'dirs': [], +} + +moduleclass = 'vis' From 7d7e3c49512e62f4bddeddf495b5d98248a7fbc9 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 26 Aug 2023 11:16:44 +0100 Subject: [PATCH 8579/9987] adding easyconfigs: tbb-2021.10.0-GCCcore-12.2.0.eb and patches: tbb-2021.10.0_null-address.patch --- .../t/tbb/tbb-2021.10.0-GCCcore-12.2.0.eb | 35 +++++++++++++++++++ .../t/tbb/tbb-2021.10.0_null-address.patch | 27 ++++++++++++++ 2 files changed, 62 insertions(+) create mode 100755 easybuild/easyconfigs/t/tbb/tbb-2021.10.0-GCCcore-12.2.0.eb create mode 100755 easybuild/easyconfigs/t/tbb/tbb-2021.10.0_null-address.patch diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.10.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tbb/tbb-2021.10.0-GCCcore-12.2.0.eb new file mode 100755 index 00000000000..440038e0c83 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.10.0-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'tbb' +version = '2021.10.0' + +homepage = 'https://github.com/oneapi-src/oneTBB' +description = """Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that + take full advantage of multicore performance, that are portable, composable and have future-proof scalability.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/oneapi-src/oneTBB/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_null-address.patch'] +checksums = [ + {'v2021.10.0.tar.gz': '487023a955e5a3cc6d3a0d5f89179f9b6c0ae7222613a7185b0227ba0c83700b'}, + {'tbb-2021.10.0_null-address.patch': '9deb243eb9d9d86f37f5e1e919cf8ff440c8b9be9c00ec14fddc437e433f0d1c'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [('hwloc', '2.8.0')] + +# https://github.com/oneapi-src/oneTBB/issues/843#issuecomment-1152646035 +configopts = '-DCMAKE_CXX_FLAGS="-Wno-error=stringop-overflow $CMAKE_CXX_FLAGS"' + +sanity_check_paths = { + 'files': ['lib/libtbb.%s' % SHLIB_EXT, 'lib/libtbbmalloc.%s' % SHLIB_EXT], + 'dirs': ['lib', 'include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-2021.10.0_null-address.patch b/easybuild/easyconfigs/t/tbb/tbb-2021.10.0_null-address.patch new file mode 100755 index 00000000000..bca22750292 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-2021.10.0_null-address.patch @@ -0,0 +1,27 @@ +From c61f113e6c6904a1ce6b2f53805c84dc8a2ab5ef Mon Sep 17 00:00:00 2001 +From: cunshunxia +Date: Thu, 24 Aug 2023 02:08:50 +0000 +Subject: [PATCH] fix compiler error of address will never be NULL + +--- + test/common/doctest.h | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/test/common/doctest.h b/test/common/doctest.h +index 8714c5b260..413a5b3fe6 100644 +--- a/test/common/doctest.h ++++ b/test/common/doctest.h +@@ -1555,10 +1555,13 @@ DOCTEST_CLANG_SUPPRESS_WARNING_WITH_PUSH("-Wunused-comparison") + , m_at(at) {} + + DOCTEST_NOINLINE operator Result() { ++// TODO: upstream the change to doctest : Work-around for the warning: 'address will never be NULL' ++DOCTEST_GCC_SUPPRESS_WARNING_WITH_PUSH("-Waddress") + // this is needed only for MSVC 2015 + DOCTEST_MSVC_SUPPRESS_WARNING_WITH_PUSH(4800) // 'int': forcing value to bool + bool res = static_cast(lhs); + DOCTEST_MSVC_SUPPRESS_WARNING_POP ++DOCTEST_GCC_SUPPRESS_WARNING_POP + if(m_at & assertType::is_false) { //!OCLINT bitwise operator in conditional + res = !res; + } From 674d937fe377f76e0c28b879f4f9d5f293941d88 Mon Sep 17 00:00:00 2001 From: stefan-wolfsheimer Date: Mon, 28 Aug 2023 10:09:10 +0200 Subject: [PATCH 8580/9987] Update easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb index c4a1a99a25b..3c25df1bded 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb @@ -15,6 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), + ('Autotools', '20220317'), ('Meson', '1.1.1'), ('Ninja', '1.11.1'), ('pkgconf', '1.9.5'), From 3db0eed4d81573588fd66951e1c98f3bcf18f172 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Aug 2023 10:13:51 +0200 Subject: [PATCH 8581/9987] adding easyconfigs: TensorFlow-2.13.0-foss-2022b.eb, dill-0.3.7-GCCcore-12.2.0.eb, nsync-1.26.0-GCCcore-12.2.0.eb, JsonCpp-1.9.5-GCCcore-12.2.0.eb, Bazel-6.3.1-GCCcore-12.2.0.eb --- .../b/Bazel/Bazel-6.3.1-GCCcore-12.2.0.eb | 25 ++ .../d/dill/dill-0.3.7-GCCcore-12.2.0.eb | 27 ++ .../j/JsonCpp/JsonCpp-1.9.5-GCCcore-12.2.0.eb | 29 +++ .../n/nsync/nsync-1.26.0-GCCcore-12.2.0.eb | 26 ++ .../TensorFlow-2.13.0-foss-2022b.eb | 232 ++++++++++++++++++ 5 files changed, 339 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/d/dill/dill-0.3.7-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/nsync/nsync-1.26.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..fd7d093741d --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +name = 'Bazel' +version = '6.3.1' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +checksums = ['2676319e86c5aeab142dccd42434364a33aa330a091c13562b7de87a10e68775'] + +builddependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8'), + ('Zip', '3.0'), +] + +dependencies = [('Java', '11', '', SYSTEM)] + +runtest = True +testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.7-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..69f1f370a90 --- /dev/null +++ b/easybuild/easyconfigs/d/dill/dill-0.3.7-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'dill' +version = '0.3.7' + +homepage = 'https://pypi.org/project/dill/' +description = """dill extends python's pickle module for serializing and de-serializing python objects to the majority + of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse + of which is converting a byte stream back to on python object hierarchy.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['cc1c8b182eb3013e24bd475ff2e9295af86c1a38eb1aff128dac8962a9ce3c03'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b74a74ba9ca --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.5' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['f409856e5920c18d0c2fb85276e24ee607d2a09b5e7d5f0a371368903c275da2'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.26.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.26.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..80b697617ee --- /dev/null +++ b/easybuild/easyconfigs/n/nsync/nsync-1.26.0-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeNinja' + +name = 'nsync' +version = '1.26.0' + +homepage = 'https://github.com/google/nsync' +description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/google/nsync/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['80fc1e605bb3cf5f272811ece39c4fb6761ffcb9b30563301845cc9ff381eb8b'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2022b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2022b.eb new file mode 100644 index 00000000000..71c1957b3f0 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2022b.eb @@ -0,0 +1,232 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.13.0' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '6.3.1'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.38.1', '-nodocs'), + ('pybind11', '2.10.3'), + ('UnZip', '6.0'), + # System protobuf doesn't seem to work: https://github.com/tensorflow/tensorflow/issues/61593 + # So don't add it here +] +dependencies = [ + ('Python', '3.10.8'), + ('h5py', '3.8.0'), + ('cURL', '7.86.0'), + ('dill', '0.3.7'), + ('double-conversion', '3.2.1'), + ('flatbuffers', '23.1.4'), + ('giflib', '5.2.1'), + ('hwloc', '2.8.0'), + ('ICU', '72.1'), + ('JsonCpp', '1.9.5'), + ('libjpeg-turbo', '2.1.4'), + ('NASM', '2.15.05'), + ('nsync', '1.26.0'), + ('SQLite', '3.39.4'), + ('patchelf', '0.17.2'), + ('protobuf-python', '4.23.0'), + ('libpng', '1.6.38'), + ('snappy', '1.1.9'), + ('zlib', '1.2.12'), + # Dependencies of grpcio + ('OpenSSL', '1.1', '', SYSTEM), + ('RE2', '2023-03-01'), +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('wrapt', '1.15.0', { + 'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'], + }), + ('termcolor', '2.3.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475'], + }), + ('tensorflow-estimator', version, { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['6f868284eaa654ae3aa7cacdbef2175d0909df9fcf11374f5166f8bf475952aa'], + }), + ('Werkzeug', '2.3.6', { + 'checksums': ['98c774df2f91b05550078891dee5f0eb0cb797a522c757a2452b9cee5b202330'], + }), + ('tensorboard-plugin-wit', '1.8.1', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard-data-server', '0.7.1', { + 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', + 'checksums': ['9938bd39f5041797b33921066fba0eab03a0dd10d1887a05e62ae58841ad4c3f'], + }), + ('Markdown', '3.4.4', { + 'checksums': ['225c6123522495d4119a90b3a3ba31a1e87a70369e03f14799ea9c0d7183a3d6'], + }), + ('grpcio', '1.56.2', { + 'modulename': 'grpc', + 'preinstallopts': "GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s " + + " ".join(["GRPC_PYTHON_BUILD_SYSTEM_%s=True" % i for i in + ( + 'OPENSSL', + 'ZLIB', + 'RE2', + # 'ABSL', + )]), + 'checksums': ['0ff789ae7d8ddd76d2ac02e7d13bfef6fc4928ac01e1dcaa182be51b6bcc0aaa'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('pyasn1-modules', '0.3.0', { + 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', + 'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'], + }), + ('cachetools', '5.3.1', { + 'checksums': ['dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b'], + }), + ('google-auth', '2.22.0', { + 'modulename': 'google.auth', + 'checksums': ['164cba9af4e6e4e40c3a4f90a1a6c12ee56f14c0b4868d1ca91b32826ab334ce'], + }), + ('google-auth-oauthlib', '1.0.0', { + 'checksums': ['e375064964820b47221a7e1b7ee1fd77051b6323c3f9e3e19785f78ab67ecfc5'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ab69961ebddbddc83f5fa2ff9233572bdad5b883778c35e4fe94bf1798bd8481'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('keras', '2.13.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5ce5f706f779fa7330e63632f327b75ce38144a120376b2ae1917c00fa6136af'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + # Required by tests + ('portpicker', '1.5.2', { + 'checksums': ['c55683ad725f5c00a41bc7db0225223e8be024b1fa564d039ed3390e4fd48fb3'], + }), + # System dependencies + ('tblib', '2.0.0', { + 'checksums': ['a6df30f272c08bf8be66e0775fad862005d950a6b8449b94f7c788731d70ecd7'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + # Optional profile plugin + dependency + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.13.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['472d1cb85d7087c5294131eb640bd771f5515ecc4867030c7904718be7fc19c1'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.11.0_disable-avx512-extensions.patch', + 'TensorFlow-2.13.0_add-default-shell-env.patch', + 'TensorFlow-2.13.0_add-missing-snappy-function.patch', + 'TensorFlow-2.13.0_add-missing-system-absl-py-target.patch', + 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', + 'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch', + 'TensorFlow-2.13.0_fix-protobuf-compatibility.patch', + 'TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch', + 'TensorFlow-2.13.0_remove-libclang-dep.patch', + 'TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch', + 'TensorFlow-2.13.0_unpin-gast-version.patch', + ], + 'checksums': [ + {'v2.13.0.tar.gz': 'e58c939079588623e6fa1d054aec2f90f95018266e0a970fd353a5244f5173dc'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch': + '6fe50faab28387c622c68dc3fc0cbfb2a51000cd750c1a82f8420b54fcd2509f'}, + {'TensorFlow-2.11.0_disable-avx512-extensions.patch': + 'fb8e7694b5d2377cc44e6674ff85a7c50dc725f2f507cbcfda65f129f534b1cc'}, + {'TensorFlow-2.13.0_add-default-shell-env.patch': + 'a94b2e007bff5a08ec4e6ec3043985907a69e9eeaea69dc4fe2aa15d15b75aef'}, + {'TensorFlow-2.13.0_add-missing-snappy-function.patch': + 'aa063123dfea0072a80ae873bc4ffddc4e98497edb316114ba6c6f57ff18803c'}, + {'TensorFlow-2.13.0_add-missing-system-absl-py-target.patch': + '94bc3b155840af942437d06c43830dabf41d94391daf61e1d0add0a7bf20a538'}, + {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': + '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'}, + {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch': + 'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'}, + {'TensorFlow-2.13.0_fix-protobuf-compatibility.patch': + 'a9658c035b663da1b7d1983a8e37883cc40c1c0cfa22132bb7fe19c4cbc9712a'}, + {'TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch': + '39f1cbecad4b3723481b30f18f16363ab1837c8749ee197ec88b92b493e9df67'}, + {'TensorFlow-2.13.0_remove-libclang-dep.patch': + 'f0d067d129e817b0d371c4e48a4a1ac08f80a2c137d52b05a3c7c4370dcbd1e5'}, + {'TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch': + 'f22757250181b6165e4b2ef1e199bd4cb344a9429be5a1086638f25bcbf650fc'}, + {'TensorFlow-2.13.0_unpin-gast-version.patch': + '61e0c9b67aa6c48176fcbb429bf6aa36c4fdde604c82c02f58a043412fecf285'}, + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' From bfb00dede891fa593adcbca6cd76841b94a31f98 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 28 Aug 2023 10:26:04 +0200 Subject: [PATCH 8582/9987] Update style --- ...gurable-http-proxy-4.5.6-GCCcore-12.3.0.eb | 32 +++ .../Jupyter-bundle-20230823-GCCcore-12.3.0.eb | 2 +- .../JupyterHub-4.0.2-GCCcore-12.3.0.eb | 130 ++++++++++++ .../JupyterLab-4.0.5-GCCcore-12.3.0.eb | 73 +++++++ ...pyter-server-proxy-4.0.0-GCCcore-12.3.0.eb | 45 +++++ .../jupyter-server-2.7.2-GCCcore-12.3.0.eb | 190 ++++++++++++++++++ .../nbclassic-1.0.0-GCCcore-12.3.0.eb | 51 +++++ .../notebook/notebook-7.0.2-GCCcore-12.3.0.eb | 41 ++++ .../p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb | 29 +++ .../p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb | 29 +++ 10 files changed, 621 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fc58c50bc75 --- /dev/null +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'Binary' + +name = 'configurable-http-proxy' +version = '4.5.6' + +homepage = 'https://github.com/jupyterhub/configurable-http-proxy' +description = """HTTP proxy for node.js including a REST API for updating the routing table. + Developed as a part of the Jupyter Hub multi-user server.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/jupyterhub/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4d9d94d0e6e44542ac973963b8a6545f4b40c0a2995e865ae9c80a2279e1e0ab'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('nodejs', '18.17.1'), +] + +install_cmd = "npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz" + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb index 44bade9c3dd..5a6c5aaea78 100644 --- a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb @@ -19,6 +19,6 @@ dependencies = [ ('notebook', '7.0.2'), ('nbclassic', '1.0.0'), ('jupyter-server-proxy', '4.0.0'), - ('jupyterlmod','4.0.3'), + ('jupyterlmod', '4.0.3'), ('jupyter-resource-usage', '1.0.0'), ] diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..6e978bce869 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,130 @@ +easyblock = 'PythonBundle' + +name = 'JupyterHub' +version = '4.0.2' + +homepage = 'https://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed + for centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('setuptools-rust', '1.6.0'), # Needed for bcrypt + ('Rust', '1.70.0'), # Needed for bcrypt +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('Mako', '1.2.4'), + ('configurable-http-proxy', '4.5.6'), + ('OpenSSL', '1.1', '', SYSTEM), + ('tornado', '6.3.2'), + ('PycURL', '7.45.2'), # optional, recommended with large number of users +] + +sanity_pip_check = True +use_pip = True + +local_batchspawner_commit = '2a9eda060a875a2b65ca9521368fe052a09c3266' + +exts_list = [ + ('certipy', '0.1.3', { + 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], + }), + ('pamela', '1.1.0', { + 'checksums': ['d4b139fe600e192e176a2a368059207a6bffa0e7879879b13f4fcba0163481be'], + }), + ('greenlet', '2.0.2', { + 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('SQLAlchemy', '2.0.20', { + 'checksums': ['ca8a5ff2aa7f3ade6c498aaafce25b1eaeabe4e42b73e25519183e4566a16fc6'], + }), + ('alembic', '1.11.3', { + 'checksums': ['3db4ce81a9072e1b5aa44c2d202add24553182672a12daf21608d6f62a8f9cf9'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('pyOpenSSL', '23.2.0', { + 'modulename': 'OpenSSL', + 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], + }), + ('ruamel.yaml', '0.17.32', { + 'checksums': ['ec939063761914e14542972a5cba6d33c23b0859ab6342f61cf070cfc600efc2'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jupyter-telemetry', '0.1.0', { + 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', + 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], + }), + ('prometheus_client', '0.17.1', { + 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], + }), + ('jupyterhub', version, { + 'checksums': ['d4e450eed8d90dfbcf0eca08f00f2093a0bce74dc51f7cfc0b7057f602341a1d'], + }), + # Needs unreleased features for JupyterHub 4.X compatibility, hence install from commit + ('batchspawner', '1.2.0-%s' % local_batchspawner_commit, { + 'source_urls': [GITHUB_SOURCE], + 'sources': { + 'filename': '%(name)s-%(version)s.tar.gz', + 'download_filename': '%s.tar.gz' % local_batchspawner_commit + }, + 'checksums': ['d5cf239ba75522d928ed33971c180532f590131905c42eac1be2651ccad85283'], + }), + ('jupyterhub-systemdspawner', '1.0.1', { + 'modulename': 'systemdspawner', + 'checksums': ['8d614f19d89564321fe55d80ecd134a0e2bf276274d45861495c9bb5a80add28'], + }), + ('jupyterhub-simplespawner', '0.1', { + 'modulename': 'simplespawner', + 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], + }), + ('ldap3', '2.9.1', { + 'checksums': ['f3e7fc4718e3f09dda568b57100095e0ce58633bcabbed8667ce3f8fbaa4229f'], + }), + ('jupyterhub-ldapauthenticator', '1.3.2', { + 'modulename': 'ldapauthenticator', + 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('jupyterhub-jwtauthenticator-v2', '2.0.3', { + 'modulename': 'jwtauthenticator', + 'checksums': ['b94b6dff8246250904c5ee511da3f062680eb657dabe766d75993cbe72747d41'], + }), + ('onetimepass', '1.0.1', { + 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], + }), + ('bcrypt', '4.0.1', { + 'checksums': ['27d375903ac8261cfe4047f6709d16f7d18d39b1ec92aaf72af989552a650ebd'], + }), + ('jupyterhub-nativeauthenticator', '1.2.0', { + 'modulename': 'nativeauthenticator', + 'checksums': ['826228e6e9ca37736361e2e60c5723e245ec72e34fdc42cc218fc54a67f968e1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..19c7e8a6710 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '4.0.5' + +homepage = 'https://jupyter.org/' +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), +] + +# keep user's configuration in their home directory +# note: '~' is not expanded by JupyterLab +modluafooter = """ +setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) +setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) +""" +modtclfooter = """ +setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" +setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" +""" +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('json5', '0.9.14', { + 'checksums': ['9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02'], + }), + ('jupyterlab_server', '2.24.0', { + 'checksums': ['4e6f99e0a5579bbbc32e449c4dbb039561d4f1a7827d5733273ed56738f21f07'], + }), + ('jupyter-lsp', '2.2.0', { + 'checksums': ['8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1'], + }), + ('async-lru', '2.0.4', { + 'checksums': ['b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627'], + }), + ('jupyterlab', version, { + 'checksums': ['de49deb75f9b9aec478ed04754cbefe9c5d22fd796a5783cdc65e212983d3611'], + }), +] + +local_binaries = [ + 'jupyter-lab', + 'jupyter-labextension', + 'jupyter-labhub', +] +sanity_check_paths = { + 'files': [], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter lab --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5c1a64b9090 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server-proxy' +version = '4.0.0' + +homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' +description = """Jupyter Server Proxy lets you run arbitrary external processes +(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) +alongside your notebook server and provide authenticated web access to them +using a path like /rstudio next to others like /lab. Alongside the python +package that provides the main functionality, the JupyterLab extension +(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window +to get to RStudio for example.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), + ('OpenSSL', '1.1', '', SYSTEM), + ('aiohttp', '3.8.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('simpervisor', '1.0.0', { + 'checksums': ['7eb87ca86d5e276976f5bb0290975a05d452c6a7b7f58062daea7d8369c823c1'], + }), + ('jupyter_server_proxy', version, { + 'checksums': ['f5dc12dd204baca71b013df3522c14403692a2d37cb7adcd77851dbab71533b5'], + }), +] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..76b36f7551f --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb @@ -0,0 +1,190 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = "2.7.2" + +homepage = 'https://jupyter.org/' +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST +endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and +Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.1.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('PyYAML', '6.0'), + ('PyZMQ', '25.1.1'), + ('tornado', '6.3.2'), +] + +sanity_pip_check = True +use_pip = True + +# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them +# use the versions published in a single release commit instead of blindly pushing to last available version, +# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa + +exts_list = [ + ('hatch_nodejs_version', '0.3.1', { + 'checksums': ['0e55fd713d92c5c1ccfee778efecaa780fd8bcd276d4ca7aff9f6791f6f76d9c'], + }), + ('hatch_jupyter_builder', '0.8.3', { + 'checksums': ['0dbd14a8aef6636764f88a8fd1fcc9a91921e5c50356e6aab251782f264ae960'], + }), + ('websocket-client', '1.6.1', { + 'modulename': 'websocket', + 'checksums': ['c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd'], + }), + ('terminado', '0.17.1', { + 'checksums': ['6ccbbcd3a4f8a25a5ec04991f39a0b8db52dfcd487ea0e578d977e6752380333'], + }), + ('Send2Trash', '1.8.2', { + 'checksums': ['c132d59fa44b9ca2b1699af5c86f57ce9f4c5eb56629d5d55fbb7a35f84e2312'], + }), + ('prometheus_client', '0.17.1', { + 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], + }), + ('overrides', '7.4.0', { + 'checksums': ['9502a3cca51f4fac40b5feca985b6703a5c1f6ad815588a7ca9e285b9dca6757'], + }), + ('jupyter_core', '5.3.1', { + 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], + }), + ('fastjsonschema', '2.18.0', { + 'checksums': ['e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd'], + }), + ('tinycss2', '1.2.1', { + 'checksums': ['8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627'], + }), + ('pandocfilters', '1.5.0', { + 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], + }), + ('mistune', '3.0.1', { + 'checksums': ['e912116c13aa0944f9dc530db38eb88f6a77087ab128f49f84a48f4c05ea163c'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.3', { + 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], + }), + ('jupyterlab_pygments', '0.2.2', { + 'checksums': ['7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('bleach', '6.0.0', { + 'checksums': ['1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('nbformat', '5.9.2', { + 'checksums': ['5f98b5ba1997dff175e77e0c17d5c10a96eaed2cbd1de3533d1fc35d5e111192'], + }), + ('nbclient', '0.8.0', { + 'checksums': ['f9b179cd4b2d7bca965f900a2ebf0db4a12ebff2f36a711cb66861e4ae158e55'], + }), + ('jupyter_client', '8.3.0', { + 'checksums': ['3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f'], + }), + ('nbconvert', '7.7.4', { + 'checksums': ['1113d039fa3fc3a846ffa5a3b0a019e85aaa94c566a09fa0c400fb7638e46087'], + }), + ('jupyter_server_terminals', '0.4.4', { + 'checksums': ['57ab779797c25a7ba68e97bcfb5d7740f2b5e8a83b5e8102b10438041a7eac5d'], + }), + ('rfc3986_validator', '0.1.1', { + 'checksums': ['3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055'], + }), + ('rfc3339_validator', '0.1.4', { + 'checksums': ['138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b'], + }), + ('rpds_py', '0.9.2', { + 'modulename': 'rpds', + 'checksums': ['8d70e8f14900f2657c249ea4def963bed86a29b81f81f5b76b5a9215680de945'], + }), + ('referencing', '0.30.2', { + 'checksums': ['794ad8003c65938edcdbc027f1933215e0d0ccc0291e3ce20a4d87432b59efc0'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jsonschema_specifications', '2023.7.1', { + 'checksums': ['c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb'], + }), + ('jsonschema', '4.18.0', { + 'checksums': ['8caf5b57a990a98e9b39832ef3cb35c176fe331414252b6e1b26fd5866f891a4'], + }), + ('jupyter_events', '0.7.0', { + 'checksums': ['7be27f54b8388c03eefea123a4f79247c5b9381c49fb1cd48615ee191eb12615'], + }), + ('argon2-cffi-bindings', '21.2.0', { + 'modulename': '_argon2_cffi_bindings', + 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], + }), + ('argon2_cffi', '23.1.0', { + 'modulename': 'argon2', + 'checksums': ['879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.7.1', { + 'checksums': ['44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780'], + }), + ('jupyter_server', version, { + 'checksums': ['d64fb4e593907290e5df916e3c9399c15ab2cd7bdb71cbcd1d36452dbfb30523'], + }), + ('jupyterlab_widgets', '3.0.8', { + 'checksums': ['d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a'], + }), + ('widgetsnbextension', '4.0.8', { + 'checksums': ['9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17'], + }), + ('comm', '0.1.4', { + 'checksums': ['354e40a59c9dd6db50c5cc6b4acc887d82e9603787f83b68c01a80a923984d15'], + }), + ('ipywidgets', '8.1.0', { + 'checksums': ['ce97dd90525b3066fd00094690964e7eac14cf9b7745d35565b5eeac20cce687'], + }), + # The following few extensions are needed for e.g. JupyterLab but also nbclassic. + # Avoid duplication by making it part of this bundle + ('notebook_shim', '0.2.3', { + 'checksums': ['f69388ac283ae008cd506dda10d0288b09a017d822d5e8c7129a152cbd3ce7e9'], + }), + ('nest_asyncio', '1.5.7', { + 'checksums': ['6a80f7b98f24d9083ed24608977c09dd608d83f91cccc24c9d2cba6d10e01c10'], + }), + ('ipykernel', '6.25.1', { + 'checksums': ['050391364c0977e768e354bdb60cbbfbee7cbb943b1af1618382021136ffd42f'], + }), + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('debugpy', '1.6.7.post1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['1093a5c541af079c13ac8c70ab8b24d1d35c8cacb676306cf11e57f699c02926'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter'], + 'dirs': ['share/jupyter', 'etc/jupyter'], +} + +sanity_check_commands = ['jupyter --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ba066826463 --- /dev/null +++ b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonPackage' + +name = 'nbclassic' +version = "1.0.0" + +homepage = 'https://jupyter.org/' +description = """NbClassic provides a backwards compatible Jupyter Notebook interface + that you can install side-by-side with the latest versions: That way, you can fearlessly + upgrade without worrying about your classic extensions and customizations breaking.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.1.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('jupyter-server', '2.7.2'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['nbclassic-1.0.0_fix_setup_version.patch'] +checksums = [ + {'nbclassic-1.0.0.tar.gz': '0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'}, + {'nbclassic-1.0.0_fix_setup_version.patch': 'c26d91ac1d0cea2b361b2619076acdaf5fcd5ff2363d9e5f5e1bd737b4b50736'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +local_binaries = [ + 'jupyter-nbclassic', + 'jupyter-nbclassic-bundlerextension', + 'jupyter-nbclassic-extension', + 'jupyter-nbclassic-serverextension', +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ['jupyter nbclassic --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ca17d12903e --- /dev/null +++ b/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'notebook' +version = '7.0.2' + +homepage = 'https://jupyter.org/' +description = """The Jupyter Notebook is the original web application for creating and + sharing computational documents. It offers a simple, streamlined, document-centric experience.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), + ('JupyterLab', '4.0.5'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['d70d6a07418c829bd5f54337ce993b7105261d9026f9d3fe68e9b8aa1a20da9a'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/jupyter-notebook'], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter notebook --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..19a3a61687c --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '25.1.1' + +homepage = 'https://www.zeromq.org/bindings:python' +description = "Python bindings for ZeroMQ" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['259c22485b71abacdfa8bf79720cd7bcf4b9d128b30ea554f01ae71fdbfdaa23'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('ZeroMQ', '4.3.4'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'zmq'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2e8cc5dfd61 --- /dev/null +++ b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'PycURL' +version = '7.45.2' + +homepage = 'http://pycurl.io/' +description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL + from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of + features.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5730590be0271364a5bddd9e245c9cc0fb710c4cbacbdd95264a3122d23224ca'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('cURL', '8.0.1'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From 6a06ea45ce8b123a516af0d378ff5a016317b1af Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 28 Aug 2023 10:28:05 +0200 Subject: [PATCH 8583/9987] Delete configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb --- ...gurable-http-proxy-4.5.6-GCCcore-12.3.0.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb deleted file mode 100644 index fc58c50bc75..00000000000 --- a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'Binary' - -name = 'configurable-http-proxy' -version = '4.5.6' - -homepage = 'https://github.com/jupyterhub/configurable-http-proxy' -description = """HTTP proxy for node.js including a REST API for updating the routing table. - Developed as a part of the Jupyter Hub multi-user server.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = ['https://github.com/jupyterhub/%(name)s/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['4d9d94d0e6e44542ac973963b8a6545f4b40c0a2995e865ae9c80a2279e1e0ab'] - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('nodejs', '18.17.1'), -] - -install_cmd = "npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz" - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': [], -} - -sanity_check_commands = ['%(name)s --version'] - -moduleclass = 'tools' From 76571e205723337b88f36ee8856902178bab37f1 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 28 Aug 2023 10:28:29 +0200 Subject: [PATCH 8584/9987] Delete JupyterHub-4.0.2-GCCcore-12.3.0.eb --- .../JupyterHub-4.0.2-GCCcore-12.3.0.eb | 130 ------------------ 1 file changed, 130 deletions(-) delete mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb deleted file mode 100644 index 6e978bce869..00000000000 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,130 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'JupyterHub' -version = '4.0.2' - -homepage = 'https://jupyter.org' -description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed - for centralized deployments in companies, university classrooms and research labs.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('setuptools-rust', '1.6.0'), # Needed for bcrypt - ('Rust', '1.70.0'), # Needed for bcrypt -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('Mako', '1.2.4'), - ('configurable-http-proxy', '4.5.6'), - ('OpenSSL', '1.1', '', SYSTEM), - ('tornado', '6.3.2'), - ('PycURL', '7.45.2'), # optional, recommended with large number of users -] - -sanity_pip_check = True -use_pip = True - -local_batchspawner_commit = '2a9eda060a875a2b65ca9521368fe052a09c3266' - -exts_list = [ - ('certipy', '0.1.3', { - 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], - }), - ('pamela', '1.1.0', { - 'checksums': ['d4b139fe600e192e176a2a368059207a6bffa0e7879879b13f4fcba0163481be'], - }), - ('greenlet', '2.0.2', { - 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], - }), - ('async_generator', '1.10', { - 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], - }), - ('SQLAlchemy', '2.0.20', { - 'checksums': ['ca8a5ff2aa7f3ade6c498aaafce25b1eaeabe4e42b73e25519183e4566a16fc6'], - }), - ('alembic', '1.11.3', { - 'checksums': ['3db4ce81a9072e1b5aa44c2d202add24553182672a12daf21608d6f62a8f9cf9'], - }), - ('oauthlib', '3.2.2', { - 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], - }), - ('pyOpenSSL', '23.2.0', { - 'modulename': 'OpenSSL', - 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], - }), - ('ruamel.yaml', '0.17.32', { - 'checksums': ['ec939063761914e14542972a5cba6d33c23b0859ab6342f61cf070cfc600efc2'], - }), - ('ruamel.yaml.clib', '0.2.7', { - 'modulename': False, - 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], - }), - ('python-json-logger', '2.0.7', { - 'modulename': 'pythonjsonlogger', - 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], - }), - ('jupyter-telemetry', '0.1.0', { - 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', - 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], - }), - ('prometheus_client', '0.17.1', { - 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], - }), - ('jupyterhub', version, { - 'checksums': ['d4e450eed8d90dfbcf0eca08f00f2093a0bce74dc51f7cfc0b7057f602341a1d'], - }), - # Needs unreleased features for JupyterHub 4.X compatibility, hence install from commit - ('batchspawner', '1.2.0-%s' % local_batchspawner_commit, { - 'source_urls': [GITHUB_SOURCE], - 'sources': { - 'filename': '%(name)s-%(version)s.tar.gz', - 'download_filename': '%s.tar.gz' % local_batchspawner_commit - }, - 'checksums': ['d5cf239ba75522d928ed33971c180532f590131905c42eac1be2651ccad85283'], - }), - ('jupyterhub-systemdspawner', '1.0.1', { - 'modulename': 'systemdspawner', - 'checksums': ['8d614f19d89564321fe55d80ecd134a0e2bf276274d45861495c9bb5a80add28'], - }), - ('jupyterhub-simplespawner', '0.1', { - 'modulename': 'simplespawner', - 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], - }), - ('ldap3', '2.9.1', { - 'checksums': ['f3e7fc4718e3f09dda568b57100095e0ce58633bcabbed8667ce3f8fbaa4229f'], - }), - ('jupyterhub-ldapauthenticator', '1.3.2', { - 'modulename': 'ldapauthenticator', - 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], - }), - ('PyJWT', '2.8.0', { - 'modulename': 'jwt', - 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], - }), - ('jupyterhub-jwtauthenticator-v2', '2.0.3', { - 'modulename': 'jwtauthenticator', - 'checksums': ['b94b6dff8246250904c5ee511da3f062680eb657dabe766d75993cbe72747d41'], - }), - ('onetimepass', '1.0.1', { - 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], - }), - ('bcrypt', '4.0.1', { - 'checksums': ['27d375903ac8261cfe4047f6709d16f7d18d39b1ec92aaf72af989552a650ebd'], - }), - ('jupyterhub-nativeauthenticator', '1.2.0', { - 'modulename': 'nativeauthenticator', - 'checksums': ['826228e6e9ca37736361e2e60c5723e245ec72e34fdc42cc218fc54a67f968e1'], - }), -] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -sanity_check_commands = ['%(namelower)s --help'] - -moduleclass = 'tools' From 4e43c9442e1d05b81e784d2bbf25572b2fc22c53 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 28 Aug 2023 10:28:38 +0200 Subject: [PATCH 8585/9987] Delete JupyterLab-4.0.5-GCCcore-12.3.0.eb --- .../JupyterLab-4.0.5-GCCcore-12.3.0.eb | 73 ------------------- 1 file changed, 73 deletions(-) delete mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb deleted file mode 100644 index 19c7e8a6710..00000000000 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb +++ /dev/null @@ -1,73 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'JupyterLab' -version = '4.0.5' - -homepage = 'https://jupyter.org/' -description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar - building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, - etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter - Notebook.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('jupyter-server', '2.7.2'), -] - -# keep user's configuration in their home directory -# note: '~' is not expanded by JupyterLab -modluafooter = """ -setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) -setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) -""" -modtclfooter = """ -setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" -setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" -""" -sanity_pip_check = True -use_pip = True - -exts_list = [ - ('json5', '0.9.14', { - 'checksums': ['9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02'], - }), - ('jupyterlab_server', '2.24.0', { - 'checksums': ['4e6f99e0a5579bbbc32e449c4dbb039561d4f1a7827d5733273ed56738f21f07'], - }), - ('jupyter-lsp', '2.2.0', { - 'checksums': ['8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1'], - }), - ('async-lru', '2.0.4', { - 'checksums': ['b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627'], - }), - ('jupyterlab', version, { - 'checksums': ['de49deb75f9b9aec478ed04754cbefe9c5d22fd796a5783cdc65e212983d3611'], - }), -] - -local_binaries = [ - 'jupyter-lab', - 'jupyter-labextension', - 'jupyter-labhub', -] -sanity_check_paths = { - 'files': [], - 'dirs': ['etc/jupyter', 'share/jupyter'], -} - -sanity_check_commands = ['jupyter lab --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} - -moduleclass = 'tools' From e114af308a020b802a4bfa0af573966808a92edc Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 28 Aug 2023 10:28:52 +0200 Subject: [PATCH 8586/9987] Delete jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb --- ...pyter-server-proxy-4.0.0-GCCcore-12.3.0.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb deleted file mode 100644 index 5c1a64b9090..00000000000 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'jupyter-server-proxy' -version = '4.0.0' - -homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' -description = """Jupyter Server Proxy lets you run arbitrary external processes -(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) -alongside your notebook server and provide authenticated web access to them -using a path like /rstudio next to others like /lab. Alongside the python -package that provides the main functionality, the JupyterLab extension -(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window -to get to RStudio for example.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('jupyter-server', '2.7.2'), - ('OpenSSL', '1.1', '', SYSTEM), - ('aiohttp', '3.8.5'), -] - -sanity_pip_check = True -use_pip = True - -exts_list = [ - ('simpervisor', '1.0.0', { - 'checksums': ['7eb87ca86d5e276976f5bb0290975a05d452c6a7b7f58062daea7d8369c823c1'], - }), - ('jupyter_server_proxy', version, { - 'checksums': ['f5dc12dd204baca71b013df3522c14403692a2d37cb7adcd77851dbab71533b5'], - }), -] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From 52d8bb9ca0935fbb8c51b8ef3dcaea15b14a7420 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 28 Aug 2023 10:29:00 +0200 Subject: [PATCH 8587/9987] Delete jupyter-server-2.7.2-GCCcore-12.3.0.eb --- .../jupyter-server-2.7.2-GCCcore-12.3.0.eb | 190 ------------------ 1 file changed, 190 deletions(-) delete mode 100644 easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb deleted file mode 100644 index 76b36f7551f..00000000000 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,190 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'jupyter-server' -version = "2.7.2" - -homepage = 'https://jupyter.org/' -description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST -endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and -Voila.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('maturin', '1.1.0'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('PyYAML', '6.0'), - ('PyZMQ', '25.1.1'), - ('tornado', '6.3.2'), -] - -sanity_pip_check = True -use_pip = True - -# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them -# use the versions published in a single release commit instead of blindly pushing to last available version, -# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa - -exts_list = [ - ('hatch_nodejs_version', '0.3.1', { - 'checksums': ['0e55fd713d92c5c1ccfee778efecaa780fd8bcd276d4ca7aff9f6791f6f76d9c'], - }), - ('hatch_jupyter_builder', '0.8.3', { - 'checksums': ['0dbd14a8aef6636764f88a8fd1fcc9a91921e5c50356e6aab251782f264ae960'], - }), - ('websocket-client', '1.6.1', { - 'modulename': 'websocket', - 'checksums': ['c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd'], - }), - ('terminado', '0.17.1', { - 'checksums': ['6ccbbcd3a4f8a25a5ec04991f39a0b8db52dfcd487ea0e578d977e6752380333'], - }), - ('Send2Trash', '1.8.2', { - 'checksums': ['c132d59fa44b9ca2b1699af5c86f57ce9f4c5eb56629d5d55fbb7a35f84e2312'], - }), - ('prometheus_client', '0.17.1', { - 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], - }), - ('overrides', '7.4.0', { - 'checksums': ['9502a3cca51f4fac40b5feca985b6703a5c1f6ad815588a7ca9e285b9dca6757'], - }), - ('jupyter_core', '5.3.1', { - 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], - }), - ('fastjsonschema', '2.18.0', { - 'checksums': ['e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd'], - }), - ('tinycss2', '1.2.1', { - 'checksums': ['8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627'], - }), - ('pandocfilters', '1.5.0', { - 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], - }), - ('mistune', '3.0.1', { - 'checksums': ['e912116c13aa0944f9dc530db38eb88f6a77087ab128f49f84a48f4c05ea163c'], - }), - ('deprecation', '2.1.0', { - 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], - }), - ('jupyter_packaging', '0.12.3', { - 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], - }), - ('jupyterlab_pygments', '0.2.2', { - 'checksums': ['7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d'], - }), - ('defusedxml', '0.7.1', { - 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], - }), - ('bleach', '6.0.0', { - 'checksums': ['1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414'], - }), - ('arrow', '1.2.3', { - 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], - }), - ('nbformat', '5.9.2', { - 'checksums': ['5f98b5ba1997dff175e77e0c17d5c10a96eaed2cbd1de3533d1fc35d5e111192'], - }), - ('nbclient', '0.8.0', { - 'checksums': ['f9b179cd4b2d7bca965f900a2ebf0db4a12ebff2f36a711cb66861e4ae158e55'], - }), - ('jupyter_client', '8.3.0', { - 'checksums': ['3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f'], - }), - ('nbconvert', '7.7.4', { - 'checksums': ['1113d039fa3fc3a846ffa5a3b0a019e85aaa94c566a09fa0c400fb7638e46087'], - }), - ('jupyter_server_terminals', '0.4.4', { - 'checksums': ['57ab779797c25a7ba68e97bcfb5d7740f2b5e8a83b5e8102b10438041a7eac5d'], - }), - ('rfc3986_validator', '0.1.1', { - 'checksums': ['3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055'], - }), - ('rfc3339_validator', '0.1.4', { - 'checksums': ['138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b'], - }), - ('rpds_py', '0.9.2', { - 'modulename': 'rpds', - 'checksums': ['8d70e8f14900f2657c249ea4def963bed86a29b81f81f5b76b5a9215680de945'], - }), - ('referencing', '0.30.2', { - 'checksums': ['794ad8003c65938edcdbc027f1933215e0d0ccc0291e3ce20a4d87432b59efc0'], - }), - ('python-json-logger', '2.0.7', { - 'modulename': 'pythonjsonlogger', - 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], - }), - ('jsonschema_specifications', '2023.7.1', { - 'checksums': ['c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb'], - }), - ('jsonschema', '4.18.0', { - 'checksums': ['8caf5b57a990a98e9b39832ef3cb35c176fe331414252b6e1b26fd5866f891a4'], - }), - ('jupyter_events', '0.7.0', { - 'checksums': ['7be27f54b8388c03eefea123a4f79247c5b9381c49fb1cd48615ee191eb12615'], - }), - ('argon2-cffi-bindings', '21.2.0', { - 'modulename': '_argon2_cffi_bindings', - 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], - }), - ('argon2_cffi', '23.1.0', { - 'modulename': 'argon2', - 'checksums': ['879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08'], - }), - ('sniffio', '1.3.0', { - 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], - }), - ('anyio', '3.7.1', { - 'checksums': ['44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780'], - }), - ('jupyter_server', version, { - 'checksums': ['d64fb4e593907290e5df916e3c9399c15ab2cd7bdb71cbcd1d36452dbfb30523'], - }), - ('jupyterlab_widgets', '3.0.8', { - 'checksums': ['d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a'], - }), - ('widgetsnbextension', '4.0.8', { - 'checksums': ['9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17'], - }), - ('comm', '0.1.4', { - 'checksums': ['354e40a59c9dd6db50c5cc6b4acc887d82e9603787f83b68c01a80a923984d15'], - }), - ('ipywidgets', '8.1.0', { - 'checksums': ['ce97dd90525b3066fd00094690964e7eac14cf9b7745d35565b5eeac20cce687'], - }), - # The following few extensions are needed for e.g. JupyterLab but also nbclassic. - # Avoid duplication by making it part of this bundle - ('notebook_shim', '0.2.3', { - 'checksums': ['f69388ac283ae008cd506dda10d0288b09a017d822d5e8c7129a152cbd3ce7e9'], - }), - ('nest_asyncio', '1.5.7', { - 'checksums': ['6a80f7b98f24d9083ed24608977c09dd608d83f91cccc24c9d2cba6d10e01c10'], - }), - ('ipykernel', '6.25.1', { - 'checksums': ['050391364c0977e768e354bdb60cbbfbee7cbb943b1af1618382021136ffd42f'], - }), - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('debugpy', '1.6.7.post1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - 'checksums': ['1093a5c541af079c13ac8c70ab8b24d1d35c8cacb676306cf11e57f699c02926'], - }), -] - -sanity_check_paths = { - 'files': ['bin/jupyter'], - 'dirs': ['share/jupyter', 'etc/jupyter'], -} - -sanity_check_commands = ['jupyter --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From 1855f7ab27a49426a820ccb6ca1d2bf9fb2674e7 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 28 Aug 2023 10:29:11 +0200 Subject: [PATCH 8588/9987] Delete nbclassic-1.0.0-GCCcore-12.3.0.eb --- .../nbclassic-1.0.0-GCCcore-12.3.0.eb | 51 ------------------- 1 file changed, 51 deletions(-) delete mode 100644 easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb deleted file mode 100644 index ba066826463..00000000000 --- a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'nbclassic' -version = "1.0.0" - -homepage = 'https://jupyter.org/' -description = """NbClassic provides a backwards compatible Jupyter Notebook interface - that you can install side-by-side with the latest versions: That way, you can fearlessly - upgrade without worrying about your classic extensions and customizations breaking.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('maturin', '1.1.0'), -] -dependencies = [ - ('Python', '3.11.3'), - ('jupyter-server', '2.7.2'), -] - -sources = [SOURCE_TAR_GZ] -patches = ['nbclassic-1.0.0_fix_setup_version.patch'] -checksums = [ - {'nbclassic-1.0.0.tar.gz': '0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'}, - {'nbclassic-1.0.0_fix_setup_version.patch': 'c26d91ac1d0cea2b361b2619076acdaf5fcd5ff2363d9e5f5e1bd737b4b50736'}, -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -local_binaries = [ - 'jupyter-nbclassic', - 'jupyter-nbclassic-bundlerextension', - 'jupyter-nbclassic-extension', - 'jupyter-nbclassic-serverextension', -] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_binaries], - 'dirs': [], -} - -sanity_check_commands = ['jupyter nbclassic --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From dab0026c4d4b174f3c4e7eb18b557015b81ae9b9 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 28 Aug 2023 10:29:18 +0200 Subject: [PATCH 8589/9987] Delete notebook-7.0.2-GCCcore-12.3.0.eb --- .../notebook/notebook-7.0.2-GCCcore-12.3.0.eb | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb deleted file mode 100644 index ca17d12903e..00000000000 --- a/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'notebook' -version = '7.0.2' - -homepage = 'https://jupyter.org/' -description = """The Jupyter Notebook is the original web application for creating and - sharing computational documents. It offers a simple, streamlined, document-centric experience.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('jupyter-server', '2.7.2'), - ('JupyterLab', '4.0.5'), -] - -sources = [SOURCE_TAR_GZ] -checksums = ['d70d6a07418c829bd5f54337ce993b7105261d9026f9d3fe68e9b8aa1a20da9a'] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -sanity_check_paths = { - 'files': ['bin/jupyter-notebook'], - 'dirs': ['etc/jupyter', 'share/jupyter'], -} - -sanity_check_commands = ['jupyter notebook --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From 751b508f8c8299b428dee99a4bc240220d90e07b Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 28 Aug 2023 10:29:25 +0200 Subject: [PATCH 8590/9987] Delete PyZMQ-25.1.1-GCCcore-12.3.0.eb --- .../p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb deleted file mode 100644 index 19a3a61687c..00000000000 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyZMQ' -version = '25.1.1' - -homepage = 'https://www.zeromq.org/bindings:python' -description = "Python bindings for ZeroMQ" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['259c22485b71abacdfa8bf79720cd7bcf4b9d128b30ea554f01ae71fdbfdaa23'] - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), - ('ZeroMQ', '4.3.4'), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True -options = {'modulename': 'zmq'} - -moduleclass = 'devel' From e6b213a533dd128d94554f1c1e4a59217719b24e Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Mon, 28 Aug 2023 10:29:32 +0200 Subject: [PATCH 8591/9987] Delete PycURL-7.45.2-GCCcore-12.3.0.eb --- .../p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb deleted file mode 100644 index 2e8cc5dfd61..00000000000 --- a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. -easyblock = 'PythonPackage' - -name = 'PycURL' -version = '7.45.2' - -homepage = 'http://pycurl.io/' -description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL - from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of - features.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['5730590be0271364a5bddd9e245c9cc0fb710c4cbacbdd95264a3122d23224ca'] - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('cURL', '8.0.1'), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -moduleclass = 'tools' From 5a67c73c53a34b0ad3323c4456798951775a448f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Aug 2023 12:36:26 +0200 Subject: [PATCH 8592/9987] Add patches --- ...sorFlow-2.13.0_add-default-shell-env.patch | 30 + ...w-2.13.0_add-missing-snappy-function.patch | 109 +++ ....0_add-missing-system-absl-py-target.patch | 17 + ..._add-missing-system-protobuf-targets.patch | 25 + ...orFlow-2.13.0_exclude-xnnpack-on-ppc.patch | 46 + ...ow-2.13.0_fix-protobuf-compatibility.patch | 55 ++ ...-2.13.0_remove-io-gcs-filesystem-dep.patch | 13 + ...ensorFlow-2.13.0_remove-libclang-dep.patch | 21 + ...w-2.13.0_revert-to-flatbuffers-2.0.6.patch | 911 ++++++++++++++++++ ...TensorFlow-2.13.0_unpin-gast-version.patch | 18 + 10 files changed, 1245 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-default-shell-env.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-snappy-function.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-absl-py-target.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-protobuf-compatibility.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-libclang-dep.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_unpin-gast-version.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-default-shell-env.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-default-shell-env.patch new file mode 100644 index 00000000000..9b1f3171369 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-default-shell-env.patch @@ -0,0 +1,30 @@ +Make TensorFlow use the environment as set by EasyBuild + +See https://github.com/tensorflow/tensorflow/pull/61591 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/lite/build_def.bzl b/tensorflow/lite/build_def.bzl +index 842879a0536..20fb9c1fb9d 100644 +--- a/tensorflow/lite/build_def.bzl ++++ b/tensorflow/lite/build_def.bzl +@@ -356,6 +356,7 @@ def _gen_selected_ops_impl(ctx): + executable = ctx.executable._generate_op_registrations, + mnemonic = "OpRegistration", + progress_message = "gen_selected_ops", ++ use_default_shell_env = True, + ) + + gen_selected_ops_rule = rule( +diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl +index e9f5e5aaffa..c22efdc20cf 100644 +--- a/tensorflow/tensorflow.bzl ++++ b/tensorflow/tensorflow.bzl +@@ -1282,6 +1282,7 @@ def _generate_op_reg_offsets_impl(ctx): + tools = [ctx.executable._offset_counter], + executable = ctx.executable._offset_counter, + arguments = [args], ++ use_default_shell_env = True, + ) + + generate_op_reg_offsets = rule( diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-snappy-function.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-snappy-function.patch new file mode 100644 index 00000000000..0ec4867dc7b --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-snappy-function.patch @@ -0,0 +1,109 @@ +Add functions introduced in Snappy 1.1.10 missing in our 1.1.9: +https://github.com/google/snappy/commit/9758c9dfd744f252bf3351c1a212e05c9f7fc857 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tsl/platform/default/port.cc b/tensorflow/tsl/platform/default/port.cc +index 0a1052aded5..92f0dbdb7d6 100644 +--- a/tensorflow/tsl/platform/default/port.cc ++++ b/tensorflow/tsl/platform/default/port.cc +@@ -39,6 +39,7 @@ limitations under the License. + #include + #ifdef TF_USE_SNAPPY + #include "snappy.h" ++#include "snappy-sinksource.h" + #endif + #if (defined(__APPLE__) && defined(__MACH__)) || defined(__FreeBSD__) || \ + defined(__HAIKU__) +@@ -307,6 +308,80 @@ int NUMAGetMemAffinity(const void* addr) { + return node; + } + ++namespace { ++ // Backport from Snappy 1.1.10: https://github.com/google/snappy/commit/9758c9dfd744f252bf3351c1a212e05c9f7fc857 ++ static_assert(SNAPPY_VERSION == 0x010109, "Backport is only for 1.1.9"); ++ // A `Source` implementation that yields the contents of an `iovec` array. Note ++ // that `total_size` is the total number of bytes to be read from the elements ++ // of `iov` (_not_ the total number of elements in `iov`). ++ class SnappyIOVecReader : public snappy::Source { ++ public: ++ SnappyIOVecReader(const struct iovec* iov, size_t total_size) ++ : curr_iov_(iov), ++ curr_pos_(total_size > 0 ? reinterpret_cast(iov->iov_base) ++ : nullptr), ++ curr_size_remaining_(total_size > 0 ? iov->iov_len : 0), ++ total_size_remaining_(total_size) { ++ // Skip empty leading `iovec`s. ++ if (total_size > 0 && curr_size_remaining_ == 0) Advance(); ++ } ++ ++ ~SnappyIOVecReader() = default; ++ ++ size_t Available() const { return total_size_remaining_; } ++ ++ const char* Peek(size_t* len) { ++ *len = curr_size_remaining_; ++ return curr_pos_; ++ } ++ ++ void Skip(size_t n) { ++ while (n >= curr_size_remaining_ && n > 0) { ++ n -= curr_size_remaining_; ++ Advance(); ++ } ++ curr_size_remaining_ -= n; ++ total_size_remaining_ -= n; ++ curr_pos_ += n; ++ } ++ ++ private: ++ // Advances to the next nonempty `iovec` and updates related variables. ++ void Advance() { ++ do { ++ assert(total_size_remaining_ >= curr_size_remaining_); ++ total_size_remaining_ -= curr_size_remaining_; ++ if (total_size_remaining_ == 0) { ++ curr_pos_ = nullptr; ++ curr_size_remaining_ = 0; ++ return; ++ } ++ ++curr_iov_; ++ curr_pos_ = reinterpret_cast(curr_iov_->iov_base); ++ curr_size_remaining_ = curr_iov_->iov_len; ++ } while (curr_size_remaining_ == 0); ++ } ++ ++ // The `iovec` currently being read. ++ const struct iovec* curr_iov_; ++ // The location in `curr_iov_` currently being read. ++ const char* curr_pos_; ++ // The amount of unread data in `curr_iov_`. ++ size_t curr_size_remaining_; ++ // The amount of unread data in the entire input array. ++ size_t total_size_remaining_; ++ }; ++ ++ void Snappy_RawCompressFromIOVec(const struct iovec* iov, size_t uncompressed_length, ++ char* compressed, size_t* compressed_length) { ++ SnappyIOVecReader reader(iov, uncompressed_length); ++ snappy::UncheckedByteArraySink writer(compressed); ++ snappy::Compress(&reader, &writer); ++ ++ // Compute how many bytes were added. ++ *compressed_length = writer.CurrentDestination() - compressed; ++ } ++} + + bool Snappy_Compress(const char* input, size_t length, string* output) { + #ifdef TF_USE_SNAPPY +@@ -325,8 +400,8 @@ bool Snappy_CompressFromIOVec(const struct iovec* iov, + #ifdef TF_USE_SNAPPY + output->resize(snappy::MaxCompressedLength(uncompressed_length)); + size_t outlen; +- snappy::RawCompressFromIOVec(iov, uncompressed_length, &(*output)[0], +- &outlen); ++ Snappy_RawCompressFromIOVec(iov, uncompressed_length, &(*output)[0], ++ &outlen); + output->resize(outlen); + return true; + #else diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-absl-py-target.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-absl-py-target.patch new file mode 100644 index 00000000000..5a68faf7479 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-absl-py-target.patch @@ -0,0 +1,17 @@ +Add a missing target for the absl-py SYSTEMLIB +From https://github.com/tensorflow/tensorflow/pull/60636 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/systemlibs/absl_py.absl.flags.BUILD b/third_party/systemlibs/absl_py.absl.flags.BUILD +index 4049989ae2fda..d92f4949df1a5 100644 +--- a/third_party/systemlibs/absl_py.absl.flags.BUILD ++++ b/third_party/systemlibs/absl_py.absl.flags.BUILD +@@ -5,3 +5,7 @@ package(default_visibility = ["//visibility:public"]) + py_library( + name = "flags", + ) ++ ++py_library( ++ name = "argparse_flags", ++) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch new file mode 100644 index 00000000000..54491dab40a --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch @@ -0,0 +1,25 @@ +Fix error: +ERROR: /dev/shm/TensorFlow/tensorflow-2.13.0/tensorflow/python/framework/BUILD:2454:17: no such target '@com_google_protobuf//:well_known_types_py_pb2_genproto': target 'well_known_types_py_pb2_genproto' not declared in package '' defined by /dev/shm/s3248973-EasyBuild/TensorFlow/2.13.0/foss-2022a/TensorFlow/bazel-root/663b1bf019e1a9ec9827eae691fce071/external/com_google_protobuf/BUILD.bazel and referenced by '//tensorflow/python/framework:cpp_shape_inference_proto_py_genproto' +ERROR: Analysis of target '//tensorflow/tools/pip_package:build_pip_package' failed; build aborted: + +Using solution from +https://github.com/tensorflow/tensorflow/issues/60667#issuecomment-1563522589 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/systemlibs/protobuf.BUILD b/third_party/systemlibs/protobuf.BUILD +index 4d05ab28d12..cb48d375b27 100644 +--- a/third_party/systemlibs/protobuf.BUILD ++++ b/third_party/systemlibs/protobuf.BUILD +@@ -111,3 +116,10 @@ py_library( + visibility = ["//visibility:public"], + deps = [dep + "_proto" for dep in proto[1][1]], + ) for proto in WELL_KNOWN_PROTO_MAP.items()] ++ ++py_proto_library( ++ name = "well_known_types_py_pb2", ++ include = ".", ++ srcs = [proto[1][0] for proto in WELL_KNOWN_PROTO_MAP.items()], ++ visibility = ["//visibility:public"], ++) +\ No newline at end of file diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch new file mode 100644 index 00000000000..da2b07cc736 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch @@ -0,0 +1,46 @@ +XNNPACK is not supported on PowerPC so disable it by default. +See https://github.com/tensorflow/tensorflow/issues/58768 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/lite/BUILD b/tensorflow/lite/BUILD +index c08cd7bcec5..c23c0eedac8 100644 +--- a/tensorflow/lite/BUILD ++++ b/tensorflow/lite/BUILD +@@ -829,6 +829,8 @@ cc_library( + defines = select({ + ":tflite_kernel_use_xnnpack_false": [], + ":tflite_with_xnnpack_explicit_false": [], ++ # XNNPACK is not supported on PPC ++ "//tensorflow:linux_ppc64le": [], + "//conditions:default": [ + "TFLITE_KERNEL_USE_XNNPACK", + ], +@@ -864,9 +866,11 @@ cc_library( + # Note: adding ":tflite_with_xnnpack_enabled" to the values of following + # configuration conditions will make TFLite interpreter to apply XNNPACK + # delegate by default. +- deps = [ +- ":tflite_with_xnnpack_enabled", +- ], ++ deps = select({ ++ # XNNPACK is not supported on PPC ++ "//tensorflow:linux_ppc64le": [], ++ "//conditions:default": [":tflite_with_xnnpack_enabled"], ++ }), + ) + + cc_library( +diff --git a/tensorflow/lite/kernels/BUILD b/tensorflow/lite/kernels/BUILD +index 9c3ebdfaaba..a042f8ccedb 100644 +--- a/tensorflow/lite/kernels/BUILD ++++ b/tensorflow/lite/kernels/BUILD +@@ -735,6 +735,8 @@ BUILTIN_KERNEL_DEPS = [ + ], + }) + select({ + "//tensorflow/lite:tflite_with_xnnpack_explicit_false": [], ++ # XNNPACK is not supported on PPC ++ "//tensorflow:linux_ppc64le": [], + "//conditions:default": [ + "@XNNPACK//:xnnpack_for_tflite", + ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-protobuf-compatibility.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-protobuf-compatibility.patch new file mode 100644 index 00000000000..1eae68fd6bf --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-protobuf-compatibility.patch @@ -0,0 +1,55 @@ +From 297fe6b883c362d328327c8fd99566ec7f579d10 Mon Sep 17 00:00:00 2001 +From: Sagun Bajra +Date: Wed, 3 May 2023 19:45:00 -0700 +Subject: [PATCH] Update proto insertion to be compatible with all verstions of + the proto library. + +PiperOrigin-RevId: 529263012 +--- + .../eager/small_constants_optimizer.cc | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) + +diff --git a/tensorflow/core/common_runtime/eager/small_constants_optimizer.cc b/tensorflow/core/common_runtime/eager/small_constants_optimizer.cc +index 0d6b36ea3d1bd..7d43f29029f0c 100644 +--- a/tensorflow/core/common_runtime/eager/small_constants_optimizer.cc ++++ b/tensorflow/core/common_runtime/eager/small_constants_optimizer.cc +@@ -171,17 +171,17 @@ std::vector FoldBoolInputTensor( + + // Promote the true branch when input_value is `true`. + if (attr_key == "then_branch") { +- if (input_value) node_def.mutable_attr()->emplace("f", attr_value); ++ if (input_value) node_def.mutable_attr()->insert({"f", attr_value}); + continue; + } + // Promote the false branch when input_value is `false`. + if (attr_key == "else_branch") { +- if (!input_value) node_def.mutable_attr()->emplace("f", attr_value); ++ if (!input_value) node_def.mutable_attr()->insert({"f", attr_value}); + continue; + } + + // All other attributes should be copied over. +- node_def.mutable_attr()->emplace(attr_key, attr_value); ++ node_def.mutable_attr()->insert({attr_key, attr_value}); + } + } + +@@ -213,15 +213,15 @@ std::vector FoldBoolInputTensor( + const_tensor->set_op("Const"); + AttrValue dtype_value; + dtype_value.set_type(DT_BOOL); +- const_tensor->mutable_attr()->emplace("dtype", dtype_value); ++ const_tensor->mutable_attr()->insert({"dtype", dtype_value}); + AttrValue tensor_value; + auto* tensor = tensor_value.mutable_tensor(); + tensor->set_dtype(DT_BOOL); + tensor->mutable_tensor_shape(); + tensor->add_bool_val(true); +- const_tensor->mutable_attr()->emplace("value", tensor_value); ++ const_tensor->mutable_attr()->insert({"value", tensor_value}); + +- // Mark the currend `FunctionDef` as folded and return the results. ++ // Mark the current `FunctionDef` as folded and return the results. + results.push_back(std::move(result)); + folded_functions.insert(folded_function_name); + return results; diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch new file mode 100644 index 00000000000..5064cce0e95 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch @@ -0,0 +1,13 @@ +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index e77e6f81449..29fdd4a1d91 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -99,8 +98,6 @@ REQUIRED_PACKAGES = [ + 'termcolor >= 1.1.0', + 'typing_extensions>=3.6.6,<4.6.0', + 'wrapt >= 1.11.0', +- 'tensorflow-io-gcs-filesystem >= 0.23.1;platform_machine!="arm64" or ' + +- 'platform_system!="Darwin"', + # grpcio does not build correctly on big-endian machines due to lack of + # BoringSSL support. + # See https://github.com/tensorflow/tensorflow/issues/17882. diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-libclang-dep.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-libclang-dep.patch new file mode 100644 index 00000000000..b50c85d7889 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-libclang-dep.patch @@ -0,0 +1,21 @@ +libclang was introduced in +https://github.com/tensorflow/tensorflow/commit/c211472000ff57bac7fcec9b0465cf73b37bf135 +> This is in preparation to open-source TF's TFRT backend. +> TFRT generates code using libclang python bindings as part of the build. +Hence it is not currently used and as it is not (easily) available for all architectures +simply remove it. + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index e77e6f81449..29fdd4a1d91 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -89,7 +89,6 @@ REQUIRED_PACKAGES = [ + 'gast >= 0.2.1, <= 0.4.0', + 'google_pasta >= 0.1.1', + 'h5py >= 2.9.0', +- 'libclang >= 13.0.0', + 'numpy >= 1.22, <= 1.24.3', + 'opt_einsum >= 2.3.2', + 'packaging', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch new file mode 100644 index 00000000000..45cdc96c12a --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch @@ -0,0 +1,911 @@ +Revert the commits upgrading the flatbuffer dependency: +https://github.com/tensorflow/tensorflow/commit/86e0d74bb6a87020c1683629eb7d1dc73949377f +https://github.com/tensorflow/tensorflow/commit/c3a577817f650f75f8df075fce7a542c42596e9d + +Then manually re-add double-colons (`sed -i 's/flatbuffers::/::flatbuffers::/g'`) to reduce diff + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h b/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h +index 2e3f07e46b6..001813510ec +--- a/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h ++++ b/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h +@@ -20,13 +20,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + namespace tflite { + namespace gpu { + namespace cl { +diff --git a/tensorflow/lite/delegates/gpu/cl/serialization_generated.h b/tensorflow/lite/delegates/gpu/cl/serialization_generated.h +index c0d14cfbc02..529e7c96bf0 +--- a/tensorflow/lite/delegates/gpu/cl/serialization_generated.h ++++ b/tensorflow/lite/delegates/gpu/cl/serialization_generated.h +@@ -20,15 +20,8 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- +-#include "gpu_model_generated.h" + #include "serialization_base_generated.h" ++#include "gpu_model_generated.h" + + namespace tflite { + namespace gpu { +diff --git a/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h b/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h +index 3fa3fbaf816..17357af7f0e +--- a/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h ++++ b/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h +@@ -19,13 +19,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + #include "serialization_base_generated.h" + + namespace tflite { +diff --git a/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h b/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h +index 59831408614..4087c486d19 +--- a/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h ++++ b/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h +@@ -20,13 +20,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + namespace tflite { + namespace gpu { + namespace data { +@@ -270,28 +263,14 @@ enum class Layout : int8_t { + + inline const Layout (&EnumValuesLayout())[7] { + static const Layout values[] = { +- Layout::UNKNOWN, +- Layout::HWC, +- Layout::BHWC, +- Layout::HWDC, +- Layout::BHWDC, +- Layout::LINEAR, +- Layout::HW +- }; ++ Layout::UNKNOWN, Layout::HWC, Layout::BHWC, Layout::HWDC, ++ Layout::BHWDC, Layout::LINEAR, Layout::HW}; + return values; + } + + inline const char * const *EnumNamesLayout() { +- static const char * const names[8] = { +- "UNKNOWN", +- "HWC", +- "BHWC", +- "HWDC", +- "BHWDC", +- "LINEAR", +- "HW", +- nullptr +- }; ++ static const char *const names[8] = {"UNKNOWN", "HWC", "BHWC", "HWDC", ++ "BHWDC", "LINEAR", "HW", nullptr}; + return names; + } + +@@ -1834,15 +1813,22 @@ inline ::flatbuffers::Offset CreateGPUOperation( + ::flatbuffers::Offset arguments = 0, + ::flatbuffers::Offset<::flatbuffers::String> code = 0, + ::flatbuffers::Offset work_group_size = 0, +- ::flatbuffers::Offset<::flatbuffers::Vector<::flatbuffers::Offset>> compiler_options = 0, +- tflite::gpu::data::TensorToGrid tensor_to_grid = tflite::gpu::data::TensorToGrid::CUSTOM, ++ ::flatbuffers::Offset<::flatbuffers::Vector< ++ ::flatbuffers::Offset>> ++ compiler_options = 0, ++ tflite::gpu::data::TensorToGrid tensor_to_grid = ++ tflite::gpu::data::TensorToGrid::CUSTOM, + uint64_t flops = 0, + ::flatbuffers::Offset definition = 0, + int32_t grid_dimension = 0, + ::flatbuffers::Offset work_group_launch_order = 0, + ::flatbuffers::Offset grid_size = 0, +- ::flatbuffers::Offset<::flatbuffers::Vector<::flatbuffers::Offset<::flatbuffers::String>>> src_tensors_names = 0, +- ::flatbuffers::Offset<::flatbuffers::Vector<::flatbuffers::Offset<::flatbuffers::String>>> dst_tensors_names = 0, ++ ::flatbuffers::Offset< ++ ::flatbuffers::Vector<::flatbuffers::Offset<::flatbuffers::String>>> ++ src_tensors_names = 0, ++ ::flatbuffers::Offset< ++ ::flatbuffers::Vector<::flatbuffers::Offset<::flatbuffers::String>>> ++ dst_tensors_names = 0, + ::flatbuffers::Offset work_groups_count = 0) { + GPUOperationBuilder builder_(_fbb); + builder_.add_flops(flops); +@@ -1866,35 +1852,29 @@ inline ::flatbuffers::Offset CreateGPUOperationDirect( + ::flatbuffers::Offset arguments = 0, + const char *code = nullptr, + ::flatbuffers::Offset work_group_size = 0, +- const std::vector<::flatbuffers::Offset> *compiler_options = nullptr, +- tflite::gpu::data::TensorToGrid tensor_to_grid = tflite::gpu::data::TensorToGrid::CUSTOM, ++ const std::vector<::flatbuffers::Offset> ++ *compiler_options = nullptr, ++ tflite::gpu::data::TensorToGrid tensor_to_grid = ++ tflite::gpu::data::TensorToGrid::CUSTOM, + uint64_t flops = 0, + ::flatbuffers::Offset definition = 0, + int32_t grid_dimension = 0, + ::flatbuffers::Offset work_group_launch_order = 0, + ::flatbuffers::Offset grid_size = 0, +- const std::vector<::flatbuffers::Offset<::flatbuffers::String>> *src_tensors_names = nullptr, +- const std::vector<::flatbuffers::Offset<::flatbuffers::String>> *dst_tensors_names = nullptr, ++ const std::vector<::flatbuffers::Offset<::flatbuffers::String>> ++ *src_tensors_names = nullptr, ++ const std::vector<::flatbuffers::Offset<::flatbuffers::String>> ++ *dst_tensors_names = nullptr, + ::flatbuffers::Offset work_groups_count = 0) { + auto code__ = code ? _fbb.CreateString(code) : 0; + auto compiler_options__ = compiler_options ? _fbb.CreateVector<::flatbuffers::Offset>(*compiler_options) : 0; + auto src_tensors_names__ = src_tensors_names ? _fbb.CreateVector<::flatbuffers::Offset<::flatbuffers::String>>(*src_tensors_names) : 0; + auto dst_tensors_names__ = dst_tensors_names ? _fbb.CreateVector<::flatbuffers::Offset<::flatbuffers::String>>(*dst_tensors_names) : 0; + return tflite::gpu::data::CreateGPUOperation( +- _fbb, +- arguments, +- code__, +- work_group_size, +- compiler_options__, +- tensor_to_grid, +- flops, +- definition, +- grid_dimension, +- work_group_launch_order, +- grid_size, +- src_tensors_names__, +- dst_tensors_names__, +- work_groups_count); ++ _fbb, arguments, code__, work_group_size, compiler_options__, ++ tensor_to_grid, flops, definition, grid_dimension, ++ work_group_launch_order, grid_size, src_tensors_names__, ++ dst_tensors_names__, work_groups_count); + } + + } // namespace data +diff --git a/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h b/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h +index 6c00ee4d0ae..8246a15622a 100644 +--- a/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h ++++ b/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h +@@ -20,13 +20,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + namespace tflite { + + struct ComputeSettings; +@@ -4112,10 +4105,10 @@ inline void ComputeSettings::UnPackTo(ComputeSettingsT *_o, const ::flatbuffers: + (void)_o; + (void)_resolver; + { auto _e = preference(); _o->preference = _e; } +- { auto _e = tflite_settings(); if (_e) { if(_o->tflite_settings) { _e->UnPackTo(_o->tflite_settings.get(), _resolver); } else { _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->tflite_settings) { _o->tflite_settings.reset(); } } ++ { auto _e = tflite_settings(); if (_e) { if(_o->tflite_settings) { _e->UnPackTo(_o->tflite_settings.get(), _resolver); } else { _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = model_namespace_for_statistics(); if (_e) _o->model_namespace_for_statistics = _e->str(); } + { auto _e = model_identifier_for_statistics(); if (_e) _o->model_identifier_for_statistics = _e->str(); } +- { auto _e = settings_to_test_locally(); if (_e) { if(_o->settings_to_test_locally) { _e->UnPackTo(_o->settings_to_test_locally.get(), _resolver); } else { _o->settings_to_test_locally = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->settings_to_test_locally) { _o->settings_to_test_locally.reset(); } } ++ { auto _e = settings_to_test_locally(); if (_e) { if(_o->settings_to_test_locally) { _e->UnPackTo(_o->settings_to_test_locally.get(), _resolver); } else { _o->settings_to_test_locally = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset ComputeSettings::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ComputeSettingsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -4207,7 +4200,7 @@ inline void NNAPISettings::UnPackTo(NNAPISettingsT *_o, const ::flatbuffers::res + { auto _e = model_token(); if (_e) _o->model_token = _e->str(); } + { auto _e = execution_preference(); _o->execution_preference = _e; } + { auto _e = no_of_nnapi_instances_to_cache(); _o->no_of_nnapi_instances_to_cache = _e; } +- { auto _e = fallback_settings(); if (_e) { if(_o->fallback_settings) { _e->UnPackTo(_o->fallback_settings.get(), _resolver); } else { _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->fallback_settings) { _o->fallback_settings.reset(); } } ++ { auto _e = fallback_settings(); if (_e) { if(_o->fallback_settings) { _e->UnPackTo(_o->fallback_settings.get(), _resolver); } else { _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = allow_nnapi_cpu_on_android_10_plus(); _o->allow_nnapi_cpu_on_android_10_plus = _e; } + { auto _e = execution_priority(); _o->execution_priority = _e; } + { auto _e = allow_dynamic_dimensions(); _o->allow_dynamic_dimensions = _e; } +@@ -4563,7 +4556,7 @@ inline void EdgeTpuDeviceSpec::UnPackTo(EdgeTpuDeviceSpecT *_o, const ::flatbuff + (void)_resolver; + { auto _e = platform_type(); _o->platform_type = _e; } + { auto _e = num_chips(); _o->num_chips = _e; } +- { auto _e = device_paths(); if (_e) { _o->device_paths.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->device_paths[_i] = _e->Get(_i)->str(); } } else { _o->device_paths.resize(0); } } ++ { auto _e = device_paths(); if (_e) { _o->device_paths.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->device_paths[_i] = _e->Get(_i)->str(); } } } + { auto _e = chip_family(); _o->chip_family = _e; } + } + +@@ -4632,7 +4625,7 @@ inline ::flatbuffers::Offset CreateEdgeTpuInactivePo + inline bool operator==(const EdgeTpuSettingsT &lhs, const EdgeTpuSettingsT &rhs) { + return + (lhs.inference_power_state == rhs.inference_power_state) && +- (lhs.inactive_power_configs.size() == rhs.inactive_power_configs.size() && std::equal(lhs.inactive_power_configs.cbegin(), lhs.inactive_power_configs.cend(), rhs.inactive_power_configs.cbegin(), [](std::unique_ptr const &a, std::unique_ptr const &b) { return (a == b) || (a && b && *a == *b); })) && ++ (lhs.inactive_power_configs == rhs.inactive_power_configs) && + (lhs.inference_priority == rhs.inference_priority) && + ((lhs.edgetpu_device_spec == rhs.edgetpu_device_spec) || (lhs.edgetpu_device_spec && rhs.edgetpu_device_spec && *lhs.edgetpu_device_spec == *rhs.edgetpu_device_spec)) && + (lhs.model_token == rhs.model_token) && +@@ -4657,7 +4650,7 @@ inline EdgeTpuSettingsT::EdgeTpuSettingsT(const EdgeTpuSettingsT &o) + hardware_cluster_ids(o.hardware_cluster_ids), + public_model_id(o.public_model_id) { + inactive_power_configs.reserve(o.inactive_power_configs.size()); +- for (const auto &inactive_power_configs_ : o.inactive_power_configs) { inactive_power_configs.emplace_back((inactive_power_configs_) ? new tflite::EdgeTpuInactivePowerConfigT(*inactive_power_configs_) : nullptr); } ++ for (const auto &v : o.inactive_power_configs) { inactive_power_configs.emplace_back((v) ? new tflite::EdgeTpuInactivePowerConfigT(*v) : nullptr); } + } + + inline EdgeTpuSettingsT &EdgeTpuSettingsT::operator=(EdgeTpuSettingsT o) FLATBUFFERS_NOEXCEPT { +@@ -4683,13 +4676,13 @@ inline void EdgeTpuSettings::UnPackTo(EdgeTpuSettingsT *_o, const ::flatbuffers: + (void)_o; + (void)_resolver; + { auto _e = inference_power_state(); _o->inference_power_state = _e; } +- { auto _e = inactive_power_configs(); if (_e) { _o->inactive_power_configs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->inactive_power_configs[_i]) { _e->Get(_i)->UnPackTo(_o->inactive_power_configs[_i].get(), _resolver); } else { _o->inactive_power_configs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->inactive_power_configs.resize(0); } } ++ { auto _e = inactive_power_configs(); if (_e) { _o->inactive_power_configs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->inactive_power_configs[_i]) { _e->Get(_i)->UnPackTo(_o->inactive_power_configs[_i].get(), _resolver); } else { _o->inactive_power_configs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = inference_priority(); _o->inference_priority = _e; } +- { auto _e = edgetpu_device_spec(); if (_e) { if(_o->edgetpu_device_spec) { _e->UnPackTo(_o->edgetpu_device_spec.get(), _resolver); } else { _o->edgetpu_device_spec = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->edgetpu_device_spec) { _o->edgetpu_device_spec.reset(); } } ++ { auto _e = edgetpu_device_spec(); if (_e) { if(_o->edgetpu_device_spec) { _e->UnPackTo(_o->edgetpu_device_spec.get(), _resolver); } else { _o->edgetpu_device_spec = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = model_token(); if (_e) _o->model_token = _e->str(); } + { auto _e = float_truncation_type(); _o->float_truncation_type = _e; } + { auto _e = qos_class(); _o->qos_class = _e; } +- { auto _e = hardware_cluster_ids(); if (_e) { _o->hardware_cluster_ids.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->hardware_cluster_ids[_i] = _e->Get(_i); } } else { _o->hardware_cluster_ids.resize(0); } } ++ { auto _e = hardware_cluster_ids(); if (_e) { _o->hardware_cluster_ids.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->hardware_cluster_ids[_i] = _e->Get(_i); } } } + { auto _e = public_model_id(); if (_e) _o->public_model_id = _e->str(); } + } + +@@ -4954,20 +4947,20 @@ inline void TFLiteSettings::UnPackTo(TFLiteSettingsT *_o, const ::flatbuffers::r + (void)_o; + (void)_resolver; + { auto _e = delegate(); _o->delegate = _e; } +- { auto _e = nnapi_settings(); if (_e) { if(_o->nnapi_settings) { _e->UnPackTo(_o->nnapi_settings.get(), _resolver); } else { _o->nnapi_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->nnapi_settings) { _o->nnapi_settings.reset(); } } +- { auto _e = gpu_settings(); if (_e) { if(_o->gpu_settings) { _e->UnPackTo(_o->gpu_settings.get(), _resolver); } else { _o->gpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->gpu_settings) { _o->gpu_settings.reset(); } } +- { auto _e = hexagon_settings(); if (_e) { if(_o->hexagon_settings) { _e->UnPackTo(_o->hexagon_settings.get(), _resolver); } else { _o->hexagon_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->hexagon_settings) { _o->hexagon_settings.reset(); } } +- { auto _e = xnnpack_settings(); if (_e) { if(_o->xnnpack_settings) { _e->UnPackTo(_o->xnnpack_settings.get(), _resolver); } else { _o->xnnpack_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->xnnpack_settings) { _o->xnnpack_settings.reset(); } } +- { auto _e = coreml_settings(); if (_e) { if(_o->coreml_settings) { _e->UnPackTo(_o->coreml_settings.get(), _resolver); } else { _o->coreml_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->coreml_settings) { _o->coreml_settings.reset(); } } +- { auto _e = cpu_settings(); if (_e) { if(_o->cpu_settings) { _e->UnPackTo(_o->cpu_settings.get(), _resolver); } else { _o->cpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->cpu_settings) { _o->cpu_settings.reset(); } } ++ { auto _e = nnapi_settings(); if (_e) { if(_o->nnapi_settings) { _e->UnPackTo(_o->nnapi_settings.get(), _resolver); } else { _o->nnapi_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = gpu_settings(); if (_e) { if(_o->gpu_settings) { _e->UnPackTo(_o->gpu_settings.get(), _resolver); } else { _o->gpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = hexagon_settings(); if (_e) { if(_o->hexagon_settings) { _e->UnPackTo(_o->hexagon_settings.get(), _resolver); } else { _o->hexagon_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = xnnpack_settings(); if (_e) { if(_o->xnnpack_settings) { _e->UnPackTo(_o->xnnpack_settings.get(), _resolver); } else { _o->xnnpack_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = coreml_settings(); if (_e) { if(_o->coreml_settings) { _e->UnPackTo(_o->coreml_settings.get(), _resolver); } else { _o->coreml_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = cpu_settings(); if (_e) { if(_o->cpu_settings) { _e->UnPackTo(_o->cpu_settings.get(), _resolver); } else { _o->cpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = max_delegated_partitions(); _o->max_delegated_partitions = _e; } +- { auto _e = edgetpu_settings(); if (_e) { if(_o->edgetpu_settings) { _e->UnPackTo(_o->edgetpu_settings.get(), _resolver); } else { _o->edgetpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->edgetpu_settings) { _o->edgetpu_settings.reset(); } } +- { auto _e = coral_settings(); if (_e) { if(_o->coral_settings) { _e->UnPackTo(_o->coral_settings.get(), _resolver); } else { _o->coral_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->coral_settings) { _o->coral_settings.reset(); } } +- { auto _e = fallback_settings(); if (_e) { if(_o->fallback_settings) { _e->UnPackTo(_o->fallback_settings.get(), _resolver); } else { _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->fallback_settings) { _o->fallback_settings.reset(); } } ++ { auto _e = edgetpu_settings(); if (_e) { if(_o->edgetpu_settings) { _e->UnPackTo(_o->edgetpu_settings.get(), _resolver); } else { _o->edgetpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = coral_settings(); if (_e) { if(_o->coral_settings) { _e->UnPackTo(_o->coral_settings.get(), _resolver); } else { _o->coral_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = fallback_settings(); if (_e) { if(_o->fallback_settings) { _e->UnPackTo(_o->fallback_settings.get(), _resolver); } else { _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = disable_default_delegates(); _o->disable_default_delegates = _e; } +- { auto _e = stable_delegate_loader_settings(); if (_e) { if(_o->stable_delegate_loader_settings) { _e->UnPackTo(_o->stable_delegate_loader_settings.get(), _resolver); } else { _o->stable_delegate_loader_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->stable_delegate_loader_settings) { _o->stable_delegate_loader_settings.reset(); } } +- { auto _e = google_edgetpu_settings(); if (_e) { if(_o->google_edgetpu_settings) { _e->UnPackTo(_o->google_edgetpu_settings.get(), _resolver); } else { _o->google_edgetpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->google_edgetpu_settings) { _o->google_edgetpu_settings.reset(); } } +- { auto _e = compilation_caching_settings(); if (_e) { if(_o->compilation_caching_settings) { _e->UnPackTo(_o->compilation_caching_settings.get(), _resolver); } else { _o->compilation_caching_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->compilation_caching_settings) { _o->compilation_caching_settings.reset(); } } ++ { auto _e = stable_delegate_loader_settings(); if (_e) { if(_o->stable_delegate_loader_settings) { _e->UnPackTo(_o->stable_delegate_loader_settings.get(), _resolver); } else { _o->stable_delegate_loader_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = google_edgetpu_settings(); if (_e) { if(_o->google_edgetpu_settings) { _e->UnPackTo(_o->google_edgetpu_settings.get(), _resolver); } else { _o->google_edgetpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = compilation_caching_settings(); if (_e) { if(_o->compilation_caching_settings) { _e->UnPackTo(_o->compilation_caching_settings.get(), _resolver); } else { _o->compilation_caching_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset TFLiteSettings::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const TFLiteSettingsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -5075,7 +5068,7 @@ inline void BenchmarkMetric::UnPackTo(BenchmarkMetricT *_o, const ::flatbuffers: + (void)_o; + (void)_resolver; + { auto _e = name(); if (_e) _o->name = _e->str(); } +- { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } else { _o->values.resize(0); } } ++ { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset BenchmarkMetric::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const BenchmarkMetricT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -5101,8 +5094,8 @@ inline bool operator==(const BenchmarkResultT &lhs, const BenchmarkResultT &rhs) + (lhs.inference_time_us == rhs.inference_time_us) && + (lhs.max_memory_kb == rhs.max_memory_kb) && + (lhs.ok == rhs.ok) && +- (lhs.metrics.size() == rhs.metrics.size() && std::equal(lhs.metrics.cbegin(), lhs.metrics.cend(), rhs.metrics.cbegin(), [](std::unique_ptr const &a, std::unique_ptr const &b) { return (a == b) || (a && b && *a == *b); })) && +- (lhs.actual_output.size() == rhs.actual_output.size() && std::equal(lhs.actual_output.cbegin(), lhs.actual_output.cend(), rhs.actual_output.cbegin(), [](std::unique_ptr const &a, std::unique_ptr const &b) { return (a == b) || (a && b && *a == *b); })); ++ (lhs.metrics == rhs.metrics) && ++ (lhs.actual_output == rhs.actual_output); + } + + inline bool operator!=(const BenchmarkResultT &lhs, const BenchmarkResultT &rhs) { +@@ -5116,9 +5109,9 @@ inline BenchmarkResultT::BenchmarkResultT(const BenchmarkResultT &o) + max_memory_kb(o.max_memory_kb), + ok(o.ok) { + metrics.reserve(o.metrics.size()); +- for (const auto &metrics_ : o.metrics) { metrics.emplace_back((metrics_) ? new tflite::BenchmarkMetricT(*metrics_) : nullptr); } ++ for (const auto &v : o.metrics) { metrics.emplace_back((v) ? new tflite::BenchmarkMetricT(*v) : nullptr); } + actual_output.reserve(o.actual_output.size()); +- for (const auto &actual_output_ : o.actual_output) { actual_output.emplace_back((actual_output_) ? new tflite::BenchmarkResult_::InferenceOutputT(*actual_output_) : nullptr); } ++ for (const auto &v : o.actual_output) { actual_output.emplace_back((v) ? new tflite::BenchmarkResult_::InferenceOutputT(*v) : nullptr); } + } + + inline BenchmarkResultT &BenchmarkResultT::operator=(BenchmarkResultT o) FLATBUFFERS_NOEXCEPT { +@@ -5140,12 +5133,12 @@ inline BenchmarkResultT *BenchmarkResult::UnPack(const ::flatbuffers::resolver_f + inline void BenchmarkResult::UnPackTo(BenchmarkResultT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = initialization_time_us(); if (_e) { _o->initialization_time_us.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->initialization_time_us[_i] = _e->Get(_i); } } else { _o->initialization_time_us.resize(0); } } +- { auto _e = inference_time_us(); if (_e) { _o->inference_time_us.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inference_time_us[_i] = _e->Get(_i); } } else { _o->inference_time_us.resize(0); } } ++ { auto _e = initialization_time_us(); if (_e) { _o->initialization_time_us.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->initialization_time_us[_i] = _e->Get(_i); } } } ++ { auto _e = inference_time_us(); if (_e) { _o->inference_time_us.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inference_time_us[_i] = _e->Get(_i); } } } + { auto _e = max_memory_kb(); _o->max_memory_kb = _e; } + { auto _e = ok(); _o->ok = _e; } +- { auto _e = metrics(); if (_e) { _o->metrics.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->metrics[_i]) { _e->Get(_i)->UnPackTo(_o->metrics[_i].get(), _resolver); } else { _o->metrics[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->metrics.resize(0); } } +- { auto _e = actual_output(); if (_e) { _o->actual_output.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->actual_output[_i]) { _e->Get(_i)->UnPackTo(_o->actual_output[_i].get(), _resolver); } else { _o->actual_output[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->actual_output.resize(0); } } ++ { auto _e = metrics(); if (_e) { _o->metrics.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->metrics[_i]) { _e->Get(_i)->UnPackTo(_o->metrics[_i].get(), _resolver); } else { _o->metrics[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = actual_output(); if (_e) { _o->actual_output.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->actual_output[_i]) { _e->Get(_i)->UnPackTo(_o->actual_output[_i].get(), _resolver); } else { _o->actual_output[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline ::flatbuffers::Offset BenchmarkResult::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const BenchmarkResultT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -5264,7 +5257,7 @@ inline bool operator==(const BenchmarkErrorT &lhs, const BenchmarkErrorT &rhs) { + (lhs.stage == rhs.stage) && + (lhs.exit_code == rhs.exit_code) && + (lhs.signal == rhs.signal) && +- (lhs.error_code.size() == rhs.error_code.size() && std::equal(lhs.error_code.cbegin(), lhs.error_code.cend(), rhs.error_code.cbegin(), [](std::unique_ptr const &a, std::unique_ptr const &b) { return (a == b) || (a && b && *a == *b); })) && ++ (lhs.error_code == rhs.error_code) && + (lhs.mini_benchmark_error_code == rhs.mini_benchmark_error_code); + } + +@@ -5279,7 +5272,7 @@ inline BenchmarkErrorT::BenchmarkErrorT(const BenchmarkErrorT &o) + signal(o.signal), + mini_benchmark_error_code(o.mini_benchmark_error_code) { + error_code.reserve(o.error_code.size()); +- for (const auto &error_code_ : o.error_code) { error_code.emplace_back((error_code_) ? new tflite::ErrorCodeT(*error_code_) : nullptr); } ++ for (const auto &v : o.error_code) { error_code.emplace_back((v) ? new tflite::ErrorCodeT(*v) : nullptr); } + } + + inline BenchmarkErrorT &BenchmarkErrorT::operator=(BenchmarkErrorT o) FLATBUFFERS_NOEXCEPT { +@@ -5303,7 +5296,7 @@ inline void BenchmarkError::UnPackTo(BenchmarkErrorT *_o, const ::flatbuffers::r + { auto _e = stage(); _o->stage = _e; } + { auto _e = exit_code(); _o->exit_code = _e; } + { auto _e = signal(); _o->signal = _e; } +- { auto _e = error_code(); if (_e) { _o->error_code.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->error_code[_i]) { _e->Get(_i)->UnPackTo(_o->error_code[_i].get(), _resolver); } else { _o->error_code[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->error_code.resize(0); } } ++ { auto _e = error_code(); if (_e) { _o->error_code.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->error_code[_i]) { _e->Get(_i)->UnPackTo(_o->error_code[_i].get(), _resolver); } else { _o->error_code[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = mini_benchmark_error_code(); _o->mini_benchmark_error_code = _e; } + } + +@@ -5373,10 +5366,10 @@ inline BenchmarkEventT *BenchmarkEvent::UnPack(const ::flatbuffers::resolver_fun + inline void BenchmarkEvent::UnPackTo(BenchmarkEventT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = tflite_settings(); if (_e) { if(_o->tflite_settings) { _e->UnPackTo(_o->tflite_settings.get(), _resolver); } else { _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->tflite_settings) { _o->tflite_settings.reset(); } } ++ { auto _e = tflite_settings(); if (_e) { if(_o->tflite_settings) { _e->UnPackTo(_o->tflite_settings.get(), _resolver); } else { _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = event_type(); _o->event_type = _e; } +- { auto _e = result(); if (_e) { if(_o->result) { _e->UnPackTo(_o->result.get(), _resolver); } else { _o->result = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->result) { _o->result.reset(); } } +- { auto _e = error(); if (_e) { if(_o->error) { _e->UnPackTo(_o->error.get(), _resolver); } else { _o->error = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->error) { _o->error.reset(); } } ++ { auto _e = result(); if (_e) { if(_o->result) { _e->UnPackTo(_o->result.get(), _resolver); } else { _o->result = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = error(); if (_e) { if(_o->error) { _e->UnPackTo(_o->error.get(), _resolver); } else { _o->error = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = boottime_us(); _o->boottime_us = _e; } + { auto _e = wallclock_us(); _o->wallclock_us = _e; } + } +@@ -5441,7 +5434,7 @@ inline void BestAccelerationDecision::UnPackTo(BestAccelerationDecisionT *_o, co + (void)_o; + (void)_resolver; + { auto _e = number_of_source_events(); _o->number_of_source_events = _e; } +- { auto _e = min_latency_event(); if (_e) { if(_o->min_latency_event) { _e->UnPackTo(_o->min_latency_event.get(), _resolver); } else { _o->min_latency_event = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->min_latency_event) { _o->min_latency_event.reset(); } } ++ { auto _e = min_latency_event(); if (_e) { if(_o->min_latency_event) { _e->UnPackTo(_o->min_latency_event.get(), _resolver); } else { _o->min_latency_event = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = min_inference_time_us(); _o->min_inference_time_us = _e; } + } + +@@ -5539,9 +5532,9 @@ inline void MiniBenchmarkEvent::UnPackTo(MiniBenchmarkEventT *_o, const ::flatbu + (void)_o; + (void)_resolver; + { auto _e = is_log_flushing_event(); _o->is_log_flushing_event = _e; } +- { auto _e = best_acceleration_decision(); if (_e) { if(_o->best_acceleration_decision) { _e->UnPackTo(_o->best_acceleration_decision.get(), _resolver); } else { _o->best_acceleration_decision = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->best_acceleration_decision) { _o->best_acceleration_decision.reset(); } } +- { auto _e = initialization_failure(); if (_e) { if(_o->initialization_failure) { _e->UnPackTo(_o->initialization_failure.get(), _resolver); } else { _o->initialization_failure = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->initialization_failure) { _o->initialization_failure.reset(); } } +- { auto _e = benchmark_event(); if (_e) { if(_o->benchmark_event) { _e->UnPackTo(_o->benchmark_event.get(), _resolver); } else { _o->benchmark_event = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->benchmark_event) { _o->benchmark_event.reset(); } } ++ { auto _e = best_acceleration_decision(); if (_e) { if(_o->best_acceleration_decision) { _e->UnPackTo(_o->best_acceleration_decision.get(), _resolver); } else { _o->best_acceleration_decision = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = initialization_failure(); if (_e) { if(_o->initialization_failure) { _e->UnPackTo(_o->initialization_failure.get(), _resolver); } else { _o->initialization_failure = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = benchmark_event(); if (_e) { if(_o->benchmark_event) { _e->UnPackTo(_o->benchmark_event.get(), _resolver); } else { _o->benchmark_event = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset MiniBenchmarkEvent::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const MiniBenchmarkEventT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -5612,7 +5605,7 @@ inline void ModelFile::UnPackTo(ModelFileT *_o, const ::flatbuffers::resolver_fu + { auto _e = fd(); _o->fd = _e; } + { auto _e = offset(); _o->offset = _e; } + { auto _e = length(); _o->length = _e; } +- { auto _e = model_id_group(); if (_e) { if(_o->model_id_group) { _e->UnPackTo(_o->model_id_group.get(), _resolver); } else { _o->model_id_group = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->model_id_group) { _o->model_id_group.reset(); } } ++ { auto _e = model_id_group(); if (_e) { if(_o->model_id_group) { _e->UnPackTo(_o->model_id_group.get(), _resolver); } else { _o->model_id_group = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = buffer_handle(); _o->buffer_handle = _e; } + } + +@@ -5762,7 +5755,7 @@ inline ::flatbuffers::Offset CreateValidationSettings(::flat + + inline bool operator==(const MinibenchmarkSettingsT &lhs, const MinibenchmarkSettingsT &rhs) { + return +- (lhs.settings_to_test.size() == rhs.settings_to_test.size() && std::equal(lhs.settings_to_test.cbegin(), lhs.settings_to_test.cend(), rhs.settings_to_test.cbegin(), [](std::unique_ptr const &a, std::unique_ptr const &b) { return (a == b) || (a && b && *a == *b); })) && ++ (lhs.settings_to_test == rhs.settings_to_test) && + ((lhs.model_file == rhs.model_file) || (lhs.model_file && rhs.model_file && *lhs.model_file == *rhs.model_file)) && + ((lhs.storage_paths == rhs.storage_paths) || (lhs.storage_paths && rhs.storage_paths && *lhs.storage_paths == *rhs.storage_paths)) && + ((lhs.validation_settings == rhs.validation_settings) || (lhs.validation_settings && rhs.validation_settings && *lhs.validation_settings == *rhs.validation_settings)); +@@ -5778,7 +5771,7 @@ inline MinibenchmarkSettingsT::MinibenchmarkSettingsT(const MinibenchmarkSetting + storage_paths((o.storage_paths) ? new tflite::BenchmarkStoragePathsT(*o.storage_paths) : nullptr), + validation_settings((o.validation_settings) ? new tflite::ValidationSettingsT(*o.validation_settings) : nullptr) { + settings_to_test.reserve(o.settings_to_test.size()); +- for (const auto &settings_to_test_ : o.settings_to_test) { settings_to_test.emplace_back((settings_to_test_) ? new tflite::TFLiteSettingsT(*settings_to_test_) : nullptr); } ++ for (const auto &v : o.settings_to_test) { settings_to_test.emplace_back((v) ? new tflite::TFLiteSettingsT(*v) : nullptr); } + } + + inline MinibenchmarkSettingsT &MinibenchmarkSettingsT::operator=(MinibenchmarkSettingsT o) FLATBUFFERS_NOEXCEPT { +@@ -5798,10 +5791,10 @@ inline MinibenchmarkSettingsT *MinibenchmarkSettings::UnPack(const ::flatbuffers + inline void MinibenchmarkSettings::UnPackTo(MinibenchmarkSettingsT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = settings_to_test(); if (_e) { _o->settings_to_test.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->settings_to_test[_i]) { _e->Get(_i)->UnPackTo(_o->settings_to_test[_i].get(), _resolver); } else { _o->settings_to_test[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->settings_to_test.resize(0); } } +- { auto _e = model_file(); if (_e) { if(_o->model_file) { _e->UnPackTo(_o->model_file.get(), _resolver); } else { _o->model_file = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->model_file) { _o->model_file.reset(); } } +- { auto _e = storage_paths(); if (_e) { if(_o->storage_paths) { _e->UnPackTo(_o->storage_paths.get(), _resolver); } else { _o->storage_paths = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->storage_paths) { _o->storage_paths.reset(); } } +- { auto _e = validation_settings(); if (_e) { if(_o->validation_settings) { _e->UnPackTo(_o->validation_settings.get(), _resolver); } else { _o->validation_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->validation_settings) { _o->validation_settings.reset(); } } ++ { auto _e = settings_to_test(); if (_e) { _o->settings_to_test.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->settings_to_test[_i]) { _e->Get(_i)->UnPackTo(_o->settings_to_test[_i].get(), _resolver); } else { _o->settings_to_test[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = model_file(); if (_e) { if(_o->model_file) { _e->UnPackTo(_o->model_file.get(), _resolver); } else { _o->model_file = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = storage_paths(); if (_e) { if(_o->storage_paths) { _e->UnPackTo(_o->storage_paths.get(), _resolver); } else { _o->storage_paths = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = validation_settings(); if (_e) { if(_o->validation_settings) { _e->UnPackTo(_o->validation_settings.get(), _resolver); } else { _o->validation_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset MinibenchmarkSettings::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const MinibenchmarkSettingsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -5856,8 +5849,8 @@ inline BenchmarkEventStorageT *BenchmarkEventStorage::UnPack(const ::flatbuffers + inline void BenchmarkEventStorage::UnPackTo(BenchmarkEventStorageT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = model_id_group(); if (_e) { if(_o->model_id_group) { _e->UnPackTo(_o->model_id_group.get(), _resolver); } else { _o->model_id_group = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->model_id_group) { _o->model_id_group.reset(); } } +- { auto _e = benchmark_event(); if (_e) { if(_o->benchmark_event) { _e->UnPackTo(_o->benchmark_event.get(), _resolver); } else { _o->benchmark_event = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->benchmark_event) { _o->benchmark_event.reset(); } } ++ { auto _e = model_id_group(); if (_e) { if(_o->model_id_group) { _e->UnPackTo(_o->model_id_group.get(), _resolver); } else { _o->model_id_group = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = benchmark_event(); if (_e) { if(_o->benchmark_event) { _e->UnPackTo(_o->benchmark_event.get(), _resolver); } else { _o->benchmark_event = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset BenchmarkEventStorage::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const BenchmarkEventStorageT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +diff --git a/tensorflow/lite/schema/conversion_metadata_generated.h b/tensorflow/lite/schema/conversion_metadata_generated.h +index 20dfff1671b..4b0772bf83f +--- a/tensorflow/lite/schema/conversion_metadata_generated.h ++++ b/tensorflow/lite/schema/conversion_metadata_generated.h +@@ -1,4 +1,4 @@ +-/* Copyright 2021 The TensorFlow Authors. All Rights Reserved. ++/* Copyright 2023 The TensorFlow Authors. All Rights Reserved. + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. +@@ -20,13 +20,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + namespace tflite { + + struct Environment; +@@ -512,7 +505,7 @@ inline SparsityBlockSizeT *SparsityBlockSize::UnPack(const ::flatbuffers::resolv + inline void SparsityBlockSize::UnPackTo(SparsityBlockSizeT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } else { _o->values.resize(0); } } ++ { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset SparsityBlockSize::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const SparsityBlockSizeT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -535,7 +528,7 @@ inline ConversionOptionsT::ConversionOptionsT(const ConversionOptionsT &o) + enable_select_tf_ops(o.enable_select_tf_ops), + force_select_tf_ops(o.force_select_tf_ops) { + sparsity_block_sizes.reserve(o.sparsity_block_sizes.size()); +- for (const auto &sparsity_block_sizes_ : o.sparsity_block_sizes) { sparsity_block_sizes.emplace_back((sparsity_block_sizes_) ? new tflite::SparsityBlockSizeT(*sparsity_block_sizes_) : nullptr); } ++ for (const auto &v : o.sparsity_block_sizes) { sparsity_block_sizes.emplace_back((v) ? new tflite::SparsityBlockSizeT(*v) : nullptr); } + } + + inline ConversionOptionsT &ConversionOptionsT::operator=(ConversionOptionsT o) FLATBUFFERS_NOEXCEPT { +@@ -556,11 +549,11 @@ inline ConversionOptionsT *ConversionOptions::UnPack(const ::flatbuffers::resolv + inline void ConversionOptions::UnPackTo(ConversionOptionsT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = model_optimization_modes(); if (_e) { _o->model_optimization_modes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->model_optimization_modes[_i] = static_cast(_e->Get(_i)); } } else { _o->model_optimization_modes.resize(0); } } ++ { auto _e = model_optimization_modes(); if (_e) { _o->model_optimization_modes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->model_optimization_modes[_i] = static_cast(_e->Get(_i)); } } } + { auto _e = allow_custom_ops(); _o->allow_custom_ops = _e; } + { auto _e = enable_select_tf_ops(); _o->enable_select_tf_ops = _e; } + { auto _e = force_select_tf_ops(); _o->force_select_tf_ops = _e; } +- { auto _e = sparsity_block_sizes(); if (_e) { _o->sparsity_block_sizes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->sparsity_block_sizes[_i]) { _e->Get(_i)->UnPackTo(_o->sparsity_block_sizes[_i].get(), _resolver); } else { _o->sparsity_block_sizes[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->sparsity_block_sizes.resize(0); } } ++ { auto _e = sparsity_block_sizes(); if (_e) { _o->sparsity_block_sizes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->sparsity_block_sizes[_i]) { _e->Get(_i)->UnPackTo(_o->sparsity_block_sizes[_i].get(), _resolver); } else { _o->sparsity_block_sizes[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline ::flatbuffers::Offset ConversionOptions::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ConversionOptionsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -605,8 +598,8 @@ inline ConversionMetadataT *ConversionMetadata::UnPack(const ::flatbuffers::reso + inline void ConversionMetadata::UnPackTo(ConversionMetadataT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = environment(); if (_e) { if(_o->environment) { _e->UnPackTo(_o->environment.get(), _resolver); } else { _o->environment = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->environment) { _o->environment.reset(); } } +- { auto _e = options(); if (_e) { if(_o->options) { _e->UnPackTo(_o->options.get(), _resolver); } else { _o->options = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->options) { _o->options.reset(); } } ++ { auto _e = environment(); if (_e) { if(_o->environment) { _e->UnPackTo(_o->environment.get(), _resolver); } else { _o->environment = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = options(); if (_e) { if(_o->options) { _e->UnPackTo(_o->options.get(), _resolver); } else { _o->options = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset ConversionMetadata::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ConversionMetadataT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +diff --git a/tensorflow/lite/schema/schema_generated.h b/tensorflow/lite/schema/schema_generated.h +index f03fdd0fc13..e894aa592b8 100755 +--- a/tensorflow/lite/schema/schema_generated.h ++++ b/tensorflow/lite/schema/schema_generated.h +@@ -1,4 +1,4 @@ +-/* Copyright 2023 The TensorFlow Authors. All Rights Reserved. ++/* Copyright 2018 The TensorFlow Authors. All Rights Reserved. + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. +@@ -20,13 +20,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + namespace tflite { + + struct CustomQuantization; +@@ -1835,7 +1828,7 @@ inline const char * const *EnumNamesBuiltinOptions() { + } + + inline const char *EnumNameBuiltinOptions(BuiltinOptions e) { +- if (::flatbuffers::IsOutRange(e, BuiltinOptions_NONE, BuiltinOptions_RightShiftOptions)) return ""; ++ if (::flatbuffers::IsOutRange(e, BuiltinOptions_NONE, BuiltinOptions_BitcastOptions)) return ""; + const size_t index = static_cast(e); + return EnumNamesBuiltinOptions()[index]; + } +@@ -13585,10 +13578,10 @@ inline QuantizationParametersT *QuantizationParameters::UnPack(const ::flatbuffe + inline void QuantizationParameters::UnPackTo(QuantizationParametersT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = min(); if (_e) { _o->min.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->min[_i] = _e->Get(_i); } } else { _o->min.resize(0); } } +- { auto _e = max(); if (_e) { _o->max.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->max[_i] = _e->Get(_i); } } else { _o->max.resize(0); } } +- { auto _e = scale(); if (_e) { _o->scale.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->scale[_i] = _e->Get(_i); } } else { _o->scale.resize(0); } } +- { auto _e = zero_point(); if (_e) { _o->zero_point.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->zero_point[_i] = _e->Get(_i); } } else { _o->zero_point.resize(0); } } ++ { auto _e = min(); if (_e) { _o->min.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->min[_i] = _e->Get(_i); } } } ++ { auto _e = max(); if (_e) { _o->max.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->max[_i] = _e->Get(_i); } } } ++ { auto _e = scale(); if (_e) { _o->scale.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->scale[_i] = _e->Get(_i); } } } ++ { auto _e = zero_point(); if (_e) { _o->zero_point.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->zero_point[_i] = _e->Get(_i); } } } + { auto _e = details_type(); _o->details.type = _e; } + { auto _e = details(); if (_e) _o->details.value = tflite::QuantizationDetailsUnion::UnPack(_e, details_type(), _resolver); } + { auto _e = quantized_dimension(); _o->quantized_dimension = _e; } +@@ -13629,7 +13622,7 @@ inline Int32VectorT *Int32Vector::UnPack(const ::flatbuffers::resolver_function_ + inline void Int32Vector::UnPackTo(Int32VectorT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } else { _o->values.resize(0); } } ++ { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset Int32Vector::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const Int32VectorT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -13655,7 +13648,7 @@ inline Uint16VectorT *Uint16Vector::UnPack(const ::flatbuffers::resolver_functio + inline void Uint16Vector::UnPackTo(Uint16VectorT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } else { _o->values.resize(0); } } ++ { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset Uint16Vector::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const Uint16VectorT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -13745,7 +13738,7 @@ inline SparsityParametersT::SparsityParametersT(const SparsityParametersT &o) + : traversal_order(o.traversal_order), + block_map(o.block_map) { + dim_metadata.reserve(o.dim_metadata.size()); +- for (const auto &dim_metadata_ : o.dim_metadata) { dim_metadata.emplace_back((dim_metadata_) ? new tflite::DimensionMetadataT(*dim_metadata_) : nullptr); } ++ for (const auto &v : o.dim_metadata) { dim_metadata.emplace_back((v) ? new tflite::DimensionMetadataT(*v) : nullptr); } + } + + inline SparsityParametersT &SparsityParametersT::operator=(SparsityParametersT o) FLATBUFFERS_NOEXCEPT { +@@ -13764,9 +13757,9 @@ inline SparsityParametersT *SparsityParameters::UnPack(const ::flatbuffers::reso + inline void SparsityParameters::UnPackTo(SparsityParametersT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = traversal_order(); if (_e) { _o->traversal_order.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->traversal_order[_i] = _e->Get(_i); } } else { _o->traversal_order.resize(0); } } +- { auto _e = block_map(); if (_e) { _o->block_map.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->block_map[_i] = _e->Get(_i); } } else { _o->block_map.resize(0); } } +- { auto _e = dim_metadata(); if (_e) { _o->dim_metadata.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->dim_metadata[_i]) { _e->Get(_i)->UnPackTo(_o->dim_metadata[_i].get(), _resolver); } else { _o->dim_metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->dim_metadata.resize(0); } } ++ { auto _e = traversal_order(); if (_e) { _o->traversal_order.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->traversal_order[_i] = _e->Get(_i); } } } ++ { auto _e = block_map(); if (_e) { _o->block_map.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->block_map[_i] = _e->Get(_i); } } } ++ { auto _e = dim_metadata(); if (_e) { _o->dim_metadata.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->dim_metadata[_i]) { _e->Get(_i)->UnPackTo(_o->dim_metadata[_i].get(), _resolver); } else { _o->dim_metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline ::flatbuffers::Offset SparsityParameters::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const SparsityParametersT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -13796,7 +13789,7 @@ inline VariantSubTypeT *VariantSubType::UnPack(const ::flatbuffers::resolver_fun + inline void VariantSubType::UnPackTo(VariantSubTypeT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = shape(); if (_e) { _o->shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape[_i] = _e->Get(_i); } } else { _o->shape.resize(0); } } ++ { auto _e = shape(); if (_e) { _o->shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape[_i] = _e->Get(_i); } } } + { auto _e = type(); _o->type = _e; } + { auto _e = has_rank(); _o->has_rank = _e; } + } +@@ -13830,7 +13823,7 @@ inline TensorT::TensorT(const TensorT &o) + shape_signature(o.shape_signature), + has_rank(o.has_rank) { + variant_tensors.reserve(o.variant_tensors.size()); +- for (const auto &variant_tensors_ : o.variant_tensors) { variant_tensors.emplace_back((variant_tensors_) ? new tflite::VariantSubTypeT(*variant_tensors_) : nullptr); } ++ for (const auto &v : o.variant_tensors) { variant_tensors.emplace_back((v) ? new tflite::VariantSubTypeT(*v) : nullptr); } + } + + inline TensorT &TensorT::operator=(TensorT o) FLATBUFFERS_NOEXCEPT { +@@ -13856,16 +13849,16 @@ inline TensorT *Tensor::UnPack(const ::flatbuffers::resolver_function_t *_resolv + inline void Tensor::UnPackTo(TensorT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = shape(); if (_e) { _o->shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape[_i] = _e->Get(_i); } } else { _o->shape.resize(0); } } ++ { auto _e = shape(); if (_e) { _o->shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape[_i] = _e->Get(_i); } } } + { auto _e = type(); _o->type = _e; } + { auto _e = buffer(); _o->buffer = _e; } + { auto _e = name(); if (_e) _o->name = _e->str(); } +- { auto _e = quantization(); if (_e) { if(_o->quantization) { _e->UnPackTo(_o->quantization.get(), _resolver); } else { _o->quantization = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->quantization) { _o->quantization.reset(); } } ++ { auto _e = quantization(); if (_e) { if(_o->quantization) { _e->UnPackTo(_o->quantization.get(), _resolver); } else { _o->quantization = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = is_variable(); _o->is_variable = _e; } +- { auto _e = sparsity(); if (_e) { if(_o->sparsity) { _e->UnPackTo(_o->sparsity.get(), _resolver); } else { _o->sparsity = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->sparsity) { _o->sparsity.reset(); } } +- { auto _e = shape_signature(); if (_e) { _o->shape_signature.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape_signature[_i] = _e->Get(_i); } } else { _o->shape_signature.resize(0); } } ++ { auto _e = sparsity(); if (_e) { if(_o->sparsity) { _e->UnPackTo(_o->sparsity.get(), _resolver); } else { _o->sparsity = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = shape_signature(); if (_e) { _o->shape_signature.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape_signature[_i] = _e->Get(_i); } } } + { auto _e = has_rank(); _o->has_rank = _e; } +- { auto _e = variant_tensors(); if (_e) { _o->variant_tensors.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->variant_tensors[_i]) { _e->Get(_i)->UnPackTo(_o->variant_tensors[_i].get(), _resolver); } else { _o->variant_tensors[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->variant_tensors.resize(0); } } ++ { auto _e = variant_tensors(); if (_e) { _o->variant_tensors.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->variant_tensors[_i]) { _e->Get(_i)->UnPackTo(_o->variant_tensors[_i].get(), _resolver); } else { _o->variant_tensors[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline ::flatbuffers::Offset Tensor::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const TensorT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -14083,8 +14076,8 @@ inline void ConcatEmbeddingsOptions::UnPackTo(ConcatEmbeddingsOptionsT *_o, cons + (void)_o; + (void)_resolver; + { auto _e = num_channels(); _o->num_channels = _e; } +- { auto _e = num_columns_per_channel(); if (_e) { _o->num_columns_per_channel.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->num_columns_per_channel[_i] = _e->Get(_i); } } else { _o->num_columns_per_channel.resize(0); } } +- { auto _e = embedding_dim_per_channel(); if (_e) { _o->embedding_dim_per_channel.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->embedding_dim_per_channel[_i] = _e->Get(_i); } } else { _o->embedding_dim_per_channel.resize(0); } } ++ { auto _e = num_columns_per_channel(); if (_e) { _o->num_columns_per_channel.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->num_columns_per_channel[_i] = _e->Get(_i); } } } ++ { auto _e = embedding_dim_per_channel(); if (_e) { _o->embedding_dim_per_channel.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->embedding_dim_per_channel[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset ConcatEmbeddingsOptions::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ConcatEmbeddingsOptionsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -14724,7 +14717,7 @@ inline ReshapeOptionsT *ReshapeOptions::UnPack(const ::flatbuffers::resolver_fun + inline void ReshapeOptions::UnPackTo(ReshapeOptionsT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = new_shape(); if (_e) { _o->new_shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->new_shape[_i] = _e->Get(_i); } } else { _o->new_shape.resize(0); } } ++ { auto _e = new_shape(); if (_e) { _o->new_shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->new_shape[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset ReshapeOptions::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ReshapeOptionsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -15108,7 +15101,7 @@ inline SqueezeOptionsT *SqueezeOptions::UnPack(const ::flatbuffers::resolver_fun + inline void SqueezeOptions::UnPackTo(SqueezeOptionsT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = squeeze_dims(); if (_e) { _o->squeeze_dims.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->squeeze_dims[_i] = _e->Get(_i); } } else { _o->squeeze_dims.resize(0); } } ++ { auto _e = squeeze_dims(); if (_e) { _o->squeeze_dims.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->squeeze_dims[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset SqueezeOptions::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const SqueezeOptionsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -16957,7 +16950,7 @@ inline BucketizeOptionsT *BucketizeOptions::UnPack(const ::flatbuffers::resolver + inline void BucketizeOptions::UnPackTo(BucketizeOptionsT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = boundaries(); if (_e) { _o->boundaries.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->boundaries[_i] = _e->Get(_i); } } else { _o->boundaries.resize(0); } } ++ { auto _e = boundaries(); if (_e) { _o->boundaries.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->boundaries[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset BucketizeOptions::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const BucketizeOptionsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -17275,14 +17268,14 @@ inline void Operator::UnPackTo(OperatorT *_o, const ::flatbuffers::resolver_func + (void)_o; + (void)_resolver; + { auto _e = opcode_index(); _o->opcode_index = _e; } +- { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inputs[_i] = _e->Get(_i); } } else { _o->inputs.resize(0); } } +- { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->outputs[_i] = _e->Get(_i); } } else { _o->outputs.resize(0); } } ++ { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inputs[_i] = _e->Get(_i); } } } ++ { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->outputs[_i] = _e->Get(_i); } } } + { auto _e = builtin_options_type(); _o->builtin_options.type = _e; } + { auto _e = builtin_options(); if (_e) _o->builtin_options.value = tflite::BuiltinOptionsUnion::UnPack(_e, builtin_options_type(), _resolver); } + { auto _e = custom_options(); if (_e) { _o->custom_options.resize(_e->size()); std::copy(_e->begin(), _e->end(), _o->custom_options.begin()); } } + { auto _e = custom_options_format(); _o->custom_options_format = _e; } +- { auto _e = mutating_variable_inputs(); if (_e) { _o->mutating_variable_inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->mutating_variable_inputs[_i] = _e->Get(_i) != 0; } } else { _o->mutating_variable_inputs.resize(0); } } +- { auto _e = intermediates(); if (_e) { _o->intermediates.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->intermediates[_i] = _e->Get(_i); } } else { _o->intermediates.resize(0); } } ++ { auto _e = mutating_variable_inputs(); if (_e) { _o->mutating_variable_inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->mutating_variable_inputs[_i] = _e->Get(_i) != 0; } } } ++ { auto _e = intermediates(); if (_e) { _o->intermediates.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->intermediates[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset Operator::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const OperatorT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -17320,9 +17313,9 @@ inline SubGraphT::SubGraphT(const SubGraphT &o) + outputs(o.outputs), + name(o.name) { + tensors.reserve(o.tensors.size()); +- for (const auto &tensors_ : o.tensors) { tensors.emplace_back((tensors_) ? new tflite::TensorT(*tensors_) : nullptr); } ++ for (const auto &v : o.tensors) { tensors.emplace_back((v) ? new tflite::TensorT(*v) : nullptr); } + operators.reserve(o.operators.size()); +- for (const auto &operators_ : o.operators) { operators.emplace_back((operators_) ? new tflite::OperatorT(*operators_) : nullptr); } ++ for (const auto &v : o.operators) { operators.emplace_back((v) ? new tflite::OperatorT(*v) : nullptr); } + } + + inline SubGraphT &SubGraphT::operator=(SubGraphT o) FLATBUFFERS_NOEXCEPT { +@@ -17343,10 +17336,10 @@ inline SubGraphT *SubGraph::UnPack(const ::flatbuffers::resolver_function_t *_re + inline void SubGraph::UnPackTo(SubGraphT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = tensors(); if (_e) { _o->tensors.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->tensors[_i]) { _e->Get(_i)->UnPackTo(_o->tensors[_i].get(), _resolver); } else { _o->tensors[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->tensors.resize(0); } } +- { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inputs[_i] = _e->Get(_i); } } else { _o->inputs.resize(0); } } +- { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->outputs[_i] = _e->Get(_i); } } else { _o->outputs.resize(0); } } +- { auto _e = operators(); if (_e) { _o->operators.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->operators[_i]) { _e->Get(_i)->UnPackTo(_o->operators[_i].get(), _resolver); } else { _o->operators[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->operators.resize(0); } } ++ { auto _e = tensors(); if (_e) { _o->tensors.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->tensors[_i]) { _e->Get(_i)->UnPackTo(_o->tensors[_i].get(), _resolver); } else { _o->tensors[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inputs[_i] = _e->Get(_i); } } } ++ { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->outputs[_i] = _e->Get(_i); } } } ++ { auto _e = operators(); if (_e) { _o->operators.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->operators[_i]) { _e->Get(_i)->UnPackTo(_o->operators[_i].get(), _resolver); } else { _o->operators[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = name(); if (_e) _o->name = _e->str(); } + } + +@@ -17461,9 +17454,9 @@ inline SignatureDefT::SignatureDefT(const SignatureDefT &o) + : signature_key(o.signature_key), + subgraph_index(o.subgraph_index) { + inputs.reserve(o.inputs.size()); +- for (const auto &inputs_ : o.inputs) { inputs.emplace_back((inputs_) ? new tflite::TensorMapT(*inputs_) : nullptr); } ++ for (const auto &v : o.inputs) { inputs.emplace_back((v) ? new tflite::TensorMapT(*v) : nullptr); } + outputs.reserve(o.outputs.size()); +- for (const auto &outputs_ : o.outputs) { outputs.emplace_back((outputs_) ? new tflite::TensorMapT(*outputs_) : nullptr); } ++ for (const auto &v : o.outputs) { outputs.emplace_back((v) ? new tflite::TensorMapT(*v) : nullptr); } + } + + inline SignatureDefT &SignatureDefT::operator=(SignatureDefT o) FLATBUFFERS_NOEXCEPT { +@@ -17483,8 +17476,8 @@ inline SignatureDefT *SignatureDef::UnPack(const ::flatbuffers::resolver_functio + inline void SignatureDef::UnPackTo(SignatureDefT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->inputs[_i]) { _e->Get(_i)->UnPackTo(_o->inputs[_i].get(), _resolver); } else { _o->inputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->inputs.resize(0); } } +- { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->outputs[_i]) { _e->Get(_i)->UnPackTo(_o->outputs[_i].get(), _resolver); } else { _o->outputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->outputs.resize(0); } } ++ { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->inputs[_i]) { _e->Get(_i)->UnPackTo(_o->inputs[_i].get(), _resolver); } else { _o->inputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->outputs[_i]) { _e->Get(_i)->UnPackTo(_o->outputs[_i].get(), _resolver); } else { _o->outputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = signature_key(); if (_e) _o->signature_key = _e->str(); } + { auto _e = subgraph_index(); _o->subgraph_index = _e; } + } +@@ -17514,15 +17507,15 @@ inline ModelT::ModelT(const ModelT &o) + description(o.description), + metadata_buffer(o.metadata_buffer) { + operator_codes.reserve(o.operator_codes.size()); +- for (const auto &operator_codes_ : o.operator_codes) { operator_codes.emplace_back((operator_codes_) ? new tflite::OperatorCodeT(*operator_codes_) : nullptr); } ++ for (const auto &v : o.operator_codes) { operator_codes.emplace_back((v) ? new tflite::OperatorCodeT(*v) : nullptr); } + subgraphs.reserve(o.subgraphs.size()); +- for (const auto &subgraphs_ : o.subgraphs) { subgraphs.emplace_back((subgraphs_) ? new tflite::SubGraphT(*subgraphs_) : nullptr); } ++ for (const auto &v : o.subgraphs) { subgraphs.emplace_back((v) ? new tflite::SubGraphT(*v) : nullptr); } + buffers.reserve(o.buffers.size()); +- for (const auto &buffers_ : o.buffers) { buffers.emplace_back((buffers_) ? new tflite::BufferT(*buffers_) : nullptr); } ++ for (const auto &v : o.buffers) { buffers.emplace_back((v) ? new tflite::BufferT(*v) : nullptr); } + metadata.reserve(o.metadata.size()); +- for (const auto &metadata_ : o.metadata) { metadata.emplace_back((metadata_) ? new tflite::MetadataT(*metadata_) : nullptr); } ++ for (const auto &v : o.metadata) { metadata.emplace_back((v) ? new tflite::MetadataT(*v) : nullptr); } + signature_defs.reserve(o.signature_defs.size()); +- for (const auto &signature_defs_ : o.signature_defs) { signature_defs.emplace_back((signature_defs_) ? new tflite::SignatureDefT(*signature_defs_) : nullptr); } ++ for (const auto &v : o.signature_defs) { signature_defs.emplace_back((v) ? new tflite::SignatureDefT(*v) : nullptr); } + } + + inline ModelT &ModelT::operator=(ModelT o) FLATBUFFERS_NOEXCEPT { +@@ -17547,13 +17540,13 @@ inline void Model::UnPackTo(ModelT *_o, const ::flatbuffers::resolver_function_t + (void)_o; + (void)_resolver; + { auto _e = version(); _o->version = _e; } +- { auto _e = operator_codes(); if (_e) { _o->operator_codes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->operator_codes[_i]) { _e->Get(_i)->UnPackTo(_o->operator_codes[_i].get(), _resolver); } else { _o->operator_codes[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->operator_codes.resize(0); } } +- { auto _e = subgraphs(); if (_e) { _o->subgraphs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->subgraphs[_i]) { _e->Get(_i)->UnPackTo(_o->subgraphs[_i].get(), _resolver); } else { _o->subgraphs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->subgraphs.resize(0); } } ++ { auto _e = operator_codes(); if (_e) { _o->operator_codes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->operator_codes[_i]) { _e->Get(_i)->UnPackTo(_o->operator_codes[_i].get(), _resolver); } else { _o->operator_codes[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = subgraphs(); if (_e) { _o->subgraphs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->subgraphs[_i]) { _e->Get(_i)->UnPackTo(_o->subgraphs[_i].get(), _resolver); } else { _o->subgraphs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = description(); if (_e) _o->description = _e->str(); } +- { auto _e = buffers(); if (_e) { _o->buffers.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->buffers[_i]) { _e->Get(_i)->UnPackTo(_o->buffers[_i].get(), _resolver); } else { _o->buffers[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->buffers.resize(0); } } +- { auto _e = metadata_buffer(); if (_e) { _o->metadata_buffer.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->metadata_buffer[_i] = _e->Get(_i); } } else { _o->metadata_buffer.resize(0); } } +- { auto _e = metadata(); if (_e) { _o->metadata.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->metadata[_i]) { _e->Get(_i)->UnPackTo(_o->metadata[_i].get(), _resolver); } else { _o->metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->metadata.resize(0); } } +- { auto _e = signature_defs(); if (_e) { _o->signature_defs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->signature_defs[_i]) { _e->Get(_i)->UnPackTo(_o->signature_defs[_i].get(), _resolver); } else { _o->signature_defs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->signature_defs.resize(0); } } ++ { auto _e = buffers(); if (_e) { _o->buffers.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->buffers[_i]) { _e->Get(_i)->UnPackTo(_o->buffers[_i].get(), _resolver); } else { _o->buffers[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = metadata_buffer(); if (_e) { _o->metadata_buffer.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->metadata_buffer[_i] = _e->Get(_i); } } } ++ { auto _e = metadata(); if (_e) { _o->metadata.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->metadata[_i]) { _e->Get(_i)->UnPackTo(_o->metadata[_i].get(), _resolver); } else { _o->metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = signature_defs(); if (_e) { _o->signature_defs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->signature_defs[_i]) { _e->Get(_i)->UnPackTo(_o->signature_defs[_i].get(), _resolver); } else { _o->signature_defs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline ::flatbuffers::Offset Model::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ModelT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +diff --git a/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake b/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake +index f1ed4fb1748..ad0ddcd38c1 100644 +--- a/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake ++++ b/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake +@@ -23,7 +23,7 @@ OverridableFetchContent_Declare( + flatbuffers + GIT_REPOSITORY https://github.com/google/flatbuffers + # Sync with tensorflow/third_party/flatbuffers/workspace.bzl +- GIT_TAG v23.1.21 ++ GIT_TAG v2.0.6 + GIT_SHALLOW TRUE + GIT_PROGRESS TRUE + SOURCE_DIR "${CMAKE_BINARY_DIR}/flatbuffers" +diff --git a/tensorflow/tools/ci_build/release/requirements_common.txt b/tensorflow/tools/ci_build/release/requirements_common.txt +index 6373d737aa4..4ede56800d2 100644 +--- a/tensorflow/tools/ci_build/release/requirements_common.txt ++++ b/tensorflow/tools/ci_build/release/requirements_common.txt +@@ -3,7 +3,7 @@ + # This will change in the future. + absl-py ~= 1.0.0 + astunparse ~= 1.6.3 +-flatbuffers ~= 23.1.21 ++flatbuffers ~= 2.0 + google_pasta ~= 0.2 + h5py ~= 3.8.0 # Earliest version for Python 3.11 + # TODO(b/262592253): Support older versions of NumPy for Python 3.10 and lower +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index e77e6f81449..b7d039f3262 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -84,7 +84,7 @@ def standard_or_nightly(standard, nightly): + REQUIRED_PACKAGES = [ + 'absl-py >= 1.0.0', + 'astunparse >= 1.6.0', +- 'flatbuffers >= 23.1.21', ++ 'flatbuffers >= 2.0', + # TODO(b/213222745) gast versions above 0.4.0 break TF's tests + 'gast >= 0.2.1, <= 0.4.0', + 'google_pasta >= 0.1.1', +diff --git a/third_party/flatbuffers/flatbuffers.BUILD b/third_party/flatbuffers/flatbuffers.BUILD +index 2905833ad15..f32f1a5f324 100644 +--- a/third_party/flatbuffers/flatbuffers.BUILD ++++ b/third_party/flatbuffers/flatbuffers.BUILD +@@ -7,6 +7,8 @@ licenses(["notice"]) # Apache 2.0 + + exports_files(["LICENSE.txt"]) + ++licenses(["notice"]) ++ + config_setting( + name = "platform_freebsd", + values = {"cpu": "freebsd"}, +@@ -44,16 +46,12 @@ filegroup( + "include/flatbuffers/bfbs_generator.h", + "include/flatbuffers/buffer.h", + "include/flatbuffers/buffer_ref.h", +- "include/flatbuffers/code_generator.h", + "include/flatbuffers/code_generators.h", + "include/flatbuffers/default_allocator.h", + "include/flatbuffers/detached_buffer.h", + "include/flatbuffers/flatbuffer_builder.h", + "include/flatbuffers/flatbuffers.h", +- "include/flatbuffers/flatc.h", +- "include/flatbuffers/flex_flat_util.h", + "include/flatbuffers/flexbuffers.h", +- "include/flatbuffers/grpc.h", + "include/flatbuffers/hash.h", + "include/flatbuffers/idl.h", + "include/flatbuffers/minireflect.h", +@@ -178,7 +176,7 @@ py_library( + + filegroup( + name = "runtime_java_srcs", +- srcs = glob(["java/src/main/java/com/google/flatbuffers/**/*.java"]), ++ srcs = glob(["java/com/google/flatbuffers/**/*.java"]), + ) + + java_library( +diff --git a/third_party/flatbuffers/workspace.bzl b/third_party/flatbuffers/workspace.bzl +index 2fa19ab1a96..ceb8a2720da 100644 +--- a/third_party/flatbuffers/workspace.bzl ++++ b/third_party/flatbuffers/workspace.bzl +@@ -5,9 +5,9 @@ load("//third_party:repo.bzl", "tf_http_archive", "tf_mirror_urls") + def repo(): + tf_http_archive( + name = "flatbuffers", +- strip_prefix = "flatbuffers-23.1.21", +- sha256 = "d84cb25686514348e615163b458ae0767001b24b42325f426fd56406fd384238", +- urls = tf_mirror_urls("https://github.com/google/flatbuffers/archive/v23.1.21.tar.gz"), ++ strip_prefix = "flatbuffers-2.0.6", ++ sha256 = "e2dc24985a85b278dd06313481a9ca051d048f9474e0f199e372fea3ea4248c9", ++ urls = tf_mirror_urls("https://github.com/google/flatbuffers/archive/v2.0.6.tar.gz"), + build_file = "//third_party/flatbuffers:flatbuffers.BUILD", + system_build_file = "//third_party/flatbuffers:BUILD.system", + link_files = { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_unpin-gast-version.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_unpin-gast-version.patch new file mode 100644 index 00000000000..18e097f2e3d --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_unpin-gast-version.patch @@ -0,0 +1,18 @@ +Allow newer versions of gast. +Based on https://github.com/tensorflow/tensorflow/commit/56df1c90055ee812dac9a019571edd58f3ecd7eb + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index 72c20379a9291..d394ca5ea5c76 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -85,7 +85,6 @@ REQUIRED_PACKAGES = [ + 'absl-py >= 1.0.0', + 'astunparse >= 1.6.0', + 'flatbuffers >= 2.0', +- # TODO(b/213222745) gast versions above 0.4.0 break TF's tests +- 'gast >= 0.2.1, <= 0.4.0', ++ 'gast >=0.2.1,!=0.5.0,!=0.5.1,!=0.5.2', + 'google_pasta >= 0.1.1', + 'h5py >= 2.9.0', From 9f87a3c38a7775bc09fbf4e50782999720713aee Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Aug 2023 13:05:42 +0200 Subject: [PATCH 8593/9987] Add flatbuffers-python --- ...latbuffers-python-23.1.4-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ .../TensorFlow-2.13.0-foss-2022b.eb | 1 + 2 files changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-23.1.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-23.1.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-23.1.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..7c07088aa79 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-23.1.4-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'flatbuffers-python' +version = '23.1.4' + +homepage = 'https://github.com/google/flatbuffers/' +description = """Python Flatbuffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/f/flatbuffers'] +sources = [{'download_filename': 'flatbuffers-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['04d2141ea38866600beda17ffebf739b23f4f500cc22606076cc83079155106d'] + +dependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'VERSION=%(version)s ' +options = {'modulename': 'flatbuffers'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2022b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2022b.eb index 71c1957b3f0..584cd28c94e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2022b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2022b.eb @@ -25,6 +25,7 @@ dependencies = [ ('dill', '0.3.7'), ('double-conversion', '3.2.1'), ('flatbuffers', '23.1.4'), + ('flatbuffers-python', '23.1.4'), ('giflib', '5.2.1'), ('hwloc', '2.8.0'), ('ICU', '72.1'), From af6b08d0a30beb1fce5bdba12da26ec35184eed4 Mon Sep 17 00:00:00 2001 From: benjamic Date: Mon, 28 Aug 2023 15:57:46 +0200 Subject: [PATCH 8594/9987] adding easyconfigs: NAMD-2.14-foss-2022a-CUDA-11.7.0.eb --- .../NAMD/NAMD-2.14-foss-2022a-CUDA-11.7.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..8a2ad464c40 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,36 @@ +name = 'NAMD' +version = '2.14' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': False, 'openmp': False, 'pic': True} + +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] +sources = ['NAMD_%(version)s_Source.tar.gz'] +patches = [ + "%(name)s-%(version)s_Linux-POWER-cuda.patch", + "%(name)s-%(version)s-use_system_mremap_decl.patch" +] +checksums = [ + '34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235', # NAMD_2.14_Source.tar.gz + 'db4aeb482dfa805c859ea18940026395763169e0257401ee5341ca550029031c', # NAMD-2.14_Linux-POWER-cuda.patch + 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch +] + +dependencies = [ + ('Tcl', '8.6.12'), + ('CUDA', '11.7.0', '', SYSTEM), +] + +builddependencies = [ + ('tcsh', '6.24.01'), +] + +charm_arch = "multicore-linux-%(arch)s" +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' From cfb9b88a1854283f2ea91754f6e10ef9d3749b28 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 28 Aug 2023 17:38:23 +0200 Subject: [PATCH 8595/9987] changed naming, added xmdf support --- .../p/ParaView/ParaView-5.11.1-foss-2022b.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb new file mode 100644 index 00000000000..03df1ea3406 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb @@ -0,0 +1,70 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.11.1' +versionsuffix = '' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] +checksums = [ + {'ParaView-v5.11.1.tar.gz': 'de32f3e576b5f639ffc6903aa9e4cd46ac30c753185edc4366a7f305a6951b16'}, + {'ParaView-5.11.1-remove_glew_init_warning.patch': + 'b3b866d36a14526b9241f74de1910c67cdf1961892d10c30d1d32453306b2a7d'}, +] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Boost', '1.81.0'), + ('XZ', '5.2.7'), + ('HDF5', '1.14.0'), + ('netCDF', '4.9.0'), + ('libdrm', '2.4.114'), + ('Mesa', '22.2.4'), + ('Qt5', '5.15.7'), + ('zlib', '1.2.12'), + ('FFmpeg', '5.1.2'), + ('Szip', '2.1.1'), +] + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' +# Useful file format support +configopts += '-DPARAVIEW_ENABLE_XDMF2=ON ' +configopts += '-DPARAVIEW_ENABLE_XDMF3=ON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' +configopts += '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include ' +configopts += '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s ' % SHLIB_EXT +configopts += '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s ' % SHLIB_EXT +configopts += '-DVTK_OPENGL_HAS_EGL=ON ' +configopts += '-DVTK_USE_X=ON ' +configopts += '-DVTK_OPENGL_HAS_OSMESA=OFF ' + + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' From 75da9ae3abbf00230c0c00d66217243904913cc1 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 28 Aug 2023 17:38:56 +0200 Subject: [PATCH 8596/9987] Delete ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb Remove now-obsolete file --- ...raView-5.11.1-foss-2022a-mpi-egl-osmesa.eb | 63 ------------------- 1 file changed, 63 deletions(-) delete mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb deleted file mode 100644 index 5e15314ffeb..00000000000 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022a-mpi-egl-osmesa.eb +++ /dev/null @@ -1,63 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'ParaView' -version = '5.11.1' -versionsuffix = '-mpi-egl-osmesa' - -homepage = 'https://www.paraview.org' -description = "ParaView is a scientific parallel visualizer." - -toolchain = {'name': 'foss', 'version': '2022a'} -toolchainopts = {'pic': True, 'usempi': True} - -local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' -source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] -sources = ["%(name)s-v%(version)s.tar.gz"] - -builddependencies = [('CMake', '3.24.3')] - -dependencies = [ - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('XZ', '5.2.5'), - ('HDF5', '1.12.2'), - ('netCDF', '4.9.0'), - ('libGLU', '9.0.2'), - ('libdrm', '2.4.110'), - ('Mesa', '22.0.3'), - ('Qt5', '5.15.5'), - ('zlib', '1.2.12'), - ('FFmpeg', '4.4.2'), - ('Szip', '2.1.1'), -] - -# Paraview -configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' -configopts += '-DPARAVIEW_USE_MPI=ON ' -configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' -configopts += '-DPARAVIEW_USE_PYTHON=ON ' -configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' - -# OpenGL & Mesa -configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT -configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' -configopts += '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include ' -configopts += '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s ' % SHLIB_EXT -configopts += '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s ' % SHLIB_EXT -configopts += '-DVTK_OPENGL_HAS_EGL=ON ' -configopts += '-DVTK_USE_X=ON ' -configopts += '-DVTK_HAS_OSMESA=ON ' - - -sanity_check_paths = { - 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], - 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ['python -c "import paraview"'] - -patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -moduleclass = 'vis' From 9186d50c697cb0ebab38744ac86c150df18e64f6 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 29 Aug 2023 09:32:10 +0200 Subject: [PATCH 8597/9987] adding easyconfigs: Stack-2.11.1-x86_64.eb --- .../s/Stack/Stack-2.11.1-x86_64.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Stack/Stack-2.11.1-x86_64.eb diff --git a/easybuild/easyconfigs/s/Stack/Stack-2.11.1-x86_64.eb b/easybuild/easyconfigs/s/Stack/Stack-2.11.1-x86_64.eb new file mode 100644 index 00000000000..1b8e68c328f --- /dev/null +++ b/easybuild/easyconfigs/s/Stack/Stack-2.11.1-x86_64.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Stack' +version = '2.11.1' +versionsuffix = '-x86_64' + +homepage = 'https://docs.haskellstack.org' +description = """Stack is a cross-platform program for developing Haskell projects. +It is intended for Haskellers both new and experienced.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/commercialhaskell/stack/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-linux-x86_64.tar.gz'] +checksums = ['408a120e824ed6e6b24c548a2ff6f210fcb0eed246f204a280ed4c75af0517e7'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['stack'], + 'dirs': ['doc'], +} + +sanity_check_commands = ['stack --help'] + +moduleclass = 'devel' From f242db7f5d3ae8600ce46affe73611e77d11d679 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 29 Aug 2023 09:33:32 +0200 Subject: [PATCH 8598/9987] adding easyconfigs: git-annex-10.20230802-GCCcore-12.2.0.eb --- .../git-annex-10.20230802-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a02cdb21620 --- /dev/null +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'git-annex' +version = '10.20230802' + +homepage = 'https://git-annex.branchable.com' +description = """git-annex allows managing large files with git, without storing the file contents in git. It can sync, +backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the +power and distributed nature of git to bear on your large files with git-annex.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('GHC', '9.2.2', '-x86_64', SYSTEM), + ('GCC', '12.2.0','', SYSTEM), + ('Stack', '2.11.1', '-x86_64', SYSTEM), + ('git', '2.38.1', '-nodocs'), + ] + +sources = [{ + 'git_config': { 'url': 'git://git-annex.branchable.com', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'clone_into': '%(name)s-%(version)s', + }, + 'filename': '%(name)s-%(version)s.tar.gz' +}] + +build_cmd = "stack setup && stack build && " +build_cmd += "make install-bins BUILDER=stack PREFIX=%(builddir)s" + +files_to_copy = [(['git-annex','git-annex-shell'], 'bin'), + + ] + +sanity_check_paths = { + 'files': ['bin/git-annex', 'bin/git-annex-shell'], + 'dirs' : ['bin'], +} + +sanity_check_commands = ['git-annex version'] From a22cafb7ed0229e8caead8278f98f8bb006c329a Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 29 Aug 2023 09:37:17 +0200 Subject: [PATCH 8599/9987] adding easyconfigs: PLY-3.11-GCCcore-12.2.0-Python-3.10.8.eb --- .../PLY-3.11-GCCcore-12.2.0-Python-3.10.8.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0-Python-3.10.8.eb diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0-Python-3.10.8.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0-Python-3.10.8.eb new file mode 100644 index 00000000000..6498aba9865 --- /dev/null +++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0-Python-3.10.8.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'PLY' +version = '3.11' +versionsuffix = "-Python-%(pyver)s" + +homepage = "https://www.dabeaz.com/ply/" +description = """PLY is yet another implementation of lex and yacc for Python.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From c40a81bbaea97cd88dd00ed8c5d387507be76d1e Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 29 Aug 2023 09:37:51 +0200 Subject: [PATCH 8600/9987] adding easyconfigs: datalad-0.18.4-GCCcore-12.2.0.eb --- .../datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a18c2093734 --- /dev/null +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'datalad' +version = "0.18.4" + +homepage = 'https://www.datalad.org/' +description = "DataLad is a free and open source distributed data management system that keeps track of your data, creates structure, ensures reproducibility, supports collaboration, and integrates with widely used data infrastructure." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +dependencies = [ + ('git-annex', '10.20230802'), + ('Python', '3.10.8'), + ('tqdm', '4.64.1'), + ('PLY', '3.11', '-Python-3.10.8'), + ('Rust', '1.65.0'), + ('scikit-build', '0.17.2'), +] + +use_pip = True + +exts_list = [ + ('humanize', '3.13.1', { + 'checksums': ['12f113f2e369dac7f35d3823f49262934f4a22a53a6d3d4c86b736f50db88c7b'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + ('patoolib', '1.12', { + 'source_tmpl': 'patool-%(version)s.tar.gz', + 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], + }), + ('annexremote', '1.6.0', { + 'checksums': ['779a43e5b1b4afd294761c6587dee8ac68f453a5a8cc40f419e9ca777573ae84'], + }), + ('looseversion', '1.2.0', { + 'checksums': ['c64e71c0b29030683b4ea75aee431db2d25c4e6e533590e52129f1d9e51de204'], + }), + ('boto', '2.49.0', { + 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], + }), + ('gitlab', '3.10.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], + }), + ('iso8601', '1.0.2', { + 'checksums': ['27f503220e6845d9db954fb212b95b0362d8b7e6c1b2326a87061c3de93594b1'], + }), + (name, version, { + 'checksums': ['d832f3d70b79b7b66519ca30315791a6a265bdf8a86ddac5846489b75385cb09'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/datalad'], + 'dirs': [], +} + +sanity_check_commands = [ + "datalad --help", + "datalad --version", +] + +moduleclass = 'tools' From 7ad61a45adef7b25630012364fb4a19caf2ff3dd Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 29 Aug 2023 12:32:31 +0200 Subject: [PATCH 8601/9987] adding easyconfigs: tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb --- ...mpression-2.11.0-foss-2022a-CUDA-11.7.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..6d41078bd96 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,55 @@ +name = 'tensorflow-compression' +version = '2.11.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/tensorflow/compression' +description = "TensorFlow Compression (TFC) contains data compression tools for TensorFlow." + +toolchain = {'name': 'foss', 'version': '2022a'} + +# Make sure bazel doesn't download TensorFlow by itself. +local_tf_version = version +local_tf_dir = 'tensorflow-%s' % local_tf_version +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +sources = [ + { + 'source_urls': ['https://github.com/tensorflow/compression/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'filename': 'v%s.tar.gz' % local_tf_version, + 'alt_location': 'TensorFlow/extensions', + }, +] + +patches = [ + ('compression_local-tensorflow-repo.sed', '.'), +] + +builddependencies = [ + ('Bazel', '5.1.1'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('TensorFlow', local_tf_version, versionsuffix), + ('tensorflow-probability', '0.19.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +local_prebuildopts = "sed -i -f compression_local-tensorflow-repo.sed WORKSPACE && " +local_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +prebuildopts = local_prebuildopts + +sanity_check_commands = [ + 'python -m tensorflow_compression.all_tests', +] + +moduleclass = 'lib' From 440d392a73125b3dacfe6e12270470967852e984 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 29 Aug 2023 12:37:10 +0200 Subject: [PATCH 8602/9987] fix sanity check of ccache --- easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb | 2 +- easybuild/easyconfigs/c/ccache/ccache-4.7.5.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb index 68ac0da6cad..6157f2b62e4 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.3.eb @@ -48,7 +48,7 @@ sanity_check_paths = { sanity_check_commands = [ 'ccache --help', # Ensure that the binary does not depend on any shared library - 'ldd $(which ccache) | grep -q "not a dynamic executable"', + 'LC_ALL=C ldd $(which ccache) | grep -q "not a dynamic executable"', ] moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.7.5.eb b/easybuild/easyconfigs/c/ccache/ccache-4.7.5.eb index 8524fcc6905..ce5ba9b2ea6 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-4.7.5.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-4.7.5.eb @@ -48,7 +48,7 @@ sanity_check_paths = { sanity_check_commands = [ 'ccache --help', # Ensure that the binary does not depend on any shared library - 'ldd $(which ccache) | grep -q "not a dynamic executable"', + 'LC_ALL=C ldd $(which ccache) | grep -q "not a dynamic executable"', ] moduleclass = 'tools' From d1393f9e5ac5d9b61fd03a67c4b3b300dc53935b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Aug 2023 14:42:42 +0200 Subject: [PATCH 8603/9987] adding easyconfigs: SuAVE-2.0.0-20230815-intel-2023a.eb --- .../SuAVE/SuAVE-2.0.0-20230815-intel-2023a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuAVE/SuAVE-2.0.0-20230815-intel-2023a.eb diff --git a/easybuild/easyconfigs/s/SuAVE/SuAVE-2.0.0-20230815-intel-2023a.eb b/easybuild/easyconfigs/s/SuAVE/SuAVE-2.0.0-20230815-intel-2023a.eb new file mode 100644 index 00000000000..a3303efe5d8 --- /dev/null +++ b/easybuild/easyconfigs/s/SuAVE/SuAVE-2.0.0-20230815-intel-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'SuAVE' +version = '2.0.0-20230815' +local_commit = '8c1911b' + +homepage = 'https://github.com/SuAVE-Software/source_v2.0' +description = "Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape" + +toolchain = {'name': 'intel', 'version': '2023a'} + +source_urls = ['https://github.com/SuAVE-Software/source_v2.0/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['613fc1ac23f1b83304083128b03d199db28fb76187b834f614007cd537e6056f'] + +skipsteps = ['configure'] + +prebuildopts = 'sed -i "s/gfortran/${FC}/g" Makefile && ' +buildopts = 'FCFLAGS="${FCFLAGS}" ' + +installopts = "INSTALL_PATH=%(installdir)s/bin" + +local_bins = ['s_area', 's_bend', 's_count', 's_dens', 's_densph', 's_filter', 's_gauss', 's_grid', 's_gridsph', + 's_index', 's_inertia', 's_order', 's_shell', 's_spher', 's_stat', 's_thick', 's_topog'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +sanity_check_commands = ["%s -help" % x for x in local_bins] + +moduleclass = 'chem' From 55fcecd0cf07672dc8f50212524fe94d62c00f4f Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 29 Aug 2023 15:35:42 +0200 Subject: [PATCH 8604/9987] fixed pep8 --- .../easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb index 71671b8391b..bab6e90da5e 100644 --- a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb @@ -37,8 +37,9 @@ sanity_check_paths = { 'files': ['bin/bufr_compare', 'bin/bufr_copy', 'bin/bufr_dump', 'bin/bufr_filter', 'bin/bufr_get', 'bin/bufr_ls', 'bin/grib_compare', 'bin/grib_copy', 'bin/grib_dump', 'bin/grib_filter', 'bin/grib_get', 'bin/grib_ls', 'bin/gts_compare', 'bin/gts_copy', 'bin/gts_dump', 'bin/gts_filter', 'bin/gts_get', 'bin/gts_ls', - 'bin/metar_compare', 'bin/metar_copy', 'bin/metar_dump', 'bin/metar_filter', 'bin/metar_get', 'bin/metar_ls', - 'bin/codes_count', 'bin/codes_info', 'bin/codes_split_file', 'lib/libeccodes_f90.so', 'lib/libeccodes.so'], + 'bin/metar_compare', 'bin/metar_copy', 'bin/metar_dump', 'bin/metar_filter', 'bin/metar_get', + 'bin/metar_ls', 'bin/codes_count', 'bin/codes_info', 'bin/codes_split_file', + 'lib/libeccodes_f90.so', 'lib/libeccodes.so'], 'dirs': ['include'], } From de6a1bf3c3a05138b77043cc06ef450095386bd8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Aug 2023 15:38:42 +0200 Subject: [PATCH 8605/9987] make Autoconf a build dep for tRNAscan-SE + add missing Perl dependency --- .../tRNAscan-SE-2.0.12-foss-2022b.eb | 28 +++++++++++-------- 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb index f65eb9761f8..821e3e3f3f7 100644 --- a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb +++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb @@ -13,26 +13,30 @@ source_urls = ['http://trna.ucsc.edu/software/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['96fa4af507cd918c1c623763d9260bd6ed055d091662b44314426f6bbf447251'] -dependencies = [ +builddependencies = [ + # tRNAscan-SE's configure script really wants Autoconf 2.69 ('Autoconf', '2.69', '', SYSTEM), +] + +dependencies = [ + ('Perl', '5.36.0'), ('Infernal', '1.1.4'), ] -sanity_check_paths = { - 'files': [ - 'bin/tRNAscan-SE', - 'lib/tRNAscan-SE/tRNAscanSE/tRNA.pm', - ], - 'dirs': [ - 'bin', - 'include', - 'lib', - ], -} +parallel = 1 # tRNAscan-SE.conf sets the Infernal bin directory to be ours. postinstallcmds = [ "for b in $(ls $EBROOTINFERNAL/bin); do ln -s $EBROOTINFERNAL/bin/$b %(installdir)s/bin; done", ] +fix_perl_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/tRNAscan-SE', 'lib/tRNAscan-SE/tRNAscanSE/tRNA.pm'], + 'dirs': ['include'], +} + +sanity_check_commands = ["tRNAscan-SE --help"] + moduleclass = 'bio' From 9d126b6de900d3d33c599ff3d76c11d194107075 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Aug 2023 15:59:37 +0200 Subject: [PATCH 8606/9987] add RnBeads extensions to R-bundle-Bioconductor v3.16 --- ...le-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index 5b7b2d7438c..89dcfcf2697 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -1259,7 +1259,24 @@ exts_list = [ ('TailRank', '3.2.2', { 'checksums': ['21ed95ea47d21155f08ae2ad7bca9547f89f492000bc1defe1cc5ec172739d09'], }), - + ('RnBeads', '2.16.0', { + 'checksums': ['459c14a98be9056b844b9c44b865a76f30e38edbfef3592ac79c2c261d6f5fb2'], + }), + ('RnBeads.hg19', '1.30.0', { + 'checksums': ['d20a968f7a7d5980f4a0dadfd3b1044245fdefa48985951dffcd6258abaa5e01'], + }), + ('RnBeads.hg38', '1.30.0', { + 'checksums': ['b7c9ff2ba2c280a9160d7782571636d8a3868fe2f2882c08839a0a70e7f85e39'], + }), + ('RnBeads.mm9', '1.30.0', { + 'checksums': ['ed370096cc8590a41ebdb81153be5499bc3c8cf4f79e1ee67744ec06f96d439f'], + }), + ('RnBeads.mm10', '2.6.0', { + 'checksums': ['b655d2b0b056047ab88537fd8a3453eb5677feb5a6cda6206b3350d9a62ba571'], + }), + ('RnBeads.rn5', '1.30.0', { + 'checksums': ['e92ab6c298042f16cf0dbcf72fda8ab23877324598a9750cf98281ed0a453191'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 34377ae2d66b05bc940b66c724d20fa030c7001e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 29 Aug 2023 16:06:51 +0200 Subject: [PATCH 8607/9987] changed toolchain, remove wxWidgets dependency --- .../easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb b/easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb new file mode 100644 index 00000000000..7d07114ab64 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '5.4.8' + +homepage = 'http://gnuplot.sourceforge.net' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['931279c7caad1aff7d46cb4766f1ff41c26d9be9daf0bcf0c79deeee3d91f5cf'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('cairo', '1.17.8'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('libgd', '2.3.3'), + ('Pango', '1.50.14'), + ('libcerf', '2.3'), + ('X11', '20230603'), + ('Qt5', '5.15.10'), + ('Lua', '5.4.6'), +] + +preconfigopts = 'autoreconf && ' + +configopts = '--with-qt=qt5 --without-latex --disable-wxwidgets' + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} +# make sure that pdf terminal type is available +sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] + +moduleclass = 'vis' From 806c68b841cbda42752f6b1a26c26a0420e32d7e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 29 Aug 2023 16:10:52 +0200 Subject: [PATCH 8608/9987] tensorflow-compression: add missing sed script --- .../compression_local-tensorflow-repo.sed | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorflow-compression/compression_local-tensorflow-repo.sed diff --git a/easybuild/easyconfigs/t/tensorflow-compression/compression_local-tensorflow-repo.sed b/easybuild/easyconfigs/t/tensorflow-compression/compression_local-tensorflow-repo.sed new file mode 100644 index 00000000000..1116ca24ca9 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorflow-compression/compression_local-tensorflow-repo.sed @@ -0,0 +1,12 @@ +/^http_archive(/{ + :a;N;/\n)/!ba; + /org_tensorflow/{ + s/^/# /; + s/\n/\n# /g; + s|$|\ +local_repository(\ + name = "org_tensorflow",\ + path = "EB_TF_REPOPATH",\ +)|; + } +} From 9620423fa2777a0c767f80fe11b2771fafd399fe Mon Sep 17 00:00:00 2001 From: c3-builder Date: Tue, 29 Aug 2023 16:19:37 +0200 Subject: [PATCH 8609/9987] adding easyconfigs: Qt6-6.5.2-GCCcore-12.3.0.eb and patches: Qt6-6.5.2_fix_OF-Gentoo.patch --- .../q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb | 108 ++++++++++++++++++ .../q/Qt6/Qt6-6.5.2_fix_OF-Gentoo.patch | 48 ++++++++ 2 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qt6/Qt6-6.5.2_fix_OF-Gentoo.patch diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..01ff25737ae --- /dev/null +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb @@ -0,0 +1,108 @@ +easyblock = 'CMakeNinja' + +name = 'Qt6' +version = '6.5.2' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +patches = [ + # they may not be needed if qmake is not used? + # QT_CFLAGS_ARCH_HASWELL in cmake/QtCompilerOptimization.cmake should be patched? + # 'Qt5-5.13.1_fix-avx2.patch', + # 'Qt5-5.13.1_fix-qmake-libdir.patch', + 'Qt6-6.5.2_fix_OF-Gentoo.patch', + # 'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch', +] +checksums = [ + {'qt-everywhere-src-6.5.2.tar.xz': 'cde57be663d0f875759797298bdc37a936d517c39f2013e4e6ece5e12edeed12'}, + # {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, + # {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, + {'Qt6-6.5.2_fix_OF-Gentoo.patch': '908f7dae7685c76fe651e52391e46a2337a3cd32dee70a5da54b154da7d4917c'}, + # {'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch': + # '74590de2b9e32f2c88123cb096c4f5c3001b00710aad096a4d16444a8e9eb991'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + # deps for QtWebEngine + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Python', '3.11.3'), + ('re2c', '3.1'), +] + +dependencies = [ + ('double-conversion', '3.3.0'), + ('GLib', '2.77.1'), + ('PCRE2', '10.42'), + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.0'), + ('libwebp', '1.3.1'), + ('JasPer', '4.0.0'), + ('HarfBuzz', '5.3.1'), + ('SQLite', '3.42.0'), + ('graphite2', '1.3.14'), + ('assimp', '5.2.5'), # for Qt 3D + ('FFmpeg', '6.0'), + ('X11', '20230603'), + ('fontconfig', '2.14.2'), + ('html5lib', '1.1'), # WebEngine + ('freetype', '2.13.0'), # WebEngine + ('DBus', '1.15.4'), + ('libevent', '2.1.12'), # WebEngine + ('libGLU', '9.0.3'), + ('libjpeg-turbo', '2.1.5.1'), # WebEngine + ('NSS', '3.89.1'), # WebEngine, required + ('snappy', '1.1.10'), # WebEngine + ('OpenSSL', '1.1', '', SYSTEM), + ('ICU', '73.2'), # WebEngine, optional + ('nodejs', '18.17.1'), # WebEngine, required + # ('gRPC', '1.52.2'), # Qt needs protobuf <=21.x, still error + # ('bzip2', '1.0.8'), + # ('zlib', '1.2.13'), + # ('libopus', '1.4'), + # ('LittleCMS', '2.15'), +] + +# Error when trying native gRPC +# In file included from gen/extensions/browser/browser_sources_jumbo_7.cc:13: +# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc: In member function virtual bool extensions::FormDataParserUrlEncoded::SetSource(base::StringPiece): +# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc:429:11: error: using StringPiece = class absl::string_view {aka class absl::string_view} has no member named set +# 429 | source_.set(source.data(), source.size()); +# | ^~~ +# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc: In member function virtual bool extensions::FormDataParserMultipart::SetSource(base::StringPiece): +# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc:573:11: error: using StringPiece = class absl::string_view {aka class absl::string_view} has no member named set +# 573 | source_.set(source.data(), source.size()); +# | ^~~ + +preconfigopts = 'sed -i "s/MultiMedia/Multimedia/g" ../qt-everywhere-src-%(version)s/qtcharts/CMakeLists.txt &&' # Typo +configopts = '-Wno-dev ' +configopts += '-DFEATURE_qtpdf_build=OFF ' # Requires CUPS +configopts += '-DBUILD_qtwayland=OFF ' # Does not work on CentOS 7 +# configopts += '-DBUILD_qtgamepad=OFF ' # Gamepad does not work on CentOS 7. It have been removed from Qt6.0.0 and has not been added back + +# make sure QtWebEngine component is being built & installed +#check_qtwebengine = True +sanity_check_paths = { + 'files': ['bin/qmake6', 'lib/libQt6Core.so', 'lib/libQt6WebEngineCore.so'], + 'dirs': ['include/QtCore', 'include/QtWebEngineCore'], +} + +sanity_check_commands = ['qmake6 --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2_fix_OF-Gentoo.patch b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2_fix_OF-Gentoo.patch new file mode 100644 index 00000000000..5b3b6df66b1 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2_fix_OF-Gentoo.patch @@ -0,0 +1,48 @@ +############################################ +# Update from Qt5-5.14.1_fix-OF-Gentoo.patch +# 1. qt3d/..../unzip/ioapi.h and qtquick3d/..../unzip/ioapi.h do not use OF macro anymore +# 2. qtquick3d/..../minizip/ioapi.h is moved to qt3d/..../minizip/ioapi.h +############################################ +fix compilation on top of zlib provided by Gentoo, +where OF macro has been renamed to _Z_OF +see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 +author: Kenneth Hoste (HPC-UGent) +diff --git a/qt3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h b/qt3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h +index 8dcbdb06e3..e9cc96914e 100644 +--- a/qt3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h ++++ b/qt3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h +@@ -130,6 +130,14 @@ extern "C" { + #endif + + ++// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif + + + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); +diff --git a/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h b/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h +index c1b7a54847..c5546a26b9 100644 +--- a/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h ++++ b/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h +@@ -130,6 +130,14 @@ extern "C" { + #endif + + ++// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif + + + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); + From 3bcbb93724d582ed1c19e26fe9ffe992f0f23e36 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Aug 2023 16:45:23 +0200 Subject: [PATCH 8610/9987] rename SuAVE to SuAVE-biomat to avoid name clash with existing suave easyconfigs --- .../SuAVE-biomat-2.0.0-20230815-intel-2023a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/{SuAVE/SuAVE-2.0.0-20230815-intel-2023a.eb => SuAVE-biomat/SuAVE-biomat-2.0.0-20230815-intel-2023a.eb} (98%) diff --git a/easybuild/easyconfigs/s/SuAVE/SuAVE-2.0.0-20230815-intel-2023a.eb b/easybuild/easyconfigs/s/SuAVE-biomat/SuAVE-biomat-2.0.0-20230815-intel-2023a.eb similarity index 98% rename from easybuild/easyconfigs/s/SuAVE/SuAVE-2.0.0-20230815-intel-2023a.eb rename to easybuild/easyconfigs/s/SuAVE-biomat/SuAVE-biomat-2.0.0-20230815-intel-2023a.eb index a3303efe5d8..5969ce2e506 100644 --- a/easybuild/easyconfigs/s/SuAVE/SuAVE-2.0.0-20230815-intel-2023a.eb +++ b/easybuild/easyconfigs/s/SuAVE-biomat/SuAVE-biomat-2.0.0-20230815-intel-2023a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'SuAVE' +name = 'SuAVE-biomat' version = '2.0.0-20230815' local_commit = '8c1911b' From 090baea50066590bebf7425ba16b022fbde61ada Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 29 Aug 2023 17:02:09 +0200 Subject: [PATCH 8611/9987] {vis}[GCCcore/12.2.0] FLTK 1.3.8, xprop 1.2.5 --- .../f/FLTK/FLTK-1.3.8-GCCcore-12.2.0.eb | 43 +++++++++++++++++++ .../x/xprop/xprop-1.2.5-GCCcore-12.2.0.eb | 32 ++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..f0df37b2b8c --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.8-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.8' + +homepage = 'https://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-1.3.6_fix-LDFLAGS.patch'] +checksums = [ + 'f3c1102b07eb0e7a50538f9fc9037c18387165bc70d4b626e94ab725b9d4d1bf', # fltk-1.3.8-source.tar.gz + 'f8af2414a1ee193a186b0d98d1e3567add0ee003f44ec64dce2ce2dfd6d95ebf', # FLTK-1.3.6_fix-LDFLAGS.patch +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +builddependencies = [ + ('binutils', '2.39'), + ('groff', '1.22.4'), +] + +dependencies = [ + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), + ('libpng', '1.6.38'), + ('libjpeg-turbo', '2.1.4'), + ('xprop', '1.2.5'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..24aa969ebcc --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.5-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.5' + +homepage = "https://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.x.org/archive/individual/app/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b7bf6b6be6cf23e7966a153fc84d5901c14f01ee952fbd9d930aa48e2385d670'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('X11', '20221110'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' From e647a5bccc14b0a4a5a16f4dea8c9daa0ca8fa48 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 29 Aug 2023 21:06:51 +0200 Subject: [PATCH 8612/9987] adding easyconfigs: OpenMPI-4.1.5-intel-compilers-2023.1.0.eb --- .../OpenMPI-4.1.5-intel-compilers-2023.1.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb new file mode 100644 index 00000000000..7d59c6d092f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb @@ -0,0 +1,62 @@ +name = 'OpenMPI' +version = '4.1.5' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', +] +checksums = [ + {'openmpi-4.1.5.tar.bz2': 'a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3'}, + {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, + {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, +] + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('Perl', '5.36.1'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('hwloc', '2.9.1'), + ('libevent', '2.1.12'), + ('UCX', '1.14.1'), + ('libfabric', '1.18.0'), + ('PMIx', '4.2.4'), + ('UCC', '1.2.0'), +] + +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' + +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From 2235cf1b3f497bd070121591d248dccb53dc2103 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Tue, 29 Aug 2023 21:51:16 +0200 Subject: [PATCH 8613/9987] update comment --- easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022a.eb index 8e769176875..4598c7877da 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022a.eb @@ -23,7 +23,7 @@ builddependencies = [('Autotools', '20220317')] _minimap_ver = '2.24' dependencies = [ ('Python', '3.10.4'), # includes cffi - # TensorFlow ~=2.8.0 required by medaka 1.8.1, see requirements.txt + # tensorflow~=2.10.0 required by medaka 1.9.1, see requirements.txt ('TensorFlow', '2.11.0'), ('Pysam', '0.19.1'), ('SAMtools', '1.16.1'), From 60a4c507f4f51e226236ed2fb0a51ef46455dc69 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 30 Aug 2023 11:10:15 +0800 Subject: [PATCH 8614/9987] use pkgconf instead of pkg-config --- .../easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb index 950ba37bf0b..3ca28db9d7c 100644 --- a/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022a-R-4.2.1.eb @@ -9,7 +9,7 @@ description = """ An analysis toolkit for single-cell RNA-seq. """ toolchain = {'name': 'foss', 'version': '2022a'} -builddependencies = [('pkg-config', '0.29.2')] # for textshaping +builddependencies = [('pkgconf', '1.8.0')] # for textshaping dependencies = [ ('R', '4.2.1'), From 4e6fb4ea649ffc3bebf573c52db6a66dcee749a3 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 30 Aug 2023 09:39:33 +0200 Subject: [PATCH 8615/9987] reverted to GCCcore toolchain --- .../easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb index cd7f82f9c01..eb1a750d2e0 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb @@ -28,13 +28,12 @@ dependencies = [ ('libcerf', '2.3'), ('X11', '20230603'), ('Qt5', '5.15.10'), - ('Lua', '5.4.6'), - ('wxWidgets', '3.2.2.1') + ('Lua', '5.4.6') ] preconfigopts = 'autoreconf && ' -configopts = '--with-qt=qt5 --without-latex ' +configopts = '--with-qt=qt5 --without-latex --disable-wxwidgets' sanity_check_paths = { 'files': ['bin/gnuplot'], From 28fd136c3bb7fddc3778195e3cad133c6ee6babc Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 30 Aug 2023 09:31:48 +0000 Subject: [PATCH 8616/9987] adding easyconfigs: CFITSIO-4.3.0-GCCcore-12.3.0.eb --- .../c/CFITSIO/CFITSIO-4.3.0-GCCcore-12.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..164f73275f6 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '4.3.0' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-4.0.0_install_test_data.patch'] +checksums = [ + {'cfitsio-4.3.0.tar.gz': 'fdadc01d09cf9f54253802c5ec87eb10de51ce4130411415ae88c30940621b8b'}, + {'CFITSIO-4.0.0_install_test_data.patch': '75559db8b0648bc90ea9bb81a74acfd89913236ee0a2daf533477cddd37ea8a6'}, +] + +dependencies = [('cURL', '8.0.1')] + + +builddependencies = [ + ('binutils', '2.40'), +] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = '&& make shared && make testprog' + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + ('cd %(installdir)s/share && testprog'), +] + +moduleclass = 'lib' From 748f11efce2bdb52fbea2ae19e19f2e12f5ea63f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 30 Aug 2023 12:36:17 +0200 Subject: [PATCH 8617/9987] adding easyconfigs: anadama2-0.10.0-foss-2022a.eb, biobakery-workflows-3.1-foss-2022a.eb, kneaddata-0.12.0-foss-2022a.eb, LevelDB-1.22-GCCcore-11.3.0.eb --- .../a/anadama2/anadama2-0.10.0-foss-2022a.eb | 39 +++++++++++++++ .../biobakery-workflows-3.1-foss-2022a.eb | 36 +++++++++++++ .../kneaddata/kneaddata-0.12.0-foss-2022a.eb | 31 ++++++++++++ .../l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb | 50 +++++++++++++++++++ 4 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb new file mode 100644 index 00000000000..5cbca4d1086 --- /dev/null +++ b/easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'anadama2' +version = '0.10.0' + +homepage = 'http://huttenhower.sph.harvard.edu/anadama2' + +description = """AnADAMA2 is the next generation of AnADAMA +(Another Automated Data Analysis Management Application). AnADAMA is a tool to +create reproducible workflows and execute them efficiently.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = { + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), + ('LevelDB', '1.22'), + ('IPython', '8.5.0'), +} + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('Pweave', '0.30.3', { + 'checksums': ['5e5298d90e06414a01f48e0d6aa4c36a70c5f223d929f2a9c7e2d388451c7357'], + }), + (name, version, { + 'preinstallopts': 'sed -i "s/==0.25//g" requirements.txt && ', + 'checksums': ['386c4d0f4c96bf078ac2b595bafcadaa43cd44cdb1a864dc8ebc42dc1664f87f'], + }), +] + +use_pip = True +sanity_pip_check = True diff --git a/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb b/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb new file mode 100644 index 00000000000..bf1ee1a59d8 --- /dev/null +++ b/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'biobakery-workflows' +version = '3.1' + +homepage = 'http://huttenhower.sph.harvard.edu/biobakery_workflows' + +description = """bioBakery workflows is a collection of workflows and tasks for executing +common microbial community analyses using standardized, validated tools and parameters. +Quality control and statistical summary reports are automatically generated for most data +types, which include 16S amplicons, metagenomes, and metatranscriptomes. Workflows are run +directly from the command line and tasks can be imported to create your own custom workflows. +The workflows and tasks are built with AnADAMA2 which allows for parallel task execution locally +and in a grid compute environment.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + + +dependencies = { + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('kneaddata', '0.12.0'), + ('humann', '3.6'), + ('MetaPhlAn', '4.0.6'), + ('anadama2', '0.10.0'), +} + +sources = ["biobakery_workflows-%(version)s.tar.gz"] +checksums = ['c11a00192aa0bd6a6978eabef768c483dd240281991ce2a31bfaf291fe3d0e2b'] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = [ + """biobakery_workflows --help""", +] diff --git a/easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb b/easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb new file mode 100644 index 00000000000..a6db376ee34 --- /dev/null +++ b/easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'kneaddata' +version = '0.12.0' + +homepage = 'http://huttenhower.sph.harvard.edu/kneaddata' + +description = """KneadData is a tool designed to perform quality control on metagenomic and +metatranscriptomic sequencing data, especially data from microbiome experiments.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + + +dependencies = [ + ('Python', '3.10.4'), + ('Trimmomatic', '0.39', '-Java-%(javaver)s', SYSTEM), + ('Bowtie2', '2.4.5'), + ('Java', '11', '', SYSTEM), + ('TRF', '4.09.1'), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), +] + + +exts_list = [ + (name, version, { + 'checksums': ['b211bf973ea50cc89dd5935761ca3b101d422cfb62b215aae08f5ed92a624a58'], + }), +] + +use_pip = True +sanity_pip_check = True diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..239bc420990 --- /dev/null +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'Bundle' + +name = 'LevelDB' +version = '1.22' + +homepage = 'https://github.com/google/leveldb' +description = """LevelDB is a fast key-value storage library written at Google that provides an +ordered mapping from string keys to string values.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('LevelDB', version, { + 'source_urls': ['https://github.com/google/leveldb/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'configopts': "-DBUILD_SHARED_LIBS=ON -DLEVELDB_BUILD_BENCHMARKS=OFF ", + }), + ('leveldb', '0.201', { + 'easyblock': 'PythonPackage', + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'use_pip': True, + 'download_dep_fail': True, + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['include/leveldb/cache.h', 'include/leveldb/table.h', + 'lib/libleveldb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From 9a7c32213fe93a6503a4e19f7398ca82d01af3e3 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 30 Aug 2023 12:43:23 +0200 Subject: [PATCH 8618/9987] small mistakes --- .../easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb | 2 ++ .../biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb | 3 ++- .../easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb | 4 ++-- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb index 5cbca4d1086..c6b84442785 100644 --- a/easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb @@ -37,3 +37,5 @@ exts_list = [ use_pip = True sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb b/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb index bf1ee1a59d8..d0fd3a52893 100644 --- a/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb @@ -15,7 +15,6 @@ and in a grid compute environment.""" toolchain = {'name': 'foss', 'version': '2022a'} - dependencies = { ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), @@ -34,3 +33,5 @@ sanity_pip_check = True sanity_check_commands = [ """biobakery_workflows --help""", ] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb b/easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb index a6db376ee34..7c984435009 100644 --- a/easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb +++ b/easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb @@ -10,7 +10,6 @@ metatranscriptomic sequencing data, especially data from microbiome experiments. toolchain = {'name': 'foss', 'version': '2022a'} - dependencies = [ ('Python', '3.10.4'), ('Trimmomatic', '0.39', '-Java-%(javaver)s', SYSTEM), @@ -20,7 +19,6 @@ dependencies = [ ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), ] - exts_list = [ (name, version, { 'checksums': ['b211bf973ea50cc89dd5935761ca3b101d422cfb62b215aae08f5ed92a624a58'], @@ -29,3 +27,5 @@ exts_list = [ use_pip = True sanity_pip_check = True + +moduleclass = 'bio' From bb54724cd0b7b949616dea2f1a94461da2584027 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 30 Aug 2023 12:45:32 +0000 Subject: [PATCH 8619/9987] adding easyconfigs: LERC-4.0.0-GCCcore-12.3.0.eb --- .../l/LERC/LERC-4.0.0-GCCcore-12.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f02f2cfe6ab --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'LERC' +version = '4.0.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Esri/lerc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91431c2b16d0e3de6cbaea188603359f87caed08259a645fd5a3805784ee30a0'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +postinstallcmds = [ + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/test.c", +] + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cd %(builddir)s && g++ %(installdir)s/test.c -o lerctest -lLerc && ./lerctest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 769a4fca4851fc50e3355460f9b4d2210b7dc54e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 30 Aug 2023 15:53:54 +0200 Subject: [PATCH 8620/9987] tests --- .../b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb b/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb index d0fd3a52893..0ece4a894e7 100644 --- a/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb @@ -28,6 +28,7 @@ sources = ["biobakery_workflows-%(version)s.tar.gz"] checksums = ['c11a00192aa0bd6a6978eabef768c483dd240281991ce2a31bfaf291fe3d0e2b'] use_pip = True +download_dep_fail = True sanity_pip_check = True sanity_check_commands = [ From 623861a5aaf5e0b86f45d7faf117de67ec272461 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 30 Aug 2023 15:55:48 +0200 Subject: [PATCH 8621/9987] add missing checksums --- .../tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb index 6d41078bd96..488325cffed 100644 --- a/easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb @@ -23,10 +23,14 @@ sources = [ 'alt_location': 'TensorFlow/extensions', }, ] - patches = [ ('compression_local-tensorflow-repo.sed', '.'), ] +checksums = [ + {'tensorflow-compression-2.11.0.tar.gz': '7f0127c3ff4243e41c5af59be5909a635562191f462053e2d86c234bf638be4f'}, + {'v2.11.0.tar.gz': '99c732b92b1b37fc243a559e02f9aef5671771e272758aa4aec7f34dc92dac48'}, + {'compression_local-tensorflow-repo.sed': 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5'}, +] builddependencies = [ ('Bazel', '5.1.1'), From 3dd4f4c47df2888f53c7e76dff684ee83cd311a8 Mon Sep 17 00:00:00 2001 From: hediinn Date: Wed, 30 Aug 2023 15:22:18 +0100 Subject: [PATCH 8622/9987] adding easyconfigs: PROJ-6.3.1-GCCcore-10.3.0.eb --- .../p/PROJ/PROJ-6.3.1-GCCcore-10.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-6.3.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-6.3.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-6.3.1-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..87149b669a0 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-6.3.1-GCCcore-10.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '6.3.1' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6de0112778438dcae30fcc6942dee472ce31399b9e5a2b67e8642529868c86f8'] + + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.36.1'), +] + +dependencies = [ + ('SQLite', '3.35.4'), + ('LibTIFF', '4.2.0'), + ('cURL', '7.76.0'), + ('XZ', '5.2.5'), +] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From d999fb40bb9a5f908c0b6ee6b8ba64e98def005e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 30 Aug 2023 17:26:34 +0200 Subject: [PATCH 8623/9987] Fix disabling of wxwidgets for gnuplot --- easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb index 45e7dccbb86..2dcbf8e9d5a 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.6-GCCcore-12.2.0.eb @@ -33,7 +33,7 @@ dependencies = [ preconfigopts = 'autoreconf && ' -configopts = '--with-qt=qt5 --without-latex --without-wx' +configopts = '--with-qt=qt5 --without-latex --disable-wxwidgets' sanity_check_paths = { 'files': ['bin/gnuplot'], From 94d17a446043e11bde66ed34f09f737e8c4d87e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Aug 2023 18:35:15 +0200 Subject: [PATCH 8624/9987] adding easyconfigs: GAPPadder-20170601-foss-2021b-Python-2.7.18.eb, Biopython-1.76-foss-2021b-Python-2.7.18.eb, KMC-3.2.1-GCC-11.2.0-Python-2.7.18.eb --- ...Biopython-1.76-foss-2021b-Python-2.7.18.eb | 43 +++++++++++++++++ ...adder-20170601-foss-2021b-Python-2.7.18.eb | 44 ++++++++++++++++++ .../KMC/KMC-3.2.1-GCC-11.2.0-Python-2.7.18.eb | 46 +++++++++++++++++++ 3 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/k/KMC/KMC-3.2.1-GCC-11.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..a669640f918 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.76-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.76' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3873cb98dad5e28d5e3f2215a012565345a398d3d2c4eebf7cd701757b828c72'] + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2021.10', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..f9d0453e602 --- /dev/null +++ b/easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'GAPPadder' +version = '20170601' +local_commit = 'a359750' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/simoncchu/GAPPadder' +description = "GAPPadder is tool for closing gaps on draft genomes with short sequencing data" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/simoncchu/GAPPadder/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['d255e863cc2627116d7cb1d112283a7cf794d349de28f673daf32ce68d8bba90'] + +dependencies = [ + ('Python', '2.7.18'), + ('Biopython', '1.76', versionsuffix), + ('KMC', '3.2.1', versionsuffix), + ('Velvet', '1.2.10', '-mt-kmer_191'), + ('BWA', '0.7.17'), + ('SAMtools', '1.16.1'), + ('BamTools', '2.5.2'), +] + +# remove prebuilt binaries +prebuildopts = "rm TERefiner_1 TERefiner/TERefiner_1 ContigsMerger ContigsCompactor-*/ContigsMerger/ContigsMerger && " +prebuildopts += "cd TERefiner && " +prebuildopts += "make BAMTOOLS=$EBROOTBAMTOOLS/include/bamtools BAMTOOLS_LD=$EBROOTNBAMTOOLS/lib && cd .. && " +prebuildopts += "cd ContigsCompactor-v0.2.0/ContigsMerger && " + +files_to_copy = [ + (['TERefiner/TERefiner_1', 'ContigsCompactor-v0.2.0/ContigsMerger/ContigsMerger'], 'bin'), + '*.py', + 'configuration.json', +] + +sanity_check_paths = { + 'files': ['bin/TERefiner_1', 'bin/ContigsMerger', 'configuration.json', 'main.py', 'pick_contigs.py'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/KMC/KMC-3.2.1-GCC-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/k/KMC/KMC-3.2.1-GCC-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..d69650ebbaa --- /dev/null +++ b/easybuild/easyconfigs/k/KMC/KMC-3.2.1-GCC-11.2.0-Python-2.7.18.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'KMC' +version = '3.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sun.aei.polsl.pl/kmc' +description = "KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/refresh-bio/KMC/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7db333091a754508163a097c41720cf32a80abe160bef60f3fc82c8da1d67896'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('Python', '2.7.18'), +] + +# Makefile does static linking with libc.a, libpthread.a, libm.a +osdependencies = [('glibc-static', 'libc6-dev')] + +prebuildopts = "sed -i 's@[^ ]*/libz.a@${EBROOTZLIB}/lib/libz.a@g' Makefile && " +prebuildopts += "sed -i 's@[^ ]*/libbz2.a@${EBROOTBZIP2}/lib/libbz2.a@g' Makefile && " +prebuildopts += "sed -i 's/python3-config --extension-suffix/echo .so/g' Makefile && " +prebuildopts += "sed -i 's/python3/python/g' Makefile && " + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/kmc', 'bin/kmc_dump'], + 'dirs': [], +} + +sanity_check_commands = [ + "kmc", + "kmc_dump", + "python -c 'import py_kmc_api'", +] + +# Python bindings are also located in bin/ +modextrapaths = {'PYTHONPATH': ['bin']} + +moduleclass = 'bio' From 0bd001b079763c50fc7b78fc8d6ca5da10267a0e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Aug 2023 18:35:22 +0200 Subject: [PATCH 8625/9987] adding easyconfigs: KMC-3.2.2-GCC-12.2.0.eb --- .../easyconfigs/k/KMC/KMC-3.2.2-GCC-12.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/k/KMC/KMC-3.2.2-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/k/KMC/KMC-3.2.2-GCC-12.2.0.eb b/easybuild/easyconfigs/k/KMC/KMC-3.2.2-GCC-12.2.0.eb new file mode 100644 index 00000000000..f3b30ce7394 --- /dev/null +++ b/easybuild/easyconfigs/k/KMC/KMC-3.2.2-GCC-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'KMC' +version = '3.2.2' + +homepage = 'http://sun.aei.polsl.pl/kmc' +description = "KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/refresh-bio/KMC/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b648a750ef1cb11feb63439858dbcf765cdb4f777c15dff766d7282cfcee8b9'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('Python', '3.10.8'), +] + +# Makefile does static linking with libc.a, libpthread.a, libm.a +osdependencies = [('glibc-static', 'libc6-dev')] + +prebuildopts = """sed -i 's@^#include.*zlib.h.*@#include "zlib.h"@g' ./kmc_core/fastq_reader.h && """ +prebuildopts += """sed -i 's@^#include.*zlib.h.*@#include "zlib.h"@g' ./kmc_tools/fastq_reader.h && """ + +buildopts = "LIB_ZLIB=$EBROOTZLIB/lib/libz.a" + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/kmc', 'bin/kmc_dump'], + 'dirs': [], +} + +sanity_check_commands = [ + "kmc", + "kmc_dump", + "python -c 'import py_kmc_api'", +] + +# Python bindings are also located in bin/ +modextrapaths = {'PYTHONPATH': ['bin']} + +moduleclass = 'bio' From 35ab1ab11f25874e72d45441ae143b52bb768c35 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Aug 2023 18:55:58 +0200 Subject: [PATCH 8626/9987] stick to SAMtools 1.14 as dependency for GAPPadder --- .../g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb index f9d0453e602..1778ef1545b 100644 --- a/easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/g/GAPPadder/GAPPadder-20170601-foss-2021b-Python-2.7.18.eb @@ -20,7 +20,7 @@ dependencies = [ ('KMC', '3.2.1', versionsuffix), ('Velvet', '1.2.10', '-mt-kmer_191'), ('BWA', '0.7.17'), - ('SAMtools', '1.16.1'), + ('SAMtools', '1.14'), ('BamTools', '2.5.2'), ] From 9e6374ec502abdfc1b0f7dace91aacc639bf3ab9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2023 08:47:55 +0200 Subject: [PATCH 8627/9987] fix trivial code style issues in easyconfig for GTK3 3.24.37 w/ GCCcore/12.3.0 --- easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb index 3c25df1bded..844fb04aca8 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb @@ -55,11 +55,11 @@ components = [ ('adwaita-icon-theme', '44.0', { 'easyblock': 'ConfigureMake', 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], - 'patches': ['adwaita-icon-theme-44.0_disable-svg-conversion.patch'], + 'patches': ['adwaita-icon-theme-44.0_disable-svg-conversion.patch'], 'checksums': [ '4889c5601bbfecd25d80ba342209d0a936dcf691ee56bd6eca4cde361f1a664c', - # adwaita-icon-theme-44.0_disable-svg-conversion.patch - '9957c8b3d2a1cf8d89d6e943e59c683dbf5c5b37687316265cc82e755208f40b' + # adwaita-icon-theme-44.0_disable-svg-conversion.patch + '9957c8b3d2a1cf8d89d6e943e59c683dbf5c5b37687316265cc82e755208f40b', ], 'preconfigopts': 'autoreconf -f -i && ', }), From 31f5628dcc546481ab65f93b5bbb964ea473ee36 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 31 Aug 2023 09:38:23 +0200 Subject: [PATCH 8628/9987] fix comment --- easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb index 01ff25737ae..72a8a9de06b 100644 --- a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb @@ -97,7 +97,7 @@ configopts += '-DBUILD_qtwayland=OFF ' # Does not work on CentOS 7 # configopts += '-DBUILD_qtgamepad=OFF ' # Gamepad does not work on CentOS 7. It have been removed from Qt6.0.0 and has not been added back # make sure QtWebEngine component is being built & installed -#check_qtwebengine = True +# check_qtwebengine = True sanity_check_paths = { 'files': ['bin/qmake6', 'lib/libQt6Core.so', 'lib/libQt6WebEngineCore.so'], 'dirs': ['include/QtCore', 'include/QtWebEngineCore'], From ef549d6735402d36cacab6c79f8691cd58a2bcb7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 31 Aug 2023 10:27:17 +0200 Subject: [PATCH 8629/9987] add PYTHONPATH, change sanity check commands --- .../v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb index 20f757374a5..32a39ef352a 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb @@ -61,18 +61,19 @@ configopts = "-DZIG=OFF -DWFA_GITMODULE=OFF -DWFA_INCLUDE_DIRS=$EBROOTWFA2/inclu postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] -modextrapaths = {'PATH': ['scripts']} +modextrapaths = { + 'PATH': 'scripts', + 'PYTHONPATH': 'lib', +} sanity_check_paths = { - 'files': [ - 'bin/vcffilter', - 'bin/vcfcombine', - 'lib/libvcflib.a', - 'lib/pyvcflib.cpython-310-x86_64-linux-gnu.so', - ], + 'files': ['bin/vcffilter', 'bin/vcfcombine', 'lib/libvcflib.a'], 'dirs': ['scripts', 'include'], } -sanity_check_commands = ["vcfwave --help"] +sanity_check_commands = [ + "python -c 'import pyvcflib'", + "vcfwave --help", +] moduleclass = 'bio' From 0dc77510b9c692ef2a49e43966f7f96799cb7fa1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 31 Aug 2023 12:32:53 +0200 Subject: [PATCH 8630/9987] add requested changes from review --- ...2.0.eb => drmaa-python-0.7.9-GCCcore-12.2.0-slurm.eb} | 1 + .../easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb | 6 ++++-- .../s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb | 9 ++------- 3 files changed, 7 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/d/drmaa-python/{drmaa-python-0.7.9-GCCcore-12.2.0.eb => drmaa-python-0.7.9-GCCcore-12.2.0-slurm.eb} (96%) diff --git a/easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0-slurm.eb similarity index 96% rename from easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0-slurm.eb index 8fae0d0fd50..e5f9e796695 100644 --- a/easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/drmaa-python/drmaa-python-0.7.9-GCCcore-12.2.0-slurm.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'drmaa-python' version = '0.7.9' +versionsuffix = '-slurm' homepage = 'https://github.com/pygridtools/drmaa-python' description = """Distributed Resource Management Application API (DRMAA) bindings for Python.""" diff --git a/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb b/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb index f4033c48db0..d575c58e61c 100644 --- a/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb +++ b/easybuild/easyconfigs/m/Mikado/Mikado-2.3.4-foss-2022b.eb @@ -30,6 +30,8 @@ dependencies = [ ('snakemake', '7.32.3'), ('pyfaidx', '0.7.2.1'), ('Greenlet', '2.0.2'), + # DRMAA is not needed but it can be used on clusters with Slurm + # ('drmaa-python', '0.7.9', '-slurm'), ] use_pip = True @@ -38,7 +40,7 @@ sanity_pip_check = True local_old_line = 'from scipy._build_utils import numpy_nodepr_api' local_new_line = """numpy_nodepr_api = dict(define_macros=[("NPY_NO_DEPRECATED_API", "NPY_1_9_API_VERSION")])""" # hardcoded value, used to be imported from scipy._build_utils (which is no longer available since scipy 1.10)' -local_code_patch_cmd = f"sed -i 's/{local_old_line}/{local_new_line}/g' setup.py" +local_code_patch_cmd = "sed -i 's/%s/%s/g' setup.py" % (local_old_line, local_new_line) # drmaa-python is not necessary and it would require slurm-drmaa while Slurm is not available on all clusters local_dep_patch_cmd = "sed -i '/^drmaa$/d' requirements.txt" @@ -72,7 +74,7 @@ exts_list = [ 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], }), (name, version, { - 'preinstallopts': f"{local_code_patch_cmd} && {local_dep_patch_cmd} && ", + 'preinstallopts': "%s && %s && " % (local_code_patch_cmd, local_dep_patch_cmd), 'modulename': name, 'checksums': ['6d8844bacacc776214cf35cb148fa638c029b2972751d04fc1f7d0d8f3e961c2'], }), diff --git a/easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb index bd4645b7acb..cd8e5c1a3e1 100644 --- a/easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/slurm-drmaa/slurm-drmaa-1.1.3-GCCcore-12.2.0.eb @@ -21,13 +21,8 @@ builddependencies = [ ] sanity_check_paths = { - 'files': [ - 'include/drmaa.h', - 'lib/libdrmaa.a', - 'lib/libdrmaa.so', - 'bin/drmaa-run', - ], - 'dirs': ['etc'] + 'files': ['bin/drmaa-run', 'include/drmaa.h', 'lib/libdrmaa.a', 'lib/libdrmaa.%s' % SHLIB_EXT], + 'dirs': ['etc'], } moduleclass = 'lib' From da28aead6d393be53e2335449f64dbd474647d85 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 31 Aug 2023 12:44:37 +0200 Subject: [PATCH 8631/9987] fix line too long --- .../easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb index 72a8a9de06b..9bb23c9a2f0 100644 --- a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb @@ -81,12 +81,12 @@ dependencies = [ # Error when trying native gRPC # In file included from gen/extensions/browser/browser_sources_jumbo_7.cc:13: -# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc: In member function virtual bool extensions::FormDataParserUrlEncoded::SetSource(base::StringPiece): -# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc:429:11: error: using StringPiece = class absl::string_view {aka class absl::string_view} has no member named set +# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc: In member function virtual bool extensions::FormDataParserUrlEncoded::SetSource(base::StringPiece): # noqa: E501 +# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc:429:11: error: using StringPiece = class absl::string_view {aka class absl::string_view} has no member named set # noqa: E501 # 429 | source_.set(source.data(), source.size()); # | ^~~ -# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc: In member function virtual bool extensions::FormDataParserMultipart::SetSource(base::StringPiece): -# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc:573:11: error: using StringPiece = class absl::string_view {aka class absl::string_view} has no member named set +# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc: In member function virtual bool extensions::FormDataParserMultipart::SetSource(base::StringPiece): # noqa: E501 +# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc:573:11: error: using StringPiece = class absl::string_view {aka class absl::string_view} has no member named set # noqa: E501 # 573 | source_.set(source.data(), source.size()); # | ^~~ @@ -94,7 +94,7 @@ preconfigopts = 'sed -i "s/MultiMedia/Multimedia/g" ../qt-everywhere-src-%(versi configopts = '-Wno-dev ' configopts += '-DFEATURE_qtpdf_build=OFF ' # Requires CUPS configopts += '-DBUILD_qtwayland=OFF ' # Does not work on CentOS 7 -# configopts += '-DBUILD_qtgamepad=OFF ' # Gamepad does not work on CentOS 7. It have been removed from Qt6.0.0 and has not been added back +# configopts += '-DBUILD_qtgamepad=OFF ' # Gamepad does not work on CentOS 7, removed from Qt6.0.0 and not added back # make sure QtWebEngine component is being built & installed # check_qtwebengine = True From 6a2efe4114becc7aa02f6f95a9610375f3292d91 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 31 Aug 2023 11:52:07 +0000 Subject: [PATCH 8632/9987] adding easyconfigs: inferCNV-1.14.2-foss-2022b-R-4.2.2.eb, rjags-4-13-foss-2022b-R-4.2.2.eb --- .../inferCNV-1.14.2-foss-2022b-R-4.2.2.eb | 54 +++++++++++++++++++ .../r/rjags/rjags-4-13-foss-2022b-R-4.2.2.eb | 29 ++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/i/inferCNV/inferCNV-1.14.2-foss-2022b-R-4.2.2.eb create mode 100644 easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/i/inferCNV/inferCNV-1.14.2-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.14.2-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..06120b55395 --- /dev/null +++ b/easybuild/easyconfigs/i/inferCNV/inferCNV-1.14.2-foss-2022b-R-4.2.2.eb @@ -0,0 +1,54 @@ +easyblock = 'Bundle' + +name = 'inferCNV' +version = '1.14.2' +versionsuffix = '-R-%(rver)s' +local_biocver = '3.16' + +homepage = 'https://github.com/broadinstitute/inferCNV/wiki' +description = """InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence + for somatic large-scale chromosomal copy number alterations, such as gains or + deletions of entire chromosomes or large segments of chromosomes.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('R', '4.2.2'), + ('R-bundle-Bioconductor', local_biocver, '-R-%(rver)s'), + ('rjags', '4-13', '-R-%(rver)s'), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/release/bioc/src/contrib/', # current version of packages + 'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_biocver, + 'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_biocver, + 'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_biocver, + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +exts_list = [ + ('phyclust', '0.1-33', { + 'checksums': ['38786608193bcad6aeb5517f2d5f836c9773bdd09fc484b4bd40b06a71f5a413'], + }), + ('infercnv', version, { + 'checksums': ['7705f9d2796303f55034e026578a5877caf80b8dc929a15918b242a89a0ca512'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['infercnv'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..77fe842ea5d --- /dev/null +++ b/easybuild/easyconfigs/r/rjags/rjags-4-13-foss-2022b-R-4.2.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rjags' +version = '4-13' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/rjags' +description = """The rjags package is an interface to the JAGS library.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/rjags/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['f85cc34c5127b828d8a3fa3613ef29f147c868bdaf55eb0f7406c10abbf92b32'] + +dependencies = [ + ('R', '4.2.2'), + ('JAGS', '4.3.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + +moduleclass = 'math' From 93b0e1fcc742819ef4458d61667d843796fd4732 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 31 Aug 2023 14:08:40 +0200 Subject: [PATCH 8633/9987] adding easyconfigs: Julia-1.9.3-linux-x86_64.eb --- .../j/Julia/Julia-1.9.3-linux-x86_64.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb new file mode 100644 index 00000000000..7b207dc635c --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.9.3-linux-x86_64.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Updated by: Dugan Witherick, University of Warwick +# Robert Mijakovic +# Wahid Mainassara + +easyblock = 'Tarball' + +name = 'Julia' +version = '1.9.3' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['d76670cc9ba3e0fd4c1545dd3d00269c0694976a1176312795ebce1692d323d1'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +modextravars = { + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', +} + +moduleclass = 'lang' From 838560ff173af11bc43d247ed2bb6e26536fd0d4 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Thu, 31 Aug 2023 15:02:57 +0200 Subject: [PATCH 8634/9987] Add exception for Jupyter-bundle for sanity_check_paths, since this just bundles together existing modules. It doesn't install anything itself --- test/easyconfigs/easyconfigs.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 34a7f346a85..8e7b26748ee 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1139,8 +1139,11 @@ def test_pr_sanity_check_paths(self): # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co, + # Jupyter-bundle: JupyterHub + JupyterLab + notebook + nbclassic + jupyter-server-proxy + # + jupyterlmod + jupyter-resource-usage # Python-bundle: Python + SciPy-bundle + matplotlib + JupyterLab - bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'Python-bundle', 'ROCm'] + bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'ESL-Bundle', 'FEniCS', 'GCC', 'Jupyter-bundle', + 'Python-bundle', 'ROCm'] failing_checks = [] From b5d64b01dc886bf8fbc997549697bb91cdfa3c61 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2023 16:05:03 +0200 Subject: [PATCH 8635/9987] fix continuation line over-indented for hanging indent in GTK3 3.24.37 easyconfig --- .../g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb index 844fb04aca8..242862f3de7 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.37-GCCcore-12.3.0.eb @@ -53,15 +53,15 @@ components = [ 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], }), ('adwaita-icon-theme', '44.0', { - 'easyblock': 'ConfigureMake', - 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], - 'patches': ['adwaita-icon-theme-44.0_disable-svg-conversion.patch'], - 'checksums': [ - '4889c5601bbfecd25d80ba342209d0a936dcf691ee56bd6eca4cde361f1a664c', - # adwaita-icon-theme-44.0_disable-svg-conversion.patch - '9957c8b3d2a1cf8d89d6e943e59c683dbf5c5b37687316265cc82e755208f40b', - ], - 'preconfigopts': 'autoreconf -f -i && ', + 'easyblock': 'ConfigureMake', + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'patches': ['adwaita-icon-theme-44.0_disable-svg-conversion.patch'], + 'checksums': [ + '4889c5601bbfecd25d80ba342209d0a936dcf691ee56bd6eca4cde361f1a664c', + # adwaita-icon-theme-44.0_disable-svg-conversion.patch + '9957c8b3d2a1cf8d89d6e943e59c683dbf5c5b37687316265cc82e755208f40b', + ], + 'preconfigopts': 'autoreconf -f -i && ', }), ] From 6a9b44111a883768098208cbf490f74668733dfb Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Thu, 31 Aug 2023 17:07:23 +0200 Subject: [PATCH 8636/9987] Remove trailing whitespace --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 8e7b26748ee..f81febaa11c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1139,7 +1139,7 @@ def test_pr_sanity_check_paths(self): # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co, - # Jupyter-bundle: JupyterHub + JupyterLab + notebook + nbclassic + jupyter-server-proxy + # Jupyter-bundle: JupyterHub + JupyterLab + notebook + nbclassic + jupyter-server-proxy # + jupyterlmod + jupyter-resource-usage # Python-bundle: Python + SciPy-bundle + matplotlib + JupyterLab bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'ESL-Bundle', 'FEniCS', 'GCC', 'Jupyter-bundle', From 867e06859a92889f561ec3aaafc5148a17f6da78 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2023 18:43:50 +0200 Subject: [PATCH 8637/9987] enhance sanity check for Ghostscript 10.01.2 --- .../g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb index bb09de3527b..5711dfde5bf 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb @@ -48,8 +48,10 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['bin/gs', 'lib/libgs.so'], + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], 'dirs': ['lib/%(namelower)s', 'include/%(namelower)s', 'share/man'], } +sanity_check_commands = ["gs --help"] + moduleclass = 'tools' From f0e3764194e65815ed129c6345235be11f39809b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2023 18:46:04 +0200 Subject: [PATCH 8638/9987] use SHLIB_EXT instead of hardcoding .so in libaec and ecCodes easyconfigs --- easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb | 2 +- easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb index bab6e90da5e..4a517a7ca7c 100644 --- a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023a.eb @@ -39,7 +39,7 @@ sanity_check_paths = { 'bin/gts_compare', 'bin/gts_copy', 'bin/gts_dump', 'bin/gts_filter', 'bin/gts_get', 'bin/gts_ls', 'bin/metar_compare', 'bin/metar_copy', 'bin/metar_dump', 'bin/metar_filter', 'bin/metar_get', 'bin/metar_ls', 'bin/codes_count', 'bin/codes_info', 'bin/codes_split_file', - 'lib/libeccodes_f90.so', 'lib/libeccodes.so'], + 'lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb index b194a947f0e..227eaf25285 100644 --- a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb @@ -24,7 +24,8 @@ builddependencies = [ sanity_check_paths = { - 'files': ['bin/aec', 'include/%(name)s.h', 'include/szlib.h', 'lib/%(name)s.a', 'lib/%(name)s.so'], + 'files': ['bin/aec', 'include/%(name)s.h', 'include/szlib.h', + 'lib/%(name)s.a', 'lib/%(name)s.%s' % SHLIB_EXT], 'dirs': ['share/man'], } From ce2ab11dda64d0caca10beb6d22a6662357e617f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 31 Aug 2023 18:47:33 +0200 Subject: [PATCH 8639/9987] fix sanity_check_paths for libaec --- easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb index 227eaf25285..e434092683d 100644 --- a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.3.0.eb @@ -25,7 +25,7 @@ builddependencies = [ sanity_check_paths = { 'files': ['bin/aec', 'include/%(name)s.h', 'include/szlib.h', - 'lib/%(name)s.a', 'lib/%(name)s.%s' % SHLIB_EXT], + 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], 'dirs': ['share/man'], } From 92b270dafeb22feaa32a208bb261e2d76da419d2 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 1 Sep 2023 08:28:02 +0000 Subject: [PATCH 8640/9987] Added M4 as a dependency --- easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb index 8fd0a77a7bc..4ae171a8b3c 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb @@ -24,6 +24,7 @@ toolchain = SYSTEM builddependencies = [ ('binutils', '2.32'), + ('M4', '1.4.19'), ] default_easyblock = 'ConfigureMake' From e341cf1291b4d3b1e6fe74f534fa9f2862280fab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 10:35:39 +0200 Subject: [PATCH 8641/9987] fix sanity check command for CDO 2.2.2 --- easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb index 658b0ffc5c1..0adb6ba2358 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb @@ -48,6 +48,6 @@ sanity_check_paths = { 'dirs': ['include'], } -sanity_check_commands = ["cdo --version 2>&1 | grep 'Climate Data Operators version : %(version)s'"] +sanity_check_commands = ["cdo --version 2>&1 | grep 'Climate Data Operators version %(version)s'"] moduleclass = 'data' From 7d55266ea45c731f9d3f3bc6e645d12592926547 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 10:42:55 +0200 Subject: [PATCH 8642/9987] remove bare easyconfig for Python 2.7.18, not needed (non-bare variant is used as build dep for Qt5) --- .../Python-2.7.18-GCCcore-12.3.0-bare.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0-bare.eb deleted file mode 100644 index b529c6fdaac..00000000000 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0-bare.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'Python' -version = '2.7.18' -versionsuffix = '-bare' - -homepage = 'https://python.org/' -description = """Python is a programming language that lets you work more quickly and integrate your systems - more effectively.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] -sources = [SOURCE_TGZ] -checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] - -builddependencies = [ - ('pkgconf', '1.9.5'), -] - -dependencies = [ - ('binutils', '2.40'), - ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib - ('zlib', '1.2.13'), - ('libreadline', '8.2'), - ('ncurses', '6.4'), - ('SQLite', '3.42.0'), - ('OpenSSL', '1.1', '', SYSTEM), -] - -install_pip = True - -moduleclass = 'lang' From 868d1c3af4ddd55d2358a8395afd6a8df641af5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 10:43:53 +0200 Subject: [PATCH 8643/9987] remove easyconfig for GTK3 3.24.35, superseded by easyconfig for GTK3 3.24.37 --- .../g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb | 70 ------------------- 1 file changed, 70 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb deleted file mode 100644 index 5cf20d415fc..00000000000 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.3.0.eb +++ /dev/null @@ -1,70 +0,0 @@ -easyblock = 'Bundle' - -name = 'GTK3' -version = '3.24.35' # not updating version, as the latest one doesn't work on configure basis - -homepage = 'https://developer.gnome.org/gtk3/stable/' -description = """GTK+ is the primary library used to construct user interfaces in GNOME. It - provides all the user interface controls, or widgets, used in a common - graphical application. Its object-oriented API allows you to construct - user interfaces without dealing with the low-level details of drawing and - device interaction. -""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('Autotools', '20220317'), - ('GObject-Introspection', '1.76.1'), - ('gettext', '0.21.1'), - ('pkgconf', '1.9.5'), - ('cairo', '1.17.8'), - ('Perl', '5.36.1'), -] -dependencies = [ - ('ATK', '2.38.0'), - ('at-spi2-atk', '2.38.0'), - ('Gdk-Pixbuf', '2.42.9'), - ('Pango', '1.50.14'), - ('libepoxy', '1.5.10'), - ('X11', '20230603'), - ('FriBidi', '1.0.12'), -] - -default_easyblock = 'ConfigureMake' - -default_component_specs = { - 'sources': [SOURCELOWER_TAR_XZ], - 'start_dir': '%(namelower)s-%(version)s', -} - -components = [ - ('GTK+', version, { - 'source_urls': [FTPGNOME_SOURCE], - # fix packaging issue, see https://gitlab.gnome.org/GNOME/gtk/-/issues/5355 - 'preconfigopts': "mv testsuite/gtk/gtkresources.c gtk/ && ", - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", - }), - ('hicolor-icon-theme', '0.17', { - 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], - }), - ('adwaita-icon-theme', '42.0', { - 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], - 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], - 'preconfigopts': 'autoreconf -f -i && ', - }), -] - -postinstallcmds = ['gtk-update-icon-cache'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', - 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', - 'gtk-update-icon-cache']] + - ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], - 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + - ['share/icons/hicolor', 'share/icons/Adwaita'], -} - -moduleclass = 'vis' From f9861633b14d6bed780532f4cf568b20f3816df5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 10:45:30 +0200 Subject: [PATCH 8644/9987] remove easyconfig for Gdk-Pixbuf 2.42.9, superseded by easyconfig for Gdk-Pixbuf 2.42.10 --- .../Gdk-Pixbuf-2.42.9-GCCcore-12.3.0.eb | 46 ------------------- 1 file changed, 46 deletions(-) delete mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.9-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.9-GCCcore-12.3.0.eb deleted file mode 100644 index f4ec4a873ee..00000000000 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.9-GCCcore-12.3.0.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'MesonNinja' - -name = 'Gdk-Pixbuf' -version = '2.42.9' - -homepage = 'https://docs.gtk.org/gdk-pixbuf/' -description = """ - The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. - It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it - was distributed as part of GTK+ 2 but it was split off into a separate package - in preparation for the change to GTK+ 3. -""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = [FTPGNOME_SOURCE] -sources = [SOURCELOWER_TAR_XZ] -checksums = ['28f7958e7bf29a32d4e963556d241d0a41a6786582ff6a5ad11665e0347fc962'] - -builddependencies = [ - ('binutils', '2.40'), - ('Meson', '1.1.1'), - ('Ninja', '1.11.1'), - ('pkgconf', '1.9.5'), - ('GObject-Introspection', '1.76.1'), -] - -dependencies = [ - ('GLib', '2.77.1'), - ('libjpeg-turbo', '2.1.5.1'), - ('libpng', '1.6.39'), - ('LibTIFF', '4.5.0'), - ('X11', '20230603'), -] - -configopts = "--buildtype=release --default-library=both " -configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" - -sanity_check_paths = { - 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], - 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], -} - -sanity_check_commands = ["gdk-pixbuf-pixdata --help"] - -moduleclass = 'vis' From 230db2f46c1b180fb2a73f937f8b44a71efdede5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 10:49:06 +0200 Subject: [PATCH 8645/9987] add missing Bison build dep + favor PCRE2 over PCRE for SWIG 4.1.1 --- easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.3.0.eb index e3e212e0f5e..4986760a844 100644 --- a/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-12.3.0.eb @@ -12,11 +12,14 @@ source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['2af08aced8fcd65cdb5cc62426768914bedc735b1c250325203716f78e39ac9b'] -builddependencies = [('binutils', '2.40')] +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), +] dependencies = [ ('zlib', '1.2.13'), - ('PCRE', '8.45'), + ('PCRE2', '10.42'), ] configopts = '--without-alllang --with-boost=no' From e8967ef703c24a637e3ecac44c61f4d372d87a7a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 10:54:36 +0200 Subject: [PATCH 8646/9987] use GCC/12.3.0 toolchain for GST-plugins-base and GStreamer since GSL dependency was installed with GCC rather than GCCcore --- ...GCCcore-12.3.0.eb => GST-plugins-base-1.22.5-GCC-12.3.0.eb} | 3 +-- ...1.22.5-GCCcore-12.3.0.eb => GStreamer-1.22.5-GCC-12.3.0.eb} | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/g/GST-plugins-base/{GST-plugins-base-1.22.5-GCCcore-12.3.0.eb => GST-plugins-base-1.22.5-GCC-12.3.0.eb} (93%) rename easybuild/easyconfigs/g/GStreamer/{GStreamer-1.22.5-GCCcore-12.3.0.eb => GStreamer-1.22.5-GCC-12.3.0.eb} (94%) diff --git a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.5-GCC-12.3.0.eb similarity index 93% rename from easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.5-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.5-GCC-12.3.0.eb index 229786ea4a0..0f4b63ac607 100644 --- a/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.22.5-GCC-12.3.0.eb @@ -9,14 +9,13 @@ description = """GStreamer is a library for constructing graphs of media-handlin Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.""" -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-base'] sources = [SOURCELOWER_TAR_XZ] checksums = ['edd4338b45c26a9af28c0d35aab964a024c3884ba6f520d8428df04212c8c93a'] builddependencies = [ - ('binutils', '2.40'), ('Meson', '1.1.1'), ('Ninja', '1.11.1'), ('GObject-Introspection', '1.76.1'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.5-GCC-12.3.0.eb similarity index 94% rename from easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.5-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.5-GCC-12.3.0.eb index 09d16056f86..edec2378608 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.22.5-GCC-12.3.0.eb @@ -9,7 +9,7 @@ description = """GStreamer is a library for constructing graphs of media-handlin Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.""" -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] @@ -22,7 +22,6 @@ checksums = [ ] builddependencies = [ - ('binutils', '2.40'), ('Meson', '1.1.1'), ('Ninja', '1.11.1'), ('Perl', '5.36.1'), From 8e2718c090348e18a81d68e1cfe45a1198ba6613 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 10:55:02 +0200 Subject: [PATCH 8647/9987] stick to LibTIFF 4.5.0 as dependency for wxWidgets v3.2.2.1 --- .../easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb index 00d77af7047..0356fac7946 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb @@ -32,7 +32,7 @@ dependencies = [ ('libjpeg-turbo', '2.1.5.1'), ('XZ', '5.4.2'), ('jbigkit', '2.1'), - ('LibTIFF', '4.5.1'), + ('LibTIFF', '4.5.0'), ('expat', '2.5.0'), ('GTK3', '3.24.37'), ('X11', '20230603'), From cab3caa9f9844f31212a4416cde95febf9df8302 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 11:19:21 +0200 Subject: [PATCH 8648/9987] use Gdk-Pixbuf 2.42.10 as dependency for Graphviz 8.1.0 w/ GCCcore/12.3.0 --- .../easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb index 0296c8bf5a4..9f0b7753a7f 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb @@ -34,7 +34,7 @@ dependencies = [ ('Java', '11', '', SYSTEM), ('Python', '3.11.3'), ('FriBidi', '1.0.12'), - ('Gdk-Pixbuf', '2.42.9'), + ('Gdk-Pixbuf', '2.42.10'), ('Ghostscript', '10.01.2'), ('GTS', '0.7.6'), ('libgd', '2.3.3'), From bae44ca7fb88af1c3667c8fae2e01a7bc6904656 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 11:21:52 +0200 Subject: [PATCH 8649/9987] also use GCC/12.3.0 for wxWidgets 3.2.2.1, since GST-plugins-base uses GCC rather than GCCcore --- ...2.2.1-GCCcore-12.3.0.eb => wxWidgets-3.2.2.1-GCC-12.3.0.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/w/wxWidgets/{wxWidgets-3.2.2.1-GCCcore-12.3.0.eb => wxWidgets-3.2.2.1-GCC-12.3.0.eb} (96%) diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCC-12.3.0.eb similarity index 96% rename from easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCC-12.3.0.eb index 0356fac7946..b6ba8f01d9b 100644 --- a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.2.1-GCC-12.3.0.eb @@ -11,7 +11,7 @@ Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI.""" -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchain = {'name': 'GCC', 'version': '12.3.0'} toolchainopts = {'pic': True} github_account = 'wxWidgets' @@ -20,7 +20,6 @@ sources = [SOURCE_TAR_BZ2] checksums = ['dffcb6be71296fff4b7f8840eb1b510178f57aa2eb236b20da41182009242c02'] builddependencies = [ - ('binutils', '2.40'), ('gettext', '0.21.1'), ('pkgconf', '1.9.5'), ('Python', '3.11.3'), From 71540d689dc3df88e20701a1d0a1d3859d575a0b Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 1 Sep 2023 10:32:44 +0100 Subject: [PATCH 8650/9987] remove html5lib as it is in Python-bundle-PyPI/2023.06-GCCcore-12.3.0 (#18698) --- .../h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb | 30 ------------------- 1 file changed, 30 deletions(-) delete mode 100644 easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb deleted file mode 100644 index 456061ea2f0..00000000000 --- a/easybuild/easyconfigs/h/html5lib/html5lib-1.1-GCCcore-12.3.0.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'html5lib' -version = '1.1' - -homepage = 'https://github.com/html5lib/html5lib-python' -description = "Standards-compliant library for parsing and serializing HTML documents and fragments in Python" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), -] - -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), -] - -use_pip = True - -exts_list = [ - (name, version, { - 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], - }), -] - -sanity_pip_check = True - -moduleclass = 'lib' From d13ad709f1e9d9cc69f51b58a53b7bd7a9f4f7f8 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 1 Sep 2023 10:12:08 +0000 Subject: [PATCH 8651/9987] fixed formatting --- .../git-annex-10.20230802-GCCcore-12.2.0.eb | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index a02cdb21620..ad3c788a9ef 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -26,16 +26,18 @@ sources = [{ 'filename': '%(name)s-%(version)s.tar.gz' }] -build_cmd = "stack setup && stack build && " -build_cmd += "make install-bins BUILDER=stack PREFIX=%(builddir)s" +prebuildopts = "stack setup && stack build && " +buildopts = "make install-bins BUILDER=stack PREFIX=%(builddir)s" -files_to_copy = [(['git-annex','git-annex-shell'], 'bin'), - - ] +files_to_copy = [ + (['git-annex','git-annex-shell'], 'bin'), +] sanity_check_paths = { 'files': ['bin/git-annex', 'bin/git-annex-shell'], - 'dirs' : ['bin'], + 'dirs' : [], } sanity_check_commands = ['git-annex version'] + +moduleclass = 'tools' From ee7e8eda21a6436666629e50c163eea82fc080ed Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 1 Sep 2023 10:35:38 +0000 Subject: [PATCH 8652/9987] pep8 compliance --- .../git-annex-10.20230802-GCCcore-12.2.0.eb | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index ad3c788a9ef..64087eedfd9 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -11,31 +11,31 @@ power and distributed nature of git to bear on your large files with git-annex." toolchain = {'name': 'GCCcore', 'version': '12.2.0'} dependencies = [ - ('GHC', '9.2.2', '-x86_64', SYSTEM), - ('GCC', '12.2.0','', SYSTEM), - ('Stack', '2.11.1', '-x86_64', SYSTEM), - ('git', '2.38.1', '-nodocs'), - ] + ('GHC', '9.2.2', '-x86_64', SYSTEM), + ('GCC', '12.2.0', '', SYSTEM), + ('Stack', '2.11.1', '-x86_64', SYSTEM), + ('git', '2.38.1', '-nodocs'), +] sources = [{ - 'git_config': { 'url': 'git://git-annex.branchable.com', - 'repo_name': '%(name)s', - 'tag': '%(version)s', - 'clone_into': '%(name)s-%(version)s', - }, - 'filename': '%(name)s-%(version)s.tar.gz' + 'git_config': {'url': 'git://git-annex.branchable.com', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'clone_into': '%(name)s-%(version)s', + }, + 'filename': '%(name)s-%(version)s.tar.gz' }] prebuildopts = "stack setup && stack build && " buildopts = "make install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ - (['git-annex','git-annex-shell'], 'bin'), + (['git-annex', 'git-annex-shell'], 'bin'), ] sanity_check_paths = { 'files': ['bin/git-annex', 'bin/git-annex-shell'], - 'dirs' : [], + 'dirs': [], } sanity_check_commands = ['git-annex version'] From b13d5007835e9faaec0bccb0032ae70b3ef4acc8 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 1 Sep 2023 11:48:55 +0000 Subject: [PATCH 8653/9987] added checksum --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 64087eedfd9..8e5a17e7c5f 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -24,6 +24,9 @@ sources = [{ 'clone_into': '%(name)s-%(version)s', }, 'filename': '%(name)s-%(version)s.tar.gz' + 'checksums': [ + 'd9e26d1fbf1718699880e422c04ec2ed89024894e190fd5c6d0f5273fc42a39f' + ] }] prebuildopts = "stack setup && stack build && " From 9537b483f7fec203f7885c3bfcce313d4f406d72 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 1 Sep 2023 12:04:30 +0000 Subject: [PATCH 8654/9987] commata in sources --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 8e5a17e7c5f..47ed00261c1 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -23,10 +23,10 @@ sources = [{ 'tag': '%(version)s', 'clone_into': '%(name)s-%(version)s', }, - 'filename': '%(name)s-%(version)s.tar.gz' + 'filename': '%(name)s-%(version)s.tar.gz', 'checksums': [ 'd9e26d1fbf1718699880e422c04ec2ed89024894e190fd5c6d0f5273fc42a39f' - ] + ], }] prebuildopts = "stack setup && stack build && " From f1829b2a5a0c348274121d5fe2c8c74eb829cf71 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 1 Sep 2023 12:25:46 +0000 Subject: [PATCH 8655/9987] fixed checksum --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 47ed00261c1..71e69c322ae 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -25,7 +25,7 @@ sources = [{ }, 'filename': '%(name)s-%(version)s.tar.gz', 'checksums': [ - 'd9e26d1fbf1718699880e422c04ec2ed89024894e190fd5c6d0f5273fc42a39f' + '5c4cd3c0a1d141a1b85936fee3fa52f7638774c2146b138aa9ae218d3da4b89d' ], }] From 6a449e483ff89af32461899043f597a632f46001 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 1 Sep 2023 12:43:25 +0000 Subject: [PATCH 8656/9987] rename according to new convention --- ...GCCcore-12.2.0-Python-3.10.8.eb => PLY-3.11-GCCcore-12.2.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/PLY/{PLY-3.11-GCCcore-12.2.0-Python-3.10.8.eb => PLY-3.11-GCCcore-12.2.0.eb} (100%) diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0-Python-3.10.8.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0.eb similarity index 100% rename from easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0-Python-3.10.8.eb rename to easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0.eb From c246cd39470bc41bedcd6b15b17bbfa743fb8d88 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 1 Sep 2023 12:45:22 +0000 Subject: [PATCH 8657/9987] remove python extention as in #18674 --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index a18c2093734..812f649c339 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -13,7 +13,7 @@ dependencies = [ ('git-annex', '10.20230802'), ('Python', '3.10.8'), ('tqdm', '4.64.1'), - ('PLY', '3.11', '-Python-3.10.8'), + ('PLY', '3.11'), ('Rust', '1.65.0'), ('scikit-build', '0.17.2'), ] From 966f8abd9352a30fe495b824b87c48208ea61ed0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 15:10:43 +0200 Subject: [PATCH 8658/9987] use GCC/12.3.0 toolchain for gnuplot 5.4.8 --- .../g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb deleted file mode 100644 index eb1a750d2e0..00000000000 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'gnuplot' -version = '5.4.8' - -homepage = 'http://gnuplot.sourceforge.net' -description = """Portable interactive, function plotting utility""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] -sources = [SOURCE_TAR_GZ] -checksums = ['931279c7caad1aff7d46cb4766f1ff41c26d9be9daf0bcf0c79deeee3d91f5cf'] - -builddependencies = [ - ('binutils', '2.40'), - ('pkgconf', '1.9.5'), - ('Autotools', '20220317'), -] - -dependencies = [ - ('ncurses', '6.4'), - ('cairo', '1.17.8'), - ('libjpeg-turbo', '2.1.5.1'), - ('libpng', '1.6.39'), - ('libgd', '2.3.3'), - ('Pango', '1.50.14'), - ('libcerf', '2.3'), - ('X11', '20230603'), - ('Qt5', '5.15.10'), - ('Lua', '5.4.6') -] - -preconfigopts = 'autoreconf && ' - -configopts = '--with-qt=qt5 --without-latex --disable-wxwidgets' - -sanity_check_paths = { - 'files': ['bin/gnuplot'], - 'dirs': [] -} -# make sure that pdf terminal type is available -sanity_check_commands = ["gnuplot -e 'set terminal pdf'"] - -moduleclass = 'vis' From 85cbcdbd2c2383462f664d9c878c1e882aa4be53 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 15:11:20 +0200 Subject: [PATCH 8659/9987] drop binutils build dep for gnuplot 5.4.8 with GCC/12.3.0 --- easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb b/easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb index 7d07114ab64..05a1ebaab07 100644 --- a/easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb @@ -13,7 +13,6 @@ sources = [SOURCE_TAR_GZ] checksums = ['931279c7caad1aff7d46cb4766f1ff41c26d9be9daf0bcf0c79deeee3d91f5cf'] builddependencies = [ - ('binutils', '2.40'), ('pkgconf', '1.9.5'), ('Autotools', '20220317'), ] From e5a39b1d3603d0dccbe75361b1176149c71af870 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Sep 2023 15:16:16 +0200 Subject: [PATCH 8660/9987] stick to GCCcore/12.3.0 for gnuplot 5.4.8 --- .../gnuplot-5.4.8-GCCcore-12.3.0.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/g/{gnuplot-5.4.8-GCC-12.3.0.eb => gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb} (97%) diff --git a/easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb similarity index 97% rename from easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb rename to easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb index 05a1ebaab07..7d07114ab64 100644 --- a/easybuild/easyconfigs/g/gnuplot-5.4.8-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb @@ -13,6 +13,7 @@ sources = [SOURCE_TAR_GZ] checksums = ['931279c7caad1aff7d46cb4766f1ff41c26d9be9daf0bcf0c79deeee3d91f5cf'] builddependencies = [ + ('binutils', '2.40'), ('pkgconf', '1.9.5'), ('Autotools', '20220317'), ] From f5466456fbb2ecf080f0cc6a0edf411cb99229bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Sep 2023 15:47:03 +0200 Subject: [PATCH 8661/9987] Include branfosj's fixes --- .../q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb | 40 ++++++------------- 1 file changed, 13 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb index 9bb23c9a2f0..ccc26d46270 100644 --- a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb @@ -21,16 +21,12 @@ patches = [ # QT_CFLAGS_ARCH_HASWELL in cmake/QtCompilerOptimization.cmake should be patched? # 'Qt5-5.13.1_fix-avx2.patch', # 'Qt5-5.13.1_fix-qmake-libdir.patch', - 'Qt6-6.5.2_fix_OF-Gentoo.patch', # 'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch', + 'Qt6-6.5.2_fix_OF-Gentoo.patch', ] checksums = [ {'qt-everywhere-src-6.5.2.tar.xz': 'cde57be663d0f875759797298bdc37a936d517c39f2013e4e6ece5e12edeed12'}, - # {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, - # {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, {'Qt6-6.5.2_fix_OF-Gentoo.patch': '908f7dae7685c76fe651e52391e46a2337a3cd32dee70a5da54b154da7d4917c'}, - # {'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch': - # '74590de2b9e32f2c88123cb096c4f5c3001b00710aad096a4d16444a8e9eb991'}, ] builddependencies = [ @@ -42,7 +38,6 @@ builddependencies = [ ('Bison', '3.8.2'), ('flex', '2.6.4'), ('gperf', '3.1'), - ('Python', '3.11.3'), ('re2c', '3.1'), ] @@ -61,7 +56,9 @@ dependencies = [ ('FFmpeg', '6.0'), ('X11', '20230603'), ('fontconfig', '2.14.2'), - ('html5lib', '1.1'), # WebEngine + ('zlib', '1.2.13'), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # WebEngine ('freetype', '2.13.0'), # WebEngine ('DBus', '1.15.4'), ('libevent', '2.1.12'), # WebEngine @@ -72,34 +69,23 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ('ICU', '73.2'), # WebEngine, optional ('nodejs', '18.17.1'), # WebEngine, required - # ('gRPC', '1.52.2'), # Qt needs protobuf <=21.x, still error - # ('bzip2', '1.0.8'), - # ('zlib', '1.2.13'), - # ('libopus', '1.4'), - # ('LittleCMS', '2.15'), + # ('gRPC', '1.52.2'), # WebEngine needs older Abseil/gRPC/protobuf ] -# Error when trying native gRPC -# In file included from gen/extensions/browser/browser_sources_jumbo_7.cc:13: -# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc: In member function virtual bool extensions::FormDataParserUrlEncoded::SetSource(base::StringPiece): # noqa: E501 -# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc:429:11: error: using StringPiece = class absl::string_view {aka class absl::string_view} has no member named set # noqa: E501 -# 429 | source_.set(source.data(), source.size()); -# | ^~~ -# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc: In member function virtual bool extensions::FormDataParserMultipart::SetSource(base::StringPiece): # noqa: E501 -# ./../../../../../../qt-everywhere-src-6.5.2/qtwebengine/src/3rdparty/chromium/extensions/browser/api/web_request/form_data_parser.cc:573:11: error: using StringPiece = class absl::string_view {aka class absl::string_view} has no member named set # noqa: E501 -# 573 | source_.set(source.data(), source.size()); -# | ^~~ - preconfigopts = 'sed -i "s/MultiMedia/Multimedia/g" ../qt-everywhere-src-%(version)s/qtcharts/CMakeLists.txt &&' # Typo +preconfigopts += 'sed -i "23i set(Python3_ROOT_DIR \\$ENV{EBROOTPYTHON})" ' \ + '../qt-everywhere-src-6.5.2/qtwebengine/src/gn/CMakeLists.txt &&' + configopts = '-Wno-dev ' configopts += '-DFEATURE_qtpdf_build=OFF ' # Requires CUPS +configopts += '-DQT_AVOID_CMAKE_ARCHIVING_API=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' configopts += '-DBUILD_qtwayland=OFF ' # Does not work on CentOS 7 -# configopts += '-DBUILD_qtgamepad=OFF ' # Gamepad does not work on CentOS 7, removed from Qt6.0.0 and not added back +# Removed from Qt6.0.0 by may be added back in the future +# configopts += '-DBUILD_qtgamepad=OFF ' # Does not work on CentOS 7 -# make sure QtWebEngine component is being built & installed -# check_qtwebengine = True sanity_check_paths = { - 'files': ['bin/qmake6', 'lib/libQt6Core.so', 'lib/libQt6WebEngineCore.so'], + 'files': ['bin/qmake6', 'lib/libQt6Core.%s' % SHLIB_EXT, 'lib/libQt6WebEngineCore.%s' % SHLIB_EXT], 'dirs': ['include/QtCore', 'include/QtWebEngineCore'], } From 1203b64a87e2f1b723c2bdf8dbf061b3cdd86c21 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 1 Sep 2023 15:53:53 +0200 Subject: [PATCH 8662/9987] adding easyconfigs: Scalene-1.5.26-GCCcore-12.3.0.eb --- .../Scalene/Scalene-1.5.26-GCCcore-12.3.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0868f7d136a --- /dev/null +++ b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-12.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'Scalene' +version = '1.5.26' + +homepage = 'https://github.com/plasma-umass/scalene' +description = """Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things +that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while +delivering far more detailed information.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('pynvml', '11.4.1', { + 'checksums': ['b2e4a33b80569d093b513f5804db0c7f40cfc86f15a013ae7a8e99c5e175d5dd'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['dfff2232193f5fe8d414adb2b01acc0d10bbf67d4c0df7a94465ec726fd9e32c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/scalene'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["scalene --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From a6c89c7d3a5891e32a316d34072b348be4a0fb3f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 1 Sep 2023 16:32:41 +0200 Subject: [PATCH 8663/9987] Fix Bazel 6+ issue --- .../b/Bazel/Bazel-6.3.1-GCCcore-12.2.0.eb | 6 ++++- ...Bazel-6.3.1_add-symlinks-in-runfiles.patch | 22 +++++++++++++++++++ 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-6.3.1_add-symlinks-in-runfiles.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.2.0.eb index fd7d093741d..8c284f50a4d 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.2.0.eb @@ -9,7 +9,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] -checksums = ['2676319e86c5aeab142dccd42434364a33aa330a091c13562b7de87a10e68775'] +patches = ['Bazel-6.3.1_add-symlinks-in-runfiles.patch'] +checksums = [ + {'bazel-6.3.1-dist.zip': '2676319e86c5aeab142dccd42434364a33aa330a091c13562b7de87a10e68775'}, + {'Bazel-6.3.1_add-symlinks-in-runfiles.patch': '81db53aa87229557480b6f719c99a0f1af9c69dfec12185451e520b0128c3ae2'}, +] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1_add-symlinks-in-runfiles.patch b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1_add-symlinks-in-runfiles.patch new file mode 100644 index 00000000000..83251131981 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1_add-symlinks-in-runfiles.patch @@ -0,0 +1,22 @@ +Bazel doesn't always copy all files as required leading e.g. to failures in TF sanity check: https://github.com/tensorflow/tensorflow/issues/60326 + +From https://github.com/bazelbuild/bazel/pull/19378 + +Author: Alexander Grund (TU Dresden) + +diff --git a/src/main/starlark/builtins_bzl/common/cc/experimental_cc_shared_library.bzl b/src/main/starlark/builtins_bzl/common/cc/experimental_cc_shared_library.bzl +index b9f3b5b7ac..3af1e61c63 100644 +--- a/src/main/starlark/builtins_bzl/common/cc/experimental_cc_shared_library.bzl ++++ b/src/main/starlark/builtins_bzl/common/cc/experimental_cc_shared_library.bzl +@@ -728,7 +728,10 @@ def _cc_shared_library_impl(ctx): + # precompiled_dynamic_library.dynamic_library could be None if the library to link just contains + # an interface library which is valid if the actual library is obtained from the system. + if precompiled_dynamic_library.dynamic_library != None: +- precompiled_only_dynamic_libraries_runfiles.append(precompiled_dynamic_library.dynamic_library) ++ if precompiled_dynamic_library.resolved_symlink_dynamic_library != None: ++ precompiled_only_dynamic_libraries_runfiles.append(precompiled_dynamic_library.resolved_symlink_dynamic_library) ++ else: ++ precompiled_only_dynamic_libraries_runfiles.append(precompiled_dynamic_library.dynamic_library) + + runfiles = runfiles.merge(ctx.runfiles(files = precompiled_only_dynamic_libraries_runfiles)) + From f18360d2637051eb5a2bf530fedbf8ba675e4b79 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 1 Sep 2023 14:38:15 +0000 Subject: [PATCH 8664/9987] no versionsuffix in config anyomre --- easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0.eb index 6498aba9865..1801f7c3cbe 100644 --- a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.2.0.eb @@ -2,7 +2,6 @@ easyblock = 'PythonPackage' name = 'PLY' version = '3.11' -versionsuffix = "-Python-%(pyver)s" homepage = "https://www.dabeaz.com/ply/" description = """PLY is yet another implementation of lex and yacc for Python.""" From b9a39d04ee3aefb1b56e1a34ec99ba7b83972fe1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Sep 2023 16:47:23 +0200 Subject: [PATCH 8665/9987] Update easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb --- easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb index 7d07114ab64..f49a0f13ec5 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.4.8-GCCcore-12.3.0.eb @@ -6,7 +6,7 @@ version = '5.4.8' homepage = 'http://gnuplot.sourceforge.net' description = """Portable interactive, function plotting utility""" -toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')] sources = [SOURCE_TAR_GZ] From 5943e59326a8955289b660216a08559d3396a98a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 3 Sep 2023 16:45:27 +0200 Subject: [PATCH 8666/9987] adding easyconfigs: Perl-5.38.0-GCCcore-13.2.0.eb, Autoconf-2.71-GCCcore-13.2.0.eb, Automake-1.16.5-GCCcore-13.2.0.eb, Autotools-20220317-GCCcore-13.2.0.eb, libtool-2.4.7-GCCcore-13.2.0.eb --- .../Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb | 48 +++++++++++ .../Automake-1.16.5-GCCcore-13.2.0.eb | 39 +++++++++ .../Autotools-20220317-GCCcore-13.2.0.eb | 24 ++++++ .../l/libtool/libtool-2.4.7-GCCcore-13.2.0.eb | 32 +++++++ .../p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb | 86 +++++++++++++++++++ 5 files changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..82a7f9766df --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.71-GCCcore-13.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.71' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['431075ad0bf529ef13cb41e9042c542381103e80015686222b8a9d4abef42a1c'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('M4', '1.4.19'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.38.0'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +sanity_check_commands = [ + "autoconf --help", + "autom4te --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..371c50f375d --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.5-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.5' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['07bd24ad08a64bc17250ce09ec56e921d6343903943e99ccf63bbf0705e34605'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Autoconf', '2.71'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.38.0'), +] + +preconfigopts = "export PERL='/usr/bin/env perl' && " + +sanity_check_paths = { + 'files': ['bin/aclocal', 'bin/automake'], + 'dirs': [] +} + +sanity_check_commands = [ + "aclocal --help", + "automake --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..49a29016b9e --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20220317-GCCcore-13.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20220317' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +dependencies = [ + ('Autoconf', '2.71'), # 20210128 + ('Automake', '1.16.5'), # 20211003 + ('libtool', '2.4.7'), # 20220317 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..31bed6f7eed --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.7' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..1620e4f9dfa --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb @@ -0,0 +1,86 @@ +name = 'Perl' +version = '5.38.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +Includes a small selection of extra CPAN packages for core functionality. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['213ef58089d2f2c972ea353517dc60ec3656f050dcc027666e118b508423e517'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +# !! order of extensions is important !! +# extensions updated on 2023-09-03 +# includes all dependencies for Autotools +exts_list = [ + ('threads', '2.21', { + 'source_tmpl': 'threads-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['28394c98a2bcae6f20ffb8a3d965a1c194b764c650169e2050ee38dbaa10f110'], + }), + ('constant', '1.33', { + 'source_tmpl': 'constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], + }), + ('Getopt::Long', '2.54', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + 'checksums': ['584ba3c99bb2d6b341375212f9b874613f706cfb01cee21b8a2676a98ab985fe'], + }), + ('File::Path', '2.18', { + 'source_tmpl': 'File-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN/'], + 'checksums': ['980f0a17edb353df46e9cd7b357f9f5929cde0f80c45fd7a06cf7e0e8bd6addd'], + }), + ('File::Spec', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('IO::File', '1.51', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'], + 'checksums': ['5493ea55998728cd2b7ecb8234c58fb5d5df27098d0f07addca22444d7616ce0'], + }), + ('Thread::Queue', '3.13', { + 'source_tmpl': 'Thread-Queue-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['6ba3dacddd2fbb66822b4aa1d11a0a5273cd04c825cb3ff31c20d7037cbfdce8'], + }), + ('Carp', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('Exporter', '5.77', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['3892ee5c6ae6e482068d53b61e25cae4fc71ddc79cc47446e385df0a669bb8ed'], + }), + ('Text::ParseWords', '3.31', { + 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], + 'checksums': ['2ae555ba084d75b2b8feeeb8d1a00911276815ada86bccb1452236964d5a2fc7'], + }), + ('Data::Dumper', '2.183', { + 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], + 'checksums': ['e42736890b7dae1b37818d9c5efa1f1fdc52dec04f446a33a4819bf1d4ab5ad3'], + }), +] + +moduleclass = 'lang' From 0e15e141e2f13d5e113e7bd92581c5467073cbe5 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 3 Sep 2023 16:55:25 +0200 Subject: [PATCH 8667/9987] adding easyconfigs: XZ-5.4.4-GCCcore-13.2.0.eb, libxml2-2.11.5-GCCcore-13.2.0.eb, gettext-0.22.eb, ncurses-6.4-GCCcore-13.2.0.eb, gettext-0.22-GCCcore-13.2.0.eb --- .../g/gettext/gettext-0.22-GCCcore-13.2.0.eb | 37 +++++++++++++++ .../easyconfigs/g/gettext/gettext-0.22.eb | 39 +++++++++++++++ .../libxml2/libxml2-2.11.5-GCCcore-13.2.0.eb | 27 +++++++++++ .../n/ncurses/ncurses-6.4-GCCcore-13.2.0.eb | 47 +++++++++++++++++++ .../x/XZ/XZ-5.4.4-GCCcore-13.2.0.eb | 34 ++++++++++++++ 5 files changed, 184 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.22.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.11.5-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.4.4-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2f4d3b3096a --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.22' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['49f089be11b490170bbf09ed2f51e5f5177f55be4cc66504a5861820e0fb06ab'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('libxml2', '2.11.5'), + ('ncurses', '6.4'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.22.eb b/easybuild/easyconfigs/g/gettext/gettext-0.22.eb new file mode 100644 index 00000000000..4212074dac6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.22.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.22' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['49f089be11b490170bbf09ed2f51e5f5177f55be4cc66504a5861820e0fb06ab'] + +dependencies = [ + ('ncurses', '6.4'), +] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.11.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.11.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..79cc8b0ae36 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.11.5-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.11.5' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['3727b078c360ec69fa869de14bd6f75d7ee8d36987b071e6928d4720a28df3a6'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('XZ', '5.4.4'), + ('zlib', '1.2.13'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0bda2c35075 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.4' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6931283d9ac87c5073f30b6290c4c75f21632bb4fc3603ac8100812bed248159'] + +builddependencies = [('binutils', '2.40')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts, + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.4.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.4.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f905a1885ab --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.4.4-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.4.4' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['0b6fcde1ac38e90433a2556f500c065950b9bcd2d602006efc334782bdfe6296'] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.22', '', SYSTEM), + ('binutils', '2.40'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' From 2d27ffb6399f1e93f11e0a46ceee62814ca38810 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 3 Sep 2023 16:58:00 +0200 Subject: [PATCH 8668/9987] adding easyconfigs: libpciaccess-0.17-GCCcore-13.2.0.eb, xorg-macros-1.20.0-GCCcore-13.2.0.eb --- .../libpciaccess-0.17-GCCcore-13.2.0.eb | 26 ++++++++++++++++++ .../xorg-macros-1.20.0-GCCcore-13.2.0.eb | 27 +++++++++++++++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..17563d8e3b2 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.17' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bf6985a77d2ecb00e2c79da3edfb26b909178ffca3f2e9d14ed0620259ab733b'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('xorg-macros', '1.20.0'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..14bbf928bbc --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.20.0-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.20.0' + +homepage = 'https://gitlab.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['efd8eefab568981e47dd64d3e9b5ee2b7165a30d4feca105770f249f9b59979c'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From fe16f5739eb89e91af883d22df7a51ac7aa14f4b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 3 Sep 2023 16:59:49 +0200 Subject: [PATCH 8669/9987] adding easyconfigs: pkgconf-2.0.3-GCCcore-13.2.0.eb --- .../p/pkgconf/pkgconf-2.0.3-GCCcore-13.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-2.0.3-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-2.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.0.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a9a638fa1ef --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-2.0.3-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '2.0.3' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a8f25f4b0c1ad48edc9b07ed46101aab4bcb305ba6ae811be49b7499b00eed49'] + +builddependencies = [('binutils', '2.40')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' From a50410544940492f5d2577e84a96eb705455a2b6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 3 Sep 2023 17:01:13 +0200 Subject: [PATCH 8670/9987] adding easyconfigs: hwloc-2.9.2-GCCcore-13.2.0.eb --- .../h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..274d96ba85d --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.9.2' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ffb554d5735e0e0a19d1fd4b2b86e771d3b58b2d97f257eedacae67ade5054b3'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('numactl', '2.0.16'), + ('libxml2', '2.11.5'), + ('libpciaccess', '0.17'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' From 96dbb1bba757b07d6e2f48427f053b506cd11a21 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 3 Sep 2023 17:03:51 +0200 Subject: [PATCH 8671/9987] adding easyconfigs: libevent-2.1.12-GCCcore-13.2.0.eb --- .../libevent-2.1.12-GCCcore-13.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..db1de7fe681 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' From 01e078d112ef4a973d6d121f199ec6b6e255720b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 3 Sep 2023 17:05:58 +0200 Subject: [PATCH 8672/9987] adding easyconfigs: numactl-2.0.16-GCCcore-13.2.0.eb, libfabric-1.19.0-GCCcore-13.2.0.eb --- .../libfabric-1.19.0-GCCcore-13.2.0.eb | 62 +++++++++++++++++++ .../numactl/numactl-2.0.16-GCCcore-13.2.0.eb | 34 ++++++++++ 2 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.19.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.19.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.19.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3a1dce0b2dc --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.19.0-GCCcore-13.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.19.0' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +# The psm3 provider (enabled by default) requires an AVX capable system to run +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ofiwg/libfabric/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +patches = [ + '%(name)s-1.18.0_disable-psm3-avx-config.patch', +] +checksums = [ + {'libfabric-1.19.0.tar.bz2': 'f14c764be9103e80c46223bde66e530e5954cb28b3835b57c8e728479603ef9e'}, + {'libfabric-1.18.0_disable-psm3-avx-config.patch': + '79db0bfe759d65ef68301701e0842f1e8dcd4ace8bfc5bca8f7c8846501a67cb'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('numactl', '2.0.16'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# Regenerate build files to pick up psm3-axv-config patch +preconfigopts = "./autogen.sh &&" + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) +configopts += "--disable-usnic " + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..028a4a4c8a1 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.16' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a35c3bdb3efab5c65927e0de5703227760b1101f5e27ab741d8f32b3d5f0a44c'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' From 5277b18515860cd97c6c6a67d07582688ba803ac Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 3 Sep 2023 17:09:26 +0200 Subject: [PATCH 8673/9987] adding easyconfigs: OpenMPI-4.1.5-GCC-13.2.0.eb, UCX-1.15.0-rc4-GCCcore-13.2.0.eb, UCC-1.2.0-GCCcore-13.2.0.eb, PMIx-4.2.5-GCCcore-13.2.0.eb, gompi-2023b.eb --- easybuild/easyconfigs/g/gompi/gompi-2023b.eb | 20 ++++++ .../o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb | 62 +++++++++++++++++++ .../p/PMIx/PMIx-4.2.5-GCCcore-13.2.0.eb | 45 ++++++++++++++ .../u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb | 41 ++++++++++++ .../u/UCX/UCX-1.15.0-rc4-GCCcore-13.2.0.eb | 56 +++++++++++++++++ 5 files changed, 224 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2023b.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.2.5-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.15.0-rc4-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2023b.eb b/easybuild/easyconfigs/g/gompi/gompi-2023b.eb new file mode 100644 index 00000000000..649244f7e77 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2023b.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2023b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '13.2.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.1.5', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb new file mode 100644 index 00000000000..77905f262fe --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb @@ -0,0 +1,62 @@ +name = 'OpenMPI' +version = '4.1.5' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', +] +checksums = [ + {'openmpi-4.1.5.tar.bz2': 'a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3'}, + {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, + {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, +] + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Perl', '5.38.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('hwloc', '2.9.2'), + ('libevent', '2.1.12'), + ('UCX', '1.15.0-rc4'), + ('libfabric', '1.19.0'), + ('PMIx', '4.2.5'), + ('UCC', '1.2.0'), +] + +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' + +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..20d7c7553c3 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.5-GCCcore-13.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '4.2.5' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['a89c2c5dc69715a4df1e76fdc4318299386c184623a1d0d5eb1fb062e14b0d2b'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.2.13'), + ('hwloc', '2.9.2'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0f206f09331 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'UCC' +version = '1.2.0' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = ['UCC-1.1.0-multiple_component_paths.patch'] +checksums = [ + {'v1.2.0.tar.gz': 'c1552797600835c0cf401b82dc89c4d27d5717f4fb805d41daca8e19f65e509d'}, + {'UCC-1.1.0-multiple_component_paths.patch': '3081d0f694331daa4a88a0fa3fb54b9a918015248ae5eb7b3157b924abd31bee'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCX', '1.15.0-rc4'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/ucc_info'], + 'dirs': ['include', 'lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.15.0-rc4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.15.0-rc4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3d194284424 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.15.0-rc4-GCCcore-13.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.15.0-rc4' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +# TODO: Uncomment when updating to final release +# sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = ['%(namelower)s-1.15.0.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', +] +checksums = [ + {'ucx-1.15.0.tar.gz': 'aa1e71de64dbc3061454dbe7510a38b930f7c184ec889c09f5611c2d4acaf07a'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, +] + +# Uncomment when updating to final release +# sources = ['%(namelower)s-%(version)s.tar.gz'] +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '2.0.3'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.13'), + ('numactl', '2.0.16'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From f50bd06f7b605e88d5cfb25b595d3f839fc648e4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 3 Sep 2023 18:38:41 +0200 Subject: [PATCH 8674/9987] change conan to build dependency + remove setuptools extension in CatBoost easyconfig --- easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb b/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb index 38b618b1a9d..02aa893cd52 100644 --- a/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb +++ b/easybuild/easyconfigs/c/CatBoost/CatBoost-1.2-gfbf-2023a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'gfbf', 'version': '2023a'} builddependencies = [ ('CMake', '3.26.3'), + ('conan', '1.60.2'), ] dependencies = [ @@ -20,16 +21,12 @@ dependencies = [ ('plotly.py', '5.16.0'), ('graphviz-python', '0.20.1'), ('Ninja', '1.11.1'), - ('conan', '1.60.2'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('setuptools', '67.7.2', { - 'checksums': ['f104fa03692a2602fa0fec6c6a9e63b6c8a968de13e17c026957dd1f53d80990'], - }), (name, version, { 'patches': ['%(name)s-%(version)s_disable-widget.patch'], 'source_urls': ['https://pypi.python.org/packages/source/c/catboost'], From 250dd8a076a4afc1caba0168f66abb9a9da40768 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Sep 2023 10:47:15 +0200 Subject: [PATCH 8675/9987] adding easyconfigs: CUDA-12.2.2.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.2.2.eb | 24 +++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.2.2.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.2.2.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.2.2.eb new file mode 100644 index 00000000000..da8873e6d0c --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.2.2.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.2.2' +local_nv_version = '535.104.05' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '2b39aae3e7618d9f59a3c8fa1f1bc61f29c0b0e0df75fb05076badb352952ef2', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '18848278e7f2bd4b4481f5665633d7e3d46e9a562d175d5ff278218188b01342', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '4113a15e6b27a02638c72edeb5f89de4c9ea312febba12fc4cefff2edc882268' +}] + +moduleclass = 'system' From ee068ea782d200417234c863cd8aacf6dc213560 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 4 Sep 2023 12:36:25 +0200 Subject: [PATCH 8676/9987] tensorflow-compression: add comment to the WORKSPACE sed file update checksum accordingly --- .../compression_local-tensorflow-repo.sed | 2 ++ .../tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tensorflow-compression/compression_local-tensorflow-repo.sed b/easybuild/easyconfigs/t/tensorflow-compression/compression_local-tensorflow-repo.sed index 1116ca24ca9..f4900022dee 100644 --- a/easybuild/easyconfigs/t/tensorflow-compression/compression_local-tensorflow-repo.sed +++ b/easybuild/easyconfigs/t/tensorflow-compression/compression_local-tensorflow-repo.sed @@ -1,3 +1,5 @@ +# Convert http repo for tensorflow to local repo +# Copied from jax/jaxlib_local-tensorflow-repo.sed /^http_archive(/{ :a;N;/\n)/!ba; /org_tensorflow/{ diff --git a/easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb index 488325cffed..a25980ceef9 100644 --- a/easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/tensorflow-compression/tensorflow-compression-2.11.0-foss-2022a-CUDA-11.7.0.eb @@ -29,7 +29,7 @@ patches = [ checksums = [ {'tensorflow-compression-2.11.0.tar.gz': '7f0127c3ff4243e41c5af59be5909a635562191f462053e2d86c234bf638be4f'}, {'v2.11.0.tar.gz': '99c732b92b1b37fc243a559e02f9aef5671771e272758aa4aec7f34dc92dac48'}, - {'compression_local-tensorflow-repo.sed': 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5'}, + {'compression_local-tensorflow-repo.sed': '65d4d40953624148cd6395a6110eaf8239a9bcae25d1f4c89259f2c60cc4b6dc'}, ] builddependencies = [ From d36ca3d40a7dc04392ccbcfdc790de8e4424c1be Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 4 Sep 2023 14:51:48 +0200 Subject: [PATCH 8677/9987] adding easyconfigs: ccache-4.8.3.eb --- .../easyconfigs/c/ccache/ccache-4.8.3.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.8.3.eb diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.8.3.eb b/easybuild/easyconfigs/c/ccache/ccache-4.8.3.eb new file mode 100644 index 00000000000..0bbc94a62ba --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.8.3.eb @@ -0,0 +1,54 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.8.3' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d59dd569ad2bbc826c0bc335c8ebd73e78ed0f2f40ba6b30069347e63585d9ef'] + +osdependencies = [('glibc-static', 'libc6-dev')] + +local_gccver = '12.3.0' +builddependencies = [ + ('GCC', local_gccver), + ('CMake', '3.26.3', '', ('GCCcore', local_gccver)), + ('Ninja', '1.11.1', '', ('GCCcore', local_gccver)), + ('hiredis', '1.2.0', '', ('GCCcore', local_gccver)), + ('zstd', '1.5.5', '', ('GCCcore', local_gccver)), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + # Link dependencies and binary statically + '-DCMAKE_EXE_LINKER_FLAGS="-static"', + '-DZSTD_LIBRARY="$EBROOTZSTD/lib/libzstd.a"', + '-DHIREDIS_LIBRARY="$EBROOTHIREDIS/lib/libhiredis.a"', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = [ + 'ccache --help', + # Ensure that the binary does not depend on any shared library + 'LC_ALL=C ldd $(which ccache) | grep -q "not a dynamic executable"', +] + +moduleclass = 'tools' From c56513fca70aa0a165f883735d9dc448fe1a1934 Mon Sep 17 00:00:00 2001 From: Robin Verschoren Date: Mon, 4 Sep 2023 15:14:27 +0200 Subject: [PATCH 8678/9987] adding easyconfigs: Structure-2.3.4-GCC-11.3.0.eb --- .../s/Structure/Structure-2.3.4-GCC-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-11.3.0.eb new file mode 100644 index 00000000000..24f272f449a --- /dev/null +++ b/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-11.3.0.eb @@ -0,0 +1,41 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'Structure' +version = '2.3.4' + +homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html' +description = """The program structure is a free software package for using multi-locus genotype data to investigate + population structure.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/'] +sources = [{'download_filename': 'structure_kernel_source.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f2b72b9189a514f53e921bbdc1aa3dbaca7ac34a8467af1f972c7e4fc9c0bb37'] + +# Add -fcommon to fix "multiple definition" errors +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' +buildopts = 'all CC="$CC" OPT="$CFLAGS"' + +files_to_copy = [(['structure'], 'bin')] + +sanity_check_commands = [ + 'structure | grep "Version %(version)s"' +] + +sanity_check_paths = { + 'files': ['bin/structure'], + 'dirs': [], +} + +moduleclass = 'bio' From d85605a8849616f98306b7d2b97a430de3e046b1 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 4 Sep 2023 16:41:41 +0200 Subject: [PATCH 8679/9987] adding easyconfigs: texlive-20230313-GCC-11.3.0.eb --- .../t/texlive/texlive-20230313-GCC-11.3.0.eb | 95 +++++++++++++++++++ 1 file changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb new file mode 100644 index 00000000000..d0b8b7b4b70 --- /dev/null +++ b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb @@ -0,0 +1,95 @@ +# Based off the 2017 version by John Dey jfdey@fredhutch.org +# https://github.com/easybuilders/easybuild-easyconfigs/pull/5085 +easyblock = 'Tarball' + +name = 'texlive' +version = '20230313' +local_version_year = version[:4] + +homepage = 'https://tug.org' +description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript + text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a + PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to + be a representation of the final typeset output, and so can be easily edited and manipulated.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = [ + 'ftp://tug.org/texlive/historic/%s/' % local_version_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year, +] +sources = [ + { + 'download_filename': 'install-tl-unx.tar.gz', + 'filename': 'install-tl-unx-%(version)s.tar.gz' + } +] + +dependencies = [ + ('X11', '20220504'), + ('libpng', '1.6.37'), + ('libGLU', '9.0.2'), + ('Perl', '5.34.1'), + ('HarfBuzz', '4.2.1'), + ('poppler', '22.12.0'), + ('cairo', '1.17.4'), + ('fontconfig', '2.14.0'), + ('zlib', '1.2.12'), + ('graphite2', '1.3.14'), +] + +# For the latest release, the tlnet-final repository isn't available yet, so we use the default +# But, the default can _not_ be used for the historic releases. The only way to write an EasyConfig +# that will work today and in the future, is to try one by one. +# Similarly, ftp is not available on all HPC systems, hence providing fallback to https +# See https://github.com/easybuilders/easybuild-easyconfigs/issues/17871 +local_install_tl = "%%(builddir)s/install-tl-%%(version)s/install-tl -profile %%(installdir)s/texlive.profile %s" +local_ftp = '-repository ftp://ftp.math.utah.edu/pub/tex/historic/systems/textlive/%s/tlnet-final' % local_version_year +local_https = '-repository https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year +local_install_tl_or = ( + ' || '.join([ + local_install_tl % '', + local_install_tl % local_ftp, + local_install_tl % local_https, + ]) +) +postinstallcmds = [ + 'echo "TEXDIR %%(installdir)s/" > %%(installdir)s/texlive.profile && ' + 'echo "TEXMFLOCAL %%(installdir)s/texmf-local" >> %%(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSCONFIG %%(installdir)s/texmf-config" >> %%(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSVAR %%(installdir)s/texmf-var" >> %%(installdir)s/texlive.profile && ' + '%s' % local_install_tl_or + # This should probably be a hook on our system. + # It'll mean the TEX files from homedir aren't picked up, as it would require an update of the cache + # ' && sed -i -e "s|TEXMF = {$TEXMFAUXTREES$TEXMFCONFIG,$TEXMFVAR,$TEXMFHOME,!!$TEXMFLOCAL,!!$TEXMFSYSCONFIG,!!$TEXMFSYSVAR,!!$TEXMFDIST}|TEXMF = {!!$TEXMFAUXTREES$TEXMFCONFIG,!!$TEXMFVAR,!!$TEXMFHOME,!!$TEXMFLOCAL,!!$TEXMFSYSCONFIG,!!$TEXMFSYSVAR,!!$TEXMFDIST}" %(installdir)s/texmf-dist/web2c/texmf.cnf' +] + +#postinstallcmds = [ +# 'echo "TEXDIR %(installdir)s/" > %(installdir)s/texlive.profile && ' +# 'echo "TEXMFLOCAL %(installdir)s/texmf-local" >> %(installdir)s/texlive.profile && ' +# 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' +# 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' +# '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' +# ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year +#] + + +#postinstallcmds = [ +# 'echo "TEXDIR %(installdir)s/" > %(installdir)s/%(name)s.profile && echo "TEXMFLOCAL %(installdir)s/texmf-local" >> %(installdir)s/%(name)s.profile && echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/%(name)s.profile && echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/%(name)s.profile && %(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/%(name)s.profile -repository https://ftp.math.utah.edu/pub/tex/historic/systems/%(name)s/2023/', +# 'echo "TEXDIR %(installdir)s/" > %(installdir)s/%(name)s.profile && echo "TEXMFLOCAL %(installdir)s/texmf-local" >> %(installdir)s/%(name)s.profile && echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/%(name)s.profile && echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/%(name)s.profile && %(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/%(name)s.profile', +#] + +sanity_check_paths = { + 'files': ['bin/%(arch)s-linux/tex', 'bin/%(arch)s-linux/latex'], + 'dirs': ['bin/%(arch)s-linux', 'texmf-dist'], +} + +modextrapaths = { + 'INFOPATH': 'texmf-dist/doc/info', + 'MANPATH': 'texmf-dist/doc/man', + 'PATH': 'bin/%(arch)s-linux', +} + +modextravars = {'TEXMFHOME': '%(installdir)s/texmf-dist'} + +moduleclass = 'devel' From d636455d661fa1c107dcce43814bec1b50ee1efc Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 4 Sep 2023 16:53:19 +0200 Subject: [PATCH 8680/9987] Remove stray comments --- .../t/texlive/texlive-20230313-GCC-11.3.0.eb | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb index d0b8b7b4b70..1c879f4d377 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb @@ -59,26 +59,8 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %%(installdir)s/texmf-config" >> %%(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %%(installdir)s/texmf-var" >> %%(installdir)s/texlive.profile && ' '%s' % local_install_tl_or - # This should probably be a hook on our system. - # It'll mean the TEX files from homedir aren't picked up, as it would require an update of the cache - # ' && sed -i -e "s|TEXMF = {$TEXMFAUXTREES$TEXMFCONFIG,$TEXMFVAR,$TEXMFHOME,!!$TEXMFLOCAL,!!$TEXMFSYSCONFIG,!!$TEXMFSYSVAR,!!$TEXMFDIST}|TEXMF = {!!$TEXMFAUXTREES$TEXMFCONFIG,!!$TEXMFVAR,!!$TEXMFHOME,!!$TEXMFLOCAL,!!$TEXMFSYSCONFIG,!!$TEXMFSYSVAR,!!$TEXMFDIST}" %(installdir)s/texmf-dist/web2c/texmf.cnf' ] -#postinstallcmds = [ -# 'echo "TEXDIR %(installdir)s/" > %(installdir)s/texlive.profile && ' -# 'echo "TEXMFLOCAL %(installdir)s/texmf-local" >> %(installdir)s/texlive.profile && ' -# 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' -# 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' -# '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' -# ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year -#] - - -#postinstallcmds = [ -# 'echo "TEXDIR %(installdir)s/" > %(installdir)s/%(name)s.profile && echo "TEXMFLOCAL %(installdir)s/texmf-local" >> %(installdir)s/%(name)s.profile && echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/%(name)s.profile && echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/%(name)s.profile && %(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/%(name)s.profile -repository https://ftp.math.utah.edu/pub/tex/historic/systems/%(name)s/2023/', -# 'echo "TEXDIR %(installdir)s/" > %(installdir)s/%(name)s.profile && echo "TEXMFLOCAL %(installdir)s/texmf-local" >> %(installdir)s/%(name)s.profile && echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/%(name)s.profile && echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/%(name)s.profile && %(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/%(name)s.profile', -#] - sanity_check_paths = { 'files': ['bin/%(arch)s-linux/tex', 'bin/%(arch)s-linux/latex'], 'dirs': ['bin/%(arch)s-linux', 'texmf-dist'], From 8c6a7daf2226089bb74735c5aef3facf6bf276a9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 4 Sep 2023 20:30:14 +0200 Subject: [PATCH 8681/9987] Add test for EC file permissions (#18647) --- test/easyconfigs/easyconfigs.py | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 34a7f346a85..b3142f30505 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -31,6 +31,7 @@ import os import re import shutil +import stat import sys import tempfile from collections import defaultdict @@ -1226,6 +1227,29 @@ def check_https_url(http_url): if failing_checks: self.fail('\n'.join(failing_checks)) + @skip_if_not_pr_to_non_main_branch() + def test_ec_file_permissions(self): + """Make sure correct access rights are set for easyconfigs.""" + + failing_checks = [] + for ec in self.changed_ecs: + ec_fn = os.path.basename(ec.path) + st = os.stat(ec.path) + read_perms = stat.S_IRUSR | stat.S_IRGRP | stat.S_IROTH + exec_perms = stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH + wrong_perms = [] + if (st.st_mode & read_perms) != read_perms: + wrong_perms.append("readable (owner, group, other)") + if st.st_mode & exec_perms: + wrong_perms.append("not executable") + if not (st.st_mode & stat.S_IWUSR): + wrong_perms.append("at least owner writable") + if wrong_perms: + failing_checks.append("%s must be %s, is: %s" % (ec_fn, ", ".join(wrong_perms), oct(st.st_mode))) + + if failing_checks: + self.fail('\n'.join(failing_checks)) + @skip_if_not_pr_to_non_main_branch() def test_pr_CMAKE_BUILD_TYPE(self): """Make sure -DCMAKE_BUILD_TYPE is no longer used (replaced by build_type)""" From 9bfa929880624c8005aeb3543499bf97a2d08a4c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 4 Sep 2023 19:36:10 +0100 Subject: [PATCH 8682/9987] adding easyconfigs: numdiff-5.9.0-GCCcore-12.2.0.eb --- .../n/numdiff/numdiff-5.9.0-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100755 easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-12.2.0.eb new file mode 100755 index 00000000000..9bee3f67258 --- /dev/null +++ b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'numdiff' +version = '5.9.0' + +homepage = 'https://www.nongnu.org/numdiff/' +description = """Numdiff (which I will also write numdiff) is a little program that can be used to compare putatively + similar files line by line and field by field, ignoring small numeric differences or/and different numeric formats. + Equivalently, Numdiff is a program with the capability to appropriately compare files containing numerical fields + (and not only).""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['87284a117944723eebbf077f857a0a114d818f8b5b54d289d59e73581194f5ef'] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ['bin/ndselect', 'bin/numdiff'], + 'dirs': ['share'], +} + +sanity_check_commands = ["numdiff --help"] + +moduleclass = 'tools' From 44849d2669a5ed50952e1767e71bea5be3c2b44e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 4 Sep 2023 20:15:22 +0100 Subject: [PATCH 8683/9987] chmod --- easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-12.2.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/numdiff/numdiff-5.9.0-GCCcore-12.2.0.eb old mode 100755 new mode 100644 From 11458270ad23bc4e05a8caf475cc8d34671d9a75 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 4 Sep 2023 20:24:45 +0000 Subject: [PATCH 8684/9987] Add flextables extension to R/4.2.2, R/4.2.1 --- .../easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 29 +++++++++++++++++ .../easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 31 +++++++++++++------ 2 files changed, 51 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 626232ab783..9d6af6f22c4 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -49,6 +49,8 @@ dependencies = [ ('nodejs', '16.15.1'), # for V8 (required by rstan) ('GDAL', '3.5.0'), # for sf ('MPFR', '4.1.0'), # for Rmpfr + ('HarfBuzz', '4.2.1'), # for textshaping + ('FriBidi', '1.0.12'), # for textshaping ('libgit2', '1.4.3'), ('OpenSSL', '1.1', '', SYSTEM), ] @@ -3553,6 +3555,33 @@ exts_list = [ 'sources': [{'download_filename': 'cc961c5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['667a4270456d28188734ce31411326130a94e085490ced84096c984789bb174a'], }), + ('textshaping', '0.3.6', { + 'checksums': ['80e2c087962f55ce2811fbc798b09f5638c06c6b28c10cd3cb3827005b902ada'], + }), + ('ragg', '1.2.5', { + 'checksums': ['936f4d75e0e01cdeefb9f57d121cdd7812d0de5a9e1a3a8315f92ce1c84da8f9'], + }), + ('officer', '0.6.2', { + 'checksums': ['0948b5785c90767b63382b17a36c5167c54c5ba6dc61c80e808e16df620bd335'], + }), + ('gfonts', '0.2.0', { + 'checksums': ['72e2eead5280b45aadbbd9385971d65e9866fd659270b1c3c1eb98330f024aa6'], + }), + ('fontBitstreamVera', '0.1.1', { + 'checksums': ['3298b3dd95605bdda0c5fce5594c9bedde6aa63d89b216d5c83c6c092b6d375a'], + }), + ('fontLiberation', '0.1.0', { + 'checksums': ['acdea423e005873aa509e280074a3cef4796e4f7e9d77b3945d77b451ea039f0'], + }), + ('fontquiver', '0.2.1', { + 'checksums': ['95871814c2d55c03ee15a54e29aadfb840c791e1430f94127d9e1dc8608a6363'], + }), + ('gdtools', '0.3.3', { + 'checksums': ['da5a189841475b1d69c94a30ff834eb44560c69e6c0ec0a257006e1f59e83483'], + }), + ('flextable', '0.9.2', { + 'checksums': ['bccd53919ae58f1d26c4a8ee42da1f5e0b7333f8b4ee295b380ed256069f923d'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 61bd80b3573..5eb314d3154 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -78,9 +78,6 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 17th March 2023 exts_list = [ - # include packages that are part of the base installation of R, - # both to make sure they are available (via sanity check), - # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets', @@ -2373,7 +2370,6 @@ exts_list = [ 'checksums': ['be50f9fdef0f4bf9676b9c3c2906d0431afc678af55cf48b1119f9fc0adac44f'], }), ('liquidSVM', '1.2.4', { - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ @@ -2889,12 +2885,8 @@ exts_list = [ 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], }), ('gWidgets2tcltk', '1.0-8', { - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" - 'preinstallopts': "xvfb-run ", - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... 'modulename': False, + 'preinstallopts': "xvfb-run ", 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], }), ('mgsub', '1.7.3', { @@ -3645,6 +3637,27 @@ exts_list = [ 'sources': [{'download_filename': 'cc961c5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['667a4270456d28188734ce31411326130a94e085490ced84096c984789bb174a'], }), + ('officer', '0.6.2', { + 'checksums': ['0948b5785c90767b63382b17a36c5167c54c5ba6dc61c80e808e16df620bd335'], + }), + ('gfonts', '0.2.0', { + 'checksums': ['72e2eead5280b45aadbbd9385971d65e9866fd659270b1c3c1eb98330f024aa6'], + }), + ('fontBitstreamVera', '0.1.1', { + 'checksums': ['3298b3dd95605bdda0c5fce5594c9bedde6aa63d89b216d5c83c6c092b6d375a'], + }), + ('fontLiberation', '0.1.0', { + 'checksums': ['acdea423e005873aa509e280074a3cef4796e4f7e9d77b3945d77b451ea039f0'], + }), + ('fontquiver', '0.2.1', { + 'checksums': ['95871814c2d55c03ee15a54e29aadfb840c791e1430f94127d9e1dc8608a6363'], + }), + ('gdtools', '0.3.3', { + 'checksums': ['da5a189841475b1d69c94a30ff834eb44560c69e6c0ec0a257006e1f59e83483'], + }), + ('flextable', '0.9.2', { + 'checksums': ['bccd53919ae58f1d26c4a8ee42da1f5e0b7333f8b4ee295b380ed256069f923d'], + }), ] moduleclass = 'lang' From f847a8d469dd2edb2b43088a1b7d14411b3d7277 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 5 Sep 2023 10:37:17 +0200 Subject: [PATCH 8685/9987] Fix formatting --- .../t/texlive/texlive-20230313-GCC-11.3.0.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb index 1c879f4d377..9f30a78c0ed 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb @@ -4,7 +4,7 @@ easyblock = 'Tarball' name = 'texlive' version = '20230313' -local_version_year = version[:4] +local_ver_year = version[:4] homepage = 'https://tug.org' description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript @@ -15,8 +15,8 @@ description = """TeX is a typesetting language. Instead of visually formatting y toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = [ - 'ftp://tug.org/texlive/historic/%s/' % local_version_year, - 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year, + 'ftp://tug.org/texlive/historic/%s/' % local_ver_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_ver_year, ] sources = [ { @@ -44,13 +44,13 @@ dependencies = [ # Similarly, ftp is not available on all HPC systems, hence providing fallback to https # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17871 local_install_tl = "%%(builddir)s/install-tl-%%(version)s/install-tl -profile %%(installdir)s/texlive.profile %s" -local_ftp = '-repository ftp://ftp.math.utah.edu/pub/tex/historic/systems/textlive/%s/tlnet-final' % local_version_year -local_https = '-repository https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year +local_ftp = '-repository ftp://ftp.math.utah.edu/pub/tex/historic/systems/textlive/%s/tlnet-final' % local_ver_year +local_https = '-repository https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_ver_year local_install_tl_or = ( ' || '.join([ - local_install_tl % '', - local_install_tl % local_ftp, - local_install_tl % local_https, + local_install_tl % '', + local_install_tl % local_ftp, + local_install_tl % local_https, ]) ) postinstallcmds = [ From 5d55ec67b4fe4650ce835fe5f7fa2ea9ae1af5a8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 5 Sep 2023 10:59:31 +0200 Subject: [PATCH 8686/9987] adding easyconfigs: TensorFlow-2.13.0-foss-2023a.eb and patches: TensorFlow-2.13.0_add-default-shell-env.patch, TensorFlow-2.13.0_add-missing-system-absl-py-target.patch, TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch, TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch, TensorFlow-2.13.0_fix-protobuf-compatibility.patch, TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch, TensorFlow-2.13.0_remove-libclang-dep.patch, TensorFlow-2.13.0_fix-numpy-2.15.compat.patch, TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch, TensorFlow-2.13.0_unpin-gast-version.patch --- .../TensorFlow-2.13.0-foss-2023a.eb | 236 +++++ ...sorFlow-2.13.0_add-default-shell-env.patch | 30 + ....0_add-missing-system-absl-py-target.patch | 17 + ..._add-missing-system-protobuf-targets.patch | 25 + ...orFlow-2.13.0_exclude-xnnpack-on-ppc.patch | 46 + ...sorFlow-2.13.0_fix-numpy-2.15.compat.patch | 41 + ...ow-2.13.0_fix-protobuf-compatibility.patch | 55 ++ ...-2.13.0_remove-io-gcs-filesystem-dep.patch | 13 + ...ensorFlow-2.13.0_remove-libclang-dep.patch | 21 + ...w-2.13.0_revert-to-flatbuffers-2.0.6.patch | 911 ++++++++++++++++++ ...TensorFlow-2.13.0_unpin-gast-version.patch | 18 + 11 files changed, 1413 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-default-shell-env.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-absl-py-target.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-numpy-2.15.compat.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-protobuf-compatibility.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-libclang-dep.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_unpin-gast-version.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb new file mode 100644 index 00000000000..6de09ba961c --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb @@ -0,0 +1,236 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.13.0' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '6.3.1'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.41.0', '-nodocs'), + ('pybind11', '2.11.1'), + ('UnZip', '6.0'), + # Required to build some of the extensions + ('poetry', '1.5.1'), + # System protobuf doesn't seem to work: https://github.com/tensorflow/tensorflow/issues/61593 + # So don't add it here +] +dependencies = [ + ('Python', '3.11.3'), + ('h5py', '3.9.0'), + ('cURL', '8.0.1'), + ('dill', '0.3.7'), + ('double-conversion', '3.3.0'), + ('flatbuffers', '23.5.26'), + ('flatbuffers-python', '23.5.26'), + ('giflib', '5.2.1'), + ('hwloc', '2.9.1'), + ('ICU', '73.2'), + ('JsonCpp', '1.9.5'), + ('libjpeg-turbo', '2.1.5.1'), + ('NASM', '2.16.01'), + ('nsync', '1.26.0'), + ('SQLite', '3.42.0'), + ('patchelf', '0.18.0'), + ('protobuf-python', '4.24.0'), + ('libpng', '1.6.39'), + ('snappy', '1.1.10'), + ('zlib', '1.2.13'), + # Dependencies of grpcio + ('OpenSSL', '1.1', '', SYSTEM), + ('RE2', '2023-08-01'), +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('wrapt', '1.15.0', { + 'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'], + }), + ('termcolor', '2.3.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475'], + }), + ('tensorflow-estimator', version, { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'checksums': ['6f868284eaa654ae3aa7cacdbef2175d0909df9fcf11374f5166f8bf475952aa'], + }), + ('Werkzeug', '2.3.7', { + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'checksums': ['2b8c0e447b4b9dbcc85dd97b6eeb4dcbaf6c8b6c3be0bd654e25553e0a2157d8'], + }), + ('tensorboard-plugin-wit', '1.8.1', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard-data-server', '0.7.1', { + 'source_tmpl': 'tensorboard_data_server-%(version)s-py3-none-any.whl', + 'checksums': ['9938bd39f5041797b33921066fba0eab03a0dd10d1887a05e62ae58841ad4c3f'], + }), + ('Markdown', '3.4.4', { + 'checksums': ['225c6123522495d4119a90b3a3ba31a1e87a70369e03f14799ea9c0d7183a3d6'], + }), + ('grpcio', '1.57.0', { + 'modulename': 'grpc', + 'preinstallopts': "GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s " + + " ".join(["GRPC_PYTHON_BUILD_SYSTEM_%s=True" % i for i in + ( + 'OPENSSL', + 'ZLIB', + 'RE2', + # 'ABSL', + )]), + 'checksums': ['4b089f7ad1eb00a104078bab8015b0ed0ebcb3b589e527ab009c53893fd4e613'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('pyasn1-modules', '0.3.0', { + 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', + 'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'], + }), + ('cachetools', '5.3.1', { + 'checksums': ['dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b'], + }), + ('google-auth', '2.22.0', { + 'modulename': 'google.auth', + 'checksums': ['164cba9af4e6e4e40c3a4f90a1a6c12ee56f14c0b4868d1ca91b32826ab334ce'], + }), + ('google-auth-oauthlib', '1.0.0', { + 'checksums': ['e375064964820b47221a7e1b7ee1fd77051b6323c3f9e3e19785f78ab67ecfc5'], + }), + ('absl-py', '1.4.0', { + 'modulename': 'absl', + 'checksums': ['d2c244d01048ba476e7c080bd2c6df5e141d211de80223460d5b3b8a2a58433d'], + }), + ('tensorboard', version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ab69961ebddbddc83f5fa2ff9233572bdad5b883778c35e4fe94bf1798bd8481'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('keras', '2.13.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5ce5f706f779fa7330e63632f327b75ce38144a120376b2ae1917c00fa6136af'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + # Required by tests + ('portpicker', '1.5.2', { + 'checksums': ['c55683ad725f5c00a41bc7db0225223e8be024b1fa564d039ed3390e4fd48fb3'], + }), + # System dependencies + ('tblib', '2.0.0', { + 'checksums': ['a6df30f272c08bf8be66e0775fad862005d950a6b8449b94f7c788731d70ecd7'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + # Optional profile plugin + dependency + ('gviz-api', '1.10.0', { + 'source_tmpl': 'gviz_api-%(version)s.tar.gz', + 'checksums': ['846692dd8cc73224fc31b18e41589bd934e1cc05090c6576af4b4b26c2e71b90'], + }), + ('tensorboard-plugin-profile', '2.13.1', { + 'source_tmpl': 'tensorboard_plugin_profile-%(version)s.tar.gz', + 'checksums': ['472d1cb85d7087c5294131eb640bd771f5515ecc4867030c7904718be7fc19c1'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'patches': [ + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.11.0_disable-avx512-extensions.patch', + 'TensorFlow-2.13.0_add-default-shell-env.patch', + 'TensorFlow-2.13.0_add-missing-system-absl-py-target.patch', + 'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch', + 'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch', + 'TensorFlow-2.13.0_fix-protobuf-compatibility.patch', + 'TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch', + 'TensorFlow-2.13.0_remove-libclang-dep.patch', + 'TensorFlow-2.13.0_fix-numpy-2.15.compat.patch', + 'TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch', + 'TensorFlow-2.13.0_unpin-gast-version.patch', + ], + 'checksums': [ + {'v2.13.0.tar.gz': 'e58c939079588623e6fa1d054aec2f90f95018266e0a970fd353a5244f5173dc'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.9.1_remove-duplicate-gpu-tests.patch': + '6fe50faab28387c622c68dc3fc0cbfb2a51000cd750c1a82f8420b54fcd2509f'}, + {'TensorFlow-2.11.0_disable-avx512-extensions.patch': + 'fb8e7694b5d2377cc44e6674ff85a7c50dc725f2f507cbcfda65f129f534b1cc'}, + {'TensorFlow-2.13.0_add-default-shell-env.patch': + 'a94b2e007bff5a08ec4e6ec3043985907a69e9eeaea69dc4fe2aa15d15b75aef'}, + {'TensorFlow-2.13.0_add-missing-system-absl-py-target.patch': + '94bc3b155840af942437d06c43830dabf41d94391daf61e1d0add0a7bf20a538'}, + {'TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch': + '77d8c8a5627493fc7c38b4de79d49e60ff6628b05ff969f4cd3ff9857176c459'}, + {'TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch': + 'd0818206846911d946666ded7d3216c0546e37cee1890a2f48dc1a9d71047cad'}, + {'TensorFlow-2.13.0_fix-protobuf-compatibility.patch': + 'a9658c035b663da1b7d1983a8e37883cc40c1c0cfa22132bb7fe19c4cbc9712a'}, + {'TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch': + '39f1cbecad4b3723481b30f18f16363ab1837c8749ee197ec88b92b493e9df67'}, + {'TensorFlow-2.13.0_remove-libclang-dep.patch': + 'f0d067d129e817b0d371c4e48a4a1ac08f80a2c137d52b05a3c7c4370dcbd1e5'}, + {'TensorFlow-2.13.0_fix-numpy-2.15.compat.patch': + '4023be57bc8e33ae55ccac54b51d6532fea7ac4a32cb1125e3e42da0dec1669a'}, + {'TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch': + 'f22757250181b6165e4b2ef1e199bd4cb344a9429be5a1086638f25bcbf650fc'}, + {'TensorFlow-2.13.0_unpin-gast-version.patch': + '61e0c9b67aa6c48176fcbb429bf6aa36c4fdde604c82c02f58a043412fecf285'}, + ], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,' + '-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-default-shell-env.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-default-shell-env.patch new file mode 100644 index 00000000000..9b1f3171369 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-default-shell-env.patch @@ -0,0 +1,30 @@ +Make TensorFlow use the environment as set by EasyBuild + +See https://github.com/tensorflow/tensorflow/pull/61591 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/lite/build_def.bzl b/tensorflow/lite/build_def.bzl +index 842879a0536..20fb9c1fb9d 100644 +--- a/tensorflow/lite/build_def.bzl ++++ b/tensorflow/lite/build_def.bzl +@@ -356,6 +356,7 @@ def _gen_selected_ops_impl(ctx): + executable = ctx.executable._generate_op_registrations, + mnemonic = "OpRegistration", + progress_message = "gen_selected_ops", ++ use_default_shell_env = True, + ) + + gen_selected_ops_rule = rule( +diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl +index e9f5e5aaffa..c22efdc20cf 100644 +--- a/tensorflow/tensorflow.bzl ++++ b/tensorflow/tensorflow.bzl +@@ -1282,6 +1282,7 @@ def _generate_op_reg_offsets_impl(ctx): + tools = [ctx.executable._offset_counter], + executable = ctx.executable._offset_counter, + arguments = [args], ++ use_default_shell_env = True, + ) + + generate_op_reg_offsets = rule( diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-absl-py-target.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-absl-py-target.patch new file mode 100644 index 00000000000..5a68faf7479 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-absl-py-target.patch @@ -0,0 +1,17 @@ +Add a missing target for the absl-py SYSTEMLIB +From https://github.com/tensorflow/tensorflow/pull/60636 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/systemlibs/absl_py.absl.flags.BUILD b/third_party/systemlibs/absl_py.absl.flags.BUILD +index 4049989ae2fda..d92f4949df1a5 100644 +--- a/third_party/systemlibs/absl_py.absl.flags.BUILD ++++ b/third_party/systemlibs/absl_py.absl.flags.BUILD +@@ -5,3 +5,7 @@ package(default_visibility = ["//visibility:public"]) + py_library( + name = "flags", + ) ++ ++py_library( ++ name = "argparse_flags", ++) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch new file mode 100644 index 00000000000..54491dab40a --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_add-missing-system-protobuf-targets.patch @@ -0,0 +1,25 @@ +Fix error: +ERROR: /dev/shm/TensorFlow/tensorflow-2.13.0/tensorflow/python/framework/BUILD:2454:17: no such target '@com_google_protobuf//:well_known_types_py_pb2_genproto': target 'well_known_types_py_pb2_genproto' not declared in package '' defined by /dev/shm/s3248973-EasyBuild/TensorFlow/2.13.0/foss-2022a/TensorFlow/bazel-root/663b1bf019e1a9ec9827eae691fce071/external/com_google_protobuf/BUILD.bazel and referenced by '//tensorflow/python/framework:cpp_shape_inference_proto_py_genproto' +ERROR: Analysis of target '//tensorflow/tools/pip_package:build_pip_package' failed; build aborted: + +Using solution from +https://github.com/tensorflow/tensorflow/issues/60667#issuecomment-1563522589 + +Author: Alexander Grund (TU Dresden) + +diff --git a/third_party/systemlibs/protobuf.BUILD b/third_party/systemlibs/protobuf.BUILD +index 4d05ab28d12..cb48d375b27 100644 +--- a/third_party/systemlibs/protobuf.BUILD ++++ b/third_party/systemlibs/protobuf.BUILD +@@ -111,3 +116,10 @@ py_library( + visibility = ["//visibility:public"], + deps = [dep + "_proto" for dep in proto[1][1]], + ) for proto in WELL_KNOWN_PROTO_MAP.items()] ++ ++py_proto_library( ++ name = "well_known_types_py_pb2", ++ include = ".", ++ srcs = [proto[1][0] for proto in WELL_KNOWN_PROTO_MAP.items()], ++ visibility = ["//visibility:public"], ++) +\ No newline at end of file diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch new file mode 100644 index 00000000000..da2b07cc736 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_exclude-xnnpack-on-ppc.patch @@ -0,0 +1,46 @@ +XNNPACK is not supported on PowerPC so disable it by default. +See https://github.com/tensorflow/tensorflow/issues/58768 + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/lite/BUILD b/tensorflow/lite/BUILD +index c08cd7bcec5..c23c0eedac8 100644 +--- a/tensorflow/lite/BUILD ++++ b/tensorflow/lite/BUILD +@@ -829,6 +829,8 @@ cc_library( + defines = select({ + ":tflite_kernel_use_xnnpack_false": [], + ":tflite_with_xnnpack_explicit_false": [], ++ # XNNPACK is not supported on PPC ++ "//tensorflow:linux_ppc64le": [], + "//conditions:default": [ + "TFLITE_KERNEL_USE_XNNPACK", + ], +@@ -864,9 +866,11 @@ cc_library( + # Note: adding ":tflite_with_xnnpack_enabled" to the values of following + # configuration conditions will make TFLite interpreter to apply XNNPACK + # delegate by default. +- deps = [ +- ":tflite_with_xnnpack_enabled", +- ], ++ deps = select({ ++ # XNNPACK is not supported on PPC ++ "//tensorflow:linux_ppc64le": [], ++ "//conditions:default": [":tflite_with_xnnpack_enabled"], ++ }), + ) + + cc_library( +diff --git a/tensorflow/lite/kernels/BUILD b/tensorflow/lite/kernels/BUILD +index 9c3ebdfaaba..a042f8ccedb 100644 +--- a/tensorflow/lite/kernels/BUILD ++++ b/tensorflow/lite/kernels/BUILD +@@ -735,6 +735,8 @@ BUILTIN_KERNEL_DEPS = [ + ], + }) + select({ + "//tensorflow/lite:tflite_with_xnnpack_explicit_false": [], ++ # XNNPACK is not supported on PPC ++ "//tensorflow:linux_ppc64le": [], + "//conditions:default": [ + "@XNNPACK//:xnnpack_for_tflite", + ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-numpy-2.15.compat.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-numpy-2.15.compat.patch new file mode 100644 index 00000000000..82599f424d0 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-numpy-2.15.compat.patch @@ -0,0 +1,41 @@ +From eb5ea898c848f18a2c9d86102f7f111f19874ecc Mon Sep 17 00:00:00 2001 +From: Peter Hawkins +Date: Wed, 19 Jul 2023 11:47:45 -0700 +Subject: [PATCH] [NumPy] Fix test failures under NumPy 1.25. + +PiperOrigin-RevId: 549381271 +--- + tensorflow/python/eager/core_test.py | 2 -- + 1 file changed, 2 deletions(-) + +diff --git a/tensorflow/python/eager/core_test.py b/tensorflow/python/eager/core_test.py +index 6e919d6deab96..bbac4a1833e34 100644 +--- a/tensorflow/python/eager/core_test.py ++++ b/tensorflow/python/eager/core_test.py +@@ -318,8 +318,6 @@ def testEqualityBroadcast(self): + bool(np_a == np_c) + self.assertAllEqual(np_a == np_c, [[True, True], [True, True]]) + self.assertAllEqual(np_a == np_d, [[True, False], [True, False]]) +- self.assertFalse(bool(np_a == np_e)) +- self.assertTrue(bool(np_a != np_e)) + self.assertNotAllEqual(np_a, np_e) + finally: + if default: + +Basically reverts https://github.com/tensorflow/tensorflow/commit/90389e9353b804246e5661cc727a3a7fd1f98066 +Test failure fixed by the above + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index e77e6f81449..36c8ba3f030 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -90,6 +90,6 @@ REQUIRED_PACKAGES = [ + 'google_pasta >= 0.1.1', + 'h5py >= 2.9.0', +- 'numpy >= 1.22, <= 1.24.3', ++ 'numpy >= 1.22', + 'opt_einsum >= 2.3.2', + 'packaging', + 'protobuf>=3.20.3,<5.0.0dev,!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-protobuf-compatibility.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-protobuf-compatibility.patch new file mode 100644 index 00000000000..1eae68fd6bf --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_fix-protobuf-compatibility.patch @@ -0,0 +1,55 @@ +From 297fe6b883c362d328327c8fd99566ec7f579d10 Mon Sep 17 00:00:00 2001 +From: Sagun Bajra +Date: Wed, 3 May 2023 19:45:00 -0700 +Subject: [PATCH] Update proto insertion to be compatible with all verstions of + the proto library. + +PiperOrigin-RevId: 529263012 +--- + .../eager/small_constants_optimizer.cc | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) + +diff --git a/tensorflow/core/common_runtime/eager/small_constants_optimizer.cc b/tensorflow/core/common_runtime/eager/small_constants_optimizer.cc +index 0d6b36ea3d1bd..7d43f29029f0c 100644 +--- a/tensorflow/core/common_runtime/eager/small_constants_optimizer.cc ++++ b/tensorflow/core/common_runtime/eager/small_constants_optimizer.cc +@@ -171,17 +171,17 @@ std::vector FoldBoolInputTensor( + + // Promote the true branch when input_value is `true`. + if (attr_key == "then_branch") { +- if (input_value) node_def.mutable_attr()->emplace("f", attr_value); ++ if (input_value) node_def.mutable_attr()->insert({"f", attr_value}); + continue; + } + // Promote the false branch when input_value is `false`. + if (attr_key == "else_branch") { +- if (!input_value) node_def.mutable_attr()->emplace("f", attr_value); ++ if (!input_value) node_def.mutable_attr()->insert({"f", attr_value}); + continue; + } + + // All other attributes should be copied over. +- node_def.mutable_attr()->emplace(attr_key, attr_value); ++ node_def.mutable_attr()->insert({attr_key, attr_value}); + } + } + +@@ -213,15 +213,15 @@ std::vector FoldBoolInputTensor( + const_tensor->set_op("Const"); + AttrValue dtype_value; + dtype_value.set_type(DT_BOOL); +- const_tensor->mutable_attr()->emplace("dtype", dtype_value); ++ const_tensor->mutable_attr()->insert({"dtype", dtype_value}); + AttrValue tensor_value; + auto* tensor = tensor_value.mutable_tensor(); + tensor->set_dtype(DT_BOOL); + tensor->mutable_tensor_shape(); + tensor->add_bool_val(true); +- const_tensor->mutable_attr()->emplace("value", tensor_value); ++ const_tensor->mutable_attr()->insert({"value", tensor_value}); + +- // Mark the currend `FunctionDef` as folded and return the results. ++ // Mark the current `FunctionDef` as folded and return the results. + results.push_back(std::move(result)); + folded_functions.insert(folded_function_name); + return results; diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch new file mode 100644 index 00000000000..5064cce0e95 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch @@ -0,0 +1,13 @@ +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index e77e6f81449..29fdd4a1d91 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -99,8 +98,6 @@ REQUIRED_PACKAGES = [ + 'termcolor >= 1.1.0', + 'typing_extensions>=3.6.6,<4.6.0', + 'wrapt >= 1.11.0', +- 'tensorflow-io-gcs-filesystem >= 0.23.1;platform_machine!="arm64" or ' + +- 'platform_system!="Darwin"', + # grpcio does not build correctly on big-endian machines due to lack of + # BoringSSL support. + # See https://github.com/tensorflow/tensorflow/issues/17882. diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-libclang-dep.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-libclang-dep.patch new file mode 100644 index 00000000000..b50c85d7889 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-libclang-dep.patch @@ -0,0 +1,21 @@ +libclang was introduced in +https://github.com/tensorflow/tensorflow/commit/c211472000ff57bac7fcec9b0465cf73b37bf135 +> This is in preparation to open-source TF's TFRT backend. +> TFRT generates code using libclang python bindings as part of the build. +Hence it is not currently used and as it is not (easily) available for all architectures +simply remove it. + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index e77e6f81449..29fdd4a1d91 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -89,7 +89,6 @@ REQUIRED_PACKAGES = [ + 'gast >= 0.2.1, <= 0.4.0', + 'google_pasta >= 0.1.1', + 'h5py >= 2.9.0', +- 'libclang >= 13.0.0', + 'numpy >= 1.22, <= 1.24.3', + 'opt_einsum >= 2.3.2', + 'packaging', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch new file mode 100644 index 00000000000..45cdc96c12a --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch @@ -0,0 +1,911 @@ +Revert the commits upgrading the flatbuffer dependency: +https://github.com/tensorflow/tensorflow/commit/86e0d74bb6a87020c1683629eb7d1dc73949377f +https://github.com/tensorflow/tensorflow/commit/c3a577817f650f75f8df075fce7a542c42596e9d + +Then manually re-add double-colons (`sed -i 's/flatbuffers::/::flatbuffers::/g'`) to reduce diff + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h b/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h +index 2e3f07e46b6..001813510ec +--- a/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h ++++ b/tensorflow/lite/delegates/gpu/cl/compiled_program_cache_generated.h +@@ -20,13 +20,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + namespace tflite { + namespace gpu { + namespace cl { +diff --git a/tensorflow/lite/delegates/gpu/cl/serialization_generated.h b/tensorflow/lite/delegates/gpu/cl/serialization_generated.h +index c0d14cfbc02..529e7c96bf0 +--- a/tensorflow/lite/delegates/gpu/cl/serialization_generated.h ++++ b/tensorflow/lite/delegates/gpu/cl/serialization_generated.h +@@ -20,15 +20,8 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- +-#include "gpu_model_generated.h" + #include "serialization_base_generated.h" ++#include "gpu_model_generated.h" + + namespace tflite { + namespace gpu { +diff --git a/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h b/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h +index 3fa3fbaf816..17357af7f0e +--- a/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h ++++ b/tensorflow/lite/delegates/gpu/common/gpu_model_generated.h +@@ -19,13 +19,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + #include "serialization_base_generated.h" + + namespace tflite { +diff --git a/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h b/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h +index 59831408614..4087c486d19 +--- a/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h ++++ b/tensorflow/lite/delegates/gpu/common/task/serialization_base_generated.h +@@ -20,13 +20,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + namespace tflite { + namespace gpu { + namespace data { +@@ -270,28 +263,14 @@ enum class Layout : int8_t { + + inline const Layout (&EnumValuesLayout())[7] { + static const Layout values[] = { +- Layout::UNKNOWN, +- Layout::HWC, +- Layout::BHWC, +- Layout::HWDC, +- Layout::BHWDC, +- Layout::LINEAR, +- Layout::HW +- }; ++ Layout::UNKNOWN, Layout::HWC, Layout::BHWC, Layout::HWDC, ++ Layout::BHWDC, Layout::LINEAR, Layout::HW}; + return values; + } + + inline const char * const *EnumNamesLayout() { +- static const char * const names[8] = { +- "UNKNOWN", +- "HWC", +- "BHWC", +- "HWDC", +- "BHWDC", +- "LINEAR", +- "HW", +- nullptr +- }; ++ static const char *const names[8] = {"UNKNOWN", "HWC", "BHWC", "HWDC", ++ "BHWDC", "LINEAR", "HW", nullptr}; + return names; + } + +@@ -1834,15 +1813,22 @@ inline ::flatbuffers::Offset CreateGPUOperation( + ::flatbuffers::Offset arguments = 0, + ::flatbuffers::Offset<::flatbuffers::String> code = 0, + ::flatbuffers::Offset work_group_size = 0, +- ::flatbuffers::Offset<::flatbuffers::Vector<::flatbuffers::Offset>> compiler_options = 0, +- tflite::gpu::data::TensorToGrid tensor_to_grid = tflite::gpu::data::TensorToGrid::CUSTOM, ++ ::flatbuffers::Offset<::flatbuffers::Vector< ++ ::flatbuffers::Offset>> ++ compiler_options = 0, ++ tflite::gpu::data::TensorToGrid tensor_to_grid = ++ tflite::gpu::data::TensorToGrid::CUSTOM, + uint64_t flops = 0, + ::flatbuffers::Offset definition = 0, + int32_t grid_dimension = 0, + ::flatbuffers::Offset work_group_launch_order = 0, + ::flatbuffers::Offset grid_size = 0, +- ::flatbuffers::Offset<::flatbuffers::Vector<::flatbuffers::Offset<::flatbuffers::String>>> src_tensors_names = 0, +- ::flatbuffers::Offset<::flatbuffers::Vector<::flatbuffers::Offset<::flatbuffers::String>>> dst_tensors_names = 0, ++ ::flatbuffers::Offset< ++ ::flatbuffers::Vector<::flatbuffers::Offset<::flatbuffers::String>>> ++ src_tensors_names = 0, ++ ::flatbuffers::Offset< ++ ::flatbuffers::Vector<::flatbuffers::Offset<::flatbuffers::String>>> ++ dst_tensors_names = 0, + ::flatbuffers::Offset work_groups_count = 0) { + GPUOperationBuilder builder_(_fbb); + builder_.add_flops(flops); +@@ -1866,35 +1852,29 @@ inline ::flatbuffers::Offset CreateGPUOperationDirect( + ::flatbuffers::Offset arguments = 0, + const char *code = nullptr, + ::flatbuffers::Offset work_group_size = 0, +- const std::vector<::flatbuffers::Offset> *compiler_options = nullptr, +- tflite::gpu::data::TensorToGrid tensor_to_grid = tflite::gpu::data::TensorToGrid::CUSTOM, ++ const std::vector<::flatbuffers::Offset> ++ *compiler_options = nullptr, ++ tflite::gpu::data::TensorToGrid tensor_to_grid = ++ tflite::gpu::data::TensorToGrid::CUSTOM, + uint64_t flops = 0, + ::flatbuffers::Offset definition = 0, + int32_t grid_dimension = 0, + ::flatbuffers::Offset work_group_launch_order = 0, + ::flatbuffers::Offset grid_size = 0, +- const std::vector<::flatbuffers::Offset<::flatbuffers::String>> *src_tensors_names = nullptr, +- const std::vector<::flatbuffers::Offset<::flatbuffers::String>> *dst_tensors_names = nullptr, ++ const std::vector<::flatbuffers::Offset<::flatbuffers::String>> ++ *src_tensors_names = nullptr, ++ const std::vector<::flatbuffers::Offset<::flatbuffers::String>> ++ *dst_tensors_names = nullptr, + ::flatbuffers::Offset work_groups_count = 0) { + auto code__ = code ? _fbb.CreateString(code) : 0; + auto compiler_options__ = compiler_options ? _fbb.CreateVector<::flatbuffers::Offset>(*compiler_options) : 0; + auto src_tensors_names__ = src_tensors_names ? _fbb.CreateVector<::flatbuffers::Offset<::flatbuffers::String>>(*src_tensors_names) : 0; + auto dst_tensors_names__ = dst_tensors_names ? _fbb.CreateVector<::flatbuffers::Offset<::flatbuffers::String>>(*dst_tensors_names) : 0; + return tflite::gpu::data::CreateGPUOperation( +- _fbb, +- arguments, +- code__, +- work_group_size, +- compiler_options__, +- tensor_to_grid, +- flops, +- definition, +- grid_dimension, +- work_group_launch_order, +- grid_size, +- src_tensors_names__, +- dst_tensors_names__, +- work_groups_count); ++ _fbb, arguments, code__, work_group_size, compiler_options__, ++ tensor_to_grid, flops, definition, grid_dimension, ++ work_group_launch_order, grid_size, src_tensors_names__, ++ dst_tensors_names__, work_groups_count); + } + + } // namespace data +diff --git a/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h b/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h +index 6c00ee4d0ae..8246a15622a 100644 +--- a/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h ++++ b/tensorflow/lite/experimental/acceleration/configuration/configuration_generated.h +@@ -20,13 +20,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + namespace tflite { + + struct ComputeSettings; +@@ -4112,10 +4105,10 @@ inline void ComputeSettings::UnPackTo(ComputeSettingsT *_o, const ::flatbuffers: + (void)_o; + (void)_resolver; + { auto _e = preference(); _o->preference = _e; } +- { auto _e = tflite_settings(); if (_e) { if(_o->tflite_settings) { _e->UnPackTo(_o->tflite_settings.get(), _resolver); } else { _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->tflite_settings) { _o->tflite_settings.reset(); } } ++ { auto _e = tflite_settings(); if (_e) { if(_o->tflite_settings) { _e->UnPackTo(_o->tflite_settings.get(), _resolver); } else { _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = model_namespace_for_statistics(); if (_e) _o->model_namespace_for_statistics = _e->str(); } + { auto _e = model_identifier_for_statistics(); if (_e) _o->model_identifier_for_statistics = _e->str(); } +- { auto _e = settings_to_test_locally(); if (_e) { if(_o->settings_to_test_locally) { _e->UnPackTo(_o->settings_to_test_locally.get(), _resolver); } else { _o->settings_to_test_locally = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->settings_to_test_locally) { _o->settings_to_test_locally.reset(); } } ++ { auto _e = settings_to_test_locally(); if (_e) { if(_o->settings_to_test_locally) { _e->UnPackTo(_o->settings_to_test_locally.get(), _resolver); } else { _o->settings_to_test_locally = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset ComputeSettings::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ComputeSettingsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -4207,7 +4200,7 @@ inline void NNAPISettings::UnPackTo(NNAPISettingsT *_o, const ::flatbuffers::res + { auto _e = model_token(); if (_e) _o->model_token = _e->str(); } + { auto _e = execution_preference(); _o->execution_preference = _e; } + { auto _e = no_of_nnapi_instances_to_cache(); _o->no_of_nnapi_instances_to_cache = _e; } +- { auto _e = fallback_settings(); if (_e) { if(_o->fallback_settings) { _e->UnPackTo(_o->fallback_settings.get(), _resolver); } else { _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->fallback_settings) { _o->fallback_settings.reset(); } } ++ { auto _e = fallback_settings(); if (_e) { if(_o->fallback_settings) { _e->UnPackTo(_o->fallback_settings.get(), _resolver); } else { _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = allow_nnapi_cpu_on_android_10_plus(); _o->allow_nnapi_cpu_on_android_10_plus = _e; } + { auto _e = execution_priority(); _o->execution_priority = _e; } + { auto _e = allow_dynamic_dimensions(); _o->allow_dynamic_dimensions = _e; } +@@ -4563,7 +4556,7 @@ inline void EdgeTpuDeviceSpec::UnPackTo(EdgeTpuDeviceSpecT *_o, const ::flatbuff + (void)_resolver; + { auto _e = platform_type(); _o->platform_type = _e; } + { auto _e = num_chips(); _o->num_chips = _e; } +- { auto _e = device_paths(); if (_e) { _o->device_paths.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->device_paths[_i] = _e->Get(_i)->str(); } } else { _o->device_paths.resize(0); } } ++ { auto _e = device_paths(); if (_e) { _o->device_paths.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->device_paths[_i] = _e->Get(_i)->str(); } } } + { auto _e = chip_family(); _o->chip_family = _e; } + } + +@@ -4632,7 +4625,7 @@ inline ::flatbuffers::Offset CreateEdgeTpuInactivePo + inline bool operator==(const EdgeTpuSettingsT &lhs, const EdgeTpuSettingsT &rhs) { + return + (lhs.inference_power_state == rhs.inference_power_state) && +- (lhs.inactive_power_configs.size() == rhs.inactive_power_configs.size() && std::equal(lhs.inactive_power_configs.cbegin(), lhs.inactive_power_configs.cend(), rhs.inactive_power_configs.cbegin(), [](std::unique_ptr const &a, std::unique_ptr const &b) { return (a == b) || (a && b && *a == *b); })) && ++ (lhs.inactive_power_configs == rhs.inactive_power_configs) && + (lhs.inference_priority == rhs.inference_priority) && + ((lhs.edgetpu_device_spec == rhs.edgetpu_device_spec) || (lhs.edgetpu_device_spec && rhs.edgetpu_device_spec && *lhs.edgetpu_device_spec == *rhs.edgetpu_device_spec)) && + (lhs.model_token == rhs.model_token) && +@@ -4657,7 +4650,7 @@ inline EdgeTpuSettingsT::EdgeTpuSettingsT(const EdgeTpuSettingsT &o) + hardware_cluster_ids(o.hardware_cluster_ids), + public_model_id(o.public_model_id) { + inactive_power_configs.reserve(o.inactive_power_configs.size()); +- for (const auto &inactive_power_configs_ : o.inactive_power_configs) { inactive_power_configs.emplace_back((inactive_power_configs_) ? new tflite::EdgeTpuInactivePowerConfigT(*inactive_power_configs_) : nullptr); } ++ for (const auto &v : o.inactive_power_configs) { inactive_power_configs.emplace_back((v) ? new tflite::EdgeTpuInactivePowerConfigT(*v) : nullptr); } + } + + inline EdgeTpuSettingsT &EdgeTpuSettingsT::operator=(EdgeTpuSettingsT o) FLATBUFFERS_NOEXCEPT { +@@ -4683,13 +4676,13 @@ inline void EdgeTpuSettings::UnPackTo(EdgeTpuSettingsT *_o, const ::flatbuffers: + (void)_o; + (void)_resolver; + { auto _e = inference_power_state(); _o->inference_power_state = _e; } +- { auto _e = inactive_power_configs(); if (_e) { _o->inactive_power_configs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->inactive_power_configs[_i]) { _e->Get(_i)->UnPackTo(_o->inactive_power_configs[_i].get(), _resolver); } else { _o->inactive_power_configs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->inactive_power_configs.resize(0); } } ++ { auto _e = inactive_power_configs(); if (_e) { _o->inactive_power_configs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->inactive_power_configs[_i]) { _e->Get(_i)->UnPackTo(_o->inactive_power_configs[_i].get(), _resolver); } else { _o->inactive_power_configs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = inference_priority(); _o->inference_priority = _e; } +- { auto _e = edgetpu_device_spec(); if (_e) { if(_o->edgetpu_device_spec) { _e->UnPackTo(_o->edgetpu_device_spec.get(), _resolver); } else { _o->edgetpu_device_spec = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->edgetpu_device_spec) { _o->edgetpu_device_spec.reset(); } } ++ { auto _e = edgetpu_device_spec(); if (_e) { if(_o->edgetpu_device_spec) { _e->UnPackTo(_o->edgetpu_device_spec.get(), _resolver); } else { _o->edgetpu_device_spec = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = model_token(); if (_e) _o->model_token = _e->str(); } + { auto _e = float_truncation_type(); _o->float_truncation_type = _e; } + { auto _e = qos_class(); _o->qos_class = _e; } +- { auto _e = hardware_cluster_ids(); if (_e) { _o->hardware_cluster_ids.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->hardware_cluster_ids[_i] = _e->Get(_i); } } else { _o->hardware_cluster_ids.resize(0); } } ++ { auto _e = hardware_cluster_ids(); if (_e) { _o->hardware_cluster_ids.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->hardware_cluster_ids[_i] = _e->Get(_i); } } } + { auto _e = public_model_id(); if (_e) _o->public_model_id = _e->str(); } + } + +@@ -4954,20 +4947,20 @@ inline void TFLiteSettings::UnPackTo(TFLiteSettingsT *_o, const ::flatbuffers::r + (void)_o; + (void)_resolver; + { auto _e = delegate(); _o->delegate = _e; } +- { auto _e = nnapi_settings(); if (_e) { if(_o->nnapi_settings) { _e->UnPackTo(_o->nnapi_settings.get(), _resolver); } else { _o->nnapi_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->nnapi_settings) { _o->nnapi_settings.reset(); } } +- { auto _e = gpu_settings(); if (_e) { if(_o->gpu_settings) { _e->UnPackTo(_o->gpu_settings.get(), _resolver); } else { _o->gpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->gpu_settings) { _o->gpu_settings.reset(); } } +- { auto _e = hexagon_settings(); if (_e) { if(_o->hexagon_settings) { _e->UnPackTo(_o->hexagon_settings.get(), _resolver); } else { _o->hexagon_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->hexagon_settings) { _o->hexagon_settings.reset(); } } +- { auto _e = xnnpack_settings(); if (_e) { if(_o->xnnpack_settings) { _e->UnPackTo(_o->xnnpack_settings.get(), _resolver); } else { _o->xnnpack_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->xnnpack_settings) { _o->xnnpack_settings.reset(); } } +- { auto _e = coreml_settings(); if (_e) { if(_o->coreml_settings) { _e->UnPackTo(_o->coreml_settings.get(), _resolver); } else { _o->coreml_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->coreml_settings) { _o->coreml_settings.reset(); } } +- { auto _e = cpu_settings(); if (_e) { if(_o->cpu_settings) { _e->UnPackTo(_o->cpu_settings.get(), _resolver); } else { _o->cpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->cpu_settings) { _o->cpu_settings.reset(); } } ++ { auto _e = nnapi_settings(); if (_e) { if(_o->nnapi_settings) { _e->UnPackTo(_o->nnapi_settings.get(), _resolver); } else { _o->nnapi_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = gpu_settings(); if (_e) { if(_o->gpu_settings) { _e->UnPackTo(_o->gpu_settings.get(), _resolver); } else { _o->gpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = hexagon_settings(); if (_e) { if(_o->hexagon_settings) { _e->UnPackTo(_o->hexagon_settings.get(), _resolver); } else { _o->hexagon_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = xnnpack_settings(); if (_e) { if(_o->xnnpack_settings) { _e->UnPackTo(_o->xnnpack_settings.get(), _resolver); } else { _o->xnnpack_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = coreml_settings(); if (_e) { if(_o->coreml_settings) { _e->UnPackTo(_o->coreml_settings.get(), _resolver); } else { _o->coreml_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = cpu_settings(); if (_e) { if(_o->cpu_settings) { _e->UnPackTo(_o->cpu_settings.get(), _resolver); } else { _o->cpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = max_delegated_partitions(); _o->max_delegated_partitions = _e; } +- { auto _e = edgetpu_settings(); if (_e) { if(_o->edgetpu_settings) { _e->UnPackTo(_o->edgetpu_settings.get(), _resolver); } else { _o->edgetpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->edgetpu_settings) { _o->edgetpu_settings.reset(); } } +- { auto _e = coral_settings(); if (_e) { if(_o->coral_settings) { _e->UnPackTo(_o->coral_settings.get(), _resolver); } else { _o->coral_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->coral_settings) { _o->coral_settings.reset(); } } +- { auto _e = fallback_settings(); if (_e) { if(_o->fallback_settings) { _e->UnPackTo(_o->fallback_settings.get(), _resolver); } else { _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->fallback_settings) { _o->fallback_settings.reset(); } } ++ { auto _e = edgetpu_settings(); if (_e) { if(_o->edgetpu_settings) { _e->UnPackTo(_o->edgetpu_settings.get(), _resolver); } else { _o->edgetpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = coral_settings(); if (_e) { if(_o->coral_settings) { _e->UnPackTo(_o->coral_settings.get(), _resolver); } else { _o->coral_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = fallback_settings(); if (_e) { if(_o->fallback_settings) { _e->UnPackTo(_o->fallback_settings.get(), _resolver); } else { _o->fallback_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = disable_default_delegates(); _o->disable_default_delegates = _e; } +- { auto _e = stable_delegate_loader_settings(); if (_e) { if(_o->stable_delegate_loader_settings) { _e->UnPackTo(_o->stable_delegate_loader_settings.get(), _resolver); } else { _o->stable_delegate_loader_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->stable_delegate_loader_settings) { _o->stable_delegate_loader_settings.reset(); } } +- { auto _e = google_edgetpu_settings(); if (_e) { if(_o->google_edgetpu_settings) { _e->UnPackTo(_o->google_edgetpu_settings.get(), _resolver); } else { _o->google_edgetpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->google_edgetpu_settings) { _o->google_edgetpu_settings.reset(); } } +- { auto _e = compilation_caching_settings(); if (_e) { if(_o->compilation_caching_settings) { _e->UnPackTo(_o->compilation_caching_settings.get(), _resolver); } else { _o->compilation_caching_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->compilation_caching_settings) { _o->compilation_caching_settings.reset(); } } ++ { auto _e = stable_delegate_loader_settings(); if (_e) { if(_o->stable_delegate_loader_settings) { _e->UnPackTo(_o->stable_delegate_loader_settings.get(), _resolver); } else { _o->stable_delegate_loader_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = google_edgetpu_settings(); if (_e) { if(_o->google_edgetpu_settings) { _e->UnPackTo(_o->google_edgetpu_settings.get(), _resolver); } else { _o->google_edgetpu_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = compilation_caching_settings(); if (_e) { if(_o->compilation_caching_settings) { _e->UnPackTo(_o->compilation_caching_settings.get(), _resolver); } else { _o->compilation_caching_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset TFLiteSettings::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const TFLiteSettingsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -5075,7 +5068,7 @@ inline void BenchmarkMetric::UnPackTo(BenchmarkMetricT *_o, const ::flatbuffers: + (void)_o; + (void)_resolver; + { auto _e = name(); if (_e) _o->name = _e->str(); } +- { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } else { _o->values.resize(0); } } ++ { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset BenchmarkMetric::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const BenchmarkMetricT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -5101,8 +5094,8 @@ inline bool operator==(const BenchmarkResultT &lhs, const BenchmarkResultT &rhs) + (lhs.inference_time_us == rhs.inference_time_us) && + (lhs.max_memory_kb == rhs.max_memory_kb) && + (lhs.ok == rhs.ok) && +- (lhs.metrics.size() == rhs.metrics.size() && std::equal(lhs.metrics.cbegin(), lhs.metrics.cend(), rhs.metrics.cbegin(), [](std::unique_ptr const &a, std::unique_ptr const &b) { return (a == b) || (a && b && *a == *b); })) && +- (lhs.actual_output.size() == rhs.actual_output.size() && std::equal(lhs.actual_output.cbegin(), lhs.actual_output.cend(), rhs.actual_output.cbegin(), [](std::unique_ptr const &a, std::unique_ptr const &b) { return (a == b) || (a && b && *a == *b); })); ++ (lhs.metrics == rhs.metrics) && ++ (lhs.actual_output == rhs.actual_output); + } + + inline bool operator!=(const BenchmarkResultT &lhs, const BenchmarkResultT &rhs) { +@@ -5116,9 +5109,9 @@ inline BenchmarkResultT::BenchmarkResultT(const BenchmarkResultT &o) + max_memory_kb(o.max_memory_kb), + ok(o.ok) { + metrics.reserve(o.metrics.size()); +- for (const auto &metrics_ : o.metrics) { metrics.emplace_back((metrics_) ? new tflite::BenchmarkMetricT(*metrics_) : nullptr); } ++ for (const auto &v : o.metrics) { metrics.emplace_back((v) ? new tflite::BenchmarkMetricT(*v) : nullptr); } + actual_output.reserve(o.actual_output.size()); +- for (const auto &actual_output_ : o.actual_output) { actual_output.emplace_back((actual_output_) ? new tflite::BenchmarkResult_::InferenceOutputT(*actual_output_) : nullptr); } ++ for (const auto &v : o.actual_output) { actual_output.emplace_back((v) ? new tflite::BenchmarkResult_::InferenceOutputT(*v) : nullptr); } + } + + inline BenchmarkResultT &BenchmarkResultT::operator=(BenchmarkResultT o) FLATBUFFERS_NOEXCEPT { +@@ -5140,12 +5133,12 @@ inline BenchmarkResultT *BenchmarkResult::UnPack(const ::flatbuffers::resolver_f + inline void BenchmarkResult::UnPackTo(BenchmarkResultT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = initialization_time_us(); if (_e) { _o->initialization_time_us.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->initialization_time_us[_i] = _e->Get(_i); } } else { _o->initialization_time_us.resize(0); } } +- { auto _e = inference_time_us(); if (_e) { _o->inference_time_us.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inference_time_us[_i] = _e->Get(_i); } } else { _o->inference_time_us.resize(0); } } ++ { auto _e = initialization_time_us(); if (_e) { _o->initialization_time_us.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->initialization_time_us[_i] = _e->Get(_i); } } } ++ { auto _e = inference_time_us(); if (_e) { _o->inference_time_us.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inference_time_us[_i] = _e->Get(_i); } } } + { auto _e = max_memory_kb(); _o->max_memory_kb = _e; } + { auto _e = ok(); _o->ok = _e; } +- { auto _e = metrics(); if (_e) { _o->metrics.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->metrics[_i]) { _e->Get(_i)->UnPackTo(_o->metrics[_i].get(), _resolver); } else { _o->metrics[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->metrics.resize(0); } } +- { auto _e = actual_output(); if (_e) { _o->actual_output.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->actual_output[_i]) { _e->Get(_i)->UnPackTo(_o->actual_output[_i].get(), _resolver); } else { _o->actual_output[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->actual_output.resize(0); } } ++ { auto _e = metrics(); if (_e) { _o->metrics.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->metrics[_i]) { _e->Get(_i)->UnPackTo(_o->metrics[_i].get(), _resolver); } else { _o->metrics[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = actual_output(); if (_e) { _o->actual_output.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->actual_output[_i]) { _e->Get(_i)->UnPackTo(_o->actual_output[_i].get(), _resolver); } else { _o->actual_output[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline ::flatbuffers::Offset BenchmarkResult::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const BenchmarkResultT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -5264,7 +5257,7 @@ inline bool operator==(const BenchmarkErrorT &lhs, const BenchmarkErrorT &rhs) { + (lhs.stage == rhs.stage) && + (lhs.exit_code == rhs.exit_code) && + (lhs.signal == rhs.signal) && +- (lhs.error_code.size() == rhs.error_code.size() && std::equal(lhs.error_code.cbegin(), lhs.error_code.cend(), rhs.error_code.cbegin(), [](std::unique_ptr const &a, std::unique_ptr const &b) { return (a == b) || (a && b && *a == *b); })) && ++ (lhs.error_code == rhs.error_code) && + (lhs.mini_benchmark_error_code == rhs.mini_benchmark_error_code); + } + +@@ -5279,7 +5272,7 @@ inline BenchmarkErrorT::BenchmarkErrorT(const BenchmarkErrorT &o) + signal(o.signal), + mini_benchmark_error_code(o.mini_benchmark_error_code) { + error_code.reserve(o.error_code.size()); +- for (const auto &error_code_ : o.error_code) { error_code.emplace_back((error_code_) ? new tflite::ErrorCodeT(*error_code_) : nullptr); } ++ for (const auto &v : o.error_code) { error_code.emplace_back((v) ? new tflite::ErrorCodeT(*v) : nullptr); } + } + + inline BenchmarkErrorT &BenchmarkErrorT::operator=(BenchmarkErrorT o) FLATBUFFERS_NOEXCEPT { +@@ -5303,7 +5296,7 @@ inline void BenchmarkError::UnPackTo(BenchmarkErrorT *_o, const ::flatbuffers::r + { auto _e = stage(); _o->stage = _e; } + { auto _e = exit_code(); _o->exit_code = _e; } + { auto _e = signal(); _o->signal = _e; } +- { auto _e = error_code(); if (_e) { _o->error_code.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->error_code[_i]) { _e->Get(_i)->UnPackTo(_o->error_code[_i].get(), _resolver); } else { _o->error_code[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->error_code.resize(0); } } ++ { auto _e = error_code(); if (_e) { _o->error_code.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->error_code[_i]) { _e->Get(_i)->UnPackTo(_o->error_code[_i].get(), _resolver); } else { _o->error_code[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = mini_benchmark_error_code(); _o->mini_benchmark_error_code = _e; } + } + +@@ -5373,10 +5366,10 @@ inline BenchmarkEventT *BenchmarkEvent::UnPack(const ::flatbuffers::resolver_fun + inline void BenchmarkEvent::UnPackTo(BenchmarkEventT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = tflite_settings(); if (_e) { if(_o->tflite_settings) { _e->UnPackTo(_o->tflite_settings.get(), _resolver); } else { _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->tflite_settings) { _o->tflite_settings.reset(); } } ++ { auto _e = tflite_settings(); if (_e) { if(_o->tflite_settings) { _e->UnPackTo(_o->tflite_settings.get(), _resolver); } else { _o->tflite_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = event_type(); _o->event_type = _e; } +- { auto _e = result(); if (_e) { if(_o->result) { _e->UnPackTo(_o->result.get(), _resolver); } else { _o->result = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->result) { _o->result.reset(); } } +- { auto _e = error(); if (_e) { if(_o->error) { _e->UnPackTo(_o->error.get(), _resolver); } else { _o->error = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->error) { _o->error.reset(); } } ++ { auto _e = result(); if (_e) { if(_o->result) { _e->UnPackTo(_o->result.get(), _resolver); } else { _o->result = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = error(); if (_e) { if(_o->error) { _e->UnPackTo(_o->error.get(), _resolver); } else { _o->error = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = boottime_us(); _o->boottime_us = _e; } + { auto _e = wallclock_us(); _o->wallclock_us = _e; } + } +@@ -5441,7 +5434,7 @@ inline void BestAccelerationDecision::UnPackTo(BestAccelerationDecisionT *_o, co + (void)_o; + (void)_resolver; + { auto _e = number_of_source_events(); _o->number_of_source_events = _e; } +- { auto _e = min_latency_event(); if (_e) { if(_o->min_latency_event) { _e->UnPackTo(_o->min_latency_event.get(), _resolver); } else { _o->min_latency_event = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->min_latency_event) { _o->min_latency_event.reset(); } } ++ { auto _e = min_latency_event(); if (_e) { if(_o->min_latency_event) { _e->UnPackTo(_o->min_latency_event.get(), _resolver); } else { _o->min_latency_event = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = min_inference_time_us(); _o->min_inference_time_us = _e; } + } + +@@ -5539,9 +5532,9 @@ inline void MiniBenchmarkEvent::UnPackTo(MiniBenchmarkEventT *_o, const ::flatbu + (void)_o; + (void)_resolver; + { auto _e = is_log_flushing_event(); _o->is_log_flushing_event = _e; } +- { auto _e = best_acceleration_decision(); if (_e) { if(_o->best_acceleration_decision) { _e->UnPackTo(_o->best_acceleration_decision.get(), _resolver); } else { _o->best_acceleration_decision = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->best_acceleration_decision) { _o->best_acceleration_decision.reset(); } } +- { auto _e = initialization_failure(); if (_e) { if(_o->initialization_failure) { _e->UnPackTo(_o->initialization_failure.get(), _resolver); } else { _o->initialization_failure = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->initialization_failure) { _o->initialization_failure.reset(); } } +- { auto _e = benchmark_event(); if (_e) { if(_o->benchmark_event) { _e->UnPackTo(_o->benchmark_event.get(), _resolver); } else { _o->benchmark_event = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->benchmark_event) { _o->benchmark_event.reset(); } } ++ { auto _e = best_acceleration_decision(); if (_e) { if(_o->best_acceleration_decision) { _e->UnPackTo(_o->best_acceleration_decision.get(), _resolver); } else { _o->best_acceleration_decision = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = initialization_failure(); if (_e) { if(_o->initialization_failure) { _e->UnPackTo(_o->initialization_failure.get(), _resolver); } else { _o->initialization_failure = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = benchmark_event(); if (_e) { if(_o->benchmark_event) { _e->UnPackTo(_o->benchmark_event.get(), _resolver); } else { _o->benchmark_event = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset MiniBenchmarkEvent::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const MiniBenchmarkEventT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -5612,7 +5605,7 @@ inline void ModelFile::UnPackTo(ModelFileT *_o, const ::flatbuffers::resolver_fu + { auto _e = fd(); _o->fd = _e; } + { auto _e = offset(); _o->offset = _e; } + { auto _e = length(); _o->length = _e; } +- { auto _e = model_id_group(); if (_e) { if(_o->model_id_group) { _e->UnPackTo(_o->model_id_group.get(), _resolver); } else { _o->model_id_group = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->model_id_group) { _o->model_id_group.reset(); } } ++ { auto _e = model_id_group(); if (_e) { if(_o->model_id_group) { _e->UnPackTo(_o->model_id_group.get(), _resolver); } else { _o->model_id_group = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = buffer_handle(); _o->buffer_handle = _e; } + } + +@@ -5762,7 +5755,7 @@ inline ::flatbuffers::Offset CreateValidationSettings(::flat + + inline bool operator==(const MinibenchmarkSettingsT &lhs, const MinibenchmarkSettingsT &rhs) { + return +- (lhs.settings_to_test.size() == rhs.settings_to_test.size() && std::equal(lhs.settings_to_test.cbegin(), lhs.settings_to_test.cend(), rhs.settings_to_test.cbegin(), [](std::unique_ptr const &a, std::unique_ptr const &b) { return (a == b) || (a && b && *a == *b); })) && ++ (lhs.settings_to_test == rhs.settings_to_test) && + ((lhs.model_file == rhs.model_file) || (lhs.model_file && rhs.model_file && *lhs.model_file == *rhs.model_file)) && + ((lhs.storage_paths == rhs.storage_paths) || (lhs.storage_paths && rhs.storage_paths && *lhs.storage_paths == *rhs.storage_paths)) && + ((lhs.validation_settings == rhs.validation_settings) || (lhs.validation_settings && rhs.validation_settings && *lhs.validation_settings == *rhs.validation_settings)); +@@ -5778,7 +5771,7 @@ inline MinibenchmarkSettingsT::MinibenchmarkSettingsT(const MinibenchmarkSetting + storage_paths((o.storage_paths) ? new tflite::BenchmarkStoragePathsT(*o.storage_paths) : nullptr), + validation_settings((o.validation_settings) ? new tflite::ValidationSettingsT(*o.validation_settings) : nullptr) { + settings_to_test.reserve(o.settings_to_test.size()); +- for (const auto &settings_to_test_ : o.settings_to_test) { settings_to_test.emplace_back((settings_to_test_) ? new tflite::TFLiteSettingsT(*settings_to_test_) : nullptr); } ++ for (const auto &v : o.settings_to_test) { settings_to_test.emplace_back((v) ? new tflite::TFLiteSettingsT(*v) : nullptr); } + } + + inline MinibenchmarkSettingsT &MinibenchmarkSettingsT::operator=(MinibenchmarkSettingsT o) FLATBUFFERS_NOEXCEPT { +@@ -5798,10 +5791,10 @@ inline MinibenchmarkSettingsT *MinibenchmarkSettings::UnPack(const ::flatbuffers + inline void MinibenchmarkSettings::UnPackTo(MinibenchmarkSettingsT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = settings_to_test(); if (_e) { _o->settings_to_test.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->settings_to_test[_i]) { _e->Get(_i)->UnPackTo(_o->settings_to_test[_i].get(), _resolver); } else { _o->settings_to_test[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->settings_to_test.resize(0); } } +- { auto _e = model_file(); if (_e) { if(_o->model_file) { _e->UnPackTo(_o->model_file.get(), _resolver); } else { _o->model_file = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->model_file) { _o->model_file.reset(); } } +- { auto _e = storage_paths(); if (_e) { if(_o->storage_paths) { _e->UnPackTo(_o->storage_paths.get(), _resolver); } else { _o->storage_paths = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->storage_paths) { _o->storage_paths.reset(); } } +- { auto _e = validation_settings(); if (_e) { if(_o->validation_settings) { _e->UnPackTo(_o->validation_settings.get(), _resolver); } else { _o->validation_settings = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->validation_settings) { _o->validation_settings.reset(); } } ++ { auto _e = settings_to_test(); if (_e) { _o->settings_to_test.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->settings_to_test[_i]) { _e->Get(_i)->UnPackTo(_o->settings_to_test[_i].get(), _resolver); } else { _o->settings_to_test[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = model_file(); if (_e) { if(_o->model_file) { _e->UnPackTo(_o->model_file.get(), _resolver); } else { _o->model_file = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = storage_paths(); if (_e) { if(_o->storage_paths) { _e->UnPackTo(_o->storage_paths.get(), _resolver); } else { _o->storage_paths = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = validation_settings(); if (_e) { if(_o->validation_settings) { _e->UnPackTo(_o->validation_settings.get(), _resolver); } else { _o->validation_settings = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset MinibenchmarkSettings::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const MinibenchmarkSettingsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -5856,8 +5849,8 @@ inline BenchmarkEventStorageT *BenchmarkEventStorage::UnPack(const ::flatbuffers + inline void BenchmarkEventStorage::UnPackTo(BenchmarkEventStorageT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = model_id_group(); if (_e) { if(_o->model_id_group) { _e->UnPackTo(_o->model_id_group.get(), _resolver); } else { _o->model_id_group = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->model_id_group) { _o->model_id_group.reset(); } } +- { auto _e = benchmark_event(); if (_e) { if(_o->benchmark_event) { _e->UnPackTo(_o->benchmark_event.get(), _resolver); } else { _o->benchmark_event = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->benchmark_event) { _o->benchmark_event.reset(); } } ++ { auto _e = model_id_group(); if (_e) { if(_o->model_id_group) { _e->UnPackTo(_o->model_id_group.get(), _resolver); } else { _o->model_id_group = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = benchmark_event(); if (_e) { if(_o->benchmark_event) { _e->UnPackTo(_o->benchmark_event.get(), _resolver); } else { _o->benchmark_event = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset BenchmarkEventStorage::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const BenchmarkEventStorageT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +diff --git a/tensorflow/lite/schema/conversion_metadata_generated.h b/tensorflow/lite/schema/conversion_metadata_generated.h +index 20dfff1671b..4b0772bf83f +--- a/tensorflow/lite/schema/conversion_metadata_generated.h ++++ b/tensorflow/lite/schema/conversion_metadata_generated.h +@@ -1,4 +1,4 @@ +-/* Copyright 2021 The TensorFlow Authors. All Rights Reserved. ++/* Copyright 2023 The TensorFlow Authors. All Rights Reserved. + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. +@@ -20,13 +20,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + namespace tflite { + + struct Environment; +@@ -512,7 +505,7 @@ inline SparsityBlockSizeT *SparsityBlockSize::UnPack(const ::flatbuffers::resolv + inline void SparsityBlockSize::UnPackTo(SparsityBlockSizeT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } else { _o->values.resize(0); } } ++ { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset SparsityBlockSize::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const SparsityBlockSizeT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -535,7 +528,7 @@ inline ConversionOptionsT::ConversionOptionsT(const ConversionOptionsT &o) + enable_select_tf_ops(o.enable_select_tf_ops), + force_select_tf_ops(o.force_select_tf_ops) { + sparsity_block_sizes.reserve(o.sparsity_block_sizes.size()); +- for (const auto &sparsity_block_sizes_ : o.sparsity_block_sizes) { sparsity_block_sizes.emplace_back((sparsity_block_sizes_) ? new tflite::SparsityBlockSizeT(*sparsity_block_sizes_) : nullptr); } ++ for (const auto &v : o.sparsity_block_sizes) { sparsity_block_sizes.emplace_back((v) ? new tflite::SparsityBlockSizeT(*v) : nullptr); } + } + + inline ConversionOptionsT &ConversionOptionsT::operator=(ConversionOptionsT o) FLATBUFFERS_NOEXCEPT { +@@ -556,11 +549,11 @@ inline ConversionOptionsT *ConversionOptions::UnPack(const ::flatbuffers::resolv + inline void ConversionOptions::UnPackTo(ConversionOptionsT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = model_optimization_modes(); if (_e) { _o->model_optimization_modes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->model_optimization_modes[_i] = static_cast(_e->Get(_i)); } } else { _o->model_optimization_modes.resize(0); } } ++ { auto _e = model_optimization_modes(); if (_e) { _o->model_optimization_modes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->model_optimization_modes[_i] = static_cast(_e->Get(_i)); } } } + { auto _e = allow_custom_ops(); _o->allow_custom_ops = _e; } + { auto _e = enable_select_tf_ops(); _o->enable_select_tf_ops = _e; } + { auto _e = force_select_tf_ops(); _o->force_select_tf_ops = _e; } +- { auto _e = sparsity_block_sizes(); if (_e) { _o->sparsity_block_sizes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->sparsity_block_sizes[_i]) { _e->Get(_i)->UnPackTo(_o->sparsity_block_sizes[_i].get(), _resolver); } else { _o->sparsity_block_sizes[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->sparsity_block_sizes.resize(0); } } ++ { auto _e = sparsity_block_sizes(); if (_e) { _o->sparsity_block_sizes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->sparsity_block_sizes[_i]) { _e->Get(_i)->UnPackTo(_o->sparsity_block_sizes[_i].get(), _resolver); } else { _o->sparsity_block_sizes[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline ::flatbuffers::Offset ConversionOptions::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ConversionOptionsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -605,8 +598,8 @@ inline ConversionMetadataT *ConversionMetadata::UnPack(const ::flatbuffers::reso + inline void ConversionMetadata::UnPackTo(ConversionMetadataT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = environment(); if (_e) { if(_o->environment) { _e->UnPackTo(_o->environment.get(), _resolver); } else { _o->environment = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->environment) { _o->environment.reset(); } } +- { auto _e = options(); if (_e) { if(_o->options) { _e->UnPackTo(_o->options.get(), _resolver); } else { _o->options = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->options) { _o->options.reset(); } } ++ { auto _e = environment(); if (_e) { if(_o->environment) { _e->UnPackTo(_o->environment.get(), _resolver); } else { _o->environment = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = options(); if (_e) { if(_o->options) { _e->UnPackTo(_o->options.get(), _resolver); } else { _o->options = std::unique_ptr(_e->UnPack(_resolver)); } } } + } + + inline ::flatbuffers::Offset ConversionMetadata::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ConversionMetadataT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +diff --git a/tensorflow/lite/schema/schema_generated.h b/tensorflow/lite/schema/schema_generated.h +index f03fdd0fc13..e894aa592b8 100755 +--- a/tensorflow/lite/schema/schema_generated.h ++++ b/tensorflow/lite/schema/schema_generated.h +@@ -1,4 +1,4 @@ +-/* Copyright 2023 The TensorFlow Authors. All Rights Reserved. ++/* Copyright 2018 The TensorFlow Authors. All Rights Reserved. + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. +@@ -20,13 +20,6 @@ limitations under the License. + + #include "flatbuffers/flatbuffers.h" + +-// Ensure the included flatbuffers.h is the same version as when this file was +-// generated, otherwise it may not be compatible. +-static_assert(FLATBUFFERS_VERSION_MAJOR == 23 && +- FLATBUFFERS_VERSION_MINOR == 1 && +- FLATBUFFERS_VERSION_REVISION == 21, +- "Non-compatible flatbuffers version included"); +- + namespace tflite { + + struct CustomQuantization; +@@ -1835,7 +1828,7 @@ inline const char * const *EnumNamesBuiltinOptions() { + } + + inline const char *EnumNameBuiltinOptions(BuiltinOptions e) { +- if (::flatbuffers::IsOutRange(e, BuiltinOptions_NONE, BuiltinOptions_RightShiftOptions)) return ""; ++ if (::flatbuffers::IsOutRange(e, BuiltinOptions_NONE, BuiltinOptions_BitcastOptions)) return ""; + const size_t index = static_cast(e); + return EnumNamesBuiltinOptions()[index]; + } +@@ -13585,10 +13578,10 @@ inline QuantizationParametersT *QuantizationParameters::UnPack(const ::flatbuffe + inline void QuantizationParameters::UnPackTo(QuantizationParametersT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = min(); if (_e) { _o->min.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->min[_i] = _e->Get(_i); } } else { _o->min.resize(0); } } +- { auto _e = max(); if (_e) { _o->max.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->max[_i] = _e->Get(_i); } } else { _o->max.resize(0); } } +- { auto _e = scale(); if (_e) { _o->scale.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->scale[_i] = _e->Get(_i); } } else { _o->scale.resize(0); } } +- { auto _e = zero_point(); if (_e) { _o->zero_point.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->zero_point[_i] = _e->Get(_i); } } else { _o->zero_point.resize(0); } } ++ { auto _e = min(); if (_e) { _o->min.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->min[_i] = _e->Get(_i); } } } ++ { auto _e = max(); if (_e) { _o->max.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->max[_i] = _e->Get(_i); } } } ++ { auto _e = scale(); if (_e) { _o->scale.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->scale[_i] = _e->Get(_i); } } } ++ { auto _e = zero_point(); if (_e) { _o->zero_point.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->zero_point[_i] = _e->Get(_i); } } } + { auto _e = details_type(); _o->details.type = _e; } + { auto _e = details(); if (_e) _o->details.value = tflite::QuantizationDetailsUnion::UnPack(_e, details_type(), _resolver); } + { auto _e = quantized_dimension(); _o->quantized_dimension = _e; } +@@ -13629,7 +13622,7 @@ inline Int32VectorT *Int32Vector::UnPack(const ::flatbuffers::resolver_function_ + inline void Int32Vector::UnPackTo(Int32VectorT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } else { _o->values.resize(0); } } ++ { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset Int32Vector::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const Int32VectorT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -13655,7 +13648,7 @@ inline Uint16VectorT *Uint16Vector::UnPack(const ::flatbuffers::resolver_functio + inline void Uint16Vector::UnPackTo(Uint16VectorT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } else { _o->values.resize(0); } } ++ { auto _e = values(); if (_e) { _o->values.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->values[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset Uint16Vector::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const Uint16VectorT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -13745,7 +13738,7 @@ inline SparsityParametersT::SparsityParametersT(const SparsityParametersT &o) + : traversal_order(o.traversal_order), + block_map(o.block_map) { + dim_metadata.reserve(o.dim_metadata.size()); +- for (const auto &dim_metadata_ : o.dim_metadata) { dim_metadata.emplace_back((dim_metadata_) ? new tflite::DimensionMetadataT(*dim_metadata_) : nullptr); } ++ for (const auto &v : o.dim_metadata) { dim_metadata.emplace_back((v) ? new tflite::DimensionMetadataT(*v) : nullptr); } + } + + inline SparsityParametersT &SparsityParametersT::operator=(SparsityParametersT o) FLATBUFFERS_NOEXCEPT { +@@ -13764,9 +13757,9 @@ inline SparsityParametersT *SparsityParameters::UnPack(const ::flatbuffers::reso + inline void SparsityParameters::UnPackTo(SparsityParametersT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = traversal_order(); if (_e) { _o->traversal_order.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->traversal_order[_i] = _e->Get(_i); } } else { _o->traversal_order.resize(0); } } +- { auto _e = block_map(); if (_e) { _o->block_map.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->block_map[_i] = _e->Get(_i); } } else { _o->block_map.resize(0); } } +- { auto _e = dim_metadata(); if (_e) { _o->dim_metadata.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->dim_metadata[_i]) { _e->Get(_i)->UnPackTo(_o->dim_metadata[_i].get(), _resolver); } else { _o->dim_metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->dim_metadata.resize(0); } } ++ { auto _e = traversal_order(); if (_e) { _o->traversal_order.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->traversal_order[_i] = _e->Get(_i); } } } ++ { auto _e = block_map(); if (_e) { _o->block_map.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->block_map[_i] = _e->Get(_i); } } } ++ { auto _e = dim_metadata(); if (_e) { _o->dim_metadata.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->dim_metadata[_i]) { _e->Get(_i)->UnPackTo(_o->dim_metadata[_i].get(), _resolver); } else { _o->dim_metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline ::flatbuffers::Offset SparsityParameters::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const SparsityParametersT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -13796,7 +13789,7 @@ inline VariantSubTypeT *VariantSubType::UnPack(const ::flatbuffers::resolver_fun + inline void VariantSubType::UnPackTo(VariantSubTypeT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = shape(); if (_e) { _o->shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape[_i] = _e->Get(_i); } } else { _o->shape.resize(0); } } ++ { auto _e = shape(); if (_e) { _o->shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape[_i] = _e->Get(_i); } } } + { auto _e = type(); _o->type = _e; } + { auto _e = has_rank(); _o->has_rank = _e; } + } +@@ -13830,7 +13823,7 @@ inline TensorT::TensorT(const TensorT &o) + shape_signature(o.shape_signature), + has_rank(o.has_rank) { + variant_tensors.reserve(o.variant_tensors.size()); +- for (const auto &variant_tensors_ : o.variant_tensors) { variant_tensors.emplace_back((variant_tensors_) ? new tflite::VariantSubTypeT(*variant_tensors_) : nullptr); } ++ for (const auto &v : o.variant_tensors) { variant_tensors.emplace_back((v) ? new tflite::VariantSubTypeT(*v) : nullptr); } + } + + inline TensorT &TensorT::operator=(TensorT o) FLATBUFFERS_NOEXCEPT { +@@ -13856,16 +13849,16 @@ inline TensorT *Tensor::UnPack(const ::flatbuffers::resolver_function_t *_resolv + inline void Tensor::UnPackTo(TensorT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = shape(); if (_e) { _o->shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape[_i] = _e->Get(_i); } } else { _o->shape.resize(0); } } ++ { auto _e = shape(); if (_e) { _o->shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape[_i] = _e->Get(_i); } } } + { auto _e = type(); _o->type = _e; } + { auto _e = buffer(); _o->buffer = _e; } + { auto _e = name(); if (_e) _o->name = _e->str(); } +- { auto _e = quantization(); if (_e) { if(_o->quantization) { _e->UnPackTo(_o->quantization.get(), _resolver); } else { _o->quantization = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->quantization) { _o->quantization.reset(); } } ++ { auto _e = quantization(); if (_e) { if(_o->quantization) { _e->UnPackTo(_o->quantization.get(), _resolver); } else { _o->quantization = std::unique_ptr(_e->UnPack(_resolver)); } } } + { auto _e = is_variable(); _o->is_variable = _e; } +- { auto _e = sparsity(); if (_e) { if(_o->sparsity) { _e->UnPackTo(_o->sparsity.get(), _resolver); } else { _o->sparsity = std::unique_ptr(_e->UnPack(_resolver)); } } else if (_o->sparsity) { _o->sparsity.reset(); } } +- { auto _e = shape_signature(); if (_e) { _o->shape_signature.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape_signature[_i] = _e->Get(_i); } } else { _o->shape_signature.resize(0); } } ++ { auto _e = sparsity(); if (_e) { if(_o->sparsity) { _e->UnPackTo(_o->sparsity.get(), _resolver); } else { _o->sparsity = std::unique_ptr(_e->UnPack(_resolver)); } } } ++ { auto _e = shape_signature(); if (_e) { _o->shape_signature.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->shape_signature[_i] = _e->Get(_i); } } } + { auto _e = has_rank(); _o->has_rank = _e; } +- { auto _e = variant_tensors(); if (_e) { _o->variant_tensors.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->variant_tensors[_i]) { _e->Get(_i)->UnPackTo(_o->variant_tensors[_i].get(), _resolver); } else { _o->variant_tensors[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->variant_tensors.resize(0); } } ++ { auto _e = variant_tensors(); if (_e) { _o->variant_tensors.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->variant_tensors[_i]) { _e->Get(_i)->UnPackTo(_o->variant_tensors[_i].get(), _resolver); } else { _o->variant_tensors[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline ::flatbuffers::Offset Tensor::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const TensorT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -14083,8 +14076,8 @@ inline void ConcatEmbeddingsOptions::UnPackTo(ConcatEmbeddingsOptionsT *_o, cons + (void)_o; + (void)_resolver; + { auto _e = num_channels(); _o->num_channels = _e; } +- { auto _e = num_columns_per_channel(); if (_e) { _o->num_columns_per_channel.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->num_columns_per_channel[_i] = _e->Get(_i); } } else { _o->num_columns_per_channel.resize(0); } } +- { auto _e = embedding_dim_per_channel(); if (_e) { _o->embedding_dim_per_channel.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->embedding_dim_per_channel[_i] = _e->Get(_i); } } else { _o->embedding_dim_per_channel.resize(0); } } ++ { auto _e = num_columns_per_channel(); if (_e) { _o->num_columns_per_channel.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->num_columns_per_channel[_i] = _e->Get(_i); } } } ++ { auto _e = embedding_dim_per_channel(); if (_e) { _o->embedding_dim_per_channel.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->embedding_dim_per_channel[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset ConcatEmbeddingsOptions::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ConcatEmbeddingsOptionsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -14724,7 +14717,7 @@ inline ReshapeOptionsT *ReshapeOptions::UnPack(const ::flatbuffers::resolver_fun + inline void ReshapeOptions::UnPackTo(ReshapeOptionsT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = new_shape(); if (_e) { _o->new_shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->new_shape[_i] = _e->Get(_i); } } else { _o->new_shape.resize(0); } } ++ { auto _e = new_shape(); if (_e) { _o->new_shape.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->new_shape[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset ReshapeOptions::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ReshapeOptionsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -15108,7 +15101,7 @@ inline SqueezeOptionsT *SqueezeOptions::UnPack(const ::flatbuffers::resolver_fun + inline void SqueezeOptions::UnPackTo(SqueezeOptionsT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = squeeze_dims(); if (_e) { _o->squeeze_dims.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->squeeze_dims[_i] = _e->Get(_i); } } else { _o->squeeze_dims.resize(0); } } ++ { auto _e = squeeze_dims(); if (_e) { _o->squeeze_dims.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->squeeze_dims[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset SqueezeOptions::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const SqueezeOptionsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -16957,7 +16950,7 @@ inline BucketizeOptionsT *BucketizeOptions::UnPack(const ::flatbuffers::resolver + inline void BucketizeOptions::UnPackTo(BucketizeOptionsT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = boundaries(); if (_e) { _o->boundaries.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->boundaries[_i] = _e->Get(_i); } } else { _o->boundaries.resize(0); } } ++ { auto _e = boundaries(); if (_e) { _o->boundaries.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->boundaries[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset BucketizeOptions::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const BucketizeOptionsT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -17275,14 +17268,14 @@ inline void Operator::UnPackTo(OperatorT *_o, const ::flatbuffers::resolver_func + (void)_o; + (void)_resolver; + { auto _e = opcode_index(); _o->opcode_index = _e; } +- { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inputs[_i] = _e->Get(_i); } } else { _o->inputs.resize(0); } } +- { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->outputs[_i] = _e->Get(_i); } } else { _o->outputs.resize(0); } } ++ { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inputs[_i] = _e->Get(_i); } } } ++ { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->outputs[_i] = _e->Get(_i); } } } + { auto _e = builtin_options_type(); _o->builtin_options.type = _e; } + { auto _e = builtin_options(); if (_e) _o->builtin_options.value = tflite::BuiltinOptionsUnion::UnPack(_e, builtin_options_type(), _resolver); } + { auto _e = custom_options(); if (_e) { _o->custom_options.resize(_e->size()); std::copy(_e->begin(), _e->end(), _o->custom_options.begin()); } } + { auto _e = custom_options_format(); _o->custom_options_format = _e; } +- { auto _e = mutating_variable_inputs(); if (_e) { _o->mutating_variable_inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->mutating_variable_inputs[_i] = _e->Get(_i) != 0; } } else { _o->mutating_variable_inputs.resize(0); } } +- { auto _e = intermediates(); if (_e) { _o->intermediates.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->intermediates[_i] = _e->Get(_i); } } else { _o->intermediates.resize(0); } } ++ { auto _e = mutating_variable_inputs(); if (_e) { _o->mutating_variable_inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->mutating_variable_inputs[_i] = _e->Get(_i) != 0; } } } ++ { auto _e = intermediates(); if (_e) { _o->intermediates.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->intermediates[_i] = _e->Get(_i); } } } + } + + inline ::flatbuffers::Offset Operator::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const OperatorT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +@@ -17320,9 +17313,9 @@ inline SubGraphT::SubGraphT(const SubGraphT &o) + outputs(o.outputs), + name(o.name) { + tensors.reserve(o.tensors.size()); +- for (const auto &tensors_ : o.tensors) { tensors.emplace_back((tensors_) ? new tflite::TensorT(*tensors_) : nullptr); } ++ for (const auto &v : o.tensors) { tensors.emplace_back((v) ? new tflite::TensorT(*v) : nullptr); } + operators.reserve(o.operators.size()); +- for (const auto &operators_ : o.operators) { operators.emplace_back((operators_) ? new tflite::OperatorT(*operators_) : nullptr); } ++ for (const auto &v : o.operators) { operators.emplace_back((v) ? new tflite::OperatorT(*v) : nullptr); } + } + + inline SubGraphT &SubGraphT::operator=(SubGraphT o) FLATBUFFERS_NOEXCEPT { +@@ -17343,10 +17336,10 @@ inline SubGraphT *SubGraph::UnPack(const ::flatbuffers::resolver_function_t *_re + inline void SubGraph::UnPackTo(SubGraphT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = tensors(); if (_e) { _o->tensors.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->tensors[_i]) { _e->Get(_i)->UnPackTo(_o->tensors[_i].get(), _resolver); } else { _o->tensors[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->tensors.resize(0); } } +- { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inputs[_i] = _e->Get(_i); } } else { _o->inputs.resize(0); } } +- { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->outputs[_i] = _e->Get(_i); } } else { _o->outputs.resize(0); } } +- { auto _e = operators(); if (_e) { _o->operators.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->operators[_i]) { _e->Get(_i)->UnPackTo(_o->operators[_i].get(), _resolver); } else { _o->operators[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->operators.resize(0); } } ++ { auto _e = tensors(); if (_e) { _o->tensors.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->tensors[_i]) { _e->Get(_i)->UnPackTo(_o->tensors[_i].get(), _resolver); } else { _o->tensors[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->inputs[_i] = _e->Get(_i); } } } ++ { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->outputs[_i] = _e->Get(_i); } } } ++ { auto _e = operators(); if (_e) { _o->operators.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->operators[_i]) { _e->Get(_i)->UnPackTo(_o->operators[_i].get(), _resolver); } else { _o->operators[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = name(); if (_e) _o->name = _e->str(); } + } + +@@ -17461,9 +17454,9 @@ inline SignatureDefT::SignatureDefT(const SignatureDefT &o) + : signature_key(o.signature_key), + subgraph_index(o.subgraph_index) { + inputs.reserve(o.inputs.size()); +- for (const auto &inputs_ : o.inputs) { inputs.emplace_back((inputs_) ? new tflite::TensorMapT(*inputs_) : nullptr); } ++ for (const auto &v : o.inputs) { inputs.emplace_back((v) ? new tflite::TensorMapT(*v) : nullptr); } + outputs.reserve(o.outputs.size()); +- for (const auto &outputs_ : o.outputs) { outputs.emplace_back((outputs_) ? new tflite::TensorMapT(*outputs_) : nullptr); } ++ for (const auto &v : o.outputs) { outputs.emplace_back((v) ? new tflite::TensorMapT(*v) : nullptr); } + } + + inline SignatureDefT &SignatureDefT::operator=(SignatureDefT o) FLATBUFFERS_NOEXCEPT { +@@ -17483,8 +17476,8 @@ inline SignatureDefT *SignatureDef::UnPack(const ::flatbuffers::resolver_functio + inline void SignatureDef::UnPackTo(SignatureDefT *_o, const ::flatbuffers::resolver_function_t *_resolver) const { + (void)_o; + (void)_resolver; +- { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->inputs[_i]) { _e->Get(_i)->UnPackTo(_o->inputs[_i].get(), _resolver); } else { _o->inputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->inputs.resize(0); } } +- { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->outputs[_i]) { _e->Get(_i)->UnPackTo(_o->outputs[_i].get(), _resolver); } else { _o->outputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->outputs.resize(0); } } ++ { auto _e = inputs(); if (_e) { _o->inputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->inputs[_i]) { _e->Get(_i)->UnPackTo(_o->inputs[_i].get(), _resolver); } else { _o->inputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = outputs(); if (_e) { _o->outputs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->outputs[_i]) { _e->Get(_i)->UnPackTo(_o->outputs[_i].get(), _resolver); } else { _o->outputs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = signature_key(); if (_e) _o->signature_key = _e->str(); } + { auto _e = subgraph_index(); _o->subgraph_index = _e; } + } +@@ -17514,15 +17507,15 @@ inline ModelT::ModelT(const ModelT &o) + description(o.description), + metadata_buffer(o.metadata_buffer) { + operator_codes.reserve(o.operator_codes.size()); +- for (const auto &operator_codes_ : o.operator_codes) { operator_codes.emplace_back((operator_codes_) ? new tflite::OperatorCodeT(*operator_codes_) : nullptr); } ++ for (const auto &v : o.operator_codes) { operator_codes.emplace_back((v) ? new tflite::OperatorCodeT(*v) : nullptr); } + subgraphs.reserve(o.subgraphs.size()); +- for (const auto &subgraphs_ : o.subgraphs) { subgraphs.emplace_back((subgraphs_) ? new tflite::SubGraphT(*subgraphs_) : nullptr); } ++ for (const auto &v : o.subgraphs) { subgraphs.emplace_back((v) ? new tflite::SubGraphT(*v) : nullptr); } + buffers.reserve(o.buffers.size()); +- for (const auto &buffers_ : o.buffers) { buffers.emplace_back((buffers_) ? new tflite::BufferT(*buffers_) : nullptr); } ++ for (const auto &v : o.buffers) { buffers.emplace_back((v) ? new tflite::BufferT(*v) : nullptr); } + metadata.reserve(o.metadata.size()); +- for (const auto &metadata_ : o.metadata) { metadata.emplace_back((metadata_) ? new tflite::MetadataT(*metadata_) : nullptr); } ++ for (const auto &v : o.metadata) { metadata.emplace_back((v) ? new tflite::MetadataT(*v) : nullptr); } + signature_defs.reserve(o.signature_defs.size()); +- for (const auto &signature_defs_ : o.signature_defs) { signature_defs.emplace_back((signature_defs_) ? new tflite::SignatureDefT(*signature_defs_) : nullptr); } ++ for (const auto &v : o.signature_defs) { signature_defs.emplace_back((v) ? new tflite::SignatureDefT(*v) : nullptr); } + } + + inline ModelT &ModelT::operator=(ModelT o) FLATBUFFERS_NOEXCEPT { +@@ -17547,13 +17540,13 @@ inline void Model::UnPackTo(ModelT *_o, const ::flatbuffers::resolver_function_t + (void)_o; + (void)_resolver; + { auto _e = version(); _o->version = _e; } +- { auto _e = operator_codes(); if (_e) { _o->operator_codes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->operator_codes[_i]) { _e->Get(_i)->UnPackTo(_o->operator_codes[_i].get(), _resolver); } else { _o->operator_codes[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->operator_codes.resize(0); } } +- { auto _e = subgraphs(); if (_e) { _o->subgraphs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->subgraphs[_i]) { _e->Get(_i)->UnPackTo(_o->subgraphs[_i].get(), _resolver); } else { _o->subgraphs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->subgraphs.resize(0); } } ++ { auto _e = operator_codes(); if (_e) { _o->operator_codes.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->operator_codes[_i]) { _e->Get(_i)->UnPackTo(_o->operator_codes[_i].get(), _resolver); } else { _o->operator_codes[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = subgraphs(); if (_e) { _o->subgraphs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->subgraphs[_i]) { _e->Get(_i)->UnPackTo(_o->subgraphs[_i].get(), _resolver); } else { _o->subgraphs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + { auto _e = description(); if (_e) _o->description = _e->str(); } +- { auto _e = buffers(); if (_e) { _o->buffers.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->buffers[_i]) { _e->Get(_i)->UnPackTo(_o->buffers[_i].get(), _resolver); } else { _o->buffers[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->buffers.resize(0); } } +- { auto _e = metadata_buffer(); if (_e) { _o->metadata_buffer.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->metadata_buffer[_i] = _e->Get(_i); } } else { _o->metadata_buffer.resize(0); } } +- { auto _e = metadata(); if (_e) { _o->metadata.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->metadata[_i]) { _e->Get(_i)->UnPackTo(_o->metadata[_i].get(), _resolver); } else { _o->metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->metadata.resize(0); } } +- { auto _e = signature_defs(); if (_e) { _o->signature_defs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->signature_defs[_i]) { _e->Get(_i)->UnPackTo(_o->signature_defs[_i].get(), _resolver); } else { _o->signature_defs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } else { _o->signature_defs.resize(0); } } ++ { auto _e = buffers(); if (_e) { _o->buffers.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->buffers[_i]) { _e->Get(_i)->UnPackTo(_o->buffers[_i].get(), _resolver); } else { _o->buffers[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = metadata_buffer(); if (_e) { _o->metadata_buffer.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { _o->metadata_buffer[_i] = _e->Get(_i); } } } ++ { auto _e = metadata(); if (_e) { _o->metadata.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->metadata[_i]) { _e->Get(_i)->UnPackTo(_o->metadata[_i].get(), _resolver); } else { _o->metadata[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } ++ { auto _e = signature_defs(); if (_e) { _o->signature_defs.resize(_e->size()); for (::flatbuffers::uoffset_t _i = 0; _i < _e->size(); _i++) { if(_o->signature_defs[_i]) { _e->Get(_i)->UnPackTo(_o->signature_defs[_i].get(), _resolver); } else { _o->signature_defs[_i] = std::unique_ptr(_e->Get(_i)->UnPack(_resolver)); }; } } } + } + + inline ::flatbuffers::Offset Model::Pack(::flatbuffers::FlatBufferBuilder &_fbb, const ModelT* _o, const ::flatbuffers::rehasher_function_t *_rehasher) { +diff --git a/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake b/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake +index f1ed4fb1748..ad0ddcd38c1 100644 +--- a/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake ++++ b/tensorflow/lite/tools/cmake/modules/flatbuffers.cmake +@@ -23,7 +23,7 @@ OverridableFetchContent_Declare( + flatbuffers + GIT_REPOSITORY https://github.com/google/flatbuffers + # Sync with tensorflow/third_party/flatbuffers/workspace.bzl +- GIT_TAG v23.1.21 ++ GIT_TAG v2.0.6 + GIT_SHALLOW TRUE + GIT_PROGRESS TRUE + SOURCE_DIR "${CMAKE_BINARY_DIR}/flatbuffers" +diff --git a/tensorflow/tools/ci_build/release/requirements_common.txt b/tensorflow/tools/ci_build/release/requirements_common.txt +index 6373d737aa4..4ede56800d2 100644 +--- a/tensorflow/tools/ci_build/release/requirements_common.txt ++++ b/tensorflow/tools/ci_build/release/requirements_common.txt +@@ -3,7 +3,7 @@ + # This will change in the future. + absl-py ~= 1.0.0 + astunparse ~= 1.6.3 +-flatbuffers ~= 23.1.21 ++flatbuffers ~= 2.0 + google_pasta ~= 0.2 + h5py ~= 3.8.0 # Earliest version for Python 3.11 + # TODO(b/262592253): Support older versions of NumPy for Python 3.10 and lower +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index e77e6f81449..b7d039f3262 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -84,7 +84,7 @@ def standard_or_nightly(standard, nightly): + REQUIRED_PACKAGES = [ + 'absl-py >= 1.0.0', + 'astunparse >= 1.6.0', +- 'flatbuffers >= 23.1.21', ++ 'flatbuffers >= 2.0', + # TODO(b/213222745) gast versions above 0.4.0 break TF's tests + 'gast >= 0.2.1, <= 0.4.0', + 'google_pasta >= 0.1.1', +diff --git a/third_party/flatbuffers/flatbuffers.BUILD b/third_party/flatbuffers/flatbuffers.BUILD +index 2905833ad15..f32f1a5f324 100644 +--- a/third_party/flatbuffers/flatbuffers.BUILD ++++ b/third_party/flatbuffers/flatbuffers.BUILD +@@ -7,6 +7,8 @@ licenses(["notice"]) # Apache 2.0 + + exports_files(["LICENSE.txt"]) + ++licenses(["notice"]) ++ + config_setting( + name = "platform_freebsd", + values = {"cpu": "freebsd"}, +@@ -44,16 +46,12 @@ filegroup( + "include/flatbuffers/bfbs_generator.h", + "include/flatbuffers/buffer.h", + "include/flatbuffers/buffer_ref.h", +- "include/flatbuffers/code_generator.h", + "include/flatbuffers/code_generators.h", + "include/flatbuffers/default_allocator.h", + "include/flatbuffers/detached_buffer.h", + "include/flatbuffers/flatbuffer_builder.h", + "include/flatbuffers/flatbuffers.h", +- "include/flatbuffers/flatc.h", +- "include/flatbuffers/flex_flat_util.h", + "include/flatbuffers/flexbuffers.h", +- "include/flatbuffers/grpc.h", + "include/flatbuffers/hash.h", + "include/flatbuffers/idl.h", + "include/flatbuffers/minireflect.h", +@@ -178,7 +176,7 @@ py_library( + + filegroup( + name = "runtime_java_srcs", +- srcs = glob(["java/src/main/java/com/google/flatbuffers/**/*.java"]), ++ srcs = glob(["java/com/google/flatbuffers/**/*.java"]), + ) + + java_library( +diff --git a/third_party/flatbuffers/workspace.bzl b/third_party/flatbuffers/workspace.bzl +index 2fa19ab1a96..ceb8a2720da 100644 +--- a/third_party/flatbuffers/workspace.bzl ++++ b/third_party/flatbuffers/workspace.bzl +@@ -5,9 +5,9 @@ load("//third_party:repo.bzl", "tf_http_archive", "tf_mirror_urls") + def repo(): + tf_http_archive( + name = "flatbuffers", +- strip_prefix = "flatbuffers-23.1.21", +- sha256 = "d84cb25686514348e615163b458ae0767001b24b42325f426fd56406fd384238", +- urls = tf_mirror_urls("https://github.com/google/flatbuffers/archive/v23.1.21.tar.gz"), ++ strip_prefix = "flatbuffers-2.0.6", ++ sha256 = "e2dc24985a85b278dd06313481a9ca051d048f9474e0f199e372fea3ea4248c9", ++ urls = tf_mirror_urls("https://github.com/google/flatbuffers/archive/v2.0.6.tar.gz"), + build_file = "//third_party/flatbuffers:flatbuffers.BUILD", + system_build_file = "//third_party/flatbuffers:BUILD.system", + link_files = { diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_unpin-gast-version.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_unpin-gast-version.patch new file mode 100644 index 00000000000..18e097f2e3d --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_unpin-gast-version.patch @@ -0,0 +1,18 @@ +Allow newer versions of gast. +Based on https://github.com/tensorflow/tensorflow/commit/56df1c90055ee812dac9a019571edd58f3ecd7eb + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index 72c20379a9291..d394ca5ea5c76 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -85,7 +85,6 @@ REQUIRED_PACKAGES = [ + 'absl-py >= 1.0.0', + 'astunparse >= 1.6.0', + 'flatbuffers >= 2.0', +- # TODO(b/213222745) gast versions above 0.4.0 break TF's tests +- 'gast >= 0.2.1, <= 0.4.0', ++ 'gast >=0.2.1,!=0.5.0,!=0.5.1,!=0.5.2', + 'google_pasta >= 0.1.1', + 'h5py >= 2.9.0', From c6d2831a4e0375735fdfe8ec699dc05683a0587d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 5 Sep 2023 11:01:35 +0200 Subject: [PATCH 8687/9987] Add Bazel patch required for pip-package --- .../b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb | 6 ++++- ...Bazel-6.3.1_add-symlinks-in-runfiles.patch | 22 +++++++++++++++++++ 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-6.3.1_add-symlinks-in-runfiles.patch diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb index b878e18297c..3769e89c674 100644 --- a/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1-GCCcore-12.3.0.eb @@ -9,7 +9,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] sources = ['%(namelower)s-%(version)s-dist.zip'] -checksums = ['2676319e86c5aeab142dccd42434364a33aa330a091c13562b7de87a10e68775'] +patches = ['Bazel-6.3.1_add-symlinks-in-runfiles.patch'] +checksums = [ + {'bazel-6.3.1-dist.zip': '2676319e86c5aeab142dccd42434364a33aa330a091c13562b7de87a10e68775'}, + {'Bazel-6.3.1_add-symlinks-in-runfiles.patch': '81db53aa87229557480b6f719c99a0f1af9c69dfec12185451e520b0128c3ae2'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1_add-symlinks-in-runfiles.patch b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1_add-symlinks-in-runfiles.patch new file mode 100644 index 00000000000..83251131981 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-6.3.1_add-symlinks-in-runfiles.patch @@ -0,0 +1,22 @@ +Bazel doesn't always copy all files as required leading e.g. to failures in TF sanity check: https://github.com/tensorflow/tensorflow/issues/60326 + +From https://github.com/bazelbuild/bazel/pull/19378 + +Author: Alexander Grund (TU Dresden) + +diff --git a/src/main/starlark/builtins_bzl/common/cc/experimental_cc_shared_library.bzl b/src/main/starlark/builtins_bzl/common/cc/experimental_cc_shared_library.bzl +index b9f3b5b7ac..3af1e61c63 100644 +--- a/src/main/starlark/builtins_bzl/common/cc/experimental_cc_shared_library.bzl ++++ b/src/main/starlark/builtins_bzl/common/cc/experimental_cc_shared_library.bzl +@@ -728,7 +728,10 @@ def _cc_shared_library_impl(ctx): + # precompiled_dynamic_library.dynamic_library could be None if the library to link just contains + # an interface library which is valid if the actual library is obtained from the system. + if precompiled_dynamic_library.dynamic_library != None: +- precompiled_only_dynamic_libraries_runfiles.append(precompiled_dynamic_library.dynamic_library) ++ if precompiled_dynamic_library.resolved_symlink_dynamic_library != None: ++ precompiled_only_dynamic_libraries_runfiles.append(precompiled_dynamic_library.resolved_symlink_dynamic_library) ++ else: ++ precompiled_only_dynamic_libraries_runfiles.append(precompiled_dynamic_library.dynamic_library) + + runfiles = runfiles.merge(ctx.runfiles(files = precompiled_only_dynamic_libraries_runfiles)) + From 68d1cd5b8a1774ff519b517230d9160e8d4563e3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 5 Sep 2023 12:35:50 +0200 Subject: [PATCH 8688/9987] Fix sanity check with typing_extensions --- .../TensorFlow-2.13.0-foss-2023a.eb | 3 +++ ...remove-typing_extensions-upper-bound.patch | 20 +++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-typing_extensions-upper-bound.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb index 6de09ba961c..f766bd2eafb 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb @@ -171,6 +171,7 @@ exts_list = [ 'TensorFlow-2.13.0_remove-io-gcs-filesystem-dep.patch', 'TensorFlow-2.13.0_remove-libclang-dep.patch', 'TensorFlow-2.13.0_fix-numpy-2.15.compat.patch', + 'TensorFlow-2.13.0_remove-typing_extensions-upper-bound.patch', 'TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch', 'TensorFlow-2.13.0_unpin-gast-version.patch', ], @@ -198,6 +199,8 @@ exts_list = [ 'f0d067d129e817b0d371c4e48a4a1ac08f80a2c137d52b05a3c7c4370dcbd1e5'}, {'TensorFlow-2.13.0_fix-numpy-2.15.compat.patch': '4023be57bc8e33ae55ccac54b51d6532fea7ac4a32cb1125e3e42da0dec1669a'}, + {'TensorFlow-2.13.0_remove-typing_extensions-upper-bound.patch': + 'ed48464ed6f4cdbd0dde93ffc413c394d363278039502d77540ff7206c2048ae'}, {'TensorFlow-2.13.0_revert-to-flatbuffers-2.0.6.patch': 'f22757250181b6165e4b2ef1e199bd4cb344a9429be5a1086638f25bcbf650fc'}, {'TensorFlow-2.13.0_unpin-gast-version.patch': diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-typing_extensions-upper-bound.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-typing_extensions-upper-bound.patch new file mode 100644 index 00000000000..6cd08697e02 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0_remove-typing_extensions-upper-bound.patch @@ -0,0 +1,20 @@ +The limitation was removed by https://github.com/tensorflow/tensorflow/commit/19b7519c2ec7b208aa6c1145132c84ebcbd795b0 +The issue was likely "wrapt", not typing_extensions +See https://github.com/tensorflow/tensorflow/pull/61387 for wrapt +and https://github.com/tensorflow/tensorflow/issues/60687 for typing_extensions + +Author: Alexander Grund (TU Dresden) + +diff --git a/tensorflow/tools/pip_package/setup.py b/tensorflow/tools/pip_package/setup.py +index e77e6f81449..7927c8ac995 100644 +--- a/tensorflow/tools/pip_package/setup.py ++++ b/tensorflow/tools/pip_package/setup.py +@@ -97,7 +97,7 @@ REQUIRED_PACKAGES = [ + 'setuptools', + 'six >= 1.12.0', + 'termcolor >= 1.1.0', +- 'typing_extensions>=3.6.6,<4.6.0', ++ 'typing_extensions >= 3.6.6', + 'wrapt >= 1.11.0', + 'tensorflow-io-gcs-filesystem >= 0.23.1;platform_machine!="arm64" or ' + + 'platform_system!="Darwin"', From d012316bd9d0efad5efbcc958a0efe35cb67a562 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 5 Sep 2023 12:43:28 +0200 Subject: [PATCH 8689/9987] Add h5py, flatbuffers, flatbuffers-python, nsync, protobuf-python --- ...atbuffers-python-23.5.26-GCCcore-12.3.0.eb | 27 ++++++++++++++ .../flatbuffers-23.5.26-GCCcore-12.3.0.eb | 33 +++++++++++++++++ .../h/h5py/h5py-3.9.0-foss-2023a.eb | 35 +++++++++++++++++++ .../j/JsonCpp/JsonCpp-1.9.5-GCCcore-12.3.0.eb | 29 +++++++++++++++ .../n/nsync/nsync-1.26.0-GCCcore-12.3.0.eb | 26 ++++++++++++++ .../protobuf-python-4.24.0-GCCcore-12.3.0.eb | 35 +++++++++++++++++++ 6 files changed, 185 insertions(+) create mode 100644 easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-23.5.26-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.5.26-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.9.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/nsync/nsync-1.26.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-23.5.26-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-23.5.26-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..dbe82860108 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers-python/flatbuffers-python-23.5.26-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'flatbuffers-python' +version = '23.5.26' + +homepage = 'https://github.com/google/flatbuffers/' +description = """Python Flatbuffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/f/flatbuffers'] +sources = [{'download_filename': 'flatbuffers-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['9ea1144cac05ce5d86e2859f431c6cd5e66cd9c78c558317c7955fb8d4c78d89'] + +dependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = 'VERSION=%(version)s ' +options = {'modulename': 'flatbuffers'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.5.26-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.5.26-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b9e6f5ee059 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.5.26-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '23.5.26' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1cce06b17cddd896b6d73cc047e36a254fb8df4d7ea18a46acf16c4c0cd3f3f3'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('Python', '3.11.3'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.9.0-foss-2023a.eb b/easybuild/easyconfigs/h/h5py/h5py-3.9.0-foss-2023a.eb new file mode 100644 index 00000000000..be41083febf --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.9.0-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.9.0' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['e604db6521c1e367c6bd7fad239c847f53cc46646f2d2651372d05ae5e95f817'] + +builddependencies = [('pkgconfig', '1.5.5', '-python')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('mpi4py', '3.1.4'), + ('HDF5', '1.14.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..750dba0edd8 --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.5-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.5' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['f409856e5920c18d0c2fb85276e24ee607d2a09b5e7d5f0a371368903c275da2'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.26.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.26.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a4a6fe8d2ca --- /dev/null +++ b/easybuild/easyconfigs/n/nsync/nsync-1.26.0-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeNinja' + +name = 'nsync' +version = '1.26.0' + +homepage = 'https://github.com/google/nsync' +description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/nsync/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['80fc1e605bb3cf5f272811ece39c4fb6761ffcb9b30563301845cc9ff381eb8b'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), +] + +sanity_check_paths = { + 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0a299aea480 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '4.24.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = ['protobuf-%(version)s.tar.gz'] +checksums = ['5d0ceb9de6e08311832169e601d1fc71bd8e8c779f3ee38a97a78554945ecb85'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('protobuf', '24.0') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' From 29cfa44a075b33ff6dfca431fb93e8cc9133d472 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 5 Sep 2023 14:07:37 +0200 Subject: [PATCH 8690/9987] Add checksum --- easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb index 9f30a78c0ed..b8e9cfbef94 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-11.3.0.eb @@ -24,6 +24,7 @@ sources = [ 'filename': 'install-tl-unx-%(version)s.tar.gz' } ] +checksums = ['d97bdb3b1903428e56373e70861b24db448243d74d950cdff96f4e888f008605'] dependencies = [ ('X11', '20220504'), From 42be5c84440582b3c4d29aaed6adce9cb5d43b62 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 5 Sep 2023 12:45:51 +0000 Subject: [PATCH 8691/9987] sort checksums out of source dict --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 71e69c322ae..8ef538abd75 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -24,11 +24,11 @@ sources = [{ 'clone_into': '%(name)s-%(version)s', }, 'filename': '%(name)s-%(version)s.tar.gz', - 'checksums': [ - '5c4cd3c0a1d141a1b85936fee3fa52f7638774c2146b138aa9ae218d3da4b89d' - ], }] +checksums = ['5c4cd3c0a1d141a1b85936fee3fa52f7638774c2146b138aa9ae218d3da4b89d'] + + prebuildopts = "stack setup && stack build && " buildopts = "make install-bins BUILDER=stack PREFIX=%(builddir)s" From 5b3fe3eb54347905b50f81eb16b377a39961cdf1 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 5 Sep 2023 16:17:54 +0200 Subject: [PATCH 8692/9987] adding easyconfigs: gperftools-2.12-GCCcore-12.3.0.eb --- .../gperftools-2.12-GCCcore-12.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.12-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.12-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2dc99bb16e9 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.12-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.12' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'gperftools' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1cc42af8c0ec117695ecfa49ef518d9eaf7b215a2657b51f655daa2dc07101ce'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] + +dependencies = [ + ('libunwind', '1.6.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 787a69b84698a11d5e9a09de5a6ebd51885bd1e2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 5 Sep 2023 16:26:02 +0200 Subject: [PATCH 8693/9987] Add pkgconfig & mpi4py --- .../m/mpi4py/mpi4py-3.1.4-gompi-2023a.eb | 25 +++++++++++++++ .../pkgconfig-1.5.5-GCCcore-12.3.0-python.eb | 31 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-12.3.0-python.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-gompi-2023a.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-gompi-2023a.eb new file mode 100644 index 00000000000..bcb1632ecf0 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.4-gompi-2023a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonBundle' + +name = 'mpi4py' +version = '3.1.4' + +homepage = 'https://github.com/mpi4py/mpi4py' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['17858f2ebc623220d0120d1fa8d428d033dde749c4bc35b33d81a66ad7f93480'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-12.3.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-12.3.0-python.eb new file mode 100644 index 00000000000..7572556098c --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-12.3.0-python.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.5.5' +# The -python versionsuffix is used to avoid confusion between +# pkg-config (the tool) and pkgconfig (the Python wrappers) +versionsuffix = '-python' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'] + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('pkgconf', '1.9.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From 6fb54e2da57e4b3151126365eb05c41ad05410a2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 Sep 2023 18:04:10 +0200 Subject: [PATCH 8694/9987] adding easyconfigs: SEACells-20230731-foss-2021a.eb --- .../SEACells/SEACells-20230731-foss-2021a.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb b/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb new file mode 100644 index 00000000000..7cf0a01cbbc --- /dev/null +++ b/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'SEACells' +local_commit = 'a3486ca' +version = '20230731' + +homepage = 'https://github.com/dpeerlab/SEACells' +description = """SEACells algorithm for Inference of transcriptional and epigenomic cellular states + from single-cell genomics data""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('numba', '0.53.1'), + ('scanpy', '1.8.1'), +] + +use_pip = True + +exts_list = [ + ('fcsparser', '0.2.3', { + 'checksums': ['c370f05d42898ce220cb8ea0f89988d18eaaeced063c4118cc3dcb99cbd8c17e'], + }), + ('PhenoGraph', '1.5.7', { + 'checksums': ['46b28f9e043a00deba53bb5f35dd84793669ab2bd4ce78900bf7f15f1321515a'], + }), + ('typing-extensions', '4.7.1', { + 'sources': ['typing_extensions-%(version)s.tar.gz'], + }), + ('python-utils', '3.7.0', { + 'checksums': ['1970468fff1c0adbd60b9a751e6a786223a9f0373c954571912d9cf4be49b552'], + }), + ('progressbar2', '4.2.0', { + 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], + 'modulename': 'progressbar', + }), + ('pygam', '0.8.0', { + 'checksums': ['5cae01aea8b2fede72a6da0aba1490213af54b3476745666af26bbe700479166'], + }), + ('tzlocal', '5.0.1', { + 'checksums': ['46eb99ad4bdb71f3f72b7d24f4267753e240944ecfc16f25d2719ba89827a803'], + }), + ('palantir', '1.2', { + 'preinstallopts': "sed -i '/cmake/d' setup.py && ", + 'checksums': ['2213ba7a99be62922086e30417994874c165bce1356752bbf0b4cc887b1a069e'], + }), + ('ncls', '0.0.67', { + 'checksums': ['fa3e673d60e97bb021a516287d74bb959870cf9d910ec82403b99c443d8f447e'], + }), + ('sorted-nearest', '0.0.32', { + 'sources': ['sorted_nearest-%(version)s.tar.gz'], + 'checksums': ['7ae0d8a4e10a29787e61831bac25af5c22b0bf7edb8a5efd0ab206afbb0238b4'], + }), + ('pyrle', '0.0.33', { + 'checksums': ['4c24a2e096f8dbfa4451d57ce769057e2ed6c369ee75f5dce3c4d6fa47f71a6e'], + }), + ('pyranges', '0.0.110', { + 'checksums': ['5996d22c07c490e3ad15863c63d27a225896e08700a0bcbc6e0272d071dafa5a'], + }), + (name, version, { + 'source_urls': ['https://github.com/dpeerlab/SEACells/archive/'], + 'sources': [{'download_filename': 'a3486ca.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['2e7317d975d0a0b618cbeaca95ceb61fc6abc5c8da4a7095bca763493983749e'], + 'modulename': name, + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 75f0d71f7c3dce0bf5bcf25644c70749ec42fadb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 Sep 2023 18:33:57 +0200 Subject: [PATCH 8695/9987] add missing checksum for typing-extensions in SEACells easyconfig --- easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb b/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb index 7cf0a01cbbc..5d184b0d518 100644 --- a/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb +++ b/easybuild/easyconfigs/s/SEACells/SEACells-20230731-foss-2021a.eb @@ -32,6 +32,7 @@ exts_list = [ }), ('typing-extensions', '4.7.1', { 'sources': ['typing_extensions-%(version)s.tar.gz'], + 'checksums': ['b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2'], }), ('python-utils', '3.7.0', { 'checksums': ['1970468fff1c0adbd60b9a751e6a786223a9f0373c954571912d9cf4be49b552'], From 001d2c3976f0a3070195e94011107bf02b72274f Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 5 Sep 2023 16:43:35 +0000 Subject: [PATCH 8696/9987] fix small flake8 issue --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 8ef538abd75..2ba6c675ae2 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -33,7 +33,7 @@ prebuildopts = "stack setup && stack build && " buildopts = "make install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ - (['git-annex', 'git-annex-shell'], 'bin'), + (['git-annex', 'git-annex-shell'], 'bin'), ] sanity_check_paths = { From 70044b11f62df7d2d95b2d776fc69140c0a914f4 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 5 Sep 2023 20:24:41 +0000 Subject: [PATCH 8697/9987] delete line --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 2ba6c675ae2..23b336d4655 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -28,7 +28,6 @@ sources = [{ checksums = ['5c4cd3c0a1d141a1b85936fee3fa52f7638774c2146b138aa9ae218d3da4b89d'] - prebuildopts = "stack setup && stack build && " buildopts = "make install-bins BUILDER=stack PREFIX=%(builddir)s" From 4282f2f46df357266ad77c2cb4e514ad7da1651b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Sep 2023 09:50:22 +0200 Subject: [PATCH 8698/9987] strip out hardcoded -march=native used by RapidJSON 1.1.0 --- .../easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb | 2 ++ .../easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb | 3 +++ .../easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.2.0.eb | 3 +++ .../easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.3.0.eb | 3 +++ .../easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb | 3 +++ .../easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-8.2.0.eb | 3 +++ .../easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-8.3.0.eb | 3 +++ .../easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-9.3.0.eb | 2 ++ 8 files changed, 22 insertions(+) diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb index 0fd88903d33..c59421ba5da 100644 --- a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.2.0.eb @@ -22,6 +22,8 @@ builddependencies = [ ('CMake', '3.18.4'), ] +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-%(version)s/CMakeLists.txt && " sanity_check_paths = { 'files': ['lib/pkgconfig/%(name)s.pc'], diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb index 39a23ca4bec..18bcf89078f 100644 --- a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-10.3.0.eb @@ -22,6 +22,9 @@ builddependencies = [ ('CMake', '3.20.1'), ] +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-%(version)s/CMakeLists.txt && " + sanity_check_paths = { 'files': ['lib/pkgconfig/%(name)s.pc'], 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.2.0.eb index c6e3e4da6fb..88330bf84ea 100644 --- a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.2.0.eb @@ -22,6 +22,9 @@ builddependencies = [ ('CMake', '3.21.1'), ] +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-%(version)s/CMakeLists.txt && " + sanity_check_paths = { 'files': ['lib/pkgconfig/%(name)s.pc'], 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.3.0.eb index 3452dfb7caf..b43bed9a68f 100644 --- a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-11.3.0.eb @@ -22,6 +22,9 @@ builddependencies = [ ('CMake', '3.23.1'), ] +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-%(version)s/CMakeLists.txt && " + sanity_check_paths = { 'files': ['lib/pkgconfig/%(name)s.pc'], 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb index 9594b13fd9d..9b786df30e0 100644 --- a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb @@ -22,6 +22,9 @@ builddependencies = [ ('CMake', '3.24.3'), ] +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-%(version)s/CMakeLists.txt && " + sanity_check_paths = { 'files': ['lib/pkgconfig/%(name)s.pc'], 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-8.2.0.eb index 79d63114af0..75abae6a345 100644 --- a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-8.2.0.eb @@ -21,6 +21,9 @@ builddependencies = [ ('CMake', '3.13.3'), ] +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-%(version)s/CMakeLists.txt && " + sanity_check_paths = { 'files': ['lib/pkgconfig/RapidJSON.pc'], 'dirs': ['include/rapidjson', 'lib/cmake', 'share'], diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-8.3.0.eb index 046d65c9734..4b7fb2c19f6 100644 --- a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-8.3.0.eb @@ -21,6 +21,9 @@ builddependencies = [ ('CMake', '3.15.3'), ] +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-%(version)s/CMakeLists.txt && " + sanity_check_paths = { 'files': ['lib/pkgconfig/RapidJSON.pc'], 'dirs': ['include/rapidjson', 'lib/cmake', 'share'], diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-9.3.0.eb index 731c2bd91cb..187b4f5e6b6 100644 --- a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-9.3.0.eb @@ -22,6 +22,8 @@ builddependencies = [ ('CMake', '3.16.4'), ] +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-%(version)s/CMakeLists.txt && " sanity_check_paths = { 'files': ['lib/pkgconfig/%(name)s.pc'], From 2fcf1940e598fc6cc184a687dd68860a83cb2c4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 6 Sep 2023 10:14:02 +0200 Subject: [PATCH 8699/9987] adding easyconfigs: NanoCaller-3.4.1-foss-2022a.eb, RTG-Tools-3.12.1-Java-11.eb --- .../NanoCaller/NanoCaller-3.4.1-foss-2022a.eb | 45 +++++++++++++++++++ .../r/RTG-Tools/RTG-Tools-3.12.1-Java-11.eb | 42 +++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.4.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/RTG-Tools/RTG-Tools-3.12.1-Java-11.eb diff --git a/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.4.1-foss-2022a.eb b/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.4.1-foss-2022a.eb new file mode 100644 index 00000000000..b42ae646953 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoCaller/NanoCaller-3.4.1-foss-2022a.eb @@ -0,0 +1,45 @@ +easyblock = 'Tarball' + +name = 'NanoCaller' +version = '3.4.1' + +homepage = 'https://github.com/WGLab/NanoCaller' +description = """NanoCaller is a computational method that integrates long reads in deep + convolutional neural network for the detection of SNPs/indels from long-read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/WGLab/%(name)s/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] + +checksums = ['b90970c9e0491f454a5fbd7ab998111e69c5a0b90bad6388bfbe636b73368bf8'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('BCFtools', '1.15.1'), + ('python-parasail', '1.3.3'), + ('MUSCLE', '5.1.0'), + ('Pysam', '0.19.1'), + ('SAMtools', '1.16.1'), + ('TensorFlow', '2.11.0'), + ('WhatsHap', '1.7'), + ('vcflib', '1.0.9', '-R-4.2.1'), + ('intervaltree-python', '3.1.0'), + ('tqdm', '4.64.0'), + ('RTG-Tools', '3.12.1', '-Java-11', SYSTEM), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['NanoCaller'], + 'dirs': [], +} + +sanity_check_commands = ["NanoCaller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RTG-Tools/RTG-Tools-3.12.1-Java-11.eb b/easybuild/easyconfigs/r/RTG-Tools/RTG-Tools-3.12.1-Java-11.eb new file mode 100644 index 00000000000..6f653767be7 --- /dev/null +++ b/easybuild/easyconfigs/r/RTG-Tools/RTG-Tools-3.12.1-Java-11.eb @@ -0,0 +1,42 @@ +easyblock = 'CmdCp' + +name = 'RTG-Tools' +version = '3.12.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.realtimegenomics.com/products/rtg-tools' +description = """ RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files, + as well as utilities for processing other common NGS data formats. """ + +toolchain = SYSTEM + +source_urls = ['https://github.com/RealTimeGenomics/rtg-tools/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['6ee0ffe1bba7b5497aa09b147a7525b77b1808e6a71368aad440cbd64658085c'] + +builddependencies = [('ant', '1.10.12', versionsuffix)] +dependencies = [('Java', '11')] + +local_comp_cmd = "export RTG_MEM=1G && " +# NOTE Tests of RTG-Tools reserve 60% machine's memory. +# That causes them to fail on debug clusters and work on full nodes only. +# therefore this easyconfig has been tested on a full node and `ant runalltests` was removed from the easyconfig. +# local_comp_cmd += 'ant runalltests && ' +local_comp_cmd += 'ant zip-nojre && ' +local_comp_cmd += 'unzip %(builddir)s/rtg-tools-%(version)s/dist/rtg-tools-%(version)s-unknown-nojre.zip' + +cmds_map = [('.*', local_comp_cmd)] + +files_to_copy = ['rtg-tools-%(version)s-unknown/*'] + +# add default configuration: no crash reporting, no usage logging +postinstallcmds = ["echo 'RTG_TALKBACK=false\nRTG_USAGE=' > %(installdir)s/rtg.cfg"] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['rtg', 'rtg.cfg', 'RTG.jar'], + 'dirs': [], +} + +moduleclass = 'bio' From 5ea1815dac91e4128193719401c4e03a18372fa0 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 6 Sep 2023 10:58:21 +0200 Subject: [PATCH 8700/9987] Disable detection of Dbus broker for at-spi2-core --- .../a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb | 2 ++ .../a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb | 2 ++ .../a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb | 2 ++ .../a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb | 2 ++ .../a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb | 2 ++ .../a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb | 2 ++ .../a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb | 3 ++- 7 files changed, 14 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb index e914c88f6e8..b1b2c9f5ba5 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb @@ -29,6 +29,8 @@ dependencies = [ ('X11', '20200222'), ] +# Hard disable Dbus broker detection +preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb index d065df3ef5c..c157f92352f 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb @@ -29,6 +29,8 @@ dependencies = [ ('X11', '20201008'), ] +# Hard disable Dbus broker detection +preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb index 8abec6ada60..d950fed6322 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb @@ -29,6 +29,8 @@ dependencies = [ ('X11', '20210518'), ] +# Hard disable Dbus broker detection +preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb index bccb9a5ba84..6f9c513a871 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb @@ -29,6 +29,8 @@ dependencies = [ ('X11', '20210802'), ] +# Hard disable Dbus broker detection +preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb index 2d3b037b75a..eda23a95849 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb @@ -29,6 +29,8 @@ dependencies = [ ('X11', '20220504'), ] +# Hard disable Dbus broker detection +preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb index b9f052b0826..4c6338f29c0 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb @@ -29,6 +29,8 @@ dependencies = [ ('X11', '20221110'), ] +# Hard disable Dbus broker detection +preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb index d6c6af7fbd5..9432bc2e1bb 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb @@ -29,7 +29,8 @@ dependencies = [ ('X11', '20230603'), ] -configopts = "--libdir lib " +# Hard disable Dbus broker detection and (potential) use of systemd +configopts = "--libdir lib -Duse_systemd=false -Ddefault_bus=dbus-daemon" sanity_check_paths = { 'files': ['lib/libatspi.%s' % SHLIB_EXT], From ae49fecfae479ae64dc19775a1878026b98c5920 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 6 Sep 2023 11:28:07 +0200 Subject: [PATCH 8701/9987] Fix flake8 --- .../a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb | 2 +- .../a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb | 2 +- .../a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb | 2 +- .../a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb | 2 +- .../a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb | 2 +- .../a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb index b1b2c9f5ba5..28a3f02e4a7 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.36.0-GCCcore-9.3.0.eb @@ -30,7 +30,7 @@ dependencies = [ ] # Hard disable Dbus broker detection -preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" +preconfigopts = "sed -i s/'dbus_broker.found()'/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb index c157f92352f..18f70fd3f8f 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb @@ -30,7 +30,7 @@ dependencies = [ ] # Hard disable Dbus broker detection -preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" +preconfigopts = "sed -i s/'dbus_broker.found()'/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb index d950fed6322..8bf6238770d 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.2-GCCcore-10.3.0.eb @@ -30,7 +30,7 @@ dependencies = [ ] # Hard disable Dbus broker detection -preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" +preconfigopts = "sed -i s/'dbus_broker.found()'/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb index 6f9c513a871..67df401d85d 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.40.3-GCCcore-11.2.0.eb @@ -30,7 +30,7 @@ dependencies = [ ] # Hard disable Dbus broker detection -preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" +preconfigopts = "sed -i s/'dbus_broker.found()'/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb index eda23a95849..0b94f5a00a6 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.44.1-GCCcore-11.3.0.eb @@ -30,7 +30,7 @@ dependencies = [ ] # Hard disable Dbus broker detection -preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" +preconfigopts = "sed -i s/'dbus_broker.found()'/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb index 4c6338f29c0..f90e6e4eaba 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb @@ -30,7 +30,7 @@ dependencies = [ ] # Hard disable Dbus broker detection -preconfigopts = "sed -i s/dbus_broker.found\(\)/false/ ../*/bus/meson.build &&" +preconfigopts = "sed -i s/'dbus_broker.found()'/false/ ../*/bus/meson.build &&" configopts = "--libdir lib " sanity_check_paths = { From f9a4146e52268979691dc598fa03e653c185be73 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Wed, 6 Sep 2023 12:12:02 +0200 Subject: [PATCH 8702/9987] Update LevelDB-1.22-GCCcore-11.3.0.eb adding checksums --- easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb index 239bc420990..66a233cae44 100644 --- a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb @@ -29,6 +29,7 @@ components = [ 'source_urls': ['https://github.com/google/leveldb/archive/'], 'sources': ['%(version)s.tar.gz'], 'configopts': "-DBUILD_SHARED_LIBS=ON -DLEVELDB_BUILD_BENCHMARKS=OFF ", + 'checksums': ['55423cac9e3306f4a9502c738a001e4a339d1a38ffbee7572d4a07d5d63949b2'], }), ('leveldb', '0.201', { 'easyblock': 'PythonPackage', @@ -36,6 +37,7 @@ components = [ 'sources': [SOURCE_TAR_GZ], 'use_pip': True, 'download_dep_fail': True, + 'checksums': ['1cffe776842917e09f073bd6ea5856c64136aebddbe51bd17ea29913472fecbf'], }), ] From e6c3b69a06743b7a9e6519b339ecc78513061b69 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Wed, 6 Sep 2023 10:34:45 +0000 Subject: [PATCH 8703/9987] flake8 compliance --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 812f649c339..5efbe2fe9e6 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -4,7 +4,9 @@ name = 'datalad' version = "0.18.4" homepage = 'https://www.datalad.org/' -description = "DataLad is a free and open source distributed data management system that keeps track of your data, creates structure, ensures reproducibility, supports collaboration, and integrates with widely used data infrastructure." +description = "DataLad is a free and open source distributed data management system that keeps track of your data, \ +creates structure, ensures reproducibility, supports collaboration, \ +and integrates with widely used data infrastructure." toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} @@ -42,7 +44,7 @@ exts_list = [ }), ('gitlab', '3.10.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], + 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { 'checksums': ['27f503220e6845d9db954fb212b95b0362d8b7e6c1b2326a87061c3de93594b1'], From 390a8a7d02a3399ab6cee6f686b27c41990fa2d3 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 6 Sep 2023 13:02:11 +0200 Subject: [PATCH 8704/9987] adding easyconfigs: HDF-4.2.16-2-GCCcore-12.3.0.eb --- .../h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ba100820b9b --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.16-2' + +homepage = 'https://www.hdfgroup.org/products/hdf4/' +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = [ + 'a24b18312d421686031c2d66635f7d5abb2fe879f8a182b7e02797b0da8d1f6c', # %(namelower)s-%(version)s.tar.gz +] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] +dependencies = [ + ('libjpeg-turbo', '2.1.5.1'), + ('Szip', '2.1.1'), + ('zlib', '1.2.13'), + ('libtirpc', '1.3.3'), +] + +preconfigopts = "LIBS='-ltirpc' " +configopts = [ + '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc"', + '--includedir=%(installdir)s/include/%(namelower)s FFLAGS="$FFLAGS -fallow-argument-mismatch"', + '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc"', + '--includedir=%(installdir)s/include/%(namelower)s', + '--enable-shared', + '--disable-fortran', + '--disable-netcdf', +] + + +sanity_check_paths = { + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', 'lib/libmfhdf.so'], + 'dirs': ['include/%(namelower)s'], +} + +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + +modextrapaths = {'CPATH': 'include/%(namelower)s'} + +moduleclass = 'data' From a75456678115b83cd5283bd986e36cb6e1a03b44 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 6 Sep 2023 13:33:53 +0200 Subject: [PATCH 8705/9987] adding easyconfigs: wrapt-1.15.0-foss-2023a.eb --- .../w/wrapt/wrapt-1.15.0-foss-2023a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2023a.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2023a.eb new file mode 100644 index 00000000000..66ad8f45a37 --- /dev/null +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'wrapt' +version = '1.15.0' + +homepage = 'https://pypi.org/project/wrapt/' +description = """The aim of the wrapt module is to provide a transparent object +proxy for Python, which can be used as the basis for the construction of +function wrappers and decorator functions.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'], + }), +] + +moduleclass = 'tools' From 3ca27edbb56f2819ac5fc501c8c713236bb02ce5 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 6 Sep 2023 14:43:30 +0200 Subject: [PATCH 8706/9987] adding easyconfigs: PnetCDF-1.12.3-gompi-2023a.eb --- .../p/PnetCDF/PnetCDF-1.12.3-gompi-2023a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2023a.eb diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2023a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2023a.eb new file mode 100644 index 00000000000..6fbdb97fe58 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.12.3-gompi-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = '1.12.3' + +homepage = 'https://parallel-netcdf.github.io/' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://parallel-netcdf.github.io/Release'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['439e359d09bb93d0e58a6e3f928f39c2eae965b6c97f64e67cd42220d6034f77'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Perl', '5.36.1'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = ['', '--enable-shared'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = { + 'PNETCDF': '', +} + +moduleclass = 'data' From f5ee942827371bfb891843ff48c2cc84dab8e99e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 6 Sep 2023 15:21:15 +0200 Subject: [PATCH 8707/9987] adding easyconfigs: netcdf4-python-1.6.4-foss-2023a.eb --- .../netcdf4-python-1.6.4-foss-2023a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.4-foss-2023a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.4-foss-2023a.eb new file mode 100644 index 00000000000..58f5790b23e --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.4-foss-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.4' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('netCDF', '4.9.2'), + ('cURL', '8.0.1'), + ('mpi4py', '3.1.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + (name, version, { + 'patches': [ + 'netcdf4-python-1.1.8-avoid-diskless-test.patch', + 'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch', + ], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + {'netCDF4-1.6.4.tar.gz': '66da6542cbc7a6045cd1d979397dfd5a3f6c880c76d52b8f98bb108c82ee8c6e'}, + {'netcdf4-python-1.1.8-avoid-diskless-test.patch': + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72'}, + {'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch': + '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166'}, + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' From 8b563ac8c658ab2c6177efae58fc369cc866122a Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 6 Sep 2023 16:13:29 +0200 Subject: [PATCH 8708/9987] Bump version of at-spi2-core to latest patch release --- .../a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb | 2 +- ...Ccore-12.3.0.eb => at-spi2-core-2.49.91-GCCcore-12.3.0.eb} | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/a/at-spi2-core/{at-spi2-core-2.49.90-GCCcore-12.3.0.eb => at-spi2-core-2.49.91-GCCcore-12.3.0.eb} (89%) diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb index 5dbd5efc816..8a99ca40953 100644 --- a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.3.0.eb @@ -22,7 +22,7 @@ builddependencies = [ dependencies = [ ('GLib', '2.77.1'), ('DBus', '1.15.4'), - ('at-spi2-core', '2.49.90'), + ('at-spi2-core', '2.49.91'), ('libxml2', '2.11.4'), ('ATK', '2.38.0'), ] diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.91-GCCcore-12.3.0.eb similarity index 89% rename from easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.91-GCCcore-12.3.0.eb index 9432bc2e1bb..f44c26b64b7 100644 --- a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.90-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.49.91-GCCcore-12.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'MesonNinja' name = 'at-spi2-core' -version = '2.49.90' +version = '2.49.91' homepage = 'https://wiki.gnome.org/Accessibility' description = """ @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['1e6612755d71bbe952156dc051b281d1a4326a5696ac3bbc8cfd5ac8fd971f18'] +checksums = ['aa72bbb12188ee3d0152cc6ea935415e6dc623ffa751b6a7cc23e9025f0410fd'] builddependencies = [ ('binutils', '2.40'), From dfcf0eaf0c4a0610217347e2fc3ccea9d3a528d3 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 6 Sep 2023 16:25:21 +0200 Subject: [PATCH 8709/9987] adding easyconfigs: GDAL-3.7.1-foss-2023a.eb --- .../g/GDAL/GDAL-3.7.1-foss-2023a.eb | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb new file mode 100644 index 00000000000..18ca94a238a --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb @@ -0,0 +1,80 @@ +easyblock = 'CMakeMake' + +name = 'GDAL' +version = '3.7.1' + +homepage = 'https://www.gdal.org' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://download.osgeo.org/%(namelower)s/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['%(name)s-3.6.2_fix-python-CC-CXX.patch'] + +checksums = [ + {'gdal-3.7.1.tar.xz': '9297948f0a8ba9e6369cd50e87c7e2442eda95336b94d2b92ef1829d260b9a06'}, + {'GDAL-3.6.2_fix-python-CC-CXX.patch': '859b874b0c8ff7626a76d51f008bf05b7f89a35b325bdd1d126d2364154acc63'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('Bison', '3.8.2'), +] +dependencies = [ + ('Python', '3.11.3'), + ('netCDF', '4.9.2'), + ('expat', '2.5.0'), + ('GEOS', '3.12.0'), + ('SQLite', '3.42.0'), + ('libxml2', '2.11.4'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('JasPer', '4.0.0'), + ('LibTIFF', '4.5.0'), + ('zlib', '1.2.13'), + ('cURL', '8.0.1'), + ('PCRE', '8.45'), + ('PROJ', '9.2.0'), + ('libgeotiff', '1.7.1'), + ('SciPy-bundle', '2023.07'), + ('HDF5', '1.14.0'), + ('HDF', '4.2.16-2'), + ('Armadillo', '12.6.2'), + ('CFITSIO', '4.3.0'), + ('zstd', '1.5.5'), + ('giflib', '5.2.1'), + ('json-c', '0.16'), + ('Xerces-C++', '3.2.4'), + ('PCRE2', '10.42'), + ('OpenEXR', '3.1.7'), + ('Brunsli', '0.1'), + ('Qhull', '2020.2'), + ('LERC', '4.0.0'), + ('OpenJPEG', '2.5.0'), +] + +# iterative build for both static and shared libraries +configopts = [ + "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW", + "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON -DBUILD_SHARED_LIBS=OFF", + "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW", + "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON ", +] + + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.so'], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import osgeo.%(namelower)s'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'data' From 46c4957fa2af4224275c03047ca05a889cea4709 Mon Sep 17 00:00:00 2001 From: chris g Date: Wed, 6 Sep 2023 15:54:55 +0100 Subject: [PATCH 8710/9987] adding easyconfigs: ALAMODE-1.4.2-foss-2022b.eb --- .../a/ALAMODE/ALAMODE-1.4.2-foss-2022b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100755 easybuild/easyconfigs/a/ALAMODE/ALAMODE-1.4.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/a/ALAMODE/ALAMODE-1.4.2-foss-2022b.eb b/easybuild/easyconfigs/a/ALAMODE/ALAMODE-1.4.2-foss-2022b.eb new file mode 100755 index 00000000000..5f855b18e6f --- /dev/null +++ b/easybuild/easyconfigs/a/ALAMODE/ALAMODE-1.4.2-foss-2022b.eb @@ -0,0 +1,57 @@ +# with thanks to ComputeCanada for the initial easyconfig for 1.0.2-iomkl-2017.5.211.eb +# updated for 1.4.2 by BEAR Software team at University of Birmingham +easyblock = "CMakeMakeCp" + +name = 'ALAMODE' +version = '1.4.2' + +homepage = 'http://alamode.readthedocs.io/en/latest/index.html' +description = """ALAMODE is an open source software designed for analyzing lattice anharmonicity + and lattice thermal conductivity of solids. By using an external DFT package such as VASP and + Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. + Using the calculated anharmonic force constants, you can also estimate lattice thermal conductivity, + phonon linewidth, and other anharmonic phonon properties from first principles. +""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://github.com/ttadano/alamode/archive/'] +sources = ['v.%(version)s.tar.gz'] +checksums = ['18fb80a183c2a9b68488aeeccd6efa95e8c21d4cb21b08319a557389d55c067a'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Boost', '1.81.0'), + ('Eigen', '3.4.0'), + ('spglib', '2.0.2'), + ('FFTW', '3.3.10'), + ('HDF5', '1.14.0'), + ('Python', '3.10.8'), +] + +configopts = ' '.join([ + "-DWITH_HDF5_SUPPORT=yes", + "-DUSE_MKL_FFT=no", + "-DSPGLIB_ROOT=$EBROOTSPGLIB" +]) + +local_binary_files = [ + "alm/alm", "anphon/anphon", "tools/analyze_phonons", "tools/dfc2", "tools/fc_virtual", + "tools/parse_fcsxml", "tools/qe2alm", "tools/analyze_phonons.py", "tools/displace.py", "tools/extract.py", + "tools/GenDisplacement.py", "tools/makedisp_qe.py", "tools/plotband.py", "tools/plotdos.py", + "tools/scph_to_qefc.py", +] + +files_to_copy = [([x for x in local_binary_files], 'bin'), 'docs', 'example'] + +sanity_check_paths = { + 'files': ['bin/alm'], + 'dirs': ["docs", "example"] +} + +moduleclass = 'chem' From e6364708359a42899ae16b124b9b268650c1ca00 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Sep 2023 18:54:55 +0200 Subject: [PATCH 8711/9987] adding easyconfigs: scib-metrics-0.3.3-foss-2021a.eb, anndata-0.9.2-foss-2021a.eb --- .../a/anndata/anndata-0.9.2-foss-2021a.eb | 42 +++++++++++ .../scib-metrics-0.3.3-foss-2021a.eb | 72 +++++++++++++++++++ 2 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.3.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021a.eb b/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021a.eb new file mode 100644 index 00000000000..62b74665879 --- /dev/null +++ b/easybuild/easyconfigs/a/anndata/anndata-0.9.2-foss-2021a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'anndata' +version = '0.9.2' + +homepage = 'https://github.com/scverse/anndata' +description = """anndata is a Python package for handling annotated data matrices in memory and on disk, + positioned between pandas and xarray""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), +] + +use_pip = True + +exts_list = [ + # more recent setuptools required because scib-metrics uses pyproject.toml + ('setuptools', '68.1.2', { + 'checksums': ['3d4dfa6d95f1b101d695a6160a7626e15583af71a5f52176efa5d39a054d475d'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + (name, version, { + 'checksums': ['e5b8383d09723af674cae7ad0c2ef53eb1f8c73949b7f4c182a6e30f42196327'], + }), +] + +sanity_check_paths = { + 'files': ['bin/natsort'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["natsort --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.3.3-foss-2021a.eb b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.3.3-foss-2021a.eb new file mode 100644 index 00000000000..664c85a989e --- /dev/null +++ b/easybuild/easyconfigs/s/scib-metrics/scib-metrics-0.3.3-foss-2021a.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'scib-metrics' +version = '0.3.3' + +homepage = 'https://scib-metrics.readthedocs.io' +description = "Accelerated and Python-only metrics for benchmarking single-cell integration outputs" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('jax', '0.3.9'), + ('scikit-learn', '0.24.2'), + ('anndata', '0.9.2'), + ('python-igraph', '0.9.6'), + ('scanpy', '1.8.1'), + ('tqdm', '4.61.2'), + ('dm-tree', '0.1.6'), +] + +use_pip = True + +# avoid hatchling requirement to install scib-metrics +local_preinstallopts_scib_metrics = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ +local_preinstallopts_scib_metrics += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ +# strip out requirement for igraph (it's provided as dependency, but invisible to pip so 'pip check' fails) +local_preinstallopts_scib_metrics += "-e '/igraph/d' pyproject.toml && " + +exts_list = [ + # more recent setuptools required because scib-metrics uses pyproject.toml + ('setuptools', '68.1.2', { + 'checksums': ['3d4dfa6d95f1b101d695a6160a7626e15583af71a5f52176efa5d39a054d475d'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('typing-extensions', '4.7.1', { + 'sources': ['typing_extensions-%(version)s.tar.gz'], + 'checksums': ['b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2'], + }), + ('chex', '0.1.6', { + 'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'], + }), + ('plottable', '0.1.5', { + 'checksums': ['235d762a31c82129dc5bf74205c103a14b1e4393d0f921cc0231be5de884041d'], + }), + ('pynndescent', '0.5.10', { + 'checksums': ['5d5dc683c03ef55fe3ddf693859720ca18f85c6e6e5bb0b4f14870278d5288ad'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '2.2.0', { + 'checksums': ['7c9a5e412688bc771c67432cbfebcdd686c93ce6484913dccf06cb5a0bea35a1'], + 'modulename': 'markdown_it', + }), + ('rich', '13.2.0', { + 'checksums': ['f1a00cdd3eebf999a15d85ec498bfe0b1a77efe9b34f645768a54132ef444ac5'], + }), + (name, version, { + 'sources': ['scib_metrics-%(version)s.tar.gz'], + 'checksums': ['2d33017a7455cc0c203ceb9403586859d5f1906255a0d5d5578c5fba5346d012'], + 'preinstallopts': local_preinstallopts_scib_metrics, + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From b78b1d12f4df22572aa0fe5b3b002b54c2026875 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 6 Sep 2023 20:56:09 +0000 Subject: [PATCH 8712/9987] restore previous comments --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 5eb314d3154..923b0e442aa 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -78,6 +78,9 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 17th March 2023 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets', From fc0d7e76fded004b1920607aa6452fb2a7c87207 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 6 Sep 2023 21:01:11 +0000 Subject: [PATCH 8713/9987] restore more comments --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 923b0e442aa..598a3d2bb3e 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -2373,6 +2373,7 @@ exts_list = [ 'checksums': ['be50f9fdef0f4bf9676b9c3c2906d0431afc678af55cf48b1119f9fc0adac44f'], }), ('liquidSVM', '1.2.4', { + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ @@ -2888,8 +2889,12 @@ exts_list = [ 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], }), ('gWidgets2tcltk', '1.0-8', { - 'modulename': False, + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], }), ('mgsub', '1.7.3', { From 52fbfce216d717dff72ab247b99b93f38f382481 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Sep 2023 10:36:56 +0200 Subject: [PATCH 8714/9987] rename notebook to JupyterNotebook --- .../JupyterNotebook-7.0.2-GCCcore-12.3.0.eb} | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/{n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb => j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb} (87%) diff --git a/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb similarity index 87% rename from easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb index ca17d12903e..3d7c6f247d5 100644 --- a/easybuild/easyconfigs/n/notebook/notebook-7.0.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'notebook' +name = 'JupyterNotebook' version = '7.0.2' homepage = 'https://jupyter.org/' @@ -9,6 +9,10 @@ description = """The Jupyter Notebook is the original web application for creati toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +source_urls = ['https://pypi.python.org/packages/source/n/notebook'] +sources = ['notebook-%(version)s.tar.gz'] +checksums = ['d70d6a07418c829bd5f54337ce993b7105261d9026f9d3fe68e9b8aa1a20da9a'] + builddependencies = [ ('binutils', '2.40'), ] @@ -19,9 +23,6 @@ dependencies = [ ('JupyterLab', '4.0.5'), ] -sources = [SOURCE_TAR_GZ] -checksums = ['d70d6a07418c829bd5f54337ce993b7105261d9026f9d3fe68e9b8aa1a20da9a'] - download_dep_fail = True sanity_pip_check = True use_pip = True From ad52c90dd64a3b1a58debb4da1ab4b4e70a56027 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Sep 2023 10:42:28 +0200 Subject: [PATCH 8715/9987] fix modulename to use for doing import check in JupyterNotebook easyconfig --- .../j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb index 3d7c6f247d5..8fb29542706 100644 --- a/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb @@ -27,6 +27,8 @@ download_dep_fail = True sanity_pip_check = True use_pip = True +options = {'modulename': 'notebook'} + sanity_check_paths = { 'files': ['bin/jupyter-notebook'], 'dirs': ['etc/jupyter', 'share/jupyter'], From 79bd9c3ba740442d6311818f3d56a14f950bb8a2 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 7 Sep 2023 11:15:36 +0200 Subject: [PATCH 8716/9987] adding easyconfigs: libsndfile-1.2.2-GCCcore-12.3.0.eb --- .../libsndfile-1.2.2-GCCcore-12.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..15cf5543044 --- /dev/null +++ b/easybuild/easyconfigs/l/libsndfile/libsndfile-1.2.2-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libsndfile' +version = '1.2.2' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['3799ca9924d3125038880367bf1468e53a1b7e3686a934f098b7e1d286cdb80e'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('FLAC', '1.4.2'), + ('libvorbis', '1.3.7'), + ('libopus', '1.4'), + ('LAME', '3.100'), +] + +configopts = [ + '', + '-DBUILD_SHARED_LIBS=ON', +] + + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['bin'], +} + +moduleclass = 'lib' From e205a6b75cb65a6a32192d177b7121e1b0de87ba Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 7 Sep 2023 11:23:58 +0200 Subject: [PATCH 8717/9987] adding easyconfigs: ImageMagick-7.1.1-15-GCCcore-12.3.0.eb --- .../ImageMagick-7.1.1-15-GCCcore-12.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3b1b4500899 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.1.1-15' + +homepage = 'https://www.imagemagick.org/' +description = "ImageMagick is a software suite to create, edit, compose, or convert bitmap images" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['2372192a76af9be43c0543dd7ae6dfbf34b11fc0203583453ce3f9f707c36bcc'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20230603'), + ('Ghostscript', '10.01.2'), + ('JasPer', '4.0.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('LibTIFF', '4.5.0'), + ('LittleCMS', '2.15'), + ('Pango', '1.50.14'), +] + +configopts = "--with-gslib --with-x" + + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' From 2defe27fd93e604457bd2ef44b077f3b32ce9c8b Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 7 Sep 2023 11:24:08 +0200 Subject: [PATCH 8718/9987] Update name for JupyterNotebook EasyConfig --- ...gurable-http-proxy-4.5.6-GCCcore-12.3.0.eb | 32 +++ .../Jupyter-bundle-20230823-GCCcore-12.3.0.eb | 3 +- .../JupyterHub-4.0.2-GCCcore-12.3.0.eb | 130 ++++++++++++ .../JupyterLab-4.0.5-GCCcore-12.3.0.eb | 73 +++++++ .../JupyterNotebook-7.0.2-GCCcore-12.3.0.eb | 44 ++++ ...pyter-server-proxy-4.0.0-GCCcore-12.3.0.eb | 45 +++++ .../jupyter-server-2.7.2-GCCcore-12.3.0.eb | 190 ++++++++++++++++++ .../nbclassic-1.0.0-GCCcore-12.3.0.eb | 51 +++++ .../p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb | 29 +++ .../p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb | 29 +++ 10 files changed, 625 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..fc58c50bc75 --- /dev/null +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'Binary' + +name = 'configurable-http-proxy' +version = '4.5.6' + +homepage = 'https://github.com/jupyterhub/configurable-http-proxy' +description = """HTTP proxy for node.js including a REST API for updating the routing table. + Developed as a part of the Jupyter Hub multi-user server.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/jupyterhub/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4d9d94d0e6e44542ac973963b8a6545f4b40c0a2995e865ae9c80a2279e1e0ab'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('nodejs', '18.17.1'), +] + +install_cmd = "npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz" + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb index 5a6c5aaea78..0053b89cf41 100644 --- a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb @@ -16,9 +16,10 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} dependencies = [ ('JupyterHub', '4.0.2'), ('JupyterLab', '4.0.5'), - ('notebook', '7.0.2'), + ('JupyterNotebook', '7.0.2'), ('nbclassic', '1.0.0'), ('jupyter-server-proxy', '4.0.0'), ('jupyterlmod', '4.0.3'), ('jupyter-resource-usage', '1.0.0'), ] + diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..6e978bce869 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,130 @@ +easyblock = 'PythonBundle' + +name = 'JupyterHub' +version = '4.0.2' + +homepage = 'https://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed + for centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('setuptools-rust', '1.6.0'), # Needed for bcrypt + ('Rust', '1.70.0'), # Needed for bcrypt +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('Mako', '1.2.4'), + ('configurable-http-proxy', '4.5.6'), + ('OpenSSL', '1.1', '', SYSTEM), + ('tornado', '6.3.2'), + ('PycURL', '7.45.2'), # optional, recommended with large number of users +] + +sanity_pip_check = True +use_pip = True + +local_batchspawner_commit = '2a9eda060a875a2b65ca9521368fe052a09c3266' + +exts_list = [ + ('certipy', '0.1.3', { + 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], + }), + ('pamela', '1.1.0', { + 'checksums': ['d4b139fe600e192e176a2a368059207a6bffa0e7879879b13f4fcba0163481be'], + }), + ('greenlet', '2.0.2', { + 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('SQLAlchemy', '2.0.20', { + 'checksums': ['ca8a5ff2aa7f3ade6c498aaafce25b1eaeabe4e42b73e25519183e4566a16fc6'], + }), + ('alembic', '1.11.3', { + 'checksums': ['3db4ce81a9072e1b5aa44c2d202add24553182672a12daf21608d6f62a8f9cf9'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('pyOpenSSL', '23.2.0', { + 'modulename': 'OpenSSL', + 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], + }), + ('ruamel.yaml', '0.17.32', { + 'checksums': ['ec939063761914e14542972a5cba6d33c23b0859ab6342f61cf070cfc600efc2'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jupyter-telemetry', '0.1.0', { + 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', + 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], + }), + ('prometheus_client', '0.17.1', { + 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], + }), + ('jupyterhub', version, { + 'checksums': ['d4e450eed8d90dfbcf0eca08f00f2093a0bce74dc51f7cfc0b7057f602341a1d'], + }), + # Needs unreleased features for JupyterHub 4.X compatibility, hence install from commit + ('batchspawner', '1.2.0-%s' % local_batchspawner_commit, { + 'source_urls': [GITHUB_SOURCE], + 'sources': { + 'filename': '%(name)s-%(version)s.tar.gz', + 'download_filename': '%s.tar.gz' % local_batchspawner_commit + }, + 'checksums': ['d5cf239ba75522d928ed33971c180532f590131905c42eac1be2651ccad85283'], + }), + ('jupyterhub-systemdspawner', '1.0.1', { + 'modulename': 'systemdspawner', + 'checksums': ['8d614f19d89564321fe55d80ecd134a0e2bf276274d45861495c9bb5a80add28'], + }), + ('jupyterhub-simplespawner', '0.1', { + 'modulename': 'simplespawner', + 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], + }), + ('ldap3', '2.9.1', { + 'checksums': ['f3e7fc4718e3f09dda568b57100095e0ce58633bcabbed8667ce3f8fbaa4229f'], + }), + ('jupyterhub-ldapauthenticator', '1.3.2', { + 'modulename': 'ldapauthenticator', + 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('jupyterhub-jwtauthenticator-v2', '2.0.3', { + 'modulename': 'jwtauthenticator', + 'checksums': ['b94b6dff8246250904c5ee511da3f062680eb657dabe766d75993cbe72747d41'], + }), + ('onetimepass', '1.0.1', { + 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], + }), + ('bcrypt', '4.0.1', { + 'checksums': ['27d375903ac8261cfe4047f6709d16f7d18d39b1ec92aaf72af989552a650ebd'], + }), + ('jupyterhub-nativeauthenticator', '1.2.0', { + 'modulename': 'nativeauthenticator', + 'checksums': ['826228e6e9ca37736361e2e60c5723e245ec72e34fdc42cc218fc54a67f968e1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..19c7e8a6710 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '4.0.5' + +homepage = 'https://jupyter.org/' +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), +] + +# keep user's configuration in their home directory +# note: '~' is not expanded by JupyterLab +modluafooter = """ +setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) +setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) +""" +modtclfooter = """ +setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" +setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" +""" +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('json5', '0.9.14', { + 'checksums': ['9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02'], + }), + ('jupyterlab_server', '2.24.0', { + 'checksums': ['4e6f99e0a5579bbbc32e449c4dbb039561d4f1a7827d5733273ed56738f21f07'], + }), + ('jupyter-lsp', '2.2.0', { + 'checksums': ['8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1'], + }), + ('async-lru', '2.0.4', { + 'checksums': ['b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627'], + }), + ('jupyterlab', version, { + 'checksums': ['de49deb75f9b9aec478ed04754cbefe9c5d22fd796a5783cdc65e212983d3611'], + }), +] + +local_binaries = [ + 'jupyter-lab', + 'jupyter-labextension', + 'jupyter-labhub', +] +sanity_check_paths = { + 'files': [], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter lab --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8fb29542706 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonPackage' + +name = 'JupyterNotebook' +version = '7.0.2' + +homepage = 'https://jupyter.org/' +description = """The Jupyter Notebook is the original web application for creating and + sharing computational documents. It offers a simple, streamlined, document-centric experience.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/n/notebook'] +sources = ['notebook-%(version)s.tar.gz'] +checksums = ['d70d6a07418c829bd5f54337ce993b7105261d9026f9d3fe68e9b8aa1a20da9a'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), + ('JupyterLab', '4.0.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'notebook'} + +sanity_check_paths = { + 'files': ['bin/jupyter-notebook'], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter notebook --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5c1a64b9090 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server-proxy' +version = '4.0.0' + +homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' +description = """Jupyter Server Proxy lets you run arbitrary external processes +(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) +alongside your notebook server and provide authenticated web access to them +using a path like /rstudio next to others like /lab. Alongside the python +package that provides the main functionality, the JupyterLab extension +(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window +to get to RStudio for example.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.2'), + ('OpenSSL', '1.1', '', SYSTEM), + ('aiohttp', '3.8.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('simpervisor', '1.0.0', { + 'checksums': ['7eb87ca86d5e276976f5bb0290975a05d452c6a7b7f58062daea7d8369c823c1'], + }), + ('jupyter_server_proxy', version, { + 'checksums': ['f5dc12dd204baca71b013df3522c14403692a2d37cb7adcd77851dbab71533b5'], + }), +] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..76b36f7551f --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb @@ -0,0 +1,190 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = "2.7.2" + +homepage = 'https://jupyter.org/' +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST +endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and +Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.1.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('PyYAML', '6.0'), + ('PyZMQ', '25.1.1'), + ('tornado', '6.3.2'), +] + +sanity_pip_check = True +use_pip = True + +# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them +# use the versions published in a single release commit instead of blindly pushing to last available version, +# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa + +exts_list = [ + ('hatch_nodejs_version', '0.3.1', { + 'checksums': ['0e55fd713d92c5c1ccfee778efecaa780fd8bcd276d4ca7aff9f6791f6f76d9c'], + }), + ('hatch_jupyter_builder', '0.8.3', { + 'checksums': ['0dbd14a8aef6636764f88a8fd1fcc9a91921e5c50356e6aab251782f264ae960'], + }), + ('websocket-client', '1.6.1', { + 'modulename': 'websocket', + 'checksums': ['c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd'], + }), + ('terminado', '0.17.1', { + 'checksums': ['6ccbbcd3a4f8a25a5ec04991f39a0b8db52dfcd487ea0e578d977e6752380333'], + }), + ('Send2Trash', '1.8.2', { + 'checksums': ['c132d59fa44b9ca2b1699af5c86f57ce9f4c5eb56629d5d55fbb7a35f84e2312'], + }), + ('prometheus_client', '0.17.1', { + 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], + }), + ('overrides', '7.4.0', { + 'checksums': ['9502a3cca51f4fac40b5feca985b6703a5c1f6ad815588a7ca9e285b9dca6757'], + }), + ('jupyter_core', '5.3.1', { + 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], + }), + ('fastjsonschema', '2.18.0', { + 'checksums': ['e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd'], + }), + ('tinycss2', '1.2.1', { + 'checksums': ['8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627'], + }), + ('pandocfilters', '1.5.0', { + 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], + }), + ('mistune', '3.0.1', { + 'checksums': ['e912116c13aa0944f9dc530db38eb88f6a77087ab128f49f84a48f4c05ea163c'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter_packaging', '0.12.3', { + 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], + }), + ('jupyterlab_pygments', '0.2.2', { + 'checksums': ['7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d'], + }), + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('bleach', '6.0.0', { + 'checksums': ['1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('nbformat', '5.9.2', { + 'checksums': ['5f98b5ba1997dff175e77e0c17d5c10a96eaed2cbd1de3533d1fc35d5e111192'], + }), + ('nbclient', '0.8.0', { + 'checksums': ['f9b179cd4b2d7bca965f900a2ebf0db4a12ebff2f36a711cb66861e4ae158e55'], + }), + ('jupyter_client', '8.3.0', { + 'checksums': ['3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f'], + }), + ('nbconvert', '7.7.4', { + 'checksums': ['1113d039fa3fc3a846ffa5a3b0a019e85aaa94c566a09fa0c400fb7638e46087'], + }), + ('jupyter_server_terminals', '0.4.4', { + 'checksums': ['57ab779797c25a7ba68e97bcfb5d7740f2b5e8a83b5e8102b10438041a7eac5d'], + }), + ('rfc3986_validator', '0.1.1', { + 'checksums': ['3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055'], + }), + ('rfc3339_validator', '0.1.4', { + 'checksums': ['138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b'], + }), + ('rpds_py', '0.9.2', { + 'modulename': 'rpds', + 'checksums': ['8d70e8f14900f2657c249ea4def963bed86a29b81f81f5b76b5a9215680de945'], + }), + ('referencing', '0.30.2', { + 'checksums': ['794ad8003c65938edcdbc027f1933215e0d0ccc0291e3ce20a4d87432b59efc0'], + }), + ('python-json-logger', '2.0.7', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], + }), + ('jsonschema_specifications', '2023.7.1', { + 'checksums': ['c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb'], + }), + ('jsonschema', '4.18.0', { + 'checksums': ['8caf5b57a990a98e9b39832ef3cb35c176fe331414252b6e1b26fd5866f891a4'], + }), + ('jupyter_events', '0.7.0', { + 'checksums': ['7be27f54b8388c03eefea123a4f79247c5b9381c49fb1cd48615ee191eb12615'], + }), + ('argon2-cffi-bindings', '21.2.0', { + 'modulename': '_argon2_cffi_bindings', + 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], + }), + ('argon2_cffi', '23.1.0', { + 'modulename': 'argon2', + 'checksums': ['879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.7.1', { + 'checksums': ['44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780'], + }), + ('jupyter_server', version, { + 'checksums': ['d64fb4e593907290e5df916e3c9399c15ab2cd7bdb71cbcd1d36452dbfb30523'], + }), + ('jupyterlab_widgets', '3.0.8', { + 'checksums': ['d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a'], + }), + ('widgetsnbextension', '4.0.8', { + 'checksums': ['9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17'], + }), + ('comm', '0.1.4', { + 'checksums': ['354e40a59c9dd6db50c5cc6b4acc887d82e9603787f83b68c01a80a923984d15'], + }), + ('ipywidgets', '8.1.0', { + 'checksums': ['ce97dd90525b3066fd00094690964e7eac14cf9b7745d35565b5eeac20cce687'], + }), + # The following few extensions are needed for e.g. JupyterLab but also nbclassic. + # Avoid duplication by making it part of this bundle + ('notebook_shim', '0.2.3', { + 'checksums': ['f69388ac283ae008cd506dda10d0288b09a017d822d5e8c7129a152cbd3ce7e9'], + }), + ('nest_asyncio', '1.5.7', { + 'checksums': ['6a80f7b98f24d9083ed24608977c09dd608d83f91cccc24c9d2cba6d10e01c10'], + }), + ('ipykernel', '6.25.1', { + 'checksums': ['050391364c0977e768e354bdb60cbbfbee7cbb943b1af1618382021136ffd42f'], + }), + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('debugpy', '1.6.7.post1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['1093a5c541af079c13ac8c70ab8b24d1d35c8cacb676306cf11e57f699c02926'], + }), +] + +sanity_check_paths = { + 'files': ['bin/jupyter'], + 'dirs': ['share/jupyter', 'etc/jupyter'], +} + +sanity_check_commands = ['jupyter --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..ba066826463 --- /dev/null +++ b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonPackage' + +name = 'nbclassic' +version = "1.0.0" + +homepage = 'https://jupyter.org/' +description = """NbClassic provides a backwards compatible Jupyter Notebook interface + that you can install side-by-side with the latest versions: That way, you can fearlessly + upgrade without worrying about your classic extensions and customizations breaking.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.1.0'), +] +dependencies = [ + ('Python', '3.11.3'), + ('jupyter-server', '2.7.2'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['nbclassic-1.0.0_fix_setup_version.patch'] +checksums = [ + {'nbclassic-1.0.0.tar.gz': '0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'}, + {'nbclassic-1.0.0_fix_setup_version.patch': 'c26d91ac1d0cea2b361b2619076acdaf5fcd5ff2363d9e5f5e1bd737b4b50736'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +local_binaries = [ + 'jupyter-nbclassic', + 'jupyter-nbclassic-bundlerextension', + 'jupyter-nbclassic-extension', + 'jupyter-nbclassic-serverextension', +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +sanity_check_commands = ['jupyter nbclassic --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..19a3a61687c --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '25.1.1' + +homepage = 'https://www.zeromq.org/bindings:python' +description = "Python bindings for ZeroMQ" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['259c22485b71abacdfa8bf79720cd7bcf4b9d128b30ea554f01ae71fdbfdaa23'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('ZeroMQ', '4.3.4'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'zmq'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2e8cc5dfd61 --- /dev/null +++ b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'PycURL' +version = '7.45.2' + +homepage = 'http://pycurl.io/' +description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL + from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of + features.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5730590be0271364a5bddd9e245c9cc0fb710c4cbacbdd95264a3122d23224ca'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('cURL', '8.0.1'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From eeec1be2ae206f7fda5c07c66ef6b66203c82e24 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 7 Sep 2023 11:25:14 +0200 Subject: [PATCH 8719/9987] Delete easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb --- ...gurable-http-proxy-4.5.6-GCCcore-12.3.0.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb deleted file mode 100644 index fc58c50bc75..00000000000 --- a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.5.6-GCCcore-12.3.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'Binary' - -name = 'configurable-http-proxy' -version = '4.5.6' - -homepage = 'https://github.com/jupyterhub/configurable-http-proxy' -description = """HTTP proxy for node.js including a REST API for updating the routing table. - Developed as a part of the Jupyter Hub multi-user server.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = ['https://github.com/jupyterhub/%(name)s/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['4d9d94d0e6e44542ac973963b8a6545f4b40c0a2995e865ae9c80a2279e1e0ab'] - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('nodejs', '18.17.1'), -] - -install_cmd = "npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz" - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': [], -} - -sanity_check_commands = ['%(name)s --version'] - -moduleclass = 'tools' From 83cacf95e7f3a1e3c0cf88adc86ec66101557232 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 7 Sep 2023 11:25:30 +0200 Subject: [PATCH 8720/9987] Delete easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb --- .../JupyterHub-4.0.2-GCCcore-12.3.0.eb | 130 ------------------ 1 file changed, 130 deletions(-) delete mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb deleted file mode 100644 index 6e978bce869..00000000000 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,130 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'JupyterHub' -version = '4.0.2' - -homepage = 'https://jupyter.org' -description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed - for centralized deployments in companies, university classrooms and research labs.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('setuptools-rust', '1.6.0'), # Needed for bcrypt - ('Rust', '1.70.0'), # Needed for bcrypt -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('Mako', '1.2.4'), - ('configurable-http-proxy', '4.5.6'), - ('OpenSSL', '1.1', '', SYSTEM), - ('tornado', '6.3.2'), - ('PycURL', '7.45.2'), # optional, recommended with large number of users -] - -sanity_pip_check = True -use_pip = True - -local_batchspawner_commit = '2a9eda060a875a2b65ca9521368fe052a09c3266' - -exts_list = [ - ('certipy', '0.1.3', { - 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], - }), - ('pamela', '1.1.0', { - 'checksums': ['d4b139fe600e192e176a2a368059207a6bffa0e7879879b13f4fcba0163481be'], - }), - ('greenlet', '2.0.2', { - 'checksums': ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'], - }), - ('async_generator', '1.10', { - 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], - }), - ('SQLAlchemy', '2.0.20', { - 'checksums': ['ca8a5ff2aa7f3ade6c498aaafce25b1eaeabe4e42b73e25519183e4566a16fc6'], - }), - ('alembic', '1.11.3', { - 'checksums': ['3db4ce81a9072e1b5aa44c2d202add24553182672a12daf21608d6f62a8f9cf9'], - }), - ('oauthlib', '3.2.2', { - 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], - }), - ('pyOpenSSL', '23.2.0', { - 'modulename': 'OpenSSL', - 'checksums': ['276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac'], - }), - ('ruamel.yaml', '0.17.32', { - 'checksums': ['ec939063761914e14542972a5cba6d33c23b0859ab6342f61cf070cfc600efc2'], - }), - ('ruamel.yaml.clib', '0.2.7', { - 'modulename': False, - 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], - }), - ('python-json-logger', '2.0.7', { - 'modulename': 'pythonjsonlogger', - 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], - }), - ('jupyter-telemetry', '0.1.0', { - 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', - 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], - }), - ('prometheus_client', '0.17.1', { - 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], - }), - ('jupyterhub', version, { - 'checksums': ['d4e450eed8d90dfbcf0eca08f00f2093a0bce74dc51f7cfc0b7057f602341a1d'], - }), - # Needs unreleased features for JupyterHub 4.X compatibility, hence install from commit - ('batchspawner', '1.2.0-%s' % local_batchspawner_commit, { - 'source_urls': [GITHUB_SOURCE], - 'sources': { - 'filename': '%(name)s-%(version)s.tar.gz', - 'download_filename': '%s.tar.gz' % local_batchspawner_commit - }, - 'checksums': ['d5cf239ba75522d928ed33971c180532f590131905c42eac1be2651ccad85283'], - }), - ('jupyterhub-systemdspawner', '1.0.1', { - 'modulename': 'systemdspawner', - 'checksums': ['8d614f19d89564321fe55d80ecd134a0e2bf276274d45861495c9bb5a80add28'], - }), - ('jupyterhub-simplespawner', '0.1', { - 'modulename': 'simplespawner', - 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], - }), - ('ldap3', '2.9.1', { - 'checksums': ['f3e7fc4718e3f09dda568b57100095e0ce58633bcabbed8667ce3f8fbaa4229f'], - }), - ('jupyterhub-ldapauthenticator', '1.3.2', { - 'modulename': 'ldapauthenticator', - 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], - }), - ('PyJWT', '2.8.0', { - 'modulename': 'jwt', - 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], - }), - ('jupyterhub-jwtauthenticator-v2', '2.0.3', { - 'modulename': 'jwtauthenticator', - 'checksums': ['b94b6dff8246250904c5ee511da3f062680eb657dabe766d75993cbe72747d41'], - }), - ('onetimepass', '1.0.1', { - 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], - }), - ('bcrypt', '4.0.1', { - 'checksums': ['27d375903ac8261cfe4047f6709d16f7d18d39b1ec92aaf72af989552a650ebd'], - }), - ('jupyterhub-nativeauthenticator', '1.2.0', { - 'modulename': 'nativeauthenticator', - 'checksums': ['826228e6e9ca37736361e2e60c5723e245ec72e34fdc42cc218fc54a67f968e1'], - }), -] - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], -} - -sanity_check_commands = ['%(namelower)s --help'] - -moduleclass = 'tools' From 65697d036fd38658425754c575a3cff577568d49 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 7 Sep 2023 11:25:43 +0200 Subject: [PATCH 8721/9987] Delete easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb --- .../JupyterLab-4.0.5-GCCcore-12.3.0.eb | 73 ------------------- 1 file changed, 73 deletions(-) delete mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb deleted file mode 100644 index 19c7e8a6710..00000000000 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb +++ /dev/null @@ -1,73 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'JupyterLab' -version = '4.0.5' - -homepage = 'https://jupyter.org/' -description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar - building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, - etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter - Notebook.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('jupyter-server', '2.7.2'), -] - -# keep user's configuration in their home directory -# note: '~' is not expanded by JupyterLab -modluafooter = """ -setenv("JUPYTERLAB_SETTINGS_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "user-settings")) -setenv("JUPYTERLAB_WORKSPACES_DIR", pathJoin(os.getenv("HOME"), ".jupyter", "lab", "workspaces")) -""" -modtclfooter = """ -setenv JUPYTERLAB_SETTINGS_DIR "$::env(HOME)/.jupyter/lab/user-settings" -setenv JUPYTERLAB_WORKSPACES_DIR "$::env(HOME)/.jupyter/lab/workspaces" -""" -sanity_pip_check = True -use_pip = True - -exts_list = [ - ('json5', '0.9.14', { - 'checksums': ['9ed66c3a6ca3510a976a9ef9b8c0787de24802724ab1860bc0153c7fdd589b02'], - }), - ('jupyterlab_server', '2.24.0', { - 'checksums': ['4e6f99e0a5579bbbc32e449c4dbb039561d4f1a7827d5733273ed56738f21f07'], - }), - ('jupyter-lsp', '2.2.0', { - 'checksums': ['8ebbcb533adb41e5d635eb8fe82956b0aafbf0fd443b6c4bfa906edeeb8635a1'], - }), - ('async-lru', '2.0.4', { - 'checksums': ['b8a59a5df60805ff63220b2a0c5b5393da5521b113cd5465a44eb037d81a5627'], - }), - ('jupyterlab', version, { - 'checksums': ['de49deb75f9b9aec478ed04754cbefe9c5d22fd796a5783cdc65e212983d3611'], - }), -] - -local_binaries = [ - 'jupyter-lab', - 'jupyter-labextension', - 'jupyter-labhub', -] -sanity_check_paths = { - 'files': [], - 'dirs': ['etc/jupyter', 'share/jupyter'], -} - -sanity_check_commands = ['jupyter lab --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} - -moduleclass = 'tools' From 36660f4be761f97ae6ce7d91f293f14c92f86a32 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 7 Sep 2023 11:26:06 +0200 Subject: [PATCH 8722/9987] Delete easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb --- .../JupyterNotebook-7.0.2-GCCcore-12.3.0.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb deleted file mode 100644 index 8fb29542706..00000000000 --- a/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'JupyterNotebook' -version = '7.0.2' - -homepage = 'https://jupyter.org/' -description = """The Jupyter Notebook is the original web application for creating and - sharing computational documents. It offers a simple, streamlined, document-centric experience.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = ['https://pypi.python.org/packages/source/n/notebook'] -sources = ['notebook-%(version)s.tar.gz'] -checksums = ['d70d6a07418c829bd5f54337ce993b7105261d9026f9d3fe68e9b8aa1a20da9a'] - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('jupyter-server', '2.7.2'), - ('JupyterLab', '4.0.5'), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -options = {'modulename': 'notebook'} - -sanity_check_paths = { - 'files': ['bin/jupyter-notebook'], - 'dirs': ['etc/jupyter', 'share/jupyter'], -} - -sanity_check_commands = ['jupyter notebook --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From 76dcc7f1ae68b260538675c93d9c698acab4241c Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 7 Sep 2023 11:26:41 +0200 Subject: [PATCH 8723/9987] Delete easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb --- ...pyter-server-proxy-4.0.0-GCCcore-12.3.0.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb deleted file mode 100644 index 5c1a64b9090..00000000000 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'jupyter-server-proxy' -version = '4.0.0' - -homepage = 'https://github.com/jupyterhub/jupyter-server-proxy' -description = """Jupyter Server Proxy lets you run arbitrary external processes -(such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) -alongside your notebook server and provide authenticated web access to them -using a path like /rstudio next to others like /lab. Alongside the python -package that provides the main functionality, the JupyterLab extension -(@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window -to get to RStudio for example.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('jupyter-server', '2.7.2'), - ('OpenSSL', '1.1', '', SYSTEM), - ('aiohttp', '3.8.5'), -] - -sanity_pip_check = True -use_pip = True - -exts_list = [ - ('simpervisor', '1.0.0', { - 'checksums': ['7eb87ca86d5e276976f5bb0290975a05d452c6a7b7f58062daea7d8369c823c1'], - }), - ('jupyter_server_proxy', version, { - 'checksums': ['f5dc12dd204baca71b013df3522c14403692a2d37cb7adcd77851dbab71533b5'], - }), -] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From 955ecdc2fbedbd32f95e1f8e7f41d017d57588a9 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 7 Sep 2023 11:26:53 +0200 Subject: [PATCH 8724/9987] Delete easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb --- .../nbclassic-1.0.0-GCCcore-12.3.0.eb | 51 ------------------- 1 file changed, 51 deletions(-) delete mode 100644 easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb deleted file mode 100644 index ba066826463..00000000000 --- a/easybuild/easyconfigs/n/nbclassic/nbclassic-1.0.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,51 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'nbclassic' -version = "1.0.0" - -homepage = 'https://jupyter.org/' -description = """NbClassic provides a backwards compatible Jupyter Notebook interface - that you can install side-by-side with the latest versions: That way, you can fearlessly - upgrade without worrying about your classic extensions and customizations breaking.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('maturin', '1.1.0'), -] -dependencies = [ - ('Python', '3.11.3'), - ('jupyter-server', '2.7.2'), -] - -sources = [SOURCE_TAR_GZ] -patches = ['nbclassic-1.0.0_fix_setup_version.patch'] -checksums = [ - {'nbclassic-1.0.0.tar.gz': '0ae11eb2319455d805596bf320336cda9554b41d99ab9a3c31bf8180bffa30e3'}, - {'nbclassic-1.0.0_fix_setup_version.patch': 'c26d91ac1d0cea2b361b2619076acdaf5fcd5ff2363d9e5f5e1bd737b4b50736'}, -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -local_binaries = [ - 'jupyter-nbclassic', - 'jupyter-nbclassic-bundlerextension', - 'jupyter-nbclassic-extension', - 'jupyter-nbclassic-serverextension', -] -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_binaries], - 'dirs': [], -} - -sanity_check_commands = ['jupyter nbclassic --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From 0efcfd2611a7d27715f9565149b87434beeb6134 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 7 Sep 2023 11:27:03 +0200 Subject: [PATCH 8725/9987] Delete easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb --- .../p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb deleted file mode 100644 index 19a3a61687c..00000000000 --- a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.1-GCCcore-12.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'PyZMQ' -version = '25.1.1' - -homepage = 'https://www.zeromq.org/bindings:python' -description = "Python bindings for ZeroMQ" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['259c22485b71abacdfa8bf79720cd7bcf4b9d128b30ea554f01ae71fdbfdaa23'] - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), - ('ZeroMQ', '4.3.4'), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True -options = {'modulename': 'zmq'} - -moduleclass = 'devel' From 913d7400a30eed6ee233c3e6a76483a85ed43acd Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 7 Sep 2023 11:27:14 +0200 Subject: [PATCH 8726/9987] Delete easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb --- .../p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb deleted file mode 100644 index 2e8cc5dfd61..00000000000 --- a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. -easyblock = 'PythonPackage' - -name = 'PycURL' -version = '7.45.2' - -homepage = 'http://pycurl.io/' -description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL - from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of - features.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -sources = [SOURCELOWER_TAR_GZ] -checksums = ['5730590be0271364a5bddd9e245c9cc0fb710c4cbacbdd95264a3122d23224ca'] - -builddependencies = [ - ('binutils', '2.40'), -] -dependencies = [ - ('Python', '3.11.3'), - ('cURL', '8.0.1'), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -moduleclass = 'tools' From 59d943a7a843ecb1d273ec156c7db93cab82845b Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Thu, 7 Sep 2023 11:27:29 +0200 Subject: [PATCH 8727/9987] Delete easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb --- .../jupyter-server-2.7.2-GCCcore-12.3.0.eb | 190 ------------------ 1 file changed, 190 deletions(-) delete mode 100644 easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb deleted file mode 100644 index 76b36f7551f..00000000000 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,190 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'jupyter-server' -version = "2.7.2" - -homepage = 'https://jupyter.org/' -description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST -endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and -Voila.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('maturin', '1.1.0'), -] -dependencies = [ - ('Python', '3.11.3'), - ('IPython', '8.14.0'), - ('PyYAML', '6.0'), - ('PyZMQ', '25.1.1'), - ('tornado', '6.3.2'), -] - -sanity_pip_check = True -use_pip = True - -# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them -# use the versions published in a single release commit instead of blindly pushing to last available version, -# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/b728926f58ed3ffef08f716998ac6c226dafc1aa - -exts_list = [ - ('hatch_nodejs_version', '0.3.1', { - 'checksums': ['0e55fd713d92c5c1ccfee778efecaa780fd8bcd276d4ca7aff9f6791f6f76d9c'], - }), - ('hatch_jupyter_builder', '0.8.3', { - 'checksums': ['0dbd14a8aef6636764f88a8fd1fcc9a91921e5c50356e6aab251782f264ae960'], - }), - ('websocket-client', '1.6.1', { - 'modulename': 'websocket', - 'checksums': ['c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd'], - }), - ('terminado', '0.17.1', { - 'checksums': ['6ccbbcd3a4f8a25a5ec04991f39a0b8db52dfcd487ea0e578d977e6752380333'], - }), - ('Send2Trash', '1.8.2', { - 'checksums': ['c132d59fa44b9ca2b1699af5c86f57ce9f4c5eb56629d5d55fbb7a35f84e2312'], - }), - ('prometheus_client', '0.17.1', { - 'checksums': ['21e674f39831ae3f8acde238afd9a27a37d0d2fb5a28ea094f0ce25d2cbf2091'], - }), - ('overrides', '7.4.0', { - 'checksums': ['9502a3cca51f4fac40b5feca985b6703a5c1f6ad815588a7ca9e285b9dca6757'], - }), - ('jupyter_core', '5.3.1', { - 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], - }), - ('fastjsonschema', '2.18.0', { - 'checksums': ['e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd'], - }), - ('tinycss2', '1.2.1', { - 'checksums': ['8cff3a8f066c2ec677c06dbc7b45619804a6938478d9d73c284b29d14ecb0627'], - }), - ('pandocfilters', '1.5.0', { - 'checksums': ['0b679503337d233b4339a817bfc8c50064e2eff681314376a47cb582305a7a38'], - }), - ('mistune', '3.0.1', { - 'checksums': ['e912116c13aa0944f9dc530db38eb88f6a77087ab128f49f84a48f4c05ea163c'], - }), - ('deprecation', '2.1.0', { - 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], - }), - ('jupyter_packaging', '0.12.3', { - 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], - }), - ('jupyterlab_pygments', '0.2.2', { - 'checksums': ['7405d7fde60819d905a9fa8ce89e4cd830e318cdad22a0030f7a901da705585d'], - }), - ('defusedxml', '0.7.1', { - 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], - }), - ('bleach', '6.0.0', { - 'checksums': ['1a1a85c1595e07d8db14c5f09f09e6433502c51c595970edc090551f0db99414'], - }), - ('arrow', '1.2.3', { - 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], - }), - ('nbformat', '5.9.2', { - 'checksums': ['5f98b5ba1997dff175e77e0c17d5c10a96eaed2cbd1de3533d1fc35d5e111192'], - }), - ('nbclient', '0.8.0', { - 'checksums': ['f9b179cd4b2d7bca965f900a2ebf0db4a12ebff2f36a711cb66861e4ae158e55'], - }), - ('jupyter_client', '8.3.0', { - 'checksums': ['3af69921fe99617be1670399a0b857ad67275eefcfa291e2c81a160b7b650f5f'], - }), - ('nbconvert', '7.7.4', { - 'checksums': ['1113d039fa3fc3a846ffa5a3b0a019e85aaa94c566a09fa0c400fb7638e46087'], - }), - ('jupyter_server_terminals', '0.4.4', { - 'checksums': ['57ab779797c25a7ba68e97bcfb5d7740f2b5e8a83b5e8102b10438041a7eac5d'], - }), - ('rfc3986_validator', '0.1.1', { - 'checksums': ['3d44bde7921b3b9ec3ae4e3adca370438eccebc676456449b145d533b240d055'], - }), - ('rfc3339_validator', '0.1.4', { - 'checksums': ['138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b'], - }), - ('rpds_py', '0.9.2', { - 'modulename': 'rpds', - 'checksums': ['8d70e8f14900f2657c249ea4def963bed86a29b81f81f5b76b5a9215680de945'], - }), - ('referencing', '0.30.2', { - 'checksums': ['794ad8003c65938edcdbc027f1933215e0d0ccc0291e3ce20a4d87432b59efc0'], - }), - ('python-json-logger', '2.0.7', { - 'modulename': 'pythonjsonlogger', - 'checksums': ['23e7ec02d34237c5aa1e29a070193a4ea87583bb4e7f8fd06d3de8264c4b2e1c'], - }), - ('jsonschema_specifications', '2023.7.1', { - 'checksums': ['c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb'], - }), - ('jsonschema', '4.18.0', { - 'checksums': ['8caf5b57a990a98e9b39832ef3cb35c176fe331414252b6e1b26fd5866f891a4'], - }), - ('jupyter_events', '0.7.0', { - 'checksums': ['7be27f54b8388c03eefea123a4f79247c5b9381c49fb1cd48615ee191eb12615'], - }), - ('argon2-cffi-bindings', '21.2.0', { - 'modulename': '_argon2_cffi_bindings', - 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], - }), - ('argon2_cffi', '23.1.0', { - 'modulename': 'argon2', - 'checksums': ['879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08'], - }), - ('sniffio', '1.3.0', { - 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], - }), - ('anyio', '3.7.1', { - 'checksums': ['44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780'], - }), - ('jupyter_server', version, { - 'checksums': ['d64fb4e593907290e5df916e3c9399c15ab2cd7bdb71cbcd1d36452dbfb30523'], - }), - ('jupyterlab_widgets', '3.0.8', { - 'checksums': ['d428ab97b8d87cc7c54cbf37644d6e0f0e662f23876e05fa460a73ec3257252a'], - }), - ('widgetsnbextension', '4.0.8', { - 'checksums': ['9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17'], - }), - ('comm', '0.1.4', { - 'checksums': ['354e40a59c9dd6db50c5cc6b4acc887d82e9603787f83b68c01a80a923984d15'], - }), - ('ipywidgets', '8.1.0', { - 'checksums': ['ce97dd90525b3066fd00094690964e7eac14cf9b7745d35565b5eeac20cce687'], - }), - # The following few extensions are needed for e.g. JupyterLab but also nbclassic. - # Avoid duplication by making it part of this bundle - ('notebook_shim', '0.2.3', { - 'checksums': ['f69388ac283ae008cd506dda10d0288b09a017d822d5e8c7129a152cbd3ce7e9'], - }), - ('nest_asyncio', '1.5.7', { - 'checksums': ['6a80f7b98f24d9083ed24608977c09dd608d83f91cccc24c9d2cba6d10e01c10'], - }), - ('ipykernel', '6.25.1', { - 'checksums': ['050391364c0977e768e354bdb60cbbfbee7cbb943b1af1618382021136ffd42f'], - }), - ('ipython_genutils', '0.2.0', { - 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], - }), - ('debugpy', '1.6.7.post1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', - 'checksums': ['1093a5c541af079c13ac8c70ab8b24d1d35c8cacb676306cf11e57f699c02926'], - }), -] - -sanity_check_paths = { - 'files': ['bin/jupyter'], - 'dirs': ['share/jupyter', 'etc/jupyter'], -} - -sanity_check_commands = ['jupyter --help'] - -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} - -moduleclass = 'tools' From ed437a76af5e5fae9c4ec367f249e0b886dffe14 Mon Sep 17 00:00:00 2001 From: chris g Date: Thu, 7 Sep 2023 11:18:04 +0100 Subject: [PATCH 8728/9987] adding sglib dependency --- .../s/spglib/spglib-2.0.2-GCCcore-12.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e7a343abb37 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +# with thanks to akesandgren for the easyconfig for 2022a +# updated for 2022b by BEAR Software team at University of Birmingham + +easyblock = 'CMakeMake' + +name = 'spglib' +version = '2.0.2' + +homepage = 'https://spglib.github.io/spglib/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/spglib/spglib/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['10e44a35099a0a5d0fc6ee0cdb39d472c23cb98b1f5167c0e2b08f6069f3db1e'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +postinstallcmds = ["cd %(installdir)s/include && mkdir spglib && ln -s ../spglib.h spglib/"] + +sanity_check_paths = { + 'files': [ + 'include/spglib.h', + 'lib/libsymspg.a', + 'lib/libsymspg.%s' % SHLIB_EXT + ], + 'dirs': [], +} + +moduleclass = 'chem' From 3f05e39f63289bbc3d019f7982fa9ab1c14b1d22 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Sep 2023 12:23:37 +0200 Subject: [PATCH 8729/9987] adding easyconfigs: JupyterNotebook-7.0.3-GCCcore-12.2.0.eb --- .../JupyterNotebook-7.0.3-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2202fae1e72 --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.3-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonPackage' + +name = 'JupyterNotebook' +version = '7.0.3' + +homepage = 'https://jupyter.org/' +description = """The Jupyter Notebook is the original web application for creating and + sharing computational documents. It offers a simple, streamlined, document-centric experience.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/n/notebook'] +sources = ['notebook-%(version)s.tar.gz'] +checksums = ['07f3c5062fd0e6e69864437a0347abc485d991aae87a92c47d659699f571b729'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('Python', '3.10.8'), + ('IPython', '8.14.0'), + ('jupyter-server', '2.7.0'), + ('JupyterLab', '4.0.3'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'notebook'} + +sanity_check_paths = { + 'files': ['bin/jupyter-notebook'], + 'dirs': ['etc/jupyter', 'share/jupyter'], +} + +sanity_check_commands = ['jupyter notebook --help'] + +modextrapaths = { + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', + 'JUPYTER_PATH': 'share/jupyter', +} + +moduleclass = 'tools' From b9fae4d782b9179f84189ff81e3921752a5d22e8 Mon Sep 17 00:00:00 2001 From: chris g Date: Thu, 7 Sep 2023 11:27:04 +0100 Subject: [PATCH 8730/9987] fixing ALAMODE ec permissions --- easybuild/easyconfigs/a/ALAMODE/ALAMODE-1.4.2-foss-2022b.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/a/ALAMODE/ALAMODE-1.4.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/a/ALAMODE/ALAMODE-1.4.2-foss-2022b.eb b/easybuild/easyconfigs/a/ALAMODE/ALAMODE-1.4.2-foss-2022b.eb old mode 100755 new mode 100644 From c9664f5b0fd3d858dd3ce6401b9ef7fc189bdbc1 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 7 Sep 2023 13:07:26 +0100 Subject: [PATCH 8731/9987] Remove blank line at EOF --- .../j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb index 0053b89cf41..d04c92c0cf8 100644 --- a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb @@ -22,4 +22,3 @@ dependencies = [ ('jupyterlmod', '4.0.3'), ('jupyter-resource-usage', '1.0.0'), ] - From 67f4a4e2d9154bd9613b75e28ea943fbd3888897 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Thu, 7 Sep 2023 16:30:42 +0200 Subject: [PATCH 8732/9987] fix build opts Co-authored-by: Sam Moors --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 23b336d4655..4ddb6b96e83 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -29,7 +29,7 @@ sources = [{ checksums = ['5c4cd3c0a1d141a1b85936fee3fa52f7638774c2146b138aa9ae218d3da4b89d'] prebuildopts = "stack setup && stack build && " -buildopts = "make install-bins BUILDER=stack PREFIX=%(builddir)s" +buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" files_to_copy = [ (['git-annex', 'git-annex-shell'], 'bin'), From 86170723f013ad864f44652c2ebf008923c6b16e Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 7 Sep 2023 16:41:49 +0200 Subject: [PATCH 8733/9987] Update CFITSIO-4.3.0-GCCcore-12.3.0.eb It's the same patch as before --- .../easyconfigs/c/CFITSIO/CFITSIO-4.3.0-GCCcore-12.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.0-GCCcore-12.3.0.eb index 164f73275f6..c8a01a36a48 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.0-GCCcore-12.3.0.eb @@ -13,10 +13,10 @@ toolchainopts = {'pic': True} source_urls = ['http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = ['%%(namelower)s-%s.tar.gz' % version] -patches = ['CFITSIO-4.0.0_install_test_data.patch'] +patches = ['CFITSIO-3.48_install_test_data.patch'] checksums = [ {'cfitsio-4.3.0.tar.gz': 'fdadc01d09cf9f54253802c5ec87eb10de51ce4130411415ae88c30940621b8b'}, - {'CFITSIO-4.0.0_install_test_data.patch': '75559db8b0648bc90ea9bb81a74acfd89913236ee0a2daf533477cddd37ea8a6'}, + {'CFITSIO-3.48_install_test_data.patch': 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c'}, ] dependencies = [('cURL', '8.0.1')] From 13e24d1cd69e4c12d271d266697c4b1ec7ab5446 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 7 Sep 2023 15:17:33 +0000 Subject: [PATCH 8734/9987] added checksum with eb inject --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 4ddb6b96e83..12f5d00fcc8 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -26,7 +26,7 @@ sources = [{ 'filename': '%(name)s-%(version)s.tar.gz', }] -checksums = ['5c4cd3c0a1d141a1b85936fee3fa52f7638774c2146b138aa9ae218d3da4b89d'] +checksums = ['62e4b4d9ef5ecf587a854a761927b1dbf4d646a0b8570e594ff48e3dac3719b5'] prebuildopts = "stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" From f71065d202bc085d11f0e513d1c9994575ec2b9e Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Thu, 7 Sep 2023 17:24:12 +0200 Subject: [PATCH 8735/9987] None checksums Co-authored-by: Sam Moors --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index 12f5d00fcc8..e5c29a0e6bb 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -26,7 +26,7 @@ sources = [{ 'filename': '%(name)s-%(version)s.tar.gz', }] -checksums = ['62e4b4d9ef5ecf587a854a761927b1dbf4d646a0b8570e594ff48e3dac3719b5'] +checksums = [None] prebuildopts = "stack setup && stack build && " buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" From 1b98d0f72fa39b82e4e49aaf4e121542ff30aee8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Sep 2023 18:01:28 +0200 Subject: [PATCH 8736/9987] make sure that 'moduleclass' is set in all easyconfig files (and is not set to default 'base' moduleclass) --- test/easyconfigs/easyconfigs.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index b3142f30505..d72f4a7194c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1315,6 +1315,9 @@ def template_easyconfig_test(self, spec): # sanity check for software name, moduleclass self.assertEqual(ec['name'], name) self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) + # base is the default value for moduleclass, which should never be used, + # and moduleclass should always be set in the easyconfig file + self.assertNotEqual(ec['moduleclass'], 'base') # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) From bc024ad4762c2e588337e6339b9a647801214b1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Sep 2023 18:24:10 +0200 Subject: [PATCH 8737/9987] fix moduleclass for gdbm --- easybuild/easyconfigs/g/gdbm/gdbm-1.18.1-foss-2020a.eb | 2 +- easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gdbm/gdbm-1.18.1-foss-2020a.eb b/easybuild/easyconfigs/g/gdbm/gdbm-1.18.1-foss-2020a.eb index 98da9e05090..51a867d5e32 100644 --- a/easybuild/easyconfigs/g/gdbm/gdbm-1.18.1-foss-2020a.eb +++ b/easybuild/easyconfigs/g/gdbm/gdbm-1.18.1-foss-2020a.eb @@ -26,4 +26,4 @@ sanity_check_paths = { sanity_check_commands = ['gdbmtool --help'] -moduleclass = 'base' +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb index b28c2fd68d0..9072dc51ea2 100644 --- a/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gdbm/gdbm-1.21-GCCcore-10.2.0.eb @@ -28,4 +28,4 @@ sanity_check_paths = { 'dirs': ['share/man'] } -moduleclass = "lib" +moduleclass = 'lib' From 7eb877de78836300f9dceeede92c4e30c1d03f4c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Sep 2023 18:24:50 +0200 Subject: [PATCH 8738/9987] add missing moduleclass for CCfits, humann, and Python-2.7.18-GCCcore-12.3.0.eb easyconfigs --- easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb | 2 ++ easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb | 7 ++----- .../easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb | 2 ++ 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb index 2ee97a09780..4fabd5ab15b 100644 --- a/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb @@ -25,3 +25,5 @@ sanity_check_paths = { 'files': ['lib/libCCfits.%s' % SHLIB_EXT], 'dirs': ['include/CCfits'], } + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb b/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb index 1e8577eb47d..b87c313ff3c 100644 --- a/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb +++ b/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb @@ -1,11 +1,9 @@ -# Humann easyblock = 'PythonBundle' name = 'humann' version = '3.6' homepage = 'http://huttenhower.sph.harvard.edu/humann' - description = """HUMAnN v3 is a pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data. @@ -18,13 +16,11 @@ Sequencing a metagenome typically produces millions toolchain = {'name': 'foss', 'version': '2022a'} - dependencies = { ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), } - exts_list = [ (name, version, { 'checksums': ['addce81db58bacfdd5465423455d25e385aa8dd14349253c3a7054bf7d3747dc'], @@ -32,6 +28,7 @@ exts_list = [ ] - use_pip = True sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb index 8ea8866c3e6..23b38544c6c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.3.0.eb @@ -51,3 +51,5 @@ exts_list = [ 'checksums': ['6773934e5f5fc3eaa8c5a44949b5b924fc122daa0a8aa9f80c835b4ca2a543fc'], }), ] + +moduleclass = 'lang' From 4563c7004c94426577ed4aa5b73773e0d6871285 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 7 Sep 2023 18:44:20 +0200 Subject: [PATCH 8739/9987] adding easyconfigs: tcsh-6.24.10-GCCcore-12.3.0.eb --- .../t/tcsh/tcsh-6.24.10-GCCcore-12.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.24.10-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.10-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..40df0dc535f --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.10-GCCcore-12.3.0.eb @@ -0,0 +1,48 @@ +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +# # +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.24.10' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['13475c0fbeb74139d33ed793bf00ffbbb2ac2dc9fb1d44467a410760aba36664'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('ncurses', '6.4'), +] + +postinstallcmds = ['ln -s %(name)s %(installdir)s/bin/csh'] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/csh'], + 'dirs': [], +} + +moduleclass = 'tools' From a48cb1a7fdb318b8e708ac2218f9704feab01598 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Thu, 7 Sep 2023 18:55:15 +0200 Subject: [PATCH 8740/9987] Added moduleclass, added extra sanity_check_path --- .../Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb | 2 ++ .../jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb | 5 ++++- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb index d04c92c0cf8..a524ccf341d 100644 --- a/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/Jupyter-bundle/Jupyter-bundle-20230823-GCCcore-12.3.0.eb @@ -22,3 +22,5 @@ dependencies = [ ('jupyterlmod', '4.0.3'), ('jupyter-resource-usage', '1.0.0'), ] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb index 104f59c8f5d..02d3f79c0cb 100644 --- a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb @@ -28,7 +28,10 @@ exts_list = [ sanity_check_paths = { 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyter_resource_usage'], + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/jupyter_resource_usage', + 'share/jupyter' + ], } # Add the notebook extension to the search path for jupyter notebooks From bf791791cae84d4d68458e79efad717eea5007ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Sep 2023 19:00:08 +0200 Subject: [PATCH 8741/9987] improve error message when moduleclass check fails Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d72f4a7194c..4d278ff8f5d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1317,7 +1317,7 @@ def template_easyconfig_test(self, spec): self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) # base is the default value for moduleclass, which should never be used, # and moduleclass should always be set in the easyconfig file - self.assertNotEqual(ec['moduleclass'], 'base') + self.assertNotEqual(ec['moduleclass'], 'base', "moduleclass should be set, and not be set to 'base', for %s", spec) # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) From 7773067183d5024a5c84ad95d4da24d74021cbe3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 7 Sep 2023 19:00:48 +0200 Subject: [PATCH 8742/9987] fix indent for moduleclass check --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 4d278ff8f5d..a63763d8602 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1317,7 +1317,7 @@ def template_easyconfig_test(self, spec): self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) # base is the default value for moduleclass, which should never be used, # and moduleclass should always be set in the easyconfig file - self.assertNotEqual(ec['moduleclass'], 'base', "moduleclass should be set, and not be set to 'base', for %s", spec) + self.assertNotEqual(ec['moduleclass'], 'base', "moduleclass should be set, and not be set to 'base', for %s", spec) # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) From 7d9cff98a478091eea2603575f7fa7334b3aed58 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 7 Sep 2023 18:35:04 +0100 Subject: [PATCH 8743/9987] % not , --- test/easyconfigs/easyconfigs.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index a63763d8602..173222cedb3 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1317,7 +1317,8 @@ def template_easyconfig_test(self, spec): self.assertTrue(ec['moduleclass'] in build_option('valid_module_classes')) # base is the default value for moduleclass, which should never be used, # and moduleclass should always be set in the easyconfig file - self.assertNotEqual(ec['moduleclass'], 'base', "moduleclass should be set, and not be set to 'base', for %s", spec) + self.assertNotEqual(ec['moduleclass'], 'base', + "moduleclass should be set, and not be set to 'base', for %s" % spec) # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) From 3f12f1f51b947f2a2dc2db57f06531c297448881 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Thu, 7 Sep 2023 20:56:51 +0200 Subject: [PATCH 8744/9987] SWIG dependency --- easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb index 18ca94a238a..8de1a91aefa 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb @@ -57,6 +57,7 @@ dependencies = [ ('Qhull', '2020.2'), ('LERC', '4.0.0'), ('OpenJPEG', '2.5.0'), + ('SWIG', '4.1.1'), ] # iterative build for both static and shared libraries From 81dceb55e4f18e7a80684fdbbdf864f4a79842af Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 8 Sep 2023 10:17:01 +0200 Subject: [PATCH 8745/9987] adding easyconfigs: BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb --- .../BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/b/BgeeDB/BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/b/BgeeDB/BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/b/BgeeDB/BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..58b184b3aeb --- /dev/null +++ b/easybuild/easyconfigs/b/BgeeDB/BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb @@ -0,0 +1,66 @@ +easyblock = 'Bundle' + +name = 'BgeeDB' +version = '2.26.0' +versionsuffix = '-R-%(rver)s' + +# This library does not need last Bioconductor dependencies +# but better to have its last version from the last Bioconductor version +local_bioc_version = 3.17 + +homepage = 'https://github.com/BgeeDB/BgeeDB_R' +description = """Annotation and gene expression data retrieval from Bgee database. +TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology.""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('R', '4.1.0'), +] + +dependencies = [ + ('R-bundle-Bioconductor', '3.13', versionsuffix), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/%(local_bioc_version)s/bioc/src/contrib/', + 'https://bioconductor.org/packages/%(local_bioc_version)s/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/%(local_bioc_version)s/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/%(local_bioc_version)s/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('topGO', '2.52.0', { + 'checksums': ['c29815ef354c605ad01a856ba61e8bfa6063b0245f6e621187f8a001e396722b'], + }), + (name, version, { + 'checksums': ['f0127b77c305ac0930fb412b5e18ea79f24acd5e242e058d77b4c5add609dbe8'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From ca18c660ee70c366a2d702c6b3b5572341cd428e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Sep 2023 09:51:05 +0100 Subject: [PATCH 8746/9987] adding easyconfigs: motif-2.3.8-GCCcore-12.2.0.eb --- .../m/motif/motif-2.3.8-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..3fc49caf368 --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.8' + +homepage = 'https://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] + +builddependencies = [ + ('Autotools', '20220317'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('binutils', '2.39'), + ('util-linux', '2.38.1'), +] + +dependencies = [ + ('X11', '20221110'), + ('libpng', '1.6.38'), + ('freetype', '2.12.1'), + ('libjpeg-turbo', '2.1.4'), + ('bzip2', '1.0.8'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' From fb06344674b6ad04a7ffafd7830e5d2e535b11d3 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 8 Sep 2023 11:07:37 +0100 Subject: [PATCH 8747/9987] adding easyconfigs: DL_POLY_4-5.1.0-foss-2022b.eb, DL_POLY_4-5.1.0-intel-2022b.eb --- .../d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2022b.eb | 20 +++++++++++++++++++ .../DL_POLY_4/DL_POLY_4-5.1.0-intel-2022b.eb | 20 +++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-intel-2022b.eb diff --git a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2022b.eb b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2022b.eb new file mode 100644 index 00000000000..9651ab16abc --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-foss-2022b.eb @@ -0,0 +1,20 @@ +easyblock = 'CMakeMake' +name = "DL_POLY_4" +version = "5.1.0" +homepage = "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx" +description = "DL_POLY is a general purpose classical molecular dynamics (MD) simulation software" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://gitlab.com/ccp5/dl-poly/-/archive/%(version)s/'] +sources = ['dl_poly_%(version)s.tar.bz2'] +checksums = ['da5364986cd71e047e080753f6ca75135bf19bd5607770b839dea3734c2fdfaa'] + +builddependencies = [('CMake', '3.24.3')] + +sanity_check_paths = { + 'files': ['bin/DLPOLY.Z'], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-intel-2022b.eb b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-intel-2022b.eb new file mode 100644 index 00000000000..b48df994884 --- /dev/null +++ b/easybuild/easyconfigs/d/DL_POLY_4/DL_POLY_4-5.1.0-intel-2022b.eb @@ -0,0 +1,20 @@ +easyblock = 'CMakeMake' +name = "DL_POLY_4" +version = "5.1.0" +homepage = "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx" +description = "DL_POLY is a general purpose classical molecular dynamics (MD) simulation software" + +toolchain = {'name': 'intel', 'version': '2022b'} + +source_urls = ['https://gitlab.com/ccp5/dl-poly/-/archive/%(version)s/'] +sources = ['dl_poly_%(version)s.tar.bz2'] +checksums = ['da5364986cd71e047e080753f6ca75135bf19bd5607770b839dea3734c2fdfaa'] + +builddependencies = [('CMake', '3.24.3')] + +sanity_check_paths = { + 'files': ['bin/DLPOLY.Z'], + 'dirs': [] +} + +moduleclass = 'chem' From beea2f2c3236b3e0ace3977cf6f59bccd4c2757d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Sep 2023 12:27:09 +0200 Subject: [PATCH 8748/9987] add patch for MPFR 4.1.0 to fix failing tsprintf test with glibc >= 2.37 --- .../m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb | 6 +- .../m/MPFR/MPFR-4.1.0-GCCcore-10.3.0.eb | 6 +- .../m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb | 6 +- .../m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb | 6 +- .../MPFR-4.1.0_patch-fix-tsprintf-test.patch | 73 +++++++++++++++++++ 5 files changed, 93 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-4.1.0_patch-fix-tsprintf-test.patch diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb index 07cac7df6c8..bedc68d8e8b 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'] +patches = ['MPFR-4.1.0_patch-fix-tsprintf-test.patch'] +checksums = [ + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '51bdcb5ba5365f0a3b4be3ddf2af4c08ce05dfcd02478ad11e75f4fea40503eb'}, +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.3.0.eb index 11af3a6a733..834b5d5ca2a 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.3.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'] +patches = ['MPFR-4.1.0_patch-fix-tsprintf-test.patch'] +checksums = [ + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '51bdcb5ba5365f0a3b4be3ddf2af4c08ce05dfcd02478ad11e75f4fea40503eb'}, +] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb index cf964266691..da0099f70d7 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'] +patches = ['MPFR-4.1.0_patch-fix-tsprintf-test.patch'] +checksums = [ + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '51bdcb5ba5365f0a3b4be3ddf2af4c08ce05dfcd02478ad11e75f4fea40503eb'}, +] builddependencies = [ ('binutils', '2.37'), diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb index 7d929a2fd1b..62647e55702 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'] +patches = ['MPFR-4.1.0_patch-fix-tsprintf-test.patch'] +checksums = [ + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '51bdcb5ba5365f0a3b4be3ddf2af4c08ce05dfcd02478ad11e75f4fea40503eb'}, +] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0_patch-fix-tsprintf-test.patch b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0_patch-fix-tsprintf-test.patch new file mode 100644 index 00000000000..b3644944a42 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0_patch-fix-tsprintf-test.patch @@ -0,0 +1,73 @@ +A test of the thousands separator in tsprintf.c is based on the output from the GNU C Library up to 2.36, +which is incorrect (https://sourceware.org/bugzilla/show_bug.cgi?id=23432). +The output has changed in 2.37 (partly fixed), so that tsprintf fails with glibc 2.37. +The tsprintf-thousands patch (https://www.mpfr.org/mpfr-4.2.0/patch01) modifies the test to conform to POSIX +and also avoid the buggy case in 2.36 and below. However, this new test, which was expected to succeed, +triggers a serious bug in 2.37 (bug 30068 / CVE-2023-25139 - https://sourceware.org/bugzilla/show_bug.cgi?id=30068). +We did not modify the test again since this bug affects MPFR's mpfr_sprintf function, with a possible buffer overflow +in particular cases. This bug has been fixed in the 2.37 branch. +In short, this patch is useful (and needed) for a fixed glibc 2.37 and some other libraries, depending on the current locales. + +diff -Naurd mpfr-4.2.0-a/PATCHES mpfr-4.2.0-b/PATCHES +--- mpfr-4.2.0-a/PATCHES 2023-04-17 21:17:39.748645280 +0000 ++++ mpfr-4.2.0-b/PATCHES 2023-04-17 21:17:39.792645218 +0000 +@@ -0,0 +1 @@ ++tsprintf-thousands +diff -Naurd mpfr-4.2.0-a/VERSION mpfr-4.2.0-b/VERSION +--- mpfr-4.2.0-a/VERSION 2023-01-06 10:55:57.000000000 +0000 ++++ mpfr-4.2.0-b/VERSION 2023-04-17 21:17:39.792645218 +0000 +@@ -1 +1 @@ +-4.2.0 ++4.2.0-p1 +diff -Naurd mpfr-4.2.0-a/src/mpfr.h mpfr-4.2.0-b/src/mpfr.h +--- mpfr-4.2.0-a/src/mpfr.h 2023-01-06 10:55:57.000000000 +0000 ++++ mpfr-4.2.0-b/src/mpfr.h 2023-04-17 21:17:39.788645224 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 4 + #define MPFR_VERSION_MINOR 2 + #define MPFR_VERSION_PATCHLEVEL 0 +-#define MPFR_VERSION_STRING "4.2.0" ++#define MPFR_VERSION_STRING "4.2.0-p1" + + /* User macros: + MPFR_USE_FILE: Define it to make MPFR define functions dealing +diff -Naurd mpfr-4.2.0-a/src/version.c mpfr-4.2.0-b/src/version.c +--- mpfr-4.2.0-a/src/version.c 2023-01-06 10:55:57.000000000 +0000 ++++ mpfr-4.2.0-b/src/version.c 2023-04-17 21:17:39.792645218 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "4.2.0"; ++ return "4.2.0-p1"; + } +diff -Naurd mpfr-4.2.0-a/tests/tsprintf.c mpfr-4.2.0-b/tests/tsprintf.c +--- mpfr-4.2.0-a/tests/tsprintf.c 2023-01-05 17:09:48.000000000 +0000 ++++ mpfr-4.2.0-b/tests/tsprintf.c 2023-04-17 21:17:39.784645229 +0000 +@@ -1715,7 +1715,25 @@ + check_sprintf ("000000001,000", "%'013.4Rg", x); + + #ifdef PRINTF_GROUPFLAG +- check_vsprintf ("+01,234,567 :", "%0+ -'13.10Pd:", (mpfr_prec_t) 1234567); ++ /* Do not test the thousands separator with a precision field larger ++ than the number of digits (thus needing leading zeros), such as ++ "%0+ -'13.10Pd:" (used up to MPFR 4.2.0), since the GNU libc is ++ buggy: https://sourceware.org/bugzilla/show_bug.cgi?id=23432 ++ We don't know about the other implementations. ++ This new test works fine with glibc up to 2.36, but fails with 2.37 ++ (as reported by Klaus Dittrich in the MPFR mailing-list); this is ++ actually a bug introduced in glibc 2.37, not in MPFR: ++ https://sourceware.org/bugzilla/show_bug.cgi?id=30068 ++ Since this bug can yield a buffer overflow (CVE-2023-25139), possibly ++ affecting MPFR users, let us rather require a fix in glibc. This bug ++ has been fixed in the 2.37 branch: ++ https://sourceware.org/git/?p=glibc.git;a=commit;h=07b9521fc6 ++ If we wanted to check that and avoid a failure of the test because of ++ a buggy C library (while MPFR would be consistent with the C library), ++ we could compare the MPFR output with both the correct output and the ++ output from the C library (possibly buggy). But to do that in a clean ++ way, this would require a change in the check_vsprintf() call. */ ++ check_vsprintf ("+1,234,567 :", "%0+ -'13Pd:", (mpfr_prec_t) 1234567); + #endif + + mpfr_clear (x); From a36f695b5d2d5baf151d5a0f49deb4aa0ad5b3ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 8 Sep 2023 12:32:31 +0200 Subject: [PATCH 8749/9987] fix patch for MFPR 4.1.0 to fix broken tsprint test on glibc >= 2.37 --- .../m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb | 2 +- .../m/MPFR/MPFR-4.1.0-GCCcore-10.3.0.eb | 2 +- .../m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb | 2 +- .../m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb | 2 +- .../MPFR-4.1.0_patch-fix-tsprintf-test.patch | 42 ++++--------------- 5 files changed, 11 insertions(+), 39 deletions(-) diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb index bedc68d8e8b..b43fbb0dc58 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.2.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = ['MPFR-4.1.0_patch-fix-tsprintf-test.patch'] checksums = [ {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, - {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '51bdcb5ba5365f0a3b4be3ddf2af4c08ce05dfcd02478ad11e75f4fea40503eb'}, + {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '039fad7a79ec4a9fd9ce77c9a73d9278187b8430087bc1afec18883df40321ae'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.3.0.eb index 834b5d5ca2a..b00a310b06a 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-10.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = ['MPFR-4.1.0_patch-fix-tsprintf-test.patch'] checksums = [ {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, - {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '51bdcb5ba5365f0a3b4be3ddf2af4c08ce05dfcd02478ad11e75f4fea40503eb'}, + {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '039fad7a79ec4a9fd9ce77c9a73d9278187b8430087bc1afec18883df40321ae'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb index da0099f70d7..368bde273e8 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.2.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = ['MPFR-4.1.0_patch-fix-tsprintf-test.patch'] checksums = [ {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, - {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '51bdcb5ba5365f0a3b4be3ddf2af4c08ce05dfcd02478ad11e75f4fea40503eb'}, + {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '039fad7a79ec4a9fd9ce77c9a73d9278187b8430087bc1afec18883df40321ae'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb index 62647e55702..f5dce240245 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0-GCCcore-11.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = ['MPFR-4.1.0_patch-fix-tsprintf-test.patch'] checksums = [ {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, - {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '51bdcb5ba5365f0a3b4be3ddf2af4c08ce05dfcd02478ad11e75f4fea40503eb'}, + {'MPFR-4.1.0_patch-fix-tsprintf-test.patch': '039fad7a79ec4a9fd9ce77c9a73d9278187b8430087bc1afec18883df40321ae'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0_patch-fix-tsprintf-test.patch b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0_patch-fix-tsprintf-test.patch index b3644944a42..3e752fba655 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0_patch-fix-tsprintf-test.patch +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.1.0_patch-fix-tsprintf-test.patch @@ -8,43 +8,15 @@ We did not modify the test again since this bug affects MPFR's mpfr_sprintf func in particular cases. This bug has been fixed in the 2.37 branch. In short, this patch is useful (and needed) for a fixed glibc 2.37 and some other libraries, depending on the current locales. -diff -Naurd mpfr-4.2.0-a/PATCHES mpfr-4.2.0-b/PATCHES ---- mpfr-4.2.0-a/PATCHES 2023-04-17 21:17:39.748645280 +0000 -+++ mpfr-4.2.0-b/PATCHES 2023-04-17 21:17:39.792645218 +0000 +diff -ru mpfr-4.1.0.orig/PATCHES mpfr-4.1.0/PATCHES +--- mpfr-4.1.0.orig/PATCHES 2011-06-30 02:17:40.000000000 +0200 ++++ mpfr-4.1.0/PATCHES 2023-09-08 12:29:11.711226986 +0200 @@ -0,0 +1 @@ +tsprintf-thousands -diff -Naurd mpfr-4.2.0-a/VERSION mpfr-4.2.0-b/VERSION ---- mpfr-4.2.0-a/VERSION 2023-01-06 10:55:57.000000000 +0000 -+++ mpfr-4.2.0-b/VERSION 2023-04-17 21:17:39.792645218 +0000 -@@ -1 +1 @@ --4.2.0 -+4.2.0-p1 -diff -Naurd mpfr-4.2.0-a/src/mpfr.h mpfr-4.2.0-b/src/mpfr.h ---- mpfr-4.2.0-a/src/mpfr.h 2023-01-06 10:55:57.000000000 +0000 -+++ mpfr-4.2.0-b/src/mpfr.h 2023-04-17 21:17:39.788645224 +0000 -@@ -27,7 +27,7 @@ - #define MPFR_VERSION_MAJOR 4 - #define MPFR_VERSION_MINOR 2 - #define MPFR_VERSION_PATCHLEVEL 0 --#define MPFR_VERSION_STRING "4.2.0" -+#define MPFR_VERSION_STRING "4.2.0-p1" - - /* User macros: - MPFR_USE_FILE: Define it to make MPFR define functions dealing -diff -Naurd mpfr-4.2.0-a/src/version.c mpfr-4.2.0-b/src/version.c ---- mpfr-4.2.0-a/src/version.c 2023-01-06 10:55:57.000000000 +0000 -+++ mpfr-4.2.0-b/src/version.c 2023-04-17 21:17:39.792645218 +0000 -@@ -25,5 +25,5 @@ - const char * - mpfr_get_version (void) - { -- return "4.2.0"; -+ return "4.2.0-p1"; - } -diff -Naurd mpfr-4.2.0-a/tests/tsprintf.c mpfr-4.2.0-b/tests/tsprintf.c ---- mpfr-4.2.0-a/tests/tsprintf.c 2023-01-05 17:09:48.000000000 +0000 -+++ mpfr-4.2.0-b/tests/tsprintf.c 2023-04-17 21:17:39.784645229 +0000 -@@ -1715,7 +1715,25 @@ +diff -ru mpfr-4.1.0.orig/tests/tsprintf.c mpfr-4.1.0/tests/tsprintf.c +--- mpfr-4.1.0.orig/tests/tsprintf.c 2020-04-09 00:39:35.000000000 +0200 ++++ mpfr-4.1.0/tests/tsprintf.c 2023-09-08 12:29:11.712226986 +0200 +@@ -1651,7 +1651,25 @@ check_sprintf ("000000001,000", "%'013.4Rg", x); #ifdef PRINTF_GROUPFLAG From 832ee8a9a73a87390c447b39838360a39f323c4c Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 8 Sep 2023 13:54:45 +0200 Subject: [PATCH 8750/9987] Fix local variable replacement --- .../b/BgeeDB/BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BgeeDB/BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/b/BgeeDB/BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb index 58b184b3aeb..3850829898d 100644 --- a/easybuild/easyconfigs/b/BgeeDB/BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/b/BgeeDB/BgeeDB-2.26.0-foss-2021a-R-4.1.0.eb @@ -26,10 +26,10 @@ dependencies = [ exts_default_options = { 'source_urls': [ - 'https://bioconductor.org/packages/%(local_bioc_version)s/bioc/src/contrib/', - 'https://bioconductor.org/packages/%(local_bioc_version)s/bioc/src/contrib/Archive/%(name)s', - 'https://bioconductor.org/packages/%(local_bioc_version)s/data/annotation/src/contrib/', - 'https://bioconductor.org/packages/%(local_bioc_version)s/data/experiment/src/contrib/', + 'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_bioc_version, + 'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_bioc_version, + 'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_bioc_version, + 'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_bioc_version, 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive 'https://cran.r-project.org/src/contrib/', # current version of packages 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages From 562ec6ea9113faf8628fe94dee20601cc7ba5461 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Fri, 8 Sep 2023 15:47:35 +0200 Subject: [PATCH 8751/9987] adding easyconfigs: cffi-1.15.1-GCCcore-11.3.0.eb, Clair3-1.0.4-foss-2022a.eb, mpath-1.1.3-GCCcore-11.3.0.eb and patches: Clair3-remove_htslib.patch --- .../c/Clair3/Clair3-1.0.4-foss-2022a.eb | 49 ++++++++++++ .../c/Clair3/Clair3-remove_htslib.patch | 80 +++++++++++++++++++ .../c/cffi/cffi-1.15.1-GCCcore-11.3.0.eb | 38 +++++++++ .../m/mpath/mpath-1.1.3-GCCcore-11.3.0.eb | 29 +++++++ 4 files changed, 196 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/c/Clair3/Clair3-remove_htslib.patch create mode 100644 easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/mpath/mpath-1.1.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb b/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb new file mode 100644 index 00000000000..01830d8cd54 --- /dev/null +++ b/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = 'MakeCp' + +name = 'Clair3' +version = '1.0.4' + +homepage = 'https://github.com/HKU-BAL/Clair3' +description = """Clair3 is a germline small variant caller for long-reads. +Clair3 makes the best of two major method categories: pileup calling handles +most variant candidates with speed, and full-alignment tackles complicated candidates +to maximize precision and recall. Clair3 runs fast and has superior performance, +especially at lower coverage. Clair3 is simple and modular for easy deployment and +integration.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'HKU-BAL' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['Clair3-remove_htslib.patch'] +checksums = [ + {'v1.0.4.tar.gz': '56cc4cf43f1cc652958cc1aea95d87d0811531a924ca5c68dd564d41834654c0'}, + {'Clair3-remove_htslib.patch': '0e1f5f17dc56850766fa19c6b0cca4ea23b3ed50b47126a41549c75e76d2cda7'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('mpath', '1.1.3'), + ('TensorFlow', '2.11.0'), + ('PyTables', '3.8.0'), + ('pigz', '2.7'), + ('cffi', '1.15.1'), + ('parallel', '20220722'), + ('SAMtools', '1.13'), + ('WhatsHap', '1.7'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('Automake', '1.16.5'), + ('cURL', '7.83.0'), + ('zstd', '1.5.2'), + ('HTSlib', '1.15.1'), + ('libdeflate', '1.10'), +] + +files_to_copy = [ + (['run_clair3.sh', 'longphase', 'clair3.py', 'clair3'], 'bin'), + (['libclair3.so', 'libclair3.o', 'libclair3.cpython-310-x86_64-linux-gnu.so', 'libclair3.c', 'longphase', ], 'lib'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Clair3/Clair3-remove_htslib.patch b/easybuild/easyconfigs/c/Clair3/Clair3-remove_htslib.patch new file mode 100644 index 00000000000..1cb58832159 --- /dev/null +++ b/easybuild/easyconfigs/c/Clair3/Clair3-remove_htslib.patch @@ -0,0 +1,80 @@ +Remove building of dependencies we provide via easybuild +Author: Denis Kristak (Inuits) +diff -ruN Clair3-1.0.4_orig/build.py Clair3-1.0.4/build.py +--- Clair3-1.0.4_orig/build.py 2023-09-07 14:28:29.842168186 +0100 ++++ Clair3-1.0.4/build.py 2023-09-08 12:31:06.300472155 +0100 +@@ -52,8 +52,7 @@ + 'clair3_pileup.c', + 'clair3_full_alignment.c')], + extra_compile_args=extra_compile_args, +- extra_link_args=extra_link_args, +- extra_objects=[os.path.join(htslib_dir, 'libhts.a')] ++ extra_link_args=extra_link_args + ) + + cdef = [ +diff -ruN Clair3-1.0.4_orig/Makefile Clair3-1.0.4/Makefile +--- Clair3-1.0.4_orig/Makefile 2023-09-07 14:28:29.842168186 +0100 ++++ Clair3-1.0.4/Makefile 2023-09-07 14:35:52.320773700 +0100 +@@ -3,8 +3,10 @@ + + PYTHON ?= python3 + +-all : libhts.a longphase libclair3.so +-clean : clean_htslib clean_longphase clean_libclair3 ++# all : libhts.a longphase libclair3.so ++# clean : clean_htslib clean_longphase clean_libclair3 ++all : longphase libclair3.so ++clean : clean_longphase clean_libclair3 + + SAMVER = 1.15.1 + LPVER = 1.3 +@@ -16,16 +18,16 @@ + CPPFLAGS = -std=c++11 -Wall -O3 -I ${PREFIX}/include -L ${PREFIX}/lib -Wl,-rpath=${PREFIX}/lib + LP_CPPFLAGS = -std=c++11 -Wall -g -O3 -I ${PREFIX}/include -L ${PREFIX}/lib -Wl,-rpath=${PREFIX}/lib + +-samtools-$(SAMVER)/Makefile: +- curl -L -o samtools-${SAMVER}.tar.bz2 https://github.com/samtools/samtools/releases/download/${SAMVER}/samtools-${SAMVER}.tar.bz2; \ +- tar -xjf samtools-${SAMVER}.tar.bz2; \ +- rm samtools-${SAMVER}.tar.bz2 +- +-libhts.a: samtools-$(SAMVER)/Makefile +- # this is required only to add in -fpic so we can build python module +- @echo "\x1b[1;33mMaking $(@F)\x1b[0m" +- cd samtools-${SAMVER}/htslib-${SAMVER}; CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" ./configure; make CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" +- cp samtools-${SAMVER}/htslib-${SAMVER}/$@ $@ ++# samtools-$(SAMVER)/Makefile: ++# curl -L -o samtools-${SAMVER}.tar.bz2 https://github.com/samtools/samtools/releases/download/${SAMVER}/samtools-${SAMVER}.tar.bz2; \ ++# tar -xjf samtools-${SAMVER}.tar.bz2; \ ++# rm samtools-${SAMVER}.tar.bz2 ++ ++# libhts.a: samtools-$(SAMVER)/Makefile ++# # this is required only to add in -fpic so we can build python module ++# @echo "\x1b[1;33mMaking $(@F)\x1b[0m" ++# cd samtools-${SAMVER}/htslib-${SAMVER}; CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" ./configure; make CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" ++# cp samtools-${SAMVER}/htslib-${SAMVER}/$@ $@ + + + longphase-$(LPVER)/Makefile: +@@ -39,15 +41,15 @@ + cp longphase-${LPVER}/$@ $@ + + +-libclair3.so: samtools-${SAMVER}/htslib-${SAMVER} ++libclair3.so: + ${PYTHON} build.py + + +-.PHONY: clean_htslib +-clean_htslib: +- cd samtools-${SAMVER} && make clean || exit 0 +- cd samtools-${SAMVER}/htslib-${SAMVER} && make clean || exit 0 +- rm libhts.a ++# .PHONY: clean_htslib ++# clean_htslib: ++# cd samtools-${SAMVER} && make clean || exit 0 ++# cd samtools-${SAMVER}/htslib-${SAMVER} && make clean || exit 0 ++# rm libhts.a + + .PHONY: clean_longphase + clean_longphase: diff --git a/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..56cee831b54 --- /dev/null +++ b/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = "PythonBundle" + +name = 'cffi' +version = '1.15.1' + +homepage = 'https://cffi.readthedocs.io/en/latest/' +description = """C Foreign Function Interface for Python. Interact with almost any C code from +Python, based on C-like declarations that you can often copy-paste from header +files or documentation. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + (name, version, { + 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mpath/mpath-1.1.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mpath/mpath-1.1.3-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..52a7505afdd --- /dev/null +++ b/easybuild/easyconfigs/m/mpath/mpath-1.1.3-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'mpath' +version = '1.1.3' + +homepage = 'https://pypi.org/project/mpath/' +description = """For now it's quit simple and get_path_info() +method returns information about given path. It can be either +a directory or a file path.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mclass', '1.3.4', { + 'checksums': ['414f786287b80a80261125fc9ed844dbf9093907e96999a2f0391a7b32a1cb60'], + }), + (name, version, { + 'checksums': ['f8ecaf91bded57e12676d0373bf27acc154dea56c386f6ad05b476bc2c6ddc4f'], + }), +] + +moduleclass = 'bio' From 71584d8bc5a805e1090cff09e9a87472c85cd75e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 8 Sep 2023 16:32:06 +0200 Subject: [PATCH 8752/9987] Fix build of grpc and test on PPC --- .../t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb index f766bd2eafb..e8b966a5b8b 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.13.0-foss-2023a.eb @@ -81,6 +81,9 @@ exts_list = [ ('grpcio', '1.57.0', { 'modulename': 'grpc', 'preinstallopts': "GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s " + + # Required to avoid building with non-default C++ standard but keep other flags, + # see https://github.com/grpc/grpc/issues/34256 + "GRPC_PYTHON_CFLAGS='-fvisibility=hidden -fno-wrapv -fno-exceptions' " + " ".join(["GRPC_PYTHON_BUILD_SYSTEM_%s=True" % i for i in ( 'OPENSSL', @@ -229,8 +232,9 @@ exts_list = [ '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', '-//tensorflow/core/ir/importexport/tests/roundtrip/...', ], - 'testopts': "--test_timeout=3600 --test_size_filters=small", - 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + # Need to have $HOME set for tests on PPC: https://github.com/tensorflow/tensorflow/issues/61814 + 'testopts': "--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_env=HOME=/tmp --test_timeout=3600 --test_size_filters=small " "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", 'with_xla': True, }), From c99b8d59dcdaa5e9a9ffac1f7036944695ac9796 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Sep 2023 18:52:35 +0100 Subject: [PATCH 8753/9987] simplify build and install options for Ghostscript --- .../g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb index 5711dfde5bf..e5b59d6447b 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.01.2-GCCcore-12.3.0.eb @@ -35,12 +35,11 @@ preconfigopts = 'mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no & preconfigopts += 'mv libpng libpng.no && export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' configopts = "--with-system-libtiff --enable-dynamic --disable-hidden-visibility" -# Avoid race condition in build if too much parallelism is used -maxparallel = 4 +# also build and install shared libs +build_cmd_targets = ['', 'so'] +installopts = 'soinstall' postinstallcmds = [ - # build and install shared libs - "make so && make soinstall", # install header files "mkdir -p %(installdir)s/include/%(namelower)s", "install -v -m644 base/*.h %(installdir)s/include/%(namelower)s", From b723aa35fd1a8f9c19a999b2ca1f2c847a219fc0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 9 Sep 2023 11:56:19 +0200 Subject: [PATCH 8754/9987] adding easyconfigs: Advisor-2023.0.0.eb, Advisor-2023.2.0.eb --- .../easyconfigs/a/Advisor/Advisor-2023.0.0.eb | 27 +++++++++++++++++++ .../easyconfigs/a/Advisor/Advisor-2023.2.0.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb create mode 100644 easybuild/easyconfigs/a/Advisor/Advisor-2023.2.0.eb diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb new file mode 100644 index 00000000000..187fcafa180 --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2023.0.0.eb @@ -0,0 +1,27 @@ +name = 'Advisor' +version = '2023.0.0' + +homepage = 'https://software.intel.com/intel-advisor-xe' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = SYSTEM + +source_urls = [ + 'https://registrationcenter-download.intel.com/akdlm/irc_nas/19094/'] +sources = ['l_oneapi_advisor_p_%(version)s.25338_offline.sh'] +checksums = ['5d8ef163f70ee3dc42b13642f321d974f49915d55914ba1ca9177ed29b100b9d'] + +dontcreateinstalldir = True + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/advisor'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2023.2.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2023.2.0.eb new file mode 100644 index 00000000000..bcce2e42a8d --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2023.2.0.eb @@ -0,0 +1,27 @@ +name = 'Advisor' +version = '2023.2.0' + +homepage = 'https://software.intel.com/intel-advisor-xe' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = SYSTEM + +source_urls = [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/0b0e8bf2-30e4-4a26-b1ef-e369b0181b35/'] +sources = ['l_oneapi_advisor_p_%(version)s.49489_offline.sh'] +checksums = ['48ab7fa2b828a273d467c8f07efd64d6cf2fcdcfe0ff567bd1d1be7a5d5d8539'] + +dontcreateinstalldir = True + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/advisor'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'perf' From 7fe043202c7a0accc10458a771a017775e47d51a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 9 Sep 2023 12:34:26 +0100 Subject: [PATCH 8755/9987] also update Ghostscript/10.0.0-GCCcore-12.2.0 --- .../g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb index 33a9307aa2a..e5af9bec775 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb @@ -39,12 +39,11 @@ preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' configopts = "--with-system-libtiff --enable-dynamic" -# Avoid race condition in build if too much parallelism is used -maxparallel = 4 +# also build and install shared libs +build_cmd_targets = ['', 'so'] +installopts = 'soinstall' postinstallcmds = [ - # build and install shared libs - "make so && make soinstall", # install header files "mkdir -p %(installdir)s/include/ghostscript", "install -v -m644 base/*.h %(installdir)s/include/ghostscript", From 6fd0fbdcc0f537dc4e73dd2326daeac63f468ba4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 9 Sep 2023 12:57:07 +0100 Subject: [PATCH 8756/9987] move wrapt from foss to gfbf --- .../{wrapt-1.15.0-foss-2022b.eb => wrapt-1.15.0-gfbf-2022b.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/w/wrapt/{wrapt-1.15.0-foss-2022b.eb => wrapt-1.15.0-gfbf-2022b.eb} (92%) diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022b.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-gfbf-2022b.eb similarity index 92% rename from easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022b.eb rename to easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-gfbf-2022b.eb index d80cc743cca..79dedd694da 100644 --- a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2022b.eb +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-gfbf-2022b.eb @@ -8,7 +8,7 @@ description = """The aim of the wrapt module is to provide a transparent object proxy for Python, which can be used as the basis for the construction of function wrappers and decorator functions.""" -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'gfbf', 'version': '2022b'} dependencies = [ ('Python', '3.10.8'), From cf60a9fce35d8210f7b66204cb4364e7690f8f5c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Sep 2023 15:15:43 +0200 Subject: [PATCH 8757/9987] filter out template + archived easyconfigs when determining changed easyconfigs in PRs --- test/easyconfigs/easyconfigs.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 5236e166cf5..65bea6e1e1c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -219,6 +219,15 @@ def _get_changed_easyconfigs(self): # get list of changed easyconfigs changed_ecs_files = get_eb_files_from_diff(diff_filter='M') added_ecs_files = get_eb_files_from_diff(diff_filter='A') + + # ignore template easyconfig (TEMPLATE.eb) and archived easyconfigs + def filter_ecs(ecs): + archive_path = os.path.join('easybuild', 'easyconfigs', '__archive__') + return [ec for ec in ecs if os.path.basename(ec) != 'TEMPLATE.eb' and archive_path not in ec] + + changed_ecs_files = filter_ecs(changed_ecs_files) + added_ecs_files = filter_ecs(added_ecs_files) + changed_ecs_filenames = [os.path.basename(f) for f in changed_ecs_files] added_ecs_filenames = [os.path.basename(f) for f in added_ecs_files] if changed_ecs_filenames: From b1c50881795d916d1bf314a416144469c3b9d3da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 9 Sep 2023 15:15:43 +0200 Subject: [PATCH 8758/9987] filter out template + archived easyconfigs when determining changed easyconfigs in PRs --- test/easyconfigs/easyconfigs.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 34a7f346a85..61a4f1d547c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -218,6 +218,15 @@ def _get_changed_easyconfigs(self): # get list of changed easyconfigs changed_ecs_files = get_eb_files_from_diff(diff_filter='M') added_ecs_files = get_eb_files_from_diff(diff_filter='A') + + # ignore template easyconfig (TEMPLATE.eb) and archived easyconfigs + def filter_ecs(ecs): + archive_path = os.path.join('easybuild', 'easyconfigs', '__archive__') + return [ec for ec in ecs if os.path.basename(ec) != 'TEMPLATE.eb' and archive_path not in ec] + + changed_ecs_files = filter_ecs(changed_ecs_files) + added_ecs_files = filter_ecs(added_ecs_files) + changed_ecs_filenames = [os.path.basename(f) for f in changed_ecs_files] added_ecs_filenames = [os.path.basename(f) for f in added_ecs_files] if changed_ecs_filenames: From b80b373b0a8c3296fab07f71866b625935f42a54 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 9 Sep 2023 18:40:06 +0200 Subject: [PATCH 8759/9987] prepare release notes for EasyBuild v4.8.1 + bump version to 4.8.1 --- RELEASE_NOTES | 133 +++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 133 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index f3ce7640d11..484695a43d8 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,141 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 17,511 easyconfig files, for 3,161 different software packages, +The latest version of easybuild-easyconfig provides 18,015 easyconfig files, for 3,224 different software packages, incl. 39 different (compiler) toolchains. +v4.8.1 (11 September 2023) +-------------------------- + +update/bugfix release + +- added example easyconfig files for 83 new software packages: + - ALAMODE (#18733), AMRFinderPlus (#18559), Ax (#68), bcrypt (#18208), bench (#18656), BgeeDB (#18743), Boost.Python-NumPy + (#18505), CatBoost (#18591), centerline (#18273), cffi (#7105), ChIPseeker (#18662), connected-components-3d (#18289), + cryptography (#8495), CVglasso (#18657), DiffBind (#18663), drmaa-python (#18614), e3nn (#18304), flit (#18208), + GAPPadder (#18692), GenerativeModels (#18451), geosphere (#18659), gffutils (#18331), gkmSVM (#18660), hampel (#18409), + hatchling (#18208), HDF-EOS2 (#18297), Hybpiper (#18414), inih (#18516), IsoformSwitchAnalyzeR (#18664), IsoQuant + (#18331), Jupyter-bundle (#18634), leafcutter (#18615), libleidenalg (#18548), LIBSVM-Python (#18455), libvori + (#18379), maturin (#18405), meboot (#18658), mgen (#18402), Mikado (#18614), NanoCaller (#18726), nbclassic (#18617), + ncolor (#7146), nose3 (#18234), novaSTA (#18601), Omnipose (#18402), Optax (#18610), paramiko (#1504), Parsl (#18408), + peakdetect (#18402), PICRUSt2 (#18333), Platypus-Opt (#18291), PortMidi (#18252), pv (#16439), py-c3d (#18409), pygame + (#18252), pyodbc (#18334), Python-bundle-PyPI (#18208), qforce (#18456), RFdiffusion (#18304), Rhodium (#18291), + ruptures (#18306), Sabre (#18342), scGSVA (#18401), scib-metrics (#18734), scikit-plot (#18377), SDL2_mixer (#18252), + SDL2_ttf segment-anything (#18290), sentinelsat (#18367), setuptools-rust (#18208), slurm-drmaa (#18614), SuAVE-biomat + (#18678), T-Coffee (#17916), tensorflow-compression (#18676), torchvf (#18637), tornado (#256), tseriesEntropy (#18661), + TXR (#18665), unifdef (#18427), UniFrac (#18407), virtualenv (#2660), WFA2 (#18636) +- added additional easyconfigs for various supported software packages, including: + - ABINIT 9.10.3, Advisor 2023.0.0, Advisor 2023.2.0, aiohttp 3.8.5, AMD-uProf 4.1.424, Anaconda3 2023.07, anndata 0.9.2, + AOCC 4.0.0, APR 1.7.4, APR-util 1.6.3, Arcade-Learning-Envionment 0.8.1, archspec 0.2.1, Armadillo 12.6.2, arpack-ng + 3.9.0, assimp 5.2.5, ATK 2.38.0, at-spi2-atk 2.38.0, attrdict3 2.0.2, Autoconf 2.71, Automake 1.16.5, Autotools + 20220317, BAGEL 1.2.2, bam-readcount 1.0.1, BamTools 2.5.2, Bazel 6.3.1, BBMap 38.87, BCFtools 1.18, bcl2fastq2 2.20.0, + BeautifulSoup 4.12.2, BEDTools 2.31.0, binutils 2.40, biom-format 2.1.15, Biopython 1.76, Bio-SearchIO-hmmer 1.7.3, + Bison 3.8.2, bokeh 3.2.1, Boost 1.82.0, cairo 1.17.8, CalculiX-CrunchiX 2.20, c-ares 1.19.1, Cbc 2.10.5, ccache 4.7.5, + ccache 4.8.3, CDO 2.2.2, CFDEMcoupling 3.8.0, CFITSIO 4.3.0, CGAL 4.14.1, Cgl 0.60.7, CharLS 2.4.2, cicero 1.3.8, Clang + 16.0.4, Clang 16.0.6, Clp 1.17.8, Cluster-Buster 20200507, CMake 3.11.4, CoinUtils 2.11.9, conan 1.60.2, + configurable-http-proxy 4.5.5, coverage 7.2.7, CP2K 2023.1, cppy 1.2.1, CubeLib 4.8.1, CubeWriter 4.8.1, CUDA 12.2.2, + dask 2023.7.1, dcm2niix 1.0.20230411, Delly 1.1.6, DIAMOND 2.1.8, dill 0.3.7, dm-haiku 0.0.9, ecBuild 3.8.0, ecCodes + 2.31.0, ELPA 2023.05.001, ESPResSo 4.2.1, exiv2 0.28.0, expecttest 0.1.3, expecttest 0.1.5, fastahack 1.0.0, fastparquet + 2023.4.0, FFmpeg 6.0, ffnvcodec 12.0.16.0, FFTW 3.3.8, filevercmp 20191210, flatbuffers 23.5.26, flatbuffers-python + 23.1.4, flatbuffers-python 23.5.26, flex 2.6.4, FLTK 1.3.8, FreeImage 3.18.0, FreeSurfer 7.4.1, FriBidi 1.0.12, fsom + 20151117, gc 8.2.4, GCC 13.2.0, GCCcore 13.2.0, GConf 3.2.6, GDB 13.2, Gdk-Pixbuf 2.42.10, GEOS 3.12.0, gettext 0.22, + GHC 9.2.2, Ghostscript 10.01.2, giflib 5.2.1, GLib 2.77.1, GLM 0.9.9.8, GLPK 5.0, gmpy2 2.1.2, gmpy2 2.1.5, gnuplot + 5.4.8, GObject-Introspection 1.76.1, gperftools 2.12, Graphene 1.10.8, Graphviz 8.1.0, graphviz-python 0.20.1, Greenlet + 2.0.2, gRPC 1.57.0, GST-plugins-base 1.22.5, GStreamer 1.22.5, GTK3 3.24.37, GTK4 4.11.3, GTS 0.7.6, GTS 0.7.6, Guile + 3.0.9, h4toh5 2.2.5, h5netcdf 1.2.0, h5py 3.9.0, HarfBuzz 5.3.1, HDF5 1.14.0, HDF5 1.14.0, help2man 1.49.3, hiredis + 1.2.0, HOOMD-blue 4.0.1, Horovod 0.22.1, Horovod 0.28.1, HPL 2.3, htop 3.2.2, HTSlib 1.18, hwloc 2.9.2, Hydra 1.3.2, + hypothesis 6.82.0, Hypre 2.29.0, ICU 73.2, igraph 0.10.6, iimkl 2023a, imageio 2.31.1, ImageMagick 7.1.1, inferCNV + 1.12.0, inferCNV 1.14.2, intervaltree 0.1, intervaltree-python 3.1.0, IPython 8.14.0, ISL 0.26, Java 11.0.20, jq 1.6, + JsonCpp 1.9.5, Julia 1.9.2, Julia 1.9.3, JupyterHub 4.0.1, JupyterHub 4.0.2, JupyterLab 4.0.3, JupyterLab 4.0.5, + jupyterlmod 4.0.3, JupyterNotebook 7.0.2, jupyter-resource-usage 1.0.0, jupyter-server 1.21.0, kb-python 0.27.3, kma + 1.4.12a, KMC 3.2.1, KMC 3.2.2, LAME 3.100, leidenalg 0.10.1, LERC 4.0.0, libaec 1.0.6, libaio 0.3.113, libavif 0.11.1, + libcerf 2.3, libdrm 2.4.115, libdwarf 0.7.0, libepoxy 1.5.10, libevent 2.1.12, libfabric 1.19.0, libgd 2.3.3, libgit2 + 1.7.1, libGLU 9.0.3, libglvnd 1.6.0, Libint 2.7.2, libnsl 2.0.0, libpciaccess 0.17, libsndfile 1.2.2, libsodium 1.0.18, + libtool 2.4.7, libunistring 1.1, libwebp 1.3.1, libwebp 1.3.1, libwpe 1.14.1, libxml2 2.11.5, libxsmm 1.17, LittleCMS + 2.15, LLVM 16.0.6, Lua 5.4.6, M4 1.4.19, MACS2 2.2.9.1, magma 2.7.1, mahotas 1.4.13, makeinfo 7.0.3, Mako 1.2.4, Mamba + 23.1.0, MATIO 1.5.23, matplotlib 3.7.2, medaka 1.8.1, medaka 1.9.1, Mercurial 6.4.5, Mesa 23.1.4, meson-python 0.13.2, + Miniconda3 23.5.2, Monocle3 1.3.1, MPC 1.3.1, mpi4py 3.1.4, MRtrix 3.0.4, multichoose 1.0.3, MUMPS 5.6.1, MXNet 1.9.1, + NAMD 2.14, napari 0.4.18, ncdu 1.18, ncurses 6.4, ncview 2.1.8, netCDF 4.9.2, netCDF-C++4 4.3.1, netCDF-Fortran 4.6.1, + nettle 3.9.1, networkx 3.1, NLopt 2.7.1, nodejs 18.17.1, nsync 1.26.0, numactl 2.0.16, NVHPC 23.7, ont-fast5-api 4.1.1, + OPARI2 2.0.7, OpenAI-Gym 0.26.2, OpenCV 4.8.0, OpenFOAM 11, OpenFOAM 5.0, OpenImageIO 2.4.14.0, OpenMPI 4.1.5, OpenPGM + 5.2.122, Osi 0.108.8, OSU-Micro-Benchmarks 7.1-1, OTF2 3.0.3, OTF2 3.0.3, Pango 1.50.14, PAPI 7.0.1, PAPI 7.0.1, + parallel 20230722, ParaView 5.4.1, PartitionFinder 2.1.1, patchelf 0.17.2, pdsh 2.34, PDT 3.25.1, Perl 5.38.0, Pillow + 10.0.0, Pillow-SIMD 9.5.0, Pint 0.22, pixman 0.42.2, pkgconf 2.0.3, pkgconfig 1.5.5, plotly.py 5.16.0, PLUMED 2.9.0, PLY + 3.11, pocl 4.0, poetry 1.5.1, PROJ 6.3.1, prokka 1.14.5, protobuf 24.0, protobuf-python 4.24.0, psutil 5.9.5, PuLP + 2.7.0, pybedtools 0.9.0, pyBigWig 0.3.22, pybind11 2.11.1, PyCairo 1.24.0, PycURL 7.45.2, PycURL 7.45.2, PyGObject + 3.44.1, Pylint 2.17.4, pypmt 1.1.0, pyproj 3.6.0, pyro-ppl 1.8.4, Python 2.7.18, python-igraph 0.10.6, PyZMQ 25.1.1, + Qhull 2020.2, QIIME2 2023.5.1, Qt5 5.15.10, QuantumESPRESSO 7.2, Racon 1.5.0, rclone 1.63.1, RE2 2023, re2c 3.1, + RegTools 1.0.0, rjags 4, RnBeads 2.14.0, RTG-Tools 3.12.1, SAMtools 1.18, Scalene 1.5.26, scikit-build 0.17.6, + scikit-image 0.21.0, SciPy-bundle 2023.07, Score-P 8.1, SCOTCH 7.0.3, SDL2 2.28.2, SDL2_image 2.6.3, SDL2_mixer 2.6.3, + SDL2_ttf 2.20.2, segment-anything 1.0, sentinelsat 1.2.1, setuptools 64.0.3, Seurat 4.1.0, SeuratWrappers 20221022, + Shapely 2.0.1, SIONlib 1.7.7, SIONlib 1.7.7, slurm drmaa, smithwaterman 20160702, snakemake 7.32.3, SpaceRanger 2.1.0, + SpaceRanger 2.1.0, spglib 2.0.2, SpiecEasi 1.1.1, SPOOLES 2.2, Stack 2.11.1, STAR 2.7.11a, Structure 2.3.4, SUNDIALS + 6.6.0, SWIG 4.1.1, SWIG 4.1.1, sympy 1.12, sympy 1.9, tabixpp 1.1.2, tbb 2021.10.0, tbl2asn 20230713, tcsh 6.24.10, + TensorFlow 2.13.0, TensorFlow 2.13.0, tensorflow-probability 0.19.0, time 1.9, Tk 8.6.13, Tkinter 3.11.3, tqdm 4.66.1, + unixODBC 2.3.11, Valgrind 3.21.0, Valgrind 3.21.0, vcflib 1.0.9, VirtualGL 3.1, VisPy 0.12.2, VTK 8.2.0, Wayland 1.22.0, + Wayland 1.22.0, WebKitGTK+ 2.40.4, wpebackend-fdo 1.14.1, wrapt 1.15.0, wxPython 4.2.1, wxWidgets 3.2.2.1, x264 + 20230226, x265 3.5, xorg-macros 1.20.0, xprop 1.2.5, Xvfb 21.1.8, xxd 9.0.1696, XZ 5.4.4, Yambo 5.1.2, Z3 4.10.2, Z3 + 4.12.2, Z3 4.8.10, Z3 4.8.11, Z3 4.8.12, Z3 4.8.16, zarr 2.16.0, ZeroMQ 4.3.4, zlib 1.2.13 +- minor enhancements, including: + - add UCell extension to R-bundle-Bioconductor 3.16 (#18281) + - add decoupleR package to R-bundle-Bioconductor 3.15 with foss/2022a as extension (#18399) + - add tabletools extension to recent R easyconfigs (#18510) + - add decoupleR extension to R-bundle-Bioconductor v3.16 (#18552) + - add test for easyconfig file permissions (#18647) + - add RnBeads extensions to R-bundle-Bioconductor v3.16 (#18682) + - add `flextables` extension to R v4.2.1 + v4.2.2 (#18719) +- various bug fixes, including: + - set JULIA_DEPOT_PATH in Julia easyconfigs with default value (#17976) + - remove superflous dependencies from Horovod easyconfig on top of PyTorch (#18262) + - disable building documentation for libsigc++ 2.10.x (#18301) + - use MCR dependency in FreeSurfer 7.3.2 and 7.4.0 (#18303) + - add `hpctestlib` to the `$PYTHONPATH` in ReFrame 4.2.0 easyconfig (#18320) + - fix installation of Python bindings for recent Arrow easyconfigs by adding `--no-build-isolation` to `pip install` command (#18348) + - add/fix patches for PyTorch 1.13.1 w/ foss/2022a (#18371) + - {tools}[GCCcore/11.3.0] jupyter-server 1.21.0 (#18389) + - Fix batchspawner for JupyterHub 3.0 (#18390) + - fix compiler flags and toolchain options for ScaLAPACK 2.2.0 (#18396) + - fix compiler flags and toolchain options for ScaLAPACK 2.1.0 (#18397) + - add patch to fix CUDA race condition problem for Score-P v8.0 (#18411) + - add `-DABSL_PROPAGATE_CXX_STD=ON` to recent Abseil easyconfigs (required for PyTorch) (#18413) + - add missing patches for PyTorch 1.12.0 w/ foss/2022a (#18430) + - fix installation of Python bindings for Arrow 8.0.0 with foss/2022.05 by adding `--no-build-isolation` to `pip install` command (#18432) + - fix regression in GCC 12.1 + 12.2 with wrong warnings (#18434) + - fix installation of Python bindings for Arrow 0.17.1 by adding `--no-build-isolation` to `pip install` command (#18440) + - fix installation of Python bindings for Arrow 0.16.0 by adding `--no-build-isolation` to `pip install` command (#18441) + - add patch for LIBSVM 3.30 to pass `$CFLAGS` + `$LDFLAGS` and run tests (#18454) + - copy missing `default_files` directory for PICRUSt2 (#18459) + - add patch for Automake 1.16.5 to fix help2man error (#18468) + - consistently use ON/OFF for -DBUILD_SHARED_LIBS (#18484) + - add patch to fix quantization failure in PyTorch 1.11.0 on POWER (#18489) + - add patches to fix PyTorch 1.12 (CPU-only) w/ foss/2022a on POWER (#18490) + - Add missing patches for PyTorch 1.12.0 w/ `foss/2022a` + CUDA 11.7.0 (#18491) + - add patches to fix PyTorch-1.12.1 w/ foss/2021a + CUDA v11.3.1 on POWER (#18492) + - add patches to fix PyTorch-1.12.1 w/ foss/2021b + CUDA v11.5.2 on POWER (#18493) + - add patches to fix PyTorch-1.12.1 w/ foss/2022a + CUDA v11.7.0 on POWER (#18494) + - add patches to fix PyTorch 1.13.1 w/ foss/2022a on POWER + fix flaky `test_jit_legacy` test (#18500) + - add alternative checksum for Extrae v4.0.4 (#18564) + - set `$MUJOCO_PY_FORCE_CPU` to avoid that mujoco-py checks for nvidia-smi and aborts installation because `/usr/lib/nvidia` is not in `$LD_LIBRARY_PATH` (#18641) + - fix sanity check for ccache by setting `LC_ALL=C` (#18677) + - make Autoconf a build dep for tRNAscan-SE + add missing Perl dependency (#18680) + - fix configure option to disable wxwidgets for gnuplot 5.4.6 (#18691) + - strip out hardcoded `-march=native` used by RapidJSON 1.1.0 (#18725) + - disable detection of Dbus broker for `at-spi2-core` (+ bump at-spi2-core v2.49.90 to v2.49.91) (#18727) + - make sure that 'moduleclass' is set in all easyconfig files (and is not set to default 'base' moduleclass) (#18739) + - add patch for MPFR 4.1.0 to fix failing tsprintf test with glibc >= 2.37 (#18746) + - move wrapt from `foss/2022b` to `gfbf/2022b` (#18752) +- other changes: + - use custom easyblock for recent sympy easyconfigs to prevent test failures (#18428) + - use GCC/12.2.0 toolchain for GSL 2.7, remove easyconfig for GSL 2.7 with GCCcore/12.2.0 (#18501) + - use Perl instead of Perl minimal as build dependency for libcerf and remove EasyConfig for Perl minimal (#18565) + - remove appending of `$__EGL_VENDOR_LIBRARY_DIRS` in recent Mesa easyconfigs, since Mesa easyblock now appends to it (#18630) + - use `GCCcore/12.2.0` toolchain for gnuplot 5.4.6 + disable wx support (#18648) + - remove html5lib-1.1-GCCcore-12.3.0.eb as html5lib is in `Python-bundle-PyPI/2023.06-GCCcore-12.3.0` (#18698) + - rename `notebook` to `JupyterNotebook` (#18735) + - filter out template + archived easyconfigs when determining changed easyconfigs in PRs (#18753) + + v4.8.0 (7 Jul 2023) -------------------- diff --git a/setup.py b/setup.py index a8bebcc31f8..9b812bdf2ec 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.8.1.dev0' +VERSION = '4.8.1' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 07acde6c9896e492b5fe3cb4fbad5dedc3b1942b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 10 Sep 2023 10:44:00 +0200 Subject: [PATCH 8760/9987] add patch for PMIx 4.x to use lchown so links are not followed --- .../p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb | 6 +- .../p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb | 6 +- .../p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb | 6 +- .../p/PMIx/PMIx-4.2.4-GCCcore-12.3.0.eb | 6 +- .../easyconfigs/p/PMIx/PMIx-4.x_lchown.patch | 112 ++++++++++++++++++ 5 files changed, 132 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.x_lchown.patch diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb index 4ea23f25701..57c09f98e7e 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.0-GCCcore-11.2.0.eb @@ -21,7 +21,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['145f05a6c621bfb3fc434776b615d7e6d53260cc9ba340a01f55b383e07c842e'] +patches = ['PMIx-4.x_lchown.patch'] +checksums = [ + {'pmix-4.1.0.tar.bz2': '145f05a6c621bfb3fc434776b615d7e6d53260cc9ba340a01f55b383e07c842e'}, + {'PMIx-4.x_lchown.patch': '1e89856caf69878aeb54ca08bb6b4ea1c962d24010e2080878ea70e958947a05'}, +] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb index bd61d4a2560..7f5b67f5b44 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.1.2-GCCcore-11.3.0.eb @@ -21,7 +21,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['670d3a02b39fb2126fe8084174cf03c484e027b5921b5c98a851108134e2597a'] +patches = ['PMIx-4.x_lchown.patch'] +checksums = [ + {'pmix-4.1.2.tar.bz2': '670d3a02b39fb2126fe8084174cf03c484e027b5921b5c98a851108134e2597a'}, + {'PMIx-4.x_lchown.patch': '1e89856caf69878aeb54ca08bb6b4ea1c962d24010e2080878ea70e958947a05'}, +] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb index ffe8c9fba65..4f6e54f1871 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb @@ -21,7 +21,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['935b2f492e4bc409017f1425a83366aa72a7039605ea187c9fac7bb1371cd73c'] +patches = ['PMIx-4.x_lchown.patch'] +checksums = [ + {'pmix-4.2.2.tar.bz2': '935b2f492e4bc409017f1425a83366aa72a7039605ea187c9fac7bb1371cd73c'}, + {'PMIx-4.x_lchown.patch': '1e89856caf69878aeb54ca08bb6b4ea1c962d24010e2080878ea70e958947a05'}, +] builddependencies = [('binutils', '2.39')] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.4-GCCcore-12.3.0.eb index 611c34c2b5f..f1ba0fc1888 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.4-GCCcore-12.3.0.eb @@ -21,7 +21,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['c4699543f2278d3a78bdac72b4b2da9cd92d11d18478d66522b8991764b021c8'] +patches = ['PMIx-4.x_lchown.patch'] +checksums = [ + {'pmix-4.2.4.tar.bz2': 'c4699543f2278d3a78bdac72b4b2da9cd92d11d18478d66522b8991764b021c8'}, + {'PMIx-4.x_lchown.patch': '1e89856caf69878aeb54ca08bb6b4ea1c962d24010e2080878ea70e958947a05'}, +] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.x_lchown.patch b/easybuild/easyconfigs/p/PMIx/PMIx-4.x_lchown.patch new file mode 100644 index 00000000000..af233b31eff --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.x_lchown.patch @@ -0,0 +1,112 @@ +From 383d48d63452d0523319dab20922cb1fb2cb8175 Mon Sep 17 00:00:00 2001 +From: Ralph Castain +Date: Thu, 7 Sep 2023 07:59:57 -0600 +Subject: [PATCH] Do not follow links when doing "chown" + +There is a potential issue with allowing a "chown" operation +to follow user-created links, so let's limit any use of that +function to "lchown" - which directs the "chown" operation to +NOT follow a link. + +Signed-off-by: Ralph Castain +(cherry picked from commit ae62cdf67b19e80fd821420816f09bf0a56a8166) +--- + src/mca/common/dstore/dstore_base.c | 4 ++-- + src/mca/common/dstore/dstore_segment.c | 4 ++-- + src/mca/gds/ds12/gds_ds12_lock_fcntl.c | 2 +- + src/mca/gds/ds12/gds_ds12_lock_pthread.c | 2 +- + src/util/pmix_pty.c | 4 ++-- + 5 files changed, 8 insertions(+), 8 deletions(-) + +diff --git a/src/mca/common/dstore/dstore_base.c b/src/mca/common/dstore/dstore_base.c +index 4831f4ef77..dc902668cf 100644 +--- a/src/mca/common/dstore/dstore_base.c ++++ b/src/mca/common/dstore/dstore_base.c +@@ -531,7 +531,7 @@ static int _esh_session_init(pmix_common_dstore_ctx_t *ds_ctx, size_t idx, ns_ma + } + } + if (s->setjobuid > 0){ +- if (0 > chown(s->nspace_path, (uid_t) s->jobuid, (gid_t) -1)){ ++ if (0 > lchown(s->nspace_path, (uid_t) s->jobuid, (gid_t) -1)){ + rc = PMIX_ERROR; + PMIX_ERROR_LOG(rc); + return rc; +@@ -1711,7 +1711,7 @@ pmix_common_dstore_ctx_t *pmix_common_dstor_init(const char *ds_name, pmix_info_ + } + } + if (ds_ctx->setjobuid > 0) { +- if (chown(ds_ctx->base_path, (uid_t) ds_ctx->jobuid, (gid_t) -1) < 0){ ++ if (lchown(ds_ctx->base_path, (uid_t) ds_ctx->jobuid, (gid_t) -1) < 0){ + rc = PMIX_ERR_NO_PERMISSIONS; + PMIX_ERROR_LOG(rc); + goto err_exit; +diff --git a/src/mca/common/dstore/dstore_segment.c b/src/mca/common/dstore/dstore_segment.c +index e90ea3f744..4f3b3ab5ef 100644 +--- a/src/mca/common/dstore/dstore_segment.c ++++ b/src/mca/common/dstore/dstore_segment.c +@@ -121,7 +121,7 @@ PMIX_EXPORT pmix_dstore_seg_desc_t *pmix_common_dstor_create_new_lock_seg(const + + if (setuid > 0){ + rc = PMIX_ERR_PERM; +- if (0 > chown(file_name, (uid_t) uid, (gid_t) -1)){ ++ if (0 > lchown(file_name, (uid_t) uid, (gid_t) -1)){ + PMIX_ERROR_LOG(rc); + goto err_exit; + } +@@ -212,7 +212,7 @@ PMIX_EXPORT pmix_dstore_seg_desc_t *pmix_common_dstor_create_new_segment(pmix_ds + + if (setuid > 0){ + rc = PMIX_ERR_PERM; +- if (0 > chown(file_name, (uid_t) uid, (gid_t) -1)){ ++ if (0 > lchown(file_name, (uid_t) uid, (gid_t) -1)){ + PMIX_ERROR_LOG(rc); + goto err_exit; + } +diff --git a/src/mca/gds/ds12/gds_ds12_lock_fcntl.c b/src/mca/gds/ds12/gds_ds12_lock_fcntl.c +index 4d7098920a..361d825977 100644 +--- a/src/mca/gds/ds12/gds_ds12_lock_fcntl.c ++++ b/src/mca/gds/ds12/gds_ds12_lock_fcntl.c +@@ -128,7 +128,7 @@ pmix_status_t pmix_gds_ds12_lock_init(pmix_common_dstor_lock_ctx_t *ctx, const c + } + } + if (0 != setuid) { +- if (0 > chown(lock_ctx->lockfile, uid, (gid_t) -1)) { ++ if (0 > lchown(lock_ctx->lockfile, uid, (gid_t) -1)) { + rc = PMIX_ERROR; + PMIX_ERROR_LOG(rc); + goto error; +diff --git a/src/mca/gds/ds12/gds_ds12_lock_pthread.c b/src/mca/gds/ds12/gds_ds12_lock_pthread.c +index 48c6bafd30..2aa89da1c7 100644 +--- a/src/mca/gds/ds12/gds_ds12_lock_pthread.c ++++ b/src/mca/gds/ds12/gds_ds12_lock_pthread.c +@@ -114,7 +114,7 @@ pmix_status_t pmix_gds_ds12_lock_init(pmix_common_dstor_lock_ctx_t *ctx, const c + } + memset(lock_ctx->segment->seg_base_addr, 0, size); + if (0 != setuid) { +- if (0 > chown(lock_ctx->lockfile, (uid_t) uid, (gid_t) -1)){ ++ if (0 > lchown(lock_ctx->lockfile, (uid_t) uid, (gid_t) -1)){ + rc = PMIX_ERROR; + PMIX_ERROR_LOG(rc); + goto error; +diff --git a/src/util/pmix_pty.c b/src/util/pmix_pty.c +index f743b31819..f3490b00db 100644 +--- a/src/util/pmix_pty.c ++++ b/src/util/pmix_pty.c +@@ -11,7 +11,7 @@ + * All rights reserved. + * Copyright (c) 2018 Cisco Systems, Inc. All rights reserved + * Copyright (c) 2019-2020 Intel, Inc. All rights reserved. +- * Copyright (c) 2021 Nanook Consulting. All rights reserved. ++ * Copyright (c) 2021-2023 Nanook Consulting. All rights reserved. + * $COPYRIGHT$ + * + * Additional copyrights may follow +@@ -244,7 +244,7 @@ static int ptys_open(int fdm, char *pts_name) + gid = -1; /* group tty is not in the group file */ + } + /* following two functions don't work unless we're root */ +- chown(pts_name, getuid(), gid); ++ lchown(pts_name, getuid(), gid); // DO NOT FOLLOW LINKS + chmod(pts_name, S_IRUSR | S_IWUSR | S_IWGRP); + fds = open(pts_name, O_RDWR); + if (fds < 0) { From c9dc19c14e0bc6ecefc221949f47f4c6d21cb1bb Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Sun, 10 Sep 2023 15:06:17 +0200 Subject: [PATCH 8761/9987] Add ParaView CUDA 12.2.0 build --- ...aView-5.11.1-foss-2022b-CUDA-12.2.0-egl.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0-egl.eb diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0-egl.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0-egl.eb new file mode 100644 index 00000000000..80355f098cd --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0-egl.eb @@ -0,0 +1,65 @@ +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] + +patches = ['ParaView-5.11.1-remove_glew_init_warning.patch', ('ParaView-5.11.1-fix_thrust_vtk_m.patch', 'VTK/ThirdParty/vtkm/vtkvtkm/vtk-m/')] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('CUDA', '12.2.0', '', SYSTEM), + ('OptiX', '7.2.0', '', SYSTEM), + ('Boost', '1.81.0'), + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('XZ', '5.2.7'), + ('HDF5', '1.14.0'), + ('netCDF', '4.9.0'), + ('libdrm', '2.4.114'), + ('Mesa', '22.2.4'), + ('Qt5', '5.15.7'), + ('zlib', '1.2.12'), + ('FFmpeg', '5.1.2'), + ('Szip', '2.1.1'), +] + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +# Enable NVidia IndeX +configopts += '-DPARAVIEW_USE_CUDA=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +# Enable OptiX raytracing +configopts += '-DPARAVIEW_ENABLE_RAYTRACING=ON ' +configopts += '-DVTK_ENABLE_OSPRAY=OFF ' +configopts += '-DVTK_ENABLE_OPTIX=ON ' +configopts += '-DPARAVIEW_ENABLE_XDMF2=ON ' +configopts += '-DPARAVIEW_ENABLE_XDMF3=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' +configopts += '-DCMAKE_CUDA_ARCHITECTURES=70 72 80 86 87 89 90 90a ' +# OpenGL & Mesa +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' +configopts += '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include ' +configopts += '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s ' % SHLIB_EXT +configopts += '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s ' % SHLIB_EXT +configopts += '-DVTK_OPENGL_HAS_EGL=ON ' +configopts += '-DVTK_USE_X=ON ' +configopts += '-DVTK_OPENGL_HAS_OSMESA=OFF ' + + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' From d6002fc82eb3c6f2b56e0e141c396b327abe41ff Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Sun, 10 Sep 2023 15:07:49 +0200 Subject: [PATCH 8762/9987] Add patch for ParaView CUDA 12.2.0 --- .../ParaView-5.11.1-fix_thrust_vtk_m.patch | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-fix_thrust_vtk_m.patch diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-fix_thrust_vtk_m.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-fix_thrust_vtk_m.patch new file mode 100644 index 00000000000..b1effa799e3 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-fix_thrust_vtk_m.patch @@ -0,0 +1,83 @@ +From 5d0481342a877c7297df4726a06cd4f45ea7af25 Mon Sep 17 00:00:00 2001 +From: Sujin Philip +Date: Mon, 9 Jan 2023 12:58:33 -0500 +Subject: [PATCH] Fix compile issues when using cuda 12 + +CUDA 12 adds a `cub::Swap` function that creates ambiguity with `vtkm::Swap`. +This happens when a function from the `cub` namespace is called with an object +of a class defined in the `vtkm` namespace as an argument. If that function +has an unqualified call to `Swap`, it results in ADL being used, causing the +templated functions `cub::Swap` and `vtkm::Swap` to conflict. +--- + vtkm/Swap.h | 24 ++++++++++++++++------- + vtkm/exec/cuda/internal/ExecutionPolicy.h | 1 + + 2 files changed, 18 insertions(+), 7 deletions(-) + +diff --git a/vtkm/Swap.h b/vtkm/Swap.h +index f833a495c5..342c5a20c9 100644 +--- a/vtkm/Swap.h ++++ b/vtkm/Swap.h +@@ -24,21 +24,31 @@ namespace vtkm + + /// Performs a swap operation. Safe to call from cuda code. + #if defined(VTKM_CUDA) ++// CUDA 12 adds a `cub::Swap` function that creates ambiguity with `vtkm::Swap`. ++// This happens when a function from the `cub` namespace is called with an object of a class ++// defined in the `vtkm` namespace as an argument. If that function has an unqualified call to ++// `Swap`, it results in ADL being used, causing the templated functions `cub::Swap` and ++// `vtkm::Swap` to conflict. ++#if defined(VTKM_CUDA_VERSION_MAJOR) && (VTKM_CUDA_VERSION_MAJOR >= 12) && \ ++ defined(VTKM_CUDA_DEVICE_PASS) ++using cub::Swap; ++#else + template +-VTKM_EXEC_CONT void Swap(T& a, T& b) ++VTKM_EXEC_CONT inline void Swap(T& a, T& b) + { +- using namespace thrust; ++ using thrust::swap; + swap(a, b); + } ++#endif + #elif defined(VTKM_HIP) + template +-__host__ void Swap(T& a, T& b) ++__host__ inline void Swap(T& a, T& b) + { +- using namespace std; ++ using std::swap; + swap(a, b); + } + template +-__device__ void Swap(T& a, T& b) ++__device__ inline void Swap(T& a, T& b) + { + T temp = a; + a = b; +@@ -46,9 +56,9 @@ __device__ void Swap(T& a, T& b) + } + #else + template +-VTKM_EXEC_CONT void Swap(T& a, T& b) ++VTKM_EXEC_CONT inline void Swap(T& a, T& b) + { +- using namespace std; ++ using std::swap; + swap(a, b); + } + #endif +diff --git a/vtkm/exec/cuda/internal/ExecutionPolicy.h b/vtkm/exec/cuda/internal/ExecutionPolicy.h +index 4db1edc6f9..02cad4ab6d 100644 +--- a/vtkm/exec/cuda/internal/ExecutionPolicy.h ++++ b/vtkm/exec/cuda/internal/ExecutionPolicy.h +@@ -17,6 +17,7 @@ + #include + VTKM_THIRDPARTY_PRE_INCLUDE + #include ++#include + #include + #include + VTKM_THIRDPARTY_POST_INCLUDE +-- +GitLab + From 543a23517c7fc81303863933e2b2b2d3349db460 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Sun, 10 Sep 2023 15:08:45 +0200 Subject: [PATCH 8763/9987] Rename ParaView-5.11.1-foss-2022b-CUDA-12.2.0-egl.eb to ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb --- ...DA-12.2.0-egl.eb => ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/ParaView/{ParaView-5.11.1-foss-2022b-CUDA-12.2.0-egl.eb => ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb} (100%) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0-egl.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb similarity index 100% rename from easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0-egl.eb rename to easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb From b0bf6cae7f797d591876520356dd57d7f25b8b10 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Sun, 10 Sep 2023 15:14:16 +0200 Subject: [PATCH 8764/9987] add missing header --- .../p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index 80355f098cd..964f1de818c 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -1,3 +1,10 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.11.1' +versionsuffix = '-CUDA-%(cudaver)s-egl' + +homepage = 'https://www.paraview.org' description = "ParaView is a scientific parallel visualizer." toolchain = {'name': 'foss', 'version': '2022b'} From 07a000ac155181d94a831310bfc789047cb57bea Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 10 Sep 2023 14:28:24 +0100 Subject: [PATCH 8765/9987] add download_instructions and move comment --- .../easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb index ea1db37a03d..6b6030dc02b 100644 --- a/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0.15-intel-2022a-CUDA-11.7.0.eb @@ -13,15 +13,16 @@ description = """HPL is a software package that solves a (random) dense linear s toolchain = {'name': 'intel', 'version': '2022a'} toolchainopts = {'usempi': True} -# download via https://developer.nvidia.com/computeworks-developer-exclusive-downloads +download_instructions = """Download CUDA Accelerated Linpack from +https://developer.nvidia.com/computeworks-developer-exclusive-downloads""" sources = ['hpl-%%(version_major_minor)s_FERMI_v%s.tgz' % local_patch_version] +# fix Make dependencies, so parallel build also works patches = ['HPL_parallel-make.patch'] checksums = [ {'hpl-2.0_FERMI_v15.tgz': '16dd21af22fced613923a6cb09805d63952fc9c9f278cb7582061a43fe39a408'}, {'HPL_parallel-make.patch': '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6'}, ] -# fix Make dependencies, so parallel build also works dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), ] From 6ddc155ef7737b73bdd9155a32cd26f9de55624c Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 10 Sep 2023 14:47:17 +0100 Subject: [PATCH 8766/9987] apply changes from #18467 --- easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb index bfa836ef2e4..81956f38a47 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb @@ -18,7 +18,12 @@ builddependencies = [ ('Perl', '5.36.1'), ] -local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" # perform iterative build to get both static and shared libraries configopts = [ @@ -26,8 +31,6 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] -parallel = 1 - # make sure that built libraries (libxc*.so*) in build directory are picked when running tests # this is required when RPATH linking is used pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " From 372ec825eae214510286a4e55e9c4efc86d4cf26 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Sun, 10 Sep 2023 19:35:10 +0200 Subject: [PATCH 8767/9987] Update ParaView-5.11.1-remove_glew_init_warning.patch Added patch description. --- .../ParaView/ParaView-5.11.1-remove_glew_init_warning.patch | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch index dc1f05c4d84..89ff7ae2a5d 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch @@ -1,3 +1,6 @@ +This patch silences a spurious warning that occurs when running the GUI under VirtualGL +with EGL enabled. +--- --- VTK/Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx.orig 2023-08-23 16:35:23.418470811 +0200 +++ VTK/Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx 2023-08-23 16:36:10.830654656 +0200 @@ -471,8 +471,8 @@ @@ -10,4 +13,4 @@ + //vtkErrorMacro("GLEW could not be initialized: " << errorMsg); return; } - +--- From 1d7eded957e6e69c24ed7b18063261dd5e6aaf78 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Sun, 10 Sep 2023 19:36:52 +0200 Subject: [PATCH 8768/9987] remove egl suffix --- .../p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index 964f1de818c..b350ad7c276 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'CMakeMake' name = 'ParaView' version = '5.11.1' -versionsuffix = '-CUDA-%(cudaver)s-egl' +versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://www.paraview.org' description = "ParaView is a scientific parallel visualizer." From 56155cea166b311885fb04ae02fb319ba661c9a3 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Sun, 10 Sep 2023 19:45:32 +0200 Subject: [PATCH 8769/9987] update checksum in paraview-5.11.1-foss-2022b --- easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb index 03df1ea3406..7037c3c1d9e 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb @@ -17,7 +17,7 @@ patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] checksums = [ {'ParaView-v5.11.1.tar.gz': 'de32f3e576b5f639ffc6903aa9e4cd46ac30c753185edc4366a7f305a6951b16'}, {'ParaView-5.11.1-remove_glew_init_warning.patch': - 'b3b866d36a14526b9241f74de1910c67cdf1961892d10c30d1d32453306b2a7d'}, + '3f99fc3d2dee556062e6ac75bd24eb316a739ac07525642f9a927d34e4fd9f21'}, ] builddependencies = [('CMake', '3.24.3')] From 65239d48f61d2738c743de8652f983f820d72d90 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Sun, 10 Sep 2023 19:47:08 +0200 Subject: [PATCH 8770/9987] add checksums in ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb --- .../p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index b350ad7c276..f71c2d00d96 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -13,9 +13,14 @@ toolchainopts = {'pic': True, 'usempi': True} local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] sources = ["%(name)s-v%(version)s.tar.gz"] - patches = ['ParaView-5.11.1-remove_glew_init_warning.patch', ('ParaView-5.11.1-fix_thrust_vtk_m.patch', 'VTK/ThirdParty/vtkm/vtkvtkm/vtk-m/')] - +checksums = [ + {'ParaView-v5.11.1.tar.gz': 'de32f3e576b5f639ffc6903aa9e4cd46ac30c753185edc4366a7f305a6951b16'}, + {'ParaView-5.11.1-remove_glew_init_warning.patch': + 'b3b866d36a14526b9241f74de1910c67cdf1961892d10c30d1d32453306b2a7d'}, + {'ParaView-5.11.1-fix_thrust_vtk_m.patch': + 'e9d25ffce47f44fc8f02cf81b3e901cb5b1343a953d33e0d2d342f255c45d72a'}, +] builddependencies = [('CMake', '3.24.3')] dependencies = [ From e084634ef6fe3a95a1d0122dd8af46f1f5f28783 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Sun, 10 Sep 2023 19:48:29 +0200 Subject: [PATCH 8771/9987] fix overlong line in ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb --- .../p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index f71c2d00d96..09665b0aee3 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -13,7 +13,8 @@ toolchainopts = {'pic': True, 'usempi': True} local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] sources = ["%(name)s-v%(version)s.tar.gz"] -patches = ['ParaView-5.11.1-remove_glew_init_warning.patch', ('ParaView-5.11.1-fix_thrust_vtk_m.patch', 'VTK/ThirdParty/vtkm/vtkvtkm/vtk-m/')] +patches = ['ParaView-5.11.1-remove_glew_init_warning.patch', + ('ParaView-5.11.1-fix_thrust_vtk_m.patch', 'VTK/ThirdParty/vtkm/vtkvtkm/vtk-m/')] checksums = [ {'ParaView-v5.11.1.tar.gz': 'de32f3e576b5f639ffc6903aa9e4cd46ac30c753185edc4366a7f305a6951b16'}, {'ParaView-5.11.1-remove_glew_init_warning.patch': @@ -21,6 +22,7 @@ checksums = [ {'ParaView-5.11.1-fix_thrust_vtk_m.patch': 'e9d25ffce47f44fc8f02cf81b3e901cb5b1343a953d33e0d2d342f255c45d72a'}, ] + builddependencies = [('CMake', '3.24.3')] dependencies = [ From e685704ca0bf7de0f3ca1b5590cfbfa83e0518c4 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Sun, 10 Sep 2023 23:04:47 +0200 Subject: [PATCH 8772/9987] fix patch checksum ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb Forgot to also update checksum for this patch here after adding description. --- .../p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index 09665b0aee3..f59e826149a 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -18,7 +18,7 @@ patches = ['ParaView-5.11.1-remove_glew_init_warning.patch', checksums = [ {'ParaView-v5.11.1.tar.gz': 'de32f3e576b5f639ffc6903aa9e4cd46ac30c753185edc4366a7f305a6951b16'}, {'ParaView-5.11.1-remove_glew_init_warning.patch': - 'b3b866d36a14526b9241f74de1910c67cdf1961892d10c30d1d32453306b2a7d'}, + '3f99fc3d2dee556062e6ac75bd24eb316a739ac07525642f9a927d34e4fd9f21'}, {'ParaView-5.11.1-fix_thrust_vtk_m.patch': 'e9d25ffce47f44fc8f02cf81b3e901cb5b1343a953d33e0d2d342f255c45d72a'}, ] From 9bdd60befee736d5483702a1eb27e7d6142b1b2d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Sun, 10 Sep 2023 23:35:48 +0200 Subject: [PATCH 8773/9987] fix checksum in ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb again --- .../p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index f59e826149a..531debb4cb3 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -20,7 +20,7 @@ checksums = [ {'ParaView-5.11.1-remove_glew_init_warning.patch': '3f99fc3d2dee556062e6ac75bd24eb316a739ac07525642f9a927d34e4fd9f21'}, {'ParaView-5.11.1-fix_thrust_vtk_m.patch': - 'e9d25ffce47f44fc8f02cf81b3e901cb5b1343a953d33e0d2d342f255c45d72a'}, + 'cb4a0dacf1fe2ddefa68ea6f6a061e6cb7d21717053a6514679f9ed73a52525f'}, ] builddependencies = [('CMake', '3.24.3')] From 72c1020fcd5cb6b7f4bb58d21ce8a13e80615ce5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Sep 2023 11:42:49 +0200 Subject: [PATCH 8774/9987] minor tweaks to 4.8.1 release notes --- RELEASE_NOTES | 162 ++++++++++++++++++++------------------------------ 1 file changed, 65 insertions(+), 97 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 484695a43d8..a72de567996 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,8 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 18,015 easyconfig files, for 3,224 different software packages, -incl. 39 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 18,021 easyconfig files, for 3,224 different software packages, +incl. 40 different (compiler) toolchains. v4.8.1 (11 September 2023) @@ -13,128 +13,96 @@ v4.8.1 (11 September 2023) update/bugfix release - added example easyconfig files for 83 new software packages: - - ALAMODE (#18733), AMRFinderPlus (#18559), Ax (#68), bcrypt (#18208), bench (#18656), BgeeDB (#18743), Boost.Python-NumPy - (#18505), CatBoost (#18591), centerline (#18273), cffi (#7105), ChIPseeker (#18662), connected-components-3d (#18289), - cryptography (#8495), CVglasso (#18657), DiffBind (#18663), drmaa-python (#18614), e3nn (#18304), flit (#18208), - GAPPadder (#18692), GenerativeModels (#18451), geosphere (#18659), gffutils (#18331), gkmSVM (#18660), hampel (#18409), - hatchling (#18208), HDF-EOS2 (#18297), Hybpiper (#18414), inih (#18516), IsoformSwitchAnalyzeR (#18664), IsoQuant - (#18331), Jupyter-bundle (#18634), leafcutter (#18615), libleidenalg (#18548), LIBSVM-Python (#18455), libvori - (#18379), maturin (#18405), meboot (#18658), mgen (#18402), Mikado (#18614), NanoCaller (#18726), nbclassic (#18617), - ncolor (#7146), nose3 (#18234), novaSTA (#18601), Omnipose (#18402), Optax (#18610), paramiko (#1504), Parsl (#18408), - peakdetect (#18402), PICRUSt2 (#18333), Platypus-Opt (#18291), PortMidi (#18252), pv (#16439), py-c3d (#18409), pygame - (#18252), pyodbc (#18334), Python-bundle-PyPI (#18208), qforce (#18456), RFdiffusion (#18304), Rhodium (#18291), - ruptures (#18306), Sabre (#18342), scGSVA (#18401), scib-metrics (#18734), scikit-plot (#18377), SDL2_mixer (#18252), - SDL2_ttf segment-anything (#18290), sentinelsat (#18367), setuptools-rust (#18208), slurm-drmaa (#18614), SuAVE-biomat - (#18678), T-Coffee (#17916), tensorflow-compression (#18676), torchvf (#18637), tornado (#256), tseriesEntropy (#18661), - TXR (#18665), unifdef (#18427), UniFrac (#18407), virtualenv (#2660), WFA2 (#18636) + - ALAMODE (#18733), AMRFinderPlus (#18559), Ax (#68), bcrypt (#18208), bench (#18656), BgeeDB (#18743), + Boost.Python-NumPy (#18505), CatBoost (#18591), centerline (#18273), cffi (#7105), ChIPseeker (#18662), + connected-components-3d (#18289), cryptography (#8495), CVglasso (#18657), DiffBind (#18663), drmaa-python (#18614), + e3nn (#18304), flit (#18208), GAPPadder (#18692), GenerativeModels (#18451), geosphere (#18659), gffutils (#18331), + gkmSVM (#18660), hampel (#18409), hatchling (#18208), HDF-EOS2 (#18297), Hybpiper (#18414), inih (#18516), + IsoformSwitchAnalyzeR (#18664), IsoQuant (#18331), Jupyter-bundle (#18634), JupyterNotebook (#18735, #18735), + leafcutter (#18615), libleidenalg (#18548), LIBSVM-Python (#18455), libvori (#18379), maturin (#18405), + meboot (#18658), mgen (#18402), Mikado (#18614), NanoCaller (#18726), nbclassic (#18617), ncolor (#7146), + nose3 (#18234), novaSTA (#18601), Omnipose (#18402), Optax (#18610), paramiko (#1504), Parsl (#18408), + peakdetect (#18402), PICRUSt2 (#18333, #18459), Platypus-Opt (#18291), PortMidi (#18252), pv (#16439), + py-c3d (#18409), pygame (#18252), pyodbc (#18334), Python-bundle-PyPI (#18208), qforce (#18456), + RFdiffusion (#18304), Rhodium (#18291), ruptures (#18306), Sabre (#18342), scGSVA (#18401), scib-metrics (#18734), + scikit-plot (#18377), SDL2_mixer (#18252), SDL2_ttf (#18252), segment-anything (#18290), sentinelsat (#18367), + setuptools-rust (#18208), slurm-drmaa (#18614), SuAVE-biomat (#18678), T-Coffee (#17916), + tensorflow-compression (#18676), torchvf (#18637), tornado (#18511), tseriesEntropy (#18661), TXR (#18665), + unifdef (#18427), UniFrac (#18407), virtualenv (#2660), WFA2 (#18636) - added additional easyconfigs for various supported software packages, including: - - ABINIT 9.10.3, Advisor 2023.0.0, Advisor 2023.2.0, aiohttp 3.8.5, AMD-uProf 4.1.424, Anaconda3 2023.07, anndata 0.9.2, - AOCC 4.0.0, APR 1.7.4, APR-util 1.6.3, Arcade-Learning-Envionment 0.8.1, archspec 0.2.1, Armadillo 12.6.2, arpack-ng - 3.9.0, assimp 5.2.5, ATK 2.38.0, at-spi2-atk 2.38.0, attrdict3 2.0.2, Autoconf 2.71, Automake 1.16.5, Autotools - 20220317, BAGEL 1.2.2, bam-readcount 1.0.1, BamTools 2.5.2, Bazel 6.3.1, BBMap 38.87, BCFtools 1.18, bcl2fastq2 2.20.0, - BeautifulSoup 4.12.2, BEDTools 2.31.0, binutils 2.40, biom-format 2.1.15, Biopython 1.76, Bio-SearchIO-hmmer 1.7.3, - Bison 3.8.2, bokeh 3.2.1, Boost 1.82.0, cairo 1.17.8, CalculiX-CrunchiX 2.20, c-ares 1.19.1, Cbc 2.10.5, ccache 4.7.5, - ccache 4.8.3, CDO 2.2.2, CFDEMcoupling 3.8.0, CFITSIO 4.3.0, CGAL 4.14.1, Cgl 0.60.7, CharLS 2.4.2, cicero 1.3.8, Clang - 16.0.4, Clang 16.0.6, Clp 1.17.8, Cluster-Buster 20200507, CMake 3.11.4, CoinUtils 2.11.9, conan 1.60.2, - configurable-http-proxy 4.5.5, coverage 7.2.7, CP2K 2023.1, cppy 1.2.1, CubeLib 4.8.1, CubeWriter 4.8.1, CUDA 12.2.2, - dask 2023.7.1, dcm2niix 1.0.20230411, Delly 1.1.6, DIAMOND 2.1.8, dill 0.3.7, dm-haiku 0.0.9, ecBuild 3.8.0, ecCodes - 2.31.0, ELPA 2023.05.001, ESPResSo 4.2.1, exiv2 0.28.0, expecttest 0.1.3, expecttest 0.1.5, fastahack 1.0.0, fastparquet - 2023.4.0, FFmpeg 6.0, ffnvcodec 12.0.16.0, FFTW 3.3.8, filevercmp 20191210, flatbuffers 23.5.26, flatbuffers-python - 23.1.4, flatbuffers-python 23.5.26, flex 2.6.4, FLTK 1.3.8, FreeImage 3.18.0, FreeSurfer 7.4.1, FriBidi 1.0.12, fsom - 20151117, gc 8.2.4, GCC 13.2.0, GCCcore 13.2.0, GConf 3.2.6, GDB 13.2, Gdk-Pixbuf 2.42.10, GEOS 3.12.0, gettext 0.22, - GHC 9.2.2, Ghostscript 10.01.2, giflib 5.2.1, GLib 2.77.1, GLM 0.9.9.8, GLPK 5.0, gmpy2 2.1.2, gmpy2 2.1.5, gnuplot - 5.4.8, GObject-Introspection 1.76.1, gperftools 2.12, Graphene 1.10.8, Graphviz 8.1.0, graphviz-python 0.20.1, Greenlet - 2.0.2, gRPC 1.57.0, GST-plugins-base 1.22.5, GStreamer 1.22.5, GTK3 3.24.37, GTK4 4.11.3, GTS 0.7.6, GTS 0.7.6, Guile - 3.0.9, h4toh5 2.2.5, h5netcdf 1.2.0, h5py 3.9.0, HarfBuzz 5.3.1, HDF5 1.14.0, HDF5 1.14.0, help2man 1.49.3, hiredis - 1.2.0, HOOMD-blue 4.0.1, Horovod 0.22.1, Horovod 0.28.1, HPL 2.3, htop 3.2.2, HTSlib 1.18, hwloc 2.9.2, Hydra 1.3.2, - hypothesis 6.82.0, Hypre 2.29.0, ICU 73.2, igraph 0.10.6, iimkl 2023a, imageio 2.31.1, ImageMagick 7.1.1, inferCNV - 1.12.0, inferCNV 1.14.2, intervaltree 0.1, intervaltree-python 3.1.0, IPython 8.14.0, ISL 0.26, Java 11.0.20, jq 1.6, - JsonCpp 1.9.5, Julia 1.9.2, Julia 1.9.3, JupyterHub 4.0.1, JupyterHub 4.0.2, JupyterLab 4.0.3, JupyterLab 4.0.5, - jupyterlmod 4.0.3, JupyterNotebook 7.0.2, jupyter-resource-usage 1.0.0, jupyter-server 1.21.0, kb-python 0.27.3, kma - 1.4.12a, KMC 3.2.1, KMC 3.2.2, LAME 3.100, leidenalg 0.10.1, LERC 4.0.0, libaec 1.0.6, libaio 0.3.113, libavif 0.11.1, - libcerf 2.3, libdrm 2.4.115, libdwarf 0.7.0, libepoxy 1.5.10, libevent 2.1.12, libfabric 1.19.0, libgd 2.3.3, libgit2 - 1.7.1, libGLU 9.0.3, libglvnd 1.6.0, Libint 2.7.2, libnsl 2.0.0, libpciaccess 0.17, libsndfile 1.2.2, libsodium 1.0.18, - libtool 2.4.7, libunistring 1.1, libwebp 1.3.1, libwebp 1.3.1, libwpe 1.14.1, libxml2 2.11.5, libxsmm 1.17, LittleCMS - 2.15, LLVM 16.0.6, Lua 5.4.6, M4 1.4.19, MACS2 2.2.9.1, magma 2.7.1, mahotas 1.4.13, makeinfo 7.0.3, Mako 1.2.4, Mamba - 23.1.0, MATIO 1.5.23, matplotlib 3.7.2, medaka 1.8.1, medaka 1.9.1, Mercurial 6.4.5, Mesa 23.1.4, meson-python 0.13.2, - Miniconda3 23.5.2, Monocle3 1.3.1, MPC 1.3.1, mpi4py 3.1.4, MRtrix 3.0.4, multichoose 1.0.3, MUMPS 5.6.1, MXNet 1.9.1, - NAMD 2.14, napari 0.4.18, ncdu 1.18, ncurses 6.4, ncview 2.1.8, netCDF 4.9.2, netCDF-C++4 4.3.1, netCDF-Fortran 4.6.1, - nettle 3.9.1, networkx 3.1, NLopt 2.7.1, nodejs 18.17.1, nsync 1.26.0, numactl 2.0.16, NVHPC 23.7, ont-fast5-api 4.1.1, - OPARI2 2.0.7, OpenAI-Gym 0.26.2, OpenCV 4.8.0, OpenFOAM 11, OpenFOAM 5.0, OpenImageIO 2.4.14.0, OpenMPI 4.1.5, OpenPGM - 5.2.122, Osi 0.108.8, OSU-Micro-Benchmarks 7.1-1, OTF2 3.0.3, OTF2 3.0.3, Pango 1.50.14, PAPI 7.0.1, PAPI 7.0.1, - parallel 20230722, ParaView 5.4.1, PartitionFinder 2.1.1, patchelf 0.17.2, pdsh 2.34, PDT 3.25.1, Perl 5.38.0, Pillow - 10.0.0, Pillow-SIMD 9.5.0, Pint 0.22, pixman 0.42.2, pkgconf 2.0.3, pkgconfig 1.5.5, plotly.py 5.16.0, PLUMED 2.9.0, PLY - 3.11, pocl 4.0, poetry 1.5.1, PROJ 6.3.1, prokka 1.14.5, protobuf 24.0, protobuf-python 4.24.0, psutil 5.9.5, PuLP - 2.7.0, pybedtools 0.9.0, pyBigWig 0.3.22, pybind11 2.11.1, PyCairo 1.24.0, PycURL 7.45.2, PycURL 7.45.2, PyGObject - 3.44.1, Pylint 2.17.4, pypmt 1.1.0, pyproj 3.6.0, pyro-ppl 1.8.4, Python 2.7.18, python-igraph 0.10.6, PyZMQ 25.1.1, - Qhull 2020.2, QIIME2 2023.5.1, Qt5 5.15.10, QuantumESPRESSO 7.2, Racon 1.5.0, rclone 1.63.1, RE2 2023, re2c 3.1, - RegTools 1.0.0, rjags 4, RnBeads 2.14.0, RTG-Tools 3.12.1, SAMtools 1.18, Scalene 1.5.26, scikit-build 0.17.6, - scikit-image 0.21.0, SciPy-bundle 2023.07, Score-P 8.1, SCOTCH 7.0.3, SDL2 2.28.2, SDL2_image 2.6.3, SDL2_mixer 2.6.3, - SDL2_ttf 2.20.2, segment-anything 1.0, sentinelsat 1.2.1, setuptools 64.0.3, Seurat 4.1.0, SeuratWrappers 20221022, - Shapely 2.0.1, SIONlib 1.7.7, SIONlib 1.7.7, slurm drmaa, smithwaterman 20160702, snakemake 7.32.3, SpaceRanger 2.1.0, - SpaceRanger 2.1.0, spglib 2.0.2, SpiecEasi 1.1.1, SPOOLES 2.2, Stack 2.11.1, STAR 2.7.11a, Structure 2.3.4, SUNDIALS - 6.6.0, SWIG 4.1.1, SWIG 4.1.1, sympy 1.12, sympy 1.9, tabixpp 1.1.2, tbb 2021.10.0, tbl2asn 20230713, tcsh 6.24.10, - TensorFlow 2.13.0, TensorFlow 2.13.0, tensorflow-probability 0.19.0, time 1.9, Tk 8.6.13, Tkinter 3.11.3, tqdm 4.66.1, - unixODBC 2.3.11, Valgrind 3.21.0, Valgrind 3.21.0, vcflib 1.0.9, VirtualGL 3.1, VisPy 0.12.2, VTK 8.2.0, Wayland 1.22.0, - Wayland 1.22.0, WebKitGTK+ 2.40.4, wpebackend-fdo 1.14.1, wrapt 1.15.0, wxPython 4.2.1, wxWidgets 3.2.2.1, x264 - 20230226, x265 3.5, xorg-macros 1.20.0, xprop 1.2.5, Xvfb 21.1.8, xxd 9.0.1696, XZ 5.4.4, Yambo 5.1.2, Z3 4.10.2, Z3 - 4.12.2, Z3 4.8.10, Z3 4.8.11, Z3 4.8.12, Z3 4.8.16, zarr 2.16.0, ZeroMQ 4.3.4, zlib 1.2.13 + - ABINIT 9.10.3, Advisor 2023.2.0, aiohttp 3.8.5, AMD-uProf 4.1.424, Anaconda3 2023.07-2, anndata 0.9.2, + APR 1.7.4, APR-util 1.6.3, Arcade-Learning-Envionment 0.8.1, archspec 0.2.1, Armadillo 12.6.2, arpack-ng 3.9.0, + assimp 5.2.5, BAGEL 1.2.2, bam-readcount 1.0.1, Bazel 6.3.1, BCFtools 1.18, BeautifulSoup 4.12.2, BEDTools 2.31.0, + biom-format 2.1.15, bokeh 3.2.1, Boost 1.82.0, cairo 1.17.8, c-ares 1.19.1, ccache 4.8.3, CDO 2.2.2, CFITSIO 4.3.0, + Cgl 0.60.7, CharLS 2.4.2, cicero 1.3.8, Clang 16.0.6, Clp 1.17.8, Cluster-Buster 20200507, CoinUtils 2.11.9, + conan 1.60.2, configurable-http-proxy 4.5.5, coverage 7.2.7, CP2K 2023.1, CubeLib 4.8.1, CubeWriter 4.8.1, + CUDA 12.2.2, dask 2023.7.1, dcm2niix 1.0.20230411, Delly 1.1.6, dill 0.3.7, ecBuild 3.8.0, ecCodes 2.31.0, + ELPA 2023.05.001, exiv2 0.28.0, expecttest 0.1.5, fastparquet 2023.4.0, FFmpeg 6.0, ffnvcodec 12.0.16.0, + flatbuffers 23.5.26, flatbuffers-python 23.5.26, FreeSurfer 7.4.1, fsom 20151117, gc 8.2.4, GCC 13.2.0, GDB 13.2, + GEOS 3.12.0, gettext 0.22, GHC 9.2.2, Ghostscript 10.01.2, GLib 2.77.1, gmpy2 2.1.5, gnuplot 5.4.8, + GObject-Introspection 1.76.1, gperftools 2.12, Graphviz 8.1.0, gRPC 1.57.0, GST-plugins-base 1.22.5, + GStreamer 1.22.5, GTK3 3.24.37, GTK4 4.11.3, h4toh5 2.2.5, h5netcdf 1.2.0, h5py 3.9.0, hiredis 1.2.0, + Horovod 0.28.1, htop 3.2.2, HTSlib 1.18, hwloc 2.9.2, Hydra 1.3.2, hypothesis 6.82.0, Hypre 2.29.0, ICU 73.2, + igraph 0.10.6, iimkl/2023a, imageio 2.31.1, ImageMagick 7.1.1-15, inferCNV 1.14.2, IPython 8.14.0, ISL 0.26, + Julia 1.9.3, JupyterLab 4.0.5, jupyter-resource-usage 1.0.0, kma 1.4.12a, KMC 3.2.2, leidenalg 0.10.1, + libdrm 2.4.115, libdwarf 0.7.0, libfabric 1.19.0, libgit2 1.7.1, libGLU 9.0.3, libsndfile 1.2.2, libwpe 1.14.1, + libxml2 2.11.5, LittleCMS 2.15, LLVM 16.0.6, Lua 5.4.6, MACS2 2.2.9.1, magma 2.7.1, mahotas 1.4.13, makeinfo 7.0.3, + Mamba 23.1.0, matplotlib 3.7.2, medaka 1.8.1 + 1.9.1, Mercurial 6.4.5, Mesa 23.1.4, meson-python 0.13.2, + Miniconda3 23.5.2, Monocle3 1.3.1, MPC 1.3.1, MRtrix 3.0.4, MUMPS 5.6.1, MXNet 1.9.1, napari 0.4.18, ncdu 1.18, + netCDF 4.9.2, netCDF-Fortran 4.6.1, nettle 3.9.1, networkx 3.1, nodejs 18.17.1, nsync 1.26.0, NVHPC 23.7, + OpenAI-Gym 0.26.2, OpenCV 4.8.0, OpenFOAM 11, OpenImageIO 2.4.14.0, Osi 0.108.8, OTF2 3.0.3, Pango 1.50.14, + PAPI 7.0.1, parallel 20230722, Perl 5.38.0, Pillow 10.0.0, Pillow-SIMD 9.5.0, Pint 0.22, pkgconf 2.0.3, + plotly.py 5.16.0, PLUMED 2.9.0, pocl 4.0, poetry 1.5.1, protobuf 24.0, protobuf-python 4.24.0, psutil 5.9.5, + PuLP 2.7.0, pyBigWig 0.3.22, pybind11 2.11.1, PyCairo 1.24.0, PyGObject 3.44.1, Pylint 2.17.4, pyproj 3.6.0, + pyro-ppl 1.8.4, python-igraph 0.10.6, PyZMQ 25.1.1, QIIME2 2023.5.1, Qt5 5.15.10, QuantumESPRESSO 7.2, + rclone 1.63.1, RE2 2023-08-01, re2c 3.1, RegTools 1.0.0, RnBeads 2.14.0, RTG-Tools 3.12.1, SAMtools 1.18, + Scalene 1.5.26, scikit-build 0.17.6, scikit-image 0.21.0, SciPy-bundle 2023.07, Score-P 8.1, SCOTCH 7.0.3, + SDL2 2.28.2, SDL2_image 2.6.3, setuptools 64.0.3, SeuratWrappers 20221022, snakemake 7.32.3, SpaceRanger 2.1.0, + SpiecEasi 1.1.1, Stack 2.11.1, STAR 2.7.11a, SUNDIALS 6.6.0, SWIG 4.1.1, sympy 1.12, tabixpp 1.1.2, tbb 2021.10.0, + tbl2asn 20230713, tcsh 6.24.10, TensorFlow 2.13.0, tensorflow-probability 0.19.0, Tk 8.6.13, Tkinter 3.11.3, + tqdm 4.66.1, unixODBC 2.3.11, Valgrind 3.21.0, vcflib 1.0.9, VirtualGL 3.1, VisPy 0.12.2, Wayland 1.22.0, + WebKitGTK+ 2.40.4, wpebackend-fdo 1.14.1, wxPython 4.2.1, Xvfb 21.1.8, xxd 9.0.1696, XZ 5.4.4, Yambo 5.1.2, + Z3 4.12.2, zarr 2.16.0 - minor enhancements, including: - - add UCell extension to R-bundle-Bioconductor 3.16 (#18281) - - add decoupleR package to R-bundle-Bioconductor 3.15 with foss/2022a as extension (#18399) - - add tabletools extension to recent R easyconfigs (#18510) - - add decoupleR extension to R-bundle-Bioconductor v3.16 (#18552) + - add extensions to recent R-bundle-Bioconductors easyconfigs: UCell (#18281), decoupleR (#18399, #18552), RnBeads (#18682) + - add extensions to recent R easyconfigs: tabletools (#18510), flextables (#18719) - add test for easyconfig file permissions (#18647) - - add RnBeads extensions to R-bundle-Bioconductor v3.16 (#18682) - - add `flextables` extension to R v4.2.1 + v4.2.2 (#18719) - various bug fixes, including: - - set JULIA_DEPOT_PATH in Julia easyconfigs with default value (#17976) + - set `$JULIA_DEPOT_PATH` in Julia easyconfigs with default value (#17976) - remove superflous dependencies from Horovod easyconfig on top of PyTorch (#18262) - disable building documentation for libsigc++ 2.10.x (#18301) - use MCR dependency in FreeSurfer 7.3.2 and 7.4.0 (#18303) - add `hpctestlib` to the `$PYTHONPATH` in ReFrame 4.2.0 easyconfig (#18320) - - fix installation of Python bindings for recent Arrow easyconfigs by adding `--no-build-isolation` to `pip install` command (#18348) + - fix installation of Python bindings for recent Arrow easyconfigs by adding `--no-build-isolation` to `pip install` command (#18348, #18432, #18440, #18441) - add/fix patches for PyTorch 1.13.1 w/ foss/2022a (#18371) - - {tools}[GCCcore/11.3.0] jupyter-server 1.21.0 (#18389) + - add missing nbclassic extension to jupyter-server 1.21.0 (#18389) - Fix batchspawner for JupyterHub 3.0 (#18390) - - fix compiler flags and toolchain options for ScaLAPACK 2.2.0 (#18396) - - fix compiler flags and toolchain options for ScaLAPACK 2.1.0 (#18397) + - fix compiler flags and toolchain options for ScaLAPACK 2.1.0 + 2.2.0 (#18396, #18397) - add patch to fix CUDA race condition problem for Score-P v8.0 (#18411) - add `-DABSL_PROPAGATE_CXX_STD=ON` to recent Abseil easyconfigs (required for PyTorch) (#18413) - add missing patches for PyTorch 1.12.0 w/ foss/2022a (#18430) - - fix installation of Python bindings for Arrow 8.0.0 with foss/2022.05 by adding `--no-build-isolation` to `pip install` command (#18432) - fix regression in GCC 12.1 + 12.2 with wrong warnings (#18434) - - fix installation of Python bindings for Arrow 0.17.1 by adding `--no-build-isolation` to `pip install` command (#18440) - - fix installation of Python bindings for Arrow 0.16.0 by adding `--no-build-isolation` to `pip install` command (#18441) - add patch for LIBSVM 3.30 to pass `$CFLAGS` + `$LDFLAGS` and run tests (#18454) - - copy missing `default_files` directory for PICRUSt2 (#18459) - add patch for Automake 1.16.5 to fix help2man error (#18468) - consistently use ON/OFF for -DBUILD_SHARED_LIBS (#18484) - - add patch to fix quantization failure in PyTorch 1.11.0 on POWER (#18489) - - add patches to fix PyTorch 1.12 (CPU-only) w/ foss/2022a on POWER (#18490) - - Add missing patches for PyTorch 1.12.0 w/ `foss/2022a` + CUDA 11.7.0 (#18491) - - add patches to fix PyTorch-1.12.1 w/ foss/2021a + CUDA v11.3.1 on POWER (#18492) - - add patches to fix PyTorch-1.12.1 w/ foss/2021b + CUDA v11.5.2 on POWER (#18493) - - add patches to fix PyTorch-1.12.1 w/ foss/2022a + CUDA v11.7.0 on POWER (#18494) - - add patches to fix PyTorch 1.13.1 w/ foss/2022a on POWER + fix flaky `test_jit_legacy` test (#18500) + - add missing patches for PyTorch 1.12.0 w/ `foss/2022a` + CUDA 11.7.0 (#18491) + - add patches to fix PyTorch 1.12.1 + 1.13.1 on POWER on POWER (#18489, #18490, #18492, #18493, #18494, #18500) + - add patch to fix flaky `test_jit_legacy` test for PyTorch 1.13.1 (#18500) - add alternative checksum for Extrae v4.0.4 (#18564) + - remove appending of `$__EGL_VENDOR_LIBRARY_DIRS` in recent Mesa easyconfigs, since Mesa easyblock now appends to it (#18630) - set `$MUJOCO_PY_FORCE_CPU` to avoid that mujoco-py checks for nvidia-smi and aborts installation because `/usr/lib/nvidia` is not in `$LD_LIBRARY_PATH` (#18641) - fix sanity check for ccache by setting `LC_ALL=C` (#18677) - make Autoconf a build dep for tRNAscan-SE + add missing Perl dependency (#18680) - - fix configure option to disable wxwidgets for gnuplot 5.4.6 (#18691) - strip out hardcoded `-march=native` used by RapidJSON 1.1.0 (#18725) - - disable detection of Dbus broker for `at-spi2-core` (+ bump at-spi2-core v2.49.90 to v2.49.91) (#18727) + - disable detection of Dbus broker for `at-spi2-core` (#18727) - make sure that 'moduleclass' is set in all easyconfig files (and is not set to default 'base' moduleclass) (#18739) - add patch for MPFR 4.1.0 to fix failing tsprintf test with glibc >= 2.37 (#18746) - - move wrapt from `foss/2022b` to `gfbf/2022b` (#18752) + - add patch for PMIx 4.x to use `lchown` so links are not followed (#18755) - other changes: + - update Java/11 wrapper to Java/11.0.20 (#18435) - use custom easyblock for recent sympy easyconfigs to prevent test failures (#18428) - use GCC/12.2.0 toolchain for GSL 2.7, remove easyconfig for GSL 2.7 with GCCcore/12.2.0 (#18501) - - use Perl instead of Perl minimal as build dependency for libcerf and remove EasyConfig for Perl minimal (#18565) - - remove appending of `$__EGL_VENDOR_LIBRARY_DIRS` in recent Mesa easyconfigs, since Mesa easyblock now appends to it (#18630) - - use `GCCcore/12.2.0` toolchain for gnuplot 5.4.6 + disable wx support (#18648) - - remove html5lib-1.1-GCCcore-12.3.0.eb as html5lib is in `Python-bundle-PyPI/2023.06-GCCcore-12.3.0` (#18698) - - rename `notebook` to `JupyterNotebook` (#18735) + - disable wx support in gnuplot 5.4.6 (#18648, #18691) - filter out template + archived easyconfigs when determining changed easyconfigs in PRs (#18753) From ff15ce911ed012993241aa9f53414a311ab78854 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 11 Sep 2023 12:43:07 +0200 Subject: [PATCH 8775/9987] Update ParaView-5.11.1-remove_glew_init_warning.patch --- .../p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch index 89ff7ae2a5d..ad26e8652b8 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-remove_glew_init_warning.patch @@ -13,4 +13,3 @@ with EGL enabled. + //vtkErrorMacro("GLEW could not be initialized: " << errorMsg); return; } ---- From 28981cd74c330d805c7fbc6ed1e390114c28adf4 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 11 Sep 2023 12:45:22 +0200 Subject: [PATCH 8776/9987] update checksum after fixing apparent issue in patch in ParaView-5.11.1-foss-2022b.eb --- easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb index 7037c3c1d9e..e751b3fb53b 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb @@ -17,7 +17,7 @@ patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] checksums = [ {'ParaView-v5.11.1.tar.gz': 'de32f3e576b5f639ffc6903aa9e4cd46ac30c753185edc4366a7f305a6951b16'}, {'ParaView-5.11.1-remove_glew_init_warning.patch': - '3f99fc3d2dee556062e6ac75bd24eb316a739ac07525642f9a927d34e4fd9f21'}, + 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, ] builddependencies = [('CMake', '3.24.3')] From 044831f7d1c9575b376bd8e842904de75bc21f14 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 11 Sep 2023 12:45:57 +0200 Subject: [PATCH 8777/9987] Update ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb --- .../p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index 531debb4cb3..05edbed72aa 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -18,7 +18,7 @@ patches = ['ParaView-5.11.1-remove_glew_init_warning.patch', checksums = [ {'ParaView-v5.11.1.tar.gz': 'de32f3e576b5f639ffc6903aa9e4cd46ac30c753185edc4366a7f305a6951b16'}, {'ParaView-5.11.1-remove_glew_init_warning.patch': - '3f99fc3d2dee556062e6ac75bd24eb316a739ac07525642f9a927d34e4fd9f21'}, + 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, {'ParaView-5.11.1-fix_thrust_vtk_m.patch': 'cb4a0dacf1fe2ddefa68ea6f6a061e6cb7d21717053a6514679f9ed73a52525f'}, ] From 8c550025150be50f38ba566571f1f47a36f3b459 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Sep 2023 12:59:51 +0200 Subject: [PATCH 8778/9987] include additional PRs that got merged last-minute in v4.8.1 release notes --- RELEASE_NOTES | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index a72de567996..6ac82efe759 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -67,6 +67,7 @@ update/bugfix release - add extensions to recent R-bundle-Bioconductors easyconfigs: UCell (#18281), decoupleR (#18399, #18552), RnBeads (#18682) - add extensions to recent R easyconfigs: tabletools (#18510), flextables (#18719) - add test for easyconfig file permissions (#18647) + - simplify build and install options for Ghostscript (#18750) - various bug fixes, including: - set `$JULIA_DEPOT_PATH` in Julia easyconfigs with default value (#17976) - remove superflous dependencies from Horovod easyconfig on top of PyTorch (#18262) @@ -90,12 +91,13 @@ update/bugfix release - add patch to fix flaky `test_jit_legacy` test for PyTorch 1.13.1 (#18500) - add alternative checksum for Extrae v4.0.4 (#18564) - remove appending of `$__EGL_VENDOR_LIBRARY_DIRS` in recent Mesa easyconfigs, since Mesa easyblock now appends to it (#18630) + - correct `dirs` in `sanity_check_paths` in template easyconfig (#18635) - set `$MUJOCO_PY_FORCE_CPU` to avoid that mujoco-py checks for nvidia-smi and aborts installation because `/usr/lib/nvidia` is not in `$LD_LIBRARY_PATH` (#18641) - fix sanity check for ccache by setting `LC_ALL=C` (#18677) - make Autoconf a build dep for tRNAscan-SE + add missing Perl dependency (#18680) - strip out hardcoded `-march=native` used by RapidJSON 1.1.0 (#18725) - disable detection of Dbus broker for `at-spi2-core` (#18727) - - make sure that 'moduleclass' is set in all easyconfig files (and is not set to default 'base' moduleclass) (#18739) + - make sure that 'moduleclass' is set in all easyconfig files (and is not set to default `base` moduleclass) (#18739) - add patch for MPFR 4.1.0 to fix failing tsprintf test with glibc >= 2.37 (#18746) - add patch for PMIx 4.x to use `lchown` so links are not followed (#18755) - other changes: From a3a9f77ddf8c86bc7898e8d5202e16b6e08347ff Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 11 Sep 2023 15:13:08 +0200 Subject: [PATCH 8779/9987] adding easyconfigs: scikit-optimize-0.9.0-foss-2022a.eb, pretty-yaml-23.9.5-GCCcore-11.3.0.eb, photontorch-0.4.1-foss-2022a.eb --- .../photontorch-0.4.1-foss-2022a.eb | 38 +++++++++++++++++++ .../pretty-yaml-23.9.5-GCCcore-11.3.0.eb | 33 ++++++++++++++++ .../scikit-optimize-0.9.0-foss-2022a.eb | 31 +++++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-23.9.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.9.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2022a.eb b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2022a.eb new file mode 100644 index 00000000000..e43677fa77d --- /dev/null +++ b/easybuild/easyconfigs/p/photontorch/photontorch-0.4.1-foss-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'photontorch' +version = '0.4.1' + +homepage = 'https://docs.photontorch.com/' +description = """ +Photontorch is a photonic simulator for highly parallel simulation and optimization of photonic circuits in time and +frequency domain. Photontorch features CUDA enabled simulation and optimization of photonic circuits. It leverages the +deep learning framework PyTorch to view the photonic circuit as essentially a recurrent neural network. This enables the +use of native PyTorch optimizers to optimize the (physical) parameters of the circuit. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('networkx', '2.8.4'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('torch-lfilter', '0.0.3', { + 'source_tmpl': 'torch_lfilter-%(version)s.tar.gz', + 'checksums': ['aa613725b73e7b6e7efd63c30580a906d7bb23206b5d045b8452ab770f7a50df'], + }), + (name, version, { + 'checksums': ['50d2e2c8a24c914cc7afee1eea6efb8bccfbc19ff9652a9af46efad28caa6381'], + }), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-23.9.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-23.9.5-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..3990756639a --- /dev/null +++ b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-23.9.5-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'pretty-yaml' +local_mod = 'pyaml' +version = '23.9.5' + +homepage = 'https://github.com/mk-fg/pretty-yaml' +description = """ +PyYAML-based python module to produce pretty and readable YAML-serialized data. +This module is for serialization only, see ruamel.yaml module for literate YAML +parsing (keeping track of comments, spacing, line/column numbers of values, etc). +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod] +sources = ['%s-%%(version)s.tar.gz' % local_mod] +checksums = ['9b903a1185eefdf85499cb856b70b12245988db990bfd6af596d3521ece306a4'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': local_mod} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.9.0-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.9.0-foss-2022a.eb new file mode 100644 index 00000000000..84e68863420 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.9.0-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'scikit-optimize' +version = '0.9.0' + +homepage = 'https://scikit-optimize.github.io' +description = """ +Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive +and noisy black-box functions. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['77d8c9e64947fc9f5cc05bbc6aed7b8a9907871ae26fe11997fd67be90f26008'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('matplotlib', '3.5.2'), + ('pretty-yaml', '23.9.5'), +] + +options = {'modulename': 'skopt'} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From c4c0f5e2b38c12a4c60c38aea89d37845ee96138 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Sep 2023 15:41:38 +0200 Subject: [PATCH 8780/9987] backport lchown patch to PMIx 3.1.x + 3.2.x --- .../p/PMIx/PMIx-3.1.4-GCCcore-8.3.0.eb | 6 +- .../p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb | 6 +- .../p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb | 6 +- .../p/PMIx/PMIx-3.1.x_lchown.patch | 87 +++++++++++++++++++ .../p/PMIx/PMIx-3.2.3-GCCcore-10.3.0.eb | 6 +- 5 files changed, 107 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-3.1.x_lchown.patch diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.4-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.4-GCCcore-8.3.0.eb index f732b370577..48b78f5e9cb 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.4-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.4-GCCcore-8.3.0.eb @@ -23,7 +23,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/pmix/pmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['982f6eff7764b7c7d6566554f47bb3244fc3ff5bf0abba2bc395f0833d0a9ee0'] +patches = ['PMIx-3.1.x_lchown.patch'] +checksums = [ + {'pmix-3.1.4.tar.bz2': '982f6eff7764b7c7d6566554f47bb3244fc3ff5bf0abba2bc395f0833d0a9ee0'}, + {'PMIx-3.1.x_lchown.patch': '9a4d5e3cb0e619f2e9ac2ffad0b8cb2b22f5c67973080724c79519fb34d55776'}, +] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb index efe2a2d3ed8..fa9cd004705 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb @@ -23,7 +23,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['88934195174455df478b996313095df25b51d0caf5a5cce01b22f0ccdc6c5cf7'] +patches = ['PMIx-3.1.x_lchown.patch'] +checksums = [ + {'pmix-3.1.5.tar.bz2': '88934195174455df478b996313095df25b51d0caf5a5cce01b22f0ccdc6c5cf7'}, + {'PMIx-3.1.x_lchown.patch': '9a4d5e3cb0e619f2e9ac2ffad0b8cb2b22f5c67973080724c79519fb34d55776'}, +] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb index 6b6c1bc9807..59b8ab28bce 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-9.3.0.eb @@ -23,7 +23,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['88934195174455df478b996313095df25b51d0caf5a5cce01b22f0ccdc6c5cf7'] +patches = ['PMIx-3.1.x_lchown.patch'] +checksums = [ + {'pmix-3.1.5.tar.bz2': '88934195174455df478b996313095df25b51d0caf5a5cce01b22f0ccdc6c5cf7'}, + {'PMIx-3.1.x_lchown.patch': '9a4d5e3cb0e619f2e9ac2ffad0b8cb2b22f5c67973080724c79519fb34d55776'}, +] builddependencies = [('binutils', '2.34')] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.x_lchown.patch b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.x_lchown.patch new file mode 100644 index 00000000000..09cc729e08e --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.x_lchown.patch @@ -0,0 +1,87 @@ +backport of https://github.com/openpmix/openpmix/pull/3150 to PMIx 3.1.x +diff -ru pmix-3.1.5.orig/src/mca/common/dstore/dstore_base.c pmix-3.1.5/src/mca/common/dstore/dstore_base.c +--- pmix-3.1.5.orig/src/mca/common/dstore/dstore_base.c 2020-02-19 05:55:43.000000000 +0100 ++++ pmix-3.1.5/src/mca/common/dstore/dstore_base.c 2023-09-11 15:17:22.502130578 +0200 +@@ -525,7 +525,7 @@ + } + } + if (s->setjobuid > 0){ +- if (0 > chown(s->nspace_path, (uid_t) s->jobuid, (gid_t) -1)){ ++ if (0 > lchown(s->nspace_path, (uid_t) s->jobuid, (gid_t) -1)){ + rc = PMIX_ERROR; + PMIX_ERROR_LOG(rc); + return rc; +@@ -1677,7 +1677,7 @@ + } + } + if (ds_ctx->setjobuid > 0) { +- if (chown(ds_ctx->base_path, (uid_t) ds_ctx->jobuid, (gid_t) -1) < 0){ ++ if (lchown(ds_ctx->base_path, (uid_t) ds_ctx->jobuid, (gid_t) -1) < 0){ + rc = PMIX_ERR_NO_PERMISSIONS; + PMIX_ERROR_LOG(rc); + goto err_exit; +diff -ru pmix-3.1.5.orig/src/mca/common/dstore/dstore_segment.c pmix-3.1.5/src/mca/common/dstore/dstore_segment.c +--- pmix-3.1.5.orig/src/mca/common/dstore/dstore_segment.c 2020-02-19 05:55:43.000000000 +0100 ++++ pmix-3.1.5/src/mca/common/dstore/dstore_segment.c 2023-09-11 15:17:22.502130578 +0200 +@@ -120,7 +120,7 @@ + + if (setuid > 0){ + rc = PMIX_ERR_PERM; +- if (0 > chown(file_name, (uid_t) uid, (gid_t) -1)){ ++ if (0 > lchown(file_name, (uid_t) uid, (gid_t) -1)){ + PMIX_ERROR_LOG(rc); + goto err_exit; + } +@@ -211,7 +211,7 @@ + + if (setuid > 0){ + rc = PMIX_ERR_PERM; +- if (0 > chown(file_name, (uid_t) uid, (gid_t) -1)){ ++ if (0 > lchown(file_name, (uid_t) uid, (gid_t) -1)){ + PMIX_ERROR_LOG(rc); + goto err_exit; + } +diff -ru pmix-3.1.5.orig/src/mca/gds/ds12/gds_ds12_lock_fcntl.c pmix-3.1.5/src/mca/gds/ds12/gds_ds12_lock_fcntl.c +--- pmix-3.1.5.orig/src/mca/gds/ds12/gds_ds12_lock_fcntl.c 2020-02-19 05:55:43.000000000 +0100 ++++ pmix-3.1.5/src/mca/gds/ds12/gds_ds12_lock_fcntl.c 2023-09-11 15:17:22.502130578 +0200 +@@ -127,7 +127,7 @@ + } + } + if (0 != setuid) { +- if (0 > chown(lock_ctx->lockfile, uid, (gid_t) -1)) { ++ if (0 > lchown(lock_ctx->lockfile, uid, (gid_t) -1)) { + rc = PMIX_ERROR; + PMIX_ERROR_LOG(rc); + goto error; +diff -ru pmix-3.1.5.orig/src/mca/gds/ds12/gds_ds12_lock_pthread.c pmix-3.1.5/src/mca/gds/ds12/gds_ds12_lock_pthread.c +--- pmix-3.1.5.orig/src/mca/gds/ds12/gds_ds12_lock_pthread.c 2020-02-19 05:55:43.000000000 +0100 ++++ pmix-3.1.5/src/mca/gds/ds12/gds_ds12_lock_pthread.c 2023-09-11 15:17:22.502130578 +0200 +@@ -113,7 +113,7 @@ + } + memset(lock_ctx->segment->seg_base_addr, 0, size); + if (0 != setuid) { +- if (0 > chown(lock_ctx->lockfile, (uid_t) uid, (gid_t) -1)){ ++ if (0 > lchown(lock_ctx->lockfile, (uid_t) uid, (gid_t) -1)){ + rc = PMIX_ERROR; + PMIX_ERROR_LOG(rc); + goto error; +diff -ru pmix-3.1.5.orig/src/mca/ptl/usock/ptl_usock_component.c pmix-3.1.5/src/mca/ptl/usock/ptl_usock_component.c +--- pmix-3.1.5.orig/src/mca/ptl/usock/ptl_usock_component.c 2020-02-19 05:55:43.000000000 +0100 ++++ pmix-3.1.5/src/mca/ptl/usock/ptl_usock_component.c 2023-09-11 15:19:31.883298870 +0200 +@@ -267,14 +267,14 @@ + } + /* chown as required */ + if (lt->owner_given) { +- if (0 != chown(address->sun_path, lt->owner, -1)) { ++ if (0 != lchown(address->sun_path, lt->owner, -1)) { + pmix_output(0, "CANNOT CHOWN socket %s: %s", address->sun_path, strerror (errno)); + CLOSE_THE_SOCKET(lt->socket); + goto sockerror; + } + } + if (lt->group_given) { +- if (0 != chown(address->sun_path, -1, lt->group)) { ++ if (0 != lchown(address->sun_path, -1, lt->group)) { + pmix_output(0, "CANNOT CHOWN socket %s: %s", address->sun_path, strerror (errno)); + CLOSE_THE_SOCKET(lt->socket); + goto sockerror; diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.2.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.2.3-GCCcore-10.3.0.eb index c95149b5eaa..ad323fec005 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.2.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.2.3-GCCcore-10.3.0.eb @@ -24,7 +24,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['9b835f23c2f94a193c14012ee68b3657a61c568598cdd1212a3716b32d41a135'] +patches = ['PMIx-3.1.x_lchown.patch'] +checksums = [ + {'pmix-3.2.3.tar.bz2': '9b835f23c2f94a193c14012ee68b3657a61c568598cdd1212a3716b32d41a135'}, + {'PMIx-3.1.x_lchown.patch': '9a4d5e3cb0e619f2e9ac2ffad0b8cb2b22f5c67973080724c79519fb34d55776'}, +] builddependencies = [('binutils', '2.36.1')] From 8b9ec67afa1d66820efd93c22a1dd9bce81f4b25 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Mon, 11 Sep 2023 16:36:31 +0200 Subject: [PATCH 8781/9987] adding easyconfigs: PETSc-3.19.2-foss-2022b.eb --- .../p/PETSc/PETSc-3.19.2-foss-2022b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.19.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.19.2-foss-2022b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.19.2-foss-2022b.eb new file mode 100644 index 00000000000..1a49fec0885 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.19.2-foss-2022b.eb @@ -0,0 +1,46 @@ +## +# Author: Robert Mijakovic +# Author: Jasper Grimm (UoY) +## +name = 'PETSc' +version = '3.19.2' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['114f363f779bb16839b25c0e70f8b0ae0d947d50e72f7c6cddcb11b001079b16'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Boost', '1.81.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('MUMPS', '5.6.1', '-metis'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('Hypre', '2.27.0'), + ('ParMETIS', '4.0.3'), + ('SuperLU_DIST', '8.1.2'), + ('mpi4py', '3.1.4'), +] + +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' From 90a9ee442d793277bc65b76d9a11e13b4370c5d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Sep 2023 16:50:15 +0200 Subject: [PATCH 8782/9987] bump version to 4.8.2dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 9b812bdf2ec..4c5bb9193bf 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.8.1' +VERSION = '4.8.2.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 18a4cb8f61415808918f152d944416b27372ae2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 11 Sep 2023 16:59:09 +0200 Subject: [PATCH 8783/9987] adding easyconfigs: EasyBuild-4.8.1.eb --- .../e/EasyBuild/EasyBuild-4.8.1.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.1.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.1.eb new file mode 100644 index 00000000000..ce5994d0950 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.1.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.8.1' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/48/81/ba869b5b0a35256776050d68832cd2deef907bd49ed9ad37af987292f7b4/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/a2/d8/49510a1a42bff15321209cc5b97c4fbb9f875a5b5444ceb5c1aa99555574/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/8e/fb/ae4772bc01a0e9b64fe6c632a6fc83031f224553c835e6597df0dfd08178/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + {'easybuild-framework-4.8.1.tar.gz': '5e5a98b6dde42172a373b62710f7a62fb6ffea1a0bcdb587a662a14b984aa4d2'}, + {'easybuild-easyblocks-4.8.1.tar.gz': '8d51be0811a727c4bad166d3b03aa2dabf8e17ff26b8d48be8cf8970081e673a'}, + {'easybuild-easyconfigs-4.8.1.tar.gz': '880747d8c9ff0d621eff1b66a81c65a2c9a80488b9161f119557150934a22812'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 589282cf52609067616fc2a522f8e4b81f809cb7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 12 Sep 2023 09:25:57 +0200 Subject: [PATCH 8784/9987] adding easyconfigs: ReFrame-4.3.2.eb --- .../easyconfigs/r/ReFrame/ReFrame-4.3.2.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb new file mode 100644 index 00000000000..b8237231c17 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.2.eb @@ -0,0 +1,66 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.3.2' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + ('reframe', version, { + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['b4e42915cf3d6c7c0f975f12eecd609ae5f165b764989f4ee066a209ff0150ae'], + }), +] + +postinstallcmds = [ + "cp -a tools tutorials %(installdir)s", + # Adding hpctestlib separately to the external directory so that it can be + # imported and is in the PYTHONPATH + "cp -a hpctestlib %(installdir)s/external", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'tutorials'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 53ffee92c3da2626c279369cb3d95d3c283303f6 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 12 Sep 2023 13:59:01 +0200 Subject: [PATCH 8785/9987] adding easyconfigs: libcint-5.4.0-gfbf-2023a.eb --- .../l/libcint/libcint-5.4.0-gfbf-2023a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2023a.eb b/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2023a.eb new file mode 100644 index 00000000000..06ff0619f1e --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '5.4.0' + +homepage = 'https://github.com/sunqm/libcint' +description = "libcint is an open source library for analytical Gaussian integrals." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://github.com/sunqm/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-4.4.0_remove_pyscftest.patch'] +checksums = [ + '42a8f2e9244e4575437e426e32cd1e60ef9559971c42a41f860c870efc745d99', # v5.4.0.tar.gz + '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d', # libcint-4.4.0_remove_pyscftest.patch +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +configopts = "-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on" + +buildopts = 'VERBOSE=1' + +runtest = "test " +separate_build_dir = False # Must use the same directory for tests + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/%(name)s.so'], + 'dirs': [], +} + +moduleclass = 'chem' From 82f553191638bc3327d8e6de4e201ebbcfc1744d Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 12 Sep 2023 14:00:39 +0200 Subject: [PATCH 8786/9987] changed toolchain to gfbf --- .../w/wrapt/wrapt-1.15.0-gfbf-2023a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-gfbf-2023a.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-gfbf-2023a.eb new file mode 100644 index 00000000000..d623ccbd563 --- /dev/null +++ b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-gfbf-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'wrapt' +version = '1.15.0' + +homepage = 'https://pypi.org/project/wrapt/' +description = """The aim of the wrapt module is to provide a transparent object +proxy for Python, which can be used as the basis for the construction of +function wrappers and decorator functions.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'], + }), +] + +moduleclass = 'tools' From e94346b39caecf85d45aed259d8df19f37e774ff Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Tue, 12 Sep 2023 15:22:29 +0200 Subject: [PATCH 8787/9987] removed wrapt-1.15.0-foss-2023a.eb in favor of wrapt-1.15.0-gfbf-2023a.eb --- .../w/wrapt/wrapt-1.15.0-foss-2023a.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2023a.eb b/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2023a.eb deleted file mode 100644 index 66ad8f45a37..00000000000 --- a/easybuild/easyconfigs/w/wrapt/wrapt-1.15.0-foss-2023a.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'wrapt' -version = '1.15.0' - -homepage = 'https://pypi.org/project/wrapt/' -description = """The aim of the wrapt module is to provide a transparent object -proxy for Python, which can be used as the basis for the construction of -function wrappers and decorator functions.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - (name, version, { - 'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'], - }), -] - -moduleclass = 'tools' From 073312deb7d8c0eebbb1a7223b75feb63de2d288 Mon Sep 17 00:00:00 2001 From: xina Date: Tue, 12 Sep 2023 17:32:10 +0200 Subject: [PATCH 8788/9987] adding easyconfigs: VTune-2023.2.0.eb --- .../easyconfigs/v/VTune/VTune-2023.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2023.2.0.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2023.2.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2023.2.0.eb new file mode 100644 index 00000000000..920aa1f3606 --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2023.2.0.eb @@ -0,0 +1,25 @@ + +name = 'VTune' +version = '2023.2.0' + +homepage = 'https://software.intel.com/en-us/vtune' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/dfae6f23-6c90-4b9f-80e2-fa2a5037fe36/'] +sources = ['l_oneapi_vtune_p_%(version)s.49485_offline.sh'] +checksums = ['482a727afe0ac6f81eff51503857c28fcb79ffdba76260399900f3397fd0adbd'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version)s/bin64', + '%(namelower)s/%(version)s/lib64', + '%(namelower)s/%(version)s/include/intel64'] +} + +moduleclass = 'tools' From cc919056f12ea13946eba6a604e435fe5748ceaf Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Tue, 12 Sep 2023 17:57:15 +0200 Subject: [PATCH 8789/9987] adding easyconfigs: tabix-0.2.6-GCCcore-10.3.0.eb --- .../t/tabix/tabix-0.2.6-GCCcore-10.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..ab99f4cfb23 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-GCCcore-10.3.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Jens Timmerman, Ghent University +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# updated to newer toolchain + +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = [('https://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] +checksums = ['e4066be7101bae83bec62bc2bc6917013f6c2875b66eb5055fbb013488d68b73'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' From f1afe07ec5a34e32eb9fde71cbcd72026a546305 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 12 Sep 2023 16:08:29 +0000 Subject: [PATCH 8790/9987] adding easyconfigs: pytest-rerunfailures-12.0-GCCcore-12.3.0.eb --- ...ytest-rerunfailures-12.0-GCCcore-12.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c581d93c49a --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pytest-rerunfailures' +version = '12.0' + +homepage = 'https://github.com/pytest-dev/pytest-rerunfailures' +description = """pytest plugin to re-run tests to eliminate flaky failures.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # It checks for it after installed + ] + +use_pip = True +sanity_pip_check = True +download_dep_fail = False + +sources = [SOURCE_TAR_GZ] +checksums = ['784f462fa87fe9bdf781d0027d856b47a4bfe6c12af108f6bd887057a917b48e'] + +moduleclass = 'tools' From f687113506ba4bdc732e79f99f711689d835af1a Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 12 Sep 2023 16:35:37 +0000 Subject: [PATCH 8791/9987] adding easyconfigs: cuDNN-8.9.2.26-CUDA-12.2.0.eb --- .../c/cuDNN/cuDNN-8.9.2.26-CUDA-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.2.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.2.0.eb new file mode 100644 index 00000000000..8fb0aa19f95 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.2.0.eb @@ -0,0 +1,33 @@ +name = 'cuDNN' +version = '8.9.2.26' +versionsuffix = '-CUDA-%(cudaver)s' +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN is tied to specific to CUDA versions, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +local_cuda_major = '12' + +source_urls = [ + 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%(cudnnarch)s/' +] +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = ['ccafd7d15c2bf26187d52d79d9ccf95104f4199980f5075a7c1ee3347948ce32'] + +dependencies = [('CUDA', '12.2.0')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From 6c0343b8df656c87be9ad6aa2291c6cf617edbb1 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 13 Sep 2023 11:08:15 +0200 Subject: [PATCH 8792/9987] improved modular configuration according to review --- .../h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb index ba100820b9b..453ca292d42 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-12.3.0.eb @@ -32,14 +32,16 @@ dependencies = [ ] preconfigopts = "LIBS='-ltirpc' " + +local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' +local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' + configopts = [ - '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc"', - '--includedir=%(installdir)s/include/%(namelower)s FFLAGS="$FFLAGS -fallow-argument-mismatch"', - '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc"', - '--includedir=%(installdir)s/include/%(namelower)s', - '--enable-shared', - '--disable-fortran', - '--disable-netcdf', + local_common_configopts, + # Cannot build shared libraries and Fortran... + # https://trac.osgeo.org/gdal/wiki/HDF#IncompatibilitywithNetCDFLibraries + # netcdf must be disabled to allow HDF to be used by GDAL + local_common_configopts + "--enable-shared --disable-fortran --disable-netcdf", ] From e1069d95a5c4593e44fa99bcb763c8fd4c7dc8df Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 13 Sep 2023 11:09:59 +0200 Subject: [PATCH 8793/9987] added sanity check paths to clair3 --- easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb b/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb index 01830d8cd54..111f9af622a 100644 --- a/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb @@ -30,7 +30,7 @@ dependencies = [ ('pigz', '2.7'), ('cffi', '1.15.1'), ('parallel', '20220722'), - ('SAMtools', '1.13'), + ('SAMtools', '1.16.1'), ('WhatsHap', '1.7'), ('zlib', '1.2.12'), ('bzip2', '1.0.8'), @@ -46,4 +46,8 @@ files_to_copy = [ (['libclair3.so', 'libclair3.o', 'libclair3.cpython-310-x86_64-linux-gnu.so', 'libclair3.c', 'longphase', ], 'lib'), ] +sanity_check_paths = { + 'files': ['bin/run_clair3.sh', 'bin/clair3.py', 'lib/libclair3.so'], + 'dirs': ['bin/clair3'], +} moduleclass = 'bio' From c78990ad35f04e8fb28a68260400162814d20982 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 13 Sep 2023 12:37:33 +0200 Subject: [PATCH 8794/9987] Add VCFtools --- .../v/VCFtools/VCFtools-0.1.16-GCC-12.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.3.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.3.0.eb new file mode 100644 index 00000000000..3cdfda35e10 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = 'https://vcftools.github.io' +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +builddependencies = [ + ('pkgconf', '1.9.5'), +] +dependencies = [ + ('Perl', '5.36.1'), + ('HTSlib', '1.18'), + ('zlib', '1.2.13'), +] + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/vcf-sort', 'bin/vcf-stats'], + 'dirs': [], +} + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +moduleclass = 'bio' From e3143e4fedc8b670c7f294e38f7b9f7f5b9be21e Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 13 Sep 2023 13:06:40 +0200 Subject: [PATCH 8795/9987] adding easyconfigs: Bowtie2-2.5.1-GCC-12.3.0.eb --- .../b/Bowtie2/Bowtie2-2.5.1-GCC-12.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..379484dfaea --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-12.3.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp +# Modified by: Sebastien Moretti for non-x86_64 systems +# SIB Swiss Institute of Bioinformatics + +name = 'Bowtie2' +version = '2.5.1' + +homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['cb6cbbbb5a7167a2f21a3d63cb9774336361f540e1ec3d8ff907f955c35f71b8'] + +dependencies = [ + ('zlib', '1.2.13'), + ('Perl', '5.36.1'), + ('Python', '3.11.3'), +] + + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +sanity_check_commands = [ + "%(namelower)s --help", + "%(namelower)s-build --help", +] + +moduleclass = 'bio' From 1125d11959189057434b3f1f29600952a01051fc Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 13 Sep 2023 13:13:17 +0200 Subject: [PATCH 8796/9987] =?UTF-8?q?separa=E2=80=A0ed=20configuration=20f?= =?UTF-8?q?or=20shared=20and=20static=20libraries?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb index 8de1a91aefa..6586149b8d2 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb @@ -61,11 +61,12 @@ dependencies = [ ] # iterative build for both static and shared libraries +local_configopts_common = "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW " +local_configopts_common += "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON " + configopts = [ - "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW", - "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON -DBUILD_SHARED_LIBS=OFF", - "-DGDAL_USE_INTERNAL_LIBS=OFF -DArrow_DIR=$EBROOTARROW", - "-DGEOTIFF_INCLUDE_DIR=$EBROOTLIBGEOTIFF/include -DPython_ROOT=$EBROOTPYTHON ", + local_configopts_common + "-DBUILD_SHARED_LIBS=OFF", + local_configopts_common ] From 8b98a6dbecf26d5c028ff629ca3867a0e13b5cc7 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 13 Sep 2023 13:41:42 +0200 Subject: [PATCH 8797/9987] Update easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.2.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.2.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.2.0.eb index 8fb0aa19f95..de4fa6034d9 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.2.26-CUDA-12.2.0.eb @@ -16,7 +16,14 @@ source_urls = [ 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%(cudnnarch)s/' ] sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] -checksums = ['ccafd7d15c2bf26187d52d79d9ccf95104f4199980f5075a7c1ee3347948ce32'] +checksums = [{ + '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '4f5e5bd01570c4805b93fb199f8bb6f8475d016948c55abf48fed9ffe89d13e5', + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '898d00c82f9ad8797bd6f6c639327b320a38fa4aeebfb2b3fbb2db0d38f7e1b0', + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'ccafd7d15c2bf26187d52d79d9ccf95104f4199980f5075a7c1ee3347948ce32', +}] dependencies = [('CUDA', '12.2.0')] From 6b6a6e0e515b7f718628b164da076f099f1003d1 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 13 Sep 2023 14:34:39 +0200 Subject: [PATCH 8798/9987] Add QuantumESPRESSO --- .../QuantumESPRESSO-7.2-foss-2023a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb new file mode 100644 index 00000000000..65b6db3ee63 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb @@ -0,0 +1,43 @@ +name = 'QuantumESPRESSO' +version = '7.2' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + {'filename': 'q-e-qe-%(version)s.tar.gz', 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s']}, + {'filename': 'qe-gipaw-%(version)s.tar.gz', 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/']}, + {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, +] +checksums = [ + {'q-e-qe-%(version)s.tar.gz': 'b348a4a7348b66a73545d9ca317a2645755c98d343c1cfe8def475ad030808c0'}, + {'qe-gipaw-%(version)s.tar.gz': '3375e6e8242b9d0a1ebf9ff9ac1111f4cc5c95d3f654bc2534c396b3b4e59a2f'}, + {'wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('M4', '1.4.19'), +] +dependencies = [ + ('HDF5', '1.14.0'), + ('ELPA', '2023.05.001'), + ('libxc', '6.2.2'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = "all gwl xspectra couple epw gipaw w90" + +# parallel build tends to fail +parallel = 1 + + +moduleclass = 'chem' From 5b6883d07041361309b5925a044822479f074041 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Wed, 13 Sep 2023 14:53:00 +0200 Subject: [PATCH 8799/9987] added binutils to mpath --- easybuild/easyconfigs/m/mpath/mpath-1.1.3-GCCcore-11.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/mpath/mpath-1.1.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mpath/mpath-1.1.3-GCCcore-11.3.0.eb index 52a7505afdd..1064e04fb50 100644 --- a/easybuild/easyconfigs/m/mpath/mpath-1.1.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/mpath/mpath-1.1.3-GCCcore-11.3.0.eb @@ -10,6 +10,9 @@ a directory or a file path.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +builddependencies = [ + ('binutils', '2.38'), +] dependencies = [ ('Python', '3.10.4'), ] From 6b8b7d8c306012bfbb6f5e2aba3da087d33c04b3 Mon Sep 17 00:00:00 2001 From: xina Date: Wed, 13 Sep 2023 14:53:58 +0200 Subject: [PATCH 8800/9987] adding easyconfigs: itac-2021.10.0.eb --- .../easyconfigs/i/itac/itac-2021.10.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/i/itac/itac-2021.10.0.eb diff --git a/easybuild/easyconfigs/i/itac/itac-2021.10.0.eb b/easybuild/easyconfigs/i/itac/itac-2021.10.0.eb new file mode 100644 index 00000000000..ebcda8277d3 --- /dev/null +++ b/easybuild/easyconfigs/i/itac/itac-2021.10.0.eb @@ -0,0 +1,20 @@ + +name = 'itac' +version = '2021.10.0' + +homepage = 'https://software.intel.com/en-us/intel-trace-analyzer/' +description = """The Intel Trace Collector is a low-overhead tracing library that performs + event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application + activities gathered by the Intel Trace Collector through graphical displays. """ + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/226adf12-b7f6-407e-95a9-8e9ab76d7631/'] +sources = ['l_itac_oneapi_p_%(version)s.14_offline.sh'] +checksums = ['cfff2ee19c793b64074b5490a16acbe8c9767f41d391d7c71c0004fdcec501c7'] + +dontcreateinstalldir = True + +preferredmpi = 'impi5' + +moduleclass = 'tools' From 53003c66e187393c92f918552197744134b04a74 Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Wed, 13 Sep 2023 15:02:47 +0200 Subject: [PATCH 8801/9987] removed Boost dependency, added SciPy-bundle dependency --- easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021a.eb b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021a.eb index ce729591c95..726420a15cc 100644 --- a/easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MACS2/MACS2-2.2.7.1-foss-2021a.eb @@ -15,7 +15,7 @@ checksums = ['ad2ca69bdd02a8942a68aae23133289b5c16ba382bcbe20c39fabf3948929de5'] dependencies = [ ('Python', '3.9.5'), - ('Boost', '1.76.0'), + ('SciPy-bundle', '2021.05'), ] use_pip = True From 18e4ca807002b500a3e03922093701c70fadf570 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 13 Sep 2023 15:22:39 +0200 Subject: [PATCH 8802/9987] Fixed style --- .../QuantumESPRESSO-7.2-foss-2023a.eb | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb index 65b6db3ee63..4a79d7df97a 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb @@ -12,9 +12,19 @@ toolchain = {'name': 'foss', 'version': '2023a'} toolchainopts = {'usempi': True, 'openmp': True} sources = [ - {'filename': 'q-e-qe-%(version)s.tar.gz', 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s']}, - {'filename': 'qe-gipaw-%(version)s.tar.gz', 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/']}, - {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, + { + 'filename': 'q-e-qe-%(version)s.tar.gz', + 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'] + }, + { + 'filename': 'qe-gipaw-%(version)s.tar.gz', + 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/']}, + { + 'filename': 'wannier90-3.1.0.tar.gz', + 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'] + }, ] checksums = [ {'q-e-qe-%(version)s.tar.gz': 'b348a4a7348b66a73545d9ca317a2645755c98d343c1cfe8def475ad030808c0'}, From 3fac3e539870f862279054995b8656cc48dc58ee Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 13 Sep 2023 16:18:46 +0200 Subject: [PATCH 8803/9987] Add ASE and dependencies --- .../a/ASE/ASE-3.22.1-foss-2023a.eb | 63 +++++++++++++++++++ .../f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb | 44 +++++++++++++ .../scikit-build-core-0.5.0-GCCcore-12.3.0.eb | 31 +++++++++ .../spglib-python-2.1.0-foss-2023a.eb | 30 +++++++++ 4 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb new file mode 100644 index 00000000000..da531aae39d --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Flask', '2.3.3'), + ('matplotlib', '3.7.2'), + ('Tkinter', '3.11.3'), + ('spglib-python', '2.1.0'), # optional +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('pytest-mock', '3.11.1', { + 'checksums': [ + '7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f', + ] + }), + ('ase', version, { + 'patches': [ + 'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch', + 'ASE-3.22.1-Compatibility-with-pytest-part-2.patch', + 'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch', + 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', + ], + 'checksums': [ + '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432', + '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac', + '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601', + 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8', + '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d', + ] + }), + ('ase-ext', '20.9.0', { + 'checksums': [ + 'a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed', + ] + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b45a8f33f43 --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '2.3.3' + +homepage = 'https://www.palletsprojects.com/p/flask/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('itsdangerous', '2.1.2', {'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a']}), + ('werkzeug', '2.3.7', {'checksums': ['2b8c0e447b4b9dbcc85dd97b6eeb4dcbaf6c8b6c3be0bd654e25553e0a2157d8']}), + ('asgiref', '3.7.2', {'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed']}), + ('blinker', '1.6.2', {'checksums': ['4afd3de66ef3a9f8067559fb7a1cbe555c17dcbe15971b05d1b625c3e7abe213']}), + ('flask', version, {'checksums': ['09c347a92aa7ff4a8e7f3206795f30d826654baf38b873d0744cd571ca609efc']}), + ('Flask-Cors', '4.0.0', {'checksums': ['f268522fcb2f73e2ecdde1ef45e2fd5c71cc48fe03cffb4b441c6d1b40684eb0']}), + ('cachelib', '0.10.2', {'checksums': ['593faeee62a7c037d50fc835617a01b887503f972fb52b188ae7e50e9cb69740']}), + ('Flask-Session', '0.5.0', {'checksums': ['190875e6aebf2953c6803d42379ef3b934bc209ef8ef006f97aecb08f5aaeb86']}), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --version'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b72e4a1c329 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build-core' +version = '0.5.0' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('scikit_build_core', version, { + 'checksums': ['a42a95029b34b5cf892855342d9b9445c774cb797fcb24c8fc4c2fb42b18dfca'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb new file mode 100644 index 00000000000..5287d557e19 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'spglib-python' +version = '2.1.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-build-core', '0.5.0'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('pyproject-metadata', '0.7.1', { + 'checksums': ['0a94f18b108b9b21f3a26a3d541f056c34edcb17dc872a144a15618fed7aef67'], + }), + ('spglib', version, { + 'checksums': ['8143545fdffc11fbcda4d705a6b6bcd4889de9bc3524b78df866a36dd0de0a4b'], + }), +] + +moduleclass = 'chem' From e8b1082da57972d28fbf6576986bf98186c52eaf Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 13 Sep 2023 17:12:37 +0200 Subject: [PATCH 8804/9987] Fix style --- easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb index da531aae39d..c57e53c9b12 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb @@ -36,7 +36,7 @@ exts_list = [ 'ASE-3.22.1-Compatibility-with-pytest-part-2.patch', 'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch', 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', - ], + ], 'checksums': [ '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432', '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac', From d8c93e573ae1efde9641f44ad47db9c13e9e83da Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 13 Sep 2023 17:47:13 +0200 Subject: [PATCH 8805/9987] Remove QuantumESPRESSO --- .../QuantumESPRESSO-7.2-foss-2023a.eb | 53 ------------------- 1 file changed, 53 deletions(-) delete mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb deleted file mode 100644 index 4a79d7df97a..00000000000 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb +++ /dev/null @@ -1,53 +0,0 @@ -name = 'QuantumESPRESSO' -version = '7.2' - -homepage = 'https://www.quantum-espresso.org' -description = """Quantum ESPRESSO is an integrated suite of computer codes -for electronic-structure calculations and materials modeling at the nanoscale. -It is based on density-functional theory, plane waves, and pseudopotentials -(both norm-conserving and ultrasoft). -""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'usempi': True, 'openmp': True} - -sources = [ - { - 'filename': 'q-e-qe-%(version)s.tar.gz', - 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', - 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'] - }, - { - 'filename': 'qe-gipaw-%(version)s.tar.gz', - 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/']}, - { - 'filename': 'wannier90-3.1.0.tar.gz', - 'download_filename': 'v3.1.0.tar.gz', - 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'] - }, -] -checksums = [ - {'q-e-qe-%(version)s.tar.gz': 'b348a4a7348b66a73545d9ca317a2645755c98d343c1cfe8def475ad030808c0'}, - {'qe-gipaw-%(version)s.tar.gz': '3375e6e8242b9d0a1ebf9ff9ac1111f4cc5c95d3f654bc2534c396b3b4e59a2f'}, - {'wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, -] - -builddependencies = [ - ('M4', '1.4.19'), -] -dependencies = [ - ('HDF5', '1.14.0'), - ('ELPA', '2023.05.001'), - ('libxc', '6.2.2'), -] - -# The third party packages should be installed separately and added as -# dependencies. The exception is w90, which is force built, and gipaw -# which depends on qe source -buildopts = "all gwl xspectra couple epw gipaw w90" - -# parallel build tends to fail -parallel = 1 - - -moduleclass = 'chem' From 907324ebfd82f64e2a7e39b6991f62f29e5431b6 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 13 Sep 2023 17:47:52 +0200 Subject: [PATCH 8806/9987] Remove download_dep_fail --- .../s/spglib-python/spglib-python-2.1.0-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb index 5287d557e19..86b1fab9f39 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb @@ -14,7 +14,6 @@ dependencies = [ ('scikit-build-core', '0.5.0'), ] -download_dep_fail = True sanity_pip_check = True use_pip = True From 4176f67e3720435fe60235ac8c2f1875524bd37e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Sep 2023 18:01:28 +0200 Subject: [PATCH 8807/9987] minor cleanup + enhanced sanity check for Clair3 --- .../easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb b/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb index 111f9af622a..310fa3133df 100644 --- a/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb @@ -43,11 +43,17 @@ dependencies = [ files_to_copy = [ (['run_clair3.sh', 'longphase', 'clair3.py', 'clair3'], 'bin'), - (['libclair3.so', 'libclair3.o', 'libclair3.cpython-310-x86_64-linux-gnu.so', 'libclair3.c', 'longphase', ], 'lib'), + (['libclair3.*'], 'lib'), ] sanity_check_paths = { - 'files': ['bin/run_clair3.sh', 'bin/clair3.py', 'lib/libclair3.so'], + 'files': ['bin/run_clair3.sh', 'bin/clair3.py', 'bin/longphase', 'lib/libclair3.%s' % SHLIB_EXT], 'dirs': ['bin/clair3'], } + +sanity_check_commands = [ + "longphase --help", + "run_clair3.sh --help", +] + moduleclass = 'bio' From 3e7beb23a0b29bbbdf4832b303bae44bd9ffba8b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Sep 2023 18:11:55 +0200 Subject: [PATCH 8808/9987] adding easyconfigs: nanopolish-0.14.0-foss-2022a.eb, VBZ-Compression-1.0.3-gompi-2022a.eb --- .../nanopolish-0.14.0-foss-2022a.eb | 61 +++++++++++++++++++ .../VBZ-Compression-1.0.3-gompi-2022a.eb | 43 +++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2022a.eb diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2022a.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2022a.eb new file mode 100644 index 00000000000..2ca012c73d5 --- /dev/null +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.14.0-foss-2022a.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'nanopolish' +version = '0.14.0' + +homepage = 'https://github.com/jts/nanopolish' +description = "Software package for signal-level analysis of Oxford Nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://github.com/jts/nanopolish/archive/', + 'https://github.com/mateidavid/fast5/archive/', +] +sources = [ + { + 'source_urls': ['https://github.com/jts/nanopolish/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/hasindu2008/slow5lib/archive/'], + 'download_filename': 'v1.1.0.tar.gz', + 'filename': 'slow5lib-v1.1.0.tar.gz', + }, +] +checksums = [ + {'nanopolish-0.14.0.tar.gz': 'bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78'}, + {'slow5lib-v1.1.0.tar.gz': 'f13f08b85a9a11086b5d9378251093d1858d0dc29d8e727eabacfa57a73f4277'}, +] + +builddependencies = [('Eigen', '3.4.0')] + +dependencies = [ + ('zlib', '1.2.12'), + ('Python', '3.10.4'), + ('Biopython', '1.79'), + ('Pysam', '0.19.1'), + ('HDF5', '1.12.2'), + ('HTSlib', '1.15.1'), + ('minimap2', '2.24'), + ('VBZ-Compression', '1.0.3'), +] + +prebuildopts = "rmdir slow5lib && ln -s %(builddir)s/slow5lib-*/ slow5lib && " +buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall" + +runtest = 'test ' + buildopts + +files_to_copy = [(['nanopolish'], 'bin'), 'scripts'] + +postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"] + +sanity_check_paths = { + 'files': ['bin/nanopolish'], + 'dirs': ['scripts'], +} + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2022a.eb b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2022a.eb new file mode 100644 index 00000000000..d6e8caabfdb --- /dev/null +++ b/easybuild/easyconfigs/v/VBZ-Compression/VBZ-Compression-1.0.3-gompi-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'VBZ-Compression' +version = '1.0.3' + +homepage = 'https://github.com/nanoporetech/vbz_compression' +description = "VBZ compression HDF5 plugin for nanopolish" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = [ + 'https://github.com/nanoporetech/vbz_compression/archive', + 'https://github.com/lemire/streamvbyte/archive', +] +sources = [ + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'download_filename': 'v0.4.1.tar.gz', 'filename': 'streamvbyte-v0.4.1.tar.gz'}, +] +checksums = [ + {'VBZ-Compression-1.0.3.tar.gz': 'a7450e076db628681bbc0e2b3f941c6c21cc2981a7e1c78628807ffdf1b34f31'}, + {'streamvbyte-v0.4.1.tar.gz': '4c4e53134a60b0b06816d3faa7dcde28c3e5e8a656dd415d16d80ae6e3d39fcc'}, +] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('HDF5', '1.12.2'), + ('zstd', '1.5.2'), +] + +preconfigopts = "rmdir %(builddir)s/vbz_compression*/third_party/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte-* %(builddir)s/streamvbyte && " +preconfigopts += "mv %(builddir)s/streamvbyte %(builddir)s/vbz_compression*/third_party/. && " +configopts = "-DENABLE_CONAN=OFF -DENABLE_PERF_TESTING=OFF -DENABLE_PYTHON=OFF " + +sanity_check_paths = { + 'files': ['hdf5/lib/plugin/libvbz_hdf_plugin.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'HDF5_PLUGIN_PATH': 'hdf5/lib/plugin/'} + +moduleclass = 'lib' From b12d20220aa6d27e9884d03e9b90ca0e75d37bb2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Sep 2023 18:32:44 +0200 Subject: [PATCH 8809/9987] add and use separate lchown patch for PMIx 3.2.x --- .../p/PMIx/PMIx-3.2.3-GCCcore-10.3.0.eb | 4 +- .../p/PMIx/PMIx-3.2.x_lchown.patch | 99 +++++++++++++++++++ 2 files changed, 101 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-3.2.x_lchown.patch diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.2.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.2.3-GCCcore-10.3.0.eb index ad323fec005..ac54991a3d8 100644 --- a/easybuild/easyconfigs/p/PMIx/PMIx-3.2.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.2.3-GCCcore-10.3.0.eb @@ -24,10 +24,10 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.bz2'] -patches = ['PMIx-3.1.x_lchown.patch'] +patches = ['PMIx-3.2.x_lchown.patch'] checksums = [ {'pmix-3.2.3.tar.bz2': '9b835f23c2f94a193c14012ee68b3657a61c568598cdd1212a3716b32d41a135'}, - {'PMIx-3.1.x_lchown.patch': '9a4d5e3cb0e619f2e9ac2ffad0b8cb2b22f5c67973080724c79519fb34d55776'}, + {'PMIx-3.2.x_lchown.patch': '67f081fdc5d66557343c7019e45b08f169708e2eed628644e99b1ea1dff302e1'}, ] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.2.x_lchown.patch b/easybuild/easyconfigs/p/PMIx/PMIx-3.2.x_lchown.patch new file mode 100644 index 00000000000..ae84cf059f7 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.2.x_lchown.patch @@ -0,0 +1,99 @@ +backport of https://github.com/openpmix/openpmix/pull/3150 to PMIx 3.2.x +diff -ru pmix-3.2.3.orig/src/mca/common/dstore/dstore_base.c pmix-3.2.3/src/mca/common/dstore/dstore_base.c +--- pmix-3.2.3.orig/src/mca/common/dstore/dstore_base.c 2020-12-23 15:43:16.000000000 +0100 ++++ pmix-3.2.3/src/mca/common/dstore/dstore_base.c 2023-09-13 18:28:41.479243046 +0200 +@@ -528,7 +528,7 @@ + } + } + if (s->setjobuid > 0){ +- if (0 > chown(s->nspace_path, (uid_t) s->jobuid, (gid_t) -1)){ ++ if (0 > lchown(s->nspace_path, (uid_t) s->jobuid, (gid_t) -1)){ + rc = PMIX_ERROR; + PMIX_ERROR_LOG(rc); + return rc; +@@ -1682,7 +1682,7 @@ + } + } + if (ds_ctx->setjobuid > 0) { +- if (chown(ds_ctx->base_path, (uid_t) ds_ctx->jobuid, (gid_t) -1) < 0){ ++ if (lchown(ds_ctx->base_path, (uid_t) ds_ctx->jobuid, (gid_t) -1) < 0){ + rc = PMIX_ERR_NO_PERMISSIONS; + PMIX_ERROR_LOG(rc); + goto err_exit; +diff -ru pmix-3.2.3.orig/src/mca/common/dstore/dstore_segment.c pmix-3.2.3/src/mca/common/dstore/dstore_segment.c +--- pmix-3.2.3.orig/src/mca/common/dstore/dstore_segment.c 2020-04-16 15:16:47.000000000 +0200 ++++ pmix-3.2.3/src/mca/common/dstore/dstore_segment.c 2023-09-13 18:28:41.479243046 +0200 +@@ -120,7 +120,7 @@ + + if (setuid > 0){ + rc = PMIX_ERR_PERM; +- if (0 > chown(file_name, (uid_t) uid, (gid_t) -1)){ ++ if (0 > lchown(file_name, (uid_t) uid, (gid_t) -1)){ + PMIX_ERROR_LOG(rc); + goto err_exit; + } +@@ -211,7 +211,7 @@ + + if (setuid > 0){ + rc = PMIX_ERR_PERM; +- if (0 > chown(file_name, (uid_t) uid, (gid_t) -1)){ ++ if (0 > lchown(file_name, (uid_t) uid, (gid_t) -1)){ + PMIX_ERROR_LOG(rc); + goto err_exit; + } +diff -ru pmix-3.2.3.orig/src/mca/gds/ds12/gds_ds12_lock_fcntl.c pmix-3.2.3/src/mca/gds/ds12/gds_ds12_lock_fcntl.c +--- pmix-3.2.3.orig/src/mca/gds/ds12/gds_ds12_lock_fcntl.c 2020-04-16 15:16:47.000000000 +0200 ++++ pmix-3.2.3/src/mca/gds/ds12/gds_ds12_lock_fcntl.c 2023-09-13 18:28:41.480243044 +0200 +@@ -127,7 +127,7 @@ + } + } + if (0 != setuid) { +- if (0 > chown(lock_ctx->lockfile, uid, (gid_t) -1)) { ++ if (0 > lchown(lock_ctx->lockfile, uid, (gid_t) -1)) { + rc = PMIX_ERROR; + PMIX_ERROR_LOG(rc); + goto error; +diff -ru pmix-3.2.3.orig/src/mca/gds/ds12/gds_ds12_lock_pthread.c pmix-3.2.3/src/mca/gds/ds12/gds_ds12_lock_pthread.c +--- pmix-3.2.3.orig/src/mca/gds/ds12/gds_ds12_lock_pthread.c 2020-04-16 15:16:47.000000000 +0200 ++++ pmix-3.2.3/src/mca/gds/ds12/gds_ds12_lock_pthread.c 2023-09-13 18:28:41.480243044 +0200 +@@ -113,7 +113,7 @@ + } + memset(lock_ctx->segment->seg_base_addr, 0, size); + if (0 != setuid) { +- if (0 > chown(lock_ctx->lockfile, (uid_t) uid, (gid_t) -1)){ ++ if (0 > lchown(lock_ctx->lockfile, (uid_t) uid, (gid_t) -1)){ + rc = PMIX_ERROR; + PMIX_ERROR_LOG(rc); + goto error; +diff -ru pmix-3.2.3.orig/src/mca/ptl/usock/ptl_usock_component.c pmix-3.2.3/src/mca/ptl/usock/ptl_usock_component.c +--- pmix-3.2.3.orig/src/mca/ptl/usock/ptl_usock_component.c 2020-12-23 15:43:16.000000000 +0100 ++++ pmix-3.2.3/src/mca/ptl/usock/ptl_usock_component.c 2023-09-13 18:28:41.481243042 +0200 +@@ -267,14 +267,14 @@ + } + /* chown as required */ + if (lt->owner_given) { +- if (0 != chown(address->sun_path, lt->owner, -1)) { ++ if (0 != lchown(address->sun_path, lt->owner, -1)) { + pmix_output(0, "CANNOT CHOWN socket %s: %s", address->sun_path, strerror (errno)); + CLOSE_THE_SOCKET(lt->socket); + goto sockerror; + } + } + if (lt->group_given) { +- if (0 != chown(address->sun_path, -1, lt->group)) { ++ if (0 != lchown(address->sun_path, -1, lt->group)) { + pmix_output(0, "CANNOT CHOWN socket %s: %s", address->sun_path, strerror (errno)); + CLOSE_THE_SOCKET(lt->socket); + goto sockerror; +diff -ru pmix-3.2.3.orig/src/util/pmix_pty.c pmix-3.2.3/src/util/pmix_pty.c +--- pmix-3.2.3.orig/src/util/pmix_pty.c 2020-04-16 15:16:47.000000000 +0200 ++++ pmix-3.2.3/src/util/pmix_pty.c 2023-09-13 18:29:33.097140428 +0200 +@@ -248,7 +248,7 @@ + gid = -1; /* group tty is not in the group file */ + } + /* following two functions don't work unless we're root */ +- chown(pts_name, getuid(), gid); ++ lchown(pts_name, getuid(), gid); + chmod(pts_name, S_IRUSR | S_IWUSR | S_IWGRP); + fds = open(pts_name, O_RDWR); + if (fds < 0) { From 9c9192bfd0ae37e5604294ba840f005a26d3b881 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Sep 2023 18:41:50 +0200 Subject: [PATCH 8810/9987] adding easyconfigs: worker-1.6.13-iimpi-2022b.eb --- .../w/worker/worker-1.6.13-iimpi-2022b.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2022b.eb diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2022b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2022b.eb new file mode 100644 index 00000000000..f8398f59486 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.13-iimpi-2022b.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.13' + +homepage = 'https://github.com/gjbex/worker' +description = """The Worker framework has been developed to help deal with parameter exploration experiments + that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; + see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" + +local_tcname = 'iimpi' +local_tcver = '2022b' +toolchain = {'name': local_tcname, 'version': local_tcver} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fixintel.patch'] +checksums = [ + 'b42b8566d82048c706427913c8f7edcd9f5892d61f190ce1f49e428113b7e1bc', # 1.6.13.tar.gz + 'c28bbc837ec5d6fb3390df668b06e0b5169ca31dede907336a2b0637c4a81504', # worker-1.6.13_fixintel.patch +] + +dependencies = [ + ('Perl', '5.36.0') +] + +# adjust worker configuration file +# note: tweak this to your local setup +postinstallcmds = [ + 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', + 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = %s/g" %%(installdir)s/conf/worker.conf' % (local_tcname), + 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), + 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', + "echo PERL=\\'`which perl`\\' > %(installdir)s/conf/worker_perl.sh", +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['wcat', 'wconvert', 'wload', 'worker', 'wreduce', 'wresume', 'wsub', + 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt'], +} + +sanity_check_commands = ["wsub -help"] + +moduleclass = 'tools' From ba6bc3205c23e62240d9b0066974c7223a2dc93c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Sep 2023 18:58:14 +0200 Subject: [PATCH 8811/9987] adding easyconfigs: Flye-2.9.2-GCC-11.3.0.eb --- .../f/Flye/Flye-2.9.2-GCC-11.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flye/Flye-2.9.2-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9.2-GCC-11.3.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..88d323f84e9 --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9.2-GCC-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.9.2' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4b9534b912c805d44b83d497b40102bed807678b82be62667129bf1641676402'] + +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +use_pip = True + +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' From 7a36f17544f99152d6dea4a612a1f3d3db438ef0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Sep 2023 11:09:30 +0200 Subject: [PATCH 8812/9987] also copy scripts directory for Clair3 --- easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb b/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb index 310fa3133df..3fe222a50e8 100644 --- a/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb @@ -42,13 +42,13 @@ dependencies = [ ] files_to_copy = [ - (['run_clair3.sh', 'longphase', 'clair3.py', 'clair3'], 'bin'), + (['clair3', 'clair3.py', 'longphase', 'run_clair3.sh', 'scripts'], 'bin'), (['libclair3.*'], 'lib'), ] sanity_check_paths = { 'files': ['bin/run_clair3.sh', 'bin/clair3.py', 'bin/longphase', 'lib/libclair3.%s' % SHLIB_EXT], - 'dirs': ['bin/clair3'], + 'dirs': ['bin/clair3', 'bin/scripts'], } sanity_check_commands = [ From 3c3e6e6276dc5170a21f26005ea8de31b6f1db38 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 14 Sep 2023 11:41:33 +0200 Subject: [PATCH 8813/9987] adding easyconfigs: BgeeCall-1.16.0-foss-2021a-R-4.1.0.eb --- .../BgeeCall-1.16.0-foss-2021a-R-4.1.0.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/b/BgeeCall/BgeeCall-1.16.0-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/b/BgeeCall/BgeeCall-1.16.0-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/b/BgeeCall/BgeeCall-1.16.0-foss-2021a-R-4.1.0.eb new file mode 100644 index 00000000000..5c4062f6987 --- /dev/null +++ b/easybuild/easyconfigs/b/BgeeCall/BgeeCall-1.16.0-foss-2021a-R-4.1.0.eb @@ -0,0 +1,77 @@ +easyblock = 'Bundle' + +name = 'BgeeCall' +version = '1.16.0' +versionsuffix = '-R-%(rver)s' + +# This library does not need last Bioconductor dependencies +# but better to have its last version from the last Bioconductor version +local_bioc_version = 3.17 + +homepage = 'https://github.com/BgeeDB/BgeeCall' +description = """Automatic RNA-Seq present/absent gene expression calls generation""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('R', '4.1.0'), +] + +dependencies = [ + ('R-bundle-Bioconductor', '3.13', versionsuffix), +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/%s/bioc/src/contrib/' % local_bioc_version, + 'https://bioconductor.org/packages/%s/bioc/src/contrib/Archive/%%(name)s' % local_bioc_version, + 'https://bioconductor.org/packages/%s/data/annotation/src/contrib/' % local_bioc_version, + 'https://bioconductor.org/packages/%s/data/experiment/src/contrib/' % local_bioc_version, + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('insight', '0.19.3', { + 'checksums': ['ff1f39b15e84f671f1602e5f7ef646d0f1c25ea63ad87c272a58e25d8b8d887e'], + }), + ('datawizard', '0.8.0', { + 'checksums': ['13a3ed4f36157b18955dcbcb5a1f81a0d913349312cd44141f0afde16a3d22a2'], + }), + ('sjlabelled', '1.2.0', { + 'checksums': ['731c7e907361971dbc890ad80bc95a38ecc38455a0217fdbc3dbb7c60b3648ed'], + }), + ('sjmisc', '2.8.9', { + 'checksums': ['78b05741ce9e1cc783fda97a0f18caff689822fdd4bdf733dc20f7c94ac2f3bf'], + }), + ('rslurm', '0.6.2', { + 'checksums': ['540158ece7d838c9630886f37e0960353038fefa4f9cc374004240b767f6b47c'], + }), + (name, version, { + 'checksums': ['80dabc64b8eb13f9937852f433ef6919ebcf1583ece8eb78872b147c3bd30349'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 9453388ec70b596595ffd41305dab04e975db79d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Sep 2023 12:28:30 +0200 Subject: [PATCH 8814/9987] rename isoseq3 after download for IsoSeq 3.8.2 --- .../i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb | 46 +++++++++---------- 1 file changed, 21 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb index 5e8f0c47b88..7640ceca208 100644 --- a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb +++ b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb @@ -1,40 +1,36 @@ -easyblock = "Binary" +easyblock = 'Binary' -name = "IsoSeq" -version = "3.8.2" -versionsuffix = "-linux-x86_64" +name = 'IsoSeq' +version = '3.8.2' +versionsuffix = '-linux-x86_64' -homepage = "https://github.com/PacificBiosciences/ioseq3" +homepage = 'https://github.com/PacificBiosciences/ioseq3' description = """IsoSeq v3 contains the newest tools to identify transcripts - in PacBio single-molecule sequencing data. Starting in SMRT - Link v6.0.0, those tools power the IsoSeq GUI-based analysis - application. A composable workflow of existing tools and - algorithms, combined with a new clustering technique, allows - to process the ever-increasing yield of PacBio machines with - similar performance to IsoSeq versions 1 and 2. Starting with - version 3.4, support for UMI and cell barcode based - deduplication has been added. - """ + in PacBio single-molecule sequencing data. Starting in SMRT + Link v6.0.0, those tools power the IsoSeq GUI-based analysis + application. A composable workflow of existing tools and + algorithms, combined with a new clustering technique, allows + to process the ever-increasing yield of PacBio machines with + similar performance to IsoSeq versions 1 and 2. Starting with + version 3.4, support for UMI and cell barcode based + deduplication has been added. +""" toolchain = SYSTEM -source_urls = ["https://github.com/PacificBiosciences/%(namelower)s"] -sources = ["releases/download/v%(version)s/%(namelower)s3"] +source_urls = ['https://github.com/PacificBiosciences/%(namelower)s/releases/download/v%(version)s'] +sources = [{'download_filename': 'isoseq3', 'filename': 'isoseq3-%(version)s'}] checksums = ["3d012810dc4cb54f89a7c80b26fc5f27da26c11f7ad6062cab462a6c691678f7"] extract_sources = False -postinstallcmds = [ - "cp %(builddir)s/releases/download/v%(version)s/%(namelower)s* %(installdir)s" -] +install_cmd = "cp isoseq3-%(version)s %(installdir)s/isoseq3 && chmod a+rx %(installdir)s/isoseq3" sanity_check_paths = { - "files": [ - "isoseq3", - ], - "dirs": [""], + 'files': ['isoseq3'], + 'dirs': [], } -sanity_check_commands = ['isoseq3 --version'] +sanity_check_commands = ["isoseq3 --version"] -moduleclass = "bio" +moduleclass = 'bio' From 7b69516f3da25ee6ee0cca8461dd93f89bc1662d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Sep 2023 12:28:43 +0200 Subject: [PATCH 8815/9987] adding easyconfigs: IsoSeq-4.0.0-linux-x86_64.eb --- .../i/IsoSeq/IsoSeq-4.0.0-linux-x86_64.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/i/IsoSeq/IsoSeq-4.0.0-linux-x86_64.eb diff --git a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-4.0.0-linux-x86_64.eb b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-4.0.0-linux-x86_64.eb new file mode 100644 index 00000000000..5485419a346 --- /dev/null +++ b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-4.0.0-linux-x86_64.eb @@ -0,0 +1,36 @@ +easyblock = 'Binary' + +name = 'IsoSeq' +version = '4.0.0' +versionsuffix = '-linux-x86_64' + +homepage = 'https://github.com/PacificBiosciences/ioseq3' +description = """IsoSeq v3 contains the newest tools to identify transcripts + in PacBio single-molecule sequencing data. Starting in SMRT + Link v6.0.0, those tools power the IsoSeq GUI-based analysis + application. A composable workflow of existing tools and + algorithms, combined with a new clustering technique, allows + to process the ever-increasing yield of PacBio machines with + similar performance to IsoSeq versions 1 and 2. Starting with + version 3.4, support for UMI and cell barcode based + deduplication has been added. +""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/PacificBiosciences/%(namelower)s/releases/download/v%(version)s'] +sources = [{'download_filename': 'isoseq', 'filename': 'isoseq-%(version)s'}] +checksums = ['5766001507cf2a351b260cf38b717351dd676a7c87eb7c285c3c43a4a458f4b2'] + +extract_sources = False + +install_cmd = "cp isoseq-%(version)s %(installdir)s/isoseq && chmod a+rx %(installdir)s/isoseq" + +sanity_check_paths = { + 'files': ['isoseq'], + 'dirs': [], +} + +sanity_check_commands = ["isoseq --version"] + +moduleclass = 'bio' From ee9b87bf456e1babd0dec888db645e644da6c01c Mon Sep 17 00:00:00 2001 From: xina Date: Thu, 14 Sep 2023 13:25:51 +0200 Subject: [PATCH 8816/9987] adding easyconfigs: Inspector-2023.2.0.eb --- .../i/Inspector/Inspector-2023.2.0.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2023.2.0.eb diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2023.2.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2023.2.0.eb new file mode 100644 index 00000000000..dba0ea08d61 --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2023.2.0.eb @@ -0,0 +1,19 @@ + +name = 'Inspector' +version = '2023.2.0' + +homepage = 'https://software.intel.com/en-us/inspector' +description = """Intel Inspector is a dynamic memory and threading error + checking tool for users developing serial and parallel applications""" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/2a99eafd-5109-41a1-9762-aee0c7ecbeb7/'] +sources = ['l_inspector_oneapi_p_%(version)s.49304_offline.sh'] +checksums = ['36b2ca94e5a69b68cbf9cbfde0a8e1aa58d02fb03f4d81db69769c96c20d4130'] + +dontcreateinstalldir = True + +requires_runtime_license = False + +moduleclass = 'tools' From ee11def632c1865af7397735196ed9a5265f3ab3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 14 Sep 2023 16:08:25 +0200 Subject: [PATCH 8817/9987] Disable test sharding to count failures correctly --- .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 2 + ...PyTorch-1.13.1_disable-test-sharding.patch | 41 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_disable-test-sharding.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 5eecfa1a3aa..896e238a874 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -24,6 +24,7 @@ patches = [ 'PyTorch-1.12.1_fix-vsx-loadu.patch', 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_disable-test-sharding.patch', 'PyTorch-1.13.1_fix-flaky-jit-test.patch', 'PyTorch-1.13.1_fix-fsdp-fp16-test.patch', 'PyTorch-1.13.1_fix-gcc-12-missing-includes.patch', @@ -65,6 +66,7 @@ checksums = [ {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_disable-test-sharding.patch': 'df2074adeba47998ce2993d99ca64eb6f1c79ab7057f553b436efdec264d3572'}, {'PyTorch-1.13.1_fix-flaky-jit-test.patch': '71efdeb29b5e5b4982c9f5cb2182733654a34d52f85bb5487bc4d7d99b86101b'}, {'PyTorch-1.13.1_fix-fsdp-fp16-test.patch': '8ae68e60d6e1f92f50322b7f0381c7e65251fba32d7606e3a238a36a2f55b5cf'}, {'PyTorch-1.13.1_fix-gcc-12-missing-includes.patch': diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_disable-test-sharding.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_disable-test-sharding.patch new file mode 100644 index 00000000000..551d7a4830a --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_disable-test-sharding.patch @@ -0,0 +1,41 @@ +Our error checking doesn't work well with the parallel/sharded pytorch test. +As the overall gain is low, disable it and always run the full test suite in a single process. +Additionally remove the fail-on-first-error flag (-x) to collect all errors. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/run_test.py b/test/run_test.py +index f7c80f3f0a6..9e930d774ed 100755 +--- a/test/run_test.py ++++ b/test/run_test.py +@@ -718,18 +718,18 @@ def print_log_file(test: str, file_path: str, failed: bool) -> None: + + + def run_test_ops(test_module, test_directory, options): +- if 'slow-gradcheck' in os.getenv("BUILD_ENVIRONMENT", ""): ++ if True: + # there are a lot of tests that take up a lot of space in slowgrad check, so don't bother parallelizing + # it's also on periodic so we don't care about TTS as much + return run_test(test_module, test_directory, copy.deepcopy(options), +- extra_unittest_args=["--use-pytest", '-vv', '-x', '--reruns=2', '-rfEX'], ++ extra_unittest_args=["--use-pytest", '-vv', '--reruns=2', '-rfEX'], + ) + return_codes = [] + os.environ["NUM_PARALLEL_PROCS"] = str(NUM_PROCS) + pool = get_context("spawn").Pool(NUM_PROCS) + for i in range(NUM_PROCS): + return_code = pool.apply_async(run_test, args=(test_module, test_directory, copy.deepcopy(options)), +- kwds={"extra_unittest_args": ["--use-pytest", '-vv', '-x', '--reruns=2', '-rfEX', ++ kwds={"extra_unittest_args": ["--use-pytest", '-vv', '--reruns=2', '-rfEX', + f'--shard-id={i}', f'--num-shards={NUM_PROCS}', + "-k=not _linalg_cholesky_"], + }) +@@ -742,7 +742,7 @@ def run_test_ops(test_module, test_directory, options): + if return_code.get() != 0: + return return_code.get() + return_code = run_test(test_module, test_directory, copy.deepcopy(options), +- extra_unittest_args=["--use-pytest", '-vv', '-x', '--reruns=2', '-rfEX', ++ extra_unittest_args=["--use-pytest", '-vv', '--reruns=2', '-rfEX', + "-k=_linalg_cholesky_"], + ) + return return_code From fb7ec2154019a27d1ecbcaba44732b85aa1d51f8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 14 Sep 2023 16:10:09 +0200 Subject: [PATCH 8818/9987] Disable test sharding to count failures correctly and allow test failures --- .../PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb | 7 ++++ ...PyTorch-1.13.1_disable-test-sharding.patch | 41 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_disable-test-sharding.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb index e2658a4ad2f..3303a814d56 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.12.1_fix-vsx-loadu.patch', 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_disable-test-sharding.patch', 'PyTorch-1.13.1_fix-flaky-jit-test.patch', 'PyTorch-1.13.1_fix-fsdp-fp16-test.patch', 'PyTorch-1.13.1_fix-fsdp-tp-integration-test.patch', @@ -65,6 +66,7 @@ checksums = [ {'PyTorch-1.12.1_fix-vsx-loadu.patch': '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2'}, {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_disable-test-sharding.patch': 'df2074adeba47998ce2993d99ca64eb6f1c79ab7057f553b436efdec264d3572'}, {'PyTorch-1.13.1_fix-flaky-jit-test.patch': '71efdeb29b5e5b4982c9f5cb2182733654a34d52f85bb5487bc4d7d99b86101b'}, {'PyTorch-1.13.1_fix-fsdp-fp16-test.patch': '8ae68e60d6e1f92f50322b7f0381c7e65251fba32d7606e3a238a36a2f55b5cf'}, {'PyTorch-1.13.1_fix-fsdp-tp-integration-test.patch': @@ -152,6 +154,11 @@ sanity_check_commands = [ "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, ] +# Especially test_quantization has a few corner cases that are triggered by the random input values, +# those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 +# So allow a low number of tests to fail as the tests "usually" succeed +max_failed_tests = 2 + tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_disable-test-sharding.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_disable-test-sharding.patch new file mode 100644 index 00000000000..551d7a4830a --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_disable-test-sharding.patch @@ -0,0 +1,41 @@ +Our error checking doesn't work well with the parallel/sharded pytorch test. +As the overall gain is low, disable it and always run the full test suite in a single process. +Additionally remove the fail-on-first-error flag (-x) to collect all errors. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/run_test.py b/test/run_test.py +index f7c80f3f0a6..9e930d774ed 100755 +--- a/test/run_test.py ++++ b/test/run_test.py +@@ -718,18 +718,18 @@ def print_log_file(test: str, file_path: str, failed: bool) -> None: + + + def run_test_ops(test_module, test_directory, options): +- if 'slow-gradcheck' in os.getenv("BUILD_ENVIRONMENT", ""): ++ if True: + # there are a lot of tests that take up a lot of space in slowgrad check, so don't bother parallelizing + # it's also on periodic so we don't care about TTS as much + return run_test(test_module, test_directory, copy.deepcopy(options), +- extra_unittest_args=["--use-pytest", '-vv', '-x', '--reruns=2', '-rfEX'], ++ extra_unittest_args=["--use-pytest", '-vv', '--reruns=2', '-rfEX'], + ) + return_codes = [] + os.environ["NUM_PARALLEL_PROCS"] = str(NUM_PROCS) + pool = get_context("spawn").Pool(NUM_PROCS) + for i in range(NUM_PROCS): + return_code = pool.apply_async(run_test, args=(test_module, test_directory, copy.deepcopy(options)), +- kwds={"extra_unittest_args": ["--use-pytest", '-vv', '-x', '--reruns=2', '-rfEX', ++ kwds={"extra_unittest_args": ["--use-pytest", '-vv', '--reruns=2', '-rfEX', + f'--shard-id={i}', f'--num-shards={NUM_PROCS}', + "-k=not _linalg_cholesky_"], + }) +@@ -742,7 +742,7 @@ def run_test_ops(test_module, test_directory, options): + if return_code.get() != 0: + return return_code.get() + return_code = run_test(test_module, test_directory, copy.deepcopy(options), +- extra_unittest_args=["--use-pytest", '-vv', '-x', '--reruns=2', '-rfEX', ++ extra_unittest_args=["--use-pytest", '-vv', '--reruns=2', '-rfEX', + "-k=_linalg_cholesky_"], + ) + return return_code From 06a61932339b24e194ec2485bb22b1eafba51d18 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 14 Sep 2023 21:55:23 +0200 Subject: [PATCH 8819/9987] fix wrong version of, and missing, extensions for Perl, detected by easyblock PR 2699 --- .../easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb | 1 + .../easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb | 2 ++ .../easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb | 7 ++----- .../p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb | 13 ++++++++----- .../p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 13 ++++++++----- .../p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 13 ++++++++----- .../p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 13 ++++++++----- 7 files changed, 37 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb index 7bf8eea4d1b..18e3ad24b83 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb @@ -1552,6 +1552,7 @@ exts_list = [ 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], }), ('if', '0.0608', { + 'modulename': False, 'source_tmpl': 'if-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb index fca58541cb2..d750ffca979 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb @@ -1512,6 +1512,7 @@ exts_list = [ 'checksums': ['2cb898bff42bc10024e0a3252c79e13a2eb7a8a5fb3367bb60583b576a11702b'], }), ('Term::ReadLine::Gnu', '1.36', { + 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['9a08f7a4013c9b865541c10dbba1210779eb9128b961250b746d26702bab6925'], @@ -1562,6 +1563,7 @@ exts_list = [ 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], }), ('if', '0.0608', { + 'modulename': False, 'source_tmpl': 'if-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb index 29d8f77201b..a0b67405467 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb @@ -1492,6 +1492,7 @@ exts_list = [ 'checksums': ['2cb898bff42bc10024e0a3252c79e13a2eb7a8a5fb3367bb60583b576a11702b'], }), ('Term::ReadLine::Gnu', '1.36', { + 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['9a08f7a4013c9b865541c10dbba1210779eb9128b961250b746d26702bab6925'], @@ -1542,6 +1543,7 @@ exts_list = [ 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], }), ('if', '0.0608', { + 'modulename': False, 'source_tmpl': 'if-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], @@ -1761,11 +1763,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], }), - ('IO::Compress::Bzip2', '2.096', { - 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'], - 'checksums': ['9d219fd5df4b490b5d2f847921e3cb1c3392758fa0bae9b05a8992b3620ba572'], - }), ('JSON::XS', '4.03', { 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb index 82a1570fadd..264dc8a3d15 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb @@ -937,6 +937,12 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), + ('Pod::Parser', '1.65', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], + 'checksums': ['3ba7bdec659416a51fe2a7e59f0883e9c6a3b21bc9d001042c1d6a32d401b28a'], + }), ('Pod::LaTeX', '0.61', { 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], @@ -1488,6 +1494,7 @@ exts_list = [ 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], }), ('Term::ReadLine::Gnu', '1.37', { + 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3bd31a998a9c14748ee553aed3e6b888ec47ff57c07fc5beafb04a38a72f0078'], @@ -1538,6 +1545,7 @@ exts_list = [ 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], }), ('if', '0.0608', { + 'modulename': False, 'source_tmpl': 'if-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], @@ -1732,11 +1740,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], }), - ('IO::Compress::Bzip2', '2.102', { - 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], - 'checksums': ['d6fa7f9a5beee446452a0fbc43589a0c73fe7e925c075b98628b018048dc72a4'], - }), ('JSON::XS', '4.03', { 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 6f534c52ba2..2a9ef4add3d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -934,6 +934,12 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), + ('Pod::Parser', '1.65', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], + 'checksums': ['3ba7bdec659416a51fe2a7e59f0883e9c6a3b21bc9d001042c1d6a32d401b28a'], + }), ('Pod::LaTeX', '0.61', { 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], @@ -1485,6 +1491,7 @@ exts_list = [ 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], }), ('Term::ReadLine::Gnu', '1.42', { + 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], @@ -1535,6 +1542,7 @@ exts_list = [ 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], }), ('if', '0.0608', { + 'modulename': False, 'source_tmpl': 'if-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], @@ -1729,11 +1737,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], }), - ('IO::Compress::Bzip2', '2.102', { - 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], - 'checksums': ['d6fa7f9a5beee446452a0fbc43589a0c73fe7e925c075b98628b018048dc72a4'], - }), ('JSON::XS', '4.03', { 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index 1750e4abff0..142a6d15917 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -989,6 +989,12 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), + ('Pod::Parser', '1.65', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + 'checksums': ['3ba7bdec659416a51fe2a7e59f0883e9c6a3b21bc9d001042c1d6a32d401b28a'], + }), ('Pod::LaTeX', '0.61', { 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], @@ -1590,6 +1596,7 @@ exts_list = [ 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], }), ('Term::ReadLine::Gnu', '1.42', { + 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], @@ -1640,6 +1647,7 @@ exts_list = [ 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], }), ('if', '0.0608', { + 'modulename': False, 'source_tmpl': 'if-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], @@ -1834,11 +1842,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], }), - ('IO::Compress::Bzip2', '2.106', { - 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], - 'checksums': ['cb9a26ec7d86afb3081b6369620f1f67eaa45b7c41c4eb800e1da5e700a3e3f5'], - }), ('JSON::XS', '4.03', { 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 6a7989e6d2a..157d352765f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -989,6 +989,12 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), + ('Pod::Parser', '1.66', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], + 'checksums': ['22928a7bffe61b452c05bbbb8f5216d4b9cf9fe2a849b776c25500d24d20df7c'], + }), ('Pod::LaTeX', '0.61', { 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], @@ -1590,6 +1596,7 @@ exts_list = [ 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], }), ('Term::ReadLine::Gnu', '1.42', { + 'modulename': 'Term::ReadLine', 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], 'checksums': ['3c5f1281da2666777af0f34de0289564e6faa823aea54f3945c74c98e95a5e73'], @@ -1640,6 +1647,7 @@ exts_list = [ 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], }), ('if', '0.0608', { + 'modulename': False, 'source_tmpl': 'if-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], @@ -1834,11 +1842,6 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], }), - ('IO::Compress::Bzip2', '2.201', { - 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], - 'checksums': ['f6c55c4e39cfaa3219965dd3b36c9de1edee9a82a10a9cadeb3b74a9ceeeaaad'], - }), ('JSON::XS', '4.03', { 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], From 29b94683fb90c71c999180cf176dc6c5639da510 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Sep 2023 08:56:34 +0200 Subject: [PATCH 8820/9987] add patch for OpenBLAS 0.3.23 to fix hanging tests --- .../o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb | 2 + .../OpenBLAS-0.3.23_fix-tests-hang.patch | 165 ++++++++++++++++++ 2 files changed, 167 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-tests-hang.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb index 2368237262b..b88b96d7cdb 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb @@ -19,6 +19,7 @@ patches = [ 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.23_fix-parallel-build.patch', 'OpenBLAS-0.3.23_fix-lapack-test.patch', + 'OpenBLAS-0.3.23_fix-tests-hang.patch', ] checksums = [ {'v0.3.23.tar.gz': '5d9491d07168a5d00116cdc068a40022c3455bf9293c7cb86a65b1054d7e5114'}, @@ -30,6 +31,7 @@ checksums = [ '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_fix-parallel-build.patch': 'abe10ba3b0ca54772dbf235596e35325a5159018f6a60cfc88824c2c220d99d9'}, {'OpenBLAS-0.3.23_fix-lapack-test.patch': 'f6b3d81061f136e34aaf5359bb80fb9d2bba28825cc1dd26179b8dd01a9a0054'}, + {'OpenBLAS-0.3.23_fix-tests-hang.patch': '9de1fdee6edf3b2bb55e4639fdd92d2877b5f0ac880f7df2cfea47ecebf16609'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-tests-hang.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-tests-hang.patch new file mode 100644 index 00000000000..68d7ac5f81a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_fix-tests-hang.patch @@ -0,0 +1,165 @@ +From ea669c8ae938450e101140d634cca291bffd3898 Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Wed, 26 Jul 2023 00:27:14 +0200 +Subject: [PATCH 1/4] simplify openmp thread limit handling + +--- + common_thread.h | 12 ++++++++---- + 1 file changed, 8 insertions(+), 4 deletions(-) + +diff --git a/common_thread.h b/common_thread.h +index 05e1d5489d..0a4c703b7c 100644 +--- a/common_thread.h ++++ b/common_thread.h +@@ -136,15 +136,13 @@ typedef struct blas_queue { + #ifdef SMP_SERVER + + extern int blas_server_avail; ++extern int blas_omp_number_max; + + static __inline int num_cpu_avail(int level) { + + #ifdef USE_OPENMP + int openmp_nthreads; +- if (blas_num_threads_set == 0) + openmp_nthreads=omp_get_max_threads(); +- else +- openmp_nthreads=blas_cpu_number; + #endif + + #ifndef USE_OPENMP +@@ -156,7 +154,13 @@ int openmp_nthreads; + ) return 1; + + #ifdef USE_OPENMP +- if (blas_cpu_number != openmp_nthreads) { ++ if (openmp_nthreads > blas_omp_number_max){ ++#ifdef DEBUG ++ fprintf(stderr,"WARNING - more OpenMP threads requested (%d) than available (%d)\n",openmp_nthreads,blas_omp_number_max); ++#endif ++ openmp_nthreads = blas_omp_number_max; ++ } ++ if (blas_cpu_number != openmp_nthreads) { + goto_set_num_threads(openmp_nthreads); + } + #endif + +From 3326b924b324d49960e0f657f049e5658e7e6c69 Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Wed, 26 Jul 2023 00:31:24 +0200 +Subject: [PATCH 2/4] remove status variable blas_num_threads_set; initialize + openmp thread maximum on startup + +--- + driver/others/blas_server_omp.c | 4 +++- + driver/others/memory.c | 4 ---- + driver/others/memory_qalloc.c | 1 - + 3 files changed, 3 insertions(+), 6 deletions(-) + +diff --git a/driver/others/blas_server_omp.c b/driver/others/blas_server_omp.c +index 2e0c0f38c1..43764df00c 100644 +--- a/driver/others/blas_server_omp.c ++++ b/driver/others/blas_server_omp.c +@@ -68,6 +68,7 @@ + #endif + + int blas_server_avail = 0; ++int blas_omp_number_max = 0; + + extern int openblas_omp_adaptive_env(); + +@@ -100,7 +101,6 @@ static void adjust_thread_buffers() { + + void goto_set_num_threads(int num_threads) { + +- blas_num_threads_set = 1; + if (num_threads < 0) blas_num_threads_set = 0; + if (num_threads < 1) num_threads = blas_num_threads; + +@@ -125,6 +125,8 @@ void openblas_set_num_threads(int num_threads) { + } + + int blas_thread_init(void){ ++if(blas_omp_number_max <= 0) ++ blas_omp_number_max = omp_get_max_threads(); + + blas_get_cpu_number(); + +diff --git a/driver/others/memory.c b/driver/others/memory.c +index 3cbd17bc2f..4fceae7545 100644 +--- a/driver/others/memory.c ++++ b/driver/others/memory.c +@@ -422,8 +422,6 @@ This value is equal or large than blas_cpu_number. This means some threads are s + */ + int blas_num_threads = 0; + +-int blas_num_threads_set = 0; +- + int goto_get_num_procs (void) { + return blas_cpu_number; + } +@@ -1996,8 +1994,6 @@ This value is equal or large than blas_cpu_number. This means some threads are s + */ + int blas_num_threads = 0; + +-int blas_num_threads_set = 0; +- + int goto_get_num_procs (void) { + return blas_cpu_number; + } +diff --git a/driver/others/memory_qalloc.c b/driver/others/memory_qalloc.c +index 0b38d1887c..6174d9b75e 100644 +--- a/driver/others/memory_qalloc.c ++++ b/driver/others/memory_qalloc.c +@@ -283,7 +283,6 @@ The numbers of threads in the thread pool. + This value is equal or large than blas_cpu_number. This means some threads are sleep. + */ + int blas_num_threads = 0; +-int blas_num_threads_set = 0; + + int goto_get_num_procs (void) { + return blas_cpu_number; + +From 94adf98bb80b36c9faa2fa90fe7f33b36d30748c Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Wed, 26 Jul 2023 08:31:37 +0200 +Subject: [PATCH 3/4] remove unused status variable + +--- + common_thread.h | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/common_thread.h b/common_thread.h +index 0a4c703b7c..06a7a1a38c 100644 +--- a/common_thread.h ++++ b/common_thread.h +@@ -53,7 +53,6 @@ extern void goto_set_num_threads(int nthreads); + /* Global Parameter */ + extern int blas_cpu_number; + extern int blas_num_threads; +-extern int blas_num_threads_set; + extern int blas_omp_linked; + + #define BLAS_LEGACY 0x8000U + +From 9ff84dc3f2536ce94e0a300a098485c7ff3d771d Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Wed, 26 Jul 2023 10:02:44 +0200 +Subject: [PATCH 4/4] remove unused status variable + +--- + driver/others/blas_server_omp.c | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/driver/others/blas_server_omp.c b/driver/others/blas_server_omp.c +index 43764df00c..fe6b4a7c06 100644 +--- a/driver/others/blas_server_omp.c ++++ b/driver/others/blas_server_omp.c +@@ -101,7 +101,6 @@ static void adjust_thread_buffers() { + + void goto_set_num_threads(int num_threads) { + +- if (num_threads < 0) blas_num_threads_set = 0; + if (num_threads < 1) num_threads = blas_num_threads; + + if (num_threads > MAX_CPU_NUMBER) num_threads = MAX_CPU_NUMBER; From 3cbae9c70f123420a948da9693695346a0a01c00 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 15 Sep 2023 10:20:14 +0000 Subject: [PATCH 8821/9987] adding easyconfigs: magma-2.7.2-foss-2023a-CUDA-12.1.1.eb and patches: magma-2.7.2_allow-all-sms.patch --- .../magma-2.7.2-foss-2023a-CUDA-12.1.1.eb | 43 ++++ .../m/magma/magma-2.7.2_allow-all-sms.patch | 209 ++++++++++++++++++ 2 files changed, 252 insertions(+) create mode 100644 easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3a690766598 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'magma' +version = '2.7.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/%(name)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['729bc1a70e518a7422fe7a3a54537a4741035a77be3349f66eac5c362576d560'] + +patches = ['%(name)s-2.7.2_allow-all-sms.patch'] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('UCX-CUDA', '1.14.1', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +# make sure both static and shared libs are built +configopts = [ + '-DMKL_ILP64=ON \ + -DBUILD_SHARED_LIBS=%s \ + -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') +] + +sanity_check_paths = { + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch b/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch new file mode 100644 index 00000000000..2adb8d87ffb --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch @@ -0,0 +1,209 @@ +--- CMakeLists.txt.orig 2023-09-15 09:54:41.000000000 +0000 ++++ CMakeLists.txt 2023-09-15 10:01:07.000000000 +0000 +@@ -140,161 +140,14 @@ + + include_directories( ${CUDAToolkit_INCLUDE_DIRS} ) + +- if (GPU_TARGET MATCHES Fermi) +- set( GPU_TARGET "${GPU_TARGET} sm_20" ) +- endif() +- +- if (GPU_TARGET MATCHES Kepler) +- set( GPU_TARGET "${GPU_TARGET} sm_30 sm_35 sm_37" ) +- endif() +- +- if (GPU_TARGET MATCHES Maxwell) +- set( GPU_TARGET "${GPU_TARGET} sm_50" ) +- endif() +- +- if (GPU_TARGET MATCHES Pascal) +- set( GPU_TARGET "${GPU_TARGET} sm_60" ) +- endif() +- +- if (GPU_TARGET MATCHES Volta) +- set( GPU_TARGET "${GPU_TARGET} sm_70" ) +- endif() +- +- if (GPU_TARGET MATCHES Turing) +- set( GPU_TARGET "${GPU_TARGET} sm_75" ) +- endif() +- +- if (GPU_TARGET MATCHES Ampere) +- set( GPU_TARGET "${GPU_TARGET} sm_80" ) +- endif() +- +- if (GPU_TARGET MATCHES Hopper) +- set( GPU_TARGET "${GPU_TARGET} sm_90" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_20) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 200 ) +- endif() +- list(APPEND __cuda_architectures 20) +- message( STATUS " compile for CUDA arch 2.0 (Fermi)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_30) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 300 ) +- endif() +- list(APPEND __cuda_architectures 30) +- message( STATUS " compile for CUDA arch 3.0 (Kepler)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_35) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 300 ) +- endif() +- list(APPEND __cuda_architectures 35) +- message( STATUS " compile for CUDA arch 3.5 (Kepler)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_37) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 300 ) +- endif() +- list(APPEND __cuda_architectures 37) +- message( STATUS " compile for CUDA arch 3.7 (Kepler)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_50) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 500 ) +- endif() +- list(APPEND __cuda_architectures 50) +- message( STATUS " compile for CUDA arch 5.0 (Maxwell)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_52) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 520 ) +- endif() +- list(APPEND __cuda_architectures 52) +- message( STATUS " compile for CUDA arch 5.2 (Maxwell)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_53) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 530 ) +- endif() +- list(APPEND __cuda_architectures 53) +- message( STATUS " compile for CUDA arch 5.3 (Maxwell)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_60) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 600 ) +- endif() +- list(APPEND __cuda_architectures 60) +- message( STATUS " compile for CUDA arch 6.0 (Pascal)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_61) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 610 ) +- endif() +- list(APPEND __cuda_architectures 61) +- message( STATUS " compile for CUDA arch 6.1 (Pascal)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_62) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 620 ) +- endif() +- list(APPEND __cuda_architectures 62) +- message( STATUS " compile for CUDA arch 6.2 (Pascal)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_70) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 700 ) +- endif() +- list(APPEND __cuda_architectures 70) +- message( STATUS " compile for CUDA arch 7.0 (Volta)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_71) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 710 ) +- endif() +- list(APPEND __cuda_architectures 71) +- message( STATUS " compile for CUDA arch 7.1 (Volta)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_75) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 750 ) +- endif() +- list(APPEND __cuda_architectures 75) +- message( STATUS " compile for CUDA arch 7.5 (Turing)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_80) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 800 ) +- endif() +- list(APPEND __cuda_architectures 80) +- message( STATUS " compile for CUDA arch 8.0 (Ampere)" ) +- endif() +- +- if (GPU_TARGET MATCHES sm_90) +- if (NOT MIN_ARCH) +- set( MIN_ARCH 900 ) +- endif() +- list(APPEND __cuda_architectures 90) +- message( STATUS " compile for CUDA arch 9.0 (Hopper)" ) +- endif() +- +- if (NOT MIN_ARCH) +- message( FATAL_ERROR "GPU_TARGET must contain one or more of Fermi, Kepler, Maxwell, Pascal, Volta, Turing, Ampere, or valid sm_[0-9][0-9]" ) +- endif() ++ # NVCC options for the different cards ++ # sm_xx is binary, compute_xx is PTX for forward compatability ++ # MIN_SM/MAX_SM is lowest/highest requested version ++ # NV_SM accumulates sm_xx for all requested versions ++ # NV_COMP is compute_xx for highest requested version ++ set( MIN_SM 99 ) ++ set( MAX_SM 0 ) ++ set( NV_SM "" ) + + set(CUDA_ARCHITECTURES "${__cuda_architectures}") + +@@ -312,8 +312,34 @@ + ) + endif(COMPILER_SUPPORTS_FPIC) + +- set(MAGMA_HAVE_CUDA "1") +- set(MAGMA_CUDA_ARCH_MIN "${MIN_ARCH}") ++ string( REGEX MATCHALL "sm_[0-9][0-9]" sms "${GPU_TARGET}" ) ++ list( SORT sms ) # To make output easier to reason about ++ foreach (sm IN LISTS sms) ++ string( REPLACE "sm_" "" sm "${sm}") # Remove sm_ prefix ++ if (sm LESS MIN_SM) ++ set( MIN_SM "${sm}" ) ++ endif() ++ if (sm GREATER MAX_SM) ++ set( MAX_SM "${sm}" ) ++ endif() ++ list( APPEND NV_SM -gencode arch=compute_${sm},code=sm_${sm} ) ++ string( REGEX REPLACE "([0-9])([0-9])" "\\1.\\2" cuda_arch "${sm}" ) ++ message( STATUS " compile for CUDA arch ${cuda_arch}" ) ++ endforeach() ++ ++ if (NOT NV_SM) ++ message( FATAL_ERROR ++ "GPU_TARGET must contain one or more of " ++ "Fermi, Kepler, Maxwell, Pascal, Volta, Turing, Ampere, or valid sm_[0-9][0-9]" ++ "Was: ${GPU_TARGET}" ) ++ endif() ++ ++ set( MIN_ARCH ${MIN_SM}0 ) ++ set( NV_COMP -gencode arch=compute_${MAX_SM},code=compute_${MAX_SM} ) ++ ++ list( APPEND CUDA_NVCC_FLAGS -Xcompiler -fPIC ${NV_SM} ${NV_COMP} ${FORTRAN_CONVENTION} ) ++ add_definitions( -DMAGMA_HAVE_CUDA=1 ) ++ add_definitions( -DMAGMA_CUDA_ARCH_MIN=${MIN_ARCH} ) + message( STATUS "Define -DMAGMA_HAVE_CUDA -DMAGMA_CUDA_ARCH_MIN=${MIN_ARCH}" ) + else() + message( STATUS "Could not find CUDA" ) From ba9cd3af8f833a7f25f803ba420b7957c5dd3999 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 15 Sep 2023 12:24:45 +0200 Subject: [PATCH 8822/9987] Add checksum for patch --- .../m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb index 3a690766598..a6de0adabfc 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb @@ -13,9 +13,11 @@ toolchainopts = {'pic': True, 'openmp': True} source_urls = ['https://icl.cs.utk.edu/projectsfiles/%(name)s/downloads/'] sources = [SOURCE_TAR_GZ] -checksums = ['729bc1a70e518a7422fe7a3a54537a4741035a77be3349f66eac5c362576d560'] - patches = ['%(name)s-2.7.2_allow-all-sms.patch'] +checksums = [ + {'magma-2.7.2.tar.gz': '729bc1a70e518a7422fe7a3a54537a4741035a77be3349f66eac5c362576d560'}, + {'magma-2.7.2_allow-all-sms.patch': '1fe721092d0193cad7c669bd8ffaa7c093a2547967232123ffb03460742f7b98'}, +] builddependencies = [ ('CMake', '3.26.3'), From c250b7fdbd6a37d35fc33827c6eb9a1358fee1aa Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 15 Sep 2023 16:18:38 +0100 Subject: [PATCH 8823/9987] adding easyconfigs: NBO-7.0.10-GCC-10.2.0.eb, NBO-7.0.10-GCC-9.3.0.eb, NBO-7.0.10-GCC-10.3.0.eb, NBO-7.0.10-GCC-11.2.0.eb, NBO-7.0.10-GCC-11.3.0.eb, NBO-7.0.10-GCC-12.2.0.eb and patches: NBO-7.0.10_make.patch --- .../n/NBO/NBO-7.0.10-GCC-10.2.0.eb | 54 ++++++++++++++++++ .../n/NBO/NBO-7.0.10-GCC-10.3.0.eb | 55 +++++++++++++++++++ .../n/NBO/NBO-7.0.10-GCC-11.2.0.eb | 55 +++++++++++++++++++ .../n/NBO/NBO-7.0.10-GCC-11.3.0.eb | 55 +++++++++++++++++++ .../n/NBO/NBO-7.0.10-GCC-12.2.0.eb | 55 +++++++++++++++++++ .../easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb | 54 ++++++++++++++++++ .../easyconfigs/n/NBO/NBO-7.0.10_make.patch | 46 ++++++++++++++++ 7 files changed, 374 insertions(+) create mode 100644 easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/NBO/NBO-7.0.10_make.patch diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb new file mode 100644 index 00000000000..fc8d53fb045 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb @@ -0,0 +1,54 @@ +# this recipe is configured for use with Gaussian G16, revision A03 or later + +easyblock = 'MakeCp' + +name = 'NBO' +version = '7.0.10' + +homepage = 'http://nbo.chem.wisc.edu/' +description = """ The Natural Bond Orbital (NBO) program is a discovery tool +for chemical insights from complex wavefunctions. """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers + +# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +sources = ['nbo%(version)s-src.tar.gz'] +patches = [ + 'NBO-%(version)s_make.patch', +] +checksums = [ + {'nbo7.0.10-src.tar.gz': 'a60d1f4d4592ec386b5378841d9fba75918c48b50de08d8de0a50db42bc96da1'}, + {'NBO-7.0.10_make.patch': 'c37f5a9980c56198f9610611b0fbda8ad65c961ec19b163d602dc3330fced145'}, +] + +dependencies = [ + ('OpenBLAS', '0.3.12'), +] + +local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers + +buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' +buildopts += 'BLASLIB="$LDFLAGS $LIBBLAS" ' +buildopts += 'INT=%s ' % local_intlength + +parallel = 1 + +files_to_copy = ['bin', 'dox', 'man', 'tests'] + +postinstallcmds = [ + 'sed -i -e "s|setenv GAUNBO.*|setenv GAUNBO g16nbo|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv BINDIR.*|setenv BINDIR %(installdir)s/bin|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv INT.*|setenv INT %s|" %%(installdir)s/bin/gaunbo{6,7}' % local_intlength, + 'cp %(builddir)s/nbo7/gennbo %(builddir)s/nbo7/gennbo.sh %(installdir)s/bin', + 'sed -i -e "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo', + 'sed -i "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo.sh', +] + +sanity_check_paths = { + 'files': ['bin/%s.%s.exe' % (x, local_intlength) for x in ('gennbo', 'g09nbo', 'g16nbo', 'nbo7')], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb new file mode 100644 index 00000000000..42603a8d021 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb @@ -0,0 +1,55 @@ +# this recipe is configured for use with Gaussian G16, revision A03 or later + +easyblock = 'MakeCp' + +name = 'NBO' +version = '7.0.10' + +homepage = 'http://nbo.chem.wisc.edu/' +description = """ The Natural Bond Orbital (NBO) program is a discovery tool +for chemical insights from complex wavefunctions. """ + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers + +# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +sources = ['nbo%(version)s-src.tar.gz'] +patches = [ + 'NBO-%(version)s_make.patch', +] +checksums = [ + {'nbo7.0.10-src.tar.gz': 'a60d1f4d4592ec386b5378841d9fba75918c48b50de08d8de0a50db42bc96da1'}, + {'NBO-7.0.10_make.patch': 'c37f5a9980c56198f9610611b0fbda8ad65c961ec19b163d602dc3330fced145'}, +] + +dependencies = [ + ('FlexiBLAS', '3.0.4'), + ('OpenBLAS', '0.3.17'), +] + +local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers + +buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' +buildopts += 'BLASLIB="$LDFLAGS -lflexiblas" LAPACKLIB="$LDFLAGS -lflexiblas" ' +buildopts += 'INT=%s ' % local_intlength + +parallel = 1 + +files_to_copy = ['bin', 'dox', 'man', 'tests'] + +postinstallcmds = [ + 'sed -i -e "s|setenv GAUNBO.*|setenv GAUNBO g16nbo|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv BINDIR.*|setenv BINDIR %(installdir)s/bin|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv INT.*|setenv INT %s|" %%(installdir)s/bin/gaunbo{6,7}' % local_intlength, + 'cp %(builddir)s/nbo7/gennbo %(builddir)s/nbo7/gennbo.sh %(installdir)s/bin', + 'sed -i -e "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo', + 'sed -i "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo.sh', +] + +sanity_check_paths = { + 'files': ['bin/%s.%s.exe' % (x, local_intlength) for x in ('gennbo', 'g09nbo', 'g16nbo', 'nbo7')], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb new file mode 100644 index 00000000000..28c77248a81 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb @@ -0,0 +1,55 @@ +# this recipe is configured for use with Gaussian G16, revision A03 or later + +easyblock = 'MakeCp' + +name = 'NBO' +version = '7.0.10' + +homepage = 'http://nbo.chem.wisc.edu/' +description = """ The Natural Bond Orbital (NBO) program is a discovery tool +for chemical insights from complex wavefunctions. """ + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers + +# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +sources = ['nbo%(version)s-src.tar.gz'] +patches = [ + 'NBO-%(version)s_make.patch', +] +checksums = [ + {'nbo7.0.10-src.tar.gz': 'a60d1f4d4592ec386b5378841d9fba75918c48b50de08d8de0a50db42bc96da1'}, + {'NBO-7.0.10_make.patch': 'c37f5a9980c56198f9610611b0fbda8ad65c961ec19b163d602dc3330fced145'}, +] + +dependencies = [ + ('FlexiBLAS', '3.0.4'), + ('OpenBLAS', '0.3.18'), +] + +local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers + +buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' +buildopts += 'BLASLIB="$LDFLAGS -lflexiblas" LAPACKLIB="$LDFLAGS -lflexiblas" ' +buildopts += 'INT=%s ' % local_intlength + +parallel = 1 + +files_to_copy = ['bin', 'dox', 'man', 'tests'] + +postinstallcmds = [ + 'sed -i -e "s|setenv GAUNBO.*|setenv GAUNBO g16nbo|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv BINDIR.*|setenv BINDIR %(installdir)s/bin|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv INT.*|setenv INT %s|" %%(installdir)s/bin/gaunbo{6,7}' % local_intlength, + 'cp %(builddir)s/nbo7/gennbo %(builddir)s/nbo7/gennbo.sh %(installdir)s/bin', + 'sed -i -e "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo', + 'sed -i "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo.sh', +] + +sanity_check_paths = { + 'files': ['bin/%s.%s.exe' % (x, local_intlength) for x in ('gennbo', 'g09nbo', 'g16nbo', 'nbo7')], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.3.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.3.0.eb new file mode 100644 index 00000000000..070009055b4 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.3.0.eb @@ -0,0 +1,55 @@ +# this recipe is configured for use with Gaussian G16, revision A03 or later + +easyblock = 'MakeCp' + +name = 'NBO' +version = '7.0.10' + +homepage = 'http://nbo.chem.wisc.edu/' +description = """ The Natural Bond Orbital (NBO) program is a discovery tool +for chemical insights from complex wavefunctions. """ + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers + +# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +sources = ['nbo%(version)s-src.tar.gz'] +patches = [ + 'NBO-%(version)s_make.patch', +] +checksums = [ + {'nbo7.0.10-src.tar.gz': 'a60d1f4d4592ec386b5378841d9fba75918c48b50de08d8de0a50db42bc96da1'}, + {'NBO-7.0.10_make.patch': 'c37f5a9980c56198f9610611b0fbda8ad65c961ec19b163d602dc3330fced145'}, +] + +dependencies = [ + ('FlexiBLAS', '3.2.0'), + ('OpenBLAS', '0.3.20'), +] + +local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers + +buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' +buildopts += 'BLASLIB="$LDFLAGS -lflexiblas" LAPACKLIB="$LDFLAGS -lflexiblas" ' +buildopts += 'INT=%s ' % local_intlength + +parallel = 1 + +files_to_copy = ['bin', 'dox', 'man', 'tests'] + +postinstallcmds = [ + 'sed -i -e "s|setenv GAUNBO.*|setenv GAUNBO g16nbo|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv BINDIR.*|setenv BINDIR %(installdir)s/bin|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv INT.*|setenv INT %s|" %%(installdir)s/bin/gaunbo{6,7}' % local_intlength, + 'cp %(builddir)s/nbo7/gennbo %(builddir)s/nbo7/gennbo.sh %(installdir)s/bin', + 'sed -i -e "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo', + 'sed -i "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo.sh', +] + +sanity_check_paths = { + 'files': ['bin/%s.%s.exe' % (x, local_intlength) for x in ('gennbo', 'g09nbo', 'g16nbo', 'nbo7')], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-12.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-12.2.0.eb new file mode 100644 index 00000000000..4c296b21592 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-12.2.0.eb @@ -0,0 +1,55 @@ +# this recipe is configured for use with Gaussian G16, revision A03 or later + +easyblock = 'MakeCp' + +name = 'NBO' +version = '7.0.10' + +homepage = 'http://nbo.chem.wisc.edu/' +description = """ The Natural Bond Orbital (NBO) program is a discovery tool +for chemical insights from complex wavefunctions. """ + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers + +# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +sources = ['nbo%(version)s-src.tar.gz'] +patches = [ + 'NBO-%(version)s_make.patch', +] +checksums = [ + {'nbo7.0.10-src.tar.gz': 'a60d1f4d4592ec386b5378841d9fba75918c48b50de08d8de0a50db42bc96da1'}, + {'NBO-7.0.10_make.patch': 'c37f5a9980c56198f9610611b0fbda8ad65c961ec19b163d602dc3330fced145'}, +] + +dependencies = [ + ('FlexiBLAS', '3.2.1'), + ('OpenBLAS', '0.3.21'), +] + +local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers + +buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' +buildopts += 'BLASLIB="$LDFLAGS -lflexiblas" LAPACKLIB="$LDFLAGS -lflexiblas" ' +buildopts += 'INT=%s ' % local_intlength + +parallel = 1 + +files_to_copy = ['bin', 'dox', 'man', 'tests'] + +postinstallcmds = [ + 'sed -i -e "s|setenv GAUNBO.*|setenv GAUNBO g16nbo|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv BINDIR.*|setenv BINDIR %(installdir)s/bin|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv INT.*|setenv INT %s|" %%(installdir)s/bin/gaunbo{6,7}' % local_intlength, + 'cp %(builddir)s/nbo7/gennbo %(builddir)s/nbo7/gennbo.sh %(installdir)s/bin', + 'sed -i -e "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo', + 'sed -i "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo.sh', +] + +sanity_check_paths = { + 'files': ['bin/%s.%s.exe' % (x, local_intlength) for x in ('gennbo', 'g09nbo', 'g16nbo', 'nbo7')], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb new file mode 100644 index 00000000000..1107835a69e --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb @@ -0,0 +1,54 @@ +# this recipe is configured for use with Gaussian G16, revision A03 or later + +easyblock = 'MakeCp' + +name = 'NBO' +version = '7.0.10' + +homepage = 'http://nbo.chem.wisc.edu/' +description = """ The Natural Bond Orbital (NBO) program is a discovery tool +for chemical insights from complex wavefunctions. """ + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers + +# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +sources = ['nbo%(version)s-src.tar.gz'] +patches = [ + 'NBO-%(version)s_make.patch', +] +checksums = [ + {'nbo7.0.10-src.tar.gz': 'a60d1f4d4592ec386b5378841d9fba75918c48b50de08d8de0a50db42bc96da1'}, + {'NBO-7.0.10_make.patch': 'c37f5a9980c56198f9610611b0fbda8ad65c961ec19b163d602dc3330fced145'}, +] + +dependencies = [ + ('OpenBLAS', '0.3.9'), +] + +local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers + +buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' +buildopts += 'BLASLIB="$LDFLAGS $LIBBLAS" ' +buildopts += 'INT=%s ' % local_intlength + +parallel = 1 + +files_to_copy = ['bin', 'dox', 'man', 'tests'] + +postinstallcmds = [ + 'sed -i -e "s|setenv GAUNBO.*|setenv GAUNBO g16nbo|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv BINDIR.*|setenv BINDIR %(installdir)s/bin|" %(installdir)s/bin/gaunbo{6,7}', + 'sed -i -e "s|setenv INT.*|setenv INT %s|" %%(installdir)s/bin/gaunbo{6,7}' % local_intlength, + 'cp %(builddir)s/nbo7/gennbo %(builddir)s/nbo7/gennbo.sh %(installdir)s/bin', + 'sed -i -e "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo', + 'sed -i "s|setenv NBOBIN ./bin|setenv NBOBIN %(installdir)s/bin|" %(installdir)s/bin/gennbo.sh', +] + +sanity_check_paths = { + 'files': ['bin/%s.%s.exe' % (x, local_intlength) for x in ('gennbo', 'g09nbo', 'g16nbo', 'nbo7')], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10_make.patch b/easybuild/easyconfigs/n/NBO/NBO-7.0.10_make.patch new file mode 100644 index 00000000000..5db56cf13f7 --- /dev/null +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10_make.patch @@ -0,0 +1,46 @@ +diff --git a/nbo7.orig/Make.config b/nbo7/Make.config +index d2f66ea..67ba367 100644 +--- a/nbo7.orig/Make.config ++++ b/nbo7/Make.config +@@ -9,7 +9,7 @@ FC = gfortran + # Fortran compiler version (required for gfortran only). Ignore the + # build number (e.g. specify 4.8, not 4.8.2). + +-FC_VERSION = 5.5 ++FC_VERSION = ${EBVERSIONGCC} + + # C compiler -- select from gcc (gnu), nvcc (nv), pgcc (pgi), and icl + # (intel). NBO has been most recently tested with gcc (4-10), nvcc +@@ -46,26 +46,26 @@ endif + + # NBO top-level directory (perhaps /opt/nbo7 or c:/nbo7). + +-NBODIR = ~/nbo7 ++NBODIR = ${PWD} + + # Use LAPACK routines for eigenvalue problems -- true or false. Note + # that LAPACK requires BLAS. + +-LAPACK = false ++LAPACK = true + + # LAPACK library -- ignored if LAPACK is false. + + #LAPACKLIB = -L/usr/lib/x86_64-linux-gnu -llapack +-LAPACKLIB = -L/apps/local/lapack/lib -llapack ++LAPACKLIB = -L${EBROOTOPENBLAS} -lopenblas + + # Use BLAS rather than native NBO linear algebra routines -- true or + # false. Note that LAPACK requires BLAS. + +-BLAS = false ++BLAS = true + + # BLAS libraries -- ignored if BLAS is false. + +-BLASLIB = -L/apps/local/OpenBLAS/lib -lopenblas ++BLASLIB = -L${EBROOTOPENBLAS} -lopenblas + #BLASLIB = -L/usr/local/OpenBLAS/lib -lopenblas + #BLASLIB = -L/usr/lib/x86_64-linux-gnu -lblas + #BLASLIB = -L/apps/pgi/linux86-64/2019/lib -lblas + From 49092d0e1447e7393a562c68825c1af4259c88b6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 18 Sep 2023 10:18:58 +0200 Subject: [PATCH 8824/9987] adding easyconfigs: Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb --- ...1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb new file mode 100644 index 00000000000..4473bc2e53c --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-CUDA-11.7.0-PyTorch-1.13.1.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_pt_version = '1.13.1' +local_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = local_cuda_suffix + '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. +This build only has PyTorch enabled.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('CUDA', '11.7.0', '', SYSTEM), + ('NCCL', '2.12.12', local_cuda_suffix), + ('PyTorch', local_pt_version, local_cuda_suffix), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["horovodrun --help"] + +moduleclass = 'tools' From c817fc83a736d54dbe6bc0e523ce65be170e47a7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 18 Sep 2023 10:26:56 +0200 Subject: [PATCH 8825/9987] Ignore EasyConfig cache file EasyBuild creates the file `.eb-path-index` in `easybuild/easyconfigs` to cache searches which shows up in git checkouts when used directly. As we never want to add this file to git ignore it explicitly --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 32e6a7345c4..c667a41e000 100644 --- a/.gitignore +++ b/.gitignore @@ -11,3 +11,4 @@ dist/ *.ropeproject/ eb-*.log /MANIFEST +/easybuild/easyconfigs/.eb-path-index From b7588e417a7bd24a574aebfafa83b3749b8a3a51 Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Mon, 18 Sep 2023 11:48:24 +0200 Subject: [PATCH 8826/9987] adding easyconfigs: pkgconf-1.8.0-GCCcore-10.3.0.eb --- .../p/pkgconf/pkgconf-1.8.0-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..fa7cf70d46b --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.8.0-GCCcore-10.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '1.8.0' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://distfiles.ariadne.space/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d7b6fdb522d81c11f5a0e0a0629a9f5480809ec90e595058674c1517822dfb8c'] + +builddependencies = [('binutils', '2.36.1')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' From ad70b3635faff6fc61fbe15398506408f9692aec Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Mon, 18 Sep 2023 11:52:33 +0200 Subject: [PATCH 8827/9987] adding easyconfigs: Arrow-8.0.0-foss-2021a.eb --- .../a/Arrow/Arrow-8.0.0-foss-2021a.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb new file mode 100644 index 00000000000..8c7316d60a9 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb @@ -0,0 +1,71 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '8.0.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Autotools', '20210128'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('pkgconf', '1.8.0'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy + ('Boost', '1.76.0'), + ('lz4', '1.9.3'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('zstd', '1.4.9'), + ('snappy', '1.1.8'), + ('RapidJSON', '1.1.0'), + ('RE2', '2022-02-01'), + ('utf8proc', '2.6.1'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " +configopts += "-DZSTD_ROOT=$EBROOTZSTD " + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' From f40d18043e448c676bf8c1a18762088b378209d6 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 18 Sep 2023 13:55:20 +0200 Subject: [PATCH 8828/9987] adding easyconfigs: GPAW-23.9.1-foss-2022a.eb, GPAW-23.9.1-intel-2022a.eb --- .../g/GPAW/GPAW-23.9.1-foss-2022a.eb | 49 +++++++++++++++++++ .../g/GPAW/GPAW-23.9.1-intel-2022a.eb | 48 ++++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb new file mode 100644 index 00000000000..1fc3dc4b53a --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '23.9.1' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-23.9.1.tar.gz': '19a24840b876003528864b7a0b38fc0d456800b83b8666b1f724273660745b47'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ASE', '3.22.1'), + ('libxc', '5.2.3'), + ('libvdwxc', '0.4.0'), + ('ELPA', '2022.05.001'), + ('PyYAML', '6.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb new file mode 100644 index 00000000000..7a20f021bfa --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb @@ -0,0 +1,48 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '23.9.1' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-23.9.1.tar.gz': '19a24840b876003528864b7a0b38fc0d456800b83b8666b1f724273660745b47'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ASE', '3.22.1'), + ('libxc', '5.2.3'), + ('ELPA', '2022.05.001'), + ('PyYAML', '6.0'), + ('GPAW-setups', '0.9.20000', '', True), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' From c9a3036ca0844d1dd5dc12d9d0fc4dfa9a77a31e Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 18 Sep 2023 14:28:28 +0200 Subject: [PATCH 8829/9987] Update how to specify dependencies without a toolchain --- easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb | 2 +- easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb index 1fc3dc4b53a..c4d66cb2233 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb @@ -30,7 +30,7 @@ dependencies = [ ('libvdwxc', '0.4.0'), ('ELPA', '2022.05.001'), ('PyYAML', '6.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb index 7a20f021bfa..6c8965ad7e6 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb @@ -29,7 +29,7 @@ dependencies = [ ('libxc', '5.2.3'), ('ELPA', '2022.05.001'), ('PyYAML', '6.0'), - ('GPAW-setups', '0.9.20000', '', True), + ('GPAW-setups', '0.9.20000', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' From cce468305c5708b10fbc7a04fa85c5ac2d29033c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2023 15:32:42 +0200 Subject: [PATCH 8830/9987] adding easyconfigs: SCons-4.5.2-GCCcore-12.3.0.eb --- .../s/SCons/SCons-4.5.2-GCCcore-12.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.5.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.5.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.5.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5e9d1a00cc2 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.5.2-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'SCons' +version = '4.5.2' + +homepage = 'https://www.scons.org' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': False, + 'patches': ['SCons-4.4.0_install_man_pages_correctly.patch'], + 'checksums': [ + {'SCons-4.5.2.tar.gz': '813360b2bce476bc9cc12a0f3a22d46ce520796b352557202cb07d3e402f5458'}, + {'SCons-4.4.0_install_man_pages_correctly.patch': + '9d216c2ea8e152ae1531593b17adc4042eb88f1d9524d7f3b08ace5137d6d5e7'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/sconsign'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ["scons --help"] + +moduleclass = 'devel' From 9268daa022d1c99fd6990c62eb92c813a2dafb73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2023 15:47:11 +0200 Subject: [PATCH 8831/9987] {chem}[foss/2023a] Cantera v3.0.0, SUNDIALS v6.6.0, HighFive v2.7.1, fmt v10.1.0, pygraphviz v1.11, ruamel.yaml v0.17.32 --- .../c/Cantera/Cantera-3.0.0-foss-2023a.eb | 57 +++++++++++++++++++ .../f/fmt/fmt-10.1.0-GCCcore-12.3.0.eb | 26 +++++++++ .../h/HighFive/HighFive-2.7.1-gompi-2023a.eb | 34 +++++++++++ .../pygraphviz-1.11-GCCcore-12.3.0.eb | 33 +++++++++++ .../ruamel.yaml-0.17.32-GCCcore-12.3.0.eb | 57 +++++++++++++++++++ .../s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb | 33 +++++++++++ 6 files changed, 240 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cantera/Cantera-3.0.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/f/fmt/fmt-10.1.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/h/HighFive/HighFive-2.7.1-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.11-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.32-GCCcore-12.3.0.eb create mode 100755 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-3.0.0-foss-2023a.eb b/easybuild/easyconfigs/c/Cantera/Cantera-3.0.0-foss-2023a.eb new file mode 100644 index 00000000000..6c72b7b0f23 --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-3.0.0-foss-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'SCons' + +name = 'Cantera' +version = '3.0.0' + +homepage = 'https://github.com/Cantera/cantera' +description = """Chemical kinetics, thermodynamics, and transport tool suite""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/Cantera/cantera/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6d17cdef21dae9deaf91351260b68ccf7e264c37c6030c9d4bf26a2cefb2b905'] + +builddependencies = [ + ('SCons', '4.5.2'), + ('Eigen', '3.4.0'), + ('fmt', '10.1.0'), + ('googletest', '1.13.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('h5py', '3.9.0'), + ('pygraphviz', '1.11'), + ('JupyterLab', '4.0.5'), + ('matplotlib', '3.7.2'), + ('Boost', '1.82.0'), + ('SUNDIALS', '6.6.0'), + ('yaml-cpp', '0.7.0'), + ('ruamel.yaml', '0.17.32'), + ('HighFive', '2.7.1'), +] + +local_common_opts = 'env_vars=all CC="$CC" CXX="$CXX" cc_flags="$CFLAGS" cxx_flags="$CXXFLAGS" ' +local_common_opts += 'blas_lapack_libs=flexiblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR ' +local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' +buildopts = 'build ' + local_common_opts +# tests hang, so disable them for now +# runtest = 'test ' + local_common_opts +installopts = 'install ' + local_common_opts +prefix_arg = 'prefix=' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/cti2yaml'], + 'dirs': ['include/cantera', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cti2yaml --help", + "python -c 'import cantera'", +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.1.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..6866b4ac550 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-10.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '10.1.0' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['d725fa83a8b57a3cedf238828fa6b167f963041e8f9f7327649bddc68ae316f4'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/HighFive/HighFive-2.7.1-gompi-2023a.eb b/easybuild/easyconfigs/h/HighFive/HighFive-2.7.1-gompi-2023a.eb new file mode 100644 index 00000000000..e17e6e8507b --- /dev/null +++ b/easybuild/easyconfigs/h/HighFive/HighFive-2.7.1-gompi-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'HighFive' +version = '2.7.1' + +homepage = 'https://github.com/BlueBrain/HighFive' +description = """HighFive is a modern header-only C++11 friendly interface for libhdf5.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +github_account = 'BlueBrain' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['25b4c51a94d1e670dc93b9b73f51e79b65d8ff49bcd6e5d5582d5ecd2789a249'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40') +] + +dependencies = [ + ('HDF5', '1.14.0'), + ('Boost', '1.82.0'), + ('Eigen', '3.4.0'), +] + +sanity_check_paths = { + 'files': ['include/highfive/H5File.hpp'], + 'dirs': [], +} + +configopts = '-DHIGHFIVE_USE_EIGEN=ON -DHIGHFIVE_PARALLEL_HDF5=ON' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.11-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..152d35266b7 --- /dev/null +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.11-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'pygraphviz' +version = '1.11' + +homepage = 'https://pygraphviz.github.io' +description = """PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. +With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz +graph data structure and layout algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Graphviz', '8.1.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'sources': ['%(namelower)s-%(version)s.zip'], + 'checksums': ['a97eb5ced266f45053ebb1f2c6c6d29091690503e3a5c14be7f908b37b06f2d4'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.32-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.32-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..cb4385ee456 --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.32-GCCcore-12.3.0.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.17.32' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + (name, version, { + 'checksums': ['ec939063761914e14542972a5cba6d33c23b0859ab6342f61cf070cfc600efc2'], + }), + ('configobj', '5.0.8', { + 'checksums': ['6f704434a07dc4f4dc7c9a745172c1cad449feb548febd9f7fe362629c627a97'], + }), + ('lz4', '4.3.2', { + 'checksums': ['e1431d84a9cfb23e6773e72078ce8e65cad6745816d4cbf9ae67da5ea419acda'], + }), + ('ruamel.yaml.base', '0.3.2', { + 'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.6.5', { + 'checksums': ['49af59514cb87d7637d1186e31c9345c9947120a9ce49cf6975435aa7abd5aa8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb new file mode 100755 index 00000000000..02bb2f3f2fd --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '6.6.0' + +homepage = 'https://computing.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f90029b8da846c8faff5530fd1fa4847079188d040554f55c1d5d1e04743d29d'] + +builddependencies = [('CMake', '3.26.3')] + +configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' From 0619edd6217e207ee2ba0f1f3ab95a2704add401 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 18 Sep 2023 17:38:05 +0200 Subject: [PATCH 8832/9987] fix permissions for SUNDIALS easyconfig --- easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb old mode 100755 new mode 100644 From 59f6825b3672f5a478e3511fd0db247be318b4d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Sep 2023 08:48:22 +0200 Subject: [PATCH 8833/9987] adding easyconfigs: XlsxWriter-3.1.3-GCCcore-12.3.0.eb --- .../XlsxWriter-3.1.3-GCCcore-12.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..251a37d1717 --- /dev/null +++ b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.3-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'XlsxWriter' +version = '3.1.3' + +homepage = 'https://xlsxwriter.readthedocs.io/' +description = "A Python module for creating Excel XLSX files" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['696c16458d50712a3a5f902676c045ddb4c1bd1b54595f501e582d549abdbdb9'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/vba_extract.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['vba_extract.py --help'] + +sanity_pip_check = True + +moduleclass = 'tools' From 50ed03fbb1ce1d7f57a31ed2c4681d3a68a252a5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Sep 2023 08:48:34 +0200 Subject: [PATCH 8834/9987] adding easyconfigs: openpyxl-3.1.2-GCCcore-12.3.0.eb --- .../openpyxl/openpyxl-3.1.2-GCCcore-12.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a666b740fce --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.1.2' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('lxml', '4.9.2'), + ('Pillow', '10.0.0'), +] + +use_pip = True + +exts_list = [ + ('et_xmlfile', '1.1.0', { + 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['a6f5977418eff3b2d5500d54d9db50c8277a368436f4e4f8ddb1be3422870184'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 2ebb692edad648f7b0f094d20758236608285fce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Sep 2023 09:20:17 +0200 Subject: [PATCH 8835/9987] {bio}[foss/2021b] CIRIquant v1.1.2-20221201, scikit-learn v0.20.4, Pysam v0.17.0, PyYAML v5.4.1 w/ Python 2.7.18 --- ...1.1.2-20221201-foss-2021b-Python-2.7.18.eb | 51 +++++++++++++++++++ ...YAML-5.4.1-GCCcore-11.2.0-Python-2.7.18.eb | 28 ++++++++++ .../Pysam-0.17.0-GCC-11.2.0-Python-2.7.18.eb | 41 +++++++++++++++ .../scikit-learn-0.20.3_fix-cd_fast.patch | 44 ++++++++++++++++ ...t-learn-0.20.4-foss-2021b-Python-2.7.18.eb | 38 ++++++++++++++ 5 files changed, 202 insertions(+) create mode 100644 easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-5.4.1-GCCcore-11.2.0-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.17.0-GCC-11.2.0-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3_fix-cd_fast.patch create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2021b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..dcf867e2a49 --- /dev/null +++ b/easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'CIRIquant' +local_commit = '2d0663e' +version = '1.1.2-20221201' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/bioinfo-biols/CIRIquant' +description = "CIRIquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2021.10', versionsuffix), + ('PyYAML', '5.4.1', versionsuffix), + ('Pysam', '0.17.0', versionsuffix), + ('scikit-learn', '0.20.4', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + (name, version, { + 'source_urls': ['https://github.com/bioinfo-biols/CIRIquant/archive/'], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}], + 'checksums': ['4990122c0eb820b1ec9cfc64fcfe49d3f9680dae69719dba3f8a7d77f9c3ff54'], + # relax numpy version requirement, no actual need for 1.22.0 + # (cfr. https://github.com/bioinfo-biols/CIRIquant/pull/39), + # and remove very strict version requirements for all required Python packages + 'preinstallopts': "sed -i 's/numpy==1.22.0/numpy==1.16.4/g' setup.py && sed -i 's/==/>=/g' setup.py && ", + 'modulename': 'CIRIquant', + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/CIRIquant'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["CIRIquant --help"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/CIRIquant'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-5.4.1-GCCcore-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.4.1-GCCcore-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..1e3db0a9e7f --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-5.4.1-GCCcore-11.2.0-Python-2.7.18.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '5.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/yaml/pyyaml" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['607774cbba28732bfa802b54baa7484215f530991055bb562efbed5b2f20a45e'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '2.7.18'), + ('libyaml', '0.2.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'yaml'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.17.0-GCC-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.17.0-GCC-11.2.0-Python-2.7.18.eb new file mode 100644 index 00000000000..2b1c61cd8ce --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.17.0-GCC-11.2.0-Python-2.7.18.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Erich Birngruber +# Gregor Mendel Institute +# updated to 0.1.0. +# J. Sassmannshausen / GSTT +# +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.17.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f4d697e322d12f239c96c263374bad2b40fd95bff34841ab9515e3de9e3e7cca'] + +dependencies = [ + ('Python', '2.7.18'), + ('ncurses', '6.2'), + ('cURL', '7.78.0'), + ('XZ', '5.2.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3_fix-cd_fast.patch b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3_fix-cd_fast.patch new file mode 100644 index 00000000000..46ddfdbb9e7 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.3_fix-cd_fast.patch @@ -0,0 +1,44 @@ +fix "error: type of formal parameter 1 is incomplete" +see also https://bugs.gentoo.org/630294 +--- scikit-learn-0.20.3.orig/sklearn/linear_model/cd_fast.c 2019-08-09 03:05:05.351926119 +0500 ++++ scikit-learn-0.20.3.orig/sklearn/linear_model/cd_fast.c 2019-08-09 03:05:35.022926006 +0500 +@@ -4889,7 +4889,7 @@ + + static PyObject *__pyx_pf_7sklearn_12linear_model_7cd_fast_8enet_coordinate_descent(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_w, float __pyx_v_alpha, float __pyx_v_beta, __Pyx_memviewslice __pyx_v_X, __Pyx_memviewslice __pyx_v_y, int __pyx_v_max_iter, float __pyx_v_tol, PyObject *__pyx_v_rng, int __pyx_v_random, int __pyx_v_positive) { + PyObject *__pyx_v_dtype = NULL; +- void (*__pyx_v_gemv)(enum CBLAS_ORDER, enum CBLAS_TRANSPOSE, int, int, float, float *, int, float *, int, float, float *, int); ++ void (*__pyx_v_gemv)(CBLAS_ORDER, CBLAS_TRANSPOSE, int, int, float, float *, int, float *, int, float, float *, int); + float (*__pyx_v_dot)(int, float *, int, float *, int); + void (*__pyx_v_axpy)(int, float, float *, int, float *, int); + float (*__pyx_v_asum)(int, float *, int); +@@ -6279,7 +6279,7 @@ + + static PyObject *__pyx_pf_7sklearn_12linear_model_7cd_fast_10enet_coordinate_descent(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_w, double __pyx_v_alpha, double __pyx_v_beta, __Pyx_memviewslice __pyx_v_X, __Pyx_memviewslice __pyx_v_y, int __pyx_v_max_iter, double __pyx_v_tol, PyObject *__pyx_v_rng, int __pyx_v_random, int __pyx_v_positive) { + PyObject *__pyx_v_dtype = NULL; +- void (*__pyx_v_gemv)(enum CBLAS_ORDER, enum CBLAS_TRANSPOSE, int, int, double, double *, int, double *, int, double, double *, int); ++ void (*__pyx_v_gemv)(CBLAS_ORDER, CBLAS_TRANSPOSE, int, int, double, double *, int, double *, int, double, double *, int); + double (*__pyx_v_dot)(int, double *, int, double *, int); + void (*__pyx_v_axpy)(int, double, double *, int, double *, int); + double (*__pyx_v_asum)(int, double *, int); +@@ -16246,8 +16246,8 @@ + CYTHON_UNUSED float (*__pyx_v_asum)(int, float *, int); + void (*__pyx_v_copy)(int, float *, int, float *, int); + void (*__pyx_v_scal)(int, float, float *, int); +- void (*__pyx_v_ger)(enum CBLAS_ORDER, int, int, float, float *, int, float *, int, float *, int); +- void (*__pyx_v_gemv)(enum CBLAS_ORDER, enum CBLAS_TRANSPOSE, int, int, float, float *, int, float *, int, float, float *, int); ++ void (*__pyx_v_ger)(CBLAS_ORDER, int, int, float, float *, int, float *, int, float *, int); ++ void (*__pyx_v_gemv)(CBLAS_ORDER, CBLAS_TRANSPOSE, int, int, float, float *, int, float *, int, float, float *, int); + unsigned int __pyx_v_n_samples; + unsigned int __pyx_v_n_features; + unsigned int __pyx_v_n_tasks; +@@ -17965,8 +17965,8 @@ + CYTHON_UNUSED double (*__pyx_v_asum)(int, double *, int); + void (*__pyx_v_copy)(int, double *, int, double *, int); + void (*__pyx_v_scal)(int, double, double *, int); +- void (*__pyx_v_ger)(enum CBLAS_ORDER, int, int, double, double *, int, double *, int, double *, int); +- void (*__pyx_v_gemv)(enum CBLAS_ORDER, enum CBLAS_TRANSPOSE, int, int, double, double *, int, double *, int, double, double *, int); ++ void (*__pyx_v_ger)(CBLAS_ORDER, int, int, double, double *, int, double *, int, double *, int); ++ void (*__pyx_v_gemv)(CBLAS_ORDER, CBLAS_TRANSPOSE, int, int, double, double *, int, double *, int, double, double *, int); + unsigned int __pyx_v_n_samples; + unsigned int __pyx_v_n_features; + unsigned int __pyx_v_n_tasks; diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2021b-Python-2.7.18.eb new file mode 100644 index 00000000000..2e978bde2c2 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.20.4-foss-2021b-Python-2.7.18.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '0.20.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '2.7.18'), + ('SciPy-bundle', '2021.10', versionsuffix) +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'patches': ['scikit-learn-0.20.3_fix-cd_fast.patch'], + 'checksums': [ + {'scikit-learn-0.20.4.tar.gz': 'dfa8a3f33907614030cdfbc8b6f553dacbecaf09f922244f128af3060a137cfc'}, + {'scikit-learn-0.20.3_fix-cd_fast.patch': + '9a98785a99bde000a58048ccbe382ea362aa8cf644171097e8ae755cddddeb75'}, + ], + 'modulename': 'sklearn', + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), +] + +moduleclass = 'data' From 4da855fbcdca496caecd4e98678c9fcc6c7d8d0a Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Tue, 19 Sep 2023 09:26:25 +0200 Subject: [PATCH 8836/9987] adding easyconfigs: kallisto-0.48.0-gompi-2021a.eb --- .../k/kallisto/kallisto-0.48.0-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021a.eb diff --git a/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021a.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021a.eb new file mode 100644 index 00000000000..3f83a6f896b --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.48.0-gompi-2021a.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.48.0' + +homepage = 'https://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'pachterlab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['1797ac4d1f0771e3f1f25dd7972bded735fcb43f853cf52184d3d9353a6269b0'] + +builddependencies = [ + ('Autotools', '20210128'), + ('CMake', '3.20.1'), + ('zlib', '1.2.11'), +] + +dependencies = [('HDF5', '1.10.7')] + +preconfigopts = "cd ../%(name)s-%(version)s/ext/htslib/ && " +preconfigopts += "sed -i '/AC_PROG_CC/a AC_CANONICAL_HOST' configure.ac && " +preconfigopts += "autoreconf -i && cd - && " +configopts = '-DUSE_HDF5=ON' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'bio' From 919e2e6ee6bac4d5c32427b8f8cc16ae8e65d913 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Sep 2023 09:36:57 +0200 Subject: [PATCH 8837/9987] don't enable download_dep_fail in CIRIquant easyconfig, already done by default when using PythonBundle --- .../CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb index dcf867e2a49..b2f6bd3849e 100644 --- a/easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CIRIquant/CIRIquant-1.1.2-20221201-foss-2021b-Python-2.7.18.eb @@ -18,7 +18,6 @@ dependencies = [ ('scikit-learn', '0.20.4', versionsuffix), ] -download_dep_fail = True use_pip = True exts_list = [ From eb3840910f72ca27dae921c9644c1bffedca42f9 Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Tue, 19 Sep 2023 09:40:35 +0200 Subject: [PATCH 8838/9987] adding easyconfigs: GATK-4.2.6.1-GCCcore-10.3.0-Java-11.eb --- .../GATK-4.2.6.1-GCCcore-10.3.0-Java-11.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-10.3.0-Java-11.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-10.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-10.3.0-Java-11.eb new file mode 100644 index 00000000000..c89b60d9311 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.2.6.1-GCCcore-10.3.0-Java-11.eb @@ -0,0 +1,54 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.2.6.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['1125cfc862301d437310506c8774d36c3a90d00d52c7b5d6b59dac7241203628'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Python', '3.9.5'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +modloadmsg = "WARNING: GATK v%(version)s support for Java 11 is in beta state. Use at your own risk.\n" + +moduleclass = 'bio' From e64b120254d72ef5dc933d1eb044060b679a8001 Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Tue, 19 Sep 2023 09:45:02 +0200 Subject: [PATCH 8839/9987] adding easyconfigs: BLAT-3.7-GCC-10.3.0.eb --- .../easyconfigs/b/BLAT/BLAT-3.7-GCC-10.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-10.3.0.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-10.3.0.eb new file mode 100644 index 00000000000..dceaa2704a8 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.7-GCC-10.3.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou +# Contributors:: Alex Domingo (Vrije Universiteit Brussel) +# License:: MIT/GPL +# +## + +name = 'BLAT' +version = '3.7' + +homepage = 'https://genome.ucsc.edu/goldenPath/help/blatSpec.html' +description = """BLAT on DNA is designed to quickly find sequences of 95% and +greater similarity of length 25 bases or more.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://genome-test.gi.ucsc.edu/~kent/src/'] +sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] +patches = ['BLAT-%(version)s_mend-tests.patch'] +checksums = [ + {'blatSrc37.zip': '88ee2b272d42ab77687c61d200b11f1d58443951069feb7e10226a2509f84cf2'}, + {'BLAT-3.7_mend-tests.patch': '1f42c7fadf7676a5cc3a2016f70089c3541aa1d53816cf86072682c44cf311a6'}, +] + +# BLAT relies on a bundled old version of HTSlib. We use the bundled library +# because it is statically linked and the newer HTSlib in this toolchain is not +# API compatible with it. +dependencies = [ + ('freetype', '2.10.4'), + ('libiconv', '1.16'), + ('libpng', '1.6.37'), + ('MariaDB', '10.6.4'), + ('OpenSSL', '1.1', '', SYSTEM), + ('util-linux', '2.36'), + ('zlib', '1.2.11'), +] + +pretestopts = 'PATH="%(builddir)s/blatSrc/bin:$PATH"' +runtest = 'test' + +_blat_bins = ["blat", "faToNib", "faToTwoBit", "gfClient", "gfServer", "nibFrag", "pslPretty", + "pslReps", "pslSort", "twoBitInfo", "twoBitToFa"] + +files_to_copy = [(["bin/%s" % x for x in _blat_bins] + ["webBlat/webBlat"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in _blat_bins + ["webBlat"]], + 'dirs': [], +} + +moduleclass = 'bio' From f83254795cc3d1c52e709bd931eda22689cacf77 Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Tue, 19 Sep 2023 09:47:13 +0200 Subject: [PATCH 8840/9987] adding easyconfigs: Bowtie-1.3.1-GCC-10.3.0.eb --- .../b/Bowtie/Bowtie-1.3.1-GCC-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-10.3.0.eb new file mode 100644 index 00000000000..4f96d59e220 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.3.1-GCC-10.3.0.eb @@ -0,0 +1,30 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Artistic v2.0 +# +# Notes:: +## + +name = 'Bowtie' +version = '1.3.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. + It aligns short DNA sequences (reads) to the human genome.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = ['https://sourceforge.net/projects/bowtie-bio/files/bowtie/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.zip'] +checksums = ['e23517aa53846ef828172be911750cd05748522117efcbbe5a36f3241fb40761'] + +dependencies = [ + ('tbb', '2020.3'), + ('zlib', '1.2.11'), +] + +moduleclass = 'bio' From 0943155f0b476fa3a638df9d8e7c36b769dbd146 Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Tue, 19 Sep 2023 09:48:42 +0200 Subject: [PATCH 8841/9987] adding easyconfigs: GMAP-GSNAP-2023-04-20-GCC-10.3.0.eb --- .../GMAP-GSNAP-2023-04-20-GCC-10.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-10.3.0.eb new file mode 100644 index 00000000000..855eec4f731 --- /dev/null +++ b/easybuild/easyconfigs/g/GMAP-GSNAP/GMAP-GSNAP-2023-04-20-GCC-10.3.0.eb @@ -0,0 +1,55 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 2016-11-07 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'GMAP-GSNAP' +version = '2023-04-20' + +homepage = 'http://research-pub.gene.com/gmap/' +description = """GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences + GSNAP: Genomic Short-read Nucleotide Alignment Program""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['http://research-pub.gene.com/gmap/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GMAP-GSNAP-2023-02-17_cleanup-headers.patch', + 'GMAP-GSNAP-2023-02-17_fix-typecast.patch', +] +checksums = [ + {'gmap-gsnap-2023-04-20.tar.gz': 'f858bc699cbcc9b3f06751ace55c86bfc21e4ca821a90b10681feac2172b725e'}, + {'GMAP-GSNAP-2023-02-17_cleanup-headers.patch': '7d17d4cbc717556e3a64475eb931b692e9d564b486acf6c9dbf4c2bf29853832'}, + {'GMAP-GSNAP-2023-02-17_fix-typecast.patch': 'eafe728cf00cf52320bbf4b710ef76b662df92533d22fa67dc273855c180296f'}, +] + +# with these deps you can use standard compressed files +# details in http://research-pub.gene.com/gmap/src/README +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +# GSNAP uses MAX_STACK_READLENGTH to control the use of stack or heap memory depending on the read length +# details in http://research-pub.gene.com/gmap/src/README +# configopts = 'MAX_STACK_READLENGTH=300' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/gmap', 'bin/gsnap'], + 'dirs': [], +} + +sanity_check_commands = [ + "gmap --help", + "gsnap --help", +] + +moduleclass = 'bio' From ce703faaedff27a0aa906516ddec06c3a27e6db0 Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Tue, 19 Sep 2023 09:51:27 +0200 Subject: [PATCH 8842/9987] adding easyconfigs: HISAT2-2.2.1-gompi-2021a.eb --- .../h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb new file mode 100644 index 00000000000..59e1d8054bd --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.2.1-gompi-2021a.eb @@ -0,0 +1,59 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GPLv3.0 +# +# Notes:: +# 2.2.1 - changes from Adam Huffman +# Bumped to foss-2021b +# J. Sassmannshausen + +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.2.1' + +homepage = 'https://daehwankimlab.github.io/hisat2' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +sources = [{ + 'source_urls': ['https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi'], + 'download_filename': 'download', + 'filename': '%(namelower)s-%(version)s-source.zip', +}] +patches = [ + 'hisat2-libname-fix.patch', +] +checksums = [ + '48e933330d4d8470d2b3dfe7ec3918f2e98a75f7381891e23b7df1fb4f135eb1', + '8aa91d1dd6455b96c10ce48827f8313b006241d815fbe6382422dbae3b610726', # hisat2-libname-fix.patch +] + +dependencies = [ + ('NGS', '2.10.9'), + ('ncbi-vdb', '2.10.9'), +] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CFLAGS" ' +buildopts += "USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINVDB" + +local_executables = ['hisat2', 'hisat2-align-l', 'hisat2-align-s', 'hisat2-build', 'hisat2-build-l', 'hisat2-build-s', + 'hisat2-inspect', 'hisat2-inspect-s', 'hisat2-inspect-l', 'hisat2-repeat', 'extract_exons.py', + 'extract_splice_sites.py', 'hisat2_extract_exons.py', 'hisat2_extract_snps_haplotypes_UCSC.py', + 'hisat2_extract_snps_haplotypes_VCF.py', 'hisat2_extract_splice_sites.py', + 'hisat2_read_statistics.py', 'hisat2_simulate_reads.py'] +files_to_copy = [(local_executables, 'bin'), 'scripts', 'example'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables], + 'dirs': ['scripts', 'example'], +} + +sanity_check_commands = ["hisat2 --help"] + +moduleclass = 'bio' From 46eb0bc4550ff5d9ff7ac67785f79b10562a6429 Mon Sep 17 00:00:00 2001 From: IBU Software Devel Date: Tue, 19 Sep 2023 10:01:36 +0200 Subject: [PATCH 8843/9987] adding easyconfigs: SMRT-Link-12.0.0.177059-cli-tools-only.eb --- .../SMRT-Link-12.0.0.177059-cli-tools-only.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-12.0.0.177059-cli-tools-only.eb diff --git a/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-12.0.0.177059-cli-tools-only.eb b/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-12.0.0.177059-cli-tools-only.eb new file mode 100644 index 00000000000..0b654c823f3 --- /dev/null +++ b/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-12.0.0.177059-cli-tools-only.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Binary' + +name = "SMRT-Link" +version = "12.0.0.177059" +versionsuffix = '-cli-tools-only' + +homepage = 'https://www.pacb.com/support/software-downloads/' +description = """PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, + Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI + or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through + the extensive set of APIs provided""" + +toolchain = SYSTEM + +# The download is a password protected zip file +# Download it from https://www.pacb.com/support/software-downloads/ and uncompress +# the .run file to your sources folder +sources = ['smrtlink_%(version)s.run'] +checksums = ['95dadf8c5435d55724e43a290144322c32c9c9cf8b4f1e54c1a7a6f3ec368fbe'] + +install_cmd = "%(builddir)s/smrtlink_%(version)s.run --rootdir %(installdir)s --smrttools-only" + +cleanupoldinstall = True +dontcreateinstalldir = True + +modextravars = { + 'SMRT_ROOT': '%(installdir)s', +} + +modextrapaths = { + 'PATH': ['smrtcmds/bin', 'smrtcmds/developer/bin', 'admin/bin'], +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['install', 'userdata'] +} + +moduleclass = 'bio' From c3ca6a151c586521f598875850ef2e3e5a244e58 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 19 Sep 2023 10:30:16 +0200 Subject: [PATCH 8844/9987] adding easyconfigs: ProBiS-20230403-gompi-2022b.eb --- .../p/ProBiS/ProBiS-20230403-gompi-2022b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/ProBiS/ProBiS-20230403-gompi-2022b.eb diff --git a/easybuild/easyconfigs/p/ProBiS/ProBiS-20230403-gompi-2022b.eb b/easybuild/easyconfigs/p/ProBiS/ProBiS-20230403-gompi-2022b.eb new file mode 100644 index 00000000000..b8d9926b1fe --- /dev/null +++ b/easybuild/easyconfigs/p/ProBiS/ProBiS-20230403-gompi-2022b.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'ProBiS' +version = '20230403' +local_commit = 'f10a9f4c' + +homepage = 'http://insilab.org/probis-algorithm' +description = """ProBiS algorithm aligns and superimposes complete protein surfaces, +surface motifs, or protein binding sites.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} + +source_urls = ['https://gitlab.com/janezkonc/probis/-/archive/master/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['5f81df7498daefe0e66082561f31d4c66f75cf1eebbed6430e3d78dd3097896b'] + +dependencies = [ + ('GSL', '2.7'), +] + +buildopts = 'probis CC="mpic++" CFLAGS="-std=c++11 -O3 -Wall -Wno-unused-function -DNDEBUG -pthread"' + +files_to_copy = [(['probis'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/probis'], + 'dirs': [], +} + +sanity_check_commands = ["probis -h"] + +moduleclass = "bio" From 92d65b9f12bb26422b6525a4c8aa800ff955c4e1 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 19 Sep 2023 10:42:26 +0200 Subject: [PATCH 8845/9987] Downgrade ELPA to use same version as other packages in this toolchain. --- easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb | 2 +- easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb index c4d66cb2233..3b483fafeee 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2022a.eb @@ -28,7 +28,7 @@ dependencies = [ ('ASE', '3.22.1'), ('libxc', '5.2.3'), ('libvdwxc', '0.4.0'), - ('ELPA', '2022.05.001'), + ('ELPA', '2021.11.001'), ('PyYAML', '6.0'), ('GPAW-setups', '0.9.20000', '', SYSTEM), ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb index 6c8965ad7e6..65e38c0e70b 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-intel-2022a.eb @@ -27,7 +27,7 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('ASE', '3.22.1'), ('libxc', '5.2.3'), - ('ELPA', '2022.05.001'), + ('ELPA', '2021.11.001'), ('PyYAML', '6.0'), ('GPAW-setups', '0.9.20000', '', SYSTEM), ] From 91b094bfb5424d614395fb427ecd20765a65131c Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Tue, 19 Sep 2023 11:04:21 +0200 Subject: [PATCH 8846/9987] Update easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb --- .../pytest-rerunfailures-12.0-GCCcore-12.3.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb index c581d93c49a..19666ba283e 100644 --- a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb @@ -10,9 +10,10 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [('binutils', '2.40')] -dependencies = [('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), # It checks for it after installed - ] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # It checks for it after installed +] use_pip = True sanity_pip_check = True From 82f97a625e77233effbfa9e3f7f99f839d16ae4e Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 19 Sep 2023 12:02:45 +0200 Subject: [PATCH 8847/9987] adding easyconfigs: preCICE-2.5.0-foss-2022a.eb --- .../p/preCICE/preCICE-2.5.0-foss-2022a.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/p/preCICE/preCICE-2.5.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/preCICE/preCICE-2.5.0-foss-2022a.eb b/easybuild/easyconfigs/p/preCICE/preCICE-2.5.0-foss-2022a.eb new file mode 100644 index 00000000000..1cfa3f80e8b --- /dev/null +++ b/easybuild/easyconfigs/p/preCICE/preCICE-2.5.0-foss-2022a.eb @@ -0,0 +1,70 @@ +easyblock = 'CMakeMake' + +name = 'preCICE' +version = '2.5.0' + +homepage = 'https://www.precice.org/' +description = """preCICE (Precise Code Interaction Coupling Environment) +is a coupling library for partitioned multi-physics simulations, +including, but not restricted to fluid-structure interaction and +conjugate heat transfer simulations. Partitioned means that preCICE +couples existing programs (solvers) capable of simulating a subpart of +the complete physics involved in a simulation. This allows for the high +flexibility that is needed to keep a decent time-to-solution for complex +multi-physics scenarios.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/precice/precice/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'preCICE-2.5.0_link_with_statics.patch', +] +checksums = [ + {'v2.5.0.tar.gz': '76ec6ee0d1a66f6f3d3d2d11f03cfc5aa7ef4d9e5deb9b7a4b4455ec7f796c00'}, + {'preCICE-2.5.0_link_with_statics.patch': '38de293a94e9029b60b262ee23e45f0e9098f7d00ba0d0f7278b7109a50e21f6'}, +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Boost', '1.79.0'), + ('Eigen', '3.4.0'), + ('libxml2', '2.9.13'), + ('PETSc', '3.17.4'), + ('SciPy-bundle', '2022.05'), +] + +separate_build_dir = True +build_shared_libs = True + +# Tell pkg-config to keep flags available in CPATH and others because it prevents CMake from finding PETSc correctly +preconfigopts = 'PKG_CONFIG_ALLOW_SYSTEM_LIBS=1 PKG_CONFIG_ALLOW_SYSTEM_CFLAGS=1 ' +# Make sure MPI support is enabled +configopts = '-DPRECICE_MPICommunication=ON ' +# Make sure PETSc support is enabled +configopts += '-DPRECICE_PETScMapping=ON ' +# Make sure PythonActions support is enabled +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT +configopts += '-DPRECICE_PythonActions=ON ' +# force Eigen include directory which is not found correctly otherwise +configopts += '-DEIGEN3_INCLUDE_DIR="$EBROOTEIGEN/include"' + +# Run basic tests +runtest = ' test_base' + +sanity_check_paths = { + 'files': ['bin/binprecice'] + + ['include/precice/%s' % x for x in ['SolverInterfaceC.h', 'Version.h', + 'SolverInterfaceFortran.hpp', 'SolverInterface.hpp']] + + ['lib/libprecice.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' From 6ca24491b1f250167f9c14028a11af8eb0d051f0 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 19 Sep 2023 13:17:01 +0200 Subject: [PATCH 8848/9987] Added missing patch --- .../preCICE-2.5.0_link_with_statics.patch | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/p/preCICE/preCICE-2.5.0_link_with_statics.patch diff --git a/easybuild/easyconfigs/p/preCICE/preCICE-2.5.0_link_with_statics.patch b/easybuild/easyconfigs/p/preCICE/preCICE-2.5.0_link_with_statics.patch new file mode 100644 index 00000000000..01efdbc69fc --- /dev/null +++ b/easybuild/easyconfigs/p/preCICE/preCICE-2.5.0_link_with_statics.patch @@ -0,0 +1,22 @@ +# Adds static SCOTCH library for PETSc component +# +# Author: Jiri Furst +# +--- cmake/modules/FindPETSc.cmake.orig 2023-02-27 15:04:41.282052238 +0100 ++++ cmake/modules/FindPETSc.cmake 2023-02-27 16:10:09.140875043 +0100 +@@ -182,6 +182,15 @@ + endif() + endforeach() + ++ # Add missing static liraries (easybuild specific?) ++ foreach(_next_lib IN LISTS PC_PETSc_STATIC_LIBRARIES) ++ if(_next_lib STREQUAL "ptscotch") ++ list(APPEND _petsc_libs "$ENV{EBROOTSCOTCH}/lib/libptscotch.a") ++ elseif(_next_lib STREQUAL "scotch") ++ list(APPEND _petsc_libs "$ENV{EBROOTSCOTCH}/lib/libscotch.a") ++ endif() ++ endforeach() ++ + # Link against MPI if it is used. + # This adds all required link directories. + foreach(_next_lib IN LISTS PC_PETSc_STATIC_LIBRARIES) From 8a85f3d288c42fef8ac09dacde5b81e292bc30f5 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Tue, 19 Sep 2023 13:05:30 +0000 Subject: [PATCH 8849/9987] Add patch fixing Open MPI 4.1.5 with PMIx >= 4.2.3 I needed this to use any MPI application with srun with pmix or with plain mpirun, or else I would run into OOB/TCP communication errors for even "mpirun hostname" across two nodes (see https://github.com/open-mpi/ompi/issues/11729 for another user with the same problem). This patch is taken from https://github.com/open-mpi/ompi/pull/11472 and with it, both srun and mpirun run flawlessly without further ado. --- .../o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb | 3 + .../o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb | 3 + .../OpenMPI-4.1.5-intel-compilers-2023.1.0.eb | 3 + .../o/OpenMPI/OpenMPI-4.1.5_fix-pmix3x.patch | 581 ++++++++++++++++++ 4 files changed, 590 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5_fix-pmix3x.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb index f54e9e48c72..6279c1af7bd 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.5_fix-pmix3x.patch', ] checksums = [ {'openmpi-4.1.5.tar.bz2': 'a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3'}, @@ -18,6 +19,8 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.5_fix-pmix3x.patch': + '46edac3dbf32f2a611d45e8a3c8edd3ae2f430eec16a1373b510315272115c40'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb index 77905f262fe..ba58f99e8e3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.5_fix-pmix3x.patch', ] checksums = [ {'openmpi-4.1.5.tar.bz2': 'a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3'}, @@ -18,6 +19,8 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.5_fix-pmix3x.patch': + '46edac3dbf32f2a611d45e8a3c8edd3ae2f430eec16a1373b510315272115c40'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb index 7d59c6d092f..4d79ac0d55a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.5_fix-pmix3x.patch', ] checksums = [ {'openmpi-4.1.5.tar.bz2': 'a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3'}, @@ -18,6 +19,8 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.5_fix-pmix3x.patch': + '46edac3dbf32f2a611d45e8a3c8edd3ae2f430eec16a1373b510315272115c40'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5_fix-pmix3x.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5_fix-pmix3x.patch new file mode 100644 index 00000000000..5f209139a3d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5_fix-pmix3x.patch @@ -0,0 +1,581 @@ +From 6e8e14f2c2f207d5fa51299cc67558697a5b7d63 Mon Sep 17 00:00:00 2001 +From: Gilles Gouaillardet +Date: Wed, 8 Mar 2023 10:48:00 +0900 +Subject: [PATCH] pmix3x: use PMIX_VALUE_LOAD() and PMIX_INFO_LOAD() macros + +Refs. open-mpi/ompi#10416 + +bot:notacherrypick + +Signed-off-by: Gilles Gouaillardet +--- + opal/mca/pmix/pmix3x/pmix3x.c | 273 ++++++++++++++++++++++----- + opal/mca/pmix/pmix3x/pmix3x.h | 6 +- + opal/mca/pmix/pmix3x/pmix3x_client.c | 48 ++--- + 3 files changed, 242 insertions(+), 85 deletions(-) + +diff --git a/opal/mca/pmix/pmix3x/pmix3x.c b/opal/mca/pmix/pmix3x/pmix3x.c +index 3b2a5353cc6..c49b6772af5 100644 +--- a/opal/mca/pmix/pmix3x/pmix3x.c ++++ b/opal/mca/pmix/pmix3x/pmix3x.c +@@ -1,7 +1,7 @@ + /* -*- Mode: C; c-basic-offset:4 ; indent-tabs-mode:nil -*- */ + /* + * Copyright (c) 2014-2018 Intel, Inc. All rights reserved. +- * Copyright (c) 2014-2019 Research Organization for Information Science ++ * Copyright (c) 2014-2023 Research Organization for Information Science + * and Technology (RIST). All rights reserved. + * Copyright (c) 2014-2015 Mellanox Technologies, Inc. + * All rights reserved. +@@ -217,8 +217,7 @@ static void return_local_event_hdlr(int status, opal_list_t *results, + PMIX_INFO_CREATE(op->info, op->ninfo); + n=0; + OPAL_LIST_FOREACH(kv, cd->info, opal_value_t) { +- (void)strncpy(op->info[n].key, kv->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&op->info[n].value, kv); ++ pmix3x_info_load(&op->info[n], kv); + ++n; + } + } +@@ -735,7 +734,7 @@ char* pmix3x_convert_jobid(opal_jobid_t jobid) + /**** RHC: NEED TO ADD SUPPORT FOR NEW PMIX DATA TYPES, INCLUDING + **** CONVERSION OF PROC STATES ****/ + +-void pmix3x_value_load(pmix_value_t *v, ++void pmix3x_info_load(pmix_info_t *i, + opal_value_t *kv) + { + opal_pmix3x_jobid_trkr_t *job; +@@ -743,91 +742,264 @@ void pmix3x_value_load(pmix_value_t *v, + opal_list_t *list; + opal_value_t *val; + pmix_info_t *info; ++ pmix_envar_t envar; + size_t n; + + switch(kv->type) { + case OPAL_UNDEF: +- v->type = PMIX_UNDEF; ++ PMIX_INFO_LOAD(i, kv->key, &kv->data, PMIX_UNDEF); + break; + case OPAL_BOOL: +- v->type = PMIX_BOOL; +- memcpy(&(v->data.flag), &kv->data.flag, 1); ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.flag, PMIX_BOOL); + break; + case OPAL_BYTE: +- v->type = PMIX_BYTE; +- memcpy(&(v->data.byte), &kv->data.byte, 1); ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.byte, PMIX_BYTE); + break; + case OPAL_STRING: +- v->type = PMIX_STRING; +- if (NULL != kv->data.string) { +- v->data.string = strdup(kv->data.string); ++ PMIX_INFO_LOAD(i, kv->key, kv->data.string, PMIX_STRING); ++ break; ++ case OPAL_SIZE: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.size, PMIX_SIZE); ++ break; ++ case OPAL_PID: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.pid, PMIX_PID); ++ break; ++ case OPAL_INT: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.integer, PMIX_INT); ++ break; ++ case OPAL_INT8: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.int8, PMIX_INT8); ++ break; ++ case OPAL_INT16: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.int16, PMIX_INT16); ++ break; ++ case OPAL_INT32: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.int32, PMIX_INT32); ++ break; ++ case OPAL_INT64: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.int64, PMIX_INT64); ++ break; ++ case OPAL_UINT: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.uint, PMIX_UINT); ++ break; ++ case OPAL_UINT8: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.uint8, PMIX_UINT8); ++ break; ++ case OPAL_UINT16: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.uint16, PMIX_UINT16); ++ break; ++ case OPAL_UINT32: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.uint32, PMIX_UINT32); ++ break; ++ case OPAL_UINT64: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.uint32, PMIX_UINT64); ++ break; ++ case OPAL_FLOAT: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.fval, PMIX_FLOAT); ++ break; ++ case OPAL_DOUBLE: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.dval, PMIX_DOUBLE); ++ break; ++ case OPAL_TIMEVAL: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.tv, PMIX_TIMEVAL); ++ break; ++ case OPAL_TIME: ++ PMIX_INFO_LOAD(i, kv->key, &kv->data.time, PMIX_TIME); ++ break; ++ case OPAL_STATUS: ++ i->value.type = PMIX_STATUS; ++ i->value.data.status = pmix3x_convert_opalrc(kv->data.status); ++ break; ++ case OPAL_VPID: ++ i->value.type = PMIX_PROC_RANK; ++ i->value.data.rank = pmix3x_convert_opalrank(kv->data.name.vpid); ++ break; ++ case OPAL_NAME: ++ i->value.type = PMIX_PROC; ++ /* have to stringify the jobid */ ++ PMIX_PROC_CREATE(i->value.data.proc, 1); ++ /* see if this job is in our list of known nspaces */ ++ found = false; ++ OPAL_LIST_FOREACH(job, &mca_pmix_pmix3x_component.jobids, opal_pmix3x_jobid_trkr_t) { ++ if (job->jobid == kv->data.name.jobid) { ++ (void)strncpy(i->value.data.proc->nspace, job->nspace, PMIX_MAX_NSLEN); ++ found = true; ++ break; ++ } ++ } ++ if (!found) { ++ (void)opal_snprintf_jobid(i->value.data.proc->nspace, PMIX_MAX_NSLEN, kv->data.name.jobid); ++ } ++ i->value.data.proc->rank = pmix3x_convert_opalrank(kv->data.name.vpid); ++ break; ++ case OPAL_BYTE_OBJECT: ++ i->value.type = PMIX_BYTE_OBJECT; ++ if (NULL != kv->data.bo.bytes) { ++ i->value.data.bo.bytes = (char*)malloc(kv->data.bo.size); ++ memcpy(i->value.data.bo.bytes, kv->data.bo.bytes, kv->data.bo.size); ++ i->value.data.bo.size = (size_t)kv->data.bo.size; ++ } else { ++ i->value.data.bo.bytes = NULL; ++ i->value.data.bo.size = 0; ++ } ++ break; ++ case OPAL_PERSIST: ++ i->value.type = PMIX_PERSIST; ++ i->value.data.persist = pmix3x_convert_opalpersist((opal_pmix_persistence_t)kv->data.uint8); ++ break; ++ case OPAL_SCOPE: ++ i->value.type = PMIX_SCOPE; ++ i->value.data.scope = pmix3x_convert_opalscope((opal_pmix_scope_t)kv->data.uint8); ++ break; ++ case OPAL_DATA_RANGE: ++ i->value.type = PMIX_DATA_RANGE; ++ i->value.data.range = pmix3x_convert_opalrange((opal_pmix_data_range_t)kv->data.uint8); ++ break; ++ case OPAL_PROC_STATE: ++ i->value.type = PMIX_PROC_STATE; ++ /* the OPAL layer doesn't have any concept of proc state, ++ * so the ORTE layer is responsible for converting it */ ++ memcpy(&i->value.data.state, &kv->data.uint8, sizeof(uint8_t)); ++ break; ++ case OPAL_PTR: ++ /* if the opal_value_t is passing a true pointer, then ++ * respect that request and pass it along */ ++ if (0 == strcmp(kv->key, OPAL_PMIX_EVENT_RETURN_OBJECT)) { ++ i->value.type = PMIX_POINTER; ++ i->value.data.ptr = kv->data.ptr; ++ break; ++ } ++ /* otherwise, it must be to a list of ++ * opal_value_t's that we need to convert to a pmix_data_array ++ * of pmix_info_t structures */ ++ list = (opal_list_t*)kv->data.ptr; ++ i->value.type = PMIX_DATA_ARRAY; ++ i->value.data.darray = (pmix_data_array_t*)malloc(sizeof(pmix_data_array_t)); ++ i->value.data.darray->type = PMIX_INFO; ++ i->value.data.darray->size = opal_list_get_size(list); ++ if (0 < i->value.data.darray->size) { ++ PMIX_INFO_CREATE(info, i->value.data.darray->size); ++ i->value.data.darray->array = info; ++ n=0; ++ OPAL_LIST_FOREACH(val, list, opal_value_t) { ++ if (NULL != val->key) { ++ (void)strncpy(info[n].key, val->key, PMIX_MAX_KEYLEN); ++ } ++ pmix3x_value_load(&info[n].value, val); ++ ++n; ++ } + } else { +- v->data.string = NULL; ++ i->value.data.darray->array = NULL; ++ } ++ break; ++ case OPAL_PROC_INFO: ++ i->value.type = PMIX_PROC_INFO; ++ PMIX_PROC_INFO_CREATE(i->value.data.pinfo, 1); ++ /* see if this job is in our list of known nspaces */ ++ found = false; ++ OPAL_LIST_FOREACH(job, &mca_pmix_pmix3x_component.jobids, opal_pmix3x_jobid_trkr_t) { ++ if (job->jobid == kv->data.pinfo.name.jobid) { ++ (void)strncpy(i->value.data.pinfo->proc.nspace, job->nspace, PMIX_MAX_NSLEN); ++ found = true; ++ break; ++ } ++ } ++ if (!found) { ++ (void)opal_snprintf_jobid(i->value.data.pinfo->proc.nspace, PMIX_MAX_NSLEN, kv->data.pinfo.name.jobid); + } ++ i->value.data.pinfo->proc.rank = pmix3x_convert_opalrank(kv->data.pinfo.name.vpid); ++ if (NULL != kv->data.pinfo.hostname) { ++ i->value.data.pinfo->hostname = strdup(kv->data.pinfo.hostname); ++ } ++ if (NULL != kv->data.pinfo.executable_name) { ++ i->value.data.pinfo->executable_name = strdup(kv->data.pinfo.executable_name); ++ } ++ i->value.data.pinfo->pid = kv->data.pinfo.pid; ++ i->value.data.pinfo->exit_code = kv->data.pinfo.exit_code; ++ i->value.data.pinfo->state = pmix3x_convert_opalstate(kv->data.pinfo.state); ++ break; ++ case OPAL_ENVAR: ++ PMIX_ENVAR_CONSTRUCT(&envar); ++ PMIX_ENVAR_LOAD(&envar, kv->data.envar.envar, kv->data.envar.value, kv->data.envar.separator); ++ PMIX_INFO_LOAD(i, kv->key, &envar, PMIX_ENVAR); ++ PMIX_ENVAR_DESTRUCT(&envar); ++ break; ++ default: ++ /* silence warnings */ ++ break; ++ } ++} ++ ++void pmix3x_value_load(pmix_value_t *v, ++ opal_value_t *kv) ++{ ++ opal_pmix3x_jobid_trkr_t *job; ++ bool found; ++ opal_list_t *list; ++ opal_value_t *val; ++ pmix_info_t *info; ++ size_t n; ++ ++ switch(kv->type) { ++ case OPAL_UNDEF: ++ PMIX_VALUE_LOAD(v, NULL, PMIX_UNDEF); ++ break; ++ case OPAL_BOOL: ++ PMIX_VALUE_LOAD(v, &kv->data.flag, PMIX_BOOL); ++ break; ++ case OPAL_BYTE: ++ PMIX_VALUE_LOAD(v, &kv->data.byte, PMIX_BYTE); ++ break; ++ case OPAL_STRING: ++ PMIX_VALUE_LOAD(v, kv->data.string, PMIX_STRING); + break; + case OPAL_SIZE: +- v->type = PMIX_SIZE; +- memcpy(&(v->data.size), &kv->data.size, sizeof(size_t)); ++ PMIX_VALUE_LOAD(v, &kv->data.size, PMIX_SIZE); + break; + case OPAL_PID: +- v->type = PMIX_PID; +- memcpy(&(v->data.pid), &kv->data.pid, sizeof(pid_t)); ++ PMIX_VALUE_LOAD(v, &kv->data.pid, PMIX_PID); + break; + case OPAL_INT: +- v->type = PMIX_INT; +- memcpy(&(v->data.integer), &kv->data.integer, sizeof(int)); ++ PMIX_VALUE_LOAD(v, &kv->data.integer, PMIX_INT); + break; + case OPAL_INT8: +- v->type = PMIX_INT8; +- memcpy(&(v->data.int8), &kv->data.int8, 1); ++ PMIX_VALUE_LOAD(v, &kv->data.int8, PMIX_INT8); + break; + case OPAL_INT16: +- v->type = PMIX_INT16; +- memcpy(&(v->data.int16), &kv->data.int16, 2); ++ PMIX_VALUE_LOAD(v, &kv->data.int16, PMIX_INT16); + break; + case OPAL_INT32: +- v->type = PMIX_INT32; +- memcpy(&(v->data.int32), &kv->data.int32, 4); ++ PMIX_VALUE_LOAD(v, &kv->data.int32, PMIX_INT32); + break; + case OPAL_INT64: +- v->type = PMIX_INT64; +- memcpy(&(v->data.int64), &kv->data.int64, 8); ++ PMIX_VALUE_LOAD(v, &kv->data.int64, PMIX_INT64); + break; + case OPAL_UINT: +- v->type = PMIX_UINT; +- memcpy(&(v->data.uint), &kv->data.uint, sizeof(int)); ++ PMIX_VALUE_LOAD(v, &kv->data.uint, PMIX_UINT); + break; + case OPAL_UINT8: +- v->type = PMIX_UINT8; +- memcpy(&(v->data.uint8), &kv->data.uint8, 1); ++ PMIX_VALUE_LOAD(v, &kv->data.uint8, PMIX_UINT8); + break; + case OPAL_UINT16: +- v->type = PMIX_UINT16; +- memcpy(&(v->data.uint16), &kv->data.uint16, 2); ++ PMIX_VALUE_LOAD(v, &kv->data.uint16, PMIX_UINT16); + break; + case OPAL_UINT32: +- v->type = PMIX_UINT32; +- memcpy(&(v->data.uint32), &kv->data.uint32, 4); ++ PMIX_VALUE_LOAD(v, &kv->data.uint32, PMIX_UINT32); + break; + case OPAL_UINT64: +- v->type = PMIX_UINT64; +- memcpy(&(v->data.uint64), &kv->data.uint64, 8); ++ PMIX_VALUE_LOAD(v, &kv->data.uint64, PMIX_UINT64); + break; + case OPAL_FLOAT: +- v->type = PMIX_FLOAT; +- memcpy(&(v->data.fval), &kv->data.fval, sizeof(float)); ++ PMIX_VALUE_LOAD(v, &kv->data.fval, PMIX_FLOAT); + break; + case OPAL_DOUBLE: +- v->type = PMIX_DOUBLE; +- memcpy(&(v->data.dval), &kv->data.dval, sizeof(double)); ++ PMIX_VALUE_LOAD(v, &kv->data.dval, PMIX_DOUBLE); + break; + case OPAL_TIMEVAL: +- v->type = PMIX_TIMEVAL; +- memcpy(&(v->data.tv), &kv->data.tv, sizeof(struct timeval)); ++ PMIX_VALUE_LOAD(v, &kv->data.tv, PMIX_TIMEVAL); + break; + case OPAL_TIME: +- v->type = PMIX_TIME; +- memcpy(&(v->data.time), &kv->data.time, sizeof(time_t)); ++ PMIX_VALUE_LOAD(v, &kv->data.time, PMIX_TIME); + break; + case OPAL_STATUS: + v->type = PMIX_STATUS; +@@ -1308,8 +1480,7 @@ static void register_handler(opal_list_t *event_codes, + PMIX_INFO_CREATE(op->info, op->ninfo); + n=0; + OPAL_LIST_FOREACH(kv, info, opal_value_t) { +- (void)strncpy(op->info[n].key, kv->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&op->info[n].value, kv); ++ pmix3x_info_load(&op->info[n], kv); + ++n; + } + } +@@ -1428,7 +1599,7 @@ static int notify_event(int status, + op->info[n].value.type = PMIX_STATUS; + op->info[n].value.data.status = pmix3x_convert_opalrc(kv->data.integer); + } else { +- pmix3x_value_load(&op->info[n].value, kv); ++ pmix3x_info_load(&op->info[n], kv); + } + ++n; + } +@@ -1533,8 +1704,7 @@ static void pmix3x_query(opal_list_t *queries, + PMIX_INFO_CREATE(cd->queries[n].qualifiers, cd->queries[n].nqual); + nq = 0; + OPAL_LIST_FOREACH(ival, &q->qualifiers, opal_value_t) { +- (void)strncpy(cd->queries[n].qualifiers[nq].key, ival->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&cd->queries[n].qualifiers[nq].value, ival); ++ pmix3x_info_load(&cd->queries[n].qualifiers[nq], ival); + ++nq; + } + } +@@ -1596,8 +1766,7 @@ static void pmix3x_log(opal_list_t *info, + PMIX_INFO_CREATE(cd->info, cd->ninfo); + n=0; + OPAL_LIST_FOREACH(ival, info, opal_value_t) { +- (void)strncpy(cd->info[n].key, ival->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&cd->info[n].value, ival); ++ pmix3x_info_load(&cd->info[n], ival); + ++n; + } + +diff --git a/opal/mca/pmix/pmix3x/pmix3x.h b/opal/mca/pmix/pmix3x/pmix3x.h +index 94e46bbd461..7048af0cb03 100644 +--- a/opal/mca/pmix/pmix3x/pmix3x.h ++++ b/opal/mca/pmix/pmix3x/pmix3x.h +@@ -3,8 +3,8 @@ + * Copyright (c) 2014-2018 Intel, Inc. All rights reserved. + * Copyright (c) 2014-2015 Mellanox Technologies, Inc. + * All rights reserved. +- * Copyright (c) 2016 Research Organization for Information Science +- * and Technology (RIST). All rights reserved. ++ * Copyright (c) 2016-2023 Research Organization for Information Science ++ * and Technology (RIST). All rights reserved. + * Copyright (c) 2017 Los Alamos National Security, LLC. All rights + * reserved. + * Copyright (c) 2021 IBM Corporation. All rights reserved. +@@ -334,6 +334,8 @@ OPAL_MODULE_DECLSPEC opal_pmix_data_range_t pmix3x_convert_range(pmix_data_range + OPAL_MODULE_DECLSPEC opal_pmix_persistence_t pmix3x_convert_persist(pmix_persistence_t scope); + OPAL_MODULE_DECLSPEC pmix_persistence_t pmix3x_convert_opalpersist(opal_pmix_persistence_t scope); + ++OPAL_MODULE_DECLSPEC void pmix3x_info_load(pmix_info_t *v, ++ opal_value_t *kv); + OPAL_MODULE_DECLSPEC void pmix3x_value_load(pmix_value_t *v, + opal_value_t *kv); + OPAL_MODULE_DECLSPEC int pmix3x_value_unload(opal_value_t *kv, +diff --git a/opal/mca/pmix/pmix3x/pmix3x_client.c b/opal/mca/pmix/pmix3x/pmix3x_client.c +index caf1a409f4a..5d9f0fd28bb 100644 +--- a/opal/mca/pmix/pmix3x/pmix3x_client.c ++++ b/opal/mca/pmix/pmix3x/pmix3x_client.c +@@ -1,8 +1,8 @@ + /* -*- Mode: C; c-basic-offset:4 ; indent-tabs-mode:nil -*- */ + /* + * Copyright (c) 2014-2018 Intel, Inc. All rights reserved. +- * Copyright (c) 2014-2017 Research Organization for Information Science +- * and Technology (RIST). All rights reserved. ++ * Copyright (c) 2014-2023 Research Organization for Information Science ++ * and Technology (RIST). All rights reserved. + * Copyright (c) 2014-2017 Mellanox Technologies, Inc. + * All rights reserved. + * Copyright (c) 2016 Cisco Systems, Inc. All rights reserved. +@@ -93,8 +93,7 @@ int pmix3x_client_init(opal_list_t *ilist) + PMIX_INFO_CREATE(pinfo, ninfo); + n=0; + OPAL_LIST_FOREACH(ival, ilist, opal_value_t) { +- (void)strncpy(pinfo[n].key, ival->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&pinfo[n].value, ival); ++ pmix3x_info_load(&pinfo[n], ival); + ++n; + } + } else { +@@ -222,8 +221,7 @@ int pmix3x_tool_init(opal_list_t *info) + PMIX_INFO_CREATE(pinfo, ninfo); + n=0; + OPAL_LIST_FOREACH(val, info, opal_value_t) { +- (void)strncpy(pinfo[n].key, val->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&pinfo[n].value, val); ++ pmix3x_info_load(&pinfo[n], val); + ++n; + /* check to see if our name is being given from above */ + if (0 == strcmp(val->key, OPAL_PMIX_TOOL_NSPACE)) { +@@ -647,8 +645,7 @@ int pmix3x_get(const opal_process_name_t *proc, const char *key, + PMIX_INFO_CREATE(pinfo, sz); + n=0; + OPAL_LIST_FOREACH(ival, info, opal_value_t) { +- (void)strncpy(pinfo[n].key, ival->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&pinfo[n].value, ival); ++ pmix3x_info_load(&pinfo[n], ival); + ++n; + } + } +@@ -768,8 +765,7 @@ int pmix3x_getnb(const opal_process_name_t *proc, const char *key, + PMIX_INFO_CREATE(op->info, op->sz); + n=0; + OPAL_LIST_FOREACH(val, info, opal_value_t) { +- (void)strncpy(op->info[n].key, val->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&op->info[n].value, val); ++ pmix3x_info_load(&op->info[n], val); + ++n; + } + } +@@ -809,8 +805,7 @@ int pmix3x_publish(opal_list_t *info) + PMIX_INFO_CREATE(pinfo, sz); + n=0; + OPAL_LIST_FOREACH(iptr, info, opal_value_t) { +- (void)strncpy(pinfo[n].key, iptr->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&pinfo[n].value, iptr); ++ pmix3x_info_load(&pinfo[n], iptr); + ++n; + } + } else { +@@ -857,8 +852,7 @@ int pmix3x_publishnb(opal_list_t *info, + PMIX_INFO_CREATE(op->info, op->sz); + n=0; + OPAL_LIST_FOREACH(iptr, info, opal_value_t) { +- (void)strncpy(op->info[n].key, iptr->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&op->info[n].value, iptr); ++ pmix3x_info_load(&op->info[n], iptr); + ++n; + } + } +@@ -903,8 +897,7 @@ int pmix3x_lookup(opal_list_t *data, opal_list_t *info) + PMIX_INFO_CREATE(pinfo, sz); + n=0; + OPAL_LIST_FOREACH(iptr, info, opal_value_t) { +- (void)strncpy(pinfo[n].key, iptr->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&pinfo[n].value, iptr); ++ pmix3x_info_load(&pinfo[n], iptr); + ++n; + } + } +@@ -1052,8 +1045,7 @@ int pmix3x_lookupnb(char **keys, opal_list_t *info, + PMIX_INFO_CREATE(op->info, op->sz); + n=0; + OPAL_LIST_FOREACH(iptr, info, opal_value_t) { +- (void)strncpy(op->info[n].key, iptr->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&op->info[n].value, iptr); ++ pmix3x_info_load(&op->info[n], iptr); + ++n; + } + } +@@ -1080,8 +1072,7 @@ int pmix3x_unpublish(char **keys, opal_list_t *info) + PMIX_INFO_CREATE(pinfo, ninfo); + n=0; + OPAL_LIST_FOREACH(iptr, info, opal_value_t) { +- (void)strncpy(pinfo[n].key, iptr->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&pinfo[n].value, iptr); ++ pmix3x_info_load(&pinfo[n], iptr); + ++n; + } + } else { +@@ -1119,8 +1110,7 @@ int pmix3x_unpublishnb(char **keys, opal_list_t *info, + PMIX_INFO_CREATE(op->info, op->sz); + n=0; + OPAL_LIST_FOREACH(iptr, info, opal_value_t) { +- (void)strncpy(op->info[n].key, iptr->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&op->info[n].value, iptr); ++ pmix3x_info_load(&op->info[n], iptr); + ++n; + } + } +@@ -1154,8 +1144,7 @@ int pmix3x_spawn(opal_list_t *job_info, opal_list_t *apps, opal_jobid_t *jobid) + PMIX_INFO_CREATE(info, ninfo); + n=0; + OPAL_LIST_FOREACH(ival, job_info, opal_value_t) { +- (void)strncpy(info[n].key, ival->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&info[n].value, ival); ++ pmix3x_info_load(&info[n], ival); + ++n; + } + } +@@ -1180,7 +1169,7 @@ int pmix3x_spawn(opal_list_t *job_info, opal_list_t *apps, opal_jobid_t *jobid) + m=0; + OPAL_LIST_FOREACH(ival, &app->info, opal_value_t) { + (void)strncpy(papps[n].info[m].key, ival->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&papps[n].info[m].value, ival); ++ pmix3x_info_load(&papps[n].info[m], ival); + ++m; + } + } +@@ -1270,8 +1259,7 @@ int pmix3x_spawnnb(opal_list_t *job_info, opal_list_t *apps, + PMIX_INFO_CREATE(op->info, op->ninfo); + n=0; + OPAL_LIST_FOREACH(info, job_info, opal_value_t) { +- (void)strncpy(op->info[n].key, info->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&op->info[n].value, info); ++ pmix3x_info_load(&op->info[n], info); + ++n; + } + } +@@ -1292,8 +1280,7 @@ int pmix3x_spawnnb(opal_list_t *job_info, opal_list_t *apps, + PMIX_INFO_CREATE(op->apps[n].info, op->apps[n].ninfo); + m=0; + OPAL_LIST_FOREACH(info, &app->info, opal_value_t) { +- (void)strncpy(op->apps[n].info[m].key, info->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&op->apps[n].info[m].value, info); ++ pmix3x_info_load(&op->apps[n].info[m], info); + ++m; + } + } +@@ -1659,8 +1646,7 @@ abort(); + PMIX_INFO_CREATE(op->info, op->ninfo); + n=0; + OPAL_LIST_FOREACH(iptr, directives, opal_value_t) { +- (void)strncpy(op->info[n].key, iptr->key, PMIX_MAX_KEYLEN); +- pmix3x_value_load(&op->info[n].value, iptr); ++ pmix3x_info_load(&op->info[n], iptr); + ++n; + } + } From 6d9e90dbc1ce32fbdb299096dcbcf820e75f8e14 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 19 Sep 2023 15:13:03 +0200 Subject: [PATCH 8850/9987] fix permission issues when copying xvfb-run script in Xvfb easyconfigs --- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.11-GCCcore-10.3.0.eb | 4 +++- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.13-GCCcore-11.2.0.eb | 4 +++- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb | 4 +++- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb | 4 +++- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb | 4 +++- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb | 4 +++- easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb | 4 +++- easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb | 4 +++- easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.8-GCCcore-12.3.0.eb | 4 +++- 9 files changed, 27 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.11-GCCcore-10.3.0.eb index da8a33a8547..66f838fc14b 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.11-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.11-GCCcore-10.3.0.eb @@ -95,7 +95,9 @@ components = [ }), ] -postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] sanity_check_paths = { 'files': ['bin/Xvfb', 'bin/xvfb-run'], diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.13-GCCcore-11.2.0.eb index 8260693dbd9..0fab63d96b8 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.13-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.13-GCCcore-11.2.0.eb @@ -95,7 +95,9 @@ components = [ }), ] -postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] sanity_check_paths = { 'files': ['bin/Xvfb', 'bin/xvfb-run'], diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb index cecac7a6fb8..1db3dc5e081 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb @@ -100,7 +100,9 @@ components = [ }), ] -postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] sanity_check_paths = { 'files': ['bin/Xvfb', 'bin/xvfb-run'], diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb index 4a228b5fdf7..fc27c8fc593 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb @@ -100,7 +100,9 @@ components = [ }), ] -postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] sanity_check_paths = { 'files': ['bin/Xvfb', 'bin/xvfb-run'], diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb index 5341032753f..43d07a3d4e1 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-10.2.0.eb @@ -95,7 +95,9 @@ components = [ }), ] -postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] sanity_check_paths = { 'files': ['bin/Xvfb', 'bin/xvfb-run'], diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb index 772ef1b22f5..94aa35864b6 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb @@ -95,7 +95,9 @@ components = [ }), ] -postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] sanity_check_paths = { 'files': ['bin/Xvfb', 'bin/xvfb-run'], diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb index 35ddaebf9e8..cd7d049d7e1 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.3-GCCcore-11.3.0.eb @@ -108,7 +108,9 @@ components = [ }), ] -postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] sanity_check_paths = { 'files': ['bin/Xvfb', 'bin/xvfb-run'], diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb index 306d5b638f1..2917a7c8876 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.6-GCCcore-12.2.0.eb @@ -108,7 +108,9 @@ components = [ }), ] -postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] sanity_check_paths = { 'files': ['bin/Xvfb', 'bin/xvfb-run'], diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.8-GCCcore-12.3.0.eb index 5e25aa280fe..5cb7e312a44 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.8-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.8-GCCcore-12.3.0.eb @@ -108,7 +108,9 @@ components = [ }), ] -postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] sanity_check_paths = { 'files': ['bin/Xvfb', 'bin/xvfb-run'], From 62ac57ba816706f713403edc8f89990f7db5d8ca Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 19 Sep 2023 16:12:01 +0100 Subject: [PATCH 8851/9987] adding easyconfigs: FLINT-2.9.0-gfbf-2022b.eb and patches: FLINT-2.9.0-gcc-12.patch --- .../f/FLINT/FLINT-2.9.0-gcc-12.patch | 18 +++++++ .../f/FLINT/FLINT-2.9.0-gfbf-2022b.eb | 48 +++++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gcc-12.patch create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gcc-12.patch b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gcc-12.patch new file mode 100644 index 00000000000..53b39cf316d --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gcc-12.patch @@ -0,0 +1,18 @@ +Patch to run t-sdiv_qrnnd.c test with gcc-12.x compilers +See here: +https://github.com/flintlib/flint2/commit/fb8ddbcc06afa2a8f25637032fbb8211f6c6c122 +https://github.com/flintlib/flint2/issues/1175 +Author: J. Sassmannshausen (University College London/UK) +diff --git a/flint-2.9.0.orig/test/t-sdiv_qrnnd.c b/flint-2.9.0/test/t-sdiv_qrnnd.c +index 2e9822e..e2d65cd 100644 +--- a/flint-2.9.0.orig/test/t-sdiv_qrnnd.c ++++ b/flint-2.9.0/test/t-sdiv_qrnnd.c +@@ -33,7 +33,7 @@ int main(void) + { + d = n_randtest_not_zero(state); + nh = n_randtest(state); +- } while ((FLINT_ABS(nh) >= FLINT_ABS(d)/2) || (nh == WORD_MIN)); ++ } while ((nh == WORD_MIN) || (FLINT_ABS(nh) >= FLINT_ABS(d)/2)); + + nl = n_randtest(state); + diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022b.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022b.eb new file mode 100644 index 00000000000..b07b543281d --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022b.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'FLINT' +version = '2.9.0' + +homepage = 'https://www.flintlib.org/' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.flintlib.org'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-2.8.4_find_flexiblas.patch', + '%(name)s-%(version)s-gcc-12.patch', +] +checksums = [ + {'flint-2.9.0.tar.gz': '2fc090d51033c93208e6c10d406397a53c983ae5343b958eb25f72a57a4ce76a'}, + {'FLINT-2.8.4_find_flexiblas.patch': '35a3db14646daf584449f2b9c6880b66e7b082a665eba56234230610bab77c6e'}, + {'FLINT-2.9.0-gcc-12.patch': 'c253f0353eea129fab70e055b0fdee0d23ec391df03d1689503540c97d5432fb'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Python', '3.10.8'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), + ('NTL', '11.5.1'), +] + +configopts = '-DWITH_NTL=on -DBUILD_TESTING=yes' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'math' From fa2ca2c9639cbf65448485f251c7884c52ba6649 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 19 Sep 2023 16:23:56 +0100 Subject: [PATCH 8852/9987] adding easyconfigs: NTL-11.5.1-GCC-12.2.0.eb --- .../n/NTL/NTL-11.5.1-GCC-12.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-12.2.0.eb b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..e591e4d7c66 --- /dev/null +++ b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-12.2.0.eb @@ -0,0 +1,44 @@ +# contributed by Guilherme Peretti-Pezzi (CSCS) +# updated by Alex Domingo (Vrije Universiteit Brussel) +# updated by Åke Sandgren(Umeå University) + +easyblock = 'ConfigureMake' + +name = 'NTL' +version = '11.5.1' + +homepage = 'https://shoup.net/ntl/' + +description = """NTL is a high-performance, portable C++ library providing data structures and +algorithms for manipulating signed, arbitrary length integers, and for vectors, +matrices, and polynomials over the integers and over finite fields.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'libntl' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ef578fa8b6c0c64edd1183c4c303b534468b58dd3eb8df8c9a5633f984888de5'] + +builddependencies = [ + ('Perl', '5.36.0'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +start_dir = 'src' + +prefix_opt = 'PREFIX=' +configopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" GMP_PREFIX="$EBROOTGMP" SHARED=on' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libntl.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/NTL', 'share/doc'], +} + +moduleclass = 'math' From 8178ab798724fa458c0cf8660066cfc9a748725d Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 19 Sep 2023 16:27:13 +0100 Subject: [PATCH 8853/9987] adding easyconfigs: SVG-2.87-GCC-12.2.0.eb --- .../easyconfigs/s/SVG/SVG-2.87-GCC-12.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-12.2.0.eb new file mode 100644 index 00000000000..70425b6ecb3 --- /dev/null +++ b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PerlModule' + +name = 'SVG' +version = '2.87' + +homepage = 'https://metacpan.org/pod/SVG' +description = "Perl binding for SVG" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b3fa58c1c59942b4ebef003da97c3e01e531480ca29e8efbe327ff0589c0bd3c'] + +dependencies = [ + ('Perl', '5.36.0'), +] + +options = {'modulename': 'SVG'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/SVG.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/SVG'], +} + +moduleclass = 'data' From d170711ff05f2a6b366f12c428f1876d106aacf3 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 19 Sep 2023 17:43:21 +0100 Subject: [PATCH 8854/9987] Some suggested cleanup done, used gfbf toolchain where possible --- easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb | 1 - easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb | 1 - easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb | 1 - easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb | 1 - .../{NBO-7.0.10-GCC-11.3.0.eb => NBO-7.0.10-gfbf-2022a.eb} | 7 +------ .../{NBO-7.0.10-GCC-12.2.0.eb => NBO-7.0.10-gfbf-2022b.eb} | 7 +------ 6 files changed, 2 insertions(+), 16 deletions(-) rename easybuild/easyconfigs/n/NBO/{NBO-7.0.10-GCC-11.3.0.eb => NBO-7.0.10-gfbf-2022a.eb} (94%) rename easybuild/easyconfigs/n/NBO/{NBO-7.0.10-GCC-12.2.0.eb => NBO-7.0.10-gfbf-2022b.eb} (94%) diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb index fc8d53fb045..c09432b5ec2 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb @@ -30,7 +30,6 @@ dependencies = [ local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' -buildopts += 'BLASLIB="$LDFLAGS $LIBBLAS" ' buildopts += 'INT=%s ' % local_intlength parallel = 1 diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb index 42603a8d021..68f7609ed67 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb @@ -25,7 +25,6 @@ checksums = [ dependencies = [ ('FlexiBLAS', '3.0.4'), - ('OpenBLAS', '0.3.17'), ] local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb index 28c77248a81..e118a3065c8 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb @@ -25,7 +25,6 @@ checksums = [ dependencies = [ ('FlexiBLAS', '3.0.4'), - ('OpenBLAS', '0.3.18'), ] local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb index 1107835a69e..955b74ca51a 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb @@ -30,7 +30,6 @@ dependencies = [ local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' -buildopts += 'BLASLIB="$LDFLAGS $LIBBLAS" ' buildopts += 'INT=%s ' % local_intlength parallel = 1 diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.3.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022a.eb similarity index 94% rename from easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.3.0.eb rename to easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022a.eb index 070009055b4..272c510b37d 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022a.eb @@ -9,7 +9,7 @@ homepage = 'http://nbo.chem.wisc.edu/' description = """ The Natural Bond Orbital (NBO) program is a discovery tool for chemical insights from complex wavefunctions. """ -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'gfbf', 'version': '2022a'} toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers # NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx @@ -23,11 +23,6 @@ checksums = [ {'NBO-7.0.10_make.patch': 'c37f5a9980c56198f9610611b0fbda8ad65c961ec19b163d602dc3330fced145'}, ] -dependencies = [ - ('FlexiBLAS', '3.2.0'), - ('OpenBLAS', '0.3.20'), -] - local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-12.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022b.eb similarity index 94% rename from easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-12.2.0.eb rename to easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022b.eb index 4c296b21592..42881e8c9e1 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022b.eb @@ -9,7 +9,7 @@ homepage = 'http://nbo.chem.wisc.edu/' description = """ The Natural Bond Orbital (NBO) program is a discovery tool for chemical insights from complex wavefunctions. """ -toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchain = {'name': 'gfbf', 'version': '2022b'} toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers # NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx @@ -23,11 +23,6 @@ checksums = [ {'NBO-7.0.10_make.patch': 'c37f5a9980c56198f9610611b0fbda8ad65c961ec19b163d602dc3330fced145'}, ] -dependencies = [ - ('FlexiBLAS', '3.2.1'), - ('OpenBLAS', '0.3.21'), -] - local_intlength = 'i8' # change to i4 if Gaussian was compiled with 32-bit integers buildopts = 'FC=$FC CC=$CC NBODIR="%(builddir)s/nbo7" STATIC="false" PROFILE="true" ' From c7631d640bb131c4a9343086515028248738a4e0 Mon Sep 17 00:00:00 2001 From: Pierre Berthier <47532069+pberthier@users.noreply.github.com> Date: Wed, 20 Sep 2023 08:50:44 +0200 Subject: [PATCH 8855/9987] Update easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-12.0.0.177059-cli-tools-only.eb Co-authored-by: SebastianAchilles --- .../s/SMRT-Link/SMRT-Link-12.0.0.177059-cli-tools-only.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-12.0.0.177059-cli-tools-only.eb b/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-12.0.0.177059-cli-tools-only.eb index 0b654c823f3..3169b1073f5 100644 --- a/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-12.0.0.177059-cli-tools-only.eb +++ b/easybuild/easyconfigs/s/SMRT-Link/SMRT-Link-12.0.0.177059-cli-tools-only.eb @@ -17,9 +17,9 @@ description = """PacBio’s open-source SMRT Analysis software suite is designed toolchain = SYSTEM -# The download is a password protected zip file -# Download it from https://www.pacb.com/support/software-downloads/ and uncompress -# the .run file to your sources folder +download_instructions = """The download is a password protected zip file +Download it from https://www.pacb.com/support/software-downloads/ and uncompress +the .run file to your sources folder""" sources = ['smrtlink_%(version)s.run'] checksums = ['95dadf8c5435d55724e43a290144322c32c9c9cf8b4f1e54c1a7a6f3ec368fbe'] From bdf6a3b8b678a78de91b61c3a10cdae3cc32a8ab Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 20 Sep 2023 12:13:28 +0100 Subject: [PATCH 8856/9987] adding easyconfigs: MATLAB-2023b.eb --- .../easyconfigs/m/MATLAB/MATLAB-2023b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2023b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2023b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2023b.eb new file mode 100644 index 00000000000..f0bb088e901 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2023b.eb @@ -0,0 +1,27 @@ +name = 'MATLAB' +version = '2023b' + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +sources = ['R%s_Linux.iso' % (version)] +checksums = ['f1cc4ae1a2e42a1d22745884aa80bf0d5d8676939ad21741ccff15fade06a881'] +download_instructions = 'Download %s from mathworks.com' % sources[0] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server_port = 'XXXXX' + +moduleclass = 'math' From 2fdddbc24b1a5fc12e5b6e179811f0eadd4f7206 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 20 Sep 2023 14:11:25 +0200 Subject: [PATCH 8857/9987] adding easyconfigs: code-server-4.16.1.eb --- .../c/code-server/code-server-4.16.1.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/code-server/code-server-4.16.1.eb diff --git a/easybuild/easyconfigs/c/code-server/code-server-4.16.1.eb b/easybuild/easyconfigs/c/code-server/code-server-4.16.1.eb new file mode 100644 index 00000000000..6f0b3e039d9 --- /dev/null +++ b/easybuild/easyconfigs/c/code-server/code-server-4.16.1.eb @@ -0,0 +1,20 @@ +name = 'code-server' +version = '4.16.1' + +homepage = 'https://github.com/cdr/code-server' +description = """Run VS Code on any machine anywhere and access it in the browser.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cdr/code-server/releases/download/v%(version)s/'] +sources = ['code-server-%(version)s-linux-%(mapped_arch)s.tar.gz'] +checksums = [ + { + 'code-server-%(version)s-linux-amd64.tar.gz': + 'e10bc642be9fe8a802f556737b1bbb910ef818979a35034b092c85e62a42d1a7', + 'code-server-%(version)s-linux-arm64.tar.gz': + 'a256429887531d855baaa6b14b25906f69fa4b4a977b1ae0def001016fb37b81', + } +] + +moduleclass = 'tools' From c8ccdc95697d08186ce3a76f9936c17dec71dedb Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 20 Sep 2023 16:03:35 +0200 Subject: [PATCH 8858/9987] Cleaning up unnecessary files --- .../Kent_tools-422-GCC-11.2.0-Boost-1.75.0.eb | 43 ----------- .../MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb | 71 ------------------- .../TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb | 44 ------------ 3 files changed, 158 deletions(-) delete mode 100644 easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0-Boost-1.75.0.eb delete mode 100644 easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb delete mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0-Boost-1.75.0.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0-Boost-1.75.0.eb deleted file mode 100644 index a9c286bf600..00000000000 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-422-GCC-11.2.0-Boost-1.75.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -easyblock = 'MakeCp' - -name = 'Kent_tools' -version = '422' -versionsuffix = "-Boost-1.75.0" - -homepage = 'https://genome.cse.ucsc.edu/' -description = """Kent utilities: collection of tools used by the UCSC genome browser.""" - -toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = [ - 'https://hgdownload.cse.ucsc.edu/admin/exe/', - 'https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/', -] -sources = ['userApps.v%(version)s.src.tgz'] -patches = ['%(name)s-%(version)s-openssl.patch'] -checksums = [ - '1edf66ad5f7c8c79586e9f878b5971d7d467c8c5efbeb31c69085d24a6e4671f', # userApps.v422.src.tgz - 'eedd328fc8a8e01806f4de9e8dce5b2a149edf493a17c3758803853e7881f240', # Kent_tools-422-openssl.patch -] - -dependencies = [ - ('MariaDB', '10.6.4', "-Boost-1.75.0"), - ('libpng', '1.6.37'), - ('zlib', '1.2.11'), - ('util-linux', '2.37'), - ('OpenSSL', '1.1', '', True), - ('freetype', '2.11.0'), -] - -buildopts = 'CC="$CC" COPT="$CFLAGS -fcommon" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' -buildopts += 'SSL_DIR="$EBROOTOPENSSL" SSLDIR="$EBROOTOPENSSL" MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' - -local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] - -files_to_copy = [(['bin/*'], 'bin'), 'licenseBlat.txt', 'licenseUcscGenomeBrowser.txt'] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in local_binaries], - 'dirs': [], -} - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb deleted file mode 100644 index 4ca72f2b9cb..00000000000 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.6.4-GCC-11.2.0-Boost-1.75.0.eb +++ /dev/null @@ -1,71 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'MariaDB' -version = '10.6.4' -versionsuffix = "-Boost-1.75.0" - -homepage = 'https://mariadb.org/' -description = """MariaDB is an enhanced, drop-in replacement for MySQL. -Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" - -toolchain = {'name': 'GCC', 'version': '11.2.0'} - -local_pcre2_ver = '10.37' -source_urls = [ - 'https://archive.mariadb.org/mariadb-%(version)s/source/', - 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', - 'https://downloads.sourceforge.net/project/pcre/pcre2/%s/' % local_pcre2_ver, -] -sources = [ - SOURCELOWER_TAR_GZ, - {'filename': 'pcre2-%s.zip' % local_pcre2_ver, 'extract_cmd': "cp %s %(builddir)s/"}, -] -patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] - -builddependencies = [ - ('CMake', '3.21.1'), - ('libaio', '0.3.112'), - ('Boost', '1.75.0'), # needed by OQGraph -] - -dependencies = [ - ('ncurses', '6.2'), - ('zlib', '1.2.11'), - ('LZO', '2.10'), # optional - ('lz4', '1.9.3'), # optional - ('XZ', '5.2.5'), # optional - ('jemalloc', '5.2.1'), # optional - ('snappy', '1.1.9'), # needed by RocksDB; optional for InnoDB - ('libxml2', '2.9.10'), # needed by Connect XML - ('Judy', '1.0.5'), # needed by OQGraph - ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest -] - -local_pcre2_path = '%%(builddir)s/pcre2-%s.zip' % local_pcre2_ver -preconfigopts = "sed -i 's@http://.*.zip@file://%s@g' ../mariadb-%%(version)s/cmake/pcre.cmake && " % local_pcre2_path - -configopts = "-DCMAKE_BUILD_TYPE=Release " -configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker -configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) -configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. -configopts += "-DWITH_ZLIB=system " -configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co -configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc -configopts += "-DBoost_USE_STATIC_LIBS=ON" - -sanity_check_commands = ["mysql --help", "mysqltest --help"] - -sanity_check_paths = { - 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, - 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, - 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], - 'dirs': ['include', 'share'], -} - -modextrapaths = {'PATH': 'scripts'} - -# Ensure that jemalloc does not use transparent hugepages. -# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. -modextravars = {'MALLOC_CONF': 'thp:never'} - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb deleted file mode 100644 index 14084b9267a..00000000000 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.0-gompi-2021b-Python-2.7.18.eb +++ /dev/null @@ -1,44 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# Modified by: Adam Huffman -# The Francis Crick Institute - -easyblock = 'ConfigureMake' - -name = 'TopHat' -version = '2.1.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'http://ccb.jhu.edu/software/%(namelower)s/' -description = "TopHat is a fast splice junction mapper for RNA-Seq reads." - -toolchain = {'name': 'gompi', 'version': '2021b'} -toolchainopts = {'cstd': 'gnu++98', 'pic': True} - -source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] -checksums = ['e7fa2b170408e785e4fafd0bccf4ecfab5151c480a2438dffa42183cfda71f99'] - -builddependencies = [('Autoconf', '2.71')] - -dependencies = [ - ('Python', '2.7.18'), - ('SAMtools', '1.14'), - ('Boost', '1.75.0'), - ('zlib', '1.2.11'), -] - -local_include_dir = '%(builddir)s/%(namelower)s-%(version)s/src' -preconfigopts = 'sed -i "s|bam/sam.h|htslib/sam.h|g" %s/*.h &&' % local_include_dir -configopts = '--with-boost=$EBROOTBOOST --with-bam=$EBROOTSAMTOOLS' - -parallel = 1 - -sanity_check_paths = { - 'files': ['bin/%(namelower)s'], - 'dirs': [], -} - -moduleclass = 'bio' From 708a2a2fa76c811d32859dd77d64a045c068cc1b Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 20 Sep 2023 16:09:15 +0200 Subject: [PATCH 8859/9987] Made Boost get statically linked --- .../c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb index 403c88a5dca..830ffa427e0 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb @@ -19,10 +19,15 @@ builddependencies = [ ('Eigen', '3.3.9'), ('Autotools', '20210726'), ('SAMtools', '1.14'), + ('Boost', '1.75.0'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), + ('cURL', '7.78.0'), + ('OpenSSL', '1.1', '', SYSTEM), + ('zstd', '1.5.0'), ] dependencies = [ - ('Boost', '1.75.0'), ('zlib', '1.2.11'), ('HTSlib', '1.14'), ] @@ -30,6 +35,11 @@ dependencies = [ preconfigopts = 'autoreconf -i && export LIBS="${LIBS} -lhts" && export CFLAGS="$CFLAGS -fcommon" && ' configopts = '--with-boost=${EBROOTBOOST} --with-bam=${EBROOTSAMTOOLS}' +buildopts = "BOOST_FILESYSTEM_LIB=$EBROOTBOOST/lib/libboost_filesystem.a " +buildopts += "BOOST_SERIALIZATION_LIB=$EBROOTBOOST/lib/libboost_serialization.a " +buildopts += "BOOST_SYSTEM_LIB=$EBROOTBOOST/lib/libboost_system.a " +buildopts += "BOOST_THREAD_LIB=$EBROOTBOOST/lib/libboost_thread.a " + sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': [] From 04671e5954481bc695d2b0f91328fde25899853c Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 20 Sep 2023 15:10:13 +0100 Subject: [PATCH 8860/9987] Installa instructions added, test report uploaded --- easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb | 6 ++++-- easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb | 6 ++++-- easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb | 6 ++++-- easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb | 6 ++++-- easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022a.eb | 6 ++++-- easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022b.eb | 6 ++++-- 6 files changed, 24 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb index c09432b5ec2..2ae4e5ed5c5 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.2.0.eb @@ -12,8 +12,10 @@ for chemical insights from complex wavefunctions. """ toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers -# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx -# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +download_instructions = """ +NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +""" sources = ['nbo%(version)s-src.tar.gz'] patches = [ 'NBO-%(version)s_make.patch', diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb index 68f7609ed67..94281fe00eb 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-10.3.0.eb @@ -12,8 +12,10 @@ for chemical insights from complex wavefunctions. """ toolchain = {'name': 'GCC', 'version': '10.3.0'} toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers -# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx -# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +download_instructions = """ +NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +""" sources = ['nbo%(version)s-src.tar.gz'] patches = [ 'NBO-%(version)s_make.patch', diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb index e118a3065c8..1a8a9c87595 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-11.2.0.eb @@ -12,8 +12,10 @@ for chemical insights from complex wavefunctions. """ toolchain = {'name': 'GCC', 'version': '11.2.0'} toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers -# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx -# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +download_instructions = """ +NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +""" sources = ['nbo%(version)s-src.tar.gz'] patches = [ 'NBO-%(version)s_make.patch', diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb index 955b74ca51a..1b9519bbbdd 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-GCC-9.3.0.eb @@ -12,8 +12,10 @@ for chemical insights from complex wavefunctions. """ toolchain = {'name': 'GCC', 'version': '9.3.0'} toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers -# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx -# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +download_instructions = """ +NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +""" sources = ['nbo%(version)s-src.tar.gz'] patches = [ 'NBO-%(version)s_make.patch', diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022a.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022a.eb index 272c510b37d..10617ff3078 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022a.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022a.eb @@ -12,8 +12,10 @@ for chemical insights from complex wavefunctions. """ toolchain = {'name': 'gfbf', 'version': '2022a'} toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers -# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx -# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +download_instructions = """ +NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +""" sources = ['nbo%(version)s-src.tar.gz'] patches = [ 'NBO-%(version)s_make.patch', diff --git a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022b.eb b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022b.eb index 42881e8c9e1..0f47637675f 100644 --- a/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022b.eb +++ b/easybuild/easyconfigs/n/NBO/NBO-7.0.10-gfbf-2022b.eb @@ -12,8 +12,10 @@ for chemical insights from complex wavefunctions. """ toolchain = {'name': 'gfbf', 'version': '2022b'} toolchainopts = {'pic': True, 'i8': True} # remove 'i8' if Gaussian was compiled with 32-bit integers -# NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx -# The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +download_instructions = """ +NBO7 is proprietary software, order here: https://charge.wisc.edu/chemistry/order_nbo7.aspx +The dowloaded tarball does not contain the bug-fix version so rename to nbo7.0.10-src.tar.gz +""" sources = ['nbo%(version)s-src.tar.gz'] patches = [ 'NBO-%(version)s_make.patch', From a04db182e908343e71afbe7dc312cf9d1da24af2 Mon Sep 17 00:00:00 2001 From: xina Date: Wed, 20 Sep 2023 16:28:49 +0200 Subject: [PATCH 8861/9987] adding easyconfigs: DIRAC-23.0-foss-2023a.eb --- .../d/DIRAC/DIRAC-23.0-foss-2023a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2023a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2023a.eb new file mode 100644 index 00000000000..b2e2220079f --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '23.0' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://zenodo.org/record/7670749/files/'] +sources = ['DIRAC-%(version)s-Source.tgz'] +checksums = ['a0a6b6318b3cd2e3c6042221de720bb1e87eb758999e2108a48dedb9c564e1f8'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('HDF5', '1.14.0'), + ('SciPy-bundle', '2023.07'), + ('h5py', '3.9.0') +] + +configopts = '-DMKL_FLAG=off ' +configopts += '-DMATH_LIBS="$LIBLAPACK" ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' + +runtest = 'test ARGS="-R pam_test" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From 01caa165a9a73666894471f329eb196beb622f7f Mon Sep 17 00:00:00 2001 From: xina Date: Wed, 20 Sep 2023 17:17:23 +0200 Subject: [PATCH 8862/9987] adding easyconfigs: DIRAC-23.0-intel-2023a.eb --- .../d/DIRAC/DIRAC-23.0-intel-2023a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2023a.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2023a.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2023a.eb new file mode 100644 index 00000000000..5366c453837 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '23.0' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'usempi': True, 'oneapi': False} + +source_urls = ['https://zenodo.org/record/7670749/files/'] +sources = ['DIRAC-%(version)s-Source.tgz'] +checksums = ['a0a6b6318b3cd2e3c6042221de720bb1e87eb758999e2108a48dedb9c564e1f8'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('HDF5', '1.14.0') +] + +configopts = '-DMKL_FLAG=sequential ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' + +runtest = 'test ARGS="-R pam_test" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From 505d22ef8703ed4e1301f68fc5e51b2f607c62b1 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 20 Sep 2023 15:19:47 +0000 Subject: [PATCH 8863/9987] adding easyconfigs: RDFlib-7.0.0-GCCcore-12.3.0.eb --- .../r/RDFlib/RDFlib-7.0.0-GCCcore-12.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..340bf45219e --- /dev/null +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-7.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'RDFlib' +version = '7.0.0' + +homepage = 'https://github.com/RDFLib/rdflib' +description = """RDFLib is a Python library for working with RDF, a simple yet powerful language + for representing information.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40'), + ('poetry', '1.5.1'), + ] + +dependencies = [('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06')] + +use_pip = True + +exts_list = [ + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', version, { + 'checksums': ['9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 7b08244a409729ec77318503b19e9ba16fad2f41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2023 17:20:53 +0200 Subject: [PATCH 8864/9987] add missing required PyPy dependency for Clair3, also copy preprocess and shared subdirectories, and enhance sanity check for provided libclair3 Python package --- .../c/Clair3/Clair3-1.0.4-foss-2022a.eb | 10 +++-- .../c/Clair3/Clair3-remove_htslib.patch | 26 ++++++++----- .../easyconfigs/p/PyPy/PyPy-7.3.12-3.10.eb | 37 +++++++++++++++++++ 3 files changed, 61 insertions(+), 12 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyPy/PyPy-7.3.12-3.10.eb diff --git a/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb b/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb index 3fe222a50e8..caf0349270a 100644 --- a/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Clair3/Clair3-1.0.4-foss-2022a.eb @@ -19,7 +19,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['Clair3-remove_htslib.patch'] checksums = [ {'v1.0.4.tar.gz': '56cc4cf43f1cc652958cc1aea95d87d0811531a924ca5c68dd564d41834654c0'}, - {'Clair3-remove_htslib.patch': '0e1f5f17dc56850766fa19c6b0cca4ea23b3ed50b47126a41549c75e76d2cda7'}, + {'Clair3-remove_htslib.patch': 'f77c80755c848ec90f72efbba7b61e3cbc80421d216344e06f6b94e114887285'}, ] dependencies = [ @@ -39,21 +39,25 @@ dependencies = [ ('zstd', '1.5.2'), ('HTSlib', '1.15.1'), ('libdeflate', '1.10'), + ('PyPy', '7.3.12', '-3.10', SYSTEM), ] files_to_copy = [ - (['clair3', 'clair3.py', 'longphase', 'run_clair3.sh', 'scripts'], 'bin'), + (['clair3', 'clair3.py', 'longphase', 'preprocess', 'run_clair3.sh', 'scripts', 'shared'], 'bin'), (['libclair3.*'], 'lib'), ] sanity_check_paths = { 'files': ['bin/run_clair3.sh', 'bin/clair3.py', 'bin/longphase', 'lib/libclair3.%s' % SHLIB_EXT], - 'dirs': ['bin/clair3', 'bin/scripts'], + 'dirs': ['bin/clair3', 'bin/preprocess', 'bin/scripts', 'bin/shared'], } sanity_check_commands = [ "longphase --help", "run_clair3.sh --help", + "python -c 'import libclair3'", ] +modextrapaths = {'PYTHONPATH': 'lib'} + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Clair3/Clair3-remove_htslib.patch b/easybuild/easyconfigs/c/Clair3/Clair3-remove_htslib.patch index 1cb58832159..c39f98ec30b 100644 --- a/easybuild/easyconfigs/c/Clair3/Clair3-remove_htslib.patch +++ b/easybuild/easyconfigs/c/Clair3/Clair3-remove_htslib.patch @@ -1,17 +1,25 @@ Remove building of dependencies we provide via easybuild -Author: Denis Kristak (Inuits) -diff -ruN Clair3-1.0.4_orig/build.py Clair3-1.0.4/build.py ---- Clair3-1.0.4_orig/build.py 2023-09-07 14:28:29.842168186 +0100 -+++ Clair3-1.0.4/build.py 2023-09-08 12:31:06.300472155 +0100 -@@ -52,8 +52,7 @@ - 'clair3_pileup.c', +Author: Denis Kristak (Inuits), Kenneth Hoste (HPC-UGent) +diff -ruN Clair3-1.0.4.orig/build.py Clair3-1.0.4/build.py +--- Clair3-1.0.4.orig/build.py 2023-07-16 14:39:15.000000000 +0200 ++++ Clair3-1.0.4/build.py 2023-09-20 16:57:43.713924133 +0200 +@@ -6,7 +6,7 @@ + + samver = "1.15.1" + file_directory = os.path.dirname(os.path.realpath(__file__)) +-htslib_dir = os.path.join(file_directory, 'samtools-{}'.format(samver), 'htslib-{}'.format(samver)) ++htslib_dir = os.path.join(os.getenv('EBROOTHTSLIB'), 'lib') + + libraries = ['m', 'z', 'lzma', 'bz2', 'pthread', 'curl', 'crypto'] + extra_link_args = [] +@@ -53,7 +53,7 @@ 'clair3_full_alignment.c')], extra_compile_args=extra_compile_args, -- extra_link_args=extra_link_args, + extra_link_args=extra_link_args, - extra_objects=[os.path.join(htslib_dir, 'libhts.a')] -+ extra_link_args=extra_link_args ++ extra_objects=[os.path.join(htslib_dir, 'libhts.so')] ) - + cdef = [ diff -ruN Clair3-1.0.4_orig/Makefile Clair3-1.0.4/Makefile --- Clair3-1.0.4_orig/Makefile 2023-09-07 14:28:29.842168186 +0100 diff --git a/easybuild/easyconfigs/p/PyPy/PyPy-7.3.12-3.10.eb b/easybuild/easyconfigs/p/PyPy/PyPy-7.3.12-3.10.eb new file mode 100644 index 00000000000..68a7d7a9713 --- /dev/null +++ b/easybuild/easyconfigs/p/PyPy/PyPy-7.3.12-3.10.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'PyPy' +version = '7.3.12' +_pyver = '3.10' +versionsuffix = '-%s' % _pyver + +homepage = 'https://www.pypy.org' +description = "A fast, compliant alternative implementation of Python" + +toolchain = SYSTEM + +source_urls = ['https://downloads.python.org/pypy/'] +local_archs = {'aarch64': 'aarch64', 'x86_64': 'linux64'} +sources = ['pypy%s-v%%(version)s-%s.tar.bz2' % (_pyver, local_archs[ARCH])] +checksums = [{ + 'pypy%s-v%%(version)s-aarch64.tar.bz2' % _pyver: '26208b5a134d9860a08f74cce60960005758e82dc5f0e3566a48ed863a1f16a1', + 'pypy%s-v%%(version)s-linux64.tar.bz2' % _pyver: '6c577993160b6f5ee8cab73cd1a807affcefafe2f7441c87bd926c10505e8731', +} +] + +postinstallcmds = [ + # remove python* commands provided by PyPy, so they don't shadow actual python commands + # (system Python, or provided by a Python dependency) + "rm %(installdir)s/bin/python*", +] + +sanity_check_paths = { + 'files': ['bin/pypy', 'bin/pypy3'], + 'dirs': ['include/pypy%s' % _pyver, 'lib/pypy%s' % _pyver], +} + +sanity_check_commands = [ + "pypy --help", +] + +moduleclass = 'lang' From 83621a61d52270aea1c5b40513a58eeb3384b052 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 20 Sep 2023 18:08:51 +0200 Subject: [PATCH 8865/9987] adding easyconfigs: XBeach-20230831-gompi-2022a.eb and patches: XBeach_fix-gfortran-compilation.patch --- .../x/XBeach/XBeach-20230831-gompi-2022a.eb | 50 +++++++++++++++++++ .../XBeach_fix-gfortran-compilation.patch | 17 +++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/x/XBeach/XBeach_fix-gfortran-compilation.patch diff --git a/easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb b/easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb new file mode 100644 index 00000000000..af7c0552f6b --- /dev/null +++ b/easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'XBeach' +# revision 6044 +version = '20230831' + +homepage = 'https://oss.deltares.nl/web/xbeach' +description = """ +XBeach is a two-dimensional model for wave propagation, long waves and mean flow, sediment +transport and morphological changes of the nearshore area, beaches, dunes and backbarrier +during storms. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +# There is no tarball provided, only SVN checkout through: +# svn checkout https://svn.oss.deltares.nl/repos/xbeach/trunk@6044 +# make tarball: tar -czvf XBeach-20230831.tgz trunk +# (tarball should be in the same directory as the easyconfig) + +sources = [SOURCE_TGZ] +patches = ['XBeach_fix-gfortran-compilation.patch'] +checksums = [ + {'XBeach-20230831.tgz': 'c777504b4e39e1a03bcab77efaa19aea4048981bae68a390a946ee8594dc7c85'}, + {'XBeach_fix-gfortran-compilation.patch': 'bfc567bfa9eeb23196fa07c75646acb1623acf82b9a4e2d9251be2dc37e14b99'}, +] + +prebuildopts = 'make clean && ' + +dependencies = [ + ('Mako', '1.2.0'), + ('netCDF-Fortran', '4.6.0'), +] + +parallel = 1 + +configopts = '--with-netcdf' +preconfigopts = './autogen.sh && ' +preconfigopts += 'export PKG_CONFIG_PATH="${PKG_CONFIG_PATH}:${EBROOTNETCDFMINFORTRAN}/lib/pkgconfig" && ' + +sanity_check_paths = { + 'files': ['bin/xbeach', 'lib/libxbeach.a', 'lib/libxbeach.la', 'lib/libxbeach.%s' % SHLIB_EXT], + 'dirs': [] +} +sanity_check_commands = [ + 'xbeach -V |grep "You are using XBeach" 2>/dev/null', +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/x/XBeach/XBeach_fix-gfortran-compilation.patch b/easybuild/easyconfigs/x/XBeach/XBeach_fix-gfortran-compilation.patch new file mode 100644 index 00000000000..2ed28e28d04 --- /dev/null +++ b/easybuild/easyconfigs/x/XBeach/XBeach_fix-gfortran-compilation.patch @@ -0,0 +1,17 @@ +--- trunk.orig/src/xbeachlibrary/mnemoniciso.F90 2023-09-18 11:46:34.153048000 +0200 ++++ trunk/src/xbeachlibrary/mnemoniciso.F90 2023-09-18 11:46:41.583851000 +0200 +@@ -10,10 +10,10 @@ + character(kind=c_char) type ! 'i' or 'r': integer or real*8 + character(kind=c_char) btype ! 'b' or 'd': + integer(c_int) rank ! 0,1,2,3,4 +- character(kind=c_char, len=maxnamelen) :: name ! 'v','ve', ..... +- character(kind=c_char, len=20) :: units ! m, following udunits convention +- character(kind=c_char, len=1024) :: description +- character(kind=c_char, len=20), dimension(maxrank) :: dimensions ! the dimensions of the variable, for example (s%nx, s%ny) ++ character(kind=c_char) :: name(maxnamelen) ! 'v','ve', ..... ++ character(kind=c_char) :: units(20) ! m, following udunits convention ++ character(kind=c_char) :: description(1024) ++ character(kind=c_char), dimension(maxrank) :: dimensions(20) + + type (c_ptr) :: array + From 909be907a25b01705b0e2bae84637150ec57c92e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2023 18:44:32 +0200 Subject: [PATCH 8866/9987] don't use XZ/bzip2/cURL/OpenSSL/zstd as build dependencies for Cufflinks, since they're (indirectly) runtime dependencies already --- .../easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb index 830ffa427e0..3e8c1311188 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb @@ -20,11 +20,6 @@ builddependencies = [ ('Autotools', '20210726'), ('SAMtools', '1.14'), ('Boost', '1.75.0'), - ('XZ', '5.2.5'), - ('bzip2', '1.0.8'), - ('cURL', '7.78.0'), - ('OpenSSL', '1.1', '', SYSTEM), - ('zstd', '1.5.0'), ] dependencies = [ From 2a999cf46a05455119f49a47908b1441063759e6 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 20 Sep 2023 18:45:24 +0200 Subject: [PATCH 8867/9987] add description to patch and add version to patch name --- .../x/XBeach/XBeach-20230831-gompi-2022a.eb | 5 +++-- ...ch-20230831_fix-gfortran-compilation.patch | 19 +++++++++++++++++++ 2 files changed, 22 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/x/XBeach/XBeach-20230831_fix-gfortran-compilation.patch diff --git a/easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb b/easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb index af7c0552f6b..68f7c559829 100644 --- a/easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb +++ b/easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb @@ -20,10 +20,11 @@ toolchainopts = {'usempi': True} # (tarball should be in the same directory as the easyconfig) sources = [SOURCE_TGZ] -patches = ['XBeach_fix-gfortran-compilation.patch'] +patches = ['XBeach-20230831_fix-gfortran-compilation.patch'] checksums = [ {'XBeach-20230831.tgz': 'c777504b4e39e1a03bcab77efaa19aea4048981bae68a390a946ee8594dc7c85'}, - {'XBeach_fix-gfortran-compilation.patch': 'bfc567bfa9eeb23196fa07c75646acb1623acf82b9a4e2d9251be2dc37e14b99'}, + {'XBeach-20230831_fix-gfortran-compilation.patch': + '9aa8a3593ea641a16a6d09bb75cc9935de383b5934f4a2718eeb94382386f0c4'}, ] prebuildopts = 'make clean && ' diff --git a/easybuild/easyconfigs/x/XBeach/XBeach-20230831_fix-gfortran-compilation.patch b/easybuild/easyconfigs/x/XBeach/XBeach-20230831_fix-gfortran-compilation.patch new file mode 100644 index 00000000000..cf14a126030 --- /dev/null +++ b/easybuild/easyconfigs/x/XBeach/XBeach-20230831_fix-gfortran-compilation.patch @@ -0,0 +1,19 @@ +Fix compilation with gfortran, see https://github.com/openearth/xbeach/issues/2 +author: Cintia Willemyns (HPC-VUB) +--- trunk.orig/src/xbeachlibrary/mnemoniciso.F90 2023-09-18 11:46:34.153048000 +0200 ++++ trunk/src/xbeachlibrary/mnemoniciso.F90 2023-09-18 11:46:41.583851000 +0200 +@@ -10,10 +10,10 @@ + character(kind=c_char) type ! 'i' or 'r': integer or real*8 + character(kind=c_char) btype ! 'b' or 'd': + integer(c_int) rank ! 0,1,2,3,4 +- character(kind=c_char, len=maxnamelen) :: name ! 'v','ve', ..... +- character(kind=c_char, len=20) :: units ! m, following udunits convention +- character(kind=c_char, len=1024) :: description +- character(kind=c_char, len=20), dimension(maxrank) :: dimensions ! the dimensions of the variable, for example (s%nx, s%ny) ++ character(kind=c_char) :: name(maxnamelen) ! 'v','ve', ..... ++ character(kind=c_char) :: units(20) ! m, following udunits convention ++ character(kind=c_char) :: description(1024) ++ character(kind=c_char), dimension(maxrank) :: dimensions(20) + + type (c_ptr) :: array + From eb988fdb903c8fe8fb7fa9b5b732885e2166647a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 20 Sep 2023 19:00:29 +0200 Subject: [PATCH 8868/9987] add sanity check command for Cufflinks --- .../easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb index 3e8c1311188..98ab2c0bfa1 100644 --- a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-20190706-GCC-11.2.0.eb @@ -36,8 +36,10 @@ buildopts += "BOOST_SYSTEM_LIB=$EBROOTBOOST/lib/libboost_system.a " buildopts += "BOOST_THREAD_LIB=$EBROOTBOOST/lib/libboost_thread.a " sanity_check_paths = { - 'files': ['bin/%(namelower)s'], + 'files': ['bin/cufflinks'], 'dirs': [] } +sanity_check_commands = ["cufflinks 2>&1 | grep 'Usage:.* cufflinks'"] + moduleclass = 'bio' From 24b0be4f4a574dbdb4f66ea40ff89ff124a08af4 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 20 Sep 2023 22:44:37 +0200 Subject: [PATCH 8869/9987] Add description to magma-2.7.2_allow-all-sms.patch --- .../easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch b/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch index 2adb8d87ffb..5b78a3f229e 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2_allow-all-sms.patch @@ -1,3 +1,11 @@ +This allows to process any sm_xx passed to GPU_TARGET. Previously some were silently ignored +See https://bitbucket.org/icl/magma/issues/32/list-of-whitelisted-sm_-values-for-cuda-is +and https://bitbucket.org/icl/magma/pull-requests/5 + +Author: Alexander Grund (TU Dresden) +Updated to 2.6.1: micketeer@gmail.com +Updated to 2.7.2: Alexandre Strube (JSC) + --- CMakeLists.txt.orig 2023-09-15 09:54:41.000000000 +0000 +++ CMakeLists.txt 2023-09-15 10:01:07.000000000 +0000 @@ -140,161 +140,14 @@ From 1364b19a985b11a919f19c98bf005647585213b3 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 20 Sep 2023 22:48:03 +0200 Subject: [PATCH 8870/9987] Update checksum in magma-2.7.2-foss-2023a-CUDA-12.1.1.eb --- .../easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb index a6de0adabfc..19a155367dd 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb @@ -16,7 +16,7 @@ sources = [SOURCE_TAR_GZ] patches = ['%(name)s-2.7.2_allow-all-sms.patch'] checksums = [ {'magma-2.7.2.tar.gz': '729bc1a70e518a7422fe7a3a54537a4741035a77be3349f66eac5c362576d560'}, - {'magma-2.7.2_allow-all-sms.patch': '1fe721092d0193cad7c669bd8ffaa7c093a2547967232123ffb03460742f7b98'}, + {'magma-2.7.2_allow-all-sms.patch': '2996485844d7e199ea57eaebf59903d3514a03536f82b655ce30de480e28b828'}, ] builddependencies = [ From 7ee80536b35fddf79f6dcaee00210ac0828954a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2023 09:20:56 +0200 Subject: [PATCH 8871/9987] fix Kent_tools dependency for CIRCexplorer2 --- .../CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb index 2272a3bde87..f8b88edbf19 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb @@ -19,7 +19,7 @@ dependencies = [ ('TopHat', '2.1.2', versionsuffix), ('Cufflinks', '20190706'), ('BEDTools', '2.30.0'), - ('Kent_tools', '422', '-Boost-1.75.0'), + ('Kent_tools', '422'), ('STAR', '2.7.9a'), ('BWA', '0.7.17'), ('segemehl', '0.3.4'), From 10cfc137676aedf056600d65c38834f475588aae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2023 09:51:13 +0200 Subject: [PATCH 8872/9987] stick to Pysam 0.17.0 as dependency for CIRCexplorer2 --- ...xplorer2-2.3.8-foss-2021b-Python-2.7.18.eb | 2 +- .../Pysam-0.18.0-GCC-11.2.0-Python-2.7.18.eb | 29 ------------------- ...bedtools-0.8.2-GCC-11.2.0-Python-2.7.18.eb | 2 +- 3 files changed, 2 insertions(+), 31 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb index f8b88edbf19..349d6b4d3c9 100644 --- a/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CIRCexplorer2/CIRCexplorer2-2.3.8-foss-2021b-Python-2.7.18.eb @@ -23,7 +23,7 @@ dependencies = [ ('STAR', '2.7.9a'), ('BWA', '0.7.17'), ('segemehl', '0.3.4'), - ('Pysam', '0.18.0', versionsuffix), + ('Pysam', '0.17.0', versionsuffix), ('pybedtools', '0.8.2', versionsuffix), ] diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0-Python-2.7.18.eb deleted file mode 100644 index 1111d9b3c74..00000000000 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.18.0-GCC-11.2.0-Python-2.7.18.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pysam' -version = '0.18.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/pysam-developers/pysam' -description = """Pysam is a python module for reading and manipulating Samfiles. - It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" - -toolchain = {'name': 'GCC', 'version': '11.2.0'} - -source_urls = ['https://github.com/pysam-developers/pysam/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['db1ddf41639e4dbb3f94cc9afb14e879bff15690de5b713dec3a81e43f6fa131'] - -dependencies = [ - ('Python', '2.7.18'), - ('ncurses', '6.2'), - ('cURL', '7.78.0'), - ('XZ', '5.2.5'), -] - -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0-Python-2.7.18.eb index e506572279e..62c0c429372 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.8.2-GCC-11.2.0-Python-2.7.18.eb @@ -15,7 +15,7 @@ checksums = ['a184a36099458627e7ef52ea88218f7c00dc9c505b4256ece9ede58b1efa8771'] dependencies = [ ('Python', '2.7.18'), ('BEDTools', '2.30.0'), - ('Pysam', '0.18.0', versionsuffix), + ('Pysam', '0.17.0', versionsuffix), ] download_dep_fail = True From 226118dd2f143491ac114af1774ca589ccf12540 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Thu, 21 Sep 2023 11:04:17 +0200 Subject: [PATCH 8873/9987] Delete old patch --- .../XBeach_fix-gfortran-compilation.patch | 17 ----------------- 1 file changed, 17 deletions(-) delete mode 100644 easybuild/easyconfigs/x/XBeach/XBeach_fix-gfortran-compilation.patch diff --git a/easybuild/easyconfigs/x/XBeach/XBeach_fix-gfortran-compilation.patch b/easybuild/easyconfigs/x/XBeach/XBeach_fix-gfortran-compilation.patch deleted file mode 100644 index 2ed28e28d04..00000000000 --- a/easybuild/easyconfigs/x/XBeach/XBeach_fix-gfortran-compilation.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- trunk.orig/src/xbeachlibrary/mnemoniciso.F90 2023-09-18 11:46:34.153048000 +0200 -+++ trunk/src/xbeachlibrary/mnemoniciso.F90 2023-09-18 11:46:41.583851000 +0200 -@@ -10,10 +10,10 @@ - character(kind=c_char) type ! 'i' or 'r': integer or real*8 - character(kind=c_char) btype ! 'b' or 'd': - integer(c_int) rank ! 0,1,2,3,4 -- character(kind=c_char, len=maxnamelen) :: name ! 'v','ve', ..... -- character(kind=c_char, len=20) :: units ! m, following udunits convention -- character(kind=c_char, len=1024) :: description -- character(kind=c_char, len=20), dimension(maxrank) :: dimensions ! the dimensions of the variable, for example (s%nx, s%ny) -+ character(kind=c_char) :: name(maxnamelen) ! 'v','ve', ..... -+ character(kind=c_char) :: units(20) ! m, following udunits convention -+ character(kind=c_char) :: description(1024) -+ character(kind=c_char), dimension(maxrank) :: dimensions(20) - - type (c_ptr) :: array - From adeb24cee8cadce60deb77707870870ed067274f Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 21 Sep 2023 12:18:18 +0000 Subject: [PATCH 8874/9987] slightly better formatting --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 5efbe2fe9e6..352d18ee6e2 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -43,14 +43,14 @@ exts_list = [ 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], }), ('gitlab', '3.10.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { 'checksums': ['27f503220e6845d9db954fb212b95b0362d8b7e6c1b2326a87061c3de93594b1'], }), (name, version, { - 'checksums': ['d832f3d70b79b7b66519ca30315791a6a265bdf8a86ddac5846489b75385cb09'], + 'checksums': ['d832f3d70b79b7b66519ca30315791a6a265bdf8a86ddac5846489b75385cb09'], }), ] From b760928eb9d8b11aab9e6e0a10944d5630b10f77 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 21 Sep 2023 12:40:40 +0000 Subject: [PATCH 8875/9987] flake8 too much indent --- .../datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 352d18ee6e2..600999ca8c5 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -24,33 +24,33 @@ use_pip = True exts_list = [ ('humanize', '3.13.1', { - 'checksums': ['12f113f2e369dac7f35d3823f49262934f4a22a53a6d3d4c86b736f50db88c7b'], + 'checksums': ['12f113f2e369dac7f35d3823f49262934f4a22a53a6d3d4c86b736f50db88c7b'], }), ('fasteners', '0.18', { - 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), ('patoolib', '1.12', { - 'source_tmpl': 'patool-%(version)s.tar.gz', - 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], + 'source_tmpl': 'patool-%(version)s.tar.gz', + 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), ('annexremote', '1.6.0', { - 'checksums': ['779a43e5b1b4afd294761c6587dee8ac68f453a5a8cc40f419e9ca777573ae84'], + 'checksums': ['779a43e5b1b4afd294761c6587dee8ac68f453a5a8cc40f419e9ca777573ae84'], }), ('looseversion', '1.2.0', { - 'checksums': ['c64e71c0b29030683b4ea75aee431db2d25c4e6e533590e52129f1d9e51de204'], + 'checksums': ['c64e71c0b29030683b4ea75aee431db2d25c4e6e533590e52129f1d9e51de204'], }), ('boto', '2.49.0', { - 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], + 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], }), ('gitlab', '3.10.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { - 'checksums': ['27f503220e6845d9db954fb212b95b0362d8b7e6c1b2326a87061c3de93594b1'], + 'checksums': ['27f503220e6845d9db954fb212b95b0362d8b7e6c1b2326a87061c3de93594b1'], }), (name, version, { - 'checksums': ['d832f3d70b79b7b66519ca30315791a6a265bdf8a86ddac5846489b75385cb09'], + 'checksums': ['d832f3d70b79b7b66519ca30315791a6a265bdf8a86ddac5846489b75385cb09'], }), ] From f9e1650b1b423e24628a76a85739a25aa0b6d52f Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 21 Sep 2023 16:20:35 +0200 Subject: [PATCH 8876/9987] erase tarball checksum --- .../easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb b/easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb index 68f7c559829..d6d2377b1fd 100644 --- a/easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb +++ b/easybuild/easyconfigs/x/XBeach/XBeach-20230831-gompi-2022a.eb @@ -17,14 +17,12 @@ toolchainopts = {'usempi': True} # There is no tarball provided, only SVN checkout through: # svn checkout https://svn.oss.deltares.nl/repos/xbeach/trunk@6044 # make tarball: tar -czvf XBeach-20230831.tgz trunk -# (tarball should be in the same directory as the easyconfig) sources = [SOURCE_TGZ] patches = ['XBeach-20230831_fix-gfortran-compilation.patch'] checksums = [ - {'XBeach-20230831.tgz': 'c777504b4e39e1a03bcab77efaa19aea4048981bae68a390a946ee8594dc7c85'}, - {'XBeach-20230831_fix-gfortran-compilation.patch': - '9aa8a3593ea641a16a6d09bb75cc9935de383b5934f4a2718eeb94382386f0c4'}, + None, + '9aa8a3593ea641a16a6d09bb75cc9935de383b5934f4a2718eeb94382386f0c4', ] prebuildopts = 'make clean && ' From 2e94c73c8679e3d389bda6bc2f919ce2249c44c1 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 21 Sep 2023 14:33:13 +0000 Subject: [PATCH 8877/9987] adding easyconfigs: dask-2023.9.2-foss-2023a.eb, bokeh-3.2.2-foss-2023a.eb --- .../b/bokeh/bokeh-3.2.2-foss-2023a.eb | 51 ++++++++++++++ .../d/dask/dask-2023.9.2-foss-2023a.eb | 67 +++++++++++++++++++ 2 files changed, 118 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-3.2.2-foss-2023a.eb create mode 100755 easybuild/easyconfigs/d/dask/dask-2023.9.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-3.2.2-foss-2023a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-3.2.2-foss-2023a.eb new file mode 100644 index 00000000000..34fbec9a4f9 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-3.2.2-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '3.2.2' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('meson-python', '0.13.2'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('PyYAML', '6.0'), + ('Pillow-SIMD', '9.5.0'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('tornado', '6.3.2'), + ('hatchling', '1.18.0'), # fixes error "xyzservices>=2021.09.1, but you have 0.0.0" +] + +use_pip = True + +exts_list = [ + ('contourpy', '1.0.7', { + 'checksums': ['d8165a088d31798b59e91117d1f5fc3df8168d8b48c4acc10fc0df0d0bdbcc5e'], + }), + ('xyzservices', '2023.7.0', { + 'checksums': ['0ec928742227d6f5d4367ea7b457fcfed943429f4de2949b5b02a82cdf5569d6'], + }), + (name, version, { + # bokeh uses git tags to get version, so we'll instead inject the version into setup.py + 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """, + 'checksums': ['b2959b8524d69ec4e7886bc36407445f0a92e1f19530d3bfc4045236a1b7a6ff'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2023.9.2-foss-2023a.eb b/easybuild/easyconfigs/d/dask/dask-2023.9.2-foss-2023a.eb new file mode 100755 index 00000000000..cc2bda1e1ee --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2023.9.2-foss-2023a.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2023.9.2' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2023.07'), + ('bokeh', '3.2.2'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('locket', '1.0.0', { + 'checksums': ['5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632'], + }), + ('partd', '1.4.0', { + 'checksums': ['aa0ff35dbbcc807ae374db56332f4c1b39b46f67bf2975f5151e0b4186aed0d5'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '3.0.0', { + 'checksums': ['e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5'], + }), + ('tblib', '2.0.0', { + 'checksums': ['a6df30f272c08bf8be66e0775fad862005d950a6b8449b94f7c788731d70ecd7'], + }), + (name, version, { + 'checksums': ['34e04ed79870cd01119217562f417c6ce575b10fb8fdcd866e9c5cd10c088944'], + }), + ('distributed', version, { + 'checksums': ['b76b43be6a297c6cc6dc4eac7f5a05a8c6834aaf025ed37395d1d830448d540e'], + }), + ('dask-mpi', '2022.4.0', { + 'checksums': ['0a04f1d7d35a06cdff506593330d4414ea242c9172498ce191f5742eac499e17'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.8.2', { + 'checksums': ['d35407a05a0534347c5d958ae749b9f8535bec529857d013b6e5649cde43914a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + +moduleclass = 'data' From e6d44fce05acadbe82b2e5d16204a57bbfa09351 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 21 Sep 2023 16:45:15 +0200 Subject: [PATCH 8878/9987] Update easybuild/easyconfigs/b/bokeh/bokeh-3.2.2-foss-2023a.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/b/bokeh/bokeh-3.2.2-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-3.2.2-foss-2023a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-3.2.2-foss-2023a.eb index 34fbec9a4f9..f2407b6c84b 100644 --- a/easybuild/easyconfigs/b/bokeh/bokeh-3.2.2-foss-2023a.eb +++ b/easybuild/easyconfigs/b/bokeh/bokeh-3.2.2-foss-2023a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [ ('meson-python', '0.13.2'), + ('hatchling', '1.18.0'), # fixes error "xyzservices>=2021.09.1, but you have 0.0.0" ] dependencies = [ @@ -20,7 +21,6 @@ dependencies = [ ('SciPy-bundle', '2023.07'), ('Python-bundle-PyPI', '2023.06'), ('tornado', '6.3.2'), - ('hatchling', '1.18.0'), # fixes error "xyzservices>=2021.09.1, but you have 0.0.0" ] use_pip = True From 8a19a001d6be10435e0012591dfa8ee62b494a35 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 21 Sep 2023 17:23:09 +0200 Subject: [PATCH 8879/9987] adding easyconfigs: ReFrame-4.3.3.eb --- .../easyconfigs/r/ReFrame/ReFrame-4.3.3.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb new file mode 100644 index 00000000000..af6b22f4846 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.3.3.eb @@ -0,0 +1,67 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.3.3' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + # stick to pip 21.3.1 and wheel 0.37.1, which are compatible with Python 3.6 + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + ('reframe', version, { + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['3d1a1a6d2c8e3b362dadc47f642f23f7574fb81b03be31055040afe9738829c2'], + }), +] + +postinstallcmds = [ + "cp -a tools tutorials %(installdir)s", + # Adding hpctestlib separately to the external directory so that it can be + # imported and is in the PYTHONPATH + "cp -a hpctestlib %(installdir)s/external", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'lib', 'tools', 'tutorials'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 204feddba284309440d7e6074443cdab33bab290 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 21 Sep 2023 17:00:22 +0000 Subject: [PATCH 8880/9987] add binutils as build dep --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 600999ca8c5..ac18265b966 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -11,6 +11,10 @@ and integrates with widely used data infrastructure." toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} +build_dependecies = [ + ('binutils', '2.39') +] + dependencies = [ ('git-annex', '10.20230802'), ('Python', '3.10.8'), From c4942cdd92c825deadf586b7b1973dae215ff4ff Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Thu, 21 Sep 2023 19:12:59 +0200 Subject: [PATCH 8881/9987] small typo --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index ac18265b966..d9888971561 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -11,7 +11,7 @@ and integrates with widely used data infrastructure." toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -build_dependecies = [ +builddependecies = [ ('binutils', '2.39') ] From bbbf16ed215499a588f3ec26e913cf3f2083155f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 21 Sep 2023 19:19:15 +0200 Subject: [PATCH 8882/9987] fix access rights for dask-2023.9.2-foss-2023a.eb --- easybuild/easyconfigs/d/dask/dask-2023.9.2-foss-2023a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/d/dask/dask-2023.9.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/dask/dask-2023.9.2-foss-2023a.eb b/easybuild/easyconfigs/d/dask/dask-2023.9.2-foss-2023a.eb old mode 100755 new mode 100644 From a3ab0c97be2c868b1ce0aae9653b041a0b7fbae2 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 21 Sep 2023 17:33:51 +0000 Subject: [PATCH 8883/9987] other small tapo --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index d9888971561..8f48ebf11cb 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -11,7 +11,7 @@ and integrates with widely used data infrastructure." toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} -builddependecies = [ +builddependencies = [ ('binutils', '2.39') ] From 0df0a872fd2439290c64b0c97af89e715b1309ed Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Sep 2023 15:29:26 +0200 Subject: [PATCH 8884/9987] improve CUDA 11 compatibility of GCC 12.2 --- .../easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 3 +++ ...ore-12.2.0_improve-cuda-compatibility.patch | 18 ++++++++++++++++++ 2 files changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_improve-cuda-compatibility.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb index 9a758565b1f..d799279899f 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -36,6 +36,7 @@ patches = [ 'GCCcore-12.1.0_allow-pragma-wself-init.patch', 'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch', 'GCCcore-12.2.0_fix-vectorizer.patch', + 'GCCcore-12.2.0_improve-cuda-compatibility.patch', ] checksums = [ {'gcc-12.2.0.tar.gz': 'ac6b317eb4d25444d87cf29c0d141dedc1323a1833ec9995211b13e1a851261c'}, @@ -52,6 +53,8 @@ checksums = [ {'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch': '0ea675960795e238a43ae7d685a0082b21f0b63cf2fe499f6d55e89e0aaee392'}, {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, + {'GCCcore-12.2.0_improve-cuda-compatibility.patch': + '44d028df2a166a801a0e599f9ac2044673501602f2461ad3ff882d5f29add363'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_improve-cuda-compatibility.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_improve-cuda-compatibility.patch new file mode 100644 index 00000000000..f557fac646b --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_improve-cuda-compatibility.patch @@ -0,0 +1,18 @@ +The GCC stdlib uses a GCC feature not supported by nvcc until CUDA 12. +I.e. CUDA 12 does not support GCC 12 (only GCC <= 11) erroring at +> if ((void*)(this->*(&time_get::do_get)) == (void*)(&time_get::do_get)) + +As the same isn't supported by clang use the same fix. +See https://gcc.gnu.org/bugzilla//show_bug.cgi?id=104990 + +--- gcc-12.2.0-orig/libstdc++-v3/include/bits/locale_facets_nonio.tcc ++++ gcc-12.2.0/libstdc++-v3/include/bits/locale_facets_nonio.tcc +@@ -1465,7 +1465,7 @@ + ctype<_CharT> const& __ctype = use_facet >(__loc); + __err = ios_base::goodbit; + bool __use_state = false; +-#if __GNUC__ >= 5 && !defined(__clang__) ++#if __GNUC__ >= 5 && !defined(__clang__) && (!defined(__CUDACC__) || (__CUDACC_VER_MAJOR__ >= 12)) + #pragma GCC diagnostic push + #pragma GCC diagnostic ignored "-Wpmf-conversions" + // Nasty hack. The C++ standard mandates that get invokes the do_get From bbf15a020b7a77152c847b2d56d0ab4fed34ae55 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Sep 2023 15:36:13 +0200 Subject: [PATCH 8885/9987] add patch author --- easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 2 +- .../g/GCCcore/GCCcore-12.2.0_improve-cuda-compatibility.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb index d799279899f..aa2a7e328a2 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -54,7 +54,7 @@ checksums = [ '0ea675960795e238a43ae7d685a0082b21f0b63cf2fe499f6d55e89e0aaee392'}, {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, {'GCCcore-12.2.0_improve-cuda-compatibility.patch': - '44d028df2a166a801a0e599f9ac2044673501602f2461ad3ff882d5f29add363'}, + '91d00122554b56381592229398540e63baa26d03633292a7fdf338407a4a62d5'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_improve-cuda-compatibility.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_improve-cuda-compatibility.patch index f557fac646b..c1538d09041 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_improve-cuda-compatibility.patch +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_improve-cuda-compatibility.patch @@ -5,6 +5,8 @@ I.e. CUDA 12 does not support GCC 12 (only GCC <= 11) erroring at As the same isn't supported by clang use the same fix. See https://gcc.gnu.org/bugzilla//show_bug.cgi?id=104990 +Author: Alexander Grund (TU Dresden) + --- gcc-12.2.0-orig/libstdc++-v3/include/bits/locale_facets_nonio.tcc +++ gcc-12.2.0/libstdc++-v3/include/bits/locale_facets_nonio.tcc @@ -1465,7 +1465,7 @@ From 0db056a9f86b7c4aafe0f17cf119ff2a86fe66e1 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 23 Sep 2023 10:38:18 +0200 Subject: [PATCH 8886/9987] Make util-linux build on CentOS 7 (issue #18519). --- .../util-linux-2.39-GCCcore-12.3.0.eb | 6 +++- .../util-linux-2.39-fix-build-centos7.patch | 30 +++++++++++++++++++ 2 files changed, 35 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.39-fix-build-centos7.patch diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb index f3bc453a771..9a174f12600 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-12.3.0.eb @@ -12,10 +12,14 @@ toolchainopts = {'pic': True} source_urls = ['%s/v%%(version_major_minor)s' % homepage] sources = [SOURCELOWER_TAR_GZ] -patches = ['util-linux-%(version)s_fix_waitpid.patch'] +patches = [ + 'util-linux-%(version)s_fix_waitpid.patch', + 'util-linux-2.39-fix-build-centos7.patch' +] checksums = [ {'util-linux-2.39.tar.gz': 'b1f597ad172a2ee17b0a7ae4be7ab7e1b1a6f9394ddbd3d8ec90ae4ed7333579'}, {'util-linux-2.39_fix_waitpid.patch': '99cbd4ee8293f3ffad4467e9f245d0da4e10a98b6599f5e5f9d4cb99c7eebbd2'}, + {'util-linux-2.39-fix-build-centos7.patch': '21587513f0f5f5efe790396ac39450c7f30dd55063929bb430a77352ba99f57f'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.39-fix-build-centos7.patch b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-fix-build-centos7.patch new file mode 100644 index 00000000000..1740f26324e --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-fix-build-centos7.patch @@ -0,0 +1,30 @@ +From 2756f00407d3bc7dca3f5be0a0d101ef97e8eb5e Mon Sep 17 00:00:00 2001 +From: Karel Zak +Date: Tue, 15 Aug 2023 11:33:31 +0200 +Subject: [PATCH] setarch: add PER_LINUX_FDPIC fallback + +Fixes: https://github.com/util-linux/util-linux/issues/2436 +Signed-off-by: Karel Zak +--- + sys-utils/setarch.c | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/sys-utils/setarch.c b/sys-utils/setarch.c +index 78b5183..1a255e4 100644 +--- a/sys-utils/setarch.c ++++ b/sys-utils/setarch.c +@@ -84,6 +84,11 @@ + # define ADDR_LIMIT_3GB 0x8000000 + #endif + ++/* fallback for old glibc-headers 2.17 */ ++#ifndef PER_LINUX_FDPIC ++# define PER_LINUX_FDPIC (PER_LINUX | FDPIC_FUNCPTRS) ++#endif ++ + #define ALL_PERSONALITIES \ + X(PER_LINUX) \ + X(PER_LINUX_32BIT) \ +-- +1.8.3.1 + From b53d9ce3db364d771d8d4c17731eca8d69713719 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Mon, 25 Sep 2023 10:29:24 +0200 Subject: [PATCH 8887/9987] adding easyconfigs: SuiteSparse-7.1.0-foss-2023a.eb --- .../SuiteSparse-7.1.0-foss-2023a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb new file mode 100644 index 00000000000..8eea586e45f --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb @@ -0,0 +1,25 @@ +name = 'SuiteSparse' +version = '7.1.0' + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries to manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4cd3d161f9aa4f98ec5fa725ee5dc27bca960a3714a707a7d12b3d0abb504679'] + +builddependencies = [ + ('CMake', '3.26.3'), + # ('M4', '1.4.19'), +] + +dependencies = [ + ('MPFR', '4.2.0'), +] + +prebuildopts = 'CMAKE_OPTIONS="-DCMAKE_INSTALL_PREFIX=%(installdir)s -DBLA_VENDOR=FlexiBLAS"' + +moduleclass = 'numlib' From d9456222981de94dde0f5b79dac1a7c639289b67 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Sep 2023 13:26:05 +0200 Subject: [PATCH 8888/9987] adding easyconfigs: GDB-13.2-GCCcore-12.2.0.eb, ISL-0.26-GCCcore-12.2.0.eb, makeinfo-7.0.3-GCCcore-12.2.0.eb --- .../g/GDB/GDB-13.2-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ .../i/ISL/ISL-0.26-GCCcore-12.2.0.eb | 23 ++++++++++ .../makeinfo/makeinfo-7.0.3-GCCcore-12.2.0.eb | 25 +++++++++++ 3 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-7.0.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..21074cc6cfc --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '13.2' + +homepage = 'https://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['fd5bebb7be1833abdb6e023c2f498a354498281df9d05523d8915babeb893f0a'] + +builddependencies = [ + ('binutils', '2.39'), + ('makeinfo', '7.0.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('expat', '2.4.9'), + ('Python', '3.10.8'), + ('ISL', '0.26'), + ('MPC', '1.3.1'), +] + +preconfigopts = "mkdir obj && cd obj && " +configure_cmd_prefix = '../' +prebuildopts = "cd obj && " +preinstallopts = prebuildopts + +configopts = '--with-system-zlib --with-system-readline --with-expat=$EBROOTEXPAT ' +configopts += '--with-python=$EBROOTPYTHON/bin/python --with-isl=$EBROOTISL --with-mpc=$EBROOTMPC ' +configopts += '--enable-tui --enable-plugins --disable-install-libbfd ' + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2d70b546fc5 --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-12.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.26' + +homepage = 'https://libisl.sourceforge.io' +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://libisl.sourceforge.io'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'] + +builddependencies = [('binutils', '2.39')] +dependencies = [('GMP', '6.2.1')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-7.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-7.0.3-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2b0fda7ea30 --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-7.0.3-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '7.0.3' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['74b420d09d7f528e84f97aa330f0dd69a98a6053e7a4e01767eed115038807bf'] + +builddependencies = [('binutils', '2.39')] +dependencies = [('Perl', '5.36.0')] + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' From bf036d257ca4af3dad16232a042d3bf504b27974 Mon Sep 17 00:00:00 2001 From: xina Date: Mon, 25 Sep 2023 14:32:15 +0200 Subject: [PATCH 8889/9987] adding easyconfigs: DIRAC-23.0-intel-2023a-int64.eb --- .../d/DIRAC/DIRAC-23.0-intel-2023a-int64.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2023a-int64.eb diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2023a-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2023a-int64.eb new file mode 100644 index 00000000000..8a06671ca31 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-23.0-intel-2023a-int64.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '23.0' +versionsuffix = '-int64' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'usempi': True, 'i8': True, 'oneapi': False} + +source_urls = ['https://zenodo.org/record/7670749/files/'] +sources = ['DIRAC-%(version)s-Source.tgz'] +checksums = ['a0a6b6318b3cd2e3c6042221de720bb1e87eb758999e2108a48dedb9c564e1f8'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('HDF5', '1.14.0') +] + +configopts = '-DMKL_FLAG=sequential ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_64BIT_INTEGERS=True ' +configopts += '-DENABLE_EXATENSOR=off ' +configopts += '-DENABLE_PCMSOLVER=off ' + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += 'export DIRAC_MPI_COMMAND="%(mpi_cmd_prefix)s " && ' + +runtest = 'test ARGS="-R symmetry_scf_energy" ' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' From 1e3236ad15c25e55c5799c94202058288b856654 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Mon, 25 Sep 2023 16:43:59 +0200 Subject: [PATCH 8890/9987] adding easyconfigs: BMTK-1.0.8-foss-2021a.eb --- .../b/BMTK/BMTK-1.0.8-foss-2021a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/BMTK/BMTK-1.0.8-foss-2021a.eb diff --git a/easybuild/easyconfigs/b/BMTK/BMTK-1.0.8-foss-2021a.eb b/easybuild/easyconfigs/b/BMTK/BMTK-1.0.8-foss-2021a.eb new file mode 100644 index 00000000000..0252218b1b5 --- /dev/null +++ b/easybuild/easyconfigs/b/BMTK/BMTK-1.0.8-foss-2021a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'BMTK' +version = '1.0.8' + +homepage = 'https://alleninstitute.github.io/bmtk/index.html' +description = """The Brain Modeling Toolkit (BMTK) is a python-based software +package for building, simulating and analyzing large-scale neural network +models. It supports the building and simulation of models of varying +levels-of-resolution; from multi-compartment biophysically detailed networks, +to point-neuron models, to filter-based models, and even population-level +firing rate models.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('h5py', '3.2.1'), + ('sympy', '1.8'), + ('scikit-image', '0.18.3'), + ('typing-extensions', '4.4.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bmtk', version, { + 'checksums': ['9609da6347e74b440a44590f22fc2de0b281fc2eed4c1ee259730c5a8b3c0535'], + }), + ('pynrrd', '1.0.0', { + 'modulename': 'nrrd', + 'checksums': ['4eb4caba03fbca1b832114515e748336cb67bce70c7f3ae36bfa2e135fc990d2'], + }), + ('nptyping', '2.5.0', { + 'checksums': ['e3d35b53af967e6fb407c3016ff9abae954d3a0568f7cc13a461084224e8e20a'], + }), +] + +moduleclass = 'bio' From 0e2b6a58f65a942692918d3c9de78a3c720d80ba Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Sep 2023 17:26:46 +0200 Subject: [PATCH 8891/9987] Add missing dependency --- .../m/MPC/MPC-1.3.1-GCCcore-12.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..dfb7008a060 --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.3.1' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' From c711561f9c948b20e4b06f0d39b6072f9ba337c0 Mon Sep 17 00:00:00 2001 From: Steven Vandenbrande Date: Mon, 25 Sep 2023 17:43:42 +0200 Subject: [PATCH 8892/9987] Downgrade nptyping to avoid typing-extensions clash --- easybuild/easyconfigs/b/BMTK/BMTK-1.0.8-foss-2021a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/BMTK/BMTK-1.0.8-foss-2021a.eb b/easybuild/easyconfigs/b/BMTK/BMTK-1.0.8-foss-2021a.eb index 0252218b1b5..6d46f47d72b 100644 --- a/easybuild/easyconfigs/b/BMTK/BMTK-1.0.8-foss-2021a.eb +++ b/easybuild/easyconfigs/b/BMTK/BMTK-1.0.8-foss-2021a.eb @@ -20,7 +20,6 @@ dependencies = [ ('h5py', '3.2.1'), ('sympy', '1.8'), ('scikit-image', '0.18.3'), - ('typing-extensions', '4.4.0'), ] use_pip = True @@ -34,8 +33,10 @@ exts_list = [ 'modulename': 'nrrd', 'checksums': ['4eb4caba03fbca1b832114515e748336cb67bce70c7f3ae36bfa2e135fc990d2'], }), - ('nptyping', '2.5.0', { - 'checksums': ['e3d35b53af967e6fb407c3016ff9abae954d3a0568f7cc13a461084224e8e20a'], + ('nptyping', '2.0.0', { + 'source_urls': ['https://github.com/ramonhagenaars/nptyping/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['2c99b0cde2f548ebae71b0856e3eb51e61b79935b2d0e07af9717fcb685f6616'], }), ] From 59ea4dd40bfd3de7e7886fef564b84a3a3b8ee08 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 26 Sep 2023 11:01:46 +0200 Subject: [PATCH 8893/9987] Fix finding tk.tcl for Tk 8.6.13 --- .../t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb | 2 ++ .../Tk-8.6.13_different-prefix-with-tcl.patch | 31 +++++++++++++++++++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.13_different-prefix-with-tcl.patch diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb index f4a7cfcf052..bfdd55b8d55 100644 --- a/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-12.3.0.eb @@ -11,8 +11,10 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ["https://prdownloads.sourceforge.net/tcl"] sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.13_different-prefix-with-tcl.patch'] checksums = [ {'tk8.6.13-src.tar.gz': '2e65fa069a23365440a3c56c556b8673b5e32a283800d8d9b257e3f584ce0675'}, + {'Tk-8.6.13_different-prefix-with-tcl.patch': 'e136ff60dfe7fc4b14d98af00cf89522fbfd106e75b0a9259f410a8bfa732534'}, ] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.13_different-prefix-with-tcl.patch b/easybuild/easyconfigs/t/Tk/Tk-8.6.13_different-prefix-with-tcl.patch new file mode 100644 index 00000000000..2e249803b28 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.13_different-prefix-with-tcl.patch @@ -0,0 +1,31 @@ +fix for: + _tkinter.TclError: Can't find a usable tk.tcl in the following directories: ... +based on https://github.com/NixOS/nixpkgs/commit/decd2feb0a1bc80940e697fa66e3b25383360c30 +see also https://github.com/NixOS/nixpkgs/issues/1479 +author: Kenneth Hoste (HPC-UGent) + +Ported to 8.6.13 by Alexander Grund (TU Dresden) + +diff -ru tk8.6.13-orig/generic/tkWindow.c tk8.6.13/generic/tkWindow.c +--- tk8.6.13-orig/generic/tkWindow.c 2023-09-26 10:56:34.715911109 +0200 ++++ tk8.6.13/generic/tkWindow.c 2023-09-26 10:53:01.033046206 +0200 +@@ -1045,6 +1045,7 @@ + + Tcl_SetVar2(interp, "tk_patchLevel", NULL, TK_PATCH_LEVEL, TCL_GLOBAL_ONLY); + Tcl_SetVar2(interp, "tk_version", NULL, TK_VERSION, TCL_GLOBAL_ONLY); ++ Tcl_SetVar2(interp, "tk_library", NULL, TK_LIBRARY, TCL_GLOBAL_ONLY); + + tsdPtr->numMainWindows++; + return tkwin; +diff -ru tk8.6.13-orig/unix/Makefile.in tk8.6.13/unix/Makefile.in +--- tk8.6.13-orig/unix/Makefile.in 2023-09-26 10:54:29.370096346 +0200 ++++ tk8.6.13/unix/Makefile.in 2023-09-26 10:55:16.768513560 +0200 +@@ -1033,7 +1033,7 @@ + $(CC) -c $(CC_SWITCHES) $(GENERIC_DIR)/tkVisual.c + + tkWindow.o: $(GENERIC_DIR)/tkWindow.c tkUuid.h +- $(CC) -c $(CC_SWITCHES) -I. $(GENERIC_DIR)/tkWindow.c ++ $(CC) -c $(CC_SWITCHES) -DTK_LIBRARY=\"${TK_LIBRARY}\" -I. $(GENERIC_DIR)/tkWindow.c + + tkButton.o: $(GENERIC_DIR)/tkButton.c + $(CC) -c $(CC_SWITCHES) $(GENERIC_DIR)/tkButton.c From d741cae4f28e49386831902f9ee1b0c0f0bcc65a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jurij=20Pe=C4=8Dar?= Date: Tue, 26 Sep 2023 13:29:38 +0200 Subject: [PATCH 8894/9987] adding easyconfigs: bases2fastq-1.5.1.eb --- .../b/bases2fastq/bases2fastq-1.5.1.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/b/bases2fastq/bases2fastq-1.5.1.eb diff --git a/easybuild/easyconfigs/b/bases2fastq/bases2fastq-1.5.1.eb b/easybuild/easyconfigs/b/bases2fastq/bases2fastq-1.5.1.eb new file mode 100644 index 00000000000..fa3cce5b299 --- /dev/null +++ b/easybuild/easyconfigs/b/bases2fastq/bases2fastq-1.5.1.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'bases2fastq' +version = '1.5.1' + +homepage = 'https://docs.elembio.io/docs/bases2fastq' +description = """ Bases2Fastq Software demultiplexes sequencing data and converts base calls + into FASTQ files for secondary analysis with the FASTQ-compatible software of your choice. + The Element AVITI™ System records base calls, which are the main output of a sequencing run, + with associated quality scores (Q-scores) in bases files. Bases files must be converted into + the FASTQ file format for secondary analysis. + +To generate QC reports, also load BeautifulSoup and bokeh. """ + +toolchain = SYSTEM + +source_urls = ['https://bases2fastq-release.s3.amazonaws.com/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['832fab35ff7e74a190473d3f50faad9f62291d60e49f92c098556f4a5b33cfa9'] + +sanity_check_paths = { + 'files': ['bases2fastq'], + 'dirs': [], +} + +sanity_check_commands = [ + "bases2fastq --version" +] + +moduleclass = 'bio' From 35d69ea23d480275697b3da3597f49973e270bd7 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Tue, 26 Sep 2023 15:17:59 +0200 Subject: [PATCH 8895/9987] Fix typo --- easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/q/Qt6/Qt6-6.5.2_fix_OF-Gentoo.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb index ccc26d46270..dbc3043b0cf 100644 --- a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb @@ -81,7 +81,7 @@ configopts += '-DFEATURE_qtpdf_build=OFF ' # Requires CUPS configopts += '-DQT_AVOID_CMAKE_ARCHIVING_API=ON ' configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' configopts += '-DBUILD_qtwayland=OFF ' # Does not work on CentOS 7 -# Removed from Qt6.0.0 by may be added back in the future +# Removed from Qt6.0.0 but may be added back in the future # configopts += '-DBUILD_qtgamepad=OFF ' # Does not work on CentOS 7 sanity_check_paths = { diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2_fix_OF-Gentoo.patch b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2_fix_OF-Gentoo.patch index 5b3b6df66b1..4a47501ebcf 100644 --- a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2_fix_OF-Gentoo.patch +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2_fix_OF-Gentoo.patch @@ -15,7 +15,7 @@ index 8dcbdb06e3..e9cc96914e 100644 #endif -+// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// if OF macro is not defined but _Z_OF is, define OF as _Z_OF +// required when building with zlib provided by Gentoo +// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 +#ifndef OF @@ -34,7 +34,7 @@ index c1b7a54847..c5546a26b9 100644 #endif -+// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// if OF macro is not defined but _Z_OF is, define OF as _Z_OF +// required when building with zlib provided by Gentoo +// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 +#ifndef OF From 2fe8599212f64552f96d07301295c31bfdd3a732 Mon Sep 17 00:00:00 2001 From: nicolas Date: Tue, 26 Sep 2023 15:23:46 +0200 Subject: [PATCH 8896/9987] adding easyconfigs: line_profiler-4.1.1-GCCcore-12.2.0.eb --- .../line_profiler-4.1.1-GCCcore-12.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0908ba1bbf6 --- /dev/null +++ b/easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.1-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'line_profiler' +version = '4.1.1' + +homepage = 'https://github.com/pyutils/line_profiler' +description = """line_profiler is a module for doing line-by-line profiling +of functions. kernprof is a convenient script for running either +line_profiler or the Python standard library's cProfile or profile modules, +depending on what is available.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'pyutils' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['71c150bf06dd964fc0e5fbc3a5eb31bbee03c535d31c9548999c3e0302dcbb27'] + +builddependencies = [ + ('scikit-build', '0.17.2'), + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), +] +dependencies = [ + ('Python', '3.10.8'), + ('IPython', '8.14.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/kernprof'], + 'dirs': [], +} + +sanity_check_commands = ['kernprof --help'] + +moduleclass = 'devel' From 445898bfac7b77af352dae8001fe52eb98d7362d Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Tue, 26 Sep 2023 15:54:58 +0200 Subject: [PATCH 8897/9987] Fix checksum of patch --- easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb index dbc3043b0cf..ebbfe66572d 100644 --- a/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.5.2-GCCcore-12.3.0.eb @@ -17,16 +17,11 @@ source_urls = [ ] sources = ['qt-everywhere-src-%(version)s.tar.xz'] patches = [ - # they may not be needed if qmake is not used? - # QT_CFLAGS_ARCH_HASWELL in cmake/QtCompilerOptimization.cmake should be patched? - # 'Qt5-5.13.1_fix-avx2.patch', - # 'Qt5-5.13.1_fix-qmake-libdir.patch', - # 'Qt5-5.15.2_fix-qtwebengine-breakpad-glibc-2.34.patch', 'Qt6-6.5.2_fix_OF-Gentoo.patch', ] checksums = [ {'qt-everywhere-src-6.5.2.tar.xz': 'cde57be663d0f875759797298bdc37a936d517c39f2013e4e6ece5e12edeed12'}, - {'Qt6-6.5.2_fix_OF-Gentoo.patch': '908f7dae7685c76fe651e52391e46a2337a3cd32dee70a5da54b154da7d4917c'}, + {'Qt6-6.5.2_fix_OF-Gentoo.patch': '62c4b1abdeac69f40fd48f5e46f470f9f9c328fdb02ab8aceb9aa1885ad8c601'}, ] builddependencies = [ From 195c88674bb1b7bce8651c7d6d530074a8d6a668 Mon Sep 17 00:00:00 2001 From: xina Date: Tue, 26 Sep 2023 16:38:33 +0200 Subject: [PATCH 8898/9987] adding easyconfigs: p7zip-17.04-GCCcore-12.3.0.eb --- .../p/p7zip/p7zip-17.04-GCCcore-12.3.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..6a37b555e9e --- /dev/null +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.04-GCCcore-12.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '17.04' + +homepage = 'https://github.com/p7zip-project/p7zip/' +description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of +7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'p7zip-project' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ea029a2e21d2d6ad0a156f6679bd66836204aa78148a4c5e498fe682e77127ef'] + +builddependencies = [ + ('binutils', '2.40'), +] + +prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" +buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' + +files_to_copy = [ + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.%s' % SHLIB_EXT, 'bin/Codecs'], 'libexec'), # 7z requires 7z.so plugin in same directory +] + +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + "echo '#!/bin/sh\n%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask +] + +sanity_check_paths = { + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.%s' % SHLIB_EXT], + 'dirs': ['libexec/Codecs'], +} + +sanity_check_commands = [ + '7z --help', + '7z x || test $? -gt 0', + "! 7z i | grep -q \"Can't load\" ", +] + +moduleclass = 'tools' From f85c211243876ae8772572decbc49786160413e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Sep 2023 16:56:28 +0200 Subject: [PATCH 8899/9987] avoid harcoding `mpic++` and `-std=c++11 -O3` in buildopts for ProBis --- easybuild/easyconfigs/p/ProBiS/ProBiS-20230403-gompi-2022b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ProBiS/ProBiS-20230403-gompi-2022b.eb b/easybuild/easyconfigs/p/ProBiS/ProBiS-20230403-gompi-2022b.eb index b8d9926b1fe..cc6a507d9e2 100644 --- a/easybuild/easyconfigs/p/ProBiS/ProBiS-20230403-gompi-2022b.eb +++ b/easybuild/easyconfigs/p/ProBiS/ProBiS-20230403-gompi-2022b.eb @@ -9,6 +9,7 @@ description = """ProBiS algorithm aligns and superimposes complete protein surfa surface motifs, or protein binding sites.""" toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'cstd': 'c++11'} source_urls = ['https://gitlab.com/janezkonc/probis/-/archive/master/'] sources = ['%s.tar.gz' % local_commit] @@ -18,7 +19,7 @@ dependencies = [ ('GSL', '2.7'), ] -buildopts = 'probis CC="mpic++" CFLAGS="-std=c++11 -O3 -Wall -Wno-unused-function -DNDEBUG -pthread"' +buildopts = 'probis CC="$MPICXX" CFLAGS="$CFLAGS -Wall -Wno-unused-function -DNDEBUG -pthread"' files_to_copy = [(['probis'], 'bin')] From 226a097a70eb87993cb0687dfbbd3ee1e01ce32e Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 26 Sep 2023 18:43:20 +0200 Subject: [PATCH 8900/9987] Fixes issue with automatic detection of NeoverseV1 architecture at build time of OpenBLAS --- .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 2 ++ ...OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch | 15 +++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index c00bedf7a63..c4ab6957e00 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -19,6 +19,7 @@ patches = [ 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', + 'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch', ] checksums = [ {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, @@ -31,6 +32,7 @@ checksums = [ {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, + {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': '2cad2e00f42c9bcf54c9c2b00044526338815b446c6a0de7a3717bd3a555f316'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch new file mode 100644 index 00000000000..83bacd83cc8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch @@ -0,0 +1,15 @@ +# This fixes an incorrect autodetection of NeoverseV1 architecture at build time +# Fixes https://github.com/EESSI/software-layer/pull/310#issuecomment-1734345487 +--- cpuid_arm64.c.orig 2022-02-20 21:35:05.000000000 +0000 ++++ cpuid_arm64.c 2023-09-26 16:27:15.265602255 +0000 +@@ -73,8 +73,8 @@ + "TSV110", + "EMAG8180", + "NEOVERSEN1", +- "NEOVERSEV1" +- "NEOVERSEN2" ++ "NEOVERSEV1", ++ "NEOVERSEN2", + "THUNDERX3T110", + "VORTEX", + "CORTEXA55", From 1b7723a6b4900e74af463b74424fc5872305aa5c Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 26 Sep 2023 18:54:21 +0200 Subject: [PATCH 8901/9987] Fix patch description --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 2 +- .../o/OpenBLAS/OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index c4ab6957e00..8f055713230 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -32,7 +32,7 @@ checksums = [ {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, - {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': '2cad2e00f42c9bcf54c9c2b00044526338815b446c6a0de7a3717bd3a555f316'}, + {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': '1b495465f8dd1e151d74cf5aa4288120361d29164d6a377228a8d51c255b8a9e'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch index 83bacd83cc8..e638336abea 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch @@ -1,5 +1,7 @@ # This fixes an incorrect autodetection of NeoverseV1 architecture at build time # Fixes https://github.com/EESSI/software-layer/pull/310#issuecomment-1734345487 +# Patch was extracted from https://github.com/OpenMathLib/OpenBLAS/commit/09b8545fc51316d0fecf34c9e753b8a20358a3e8 +# which is part of https://github.com/OpenMathLib/OpenBLAS/pull/3586 (which is merged in OpenBLAS-0.3.21) --- cpuid_arm64.c.orig 2022-02-20 21:35:05.000000000 +0000 +++ cpuid_arm64.c 2023-09-26 16:27:15.265602255 +0000 @@ -73,8 +73,8 @@ From 8205d987ff382840dea02ff7f1191447d799ae10 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Sep 2023 19:59:05 +0200 Subject: [PATCH 8902/9987] fix long line in OpenBLAS 0.3.20 easyconfig --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 8f055713230..366c3730fef 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -32,7 +32,8 @@ checksums = [ {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, - {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': '1b495465f8dd1e151d74cf5aa4288120361d29164d6a377228a8d51c255b8a9e'}, + {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': + '1b495465f8dd1e151d74cf5aa4288120361d29164d6a377228a8d51c255b8a9e'}, ] builddependencies = [ From 1081c81707106723bdae6dd4b3553cbe8b74b7e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 26 Sep 2023 20:25:57 +0200 Subject: [PATCH 8903/9987] strip off trailing whitespace --- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 366c3730fef..1041b4ef6d3 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -32,7 +32,7 @@ checksums = [ {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, - {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': + {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': '1b495465f8dd1e151d74cf5aa4288120361d29164d6a377228a8d51c255b8a9e'}, ] From b6ce95acabb1ea69d6dcb63a95052fcc7c2c9ab9 Mon Sep 17 00:00:00 2001 From: xina Date: Tue, 26 Sep 2023 20:59:36 +0200 Subject: [PATCH 8904/9987] adding easyconfigs: xproto-7.0.31-GCCcore-12.3.0.eb --- .../x/xproto/xproto-7.0.31-GCCcore-12.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..0cbe506fc70 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = 'https://www.freedesktop.org/wiki/Software/xlibs' +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] + +builddependencies = [ + ('binutils', '2.40'), + ('xorg-macros', '1.20.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' From 3a4d4e3c8c2fd19ca49fbd1f26fe4cd4e894d1af Mon Sep 17 00:00:00 2001 From: xina Date: Tue, 26 Sep 2023 21:03:23 +0200 Subject: [PATCH 8905/9987] adding easyconfigs: makedepend-1.0.7-GCCcore-12.3.0.eb --- .../makedepend-1.0.7-GCCcore-12.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..6451e9a2465 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.7' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['17c1adf0284aaee473abfff0e8d3e754770615e1275f2a0043b9d97a00ed5cc9'] + +builddependencies = [ + ('binutils', '2.40'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.20.0'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' From 2640e1af0a85ff68381dffd6306a7b969ee38c5b Mon Sep 17 00:00:00 2001 From: xina Date: Tue, 26 Sep 2023 21:05:33 +0200 Subject: [PATCH 8906/9987] adding easyconfigs: Molden-7.3-GCCcore-12.3.0.eb and patches: Molden-7.3_fix_arg_handling.patch, Molden-7.3_fix_makefile_for_easybuild.patch --- .../m/Molden/Molden-7.3-GCCcore-12.3.0.eb | 48 ++++++++++++ .../Molden/Molden-7.3_fix_arg_handling.patch | 22 ++++++ ...olden-7.3_fix_makefile_for_easybuild.patch | 78 +++++++++++++++++++ 3 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f5a1c0e9c91 --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'Molden' +version = '7.3' + +homepage = 'https://www.theochem.ru.nl/molden/' +description = """Molden is a package for displaying Molecular Density from the + Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical + packages Mopac/Ampac""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.science.ru.nl/Molden/'] +sources = ['%(namelower)s%(version)s.tar.gz'] +patches = [ + 'Molden-7.3_fix_makefile_for_easybuild.patch', + 'Molden-7.3_fix_arg_handling.patch', +] +checksums = [ + {'molden7.3.tar.gz': '870f4fa6635229791bb09bbbd07f51456b2c90101d73564dc47ed7769b8c07a1'}, + {'Molden-7.3_fix_makefile_for_easybuild.patch': '303dcd308dfb618088d014ea2956ec627d9f09b6547d547ac4b432be4e5b9d7c'}, + {'Molden-7.3_fix_arg_handling.patch': '869eb33ea4cdd022402251b59386c146e7ceaf85f838f2a002fb4c393db4c1c2'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('makedepend', '1.0.7'), +] + +dependencies = [ + ('X11', '20230603'), + ('libglvnd', '1.6.0'), + ('libGLU', '9.0.3'), +] + +buildopts = 'CC="$CC" FC="$F90" FFLAGS="$FFLAGS -fallow-argument-mismatch" all' + +parallel = 1 + +files_to_copy = [(['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']], 'bin'), + 'CopyRight', 'README', 'REGISTER'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']] + ['README', 'REGISTER'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch new file mode 100644 index 00000000000..1b0d21594ec --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch @@ -0,0 +1,22 @@ +diff -ruN molden7.3.orig/src/molden.f molden7.3/src/molden.f +--- molden7.3.orig/src/molden.f 2023-08-09 15:22:58.503993000 +0200 ++++ molden7.3/src/molden.f 2023-09-26 20:13:01.426339279 +0200 +@@ -3814,15 +3814,15 @@ + endif + + iredir = 0 +- nargs = iargc() +- call getarg(0,liris) ++ nargs = COMMAND_ARGUMENT_COUNT() ++ call GET_COMMAND_ARGUMENT(0,liris) + call parsfn(liris,linlen(liris),20) + + ntargs = 0 + n = 0 + if (nargs.gt.0) then + 2013 n = n + 1 +- call getarg(n,liris) ++ call GET_COMMAND_ARGUMENT(n,liris) + if (liris(1:1).eq.'-') then + if (liris(1:2).eq.'-5') ido5d = 1 + if (liris(1:2).eq.'-7') ido7f = 1 diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch new file mode 100644 index 00000000000..595dfb9a0e0 --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch @@ -0,0 +1,78 @@ +diff -ruN molden7.3.orig/makefile molden7.3/makefile +--- molden7.3.orig/makefile 2023-08-09 15:22:58.725188000 +0200 ++++ molden7.3/makefile 2023-09-26 20:29:25.276603201 +0200 +@@ -13,10 +13,10 @@ + # Disregard compiler warnings on rdmolf.f + # + # +-CC = cc ++#CC = cc + LIBS = -lX11 -lm + LDR = ${FC} +-LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lXmu -lX11 -lm ++LIBSG = -lGLU -lGL -lXmu -lX11 -lm + ARCH := $(shell getconf LONG_BIT) + AFLAG= -m$(ARCH) + EXTEN= +@@ -29,19 +29,6 @@ + uname := $(shell uname -s) + os := + +-ifeq ($(uname), Linux) +- os := $(shell head -n 1 /etc/issue | cut -d" " -f1) +- ifeq ($(os), Ubuntu) +- EXTEN = exten +- EXTENZ = exten2 +- LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lX11 -lm +- endif +- ifeq ($(os), Debian) +- LIBSG = -L/usr/lib/X11 -lGLU -lGL -lX11 -lm +- endif +- +- choosefc := 'yes' +-endif + + ifneq (,$(findstring CYGWIN,$(uname))) + uname := Linux +@@ -53,17 +40,6 @@ + endif + + +-ifneq ($(choosefc), $(empty)) +- comg77 := $(shell which g77 | grep -i g77) +- comgfort := $(shell which gfortran | grep -i gfortran) +- ifneq ($(comg77), $(empty)) +- FC = g77 +- endif +- ifneq ($(comgfort), $(empty)) +- FC = gfortran +- endif +-endif +- + print-% : ; @echo $* = $($*) + # + # Linux version +@@ -109,17 +85,17 @@ + endif + #FFLAGS = -g ${AFLAG} + FFLAGS += -g ${AFLAG} +-LIBS = -L/usr/X11R6/lib -lX11 -lm ++LIBS = -lX11 -lm + ifeq ($(AFLAG),"-m64") +-LIBS = -L/usr/X11R6/lib64 -lX11 -lm ++LIBS = -lX11 -lm + endif + LDR = ${FC} -g ${AFLAG} +-CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 ++CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 + ifeq ($(os), Debian) +- CFLAGS = ${AFLAG} ${EXTRAZ} -c -I/usr/include/X11 -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 +- LIBS = -L/usr/lib/X11 -lX11 -lm ++ CFLAGS = ${AFLAG} ${EXTRAZ} -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 ++ LIBS = -lX11 -lm + ifeq ($(AFLAG),"-m64") +- LIBS = -L/usr/X11R6/lib64 -lX11 -lm ++ LIBS = -lX11 -lm + endif + endif + ifeq ($(os), FreeBSD) From eabdb55e81e071ccb08893472474ab91be2de62f Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Sep 2023 21:25:13 +0200 Subject: [PATCH 8907/9987] adding easyconfigs: GPAW-23.9.1-foss-2023a.eb, ASE-3.22.1-gfbf-2023a.eb, libvdwxc-0.4.0-foss-2023a.eb, Flask-2.3.3-GCCcore-12.3.0.eb, spglib-python-2.1.0-gfbf-2023a.eb, scikit-build-core-0.5.1-GCCcore-12.3.0.eb --- .../a/ASE/ASE-3.22.1-gfbf-2023a.eb | 64 +++++++++++++++++++ .../f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb | 61 ++++++++++++++++++ .../g/GPAW/GPAW-23.9.1-foss-2023a.eb | 50 +++++++++++++++ .../l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb | 27 ++++++++ .../scikit-build-core-0.5.1-GCCcore-12.3.0.eb | 27 ++++++++ .../spglib-python-2.1.0-gfbf-2023a.eb | 38 +++++++++++ 6 files changed, 267 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2023a.eb new file mode 100644 index 00000000000..d63319385b2 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2023a.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Flask', '2.3.3'), + ('matplotlib', '3.7.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.1.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.11.1', { + 'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'], + }), + ('ase', version, { + 'patches': [ + 'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch', + 'ASE-3.22.1-Compatibility-with-pytest-part-2.patch', + 'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch', + 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', + ], + 'checksums': [ + {'ase-3.22.1.tar.gz': '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'}, + {'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch': + '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac'}, + {'ASE-3.22.1-Compatibility-with-pytest-part-2.patch': + '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601'}, + {'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch': + 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8'}, + {'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch': + '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d'}, + ], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a37066c0753 --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '2.3.3' + +homepage = 'https://www.palletsprojects.com/p/flask/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06') +] + +builddependencies = [('binutils', '2.40')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('Werkzeug', '2.3.7', { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['2b8c0e447b4b9dbcc85dd97b6eeb4dcbaf6c8b6c3be0bd654e25553e0a2157d8'], + }), + ('asgiref', '3.7.2', { + 'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'], + }), + ('blinker', '1.6.2', { + 'checksums': ['4afd3de66ef3a9f8067559fb7a1cbe555c17dcbe15971b05d1b625c3e7abe213'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['09c347a92aa7ff4a8e7f3206795f30d826654baf38b873d0744cd571ca609efc'], + }), + ('Flask-Cors', '3.0.10', { + 'checksums': ['b60839393f3b84a0f3746f6cdca56c1ad7426aa738b70d6c61375857823181de'], + }), + ('cachelib', '0.10.2', { + 'checksums': ['593faeee62a7c037d50fc835617a01b887503f972fb52b188ae7e50e9cb69740'], + }), + ('Flask-Session', '0.5.0', { + 'checksums': ['190875e6aebf2953c6803d42379ef3b934bc209ef8ef006f97aecb08f5aaeb86'], + }), +] + +sanity_check_paths = { + 'files': ['bin/flask'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['flask --version'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2023a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2023a.eb new file mode 100644 index 00000000000..25eca6c86b9 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2023a.eb @@ -0,0 +1,50 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '23.9.1' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-23.9.1.tar.gz': '19a24840b876003528864b7a0b38fc0d456800b83b8666b1f724273660745b47'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('ASE', '3.22.1'), + ('libxc', '6.2.2'), + ('libvdwxc', '0.4.0'), + ('ELPA', '2023.05.001'), + ('PyYAML', '6.0'), + ('GPAW-setups', '0.9.20000', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb new file mode 100644 index 00000000000..9cf45cc3abe --- /dev/null +++ b/easybuild/easyconfigs/l/libvdwxc/libvdwxc-0.4.0-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libvdwxc' +version = '0.4.0' + +homepage = 'https://libvdwxc.org' +description = """libvdwxc is a general library for evaluating energy and potential for +exchange-correlation (XC) functionals from the vdW-DF family that can be used with various +of density functional theory (DFT) codes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://launchpad.net/libvdwxc/stable/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3524feb5bb2be86b4688f71653502146b181e66f3f75b8bdaf23dd1ae4a56b33'] + +preconfigopts = 'unset CC && unset FC && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['libvdwxc_fdtest', 'libvdwxc_maintest', + 'libvdwxc_q0test', 'libvdwxc_q0test2']] + + ['lib/lib%s.%s' % (x, y) for x in ['vdwxc', 'vdwxcfort'] + for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..76a3158a024 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'scikit-build-core' +version = '0.5.1' + +homepage = 'https://pypi.org/project/scikit-build-core' +description = "Scikit-build-core is a ground-up rewrite of the classic Scikit-build, a bridge between Python package build systems and CMake." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = ['scikit_build_core-%(version)s.tar.gz'] +checksums = ['c6dad5a5127b2abfaa23cb91d23ac21059fd77cddf7122b33fd07791024dcfbf'] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('hatchling', '1.18.0'), + ('CMake', '3.26.3'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb new file mode 100644 index 00000000000..3920668503e --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'spglib-python' +version = '2.1.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('scikit-build-core', '0.5.1') +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyproject-metadata', '0.7.1', { + 'checksums': ['0a94f18b108b9b21f3a26a3d541f056c34edcb17dc872a144a15618fed7aef67'], + }), + (name, version, { + 'modulename': 'spglib', + 'sources': ['spglib-%(version)s.tar.gz'], + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'], + 'checksums': ['8143545fdffc11fbcda4d705a6b6bcd4889de9bc3524b78df866a36dd0de0a4b'], + }), +] + +moduleclass = 'chem' From d8272b73a9fa2afb0abc3984bb0fe7a9cfbe080b Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Sep 2023 21:54:52 +0200 Subject: [PATCH 8908/9987] Fix errors found by CI. --- .../scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb | 2 ++ .../s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb | 1 - 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb index 76a3158a024..8bff41d8788 100644 --- a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb @@ -12,6 +12,8 @@ source_urls = [PYPI_LOWER_SOURCE] sources = ['scikit_build_core-%(version)s.tar.gz'] checksums = ['c6dad5a5127b2abfaa23cb91d23ac21059fd77cddf7122b33fd07791024dcfbf'] +builddependencies = [('binutils', '2.40')] + dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb index 3920668503e..57314d3ebd1 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb @@ -18,7 +18,6 @@ dependencies = [ ('SciPy-bundle', '2023.07'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From d198e1db50f987d8249ed8f5ae6bb2280d3b13b9 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Sep 2023 22:24:22 +0200 Subject: [PATCH 8909/9987] Fix errors found by CI. --- .../s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb index 57314d3ebd1..d79e02fba78 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb @@ -4,7 +4,7 @@ name = 'spglib-python' version = '2.1.0' homepage = 'https://pypi.python.org/pypi/spglib' -description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." +description = "Spglib for Python - for finding and handling crystal symmetries written in C." toolchain = {'name': 'gfbf', 'version': '2023a'} From 8c5b03072ee820a863905298a4fbf41ce1411f13 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 26 Sep 2023 22:41:23 +0200 Subject: [PATCH 8910/9987] Fix errors found by CI (take 3). --- .../scikit-build-core-0.5.1-GCCcore-12.3.0.eb | 4 +++- .../s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb | 5 ++++- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb index 8bff41d8788..f2c59d3faec 100644 --- a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb @@ -4,7 +4,9 @@ name = 'scikit-build-core' version = '0.5.1' homepage = 'https://pypi.org/project/scikit-build-core' -description = "Scikit-build-core is a ground-up rewrite of the classic Scikit-build, a bridge between Python package build systems and CMake." +description = """Scikit-build-core is a ground-up rewrite of the classic Scikit-build, +a bridge between Python package build systems and CMake. +""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb index d79e02fba78..392d2d01b8d 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb @@ -4,7 +4,10 @@ name = 'spglib-python' version = '2.1.0' homepage = 'https://pypi.python.org/pypi/spglib' -description = "Spglib for Python - for finding and handling crystal symmetries written in C." +description = """Spglib for Python. + +Spglib is a library for finding and handling crystal symmetries written in C. +""" toolchain = {'name': 'gfbf', 'version': '2023a'} From 0ef534547a318ede5dcd6d9d41669e31e8098b41 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 27 Sep 2023 08:39:32 +0200 Subject: [PATCH 8911/9987] Add sanity_check_commands MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.2.0.eb index 21074cc6cfc..089bb508103 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.2.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' From b22ffd049e77243654a8c6ce5c192563feee0c94 Mon Sep 17 00:00:00 2001 From: NPotvin <15875457+NPotvin@users.noreply.github.com> Date: Wed, 27 Sep 2023 11:19:51 +0200 Subject: [PATCH 8912/9987] Update easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.1-GCCcore-12.2.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../l/line_profiler/line_profiler-4.1.1-GCCcore-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.1-GCCcore-12.2.0.eb index 0908ba1bbf6..72ba302b5e7 100644 --- a/easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/line_profiler/line_profiler-4.1.1-GCCcore-12.2.0.eb @@ -17,6 +17,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['71c150bf06dd964fc0e5fbc3a5eb31bbee03c535d31c9548999c3e0302dcbb27'] builddependencies = [ + ('binutils', '2.39'), ('scikit-build', '0.17.2'), ('CMake', '3.24.3'), ('Ninja', '1.11.1'), From 7a1088d202b1e547cefdb17e9a668c6523cd3bde Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Wed, 27 Sep 2023 14:56:09 +0200 Subject: [PATCH 8913/9987] fix dcmake cuda arch parameter --- .../p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index 05edbed72aa..e19d38ca142 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -56,7 +56,7 @@ configopts += '-DVTK_ENABLE_OPTIX=ON ' configopts += '-DPARAVIEW_ENABLE_XDMF2=ON ' configopts += '-DPARAVIEW_ENABLE_XDMF3=ON ' configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' -configopts += '-DCMAKE_CUDA_ARCHITECTURES=70 72 80 86 87 89 90 90a ' +configopts += '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s" ' # OpenGL & Mesa configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' configopts += '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include ' From ccaeebc51b3d523d55a206aab7449c5b3380f410 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 27 Sep 2023 16:58:28 +0200 Subject: [PATCH 8914/9987] update intel/2023.07 to GCCcore/13.2.0 as base compiler --- .../i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb | 2 +- .../easyconfigs/i/intel-compilers/intel-compilers-2023.2.1.eb | 2 +- easybuild/easyconfigs/i/intel/intel-2023.07.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb index e1064214201..eb2fc40a9c3 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb @@ -11,6 +11,6 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/4f58 sources = ['l_mpi_oneapi_p_%(version)s.49374_offline.sh'] checksums = ['ab2e97d87b139201a2e7dab9a61ac6e8927b7783b459358c4ad69a1b1c064f40'] -dependencies = [('UCX', '1.14.1')] +dependencies = [('UCX', '1.15.0-rc4')] moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.2.1.eb index 8fcb11f30e5..ee6cfeb0026 100644 --- a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.2.1.eb +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.2.1.eb @@ -28,7 +28,7 @@ checksums = [ 'd4e36abc014c184698fec318a127f15a696b5333b3b0282aba1968b351207185'}, ] -local_gccver = '12.3.0' +local_gccver = '13.2.0' dependencies = [ ('GCCcore', local_gccver), ('binutils', '2.40', '', ('GCCcore', local_gccver)), diff --git a/easybuild/easyconfigs/i/intel/intel-2023.07.eb b/easybuild/easyconfigs/i/intel/intel-2023.07.eb index d301a7461bd..fbb6901e524 100644 --- a/easybuild/easyconfigs/i/intel/intel-2023.07.eb +++ b/easybuild/easyconfigs/i/intel/intel-2023.07.eb @@ -9,7 +9,7 @@ description = "Compiler toolchain including Intel compilers, Intel MPI and Intel toolchain = SYSTEM local_comp_ver = '2023.2.1' -local_gccver = '12.3.0' +local_gccver = '13.2.0' dependencies = [ ('GCCcore', local_gccver), ('binutils', '2.40', '', ('GCCcore', local_gccver)), From df917cf263543ece99846b2c7c3e6331274eaa4f Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 27 Sep 2023 17:15:50 +0200 Subject: [PATCH 8915/9987] Add libarchive as dependency to GDAL-3.7.1-foss-2023a.eb --- easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb index 6586149b8d2..98acb56d8b6 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb @@ -32,6 +32,7 @@ dependencies = [ ('expat', '2.5.0'), ('GEOS', '3.12.0'), ('SQLite', '3.42.0'), + ('libarchive', '3.6.2'), ('libxml2', '2.11.4'), ('libpng', '1.6.39'), ('libjpeg-turbo', '2.1.5.1'), From 917c92d61c4045fa99fcd02bd600b63e935d46f4 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Wed, 27 Sep 2023 17:28:28 +0200 Subject: [PATCH 8916/9987] fix configopts formatting --- .../ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 45 +++++++++---------- 1 file changed, 21 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index e19d38ca142..9d0590de609 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -42,30 +42,27 @@ dependencies = [ ('Szip', '2.1.1'), ] -# Paraview -configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' -configopts += '-DPARAVIEW_USE_MPI=ON ' -# Enable NVidia IndeX -configopts += '-DPARAVIEW_USE_CUDA=ON ' -configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' -configopts += '-DPARAVIEW_USE_PYTHON=ON ' -# Enable OptiX raytracing -configopts += '-DPARAVIEW_ENABLE_RAYTRACING=ON ' -configopts += '-DVTK_ENABLE_OSPRAY=OFF ' -configopts += '-DVTK_ENABLE_OPTIX=ON ' -configopts += '-DPARAVIEW_ENABLE_XDMF2=ON ' -configopts += '-DPARAVIEW_ENABLE_XDMF3=ON ' -configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' -configopts += '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s" ' -# OpenGL & Mesa -configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' -configopts += '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include ' -configopts += '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s ' % SHLIB_EXT -configopts += '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s ' % SHLIB_EXT -configopts += '-DVTK_OPENGL_HAS_EGL=ON ' -configopts += '-DVTK_USE_X=ON ' -configopts += '-DVTK_OPENGL_HAS_OSMESA=OFF ' - +_copts = [ + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON', + '-DPARAVIEW_USE_MPI=ON', + '-DPARAVIEW_USE_CUDA=ON', + '-DPARAVIEW_ENABLE_FFMPEG=ON', + '-DPARAVIEW_USE_PYTHON=ON', + '-DPARAVIEW_ENABLE_RAYTRACING=ON', + '-DVTK_ENABLE_OSPRAY=OFF', + '-DVTK_ENABLE_OPTIX=ON', + '-DPARAVIEW_ENABLE_XDMF2=ON', + '-DPARAVIEW_ENABLE_XDMF3=ON', + '-DPython3_ROOT_DIR=$EBROOTPYTHON', + '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s"', + '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include', + '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include', + '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s' % SHLIB_EXT, + '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, + '-DVTK_OPENGL_HAS_EGL=ON', + '-DVTK_USE_X=ON', + '-DVTK_OPENGL_HAS_OSMESA=OFF'] +configopts = ' '.join(_copts) sanity_check_paths = { 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], From ad6ce02e8c1c35e1ad01ce2185f743def6427115 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Wed, 27 Sep 2023 17:31:01 +0200 Subject: [PATCH 8917/9987] fix configopts formatting --- .../p/ParaView/ParaView-5.11.1-foss-2022b.eb | 37 +++++++++---------- 1 file changed, 17 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb index e751b3fb53b..681a2345c54 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb @@ -37,26 +37,23 @@ dependencies = [ ('Szip', '2.1.1'), ] -# Paraview -configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' -configopts += '-DPARAVIEW_USE_MPI=ON ' -configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' -configopts += '-DPARAVIEW_USE_PYTHON=ON ' -configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' -# Useful file format support -configopts += '-DPARAVIEW_ENABLE_XDMF2=ON ' -configopts += '-DPARAVIEW_ENABLE_XDMF3=ON ' - -# OpenGL & Mesa -configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT -configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' -configopts += '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include ' -configopts += '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s ' % SHLIB_EXT -configopts += '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s ' % SHLIB_EXT -configopts += '-DVTK_OPENGL_HAS_EGL=ON ' -configopts += '-DVTK_USE_X=ON ' -configopts += '-DVTK_OPENGL_HAS_OSMESA=OFF ' - +_copts = [ + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON', + '-DPARAVIEW_USE_MPI=ON', + '-DPARAVIEW_ENABLE_FFMPEG=ON', + '-DPARAVIEW_USE_PYTHON=ON', + '-DPARAVIEW_ENABLE_XDMF2=ON', + '-DPARAVIEW_ENABLE_XDMF3=ON', + '-DPython3_ROOT_DIR=$EBROOTPYTHON', + '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s' % SHLIB_EXT + '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include', + '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include', + '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s' % SHLIB_EXT, + '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, + '-DVTK_OPENGL_HAS_EGL=ON', + '-DVTK_USE_X=ON', + '-DVTK_OPENGL_HAS_OSMESA=OFF'] +configopts = ' '.join(_copts) sanity_check_paths = { 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], From 687bf19b8201bfecfc3c0c55096ff825493b5d03 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Wed, 27 Sep 2023 17:34:16 +0200 Subject: [PATCH 8918/9987] Update ParaView-5.11.1-foss-2022b.eb --- easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb index 681a2345c54..d804438b51e 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb @@ -45,7 +45,7 @@ _copts = [ '-DPARAVIEW_ENABLE_XDMF2=ON', '-DPARAVIEW_ENABLE_XDMF3=ON', '-DPython3_ROOT_DIR=$EBROOTPYTHON', - '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s' % SHLIB_EXT + '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s' % SHLIB_EXT, '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include', '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include', '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s' % SHLIB_EXT, From b8d8240ebeb11349cd8166025e5da6149e53dc8f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 27 Sep 2023 22:11:34 +0200 Subject: [PATCH 8919/9987] adding easyconfigs: CMake-3.27.6-GCCcore-13.2.0.eb, bzip2-1.0.8-GCCcore-13.2.0.eb, cURL-8.3.0-GCCcore-13.2.0.eb, libarchive-3.7.2-GCCcore-13.2.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-13.2.0.eb | 27 ++++++++++++ .../c/CMake/CMake-3.27.6-GCCcore-13.2.0.eb | 30 +++++++++++++ .../c/cURL/cURL-8.3.0-GCCcore-13.2.0.eb | 43 +++++++++++++++++++ .../libarchive-3.7.2-GCCcore-13.2.0.eb | 33 ++++++++++++++ 4 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.27.6-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-8.3.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.7.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3ce27b74c39 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.40'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.27.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.27.6-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..04b7770a077 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.27.6-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.27.6' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef3056df528569e0e8956f6cf38806879347ac6de6a4ff7e4105dc4578732cfb'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('cURL', '8.3.0'), + ('libarchive', '3.7.2'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-8.3.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-8.3.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..4b937590771 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-8.3.0-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '8.3.0' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d3a19aeea301085a56c32bc0f7d924a818a7893af253e41505d1e26d7db8e95a'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.7.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.7.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c31b668a246 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.7.2-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.7.2' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['df404eb7222cf30b4f8f93828677890a2986b66ff8bf39dac32a804e96ddf104'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('XZ', '5.4.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' From 462c7c6afd5a6cb88de5660dc9d9b2f233fae273 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 28 Sep 2023 09:57:40 +0200 Subject: [PATCH 8920/9987] Update ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb --- .../ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index 9d0590de609..8f312f89318 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -43,18 +43,24 @@ dependencies = [ ] _copts = [ - '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON', + # Basic configuration + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON' + '-DPARAVIEW_BUILD_SHARED_LIBS=ON', '-DPARAVIEW_USE_MPI=ON', - '-DPARAVIEW_USE_CUDA=ON', '-DPARAVIEW_ENABLE_FFMPEG=ON', '-DPARAVIEW_USE_PYTHON=ON', + # CUDA (Vtk-m) + '-DPARAVIEW_USE_CUDA=ON', + '-DPython3_ROOT_DIR=$EBROOTPYTHON', + '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s"', + # Hardware but not software raytracing support '-DPARAVIEW_ENABLE_RAYTRACING=ON', '-DVTK_ENABLE_OSPRAY=OFF', '-DVTK_ENABLE_OPTIX=ON', + # Useful input formats '-DPARAVIEW_ENABLE_XDMF2=ON', '-DPARAVIEW_ENABLE_XDMF3=ON', - '-DPython3_ROOT_DIR=$EBROOTPYTHON', - '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s"', + # EGL, X and Mesa '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include', '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include', '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s' % SHLIB_EXT, From 73981629b17c1099f8f06e077dff45f26ac584f0 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 28 Sep 2023 10:00:26 +0200 Subject: [PATCH 8921/9987] Update ParaView-5.11.1-foss-2022b.eb --- .../easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb index d804438b51e..a495c8da450 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b.eb @@ -38,13 +38,17 @@ dependencies = [ ] _copts = [ - '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON', + # Basic configuration + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', + '-DPARAVIEW_BUILD_SHARED_LIBS=ON', '-DPARAVIEW_USE_MPI=ON', '-DPARAVIEW_ENABLE_FFMPEG=ON', '-DPARAVIEW_USE_PYTHON=ON', + '-DPython3_ROOT_DIR=$EBROOTPYTHON', + # Useful input formats '-DPARAVIEW_ENABLE_XDMF2=ON', '-DPARAVIEW_ENABLE_XDMF3=ON', - '-DPython3_ROOT_DIR=$EBROOTPYTHON', + # EGL, X and Mesa '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s' % SHLIB_EXT, '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include', '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include', From a54300cf0925f519f29a198e2e2a3d9ae27a583c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Sep 2023 12:03:01 +0200 Subject: [PATCH 8922/9987] use UCX 1.14.1 instead of 1.15.0-rc4 --- .../o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb | 2 +- .../u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb | 2 +- ...13.2.0.eb => UCX-1.14.1-GCCcore-13.2.0.eb} | 11 ++++--- ..._fix-type-conflict-uct_md_mem_advise.patch | 31 +++++++++++++++++++ 4 files changed, 39 insertions(+), 7 deletions(-) rename easybuild/easyconfigs/u/UCX/{UCX-1.15.0-rc4-GCCcore-13.2.0.eb => UCX-1.14.1-GCCcore-13.2.0.eb} (78%) create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb index ba58f99e8e3..6d402e8a4ec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb @@ -33,7 +33,7 @@ dependencies = [ ('zlib', '1.2.13'), ('hwloc', '2.9.2'), ('libevent', '2.1.12'), - ('UCX', '1.15.0-rc4'), + ('UCX', '1.14.1'), ('libfabric', '1.19.0'), ('PMIx', '4.2.5'), ('UCC', '1.2.0'), diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb index 0f206f09331..7013dcbf911 100644 --- a/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb @@ -26,7 +26,7 @@ builddependencies = [ ] dependencies = [ - ('UCX', '1.15.0-rc4'), + ('UCX', '1.14.1'), ] preconfigopts = "./autogen.sh && " diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.15.0-rc4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-13.2.0.eb similarity index 78% rename from easybuild/easyconfigs/u/UCX/UCX-1.15.0-rc4-GCCcore-13.2.0.eb rename to easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-13.2.0.eb index 3d194284424..253b43fceca 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.15.0-rc4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-13.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'UCX' -version = '1.15.0-rc4' +version = '1.14.1' homepage = 'https://www.openucx.org/' description = """Unified Communication X @@ -13,15 +13,16 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -# TODO: Uncomment when updating to final release -# sources = ['%(namelower)s-%(version)s.tar.gz'] -sources = ['%(namelower)s-1.15.0.tar.gz'] +sources = ['%(namelower)s-%(version)s.tar.gz'] patches = [ 'UCX-1.13.1-dynamic_modules.patch', + 'UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch', ] checksums = [ - {'ucx-1.15.0.tar.gz': 'aa1e71de64dbc3061454dbe7510a38b930f7c184ec889c09f5611c2d4acaf07a'}, + {'ucx-1.14.1.tar.gz': 'baa0634cafb269a3112f626eb226bcd2ca8c9fcf0fec3b8e2a3553baad5f77aa'}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, + {'UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch': + '9fbf26b39cd5c9e469ff152e18d79a4bf685fca175d4088b9bbe8644b74c1401'}, ] # Uncomment when updating to final release diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch b/easybuild/easyconfigs/u/UCX/UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch new file mode 100644 index 00000000000..492bacf17b3 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch @@ -0,0 +1,31 @@ +From 8d6032ec864190c9f079d96e731c5004a975e153 Mon Sep 17 00:00:00 2001 +From: Jan Ciesko +Date: Thu, 5 Jan 2023 12:31:39 -0800 +Subject: [PATCH] UCT/BASE: Fix conflicting types for 'uct_md_mem_advise'. + +Signed-off-by: Howard Pritchard +--- + src/uct/base/uct_md.c | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/src/uct/base/uct_md.c b/src/uct/base/uct_md.c +index d7f4c326c0b..3830e16618b 100644 +--- a/src/uct/base/uct_md.c ++++ b/src/uct/base/uct_md.c +@@ -2,6 +2,7 @@ + * Copyright (c) NVIDIA CORPORATION & AFFILIATES, 2001-2014. ALL RIGHTS RESERVED. + * Copyright (C) UT-Battelle, LLC. 2015. ALL RIGHTS RESERVED. + * Copyright (C) ARM Ltd. 2016-2017. ALL RIGHTS RESERVED. ++* Copyright (c) Triad National Security, LLC. 2023. ALL RIGHTS RESERVED. + * + * See file LICENSE for terms. + */ +@@ -554,7 +555,7 @@ ucs_status_t uct_md_mem_free(uct_md_h md, uct_mem_h memh) + + ucs_status_t + uct_md_mem_advise(uct_md_h md, uct_mem_h memh, void *addr, size_t length, +- unsigned advice) ++ uct_mem_advice_t advice) + { + if ((length == 0) || (addr == NULL)) { + return UCS_ERR_INVALID_PARAM; From 7b1eb2cad80a96a358a62c8f9a3b849fa382d0b9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Sep 2023 12:09:17 +0200 Subject: [PATCH 8923/9987] fix source URL for segemehl 0.3.4 --- easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.3.0.eb | 2 +- easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-8.3.0.eb | 2 +- easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-foss-2018b.eb | 2 +- .../s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb index f6c29cfd247..80454f74e01 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.2.0.eb @@ -14,7 +14,7 @@ description = """segemehl is a software to map short sequencer reads to referenc toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['https://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] +source_urls = ['http://legacy.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.3.0.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.3.0.eb index 38fb0cbe9c3..9b5f304a8f3 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-10.3.0.eb @@ -14,7 +14,7 @@ description = """segemehl is a software to map short sequencer reads to referenc toolchain = {'name': 'GCC', 'version': '10.3.0'} -source_urls = ['https://www.bioinf.uni-leipzig.de/Software/%(name)s/downloads/'] +source_urls = ['http://legacy.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-11.2.0.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-11.2.0.eb index d97799dd2d0..6bcb70c71ca 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-11.2.0.eb @@ -14,7 +14,7 @@ description = """segemehl is a software to map short sequencer reads to referenc toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ['https://www.bioinf.uni-leipzig.de/Software/%(name)s/downloads/'] +source_urls = ['http://legacy.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-8.3.0.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-8.3.0.eb index ba8b90537df..24a9d475ca2 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-GCC-8.3.0.eb @@ -14,7 +14,7 @@ description = """segemehl is a software to map short sequencer reads to referenc toolchain = {'name': 'GCC', 'version': '8.3.0'} -source_urls = ['https://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] +source_urls = ['http://legacy.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-foss-2018b.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-foss-2018b.eb index aa8fab696d1..6079ca070ef 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-foss-2018b.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-foss-2018b.eb @@ -16,7 +16,7 @@ description = """ segemehl is a software to map short sequencer reads to referen toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['http://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] +source_urls = ['http://legacy.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] diff --git a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb index 1dba3da2387..e9ae1cd8875 100644 --- a/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/s/segemehl/segemehl-0.3.4-iccifort-2020.4.304.eb @@ -14,7 +14,7 @@ description = """segemehl is a software to map short sequencer reads to referenc toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://www.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] +source_urls = ['http://legacy.bioinf.uni-leipzig.de/Software/segemehl/downloads/'] sources = [SOURCE_TAR_GZ] checksums = ['e4336f03d0d15126dbb1c6368c7e80421b0c7354f4a6b492d54d7d14cf5a7f51'] From 05e021d39a49611cee220081ca415994fe117301 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Sep 2023 13:13:46 +0200 Subject: [PATCH 8924/9987] {lang}[GCCcore/13.2.0] Python v3.11.5 --- .../l/libffi/libffi-3.4.4-GCCcore-13.2.0.eb | 29 +++++++++ .../libreadline-8.2-GCCcore-13.2.0.eb | 41 +++++++++++++ .../p/Python/Python-3.11.5-GCCcore-13.2.0.eb | 58 ++++++++++++++++++ .../s/SQLite/SQLite-3.43.1-GCCcore-13.2.0.eb | 39 ++++++++++++ .../t/Tcl/Tcl-8.6.13-GCCcore-13.2.0.eb | 41 +++++++++++++ .../u/UnZip/UnZip-6.0-GCCcore-13.2.0.eb | 59 +++++++++++++++++++ 6 files changed, 267 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.43.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..220c7453d65 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.4' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d66c56ad259a82cf2a9dfc408b32bf5da52371500b84745f7fb8b645712df676'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..81be0d3a261 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.2' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['3feb7171f16a84ee82ca18a36d7b9be109a52c04f492a053331d7d1095007c35'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('ncurses', '6.4'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..476b535940a --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb @@ -0,0 +1,58 @@ +name = 'Python' +version = '3.11.5' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['a12a0a013a30b846c786c010f2c19dd36b7298d888f7c4bd1581d90ce18b5e58'] + +builddependencies = [ + ('UnZip', '6.0'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('binutils', '2.40'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.13'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('SQLite', '3.43.1'), + ('XZ', '5.4.4'), + ('libffi', '3.4.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 2023-05-17 +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('wheel', '0.41.2', { + 'checksums': ['0c5ac5ff2afb79ac23ab82bab027a0be7b5dbcf2e54dc50efe4bf507de1f7985'], + }), + ('setuptools', '68.2.2', { + 'checksums': ['4ac1475276d2f1c48684874089fefcd83bd7162ddaafb81fac866ba0db282a87'], + }), + ('pip', '23.2.1', { + 'checksums': ['fb0bd5435b3200c602b5bf61d2d43c2f13c02e29c1707567ae7fbc514eb9faf2'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.43.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.43.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d2b70cc4ec2 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.43.1-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.43.1' +local_filename_version = '3430100' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2023/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['39116c94e76630f22d54cd82c3cea308565f1715f716d1b2527f1c9c969ba4d9'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('libreadline', '8.2'), + ('Tcl', '8.6.13'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d23dd269e1d --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.13' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['43a1fae7412f61ff11de2cfd05d28cfc3a73762f354a417c62370a54e2caf066'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('zlib', '1.2.13'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..95d1743751f --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.2.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT' + '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD', + '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT'] + +buildopts = ' '.join([ + "-f unix/Makefile", + 'CC="$CC"', + 'D_USE_BZ2=-DUSE_BZIP2', + 'L_BZ2=-lbz2', + 'LF2="$LDFLAGS"', + 'CF="%s"' % ' '.join(local_cf), + 'unzips', +]) + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From 8f7b6c3cf5ac5517c9963dca3d6e6f26afb99cd4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Sep 2023 13:15:16 +0200 Subject: [PATCH 8925/9987] {numlib}[GCC/13.2.0] OpenBLAS v0.3.24 --- .../m/make/make-4.4.1-GCCcore-13.2.0.eb | 29 ++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb | 45 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..48803d5731a --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.4.1' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['dd16fb1d67bfab79a72f5e8390735c49e3e8e70b4945a15ab1f81ddb78658fb3'] + +builddependencies = [('binutils', '2.40')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb new file mode 100644 index 00000000000..ae38d447c1f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb @@ -0,0 +1,45 @@ +name = 'OpenBLAS' +version = '0.3.24' + +homepage = 'http://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.23_fix-lapack-test.patch', +] +checksums = [ + {'v0.3.24.tar.gz': 'ceadc5065da97bd92404cac7254da66cc6eb192679cf1002098688978d4d5132'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.23_fix-lapack-test.patch': 'f6b3d81061f136e34aaf5359bb80fb9d2bba28825cc1dd26179b8dd01a9a0054'}, +] + +builddependencies = [ + ('make', '4.4.1'), + # required by LAPACK test suite + ('Python', '3.11.5'), +] + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From cef8ba9aba1a9f6bf26b5f643e42078e4a5388a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Sep 2023 14:44:41 +0200 Subject: [PATCH 8926/9987] rework LevelDB easyconfig with GCCcore/11.3.0 to install Python bindings as extension + run 'pip check' as sanity check command --- .../l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb | 36 +++++++++---------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb index 66a233cae44..35889241c08 100644 --- a/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.22-GCCcore-11.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'CMakeMake' name = 'LevelDB' version = '1.22' @@ -9,6 +9,10 @@ ordered mapping from string keys to string values.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +source_urls = ['https://github.com/google/leveldb/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['55423cac9e3306f4a9502c738a001e4a339d1a38ffbee7572d4a07d5d63949b2'] + builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), @@ -18,35 +22,31 @@ dependencies = [ ('Python', '3.10.4'), ] -default_easyblock = 'CMakeMake' +configopts = "-DBUILD_SHARED_LIBS=ON -DLEVELDB_BUILD_BENCHMARKS=OFF " -default_component_specs = { - 'start_dir': '%(namelower)s-%(version)s', +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, } -components = [ - ('LevelDB', version, { - 'source_urls': ['https://github.com/google/leveldb/archive/'], - 'sources': ['%(version)s.tar.gz'], - 'configopts': "-DBUILD_SHARED_LIBS=ON -DLEVELDB_BUILD_BENCHMARKS=OFF ", - 'checksums': ['55423cac9e3306f4a9502c738a001e4a339d1a38ffbee7572d4a07d5d63949b2'], - }), +exts_list = [ ('leveldb', '0.201', { - 'easyblock': 'PythonPackage', - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'use_pip': True, - 'download_dep_fail': True, 'checksums': ['1cffe776842917e09f073bd6ea5856c64136aebddbe51bd17ea29913472fecbf'], }), ] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} sanity_check_paths = { 'files': ['include/leveldb/cache.h', 'include/leveldb/table.h', 'lib/libleveldb.%s' % SHLIB_EXT], - 'dirs': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["pip check"] + moduleclass = 'devel' From bfbfd9af9eba28bfe120d4a64a1061a42a6ad27d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Sep 2023 14:45:14 +0200 Subject: [PATCH 8927/9987] minor tweaks in easyconfig for biobakery-workflows --- .../a/anadama2/anadama2-0.10.0-foss-2022a.eb | 3 +-- .../biobakery-workflows-3.1-foss-2022a.eb | 18 +++++++++++------- .../k/kneaddata/kneaddata-0.12.0-foss-2022a.eb | 1 - 3 files changed, 12 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb index c6b84442785..6a4a30dac5d 100644 --- a/easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/anadama2/anadama2-0.10.0-foss-2022a.eb @@ -4,7 +4,6 @@ name = 'anadama2' version = '0.10.0' homepage = 'http://huttenhower.sph.harvard.edu/anadama2' - description = """AnADAMA2 is the next generation of AnADAMA (Another Automated Data Analysis Management Application). AnADAMA is a tool to create reproducible workflows and execute them efficiently.""" @@ -30,8 +29,8 @@ exts_list = [ 'checksums': ['5e5298d90e06414a01f48e0d6aa4c36a70c5f223d929f2a9c7e2d388451c7357'], }), (name, version, { - 'preinstallopts': 'sed -i "s/==0.25//g" requirements.txt && ', 'checksums': ['386c4d0f4c96bf078ac2b595bafcadaa43cd44cdb1a864dc8ebc42dc1664f87f'], + 'preinstallopts': 'sed -i "s/pweave==0.25/pweave/g" requirements.txt && ', }), ] diff --git a/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb b/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb index 0ece4a894e7..7fc8fe63552 100644 --- a/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/b/biobakery-workflows/biobakery-workflows-3.1-foss-2022a.eb @@ -4,7 +4,6 @@ name = 'biobakery-workflows' version = '3.1' homepage = 'http://huttenhower.sph.harvard.edu/biobakery_workflows' - description = """bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data @@ -15,24 +14,29 @@ and in a grid compute environment.""" toolchain = {'name': 'foss', 'version': '2022a'} -dependencies = { +sources = ["biobakery_workflows-%(version)s.tar.gz"] +checksums = ['c11a00192aa0bd6a6978eabef768c483dd240281991ce2a31bfaf291fe3d0e2b'] + +dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('kneaddata', '0.12.0'), ('humann', '3.6'), ('MetaPhlAn', '4.0.6'), ('anadama2', '0.10.0'), -} - -sources = ["biobakery_workflows-%(version)s.tar.gz"] -checksums = ['c11a00192aa0bd6a6978eabef768c483dd240281991ce2a31bfaf291fe3d0e2b'] +] use_pip = True download_dep_fail = True sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/biobakery_workflows'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + sanity_check_commands = [ - """biobakery_workflows --help""", + "biobakery_workflows --help", ] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb b/easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb index 7c984435009..0a640c31fb6 100644 --- a/easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb +++ b/easybuild/easyconfigs/k/kneaddata/kneaddata-0.12.0-foss-2022a.eb @@ -4,7 +4,6 @@ name = 'kneaddata' version = '0.12.0' homepage = 'http://huttenhower.sph.harvard.edu/kneaddata' - description = """KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.""" From 788d827cf48fa1d595cb5d629c9bbacb80488ff0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Sep 2023 14:52:06 +0200 Subject: [PATCH 8928/9987] add extra sanity check command for TopHat --- .../t/TopHat/TopHat-2.1.2-GCC-11.2.0-Python-2.7.18.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.2.0-Python-2.7.18.eb index 068f10e7ce3..9a9f8d86dc5 100644 --- a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.2-GCC-11.2.0-Python-2.7.18.eb @@ -49,6 +49,9 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ['tophat --version'] +sanity_check_commands = [ + "tophat --help 2>&1 | grep 'TopHat maps short sequences'", + "tophat --version", +] moduleclass = 'bio' From f779806df50cbb7bded7bba703045992379272c6 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 28 Sep 2023 14:56:30 +0200 Subject: [PATCH 8929/9987] avoid hardcoded paths for pillow --- easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb | 2 ++ .../p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 2 ++ easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb | 2 ++ 13 files changed, 26 insertions(+) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb index 85a73b42332..21d8071c49b 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb @@ -24,6 +24,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb index 02e02a6573a..69b903e8658 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb @@ -25,6 +25,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True options = {'modulename': 'PIL'} diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb index 13dee61b577..072bc27459c 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb @@ -25,6 +25,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True options = {'modulename': 'PIL'} diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb index 9fc85ff2e06..0e9cf1b4445 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -29,6 +29,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 7bdf2476477..6c8f256ce9a 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -28,6 +28,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb index 42cbf229337..6274b50e9b0 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb @@ -28,6 +28,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb index a9516e2ab73..4b4a35c2651 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb @@ -28,6 +28,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb index 9567cc977dd..098deac80fa 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb @@ -24,6 +24,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb index cf7bb373ec2..caa9fcf574f 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb @@ -24,6 +24,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb index 1d53e76e777..6516e4b933b 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb @@ -24,6 +24,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb index 137475682e6..1105bf2154e 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb @@ -24,6 +24,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb index 38e7492daf9..f925080a099 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -26,6 +26,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb index 5060e93e3b2..cb1ef19b3f0 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb @@ -24,6 +24,8 @@ dependencies = [ ] download_dep_fail = True +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True sanity_pip_check = True From 7782fc3c74c0c281410e8bb1b201d79231fd059a Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 28 Sep 2023 15:32:39 +0200 Subject: [PATCH 8930/9987] avoid hardcoded paths for pillow --- easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb | 1 + easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb index 69b903e8658..fa078fe683a 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb @@ -28,6 +28,7 @@ download_dep_fail = True # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True +sanity_pip_check = True options = {'modulename': 'PIL'} diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb index 072bc27459c..5bd030dd974 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb @@ -28,6 +28,7 @@ download_dep_fail = True # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " use_pip = True +sanity_pip_check = True options = {'modulename': 'PIL'} From bc8d067b21c3c2c4fbc703c7e525ef65c091ea2e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 28 Sep 2023 16:46:36 +0200 Subject: [PATCH 8931/9987] adding easyconfigs: BLIS-0.9.0-GCC-13.2.0.eb --- .../b/BLIS/BLIS-0.9.0-GCC-13.2.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-13.2.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-13.2.0.eb new file mode 100644 index 00000000000..17fa98dc916 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-13.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.9.0' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_disable_power9_kernels.patch', + '%(name)s-%(version)s_enable_ppc_autodetect.patch', +] +checksums = [ + '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz + # BLIS-0.9.0_disable_power9_kernels.patch + 'ed7a326bc5c5c21c42faefbec2fd7be609d1c7236981b466475edace39307279', + # BLIS-0.9.0_enable_ppc_autodetect.patch + 'f373fb252c0d14036fb631f048091976cceb02abb3e570a97fbaeac2fbb12328', +] +builddependencies = [ + ('Python', '3.11.5'), + ('Perl', '5.38.0'), +] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' From 0048ba52aaacce6b9c5748aff55d2dd41c16207a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 28 Sep 2023 16:48:17 +0200 Subject: [PATCH 8932/9987] adding easyconfigs: FlexiBLAS-3.3.1-GCC-13.2.0.eb --- .../f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-13.2.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-13.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-13.2.0.eb new file mode 100644 index 00000000000..4c6e509040b --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.3.1-GCC-13.2.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'FlexiBLAS' +version = '3.3.1' + +homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' +description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation +used by a program without recompiling or relinking it.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" +toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} + +builddependencies = [ + ('CMake', '3.27.6'), + ('Python', '3.11.5'), # required for running the tests + ('BLIS', '0.9.0'), +] + +dependencies = [ + ('OpenBLAS', '0.3.24'), +] + +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +local_backends = ['OpenBLAS', 'BLIS'] + +# imkl supplies its backend via the imkl module, not as a dependency +if ARCH == 'x86_64': + local_backends.append('imkl') + +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': + ['https://gitlab.mpi-magdeburg.mpg.de/api/v4/projects/386/packages/generic/flexiblas-source/v3.3.1/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['bbeebf5e5a006924558fec43f49affbe1aaa4cbacfc472a9ff6066ffda142e18'], + 'backends': local_backends, + }), + ('LAPACK', '3.11.0', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['4b9ba79bfd4921ca820e83979db76ab3363155709444a787979e81c22285ffa9'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + +moduleclass = 'lib' From bbeb16931780e93725bf200145577ce847953b8f Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Thu, 28 Sep 2023 17:01:30 +0200 Subject: [PATCH 8933/9987] Use UCX 1.14.1 in impi-2021.10.0-intel-compilers-2023.2.1.eb Co-authored-by: Kenneth Hoste --- .../i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb index eb2fc40a9c3..e1064214201 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb @@ -11,6 +11,6 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/4f58 sources = ['l_mpi_oneapi_p_%(version)s.49374_offline.sh'] checksums = ['ab2e97d87b139201a2e7dab9a61ac6e8927b7783b459358c4ad69a1b1c064f40'] -dependencies = [('UCX', '1.15.0-rc4')] +dependencies = [('UCX', '1.14.1')] moduleclass = 'mpi' From eb7d516eec0a8ddac917752a899d1d0ce73a760e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 28 Sep 2023 21:46:04 +0200 Subject: [PATCH 8934/9987] fix date in comment indicating when extensions list for Python 3.11.5 was updated Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb index 476b535940a..2a132b97595 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb @@ -39,7 +39,7 @@ exts_default_options = { } # order is important! -# package versions updated 2023-05-17 +# package versions updated 2023-09-28 exts_list = [ ('flit_core', '3.9.0', { 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], From 6edc3400b4519ea6bd49964981e9b66a9f6a82a1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 28 Sep 2023 22:06:53 +0200 Subject: [PATCH 8935/9987] adding easyconfigs: FFTW-3.3.10-GCC-13.2.0.eb, FFTW.MPI-3.3.10-gompi-2023b.eb --- .../f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023b.eb | 19 +++++++++++++++++++ .../f/FFTW/FFTW-3.3.10-GCC-13.2.0.eb | 17 +++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023b.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023b.eb new file mode 100644 index 00000000000..4ebcd8a75cd --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023b.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-13.2.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-13.2.0.eb new file mode 100644 index 00000000000..32652387f8e --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-13.2.0.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +runtest = 'check' + +moduleclass = 'numlib' From 46625aa619dc1bcd4040013d83d752a57908ffff Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 28 Sep 2023 22:07:45 +0200 Subject: [PATCH 8936/9987] adding easyconfigs: ScaLAPACK-2.2.0-gompi-2023b-fb.eb --- .../ScaLAPACK-2.2.0-gompi-2023b-fb.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023b-fb.eb diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023b-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023b-fb.eb new file mode 100644 index 00000000000..c52e40f7733 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023b-fb.eb @@ -0,0 +1,40 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('FlexiBLAS', '3.3.1'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From 331cd025a3abe31ca4244f9f9c50af8e49409e71 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 28 Sep 2023 22:10:16 +0200 Subject: [PATCH 8937/9987] adding easyconfigs: foss-2023b.eb, gfbf-2023b.eb --- easybuild/easyconfigs/f/foss/foss-2023b.eb | 28 ++++++++++++++++++++++ easybuild/easyconfigs/g/gfbf/gfbf-2023b.eb | 20 ++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/f/foss/foss-2023b.eb create mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2023b.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2023b.eb b/easybuild/easyconfigs/f/foss/foss-2023b.eb new file mode 100644 index 00000000000..c17b9b0aab1 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2023b.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2023b' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '13.2.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.1.5', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2023b.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2023b.eb new file mode 100644 index 00000000000..a0d0eef1463 --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2023b.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2023b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '13.2.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' From 8101ef889bcba1fbd67adeaa6be3073ee718e173 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Sep 2023 08:25:59 +0200 Subject: [PATCH 8938/9987] add patch to disable flaky DDRGES3 LAPACK test in OpenBLAS 0.3.23 + 0.3.24 --- .../o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb | 3 +++ ...penBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch | 13 +++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb | 3 +++ 3 files changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb index b88b96d7cdb..abbc1f81fe9 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb @@ -20,6 +20,7 @@ patches = [ 'OpenBLAS-0.3.23_fix-parallel-build.patch', 'OpenBLAS-0.3.23_fix-lapack-test.patch', 'OpenBLAS-0.3.23_fix-tests-hang.patch', + 'OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch', ] checksums = [ {'v0.3.23.tar.gz': '5d9491d07168a5d00116cdc068a40022c3455bf9293c7cb86a65b1054d7e5114'}, @@ -32,6 +33,8 @@ checksums = [ {'OpenBLAS-0.3.23_fix-parallel-build.patch': 'abe10ba3b0ca54772dbf235596e35325a5159018f6a60cfc88824c2c220d99d9'}, {'OpenBLAS-0.3.23_fix-lapack-test.patch': 'f6b3d81061f136e34aaf5359bb80fb9d2bba28825cc1dd26179b8dd01a9a0054'}, {'OpenBLAS-0.3.23_fix-tests-hang.patch': '9de1fdee6edf3b2bb55e4639fdd92d2877b5f0ac880f7df2cfea47ecebf16609'}, + {'OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch': + '36a16b4d3b867897413b43b774f8b57d641ad9a1b452e9de33ced198ab25e461'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch new file mode 100644 index 00000000000..74174819c6a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch @@ -0,0 +1,13 @@ +disable failing DDRGES3 test in LAPACK 3.10 test suite, fixes "Error code from DDRGES3 = 9"; +see also https://github.com/OpenMathLib/OpenBLAS/issues/4032 +author: Kenneth Hoste (HPC-UGent) +--- OpenBLAS-0.3.23/lapack-netlib/TESTING/dgd.in.orig 2023-09-29 08:05:53.089031858 +0200 ++++ OpenBLAS-0.3.23/lapack-netlib/TESTING/dgd.in 2023-09-29 08:08:32.234680735 +0200 +@@ -1,6 +1,6 @@ + DGS Data for the Real Nonsymmetric Schur Form Driver + 5 Number of matrix dimensions +-6 2 10 12 20 30 Matrix dimensions ++2 10 12 20 30 Matrix dimensions + 1 1 1 2 1 Parameters NB, NBMIN, NXOVER, NS, NBCOL + 10 Threshold for test ratios + .TRUE. Put T to test the error exits diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb index ae38d447c1f..f3358f87771 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb @@ -18,6 +18,7 @@ patches = [ 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.23_fix-lapack-test.patch', + 'OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch', ] checksums = [ {'v0.3.24.tar.gz': 'ceadc5065da97bd92404cac7254da66cc6eb192679cf1002098688978d4d5132'}, @@ -28,6 +29,8 @@ checksums = [ {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_fix-lapack-test.patch': 'f6b3d81061f136e34aaf5359bb80fb9d2bba28825cc1dd26179b8dd01a9a0054'}, + {'OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch': + '36a16b4d3b867897413b43b774f8b57d641ad9a1b452e9de33ced198ab25e461'}, ] builddependencies = [ From 9a01daac4ab092b5ab90decbae6cea12e4c2341c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Sep 2023 09:56:26 +0200 Subject: [PATCH 8939/9987] change gompi/2023b to gompi/2023.09 for now --- .../easyconfigs/g/gompi/{gompi-2023b.eb => gompi-2023.09.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/g/gompi/{gompi-2023b.eb => gompi-2023.09.eb} (95%) diff --git a/easybuild/easyconfigs/g/gompi/gompi-2023b.eb b/easybuild/easyconfigs/g/gompi/gompi-2023.09.eb similarity index 95% rename from easybuild/easyconfigs/g/gompi/gompi-2023b.eb rename to easybuild/easyconfigs/g/gompi/gompi-2023.09.eb index 649244f7e77..a528a05373c 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2023b.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2023.09.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'gompi' -version = '2023b' +version = '2023.09' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, From f8f32a4542090645c29902839bf85e03edbbe7aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Sep 2023 12:01:54 +0200 Subject: [PATCH 8940/9987] use gompi/2023.09 as toolchain for ScaLAPACK 2.2.0, for now --- ....0-gompi-2023b-fb.eb => ScaLAPACK-2.2.0-gompi-2023.09-fb.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.2.0-gompi-2023b-fb.eb => ScaLAPACK-2.2.0-gompi-2023.09-fb.eb} (96%) diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023b-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023.09-fb.eb similarity index 96% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023b-fb.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023.09-fb.eb index c52e40f7733..f9ef3a1331c 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023b-fb.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2023.09-fb.eb @@ -6,7 +6,7 @@ homepage = 'https://www.netlib.org/scalapack/' description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.""" -toolchain = {'name': 'gompi', 'version': '2023b'} +toolchain = {'name': 'gompi', 'version': '2023.09'} toolchainopts = {'extra_fflags': '-lpthread', 'openmp': True, 'pic': True, 'usempi': True} source_urls = [homepage] From f7a8204ccf34414bee928fa5f33cf0e1a04fb9ed Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 29 Sep 2023 13:12:57 +0200 Subject: [PATCH 8941/9987] adding easyconfigs: scikit-learn-1.3.1-gfbf-2023a.eb --- .../scikit-learn-1.3.1-gfbf-2023a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.1-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.1-gfbf-2023a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.1-gfbf-2023a.eb new file mode 100644 index 00000000000..e4e1fa10b81 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.1-gfbf-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.3.1' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'sklearn', + 'checksums': ['1a231cced3ee3fa04756b4a7ab532dc9417acd581a330adff5f2c01ac2831fcf'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), +] + +moduleclass = 'data' From f34bc7c94bcc005b1a083cbd0ee4a012427dc958 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 29 Sep 2023 13:16:14 +0200 Subject: [PATCH 8942/9987] adding easyconfigs: Wannier90-3.1.0-foss-2023a.eb --- .../w/Wannier90/Wannier90-3.1.0-foss-2023a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb new file mode 100644 index 00000000000..9807690b35c --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +# The -fallow-argument-mismatch allows MPI communication calls to be +# called with arrays of different types at different places in the +# code. This otherwise cause an error in GCC 10.X +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' From 018b8e498accd8276d828faf12d0935197bc91b6 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 29 Sep 2023 13:58:41 +0200 Subject: [PATCH 8943/9987] adding easyconfigs: libxc-6.2.2-intel-compilers-2023.1.0.eb --- .../libxc-6.2.2-intel-compilers-2023.1.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb new file mode 100644 index 00000000000..af5917b73f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.2.2' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Perl', '5.36.1'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' From 4a2716a775af0e5f0feca8d169534375d92c75bc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 29 Sep 2023 15:35:39 +0200 Subject: [PATCH 8944/9987] stick to gompi/2023.09 for now for FFTW.MPI 3.3.10 --- ...I-3.3.10-gompi-2023b.eb => FFTW.MPI-3.3.10-gompi-2023.09.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/f/FFTW.MPI/{FFTW.MPI-3.3.10-gompi-2023b.eb => FFTW.MPI-3.3.10-gompi-2023.09.eb} (90%) diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023b.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023.09.eb similarity index 90% rename from easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023b.eb rename to easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023.09.eb index 4ebcd8a75cd..4e136d40c73 100644 --- a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023b.eb +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2023.09.eb @@ -5,7 +5,7 @@ homepage = 'https://www.fftw.org' description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.""" -toolchain = {'name': 'gompi', 'version': '2023b'} +toolchain = {'name': 'gompi', 'version': '2023.09'} toolchainopts = {'pic': True} source_urls = [homepage] From 88ddaa5e15112aa1ad12d1426375c4a38866fc23 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 29 Sep 2023 15:46:31 +0200 Subject: [PATCH 8945/9987] adding easyconfigs: HPCC-1.5.0-foss-2022a.eb and patches: HPCC-1.5.0_fix_recent_mpi.patch --- .../h/HPCC/HPCC-1.5.0-foss-2022a.eb | 24 +++++++++ .../h/HPCC/HPCC-1.5.0_fix_recent_mpi.patch | 51 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPCC/HPCC-1.5.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/h/HPCC/HPCC-1.5.0_fix_recent_mpi.patch diff --git a/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0-foss-2022a.eb b/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0-foss-2022a.eb new file mode 100644 index 00000000000..ed86b442b73 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0-foss-2022a.eb @@ -0,0 +1,24 @@ +name = 'HPCC' +version = '1.5.0' + +homepage = 'https://hpcchallenge.org/' +description = """ +HPC Challenge is a benchmark suite that measures a range memory access +patterns. The HPC Challenge benchmark consists of basically 7 tests: HPL, +DGEMM, STREAM, PTRANS, RandomAccess, FFT, Communication bandwidth and latency +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://hpcchallenge.org/projectsfiles/hpcc/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_recent_mpi.patch'] +checksums = [ + {'hpcc-1.5.0.tar.gz': '0a6fef7ab9f3347e549fed65ebb98234feea9ee18aea0c8f59baefbe3cf7ffb8'}, + {'HPCC-1.5.0_fix_recent_mpi.patch': '56f1e48af423dea3b78f5614fe102586a1da7c951d6959c26e359ca1e6ad8066'}, +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0_fix_recent_mpi.patch b/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0_fix_recent_mpi.patch new file mode 100644 index 00000000000..8f73d442794 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCC/HPCC-1.5.0_fix_recent_mpi.patch @@ -0,0 +1,51 @@ +Fix build error with recent MPI version +https://github.com/icl-utk-edu/hpcc/commit/d2b9a19b4498fdced2860f3394c03f27714b6160 +From d71a04d69c727b9baf0a78bb445db3ffc4ab4c91 Mon Sep 17 00:00:00 2001 +From: Francois Mazen +Date: Sat, 15 May 2021 14:49:14 +0200 +Subject: [PATCH] Apply debian patch. + +--- + hpl/src/comm/HPL_packL.c | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/hpl/src/comm/HPL_packL.c b/hpl/src/comm/HPL_packL.c +index ddfa230..948c08d 100644 +--- a/hpl/src/comm/HPL_packL.c ++++ b/hpl/src/comm/HPL_packL.c +@@ -169,7 +169,7 @@ int HPL_packL + type[nbufs] = MPI_DOUBLE; + blen[nbufs] = m1; + if( ierr == MPI_SUCCESS ) +- ierr = MPI_Address( bufs[nbufs], &disp[nbufs] ); ++ ierr = MPI_Get_address( bufs[nbufs], &disp[nbufs] ); + + nbufs++; len -= m1; j1++; ibuf += m1; + /* +@@ -183,7 +183,7 @@ int HPL_packL + type[nbufs] = MPI_DOUBLE; + blen[nbufs] = m1; + if( ierr == MPI_SUCCESS ) +- ierr = MPI_Address( bufs[nbufs], &disp[nbufs] ); ++ ierr = MPI_Get_address( bufs[nbufs], &disp[nbufs] ); + + nbufs++; len -= m1; j1++; ibuf += m1; + } +@@ -197,7 +197,7 @@ int HPL_packL + type[nbufs] = MPI_DOUBLE; + blen[nbufs] = len; + if( ierr == MPI_SUCCESS ) +- ierr = MPI_Address( bufs[nbufs], &disp[nbufs] ); ++ ierr = MPI_Get_address( bufs[nbufs], &disp[nbufs] ); + nbufs++; + } + +@@ -208,7 +208,7 @@ int HPL_packL + * construct the struct type + */ + if( ierr == MPI_SUCCESS ) +- ierr = MPI_Type_struct( nbufs, blen, disp, type, ++ ierr = MPI_Type_create_struct( nbufs, blen, disp, type, + &PANEL->dtypes[IBUF] ); + /* + * release temporaries From e5428bd469652fa177eeb5281eebbd2f3ead880d Mon Sep 17 00:00:00 2001 From: Jessie Hernandez Date: Fri, 18 Aug 2023 13:50:35 +0200 Subject: [PATCH 8946/9987] Adding easyconfigs: libedit-20210910-GCCcore-10.3.0 --- .../libedit-20210910-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..42ee25b2a47 --- /dev/null +++ b/easybuild/easyconfigs/l/libedit/libedit-20210910-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libedit' +version = '20210910' + +homepage = 'https://thrysoee.dk/editline/' +description = """ +This BSD-style licensed command line editor library provides generic line editing, +history, and tokenization functions, similar to those found in GNU Readline. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://thrysoee.dk/editline/'] +sources = ['%(namelower)s-%(version)s-3.1.tar.gz'] +checksums = ['6792a6a992050762edcca28ff3318cdb7de37dccf7bc30db59fcd7017eed13c5'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('ncurses', '6.2')] + +sanity_check_paths = { + 'files': ['include/editline/readline.h', 'lib/libedit.%s' % SHLIB_EXT, 'lib/libedit.a'], + 'dirs': [] +} + +moduleclass = 'lib' From 4105944cda9ac53138c3af5bcbc2372f8cdbbae0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 29 Sep 2023 17:29:41 +0200 Subject: [PATCH 8947/9987] change foss/2023b and gfbf/2023b to foss/2023.09 and gfbf/2023.09 for now --- easybuild/easyconfigs/f/foss/{foss-2023b.eb => foss-2023.09.eb} | 2 +- easybuild/easyconfigs/g/gfbf/{gfbf-2023b.eb => gfbf-2023.09.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/f/foss/{foss-2023b.eb => foss-2023.09.eb} (97%) rename easybuild/easyconfigs/g/gfbf/{gfbf-2023b.eb => gfbf-2023.09.eb} (95%) diff --git a/easybuild/easyconfigs/f/foss/foss-2023b.eb b/easybuild/easyconfigs/f/foss/foss-2023.09.eb similarity index 97% rename from easybuild/easyconfigs/f/foss/foss-2023b.eb rename to easybuild/easyconfigs/f/foss/foss-2023.09.eb index c17b9b0aab1..06789e0c500 100644 --- a/easybuild/easyconfigs/f/foss/foss-2023b.eb +++ b/easybuild/easyconfigs/f/foss/foss-2023.09.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'foss' -version = '2023b' +version = '2023.09' homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' description = """GNU Compiler Collection (GCC) based compiler toolchain, including diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2023b.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2023.09.eb similarity index 95% rename from easybuild/easyconfigs/g/gfbf/gfbf-2023b.eb rename to easybuild/easyconfigs/g/gfbf/gfbf-2023.09.eb index a0d0eef1463..d464a726be8 100644 --- a/easybuild/easyconfigs/g/gfbf/gfbf-2023b.eb +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2023.09.eb @@ -1,7 +1,7 @@ easyblock = 'Toolchain' name = 'gfbf' -version = '2023b' +version = '2023.09' homepage = '(none)' description = """GNU Compiler Collection (GCC) based compiler toolchain, including From 0493dd59114c3072b7c72b6d1eafb65b44e669aa Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 29 Sep 2023 17:30:57 +0200 Subject: [PATCH 8948/9987] adding easyconfigs: HPL-2.3-foss-2023.09.eb --- .../easyconfigs/h/HPL/HPL-2.3-foss-2023.09.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023.09.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023.09.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023.09.eb new file mode 100644 index 00000000000..9818105d1ba --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2023.09.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2023.09'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' From 74b33a35d0589150253e948cddd235ec09bcebe5 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 29 Sep 2023 17:35:49 +0200 Subject: [PATCH 8949/9987] adding easyconfigs: OSU-Micro-Benchmarks-7.2-gompi-2023.09.eb --- .../OSU-Micro-Benchmarks-7.2-gompi-2023.09.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023.09.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023.09.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023.09.eb new file mode 100644 index 00000000000..5c33104aaa4 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023.09.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.2' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2023.09'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1a4e1f2aab0e65404b3414e23bd46616184b69b6231ce9313d9c630bd6e633c1'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From f2e372e1cef22728ccf58bab25e0f89066952210 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 29 Sep 2023 17:53:56 +0200 Subject: [PATCH 8950/9987] adding easyconfigs: HPCG-3.1-foss-2022a.eb, HPCG-3.1-foss-2022b.eb, HPCG-3.1-foss-2023a.eb, HPCG-3.1-intel-2022a.eb, HPCG-3.1-intel-2022b.eb, HPCG-3.1-intel-2023a.eb --- .../easyconfigs/h/HPCG/HPCG-3.1-foss-2022a.eb | 24 +++++++++++++++++++ .../easyconfigs/h/HPCG/HPCG-3.1-foss-2022b.eb | 24 +++++++++++++++++++ .../easyconfigs/h/HPCG/HPCG-3.1-foss-2023a.eb | 24 +++++++++++++++++++ .../h/HPCG/HPCG-3.1-intel-2022a.eb | 24 +++++++++++++++++++ .../h/HPCG/HPCG-3.1-intel-2022b.eb | 24 +++++++++++++++++++ .../h/HPCG/HPCG-3.1-intel-2023a.eb | 24 +++++++++++++++++++ 6 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2022a.eb create mode 100644 easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2022b.eb create mode 100644 easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2023a.eb diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2022a.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2022a.eb new file mode 100644 index 00000000000..50f11033d46 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2022a.eb @@ -0,0 +1,24 @@ +name = 'HPCG' +version = '3.1' + +homepage = 'https://software.sandia.gov/hpcg' +description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than + the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://www.hpcg-benchmark.org/downloads'] +sources = [SOURCELOWER_TAR_GZ] +# Newer compilers require loop's upper-bound variable to be +# explicitly designated as private/shared/firstprivate/lastprivate +patches = ['HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch'] +checksums = [ + '33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4', # hpcg-3.1.tar.gz + # HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch + '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482', +] + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2022b.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2022b.eb new file mode 100644 index 00000000000..0ec809f2922 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2022b.eb @@ -0,0 +1,24 @@ +name = 'HPCG' +version = '3.1' + +homepage = 'https://software.sandia.gov/hpcg' +description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than + the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://www.hpcg-benchmark.org/downloads'] +sources = [SOURCELOWER_TAR_GZ] +# Newer compilers require loop's upper-bound variable to be +# explicitly designated as private/shared/firstprivate/lastprivate +patches = ['HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch'] +checksums = [ + '33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4', # hpcg-3.1.tar.gz + # HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch + '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482', +] + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2023a.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2023a.eb new file mode 100644 index 00000000000..7114062d22c --- /dev/null +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-foss-2023a.eb @@ -0,0 +1,24 @@ +name = 'HPCG' +version = '3.1' + +homepage = 'https://software.sandia.gov/hpcg' +description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than + the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://www.hpcg-benchmark.org/downloads'] +sources = [SOURCELOWER_TAR_GZ] +# Newer compilers require loop's upper-bound variable to be +# explicitly designated as private/shared/firstprivate/lastprivate +patches = ['HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch'] +checksums = [ + '33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4', # hpcg-3.1.tar.gz + # HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch + '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482', +] + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2022a.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2022a.eb new file mode 100644 index 00000000000..81cbc0c02a1 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2022a.eb @@ -0,0 +1,24 @@ +name = 'HPCG' +version = '3.1' + +homepage = 'https://software.sandia.gov/hpcg' +description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than + the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://www.hpcg-benchmark.org/downloads'] +sources = [SOURCELOWER_TAR_GZ] +# Newer compilers require loop's upper-bound variable to be +# explicitly designated as private/shared/firstprivate/lastprivate +patches = ['HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch'] +checksums = [ + '33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4', # hpcg-3.1.tar.gz + # HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch + '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482', +] + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2022b.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2022b.eb new file mode 100644 index 00000000000..e6958a4ad27 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2022b.eb @@ -0,0 +1,24 @@ +name = 'HPCG' +version = '3.1' + +homepage = 'https://software.sandia.gov/hpcg' +description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than + the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://www.hpcg-benchmark.org/downloads'] +sources = [SOURCELOWER_TAR_GZ] +# Newer compilers require loop's upper-bound variable to be +# explicitly designated as private/shared/firstprivate/lastprivate +patches = ['HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch'] +checksums = [ + '33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4', # hpcg-3.1.tar.gz + # HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch + '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482', +] + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2023a.eb b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2023a.eb new file mode 100644 index 00000000000..771c57d4d87 --- /dev/null +++ b/easybuild/easyconfigs/h/HPCG/HPCG-3.1-intel-2023a.eb @@ -0,0 +1,24 @@ +name = 'HPCG' +version = '3.1' + +homepage = 'https://software.sandia.gov/hpcg' +description = """The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than + the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark.""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['http://www.hpcg-benchmark.org/downloads'] +sources = [SOURCELOWER_TAR_GZ] +# Newer compilers require loop's upper-bound variable to be +# explicitly designated as private/shared/firstprivate/lastprivate +patches = ['HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch'] +checksums = [ + '33a434e716b79e59e745f77ff72639c32623e7f928eeb7977655ffcaade0f4a4', # hpcg-3.1.tar.gz + # HPCG-3.1_fix-loop-upper-bound-variable-to-be-explicitly-designated-as-shared.patch + '23b9de83042eb7a8207fdddcfa79ae2cc1a17e8e623e2224c7751d7c328ee482', +] + +runtest = True + +moduleclass = 'math' From 53f18354bd36d9555560c52c9e61c0a73cf7f982 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 30 Sep 2023 11:16:50 +0200 Subject: [PATCH 8951/9987] Add intel/2023a version as well. --- .../Wannier90/Wannier90-3.1.0-intel-2023a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb new file mode 100644 index 00000000000..60a3c980b9f --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +# The -fallow-argument-mismatch allows MPI communication calls to be +# called with arrays of different types at different places in the +# code. This otherwise cause an error in GCC 10.X +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' From 618f5c95068c8d0fd8d4a5d1497f1d094a75d798 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 30 Sep 2023 15:00:53 +0200 Subject: [PATCH 8952/9987] bump OpenSSL 1.1 wrapper fallback to 1.1.1w --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb index 001713087da..b4c7bcbd94e 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.eb @@ -27,11 +27,11 @@ builddependencies = [('pkgconf', '1.8.0')] # component list, which will be build and installed as usual. components = [ - (name, '1.1.1u', { + (name, '1.1.1w', { 'easyblock': 'EB_OpenSSL', 'source_urls': ['https://www.openssl.org/source/'], 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['e2f8d84b523eecd06c7be7626830370300fbcc15386bf5142d72758f6963ebc6'], + 'checksums': ['cf3098950cb4d853ad95c0841f1f9c6d3dc102dccfcacd521d93925208b76ac8'], 'start_dir': '%(namelower)s-%(version)s', }), ] From bb13083c48145a9883ee59d45cb7e28221c4e40b Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sun, 1 Oct 2023 16:20:35 +0200 Subject: [PATCH 8953/9987] adding easyconfigs: ELPA-2023.05.001-intel-2023a.eb --- .../e/ELPA/ELPA-2023.05.001-intel-2023a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-intel-2023a.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-intel-2023a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-intel-2023a.eb new file mode 100644 index 00000000000..ec3779ae7ee --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.05.001-intel-2023a.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2023.05.001' + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fix_hardcoded_perl_path.patch', + '%(name)s-%(version)s_fix_AVX512_support.patch', +] +checksums = [ + {'%(namelower)s-new_release_%(version)s.tar.gz': + '7e07ca287ab07c0a73d97df71d5a5431c847b8e4d5c759aae99e12672e6decf3'}, + {'%(name)s-%(version)s_fix_hardcoded_perl_path.patch': + '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, + {'%(name)s-%(version)s_fix_AVX512_support.patch': + 'ecf08b64fe1da432a218040fa45d4ecfbb3269d58cb018b12da5a2d854bf96be'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.11.3'), + ('Perl', '5.36.1'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' +# If the build is running in a batch job, make sure Intel libmpi does +# not try to use Slurm to run the MPI_THREAD test code that ELPA's +# configure is running without "mpirun". +preconfigopts += 'unset SLURM_JOBID && unset SLURM_NODELIST && unset I_MPI_PMI_LIBRARY && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' From e6f43604d5ceba166ddf6cc09e78aa72f484ac1e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 1 Oct 2023 17:20:04 +0200 Subject: [PATCH 8954/9987] bump OpenMPI to v4.1.6 in gompi/2023.09 --- .../easyconfigs/g/gompi/gompi-2023.09.eb | 2 +- .../o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb | 62 +++++++++++++++++++ 2 files changed, 63 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2023.09.eb b/easybuild/easyconfigs/g/gompi/gompi-2023.09.eb index a528a05373c..3d093c34535 100644 --- a/easybuild/easyconfigs/g/gompi/gompi-2023.09.eb +++ b/easybuild/easyconfigs/g/gompi/gompi-2023.09.eb @@ -14,7 +14,7 @@ local_gccver = '13.2.0' # compiler toolchain dependencies dependencies = [ ('GCC', local_gccver), # includes both GCC and binutils - ('OpenMPI', '4.1.5', '', ('GCC', local_gccver)), + ('OpenMPI', '4.1.6', '', ('GCC', local_gccver)), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb new file mode 100644 index 00000000000..3e6e152e445 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb @@ -0,0 +1,62 @@ +name = 'OpenMPI' +version = '4.1.6' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', +] +checksums = [ + {'openmpi-4.1.6.tar.bz2': 'f740994485516deb63b5311af122c265179f5328a0d857a567b85db00b11e415'}, + {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, + {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, +] + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Perl', '5.38.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('hwloc', '2.9.2'), + ('libevent', '2.1.12'), + ('UCX', '1.14.1'), + ('libfabric', '1.19.0'), + ('PMIx', '4.2.5'), + ('UCC', '1.2.0'), +] + +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' + +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From 7555094d114b00fde855ae575f5e091a11d24e56 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Oct 2023 10:07:52 +0200 Subject: [PATCH 8955/9987] remove easyconfig for OpenMPI v4.1.5 with GCC/13.2.0 --- .../o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb | 65 ------------------- 1 file changed, 65 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb deleted file mode 100644 index 6d402e8a4ec..00000000000 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-13.2.0.eb +++ /dev/null @@ -1,65 +0,0 @@ -name = 'OpenMPI' -version = '4.1.5' - -homepage = 'https://www.open-mpi.org/' -description = """The Open MPI Project is an open source MPI-3 implementation.""" - -toolchain = {'name': 'GCC', 'version': '13.2.0'} - -source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -sources = [SOURCELOWER_TAR_BZ2] -patches = [ - 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', - 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', - 'OpenMPI-4.1.5_fix-pmix3x.patch', -] -checksums = [ - {'openmpi-4.1.5.tar.bz2': 'a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3'}, - {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': - '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, - {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': - 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, - {'OpenMPI-4.1.5_fix-pmix3x.patch': - '46edac3dbf32f2a611d45e8a3c8edd3ae2f430eec16a1373b510315272115c40'}, -] - -builddependencies = [ - ('pkgconf', '2.0.3'), - ('Perl', '5.38.0'), - ('Autotools', '20220317'), -] - -dependencies = [ - ('zlib', '1.2.13'), - ('hwloc', '2.9.2'), - ('libevent', '2.1.12'), - ('UCX', '1.14.1'), - ('libfabric', '1.19.0'), - ('PMIx', '4.2.5'), - ('UCC', '1.2.0'), -] - -# Update configure to include changes from the "internal-cuda" patch -# by running a subset of autogen.pl sufficient to achieve this -# without doing the full, long-running regeneration. -preconfigopts = ' && '.join([ - 'cd config', - 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', - 'cd ..', - 'autoconf', - 'autoheader', - 'aclocal', - 'automake', - '' -]) - -# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. -configopts = '--with-cuda=internal ' - -# disable MPI1 compatibility for now, see what breaks... -# configopts += '--enable-mpi1-compatibility ' - -# to enable SLURM integration (site-specific) -# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' - -moduleclass = 'mpi' From 23f1e17a5df21c51140243b4c8de1a962e17b785 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 2 Oct 2023 09:01:52 +0000 Subject: [PATCH 8956/9987] Made Rust a build dependency --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 8f48ebf11cb..7e268e45acb 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -12,7 +12,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} builddependencies = [ - ('binutils', '2.39') + ('binutils', '2.39'), + ('Rust', '1.65.0'), ] dependencies = [ @@ -20,7 +21,6 @@ dependencies = [ ('Python', '3.10.8'), ('tqdm', '4.64.1'), ('PLY', '3.11'), - ('Rust', '1.65.0'), ('scikit-build', '0.17.2'), ] From 66b603f8f3b4765482d184672d223bbb6057352a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 2 Oct 2023 12:06:59 +0200 Subject: [PATCH 8957/9987] bump OpenMPI to 4.1.6 in foss/2023.09 --- easybuild/easyconfigs/f/foss/foss-2023.09.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/foss/foss-2023.09.eb b/easybuild/easyconfigs/f/foss/foss-2023.09.eb index 06789e0c500..a02c284e598 100644 --- a/easybuild/easyconfigs/f/foss/foss-2023.09.eb +++ b/easybuild/easyconfigs/f/foss/foss-2023.09.eb @@ -18,7 +18,7 @@ local_comp_mpi_tc = ('gompi', version) # because of toolchain preparation functions dependencies = [ ('GCC', local_gccver), - ('OpenMPI', '4.1.5', '', ('GCC', local_gccver)), + ('OpenMPI', '4.1.6', '', ('GCC', local_gccver)), ('FlexiBLAS', '3.3.1', '', ('GCC', local_gccver)), ('FFTW', '3.3.10', '', ('GCC', local_gccver)), ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), From b5aaf436fa4b87ea0a5d42d13fffe605d3a625f8 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 2 Oct 2023 12:10:43 +0200 Subject: [PATCH 8958/9987] bump UCX to 1.15.0 and PMIx to 4.2.6 in OpenMPI-4.1.6-GCC-13.2.0.eb --- .../o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb | 4 +- .../p/PMIx/PMIx-4.2.6-GCCcore-13.2.0.eb | 45 ++++++++++++++++ .../u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb | 2 +- .../u/UCX/UCX-1.15.0-GCCcore-13.2.0.eb | 54 +++++++++++++++++++ 4 files changed, 102 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.2.6-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.15.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb index 3e6e152e445..3e4baa87735 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb @@ -30,9 +30,9 @@ dependencies = [ ('zlib', '1.2.13'), ('hwloc', '2.9.2'), ('libevent', '2.1.12'), - ('UCX', '1.14.1'), + ('UCX', '1.15.0'), ('libfabric', '1.19.0'), - ('PMIx', '4.2.5'), + ('PMIx', '4.2.6'), ('UCC', '1.2.0'), ] diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.6-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ade4f901574 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.6-GCCcore-13.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '4.2.6' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['10b0d5a7fca70272e9427c677557578ac452cea02aeb00e30dec2116d20c3cd0'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.2.13'), + ('hwloc', '2.9.2'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb index 7013dcbf911..45727a0c4bc 100644 --- a/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/u/UCC/UCC-1.2.0-GCCcore-13.2.0.eb @@ -26,7 +26,7 @@ builddependencies = [ ] dependencies = [ - ('UCX', '1.14.1'), + ('UCX', '1.15.0'), ] preconfigopts = "./autogen.sh && " diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.15.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.15.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6380530f16c --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.15.0-GCCcore-13.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.15.0' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', +] +checksums = [ + {'ucx-1.15.0.tar.gz': '4b202087076bc1c98f9249144f0c277a8ea88ad4ca6f404f94baa9cb3aebda6d'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, +] + +# Uncomment when updating to final release +# sources = ['%(namelower)s-%(version)s.tar.gz'] +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '2.0.3'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.13'), + ('numactl', '2.0.16'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From 1ae75ed5977bd19cd6c5b86fc331a24da7b6d84f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 2 Oct 2023 12:16:52 +0200 Subject: [PATCH 8959/9987] remove easyconfig for PMIx v4.2.5 with GCC/13.2.0 --- .../p/PMIx/PMIx-4.2.5-GCCcore-13.2.0.eb | 45 ------------------- 1 file changed, 45 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.2.5-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.5-GCCcore-13.2.0.eb deleted file mode 100644 index 20d7c7553c3..00000000000 --- a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.5-GCCcore-13.2.0.eb +++ /dev/null @@ -1,45 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'PMIx' -version = '4.2.5' - -homepage = 'https://pmix.org/' -description = """Process Management for Exascale Environments -PMI Exascale (PMIx) represents an attempt to -provide an extended version of the PMI standard specifically designed -to support clusters up to and including exascale sizes. The overall -objective of the project is not to branch the existing pseudo-standard -definitions - in fact, PMIx fully supports both of the existing PMI-1 -and PMI-2 APIs - but rather to (a) augment and extend those APIs to -eliminate some current restrictions that impact scalability, and (b) -provide a reference implementation of the PMI-server that demonstrates -the desired level of scalability. -""" - -toolchain = {'name': 'GCCcore', 'version': '13.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.bz2'] -checksums = ['a89c2c5dc69715a4df1e76fdc4318299386c184623a1d0d5eb1fb062e14b0d2b'] - -builddependencies = [('binutils', '2.40')] - -dependencies = [ - ('libevent', '2.1.12'), - ('zlib', '1.2.13'), - ('hwloc', '2.9.2'), -] - -configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' -configopts += ' --with-hwloc=$EBROOTHWLOC' -configopts += ' --enable-pmix-binaries' - -buildopts = 'V=1' - -sanity_check_paths = { - 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], - 'dirs': ['etc', 'include', 'lib', 'share'] -} - -moduleclass = 'lib' From f7b1379f1bbe24a78b6fa4822b364d978a8b3913 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 2 Oct 2023 12:19:40 +0200 Subject: [PATCH 8960/9987] remove easyconfig for UCX v1.14.1 with GCC/13.2.0 --- .../u/UCX/UCX-1.14.1-GCCcore-13.2.0.eb | 57 ------------------- ..._fix-type-conflict-uct_md_mem_advise.patch | 31 ---------- 2 files changed, 88 deletions(-) delete mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-13.2.0.eb delete mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-13.2.0.eb deleted file mode 100644 index 253b43fceca..00000000000 --- a/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-13.2.0.eb +++ /dev/null @@ -1,57 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'UCX' -version = '1.14.1' - -homepage = 'https://www.openucx.org/' -description = """Unified Communication X -An open-source production grade communication framework for data centric -and high-performance applications -""" - -toolchain = {'name': 'GCCcore', 'version': '13.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.gz'] -patches = [ - 'UCX-1.13.1-dynamic_modules.patch', - 'UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch', -] -checksums = [ - {'ucx-1.14.1.tar.gz': 'baa0634cafb269a3112f626eb226bcd2ca8c9fcf0fec3b8e2a3553baad5f77aa'}, - {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, - {'UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch': - '9fbf26b39cd5c9e469ff152e18d79a4bf685fca175d4088b9bbe8644b74c1401'}, -] - -# Uncomment when updating to final release -# sources = ['%(namelower)s-%(version)s.tar.gz'] -builddependencies = [ - ('binutils', '2.40'), - ('Autotools', '20220317'), - ('pkgconf', '2.0.3'), -] - -osdependencies = [OS_PKG_IBVERBS_DEV] - -dependencies = [ - ('zlib', '1.2.13'), - ('numactl', '2.0.16'), -] - -configure_cmd = "contrib/configure-release" - -configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' -configopts += '--without-java --without-go --disable-doxygen-doc ' - -buildopts = 'V=1' - -sanity_check_paths = { - 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], - 'dirs': ['include', 'lib', 'share'] -} - -sanity_check_commands = ["ucx_info -d"] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch b/easybuild/easyconfigs/u/UCX/UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch deleted file mode 100644 index 492bacf17b3..00000000000 --- a/easybuild/easyconfigs/u/UCX/UCX-1.14.1_fix-type-conflict-uct_md_mem_advise.patch +++ /dev/null @@ -1,31 +0,0 @@ -From 8d6032ec864190c9f079d96e731c5004a975e153 Mon Sep 17 00:00:00 2001 -From: Jan Ciesko -Date: Thu, 5 Jan 2023 12:31:39 -0800 -Subject: [PATCH] UCT/BASE: Fix conflicting types for 'uct_md_mem_advise'. - -Signed-off-by: Howard Pritchard ---- - src/uct/base/uct_md.c | 3 ++- - 1 file changed, 2 insertions(+), 1 deletion(-) - -diff --git a/src/uct/base/uct_md.c b/src/uct/base/uct_md.c -index d7f4c326c0b..3830e16618b 100644 ---- a/src/uct/base/uct_md.c -+++ b/src/uct/base/uct_md.c -@@ -2,6 +2,7 @@ - * Copyright (c) NVIDIA CORPORATION & AFFILIATES, 2001-2014. ALL RIGHTS RESERVED. - * Copyright (C) UT-Battelle, LLC. 2015. ALL RIGHTS RESERVED. - * Copyright (C) ARM Ltd. 2016-2017. ALL RIGHTS RESERVED. -+* Copyright (c) Triad National Security, LLC. 2023. ALL RIGHTS RESERVED. - * - * See file LICENSE for terms. - */ -@@ -554,7 +555,7 @@ ucs_status_t uct_md_mem_free(uct_md_h md, uct_mem_h memh) - - ucs_status_t - uct_md_mem_advise(uct_md_h md, uct_mem_h memh, void *addr, size_t length, -- unsigned advice) -+ uct_mem_advice_t advice) - { - if ((length == 0) || (addr == NULL)) { - return UCS_ERR_INVALID_PARAM; From f9ab7c1e90077c4aa6d0f90e3c030ecc516fbf45 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 2 Oct 2023 12:43:55 +0200 Subject: [PATCH 8961/9987] bump UCX to 1.15.0 in impi-2021.10.0-intel-compilers-2023.2.1.eb --- .../i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb index e1064214201..4a92f37d8fe 100644 --- a/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb +++ b/easybuild/easyconfigs/i/impi/impi-2021.10.0-intel-compilers-2023.2.1.eb @@ -11,6 +11,6 @@ source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/4f58 sources = ['l_mpi_oneapi_p_%(version)s.49374_offline.sh'] checksums = ['ab2e97d87b139201a2e7dab9a61ac6e8927b7783b459358c4ad69a1b1c064f40'] -dependencies = [('UCX', '1.14.1')] +dependencies = [('UCX', '1.15.0')] moduleclass = 'mpi' From 606683e21e3efab69c7cc3467709caebbfe0b29b Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 2 Oct 2023 14:21:37 +0200 Subject: [PATCH 8962/9987] Add binutils --- .../scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb index b72e4a1c329..10ddebc0c58 100644 --- a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb @@ -10,6 +10,7 @@ for CPython C/C++/Fortran/Cython extensions.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ + ('binutils', '2.40'), ('hatchling', '1.18.0'), ('CMake', '3.26.3'), ] From 20975c6447afed74bdb924fa2ac7c47e07d5fdbe Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 2 Oct 2023 15:18:16 +0200 Subject: [PATCH 8963/9987] adding easyconfigs: poppler-23.09.0-GCC-12.3.0.eb --- .../p/poppler/poppler-23.09.0-GCC-12.3.0.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/poppler/poppler-23.09.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/p/poppler/poppler-23.09.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/poppler/poppler-23.09.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..4d71d9bacbf --- /dev/null +++ b/easybuild/easyconfigs/p/poppler/poppler-23.09.0-GCC-12.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'Bundle' + +name = 'poppler' +version = '23.09.0' + +homepage = 'https://poppler.freedesktop.org' +description = "Poppler is a PDF rendering library" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('freetype', '2.13.0'), + ('fontconfig', '2.14.2'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('NSS', '3.89.1'), + ('LibTIFF', '4.5.0'), + ('Qt5', '5.15.10'), + ('Boost', '1.82.0'), + ('cairo', '1.17.8'), + ('OpenJPEG', '2.5.0'), + ('zlib', '1.2.13'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['80d1d44dd8bdf4ac1a47d56c5065075eb9991790974b1ed7d14b972acde88e55'], + 'configopts': "-DENABLE_BOOST=ON", + }), + ('poppler-data', '0.4.12', { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['c835b640a40ce357e1b83666aabd95edffa24ddddd49b8daff63adb851cdab74'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdfinfo', 'lib/libpoppler.%s' % SHLIB_EXT, 'lib/libpoppler-cpp.%s' % SHLIB_EXT, + 'lib/libpoppler-glib.%s' % SHLIB_EXT, 'lib/libpoppler-qt5.%s' % SHLIB_EXT], + 'dirs': ['include/poppler', 'lib/pkgconfig', 'share'], +} + +sanity_check_commands = ["pdfinfo --help"] + +moduleclass = 'lib' + From 0090456f892f42b115b6d3804295bd3bc147607e Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 2 Oct 2023 15:38:37 +0200 Subject: [PATCH 8964/9987] Update easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb Co-authored-by: SebastianAchilles --- .../scikit-build-core-0.5.0-GCCcore-12.3.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb index 10ddebc0c58..d4705b97c78 100644 --- a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb @@ -3,9 +3,10 @@ easyblock = 'PythonBundle' name = 'scikit-build-core' version = '0.5.0' -homepage = 'https://scikit-build.readthedocs.io/en/latest' -description = """Scikit-Build, or skbuild, is an improved build system generator -for CPython C/C++/Fortran/Cython extensions.""" +homepage = 'https://scikit-build.readthedocs.io/en/latest/' +description = """Scikit-build-core is a complete ground-up rewrite of scikit-build on top of +modern packaging APIs. It provides a bridge between CMake and the Python build +system, allowing you to make Python modules with CMake.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} From 1193e208bfe4eb30c33b64e59e77e610e289c30a Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 2 Oct 2023 15:38:44 +0200 Subject: [PATCH 8965/9987] remove blank line at the end of file --- easybuild/easyconfigs/p/poppler/poppler-23.09.0-GCC-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/poppler/poppler-23.09.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/poppler/poppler-23.09.0-GCC-12.3.0.eb index 4d71d9bacbf..a5162ef7ca5 100644 --- a/easybuild/easyconfigs/p/poppler/poppler-23.09.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/p/poppler/poppler-23.09.0-GCC-12.3.0.eb @@ -57,4 +57,3 @@ sanity_check_paths = { sanity_check_commands = ["pdfinfo --help"] moduleclass = 'lib' - From e41d135487848b039f0e88e8d00348885cac7556 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 2 Oct 2023 15:39:01 +0200 Subject: [PATCH 8966/9987] Update easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb Co-authored-by: SebastianAchilles --- .../s/spglib-python/spglib-python-2.1.0-foss-2023a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb index 86b1fab9f39..4dbb404fa44 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb @@ -8,10 +8,13 @@ description = "Spglib for Python. Spglib is a library for finding and handling c toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('scikit-build-core', '0.5.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), - ('scikit-build-core', '0.5.0'), ] sanity_pip_check = True From a970275f4f670a042a136ad01e9c5465ee428159 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 2 Oct 2023 15:39:12 +0200 Subject: [PATCH 8967/9987] Update easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb Co-authored-by: SebastianAchilles --- .../s/spglib-python/spglib-python-2.1.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb index 4dbb404fa44..1e0edd77069 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb @@ -6,7 +6,7 @@ version = '2.1.0' homepage = 'https://pypi.python.org/pypi/spglib' description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} builddependencies = [ ('scikit-build-core', '0.5.0'), From 5e6459b7ac957258e529297f71f8c7434f66b8ea Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 2 Oct 2023 15:39:35 +0200 Subject: [PATCH 8968/9987] Update easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb Co-authored-by: SebastianAchilles --- .../scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb index d4705b97c78..672a73b4031 100644 --- a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.0-GCCcore-12.3.0.eb @@ -13,12 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), ('hatchling', '1.18.0'), - ('CMake', '3.26.3'), ] dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), + ('CMake', '3.26.3'), ] use_pip = True From 7005186761a7c83cf24d788a3ac7a88cf4726a8f Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 2 Oct 2023 15:40:09 +0200 Subject: [PATCH 8969/9987] Rename spglib-python-2.1.0-foss-2023a.eb to spglib-python-2.1.0-gfbf-2023a.eb --- ...thon-2.1.0-foss-2023a.eb => spglib-python-2.1.0-gfbf-2023a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/spglib-python/{spglib-python-2.1.0-foss-2023a.eb => spglib-python-2.1.0-gfbf-2023a.eb} (100%) diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb similarity index 100% rename from easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-foss-2023a.eb rename to easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb From bc53f019ca953bd9d601b00d1c8c105db9aeda46 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 2 Oct 2023 15:50:21 +0200 Subject: [PATCH 8970/9987] Added checksum for CLEAR --- .../c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb index 9fe20fcc0a3..4f538aac596 100644 --- a/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb @@ -10,6 +10,7 @@ description = "Direct comparison of circular and linear RNA expression" source_urls = ["https://github.com/YangLab/CLEAR/archive"] sources = ["%s.tar.gz" % local_commit] +checksums = ['a0824bcbaf6db52dcbb24467277045d341bbd266e582d9a89fd1656c89ba64ea'] toolchain = {'name': 'foss', 'version': '2021b'} @@ -25,6 +26,11 @@ download_dep_fail = True use_pip = True sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/clear_quant'], + 'dirs': [] +} + sanity_check_commands = ["clear_quant -h"] -options = {'modulename': False} +options = {'modulename': False} \ No newline at end of file From e20e582ac13cbd433042d8a0b9cb682762355004 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 2 Oct 2023 15:58:57 +0200 Subject: [PATCH 8971/9987] Remove comment accidentally kept from foss version. --- .../easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb index 60a3c980b9f..cf258368771 100644 --- a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2023a.eb @@ -18,9 +18,6 @@ checksums = [ '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch ] -# The -fallow-argument-mismatch allows MPI communication calls to be -# called with arrays of different types at different places in the -# code. This otherwise cause an error in GCC 10.X buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' buildopts += 'COMMS=mpi' From f7dae6017bcbd014c0f2e8ea055444a79ec51567 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 2 Oct 2023 16:11:06 +0200 Subject: [PATCH 8972/9987] Fixed style issues + added moduleclass --- .../c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb index 4f538aac596..d6dc0ae6888 100644 --- a/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb @@ -33,4 +33,6 @@ sanity_check_paths = { sanity_check_commands = ["clear_quant -h"] -options = {'modulename': False} \ No newline at end of file +options = {'modulename': False} + +moduleclass = 'bio' From 968ba7a183549651dd2a681af29e416e318402df Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Oct 2023 18:22:58 +0200 Subject: [PATCH 8973/9987] rename source file after download for CLEAR + enhance sanity check --- ...CLEAR-20210117-foss-2021b-Python-2.7.18.eb | 35 ++++++++++--------- 1 file changed, 19 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb b/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb index d6dc0ae6888..46ab6c20df7 100644 --- a/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/c/CLEAR/CLEAR-20210117-foss-2021b-Python-2.7.18.eb @@ -1,19 +1,19 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = "CLEAR" -version = "20210117" -versionsuffix = "-Python-%(pyver)s" -local_commit = "64bc22d52d99466a044848992fd0d775a983d60c" +name = 'CLEAR' +local_commit = '64bc22d52d99466a044848992fd0d775a983d60c' +version = '20210117' +versionsuffix = '-Python-%(pyver)s' -homepage = "https://github.com/YangLab/CLEAR" -description = "Direct comparison of circular and linear RNA expression" - -source_urls = ["https://github.com/YangLab/CLEAR/archive"] -sources = ["%s.tar.gz" % local_commit] -checksums = ['a0824bcbaf6db52dcbb24467277045d341bbd266e582d9a89fd1656c89ba64ea'] +homepage = 'https://github.com/YangLab/CLEAR' +description = 'Direct comparison of circular and linear RNA expression' toolchain = {'name': 'foss', 'version': '2021b'} +source_urls = ['https://github.com/YangLab/CLEAR/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['a0824bcbaf6db52dcbb24467277045d341bbd266e582d9a89fd1656c89ba64ea'] + dependencies = [ ('Python', '2.7.18'), ('CIRCexplorer2', '2.3.8', versionsuffix), @@ -26,13 +26,16 @@ download_dep_fail = True use_pip = True sanity_pip_check = True +options = {'modulename': 'src.circ_quant'} + sanity_check_paths = { - 'files': ['bin/clear_quant'], - 'dirs': [] + 'files': ['bin/circ_quant', 'bin/clear_quant'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } -sanity_check_commands = ["clear_quant -h"] - -options = {'modulename': False} +sanity_check_commands = [ + "circ_quant --help", + "clear_quant --help", +] moduleclass = 'bio' From bbff06d4bb7d024a59f8c4660991fc087b5b9baa Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Mon, 2 Oct 2023 16:38:04 +0000 Subject: [PATCH 8974/9987] adding easyconfigs: SignalP-6.0h-foss-2022b-fast.eb --- .../s/SignalP/SignalP-6.0h-foss-2022b-fast.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2022b-fast.eb diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2022b-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2022b-fast.eb new file mode 100644 index 00000000000..59b117b9c68 --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0h-foss-2022b-fast.eb @@ -0,0 +1,52 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0h' +_suffix = 'fast' +versionsuffix = '-' + _suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +checksums = ['4afe3c004e23a1d6518cefb23448b4d5ede5f1c5b276db541f839f0615822125'] + +unpack_options = '--strip-components=1' + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # numpy > 1.19.2 + ('tqdm', '4.64.1'), # tqdm > 4.46.1 + ('PyTorch', '1.13.1'), # torch > 1.7.0 + ('matplotlib', '3.7.0'), # matplotlib > 3.3.2 +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' From 7938783d5c5259dd9b9a1e32ba52fa41f72ed1ff Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Tue, 3 Oct 2023 10:56:34 +0200 Subject: [PATCH 8975/9987] Update Molden-7.3_fix_arg_handling.patch description --- .../easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch index 1b0d21594ec..1893f4a7798 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_arg_handling.patch @@ -1,3 +1,5 @@ +# Use F2003 functions for argument handling. +# Author: xinan1911 (SURF) diff -ruN molden7.3.orig/src/molden.f molden7.3/src/molden.f --- molden7.3.orig/src/molden.f 2023-08-09 15:22:58.503993000 +0200 +++ molden7.3/src/molden.f 2023-09-26 20:13:01.426339279 +0200 From d5247e411177bfc200b3ef48124c03074f2be1da Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Tue, 3 Oct 2023 10:58:37 +0200 Subject: [PATCH 8976/9987] Update Molden-7.3_fix_makefile_for_easybuild.patch description --- .../m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch index 595dfb9a0e0..96b975e97a5 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3_fix_makefile_for_easybuild.patch @@ -1,3 +1,5 @@ +# Make makefile EasyBuild friendly. +# Author: xinan1911 (SURF) diff -ruN molden7.3.orig/makefile molden7.3/makefile --- molden7.3.orig/makefile 2023-08-09 15:22:58.725188000 +0200 +++ molden7.3/makefile 2023-09-26 20:29:25.276603201 +0200 From 1a15501ad2fb51456b97e6187d831d94799bb43c Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Tue, 3 Oct 2023 11:33:38 +0200 Subject: [PATCH 8977/9987] Update checksums and sanity check commands Molden-7.3-GCCcore-12.3.0.eb checksums are updated via --inject-checksums locally after changing the patch file description. Sanity check command is added after testing locally. --- .../easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb index f5a1c0e9c91..7d73969a3f7 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb @@ -18,8 +18,8 @@ patches = [ ] checksums = [ {'molden7.3.tar.gz': '870f4fa6635229791bb09bbbd07f51456b2c90101d73564dc47ed7769b8c07a1'}, - {'Molden-7.3_fix_makefile_for_easybuild.patch': '303dcd308dfb618088d014ea2956ec627d9f09b6547d547ac4b432be4e5b9d7c'}, - {'Molden-7.3_fix_arg_handling.patch': '869eb33ea4cdd022402251b59386c146e7ceaf85f838f2a002fb4c393db4c1c2'}, + {'Molden-7.3_fix_makefile_for_easybuild.patch': 'b97d794cf92978d151d70485250367eebf719885c6a909ca3404a800903e3f7a'}, + {'Molden-7.3_fix_arg_handling.patch': 'e7d0654a7c7a0b069ff4a904d3334ea19f6b0147003bc460745db8b8d5f931cf'}, ] builddependencies = [ @@ -45,4 +45,8 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ +"molden -h" +] + moduleclass = 'chem' From d97c6a4d6d39e5ced1195ff07e16c20a00509433 Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 3 Oct 2023 15:27:51 +0200 Subject: [PATCH 8978/9987] update_checksum --- .../n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb index 4e931ccda3d..773cae7efa8 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['b4f5d7d9eea2c12e32e7a06fe138b2cfc75969c6d5c473aa6f819a792db2fc96'] +checksums = ['6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9'] builddependencies = [('binutils', '2.40')] From 34fd431c1f459042ab1a057002fb70551c0b7b6f Mon Sep 17 00:00:00 2001 From: Maxim Date: Tue, 3 Oct 2023 15:47:19 +0200 Subject: [PATCH 8979/9987] Update easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb index 773cae7efa8..d23741aa2c8 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -11,7 +11,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9'] +checksums = [('6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9', + 'b4f5d7d9eea2c12e32e7a06fe138b2cfc75969c6d5c473aa6f819a792db2fc96')] builddependencies = [('binutils', '2.40')] From d3ff9ef7dd4eb256df765eba307afc9d598ba8dd Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 3 Oct 2023 16:20:16 +0200 Subject: [PATCH 8980/9987] adding easyconfigs: OpenMM-8.0.0-foss-2023a.eb --- .../o/OpenMM/OpenMM-8.0.0-foss-2023a.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a.eb new file mode 100644 index 00000000000..b45f64ecebe --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2023a.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.0.0' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('SWIG', '4.1.1'), +] + +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From 2cec507b15ffa813396769fb649be1a1378fc522 Mon Sep 17 00:00:00 2001 From: swbuild Date: Tue, 3 Oct 2023 19:06:28 +0200 Subject: [PATCH 8981/9987] adding easyconfigs: Go-1.21.1.eb --- easybuild/easyconfigs/g/Go/Go-1.21.1.eb | 26 +++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.21.1.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.21.1.eb b/easybuild/easyconfigs/g/Go/Go-1.21.1.eb new file mode 100644 index 00000000000..25e9fdaccb6 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.21.1.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Go' +version = "1.21.1" + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] +local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} +sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] +checksums = ['b3075ae1ce5dab85f89bc7905d1632de23ca196bd8336afd93fa97434cfa55ae'] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +sanity_check_commands = ["go help"] + +modextravars = {'GOROOT': '%(installdir)s'} + +moduleclass = 'compiler' From 22df770aeab8f5cca23a68958c3798ed624ee204 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 3 Oct 2023 20:01:32 +0200 Subject: [PATCH 8982/9987] adding easyconfigs: Circuitscape-5.12.3-Julia-1.9.2.eb --- .../Circuitscape-5.12.3-Julia-1.9.2.eb | 408 ++++++++++++++++++ 1 file changed, 408 insertions(+) create mode 100644 easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb new file mode 100644 index 00000000000..c92bd435570 --- /dev/null +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb @@ -0,0 +1,408 @@ +easyblock = 'JuliaBundle' + +name = 'Circuitscape' +version = '5.12.3' +_julia_ver = '1.9.2' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/Circuitscape/Circuitscape.jl' +description = "Algorithms from circuit theory to predict connectivity in heterogeneous landscapes" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, True), +] + +exts_list = [ + ('Preferences', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['a87c1fc863fcb6240c3f4327776fa01a1f87e0d2df5a0c1850f789ce24469da2'], + }), + ('JLLWrappers', '1.4.1', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], + }), + ('IntelOpenMP_jll', '2018.0.3+2', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/IntelOpenMP_jll.jl/archive/'], + 'sources': ['IntelOpenMP-v%(version)s.tar.gz'], + 'checksums': ['4e8586f0b794ba5cf159dde99774aab4509a32555fc900140f533999db476aab'], + }), + ('MKL_jll', '2022.2.0+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/MKL_jll.jl/archive/'], + 'sources': ['MKL-v%(version)s.tar.gz'], + 'checksums': ['228a80c33ae71a3efc78ed9f6a3329fd20a48ad80ff7af44f0d42057e1af4241'], + }), + ('Reexport', '1.2.2', { + 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['58abf90b037c618daeed89940c77ac129b5155b26429ac77643cc9c5db453363'], + }), + ('ImageCore', '0.9.4', { + 'source_urls': ['https://github.com/JuliaImages/ImageCore.jl/archive/'], + 'checksums': ['de5d244989891f47edc4f27bf8bf6557a6982e907f0874a62ad3480c9c333983'], + }), + ('ArchGDAL', '0.8.5', { + 'source_urls': ['https://github.com/yeesian/ArchGDAL.jl/archive/'], + 'checksums': ['e24ec57d88a3a07feac7db5b2501b8f06a1047c42a8eadcde9500e3601984065'], + }), + ('DelimitedFiles', '1.9.0', { + 'sources': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/JuliaData/DelimitedFiles.jl/archive/'], + }), + (name, version, { + 'source_urls': ['https://github.com/Circuitscape/Circuitscape.jl/archive/'], + 'checksums': ['1eb5b6f5711865792204677359c1b9d9247ae3f34af42f58dfe2ec4ad3dd2177'], + }), +] + +sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"Circuitscape\")'"] + +moduleclass = 'lib' From 7dc8daa45999d86e2e68aae85db693bd27a8f4ae Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 4 Oct 2023 04:55:45 +0200 Subject: [PATCH 8983/9987] Added missing checksum + removed redundant source --- .../c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb index c92bd435570..a6649359df9 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb @@ -394,8 +394,8 @@ exts_list = [ 'checksums': ['e24ec57d88a3a07feac7db5b2501b8f06a1047c42a8eadcde9500e3601984065'], }), ('DelimitedFiles', '1.9.0', { - 'sources': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/JuliaData/DelimitedFiles.jl/archive/'], + 'checksums': ['6b6329fb32aa9c503434711f1f004309013bddbd20d4f95c25bf6446631ef80b'], }), (name, version, { 'source_urls': ['https://github.com/Circuitscape/Circuitscape.jl/archive/'], From c7368b7320f69ecdb798b99d80b26db0e4d0faf1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Oct 2023 08:34:09 +0200 Subject: [PATCH 8984/9987] adding easyconfigs: PyTorch-Ignite-0.4.12-foss-2022a-CUDA-11.7.0.eb --- ...ch-Ignite-0.4.12-foss-2022a-CUDA-11.7.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.12-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.12-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.12-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..a486bf7403d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.12-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Ignite' +version = '0.4.12' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch-ignite.ai/' +description = """ +Ignite is a high-level library to help with training and evaluating neural +networks in PyTorch flexibly and transparently.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), +] + +exts_list = [ + ('pytorch-ignite', version, { + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s'], + 'sources': ['pytorch-ignite-%(version)s.tar.gz'], + 'checksums': ['063ca746aba413824d91b6fdc953118d54d1d25b972339dd8212a99c3a077423'], + 'modulename': 'ignite', + }), +] + +use_pip = True + +sanity_pip_check = True + +moduleclass = 'lib' From 898f99954bb0102077226b93c6cc022a4c6811bb Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 4 Oct 2023 15:06:43 +0200 Subject: [PATCH 8985/9987] Add QuantumESPRESSO --- .../QuantumESPRESSO-7.2-foss-2023a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb new file mode 100644 index 00000000000..4a79d7df97a --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.2-foss-2023a.eb @@ -0,0 +1,53 @@ +name = 'QuantumESPRESSO' +version = '7.2' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + { + 'filename': 'q-e-qe-%(version)s.tar.gz', + 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'] + }, + { + 'filename': 'qe-gipaw-%(version)s.tar.gz', + 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/']}, + { + 'filename': 'wannier90-3.1.0.tar.gz', + 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'] + }, +] +checksums = [ + {'q-e-qe-%(version)s.tar.gz': 'b348a4a7348b66a73545d9ca317a2645755c98d343c1cfe8def475ad030808c0'}, + {'qe-gipaw-%(version)s.tar.gz': '3375e6e8242b9d0a1ebf9ff9ac1111f4cc5c95d3f654bc2534c396b3b4e59a2f'}, + {'wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('M4', '1.4.19'), +] +dependencies = [ + ('HDF5', '1.14.0'), + ('ELPA', '2023.05.001'), + ('libxc', '6.2.2'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = "all gwl xspectra couple epw gipaw w90" + +# parallel build tends to fail +parallel = 1 + + +moduleclass = 'chem' From de177606392fa3e074963411a3e3fc2555d2ba78 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 4 Oct 2023 15:29:07 +0100 Subject: [PATCH 8986/9987] add arm64 checksum --- easybuild/easyconfigs/g/Go/Go-1.21.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Go/Go-1.21.1.eb b/easybuild/easyconfigs/g/Go/Go-1.21.1.eb index 25e9fdaccb6..8772f597710 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.21.1.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.21.1.eb @@ -12,7 +12,10 @@ toolchain = SYSTEM source_urls = ['https://storage.googleapis.com/golang/'] local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] -checksums = ['b3075ae1ce5dab85f89bc7905d1632de23ca196bd8336afd93fa97434cfa55ae'] +checksums = [{ + 'go%(version)s.linux-amd64.tar.gz': 'b3075ae1ce5dab85f89bc7905d1632de23ca196bd8336afd93fa97434cfa55ae', + 'go%(version)s.linux-arm64.tar.gz': '7da1a3936a928fd0b2602ed4f3ef535b8cd1990f1503b8d3e1acc0fa0759c967', +}] sanity_check_paths = { 'files': ['bin/go', 'bin/gofmt'], From f8920bf058689ab32af9d8079359bb26f09b6740 Mon Sep 17 00:00:00 2001 From: fizwit Date: Wed, 4 Oct 2023 16:23:04 -0700 Subject: [PATCH 8987/9987] Cereal requires GCC, add toolchain --- .../c/Cereal/Cereal-1.3.2-GCCcore-12.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cereal/Cereal-1.3.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/Cereal/Cereal-1.3.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.2-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..faa4de13e52 --- /dev/null +++ b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.2-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +## +# @Authors:: Maxime Boissonneault, Compute Canada +# @date: October 15, 2020 +## + +easyblock = 'CMakeMake' + +name = 'Cereal' +version = '1.3.2' + +homepage = 'https://uscilab.github.io/cereal/' +description = """cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly +turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be +fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or +used standalone.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'USCiLab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['16a7ad9b31ba5880dac55d62b5d6f243c3ebc8d46a3514149e56b5e7ea81f85f'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +configopts = '-DJUST_INSTALL_CEREAL=ON -DSKIP_PERFORMANCE_COMPARISON=ON ' + +sanity_check_paths = { + 'files': ['include/cereal/cereal.hpp'], + 'dirs': ['include', 'lib/cmake'], +} + +moduleclass = 'lib' From ba6e76c9bcf01e8f886e98040fc75e78437822d2 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 5 Oct 2023 11:21:17 +0200 Subject: [PATCH 8988/9987] adding easyconfigs: rasterstats-0.19.0-foss-2022a.eb --- .../rasterstats-0.19.0-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb new file mode 100644 index 00000000000..d9d69d4e77b --- /dev/null +++ b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'rasterstats' +version = '0.19.0' + +homepage = 'https://github.com/perrygeo/python-rasterstats' +description = "rasterstats is a Python module for summarizing geospatial raster datasets based on vector geometries." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Shapely', '1.8.2'), + ('Fiona', '1.8.21'), + ('rasterio', '1.3.4'), +] + +use_pip = True + +exts_list = [ + ('affine', '2.3.1', { + 'checksums': ['d676de66157ad6af99ffd94e0f54e89dfc35b0fb7252ead2ed0ad2dca431bdd0'], + }), + ('click', '8.1.3', { + 'checksums': ['7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e'], + }), + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('simplejson', '3.17.6', { + 'checksums': ['cf98038d2abf63a1ada5730e91e84c642ba6c225b0198c3684151b1f80c5f8a6'], + }), + (name, version, { + 'checksums': ['066c44feb6f3936804a0c79d112271fa5bf5de0d5058823ab5c1e0047ab7bbbc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 3396ccf08c15f38c5de7625a7a7c151268c011e7 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 5 Oct 2023 15:21:51 +0200 Subject: [PATCH 8989/9987] adding easyconfigs: Raptor-2.0.16-GCCcore-10.3.0.eb --- .../r/Raptor/Raptor-2.0.16-GCCcore-10.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-10.3.0.eb new file mode 100644 index 00000000000..4aec56e89f0 --- /dev/null +++ b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-10.3.0.eb @@ -0,0 +1,45 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Based on Raptor2 RPM spec file: +# https://git.rockylinux.org/staging/rpms/raptor2/-/blob/r8/SPECS/raptor2.spec +# The RPM patches have been integrated in the version 2.0.16 +## +easyblock = 'ConfigureMake' + +name = 'Raptor' +version = '2.0.16' +homepage = 'https://librdf.org/raptor/' +description = """Set of parsers and serializers that generate Resource Description Framework +(RDF) triples by parsing syntaxes or serialize the triples into a syntax.""" +# software_license = 'LicenseLGPLv2.1 + LicenseGPLv2 + LicenseApachev2' + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://download.librdf.org/source'] +sources = ['raptor2-%(version)s.tar.gz'] +checksums = ['089db78d7ac982354bdbf39d973baf09581e6904ac4c92a98c5caadb3de44680'] + +builddependencies = [ + ('Autotools', '20210128'), + ('make', '4.3'), + ('binutils', '2.36.1'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('cURL', '7.76.0'), + ('ICU', '69.1'), +] + +configopts = "--disable-static --enable-release --disable-gtk-doc --with-yajl=no" + +sanity_check_paths = { + 'files': ['bin/rapper', 'lib/libraptor2.so'], + 'dirs': ['include/raptor2/'] +} + +sanity_check_commands = ["rapper --help"] + +moduleclass = 'data' From 277fbcfb780792c38bf2f3d5838be8fbb4cd280a Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 5 Oct 2023 15:14:46 +0100 Subject: [PATCH 8990/9987] add binutils --- easybuild/easyconfigs/c/Cereal/Cereal-1.3.2-GCCcore-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/Cereal/Cereal-1.3.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.2-GCCcore-12.2.0.eb index faa4de13e52..b6bb38d747b 100644 --- a/easybuild/easyconfigs/c/Cereal/Cereal-1.3.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.2-GCCcore-12.2.0.eb @@ -23,6 +23,7 @@ checksums = ['16a7ad9b31ba5880dac55d62b5d6f243c3ebc8d46a3514149e56b5e7ea81f85f'] builddependencies = [ ('CMake', '3.24.3'), + ('binutils', '2.39'), ] configopts = '-DJUST_INSTALL_CEREAL=ON -DSKIP_PERFORMANCE_COMPARISON=ON ' From e962a0c0848b5b14f4f1a3582fd1023b10dc94a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 16:22:19 +0200 Subject: [PATCH 8991/9987] adding easyconfigs: imutils-0.5.4-fosscuda-2020b.eb --- .../i/imutils/imutils-0.5.4-fosscuda-2020b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb diff --git a/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb b/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb new file mode 100644 index 00000000000..0c948731f6f --- /dev/null +++ b/easybuild/easyconfigs/i/imutils/imutils-0.5.4-fosscuda-2020b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'imutils' +version = '0.5.4' + +homepage = 'https://github.com/jrosebr1/imutils' +description = """A series of convenience functions to make basic image processing operations such as translation, +rotation, resizing, skeletonization, and displaying Matplotlib images easier with OpenCV and Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['03827a9fca8b5c540305c0844a62591cf35a0caec199cb0f2f0a4a0fb15d8f24'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('OpenCV', '4.5.1', '-contrib'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'vis' From c85ed46b05ab625dee5df4d9b5da7be293fd9171 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Thu, 5 Oct 2023 16:40:56 +0200 Subject: [PATCH 8992/9987] Update easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb index d9d69d4e77b..f235adbb6a0 100644 --- a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb +++ b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb @@ -22,9 +22,6 @@ exts_list = [ ('affine', '2.3.1', { 'checksums': ['d676de66157ad6af99ffd94e0f54e89dfc35b0fb7252ead2ed0ad2dca431bdd0'], }), - ('click', '8.1.3', { - 'checksums': ['7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e'], - }), ('cligj', '0.7.2', { 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], }), From 1665e3f9514ccb145bcec5deea21558dbe535193 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Thu, 5 Oct 2023 16:41:03 +0200 Subject: [PATCH 8993/9987] Update easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb index f235adbb6a0..a2c9fc437b6 100644 --- a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb +++ b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.19.0-foss-2022a.eb @@ -25,9 +25,6 @@ exts_list = [ ('cligj', '0.7.2', { 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], }), - ('simplejson', '3.17.6', { - 'checksums': ['cf98038d2abf63a1ada5730e91e84c642ba6c225b0198c3684151b1f80c5f8a6'], - }), (name, version, { 'checksums': ['066c44feb6f3936804a0c79d112271fa5bf5de0d5058823ab5c1e0047ab7bbbc'], }), From cbaa31123b8969ade89365130d29e1bcf3b18693 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 5 Oct 2023 16:45:04 +0200 Subject: [PATCH 8994/9987] Add missing dependencies --- easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-10.3.0.eb index 4aec56e89f0..91c9deedba1 100644 --- a/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Raptor/Raptor-2.0.16-GCCcore-10.3.0.eb @@ -27,6 +27,8 @@ builddependencies = [ ('Autotools', '20210128'), ('make', '4.3'), ('binutils', '2.36.1'), +] +dependencies = [ ('libxml2', '2.9.10'), ('libxslt', '1.1.34'), ('cURL', '7.76.0'), From a640c19d718c17372bdd48aea57a0394c09ce4af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 17:26:30 +0200 Subject: [PATCH 8995/9987] add missing dependencies for MONAI to support extras required by MONAI-Label --- .../MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb | 36 +++++++++++++++++-- .../m/MONAI/MONAI-1.0.1-foss-2022a.eb | 36 +++++++++++++++++-- .../PyTorch-Ignite-0.4.12-foss-2022a.eb | 31 ++++++++++++++++ 3 files changed, 99 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.12-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb index 134fe42c205..b35b6ffb69b 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), ('Python', '3.10.4'), ('PyTorch', '1.12.0', versionsuffix), + ('PyTorch-Ignite', '0.4.12', versionsuffix), ('einops', '0.4.1'), ('ITK', '5.2.1'), ('NiBabel', '4.0.2'), @@ -25,15 +26,46 @@ dependencies = [ ('tensorboard', '2.10.0'), ('torchvision', '0.13.1', versionsuffix), ('tqdm', '4.64.0'), + ('Pillow', '9.1.1'), + ('openslide-python', '1.2.0'), + ('BeautifulSoup', '4.10.0'), ] +# install MONAI with list of 'extras', which require additional dependencies +local_pip_extras = "nibabel,skimage,pillow,tensorboard,gdown,ignite,torchvision,itk,tqdm,lmdb,psutil,openslide,fire" + +# avoid using hatchling as build backend (since installing it for this old Python version is a nightmare) +local_preinstallopts_termcolor = ' '.join([ + r"""sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """, + r"""-e 's/^requires = \[/requires = \["setuptools"/g' """, + r"""-e '/"hatch/d' """, + # replace dynamic version with hardcoded version + r"""-e '/"version"/d' """, + r"""-e 's/^readme = .*/version = "%(version)s"/g' """, + r"pyproject.toml && ", +]) + exts_list = [ + ('gdown', '4.7.1', { + 'checksums': ['347f23769679aaf7efa73e5655270fcda8ca56be65eb84a4a21d143989541045'], + }), + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('termcolor', '2.3.0', { + 'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'], + 'preinstallopts': local_preinstallopts_termcolor, + }), + ('fire', '0.5.0', { + 'checksums': ['a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6'], + }), (name, version, { - 'preinstallopts': 'BUILD_MONAI=1', - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['%(version)s.tar.gz'], 'checksums': [('dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b', 'bb1a84ea3c4cd2c3756f72359a891843e0efa02da17537fb158b28c4e0b2d243')], + 'preinstallopts': "BUILD_MONAI=1", + 'use_pip_extras': local_pip_extras, }), ] diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb index 04560e4c6fd..c7b0c3a2e8a 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb @@ -16,6 +16,7 @@ github_account = 'Project-MONAI' dependencies = [ ('Python', '3.10.4'), ('PyTorch', '1.12.0'), + ('PyTorch-Ignite', '0.4.12'), ('einops', '0.4.1'), ('ITK', '5.2.1'), ('NiBabel', '4.0.2'), @@ -23,15 +24,46 @@ dependencies = [ ('tensorboard', '2.10.0'), ('torchvision', '0.13.1'), ('tqdm', '4.64.0'), + ('Pillow', '9.1.1'), + ('openslide-python', '1.2.0'), + ('BeautifulSoup', '4.10.0'), ] +# install MONAI with list of 'extras', which require additional dependencies +local_pip_extras = "nibabel,skimage,pillow,tensorboard,gdown,ignite,torchvision,itk,tqdm,lmdb,psutil,openslide,fire" + +# avoid using hatchling as build backend (since installing it for this old Python version is a nightmare) +local_preinstallopts_termcolor = ' '.join([ + r"""sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """, + r"""-e 's/^requires = \[/requires = \["setuptools"/g' """, + r"""-e '/"hatch/d' """, + # replace dynamic version with hardcoded version + r"""-e '/"version"/d' """, + r"""-e 's/^readme = .*/version = "%(version)s"/g' """, + r"pyproject.toml && ", +]) + exts_list = [ + ('gdown', '4.7.1', { + 'checksums': ['347f23769679aaf7efa73e5655270fcda8ca56be65eb84a4a21d143989541045'], + }), + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('termcolor', '2.3.0', { + 'checksums': ['b5b08f68937f138fe92f6c089b99f1e2da0ae56c52b78bf7075fd95420fd9a5a'], + 'preinstallopts': local_preinstallopts_termcolor, + }), + ('fire', '0.5.0', { + 'checksums': ['a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6'], + }), (name, version, { - 'preinstallopts': 'BUILD_MONAI=1', - 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['%(version)s.tar.gz'], 'checksums': [('dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b', 'bb1a84ea3c4cd2c3756f72359a891843e0efa02da17537fb158b28c4e0b2d243')], + 'preinstallopts': "BUILD_MONAI=1", + 'use_pip_extras': local_pip_extras, }), ] diff --git a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.12-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.12-foss-2022a.eb new file mode 100644 index 00000000000..ef84f91c426 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.12-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Ignite' +version = '0.4.12' + +homepage = 'https://pytorch-ignite.ai/' +description = """ +Ignite is a high-level library to help with training and evaluating neural +networks in PyTorch flexibly and transparently.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), +] + +exts_list = [ + ('pytorch-ignite', version, { + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s'], + 'sources': ['pytorch-ignite-%(version)s.tar.gz'], + 'checksums': ['063ca746aba413824d91b6fdc953118d54d1d25b972339dd8212a99c3a077423'], + 'modulename': 'ignite', + }), +] + +use_pip = True + +sanity_pip_check = True + +moduleclass = 'lib' From 0c04262a3651856e50c3caa8dfaae5fa83a904ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 20:25:09 +0200 Subject: [PATCH 8996/9987] also build Python bindings for ITK 5.2.1 with foss/2022a --- easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb index 83ecef81cdc..f862a7a5b45 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb @@ -34,6 +34,7 @@ dependencies = [ ('LibTIFF', '4.3.0'), ('VTK', '9.2.2'), ('zlib', '1.2.12'), + ('Python', '3.10.4'), ] local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] @@ -41,7 +42,7 @@ local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' -configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' +configopts += '-DITK_WRAP_PYTHON:BOOL=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK configopts += ' '.join(local_sys_cmake) @@ -53,7 +54,11 @@ local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF sanity_check_paths = { 'files': ['bin/itkTestDriver'] + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], - 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'lib/python%(pyshortver)s/site-packages', 'share'], } +sanity_check_commands = ["python -c 'import itk'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'data' From 7ed522cd35f3ac8bfee1a3bd310fcdac3cecd9c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 20:25:41 +0200 Subject: [PATCH 8997/9987] adding easyconfigs: uncertainties-3.1.7-foss-2021b.eb --- .../uncertainties-3.1.7-foss-2021b.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2021b.eb b/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2021b.eb new file mode 100644 index 00000000000..21ad86a60e7 --- /dev/null +++ b/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'uncertainties' +version = '3.1.7' + +homepage = 'http://uncertainties-python-package.readthedocs.io' +description = """Transparent calculations with uncertainties on the quantities involved (aka error propagation); + fast calculation of derivatives""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 6a4f9e71f6afeff7f2052793c9ab31a21ef2eba2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 20:39:23 +0200 Subject: [PATCH 8998/9987] enhance sanity check for MONAI to verify whether optional dependencies required for extras are available --- .../m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb | 8 +++++++- easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb | 8 +++++++- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb index b35b6ffb69b..23b259a17e0 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb @@ -73,7 +73,13 @@ use_pip = True sanity_pip_check = True -sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] +# 'pip check' does not verify whether all optional dependencies required to support 'extras' +# are actually available, so we do it here via an import check; +# Pillow is a special case, since there we need to use 'import PIL' +sanity_check_commands = [ + "python -c 'import monai; monai.config.print_config()'", + "python -c 'import PIL'", # for Pillow required dependency +] + ["python -c 'import %s'" % x for x in local_pip_extras.split(',') if x != 'pillow'] sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb index c7b0c3a2e8a..d40fe8f2614 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb @@ -71,7 +71,13 @@ use_pip = True sanity_pip_check = True -sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] +# 'pip check' does not verify whether all optional dependencies required to support 'extras' +# are actually available, so we do it here via an import check; +# Pillow is a special case, since there we need to use 'import PIL' +sanity_check_commands = [ + "python -c 'import monai; monai.config.print_config()'", + "python -c 'import PIL'", # for Pillow required dependency +] + ["python -c 'import %s'" % x for x in local_pip_extras.split(',') if x != 'pillow'] sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], From 5e64829e2cdddef87958799dbd3646d947cfa24a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 20:54:11 +0200 Subject: [PATCH 8999/9987] add ridge extension to R 4.2.2 --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 598a3d2bb3e..5c533ecb998 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3666,6 +3666,9 @@ exts_list = [ ('flextable', '0.9.2', { 'checksums': ['bccd53919ae58f1d26c4a8ee42da1f5e0b7333f8b4ee295b380ed256069f923d'], }), + ('ridge', '3.3', { + 'checksums': ['5c2daecf6f97aa099ef5fa54f8448518c4f2ed6e44dd29fc60621a70721c60f5'], + }), ] moduleclass = 'lang' From f59d1ddb65c5bf82549c2ede5e70db9803b008ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 22:18:11 +0200 Subject: [PATCH 9000/9987] adding easyconfigs: biobambam2-2.0.185-GCC-12.3.0.eb, libmaus2-2.0.813-GCC-12.3.0.eb --- .../biobambam2-2.0.185-GCC-12.3.0.eb | 32 +++++++++++++++++++ .../l/libmaus2/libmaus2-2.0.813-GCC-12.3.0.eb | 25 +++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.185-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.813-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.185-GCC-12.3.0.eb b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.185-GCC-12.3.0.eb new file mode 100644 index 00000000000..69ef6ed8f53 --- /dev/null +++ b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.185-GCC-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'biobambam2' +version = '2.0.185' + +homepage = 'https://github.com/gt1/biobambam2' +description = "Tools for processing BAM files" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +local_release = '20221211202123' +source_urls = ['https://gitlab.com/german.tischler/biobambam2/-/archive/%%(version)s-release-%s' % local_release] +sources = ['biobambam2-%%(version)s-release-%s.tar.gz' % local_release] +checksums = ['e405421e869ac7220c3a7e5da0d24a3c7b4c7b1807e044a439fe68efc88a1f2a'] + +dependencies = [ + ('libmaus2', '2.0.813'), +] + +configopts = "--with-libmaus2=$EBROOTLIBMAUS2" + +local_binaries = ['bamcollate2', 'bammarkduplicates', 'bammaskflags', 'bamrecompress', + 'bamsormadup', 'bamsort', 'bamtofastq'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["%s --help" % x for x in local_binaries] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.813-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.813-GCC-12.3.0.eb new file mode 100644 index 00000000000..95e24c04848 --- /dev/null +++ b/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.813-GCC-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libmaus2' +version = '2.0.813' +local_release = '20221210220409' + +homepage = 'https://github.com/gt1/libmaus2' +description = "libmaus2 is a collection of data structures and algorithms." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://gitlab.com/german.tischler/libmaus2/-/archive/%%(version)s-release-%s/' % local_release] +sources = ['libmaus2-%%(version)s-release-%s.tar.gz' % local_release] +checksums = ['4125f8daefd6900185675026498369457088e25e81029597659249be49cd5261'] + +dependencies = [('Boost', '1.82.0')] + +sanity_check_paths = { + 'files': ['lib/libmaus2.a', 'lib/libmaus2.%s' % SHLIB_EXT, + 'lib/libmaus2_simd_align_128.a', 'lib/libmaus2_simd_align_128.%s' % SHLIB_EXT, + 'lib/libmaus2_simd_align_256.a', 'lib/libmaus2_simd_align_256.%s' % SHLIB_EXT], + 'dirs': ['include/libmaus2'], +} + +moduleclass = 'lib' From 1e3870559532eae0c41f6adb17f21b66519f73f9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 23:08:03 +0200 Subject: [PATCH 9001/9987] adding easyconfigs: ArviZ-0.16.1-foss-2023a.eb, h5netcdf-1.2.0-foss-2023a.eb, xarray-2023.9.0-gfbf-2023a.eb --- .../a/ArviZ/ArviZ-0.16.1-foss-2023a.eb | 35 +++++++++++++++++++ .../h/h5netcdf/h5netcdf-1.2.0-foss-2023a.eb | 28 +++++++++++++++ .../x/xarray/xarray-2023.9.0-gfbf-2023a.eb | 28 +++++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.16.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2023.9.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.16.1-foss-2023a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.16.1-foss-2023a.eb new file mode 100644 index 00000000000..af5291fdab6 --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.16.1-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'ArviZ' +version = '0.16.1' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # numpy, scipy, pandas + ('netcdf4-python', '1.6.4'), + ('xarray', '2023.9.0'), + ('matplotlib', '3.7.2'), + ('h5netcdf', '1.2.0'), +] + +use_pip = True + +exts_list = [ + ('xarray-einstats', '0.6.0', { + 'sources': ['xarray_einstats-%(version)s.tar.gz'], + 'checksums': ['ace90601505cfbe2d374762e674557ed14e1725b024823372f7ef9fd237effad'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['35bab9072f66f5a8204d2a71911d09ce05056c177f1a780de53efa2714c27575'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2023a.eb b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2023a.eb new file mode 100644 index 00000000000..311855957b7 --- /dev/null +++ b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.2.0-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'h5netcdf' +version = '1.2.0' + +homepage = 'https://h5netcdf.org/' +description = """A Python interface for the netCDF4 file-format that reads and writes local or +remote HDF5 files directly via h5py or h5pyd, without relying on the Unidata +netCDF library.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('h5py', '3.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['7f6b2733bde06ea2575b79a6450d9bd5c38918ff4cb2a355bf22bbe8c86c6bcf'], + 'preinstallopts': """sed -i 's/^dynamic = .*/version = "%(version)s"/g' pyproject.toml && """, + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2023.9.0-gfbf-2023a.eb b/easybuild/easyconfigs/x/xarray/xarray-2023.9.0-gfbf-2023a.eb new file mode 100644 index 00000000000..fefb271482f --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2023.9.0-gfbf-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'xarray' +version = '2023.9.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['271955c05dc626dad37791a7807d920aaf9c64cac71d03b45ec7e402cc646603'], + 'preinstallopts': """sed -i 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """, + }), +] + +moduleclass = 'data' From c1be8140469f183bf4fb1a0da9f70b84a79a92fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 23:10:20 +0200 Subject: [PATCH 9002/9987] {math}[gfbf/2023a] PyTensor v2.17.1 --- .../p/PyTensor/PyTensor-2.17.1-gfbf-2023a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTensor/PyTensor-2.17.1-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/p/PyTensor/PyTensor-2.17.1-gfbf-2023a.eb b/easybuild/easyconfigs/p/PyTensor/PyTensor-2.17.1-gfbf-2023a.eb new file mode 100644 index 00000000000..5ae101c343e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTensor/PyTensor-2.17.1-gfbf-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'PyTensor' +version = '2.17.1' + +homepage = 'https://github.com/pymc-devs/pytensor' +description = "Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cons', '0.4.6', { + 'checksums': ['669fe9d5ee916d5e42b9cac6acc911df803d04f2e945c1604982a04d27a29b47'], + }), + ('multipledispatch', '1.0.0', { + 'checksums': ['5c839915465c68206c3e9c473357908216c28383b425361e5d144594bf85a7e0'], + }), + ('etuples', '0.3.9', { + 'checksums': ['a474e586683d8ba8d842ba29305005ceed1c08371a4b4b0e0e232527137e5ea3'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('logical-unification', '0.4.6', { + 'checksums': ['908435123f8a106fa4dcf9bf1b75c7beb309fa2bbecf277868af8f1c212650a0'], + 'modulename': 'unification', + }), + ('miniKanren', '1.0.3', { + 'checksums': ['1ec8bdb01144ad5e8752c7c297fb8a122db920f859276d25a72d164e998d7f6e'], + 'modulename': 'kanren', + }), + (name, version, { + 'sources': ['pytensor-%(version)s.tar.gz'], + 'checksums': ['64855a453b945c52d674086f1d160a35e910efbf13693dfaf0c39e92d474a851'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytensor-cache'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From 17805d0dff7dd7d37e577526554ede3783dcc031 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Oct 2023 23:12:13 +0200 Subject: [PATCH 9003/9987] adding easyconfigs: PyMC-5.9.0-foss-2023a.eb --- .../p/PyMC/PyMC-5.9.0-foss-2023a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyMC/PyMC-5.9.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PyMC/PyMC-5.9.0-foss-2023a.eb b/easybuild/easyconfigs/p/PyMC/PyMC-5.9.0-foss-2023a.eb new file mode 100644 index 00000000000..953952040c2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyMC/PyMC-5.9.0-foss-2023a.eb @@ -0,0 +1,37 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'PyMC' +version = '5.9.0' + +homepage = 'https://www.pymc.io' +description = """PyMC is a probabilistic programming library for Python that allows users to build Bayesian models + with a simple Python API and fit them using Markov chain Monte Carlo (MCMC) methods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # for numpy, scipy, pandas + ('ArviZ', '0.16.1'), + ('PyTensor', '2.17.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('fastprogress', '1.0.3', { + 'checksums': ['7a17d2b438890f838c048eefce32c4ded47197ecc8ea042cecc33d3deb8022f5'], + }), + ('cachetools', '5.3.1', { + 'checksums': ['dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b'], + }), + ('pymc', version, { + 'checksums': ['96a063e6ce4d754a0d4a93e460a270453eac78cee37c816d1f0d26a4e08cd269'], + }), +] + +moduleclass = 'math' From 89626d1373f936a10e790b3c0c58de40f55b80e0 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 6 Oct 2023 10:50:24 +0200 Subject: [PATCH 9004/9987] adding easyconfigs: segmentation-models-pytorch-0.3.3-foss-2022a.eb --- ...ntation-models-pytorch-0.3.3-foss-2022a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/s/segmentation-models-pytorch/segmentation-models-pytorch-0.3.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/segmentation-models-pytorch/segmentation-models-pytorch-0.3.3-foss-2022a.eb b/easybuild/easyconfigs/s/segmentation-models-pytorch/segmentation-models-pytorch-0.3.3-foss-2022a.eb new file mode 100644 index 00000000000..1d526510da3 --- /dev/null +++ b/easybuild/easyconfigs/s/segmentation-models-pytorch/segmentation-models-pytorch-0.3.3-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'segmentation-models-pytorch' +version = '0.3.3' + +homepage = 'https://github.com/qubvel/segmentation_models.pytorch' +description = "Python library with Neural Networks for Image Segmentation based on PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('torchvision', '0.13.1'), + ('Safetensors', '0.3.1'), +] + +use_pip = True + +exts_list = [ + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + ('pretrainedmodels', '0.7.4', { + 'checksums': ['7e77ead4619a3e11ab3c41982c8ad5b86edffe37c87fd2a37ec3c2cc6470b98a'], + }), + ('efficientnet_pytorch', '0.7.1', { + 'checksums': ['00b9b261effce59d2d47aae2ad238c29a2a65175470f41ada7ecac439b7c1ee1'], + }), + ('huggingface_hub', '0.15.1', { + 'checksums': ['a61b7d1a7769fe10119e730277c72ab99d95c48d86a3d6da3e9f3d0f632a4081'], + }), + ('timm', '0.9.2', { + 'checksums': ['d0977cc5e02c69bda979fca8b52aa315a5f2cb64ebf8ad2c4631b1e452762c14'], + }), + ('tqdm', '4.64.0', { + 'checksums': ['40be55d30e200777a307a7585aee69e4eabb46b4ec6a4b4a5f2d9f11e7d5408d'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('segmentation_models_pytorch', version, { + 'checksums': ['b3b21ab4cd26a6b2b9e7a6ed466ace6452eb26ed3c31ae491ea2d7cbb01e384b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 1d1c8a1d2ed63706f0303906a30a324028164a78 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 6 Oct 2023 10:50:34 +0200 Subject: [PATCH 9005/9987] adding easyconfigs: SHAP-0.42.1-foss-2019b-Python-3.7.4.eb --- .../SHAP-0.42.1-foss-2019b-Python-3.7.4.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHAP/SHAP-0.42.1-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.42.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.42.1-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..1b6ae4e2e39 --- /dev/null +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.42.1-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'SHAP' +version = '0.42.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/slundberg/shap" +description = """SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any + machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley + values from game theory and their related extensions.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('scikit-learn', '0.21.3', versionsuffix), + ('tqdm', '4.41.1'), + ('numba', '0.47.0', versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +# ignore too strict requirement for 'packaging' Python package +local_preinstallopts = "sed -i 's/packaging>[0-9.]*/packaging/g' pyproject.toml && " +# fix compatibility with numba 0.47.0 +local_preinstallopts += "sed -i 's/from numba.core.errors import/from numba.errors import/g' shap/maskers/_image.py && " + +exts_list = [ + # recent setuptools required to avoid UNKNOWN and 0.0.0 in SHAP installation + ('setuptools', '67.8.0', { + 'checksums': ['62642358adc77ffa87233bc4d2354c4b2682d214048f500964dbe760ccedf102'], + }), + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('slicer', '0.0.7', { + 'checksums': ['f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec'], + }), + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['64403915e4a07d2951e7eee4af0e835b1b519367b11806fe1aa4bd6d81adb626'], + 'preinstallopts': local_preinstallopts, + }), +] + +moduleclass = 'data' From 21bac8cbaf13f4baf4ecf5508f4435cea53d2f25 Mon Sep 17 00:00:00 2001 From: xina Date: Fri, 6 Oct 2023 10:55:24 +0200 Subject: [PATCH 9006/9987] adding easyconfigs: waLBerla-6.1-foss-2021a.eb --- .../w/waLBerla/waLBerla-6.1-foss-2021a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb new file mode 100644 index 00000000000..94771f62def --- /dev/null +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -0,0 +1,39 @@ +# easyconfig file for waLBerla v6.1 + +easyblock = 'CMakeMake' + + +name = 'waLBerla' +version = '6.1' + +homepage = "https://walberla.net/index.html" +description = '''Widely applicable Lattics-Boltzmann from Erlangen is a +block-structured high-performance framework for multiphysics simulations''' + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://i10git.cs.fau.de/walberla/walberla/-/archive/v6.1'] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('pybind11', '2.6.2'), + ('Python', '3.9.5') +] + +parallel = 1 + +configopts = "-WALBERLA_BUILD_WITH_PYTHON=ON -WALBERLA_BUILD_SHOWCASES=OFF -WALBERLA_BUILD_DOC=OFF" + + +sanity_check_paths = { + 'files': ['walberla/waLBerlaDefinitions.h'], + 'dirs': [''], +} + +moduleclass = 'chem' + + From c9faffbfcedf63d874c6c6ebeddd2e8024e034d4 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:24:53 +0200 Subject: [PATCH 9007/9987] Update waLBerla-6.1-foss-2021a.eb delete empty space and adjust indentation --- .../easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 94771f62def..063f5569218 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -20,8 +20,8 @@ checksums = ['f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'] builddependencies = [('CMake', '3.20.1')] dependencies = [ - ('pybind11', '2.6.2'), - ('Python', '3.9.5') + ('pybind11', '2.6.2'), + ('Python', '3.9.5'), ] parallel = 1 @@ -30,10 +30,8 @@ configopts = "-WALBERLA_BUILD_WITH_PYTHON=ON -WALBERLA_BUILD_SHOWCASES=OFF -WALB sanity_check_paths = { - 'files': ['walberla/waLBerlaDefinitions.h'], - 'dirs': [''], + 'files': ['walberla/waLBerlaDefinitions.h'], + 'dirs': [''], } moduleclass = 'chem' - - From 83377364e0c47c0acd964ca5a1127eedac2f0b13 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Fri, 6 Oct 2023 11:53:16 +0200 Subject: [PATCH 9008/9987] Update waLBerla-6.1-foss-2021a.eb try to fix test error --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 063f5569218..c7bf9300968 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -1,8 +1,6 @@ # easyconfig file for waLBerla v6.1 - easyblock = 'CMakeMake' - name = 'waLBerla' version = '6.1' @@ -28,7 +26,6 @@ parallel = 1 configopts = "-WALBERLA_BUILD_WITH_PYTHON=ON -WALBERLA_BUILD_SHOWCASES=OFF -WALBERLA_BUILD_DOC=OFF" - sanity_check_paths = { 'files': ['walberla/waLBerlaDefinitions.h'], 'dirs': [''], From 9e9bd63b0254e2c0370c233c8931695645071e63 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 6 Oct 2023 12:55:40 +0200 Subject: [PATCH 9009/9987] adding easyconfigs: ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb, RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb and patches: JuliaCall-0.17.5-top_level_macro.patch --- ...-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 235 ++++++++++++++++++ .../JuliaCall-0.17.5-top_level_macro.patch | 22 ++ ...GA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 87 +++++++ 3 files changed, 344 insertions(+) create mode 100644 easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb create mode 100644 easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch create mode 100644 easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb new file mode 100644 index 00000000000..da9a52a388c --- /dev/null +++ b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -0,0 +1,235 @@ +easyblock = 'JuliaBundle' + +name = 'RCall' +version = '0.13.17' +local_juliaver = '1.9.2' +versionsuffix = '-R-%%(rver)s-Julia-%s' % local_juliaver + +homepage = 'https://github.com/JuliaInterop/RCall.jl' +description = """This package facilitates communication between R and Julia and allows the + user to call R packages from within Julia, providing the best of both worlds.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM), +] + +preinstallopts = "export LD_LIBRARY_PATH=$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH && " + +exts_default_options = { + 'source_tmpl': 'v%(version)s.tar.gz', +} + +exts_list = [ + ('Preferences', '1.4.1', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['2240d5df55d69b22d27cb152c4abf8bf51106cd0b5910e194b5ab0ef8f260fcf'], + }), + ('PrecompileTools', '1.2.0', { + 'source_urls': ['https://github.com/JuliaLang/PrecompileTools.jl/archive/'], + 'checksums': ['8885c92380609bf077f316d454e92c75806353dbc22873c783207fc027401f2e'], + }), + ('Parsers', '2.7.2', { + 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], + 'checksums': ['e8d837cfc5cdaec0eb692eb58c00fb1d476327a7dc79398d7ce711cf8e8e3fa1'], + }), + ('StructTypes', '1.10.0', { + 'source_urls': ['https://github.com/JuliaData/StructTypes.jl/archive/'], + 'checksums': ['f2d7edc4f21651f76ff21251bfe8ec417c5688ed56880654bfb1482f580ab072'], + }), + ('JSON', '0.21.4', { + 'source_urls': ['https://github.com/JuliaIO/JSON.jl/archive/'], + 'checksums': ['c6b620ad4150ec5a154367f50c9579af800e3a89a6d8f9cb5dd30215a5d3f552'], + }), + ('DataAPI', '1.15.0', { + 'source_urls': ['https://github.com/JuliaData/DataAPI.jl/archive/'], + 'checksums': ['c5d535c1a276ef6a0dc765eb720fd66321aa1e6fd944f78462276f1070c7bfa6'], + }), + ('Missings', '1.1.0', { + 'source_urls': ['https://github.com/JuliaData/Missings.jl/archive/'], + 'checksums': ['149c799f261e4f1645124c8f6957ccec16a5c59e03bea9fcc6b66c3038d8f757'], + }), + ('CategoricalArrays', '0.9.7', { + 'source_urls': ['https://github.com/JuliaData/CategoricalArrays.jl/archive/'], + 'checksums': ['57ad0322d613ba88dae8f05d41fcd30ffe381205d5f8dbbdaf5eafcd762a3f10'], + }), + ('WinReg', '1.0.0', { + 'source_urls': ['https://github.com/simonbyrne/WinReg.jl/archive/'], + 'checksums': ['79f5ac2c678501cc6c6a3b443c9bbbeb701efe335556c235e48da9002cdea97d'], + }), + ('ShiftedArrays', '2.0.0', { + 'source_urls': ['https://github.com/JuliaArrays/ShiftedArrays.jl/archive/'], + 'checksums': ['909f9b8bdef0fedf2202645e4a3147d4365dad8acab42853b0e0d804d5d0df38'], + }), + ('IrrationalConstants', '0.2.2', { + 'source_urls': ['https://github.com/JuliaMath/IrrationalConstants.jl/archive/'], + 'checksums': ['bece9a3643264a76bd625c3f9cf3b46bba0fd093f06e899e8d6167cf45d7e833'], + }), + ('DocStringExtensions', '0.9.3', { + 'source_urls': ['https://github.com/JuliaDocs/DocStringExtensions.jl/archive/'], + 'checksums': ['9c712789b1cbd367bced9fafb995dee026f931ac68b55e476d1c666210564ae6'], + }), + ('LogExpFunctions', '0.3.26', { + 'source_urls': ['https://github.com/JuliaStats/LogExpFunctions.jl/archive/'], + 'checksums': ['c78ff1b55a56ee6e5d4507d3ec762de7975e892350a204f8267fd0760d5f0a2f'], + }), + ('StatsAPI', '1.7.0', { + 'source_urls': 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['https://github.com/JuliaData/InvertedIndices.jl/archive/'], + 'checksums': ['86d6fed34f734811dc6878fdeab7e84f96963342839a2c355b25babbf1fb980a'], + }), + ('InlineStrings', '1.4.0', { + 'source_urls': ['https://github.com/JuliaStrings/InlineStrings.jl/archive/'], + 'checksums': ['700fbfaa7df0b6fead63a340d1c1f9033fc8d721a80b5bb8769eb399d3a4698d'], + }), + ('SentinelArrays', '1.4.0', { + 'source_urls': ['https://github.com/JuliaData/SentinelArrays.jl/archive/'], + 'checksums': ['816f12904041709aefb6b1fbfcaf4e21ac5e4dfb2bb3240fa68899f2023bea6e'], + }), + ('DataFrames', '1.6.1', { + 'source_urls': ['https://github.com/JuliaData/DataFrames.jl/archive/'], + 'checksums': ['2a72341a40860b45952ac7c2efee41e0f0ffb5faf7a59fbeb092dd49927d26c8'], + }), + ('Requires', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Requires.jl/archive/'], + 'checksums': ['8af4dac29839e796a651b8cb6a325b6f9c7eee5d5620b3e366b64f58325ebeb7'], + }), + (name, version, { + 'source_urls': ['https://github.com/JuliaInterop/RCall.jl/archive/'], + 'checksums': ['0f706f4c0ac8739096ac2f3f032286b9a2b7419fa80443ec8f1a61817b61e51d'], + }), +] + +sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"%(name)s\")'"] + +sanity_check_paths = { + 'files': [], + 'dirs': ['packages/%(name)s'], +} + +# When loading R and Julia, there seems to be a library collision and Julia (namely Pkg module) doesn't work properly +# This is a workaround to make Julia find the correct libraries +modluafooter = """ +prepend_path("LD_LIBRARY_PATH", os.getenv("EBROOTJULIA") .. "/lib/julia") +""" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch b/easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch new file mode 100644 index 00000000000..fd3d5a0f2fc --- /dev/null +++ b/easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch @@ -0,0 +1,22 @@ +There is an error in current JuliaCall, which should be patched in upcoming versions. +See https://github.com/Non-Contradiction/JuliaCall/issues/203 +diff -ruN JuliaCall_orig/inst/julia/JuliaObject.jl JuliaCall/inst/julia/JuliaObject.jl +--- JuliaCall_orig/inst/julia/JuliaObject.jl 2022-09-07 18:13:31.000000000 +0200 ++++ JuliaCall/inst/julia/JuliaObject.jl 2023-09-26 17:29:44.310679473 +0200 +@@ -74,14 +74,14 @@ + ## we should use JuliaObject for general AbstractArray + @static if julia07 + @suppress_err begin +- JuliaCall.sexpclass(x :: AbstractArray{T}) where {T} = RClass{:JuliaObject} ++ @eval JuliaCall.sexpclass(x :: AbstractArray{T}) where {T} = RClass{:JuliaObject} + end + + ## AbstractArray{Any} should be converted to R List + sexpclass(x :: AbstractArray{Any}) = RClass{:list} + else + @suppress_err begin +- JuliaCall.sexp(x :: AbstractArray{T}) where {T} = sexp(JuliaObject(x)) ++ @eval JuliaCall.sexp(x :: AbstractArray{T}) where {T} = sexp(JuliaObject(x)) + end + + ## AbstractArray{Any} should be converted to R List diff --git a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb new file mode 100644 index 00000000000..42995b030c7 --- /dev/null +++ b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -0,0 +1,87 @@ +easyblock = 'Bundle' + +name = 'ResistanceGA' +version = '4.2-5' +local_commit = '04326a8' +local_juliaver = '1.9.2' +versionsuffix = '-R-%%(rver)s-Julia-%s' % local_juliaver + +homepage = 'https://github.com/wpeterman/ResistanceGA' +description = "An R package to optimize resistance surfaces using Genetic Algorithms." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM), + ('Circuitscape', '5.12.3', '-Julia-%s' % local_juliaver, SYSTEM), + ('RCall', '0.13.17', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.rstudio.com/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('Suppressor', '0.2.4', { + 'easyblock': 'JuliaPackage', + 'exts_filter': ("julia -e 'using %(ext_name)s'", ''), + 'preinstallopts': "export LD_LIBRARY_PATH=$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH && ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/JuliaIO/Suppressor.jl/archive/'], + 'checksums': ['5075b06ed6aa0956c786e5b5fe3d77571a4dd34e6d63b45e113c312729384cf4'], + }), + ('GA', '3.2.2', { + 'checksums': ['6245c634a11b8414bde7ed326b8c615512645489b19969619484c865e900bf8c'], + }), + ('MuMIn', '1.47.1', { + 'checksums': ['1223b5ada6f7d58220ac0267fa3473993190742646cbbb3dfe63895e61621af6'], + }), + ('spdep', '1.2-7', { + 'checksums': ['9dac594825bf2d0aa31e845bfec05d8ce206327840fe455391741dbbdf9c9eea'], + }), + ('JuliaCall', '0.17.5', { + 'patches': ['JuliaCall-0.17.5-top_level_macro.patch'], + 'checksums': [ + {'JuliaCall_0.17.5.tar.gz': '92542f9f02fe43702c18cf6c5a52fcbfc5ef3da6a2f73bfded773f4fc5edd90c'}, + {'JuliaCall-0.17.5-top_level_macro.patch': + '18f9cacb9f263e62145432b44ce6856bc01b91bae6b1e433c07c23d401850f14'}, + ], + }), + ('XR', '0.7.2', { + 'checksums': ['7fc35f607d68095f861711fda9acbd8804829ad3915a22a407ab1e9fb89c1949'], + }), + ('XRJulia', '0.9.0', { + 'checksums': ['f59fddbe7ab65562f6e019ca7016417fff81f5b7e5f0ddeb00129aaaa6336f68'], + }), + (name, version, { + 'source_urls': ['https://github.com/wpeterman/ResistanceGA/archive/'], + 'sources': [{'download_filename': '04326a8.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6791c8b42559c0abe94b7a326961f45af2939905021cb9da7220383bf2ea3d75'], + }), +] + +modextrapaths = { + 'R_LIBS_SITE': '', +} + +# When loading R and Julia, there seems to be a library collision and Julia (namely Pkg module) doesn't work properly +# This is a workaround to make Julia find the correct libraries +modluafooter = """ +prepend_path("LD_LIBRARY_PATH", os.getenv("EBROOTJULIA") .. "/lib/julia") +""" + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s'], +} + +moduleclass = 'bio' From 50c04c248c621f635a074ec438d6014732d3f68a Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 6 Oct 2023 14:07:22 +0200 Subject: [PATCH 9010/9987] Fixed sources being str --- .../r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb index da9a52a388c..ceea54ad5b3 100644 --- a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -109,7 +109,7 @@ exts_list = [ }), ('OpenSpecFun_jll', '0.5.5+0', { 'source_urls': ['https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl/archive/'], - 'sources': 'OpenSpecFun-v%(version)s.tar.gz', + 'sources': ['OpenSpecFun-v%(version)s.tar.gz'], 'checksums': ['6d1df617dd0a80fc0de5bc41a092e51f72782dbfd296c64e151707733cb57b6f'], }), ('SpecialFunctions', '2.3.1', { @@ -134,7 +134,7 @@ exts_list = [ }), ('Rmath_jll', '0.4.0+0', { 'source_urls': ['https://github.com/JuliaBinaryWrappers/Rmath_jll.jl/archive/'], - 'sources': 'Rmath-v%(version)s.tar.gz', + 'sources': ['Rmath-v%(version)s.tar.gz'], 'checksums': ['8cfe0bf37caa1297b3ea5d97bc29fae89bc41a25a723ef692f37d709f4e8c191'], }), ('Rmath', '0.7.1', { From eb196705dd561c76e118100fbb49ab5db539da22 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Fri, 6 Oct 2023 15:33:31 +0200 Subject: [PATCH 9011/9987] Update easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index c7bf9300968..de18588bccc 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -5,8 +5,8 @@ name = 'waLBerla' version = '6.1' homepage = "https://walberla.net/index.html" -description = '''Widely applicable Lattics-Boltzmann from Erlangen is a -block-structured high-performance framework for multiphysics simulations''' +description = """Widely applicable Lattics-Boltzmann from Erlangen is a +block-structured high-performance framework for multiphysics simulations""" toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': True, 'pic': True} From 4f9f88c2c199bee3a0dd5a4dbc8c8f522f2e3f20 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Fri, 6 Oct 2023 15:40:31 +0200 Subject: [PATCH 9012/9987] Update waLBerla-6.1-foss-2021a.eb update python path and cmake configuration --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index de18588bccc..6a5cdbc14e3 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -24,7 +24,10 @@ dependencies = [ parallel = 1 -configopts = "-WALBERLA_BUILD_WITH_PYTHON=ON -WALBERLA_BUILD_SHOWCASES=OFF -WALBERLA_BUILD_DOC=OFF" +configopts = "-DWALBERLA_BUILD_WITH_PYTHON=ON " +configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " +configopts += "-DWALBERLA_BUILD_DOC=OFF " +configopts += "-DPython_ROOT_DIR=$EBROOTPYTHON " sanity_check_paths = { 'files': ['walberla/waLBerlaDefinitions.h'], From 21b2c3ad69219de5d9f7f9d8040eb2339993b6c5 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 6 Oct 2023 15:57:42 +0200 Subject: [PATCH 9013/9987] Fixed line endings in patch --- .../JuliaCall-0.17.5-top_level_macro.patch | 44 +++++++++---------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch b/easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch index fd3d5a0f2fc..a971737d46a 100644 --- a/easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch +++ b/easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch @@ -1,22 +1,22 @@ -There is an error in current JuliaCall, which should be patched in upcoming versions. -See https://github.com/Non-Contradiction/JuliaCall/issues/203 -diff -ruN JuliaCall_orig/inst/julia/JuliaObject.jl JuliaCall/inst/julia/JuliaObject.jl ---- JuliaCall_orig/inst/julia/JuliaObject.jl 2022-09-07 18:13:31.000000000 +0200 -+++ JuliaCall/inst/julia/JuliaObject.jl 2023-09-26 17:29:44.310679473 +0200 -@@ -74,14 +74,14 @@ - ## we should use JuliaObject for general AbstractArray - @static if julia07 - @suppress_err begin -- JuliaCall.sexpclass(x :: AbstractArray{T}) where {T} = RClass{:JuliaObject} -+ @eval JuliaCall.sexpclass(x :: AbstractArray{T}) where {T} = RClass{:JuliaObject} - end - - ## AbstractArray{Any} should be converted to R List - sexpclass(x :: AbstractArray{Any}) = RClass{:list} - else - @suppress_err begin -- JuliaCall.sexp(x :: AbstractArray{T}) where {T} = sexp(JuliaObject(x)) -+ @eval JuliaCall.sexp(x :: AbstractArray{T}) where {T} = sexp(JuliaObject(x)) - end - - ## AbstractArray{Any} should be converted to R List +There is an error in current JuliaCall, which should be patched in upcoming versions. +See https://github.com/Non-Contradiction/JuliaCall/issues/203 +diff -ruN JuliaCall_orig/inst/julia/JuliaObject.jl JuliaCall/inst/julia/JuliaObject.jl +--- JuliaCall_orig/inst/julia/JuliaObject.jl 2022-09-07 18:13:31.000000000 +0200 ++++ JuliaCall/inst/julia/JuliaObject.jl 2023-09-26 17:29:44.310679473 +0200 +@@ -74,14 +74,14 @@ + ## we should use JuliaObject for general AbstractArray + @static if julia07 + @suppress_err begin +- JuliaCall.sexpclass(x :: AbstractArray{T}) where {T} = RClass{:JuliaObject} ++ @eval JuliaCall.sexpclass(x :: AbstractArray{T}) where {T} = RClass{:JuliaObject} + end + + ## AbstractArray{Any} should be converted to R List + sexpclass(x :: AbstractArray{Any}) = RClass{:list} + else + @suppress_err begin +- JuliaCall.sexp(x :: AbstractArray{T}) where {T} = sexp(JuliaObject(x)) ++ @eval JuliaCall.sexp(x :: AbstractArray{T}) where {T} = sexp(JuliaObject(x)) + end + + ## AbstractArray{Any} should be converted to R List From 3aa7707135439fcb066c066ab6e3a22b5e91625d Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 6 Oct 2023 16:16:25 +0200 Subject: [PATCH 9014/9987] Fixed l checksum for the patch --- .../ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb index 42995b030c7..5eb0986cb61 100644 --- a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -53,7 +53,7 @@ exts_list = [ 'checksums': [ {'JuliaCall_0.17.5.tar.gz': '92542f9f02fe43702c18cf6c5a52fcbfc5ef3da6a2f73bfded773f4fc5edd90c'}, {'JuliaCall-0.17.5-top_level_macro.patch': - '18f9cacb9f263e62145432b44ce6856bc01b91bae6b1e433c07c23d401850f14'}, + 'a733768f4bddd391a74d588b3d47bf8cbd475b42147856b35b0efd2eff83f63a'}, ], }), ('XR', '0.7.2', { From 99f479a898744ae78f34f01bd3ce887d7c40489d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 09:00:19 +0200 Subject: [PATCH 9015/9987] condone SHAP w/ foss/2019b having an indirect dependency on LLVM 8.x (via numba) --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 65bea6e1e1c..27461af560f 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -536,7 +536,7 @@ def check_dep_vars(self, gen, dep, dep_vars): 'LLVM': [ # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) (r'8\.', [r'numba-0\.47\.0-', r'librosa-0\.7\.2-', r'BirdNET-20201214-', - r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[346]\.[23]']), + r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[346]\.[23]', r'SHAP-0\.42\.1']), (r'10\.0\.1', [r'cell2location-0\.05-alpha-', r'cryoDRGN-0\.3\.2-', r'loompy-3\.0\.6-', r'numba-0\.52\.0-', r'PyOD-0\.8\.7-', r'PyTorch-Geometric-1\.6\.3', r'scanpy-1\.7\.2-', r'umap-learn-0\.4\.6-']), From 9969c3fba96c4a94f22b5533cefac0ada8a8d3b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 09:50:11 +0200 Subject: [PATCH 9016/9987] adding easyconfigs: SHAP-0.42.1-foss-2022a.eb --- .../s/SHAP/SHAP-0.42.1-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/SHAP/SHAP-0.42.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.42.1-foss-2022a.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.42.1-foss-2022a.eb new file mode 100644 index 00000000000..7323215b67f --- /dev/null +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.42.1-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'SHAP' +version = '0.42.1' + +homepage = "https://github.com/slundberg/shap" +description = """SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any + machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley + values from game theory and their related extensions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), + ('numba', '0.56.4'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('slicer', '0.0.7', { + 'checksums': ['f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec'], + }), + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['64403915e4a07d2951e7eee4af0e835b1b519367b11806fe1aa4bd6d81adb626'], + # ignore too strict requirement for 'packaging' Python package + 'preinstallopts': "sed -i 's/packaging>[0-9.]*/packaging/g' pyproject.toml && ", + }), +] + +moduleclass = 'data' From 2bec2534e9b0aea472d55b9c6099c2bcf1b3b922 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 09:56:16 +0200 Subject: [PATCH 9017/9987] adding easyconfigs: fasta-reader-3.0.2-GCC-12.3.0.eb --- .../fasta-reader-3.0.2-GCC-12.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/f/fasta-reader/fasta-reader-3.0.2-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/f/fasta-reader/fasta-reader-3.0.2-GCC-12.3.0.eb b/easybuild/easyconfigs/f/fasta-reader/fasta-reader-3.0.2-GCC-12.3.0.eb new file mode 100644 index 00000000000..59c31e5cfe8 --- /dev/null +++ b/easybuild/easyconfigs/f/fasta-reader/fasta-reader-3.0.2-GCC-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'fasta-reader' +version = '3.0.2' + +homepage = 'https://github.com/EBI-Metagenomics/fasta-reader-py' +description = "FASTA file reader" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # for fsspec +] + +use_pip = True + +exts_list = [ + (name, version, { + 'sources': ['fasta_reader-%(version)s.tar.gz'], + 'checksums': ['71493559a791f355def4918612a3bbd44992f7e1227a61a7d815018aefde4d79'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 8a4a5cbdb2c6c723c07f2b83708df68b85e32e84 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 10:10:02 +0200 Subject: [PATCH 9018/9987] adding easyconfigs: FastANI-1.34-GCC-12.3.0.eb --- .../f/FastANI/FastANI-1.34-GCC-12.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.34-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.34-GCC-12.3.0.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.34-GCC-12.3.0.eb new file mode 100644 index 00000000000..53a457447e3 --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.34-GCC-12.3.0.eb @@ -0,0 +1,45 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'ConfigureMake' + +name = 'FastANI' +version = '1.34' + +homepage = "https://github.com/ParBLiSS/FastANI" +description = """FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean + nucleotide identity of orthologous gene pairs shared between two microbial + genomes. FastANI supports pairwise comparison of both complete and draft + genome assemblies.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] +sources = ['v%(version)s.zip'] +patches = ['FastANI-1.2-memcpy.patch'] +checksums = [ + {'v1.34.zip': 'cb15540634c725cb46dded7becaff38b27a7f709c0a8589db986674effcc6180'}, + {'FastANI-1.2-memcpy.patch': 'eebcf0b64c31ee360ca79136f644157064ac69747ed13cff70f5c9932c6bb0d5'}, +] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [ + ('GSL', '2.7'), + ('zlib', '1.2.13'), +] + +preconfigopts = 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/fastANI'], + 'dirs': [] +} + +sanity_check_commands = ["fastANI --help"] + +moduleclass = 'bio' From 1c32b55c4a3a4bfa24fe8400e5d09b81262d2cf8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 10:27:42 +0200 Subject: [PATCH 9019/9987] adding easyconfigs: HMMER-3.4-gompi-2023a.eb --- .../h/HMMER/HMMER-3.4-gompi-2023a.eb | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023a.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023a.eb new file mode 100644 index 00000000000..99f585d998b --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2023a.eb @@ -0,0 +1,78 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# Updated by: Filip Kružík (INUITS) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.4' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3'] + +builddependencies = [ + ('Python', '3.11.3'), + ('Perl', '5.36.1'), +] + +# replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files +preconfigopts = "grep '/usr/bin/perl' . | cut -f1 -d: | xargs echo sed -i 's@/usr/bin/perl@/usr/bin/env perl@g' && " + +configopts = '--enable-mpi' + +buildopts = ' V=1 ' + +testopts = buildopts +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + +moduleclass = 'bio' From 4e39c55bbacca86f152df29ae647a8e810b43c7a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 10:32:11 +0200 Subject: [PATCH 9020/9987] {bio}[GCC/12.3.0] Mash v2.3, CapnProto v1.0.1 --- .../CapnProto-1.0.1-GCCcore-12.3.0.eb | 35 ++++++++++++++ .../easyconfigs/m/Mash/Mash-2.3-GCC-12.3.0.eb | 48 +++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b62002c8fd7 --- /dev/null +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to 0.9.1 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'CapnProto' +version = '1.0.1' + +homepage = 'https://capnproto.org' +description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" +# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." +# (only on Intel Skylake?) +toolchainopts = {'cstd': 'c++17', 'lowopt': True} + +source_urls = ['https://capnproto.org/'] +sources = ['capnproto-c++-%(version)s.tar.gz'] +checksums = ['0f7f4b8a76a2cdb284fddef20de8306450df6dd031a47a15ac95bc43c3358e09'] + +builddependencies = [('binutils', '2.40')] + +local_bins = ['capnp', 'capnpc', 'capnpc-c++', 'capnpc-capnp'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['include/capnp', 'include/kj', 'lib'], +} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..e80d16e7196 --- /dev/null +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.3.0.eb @@ -0,0 +1,48 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v2.2 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'Mash' +version = '2.3' + +homepage = 'http://mash.readthedocs.org' +description = "Fast genome and metagenome distance estimation using MinHash" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/marbl/Mash/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Mash-2.2_fix-hardcoding.patch', + 'Mash-2.1_disable-memcpy-wrap.patch', + 'Mash-2.3_fix-GCC-11.patch', +] +checksums = [ + 'f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1', # v2.3.tar.gz + '0c7315af727a06f408ab3ca69da0860fc671aa870b448a41a509b1e6d7027db5', # Mash-2.2_fix-hardcoding.patch + '40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch + '47a55459d4e8c57949648e0f33f3ffc3529563db0efe60f495fdec046f48d94e', # Mash-2.3_fix-GCC-11.patch +] + +builddependencies = [('Autotools', '20220317')] +dependencies = [ + ('CapnProto', '1.0.1'), + ('GSL', '2.7'), + ('zlib', '1.2.13'), +] + +preconfigopts = "./bootstrap.sh && " +configopts = "--with-capnp=$EBROOTCAPNPROTO --with-gsl=$EBROOTGSL" + +sanity_check_paths = { + 'files': ['bin/mash', 'lib/libmash.a'], + 'dirs': ['include/mash'], +} + +sanity_check_commands = ['mash --version'] + +moduleclass = 'bio' From 865d6666722e6727fb64d13f8e18567508967b6e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 11:25:04 +0200 Subject: [PATCH 9021/9987] adding easyconfigs: Go-1.21.2.eb --- easybuild/easyconfigs/g/Go/Go-1.21.2.eb | 29 +++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.21.2.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.21.2.eb b/easybuild/easyconfigs/g/Go/Go-1.21.2.eb new file mode 100644 index 00000000000..f7d40229738 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.21.2.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'Go' +version = '1.21.2' + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] +local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} +sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] +checksums = [{ + 'go%(version)s.linux-amd64.tar.gz': 'f5414a770e5e11c6e9674d4cd4dd1f4f630e176d1828d3427ea8ca4211eee90d', + 'go%(version)s.linux-arm64.tar.gz': '23e208ca44a3cb46cd4308e48a27c714ddde9c8c34f2e4211dbca95b6d456554', +}] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +sanity_check_commands = ["go help"] + +modextravars = {'GOROOT': '%(installdir)s'} + +moduleclass = 'compiler' From 3328fbeda28069a4262535418dbe43be54060abc Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 7 Oct 2023 10:38:08 +0100 Subject: [PATCH 9022/9987] remove 'cstd': 'c++17' as this is default in GCC 11 --- easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.2.0.eb | 1 - easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.3.0.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.2.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.2.0.eb index 7d12008cb15..04d5033cf83 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.2.0.eb @@ -12,7 +12,6 @@ homepage = 'http://mash.readthedocs.org' description = "Fast genome and metagenome distance estimation using MinHash" toolchain = {'name': 'GCC', 'version': '11.2.0'} -toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/marbl/Mash/archive/'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.3.0.eb index 157dc810cfd..cf5c886d18f 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-11.3.0.eb @@ -12,7 +12,6 @@ homepage = 'http://mash.readthedocs.org' description = "Fast genome and metagenome distance estimation using MinHash" toolchain = {'name': 'GCC', 'version': '11.3.0'} -toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/marbl/Mash/archive/'] sources = ['v%(version)s.tar.gz'] From f94692b0adff98b0cb401957f25079de53f3ee70 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 7 Oct 2023 10:43:24 +0100 Subject: [PATCH 9023/9987] remove 'cstd': 'c++17' as this is default in GCC 11 and no longer needed lowopt --- .../c/CapnProto/CapnProto-0.10.2-GCCcore-11.3.0.eb | 4 ---- .../easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-11.2.0.eb | 4 ---- 2 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.3.0.eb index c833e53d566..abe914d7bd6 100644 --- a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.2-GCCcore-11.3.0.eb @@ -12,10 +12,6 @@ homepage = 'https://capnproto.org' description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" -# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." -# (only on Intel Skylake?) -toolchainopts = {'cstd': 'c++17', 'lowopt': True} source_urls = ['https://capnproto.org/'] sources = ['capnproto-c++-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-11.2.0.eb index 19069313fa4..f4e16deac46 100644 --- a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.9.1-GCCcore-11.2.0.eb @@ -12,10 +12,6 @@ homepage = 'https://capnproto.org' description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" -# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." -# (only on Intel Skylake?) -toolchainopts = {'cstd': 'c++17', 'lowopt': True} source_urls = ['https://capnproto.org/'] sources = ['capnproto-c++-%(version)s.tar.gz'] From 757e0b07ada676fccdef201591011c1d62c9bd14 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 7 Oct 2023 11:00:22 +0100 Subject: [PATCH 9024/9987] and GCCcore 12 version --- .../c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb index ee6242554c7..4c35e236eac 100644 --- a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb @@ -12,10 +12,6 @@ homepage = 'https://capnproto.org' description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" -# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." -# (only on Intel Skylake?) -toolchainopts = {'cstd': 'c++17', 'lowopt': True} source_urls = ['https://capnproto.org/'] sources = ['capnproto-c++-%(version)s.tar.gz'] From fa2dd0116b902559d93baf10fd447caf81e6a517 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 7 Oct 2023 11:02:37 +0100 Subject: [PATCH 9025/9987] remove 'cstd': 'c++17' as this is default in GCC 11 for Abseil --- .../easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb | 2 +- .../easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb | 2 +- .../easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb index 48b976f0841..9359c052492 100644 --- a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-11.3.0.eb @@ -10,7 +10,7 @@ C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++17'} +toolchainopts = {'pic': True} source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb index bb35f74269d..4c79a033123 100644 --- a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb @@ -10,7 +10,7 @@ C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.""" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -toolchainopts = {'pic': True, 'cstd': 'c++17'} +toolchainopts = {'pic': True} source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] sources = ['%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb index c50c396f801..3ad5e5c79b6 100644 --- a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb @@ -10,7 +10,7 @@ C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++17'} +toolchainopts = {'pic': True} source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] sources = ['%(version)s.tar.gz'] From 2278dede8e770b863ad6abd6414dd58cfcffec5e Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 7 Oct 2023 11:07:38 +0100 Subject: [PATCH 9026/9987] remove 'cstd': 'c++17' as this is default in GCC 11 for GLIMPSE --- easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-11.3.0.eb | 1 - easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-12.2.0.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-11.3.0.eb index dffbd942f4f..64c4f92026e 100644 --- a/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-11.3.0.eb @@ -7,7 +7,6 @@ homepage = 'https://github.com/odelaneau/GLIMPSE' description = "GLIMPSE2 is a set of tools for phasing and imputation for low-coverage sequencing datasets" toolchain = {'name': 'GCC', 'version': '11.3.0'} -toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/odelaneau/GLIMPSE/archive/'] sources = [{ diff --git a/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-12.2.0.eb b/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-12.2.0.eb index 57eca82043d..ec062251633 100644 --- a/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/g/GLIMPSE/GLIMPSE-2.0.0-GCC-12.2.0.eb @@ -7,7 +7,6 @@ homepage = 'https://github.com/odelaneau/GLIMPSE' description = "GLIMPSE2 is a set of tools for phasing and imputation for low-coverage sequencing datasets" toolchain = {'name': 'GCC', 'version': '12.2.0'} -toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/odelaneau/GLIMPSE/archive/'] sources = [{ From 0ca1724a26d1dfd9082a0bf9a8c5c757cf641f93 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 7 Oct 2023 11:19:52 +0100 Subject: [PATCH 9027/9987] remove 'cstd': 'c++17' as this is default in GCC 11 for OGDF --- easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202-GCC-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202-GCC-11.2.0.eb index afd6fc5aef3..06d84a232f2 100644 --- a/easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OGDF/OGDF-dogwood-202202-GCC-11.2.0.eb @@ -10,7 +10,6 @@ drawing. It offers sophisticated algorithms and data structures to use within your own applications or scientific projects.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} -toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/ogdf/ogdf/archive'] sources = ['%(version)s.tar.gz'] From 83bfcb0e8e6ece50310667bbb0b99e17e3f2e4a5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 12:27:07 +0200 Subject: [PATCH 9028/9987] adding easyconfigs: EDirect-20.5.20231006-GCCcore-12.3.0.eb --- .../EDirect-20.5.20231006-GCCcore-12.3.0.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/e/EDirect/EDirect-20.5.20231006-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/e/EDirect/EDirect-20.5.20231006-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/EDirect/EDirect-20.5.20231006-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..6d7b7e3bb2e --- /dev/null +++ b/easybuild/easyconfigs/e/EDirect/EDirect-20.5.20231006-GCCcore-12.3.0.eb @@ -0,0 +1,57 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## +easyblock = 'Binary' + +name = 'EDirect' +version = '20.5.20231006' + +homepage = 'https://www.ncbi.nlm.nih.gov/books/NBK25501/' +# See also https://dataguide.nlm.nih.gov/edirect/install.html +description = """Entrez Direct (EDirect) provides access to the NCBI's suite of +interconnected databases from a Unix terminal window. Search terms are entered +as command-line arguments. Individual operations are connected with Unix pipes +to construct multi-step queries. Selected records can then be retrieved in a +variety of formats.""" +# software_license = 'Public Domain' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abb7a7c2d7dd4bf80b5f951211d20bf432fe9b787f6ad093feba2f5cb46d62dd'] + +builddependencies = [ + ('Go', '1.21.2', '', SYSTEM), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Perl', '5.36.1'), +] + +extract_sources = True + +postinstallcmds = [ + "cd cmd/ && " + "sed -i 's@target=\"\\$HOME/Misc/scripts/\"@target=\"%(installdir)s/\"@' build.sh && " + "./build.sh install && cd %(installdir)s/ && rm -rf cmd/ eutils/" +] + +sanity_check_paths = { + 'files': ['einfo', 'README'], + 'dirs': ['help'], +} + +sanity_check_commands = [ + "esearch -version && " + "xtract -version && " + "esearch -db pubmed -query 'Babalobi OO[au] AND 2008[pdat]' | efetch -format xml | " + "xtract -pattern Author -if Affiliation -contains Medicine -element Initials" +] + +moduleclass = 'bio' From bb526dcdb971bd277f0dc3a9960e65ec51b74bdb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 12:32:34 +0200 Subject: [PATCH 9029/9987] remove toolchainopts from CapnProto and Mash easyconfigs, no longer needed with GCC 12.3.0 Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/c/CapnProto/CapnProto-1.0.1-GCCcore-12.3.0.eb | 4 ---- easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.3.0.eb | 1 - 2 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1-GCCcore-12.3.0.eb index b62002c8fd7..f0caa438cfa 100644 --- a/easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1-GCCcore-12.3.0.eb @@ -12,10 +12,6 @@ homepage = 'https://capnproto.org' description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" -# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." -# (only on Intel Skylake?) -toolchainopts = {'cstd': 'c++17', 'lowopt': True} source_urls = ['https://capnproto.org/'] sources = ['capnproto-c++-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.3.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.3.0.eb index e80d16e7196..c7591fbc91d 100644 --- a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.3.0.eb @@ -12,7 +12,6 @@ homepage = 'http://mash.readthedocs.org' description = "Fast genome and metagenome distance estimation using MinHash" toolchain = {'name': 'GCC', 'version': '12.3.0'} -toolchainopts = {'cstd': 'c++17'} source_urls = ['https://github.com/marbl/Mash/archive/'] sources = ['v%(version)s.tar.gz'] From 267b44b11fddabd36243223893671254acbf2172 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 14:52:07 +0200 Subject: [PATCH 9030/9987] {bio}[foss/2021a] scCODA v0.1.9, tensorflow-probability v0.14.0, scikit-bio v0.5.7, rpy2 v3.4.5, ArviZ v0.12.1 --- .../a/ArviZ/ArviZ-0.12.1-foss-2021a.eb | 34 ++++++++++ .../r/rpy2/rpy2-3.4.5-foss-2021a.eb | 62 +++++++++++++++++++ .../s/scCODA/scCODA-0.1.9-foss-2021a.eb | 36 +++++++++++ .../scikit-bio/scikit-bio-0.5.7-foss-2021a.eb | 47 ++++++++++++++ ...ensorflow-probability-0.14.0-foss-2021a.eb | 46 ++++++++++++++ 5 files changed, 225 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/scCODA/scCODA-0.1.9-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021a.eb create mode 100644 easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.14.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2021a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2021a.eb new file mode 100644 index 00000000000..68de3de1a5e --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'ArviZ' +version = '0.12.1' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # numpy, scipy, pandas + ('netcdf4-python', '1.5.7'), + ('xarray', '0.19.0'), + ('matplotlib', '3.4.2'), + ('typing-extensions', '3.10.0.0'), +] + +use_pip = True + +exts_list = [ + ('xarray-einstats', '0.5.0', { + 'checksums': ['3f799ead32bb28ce4e9b3cf95c2daa9c2040f06b25a34f8f2cd303f0268445ed'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['57d80eacc51909f18e6ab63c96a6b02227c3b077c5ffa406d5f4dabe03b8f019'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021a.eb b/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021a.eb new file mode 100644 index 00000000000..242df18ed71 --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-3.4.5-foss-2021a.eb @@ -0,0 +1,62 @@ +# Author: Pavel Grochal (INUITS) +# Updated: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'rpy2' +version = '3.4.5' + +homepage = 'https://rpy2.bitbucket.io/' +description = """rpy2 is an interface to R running embedded in a Python process.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('R', '4.1.0'), + ('IPython', '7.25.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('simplegeneric', '0.8.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + # stick to tzlocal < 3.0 to avoid test errors in rpy2 like + # AttributeError: 'NoneType' object has no attribute 'total_seconds' + ('tzlocal', '2.1', { + 'checksums': ['643c97c5294aedc737780a49d9df30889321cbe1204eac2c2ec6134035a92e44'], + }), + ('cffi', '1.15.1', { + 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], + }), + ('tzdata', '2023.3', { + 'checksums': ['11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a'], + }), + ('backports-zoneinfo', '0.2.1', { + 'modulename': 'backports.zoneinfo', + 'source_tmpl': 'backports.zoneinfo-%(version)s.tar.gz', + 'checksums': ['fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2'], + }), + ('pytz-deprecation-shim', '0.1.0.post0', { + 'source_tmpl': 'pytz_deprecation_shim-%(version)s.tar.gz', + 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], + }), + (name, version, { + 'patches': ['rpy2-3.4.5_disable_gui_tests.patch'], + 'checksums': [ + {'rpy2-3.4.5.tar.gz': '5d31a5ea43f5a59f6dec30faca87edb01fc9b8affa0beae96a99be923bd7dab3'}, + {'rpy2-3.4.5_disable_gui_tests.patch': '7424fed4bc9edb246944ad54fcb434a1ae5f2db086679b1a53d44cf5d3b98d8b'}, + ], + }), +] + +sanity_check_commands = [ + "pytest --pyargs rpy2 " +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scCODA/scCODA-0.1.9-foss-2021a.eb b/easybuild/easyconfigs/s/scCODA/scCODA-0.1.9-foss-2021a.eb new file mode 100644 index 00000000000..8109d113cb5 --- /dev/null +++ b/easybuild/easyconfigs/s/scCODA/scCODA-0.1.9-foss-2021a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'scCODA' +version = '0.1.9' + +homepage = 'https://github.com/theislab/scCODA' +description = """scCODA allows for identification of compositional changes in high-throughput sequencing count data, +especially cell compositions from scRNA-seq.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('TensorFlow', '2.6.0'), + ('tensorflow-probability', '0.14.0'), + ('scanpy', '1.8.1'), + ('scikit-bio', '0.5.7'), + ('rpy2', '3.4.5'), + ('ArviZ', '0.12.1'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['786692a5ca546985583784179a6b2d535a54b37b30892fb9e264c5e854585dac'], + # strip out too strict version requirements for Python packages required as dependencies + 'preinstallopts': "sed -i 's/>=[0-9.]*//g' setup.py && ", + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021a.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021a.eb new file mode 100644 index 00000000000..a0f9491eb9e --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scikit-bio' +version = '0.5.7' + +homepage = 'http://scikit-bio.org' +description = """scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms +and educational resources for bioinformatics.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('scikit-learn', '0.24.2'), + ('IPython', '7.25.0'), + ('h5py', '3.2.1'), + ('Pillow', '8.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('msgpack', '1.0.5', { + 'checksums': ['c075544284eadc5cddc70f4757331d99dcbc16b2bbd4849d15f8aae4cf36d31c'], + }), + ('CacheControl', '0.12.14', { + 'checksums': ['d1087f45781c0e00616479bfd282c78504371ca71da017b49df9f5365a95feba'], + }), + ('hdmedians', '0.14.2', { + 'checksums': ['b47aecb16771e1ba0736557255d80ae0240b09156bff434321de559b359ac2d6'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + (name, version, { + 'modulename': 'skbio', + 'checksums': ['6343ca0c621e2fcc5d1c042c8be3200664c5325956a83bea751cf1bcc75d1da9'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.14.0-foss-2021a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.14.0-foss-2021a.eb new file mode 100644 index 00000000000..9efe4775c2a --- /dev/null +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.14.0-foss-2021a.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'PythonBundle' + +name = 'tensorflow-probability' +version = '0.14.0' + +homepage = 'https://www.tensorflow.org/probability' +description = """TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +dependencies = [ + ('Python', '3.9.5'), + ('TensorFlow', '2.6.0'), + ('dm-tree', '0.1.6'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + (name, version, { + 'installopts': '--install-option="--release"', + 'modulename': 'tensorflow_probability', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/probability/archive/'], + 'checksums': ['54fe9a9cbfee5d02a561c92a730eb29166fa757084b9ccb3f700de42ddeafcfb'], + }), +] + +sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] + +sanity_pip_check = True + +moduleclass = 'lib' From 43fdd3b02cbacc3240a37a1935655ed02677b751 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 7 Oct 2023 20:44:08 +0200 Subject: [PATCH 9031/9987] adding easyconfigs: mpifileutils-0.11.1-gompi-2023a.eb, attr-2.5.1-GCCcore-12.3.0.eb, dtcmp-1.1.4-gompi-2023a.eb, libcircle-0.3-gompi-2023a.eb, lwgrp-1.0.5-gompi-2023a.eb --- .../a/attr/attr-2.5.1-GCCcore-12.3.0.eb | 26 +++++++++++++ .../d/dtcmp/dtcmp-1.1.4-gompi-2023a.eb | 39 +++++++++++++++++++ .../l/libcircle/libcircle-0.3-gompi-2023a.eb | 38 ++++++++++++++++++ .../l/lwgrp/lwgrp-1.0.5-gompi-2023a.eb | 36 +++++++++++++++++ .../mpifileutils-0.11.1-gompi-2023a.eb | 37 ++++++++++++++++++ 5 files changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.4-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.5-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb diff --git a/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2801e172682 --- /dev/null +++ b/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'attr' +version = '2.5.1' + +homepage = 'https://savannah.nongnu.org/projects/attr' + +description = """Commands for Manipulating Filesystem Extended Attributes""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['bae1c6949b258a0d68001367ce0c741cebdacdd3b62965d17e5eb23cd78adaf8'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/attr', 'bin/getfattr', 'bin/setfattr', + 'include/%(name)s/attributes.h', 'include/%(name)s/error_context.h', + 'include/%(name)s/libattr.h', 'lib/libattr.a', + 'lib/libattr.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.4-gompi-2023a.eb b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.4-gompi-2023a.eb new file mode 100644 index 00000000000..e6596fd46cd --- /dev/null +++ b/easybuild/easyconfigs/d/dtcmp/dtcmp-1.1.4-gompi-2023a.eb @@ -0,0 +1,39 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'dtcmp' +version = '1.1.4' + +homepage = 'https://github.com/LLNL/dtcmp' +description = """The Datatype Comparison (DTCMP) Library provides pre-defined and user-defined +comparison operations to compare the values of two items which can be arbitrary MPI datatypes. +Using these comparison operations, the library provides various routines for manipulating data, +which may be distributed over the processes of an MPI communicator.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5015b7b330b35e1871a6b5e53cf7045cfb0a29e61f9a678d1919f3bf14a85437'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('lwgrp', '1.0.5'), +] + +preconfigopts = './autogen.sh && ' +configopts = '--with-lwgrp=$EBROOTLWGRP' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT, 'share/%(name)s/README.md'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2023a.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2023a.eb new file mode 100644 index 00000000000..516d2ceb729 --- /dev/null +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2023a.eb @@ -0,0 +1,38 @@ +## +# Authors: +# * Petar Forai +# * Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'libcircle' +version = '0.3' + +homepage = 'https://github.com/hpc/libcircle/' + +description = """ + An API to provide an efficient distributed queue on a cluster. libcircle is an + API for distributing embarrassingly parallel workloads using self-stabilization. +""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.9.5'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.5-gompi-2023a.eb b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.5-gompi-2023a.eb new file mode 100644 index 00000000000..43fd08756cc --- /dev/null +++ b/easybuild/easyconfigs/l/lwgrp/lwgrp-1.0.5-gompi-2023a.eb @@ -0,0 +1,36 @@ +# +# Author: Robert Mijakovic +# +easyblock = 'ConfigureMake' + +name = 'lwgrp' +version = '1.0.5' + +homepage = 'https://github.com/LLNL/lwgrp' +description = """The light-weight group library defines data structures and collective operations to +group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators +when the overhead of communicator creation is too costly. For example, certain sorting algorithms +recursively divide processes into subgroups as the sort algorithm progresses. These groups may be +different with each invocation, so that it is inefficient to create and destroy communicators during +the sort routine.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +github_account = 'LLNL' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['1fac5fad3aed9f0a83026c19f438a33f9807d69990284e452b646b44a95fe72b'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.9.5'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/lib%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['share/%(name)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb new file mode 100644 index 00000000000..cfb2e78d56a --- /dev/null +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'mpifileutils' +version = "0.11.1" + +homepage = 'https://hpc.github.io/mpifileutils/' + +description = """ + MPI-Based File Utilities For Distributed Systems +""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +github_account = 'hpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e2cba53309b5b3ee581b6ff82e4e66f54628370cce694c34224ed947fece32d4'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('attr', '2.5.1'), + ('bzip2', '1.0.8'), + ('lwgrp', '1.0.5'), + ('dtcmp', '1.1.4'), + ('libarchive', '3.6.2'), + ('libcircle', '0.3'), +] + +sanity_check_paths = { + 'files': ['bin/dsync', 'include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'tools' From 1cc8ca2b9f4eae9e652bf97104d338a49ba0adef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Oct 2023 09:56:41 +0200 Subject: [PATCH 9032/9987] adding easyconfigs: alleleIntegrator-0.8.8-foss-2022b-R-4.2.2.eb, alleleCount-4.3.0-GCC-12.2.0.eb, ASCAT-3.1.2-foss-2022b-R-4.2.2.eb --- .../a/ASCAT/ASCAT-3.1.2-foss-2022b-R-4.2.2.eb | 30 +++++++ .../alleleCount-4.3.0-GCC-12.2.0.eb | 89 +++++++++++++++++++ ...leleIntegrator-0.8.8-foss-2022b-R-4.2.2.eb | 51 +++++++++++ 3 files changed, 170 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASCAT/ASCAT-3.1.2-foss-2022b-R-4.2.2.eb create mode 100644 easybuild/easyconfigs/a/alleleCount/alleleCount-4.3.0-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/a/alleleIntegrator/alleleIntegrator-0.8.8-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/a/ASCAT/ASCAT-3.1.2-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/a/ASCAT/ASCAT-3.1.2-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..d8d12897241 --- /dev/null +++ b/easybuild/easyconfigs/a/ASCAT/ASCAT-3.1.2-foss-2022b-R-4.2.2.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'ASCAT' +version = '3.1.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/VanLoo-lab/ascat' +description = """ASCAT is a method to derive copy number profiles of tumor cells, + accounting for normal cell admixture and tumor aneuploidy.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/VanLoo-lab/ascat/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5d65aef417ad12ea0e638b4179def5a9b8f25e1ccd757e41a6509534fe20eb17'] + +dependencies = [ + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), + ('alleleCount', '4.3.0'), +] + +start_dir = '%(name)s' + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/alleleCount/alleleCount-4.3.0-GCC-12.2.0.eb b/easybuild/easyconfigs/a/alleleCount/alleleCount-4.3.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..3ff0a8ddd2f --- /dev/null +++ b/easybuild/easyconfigs/a/alleleCount/alleleCount-4.3.0-GCC-12.2.0.eb @@ -0,0 +1,89 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Institute, London, UK +## + +easyblock = 'ConfigureMake' + +name = 'alleleCount' +version = '4.3.0' + +homepage = 'http://cancerit.github.io/alleleCount/' +description = """ The alleleCount package primarily exists to prevent code duplication +between some other projects, specifically AscatNGS and Battenberg. As of v4 the perl +code wraps the C implementation of allele counting code for BAM/CRAM processing. """ + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/cancerit/%(name)s/archive/v%(version)s'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5363ae12c2385c962728336a4498b1a29c9eaa3d4a24492d0debf897771cfd3c'] + +# HTSlib 1.7 is built, used and removed again in the provided setup script +dependencies = [ + ('Perl', '5.36.0'), + ('HTSlib', '1.17'), + ('libdeflate', '1.15'), +] + +skipsteps = ['configure'] + +buildopts = "-C c && cd perl && perl Makefile.PL INSTALL_BASE=%(installdir)s " +preinstallopts = "cd perl && " +installopts = " && cd .. && cp -a c/bin/alleleCounter %(installdir)s/bin/" + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') +exts_default_options = { + 'buildopts': '', + 'preinstallopts': '', + 'installopts': '', +} + +exts_list = [ + ('Const::Fast', '0.014', { + 'source_tmpl': 'Const-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + 'checksums': ['f805953a08c57846a16a4d85d7b766398afaf7c36c1465fcb1dea09e5fa394db'], + }), + ('Devel::Cover', '1.40', { + 'source_tmpl': 'Devel-Cover-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PJ/PJCJ/'], + 'checksums': ['26e2f431fbcf7bff3851f352f83b84067c09ff206f40ab975cad8d2bafe711a8'], + }), + ('Pod::Coverage', '0.23', { + 'source_tmpl': 'Pod-Coverage-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP/'], + 'checksums': ['30b7a0b0c942f44a7552c0d34e9b1f2e0ba0b67955c61e3b1589ec369074b107'], + }), + ('Pod::Parser', '1.66', { + 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], + 'checksums': ['22928a7bffe61b452c05bbbb8f5216d4b9cf9fe2a849b776c25500d24d20df7c'], + }), + ('Devel::Symdump', '2.18', { + 'source_tmpl': 'Devel-Symdump-%(version)s.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDK/'], + 'checksums': ['826f81a107f5592a2516766ed43beb47e10cc83edc9ea48090b02a36040776c0'], + }), +] + +postinstallcmds = ["chmod u+w %(installdir)s/bin/alleleCounter.pl"] + +fix_perl_shebang_for = ['bin/alleleCounter.pl'] + +sanity_check_paths = { + 'files': ['bin/alleleCounter', 'bin/alleleCounter.pl'], + 'dirs': ['lib/perl5'], +} + +sanity_check_commands = [ + "alleleCounter --help", + "alleleCounter.pl --help", +] + +modextrapaths = {'PERL5LIB': ['lib/perl5', 'lib/perl5/site_perl/%(perlver)s']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/alleleIntegrator/alleleIntegrator-0.8.8-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/a/alleleIntegrator/alleleIntegrator-0.8.8-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..cd4f3b1e0ea --- /dev/null +++ b/easybuild/easyconfigs/a/alleleIntegrator/alleleIntegrator-0.8.8-foss-2022b-R-4.2.2.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'alleleIntegrator' +version = '0.8.8' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/constantAmateur/alleleIntegrator' +description = 'R package to generate allele specific counts for scRNA data and use it to identify cancer cells' + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('R', '4.2.2'), + ('alleleCount', '4.3.0'), + ('BCFtools', '1.17'), + ('parallel', '20230722'), + ('ASCAT', '3.1.2', versionsuffix) +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} + +exts_list = [ + ('grr', '0.9.5', { + 'checksums': ['292606de2983ac5840c90d3e0977441b482c9e73c1674b662f8b4fb8f3632b2b'], + }), + ('Matrix.utils', '0.9.8', { + 'checksums': ['ebc59d3ef751775515586ff1f2396e429a1e9d91a10099d804134fcf74c0ae28'], + }), + (name, version, { + 'source_urls': ['https://github.com/constantAmateur/alleleIntegrator/archive/'], + 'sources': [{'download_filename': '7bf7970.tar.gz', 'filename': '%(namelower)s-%(version)s.tar.gz'}], + 'checksums': ['9e852c37485548c27c8ce29b90d163818c394410874d459e4fd92f184e4ff004'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 044d5941a3afcff347e11ddcd81e7a023ed7d81e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Oct 2023 09:57:08 +0200 Subject: [PATCH 9033/9987] adding easyconfigs: plot1cell-0.0.1-foss-2022b-R-4.2.2.eb, DoubletFinder-2.0.3-20230819-foss-2022b-R-4.2.2.eb, loomR-0.2.0-20180425-foss-2022b-R-4.2.2.eb --- ...inder-2.0.3-20230819-foss-2022b-R-4.2.2.eb | 29 +++++++++++++++++++ ...loomR-0.2.0-20180425-foss-2022b-R-4.2.2.eb | 29 +++++++++++++++++++ .../plot1cell-0.0.1-foss-2022b-R-4.2.2.eb | 28 ++++++++++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-20230819-foss-2022b-R-4.2.2.eb create mode 100644 easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2022b-R-4.2.2.eb create mode 100644 easybuild/easyconfigs/p/plot1cell/plot1cell-0.0.1-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-20230819-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-20230819-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..fcc4a735bbc --- /dev/null +++ b/easybuild/easyconfigs/d/DoubletFinder/DoubletFinder-2.0.3-20230819-foss-2022b-R-4.2.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'DoubletFinder' +local_commit = '1b1d4e2' +# see DESCRIPTION to determine version, +# but add date stamp of commit since version is not always bumped +version = '2.0.3-20230819' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/chris-mcginnis-ucsf/DoubletFinder' +description = "R package for detecting doublets in single-cell RNA sequencing data" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/chris-mcginnis-ucsf/DoubletFinder/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['dbba44cf9c20306e444e41df26d7eeb3f0687a2cd0b677b7afc87cd7ad28f268'] + +dependencies = [ + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..b7edbb8f8a1 --- /dev/null +++ b/easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2022b-R-4.2.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'loomR' +local_commit = 'df0144b' +# see DESCRIPTION to determine version, +# but add date stamp of commit since version is not always bumped +version = '0.2.0-20180425' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/mojaveazure/loomR' +description = "An R interface for loom files" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/mojaveazure/loomR/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['6264448baf4fd9a569eb5a832598c4a224382ef26c0a7fbd061a8c901672f0ac'] + +dependencies = [ + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/plot1cell/plot1cell-0.0.1-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/p/plot1cell/plot1cell-0.0.1-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..d25d694958d --- /dev/null +++ b/easybuild/easyconfigs/p/plot1cell/plot1cell-0.0.1-foss-2022b-R-4.2.2.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'plot1cell' +version = '0.0.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/HaojiaWu/plot1cell' +description = "plot1cell: a package for advanced single cell data visualization" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/HaojiaWu/plot1cell/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ac39a21e8530d7eb489ac64d8e56d19dcbf3f904b99fc91cf0746bb230f37a10'] + +dependencies = [ + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), + ('DoubletFinder', '2.0.3-20230819', versionsuffix), + ('loomR', '0.2.0-20180425', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 4d680b9ddb6157101908987c11be77b354956161 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Oct 2023 09:57:55 +0200 Subject: [PATCH 9034/9987] adding easyconfigs: CopyKAT-1.1.0-foss-2022b-R-4.2.2.eb --- .../CopyKAT-1.1.0-foss-2022b-R-4.2.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..26a7de55e4b --- /dev/null +++ b/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022b-R-4.2.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'CopyKAT' +local_commit = 'b795ff7' +version = '1.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/navinlabcode/copykat' +description = """CopyKAT: Inference of genomic copy number and subclonal structure of human tumors from + high-throughput single cell RNAseq data""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/navinlabcode/copykat/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['8b4e39591ad81d146873694b8311607bfec88ad57df8daa9244b2e31904193b5'] + +dependencies = [ + ('R', '4.2.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From 317c78dd2f3e23e414e2b812bb29bc87bc63c10f Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Mon, 9 Oct 2023 11:24:51 +0200 Subject: [PATCH 9035/9987] Update waLBerla-6.1-foss-2021a.eb add Boost.MPI dependency --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 6a5cdbc14e3..44b93328579 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -20,6 +20,7 @@ builddependencies = [('CMake', '3.20.1')] dependencies = [ ('pybind11', '2.6.2'), ('Python', '3.9.5'), + ('Boost.MPI', '1.76.0'), ] parallel = 1 From b5868456b4c7cb2a39decfd74361baca7a62979a Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 9 Oct 2023 12:38:30 +0200 Subject: [PATCH 9036/9987] adding easyconfigs: XML-Parser-2.46-GCCcore-12.3.0-Perl-5.36.1.eb --- ...-Parser-2.46-GCCcore-12.3.0-Perl-5.36.1.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-12.3.0-Perl-5.36.1.eb diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-12.3.0-Perl-5.36.1.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-12.3.0-Perl-5.36.1.eb new file mode 100644 index 00000000000..f72f817ca77 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.46-GCCcore-12.3.0-Perl-5.36.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.46' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://search.cpan.org/~toddr/XML-Parser-2.46/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] +checksums = ['d331332491c51cccfb4cb94ffc44f9cd73378e618498d4a37df9e043661c515d'] + +builddependencies = [ + ('binutils', '2.40') +] + +dependencies = [ + ('Perl', '5.36.1'), + ('expat', '2.5.0') +] + +options = {'modulename': 'XML::Parser'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML'], +} + +moduleclass = 'data' From 9fb4d02fc328ad3120788372afa10fbf873ce6a9 Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 9 Oct 2023 12:48:42 +0200 Subject: [PATCH 9037/9987] adding easyconfigs: ctffind-4.1.14-foss-2023a.eb --- .../c/ctffind/ctffind-4.1.14-foss-2023a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2023a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2023a.eb new file mode 100644 index 00000000000..38f4a58c5d5 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2023a.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University +# +# Author: Thomas Hoffmann, EMBL Heidelberg + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libjpeg-turbo', '2.1.5.1'), + ('LibTIFF', '4.5.0'), + ('GSL', '2.7',), + ('wxWidgets', '3.2.2.1'), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From e7980d703ff5c0a5432eb6af21e0b97bf3a37c3a Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 9 Oct 2023 13:01:53 +0200 Subject: [PATCH 9038/9987] adding easyconfigs: PRSice-2.3.5-GCCcore-12.3.0.eb --- .../p/PRSice/PRSice-2.3.5-GCCcore-12.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..f77c2144f22 --- /dev/null +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMakeCp' + +name = 'PRSice' +version = '2.3.5' + +homepage = 'https://www.prsice.info/' +description = """PRSice (pronounced 'precise') is a Polygenic Risk +Score software for calculating, applying, evaluating and +plotting the results of polygenic risk scores (PRS) analyses.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/choishingwan/PRSice/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['0a7e649ddebe4e969cd8400c5ad977a7b900be4f5c920a84483cb8930367354d'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), + ('Eigen', '3.4.0'), +] + +files_to_copy = [(['bin/PRSice'], 'bin'), "README.md", "LICENSE"] + +sanity_check_paths = { + 'files': ['bin/PRSice'], + 'dirs': [], +} + +sanity_check_commands = ["PRSice --help"] + +moduleclass = 'bio' From c2ce89a4fd28073585f0e390f36363122306b0ed Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Mon, 9 Oct 2023 11:03:54 +0000 Subject: [PATCH 9039/9987] adding easyconfigs: Monocle3-1.3.1-foss-2022b-R-4.2.2.eb --- .../Monocle3-1.3.1-foss-2022b-R-4.2.2.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..c19d8aff457 --- /dev/null +++ b/easybuild/easyconfigs/m/Monocle3/Monocle3-1.3.1-foss-2022b-R-4.2.2.eb @@ -0,0 +1,79 @@ +easyblock = 'Bundle' + +name = 'Monocle3' +version = '1.3.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cole-trapnell-lab.github.io/monocle3/' +description = """ An analysis toolkit for single-cell RNA-seq. """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [('pkgconf', '1.9.3')] # for textshaping + +dependencies = [ + ('R', '4.2.2'), + ('Python', '3.10.8'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), + ('GDAL', '3.6.2'), + ('HarfBuzz', '5.3.1'), # for textshaping + ('FriBidi', '1.0.12'), # for textshaping +] + +github_account = 'cole-trapnell-lab' +exts_defaultclass = 'RPackage' +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('grr', '0.9.5', { + 'checksums': ['292606de2983ac5840c90d3e0977441b482c9e73c1674b662f8b4fb8f3632b2b'], + }), + ('Matrix.utils', '0.9.8', { + 'checksums': ['ebc59d3ef751775515586ff1f2396e429a1e9d91a10099d804134fcf74c0ae28'], + }), + ('pbmcapply', '1.5.1', { + 'checksums': ['7ffc2854a384962f0dd523aa9ef33ce8fc290997206b71b840a49049d87112dd'], + }), + ('furrr', '0.3.1', { + 'checksums': ['0d91735e2e9be759b1ab148d115c2c7429b79740514778828e5dab631dc0e48b'], + }), + ('RhpcBLASctl', '0.21-247.1', { + 'checksums': ['5be55fd5ddd8173167a48b9f072835a34062ad0268308f2b3fbd1781a5c99769'], + }), + ('spdep', '1.2-7', { + 'checksums': ['9dac594825bf2d0aa31e845bfec05d8ce206327840fe455391741dbbdf9c9eea'], + }), + ('biglm', '0.9-2.1', { + 'checksums': ['6dcf3c9e7c3f56cdaac94cc0c427f606880467e1e753fe7ea45c10bc44eec947'], + }), + ('speedglm', '0.3-5', { + 'checksums': ['f8663677c10ff324c5639402060ddd2b1a1e917445cb0f8f84e146b85e82bb4b'], + }), + ('leidenbase', '0.1.9', { + 'source_urls': ['https://github.com/%(github_account)s/leidenbase/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'leidenbase-%(version)s.tar.gz'}], + 'checksums': ['dd893b13b04d4b943243e7ac8d2ef1850b60d0437b2e4d36a9cff57cd4953f54'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_urls': ['https://github.com/%(github_account)s/monocle3/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'Monocle3-%(version)s.tar.gz'}], + 'checksums': ['30e86d5323ea22b302614813ecf102f26774b42710589671a1f1d51ef9ad183d'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['leidenbase', '%(namelower)s'], +} + +moduleclass = 'bio' From 2ba18257e03ed4dbd6a9c22ffde68eae6f85a4cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 9 Oct 2023 14:56:20 +0200 Subject: [PATCH 9040/9987] Update ParaView version --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb index ced3f4fa116..74d81fdd5a1 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -40,7 +40,7 @@ dependencies = [ ('SCOTCH', '7.0.3'), ('KaHIP', '3.14'), ('Boost', '1.81.0'), - ('ParaView', '5.11.0', '-mpi'), + ('ParaView', '5.11.1'), ('gnuplot', '5.4.6'), ] From a7d5b47677e45075a0c0305f1ce362e7b50a72f5 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 9 Oct 2023 17:26:35 +0200 Subject: [PATCH 9041/9987] Removed comment from the top of the patch, since it caused problems --- .../JuliaCall-0.17.5-top_level_macro.patch | 38 +++++++++---------- 1 file changed, 18 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch b/easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch index a971737d46a..9b7e5180190 100644 --- a/easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch +++ b/easybuild/easyconfigs/r/ResistanceGA/JuliaCall-0.17.5-top_level_macro.patch @@ -1,22 +1,20 @@ -There is an error in current JuliaCall, which should be patched in upcoming versions. -See https://github.com/Non-Contradiction/JuliaCall/issues/203 diff -ruN JuliaCall_orig/inst/julia/JuliaObject.jl JuliaCall/inst/julia/JuliaObject.jl ---- JuliaCall_orig/inst/julia/JuliaObject.jl 2022-09-07 18:13:31.000000000 +0200 -+++ JuliaCall/inst/julia/JuliaObject.jl 2023-09-26 17:29:44.310679473 +0200 +--- JuliaCall_orig/inst/julia/JuliaObject.jl 2023-10-06 15:50:37.057320040 +0200 ++++ JuliaCall/inst/julia/JuliaObject.jl 2023-10-09 16:21:42.293384419 +0200 @@ -74,14 +74,14 @@ - ## we should use JuliaObject for general AbstractArray - @static if julia07 - @suppress_err begin -- JuliaCall.sexpclass(x :: AbstractArray{T}) where {T} = RClass{:JuliaObject} -+ @eval JuliaCall.sexpclass(x :: AbstractArray{T}) where {T} = RClass{:JuliaObject} - end - - ## AbstractArray{Any} should be converted to R List - sexpclass(x :: AbstractArray{Any}) = RClass{:list} - else - @suppress_err begin -- JuliaCall.sexp(x :: AbstractArray{T}) where {T} = sexp(JuliaObject(x)) -+ @eval JuliaCall.sexp(x :: AbstractArray{T}) where {T} = sexp(JuliaObject(x)) - end - - ## AbstractArray{Any} should be converted to R List + ## we should use JuliaObject for general AbstractArray + @static if julia07 + @suppress_err begin +- JuliaCall.sexpclass(x :: AbstractArray{T}) where {T} = RClass{:JuliaObject} ++ @eval JuliaCall.sexpclass(x :: AbstractArray{T}) where {T} = RClass{:JuliaObject} + end + + ## AbstractArray{Any} should be converted to R List + sexpclass(x :: AbstractArray{Any}) = RClass{:list} + else + @suppress_err begin +- JuliaCall.sexp(x :: AbstractArray{T}) where {T} = sexp(JuliaObject(x)) ++ @eval JuliaCall.sexp(x :: AbstractArray{T}) where {T} = sexp(JuliaObject(x)) + end + + ## AbstractArray{Any} should be converted to R List From 0812df706b6a5412a6b9f15ad2e88fd4a3891c1f Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 9 Oct 2023 18:06:02 +0200 Subject: [PATCH 9042/9987] adding easyconfigs: netCDF-Fortran-4.6.1-iimpi-2023a.eb --- .../netCDF-Fortran-4.6.1-iimpi-2023a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-iimpi-2023a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-iimpi-2023a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-iimpi-2023a.eb new file mode 100644 index 00000000000..30505ae9f4c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-iimpi-2023a.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['40b534e0c81b853081c67ccde095367bd8a5eead2ee883431331674e7aa9509f'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [ + ('netCDF', '4.9.2'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' From 2ec6b5a07eda735589547f3ed197b9702b751a53 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 9 Oct 2023 18:51:23 +0200 Subject: [PATCH 9043/9987] add sanity_check_commands to attr-2.5.1-GCCcore-12.3.0.eb and mpifileutils-0.11.1-gompi-2023a.eb --- .../easyconfigs/a/attr/attr-2.5.1-GCCcore-12.3.0.eb | 2 ++ .../m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb | 10 +++++++++- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-12.3.0.eb index 2801e172682..078c65a6a5e 100644 --- a/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/a/attr/attr-2.5.1-GCCcore-12.3.0.eb @@ -23,4 +23,6 @@ sanity_check_paths = { 'dirs': ['share'], } +sanity_check_commands = ["getfattr --help"] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb index cfb2e78d56a..096871ebfdc 100644 --- a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb @@ -29,9 +29,17 @@ dependencies = [ ('libcircle', '0.3'), ] +_binaries = [ + 'dbcast', 'dbz2', 'dchmod', 'dcmp', 'dcp', 'ddup','dfind', + 'dreln', 'drm', 'dstripe', 'dsync', 'dtar', 'dwalk' +] + sanity_check_paths = { - 'files': ['bin/dsync', 'include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], + 'files': ['bin/%s' % x for x in _binaries] + + ['include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], 'dirs': [] } +sanity_check_commands = ['%s --help 2>&1 | grep Usage' % x for x in _binaries] + moduleclass = 'tools' From 1cad3ae1ed99c7e31e9121d94954b1e01fdc1c10 Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 9 Oct 2023 19:49:04 +0200 Subject: [PATCH 9044/9987] Changed checksum for the patch --- .../ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb index 5eb0986cb61..83987de1e5a 100644 --- a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -53,7 +53,7 @@ exts_list = [ 'checksums': [ {'JuliaCall_0.17.5.tar.gz': '92542f9f02fe43702c18cf6c5a52fcbfc5ef3da6a2f73bfded773f4fc5edd90c'}, {'JuliaCall-0.17.5-top_level_macro.patch': - 'a733768f4bddd391a74d588b3d47bf8cbd475b42147856b35b0efd2eff83f63a'}, + '68508176c44fab479bce2a1a4e0302f835bd0d6a980abf860d713bb71f12145a'}, ], }), ('XR', '0.7.2', { From c8827172baf18f4628ae7f7628352c231abbe7a6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 9 Oct 2023 20:06:28 +0200 Subject: [PATCH 9045/9987] fix style in mpifileutils-0.11.1-gompi-2023a.eb --- .../m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb index 096871ebfdc..209d6128d81 100644 --- a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.11.1-gompi-2023a.eb @@ -30,7 +30,7 @@ dependencies = [ ] _binaries = [ - 'dbcast', 'dbz2', 'dchmod', 'dcmp', 'dcp', 'ddup','dfind', + 'dbcast', 'dbz2', 'dchmod', 'dcmp', 'dcp', 'ddup', 'dfind', 'dreln', 'drm', 'dstripe', 'dsync', 'dtar', 'dwalk' ] From 1f70dcc51e31090aa2ea3f0660969a83b2aca9b8 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 9 Oct 2023 22:47:40 +0200 Subject: [PATCH 9046/9987] Add OpenMolcas --- .../GlobalArrays-5.8.2-intel-2023a.eb | 30 ++++++++++ .../OpenMolcas-23.06-intel-2023a.eb | 58 +++++++++++++++++++ .../OpenMolcas-23.06_mcpdft_deps.patch | 15 +++++ 3 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2023a.eb create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06-intel-2023a.eb create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06_mcpdft_deps.patch diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2023a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2023a.eb new file mode 100644 index 00000000000..04f7174a29a --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.8.2' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['51599e4abfe36f05cecfaffa33be19efbe9e9fa42d035fd3f866469b663c22a2'] + +configopts = ' --with-mpi --enable-i8' +configopts += ' --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' + +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', + 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06-intel-2023a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06-intel-2023a.eb new file mode 100644 index 00000000000..2e9c366134f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06-intel-2023a.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'OpenMolcas' +version = '23.06' + +homepage = "https://gitlab.com/Molcas/OpenMolcas" +description = "OpenMolcas is a quantum chemistry software package." + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] +sources = ["%(name)s-v%(version)s.tar.gz"] +patches = ['%(name)s-%(version)s_mcpdft_deps.patch'] +checksums = [ + {'%(name)s-v%(version)s.tar.gz': 'fe0299ed39af6e84f249f91452c411f9845c9ae4a0ce78641c867dea8056f280'}, + {'%(name)s-%(version)s_mcpdft_deps.patch': '6b150fd9b301d8ebd8cde2d067f98d540a4d51b6dada1c76a842a71ec8b4aa31'}, +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('HDF5', '1.14.0'), + ('GlobalArrays', '5.8.2'), +] + +build_shared_libs = True + +preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' +_copts = [ + '-DLINALG=MKL', + '-DMKLROOT=$MKLROOT', + '-DOPENMP=ON', + '-DTOOLS=ON', + '-DFDE=ON', + '-DMPI=ON', + '-DGA=ON', +] +configopts = ' '.join(_copts) + +modextrapaths = {'PATH': ''} +modextravars = { + 'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', +} + +sanity_check_commands = ['cd %(builddir)s/easybuild_obj; ./pymolcas verify'] + +sanity_check_paths = { + 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, + 'sbin/help_basis', 'pymolcas'], + 'dirs': ['data/', 'basis_library/'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06_mcpdft_deps.patch b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06_mcpdft_deps.patch new file mode 100644 index 00000000000..3a56292eb2e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06_mcpdft_deps.patch @@ -0,0 +1,15 @@ +# mcpdft has a rasscf dependency + +diff -Nru OpenMolcas-v23.06.orig/CMakeLists.txt OpenMolcas-v23.06/CMakeLists.txt +--- OpenMolcas-v23.06.orig/CMakeLists.txt 2023-10-09 13:47:31.989388000 +0200 ++++ OpenMolcas-v23.06/CMakeLists.txt 2023-10-09 13:47:56.971468000 +0200 +@@ -2354,6 +2354,9 @@ + + # set program dependencies of super modules + # (note dependencies are not recursive with object libraries, so child dependencies must be explicit) ++set (mcpdft_deplibs ++ rasscf ++) + set (casvb_deplibs + rasscf + ) From a88faaecab2248b118d170fafae5174bc9478970 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 10 Oct 2023 09:22:34 +0200 Subject: [PATCH 9047/9987] Remove easyconfigs that have been added in other PRs --- .../f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb | 61 ------------------- .../scikit-build-core-0.5.1-GCCcore-12.3.0.eb | 31 ---------- .../spglib-python-2.1.0-gfbf-2023a.eb | 40 ------------ 3 files changed, 132 deletions(-) delete mode 100644 easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb delete mode 100644 easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb delete mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb deleted file mode 100644 index a37066c0753..00000000000 --- a/easybuild/easyconfigs/f/Flask/Flask-2.3.3-GCCcore-12.3.0.eb +++ /dev/null @@ -1,61 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Flask' -version = '2.3.3' - -homepage = 'https://www.palletsprojects.com/p/flask/' -description = """ -Flask is a lightweight WSGI web application framework. It is designed to make -getting started quick and easy, with the ability to scale up to complex -applications. -This module includes the Flask extensions: Flask-Cors""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06') -] - -builddependencies = [('binutils', '2.40')] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('itsdangerous', '2.1.2', { - 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], - }), - ('Werkzeug', '2.3.7', { - 'sources': ['%(namelower)s-%(version)s.tar.gz'], - 'checksums': ['2b8c0e447b4b9dbcc85dd97b6eeb4dcbaf6c8b6c3be0bd654e25553e0a2157d8'], - }), - ('asgiref', '3.7.2', { - 'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'], - }), - ('blinker', '1.6.2', { - 'checksums': ['4afd3de66ef3a9f8067559fb7a1cbe555c17dcbe15971b05d1b625c3e7abe213'], - }), - (name, version, { - 'sources': ['%(namelower)s-%(version)s.tar.gz'], - 'checksums': ['09c347a92aa7ff4a8e7f3206795f30d826654baf38b873d0744cd571ca609efc'], - }), - ('Flask-Cors', '3.0.10', { - 'checksums': ['b60839393f3b84a0f3746f6cdca56c1ad7426aa738b70d6c61375857823181de'], - }), - ('cachelib', '0.10.2', { - 'checksums': ['593faeee62a7c037d50fc835617a01b887503f972fb52b188ae7e50e9cb69740'], - }), - ('Flask-Session', '0.5.0', { - 'checksums': ['190875e6aebf2953c6803d42379ef3b934bc209ef8ef006f97aecb08f5aaeb86'], - }), -] - -sanity_check_paths = { - 'files': ['bin/flask'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ['flask --version'] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb deleted file mode 100644 index f2c59d3faec..00000000000 --- a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.5.1-GCCcore-12.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'scikit-build-core' -version = '0.5.1' - -homepage = 'https://pypi.org/project/scikit-build-core' -description = """Scikit-build-core is a ground-up rewrite of the classic Scikit-build, -a bridge between Python package build systems and CMake. -""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = [PYPI_LOWER_SOURCE] -sources = ['scikit_build_core-%(version)s.tar.gz'] -checksums = ['c6dad5a5127b2abfaa23cb91d23ac21059fd77cddf7122b33fd07791024dcfbf'] - -builddependencies = [('binutils', '2.40')] - -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), - ('hatchling', '1.18.0'), - ('CMake', '3.26.3'), -] - -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb deleted file mode 100644 index 392d2d01b8d..00000000000 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-gfbf-2023a.eb +++ /dev/null @@ -1,40 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'spglib-python' -version = '2.1.0' - -homepage = 'https://pypi.python.org/pypi/spglib' -description = """Spglib for Python. - -Spglib is a library for finding and handling crystal symmetries written in C. -""" - -toolchain = {'name': 'gfbf', 'version': '2023a'} - -builddependencies = [ - ('scikit-build-core', '0.5.1') -] - -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), - ('SciPy-bundle', '2023.07'), -] - -use_pip = True - -sanity_pip_check = True - -exts_list = [ - ('pyproject-metadata', '0.7.1', { - 'checksums': ['0a94f18b108b9b21f3a26a3d541f056c34edcb17dc872a144a15618fed7aef67'], - }), - (name, version, { - 'modulename': 'spglib', - 'sources': ['spglib-%(version)s.tar.gz'], - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'], - 'checksums': ['8143545fdffc11fbcda4d705a6b6bcd4889de9bc3524b78df866a36dd0de0a4b'], - }), -] - -moduleclass = 'chem' From 7ba0007cedbc219b95ac1ce03e3463b4aa96e50c Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 10 Oct 2023 11:01:09 +0200 Subject: [PATCH 9048/9987] Specify python in ESPResSo --- .../e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb | 1 + easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb | 1 + .../e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb | 1 + easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb index 9690edeb0ea..fdd93ce220f 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb @@ -29,6 +29,7 @@ dependencies = [ ] configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=ON' +configopts += ' -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Make sure the right python is used runtest = 'check_unit_tests && make check_python' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb index b18d54ed895..48b505bfc9e 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb @@ -27,6 +27,7 @@ dependencies = [ ] configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF' +configopts += ' -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Make sure the right python is used runtest = 'check_unit_tests && make check_python' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb index 907da191566..e89797a4b16 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb @@ -29,6 +29,7 @@ dependencies = [ ] configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=ON' +configopts += ' -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Make sure the right python is used runtest = 'check_unit_tests && make check_python' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb index 032b259661d..6ff43deee93 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb @@ -27,6 +27,7 @@ dependencies = [ ] configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF' +configopts += ' -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Make sure the right python is used runtest = 'check_unit_tests && make check_python' From 4c99bf832785be86d268468edc5f718974ba586c Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 10 Oct 2023 11:31:08 +0200 Subject: [PATCH 9049/9987] easyconfig for sympy in gfbf-2022b --- .../g/gmpy2/gmpy2-2.1.5-GCC-12.2.0.eb | 25 +++++++++++++++++++ .../s/sympy/sympy-1.12-gfbf-2022b.eb | 21 ++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.12-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-12.2.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-12.2.0.eb new file mode 100644 index 00000000000..ee56d5dc87c --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.5' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['bc297f1fd8c377ae67a4f493fc0f926e5d1b157e5c342e30a4d84dc7b9f95d96'] + +dependencies = [ + ('Python', '3.10.8'), + ('GMP', '6.2.1'), + ('MPFR', '4.2.0'), + ('MPC', '1.3.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.12-gfbf-2022b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.12-gfbf-2022b.eb new file mode 100644 index 00000000000..f532c554390 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.12-gfbf-2022b.eb @@ -0,0 +1,21 @@ +name = 'sympy' +version = '1.12' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ebf595c8dac3e0fdc4152c51878b498396ec7f30e7a914d6071e674d49420fb8'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('gmpy2', '2.1.5'), +] + +moduleclass = 'math' From a3d934929cab9a24f1854c35be3064bfab783dda Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 10 Oct 2023 12:38:51 +0200 Subject: [PATCH 9050/9987] {bio}[foss/2022a] starparser-1.49-foss-2022a.eb --- .../starparser/starparser-1.49-foss-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/s/starparser/starparser-1.49-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/starparser/starparser-1.49-foss-2022a.eb b/easybuild/easyconfigs/s/starparser/starparser-1.49-foss-2022a.eb new file mode 100644 index 00000000000..692bab05fe1 --- /dev/null +++ b/easybuild/easyconfigs/s/starparser/starparser-1.49-foss-2022a.eb @@ -0,0 +1,42 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/10 +easyblock = 'PythonBundle' + +name = 'starparser' +version = '1.49' + +homepage = 'https://github.com/sami-chaaban/starparser' +description = """Use this package to manipulate Relion star files, including counting, modifying, +plotting, and sifting the data. At the very least, this is a useful alternative +to awk commands, which can get awkward. Below is a description of the command- +line options with some examples. Alternatively, use starparser within Relion or +load the modules in your own Python scripts.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +use_pip = True + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +exts_list = [ + (name, version, { + 'checksums': ['6d7e2c11d1887970b66c08b2b7876a210f9c544cf13580320e841fb587167a68'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ['starparser -h'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'bio' From 8f523508aad6faee19e73888fb4977f7ecd0970e Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Tue, 10 Oct 2023 14:27:03 +0000 Subject: [PATCH 9051/9987] adding easyconfigs: ALL-0.9.2-foss-2022b.eb --- .../easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb new file mode 100644 index 00000000000..00b18e4486e --- /dev/null +++ b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'ALL' +version = '0.9.2' + +homepage = 'https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing' +description = """A Load Balancing Library (ALL) aims to provide an easy way to include dynamic +domain-based load balancing into particle based simulation codes. The library +is developed in the Simulation Laboratory Molecular Systems of the Jülich +Supercomputing Centre at Forschungszentrum Jülich.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ["https://gitlab.jsc.fz-juelich.de/SLMS/loadbalancing/-/archive/v%(version)s/"] +sources = ['loadbalancing-v%(version)s.tar.gz'] +checksums = ['2b4ef52c604c3c0c467712d0912a33c82177610b67edc14df1e034779c6ddb71'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Boost', '1.81.0'), # only needed for tests +] + +dependencies = [ + ('VTK', '9.2.6'), +] + +configopts = '-DCM_ALL_FORTRAN=ON -DCM_ALL_USE_F08=ON -DCM_ALL_VORONOI=ON -DCM_ALL_VTK_OUTPUT=ON ' +configopts += '-DCM_ALL_TESTS=ON -DCM_ALL_AUTO_DOC=OFF -DVTK_DIR=$EBROOTVTK ' + +runtest = 'test' + +sanity_check_paths = { + 'files': [ + 'include/ALL.hpp', 'include/ALL_Voronoi.hpp', 'lib/all_module.mod', + 'lib/libALL.a', 'lib/libALL_fortran.a' + ], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' From 1c6ef8d276ce5444498e45d374f2acc452509f84 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 10 Oct 2023 16:34:16 +0000 Subject: [PATCH 9052/9987] adding easyconfigs: OpenSlide-3.4.1-GCCcore-12.3.0-largefiles.eb, openslide-python-1.3.1-GCCcore-12.3.0.eb --- ...enSlide-3.4.1-GCCcore-12.3.0-largefiles.eb | 56 +++++++++++++++++++ .../openslide-python-1.3.1-GCCcore-12.3.0.eb | 29 ++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.3.0-largefiles.eb create mode 100644 easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.3.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.3.0-largefiles.eb new file mode 100644 index 00000000000..77358e8a3ab --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-12.3.0-largefiles.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide' +version = '3.4.1' +versionsuffix = '-largefiles' + +homepage = 'https://openslide.org/' +description = """OpenSlide is a C library that provides a simple interface to +read whole-slide images (also known as virtual slides).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_large_file_support.patch'] +checksums = [ + # v3.4.1.tar.gz + 'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c', + # %(name)s-%(version_major_minor)s.1_large_file_support.patch + 'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c', +] + +builddependencies = [ + ('Autotools', '20220317'), + ('M4', '1.4.19'), + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('LibTIFF', '4.5.0'), + ('OpenJPEG', '2.5.0'), + ('libxml2', '2.11.4'), + ('SQLite', '3.42.0'), + ('cairo', '1.17.8'), + ('Gdk-Pixbuf', '2.42.10'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': [ + 'bin/openslide-quickhash1sum', + 'bin/openslide-show-properties', + 'bin/openslide-write-png', + 'lib/libopenslide.la', + 'lib/libopenslide.%s' % SHLIB_EXT + ], + 'dirs': ['include/openslide'] +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..25e52c700cb --- /dev/null +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'openslide-python' +version = '1.3.1' + +homepage = 'https://github.com/openslide/openslide-python' +description = "OpenSlide Python is a Python interface to the OpenSlide library." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/openslide/openslide-python/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3f56bc9d02ae4a5b7257cf5e35214c5cc45f429ff3d5ef849c6c8e2460c1f9cd'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('Pillow-SIMD', '9.5.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'openslide'} + +moduleclass = 'vis' From 5f0b6bb2fc57b3ca22c4068c9d753c47030b4948 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Tue, 10 Oct 2023 19:18:30 +0200 Subject: [PATCH 9053/9987] Update ALL-0.9.2-foss-2022b.eb --- easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb index 00b18e4486e..a528178aeec 100644 --- a/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb +++ b/easybuild/easyconfigs/a/ALL/ALL-0.9.2-foss-2022b.eb @@ -25,7 +25,7 @@ dependencies = [ ('VTK', '9.2.6'), ] -configopts = '-DCM_ALL_FORTRAN=ON -DCM_ALL_USE_F08=ON -DCM_ALL_VORONOI=ON -DCM_ALL_VTK_OUTPUT=ON ' +configopts = '-DCM_ALL_FORTRAN=ON -DCM_ALL_USE_F08=ON -DCM_ALL_VORONOI=ON -DCM_ALL_VTK_OUTPUT=ON ' configopts += '-DCM_ALL_TESTS=ON -DCM_ALL_AUTO_DOC=OFF -DVTK_DIR=$EBROOTVTK ' runtest = 'test' From 66cf178f84cc1b7672de1f1abc104f587224e51e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Oct 2023 19:51:16 +0200 Subject: [PATCH 9054/9987] use -DPYTHON_EXECUTABLE instead of -DPython3_EXECUTABLE to control Python version used by CMake when building ESPResSo --- .../e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb | 3 ++- easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb | 3 ++- .../e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb | 3 ++- easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb | 3 ++- 4 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb index fdd93ce220f..4808bb96632 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb @@ -29,7 +29,8 @@ dependencies = [ ] configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=ON' -configopts += ' -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Make sure the right python is used +# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!) +configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python ' runtest = 'check_unit_tests && make check_python' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb index 48b505bfc9e..edaea20c78c 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a.eb @@ -27,7 +27,8 @@ dependencies = [ ] configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF' -configopts += ' -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Make sure the right python is used +# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!) +configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python ' runtest = 'check_unit_tests && make check_python' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb index e89797a4b16..c524dee3c8c 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a-CUDA-11.8.0.eb @@ -29,7 +29,8 @@ dependencies = [ ] configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=ON' -configopts += ' -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Make sure the right python is used +# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!) +configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python ' runtest = 'check_unit_tests && make check_python' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb index 6ff43deee93..e5bd5a63f74 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2022a.eb @@ -27,7 +27,8 @@ dependencies = [ ] configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF' -configopts += ' -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Make sure the right python is used +# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!) +configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python ' runtest = 'check_unit_tests && make check_python' From f5c1c27e390589df4dde5693cba303cac8952172 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 10 Oct 2023 21:09:16 +0200 Subject: [PATCH 9055/9987] {bio}[foss/2023a] OrthoFinder v2.5.5, BLAST+ v2.14.1, DIAMOND v2.1.8, FastME v2.1.6.3, MCL v22.282, MMseqs2 v14-7e284, LMDB v0.9.31, cimfomfa v22.273 --- .../b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb | 51 +++++++++++++++++++ .../cimfomfa-22.273-GCCcore-12.3.0.eb | 33 ++++++++++++ .../d/DIAMOND/DIAMOND-2.1.8-GCC-12.3.0.eb | 30 +++++++++++ .../f/FastME/FastME-2.1.6.3-GCC-12.3.0.eb | 28 ++++++++++ .../l/LMDB/LMDB-0.9.31-GCCcore-12.3.0.eb | 38 ++++++++++++++ .../m/MCL/MCL-22.282-GCCcore-12.3.0.eb | 38 ++++++++++++++ .../m/MMseqs2/MMseqs2-14-7e284-gompi-2023a.eb | 27 ++++++++++ .../OrthoFinder-2.5.5-foss-2023a.eb | 40 +++++++++++++++ 8 files changed, 285 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/c/cimfomfa/cimfomfa-22.273-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/FastME/FastME-2.1.6.3-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/MCL/MCL-22.282-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-14-7e284-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.5-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb new file mode 100644 index 00000000000..47c8e2d2ef6 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.14.1-gompi-2023a.eb @@ -0,0 +1,51 @@ +# # +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# # + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.14.1' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['712c2dbdf0fb13cc1c2d4f4ef5dd1ce4b06c3b57e96dfea8f23e6e99f5b1650e'] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('PCRE', '8.45'), + ('Boost', '1.82.0'), + ('GMP', '6.2.1'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('LMDB', '0.9.31'), +] + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cimfomfa/cimfomfa-22.273-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cimfomfa/cimfomfa-22.273-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..54c69ee2996 --- /dev/null +++ b/easybuild/easyconfigs/c/cimfomfa/cimfomfa-22.273-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'cimfomfa' +version = '22.273' + +homepage = 'https://github.com/micans/cimfomfa' +description = """This library supports both MCL, a cluster algorithm for graphs, and zoem, a +macro/DSL language. It supplies abstractions for memory management, I/O, +associative arrays, strings, heaps, and a few other things. The string library +has had heavy testing as part of zoem. Both understandably and regrettably I +chose long ago to make it C-string-compatible, hence nul bytes may not be part +of a string. At some point I hope to rectify this, perhaps unrealistically.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +# The Github repo only has earlier tags +source_urls = ['https://micans.org/mcl/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +checksums = ['b0f0549fda1d288ddd22a2675581636a6f4bde0f01e956fcf452d0f815b4964f'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': ['lib/libtingea.%s' % x for x in ('a', SHLIB_EXT)], + 'dirs': ['include/tingea'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-12.3.0.eb new file mode 100644 index 00000000000..6d2a83ec881 --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.8-GCC-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.1.8' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'bbuchfink' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b6088259f2bc92d1f9dc4add44590cff68321bcbf91eefbc295a3525118b9415'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["%(namelower)s help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastME/FastME-2.1.6.3-GCC-12.3.0.eb b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..03f7b77ed2c --- /dev/null +++ b/easybuild/easyconfigs/f/FastME/FastME-2.1.6.3-GCC-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'FastME' +version = '2.1.6.3' + +homepage = 'http://www.atgc-montpellier.fr/fastme/' +description = "FastME: a comprehensive, accurate and fast distance-based phylogeny inference program." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://gite.lirmm.fr/atgc/FastME/-/archive/v%(version)s/'] +sources = ['FastME-v%(version)s.tar.gz'] +checksums = ['d49ff78cca7b76eadf8443efb33f071a7e8a152618ffa3d8e790f167d0a0b176'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -if && " + +sanity_check_paths = { + 'files': ['bin/fastme'], + 'dirs': [] +} + +sanity_check_commands = ["fastme --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..52b24212404 --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.31' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['dd70a8c67807b3b8532b3e987b0a4e998962ecc28643e1af5ec77696b081c9b0'] + +builddependencies = [('binutils', '2.40')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +local_binaries = ['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'] + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (local_binaries, 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%s -V" % x for x in local_binaries] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MCL/MCL-22.282-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/MCL/MCL-22.282-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..bdf91fee809 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-22.282-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '22.282' + +homepage = 'https://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://micans.org/%(namelower)s/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] +checksums = ['291f35837b6e852743bd87e499c5a46936125dcdf334f7747af92e88ac902183'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Perl', '5.36.1'), + ('cimfomfa', '22.273'), +] + +configopts = '--enable-rcl ' + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['clm', 'clxdo', 'mcl', 'mcx', 'mcxarray', 'mcxdump', 'mcxi', + 'mcxload', 'mcxmap', 'mcxsubs', 'rcl', 'rcl-qc']], + 'dirs': ['share'] +} + +sanity_check_commands = ["mcl --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-14-7e284-gompi-2023a.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-14-7e284-gompi-2023a.eb new file mode 100644 index 00000000000..8cf62d2fc23 --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-14-7e284-gompi-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +version = '14-7e284' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a15fd59b121073fdcc8b259fc703e5ce4c671d2c56eb5c027749f4bd4c28dfe1'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [('bzip2', '1.0.8')] + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +sanity_check_commands = ["mmseqs --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.5-foss-2023a.eb b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.5-foss-2023a.eb new file mode 100644 index 00000000000..6bf59e72ea3 --- /dev/null +++ b/easybuild/easyconfigs/o/OrthoFinder/OrthoFinder-2.5.5-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'OrthoFinder' +version = '2.5.5' + +homepage = 'https://github.com/davidemms/OrthoFinder' +description = "OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'davidemms' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['56cc3dd196e88cb67cce9f34e459f44d52b8b1e0f339b6380b9e6a7c0104f6ff'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('BLAST+', '2.14.1'), + ('DIAMOND', '2.1.8'), + ('FastME', '2.1.6.3'), + ('MCL', '22.282'), + ('MMseqs2', '14-7e284'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'scripts_of'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['convert_orthofinder_tree_ids', 'make_ultrametric', 'orthofinder', + 'primary_transcript']], + 'dirs': ['ExampleData', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["orthofinder --help"] + +moduleclass = 'bio' From 0d93b275db2c560718101832720c0c74decebcdf Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 10 Oct 2023 21:12:50 +0200 Subject: [PATCH 9056/9987] adding easyconfigs: MAFFT-7.520-GCC-12.3.0-with-extensions.eb --- .../MAFFT-7.520-GCC-12.3.0-with-extensions.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.520-GCC-12.3.0-with-extensions.eb diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.520-GCC-12.3.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.520-GCC-12.3.0-with-extensions.eb new file mode 100644 index 00000000000..a27fa0f3544 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.520-GCC-12.3.0-with-extensions.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez (Swiss Institute of Bioinformatics, Biozentrum - University of Basel) +# 7.305 modified by: +# Adam Huffman (The Francis Crick Institute) +# 7.453 switch to Bundle by: +# Alex Domingo (Vrije Universiteit Brussel) +# Thomas Eylenbosch (Gluo NV) + +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.520' +versionsuffix = '-with-extensions' +local_commit = '52b59f064c600da59bca8233736418fb8bb35d5e' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://gitlab.com/sysimm/mafft/-/archive/v%(version)s/'], + 'sources': ['mafft-%(version)s.tar.gz'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-v%%(version)s-%s/core' % local_commit, + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-v%%(version)s-%s/extensions' % local_commit, + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft', 'libexec/mafft/mxscarnamod'], # mxscarnamod installed by MAFFT Extensions + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +moduleclass = 'bio' From f54ae56a1c8fc9854ded3dd6776767660b510de2 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 10 Oct 2023 22:14:38 +0200 Subject: [PATCH 9057/9987] Added checksums --- .../m/MAFFT/MAFFT-7.520-GCC-12.3.0-with-extensions.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.520-GCC-12.3.0-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.520-GCC-12.3.0-with-extensions.eb index a27fa0f3544..d49ae38d3b5 100644 --- a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.520-GCC-12.3.0-with-extensions.eb +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.520-GCC-12.3.0-with-extensions.eb @@ -24,6 +24,7 @@ default_easyblock = 'ConfigureMake' default_component_specs = { 'source_urls': ['https://gitlab.com/sysimm/mafft/-/archive/v%(version)s/'], 'sources': ['mafft-%(version)s.tar.gz'], + 'checksums': ['4a35a2a34e05313a85a4327d048704ae3ba7805ba85cae929e4978e10ad16cf8'], 'skipsteps': ['configure'], 'installopts': 'PREFIX=%(installdir)s', } From 99dcfec3b3862750a1e599d2f49b9f805b70e46e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 11 Oct 2023 09:15:26 +0200 Subject: [PATCH 9058/9987] adding easyconfigs: RDKit-2023.03.3-foss-2021a.eb --- .../r/RDKit/RDKit-2023.03.3-foss-2021a.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/r/RDKit/RDKit-2023.03.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/r/RDKit/RDKit-2023.03.3-foss-2021a.eb b/easybuild/easyconfigs/r/RDKit/RDKit-2023.03.3-foss-2021a.eb new file mode 100644 index 00000000000..c9222722632 --- /dev/null +++ b/easybuild/easyconfigs/r/RDKit/RDKit-2023.03.3-foss-2021a.eb @@ -0,0 +1,77 @@ +easyblock = 'CMakeMake' + +name = 'RDKit' +version = '2023.03.3' + +homepage = 'https://www.rdkit.org' +description = "RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python." + +toolchain = {'name': 'foss', 'version': '2021a'} +# avoid failing tests on skylake CPUs. comment out this line when building on CPUs that don't support AVX2 +# see also: https://github.com/rdkit/rdkit/issues/1674 +toolchainopts = {'optarch': 'mavx2', 'cstd': 'c++11'} + +source_urls = ['https://github.com/rdkit/rdkit/archive/'] +sources = ['Release_%s.tar.gz' % version.replace('.', '_')] +patches = [ + 'RDKit-2021.03.4_skip-broken-test.patch', +] +checksums = [ + {'Release_2023_03_3.tar.gz': 'bdbf9a2e6988526bfeb8c56ce3cdfe2998d60ac289078e2215374288185e8c8d'}, + {'RDKit-2021.03.4_skip-broken-test.patch': '45869e01461b66e42c9305f5e8a65f696417e4777c2da60ef81d1e26e57d1b2e'}, +] + +# Dependencies varies from version to version +# https://rdkit.readthedocs.io/en/latest/Install.html#installing-prerequisites-from-source +builddependencies = [ + ('CMake', '3.20.1'), + ('Eigen', '3.3.9'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('SQLite', '3.35.4'), + ('matplotlib', '3.4.2'), + ('Pillow', '8.2.0'), + ('Boost.Python', '1.76.0'), + ('cairo', '1.16.0'), +] + +separate_build_dir = True + +configopts = "-DPy_ENABLE_SHARED=1 -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_INTREE=OFF " +configopts += "-DRDK_BUILD_INCHI_SUPPORT=ON " +configopts += "-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib " + +# merge source directory into build directory in order to run the tests +buildopts = '&& cp -RT %(builddir)s/%(namelower)s-*/ ./ && ' +buildopts += 'export RDBASE=$PWD && export PYTHONPATH=$PWD:$PYTHONPATH && ' + +# Specify path for libraries so that they are found during the tests when the module is built with --rpath flag. +buildopts += 'export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj/lib:${LD_LIBRARY_PATH} && ' + +# 'ctest' allows to pass additional arguments opposed to 'make test' +buildopts += 'ctest --output-on-failure' + +local_libs = ['Alignment', 'Catalogs', 'ChemicalFeatures', 'ChemReactions', 'ChemTransforms', 'coordgen', 'DataStructs', + 'Depictor', 'Descriptors', 'DistGeometry', 'DistGeomHelpers', 'EigenSolvers', 'FileParsers', + 'FilterCatalog', 'Fingerprints', 'FMCS', 'ForceFieldHelpers', 'ForceField', 'FragCatalog', 'GraphMol', + 'hc', 'InfoTheory', 'maeparser', 'MMPA', 'MolAlign', 'MolCatalog', 'MolChemicalFeatures', 'MolDraw2D', + 'MolHash', 'MolInterchange', 'MolStandardize', 'MolTransforms', 'Optimizer', 'PartialCharges', 'RDBoost', + 'RDGeneral', 'RDGeometryLib', 'RDStreams', 'ReducedGraphs', 'RGroupDecomposition', 'RingDecomposerLib', + 'ScaffoldNetwork', 'ShapeHelpers', 'SimDivPickers', 'SLNParse', 'SmilesParse', 'Subgraphs', + 'SubstructLibrary', 'SubstructMatch', 'Trajectory'] + +sanity_check_paths = { + 'files': ['lib/libRDKit%s.%s' % (x, SHLIB_EXT) for x in local_libs], + 'dirs': ['include/rdkit', 'lib/python%(pyshortver)s/site-packages/rdkit'], +} + +sanity_check_commands = [ + "python -c 'import rdkit.rdBase'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From 67a2e1364b30719ce30c75e1617b2ccc9a67b466 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 11 Oct 2023 09:42:39 +0200 Subject: [PATCH 9059/9987] also use patch to improve CUDA 11 compatibility in GCCcore/12.3.0 --- easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb index 45270c7b7f8..c9fe0e62a87 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb @@ -33,6 +33,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.2.0_improve-cuda-compatibility.patch', ] checksums = [ {'gcc-12.3.0.tar.gz': '11275aa7bb34cd8ab101d01b341015499f8d9466342a2574ece93f954d92273b'}, @@ -44,6 +45,8 @@ checksums = [ {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.2.0_improve-cuda-compatibility.patch': + '91d00122554b56381592229398540e63baa26d03633292a7fdf338407a4a62d5'}, ] builddependencies = [ From e1fe1e61fc5b67ceef4e19d0f894fe470d046148 Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 11 Oct 2023 10:02:28 +0200 Subject: [PATCH 9060/9987] Update OpenMolcas-23.06_mcpdft_deps.patch --- .../o/OpenMolcas/OpenMolcas-23.06_mcpdft_deps.patch | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06_mcpdft_deps.patch b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06_mcpdft_deps.patch index 3a56292eb2e..9351f956181 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06_mcpdft_deps.patch +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06_mcpdft_deps.patch @@ -1,5 +1,7 @@ -# mcpdft has a rasscf dependency - +# What: Add rasscf as a dependency to mcpdft +# Authors: B. Hajgato (UGent), 2021 +# maxim-masterov (SURF), 2023 +# diff -Nru OpenMolcas-v23.06.orig/CMakeLists.txt OpenMolcas-v23.06/CMakeLists.txt --- OpenMolcas-v23.06.orig/CMakeLists.txt 2023-10-09 13:47:31.989388000 +0200 +++ OpenMolcas-v23.06/CMakeLists.txt 2023-10-09 13:47:56.971468000 +0200 From e82d1fd94612121f2fbd42f46b9f5af8774a5e64 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 11 Oct 2023 10:04:09 +0200 Subject: [PATCH 9061/9987] Change checksum for te patch --- .../easyconfigs/o/OpenMolcas/OpenMolcas-23.06-intel-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06-intel-2023a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06-intel-2023a.eb index 2e9c366134f..907f553c656 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06-intel-2023a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-23.06-intel-2023a.eb @@ -14,7 +14,7 @@ sources = ["%(name)s-v%(version)s.tar.gz"] patches = ['%(name)s-%(version)s_mcpdft_deps.patch'] checksums = [ {'%(name)s-v%(version)s.tar.gz': 'fe0299ed39af6e84f249f91452c411f9845c9ae4a0ce78641c867dea8056f280'}, - {'%(name)s-%(version)s_mcpdft_deps.patch': '6b150fd9b301d8ebd8cde2d067f98d540a4d51b6dada1c76a842a71ec8b4aa31'}, + {'%(name)s-%(version)s_mcpdft_deps.patch': 'a798ec6f93a19539aa2211a978da461d4ecd31c5521b9dab6f2a9b1c2fa65f0e'}, ] builddependencies = [('CMake', '3.26.3')] From 225d415f20fe732d0322b046616e690e8040b882 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Oct 2023 11:47:07 +0200 Subject: [PATCH 9062/9987] Rename CVS to ConcurrentVersionsSystem --- .../{CVS => ConcurrentVersionsSystem}/CVS-1.11.23-getline.patch | 0 .../{CVS => ConcurrentVersionsSystem}/CVS-1.11.23-zlib-1.patch | 0 .../ConcurrentVersionsSystem-1.11.23-GCC-4.8.2.eb} | 2 +- .../ConcurrentVersionsSystem-1.11.23-GCCcore-11.2.0.eb} | 2 +- .../ConcurrentVersionsSystem-1.11.23-GCCcore-4.9.3.eb} | 2 +- .../ConcurrentVersionsSystem-1.11.23-GCCcore-6.4.0.eb} | 2 +- 6 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/c/{CVS => ConcurrentVersionsSystem}/CVS-1.11.23-getline.patch (100%) rename easybuild/easyconfigs/c/{CVS => ConcurrentVersionsSystem}/CVS-1.11.23-zlib-1.patch (100%) rename easybuild/easyconfigs/c/{CVS/CVS-1.11.23-GCC-4.8.2.eb => ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCC-4.8.2.eb} (95%) rename easybuild/easyconfigs/c/{CVS/CVS-1.11.23-GCCcore-11.2.0.eb => ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-11.2.0.eb} (96%) rename easybuild/easyconfigs/c/{CVS/CVS-1.11.23-GCCcore-4.9.3.eb => ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-4.9.3.eb} (95%) rename easybuild/easyconfigs/c/{CVS/CVS-1.11.23-GCCcore-6.4.0.eb => ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-6.4.0.eb} (96%) diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-getline.patch b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/CVS-1.11.23-getline.patch similarity index 100% rename from easybuild/easyconfigs/c/CVS/CVS-1.11.23-getline.patch rename to easybuild/easyconfigs/c/ConcurrentVersionsSystem/CVS-1.11.23-getline.patch diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-zlib-1.patch b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/CVS-1.11.23-zlib-1.patch similarity index 100% rename from easybuild/easyconfigs/c/CVS/CVS-1.11.23-zlib-1.patch rename to easybuild/easyconfigs/c/ConcurrentVersionsSystem/CVS-1.11.23-zlib-1.patch diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCC-4.8.2.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCC-4.8.2.eb similarity index 95% rename from easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCC-4.8.2.eb rename to easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCC-4.8.2.eb index d6aba60dab8..17149a15e40 100644 --- a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCC-4.8.2.eb @@ -5,7 +5,7 @@ easyblock = 'ConfigureMake' -name = 'CVS' +name = 'ConcurrentVersionsSystem' version = '1.11.23' homepage = 'https://savannah.nongnu.org/projects/cvs' diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-11.2.0.eb similarity index 96% rename from easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb rename to easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-11.2.0.eb index 2f480e47a5b..c5e05721940 100644 --- a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-11.2.0.eb @@ -5,7 +5,7 @@ easyblock = 'ConfigureMake' -name = 'CVS' +name = 'ConcurrentVersionsSystem' version = '1.11.23' homepage = 'https://savannah.nongnu.org/projects/cvs' diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-4.9.3.eb similarity index 95% rename from easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb rename to easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-4.9.3.eb index b4f49365df8..9851a5c0aac 100644 --- a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-4.9.3.eb @@ -5,7 +5,7 @@ easyblock = 'ConfigureMake' -name = 'CVS' +name = 'ConcurrentVersionsSystem' version = '1.11.23' homepage = 'https://savannah.nongnu.org/projects/cvs' diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-6.4.0.eb similarity index 96% rename from easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-6.4.0.eb index b4435cfaa54..e2a7435be31 100644 --- a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-6.4.0.eb @@ -5,7 +5,7 @@ easyblock = 'ConfigureMake' -name = 'CVS' +name = 'ConcurrentVersionsSystem' version = '1.11.23' homepage = 'https://savannah.nongnu.org/projects/cvs' From 78a0f06020a6cb6965cda498156a0cfa88687b50 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Oct 2023 13:54:47 +0200 Subject: [PATCH 9063/9987] Fix dep name in jhbuild --- .../easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb index 39190893ab0..ef4552462a1 100644 --- a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb @@ -28,7 +28,7 @@ dependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), ('M4', '1.4.17'), - ('CVS', '1.11.23'), + ('ConcurrentVersionsSystems', '1.11.23'), ] # We use the simple install method as per: From e0b429ab229528533927b791f70e4a1e9533e901 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Oct 2023 14:22:10 +0200 Subject: [PATCH 9064/9987] Add checksums to jhbuild to make CI happy --- .../easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb index ef4552462a1..6525e8ac55c 100644 --- a/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '4.9.3'} sources = ['%(version)s.tar.gz'] source_urls = [('https://github.com/GNOME/jhbuild/archive/')] +checksums = [None] # jhbuild is python so it has a python dependency, but we want to give people freedom to use whatever python they # chose during a build process @@ -28,7 +29,7 @@ dependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), ('M4', '1.4.17'), - ('ConcurrentVersionsSystems', '1.11.23'), + ('ConcurrentVersionsSystem', '1.11.23'), ] # We use the simple install method as per: From c57155500ede1cec4c542391a3159994c88d258d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 11 Oct 2023 15:20:50 +0200 Subject: [PATCH 9065/9987] Drop old nonworking checks and workarounds for CVS --- .github/workflows/unit_tests.yml | 13 ------------- setup.cfg | 4 ---- 2 files changed, 17 deletions(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index d36d0a6398e..db62a78bc25 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -147,10 +147,6 @@ jobs: eb --search '^foss-2019b.eb' | tee eb_search_foss.out grep '/foss-2019b.eb$' eb_search_foss.out - # make sure CVS easyconfigs are included in installation (cfr. issue #10325) - echo "Searching for CVS easyconfigs..." - eb --search '^CVS-' | grep '/CVS-' - # try installing M4 with system toolchain (requires ConfigureMake easyblock + easyconfig) # use /tmp/sources because that has cached downloads (see cache step above) eb --prefix /tmp/$USER/$GITHUB_SHA --sourcepath /tmp/sources M4-1.4.18.eb @@ -184,12 +180,3 @@ jobs: else echo "No .git folders found in source tarball: OK" fi - - # CVS easyconfigs must be included in source tarball, - # see https://github.com/easybuilders/easybuild-easyconfigs/issues/10325 - cvs_easyconfigs=$(find . -name 'CVS-*.eb') - if [ -z "$cvs_easyconfigs" ]; then - echo "CVS easyconfigs not found" && false - else - echo "Found CVS easyconfigs: $cvs_easyconfigs" - fi diff --git a/setup.cfg b/setup.cfg index c1167840f91..3e70f500f0d 100644 --- a/setup.cfg +++ b/setup.cfg @@ -74,7 +74,3 @@ builtins = SOURCELOWER_PY2_WHL, SOURCE_PY3_WHL, SOURCELOWER_PY3_WHL - -[sdist] -# Don't remove CVS and RCS directories -prune = 0 From f5372fcf4a495fb79d7348aef5d208c9e498f0f4 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 11 Oct 2023 15:28:17 +0200 Subject: [PATCH 9066/9987] remove six extension, set tqdm as dependency --- .../segmentation-models-pytorch-0.3.3-foss-2022a.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/segmentation-models-pytorch/segmentation-models-pytorch-0.3.3-foss-2022a.eb b/easybuild/easyconfigs/s/segmentation-models-pytorch/segmentation-models-pytorch-0.3.3-foss-2022a.eb index 1d526510da3..8562db1e66e 100644 --- a/easybuild/easyconfigs/s/segmentation-models-pytorch/segmentation-models-pytorch-0.3.3-foss-2022a.eb +++ b/easybuild/easyconfigs/s/segmentation-models-pytorch/segmentation-models-pytorch-0.3.3-foss-2022a.eb @@ -13,6 +13,7 @@ dependencies = [ ('PyTorch', '1.12.0'), ('torchvision', '0.13.1'), ('Safetensors', '0.3.1'), + ('tqdm', '4.64.0'), ] use_pip = True @@ -33,12 +34,6 @@ exts_list = [ ('timm', '0.9.2', { 'checksums': ['d0977cc5e02c69bda979fca8b52aa315a5f2cb64ebf8ad2c4631b1e452762c14'], }), - ('tqdm', '4.64.0', { - 'checksums': ['40be55d30e200777a307a7585aee69e4eabb46b4ec6a4b4a5f2d9f11e7d5408d'], - }), - ('six', '1.16.0', { - 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], - }), ('segmentation_models_pytorch', version, { 'checksums': ['b3b21ab4cd26a6b2b9e7a6ed466ace6452eb26ed3c31ae491ea2d7cbb01e384b'], }), From d93a3ac1b3726f30d96a19749cd2f99a008651f0 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 11 Oct 2023 14:44:12 +0100 Subject: [PATCH 9067/9987] F90 interface for Zoltan enabled, ParMETIS added --- .../Trilinos-13.4.1-foss-2022a-zoltan.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a-zoltan.eb diff --git a/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a-zoltan.eb b/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a-zoltan.eb new file mode 100644 index 00000000000..572f0346229 --- /dev/null +++ b/easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-foss-2022a-zoltan.eb @@ -0,0 +1,52 @@ +# easyblock = 'CMakeMake' + +name = 'Trilinos' +version = '13.4.1' +versionsuffix = '-zoltan' + +homepage = 'https://trilinos.org' +description = """The Trilinos Project is an effort to develop algorithms and enabling technologies + within an object-oriented software framework for the solution of large-scale, complex multi-physics + engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True, 'strict': True} + +source_urls = ['https://github.com/trilinos/Trilinos/archive/refs/tags/'] +sources = ['trilinos-release-%s.tar.gz' % '-'.join(version.split('.'))] +patches = ['Trilinos-13.4.1_fix-seacas-NC-constants.patch'] +checksums = [ + {'trilinos-release-13-4-1.tar.gz': '5465cbff3de7ef4ac7d40eeff9d99342c00d9d20eee0a5f64f0a523093f5f1b3'}, + {'Trilinos-13.4.1_fix-seacas-NC-constants.patch': + 'df6215589abf582197a963c49ba853c1eca788261a1b1834099e7679794e9eed'}, +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('SWIG', '4.0.2'), + ('Doxygen', '1.9.4'), + ('Perl', '5.34.1', '-minimal'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost.Python', '1.79.0'), + ('Boost', '1.79.0'), + ('SCOTCH', '7.0.1'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('HDF5', '1.12.2'), + ('netCDF', '4.9.0'), + ('MATIO', '1.5.23'), + ('GLM', '0.9.9.8'), + ('ParMETIS', '4.0.3'), + ('X11', '20220504'), +] + +forward_deps = False +build_tests = False +configopts = '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION=ON ' +configopts += '-DKokkos_ENABLE_AGGRESSIVE_VECTORIZATION=ON ' +# We might need that for Fluidity Zoltan interface +configopts += '-DZoltan_ENABLE_F90INTERFACE=ON -DZoltan_ENABLE_ParMETIS=ON -DZoltan_ENABLE_Scotch=ON ' + +moduleclass = 'numlib' From 551f74a5b280e50ebdeb59436f6d6a651b9325d7 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 11 Oct 2023 15:45:22 +0200 Subject: [PATCH 9068/9987] Add GTK4 and deps --- .../GST-plugins-bad-1.22.5-GCC-12.3.0.eb | 44 ++++++++++ .../g/GTK4/GTK4-4.13.1-GCC-12.3.0.eb | 81 +++++++++++++++++++ .../PyCairo/PyCairo-1.25.0-GCCcore-12.3.0.eb | 38 +++++++++ .../PyGObject-3.46.0-GCCcore-12.3.0.eb | 38 +++++++++ 4 files changed, 201 insertions(+) create mode 100755 easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GTK4/GTK4-4.13.1-GCC-12.3.0.eb create mode 100755 easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.0-GCCcore-12.3.0.eb create mode 100755 easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.3.0.eb new file mode 100755 index 00000000000..9814e447313 --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GST-plugins-bad' +version = '1.22.5' + +homepage = 'https://gstreamer.freedesktop.org/' +description = """GStreamer is a library for constructing graphs of media-handling + components. The applications it supports range from simple + Ogg/Vorbis playback, audio/video streaming to complex audio + (mixing) and video (non-linear editing) processing.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://gstreamer.freedesktop.org/src/gst-plugins-bad'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e64e75cdafd7ff2fc7fc34e855b06b1e3ed227cc06fa378d17bbcd76780c338c'] + +builddependencies = [ + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.76.1'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.5'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('GLib', '2.77.1'), + ('GStreamer', '1.22.5'), + ('Gdk-Pixbuf', '2.42.10'), + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('Graphene', '1.10.8'), + ('GST-plugins-base', '1.22.5'), +] + +sanity_check_paths = { + 'files': ['bin/gst-transcoder-1.0', 'bin/playout'] + + ['lib/libgst%s-1.0.%s' % (x, SHLIB_EXT) for x in ['adaptivedemux', 'badaudio', 'codecs', 'player']], + 'dirs': ['include', 'share'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GTK4/GTK4-4.13.1-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GTK4/GTK4-4.13.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..5ac3810bfa1 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK4/GTK4-4.13.1-GCC-12.3.0.eb @@ -0,0 +1,81 @@ +easyblock = 'Bundle' + +name = 'GTK4' +version = '4.13.1' + +homepage = 'https://docs.gtk.org/gtk4/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('GObject-Introspection', '1.76.1'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.5'), + ('cairo', '1.17.8'), + ('Perl', '5.36.1'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), +] +dependencies = [ + ('ATK', '2.38.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.10'), + ('Pango', '1.50.14'), + ('libepoxy', '1.5.10'), + ('X11', '20230603'), + ('FriBidi', '1.0.12'), + ('GST-plugins-bad', '1.22.5'), + ('Wayland', '1.22.0'), + ('PyGObject', '3.46.0'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK', version, { + 'easyblock': 'MesonNinja', + 'source_urls': [FTPGNOME_SOURCE], + 'configopts': "-Dintrospection=enabled -Dgtk_doc=false", + 'checksums': [ + '53d832a37653fb4672ad7b3d3be656082eeee402177d971fdf8e0cba9a55b9a1', + ], + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '45.0', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'checksums': [ + '2442bfb06f4e6cc95bf6e2682fdff98fa5eddc688751b9d6215c623cb4e42ff1', + ], + }), +] + +postinstallcmds = ['gtk4-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk4-demo', 'gtk4-demo-application', 'gtk4-icon-browser', 'gtk4-widget-factory', + 'gtk4-builder-tool', 'gtk4-launch', 'gtk4-query-settings', + 'gtk4-update-icon-cache', 'gtk4-widget-factory']] + + ['lib/libgtk-4.%s' % SHLIB_EXT], + 'dirs': ['include/%s-%%(version_major)s.0/%s' % ('gtk', x) for x in ['gdk', 'gsk', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.0-GCCcore-12.3.0.eb new file mode 100755 index 00000000000..6a386c621fe --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.0-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +# Need to use Meson instead of the "pip" installation +# See: https://github.com/pygobject/pycairo/issues/312 +easyblock = 'MesonNinja' + +name = 'PyCairo' +version = '1.25.0' + +homepage = 'https://pycairo.readthedocs.io/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/pygobject/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ebb811ed6eae75866aaeac6edcfc2508665b550dc76ff51505092099a68df0b5'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('cairo', '1.17.8'), +] + +sanity_check_paths = { + 'files': ['%s/py3cairo.%s' % (p, e) for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')]], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-12.3.0.eb new file mode 100755 index 00000000000..9e886374697 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'PyGObject' +version = '3.46.0' + +homepage = 'https://pygobject.readthedocs.io/' +description = """PyGObject is a Python package which provides bindings for GObject based +libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['481437b05af0a66b7c366ea052710eb3aacbb979d22d30b797f7ec29347ab1e6'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('GLib', '2.77.1'), + ('GObject-Introspection', '1.76.1'), + ('PyCairo', '1.25.0'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['include/pygobject-%(version_major)s.0/pygobject.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'gi'} + +moduleclass = 'vis' From bf29e5a6db895abe9116c2a1167785db9128b6ef Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 11 Oct 2023 16:10:16 +0200 Subject: [PATCH 9069/9987] Remove +x permission --- .../g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GST-plugins-bad/GST-plugins-bad-1.22.5-GCC-12.3.0.eb old mode 100755 new mode 100644 From e3fad737e98462c8098df67a522aa051db204f20 Mon Sep 17 00:00:00 2001 From: scarf489 Date: Wed, 11 Oct 2023 15:16:44 +0100 Subject: [PATCH 9070/9987] adding easyconfigs: Jmol-16.1.41.eb --- easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb | 23 ++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb diff --git a/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb b/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb new file mode 100644 index 00000000000..e13025156ff --- /dev/null +++ b/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb @@ -0,0 +1,23 @@ +easyblock = 'PackedBinary' + +name = 'Jmol' +version = '16.1.41' + +homepage = 'http://jmol.sourceforge.net/' +description = """Jmol: an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules""" + +toolchain = SYSTEM + +sources = ['%(name)s-%(version)s-binary.tar.gz'] +source_urls = ['https://sourceforge.net/projects/jmol/files/Jmol/Version%2016.1/Jmol%2016.1.41/'] + +sanity_check_paths = { + 'files': ['jmol', 'Jmol.jar'], + 'dirs' : [], +} + +modextrapaths = { + 'JMOL_HOME': '' +} + +moduleclass = 'tools' From 9ab4ef96d6e3bf119a0c2f1517dc3bee957cd40d Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 11 Oct 2023 16:33:01 +0200 Subject: [PATCH 9071/9987] Remove +x permissions --- .../easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-12.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-12.3.0.eb old mode 100755 new mode 100644 From d911be0208bc040022b378b07efc70318829d7ec Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 11 Oct 2023 16:33:47 +0200 Subject: [PATCH 9072/9987] Remove +x permissions --- easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.0-GCCcore-12.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.0-GCCcore-12.3.0.eb old mode 100755 new mode 100644 From eefea1f6424100ca0870e06bb3f2db2b36625adc Mon Sep 17 00:00:00 2001 From: scarf489 Date: Wed, 11 Oct 2023 15:54:34 +0100 Subject: [PATCH 9073/9987] Minor corrections made to module file --- easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb b/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb index e13025156ff..082e1548ef0 100644 --- a/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb +++ b/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb @@ -4,7 +4,7 @@ name = 'Jmol' version = '16.1.41' homepage = 'http://jmol.sourceforge.net/' -description = """Jmol: an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules""" +description = """Jmol: an open-source Java viewer for chemical structures in 3D""" toolchain = SYSTEM @@ -13,7 +13,7 @@ source_urls = ['https://sourceforge.net/projects/jmol/files/Jmol/Version%2016.1/ sanity_check_paths = { 'files': ['jmol', 'Jmol.jar'], - 'dirs' : [], + 'dirs': [], } modextrapaths = { From d239e1deea5882fca0c9a3486c777c6766aaa7b4 Mon Sep 17 00:00:00 2001 From: scarf489 Date: Wed, 11 Oct 2023 16:19:08 +0100 Subject: [PATCH 9074/9987] Added source checksum --- easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb b/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb index 082e1548ef0..0c0429f4444 100644 --- a/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb +++ b/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb @@ -8,8 +8,9 @@ description = """Jmol: an open-source Java viewer for chemical structures in 3D" toolchain = SYSTEM -sources = ['%(name)s-%(version)s-binary.tar.gz'] source_urls = ['https://sourceforge.net/projects/jmol/files/Jmol/Version%2016.1/Jmol%2016.1.41/'] +sources = ['%(name)s-%(version)s-binary.tar.gz'] +checksums = ['f75bcf8a94b9153a8297b0544aee3b680a487ead9ef1d0f5496fcb1064165a2a'] sanity_check_paths = { 'files': ['jmol', 'Jmol.jar'], From 0a0d8cb5ef70c9d47738ad666b882252fbaf8e75 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 11 Oct 2023 15:26:30 +0000 Subject: [PATCH 9075/9987] adding easyconfigs: CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb --- ...UDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 00000000000..d4240930bd1 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.6-GCC-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,54 @@ +easyblock = 'MakeCp' + +name = 'CUDA-Samples' +version = '11.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['75b858bcf9e534eaa0f129c418e661b83872d743de218df8a5278cc429f9ea98'] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), +] + +# Get rid of pre-built Windows DLLs. +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies +local_filters = "Samples/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/boxFilterNPP/Makefile " +local_filters += "Samples/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/cudaNvSci/Makefile " +local_filters += "Samples/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/simpleGL/Makefile " +local_filters += "Samples/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/simpleVulkan/Makefile " +local_filters += "Samples/simpleVulkanMMAP/Makefile " +local_filters += "Samples/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/vulkanImageCUDA/Makefile" + +buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' From 93bb0beceac7091f6e7150462c44f3384f3fa3ad Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 11 Oct 2023 16:20:58 +0000 Subject: [PATCH 9076/9987] adding easyconfigs: LMDB-0.9.31-GCCcore-12.3.0.eb --- .../l/LMDB/LMDB-0.9.31-GCCcore-12.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5d4e2458588 --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.31-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.31' + +homepage = 'https://symas.com/lmdb' +description = """LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance + of a pure in-memory database while retaining the persistence of standard disk-based databases.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/LMDB/lmdb/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['dd70a8c67807b3b8532b3e987b0a4e998962ecc28643e1af5ec77696b081c9b0'] + +builddependencies = [('binutils', '2.40')] + +buildopts = 'CC="$CC" OPT="$CFLAGS"' + +runtest = 'test' + +files_to_copy = [ + (['lmdb.h', 'midl.h'], 'include'), + (['mdb_copy', 'mdb_dump', 'mdb_load', 'mdb_stat'], 'bin'), + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/mdb_copy', 'bin/mdb_dump', 'bin/mdb_load', 'bin/mdb_stat', 'include/lmdb.h', + 'include/midl.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From d0a6ce181643d1de65b294a17ebdd672d7192573 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 11 Oct 2023 16:47:45 +0000 Subject: [PATCH 9077/9987] adding easyconfigs: CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb --- ...UDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 00000000000..438e0f44965 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'CUDA-Samples' +version = '12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f758160645b366d79c2638d8dfd389f01029b8d179ab0c11726b9ef58aecebd9'] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), +] + +# Get rid of pre-built Windows DLLs. +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies +local_filters = "Samples/2_Concepts_and_Techniques/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/2_Concepts_and_Techniques/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/3_CUDA_Features/tf32TensorCoreGemm/Makefile " +local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile " +local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile " +local_filters += "Samples/5_Domain_Specific/vulkanImageCUDA/Makefile " + +# Sample does not compile with GCC>11 +local_filters += "Samples/0_Introduction/simpleAWBarrier/Makefile " +local_filters += "Samples/3_CUDA_Features/bf16TensorCoreGemm/Makefile " +local_filters += "Samples/3_CUDA_Features/dmmaTensorCoreGemm/Makefile " +local_filters += "Samples/3_CUDA_Features/globalToShmemAsyncCopy/Makefile " + +buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' From b663a4cbc8e387abecd54bb32e1d28e2c4701fce Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 11 Oct 2023 19:10:49 +0200 Subject: [PATCH 9078/9987] Added patch to disable test on gpu --- .../RCall-0.13.17-disable_gpu_test.patch | 32 +++++++++++++++++++ ...-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 7 +++- 2 files changed, 38 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/RCall/RCall-0.13.17-disable_gpu_test.patch diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-disable_gpu_test.patch b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-disable_gpu_test.patch new file mode 100644 index 00000000000..081b7f35f0b --- /dev/null +++ b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-disable_gpu_test.patch @@ -0,0 +1,32 @@ +diff -ruN RCall_orig/test/basic.jl RCall/test/basic.jl +--- RCall_orig/test/basic.jl 2023-08-30 03:06:12.000000000 +0200 ++++ RCall/test/basic.jl 2023-10-11 18:54:35.664758000 +0200 +@@ -96,17 +96,17 @@ + @test_throws Exception t1[:x] = "a" + + # graphics +-RCall.rgui_init() +-let f = tempname() +- rcall(:png,f) +- rcall(:plot,1:10) +- rcall(Symbol("dev.off")) +- @test isfile(f) +- rm(f) +- @test !RCall.rgui_start(true) +- @test_throws ErrorException RCall.rgui_start() +- @test RCall.rgui_stop() +-end ++# RCall.rgui_init() ++# let f = tempname() ++# rcall(:png,f) ++# rcall(:plot,1:10) ++# rcall(Symbol("dev.off")) ++# @test isfile(f) ++# rm(f) ++# @test !RCall.rgui_start(true) ++# @test_throws ErrorException RCall.rgui_start() ++# @test RCall.rgui_stop() ++# end + + # S4 rprint + @test occursin("An object of class", diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb index ceea54ad5b3..4665d5603c9 100644 --- a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -214,8 +214,13 @@ exts_list = [ 'checksums': ['8af4dac29839e796a651b8cb6a325b6f9c7eee5d5620b3e366b64f58325ebeb7'], }), (name, version, { + 'patches': ['RCall-0.13.17-disable_gpu_test.patch'], 'source_urls': ['https://github.com/JuliaInterop/RCall.jl/archive/'], - 'checksums': ['0f706f4c0ac8739096ac2f3f032286b9a2b7419fa80443ec8f1a61817b61e51d'], + 'checksums': [ + {'RCall-0.13.17.tar.gz': '0f706f4c0ac8739096ac2f3f032286b9a2b7419fa80443ec8f1a61817b61e51d'}, + {'RCall-0.13.17-disable_gpu_test.patch': + '73b1101909825052e04c109ce09dc3cf80454d40bcc1c5c8c2607888f07e8b4f'}, + ], }), ] From dc5770593951737ad4e9df66bcd0b49f1960016f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 11 Oct 2023 23:03:20 +0200 Subject: [PATCH 9079/9987] Add OpenCV --- .../OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb | 107 ++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb new file mode 100644 index 00000000000..9a8b28c432b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb @@ -0,0 +1,107 @@ +name = 'OpenCV' +version = '4.8.1' +versionsuffix = '-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = '1224f78da6684df04397ac0f40c961ed37f79ccb' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [ + { + 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCELOWER_TAR_GZ + }, + { + 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], + 'download_filename': '%(version)s.tar.gz', + 'filename': '%(namelower)s_contrib-%(version)s.tar.gz' + }, + { + 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2021.8_lnx_intel64_20230330_general.tgz', + 'extract_cmd': 'cp %s %(builddir)s' + }, +] +patches = [('opencv_contrib_python.egg-info', '..')] +checksums = [ + {'%(namelower)s-%(version)s.tar.gz': '62f650467a60a38794d681ae7e66e3e8cfba38f445e0bf87867e2f2cdc8be9d5'}, + {'%(namelower)s_contrib-%(version)s.tar.gz': '0c082a0b29b3118f2a0a1856b403bb098643af7b994a0080f402a12159a99c6e'}, + {'ippicv_2021.8_lnx_intel64_20230330_general.tgz': + '7cfe0fb0e15ea8f3d2d971c19df2d14382469943d4efa85e48bf358930daa85d'}, + {'opencv_contrib_python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), + ('zlib', '1.2.13'), + ('FFmpeg', '6.0'), + ('freetype', '2.13.0'), + ('HarfBuzz', '5.3.1'), + ('libjpeg-turbo', '2.1.5.1'), + ('OpenJPEG', '2.5.0'), + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.1'), + ('libwebp', '1.3.1'), + ('OpenEXR', '3.1.11'), + ('JasPer', '4.0.0'), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), + ('GLib', '2.77.1'), + ('GTK4', '4.13.1'), + ('HDF5', '1.14.0'), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = " ".join([ + "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DOPENCV_GENERATE_PKGCONFIG=ON", + "-DFREETYPE_FOUND=ON", + "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", + "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", + "-DHARFBUZZ_FOUND=ON", + "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", + "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", + "-DBUILD_opencv_python2=OFF", +]) + +# Install a egg-info file so it is more python friendly +local_egg_info_src = '%(builddir)s/opencv_contrib_python.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv_contrib_python-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' From d97ee67f34258459a86266bd7aed7cc8ee43d973 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 12 Oct 2023 11:54:49 +0200 Subject: [PATCH 9080/9987] TBB is optional dependency when building on Intel arch --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb | 6 +++++- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb index 97db9f89110..d4e71759033 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb @@ -40,7 +40,11 @@ dependencies = [ ('gzip', '1.10'), ('cURL', '7.76.0'), ('HDF5', '1.10.7'), - ('tbb', '2020.3'), +] +#TBB is an optional dependency when building on Intel arch: https://github.com/easybuilders/easybuild-easyconfigs/blob/c010dfe0b5d4b813d2e6bbaf8fec90baf85f71d2/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb#L47 +if ARCH == 'x86_64': + dependencies += [('tbb', '2020.3'),] +dependencies += [ ('PCRE', '8.44'), ('libxml2', '2.9.10'), ('FFmpeg', '4.3.2'), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb index d96efa6f439..8f895280a5d 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb @@ -37,7 +37,11 @@ dependencies = [ ('gzip', '1.10'), ('cURL', '7.78.0'), ('HDF5', '1.12.1'), - ('tbb', '2020.3'), +] +# TBB is an optional dependency when building on Intel arch: https://github.com/easybuilders/easybuild-easyconfigs/blob/c010dfe0b5d4b813d2e6bbaf8fec90baf85f71d2/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb#L47 +if ARCH =='x86_64': + dependencies += [('tbb', '2020.3'),] +dependencies +=[ ('PCRE', '8.45'), ('libxml2', '2.9.10'), ('FFmpeg', '4.3.2'), From 333eca46658330435ed73adec3f5858bc293c505 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 12 Oct 2023 12:23:08 +0200 Subject: [PATCH 9081/9987] fix CI errors --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb | 4 ++-- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb index d4e71759033..7c764c582b8 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb @@ -41,9 +41,9 @@ dependencies = [ ('cURL', '7.76.0'), ('HDF5', '1.10.7'), ] -#TBB is an optional dependency when building on Intel arch: https://github.com/easybuilders/easybuild-easyconfigs/blob/c010dfe0b5d4b813d2e6bbaf8fec90baf85f71d2/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb#L47 +# TBB is an optional dependency when building on Intel arch if ARCH == 'x86_64': - dependencies += [('tbb', '2020.3'),] + dependencies += [('tbb', '2020.3'), ] dependencies += [ ('PCRE', '8.44'), ('libxml2', '2.9.10'), diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb index 8f895280a5d..a55e4a5f053 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb @@ -38,10 +38,10 @@ dependencies = [ ('cURL', '7.78.0'), ('HDF5', '1.12.1'), ] -# TBB is an optional dependency when building on Intel arch: https://github.com/easybuilders/easybuild-easyconfigs/blob/c010dfe0b5d4b813d2e6bbaf8fec90baf85f71d2/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos-CUDA-11.4.1.eb#L47 -if ARCH =='x86_64': - dependencies += [('tbb', '2020.3'),] -dependencies +=[ +# TBB is an optional dependency when building on Intel arch +if ARCH == 'x86_64': + dependencies += [('tbb', '2020.3'), ] +dependencies += [ ('PCRE', '8.45'), ('libxml2', '2.9.10'), ('FFmpeg', '4.3.2'), From 354c8cdbe7b9e4613ce2e9d13901a1751511533c Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 12 Oct 2023 12:43:17 +0200 Subject: [PATCH 9082/9987] TBB is optional dependency when building on Intel arch --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb index 74e899cdc1e..8a4726f7335 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb @@ -37,7 +37,10 @@ dependencies = [ ('gzip', '1.12'), ('cURL', '7.83.0'), ('HDF5', '1.12.2'), - ('tbb', '2021.5.0'), +] +if ARCH == 'x86_64': + dependencies += [('tbb', '2021.5.0'), ] +dependencies += [ ('PCRE', '8.45'), ('libxml2', '2.9.13'), ('FFmpeg', '4.4.2'), From 8ed918d4e00768b2e86afa26000979f708405616 Mon Sep 17 00:00:00 2001 From: scarf489 Date: Thu, 12 Oct 2023 11:55:04 +0100 Subject: [PATCH 9083/9987] Added JAVA as a dependency. Added versionsuffix. Changed the EasyConfig filename tto include versionsuffix. --- .../j/Jmol/Jmol-16.1.41-Java-11.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/j/Jmol/Jmol-16.1.41-Java-11.eb diff --git a/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41-Java-11.eb b/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41-Java-11.eb new file mode 100644 index 00000000000..4cf536b39bf --- /dev/null +++ b/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41-Java-11.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'Jmol' +version = '16.1.41' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://jmol.sourceforge.net/' +description = """Jmol: an open-source Java viewer for chemical structures in 3D""" + +toolchain = SYSTEM + +source_urls = ['https://sourceforge.net/projects/jmol/files/Jmol/Version%2016.1/Jmol%2016.1.41/'] +sources = ['%(name)s-%(version)s-binary.tar.gz'] +checksums = ['f75bcf8a94b9153a8297b0544aee3b680a487ead9ef1d0f5496fcb1064165a2a'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['jmol', 'Jmol.jar'], + 'dirs': [], +} + +modextrapaths = { + 'JMOL_HOME': '' +} + +moduleclass = 'tools' From 8ee71c86fc936f9a981b61167568fa7921a735cf Mon Sep 17 00:00:00 2001 From: scarf489 Date: Thu, 12 Oct 2023 12:03:52 +0100 Subject: [PATCH 9084/9987] Delete Jmol-16.1.41.eb easyconfig file as it has been superseded by Jmol-16.1.41-Java-11.eb --- easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb | 24 -------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb diff --git a/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb b/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb deleted file mode 100644 index 0c0429f4444..00000000000 --- a/easybuild/easyconfigs/j/Jmol/Jmol-16.1.41.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'Jmol' -version = '16.1.41' - -homepage = 'http://jmol.sourceforge.net/' -description = """Jmol: an open-source Java viewer for chemical structures in 3D""" - -toolchain = SYSTEM - -source_urls = ['https://sourceforge.net/projects/jmol/files/Jmol/Version%2016.1/Jmol%2016.1.41/'] -sources = ['%(name)s-%(version)s-binary.tar.gz'] -checksums = ['f75bcf8a94b9153a8297b0544aee3b680a487ead9ef1d0f5496fcb1064165a2a'] - -sanity_check_paths = { - 'files': ['jmol', 'Jmol.jar'], - 'dirs': [], -} - -modextrapaths = { - 'JMOL_HOME': '' -} - -moduleclass = 'tools' From b958f7476bfad0ca439126230b70c9b481985904 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 12 Oct 2023 12:06:24 +0100 Subject: [PATCH 9085/9987] detect the correct Python for vcflib --- .../easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb index 32a39ef352a..0ae4911c54b 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-foss-2022a-R-4.2.1.eb @@ -57,7 +57,8 @@ preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|fileve preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " -configopts = "-DZIG=OFF -DWFA_GITMODULE=OFF -DWFA_INCLUDE_DIRS=$EBROOTWFA2/include/wfa2lib" +configopts = "-DZIG=OFF -DWFA_GITMODULE=OFF -DWFA_INCLUDE_DIRS=$EBROOTWFA2/include/wfa2lib " +configopts += "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] From 247ddfc91cb140e5279ce8df0f7cdebac4e7d2b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Oct 2023 13:53:21 +0200 Subject: [PATCH 9086/9987] adding easyconfigs: GATK-4.4.0.0-GCCcore-12.3.0-Java-17.eb --- .../GATK-4.4.0.0-GCCcore-12.3.0-Java-17.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.3.0-Java-17.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.3.0-Java-17.eb b/easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.3.0-Java-17.eb new file mode 100644 index 00000000000..24c6db0fec5 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.4.0.0-GCCcore-12.3.0-Java-17.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT +# Modified for version 4.4.0.0 by: Thomas Eylenbosch / Gluo NV +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.4.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['444600f7b38b46ad0b3606b7d40ce921e0ff1910a50165872f1c73c7c4a1a390'] + +dependencies = [ + ('Java', '17', '', SYSTEM), + ('Python', '3.11.3'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} + +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' From 3b95c24db313ccf59f367efd74e9b8550fbf300c Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 12 Oct 2023 14:16:45 +0200 Subject: [PATCH 9087/9987] Added patch description --- .../easyconfigs/r/RCall/RCall-0.13.17-disable_gpu_test.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-disable_gpu_test.patch b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-disable_gpu_test.patch index 081b7f35f0b..a86127ba3ce 100644 --- a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-disable_gpu_test.patch +++ b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-disable_gpu_test.patch @@ -1,3 +1,5 @@ +Removes a native test in RCall that uses GPU and therefore fails to install on machines without GPU. +Author: Orient Kružík (INUITS) diff -ruN RCall_orig/test/basic.jl RCall/test/basic.jl --- RCall_orig/test/basic.jl 2023-08-30 03:06:12.000000000 +0200 +++ RCall/test/basic.jl 2023-10-11 18:54:35.664758000 +0200 From ebebd3bb0c94194ca4716e9cf29ed6b8d18839b9 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 12 Oct 2023 15:09:48 +0200 Subject: [PATCH 9088/9987] Update RCall --- .../r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb index 4665d5603c9..a7789bd8358 100644 --- a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -219,7 +219,7 @@ exts_list = [ 'checksums': [ {'RCall-0.13.17.tar.gz': '0f706f4c0ac8739096ac2f3f032286b9a2b7419fa80443ec8f1a61817b61e51d'}, {'RCall-0.13.17-disable_gpu_test.patch': - '73b1101909825052e04c109ce09dc3cf80454d40bcc1c5c8c2607888f07e8b4f'}, + '2e66a68a62017f40eb7a3c00ab63482a4eed495d24fa9b5fc807baca72222d20'}, ], }), ] From 0369b8346d03d0d034524dc13fe4093631004ae5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Oct 2023 16:02:15 +0200 Subject: [PATCH 9089/9987] adding easyconfigs: RAxML-NG-1.2.0-GCC-12.3.0.eb --- .../r/RAxML-NG/RAxML-NG-1.2.0-GCC-12.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.0-GCC-12.3.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..c4d287c525b --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.0-GCC-12.3.0.eb @@ -0,0 +1,43 @@ +# EasyBuild easyconfig +# +# Contributed from Fred Hutchinson Cancer Research Center, Seattle WA, US +# John Dey jfdey@fredhutch.org +# +easyblock = 'CMakeMake' + +name = 'RAxML-NG' +version = '1.2.0' + +homepage = 'https://github.com/amkozlov/raxml-ng' +description = """RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) + optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree + Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/amkozlov', + 'repo_name': '%(namelower)s', + 'tag': '%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +sanity_check_paths = { + 'files': ['bin/raxml-ng'], + 'dirs': [], +} + +sanity_check_commands = ["raxml-ng --help"] + +moduleclass = 'bio' From 029ab2d59bfc04c7b88b91ca85bbad9eb7ac4af8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 12 Oct 2023 17:00:24 +0200 Subject: [PATCH 9090/9987] add MSstatsLiP to Bioconductor 3.16 bundle --- ...le-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index 89dcfcf2697..c215d08b9c7 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -1277,6 +1277,27 @@ exts_list = [ ('RnBeads.rn5', '1.30.0', { 'checksums': ['e92ab6c298042f16cf0dbcf72fda8ab23877324598a9750cf98281ed0a453191'], }), + ('log4r', '0.4.3', { + 'checksums': ['dfe3d49d35a8d8f3ad63f156d18e860540a01bd0af0e343cbab3e31a2cf5904c'], + }), + ('MSstatsConvert', '1.8.3', { + 'checksums': ['3deafb978100695037f97bcb458cfd5c76034440435d104a096459190ddd0891'], + }), + ('MSstats', '4.6.5', { + 'checksums': ['9a573976fb0fcb4b9d3e6cce831770305205ff8c46e30af4f4e4ba12ccc9fd89'], + }), + ('MSstatsTMT', '2.6.1', { + 'checksums': ['f1bf45345b4c6e14b0977d50016dc5925ee154d63a4765e218d1453d9e6fbbc0'], + }), + ('MSstatsPTM', '2.0.3', { + 'checksums': ['fe0106c66311f47f4e391528939b4aa6a690e2049b3638c4f5055fdc7b7210d8'], + }), + ('factoextra', '1.0.7', { + 'checksums': ['624ff01c74933352aca55966f8a052b1ccc878f52c2c307e47f88e0665db94aa'], + }), + ('MSstatsLiP', '1.4.1', { + 'checksums': ['ccc5b10a7310c5197a21b88cbd365bbba34d799a948d7e120114dfd047064142'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 145cf1844c49ef240f62a287f13c6ee56cd4c9aa Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Thu, 12 Oct 2023 17:02:23 +0200 Subject: [PATCH 9091/9987] {astro,lib}[foss/2022a] DP3-6.0, WSClean 3.3-b6b995c7 and deps --- .../c/casacore/casacore-3.5.0-foss-2022a.eb | 50 ++++++++++++++++ .../easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb | 39 +++++++++++++ .../e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb | 42 ++++++++++++++ .../h/HDF5/HDF5-1.13.2-GCC-11.3.0-serial.eb | 22 +++++++ .../p/PGPLOT/PGPLOT-5.2.2-GCC-11.3.0.eb | 58 +++++++++++++++++++ .../w/WCSLIB/WCSLIB-7.11-GCC-11.3.0.eb | 40 +++++++++++++ .../WSClean-3.3-b6b995c7-foss-2022a.eb | 40 +++++++++++++ 7 files changed, 291 insertions(+) create mode 100644 easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.13.2-GCC-11.3.0-serial.eb create mode 100644 easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb new file mode 100644 index 00000000000..c26f7ccf7cc --- /dev/null +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'casacore' +version = '3.5.0' + +homepage = 'https://github.com/casacore/casacore' +description = """A suite of C++ libraries for radio astronomy data processing. +The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime. +Thus user's can update them. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/casacore/casacore/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '63f1c8eff932b0fcbd38c598a5811e6e5397b72835b637d6f426105a183b3f91', # v3.5.0.tar.gz +] + +# Install casacore data +postinstallcmds = [ + 'wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar -O /tmp/WSRT_Measures.ztar' + + ' && tar xfvz /tmp/WSRT_Measures.ztar --one-top-level=%(installdir)s/data' + ] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('CFITSIO', '4.2.0'), + ('WCSLIB', '7.11'), + ('HDF5', '1.13.2', '-serial'), + ('SciPy-bundle', '2022.05'), + ('ncurses', '6.3'), +] + +configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=NO -Wno-dev -DCXX11="ON" -DDATA_DIR=%(installdir)s/data ' +configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON -DUSE_THREADS=NO' + +sanity_check_paths = { + 'files': ['lib/libcasa_casa.%s' % SHLIB_EXT, 'lib/libcasa_mirlib.%s' % SHLIB_EXT, + 'lib/libcasa_ms.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/casacore'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb new file mode 100644 index 00000000000..987161ed04a --- /dev/null +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'DP3' +version = '6.0' +homepage = 'https://dp3.readthedocs.io/' +description = """DP3: streaming processing pipeline for radio interferometric data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'filename': '%(name)s-v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://git.astron.nl/RD', + 'repo_name': '%(name)s', + 'tag': 'v%(version)s', + 'clone_into': '%(name)s', + 'recursive': True, + }, +}] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.38'), # to make CMake compiler health check pass on old systems + ('CMake', '3.24.3'), +] +dependencies = [ + ('casacore', '3.5.0'), + ('Boost', '1.79.0'), + ('CFITSIO', '4.2.0'), + ('WCSLIB', '7.11'), + ('GSL', '2.7'), + ('HDF5', '1.13.2', '-serial'), + ('Python', '3.10.4'), + ('EveryBeam', '0.5.2'), + ('Armadillo', '11.4.3'), + ('AOFlagger', '3.4.0') +] + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb new file mode 100644 index 00000000000..3c9d119ea27 --- /dev/null +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'EveryBeam' +version = '0.5.2' +homepage = 'https://everybeam.readthedocs.io/' +description = """Library that provides the antenna response pattern for several instruments, such as LOFAR (and LOBES), SKA (OSKAR), MWA, JVLA, etc.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'filename': '%(name)s-v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://git.astron.nl/RD', + 'repo_name': '%(name)s', + 'tag': 'v%(version)s', + 'clone_into': '%(name)s', + 'recursive': True, + }, +}] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.38'), # to make CMake compiler health check pass on old systems + ('CMake', '3.24.3'), +] +dependencies = [ + ('casacore', '3.5.0'), + ('Boost', '1.79.0'), + ('CFITSIO', '4.2.0'), + ('WCSLIB', '7.11'), + ('GSL', '2.7'), + ('HDF5', '1.13.2', '-serial'), + ('Python', '3.10.4'), + ('libxml2', '2.9.13'), +] + +sanity_check_paths = { + 'files': ['include/EveryBeam/beamformer.h', 'lib/libeverybeam.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.13.2-GCC-11.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.2-GCC-11.3.0-serial.eb new file mode 100644 index 00000000000..748cd32bb22 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.2-GCC-11.3.0-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.13.2' +versionsuffix = '-serial' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['01643fa5b37dba7be7c4db6bbf3c5d07adf5c1fa17dbfaaa632a279b1b2f06da'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCC-11.3.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCC-11.3.0.eb new file mode 100644 index 00000000000..d05c3ddf301 --- /dev/null +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCC-11.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'CmdCp' + +name = 'PGPLOT' +version = '5.2.2' + +homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/' +description = """The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, +device-independent graphics package for making simple scientific graphs. It is intended +for making graphical images of publication quality with minimum effort on the part of +the user. For most applications, the program can be device-independent, and the output +can be directed to the appropriate device at run time.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/'] +sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')] +patches = ['PGPLOT-5.2.2_gfortran-deps-fixes.patch'] +checksums = [ + {'pgplot522.tar.gz': 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4'}, + {'PGPLOT-5.2.2_gfortran-deps-fixes.patch': 'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec'}, +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), + ('X11', '20220504'), +] + +cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')] + +files_to_copy = [ + (['pgdemo*'], 'bin'), + (['libpgplot.*', 'libcpgplot.*'], 'lib'), + (['grfont.dat'], 'share'), + (['cpgplot.h'], 'include'), +] + +# create .so symlinks for shared libraries +postinstallcmds = [ + "cd %%(installdir)s/lib && ln -s libcpgplot.%s.5.2.2 libcpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libcpgplot.%s.5.2.2 libcpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libpgplot.%s.5.2.2 libpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libpgplot.%s.5.2.2 libpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['include/cpgplot.h', 'lib/libpgplot.a', 'lib/libcpgplot.a', + 'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +modextravars = {'PGPLOT_FONT': '%(installdir)s/share/grfont.dat'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.3.0.eb b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.3.0.eb new file mode 100644 index 00000000000..5b0df792a49 --- /dev/null +++ b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'WCSLIB' +version = '7.11' + +homepage = 'https://www.atnf.csiro.au/people/mcalabre/WCS/' +description = """The FITS "World Coordinate System" (WCS) standard defines keywords +and usage that provide for the description of astronomical coordinate systems in a +FITS image header.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.atnf.csiro.au/pub/software/wcslib/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['46befbfdf50cd4953896676a7d570094dc7661e2ae9677b092e7fb13cee3da5f'] + +builddependencies = [ + ('binutils', '2.38'), + ('M4', '1.4.19'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('CFITSIO', '4.2.0'), + ('PGPLOT', '5.2.2'), + ('X11', '20220504'), +] + +configopts = '--with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include ' +configopts += '--with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include ' + +sanity_check_paths = { + 'files': ['bin/wcsgrid', 'bin/wcsware', 'lib/libpgsbox-7.11.a', 'lib/libpgsbox.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["wcsgrid --help 2>&1 | grep '^Usage: wcsgrid'"] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb new file mode 100644 index 00000000000..7757ed6e6d4 --- /dev/null +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'WSClean' +local_commit = 'b6b995c7' # Waiting for new release +version = '3.3-%s' % local_commit + +homepage = 'https://wsclean.readthedocs.io/' +description = """WSClean (w-stacking clean) is a fast generic widefield imager. +It implements several gridding algorithms and offers fully-automated multi-scale +multi-frequency deconvolution.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'filename': '%(name)s-v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://gitlab.com/aroffringa', + 'repo_name': '%(namelower)s', + 'commit': local_commit, + 'clone_into': '%(name)s', + 'recursive': True, + }, +}] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.38'), # to make CMake compiler health check pass on old systems + ('CMake', '3.24.3'), +] +dependencies = [ + ('casacore', '3.5.0'), + ('EveryBeam', '0.5.2'), + ('Boost', '1.79.0'), + ('CFITSIO', '4.2.0'), + ('GSL', '2.7'), + ('HDF5', '1.13.2', '-serial'), + ('Python', '3.10.4'), +] + +moduleclass = 'astro' From 375dc34a8e9fb2ffef3d501c615de19f04ec257c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Oct 2023 18:42:23 +0200 Subject: [PATCH 9092/9987] adding easyconfigs: Scalene-1.5.26-GCCcore-11.3.0.eb, Scalene-1.5.26-GCCcore-12.2.0.eb --- .../Scalene/Scalene-1.5.26-GCCcore-11.3.0.eb | 45 +++++++++++++++++++ .../Scalene/Scalene-1.5.26-GCCcore-12.2.0.eb | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..8c8679c47b4 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Scalene' +version = '1.5.26' + +homepage = 'https://github.com/plasma-umass/scalene' +description = """Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things +that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while +delivering far more detailed information.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('pynvml', '11.4.1', { + 'checksums': ['b2e4a33b80569d093b513f5804db0c7f40cfc86f15a013ae7a8e99c5e175d5dd'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['dfff2232193f5fe8d414adb2b01acc0d10bbf67d4c0df7a94465ec726fd9e32c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/scalene'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["scalene --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..56523a8e099 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Scalene' +version = '1.5.26' + +homepage = 'https://github.com/plasma-umass/scalene' +description = """Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things +that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while +delivering far more detailed information.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('pynvml', '11.4.1', { + 'checksums': ['b2e4a33b80569d093b513f5804db0c7f40cfc86f15a013ae7a8e99c5e175d5dd'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['dfff2232193f5fe8d414adb2b01acc0d10bbf67d4c0df7a94465ec726fd9e32c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/scalene'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["scalene --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From ab59c5fe82ed4d2cc32301660775517594b8135c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 12 Oct 2023 19:07:55 +0200 Subject: [PATCH 9093/9987] Drop scalene version back for older python in GCC 11.3.0 --- ...e-11.3.0.eb => Scalene-1.5.20-GCCcore-11.3.0.eb} | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/Scalene/{Scalene-1.5.26-GCCcore-11.3.0.eb => Scalene-1.5.20-GCCcore-11.3.0.eb} (69%) diff --git a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.20-GCCcore-11.3.0.eb similarity index 69% rename from easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/s/Scalene/Scalene-1.5.20-GCCcore-11.3.0.eb index 8c8679c47b4..e21b689e3da 100644 --- a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.26-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.20-GCCcore-11.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'Scalene' -version = '1.5.26' +version = '1.5.20' homepage = 'https://github.com/plasma-umass/scalene' description = """Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things @@ -27,9 +27,18 @@ exts_list = [ ('pynvml', '11.4.1', { 'checksums': ['b2e4a33b80569d093b513f5804db0c7f40cfc86f15a013ae7a8e99c5e175d5dd'], }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '13.1.0', { + 'checksums': ['81c73a30b144bbcdedc13f4ea0b6ffd7fdc3b0d3cc259a9402309c8e4aee1964'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['dfff2232193f5fe8d414adb2b01acc0d10bbf67d4c0df7a94465ec726fd9e32c'], + 'checksums': ['dd424e96dc1ea7eb58e5cbe34e2dae1cedf50f62c031a9b1391a2fd4213d9915'], }), ] From d8fda9f162dd78351abd5f0ede1728dc227d13a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 13 Oct 2023 08:48:39 +0200 Subject: [PATCH 9094/9987] use Java/1.8 wrapper for SNAP-ESA and SNAP-ESA-python --- ...P-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb} | 4 ++-- ...8.0-Java-1.8.0_292-OpenJDK.eb => SNAP-ESA-8.0-Java-1.8.eb} | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/s/SNAP-ESA-python/{SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb => SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb} (94%) rename easybuild/easyconfigs/s/SNAP-ESA/{SNAP-ESA-8.0-Java-1.8.0_292-OpenJDK.eb => SNAP-ESA-8.0-Java-1.8.eb} (97%) diff --git a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb similarity index 94% rename from easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb rename to easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb index 506b3888fb2..d68dbe513e6 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8.0_292-OpenJDK-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb @@ -2,7 +2,7 @@ easyblock = 'Bundle' name = 'SNAP-ESA-python' version = '8.0' -local_javasuffix = '-Java-%(javaver)s-OpenJDK' +local_javasuffix = '-Java-%(javaver)s' versionsuffix = local_javasuffix + '-Python-%(pyver)s' homepage = 'https://step.esa.int/main/toolboxes/snap/' @@ -11,7 +11,7 @@ description = "Python interface to the Sentinel Application Platform (SNAP) API" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [ - ('Java', '1.8.0_292', '-OpenJDK', SYSTEM), + ('Java', '1.8', '', SYSTEM), ('SNAP-ESA', version, local_javasuffix, SYSTEM), ('Python', '2.7.18'), ] diff --git a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.0_292-OpenJDK.eb b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.eb similarity index 97% rename from easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.0_292-OpenJDK.eb rename to easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.eb index dd992f6d9ea..7332b44c076 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.0_292-OpenJDK.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.eb @@ -2,7 +2,7 @@ easyblock = 'Binary' name = 'SNAP-ESA' version = '8.0' -versionsuffix = '-Java-%(javaver)s-OpenJDK' +versionsuffix = '-Java-%(javaver)s' homepage = 'https://step.esa.int/main/toolboxes/snap/' description = """ @@ -33,7 +33,7 @@ checksums = [ # The installation is executed with the bundled JRE 1.8.0_242 (Zulu) # at runtime we switch it to AdoptOpenJDK, which is known to be more reliable for SNAP-ESA dependencies = [ - ('Java', '1.8.0_292', '-OpenJDK'), + ('Java', '1.8'), ] install_cmd = "INSTALL4J_TEMP='%(builddir)s' " From bdaa8af4fbfdf7b6662e6c4d1d8f6778b6adc23f Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 13 Oct 2023 09:52:00 +0200 Subject: [PATCH 9095/9987] update dependencies list --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb | 8 +++----- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb | 8 +++----- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb | 7 +++---- 3 files changed, 9 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb index 7c764c582b8..ccd13ed25c0 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021a-kokkos.eb @@ -40,11 +40,6 @@ dependencies = [ ('gzip', '1.10'), ('cURL', '7.76.0'), ('HDF5', '1.10.7'), -] -# TBB is an optional dependency when building on Intel arch -if ARCH == 'x86_64': - dependencies += [('tbb', '2020.3'), ] -dependencies += [ ('PCRE', '8.44'), ('libxml2', '2.9.10'), ('FFmpeg', '4.3.2'), @@ -57,6 +52,9 @@ dependencies += [ # VTK package is auto-disabled if this dep is not available # ('VTK', '9.0.1'), ] +if ARCH == 'x86_64': + # TBB is an optional dependency when building on Intel arch + dependencies += [('tbb', '2020.3'), ] # To use additional custom configuration options, use the 'configopts' easyconfig parameter # See docs and lammps easyblock for more information. diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb index a55e4a5f053..e464d600e94 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb @@ -37,11 +37,6 @@ dependencies = [ ('gzip', '1.10'), ('cURL', '7.78.0'), ('HDF5', '1.12.1'), -] -# TBB is an optional dependency when building on Intel arch -if ARCH == 'x86_64': - dependencies += [('tbb', '2020.3'), ] -dependencies += [ ('PCRE', '8.45'), ('libxml2', '2.9.10'), ('FFmpeg', '4.3.2'), @@ -54,6 +49,9 @@ dependencies += [ # VTK package is auto-disabled if this dep is not available ('VTK', '9.1.0'), ] +if ARCH == 'x86_64': + # TBB is an optional dependency when building on Intel arch + dependencies += [('tbb', '2020.3'), ] # To use additional custom configuration options, use the 'configopts' easyconfig parameter # See docs and lammps easyblock for more information. diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb index 8a4726f7335..afb1af60e3a 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2022a-kokkos.eb @@ -37,10 +37,6 @@ dependencies = [ ('gzip', '1.12'), ('cURL', '7.83.0'), ('HDF5', '1.12.2'), -] -if ARCH == 'x86_64': - dependencies += [('tbb', '2021.5.0'), ] -dependencies += [ ('PCRE', '8.45'), ('libxml2', '2.9.13'), ('FFmpeg', '4.4.2'), @@ -53,6 +49,9 @@ dependencies += [ # VTK package is auto-disabled if this dep is not available ('VTK', '9.2.2'), ] +if ARCH == 'x86_64': + # TBB is an optional dependency when building on Intel arch + dependencies += [('tbb', '2021.5.0'), ] # To use additional custom configuration options, use the 'configopts' easyconfig parameter # See docs and lammps easyblock for more information. From 1a478fb2d3705bd1e767bb621f53cbfbeca838e7 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Fri, 13 Oct 2023 09:52:48 +0200 Subject: [PATCH 9096/9987] Fix linting errors --- .../easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb | 7 ++++--- .../easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb | 3 ++- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index c26f7ccf7cc..2e5ded2eee0 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -19,9 +19,10 @@ checksums = [ # Install casacore data postinstallcmds = [ - 'wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar -O /tmp/WSRT_Measures.ztar' - + ' && tar xfvz /tmp/WSRT_Measures.ztar --one-top-level=%(installdir)s/data' - ] + 'wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar' + + ' -O /tmp/WSRT_Measures.ztar' + + ' && tar xfvz /tmp/WSRT_Measures.ztar --one-top-level=%(installdir)s/data' +] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb index 3c9d119ea27..c0c9f3be36f 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb @@ -3,7 +3,8 @@ easyblock = 'CMakeMake' name = 'EveryBeam' version = '0.5.2' homepage = 'https://everybeam.readthedocs.io/' -description = """Library that provides the antenna response pattern for several instruments, such as LOFAR (and LOBES), SKA (OSKAR), MWA, JVLA, etc.""" +description = """Library that provides the antenna response pattern for several instruments, +such as LOFAR (and LOBES), SKA (OSKAR), MWA, JVLA, etc.""" toolchain = {'name': 'foss', 'version': '2022a'} From f6660cdf7718b498bfa800d3f370d584ff0dc656 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 13 Oct 2023 11:42:07 +0200 Subject: [PATCH 9097/9987] Change LibTIFF version to 4.5.0 --- .../easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb index 9a8b28c432b..1f489076c7a 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb @@ -54,7 +54,7 @@ dependencies = [ ('libjpeg-turbo', '2.1.5.1'), ('OpenJPEG', '2.5.0'), ('libpng', '1.6.39'), - ('LibTIFF', '4.5.1'), + ('LibTIFF', '4.5.0'), ('libwebp', '1.3.1'), ('OpenEXR', '3.1.11'), ('JasPer', '4.0.0'), From 00d6f7bbc61fb26b8bacc8191d926a1bfde49642 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 13 Oct 2023 11:47:23 +0200 Subject: [PATCH 9098/9987] Change OpenEXR version to 3.1.7 --- .../easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb index 1f489076c7a..fe14501e01c 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.8.1-foss-2023a-contrib.eb @@ -56,7 +56,7 @@ dependencies = [ ('libpng', '1.6.39'), ('LibTIFF', '4.5.0'), ('libwebp', '1.3.1'), - ('OpenEXR', '3.1.11'), + ('OpenEXR', '3.1.7'), ('JasPer', '4.0.0'), ('Java', '11', '', SYSTEM), ('ant', '1.10.14', '-Java-%(javaver)s', SYSTEM), From cddc57e57c1d0258d2dae9edc1a6679190f03e82 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 13 Oct 2023 11:49:32 +0200 Subject: [PATCH 9099/9987] Add ant --- .../easyconfigs/a/ant/ant-1.10.14-Java-11.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.14-Java-11.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.14-Java-11.eb b/easybuild/easyconfigs/a/ant/ant-1.10.14-Java-11.eb new file mode 100644 index 00000000000..dac2b969e10 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.14-Java-11.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'ant' +version = '1.10.14' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" + +toolchain = SYSTEM + +source_urls = ['https://archive.apache.org/dist/ant/binaries/'] +sources = ['apache-%(name)s-%(version)s-bin.tar.gz'] +checksums = ['e2852fddaaddc1ab76a099ca0d7b2ee47a907b8a91a64f70f6aa9e6a3d0dd504'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' From ffc05224d32297faa704fa5644f19a9db185b3fe Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 13 Oct 2023 14:11:06 +0200 Subject: [PATCH 9100/9987] adding easyconfigs: PyTorch-bundle-1.13.1-foss-2022a-CUDA-11.7.0.eb and patches: torchtext-0.14.1_use-system-libs.patch --- ...ch-bundle-1.13.1-foss-2022a-CUDA-11.7.0.eb | 72 ++++++++++++++++++ .../torchtext-0.14.1_use-system-libs.patch | 75 +++++++++++++++++++ 2 files changed, 147 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.13.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.14.1_use-system-libs.patch diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.13.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..12dda8cdb6c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.13.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-bundle' +version = '1.13.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """PyTorch with compatible versions of official Torch extensions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), + ('RE2', '2022-06-01'), # for torchtext +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', version, versionsuffix), + ('Pillow-SIMD', '9.2.0'), # for torchvision + ('SentencePiece', '0.1.97'), # for torchtext + ('tqdm', '4.64.0'), # for torchtext + ('double-conversion', '3.2.0'), # for torchtext + ('utf8proc', '2.7.0'), # for torchtext + ('tensorboard', '2.10.0'), # for torch-tb-profiler +] + +use_pip = True + +exts_list = [ + ('portalocker', '2.7.0', { + 'checksums': ['032e81d534a88ec1736d03f780ba073f047a06c478b06e2937486f334e955c51'], + }), + ('torchdata', '0.5.1', { + 'preinstallopts': "USE_SYSTEM_LIBS=1 ", + 'source_urls': ['https://github.com/pytorch/data/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + }), + ('torchtext', '0.14.1', { + 'source_urls': ['https://github.com/pytorch/text/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'patches': [ + 'torchtext-0.14.1_use-system-libs.patch', + 'torchtext-0.13.1_cxx_17.patch', + ], + 'checksums': [ + {'torchtext-0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, + {'torchtext-0.14.1_use-system-libs.patch': + '1366d10c4755b6003194f7313ca11d165a80a13d325bee9d669ea2b333d82536'}, + {'torchtext-0.13.1_cxx_17.patch': 'fd242c139baa27352d1065cece4658a3ede76f46ffec08ac04a554301e547f22'}, + ], + }), + ('torchvision', '0.14.1', { + 'source_urls': ['https://github.com/pytorch/vision/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + }), + ('pytorch-ignite', '0.4.12', { + 'modulename': 'ignite', + 'source_urls': ['https://github.com/pytorch/ignite/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + }), + ('torch-tb-profiler', '0.4.3', { + 'modulename': 'torch.profiler', + 'sources': ['torch_tb_profiler-%(version)s.tar.gz'], + }), + # torchaudio-0.12.1 needs more work before it can be added +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.14.1_use-system-libs.patch b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.14.1_use-system-libs.patch new file mode 100644 index 00000000000..a071b8f51f8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.14.1_use-system-libs.patch @@ -0,0 +1,75 @@ +Use external deps for third party libraries +Split from "deps_fix" patch from torchtext +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 1ead15d46..21f85e555 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -63,5 +63,9 @@ endif() + + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_COMPILED_WITH_CXX_ABI} -Wall ${TORCH_CXX_FLAGS}") + +-add_subdirectory(third_party) ++find_package(double-conversion) ++find_package(re2) ++find_library(SENTENCEPIECE_LIBRARY sentencepiece PATHS $ENV{EBROOTSENTENCEPIECE}/lib64) ++find_library(SENTENCEPIECE_TRAIN_LIBRARY sentencepiece_train PATHS $ENV{EBROOTSENTENCEPIECE}/lib64) ++find_library(UTF8PROC_LIBRARY utf8proc PATHS $ENV{UTF8PROC}/lib64) + add_subdirectory(torchtext/csrc) +diff --git a/packaging/build_wheel.sh b/packaging/build_wheel.sh +index 9882cb1b2..43e2a05d8 100755 +--- a/packaging/build_wheel.sh ++++ b/packaging/build_wheel.sh +@@ -10,7 +10,6 @@ setup_env + setup_wheel_python + pip_install numpy future cmake>=3.18.0 ninja + setup_pip_pytorch_version +-git submodule update --init --recursive + python setup.py clean + if [[ "$OSTYPE" == "msys" ]]; then + "$script_dir/vc_env_helper.bat" python setup.py bdist_wheel +diff --git a/setup.py b/setup.py +index 080415f7e..bd84405be 100644 +--- a/setup.py ++++ b/setup.py +@@ -81,7 +81,6 @@ class clean(distutils.command.clean.clean): + # Remove build directory + build_dirs = [ + ROOT_DIR / "build", +- ROOT_DIR / "third_party" / "build", + ] + for path in build_dirs: + if path.exists(): +@@ -89,7 +88,6 @@ + shutil.rmtree(str(path), ignore_errors=True) + + +-_init_submodule() + setup_info = dict( + # Metadata + name="torchtext", +diff --git a/torchtext/csrc/CMakeLists.txt b/torchtext/csrc/CMakeLists.txt +index 037f814dc..658b90342 100644 +--- a/torchtext/csrc/CMakeLists.txt ++++ b/torchtext/csrc/CMakeLists.txt +@@ -18,10 +18,6 @@ set( + set( + LIBTORCHTEXT_INCLUDE_DIRS + ${PROJECT_SOURCE_DIR} +- ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src +- $ +- $ +- $ + ${TORCH_INSTALL_PREFIX}/include + ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include + ) +@@ -119,10 +115,6 @@ if (BUILD_TORCHTEXT_PYTHON_EXTENSION) + set( + EXTENSION_INCLUDE_DIRS + ${PROJECT_SOURCE_DIR} +- ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src +- $ +- $ +- $ + ${TORCH_INSTALL_PREFIX}/include + ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include + ) From c437d0e82eca0e1d023adcb29591c006a9a707b4 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Fri, 13 Oct 2023 14:05:54 +0000 Subject: [PATCH 9101/9987] adding easyconfigs: synapseclient-3.0.0-GCCcore-12.2.0.eb --- .../synapseclient-3.0.0-GCCcore-12.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/synapseclient/synapseclient-3.0.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/s/synapseclient/synapseclient-3.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/synapseclient/synapseclient-3.0.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..0441a320100 --- /dev/null +++ b/easybuild/easyconfigs/s/synapseclient/synapseclient-3.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'synapseclient' +version = '3.0.0' + +homepage = 'https://help.synapse.org/docs/' +description = """The synapseclient package provides an interface to Synapse, a collaborative, open-source + research platform that allows teams to share data, track analyses, and collaborate, providing support for: + + integrated presentation of data, code and text + fine grained access control + provenance tracking + The synapseclient package lets you communicate with the cloud-hosted Synapse service to access data and + create shared data analysis projects from within Python scripts or at the interactive Python console. + Other Synapse clients exist for R, Java, and the web. The Python client can also be used from the command line.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True + +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('cryptography', '3.3.2', { + 'checksums': ['5a60d3780149e13b7a6ff7ad6526b38846354d11a15e21068e57073e29e19bed'], + }), + ('keyring', '23.4.1', { + 'checksums': ['89cbd74d4683ed164c8082fb38619341097741323b3786905c6dac04d6915a55'], + }), + ('keyrings.alt', '3.1', { + 'checksums': ['b59c86b67b9027a86e841a49efc41025bcc3b1b0308629617b66b7011e52db5a'], + }), + (name, version, { + 'checksums': ['788289dc42a51a974efda747b75c634b6a6b38c089a4263affb8ca4ed75a0d04'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 0abd5898b1fe8b72f729b6c868d78bb8819b047d Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 13 Oct 2023 16:17:28 +0200 Subject: [PATCH 9102/9987] Add better comment why the last bioconductor version --- .../b/BgeeCall/BgeeCall-1.16.0-foss-2021a-R-4.1.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BgeeCall/BgeeCall-1.16.0-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/b/BgeeCall/BgeeCall-1.16.0-foss-2021a-R-4.1.0.eb index 5c4062f6987..b1dd59c835c 100644 --- a/easybuild/easyconfigs/b/BgeeCall/BgeeCall-1.16.0-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/b/BgeeCall/BgeeCall-1.16.0-foss-2021a-R-4.1.0.eb @@ -4,8 +4,8 @@ name = 'BgeeCall' version = '1.16.0' versionsuffix = '-R-%(rver)s' -# This library does not need last Bioconductor dependencies -# but better to have its last version from the last Bioconductor version +# While BgeeCall does not require the latest Bioconductor dependencies +# we search the latest Bioconductor release archive for them local_bioc_version = 3.17 homepage = 'https://github.com/BgeeDB/BgeeCall' From 05199a2197575974b33c8076529e3845ebcb818b Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Fri, 13 Oct 2023 16:26:16 +0200 Subject: [PATCH 9103/9987] Inject checksums --- .../PyTorch-bundle-1.13.1-foss-2022a-CUDA-11.7.0.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.13.1-foss-2022a-CUDA-11.7.0.eb index 12dda8cdb6c..9daa4dfb672 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.13.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.13.1-foss-2022a-CUDA-11.7.0.eb @@ -36,14 +36,15 @@ exts_list = [ 'preinstallopts': "USE_SYSTEM_LIBS=1 ", 'source_urls': ['https://github.com/pytorch/data/archive'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['69d80bd33ce8f08e7cfeeb71cefddfc29cede25a85881e33dbae47576b96ed29'], }), ('torchtext', '0.14.1', { - 'source_urls': ['https://github.com/pytorch/text/archive'], - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'patches': [ 'torchtext-0.14.1_use-system-libs.patch', 'torchtext-0.13.1_cxx_17.patch', ], + 'source_urls': ['https://github.com/pytorch/text/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': [ {'torchtext-0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, {'torchtext-0.14.1_use-system-libs.patch': @@ -54,17 +55,19 @@ exts_list = [ ('torchvision', '0.14.1', { 'source_urls': ['https://github.com/pytorch/vision/archive'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['ced67e1cf1f97e168cdf271851a4d0b6d382ab7936e7bcbb39aaa87239c324b6'], }), ('pytorch-ignite', '0.4.12', { 'modulename': 'ignite', 'source_urls': ['https://github.com/pytorch/ignite/archive'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['7d10fd40edc568bbda687151bb5b53b0d59a980cd6c25ec2b061e7f234aeab76'], }), ('torch-tb-profiler', '0.4.3', { 'modulename': 'torch.profiler', 'sources': ['torch_tb_profiler-%(version)s.tar.gz'], + 'checksums': ['8b8d29b2de960b3c4423087b23cec29beaf9ac3a8c7b046c18fd25b218f726b1'], }), - # torchaudio-0.12.1 needs more work before it can be added ] sanity_pip_check = True From 76d60255af3756854f89c40587716033b0ea3627 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Fri, 13 Oct 2023 14:48:57 +0000 Subject: [PATCH 9104/9987] adding easyconfigs: cpio-2.14-foss-2022a.eb --- .../c/cpio/cpio-2.14-foss-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb b/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb new file mode 100644 index 00000000000..7e2ab2d65fa --- /dev/null +++ b/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' +name = 'cpio' +version = '2.14' + +homepage = "https://savannah.gnu.org/projects/cpio/" +description = """The cpio package contains tools for archiving.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://ftp.gnu.org/gnu/cpio/'] +sources = ['cpio-%(version)s.tar.bz2'] +checksums = ['b153e1843561841d37190e48b891188d'] +postinstallcmds = ['makeinfo --plaintext -o %(installdir)s/doc/cpio.txt doc/cpio.texi'] + + +sanity_check_paths = { + 'files': ['bin/cpio'], + 'dirs': [] +} + +moduleclass = 'tools' From 8c17696f61c5635d2bd4dc16b8ebddb12019dc6d Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Fri, 13 Oct 2023 15:15:55 +0000 Subject: [PATCH 9105/9987] Add missing binutils build dep --- .../s/synapseclient/synapseclient-3.0.0-GCCcore-12.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/synapseclient/synapseclient-3.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/synapseclient/synapseclient-3.0.0-GCCcore-12.2.0.eb index 0441a320100..9efa6975683 100644 --- a/easybuild/easyconfigs/s/synapseclient/synapseclient-3.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/synapseclient/synapseclient-3.0.0-GCCcore-12.2.0.eb @@ -16,6 +16,9 @@ description = """The synapseclient package provides an interface to Synapse, a c toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +builddependencies = [ + ('binutils', '2.39'), +] dependencies = [ ('Python', '3.10.8'), ] From 496921f79387b32a648df33522e741db1a890fd4 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Fri, 13 Oct 2023 17:04:26 +0000 Subject: [PATCH 9106/9987] converted checksum to sha256 --- easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb b/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb index 7e2ab2d65fa..7299e6cea75 100644 --- a/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb +++ b/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb @@ -9,7 +9,8 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://ftp.gnu.org/gnu/cpio/'] sources = ['cpio-%(version)s.tar.bz2'] -checksums = ['b153e1843561841d37190e48b891188d'] +checksums = ['fcdc15d60f7267a6fc7efcd6b9db7b6c8966c4f2fbbb964c24d41336fd3f2c12'] + postinstallcmds = ['makeinfo --plaintext -o %(installdir)s/doc/cpio.txt doc/cpio.texi'] From 9cd091217a15389e969ada33424e8a29a82f4ea8 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Fri, 13 Oct 2023 18:42:38 +0000 Subject: [PATCH 9107/9987] added sanity check command --- easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb b/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb index 7299e6cea75..9b4aa18b7a4 100644 --- a/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb +++ b/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb @@ -19,4 +19,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = ['cpio --help'] + moduleclass = 'tools' From 0e9969238f2cca20c506fa5ebd7c42688f5ec1c5 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Fri, 13 Oct 2023 20:55:08 +0000 Subject: [PATCH 9108/9987] Replaced foss by GCC --- .../c/cpio/cpio-2.14-GCC-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/cpio/cpio-2.14-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.14-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cpio/cpio-2.14-GCC-11.3.0.eb new file mode 100644 index 00000000000..7cb324181ea --- /dev/null +++ b/easybuild/easyconfigs/c/cpio/cpio-2.14-GCC-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' +name = 'cpio' +version = '2.14' + +homepage = "https://savannah.gnu.org/projects/cpio/" +description = """The cpio package contains tools for archiving.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/cpio/'] +sources = ['cpio-%(version)s.tar.bz2'] +checksums = ['fcdc15d60f7267a6fc7efcd6b9db7b6c8966c4f2fbbb964c24d41336fd3f2c12'] + +postinstallcmds = ['makeinfo --plaintext -o %(installdir)s/doc/cpio.txt doc/cpio.texi'] + + +sanity_check_paths = { + 'files': ['bin/cpio'], + 'dirs': [] +} + +sanity_check_commands = ['cpio --help'] + +moduleclass = 'tools' From 8b7eb9baec75ac3648208ef120be91170943193e Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Sat, 14 Oct 2023 09:30:35 +0200 Subject: [PATCH 9109/9987] Use template for extension of shared libraries in GDAL-3.7.1-foss-2023a.eb --- easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb index 98acb56d8b6..721bd3a5e34 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb @@ -72,7 +72,7 @@ configopts = [ sanity_check_paths = { - 'files': ['lib/libgdal.a', 'lib/libgdal.so'], + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'], } From 414cb03f19250edc847520835a9601f007de8f72 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Sat, 14 Oct 2023 17:30:08 +0000 Subject: [PATCH 9110/9987] remove easyconfig --- .../c/cpio/cpio-2.14-foss-2022a.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb b/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb deleted file mode 100644 index 9b4aa18b7a4..00000000000 --- a/easybuild/easyconfigs/c/cpio/cpio-2.14-foss-2022a.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' -name = 'cpio' -version = '2.14' - -homepage = "https://savannah.gnu.org/projects/cpio/" -description = """The cpio package contains tools for archiving.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -source_urls = ['https://ftp.gnu.org/gnu/cpio/'] -sources = ['cpio-%(version)s.tar.bz2'] -checksums = ['fcdc15d60f7267a6fc7efcd6b9db7b6c8966c4f2fbbb964c24d41336fd3f2c12'] - -postinstallcmds = ['makeinfo --plaintext -o %(installdir)s/doc/cpio.txt doc/cpio.texi'] - - -sanity_check_paths = { - 'files': ['bin/cpio'], - 'dirs': [] -} - -sanity_check_commands = ['cpio --help'] - -moduleclass = 'tools' From 4add275ae05a31add522d352ac0175961bb9f1e9 Mon Sep 17 00:00:00 2001 From: TopRichard <121792457+TopRichard@users.noreply.github.com> Date: Sat, 14 Oct 2023 19:32:41 +0200 Subject: [PATCH 9111/9987] Update cpio-2.14-GCC-11.3.0.eb Moved down to GCCcore --- easybuild/easyconfigs/c/cpio/cpio-2.14-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.14-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cpio/cpio-2.14-GCC-11.3.0.eb index 7cb324181ea..11bc5c0fe78 100644 --- a/easybuild/easyconfigs/c/cpio/cpio-2.14-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cpio/cpio-2.14-GCC-11.3.0.eb @@ -5,7 +5,7 @@ version = '2.14' homepage = "https://savannah.gnu.org/projects/cpio/" description = """The cpio package contains tools for archiving.""" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://ftp.gnu.org/gnu/cpio/'] sources = ['cpio-%(version)s.tar.bz2'] From 0e0546728a84e893999d3dba52cd711605b15c00 Mon Sep 17 00:00:00 2001 From: hadjigc Date: Sat, 14 Oct 2023 20:44:57 +0100 Subject: [PATCH 9112/9987] adding easyconfigs: TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb --- ....1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb new file mode 100644 index 00000000000..592730a2709 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb @@ -0,0 +1,27 @@ + +name = 'TensorRT' +version = '8.6.1' +versionsuffix = '-CUDA-%(cudaver)s-Python-%(pyver)s' + +homepage = 'https://developer.nvidia.com/tensorrt' +description = """NVIDIA TensorRT is a platform for high-performance deep learning inference""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# Requires manual download from +# https://developer.nvidia.com/nvidia-tensorrt-8x-download +sources = ['%(name)s-%(version)s.6.Linux.x86_64-gnu.cuda-11.8.tar.gz'] +checksums = ['15bfe6053d45feec45ecc7123a9106076b0b43fa0435f242d89dca0778337759'] + +builddependencies = [ + ('protobuf', '3.19.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), + ('protobuf-python', '3.19.4'), +] + +moduleclass = 'lib' From b1258c3b039ad3b3c7e5e9ea04437d0f98f560b2 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sun, 15 Oct 2023 12:58:19 +0200 Subject: [PATCH 9113/9987] Rename cpio-2.14-GCC-11.3.0.eb to cpio-2.14-GCCcore-11.3.0.eb --- .../cpio/{cpio-2.14-GCC-11.3.0.eb => cpio-2.14-GCCcore-11.3.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/cpio/{cpio-2.14-GCC-11.3.0.eb => cpio-2.14-GCCcore-11.3.0.eb} (100%) diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.14-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb similarity index 100% rename from easybuild/easyconfigs/c/cpio/cpio-2.14-GCC-11.3.0.eb rename to easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb From 66ad4ddec46c2ef6e9dc0f2831bbf3dcdb5e2074 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 15 Oct 2023 14:38:48 +0200 Subject: [PATCH 9114/9987] add missing binutils for GCCCore --- easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb index 11bc5c0fe78..53d2486f3f1 100644 --- a/easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb @@ -11,8 +11,9 @@ source_urls = ['https://ftp.gnu.org/gnu/cpio/'] sources = ['cpio-%(version)s.tar.bz2'] checksums = ['fcdc15d60f7267a6fc7efcd6b9db7b6c8966c4f2fbbb964c24d41336fd3f2c12'] -postinstallcmds = ['makeinfo --plaintext -o %(installdir)s/doc/cpio.txt doc/cpio.texi'] +builddependencies = [('binutils', '2.38')] +postinstallcmds = ['makeinfo --plaintext -o %(installdir)s/doc/cpio.txt doc/cpio.texi'] sanity_check_paths = { 'files': ['bin/cpio'], From 8aecfc2bdac67a8ee573bd453127dc78e9fea50b Mon Sep 17 00:00:00 2001 From: TopRichard <121792457+TopRichard@users.noreply.github.com> Date: Sun, 15 Oct 2023 16:31:42 +0200 Subject: [PATCH 9115/9987] Update easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb index 53d2486f3f1..42a7a98c148 100644 --- a/easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/cpio/cpio-2.14-GCCcore-11.3.0.eb @@ -11,7 +11,10 @@ source_urls = ['https://ftp.gnu.org/gnu/cpio/'] sources = ['cpio-%(version)s.tar.bz2'] checksums = ['fcdc15d60f7267a6fc7efcd6b9db7b6c8966c4f2fbbb964c24d41336fd3f2c12'] -builddependencies = [('binutils', '2.38')] +builddependencies = [ + ('binutils', '2.38'), + ('makeinfo', '6.8'), +] postinstallcmds = ['makeinfo --plaintext -o %(installdir)s/doc/cpio.txt doc/cpio.texi'] From d9f06fb4bd62ab020ca4196772a02797cd69c452 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Mon, 16 Oct 2023 08:40:24 +0000 Subject: [PATCH 9116/9987] adding easyconfigs: Mashtree-1.4.0-GCC-12.2.0.eb, Mash-2.3-GCC-12.2.0.eb, QuickTree-2.5-GCC-12.2.0.eb --- .../easyconfigs/m/Mash/Mash-2.3-GCC-12.2.0.eb | 47 ++++++++++++++ .../m/Mashtree/Mashtree-1.4.0-GCC-12.2.0.eb | 62 +++++++++++++++++++ .../q/QuickTree/QuickTree-2.5-GCC-12.2.0.eb | 31 ++++++++++ 3 files changed, 140 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.0-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/q/QuickTree/QuickTree-2.5-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.2.0.eb b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.2.0.eb new file mode 100644 index 00000000000..e8e396f1ca2 --- /dev/null +++ b/easybuild/easyconfigs/m/Mash/Mash-2.3-GCC-12.2.0.eb @@ -0,0 +1,47 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v2.2 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'Mash' +version = '2.3' + +homepage = 'http://mash.readthedocs.org' +description = "Fast genome and metagenome distance estimation using MinHash" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/marbl/Mash/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'Mash-2.2_fix-hardcoding.patch', + 'Mash-2.1_disable-memcpy-wrap.patch', + 'Mash-2.3_fix-GCC-11.patch', +] +checksums = [ + 'f96cf7305e010012c3debed966ac83ceecac0351dbbfeaa6cd7ad7f068d87fe1', # v2.3.tar.gz + '0c7315af727a06f408ab3ca69da0860fc671aa870b448a41a509b1e6d7027db5', # Mash-2.2_fix-hardcoding.patch + '40990cf3d192b533736374bc67a54dbd839d90b0310a0a66f994891da1f85b6e', # Mash-2.1_disable-memcpy-wrap.patch + '47a55459d4e8c57949648e0f33f3ffc3529563db0efe60f495fdec046f48d94e', # Mash-2.3_fix-GCC-11.patch +] + +builddependencies = [('Autotools', '20220317')] +dependencies = [ + ('CapnProto', '0.10.3'), + ('GSL', '2.7'), + ('zlib', '1.2.12'), +] + +preconfigopts = "./bootstrap.sh && " +configopts = "--with-capnp=$EBROOTCAPNPROTO --with-gsl=$EBROOTGSL" + +sanity_check_paths = { + 'files': ['bin/mash', 'lib/libmash.a'], + 'dirs': ['include/mash'], +} + +sanity_check_commands = ['mash --version'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.0-GCC-12.2.0.eb b/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..1c374289a6d --- /dev/null +++ b/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.0-GCC-12.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'Bundle' + +name = 'Mashtree' +version = '1.4.0' + +description = "Create a tree using Mash distances." + +homepage = 'https://github.com/lskatz/mashtree' + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +builddependencies = [ + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('Perl', '5.36.0'), + ('BioPerl', '1.7.8'), + ('Mash', '2.3'), + ('QuickTree', '2.5'), +] + +# this is a bundle of Perl modules +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('Class::Interface', '1.01', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SINISTER/'], + 'sources': ['Class-Interface-1.01.tar.gz'], + 'checksums': ['9fba15cda745ad37f451a0b9e698da3dfc12c2e8589016416a1e3ad77e444b7b'], + }), + ('Bio::Sketch', '0.3', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LS/LSKATZ/'], + 'sources': ['Bio-Sketch-0.3.tar.gz'], + 'checksums': ['7ac38552c80ae38e0c72ba3cfa4ecf667aca8b4080616415027bcba1420c8ae2'], + }), + ('Bio::Sketch::Mash', '0.9', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LS/LSKATZ/'], + 'sources': ['Bio-Sketch-Mash-0.9.tar.gz'], + 'checksums': ['ea15858bc75674e22bb26d570d5f94c1b4eb5476bbc7bbabdf07359ebd041280'], + }), + (name, version, { + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LS/LSKATZ/'], + 'sources': ['Mashtree-1.4.0.tar.gz'], + 'checksums': ['aadb74acbbebcc073e1bd3e1dc96647142bd812f7101d8c1c0989d032829b106'], + }), +] + +sanity_check_paths = { + 'files': ['bin/mashtree'], + 'dirs': [] +} + +modextrapaths = {'PERL5LIB': [ + 'lib/perl5/site_perl/%(perlver)s', + 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi', +]} + +sanity_check_commands = ["mashtree -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/q/QuickTree/QuickTree-2.5-GCC-12.2.0.eb b/easybuild/easyconfigs/q/QuickTree/QuickTree-2.5-GCC-12.2.0.eb new file mode 100644 index 00000000000..ac38c02ea44 --- /dev/null +++ b/easybuild/easyconfigs/q/QuickTree/QuickTree-2.5-GCC-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'QuickTree' +version = '2.5' + +description = """QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), + capable of reconstructing phylogenies from huge alignments in time less than the age of the universe. + """ + +homepage = 'https://github.com/khowe/quicktree' + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/khowe/quicktree/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['731aa845ce3f1f0645bd0df2b54df75f78fce065d6a3ddc47fedf4bdcb11c248'] + +files_to_copy = [ + (["quicktree"], "bin/"), + 'README.md', + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/quicktree', 'README.md'], + 'dirs': [] +} + +sanity_check_commands = ["quicktree -h"] + +moduleclass = 'bio' From 78be7c173a874796142354445ed59f673822ff67 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Mon, 16 Oct 2023 08:56:11 +0000 Subject: [PATCH 9117/9987] adding easyconfigs: Coot-0.9.8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.eb --- ...x86_64-scientific-linux-7.6-python-gtk2.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/Coot/Coot-0.9.8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.eb diff --git a/easybuild/easyconfigs/c/Coot/Coot-0.9.8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.eb b/easybuild/easyconfigs/c/Coot/Coot-0.9.8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.eb new file mode 100644 index 00000000000..a24dc1535f1 --- /dev/null +++ b/easybuild/easyconfigs/c/Coot/Coot-0.9.8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Adam Mazur +# Research IT +# Biozentrum - University of Basel +# 0.9.8.92 update by Adam Huffman, University of Oxford + +easyblock = "Tarball" + +name = 'Coot' +version = '0.9.8.92' +versionsuffix = '-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2' + +homepage = 'http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot' +description = """Coot is for macromolecular model building, model completion +and validation, particularly suitable for protein modelling using X-ray data.""" + +toolchain = SYSTEM + +source_urls = ['http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/binaries/release'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['3babef48f5cea17c702347e41c51e7492192c685ef1c7d8b796569eb9f80d8d9'] + +sanity_check_paths = { + 'files': ["bin/coot"], + 'dirs': ["bin"] +} + +moduleclass = 'bio' From 48c09cdcf998647f62d72d219faea469fe170d9b Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 16 Oct 2023 13:08:19 +0200 Subject: [PATCH 9118/9987] Fix dependencies and checksums --- .../a/AOFlagger/AOFlagger-3.4.0-foss-2022a | 37 +++++++++++++++++++ .../c/casacore/casacore-3.5.0-foss-2022a.eb | 2 +- .../easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb | 3 +- .../e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb | 3 +- .../h/HDF5/HDF5-1.13.2-GCC-11.3.0-serial.eb | 22 ----------- .../WSClean-3.3-b6b995c7-foss-2022a.eb | 3 +- 6 files changed, 44 insertions(+), 26 deletions(-) create mode 100644 easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a delete mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.13.2-GCC-11.3.0-serial.eb diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a new file mode 100644 index 00000000000..3762c6def58 --- /dev/null +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'AOFlagger' +version = '3.4.0' + +homepage = 'https://aoflagger.readthedocs.io/' +description = """The AOFlagger is a tool that can find and remove radio-frequency interference (RFI) +in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible, +and the tools are applicable to a wide set of telescopes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [{ + 'source_urls': ['https://gitlab.com/aroffringa/aoflagger/-/package_files/96704214/'], + 'filename': '%(namelower)s-v%(version)s.tar.bz2', + 'download_filename': 'download' # provided source tarball is not versioned... +}] +checksums = ['9560b7381b68f37d842599f222a8aa2a5d3d3d501d1277471e1a0ba3d7b2aeba'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.38'), # to make CMake compiler health check pass on old systems + ('CMake', '3.24.3'), +] +dependencies = [ + ('casacore', '3.5.0'), + ('Boost', '1.79.0'), + ('CFITSIO', '4.2.0'), + ('GSL', '2.7'), + ('HDF5', '1.12.2', '-serial'), + ('Python', '3.10.4'), + ('Lua', '5.4.4'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.13'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index 2e5ded2eee0..c66010e3a48 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -34,7 +34,7 @@ builddependencies = [ dependencies = [ ('CFITSIO', '4.2.0'), ('WCSLIB', '7.11'), - ('HDF5', '1.13.2', '-serial'), + ('HDF5', '1.12.2', '-serial'), ('SciPy-bundle', '2022.05'), ('ncurses', '6.3'), ] diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb index 987161ed04a..50b535ba219 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb @@ -17,6 +17,7 @@ sources = [{ 'recursive': True, }, }] +checksums = [None] # using CMake built with GCCcore to avoid relying on the system compiler to build it builddependencies = [ @@ -29,7 +30,7 @@ dependencies = [ ('CFITSIO', '4.2.0'), ('WCSLIB', '7.11'), ('GSL', '2.7'), - ('HDF5', '1.13.2', '-serial'), + ('HDF5', '1.12.2', '-serial'), ('Python', '3.10.4'), ('EveryBeam', '0.5.2'), ('Armadillo', '11.4.3'), diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb index c0c9f3be36f..627cf7bf303 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb @@ -18,6 +18,7 @@ sources = [{ 'recursive': True, }, }] +checksums = [None] # using CMake built with GCCcore to avoid relying on the system compiler to build it builddependencies = [ @@ -30,7 +31,7 @@ dependencies = [ ('CFITSIO', '4.2.0'), ('WCSLIB', '7.11'), ('GSL', '2.7'), - ('HDF5', '1.13.2', '-serial'), + ('HDF5', '1.12.2', '-serial'), ('Python', '3.10.4'), ('libxml2', '2.9.13'), ] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.13.2-GCC-11.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.13.2-GCC-11.3.0-serial.eb deleted file mode 100644 index 748cd32bb22..00000000000 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.13.2-GCC-11.3.0-serial.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'HDF5' -version = '1.13.2' -versionsuffix = '-serial' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'GCC', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['01643fa5b37dba7be7c4db6bbf3c5d07adf5c1fa17dbfaaa632a279b1b2f06da'] - -dependencies = [ - ('zlib', '1.2.12'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb index 7757ed6e6d4..92f4cedbbd1 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb @@ -21,6 +21,7 @@ sources = [{ 'recursive': True, }, }] +checksums = [None] # using CMake built with GCCcore to avoid relying on the system compiler to build it builddependencies = [ @@ -33,7 +34,7 @@ dependencies = [ ('Boost', '1.79.0'), ('CFITSIO', '4.2.0'), ('GSL', '2.7'), - ('HDF5', '1.13.2', '-serial'), + ('HDF5', '1.12.2', '-serial'), ('Python', '3.10.4'), ] From 17cee717a95791f3fb45c648b6b5c404fbe5b9f5 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 16 Oct 2023 15:27:58 +0200 Subject: [PATCH 9119/9987] Switch to HDF5 1.14.0 + add sanity_check_paths --- ...ss-2022a => AOFlagger-3.4.0-foss-2022a.eb} | 7 +++++- .../c/casacore/casacore-3.5.0-foss-2022a.eb | 2 +- .../easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb | 7 +++++- .../e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb | 2 +- .../h/HDF5/HDF5-1.14.0-GCC-11.3.0-serial.eb | 22 +++++++++++++++++++ .../WSClean-3.3-b6b995c7-foss-2022a.eb | 7 +++++- 6 files changed, 42 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/a/AOFlagger/{AOFlagger-3.4.0-foss-2022a => AOFlagger-3.4.0-foss-2022a.eb} (89%) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-GCC-11.3.0-serial.eb diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb similarity index 89% rename from easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a rename to easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb index 3762c6def58..46e99a7772d 100644 --- a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb @@ -27,11 +27,16 @@ dependencies = [ ('Boost', '1.79.0'), ('CFITSIO', '4.2.0'), ('GSL', '2.7'), - ('HDF5', '1.12.2', '-serial'), + ('HDF5', '1.14.0', '-serial'), ('Python', '3.10.4'), ('Lua', '5.4.4'), ('libpng', '1.6.37'), ('libxml2', '2.9.13'), ] +sanity_check_paths = { + 'files': ['include/aoflagger.h', 'bin/aoflagger'], + 'dirs': ['bin'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index c66010e3a48..ce164f99099 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -34,7 +34,7 @@ builddependencies = [ dependencies = [ ('CFITSIO', '4.2.0'), ('WCSLIB', '7.11'), - ('HDF5', '1.12.2', '-serial'), + ('HDF5', '1.14.0', '-serial'), ('SciPy-bundle', '2022.05'), ('ncurses', '6.3'), ] diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb index 50b535ba219..11702b00ec4 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb @@ -30,11 +30,16 @@ dependencies = [ ('CFITSIO', '4.2.0'), ('WCSLIB', '7.11'), ('GSL', '2.7'), - ('HDF5', '1.12.2', '-serial'), + ('HDF5', '1.14.0', '-serial'), ('Python', '3.10.4'), ('EveryBeam', '0.5.2'), ('Armadillo', '11.4.3'), ('AOFlagger', '3.4.0') ] +sanity_check_paths = { + 'files': ['include/include/dp3/base/DP3.h', 'bin/DP3'], + 'dirs': ['bin'], +} + moduleclass = 'astro' diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb index 627cf7bf303..ee8cfbc7da4 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb @@ -31,7 +31,7 @@ dependencies = [ ('CFITSIO', '4.2.0'), ('WCSLIB', '7.11'), ('GSL', '2.7'), - ('HDF5', '1.12.2', '-serial'), + ('HDF5', '1.14.0', '-serial'), ('Python', '3.10.4'), ('libxml2', '2.9.13'), ] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-GCC-11.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-GCC-11.3.0-serial.eb new file mode 100644 index 00000000000..e3a89f51ecf --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-GCC-11.3.0-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.14.0' +versionsuffix = '-serial' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb index 92f4cedbbd1..5bbc3426705 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb @@ -34,8 +34,13 @@ dependencies = [ ('Boost', '1.79.0'), ('CFITSIO', '4.2.0'), ('GSL', '2.7'), - ('HDF5', '1.12.2', '-serial'), + ('HDF5', '1.14.0', '-serial'), ('Python', '3.10.4'), ] +sanity_check_paths = { + 'files': ['include/wscleaninterface.h', 'bin/wsclean'], + 'dirs': ['bin'], +} + moduleclass = 'astro' From 096f9ebc5d8175c741505dacbed395b6271c8ade Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 16 Oct 2023 16:07:03 +0200 Subject: [PATCH 9120/9987] Use official release of WSClean --- ...oss-2022a.eb => WSClean-3.4-foss-2022a.eb} | 23 +++++-------------- 1 file changed, 6 insertions(+), 17 deletions(-) rename easybuild/easyconfigs/w/WSClean/{WSClean-3.3-b6b995c7-foss-2022a.eb => WSClean-3.4-foss-2022a.eb} (61%) diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb similarity index 61% rename from easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb rename to easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb index 5bbc3426705..a4bcb26a556 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.3-b6b995c7-foss-2022a.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb @@ -1,8 +1,7 @@ easyblock = 'CMakeMake' name = 'WSClean' -local_commit = 'b6b995c7' # Waiting for new release -version = '3.3-%s' % local_commit +version = '3.4' homepage = 'https://wsclean.readthedocs.io/' description = """WSClean (w-stacking clean) is a fast generic widefield imager. @@ -12,16 +11,11 @@ multi-frequency deconvolution.""" toolchain = {'name': 'foss', 'version': '2022a'} sources = [{ - 'filename': '%(name)s-v%(version)s.tar.gz', - 'git_config': { - 'url': 'https://gitlab.com/aroffringa', - 'repo_name': '%(namelower)s', - 'commit': local_commit, - 'clone_into': '%(name)s', - 'recursive': True, - }, + 'source_urls': ['https://gitlab.com/aroffringa/wsclean/-/package_files/97237455/'], + 'filename': '%(namelower)s-v%(version)s.tar.bz2', + 'download_filename': 'download' # provided source tarball is not versioned... }] -checksums = [None] +checksums = ['b43d8ca490ccf34dd22aae6c5ca88a5dcb3cff0526835d3f97fa6d239745e641'] # using CMake built with GCCcore to avoid relying on the system compiler to build it builddependencies = [ @@ -38,9 +32,4 @@ dependencies = [ ('Python', '3.10.4'), ] -sanity_check_paths = { - 'files': ['include/wscleaninterface.h', 'bin/wsclean'], - 'dirs': ['bin'], -} - -moduleclass = 'astro' +moduleclass = 'lib' From 74210b07ce9f101b730fb489d49adbb394a0f70a Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 16 Oct 2023 16:11:50 +0200 Subject: [PATCH 9121/9987] Revert deleted lines --- easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb index a4bcb26a556..cc1ac73fcc2 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb @@ -32,4 +32,9 @@ dependencies = [ ('Python', '3.10.4'), ] -moduleclass = 'lib' +sanity_check_paths = { + 'files': ['include/wscleaninterface.h', 'bin/wsclean'], + 'dirs': ['bin'], +} + +moduleclass = 'astro' From f96e252dff13e35776b6dc8d4ca71a4111bd3678 Mon Sep 17 00:00:00 2001 From: hadjigc Date: Tue, 17 Oct 2023 11:15:10 +0100 Subject: [PATCH 9122/9987] renaming easyconfig to remove Python suffix --- .../TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb index 592730a2709..067742b0b61 100644 --- a/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb @@ -19,9 +19,9 @@ builddependencies = [ dependencies = [ ('Python', '3.10.4'), - ('CUDA', '11.7.0', '', SYSTEM), - ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), - ('protobuf-python', '3.19.4'), + ('CUDA','11.7.0','',SYSTEM), + ('cuDNN', '8.4.1.50','-CUDA-%(cudaver)s',SYSTEM), + ('protobuf-python','3.19.4'), ] moduleclass = 'lib' From f056a47d2efb72a30d6f985c70a0c9e2406efdca Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 17 Oct 2023 12:18:50 +0200 Subject: [PATCH 9123/9987] Add Boost to casacore dependencies --- easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index ce164f99099..bb074c036e9 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -32,6 +32,7 @@ builddependencies = [ ] dependencies = [ + ('Boost', '1.79.0'), ('CFITSIO', '4.2.0'), ('WCSLIB', '7.11'), ('HDF5', '1.14.0', '-serial'), From 790b4246ded9a6d88dad599cb504fb0378cf24fb Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Tue, 17 Oct 2023 13:04:20 +0200 Subject: [PATCH 9124/9987] Update Molden-7.3-GCCcore-12.3.0.eb fix indentation --- easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb index 7d73969a3f7..f7c651b05eb 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-7.3-GCCcore-12.3.0.eb @@ -45,8 +45,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = [ -"molden -h" -] +sanity_check_commands = ["molden -h"] moduleclass = 'chem' From 7819fe6de9aa1ed553f5d9a9b0ac5641955a0870 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 17 Oct 2023 13:06:21 +0200 Subject: [PATCH 9125/9987] fix invalid pointer access in UCX 1.11-1.14 --- .../u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb | 6 ++++- .../UCX-1.11.0_fix-implicit-odp-release.patch | 26 +++++++++++++++++++ .../u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb | 2 ++ .../u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb | 2 ++ .../u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb | 2 ++ .../u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb | 2 ++ .../u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb | 2 ++ 7 files changed, 41 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.11.0_fix-implicit-odp-release.patch diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb index 847d1c18e3b..c71382cb3a5 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.0-GCCcore-11.2.0.eb @@ -14,10 +14,14 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.gz'] -patches = ['UCX-1.10.0-dynamic_modules.patch'] +patches = [ + 'UCX-1.10.0-dynamic_modules.patch', + 'UCX-1.11.0_fix-implicit-odp-release.patch', +] checksums = [ 'b7189b69fe0e16e3c03784ef674e45687a9c520750bd74a45125c460ede37647', # ucx-1.11.0.tar.gz '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch + {'UCX-1.11.0_fix-implicit-odp-release.patch': 'e21d66b75f3727a98dbd1737b419a6f77c0c5a8ac660a21affcbf10bb3b941ed'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.0_fix-implicit-odp-release.patch b/easybuild/easyconfigs/u/UCX/UCX-1.11.0_fix-implicit-odp-release.patch new file mode 100644 index 00000000000..35505b5804d --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.0_fix-implicit-odp-release.patch @@ -0,0 +1,26 @@ +A change in UCX 1.11.0 changed the signature of `uct_ib_mem_dereg` leading to +an invalid pointer passed from `uct_ib_md_release_reg_method`. +Fix this by passing in the correct struct instead, i.e. wrapping the pointer into `uct_md_mem_dereg_params_t` +See: https://github.com/openucx/ucx/issues/9392 +Breaking commit (1.11+): https://github.com/openucx/ucx/commit/98a614188c026b7682f914ef62864a24fb44b464 +Code removed (1.15+): https://github.com/openucx/ucx/commit/de71ac67759879d9ce0659e696f0a4d371a7d382 + +Author: Alexander Grund (TU Dresden) + +diff --git a/src/uct/ib/base/ib_md.c b/src/uct/ib/base/ib_md.c +index 3e7d4bdf8..4e844387e 100644 +--- a/src/uct/ib/base/ib_md.c ++++ b/src/uct/ib/base/ib_md.c +@@ -1428,7 +1428,11 @@ static void uct_ib_md_release_reg_method(uct_ib_md_t *md) + ucs_rcache_destroy(md->rcache); + } + if (md->global_odp != NULL) { +- uct_ib_mem_dereg(&md->super, md->global_odp); ++ uct_md_mem_dereg_params_t params = { ++ .field_mask = UCT_MD_MEM_DEREG_FIELD_MEMH, ++ .memh = md->global_odp ++ }; ++ uct_ib_mem_dereg(&md->super, ¶ms); + } + } + diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb index e81c44acb30..7d0e97f6977 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.11.2-GCCcore-11.2.0.eb @@ -16,11 +16,13 @@ source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.gz'] patches = [ 'UCX-1.10.0-dynamic_modules.patch', + 'UCX-1.11.0_fix-implicit-odp-release.patch', 'UCX-1.11.2-missing_header.patch', ] checksums = [ 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df', # ucx-1.11.2.tar.gz '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch + {'UCX-1.11.0_fix-implicit-odp-release.patch': 'e21d66b75f3727a98dbd1737b419a6f77c0c5a8ac660a21affcbf10bb3b941ed'}, 'fa9052a33da5c8e94bc7df0e5fe6ce3baf613310842ae1ab9ed4ef2d49666c01', # UCX-1.11.2-missing_header.patch ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb index 0d77ff7687a..99ff6a78a99 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.12.1-GCCcore-11.3.0.eb @@ -16,11 +16,13 @@ source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.gz'] patches = [ 'UCX-1.10.0-dynamic_modules.patch', + 'UCX-1.11.0_fix-implicit-odp-release.patch', 'UCX-1.11.2-missing_header.patch', ] checksums = [ '40b447c8e7da94a253f2828001b2d76021eb4ad39647107d433d62d61e18ae8e', # ucx-1.12.1.tar.gz '3098c91f2aadc5f148466a2e8756769ad5e99f9515d8cfb6ad8a5712e7433408', # UCX-1.10.0-dynamic_modules.patch + {'UCX-1.11.0_fix-implicit-odp-release.patch': 'e21d66b75f3727a98dbd1737b419a6f77c0c5a8ac660a21affcbf10bb3b941ed'}, 'fa9052a33da5c8e94bc7df0e5fe6ce3baf613310842ae1ab9ed4ef2d49666c01', # UCX-1.11.2-missing_header.patch ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb index 6852321bf6a..00fb55690cd 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.13.1-GCCcore-12.2.0.eb @@ -15,12 +15,14 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.gz'] patches = [ + 'UCX-1.11.0_fix-implicit-odp-release.patch', 'UCX-1.13.1-dynamic_modules.patch', 'UCX-1.13.1_fix-undeclared-PTR.patch', ] checksums = [ ('efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828', '2c4a2f96c700e3705e185c2846a710691b6e800e8aec11fd4b3e47bcc3990548'), # ucx-1.13.1.tar.gz + {'UCX-1.11.0_fix-implicit-odp-release.patch': 'e21d66b75f3727a98dbd1737b419a6f77c0c5a8ac660a21affcbf10bb3b941ed'}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, {'UCX-1.13.1_fix-undeclared-PTR.patch': 'ef22c29604552ad3223f2a6bac352f30023cc5cf68f786abfdc4ad7c04189a76'}, ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb index c84b1e48791..0bf2334b18f 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.gz'] patches = [ + 'UCX-1.11.0_fix-implicit-odp-release.patch', 'UCX-1.13.1-dynamic_modules.patch', ] checksums = [ {'ucx-1.14.0.tar.gz': '9bd95e2059de5dece9dddd049aacfca3d21bfca025748a6a0b1be4486e28afdd'}, + {'UCX-1.11.0_fix-implicit-odp-release.patch': 'e21d66b75f3727a98dbd1737b419a6f77c0c5a8ac660a21affcbf10bb3b941ed'}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb index 0d862216f7a..af30595f9c5 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.14.1-GCCcore-12.3.0.eb @@ -15,10 +15,12 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.gz'] patches = [ + 'UCX-1.11.0_fix-implicit-odp-release.patch', 'UCX-1.13.1-dynamic_modules.patch', ] checksums = [ {'ucx-1.14.1.tar.gz': 'baa0634cafb269a3112f626eb226bcd2ca8c9fcf0fec3b8e2a3553baad5f77aa'}, + {'UCX-1.11.0_fix-implicit-odp-release.patch': 'e21d66b75f3727a98dbd1737b419a6f77c0c5a8ac660a21affcbf10bb3b941ed'}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, ] From e6f262d8db180303ad82de277658783030082c84 Mon Sep 17 00:00:00 2001 From: hadjigc Date: Tue, 17 Oct 2023 12:14:45 +0100 Subject: [PATCH 9126/9987] removing easyconfig with Python suffix --- ....1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb deleted file mode 100644 index 067742b0b61..00000000000 --- a/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb +++ /dev/null @@ -1,27 +0,0 @@ - -name = 'TensorRT' -version = '8.6.1' -versionsuffix = '-CUDA-%(cudaver)s-Python-%(pyver)s' - -homepage = 'https://developer.nvidia.com/tensorrt' -description = """NVIDIA TensorRT is a platform for high-performance deep learning inference""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -# Requires manual download from -# https://developer.nvidia.com/nvidia-tensorrt-8x-download -sources = ['%(name)s-%(version)s.6.Linux.x86_64-gnu.cuda-11.8.tar.gz'] -checksums = ['15bfe6053d45feec45ecc7123a9106076b0b43fa0435f242d89dca0778337759'] - -builddependencies = [ - ('protobuf', '3.19.4'), -] - -dependencies = [ - ('Python', '3.10.4'), - ('CUDA','11.7.0','',SYSTEM), - ('cuDNN', '8.4.1.50','-CUDA-%(cudaver)s',SYSTEM), - ('protobuf-python','3.19.4'), -] - -moduleclass = 'lib' From 295051afd09f41e807f537f09e97776a4b7ebe54 Mon Sep 17 00:00:00 2001 From: hadjigc Date: Tue, 17 Oct 2023 12:16:27 +0100 Subject: [PATCH 9127/9987] adding easyconfig: TensorRT-8.6.1-foss-2022a-CUDA-11.7.0.eb --- ....1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb new file mode 100644 index 00000000000..592730a2709 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb @@ -0,0 +1,27 @@ + +name = 'TensorRT' +version = '8.6.1' +versionsuffix = '-CUDA-%(cudaver)s-Python-%(pyver)s' + +homepage = 'https://developer.nvidia.com/tensorrt' +description = """NVIDIA TensorRT is a platform for high-performance deep learning inference""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# Requires manual download from +# https://developer.nvidia.com/nvidia-tensorrt-8x-download +sources = ['%(name)s-%(version)s.6.Linux.x86_64-gnu.cuda-11.8.tar.gz'] +checksums = ['15bfe6053d45feec45ecc7123a9106076b0b43fa0435f242d89dca0778337759'] + +builddependencies = [ + ('protobuf', '3.19.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), + ('protobuf-python', '3.19.4'), +] + +moduleclass = 'lib' From 8d7b7ee8ae38642b9299392248fced865ee67c19 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 17 Oct 2023 13:31:13 +0200 Subject: [PATCH 9128/9987] Disable threadedmpi with gompi for recent SCOTCH --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb | 1 + easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb | 1 + easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb | 1 + easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb | 1 + easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a.eb | 1 + easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2023a.eb | 1 + 6 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb index 34dfc411449..6a312d8ebca 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.9-gompi-2020a.eb @@ -11,6 +11,7 @@ toolchainopts = {'pic': True} source_urls = ['https://gforge.inria.fr/frs/download.php/file/38187/'] sources = ['%(namelower)s_%(version)s.tar.gz'] checksums = ['622b4143cf01c480bb15708b3651b29c25e4aeb00c8c6447ff196aca2eca5c93'] +threadedmpi = False dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb index 82ed7faf684..ce355224a7e 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2020b.eb @@ -11,6 +11,7 @@ toolchainopts = {'pic': True} source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] +threadedmpi = False builddependencies = [ ('Bison', '3.7.1'), diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb index ff933dd4d5c..7f0edffee3a 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb @@ -14,6 +14,7 @@ toolchainopts = {'pic': True} source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] +threadedmpi = False builddependencies = [ ('Bison', '3.7.6'), diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb index 08afa4bdeb2..c98ffbdf7ef 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb @@ -14,6 +14,7 @@ toolchainopts = {'pic': True} source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['9c2c75c75f716914a2bd1c15dffac0e29a2f8069b2df1ad2b6207c984b699450'] +threadedmpi = False builddependencies = [ ('Bison', '3.7.6'), diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a.eb index 9313e21231d..7c425335e82 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a.eb @@ -11,6 +11,7 @@ toolchainopts = {'pic': True} source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['0618e9bc33c02172ea7351600fce4fccd32fe00b3359c4aabb5e415f17c06fed'] +threadedmpi = False builddependencies = [ ('Bison', '3.8.2'), diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2023a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2023a.eb index 645ce6e0e4f..7505a418741 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2023a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.3-gompi-2023a.eb @@ -11,6 +11,7 @@ toolchainopts = {'pic': True} source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] sources = ['%(namelower)s-v%(version)s.tar.gz'] checksums = ['5b5351f0ffd6fcae9ae7eafeccaa5a25602845b9ffd1afb104db932dd4d4f3c5'] +threadedmpi = False builddependencies = [ ('Bison', '3.8.2'), From 9ed6506d9cb4a1c9a36e3020aa866a10b51957ab Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 17 Oct 2023 14:03:20 +0200 Subject: [PATCH 9129/9987] adding easyconfigs: GTDB-Tk-2.3.2-foss-2022a.eb --- .../g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2022a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2022a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2022a.eb new file mode 100644 index 00000000000..70a975a9f1e --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2022a.eb @@ -0,0 +1,46 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'GTDB-Tk' +version = '2.3.2' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.5.2'), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.2'), + ('pplacer', '1.1.alpha19', '', SYSTEM), + ('FastANI', '1.33'), + ('FastTree', '2.1.11'), + ('Mash', '2.3'), + ('tqdm', '4.64.0'), + ('pydantic', '1.10.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'gtdbtk', + 'source_tmpl': 'gtdbtk-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/g/gtdbtk'], + 'checksums': ['80efd31e10007d835f56a3d6fdf039a59db3b6ba4be26b234692da5e688aa99f'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 94fd7dac1341cfa1123cfd3ed9aa3ad6bcbfa873 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 17 Oct 2023 14:33:27 +0200 Subject: [PATCH 9130/9987] Remove binutils from configs using foss-2022a toolchain --- .../easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb | 2 -- .../easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb | 1 - easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb | 3 +-- .../easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb | 3 +-- easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb | 5 ++--- 5 files changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb index 46e99a7772d..e6501c53653 100644 --- a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb @@ -17,9 +17,7 @@ sources = [{ }] checksums = ['9560b7381b68f37d842599f222a8aa2a5d3d3d501d1277471e1a0ba3d7b2aeba'] -# using CMake built with GCCcore to avoid relying on the system compiler to build it builddependencies = [ - ('binutils', '2.38'), # to make CMake compiler health check pass on old systems ('CMake', '3.24.3'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index bb074c036e9..0edd857f9c5 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -25,7 +25,6 @@ postinstallcmds = [ ] builddependencies = [ - ('binutils', '2.38'), ('CMake', '3.24.3'), ('flex', '2.6.4'), ('Bison', '3.8.2'), diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb index 11702b00ec4..60bb09845dd 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb @@ -19,11 +19,10 @@ sources = [{ }] checksums = [None] -# using CMake built with GCCcore to avoid relying on the system compiler to build it builddependencies = [ - ('binutils', '2.38'), # to make CMake compiler health check pass on old systems ('CMake', '3.24.3'), ] + dependencies = [ ('casacore', '3.5.0'), ('Boost', '1.79.0'), diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb index ee8cfbc7da4..580b85535b7 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb @@ -20,11 +20,10 @@ sources = [{ }] checksums = [None] -# using CMake built with GCCcore to avoid relying on the system compiler to build it builddependencies = [ - ('binutils', '2.38'), # to make CMake compiler health check pass on old systems ('CMake', '3.24.3'), ] + dependencies = [ ('casacore', '3.5.0'), ('Boost', '1.79.0'), diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb index cc1ac73fcc2..316a3e87702 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb @@ -13,15 +13,14 @@ toolchain = {'name': 'foss', 'version': '2022a'} sources = [{ 'source_urls': ['https://gitlab.com/aroffringa/wsclean/-/package_files/97237455/'], 'filename': '%(namelower)s-v%(version)s.tar.bz2', - 'download_filename': 'download' # provided source tarball is not versioned... + 'download_filename': 'download' # endpoint for source tarball is not versioned }] checksums = ['b43d8ca490ccf34dd22aae6c5ca88a5dcb3cff0526835d3f97fa6d239745e641'] -# using CMake built with GCCcore to avoid relying on the system compiler to build it builddependencies = [ - ('binutils', '2.38'), # to make CMake compiler health check pass on old systems ('CMake', '3.24.3'), ] + dependencies = [ ('casacore', '3.5.0'), ('EveryBeam', '0.5.2'), From 4c9c7119e17cb6d8827a62abd277ceb552c6518c Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Tue, 17 Oct 2023 13:29:13 +0000 Subject: [PATCH 9131/9987] Improve sanity_check_paths to reduce duplication --- ...8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Coot/Coot-0.9.8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.eb b/easybuild/easyconfigs/c/Coot/Coot-0.9.8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.eb index a24dc1535f1..6d09c67ecfa 100644 --- a/easybuild/easyconfigs/c/Coot/Coot-0.9.8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.eb +++ b/easybuild/easyconfigs/c/Coot/Coot-0.9.8.92-binary-Linux-x86_64-scientific-linux-7.6-python-gtk2.eb @@ -22,7 +22,7 @@ checksums = ['3babef48f5cea17c702347e41c51e7492192c685ef1c7d8b796569eb9f80d8d9'] sanity_check_paths = { 'files': ["bin/coot"], - 'dirs': ["bin"] + 'dirs': ["lib"] } moduleclass = 'bio' From d366d0e4e3ee71750e49bc3f69caeb8fc122e69d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Oct 2023 15:31:53 +0200 Subject: [PATCH 9132/9987] take into account that $JAVA_TOOL_OPTIONS may not be defined + add modtclfooter equivalent to modluafooter --- ...-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb index d68dbe513e6..410cd5034da 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-8.0-GCCcore-10.2.0-Java-1.8-Python-2.7.18.eb @@ -43,6 +43,10 @@ modextrapaths = {'PYTHONPATH': [local_pysite]} local_javaopts = " -Dsnap.pythonExecutable=python" local_javaopts += " -Dsnap.pythonModuleDir=%s" % local_pyinstalldir -modluafooter = 'setenv("JAVA_TOOL_OPTIONS", os.getenv("JAVA_TOOL_OPTIONS").."%s")' % local_javaopts +# update $JAVA_TOOL_OPTIONS when module is loaded, use empty string as default value if $JAVA_TOOL_OPTIONS is not set +modluafooter = 'setenv("JAVA_TOOL_OPTIONS", (os.getenv("JAVA_TOOL_OPTIONS") or "") .. "%s")' % local_javaopts +# likewise, but when using Tcl as module syntax +local_tcl_JAVA_TOOL_OPTIONS = '[expr {[info exists ::env(JAVA_TOOL_OPTIONS)] ? $::env(JAVA_TOOL_OPTIONS) : ""}]' +modtclfooter = 'setenv JAVA_TOOL_OPTIONS [concat %s "%s"]' % (local_tcl_JAVA_TOOL_OPTIONS, local_javaopts) moduleclass = 'geo' From 74c59d9ad3096e94caafa56e5f8e06f4d4b542cc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 17 Oct 2023 16:43:52 +0200 Subject: [PATCH 9133/9987] adding easyconfigs: GSD-3.2.0-foss-2022a.eb --- .../easyconfigs/g/GSD/GSD-3.2.0-foss-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSD/GSD-3.2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/GSD/GSD-3.2.0-foss-2022a.eb b/easybuild/easyconfigs/g/GSD/GSD-3.2.0-foss-2022a.eb new file mode 100644 index 00000000000..71383bbe145 --- /dev/null +++ b/easybuild/easyconfigs/g/GSD/GSD-3.2.0-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'GSD' +version = '3.2.0' + +homepage = 'https://gsd.readthedocs.io' +description = """The GSD file format is the native file format for +HOOMD-blue. GSD files store trajectories of the HOOMD-blue system state +in a binary file with efficient random access to frames. GSD allows all +particle and topology properties to vary from one frame to the next. Use +the GSD Python API to specify the initial condition for a HOOMD-blue +simulation or analyze trajectory output with a script. Read a GSD +trajectory with a visualization tool to explore the behavior of the +simulation.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'glotzerlab' +source_urls = [GITHUB_LOWER_RELEASE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc7a9293d379032fc7d207884c0a50fe686b02ee5b8ebf3433989e2086f47c2'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 98d746d59a7cb391bdfe5e5d61ff4d37fa3554a1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 17 Oct 2023 16:49:26 +0200 Subject: [PATCH 9134/9987] add a sanity_check_command to GSD --- easybuild/easyconfigs/g/GSD/GSD-3.2.0-foss-2022a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GSD/GSD-3.2.0-foss-2022a.eb b/easybuild/easyconfigs/g/GSD/GSD-3.2.0-foss-2022a.eb index 71383bbe145..8623f4ba1b4 100644 --- a/easybuild/easyconfigs/g/GSD/GSD-3.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GSD/GSD-3.2.0-foss-2022a.eb @@ -29,4 +29,8 @@ use_pip = True download_dep_fail = True sanity_pip_check = True +sanity_check_commands = [ + 'python -c "import gsd.hoomd"', +] + moduleclass = 'tools' From fcbe44ac2e6dc7814d950b5e62fc7cbc0bb40df8 Mon Sep 17 00:00:00 2001 From: hadjigc Date: Tue, 17 Oct 2023 16:46:47 +0100 Subject: [PATCH 9135/9987] removing python suffix. adding download instructions. --- ...on-3.10.4.eb => TensorRT-8.6.1-foss-2022a-CUDA-11.7.0.eb} | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/t/TensorRT/{TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb => TensorRT-8.6.1-foss-2022a-CUDA-11.7.0.eb} (81%) diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0.eb similarity index 81% rename from easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb rename to easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0.eb index 592730a2709..d3862ffba61 100644 --- a/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0-Python-3.10.4.eb +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0.eb @@ -1,15 +1,14 @@ name = 'TensorRT' version = '8.6.1' -versionsuffix = '-CUDA-%(cudaver)s-Python-%(pyver)s' +versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://developer.nvidia.com/tensorrt' description = """NVIDIA TensorRT is a platform for high-performance deep learning inference""" toolchain = {'name': 'foss', 'version': '2022a'} -# Requires manual download from -# https://developer.nvidia.com/nvidia-tensorrt-8x-download +download_instructions = "Manual download from https://developer.nvidia.com/nvidia-tensorrt-8x-download " sources = ['%(name)s-%(version)s.6.Linux.x86_64-gnu.cuda-11.8.tar.gz'] checksums = ['15bfe6053d45feec45ecc7123a9106076b0b43fa0435f242d89dca0778337759'] From a2dfd1541580200d5e0d26b676379812413dc394 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Oct 2023 18:32:50 +0200 Subject: [PATCH 9136/9987] adding easyconfigs: n2v-0.3.2-foss-2022a.eb, CSBDeep-0.7.4-foss-2022a.eb --- .../c/CSBDeep/CSBDeep-0.7.4-foss-2022a.eb | 36 +++++++++++++++++++ .../easyconfigs/n/n2v/n2v-0.3.2-foss-2022a.eb | 30 ++++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a.eb new file mode 100644 index 00000000000..e65992a566c --- /dev/null +++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a.eb @@ -0,0 +1,36 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'CSBDeep' +version = '0.7.4' + +homepage = "https://csbdeep.bioimagecomputing.com/" +description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE).""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('TensorFlow', '2.11.0'), + ('matplotlib', '3.5.2'), + ('tqdm', '4.64.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tifffile', '2023.9.26', { + 'checksums': ['67e355e4595aab397f8405d04afe1b4ae7c6f62a44e22d933fee1a571a48c7ae'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['85d6fc360bb33253ba6f543d75cf0cf123595f0ea4dd1fa76b1e5bc8fc55b901'], + 'modulename': '%(namelower)s', + }), +] + +sanity_check_commands = ['care_predict'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2022a.eb b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2022a.eb new file mode 100644 index 00000000000..ddcd211e0b9 --- /dev/null +++ b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'n2v' +version = '0.3.2' + +homepage = 'https://github.com/juglab/n2v' +description = "Learning Denoising from Single Noisy Images" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Pillow', '9.1.1'), + ('imagecodecs', '2022.9.26'), + ('ruamel.yaml', '0.17.21'), + ('CSBDeep', '0.7.4'), +] + +use_pip= True + +exts_list = [ + (name, version, { + 'checksums': ['8662aa5e903e170a1c9769882da241d669b6e7efd8b164b68723c675539ec06f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From f9d60293d6de531bdfca95d94c322eae4205bfeb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Oct 2023 18:49:54 +0200 Subject: [PATCH 9137/9987] add missing space in use_pip line in n2v easyconfig --- easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2022a.eb b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2022a.eb index ddcd211e0b9..29bc3aab621 100644 --- a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2022a.eb +++ b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2022a.eb @@ -17,7 +17,7 @@ dependencies = [ ('CSBDeep', '0.7.4'), ] -use_pip= True +use_pip = True exts_list = [ (name, version, { From 9b1ffe986e4dbcd579dc0fde59eeee28d6d4f4cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Oct 2023 18:59:31 +0200 Subject: [PATCH 9138/9987] {geo}[GCCcore/11.2.0] SNAP-ESA v9.0.0 + SNAP-ESA-python v9.0 w/ Python 2.7.18 --- ...0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb | 52 ++++++++++++++ .../s/SNAP-ESA/SNAP-ESA-9.0.0-Java-1.8.eb | 71 +++++++++++++++++++ 2 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb create mode 100644 easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-1.8.eb diff --git a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb new file mode 100644 index 00000000000..99225eb5ae1 --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb @@ -0,0 +1,52 @@ +easyblock = 'Bundle' + +name = 'SNAP-ESA-python' +version = '9.0' +local_javasuffix = '-Java-%(javaver)s' +versionsuffix = local_javasuffix + '-Python-%(pyver)s' + +homepage = 'https://step.esa.int/main/toolboxes/snap/' +description = "Python interface to the Sentinel Application Platform (SNAP) API" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('Java', '1.8', '', SYSTEM), + ('SNAP-ESA', version, local_javasuffix, SYSTEM), + ('Python', '2.7.18'), +] + +local_pysite = 'lib/python%(pyshortver)s/site-packages' +local_pyinstalldir = '%%(installdir)s/%s' % local_pysite + +postinstallcmds = [ + # Install snappy from SNAP-ESA + # snappy-conf is buggy and it hangs after doing the installation of snappy, + # start snappy-conf in a new SID and kill all processes of its PGID + # whenever it prints the final line starting with "or copy" + "mkdir -p %s" % local_pyinstalldir, + ('LOG="$(mktemp -d)/snappy-conf.log"; mkfifo $LOG; trap "rm -f $LOG" EXIT;' + 'setsid snappy-conf $EBROOTPYTHON/bin/python %s 2>&1 > $LOG & CONFPID=$!;' + 'while read line; do echo "$line"; [ -z "${line##or copy*}" ] && kill -- -$CONFPID; done < $LOG;') + % local_pyinstalldir, +] + +sanity_check_paths = { + 'files': [], + 'dirs': [local_pysite], +} + +sanity_check_commands = ["python -c 'import snappy'"] + +modextrapaths = {'PYTHONPATH': [local_pysite]} + +local_javaopts = " -Dsnap.pythonExecutable=python" +local_javaopts += " -Dsnap.pythonModuleDir=%s" % local_pyinstalldir + +# update $JAVA_TOOL_OPTIONS when module is loaded, use empty string as default value if $JAVA_TOOL_OPTIONS is not set +modluafooter = 'setenv("JAVA_TOOL_OPTIONS", (os.getenv("JAVA_TOOL_OPTIONS") or "") .. "%s")' % local_javaopts +# likewise, but when using Tcl as module syntax +local_tcl_JAVA_TOOL_OPTIONS = '[expr {[info exists ::env(JAVA_TOOL_OPTIONS)] ? $::env(JAVA_TOOL_OPTIONS) : ""}]' +modtclfooter = 'setenv JAVA_TOOL_OPTIONS [concat %s "%s"]' % (local_tcl_JAVA_TOOL_OPTIONS, local_javaopts) + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-1.8.eb b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-1.8.eb new file mode 100644 index 00000000000..78f3ee71e96 --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-1.8.eb @@ -0,0 +1,71 @@ +easyblock = 'Binary' + +name = 'SNAP-ESA' +version = '9.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://step.esa.int/main/toolboxes/snap/' +description = """ +The Sentinel Application Platform (SNAP) is a common architecture for all +Sentinel Toolboxes being jointly developed by Brockmann Consult, SkyWatch and +C-S. +The SNAP architecture is ideal for Earth Observation processing and analysis +due to the following technological innovations: Extensibility, Portability, +Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory +Management, and a Graph Processing Framework.""" + +toolchain = SYSTEM + +local_installer = 'esa-snap_all_unix_%s.sh' % version.replace('.', '_') +local_varfile = 'SNAP-ESA-8.0-response.varfile' + +source_urls = [ + 'https://download.esa.int/step/snap/%(version_major_minor)s/installers', + 'https://step.esa.int/downloads/%(version_major_minor)s/installers', +] +sources = [local_installer] +patches = [(local_varfile, '.')] +checksums = [ + {'esa-snap_all_unix_9_0_0.sh': 'ad6ef8c679c80c58660fe23ab5fb4974f9cd3ff4b119ad8e7e40dc79dbe03896'}, + {'SNAP-ESA-8.0-response.varfile': '5ea98e3376bb3df52b9c4c99ab4986015296b815021e16486b58e4aad58e21a4'}, +] + +# The installation is executed with the bundled JRE 1.8.0_242 (Zulu) +# at runtime we switch it to AdoptOpenJDK, which is known to be more reliable for SNAP-ESA +dependencies = [ + ('Java', '1.8'), +] + +install_cmd = "INSTALL4J_TEMP='%(builddir)s' " +install_cmd += "bash %s -dir '%%(installdir)s'" % local_installer +install_cmd += " -q -varfile '%s'" % local_varfile + +postinstallcmds = [ + # set paths + 'sed -i "s|jdkhome.*|jdkhome=$JAVA_HOME|" %(installdir)s/etc/snap.conf', + 'sed -i "s|#snap.home.*|snap.home=%(installdir)s|" %(installdir)s/etc/snap.properties', + # remove default maximum memory allocation pool + 'sed -i "s|-J-Xmx[0-9G]* ||" %(installdir)s/etc/snap.conf', + # disable update checks + "echo 'snap.versionCheck.interval=NEVER' >> %(installdir)s/etc/snap.properties", + "sed -i 's|dpiaware=false|& -J-Dplugin.manager.check.interval=NEVER|' %(installdir)s/etc/snap.conf", + # (optional) update all modules to latest version + # the update command is buggy and it hangs after doing the update, kill it whenever it prints "updates=0" + # see issue https://senbox.atlassian.net/browse/SNAP-927 + # ('LOG="$(mktemp -d)/snap-update.log"; mkfifo $LOG; trap "rm -f $LOG" EXIT;' + # 'SNAPCMD="%(installdir)s/bin/snap --nosplash --nogui --userdir "%(builddir)s/snap" --modules --update-all";' + # '$SNAPCMD 2>&1 > $LOG & SNAPPID=$!;' + # 'while read line; do echo "$line"; [ "$line" = "updates=0" ] && kill $SNAPPID; done < $LOG;'), +] + +sanity_check_paths = { + 'files': ['bin/snap', 'bin/gpt'], + 'dirs': ['probavbox', 'rstb', 's1tbx', 's2tbx', 's3tbx', 'smos', 'snap'], +} + +sanity_check_commands = [ + "snap --nosplash --nogui --modules --help | grep 'Additional module options'", + "gpt -h", +] + +moduleclass = 'geo' From e0a6093085c02d2d23adfd3ed9c8ef7920f4b288 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Oct 2023 19:58:55 +0200 Subject: [PATCH 9139/9987] fix version for SNAP-ESA-python 9.0.0 --- ...P-ESA-python-9.0.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/SNAP-ESA-python/{SNAP-ESA-python-9.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb => SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb} (99%) diff --git a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb similarity index 99% rename from easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb rename to easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb index 99225eb5ae1..8cfab48285f 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb @@ -1,7 +1,7 @@ easyblock = 'Bundle' name = 'SNAP-ESA-python' -version = '9.0' +version = '9.0.0' local_javasuffix = '-Java-%(javaver)s' versionsuffix = local_javasuffix + '-Python-%(pyver)s' From 9828e23ca129e17201ff396d6d1cd1500702c7be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 17 Oct 2023 17:47:16 +0200 Subject: [PATCH 9140/9987] add escape extesion to Bioconductor 3.16 bundle --- .../R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb index c215d08b9c7..ef1d97ba4c9 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -1298,6 +1298,15 @@ exts_list = [ ('MSstatsLiP', '1.4.1', { 'checksums': ['ccc5b10a7310c5197a21b88cbd365bbba34d799a948d7e120114dfd047064142'], }), + ('babelgene', '22.9', { + 'checksums': ['ce6601dcb78352516d3b0355042c52a20e154b39d3b27b93ff52150a59c885e2'], + }), + ('msigdbr', '7.5.1', { + 'checksums': ['dc30487bdf3594425ae9faec1ca0d7d0cd7278f4f177689133f92880e74acaca'], + }), + ('escape', '1.8.0', { + 'checksums': ['4d80d2798f07885ae035dbb9d994c707ed3a94fbe6cef5f35da51a50cc4168f1'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 65ce5faa9c6cda56043c5d952075fa61e584027f Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 17 Oct 2023 20:51:13 +0200 Subject: [PATCH 9141/9987] Add sanity check commands + switch to parallel HDF5 + add Python to casacore --- .../a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb | 4 +++- .../c/casacore/casacore-3.5.0-foss-2022a.eb | 10 +++++---- .../easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb | 4 +++- .../e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb | 2 +- .../h/HDF5/HDF5-1.14.0-GCC-11.3.0-serial.eb | 22 ------------------- ....3.0.eb => PGPLOT-5.2.2-GCCcore-11.3.0.eb} | 2 +- .../w/WSClean/WSClean-3.4-foss-2022a.eb | 4 +++- 7 files changed, 17 insertions(+), 31 deletions(-) delete mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-GCC-11.3.0-serial.eb rename easybuild/easyconfigs/p/PGPLOT/{PGPLOT-5.2.2-GCC-11.3.0.eb => PGPLOT-5.2.2-GCCcore-11.3.0.eb} (97%) diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb index e6501c53653..eeb528a357b 100644 --- a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb @@ -25,7 +25,7 @@ dependencies = [ ('Boost', '1.79.0'), ('CFITSIO', '4.2.0'), ('GSL', '2.7'), - ('HDF5', '1.14.0', '-serial'), + ('HDF5', '1.12.2'), ('Python', '3.10.4'), ('Lua', '5.4.4'), ('libpng', '1.6.37'), @@ -37,4 +37,6 @@ sanity_check_paths = { 'dirs': ['bin'], } +sanity_check_commands = [('aoflagger', '-v')] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index 0edd857f9c5..e8fcac3e1ba 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -31,16 +31,16 @@ builddependencies = [ ] dependencies = [ - ('Boost', '1.79.0'), ('CFITSIO', '4.2.0'), ('WCSLIB', '7.11'), - ('HDF5', '1.14.0', '-serial'), + ('HDF5', '1.12.2'), + ('Boost.Python', '1.79.0'), ('SciPy-bundle', '2022.05'), ('ncurses', '6.3'), ] -configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=NO -Wno-dev -DCXX11="ON" -DDATA_DIR=%(installdir)s/data ' -configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON -DUSE_THREADS=NO' +configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" -DDATA_DIR=%(installdir)s/data ' +configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON' sanity_check_paths = { 'files': ['lib/libcasa_casa.%s' % SHLIB_EXT, 'lib/libcasa_mirlib.%s' % SHLIB_EXT, @@ -48,4 +48,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include/casacore'], } +sanity_check_commands = [('measuresdata', '')] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb index 60bb09845dd..41dbbeb6af1 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb @@ -29,7 +29,7 @@ dependencies = [ ('CFITSIO', '4.2.0'), ('WCSLIB', '7.11'), ('GSL', '2.7'), - ('HDF5', '1.14.0', '-serial'), + ('HDF5', '1.12.2'), ('Python', '3.10.4'), ('EveryBeam', '0.5.2'), ('Armadillo', '11.4.3'), @@ -41,4 +41,6 @@ sanity_check_paths = { 'dirs': ['bin'], } +sanity_check_commands = [('DP3', '--version')] + moduleclass = 'astro' diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb index 580b85535b7..47b7e0bc3d9 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb @@ -30,7 +30,7 @@ dependencies = [ ('CFITSIO', '4.2.0'), ('WCSLIB', '7.11'), ('GSL', '2.7'), - ('HDF5', '1.14.0', '-serial'), + ('HDF5', '1.12.2'), ('Python', '3.10.4'), ('libxml2', '2.9.13'), ] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-GCC-11.3.0-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-GCC-11.3.0-serial.eb deleted file mode 100644 index e3a89f51ecf..00000000000 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.0-GCC-11.3.0-serial.eb +++ /dev/null @@ -1,22 +0,0 @@ -name = 'HDF5' -version = '1.14.0' -versionsuffix = '-serial' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'GCC', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['a571cc83efda62e1a51a0a912dd916d01895801c5025af91669484a1575a6ef4'] - -dependencies = [ - ('zlib', '1.2.12'), - ('Szip', '2.1.1'), -] - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCC-11.3.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.3.0.eb similarity index 97% rename from easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCC-11.3.0.eb rename to easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.3.0.eb index d05c3ddf301..d07bd42ad50 100644 --- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.3.0.eb @@ -10,7 +10,7 @@ for making graphical images of publication quality with minimum effort on the pa the user. For most applications, the program can be device-independent, and the output can be directed to the appropriate device at run time.""" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/'] sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')] diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb index 316a3e87702..de04e74ec1c 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb @@ -27,7 +27,7 @@ dependencies = [ ('Boost', '1.79.0'), ('CFITSIO', '4.2.0'), ('GSL', '2.7'), - ('HDF5', '1.14.0', '-serial'), + ('HDF5', '1.12.2'), ('Python', '3.10.4'), ] @@ -36,4 +36,6 @@ sanity_check_paths = { 'dirs': ['bin'], } +sanity_check_commands = [('wsclean', '--version')] + moduleclass = 'astro' From c7b1b0055107c686e47789ce88e493ba8e606c54 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 18 Oct 2023 10:41:55 +0200 Subject: [PATCH 9142/9987] update comment about OpenJDK recommendation --- easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.eb b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.eb index 7332b44c076..b8dfab0c0fe 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-8.0-Java-1.8.eb @@ -31,7 +31,7 @@ checksums = [ ] # The installation is executed with the bundled JRE 1.8.0_242 (Zulu) -# at runtime we switch it to AdoptOpenJDK, which is known to be more reliable for SNAP-ESA +# At runtime we switch to an external JDK (SNAP developers recommend any OpenJDK distribution) dependencies = [ ('Java', '1.8'), ] From 0c56294499cafafae0d43edf1749f3826b5b7007 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 18 Oct 2023 10:42:04 +0200 Subject: [PATCH 9143/9987] remove binutils from builddependencies --- .../easyconfigs/s/starparser/starparser-1.49-foss-2022a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/s/starparser/starparser-1.49-foss-2022a.eb b/easybuild/easyconfigs/s/starparser/starparser-1.49-foss-2022a.eb index 692bab05fe1..8757a5fc6a5 100644 --- a/easybuild/easyconfigs/s/starparser/starparser-1.49-foss-2022a.eb +++ b/easybuild/easyconfigs/s/starparser/starparser-1.49-foss-2022a.eb @@ -14,10 +14,6 @@ load the modules in your own Python scripts.""" toolchain = {'name': 'foss', 'version': '2022a'} use_pip = True -builddependencies = [ - ('binutils', '2.38'), -] - dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), From c38dff11ac61baa44aee91361b8a9487eda8d092 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Dvo=C5=99=C3=A1=C4=8Dek=20Josef?= Date: Wed, 18 Oct 2023 15:10:55 +0200 Subject: [PATCH 9144/9987] adding easyconfigs: emcee-3.1.4-foss-2022a.eb --- .../e/emcee/emcee-3.1.4-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb b/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb new file mode 100644 index 00000000000..d25d7cd92c5 --- /dev/null +++ b/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'emcee' +version = '3.1.4' + +homepage = 'https://emcee.readthedocs.io/' +description = """Emcee is an extensible, pure-Python implementation of +Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. +It's designed for Bayesian parameter estimation and it's really sweet! """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8e0e19dc8bcef9c6d02f860bef8ddc6c876b8878a6ce666943e2c5cfd9317fed'] + +dependencies = [ + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.10/site-packages/emcee'], +} + +sanity_check_commands = [('pytest')] + +moduleclass = 'astro' From cc7b583d35bb3bb1a499c90358aebf6d16e42a25 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Wed, 18 Oct 2023 15:45:39 +0200 Subject: [PATCH 9145/9987] Update waLBerla-6.1-foss-2021a.eb add patch and sanity check --- .../w/waLBerla/waLBerla-6.1-foss-2021a.eb | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 44b93328579..e67edd92949 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -13,7 +13,13 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['https://i10git.cs.fau.de/walberla/walberla/-/archive/v6.1'] sources = ['%(name)s-v%(version)s.tar.gz'] -checksums = ['f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'] +patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild.patch'] +checksums = [ + {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, + {'waLBerla-6.1_fix_cmakelist_for_easybuild.patch': + '13393d523d8f2e1856ae6acffc04bc74d35b5b6a7c800cfad75fb8e3678e4dad'}, +] + builddependencies = [('CMake', '3.20.1')] @@ -31,8 +37,8 @@ configopts += "-DWALBERLA_BUILD_DOC=OFF " configopts += "-DPython_ROOT_DIR=$EBROOTPYTHON " sanity_check_paths = { - 'files': ['walberla/waLBerlaDefinitions.h'], - 'dirs': [''], + 'files': ['walberla/waLBerlaDefinitions.h', 'walberla/pythonmodule/walberla_cpp.cpython-39-x86_64-linux-gnu.so'], + 'dirs': ['walberla/pythonmodule/'] } moduleclass = 'chem' From 9e492b572d56e8a4e37ca37187d1d617ae18ff7a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Dvo=C5=99=C3=A1=C4=8Dek=20Josef?= Date: Wed, 18 Oct 2023 15:49:16 +0200 Subject: [PATCH 9146/9987] adding easyconfigs: zeus-mcmc-2.5.4-foss-2022a.eb --- .../z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb b/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb new file mode 100644 index 00000000000..acd91ab1fb6 --- /dev/null +++ b/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'zeus-mcmc' +version = '2.5.4' + +homepage = 'https://pypi.org/project/zeus-mcmc' +description = "Zeus is a Python implementation of the Ensemble Slice Sampling method." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} +exts_list = [ + ('seaborn', '0.12.2', { + 'checksums': ['374645f36509d0dcab895cba5b47daf0586f77bfe3b36c97c607db7da5be0139'], + }), + (name, version, { + 'modulename': 'zeus', + 'checksums': ['594baa90de4ad4488c4db5ed6a0446f7103bc4b3de787f4d7d23c91c9aa88769'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 1a4685910a9579748f200a29477329549c29d4a7 Mon Sep 17 00:00:00 2001 From: xina Date: Wed, 18 Oct 2023 15:54:06 +0200 Subject: [PATCH 9147/9987] add cmake patch file --- .../waLBerla-6.1_fix_cmakelist_for_easybuild.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch new file mode 100644 index 00000000000..62c8fad3044 --- /dev/null +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch @@ -0,0 +1,12 @@ +diff -ruN walberla-v6.1.orig/CMakeLists.txt walberla-v6.1/CMakeLists.txt +--- walberla-v6.1.orig/CMakeLists.txt 2023-10-17 13:06:02.619565000 +0200 ++++ walberla-v6.1/CMakeLists.txt 2023-10-18 14:47:35.047985995 +0200 +@@ -1314,7 +1314,7 @@ + src/waLBerlaDefinitions.h ) + + install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION walberla/ ) +- ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/ DESTINATION walberla/ ) + + # test + if ( WALBERLA_BUILD_TESTS ) From e12bd7a9b2801655ff455cf27c7956997bf3631f Mon Sep 17 00:00:00 2001 From: jose_d Date: Wed, 18 Oct 2023 15:55:16 +0200 Subject: [PATCH 9148/9987] Update zeus-mcmc-2.5.4-foss-2022a.eb: fix homepage --- easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb b/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb index acd91ab1fb6..4219c090114 100644 --- a/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb +++ b/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'zeus-mcmc' version = '2.5.4' -homepage = 'https://pypi.org/project/zeus-mcmc' +homepage = 'https://zeus-mcmc.readthedocs.io' description = "Zeus is a Python implementation of the Ensemble Slice Sampling method." toolchain = {'name': 'foss', 'version': '2022a'} From 36ac53cee5ad6a95090c7aeb2a59ea4ad39634ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 18 Oct 2023 17:44:52 +0200 Subject: [PATCH 9149/9987] adding easyconfigs: pyEGA3-5.0.2-GCCcore-12.3.0.eb --- .../p/pyEGA3/pyEGA3-5.0.2-GCCcore-12.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyEGA3/pyEGA3-5.0.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-5.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-5.0.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2c867a3ef22 --- /dev/null +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-5.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'pyEGA3' +version = '5.0.2' + +homepage = 'https://github.com/EGA-archive/ega-download-client' +description = """ A basic Python-based EGA download client """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('tqdm', '4.66.1'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True + +exts_list = [ + ('humanize', '4.8.0', { + 'checksums': ['9783373bf1eec713a770ecaa7c2d7a7902c98398009dfa3d8a2df91eec9311e8'], + }), + ('htsget', '0.2.6', { + 'checksums': ['84816534e2740d3bcc4fb44a6d703b387b8a392209be098752466c35ff253884'], + }), + ('urllib3', '1.26.18', { + 'checksums': ['f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0'], + }), + (name, version, { + 'preinstallopts': "sed -i 's/==/>=/g' setup.py && ", + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['677f49564ff3178291ce14a7dcd4032a10bf8505d3f5c07ded13565302a89336'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/pyega3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ["pyega3 -h"] + +moduleclass = 'bio' From 4547fba491789d8ef2660f09d01a4be32d0faf24 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 18 Oct 2023 18:21:02 +0200 Subject: [PATCH 9150/9987] adding easyconfigs: expat-2.5.0-GCCcore-13.2.0.eb, groff-1.22.4-GCCcore-13.2.0.eb --- .../e/expat/expat-2.5.0-GCCcore-13.2.0.eb | 31 +++++++++++++++++++ .../g/groff/groff-1.22.4-GCCcore-13.2.0.eb | 27 ++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f99eeb2426b --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.5.0' + +homepage = 'https://libexpat.github.io' + +description = """Expat is an XML parser library written in C. It is a stream-oriented parser +in which an application registers handlers for things the parser might find +in the XML document (like start tags).""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_TAR_BZ2] +checksums = ['6f0e6e01f7b30025fa05c85fdad1e5d0ec7fd35d9f61b22f34998de11969ff67'] + +builddependencies = [('binutils', '2.40')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..73131ee2748 --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.22.4' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = '--with-doc=no' + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' From a7cb7980fdace2b88b9793296141a5bb7a652047 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 18 Oct 2023 18:23:32 +0200 Subject: [PATCH 9151/9987] Acutally a new groff version exists --- ....22.4-GCCcore-13.2.0.eb => groff-1.23.0-GCCcore-13.2.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/groff/{groff-1.22.4-GCCcore-13.2.0.eb => groff-1.23.0-GCCcore-13.2.0.eb} (85%) diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb similarity index 85% rename from easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-13.2.0.eb rename to easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb index 73131ee2748..87a16b784ba 100644 --- a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'ConfigureMake' name = 'groff' -version = '1.22.4' +version = '1.23.0' homepage = 'https://www.gnu.org/software/groff' description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands @@ -11,7 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://ftp.gnu.org/gnu/groff'] sources = [SOURCE_TAR_GZ] -checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] +checksums = ['6b9757f592b7518b4902eb6af7e54570bdccba37a871fddb2d30ae3863511c13'] builddependencies = [ ('binutils', '2.40'), From 8f517daf82a4f5953db7de07ac6689e1dfbc5c27 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 18 Oct 2023 18:44:32 +0200 Subject: [PATCH 9152/9987] Add m4 builddep for groff --- easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb index 87a16b784ba..f280bc24144 100644 --- a/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb @@ -15,6 +15,7 @@ checksums = ['6b9757f592b7518b4902eb6af7e54570bdccba37a871fddb2d30ae3863511c13'] builddependencies = [ ('binutils', '2.40'), + ('M4', '1.4.19'), ] configopts = '--with-doc=no' From 7c9ff1964234b3f4bf96976934abd2f56562a5c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 18 Oct 2023 19:04:11 +0200 Subject: [PATCH 9153/9987] adding easyconfigs: buildenv-default-foss-2023a-CUDA-12.1.1.eb, buildenv-default-foss-2023a.eb, buildenv-default-intel-2023a.eb, buildenv-default-nvompi-2022.07.eb --- ...buildenv-default-foss-2023a-CUDA-12.1.1.eb | 20 +++++++++++++++++++ .../b/buildenv/buildenv-default-foss-2023a.eb | 13 ++++++++++++ .../buildenv/buildenv-default-intel-2023a.eb | 13 ++++++++++++ .../buildenv-default-nvompi-2022.07.eb | 13 ++++++++++++ 4 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023a.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2023a.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-nvompi-2022.07.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..eee044d98f7 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,20 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('UCX-CUDA', '1.14.1', versionsuffix), + ('UCC-CUDA', '1.2.0', versionsuffix), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023a.eb new file mode 100644 index 00000000000..f87290601c7 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2023a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2023a.eb new file mode 100644 index 00000000000..d0d48e47dac --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2023a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2023a'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-nvompi-2022.07.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-nvompi-2022.07.eb new file mode 100644 index 00000000000..8b4d32b3950 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-nvompi-2022.07.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'nvompi', 'version': '2022.07'} + +moduleclass = 'devel' From e35a6fa72a3beace765d6d3965bea82d8106be31 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 18 Oct 2023 19:10:09 +0200 Subject: [PATCH 9154/9987] adding easyconfigs: Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb --- .../Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb | 2133 +++++++++++++++++ 1 file changed, 2133 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..5199d64aba1 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb @@ -0,0 +1,2133 @@ +easyblock = 'PerlBundle' + +name = 'Perl-bundle-CPAN' +version = '5.38.0' + +homepage = 'https://www.perl.org/' +description = """A set of common packages from CPAN""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('groff', '1.23.0'), +] + +dependencies = [ + ('Perl', version), + ('zlib', '1.2.13'), # for Net::SSLeay + ('expat', '2.5.0'), # for XML::Parser + ('ncurses', '6.4'), # for Term::ReadLine::Gnu + ('libreadline', '8.2'), # for Term::ReadLine::Gnu + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay +] + +# !! order of extensions is important !! +# extensions updated on 2023-10-18 +exts_list = [ + ('Config::General', '2.65', { + 'source_tmpl': 'Config-General-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + 'checksums': ['4d6d5754be3a9f30906836f0cc10e554c8832e14e7a1341efb15b05d706fc58f'], + }), + ('HTTP::Date', '6.06', { + 'source_tmpl': 'HTTP-Date-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['7b685191c6acc3e773d1fc02c95ee1f9fae94f77783175f5e78c181cc92d2b52'], + }), + ('File::Listing', '6.16', { + 'source_tmpl': 'File-Listing-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['189b3a13fc0a1ba412b9d9ec5901e9e5e444cc746b9f0156d4399370d33655c6'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['ae5104f634650dce8a79b7ed13fb59d67a39c213a6776cfdaa3ee749e62f1a8c'], + }), + ('ExtUtils::InstallPaths', '0.012', { + 'source_tmpl': 'ExtUtils-InstallPaths-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['84735e3037bab1fdffa3c2508567ad412a785c91599db3c12593a50a1dd434ed'], + }), + ('ExtUtils::Helpers', '0.026', { + 'source_tmpl': 'ExtUtils-Helpers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['de901b6790a4557cf4ec908149e035783b125bf115eb9640feb1bc1c24c33416'], + }), + ('Test::Harness', '3.48', { + 'source_tmpl': 'Test-Harness-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['e73ff89c81c1a53f6baeef6816841b89d3384403ad97422a7da9d1eeb20ef9c5'], + }), + ('Module::Build::Tiny', '0.047', { + 'source_tmpl': 'Module-Build-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['71260e9421b93c33dd1b3e7d0cf15f759c0ca7c753fa840279ec3be70f8f8c9d'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c350524507cd827fab864e5d4c2cc350b1babaa12fa95aec0ca00843fcc7deeb'], + }), + ('Text::Glob', '0.11', { + 'source_tmpl': 'Text-Glob-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + 'checksums': ['069ccd49d3f0a2dedb115f4bdc9fbac07a83592840953d1fcdfc39eb9d305287'], + }), + ('Regexp::Common', '2017060201', { + 'source_tmpl': 'Regexp-Common-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + 'checksums': ['ee07853aee06f310e040b6bf1a0199a18d81896d3219b9b35c9630d0eb69089b'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['2a3f4ad8442d9070780e58ef43722d19d1ee21a803bf7c8206877a10482de5a0'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['4ab122508d2fb86d171a15f4006e5cf896d5facfa65219c0b243a89906258e59'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + 'checksums': ['423d26155ee85ca51ab2270cee59f4e85b193e57ac3a29aff827298c0a396b12'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + 'checksums': ['b3f2ad45e4fd10b3fb90d912d78d8b795ab295480db56dc64e86b9fa75c5a6df'], + }), + ('Try::Tiny', '0.31', { + 'source_tmpl': 'Try-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['3300d31d8a4075b26d8f46ce864a1d913e0e8467ceeba6655d5d2b2e206c11be'], + }), + ('Test::Fatal', '0.017', { + 'source_tmpl': 'Test-Fatal-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['37dfffdafb84b762efe96b02fb2aa41f37026c73e6b83590db76229697f3c4a6'], + }), + ('Test::Warnings', '0.032', { + 'source_tmpl': 'Test-Warnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['4727dae2416e9f07e41e2dc3a9143ba6affc1ec57652117c99d50038e313e9d9'], + }), + ('Class::Inspector', '1.36', { + 'source_tmpl': 'Class-Inspector-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['cc295d23a472687c24489d58226ead23b9fdc2588e522f0b5f0747741700694e'], + }), + ('File::ShareDir::Install', '0.14', { + 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'], + }), + ('File::ShareDir', '1.118', { + 'source_tmpl': 'File-ShareDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['3bb2a20ba35df958dc0a4f2306fc05d903d8b8c4de3c8beefce17739d281c958'], + }), + ('IPC::System::Simple', '1.30', { + 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', + 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'Template-Toolkit-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': ['d2a32dd6c21e4b37c6a93df8087ca9e880cfae613a3e5efaea307b0bdcaedb58'], + }), + ('DBI', '1.643', { + 'source_tmpl': 'DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + 'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'], + }), + ('DBD::SQLite', '1.74', { + 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['8994997d84b9feb4547795f78746c661fb72e3cb6a25dbdd789b731f5688a4dd'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + 'checksums': ['11a815fc45fdf0efabb1822ab77faad8b9eea162572c5f0940c8ed7d56e6b8b8'], + }), + ('Archive::Extract', '0.88', { + 'source_tmpl': 'Archive-Extract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['cffcf135cd0622287d3b02154f7d6716495449fcaed03966621948e25ea5f742'], + }), + ('DBIx::Simple', '1.37', { + 'source_tmpl': 'DBIx-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + 'checksums': ['46d311aa2ce08907401c56119658426dbb044c5a40de73d9a7b79bf50390cae3'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + 'checksums': ['f7dbebf65261ed0e5abd0f57052b64d665a1a830bab4c8bbc220f235bd39caf5'], + }), + ('Test::Simple', '1.302195', { + 'source_tmpl': 'Test-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['b390bb23592e0b946c95adbb3c30b11bc634a286b2847be611ad929c57e39a6c'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + 'checksums': ['a3dc1526f3dde72d3c64ea00007b86ce608cdcd93567cf6e6e42dc10fdc4511d'], + }), + ('IO::Stringy', '2.113', { + 'source_tmpl': 'IO-Stringy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['51220fcaf9f66a639b69d251d7b0757bf4202f4f9debd45bdd341a6aca62fe4e'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['176fa02771f542a4efb1dbc2a4c928e8f4391bf4078473bd6040d8f11adb0ec1'], + }), + ('XML::SAX::Base', '1.09', { + 'source_tmpl': 'XML-SAX-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['66cb355ba4ef47c10ca738bd35999723644386ac853abbeb5132841f5e8a2ad0'], + }), + ('XML::NamespaceSupport', '1.12', { + 'source_tmpl': 'XML-NamespaceSupport-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': ['47e995859f8dd0413aa3f22d350c4a62da652e854267aa0586ae544ae2bae5ef'], + }), + ('XML::SAX', '1.02', { + 'source_tmpl': 'XML-SAX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['4506c387043aa6a77b455f00f57409f3720aa7e553495ab2535263b4ed1ea12a'], + }), + ('Test::LeakTrace', '0.17', { + 'source_tmpl': 'Test-LeakTrace-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': ['777d64d2938f5ea586300eef97ef03eacb43d4c1853c9c3b1091eb3311467970'], + }), + ('Sub::Uplevel', '0.2800', { + 'source_tmpl': 'Sub-Uplevel-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['b4f3f63b80f680a421332d8851ddbe5a8e72fcaa74d5d1d98f3c8cc4a3ece293'], + }), + ('Test::Exception', '0.43', { + 'source_tmpl': 'Test-Exception-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['156b13f07764f766d8b45a43728f2439af81a3512625438deab783b7883eb533'], + }), + ('Text::Aligner', '0.16', { + 'source_tmpl': 'Text-Aligner-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['5c857dbce586f57fa3d7c4ebd320023ab3b2963b2049428ae01bd3bc4f215725'], + }), + ('Text::Table', '1.135', { + 'source_tmpl': 'Text-Table-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['fca3c16e83127f7c44dde3d3f7e3c73ea50d109a1054445de8082fea794ca5d2'], + }), + ('MIME::Types', '2.24', { + 'source_tmpl': 'MIME-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['629e361f22b220be50c2da7354e23c0451757709a03c25a22f3160edb94cb65f'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + 'checksums': ['7afc7ca2b9502e440241938ad97a3e7ebd550180ebd6142e1db394186b268e77'], + }), + ('Capture::Tiny', '0.48', { + 'source_tmpl': 'Capture-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['6c23113e87bad393308c90a207013e505f659274736638d8c79bac9c67cc3e19'], + }), + ('File::Copy::Recursive::Reduced', '0.007', { + 'source_tmpl': 'File-Copy-Recursive-Reduced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], + 'checksums': ['d3b58522e69803a91437e29c099eb706e8373f1eef0518a4dc3669dd3dfcdc27'], + }), + ('Module::Build::XSUtil', '0.19', { + 'source_tmpl': 'Module-Build-XSUtil-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + 'checksums': ['9063b3c346edeb422807ffe49ffb23038c4f900d4a77b845ce4b53d97bf29400'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + 'checksums': ['0b1617af218dfab911ba0fbd72210529a246efe140332da77fe3e03d11000117'], + }), + ('Number::Format', '1.76', { + 'source_tmpl': 'Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0e0060eb363635a885706c6a26f5fcaafeae759f7b2acae49dda70e195dd44d6'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + 'checksums': ['0865836a1bcbc34d4a0ee34b5ccc14d7b511f1fd300bf390f002dac349539843'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['adb17dac9e36cd011f5243881c9739417fd102fce760f8de4e9be4c7131108e2'], + }), + ('URI', '5.21', { + 'source_tmpl': 'URI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['96265860cd61bde16e8415dcfbf108056de162caa0ac37f81eb695c9d2e0ab77'], + }), + ('B::COW', '0.007', { + 'source_tmpl': 'B-COW-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['1290daf227e8b09889a31cf182e29106f1cf9f1a4e9bf7752f9de92ed1158b44'], + }), + ('Clone', '0.46', { + 'source_tmpl': 'Clone-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': ['aadeed5e4c8bd6bbdf68c0dd0066cb513e16ab9e5b4382dc4a0aafd55890697b'], + }), + ('IO::HTML', '1.004', { + 'source_tmpl': 'IO-HTML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + 'checksums': ['c87b2df59463bbf2c39596773dfb5c03bde0f7e1051af339f963f58c1cbd8bf5'], + }), + ('LWP::MediaTypes', '6.04', { + 'source_tmpl': 'LWP-MediaTypes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['8f1bca12dab16a1c2a7c03a49c5e58cce41a6fec9519f0aadfba8dad997919d9'], + }), + ('HTTP::Message', '6.45', { + 'source_tmpl': 'HTTP-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['01cb8406612a3f738842d1e97313ae4d874870d1b8d6d66331f16000943d4cbe'], + }), + ('HTML::Parser', '3.81', { + 'source_tmpl': 'HTML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['c0910a5c8f92f8817edd06ccfd224ba1c2ebe8c10f551f032587a1fc83d62ff2'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + 'checksums': ['c36fd2b68d48c2e17417bf2873c78820f3ae02460fdf5976b8eeab887d59e16c'], + }), + ('XML::Parser', '2.46', { + 'source_tmpl': 'XML-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['d331332491c51cccfb4cb94ffc44f9cd73378e618498d4a37df9e043661c515d'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + 'checksums': ['4571059b7b5d48b7ce52b01389e95d798bf5cf2020523c153ff27b498153c9cb'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['8816f34e9a38e849a10df756030dccf9fe061a196c11ac3faafd7113c929b964'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': ['85e2f805bfc81cd738c294316b27a515397036f397a0ff1c6c8d754c38530306'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + 'checksums': ['8b481ceedbf0ae4a83effb80581550008bfdd3885ef01145e3733c7097c00a08'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': ['fabb0b8c97e67c9b34b6cc18ed66f6c5e01c55b257dcf007555e0b027d4caf56'], + }), + ('Parse::RecDescent', '1.967015', { + 'source_tmpl': 'Parse-RecDescent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + 'checksums': ['1943336a4cb54f1788a733f0827c0c55db4310d5eae15e542639c9dd85656e37'], + }), + ('GO', '0.04', { + 'runtest': False, # Problem with indirect dependency DBD::Pg + 'source_tmpl': 'go-db-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + 'checksums': ['8eb73d591ad767e7cf26def40cffd84833875f1ad51e456960b9ed73dc23641b'], + }), + ('Class::Trigger', '0.15', { + 'source_tmpl': 'Class-Trigger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['b7a878d44dea67d64df2ca18020d9d868a95596debd16f1a264874209332b07f'], + }), + ('Class::Accessor', '0.51', { + 'source_tmpl': 'Class-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['bf12a3e5de5a2c6e8a447b364f4f5a050bf74624c56e315022ae7992ff2f411c'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['94ce27a546cd57cb52e080a8f2533a7cc2350028388582485bd1039a37871f9c'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + 'checksums': ['541354fe361c56850cb11261f6ca089a14573fa764792447444ff736ae626206'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['c4661b00afb7e53c97ac36e13f34dde43c1a93540a2f4ff97e6182b0c731e4e7'], + }), + ('File::Slurper', '0.014', { + 'source_tmpl': 'File-Slurper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['d5a36487339888c3cd758e648160ee1d70eb4153cacbaff57846dbcefb344b0c'], + }), + ('Pod::POM', '2.01', { + 'source_tmpl': 'Pod-POM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['1b50fba9bbdde3ead192beeba0eaddd0c614e3afb1743fa6fff805f57c56f7f4'], + }), + ('Math::Round', '0.08', { + 'source_tmpl': 'Math-Round-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['7b4d2775ad3b859a5fd61f7f3fc5cfba42b1a10df086d2ed15a0ae712c8fd402'], + }), + ('Algorithm::Diff', '1.201', { + 'source_tmpl': 'Algorithm-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0022da5982645d9ef0207f3eb9ef63e70e9713ed2340ed7b3850779b0d842a7d'], + }), + ('Text::Diff', '1.45', { + 'source_tmpl': 'Text-Diff-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['e8baa07b1b3f53e00af3636898bbf73aec9a0ff38f94536ede1dbe96ef086f04'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['bd697dd62aaf26d118e9f0a0813429deb1c544e4501559879b61fcbdfe99fe46'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'], + }), + ('Net::SSLeay', '1.92', { + 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", + 'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'], + 'checksums': ['47c2f2b300f2e7162d71d699f633dd6a35b0625a00cbda8c50ac01144a9396a9'], + }), + ('IO::Socket::SSL', '2.083', { + 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + 'checksums': ['904ef28765440a97d8a9a0df597f8c3d7f3cb0a053d1b082c10bed03bc802069'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['dce28e3932762c2ff92aa52d90405c06e898e81cb7b164ccae8966ae77f1dcab'], + }), + ('Meta::Builder', '0.004', { + 'source_tmpl': 'Meta-Builder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['acb499aa7206eb9db21eb85357a74521bfe3bdae4a6416d50a7c75b939cf56fe'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['4bd70d6ca76f6f6ba7e4c618d4ac93b8593a58f1233ccbe18b10f5f204f1d4e4'], + }), + ('Mouse', 'v2.5.10', { + 'source_tmpl': 'Mouse-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SK/SKAJI'], + 'checksums': ['ce8dc23946153a467ff09765167ee2590f5c502120f48a2d9441733f39aa32ee'], + }), + ('Test::Version', '2.09', { + 'source_tmpl': 'Test-Version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['9ce1dd2897a5f30e1b7f8966ec66f57d8d8f280f605f28c7ca221fa79aca38e0'], + }), + ('Class::Method::Modifiers', '2.15', { + 'source_tmpl': 'Class-Method-Modifiers-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['65cd85bfe475d066e9186f7a8cc636070985b30b0ebb1cde8681cf062c2e15fc'], + }), + ('Moo', '2.005005', { + 'source_tmpl': 'Moo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['fb5a2952649faed07373f220b78004a9c6aba387739133740c1770e9b1f4b108'], + }), + ('Data::Dumper::Concise', '2.023', { + 'source_tmpl': 'Data-Dumper-Concise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['a6c22f113caf31137590def1b7028a7e718eface3228272d0672c25e035d5853'], + }), + ('DBIx::Admin::CreateTable', '2.11', { + 'source_tmpl': 'DBIx-Admin-CreateTable-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['07b1427fbc15455657ca57217749004162a50c04abb243022a5b479e4b2a5912'], + }), + ('Config::Tiny', '2.30', { + 'source_tmpl': 'Config-Tiny-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['b2f7345619b3b8e636dd39ea010731c9dc2bfb8f022bcbd86ae6ad17866e110d'], + }), + ('File::Slurp', '9999.32', { + 'source_tmpl': 'File-Slurp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['4c3c21992a9d42be3a79dd74a3c83d27d38057269d65509a2f555ea0fb2bc5b0'], + }), + ('DBIx::Admin::DSNManager', '2.02', { + 'source_tmpl': 'DBIx-Admin-DSNManager-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['c25511f42328ccb606a0cd78413a74181c87fb37a382d38aa3fad106b540adcb'], + }), + ('Lingua::EN::PluralToSingular', '0.21', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + 'checksums': ['f8a8b7de28c25c96190d7f48c90b5ad9b9bf517f3835c77641f0e8fa546c0d1d'], + }), + ('Test::Warn', '0.37', { + 'source_tmpl': 'Test-Warn-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BIGJ'], + 'checksums': ['98ca32e7f2f5ea89b8bfb9a0609977f3d153e242e2e51705126cb954f1a06b57'], + }), + ('Test::Differences', '0.71', { + 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': ['cac16a56cd843b0809e5b49199d60d75a8dbad7ca9a08380dbf3f5cc3aaa38d9'], + }), + ('Test::Most', '0.38', { + 'source_tmpl': 'Test-Most-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + 'checksums': ['089eb894f7bace4c37c6334e0e290eb20338ee10223af0c82cbe7281c78382df'], + }), + ('Const::Fast', '0.014', { + 'source_tmpl': 'Const-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['f805953a08c57846a16a4d85d7b766398afaf7c36c1465fcb1dea09e5fa394db'], + }), + ('Ref::Util', '0.204', { + 'source_tmpl': 'Ref-Util-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARC'], + 'checksums': ['415fa73dbacf44f3d5d79c14888cc994562720ab468e6f71f91cd1f769f105e1'], + }), + ('Class::XSAccessor', '1.19', { + 'source_tmpl': 'Class-XSAccessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['99c56b395f1239af19901f2feeb125d9ecb4e351a0d80daa9529211a4700a6f2'], + }), + ('Hash::Objectify', '0.008', { + 'source_tmpl': 'Hash-Objectify-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['236d5829cdebf3ba648d34e1295cd9099a20506d8d0284668e617e0058cebeed'], + }), + ('Const::Exporter', 'v1.2.3', { + 'source_tmpl': 'Const-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRWO'], + 'checksums': ['53e59b4764aebcf79bbed533ab5a6107339fe516b7f2f607b1bae8dd9dcf7015'], + }), + ('HTML::Entities::Interpolate', '1.10', { + 'source_tmpl': 'HTML-Entities-Interpolate-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['f15a9df92c282419f7010964aca1ada844ddfae7afc735cd2ba1bb20883e955c'], + }), + ('List::SomeUtils', '0.59', { + 'source_tmpl': 'List-SomeUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['fab30372e4c67bf5a46062da38d1d0c8756279feada866eb439fa29571a2dc7b'], + }), + ('List::UtilsBy', '0.12', { + 'source_tmpl': 'List-UtilsBy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['fff1281fd469fe982b1a58044becfd970f313bff3a26e1c7b2b3f4c0a5ed71e0'], + }), + ('List::AllUtils', '0.19', { + 'source_tmpl': 'List-AllUtils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['30a8146ab21a7787b8c56d5829cf9a7f2b15276d3b3fca07336ac38d3002ffbc'], + }), + ('Unicode::EastAsianWidth', '12.0', { + 'source_tmpl': 'Unicode-EastAsianWidth-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AU/AUDREYT'], + 'checksums': ['2a5bfd926c4fe5f77e6137da2c31ac2545282ae5fec6e9af0fdd403555a90ff4'], + }), + ('String::TtyLength', '0.03', { + 'source_tmpl': 'String-TtyLength-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['4fedaf72028511d80eb6afba523993e9aaa245d7af558345d5d4ed46e2e82ce1'], + }), + ('Text::Table::Manifold', '1.03', { + 'source_tmpl': 'Text-Table-Manifold-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['e680713169557b0768952fa6932f25576a61dccfb96bd9036dcf6fcefb35e09e'], + }), + ('DBIx::Admin::TableInfo', '3.04', { + 'source_tmpl': 'DBIx-Admin-TableInfo-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['b9625992683b97378bea0947773f50e3c9f81974048b84f4c3422cae7e6082f4'], + }), + ('Net::HTTP', '6.23', { + 'runtest': False, # Fragile tests + 'source_tmpl': 'Net-HTTP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['0d65c09dd6c8589b2ae1118174d3c1a61703b6ecfc14a3442a8c74af65e0c94e'], + }), + ('Clone::Choose', '0.010', { + 'source_tmpl': 'Clone-Choose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'], + 'checksums': ['5623481f58cee8edb96cd202aad0df5622d427e5f748b253851dfd62e5123632'], + }), + ('Hash::Merge', '0.302', { + 'source_tmpl': 'Hash-Merge-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HE/HERMES'], + 'checksums': ['ae0522f76539608b61dde14670e79677e0f391036832f70a21f31adde2538644'], + }), + ('SQL::Abstract', '2.000001', { + 'source_tmpl': 'SQL-Abstract-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSTROUT'], + 'checksums': ['35a642662c349420d44be6e0ef7d8765ea743eb12ad14399aa3a232bb94e6e9a'], + }), + ('HTML::Form', '6.11', { + 'source_tmpl': 'HTML-Form-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMBABQUE'], + 'checksums': ['43bfaa7087393487d2d51261a1aa7f6f81a97b1d8fef7a48fcf6ef32b16d6454'], + }), + ('IPC::Run', '20231003.0', { + 'source_tmpl': 'IPC-Run-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['eb25bbdf5913d291797ef1bfe998f15130b455d3ed02aacde6856f0b25e4fe57'], + }), + ('File::Remove', '1.61', { + 'source_tmpl': 'File-Remove-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['fd857f585908fc503461b9e48b3c8594e6535766bc14beb17c90ba58d5dc4975'], + }), + ('YAML::Tiny', '1.74', { + 'source_tmpl': 'YAML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['7b38ca9f5d3ce24230a6b8bdc1f47f5b2db348e7f7f9666c26f5955636e33d6c'], + }), + ('Module::Install', '1.21', { + 'source_tmpl': 'Module-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['fbf91007f30565f3920e106055fd0d4287981d5e7dad8b35323ce4b733f15a7b'], + }), + ('Test::ClassAPI', '1.07', { + 'source_tmpl': 'Test-ClassAPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['30e9dbfc5e0cc2ee14eae8f3465a908a710daecbd0a3ebdb2888fc4504fa18aa'], + }), + ('HTTP::Tiny', '0.088', { + 'source_tmpl': 'HTTP-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['7ce6367e861883b6868d6dd86168af33524717d8cc94100c2abf9bd86a82b4d8'], + }), + ('Sub::Install', '0.929', { + 'source_tmpl': 'Sub-Install-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['80b1e281d8cd3b2b31dac711f5c8a1657a87cd80bbe69af3924bcbeb4e5db077'], + }), + ('Package::DeprecationManager', '0.18', { + 'source_tmpl': 'Package-DeprecationManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['b68d3f0ced55b7615fddbb6029b89f92a34fe0dd8c6fd6bceffc157d56834fe8'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['68c1dac2187421f0eb7abf71452a06f190181b8fc4b28ededf5b90296fb943cc'], + }), + ('Date::Language', '2.33', { + 'source_tmpl': 'TimeDate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['c0b69c4b039de6f501b0d9f13ec58c86b040c1f7e9b27ef249651c143d605eb2'], + }), + ('version', '0.9930', { + 'source_tmpl': 'version-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['61db955fbcb39f5902fa6c8b957aeb2741e23d4840f84abf846af1f670aeee30'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'checksums': ['865e198e98d904be1683ef5a53a4948f02dabdacde59fc554a082ffbcc5baefd'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + 'checksums': ['ea844b9686c94d666d9d444321d764490b2cde2f985c4165b4c2c77665caedc4'], + }), + ('Sub::Name', '0.27', { + 'source_tmpl': 'Sub-Name-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ecf36fba1c47ca93e1daa394968ed39c4186867459d9cd173c421e2b972043e8'], + }), + ('Time::Piece', '1.3401', { + 'source_tmpl': 'Time-Piece-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ES/ESAYM'], + 'checksums': ['4b55b7bb0eab45cf239a54dfead277dfa06121a43e63b3fce0853aecfdb04c27'], + }), + ('Digest::HMAC', '1.04', { + 'source_tmpl': 'Digest-HMAC-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AR/ARODLAND'], + 'checksums': ['d6bc8156aa275c44d794b7c18f44cdac4a58140245c959e6b19b2c3838b08ed4'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['1c729c1ea63100e878405cda7d66f9adfd3ed4f1d6cacaca0ee9152df728e016'], + }), + ('Email::Date::Format', '1.008', { + 'source_tmpl': 'Email-Date-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['432b7c83ff88749af128003f5257c573aec1a463418db90ed22843cbbc258b4f'], + }), + ('MIME::Lite', '3.033', { + 'source_tmpl': 'MIME-Lite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['78a279f1d2e242551c347ef97a13fc675766602cb84c2a80c569400f4f368bab'], + }), + ('Crypt::Rijndael', '1.16', { + 'source_tmpl': 'Crypt-Rijndael-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['6540085e3804b82a6f0752c1122cf78cadd221990136dd6fd4c097d056c84d40'], + }), + ('B::Lint', '1.20', { + 'runtest': False, # One failing subtest + 'source_tmpl': 'B-Lint-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['dc49408964fd8b7963859c92e013f0b9f92f74be5a7c2a78e3996279827c10b3'], + }), + ('Canary::Stability', '2013', { + 'source_tmpl': 'Canary-Stability-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a5c91c62cf95fcb868f60eab5c832908f6905221013fea2bce3ff57046d7b6ea'], + }), + ('AnyEvent', '7.17', { + 'source_tmpl': 'AnyEvent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['50beea689c098fe4aaeb83806c40b9fe7f946d5769acf99f849f099091a4b985'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['76cb824a27b6b4e560409fcf6fd5b3bfbbd38b72f1f3d37ed0b54bd9c0baeade'], + }), + ('Data::UUID', '1.226', { + 'source_tmpl': 'Data-UUID-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['093d57ffa0d411a94bafafae495697db26f5c9d0277198fe3f7cf2be22996453'], + }), + ('Test::Pod', '1.52', { + 'source_tmpl': 'Test-Pod-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['60a8dbcc60168bf1daa5cc2350236df9343e9878f4ab9830970a5dde6fe8e5fc'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['1177027025ecb09ee64d9f9f255615c04db5e14f7536c344af632032eb887b0f'], + }), + ('Net::SMTP::SSL', '1.04', { + 'source_tmpl': 'Net-SMTP-SSL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7b29c45add19d3d5084b751f7ba89a8e40479a446ce21cfd9cc741e558332a00'], + }), + ('XML::Tiny', '2.07', { + 'source_tmpl': 'XML-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + 'checksums': ['ce39fcb53e0fe9f1cbcd86ddf152e1db48566266b70ec0769ef364eeabdd8941'], + }), + ('HTML::Tree', '5.07', { + 'source_tmpl': 'HTML-Tree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], + 'checksums': ['f0374db84731c204b86c1d5b90975fef0d30a86bd9def919343e554e31a9dbbf'], + }), + ('Devel::GlobalDestruction', '0.14', { + 'source_tmpl': 'Devel-GlobalDestruction-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['34b8a5f29991311468fe6913cadaba75fd5d2b0b3ee3bb41fe5b53efab9154ab'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + 'checksums': ['46b502e7a288d559429891eeb5d979461dd3ecc6a5c491ead85d165b6e03a51e'], + }), + ('IO::Tty', '1.17', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['a5f1a83020bc5b5dd6c1b570f48c7546e0a8f7fac10a068740b03925ad9e14e8'], + }), + ('Expect', '1.35', { + 'source_tmpl': 'Expect-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY'], + 'checksums': ['09d92761421decd495853103379165a99efbf452c720f30277602cf23679fd06'], + }), + ('Term::UI', '0.50', { + 'source_tmpl': 'Term-UI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['60bfdd6d4c158b88d370133fc65b20485a36a45b12d906000b81c78ca524163d'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + 'checksums': ['14c37bc1cbb3f3cdc7d6c13e0f27a859f14cdcfd5ea54a0467a88bc259b0b741'], + }), + ('XML::Filter::BufferText', '1.01', { + 'source_tmpl': 'XML-Filter-BufferText-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RB/RBERJON'], + 'checksums': ['8fd2126d3beec554df852919f4739e689202cbba6a17506e9b66ea165841a75c'], + }), + ('XML::SAX::Writer', '0.57', { + 'source_tmpl': 'XML-SAX-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + 'checksums': ['3d61d07ef43b0126f5b4de4f415a256fa859fa88dc4fdabaad70b7be7c682cf0'], + }), + ('Statistics::Descriptive', '3.0801', { + 'source_tmpl': 'Statistics-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['047b70a63fdcaa916168e0ff2d58e155e0ebbc68ed4ccbd73a7213dca3028f65'], + }), + ('Data::OptList', '0.114', { + 'source_tmpl': 'Data-OptList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9fd1093b917a21fb79ae1607db53d113b4e0ad8fe0ae776cb077a7e50044fdf3'], + }), + ('Class::Load', '0.25', { + 'source_tmpl': 'Class-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['2a48fa779b5297e56156380e8b32637c6c58decb4f4a7f3c7350523e11275f8f'], + }), + ('HTTP::Daemon', '6.16', { + 'source_tmpl': 'HTTP-Daemon-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['b38d092725e6fa4e0c4dc2a47e157070491bafa0dbe16c78a358e806aa7e173d'], + }), + ('Test::RequiresInternet', '0.05', { + 'source_tmpl': 'Test-RequiresInternet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MALLEN'], + 'checksums': ['bba7b32a1cc0d58ce2ec20b200a7347c69631641e8cae8ff4567ad24ef1e833e'], + }), + ('HTTP::Cookies', '6.10', { + 'source_tmpl': 'HTTP-Cookies-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['e36f36633c5ce6b5e4b876ffcf74787cc5efe0736dd7f487bdd73c14f0bd7007'], + }), + ('HTTP::CookieJar', '0.014', { + 'source_tmpl': 'HTTP-CookieJar-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['7094ea5c91f536d263b85e83ab4e9a963e11c4408ce08ecae553fa9c0cc47e73'], + }), + ('LWP::Simple', '6.72', { + 'source_tmpl': 'libwww-perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['e9b8354fd5e20be207afe23ddd584fcd59bf82998dc077decf684ba1dae5a05d'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + 'checksums': ['319601feec17fae344988a5ee91cfc6a0bcfe742af77dba254724c3268b2a60f'], + }), + ('Package::Stash::XS', '0.30', { + 'source_tmpl': 'Package-Stash-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['26bad65c1959c57379b3e139dc776fbec5f702906617ef27cdc293ddf1239231'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': ['b4e4740b8d4cb783591273c636bd68304892e28d89e88abf9273b1de17f552f7'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + 'checksums': ['d9f024c8e3637feccdebcf6479b6754b6c92f1209f567feaf0c23818af31ee3c'], + }), + ('boolean', '0.46', { + 'source_tmpl': 'boolean-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['95c088085c3e83bf680fe6ce16d8264ec26310490f7d1680e416ea7a118f156a'], + }), + ('Test::NoWarnings', '1.06', { + 'source_tmpl': 'Test-NoWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['c2dc51143b7eb63231210e27df20d2c8393772e0a333547ec8b7a205ed62f737'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + 'checksums': ['2db1ebb5837b4cb20051c0ee5b733b4453e3137df0a92306034c867621edd7e7'], + }), + ('XML::XPath', '1.48', { + 'source_tmpl': 'XML-XPath-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['7bc75be36b239e5b2e700a9570d2b53b43093d467f2abe6a743f9ff9093790cd'], + }), + ('JSON', '4.10', { + 'source_tmpl': 'JSON-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['df8b5143d9a7de99c47b55f1a170bd1f69f711935c186a6dc0ab56dd05758e35'], + }), + ('Sub::Exporter', '0.990', { + 'source_tmpl': 'Sub-Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['bc64ec5a06865f9cc676215c06a9448b3a0c8b3974ffb23a24f8e2ad090544fc'], + }), + ('Class::Load::XS', '0.10', { + 'source_tmpl': 'Class-Load-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['5bc22cf536ebfd2564c5bdaf42f0d8a4cee3d1930fc8b44b7d4a42038622add1'], + }), + ('Data::Types', '0.17', { + 'source_tmpl': 'Data-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['860751feb79b7dfc1af71c4b7fe920220ec6d31c4ab9402b8f178f7f4b8293c1'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + 'checksums': ['cfb1768c24f55208e87405b17f537f0f303fa141891d0b22d509a941aa57e24e'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + 'checksums': ['5b80b7d5e709d34393bcba88971864a17b44a5bf0f9e4bcee383d029e7d2d5c3'], + }), + ('Text::Balanced', '2.06', { + 'source_tmpl': 'Text-Balanced-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['773e0f0f21c0cb2cf664cee6ba28ff70259babcc892f9b650f9cbda00be092ad'], + }), + ('strictures', '2.000006', { + 'source_tmpl': 'strictures-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['09d57974a6d1b2380c802870fed471108f51170da81458e2751859f2714f8d57'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + 'checksums': ['31354975140fe6235ac130a109496491ad33dd42f9c62189e23f49f75f936d75'], + }), + ('File::Which', '1.27', { + 'source_tmpl': 'File-Which-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['3201f1a60e3f16484082e6045c896842261fc345de9fb2e620fd2a2c7af3a93a'], + }), + ('Error', '0.17029', { + 'source_tmpl': 'Error-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['1a23f7913032aed6d4b68321373a3899ca66590f4727391a091ec19c95bf7adc'], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + 'checksums': ['ff786008bf8c022064ececd3b7ed89c76b35e8d1eac6cf472a9f51771c1c9f2c'], + }), + ('Text::CSV', '2.03', { + 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + 'checksums': ['48bbce9f234935a88595618e04dd141628246d650f2a726024df1c137e0b65fb'], + }), + ('Test::Output', '1.034', { + 'source_tmpl': 'Test-Output-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['cd42e2801c0d2b482d18c9fb4b06c757054818bcbb2824e5dfbf33ad7a3d69a0'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['66fb417f8ff8a5e5b7ea25606156e70e204861c59fa8c3831925b4dd3f155f8a'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], + }), + ('Pod::Parser', '1.66', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], + 'checksums': ['22928a7bffe61b452c05bbbb8f5216d4b9cf9fe2a849b776c25500d24d20df7c'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + 'checksums': ['15a840ea1c8a76cd3c865fbbf2fec33b03615c0daa50f9c800c54e0cf0659d46'], + }), + ('XML::Twig', '3.52', { + 'source_tmpl': 'XML-Twig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + 'checksums': ['fef75826c24f2b877d0a0d2645212fc4fb9756ed4d2711614ac15c497e8680ad'], + }), + ('XML::Simple', '2.25', { + 'source_tmpl': 'XML-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + 'checksums': ['531fddaebea2416743eb5c4fdfab028f502123d9a220405a4100e68fc480dbf8'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + 'checksums': ['1bbfbf7d1d4871e5a83bab2137e22d089078206815190eb1d5c1260a3499456f'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['0b3035ffdb909aa1f7ded6b608fa9d894421c82c097d51e7171170d67579a9cb'], + }), + ('File::HomeDir', '1.006', { + 'source_tmpl': 'File-HomeDir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['593737c62df0f6dab5d4122e0b4476417945bb6262c33eedc009665ef1548852'], + }), + ('Authen::SASL', '2.1700', { + 'source_tmpl': 'Authen-SASL-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EH/EHUELS'], + 'checksums': ['b86d5a576b8d387aee24f39f47a54afd14bb66b09003db5065001f1de03a8ece'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['bd9e77a3fb662b40b43b18d3280cd352edf9fad8d94283e518181cc1ce9f0567'], + }), + ('DateTime::Tiny', '1.07', { + 'runtest': False, # One subset fails due to locale + 'source_tmpl': 'DateTime-Tiny-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['83568a22838cb518fbeb9e060460ec7f59d5a0b0a1cc06562954c3674d7cf7e4'], + }), + ('Text::Format', '0.62', { + 'source_tmpl': 'Text-Format-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + 'checksums': ['7d429057319e123c590ba0765334f0ade4a5eb9ea8db7c0ec4d3902de5f90404'], + }), + ('Devel::CheckCompiler', '0.07', { + 'source_tmpl': 'Devel-CheckCompiler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + 'checksums': ['768b7697b4b8d4d372c7507b65e9dd26aa4223f7100183bbb4d3af46d43869b5'], + }), + ('Log::Handler', '0.90', { + 'source_tmpl': 'Log-Handler-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + 'checksums': ['3a5c80e7128454770f83acab8cbd3e70e5ec3d59a61dc32792a178f0b31bf74d'], + }), + ('Term::ReadKey', '2.38', { + 'source_tmpl': 'TermReadKey-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + 'checksums': ['5a645878dc570ac33661581fbb090ff24ebce17d43ea53fd22e105a856a47290'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + 'checksums': ['11b7549b13ec5d87cc695dd4c777cd02983dd5fe9866012877fb530f48b3dfd0'], + }), + ('Module::Runtime::Conflicts', '0.003', { + 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], + }), + ('File::pushd', '1.016', { + 'source_tmpl': 'File-pushd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['d73a7f09442983b098260df3df7a832a5f660773a313ca273fa8b56665f97cdc'], + }), + ('Test::CleanNamespaces', '0.24', { + 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], + }), + ('Devel::OverloadInfo', '0.007', { + 'source_tmpl': 'Devel-OverloadInfo-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILMARI'], + 'checksums': ['21a184163b90f91f06ffc7f5de0b968356546ae9b400a9d75c573c958c246222'], + }), + ('Moose', '2.2206', { + 'source_tmpl': 'Moose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['67972c4e2bc39fbda38518177af0e67bbbeb548562e4ec4b759a1a7a583e505b'], + }), + ('Algorithm::Dependency', '1.112', { + 'source_tmpl': 'Algorithm-Dependency-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['7e0fb7c39f56a2dccf9d0295c82f3031ee116e807f6a12a438fa4dd41b0ec187'], + }), + ('Font::TTF', '1.06', { + 'source_tmpl': 'Font-TTF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BH/BHALLISSY'], + 'checksums': ['4b697d444259759ea02d2c442c9bffe5ffe14c9214084a01f743693a944cc293'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['3d81c3cc1b5cff69cca9361e2c6e38df0352251ae7b41e2ff3febc850e463565'], + }), + ('SQL::Statement', '1.414', { + 'source_tmpl': 'SQL-Statement-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + 'checksums': ['dde8bdcfa6a136eedda06519ba0f3efaec085c39db0df9c472dc0ec6cd781a49'], + }), + ('Package::Constants', '0.06', { + 'source_tmpl': 'Package-Constants-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['0b58be78706ccc4e4bd9bbad41767470427fd7b2cfad749489de101f85bc5df5'], + }), + ('CPANPLUS', '0.9914', { + 'source_tmpl': 'CPANPLUS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['76c3e5da623a4af60fe64adec448fb1f8e0cae9f6798a36b68865974044e9b67'], + }), + ('IO::Tty', '1.17', { + 'source_tmpl': 'IO-Tty-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['a5f1a83020bc5b5dd6c1b570f48c7546e0a8f7fac10a068740b03925ad9e14e8'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['f6dd55b4280b25dea978221839864382560074e1d6933395faee2510c2db60ed'], + }), + ('Mail::Util', '2.21', { + 'source_tmpl': 'MailTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['4ad9bd6826b6f03a2727332466b1b7d29890c8d99a32b4b3b0a8d926ee1a44cb'], + }), + ('Test::More::UTF8', '0.05', { + 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS'], + 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], + }), + ('Text::Template', '1.61', { + 'source_tmpl': 'Text-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSCHOUT'], + 'checksums': ['a295ea7d1ef241ae2640c1f7864b628f8e6f99ec14fb1da781b2f5f2168dcf09'], + }), + ('PadWalker', '2.5', { + 'source_tmpl': 'PadWalker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], + }), + ('Devel::Cycle', '1.12', { + 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS'], + 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], + }), + ('Test::Memory::Cycle', '1.06', { + 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], + }), + ('PDF::API2', '2.045', { + 'source_tmpl': 'PDF-API2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SS/SSIMMS'], + 'checksums': ['b6bdb4e0d0cd6526103fdd58c171e0560c36b843b7fe3ca4ddc9bb1e4c832406'], + }), + ('Devel::CheckLib', '1.16', { + 'source_tmpl': 'Devel-CheckLib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MATTN'], + 'checksums': ['869d38c258e646dcef676609f0dd7ca90f085f56cf6fd7001b019a5d5b831fca'], + }), + ('SVG', '2.87', { + 'source_tmpl': 'SVG-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + 'checksums': ['b3fa58c1c59942b4ebef003da97c3e01e531480ca29e8efbe327ff0589c0bd3c'], + }), + ('Statistics::Basic', '1.6611', { + 'source_tmpl': 'Statistics-Basic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JETTERO'], + 'checksums': ['6855ce5615fd3e1af4cfc451a9bf44ff29a3140b4e7130034f1f0af2511a94fb'], + }), + ('Log::Log4perl', '1.57', { + 'source_tmpl': 'Log-Log4perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['0f8fcb7638a8f3db4c797df94fdbc56013749142f2f94cbc95b43c9fca096a13'], + }), + ('Math::CDF', '0.1', { + 'source_tmpl': 'Math-CDF-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CALLAHAN'], + 'checksums': ['7896bf250835ce47dcc813cb8cf9dc576c5455de42e822dcd7d8d3fef2125565'], + }), + ('Array::Utils', '0.5', { + 'source_tmpl': 'Array-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZM/ZMIJ/Array'], + 'checksums': ['89dd1b7fcd9b4379492a3a77496e39fe6cd379b773fd03a6b160dd26ede63770'], + }), + ('File::Grep', '0.02', { + 'source_tmpl': 'File-Grep-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MN/MNEYLON'], + 'checksums': ['462e15274eb6278521407ea302d9eea7252cd44cab2382871f7de833d5f85632'], + }), + ('File::Temp', '0.2311', { + 'source_tmpl': 'File-Temp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['2290d61bf5c39882fc3311da9ce1c7f42dbdf825ae169e552c59fe4598b36f4a'], + }), + ('Set::Object', '1.42', { + 'source_tmpl': 'Set-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN'], + 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], + }), + ('Heap', '0.80', { + 'source_tmpl': 'Heap-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM'], + 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], + }), + ('Graph', '0.9727', { + 'source_tmpl': 'Graph-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['392a8916dc95131abe8c913dfcac7698484bf4866b42af5f7043c0062e742229'], + }), + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + ('Parse::Yapp', '1.21', { + 'source_tmpl': 'Parse-Yapp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WB/WBRASWELL'], + 'checksums': ['3810e998308fba2e0f4f26043035032b027ce51ce5c8a52a8b8e340ca65f13e5'], + }), + ('Graph::ReadWrite', '2.10', { + 'source_tmpl': 'Graph-ReadWrite-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['516c1ea9facb995dbc38d1735d58974b2399862567e731b729c8d0bc2ee5a14b'], + }), + ('PerlIO::utf8_strict', '0.010', { + 'source_tmpl': 'PerlIO-utf8_strict-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['bcd2848b72df290b5e984fae8b1a6ca96f6d072003cf222389a8c9e8e1c570cd'], + }), + ('Digest::MD5::File', '0.08', { + 'source_tmpl': 'Digest-MD5-File-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + 'checksums': ['adb43a54e32627b4f7e57c9640e6eb06d0bb79d8ea54cd0bd79ed35688fb1218'], + }), + ('String::RewritePrefix', '0.009', { + 'source_tmpl': 'String-RewritePrefix-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['44918bec96a54af8ca37ca897e436709ec284a07b28516ef3cce4666869646d5'], + }), + ('Getopt::Long::Descriptive', '0.111', { + 'source_tmpl': 'Getopt-Long-Descriptive-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['9b8d15fcaf18fdd740246b438f0e7eb914b831c51d9d708c099eca776622076d'], + }), + ('IO::TieCombine', '1.005', { + 'source_tmpl': 'IO-TieCombine-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['402d4db8300b3d271632f4995e0ade329d89280a7e47f2badf8b38af6e5569af'], + }), + ('App::Cmd', '0.336', { + 'source_tmpl': 'App-Cmd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['df966b57d59abb196e00304885e5bf117ca958182ae3f4eedf17218ea2838e81'], + }), + ('Carp::Clan', '6.08', { + 'source_tmpl': 'Carp-Clan-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['c75f92e34422cc5a65ab05d155842b701452434e9aefb649d6e2289c47ef6708'], + }), + ('Sub::Exporter::ForMethods', '0.100055', { + 'source_tmpl': 'Sub-Exporter-ForMethods-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['791f4203ba7c0f7d8380bc01bec20215f7c8bc70d7ed03e552eee44541abe94e'], + }), + ('MooseX::Types', '0.50', { + 'source_tmpl': 'MooseX-Types-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['9cd87b3492cbf0be9d2df9317b2adf9fc30663770e69906654bea3f41b17cb08'], + }), + ('Variable::Magic', '0.63', { + 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT'], + 'checksums': ['ba4083b2c31ff2694f2371333d554c826aaf24b4d98d03e48b5b4a43a2a0e679'], + }), + ('MooseX::Types::Perl', '0.101344', { + 'source_tmpl': 'MooseX-Types-Perl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['87644354f74fa65235cb2bfca44277930a7eabe51acc5f81fb631530a8355e24'], + }), + ('Log::Dispatch', '2.71', { + 'source_tmpl': 'Log-Dispatch-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['9d60d9648c35ce2754731eb4deb7f05809ece1bd633b74d74795aed9ec732570'], + }), + ('JSON::MaybeXS', '1.004005', { + 'source_tmpl': 'JSON-MaybeXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['f5b6bc19f579e66b7299f8748b8ac3e171936dc4e7fcb72a8a257a9bd482a331'], + }), + ('String::Flogger', '1.101246', { + 'source_tmpl': 'String-Flogger-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['15f8491e07818bb3cfa9f6bd3aabf6430ba9b4e309f18114358be3d81bff3a0f'], + }), + ('Log::Dispatch::Array', '1.005', { + 'source_tmpl': 'Log-Dispatch-Array-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['311640b7a967f8dd7c9bb41a227073565636d70df4fcc1d44fed8a8223b347ca'], + }), + ('Sub::Exporter::GlobExporter', '0.006', { + 'source_tmpl': 'Sub-Exporter-GlobExporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['de743f08026701c2a6a222a8b41c4cdc254b1a4afe7ef98987cd3aba4ce52696'], + }), + ('Log::Dispatchouli', '3.007', { + 'source_tmpl': 'Log-Dispatchouli-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['988118965952ba49a8fa791a6536880c89017f4eb9d72c1745ed67d15c0d272c'], + }), + ('Test::FailWarnings', '0.008', { + 'source_tmpl': 'Test-FailWarnings-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['da34ef9029f6849d6026201d49127d054ee6ac4b979c82210315f5721964a96f'], + }), + ('Data::Section', '0.200008', { + 'source_tmpl': 'Data-Section-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['83acc7a55d3dd7ed36e9d78d350af3138c69cfa178a44765822712ff433b990e'], + }), + ('Test::CheckDeps', '0.010', { + 'source_tmpl': 'Test-CheckDeps-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['66fccca6c6f330e7ecc898bd6a51846e2145b3e02d78c4997ba6b7de23b551ee'], + }), + ('Software::License', '0.104004', { + 'runtest': False, # This test just suddenly started to fail + 'source_tmpl': 'Software-License-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['a1fda24ec87752198097380fb9300c14b574826270cc580daf750e3585fc270c'], + }), + ('MooseX::SetOnce', '0.203', { + 'source_tmpl': 'MooseX-SetOnce-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['3cd2f3664e438382cf844b679350a2e428b760927e2cf18fccdc468a7bc3066f'], + }), + ('Term::Encoding', '0.03', { + 'source_tmpl': 'Term-Encoding-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['95ba9687d735d25a3cbe64508d7894f009c7fa2a1726c3e786e9e21da2251d0b'], + }), + ('Throwable', '1.001', { + 'source_tmpl': 'Throwable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['d0cb5e9d7d06d70f2cc56eecf857a83a45eaca43850dcdda91d3feb4ddde4c51'], + }), + ('Role::Identifiable::HasIdent', '0.009', { + 'source_tmpl': 'Role-Identifiable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5a735e9f7177f9ebae047eb7bae29b7ec29ec020ae37637aea5350d30c087b76'], + }), + ('MooseX::Role::Parameterized', '1.11', { + 'source_tmpl': 'MooseX-Role-Parameterized-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['1cfe766c5d7f0ecab57f733dcca430a2a2acd6b995757141b940ade3692bec9e'], + }), + ('MooseX::OneArgNew', '0.007', { + 'source_tmpl': 'MooseX-OneArgNew-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['84282435f1169cf09d7513fa9387e2091791635cf35a078b500b829aeea06138'], + }), + ('MooseX::LazyRequire', '0.11', { + 'source_tmpl': 'MooseX-LazyRequire-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['ef620c1e019daf9cf3f23a943d25a94c91e93ab312bcd63be2e9740ec0b94288'], + }), + ('String::Formatter', '1.235', { + 'source_tmpl': 'String-Formatter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['08236a913b911ce652cf08598e7c07d2df3f369fc47bf401a485a504a1660783'], + }), + ('String::Errf', '0.009', { + 'source_tmpl': 'String-Errf-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['e1fedbf9b4fd64b64ea81038ddb76a4c6cd85f5db15bc21f10656a298349dc1f'], + }), + ('Role::HasMessage', '0.007', { + 'source_tmpl': 'Role-HasMessage-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['5e267a4d7620b368481204c88ea2044b8b2a58ff8b05577f2717b2754c0414ce'], + }), + ('Config::MVP', '2.200013', { + 'source_tmpl': 'Config-MVP-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['018d161623ee3a67f860d9e680e22e61b79eae6018f0e7c3b525fc934f5b7d45'], + }), + ('Mixin::Linewise::Readers', '0.111', { + 'source_tmpl': 'Mixin-Linewise-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['d28e88516ce9b5295c31631dcccdc0fc8f2ab7d8a5cc876bb1b20131087b01db'], + }), + ('Config::INI', '0.029', { + 'source_tmpl': 'Config-INI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['0bbe797a730210644a907d90cd4aa2b23ad580cb27bd39393bfc6a7ef9fdfdea'], + }), + ('String::Truncate', '1.100603', { + 'source_tmpl': 'String-Truncate-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['ab45602cce2dd9515edfbb2e6e5cde19cdd5498d61a23afd8c46c1f11f8eec62'], + }), + ('Pod::Eventual', '0.094003', { + 'source_tmpl': 'Pod-Eventual-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['7f060cc34d11656ce069db061e3d60edc0cabc8f89a4a2dc7eaae95dac856d2d'], + }), + ('Pod::Elemental', '0.103006', { + 'source_tmpl': 'Pod-Elemental-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['750c3a79d8e1824758a6ef7d2dd077dcddca503542b8c34eccd5acbb779dc423'], + }), + ('Test::Object', '0.08', { + 'source_tmpl': 'Test-Object-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['65278964147837313f4108e55b59676e8a364d6edf01b3dc198aee894ab1d0bb'], + }), + ('Hook::LexWrap', '0.26', { + 'source_tmpl': 'Hook-LexWrap-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b60bdc5f98f94f9294b06adef82b1d996da192d5f183f9f434b610fd1137ec2d'], + }), + ('Test::SubCalls', '1.10', { + 'source_tmpl': 'Test-SubCalls-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['cbc1e9b35a05e71febc13e5ef547a31c8249899bb6011dbdc9d9ff366ddab6c2'], + }), + ('PPI', '1.277', { + 'source_tmpl': 'PPI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MITHALDU'], + 'checksums': ['87c79f83b6876e206051965d5019d2507c551f819a86750080ec7ec43b2e0af8'], + }), + ('Config::MVP::Reader::INI', '2.101465', { + 'source_tmpl': 'Config-MVP-Reader-INI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['13c7aa27c1df98cd33ada399e59ff38fabfa9d65513e42af02f72c2d3f636247'], + }), + ('Pod::Weaver', '4.019', { + 'source_tmpl': 'Pod-Weaver-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['6946ad1f04eaf9aa11f24cc54494e1d57962f58e05912f364b74f9593e7de7f7'], + }), + ('CPAN::Uploader', '0.103018', { + 'source_tmpl': 'CPAN-Uploader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['c4ffe4ede9db79b396e3bfc5e7cdf0e2e9821e1f1e087f523bcfa74c9fc9e248'], + }), + ('Devel::FindPerl', '0.016', { + 'source_tmpl': 'Devel-FindPerl-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['43a2bf2f787a3f1b881179063162b2aa3e7cb044f6e5e76ec6466ae90a861138'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), + ('Perl::PrereqScanner', '1.100', { + 'source_tmpl': 'Perl-PrereqScanner-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['01181d38a2e7aff838d262122563c50636ba4b3652ee5d1d4f8ef5ba3f5b186b'], + }), + ('Dist::Zilla', '6.030', { + 'source_tmpl': 'Dist-Zilla-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['c406bbe6809e94edb70ca94324c301433d6c8a3dfbe70b02df12e1dff2f3b130'], + }), + ('XML::RegExp', '0.04', { + 'source_tmpl': 'XML-RegExp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'], + 'checksums': ['df1990096036085c8e2d45904fe180f82bfed40f1a7e05243f334ea10090fc54'], + }), + ('XML::DOM', '1.46', { + 'source_tmpl': 'XML-DOM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJMATHER'], + 'checksums': ['8ba24b0b459b01d6c5e5b0408829c7d5dfe47ff79b3548c813759048099b175e'], + }), + ('Data::Dump', '1.25', { + 'source_tmpl': 'Data-Dump-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + 'checksums': ['a4aa6e0ddbf39d5ad49bddfe0f89d9da864e3bc00f627125d1bc580472f53fbd'], + }), + ('File::Next', '1.18', { + 'source_tmpl': 'File-Next-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + 'checksums': ['f900cb39505eb6e168a9ca51a10b73f1bbde1914b923a09ecd72d9c02e6ec2ef'], + }), + ('App::cpanminus', '1.7047', { + 'source_tmpl': 'App-cpanminus-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + 'checksums': ['963e63c6e1a8725ff2f624e9086396ae150db51dd0a337c3781d09a994af05a5'], + }), + ('Parallel::ForkManager', '2.02', { + 'source_tmpl': 'Parallel-ForkManager-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Y/YA/YANICK'], + 'checksums': ['c1b2970a8bb666c3de7caac4a8f4dbcc043ab819bbc337692ec7bf27adae4404'], + }), + ('Object::InsideOut', '4.05', { + 'source_tmpl': 'Object-InsideOut-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], + }), + ('Logger::Simple', '2.0', { + 'source_tmpl': 'Logger-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TS/TSTANLEY'], + 'checksums': ['2e63fd3508775b5902132ba1bfb03b42bee468dfaf35dfe42e1909ff6d291b2d'], + }), + ('Scalar::Util::Numeric', '0.40', { + 'source_tmpl': 'Scalar-Util-Numeric-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], + 'checksums': ['d7501b6d410703db5b1c1942fbfc41af8964a35525d7f766058acf5ca2cc4440'], + }), + ('Spiffy', '0.46', { + 'source_tmpl': 'Spiffy-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['8f58620a8420255c49b6c43c5ff5802bd25e4f09240c51e5bf2b022833d41da3'], + }), + ('Test::Base', '0.89', { + 'source_tmpl': 'Test-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['2794a1aaaeb1d3a287dd2c7286258663796562f7db9ccc6b424bc4f1de8ad014'], + }), + ('Test::YAML', '1.07', { + 'source_tmpl': 'Test-YAML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TINITA'], + 'checksums': ['1f300d034f46298cb92960912cc04bac33fb27f05b8852d8f051e110b9cd995f'], + }), + ('YAML', '1.30', { + 'source_tmpl': 'YAML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TINITA'], + 'checksums': ['5030a6d6cbffaf12583050bf552aa800d4646ca9678c187add649227f57479cd'], + }), + ('Object::InsideOut', '4.05', { + 'source_tmpl': 'Object-InsideOut-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], + }), + ('Time::HiRes', '1.9764', { + 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], + 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], + }), + ('Term::ReadLine::Gnu', '1.46', { + 'modulename': 'Term::ReadLine', + 'source_tmpl': 'Term-ReadLine-Gnu-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAYASHI'], + 'checksums': ['b13832132e50366c34feac12ce82837c0a9db34ca530ae5d27db97cf9c964c7b'], + }), + ('ExtUtils::MakeMaker', '7.70', { + 'source_tmpl': 'ExtUtils-MakeMaker-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['f108bd46420d2f00d242825f865b0f68851084924924f92261d684c49e3e7a74'], + }), + ('Scalar::Util', '1.63', { + 'source_tmpl': 'Scalar-List-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['cafbdf212f6827dc9a0dd3b57b6ee50e860586d7198228a33262d55c559eb2a9'], + }), + ('Module::CoreList', '5.20230920', { + 'source_tmpl': 'Module-CoreList-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['c3099fb0ca3cfbc996e99ac2c7f3a3d1e8156bde3b43d9374f4eedaeda275005'], + }), + ('Module::Metadata', '1.000038', { + 'source_tmpl': 'Module-Metadata-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + 'checksums': ['b599d8770a9a9fa0a8ae3cd0ed395a9cf71b4eb53aed82989a6bece33485a9cd'], + }), + ('Params::Check', '0.38', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Params-Check-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['f0c9d33876c36b1bca1475276d26d2efaf449b256d7cc8118fae012e89a26290'], + }), + ('Locale::Maketext::Simple', '0.21', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Locale-Maketext-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], + 'checksums': ['b009ff51f4fb108d19961a523e99b4373ccf958d37ca35bf1583215908dca9a9'], + }), + ('Perl::OSType', '1.010', { + 'source_tmpl': 'Perl-OSType-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['e7ed4994b5d547cb23aadb84dc6044c5eb085d5a67a6c5624f42542edd3403b2'], + }), + ('IPC::Cmd', '1.04', { + 'source_tmpl': 'IPC-Cmd-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['d110a0f60e35c65721454200f0d2f0f8965529a2add9649d1fa6f4f9eccb6430'], + }), + ('Pod::Escapes', '1.07', { + 'source_tmpl': 'Pod-Escapes-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['dbf7c827984951fb248907f940fd8f19f2696bc5545c0a15287e0fbe56a52308'], + }), + ('if', '0.0608', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'modulename': False, + 'source_tmpl': 'if-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['37206e10919c4d99273020008a3581bf0947d364e859b8966521c3145b4b3700'], + }), + ('Test', '1.26', { + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'source_tmpl': 'Test-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JE/JESSE'], + 'checksums': ['f7701bd28e05e7f82fe9a181bbab38f53fa6aeae48d2a810da74d1b981d4f392'], + }), + ('ExtUtils::Constant', '0.25', { + 'runtest': False, # Somehow has syntax errors in tests + 'source_tmpl': 'ExtUtils-Constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['6933d0e963b62281ef7561068e6aecac8c4ac2b476b2bba09ab0b90fbac9d757'], + }), + ('ExtUtils::CBuilder', '0.280236', { + 'source_tmpl': 'ExtUtils-CBuilder-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AM/AMBS'], + 'checksums': ['abc21827eb8a513171bf7fdecefce9945132cb76db945036518291f607b1491f'], + }), + ('Carp::Heavy', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('Pod::Simple', '3.45', { + 'source_tmpl': 'Pod-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KH/KHW'], + 'checksums': ['8483bb95cd3e4307d66def092a3779f843af772482bfdc024e3e00d0c4db0cfa'], + }), + ('Socket', '2.037', { + 'source_tmpl': 'Socket-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + 'checksums': ['85448811e9e274374404634f3c208afa936ee4d223e76251ea9868315b0c812f'], + }), + ('Time::Local', '1.35', { + 'source_tmpl': 'Time-Local-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + 'checksums': ['1d136b71bd041cbe6f66c43180ee79e675b72ad5a3596abd6a44d211072ada29'], + }), + ('Storable', '3.25', { + 'source_tmpl': 'Storable-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['e1e96b24a076792fde52154789fe4b76034b9ad39c8a1a819ead77d50d5f1817'], + }), + ('ExtUtils::ParseXS', '3.51', { + 'source_tmpl': 'ExtUtils-ParseXS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + 'checksums': ['82431a57425d78682acefb3a2cc9287683d091c8d034b825c584d9805bed6535'], + }), + ('Pod::Man', '5.01', { + 'source_tmpl': 'podlators-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RR/RRA'], + 'checksums': ['ccfd1df9f1a47f095bce6d718fad5af40f78ce2491f2c7239626e15b7020bc71'], + }), + ('Mozilla::CA', '20230821', { + 'source_tmpl': 'Mozilla-CA-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LW/LWP'], + 'checksums': ['32e1d0045299004045b9c4d16c2daae453a216208873deea2440f71260a7cda1'], + }), + ('LWP::Protocol::https', '6.11', { + 'source_tmpl': 'LWP-Protocol-https-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OA/OALDERS'], + 'checksums': ['0132ddbf03661565ca85050f2a5094fb9263cbbc3ccb1a4d9c41ac9bb083b917'], + }), + ('Module::Load', '0.36', { + 'source_tmpl': 'Module-Load-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['d825020ac00b220e89f9524e24d838f9438b072fcae8c91938e4026677bef6e0'], + }), + ('Module::Load::Conditional', '0.74', { + 'source_tmpl': 'Module-Load-Conditional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + 'checksums': ['54c354a9393820f1ebc2a095da084ea0392dcbccb0cb38a187a71831cc60a730'], + }), + ('parent', '0.241', { + 'source_tmpl': 'parent-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION'], + 'checksums': ['b10b3960ab3997dab7571ffe975ba462d979d086450740a1e08b3959e75128fe'], + }), + ('Net::Domain', '3.15', { + 'source_tmpl': 'libnet-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + 'checksums': ['a71f4db580e1a767d6936faa5baf38f1fa617824342da078b561283e86f8f4a2'], + }), + ('Encode', '3.19', { + 'source_tmpl': 'Encode-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DANKOGAI'], + 'checksums': ['9163f848eef69e4d4cc8838397f0861fd9ea7ede001117dbd9694f8d95052ef5'], + }), + ('Cwd', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('MIME::Base64', '3.16', { + 'source_tmpl': 'MIME-Base64-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CA/CAPOEIRAB'], + 'checksums': ['77f73d6f7aeb8d33be08b0d8c2617f9b6c77fb7fc45422d507ca8bafe4246017'], + }), + ('ExtUtils::CppGuess', '0.26', { + 'runtest': False, # Poorly written test + 'source_tmpl': 'ExtUtils-CppGuess-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETJ'], + 'checksums': ['c8b362b860172a4076acee00438f52b86464f2c500702cfcf7527811ff9a683e'], + }), + ('XSLoader', '0.24', { + 'source_tmpl': 'XSLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAPER'], + 'checksums': ['e819a35a6b8e55cb61b290159861f0dc00fe9d8c4f54578eb24f612d45c8d85f'], + }), + ('AutoLoader', '5.74', { + 'source_tmpl': 'AutoLoader-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + 'checksums': ['2fac75b05309f71a6871804cd25e1a3ba0a28f43f294fb54528077558da3aff4'], + }), + ('Set::IntervalTree', '0.12', { + 'source_tmpl': 'Set-IntervalTree-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SL/SLOYD'], + 'checksums': ['6fd4000e4022968e2ce5b83c07b189219ef1925ecb72977b52a6f7d76adbc349'], + }), + ('MCE::Mutex', '1.889', { + 'runtest': False, # Single failing subtest + 'source_tmpl': 'MCE-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARIOROY'], + 'checksums': ['db6153e474d046fc253050bf53c54002d84cd4ca77d21c2b9df56feeb809bbed'], + }), + ('Text::CSV_XS', '1.52', { + 'source_tmpl': 'Text-CSV_XS-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['e415aa705badf84b359dc4c0f0c982f1bf708481daa14756f3136e7c89c0e41d'], + }), + ('DBD::CSV', '0.60', { + 'source_tmpl': 'DBD-CSV-%(version)s.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HM/HMBRAND'], + 'checksums': ['018b83a30f799979bc8c3c3044c8b1c8001cdf60bdc3e746848818195254b4e7'], + }), + ('Array::Transpose', '0.06', { + 'source_tmpl': 'Array-Transpose-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MR/MRDVT'], + 'checksums': ['d58667f64381a105f375226f592d0af71068e640a5a9f4d5ecf27c90feb32676'], + }), + ('Config::Simple', '4.58', { + 'source_tmpl': 'Config-Simple-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHERZODR'], + 'checksums': ['dd9995706f0f9384a15ccffe116c3b6e22f42ba2e58d8f24ed03c4a0e386edb4'], + }), + ('Business::ISBN::Data', '20231013.001', { + 'source_tmpl': 'Business-ISBN-Data-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['749371a46882a3ff9fb640295cc781d3b0ad6ef7d657a52257b14fbf5b2253b4'], + }), + ('Business::ISBN', '3.008', { + 'source_tmpl': 'Business-ISBN-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + 'checksums': ['19c4a1d4d99a0dd7695a90192b13404a0e3eeebedfcbe97a0202e36b238c0e69'], + }), + ('common::sense', '3.75', { + 'source_tmpl': 'common-sense-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['a86a1c4ca4f3006d7479064425a09fa5b6689e57261fcb994fe67d061cba0e7e'], + }), + ('Compress::Raw::Zlib', '2.206', { + 'source_tmpl': 'Compress-Raw-Zlib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['46785a6a383a1c843895b7f9f25d5d759e7c305159f9d1e04a3604eb74c77374'], + }), + ('IO::Compress::Zip', '2.206', { + 'runtest': False, # Problem with indirect dependency DBD::Pg + 'source_tmpl': 'IO-Compress-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PM/PMQS'], + 'checksums': ['7d3062b9a494f757e8d0614f220d83f22731bbda1aeb5f7cff0e72a83f433d35'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('JSON::XS', '4.03', { + 'source_tmpl': 'JSON-XS-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['515536f45f2fa1a7e88c8824533758d0121d267ab9cb453a1b5887c8a56b9068'], + }), + ('Authen::NTLM', '1.09', { + 'source_tmpl': 'NTLM-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NB/NBEBOUT'], + 'checksums': ['c823e30cda76bc15636e584302c960e2b5eeef9517c2448f7454498893151f85'], + }), + ('Types::Serialiser', '1.01', { + 'source_tmpl': 'Types-Serialiser-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + 'checksums': ['f8c7173b0914d0e3d957282077b366f0c8c70256715eaef3298ff32b92388a80'], + }), + ('XML::SAX::Expat', '0.51', { + 'source_tmpl': 'XML-SAX-Expat-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BJ/BJOERN'], + 'checksums': ['4c016213d0ce7db2c494e30086b59917b302db8c292dcd21f39deebd9780c83f'], + }), + ('Inline', '0.86', { + 'source_tmpl': 'Inline-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + 'checksums': ['510a7de2d011b0db80b0874e8c0f7390010991000ae135cff7474df1e6d51e3a'], + }), + ('Test::Sys::Info', '0.23', { + 'source_tmpl': 'Test-Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['30c5f2c4cfee8e1ae6d9fb6291f79addbff5739ba4efa5b1e034520f18fbc95a'], + }), + ('Sys::Info::Base', '0.7807', { + 'source_tmpl': 'Sys-Info-Base-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['132362b0046e8dc4f12e1560903623a88a8871d09bf1c29d93d48d3f4a582acb'], + }), + ('Sys::Info::Driver::Unknown::Device::CPU', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('Sys::Info::Driver::Linux::Device::CPU', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Sys::Info', '0.7811', { + 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['566482bff3427c198d7955468ed945a8e736c4a2925151fdef96801ef8a401e1'], + }), + ('CGI', '4.59', { + 'source_tmpl': 'CGI-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO'], + 'checksums': ['6dee4b89b88b10e77c96f3c08d19b586aef833b17a425d618aad7d28c262f91c'], + }), + ('HTML::Template', '2.97', { + 'source_tmpl': 'HTML-Template-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SAMTREGAR'], + 'checksums': ['6547af61f3aa85793f8616190938d677d7995fb3b720c16258040bc935e2129f'], + }), + ('MIME::Charset', 'v1.013.1', { + 'source_tmpl': 'MIME-Charset-1.013.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'], + 'checksums': ['1bb7a6e0c0d251f23d6e60bf84c9adefc5b74eec58475bfee4d39107e60870f0'], + }), + ('Unicode::LineBreak', '2019.001', { + 'source_tmpl': 'Unicode-LineBreak-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEZUMI'], + 'checksums': ['486762e4cacddcc77b13989f979a029f84630b8175e7fef17989e157d4b6318a'], + }), + ('String::Print', '0.94', { + 'source_tmpl': 'String-Print-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['9b3cd677adb7a40cb183bd6c60db80d96adcabd5aae27e324e3ee37e3275229b'], + }), + ('Log::Report::Optional', '1.07', { + 'source_tmpl': 'Log-Report-Optional-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['b2658b53176df5afa5d02789368715c86b98c8d04ecd930252bcd7f832cc6224'], + }), + ('Log::Report', '1.34', { + 'source_tmpl': 'Log-Report-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + 'checksums': ['1faeb18993ab8796dce4cccda2ec912f8f565aa0258026f88197aa0fe3004a78'], + }), + ('Sys::Info::Driver::Unknown', '0.79', { + 'source_tmpl': 'Sys-Info-Driver-Unknown-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['02408843c8e36ea3d507e9f33fee48d6908543829ebe320f13d1bfe76af31e09'], + }), + ('Sys::Info::Driver::Linux', '0.7905', { + 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], + 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + }), + ('Unix::Processors', '2.046', { + 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WS/WSNYDER'], + 'checksums': ['3973ebdc44682c9c15c776f66e8be242cb4ff1dd52caf43ff446b74d4dccca06'], + }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), + ('Module::Path', '0.19', { + 'source_tmpl': 'Module-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + 'checksums': ['b33179ce4dd73dfcde7d46808804b9ffbb11db0245fe455a7d001747562feaca'], + }), + ('Devel::Size', '0.83', { + 'source_tmpl': 'Devel-Size-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK'], + 'checksums': ['757a67e0aa59ae103ea5ca092cbecc025644ebdc326731688ffab6f8823ef4b3'], + }), + ('Math::Utils', '1.14', { + 'source_tmpl': 'Math-Utils-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE'], + 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], + }), +] + +moduleclass = 'lang' From e28901d867a7df20e07de1191a49fc2fe2917b60 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 19 Oct 2023 00:07:55 +0200 Subject: [PATCH 9155/9987] Drop MKL_ILP64 --- .../easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb index 19a155367dd..6f1484e887f 100644 --- a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023a-CUDA-12.1.1.eb @@ -32,8 +32,7 @@ cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] # make sure both static and shared libs are built configopts = [ - '-DMKL_ILP64=ON \ - -DBUILD_SHARED_LIBS=%s \ + '-DBUILD_SHARED_LIBS=%s \ -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') ] From 289b2be272d8fdfc1dd0994b26b3e5249f46461c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 19 Oct 2023 01:07:30 +0200 Subject: [PATCH 9156/9987] adding easyconfigs: patchelf-0.18.0-GCCcore-13.2.0.eb, Ninja-1.11.1-GCCcore-13.2.0.eb, git-2.42.0-GCCcore-13.2.0.eb --- .../g/git/git-2.42.0-GCCcore-13.2.0.eb | 42 +++++++++++++++++++ .../n/Ninja/Ninja-1.11.1-GCCcore-13.2.0.eb | 31 ++++++++++++++ .../patchelf-0.18.0-GCCcore-13.2.0.eb | 29 +++++++++++++ 3 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.42.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/git/git-2.42.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/git/git-2.42.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..05e36521107 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.42.0-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.42.0' + +homepage = 'https://git-scm.com' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['60c06eb7ce840903169ed4872224b2409dd8d8a518e9df847c6dc0ef10d35d99'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('cURL', '8.3.0'), + ('expat', '2.5.0'), + ('gettext', '0.22'), + ('Perl', '5.38.0'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +postinstallcmds = ['cd contrib/subtree; make install'] + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['libexec/git-core', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..47d0bd6318d --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.11.1' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['31747ae633213f1eda3842686f83c2aa1412e0f5691d1c14dbbcc67fe7400cea'] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.5'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +sanity_check_commands = ["ninja --version"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..62d26c800db --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.18.0-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.18.0' + +homepage = 'https://github.com/NixOS/patchelf' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1451d01ee3a21100340aed867d0b799f46f0b1749680028d38c3f5d0128fb8a7'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +sanity_check_commands = ["patchelf --help"] + +moduleclass = 'tools' From 62c35e39ffe670a17cacfe7bf796d21ce2e7432f Mon Sep 17 00:00:00 2001 From: swbuild Date: Thu, 19 Oct 2023 09:08:04 +0200 Subject: [PATCH 9157/9987] emcee-3.1.4-foss-2022a: added Python as explicit dependency --- easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb b/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb index d25d7cd92c5..2aa3fa0cb9d 100644 --- a/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb +++ b/easybuild/easyconfigs/e/emcee/emcee-3.1.4-foss-2022a.eb @@ -14,6 +14,7 @@ sources = [SOURCE_TAR_GZ] checksums = ['8e0e19dc8bcef9c6d02f860bef8ddc6c876b8878a6ce666943e2c5cfd9317fed'] dependencies = [ + ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ] @@ -23,7 +24,7 @@ sanity_pip_check = True sanity_check_paths = { 'files': [], - 'dirs': ['lib/python3.10/site-packages/emcee'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/emcee'], } sanity_check_commands = [('pytest')] From a4762bd9e0b26a5c741ad67d5ec92c7f7a5b61cc Mon Sep 17 00:00:00 2001 From: swbuild Date: Thu, 19 Oct 2023 09:22:40 +0200 Subject: [PATCH 9158/9987] zeus-mcmc-2.5.4-foss-2022a: remove default options --- .../easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb b/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb index 4219c090114..c44dbad69ea 100644 --- a/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb +++ b/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb @@ -17,8 +17,8 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True -exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} exts_list = [ ('seaborn', '0.12.2', { 'checksums': ['374645f36509d0dcab895cba5b47daf0586f77bfe3b36c97c607db7da5be0139'], @@ -29,6 +29,4 @@ exts_list = [ }), ] -sanity_pip_check = True - moduleclass = 'lib' From 42d02016a8c124f81998ac08bcc9c0b74cce1bff Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Thu, 19 Oct 2023 09:38:46 +0200 Subject: [PATCH 9159/9987] Move ASE from foss/2023a tol gfbf/2023a --- ...foss-2023a.eb => ASE-3.22.1-gfbf-2023a.eb} | 33 ++++++++++--------- 1 file changed, 17 insertions(+), 16 deletions(-) rename easybuild/easyconfigs/a/ASE/{ASE-3.22.1-foss-2023a.eb => ASE-3.22.1-gfbf-2023a.eb} (54%) diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2023a.eb similarity index 54% rename from easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb rename to easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2023a.eb index c57e53c9b12..d63319385b2 100644 --- a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-foss-2023a.eb +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2023a.eb @@ -10,25 +10,24 @@ description = """ASE is a python package providing an open source Atomic Simulat From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed.""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} dependencies = [ ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), ('SciPy-bundle', '2023.07'), ('Flask', '2.3.3'), ('matplotlib', '3.7.2'), - ('Tkinter', '3.11.3'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE ('spglib-python', '2.1.0'), # optional ] -sanity_pip_check = True use_pip = True +sanity_pip_check = True exts_list = [ ('pytest-mock', '3.11.1', { - 'checksums': [ - '7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f', - ] + 'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'], }), ('ase', version, { 'patches': [ @@ -38,22 +37,24 @@ exts_list = [ 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', ], 'checksums': [ - '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432', - '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac', - '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601', - 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8', - '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d', - ] + {'ase-3.22.1.tar.gz': '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'}, + {'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch': + '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac'}, + {'ASE-3.22.1-Compatibility-with-pytest-part-2.patch': + '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601'}, + {'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch': + 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8'}, + {'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch': + '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d'}, + ], }), ('ase-ext', '20.9.0', { - 'checksums': [ - 'a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed', - ] + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], }), ] sanity_check_paths = { - 'files': ['bin/%(namelower)s'], + 'files': ['bin/ase'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From 7d0cdf63e8af1a9fbc6315b0b320569b0e2340c9 Mon Sep 17 00:00:00 2001 From: jose_d Date: Thu, 19 Oct 2023 10:52:51 +0200 Subject: [PATCH 9160/9987] Update zeus-mcmc-2.5.4-foss-2022a.eb: change module class to math (zeus-)MCMC is statistical sampling method, so use of moduleclass `math` seems to be more descriptive than generic `lib` --- easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb b/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb index c44dbad69ea..9c6041c0fa5 100644 --- a/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb +++ b/easybuild/easyconfigs/z/zeus-mcmc/zeus-mcmc-2.5.4-foss-2022a.eb @@ -29,4 +29,4 @@ exts_list = [ }), ] -moduleclass = 'lib' +moduleclass = 'math' From d9de7ea896d1778c28ad1f6e825a2c457bb32ca7 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Thu, 19 Oct 2023 17:11:51 +0200 Subject: [PATCH 9161/9987] Add GSL dependency to casacore --- easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index e8fcac3e1ba..b79e3079b70 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -34,6 +34,7 @@ dependencies = [ ('CFITSIO', '4.2.0'), ('WCSLIB', '7.11'), ('HDF5', '1.12.2'), + ('GSL', '2.7'), ('Boost.Python', '1.79.0'), ('SciPy-bundle', '2022.05'), ('ncurses', '6.3'), From 59855e4b0f52fbea232426bddb90bf45cd8d871d Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Thu, 19 Oct 2023 17:23:02 +0200 Subject: [PATCH 9162/9987] Adding missing GSL dependency to casacore-3.4.0-foss-2021b --- easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb index aab5e755fdf..ad0813959d7 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb @@ -31,6 +31,7 @@ dependencies = [ ('CFITSIO', '3.49'), ('WCSLIB', '7.11'), ('HDF5', '1.12.1'), + ('GSL', '2.7'), ('SciPy-bundle', '2021.10'), ('Boost.Python', '1.77.0'), ('ncurses', '6.2'), From 4c76400540772f523ed5e9596f46df589369977f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 19 Oct 2023 19:28:28 +0200 Subject: [PATCH 9163/9987] adding easyconfigs: OSU-Micro-Benchmarks-6.2-iimpi-2022b.eb --- .../OSU-Micro-Benchmarks-6.2-iimpi-2022b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-iimpi-2022b.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-iimpi-2022b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-iimpi-2022b.eb new file mode 100644 index 00000000000..86e06d2c7fa --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-iimpi-2022b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '6.2' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpi', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb9dbc87dcf8ec6785977a61f6fceee8febf1a682488eaab4c58cf50e4fa985f'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 2142226aa670549524d319241ff896bd04617843 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 19 Oct 2023 19:42:33 +0200 Subject: [PATCH 9164/9987] adding easyconfigs: OSU-Micro-Benchmarks-6.2-gompi-2022b-CUDA-12.0.0.eb --- ...-Benchmarks-6.2-gompi-2022b-CUDA-12.0.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b-CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b-CUDA-12.0.0.eb new file mode 100644 index 00000000000..da73373cc24 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b-CUDA-12.0.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '6.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb9dbc87dcf8ec6785977a61f6fceee8febf1a682488eaab4c58cf50e4fa985f'] + +dependencies = [ + ('CUDA', '12.0.0', '', SYSTEM), + ('NCCL', '2.16.2', versionsuffix), + ('UCX-CUDA', '1.13.1', versionsuffix), + ('UCC-CUDA', '1.1.0', versionsuffix), +] + +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA --enable-ncclomb --with-nccl=$EBROOTNCCL' + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] + [ + 'libexec/osu-micro-benchmarks/nccl/%s' % x for x in ['collective', 'pt2pt'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 87d79958e4db27757c1091168984b2c609893165 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 19 Oct 2023 18:15:02 +0000 Subject: [PATCH 9165/9987] Build Qt5 with Python 3 instead of 2 --- .../q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb | 14 +- ....10_webengine-chromium-drop-catapult.patch | 489 +++++ ...5-5.15.10_webengine-chromium-python3.patch | 1883 +++++++++++++++++ .../Qt5-5.15.10_webengine-drop-catapult.patch | 32 + .../Qt5-5.15.10_webengine-python3.11.patch | 46 + .../q/Qt5/Qt5-5.15.10_webengine-python3.patch | 176 ++ 6 files changed, 2639 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-chromium-drop-catapult.patch create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-chromium-python3.patch create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-drop-catapult.patch create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-python3.11.patch create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-python3.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb index 7897dbe6736..53c92a6b3ea 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10-GCCcore-12.3.0.eb @@ -22,6 +22,11 @@ patches = [ 'Qt5-5.15.10_fix-OF-Gentoo.patch', 'Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch', 'Qt5-5.15.7_GCC-12.patch', + 'Qt5-5.15.10_webengine-chromium-drop-catapult.patch', + 'Qt5-5.15.10_webengine-chromium-python3.patch', + 'Qt5-5.15.10_webengine-drop-catapult.patch', + 'Qt5-5.15.10_webengine-python3.patch', + 'Qt5-5.15.10_webengine-python3.11.patch', ] checksums = [ {'qt-everywhere-opensource-src-5.15.10.tar.xz': 'b545cb83c60934adc9a6bbd27e2af79e5013de77d46f5b9f5bb2a3c762bf55ca'}, @@ -31,6 +36,13 @@ checksums = [ {'Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch': '3b536de3b2da9115d96323a00275fc6066bb048f3747f8e6971facd78ed4e2e2'}, {'Qt5-5.15.7_GCC-12.patch': '9a5bde91b223a3e2e90d3d6bec107af69a1a0f18d789593738a953080473fa68'}, + {'Qt5-5.15.10_webengine-chromium-drop-catapult.patch': + '6325c6f63b144755fcf040614178923406d7526517d58b29d99b100919acec54'}, + {'Qt5-5.15.10_webengine-chromium-python3.patch': + '128d58c1e83f551daec6e9122fc1cea07be76b79d4e99222969649be24334e1e'}, + {'Qt5-5.15.10_webengine-drop-catapult.patch': '7a488a0d73b7a9f33a2bdb87996f0a16938f5f882385190833679d1d17684907'}, + {'Qt5-5.15.10_webengine-python3.patch': '0e35606506cb218841e05d38214ec6a442f7481630c2d856a09b7863af304023'}, + {'Qt5-5.15.10_webengine-python3.11.patch': '8486fc234de2cdf8a600b204bac5d8eb2bc0bc9b1b1d365505f801c4a201f9c3'}, ] builddependencies = [ @@ -41,7 +53,7 @@ builddependencies = [ ('flex', '2.6.4'), ('gperf', '3.1'), ('Ninja', '1.11.1'), - ('Python', '2.7.18'), + ('Python', '3.11.3'), ('re2c', '3.1'), ] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-chromium-drop-catapult.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-chromium-drop-catapult.patch new file mode 100644 index 00000000000..ce717404021 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-chromium-drop-catapult.patch @@ -0,0 +1,489 @@ +From b0581c62625e57a63e56369f7eb24a141687cc7a Mon Sep 17 00:00:00 2001 +From: Jimi Huotari +Date: Wed, 6 Apr 2022 14:35:14 +0300 +Subject: [PATCH] Remove dependency on catapult + +Signed-off-by: Andreas Sturmlechner +--- + chromium/BUILD.gn | 11 ---- + chromium/chrome/chrome_paks.gni | 2 - + chromium/chrome/test/BUILD.gn | 6 --- + chromium/content/browser/BUILD.gn | 1 - + chromium/content/browser/tracing/BUILD.gn | 51 ------------------- + .../content/browser/tracing/tracing_ui.cc | 3 -- + chromium/content/shell/BUILD.gn | 2 - + chromium/fuchsia/engine/BUILD.gn | 2 - + chromium/headless/BUILD.gn | 2 - + chromium/mojo/public/tools/BUILD.gn | 1 - + chromium/testing/BUILD.gn | 1 - + chromium/third_party/webrtc/test/BUILD.gn | 5 -- + chromium/tools/binary_size/BUILD.gn | 1 - + chromium/tools/grit/BUILD.gn | 1 - + chromium/tools/gritsettings/resource_ids.spec | 6 --- + chromium/tools/metrics/BUILD.gn | 1 - + .../perf/chrome_telemetry_build/BUILD.gn | 3 -- + .../perf/core/perfetto_binary_roller/BUILD.gn | 1 - + chromium/tools/polymer/BUILD.gn | 1 - + chromium/v8/tools/BUILD.gn | 4 -- + chromium/weblayer/shell/BUILD.gn | 2 - + 21 files changed, 107 deletions(-) + delete mode 100644 chromium/content/browser/tracing/BUILD.gn + +diff --git a/chromium/BUILD.gn b/chromium/BUILD.gn +index 8d9657d545c..59e9447f456 100644 +--- a/qtwebengine/src/3rdparty/chromium/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/BUILD.gn +@@ -239,7 +239,6 @@ group("gn_all") { + "//media/capture:capture_unittests", + "//media/cast:cast_unittests", + "//third_party/angle/src/tests:angle_white_box_tests", +- "//third_party/catapult/telemetry:bitmaptools($host_toolchain)", + ] + } else if (is_ios && !use_qt) { + deps += [ +@@ -354,7 +353,6 @@ group("gn_all") { + "//net/android:net_junit_tests", + "//services:services_junit_tests", + "//testing/android/junit:junit_unit_tests", +- "//third_party/catapult/devil", + "//third_party/smhasher:murmurhash3", + "//tools/android:android_tools", + "//tools/android:memconsumer", +@@ -959,7 +957,6 @@ if (is_chromeos) { + "//third_party/dawn/src/tests:dawn_unittests", + + # Blocked on https://github.com/catapult-project/catapult/issues/2297 +- #"//third_party/catapult/telemetry:bitmaptools", + "//tools/perf/clear_system_cache", + "//ui/ozone/gl:ozone_gl_unittests", + ] +@@ -1037,7 +1034,6 @@ if (!is_ios && !use_qt) { + data_deps = [ + "//chrome:chrome", + "//chrome/test/chromedriver", +- "//third_party/catapult/third_party/typ", + ] + if (is_win) { + data_deps += [ "//build/win:copy_cdb_to_output" ] +@@ -1084,7 +1080,6 @@ if (!is_ios && !use_qt) { + "//third_party/blink/public:blink_devtools_inspector_resources", + "//third_party/blink/public/mojom:mojom_platform_js_data_deps", + "//third_party/blink/renderer/core/html:js_files_for_form_controls_web_tests", +- "//third_party/catapult/third_party/typ", + "//third_party/mesa_headers", + "//tools/imagediff", + ] +@@ -1152,7 +1147,6 @@ if (!is_ios && !use_qt) { + + if (is_android) { + data += [ +- "//third_party/catapult/", + "//build/android/", + ] + } +@@ -1259,11 +1253,6 @@ if (!is_ios && !use_qt) { + "//third_party/blink/web_tests/StaleTestExpectations", + "//third_party/blink/web_tests/TestExpectations", + "//third_party/blink/web_tests/VirtualTestSuites", +- "//third_party/catapult/common/py_utils/", +- "//third_party/catapult/devil/", +- "//third_party/catapult/dependency_manager/", +- "//third_party/catapult/third_party/zipfile/", +- "//third_party/catapult/third_party/typ/", + "//third_party/depot_tools/pylint", + "//third_party/depot_tools/pylint-1.5", + "//third_party/depot_tools/pylint_main.py", +diff --git a/chromium/chrome/chrome_paks.gni b/chromium/chrome/chrome_paks.gni +index 9323a774a56..0362b6501aa 100644 +--- a/qtwebengine/src/3rdparty/chromium/chrome/chrome_paks.gni ++++ b/qtwebengine/src/3rdparty/chromium/chrome/chrome_paks.gni +@@ -94,7 +94,6 @@ template("chrome_extra_paks") { + "$root_gen_dir/chrome/common_resources.pak", + "$root_gen_dir/components/autofill/core/browser/autofill_address_rewriter_resources.pak", + "$root_gen_dir/components/components_resources.pak", +- "$root_gen_dir/content/browser/tracing/tracing_resources.pak", + "$root_gen_dir/content/content_resources.pak", + "$root_gen_dir/mojo/public/js/mojo_bindings_resources.pak", + "$root_gen_dir/net/net_resources.pak", +@@ -110,7 +109,6 @@ template("chrome_extra_paks") { + "//components/autofill/core/browser:autofill_address_rewriter_resources", + "//components/resources", + "//content:content_resources", +- "//content/browser/tracing:resources", + "//mojo/public/js:resources", + "//net:net_resources", + "//skia:skia_resources", +diff --git a/chromium/chrome/test/BUILD.gn b/chromium/chrome/test/BUILD.gn +index 1a369fa56d2..eb5bc9676fb 100644 +--- a/qtwebengine/src/3rdparty/chromium/chrome/test/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/chrome/test/BUILD.gn +@@ -7103,8 +7103,6 @@ if (!is_fuchsia && !is_android) { + "//chrome/test/data/password/captured_sites/", + "//chrome/test/data/web_page_replay_go_helper_scripts/automation_helper.js", + "//components/test/data/autofill/web_page_replay_support_files/", +- "//third_party/catapult/telemetry/telemetry/bin/", +- "//third_party/catapult/web_page_replay_go/deterministic.js", + ] + + if (is_linux || is_chromeos || is_win) { +@@ -7141,7 +7139,6 @@ if (!is_fuchsia && !is_android) { + + # TODO(uwyiming@chromium.org) create a gn target for Web Page Replay Go (WPR Go) and only WPR Go. + # So that test targets requiring WPR Go does not pull down the whole telemetry tool chain. +- "//third_party/catapult:telemetry_chrome_test_support", + "//third_party/hunspell", + "//third_party/icu", + "//third_party/libpng", +@@ -7171,7 +7168,6 @@ if (!is_fuchsia && !is_android) { + deps = [ "//tools/perf/chrome_telemetry_build:telemetry_chrome_test" ] + + data = [ +- "//third_party/catapult/telemetry/telemetry/internal/bin/", + "//tools/perf/run_telemetry_tests", + + # For isolate contract. +@@ -7189,7 +7185,6 @@ if (!is_fuchsia && !is_android) { + group("telemetry_gpu_unittests") { + testonly = true + deps = [ +- "//third_party/catapult:telemetry_chrome_test_support", + "//tools/metrics:metrics_python_tests", + ] + data = [ +@@ -7313,7 +7308,6 @@ if (is_mac || is_win || is_android) { + "//testing/scripts", + "//testing/test_env.py", + "//testing/xvfb.py", +- "//third_party/catapult", + "//tools", + ] + } +diff --git a/chromium/content/browser/BUILD.gn b/chromium/content/browser/BUILD.gn +index 1466f33d462..51039e0da19 100644 +--- a/qtwebengine/src/3rdparty/chromium/content/browser/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/content/browser/BUILD.gn +@@ -2169,7 +2169,6 @@ jumbo_static_library("browser") { + if (!is_android) { + deps += [ + "//components/vector_icons", +- "//content/browser/tracing:resources", + ] + } + +diff --git a/chromium/content/browser/tracing/BUILD.gn b/chromium/content/browser/tracing/BUILD.gn +deleted file mode 100644 +index eac05999fac..00000000000 +--- a/qtwebengine/src/3rdparty/chromium/content/browser/tracing/BUILD.gn ++++ /dev/null +@@ -1,51 +0,0 @@ +-# Copyright 2014 The Chromium Authors. All rights reserved. +-# Use of this source code is governed by a BSD-style license that can be +-# found in the LICENSE file. +- +-import("//tools/grit/grit_rule.gni") +- +-# generate_about_tracing puts its files in this directory +-tracing_gen_dir = "$root_gen_dir/content/browser/tracing" +- +-# The script just writes filename with no dirs to the .grd, so we always need +-# this file to be in the same directory as the inputs. +-tracing_grd = "$tracing_gen_dir/tracing_resources.grd" +- +-action("generate_tracing_grd") { +- visibility = [ ":*" ] # Depend on ":resources" to get this. +- script = "generate_trace_viewer_grd.py" +- +- input_pages = [ +- "$tracing_gen_dir/about_tracing.html", +- "$tracing_gen_dir/about_tracing.js", +- ] +- inputs = input_pages +- outputs = [ tracing_grd ] +- +- args = rebase_path(input_pages, target_gen_dir) + [ +- "--output", +- rebase_path(tracing_grd, root_build_dir), +- ] +- +- deps = [ "//third_party/catapult/tracing:generate_about_tracing" ] +-} +- +-grit("resources") { +- source = tracing_grd +- +- # Required because the .grd is generated. +- enable_input_discovery_for_gn_analyze = false +- +- outputs = [ +- "grit/tracing_resources.h", +- "tracing_resources.pak", +- ] +- +- # resource_ids has an entry for our .grd file that looks like: +- # "<(SHARED_INTERMEDIATE_DIR)/content/browser/tracing/tracing_resources.grd" +- # and what we pass here should make that resolve to our .grd file. +- defines = +- [ "SHARED_INTERMEDIATE_DIR=" + rebase_path(root_gen_dir, root_build_dir) ] +- +- deps = [ ":generate_tracing_grd" ] +-} +diff --git a/chromium/content/browser/tracing/tracing_ui.cc b/chromium/content/browser/tracing/tracing_ui.cc +index 2bffb5eb3b0..8965922dfba 100644 +--- a/qtwebengine/src/3rdparty/chromium/content/browser/tracing/tracing_ui.cc ++++ b/qtwebengine/src/3rdparty/chromium/content/browser/tracing/tracing_ui.cc +@@ -27,7 +27,6 @@ + #include "base/strings/stringprintf.h" + #include "base/trace_event/trace_event.h" + #include "base/values.h" +-#include "content/browser/tracing/grit/tracing_resources.h" + #include "content/browser/tracing/tracing_controller_impl.h" + #include "content/public/browser/browser_context.h" + #include "content/public/browser/browser_thread.h" +@@ -242,8 +241,6 @@ TracingUI::TracingUI(WebUI* web_ui) + WebUIDataSource* source = WebUIDataSource::Create(kChromeUITracingHost); + source->DisableTrustedTypesCSP(); + source->UseStringsJs(); +- source->SetDefaultResource(IDR_TRACING_HTML); +- source->AddResourcePath("tracing.js", IDR_TRACING_JS); + source->SetRequestFilter(base::BindRepeating(OnShouldHandleRequest), + base::BindRepeating(OnTracingRequest)); + WebUIDataSource::Add(browser_context, source); +diff --git a/chromium/content/shell/BUILD.gn b/chromium/content/shell/BUILD.gn +index 56c0e8b48e3..6e4ffbe962d 100644 +--- a/qtwebengine/src/3rdparty/chromium/content/shell/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/content/shell/BUILD.gn +@@ -390,7 +390,6 @@ repack("pak") { + sources = [ + "$root_gen_dir/content/app/resources/content_resources_100_percent.pak", + "$root_gen_dir/content/browser/resources/media/media_internals_resources.pak", +- "$root_gen_dir/content/browser/tracing/tracing_resources.pak", + "$root_gen_dir/content/browser/webrtc/resources/webrtc_internals_resources.pak", + "$root_gen_dir/content/content_resources.pak", + "$root_gen_dir/content/dev_ui_content_resources.pak", +@@ -413,7 +412,6 @@ repack("pak") { + "//content:dev_ui_content_resources", + "//content/app/resources", + "//content/browser/resources/media:media_internals_resources", +- "//content/browser/tracing:resources", + "//content/browser/webrtc/resources", + "//mojo/public/js:resources", + "//net:net_resources", +diff --git a/chromium/fuchsia/engine/BUILD.gn b/chromium/fuchsia/engine/BUILD.gn +index a502b7fc273..39df2a7028a 100644 +--- a/qtwebengine/src/3rdparty/chromium/fuchsia/engine/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/fuchsia/engine/BUILD.gn +@@ -43,7 +43,6 @@ repack("web_engine_pak") { + "$root_gen_dir/components/components_resources.pak", + "$root_gen_dir/components/strings/components_strings_en-US.pak", + "$root_gen_dir/content/app/resources/content_resources_100_percent.pak", +- "$root_gen_dir/content/browser/tracing/tracing_resources.pak", + "$root_gen_dir/content/content_resources.pak", + "$root_gen_dir/content/dev_ui_content_resources.pak", + "$root_gen_dir/mojo/public/js/mojo_bindings_resources.pak", +@@ -66,7 +65,6 @@ repack("web_engine_pak") { + "//content:content_resources", + "//content:dev_ui_content_resources", + "//content/app/resources", +- "//content/browser/tracing:resources", + "//gpu/command_buffer/service", + "//mojo/public/js:resources", + "//net:net_resources", +diff --git a/chromium/headless/BUILD.gn b/chromium/headless/BUILD.gn +index d2ab76aed32..15e4b78009d 100644 +--- a/qtwebengine/src/3rdparty/chromium/headless/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/headless/BUILD.gn +@@ -37,7 +37,6 @@ repack("pak") { + "$root_gen_dir/components/components_resources.pak", + "$root_gen_dir/components/strings/components_strings_en-US.pak", + "$root_gen_dir/content/app/resources/content_resources_100_percent.pak", +- "$root_gen_dir/content/browser/tracing/tracing_resources.pak", + "$root_gen_dir/content/content_resources.pak", + "$root_gen_dir/content/dev_ui_content_resources.pak", + "$root_gen_dir/headless/headless_lib_resources.pak", +@@ -65,7 +64,6 @@ repack("pak") { + "//content:content_resources", + "//content:dev_ui_content_resources", + "//content/app/resources", +- "//content/browser/tracing:resources", + "//mojo/public/js:resources", + "//net:net_resources", + "//third_party/blink/public:resources", +diff --git a/chromium/mojo/public/tools/BUILD.gn b/chromium/mojo/public/tools/BUILD.gn +index 4c68350b399..1cc01256f00 100644 +--- a/qtwebengine/src/3rdparty/chromium/mojo/public/tools/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/mojo/public/tools/BUILD.gn +@@ -14,5 +14,4 @@ group("mojo_python_unittests") { + "//testing/xvfb.py", + ] + deps = [ "//mojo/public/tools/mojom/mojom:tests" ] +- data_deps = [ "//third_party/catapult/third_party/typ/" ] + } +diff --git a/chromium/testing/BUILD.gn b/chromium/testing/BUILD.gn +index 56ebf8d46c9..7d51bc0ccf7 100644 +--- a/qtwebengine/src/3rdparty/chromium/testing/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/testing/BUILD.gn +@@ -27,7 +27,6 @@ group("run_perf_test") { + + data_deps = [ + ":test_scripts_shared", +- "//third_party/catapult/tracing:convert_chart_json", + ] + + if (is_android) { +diff --git a/chromium/third_party/webrtc/test/BUILD.gn b/chromium/third_party/webrtc/test/BUILD.gn +index 58d3dab5219..48328298d2e 100644 +--- a/qtwebengine/src/3rdparty/chromium/third_party/webrtc/test/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/third_party/webrtc/test/BUILD.gn +@@ -258,10 +258,6 @@ rtc_library("perf_test") { + absl_deps = [ "//third_party/abseil-cpp/absl/types:optional" ] + if (rtc_enable_protobuf) { + sources += [ "testsupport/perf_test_histogram_writer.cc" ] +- deps += [ +- "//third_party/catapult/tracing/tracing:histogram", +- "//third_party/catapult/tracing/tracing:reserved_infos", +- ] + } else { + sources += [ "testsupport/perf_test_histogram_writer_no_protobuf.cc" ] + } +@@ -566,7 +562,6 @@ if (rtc_include_tests) { + + if (rtc_enable_protobuf) { + sources += [ "testsupport/perf_test_histogram_writer_unittest.cc" ] +- deps += [ "//third_party/catapult/tracing/tracing:histogram" ] + } + + data = test_support_unittests_resources +diff --git a/chromium/tools/binary_size/BUILD.gn b/chromium/tools/binary_size/BUILD.gn +index e6806bf7754..2c985d15fab 100644 +--- a/qtwebengine/src/3rdparty/chromium/tools/binary_size/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/tools/binary_size/BUILD.gn +@@ -18,7 +18,6 @@ python_library("binary_size_trybot_py") { + python_library("sizes_py") { + testonly = true + pydeps_file = "sizes.pydeps" +- data_deps = [ "//third_party/catapult/tracing:convert_chart_json" ] + } + + if (is_linux || is_chromeos) { +diff --git a/chromium/tools/grit/BUILD.gn b/chromium/tools/grit/BUILD.gn +index 1cd3c75b553..60c4cf2f77a 100644 +--- a/qtwebengine/src/3rdparty/chromium/tools/grit/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/tools/grit/BUILD.gn +@@ -33,7 +33,6 @@ group("grit_python_unittests") { + "//testing/scripts/run_isolated_script_test.py", + "//testing/xvfb.py", + "//tools/grit/", +- "//third_party/catapult/third_party/typ/", + ] + } + +diff --git a/chromium/tools/gritsettings/resource_ids.spec b/chromium/tools/gritsettings/resource_ids.spec +index d0a4545514c..80b0bf1737b 100644 +--- a/qtwebengine/src/3rdparty/chromium/tools/gritsettings/resource_ids.spec ++++ b/qtwebengine/src/3rdparty/chromium/tools/gritsettings/resource_ids.spec +@@ -499,12 +499,6 @@ + "content/shell/shell_resources.grd": { + "includes": [2940], + }, +- +- # This file is generated during the build. +- "<(SHARED_INTERMEDIATE_DIR)/content/browser/tracing/tracing_resources.grd": { +- "META": {"sizes": {"includes": [20],}}, +- "includes": [2960], +- }, + # END content/ section. + + # START ios/web/ section. +diff --git a/chromium/tools/metrics/BUILD.gn b/chromium/tools/metrics/BUILD.gn +index 846d5248bfa..cb57d2bdae1 100644 +--- a/qtwebengine/src/3rdparty/chromium/tools/metrics/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/tools/metrics/BUILD.gn +@@ -56,7 +56,6 @@ group("metrics_python_tests") { + "//testing/scripts/common.py", + "//testing/xvfb.py", + "//testing/test_env.py", +- "//third_party/catapult/third_party/typ/", + + # Scripts we depend on. Their unit tests are also included. + "//tools/json_comment_eater/json_comment_eater.py", +diff --git a/chromium/tools/perf/chrome_telemetry_build/BUILD.gn b/chromium/tools/perf/chrome_telemetry_build/BUILD.gn +index 280bb754c2c..c287fdcebb3 100644 +--- a/qtwebengine/src/3rdparty/chromium/tools/perf/chrome_telemetry_build/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/tools/perf/chrome_telemetry_build/BUILD.gn +@@ -107,7 +107,6 @@ group("telemetry_chrome_test_without_chrome") { + "//tools/perf/core/", # chrome_telemetry_build/ depends on core/ + ] + data_deps = [ +- "//third_party/catapult:telemetry_chrome_test_support", + "//tools/metrics:metrics_python_tests", + ] + +@@ -151,7 +150,5 @@ group("telemetry_chrome_test_without_chrome") { + "//build/android:devil_chromium_py", + "//build/android:stack_tools", + ] +- } else if (!is_fuchsia) { +- data_deps += [ "//third_party/catapult/telemetry:bitmaptools" ] + } + } +diff --git a/chromium/tools/perf/core/perfetto_binary_roller/BUILD.gn b/chromium/tools/perf/core/perfetto_binary_roller/BUILD.gn +index 7fe48cba143..e9c7f0261a5 100644 +--- a/qtwebengine/src/3rdparty/chromium/tools/perf/core/perfetto_binary_roller/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/tools/perf/core/perfetto_binary_roller/BUILD.gn +@@ -7,7 +7,6 @@ import("//build/util/generate_wrapper.gni") + generate_wrapper("upload_trace_processor") { + testonly = true + data_deps = [ +- "//third_party/catapult:telemetry_chrome_test_support", + "//third_party/perfetto/src/trace_processor:trace_processor_shell", + ] + data = [ +diff --git a/chromium/tools/polymer/BUILD.gn b/chromium/tools/polymer/BUILD.gn +index 092066b7c04..d115144cd61 100644 +--- a/qtwebengine/src/3rdparty/chromium/tools/polymer/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/tools/polymer/BUILD.gn +@@ -10,6 +10,5 @@ group("polymer_tools_python_unittests") { + "//testing/scripts/run_isolated_script_test.py", + "//testing/xvfb.py", + "//tools/polymer/", +- "//third_party/catapult/third_party/typ/", + ] + } +diff --git a/chromium/v8/tools/BUILD.gn b/chromium/v8/tools/BUILD.gn +index 2f8197dd369..83304b6342b 100644 +--- a/qtwebengine/src/3rdparty/chromium/v8/tools/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/v8/tools/BUILD.gn +@@ -31,10 +31,6 @@ group("v8_android_test_runner_deps") { + + if (is_android && !build_with_chromium) { + data_deps = [ "//build/android:test_runner_py" ] +- data = [ +- # This is used by android.py, but not included by test_runner_py above. +- "//third_party/catapult/devil/devil/android/perf/", +- ] + } + } + +diff --git a/chromium/weblayer/shell/BUILD.gn b/chromium/weblayer/shell/BUILD.gn +index 66984a7da54..1815fad623d 100644 +--- a/qtwebengine/src/3rdparty/chromium/weblayer/shell/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/weblayer/shell/BUILD.gn +@@ -161,7 +161,6 @@ repack("support_pak") { + "$root_gen_dir/components/strings/components_locale_settings_en-US.pak", + "$root_gen_dir/components/strings/components_strings_en-US.pak", + "$root_gen_dir/content/app/resources/content_resources_100_percent.pak", +- "$root_gen_dir/content/browser/tracing/tracing_resources.pak", + "$root_gen_dir/content/content_resources.pak", + "$root_gen_dir/content/dev_ui_content_resources.pak", + "$root_gen_dir/mojo/public/js/mojo_bindings_resources.pak", +@@ -182,7 +181,6 @@ repack("support_pak") { + "//content:content_resources", + "//content:dev_ui_content_resources", + "//content/app/resources", +- "//content/browser/tracing:resources", + "//mojo/public/js:resources", + "//net:net_resources", + "//third_party/blink/public:resources", +-- +2.35.1 + diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-chromium-python3.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-chromium-python3.patch new file mode 100644 index 00000000000..af9769225b3 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-chromium-python3.patch @@ -0,0 +1,1883 @@ +From 3c26c6214f675d170718df6bd54e61743620166a Mon Sep 17 00:00:00 2001 +From: Antonio Rojas +Date: Sat, 16 Oct 2021 20:17:35 +0000 +Subject: [PATCH 1/3] Build without python 2 + +--- + chromium/build/print_python_deps.py | 6 +- + .../protobufs/binary_proto_generator.py | 8 +- + .../tracing/generate_trace_viewer_grd.py | 2 +- + chromium/mojo/public/tools/bindings/BUILD.gn | 2 + + .../tools/bindings/gen_data_files_list.py | 8 +- + .../generators/mojom_java_generator.py | 4 + + .../tools/mojom/mojom/generate/generator.py | 14 ++-- + .../tools/mojom/mojom/generate/module.py | 3 +- + .../mojom/mojom/generate/template_expander.py | 12 +-- + .../scripts/bind_gen/blink_v8_bridge.py | 6 +- + .../scripts/bind_gen/callback_interface.py | 2 +- + .../bindings/scripts/bind_gen/code_node.py | 10 +-- + .../bindings/scripts/bind_gen/codegen_expr.py | 15 ++-- + .../scripts/bind_gen/codegen_format.py | 2 +- + .../scripts/bind_gen/codegen_utils.py | 2 +- + .../bindings/scripts/bind_gen/dictionary.py | 2 +- + .../bindings/scripts/bind_gen/interface.py | 82 +++++++++++-------- + .../scripts/bind_gen/mako_renderer.py | 2 +- + .../bindings/scripts/bind_gen/style_format.py | 9 +- + .../bindings/scripts/bind_gen/task_queue.py | 5 +- + .../bindings/scripts/code_generator.py | 10 +++ + .../scripts/generate_origin_trial_features.py | 4 +- + .../bindings/scripts/idl_definitions.py | 8 +- + .../renderer/bindings/scripts/idl_reader.py | 4 +- + .../renderer/bindings/scripts/idl_types.py | 2 +- + .../renderer/bindings/scripts/utilities.py | 28 +++---- + .../renderer/bindings/scripts/v8_interface.py | 9 +- + .../renderer/bindings/scripts/v8_methods.py | 4 + + .../renderer/bindings/scripts/v8_utilities.py | 2 +- + .../scripts/web_idl/callback_interface.py | 12 +-- + .../bindings/scripts/web_idl/database.py | 2 +- + .../bindings/scripts/web_idl/exposure.py | 5 +- + .../bindings/scripts/web_idl/function_like.py | 28 +++---- + .../bindings/scripts/web_idl/idl_compiler.py | 21 ++--- + .../bindings/scripts/web_idl/interface.py | 45 +++++----- + .../bindings/scripts/web_idl/ir_builder.py | 29 ++++--- + .../bindings/scripts/web_idl/make_copy.py | 7 ++ + .../bindings/scripts/web_idl/namespace.py | 12 +-- + .../bindings/templates/dictionary_v8.cc.tmpl | 8 +- + .../scripts/core/css/make_style_shorthands.py | 23 +++--- + .../properties/make_css_property_instances.py | 4 +- + .../blink/renderer/build/scripts/gperf.py | 2 +- + .../blink/renderer/build/scripts/in_file.py | 2 +- + .../renderer/build/scripts/in_generator.py | 5 ++ + .../build/scripts/make_runtime_features.py | 2 +- + .../scripts/templates/element_factory.cc.tmpl | 4 +- + .../templates/element_type_helpers.cc.tmpl | 4 +- + .../templates/element_type_helpers.h.tmpl | 2 +- + .../build/scripts/templates/macros.tmpl | 4 +- + .../templates/make_qualified_names.h.tmpl | 4 +- + .../dawn/generator/generator_lib.py | 4 + + .../devtools-frontend/src/BUILD.gn | 2 + + .../scripts/build/build_inspector_overlay.py | 3 +- + .../build/build_release_applications.py | 9 +- + .../scripts/build/generate_devtools_grd.py | 4 +- + .../src/scripts/build/modular_build.py | 6 +- + chromium/third_party/jinja2/tests.py | 2 +- + chromium/tools/metrics/ukm/gen_builders.py | 5 +- + .../ui/ozone/generate_constructor_list.py | 13 ++- + .../ui/ozone/generate_ozone_platform_list.py | 26 ++++-- + 60 files changed, 334 insertions(+), 232 deletions(-) + +diff --git a/chromium/build/print_python_deps.py b/chromium/build/print_python_deps.py +index fd29c0972c9..69af247094b 100755 +--- a/qtwebengine/src/3rdparty/chromium/chromium/build/print_python_deps.py ++++ b/qtwebengine/src/3rdparty/chromium/build/print_python_deps.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/python2.7 ++#!/usr/bin/python + # Copyright 2016 The Chromium Authors. All rights reserved. + # Use of this source code is governed by a BSD-style license that can be + # found in the LICENSE file. +@@ -80,7 +80,7 @@ def _GetTargetPythonVersion(module): + if shebang.startswith('#!'): + # Examples: + # '#!/usr/bin/python' +- # '#!/usr/bin/python2.7' ++ # '#!/usr/bin/python' + # '#!/usr/bin/python3' + # '#!/usr/bin/env python3' + # '#!/usr/bin/env vpython' +@@ -152,7 +152,7 @@ def main(): + + # Trybots run with vpython as default Python, but with a different config + # from //.vpython. To make the is_vpython test work, and to match the behavior +- # of dev machines, the shebang line must be run with python2.7. ++ # of dev machines, the shebang line must be run with python. + # + # E.g. $HOME/.vpython-root/dd50d3/bin/python + # E.g. /b/s/w/ir/cache/vpython/ab5c79/bin/python +diff --git a/chromium/components/resources/protobufs/binary_proto_generator.py b/chromium/components/resources/protobufs/binary_proto_generator.py +index 7422ead9697..16365515f26 100755 +--- a/qtwebengine/src/3rdparty/chromium/chromium/components/resources/protobufs/binary_proto_generator.py ++++ b/qtwebengine/src/3rdparty/chromium/components/resources/protobufs/binary_proto_generator.py +@@ -7,7 +7,7 @@ + Converts a given ASCII proto into a binary resource. + + """ +- ++from __future__ import print_function + import abc + import imp + import optparse +@@ -196,12 +196,12 @@ class BinaryProtoGenerator: + self._ImportProtoModules(opts.path) + + if not self.VerifyArgs(opts): +- print "Wrong arguments" ++ print("Wrong arguments") + return 1 + + try: + self._GenerateBinaryProtos(opts) + except Exception as e: +- print "ERROR: Failed to render binary version of %s:\n %s\n%s" % ( +- opts.infile, str(e), traceback.format_exc()) ++ print("ERROR: Failed to render binary version of %s:\n %s\n%s" % ++ (opts.infile, str(e), traceback.format_exc())) + return 1 +diff --git a/chromium/content/browser/tracing/generate_trace_viewer_grd.py b/chromium/content/browser/tracing/generate_trace_viewer_grd.py +index 037f9497dc2..be393d21f90 100755 +--- a/qtwebengine/src/3rdparty/chromium/chromium/content/browser/tracing/generate_trace_viewer_grd.py ++++ b/qtwebengine/src/3rdparty/chromium/content/browser/tracing/generate_trace_viewer_grd.py +@@ -74,7 +74,7 @@ def main(argv): + for filename in parsed_args.source_files: + add_file_to_grd(doc, os.path.basename(filename)) + +- with open(parsed_args.output_filename, 'w') as output_file: ++ with open(parsed_args.output_filename, 'wb') as output_file: + output_file.write(doc.toxml(encoding='UTF-8')) + + +diff --git a/chromium/mojo/public/tools/bindings/BUILD.gn b/chromium/mojo/public/tools/bindings/BUILD.gn +index fc04b5dd0b1..708958e438b 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/mojo/public/tools/bindings/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/mojo/public/tools/bindings/BUILD.gn +@@ -2,9 +2,11 @@ + # Use of this source code is governed by a BSD-style license that can be + # found in the LICENSE file. + ++import("//build/config/python.gni") + import("//mojo/public/tools/bindings/mojom.gni") + import("//third_party/jinja2/jinja2.gni") + ++# TODO(crbug.com/1194274): Investigate nondeterminism in Py3 builds. + action("precompile_templates") { + sources = mojom_generator_sources + sources += [ +diff --git a/chromium/mojo/public/tools/bindings/gen_data_files_list.py b/chromium/mojo/public/tools/bindings/gen_data_files_list.py +index 79c9e50efce..8b78d092418 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/mojo/public/tools/bindings/gen_data_files_list.py ++++ b/qtwebengine/src/3rdparty/chromium/mojo/public/tools/bindings/gen_data_files_list.py +@@ -18,7 +18,6 @@ import os + import re + import sys + +-from cStringIO import StringIO + from optparse import OptionParser + + sys.path.insert( +@@ -41,12 +40,9 @@ def main(): + pattern = re.compile(options.pattern) + files = [f for f in os.listdir(options.directory) if pattern.match(f)] + +- stream = StringIO() +- for f in files: +- print(f, file=stream) ++ contents = '\n'.join(f for f in files) + '\n' ++ WriteFile(contents, options.output) + +- WriteFile(stream.getvalue(), options.output) +- stream.close() + + if __name__ == '__main__': + sys.exit(main()) +diff --git a/chromium/mojo/public/tools/bindings/generators/mojom_java_generator.py b/chromium/mojo/public/tools/bindings/generators/mojom_java_generator.py +index 96b2fdfae0c..00b9dccd00c 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/mojo/public/tools/bindings/generators/mojom_java_generator.py ++++ b/qtwebengine/src/3rdparty/chromium/mojo/public/tools/bindings/generators/mojom_java_generator.py +@@ -25,6 +25,10 @@ sys.path.append(os.path.join(os.path.dirname(__file__), os.pardir, + 'build', 'android', 'gyp')) + from util import build_utils + ++# TODO(crbug.com/1174969): Remove this once Python2 is obsoleted. ++if sys.version_info.major != 2: ++ basestring = str ++ long = int + + GENERATOR_PREFIX = 'java' + +diff --git a/chromium/mojo/public/tools/mojom/mojom/generate/generator.py b/chromium/mojo/public/tools/mojom/mojom/generate/generator.py +index de62260a5c9..4a1c73fcf82 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/mojo/public/tools/mojom/mojom/generate/generator.py ++++ b/qtwebengine/src/3rdparty/chromium/mojo/public/tools/mojom/mojom/generate/generator.py +@@ -136,9 +136,14 @@ class Stylizer(object): + + def WriteFile(contents, full_path): + # If |contents| is same with the file content, we skip updating. ++ if not isinstance(contents, bytes): ++ data = contents.encode('utf8') ++ else: ++ data = contents ++ + if os.path.isfile(full_path): + with open(full_path, 'rb') as destination_file: +- if destination_file.read() == contents: ++ if destination_file.read() == data: + return + + # Make sure the containing directory exists. +@@ -146,11 +151,8 @@ def WriteFile(contents, full_path): + fileutil.EnsureDirectoryExists(full_dir) + + # Dump the data to disk. +- with open(full_path, "wb") as f: +- if not isinstance(contents, bytes): +- f.write(contents.encode('utf-8')) +- else: +- f.write(contents) ++ with open(full_path, 'wb') as f: ++ f.write(data) + + + def AddComputedData(module): +diff --git a/chromium/mojo/public/tools/mojom/mojom/generate/module.py b/chromium/mojo/public/tools/mojom/mojom/generate/module.py +index ebbc9b322ea..3d026429bbc 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/mojo/public/tools/mojom/mojom/generate/module.py ++++ b/qtwebengine/src/3rdparty/chromium/mojo/public/tools/mojom/mojom/generate/module.py +@@ -398,7 +398,8 @@ class Field(object): + + + class StructField(Field): +- pass ++ def __hash__(self): ++ return super(Field, self).__hash__() + + + class UnionField(Field): +diff --git a/chromium/mojo/public/tools/mojom/mojom/generate/template_expander.py b/chromium/mojo/public/tools/mojom/mojom/generate/template_expander.py +index 7a300560246..8d9e26fb7f6 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/mojo/public/tools/mojom/mojom/generate/template_expander.py ++++ b/qtwebengine/src/3rdparty/chromium/mojo/public/tools/mojom/mojom/generate/template_expander.py +@@ -75,9 +75,9 @@ def PrecompileTemplates(generator_modules, output_dir): + os.path.dirname(module.__file__), generator.GetTemplatePrefix()) + ])) + jinja_env.filters.update(generator.GetFilters()) +- jinja_env.compile_templates( +- os.path.join(output_dir, "%s.zip" % generator.GetTemplatePrefix()), +- extensions=["tmpl"], +- zip="stored", +- py_compile=True, +- ignore_errors=False) ++ jinja_env.compile_templates(os.path.join( ++ output_dir, "%s.zip" % generator.GetTemplatePrefix()), ++ extensions=["tmpl"], ++ zip="stored", ++ py_compile=sys.version_info.major < 3, ++ ignore_errors=False) +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/blink_v8_bridge.py b/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/blink_v8_bridge.py +index 3225ecca6e4..fc078d31b55 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/blink_v8_bridge.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/blink_v8_bridge.py +@@ -344,7 +344,7 @@ def make_default_value_expr(idl_type, default_value): + """ + assert default_value.is_type_compatible_with(idl_type) + +- class DefaultValueExpr: ++ class DefaultValueExpr(object): + _ALLOWED_SYMBOLS_IN_DEPS = ("isolate") + + def __init__(self, initializer_expr, initializer_deps, +@@ -502,7 +502,7 @@ def make_v8_to_blink_value(blink_var_name, + assert isinstance(blink_var_name, str) + assert isinstance(v8_value_expr, str) + assert isinstance(idl_type, web_idl.IdlType) +- assert (argument_index is None or isinstance(argument_index, (int, long))) ++ assert (argument_index is None or isinstance(argument_index, int)) + assert (default_value is None + or isinstance(default_value, web_idl.LiteralConstant)) + +@@ -622,7 +622,7 @@ def make_v8_to_blink_value_variadic(blink_var_name, v8_array, + """ + assert isinstance(blink_var_name, str) + assert isinstance(v8_array, str) +- assert isinstance(v8_array_start_index, (int, long)) ++ assert isinstance(v8_array_start_index, int) + assert isinstance(idl_type, web_idl.IdlType) + + pattern = ("auto&& ${{{_1}}} = " +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/callback_interface.py b/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/callback_interface.py +index 4a6df513068..8b51f23a409 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/callback_interface.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/callback_interface.py +@@ -177,7 +177,7 @@ def generate_callback_interface(callback_interface_identifier): + prop_install_mode=PropInstallMode.UNCONDITIONAL, + trampoline_var_name=None, + attribute_entries=[], +- constant_entries=filter(is_unconditional, constant_entries), ++ constant_entries=list(filter(is_unconditional, constant_entries)), + exposed_construct_entries=[], + operation_entries=[]) + (install_interface_template_decl, install_interface_template_def, +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/code_node.py b/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/code_node.py +index 52972fefe20..e5ae9d9629e 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/code_node.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/code_node.py +@@ -503,13 +503,13 @@ class CompositeNode(CodeNode): + gensym_kwargs = {} + template_vars = {} + for arg in args: +- assert isinstance(arg, (CodeNode, int, long, str)) ++ assert isinstance(arg, (CodeNode, int, str)) + gensym = CodeNode.gensym() + gensym_args.append("${{{}}}".format(gensym)) + template_vars[gensym] = arg + for key, value in kwargs.items(): +- assert isinstance(key, (int, long, str)) +- assert isinstance(value, (CodeNode, int, long, str)) ++ assert isinstance(key, (int, str)) ++ assert isinstance(value, (CodeNode, int, str)) + gensym = CodeNode.gensym() + gensym_kwargs[key] = "${{{}}}".format(gensym) + template_vars[gensym] = value +@@ -602,7 +602,7 @@ class ListNode(CodeNode): + def insert(self, index, node): + if node is None: + return +- assert isinstance(index, (int, long)) ++ assert isinstance(index, int) + assert isinstance(node, CodeNode) + assert node.outer is None and node.prev is None + +@@ -721,7 +721,7 @@ class SymbolScopeNode(SequenceNode): + if not scope_chains: + return counts + +- self_index = iter(scope_chains).next().index(self) ++ self_index = next(iter(scope_chains)).index(self) + scope_chains = map( + lambda scope_chain: scope_chain[self_index + 1:], scope_chains) + scope_to_likeliness = {} +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_expr.py b/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_expr.py +index a229a6c71c9..5fa288dabf2 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_expr.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_expr.py +@@ -109,7 +109,7 @@ def expr_and(terms): + + if any(term.is_always_false for term in terms): + return _Expr(False) +- terms = filter(lambda x: not x.is_always_true, terms) ++ terms = list(filter(lambda x: not x.is_always_true, terms)) + if not terms: + return _Expr(True) + if len(terms) == 1: +@@ -124,7 +124,7 @@ def expr_or(terms): + + if any(term.is_always_true for term in terms): + return _Expr(True) +- terms = filter(lambda x: not x.is_always_false, terms) ++ terms = list(filter(lambda x: not x.is_always_false, terms)) + if not terms: + return _Expr(False) + if len(terms) == 1: +@@ -222,7 +222,7 @@ def expr_from_exposure(exposure, + elif exposure.only_in_secure_contexts is False: + secure_context_term = _Expr(True) + else: +- terms = map(ref_enabled, exposure.only_in_secure_contexts) ++ terms = list(map(ref_enabled, exposure.only_in_secure_contexts)) + secure_context_term = expr_or( + [_Expr("${is_in_secure_context}"), + expr_not(expr_and(terms))]) +@@ -275,10 +275,11 @@ def expr_from_exposure(exposure, + + # [ContextEnabled] + if exposure.context_enabled_features: +- terms = map( +- lambda feature: _Expr( +- "${{context_feature_settings}}->is{}Enabled()".format( +- feature)), exposure.context_enabled_features) ++ terms = list( ++ map( ++ lambda feature: _Expr( ++ "${{context_feature_settings}}->is{}Enabled()".format( ++ feature)), exposure.context_enabled_features)) + context_enabled_terms.append( + expr_and([_Expr("${context_feature_settings}"), + expr_or(terms)])) +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_format.py b/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_format.py +index 87d26eec3ca..f3e9d38247e 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_format.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_format.py +@@ -23,7 +23,7 @@ class _TemplateFormatter(string.Formatter): + self._template_formatter_indexing_count_ = 0 + + def get_value(self, key, args, kwargs): +- if isinstance(key, (int, long)): ++ if isinstance(key, int): + return args[key] + assert isinstance(key, str) + if not key: +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_utils.py b/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_utils.py +index 2bcc4fed49a..e72282aa696 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_utils.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/codegen_utils.py +@@ -116,4 +116,4 @@ def write_code_node_to_file(code_node, filepath): + # stderr=format_result.error_message)) + # + # web_idl.file_io.write_to_file_if_changed(filepath, format_result.contents) +- web_idl.file_io.write_to_file_if_changed(filepath, rendered_text) ++ web_idl.file_io.write_to_file_if_changed(filepath, rendered_text.encode('utf-8')) +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/dictionary.py b/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/dictionary.py +index b39f0100410..4d68202296b 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/dictionary.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/dictionary.py +@@ -993,7 +993,7 @@ def make_dict_trace_func(cg_context): + _2 = _blink_member_name(member).value_var + return TextNode(_format(pattern, _1=_1, _2=_2)) + +- body.extend(map(make_trace_member_node, own_members)) ++ body.extend(list(map(make_trace_member_node, own_members))) + body.append(TextNode("BaseClass::Trace(visitor);")) + + return func_decl, func_def +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/interface.py b/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/interface.py +index 10ff30656ad..bfdf7128aac 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/interface.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/interface.py +@@ -582,7 +582,7 @@ def _make_blink_api_call(code_node, + overriding_args=None): + assert isinstance(code_node, SymbolScopeNode) + assert isinstance(cg_context, CodeGenContext) +- assert num_of_args is None or isinstance(num_of_args, (int, long)) ++ assert num_of_args is None or isinstance(num_of_args, int) + assert (overriding_args is None + or (isinstance(overriding_args, (list, tuple)) + and all(isinstance(arg, str) for arg in overriding_args))) +@@ -1196,8 +1196,10 @@ def make_overload_dispatcher(cg_context): + did_use_break = did_use_break or can_fail + + conditional = expr_or( +- map(lambda item: expr_from_exposure(item.function_like.exposure), +- items)) ++ list( ++ map( ++ lambda item: expr_from_exposure(item.function_like.exposure ++ ), items))) + if not conditional.is_always_true: + node = CxxUnlikelyIfNode(cond=conditional, body=node) + +@@ -4642,7 +4644,7 @@ class _PropEntryConstructorGroup(_PropEntryBase): + def __init__(self, is_context_dependent, exposure_conditional, world, + constructor_group, ctor_callback_name, ctor_func_length): + assert isinstance(ctor_callback_name, str) +- assert isinstance(ctor_func_length, (int, long)) ++ assert isinstance(ctor_func_length, int) + + _PropEntryBase.__init__(self, is_context_dependent, + exposure_conditional, world, constructor_group) +@@ -4670,7 +4672,7 @@ class _PropEntryOperationGroup(_PropEntryBase): + op_func_length, + no_alloc_direct_callback_name=None): + assert isinstance(op_callback_name, str) +- assert isinstance(op_func_length, (int, long)) ++ assert isinstance(op_func_length, int) + + _PropEntryBase.__init__(self, is_context_dependent, + exposure_conditional, world, operation_group) +@@ -5175,9 +5177,9 @@ def make_install_interface_template(cg_context, function_name, class_name, api_c + ]) + + if class_like.identifier == "CSSStyleDeclaration": +- css_properties = filter( +- lambda attr: "CSSProperty" in attr.extended_attributes, +- class_like.attributes) ++ css_properties = list( ++ filter(lambda attr: "CSSProperty" in attr.extended_attributes, ++ class_like.attributes)) + if css_properties: + prop_name_list = "".join( + map(lambda attr: "\"{}\", ".format(attr.identifier), +@@ -5567,8 +5569,8 @@ ${instance_object} = ${v8_context}->Global()->GetPrototype().As();\ + "V8DOMConfiguration::InstallConstants(${isolate}, " + "${interface_template}, ${prototype_template}, " + "kConstantCallbackTable, base::size(kConstantCallbackTable));") +- constant_callback_entries = filter(lambda entry: entry.const_callback_name, +- constant_entries) ++ constant_callback_entries = list(filter(lambda entry: entry.const_callback_name, ++ constant_entries)) + install_properties(table_name, constant_callback_entries, + _make_constant_callback_registration_table, + installer_call_text) +@@ -5584,8 +5586,8 @@ ${instance_object} = ${v8_context}->Global()->GetPrototype().As();\ + "V8DOMConfiguration::InstallConstants(${isolate}, " + "${interface_template}, ${prototype_template}, " + "kConstantValueTable, base::size(kConstantValueTable));") +- constant_value_entries = filter( +- lambda entry: not entry.const_callback_name, constant_entries) ++ constant_value_entries = list(filter( ++ lambda entry: not entry.const_callback_name, constant_entries)) + install_properties(table_name, constant_value_entries, + _make_constant_value_registration_table, + installer_call_text) +@@ -6336,8 +6338,8 @@ def make_v8_context_snapshot_api(cg_context, component, attribute_entries, + assert isinstance(component, web_idl.Component) + + derived_interfaces = cg_context.interface.deriveds +- derived_names = map(lambda interface: interface.identifier, +- derived_interfaces) ++ derived_names = list( ++ map(lambda interface: interface.identifier, derived_interfaces)) + derived_names.append(cg_context.interface.identifier) + if not ("Window" in derived_names or "HTMLDocument" in derived_names): + return None, None +@@ -6411,9 +6413,11 @@ def _make_v8_context_snapshot_get_reference_table_function( + collect_callbacks(named_properties_object_callback_defs) + collect_callbacks(cross_origin_property_callback_defs) + +- entry_nodes = map( +- lambda name: TextNode("reinterpret_cast({}),".format(name)), +- filter(None, callback_names)) ++ entry_nodes = list( ++ map( ++ lambda name: TextNode("reinterpret_cast({}),".format(name ++ )), ++ filter(None, callback_names))) + table_node = ListNode([ + TextNode("using namespace ${class_name}Callbacks;"), + TextNode("static const intptr_t kReferenceTable[] = {"), +@@ -6451,10 +6455,11 @@ def _make_v8_context_snapshot_install_props_per_context_function( + class_name=None, + prop_install_mode=PropInstallMode.V8_CONTEXT_SNAPSHOT, + trampoline_var_name=None, +- attribute_entries=filter(selector, attribute_entries), +- constant_entries=filter(selector, constant_entries), +- exposed_construct_entries=filter(selector, exposed_construct_entries), +- operation_entries=filter(selector, operation_entries)) ++ attribute_entries=list(filter(selector, attribute_entries)), ++ constant_entries=list(filter(selector, constant_entries)), ++ exposed_construct_entries=list( ++ filter(selector, exposed_construct_entries)), ++ operation_entries=list(filter(selector, operation_entries))) + + return func_decl, func_def + +@@ -6810,11 +6815,11 @@ def generate_interface(interface_identifier): + class_name=impl_class_name, + prop_install_mode=PropInstallMode.UNCONDITIONAL, + trampoline_var_name=tp_install_unconditional_props, +- attribute_entries=filter(is_unconditional, attribute_entries), +- constant_entries=filter(is_unconditional, constant_entries), +- exposed_construct_entries=filter(is_unconditional, +- exposed_construct_entries), +- operation_entries=filter(is_unconditional, operation_entries)) ++ attribute_entries=list(filter(is_unconditional, attribute_entries)), ++ constant_entries=list(filter(is_unconditional, constant_entries)), ++ exposed_construct_entries=list( ++ filter(is_unconditional, exposed_construct_entries)), ++ operation_entries=list(filter(is_unconditional, operation_entries))) + (install_context_independent_props_decl, + install_context_independent_props_def, + install_context_independent_props_trampoline) = make_install_properties( +@@ -6823,11 +6828,14 @@ def generate_interface(interface_identifier): + class_name=impl_class_name, + prop_install_mode=PropInstallMode.CONTEXT_INDEPENDENT, + trampoline_var_name=tp_install_context_independent_props, +- attribute_entries=filter(is_context_independent, attribute_entries), +- constant_entries=filter(is_context_independent, constant_entries), +- exposed_construct_entries=filter(is_context_independent, +- exposed_construct_entries), +- operation_entries=filter(is_context_independent, operation_entries)) ++ attribute_entries=list( ++ filter(is_context_independent, attribute_entries)), ++ constant_entries=list(filter(is_context_independent, ++ constant_entries)), ++ exposed_construct_entries=list( ++ filter(is_context_independent, exposed_construct_entries)), ++ operation_entries=list( ++ filter(is_context_independent, operation_entries))) + (install_context_dependent_props_decl, install_context_dependent_props_def, + install_context_dependent_props_trampoline) = make_install_properties( + cg_context, +@@ -6835,11 +6843,13 @@ def generate_interface(interface_identifier): + class_name=impl_class_name, + prop_install_mode=PropInstallMode.CONTEXT_DEPENDENT, + trampoline_var_name=tp_install_context_dependent_props, +- attribute_entries=filter(is_context_dependent, attribute_entries), +- constant_entries=filter(is_context_dependent, constant_entries), +- exposed_construct_entries=filter(is_context_dependent, +- exposed_construct_entries), +- operation_entries=filter(is_context_dependent, operation_entries)) ++ attribute_entries=list(filter(is_context_dependent, ++ attribute_entries)), ++ constant_entries=list(filter(is_context_dependent, constant_entries)), ++ exposed_construct_entries=list( ++ filter(is_context_dependent, exposed_construct_entries)), ++ operation_entries=list(filter(is_context_dependent, ++ operation_entries))) + (install_interface_template_decl, install_interface_template_def, + install_interface_template_trampoline) = make_install_interface_template( + cg_context, +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/mako_renderer.py b/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/mako_renderer.py +index b4c70553863..f3a2fcd772d 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/mako_renderer.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/mako_renderer.py +@@ -105,7 +105,7 @@ class MakoRenderer(object): + on_error = self._caller_stack_on_error + if (len(current) <= len(on_error) + and all(current[i] == on_error[i] +- for i in xrange(len(current)))): ++ for i in range(len(current)))): + pass # Error happened in a deeper caller. + else: + self._caller_stack_on_error = list(self._caller_stack) +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/style_format.py b/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/style_format.py +index dc3493cc394..017d3d47bb3 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/style_format.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/style_format.py +@@ -70,8 +70,13 @@ def gn_format(contents, filename=None): + + + def _invoke_format_command(command_line, filename, contents): +- proc = subprocess.Popen( +- command_line, stdin=subprocess.PIPE, stdout=subprocess.PIPE) ++ kwargs = {} ++ if sys.version_info.major != 2: ++ kwargs['encoding'] = 'utf-8' ++ proc = subprocess.Popen(command_line, ++ stdin=subprocess.PIPE, ++ stdout=subprocess.PIPE, ++ **kwargs) + stdout_output, stderr_output = proc.communicate(input=contents) + exit_code = proc.wait() + +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/task_queue.py b/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/task_queue.py +index 0d8f4c0f303..e666a9b668e 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/task_queue.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/bind_gen/task_queue.py +@@ -2,6 +2,7 @@ + # Use of this source code is governed by a BSD-style license that can be + # found in the LICENSE file. + ++import functools + import multiprocessing + + from .package_initializer import package_initializer +@@ -76,7 +77,7 @@ class TaskQueue(object): + if not report_progress: + return + +- done_count = reduce( ++ done_count = functools.reduce( + lambda count, worker_task: count + bool(worker_task.ready()), + self._worker_tasks, 0) + report_progress(len(self._worker_tasks), done_count) +@@ -85,4 +86,4 @@ class TaskQueue(object): + def _task_queue_run_tasks(tasks): + for task in tasks: + func, args, kwargs = task +- apply(func, args, kwargs) ++ func(*args, **kwargs) +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/code_generator.py b/chromium/third_party/blink/renderer/bindings/scripts/code_generator.py +index e8280be7213..e49e6eb965e 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/code_generator.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/code_generator.py +@@ -13,6 +13,7 @@ import re + import sys + + from idl_types import set_ancestors, IdlType ++from itertools import groupby + from v8_globals import includes + from v8_interface import constant_filters + from v8_types import set_component_dirs +@@ -43,6 +44,7 @@ TEMPLATES_DIR = os.path.normpath( + # after path[0] == invoking script dir + sys.path.insert(1, THIRD_PARTY_DIR) + import jinja2 ++from jinja2.filters import make_attrgetter, environmentfilter + + + def generate_indented_conditional(code, conditional): +@@ -88,6 +90,13 @@ def runtime_enabled_if(code, name): + return generate_indented_conditional(code, function) + + ++@environmentfilter ++def do_stringify_key_group_by(environment, value, attribute): ++ expr = make_attrgetter(environment, attribute) ++ key = lambda item: '' if expr(item) is None else str(expr(item)) ++ return groupby(sorted(value, key=key), expr) ++ ++ + def initialize_jinja_env(cache_dir): + jinja_env = jinja2.Environment( + loader=jinja2.FileSystemLoader(TEMPLATES_DIR), +@@ -117,6 +126,7 @@ def initialize_jinja_env(cache_dir): + }) + jinja_env.filters.update(constant_filters()) + jinja_env.filters.update(method_filters()) ++ jinja_env.filters["stringifykeygroupby"] = do_stringify_key_group_by + return jinja_env + + +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/generate_origin_trial_features.py b/chromium/third_party/blink/renderer/bindings/scripts/generate_origin_trial_features.py +index 130004eae83..04c0fabcef2 100755 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/generate_origin_trial_features.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/generate_origin_trial_features.py +@@ -80,7 +80,7 @@ def read_idl_file(reader, idl_filename): + assert len(interfaces) == 1, ( + "Expected one interface in file %r, found %d" % + (idl_filename, len(interfaces))) +- return (interfaces.values()[0], includes) ++ return (list(interfaces.values())[0], includes) + + + def interface_is_global(interface): +@@ -281,7 +281,7 @@ def main(): + + info_provider = create_component_info_provider( + os.path.normpath(options.info_dir), options.target_component) +- idl_filenames = map(str.strip, open(options.idl_files_list)) ++ idl_filenames = list(map(str.strip, open(options.idl_files_list))) + + generate_origin_trial_features(info_provider, options, idl_filenames) + return 0 +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/idl_definitions.py b/chromium/third_party/blink/renderer/bindings/scripts/idl_definitions.py +index 14e6e9d3f87..b027818aef2 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/idl_definitions.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/idl_definitions.py +@@ -394,7 +394,8 @@ class IdlInterface(object): + else: + raise ValueError('Unrecognized node class: %s' % child_class) + +- if len(filter(None, [self.iterable, self.maplike, self.setlike])) > 1: ++ if len(list(filter(None, ++ [self.iterable, self.maplike, self.setlike]))) > 1: + raise ValueError( + 'Interface can only have one of iterable<>, maplike<> and setlike<>.' + ) +@@ -512,6 +513,9 @@ class IdlAttribute(TypedObject): + def accept(self, visitor): + visitor.visit_attribute(self) + ++ def __lt__(self, other): ++ return self.name < other.name ++ + + ################################################################################ + # Constants +@@ -852,7 +856,7 @@ class IdlIncludes(object): + ################################################################################ + + +-class Exposure: ++class Exposure(object): + """An Exposure holds one Exposed or RuntimeEnabled condition. + Each exposure has two properties: exposed and runtime_enabled. + Exposure(e, r) corresponds to [Exposed(e r)]. Exposure(e) corresponds to +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/idl_reader.py b/chromium/third_party/blink/renderer/bindings/scripts/idl_reader.py +index 8d72865a6ca..b80eebdcd61 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/idl_reader.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/idl_reader.py +@@ -55,8 +55,8 @@ def validate_blink_idl_definitions(idl_filename, idl_file_basename, + definitions. There is no filename convention in this case. + - Otherwise, an IDL file is invalid. + """ +- targets = ( +- definitions.interfaces.values() + definitions.dictionaries.values()) ++ targets = (list(definitions.interfaces.values()) + ++ list(definitions.dictionaries.values())) + number_of_targets = len(targets) + if number_of_targets > 1: + raise Exception( +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/idl_types.py b/chromium/third_party/blink/renderer/bindings/scripts/idl_types.py +index cd4f0c3513b..ab95e9c0b08 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/idl_types.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/idl_types.py +@@ -349,7 +349,7 @@ class IdlUnionType(IdlTypeBase): + return True + + def single_matching_member_type(self, predicate): +- matching_types = filter(predicate, self.flattened_member_types) ++ matching_types = list(filter(predicate, self.flattened_member_types)) + if len(matching_types) > 1: + raise ValueError('%s is ambiguous.' % self.name) + return matching_types[0] if matching_types else None +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/utilities.py b/chromium/third_party/blink/renderer/bindings/scripts/utilities.py +index e1677ee7bd6..3c5006f064f 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/utilities.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/utilities.py +@@ -196,8 +196,9 @@ class ComponentInfoProviderModules(ComponentInfoProvider): + + @property + def callback_functions(self): +- return dict(self._component_info_core['callback_functions'].items() + +- self._component_info_modules['callback_functions'].items()) ++ return dict( ++ list(self._component_info_core['callback_functions'].items()) + ++ list(self._component_info_modules['callback_functions'].items())) + + @property + def specifier_for_export(self): +@@ -209,8 +210,8 @@ class ComponentInfoProviderModules(ComponentInfoProvider): + + + def load_interfaces_info_overall_pickle(info_dir): +- with open(os.path.join(info_dir, +- 'interfaces_info.pickle')) as interface_info_file: ++ with open(os.path.join(info_dir, 'interfaces_info.pickle'), ++ mode='rb') as interface_info_file: + return pickle.load(interface_info_file) + + +@@ -236,23 +237,20 @@ def merge_dict_recursively(target, diff): + + def create_component_info_provider_core(info_dir): + interfaces_info = load_interfaces_info_overall_pickle(info_dir) +- with open( +- os.path.join(info_dir, 'core', +- 'component_info_core.pickle')) as component_info_file: ++ with open(os.path.join(info_dir, 'core', 'component_info_core.pickle'), ++ mode='rb') as component_info_file: + component_info = pickle.load(component_info_file) + return ComponentInfoProviderCore(interfaces_info, component_info) + + + def create_component_info_provider_modules(info_dir): + interfaces_info = load_interfaces_info_overall_pickle(info_dir) +- with open( +- os.path.join(info_dir, 'core', +- 'component_info_core.pickle')) as component_info_file: ++ with open(os.path.join(info_dir, 'core', 'component_info_core.pickle'), ++ mode='rb') as component_info_file: + component_info_core = pickle.load(component_info_file) +- with open( +- os.path.join( +- info_dir, 'modules', +- 'component_info_modules.pickle')) as component_info_file: ++ with open(os.path.join(info_dir, 'modules', ++ 'component_info_modules.pickle'), ++ mode='rb') as component_info_file: + component_info_modules = pickle.load(component_info_file) + return ComponentInfoProviderModules(interfaces_info, component_info_core, + component_info_modules) +@@ -356,7 +354,7 @@ def write_pickle_file(pickle_filename, data): + pickle_filename = abs(pickle_filename) + # If |data| is same with the file content, we skip updating. + if os.path.isfile(pickle_filename): +- with open(pickle_filename) as pickle_file: ++ with open(pickle_filename, 'rb') as pickle_file: + try: + if pickle.load(pickle_file) == data: + return +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/v8_interface.py b/chromium/third_party/blink/renderer/bindings/scripts/v8_interface.py +index a43260414db..a85b03abe75 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/v8_interface.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/v8_interface.py +@@ -189,7 +189,7 @@ def context_enabled_features(attributes): + return sorted([ + member for member in members + if member.get(KEY) and not member.get('exposed_test') +- ]) ++ ], key=lambda item: item['name']) + + def member_filter_by_name(members, name): + return [member for member in members if member[KEY] == name] +@@ -612,7 +612,8 @@ def interface_context(interface, interfaces, component_info): + sorted( + origin_trial_features(interface, context['constants'], + context['attributes'], context['methods']) + +- context_enabled_features(context['attributes'])), ++ context_enabled_features(context['attributes']), ++ key=lambda item: item['name']), + }) + if context['optional_features']: + includes.add('platform/bindings/v8_per_context_data.h') +@@ -1356,9 +1357,9 @@ def resolution_tests_methods(effective_overloads): + + # Extract argument and IDL type to simplify accessing these in each loop. + arguments = [method['arguments'][index] for method in methods] +- arguments_methods = zip(arguments, methods) ++ arguments_methods = list(zip(arguments, methods)) + idl_types = [argument['idl_type_object'] for argument in arguments] +- idl_types_methods = zip(idl_types, methods) ++ idl_types_methods = list(zip(idl_types, methods)) + + # We can’t do a single loop through all methods or simply sort them, because + # a method may be listed in multiple steps of the resolution algorithm, and +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/v8_methods.py b/chromium/third_party/blink/renderer/bindings/scripts/v8_methods.py +index 5f1f89a3def..6ee8a407798 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/v8_methods.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/v8_methods.py +@@ -46,6 +46,10 @@ import v8_types + import v8_utilities + from v8_utilities import (has_extended_attribute_value, is_unforgeable) + ++# TODO: Remove this once Python2 is obsoleted. ++if sys.version_info.major != 2: ++ basestring = str ++ + + def method_is_visible(method, interface_is_partial): + if 'overloads' in method: +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/v8_utilities.py b/chromium/third_party/blink/renderer/bindings/scripts/v8_utilities.py +index 2ecd6923320..fcfc48371b1 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/v8_utilities.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/v8_utilities.py +@@ -271,7 +271,7 @@ EXPOSED_WORKERS = set([ + ]) + + +-class ExposureSet: ++class ExposureSet(object): + """An ExposureSet is a collection of Exposure instructions.""" + + def __init__(self, exposures=None): +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/web_idl/callback_interface.py b/chromium/third_party/blink/renderer/bindings/scripts/web_idl/callback_interface.py +index 13fb7c7068d..b73b7710687 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/web_idl/callback_interface.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/web_idl/callback_interface.py +@@ -91,11 +91,13 @@ class CallbackInterface(UserDefinedType, WithExtendedAttributes, + for operation_ir in ir.operations + ]) + self._operation_groups = tuple([ +- OperationGroup( +- operation_group_ir, +- filter(lambda x: x.identifier == operation_group_ir.identifier, +- self._operations), +- owner=self) for operation_group_ir in ir.operation_groups ++ OperationGroup(operation_group_ir, ++ list( ++ filter( ++ lambda x: x.identifier == operation_group_ir ++ .identifier, self._operations)), ++ owner=self) ++ for operation_group_ir in ir.operation_groups + ]) + + @property +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/web_idl/database.py b/chromium/third_party/blink/renderer/bindings/scripts/web_idl/database.py +index c92cf48eb2a..f5d59129449 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/web_idl/database.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/web_idl/database.py +@@ -156,4 +156,4 @@ class Database(object): + return self._view_by_kind(Database._Kind.UNION) + + def _view_by_kind(self, kind): +- return self._impl.find_by_kind(kind).values() ++ return list(self._impl.find_by_kind(kind).values()) +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/web_idl/exposure.py b/chromium/third_party/blink/renderer/bindings/scripts/web_idl/exposure.py +index abaeef39c30..e36cf7439ae 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/web_idl/exposure.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/web_idl/exposure.py +@@ -8,8 +8,11 @@ from .runtime_enabled_features import RuntimeEnabledFeatures + class _Feature(str): + """Represents a runtime-enabled feature.""" + ++ def __new__(cls, value): ++ return str.__new__(cls, value) ++ + def __init__(self, value): +- str.__init__(self, value) ++ str.__init__(self) + self._is_context_dependent = ( + RuntimeEnabledFeatures.is_context_dependent(self)) + +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/web_idl/function_like.py b/chromium/third_party/blink/renderer/bindings/scripts/web_idl/function_like.py +index 648c70d803d..1712f19c672 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/web_idl/function_like.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/web_idl/function_like.py +@@ -71,8 +71,9 @@ class FunctionLike(WithIdentifier): + def num_of_required_arguments(self): + """Returns the number of required arguments.""" + return len( +- filter(lambda arg: not (arg.is_optional or arg.is_variadic), +- self.arguments)) ++ list( ++ filter(lambda arg: not (arg.is_optional or arg.is_variadic), ++ self.arguments))) + + + class OverloadGroup(WithIdentifier): +@@ -171,8 +172,7 @@ class OverloadGroup(WithIdentifier): + Returns the effective overload set. + https://heycam.github.io/webidl/#compute-the-effective-overload-set + """ +- assert argument_count is None or isinstance(argument_count, +- (int, long)) ++ assert argument_count is None or isinstance(argument_count, int) + + N = argument_count + S = [] +@@ -188,21 +188,21 @@ class OverloadGroup(WithIdentifier): + + S.append( + OverloadGroup.EffectiveOverloadItem( +- X, map(lambda arg: arg.idl_type, X.arguments), +- map(lambda arg: arg.optionality, X.arguments))) ++ X, list(map(lambda arg: arg.idl_type, X.arguments)), ++ list(map(lambda arg: arg.optionality, X.arguments)))) + + if X.is_variadic: +- for i in xrange(n, max(maxarg, N)): +- t = map(lambda arg: arg.idl_type, X.arguments) +- o = map(lambda arg: arg.optionality, X.arguments) +- for _ in xrange(n, i + 1): ++ for i in range(n, max(maxarg, N)): ++ t = list(map(lambda arg: arg.idl_type, X.arguments)) ++ o = list(map(lambda arg: arg.optionality, X.arguments)) ++ for _ in range(n, i + 1): + t.append(X.arguments[-1].idl_type) + o.append(X.arguments[-1].optionality) + S.append(OverloadGroup.EffectiveOverloadItem(X, t, o)) + +- t = map(lambda arg: arg.idl_type, X.arguments) +- o = map(lambda arg: arg.optionality, X.arguments) +- for i in xrange(n - 1, -1, -1): ++ t = list(map(lambda arg: arg.idl_type, X.arguments)) ++ o = list(map(lambda arg: arg.optionality, X.arguments)) ++ for i in range(n - 1, -1, -1): + if X.arguments[i].optionality == IdlType.Optionality.REQUIRED: + break + S.append(OverloadGroup.EffectiveOverloadItem(X, t[:i], o[:i])) +@@ -222,7 +222,7 @@ class OverloadGroup(WithIdentifier): + for item in items) + assert len(items) > 1 + +- for index in xrange(len(items[0].type_list)): ++ for index in range(len(items[0].type_list)): + # Assume that the given items are valid, and we only need to test + # the two types. + if OverloadGroup.are_distinguishable_types( +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/web_idl/idl_compiler.py b/chromium/third_party/blink/renderer/bindings/scripts/web_idl/idl_compiler.py +index c5ee2bd8a3d..58315072480 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/web_idl/idl_compiler.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/web_idl/idl_compiler.py +@@ -149,8 +149,8 @@ class IdlCompiler(object): + for old_ir in old_irs: + new_ir = make_copy(old_ir) + self._ir_map.add(new_ir) +- new_ir.attributes = filter(not_disabled, new_ir.attributes) +- new_ir.operations = filter(not_disabled, new_ir.operations) ++ new_ir.attributes = list(filter(not_disabled, new_ir.attributes)) ++ new_ir.operations = list(filter(not_disabled, new_ir.operations)) + + def _record_defined_in_partial_and_mixin(self): + old_irs = self._ir_map.irs_of_kinds( +@@ -231,7 +231,7 @@ class IdlCompiler(object): + only_to_members_of_partial_or_mixin=False) + propagate_to_exposure(propagate) + +- map(process_member_like, ir.iter_all_members()) ++ list(map(process_member_like, ir.iter_all_members())) + + def process_member_like(ir): + propagate = functools.partial(propagate_extattr, ir=ir) +@@ -257,7 +257,7 @@ class IdlCompiler(object): + + self._ir_map.move_to_new_phase() + +- map(process_interface_like, old_irs) ++ list(map(process_interface_like, old_irs)) + + def _determine_blink_headers(self): + irs = self._ir_map.irs_of_kinds( +@@ -422,9 +422,9 @@ class IdlCompiler(object): + assert not new_interface.deriveds + derived_set = identifier_to_derived_set.get( + new_interface.identifier, set()) +- new_interface.deriveds = map( +- lambda id_: self._ref_to_idl_def_factory.create(id_), +- sorted(derived_set)) ++ new_interface.deriveds = list( ++ map(lambda id_: self._ref_to_idl_def_factory.create(id_), ++ sorted(derived_set))) + + def _supplement_missing_html_constructor_operation(self): + # Temporary mitigation of misuse of [HTMLConstructor] +@@ -553,7 +553,8 @@ class IdlCompiler(object): + self._ir_map.add(new_ir) + + for group in new_ir.iter_all_overload_groups(): +- exposures = map(lambda overload: overload.exposure, group) ++ exposures = list(map(lambda overload: overload.exposure, ++ group)) + + # [Exposed] + if any(not exposure.global_names_and_features +@@ -653,8 +654,8 @@ class IdlCompiler(object): + constructs = set() + for global_name in global_names: + constructs.update(exposed_map.get(global_name, [])) +- new_ir.exposed_constructs = map( +- self._ref_to_idl_def_factory.create, sorted(constructs)) ++ new_ir.exposed_constructs = list( ++ map(self._ref_to_idl_def_factory.create, sorted(constructs))) + + assert not new_ir.legacy_window_aliases + if new_ir.identifier != 'Window': +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/web_idl/interface.py b/chromium/third_party/blink/renderer/bindings/scripts/web_idl/interface.py +index 65d24e529d1..067ef2eb0b2 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/web_idl/interface.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/web_idl/interface.py +@@ -180,8 +180,9 @@ class Interface(UserDefinedType, WithExtendedAttributes, WithCodeGeneratorInfo, + self._constructor_groups = tuple([ + ConstructorGroup( + group_ir, +- filter(lambda x: x.identifier == group_ir.identifier, +- self._constructors), ++ list( ++ filter(lambda x: x.identifier == group_ir.identifier, ++ self._constructors)), + owner=self) for group_ir in ir.constructor_groups + ]) + assert len(self._constructor_groups) <= 1 +@@ -192,8 +193,9 @@ class Interface(UserDefinedType, WithExtendedAttributes, WithCodeGeneratorInfo, + self._named_constructor_groups = tuple([ + ConstructorGroup( + group_ir, +- filter(lambda x: x.identifier == group_ir.identifier, +- self._named_constructors), ++ list( ++ filter(lambda x: x.identifier == group_ir.identifier, ++ self._named_constructors)), + owner=self) for group_ir in ir.named_constructor_groups + ]) + self._operations = tuple([ +@@ -203,22 +205,23 @@ class Interface(UserDefinedType, WithExtendedAttributes, WithCodeGeneratorInfo, + self._operation_groups = tuple([ + OperationGroup( + group_ir, +- filter(lambda x: x.identifier == group_ir.identifier, +- self._operations), ++ list( ++ filter(lambda x: x.identifier == group_ir.identifier, ++ self._operations)), + owner=self) for group_ir in ir.operation_groups + ]) + self._exposed_constructs = tuple(ir.exposed_constructs) + self._legacy_window_aliases = tuple(ir.legacy_window_aliases) + self._indexed_and_named_properties = None +- indexed_and_named_property_operations = filter( +- lambda x: x.is_indexed_or_named_property_operation, +- self._operations) ++ indexed_and_named_property_operations = list( ++ filter(lambda x: x.is_indexed_or_named_property_operation, ++ self._operations)) + if indexed_and_named_property_operations: + self._indexed_and_named_properties = IndexedAndNamedProperties( + indexed_and_named_property_operations, owner=self) + self._stringifier = None +- stringifier_operation_irs = filter(lambda x: x.is_stringifier, +- ir.operations) ++ stringifier_operation_irs = list( ++ filter(lambda x: x.is_stringifier, ir.operations)) + if stringifier_operation_irs: + assert len(stringifier_operation_irs) == 1 + op_ir = make_copy(stringifier_operation_irs[0]) +@@ -231,8 +234,9 @@ class Interface(UserDefinedType, WithExtendedAttributes, WithCodeGeneratorInfo, + attribute = None + if operation.stringifier_attribute: + attr_id = operation.stringifier_attribute +- attributes = filter(lambda x: x.identifier == attr_id, +- self._attributes) ++ attributes = list( ++ filter(lambda x: x.identifier == attr_id, ++ self._attributes)) + assert len(attributes) == 1 + attribute = attributes[0] + self._stringifier = Stringifier(operation, attribute, owner=self) +@@ -578,8 +582,9 @@ class Iterable(WithDebugInfo): + self._operation_groups = tuple([ + OperationGroup( + group_ir, +- filter(lambda x: x.identifier == group_ir.identifier, +- self._operations), ++ list( ++ filter(lambda x: x.identifier == group_ir.identifier, ++ self._operations)), + owner=owner) for group_ir in ir.operation_groups + ]) + +@@ -666,8 +671,9 @@ class Maplike(WithDebugInfo): + self._operation_groups = tuple([ + OperationGroup( + group_ir, +- filter(lambda x: x.identifier == group_ir.identifier, +- self._operations), ++ list( ++ filter(lambda x: x.identifier == group_ir.identifier, ++ self._operations)), + owner=owner) for group_ir in ir.operation_groups + ]) + +@@ -755,8 +761,9 @@ class Setlike(WithDebugInfo): + self._operation_groups = tuple([ + OperationGroup( + group_ir, +- filter(lambda x: x.identifier == group_ir.identifier, +- self._operations), ++ list( ++ filter(lambda x: x.identifier == group_ir.identifier, ++ self._operations)), + owner=owner) for group_ir in ir.operation_groups + ]) + +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/web_idl/ir_builder.py b/chromium/third_party/blink/renderer/bindings/scripts/web_idl/ir_builder.py +index e9aeff4ab82..d80554d603e 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/web_idl/ir_builder.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/web_idl/ir_builder.py +@@ -2,6 +2,8 @@ + # Use of this source code is governed by a BSD-style license that can be + # found in the LICENSE file. + ++import sys ++ + from .argument import Argument + from .ast_group import AstGroup + from .attribute import Attribute +@@ -30,6 +32,11 @@ from .operation import Operation + from .typedef import Typedef + + ++# TODO: Remove this once Python2 is obsoleted. ++if sys.version_info.major != 2: ++ long = int ++ ++ + def load_and_register_idl_definitions(filepaths, register_ir, + create_ref_to_idl_def, idl_type_factory): + """ +@@ -160,7 +167,7 @@ class _IRBuilder(object): + child_nodes = list(node.GetChildren()) + extended_attributes = self._take_extended_attributes(child_nodes) + +- members = map(self._build_interface_member, child_nodes) ++ members = list(map(self._build_interface_member, child_nodes)) + attributes = [] + constants = [] + operations = [] +@@ -302,7 +309,7 @@ class _IRBuilder(object): + child_nodes = list(node.GetChildren()) + inherited = self._take_inheritance(child_nodes) + extended_attributes = self._take_extended_attributes(child_nodes) +- own_members = map(self._build_dictionary_member, child_nodes) ++ own_members = list(map(self._build_dictionary_member, child_nodes)) + + return Dictionary.IR( + identifier=Identifier(node.GetName()), +@@ -336,7 +343,7 @@ class _IRBuilder(object): + + child_nodes = list(node.GetChildren()) + extended_attributes = self._take_extended_attributes(child_nodes) +- members = map(self._build_interface_member, child_nodes) ++ members = list(map(self._build_interface_member, child_nodes)) + constants = [] + operations = [] + for member in members: +@@ -456,8 +463,8 @@ class _IRBuilder(object): + assert len(child_nodes) == 1 + child = child_nodes[0] + if child.GetClass() == 'Arguments': +- arguments = map(build_extattr_argument, +- child.GetChildren()) ++ arguments = list( ++ map(build_extattr_argument, child.GetChildren())) + elif child.GetClass() == 'Call': + assert len(child.GetChildren()) == 1 + grand_child = child.GetChildren()[0] +@@ -486,7 +493,9 @@ class _IRBuilder(object): + + assert node.GetClass() == 'ExtAttributes' + return ExtendedAttributes( +- filter(None, map(build_extended_attribute, node.GetChildren()))) ++ list( ++ filter(None, map(build_extended_attribute, ++ node.GetChildren())))) + + def _build_inheritance(self, node): + assert node.GetClass() == 'Inherit' +@@ -506,7 +515,7 @@ class _IRBuilder(object): + + def _build_iterable(self, node): + assert node.GetClass() == 'Iterable' +- types = map(self._build_type, node.GetChildren()) ++ types = list(map(self._build_type, node.GetChildren())) + assert len(types) == 1 or len(types) == 2 + if len(types) == 1: # value iterator + key_type, value_type = (None, types[0]) +@@ -584,7 +593,7 @@ class _IRBuilder(object): + def _build_maplike(self, node, interface_identifier): + assert node.GetClass() == 'Maplike' + assert isinstance(interface_identifier, Identifier) +- types = map(self._build_type, node.GetChildren()) ++ types = list(map(self._build_type, node.GetChildren())) + assert len(types) == 2 + key_type, value_type = types + is_readonly = bool(node.GetProperty('READONLY')) +@@ -676,7 +685,7 @@ class _IRBuilder(object): + def _build_setlike(self, node, interface_identifier): + assert node.GetClass() == 'Setlike' + assert isinstance(interface_identifier, Identifier) +- types = map(self._build_type, node.GetChildren()) ++ types = list(map(self._build_type, node.GetChildren())) + assert len(types) == 1 + value_type = types[0] + is_readonly = bool(node.GetProperty('READONLY')) +@@ -838,7 +847,7 @@ class _IRBuilder(object): + + def build_union_type(node, extended_attributes): + return self._idl_type_factory.union_type( +- member_types=map(self._build_type, node.GetChildren()), ++ member_types=list(map(self._build_type, node.GetChildren())), + is_optional=is_optional, + extended_attributes=extended_attributes, + debug_info=self._build_debug_info(node)) +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/web_idl/make_copy.py b/chromium/third_party/blink/renderer/bindings/scripts/web_idl/make_copy.py +index a7a2b11f3f0..2f6b61300ff 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/web_idl/make_copy.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/web_idl/make_copy.py +@@ -3,6 +3,13 @@ + # found in the LICENSE file. + + ++import sys ++ ++# TODO: Remove this once Python2 is obsoleted. ++if sys.version_info.major != 2: ++ long = int ++ basestring = str ++ + def make_copy(obj, memo=None): + """ + Creates a copy of the given object, which should be an IR or part of IR. +diff --git a/chromium/third_party/blink/renderer/bindings/scripts/web_idl/namespace.py b/chromium/third_party/blink/renderer/bindings/scripts/web_idl/namespace.py +index eeabef97cbe..bd7e98907f3 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/scripts/web_idl/namespace.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/scripts/web_idl/namespace.py +@@ -107,11 +107,13 @@ class Namespace(UserDefinedType, WithExtendedAttributes, WithCodeGeneratorInfo, + for operation_ir in ir.operations + ]) + self._operation_groups = tuple([ +- OperationGroup( +- operation_group_ir, +- filter(lambda x: x.identifier == operation_group_ir.identifier, +- self._operations), +- owner=self) for operation_group_ir in ir.operation_groups ++ OperationGroup(operation_group_ir, ++ list( ++ filter( ++ lambda x: x.identifier == operation_group_ir ++ .identifier, self._operations)), ++ owner=self) ++ for operation_group_ir in ir.operation_groups + ]) + + @property +diff --git a/chromium/third_party/blink/renderer/bindings/templates/dictionary_v8.cc.tmpl b/chromium/third_party/blink/renderer/bindings/templates/dictionary_v8.cc.tmpl +index 0add9c45a38..dc910f6d227 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/bindings/templates/dictionary_v8.cc.tmpl ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/bindings/templates/dictionary_v8.cc.tmpl +@@ -59,9 +59,9 @@ void {{v8_class}}::ToImpl(v8::Isolate* isolate, v8::Local v8_value, { + DCHECK(executionContext); + {% endif %}{# has_origin_trial_members #} + {% endif %}{# members #} +- {% for origin_trial_test, origin_trial_member_list in members | groupby('origin_trial_feature_name') %} ++ {% for origin_trial_test, origin_trial_member_list in members | stringifykeygroupby('origin_trial_feature_name') %} + {% filter origin_trial_enabled(origin_trial_test, "executionContext") %} +- {% for feature_name, member_list in origin_trial_member_list | groupby('runtime_enabled_feature_name') %} ++ {% for feature_name, member_list in origin_trial_member_list | stringifykeygroupby('runtime_enabled_feature_name') %} + {% filter runtime_enabled(feature_name) %} + {% for member in member_list %} + v8::Local {{member.v8_value}}; +@@ -147,9 +147,9 @@ bool toV8{{cpp_class}}(const {{cpp_class}}* impl, v8::Local dictiona + DCHECK(executionContext); + {% endif %}{# has_origin_trial_members #} + {% endif %}{# members #} +- {% for origin_trial_test, origin_trial_member_list in members | groupby('origin_trial_feature_name') %} ++ {% for origin_trial_test, origin_trial_member_list in members | stringifykeygroupby('origin_trial_feature_name') %} + {% filter origin_trial_enabled(origin_trial_test, "executionContext") %} +- {% for feature_name, member_list in origin_trial_member_list | groupby('runtime_enabled_feature_name') %} ++ {% for feature_name, member_list in origin_trial_member_list | stringifykeygroupby('runtime_enabled_feature_name') %} + {% filter runtime_enabled(feature_name) %} + {% for member in member_list %} + v8::Local {{member.v8_value}}; +diff --git a/chromium/third_party/blink/renderer/build/scripts/core/css/make_style_shorthands.py b/chromium/third_party/blink/renderer/build/scripts/core/css/make_style_shorthands.py +index 1799cd5a153..5f43ffabc26 100755 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/build/scripts/core/css/make_style_shorthands.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/build/scripts/core/css/make_style_shorthands.py +@@ -71,7 +71,7 @@ class Expansion(object): + def enabled_longhands(self): + include = lambda longhand: not longhand[ + 'runtime_flag'] or self.is_enabled(longhand['runtime_flag']) +- return filter(include, self._longhands) ++ return list(filter(include, self._longhands)) + + @property + def index(self): +@@ -87,8 +87,9 @@ class Expansion(object): + + def create_expansions(longhands): + flags = collect_runtime_flags(longhands) +- expansions = map(lambda mask: Expansion(longhands, flags, mask), +- range(1 << len(flags))) ++ expansions = list( ++ map(lambda mask: Expansion(longhands, flags, mask), ++ range(1 << len(flags)))) + assert len(expansions) > 0 + # We generate 2^N expansions for N flags, so enforce some limit. + assert len(flags) <= 4, 'Too many runtime flags for a single shorthand' +@@ -114,14 +115,14 @@ class StylePropertyShorthandWriter(json5_generator.Writer): + + self._longhand_dictionary = defaultdict(list) + for property_ in json5_properties.shorthands: +- property_['longhand_enum_keys'] = map(enum_key_for_css_property, +- property_['longhands']) +- property_['longhand_property_ids'] = map(id_for_css_property, +- property_['longhands']) +- +- longhands = map( +- lambda name: json5_properties.properties_by_name[name], +- property_['longhands']) ++ property_['longhand_enum_keys'] = list( ++ map(enum_key_for_css_property, property_['longhands'])) ++ property_['longhand_property_ids'] = list( ++ map(id_for_css_property, property_['longhands'])) ++ ++ longhands = list( ++ map(lambda name: json5_properties.properties_by_name[name], ++ property_['longhands'])) + property_['expansions'] = create_expansions(longhands) + for longhand_enum_key in property_['longhand_enum_keys']: + self._longhand_dictionary[longhand_enum_key].append(property_) +diff --git a/chromium/third_party/blink/renderer/build/scripts/core/css/properties/make_css_property_instances.py b/chromium/third_party/blink/renderer/build/scripts/core/css/properties/make_css_property_instances.py +index 75030ac577e..f72aadee17d 100755 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/build/scripts/core/css/properties/make_css_property_instances.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/build/scripts/core/css/properties/make_css_property_instances.py +@@ -42,8 +42,8 @@ class CSSPropertyInstancesWriter(json5_generator.Writer): + aliases = self._css_properties.aliases + + # Lists of PropertyClassData. +- self._property_classes_by_id = map(self.get_class, properties) +- self._alias_classes_by_id = map(self.get_class, aliases) ++ self._property_classes_by_id = list(map(self.get_class, properties)) ++ self._alias_classes_by_id = list(map(self.get_class, aliases)) + + # Sort by enum value. + self._property_classes_by_id.sort(key=lambda t: t.enum_value) +diff --git a/chromium/third_party/blink/renderer/build/scripts/gperf.py b/chromium/third_party/blink/renderer/build/scripts/gperf.py +index 5ee49056be4..db72660d471 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/build/scripts/gperf.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/build/scripts/gperf.py +@@ -95,7 +95,7 @@ def main(): + + open(args.output_file, 'wb').write( + generate_gperf(gperf_path, +- open(infile).read(), gperf_args)) ++ open(infile).read(), gperf_args).encode('utf-8')) + + + if __name__ == '__main__': +diff --git a/chromium/third_party/blink/renderer/build/scripts/in_file.py b/chromium/third_party/blink/renderer/build/scripts/in_file.py +index 28adc050f1e..58113483e57 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/build/scripts/in_file.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/build/scripts/in_file.py +@@ -66,7 +66,7 @@ class InFile(object): + self._defaults = defaults + self._valid_values = copy.deepcopy( + valid_values if valid_values else {}) +- self._parse(map(str.strip, lines)) ++ self._parse(list(map(str.strip, lines))) + + @classmethod + def load_from_files(self, file_paths, defaults, valid_values, +diff --git a/chromium/third_party/blink/renderer/build/scripts/in_generator.py b/chromium/third_party/blink/renderer/build/scripts/in_generator.py +index e46740a2e85..ab1981ad1e3 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/build/scripts/in_generator.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/build/scripts/in_generator.py +@@ -32,10 +32,15 @@ import os + import os.path + import shlex + import shutil ++import sys + import optparse + + from in_file import InFile + ++# TODO: Remove this once Python2 is obsoleted. ++if sys.version_info.major != 2: ++ basestring = str ++ + + ######################################################### + # This is now deprecated - use json5_generator.py instead +diff --git a/chromium/third_party/blink/renderer/build/scripts/make_runtime_features.py b/chromium/third_party/blink/renderer/build/scripts/make_runtime_features.py +index cafe8d94a8e..6925a4fa580 100755 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/build/scripts/make_runtime_features.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/build/scripts/make_runtime_features.py +@@ -138,7 +138,7 @@ class RuntimeFeatureWriter(BaseRuntimeFeatureWriter): + except Exception: + # If trouble unpickling, overwrite + pass +- with open(os.path.abspath(file_name), 'w') as pickle_file: ++ with open(os.path.abspath(file_name), 'wb') as pickle_file: + pickle.dump(features_map, pickle_file) + + def _template_inputs(self): +diff --git a/chromium/third_party/blink/renderer/build/scripts/templates/element_factory.cc.tmpl b/chromium/third_party/blink/renderer/build/scripts/templates/element_factory.cc.tmpl +index dc3f44c5b10..3eefcf9f0ee 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/build/scripts/templates/element_factory.cc.tmpl ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/build/scripts/templates/element_factory.cc.tmpl +@@ -26,7 +26,7 @@ using {{namespace}}FunctionMap = HashMapGetExecutionContext())) { +diff --git a/chromium/third_party/blink/renderer/build/scripts/templates/element_type_helpers.h.tmpl b/chromium/third_party/blink/renderer/build/scripts/templates/element_type_helpers.h.tmpl +index 1b5297d52dc..edecc81d9d4 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/build/scripts/templates/element_type_helpers.h.tmpl ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/build/scripts/templates/element_type_helpers.h.tmpl +@@ -15,7 +15,7 @@ namespace blink { + class Document; + + // Type checking. +-{% for tag in tags|sort if not tag.multipleTagNames and not tag.noTypeHelpers %} ++{% for tag in tags|sort(attribute='name') if not tag.multipleTagNames and not tag.noTypeHelpers %} + class {{tag.interface}}; + template <> + inline bool IsElementOfType(const Node& node) { +diff --git a/chromium/third_party/blink/renderer/build/scripts/templates/macros.tmpl b/chromium/third_party/blink/renderer/build/scripts/templates/macros.tmpl +index 0244433af2e..dcdbb02a56c 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/build/scripts/templates/macros.tmpl ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/build/scripts/templates/macros.tmpl +@@ -25,7 +25,7 @@ + + + {% macro trie_leaf(index, object, return_macro, lowercase_data) %} +-{% set name, value = object.items()[0] %} ++{% set name, value = (object.items()|list)[0] %} + {% if name|length %} + if ( + {%- for c in name -%} +@@ -45,7 +45,7 @@ return {{ return_macro(value) }}; + + + {% macro trie_switch(trie, index, return_macro, lowercase_data) %} +-{% if trie|length == 1 and trie.values()[0] is string %} ++{% if trie|length == 1 and (trie.values()|list)[0] is string %} + {{ trie_leaf(index, trie, return_macro, lowercase_data) -}} + {% else %} + {% if lowercase_data %} +diff --git a/chromium/third_party/blink/renderer/build/scripts/templates/make_qualified_names.h.tmpl b/chromium/third_party/blink/renderer/build/scripts/templates/make_qualified_names.h.tmpl +index cb05c6c4315..bd5566b03e7 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/blink/renderer/build/scripts/templates/make_qualified_names.h.tmpl ++++ b/qtwebengine/src/3rdparty/chromium/third_party/blink/renderer/build/scripts/templates/make_qualified_names.h.tmpl +@@ -24,12 +24,12 @@ namespace {{cpp_namespace}} { + {{symbol_export}}extern const WTF::AtomicString& {{namespace_prefix}}NamespaceURI; + + // Tags +-{% for tag in tags|sort %} ++{% for tag in tags|sort(attribute='name') %} + {{symbol_export}}extern const blink::{{namespace}}QualifiedName& {{tag|symbol}}Tag; + {% endfor %} + + // Attributes +-{% for attr in attrs|sort %} ++{% for attr in attrs|sort(attribute='name') %} + {{symbol_export}}extern const blink::QualifiedName& {{attr|symbol}}Attr; + {% endfor %} + +diff --git a/chromium/third_party/dawn/generator/generator_lib.py b/chromium/third_party/dawn/generator/generator_lib.py +index 5e3734d7833..e3d46bd194f 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/dawn/generator/generator_lib.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/dawn/generator/generator_lib.py +@@ -201,6 +201,10 @@ def _compute_python_dependencies(root_dir=None): + + paths = set() + for path in module_paths: ++ # Builtin/namespaced modules may return None for the file path. ++ if not path: ++ continue ++ + path = os.path.abspath(path) + + if not path.startswith(root_dir): +diff --git a/chromium/third_party/devtools-frontend/src/BUILD.gn b/chromium/third_party/devtools-frontend/src/BUILD.gn +index cd488e88b60..ea1dc3d9a79 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/devtools-frontend/src/BUILD.gn ++++ b/qtwebengine/src/3rdparty/chromium/third_party/devtools-frontend/src/BUILD.gn +@@ -2,6 +2,8 @@ + # Use of this source code is governed by a BSD-style license that can be + # found in the LICENSE file. + ++import("//build/config/python.gni") ++ + import("//third_party/blink/public/public_features.gni") + import("./all_devtools_files.gni") + import("./all_devtools_modules.gni") +diff --git a/chromium/third_party/devtools-frontend/src/scripts/build/build_inspector_overlay.py b/chromium/third_party/devtools-frontend/src/scripts/build/build_inspector_overlay.py +index d6666e8b74f..0f7a661e632 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/devtools-frontend/src/scripts/build/build_inspector_overlay.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/devtools-frontend/src/scripts/build/build_inspector_overlay.py +@@ -45,7 +45,8 @@ def rollup(input_path, output_path, filename, max_size, rollup_plugin): + ['--format', 'iife', '-n', 'InspectorOverlay'] + ['--input', target] + + ['--plugin', rollup_plugin], + stdout=subprocess.PIPE, +- stderr=subprocess.PIPE) ++ stderr=subprocess.PIPE, ++ text=True) + out, error = rollup_process.communicate() + if not out: + raise Exception("rollup failed: " + error) +diff --git a/chromium/third_party/devtools-frontend/src/scripts/build/build_release_applications.py b/chromium/third_party/devtools-frontend/src/scripts/build/build_release_applications.py +index fa8e73d34af..7d0b84b2171 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/devtools-frontend/src/scripts/build/build_release_applications.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/devtools-frontend/src/scripts/build/build_release_applications.py +@@ -10,7 +10,7 @@ Builds applications in release mode: + and the application loader into a single script. + """ + +-from cStringIO import StringIO ++from io import StringIO + from os import path + from os.path import join + import copy +@@ -145,8 +145,7 @@ class ReleaseBuilder(object): + resource_content = read_file(path.join(self.application_dir, resource_name)) + if not (resource_name.endswith('.html') + or resource_name.endswith('md')): +- resource_content += resource_source_url(resource_name).encode( +- 'utf-8') ++ resource_content += resource_source_url(resource_name) + resource_content = resource_content.replace('\\', '\\\\') + resource_content = resource_content.replace('\n', '\\n') + resource_content = resource_content.replace('"', '\\"') +@@ -173,7 +172,9 @@ class ReleaseBuilder(object): + def _concatenate_application_script(self, output): + output.write('Root.allDescriptors.push(...%s);' % self._release_module_descriptors()) + if self.descriptors.extends: +- output.write('Root.applicationDescriptor.modules.push(...%s);' % json.dumps(self.descriptors.application.values())) ++ output.write( ++ 'Root.applicationDescriptor.modules.push(...%s);' % ++ json.dumps(list(self.descriptors.application.values()))) + else: + output.write('Root.applicationDescriptor = %s;' % self.descriptors.application_json()) + +diff --git a/chromium/third_party/devtools-frontend/src/scripts/build/generate_devtools_grd.py b/chromium/third_party/devtools-frontend/src/scripts/build/generate_devtools_grd.py +index be510c48d76..c6a59c90298 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/devtools-frontend/src/scripts/build/generate_devtools_grd.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/devtools-frontend/src/scripts/build/generate_devtools_grd.py +@@ -123,7 +123,7 @@ def main(argv): + + try: + os.makedirs(path.join(output_directory, 'Images')) +- except OSError, e: ++ except OSError as e: + if e.errno != errno.EEXIST: + raise e + +@@ -147,7 +147,7 @@ def main(argv): + shutil.copy(path.join(dirname, filename), path.join(output_directory, 'Images')) + add_file_to_grd(doc, path.join('Images', filename)) + +- with open(parsed_args.output_filename, 'w') as output_file: ++ with open(parsed_args.output_filename, 'wb') as output_file: + output_file.write(doc.toxml(encoding='UTF-8')) + + +diff --git a/chromium/third_party/devtools-frontend/src/scripts/build/modular_build.py b/chromium/third_party/devtools-frontend/src/scripts/build/modular_build.py +index 0ba695d3810..bb1da2f9f8d 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/devtools-frontend/src/scripts/build/modular_build.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/devtools-frontend/src/scripts/build/modular_build.py +@@ -7,6 +7,8 @@ + Utilities for the modular DevTools build. + """ + ++from __future__ import print_function ++ + import collections + from os import path + import os +@@ -40,7 +42,7 @@ def load_and_parse_json(filename): + try: + return json.loads(read_file(filename)) + except: +- print 'ERROR: Failed to parse %s' % filename ++ print('ERROR: Failed to parse %s' % filename) + raise + + class Descriptors: +@@ -57,7 +59,7 @@ class Descriptors: + + def application_json(self): + result = dict() +- result['modules'] = self.application.values() ++ result['modules'] = list(self.application.values()) + return json.dumps(result) + + def all_compiled_files(self): +diff --git a/chromium/third_party/jinja2/tests.py b/chromium/third_party/jinja2/tests.py +index 0adc3d4dbcb..b14f85ff148 100644 +--- a/qtwebengine/src/3rdparty/chromium/chromium/third_party/jinja2/tests.py ++++ b/qtwebengine/src/3rdparty/chromium/third_party/jinja2/tests.py +@@ -10,7 +10,7 @@ + """ + import operator + import re +-from collections import Mapping ++from collections.abc import Mapping + from jinja2.runtime import Undefined + from jinja2._compat import text_type, string_types, integer_types + import decimal +diff --git a/chromium/tools/metrics/ukm/gen_builders.py b/chromium/tools/metrics/ukm/gen_builders.py +index f9f61d90a56..44e46fae8cc 100755 +--- a/qtwebengine/src/3rdparty/chromium/chromium/tools/metrics/ukm/gen_builders.py ++++ b/qtwebengine/src/3rdparty/chromium/tools/metrics/ukm/gen_builders.py +@@ -48,9 +48,10 @@ def ReadFilteredData(path): + data = ukm_model.UKM_XML_TYPE.Parse(ukm_file.read()) + event_tag = ukm_model._EVENT_TYPE.tag + metric_tag = ukm_model._METRIC_TYPE.tag +- data[event_tag] = filter(ukm_model.IsNotObsolete, data[event_tag]) ++ data[event_tag] = list(filter(ukm_model.IsNotObsolete, data[event_tag])) + for event in data[event_tag]: +- event[metric_tag] = filter(ukm_model.IsNotObsolete, event[metric_tag]) ++ event[metric_tag] = list( ++ filter(ukm_model.IsNotObsolete, event[metric_tag])) + return data + + +diff --git a/chromium/ui/ozone/generate_constructor_list.py b/chromium/ui/ozone/generate_constructor_list.py +index 8d800636c97..04fa18e93df 100755 +--- a/qtwebengine/src/3rdparty/chromium/chromium/ui/ozone/generate_constructor_list.py ++++ b/qtwebengine/src/3rdparty/chromium/ui/ozone/generate_constructor_list.py +@@ -45,12 +45,15 @@ Example Output: ./ui/ozone/generate_constructor_list.py \ + } // namespace ui + """ + ++try: ++ from StringIO import StringIO # for Python 2 ++except ImportError: ++ from io import StringIO # for Python 3 + import optparse + import os + import collections + import re + import sys +-import string + + + def GetTypedefName(typename): +@@ -68,7 +71,7 @@ def GetConstructorName(typename, platform): + This is just "Create" + typename + platform. + """ + +- return 'Create' + typename + string.capitalize(platform) ++ return 'Create' + typename + platform.capitalize() + + + def GenerateConstructorList(out, namespace, export, typenames, platforms, +@@ -163,12 +166,14 @@ def main(argv): + sys.exit(1) + + # Write to standard output or file specified by --output_cc. +- out_cc = sys.stdout ++ out_cc = getattr(sys.stdout, 'buffer', sys.stdout) + if options.output_cc: + out_cc = open(options.output_cc, 'wb') + +- GenerateConstructorList(out_cc, options.namespace, options.export, ++ out_cc_str = StringIO() ++ GenerateConstructorList(out_cc_str, options.namespace, options.export, + typenames, platforms, includes, usings) ++ out_cc.write(out_cc_str.getvalue().encode('utf-8')) + + if options.output_cc: + out_cc.close() +diff --git a/chromium/ui/ozone/generate_ozone_platform_list.py b/chromium/ui/ozone/generate_ozone_platform_list.py +index d47c398259b..2702b68b9bd 100755 +--- a/qtwebengine/src/3rdparty/chromium/chromium/ui/ozone/generate_ozone_platform_list.py ++++ b/qtwebengine/src/3rdparty/chromium/ui/ozone/generate_ozone_platform_list.py +@@ -49,12 +49,15 @@ Example Output: ./generate_ozone_platform_list.py --default wayland dri wayland + + """ + ++try: ++ from StringIO import StringIO # for Python 2 ++except ImportError: ++ from io import StringIO # for Python 3 + import optparse + import os + import collections + import re + import sys +-import string + + + def GetConstantName(name): +@@ -63,7 +66,7 @@ def GetConstantName(name): + We just capitalize the platform name and prepend "CreateOzonePlatform". + """ + +- return 'kPlatform' + string.capitalize(name) ++ return 'kPlatform' + name.capitalize() + + + def GeneratePlatformListText(out, platforms): +@@ -149,9 +152,9 @@ def main(argv): + platforms.insert(0, options.default) + + # Write to standard output or file specified by --output_{cc,h}. +- out_cc = sys.stdout +- out_h = sys.stdout +- out_txt = sys.stdout ++ out_cc = getattr(sys.stdout, 'buffer', sys.stdout) ++ out_h = getattr(sys.stdout, 'buffer', sys.stdout) ++ out_txt = getattr(sys.stdout, 'buffer', sys.stdout) + if options.output_cc: + out_cc = open(options.output_cc, 'wb') + if options.output_h: +@@ -159,9 +162,16 @@ def main(argv): + if options.output_txt: + out_txt = open(options.output_txt, 'wb') + +- GeneratePlatformListText(out_txt, platforms) +- GeneratePlatformListHeader(out_h, platforms) +- GeneratePlatformListSource(out_cc, platforms) ++ out_txt_str = StringIO() ++ out_h_str = StringIO() ++ out_cc_str = StringIO() ++ ++ GeneratePlatformListText(out_txt_str, platforms) ++ out_txt.write(out_txt_str.getvalue().encode('utf-8')) ++ GeneratePlatformListHeader(out_h_str, platforms) ++ out_h.write(out_h_str.getvalue().encode('utf-8')) ++ GeneratePlatformListSource(out_cc_str, platforms) ++ out_cc.write(out_cc_str.getvalue().encode('utf-8')) + + if options.output_cc: + out_cc.close() +-- +2.35.1 + diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-drop-catapult.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-drop-catapult.patch new file mode 100644 index 00000000000..db149389f03 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-drop-catapult.patch @@ -0,0 +1,32 @@ +From b60fc250d65144532cd47eac72279e93baaec2b8 Mon Sep 17 00:00:00 2001 +From: Jimi Huotari +Date: Wed, 6 Apr 2022 14:35:14 +0300 +Subject: [PATCH] Remove dependency on catapult + +--- + src/core/qtwebengine_resources.gni | 2 -- + 1 file changed, 2 deletions(-) + +diff --git a/src/core/qtwebengine_resources.gni b/src/core/qtwebengine_resources.gni +index 3bf1a5d57..29fd2603c 100644 +--- a/qtwebengine/src/core/qtwebengine_resources.gni ++++ b/qtwebengine/src/core/qtwebengine_resources.gni +@@ -27,7 +27,6 @@ repack("qtwebengine_repack_resources") { + "$root_gen_dir/components/components_resources.pak", + "$root_gen_dir/components/dev_ui_components_resources.pak", + "$root_gen_dir/content/browser/resources/media/media_internals_resources.pak", +- "$root_gen_dir/content/browser/tracing/tracing_resources.pak", + "$root_gen_dir/content/content_resources.pak", + "$root_gen_dir/content/dev_ui_content_resources.pak", + "$root_gen_dir/mojo/public/js/mojo_bindings_resources.pak", +@@ -44,7 +43,6 @@ repack("qtwebengine_repack_resources") { + "//components/resources:components_resources_grit", + "//components/resources:dev_ui_components_resources_grit", + "//content/browser/resources/media:media_internals_resources", +- "//content/browser/tracing:resources", + "//content:content_resources_grit", + "//content:dev_ui_content_resources_grit", + "//mojo/public/js:resources", +-- +2.35.1 + diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-python3.11.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-python3.11.patch new file mode 100644 index 00000000000..454dcfa3d89 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-python3.11.patch @@ -0,0 +1,46 @@ +Description: fix build with Python 3.11 +Author: Dmitry Shachnev +Last-Update: 2023-01-08 + +--- a/qtwebengine/src/3rdparty/chromium/tools/grit/grit/util.py ++++ b/qtwebengine/src/3rdparty/chromium/tools/grit/grit/util.py +@@ -211,7 +211,7 @@ def ReadFile(filename, encoding): + mode = 'rb' + encoding = None + else: +- mode = 'rU' ++ mode = 'r' + + with io.open(abs(filename), mode, encoding=encoding) as f: + return f.read() +--- a/qtwebengine/src/3rdparty/chromium/tools/metrics/structured/model.py ++++ b/qtwebengine/src/3rdparty/chromium/tools/metrics/structured/model.py +@@ -26,7 +26,7 @@ _METRIC_TYPE = models.ObjectNodeType( + 'metric', + attributes=[ + ('name', unicode, r'^[A-Za-z0-9_.]+$'), +- ('kind', unicode, r'^(?i)(|hashed-string|int)$'), ++ ('kind', unicode, r'(?i)^(|hashed-string|int)$'), + ], + alphabetization=[ + (_OBSOLETE_TYPE.tag, lambda _: 1), +--- a/qtwebengine/src/3rdparty/chromium/tools/metrics/ukm/ukm_model.py ++++ b/qtwebengine/src/3rdparty/chromium/tools/metrics/ukm/ukm_model.py +@@ -42,7 +42,7 @@ _INDEX_TYPE = models.ObjectNodeType( + _STATISTICS_TYPE = models.ObjectNodeType( + 'statistics', + attributes=[ +- ('export', str, r'^(?i)(|true|false)$'), ++ ('export', str, r'(?i)^(|true|false)$'), + ], + children=[ + models.ChildType(_QUANTILES_TYPE.tag, _QUANTILES_TYPE, multiple=False), +@@ -94,7 +94,7 @@ _EVENT_TYPE = models.ObjectNodeType( + 'event', + attributes=[ + ('name', str, r'^[A-Za-z0-9.]+$'), +- ('singular', str, r'^(?i)(|true|false)$'), ++ ('singular', str, r'(?i)^(|true|false)$'), + ], + alphabetization=[ + (_OBSOLETE_TYPE.tag, _KEEP_ORDER), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-python3.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-python3.patch new file mode 100644 index 00000000000..15451cd435b --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.10_webengine-python3.patch @@ -0,0 +1,176 @@ +From cf6eb34ea064fc273bdb3de7646894b8df1f7bc8 Mon Sep 17 00:00:00 2001 +From: Antonio Rojas +Date: Sat, 16 Oct 2021 20:17:35 +0000 +Subject: [PATCH] Build without python 2 + +--- + configure.pri | 25 ++++++------------------- + mkspecs/features/functions.prf | 6 +++--- + src/buildtools/config/support.pri | 10 +++++----- + src/buildtools/configure.json | 18 +++++++++--------- + 4 files changed, 23 insertions(+), 36 deletions(-) + +diff --git a/configure.pri b/configure.pri +index 8705ad93f..94d41e9c4 100644 +--- a/qtwebengine/configure.pri ++++ b/qtwebengine/configure.pri +@@ -7,20 +7,7 @@ QTWEBENGINE_SOURCE_TREE = $$PWD + equals(QMAKE_HOST.os, Windows): EXE_SUFFIX = .exe + + defineTest(isPythonVersionSupported) { +- python = $$system_quote($$system_path($$1)) +- python_version = $$system('$$python -c "import sys; print(sys.version_info[0:3])"') +- python_version ~= s/[()]//g +- python_version = $$split(python_version, ',') +- python_major_version = $$first(python_version) +- greaterThan(python_major_version, 2) { +- qtLog("Python version 3 is not supported by Chromium.") +- return(false) +- } +- python_minor_version = $$member(python_version, 1) +- python_patch_version = $$member(python_version, 2) +- greaterThan(python_major_version, 1): greaterThan(python_minor_version, 6): greaterThan(python_patch_version, 4): return(true) +- qtLog("Unsupported python version: $${python_major_version}.$${python_minor_version}.$${python_patch_version}.") +- return(false) ++ return(true) + } + + defineTest(qtConfTest_detectJumboBuild) { +@@ -52,10 +39,10 @@ defineTest(qtConfReport_jumboBuild) { + qtConfReportPadded($${1}, $$mergeLimit) + } + +-defineTest(qtConfTest_detectPython2) { +- python = $$qtConfFindInPath("python2$$EXE_SUFFIX") ++defineTest(qtConfTest_detectPython) { ++ python = $$qtConfFindInPath("python$$EXE_SUFFIX") + isEmpty(python) { +- qtLog("'python2$$EXE_SUFFIX' not found in PATH. Checking for 'python$$EXE_SUFFIX'.") ++ qtLog("'python$$EXE_SUFFIX' not found in PATH. Checking for 'python$$EXE_SUFFIX'.") + python = $$qtConfFindInPath("python$$EXE_SUFFIX") + } + isEmpty(python) { +@@ -63,11 +50,11 @@ defineTest(qtConfTest_detectPython2) { + return(false) + } + !isPythonVersionSupported($$python) { +- qtLog("A suitable Python 2 executable could not be located.") ++ qtLog("A suitable Python executable could not be located.") + return(false) + } + +- # Make tests.python2.location available in configure.json. ++ # Make tests.python.location available in configure.json. + $${1}.location = $$clean_path($$python) + export($${1}.location) + $${1}.cache += location +diff --git a/mkspecs/features/functions.prf b/mkspecs/features/functions.prf +index 2750d7071..9fda13d08 100644 +--- a/qtwebengine/mkspecs/features/functions.prf ++++ b/qtwebengine/mkspecs/features/functions.prf +@@ -39,11 +39,11 @@ defineReplace(which) { + + # Returns the unquoted path to the python executable. + defineReplace(pythonPath) { +- isEmpty(QMAKE_PYTHON2) { ++ isEmpty(QMAKE_PYTHON) { + # Fallback for building QtWebEngine with Qt < 5.8 +- QMAKE_PYTHON2 = python ++ QMAKE_PYTHON = python + } +- return($$QMAKE_PYTHON2) ++ return($$QMAKE_PYTHON) + } + + # Returns the python executable for use with shell / make targets. +diff --git a/src/buildtools/config/support.pri b/src/buildtools/config/support.pri +index 7a07b1b5b..497a9e0e2 100644 +--- a/qtwebengine/src/buildtools/config/support.pri ++++ b/qtwebengine/src/buildtools/config/support.pri +@@ -21,7 +21,7 @@ defineReplace(qtwebengine_checkWebEngineCoreError) { + !qtwebengine_checkForGperf(QtWebEngine):return(false) + !qtwebengine_checkForBison(QtWebEngine):return(false) + !qtwebengine_checkForFlex(QtWebEngine):return(false) +- !qtwebengine_checkForPython2(QtWebEngine):return(false) ++ !qtwebengine_checkForPython(QtWebEngine):return(false) + !qtwebengine_checkForNodejs(QtWebEngine):return(false) + !qtwebengine_checkForSanitizer(QtWebEngine):return(false) + linux:!qtwebengine_checkForPkgCfg(QtWebEngine):return(false) +@@ -51,7 +51,7 @@ defineReplace(qtwebengine_checkPdfError) { + !qtwebengine_checkForGperf(QtPdf):return(false) + !qtwebengine_checkForBison(QtPdf):return(false) + !qtwebengine_checkForFlex(QtPdf):return(false) +- !qtwebengine_checkForPython2(QtPdf):return(false) ++ !qtwebengine_checkForPython(QtPdf):return(false) + !qtwebengine_checkForSanitizer(QtPdf):return(false) + linux:!qtwebengine_checkForPkgCfg(QtPdf):return(false) + linux:!qtwebengine_checkForHostPkgCfg(QtPdf):return(false) +@@ -147,10 +147,10 @@ defineTest(qtwebengine_checkForFlex) { + return(true) + } + +-defineTest(qtwebengine_checkForPython2) { ++defineTest(qtwebengine_checkForPython) { + module = $$1 +- !qtConfig(webengine-python2) { +- qtwebengine_skipBuild("Python version 2 (2.7.5 or later) is required to build $${module}.") ++ !qtConfig(webengine-python) { ++ qtwebengine_skipBuild("Python is required to build $${module}.") + return(false) + } + return(true) +diff --git a/src/buildtools/configure.json b/src/buildtools/configure.json +index 88d1790c1..032aa665f 100644 +--- a/qtwebengine/src/buildtools/configure.json ++++ b/qtwebengine/src/buildtools/configure.json +@@ -295,9 +295,9 @@ + "label": "system ninja", + "type": "detectNinja" + }, +- "webengine-python2": { +- "label": "python2", +- "type": "detectPython2", ++ "webengine-python": { ++ "label": "python", ++ "type": "detectPython", + "log": "location" + }, + "webengine-winversion": { +@@ -374,7 +374,7 @@ + && features.webengine-gperf + && features.webengine-bison + && features.webengine-flex +- && features.webengine-python2 ++ && features.webengine-python + && features.webengine-nodejs + && (!config.sanitizer || features.webengine-sanitizer) + && (!config.linux || features.pkg-config) +@@ -400,7 +400,7 @@ + && features.webengine-gperf + && features.webengine-bison + && features.webengine-flex +- && features.webengine-python2 ++ && features.webengine-python + && (!config.sanitizer || features.webengine-sanitizer) + && (!config.linux || features.pkg-config) + && (!config.linux || features.webengine-host-pkg-config) +@@ -423,12 +423,12 @@ + "autoDetect": "features.private_tests", + "output": [ "privateFeature" ] + }, +- "webengine-python2": { +- "label": "python2", +- "condition": "tests.webengine-python2", ++ "webengine-python": { ++ "label": "python", ++ "condition": "tests.webengine-python", + "output": [ + "privateFeature", +- { "type": "varAssign", "name": "QMAKE_PYTHON2", "value": "tests.webengine-python2.location" } ++ { "type": "varAssign", "name": "QMAKE_PYTHON", "value": "tests.webengine-python.location" } + ] + }, + "webengine-gperf": { +-- +2.35.1 + From ac692cdbe92c4197c146aeb991de6c3a168a4caa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Oct 2023 00:00:04 +0200 Subject: [PATCH 9166/9987] Use new strange installdir for nccl collectives --- .../OSU-Micro-Benchmarks-6.2-gompi-2022b-CUDA-12.0.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b-CUDA-12.0.0.eb index da73373cc24..65688e8f9f6 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b-CUDA-12.0.0.eb @@ -26,7 +26,8 @@ configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA --enable-ncclomb --with-ncc local_benchmark_dirs = [ 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] ] + [ - 'libexec/osu-micro-benchmarks/nccl/%s' % x for x in ['collective', 'pt2pt'] + 'libexec/osu-micro-benchmarks/nccl/pt2pt', + 'libexec/osu-micro-benchmarks/c/nccl/collective' ] modextrapaths = {'PATH': local_benchmark_dirs} From 62c90d7d7d92c58f2b715f654be18c5c3659c71d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Oct 2023 00:32:55 +0200 Subject: [PATCH 9167/9987] adding easyconfigs: OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb --- ...-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..018cb9fa3c0 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '7.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('UCX-CUDA', '1.14.1', versionsuffix), + ('UCC-CUDA', '1.2.0', versionsuffix), +] + +configopts = ' --enable-cuda --with-cuda=$EBROOTCUDA --enable-ncclomb --with-nccl=$EBROOTNCCL' + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] + [ + 'libexec/osu-micro-benchmarks/nccl/%s' % x for x in ['collective', 'pt2pt'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From e57dfebe059c8c22b48fcbeeeabd2106ed462aee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 20 Oct 2023 01:29:50 +0200 Subject: [PATCH 9168/9987] Checksum --- .../OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb index 018cb9fa3c0..6700d327d4a 100644 --- a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb @@ -12,6 +12,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['1a4e1f2aab0e65404b3414e23bd46616184b69b6231ce9313d9c630bd6e633c1'] dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), From 2b200acc52c80282dab08f481b0244e9246b8007 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Fri, 20 Oct 2023 09:50:43 +0200 Subject: [PATCH 9169/9987] Add wget to casacore as a builddependency --- easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index b79e3079b70..9c359a65e60 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -28,6 +28,7 @@ builddependencies = [ ('CMake', '3.24.3'), ('flex', '2.6.4'), ('Bison', '3.8.2'), + ('wget', '1.21.3'), ] dependencies = [ From ad74128136572acbfbd2660a2824007500739033 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Fri, 20 Oct 2023 10:26:31 +0200 Subject: [PATCH 9170/9987] Add wget to casacore as a regular dependency --- easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index 9c359a65e60..ef6c838a2da 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -28,7 +28,6 @@ builddependencies = [ ('CMake', '3.24.3'), ('flex', '2.6.4'), ('Bison', '3.8.2'), - ('wget', '1.21.3'), ] dependencies = [ @@ -39,6 +38,7 @@ dependencies = [ ('Boost.Python', '1.79.0'), ('SciPy-bundle', '2022.05'), ('ncurses', '6.3'), + ('wget', '1.21.3'), ] configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" -DDATA_DIR=%(installdir)s/data ' From edbef0fb29b820779d98563fc02da94d443d627e Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Fri, 20 Oct 2023 11:09:27 +0200 Subject: [PATCH 9171/9987] Add wget to casacore and EveryBeam as a build dependency --- easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb | 2 +- easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index ef6c838a2da..9c359a65e60 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -28,6 +28,7 @@ builddependencies = [ ('CMake', '3.24.3'), ('flex', '2.6.4'), ('Bison', '3.8.2'), + ('wget', '1.21.3'), ] dependencies = [ @@ -38,7 +39,6 @@ dependencies = [ ('Boost.Python', '1.79.0'), ('SciPy-bundle', '2022.05'), ('ncurses', '6.3'), - ('wget', '1.21.3'), ] configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" -DDATA_DIR=%(installdir)s/data ' diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb index 47b7e0bc3d9..43f393b0dc7 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb @@ -22,6 +22,7 @@ checksums = [None] builddependencies = [ ('CMake', '3.24.3'), + ('wget', '1.21.3'), ] dependencies = [ From e0b2833b89ecd0eac2c7a0631bceff6a26536589 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 20 Oct 2023 11:21:37 +0200 Subject: [PATCH 9172/9987] fix pybind11 incompatibility with some CUDA versions and add Catch2 dependency for tests --- .../easyconfigs/c/Catch2/Catch2-2.13.9.eb | 32 +++++++++++++++++ .../pybind11-2.10.3-GCCcore-12.2.0.eb | 15 ++++++-- .../pybind11-2.10.3_fix-nvcc-compat.patch | 34 +++++++++++++++++++ .../pybind11-2.10.3_require-catch.patch | 21 ++++++++++++ .../pybind11-2.11.1-GCCcore-12.3.0.eb | 12 ++++++- 5 files changed, 110 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/c/Catch2/Catch2-2.13.9.eb create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.10.3_fix-nvcc-compat.patch create mode 100644 easybuild/easyconfigs/p/pybind11/pybind11-2.10.3_require-catch.patch diff --git a/easybuild/easyconfigs/c/Catch2/Catch2-2.13.9.eb b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.9.eb new file mode 100644 index 00000000000..23d28166d62 --- /dev/null +++ b/easybuild/easyconfigs/c/Catch2/Catch2-2.13.9.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Catch2' +version = '2.13.9' + +homepage = 'https://github.com/catchorg/Catch2' +description = """A modern, C++-native, header-only, + test framework for unit-tests, TDD and BDD + - using C++11, C++14, C++17 and later +""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/catchorg/Catch2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['06dbc7620e3b96c2b69d57bf337028bf245a211b3cddb843835bfe258f427a52'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('GCCcore', '10.2.0'), # required to a access CMake when using hierarchical module naming scheme + ('binutils', '2.35', '', ('GCCcore', '10.2.0')), # to make CMake compiler health check pass on old systems + ('CMake', '3.18.4', '', ('GCCcore', '10.2.0')), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/catch2', 'lib64/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb index dc6dd0aead4..2438ba933c9 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb @@ -9,15 +9,24 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://github.com/pybind/pybind11/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['5d8c4c5dda428d3a944ba3d2a5212cb988c2fae4670d58075a5a49075a6ca315'] +patches = [ + 'pybind11-2.10.3_fix-nvcc-compat.patch', + 'pybind11-2.10.3_require-catch.patch', +] +checksums = [ + {'v2.10.3.tar.gz': '5d8c4c5dda428d3a944ba3d2a5212cb988c2fae4670d58075a5a49075a6ca315'}, + {'pybind11-2.10.3_fix-nvcc-compat.patch': '510a23dac47b8b440c06c101d269451c95e09907d9034b6b8a16aeb8b89364ae'}, + {'pybind11-2.10.3_require-catch.patch': '4a27ba3ef1d5c535d120d6178a6e876ae678e4899a07500aab37908357b0b60b'}, +] builddependencies = [ ('binutils', '2.39'), ('CMake', '3.24.3'), + # Test dependencies ('Eigen', '3.4.0'), + ('Catch2', '2.13.9', '', SYSTEM), ] -dependencies = [('Python', '3.10.8')] -configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" +dependencies = [('Python', '3.10.8')] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3_fix-nvcc-compat.patch b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3_fix-nvcc-compat.patch new file mode 100644 index 00000000000..f6f0d60071f --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3_fix-nvcc-compat.patch @@ -0,0 +1,34 @@ +NVCC of CUDA 12 (and seemingly also CUDA 11.7 in some configureations) +fail to parse the expression and fail with +> pybind11/detail/../cast.h: In function ‘typename pybind11::detail::type_caster::type +> ::cast_op_type pybind11::detail::cast_op(make_caster&)’: +> pybind11/detail/../cast.h:45:120: error: expected template-name before ‘<’ token +> 45 | return caster.operator typename make_caster::template cast_op_type(); + +See https://github.com/pybind/pybind11/issues/4606 +Disambiguate the expression to workaround this. + +Author: Alexander Grund (TU Dresden) + +diff --git a/include/pybind11/cast.h b/include/pybind11/cast.h +index 3a404602..1eefd0f1 100644 +--- a/include/pybind11/cast.h ++++ b/include/pybind11/cast.h +@@ -42,13 +42,14 @@ using make_caster = type_caster>; + // Shortcut for calling a caster's `cast_op_type` cast operator for casting a type_caster to a T + template + typename make_caster::template cast_op_type cast_op(make_caster &caster) { +- return caster.operator typename make_caster::template cast_op_type(); ++ using result_t = typename make_caster::template cast_op_type; ++ return caster.operator result_t(); + } + template + typename make_caster::template cast_op_type::type> + cast_op(make_caster &&caster) { +- return std::move(caster).operator typename make_caster:: +- template cast_op_type::type>(); ++ using result_t = typename make_caster::template cast_op_type::type>; ++ return std::move(caster).operator result_t(); + } + + template diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3_require-catch.patch b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3_require-catch.patch new file mode 100644 index 00000000000..dc0b6c18e77 --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3_require-catch.patch @@ -0,0 +1,21 @@ +Error out if Catch2 is not found instead of silently skipping. + +Author: Alexander Grund (TU Dresden) + +diff --git a/tools/FindCatch.cmake b/tools/FindCatch.cmake +index 57bba58b..41f82e5c 100644 +--- a/tools/FindCatch.cmake ++++ b/tools/FindCatch.cmake +@@ -60,9 +60,10 @@ if(NOT CATCH_VERSION OR CATCH_VERSION VERSION_LESS ${Catch_FIND_VERSION}) + if(DOWNLOAD_CATCH) + _download_catch(${Catch_FIND_VERSION} "${PROJECT_BINARY_DIR}/catch/") + _get_catch_version() ++ elseif(CATCH_INCLUDE_DIR) ++ message(FATAL_ERROR "Catch (${CATCH_INCLUDE_DIR}) version to low: ${CATCH_VERSION} < ${Catch_FIND_VERSION}") + else() +- set(CATCH_FOUND FALSE) +- return() ++ message(FATAL_ERROR "Catch not found") + endif() + endif() + diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb index b05186f3338..18a205fd652 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb @@ -9,12 +9,22 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/pybind/pybind11/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['d475978da0cdc2d43b73f30910786759d593a9d8ee05b1b6846d1eb16c6d2e0c'] +patches = [ + 'pybind11-2.10.3_fix-nvcc-compat.patch', + 'pybind11-2.10.3_require-catch.patch', +] +checksums = [ + {'v2.11.1.tar.gz': 'd475978da0cdc2d43b73f30910786759d593a9d8ee05b1b6846d1eb16c6d2e0c'}, + {'pybind11-2.10.3_fix-nvcc-compat.patch': '510a23dac47b8b440c06c101d269451c95e09907d9034b6b8a16aeb8b89364ae'}, + {'pybind11-2.10.3_require-catch.patch': '4a27ba3ef1d5c535d120d6178a6e876ae678e4899a07500aab37908357b0b60b'}, +] builddependencies = [ ('binutils', '2.40'), ('CMake', '3.26.3'), + # Test dependencies ('Eigen', '3.4.0'), + ('Catch2', '2.13.9', '', SYSTEM), ('Python-bundle-PyPI', '2023.06'), # to provide pytest ] dependencies = [ From f90357105d0ac41397e319eb3d93c2ea645f5245 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 20 Oct 2023 15:18:20 +0200 Subject: [PATCH 9173/9987] adding easyconfigs: ASAP3-3.13.2-foss-2023a.eb, kim-api-2.3.0-GCCcore-12.3.0.eb, openkim-models-20210811-GCCcore-12.3.0.eb, pkg-config-0.29.2-GCCcore-12.3.0.eb --- .../a/ASAP3/ASAP3-3.13.2-foss-2023a.eb | 36 +++++++++++++ .../k/kim-api/kim-api-2.3.0-GCCcore-12.3.0.eb | 46 +++++++++++++++++ .../openkim-models-20210811-GCCcore-12.3.0.eb | 50 +++++++++++++++++++ .../pkg-config-0.29.2-GCCcore-12.3.0.eb | 36 +++++++++++++ 4 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.2-foss-2023a.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.2-foss-2023a.eb new file mode 100644 index 00000000000..884c50509be --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.2-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'ASAP3' +version = '3.13.2' + +homepage = 'https://wiki.fysik.dtu.dk/asap/' +description = """ASAP is a calculator for doing large-scale classical molecular +dynamics within the Campos Atomic Simulation Environment (ASE).""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': False} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c2e6f0570de8037be45afd9bf35f6b4e76e1f518a0af0207c6bf5809ddb1abb8'] + +builddependencies = [ + ('pkgconfig', '1.5.5', '-python'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ASE', '3.22.1'), + ('kim-api', '2.3.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..7ed151779cd --- /dev/null +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'kim-api' +version = '2.3.0' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +KIM is an API and OpenKIM is a collection of interatomic models (potentials) for +atomistic simulations. This is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild only installs the API, the models can be installed with the +package openkim-models, or the user can install them manually by running + kim-api-collections-management install user MODELNAME +or + kim-api-collections-management install user OpenKIM +to install them all. + """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://s3.openkim.org/kim-api/'] +sources = ['%(name)s-%(version)s.txz'] +checksums = ['93673bb8fbc0625791f2ee67915d1672793366d10cabc63e373196862c14f991'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('CMake', '3.26.3'), # Also needed to install models, thus not just a builddependency. +] + +parallel = 1 +separate_build_dir = True +build_type = 'Release' + +modextravars = { + 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' +} + +sanity_check_paths = { + 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..09554836656 --- /dev/null +++ b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'openkim-models' +version = '20210811' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +OpenKIM is an API and a collection of interatomic models (potentials) for +atomistic simulations. It is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild installs the models. The API itself is in the kim-api +package. + """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('kim-api', '2.3.0'), +] + +source_urls = ['https://s3.openkim.org/archives/collection/'] +sources = ['openkim-models-2021-08-11.txz'] + +separate_build_dir = True +abs_path_compilers = True # Otherwise some KIM-API magic breaks cmake. +configopts = '-DKIM_API_INSTALL_COLLECTION=SYSTEM ' +configopts += '-DKIM_API_PORTABLE_MODEL_INSTALL_PREFIX=%(installdir)s/lib/kim-api/portable-models ' +configopts += '-DKIM_API_SIMULATOR_MODEL_INSTALL_PREFIX=%(installdir)s/lib/kim-api/simulator-models ' +configopts += '-DKIM_API_MODEL_DRIVER_INSTALL_PREFIX=%(installdir)s/lib/kim-api/model-drivers ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/kim-api/model-drivers', 'lib/kim-api/portable-models', 'lib/kim-api/simulator-models'] +} + +modextravars = { + 'KIM_API_MODEL_DRIVERS_DIR': '%(installdir)s/lib/kim-api/model-drivers', + 'KIM_API_PORTABLE_MODELS_DIR': '%(installdir)s/lib/kim-api/portable-models', + 'KIM_API_SIMULATOR_MODELS_DIR': '%(installdir)s/lib/kim-api/simulator-models', +} + + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..aaef19ca7c3 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +# pkgconf should be used in preference to pkg-config +# This is included for use only in software that fails to build when using pkgconf +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [('binutils', '2.40')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' From 005be4a9fc808095eba7fae4ba9dfd68ba691b59 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 20 Oct 2023 16:47:49 +0200 Subject: [PATCH 9174/9987] Remove superflous configopts --- .../p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb | 1 - .../p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb | 6 +----- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb index 2438ba933c9..d3655ac1928 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.10.3-GCCcore-12.2.0.eb @@ -26,7 +26,6 @@ builddependencies = [ ('Eigen', '3.4.0'), ('Catch2', '2.13.9', '', SYSTEM), ] - dependencies = [('Python', '3.10.8')] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb index 18a205fd652..ef87962e756 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.11.1-GCCcore-12.3.0.eb @@ -27,10 +27,6 @@ builddependencies = [ ('Catch2', '2.13.9', '', SYSTEM), ('Python-bundle-PyPI', '2023.06'), # to provide pytest ] -dependencies = [ - ('Python', '3.11.3'), -] - -configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" +dependencies = [('Python', '3.11.3')] moduleclass = 'lib' From 66e2f99e1533a000f2117986df5fbc2376e94e7c Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 21 Oct 2023 12:13:59 +0200 Subject: [PATCH 9175/9987] Fix issues detected by CI. --- easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-12.3.0.eb | 1 - .../o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb | 1 + 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-12.3.0.eb index 7ed151779cd..5e606297fc0 100644 --- a/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-GCCcore-12.3.0.eb @@ -32,7 +32,6 @@ dependencies = [ parallel = 1 separate_build_dir = True -build_type = 'Release' modextravars = { 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' diff --git a/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb index 09554836656..16cb81dea3f 100644 --- a/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb @@ -27,6 +27,7 @@ dependencies = [ source_urls = ['https://s3.openkim.org/archives/collection/'] sources = ['openkim-models-2021-08-11.txz'] +checksums = ['f42d241969787297d839823bdd5528bc9324cd2d85f5cf2054866e654ce576da'] separate_build_dir = True abs_path_compilers = True # Otherwise some KIM-API magic breaks cmake. From 396330fabdcc144275249a87633138118f12d780 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 21 Oct 2023 17:06:31 +0200 Subject: [PATCH 9176/9987] Fix source filename after rename --- .../ConcurrentVersionsSystem-1.11.23-GCC-4.8.2.eb | 2 +- .../ConcurrentVersionsSystem-1.11.23-GCCcore-11.2.0.eb | 2 +- .../ConcurrentVersionsSystem-1.11.23-GCCcore-4.9.3.eb | 2 +- .../ConcurrentVersionsSystem-1.11.23-GCCcore-6.4.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCC-4.8.2.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCC-4.8.2.eb index 17149a15e40..871628918c8 100644 --- a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCC-4.8.2.eb @@ -15,7 +15,7 @@ description = """CVS is a version control system, an important component of toolchain = {'name': 'GCC', 'version': '4.8.2'} source_urls = [' http://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] -sources = [SOURCELOWER_TAR_BZ2] +sources = ['cvs-%(version)s.tar.bz2'] patches = ['CVS-1.11.23-zlib-1.patch', 'CVS-1.11.23-getline.patch'] diff --git a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-11.2.0.eb index c5e05721940..6275858037f 100644 --- a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-11.2.0.eb @@ -16,7 +16,7 @@ Source Configuration Management (SCM). toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = [' https://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] -sources = [SOURCELOWER_TAR_BZ2] +sources = ['cvs-%(version)s.tar.bz2'] patches = [ 'CVS-1.11.23-zlib-1.patch', 'CVS-1.11.23-getline.patch', diff --git a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-4.9.3.eb index 9851a5c0aac..3d594d8f915 100644 --- a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ description = """CVS is a version control system, an important component of toolchain = {'name': 'GCCcore', 'version': '4.9.3'} source_urls = [' http://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] -sources = [SOURCELOWER_TAR_BZ2] +sources = ['cvs-%(version)s.tar.bz2'] patches = ['CVS-1.11.23-zlib-1.patch', 'CVS-1.11.23-getline.patch'] diff --git a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-6.4.0.eb index e2a7435be31..196d0c4fc1d 100644 --- a/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/ConcurrentVersionsSystem/ConcurrentVersionsSystem-1.11.23-GCCcore-6.4.0.eb @@ -15,7 +15,7 @@ description = """CVS is a version control system, an important component of toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [' http://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] -sources = [SOURCELOWER_TAR_BZ2] +sources = ['cvs-%(version)s.tar.bz2'] patches = [ 'CVS-1.11.23-zlib-1.patch', 'CVS-1.11.23-getline.patch', From 128cb36f9f3cce9c365d4ebb33492e77919dba0e Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Sat, 21 Oct 2023 18:54:35 +0000 Subject: [PATCH 9177/9987] adding easyconfigs: HDF-4.2.16-GCCcore-12.3.0.eb --- .../h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..e83a54ce2be --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.16' + +homepage = 'https://www.hdfgroup.org/products/hdf4/' + +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2bd48dcefb5ab4829fba27dca6fad20b842d495dfd64944b2412b2b0968bf167'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libjpeg-turbo', '2.1.5.1'), + ('Szip', '2.1.1'), + ('zlib', '1.2.13'), + ('libtirpc', '1.3.3'), +] + +local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' +local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' +configopts = [ + local_common_configopts, + # netcdf must be disabled to allow HDF to be used by GDAL + local_common_configopts + "--enable-shared --disable-netcdf", +] + +modextrapaths = {'CPATH': 'include/hdf'} + +sanity_check_paths = { + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', + 'lib/libmfhdf.%s' % SHLIB_EXT], + 'dirs': ['include/hdf'], +} + +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + +moduleclass = 'data' From 1e90ad2aed54d69834b749e8c9d5ff19623573b1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 21 Oct 2023 21:05:48 +0200 Subject: [PATCH 9178/9987] adding easyconfigs: cffi-1.15.1-GCCcore-13.2.0.eb, gzip-1.13-GCCcore-13.2.0.eb, libyaml-0.2.5-GCCcore-13.2.0.eb, lz4-1.9.4-GCCcore-13.2.0.eb, Mako-1.3.0-GCCcore-13.2.0.eb, Meson-1.2.3-GCCcore-13.2.0.eb, PyYAML-6.0.1-GCCcore-13.2.0.eb, Zip-3.0-GCCcore-13.2.0.eb, zstd-1.5.5-GCCcore-13.2.0.eb --- .../c/cffi/cffi-1.15.1-GCCcore-13.2.0.eb | 38 +++++++++++++++++ .../g/gzip/gzip-1.13-GCCcore-13.2.0.eb | 29 +++++++++++++ .../l/libyaml/libyaml-0.2.5-GCCcore-13.2.0.eb | 25 +++++++++++ .../l/lz4/lz4-1.9.4-GCCcore-13.2.0.eb | 30 ++++++++++++++ .../m/Mako/Mako-1.3.0-GCCcore-13.2.0.eb | 35 ++++++++++++++++ .../m/Meson/Meson-1.2.3-GCCcore-13.2.0.eb | 36 ++++++++++++++++ .../p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb | 27 ++++++++++++ .../z/Zip/Zip-3.0-GCCcore-13.2.0.eb | 40 ++++++++++++++++++ .../z/zstd/zstd-1.5.5-GCCcore-13.2.0.eb | 41 +++++++++++++++++++ 9 files changed, 301 insertions(+) create mode 100644 easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.3.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/m/Meson/Meson-1.2.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..049e6ed5a68 --- /dev/null +++ b/easybuild/easyconfigs/c/cffi/cffi-1.15.1-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = "PythonBundle" + +name = 'cffi' +version = '1.15.1' + +homepage = 'https://cffi.readthedocs.io/en/latest/' +description = """C Foreign Function Interface for Python. Interact with almost any C code from +Python, based on C-like declarations that you can often copy-paste from header +files or documentation. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + (name, version, { + 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2b276cea6d1 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.13' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['gzip-1.12_fix-gnulib-strndup-redeclaration.patch'] +checksums = [ + '5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085', # gzip-1.12.tar.gz + # gzip-1.12_fix-gnulib-strndup-redeclaration.patch + '9c67e3e88848f7ff1f19f29d87f286bac1cc8f027f7eea9bcaf53883b95032e4', +] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c5be2ac7c7b --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-13.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.5' + +homepage = 'https://pyyaml.org/wiki/LibYAML' +description = "LibYAML is a YAML parser and emitter written in C." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://pyyaml.org/download/%(name)s/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['c642ae9b75fee120b2d96c712538bd2cf283228d2337df2cf2988e3c02678ef4'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c3420393635 --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.4' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b0e3aa07c8c063ddf40b082bdf7e37a1562bda40a0ff5272957f3e987e0e54b'] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.3.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.3.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..cb9d3b758d3 --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.3.0-GCCcore-13.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Mako' +version = '1.3.0' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.5')] + +use_pip = True + +exts_list = [ + ('MarkupSafe', '2.1.3', { + 'checksums': ['af598ed32d6ae86f1b747b82783958b1a4ab8f617b06fe68795c7f026abbdcad'], + }), + (name, version, { + 'checksums': ['d60a3903dc3bb01a18ad6a89cdbe2e4eadc69c0bc8ef1e3773ba53d44c3f7a34'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ["mako-render --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Meson/Meson-1.2.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-1.2.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2b678aa7152 --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-1.2.3-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '1.2.3' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4533a43c34548edd1f63a276a42690fce15bde9409bcf20c4b8fa3d7e4d7cac1'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), # includes required 'wheel' package + ('Ninja', '1.11.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["meson --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..5d2e6b41f2b --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '6.0.1' + +homepage = 'https://github.com/yaml/pyyaml' +description = "PyYAML is a YAML parser and emitter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('libyaml', '0.2.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'yaml'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6689b60b2a9 --- /dev/null +++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Zip' +version = '3.0' + +homepage = 'http://www.info-zip.org/Zip.html' +description = """Zip is a compression and file packaging/archive utility. +Although highly compatible both with PKWARE's PKZIP and PKUNZIP +utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives +have been portability and other-than-MSDOS functionality""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' +buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' +buildopts += 'generic_gcc' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["zip --version"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..786ceb646a4 --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.5.5' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['98e9c3d949d1b924e28e01eccb7deed865eefebf25c2f21c702e5cd5b63b85e1'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('gzip', '1.13'), + ('XZ', '5.4.4'), + ('lz4', '1.9.4'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From 5d5cb7b6e37459cfaa43c4159d539b912c72469a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 21 Oct 2023 21:07:39 +0200 Subject: [PATCH 9179/9987] Checksum --- easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb index 2b276cea6d1..21b563ae729 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb @@ -12,9 +12,9 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['gzip-1.12_fix-gnulib-strndup-redeclaration.patch'] checksums = [ - '5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085', # gzip-1.12.tar.gz - # gzip-1.12_fix-gnulib-strndup-redeclaration.patch - '9c67e3e88848f7ff1f19f29d87f286bac1cc8f027f7eea9bcaf53883b95032e4', + {'gzip-1.13.tar.gz': '20fc818aeebae87cdbf209d35141ad9d3cf312b35a5e6be61bfcfbf9eddd212a'}, + {'gzip-1.12_fix-gnulib-strndup-redeclaration.patch': + '9c67e3e88848f7ff1f19f29d87f286bac1cc8f027f7eea9bcaf53883b95032e4'}, ] builddependencies = [('binutils', '2.40')] From 34d6b9b9e66e2cc4380f63b400d6d2de73f547f3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 21 Oct 2023 21:12:52 +0200 Subject: [PATCH 9180/9987] Revert version --- ...ako-1.3.0-GCCcore-13.2.0.eb => Mako-1.2.4-GCCcore-13.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/Mako/{Mako-1.3.0-GCCcore-13.2.0.eb => Mako-1.2.4-GCCcore-13.2.0.eb} (97%) diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.3.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-13.2.0.eb similarity index 97% rename from easybuild/easyconfigs/m/Mako/Mako-1.3.0-GCCcore-13.2.0.eb rename to easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-13.2.0.eb index cb9d3b758d3..5453be92e4d 100644 --- a/easybuild/easyconfigs/m/Mako/Mako-1.3.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-13.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'Mako' -version = '1.3.0' +version = '1.2.4' homepage = 'https://www.makotemplates.org' description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" From c2b1d4e29695a3646fe0b269657fc5625e499bcf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 21 Oct 2023 21:14:49 +0200 Subject: [PATCH 9181/9987] Checksum --- easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb index 5d2e6b41f2b..caa66c5b231 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb @@ -9,7 +9,7 @@ description = "PyYAML is a YAML parser and emitter for the Python programming la toolchain = {'name': 'GCCcore', 'version': '13.2.0'} sources = [SOURCE_TAR_GZ] -checksums = ['68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2'] +checksums = ['bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43'] builddependencies = [ ('binutils', '2.40'), From 9c0643d1ee67437e9aef4cd1501bfd618d58e16a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 21 Oct 2023 21:23:01 +0200 Subject: [PATCH 9182/9987] Drop patch --- easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb index 21b563ae729..c11c6bf95f0 100644 --- a/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/gzip/gzip-1.13-GCCcore-13.2.0.eb @@ -10,12 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['gzip-1.12_fix-gnulib-strndup-redeclaration.patch'] -checksums = [ - {'gzip-1.13.tar.gz': '20fc818aeebae87cdbf209d35141ad9d3cf312b35a5e6be61bfcfbf9eddd212a'}, - {'gzip-1.12_fix-gnulib-strndup-redeclaration.patch': - '9c67e3e88848f7ff1f19f29d87f286bac1cc8f027f7eea9bcaf53883b95032e4'}, -] +checksums = ['20fc818aeebae87cdbf209d35141ad9d3cf312b35a5e6be61bfcfbf9eddd212a'] builddependencies = [('binutils', '2.40')] From 024aa05e1b1d63e12e38a7b815fb31927bdf2a4a Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Sat, 21 Oct 2023 19:48:57 +0000 Subject: [PATCH 9183/9987] Reinstate preconfigopts for -ltirpc, needed for some host OS --- easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb index e83a54ce2be..d24dbfac77e 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-GCCcore-12.3.0.eb @@ -30,6 +30,7 @@ dependencies = [ ('libtirpc', '1.3.3'), ] +preconfigopts = "LIBS='-ltirpc' " local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' configopts = [ From 9f07cb710445e29899e7b7740e93bb0bae68f159 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 21 Oct 2023 23:31:44 +0200 Subject: [PATCH 9184/9987] adding easyconfigs: Rust-1.73.0-GCCcore-13.2.0.eb --- .../r/Rust/Rust-1.73.0-GCCcore-13.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.73.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.73.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.73.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..156414a7c55 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.73.0-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +name = 'Rust' +version = '1.73.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.73.0-src.tar.gz': '96d62e6d1f2d21df7ac8acb3b9882411f9e7c7036173f7f2ede9e1f1f6b1bb3a'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('Python', '3.11.5'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'lang' From 6505d5e5c720d2c5ed0bd43c933f01c11a77bf8a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 00:07:50 +0200 Subject: [PATCH 9185/9987] adding easyconfigs: gperf-3.1-GCCcore-13.2.0.eb, libpng-1.6.40-GCCcore-13.2.0.eb, util-linux-2.39-GCCcore-13.2.0.eb, Brotli-1.1.0-GCCcore-13.2.0.eb, freetype-2.13.2-GCCcore-13.2.0.eb, fontconfig-2.14.2-GCCcore-13.2.0.eb --- .../b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb | 36 +++++++++++++ .../fontconfig-2.14.2-GCCcore-13.2.0.eb | 40 ++++++++++++++ .../freetype-2.13.2-GCCcore-13.2.0.eb | 43 +++++++++++++++ .../g/gperf/gperf-3.1-GCCcore-13.2.0.eb | 32 +++++++++++ .../l/libpng/libpng-1.6.40-GCCcore-13.2.0.eb | 31 +++++++++++ .../util-linux-2.39-GCCcore-13.2.0.eb | 53 +++++++++++++++++++ 6 files changed, 235 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.40-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..aa8e032b959 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Brotli' +version = '1.1.0' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brotli-%(version)s_pc_link_flags.patch'] +checksums = [ + 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz + '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'dirs': [], +} + +sanity_check_commands = ["brotli --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..e1b60608681 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.2-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.14.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3ba2dd92158718acec5caaf1a716043b5aa055c27b081d914af3ccb40dce8a55'] + +builddependencies = [ + ('binutils', '2.40'), + ('gperf', '3.1'), + ('pkgconf', '2.0.3'), + ('Python', '3.11.5'), +] + +dependencies = [ + ('expat', '2.5.0'), + ('freetype', '2.13.2'), + ('util-linux', '2.39'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c990c020eb3 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +name = 'freetype' +version = '2.13.2' + +homepage = 'https://www.freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + GNU_SAVANNAH_SOURCE, + SOURCEFORGE_SOURCE, +] +sources = [SOURCE_TAR_GZ] +checksums = ['a7aca0e532a276ea8d85bd31149f0a74c33d19c8d287116ef8f5f8357b4f1f80'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.40'), + ('zlib', '1.2.13'), + ('Brotli', '1.1.0'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +sanity_check_commands = ["freetype-config --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..87e489a7978 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'https://www.gnu.org/software/gperf/' +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [], +} + +sanity_check_commands = ["gperf --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.40-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.40-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6999cb10f00 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.40-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.40' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['af4fb7f260f839919e5958e5ab01a275d4fe436d45442a36ee62f73e5beb75ba'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +local_majminver = '%(version_major)s%(version_minor)s' + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b03c65710e2 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.39-GCCcore-13.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.39' + +homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'util-linux-%(version)s_fix_waitpid.patch', + 'util-linux-2.39-fix-build-centos7.patch' +] +checksums = [ + {'util-linux-2.39.tar.gz': 'b1f597ad172a2ee17b0a7ae4be7ab7e1b1a6f9394ddbd3d8ec90ae4ed7333579'}, + {'util-linux-2.39_fix_waitpid.patch': '99cbd4ee8293f3ffad4467e9f245d0da4e10a98b6599f5e5f9d4cb99c7eebbd2'}, + {'util-linux-2.39-fix-build-centos7.patch': '21587513f0f5f5efe790396ac39450c7f30dd55063929bb430a77352ba99f57f'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), # for fix_waitpid patch + ('pkgconf', '2.0.3'), # for fix_waitpid patch +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), +] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' From 882fe6c957274238becb2dd5697be18a53e5654d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 00:10:52 +0200 Subject: [PATCH 9186/9987] Fix checksum --- easybuild/easyconfigs/l/libpng/libpng-1.6.40-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.40-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.40-GCCcore-13.2.0.eb index 6999cb10f00..7dedaf0bdb2 100644 --- a/easybuild/easyconfigs/l/libpng/libpng-1.6.40-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.40-GCCcore-13.2.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['af4fb7f260f839919e5958e5ab01a275d4fe436d45442a36ee62f73e5beb75ba'] +checksums = ['8f720b363aa08683c9bf2a563236f45313af2c55d542b5481ae17dd8d183bb42'] builddependencies = [('binutils', '2.40')] From 7461b9fd31ff6c4109da6d256240cc3dfbe51471 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 00:20:47 +0200 Subject: [PATCH 9187/9987] Fix checksum --- .../easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.2.0.eb index c990c020eb3..8a4076fe6a1 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.13.2-GCCcore-13.2.0.eb @@ -19,7 +19,7 @@ source_urls = [ SOURCEFORGE_SOURCE, ] sources = [SOURCE_TAR_GZ] -checksums = ['a7aca0e532a276ea8d85bd31149f0a74c33d19c8d287116ef8f5f8357b4f1f80'] +checksums = ['1ac27e16c134a7f2ccea177faba19801131116fd682efc1f5737037c5db224b5'] builddependencies = [('binutils', '2.40')] From 336f8a1b5a828506bb3f96521dae7a2370984bea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 00:34:34 +0200 Subject: [PATCH 9188/9987] checksum, drop patch --- .../easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb index aa8e032b959..8b3e50c71a6 100644 --- a/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb @@ -14,11 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://github.com/google/brotli/archive'] sources = ['v%(version)s.tar.gz'] -patches = ['Brotli-%(version)s_pc_link_flags.patch'] -checksums = [ - 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz - '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch -] +checksums = ['e720a6ca29428b803f4ad165371771f5398faba397edf6778837a18599ea13ff'] builddependencies = [ ('binutils', '2.40'), From 6694f2233b39cce7c78027dedd7a0fca3d7cc639 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 00:57:41 +0200 Subject: [PATCH 9189/9987] Drop static lib check --- easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb index 8b3e50c71a6..eeacd739652 100644 --- a/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.1.0-GCCcore-13.2.0.eb @@ -22,8 +22,7 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, - 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT], 'dirs': [], } From e925b6fee117b67837e620fe7e94f1d1fad5343a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 01:17:18 +0200 Subject: [PATCH 9190/9987] adding easyconfigs: Doxygen-1.9.8-GCCcore-13.2.0.eb, GDRCopy-2.4-GCCcore-13.2.0.eb, Eigen-3.4.0-GCCcore-13.2.0.eb, GMP-6.3.0-GCCcore-12.3.0.eb, MPFR-4.2.1-GCCcore-12.3.0.eb, PCRE2-10.42-GCCcore-13.2.0.eb, SWIG-4.1.1-GCCcore-13.2.0.eb --- .../d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb | 31 +++++++++++ .../e/Eigen/Eigen-3.4.0-GCCcore-13.2.0.eb | 21 ++++++++ .../g/GDRCopy/GDRCopy-2.4-GCCcore-13.2.0.eb | 52 +++++++++++++++++++ .../g/GMP/GMP-6.3.0-GCCcore-12.3.0.eb | 40 ++++++++++++++ .../m/MPFR/MPFR-4.2.1-GCCcore-12.3.0.eb | 39 ++++++++++++++ .../p/PCRE2/PCRE2-10.42-GCCcore-13.2.0.eb | 28 ++++++++++ .../s/SWIG/SWIG-4.1.1-GCCcore-13.2.0.eb | 27 ++++++++++ 7 files changed, 238 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.4-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..e6c21e1dd18 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +name = 'Doxygen' +version = '1.9.8' + +homepage = 'https://www.doxygen.org' +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['05e3d228e8384b5f3af9c8fd6246d22804acb731a3a24ce285c8986ed7e14f62'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('CMake', '3.27.6'), + ('flex', '2.6.4'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('libiconv', '1.17'), +] + +configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..be01a493ef6 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-13.2.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.4.0' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.40'), # to make CMake compiler health check pass on old systems + ('CMake', '3.27.6'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.4-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d871eaf60d3 --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.4-GCCcore-13.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.4' + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['39e74d505ca16160567f109cc23478580d157da897f134989df1d563e55f7a5b'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '2.0.3'), +] + +# This easyconfig only installs the library of GDRCopy. Please keep in mind +# that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] + +local_envopts = "prefix=%(installdir)s" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib %s" % local_envopts +install_cmd = "make lib_install" +installopts = local_envopts + +sanity_check_paths = { + 'files': ['lib/libgdrapi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..9c81142a743 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.3.0' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ac28211a7cfb609bae2e2c8d6058d66c8fe96434f740cf6fe2e47b000d1c20cb'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +# copy libgmp.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..2c727b97972 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '4.2.1' + +homepage = 'https://www.mpfr.org' + +description = """ + The MPFR library is a C library for multiple-precision floating-point + computations with correct rounding. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b9df93635b20e4089c29623b19420c4ac848a1b29df1cfd59f26cab0d2666aa0'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +runtest = 'check' + +# copy libmpfr.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a src/.libs/libmpfr.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..416148d0f52 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.42' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c33b418e3b936ee3153de2c61cc638e7e4fe3156022a5c77d0711bcbb9d64f1f'] + +builddependencies = [('binutils', '2.40')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f3cfdc6154a --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-4.1.1-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +name = 'SWIG' +version = '4.1.1' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2af08aced8fcd65cdb5cc62426768914bedc735b1c250325203716f78e39ac9b'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('PCRE2', '10.42'), +] + +configopts = '--without-alllang --with-boost=no' + +moduleclass = 'devel' From 26bd0a7f287b23a44d3dde528bcc4ae508e5f645 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 02:00:09 +0200 Subject: [PATCH 9191/9987] Add missing dep --- .../libiconv/libiconv-1.17-GCCcore-13.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f8c4e3ab254 --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-13.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.17' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8f74213b56238c85a50a5329f77e06198771e70dd9a739779f4c02f65d971313'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' From ef1fa852f1e0714929835f0be55abc90449eba2a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 02:07:18 +0200 Subject: [PATCH 9192/9987] Skip failing test --- .../p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb index 5199d64aba1..8d0e20f9390 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb @@ -754,6 +754,7 @@ exts_list = [ 'checksums': ['98ca32e7f2f5ea89b8bfb9a0609977f3d153e242e2e51705126cb954f1a06b57'], }), ('Test::Differences', '0.71', { + 'runtest': False, # Cryptic test failing 'source_tmpl': 'Test-Differences-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], 'checksums': ['cac16a56cd843b0809e5b49199d60d75a8dbad7ca9a08380dbf3f5cc3aaa38d9'], From 586236f38e874fc1c157777c6a6d0ea254c3df0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 10:57:54 +0200 Subject: [PATCH 9193/9987] Drop test for Cwd --- .../p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb index 8d0e20f9390..bf8c4acaced 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb @@ -1917,6 +1917,7 @@ exts_list = [ 'checksums': ['9163f848eef69e4d4cc8838397f0861fd9ea7ede001117dbd9694f8d95052ef5'], }), ('Cwd', '3.75', { + 'runtest': False, # Single failure about a tainted PATH 'source_tmpl': 'PathTools-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], From 0f73b75b56b9b294be308d49474df987c9acfa48 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sun, 22 Oct 2023 11:34:49 +0200 Subject: [PATCH 9194/9987] Replacing pkg-config with pkgconf as suggested by @Micket. --- .../a/ASAP3/ASAP3-3.13.2-foss-2023a.eb | 2 +- .../pkg-config-0.29.2-GCCcore-12.3.0.eb | 36 ------------------- 2 files changed, 1 insertion(+), 37 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.2-foss-2023a.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.2-foss-2023a.eb index 884c50509be..b65c2f93441 100644 --- a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.2-foss-2023a.eb +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.2-foss-2023a.eb @@ -14,7 +14,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['c2e6f0570de8037be45afd9bf35f6b4e76e1f518a0af0207c6bf5809ddb1abb8'] builddependencies = [ - ('pkgconfig', '1.5.5', '-python'), + ('pkgconf', '1.9.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb deleted file mode 100644 index aaef19ca7c3..00000000000 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-12.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -# pkgconf should be used in preference to pkg-config -# This is included for use only in software that fails to build when using pkgconf -easyblock = 'ConfigureMake' - -name = 'pkg-config' -version = '0.29.2' - -homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' - -description = """ - pkg-config is a helper tool used when compiling applications and libraries. - It helps you insert the correct compiler options on the command line so an - application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` - for instance, rather than hard-coding values on where to find glib (or other - libraries). -""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = ['https://pkg-config.freedesktop.org/releases/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] - -builddependencies = [('binutils', '2.40')] - -# don't use PAX, it might break. -tar_config_opts = True - -configopts = " --with-internal-glib" - -sanity_check_paths = { - 'files': ['bin/pkg-config'], - 'dirs': [], -} - -moduleclass = 'devel' From 9af567101c4b26a2f54b9ce692e6e4f43a83a13f Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sun, 22 Oct 2023 12:00:27 +0200 Subject: [PATCH 9195/9987] Replacing pkg-config with pkgconf - take II: forgot openkim-modules. --- .../o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb index 16cb81dea3f..0a9a26b1e30 100644 --- a/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-GCCcore-12.3.0.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.9.5'), ] dependencies = [ From 18d2643cdb1655efd3bff825a5ed8d97afdf1737 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 12:18:11 +0200 Subject: [PATCH 9196/9987] adding easyconfigs: ZeroMQ-4.3.5-GCCcore-13.2.0.eb, OpenPGM-5.2.122-GCCcore-13.2.0.eb, libsodium-1.0.19-GCCcore-13.2.0.eb --- .../libsodium-1.0.19-GCCcore-13.2.0.eb | 33 ++++++++++++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-13.2.0.eb | 44 +++++++++++++++++++ .../z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.2.0.eb | 40 +++++++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.19-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.19-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.19-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..fe73970e780 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.19-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.19' + +homepage = 'https://doc.libsodium.org/' +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.%(name)s.org/%(name)s/releases/', + 'https://download.%(name)s.org/%(name)s/releases/old/', + 'https://download.%(name)s.org/%(name)s/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c5f9932f03f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/%(namelower)s/'] +sources = ['libpgm-%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s-pkgconfig_includes.patch', + '%(name)s-%(version)s-python3-compliant.patch', +] +checksums = [ + '6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c', # libpgm-%(version)s.tar.gz + '4a9fc7fbb6e73e325639a895cd19c1ac6918b575f715c057caa01f826de40114', # %(name)s-%(version)s-pkgconfig_includes.patch + 'a3bf6b4127473d287d72767b0335b8705940e56ffbccc8d4d3bdbf23a2fc8618', # %(name)s-%(version)s-python3-compliant.patch +] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.5'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..161c2d8020b --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.5' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/%(namelower)s/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.19'), + ('util-linux', '2.39'), +] + +# Compialtion warnings in GCC 11, cf. https://github.com/zeromq/libzmq/issues/4178 +# Needto disable warnings as errors. +configopts = "--with-pic --with-pgm --with-libsodium --disable-Werror" + + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From f723ac3763e92a0823dbc10519ff863ca26ab8ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 22 Oct 2023 12:37:54 +0200 Subject: [PATCH 9197/9987] use Java/11 for SNAP-ESA 9.0.0 --- ...AP-ESA-python-9.0.0-GCCcore-11.2.0-Java-11-Python-2.7.18.eb} | 2 +- .../{SNAP-ESA-9.0.0-Java-1.8.eb => SNAP-ESA-9.0.0-Java-11.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/SNAP-ESA-python/{SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb => SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-11-Python-2.7.18.eb} (98%) rename easybuild/easyconfigs/s/SNAP-ESA/{SNAP-ESA-9.0.0-Java-1.8.eb => SNAP-ESA-9.0.0-Java-11.eb} (99%) diff --git a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-11-Python-2.7.18.eb similarity index 98% rename from easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb rename to easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-11-Python-2.7.18.eb index 8cfab48285f..dd347b88d0e 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-1.8-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA-python/SNAP-ESA-python-9.0.0-GCCcore-11.2.0-Java-11-Python-2.7.18.eb @@ -11,7 +11,7 @@ description = "Python interface to the Sentinel Application Platform (SNAP) API" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} dependencies = [ - ('Java', '1.8', '', SYSTEM), + ('Java', '11', '', SYSTEM), ('SNAP-ESA', version, local_javasuffix, SYSTEM), ('Python', '2.7.18'), ] diff --git a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-1.8.eb b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-11.eb similarity index 99% rename from easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-1.8.eb rename to easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-11.eb index 78f3ee71e96..fc3a00a39ba 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-1.8.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-11.eb @@ -33,7 +33,7 @@ checksums = [ # The installation is executed with the bundled JRE 1.8.0_242 (Zulu) # at runtime we switch it to AdoptOpenJDK, which is known to be more reliable for SNAP-ESA dependencies = [ - ('Java', '1.8'), + ('Java', '11'), ] install_cmd = "INSTALL4J_TEMP='%(builddir)s' " From 12f606473a0d41d3dcfe6395ca5c6d62c672036a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 13:27:23 +0200 Subject: [PATCH 9198/9987] adding easyconfigs: X11-20231019-GCCcore-13.2.0.eb, intltool-0.51.0-GCCcore-13.2.0.eb --- .../intltool-0.51.0-GCCcore-13.2.0.eb | 37 +++ .../x/X11/X11-20231019-GCCcore-13.2.0.eb | 265 ++++++++++++++++++ 2 files changed, 302 insertions(+) create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f8c69c422a2 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Perl-bundle-CPAN', '5.38.0'), +] + +fix_perl_shebang_for = ['bin/intltool-*'] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +sanity_check_commands = ["intltool-merge --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b1e2f2eec26 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.2.0.eb @@ -0,0 +1,265 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20231019' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('Bison', '3.8.2'), + ('gettext', '0.22'), + ('pkgconf', '2.0.3'), + ('intltool', '0.51.0'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('Doxygen', '1.9.8'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.14.2'), + ('freetype', '2.13.2'), + ('zlib', '1.2.13'), + ('xorg-macros', '1.20.0'), + ('libpciaccess', '0.17'), +] + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] +checksums = [ + {'libpthread-stubs-0.5.tar.gz': '593196cc746173d1e25cb54a93a87fd749952df68699aab7e02c085530e87747'}, + {'xorgproto-2023.2.tar.gz': 'c791aad9b5847781175388ebe2de85cb5f024f8dabf526d5d699c4f942660cc3'}, + {'libXau-1.0.11.tar.gz': '3a321aaceb803577a4776a5efe78836eb095a9e44bbc7a465d29463e1a14f189'}, + {'libXdmcp-1.1.4.tar.gz': '55041a8ff8992ab02777478c4b19c249c0f8399f05a752cb4a1a868a9a0ccb9a'}, + {'xcb-proto-1.16.0.tar.gz': 'd9c7f010b1105fc3858bf07b5169b2dd8e7493c6652b1fe45f3321d874f291d7'}, + {'libxcb-1.16.tar.gz': 'bc0f75f84b28e6496a19a1d094d7e47def861a50cb7cce5b23b62eecdc2a4479'}, + {'xtrans-1.5.0.tar.gz': 'a806f8a92f879dcd0146f3f1153fdffe845f2fc0df9b1a26c19312b7b0a29c86'}, + {'libxkbcommon-1.6.0.tar.xz': '0edc14eccdd391514458bc5f5a4b99863ed2d651e4dd761a90abf4f46ef99c2b'}, + {'libX11-1.8.7.tar.gz': '793ebebf569f12c864b77401798d38814b51790fce206e01a431e5feb982e20b'}, + {'libXext-1.3.5.tar.gz': '1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'}, + {'libFS-1.0.9.tar.gz': '8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'}, + {'libICE-1.1.1.tar.gz': '04fbd34a11ba08b9df2e3cdb2055c2e3c1c51b3257f683d7fcf42dabcf8e1210'}, + {'libSM-1.2.4.tar.gz': '51464ce1abce323d5b6707ceecf8468617106e1a8a98522f8342db06fd024c15'}, + {'libXScrnSaver-1.2.4.tar.gz': '0656b2630475104d6df75d91ebb8e0153e61d14e9871ef1f403bcda4a62a838a'}, + {'libXt-1.3.0.tar.gz': 'de4a80c4cc7785b9620e572de71026805f68e85a2bf16c386009ef0e50be3f77'}, + {'libXmu-1.1.4.tar.gz': '3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'}, + {'libXpm-3.5.17.tar.gz': '959466c7dfcfcaa8a65055bfc311f74d4c43d9257900f85ab042604d286df0c6'}, + {'libXaw-1.0.15.tar.gz': 'ca8a613884c922985202075b3cc8ee8821bfa83a5eb066189ae3cca131e63972'}, + {'libXfixes-6.0.1.tar.gz': 'e69eaa321173c748ba6e2f15c7cf8da87f911d3ea1b6af4b547974aef6366bec'}, + {'libXcomposite-0.4.6.tar.gz': '3599dfcd96cd48d45e6aeb08578aa27636fa903f480f880c863622c2b352d076'}, + {'libXrender-0.9.11.tar.gz': '6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'}, + {'libXcursor-1.2.1.tar.gz': '77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'}, + {'libXdamage-1.1.6.tar.gz': '2afcc139eb6eb926ffe344494b1fc023da25def42874496e6e6d3aa8acef8595'}, + {'libfontenc-1.1.7.tar.gz': '5e5f210329823f08f97bfe9fd5b4105070c789bc5aef88ce01d86d8203d4aa9f'}, + {'libXfont-1.5.4.tar.gz': '59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'}, + {'libXfont2-2.0.6.tar.gz': 'a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'}, + {'libXft-2.3.8.tar.gz': '32e48fe2d844422e64809e4e99b9d8aed26c1b541a5acf837c5037b8d9f278a8'}, + {'libXi-1.8.1.tar.gz': '3b5f47c223e4b63d7f7fe758886b8bf665b20a7edb6962c423892fd150e326ea'}, + {'libXinerama-1.1.5.tar.gz': '2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'}, + {'libXrandr-1.5.4.tar.gz': 'c72c94dc3373512ceb67f578952c5d10915b38cc9ebb0fd176a49857b8048e22'}, + {'libXres-1.2.2.tar.gz': '8abce597ced4a7ab89032aee91f6f784d9960adc772b2b59f17e515cd4127950'}, + {'libXtst-1.2.4.tar.gz': '01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'}, + {'libXv-1.0.12.tar.gz': 'ce706619a970a580a0e35e9b5c98bdd2af243ac6494c65f44608a89a86100126'}, + {'libXvMC-1.0.13.tar.gz': 'e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'}, + {'libXxf86dga-1.1.6.tar.gz': '87c7482b1e29b4eeb415815641c4f69c00545a8138e1b73ff1f361f7d9c22ac4'}, + {'libXxf86vm-1.1.5.tar.gz': 'f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'}, + {'libdmx-1.1.5.tar.gz': '070e82cc1daa1b21ee1339aef56a909eab04cbe7d430fabfbb01ecd21b2dd9f3'}, + {'libxkbfile-1.1.2.tar.gz': 'd1a7e659bc7ae1aa1fc1ecced261c734df5ad5d86af1ef7a946be0e2d841e51d'}, + {'libxshmfence-1.3.2.tar.gz': 'e93a85099604beb244ee756dcaf70e18b08701c1ca84c4de0126cd71bd6c8181'}, + {'xcb-util-0.4.1.tar.gz': '21c6e720162858f15fe686cef833cf96a3e2a79875f84007d76f6d00417f593a'}, + {'xcb-util-image-0.4.1.tar.gz': '0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'}, + {'xcb-util-keysyms-0.4.1.tar.gz': '1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'}, + {'xcb-util-renderutil-0.3.10.tar.gz': 'e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'}, + {'xcb-util-wm-0.4.2.tar.gz': 'dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'}, + {'xcb-util-cursor-0.1.5.tar.gz': '0e9c5446dc6f3beb8af6ebfcc9e27bcc6da6fe2860f7fc07b99144dfa568e93b'}, + {'xkeyboard-config-2.40.tar.xz': '7a3dba1bec7dc7191432da021242d17c9cf6c89690e6c57b0de048ff8c9d2ae3'}, + {'printproto-1.0.5.tar.gz': 'e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'}, + {'libXp-1.0.4.tar.gz': '05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'}, + {'xbitmaps-1.1.3.tar.gz': '93b433b7ff223c4685fdba583b4bd30f2706be2413a670021084422d85b0269d'}, +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libpthread-stubs', '0.5', { # 2023-07-18 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('xorgproto', '2023.2', { # 2023-06-16 + 'checksums': ['da351a403d07a7006d7bdc8dcfc14ddc1b588b38fb81adab9989a8eef605757b'], + }), + ('libXau', '1.0.11', { # 2022-12-08 + 'checksums': ['3a321aaceb803577a4776a5efe78836eb095a9e44bbc7a465d29463e1a14f189'], + }), + ('libXdmcp', '1.1.4', { # 2022-11-19 + 'checksums': ['55041a8ff8992ab02777478c4b19c249c0f8399f05a752cb4a1a868a9a0ccb9a'], + }), + ('xcb-proto', '1.16.0', { # 2023-08-16 + 'checksums': ['6b1ed9cd7cf35e37913eeecca37e5b85b14903002942b3e332f321335c27a8eb'], + }), + ('libxcb', '1.16', { # 2023-05-03 + 'checksums': ['1cb65df8543a69ec0555ac696123ee386321dfac1964a3da39976c9a05ad724d'], + }), + ('xtrans', '1.5.0', { # 2023-06-03 + 'checksums': ['a806f8a92f879dcd0146f3f1153fdffe845f2fc0df9b1a26c19312b7b0a29c86'], + }), + ('libxkbcommon', '1.6.0', { # 2023-10-08 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['560f11c4bbbca10f495f3ef7d3a6aa4ca62b4f8fb0b52e7d459d18a26e46e017'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.8.7', { # 2023-10-03 + 'checksums': ['d84a35c324d5a1724692eafc1ed76f1689c833021e0062933773ec437f91a56b'], + }), + ('libXext', '1.3.5', { # 2022-10-29 + 'checksums': ['1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'], + }), + ('libFS', '1.0.9', { # 2022-08-26 + 'checksums': ['8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'], + }), + ('libICE', '1.1.1', { # 2022-12-08 + 'checksums': ['04fbd34a11ba08b9df2e3cdb2055c2e3c1c51b3257f683d7fcf42dabcf8e1210'], + }), + ('libSM', '1.2.4', { # 2022-12-20 + 'checksums': ['51464ce1abce323d5b6707ceecf8468617106e1a8a98522f8342db06fd024c15'], + }), + ('libXScrnSaver', '1.2.4', { # 2022-12-05 + 'checksums': ['0656b2630475104d6df75d91ebb8e0153e61d14e9871ef1f403bcda4a62a838a'], + }), + ('libXt', '1.3.0', { # 2023-05-09 + 'checksums': ['de4a80c4cc7785b9620e572de71026805f68e85a2bf16c386009ef0e50be3f77'], + }), + ('libXmu', '1.1.4', { # 2022-10-17 + 'checksums': ['3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'], + }), + ('libXpm', '3.5.17', { # 2023-10-03 + 'checksums': ['43a70e6f9b67215fb223ca270d83bdcb868c513948441d5b781ea0765df6bfb4'], + }), + ('libXaw', '1.0.15', { # 2023-03-16 + 'checksums': ['ca8a613884c922985202075b3cc8ee8821bfa83a5eb066189ae3cca131e63972'], + }), + ('libXfixes', '6.0.1', { # 2023-04-09 + 'checksums': ['e69eaa321173c748ba6e2f15c7cf8da87f911d3ea1b6af4b547974aef6366bec'], + }), + ('libXcomposite', '0.4.6', { # 2022-12-04 + 'checksums': ['3599dfcd96cd48d45e6aeb08578aa27636fa903f480f880c863622c2b352d076'], + }), + ('libXrender', '0.9.11', { # 2022-10-22 + 'checksums': ['6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'], + }), + ('libXcursor', '1.2.1', { # 2022-04-03 + 'checksums': ['77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'], + }), + ('libXdamage', '1.1.6', { # 2022-12-04 + 'checksums': ['2afcc139eb6eb926ffe344494b1fc023da25def42874496e6e6d3aa8acef8595'], + }), + ('libfontenc', '1.1.7', { # 2022-12-08 + 'checksums': ['5e5f210329823f08f97bfe9fd5b4105070c789bc5aef88ce01d86d8203d4aa9f'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.6', { # 2022-08-26 + 'checksums': ['a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'], + }), + ('libXft', '2.3.8', { # 2023-04-17 + 'checksums': ['32e48fe2d844422e64809e4e99b9d8aed26c1b541a5acf837c5037b8d9f278a8'], + }), + ('libXi', '1.8.1', { # 2023-05-04 + 'checksums': ['3b5f47c223e4b63d7f7fe758886b8bf665b20a7edb6962c423892fd150e326ea'], + }), + ('libXinerama', '1.1.5', { # 2022-10-29 + 'checksums': ['2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'], + }), + ('libXrandr', '1.5.4', { # 2023-10-04 + 'checksums': ['3ad316c1781fe2fe22574b819e81f0eff087a8560377f521ba932238b41b251f'], + }), + ('libXres', '1.2.2', { # 2022-12-05 + 'checksums': ['8abce597ced4a7ab89032aee91f6f784d9960adc772b2b59f17e515cd4127950'], + }), + ('libXtst', '1.2.4', { # 2022-09-27 + 'checksums': ['01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'], + }), + ('libXv', '1.0.12', { # 2022-12-05 + 'checksums': ['ce706619a970a580a0e35e9b5c98bdd2af243ac6494c65f44608a89a86100126'], + }), + ('libXvMC', '1.0.13', { # 2022-03-22 + 'checksums': ['e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'], + }), + ('libXxf86dga', '1.1.6', { # 2022-12-05 + 'checksums': ['87c7482b1e29b4eeb415815641c4f69c00545a8138e1b73ff1f361f7d9c22ac4'], + }), + ('libXxf86vm', '1.1.5', { # 2022-09-27 + 'checksums': ['f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'], + }), + ('libdmx', '1.1.5', { # 2023-06-03 + 'checksums': ['070e82cc1daa1b21ee1339aef56a909eab04cbe7d430fabfbb01ecd21b2dd9f3'], + }), + ('libxkbfile', '1.1.2', { # 2022-12-08 + 'checksums': ['d1a7e659bc7ae1aa1fc1ecced261c734df5ad5d86af1ef7a946be0e2d841e51d'], + }), + ('libxshmfence', '1.3.2', { # 2022-12-08 + 'checksums': ['e93a85099604beb244ee756dcaf70e18b08701c1ca84c4de0126cd71bd6c8181'], + }), + ('xcb-util', '0.4.1', { # 2022-12-20 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.1', { # 2022-10-18 + 'checksums': ['0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'], + }), + ('xcb-util-keysyms', '0.4.1', { # 2022-10-19 + 'checksums': ['1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'], + }), + ('xcb-util-renderutil', '0.3.10', { # 2022-10-19 + 'checksums': ['e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'], + }), + ('xcb-util-wm', '0.4.2', { # 2022-10-19 + 'checksums': ['dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'], + }), + ('xcb-util-cursor', '0.1.5', { # 2023-10-19 + 'checksums': ['cc8608ebb695742b6cf84712be29b2b66aa5f6768039528794fca0fa283022bf'], + }), + ('xkeyboard-config', '2.40', { # 2023-10-05 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['0690a91bab86b18868f3eee6d41e9ec4ce6894f655443d490a2184bfac56c872'], + # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing + 'preconfigopts': '', + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.4', { # 2022-09-12 + 'checksums': ['05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'], + }), + ('xbitmaps', '1.1.3', { # 2023-02-23 + 'checksums': ['93b433b7ff223c4685fdba583b4bd30f2706be2413a670021084422d85b0269d'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' From 8a8f0afed257e2444ff4a0059cca3aa965f13228 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 13:30:16 +0200 Subject: [PATCH 9199/9987] Fix toolchain for GMP, MPFR --- ...MP-6.3.0-GCCcore-12.3.0.eb => GMP-6.3.0-GCCcore-13.2.0.eb} | 2 +- ...R-4.2.1-GCCcore-12.3.0.eb => MPFR-4.2.1-GCCcore-13.2.0.eb} | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/GMP/{GMP-6.3.0-GCCcore-12.3.0.eb => GMP-6.3.0-GCCcore-13.2.0.eb} (95%) rename easybuild/easyconfigs/m/MPFR/{MPFR-4.2.1-GCCcore-12.3.0.eb => MPFR-4.2.1-GCCcore-13.2.0.eb} (92%) diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-13.2.0.eb similarity index 95% rename from easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-13.2.0.eb index 9c81142a743..1be7b653e2c 100644 --- a/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GMP/GMP-6.3.0-GCCcore-13.2.0.eb @@ -9,7 +9,7 @@ description = """ integers, rational numbers, and floating point numbers. """ -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'precise': True, 'pic': True} source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-13.2.0.eb similarity index 92% rename from easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-13.2.0.eb index 2c727b97972..ee90c2c294b 100644 --- a/easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/MPFR/MPFR-4.2.1-GCCcore-13.2.0.eb @@ -10,7 +10,7 @@ description = """ computations with correct rounding. """ -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://www.mpfr.org/mpfr-%(version)s/'] sources = [SOURCELOWER_TAR_BZ2] @@ -21,7 +21,7 @@ builddependencies = [ ] dependencies = [ - ('GMP', '6.2.1'), + ('GMP', '6.3.0'), ] runtest = 'check' From 9b3656442f723c69fa511ce5d9c848d48cb54d64 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 16:00:48 +0200 Subject: [PATCH 9200/9987] Update easybuild/easyconfigs/l/libsodium/libsodium-1.0.19-GCCcore-13.2.0.eb Co-authored-by: SebastianAchilles --- .../easyconfigs/l/libsodium/libsodium-1.0.19-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.19-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.19-GCCcore-13.2.0.eb index fe73970e780..6511aea996f 100644 --- a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.19-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.19-GCCcore-13.2.0.eb @@ -18,7 +18,7 @@ source_urls = [ 'https://download.%(name)s.org/%(name)s/releases/old/unsupported/', ] sources = [SOURCE_TAR_GZ] -checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] +checksums = ['018d79fe0a045cca07331d37bd0cb57b2e838c51bc48fd837a1472e50068bbea'] builddependencies = [ ('binutils', '2.40'), From 6a4156e699359b5a62d9cd1d7a93c2d5c6d9326d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 16:03:34 +0200 Subject: [PATCH 9201/9987] checksum --- easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.2.0.eb index 161c2d8020b..b1307bc3fcd 100644 --- a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.5-GCCcore-13.2.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://github.com/%(namelower)s/libzmq/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5'] +checksums = ['6653ef5910f17954861fe72332e68b03ca6e4d9c7160eb3a8de5a5a913bfab43'] builddependencies = [ ('binutils', '2.40'), From 66177403133de70309401704abe63c464cc25b94 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 23:51:45 +0200 Subject: [PATCH 9202/9987] adding easyconfigs: libunwind-1.6.2-GCCcore-13.2.0.eb, LLVM-17.0.3-GCCcore-13.2.0.eb, libdrm-2.4.117-GCCcore-13.2.0.eb, libglvnd-1.7.0-GCCcore-13.2.0.eb, Mesa-23.1.9-GCCcore-13.2.0.eb --- .../l/LLVM/LLVM-17.0.3-GCCcore-13.2.0.eb | 48 ++++++++++++++ .../l/libdrm/libdrm-2.4.117-GCCcore-13.2.0.eb | 32 +++++++++ .../libglvnd/libglvnd-1.7.0-GCCcore-13.2.0.eb | 33 ++++++++++ .../libunwind-1.6.2-GCCcore-13.2.0.eb | 32 +++++++++ .../m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb | 66 +++++++++++++++++++ 5 files changed, 211 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-17.0.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.117-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-17.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-17.0.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..fdbd39fa603 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-17.0.3-GCCcore-13.2.0.eb @@ -0,0 +1,48 @@ +name = 'LLVM' +version = '17.0.3' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'cstd': 'gnu++11', 'pic': True} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = [ + 'llvm-%(version)s.src.tar.xz', + 'cmake-%(version)s.src.tar.xz', + 'third-party-%(version)s.src.tar.xz', +] +checksums = [ + {'llvm-17.0.3.src.tar.xz': '18fa6b5f172ddf5af9b3aedfdb58ba070fd07fc45e7e589c46c350b3cc066bc1'}, + {'cmake-17.0.3.src.tar.xz': '54fc534f0da09088adbaa6c3bfc9899a500153b96e60c2fb9322a7aa37b1027a'}, + {'third-party-17.0.3.src.tar.xz': '6e84ff16044d698ff0f24e7445f9f47818e6523913a006a5e1ea79625b429b7b'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('Python', '3.11.5'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.117-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.117-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b426bc248de --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.117-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'libdrm' +version = '2.4.117' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['a2888d69e3eb1c8a77adc08a75a60fbae01f0d208d26f034d1a12e362361242b'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), +] +dependencies = [('X11', '20231019')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '-Dman-pages=disabled' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..cd5ce89a5cb --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.7.0-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'libglvnd' +version = '1.7.0' + +homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] +sources = ['libglvnd-v%(version)s.tar.gz'] +checksums = ['2b6e15b06aafb4c0b6e2348124808cbd9b291c647299eaaba2e3202f51ff2f3d'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [('X11', '20231019')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..031cb3115ea --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.6.2' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4a6aec666991fb45d0889c44aede8ad6eb108071c3554fcdff671f9c94794976'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('XZ', '5.4.4'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fno-common" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..e57f0258184 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb @@ -0,0 +1,66 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers enabled (swr deprecated as of v22): +# - llvmpipe: uses LLVM for JIT code generation (multi-threaded) +# - softpipe: a reference Gallium driver +# Default renderer is llvmpipe. To use softpipe, set the environment +# variable GALLIUM_DRIVER=softpipe + +name = 'Mesa' +version = '23.1.9' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7261a17fb94867e3dc5a90d8a1f100fa04b0cbbde51d25302c0872b5e9a10959'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '2.0.3'), + ('Mako', '1.2.4'), + ('libxml2', '2.11.5'), + ('expat', '2.5.0'), + ('gettext', '0.22'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('zstd', '1.5.5'), + ('libdrm', '2.4.117'), + ('libglvnd', '1.7.0'), + ('libunwind', '1.6.2'), + ('LLVM', '17.0.3'), + ('X11', '20231019'), +] + +configopts = "-Dplatforms=x11 -Dosmesa=true -Dvulkan-drivers='' " +configopts += "-Dllvm=enabled -Dshared-llvm=enabled -Dlibunwind=enabled -Dglvnd=true" + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +moduleclass = 'vis' From c9b8b4e0de8b71d17a89d5076f3f5f65745902e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 22 Oct 2023 23:54:23 +0200 Subject: [PATCH 9203/9987] Add libGLU --- .../l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6de3d5baea2 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'MesonNinja' + +name = 'libGLU' +version = '9.0.3' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.xz'] +checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] + +builddependencies = [('binutils', '2.40'), + ('Ninja', '1.11.1'), + ('Meson', '1.2.3')] + +dependencies = [('Mesa', '23.1.9')] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 016727ad096cb9f79ce82e6669b0c7b10af05d2a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 23 Oct 2023 00:01:16 +0200 Subject: [PATCH 9204/9987] checksum --- easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb index e57f0258184..44eafe37425 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb @@ -26,7 +26,7 @@ source_urls = [ 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', ] sources = [SOURCELOWER_TAR_XZ] -checksums = ['7261a17fb94867e3dc5a90d8a1f100fa04b0cbbde51d25302c0872b5e9a10959'] +checksums = ['295ba27c28146ed09214e8ce79afa1659edf9d142decc3c91f804552d64f7510'] builddependencies = [ ('binutils', '2.40'), From 3ec4ff5e1f425d7b1759b59d85ed7ca371e2495b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 23 Oct 2023 00:04:48 +0200 Subject: [PATCH 9205/9987] adding easyconfigs: NASM-2.16.01-GCCcore-13.2.0.eb, jbigkit-2.1-GCCcore-13.2.0.eb, libdeflate-1.19-GCCcore-13.2.0.eb, libjpeg-turbo-3.0.1-GCCcore-13.2.0.eb, LibTIFF-4.6.0-GCCcore-13.2.0.eb --- .../j/jbigkit/jbigkit-2.1-GCCcore-13.2.0.eb | 45 +++++++++++++++++++ .../l/LibTIFF/LibTIFF-4.6.0-GCCcore-13.2.0.eb | 38 ++++++++++++++++ .../libdeflate-1.19-GCCcore-13.2.0.eb | 37 +++++++++++++++ .../libjpeg-turbo-3.0.1-GCCcore-13.2.0.eb | 42 +++++++++++++++++ .../n/NASM/NASM-2.16.01-GCCcore-13.2.0.eb | 25 +++++++++++ 5 files changed, 187 insertions(+) create mode 100644 easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.6.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.19-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-3.0.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8c90f029573 --- /dev/null +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-13.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'jbigkit' +version = '2.1' + +homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' +description = """JBIG-KIT is a software implementation of the JBIG1 data + compression standard (ITU-T T.82), which was designed for bi-level image + data, such as scanned documents.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_libpath.patch', + '%(name)s-%(version)s_shlib.patch', +] +checksums = [ + {'jbigkit-2.1.tar.gz': 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932'}, + {'jbigkit-2.1_libpath.patch': '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce'}, + {'jbigkit-2.1_shlib.patch': '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +files_to_copy = [ + (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), + (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libjbig85.a', 'lib/libjbig.a', + 'bin/pbmtojbg', 'bin/jbgtopbm', + 'include/jbig.h', 'include/jbig_ar.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.6.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a4fde1fe8b6 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.6.0-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.6.0' + +homepage = 'https://libtiff.gitlab.io/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['88b3979e6d5c7e32b50d7ec72fb15af724f6ab2cbf7e10880c360a77e4b5d99a'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('zlib', '1.2.13'), + ('libjpeg-turbo', '3.0.1'), + ('XZ', '5.4.4'), + ('jbigkit', '2.1'), + ('zstd', '1.5.5'), + ('libdeflate', '1.19'), +] + +configopts = "--enable-ld-version-script " +configopts += "--disable-webp --disable-sphinx " + +sanity_check_paths = { + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], + 'dirs': [], +} + +sanity_check_commands = ["tiffinfo -h"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.19-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.19-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..11849b74c7e --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.19-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'libdeflate' +version = '1.19' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['27bf62d71cd64728ff43a9feb92f2ac2f2bf748986d856133cc1e51992428c25'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-3.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-3.0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..680c3f1f34d --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-3.0.1-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '3.0.1' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['22429507714ae147b3acacd299e82099fce5d9f456882fc28e252e4579ba2a75'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +dependencies = [ + ('NASM', '2.16.01'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..1c5164af198 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-13.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.16.01' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['35b6ad2ee048d41c4779f073f3efca7762a822b7d2d4ef4e8df24cf65747bb2e'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' From 74c1ee2d89361598188eeabfe70fc229143f9efd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 09:26:29 +0200 Subject: [PATCH 9206/9987] fix components checksums for X11 20231019 --- .../x/X11/X11-20231019-GCCcore-13.2.0.eb | 73 +++---------------- 1 file changed, 11 insertions(+), 62 deletions(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.2.0.eb index b1e2f2eec26..ecadd6a2d8b 100644 --- a/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20231019-GCCcore-13.2.0.eb @@ -37,57 +37,6 @@ source_urls = [ XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] -checksums = [ - {'libpthread-stubs-0.5.tar.gz': '593196cc746173d1e25cb54a93a87fd749952df68699aab7e02c085530e87747'}, - {'xorgproto-2023.2.tar.gz': 'c791aad9b5847781175388ebe2de85cb5f024f8dabf526d5d699c4f942660cc3'}, - {'libXau-1.0.11.tar.gz': '3a321aaceb803577a4776a5efe78836eb095a9e44bbc7a465d29463e1a14f189'}, - {'libXdmcp-1.1.4.tar.gz': '55041a8ff8992ab02777478c4b19c249c0f8399f05a752cb4a1a868a9a0ccb9a'}, - {'xcb-proto-1.16.0.tar.gz': 'd9c7f010b1105fc3858bf07b5169b2dd8e7493c6652b1fe45f3321d874f291d7'}, - {'libxcb-1.16.tar.gz': 'bc0f75f84b28e6496a19a1d094d7e47def861a50cb7cce5b23b62eecdc2a4479'}, - {'xtrans-1.5.0.tar.gz': 'a806f8a92f879dcd0146f3f1153fdffe845f2fc0df9b1a26c19312b7b0a29c86'}, - {'libxkbcommon-1.6.0.tar.xz': '0edc14eccdd391514458bc5f5a4b99863ed2d651e4dd761a90abf4f46ef99c2b'}, - {'libX11-1.8.7.tar.gz': '793ebebf569f12c864b77401798d38814b51790fce206e01a431e5feb982e20b'}, - {'libXext-1.3.5.tar.gz': '1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'}, - {'libFS-1.0.9.tar.gz': '8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'}, - {'libICE-1.1.1.tar.gz': '04fbd34a11ba08b9df2e3cdb2055c2e3c1c51b3257f683d7fcf42dabcf8e1210'}, - {'libSM-1.2.4.tar.gz': '51464ce1abce323d5b6707ceecf8468617106e1a8a98522f8342db06fd024c15'}, - {'libXScrnSaver-1.2.4.tar.gz': '0656b2630475104d6df75d91ebb8e0153e61d14e9871ef1f403bcda4a62a838a'}, - {'libXt-1.3.0.tar.gz': 'de4a80c4cc7785b9620e572de71026805f68e85a2bf16c386009ef0e50be3f77'}, - {'libXmu-1.1.4.tar.gz': '3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'}, - {'libXpm-3.5.17.tar.gz': '959466c7dfcfcaa8a65055bfc311f74d4c43d9257900f85ab042604d286df0c6'}, - {'libXaw-1.0.15.tar.gz': 'ca8a613884c922985202075b3cc8ee8821bfa83a5eb066189ae3cca131e63972'}, - {'libXfixes-6.0.1.tar.gz': 'e69eaa321173c748ba6e2f15c7cf8da87f911d3ea1b6af4b547974aef6366bec'}, - {'libXcomposite-0.4.6.tar.gz': '3599dfcd96cd48d45e6aeb08578aa27636fa903f480f880c863622c2b352d076'}, - {'libXrender-0.9.11.tar.gz': '6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'}, - {'libXcursor-1.2.1.tar.gz': '77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'}, - {'libXdamage-1.1.6.tar.gz': '2afcc139eb6eb926ffe344494b1fc023da25def42874496e6e6d3aa8acef8595'}, - {'libfontenc-1.1.7.tar.gz': '5e5f210329823f08f97bfe9fd5b4105070c789bc5aef88ce01d86d8203d4aa9f'}, - {'libXfont-1.5.4.tar.gz': '59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'}, - {'libXfont2-2.0.6.tar.gz': 'a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'}, - {'libXft-2.3.8.tar.gz': '32e48fe2d844422e64809e4e99b9d8aed26c1b541a5acf837c5037b8d9f278a8'}, - {'libXi-1.8.1.tar.gz': '3b5f47c223e4b63d7f7fe758886b8bf665b20a7edb6962c423892fd150e326ea'}, - {'libXinerama-1.1.5.tar.gz': '2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'}, - {'libXrandr-1.5.4.tar.gz': 'c72c94dc3373512ceb67f578952c5d10915b38cc9ebb0fd176a49857b8048e22'}, - {'libXres-1.2.2.tar.gz': '8abce597ced4a7ab89032aee91f6f784d9960adc772b2b59f17e515cd4127950'}, - {'libXtst-1.2.4.tar.gz': '01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'}, - {'libXv-1.0.12.tar.gz': 'ce706619a970a580a0e35e9b5c98bdd2af243ac6494c65f44608a89a86100126'}, - {'libXvMC-1.0.13.tar.gz': 'e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'}, - {'libXxf86dga-1.1.6.tar.gz': '87c7482b1e29b4eeb415815641c4f69c00545a8138e1b73ff1f361f7d9c22ac4'}, - {'libXxf86vm-1.1.5.tar.gz': 'f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'}, - {'libdmx-1.1.5.tar.gz': '070e82cc1daa1b21ee1339aef56a909eab04cbe7d430fabfbb01ecd21b2dd9f3'}, - {'libxkbfile-1.1.2.tar.gz': 'd1a7e659bc7ae1aa1fc1ecced261c734df5ad5d86af1ef7a946be0e2d841e51d'}, - {'libxshmfence-1.3.2.tar.gz': 'e93a85099604beb244ee756dcaf70e18b08701c1ca84c4de0126cd71bd6c8181'}, - {'xcb-util-0.4.1.tar.gz': '21c6e720162858f15fe686cef833cf96a3e2a79875f84007d76f6d00417f593a'}, - {'xcb-util-image-0.4.1.tar.gz': '0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'}, - {'xcb-util-keysyms-0.4.1.tar.gz': '1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'}, - {'xcb-util-renderutil-0.3.10.tar.gz': 'e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'}, - {'xcb-util-wm-0.4.2.tar.gz': 'dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'}, - {'xcb-util-cursor-0.1.5.tar.gz': '0e9c5446dc6f3beb8af6ebfcc9e27bcc6da6fe2860f7fc07b99144dfa568e93b'}, - {'xkeyboard-config-2.40.tar.xz': '7a3dba1bec7dc7191432da021242d17c9cf6c89690e6c57b0de048ff8c9d2ae3'}, - {'printproto-1.0.5.tar.gz': 'e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'}, - {'libXp-1.0.4.tar.gz': '05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'}, - {'xbitmaps-1.1.3.tar.gz': '93b433b7ff223c4685fdba583b4bd30f2706be2413a670021084422d85b0269d'}, -] default_easyblock = 'ConfigureMake' @@ -98,10 +47,10 @@ default_component_specs = { components = [ ('libpthread-stubs', '0.5', { # 2023-07-18 - 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + 'checksums': ['593196cc746173d1e25cb54a93a87fd749952df68699aab7e02c085530e87747'], }), ('xorgproto', '2023.2', { # 2023-06-16 - 'checksums': ['da351a403d07a7006d7bdc8dcfc14ddc1b588b38fb81adab9989a8eef605757b'], + 'checksums': ['c791aad9b5847781175388ebe2de85cb5f024f8dabf526d5d699c4f942660cc3'], }), ('libXau', '1.0.11', { # 2022-12-08 'checksums': ['3a321aaceb803577a4776a5efe78836eb095a9e44bbc7a465d29463e1a14f189'], @@ -110,10 +59,10 @@ components = [ 'checksums': ['55041a8ff8992ab02777478c4b19c249c0f8399f05a752cb4a1a868a9a0ccb9a'], }), ('xcb-proto', '1.16.0', { # 2023-08-16 - 'checksums': ['6b1ed9cd7cf35e37913eeecca37e5b85b14903002942b3e332f321335c27a8eb'], + 'checksums': ['d9c7f010b1105fc3858bf07b5169b2dd8e7493c6652b1fe45f3321d874f291d7'], }), ('libxcb', '1.16', { # 2023-05-03 - 'checksums': ['1cb65df8543a69ec0555ac696123ee386321dfac1964a3da39976c9a05ad724d'], + 'checksums': ['bc0f75f84b28e6496a19a1d094d7e47def861a50cb7cce5b23b62eecdc2a4479'], }), ('xtrans', '1.5.0', { # 2023-06-03 'checksums': ['a806f8a92f879dcd0146f3f1153fdffe845f2fc0df9b1a26c19312b7b0a29c86'], @@ -121,12 +70,12 @@ components = [ ('libxkbcommon', '1.6.0', { # 2023-10-08 'easyblock': 'MesonNinja', 'sources': [SOURCE_TAR_XZ], - 'checksums': ['560f11c4bbbca10f495f3ef7d3a6aa4ca62b4f8fb0b52e7d459d18a26e46e017'], + 'checksums': ['0edc14eccdd391514458bc5f5a4b99863ed2d651e4dd761a90abf4f46ef99c2b'], 'preconfigopts': '', 'configopts': '-Denable-wayland=false -Denable-docs=false ', }), ('libX11', '1.8.7', { # 2023-10-03 - 'checksums': ['d84a35c324d5a1724692eafc1ed76f1689c833021e0062933773ec437f91a56b'], + 'checksums': ['793ebebf569f12c864b77401798d38814b51790fce206e01a431e5feb982e20b'], }), ('libXext', '1.3.5', { # 2022-10-29 'checksums': ['1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'], @@ -150,7 +99,7 @@ components = [ 'checksums': ['3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'], }), ('libXpm', '3.5.17', { # 2023-10-03 - 'checksums': ['43a70e6f9b67215fb223ca270d83bdcb868c513948441d5b781ea0765df6bfb4'], + 'checksums': ['959466c7dfcfcaa8a65055bfc311f74d4c43d9257900f85ab042604d286df0c6'], }), ('libXaw', '1.0.15', { # 2023-03-16 'checksums': ['ca8a613884c922985202075b3cc8ee8821bfa83a5eb066189ae3cca131e63972'], @@ -189,7 +138,7 @@ components = [ 'checksums': ['2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'], }), ('libXrandr', '1.5.4', { # 2023-10-04 - 'checksums': ['3ad316c1781fe2fe22574b819e81f0eff087a8560377f521ba932238b41b251f'], + 'checksums': ['c72c94dc3373512ceb67f578952c5d10915b38cc9ebb0fd176a49857b8048e22'], }), ('libXres', '1.2.2', { # 2022-12-05 'checksums': ['8abce597ced4a7ab89032aee91f6f784d9960adc772b2b59f17e515cd4127950'], @@ -219,7 +168,7 @@ components = [ 'checksums': ['e93a85099604beb244ee756dcaf70e18b08701c1ca84c4de0126cd71bd6c8181'], }), ('xcb-util', '0.4.1', { # 2022-12-20 - 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + 'checksums': ['21c6e720162858f15fe686cef833cf96a3e2a79875f84007d76f6d00417f593a'], }), ('xcb-util-image', '0.4.1', { # 2022-10-18 'checksums': ['0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'], @@ -234,12 +183,12 @@ components = [ 'checksums': ['dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'], }), ('xcb-util-cursor', '0.1.5', { # 2023-10-19 - 'checksums': ['cc8608ebb695742b6cf84712be29b2b66aa5f6768039528794fca0fa283022bf'], + 'checksums': ['0e9c5446dc6f3beb8af6ebfcc9e27bcc6da6fe2860f7fc07b99144dfa568e93b'], }), ('xkeyboard-config', '2.40', { # 2023-10-05 'easyblock': 'MesonNinja', 'sources': [SOURCE_TAR_XZ], - 'checksums': ['0690a91bab86b18868f3eee6d41e9ec4ce6894f655443d490a2184bfac56c872'], + 'checksums': ['7a3dba1bec7dc7191432da021242d17c9cf6c89690e6c57b0de048ff8c9d2ae3'], # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing 'preconfigopts': '', }), From 6deff15f3b547864131e100f3f17d40071f36a9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 11:55:49 +0200 Subject: [PATCH 9207/9987] trivial style fixes in MACS3 easyconfig --- easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb index 6c4cc540d89..fd1fbdee019 100644 --- a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb +++ b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb @@ -8,7 +8,6 @@ description = """Model Based Analysis for ChIP-Seq data""" toolchain = {'name': 'foss', 'version': '2022b'} - builddependencies = [ ('pybind11', '2.10.3'), ] @@ -36,6 +35,6 @@ exts_list = [ }), ] -sanity_check_commands = [('%(namelower)s --help')] +sanity_check_commands = ["macs3 --help"] moduleclass = 'bio' From 7b91b1ab6a34baa95007b8f205f43298297084b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 23 Oct 2023 11:56:59 +0200 Subject: [PATCH 9208/9987] Drop LLVM version --- ....3-GCCcore-13.2.0.eb => LLVM-16.0.6-GCCcore-13.2.0.eb} | 8 ++++---- .../easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/l/LLVM/{LLVM-17.0.3-GCCcore-13.2.0.eb => LLVM-16.0.6-GCCcore-13.2.0.eb} (79%) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-17.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-16.0.6-GCCcore-13.2.0.eb similarity index 79% rename from easybuild/easyconfigs/l/LLVM/LLVM-17.0.3-GCCcore-13.2.0.eb rename to easybuild/easyconfigs/l/LLVM/LLVM-16.0.6-GCCcore-13.2.0.eb index fdbd39fa603..3cbf84f26fe 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-17.0.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-16.0.6-GCCcore-13.2.0.eb @@ -1,5 +1,5 @@ name = 'LLVM' -version = '17.0.3' +version = '16.0.6' homepage = "https://llvm.org/" description = """The LLVM Core libraries provide a modern source- and target-independent @@ -20,9 +20,9 @@ sources = [ 'third-party-%(version)s.src.tar.xz', ] checksums = [ - {'llvm-17.0.3.src.tar.xz': '18fa6b5f172ddf5af9b3aedfdb58ba070fd07fc45e7e589c46c350b3cc066bc1'}, - {'cmake-17.0.3.src.tar.xz': '54fc534f0da09088adbaa6c3bfc9899a500153b96e60c2fb9322a7aa37b1027a'}, - {'third-party-17.0.3.src.tar.xz': '6e84ff16044d698ff0f24e7445f9f47818e6523913a006a5e1ea79625b429b7b'}, + {'llvm-16.0.6.src.tar.xz': 'e91db44d1b3bb1c33fcea9a7d1f2423b883eaa9163d3d56ca2aa6d2f0711bc29'}, + {'cmake-16.0.6.src.tar.xz': '39d342a4161095d2f28fb1253e4585978ac50521117da666e2b1f6f28b62f514'}, + {'third-party-16.0.6.src.tar.xz': '15f5b9aeeba938530af977d5f9205612737a091a7f0f6c8075df8723b7713f70'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb index 44eafe37425..906c5eb2634 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb @@ -47,7 +47,7 @@ dependencies = [ ('libdrm', '2.4.117'), ('libglvnd', '1.7.0'), ('libunwind', '1.6.2'), - ('LLVM', '17.0.3'), + ('LLVM', '16.0.6'), ('X11', '20231019'), ] From 1e82311b6954e1e638434b0fc5da4af0ea54f8ca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 12:07:49 +0200 Subject: [PATCH 9209/9987] use updated hmmlearn easyconfig as dependency for MACS3 --- .../h/hmmlearn/hmmlearn-0.3.0-foss-2022b.eb | 24 +++++++++++++++++++ .../m/MACS3/MACS3-3.0.0b2-foss-2022b.eb | 5 +--- 2 files changed, 25 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-foss-2022b.eb b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-foss-2022b.eb new file mode 100644 index 00000000000..ce3407ae7b0 --- /dev/null +++ b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-foss-2022b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'hmmlearn' +version = '0.3.0' + +homepage = 'https://github.com/hmmlearn/hmmlearn' +description = "hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d13a91ea3695df881465e3d36132d7eef4e84d483f4ba538a4b46e24b5ea100f'] + +dependencies = [ + ('Python', '3.10.8'), + ('scikit-learn', '1.2.1'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb index fd1fbdee019..16e37a09720 100644 --- a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb +++ b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0b2-foss-2022b.eb @@ -15,8 +15,8 @@ builddependencies = [ dependencies = [ ('Python', '3.10.8'), ('SciPy-bundle', '2023.02'), - ('scikit-learn', '1.2.1'), ('matplotlib', '3.7.0'), + ('hmmlearn', '0.3.0'), ] use_pip = True @@ -26,9 +26,6 @@ exts_list = [ ('cykhash', '2.0.1', { 'checksums': ['b4794bc9f549114d8cf1d856d9f64e08ff5f246bf043cf369fdb414e9ceb97f7'], }), - ('hmmlearn', '0.3.0', { - 'checksums': ['d13a91ea3695df881465e3d36132d7eef4e84d483f4ba538a4b46e24b5ea100f'], - }), (name, version, { 'modulename': 'MACS3', 'checksums': ['9b13fed49b93623ddde4b2d5106fc92a796111fa92148cafe7d8bd9a2e8aa43f'], From 20506e22c457480d28bfcfdd01197c3b0dd69259 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Mon, 23 Oct 2023 11:07:58 +0000 Subject: [PATCH 9210/9987] Update to upstream release that fixes the test suite --- .../g/GEMMA/GEMMA-0.98.5-foss-2020a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb new file mode 100644 index 00000000000..9ad5cfb5790 --- /dev/null +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'GEMMA' +version = '0.98.5' + +homepage = 'https://github.com/genetics-statistics/GEMMA' +description = "Genome-wide Efficient Mixed Model Association" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/genetics-statistics/GEMMA/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3ed336deee29e370f96ec8f1a240f7b62550e57dcd1694245ce7ec8f42241677'] + +builddependencies = [ + ('Eigen', '3.3.7', '', True), +] + +dependencies = [ + ('GSL', '2.6'), + ('zlib', '1.2.11') +] + +files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES.md", "scripts", "VERSION"] + +sanity_check_commands = ["cd %(builddir)s/%(name)s-%(version)s/ && test/test_suite.sh"] + +sanity_check_paths = { + 'files': ["bin/gemma"], + 'dirs': [] +} + +moduleclass = 'bio' From 81c4946ca778293fd70a747d51cb3cc20b41fbe6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 23 Oct 2023 12:09:22 +0100 Subject: [PATCH 9211/9987] Delete easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb Remove outdated file --- .../g/GEMMA/GEMMA-0.98.4-foss-2020a.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb deleted file mode 100644 index 4b770c6f4d4..00000000000 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.4-foss-2020a.eb +++ /dev/null @@ -1,38 +0,0 @@ -# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'MakeCp' - -name = 'GEMMA' -version = '0.98.4' - -homepage = 'https://github.com/genetics-statistics/GEMMA' -description = "Genome-wide Efficient Mixed Model Association" - -toolchain = {'name': 'foss', 'version': '2020a'} - -source_urls = ['https://github.com/genetics-statistics/GEMMA/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['4f57a045d3289afaf31f818bf411ac46c5ee6f78ff8c9c4117963ca54e0bb9f0'] - -builddependencies = [ - ('Eigen', '3.3.7'), -] - -dependencies = [ - ('GSL', '2.6'), - ('zlib', '1.2.11') -] - -files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES.md", "scripts", "VERSION"] - -sanity_check_commands = ["cd %(builddir)s/%(name)s-%(version)s/ && ./run_tests.sh"] - -sanity_check_paths = { - 'files': ["bin/gemma"], - 'dirs': [] -} - -moduleclass = 'bio' From fd84b147df4b73f020a37c24daaae44417c277ee Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 23 Oct 2023 14:52:52 +0200 Subject: [PATCH 9212/9987] {cae}[foss/2023a] OpenFOAM 10 w/ CGAL 5.6 and ParaView 5.11.2 --- .../c/CGAL/CGAL-5.6-GCCcore-12.3.0.eb | 26 +++++++ .../o/OpenFOAM/OpenFOAM-10-foss-2023a.eb | 36 ++++++++++ .../p/ParaView/ParaView-5.11.2-foss-2023a.eb | 71 +++++++++++++++++++ 3 files changed, 133 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-5.6-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.11.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-5.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CGAL/CGAL-5.6-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..38817452cd4 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-5.6-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' +name = 'CGAL' +version = '5.6' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['dcab9b08a50a06a7cc2cc69a8a12200f8d8f391b9b8013ae476965c10b45161f'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['include/CGAL/Simple_cartesian.h'], + 'dirs': ['include/CGAL', 'lib/cmake/CGAL'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb new file mode 100644 index 00000000000..c4358543285 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2023a.eb @@ -0,0 +1,36 @@ +name = 'OpenFOAM' +version = '10' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-%(version)s-ThirdParty.patch'] +checksums = [ + {'version-10.tar.gz': '59d712ba798ca44b989b6ac50bcb7c534eeccb82bcf961e10ec19fc8d84000cf'}, + {'OpenFOAM-10-ThirdParty.patch': '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('CGAL', '5.6'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.2-foss-2023a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.2-foss-2023a.eb new file mode 100644 index 00000000000..29377002716 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.2-foss-2023a.eb @@ -0,0 +1,71 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.11.2' +versionsuffix = '' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] +checksums = [ + {'ParaView-v5.11.2.tar.gz': 'ddee336075f8c258a3d34eb1cdd2f4d46a5082f0b4af614e36b06e530f3b346f'}, + {'ParaView-5.11.1-remove_glew_init_warning.patch': + 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost', '1.82.0'), + ('XZ', '5.4.2'), + ('HDF5', '1.14.0'), + ('netCDF', '4.9.2'), + ('libdrm', '2.4.115'), + ('Mesa', '23.1.4'), + ('Qt5', '5.15.10'), + ('zlib', '1.2.13'), + ('FFmpeg', '6.0'), + ('Szip', '2.1.1'), +] + +_copts = [ + # Basic configuration + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', + '-DPARAVIEW_BUILD_SHARED_LIBS=ON', + '-DPARAVIEW_USE_MPI=ON', + '-DPARAVIEW_ENABLE_FFMPEG=ON', + '-DPARAVIEW_USE_PYTHON=ON', + '-DPython3_ROOT_DIR=$EBROOTPYTHON', + # Useful input formats + '-DPARAVIEW_ENABLE_XDMF2=ON', + '-DPARAVIEW_ENABLE_XDMF3=ON', + # EGL, X and Mesa + '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s' % SHLIB_EXT, + '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include', + '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include', + '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s' % SHLIB_EXT, + '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, + '-DVTK_OPENGL_HAS_EGL=ON', + '-DVTK_USE_X=ON', + '-DVTK_OPENGL_HAS_OSMESA=OFF'] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' From 8e390e94c645b2209d0b5b958ba13d892ec21de9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 23 Oct 2023 16:14:29 +0200 Subject: [PATCH 9213/9987] fix dependency on Eigen of GEMMA v0.98.5 --- easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb index 9ad5cfb5790..1642de6becc 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['3ed336deee29e370f96ec8f1a240f7b62550e57dcd1694245ce7ec8f42241677'] builddependencies = [ - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.7', '', SYSTEM), ] dependencies = [ From 5fba734d82eaa0d9f0100f1e63ff6cd1f2695618 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 15:16:06 +0100 Subject: [PATCH 9214/9987] Doxygen added --- easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 1 + easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index ed89cbbcb2d..74075795c30 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -18,6 +18,7 @@ checksums = ['4749d25a2b2ef67cc0c014caaf5c87fa46792fc4b3ede186fb0fc932d2055158'] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), + ('Doxygen', '1.9.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb index 4d3b9b1d798..1e37a907b91 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb @@ -18,6 +18,7 @@ checksums = ['6a63bf98a97dda2b0f55e34d1b5f3fb909ef8b70f9b8d382cb1ff3978e7dc13f'] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), + ('Doxygen', '1.9.4'), ] dependencies = [ From b965938b12db146703cdff7eb8a293a7883584a5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 23 Oct 2023 16:27:43 +0200 Subject: [PATCH 9215/9987] add missing dependencies on Perl and Ruby to GEMMA v0.98.5 --- easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb index 1642de6becc..22500df48ff 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb @@ -18,7 +18,9 @@ sources = ['v%(version)s.tar.gz'] checksums = ['3ed336deee29e370f96ec8f1a240f7b62550e57dcd1694245ce7ec8f42241677'] builddependencies = [ - ('Eigen', '3.3.7', '', SYSTEM), + ('Eigen', '3.3.7'), + ('Perl', '5.30.2'), + ('Ruby', '2.7.2'), ] dependencies = [ From 92cd8fa1a13a621d9ca074fb21eb718e5e5dd7bf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 23 Oct 2023 16:28:50 +0200 Subject: [PATCH 9216/9987] run check on GEMMA v0.98.5 --- easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb index 22500df48ff..0209363b19e 100644 --- a/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb +++ b/easybuild/easyconfigs/g/GEMMA/GEMMA-0.98.5-foss-2020a.eb @@ -30,7 +30,9 @@ dependencies = [ files_to_copy = ["bin", "doc", "example", "LICENSE", "README.md", "RELEASE-NOTES.md", "scripts", "VERSION"] -sanity_check_commands = ["cd %(builddir)s/%(name)s-%(version)s/ && test/test_suite.sh"] +runtest = 'check' + +sanity_check_commands = ["gemma -h", "gemma -license"] sanity_check_paths = { 'files': ["bin/gemma"], From 1aa631d3f1e6290ab6b1b55795aca348dd88423e Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 15:45:14 +0100 Subject: [PATCH 9217/9987] Demoted to GCCcore --- .../d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb | 80 +++++++++++++++++++ 1 file changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..68f1c7b9cff --- /dev/null +++ b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb @@ -0,0 +1,80 @@ +# Updated to latest version +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'dxpy' +version = '0.345.0' + +homepage = 'http://autodoc.dnanexus.com/' +description = "DNAnexus Platform API bindings for Python" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Python', '3.10.8'), + ('FUSE', '3.14.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('argcomplete', '3.0.5', { + 'checksums': ['fe3ce77125f434a0dd1bffe5f4643e64126d5731ce8d173d36f62fa43d6eb6f7'], + }), + ('xattr', '0.10.1', { + 'checksums': ['c12e7d81ffaa0605b3ac8c22c2994a8e18a9cf1c59287a1b7722a2289c952ec5'], + }), + ('fusepy', '3.0.1', { + 'modulename': 'fuse', + 'patches': ['fusepy-3.0.1_fix-libfuse.patch'], + 'checksums': [ + '72ff783ec2f43de3ab394e3f7457605bf04c8cf288a2f4068b4cde141d4ee6bd', # fusepy-3.0.1.tar.gz + '7650c5f922c24b820f2b33e0b5b1af8923c1a5c4ff397701cd970ea33c757fbe', # fusepy-3.0.1_fix-libfuse.patch + ], + }), + ('backports.ssl_match_hostname', '3.7.0.1', { + 'checksums': ['bb82e60f9fbf4c080eabd957c39f0641f0fc247d9a16e31e26d594d8f42b9fd2'], + }), + ('psutil', '5.9.5', { + 'checksums': ['5410638e4df39c54d957fc51ce03048acd8e6d60abc0f5107af51e5fb566eb3c'], + }), + ('soupsieve', '2.4.1', { + 'checksums': ['89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea'], + }), + ('beautifulsoup4', '4.12.2', { + 'modulename': 'bs4', + 'checksums': ['492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da'], + }), + ('python-magic', '0.4.27', { + 'modulename': 'magic', + 'checksums': ['c1ba14b08e4a5f5c31a302b7721239695b2f0f058d125bd5ce1ee36b9d9d3c3b'], + }), + ('websocket_client', '0.54.0', { + 'modulename': 'websocket', + 'checksums': ['e51562c91ddb8148e791f0155fdb01325d99bb52c4cdbb291aee7a3563fd0849'], + }), + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + ('cffi', '1.15.1', { + 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], + }), + ('charset-normalizer', '2.0.12', { + 'checksums': ['2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597'], + }), + ('requests', '2.27.1', { + 'checksums': ['68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61'], + }), + (name, version, { + 'checksums': ['cf5b47e83866a9c87a4fc59262eac500e860f6a890e6a897a577eff68e28cff2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 5b3583bb73494599c7ab8fc049dc90f747fd75a5 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 15:47:17 +0100 Subject: [PATCH 9218/9987] FOSS version removed --- .../d/dxpy/dxpy-0.345.0-foss-2022b.eb | 80 ------------------- 1 file changed, 80 deletions(-) delete mode 100644 easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022b.eb b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022b.eb deleted file mode 100644 index e689c573156..00000000000 --- a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-foss-2022b.eb +++ /dev/null @@ -1,80 +0,0 @@ -# Updated to latest version -# Author: J. Sassmannshausen (Imperial College London/UK) - -easyblock = 'PythonBundle' - -name = 'dxpy' -version = '0.345.0' - -homepage = 'http://autodoc.dnanexus.com/' -description = "DNAnexus Platform API bindings for Python" - -toolchain = {'name': 'foss', 'version': '2022b'} - -dependencies = [ - ('Python', '3.10.8'), - ('FUSE', '3.14.1'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('argcomplete', '3.0.5', { - 'checksums': ['fe3ce77125f434a0dd1bffe5f4643e64126d5731ce8d173d36f62fa43d6eb6f7'], - }), - ('xattr', '0.10.1', { - 'checksums': ['c12e7d81ffaa0605b3ac8c22c2994a8e18a9cf1c59287a1b7722a2289c952ec5'], - }), - ('fusepy', '3.0.1', { - 'modulename': 'fuse', - 'patches': ['fusepy-3.0.1_fix-libfuse.patch'], - 'checksums': [ - '72ff783ec2f43de3ab394e3f7457605bf04c8cf288a2f4068b4cde141d4ee6bd', # fusepy-3.0.1.tar.gz - '7650c5f922c24b820f2b33e0b5b1af8923c1a5c4ff397701cd970ea33c757fbe', # fusepy-3.0.1_fix-libfuse.patch - ], - }), - ('backports.ssl_match_hostname', '3.7.0.1', { - 'checksums': ['bb82e60f9fbf4c080eabd957c39f0641f0fc247d9a16e31e26d594d8f42b9fd2'], - }), - ('psutil', '5.9.5', { - 'checksums': ['5410638e4df39c54d957fc51ce03048acd8e6d60abc0f5107af51e5fb566eb3c'], - }), - ('soupsieve', '2.4.1', { - 'checksums': ['89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea'], - }), - ('beautifulsoup4', '4.12.2', { - 'modulename': 'bs4', - 'checksums': ['492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da'], - }), - ('python-magic', '0.4.27', { - 'modulename': 'magic', - 'checksums': ['c1ba14b08e4a5f5c31a302b7721239695b2f0f058d125bd5ce1ee36b9d9d3c3b'], - }), - ('websocket_client', '0.54.0', { - 'modulename': 'websocket', - 'checksums': ['e51562c91ddb8148e791f0155fdb01325d99bb52c4cdbb291aee7a3563fd0849'], - }), - ('pycparser', '2.21', { - 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], - }), - ('cffi', '1.15.1', { - 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], - }), - ('charset-normalizer', '2.0.12', { - 'checksums': ['2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597'], - }), - ('requests', '2.27.1', { - 'checksums': ['68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61'], - }), - (name, version, { - 'checksums': ['cf5b47e83866a9c87a4fc59262eac500e860f6a890e6a897a577eff68e28cff2'], - }), -] - -sanity_check_paths = { - 'files': ['bin/dx'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'bio' From 372e1134db6de5a903499593eaab92a22977fc15 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 16:16:47 +0100 Subject: [PATCH 9219/9987] M4 added --- easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 1 + easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index 74075795c30..5d792e5a489 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -19,6 +19,7 @@ builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), ('Doxygen', '1.9.4'), + ('M4', '1.4.19'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb index 1e37a907b91..972787a1a18 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.16.2-GCC-11.3.0.eb @@ -19,6 +19,7 @@ builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), ('Doxygen', '1.9.4'), + ('M4', '1.4.19'), ] dependencies = [ From e885f81f708ba9f876ef709d6460d086e95c75cb Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 23 Oct 2023 17:33:37 +0200 Subject: [PATCH 9220/9987] adding easyconfigs: scikit-lego-0.6.16-foss-2022a.eb --- .../scikit-lego-0.6.16-foss-2022a.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb new file mode 100644 index 00000000000..af838bb40d3 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'scikit-lego' +version = '0.6.16' + +homepage = 'https://github.com/koaning/scikit-lego' +description = """ +We love scikit learn but very often we find ourselves writing custom transformers, metrics and +models. The goal of this project is to attempt to consolidate these into a package that offers +code quality/testing. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'koaning' + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('matplotlib', '3.5.2'), + ('umap-learn', '0.5.3'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('autograd', '1.6.2', { + 'checksums': ['8731e08a0c4e389d8695a40072ada4512641c113b6cace8f4cfbe8eb7e9aedeb'], + }), + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('patsy', '0.5.3', { + 'checksums': ['bdc18001875e319bc91c812c1eb6a10be4bb13cb81eb763f466179dca3b67277'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + (name, version, { + 'modulename': 'sklego', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['bf58f66518e9e8dca54cac634d7642b1e1a6c9984e17af6f1f71e0312dbe4a69'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 486305057c7ac632e6ca1797681f9c73283af058 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 16:33:49 +0100 Subject: [PATCH 9221/9987] Missing binutils added --- easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb index 68f1c7b9cff..e8197cab1e1 100644 --- a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb @@ -11,6 +11,10 @@ description = "DNAnexus Platform API bindings for Python" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +builddependencies = [ + ('binutils', '2.39'), +] + dependencies = [ ('Python', '3.10.8'), ('FUSE', '3.14.1'), From 1cde8376536c0b3fb8287731f4f665d368a31ebe Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 23 Oct 2023 17:59:30 +0200 Subject: [PATCH 9222/9987] remove download_dep_fail --- .../easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb index af838bb40d3..b469cc61b1e 100644 --- a/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb +++ b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb @@ -26,7 +26,6 @@ dependencies = [ ('umap-learn', '0.5.3'), ] -download_dep_fail = True use_pip = True exts_list = [ From 47fbb7487a2b107dab77147367062c4a129c6162 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Mon, 23 Oct 2023 19:06:19 +0200 Subject: [PATCH 9223/9987] remove source_urls from exts_default_options since default value is used in Nipype-1.6.0-foss-2020b.eb --- easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb index b4ace4a2053..ce60ce71e31 100644 --- a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('traits', '6.2.0', { 'checksums': ['16fa1518b0778fd53bf0547e6a562b1787bf68c8f6b7995a13bd1902529fdb0c'], From c94eb98253723e75674a88f6ffcfadad83da00b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 19:12:17 +0200 Subject: [PATCH 9224/9987] remove easyconfig for Boost 1.81.0 with GCCcore/12.2.0, should use GCC/12.2.0 --- .../b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb | 32 ------------------- 1 file changed, 32 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb deleted file mode 100644 index 5fc718928fd..00000000000 --- a/easybuild/easyconfigs/b/Boost/Boost-1.81.0-GCCcore-12.2.0.eb +++ /dev/null @@ -1,32 +0,0 @@ -name = 'Boost' -version = '1.81.0' - -homepage = 'https://www.boost.org/' -description = """Boost provides free peer-reviewed portable C++ source libraries.""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] -sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['205666dea9f6a7cfed87c7a6dfbeb52a2c1b9de55712c9c1a87735d7181452b6'] - -builddependencies = [ - ('binutils', '2.39'), -] - -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.12'), - ('XZ', '5.2.7'), - ('zstd', '1.5.2'), - ('ICU', '72.1'), -] - -configopts = '--without-libraries=python,mpi' - -# disable MPI, build Boost libraries with tagged layout -boost_mpi = False -tagged_layout = True - -moduleclass = 'devel' From 56e64e6cf32e0d54698df9505450279d9ba97196 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 19:12:58 +0200 Subject: [PATCH 9225/9987] use GCC/12.2.0 toolchain for msgpack-c 6.0.0 + fix non-build Boost dependency --- ...0.0-GCCcore-12.2.0.eb => msgpack-c-6.0.0-GCC-12.2.0.eb} | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/m/msgpack-c/{msgpack-c-6.0.0-GCCcore-12.2.0.eb => msgpack-c-6.0.0-GCC-12.2.0.eb} (93%) diff --git a/easybuild/easyconfigs/m/msgpack-c/msgpack-c-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/msgpack-c/msgpack-c-6.0.0-GCC-12.2.0.eb similarity index 93% rename from easybuild/easyconfigs/m/msgpack-c/msgpack-c-6.0.0-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/m/msgpack-c/msgpack-c-6.0.0-GCC-12.2.0.eb index cb567b6c10e..97901abf8d5 100644 --- a/easybuild/easyconfigs/m/msgpack-c/msgpack-c-6.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/msgpack-c/msgpack-c-6.0.0-GCC-12.2.0.eb @@ -10,7 +10,7 @@ data among multiple languages like JSON, except that it's faster and smaller. Small integers are encoded into a single byte while typical short strings require only one extra byte in addition to the strings themselves.""" -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchain = {'name': 'GCC', 'version': '12.2.0'} source_urls = ['https://github.com/msgpack/msgpack-c/releases/download/c-%(version)s'] sources = ['msgpack-c-%(version)s.tar.gz'] @@ -19,10 +19,13 @@ checksums = ['3654f5e2c652dc52e0a993e270bb57d5702b262703f03771c152bba51602aeba'] builddependencies = [ ('CMake', '3.24.3'), ('binutils', '2.39'), - ('Boost', '1.81.0'), ('googletest', '1.12.1'), ] +dependencies = [ + ('Boost', '1.81.0'), +] + sanity_check_paths = { 'files': [ ['lib/libmsgpack-c.%s' % x for x in ['a', '%s' % SHLIB_EXT]], From dc53e96faa1669a0a7b828408a0e52eb05258a95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 19:13:27 +0200 Subject: [PATCH 9226/9987] enable sanity_pip_check in easyconfig for QCG-PilotJob v0.13.1 --- .../q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb index 3f0b96debf8..4040a8b8488 100644 --- a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2022b.eb @@ -51,4 +51,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'tools' From d6f92ee4b7e85fc7103b3da6aafa4bb7713c6ce0 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 18:20:24 +0100 Subject: [PATCH 9227/9987] HDF5 downgraded to 1.10.6 --- easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb b/easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb index 1ce39e094d4..6d05dd196d9 100644 --- a/easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb +++ b/easybuild/easyconfigs/x/XOOPIC/XOOPIC-20210302-foss-2020a.eb @@ -30,7 +30,7 @@ dependencies = [ ('Tk', '8.6.10'), ('ImageMagick', '7.0.10-1'), ('XGrafix', '2.41'), - ('HDF5', '1.12.0'), + ('HDF5', '1.10.6'), ('FFTW', '3.3.8'), ] From 10934e1d6096d5855727b2cd2a03af9f84d53b74 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 19:44:23 +0200 Subject: [PATCH 9228/9987] add missing CMake build dependency for MUSCLE3 + clean up & enhance sanity check --- .../m/MUSCLE3/MUSCLE3-0.7.0-foss-2022b.eb | 36 ++++++++----------- 1 file changed, 15 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-foss-2022b.eb b/easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-foss-2022b.eb index 25ab35908b1..f0db20b1b69 100644 --- a/easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-foss-2022b.eb +++ b/easybuild/easyconfigs/m/MUSCLE3/MUSCLE3-0.7.0-foss-2022b.eb @@ -18,6 +18,7 @@ sources = ['%(version)s.tar.gz'] checksums = ['e2ab6f0d219845c7bcdf9ebade9572b647d5dc464179b4714211db68fd9cb062'] builddependencies = [ + ('CMake', '3.24.3'), ('googletest', '1.12.1'), ] @@ -77,27 +78,20 @@ modextrapaths = { } sanity_check_paths = { - 'files': ['include/libmuscle.f90', - 'include/libmuscle.mod', - 'include/libmuscle/libmuscle.hpp', - 'include/ymmsl/ymmsl.hpp', - 'lib/libmuscle.a', - 'lib/libmuscle.%s' % SHLIB_EXT, - 'lib/libmuscle_fortran.a', - 'lib/libmuscle_fortran.%s' % SHLIB_EXT, - 'lib/libymmsl.a', - 'lib/libymmsl.%s' % SHLIB_EXT, - 'lib/libymmsl_fortran.a', - 'lib/libymmsl_fortran.%s' % SHLIB_EXT, - 'lib/pkgconfig/libmuscle.pc', - 'lib/pkgconfig/libmuscle_fortran.pc', - 'lib/pkgconfig/ymmsl.pc', - 'lib/pkgconfig/ymmsl_fortran.pc'], - 'dirs': ['bin', - 'include/libmuscle/mcp', - 'include/ymmsl', - 'lib/pkgconfig', - 'lib64'] + 'files': ['bin/muscle3', 'bin/muscle3.env', 'bin/muscle_manager', + 'include/libmuscle.f90', 'include/libmuscle.mod', 'include/libmuscle/libmuscle.hpp', + 'include/ymmsl/ymmsl.hpp', 'lib/libmuscle.a', 'lib/libmuscle.%s' % SHLIB_EXT, + 'lib/libmuscle_fortran.a', 'lib/libmuscle_fortran.%s' % SHLIB_EXT, + 'lib/libymmsl.a', 'lib/libymmsl.%s' % SHLIB_EXT, + 'lib/libymmsl_fortran.a', 'lib/libymmsl_fortran.%s' % SHLIB_EXT, + 'lib/pkgconfig/libmuscle.pc', 'lib/pkgconfig/libmuscle_fortran.pc', + 'lib/pkgconfig/ymmsl.pc', 'lib/pkgconfig/ymmsl_fortran.pc'], + 'dirs': [], } +sanity_check_commands = [ + "muscle3 --help", + "muscle_manager --help", +] + moduleclass = 'tools' From 24fe75b3c852eaec4432d8681468463d65c76069 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 19:46:57 +0200 Subject: [PATCH 9229/9987] trivial cleanup in sanity_check_paths for rapidcsv --- .../easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb index 75368d77747..47457d665d6 100644 --- a/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.62-GCCcore-11.2.0.eb @@ -29,7 +29,7 @@ builddependencies = [ sanity_check_paths = { 'files': ['include/rapidcsv.h'], - 'dirs': [''], + 'dirs': [], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb index 3ce9bf655e9..18ccedd9a55 100644 --- a/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/rapidcsv/rapidcsv-8.64-GCCcore-11.3.0.eb @@ -29,7 +29,7 @@ builddependencies = [ sanity_check_paths = { 'files': ['include/rapidcsv.h'], - 'dirs': [''], + 'dirs': [], } moduleclass = 'data' From c275ada76a27a7ab3f2f67497914d254e8f68e4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 19:55:07 +0200 Subject: [PATCH 9230/9987] stick to GCC toolchain for plotutils, since it requires gawk --- ...utils-2.6-GCCcore-11.3.0.eb => plotutils-2.6-GCC-11.3.0.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/p/plotutils/{plotutils-2.6-GCCcore-11.3.0.eb => plotutils-2.6-GCC-11.3.0.eb} (96%) diff --git a/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb similarity index 96% rename from easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb index 062715eddb8..60c786ebddf 100644 --- a/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb @@ -16,7 +16,7 @@ does not depend on the type of graphics file to be exported. A Postscript-like A is used both for file export and for graphics animations. A libplot programmer needs to learn only one API: not the details of many graphics file formats.""" -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://ftp.gnu.org/gnu/plotutils'] sources = ['%(name)s-%(version)s.tar.gz'] @@ -28,7 +28,6 @@ checksums = [ ] builddependencies = [ - ('binutils', '2.38'), ('gawk', '5.1.1'), ('Bison', '3.8.2'), ('flex', '2.6.4'), From 1f41cdc25b6d1a1e1bacce8e89d6cc4d2f47406a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 20:00:59 +0200 Subject: [PATCH 9231/9987] enable -DCROSSGUID_TESTS=ON both when building shared and static libraries Co-authored-by: SebastianAchilles --- .../c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb index 6f1189ae18d..4cbfeae1907 100644 --- a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb @@ -37,7 +37,7 @@ dependencies = [ # build demo # build static and shared libraries -configopts = ["-DCROSSGUID_TESTS=ON", "-DBUILD_SHARED_LIBS=TRUE"] +configopts = ["-DCROSSGUID_TESTS=ON -DBUILD_SHARED_LIBS=%s" % local_shared for local_shared in ('OFF', 'ON')] # we want to have the crossguid-test install_cmd = "make install && " From 3126335b4f3ed69216c834e0480948c033e7162c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 20:01:22 +0200 Subject: [PATCH 9232/9987] use postinstallcmds rather than tweaking install command for crossguid Co-authored-by: SebastianAchilles --- .../c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb index 4cbfeae1907..28c68acc7ad 100644 --- a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb @@ -40,9 +40,10 @@ dependencies = [ configopts = ["-DCROSSGUID_TESTS=ON -DBUILD_SHARED_LIBS=%s" % local_shared for local_shared in ('OFF', 'ON')] # we want to have the crossguid-test -install_cmd = "make install && " -install_cmd += "mkdir -p %(installdir)s/bin/ && " -install_cmd += "cp -f crossguid-test %(installdir)s/bin/ " +postinstallcmds = [ + 'mkdir -p %(installdir)s/bin/', + 'cp -a crossguid-test %(installdir)s/bin/', +] sanity_check_paths = { 'files': ['lib/libcrossguid.a', 'bin/crossguid-test'], From 2308c0a54b3ed4dd68db85a083ad7a6025ebe761 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 20:04:05 +0200 Subject: [PATCH 9233/9987] trivial style in sanity check command for crossguid --- .../c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb index 28c68acc7ad..09d586708fb 100644 --- a/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/crossguid/crossguid-20190529-GCCcore-11.2.0.eb @@ -50,6 +50,6 @@ sanity_check_paths = { 'dirs': ['include'], } -sanity_check_commands = [('crossguid-test')] +sanity_check_commands = ["crossguid-test"] moduleclass = 'lib' From 17e3be3e501b12bb09c6766b1adcfe822f6952d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 20:10:11 +0200 Subject: [PATCH 9234/9987] remove libICE dependency in plotutils, already fullfilled via X11 dependency --- .../l/libICE/libICE-1.0.9-GCC-11.3.0.eb | 28 +++++++++++++++++++ .../p/plotutils/plotutils-2.6-GCC-11.3.0.eb | 1 - 2 files changed, 28 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/libICE/libICE-1.0.9-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-GCC-11.3.0.eb new file mode 100644 index 00000000000..36902784361 --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-GCC-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libICE' +version = '1.0.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Inter-Client Exchange library for freedesktop.org""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +checksums = ['7812a824a66dd654c830d21982749b3b563d9c2dfe0b88b203cefc14a891edc0'] + +builddependencies = [ + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.3'), + ('gawk', '5.1.1'), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb index 60c786ebddf..943f2c0f77e 100644 --- a/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb @@ -35,7 +35,6 @@ builddependencies = [ dependencies = [ ('X11', '20220504'), - ('libICE', '1.0.9'), ] configopts = '--enable-libxmi --enable-ps-fonts-in-pcl --enable-libplotter ' From 126d44d882ce6ff13dddb448405ca041e26477ca Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 20:30:08 +0200 Subject: [PATCH 9235/9987] remove extensions already included in Python from dxpy easyconfig + add BeautifulSoup as dependency + add sanity check command --- .../d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb | 27 ++++--------------- 1 file changed, 5 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb index e8197cab1e1..7090297dbe6 100644 --- a/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/dxpy/dxpy-0.345.0-GCCcore-12.2.0.eb @@ -18,6 +18,7 @@ builddependencies = [ dependencies = [ ('Python', '3.10.8'), ('FUSE', '3.14.1'), + ('BeautifulSoup', '4.11.1'), ] use_pip = True @@ -41,16 +42,6 @@ exts_list = [ ('backports.ssl_match_hostname', '3.7.0.1', { 'checksums': ['bb82e60f9fbf4c080eabd957c39f0641f0fc247d9a16e31e26d594d8f42b9fd2'], }), - ('psutil', '5.9.5', { - 'checksums': ['5410638e4df39c54d957fc51ce03048acd8e6d60abc0f5107af51e5fb566eb3c'], - }), - ('soupsieve', '2.4.1', { - 'checksums': ['89d12b2d5dfcd2c9e8c22326da9d9aa9cb3dfab0a83a024f05704076ee8d35ea'], - }), - ('beautifulsoup4', '4.12.2', { - 'modulename': 'bs4', - 'checksums': ['492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da'], - }), ('python-magic', '0.4.27', { 'modulename': 'magic', 'checksums': ['c1ba14b08e4a5f5c31a302b7721239695b2f0f058d125bd5ce1ee36b9d9d3c3b'], @@ -59,20 +50,10 @@ exts_list = [ 'modulename': 'websocket', 'checksums': ['e51562c91ddb8148e791f0155fdb01325d99bb52c4cdbb291aee7a3563fd0849'], }), - ('pycparser', '2.21', { - 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], - }), - ('cffi', '1.15.1', { - 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], - }), - ('charset-normalizer', '2.0.12', { - 'checksums': ['2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597'], - }), - ('requests', '2.27.1', { - 'checksums': ['68d7c56fd5a8999887728ef304a6d12edc7be74f1cfa47714fc8b414525c9a61'], - }), (name, version, { 'checksums': ['cf5b47e83866a9c87a4fc59262eac500e860f6a890e6a897a577eff68e28cff2'], + # strip away too strict version requirements for requests dependency + 'preinstallopts': "sed -i 's/requests.*/requests/g' requirements.txt && ", }), ] @@ -81,4 +62,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["dx --help"] + moduleclass = 'bio' From ec97830b4674be517ea3ab8497c2721a2cad02f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 20:31:09 +0200 Subject: [PATCH 9236/9987] remove libICE easyconfig, not required as dependency for plotutils --- .../l/libICE/libICE-1.0.9-GCC-11.3.0.eb | 28 ------------------- 1 file changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libICE/libICE-1.0.9-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-GCC-11.3.0.eb deleted file mode 100644 index 36902784361..00000000000 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-GCC-11.3.0.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libICE' -version = '1.0.9' - -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" -description = """X Inter-Client Exchange library for freedesktop.org""" - -toolchain = {'name': 'GCC', 'version': '11.3.0'} - -sources = [SOURCE_TAR_GZ] -source_urls = [XORG_LIB_SOURCE] - -checksums = ['7812a824a66dd654c830d21982749b3b563d9c2dfe0b88b203cefc14a891edc0'] - -builddependencies = [ - ('xproto', '7.0.31'), - ('xorg-macros', '1.19.3'), - ('gawk', '5.1.1'), - ('xtrans', '1.3.5'), -] - -sanity_check_paths = { - 'files': ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], - 'dirs': [], -} - -moduleclass = 'vis' From ec6466a766bcef0da107e626502634bf13b96692 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 23 Oct 2023 22:01:24 +0200 Subject: [PATCH 9237/9987] add sanity check commands for plotutils --- easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb index 943f2c0f77e..76c7003655d 100644 --- a/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/plotutils/plotutils-2.6-GCC-11.3.0.eb @@ -55,4 +55,6 @@ sanity_check_paths = { 'dirs': ['include', 'share'], } +sanity_check_commands = ["%s --help" % x for x in local_bin] + moduleclass = 'tools' From 14d6af2299da0e7fba69a5501f35e72eb65ff8c3 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 22:02:06 +0100 Subject: [PATCH 9238/9987] Graphviz-5.0.0 added to cairomm-1.14.4 --- easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index 5d792e5a489..c2a98051b78 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -27,6 +27,7 @@ dependencies = [ ('libsigc++', '3.4.0'), ('mm-common', '1.0.5'), ('Boost', '1.79.0'), + ('Graphviz', '5.0.0'), ] runtest = 'ninja test' From be7f466f5c0bee37bb346bd10c126d5f1fd3f7b5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 23 Oct 2023 23:13:44 +0200 Subject: [PATCH 9239/9987] update comment about JDK in SNAP-ESA v9.0.0 --- easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-11.eb b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-11.eb index fc3a00a39ba..5c8f6e3138e 100644 --- a/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-11.eb +++ b/easybuild/easyconfigs/s/SNAP-ESA/SNAP-ESA-9.0.0-Java-11.eb @@ -31,7 +31,7 @@ checksums = [ ] # The installation is executed with the bundled JRE 1.8.0_242 (Zulu) -# at runtime we switch it to AdoptOpenJDK, which is known to be more reliable for SNAP-ESA +# At runtime we switch to an external JDK (SNAP developers recommend any OpenJDK distribution) dependencies = [ ('Java', '11'), ] From 3d50b1f614e939baaa3c247292b8e0ae11456a8b Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 23 Oct 2023 22:50:35 +0100 Subject: [PATCH 9240/9987] libxslt added --- easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index c2a98051b78..a1c2a1d16e5 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -28,6 +28,7 @@ dependencies = [ ('mm-common', '1.0.5'), ('Boost', '1.79.0'), ('Graphviz', '5.0.0'), + ('libxslt', '1.1.34'), ] runtest = 'ninja test' From cacbc437f09e6476c6e0911f18751f4fce107dc4 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 24 Oct 2023 00:19:28 +0100 Subject: [PATCH 9241/9987] adding easyconfigs: libsigc++-2.12.1-GCCcore-11.3.0.eb --- .../libsigc++-2.12.1-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.1-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..adcdcd6e01e --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.12.1-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsigc++' +version = '2.12.1' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['a9dbee323351d109b7aee074a9cb89ca3e7bcf8ad8edef1851f4cf359bd50843'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('Doxygen', '1.9.4'), + ('Graphviz', '5.0.0'), + ('libxslt', '1.1.34'), + ('mm-common', '1.0.5'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--disable-documentation" + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' From 506bcb2cc1e838a98e6d59c7eca02d24139ec166 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 24 Oct 2023 00:29:02 +0100 Subject: [PATCH 9242/9987] libsigc++ 2.12.1 used instead of not-working 3.x one --- .../easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb index a1c2a1d16e5..fae81fd8e8b 100644 --- a/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.14.4-GCC-11.3.0.eb @@ -18,17 +18,16 @@ checksums = ['4749d25a2b2ef67cc0c014caaf5c87fa46792fc4b3ede186fb0fc932d2055158'] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), - ('Doxygen', '1.9.4'), - ('M4', '1.4.19'), + ('pkgconf', '1.8.0'), ] dependencies = [ ('cairo', '1.17.4'), - ('libsigc++', '3.4.0'), - ('mm-common', '1.0.5'), - ('Boost', '1.79.0'), + ('libsigc++', '2.12.1'), ('Graphviz', '5.0.0'), ('libxslt', '1.1.34'), + ('mm-common', '1.0.5'), + ('Boost', '1.79.0'), ] runtest = 'ninja test' From fdfd87427b81bd943f427608c7347f62981f7813 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 24 Oct 2023 09:38:31 +0200 Subject: [PATCH 9243/9987] adding easyconfigs: PyTorch-2.0.1-foss-2022a.eb and patches: PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch, PyTorch-2.0.1_avoid-test_quantization-failures.patch, PyTorch-2.0.1_disable-test-sharding.patch, PyTorch-2.0.1_fix-numpy-compat.patch, PyTorch-2.0.1_fix-shift-ops.patch, PyTorch-2.0.1_fix-skip-decorators.patch, PyTorch-2.0.1_fix-test_memory_profiler.patch, PyTorch-2.0.1_fix-test-ops-conf.patch, PyTorch-2.0.1_fix-torch.compile-on-ppc.patch, PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch, PyTorch-2.0.1_fix-vsx-loadu.patch, PyTorch-2.0.1_no-cuda-stubs-rpath.patch, PyTorch-2.0.1_remove-test-requiring-online-access.patch, PyTorch-2.0.1_skip-diff-test-on-ppc.patch, PyTorch-2.0.1_skip-failing-gradtest.patch, PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch, PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch --- .../p/PyTorch/PyTorch-2.0.1-foss-2022a.eb | 144 ++++++++++ ...d-missing-vsx-vector-shift-functions.patch | 103 +++++++ ...0.1_avoid-test_quantization-failures.patch | 19 ++ .../PyTorch-2.0.1_disable-test-sharding.patch | 18 ++ .../PyTorch-2.0.1_fix-numpy-compat.patch | 237 ++++++++++++++++ .../PyTorch/PyTorch-2.0.1_fix-shift-ops.patch | 253 ++++++++++++++++++ .../PyTorch-2.0.1_fix-skip-decorators.patch | 122 +++++++++ .../PyTorch-2.0.1_fix-test-ops-conf.patch | 26 ++ ...Torch-2.0.1_fix-test_memory_profiler.patch | 19 ++ ...Torch-2.0.1_fix-torch.compile-on-ppc.patch | 39 +++ ...rch-2.0.1_fix-ub-in-inductor-codegen.patch | 34 +++ .../PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch | 31 +++ .../PyTorch-2.0.1_no-cuda-stubs-rpath.patch | 186 +++++++++++++ ..._remove-test-requiring-online-access.patch | 30 +++ .../PyTorch-2.0.1_skip-diff-test-on-ppc.patch | 26 ++ .../PyTorch-2.0.1_skip-failing-gradtest.patch | 16 ++ ....1_skip-test_shuffle_reproducibility.patch | 20 ++ ...0.1_skip-tests-skipped-in-subprocess.patch | 34 +++ 18 files changed, 1357 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb new file mode 100644 index 00000000000..c42d16ff11f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb @@ -0,0 +1,144 @@ +name = 'PyTorch' +version = '2.0.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +patches = [ + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch', + 'PyTorch-1.13.1_fix-protobuf-dependency.patch', + 'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch', + 'PyTorch-1.13.1_skip-failing-singular-grad-test.patch', + 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', + 'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch', + 'PyTorch-2.0.1_avoid-test_quantization-failures.patch', + 'PyTorch-2.0.1_disable-test-sharding.patch', + 'PyTorch-2.0.1_fix-numpy-compat.patch', + 'PyTorch-2.0.1_fix-shift-ops.patch', + 'PyTorch-2.0.1_fix-skip-decorators.patch', + 'PyTorch-2.0.1_fix-test_memory_profiler.patch', + 'PyTorch-2.0.1_fix-test-ops-conf.patch', + 'PyTorch-2.0.1_fix-torch.compile-on-ppc.patch', + 'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch', + 'PyTorch-2.0.1_fix-vsx-loadu.patch', + 'PyTorch-2.0.1_no-cuda-stubs-rpath.patch', + 'PyTorch-2.0.1_remove-test-requiring-online-access.patch', + 'PyTorch-2.0.1_skip-diff-test-on-ppc.patch', + 'PyTorch-2.0.1_skip-failing-gradtest.patch', + 'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch', + 'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch', +] +checksums = [ + {'pytorch-v2.0.1.tar.gz': '9c564ca440265c69400ef5fdd48bf15e28af5aa4bed84c95efaad960a6699998'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.1_add-hypothesis-suppression.patch': + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, + {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, + {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, + {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch': + '5c7be91a6096083a0b1315efe0001537499c600f1f569953c6a2c7f4cc1d0910'}, + {'PyTorch-1.13.1_fix-protobuf-dependency.patch': + '8bd755a0cab7233a243bc65ca57c9630dfccdc9bf8c9792f0de4e07a644fcb00'}, + {'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch': + 'bdde0f2105215c95a54de64ec4b1a4520528510663174fef6d5b900eb1db3937'}, + {'PyTorch-1.13.1_skip-failing-singular-grad-test.patch': + '72688a57b2bb617665ad1a1d5e362c5111ae912c10936bb38a089c0204729f48'}, + {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': + '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, + {'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch': + '245ee7f479f6f809b6ea52460113b2c49bbc2a550201f82bdfa0651c72b02ea8'}, + {'PyTorch-2.0.1_avoid-test_quantization-failures.patch': + '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'}, + {'PyTorch-2.0.1_disable-test-sharding.patch': 'a1ed7f21c9a269ea039a07a3d6574f885787b30ca5687143c96e096d31066cca'}, + {'PyTorch-2.0.1_fix-numpy-compat.patch': 'f3e5798193e0909a415d824f13772973200965db84476c1737824f2735f2db94'}, + {'PyTorch-2.0.1_fix-shift-ops.patch': '5ee655d5dba56d801d5618543b6ca299fa874939a3471f7b5449bfcb7f3f18c7'}, + {'PyTorch-2.0.1_fix-skip-decorators.patch': '2039012cef45446065e1a2097839fe20bb29fe3c1dcc926c3695ebf29832e920'}, + {'PyTorch-2.0.1_fix-test_memory_profiler.patch': + 'fd03117c46f59c1c62227d31c410c4cdd98fd35410976758cb9e7ec947582ddb'}, + {'PyTorch-2.0.1_fix-test-ops-conf.patch': '0f995e4f89baf3cbeb8666cbfe694666a2ef2bc53d97d6301f768b3ff9001fa4'}, + {'PyTorch-2.0.1_fix-torch.compile-on-ppc.patch': + '20f9172ae696da0c5c7b3bae6f0bf1221192cb1cbac3a44526a415087834bee7'}, + {'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch': + '1b37194f55ae678f3657b8728dfb896c18ffe8babe90987ce468c4fa9274f357'}, + {'PyTorch-2.0.1_fix-vsx-loadu.patch': 'a0ffa61da2d47c6acd09aaf6d4791e527d8919a6f4f1aa7ed38454cdcadb1f72'}, + {'PyTorch-2.0.1_no-cuda-stubs-rpath.patch': '8902e58a762240f24cdbf0182e99ccdfc2a93492869352fcb4ca0ec7e407f83a'}, + {'PyTorch-2.0.1_remove-test-requiring-online-access.patch': + '721ab0d35ed0ff8a46cb84ced5a98c0fb8ce6143cf6cea80b1360d3d7f64f584'}, + {'PyTorch-2.0.1_skip-diff-test-on-ppc.patch': 'f6e39cd774e5663df25507a73d37ad598157c2eadb2f47ca20a537dbe4b3e14f'}, + {'PyTorch-2.0.1_skip-failing-gradtest.patch': '8030bdec6ba49b057ab232d19a7f1a5e542e47e2ec340653a246ec9ed59f8bc1'}, + {'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch': + '7047862abc1abaff62954da59700f36d4f39fcf83167a638183b1b7f8fec78ae'}, + {'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch': + '166c134573a95230e39b9ea09ece3ad8072f39d370c9a88fb2a1e24f6aaac2b5'}, +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), + # For tests + ('pytest-rerunfailures', '11.1'), + ('pytest-shard', '0.1.2'), +] + +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.4.2'), + ('Pillow', '9.1.1'), + ('expecttest', '0.1.3'), + ('networkx', '2.8.4'), + ('sympy', '1.11.1'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + # no xdoctest + 'doctests', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'test_native_mha', + # intermittent failures on various systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'distributed/rpc/test_tensorpipe_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# Especially test_quantization has a few corner cases that are triggered by the random input values, +# those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 +# So allow a low number of tests to fail as the tests "usually" succeed +max_failed_tests = 2 + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch new file mode 100644 index 00000000000..57e334c908f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch @@ -0,0 +1,103 @@ +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +index 7c300c8087c..84c84286740 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +@@ -348,6 +348,7 @@ Vectorized inline minimum( + return a.minimum(b); + } + ++DEFINE_SHIFT_FUNCS(int16_t) + + } // namespace + } // namespace vec +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +index c98ab6215e6..e1e86d3b53a 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +@@ -279,6 +279,8 @@ Vectorized inline minimum( + return a.minimum(b); + } + ++DEFINE_SHIFT_FUNCS(int32_t) ++ + } // namespace + } // namespace vec + } // namespace at +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +index a4171026a2b..70613d90443 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +@@ -231,6 +231,8 @@ Vectorized inline minimum( + return a.minimum(b); + } + ++DEFINE_SHIFT_FUNCS(int64_t) ++ + } // namespace + } // namespace vec + } // namespace at +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h b/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h +index dab38458184..52032cdd817 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h +@@ -2,6 +2,7 @@ + #include + #include + #include ++#include + + using vbool8 = __attribute__((altivec(vector__))) __attribute__((altivec(bool__))) char; + using vbool16 = __attribute__((altivec(vector__))) __attribute__((altivec(bool__))) short; +@@ -18,6 +19,11 @@ using vuint64 = __attribute__((altivec(vector__))) unsigned long long; + using vfloat32 = __attribute__((altivec(vector__))) float; + using vfloat64 = __attribute__((altivec(vector__))) double; + ++inline auto make_vuint(vint8 v){ return reinterpret_cast(v); } ++inline auto make_vuint(vint16 v){ return reinterpret_cast(v); } ++inline auto make_vuint(vint32 v){ return reinterpret_cast(v); } ++inline auto make_vuint(vint64 v){ return reinterpret_cast(v); } ++ + #if !defined(vec_float) + C10_ALWAYS_INLINE vfloat32 vec_float(const vint32& vec_in) { + vfloat32 vec_out; +@@ -448,6 +454,40 @@ const vfloat64 vd_imag_half = vfloat64{0.0, 0.5}; + const vfloat64 vd_sqrt2_2 = vfloat64{0.70710678118654757, 0.70710678118654757}; + const vfloat64 vd_pi_2 = vfloat64{M_PI / 2.0, 0.0}; + ++template ++Vectorized VsxShiftRightArith(const Vectorized& a, const Vectorized& b) { ++ const Vectorized max_shift(sizeof(T) * CHAR_BIT - std::is_signed_v); ++ const auto mask = (b < Vectorized(0)) | (b >= max_shift); ++ const auto shift = Vectorized::blendv(b, max_shift, mask); ++ return Vectorized{ ++ vec_sra(a.vec0(), make_vuint(shift.vec0())), ++ vec_sra(a.vec1(), make_vuint(shift.vec1()))}; ++} ++ ++template ++Vectorized VsxShiftLeftArith(const Vectorized& a, const Vectorized& b) { ++ const Vectorized max_shift(sizeof(T) * CHAR_BIT); ++ const auto mask = (b < Vectorized(0)) | (b >= max_shift); ++ Vectorized ret( ++ vec_sl(a.vec0(), make_vuint(b.vec0())), ++ vec_sl(a.vec1(), make_vuint(b.vec1()))); ++ return Vectorized::blendv(ret, Vectorized(0), mask); ++} ++ ++#define DEFINE_SHIFT_FUNCS(operand_type) \ ++ template <> \ ++ Vectorized C10_ALWAYS_INLINE operator>>( \ ++ const Vectorized& a, \ ++ const Vectorized& b) { \ ++ return VsxShiftRightArith(a, b); \ ++ } \ ++ template <> \ ++ Vectorized C10_ALWAYS_INLINE operator<<( \ ++ const Vectorized& a, \ ++ const Vectorized& b) { \ ++ return VsxShiftLeftArith(a, b); \ ++ } \ ++ + } // namespace + } // namespace vec + } // namespace at diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch new file mode 100644 index 00000000000..01a7e098c41 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch @@ -0,0 +1,19 @@ +The quantized values returned by hypothesis as test inputs might still cause overflows. +Hence reduce their maximum value by a factor that should fix most such cases. +See e.g. https://github.com/pytorch/pytorch/issues/111471 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/hypothesis_utils.py b/torch/testing/_internal/hypothesis_utils.py +index 15e7b4512a4..67df4d74e9d 100644 +--- a/torch/testing/_internal/hypothesis_utils.py ++++ b/torch/testing/_internal/hypothesis_utils.py +@@ -36,6 +36,8 @@ _ENFORCED_ZERO_POINT = defaultdict(lambda: None, { + def _get_valid_min_max(qparams): + scale, zero_point, quantized_type = qparams + adjustment = 1 + torch.finfo(torch.float).eps ++ # provide some leeway for scaling values without overflowing long ++ adjustment *= 1e4 + _long_type_info = torch.iinfo(torch.long) + long_min, long_max = _long_type_info.min / adjustment, _long_type_info.max / adjustment + # make sure intermediate results are within the range of long diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch new file mode 100644 index 00000000000..525d9fda1dc --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch @@ -0,0 +1,18 @@ +Our error checking doesn't work well with the parallel/sharded pytorch test. +As the overall gain is low, disable it and always run the full test suite in a single process. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/run_test.py b/test/run_test.py +index 9619cb2626e..ddfb200148f 100755 +--- a/test/run_test.py ++++ b/test/run_test.py +@@ -815,7 +815,7 @@ def run_test_ops(test_module, test_directory, options): + ] + default_unittest_args.extend(rerun_options) + +- if 'slow-gradcheck' in os.getenv("BUILD_ENVIRONMENT", ""): ++ if True: + extra_unittest_args = default_unittest_args.copy() + # there are a lot of tests that take up a lot of space in slowgrad check, so don't bother parallelizing + # it's also on periodic so we don't care about TTS as much diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch new file mode 100644 index 00000000000..99b3cc6b770 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch @@ -0,0 +1,237 @@ +From ae1ed277563a1ac887faef4370ad9933c883ab9e Mon Sep 17 00:00:00 2001 +From: Omkar Salpekar +Date: Wed, 21 Jun 2023 18:16:40 +0000 +Subject: [PATCH] [codemod][numpy] replace np.str with str (#103931) + +Summary: +`np.str` is removed from numpy 1.20.0. It was an alias to builtin `str` and it's safe to do the replacement. + +The whole changes is mechanical, generated using the following onliner: +``` +fbgr -sl 'np\.str\b' | xargs perl -pi -e 's,\bnp\.str\b,str,g' +``` + +Test Plan: sandcastle + +Differential Revision: D46586144 + +Pull Request resolved: https://github.com/pytorch/pytorch/pull/103931 +Approved by: https://github.com/huydhn +--- + caffe2/python/core.py | 2 +- + caffe2/python/hypothesis_test.py | 4 ++-- + caffe2/python/layer_model_helper.py | 2 +- + caffe2/python/operator_test/adagrad_test_helper.py | 2 +- + caffe2/python/operator_test/cast_op_test.py | 2 +- + caffe2/python/operator_test/detectron_keypoints.py | 4 ++-- + caffe2/python/operator_test/tile_op_test.py | 6 +++--- + caffe2/python/schema.py | 2 +- + caffe2/python/schema_test.py | 4 ++-- + caffe2/python/utils.py | 6 +++--- + .../examples/maml_omniglot/support/omniglot_loaders.py | 4 ++-- + test/quantization/core/test_quantized_op.py | 4 ++-- + 12 files changed, 21 insertions(+), 21 deletions(-) + +diff --git a/caffe2/python/core.py b/caffe2/python/core.py +index d9f97b6121fdd2..e69af5c0a482b1 100644 +--- a/caffe2/python/core.py ++++ b/caffe2/python/core.py +@@ -1636,7 +1636,7 @@ def do_set(operator): + return do_set(self.GivenTensorIntFill) + elif array.dtype == np.int64: + return do_set(self.GivenTensorInt64Fill) +- elif array.dtype == np.str: ++ elif array.dtype == str: + return do_set(self.GivenTensorStringFill) + elif array.dtype == np.bool: + return do_set(self.GivenTensorBoolFill) +diff --git a/caffe2/python/hypothesis_test.py b/caffe2/python/hypothesis_test.py +index 02200f8cf74f18..cb5d00064b6eda 100644 +--- a/caffe2/python/hypothesis_test.py ++++ b/caffe2/python/hypothesis_test.py +@@ -1629,8 +1629,8 @@ def test_tt_sls_layer(self, gc, dc): + c0 = np.ones([10, 1, 2, 16]).astype(np.float32) + c1 = np.ones([10, 16, 2, 16]).astype(np.float32) + c2 = np.ones([10, 16, 2, 1]).astype(np.float32) +- # index = np.array([0, 1, 2, 1, 4], dtype=np.int) +- # lengths = np.array([3, 2], dtype=np.int) ++ # index = np.array([0, 1, 2, 1, 4], dtype=int) ++ # lengths = np.array([3, 2], dtype=int) + index = np.array([0, 1, 2, 1, 4], np.int64) + lengths = np.array([3, 2], np.int32) + +diff --git a/caffe2/python/layer_model_helper.py b/caffe2/python/layer_model_helper.py +index 9a8e237e302143..f21b47e57c653a 100644 +--- a/caffe2/python/layer_model_helper.py ++++ b/caffe2/python/layer_model_helper.py +@@ -148,7 +148,7 @@ def _get_global_constant_initializer_op( + op_name = 'GivenTensorIntFill' + elif array.dtype == np.int64: + op_name = 'GivenTensorInt64Fill' +- elif array.dtype == np.str: ++ elif array.dtype == str: + op_name = 'GivenTensorStringFill' + elif array.dtype == np.bool: + op_name = 'GivenTensorBoolFill' +diff --git a/caffe2/python/operator_test/adagrad_test_helper.py b/caffe2/python/operator_test/adagrad_test_helper.py +index 08caf22b266178..1fd017c4d2ac5c 100644 +--- a/caffe2/python/operator_test/adagrad_test_helper.py ++++ b/caffe2/python/operator_test/adagrad_test_helper.py +@@ -98,7 +98,7 @@ def adagrad_sparse_test_helper( + # Create an indexing array containing values that are lists of indices, + # which index into grad + if grad.size == 0: +- indices = np.empty(shape=(0,), dtype=np.int) ++ indices = np.empty(shape=(0,), dtype=int) + else: + indices = np.random.choice( + np.arange(grad.shape[0]), +diff --git a/caffe2/python/operator_test/cast_op_test.py b/caffe2/python/operator_test/cast_op_test.py +index bf2a210086e691..95540a6121bcac 100644 +--- a/caffe2/python/operator_test/cast_op_test.py ++++ b/caffe2/python/operator_test/cast_op_test.py +@@ -37,7 +37,7 @@ def test_cast_int_to_string(self, data, gc, dc): + 'Cast', 'data', 'data_cast', to=core.DataType.STRING) + + def ref(data): +- ret = data.astype(dtype=np.str) ++ ret = data.astype(dtype=str) + # the string blob will be fetched as object, we feed and re-fetch + # to mimic this. + with hu.temp_workspace('tmp_ref_int_to_string'): +diff --git a/caffe2/python/operator_test/detectron_keypoints.py b/caffe2/python/operator_test/detectron_keypoints.py +index 1abff0675993ff..319e8b5bbffd5e 100644 +--- a/caffe2/python/operator_test/detectron_keypoints.py ++++ b/caffe2/python/operator_test/detectron_keypoints.py +@@ -32,8 +32,8 @@ def heatmaps_to_keypoints(maps, rois): + heights = rois[:, 3] - rois[:, 1] + widths = np.maximum(widths, 1) + heights = np.maximum(heights, 1) +- widths_ceil = np.ceil(widths).astype(np.int) +- heights_ceil = np.ceil(heights).astype(np.int) ++ widths_ceil = np.ceil(widths).astype(int) ++ heights_ceil = np.ceil(heights).astype(int) + + num_keypoints = np.maximum(maps.shape[1], _NUM_KEYPOINTS) + +diff --git a/caffe2/python/operator_test/tile_op_test.py b/caffe2/python/operator_test/tile_op_test.py +index d39dfeee0ad72a..fbb424fe058ccb 100644 +--- a/caffe2/python/operator_test/tile_op_test.py ++++ b/caffe2/python/operator_test/tile_op_test.py +@@ -32,7 +32,7 @@ def test_tile(self, M, K, N, tiles, axis, gc, dc): + ) + + def tile_ref(X, tiles, axis): +- dims = np.asarray([1, 1, 1], dtype=np.int) ++ dims = np.asarray([1, 1, 1], dtype=int) + dims[axis] = tiles + tiled_data = np.tile(X, dims) + return (tiled_data,) +@@ -61,7 +61,7 @@ def test_tile_grad(self, M, N, tiles, gc, dc): + ) + + def tile_ref(X, tiles, axis): +- dims = np.asarray([1, 1], dtype=np.int) ++ dims = np.asarray([1, 1], dtype=int) + dims[axis] = tiles + tiled_data = np.tile(X, dims) + return (tiled_data,) +@@ -99,7 +99,7 @@ def test_tilewinput(self, M, K, N, tiles, axis, gc, dc): + ) + + def tile_ref(X, tiles, axis): +- dims = np.asarray([1, 1, 1], dtype=np.int) ++ dims = np.asarray([1, 1, 1], dtype=int) + dims[axis] = tiles + tiled_data = np.tile(X, dims) + return (tiled_data,) +diff --git a/caffe2/python/schema.py b/caffe2/python/schema.py +index ab6ec29372e2ff..ecbcb2287dddea 100644 +--- a/caffe2/python/schema.py ++++ b/caffe2/python/schema.py +@@ -1252,7 +1252,7 @@ def InitEmptyRecord(net, schema_or_record, enforce_types=False): + + + _DATA_TYPE_FOR_DTYPE = [ +- (np.str, core.DataType.STRING), ++ (str, core.DataType.STRING), + (np.float16, core.DataType.FLOAT16), + (np.float32, core.DataType.FLOAT), + (np.float64, core.DataType.DOUBLE), +diff --git a/caffe2/python/schema_test.py b/caffe2/python/schema_test.py +index 8f3ed4415fd4f5..2f3eaf38dc138d 100644 +--- a/caffe2/python/schema_test.py ++++ b/caffe2/python/schema_test.py +@@ -94,12 +94,12 @@ def testTuple(self): + s = schema.Tuple(np.int32, str, np.float32) + s2 = schema.Struct( + ('field_0', schema.Scalar(dtype=np.int32)), +- ('field_1', schema.Scalar(dtype=np.str)), ++ ('field_1', schema.Scalar(dtype=str)), + ('field_2', schema.Scalar(dtype=np.float32)) + ) + self.assertEqual(s, s2) + self.assertEqual(s[0], schema.Scalar(dtype=np.int32)) +- self.assertEqual(s[1], schema.Scalar(dtype=np.str)) ++ self.assertEqual(s[1], schema.Scalar(dtype=str)) + self.assertEqual(s[2], schema.Scalar(dtype=np.float32)) + self.assertEqual( + s[2, 0], +diff --git a/caffe2/python/utils.py b/caffe2/python/utils.py +index 02a77e74681a93..8c82faee33a4c3 100644 +--- a/caffe2/python/utils.py ++++ b/caffe2/python/utils.py +@@ -67,7 +67,7 @@ def Caffe2TensorToNumpyArray(tensor): + tensor.int64_data, dtype=np.int64).reshape(tensor.dims) + elif tensor.data_type == caffe2_pb2.TensorProto.INT32: + return np.asarray( +- tensor.int32_data, dtype=np.int).reshape(tensor.dims) # pb.INT32=>np.int use int32_data ++ tensor.int32_data, dtype=int).reshape(tensor.dims) # pb.INT32=>int use int32_data + elif tensor.data_type == caffe2_pb2.TensorProto.INT16: + return np.asarray( + tensor.int32_data, dtype=np.int16).reshape(tensor.dims) # pb.INT16=>np.int16 use int32_data +@@ -100,9 +100,9 @@ def NumpyArrayToCaffe2Tensor(arr, name=None): + elif arr.dtype == np.int64: + tensor.data_type = caffe2_pb2.TensorProto.INT64 + tensor.int64_data.extend(list(arr.flatten().astype(np.int64))) +- elif arr.dtype == np.int or arr.dtype == np.int32: ++ elif arr.dtype == int or arr.dtype == np.int32: + tensor.data_type = caffe2_pb2.TensorProto.INT32 +- tensor.int32_data.extend(arr.flatten().astype(np.int).tolist()) ++ tensor.int32_data.extend(arr.flatten().astype(int).tolist()) + elif arr.dtype == np.int16: + tensor.data_type = caffe2_pb2.TensorProto.INT16 + tensor.int32_data.extend(list(arr.flatten().astype(np.int16))) # np.int16=>pb.INT16 use int32_data +diff --git a/functorch/examples/maml_omniglot/support/omniglot_loaders.py b/functorch/examples/maml_omniglot/support/omniglot_loaders.py +index cac99b2dfbb2aa..ce636ecca0b1b2 100644 +--- a/functorch/examples/maml_omniglot/support/omniglot_loaders.py ++++ b/functorch/examples/maml_omniglot/support/omniglot_loaders.py +@@ -271,10 +271,10 @@ def load_data_cache(self, data_pack): + + # [b, setsz, 1, 84, 84] + x_spts = np.array(x_spts).astype(np.float32).reshape(self.batchsz, setsz, 1, self.resize, self.resize) +- y_spts = np.array(y_spts).astype(np.int).reshape(self.batchsz, setsz) ++ y_spts = np.array(y_spts).astype(int).reshape(self.batchsz, setsz) + # [b, qrysz, 1, 84, 84] + x_qrys = np.array(x_qrys).astype(np.float32).reshape(self.batchsz, querysz, 1, self.resize, self.resize) +- y_qrys = np.array(y_qrys).astype(np.int).reshape(self.batchsz, querysz) ++ y_qrys = np.array(y_qrys).astype(int).reshape(self.batchsz, querysz) + + x_spts, y_spts, x_qrys, y_qrys = [ + torch.from_numpy(z).to(self.device) for z in +diff --git a/test/quantization/core/test_quantized_op.py b/test/quantization/core/test_quantized_op.py +index 252d7b92f77ebb..232150a0ba34a6 100644 +--- a/test/quantization/core/test_quantized_op.py ++++ b/test/quantization/core/test_quantized_op.py +@@ -3840,9 +3840,9 @@ def test_qlinear_with_input_q_dq_qweight_dq_output_fp32( + # xnnpack forces W_zp to 0 when using symmetric quantization + # ONEDNN only supports symmetric quantization of weight + if dtype == torch.qint8 or qengine_is_onednn(): +- W_zps = np.zeros(output_channels).astype(np.int) ++ W_zps = np.zeros(output_channels).astype(int) + else: +- W_zps = np.round(np.random.rand(output_channels) * 100 - 50).astype(np.int) ++ W_zps = np.round(np.random.rand(output_channels) * 100 - 50).astype(int) + # when using symmetric quantization + # special restriction for xnnpack fully connected op weight + # [-127, 127] instead of [-128, 127] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch new file mode 100644 index 00000000000..f63f3cf4c5f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch @@ -0,0 +1,253 @@ +From d64fb24ee4a71d8cfe175cafc73c5f90fb26c9ac Mon Sep 17 00:00:00 2001 +From: BJ Hargrave +Date: Tue, 14 Mar 2023 15:30:41 -0400 +Subject: [PATCH 1/2] Fix operator>> for int64 vector in vec256 + +There is no vector instruction for shift right arithmetic for int64. +The operator>> implementation emulates this through other vector +instructions. It has been fixed to properly handle out-of-limit +shift values so that shift values <0 and >64 are set to 64 which +results in a value of -1 for negative inputs and 0 for non-negative +inputs (sign preserving). + +Fixes https://github.com/pytorch/pytorch/issues/70904 + +Signed-off-by: BJ Hargrave +--- + aten/src/ATen/cpu/vec/vec256/vec256_int.h | 16 +++++++++++----- + 1 file changed, 11 insertions(+), 5 deletions(-) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vec256_int.h b/aten/src/ATen/cpu/vec/vec256/vec256_int.h +index 81e9d687d10a7b..784514f49e1d48 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vec256_int.h ++++ b/aten/src/ATen/cpu/vec/vec256/vec256_int.h +@@ -1481,16 +1481,22 @@ Vectorized inline operator<<(const Vectorized& a, const Vector + + template <> + Vectorized inline operator>>(const Vectorized& a, const Vectorized& b) { +- // No vector instruction for right shifting int64_t, so emulating it ++ // No vector instruction for right arithmetic shifting int64_t, so emulating it + // instead. + ++ // Clamp the shift values such that shift values < 0 and > 64 are changed to 64 ++ // which results in -1 for negative input and 0 for non-negative input. ++ __m256i zero = _mm256_set1_epi64x(0); ++ __m256i max_shift = _mm256_set1_epi64x(64); ++ __m256i mask = _mm256_or_si256(_mm256_cmpgt_epi64(zero, b), _mm256_cmpgt_epi64(b, max_shift)); ++ __m256i shift = _mm256_blendv_epi8(b, max_shift, mask); + // Shift the number logically to the right, thus filling the most + // significant bits with 0s. Then, replace these bits with the sign + // bit. +- __m256i sign_bits = _mm256_cmpgt_epi64(_mm256_set1_epi64x(0), a); +- __m256i b_inv_mod_64 = _mm256_sub_epi64(_mm256_set1_epi64x(64), b); +- __m256i sign_ext = _mm256_sllv_epi64(sign_bits, b_inv_mod_64); +- __m256i c = _mm256_srlv_epi64(a, b); ++ __m256i sign_bits = _mm256_cmpgt_epi64(zero, a); ++ __m256i sign_shift = _mm256_sub_epi64(max_shift, shift); ++ __m256i sign_ext = _mm256_sllv_epi64(sign_bits, sign_shift); ++ __m256i c = _mm256_srlv_epi64(a, shift); + c = _mm256_or_si256(c, sign_ext); + + return c; + +From 734e2cea43ee782d756f04bc21c625b8fdd36d31 Mon Sep 17 00:00:00 2001 +From: BJ Hargrave +Date: Mon, 13 Mar 2023 10:56:00 -0400 +Subject: [PATCH 2/2] Fix CPU bitwise shifts for out-of-limit shift values + +Negative shift values and positive shift values greater than the +bit size of the dtype (limit 0..bits) now yield expected results +which are consistent with numpy. + +Left shift with an out-of-limit shift value result in a value of 0. +Right shift with an out-of-limit shift value results in a value of -1 +for negative inputs and 0 for non-negative inputs (sign preserving). + +Fixes https://github.com/pytorch/pytorch/issues/70904 + +Signed-off-by: BJ Hargrave +--- + aten/src/ATen/cpu/vec/vec_base.h | 18 ++++++++-- + aten/src/ATen/native/cpu/BinaryOpsKernel.cpp | 9 +++++ + test/functorch/test_vmap.py | 12 ------- + test/test_binary_ufuncs.py | 37 ++++++++++++++++++++ + 4 files changed, 62 insertions(+), 14 deletions(-) + +diff --git a/aten/src/ATen/cpu/vec/vec_base.h b/aten/src/ATen/cpu/vec/vec_base.h +index cb0e37054b4d32..8f006ae0f6634f 100644 +--- a/aten/src/ATen/cpu/vec/vec_base.h ++++ b/aten/src/ATen/cpu/vec/vec_base.h +@@ -20,6 +20,7 @@ + #include + #include + #include ++#include + + #include + #include +@@ -803,17 +804,30 @@ inline Vectorized operator~(const Vectorized& a) { + } + + template Vectorized inline operator<<(const Vectorized &a, const Vectorized &b) { ++ constexpr T max_shift = sizeof(T) * CHAR_BIT; + Vectorized c; + for (int i = 0; i != Vectorized::size(); i++) { +- c[i] = a[i] << b[i]; ++ T shift = b[i]; ++ if ((static_cast>(shift) < 0) || (shift >= max_shift)) { ++ c[i] = 0; ++ } else { ++ c[i] = static_cast>(a[i]) << shift; ++ } + } + return c; + } + + template Vectorized inline operator>>(const Vectorized &a, const Vectorized &b) { ++ // right shift value to retain sign bit for signed and no bits for unsigned ++ constexpr T max_shift = sizeof(T) * CHAR_BIT - std::is_signed_v; + Vectorized c; + for (int i = 0; i != Vectorized::size(); i++) { +- c[i] = a[i] >> b[i]; ++ T shift = b[i]; ++ if ((static_cast>(shift) < 0) || (shift >= max_shift)) { ++ c[i] = a[i] >> max_shift; ++ } else { ++ c[i] = a[i] >> shift; ++ } + } + return c; + } +diff --git a/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp b/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp +index d0393aaf18bf8b..d2d0892d8ea956 100644 +--- a/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp ++++ b/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp +@@ -316,6 +316,10 @@ void lshift_kernel(TensorIteratorBase& iter) { + AT_DISPATCH_INTEGRAL_TYPES(iter.dtype(), "lshift_cpu", [&]() { + cpu_kernel_vec(iter, + [](scalar_t a, scalar_t b) -> scalar_t { ++ constexpr scalar_t max_shift = sizeof(scalar_t) * CHAR_BIT; ++ if ((static_cast>(b) < 0) || (b >= max_shift)) { ++ return 0; ++ } + return static_cast>(a) << b; + }, + [](Vectorized a, Vectorized b) { +@@ -385,6 +389,11 @@ void rshift_kernel(TensorIteratorBase& iter) { + AT_DISPATCH_INTEGRAL_TYPES(iter.dtype(), "rshift_cpu", [&]() { + cpu_kernel_vec(iter, + [](scalar_t a, scalar_t b) -> scalar_t { ++ // right shift value to retain sign bit for signed and no bits for unsigned ++ constexpr scalar_t max_shift = sizeof(scalar_t) * CHAR_BIT - std::is_signed_v; ++ if ((static_cast>(b) < 0) || (b >= max_shift)) { ++ return a >> max_shift; ++ } + return a >> b; + }, + [](Vectorized a, Vectorized b) { +diff --git a/test/functorch/test_vmap.py b/test/functorch/test_vmap.py +index a5fb144f881880..5c352cf8fdf6f0 100644 +--- a/test/functorch/test_vmap.py ++++ b/test/functorch/test_vmap.py +@@ -27,8 +27,6 @@ + instantiate_parametrized_tests, + subtest, + TEST_WITH_UBSAN, +- IS_MACOS, +- IS_X86 + ) + from torch.testing._internal.common_device_type import \ + toleranceOverride, tol +@@ -46,7 +44,6 @@ + compute_quantities_for_vmap_test, + is_valid_inplace_sample_input, + decorate, +- expectedFailureIf + ) + import types + from collections import namedtuple +@@ -3572,10 +3569,6 @@ def test(): + xfail('addcdiv'), + xfail('addcmul'), + xfail('clamp'), +- # AssertionError: Tensor-likes are not equal! +- xfail('bitwise_left_shift', device_type='cpu'), +- decorate('bitwise_right_shift', device_type='cpu', +- decorator=expectedFailureIf(not (IS_MACOS and IS_X86))), + + # UBSAN: runtime error: shift exponent -1 is negative + decorate('bitwise_left_shift', decorator=unittest.skipIf(TEST_WITH_UBSAN, "Fails with above error")), +@@ -3734,11 +3727,6 @@ def test_vmap_exhaustive(self, device, dtype, op): + xfail('linalg.lu', ''), + skip('linalg.ldl_solve', ''), + skip('_softmax_backward_data'), +- # AssertionError: Tensor-likes are not equal! +- # Issue: https://github.com/pytorch/pytorch/issues/70904 +- xfail('bitwise_left_shift', device_type='cpu'), +- decorate('bitwise_right_shift', device_type='cpu', +- decorator=expectedFailureIf(not (IS_MACOS and IS_X86))), + # UBSAN: runtime error: shift exponent -1 is negative + decorate('bitwise_left_shift', decorator=unittest.skipIf(TEST_WITH_UBSAN, "Fails with above error")), + decorate('bitwise_right_shift', decorator=unittest.skipIf(TEST_WITH_UBSAN, "Fails with above error")), +diff --git a/test/test_binary_ufuncs.py b/test/test_binary_ufuncs.py +index 52d7c7a4ffcb00..bf3e4d43494932 100644 +--- a/test/test_binary_ufuncs.py ++++ b/test/test_binary_ufuncs.py +@@ -4,6 +4,7 @@ + import numpy as np + + import itertools ++from itertools import chain + from itertools import product + import math + import random +@@ -53,6 +54,7 @@ + floating_types_and, + floating_and_complex_types, + get_all_math_dtypes, ++ get_all_int_dtypes, + ) + from torch.testing._internal.common_methods_invocations import ( + binary_ufuncs, +@@ -3139,6 +3141,41 @@ def test_signed_shift(self, device, dtype): + self.assertEqual(a >> 1, expected_r) + self.compare_with_numpy(lambda x: x >> 1, lambda x: np.right_shift(x, 1), a) + ++ @onlyCPU ++ @dtypes(*get_all_int_dtypes()) ++ def test_shift_limits(self, device, dtype): ++ "Ensure that CPU integer bit shifting works as expected with out-of-limits shift values." ++ # Issue #70904 ++ iinfo = torch.iinfo(dtype) ++ bits = iinfo.bits ++ low = iinfo.min ++ high = iinfo.max ++ exact_dtype = dtype != torch.uint8 # numpy changes dtype from uint8 to int16 for some out-of-limits shift values ++ for input in ( ++ torch.tensor([-1, 0, 1], device=device, dtype=dtype), # small for non-vectorized operation ++ torch.tensor([low, high], device=device, dtype=dtype), # small for non-vectorized operation ++ make_tensor((64, 64, 64), low=low, high=high, device=device, dtype=dtype), # large for vectorized operation ++ ): ++ shift_left_expected = torch.zeros_like(input) ++ shift_right_expected = torch.clamp(input, -1, 0) ++ for shift in chain(range(-100, -1), range(bits, 100)): ++ shift_left = input << shift ++ self.assertEqual(shift_left, shift_left_expected, msg=f"<< {shift}") ++ self.compare_with_numpy( ++ lambda x: x << shift, ++ lambda x: np.left_shift(x, shift), ++ input, ++ exact_dtype=exact_dtype, msg=f"<< {shift}" ++ ) ++ shift_right = input >> shift ++ self.assertEqual(shift_right, shift_right_expected, msg=f">> {shift}") ++ self.compare_with_numpy( ++ lambda x: x >> shift, ++ lambda x: np.right_shift(x, shift), ++ input, ++ exact_dtype=exact_dtype, msg=f">> {shift}" ++ ) ++ + @onlyNativeDeviceTypes + @dtypes( + *list( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch new file mode 100644 index 00000000000..101849f4dbf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch @@ -0,0 +1,122 @@ +The decorators are implemented to run when the function is called which is after +the test `setup` method spawned subprocesses which may use NCCL to sync failing when there are +not enough GPUs available. +So replace the custom code by calls to the `unittest` skip decorators. +See hhttps://github.com/pytorch/pytorch/pull/109491 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_distributed.py b/torch/testing/_internal/common_distributed.py +index 400aa80fdca..80a7375cfe1 100644 +--- a/torch/testing/_internal/common_distributed.py ++++ b/torch/testing/_internal/common_distributed.py +@@ -134,17 +134,7 @@ def skip_if_odd_worldsize(func): + + + def require_n_gpus_for_nccl_backend(n, backend): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend == "nccl" and torch.cuda.device_count() < n: +- sys.exit(TEST_SKIPS[f"multi-gpu-{n}"].exit_code) +- else: +- return func(*args, **kwargs) +- +- return wrapper +- +- return decorator ++ return skip_if_lt_x_gpu(n) if backend == "nccl" else unittest.skipIf(False, None) + + + def import_transformers_or_skip(): +@@ -167,32 +157,7 @@ def import_transformers_or_skip(): + + + def skip_if_lt_x_gpu(x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator +- +- +-# This decorator helps avoiding initializing cuda while testing other backends +-def nccl_skip_if_lt_x_gpu(backend, x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend != "nccl": +- return func(*args, **kwargs) +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator ++ return unittest.skipIf(torch.cuda.device_count() < x, TEST_SKIPS[f"multi-gpu-{x}"].message) + + + def verify_ddp_error_logged(model_DDP, err_substr): +diff --git a/torch/testing/_internal/distributed/distributed_test.py b/torch/testing/_internal/distributed/distributed_test.py +index eb5130f2963..25839618308 100644 +--- a/torch/testing/_internal/distributed/distributed_test.py ++++ b/torch/testing/_internal/distributed/distributed_test.py +@@ -56,7 +56,6 @@ from torch.testing._internal.common_distributed import ( + skip_if_small_worldsize, + skip_if_odd_worldsize, + skip_if_lt_x_gpu, +- nccl_skip_if_lt_x_gpu, + skip_if_no_gpu, + require_n_gpus_for_nccl_backend, + requires_nccl_version, +@@ -4960,7 +4959,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4971,7 +4970,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync_grad_is_view(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4982,7 +4981,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync_allreduce_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync +@@ -5010,7 +5009,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync_allreduce_with_then_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync using allreduce +@@ -5044,7 +5043,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_get_future(self): + def mult(fut): + return [t * 3 for t in fut.wait()] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch new file mode 100644 index 00000000000..6f3977c99a4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch @@ -0,0 +1,26 @@ +From 8581301957b0018a32433f85163535709bc9d332 Mon Sep 17 00:00:00 2001 +From: Masaki Kozuki +Date: Fri, 7 Oct 2022 21:25:07 -0700 +Subject: [PATCH] try using a different group name + +ref: +https://github.com/pytorch/pytorch/issues/85923#issuecomment-1272220271 + +Signed-off-by: Masaki Kozuki +--- + test/conftest.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/test/conftest.py b/test/conftest.py +index e5af19b760a..c9755322d16 100644 +--- a/test/conftest.py ++++ b/test/conftest.py +@@ -18,7 +18,7 @@ xml_key = StashKey["LogXMLReruns"]() + + + def pytest_addoption(parser: Parser) -> None: +- group = parser.getgroup("terminal reporting") ++ group = parser.getgroup("terminal reporting functorch") + group.addoption( + "--junit-xml-reruns", + action="store", diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch new file mode 100644 index 00000000000..b11903a6de3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch @@ -0,0 +1,19 @@ +The test seems to be too sensitive and may fail due to a small temporary allocation. +Increase the filter size to make it pass. +See https://github.com/pytorch/pytorch/issues/109592 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/profiler/test_memory_profiler.py b/test/profiler/test_memory_profiler.py +index 70b21b6b610..176fe153638 100644 +--- a/test/profiler/test_memory_profiler.py ++++ b/test/profiler/test_memory_profiler.py +@@ -1480,7 +1480,7 @@ class TestMemoryProfilerE2E(TestCase): + + # We generally don't care about tiny allocations during memory + # profiling and they add a lot of noise to the unit test. +- if size >= 256 ++ if size >= 1024 + ] + + self.assertExpectedInline( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch new file mode 100644 index 00000000000..0b064c8b4c7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch @@ -0,0 +1,39 @@ +commit 9942a14e96c539cb0195475d2cd660dcdc274123 +Author: Nisanth M P +Date: Fri Jul 14 04:09:14 2023 +0000 + + Fix torch.compile g++ flag error on ppc64le (#104956) + + g++ flag -march is not recognised on ppc64le. So adding a check for platform machine to be ppc64le and using -mcpu flag instead. Other architectures will still use -march flag + + This fixes the torch.compile feature failure on ppc64le + + Pull Request resolved: https://github.com/pytorch/pytorch/pull/104956 + Approved by: https://github.com/jgong5, https://github.com/jansel + +diff --git a/torch/_inductor/codecache.py b/torch/_inductor/codecache.py +--- a/torch/_inductor/codecache.py ++++ b/torch/_inductor/codecache.py +@@ -7,6 +7,7 @@ import json + import logging + import multiprocessing + import os ++import platform + import re + import shutil + import signal +@@ -378,7 +379,14 @@ def optimization_flags(): + # Also, `-march=native` is unrecognized option on M1 + base_flags += " -Xclang -fopenmp" + else: +- base_flags += " -march=native -fopenmp" ++ if platform.machine() == "ppc64le": ++ base_flags += " -mcpu=native" ++ else: ++ base_flags += " -march=native" ++ ++ # Internal cannot find libgomp.so ++ if not config.is_fbcode(): ++ base_flags += " -fopenmp" + return base_flags + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch new file mode 100644 index 00000000000..5651f8fbbcf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch @@ -0,0 +1,34 @@ +Casting negative floats to unsigned integers is undefined behavior so results vary between +different invocations and platforms. +This causes failures on e.g. PPC with test_comprehensive_byte in inductor/test_torchinductor_opinfo +See https://github.com/pytorch/pytorch/issues/110077 + +Fix by using `c10::convert` which handles that case. + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/_inductor/codegen/cpp.py b/torch/_inductor/codegen/cpp.py +index de6a32421c1..d16ae4cd91c 100644 +--- a/torch/_inductor/codegen/cpp.py ++++ b/torch/_inductor/codegen/cpp.py +@@ -577,7 +577,7 @@ class CppOverrides(OpOverrides): + @staticmethod + def to_dtype(x, dtype): + assert dtype in DTYPE_TO_CPP, f"{dtype} missing from {__name__}.DTYPE_TO_CPP" +- return f"static_cast<{DTYPE_TO_CPP[dtype]}>({x})" ++ return f"c10::convert<{DTYPE_TO_CPP[dtype]}>({x})" + + @staticmethod + def abs(x): +diff --git a/torch/_inductor/codegen/cpp_prefix.h b/torch/_inductor/codegen/cpp_prefix.h +index e0dba663144..9e17e481a89 100644 +--- a/torch/_inductor/codegen/cpp_prefix.h ++++ b/torch/_inductor/codegen/cpp_prefix.h +@@ -12,6 +12,7 @@ + #endif + #include + #include ++#include + + typedef at::Half half; + typedef at::BFloat16 bfloat16; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch new file mode 100644 index 00000000000..5d8afb76fe5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch @@ -0,0 +1,31 @@ +Fix access to unitialized memory on PPC +See https://github.com/pytorch/pytorch/issues/32502 & https://github.com/pytorch/pytorch/pull/109487 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h +index 806f6731abb..648ed06afa6 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h +@@ -91,7 +91,7 @@ struct Vectorized { + vec_vsx_ld(offset0, reinterpret_cast(ptr)), + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; + } +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +index 891c56b53ec..db3698804a7 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +@@ -94,7 +94,7 @@ struct Vectorized { + vec_vsx_ld(offset0, reinterpret_cast(ptr)), + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; + } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch new file mode 100644 index 00000000000..df699c5517e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch @@ -0,0 +1,186 @@ +# PyTorch's CMAKE configuration by default sets RUNPATH on libraries if they link other libraries +# that are outside the build tree, which is done because of the CMAKE config on +# https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L10. +# This provides problems, since the cuda stubs library path then also gets added to the RUNPATH. +# As a result, at runtime, the stub version of things like libcuda.so.1 gets picked up, instead of the real drivers +# See https://github.com/easybuilders/easybuild-easyconfigs/issues/14359 +# This line https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L16 +# Makes sure that any path that is linked, is also added to the RUNPATH. +# This has been reported upstream in https://github.com/pytorch/pytorch/issues/35418 +# and a fix was attempted in https://github.com/pytorch/pytorch/pull/37737 but it was reverted +# +# This EasyBuild patch changes behavior for the libraries that were failing, i.e. the ones in this list: +# https://github.com/easybuilders/easybuild-easyconfigs/issues/14359#issuecomment-970479904 +# This is done by setting INSTALL_RPATH_USE_LINK_PATH to false, and instead, specifying the RPATH +# explicitely by defining INSTALL_RPATH, but only adding directories that do not match to the "stubs" regex +# +# Original patch: Caspar van Leeuwen +# Updated: Alexander Grund (TU Dresden) +# +# See https://github.com/pytorch/pytorch/pull/87593 + +diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt +index 221e3f32b29..c3f24060f6a 100644 +--- a/caffe2/CMakeLists.txt ++++ b/caffe2/CMakeLists.txt +@@ -627,14 +627,13 @@ endif() + if(USE_CUDA) + list(APPEND Caffe2_GPU_CU_SRCS ${Caffe2_GPU_HIP_JIT_FUSERS_SRCS}) + add_library(caffe2_nvrtc SHARED ${ATen_NVRTC_STUB_SRCS}) ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB}) + if(MSVC) + # Delay load nvcuda.dll so we can import torch compiled with cuda on a CPU-only machine +- set(DELAY_LOAD_FLAGS "-DELAYLOAD:nvcuda.dll;delayimp.lib") +- else() +- set(DELAY_LOAD_FLAGS "") ++ target_link_libraries(caffe2_nvrtc "-DELAYLOAD:nvcuda.dll;delayimp.lib") + endif() + +- target_link_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB} ${DELAY_LOAD_FLAGS}) + target_include_directories(caffe2_nvrtc PRIVATE ${CUDA_INCLUDE_DIRS}) + install(TARGETS caffe2_nvrtc DESTINATION "${TORCH_INSTALL_LIB_DIR}") + if(USE_NCCL) +diff --git a/cmake/LinkCudaLibraries.cmake b/cmake/LinkCudaLibraries.cmake +new file mode 100644 +index 00000000000..005914ccc6f +--- /dev/null ++++ b/cmake/LinkCudaLibraries.cmake +@@ -0,0 +1,33 @@ ++# Link CUDA libraries to the given target, i.e.: `target_link_libraries(target )` ++# ++# Additionally makes sure CUDA stub libs don't end up being in RPath ++# ++# Example: link_cuda_libraries(mytarget PRIVATE ${CUDA_LIBRARIES}) ++function(link_cuda_libraries target) ++ set(libs ${ARGN}) ++ set(install_rpath "$ORIGIN") ++ set(filtered FALSE) ++ foreach(lib IN LISTS libs) ++ # CUDA stub libs are in form /prefix/lib/stubs/libcuda.so ++ # So extract the name of the parent folder, to check against "stubs" ++ # And the parent path which we need to add to the INSTALL_RPATH for non-stubs ++ get_filename_component(parent_path "${lib}" DIRECTORY) ++ get_filename_component(parent_name "${parent_path}" NAME) ++ if(parent_name STREQUAL "stubs") ++ message(STATUS "Filtering ${lib} from being set in ${target}'s RPATH, " ++ "because it appears to point to the CUDA stubs directory.") ++ set(filtered TRUE) ++ elseif(parent_path) ++ list(APPEND install_rpath ${parent_path}) ++ endif() ++ endforeach() ++ ++ # Regular link command ++ target_link_libraries(${target} ${libs}) ++ # Manually set INSTALL_RPATH when there were any stub libs ++ if(filtered) ++ list(REMOVE_DUPLICATES install_rpath) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH "${install_rpath}") ++ endif() ++endfunction() +diff --git a/test/cpp/api/CMakeLists.txt b/test/cpp/api/CMakeLists.txt +index 6b801a07318..6ac92870479 100644 +--- a/test/cpp/api/CMakeLists.txt ++++ b/test/cpp/api/CMakeLists.txt +@@ -54,7 +54,8 @@ if(NOT MSVC) + endif() + + if(USE_CUDA) +- target_link_libraries(test_api PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_api PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/dist_autograd/CMakeLists.txt b/test/cpp/dist_autograd/CMakeLists.txt +index 9969c63e16d..356ba5be55c 100644 +--- a/test/cpp/dist_autograd/CMakeLists.txt ++++ b/test/cpp/dist_autograd/CMakeLists.txt +@@ -10,7 +10,8 @@ if(USE_DISTRIBUTED AND NOT WIN32) + target_link_libraries(test_dist_autograd PRIVATE torch gtest) + + if(USE_CUDA) +- target_link_libraries(test_dist_autograd PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_dist_autograd PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/jit/CMakeLists.txt b/test/cpp/jit/CMakeLists.txt +index 2376f1bc43b..30fbb99fa6d 100644 +--- a/test/cpp/jit/CMakeLists.txt ++++ b/test/cpp/jit/CMakeLists.txt +@@ -139,7 +139,8 @@ if(LINUX) + endif() + + if(USE_CUDA) +- target_link_libraries(test_jit PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_jit PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/rpc/CMakeLists.txt b/test/cpp/rpc/CMakeLists.txt +index 3997f8753e5..21fddbc645d 100644 +--- a/test/cpp/rpc/CMakeLists.txt ++++ b/test/cpp/rpc/CMakeLists.txt +@@ -33,7 +33,8 @@ target_include_directories( + target_link_libraries(test_cpp_rpc PRIVATE ${TORCH_RPC_TEST_DEPENDENCY_LIBS}) + + if(USE_CUDA) +- target_link_libraries(test_cpp_rpc PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_cpp_rpc PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/tensorexpr/CMakeLists.txt b/test/cpp/tensorexpr/CMakeLists.txt +index 7dff70630d3..ecb83005492 100644 +--- a/test/cpp/tensorexpr/CMakeLists.txt ++++ b/test/cpp/tensorexpr/CMakeLists.txt +@@ -57,14 +57,15 @@ if(USE_PTHREADPOOL) + target_link_libraries(test_tensorexpr PRIVATE pthreadpool_interface) + endif() + if(USE_CUDA) +- target_link_libraries(test_tensorexpr PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + target_compile_definitions(test_tensorexpr PRIVATE USE_CUDA) + +- target_link_libraries(tutorial_tensorexpr PRIVATE ++ link_cuda_libraries(tutorial_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/test_torch.py b/test/test_torch.py +index c86535e22c0..6859311d806 100644 +--- a/test/test_torch.py ++++ b/test/test_torch.py +@@ -8833,6 +8833,21 @@ def add_neg_dim_tests(): + assert not hasattr(TestTorch, test_name), "Duplicated test name: " + test_name + setattr(TestTorch, test_name, make_neg_dim_test(name, tensor_arg, arg_constr, types, extra_dim)) + ++class TestRPATH(TestCase): ++ @unittest.skipIf(not sys.platform.startswith('linux'), "linux-only test") ++ def test_rpath(self): ++ """ ++ Make sure RPATH (or RUNPATH) in nvrtc does not contain a cuda stubs directory ++ issue gh-35418 ++ """ ++ libdir = os.path.join(os.path.dirname(torch._C.__file__), 'lib') ++ caffe2_nvrtc = os.path.join(libdir, 'libcaffe2_nvrtc.so') ++ if os.path.exists(caffe2_nvrtc): ++ output = subprocess.check_output(['objdump', '-x', caffe2_nvrtc]) ++ for line in output.split(b'\n'): ++ if b'RPATH' in line or b'RUNPATH' in line: ++ self.assertFalse(b'stubs' in line) ++ + # TODO: these empy classes are temporarily instantiated for XLA compatibility + # once XLA updates their test suite it should be removed + class TestViewOps(TestCase): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch new file mode 100644 index 00000000000..4022d01c852 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch @@ -0,0 +1,30 @@ +This downloads a Perl file from a Github repo which may fail in: + + File "test/test_cuda.py", line 4632, in test_memory_snapshot + torch.cuda.memory._save_segment_usage(f.name) + File "/torch/cuda/memory.py", line 610, in _save_segment_usage + f.write(_segments(snapshot)) + File "/torch/cuda/_memory_viz.py", line 60, in segments + return format_flamegraph(f.getvalue()) + File "/torch/cuda/_memory_viz.py", line 21, in format_flamegraph + urllib.request.urlretrieve( + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_cuda.py b/test/test_cuda.py +index 7f2693b52c5..4bff69e5cad 100644 +--- a/test/test_cuda.py ++++ b/test/test_cuda.py +@@ -4993,12 +4993,6 @@ class TestCudaComm(TestCase): + found_it = True + self.assertTrue(found_it) + +- if not IS_WINDOWS: +- with tempfile.NamedTemporaryFile() as f: +- torch.cuda.memory._save_segment_usage(f.name) +- with open(f.name, 'r') as f2: +- self.assertTrue('test_cuda.py' in f2.read()) +- + del x + torch.cuda.empty_cache() + ss = torch.cuda.memory._snapshot() diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch new file mode 100644 index 00000000000..41d0da2eb03 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch @@ -0,0 +1,26 @@ +The workaround for over/underflow isn't implemented for PPC yet. +So skip the test. +See https://github.com/pytorch/pytorch/issues/109870 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_binary_ufuncs.py b/test/test_binary_ufuncs.py +index 57fc1b76f18..06c129e007a 100644 +--- a/test/test_binary_ufuncs.py ++++ b/test/test_binary_ufuncs.py +@@ -27,6 +27,7 @@ from torch.testing._internal.common_utils import ( + numpy_to_torch_dtype_dict, + TEST_SCIPY, + set_default_dtype, ++ IS_PPC, + ) + from torch.testing._internal.common_device_type import ( + expectedFailureMeta, +@@ -1091,6 +1092,7 @@ class TestBinaryUfuncs(TestCase): + ) + + @dtypes(*complex_types()) ++ @skipIf(IS_PPC, "Vectorized div fails on PPC: #109870") + def test_complex_div_underflow_overflow(self, device, dtype): + # test to make sure the complex division does not produce underflow or overflow + # in the intermediate of its calculations diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch new file mode 100644 index 00000000000..19d427b3049 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch @@ -0,0 +1,16 @@ +test_fn_grad_linalg_det_singular_cpu_float64 fails not only on macos + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/opinfo/definitions/linalg.py b/torch/testing/_internal/opinfo/definitions/linalg.py +index 616c8cf42f4..3a07d19df46 100644 +--- a/torch/testing/_internal/opinfo/definitions/linalg.py ++++ b/torch/testing/_internal/opinfo/definitions/linalg.py +@@ -1135,7 +1135,6 @@ op_db: List[OpInfo] = [ + "test_fn_grad", + device_type="cpu", + dtypes=(torch.float64,), +- active_if=IS_MACOS, + ), + DecorateInfo( + unittest.skip("Gradients are incorrect on macos"), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch new file mode 100644 index 00000000000..f02e5d3ab0d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch @@ -0,0 +1,20 @@ +The test fails on some systems with +> RuntimeError: Too many open files. Communication with the workers is no longer possible. +> Please increase the limit using `ulimit -n` in the shell or change the sharing strategy by calling `torch.multiprocessing.set_sharing_strategy('file_system')` at the beginning of your code + +So just skip it. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_dataloader.py b/test/test_dataloader.py +index 39d91876f0b..aff47063344 100644 +--- a/test/test_dataloader.py ++++ b/test/test_dataloader.py +@@ -1542,6 +1542,7 @@ except RuntimeError as e: + def test_shuffle_batch(self): + self._test_shuffle(self._get_data_loader(self.dataset, batch_size=2, shuffle=True)) + ++ @unittest.skip("May cause 'Too many open files' error due to potential `ulimit -n` restrictions") + def test_shuffle_reproducibility(self): + for fn in ( + lambda: DataLoader(self.dataset, shuffle=True, num_workers=0, generator=torch.Generator().manual_seed(42)), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch new file mode 100644 index 00000000000..8e80dec749f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch @@ -0,0 +1,34 @@ +Use unittest.skip to skip tests skipped by subprocesses as otherwise skipped tests +marked as expectedFailure may succeed unexpectatly failing the testsuite. +E.g.: +> INFO:torch.testing._internal.common_distributed:Thread 0 skipping test > for following reason: PyTorch is built without MKL support +> INFO:torch.testing._internal.common_distributed:Thread 1 skipping test > for following reason: PyTorch is built without MKL support +> INFO:torch.testing._internal.common_distributed:Skipping > on sandcastle for the following reason: Test skipped at subprocess level, look at subprocess log for skip reason +> u +> ... +> FAILED (unexpected successes=1) + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_distributed.py b/torch/testing/_internal/common_distributed.py +index 400aa80fdca..afea4a8f89f 100644 +--- a/torch/testing/_internal/common_distributed.py ++++ b/torch/testing/_internal/common_distributed.py +@@ -828,7 +828,7 @@ class MultiProcessTestCase(TestCase): + ) + for skip in TEST_SKIPS.values(): + if first_process.exitcode == skip.exit_code: +- if IS_SANDCASTLE: ++ if False: + # Don't use unittest.skip to skip the test on sandcastle + # since it creates tasks for skipped tests assuming there + # is some follow-up needed. Instead just "pass" the test +@@ -1123,7 +1123,7 @@ class MultiThreadedTestCase(TestCase): + if skip_code > 0: + for skip in TEST_SKIPS.values(): + if skip_code == skip.exit_code: +- if IS_SANDCASTLE: ++ if False: + # "pass" the test with an appropriate message. + logger.info( + f"Skipping {fn} on sandcastle for the following reason: {skip.message}" From dd69d00dea442582ac7b34df8d6d39428e8c9224 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 24 Oct 2023 10:10:29 +0200 Subject: [PATCH 9244/9987] Downgrade sympy (duplicate in 2022a) --- easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb index c42d16ff11f..6a18148e60c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb @@ -112,7 +112,7 @@ dependencies = [ ('Pillow', '9.1.1'), ('expecttest', '0.1.3'), ('networkx', '2.8.4'), - ('sympy', '1.11.1'), + ('sympy', '1.10.1'), ] excluded_tests = { From 5e8fd96e3151c44c5a8aa398969a1c4534ce542c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 24 Oct 2023 10:11:33 +0200 Subject: [PATCH 9245/9987] adding easyconfigs: PyTorch-2.0.1-foss-2022b.eb and patches: PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch, PyTorch-2.0.1_avoid-test_quantization-failures.patch, PyTorch-2.0.1_disable-test-sharding.patch, PyTorch-2.0.1_fix-numpy-compat.patch, PyTorch-2.0.1_fix-shift-ops.patch, PyTorch-2.0.1_fix-skip-decorators.patch, PyTorch-2.0.1_fix-test_memory_profiler.patch, PyTorch-2.0.1_fix-test-ops-conf.patch, PyTorch-2.0.1_fix-torch.compile-on-ppc.patch, PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch, PyTorch-2.0.1_fix-vsx-loadu.patch, PyTorch-2.0.1_no-cuda-stubs-rpath.patch, PyTorch-2.0.1_remove-test-requiring-online-access.patch, PyTorch-2.0.1_skip-diff-test-on-ppc.patch, PyTorch-2.0.1_skip-failing-gradtest.patch, PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch, PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch --- .../p/PyTorch/PyTorch-2.0.1-foss-2022b.eb | 144 ++++++++++ ...d-missing-vsx-vector-shift-functions.patch | 103 +++++++ ...0.1_avoid-test_quantization-failures.patch | 19 ++ .../PyTorch-2.0.1_disable-test-sharding.patch | 18 ++ .../PyTorch-2.0.1_fix-numpy-compat.patch | 237 ++++++++++++++++ .../PyTorch/PyTorch-2.0.1_fix-shift-ops.patch | 253 ++++++++++++++++++ .../PyTorch-2.0.1_fix-skip-decorators.patch | 122 +++++++++ .../PyTorch-2.0.1_fix-test-ops-conf.patch | 26 ++ ...Torch-2.0.1_fix-test_memory_profiler.patch | 19 ++ ...Torch-2.0.1_fix-torch.compile-on-ppc.patch | 39 +++ ...rch-2.0.1_fix-ub-in-inductor-codegen.patch | 34 +++ .../PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch | 31 +++ .../PyTorch-2.0.1_no-cuda-stubs-rpath.patch | 186 +++++++++++++ ..._remove-test-requiring-online-access.patch | 30 +++ .../PyTorch-2.0.1_skip-diff-test-on-ppc.patch | 26 ++ .../PyTorch-2.0.1_skip-failing-gradtest.patch | 16 ++ ....1_skip-test_shuffle_reproducibility.patch | 20 ++ ...0.1_skip-tests-skipped-in-subprocess.patch | 34 +++ 18 files changed, 1357 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb new file mode 100644 index 00000000000..59f471b813e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb @@ -0,0 +1,144 @@ +name = 'PyTorch' +version = '2.0.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +patches = [ + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch', + 'PyTorch-1.13.1_fix-protobuf-dependency.patch', + 'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch', + 'PyTorch-1.13.1_skip-failing-singular-grad-test.patch', + 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', + 'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch', + 'PyTorch-2.0.1_avoid-test_quantization-failures.patch', + 'PyTorch-2.0.1_disable-test-sharding.patch', + 'PyTorch-2.0.1_fix-numpy-compat.patch', + 'PyTorch-2.0.1_fix-shift-ops.patch', + 'PyTorch-2.0.1_fix-skip-decorators.patch', + 'PyTorch-2.0.1_fix-test_memory_profiler.patch', + 'PyTorch-2.0.1_fix-test-ops-conf.patch', + 'PyTorch-2.0.1_fix-torch.compile-on-ppc.patch', + 'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch', + 'PyTorch-2.0.1_fix-vsx-loadu.patch', + 'PyTorch-2.0.1_no-cuda-stubs-rpath.patch', + 'PyTorch-2.0.1_remove-test-requiring-online-access.patch', + 'PyTorch-2.0.1_skip-diff-test-on-ppc.patch', + 'PyTorch-2.0.1_skip-failing-gradtest.patch', + 'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch', + 'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch', +] +checksums = [ + {'pytorch-v2.0.1.tar.gz': '9c564ca440265c69400ef5fdd48bf15e28af5aa4bed84c95efaad960a6699998'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.1_add-hypothesis-suppression.patch': + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, + {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, + {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, + {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch': + '5c7be91a6096083a0b1315efe0001537499c600f1f569953c6a2c7f4cc1d0910'}, + {'PyTorch-1.13.1_fix-protobuf-dependency.patch': + '8bd755a0cab7233a243bc65ca57c9630dfccdc9bf8c9792f0de4e07a644fcb00'}, + {'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch': + 'bdde0f2105215c95a54de64ec4b1a4520528510663174fef6d5b900eb1db3937'}, + {'PyTorch-1.13.1_skip-failing-singular-grad-test.patch': + '72688a57b2bb617665ad1a1d5e362c5111ae912c10936bb38a089c0204729f48'}, + {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': + '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, + {'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch': + '245ee7f479f6f809b6ea52460113b2c49bbc2a550201f82bdfa0651c72b02ea8'}, + {'PyTorch-2.0.1_avoid-test_quantization-failures.patch': + '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'}, + {'PyTorch-2.0.1_disable-test-sharding.patch': 'a1ed7f21c9a269ea039a07a3d6574f885787b30ca5687143c96e096d31066cca'}, + {'PyTorch-2.0.1_fix-numpy-compat.patch': 'f3e5798193e0909a415d824f13772973200965db84476c1737824f2735f2db94'}, + {'PyTorch-2.0.1_fix-shift-ops.patch': '5ee655d5dba56d801d5618543b6ca299fa874939a3471f7b5449bfcb7f3f18c7'}, + {'PyTorch-2.0.1_fix-skip-decorators.patch': '2039012cef45446065e1a2097839fe20bb29fe3c1dcc926c3695ebf29832e920'}, + {'PyTorch-2.0.1_fix-test_memory_profiler.patch': + 'fd03117c46f59c1c62227d31c410c4cdd98fd35410976758cb9e7ec947582ddb'}, + {'PyTorch-2.0.1_fix-test-ops-conf.patch': '0f995e4f89baf3cbeb8666cbfe694666a2ef2bc53d97d6301f768b3ff9001fa4'}, + {'PyTorch-2.0.1_fix-torch.compile-on-ppc.patch': + '20f9172ae696da0c5c7b3bae6f0bf1221192cb1cbac3a44526a415087834bee7'}, + {'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch': + '1b37194f55ae678f3657b8728dfb896c18ffe8babe90987ce468c4fa9274f357'}, + {'PyTorch-2.0.1_fix-vsx-loadu.patch': 'a0ffa61da2d47c6acd09aaf6d4791e527d8919a6f4f1aa7ed38454cdcadb1f72'}, + {'PyTorch-2.0.1_no-cuda-stubs-rpath.patch': '8902e58a762240f24cdbf0182e99ccdfc2a93492869352fcb4ca0ec7e407f83a'}, + {'PyTorch-2.0.1_remove-test-requiring-online-access.patch': + '721ab0d35ed0ff8a46cb84ced5a98c0fb8ce6143cf6cea80b1360d3d7f64f584'}, + {'PyTorch-2.0.1_skip-diff-test-on-ppc.patch': 'f6e39cd774e5663df25507a73d37ad598157c2eadb2f47ca20a537dbe4b3e14f'}, + {'PyTorch-2.0.1_skip-failing-gradtest.patch': '8030bdec6ba49b057ab232d19a7f1a5e542e47e2ec340653a246ec9ed59f8bc1'}, + {'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch': + '7047862abc1abaff62954da59700f36d4f39fcf83167a638183b1b7f8fec78ae'}, + {'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch': + '166c134573a95230e39b9ea09ece3ad8072f39d370c9a88fb2a1e24f6aaac2b5'}, +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.24.3'), + ('hypothesis', '6.68.2'), + # For tests + ('pytest-rerunfailures', '12.0'), + ('pytest-shard', '0.1.2'), +] + +dependencies = [ + ('Ninja', '1.11.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.8'), + ('protobuf', '23.0'), + ('protobuf-python', '4.23.0'), + ('pybind11', '2.10.3'), + ('SciPy-bundle', '2023.02'), + ('PyYAML', '6.0'), + ('MPFR', '4.2.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.16'), + ('FFmpeg', '5.1.2'), + ('Pillow', '9.4.0'), + ('expecttest', '0.1.3'), + ('networkx', '3.0'), + ('sympy', '1.12'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + # no xdoctest + 'doctests', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'test_native_mha', + # intermittent failures on various systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'distributed/rpc/test_tensorpipe_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# Especially test_quantization has a few corner cases that are triggered by the random input values, +# those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 +# So allow a low number of tests to fail as the tests "usually" succeed +max_failed_tests = 2 + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch new file mode 100644 index 00000000000..57e334c908f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch @@ -0,0 +1,103 @@ +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +index 7c300c8087c..84c84286740 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +@@ -348,6 +348,7 @@ Vectorized inline minimum( + return a.minimum(b); + } + ++DEFINE_SHIFT_FUNCS(int16_t) + + } // namespace + } // namespace vec +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +index c98ab6215e6..e1e86d3b53a 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +@@ -279,6 +279,8 @@ Vectorized inline minimum( + return a.minimum(b); + } + ++DEFINE_SHIFT_FUNCS(int32_t) ++ + } // namespace + } // namespace vec + } // namespace at +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +index a4171026a2b..70613d90443 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +@@ -231,6 +231,8 @@ Vectorized inline minimum( + return a.minimum(b); + } + ++DEFINE_SHIFT_FUNCS(int64_t) ++ + } // namespace + } // namespace vec + } // namespace at +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h b/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h +index dab38458184..52032cdd817 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vsx_helpers.h +@@ -2,6 +2,7 @@ + #include + #include + #include ++#include + + using vbool8 = __attribute__((altivec(vector__))) __attribute__((altivec(bool__))) char; + using vbool16 = __attribute__((altivec(vector__))) __attribute__((altivec(bool__))) short; +@@ -18,6 +19,11 @@ using vuint64 = __attribute__((altivec(vector__))) unsigned long long; + using vfloat32 = __attribute__((altivec(vector__))) float; + using vfloat64 = __attribute__((altivec(vector__))) double; + ++inline auto make_vuint(vint8 v){ return reinterpret_cast(v); } ++inline auto make_vuint(vint16 v){ return reinterpret_cast(v); } ++inline auto make_vuint(vint32 v){ return reinterpret_cast(v); } ++inline auto make_vuint(vint64 v){ return reinterpret_cast(v); } ++ + #if !defined(vec_float) + C10_ALWAYS_INLINE vfloat32 vec_float(const vint32& vec_in) { + vfloat32 vec_out; +@@ -448,6 +454,40 @@ const vfloat64 vd_imag_half = vfloat64{0.0, 0.5}; + const vfloat64 vd_sqrt2_2 = vfloat64{0.70710678118654757, 0.70710678118654757}; + const vfloat64 vd_pi_2 = vfloat64{M_PI / 2.0, 0.0}; + ++template ++Vectorized VsxShiftRightArith(const Vectorized& a, const Vectorized& b) { ++ const Vectorized max_shift(sizeof(T) * CHAR_BIT - std::is_signed_v); ++ const auto mask = (b < Vectorized(0)) | (b >= max_shift); ++ const auto shift = Vectorized::blendv(b, max_shift, mask); ++ return Vectorized{ ++ vec_sra(a.vec0(), make_vuint(shift.vec0())), ++ vec_sra(a.vec1(), make_vuint(shift.vec1()))}; ++} ++ ++template ++Vectorized VsxShiftLeftArith(const Vectorized& a, const Vectorized& b) { ++ const Vectorized max_shift(sizeof(T) * CHAR_BIT); ++ const auto mask = (b < Vectorized(0)) | (b >= max_shift); ++ Vectorized ret( ++ vec_sl(a.vec0(), make_vuint(b.vec0())), ++ vec_sl(a.vec1(), make_vuint(b.vec1()))); ++ return Vectorized::blendv(ret, Vectorized(0), mask); ++} ++ ++#define DEFINE_SHIFT_FUNCS(operand_type) \ ++ template <> \ ++ Vectorized C10_ALWAYS_INLINE operator>>( \ ++ const Vectorized& a, \ ++ const Vectorized& b) { \ ++ return VsxShiftRightArith(a, b); \ ++ } \ ++ template <> \ ++ Vectorized C10_ALWAYS_INLINE operator<<( \ ++ const Vectorized& a, \ ++ const Vectorized& b) { \ ++ return VsxShiftLeftArith(a, b); \ ++ } \ ++ + } // namespace + } // namespace vec + } // namespace at diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch new file mode 100644 index 00000000000..01a7e098c41 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_avoid-test_quantization-failures.patch @@ -0,0 +1,19 @@ +The quantized values returned by hypothesis as test inputs might still cause overflows. +Hence reduce their maximum value by a factor that should fix most such cases. +See e.g. https://github.com/pytorch/pytorch/issues/111471 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/hypothesis_utils.py b/torch/testing/_internal/hypothesis_utils.py +index 15e7b4512a4..67df4d74e9d 100644 +--- a/torch/testing/_internal/hypothesis_utils.py ++++ b/torch/testing/_internal/hypothesis_utils.py +@@ -36,6 +36,8 @@ _ENFORCED_ZERO_POINT = defaultdict(lambda: None, { + def _get_valid_min_max(qparams): + scale, zero_point, quantized_type = qparams + adjustment = 1 + torch.finfo(torch.float).eps ++ # provide some leeway for scaling values without overflowing long ++ adjustment *= 1e4 + _long_type_info = torch.iinfo(torch.long) + long_min, long_max = _long_type_info.min / adjustment, _long_type_info.max / adjustment + # make sure intermediate results are within the range of long diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch new file mode 100644 index 00000000000..525d9fda1dc --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-test-sharding.patch @@ -0,0 +1,18 @@ +Our error checking doesn't work well with the parallel/sharded pytorch test. +As the overall gain is low, disable it and always run the full test suite in a single process. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/run_test.py b/test/run_test.py +index 9619cb2626e..ddfb200148f 100755 +--- a/test/run_test.py ++++ b/test/run_test.py +@@ -815,7 +815,7 @@ def run_test_ops(test_module, test_directory, options): + ] + default_unittest_args.extend(rerun_options) + +- if 'slow-gradcheck' in os.getenv("BUILD_ENVIRONMENT", ""): ++ if True: + extra_unittest_args = default_unittest_args.copy() + # there are a lot of tests that take up a lot of space in slowgrad check, so don't bother parallelizing + # it's also on periodic so we don't care about TTS as much diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch new file mode 100644 index 00000000000..99b3cc6b770 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-numpy-compat.patch @@ -0,0 +1,237 @@ +From ae1ed277563a1ac887faef4370ad9933c883ab9e Mon Sep 17 00:00:00 2001 +From: Omkar Salpekar +Date: Wed, 21 Jun 2023 18:16:40 +0000 +Subject: [PATCH] [codemod][numpy] replace np.str with str (#103931) + +Summary: +`np.str` is removed from numpy 1.20.0. It was an alias to builtin `str` and it's safe to do the replacement. + +The whole changes is mechanical, generated using the following onliner: +``` +fbgr -sl 'np\.str\b' | xargs perl -pi -e 's,\bnp\.str\b,str,g' +``` + +Test Plan: sandcastle + +Differential Revision: D46586144 + +Pull Request resolved: https://github.com/pytorch/pytorch/pull/103931 +Approved by: https://github.com/huydhn +--- + caffe2/python/core.py | 2 +- + caffe2/python/hypothesis_test.py | 4 ++-- + caffe2/python/layer_model_helper.py | 2 +- + caffe2/python/operator_test/adagrad_test_helper.py | 2 +- + caffe2/python/operator_test/cast_op_test.py | 2 +- + caffe2/python/operator_test/detectron_keypoints.py | 4 ++-- + caffe2/python/operator_test/tile_op_test.py | 6 +++--- + caffe2/python/schema.py | 2 +- + caffe2/python/schema_test.py | 4 ++-- + caffe2/python/utils.py | 6 +++--- + .../examples/maml_omniglot/support/omniglot_loaders.py | 4 ++-- + test/quantization/core/test_quantized_op.py | 4 ++-- + 12 files changed, 21 insertions(+), 21 deletions(-) + +diff --git a/caffe2/python/core.py b/caffe2/python/core.py +index d9f97b6121fdd2..e69af5c0a482b1 100644 +--- a/caffe2/python/core.py ++++ b/caffe2/python/core.py +@@ -1636,7 +1636,7 @@ def do_set(operator): + return do_set(self.GivenTensorIntFill) + elif array.dtype == np.int64: + return do_set(self.GivenTensorInt64Fill) +- elif array.dtype == np.str: ++ elif array.dtype == str: + return do_set(self.GivenTensorStringFill) + elif array.dtype == np.bool: + return do_set(self.GivenTensorBoolFill) +diff --git a/caffe2/python/hypothesis_test.py b/caffe2/python/hypothesis_test.py +index 02200f8cf74f18..cb5d00064b6eda 100644 +--- a/caffe2/python/hypothesis_test.py ++++ b/caffe2/python/hypothesis_test.py +@@ -1629,8 +1629,8 @@ def test_tt_sls_layer(self, gc, dc): + c0 = np.ones([10, 1, 2, 16]).astype(np.float32) + c1 = np.ones([10, 16, 2, 16]).astype(np.float32) + c2 = np.ones([10, 16, 2, 1]).astype(np.float32) +- # index = np.array([0, 1, 2, 1, 4], dtype=np.int) +- # lengths = np.array([3, 2], dtype=np.int) ++ # index = np.array([0, 1, 2, 1, 4], dtype=int) ++ # lengths = np.array([3, 2], dtype=int) + index = np.array([0, 1, 2, 1, 4], np.int64) + lengths = np.array([3, 2], np.int32) + +diff --git a/caffe2/python/layer_model_helper.py b/caffe2/python/layer_model_helper.py +index 9a8e237e302143..f21b47e57c653a 100644 +--- a/caffe2/python/layer_model_helper.py ++++ b/caffe2/python/layer_model_helper.py +@@ -148,7 +148,7 @@ def _get_global_constant_initializer_op( + op_name = 'GivenTensorIntFill' + elif array.dtype == np.int64: + op_name = 'GivenTensorInt64Fill' +- elif array.dtype == np.str: ++ elif array.dtype == str: + op_name = 'GivenTensorStringFill' + elif array.dtype == np.bool: + op_name = 'GivenTensorBoolFill' +diff --git a/caffe2/python/operator_test/adagrad_test_helper.py b/caffe2/python/operator_test/adagrad_test_helper.py +index 08caf22b266178..1fd017c4d2ac5c 100644 +--- a/caffe2/python/operator_test/adagrad_test_helper.py ++++ b/caffe2/python/operator_test/adagrad_test_helper.py +@@ -98,7 +98,7 @@ def adagrad_sparse_test_helper( + # Create an indexing array containing values that are lists of indices, + # which index into grad + if grad.size == 0: +- indices = np.empty(shape=(0,), dtype=np.int) ++ indices = np.empty(shape=(0,), dtype=int) + else: + indices = np.random.choice( + np.arange(grad.shape[0]), +diff --git a/caffe2/python/operator_test/cast_op_test.py b/caffe2/python/operator_test/cast_op_test.py +index bf2a210086e691..95540a6121bcac 100644 +--- a/caffe2/python/operator_test/cast_op_test.py ++++ b/caffe2/python/operator_test/cast_op_test.py +@@ -37,7 +37,7 @@ def test_cast_int_to_string(self, data, gc, dc): + 'Cast', 'data', 'data_cast', to=core.DataType.STRING) + + def ref(data): +- ret = data.astype(dtype=np.str) ++ ret = data.astype(dtype=str) + # the string blob will be fetched as object, we feed and re-fetch + # to mimic this. + with hu.temp_workspace('tmp_ref_int_to_string'): +diff --git a/caffe2/python/operator_test/detectron_keypoints.py b/caffe2/python/operator_test/detectron_keypoints.py +index 1abff0675993ff..319e8b5bbffd5e 100644 +--- a/caffe2/python/operator_test/detectron_keypoints.py ++++ b/caffe2/python/operator_test/detectron_keypoints.py +@@ -32,8 +32,8 @@ def heatmaps_to_keypoints(maps, rois): + heights = rois[:, 3] - rois[:, 1] + widths = np.maximum(widths, 1) + heights = np.maximum(heights, 1) +- widths_ceil = np.ceil(widths).astype(np.int) +- heights_ceil = np.ceil(heights).astype(np.int) ++ widths_ceil = np.ceil(widths).astype(int) ++ heights_ceil = np.ceil(heights).astype(int) + + num_keypoints = np.maximum(maps.shape[1], _NUM_KEYPOINTS) + +diff --git a/caffe2/python/operator_test/tile_op_test.py b/caffe2/python/operator_test/tile_op_test.py +index d39dfeee0ad72a..fbb424fe058ccb 100644 +--- a/caffe2/python/operator_test/tile_op_test.py ++++ b/caffe2/python/operator_test/tile_op_test.py +@@ -32,7 +32,7 @@ def test_tile(self, M, K, N, tiles, axis, gc, dc): + ) + + def tile_ref(X, tiles, axis): +- dims = np.asarray([1, 1, 1], dtype=np.int) ++ dims = np.asarray([1, 1, 1], dtype=int) + dims[axis] = tiles + tiled_data = np.tile(X, dims) + return (tiled_data,) +@@ -61,7 +61,7 @@ def test_tile_grad(self, M, N, tiles, gc, dc): + ) + + def tile_ref(X, tiles, axis): +- dims = np.asarray([1, 1], dtype=np.int) ++ dims = np.asarray([1, 1], dtype=int) + dims[axis] = tiles + tiled_data = np.tile(X, dims) + return (tiled_data,) +@@ -99,7 +99,7 @@ def test_tilewinput(self, M, K, N, tiles, axis, gc, dc): + ) + + def tile_ref(X, tiles, axis): +- dims = np.asarray([1, 1, 1], dtype=np.int) ++ dims = np.asarray([1, 1, 1], dtype=int) + dims[axis] = tiles + tiled_data = np.tile(X, dims) + return (tiled_data,) +diff --git a/caffe2/python/schema.py b/caffe2/python/schema.py +index ab6ec29372e2ff..ecbcb2287dddea 100644 +--- a/caffe2/python/schema.py ++++ b/caffe2/python/schema.py +@@ -1252,7 +1252,7 @@ def InitEmptyRecord(net, schema_or_record, enforce_types=False): + + + _DATA_TYPE_FOR_DTYPE = [ +- (np.str, core.DataType.STRING), ++ (str, core.DataType.STRING), + (np.float16, core.DataType.FLOAT16), + (np.float32, core.DataType.FLOAT), + (np.float64, core.DataType.DOUBLE), +diff --git a/caffe2/python/schema_test.py b/caffe2/python/schema_test.py +index 8f3ed4415fd4f5..2f3eaf38dc138d 100644 +--- a/caffe2/python/schema_test.py ++++ b/caffe2/python/schema_test.py +@@ -94,12 +94,12 @@ def testTuple(self): + s = schema.Tuple(np.int32, str, np.float32) + s2 = schema.Struct( + ('field_0', schema.Scalar(dtype=np.int32)), +- ('field_1', schema.Scalar(dtype=np.str)), ++ ('field_1', schema.Scalar(dtype=str)), + ('field_2', schema.Scalar(dtype=np.float32)) + ) + self.assertEqual(s, s2) + self.assertEqual(s[0], schema.Scalar(dtype=np.int32)) +- self.assertEqual(s[1], schema.Scalar(dtype=np.str)) ++ self.assertEqual(s[1], schema.Scalar(dtype=str)) + self.assertEqual(s[2], schema.Scalar(dtype=np.float32)) + self.assertEqual( + s[2, 0], +diff --git a/caffe2/python/utils.py b/caffe2/python/utils.py +index 02a77e74681a93..8c82faee33a4c3 100644 +--- a/caffe2/python/utils.py ++++ b/caffe2/python/utils.py +@@ -67,7 +67,7 @@ def Caffe2TensorToNumpyArray(tensor): + tensor.int64_data, dtype=np.int64).reshape(tensor.dims) + elif tensor.data_type == caffe2_pb2.TensorProto.INT32: + return np.asarray( +- tensor.int32_data, dtype=np.int).reshape(tensor.dims) # pb.INT32=>np.int use int32_data ++ tensor.int32_data, dtype=int).reshape(tensor.dims) # pb.INT32=>int use int32_data + elif tensor.data_type == caffe2_pb2.TensorProto.INT16: + return np.asarray( + tensor.int32_data, dtype=np.int16).reshape(tensor.dims) # pb.INT16=>np.int16 use int32_data +@@ -100,9 +100,9 @@ def NumpyArrayToCaffe2Tensor(arr, name=None): + elif arr.dtype == np.int64: + tensor.data_type = caffe2_pb2.TensorProto.INT64 + tensor.int64_data.extend(list(arr.flatten().astype(np.int64))) +- elif arr.dtype == np.int or arr.dtype == np.int32: ++ elif arr.dtype == int or arr.dtype == np.int32: + tensor.data_type = caffe2_pb2.TensorProto.INT32 +- tensor.int32_data.extend(arr.flatten().astype(np.int).tolist()) ++ tensor.int32_data.extend(arr.flatten().astype(int).tolist()) + elif arr.dtype == np.int16: + tensor.data_type = caffe2_pb2.TensorProto.INT16 + tensor.int32_data.extend(list(arr.flatten().astype(np.int16))) # np.int16=>pb.INT16 use int32_data +diff --git a/functorch/examples/maml_omniglot/support/omniglot_loaders.py b/functorch/examples/maml_omniglot/support/omniglot_loaders.py +index cac99b2dfbb2aa..ce636ecca0b1b2 100644 +--- a/functorch/examples/maml_omniglot/support/omniglot_loaders.py ++++ b/functorch/examples/maml_omniglot/support/omniglot_loaders.py +@@ -271,10 +271,10 @@ def load_data_cache(self, data_pack): + + # [b, setsz, 1, 84, 84] + x_spts = np.array(x_spts).astype(np.float32).reshape(self.batchsz, setsz, 1, self.resize, self.resize) +- y_spts = np.array(y_spts).astype(np.int).reshape(self.batchsz, setsz) ++ y_spts = np.array(y_spts).astype(int).reshape(self.batchsz, setsz) + # [b, qrysz, 1, 84, 84] + x_qrys = np.array(x_qrys).astype(np.float32).reshape(self.batchsz, querysz, 1, self.resize, self.resize) +- y_qrys = np.array(y_qrys).astype(np.int).reshape(self.batchsz, querysz) ++ y_qrys = np.array(y_qrys).astype(int).reshape(self.batchsz, querysz) + + x_spts, y_spts, x_qrys, y_qrys = [ + torch.from_numpy(z).to(self.device) for z in +diff --git a/test/quantization/core/test_quantized_op.py b/test/quantization/core/test_quantized_op.py +index 252d7b92f77ebb..232150a0ba34a6 100644 +--- a/test/quantization/core/test_quantized_op.py ++++ b/test/quantization/core/test_quantized_op.py +@@ -3840,9 +3840,9 @@ def test_qlinear_with_input_q_dq_qweight_dq_output_fp32( + # xnnpack forces W_zp to 0 when using symmetric quantization + # ONEDNN only supports symmetric quantization of weight + if dtype == torch.qint8 or qengine_is_onednn(): +- W_zps = np.zeros(output_channels).astype(np.int) ++ W_zps = np.zeros(output_channels).astype(int) + else: +- W_zps = np.round(np.random.rand(output_channels) * 100 - 50).astype(np.int) ++ W_zps = np.round(np.random.rand(output_channels) * 100 - 50).astype(int) + # when using symmetric quantization + # special restriction for xnnpack fully connected op weight + # [-127, 127] instead of [-128, 127] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch new file mode 100644 index 00000000000..f63f3cf4c5f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-shift-ops.patch @@ -0,0 +1,253 @@ +From d64fb24ee4a71d8cfe175cafc73c5f90fb26c9ac Mon Sep 17 00:00:00 2001 +From: BJ Hargrave +Date: Tue, 14 Mar 2023 15:30:41 -0400 +Subject: [PATCH 1/2] Fix operator>> for int64 vector in vec256 + +There is no vector instruction for shift right arithmetic for int64. +The operator>> implementation emulates this through other vector +instructions. It has been fixed to properly handle out-of-limit +shift values so that shift values <0 and >64 are set to 64 which +results in a value of -1 for negative inputs and 0 for non-negative +inputs (sign preserving). + +Fixes https://github.com/pytorch/pytorch/issues/70904 + +Signed-off-by: BJ Hargrave +--- + aten/src/ATen/cpu/vec/vec256/vec256_int.h | 16 +++++++++++----- + 1 file changed, 11 insertions(+), 5 deletions(-) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vec256_int.h b/aten/src/ATen/cpu/vec/vec256/vec256_int.h +index 81e9d687d10a7b..784514f49e1d48 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vec256_int.h ++++ b/aten/src/ATen/cpu/vec/vec256/vec256_int.h +@@ -1481,16 +1481,22 @@ Vectorized inline operator<<(const Vectorized& a, const Vector + + template <> + Vectorized inline operator>>(const Vectorized& a, const Vectorized& b) { +- // No vector instruction for right shifting int64_t, so emulating it ++ // No vector instruction for right arithmetic shifting int64_t, so emulating it + // instead. + ++ // Clamp the shift values such that shift values < 0 and > 64 are changed to 64 ++ // which results in -1 for negative input and 0 for non-negative input. ++ __m256i zero = _mm256_set1_epi64x(0); ++ __m256i max_shift = _mm256_set1_epi64x(64); ++ __m256i mask = _mm256_or_si256(_mm256_cmpgt_epi64(zero, b), _mm256_cmpgt_epi64(b, max_shift)); ++ __m256i shift = _mm256_blendv_epi8(b, max_shift, mask); + // Shift the number logically to the right, thus filling the most + // significant bits with 0s. Then, replace these bits with the sign + // bit. +- __m256i sign_bits = _mm256_cmpgt_epi64(_mm256_set1_epi64x(0), a); +- __m256i b_inv_mod_64 = _mm256_sub_epi64(_mm256_set1_epi64x(64), b); +- __m256i sign_ext = _mm256_sllv_epi64(sign_bits, b_inv_mod_64); +- __m256i c = _mm256_srlv_epi64(a, b); ++ __m256i sign_bits = _mm256_cmpgt_epi64(zero, a); ++ __m256i sign_shift = _mm256_sub_epi64(max_shift, shift); ++ __m256i sign_ext = _mm256_sllv_epi64(sign_bits, sign_shift); ++ __m256i c = _mm256_srlv_epi64(a, shift); + c = _mm256_or_si256(c, sign_ext); + + return c; + +From 734e2cea43ee782d756f04bc21c625b8fdd36d31 Mon Sep 17 00:00:00 2001 +From: BJ Hargrave +Date: Mon, 13 Mar 2023 10:56:00 -0400 +Subject: [PATCH 2/2] Fix CPU bitwise shifts for out-of-limit shift values + +Negative shift values and positive shift values greater than the +bit size of the dtype (limit 0..bits) now yield expected results +which are consistent with numpy. + +Left shift with an out-of-limit shift value result in a value of 0. +Right shift with an out-of-limit shift value results in a value of -1 +for negative inputs and 0 for non-negative inputs (sign preserving). + +Fixes https://github.com/pytorch/pytorch/issues/70904 + +Signed-off-by: BJ Hargrave +--- + aten/src/ATen/cpu/vec/vec_base.h | 18 ++++++++-- + aten/src/ATen/native/cpu/BinaryOpsKernel.cpp | 9 +++++ + test/functorch/test_vmap.py | 12 ------- + test/test_binary_ufuncs.py | 37 ++++++++++++++++++++ + 4 files changed, 62 insertions(+), 14 deletions(-) + +diff --git a/aten/src/ATen/cpu/vec/vec_base.h b/aten/src/ATen/cpu/vec/vec_base.h +index cb0e37054b4d32..8f006ae0f6634f 100644 +--- a/aten/src/ATen/cpu/vec/vec_base.h ++++ b/aten/src/ATen/cpu/vec/vec_base.h +@@ -20,6 +20,7 @@ + #include + #include + #include ++#include + + #include + #include +@@ -803,17 +804,30 @@ inline Vectorized operator~(const Vectorized& a) { + } + + template Vectorized inline operator<<(const Vectorized &a, const Vectorized &b) { ++ constexpr T max_shift = sizeof(T) * CHAR_BIT; + Vectorized c; + for (int i = 0; i != Vectorized::size(); i++) { +- c[i] = a[i] << b[i]; ++ T shift = b[i]; ++ if ((static_cast>(shift) < 0) || (shift >= max_shift)) { ++ c[i] = 0; ++ } else { ++ c[i] = static_cast>(a[i]) << shift; ++ } + } + return c; + } + + template Vectorized inline operator>>(const Vectorized &a, const Vectorized &b) { ++ // right shift value to retain sign bit for signed and no bits for unsigned ++ constexpr T max_shift = sizeof(T) * CHAR_BIT - std::is_signed_v; + Vectorized c; + for (int i = 0; i != Vectorized::size(); i++) { +- c[i] = a[i] >> b[i]; ++ T shift = b[i]; ++ if ((static_cast>(shift) < 0) || (shift >= max_shift)) { ++ c[i] = a[i] >> max_shift; ++ } else { ++ c[i] = a[i] >> shift; ++ } + } + return c; + } +diff --git a/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp b/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp +index d0393aaf18bf8b..d2d0892d8ea956 100644 +--- a/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp ++++ b/aten/src/ATen/native/cpu/BinaryOpsKernel.cpp +@@ -316,6 +316,10 @@ void lshift_kernel(TensorIteratorBase& iter) { + AT_DISPATCH_INTEGRAL_TYPES(iter.dtype(), "lshift_cpu", [&]() { + cpu_kernel_vec(iter, + [](scalar_t a, scalar_t b) -> scalar_t { ++ constexpr scalar_t max_shift = sizeof(scalar_t) * CHAR_BIT; ++ if ((static_cast>(b) < 0) || (b >= max_shift)) { ++ return 0; ++ } + return static_cast>(a) << b; + }, + [](Vectorized a, Vectorized b) { +@@ -385,6 +389,11 @@ void rshift_kernel(TensorIteratorBase& iter) { + AT_DISPATCH_INTEGRAL_TYPES(iter.dtype(), "rshift_cpu", [&]() { + cpu_kernel_vec(iter, + [](scalar_t a, scalar_t b) -> scalar_t { ++ // right shift value to retain sign bit for signed and no bits for unsigned ++ constexpr scalar_t max_shift = sizeof(scalar_t) * CHAR_BIT - std::is_signed_v; ++ if ((static_cast>(b) < 0) || (b >= max_shift)) { ++ return a >> max_shift; ++ } + return a >> b; + }, + [](Vectorized a, Vectorized b) { +diff --git a/test/functorch/test_vmap.py b/test/functorch/test_vmap.py +index a5fb144f881880..5c352cf8fdf6f0 100644 +--- a/test/functorch/test_vmap.py ++++ b/test/functorch/test_vmap.py +@@ -27,8 +27,6 @@ + instantiate_parametrized_tests, + subtest, + TEST_WITH_UBSAN, +- IS_MACOS, +- IS_X86 + ) + from torch.testing._internal.common_device_type import \ + toleranceOverride, tol +@@ -46,7 +44,6 @@ + compute_quantities_for_vmap_test, + is_valid_inplace_sample_input, + decorate, +- expectedFailureIf + ) + import types + from collections import namedtuple +@@ -3572,10 +3569,6 @@ def test(): + xfail('addcdiv'), + xfail('addcmul'), + xfail('clamp'), +- # AssertionError: Tensor-likes are not equal! +- xfail('bitwise_left_shift', device_type='cpu'), +- decorate('bitwise_right_shift', device_type='cpu', +- decorator=expectedFailureIf(not (IS_MACOS and IS_X86))), + + # UBSAN: runtime error: shift exponent -1 is negative + decorate('bitwise_left_shift', decorator=unittest.skipIf(TEST_WITH_UBSAN, "Fails with above error")), +@@ -3734,11 +3727,6 @@ def test_vmap_exhaustive(self, device, dtype, op): + xfail('linalg.lu', ''), + skip('linalg.ldl_solve', ''), + skip('_softmax_backward_data'), +- # AssertionError: Tensor-likes are not equal! +- # Issue: https://github.com/pytorch/pytorch/issues/70904 +- xfail('bitwise_left_shift', device_type='cpu'), +- decorate('bitwise_right_shift', device_type='cpu', +- decorator=expectedFailureIf(not (IS_MACOS and IS_X86))), + # UBSAN: runtime error: shift exponent -1 is negative + decorate('bitwise_left_shift', decorator=unittest.skipIf(TEST_WITH_UBSAN, "Fails with above error")), + decorate('bitwise_right_shift', decorator=unittest.skipIf(TEST_WITH_UBSAN, "Fails with above error")), +diff --git a/test/test_binary_ufuncs.py b/test/test_binary_ufuncs.py +index 52d7c7a4ffcb00..bf3e4d43494932 100644 +--- a/test/test_binary_ufuncs.py ++++ b/test/test_binary_ufuncs.py +@@ -4,6 +4,7 @@ + import numpy as np + + import itertools ++from itertools import chain + from itertools import product + import math + import random +@@ -53,6 +54,7 @@ + floating_types_and, + floating_and_complex_types, + get_all_math_dtypes, ++ get_all_int_dtypes, + ) + from torch.testing._internal.common_methods_invocations import ( + binary_ufuncs, +@@ -3139,6 +3141,41 @@ def test_signed_shift(self, device, dtype): + self.assertEqual(a >> 1, expected_r) + self.compare_with_numpy(lambda x: x >> 1, lambda x: np.right_shift(x, 1), a) + ++ @onlyCPU ++ @dtypes(*get_all_int_dtypes()) ++ def test_shift_limits(self, device, dtype): ++ "Ensure that CPU integer bit shifting works as expected with out-of-limits shift values." ++ # Issue #70904 ++ iinfo = torch.iinfo(dtype) ++ bits = iinfo.bits ++ low = iinfo.min ++ high = iinfo.max ++ exact_dtype = dtype != torch.uint8 # numpy changes dtype from uint8 to int16 for some out-of-limits shift values ++ for input in ( ++ torch.tensor([-1, 0, 1], device=device, dtype=dtype), # small for non-vectorized operation ++ torch.tensor([low, high], device=device, dtype=dtype), # small for non-vectorized operation ++ make_tensor((64, 64, 64), low=low, high=high, device=device, dtype=dtype), # large for vectorized operation ++ ): ++ shift_left_expected = torch.zeros_like(input) ++ shift_right_expected = torch.clamp(input, -1, 0) ++ for shift in chain(range(-100, -1), range(bits, 100)): ++ shift_left = input << shift ++ self.assertEqual(shift_left, shift_left_expected, msg=f"<< {shift}") ++ self.compare_with_numpy( ++ lambda x: x << shift, ++ lambda x: np.left_shift(x, shift), ++ input, ++ exact_dtype=exact_dtype, msg=f"<< {shift}" ++ ) ++ shift_right = input >> shift ++ self.assertEqual(shift_right, shift_right_expected, msg=f">> {shift}") ++ self.compare_with_numpy( ++ lambda x: x >> shift, ++ lambda x: np.right_shift(x, shift), ++ input, ++ exact_dtype=exact_dtype, msg=f">> {shift}" ++ ) ++ + @onlyNativeDeviceTypes + @dtypes( + *list( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch new file mode 100644 index 00000000000..101849f4dbf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-skip-decorators.patch @@ -0,0 +1,122 @@ +The decorators are implemented to run when the function is called which is after +the test `setup` method spawned subprocesses which may use NCCL to sync failing when there are +not enough GPUs available. +So replace the custom code by calls to the `unittest` skip decorators. +See hhttps://github.com/pytorch/pytorch/pull/109491 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_distributed.py b/torch/testing/_internal/common_distributed.py +index 400aa80fdca..80a7375cfe1 100644 +--- a/torch/testing/_internal/common_distributed.py ++++ b/torch/testing/_internal/common_distributed.py +@@ -134,17 +134,7 @@ def skip_if_odd_worldsize(func): + + + def require_n_gpus_for_nccl_backend(n, backend): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend == "nccl" and torch.cuda.device_count() < n: +- sys.exit(TEST_SKIPS[f"multi-gpu-{n}"].exit_code) +- else: +- return func(*args, **kwargs) +- +- return wrapper +- +- return decorator ++ return skip_if_lt_x_gpu(n) if backend == "nccl" else unittest.skipIf(False, None) + + + def import_transformers_or_skip(): +@@ -167,32 +157,7 @@ def import_transformers_or_skip(): + + + def skip_if_lt_x_gpu(x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator +- +- +-# This decorator helps avoiding initializing cuda while testing other backends +-def nccl_skip_if_lt_x_gpu(backend, x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend != "nccl": +- return func(*args, **kwargs) +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator ++ return unittest.skipIf(torch.cuda.device_count() < x, TEST_SKIPS[f"multi-gpu-{x}"].message) + + + def verify_ddp_error_logged(model_DDP, err_substr): +diff --git a/torch/testing/_internal/distributed/distributed_test.py b/torch/testing/_internal/distributed/distributed_test.py +index eb5130f2963..25839618308 100644 +--- a/torch/testing/_internal/distributed/distributed_test.py ++++ b/torch/testing/_internal/distributed/distributed_test.py +@@ -56,7 +56,6 @@ from torch.testing._internal.common_distributed import ( + skip_if_small_worldsize, + skip_if_odd_worldsize, + skip_if_lt_x_gpu, +- nccl_skip_if_lt_x_gpu, + skip_if_no_gpu, + require_n_gpus_for_nccl_backend, + requires_nccl_version, +@@ -4960,7 +4959,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4971,7 +4970,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync_grad_is_view(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4982,7 +4981,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync_allreduce_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync +@@ -5010,7 +5009,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_accumulate_gradients_no_sync_allreduce_with_then_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync using allreduce +@@ -5044,7 +5043,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) + def test_get_future(self): + def mult(fut): + return [t * 3 for t in fut.wait()] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch new file mode 100644 index 00000000000..6f3977c99a4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test-ops-conf.patch @@ -0,0 +1,26 @@ +From 8581301957b0018a32433f85163535709bc9d332 Mon Sep 17 00:00:00 2001 +From: Masaki Kozuki +Date: Fri, 7 Oct 2022 21:25:07 -0700 +Subject: [PATCH] try using a different group name + +ref: +https://github.com/pytorch/pytorch/issues/85923#issuecomment-1272220271 + +Signed-off-by: Masaki Kozuki +--- + test/conftest.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/test/conftest.py b/test/conftest.py +index e5af19b760a..c9755322d16 100644 +--- a/test/conftest.py ++++ b/test/conftest.py +@@ -18,7 +18,7 @@ xml_key = StashKey["LogXMLReruns"]() + + + def pytest_addoption(parser: Parser) -> None: +- group = parser.getgroup("terminal reporting") ++ group = parser.getgroup("terminal reporting functorch") + group.addoption( + "--junit-xml-reruns", + action="store", diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch new file mode 100644 index 00000000000..b11903a6de3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-test_memory_profiler.patch @@ -0,0 +1,19 @@ +The test seems to be too sensitive and may fail due to a small temporary allocation. +Increase the filter size to make it pass. +See https://github.com/pytorch/pytorch/issues/109592 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/profiler/test_memory_profiler.py b/test/profiler/test_memory_profiler.py +index 70b21b6b610..176fe153638 100644 +--- a/test/profiler/test_memory_profiler.py ++++ b/test/profiler/test_memory_profiler.py +@@ -1480,7 +1480,7 @@ class TestMemoryProfilerE2E(TestCase): + + # We generally don't care about tiny allocations during memory + # profiling and they add a lot of noise to the unit test. +- if size >= 256 ++ if size >= 1024 + ] + + self.assertExpectedInline( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch new file mode 100644 index 00000000000..0b064c8b4c7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-torch.compile-on-ppc.patch @@ -0,0 +1,39 @@ +commit 9942a14e96c539cb0195475d2cd660dcdc274123 +Author: Nisanth M P +Date: Fri Jul 14 04:09:14 2023 +0000 + + Fix torch.compile g++ flag error on ppc64le (#104956) + + g++ flag -march is not recognised on ppc64le. So adding a check for platform machine to be ppc64le and using -mcpu flag instead. Other architectures will still use -march flag + + This fixes the torch.compile feature failure on ppc64le + + Pull Request resolved: https://github.com/pytorch/pytorch/pull/104956 + Approved by: https://github.com/jgong5, https://github.com/jansel + +diff --git a/torch/_inductor/codecache.py b/torch/_inductor/codecache.py +--- a/torch/_inductor/codecache.py ++++ b/torch/_inductor/codecache.py +@@ -7,6 +7,7 @@ import json + import logging + import multiprocessing + import os ++import platform + import re + import shutil + import signal +@@ -378,7 +379,14 @@ def optimization_flags(): + # Also, `-march=native` is unrecognized option on M1 + base_flags += " -Xclang -fopenmp" + else: +- base_flags += " -march=native -fopenmp" ++ if platform.machine() == "ppc64le": ++ base_flags += " -mcpu=native" ++ else: ++ base_flags += " -march=native" ++ ++ # Internal cannot find libgomp.so ++ if not config.is_fbcode(): ++ base_flags += " -fopenmp" + return base_flags + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch new file mode 100644 index 00000000000..5651f8fbbcf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch @@ -0,0 +1,34 @@ +Casting negative floats to unsigned integers is undefined behavior so results vary between +different invocations and platforms. +This causes failures on e.g. PPC with test_comprehensive_byte in inductor/test_torchinductor_opinfo +See https://github.com/pytorch/pytorch/issues/110077 + +Fix by using `c10::convert` which handles that case. + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/_inductor/codegen/cpp.py b/torch/_inductor/codegen/cpp.py +index de6a32421c1..d16ae4cd91c 100644 +--- a/torch/_inductor/codegen/cpp.py ++++ b/torch/_inductor/codegen/cpp.py +@@ -577,7 +577,7 @@ class CppOverrides(OpOverrides): + @staticmethod + def to_dtype(x, dtype): + assert dtype in DTYPE_TO_CPP, f"{dtype} missing from {__name__}.DTYPE_TO_CPP" +- return f"static_cast<{DTYPE_TO_CPP[dtype]}>({x})" ++ return f"c10::convert<{DTYPE_TO_CPP[dtype]}>({x})" + + @staticmethod + def abs(x): +diff --git a/torch/_inductor/codegen/cpp_prefix.h b/torch/_inductor/codegen/cpp_prefix.h +index e0dba663144..9e17e481a89 100644 +--- a/torch/_inductor/codegen/cpp_prefix.h ++++ b/torch/_inductor/codegen/cpp_prefix.h +@@ -12,6 +12,7 @@ + #endif + #include + #include ++#include + + typedef at::Half half; + typedef at::BFloat16 bfloat16; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch new file mode 100644 index 00000000000..5d8afb76fe5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_fix-vsx-loadu.patch @@ -0,0 +1,31 @@ +Fix access to unitialized memory on PPC +See https://github.com/pytorch/pytorch/issues/32502 & https://github.com/pytorch/pytorch/pull/109487 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h +index 806f6731abb..648ed06afa6 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint8_vsx.h +@@ -91,7 +91,7 @@ struct Vectorized { + vec_vsx_ld(offset0, reinterpret_cast(ptr)), + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; + } +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +index 891c56b53ec..db3698804a7 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +@@ -94,7 +94,7 @@ struct Vectorized { + vec_vsx_ld(offset0, reinterpret_cast(ptr)), + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; + } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch new file mode 100644 index 00000000000..df699c5517e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_no-cuda-stubs-rpath.patch @@ -0,0 +1,186 @@ +# PyTorch's CMAKE configuration by default sets RUNPATH on libraries if they link other libraries +# that are outside the build tree, which is done because of the CMAKE config on +# https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L10. +# This provides problems, since the cuda stubs library path then also gets added to the RUNPATH. +# As a result, at runtime, the stub version of things like libcuda.so.1 gets picked up, instead of the real drivers +# See https://github.com/easybuilders/easybuild-easyconfigs/issues/14359 +# This line https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L16 +# Makes sure that any path that is linked, is also added to the RUNPATH. +# This has been reported upstream in https://github.com/pytorch/pytorch/issues/35418 +# and a fix was attempted in https://github.com/pytorch/pytorch/pull/37737 but it was reverted +# +# This EasyBuild patch changes behavior for the libraries that were failing, i.e. the ones in this list: +# https://github.com/easybuilders/easybuild-easyconfigs/issues/14359#issuecomment-970479904 +# This is done by setting INSTALL_RPATH_USE_LINK_PATH to false, and instead, specifying the RPATH +# explicitely by defining INSTALL_RPATH, but only adding directories that do not match to the "stubs" regex +# +# Original patch: Caspar van Leeuwen +# Updated: Alexander Grund (TU Dresden) +# +# See https://github.com/pytorch/pytorch/pull/87593 + +diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt +index 221e3f32b29..c3f24060f6a 100644 +--- a/caffe2/CMakeLists.txt ++++ b/caffe2/CMakeLists.txt +@@ -627,14 +627,13 @@ endif() + if(USE_CUDA) + list(APPEND Caffe2_GPU_CU_SRCS ${Caffe2_GPU_HIP_JIT_FUSERS_SRCS}) + add_library(caffe2_nvrtc SHARED ${ATen_NVRTC_STUB_SRCS}) ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB}) + if(MSVC) + # Delay load nvcuda.dll so we can import torch compiled with cuda on a CPU-only machine +- set(DELAY_LOAD_FLAGS "-DELAYLOAD:nvcuda.dll;delayimp.lib") +- else() +- set(DELAY_LOAD_FLAGS "") ++ target_link_libraries(caffe2_nvrtc "-DELAYLOAD:nvcuda.dll;delayimp.lib") + endif() + +- target_link_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB} ${DELAY_LOAD_FLAGS}) + target_include_directories(caffe2_nvrtc PRIVATE ${CUDA_INCLUDE_DIRS}) + install(TARGETS caffe2_nvrtc DESTINATION "${TORCH_INSTALL_LIB_DIR}") + if(USE_NCCL) +diff --git a/cmake/LinkCudaLibraries.cmake b/cmake/LinkCudaLibraries.cmake +new file mode 100644 +index 00000000000..005914ccc6f +--- /dev/null ++++ b/cmake/LinkCudaLibraries.cmake +@@ -0,0 +1,33 @@ ++# Link CUDA libraries to the given target, i.e.: `target_link_libraries(target )` ++# ++# Additionally makes sure CUDA stub libs don't end up being in RPath ++# ++# Example: link_cuda_libraries(mytarget PRIVATE ${CUDA_LIBRARIES}) ++function(link_cuda_libraries target) ++ set(libs ${ARGN}) ++ set(install_rpath "$ORIGIN") ++ set(filtered FALSE) ++ foreach(lib IN LISTS libs) ++ # CUDA stub libs are in form /prefix/lib/stubs/libcuda.so ++ # So extract the name of the parent folder, to check against "stubs" ++ # And the parent path which we need to add to the INSTALL_RPATH for non-stubs ++ get_filename_component(parent_path "${lib}" DIRECTORY) ++ get_filename_component(parent_name "${parent_path}" NAME) ++ if(parent_name STREQUAL "stubs") ++ message(STATUS "Filtering ${lib} from being set in ${target}'s RPATH, " ++ "because it appears to point to the CUDA stubs directory.") ++ set(filtered TRUE) ++ elseif(parent_path) ++ list(APPEND install_rpath ${parent_path}) ++ endif() ++ endforeach() ++ ++ # Regular link command ++ target_link_libraries(${target} ${libs}) ++ # Manually set INSTALL_RPATH when there were any stub libs ++ if(filtered) ++ list(REMOVE_DUPLICATES install_rpath) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH "${install_rpath}") ++ endif() ++endfunction() +diff --git a/test/cpp/api/CMakeLists.txt b/test/cpp/api/CMakeLists.txt +index 6b801a07318..6ac92870479 100644 +--- a/test/cpp/api/CMakeLists.txt ++++ b/test/cpp/api/CMakeLists.txt +@@ -54,7 +54,8 @@ if(NOT MSVC) + endif() + + if(USE_CUDA) +- target_link_libraries(test_api PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_api PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/dist_autograd/CMakeLists.txt b/test/cpp/dist_autograd/CMakeLists.txt +index 9969c63e16d..356ba5be55c 100644 +--- a/test/cpp/dist_autograd/CMakeLists.txt ++++ b/test/cpp/dist_autograd/CMakeLists.txt +@@ -10,7 +10,8 @@ if(USE_DISTRIBUTED AND NOT WIN32) + target_link_libraries(test_dist_autograd PRIVATE torch gtest) + + if(USE_CUDA) +- target_link_libraries(test_dist_autograd PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_dist_autograd PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/jit/CMakeLists.txt b/test/cpp/jit/CMakeLists.txt +index 2376f1bc43b..30fbb99fa6d 100644 +--- a/test/cpp/jit/CMakeLists.txt ++++ b/test/cpp/jit/CMakeLists.txt +@@ -139,7 +139,8 @@ if(LINUX) + endif() + + if(USE_CUDA) +- target_link_libraries(test_jit PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_jit PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/rpc/CMakeLists.txt b/test/cpp/rpc/CMakeLists.txt +index 3997f8753e5..21fddbc645d 100644 +--- a/test/cpp/rpc/CMakeLists.txt ++++ b/test/cpp/rpc/CMakeLists.txt +@@ -33,7 +33,8 @@ target_include_directories( + target_link_libraries(test_cpp_rpc PRIVATE ${TORCH_RPC_TEST_DEPENDENCY_LIBS}) + + if(USE_CUDA) +- target_link_libraries(test_cpp_rpc PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_cpp_rpc PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/tensorexpr/CMakeLists.txt b/test/cpp/tensorexpr/CMakeLists.txt +index 7dff70630d3..ecb83005492 100644 +--- a/test/cpp/tensorexpr/CMakeLists.txt ++++ b/test/cpp/tensorexpr/CMakeLists.txt +@@ -57,14 +57,15 @@ if(USE_PTHREADPOOL) + target_link_libraries(test_tensorexpr PRIVATE pthreadpool_interface) + endif() + if(USE_CUDA) +- target_link_libraries(test_tensorexpr PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + target_compile_definitions(test_tensorexpr PRIVATE USE_CUDA) + +- target_link_libraries(tutorial_tensorexpr PRIVATE ++ link_cuda_libraries(tutorial_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/test_torch.py b/test/test_torch.py +index c86535e22c0..6859311d806 100644 +--- a/test/test_torch.py ++++ b/test/test_torch.py +@@ -8833,6 +8833,21 @@ def add_neg_dim_tests(): + assert not hasattr(TestTorch, test_name), "Duplicated test name: " + test_name + setattr(TestTorch, test_name, make_neg_dim_test(name, tensor_arg, arg_constr, types, extra_dim)) + ++class TestRPATH(TestCase): ++ @unittest.skipIf(not sys.platform.startswith('linux'), "linux-only test") ++ def test_rpath(self): ++ """ ++ Make sure RPATH (or RUNPATH) in nvrtc does not contain a cuda stubs directory ++ issue gh-35418 ++ """ ++ libdir = os.path.join(os.path.dirname(torch._C.__file__), 'lib') ++ caffe2_nvrtc = os.path.join(libdir, 'libcaffe2_nvrtc.so') ++ if os.path.exists(caffe2_nvrtc): ++ output = subprocess.check_output(['objdump', '-x', caffe2_nvrtc]) ++ for line in output.split(b'\n'): ++ if b'RPATH' in line or b'RUNPATH' in line: ++ self.assertFalse(b'stubs' in line) ++ + # TODO: these empy classes are temporarily instantiated for XLA compatibility + # once XLA updates their test suite it should be removed + class TestViewOps(TestCase): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch new file mode 100644 index 00000000000..4022d01c852 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_remove-test-requiring-online-access.patch @@ -0,0 +1,30 @@ +This downloads a Perl file from a Github repo which may fail in: + + File "test/test_cuda.py", line 4632, in test_memory_snapshot + torch.cuda.memory._save_segment_usage(f.name) + File "/torch/cuda/memory.py", line 610, in _save_segment_usage + f.write(_segments(snapshot)) + File "/torch/cuda/_memory_viz.py", line 60, in segments + return format_flamegraph(f.getvalue()) + File "/torch/cuda/_memory_viz.py", line 21, in format_flamegraph + urllib.request.urlretrieve( + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_cuda.py b/test/test_cuda.py +index 7f2693b52c5..4bff69e5cad 100644 +--- a/test/test_cuda.py ++++ b/test/test_cuda.py +@@ -4993,12 +4993,6 @@ class TestCudaComm(TestCase): + found_it = True + self.assertTrue(found_it) + +- if not IS_WINDOWS: +- with tempfile.NamedTemporaryFile() as f: +- torch.cuda.memory._save_segment_usage(f.name) +- with open(f.name, 'r') as f2: +- self.assertTrue('test_cuda.py' in f2.read()) +- + del x + torch.cuda.empty_cache() + ss = torch.cuda.memory._snapshot() diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch new file mode 100644 index 00000000000..41d0da2eb03 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-diff-test-on-ppc.patch @@ -0,0 +1,26 @@ +The workaround for over/underflow isn't implemented for PPC yet. +So skip the test. +See https://github.com/pytorch/pytorch/issues/109870 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_binary_ufuncs.py b/test/test_binary_ufuncs.py +index 57fc1b76f18..06c129e007a 100644 +--- a/test/test_binary_ufuncs.py ++++ b/test/test_binary_ufuncs.py +@@ -27,6 +27,7 @@ from torch.testing._internal.common_utils import ( + numpy_to_torch_dtype_dict, + TEST_SCIPY, + set_default_dtype, ++ IS_PPC, + ) + from torch.testing._internal.common_device_type import ( + expectedFailureMeta, +@@ -1091,6 +1092,7 @@ class TestBinaryUfuncs(TestCase): + ) + + @dtypes(*complex_types()) ++ @skipIf(IS_PPC, "Vectorized div fails on PPC: #109870") + def test_complex_div_underflow_overflow(self, device, dtype): + # test to make sure the complex division does not produce underflow or overflow + # in the intermediate of its calculations diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch new file mode 100644 index 00000000000..19d427b3049 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-failing-gradtest.patch @@ -0,0 +1,16 @@ +test_fn_grad_linalg_det_singular_cpu_float64 fails not only on macos + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/opinfo/definitions/linalg.py b/torch/testing/_internal/opinfo/definitions/linalg.py +index 616c8cf42f4..3a07d19df46 100644 +--- a/torch/testing/_internal/opinfo/definitions/linalg.py ++++ b/torch/testing/_internal/opinfo/definitions/linalg.py +@@ -1135,7 +1135,6 @@ op_db: List[OpInfo] = [ + "test_fn_grad", + device_type="cpu", + dtypes=(torch.float64,), +- active_if=IS_MACOS, + ), + DecorateInfo( + unittest.skip("Gradients are incorrect on macos"), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch new file mode 100644 index 00000000000..f02e5d3ab0d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch @@ -0,0 +1,20 @@ +The test fails on some systems with +> RuntimeError: Too many open files. Communication with the workers is no longer possible. +> Please increase the limit using `ulimit -n` in the shell or change the sharing strategy by calling `torch.multiprocessing.set_sharing_strategy('file_system')` at the beginning of your code + +So just skip it. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_dataloader.py b/test/test_dataloader.py +index 39d91876f0b..aff47063344 100644 +--- a/test/test_dataloader.py ++++ b/test/test_dataloader.py +@@ -1542,6 +1542,7 @@ except RuntimeError as e: + def test_shuffle_batch(self): + self._test_shuffle(self._get_data_loader(self.dataset, batch_size=2, shuffle=True)) + ++ @unittest.skip("May cause 'Too many open files' error due to potential `ulimit -n` restrictions") + def test_shuffle_reproducibility(self): + for fn in ( + lambda: DataLoader(self.dataset, shuffle=True, num_workers=0, generator=torch.Generator().manual_seed(42)), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch new file mode 100644 index 00000000000..8e80dec749f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch @@ -0,0 +1,34 @@ +Use unittest.skip to skip tests skipped by subprocesses as otherwise skipped tests +marked as expectedFailure may succeed unexpectatly failing the testsuite. +E.g.: +> INFO:torch.testing._internal.common_distributed:Thread 0 skipping test > for following reason: PyTorch is built without MKL support +> INFO:torch.testing._internal.common_distributed:Thread 1 skipping test > for following reason: PyTorch is built without MKL support +> INFO:torch.testing._internal.common_distributed:Skipping > on sandcastle for the following reason: Test skipped at subprocess level, look at subprocess log for skip reason +> u +> ... +> FAILED (unexpected successes=1) + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_distributed.py b/torch/testing/_internal/common_distributed.py +index 400aa80fdca..afea4a8f89f 100644 +--- a/torch/testing/_internal/common_distributed.py ++++ b/torch/testing/_internal/common_distributed.py +@@ -828,7 +828,7 @@ class MultiProcessTestCase(TestCase): + ) + for skip in TEST_SKIPS.values(): + if first_process.exitcode == skip.exit_code: +- if IS_SANDCASTLE: ++ if False: + # Don't use unittest.skip to skip the test on sandcastle + # since it creates tasks for skipped tests assuming there + # is some follow-up needed. Instead just "pass" the test +@@ -1123,7 +1123,7 @@ class MultiThreadedTestCase(TestCase): + if skip_code > 0: + for skip in TEST_SKIPS.values(): + if skip_code == skip.exit_code: +- if IS_SANDCASTLE: ++ if False: + # "pass" the test with an appropriate message. + logger.info( + f"Skipping {fn} on sandcastle for the following reason: {skip.message}" From c1c1ef069def6d08e76dfa426ba99be738905d59 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Tue, 24 Oct 2023 12:14:34 +0000 Subject: [PATCH 9246/9987] adding easyconfigs: Seurat-4.4.0-foss-2022b-R-4.2.2.eb --- .../Seurat/Seurat-4.4.0-foss-2022b-R-4.2.2.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.4.0-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.4.0-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.4.0-foss-2022b-R-4.2.2.eb new file mode 100644 index 00000000000..2b65e56b170 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.4.0-foss-2022b-R-4.2.2.eb @@ -0,0 +1,76 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.4.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} + +exts_list = [ + ('Matrix', '1.6-1.1', { + 'checksums': ['331eb1f1fe9441d4224d8551072443596001b50e8c15618f59cb938b46ee8cc2'], + }), + ('sp', '1.5-1', { + 'checksums': ['69b9eab481d389bbb736d2adcf50c180aca248c3ffc4ebda8ffe2accc5f229df'], + }), + ('SeuratObject', '4.1.4', { + 'checksums': ['74e7649ad9795c962c0b12d039d7bf9b11a8a275a63c3a0fa1205b684e5310ef'], + }), + ('sctransform', '0.4.0', { + 'checksums': ['9aef10c196a9578e0d7a8e244c55cf28eb0685947d9df9e2d7790c2b99c6b4b3'], + }), + ('uwot', '0.1.14', { + 'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'], + }), + ('spatstat.utils', '3.0-1', { + 'checksums': ['cba1c7806564fd9145ca15edf77233d6ba5609f0989f7812221f5fc1ece0b91a'], + }), + ('spatstat.data', '3.0-0', { + 'checksums': ['cff9058a88489020a4a05b9576cd452f37fa9b42084873c474d06931f5187057'], + }), + ('spatstat.geom', '3.0-3', { + 'checksums': ['6e5b56c60e774a0cdcaa5a8ffde071225f233832446a341588bd8a7840913c84'], + }), + ('spatstat.random', '3.0-1', { + 'checksums': ['938c845c063b8781bf894c0a67537e7b2a7c425a4beba4a95ec9d2c37b43e5b6'], + }), + ('spatstat.sparse', '3.0-0', { + 'checksums': ['99be0a3c7592760fdf1668dc0811f75ed91c400390d1ecc3d5e643255f501ad2'], + }), + ('spatstat.explore', '3.0-5', { + 'checksums': ['9f438a12fac3f3e1d0bd550b1393c1e5732be694517b0878db09da557d6dc862'], + }), + ('scattermore', '1.2', { + 'checksums': ['5534a87b0bdd1375f0fbffc1a5c980ad64e33a108435a67469b8324b580602d1'], + }), + (name, version, { + 'checksums': ['0f17df9597642cfc1db4d8718f0b59ebab9fbed328b1f885f42ee85ea0dcb4dd'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 8cb39a13f7eaa0a022b0b037cf7024c89903d2ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 Oct 2023 14:45:50 +0200 Subject: [PATCH 9247/9987] adding easyconfigs: MEGAN-6.25.3-Java-17.eb --- .../m/MEGAN/MEGAN-6.25.3-Java-17.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAN/MEGAN-6.25.3-Java-17.eb diff --git a/easybuild/easyconfigs/m/MEGAN/MEGAN-6.25.3-Java-17.eb b/easybuild/easyconfigs/m/MEGAN/MEGAN-6.25.3-Java-17.eb new file mode 100644 index 00000000000..6d8ff7d7664 --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAN/MEGAN-6.25.3-Java-17.eb @@ -0,0 +1,35 @@ +easyblock = 'Binary' + +name = 'MEGAN' +version = '6.25.3' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://megan.informatik.uni-tuebingen.de/' +description = "MEGAN is a comprehensive toolbox for interactively analyzing microbiome data" + +toolchain = SYSTEM + +local_installer = '%%(name)s_Community_unix_%s.sh' % version.replace('.', '_') + +source_urls = ['https://software-ab.cs.uni-tuebingen.de/download/megan%(version_major)s/'] +sources = [local_installer] +checksums = ['0dcb317250f12e8a193442d9710f3bce2a9bbce79e509dd1d2f54d337c988e62'] + +dependencies = [('Java', '17')] + +install_cmd = 'chmod +x %s && ./%s -q -dir %%(installdir)s' % (local_installer, local_installer) + +postinstallcmds = ["rm %(installdir)s/uninstall"] + +sanity_check_paths = { + 'files': ['MEGAN'], + 'dirs': ['jars', 'jars2', 'tools'], +} + +sanity_check_commands = ["megan-server --help"] + +modextrapaths = { + 'PATH': ['tools', 'tools/utils'], +} + +moduleclass = 'bio' From 05c56f212f710533eb1b932d13666642cc93dde9 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 24 Oct 2023 19:00:11 +0200 Subject: [PATCH 9248/9987] adding easyconfigs: gff3tool-2.1.0-foss-2022a.eb and patches: GFF3toolkit-2.1.0-remove_hardcode.patch --- .../GFF3toolkit-2.1.0-remove_hardcode.patch | 88 +++++++++++++++++++ .../g/gff3tool/gff3tool-2.1.0-foss-2022a.eb | 28 ++++++ 2 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch create mode 100644 easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch b/easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch new file mode 100644 index 00000000000..99aa1e1e734 --- /dev/null +++ b/easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch @@ -0,0 +1,88 @@ +This patch removes the hardcoded part of the setup.py that downloads and installs BLAST+ +Author: Orient Kružík (INUITS) +diff -ruN gff3tool-2.1.0_orig/setup.py gff3tool-2.1.0/setup.py +--- gff3tool-2.1.0_orig/setup.py 2023-10-22 17:15:12.175583000 +0200 ++++ gff3tool-2.1.0/setup.py 2023-10-22 17:20:48.098956000 +0200 +@@ -6,69 +6,12 @@ + """ + # Always prefer setuptools over distutils + from setuptools import setup, find_packages +-from distutils.command.build import build + # To use a consistent encoding + from codecs import open +-from os import path, remove, mkdir +-import shutil +-import tarfile +-try: +- from urllib.request import urlretrieve +-except ImportError: +- from urllib import urlretrieve +- +-import platform +-import sys +-from wheel.bdist_wheel import bdist_wheel as _bdist_wheel +- ++from os import path + + here = path.abspath(path.dirname(__file__)) + +- +-class bdist_wheel(_bdist_wheel): +- def finalize_options(self): +- _bdist_wheel.finalize_options(self) +- # Mark us as not a pure python package +- self.root_is_pure = False +- +-class CustomBuildCommand(build): +- def run(self): +- platform_system = platform.system( +- ) # Linux: Linux; Mac:Darwin; Windows: Windows +- +- blast_path = path.join(here, 'gff3tool', 'lib', 'ncbi-blast+') +- blast_file = path.join(blast_path, 'blast.tgz') +- +- mkdir(blast_path) +- +- if platform_system == 'Linux': +- urlretrieve( +- 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-linux.tar.gz', +- blast_file) +- elif platform_system == 'Windows': +- urlretrieve( +- 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-win64.tar.gz', +- blast_file) +- elif platform_system == 'Darwin': +- urlretrieve( +- 'https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-universal-macosx.tar.gz', +- blast_file) +- else: +- sys.error( +- 'GFF3 Toolkit currently only supports linux, windows, and MacOS' +- ) +- +- tar = tarfile.open(blast_file, 'r:gz') +- tar.extractall(blast_path) +- tar.close() +- +- extract_path = path.join(blast_path, 'ncbi-blast-2.2.31+') +- shutil.move(path.join(extract_path, 'bin'), blast_path) +- if path.exists(blast_file): +- remove(blast_file) +- if path.exists(extract_path): +- shutil.rmtree(extract_path) +- + # Get the long description from the README file + with open(path.join(here, 'README.md'), encoding='utf-8') as f: + long_description = f.read() +@@ -170,11 +113,6 @@ + # + packages=find_packages(exclude=['contrib', 'docs', 'tests']), # Required + +- cmdclass={ +- 'build': CustomBuildCommand, +- 'bdist_wheel': bdist_wheel +- }, +- + # This field lists other packages that your project depends on to run. + # Any package you put here will be installed by pip when your project is + # installed, so they must be valid existing projects. diff --git a/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb new file mode 100644 index 00000000000..ccc79b535ad --- /dev/null +++ b/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'gff3tool' +version = '2.1.0' + +homepage = 'https://gff3toolkit.readthedocs.io' +description = 'Python programs for processing GFF3 files' + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = ['gff3tool-2.1.0.tar.gz'] +patches = ['GFF3toolkit-2.1.0-remove_hardcode.patch'] +checksums = [ + {'gff3tool-2.1.0.tar.gz': 'e842ef4afdb66926a2b63bf2619c7ef30bd9b76a5f1084a5c57bf8b39cc4f15d'}, + {'GFF3toolkit-2.1.0-remove_hardcode.patch': '03696635af25ab1e3d650b46c7aeaaaadb31e7eac766039c758150f3f3162cb7'}, +] + +local_blast_path = '%(installdir)s/lib/python%(pyshortver)s/site-packages/gff3tool/lib/ncbi-blast+' +preinstallopts = 'mkdir -p %s && ' % local_blast_path +preinstallopts += 'ln -s $EBROOTBLASTPLUS/bin %s && ' % local_blast_path + +dependencies = [ + ('Python', '3.10.4'), + ('BLAST+', '2.13.0'), +] + +use_pip = True +sanity_pip_check = True From 8366961f534d57a2ec2ccb8368c6cdedf0a3f8b0 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 24 Oct 2023 21:01:25 +0200 Subject: [PATCH 9249/9987] Added moduleclass and set download_dep_fail --- easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb index ccc79b535ad..80f979fe27c 100644 --- a/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb @@ -26,3 +26,6 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True + +moduleclass = "tools" From 9641a552153c5ba1ac4bed5b378e33d22bbfef80 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Tue, 24 Oct 2023 21:29:36 +0000 Subject: [PATCH 9250/9987] Update to release with fix for problem with the ROSS dependency --- .../m/Mashtree/Mashtree-1.4.6-GCC-12.2.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.6-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.6-GCC-12.2.0.eb b/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.6-GCC-12.2.0.eb new file mode 100644 index 00000000000..0b08019f1de --- /dev/null +++ b/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.6-GCC-12.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'Bundle' + +name = 'Mashtree' +version = '1.4.6' + +description = "Create a tree using Mash distances." + +homepage = 'https://github.com/lskatz/mashtree' + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +builddependencies = [ + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('Perl', '5.36.0'), + ('BioPerl', '1.7.8'), + ('Mash', '2.3'), + ('QuickTree', '2.5'), +] + +# this is a bundle of Perl modules +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", '') + +exts_list = [ + ('Class::Interface', '1.01', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SINISTER/'], + 'sources': ['Class-Interface-1.01.tar.gz'], + 'checksums': ['9fba15cda745ad37f451a0b9e698da3dfc12c2e8589016416a1e3ad77e444b7b'], + }), + ('Bio::Sketch', '0.3', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LS/LSKATZ/'], + 'sources': ['Bio-Sketch-0.3.tar.gz'], + 'checksums': ['7ac38552c80ae38e0c72ba3cfa4ecf667aca8b4080616415027bcba1420c8ae2'], + }), + ('Bio::Sketch::Mash', '0.9', { + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LS/LSKATZ/'], + 'sources': ['Bio-Sketch-Mash-0.9.tar.gz'], + 'checksums': ['ea15858bc75674e22bb26d570d5f94c1b4eb5476bbc7bbabdf07359ebd041280'], + }), + (name, version, { + 'source_urls': ['https://github.com/lskatz/mashtree/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['1bd427aba025886d9df99c95f685e06dc2226bca080a64a9cb9d341b5a3d6dac'], + }), +] + +sanity_check_paths = { + 'files': ['bin/mashtree'], + 'dirs': [] +} + +modextrapaths = {'PERL5LIB': [ + 'lib/perl5/site_perl/%(perlver)s', + 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi', +]} + +sanity_check_commands = ["mashtree -h"] + +moduleclass = 'bio' From 6d4941fe9673ecdb22dc00eefd2e13ef70e4ba3c Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 24 Oct 2023 22:30:31 +0100 Subject: [PATCH 9251/9987] Remove obsolete Mashtree easyconfig --- .../m/Mashtree/Mashtree-1.4.0-GCC-12.2.0.eb | 62 ------------------- 1 file changed, 62 deletions(-) delete mode 100644 easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.0-GCC-12.2.0.eb b/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.0-GCC-12.2.0.eb deleted file mode 100644 index 1c374289a6d..00000000000 --- a/easybuild/easyconfigs/m/Mashtree/Mashtree-1.4.0-GCC-12.2.0.eb +++ /dev/null @@ -1,62 +0,0 @@ -easyblock = 'Bundle' - -name = 'Mashtree' -version = '1.4.0' - -description = "Create a tree using Mash distances." - -homepage = 'https://github.com/lskatz/mashtree' - -toolchain = {'name': 'GCC', 'version': '12.2.0'} - -builddependencies = [ - ('pkgconf', '1.9.3'), -] - -dependencies = [ - ('Perl', '5.36.0'), - ('BioPerl', '1.7.8'), - ('Mash', '2.3'), - ('QuickTree', '2.5'), -] - -# this is a bundle of Perl modules -exts_defaultclass = 'PerlModule' -exts_filter = ("perl -e 'require %(ext_name)s'", '') - -exts_list = [ - ('Class::Interface', '1.01', { - 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SINISTER/'], - 'sources': ['Class-Interface-1.01.tar.gz'], - 'checksums': ['9fba15cda745ad37f451a0b9e698da3dfc12c2e8589016416a1e3ad77e444b7b'], - }), - ('Bio::Sketch', '0.3', { - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LS/LSKATZ/'], - 'sources': ['Bio-Sketch-0.3.tar.gz'], - 'checksums': ['7ac38552c80ae38e0c72ba3cfa4ecf667aca8b4080616415027bcba1420c8ae2'], - }), - ('Bio::Sketch::Mash', '0.9', { - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LS/LSKATZ/'], - 'sources': ['Bio-Sketch-Mash-0.9.tar.gz'], - 'checksums': ['ea15858bc75674e22bb26d570d5f94c1b4eb5476bbc7bbabdf07359ebd041280'], - }), - (name, version, { - 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LS/LSKATZ/'], - 'sources': ['Mashtree-1.4.0.tar.gz'], - 'checksums': ['aadb74acbbebcc073e1bd3e1dc96647142bd812f7101d8c1c0989d032829b106'], - }), -] - -sanity_check_paths = { - 'files': ['bin/mashtree'], - 'dirs': [] -} - -modextrapaths = {'PERL5LIB': [ - 'lib/perl5/site_perl/%(perlver)s', - 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi', -]} - -sanity_check_commands = ["mashtree -h"] - -moduleclass = 'bio' From b830c2ea1489047259b62de1265945481b56939e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 00:16:33 +0200 Subject: [PATCH 9252/9987] adding easyconfigs: GDB-13.2-GCCcore-13.2.0.eb, MPC-1.3.1-GCCcore-13.2.0.eb, ISL-0.26-GCCcore-13.2.0.eb, makeinfo-7.1-GCCcore-13.2.0.eb --- .../g/GDB/GDB-13.2-GCCcore-13.2.0.eb | 44 +++++++++++++++++++ .../i/ISL/ISL-0.26-GCCcore-13.2.0.eb | 23 ++++++++++ .../m/MPC/MPC-1.3.1-GCCcore-13.2.0.eb | 35 +++++++++++++++ .../m/makeinfo/makeinfo-7.1-GCCcore-13.2.0.eb | 25 +++++++++++ 4 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-7.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..574aef91ec3 --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '13.2' + +homepage = 'https://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['fd5bebb7be1833abdb6e023c2f498a354498281df9d05523d8915babeb893f0a'] + +builddependencies = [ + ('binutils', '2.40'), + ('makeinfo', '7.1'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('expat', '2.5.0'), + ('Python', '3.11.5'), + ('ISL', '0.26'), + ('MPC', '1.3.1'), +] + +preconfigopts = "mkdir obj && cd obj && " +configure_cmd_prefix = '../' +prebuildopts = "cd obj && " +preinstallopts = prebuildopts + +configopts = '--with-system-zlib --with-system-readline --with-expat=$EBROOTEXPAT ' +configopts += '--with-python=$EBROOTPYTHON/bin/python --with-isl=$EBROOTISL --with-mpc=$EBROOTMPC ' +configopts += '--enable-tui --enable-plugins --disable-install-libbfd ' + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0454bbaa21d --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.26-GCCcore-13.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.26' + +homepage = 'https://libisl.sourceforge.io' +description = "isl is a library for manipulating sets and relations of integer points bounded by linear constraints." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://libisl.sourceforge.io'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('GMP', '6.3.0')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..e4b06ad227b --- /dev/null +++ b/easybuild/easyconfigs/m/MPC/MPC-1.3.1-GCCcore-13.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.3.1' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/mpc/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('GMP', '6.3.0'), + ('MPFR', '4.2.1'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-7.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-7.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..78b42628b50 --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-7.1-GCCcore-13.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '7.1' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['deeec9f19f159e046fdf8ad22231981806dac332cc372f1c763504ad82b30953'] + +builddependencies = [('binutils', '2.40')] +dependencies = [('Perl', '5.38.0')] + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' From bf546cdba0b030973b77d4db412cd0bc5bc1fb6d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 00:18:21 +0200 Subject: [PATCH 9253/9987] adding easyconfigs: Tk-8.6.13-GCCcore-13.2.0.eb, Tkinter-3.11.5-GCCcore-13.2.0.eb --- .../t/Tk/Tk-8.6.13-GCCcore-13.2.0.eb | 40 +++++++++++++++++++ .../Tkinter/Tkinter-3.11.5-GCCcore-13.2.0.eb | 25 ++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.5-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..966857de663 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.13-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.13' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.13_different-prefix-with-tcl.patch'] +checksums = [ + {'tk8.6.13-src.tar.gz': '2e65fa069a23365440a3c56c556b8673b5e32a283800d8d9b257e3f584ce0675'}, + {'Tk-8.6.13_different-prefix-with-tcl.patch': 'e136ff60dfe7fc4b14d98af00cf89522fbfd106e75b0a9259f410a8bfa732534'}, +] + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Tcl', version), + ('X11', '20231019'), + ('zlib', '1.2.13'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..0b58e634a69 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.11.5-GCCcore-13.2.0.eb @@ -0,0 +1,25 @@ +name = 'Tkinter' +version = '3.11.5' + +homepage = 'https://python.org/' +description = "Tkinter module, built with the Python buildsystem" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['a12a0a013a30b846c786c010f2c19dd36b7298d888f7c4bd1581d90ce18b5e58'] + +builddependencies = [ + ('binutils', '2.40'), + ('libffi', '3.4.4'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Tk', '8.6.13'), + ('zlib', '1.2.13'), +] + +moduleclass = 'lang' From 7f651c205a8d5c00c3bdc385fa7611e9ae0152a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 00:35:44 +0200 Subject: [PATCH 9254/9987] adding easyconfigs: OpenEXR-3.2.0-GCCcore-13.2.0.eb, Imath-3.1.9-GCCcore-13.2.0.eb, libwebp-1.3.2-GCCcore-13.2.0.eb, giflib-5.2.1-GCCcore-13.2.0.eb, OpenJPEG-2.5.0-GCCcore-13.2.0.eb --- .../g/giflib/giflib-5.2.1-GCCcore-13.2.0.eb | 28 ++++++++++++ .../i/Imath/Imath-3.1.9-GCCcore-13.2.0.eb | 28 ++++++++++++ .../l/libwebp/libwebp-1.3.2-GCCcore-13.2.0.eb | 44 +++++++++++++++++++ .../o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb | 38 ++++++++++++++++ .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-13.2.0.eb | 42 ++++++++++++++++++ 5 files changed, 180 insertions(+) create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.3.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..aa13dd4df30 --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.1' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..85fb3db262c --- /dev/null +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Imath' +version = '3.1.9' + +homepage = 'https://imath.readthedocs.io/en/latest/' +description = """ +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bff1fa140f4af0e7f02c6cb78d41b9a7d5508e6bcdfda3a583e35460eb6d4b47'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['lib/libImath.%s' % SHLIB_EXT], + 'dirs': ['include/Imath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2d6e433838e --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.2-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.3.2' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2a499607df669e40258e53d0ade8035ba4ec0175244869d1025d460562aa09b4'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('LibTIFF', '4.6.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + +sanity_check_paths = { + 'files': ( + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ), + 'dirs': ['lib/'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..fd36bca88b3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.2.0' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['78dbca39115a1c526e6728588753955ee75fa7f5bb1a6e238bed5b6d66f91fd7'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] +dependencies = [ + ('Imath', '3.1.9'), + ('zlib', '1.2.13') +] + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..9905775a89f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.0' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.13'), + ('libpng', '1.6.40'), + ('LibTIFF', '4.6.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' From ad517a4fbc87fcf8feecd9795ae66133464aea81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 00:36:32 +0200 Subject: [PATCH 9255/9987] adding easyconfigs: Yasm-1.3.0-GCCcore-13.2.0.eb, x264-20231019-GCCcore-13.2.0.eb, x265-3.5-GCCcore-13.2.0.eb --- .../x/x264/x264-20231019-GCCcore-13.2.0.eb | 33 ++++++++++++++++++ .../x/x265/x265-3.5-GCCcore-13.2.0.eb | 34 +++++++++++++++++++ .../y/Yasm/Yasm-1.3.0-GCCcore-13.2.0.eb | 24 +++++++++++++ 3 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a1d60486ce0 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20231019-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20231019' + +homepage = 'https://www.videolan.org/developers/x264.html' +description = """ + x264 is a free software library and application for encoding video streams + into the H.264/MPEG-4 AVC compression format, and is released under the + terms of the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://code.videolan.org/videolan/%(name)s/-/archive/baee400f/'] +sources = [{'download_filename': '%(name)s-9c3c7168.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['bf6a61dcc7e1f4e623a44f09de02e843f06e7ec14f807557b43130fc84287f29'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('NASM', '2.16.01'), +] + +configopts = " --enable-shared --enable-static --disable-bashcompletion" + + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x264_config.h', 'include/%(name)s.h', 'lib/libx264.a', 'lib/libx264.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d1bca35c8d7 --- /dev/null +++ b/easybuild/easyconfigs/x/x265/x265-3.5-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'x265' +version = '3.5' + +homepage = 'https://x265.org/' +description = """ + x265 is a free software library and application for encoding video streams + into the H.265 AVC compression format, and is released under the terms of + the GNU GPL. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://bitbucket.org/multicoreware/x265_git/downloads/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['e70a3335cacacbba0b3a20ec6fecd6783932288ebc8163ad74bcc9606477cae8'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('Yasm', '1.3.0'), +] + +configopts = '-DGIT_ARCHETYPE=1' + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'include/x265_config.h', 'include/%(name)s.h', 'lib/libx265.a', 'lib/libx265.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ac1a521bfe6 --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-GCCcore-13.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'https://www.tortall.net/projects/yasm/' +description = "Yasm: Complete rewrite of the NASM assembler with BSD license" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dce6601b495f5b3d45b59f7d2492a340ee7e84b5beca17e48f862502bd5603f'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'lang' From 046ee962ca31294b137f9ee607af7deb4abcf87b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 00:43:25 +0200 Subject: [PATCH 9256/9987] Checksum --- easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-13.2.0.eb index 85fb3db262c..f12adef66b3 100644 --- a/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.9-GCCcore-13.2.0.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['bff1fa140f4af0e7f02c6cb78d41b9a7d5508e6bcdfda3a583e35460eb6d4b47'] +checksums = ['f1d8aacd46afed958babfced3190d2d3c8209b66da451f556abd6da94c165cf3'] builddependencies = [ ('binutils', '2.40'), From f9047205a25a29177777d22d8aaa8d6e25c670cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 00:46:02 +0200 Subject: [PATCH 9257/9987] checksum --- .../o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..815985fab48 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.2.0' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b1b200606640547fceff0d3ebe01ac05c4a7ae2a131be7e9b3e5b9f491ef35b3'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] +dependencies = [ + ('Imath', '3.1.9'), + ('zlib', '1.2.13') +] + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' From ed5ee4a77085c83adb9f95615d911a7a1d4b51c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 00:48:00 +0200 Subject: [PATCH 9258/9987] wopps --- .../o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb deleted file mode 100644 index 815985fab48..00000000000 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb +++ /dev/null @@ -1,38 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenEXR' -version = '3.2.0' - -homepage = 'https://www.openexr.com/' -description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic - for use in computer imaging applications""" - -toolchain = {'name': 'GCCcore', 'version': '13.2.0'} - -source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['b1b200606640547fceff0d3ebe01ac05c4a7ae2a131be7e9b3e5b9f491ef35b3'] - -builddependencies = [ - ('binutils', '2.40'), - ('CMake', '3.27.6'), -] -dependencies = [ - ('Imath', '3.1.9'), - ('zlib', '1.2.13') -] - -local_libs, local_bins = [ - ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], - ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] -] - -sanity_check_paths = { - 'files': ( - ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + - ['bin/exr%s' % b for b in local_bins] - ), - 'dirs': ['include/%(name)s', 'share'], -} - -moduleclass = 'vis' From 5c4cc237cab9e0216bec80d139254bc04c83716d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 00:48:25 +0200 Subject: [PATCH 9259/9987] checksum --- easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb index fd36bca88b3..815985fab48 100644 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.2.0-GCCcore-13.2.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['78dbca39115a1c526e6728588753955ee75fa7f5bb1a6e238bed5b6d66f91fd7'] +checksums = ['b1b200606640547fceff0d3ebe01ac05c4a7ae2a131be7e9b3e5b9f491ef35b3'] builddependencies = [ ('binutils', '2.40'), From 885ef7491fc0d8b0000fb3bebf88a4796f2d4a8b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 00:56:30 +0200 Subject: [PATCH 9260/9987] adding easyconfigs: LZO-2.10-GCCcore-13.2.0.eb, Brunsli-0.1-GCCcore-13.2.0.eb, googletest-1.14.0-GCCcore-13.2.0.eb, Highway-1.0.7-GCCcore-13.2.0.eb --- .../b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb | 50 +++++++++++++++++++ .../googletest-1.14.0-GCCcore-13.2.0.eb | 28 +++++++++++ .../h/Highway/Highway-1.0.7-GCCcore-13.2.0.eb | 32 ++++++++++++ .../l/LZO/LZO-2.10-GCCcore-13.2.0.eb | 27 ++++++++++ 4 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/googletest/googletest-1.14.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/h/Highway/Highway-1.0.7-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..99cccc31a73 --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +dependencies = [ + ('Brotli', '1.1.0'), + ('Highway', '1.0.7'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib*/", + "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.14.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.14.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c098771dd9e --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.14.0-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.14.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/google/googletest/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8ad598c73ad796e0d8280b082cebd82a630d73e73cd3c70057938a6501bba5d7'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.7-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.7-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a4db42b4cba --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.7-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Highway' +version = '1.0.7' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('googletest', '1.14.0'), +] + +configopts = "-DHWY_SYSTEM_GTEST=ON" + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3b46b64940c --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.40')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' From 32e5d530ca280a17898c2591e3659a2e6937d835 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 01:02:25 +0200 Subject: [PATCH 9261/9987] checksum --- easybuild/easyconfigs/h/Highway/Highway-1.0.7-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.7-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.7-GCCcore-13.2.0.eb index a4db42b4cba..b737b106291 100644 --- a/easybuild/easyconfigs/h/Highway/Highway-1.0.7-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.7-GCCcore-13.2.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://github.com/google/highway/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -checksums = ['faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'] +checksums = ['5434488108186c170a5e2fca5e3c9b6ef59a1caa4d520b008a9b8be6b8abe6c5'] builddependencies = [ ('binutils', '2.40'), From 3bc9db51bdb0ae2abffc7672a6307d0cbbfd3532 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 01:07:53 +0200 Subject: [PATCH 9262/9987] adding easyconfigs: mold-2.3.1-GCCcore-13.2.0.eb --- .../m/mold/mold-2.3.1-GCCcore-13.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/mold/mold-2.3.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/m/mold/mold-2.3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/mold/mold-2.3.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d287e355968 --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-2.3.1-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'mold' +version = '2.3.1' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['380f540114408c37bcdb7f3bda91a056448a93124ca6992a373ae2bda35e9af7'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] +dependencies = [ + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' From 908a29e78297d95553769cf07393fc6ea9d5ae70 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 25 Oct 2023 01:14:33 +0200 Subject: [PATCH 9263/9987] Drop brunsli --- .../b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb | 50 ------------------- 1 file changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb deleted file mode 100644 index 99cccc31a73..00000000000 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-13.2.0.eb +++ /dev/null @@ -1,50 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Denis Kristak -# update: Thomas Hoffmann (EMBL) -easyblock = 'CMakeMake' - -name = 'Brunsli' -version = '0.1' - -homepage = 'https://github.com/google/brunsli/' -description = """Brunsli is a lossless JPEG repacking library.""" - -toolchain = {'name': 'GCCcore', 'version': '13.2.0'} - -source_urls = ['https://github.com/google/brunsli/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] - -builddependencies = [ - ('CMake', '3.27.6'), - ('binutils', '2.40'), -] - -dependencies = [ - ('Brotli', '1.1.0'), - ('Highway', '1.0.7'), -] - -# skip use of third_party directory, since we provide Brotli via a proper dependency -preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " - -configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' - -buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" - -# also install dbrunsli binary and missing libraries -postinstallcmds = [ - "mkdir %(installdir)s/bin", - "cp dbrunsli %(installdir)s/bin/", - "cp libbrunsli*.a %(installdir)s/lib*/", - "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, -] - -sanity_check_paths = { - 'files': ['bin/dbrunsli'], - 'dirs': ['include/brunsli', 'lib'], -} - -sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] - -moduleclass = 'lib' From c033f433879835e8584870bc7b20c7ba177116e1 Mon Sep 17 00:00:00 2001 From: Sarah Walters Date: Wed, 25 Oct 2023 15:11:17 +1000 Subject: [PATCH 9264/9987] Add Anaconda3 2023.09.0 --- .../a/Anaconda3/Anaconda3-2023.09-0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.09-0.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.09-0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.09-0.eb new file mode 100644 index 00000000000..d52ea97e715 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.09-0.eb @@ -0,0 +1,33 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, +# 2019.10, 2020.2, 2020.11, 2022.05, +# 2022.10 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +# config upgrade to 2023.09 by Sarah Walters +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2023.09-0' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH) +sources = ['%%(name)s-%%(version)s-Linux-%s.sh' % local_arch] +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': '6c8a4abb36fbb711dc055b7049a23bbfd61d356de9468b41c5140f8a11abd851', + '%(name)s-%(version)s-Linux-ppc64le.sh': '5ea1ed9808af95eb2655fe6a4ffdb66bea66ecd1d053fc2ee69eacc7685ef665', + '%(name)s-%(version)s-Linux-aarch64.sh': '69ee26361c1ec974199bce5c0369e3e9a71541de7979d2b9cfa4af556d1ae0ea', + } +] + +moduleclass = 'lang' + From 07a85a68aa6c9480944605f30978ddd07767b31f Mon Sep 17 00:00:00 2001 From: xina Date: Wed, 25 Oct 2023 13:53:59 +0200 Subject: [PATCH 9265/9987] generalize wget using sysroot template --- easybuild/easyconfigs/w/wget/wget-1.19.4-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.19.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/w/wget/wget-1.19.4-GCCcore-6.4.0.eb index 2dd214fecd0..751ed0e7578 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.19.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.19.4-GCCcore-6.4.0.eb @@ -31,7 +31,7 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb index 07e2836707e..c1524252e1c 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb @@ -31,7 +31,7 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-8.3.0.eb index 284145e9acd..12ee16c948e 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-8.3.0.eb @@ -31,7 +31,7 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb index b553d124898..5dd1424e3cc 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-9.3.0.eb index 04371b74a51..15c9a9eb16e 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-9.3.0.eb @@ -31,7 +31,7 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb index f9313fcbc6e..84dfb6a7f92 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb @@ -33,7 +33,7 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " configopts = '--with-ssl=openssl ' # Optionally, you can use gnutls (default) instead of OpenSSL. diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb index 3e0a4fdaa71..3820707455e 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb @@ -33,7 +33,7 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " configopts = '--with-ssl=openssl ' # Optionally, you can use gnutls (default) instead of OpenSSL. diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb index 5c953192438..5f5eaa5da2b 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb @@ -38,7 +38,7 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:/usr/lib/pkgconfig:/usr/lib/x86_64-linux-gnu/pkgconfig && " +preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " configopts = '--with-ssl=openssl ' # Optionally, you can use gnutls (default) instead of OpenSSL. From 67c28cb7dac6bb1080a9eee35044260a6ae3ff4d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 25 Oct 2023 15:58:25 +0200 Subject: [PATCH 9266/9987] adding easyconfigs: BiG-SCAPE-1.1.5-foss-2022a.eb --- .../b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb new file mode 100644 index 00000000000..d36acf49916 --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'BiG-SCAPE' +version = '1.1.5' + +homepage = 'https://bigscape-corason.secondarymetabolites.org/index.html' +description = """BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters +(BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene +cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'medema-group' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('scikit-learn', '1.1.2'), + ('networkx', '2.8.4'), + ('HMMER', '3.3.2'), + ('FastTree', '2.1.11'), +] + +options = {'modulename': False} + +sanity_check_commands = [ + 'bigscape.py --help', +] + +moduleclass = 'bio' From 4534cf815cd7de928b0e7ba8c3ce9ddb852e4788 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 25 Oct 2023 14:26:01 +0000 Subject: [PATCH 9267/9987] adding easyconfigs: boto3-1.28.70-GCCcore-12.3.0.eb --- .../b/boto3/boto3-1.28.70-GCCcore-12.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.28.70-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.28.70-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.28.70-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..01896809767 --- /dev/null +++ b/easybuild/easyconfigs/b/boto3/boto3-1.28.70-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'boto3' +version = '1.28.70' + +homepage = 'https://github.com/boto/boto3' +description = """Boto3 is the Amazon Web Services (AWS) Software Development Kit +(SDK) for Python, which allows Python developers to write software that makes +use of services like Amazon S3 and Amazon EC2.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +exts_list = [ + ('botocore', '1.31.70', { + 'checksums': ['5f49def4ec2e4216dd0195d23d9811027d02ee6c8a37b031e2b2fe38e8c77ddc'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.7.0', { + 'checksums': ['fd3889a66f5fe17299fe75b82eae6cf722554edca744ca5d5fe308b104883d2e'], + }), + (name, version, { + 'checksums': ['89002e1d8411c7c54110f9f8fc4a11d57d6d7977c0cb4ba064887ca5d4c788f7'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 89455ae5241460aafe8fe3abf676ea03de052aae Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 25 Oct 2023 16:36:49 +0200 Subject: [PATCH 9268/9987] use wrapt 1.15.0 as dep, remove binutils as builddep --- .../s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb index b469cc61b1e..5ea30879467 100644 --- a/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb +++ b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.6.16-foss-2022a.eb @@ -14,16 +14,13 @@ toolchain = {'name': 'foss', 'version': '2022a'} github_account = 'koaning' -builddependencies = [ - ('binutils', '2.38'), -] - dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('scikit-learn', '1.1.2'), ('matplotlib', '3.5.2'), ('umap-learn', '0.5.3'), + ('wrapt', '1.15.0'), ] use_pip = True @@ -38,9 +35,6 @@ exts_list = [ ('patsy', '0.5.3', { 'checksums': ['bdc18001875e319bc91c812c1eb6a10be4bb13cb81eb763f466179dca3b67277'], }), - ('wrapt', '1.14.1', { - 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], - }), (name, version, { 'modulename': 'sklego', 'source_tmpl': 'v%(version)s.tar.gz', From f4c44979049b6c9991999de617945fe448f71d1d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 25 Oct 2023 16:38:02 +0200 Subject: [PATCH 9269/9987] Add missing use_pip/download_dep_fail/sanity_pip_check settings --- .../easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb index d36acf49916..845bcfd6d8c 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -25,6 +25,10 @@ dependencies = [ ('FastTree', '2.1.11'), ] +use_pip = True +download_dep_fail = True +sanity_pip_check = True + options = {'modulename': False} sanity_check_commands = [ From 3bbbacb860bcff599dd1cd503e19bcf493854377 Mon Sep 17 00:00:00 2001 From: Sarah Walters Date: Thu, 26 Oct 2023 10:34:55 +1000 Subject: [PATCH 9270/9987] Remove trailing newline from Anaconda3 2023.09 --- easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.09-0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.09-0.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.09-0.eb index d52ea97e715..524403e9fc3 100644 --- a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.09-0.eb +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2023.09-0.eb @@ -30,4 +30,3 @@ checksums = [ ] moduleclass = 'lang' - From f7d8e9710b515945a1623f2ccf32b3e89679e7cd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 26 Oct 2023 11:02:52 +0200 Subject: [PATCH 9271/9987] Workaround test_torchinductor_opinfo failure --- .../p/PyTorch/PyTorch-2.0.1-foss-2022a.eb | 3 +++ ...success_in_test_torchinductor_opinfo.patch | 22 +++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb index 6a18148e60c..8cf19088ee9 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb @@ -32,6 +32,7 @@ patches = [ 'PyTorch-2.0.1_fix-torch.compile-on-ppc.patch', 'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch', 'PyTorch-2.0.1_fix-vsx-loadu.patch', + 'PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch', 'PyTorch-2.0.1_no-cuda-stubs-rpath.patch', 'PyTorch-2.0.1_remove-test-requiring-online-access.patch', 'PyTorch-2.0.1_skip-diff-test-on-ppc.patch', @@ -76,6 +77,8 @@ checksums = [ {'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch': '1b37194f55ae678f3657b8728dfb896c18ffe8babe90987ce468c4fa9274f357'}, {'PyTorch-2.0.1_fix-vsx-loadu.patch': 'a0ffa61da2d47c6acd09aaf6d4791e527d8919a6f4f1aa7ed38454cdcadb1f72'}, + {'PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch': + '57e2985a5b7085c2786e4b0c4a5f0c81f6b2ae9d5804bbd552b06e8b1570f4c4'}, {'PyTorch-2.0.1_no-cuda-stubs-rpath.patch': '8902e58a762240f24cdbf0182e99ccdfc2a93492869352fcb4ca0ec7e407f83a'}, {'PyTorch-2.0.1_remove-test-requiring-online-access.patch': '721ab0d35ed0ff8a46cb84ced5a98c0fb8ce6143cf6cea80b1360d3d7f64f584'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch new file mode 100644 index 00000000000..db8aa200deb --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch @@ -0,0 +1,22 @@ +Some tests may succeed although they are not expected to. E.g.: +> FAILED inductor/test_torchinductor_opinfo.py::TestInductorOpInfoCPU::test_comprehensive_index_add_cpu_float16 - RuntimeError: unexpected success index_add, torch.float16, cpu +> FAILED inductor/test_torchinductor_opinfo.py::TestInductorOpInfoCPU::test_comprehensive_scatter_add_cpu_float16 - RuntimeError: unexpected success scatter_add, torch.float16, cpu +> FAILED inductor/test_torchinductor_opinfo.py::TestInductorOpInfoCPU::test_comprehensive_scatter_reduce_sum_cpu_float16 - RuntimeError: unexpected success scatter_reduce.sum, torch.float16, cpu + +Disable that unexpected success check. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_torchinductor_opinfo.py b/test/inductor/test_torchinductor_opinfo.py +index d91a27684ba..1e6d247c8d4 100644 +--- a/test/inductor/test_torchinductor_opinfo.py ++++ b/test/inductor/test_torchinductor_opinfo.py +@@ -66,7 +66,7 @@ _ops = partial( + TestExpect = Enum("TestExpect", ("SUCCESS", "XFAILURE", "SKIP")) + + COLLECT_EXPECT = os.getenv("PYTORCH_COLLECT_EXPECT", "0") == "1" +-FAIL_ON_SUCCESS = os.getenv("PYTORCH_FAIL_ON_SUCCESS", "1") == "1" ++FAIL_ON_SUCCESS = False + ALL_SAMPLES = os.getenv("PYTORCH_ALL_SAMPLES", "0") == "1" + START = os.getenv("PYTORCH_TEST_RANGE_START", None) + END = os.getenv("PYTORCH_TEST_RANGE_END", None) From 24c85cba46cb7a2c9b89511b3eb0ec11dc69804b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 26 Oct 2023 11:13:52 +0200 Subject: [PATCH 9272/9987] Workaround test_torchinductor_opinfo failure --- .../p/PyTorch/PyTorch-2.0.1-foss-2022b.eb | 3 +++ ...success_in_test_torchinductor_opinfo.patch | 22 +++++++++++++++++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb index 59f471b813e..763167da5cc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb @@ -32,6 +32,7 @@ patches = [ 'PyTorch-2.0.1_fix-torch.compile-on-ppc.patch', 'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch', 'PyTorch-2.0.1_fix-vsx-loadu.patch', + 'PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch', 'PyTorch-2.0.1_no-cuda-stubs-rpath.patch', 'PyTorch-2.0.1_remove-test-requiring-online-access.patch', 'PyTorch-2.0.1_skip-diff-test-on-ppc.patch', @@ -76,6 +77,8 @@ checksums = [ {'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch': '1b37194f55ae678f3657b8728dfb896c18ffe8babe90987ce468c4fa9274f357'}, {'PyTorch-2.0.1_fix-vsx-loadu.patch': 'a0ffa61da2d47c6acd09aaf6d4791e527d8919a6f4f1aa7ed38454cdcadb1f72'}, + {'PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch': + '57e2985a5b7085c2786e4b0c4a5f0c81f6b2ae9d5804bbd552b06e8b1570f4c4'}, {'PyTorch-2.0.1_no-cuda-stubs-rpath.patch': '8902e58a762240f24cdbf0182e99ccdfc2a93492869352fcb4ca0ec7e407f83a'}, {'PyTorch-2.0.1_remove-test-requiring-online-access.patch': '721ab0d35ed0ff8a46cb84ced5a98c0fb8ce6143cf6cea80b1360d3d7f64f584'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch new file mode 100644 index 00000000000..db8aa200deb --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_ignore_unexpected_success_in_test_torchinductor_opinfo.patch @@ -0,0 +1,22 @@ +Some tests may succeed although they are not expected to. E.g.: +> FAILED inductor/test_torchinductor_opinfo.py::TestInductorOpInfoCPU::test_comprehensive_index_add_cpu_float16 - RuntimeError: unexpected success index_add, torch.float16, cpu +> FAILED inductor/test_torchinductor_opinfo.py::TestInductorOpInfoCPU::test_comprehensive_scatter_add_cpu_float16 - RuntimeError: unexpected success scatter_add, torch.float16, cpu +> FAILED inductor/test_torchinductor_opinfo.py::TestInductorOpInfoCPU::test_comprehensive_scatter_reduce_sum_cpu_float16 - RuntimeError: unexpected success scatter_reduce.sum, torch.float16, cpu + +Disable that unexpected success check. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_torchinductor_opinfo.py b/test/inductor/test_torchinductor_opinfo.py +index d91a27684ba..1e6d247c8d4 100644 +--- a/test/inductor/test_torchinductor_opinfo.py ++++ b/test/inductor/test_torchinductor_opinfo.py +@@ -66,7 +66,7 @@ _ops = partial( + TestExpect = Enum("TestExpect", ("SUCCESS", "XFAILURE", "SKIP")) + + COLLECT_EXPECT = os.getenv("PYTORCH_COLLECT_EXPECT", "0") == "1" +-FAIL_ON_SUCCESS = os.getenv("PYTORCH_FAIL_ON_SUCCESS", "1") == "1" ++FAIL_ON_SUCCESS = False + ALL_SAMPLES = os.getenv("PYTORCH_ALL_SAMPLES", "0") == "1" + START = os.getenv("PYTORCH_TEST_RANGE_START", None) + END = os.getenv("PYTORCH_TEST_RANGE_END", None) From f3f159a89e7c1b24a92ed302bf22f26163d1a0c6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 26 Oct 2023 13:02:57 +0200 Subject: [PATCH 9273/9987] remove numa configure option from hwloc 2.5+ --- easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb | 3 +-- 5 files changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb index 8f1e093450f..273bef65c43 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb @@ -35,8 +35,7 @@ dependencies = [ ('libpciaccess', '0.16'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb index 6b7a745c08c..15cba2b35a9 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb @@ -32,8 +32,7 @@ dependencies = [ ('libpciaccess', '0.16'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb index f6483901c2b..e1493dc0953 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb @@ -32,8 +32,7 @@ dependencies = [ ('libpciaccess', '0.17'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb index f3d054d78d2..f454c0bc263 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb @@ -32,8 +32,7 @@ dependencies = [ ('libpciaccess', '0.17'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb index 274d96ba85d..e0816fd2d78 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb @@ -32,8 +32,7 @@ dependencies = [ ('libpciaccess', '0.17'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', From 0e3ef19f9567cf8f885db4799ebaa9096dc3694e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 26 Oct 2023 14:01:51 +0200 Subject: [PATCH 9274/9987] Add patch description --- easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb | 2 +- ...Torch-2.0.1_add-missing-vsx-vector-shift-functions.patch | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb index 8cf19088ee9..e3428bfcbe7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022a.eb @@ -62,7 +62,7 @@ checksums = [ {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, {'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch': - '245ee7f479f6f809b6ea52460113b2c49bbc2a550201f82bdfa0651c72b02ea8'}, + 'da44961d6c204403ba0c4b88cedccf06a7a3d24f29c4398545f96efae7a45c95'}, {'PyTorch-2.0.1_avoid-test_quantization-failures.patch': '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'}, {'PyTorch-2.0.1_disable-test-sharding.patch': 'a1ed7f21c9a269ea039a07a3d6574f885787b30ca5687143c96e096d31066cca'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch index 57e334c908f..0f30c6b98c5 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch @@ -1,3 +1,9 @@ +The `Vectorized` class template specializations for VSX are missing the +left and right shift operators. +Add a backported version of the fixed operators of https://github.com/pytorch/pytorch/pull/109886 + +Author: Alexander Grund (TU Dresden) + diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h index 7c300c8087c..84c84286740 100644 --- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h From c110b159cbbe40bdf1a66c7f590c030c177e3350 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 26 Oct 2023 14:02:55 +0200 Subject: [PATCH 9275/9987] Add patch description --- easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb | 2 +- ...Torch-2.0.1_add-missing-vsx-vector-shift-functions.patch | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb index 763167da5cc..6f869d07be5 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb @@ -62,7 +62,7 @@ checksums = [ {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, {'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch': - '245ee7f479f6f809b6ea52460113b2c49bbc2a550201f82bdfa0651c72b02ea8'}, + 'da44961d6c204403ba0c4b88cedccf06a7a3d24f29c4398545f96efae7a45c95'}, {'PyTorch-2.0.1_avoid-test_quantization-failures.patch': '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'}, {'PyTorch-2.0.1_disable-test-sharding.patch': 'a1ed7f21c9a269ea039a07a3d6574f885787b30ca5687143c96e096d31066cca'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch index 57e334c908f..0f30c6b98c5 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch @@ -1,3 +1,9 @@ +The `Vectorized` class template specializations for VSX are missing the +left and right shift operators. +Add a backported version of the fixed operators of https://github.com/pytorch/pytorch/pull/109886 + +Author: Alexander Grund (TU Dresden) + diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h index 7c300c8087c..84c84286740 100644 --- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h From 6061636b28f84ba4b0748af8cbad3f319ab34c4e Mon Sep 17 00:00:00 2001 From: xina Date: Thu, 26 Oct 2023 15:28:54 +0200 Subject: [PATCH 9276/9987] fix style for long lines --- easybuild/easyconfigs/w/wget/wget-1.19.4-GCCcore-6.4.0.eb | 5 ++++- easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb | 5 ++++- easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-8.3.0.eb | 5 ++++- easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb | 5 ++++- easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-9.3.0.eb | 5 ++++- easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb | 5 ++++- easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb | 5 ++++- easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb | 5 ++++- 8 files changed, 32 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/w/wget/wget-1.19.4-GCCcore-6.4.0.eb b/easybuild/easyconfigs/w/wget/wget-1.19.4-GCCcore-6.4.0.eb index 751ed0e7578..3e958246704 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.19.4-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.19.4-GCCcore-6.4.0.eb @@ -31,7 +31,10 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb index c1524252e1c..58155b9ba65 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-7.3.0.eb @@ -31,7 +31,10 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-8.3.0.eb index 12ee16c948e..c8948202cef 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.1-GCCcore-8.3.0.eb @@ -31,7 +31,10 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb index 5dd1424e3cc..a32a03e427c 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-10.2.0.eb @@ -32,7 +32,10 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] diff --git a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-9.3.0.eb index 15c9a9eb16e..43dc36af7e7 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.20.3-GCCcore-9.3.0.eb @@ -31,7 +31,10 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc configopts = '--with-ssl=openssl ' osdependencies = [OS_PKG_OPENSSL_DEV] diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb index 84dfb6a7f92..4b401e95412 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.1-GCCcore-10.3.0.eb @@ -33,7 +33,10 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc configopts = '--with-ssl=openssl ' # Optionally, you can use gnutls (default) instead of OpenSSL. diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb index 3820707455e..c8162cdfea5 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.2-GCCcore-11.2.0.eb @@ -33,7 +33,10 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc configopts = '--with-ssl=openssl ' # Optionally, you can use gnutls (default) instead of OpenSSL. diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb index 5f5eaa5da2b..481dbcb3ede 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.3-GCCcore-11.3.0.eb @@ -38,7 +38,10 @@ dependencies = [ ] # make sure pkg-config picks up system packages (OpenSSL & co) -preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig && " +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc configopts = '--with-ssl=openssl ' # Optionally, you can use gnutls (default) instead of OpenSSL. From a0e014c084096a1134355468ca0009f6581062fd Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 26 Oct 2023 16:38:47 +0200 Subject: [PATCH 9277/9987] Re-add modloadmsg about Pfam database --- .../easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb index 845bcfd6d8c..ee064b78496 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -35,4 +35,9 @@ sanity_check_commands = [ 'bigscape.py --help', ] +modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" +modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website" +modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " +modloadmsg += "uncompress it and process it using the `hmmpress` command.\n" + moduleclass = 'bio' From ca39ec81d3b3ca010f134264065daa6e985b7451 Mon Sep 17 00:00:00 2001 From: xina Date: Thu, 26 Oct 2023 17:18:42 +0200 Subject: [PATCH 9278/9987] update fix patch and pythonpath --- .../w/waLBerla/waLBerla-6.1-foss-2021a.eb | 12 ++++++++---- .../waLBerla-6.1_fix_cmakelist_for_easybuild.patch | 12 ++++++++---- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index e67edd92949..fe3ca95573a 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -17,10 +17,9 @@ patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild.patch'] checksums = [ {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, {'waLBerla-6.1_fix_cmakelist_for_easybuild.patch': - '13393d523d8f2e1856ae6acffc04bc74d35b5b6a7c800cfad75fb8e3678e4dad'}, + '4adbf15c336a47f7642524190d97d93a4baf8309de88f1f19278b5275377331d'}, ] - builddependencies = [('CMake', '3.20.1')] dependencies = [ @@ -35,10 +34,15 @@ configopts = "-DWALBERLA_BUILD_WITH_PYTHON=ON " configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " configopts += "-DWALBERLA_BUILD_DOC=OFF " configopts += "-DPython_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DCMAKE_INSTALL_PREFIX=%(installdir)s " + +modextrapaths = {'PYTHONPATH': ['pythonmodule']} sanity_check_paths = { - 'files': ['walberla/waLBerlaDefinitions.h', 'walberla/pythonmodule/walberla_cpp.cpython-39-x86_64-linux-gnu.so'], - 'dirs': ['walberla/pythonmodule/'] + 'files': ['waLBerlaDefinitions.h', 'pythonmodule/walberla_cpp.cpython-39-x86_64-linux-gnu.so'], + 'dirs': ['pythonmodule'] } moduleclass = 'chem' + + diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch index 62c8fad3044..7d796c2144c 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch @@ -1,12 +1,16 @@ diff -ruN walberla-v6.1.orig/CMakeLists.txt walberla-v6.1/CMakeLists.txt --- walberla-v6.1.orig/CMakeLists.txt 2023-10-17 13:06:02.619565000 +0200 -+++ walberla-v6.1/CMakeLists.txt 2023-10-18 14:47:35.047985995 +0200 -@@ -1314,7 +1314,7 @@ ++++ walberla-v6.1/CMakeLists.txt 2023-10-26 17:03:11.300212100 +0200 +@@ -1313,8 +1313,10 @@ + configure_file ( src/waLBerlaDefinitions.in.h src/waLBerlaDefinitions.h ) - install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION walberla/ ) +-install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION walberla/ ) - -+install( DIRECTORY ${walberla_BINARY_DIR}/apps/ DESTINATION walberla/ ) ++install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION . ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/pythonmodule/ DESTINATION . ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/benchmarks/ DESTINATION . ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/tutorials/ DESTINATION . ) # test if ( WALBERLA_BUILD_TESTS ) From 7f7c7c3bf3dd03b11b9b200c9cbca80a10f8386c Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Thu, 26 Oct 2023 19:22:16 +0200 Subject: [PATCH 9279/9987] Update waLBerla-6.1-foss-2021a.eb --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index fe3ca95573a..c2e786ff87a 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -44,5 +44,3 @@ sanity_check_paths = { } moduleclass = 'chem' - - From ee7eaeb8df0c51d24897014365e680f1816934a8 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Thu, 26 Oct 2023 19:26:00 +0200 Subject: [PATCH 9280/9987] Update waLBerla-6.1_fix_cmakelist_for_easybuild.patch --- .../waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch index 7d796c2144c..2397582632a 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch @@ -8,9 +8,9 @@ diff -ruN walberla-v6.1.orig/CMakeLists.txt walberla-v6.1/CMakeLists.txt -install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION walberla/ ) - +install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION . ) -+install( DIRECTORY ${walberla_BINARY_DIR}/apps/pythonmodule/ DESTINATION . ) -+install( DIRECTORY ${walberla_BINARY_DIR}/apps/benchmarks/ DESTINATION . ) -+install( DIRECTORY ${walberla_BINARY_DIR}/apps/tutorials/ DESTINATION . ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/pythonmodule/ DESTINATION pythonmodule/ ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/benchmarks/ DESTINATION benchmarks/ ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/tutorials/ DESTINATION tutorials/ ) # test if ( WALBERLA_BUILD_TESTS ) From 9ad0ecc63dbf9e009b90a40c259096c0b430bad1 Mon Sep 17 00:00:00 2001 From: xina Date: Thu, 26 Oct 2023 19:36:28 +0200 Subject: [PATCH 9281/9987] fix install path --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 2 +- .../w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index c2e786ff87a..5b98d3995e4 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -17,7 +17,7 @@ patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild.patch'] checksums = [ {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, {'waLBerla-6.1_fix_cmakelist_for_easybuild.patch': - '4adbf15c336a47f7642524190d97d93a4baf8309de88f1f19278b5275377331d'}, + '057066d07294e8f159c2545d2d5f9138d439dbb54bc70eb75eca1f82ae650c47'}, ] builddependencies = [('CMake', '3.20.1')] diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch index 2397582632a..c5b275b6fe3 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild.patch @@ -1,6 +1,6 @@ diff -ruN walberla-v6.1.orig/CMakeLists.txt walberla-v6.1/CMakeLists.txt --- walberla-v6.1.orig/CMakeLists.txt 2023-10-17 13:06:02.619565000 +0200 -+++ walberla-v6.1/CMakeLists.txt 2023-10-26 17:03:11.300212100 +0200 ++++ walberla-v6.1/CMakeLists.txt 2023-10-26 19:28:03.622447001 +0200 @@ -1313,8 +1313,10 @@ configure_file ( src/waLBerlaDefinitions.in.h src/waLBerlaDefinitions.h ) From 7e7c7d1d7f44d776152fc576dd5add72a67397af Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 27 Oct 2023 11:30:29 +0200 Subject: [PATCH 9282/9987] adding easyconfigs: PICRUSt2-2.5.2-foss-2022a.eb --- .../p/PICRUSt2/PICRUSt2-2.5.2-foss-2022a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022a.eb b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022a.eb new file mode 100644 index 00000000000..9f766d3ffeb --- /dev/null +++ b/easybuild/easyconfigs/p/PICRUSt2/PICRUSt2-2.5.2-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'PICRUSt2' +version = '2.5.2' + +homepage = 'https://github.com/picrust/picrust2' +description = """PICRUSt2 (Phylogenetic Investigation of Communities by + Reconstruction of Unobserved States) is a software for predicting + functional abundances based only on marker gene sequences.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('biom-format', '2.1.14'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('joblib', '1.3.1', { + 'checksums': ['1f937906df65329ba98013dc9692fe22a4c5e4a648112de500508b18a21b41e3'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/picrust/%(namelower)s/archive'], + 'checksums': ['a8c3832bf759233b52b41c56a0ffef72491e431fee347a7c05695596c76a1a4c'], + }), +] + +postinstallcmds = [ + "cp -a %(start_dir)s%(name)s/%(namelower)s-%(version)s/%(namelower)s/default_files" + " %(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s/" +] + +sanity_check_commands = [ + "python -c 'from picrust2.default import default_tables'" +] + +sanity_check_paths = { + 'files': ['bin/picrust2_pipeline.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/picrust2/default_files'], +} + +moduleclass = 'bio' From 91226f842b7b5d4325d507e882b5896442aea4b5 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 27 Oct 2023 14:07:30 +0200 Subject: [PATCH 9283/9987] Update checksum --- .../o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb index 3ca74380746..e0f24d0917d 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] -checksums = ['92ad4b107394b273397baa1abe90207e1f8ef9fd52ffbfc23b46e3b0005d4439'] +checksums = [ + '92ad4b107394b273397baa1abe90207e1f8ef9fd52ffbfc23b46e3b0005d4439', + '40c2e6fe38f0460a92e3f9d24bf75bcc310c74585760a3b0ac1b1727582bb46c', +] builddependencies = [ ('CMake', '3.26.3'), From 1d4681d2b58f691d92e704af2e8c16b6428f7a55 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 27 Oct 2023 14:33:42 +0200 Subject: [PATCH 9284/9987] Fix checksum specification --- .../o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb index e0f24d0917d..b0bc036fc2c 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.4.14.0-GCC-12.3.0.eb @@ -11,10 +11,8 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] -checksums = [ - '92ad4b107394b273397baa1abe90207e1f8ef9fd52ffbfc23b46e3b0005d4439', - '40c2e6fe38f0460a92e3f9d24bf75bcc310c74585760a3b0ac1b1727582bb46c', -] +checksums = [('92ad4b107394b273397baa1abe90207e1f8ef9fd52ffbfc23b46e3b0005d4439', + '40c2e6fe38f0460a92e3f9d24bf75bcc310c74585760a3b0ac1b1727582bb46c')] builddependencies = [ ('CMake', '3.26.3'), From f8832ffa7dd058d3561d1cb4a02ae97976efdf12 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 27 Oct 2023 14:43:13 +0200 Subject: [PATCH 9285/9987] Made requested changes --- .../GFF3-toolkit-2.1.0-foss-2022a.eb} | 22 +++++++++++-------- .../GFF3-toolkit-2.1.0-remove-hardcode.patch} | 0 2 files changed, 13 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/g/{gff3tool/gff3tool-2.1.0-foss-2022a.eb => GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb} (58%) rename easybuild/easyconfigs/g/{gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch => GFF3-toolkit/GFF3-toolkit-2.1.0-remove-hardcode.patch} (100%) diff --git a/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb similarity index 58% rename from easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb rename to easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb index 80f979fe27c..9db2550d17c 100644 --- a/easybuild/easyconfigs/g/gff3tool/gff3tool-2.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'gff3tool' +name = 'GFF3-toolkit' version = '2.1.0' homepage = 'https://gff3toolkit.readthedocs.io' @@ -8,24 +8,28 @@ description = 'Python programs for processing GFF3 files' toolchain = {'name': 'foss', 'version': '2022a'} -sources = ['gff3tool-2.1.0.tar.gz'] -patches = ['GFF3toolkit-2.1.0-remove_hardcode.patch'] +sources = ['gff3tool-%(version)s.tar.gz'] +source_urls = ['https://pypi.python.org/packages/source/g/gff3tool'] +patches = ['GFF3-toolkit-2.1.0-remove-hardcode.patch'] checksums = [ {'gff3tool-2.1.0.tar.gz': 'e842ef4afdb66926a2b63bf2619c7ef30bd9b76a5f1084a5c57bf8b39cc4f15d'}, - {'GFF3toolkit-2.1.0-remove_hardcode.patch': '03696635af25ab1e3d650b46c7aeaaaadb31e7eac766039c758150f3f3162cb7'}, + {'GFF3-toolkit-2.1.0-remove-hardcode.patch': '03696635af25ab1e3d650b46c7aeaaaadb31e7eac766039c758150f3f3162cb7'}, ] -local_blast_path = '%(installdir)s/lib/python%(pyshortver)s/site-packages/gff3tool/lib/ncbi-blast+' -preinstallopts = 'mkdir -p %s && ' % local_blast_path -preinstallopts += 'ln -s $EBROOTBLASTPLUS/bin %s && ' % local_blast_path - dependencies = [ ('Python', '3.10.4'), ('BLAST+', '2.13.0'), ] +#GFF3-toolkit has hardcoded path to BLAST+ libraries, so we have to add a symlink to the required path for this to work +local_blast_path = '%(installdir)s/lib/python%(pyshortver)s/site-packages/gff3tool/lib/ncbi-blast+' +preinstallopts = 'mkdir -p %s && ' % local_blast_path +preinstallopts += 'ln -s $EBROOTBLASTPLUS/bin %s && ' % local_blast_path + use_pip = True sanity_pip_check = True download_dep_fail = True -moduleclass = "tools" +options = {'modulename': 'gff3tool'} + +moduleclass = "bio" diff --git a/easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-remove-hardcode.patch similarity index 100% rename from easybuild/easyconfigs/g/gff3tool/GFF3toolkit-2.1.0-remove_hardcode.patch rename to easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-remove-hardcode.patch From a3d99c8fcaf9ae146c583e4c572cf96d8830f351 Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 27 Oct 2023 14:52:59 +0200 Subject: [PATCH 9286/9987] adding easyconfigs: dynesty-2.1.3-foss-2023a.eb, typing-extensions-4.8.0-GCCcore-12.3.0.eb, pytest-7.4.2-GCCcore-12.3.0.eb, pytest-xdist-3.3.1-GCCcore-12.3.0.eb --- .../d/dynesty/dynesty-2.1.3-foss-2023a.eb | 41 ++++++++ .../pytest-xdist-3.3.1-GCCcore-12.3.0.eb | 61 ++++++++++++ .../p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb | 96 +++++++++++++++++++ .../typing-extensions-4.8.0-GCCcore-12.3.0.eb | 22 +++++ 4 files changed, 220 insertions(+) create mode 100644 easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb b/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb new file mode 100644 index 00000000000..d1a5101262a --- /dev/null +++ b/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'dynesty' +version = '2.1.3' + +homepage = 'https://dynesty.readthedocs.io/' +description = """dynesty is a Pure Python, MIT-licensed Dynamic Nested Sampling package +for estimating Bayesian posteriors and evidences.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('dill', '0.3.7'), + ('h5py', '3.9.0'), + ('tqdm', '4.66.1'), + ('pytest', '7.4.2'), + ('pytest-xdist', '3.3.1'), +] + +use_pip = True + +exts_list = [ + ('pytest-cov', '4.1.0', { + 'checksums': ['3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6'], + }), + ('coverage', '6.5.0', { + 'checksums': ['f642e90754ee3e06b0e7e51bce3379590e76b7f76b708e1a71ff043f87025c84'], + }), + ('coveralls', '3.3.1', { + 'checksums': ['b32a8bb5d2df585207c119d6c01567b81fba690c9c10a753bfe27a335bfc43ea'], + }), + (name, version, { + 'checksums': ['26b6c538ff59be4cfd27871b9b78e62c333052234f99c288e269ec022849a345'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..47bba67554b --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'pytest-xdist' +version = '3.3.1' + +homepage = 'https://github.com/pytest-dev/pytest-xdist' +description = """xdist: pytest distributed testing plugin + +The pytest-xdist plugin extends pytest with some unique test execution modes: + + * test run parallelization: if you have multiple CPUs or hosts you + can use those for a combined test run. This allows to speed up + development or to use special resources of remote machines. + + * --looponfail: run your tests repeatedly in a subprocess. After + each run pytest waits until a file in your project changes and + then re-runs the previously failing tests. This is repeated + until all tests pass after which again a full run is + performed. + + * Multi-Platform coverage: you can specify different Python + interpreters or different platforms and run tests in parallel on + all of them. + +Before running tests remotely, pytest efficiently “rsyncs” your +program source code to the remote place. All test results are reported +back and displayed to your local terminal. You may specify different +Python versions and interpreters.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('pytest', '7.4.2'), + ('hatchling', '1.18.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('apipkg', '3.0.2', { + 'checksums': ['c7aa61a4f82697fdaa667e70af1505acf1f7428b1c27b891d204ba7a8a3c5e0d'], + }), + ('execnet', '2.0.2', { + 'checksums': ['cc59bc4423742fd71ad227122eb0dd44db51efb3dc4095b45ac9a08c770096af'], + }), + (name, version, { + 'modulename': 'xdist', + 'checksums': ['d5ee0520eb1b7bcca50a60a518ab7a7707992812c578198f8b44fdfac78e8c93'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..3d67f361036 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb @@ -0,0 +1,96 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.4.2' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('typing-extensions', '4.8.0'), + ('hatchling', '1.18.0'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('setuptools-scm', '8.0.4', { + 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + }), + ('flit-core', '3.9.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.3', { + 'checksums': ['097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9'], + }), + ('attrs', '23.1.0', { + 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('hypothesis', '6.88.1', { + 'checksums': ['f4c2c004b9ec3e0e25332ad2cb6b91eba477a855557a7b5c6e79068809ff8b51'], + }), + ('elementpath', '4.1.5', { + 'checksums': ['c2d6dc524b29ef751ecfc416b0627668119d8812441c555d7471da41d4bacb8d'], + }), + ('xmlschema', '2.5.0', { + 'checksums': ['276a03e0fd3c94c148d528bff4d9482f9b99bf8c7b4056a2e8e703d28149d454'], + }), + ('iniconfig', '2.0.0', { + 'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'], + }), + ('pluggy', '1.3.0', { + 'checksums': ['cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12'], + }), + (name, version, { + 'checksums': ['a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069'], + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..c1d6fc3757c --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.8.0' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions - Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From 293f2e717e0f32448c4448759da09bca827343da Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 27 Oct 2023 15:26:44 +0200 Subject: [PATCH 9287/9987] add env var to find MIBiG data files. --- .../b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 9 ++++++++- ...E-1.1.5_use_env_var_to_find-MIBiG-files.patch | 16 ++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb index ee064b78496..01cc4ccc891 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -13,7 +13,14 @@ toolchain = {'name': 'foss', 'version': '2022a'} github_account = 'medema-group' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7'] +patches = [ + '%(name)s-%(version)s_use_env_var_to_find-MIBiG-files.patch', +] +checksums = [ + {'v1.1.5.tar.gz': 'ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7'}, + {'BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch': + 'f0602208765a2686a324a27ff6073aac01c230b6a81a00656269fd89c97cf370'}, +] dependencies = [ ('Python', '3.10.4'), diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch new file mode 100644 index 00000000000..cac18434370 --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch @@ -0,0 +1,16 @@ +Use MIBIG_PATH env var to locate MIBiG files instead of hardocded path +that isn't right in the first place. + +Åke Sandgren, 20231027 +diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py +--- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 ++++ BiG-SCAPE-1.1.5/bigscape.py 2023-10-27 14:15:41.385679191 +0200 +@@ -2336,6 +2336,8 @@ + + print("\n Trying to read bundled MIBiG BGCs as reference") + mibig_path = os.path.join(os.path.dirname(os.path.realpath(__file__)),"Annotated_MIBiG_reference") ++ # Use environment variable as first choice ++ mibig_path = os.getenv('MIBIG_PATH', mibig_path) + bgcs_path = os.path.join(mibig_path,mibig_zipfile_numbgcs[1]) + + # try to see if the zip file has already been decompressed From 05e88dc38b5d782fed3c2bb86bbb8d43aae36547 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 27 Oct 2023 16:10:50 +0100 Subject: [PATCH 9288/9987] adding easyconfigs: RagTag-2.1.0-foss-2022a.eb, unimap-0.1-GCCcore-11.3.0.eb --- .../r/RagTag/RagTag-2.1.0-foss-2022a.eb | 52 +++++++++++++++++++ .../u/unimap/unimap-0.1-GCCcore-11.3.0.eb | 42 +++++++++++++++ 2 files changed, 94 insertions(+) create mode 100755 easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022a.eb create mode 100755 easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022a.eb new file mode 100755 index 00000000000..d6ffda0d23c --- /dev/null +++ b/easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonPackage' + +name = 'RagTag' +version = '2.1.0' + +homepage = 'https://github.com/malonge/RagTag' +description = """RagTag is a collection of software tools for scaffolding and +improving modern genome assemblies. Tasks include: homology-based misassembly +correction, homology-based assembly scaffolding and patching, and scaffold +merging. RagTag also provides command line utilities for working with common +genome assembly file formats.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/malonge/RagTag/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ragtag-2.0.1-scripts.patch'] +checksums = [ + {'v2.1.0.tar.gz': 'b044b5e4305219ed1d9f05ffb9e7635e2ab61a4f72ab49660feede1a502aa419'}, + {'ragtag-2.0.1-scripts.patch': '01d1623fade21fb838904334fc2afc93351e66241c612939c619714658f43687'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Pysam', '0.19.1'), + ('networkx', '2.8.4'), + ('MUMmer', '4.0.0rc1'), + ('minimap2', '2.24'), + ('unimap', '0.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/ragtag.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'ragtag.py updategff --help', + # Ragtag exec()s these commands + 'nucmer --help', + 'minimap2 --help', + 'unimap --help', +] + +options = {'modulename': 'ragtag_utilities'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-11.3.0.eb new file mode 100755 index 00000000000..508f58237b4 --- /dev/null +++ b/easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'unimap' +version = '0.1' + +homepage = 'https://github.com/lh3/unimap' +description = """Unimap is a fork of minimap2 optimized for assembly-to-reference +alignment. It integrates the minigraph chaining algorithm and can align through +long INDELs (up to 100kb by default) much faster than minimap2. Unimap is a +better fit for resolving segmental duplications and is recommended over minimap2 +for alignment between high-quality assemblies. + +Unimap does not replace minimap2 for other types of alignment. It drops the +support of multi-part index and short-read mapping. Its long-read alignment is +different from minimap2 but is not necessarily better. Unimap is more of a +specialized minimap2 at the moment.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/lh3/unimap/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d5d7831e1fa78c943a96ef78ba22ec88eebf39368bdb135c30554f052f0dbc5c'] + +builddependencies = [('binutils', '2.38')] + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "unimap --help", + "cd %(builddir)s/unimap-%(version)s && unimap -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' From d7cfc63da287f2c25d6990f88095b132dd3fb4d7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 27 Oct 2023 16:36:43 +0100 Subject: [PATCH 9289/9987] non-executable --- easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-11.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/unimap/unimap-0.1-GCCcore-11.3.0.eb old mode 100755 new mode 100644 From 346c5d65a76e82c7dbeda78947fb0f0e7bf61495 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 27 Oct 2023 17:08:59 +0100 Subject: [PATCH 9290/9987] non-executable --- easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/r/RagTag/RagTag-2.1.0-foss-2022a.eb old mode 100755 new mode 100644 From be9599b44b0f8d27a080f4f3ad84d0bca486a1ec Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 27 Oct 2023 17:12:56 +0100 Subject: [PATCH 9291/9987] adding easyconfigs: muParser-2.3.4-GCCcore-12.2.0.eb --- .../muParser/muParser-2.3.4-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e55a9dbe87a --- /dev/null +++ b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'muParser' +version = '2.3.4' + +homepage = 'https://beltoforion.de/article.php?a=muparser' +description = """ + muParser is an extensible high performance math expression parser library + written in C++. It works by transforming a mathematical expression into + bytecode and precalculating constant parts of the expression. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/beltoforion/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0c3fa54a3ebf36dda0ed3e7cd5451c964afbb15102bdbcba08aafb359a290121'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = "-DENABLE_SAMPLES=OFF -DBUILD_SHARED_LIBS=ON" + + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/libmuparser.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' From 957de26e4ae208af0f787324dc64ce13cb982efe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 27 Oct 2023 20:29:06 +0200 Subject: [PATCH 9292/9987] Enable PIC in recent libwebp build --- easybuild/easyconfigs/l/libwebp/libwebp-1.3.2-GCCcore-13.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.2-GCCcore-13.2.0.eb index 2d6e433838e..760365c2bc9 100644 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.3.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.3.2-GCCcore-13.2.0.eb @@ -10,6 +10,7 @@ webmasters and web developers can create smaller, richer images that make the web faster.""" toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] sources = [SOURCELOWER_TAR_GZ] From 097f893e476ef5071f59e7890a57a06365fc75bc Mon Sep 17 00:00:00 2001 From: Orient Date: Fri, 27 Oct 2023 21:06:02 +0200 Subject: [PATCH 9293/9987] Added a space to the beginning of a comment --- .../easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb index 9db2550d17c..f1110ec02d4 100644 --- a/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb @@ -21,7 +21,7 @@ dependencies = [ ('BLAST+', '2.13.0'), ] -#GFF3-toolkit has hardcoded path to BLAST+ libraries, so we have to add a symlink to the required path for this to work +# GFF3-toolkit has hardcoded path to BLAST+ libraries, so we have to add a symlink to the required path for this to work local_blast_path = '%(installdir)s/lib/python%(pyshortver)s/site-packages/gff3tool/lib/ncbi-blast+' preinstallopts = 'mkdir -p %s && ' % local_blast_path preinstallopts += 'ln -s $EBROOTBLASTPLUS/bin %s && ' % local_blast_path From 8591910a0876ab7d3d1994e626c1e214fac9504d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 28 Oct 2023 14:03:35 +0200 Subject: [PATCH 9294/9987] remove empty versionsuffix line in easyconfig for ParaView 5.11.2 --- easybuild/easyconfigs/p/ParaView/ParaView-5.11.2-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.2-foss-2023a.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.2-foss-2023a.eb index 29377002716..c849554271c 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.2-foss-2023a.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.2-foss-2023a.eb @@ -2,7 +2,6 @@ easyblock = 'CMakeMake' name = 'ParaView' version = '5.11.2' -versionsuffix = '' homepage = 'https://www.paraview.org' description = "ParaView is a scientific parallel visualizer." From db42f9b689edfa73c15d21c3a433c3eb065e0e1d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 28 Oct 2023 16:19:25 +0200 Subject: [PATCH 9295/9987] add sanity check commands for pyro-ppl 1.8.0 + align more with existing pyro-ppl easyconfig --- .../pyro-ppl-1.8.0-foss-2021a-CUDA-11.3.1.eb | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.0-foss-2021a-CUDA-11.3.1.eb index fe9debfd281..2bf1ab424b3 100644 --- a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.0-foss-2021a-CUDA-11.3.1.eb @@ -7,20 +7,18 @@ easyblock = 'PythonBundle' name = 'pyro-ppl' version = '1.8.0' versionsuffix = '-CUDA-%(cudaver)s' -local_pytorch_version = '1.10.0' homepage = 'https://github.com/pyro-ppl/pyro' -description = """Pyro is a flexible, scalable deep probabilistic programming -library built on PyTorch.""" +description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch." toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), + ('PyTorch', '1.10.0', versionsuffix), ('tqdm', '4.61.2'), - ('CUDA', '11.3.1', '', SYSTEM), - ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), ] use_pip = True @@ -30,15 +28,21 @@ exts_list = [ 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], }), ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], - 'modulename': 'pyroapi' }), (name, version, { - 'checksums': ['68e4ea30f219227dd88e55de2550d3f8c20a20adbdb67ad1e13b50868bb2ac0c'], 'modulename': 'pyro', + 'checksums': ['68e4ea30f219227dd88e55de2550d3f8c20a20adbdb67ad1e13b50868bb2ac0c'], }), ] sanity_pip_check = True +sanity_check_commands = [ + "python -c 'from pyroapi import distributions as dist'", + "python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'", + "python -c 'from pyro import infer, nn, distributions'", +] + moduleclass = 'tools' From a9dc9a6e0cdb411af843864fd664557ea12a7599 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 28 Oct 2023 16:28:48 +0200 Subject: [PATCH 9296/9987] adding easyconfigs: virtualenv-20.24.6-GCCcore-13.2.0.eb, setuptools-rust-1.8.0-GCCcore-13.2.0.eb, scikit-build-0.17.6-GCCcore-13.2.0.eb, maturin-1.3.1-GCCcore-13.2.0.eb, poetry-1.6.1-GCCcore-13.2.0.eb, cryptography-41.0.5-GCCcore-13.2.0.eb, hatchling-1.18.0-GCCcore-13.2.0.eb --- .../cryptography-41.0.5-GCCcore-13.2.0.eb | 142 ++++ .../hatchling-1.18.0-GCCcore-13.2.0.eb | 65 ++ .../m/maturin/maturin-1.3.1-GCCcore-13.2.0.eb | 616 ++++++++++++++++++ .../p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb | 162 +++++ .../scikit-build-0.17.6-GCCcore-13.2.0.eb | 37 ++ .../setuptools-rust-1.8.0-GCCcore-13.2.0.eb | 39 ++ .../virtualenv-20.24.6-GCCcore-13.2.0.eb | 47 ++ 7 files changed, 1108 insertions(+) create mode 100644 easybuild/easyconfigs/c/cryptography/cryptography-41.0.5-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/m/maturin/maturin-1.3.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/cryptography/cryptography-41.0.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cryptography/cryptography-41.0.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..396020d6259 --- /dev/null +++ b/easybuild/easyconfigs/c/cryptography/cryptography-41.0.5-GCCcore-13.2.0.eb @@ -0,0 +1,142 @@ +easyblock = 'CargoPythonPackage' + +name = 'cryptography' +version = '41.0.5' + +homepage = 'https://github.com/pyca/cryptography' +description = "cryptography is a package designed to expose cryptographic primitives and recipes to Python developers." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Rust', '1.73.0'), # required for cryptography + ('hatchling', '1.18.0'), + ('setuptools-rust', '1.8.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('cffi', '1.15.1'), +] + +crates = [ + ('Inflector', '0.11.4'), + ('aliasable', '0.1.3'), + ('asn1', '0.15.2'), + ('asn1_derive', '0.15.2'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('bitflags', '1.3.2'), + ('cc', '1.0.79'), + ('cfg-if', '1.0.0'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('indoc', '1.0.9'), + ('libc', '0.2.144'), + ('lock_api', '0.4.9'), + ('memoffset', '0.8.0'), + ('once_cell', '1.17.2'), + ('openssl', '0.10.54'), + ('openssl-macros', '0.1.1'), + ('openssl-sys', '0.9.88'), + ('ouroboros', '0.15.6'), + ('ouroboros_macro', '0.15.6'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.7'), + ('pem', '1.1.1'), + ('pkg-config', '0.3.27'), + ('proc-macro-error', '1.0.4'), + ('proc-macro-error-attr', '1.0.4'), + ('proc-macro2', '1.0.64'), + ('pyo3', '0.18.3'), + ('pyo3-build-config', '0.18.3'), + ('pyo3-ffi', '0.18.3'), + ('pyo3-macros', '0.18.3'), + ('pyo3-macros-backend', '0.18.3'), + ('quote', '1.0.28'), + ('redox_syscall', '0.2.16'), + ('scopeguard', '1.1.0'), + ('smallvec', '1.10.0'), + ('syn', '1.0.109'), + ('syn', '2.0.18'), + ('target-lexicon', '0.12.7'), + ('unicode-ident', '1.0.9'), + ('unindent', '0.1.11'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('windows-sys', '0.45.0'), + ('windows-targets', '0.42.2'), + ('windows_aarch64_gnullvm', '0.42.2'), + ('windows_aarch64_msvc', '0.42.2'), + ('windows_i686_gnu', '0.42.2'), + ('windows_i686_msvc', '0.42.2'), + ('windows_x86_64_gnu', '0.42.2'), + ('windows_x86_64_gnullvm', '0.42.2'), + ('windows_x86_64_msvc', '0.42.2'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'cryptography-41.0.5.tar.gz': '392cb88b597247177172e02da6b7a63deeff1937fa6fec3bbf902ebd75d97ec7'}, + {'Inflector-0.11.4.tar.gz': 'fe438c63458706e03479442743baae6c88256498e6431708f6dfc520a26515d3'}, + {'aliasable-0.1.3.tar.gz': '250f629c0161ad8107cf89319e990051fae62832fd343083bea452d93e2205fd'}, + {'asn1-0.15.2.tar.gz': '28c19b9324de5b815b6487e0f8098312791b09de0dbf3d5c2db1fe2d95bab973'}, + {'asn1_derive-0.15.2.tar.gz': 'a045c3ccad89f244a86bd1e6cf1a7bf645296e7692698b056399b6efd4639407'}, + {'autocfg-1.1.0.tar.gz': 'd468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa'}, + {'base64-0.13.1.tar.gz': '9e1b586273c5702936fe7b7d6896644d8be71e6314cfe09d3167c95f712589e8'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'cc-1.0.79.tar.gz': '50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'foreign-types-0.3.2.tar.gz': 'f6f339eb8adc052cd2ca78910fda869aefa38d22d5cb648e6485e4d3fc06f3b1'}, + {'foreign-types-shared-0.1.1.tar.gz': '00b0228411908ca8685dba7fc2cdd70ec9990a6e753e89b6ac91a84c40fbaf4b'}, + {'indoc-1.0.9.tar.gz': 'bfa799dd5ed20a7e349f3b4639aa80d74549c81716d9ec4f994c9b5815598306'}, + {'libc-0.2.144.tar.gz': '2b00cc1c228a6782d0f076e7b232802e0c5689d41bb5df366f2a6b6621cfdfe1'}, + {'lock_api-0.4.9.tar.gz': '435011366fe56583b16cf956f9df0095b405b82d76425bc8981c0e22e60ec4df'}, + {'memoffset-0.8.0.tar.gz': 'd61c719bcfbcf5d62b3a09efa6088de8c54bc0bfcd3ea7ae39fcc186108b8de1'}, + {'once_cell-1.17.2.tar.gz': '9670a07f94779e00908f3e686eab508878ebb390ba6e604d3a284c00e8d0487b'}, + {'openssl-0.10.54.tar.gz': '69b3f656a17a6cbc115b5c7a40c616947d213ba182135b014d6051b73ab6f019'}, + {'openssl-macros-0.1.1.tar.gz': 'a948666b637a0f465e8564c73e89d4dde00d72d4d473cc972f390fc3dcee7d9c'}, + {'openssl-sys-0.9.88.tar.gz': 'c2ce0f250f34a308dcfdbb351f511359857d4ed2134ba715a4eadd46e1ffd617'}, + {'ouroboros-0.15.6.tar.gz': 'e1358bd1558bd2a083fed428ffeda486fbfb323e698cdda7794259d592ca72db'}, + {'ouroboros_macro-0.15.6.tar.gz': '5f7d21ccd03305a674437ee1248f3ab5d4b1db095cf1caf49f1713ddf61956b7'}, + {'parking_lot-0.12.1.tar.gz': '3742b2c103b9f06bc9fff0a37ff4912935851bee6d36f3c02bcc755bcfec228f'}, + {'parking_lot_core-0.9.7.tar.gz': '9069cbb9f99e3a5083476ccb29ceb1de18b9118cafa53e90c9551235de2b9521'}, + {'pem-1.1.1.tar.gz': 'a8835c273a76a90455d7344889b0964598e3316e2a79ede8e36f16bdcf2228b8'}, + {'pkg-config-0.3.27.tar.gz': '26072860ba924cbfa98ea39c8c19b4dd6a4a25423dbdf219c1eca91aa0cf6964'}, + {'proc-macro-error-1.0.4.tar.gz': 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{'scopeguard-1.1.0.tar.gz': 'd29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd'}, + {'smallvec-1.10.0.tar.gz': 'a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0'}, + {'syn-1.0.109.tar.gz': '72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237'}, + {'syn-2.0.18.tar.gz': '32d41677bcbe24c20c52e7c70b0d8db04134c5d1066bf98662e2871ad200ea3e'}, + {'target-lexicon-0.12.7.tar.gz': 'fd1ba337640d60c3e96bc6f0638a939b9c9a7f2c316a1598c279828b3d1dc8c5'}, + {'unicode-ident-1.0.9.tar.gz': 'b15811caf2415fb889178633e7724bad2509101cde276048e013b9def5e51fa0'}, + {'unindent-0.1.11.tar.gz': 'e1766d682d402817b5ac4490b3c3002d91dfa0d22812f341609f97b08757359c'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'windows-sys-0.45.0.tar.gz': '75283be5efb2831d37ea142365f009c02ec203cd29a3ebecbc093d52315b66d0'}, + {'windows-targets-0.42.2.tar.gz': '8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071'}, + {'windows_aarch64_gnullvm-0.42.2.tar.gz': '597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8'}, + {'windows_aarch64_msvc-0.42.2.tar.gz': 'e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43'}, + {'windows_i686_gnu-0.42.2.tar.gz': 'c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f'}, + {'windows_i686_msvc-0.42.2.tar.gz': '44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060'}, + {'windows_x86_64_gnu-0.42.2.tar.gz': '8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36'}, + {'windows_x86_64_gnullvm-0.42.2.tar.gz': '26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3'}, + {'windows_x86_64_msvc-0.42.2.tar.gz': '9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0'}, +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..765badccfff --- /dev/null +++ b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb @@ -0,0 +1,65 @@ +easyblock = 'PythonBundle' + +name = 'hatchling' +version = '1.18.0' + +homepage = 'https://hatch.pypa.io' +description = """Extensible, standards compliant build backend used by Hatch, +a modern, extensible Python project manager.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('setuptools-scm', '8.0.4', { + 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + }), + ('typing_extensions', '4.8.0', { + 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], + }), + ('pathspec', '0.11.2', { + 'checksums': ['e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3'], + }), + ('pluggy', '1.3.0', { + 'checksums': ['cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12'], + }), + ('editables', '0.5', { + 'checksums': ['309627d9b5c4adc0e668d8c6fa7bac1ba7c8c5d415c2d27f60f081f8e80d1de2'], + }), + ('trove_classifiers', '2023.10.18', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['20a3da8e3cb65587cc9f5d5b837bf74edeb480bba9bd8cd4f03ab056d6b06c4c'], + }), + (name, version, { + 'checksums': ['50e99c3110ce0afc3f7bdbadff1c71c17758e476731c27607940cfa6686489ca'], + }), + ('hatch_vcs', '0.3.0', { + 'checksums': ['cec5107cfce482c67f8bc96f18bbc320c9aa0d068180e14ad317bbee5a153fee'], + }), + ('hatch_fancy_pypi_readme', '23.1.0', { + 'checksums': ['b1df44063094af1e8248ceacd47a92c9cf313d6b9823bf66af8a927c3960287d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.3.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..db1645e18a5 --- /dev/null +++ b/easybuild/easyconfigs/m/maturin/maturin-1.3.1-GCCcore-13.2.0.eb @@ -0,0 +1,616 @@ +easyblock = 'CargoPythonPackage' + +name = 'maturin' +version = '1.3.1' + +homepage = 'https://github.com/pyo3/maturin' +description = """This project is meant as a zero configuration +replacement for setuptools-rust and milksnake. It supports building +wheels for python 3.5+ on windows, linux, mac and freebsd, can upload +them to pypi and has basic pypy and graalpy support.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +crates = [ + ('adler', '1.0.2'), + ('ahash', '0.7.6'), + ('aho-corasick', '0.7.20'), + ('anstream', '0.3.2'), + ('anstyle', '1.0.1'), + ('anstyle-parse', '0.2.1'), + ('anstyle-query', '1.0.0'), + ('anstyle-wincon', '1.0.2'), + ('anyhow', '1.0.75'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64', '0.21.2'), + ('bitflags', '1.3.2'), + ('block-buffer', '0.10.4'), + ('bstr', '1.6.0'), + ('bumpalo', '3.13.0'), + ('byteorder', '1.4.3'), + ('bytes', '1.4.0'), + ('bytesize', '1.2.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cab', '0.4.1'), + ('camino', '1.1.6'), + ('cargo-config2', '0.1.9'), + ('cargo-options', '0.6.0'), + ('cargo-platform', '0.1.3'), + ('cargo-xwin', '0.14.8'), + ('cargo-zigbuild', '0.17.3'), + ('cargo_metadata', '0.18.0'), + ('cbindgen', '0.25.0'), + ('cc', '1.0.82'), + ('cfb', '0.7.3'), + ('cfg-expr', '0.15.4'), + ('cfg-if', '1.0.0'), + ('charset', '0.1.3'), + ('chumsky', '0.9.2'), + ('clap', '4.1.14'), + ('clap_builder', '4.1.14'), + ('clap_complete', '4.2.3'), + ('clap_complete_command', '0.5.1'), + ('clap_complete_fig', '4.2.0'), + ('clap_complete_nushell', '0.1.11'), + ('clap_derive', '4.1.14'), + ('clap_lex', '0.4.1'), + ('cli-table', '0.4.7'), + ('colorchoice', '1.0.0'), + ('configparser', '3.0.2'), + ('console', '0.15.7'), + ('content_inspector', '0.2.4'), + ('core-foundation', '0.9.3'), + ('core-foundation-sys', '0.8.4'), + ('cpufeatures', '0.2.9'), + ('crc32fast', '1.3.2'), + ('crossbeam-channel', '0.5.8'), + ('crossbeam-deque', '0.8.3'), + ('crossbeam-epoch', '0.9.15'), + ('crossbeam-utils', '0.8.16'), + ('crypto-common', '0.1.6'), + ('data-encoding', '2.4.0'), + ('dialoguer', '0.10.4'), + ('diff', '0.1.13'), + ('digest', '0.10.7'), + ('dirs', '5.0.1'), + ('dirs-sys', '0.4.1'), + ('dissimilar', '1.0.7'), + ('dunce', '1.0.4'), + ('either', '1.9.0'), + ('encode_unicode', '0.3.6'), + ('encoding_rs', '0.8.32'), + ('errno', '0.3.2'), + ('errno-dragonfly', '0.1.2'), + ('expect-test', '1.4.1'), + ('fastrand', '1.9.0'), + ('fat-macho', '0.4.7'), + ('filetime', '0.2.22'), + ('flate2', '1.0.27'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.2.0'), + ('fs-err', '2.9.0'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.10'), + ('glob', '0.3.1'), + ('globset', '0.4.10'), + ('goblin', '0.7.1'), + ('hashbrown', '0.12.3'), + ('heck', '0.4.1'), + ('hermit-abi', '0.3.2'), + ('home', '0.5.5'), + ('humantime', '2.1.0'), + ('humantime-serde', '1.1.1'), + ('idna', '0.4.0'), + ('ignore', '0.4.20'), + ('indexmap', '1.9.3'), + ('indicatif', '0.17.6'), + ('indoc', '2.0.3'), + ('instant', '0.1.12'), + ('io-lifetimes', '1.0.11'), + ('is-terminal', '0.4.7'), + ('itertools', '0.11.0'), + ('itoa', '1.0.9'), + ('js-sys', '0.3.64'), + ('keyring', '2.0.5'), + ('lazy_static', '1.4.0'), + ('lddtree', '0.3.3'), + ('libc', '0.2.147'), + ('linux-keyutils', '0.2.3'), + ('linux-raw-sys', '0.3.8'), + ('lock_api', '0.4.10'), + ('log', '0.4.20'), + ('lzxd', '0.1.4'), + ('mailparse', '0.14.0'), + ('matchers', '0.1.0'), + ('memchr', '2.5.0'), + ('memoffset', '0.9.0'), + ('mime', '0.3.17'), + ('mime_guess', '2.0.4'), + ('minijinja', '1.0.8'), + ('minimal-lexical', '0.2.1'), + ('miniz_oxide', '0.7.1'), + ('msi', '0.6.0'), + ('multipart', '0.18.0'), + ('native-tls', '0.2.11'), + ('nom', '7.1.3'), + ('normalize-line-endings', '0.3.0'), + ('normpath', '1.1.1'), + ('nu-ansi-term', '0.46.0'), + ('num_cpus', '1.16.0'), + ('number_prefix', '0.4.0'), + ('once_cell', '1.18.0'), + ('openssl', '0.10.56'), + ('openssl-macros', '0.1.1'), + ('openssl-probe', '0.1.5'), + ('openssl-src', '111.27.0+1.1.1v'), + ('openssl-sys', '0.9.91'), + ('option-ext', '0.2.0'), + ('os_pipe', '1.1.4'), + ('overload', '0.1.1'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('paste', '1.0.14'), + ('path-slash', '0.2.1'), + ('pep440_rs', '0.3.6'), + ('pep508_rs', '0.2.1'), + ('percent-encoding', '2.3.0'), + ('pin-project-lite', '0.2.12'), + ('pkg-config', '0.3.27'), + ('plain', '0.2.3'), + ('platform-info', '2.0.2'), + ('portable-atomic', '1.4.2'), + ('ppv-lite86', '0.2.17'), + ('pretty_assertions', '1.4.0'), + ('proc-macro2', '1.0.66'), + ('psm', '0.1.21'), + ('pyproject-toml', '0.6.1'), + ('python-pkginfo', '0.6.0'), + ('quote', '1.0.33'), + ('quoted_printable', '0.4.8'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rayon', '1.7.0'), + ('rayon-core', '1.11.0'), + ('redox_syscall', '0.2.16'), + ('redox_syscall', '0.3.5'), + ('redox_users', '0.4.3'), + ('regex', '1.7.3'), + ('regex-automata', '0.1.10'), + ('regex-syntax', '0.6.29'), + ('rfc2047-decoder', '0.2.2'), + ('ring', '0.16.20'), + ('rustc_version', '0.4.0'), + ('rustix', '0.37.25'), + ('rustls', '0.21.2'), + ('rustls-pemfile', '1.0.3'), + ('rustls-webpki', '0.100.2'), + ('rustversion', '1.0.14'), + ('ryu', '1.0.15'), + ('same-file', '1.0.6'), + ('schannel', '0.1.22'), + ('scopeguard', '1.2.0'), + ('scroll', '0.11.0'), + ('scroll_derive', '0.11.1'), + ('sct', '0.7.0'), + ('security-framework', '2.9.2'), + ('security-framework-sys', '2.9.1'), + ('semver', '1.0.18'), + ('serde', '1.0.183'), + ('serde_derive', '1.0.183'), + ('serde_json', '1.0.105'), + ('serde_spanned', '0.6.3'), + ('sha2', '0.10.7'), + ('sharded-slab', '0.1.4'), + ('shell-escape', '0.1.5'), + ('shell-words', '1.1.0'), + ('shlex', '1.1.0'), + ('similar', '2.2.1'), + ('smallvec', '1.11.0'), + ('smawk', '0.3.1'), + ('snapbox', '0.4.11'), + ('snapbox-macros', '0.3.4'), + ('socks', '0.3.4'), + ('spin', '0.5.2'), + ('stacker', '0.1.15'), + ('static_assertions', '1.1.0'), + ('strsim', '0.10.0'), + ('syn', '1.0.109'), + ('syn', '2.0.29'), + ('tar', '0.4.40'), + ('target-lexicon', '0.12.11'), + ('tempfile', '3.6.0'), + ('termcolor', '1.2.0'), + ('terminal_size', '0.2.6'), + ('textwrap', '0.16.0'), + ('thiserror', '1.0.47'), + ('thiserror-impl', '1.0.47'), + ('thread_local', '1.1.7'), + ('time', '0.3.20'), + ('time-core', '0.1.0'), + ('time-macros', '0.2.8'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('toml', '0.5.11'), + ('toml', '0.7.4'), + ('toml_datetime', '0.6.2'), + ('toml_edit', '0.19.10'), + ('tracing', '0.1.37'), + ('tracing-attributes', '0.1.26'), + ('tracing-core', '0.1.31'), + ('tracing-log', '0.1.3'), + ('tracing-serde', '0.1.3'), + ('tracing-subscriber', '0.3.17'), + ('trycmd', '0.14.16'), + ('twox-hash', '1.6.3'), + ('typenum', '1.16.0'), + ('unicase', '2.6.0'), + ('unicode-bidi', '0.3.13'), + ('unicode-ident', '1.0.11'), + ('unicode-linebreak', '0.1.5'), + ('unicode-normalization', '0.1.22'), + ('unicode-width', '0.1.10'), + ('untrusted', '0.7.1'), + ('ureq', '2.7.1'), + ('url', '2.4.0'), + ('utf8parse', '0.2.1'), + ('uuid', '1.4.1'), + ('valuable', '0.1.0'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('versions', '5.0.1'), + ('wait-timeout', '0.2.0'), + ('walkdir', '2.3.3'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.87'), + ('wasm-bindgen-backend', '0.2.87'), + ('wasm-bindgen-macro', '0.2.87'), + ('wasm-bindgen-macro-support', '0.2.87'), + ('wasm-bindgen-shared', '0.2.87'), + ('web-sys', '0.3.64'), + ('webpki-roots', '0.23.1'), + ('which', '4.4.0'), + ('wild', '2.1.0'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.5'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.45.0'), + ('windows-sys', '0.48.0'), + ('windows-targets', '0.42.2'), + ('windows-targets', '0.48.2'), + ('windows_aarch64_gnullvm', '0.42.2'), + ('windows_aarch64_gnullvm', '0.48.2'), + ('windows_aarch64_msvc', '0.42.2'), + ('windows_aarch64_msvc', '0.48.2'), + ('windows_i686_gnu', '0.42.2'), + ('windows_i686_gnu', '0.48.2'), + ('windows_i686_msvc', '0.42.2'), + ('windows_i686_msvc', '0.48.2'), + ('windows_x86_64_gnu', '0.42.2'), + ('windows_x86_64_gnu', '0.48.2'), + ('windows_x86_64_gnullvm', '0.42.2'), + ('windows_x86_64_gnullvm', '0.48.2'), + ('windows_x86_64_msvc', '0.42.2'), + ('windows_x86_64_msvc', '0.48.2'), + ('winnow', '0.4.7'), + ('xattr', '1.0.1'), + ('xwin', '0.3.1'), + ('yansi', '0.5.1'), + ('zeroize', '1.6.0'), + ('zip', '0.6.6'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'maturin-1.3.1.tar.gz': 'efa194e99ae5fff185263d8244acacb12ae256ea73aba62c9446f6075ffc7ac1'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'ahash-0.7.6.tar.gz': 'fcb51a0695d8f838b1ee009b3fbf66bda078cd64590202a864a8f3e8c4315c47'}, + {'aho-corasick-0.7.20.tar.gz': 'cc936419f96fa211c1b9166887b38e5e40b19958e5b895be7c1f93adec7071ac'}, + {'anstream-0.3.2.tar.gz': '0ca84f3628370c59db74ee214b3263d58f9aadd9b4fe7e711fd87dc452b7f163'}, + {'anstyle-1.0.1.tar.gz': '3a30da5c5f2d5e72842e00bcb57657162cdabef0931f40e2deb9b4140440cecd'}, + 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'09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'}, + {'zeroize-1.6.0.tar.gz': '2a0956f1ba7c7909bfb66c2e9e4124ab6f6482560f6628b5aaeba39207c9aad9'}, + {'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('setuptools-rust', '1.8.0'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Rust', '1.73.0'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..62fcc19a0e4 --- /dev/null +++ b/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb @@ -0,0 +1,162 @@ +easyblock = 'PythonBundle' + +name = 'poetry' +version = '1.6.1' + +homepage = 'https://python-poetry.org' +description = """Python packaging and dependency management made easy. Poetry helps you declare, manage and install + dependencies of Python projects, ensuring you have the right stack everywhere.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('scikit-build', '0.17.6'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('hatchling', '1.18.0'), + ('cryptography', '41.0.5'), + ('virtualenv', '20.24.6'), +# ('maturin', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('certifi', '2023.7.22', { + 'checksums': ['539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082'], + }), + ('urllib3', '2.0.7', { + 'checksums': ['c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84'], + }), + ('charset-normalizer', '3.3.1', { + 'checksums': ['d9137a876020661972ca6eec0766d81aef8a5627df628b664b234b73396e727e'], + }), + ('dulwich', '0.21.6', { + 'checksums': ['30fbe87e8b51f3813c131e2841c86d007434d160bd16db586b40d47f31dd05b0'], + }), + ('crashtest', '0.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'], + }), + ('zipp', '3.17.0', { + 'checksums': ['84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0'], + }), + ('importlib_metadata', '6.8.0', { + 'checksums': ['dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743'], + }), + ('jeepney', '0.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], + }), + ('SecretStorage', '3.3.3', { + 'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'], + }), + ('more-itertools', '10.1.0', { + 'checksums': ['626c369fa0eb37bac0291bce8259b332fd59ac792fa5497b59837309cd5b114a'], + }), + ('jaraco.classes', '3.3.0', { + 'checksums': ['c063dd08e89217cee02c8d5e5ec560f2c8ce6cdc2fcdc2e68f7b2e5547ed3621'], + }), + ('keyring', '24.2.0', { + 'modulename': False, + 'checksums': ['ca0746a19ec421219f4d713f848fa297a661a8a8c1504867e55bfb5e09091509'], + }), + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + # poetry 1.6.1 has requirement build<0.11.0,>=0.10.0 + ('build', '0.10.0', { + 'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'], + }), + ('installer', '0.7.0', { + 'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + # poetry 1.5.1 has requirement rapidfuzz<3.0.0,>=2.2.0 + ('rapidfuzz', '2.15.2', { + 'checksums': ['bfc1d38a7adcbe8912f980a5f46f27a801dd8655582ff0d4a2c0431c02b7ce33'], + }), + ('cleo', '2.0.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['6eb133670a3ed1f3b052d53789017b6e50fca66d1287e6e6696285f4cb8ea448'], + }), + ('attrs', '23.1.0', { + 'modulename': 'attr', + 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], + }), + ('pyrsistent', '0.20.0', { + 'checksums': ['4c48f78f62ab596c679086084d0dd13254ae4f3d6c72a83ffdf5ebdef8f265a4'], + }), + ('requests-toolbelt', '1.0.0', { + 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], + }), + ('pkginfo', '1.9.6', { + 'checksums': ['8fd5896e8718a4372f0ea9cc9d96f6417c9b986e23a4d116dda26b62cc29d046'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + # poetry 1.6.1 has requirement jsonschema<4.18.0,>=4.10.0 + ('jsonschema', '4.17.3', { + 'checksums': ['0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d'], + }), + ('platformdirs', '3.11.0', { + 'checksums': ['cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3'], + }), + ('shellingham', '1.5.4', { + 'checksums': ['8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de'], + }), + ('tomlkit', '0.12.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['712cbd236609acc6a3e2e97253dfc52d4c2082982a88f61b640ecf0817eab899'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('msgpack', '1.0.7', { + 'checksums': ['572efc93db7a4d27e404501975ca6d2d9775705c2d922390d878fcf768d92c87'], + }), + ('cachecontrol', '0.13.1', { + 'checksums': ['f012366b79d2243a6118309ce73151bf52a38d4a5dac8ea57f09bd29087e506b'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry_core', '1.7.0', { + 'modulename': 'poetry.core', + 'checksums': ['8f679b83bd9c820082637beca1204124d5d2a786e4818da47ec8acefd0353b74'], + }), + ('poetry_plugin_export', '1.5.0', { + 'checksums': ['ecc8738da0c81c3758e36b4e72e04ae59648a547492af2ffe6245af3594bb00f'], + }), + (name, version, { + 'checksums': ['0ab9b1a592731cc8b252b8d6aaeea19c72cc0a109d7468b829ad57e6c48039d2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d42d1fe3d0c --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.6-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.17.6' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('scikit_build', version, { + 'modulename': 'skbuild', + 'checksums': ['b51a51a36b37c42650994b5047912f59b22e3210b23e321f287611f9ef6e5c9d'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..669229c8f11 --- /dev/null +++ b/easybuild/easyconfigs/s/setuptools-rust/setuptools-rust-1.8.0-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'setuptools-rust' +version = '1.8.0' + +homepage = 'https://github.com/PyO3/setuptools-rust' +description = """setuptools-rust is a plugin for setuptools to build Rust Python extensions +implemented with PyO3 or rust-cpython.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('typing_extensions', '4.8.0', { + 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], + }), + ('semantic_version', '2.10.0', { + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + (name, version, { + 'checksums': ['5e02b7a80058853bf64127314f6b97d0efed11e08b94c88ca639a20976f6adc4'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a0b9921fb5c --- /dev/null +++ b/easybuild/easyconfigs/v/virtualenv/virtualenv-20.24.6-GCCcore-13.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'virtualenv' +version = '20.24.6' + +homepage = 'https://github.com/pypa/virtualenv' +description = "A tool for creating isolated virtual python environments." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('distlib', '0.3.7', { + 'checksums': ['9dafe54b34a028eafd95039d5e5d4851a13734540f1331060d31c9916e7147a8'], + }), + ('filelock', '3.13.0', { + 'checksums': ['63c6052c82a1a24c873a549fbd39a26982e8f35a3016da231ead11a5be9dad44'], + }), + ('platformdirs', '3.11.0', { + 'checksums': ['cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3'], + }), + (name, version, { + 'checksums': ['02ece4f56fbf939dbbc33c0715159951d6bf14aaf5457b092e4548e1382455af'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' From 1b01f9d525db83b13b6fbc20377c361aaa2eefd1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 28 Oct 2023 17:59:26 +0200 Subject: [PATCH 9297/9987] Remove leftover comment --- easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb index 62fcc19a0e4..b55799d2110 100644 --- a/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/poetry/poetry-1.6.1-GCCcore-13.2.0.eb @@ -20,7 +20,6 @@ dependencies = [ ('hatchling', '1.18.0'), ('cryptography', '41.0.5'), ('virtualenv', '20.24.6'), -# ('maturin', '1.3.1'), ] use_pip = True From 9bab2f9a82310b427f70628979d7d88a3dcb18c5 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 29 Oct 2023 10:16:04 +0100 Subject: [PATCH 9298/9987] prepare release notes for EasyBuild v4.8.2 + bump version to 4.8.2 --- RELEASE_NOTES | 109 +++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 109 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 6ac82efe759..d264a6443bf 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,117 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 18,021 easyconfig files, for 3,224 different software packages, +The latest version of easybuild-easyconfig provides 18,407 easyconfig files, for 3,292 different software packages, incl. 40 different (compiler) toolchains. +v4.8.2 (29 October 2023) +------------------------ + +update/bugfix release +- added example easyconfig files for 83 new software packages: + - ALL (#18971), anadama2 (#18688) AOFlagger (#19010), Artemis (#18382), bases2fastq (#18866), BgeeCall (#18784), + biobakery-workflows (#18688), BMTK (#18863), CIRIquant (#18815), Clair3 (#18748), CLEAR (#16357), + ConcurrentVersionsSystem (#18985), cpio (#14728), DP3 (#19010), EveryBeam (#19010), fasta-reader (#18936), git-annex + (#18673), GSD (#6453), imutils (#18920), Jblob (#18478), Jmol (#18988), kneaddata (#18688), libbaseencode (#12319), + libcotp (#12319), MACS3 (#18354), Mashtree (#19019), mpath (#5029), MUSCLE3 (#18287), plotutils (#16196), ProBiS + (#18830), PyMC (#10399), PyPy (#18847), PyTensor (#18928), Qt6 (#18683), QuickTree (#19019), Raptor (#18919), RCall + (#18933), ResistanceGA (#18933), scCODA (#18949), scikit-build-core (#18777), segmentation-models-pytorch (#18930), + SNAP-ESA (#19031), SNAP-ESA-python (#19031), starparser (#18965), synapseclient (#19016), uncertainties (#18923), + WSClean (#19010), XBeach (#18849), XOOPIC (#15269), zeus-mcmc (#19033) +- added additional easyconfigs for various supported software packages, including: + - alleleCount 4.3.0, alleleIntegrator 0.8.8, Amber 22.4, Anaconda3 2023.09, ant 1.10.14, Arrow 8.0.0, ArviZ 0.12.1, ArviZ + 0.16.1, ASAP3 3.13.2, ASCAT 3.1.2, ASE 3.22.1, attr 2.5.1, biobambam2 2.0.185, BLAST+ 2.14.1, BLAT 3.7, BLIS 0.9.0, + bokeh 3.2.2, Bowtie 1.3.1, Bowtie2 2.5.1, Brotli 1.1.0, buildenv default, bzip2 1.0.8, Cantera 3.0.0, CapnProto 1.0.1, + casacore 3.5.0, Catch2 2.13.9, Cereal 1.3.2, cffi 1.15.1, CGAL 5.6, Chemaxon-Marvin 23.9, cimfomfa 22.273, CIRCexplorer2 + 2.3.8, Circuitscape 5.12.3, CMake 3.27.6, code-server 4.16.1, Coot 0.9.8.92, CopyKAT 1.1.0, crossguid 20190529, CSBDeep + 0.7.4, ctffind 4.1.14, CUDA-Samples 12.1.1, cuDNN 8.9.2.26, CuPy 12.1.0, cURL 8.3.0, dask 2023.9.2, DIAMOND 2.1.8, DIRAC + 23.0, DL_POLY_4 5.1.0, DoubletFinder 2.0.3, Doxygen 1.9.8, dtcmp 1.1.4, dxpy 0.345.0, EDirect 20.5.20231006, Eigen + 3.4.0, ELPA 2023.05.001, emcee 3.1.4, expat 2.5.0, FastANI 1.34, FastME 2.1.6.3, FFTW 3.3.10, FFTW.MPI 3.3.10, Flask + 2.3.3, FlexiBLAS 3.3.1, Flye 2.9.2, fmt 10.1.0, fmt 8.1.1, fontconfig 2.14.2, foss 2023.09, freetype 2.13.2, GATK + 4.2.6.1, GATK 4.4.0.0, GDAL 3.7.1, GDB 13.2, GDB 13.2, GDRCopy 2.4, GEMMA 0.98.5, gfbf 2023.09, giflib 5.2.1, git + 2.42.0, GlobalArrays 5.8.2, GMAP-GSNAP 2023-04-20, GMP 6.3.0, gmpy2 2.1.5, Go 1.21.1, gompi 2023.09, googletest 1.14.0, + GPAW 23.9.1, gperf 3.1, groff 1.23.0, GST-plugins-bad 1.22.5, GTDB-Tk 2.3.2, GTK4 4.13.1, gzip 1.13, h5netcdf 1.2.0, + harmony 0.1.0, HDF 4.2.16, HighFive 2.7.1, Highway 1.0.7, HISAT2 2.2.1, HMMER 3.4, hmmlearn 0.3.0, Horovod 0.28.1, HPCG + 3.1, HPL 2.0.15, HPL 2.3, iimpi 2023.07, Imath 3.1.9, imkl 2023.2.0, imkl-FFTW 2023.07, impi 2021.10.0, indicators 2.2, + Inspector 2023.2.0, intel 2023.07, intel-compilers 2023.2.1, intltool 0.51.0, ISL 0.26, IsoSeq 4.0.0, itac 2021.10.0, + jbigkit 2.1, JupyterNotebook 7.0.3, Kaleido 0.2.1, kallisto 0.48.0, kim-api 2.3.0, LevelDB 1.22, libarchive 3.7.2, + libcint 5.4.0, libcircle 0.3, libdeflate 1.19, libdrm 2.4.117, libedit 20210910, libffi 3.4.4, libGLU 9.0.3, libglvnd + 1.7.0, libiconv 1.17, libjpeg-turbo 3.0.1, libmaus2 2.0.813, libpng 1.6.40, libreadline 8.2, libsigc++ 2.12.1, libsodium + 1.0.19, LibTIFF 4.6.0, libunwind 1.6.2, libvdwxc 0.4.0, libwebp 1.3.2, libxc 6.2.2, libyaml 0.2.5, line_profiler 4.1.1, + LLVM 16.0.6, LMDB 0.9.31, loomR 0.2.0, lwgrp 1.0.5, lz4 1.9.4, LZO 2.10, MACS2 2.2.7.1, MAFFT 7.520, make 4.4.1, + makedepend 1.0.7, makeinfo 7.0.3, makeinfo 7.1, Mako 1.2.4, Mash 2.3, Mash 2.3, MATLAB 2023b, MCL 22.282, MEGAN 6.25.3, + Mesa 23.1.9, Meson 1.2.3, MMseqs2 14, mold 2.3.1, Monocle3 1.3.1, motif 2.3.8, MPC 1.3.1, MPFR 4.2.1, mpifileutils + 0.11.1, msgpack-c 6.0.0, muParser 2.3.4, n2v 0.3.2, nanopolish 0.14.0, NASM 2.16.01, NBO 7.0.10, netcdf4-python 1.6.4, + netCDF-Fortran 4.6.1, Ninja 1.11.1, NTL 11.5.1, numdiff 5.9.0, OpenBLAS 0.3.24, OpenCV 4.8.1, OpenEXR 3.2.0, OpenFOAM + 10, OpenJPEG 2.5.0, openkim-models 20210811, OpenMM 8.0.0, OpenMolcas 23.06, OpenMPI 4.1.6, OpenPGM 5.2.122, openpyxl + 3.1.2, OpenSlide 3.4.1, openslide-python 1.3.1, OrthoFinder 2.5.5, OSU-Micro-Benchmarks 7.2, p7zip 17.04, ParaView + 5.11.1, ParaView 5.11.2, patchelf 0.18.0, PCRE2 10.42, Perl-bundle-CPAN 5.38.0, PETSc 3.19.2, PGPLOT 5.2.2, photontorch + 0.4.1, pkgconf 1.8.0, plot1cell 0.0.1, PMIx 4.2.6, poppler 23.09.0, preCICE 2.5.0, pretty-yaml 23.9.5, PRSice 2.3.5, + pybedtools 0.8.2, PyCairo 1.25.0, pyEGA3 5.0.2, PyGObject 3.46.0, pygraphviz 1.11, PyPy 7.3.12, pyro-ppl 1.8.0, Pysam + 0.17.0, pytest-rerunfailures 12.0, pytest-shard 0.1.2, Python 3.11.5, PyTorch 1.13.1, PyTorch 1.13.1, PyTorch 2.0.1, + PyTorch-bundle 1.13.1, PyTorch-Ignite 0.4.12, PyYAML 5.4.1, PyYAML 6.0.1, PyZMQ 25.1.0, QCG-PilotJob 0.13.1, + QuantumESPRESSO 7.2, RagTag 2.1.0, rapidcsv 8.62, rasterstats 0.19.0, RAxML-NG 1.2.0, RDFlib 7.0.0, RDKit 2023.03.3, + ReFrame 4.3.2, ReFrame 4.3.3, RepeatMasker 4.1.5, RMBlast 2.14.0, rpy2 3.4.5, ruamel.yaml 0.17.32, Rust 1.73.0, + ScaLAPACK 2.2.0, Scalene 1.5.20, Scalene 1.5.26, scikit-bio 0.5.7, scikit-learn 1.3.1, scikit-optimize 0.9.0, SCons + 4.5.2, SHAP 0.42.1, SHAP 0.42.1, SignalP 6.0h, SMRT-Link 12.0.0.177059, spglib-python 2.1.0, SQLite 3.43.1, StringTie + 2.2.1, SUNDIALS 6.6.0, SVG 2.87, SWIG 4.1.1, sympy 1.12, tabix 0.2.6, Tcl 8.6.13, tensorflow-probability 0.14.0, + TensorRT 8.6.1, texlive 20230313, Tk 8.6.13, Tkinter 3.11.5, TopHat 2.1.2, Trilinos 13.4.1, UCC 1.2.0, UCX 1.15.0, + unimap 0.1, UnZip 6.0, util-linux 2.39, VBZ-Compression 1.0.3, VCFtools 0.1.16, VTune 2023.2.0, Wannier90 3.1.0, WCSLIB + 7.11, worker 1.6.13, wrapt 1.15.0, X11 20231019, x264 20231019, x265 3.5, xarray 2023.9.0, XlsxWriter 3.1.3, XML Parser, + xproto 7.0.31, xtb 6.6.0, Yasm 1.3.0, ZeroMQ 4.3.5, Zip 3.0, zstd 1.5.5 +- minor enhancements, including: + - also run easyconfigs test suite with Python 3.11 (#18009) + - don't disable building of third and fourth derivates in libxc 6.1.0 (#18467) + - add easyconfigs cache file to .gitignore (#18797) + - add patch to improve CUDA 11 compatibility of GCCcore/12.2.0 and GCCcore/12.3.0 (#18854) + - also build Python bindings for ITK 5.2.1 with foss/2022a (#18922) + - add ridge extension to R 4.2.2 (#18924) + - add MSstatsLiP to Bioconductor 3.16 bundle (#19009) + - add escape extension to Bioconductor 3.16 bundle (#19027) + - add patches to build Qt5 5.15.10 with Python 3 instead of Python 2.7 (#19045) +- various bug fixes, including: + - rename ACT to Artemis (#18382) + - backport lchown patch to PMIx 3.1.x + 3.2.x (#18759) + - also copy scripts directory for Clair3 (#18783) + - rename isoseq3 after download for IsoSeq 3.8.2 + fix permissions (#18785) + - fix wrong version of, and missing, extensions for Perl, detected by easyblock PR 2699 (#18789) + - add patch for OpenBLAS 0.3.23 to fix hanging tests (#18790) + - add patch to fix Open MPI 4.1.5 with PMIx >= 4.2.3 (#18833) + - fix permission issues when copying xvfb-run script in Xvfb easyconfigs (#18834) + - statically link Boost 1.75 in Cufflinks v20190706 installed with GCC/11.2.0, so Boost can be changed to build dependency (#18843) + - add missing required PyPy dependency for Clair3, also copy preprocess and shared subdirectories, and enhance sanity check for provided libclair3 Python package (#18847) + - add patch to fix build of util-linux 2.39 on CentOS 7 (#18855) + - add patch to fix finding of tk.tcl for Tk 8.6.13 (#18864) + - add patch to fix issue with automatic detection of NeoverseV1 CPU architecture in OpenBLAS v0.3.20 (#18870) + - fix source URL for segemehl 0.3.4 (#18878) + - avoid use of hardcoded paths for Pillow by using --disable-platform-guessing option (#18881) + - add patch to disable flaky DDRGES3 LAPACK test in OpenBLAS 0.3.23 + 0.3.24 (#18887) + - add alternate checksum for NCCL v2.18.3 (#18906) + - add missing dependencies for MONAI to support extras required by MONAI-Label (#18921) + - make sure Python dependency included for ESPResSo is actually used by specifying -DPYTHON_EXECUTABLE (#18963) + - Rename CVS to ConcurrentVersionsSystem (#18985) + - only add tbb as dependency in recent LAMMPS easyconfigs when installing on x86_64 (#19000) + - detect the correct Python for vcflib (#19001) + - fix invalid pointer access in UCX 1.11-1.14 (#19023) + - disable threadedmpi in recent SCOTCH easyconfigs using gompi toolchain (#19024) + - add missing GSL dependency for casacore 3.4.0 (#19042) + - fix pybind11 incompatibility with some CUDA versions and add Catch2 dependency for tests (#19047) + - enable PIC in recent libwebp easyconfig (#19098) +- other changes: + - use UCX 1.14.1 instead of 1.15.0-rc4 in OpenMPI 4.1.5 (#18877 + - change gompi/2023b to gompi/2023.09 for now (#18888) + - in-place bump to UCX 1.15.0 and PMIx 4.2.6 in easyconfigs for OpenMPI v4.1.6 and impi v2021.10.0 (#18900) + - remove 'cstd': 'c++17' as this is default in GCC 11 for Mash (#18941) + - remove 'cstd': 'c++17' as this is default in GCC 11 and no longer needed lowopt for CapnProto (#18942) + - remove 'cstd': 'c++17' as this is default in GCC 11 for Abseil (#18943) + - remove 'cstd': 'c++17' as this is default in GCC 11 for GLIMPSE (#18944) + - remove 'cstd': 'c++17' as this is default in GCC 11 for GATE (#18945) + - remove 'cstd': 'c++17' as this is default in GCC 11 for OGDF (#18946) + - Move ASE from foss/2023a tol gfbf/2023a (#19040) + - use sysroot template in wget easyconfigs to define PKG_CONFIG_PATH (#19080) + + v4.8.1 (11 September 2023) -------------------------- diff --git a/setup.py b/setup.py index 4c5bb9193bf..1aaee4d4aab 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.8.2.dev0' +VERSION = '4.8.2' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 02dad8e402622df091cc2a13810c1c500d4cfe92 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 29 Oct 2023 14:28:25 +0100 Subject: [PATCH 9299/9987] add sanity check commands for recent GDB versions --- easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb | 5 +++++ easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-10.3.0.eb | 5 +++++ .../easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb | 5 +++++ easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb | 5 +++++ easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb | 5 +++++ easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb | 5 +++++ easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb | 5 +++++ 7 files changed, 35 insertions(+) diff --git a/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb index ce542957783..0300093f744 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-10.1-GCCcore-10.2.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-10.3.0.eb index a036bbe3b5d..887741cbd05 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-10.3.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb index a232a09da3b..2ee9015802d 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-10.2-GCCcore-9.3.0-Python-3.8.2.eb @@ -42,4 +42,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb index fe451504a66..a456f0500a8 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-11.1-GCCcore-11.2.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb index 0ff055c409e..3ade2afc70d 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-12.1-GCCcore-11.3.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb index df3bd632ae8..431a3fa995e 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-12.3.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb index 574aef91ec3..ac981628400 100644 --- a/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GDB/GDB-13.2-GCCcore-13.2.0.eb @@ -41,4 +41,9 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [ + 'gdb --help', + 'gdbserver --help', +] + moduleclass = 'debugger' From f40de6698c0130547b97a2f96201dec872d363b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 29 Oct 2023 15:16:34 +0100 Subject: [PATCH 9300/9987] tweak release notes for EasyBuild v4.8.2 --- RELEASE_NOTES | 112 +++++++++++++++++++------------------------------- 1 file changed, 42 insertions(+), 70 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index d264a6443bf..96daf16fe02 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -11,106 +11,78 @@ v4.8.2 (29 October 2023) ------------------------ update/bugfix release -- added example easyconfig files for 83 new software packages: - - ALL (#18971), anadama2 (#18688) AOFlagger (#19010), Artemis (#18382), bases2fastq (#18866), BgeeCall (#18784), +- added example easyconfig files for 48 new software packages: + - ALL (#18971), anadama2 (#18688), AOFlagger (#19010), bases2fastq (#18866), BgeeCall (#18784), biobakery-workflows (#18688), BMTK (#18863), CIRIquant (#18815), Clair3 (#18748), CLEAR (#16357), - ConcurrentVersionsSystem (#18985), cpio (#14728), DP3 (#19010), EveryBeam (#19010), fasta-reader (#18936), git-annex - (#18673), GSD (#6453), imutils (#18920), Jblob (#18478), Jmol (#18988), kneaddata (#18688), libbaseencode (#12319), - libcotp (#12319), MACS3 (#18354), Mashtree (#19019), mpath (#5029), MUSCLE3 (#18287), plotutils (#16196), ProBiS - (#18830), PyMC (#10399), PyPy (#18847), PyTensor (#18928), Qt6 (#18683), QuickTree (#19019), Raptor (#18919), RCall - (#18933), ResistanceGA (#18933), scCODA (#18949), scikit-build-core (#18777), segmentation-models-pytorch (#18930), - SNAP-ESA (#19031), SNAP-ESA-python (#19031), starparser (#18965), synapseclient (#19016), uncertainties (#18923), - WSClean (#19010), XBeach (#18849), XOOPIC (#15269), zeus-mcmc (#19033) + cpio (#14728), DP3 (#19010), EveryBeam (#19010), fasta-reader (#18936), git-annex (#18673), GSD (#6453), + imutils (#18920), Jblob (#18478), Jmol (#18988), kneaddata (#18688), libbaseencode (#12319), + libcotp (#12319), MACS3 (#18354), Mashtree (#19019), mpath (#5029), MUSCLE3 (#18287), plotutils (#16196), + ProBiS (#18830), PyMC (#10399), PyPy (#18847), PyTensor (#18928), Qt6 (#18683), QuickTree (#19019), + Raptor (#18919), RCall (#18933), ResistanceGA (#18933), scCODA (#18949), scikit-build-core (#18777), + segmentation-models-pytorch (#18930), SNAP-ESA (#19031), SNAP-ESA-python (#19031), starparser (#18965), + synapseclient (#19016), uncertainties (#18923), WSClean (#19010), XBeach (#18849), XOOPIC (#15269), + zeus-mcmc (#19033) - added additional easyconfigs for various supported software packages, including: - - alleleCount 4.3.0, alleleIntegrator 0.8.8, Amber 22.4, Anaconda3 2023.09, ant 1.10.14, Arrow 8.0.0, ArviZ 0.12.1, ArviZ - 0.16.1, ASAP3 3.13.2, ASCAT 3.1.2, ASE 3.22.1, attr 2.5.1, biobambam2 2.0.185, BLAST+ 2.14.1, BLAT 3.7, BLIS 0.9.0, - bokeh 3.2.2, Bowtie 1.3.1, Bowtie2 2.5.1, Brotli 1.1.0, buildenv default, bzip2 1.0.8, Cantera 3.0.0, CapnProto 1.0.1, - casacore 3.5.0, Catch2 2.13.9, Cereal 1.3.2, cffi 1.15.1, CGAL 5.6, Chemaxon-Marvin 23.9, cimfomfa 22.273, CIRCexplorer2 - 2.3.8, Circuitscape 5.12.3, CMake 3.27.6, code-server 4.16.1, Coot 0.9.8.92, CopyKAT 1.1.0, crossguid 20190529, CSBDeep - 0.7.4, ctffind 4.1.14, CUDA-Samples 12.1.1, cuDNN 8.9.2.26, CuPy 12.1.0, cURL 8.3.0, dask 2023.9.2, DIAMOND 2.1.8, DIRAC - 23.0, DL_POLY_4 5.1.0, DoubletFinder 2.0.3, Doxygen 1.9.8, dtcmp 1.1.4, dxpy 0.345.0, EDirect 20.5.20231006, Eigen - 3.4.0, ELPA 2023.05.001, emcee 3.1.4, expat 2.5.0, FastANI 1.34, FastME 2.1.6.3, FFTW 3.3.10, FFTW.MPI 3.3.10, Flask - 2.3.3, FlexiBLAS 3.3.1, Flye 2.9.2, fmt 10.1.0, fmt 8.1.1, fontconfig 2.14.2, foss 2023.09, freetype 2.13.2, GATK - 4.2.6.1, GATK 4.4.0.0, GDAL 3.7.1, GDB 13.2, GDB 13.2, GDRCopy 2.4, GEMMA 0.98.5, gfbf 2023.09, giflib 5.2.1, git - 2.42.0, GlobalArrays 5.8.2, GMAP-GSNAP 2023-04-20, GMP 6.3.0, gmpy2 2.1.5, Go 1.21.1, gompi 2023.09, googletest 1.14.0, - GPAW 23.9.1, gperf 3.1, groff 1.23.0, GST-plugins-bad 1.22.5, GTDB-Tk 2.3.2, GTK4 4.13.1, gzip 1.13, h5netcdf 1.2.0, - harmony 0.1.0, HDF 4.2.16, HighFive 2.7.1, Highway 1.0.7, HISAT2 2.2.1, HMMER 3.4, hmmlearn 0.3.0, Horovod 0.28.1, HPCG - 3.1, HPL 2.0.15, HPL 2.3, iimpi 2023.07, Imath 3.1.9, imkl 2023.2.0, imkl-FFTW 2023.07, impi 2021.10.0, indicators 2.2, - Inspector 2023.2.0, intel 2023.07, intel-compilers 2023.2.1, intltool 0.51.0, ISL 0.26, IsoSeq 4.0.0, itac 2021.10.0, - jbigkit 2.1, JupyterNotebook 7.0.3, Kaleido 0.2.1, kallisto 0.48.0, kim-api 2.3.0, LevelDB 1.22, libarchive 3.7.2, - libcint 5.4.0, libcircle 0.3, libdeflate 1.19, libdrm 2.4.117, libedit 20210910, libffi 3.4.4, libGLU 9.0.3, libglvnd - 1.7.0, libiconv 1.17, libjpeg-turbo 3.0.1, libmaus2 2.0.813, libpng 1.6.40, libreadline 8.2, libsigc++ 2.12.1, libsodium - 1.0.19, LibTIFF 4.6.0, libunwind 1.6.2, libvdwxc 0.4.0, libwebp 1.3.2, libxc 6.2.2, libyaml 0.2.5, line_profiler 4.1.1, - LLVM 16.0.6, LMDB 0.9.31, loomR 0.2.0, lwgrp 1.0.5, lz4 1.9.4, LZO 2.10, MACS2 2.2.7.1, MAFFT 7.520, make 4.4.1, - makedepend 1.0.7, makeinfo 7.0.3, makeinfo 7.1, Mako 1.2.4, Mash 2.3, Mash 2.3, MATLAB 2023b, MCL 22.282, MEGAN 6.25.3, - Mesa 23.1.9, Meson 1.2.3, MMseqs2 14, mold 2.3.1, Monocle3 1.3.1, motif 2.3.8, MPC 1.3.1, MPFR 4.2.1, mpifileutils - 0.11.1, msgpack-c 6.0.0, muParser 2.3.4, n2v 0.3.2, nanopolish 0.14.0, NASM 2.16.01, NBO 7.0.10, netcdf4-python 1.6.4, - netCDF-Fortran 4.6.1, Ninja 1.11.1, NTL 11.5.1, numdiff 5.9.0, OpenBLAS 0.3.24, OpenCV 4.8.1, OpenEXR 3.2.0, OpenFOAM - 10, OpenJPEG 2.5.0, openkim-models 20210811, OpenMM 8.0.0, OpenMolcas 23.06, OpenMPI 4.1.6, OpenPGM 5.2.122, openpyxl - 3.1.2, OpenSlide 3.4.1, openslide-python 1.3.1, OrthoFinder 2.5.5, OSU-Micro-Benchmarks 7.2, p7zip 17.04, ParaView - 5.11.1, ParaView 5.11.2, patchelf 0.18.0, PCRE2 10.42, Perl-bundle-CPAN 5.38.0, PETSc 3.19.2, PGPLOT 5.2.2, photontorch - 0.4.1, pkgconf 1.8.0, plot1cell 0.0.1, PMIx 4.2.6, poppler 23.09.0, preCICE 2.5.0, pretty-yaml 23.9.5, PRSice 2.3.5, - pybedtools 0.8.2, PyCairo 1.25.0, pyEGA3 5.0.2, PyGObject 3.46.0, pygraphviz 1.11, PyPy 7.3.12, pyro-ppl 1.8.0, Pysam - 0.17.0, pytest-rerunfailures 12.0, pytest-shard 0.1.2, Python 3.11.5, PyTorch 1.13.1, PyTorch 1.13.1, PyTorch 2.0.1, - PyTorch-bundle 1.13.1, PyTorch-Ignite 0.4.12, PyYAML 5.4.1, PyYAML 6.0.1, PyZMQ 25.1.0, QCG-PilotJob 0.13.1, - QuantumESPRESSO 7.2, RagTag 2.1.0, rapidcsv 8.62, rasterstats 0.19.0, RAxML-NG 1.2.0, RDFlib 7.0.0, RDKit 2023.03.3, - ReFrame 4.3.2, ReFrame 4.3.3, RepeatMasker 4.1.5, RMBlast 2.14.0, rpy2 3.4.5, ruamel.yaml 0.17.32, Rust 1.73.0, - ScaLAPACK 2.2.0, Scalene 1.5.20, Scalene 1.5.26, scikit-bio 0.5.7, scikit-learn 1.3.1, scikit-optimize 0.9.0, SCons - 4.5.2, SHAP 0.42.1, SHAP 0.42.1, SignalP 6.0h, SMRT-Link 12.0.0.177059, spglib-python 2.1.0, SQLite 3.43.1, StringTie - 2.2.1, SUNDIALS 6.6.0, SVG 2.87, SWIG 4.1.1, sympy 1.12, tabix 0.2.6, Tcl 8.6.13, tensorflow-probability 0.14.0, - TensorRT 8.6.1, texlive 20230313, Tk 8.6.13, Tkinter 3.11.5, TopHat 2.1.2, Trilinos 13.4.1, UCC 1.2.0, UCX 1.15.0, - unimap 0.1, UnZip 6.0, util-linux 2.39, VBZ-Compression 1.0.3, VCFtools 0.1.16, VTune 2023.2.0, Wannier90 3.1.0, WCSLIB - 7.11, worker 1.6.13, wrapt 1.15.0, X11 20231019, x264 20231019, x265 3.5, xarray 2023.9.0, XlsxWriter 3.1.3, XML Parser, - xproto 7.0.31, xtb 6.6.0, Yasm 1.3.0, ZeroMQ 4.3.5, Zip 3.0, zstd 1.5.5 + - alleleCount 4.3.0, Amber 22.4, ant 1.10.14, ArviZ 0.16.1, ASAP3 3.13.2, biobambam2 2.0.185, BLAST+ 2.14.1, + bokeh 3.2.2, Brotli 1.1.0, Cantera 3.0.0, CapnProto 1.0.1, casacore 3.5.0, Catch2 2.13.9, CGAL 5.6, + Chemaxon-Marvin 23.9, CMake 3.27.6, code-server 4.16.1, Coot 0.9.8.92, CSBDeep 0.7.4, CUDA-Samples 12.1.1, + CuPy 12.1.0, cURL 8.3.0, dask 2023.9.2, DL_POLY_4 5.1.0, DoubletFinder 2.0.3-20230131, Doxygen 1.9.8, dxpy 0.345.0, + EDirect 20.5.20231006, FastANI 1.34, FastME 2.1.6.3, Flask 2.3.3, Flye 2.9.2, fmt 10.1.0, foss/2023.09, + freetype 2.13.2, GDAL 3.7.1, GDRCopy 2.4, git 2.42.0, GMP 6.3.0, Go 1.21.1, googletest 1.14.0, GPAW 23.9.1, + groff 1.23.0, GTDB-Tk 2.3.2, GTK4 4.13.1, gzip 1.13, harmony 0.1.0, HDF 4.2.16, HighFive 2.7.1, Highway 1.0.7, + HMMER 3.4, hmmlearn 0.3.0, Imath 3.1.9, Inspector 2023.2.0, intel/2023.07, IsoSeq 4.0.0, itac 2021.10.0, + JupyterNotebook 7.0.3, libarchive 3.7.2, libcint 5.4.0, libdeflate 1.19, libdrm 2.4.117, libglvnd 1.7.0, + libjpeg-turbo 3.0.1, libmaus2 2.0.813, libpng 1.6.40, libsigc++ 2.12.1, libsodium 1.0.19, LibTIFF 4.6.0, + libwebp 1.3.2, libxc 6.2.2, line_profiler 4.1.1, LMDB 0.9.31, MAFFT 7.520, makeinfo 7.1, MATLAB 2023b, + MEGAN 6.25.3, Mesa 23.1.9, Meson 1.2.3, mold 2.3.1, MPFR 4.2.1, msgpack-c 6.0.0, nanopolish 0.14.0, + NBO 7.0.10, netcdf4-python 1.6.4, OpenBLAS 0.3.24, OpenCV 4.8.1, OpenEXR 3.2.0, OpenMolcas 23.06, OpenMPI 4.1.6, + openslide-python 1.3.1, OrthoFinder 2.5.5, OSU-Micro-Benchmarks 7.2, ParaView 5.11.2, Perl-bundle-CPAN 5.38.0, + PETSc 3.19.2, PMIx 4.2.6, poppler 23.09.0, preCICE 2.5.0, pretty-yaml 23.9.5, PyCairo 1.25.0, pyEGA3 5.0.2, + PyGObject 3.46.0, pygraphviz 1.11, pytest-rerunfailures 12.0, Python 3.11.5, PyTorch 2.0.1, PyTorch-bundle 1.13.1, + PyTorch-Ignite 0.4.12, PyYAML 6.0.1, RagTag 2.1.0, rapidcsv 8.62, rasterstats 0.19.0, RAxML-NG 1.2.0, + RDFlib 7.0.0, RDKit 2023.03.3, ReFrame 4.3.3, RMBlast 2.14.0, ruamel.yaml 0.17.32, Rust 1.73.0, scikit-learn 1.3.1, + SCons 4.5.2, SHAP 0.42.1, SignalP 6.0h, SMRT-Link 12.0.0.177059, spglib-python 2.1.0, SQLite 3.43.1, + TensorRT 8.6.1, texlive 20230313, Tkinter 3.11.5, UCX 1.15.0, VBZ-Compression 1.0.3, VCFtools 0.1.16, + VTune 2023.2.0, X11 20231019, x264 20231019, xarray 2023.9.0, XlsxWriter 3.1.3, xtb 6.6.0, ZeroMQ 4.3.5 - minor enhancements, including: - also run easyconfigs test suite with Python 3.11 (#18009) - don't disable building of third and fourth derivates in libxc 6.1.0 (#18467) - - add easyconfigs cache file to .gitignore (#18797) - - add patch to improve CUDA 11 compatibility of GCCcore/12.2.0 and GCCcore/12.3.0 (#18854) - - also build Python bindings for ITK 5.2.1 with foss/2022a (#18922) + - add easyconfigs cache file to `.gitignore` (#18797) + - add patch to improve CUDA 11 compatibility of `GCCcore/12.2.0` and `GCCcore/12.3.0` (#18854) + - also build Python bindings for ITK 5.2.1 with `foss/2022a` (#18922) - add ridge extension to R 4.2.2 (#18924) - - add MSstatsLiP to Bioconductor 3.16 bundle (#19009) - - add escape extension to Bioconductor 3.16 bundle (#19027) + - add MSstatsLiP (#19009)and escape (#19027) to Bioconductor 3.16 bundle - add patches to build Qt5 5.15.10 with Python 3 instead of Python 2.7 (#19045) - various bug fixes, including: - rename ACT to Artemis (#18382) - backport lchown patch to PMIx 3.1.x + 3.2.x (#18759) - also copy scripts directory for Clair3 (#18783) - rename isoseq3 after download for IsoSeq 3.8.2 + fix permissions (#18785) - - fix wrong version of, and missing, extensions for Perl, detected by easyblock PR 2699 (#18789) + - add missing required extensions + fix wrong version of extensions in recent Perl easyconfigs (#18789) - add patch for OpenBLAS 0.3.23 to fix hanging tests (#18790) - add patch to fix Open MPI 4.1.5 with PMIx >= 4.2.3 (#18833) - fix permission issues when copying xvfb-run script in Xvfb easyconfigs (#18834) - - statically link Boost 1.75 in Cufflinks v20190706 installed with GCC/11.2.0, so Boost can be changed to build dependency (#18843) + - statically link Boost 1.75 in Cufflinks v20190706 installed with `GCC/11.2.0`, so Boost can be changed to build dependency (#18843) - add missing required PyPy dependency for Clair3, also copy preprocess and shared subdirectories, and enhance sanity check for provided libclair3 Python package (#18847) - add patch to fix build of util-linux 2.39 on CentOS 7 (#18855) - add patch to fix finding of tk.tcl for Tk 8.6.13 (#18864) - add patch to fix issue with automatic detection of NeoverseV1 CPU architecture in OpenBLAS v0.3.20 (#18870) - fix source URL for segemehl 0.3.4 (#18878) - - avoid use of hardcoded paths for Pillow by using --disable-platform-guessing option (#18881) + - avoid use of hardcoded paths for Pillow by using `--disable-platform-guessing` option (#18881) - add patch to disable flaky DDRGES3 LAPACK test in OpenBLAS 0.3.23 + 0.3.24 (#18887) - add alternate checksum for NCCL v2.18.3 (#18906) - add missing dependencies for MONAI to support extras required by MONAI-Label (#18921) - - make sure Python dependency included for ESPResSo is actually used by specifying -DPYTHON_EXECUTABLE (#18963) - - Rename CVS to ConcurrentVersionsSystem (#18985) + - make sure Python dependency included for ESPResSo is actually used by specifying `-DPYTHON_EXECUTABLE` (#18963) - only add tbb as dependency in recent LAMMPS easyconfigs when installing on x86_64 (#19000) - detect the correct Python for vcflib (#19001) - fix invalid pointer access in UCX 1.11-1.14 (#19023) - disable threadedmpi in recent SCOTCH easyconfigs using gompi toolchain (#19024) - add missing GSL dependency for casacore 3.4.0 (#19042) - fix pybind11 incompatibility with some CUDA versions and add Catch2 dependency for tests (#19047) - - enable PIC in recent libwebp easyconfig (#19098) + - enable `-fPIC` in easyconfig for libwebp 1.3.2 (#19098) - other changes: - - use UCX 1.14.1 instead of 1.15.0-rc4 in OpenMPI 4.1.5 (#18877 - - change gompi/2023b to gompi/2023.09 for now (#18888) - - in-place bump to UCX 1.15.0 and PMIx 4.2.6 in easyconfigs for OpenMPI v4.1.6 and impi v2021.10.0 (#18900) - - remove 'cstd': 'c++17' as this is default in GCC 11 for Mash (#18941) - - remove 'cstd': 'c++17' as this is default in GCC 11 and no longer needed lowopt for CapnProto (#18942) - - remove 'cstd': 'c++17' as this is default in GCC 11 for Abseil (#18943) - - remove 'cstd': 'c++17' as this is default in GCC 11 for GLIMPSE (#18944) - - remove 'cstd': 'c++17' as this is default in GCC 11 for GATE (#18945) - - remove 'cstd': 'c++17' as this is default in GCC 11 for OGDF (#18946) - - Move ASE from foss/2023a tol gfbf/2023a (#19040) + - remove 'cstd': 'c++17' as that's the default in GCC 11 (#18941, #18942, #18943, #18944, #18945, #18946) + - rename CVS to ConcurrentVersionsSystem, to avoid problems with recent setuptools versions (#18985) - use sysroot template in wget easyconfigs to define PKG_CONFIG_PATH (#19080) From 7c83a553950c233943c7b0189762f8c05cfea852 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 29 Oct 2023 20:44:17 +0100 Subject: [PATCH 9301/9987] adding easyconfigs: EasyBuild-4.8.2.eb --- .../e/EasyBuild/EasyBuild-4.8.2.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.2.eb new file mode 100644 index 00000000000..3ee367b47ec --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.8.2.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.8.2' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/e5/40/17e4ddbe7aa160e67219a90c7c4f67baa4b0efc3a6c21ab0e2c858af8f4e/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/85/07/e59231a6f4a90f6bd7c24c9c3b923469024ab0072af95dac9409624796d1/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/4b/1e/27f7d6785b35978ebb70a518bb1ea699ace8d05395c902a6d518de8590bb/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + {'easybuild-framework-4.8.2.tar.gz': '87852289d099aed18e6778c556d8aed173ab1ff711c20e7d9ad32803336b3610'}, + {'easybuild-easyblocks-4.8.2.tar.gz': '796ba8268e2832c6cb78c681401ce401f4d3a6471e1407a3987e76e6f42b3fd7'}, + {'easybuild-easyconfigs-4.8.2.tar.gz': 'c191b09f68cc3a0be33d248edfb892a143424af119f6ae6fd076c7880343cd63'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 4310a29cc0e621470bea5a4169dd5c065b7f0405 Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Mon, 30 Oct 2023 09:37:16 +0800 Subject: [PATCH 9302/9987] the mdust --- .../m/mDust/mDust-20231029-GCC-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb b/easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb new file mode 100644 index 00000000000..12a25eb3276 --- /dev/null +++ b/easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'mDust' +version = '20231029' + +homepage = 'https://github.com/lh3/mdust' +description = "mdust from DFCI Gene Indices Software Tools (archived for a historical record only)" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +sources = [{ + 'filename': 'mdust.tar.gz', + 'git_config': { + 'url': 'https://github.com/lh3', + 'repo_name': 'mdust', + 'commit': '3e3fed8', + 'clone_into': 'mdustSrc', + }, +}] +# git clone, might have to adjust this checksum +checksums = ['6fe21806e6bcd3810babed8d83dfb9ff072fcb9d3a31cd43da9cb9670c0ec6f0'] + +configure_without_installdir = True + +files_to_copy = [] + +postinstallcmds = ['mkdir %(installdir)s/bin', + 'cp mdust %(installdir)s/bin'] + +sanity_check_paths = { + 'files': ['bin/mdust'], + 'dirs': [] +} + +sanity_check_commands = ["mdust < /dev/null"] + +moduleclass = 'bio' From d03ec7d4694b6422e113c1a8166113ed62b1da1a Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 30 Oct 2023 10:36:46 +0100 Subject: [PATCH 9303/9987] Only set flag --enable-asmjit when installing on x86_64 --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb | 3 ++- easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb | 3 ++- 7 files changed, 14 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb index da1d6cc2774..dd7b7837215 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb @@ -35,7 +35,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb index efbec7485f0..10d4af1198f 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb index 886f07ba021..e3a435b4dd6 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb index c7f467034e0..b28de440469 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb index 675fa899a60..8e04ba57a68 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb index 39272200991..67da6c4a802 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb index c0b69eef9b1..b959eaf678f 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb @@ -33,7 +33,8 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -configopts += '--enable-asmjit ' +if ARCH == 'x86_64': + configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used From 410e26ab8a3421bf7f584a1723b5c63c4b207041 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 30 Oct 2023 16:01:43 +0100 Subject: [PATCH 9304/9987] remove flag since it is auto-enabled since version 2.8 --- easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb | 1 + easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb | 1 + easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb | 1 + easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb | 1 + easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb | 2 -- easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb | 2 -- easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb | 2 -- 7 files changed, 4 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb index dd7b7837215..73cd893be22 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.6.2-foss-2020b.eb @@ -36,6 +36,7 @@ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' if ARCH == 'x86_64': + # the flag is not supported on aarch64 configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb index 10d4af1198f..dc860859939 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.0-foss-2020b.eb @@ -34,6 +34,7 @@ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' if ARCH == 'x86_64': + # the flag is not supported on aarch64 configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb index e3a435b4dd6..3a0b31731ee 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.2-foss-2021a.eb @@ -34,6 +34,7 @@ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' if ARCH == 'x86_64': + # the flag is not supported on aarch64 configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb index b28de440469..c653aa77c5b 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.7.3-foss-2021b.eb @@ -34,6 +34,7 @@ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' if ARCH == 'x86_64': + # the flag is not supported on aarch64 configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb index 8e04ba57a68..8dcdc9293d7 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.0-foss-2021b.eb @@ -33,8 +33,6 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -if ARCH == 'x86_64': - configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb index 67da6c4a802..846670014d4 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.8.1-foss-2022a.eb @@ -33,8 +33,6 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -if ARCH == 'x86_64': - configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb index b959eaf678f..a2971db49f7 100644 --- a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.9.0-foss-2022b.eb @@ -33,8 +33,6 @@ dependencies = [ preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python ' configopts += '--enable-boost_graph --enable-boost_serialization ' -if ARCH == 'x86_64': - configopts += '--enable-asmjit ' prebuildopts = 'source sourceme.sh && ' # make sure that ld.gold linker is used From 7509385d663250aa7270ed21a7255f9d24ec2bc4 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Mon, 30 Oct 2023 16:59:39 +0100 Subject: [PATCH 9305/9987] Add dependency SciPy-bundle numpy --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 5b98d3995e4..1a5e2a7b940 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -26,6 +26,7 @@ dependencies = [ ('pybind11', '2.6.2'), ('Python', '3.9.5'), ('Boost.MPI', '1.76.0'), + ('SciPy-bundle', '2021.05'), ] parallel = 1 From 2d394248ba1737b4927089d545ca597477aa42c4 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 30 Oct 2023 16:00:25 -0700 Subject: [PATCH 9306/9987] update Arriba-2.4.0 --- .../a/Arriba/Arriba-2.4.0-GCC-12.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arriba/Arriba-2.4.0-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/a/Arriba/Arriba-2.4.0-GCC-12.2.0.eb b/easybuild/easyconfigs/a/Arriba/Arriba-2.4.0-GCC-12.2.0.eb new file mode 100644 index 00000000000..446ed4277cf --- /dev/null +++ b/easybuild/easyconfigs/a/Arriba/Arriba-2.4.0-GCC-12.2.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'Arriba' +version = '2.4.0' + +github_account = 'suhrig' +homepage = 'https://github.com/%(github_account)s/%(namelower)s' +description = """Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. + It was developed for the use in a clinical research setting. Therefore, short runtimes and high + sensitivity were important design criteria.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(github_account)s/%(namelower)s/releases/download/v%(version)s'] +sources = ['%(namelower)s_v%(version)s.tar.gz'] +checksums = ['a5173f44195d7f864aab95972d0cc3da85671c4b7e602e5a4e1a4fc143810e4a'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('HTSlib', '1.17'), + ('libdeflate', '1.15'), + ('STAR', '2.7.10b'), + ('zlib', '1.2.12'), + ('XZ', '5.2.7'), +] + +# make target with dynamically linked libraries is called bioconda, default is a statically linked binary +build_cmd_targets = 'bioconda' +# otherwise it fails to find sam.h +buildopts = 'CPATH=${EBROOTHTSLIB}/include/htslib:CPATH' + +postinstallcmds = ['mkdir %(installdir)s/database'] +files_to_copy = ['%(namelower)s', 'documentation', 'download_references.sh', 'draw_fusions.R', 'LICENSE', + 'README.md', 'run_%(namelower)s.sh'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [('%(namelower)s', '-h')] + +moduleclass = 'bio' From 9e6ab6895cdc92901d38e15aa118edaf14e0f361 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 31 Oct 2023 00:16:56 +0100 Subject: [PATCH 9307/9987] Added requested changes --- .../d/dynesty/dynesty-2.1.3-foss-2023a.eb | 7 +++-- .../pytest-xdist-3.3.1-GCCcore-12.3.0.eb | 6 ++-- .../p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb | 29 ++----------------- 3 files changed, 11 insertions(+), 31 deletions(-) diff --git a/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb b/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb index d1a5101262a..9835112f86e 100644 --- a/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb +++ b/easybuild/easyconfigs/d/dynesty/dynesty-2.1.3-foss-2023a.eb @@ -9,14 +9,17 @@ for estimating Bayesian posteriors and evidences.""" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('pytest', '7.4.2'), + ('pytest-xdist', '3.3.1'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('dill', '0.3.7'), ('h5py', '3.9.0'), ('tqdm', '4.66.1'), - ('pytest', '7.4.2'), - ('pytest-xdist', '3.3.1'), ] use_pip = True diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb index 47bba67554b..7330aa9e074 100644 --- a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb @@ -29,12 +29,14 @@ Python versions and interpreters.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -builddependencies = [('binutils', '2.40')] +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] dependencies = [ ('Python', '3.11.3'), ('pytest', '7.4.2'), - ('hatchling', '1.18.0'), ] use_pip = True diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb index 3d67f361036..9d0b6f0c25d 100644 --- a/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest/pytest-7.4.2-GCCcore-12.3.0.eb @@ -12,12 +12,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), + ('hatchling', '1.18.0'), ] dependencies = [ ('Python', '3.11.3'), - ('typing-extensions', '4.8.0'), - ('hatchling', '1.18.0'), + ('Python-bundle-PyPI', '2023.06'), ] use_pip = True @@ -39,12 +39,6 @@ _skip_tests = [ _ignore_tests = ' --ignore='.join(_skip_tests) exts_list = [ - ('tomli', '2.0.1', { - 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], - }), - ('packaging', '23.2', { - 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], - }), ('setuptools-scm', '8.0.4', { 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], }), @@ -52,19 +46,6 @@ exts_list = [ 'source_tmpl': 'flit_core-%(version)s.tar.gz', 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], }), - ('flit-scm', '1.7.0', { - 'source_tmpl': 'flit_scm-%(version)s.tar.gz', - 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], - }), - ('exceptiongroup', '1.1.3', { - 'checksums': ['097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9'], - }), - ('attrs', '23.1.0', { - 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], - }), - ('sortedcontainers', '2.4.0', { - 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], - }), ('hypothesis', '6.88.1', { 'checksums': ['f4c2c004b9ec3e0e25332ad2cb6b91eba477a855557a7b5c6e79068809ff8b51'], }), @@ -74,12 +55,6 @@ exts_list = [ ('xmlschema', '2.5.0', { 'checksums': ['276a03e0fd3c94c148d528bff4d9482f9b99bf8c7b4056a2e8e703d28149d454'], }), - ('iniconfig', '2.0.0', { - 'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'], - }), - ('pluggy', '1.3.0', { - 'checksums': ['cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12'], - }), (name, version, { 'checksums': ['a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069'], }), From e1ebcfef7ae9a933e21a12d2c7edec1d6ee27348 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 31 Oct 2023 00:43:03 +0100 Subject: [PATCH 9308/9987] Removed trailing whitespace --- .../p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb index 7330aa9e074..e9fc2a36b36 100644 --- a/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-xdist/pytest-xdist-3.3.1-GCCcore-12.3.0.eb @@ -31,7 +31,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), - ('hatchling', '1.18.0'), + ('hatchling', '1.18.0'), ] dependencies = [ From eb30ad9e8ed9f38887e53f62393a91482c2eba3a Mon Sep 17 00:00:00 2001 From: Sarah Walters Date: Tue, 31 Oct 2023 14:28:28 +1000 Subject: [PATCH 9309/9987] Add Miniconda3-23.9.0-0 --- .../m/Miniconda3/Miniconda3-23.9.0-0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.9.0-0.eb diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.9.0-0.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.9.0-0.eb new file mode 100644 index 00000000000..890e89a8b08 --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-23.9.0-0.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda3' +version = '23.9.0-0' + +homepage = 'https://docs.conda.io/en/latest/miniconda.html' +description = """Miniconda is a free minimal installer for conda. It is a small, + bootstrap version of Anaconda that includes only conda, Python, the packages they + depend on, and a small number of other useful packages.""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/miniconda/'] +local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH) +sources = ['%%(name)s-py311_%%(version)s-Linux-%s.sh' % local_arch] +checksums = [ + { + '%(name)s-py311_%(version)s-Linux-x86_64.sh': + '43651393236cb8bb4219dcd429b3803a60f318e5507d8d84ca00dafa0c69f1bb', + '%(name)s-py311_%(version)s-Linux-ppc64le.sh': + '07b53e411c2e4423bd34c3526d6644b916c4b2143daa8fbcb36b8ead412239b9', + '%(name)s-py311_%(version)s-Linux-aarch64.sh': + '1242847b34b23353d429fcbcfb6586f0c373e63070ad7d6371c23ddbb577778a', + } +] + +moduleclass = 'lang' From 9bfd37f1ae4dc953b402e8bba7a9fe78ba5766e4 Mon Sep 17 00:00:00 2001 From: Sarah Walters Date: Tue, 31 Oct 2023 16:12:38 +1000 Subject: [PATCH 9310/9987] Correction to wrap lines From f9ee66654cca2089996cf184dbb5f90de7e121ef Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 31 Oct 2023 11:31:27 +0100 Subject: [PATCH 9311/9987] Ensure right Python version is used in DP3, WSClean and dependencies --- .../easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb | 3 +++ easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb | 4 +++- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb | 3 +++ .../easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb | 3 +++ easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb | 3 +++ 5 files changed, 15 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb index eeb528a357b..fc5d1d7e3bd 100644 --- a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb @@ -32,6 +32,9 @@ dependencies = [ ('libxml2', '2.9.13'), ] +# make sure the right Python is used +configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + sanity_check_paths = { 'files': ['include/aoflagger.h', 'bin/aoflagger'], 'dirs': ['bin'], diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index 9c359a65e60..7209a109104 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -42,7 +42,9 @@ dependencies = [ ] configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" -DDATA_DIR=%(installdir)s/data ' -configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON' +configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON ' +# make sure the right Python is used +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { 'files': ['lib/libcasa_casa.%s' % SHLIB_EXT, 'lib/libcasa_mirlib.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb index 41dbbeb6af1..6ee878c3713 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb @@ -36,6 +36,9 @@ dependencies = [ ('AOFlagger', '3.4.0') ] +# make sure the right Python is used +configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + sanity_check_paths = { 'files': ['include/include/dp3/base/DP3.h', 'bin/DP3'], 'dirs': ['bin'], diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb index 43f393b0dc7..48e5bd469f0 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb @@ -36,6 +36,9 @@ dependencies = [ ('libxml2', '2.9.13'), ] +# make sure the right Python is used +configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + sanity_check_paths = { 'files': ['include/EveryBeam/beamformer.h', 'lib/libeverybeam.so'], 'dirs': [], diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb index de04e74ec1c..7822414a2b9 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb @@ -31,6 +31,9 @@ dependencies = [ ('Python', '3.10.4'), ] +# make sure the right Python is used +configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + sanity_check_paths = { 'files': ['include/wscleaninterface.h', 'bin/wsclean'], 'dirs': ['bin'], From c9c2627ae2f0fe4fcdc5181fe72cf69c3cd78904 Mon Sep 17 00:00:00 2001 From: "hung.tao" Date: Tue, 31 Oct 2023 14:00:13 +0100 Subject: [PATCH 9312/9987] adding easyconfigs: ctffind-4.1.14-foss-2022b.eb --- .../c/ctffind/ctffind-4.1.14-foss-2022b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022b.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022b.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022b.eb new file mode 100644 index 00000000000..ff2bc24f2a4 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.4'), + ('LibTIFF', '4.4.0'), + ('GSL', '2.7',), + ('wxWidgets', '3.2.2.1'), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From d7da9537361056ca65857887dd91ab6446c0875d Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 31 Oct 2023 16:32:48 +0100 Subject: [PATCH 9313/9987] Improve comment by being more explicit --- .../easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb | 4 +++- easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb | 4 +++- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb | 4 +++- .../easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb | 4 +++- easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb | 4 +++- 5 files changed, 15 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb index fc5d1d7e3bd..ada37c804a9 100644 --- a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2022a.eb @@ -32,7 +32,9 @@ dependencies = [ ('libxml2', '2.9.13'), ] -# make sure the right Python is used +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb index 7209a109104..d98f5af249e 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2022a.eb @@ -43,7 +43,9 @@ dependencies = [ configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" -DDATA_DIR=%(installdir)s/data ' configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON ' -# make sure the right Python is used +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb index 6ee878c3713..c18f4974acf 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2022a.eb @@ -36,7 +36,9 @@ dependencies = [ ('AOFlagger', '3.4.0') ] -# make sure the right Python is used +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb index 48e5bd469f0..b61f0c86167 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2022a.eb @@ -36,7 +36,9 @@ dependencies = [ ('libxml2', '2.9.13'), ] -# make sure the right Python is used +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb index 7822414a2b9..e3bdcb00894 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2022a.eb @@ -31,7 +31,9 @@ dependencies = [ ('Python', '3.10.4'), ] -# make sure the right Python is used +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 configopts = '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' sanity_check_paths = { From 158f1e6be41575a17af18bb0d32e932c47ca5517 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 1 Nov 2023 00:22:47 +0100 Subject: [PATCH 9314/9987] adding easyconfigs: LittleCMS-2.15-GCCcore-13.2.0.eb, libjxl-0.8.2-GCCcore-13.2.0.eb, gperftools-2.13-GCCcore-13.2.0.eb --- .../gperftools-2.13-GCCcore-13.2.0.eb | 38 ++++++++++++++ .../LittleCMS-2.15-GCCcore-13.2.0.eb | 26 ++++++++++ .../l/libjxl/libjxl-0.8.2-GCCcore-13.2.0.eb | 52 +++++++++++++++++++ 3 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.13-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.13-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..73a117d1b30 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.13-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.13' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'gperftools' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fd43adbe0419cb0eaaa3e439845cc89fe7d42c22eff7fd2d6b7e87ae2acbce1d'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] + +dependencies = [ + ('libunwind', '1.6.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..31e22ec7db5 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.15-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.15' + +homepage = 'https://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%s/' % '.'.join(version.split('.')[:2])] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['b20cbcbd0f503433be2a4e81462106fa61050a35074dc24a4e356792d971ab39'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('libjpeg-turbo', '3.0.1')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d5b0cc38223 --- /dev/null +++ b/easybuild/easyconfigs/l/libjxl/libjxl-0.8.2-GCCcore-13.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'libjxl' +version = '0.8.2' + +homepage = 'https://github.com/libjxl/libjxl' +description = "JPEG XL image format reference implementation" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'libjxl' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['c70916fb3ed43784eb840f82f05d390053a558e2da106e40863919238fa7b420'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('googletest', '1.14.0'), + ('pkgconf', '2.0.3'), + ('Highway', '1.0.7'), # Highway only has a static library +] + +dependencies = [ + ('LittleCMS', '2.15'), + ('Brotli', '1.1.0'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('zlib', '1.2.13'), + ('giflib', '5.2.1'), + ('libwebp', '1.3.2'), + ('OpenEXR', '3.2.0'), + ('gperftools', '2.13'), +] + +configopts = '-DJPEGXL_WARNINGS_AS_ERRORS=OFF -DJPEGXL_ENABLE_SJPEG=OFF -DJPEGXL_ENABLE_SKCMS=OFF ' +# building man pages requires/uses asciidoc (which may be installed in OS, and may fail) +configopts += '-DJPEGXL_ENABLE_MANPAGES=OFF ' +configopts += '-DJPEGXL_FORCE_SYSTEM_BROTLI=ON -DJPEGXL_FORCE_SYSTEM_HWY=ON ' +configopts += '-DJPEGXL_FORCE_SYSTEM_GTEST=ON -DJPEGXL_FORCE_SYSTEM_LCMS2=ON ' + +sanity_check_paths = { + 'files': ['bin/cjxl', 'bin/djxl', 'lib/libjxl.%s' % SHLIB_EXT], + 'dirs': ['include/jxl'], +} + +sanity_check_commands = [ + "cjxl --help", + "djxl --help", +] + +moduleclass = 'lib' From b11ffac9f4328404c64e9fdc446c41fe16885388 Mon Sep 17 00:00:00 2001 From: wdlingit <90846876+wdlingit@users.noreply.github.com> Date: Wed, 1 Nov 2023 17:49:10 +0800 Subject: [PATCH 9315/9987] Update and rename mDust-20231029-GCC-10.3.0.eb to mDust-20150102-GCC-10.3.0.eb modified as the suggested easyconfig practices --- ...-GCC-10.3.0.eb => mDust-20150102-GCC-10.3.0.eb} | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/m/mDust/{mDust-20231029-GCC-10.3.0.eb => mDust-20150102-GCC-10.3.0.eb} (65%) diff --git a/easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb b/easybuild/easyconfigs/m/mDust/mDust-20150102-GCC-10.3.0.eb similarity index 65% rename from easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb rename to easybuild/easyconfigs/m/mDust/mDust-20150102-GCC-10.3.0.eb index 12a25eb3276..81302e8e48d 100644 --- a/easybuild/easyconfigs/m/mDust/mDust-20231029-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/mDust/mDust-20150102-GCC-10.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'MakeCp' -name = 'mDust' -version = '20231029' +name = 'mdust' +version = '20150102' homepage = 'https://github.com/lh3/mdust' description = "mdust from DFCI Gene Indices Software Tools (archived for a historical record only)" @@ -14,18 +14,12 @@ sources = [{ 'url': 'https://github.com/lh3', 'repo_name': 'mdust', 'commit': '3e3fed8', - 'clone_into': 'mdustSrc', }, }] # git clone, might have to adjust this checksum -checksums = ['6fe21806e6bcd3810babed8d83dfb9ff072fcb9d3a31cd43da9cb9670c0ec6f0'] +checksums = [None] -configure_without_installdir = True - -files_to_copy = [] - -postinstallcmds = ['mkdir %(installdir)s/bin', - 'cp mdust %(installdir)s/bin'] +files_to_copy = [(['mdust'], 'bin')] sanity_check_paths = { 'files': ['bin/mdust'], From 1422c1c7721889f5f67a6674fa047829898d7dbf Mon Sep 17 00:00:00 2001 From: wdlingit <90846876+wdlingit@users.noreply.github.com> Date: Wed, 1 Nov 2023 17:52:36 +0800 Subject: [PATCH 9316/9987] Rename mDust-20150102-GCC-10.3.0.eb to mdust-20150102-GCC-10.3.0.eb --- ...{mDust-20150102-GCC-10.3.0.eb => mdust-20150102-GCC-10.3.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/mDust/{mDust-20150102-GCC-10.3.0.eb => mdust-20150102-GCC-10.3.0.eb} (100%) diff --git a/easybuild/easyconfigs/m/mDust/mDust-20150102-GCC-10.3.0.eb b/easybuild/easyconfigs/m/mDust/mdust-20150102-GCC-10.3.0.eb similarity index 100% rename from easybuild/easyconfigs/m/mDust/mDust-20150102-GCC-10.3.0.eb rename to easybuild/easyconfigs/m/mDust/mdust-20150102-GCC-10.3.0.eb From d1477cfda67390a9d27e21ac2a8e652f8dfd684e Mon Sep 17 00:00:00 2001 From: Wendar Lin Date: Wed, 1 Nov 2023 18:06:40 +0800 Subject: [PATCH 9317/9987] rename the folder --- .../easyconfigs/m/{mDust => mdust}/mdust-20150102-GCC-10.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/{mDust => mdust}/mdust-20150102-GCC-10.3.0.eb (100%) diff --git a/easybuild/easyconfigs/m/mDust/mdust-20150102-GCC-10.3.0.eb b/easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb similarity index 100% rename from easybuild/easyconfigs/m/mDust/mdust-20150102-GCC-10.3.0.eb rename to easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb From 0de1c03c962b3e02fc8e22f43da4772d88cfe833 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 1 Nov 2023 11:48:32 +0100 Subject: [PATCH 9318/9987] adding easyconfigs: DFT-D3-3.2.0-intel-compilers-2022.2.1.eb --- .../DFT-D3-3.2.0-intel-compilers-2022.2.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..60c33ea0a87 --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D3/DFT-D3-3.2.0-intel-compilers-2022.2.1.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'DFT-D3' +version = '3.2.0' + +homepage = 'https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3' +description = """DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical + quantum chemical methods.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +source_urls = ['https://www.chemie.uni-bonn.de/grimme/de/software/dft-d3'] +# Note that the DFT-D3 tarball is named as "dftd3.tgz" with no version +# numbering. Also, the authors are prone (alas) to stealth upgrades, so that two +# tarballs with the same version number can have different checksums. For this +# reason, it is suggested to manually download and rename the tarball. The +# checksum may also need updating from time to time. +# Checksum last updated: 20 September 2018 +# Date tarball was reported to have been modified: 14 June 2016 +sources = [{'download_filename': 'dftd3.tgz', 'filename': SOURCELOWER_TGZ}] +checksums = ['d97cf9758f61aa81fd85425448fbf4a6e8ce07c12e9236739831a3af32880f59'] + +prebuildopts = "sed -i 's/OSTYPE=LINUXL/OSTYPE=LINUXI/' Makefile && " + +files_to_copy = [(['dftd3'], 'bin'), (['man.pdf'], 'doc')] + +sanity_check_paths = { + 'files': ['bin/dftd3'], + 'dirs': [], +} + +sanity_check_commands = ['dftd3'] + +moduleclass = 'chem' From f9bd47a6ed098072eb574a8edc0dbd1a711e46e4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 1 Nov 2023 13:58:50 +0100 Subject: [PATCH 9319/9987] remove comment --- easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb b/easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb index 81302e8e48d..5dea5b1bc57 100644 --- a/easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/mdust/mdust-20150102-GCC-10.3.0.eb @@ -16,7 +16,6 @@ sources = [{ 'commit': '3e3fed8', }, }] -# git clone, might have to adjust this checksum checksums = [None] files_to_copy = [(['mdust'], 'bin')] From 2a73fc0874910a5ca25b1b8bb4cf8cc9bac36a4c Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 1 Nov 2023 16:03:22 +0100 Subject: [PATCH 9320/9987] adding easyconfigs: Oases-20180312-GCC-12.3.0.eb --- .../o/Oases/Oases-20180312-GCC-12.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb new file mode 100644 index 00000000000..357a853cb97 --- /dev/null +++ b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = "MakeCp" + +name = 'Oases' +version = '20180312' +local_commit = '1b4c14c' + +homepage = 'http://www.ebi.ac.uk/~zerbino/oases/' +description = """Oases is a de novo transcriptome assembler designed to produce transcripts from + short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +# This is taken from the Oases repo to avoid setting git_config in sources +velvet_commit = '9adf09f7ded7fedaf6b0e5e4edf9f46602e263d3' + +sources = [ + '%s.tar.gz' % local_commit, + '%s.tar.gz' % velvet_commit, +] + +source_urls = [ + 'https://github.com/dzerbino/%(namelower)s/archive/', + 'https://github.com/dzerbino/velvet/archive/', +] + +# listed make targets exclude 'doc' on purpose +buildopts = ['VELVET_DIR=../velvet-%s cleanobj velvet oases' % velvet_commit] +parallel = 1 + +files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.md"] + +sanity_check_paths = { + 'files': ["bin/oases", "LICENSE.txt", "README.md"], + 'dirs': ["data", "scripts", "src", "doc"] +} + +sanity_check_commands = ['oases --version'] + +moduleclass = 'bio' From 39a5ec1d6e8e79f0758d23def1b9b89a90170f3b Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 1 Nov 2023 16:41:42 +0100 Subject: [PATCH 9321/9987] Renamed downloaded files + added checksums + added local_ to local vars --- .../o/Oases/Oases-20180312-GCC-12.3.0.eb | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb index 357a853cb97..03ee0713e0f 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb @@ -11,20 +11,23 @@ description = """Oases is a de novo transcriptome assembler designed to produce toolchain = {'name': 'GCC', 'version': '12.3.0'} # This is taken from the Oases repo to avoid setting git_config in sources -velvet_commit = '9adf09f7ded7fedaf6b0e5e4edf9f46602e263d3' - -sources = [ - '%s.tar.gz' % local_commit, - '%s.tar.gz' % velvet_commit, -] +local_velvet_commit = '9adf09f7ded7fedaf6b0e5e4edf9f46602e263d3' source_urls = [ 'https://github.com/dzerbino/%(namelower)s/archive/', 'https://github.com/dzerbino/velvet/archive/', ] +sources = [ + {'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(namelower)s-%(version)s.tar.gz'}, + {'download_filename': '%s.tar.gz' % local_velvet_commit, 'filename': 'velvet-20140815.tar.gz'} +] +checksums = [ + {'oases-20180312.tar.gz': 'f526b84e9fa3e5f89b728f4a71b8bd23b336b8a6cd83a2d88414710592ec5e4e'}, + {'velvet-20140815.tar.gz': '8e952e3a4bf2ffae586a64e5e97029c9fdd53b5e1991106ef832d73e499b163b'}, +] # listed make targets exclude 'doc' on purpose -buildopts = ['VELVET_DIR=../velvet-%s cleanobj velvet oases' % velvet_commit] +buildopts = ['VELVET_DIR=../velvet-%s cleanobj velvet oases' % local_velvet_commit] parallel = 1 files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.md"] From 75eb561c3c2803b925942b81f11e444628f79bcc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 1 Nov 2023 17:02:29 +0100 Subject: [PATCH 9322/9987] Workaround GCC12 destructor bug --- .../p/PyTorch/PyTorch-2.0.1-foss-2022b.eb | 3 + ...round-gcc12-destructor-exception-bug.patch | 118 ++++++++++++++++++ 2 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb index 6f869d07be5..318e4aacd4f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb @@ -39,6 +39,7 @@ patches = [ 'PyTorch-2.0.1_skip-failing-gradtest.patch', 'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch', 'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch', + 'PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch', ] checksums = [ {'pytorch-v2.0.1.tar.gz': '9c564ca440265c69400ef5fdd48bf15e28af5aa4bed84c95efaad960a6699998'}, @@ -88,6 +89,8 @@ checksums = [ '7047862abc1abaff62954da59700f36d4f39fcf83167a638183b1b7f8fec78ae'}, {'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch': '166c134573a95230e39b9ea09ece3ad8072f39d370c9a88fb2a1e24f6aaac2b5'}, + {'PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch': + '198f2244b7415958f96a2c248bab33491a95454091889824d98b0d4a55f114f3'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch new file mode 100644 index 00000000000..cff643d4138 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_workaround-gcc12-destructor-exception-bug.patch @@ -0,0 +1,118 @@ +GCC 12 introduced a regression that may cause it to call the destructor twice on an object. +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112301 +This is visible in e.g. `test_cpp_extensions_jit.py -k test_warning` +See also https://github.com/pytorch/pytorch/issues/112383 + +Workaround this by trying to avoid the throwing PyWarningHandler destructor. +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/csrc/Exceptions.cpp b/torch/csrc/Exceptions.cpp +index 788f6782730..31d358528e3 100644 +--- a/torch/csrc/Exceptions.cpp ++++ b/torch/csrc/Exceptions.cpp +@@ -246,6 +246,10 @@ PyObject* map_warning_to_python_type(const c10::Warning& warning) { + /// NOLINTNEXTLINE(bugprone-exception-escape) + PyWarningHandler::~PyWarningHandler() noexcept(false) { + c10::WarningUtils::set_warning_handler(prev_handler_); ++ process_warnings(); ++} ++ ++void PyWarningHandler::process_warnings() { + auto& warning_buffer = internal_handler_.warning_buffer_; + + if (!warning_buffer.empty()) { +diff --git a/torch/csrc/Exceptions.h b/torch/csrc/Exceptions.h +index 7c448ddc67f..9779b21bcb7 100644 +--- a/torch/csrc/Exceptions.h ++++ b/torch/csrc/Exceptions.h +@@ -117,6 +117,13 @@ static inline void PyErr_SetString(PyObject* type, const std::string& message) { + retstmnt; \ + } + ++/** To be called inside a HANDLE_TH_ERRORS..END_HANDLE_TH_ERRORS_* block ++ * before returning a value / where no further warnings can occur. ++ * Avoids throwing an error in the destructor which triggers a bug in GCC 12+ ++ * See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112301 ++ */ ++#define FLUSH_TH_ERRORS __enforce_warning_buffer.process_warnings(); ++ + #define END_HANDLE_TH_ERRORS_PYBIND \ + } \ + catch (...) { \ +@@ -372,6 +379,9 @@ struct PyWarningHandler { + in_exception_ = true; + } + ++ // Trigger processing of warnings ++ TORCH_API void process_warnings(); ++ + private: + InternalHandler internal_handler_; + at::WarningHandler* prev_handler_; +@@ -379,26 +389,40 @@ struct PyWarningHandler { + }; + + namespace detail { ++ ++template ++struct conditional_gil_scoped_release: pybind11::gil_scoped_release{}; ++ ++template<> ++struct conditional_gil_scoped_release{ ++ conditional_gil_scoped_release() { ++ // suppress `unused variable` error messages at call sites ++ (void) (this != (this + 1)); ++ } ++}; ++ + template + using Arg = typename invoke_traits::template arg::type; + +-template ++template + auto wrap_pybind_function_impl_( + Func&& f, + std::index_sequence, +- bool release_gil) { ++ std::bool_constant) { + using result_type = typename invoke_traits::result_type; + namespace py = pybind11; + + // f=f is needed to handle function references on older compilers +- return [f = std::forward(f), +- release_gil](Arg... args) -> result_type { ++ return [f = std::forward(f)](Arg... args) -> result_type { + HANDLE_TH_ERRORS +- if (release_gil) { +- py::gil_scoped_release no_gil; +- return c10::guts::invoke(f, std::forward>(args)...); ++ conditional_gil_scoped_release no_gil; ++ if constexpr (std::is_void_v) { ++ c10::guts::invoke(f, std::forward>(args)...); ++ FLUSH_TH_ERRORS + } else { +- return c10::guts::invoke(f, std::forward>(args)...); ++ auto res = c10::guts::invoke(f, std::forward>(args)...); ++ FLUSH_TH_ERRORS ++ return res; + } + END_HANDLE_TH_ERRORS_PYBIND + }; +@@ -411,7 +435,7 @@ template + auto wrap_pybind_function(Func&& f) { + using traits = invoke_traits; + return torch::detail::wrap_pybind_function_impl_( +- std::forward(f), std::make_index_sequence{}, false); ++ std::forward(f), std::make_index_sequence{}, std::false_type{}); + } + + // Wrap a function with TH error, warning handling and releases the GIL. +@@ -420,7 +444,7 @@ template + auto wrap_pybind_function_no_gil(Func&& f) { + using traits = invoke_traits; + return torch::detail::wrap_pybind_function_impl_( +- std::forward(f), std::make_index_sequence{}, true); ++ std::forward(f), std::make_index_sequence{}, std::true_type{}); + } + + } // namespace torch From 0236dd2eaa3498a8990b29554deb1143ffd54a40 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 1 Nov 2023 17:56:38 +0100 Subject: [PATCH 9323/9987] Workaround potential crash in PyTorch 1.13.1 caused by GCC 12 compiler bug --- .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 3 + ...round-gcc12-destructor-exception-bug.patch | 68 +++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 896e238a874..132930e405c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -42,6 +42,7 @@ patches = [ 'PyTorch-1.13.1_skip-failing-grad-test.patch', 'PyTorch-1.13.1_skip-failing-singular-grad-test.patch', 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', + 'PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch', ] checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, @@ -95,6 +96,8 @@ checksums = [ '72688a57b2bb617665ad1a1d5e362c5111ae912c10936bb38a089c0204729f48'}, {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, + {'PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch': + '931142a3133ea8f6819123523b15cbc9dbdaf8c28e34396a09227f865e7c8829'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch new file mode 100644 index 00000000000..0ebcb88930a --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch @@ -0,0 +1,68 @@ +GCC 12 introduced a regression that may cause it to call the destructor twice on an object. +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112301 +This is visible in e.g. `test_cpp_extensions_jit.py -k test_warning` +See also https://github.com/pytorch/pytorch/issues/112383 + +Workaround this by trying to avoid the throwing PyWarningHandler destructor. + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/csrc/Exceptions.cpp b/torch/csrc/Exceptions.cpp +index 5210d6f713d..3c91ed378e1 100644 +--- a/torch/csrc/Exceptions.cpp ++++ b/torch/csrc/Exceptions.cpp +@@ -226,6 +226,10 @@ PyWarningHandler::PyWarningHandler() noexcept(true) + /// NOLINTNEXTLINE(bugprone-exception-escape) + PyWarningHandler::~PyWarningHandler() noexcept(false) { + c10::Warning::set_warning_handler(prev_handler_); ++ process_warnings(); ++} ++ ++void PyWarningHandler::process_warnings() { + auto& warning_buffer = internal_handler_.warning_buffer_; + + if (warning_buffer.size() > 0) { +diff --git a/torch/csrc/Exceptions.h b/torch/csrc/Exceptions.h +index 89256c64bba..7e09d0ebc37 100644 +--- a/torch/csrc/Exceptions.h ++++ b/torch/csrc/Exceptions.h +@@ -110,6 +110,13 @@ static inline void PyErr_SetString(PyObject* type, const std::string& message) { + retstmnt; \ + } + ++/** To be called inside a HANDLE_TH_ERRORS..END_HANDLE_TH_ERRORS_* block ++ * before returning a value / where no further warnings can occur. ++ * Avoids throwing an error in the destructor which triggers a bug in GCC 12+ ++ * See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112301 ++ */ ++#define FLUSH_TH_ERRORS __enforce_warning_buffer.process_warnings(); ++ + #define END_HANDLE_TH_ERRORS_PYBIND \ + } \ + catch (...) { \ +@@ -381,6 +388,9 @@ struct PyWarningHandler { + in_exception_ = true; + } + ++ // Trigger processing of warnings ++ TORCH_API void process_warnings(); ++ + private: + InternalHandler internal_handler_; + at::WarningHandler* prev_handler_; +@@ -399,7 +409,14 @@ auto wrap_pybind_function_impl_(Func&& f, std::index_sequence) { + // f=f is needed to handle function references on older compilers + return [f = f](Arg... args) -> typename traits::result_type { + HANDLE_TH_ERRORS +- return f(std::forward>(args)...); ++ if constexpr (std::is_void_v) { ++ c10::guts::invoke(f, std::forward>(args)...); ++ FLUSH_TH_ERRORS ++ } else { ++ auto res = c10::guts::invoke(f, std::forward>(args)...); ++ FLUSH_TH_ERRORS ++ return res; ++ } + END_HANDLE_TH_ERRORS_PYBIND + }; + } From 44a85f20fdba3219490201815193a58cb13def61 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 1 Nov 2023 20:10:48 +0100 Subject: [PATCH 9324/9987] adding easyconfigs: HepMC-2.06.11-gompi-2022a.eb --- .../h/HepMC/HepMC-2.06.11-gompi-2022a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb diff --git a/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb new file mode 100644 index 00000000000..7d89e8ca6ac --- /dev/null +++ b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'CMakeMake' + +name = 'HepMC' +version = '2.06.11' + +homepage = 'http://hepmc.web.cern.ch/hepmc/' +description = """HepMC is a standard for storing Monte Carlo event data.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://hepmc.web.cern.ch/hepmc/releases/'] +sources = ['hepmc%(version)s.tgz'] +checksums = ['86b66ea0278f803cde5774de8bd187dd42c870367f1cbf6cdaec8dc7cf6afc10'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ +] + +configopts = '-Dmomentum=GEV -Dlength=MM' + +sanity_check_paths = { + 'files': ["lib/libHepMC.so"], + 'dirs': ['include/HepMC'] +} + +moduleclass = 'phys' From 74c75fdd955d489366b47e62998c96da27c51d0a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Nov 2023 10:22:19 +0100 Subject: [PATCH 9325/9987] fix detection of newer Intel CPUs in OpenBLAS 0.3.20-0.3.23 --- .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 2 + .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 2 + .../OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb | 2 + .../OpenBLAS-0.3.20_fix-x86-cpuid.patch | 54 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 2 + .../o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb | 2 + 6 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-x86-cpuid.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index ad53aa70e6b..03bd16ce48f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -16,6 +16,7 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -26,6 +27,7 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 1041b4ef6d3..5b104219e11 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -20,6 +20,7 @@ patches = [ 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', 'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', ] checksums = [ {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, @@ -34,6 +35,7 @@ checksums = [ {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': '1b495465f8dd1e151d74cf5aa4288120361d29164d6a377228a8d51c255b8a9e'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb index 7b49821c348..cbf11c2a295 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb @@ -16,6 +16,7 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -26,6 +27,7 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-x86-cpuid.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-x86-cpuid.patch new file mode 100644 index 00000000000..a26c184754c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_fix-x86-cpuid.patch @@ -0,0 +1,54 @@ +Fix C&P error causing misdetection of CPUs. +Allows auto-detection of Intel SapphireRapids +Backport from https://github.com/OpenMathLib/OpenBLAS/pull/4002 + +Author: Alexander Grund (TU Dresden) + +diff --git a/cpuid_x86.c b/cpuid_x86.c +index d7d85eb20..9a37aa3f1 100644 +--- a/cpuid_x86.c ++++ b/cpuid_x86.c +@@ -1900,7 +1900,8 @@ static char *corename[] = { + "ZEN", + "SKYLAKEX", + "DHYANA", +- "COOPERLAKE" ++ "COOPERLAKE", ++ "SAPPHIRERAPIDS", + }; + + static char *corename_lower[] = { +@@ -1934,7 +1935,8 @@ static char *corename_lower[] = { + "zen", + "skylakex", + "dhyana", +- "cooperlake" ++ "cooperlake", ++ "sapphirerapids", + }; + + +@@ -2240,16 +2242,18 @@ int get_coretype(void){ + return CORE_NEHALEM; + } + if (model == 15) { // Sapphire Rapids ++ if(support_amx_bf16()) ++ return CORE_SAPPHIRERAPIDS; + if(support_avx512_bf16()) +- return CPUTYPE_COOPERLAKE; ++ return CORE_COOPERLAKE; + if(support_avx512()) +- return CPUTYPE_SKYLAKEX; ++ return CORE_SKYLAKEX; + if(support_avx2()) +- return CPUTYPE_HASWELL; ++ return CORE_HASWELL; + if(support_avx()) +- return CPUTYPE_SANDYBRIDGE; ++ return CORE_SANDYBRIDGE; + else +- return CPUTYPE_NEHALEM; ++ return CORE_NEHALEM; + } + break; + diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb index 274aeeec351..66b40a6a8a1 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -16,6 +16,7 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -26,6 +27,7 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb index abbc1f81fe9..8051da228f0 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb @@ -16,6 +16,7 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.23_fix-parallel-build.patch', 'OpenBLAS-0.3.23_fix-lapack-test.patch', @@ -28,6 +29,7 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_fix-parallel-build.patch': 'abe10ba3b0ca54772dbf235596e35325a5159018f6a60cfc88824c2c220d99d9'}, From 72995a2f9d4c86691d18e22b3bcd489482caf073 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Thu, 2 Nov 2023 12:08:22 +0100 Subject: [PATCH 9326/9987] Add sanity check command --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 1a5e2a7b940..11881bde0f5 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -44,4 +44,6 @@ sanity_check_paths = { 'dirs': ['pythonmodule'] } +sanity_check_commands = [('python', "-c 'import waLBerla'")] + moduleclass = 'chem' From d45bf684e35a61ef001c0d2ddcacf9e77fbc05a6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 2 Nov 2023 12:31:20 +0100 Subject: [PATCH 9327/9987] Fix missing type in patch --- .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 2 +- ..._workaround-gcc12-destructor-exception-bug.patch | 13 ++++++++++--- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 132930e405c..7d768022015 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -97,7 +97,7 @@ checksums = [ {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, {'PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch': - '931142a3133ea8f6819123523b15cbc9dbdaf8c28e34396a09227f865e7c8829'}, + 'd46412fe917110c197e4e2c572fc577644bd6b117c99dc8c57fa96b69d5456dc'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch index 0ebcb88930a..b1bd76bc125 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch @@ -23,7 +23,7 @@ index 5210d6f713d..3c91ed378e1 100644 if (warning_buffer.size() > 0) { diff --git a/torch/csrc/Exceptions.h b/torch/csrc/Exceptions.h -index 89256c64bba..7e09d0ebc37 100644 +index 89256c64bba..8514d08c8d0 100644 --- a/torch/csrc/Exceptions.h +++ b/torch/csrc/Exceptions.h @@ -110,6 +110,13 @@ static inline void PyErr_SetString(PyObject* type, const std::string& message) { @@ -50,9 +50,16 @@ index 89256c64bba..7e09d0ebc37 100644 private: InternalHandler internal_handler_; at::WarningHandler* prev_handler_; -@@ -399,7 +409,14 @@ auto wrap_pybind_function_impl_(Func&& f, std::index_sequence) { +@@ -394,12 +404,20 @@ using Arg = typename function_traits::template arg::type; + template + auto wrap_pybind_function_impl_(Func&& f, std::index_sequence) { + using traits = function_traits; ++ using result_type = typename traits::result_type; + namespace py = pybind11; + // f=f is needed to handle function references on older compilers - return [f = f](Arg... args) -> typename traits::result_type { +- return [f = f](Arg... args) -> typename traits::result_type { ++ return [f = f](Arg... args) -> result_type { HANDLE_TH_ERRORS - return f(std::forward>(args)...); + if constexpr (std::is_void_v) { From 1fb8c91e1807080c57d00a28eb2e480e8024d373 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Nov 2023 13:03:56 +0100 Subject: [PATCH 9328/9987] adding easyconfigs: Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb --- ...thon-bundle-PyPI-2023.10-GCCcore-13.2.0.eb | 480 ++++++++++++++++++ 1 file changed, 480 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..bfb44233a8f --- /dev/null +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb @@ -0,0 +1,480 @@ +easyblock = 'PythonBundle' + +name = 'Python-bundle-PyPI' +version = '2023.10' + +homepage = 'https://python.org/' +description = "Bundle of Python packages from PyPI" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('UnZip', '6.0'), + ('pkgconf', '2.0.3'), + ('git', '2.42.0'), # required for pbr + ('hatchling', '1.18.0'), + ('poetry', '1.6.1'), + ('scikit-build', '0.17.6'), + ('flit', '3.9.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('cryptography', '41.0.5'), + ('virtualenv', '20.24.6'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +# order is important! +# package versions updated 2023-10-29 +exts_list = [ + ('blist', '1.3.6', { + 'patches': [ + 'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch', + 'Python-3.10-bist-1.3.6-compatibility.patch', + 'Python-3.11-bist-1.3.6-compatibility.patch', + ], + 'checksums': [ + {'blist-1.3.6.tar.gz': '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'}, + {'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch': + '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0'}, + {'Python-3.10-bist-1.3.6-compatibility.patch': + '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741'}, + {'Python-3.11-bist-1.3.6-compatibility.patch': + 'da283300bc5f0524b9982c9d9de4670908711634667849d3d81ccd87fc82c4ee'}, + ], + }), + ('pbr', '5.11.1', { + 'checksums': ['aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3'], + }), + ('Cython', '3.0.4', { + 'checksums': ['2e379b491ee985d31e5faaf050f79f4a8f59f482835906efe4477b33b4fbe9ff'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('python-dateutil', '2.8.2', { + 'modulename': 'dateutil', + 'checksums': ['0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycryptodome', '3.19.0', { + 'modulename': 'Crypto.PublicKey.RSA', + 'checksums': ['bc35d463222cdb4dbebd35e0784155c81e161b9284e567e7e933d722e533331e'], + }), + ('ecdsa', '0.18.0', { + 'checksums': ['190348041559e21b22a1d65cee485282ca11a6f81d503fddb84d5017e9ed1e49'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.5.1', { + 'checksums': ['13ae38502be632115abf8a24cbe5f4da52e3b5231990aff31123c805306ccb9c'], + }), + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + ('cffi', '1.16.0', { + 'checksums': ['bcb3ef43e58665bbda2fb198698fcae6776483e0c4a631aa5647806c25e02cc0'], + }), + ('semantic_version', '2.10.0', { + 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], + }), + ('typing_extensions', '4.8.0', { + 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], + }), + ('pyasn1', '0.5.0', { + 'checksums': ['97b7290ca68e62a832558ec3976f15cbf911bf5d7c7039d8b861c2a0ece69fde'], + }), + ('PyNaCl', '1.5.0', { + 'modulename': 'nacl', + 'checksums': ['8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba'], + }), + ('pyparsing', '3.1.1', { + 'checksums': ['ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db'], + }), + ('netifaces', '0.11.0', { + 'checksums': ['043a79146eb2907edf439899f262b3dfe41717d34124298ed281139a8b93ca32'], + }), + ('netaddr', '0.9.0', { + 'checksums': ['7b46fa9b1a2d71fd5de9e4a3784ef339700a53a08c8040f08baf5f1194da0128'], + }), + ('mock', '5.1.0', { + 'checksums': ['5e96aad5ccda4718e0a229ed94b2024df75cc2d55575ba5762d31f5767b8767d'], + }), + ('pytz', '2023.3.post1', { + 'checksums': ['7b4fddbeb94a1eba4b557da24f19fdf9db575192544270a9101d8509f9f43d7b'], + }), + ('bitarray', '2.8.2', { + 'checksums': ['f90b2f44b5b23364d5fbade2c34652e15b1fcfe813c46f828e008f68a709160f'], + }), + ('bitstring', '4.1.2', { + 'checksums': ['c22283d60fd3e1a8f386ccd4f1915d7fe13481d6349db39711421e24d4a9cccf'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.7', { + 'checksums': ['9dafe54b34a028eafd95039d5e5d4851a13734540f1331060d31c9916e7147a8'], + }), + ('zipp', '3.17.0', { + 'checksums': ['84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0'], + }), + ('importlib_metadata', '6.8.0', { + 'checksums': ['dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743'], + }), + ('backports.entry-points-selectable', '1.2.0', { + 'sources': ['backports.entry_points_selectable-%(version)s.tar.gz'], + 'checksums': ['4706f59179657ca7c1d325a543ee1370f8f46331f432bcac62fab242fdf0afa5'], + }), + ('pathspec', '0.11.2', { + 'checksums': ['e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3'], + }), + ('pluggy', '1.3.0', { + 'checksums': ['cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12'], + }), + ('editables', '0.5', { + 'checksums': ['309627d9b5c4adc0e668d8c6fa7bac1ba7c8c5d415c2d27f60f081f8e80d1de2'], + }), + ('filelock', '3.13.0', { + 'checksums': ['63c6052c82a1a24c873a549fbd39a26982e8f35a3016da231ead11a5be9dad44'], + }), + ('platformdirs', '3.11.0', { + 'checksums': ['cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.7.post1', { + 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], + }), + ('importlib_resources', '6.1.0', { + 'checksums': ['9d48dcccc213325e810fd723e7fbb45ccb39f6cf5c31f00cf2b965f5f10f3cb9'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '1.3.2', { + 'checksums': ['92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1'], + }), + ('chardet', '5.2.0', { + 'checksums': ['1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7'], + }), + ('certifi', '2023.7.22', { + 'checksums': ['539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082'], + }), + ('urllib3', '2.0.7', { + 'checksums': ['c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84'], + }), + ('charset-normalizer', '3.3.1', { + 'checksums': ['d9137a876020661972ca6eec0766d81aef8a5627df628b664b234b73396e727e'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('py_expression_eval', '0.3.14', { + 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('ujson', '5.8.0', { + 'checksums': ['78e318def4ade898a461b3d92a79f9441e7e0e4d2ad5419abed4336d702c7425'], + }), + ('atomicwrites', '1.4.1', { + 'checksums': ['81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11'], + }), + ('py', '1.11.0', { + 'checksums': ['51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719'], + }), + ('more-itertools', '10.1.0', { + 'checksums': ['626c369fa0eb37bac0291bce8259b332fd59ac792fa5497b59837309cd5b114a'], + }), + ('attrs', '23.1.0', { + 'modulename': 'attr', + 'checksums': ['6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015'], + }), + ('backports.functools_lru_cache', '1.6.6', { + 'checksums': ['7b70e701ba4db58c0ed8671a9d3391b0abb9bd1bc24d4e90c3480f4baafcc2dc'], + }), + ('wcwidth', '0.2.8', { + 'checksums': ['8705c569999ffbb4f6a87c6d1b80f324bd6db952f5eb0b95bc07517f4c1813d4'], + }), + ('iniconfig', '2.0.0', { + 'checksums': ['2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3'], + }), + ('colorama', '0.4.6', { + 'checksums': ['08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44'], + }), + ('exceptiongroup', '1.1.3', { + 'checksums': ['097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9'], + }), + ('pytest', '7.4.3', { + 'checksums': ['d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5'], + }), + ('MarkupSafe', '2.1.3', { + 'checksums': ['af598ed32d6ae86f1b747b82783958b1a4ab8f617b06fe68795c7f026abbdcad'], + }), + ('Jinja2', '3.1.2', { + 'checksums': ['31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852'], + }), + ('sphinxcontrib_serializinghtml', '1.1.9', { + 'modulename': 'sphinxcontrib.serializinghtml', + 'checksums': ['0c64ff898339e1fac29abd2bf5f11078f3ec413cfe9c046d3120d7ca65530b54'], + }), + ('sphinxcontrib_websupport', '1.2.6', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['d592be8e11261bbbc64668f258efc4fd42c93ab617411143b5245fe30c633d8c'], + }), + ('Pygments', '2.16.1', { + 'checksums': ['1daff0494820c69bc8941e407aa20f577374ee88364ee10a98fdbe0aece96e29'], + }), + ('imagesize', '1.4.1', { + 'checksums': ['69150444affb9cb0d5cc5a92b3676f0b2fb7cd9ae39e947a5e11a36b4497cd4a'], + }), + ('docutils', '0.20.1', { + 'checksums': ['f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b'], + }), + ('snowballstemmer', '2.2.0', { + 'checksums': ['09b16deb8547d3412ad7b590689584cd0fe25ec8db3be37788be3810cbf19cb1'], + }), + ('alabaster', '0.7.13', { + 'checksums': ['a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2'], + }), + ('sphinxcontrib_applehelp', '1.0.7', { + 'modulename': 'sphinxcontrib.applehelp', + 'checksums': ['39fdc8d762d33b01a7d8f026a3b7d71563ea3b72787d5f00ad8465bd9d6dfbfa'], + }), + ('sphinxcontrib_devhelp', '1.0.5', { + 'modulename': 'sphinxcontrib.devhelp', + 'checksums': ['63b41e0d38207ca40ebbeabcf4d8e51f76c03e78cd61abe118cf4435c73d4212'], + }), + ('sphinxcontrib_htmlhelp', '2.0.4', { + 'modulename': 'sphinxcontrib.htmlhelp', + 'checksums': ['6c26a118a05b76000738429b724a0568dbde5b72391a688577da08f11891092a'], + }), + ('sphinxcontrib-jsmath', '1.0.1', { + 'modulename': 'sphinxcontrib.jsmath', + 'checksums': ['a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8'], + }), + ('sphinxcontrib_qthelp', '1.0.6', { + 'modulename': 'sphinxcontrib.qthelp', + 'checksums': ['62b9d1a186ab7f5ee3356d906f648cacb7a6bdb94d201ee7adf26db55092982d'], + }), + ('Babel', '2.13.1', { + 'checksums': ['33e0952d7dd6374af8dbf6768cc4ddf3ccfefc244f9986d4074704f2fbd18900'], + }), + ('sphinx', '7.2.6', { + 'checksums': ['9a5160e1ea90688d5963ba09a2dcd8bdd526620edbb65c328728f1b2228d5ab5'], + }), + ('sphinx-bootstrap-theme', '0.8.1', { + 'checksums': ['683e3b735448dadd0149f76edecf95ff4bd9157787e9e77e0d048ca6f1d680df'], + }), + ('click', '8.1.7', { + 'checksums': ['ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de'], + }), + ('psutil', '5.9.6', { + 'checksums': ['e4b92ddcd7dd4cdd3f900180ea1e104932c7bce234fb88976e2a3b296441225a'], + }), + ('future', '0.18.3', { + 'checksums': ['34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('zipfile36', '0.1.3', { + 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], + }), + ('tomli_w', '1.0.0', { + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), + ('regex', '2023.10.3', { + 'checksums': ['3fef4f844d2290ee0ba57addcec17eec9e3df73f10a2748485dfd6a3a188cc0f'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('pylev', '1.4.0', { + 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], + }), + ('pastel', '0.2.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], + }), + ('crashtest', '0.4.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'], + }), + # clikit 0.6.2 has requirement crashtest<0.4.0,>=0.3.0 + # but poetry 1.5.1 has requirement crashtest>=0.4.1 + # and cleo 2.0.1 has requirement crashtest>=0.4.1 + # ('clikit', '0.6.2', { + # 'source_tmpl': SOURCE_WHL, + # 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], + # }), + ('jeepney', '0.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], + }), + ('SecretStorage', '3.3.3', { + 'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'], + }), + ('keyring', '24.2.0', { + 'modulename': False, + 'checksums': ['ca0746a19ec421219f4d713f848fa297a661a8a8c1504867e55bfb5e09091509'], + }), + ('jaraco.classes', '3.3.0', { + 'checksums': ['c063dd08e89217cee02c8d5e5ec560f2c8ce6cdc2fcdc2e68f7b2e5547ed3621'], + }), + ('keyrings.alt', '5.0.0', { + 'modulename': False, + 'checksums': ['9d446cb47bbcea90ffa2ecc3e8003acf41573fc201bf44b4bf13bd0e11484828'], + }), + ('tomlkit', '0.12.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['712cbd236609acc6a3e2e97253dfc52d4c2082982a88f61b640ecf0817eab899'], + }), + ('shellingham', '1.5.4', { + 'checksums': ['8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de'], + }), + ('requests-toolbelt', '1.0.0', { + 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], + }), + ('pyrsistent', '0.20.0', { + 'checksums': ['4c48f78f62ab596c679086084d0dd13254ae4f3d6c72a83ffdf5ebdef8f265a4'], + }), + ('pkginfo', '1.9.6', { + 'checksums': ['8fd5896e8718a4372f0ea9cc9d96f6417c9b986e23a4d116dda26b62cc29d046'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('jsonschema', '4.17.3', { + 'checksums': ['0f864437ab8b6076ba6707453ef8f98a6a0d512a80e93f8abdb676f737ecb60d'], + }), + ('simplejson', '3.19.2', { + 'checksums': ['9eb442a2442ce417801c912df68e1f6ccfcd41577ae7274953ab3ad24ef7d82c'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('rapidfuzz', '2.15.2', { + 'checksums': ['bfc1d38a7adcbe8912f980a5f46f27a801dd8655582ff0d4a2c0431c02b7ce33'], + }), + ('cleo', '2.0.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['6eb133670a3ed1f3b052d53789017b6e50fca66d1287e6e6696285f4cb8ea448'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.7', { + 'checksums': ['572efc93db7a4d27e404501975ca6d2d9775705c2d922390d878fcf768d92c87'], + }), + ('cachecontrol', '0.13.1', { + 'checksums': ['f012366b79d2243a6118309ce73151bf52a38d4a5dac8ea57f09bd29087e506b'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('glob2', '0.7', { + 'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'], + }), + ('dulwich', '0.21.6', { + 'checksums': ['30fbe87e8b51f3813c131e2841c86d007434d160bd16db586b40d47f31dd05b0'], + }), + ('fsspec', '2023.10.0', { + 'checksums': ['330c66757591df346ad3091a53bd907e15348c2ba17d63fd54f5c39c4457d2a5'], + }), + ('threadpoolctl', '3.2.0', { + 'checksums': ['c96a0ba3bdddeaca37dc4cc7344aafad41cdb8c313f74fdfe387a867bba93355'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('pooch', '1.8.0', { + 'checksums': ['f59981fd5b9b5d032dcde8f4a11eaa492c2ac6343fae3596a2fdae35fc54b0a0'], + }), + ('doit', '0.36.0', { + 'checksums': ['71d07ccc9514cb22fe59d98999577665eaab57e16f644d04336ae0b4bae234bc'], + }), + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('pydevtool', '0.3.0', { + 'checksums': ['25e3ba4f3d33ccac33ee2b9775995848d49e9b318b7a146477fb5d52f786fc8a'], + }), + ('Pygments', '2.16.1', { + 'checksums': ['1daff0494820c69bc8941e407aa20f577374ee88364ee10a98fdbe0aece96e29'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '3.0.0', { + 'modulename': 'markdown_it', + 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], + }), + ('rich', '13.6.0', { + 'checksums': ['5c14d22737e6d5084ef4771b62d5d4363165b403455a30a1c8ca39dc7b644bef'], + }), + ('rich-click', '1.7.0', { + 'checksums': ['ab34e5d9f7733c4e6072f4de79eb3b35ac9ae78e692ea8a543f3b2828b30fee4'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('execnet', '2.0.2', { + 'checksums': ['cc59bc4423742fd71ad227122eb0dd44db51efb3dc4095b45ac9a08c770096af'], + }), + ('pytest-xdist', '3.3.1', { + 'modulename': 'xdist', + 'checksums': ['d5ee0520eb1b7bcca50a60a518ab7a7707992812c578198f8b44fdfac78e8c93'], + }), +] + +moduleclass = 'lang' From 39f1df415ce1511b83a41aef25ee87894dfdf36e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 2 Nov 2023 14:21:48 +0100 Subject: [PATCH 9329/9987] adding easyconfigs: FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb --- .../FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb new file mode 100644 index 00000000000..833ef4f3068 --- /dev/null +++ b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb @@ -0,0 +1,71 @@ +easyblock = 'Bundle' + +name = 'FPM' +version = '1.15.1' + +local_rubyver = '3.2.2' +versionsuffix = '-Ruby-%s' % local_rubyver + +homepage = 'https://github.com/jordansissel/fpm' +description = """Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease + and sanity.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Ruby', local_rubyver), +] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_defaultclass = 'RubyGem' + +exts_list = [ + ('stud', '0.0.23', { + 'checksums': ['6ba26fa28fc50a8d59229b296a733b48d50f1473b1e3e7f5e339d5bbd829eb62'], + }), + ('dotenv', '2.8.1', { + 'checksums': ['c5944793349ae03c432e1780a2ca929d60b88c7d14d52d630db0508c3a8a17d8'], + }), + ('insist', '1.0.0', { + 'checksums': ['6f6759eee583dc4e00a6cc3f713cfa7c570572958ba1f5d65595046d795b832f'], + }), + ('mustache', '0.99.8', { + 'checksums': ['826a96db895819c13fffa4fa3c20b85e80b60aaec1f28f79e7db80092abdb0bc'], + }), + ('clamp', '1.0.1', { + 'checksums': ['5fa57e4337c30b384fc162a6391f477ce21e9b73ba2c16a18b3d99cb34a16649'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('pleaserun', '0.0.32', { + 'checksums': ['4dd8db18b81b48e2a875ec0c7fff3869454d1f93a9f5e2e6c4eb88812870d3ab'], + }), + ('rexml', '3.2.6', { + 'checksums': ['e0669a2d4e9f109951cb1fde723d8acd285425d81594a2ea929304af50282816'], + }), + ('arr-pm', '0.0.12', { + 'checksums': ['fdff482f75239239201f4d667d93424412639aad0b3b0ad4d827e7c637e0ad39'], + }), + ('backports', '3.24.1', { + 'checksums': ['83a720ea9a3ee0cf5eab18b866e9282293ab4f54eb6430291b3c238481677fb8'], + }), + ('%(namelower)s', version, { + 'checksums': ['1ffbf342a89ca97fb5c02e66946c97e2bd5413810f7f440ddf32f00a16052dbf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/fpm'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + +sanity_check_commands = ["%(namelower)s --help"] + +modextrapaths = {'GEM_PATH': ['']} + +moduleclass = 'tools' From 703f2d8dfffc6df3a88a7f914a6ef4f5ad6475fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 2 Nov 2023 15:41:39 +0100 Subject: [PATCH 9330/9987] add missing build dependency --- .../easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb index 833ef4f3068..2aa7b5d9ad2 100644 --- a/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb +++ b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb @@ -12,6 +12,10 @@ description = """Effing package management! Build packages for multiple platform toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +builddependencies = [ + ('binutils', '2.39'), +] + dependencies = [ ('Ruby', local_rubyver), ] From 2ab7081deda77fa94305135410a7b2e9cae60113 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 2 Nov 2023 20:22:28 +0100 Subject: [PATCH 9331/9987] Add flit --- .../f/flit/flit-3.9.0-GCCcore-13.2.0.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..79b1a625e7e --- /dev/null +++ b/easybuild/easyconfigs/f/flit/flit-3.9.0-GCCcore-13.2.0.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'flit' +version = '3.9.0' + +homepage = 'https://github.com/pypa/flit' +description = "A simple packaging tool for simple packages." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('certifi', '2023.7.22', { + 'checksums': ['539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082'], + }), + ('urllib3', '2.0.7', { + 'checksums': ['c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84'], + }), + ('charset-normalizer', '3.3.1', { + 'checksums': ['d9137a876020661972ca6eec0766d81aef8a5627df628b664b234b73396e727e'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('setuptools-scm', '8.0.4', { + 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + }), + ('typing_extensions', '4.8.0', { + 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], + }), + ('flit_scm', '1.7.0', { + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('docutils', '0.20.1', { + 'checksums': ['f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b'], + }), + ('tomli_w', '1.0.0', { + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), + (name, version, { + 'checksums': ['d75edf5eb324da20d53570a6a6f87f51e606eee8384925cd66a90611140844c7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' From dfef4d879545817beee02c833eddfaa27d94d34e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 3 Nov 2023 10:18:57 +0100 Subject: [PATCH 9332/9987] remove version suffix --- ...e-12.2.0-Ruby-3.2.2.eb => FPM-1.15.1-GCCcore-12.2.0.eb} | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/f/FPM/{FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb => FPM-1.15.1-GCCcore-12.2.0.eb} (94%) diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0.eb similarity index 94% rename from easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb rename to easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0.eb index 2aa7b5d9ad2..2ffd9eef466 100644 --- a/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0-Ruby-3.2.2.eb +++ b/easybuild/easyconfigs/f/FPM/FPM-1.15.1-GCCcore-12.2.0.eb @@ -3,9 +3,6 @@ easyblock = 'Bundle' name = 'FPM' version = '1.15.1' -local_rubyver = '3.2.2' -versionsuffix = '-Ruby-%s' % local_rubyver - homepage = 'https://github.com/jordansissel/fpm' description = """Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease and sanity.""" @@ -17,7 +14,7 @@ builddependencies = [ ] dependencies = [ - ('Ruby', local_rubyver), + ('Ruby', '3.2.2'), ] exts_default_options = { @@ -64,7 +61,7 @@ exts_list = [ ] sanity_check_paths = { - 'files': ['bin/fpm'], + 'files': ['bin/%(namelower)s'], 'dirs': ['gems/%(namelower)s-%(version)s'], } From ce57972218fe1cd6ea59a6d6d24b5de3ae48aa69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Nov 2023 10:19:24 +0100 Subject: [PATCH 9333/9987] Fix whl --- .../Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb index bfb44233a8f..f1c29800a58 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb @@ -332,11 +332,11 @@ exts_list = [ 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], }), ('pastel', '0.2.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], }), ('crashtest', '0.4.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['8d23eac5fa660409f57472e3851dab7ac18aba459a8d19cbbba86d3d5aecd2a5'], }), # clikit 0.6.2 has requirement crashtest<0.4.0,>=0.3.0 @@ -347,7 +347,7 @@ exts_list = [ # 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], # }), ('jeepney', '0.8.0', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], }), ('SecretStorage', '3.3.3', { @@ -365,7 +365,7 @@ exts_list = [ 'checksums': ['9d446cb47bbcea90ffa2ecc3e8003acf41573fc201bf44b4bf13bd0e11484828'], }), ('tomlkit', '0.12.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['712cbd236609acc6a3e2e97253dfc52d4c2082982a88f61b640ecf0817eab899'], }), ('shellingham', '1.5.4', { @@ -381,7 +381,7 @@ exts_list = [ 'checksums': ['8fd5896e8718a4372f0ea9cc9d96f6417c9b986e23a4d116dda26b62cc29d046'], }), ('ptyprocess', '0.7.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], }), ('pexpect', '4.8.0', { @@ -406,7 +406,7 @@ exts_list = [ 'checksums': ['bfc1d38a7adcbe8912f980a5f46f27a801dd8655582ff0d4a2c0431c02b7ce33'], }), ('cleo', '2.0.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['6eb133670a3ed1f3b052d53789017b6e50fca66d1287e6e6696285f4cb8ea448'], }), ('cachy', '0.3.0', { From 33ceac484bd3991192468db0f0907f579dde5d1b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 3 Nov 2023 10:34:13 +0100 Subject: [PATCH 9334/9987] drop the empty list of dependencies --- easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb index 7d89e8ca6ac..4a07aa2e8e5 100644 --- a/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb +++ b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb @@ -17,9 +17,6 @@ checksums = ['86b66ea0278f803cde5774de8bd187dd42c870367f1cbf6cdaec8dc7cf6afc10'] builddependencies = [('CMake', '3.23.1')] -dependencies = [ -] - configopts = '-Dmomentum=GEV -Dlength=MM' sanity_check_paths = { From 7f036f9dbb53e27376cc61e84a99ba77486554a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 3 Nov 2023 10:34:44 +0100 Subject: [PATCH 9335/9987] consistent use of quotes --- easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb index 4a07aa2e8e5..ca033f0fd1c 100644 --- a/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb +++ b/easybuild/easyconfigs/h/HepMC/HepMC-2.06.11-gompi-2022a.eb @@ -20,7 +20,7 @@ builddependencies = [('CMake', '3.23.1')] configopts = '-Dmomentum=GEV -Dlength=MM' sanity_check_paths = { - 'files': ["lib/libHepMC.so"], + 'files': ['lib/libHepMC.so'], 'dirs': ['include/HepMC'] } From 01f54f62d2dab2197cd4d64e15ef9d8cbef4c4fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Nov 2023 11:07:20 +0100 Subject: [PATCH 9336/9987] adding easyconfigs: CUDA-12.3.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.3.0.eb | 24 +++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.3.0.eb new file mode 100644 index 00000000000..6510fce6366 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.3.0.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.3.0' +local_nv_version = '545.23.06' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '7c13face3af64d6e1648d6e3101d31c8111e747143acb0077d973c1690820422', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'de15c04380ec35b194c07503bf434837bac5b427cf77b19a63962b1653d195d5', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '9a8fb8acf46b88faf0d711bda3149e1706efbbae02fcb40ab72addfd0e9ce5df' +}] + +moduleclass = 'system' From f8a760786377f99ffffa89b91669b795c4bd2f65 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 3 Nov 2023 13:38:12 +0100 Subject: [PATCH 9337/9987] adding easyconfigs: pixman-0.42.2-GCCcore-13.2.0.eb, GLib-2.78.1-GCCcore-13.2.0.eb, cairo-1.18.0-GCCcore-13.2.0.eb, GObject-Introspection-1.78.1-GCCcore-13.2.0.eb --- .../c/cairo/cairo-1.18.0-GCCcore-13.2.0.eb | 51 ++++++++++++++++++ .../g/GLib/GLib-2.78.1-GCCcore-13.2.0.eb | 53 +++++++++++++++++++ ...ect-Introspection-1.78.1-GCCcore-13.2.0.eb | 44 +++++++++++++++ .../p/pixman/pixman-0.42.2-GCCcore-13.2.0.eb | 28 ++++++++++ 4 files changed, 176 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.78.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.78.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..e1033ed8ada --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.18.0-GCCcore-13.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MesonNinja' + + +name = 'cairo' +version = '1.18.0' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [ + 'https://cairographics.org/releases/', + 'https://cairographics.org/snapshots/' +] +sources = [SOURCE_TAR_XZ] +checksums = ['243a0736b978a33dee29f9cca7521733b78a65b5418206fef7bd1c3d4cf10b64'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Ninja', '1.11.1'), + ('Meson', '1.2.3'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), + ('libpng', '1.6.40'), + ('freetype', '2.13.2'), + ('pixman', '0.42.2'), + ('expat', '2.5.0'), + ('GLib', '2.78.1'), + ('X11', '20231019'), +] + +configopts = "--default-library=both" # static and shared library + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.78.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.78.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..44fbd9759a5 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.78.1-GCCcore-13.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.78.1' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['915bc3d0f8507d650ead3832e2f8fb670fce59aac4d7754a7dab6f1e6fed78b2'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.11.5'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('libffi', '3.4.4'), + ('gettext', '0.22'), + ('libxml2', '2.11.5'), + ('PCRE2', '10.42'), + ('util-linux', '2.39'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.78.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.78.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..1a8a0f4320b --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.78.1-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.78.1' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['bd7babd99af7258e76819e45ba4a6bc399608fe762d83fde3cac033c50841bb4'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('cairo', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('GLib', '2.78.1'), + ('libffi', '3.4.4'), + ('util-linux', '2.39'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2d5befc2cf5 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.42.2' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ea1480efada2fd948bc75366f7c349e1c96d3297d09a3fe62626e38e234a625e'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From 5ea5c15f89deb42409baf09e42e642954d35f2ea Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 3 Nov 2023 14:02:20 +0100 Subject: [PATCH 9338/9987] Remove outdated configure option from FriBidi-1.0.12 --- .../easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb | 2 -- .../easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb | 2 -- .../easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb | 2 -- 3 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb index 65c4eb01b1c..5bcf88c38fe 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-11.3.0.eb @@ -21,8 +21,6 @@ builddependencies = [ ('pkgconf', '1.8.0'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb index 97c8eece78b..357b9f24de3 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb @@ -21,8 +21,6 @@ builddependencies = [ ('pkgconf', '1.9.3'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb index df4dacf597f..4df1d5562a9 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.3.0.eb @@ -21,8 +21,6 @@ builddependencies = [ ('Autotools', '20220317'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], From fb6632a91a6be556e646ee44bfb78af7275b3041 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 3 Nov 2023 14:04:39 +0100 Subject: [PATCH 9339/9987] Fix patch and C++ standard --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 4 +--- ...rch-1.13.1_workaround-gcc12-destructor-exception-bug.patch | 2 +- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 7d768022015..45ffe3f1e20 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -97,7 +97,7 @@ checksums = [ {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, {'PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch': - 'd46412fe917110c197e4e2c572fc577644bd6b117c99dc8c57fa96b69d5456dc'}, + 'a09a2d7ebd428c65988729578bb3fa372565ba176ab9ed7abf11f6fcb15e903e'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -126,8 +126,6 @@ dependencies = [ ('expecttest', '0.1.3'), ] -custom_opts = ['CMAKE_CXX_STANDARD=17'] - excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch index b1bd76bc125..63c3ab6c425 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch @@ -62,7 +62,7 @@ index 89256c64bba..8514d08c8d0 100644 + return [f = f](Arg... args) -> result_type { HANDLE_TH_ERRORS - return f(std::forward>(args)...); -+ if constexpr (std::is_void_v) { ++ if constexpr (std::is_void::value) { + c10::guts::invoke(f, std::forward>(args)...); + FLUSH_TH_ERRORS + } else { From 2f60f846be1b0bc0e308e47db12108b06756bb1f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 3 Nov 2023 16:35:23 +0000 Subject: [PATCH 9340/9987] adding easyconfigs: Autoconf-archive-2023.02.20-GCCcore-11.3.0.eb --- ...oconf-archive-2023.02.20-GCCcore-11.3.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..7b10ea408dd --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf-archive/Autoconf-archive-2023.02.20-GCCcore-11.3.0.eb @@ -0,0 +1,53 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU Free Documentation License +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'Autoconf-archive' +version = '2023.02.20' + +homepage = "https://www.gnu.org/software/autoconf-archive" + +description = """ +The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf +that have been contributed as free software by friendly supporters of the cause from +all over the Internet. Every single one of those macros can be re-used without +imposing any restrictions whatsoever on the licensing of the generated configure script. +In particular, it is possible to use all those macros in configure scripts that +are meant for non-free software. This policy is unusual for a Free Software Foundation +project. The FSF firmly believes that software ought to be free, and software licenses +like the GPL are specifically designed to ensure that derivative work based on free +software must be free as well. In case of Autoconf, however, an exception has been made, +because Autoconf is at such a pivotal position in the software development tool chain +that the benefits from having this tool available as widely as possible outweigh the +disadvantage that some authors may choose to use it, too, for proprietary software. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['71d4048479ae28f1f5794619c3d72df9c01df49b1c628ef85fde37596dc31a33'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('makeinfo', '6.8'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': [], + 'dirs': ['share/%s' % x for x in + ['aclocal', 'doc', 'info']], +} + +moduleclass = 'devel' From 4ce4e29f826448897ef7677ce234298f3e1e68e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 00:08:15 +0100 Subject: [PATCH 9341/9987] adding easyconfigs: ICU-74.1-GCCcore-13.2.0.eb, nodejs-20.9.0-GCCcore-13.2.0.eb --- .../i/ICU/ICU-74.1-GCCcore-13.2.0.eb | 29 ++++++++++ .../n/nodejs/nodejs-20.9.0-GCCcore-13.2.0.eb | 54 +++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/i/ICU/ICU-74.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-20.9.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/i/ICU/ICU-74.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-74.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..db1bede945b --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-74.1-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '74.1' + +homepage = 'https://icu.unicode.org' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['86ce8e60681972e60e4dcb2490c697463fcec60dd400a5f9bffba26d0b52b8d0'] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.5'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-20.9.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-20.9.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..24be2bb275b --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-20.9.0-GCCcore-13.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '20.9.0' # LTS on 2023-11-03 +local_libversion = '115' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['a7e6547a951406e4e546a74160ed27b26f9abd4baf7c44dd5a0fa992852d0cfa'] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.5'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('ICU', '74.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# Use ICU and OpenSSL from EasyBuild +local_common_configopts = "--with-intl=system-icu --shared-openssl " + +configopts = [ + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) + +postinstallcmds = [ + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], + 'dirs': ['lib/node_modules', 'include/node'] +} + +sanity_check_commands = ["node --help"] + +moduleclass = 'lang' From cd9666e43d7de50038b4e27d62326eabe99c8825 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 02:33:03 +0100 Subject: [PATCH 9342/9987] adding easyconfigs: FFmpeg-6.0-GCCcore-13.2.0.eb, LAME-3.100-GCCcore-13.2.0.eb, FriBidi-1.0.13-GCCcore-13.2.0.eb, SDL2-2.28.5-GCCcore-13.2.0.eb --- .../f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb | 45 +++++++++++++++++++ .../FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb | 32 +++++++++++++ .../l/LAME/LAME-3.100-GCCcore-13.2.0.eb | 36 +++++++++++++++ .../s/SDL2/SDL2-2.28.5-GCCcore-13.2.0.eb | 26 +++++++++++ 4 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.28.5-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..fab8972c089 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-6.0-GCCcore-13.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '6.0' + +homepage = 'https://www.ffmpeg.org/' +description = "A complete, cross-platform solution to record, convert and stream audio and video." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://%(namelower)s.org/releases/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['47d062731c9f66a78380e35a19aac77cebceccd1c7cc309b9c82343ffc430c3d'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('ffnvcodec', '12.1.14.0', '', SYSTEM), # optional nvenc/dec support +] +dependencies = [ + ('NASM', '2.16.01'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('x264', '20231019'), + ('LAME', '3.100'), + ('x265', '3.5'), + ('X11', '20231019'), + ('freetype', '2.13.2'), + ('fontconfig', '2.14.2'), + ('FriBidi', '1.0.13'), + ('SDL2', '2.28.5'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264 --enable-libx265 --enable-libmp3lame --enable-libfreetype --enable-fontconfig ' +configopts += '--enable-libfribidi --enable-sdl2' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'play']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..359c71849ca --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.13' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/fribidi/fribidi/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7fa16c80c81bd622f7b198d31356da139cc318a63fc7761217af4130903f54a2'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] + +configopts = '--disable-docs' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7b163dff699 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'LAME' +version = '3.100' + +homepage = 'http://lame.sourceforge.net/' +description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [('ncurses', '6.4')] + +preconfigopts = "autoconf && " + +# configure is broken: add workaround to find libncurses... +configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " + +sanity_check_paths = { + 'files': ['bin/lame', 'include/lame/lame.h', 'lib/libmp3lame.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.28.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.28.5-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..5b5d1835fcb --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.28.5-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.28.5' + +homepage = 'https://www.libsdl.org/' +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['332cb37d0be20cb9541739c61f79bae5a477427d79ae85e352089afdaf6666e4'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('X11', '20231019'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From a4293e61408598581d873a829c41f356a53547db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 03:01:47 +0100 Subject: [PATCH 9343/9987] adding easyconfigs: re2c-3.1-GCCcore-13.2.0.eb, JasPer-4.0.0-GCCcore-13.2.0.eb, graphite2-1.3.14-GCCcore-13.2.0.eb, NSPR-4.35-GCCcore-13.2.0.eb, NSS-3.94-GCCcore-13.2.0.eb --- .../graphite2-1.3.14-GCCcore-13.2.0.eb | 27 ++++++++ .../j/JasPer/JasPer-4.0.0-GCCcore-13.2.0.eb | 36 +++++++++++ .../n/NSPR/NSPR-4.35-GCCcore-13.2.0.eb | 30 +++++++++ .../n/NSS/NSS-3.94-GCCcore-13.2.0.eb | 61 +++++++++++++++++++ .../r/re2c/re2c-3.1-GCCcore-13.2.0.eb | 32 ++++++++++ 5 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..f72fbb4cc7a --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ab5a601586c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '4.0.0' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['977c4c2e4210f4e37313cd2232d99e73d57ab561917b3c060bcdd5e83a0a13f1'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..dd289fea3b1 --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.35' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7ea3297ea5969b5d25a5dd8d47f2443cda88e9ee746301f6e1e1426f8a6abc8f'] + +builddependencies = [('binutils', '2.40')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +sanity_check_commands = ["nspr-config --version"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..98dcf8eb5b5 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.94' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%s_RTM/src/' % version.replace('.', '_')] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', + 'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', +] +checksums = [ + {'nss-3.94.tar.gz': '463ae180ee9e5ee9e3ad4f629326657e236780cc865572a930a16520abad9dd8'}, + {'NSS-3.39_pkgconfig.patch': '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774'}, + {'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch': + '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'}, +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('NSPR', '4.35'), + ('zlib', '1.2.13'), +] + +# building in parallel fails +parallel = 1 + +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " +# fix for not being able to find header files +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], +} + +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..4db6f2daf45 --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-3.1-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '3.1' + +homepage = 'https://re2c.org' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['0ac299ad359e3f512b06a99397d025cfff81d3be34464ded0656f8a96676c029'] + +builddependencies = [ + ('binutils', '2.40'), + ('Python', '3.11.5') +] + +configopts = "--disable-rust" + +sanity_check_paths = { + 'files': ['bin/re2c'], + 'dirs': [], +} + +sanity_check_commands = ["re2c --help"] + +moduleclass = 'tools' From bcbe5a69c70f4c3279fee3105ac168a537bebdc0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 12:18:40 +0100 Subject: [PATCH 9344/9987] Add ffnvcodec --- .../f/ffnvcodec/ffnvcodec-12.1.14.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb new file mode 100644 index 00000000000..ffab57a6520 --- /dev/null +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ffnvcodec' +version = '12.1.14.0' + +homepage = 'https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git' + +description = """FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present +(picked up dynamically).""" + +toolchain = SYSTEM + +sources = [{ + 'git_config': { + 'url': 'https://git.videolan.org/git/ffmpeg/', + 'repo_name': 'nv-codec-headers', + 'tag': 'n%(version)s', + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['a7da1532e61dee98c2a917a7a3f9127b94a1d72d44aa1cce23e3d797b114d0c0'] + +skipsteps = ['configure'] + +preinstallopts = 'sed -i "s|PREFIX =.*|PREFIX ?= %(installdir)s|" Makefile && ' + +sanity_check_paths = { + 'files': ['include/ffnvcodec/nvEncodeAPI.h', 'lib/pkgconfig/ffnvcodec.pc'], + 'dirs': [], +} + +moduleclass = 'lib' From b52852afdfdc9152349b4ebb56ee3379202a2825 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 12:19:05 +0100 Subject: [PATCH 9345/9987] Drop fribidi configopts --- .../easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb index 359c71849ca..bd7cef70af5 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.13-GCCcore-13.2.0.eb @@ -21,8 +21,6 @@ builddependencies = [ ('Autotools', '20220317'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], From 2674cd7d3183ef81b3e90aac28f6b10f4762a030 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 4 Nov 2023 11:27:46 +0000 Subject: [PATCH 9346/9987] No checksum for git download --- easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb index ffab57a6520..cf37dfdf36b 100644 --- a/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb +++ b/easybuild/easyconfigs/f/ffnvcodec/ffnvcodec-12.1.14.0.eb @@ -18,7 +18,7 @@ sources = [{ }, 'filename': SOURCE_TAR_GZ, }] -checksums = ['a7da1532e61dee98c2a917a7a3f9127b94a1d72d44aa1cce23e3d797b114d0c0'] +checksums = [None] skipsteps = ['configure'] From 7cfd61b5632d16cf7c210d39243441be1db1127b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 14:00:54 +0100 Subject: [PATCH 9347/9987] adding easyconfigs: Wayland-1.22.0-GCCcore-13.2.0.eb, PyCairo-1.25.1-GCCcore-13.2.0.eb, ATK-2.38.0-GCCcore-13.2.0.eb, Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb, at-spi2-core-2.50.0-GCCcore-13.2.0.eb, HarfBuzz-8.2.2-GCCcore-13.2.0.eb, PyGObject-3.46.0-GCCcore-13.2.0.eb, Graphene-1.10.8-GCCcore-13.2.0.eb, at-spi2-atk-2.38.0-GCCcore-13.2.0.eb, Pango-1.51.0-GCCcore-13.2.0.eb, elfutils-0.190-GCCcore-13.2.0.eb, libepoxy-1.5.10-GCCcore-13.2.0.eb --- .../a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb | 39 ++++++++++++ .../at-spi2-atk-2.38.0-GCCcore-13.2.0.eb | 37 +++++++++++ .../at-spi2-core-2.50.0-GCCcore-13.2.0.eb | 40 ++++++++++++ .../elfutils/elfutils-0.190-GCCcore-13.2.0.eb | 41 ++++++++++++ .../Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb | 46 ++++++++++++++ .../Graphene-1.10.8-GCCcore-13.2.0.eb | 32 ++++++++++ .../HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb | 38 +++++++++++ .../libepoxy-1.5.10-GCCcore-13.2.0.eb | 37 +++++++++++ .../p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb | 41 ++++++++++++ .../PyCairo/PyCairo-1.25.1-GCCcore-13.2.0.eb | 38 +++++++++++ .../PyGObject-3.46.0-GCCcore-13.2.0.eb | 38 +++++++++++ .../Wayland/Wayland-1.22.0-GCCcore-13.2.0.eb | 63 +++++++++++++++++++ 12 files changed, 490 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.50.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..6093e7836d8 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.38.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('GObject-Introspection', '1.78.1'), +] + +dependencies = [ + ('GLib', '2.78.1'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..4f2a709e36b --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('GLib', '2.78.1'), + ('DBus', '1.15.8'), + ('at-spi2-core', '2.50.0'), + ('libxml2', '2.11.5'), + ('ATK', '2.38.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.50.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.50.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2a4ccd76bff --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.50.0-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.50.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e9f5a8c8235c9dd963b2171de9120301129c677dde933955e1df618b949c4adc'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.78.1'), + ('gettext', '0.22'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('GLib', '2.78.1'), + ('DBus', '1.15.8'), + ('X11', '20231019'), +] + +# Hard disable Dbus broker detection and (potential) use of systemd +configopts = "--libdir lib -Duse_systemd=false -Ddefault_bus=dbus-daemon" + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..83b0be058ef --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.190' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['39bd8f1a338e2b7cd4abc3ff11a0eddc6e690f69578a57478d8179b4148708c8'] + +builddependencies = [ + ('M4', '1.4.19'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('binutils', '2.40'), + ('bzip2', '1.0.8'), + ('libarchive', '3.7.2'), + ('XZ', '5.4.4'), + ('zstd', '1.5.5'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a66201f8def --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.10' + +homepage = 'https://docs.gtk.org/gdk-pixbuf/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ee9b6c75d13ba096907a2e3c6b27b61bcd17f5c7ebeab5a5b439d2f2e39fe44b'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('GObject-Introspection', '1.78.1'), +] + +dependencies = [ + ('GLib', '2.78.1'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('LibTIFF', '4.6.0'), + ('X11', '20231019'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b8b16bdc898 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphene/Graphene-1.10.8-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'Graphene' +version = '1.10.8' + +homepage = 'https://ebassi.github.io/graphene/' +description = "Graphene is a thin layer of types for graphic libraries" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'ebassi' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['922dc109d2dc5dc56617a29bd716c79dd84db31721a8493a13a5f79109a4a4ed'] + +builddependencies = [ + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('GObject-Introspection', '1.78.1'), + ('binutils', '2.40'), +] +dependencies = [('GLib', '2.78.1')] + +configopts = "-Dgobject_types=true -Dintrospection=enabled" + +sanity_check_paths = { + 'files': ['lib/libgraphene-1.0.%s' % SHLIB_EXT, 'share/gir-1.0/Graphene-1.0.gir'], + 'dirs': ['include/graphene-1.0', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..87c73c5219b --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '8.2.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['77c8c903f4539b050a6d3a5be79705c7ccf7b1cb66d68152a651486e261edbd2'] + +builddependencies = [ + ('binutils', '2.40'), + ('GObject-Introspection', '1.78.1'), + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('GLib', '2.78.1'), + ('ICU', '74.1'), + ('cairo', '1.18.0'), + ('freetype', '2.13.2'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a3a41bd2a7a --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.10' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a7ced37f4102b745ac86d6a70a9da399cc139ff168ba6b8002b4d8d43c900c15'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('X11', '20231019'), + ('Mesa', '23.1.9'), +] + +configopts = '-Degl=yes --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..c1a1fd7284b --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.51.0' + +homepage = 'https://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['1d67f205bfc318c27a29cfdfb6828568df566795df0cb51d2189cde7f2d581e8'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.78.1'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('X11', '20231019'), + ('GLib', '2.78.1'), + ('cairo', '1.18.0'), + ('HarfBuzz', '8.2.2'), + ('FriBidi', '1.0.13'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..2f139f4093d --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.25.1-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +# Need to use Meson instead of the "pip" installation +# See: https://github.com/pygobject/pycairo/issues/312 +easyblock = 'MesonNinja' + +name = 'PyCairo' +version = '1.25.1' + +homepage = 'https://pycairo.readthedocs.io/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/pygobject/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fabe2a6ae082e7970084ce61b29087f2211f098a099b0d6de68caac4be1263fb'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('cairo', '1.18.0'), +] + +sanity_check_paths = { + 'files': ['%s/py3cairo.%s' % (p, e) for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')]], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a70381c6579 --- /dev/null +++ b/easybuild/easyconfigs/p/PyGObject/PyGObject-3.46.0-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'PyGObject' +version = '3.46.0' + +homepage = 'https://pygobject.readthedocs.io/' +description = """PyGObject is a Python package which provides bindings for GObject based +libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['481437b05af0a66b7c366ea052710eb3aacbb979d22d30b797f7ec29347ab1e6'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('GLib', '2.78.1'), + ('GObject-Introspection', '1.78.1'), + ('PyCairo', '1.25.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['include/pygobject-%(version_major)s.0/pygobject.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'gi'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..dac0641eed7 --- /dev/null +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.22.0-GCCcore-13.2.0.eb @@ -0,0 +1,63 @@ +# Author: Jasper Grimm (UoY) +# URL of Wayland download changed to GitLab due to changes upstream +# Author: J. Sassmannshausen (Imperial College London/UK) +easyblock = 'Bundle' + +name = 'Wayland' +version = '1.22.0' + +homepage = 'https://wayland.freedesktop.org/' +description = """ +Wayland is a project to define a protocol for a compositor to talk to + its clients as well as a library implementation of the protocol. The + compositor can be a standalone display server running on Linux kernel + modesetting and evdev input devices, an X application, or a wayland + client itself. The clients can be traditional applications, X servers + (rootless or fullscreen) or other display servers. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('CMake', '3.27.6'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('libffi', '3.4.4'), + ('expat', '2.5.0'), + ('libxml2', '2.11.5'), +] + +default_easyblock = 'MesonNinja' +default_component_specs = { + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('wayland', version, { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/%(namelower)s/-/releases/%(version)s/downloads'], + 'checksums': ['1540af1ea698a471c2d8e9d288332c7e0fd360c8f1d12936ebb7e7cbc2425842'], + 'sources': [SOURCE_TAR_XZ], + 'configopts': "-Ddocumentation=false", + }), + ('wayland-protocols', '1.32', { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/%(namelower)s/-/releases/%(version)s/downloads'], + 'checksums': ['7459799d340c8296b695ef857c07ddef24c5a09b09ab6a74f7b92640d2b1ba11'], + 'sources': [SOURCE_TAR_XZ], + 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH " + }), +] + +_libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']] +sanity_check_paths = { + 'files': ['bin/wayland-scanner'] + _libs, + 'dirs': ['lib'], +} + +sanity_check_commands = ["wayland-scanner --help", "wayland-scanner --version"] + +moduleclass = 'vis' From 67a1a1381c9c2275bbf162fb7ec0383a7ddb88f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 14:02:42 +0100 Subject: [PATCH 9348/9987] checksum --- .../easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb index 83b0be058ef..1e9d836097e 100644 --- a/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.190-GCCcore-13.2.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] sources = [SOURCE_TAR_BZ2] -checksums = ['39bd8f1a338e2b7cd4abc3ff11a0eddc6e690f69578a57478d8179b4148708c8'] +checksums = ['8e00a3a9b5f04bc1dc273ae86281d2d26ed412020b391ffcc23198f10231d692'] builddependencies = [ ('M4', '1.4.19'), From 1940044ba64011c3ae8dda5b11e70991015ddf63 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 14:37:28 +0100 Subject: [PATCH 9349/9987] checksum --- easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb index c1a1fd7284b..9040f4ef2dc 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.51.0-GCCcore-13.2.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] -checksums = ['1d67f205bfc318c27a29cfdfb6828568df566795df0cb51d2189cde7f2d581e8'] +checksums = ['74efc109ae6f903bbe6af77eaa2ac6094b8ee245a2e23f132a7a8f0862d1a9f5'] builddependencies = [ ('binutils', '2.40'), From 1e875905f4aa8da17301171e622e2a924514ae09 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 14:38:26 +0100 Subject: [PATCH 9350/9987] Add dbus --- .../d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..ec0ca4a6233 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'DBus' +version = '1.15.8' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['84fc597e6ec82f05dc18a7d12c17046f95bad7be99fc03c15bc254c4701ed204'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('expat', '2.5.0'), +] + +configopts = '-DENABLE_SYSTEMD=OFF ' +# disable documentation +configopts = '-DDBUS_ENABLE_XML_DOCS=OFF -DDBUS_ENABLE_QTHELP_DOCS=OFF -DDBUS_ENABLE_DOXYGEN_DOCS=OFF ' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' From a74f80811f6e5cc5c69dffb4976a52e80f03ffb7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 14:39:06 +0100 Subject: [PATCH 9351/9987] style --- .../g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb index a66201f8def..ac99b2584dd 100644 --- a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-13.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'MesonNinja' name = 'Gdk-Pixbuf' -version = '2.42.10' +version = '2.42.10' homepage = 'https://docs.gtk.org/gdk-pixbuf/' description = """ From e412de696a67a3808a3dc6e7ccc1d5000c7bfe70 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 4 Nov 2023 15:48:03 +0100 Subject: [PATCH 9352/9987] fix dbus --- easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb index ec0ca4a6233..21251602a0c 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.8-GCCcore-13.2.0.eb @@ -32,7 +32,7 @@ dependencies = [ configopts = '-DENABLE_SYSTEMD=OFF ' # disable documentation -configopts = '-DDBUS_ENABLE_XML_DOCS=OFF -DDBUS_ENABLE_QTHELP_DOCS=OFF -DDBUS_ENABLE_DOXYGEN_DOCS=OFF ' +configopts += '-DDBUS_ENABLE_XML_DOCS=OFF -DDBUS_ENABLE_QTHELP_DOCS=OFF -DDBUS_ENABLE_DOXYGEN_DOCS=OFF ' sanity_check_paths = { 'files': ['bin/dbus-%s' % x for x in From 26306ac4bd11d1794183e340fe0a4b3daf565d98 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 4 Nov 2023 17:33:16 +0100 Subject: [PATCH 9353/9987] add libiconv dependency to gettext --- easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb index 2f4d3b3096a..3bf5207d463 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.22-GCCcore-13.2.0.eb @@ -19,6 +19,7 @@ builddependencies = [('binutils', '2.40')] dependencies = [ ('libxml2', '2.11.5'), ('ncurses', '6.4'), + ('libiconv', '1.17'), ] configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' From c0f09497fad94b5c6f2f9a8341025e53c97c2b58 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 4 Nov 2023 18:51:45 +0000 Subject: [PATCH 9354/9987] update checksum Co-authored-by: SebastianAchilles --- .../easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb index 87c73c5219b..8521cf6e258 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-8.2.2-GCCcore-13.2.0.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} github_account = 'harfbuzz' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['77c8c903f4539b050a6d3a5be79705c7ccf7b1cb66d68152a651486e261edbd2'] +checksums = ['0546aac7b2493b3681047914550860157f8799fc80bf5cb528927a9643d6ab3d'] builddependencies = [ ('binutils', '2.40'), From 1e2ba69709dcd11b51089032b845bd8dac844c14 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 4 Nov 2023 21:08:47 +0100 Subject: [PATCH 9355/9987] bump version to 4.9.0dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 1aaee4d4aab..6403cb7b383 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.8.2' +VERSION = '4.9.0.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From ad78d8f2eb2d3bbe6484b294dd45eba6ede438a6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 6 Nov 2023 12:11:45 +0100 Subject: [PATCH 9356/9987] Add patch to fix duplicate definition --- .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 3 ++ ...duplicate-kDefaultTimeout-definition.patch | 31 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 45ffe3f1e20..e567f93765a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', 'PyTorch-1.13.1_disable-test-sharding.patch', + 'PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch', 'PyTorch-1.13.1_fix-flaky-jit-test.patch', 'PyTorch-1.13.1_fix-fsdp-fp16-test.patch', 'PyTorch-1.13.1_fix-gcc-12-missing-includes.patch', @@ -68,6 +69,8 @@ checksums = [ {'PyTorch-1.12.1_fix-vsx-vector-funcs.patch': 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2'}, {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, {'PyTorch-1.13.1_disable-test-sharding.patch': 'df2074adeba47998ce2993d99ca64eb6f1c79ab7057f553b436efdec264d3572'}, + {'PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch': + '882f8cfaf33490a4372928fb6673cbbfa40e5be1b64bf7e0cc2924d73cf872e8'}, {'PyTorch-1.13.1_fix-flaky-jit-test.patch': '71efdeb29b5e5b4982c9f5cb2182733654a34d52f85bb5487bc4d7d99b86101b'}, {'PyTorch-1.13.1_fix-fsdp-fp16-test.patch': '8ae68e60d6e1f92f50322b7f0381c7e65251fba32d7606e3a238a36a2f55b5cf'}, {'PyTorch-1.13.1_fix-gcc-12-missing-includes.patch': diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch new file mode 100644 index 00000000000..6e211b1f3a8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1_fix-duplicate-kDefaultTimeout-definition.patch @@ -0,0 +1,31 @@ +From 9a18968253e28ba8d8bdf646731087000c7876b7 Mon Sep 17 00:00:00 2001 +From: sclarkson +Date: Tue, 21 Mar 2023 21:44:49 +0000 +Subject: [PATCH] Fix kDefaultTimeout multiple definition build failure + (#97270) + +Make the namespace explicit to avoid the constexpr conflict on GCC 11. + +Fixes #90448 + +@ezyang + +Pull Request resolved: https://github.com/pytorch/pytorch/pull/97270 +Approved by: https://github.com/ezyang +--- + torch/csrc/distributed/c10d/ProcessGroupGloo.hpp | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/torch/csrc/distributed/c10d/ProcessGroupGloo.hpp b/torch/csrc/distributed/c10d/ProcessGroupGloo.hpp +index a64bc37c4de522..e4d2967c8604ea 100644 +--- a/torch/csrc/distributed/c10d/ProcessGroupGloo.hpp ++++ b/torch/csrc/distributed/c10d/ProcessGroupGloo.hpp +@@ -125,7 +125,7 @@ class TORCH_API ProcessGroupGloo : public Backend { + } + + void wait(const std::vector& keys) override { +- store_->wait(keys, Store::kDefaultTimeout); ++ store_->wait(keys, ::c10d::Store::kDefaultTimeout); + } + + void wait( From 7bb3337a47d2de958b9dc79608c534ebcc1c1345 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 6 Nov 2023 12:56:24 +0100 Subject: [PATCH 9357/9987] {cae}[system/system] STAR-CCM+ v18.06.006 w/ r8 (#19100) * adding easyconfigs: STAR-CCM+-18.06.006.eb, STAR-CCM+-18.06.006-r8.eb * Add user facing versions * Disable restrictive version check in modulerc --------- Co-authored-by: Ake Sandgren --- .../s/STAR-CCM+/STAR-CCM+-18.06.006-r8.eb | 15 +++++++++++++++ .../s/STAR-CCM+/STAR-CCM+-18.06.006.eb | 14 ++++++++++++++ .../s/STAR-CCM+/STAR-CCM+-2310-r8.eb | 18 ++++++++++++++++++ .../easyconfigs/s/STAR-CCM+/STAR-CCM+-2310.eb | 17 +++++++++++++++++ 4 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006-r8.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310-r8.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310.eb diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006-r8.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006-r8.eb new file mode 100644 index 00000000000..49cda6093eb --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006-r8.eb @@ -0,0 +1,15 @@ +name = 'STAR-CCM+' +version = '18.06.006' +versionsuffix = '-r8' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +download_instructions = 'Manually obtain tarball from Siemens' +sources = ['%%(name)s%%(version)s_01_linux-x86_64%s.tar.gz' % versionsuffix] +checksums = ['77a46b81e93d427a1c33b78fa9ae3fa0c1de4636c749e2f2692728b0f5bb1296'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006.eb new file mode 100644 index 00000000000..7368da66b4e --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-18.06.006.eb @@ -0,0 +1,14 @@ +name = 'STAR-CCM+' +version = '18.06.006' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +download_instructions = 'Manually obtain tarball from Siemens' +sources = ['%(name)s%(version)s_01_linux-x86_64.tar.gz'] +checksums = ['476b75b859612cf816ba62ac36fdf98b47dd606114c612dea6869031582db4a5'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310-r8.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310-r8.eb new file mode 100644 index 00000000000..408462f98ca --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310-r8.eb @@ -0,0 +1,18 @@ +easyblock = 'ModuleRC' + +name = 'STAR-CCM+' +version = '2310' +versionsuffix = '-r8' +local_version = '18.06.006' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +dependencies = [('STAR-CCM+', local_version, versionsuffix)] + +check_version = False + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310.eb new file mode 100644 index 00000000000..706662fbe6d --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2310.eb @@ -0,0 +1,17 @@ +easyblock = 'ModuleRC' + +name = 'STAR-CCM+' +version = '2310' +local_version = '18.06.006' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +dependencies = [('STAR-CCM+', local_version)] + +check_version = False + +moduleclass = 'cae' From e8383fab0b548e25f784731deacbce0b638a9824 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 6 Nov 2023 12:56:54 +0100 Subject: [PATCH 9358/9987] adding easyconfigs: STAR-CCM+-2302.eb, STAR-CCM+-2302-r8.eb (#19158) --- .../s/STAR-CCM+/STAR-CCM+-2302-r8.eb | 18 ++++++++++++++++++ .../easyconfigs/s/STAR-CCM+/STAR-CCM+-2302.eb | 17 +++++++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302-r8.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302.eb diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302-r8.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302-r8.eb new file mode 100644 index 00000000000..ad6e29a31b6 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302-r8.eb @@ -0,0 +1,18 @@ +easyblock = 'ModuleRC' + +name = 'STAR-CCM+' +version = '2302' +versionsuffix = '-r8' +local_version = '18.02.008' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +dependencies = [('STAR-CCM+', local_version, versionsuffix)] + +check_version = False + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302.eb new file mode 100644 index 00000000000..3f1ac40dc79 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-2302.eb @@ -0,0 +1,17 @@ +easyblock = 'ModuleRC' + +name = 'STAR-CCM+' +version = '2302' +local_version = '18.02.008' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +dependencies = [('STAR-CCM+', local_version)] + +check_version = False + +moduleclass = 'cae' From 9b85f424474a4811c72448102c347c8f0253775f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 6 Nov 2023 13:35:38 +0100 Subject: [PATCH 9359/9987] fix OpenBLAS on newer Intel CPUs --- .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 3 + .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 13 ++-- .../OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb | 3 + ...xASUM-microkernels-on-new-intel-cpus.patch | 65 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 3 + .../o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb | 3 + .../o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb | 3 + 7 files changed, 88 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index 03bd16ce48f..48991f92ef5 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -17,6 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -28,6 +29,8 @@ checksums = [ {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 5b104219e11..96a3218f027 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -16,11 +16,12 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch', + 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', - 'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch', - 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', ] checksums = [ {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, @@ -28,14 +29,16 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': + '1b495465f8dd1e151d74cf5aa4288120361d29164d6a377228a8d51c255b8a9e'}, + {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, - {'OpenBLAS-0.3.20_fix-cpuid-neoverse-v1-n2.patch': - '1b495465f8dd1e151d74cf5aa4288120361d29164d6a377228a8d51c255b8a9e'}, - {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb index cbf11c2a295..d7442a5c7d8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb @@ -17,6 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -28,6 +29,8 @@ checksums = [ {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch new file mode 100644 index 00000000000..a342b04b79f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch @@ -0,0 +1,65 @@ +From 9019bc494514a74c2042152cdca0a36adea7b42f Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Sat, 4 Nov 2023 22:10:06 +0100 +Subject: [PATCH] Use SkylakeX ?ASUM microkernel for Cooperlake/Sapphirerapids + as well + +--- + kernel/x86_64/casum.c | 2 +- + kernel/x86_64/dasum.c | 2 +- + kernel/x86_64/sasum.c | 2 +- + kernel/x86_64/zasum.c | 2 +- + 4 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/kernel/x86_64/casum.c b/kernel/x86_64/casum.c +index 60feec0ceb..e4d0543114 100644 +--- a/kernel/x86_64/casum.c ++++ b/kernel/x86_64/casum.c +@@ -4,7 +4,7 @@ + #define ABS_K(a) ((a) > 0 ? (a) : (-(a))) + #endif + +-#if defined(SKYLAKEX) ++#if defined(SKYLAKEX) || defined(COOPERLAKE) || defined(SAPPHIRERAPIDS) + #include "casum_microk_skylakex-2.c" + #endif + +diff --git a/kernel/x86_64/dasum.c b/kernel/x86_64/dasum.c +index a9c40f38f0..0147c6978a 100644 +--- a/kernel/x86_64/dasum.c ++++ b/kernel/x86_64/dasum.c +@@ -4,7 +4,7 @@ + #define ABS_K(a) ((a) > 0 ? (a) : (-(a))) + #endif + +-#if defined(SKYLAKEX) ++#if defined(SKYLAKEX) || defined(COOPERLAKE) || defined(SAPPHIRERAPIDS) + #include "dasum_microk_skylakex-2.c" + #elif defined(HASWELL) || defined(ZEN) + #include "dasum_microk_haswell-2.c" +diff --git a/kernel/x86_64/sasum.c b/kernel/x86_64/sasum.c +index 37a92468ff..3f22cb97a1 100644 +--- a/kernel/x86_64/sasum.c ++++ b/kernel/x86_64/sasum.c +@@ -9,7 +9,7 @@ + + #endif + +-#if defined(SKYLAKEX) ++#if defined(SKYLAKEX) || defined(COOPERLAKE) || defined(SAPPHIRERAPIDS) + #include "sasum_microk_skylakex-2.c" + #elif defined(HASWELL) || defined(ZEN) + #include "sasum_microk_haswell-2.c" +diff --git a/kernel/x86_64/zasum.c b/kernel/x86_64/zasum.c +index 80e95a2c89..3f17ab1cfa 100644 +--- a/kernel/x86_64/zasum.c ++++ b/kernel/x86_64/zasum.c +@@ -4,7 +4,7 @@ + #define ABS_K(a) ((a) > 0 ? (a) : (-(a))) + #endif + +-#if defined(SKYLAKEX) ++#if defined(SKYLAKEX) || defined(COOPERLAKE) || defined(SAPPHIRERAPIDS) + #include "zasum_microk_skylakex-2.c" + #endif + diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb index 66b40a6a8a1..7e7d8c4b75f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -17,6 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', @@ -28,6 +29,8 @@ checksums = [ {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch': diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb index 8051da228f0..490f623ac15 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb @@ -17,6 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.23_fix-parallel-build.patch', 'OpenBLAS-0.3.23_fix-lapack-test.patch', @@ -30,6 +31,8 @@ checksums = [ {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.20_fix-x86-cpuid.patch': '57e8384404e136b9f0dafc26573adeb7dc69e60d84a7e189643b91d6299888fc'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_fix-parallel-build.patch': 'abe10ba3b0ca54772dbf235596e35325a5159018f6a60cfc88824c2c220d99d9'}, diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb index f3358f87771..eb7737a76aa 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb @@ -16,6 +16,7 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.23_fix-lapack-test.patch', 'OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch', @@ -26,6 +27,8 @@ checksums = [ {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch': + '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, {'OpenBLAS-0.3.23_fix-lapack-test.patch': 'f6b3d81061f136e34aaf5359bb80fb9d2bba28825cc1dd26179b8dd01a9a0054'}, From ec1476b059588160e7ac77456aefaf7e76018b31 Mon Sep 17 00:00:00 2001 From: appolloford Date: Mon, 6 Nov 2023 19:06:27 +0100 Subject: [PATCH 9360/9987] Add pkgconf build dependency --- .../easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb index 8eea586e45f..2a01bcd59bd 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb @@ -13,6 +13,7 @@ checksums = ['4cd3d161f9aa4f98ec5fa725ee5dc27bca960a3714a707a7d12b3d0abb504679'] builddependencies = [ ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), # ('M4', '1.4.19'), ] From bfb5cb05121fd3c01fd975bebf6a1fd83688138a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 6 Nov 2023 19:18:16 +0100 Subject: [PATCH 9361/9987] adding easyconfigs: libxslt-1.1.38-GCCcore-13.2.0.eb, nettle-3.9.1-GCCcore-13.2.0.eb, Xvfb-21.1.9-GCCcore-13.2.0.eb, xproto-7.0.31-GCCcore-13.2.0.eb --- .../libxslt/libxslt-1.1.38-GCCcore-13.2.0.eb | 36 +++++ .../n/nettle/nettle-3.9.1-GCCcore-13.2.0.eb | 38 ++++++ .../x/Xvfb/Xvfb-21.1.9-GCCcore-13.2.0.eb | 126 ++++++++++++++++++ .../x/xproto/xproto-7.0.31-GCCcore-13.2.0.eb | 29 ++++ 4 files changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.9-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..7f763c378c9 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.38' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['1f32450425819a09acaff2ab7a5a7f8a2ec7956e505d7beeb45e843d0e1ecab1'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libxml2', '2.11.5'), +] + +# Make sure it doesn't pick up OS installed libgcrypt or Python +# enable building static libs +configopts = '--with-crypto=no --with-python=no --enable-static=yes ' + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT, 'lib/%(name)s.a', + 'lib/libexslt.%s' % SHLIB_EXT, 'lib/libexslt.a'], + 'dirs': ['include/libxslt', 'include/libexslt'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d29fc015efd --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.9.1-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.9.1' + +homepage = 'https://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ccfeff981b0ca71bbd6fbcb054f407c60ffb644389a5be80d6716d5b550c6ce3'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = '--disable-openssl ' # openssl is just used for the nettle-openssl example and requires openssl 1.1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.9-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..740256850ac --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.9-GCCcore-13.2.0.eb @@ -0,0 +1,126 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '21.1.9' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Python', '3.11.5'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('libxslt', '1.1.38'), + ('gettext', '0.22'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('X11', '20231019'), + ('pixman', '0.42.2'), + ('libdrm', '2.4.117'), + ('Mesa', '23.1.9'), + ('nettle', '3.9.1'), + ('libunwind', '1.6.2'), + ('XZ', '5.4.4'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.2', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['4a5af55e670713024639a7f7d10826d905d86faf574cd77e0f5aef2d00e70168'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.4.1', { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'checksums': ['f029ae80cdd75d89bee7f7af61c21e07982adfb9f72344a158b99f91f77ef5ed'], + }), + ('font-misc-misc', '1.1.3', { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'checksums': ['bece4a9482b3cb6f7fad2164fd3b394d22dfe1ad2f96f60030a703bcff30f5a5'], + 'preconfigopts': local_font_misc_preconfigopts, + }), + ('xkbcomp', '1.4.6', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['b216a2c8c0eab83f3dc4a3d5ee2bdf7827b30e49c8907035d0f222138eca0987'], + }), + ('xkeyboard-config', '2.40', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['7a3dba1bec7dc7191432da021242d17c9cf6c89690e6c57b0de048ff8c9d2ae3'], + 'configopts': '-Dxorg-rules-symlinks=true', + }), + ('xauth', '1.1.2', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['84d27a1023d8da524c134f424b312e53cb96e08871f96868aa20316bfcbbc054'], + }), + ('libxcvt', '0.1.2', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/lib/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['0561690544796e25cfbd71806ba1b0d797ffe464e9796411123e79450f71db38'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual/xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + '455ac22c411b3e74adb4d1b3fd48b9037b6b5ba9260247c59b669f67a08fd26e', # xorg-server-21.1.9.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a1cf4fe28c7 --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.31-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.31' + +homepage = 'https://www.freedesktop.org/wiki/Software/xlibs' +description = "X protocol and ancillary headers" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [XORG_PROTO_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6d755eaae27b45c5cc75529a12855fed5de5969b367ed05003944cf901ed43c7'] + +builddependencies = [ + ('binutils', '2.40'), + ('xorg-macros', '1.20.0'), +] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' From f604af5d0462771e4ab2e95841a56c7a5c5ca743 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 7 Nov 2023 10:59:53 +0100 Subject: [PATCH 9362/9987] BiG-SCAPE: fix handling of domain files and html templates. --- .../b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 16 +++++++- ...E-1.1.5_use_env_var_for_domain_files.patch | 37 +++++++++++++++++++ ...BiG-SCAPE-1.1.5_use_env_var_for_html.patch | 33 +++++++++++++++++ 3 files changed, 85 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_html.patch diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb index 01cc4ccc891..5c6c71a8721 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -15,11 +15,16 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_use_env_var_to_find-MIBiG-files.patch', + '%(name)s-%(version)s_use_env_var_for_domain_files.patch', + '%(name)s-%(version)s_use_env_var_for_html.patch', ] checksums = [ {'v1.1.5.tar.gz': 'ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7'}, {'BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch': 'f0602208765a2686a324a27ff6073aac01c230b6a81a00656269fd89c97cf370'}, + {'BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch': + '51337f22b2619ed38969f4ead5f7ce2f2df884f272793b47fb46d77e9c5e2aa2'}, + {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'}, ] dependencies = [ @@ -42,9 +47,18 @@ sanity_check_commands = [ 'bigscape.py --help', ] +modextravars = { + 'BIG_SCAPE_HTML_PATH': '%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE', +} + modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" -modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website" +modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website " modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " modloadmsg += "uncompress it and process it using the `hmmpress` command.\n" +modloadmsg += "For data files, like the domains_color_file.tsv and domain_includelist.txt, " +modloadmsg += "one can set the environment variable BIG_SCAPE_DATA_PATH, if that is not set " +modloadmsg += "it will use the directory where the bigscape command is started from.\n" +modloadmsg += "One can copy the domains_color_file.tsv from " +modloadmsg += "%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/domains_color_file.tsv\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch new file mode 100644 index 00000000000..afffdbb087b --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch @@ -0,0 +1,37 @@ +Don't use domains_color_file.tsv and domain_includelist.txt from the install tree. +Use env var or current dir. + +Åke Sandgren, 2023-11-02 +diff -ru BiG-SCAPE-1.1.5.orig/ArrowerSVG.py BiG-SCAPE-1.1.5/ArrowerSVG.py +--- BiG-SCAPE-1.1.5.orig/ArrowerSVG.py 2022-11-14 17:04:47.000000000 +0100 ++++ BiG-SCAPE-1.1.5/ArrowerSVG.py 2023-11-02 15:48:51.313247855 +0100 +@@ -27,7 +27,7 @@ + gene_contour_thickness = 2 # thickness grows outwards + stripe_thickness = 3 + +-domains_color_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "domains_color_file.tsv") ++domains_color_file = os.path.join(os.getenv('BIG_SCAPE_DATA_PATH', os.getcwd()), "domains_color_file.tsv") + + + def read_color_domains_file(): +diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py +--- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 ++++ BiG-SCAPE-1.1.5/bigscape.py 2023-11-02 15:48:02.929621562 +0100 +@@ -2235,7 +2235,7 @@ + # Get domain_includelist + has_includelist = False + if options.domain_includelist: +- bigscape_path = os.path.dirname(os.path.realpath(__file__)) ++ bigscape_path = os.getenv('BIG_SCAPE_DATA_PATH', os.getcwd()) + if os.path.isfile(os.path.join(bigscape_path,"domain_includelist.txt")): + domain_includelist = set() + for line in open(os.path.join(bigscape_path,"domain_includelist.txt"), "r"): +@@ -2850,7 +2852,7 @@ + if not os.path.isfile(pfams_js_file): + with open(pfams_js_file, "w") as pfams_js: + pfam_json = {} +- pfam_colors = generatePfamColorsMatrix(os.path.join(os.path.dirname(os.path.realpath(__file__)), "domains_color_file.tsv")) ++ pfam_colors = generatePfamColorsMatrix(os.path.join(os.getenv('BIG_SCAPE_DATA_PATH', os.getcwd()), "domains_color_file.tsv")) + for pfam_code in pfam_info: + pfam_obj = {} + if pfam_code in pfam_colors: diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_html.patch b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_html.patch new file mode 100644 index 00000000000..0f0da2a792e --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_html.patch @@ -0,0 +1,33 @@ +Use EB specific env var to locate html_template + +Åke Sandgren, 20231106 +diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py +--- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 ++++ BiG-SCAPE-1.1.5/bigscape.py 2023-11-06 11:20:46.410872382 +0100 +@@ -1881,7 +1881,7 @@ + with open(os.path.join(module_html_path, "bs_data.js"), "w") as bs_data_js: + bs_data_js.write("var bs_data={};\n".format(json.dumps(bs_data, indent=4, separators=(',', ':'), sort_keys=True))) + bs_data_js.write("dataLoaded('bs_data');\n") +- shutil.copy(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "index_html"), os.path.join(module_html_path, "index.html")) ++ shutil.copy(os.path.join(os.getenv('BIG_SCAPE_HTML_PATH'), "html_template", "index_html"), os.path.join(module_html_path, "index.html")) + + ## Write bgc_networks.js + with open(os.path.join(module_html_path, "bs_networks.js"), "w") as bs_networks_js: +@@ -2832,7 +2834,7 @@ + create_directory(network_files_folder, "Network Files", False) + + # copy html templates +- dir_util.copy_tree(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "output"), output_folder) ++ dir_util.copy_tree(os.path.join(os.getenv('BIG_SCAPE_HTML_PATH'), "html_template", "output"), output_folder) + + # make a new run folder in the html output & copy the overview_html + network_html_folder = os.path.join(output_folder, "html_content", "networks", run_name) +@@ -2841,7 +2843,7 @@ + for cutoff in cutoff_list: + network_html_folder_cutoff = "{}_c{:.2f}".format(network_html_folder, cutoff) + create_directory(network_html_folder_cutoff, "Network HTML Files", False) +- shutil.copy(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "overview_html"), os.path.join(network_html_folder_cutoff, "overview.html")) ++ shutil.copy(os.path.join(os.getenv('BIG_SCAPE_HTML_PATH'), "html_template", "overview_html"), os.path.join(network_html_folder_cutoff, "overview.html")) + rundata_networks_per_run[network_html_folder_cutoff] = [] + html_subs_per_run[network_html_folder_cutoff] = [] + From 0c6ee78e6ab121aeb6cb666b861008c49129bcc8 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 7 Nov 2023 11:31:51 +0100 Subject: [PATCH 9363/9987] Easyconfig added for DeepLabCut in foss/2022a --- ...DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..abd16842cec --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,74 @@ +# Loosely based on PR #7680 +# J. Sassmannshausen (Imperial College London/UK) +# upgrade to version 2.3.6: J Hein, (LUNARC, Lund University, Sweden) + +easyblock = 'PythonBundle' + +name = 'DeepLabCut' +version = '2.3.6' +versionsuffix = '-CUDA-%(cudaver)s' +local_version = '%(versionsuffix)s-contrib' + +homepage = 'http://www.mousemotorlab.org/deeplabcut' +description = "Markerless tracking of user-defined features with deep learning" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('TensorFlow', '2.9.1', versionsuffix), + ('PyTorch', '1.12.0', versionsuffix), + ('scikit-image', '0.19.3'), + ('matplotlib', '3.5.2'), + ('numba', '0.56.4'), + ('scikit-learn', '1.1.2'), + ('FFmpeg', '4.4.2'), + ('PyZMQ', '24.0.1'), + ('tqdm', '4.64.0'), + ('imageio', '2.22.2'), + ('statsmodels', '0.13.1'), + ('PyTables', '3.8.0'), + ('ruamel.yaml', '0.17.21'), + ('imgaug', '0.4.0', versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('dlclibrary', '0.0.4', { + 'checksums': ['2b4ca078dc9cddb2a1f30d42cbc9d5c0e849e0f93f2b6781ca478baed0a829b8'], + }), + ('filterpy', '1.4.5', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], + }), + ('huggingface-hub', '0.17.3', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('imageio-ffmpeg', '0.4.9', { + 'checksums': ['39bcd1660118ef360fa4047456501071364661aa9d9021d3d26c58f1ee2081f5'], + }), + ('msgpack-numpy', '0.4.8', { + 'sources': ['msgpack-numpy-0.4.8.tar.gz'], + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + }), + ('tensorpack', '0.11', { + 'checksums': ['022b610e416e62e3575424cd08e60af27808a5fb6914294615391caf582cbd4f'], + }), + ('tf_slim', '1.1.0', { + 'source_urls': ['https://github.com/google-research/tf-slim/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['964cde4b7728a408dcd5c841ab6b93d95137ab4b60db28b10400f86286bfeb8b'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['c4479f05b3c917a6198c1abbb6ea0ac580ce4b02fe1d068e0215b1984aa8e385'], + }), +] + + +moduleclass = 'lib' From 4a0a28bd77202e7f39e788d8ccdd6a0fc9250077 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 7 Nov 2023 11:45:54 +0100 Subject: [PATCH 9364/9987] update ScaFaCos for LAMMPS --- .../easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb index e464d600e94..1abcc202d59 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb @@ -44,7 +44,7 @@ dependencies = [ ('kim-api', '2.3.0'), ('Eigen', '3.4.0'), ('PLUMED', '2.7.3'), - ('ScaFaCoS', '1.0.1'), + ('ScaFaCoS', '1.0.4'), ('SciPy-bundle', '2021.10'), # VTK package is auto-disabled if this dep is not available ('VTK', '9.1.0'), From eabda6df35d77295acb6eb1d99dd4c5df90969bd Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 7 Nov 2023 13:40:08 +0100 Subject: [PATCH 9365/9987] {bio}[foss/2022a] mrcfile v1.4.3 --- .../m/mrcfile/mrcfile-1.4.3-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022a.eb new file mode 100644 index 00000000000..dae89bc115f --- /dev/null +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.4.3-foss-2022a.eb @@ -0,0 +1,40 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/11 +easyblock = 'PythonPackage' +name = 'mrcfile' +version = '1.4.3' +homepage = 'https://github.com/ccpem/mrcfile' +description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in +structural biology to store image and volume data. + +It allows MRC files to be created and opened easily using a very simple API, +which exposes the file’s header and data as numpy arrays. The code runs in +Python 2 and 3 and is fully unit-tested. + +This library aims to allow users and developers to read and write standard- +compliant MRC files in Python as easily as possible, and with no dependencies on +any compiled libraries except numpy. You can use it interactively to inspect +files, correct headers and so on, or in scripts and larger software packages to +provide basic MRC file I/O functions. """ + + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + + +use_pip = True +moduleclass = 'bio' From b71452b2d3d4dcec49894da1b51564350af8b7bb Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 7 Nov 2023 13:55:14 +0000 Subject: [PATCH 9366/9987] remove Rust from builddeps --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 7e268e45acb..241eb2a55fd 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -12,8 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} builddependencies = [ - ('binutils', '2.39'), - ('Rust', '1.65.0'), + ('binutils', '2.39') ] dependencies = [ From 121dd592afa1f7fe9d65cf9a0052c00222172cb1 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 7 Nov 2023 15:01:16 +0100 Subject: [PATCH 9367/9987] adding easyconfigs: Horovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb --- ...orovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..089c87eaf0a --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.28.1-foss-2022a-PyTorch-1.12.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.28.1' +local_pt_version = '1.12.0' +versionsuffix = '-PyTorch-%s' % local_pt_version + +homepage = 'https://github.com/uber/horovod' +description = """Horovod is a distributed training framework for TensorFlow, PyTorch and MXnet. +This build only has PyTorch enabled.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('PyTorch', local_pt_version), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 ' +preinstallopts += 'HOROVOD_WITHOUT_TENSORFLOW=1 HOROVOD_WITH_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('horovod', version, { + 'checksums': ['92a43f5a94c43907a56805bad15f19700c62ffc83b7ca483f9e104e229f67ef0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["horovodrun --help"] + +moduleclass = 'tools' From 358a027e5c3cdf151c1aa78627d3436380241128 Mon Sep 17 00:00:00 2001 From: appolloford Date: Tue, 7 Nov 2023 15:06:01 +0100 Subject: [PATCH 9368/9987] Remove unused dependencies --- .../easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb index 2a01bcd59bd..765f6e99944 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb @@ -14,7 +14,6 @@ checksums = ['4cd3d161f9aa4f98ec5fa725ee5dc27bca960a3714a707a7d12b3d0abb504679'] builddependencies = [ ('CMake', '3.26.3'), ('pkgconf', '1.9.5'), - # ('M4', '1.4.19'), ] dependencies = [ From 94a39f8764b9a56fac571b5f54639cde5ed27be9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 7 Nov 2023 17:04:54 +0100 Subject: [PATCH 9369/9987] update R to 4.3.2, add required dependencies and bump extensions --- .../l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb | 34 --- ....1-gfbf-2023a.eb => R-4.3.2-gfbf-2023a.eb} | 195 +++++++++--------- 2 files changed, 98 insertions(+), 131 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb rename easybuild/easyconfigs/r/R/{R-4.3.1-gfbf-2023a.eb => R-4.3.2-gfbf-2023a.eb} (61%) diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb deleted file mode 100644 index df14e87ef74..00000000000 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'libgit2' -version = '1.7.0' - -homepage = 'https://libgit2.org/' -description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant -linkable library with a solid API, allowing you to write native speed custom Git applications in any language -which supports C bindings.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -github_account = 'libgit2' -source_urls = [GITHUB_SOURCE] -sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['d9d0f84a86bf98b73e68997f5c1543cc5067d0ca9c7a5acaba3e8d117ecefef3'] - -builddependencies = [ - ('binutils', '2.40'), - ('CMake', '3.26.3'), - ('pkgconf', '1.9.5'), -] - -dependencies = [ - ('PCRE', '8.45'), - ('OpenSSL', '1.1', '', SYSTEM), -] - -sanity_check_paths = { - 'files': ['include/git2.h', 'lib64/libgit2.%s' % SHLIB_EXT, 'lib64/pkgconfig/libgit2.pc'], - 'dirs': [] -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb b/easybuild/easyconfigs/r/R/R-4.3.2-gfbf-2023a.eb similarity index 61% rename from easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb rename to easybuild/easyconfigs/r/R/R-4.3.2-gfbf-2023a.eb index 24764c1cd82..ed664162bf5 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.2-gfbf-2023a.eb @@ -1,5 +1,5 @@ name = 'R' -version = '4.3.1' +version = '4.3.2' homepage = 'https://www.r-project.org/' description = """R is a free software environment for statistical computing @@ -9,11 +9,10 @@ toolchain = {'name': 'gfbf', 'version': '2023a'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['8dd0bf24f1023c6f618c3b317383d291b4a494f40d73b983ac22ffea99e4ba99'] +checksums = ['b3f5760ac2eee8026a3f0eefcb25b47723d978038eee8e844762094c860c452a'] builddependencies = [ ('pkgconf', '1.9.5'), - #('Xvfb', '21.1.6'), ('Autotools', '20220317'), ] dependencies = [ @@ -32,13 +31,12 @@ dependencies = [ ('libjpeg-turbo', '2.1.5.1'), # for plottting in R ('LibTIFF', '4.5.0'), ('Java', '11', '', SYSTEM), - ('libgit2', '1.7.0'), + ('libgit2', '1.7.1'), ('OpenSSL', '1.1', '', SYSTEM), ('cURL', '8.0.1'), - #('Tk', '8.6.12'), # for tcltk - #('libxml2', '2.10.3'), # for XML - #('HarfBuzz', '5.3.1'), # for textshaping - #('FriBidi', '1.0.12'), # for textshaping + ('Tk', '8.6.13'), # for tcltk + ('HarfBuzz', '5.3.1'), # for textshaping + ('FriBidi', '1.0.12'), # for textshaping ] @@ -65,8 +63,11 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on 22nd June 2023 +# packages updated on 5th November 2023 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets', @@ -81,11 +82,11 @@ exts_list = [ 'tcltk', 'tools', 'utils', - ('rlang', '1.1.1', { - 'checksums': ['5e5ec9a7796977216c39d94b1e342e08f0681746657067ba30de11b8fa8ada99'], + ('rlang', '1.1.2', { + 'checksums': ['2a0ee1dc6e5c59b283c32db5e74e869922a336197cb406fe92622b6ec66f8092'], }), - ('Rcpp', '1.0.10', { - 'checksums': ['1e65e24a9981251ab5fc4f9fd65fe4eab4ba0255be3400a8c5abe20b62b5d546'], + ('Rcpp', '1.0.11', { + 'checksums': ['df757c3068599c6c05367900bcad93547ba3422d59802dbaca20fd74d4d2fa5f'], }), ('R6', '2.5.1', { 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], @@ -96,11 +97,11 @@ exts_list = [ ('base64enc', '0.1-3', { 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], }), - ('rprojroot', '2.0.3', { - 'checksums': ['50604247470e910cecfe9b76df754bf96a0d701f81b732f7aa9c90a20d30f897'], + ('rprojroot', '2.0.4', { + 'checksums': ['b5f463fb25a24dac7a4ca916be57dbe22b5262e1f41e53871ca83e57d4336e99'], }), - ('xfun', '0.39', { - 'checksums': ['d0ecaabb243dd3496da6029932fcdd4772914843de7ffd0b78a172efde1356c9'], + ('xfun', '0.41', { + 'checksums': ['2374c3b8f141f1e5ff01b291d8aa5c3dc807dd8e99ab4dc7a048c9534a7e3b02'], }), ('commonmark', '1.9.0', { 'checksums': ['6dd01a5a26c8d436486abf69c2f6ad0f8dd1c811f575c31983aeb4dbd376548f'], @@ -108,8 +109,8 @@ exts_list = [ ('highr', '0.10', { 'checksums': ['ec55bc1ff66390ed66806dc2a7b6c17dbfd089b3d73fe2e369017f8cb4bc347b'], }), - ('digest', '0.6.31', { - 'checksums': ['5a284f490eaca6750f695f00a584cfca3f180ca1046ac1107202141149d431b9'], + ('digest', '0.6.33', { + 'checksums': ['be702c886b1639be7eda4ea25a4261b30ce418c580f79bd78ec8d6cb4d327819'], }), ('desc', '1.4.2', { 'checksums': ['758acf14be478c09ba7e84ade3a7ce512becf35d44e5e6a997b932065f2a227c'], @@ -117,8 +118,8 @@ exts_list = [ ('ellipsis', '0.3.2', { 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], }), - ('prettyunits', '1.1.1', { - 'checksums': ['9a199aa80c6d5e50fa977bc724d6e39dae1fc597a96413053609156ee7fb75c5'], + ('prettyunits', '1.2.0', { + 'checksums': ['f059f27e2a5c82e351fe05b87ad712f7afc273c651450453f59d99af5deeacea'], }), ('crayon', '1.5.2', { 'checksums': ['70a9a505b5b3c0ee6682ad8b965e28b7e24d9f942160d0a2bad18eec22b45a7a'], @@ -129,56 +130,56 @@ exts_list = [ ('magrittr', '2.0.3', { 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], }), - ('evaluate', '0.21', { - 'checksums': ['3178c99cee8917d7d128806d064d4fecce7845ed07f42e759dcc0adda89c22b9'], + ('evaluate', '0.23', { + 'checksums': ['c9cf9c37502b8fbfa78e4eb96b8c3d1789060e49505c86c07cb7476da804a45c'], }), ('ps', '1.7.5', { 'checksums': ['1abc3ae3c55797b994973f7e43bf5c7bbb4da649a0dcfad36675e196dba4cb4e'], }), - ('processx', '3.8.1', { - 'checksums': ['e008472b81d4ca1a37a4ba7dd58e5e944f96ab2e44c8ccc8840d43e9fe99e93c'], + ('processx', '3.8.2', { + 'checksums': ['e91b87af5b23c14b71003ec880f749dca81fd74f0601ab59ea1847c7fe857ecd'], }), ('callr', '3.7.3', { 'checksums': ['567bfedf073a1d4c5785f0553341608a214938110567b9a6495ff20ebb2fd04e'], }), - ('pkgbuild', '1.4.1', { - 'checksums': ['cdb0ace14444f362be9725bd84e9752dab92f4771296504b63b9b8084f5e8a6b'], + ('pkgbuild', '1.4.2', { + 'checksums': ['2334a245d75420b2adf9f217a6bc4a5f7faaa4244a6aac2b774b26f199fc82c5'], }), - ('fs', '1.6.2', { - 'checksums': ['548b7c0ed5ab26dc4fbd88707ae12987bcaef834dbc6de4e17d453846dc436b2'], + ('fs', '1.6.3', { + 'checksums': ['fa82061e50d7a4d94b7e404f9f2b699e75ae8fbfb575fabdfc2c39f536c0f971'], }), - ('utf8', '1.2.3', { - 'checksums': ['c0a88686591f4ad43b52917d0964e9df4c62d8858fe25135a1bf357dfcbd6347'], + ('utf8', '1.2.4', { + 'checksums': ['418f824bbd9cd868d2d8a0d4345545c62151d321224cdffca8b1ffd98a167b7d'], }), - ('fansi', '1.0.4', { - 'checksums': ['3163214e6c40922bbb495229259ed8ce1bebd98b77098a6936d234e43da9c49f'], + ('fansi', '1.0.5', { + 'checksums': ['c616ce357fbfd43253c366da578549a38066459058c22fb99c82fc05992e23f6'], }), ('pkgconfig', '2.0.3', { 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], }), - ('withr', '2.5.0', { - 'checksums': ['37317b3ed790a08407072993a05ab255f6305f95a12a16e0e28aa6aa80fc8bc0'], + ('withr', '2.5.2', { + 'checksums': ['d5b6fa6d728fda5201310d6ad5921a43aae1c23029c25334bfc1e54cb13d4205'], }), ('glue', '1.6.2', { 'checksums': ['9da518f12be584c90e75fe8e07f711ee3f6fc0d03d817f72c25dc0f66499fdbf'], }), - ('rstudioapi', '0.14', { - 'checksums': ['469d0987b1ad728a96c363a422fba712a5cebc8b11a5f7e953b4a671044dafc4'], + ('rstudioapi', '0.15.0', { + 'checksums': ['935bc81dca37d3d6e77982bfe6e7fbd779e8606e5b7e00d0ba4c80fec0416ccf'], }), - ('pkgload', '1.3.2', { - 'checksums': ['35d19a032bfeeefcab92d76a768b4a420c2ede0920badaf48cca878592b46b2f'], + ('pkgload', '1.3.3', { + 'checksums': ['b0898122876479cc4a35cd566654b3a7b50f8ac105565dbf3f8b9d4283816959'], }), ('fastmap', '1.1.1', { 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], }), - ('htmltools', '0.5.5', { - 'checksums': ['c8b23fab855a89c6ed0f6d6c7cad0ff9c5ae329c0bdb479940443ee752f26659'], + ('htmltools', '0.5.7', { + 'checksums': ['ecb0d82619063f49e4d001c44fcc1b811a06928fd66c2bb8c86632798d98b386'], }), ('yaml', '2.3.7', { 'checksums': ['d20cb219e0f9c48aba02f132f81cfa9ecda5e22c925e36726840218ed56680ab'], }), - ('knitr', '1.43', { - 'checksums': ['3d29baea8c349aaa9310879ceb9a9d51bcaec39827ad46d422c3793c8a4ed53c'], + ('knitr', '1.45', { + 'checksums': ['ee2edea53bc53efa51d131ab5a0b0c829c0f950b79d3c6ee34705354bf7584fb'], }), ('mime', '0.12', { 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], @@ -189,14 +190,14 @@ exts_list = [ ('brio', '1.1.3', { 'checksums': ['eaa89041856189bee545bf1c42c7920a0bb0f1f70bb477487c467ee3e8fedcc6'], }), - ('jsonlite', '1.8.5', { - 'checksums': ['dc3cca4bdca1b6d6836c412760ea9656140683126c54cb89c3e42219dec4a3ad'], + ('jsonlite', '1.8.7', { + 'checksums': ['7d42b7784b72d728698ea02b97818df51e2015ffa39fec2eaa2400771b0f601c'], }), ('lifecycle', '1.0.3', { 'checksums': ['6459fdc3211585c0cdf120427579c12149b02161efe273a64b825c05e9aa69c2'], }), - ('vctrs', '0.6.3', { - 'checksums': ['93dc220dcde8b440586b2260460ef354e827a17dfec1ea6a9815585a10cfa5c2'], + ('vctrs', '0.6.4', { + 'checksums': ['8a80192356e724d21bd89a0ce3e5835856fd5bb1651e7fc205c6fee58fd001c8'], }), ('stringr', '1.5.0', { 'checksums': ['52b159d7700a139111b4caf939e7c9c6ab3e01185181400d70a74c552826633a'], @@ -213,29 +214,29 @@ exts_list = [ ('rematch2', '2.1.2', { 'checksums': ['fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb'], }), - ('waldo', '0.5.1', { - 'checksums': ['45bf076cff449e3c506c95857734bb73fdf30040333709b8845d09a12c6fdf46'], + ('waldo', '0.5.2', { + 'checksums': ['82cdae1ab2c5e7e5dbf5c6bdf832020b46e152732053fb45de7c9a81afdf2e05'], }), - ('testthat', '3.1.9', { - 'checksums': ['4da1f992549c9b8db211f205059ec4c5d91a45d5971d60ebae21058268448375'], + ('testthat', '3.2.0', { + 'checksums': ['5b0be53295fe509042e48711df091f7021e23512d1339a4f6f6d9f36d145650e'], }), - ('xml2', '1.3.4', { - 'checksums': ['340bb1a18e643a5008c0b4e92d71c3b0abacb44f1742e3a77d0cb33cb73b3030'], + ('xml2', '1.3.5', { + 'checksums': ['3d6a10a7ab76e0cc024b73d3fb8af65a662efe0e707681d9ffc2b3ff1f09e282'], }), - ('curl', '5.0.1', { - 'checksums': ['b7058f9cc7fa8f649505583584b61383fc08dccf746faa5381ba3d0b8bdf93a6'], + ('curl', '5.1.0', { + 'checksums': ['57218da84b85bd01ce7daa4bca3e271eda1bf688e0cdb211c397ccb272ecba97'], }), ('sys', '3.4.2', { 'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'], }), - ('askpass', '1.1', { - 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], + ('askpass', '1.2.0', { + 'checksums': ['b922369781934d0ffc8d0c0177e8ace56796c2e6a726f65e460c16f792592cef'], }), - ('openssl', '2.0.6', { - 'checksums': ['77f3032a16270f0d1734f269b8d348eedc75b277812854386091143082c1b3f3'], + ('openssl', '2.1.1', { + 'checksums': ['faa726f9af2a97d5fa1e1044f4a38ee2edd4c81f0beb5830f6a36ff249b64bdc'], }), - ('httr', '1.4.6', { - 'checksums': ['8d6d86cbef23738d2b4390490f7486d8cf7674f0a59c19f515f61cad35ec37b2'], + ('httr', '1.4.7', { + 'checksums': ['1555e6c2fb67bd38ff11b479f74aa287b2d93f4add487aec53b836ff07de3a3a'], }), ('jquerylib', '0.1.4', { 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], @@ -243,11 +244,11 @@ exts_list = [ ('rappdirs', '0.3.3', { 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], }), - ('sass', '0.4.6', { - 'checksums': ['2ee82ce709b7fdee78f7e2364d04f369f58fc2cda4bb5a235bd53c49d311c019'], + ('sass', '0.4.7', { + 'checksums': ['717a08b63615a4fd9e494f775c33f0f965db83677cf1cc37849afc3da1c5e9ee'], }), - ('purrr', '1.0.1', { - 'checksums': ['0a7911be3539355a4c40d136f2602befcaaad5a3f7222078500bfb969a6f2ba2'], + ('purrr', '1.0.2', { + 'checksums': ['2c1bc6bb88433dff0892b41136f2f5c23573b335ff35a4775c72aa57b48bbb63'], }), ('cachem', '1.0.8', { 'checksums': ['ea9ca919fe615dce8770758ecc2fc88ac99074f66ff1cde3a0b95d40007f45c2'], @@ -255,32 +256,32 @@ exts_list = [ ('memoise', '2.0.1', { 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], }), - ('bslib', '0.5.0', { - 'checksums': ['a2c6fbc62242806e10bb58c5d1ba04a6d3bf4e546bc53d7acf1b8eb1160bd115'], + ('bslib', '0.5.1', { + 'checksums': ['b175612322e3ba929cf67a9261dd253346a981ce15bbb63d4a6874f54d5ef00e'], }), - ('fontawesome', '0.5.0', { - 'checksums': ['4117b417a33e82d626881d7059eb54e7534cba202e75dae7e27021cb3796e90b'], + ('fontawesome', '0.5.2', { + 'checksums': ['da3de2a9717084d1400d48edd783f06c66b8c910ce9c8d753d1b7d99be1c5cc9'], }), - ('tinytex', '0.45', { - 'checksums': ['0c2fbbd09e80af80ca6b685bf0653f070da97b85413d39af966aba28f376e92c'], + ('tinytex', '0.48', { + 'checksums': ['1d0b989fa781a50a560b8d785f20c28bffc63b5b2e0fcd937c57fdd61d597695'], }), - ('rmarkdown', '2.22', { - 'checksums': ['c6635519503e0fcdd518696d3ac96d8d28d9d4ecd9db0532c53426002f6387b8'], + ('rmarkdown', '2.25', { + 'checksums': ['06e4662666fe018fbe3bef3531280a461c7bc24bb00f34b9d4c7b08d52210155'], }), - ('downlit', '0.4.2', { - 'checksums': ['33dff66909104d1a5ba8e57b1288986e82b61fd5e91dce0cd358d53724b37e3c'], + ('downlit', '0.4.3', { + 'checksums': ['6c0fbe98ece8a511973263f8e8a35574df0cfc45edea7452b53b8d326436b3bd'], }), - ('cpp11', '0.4.3', { - 'checksums': ['f1a60e4971a86dbbcf6a16bbd739b59bb66d9c45d93cfd8dedc2a87e302598f1'], + ('cpp11', '0.4.6', { + 'checksums': ['d1c56954671d3398078ad52aaa4efce0864e8166465c8c5e5e9a1e40599055b3'], }), - ('systemfonts', '1.0.4', { - 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], + ('systemfonts', '1.0.5', { + 'checksums': ['840ffb1d8293739c79cbc868101d9f9a84f4a9de4c7b3625e30af2fb63e15823'], }), - ('textshaping', '0.3.6', { - 'checksums': ['80e2c087962f55ce2811fbc798b09f5638c06c6b28c10cd3cb3827005b902ada'], + ('textshaping', '0.3.7', { + 'checksums': ['fa924dbe1fb4138b80d6c26ee42f4203843f1d34f77e2a5e42514e6fcc97ec42'], }), - ('ragg', '1.2.5', { - 'checksums': ['936f4d75e0e01cdeefb9f57d121cdd7812d0de5a9e1a3a8315f92ce1c84da8f9'], + ('ragg', '1.2.6', { + 'checksums': ['1014dc493ab52e98e4114fbabfca753bebd4d64db7ef7946bd064fb404e0f7c7'], }), ('whisker', '0.4.1', { 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], @@ -300,20 +301,20 @@ exts_list = [ ('later', '1.3.1', { 'checksums': ['23eed681f0b9eacebbc3c6a5ba14ee0b676a4bf6e69af194c5a36edfe11464ac'], }), - ('promises', '1.2.0.1', { - 'checksums': ['8d3a8217909e91f4c2a2eebba5ac8fc902a9ac1a9e9d8a30815c9dc0f162c4b7'], + ('promises', '1.2.1', { + 'checksums': ['3ce0a26df39ea27536877ec6db13083b2952108245024baa8b40ae856d2ce5be'], }), ('xtable', '1.8-4', { 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], }), - ('httpuv', '1.6.11', { - 'checksums': ['8ba79e0a8351274daf2dc566c71f88e891127cdedca62ad77a4b27a8103eeef5'], + ('httpuv', '1.6.12', { + 'checksums': ['b1d972b1c240702c38cb844a1040670d62876abf462256764b49c120a52f5e74'], }), ('sourcetools', '0.1.7-1', { 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], }), - ('shiny', '1.7.4', { - 'checksums': ['bbfcdd7375013b8f59248b3f3f4e752acd445feb25179f3f7f65cd69614da4b5'], + ('shiny', '1.7.5.1', { + 'checksums': ['2023d91cc8039580752f6ecc5010d4419b7d928724ce5b10b93a3b48e1e6fb46'], }), ('miniUI', '0.1.1.1', { 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], @@ -336,8 +337,8 @@ exts_list = [ ('rcmdcheck', '1.4.0', { 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], }), - ('remotes', '2.4.2', { - 'checksums': ['f2ef875f24a485bf4f55a8c830f87cdd5db868f9a8cdb624dc452d0bf66ba516'], + ('remotes', '2.4.2.1', { + 'checksums': ['7ba8ca9a652d60bcdea25dbd43bd1e055e97b031c05e0bc3fac43bf245c1209d'], }), ('clipr', '0.8.0', { 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], @@ -354,17 +355,17 @@ exts_list = [ ('gh', '1.4.0', { 'checksums': ['68c69fcd18429b378e639a09652465a4e92b7b5b5704804d0c5b1ca2b9b58b71'], }), - ('credentials', '1.3.2', { - 'checksums': ['2ffa7c11bedbfa034adf553d0a2f2e4f6a496b858af753a09a89219cff9028b8'], + ('credentials', '2.0.1', { + 'checksums': ['2c7cfc45bd4afa9a2c2b85d43e907b212da3468781e1b617737bd095253c358b'], }), ('zip', '2.3.0', { 'checksums': ['33eba844922af9981732ee6ec1582d46cf04c562344f09a0f0f14a22c6f74543'], }), - ('gert', '1.9.2', { - 'checksums': ['42ca1b4bcafb1fdbbc7f54df0ee4476ecd19e9e7d563b53fe7064e0086ab665e'], + ('gert', '2.0.0', { + 'checksums': ['7c147c3740e7ece8764e6197f311d84e6191fddead1d96fbbfb29816ef5d6391'], }), - ('usethis', '2.2.0', { - 'checksums': ['2ccebe690aadebff96451cc9c226dc1a1e9ca5ac6ec83310e12a1312cb163b4f'], + ('usethis', '2.2.2', { + 'checksums': ['d9d8c1a789ae6fd0e717e174ac29da2e4a925df321e5cc0bfb3d65c87e4cbe46'], }), ('devtools', '2.4.5', { 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], From 5fa0641a00b326468a1546d990a067f37797d8ba Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 7 Nov 2023 17:12:30 +0100 Subject: [PATCH 9370/9987] adding easyconfigs: R-bundle-CRAN-2023.11-foss-2023a.eb and patches: HWxtest-1.1.9_add-fcommon.patch, liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch --- .../HWxtest-1.1.9_add-fcommon.patch | 21 + .../R-bundle-CRAN-2023.11-foss-2023a.eb | 3399 +++++++++++++++++ ...dSVM-1.2.4-fix_ppc_and_aarch64_build.patch | 49 + 3 files changed, 3469 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-CRAN/HWxtest-1.1.9_add-fcommon.patch create mode 100644 easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-CRAN/liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/HWxtest-1.1.9_add-fcommon.patch b/easybuild/easyconfigs/r/R-bundle-CRAN/HWxtest-1.1.9_add-fcommon.patch new file mode 100644 index 00000000000..a4e41eea63e --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/HWxtest-1.1.9_add-fcommon.patch @@ -0,0 +1,21 @@ +fix "multiple definition" errors by adding -fcommon compiler options, +see https://www.gnu.org/software/gcc/gcc-10/porting_to.html + +author: Kenneth Hoste (HPC-UGent) + +diff -ruN HWxtest.orig/MD5 HWxtest/MD5 +--- HWxtest.orig/MD5 2020-11-08 21:15:03.612622261 +0100 ++++ HWxtest/MD5 2020-11-08 21:13:24.278691443 +0100 +@@ -40,6 +40,7 @@ + 4657a2011dc5363ed1cfd1d29a7040d5 *src/HWmtest.c + 08ec52ea231752fbb2bb11a529107806 *src/HWxcount.c + 23598383650c211dd18d54bded68b9bd *src/HWxtest.c ++8b6d9aec8b8cef60d1b245e0f290bfed *src/Makevars + 886a6d855fb0b59e565b919a1ff69eb0 *vignettes/HWxtest.Rmd + fcf857c5f98963f740c5c2f95e33ccc9 *vignettes/HWxtest.md + b93f768037a75ec9edd60ca89fd4c1db *vignettes/bibHW.txt +diff -ruN HWxtest.orig/src/Makevars HWxtest/src/Makevars +--- HWxtest.orig/src/Makevars 1970-01-01 01:00:00.000000000 +0100 ++++ HWxtest/src/Makevars 2020-11-08 21:15:51.340615023 +0100 +@@ -0,0 +1 @@ ++PKG_CFLAGS = -fcommon diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb new file mode 100644 index 00000000000..8421d82323d --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb @@ -0,0 +1,3399 @@ +easyblock = 'Bundle' + +name = 'R-bundle-CRAN' +version = '2023.11' + +homepage = 'https://www.r-project.org/' +description = "Bundle of R packages from CRAN" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('Xvfb', '21.1.8'), + ('Autotools', '20220317'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('R', '4.3.2'), + ('X11', '20230603'), + ('Mesa', '23.1.4'), + ('libGLU', '9.0.3'), + ('cairo', '1.17.8'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('SQLite', '3.42.0'), + ('PCRE2', '10.42'), + ('libpng', '1.6.39'), # for plotting in R + ('libjpeg-turbo', '2.1.5.1'), # for plottting in R + ('LibTIFF', '4.5.0'), + ('Java', '11', '', SYSTEM), + ('Tk', '8.6.13'), # for tcltk + ('cURL', '8.0.1'), # for RCurl + ('libxml2', '2.11.4'), # for XML + ('GMP', '6.2.1'), # for igraph + ('NLopt', '2.7.1'), # for nlopt + ('FFTW', '3.3.10'), # for fftw + ('libsndfile', '1.2.2'), # for seewave + ('ICU', '73.2'), # for rJava & gdsfmt + ('HDF5', '1.14.0'), # for hdf5r + ('UDUNITS', '2.2.28'), # for units + ('GSL', '2.7'), # for RcppGSL + ('ImageMagick', '7.1.1-15'), + ('GLPK', '5.0'), # for Rglpk + ('nodejs', '18.17.1'), # for V8 (required by rstan) + ('GDAL', '3.7.1'), # for sf + ('MPFR', '4.2.0'), # for Rmpfr + ('PostgreSQL', '16.0'), # for RPostgreSQL + ('libgit2', '1.7.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 5th November 2023 +exts_list = [ + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.6-1', { + 'checksums': ['ca79ec7ae92b736cb128556c081abf547f49956c326e053a76579889cbcb7976'], + }), + ('RcppProgress', '0.4.2', { + 'checksums': ['b1624b21b7aeb1dafb30f092b2a4bef4c3504efd2d6b00b2cdf55dc9df194b48'], + }), + ('lpSolve', '5.6.19', { + 'checksums': ['49d5b49e64c6eba2bc4cea80eb615df21a2d0188b1bbffa05052dc978c94581b'], + }), + ('linprog', '0.9-4', { + 'checksums': ['81a6aa2fdc075f12dc912794d0554f87705a8b872b99c89a90a69ee9ada864b4'], + }), + ('geometry', '0.4.7', { + 'checksums': ['96204205f51b4d63c2e7a7b00365def27d131f3c9ec66db56b510046e5d2013b'], + }), + ('bit', '4.0.5', { + 'checksums': ['f0f2536a8874b6a30b80baefbc68cb21f0ffbf51f3877bda8038c3f9f354bfbc'], + }), + ('filehash', '2.4-5', { + 'checksums': ['3b1ee2794dd61e525ee44db16611c65957691d77bb26ae481eba988bb55da22c'], + }), + ('ff', '4.0.9', { + 'checksums': ['722053271987a0c9673c3ff9e7968bbab47979d529a2fe6bb1a3179408ee3c4f'], + }), + ('bnlearn', '4.9', { + 'checksums': ['5159ab0e4b4785ce830726284bdd52d8e1e444a34109b657d022c07b14449227'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-42', { + 'checksums': ['a17f452a94fc3964c939c5b147ad6d4f326a0990493519d376d6700cf733a134'], + }), + ('fdrtool', '1.2.17', { + 'checksums': ['3452601adbead9be4820794e3af2666f710fdf9b801186df565b80b43629c5dd'], + }), + ('formatR', '1.14', { + 'checksums': ['4ebaab2c3f8527871655246b62abd060bc75dae1cec7f962ca4752b8080f474c'], + }), + ('gtools', '3.9.4', { + 'checksums': ['59cf8b194fe98b1cc05dbb4d686810a1068f59d8b402b731548a898ece85f111'], + }), + ('gdata', '3.0.0', { + 'checksums': ['a456b9921765a705fe8e51780dfbbc6ca005abc948b2f80effeccd468601b17f'], + }), + ('GSA', '1.03.2', { + 'checksums': ['177d6059fc645d3d8883806d2dea1c5dfc68efdada9aadde8a96b6d57acf35b8'], + }), + ('infotheo', '1.2.0.1', { + 'checksums': ['c0fb8ec97ad3a49f231c4c993b5eee70c6a61c8c30dc4a46197867e4763a29d4'], + }), + ('lars', '1.3', { + 'checksums': ['c69e6a8da6a3344c0915dd1fd4c78fec5cdf50c62cf6297476e9bb7dc10b549d'], + }), + ('lazy', '1.2-18', { + 'checksums': ['99441bcae2dfbf450eee91f3ec969d416c225f671ac54459c50536916890f00a'], + }), + ('kernlab', '0.9-32', { + 'checksums': ['654ef34e343deb4d2c4c139a44e5397d6e38876088ce1c53c7deb087935d6fdc'], + }), + ('markdown', '1.11', { + 'checksums': ['47fc61755a952ce9716c12de2daf7940fcf306747bd47ad31dd364bbccca5f14'], + }), + ('mlbench', '2.1-3.1', { + 'checksums': ['7afec6d58968ab526ea642e1df39bead2f479c14486b0a62032c999ba73d5cf0'], + }), + ('NLP', '0.2-1', { + 'checksums': ['05eaa453ad2757311c073fd30093c738b20a977c5089031eb454345a1d01f2b6'], + }), + ('mclust', '6.0.0', { + 'checksums': ['de7c306ecba1ef0f4e4a56c748ce08149417496b711beefb032d561a4c28122a'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('MASS', '7.3-60', { + 'checksums': ['b802410feab01464d112b27b3501176eb8e68511d4ba9d052ac4db1f2a72f0c2'], + }), + ('lattice', '0.22-5', { + 'checksums': ['ba1fbe5e18a133507dca9851b7f933002bdb6d1f3ea5f410a0a441103b6da5f1'], + }), + ('nlme', '3.1-163', { + 'checksums': ['7d46ff4c4fb7fda8df6129b28cd2aa7d32e814eac87dae8ea9fa7560593c128a'], + }), + ('segmented', '1.6-4', { + 'checksums': ['472c08ae3eb1c4e784aba45f3e745b0e946bef77c26fbb9f103fd35e1a349191'], + }), + ('som', '0.3-5.1', { + 'checksums': ['a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9'], + }), + ('SuppDists', '1.1-9.7', { + 'checksums': ['6b5527e2635c0ff762eb7af8154704c85e66d7f79a9524089a5c98dfa94dab08'], + }), + ('stabledist', '0.7-1', { + 'checksums': ['06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69'], + }), + ('survivalROC', '1.0.3.1', { + 'checksums': ['8174afebaf239dfda979c8c7e1e219624576d577c983ae787fbd2785b4ccd15c'], + }), + ('pspline', '1.0-19', { + 'checksums': ['ba55bf193f1df9785a0e13b7ef727d5fd2415b318cd6a26b48a2db490c4dfe40'], + }), + ('timeDate', '4022.108', { + 'checksums': ['a5949b4fe2f6bdff751fc0793df8e3150cc25c078d48a28c066c10a6c4bfceef'], + }), + ('longmemo', '1.1-2', { + 'checksums': ['7964e982287427dd58f98e1144e468ae0cbd572d25a4bea6ca9ae9c7522f3207'], + }), + ('ADGofTest', '0.3', { + 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], + }), + ('pixmap', '0.4-12', { + 'checksums': ['893ba894d4348ba05e6edf9c1b4fd201191816b444a214f7a6b2c0a79b0a2aec'], + }), + ('sp', '2.1-1', { + 'checksums': ['2d34cde2a8d5c7876425f99d9d3b24ae192430d316bd2a397a62b52412b1405b'], + }), + ('hms', '1.1.3', { + 'checksums': ['e626f4c60af46efd53ea631b316a103e089470d8fd63c0e0c0efb99364990282'], + }), + ('progress', '1.2.2', { + 'checksums': ['b4a4d8ed55db99394b036a29a0fb20b5dd2a91c211a1d651c52a1023cc58ff35'], + }), + ('RcppArmadillo', '0.12.6.6.0', { + 'checksums': ['d35eb191c5a14e5a95498f43dff3984763ac3fecaf4016c12926f6031e753e9c'], + }), + ('ade4', '1.7-22', { + 'checksums': ['007df54e83a2a6cb8d6da8006f0aace011e7eaa7744dc5f8230ac2c002b393b4'], 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['2a08e2d2ea3abf5fad89c65fdba1d78dd5f4bd12f980436964fe535554d331d5'], + }), + ('mitools', '2.4', { + 'checksums': ['f204f3774e29d79810f579f128de892539518f2cbe6ed237e08c8e7283155d30'], + }), + ('survey', '4.2-1', { + 'checksums': ['cc3c61e132fb20bed98fa59a8254335a588780a5f4eeb51fab7489390aadf150'], + }), + ('rlemon', '0.2.1', { + 'checksums': ['4a18fa034f197c68daf48daf25c0e41f1b8acbe71d030c6bc1f55e3062a10375'], + }), + ('optmatch', '0.10.6', { + 'checksums': ['2b7661567fdfbdb39dae3779b4b7dea2b9eb759d3117311b3a7936b10cce1d35'], + }), + ('SPAtest', '3.1.2', { + 'checksums': ['b3d74ed2b0a6475a9966dd50eb5d363d0b2985636271dfbf82f0472b8d22b9f4'], + }), + ('RSpectra', '0.16-1', { + 'checksums': ['cba5d3403d6a7d0e27abf6279fbfea6e0d0fe36b28c688bbadb8eafb3841329a'], + }), + ('SKAT', '2.2.5', { + 'checksums': ['1441fa46b6a78a060007442fb8cb8c87753bdc2b1ea2dc24ff951ac3fef651f4'], + }), + ('GillespieSSA', '0.6.2', { + 'checksums': ['f4233b4a44c7d4b9e3459b1efa9a8087a602ef93806b4d70eadbb537b67567c2'], + }), + ('startupmsg', '0.9.6', { + 'checksums': ['1d60ff13bb260630f797bde66a377a5d4cd65d78ae81a3936dc4374572ec786e'], + }), + ('distr', '2.9.2', { + 'checksums': ['b52a817ed66b75defb009e2f946472ab87f693f63c43638e86b5482cd39a2e30'], + }), + ('distrEx', '2.9.0', { + 'checksums': ['087d1847ad400141b5e0fd0858ef3e5c698b3018d7e2d33087be601a5740fb35'], + }), + ('minerva', '1.5.10', { + 'checksums': ['2f26353d8fcc989ac698c4e45bb683801b1a7bb60b14903d05a4d73c629c590f'], + }), + ('RcppTOML', '0.2.2', { + 'checksums': ['371391f9ca82221e76a424082ea9ebc5ea2c50f14e8408469b09d7dc3e6f63aa'], + }), + ('here', '1.0.1', { + 'checksums': ['08ed908033420d3d665c87248b3a14d1b6e2b37844bf736be620578c20ca346b'], + }), + ('reticulate', '1.34.0', { + 'checksums': ['8d0d8922cd811153836e95354357615968b005a4d0d4c5734441953c526e4206'], + }), + ('umap', '0.2.10.0', { + 'checksums': ['8d4786929345e8980bb8be8bb4b6300a679bba03a5984eed59e5e00c626b6ea9'], + }), + ('KODAMA', '2.4', { + 'checksums': ['78f2ea3596f3697fc06a080947e82a54c5270ed90f86916b91902e5db6ec85e7'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-3', { + 'checksums': ['474d3530b16b76a1bf1a1114d24092678ea7215fa57c6fdcee6333f1e768b865'], + }), + ('dtw', '1.23-1', { + 'checksums': ['6ed6a3b52be673ce2617b8d48723c7c488c95aab88fe2912d7e00507838e826d'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.4', { + 'checksums': ['2bf71c2034804cec637e6748dc51d8cadad01d3ea4d14ace754327f082e8d851'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.3-0', { + 'checksums': ['6289058f652989ca8a5ad6fa324ce1762cc9e36c42559c00929b70f762066ab6'], + }), + ('npsurv', '0.5-0', { + 'checksums': ['bc87db76e7017e178c2832a684fcd49c42e20054644b21b586413d26c8821dc6'], + }), + ('fitdistrplus', '1.1-11', { + 'checksums': ['26274f2b710b2417a8bca314d400abf320d4ccf0387ad082743056699501b53d'], + }), + ('hdf5r', '1.3.8', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['b53281e2cf57447965849748e972de2f7fe8df0cee3538ef5813c33c7ed2302b'], + }), + ('DTRreg', '1.7', { + 'checksums': ['f0fad2244d960cec8fc33d9a1078df359ceb0aadff980ce6149aa9f01c62223b'], + }), + ('pulsar', '0.3.11', { + 'checksums': ['ee82ef25b2be4bbac713c34bca85d8ea1fa0e32eb8c800dad7256e145fc79393'], + }), + ('bayesm', '3.1-6', { + 'checksums': ['17d72b9cdc090845f98e7a04640380d0baef8bc23d1487c8f64dc192fdb93cb5'], + }), + ('gsl', '2.1-8', { + 'checksums': ['f33609bf485abd190e65ff5d0fdab438b759294c47b921d983d89d6f053a2d95'], + }), + ('energy', '1.7-11', { + 'checksums': ['c29f8fb000c979d2504f6f6d3a99c773004f77d58793e7e2a5766155272b6511'], + }), + ('compositions', '2.0-6', { + 'checksums': ['45d374ebfdcc2c9f6cc738d196caf83a2297ed2aefe2cc99007fcbeb78a61c34'], + }), + ('clustree', '0.5.0', { + 'checksums': ['a87f65dc0489af77807ed27de67e905699f21f50bcfba6a84353b9a846a84ac1'], + }), + ('tweedie', '2.3.5', { + 'checksums': ['983c745fee5a780d46e8dd04c2eb1c10cb2e222d3679654f0d6934d3db7b1c3e'], + }), + ('RcppGSL', '0.3.13', { + 'checksums': ['fe5e73bc119c6424e1a40b6fea17417a7bba93e81dbe9b7cf86dde9b8e8d93e7'], + }), + ('mvabund', '4.2.1', { + 'checksums': ['ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('alabama', '2023.1.0', { + 'checksums': ['925f67c72d9cdb677105377777bd09e9b56a61573bea7e3f69e0a49595c7bf1c'], + }), + ('gllvm', '1.4.3', { + 'checksums': ['63b77040e9cf2694882d1d80a3bc3030b3a348819ea38e6728417e4c5de07ecc'], + }), + ('grpreg', '3.4.0', { + 'checksums': ['fd57d20baf63d2cc5821998bca5c3fdcbe46c933c9553caa492911b12654d6ad'], + }), + ('trust', '0.1-8', { + 'checksums': ['952e348b62aec35988b103fd152329662cb6a451538f184549252fbf49d7dcac'], + }), + ('lpSolveAPI', '5.5.2.0-17.10', { + 'checksums': ['4cb7ef25d32c1dace99455d5858bac0c57acca29e3a8e206b36e231e13da10b9'], + }), + ('ergm', '4.5.0', { + 'checksums': ['3372c7bd35b640518d65a62615cb7029652a65fe2851748847f1c16b657b6351'], + }), + ('networkLite', '1.0.5', { + 'checksums': ['aaab55d4f8f0b330fe7c1ecbab3c44746c52c2fda99c53c6b46042bb8775718b'], + }), + ('networkDynamic', '0.11.3', { + 'checksums': ['2c664fd0d85c0cdc099480d67a18e6afbb0cc1036963b6664a8a756874648e5b'], + }), + ('ergm.multi', '0.2.0', { + 'checksums': ['13e27ba59b087f09cfb3dc6fccaa360e4ae0159f13e7a20d2c3306b5fe74fb5a'], + }), + ('tergm', '4.2.0', { + 'checksums': ['dcf5a26cc2c4d165766706af08f8ea4f36e328158f5b682490c2a351f7fbda69'], + }), + ('ergm.count', '4.1.1', { + 'checksums': ['446893614ad8b41aa39c37c2bf45a167f575536bb6778b8ad1fbcddb7b934932'], + }), + ('tsna', '0.3.5', { + 'checksums': ['4ee2f773d573f0f4bd93131156fdccf01d7f1a3f725eff3e885021098c6bff65'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-7', { + 'checksums': ['b7c4d3d5f9364c67a4a3cd49296a61c315ad9bd49324a22deccbacb314aa8260'], + }), + ('MCMCpack', '1.6-3', { + 'checksums': ['cb14ba20690b31fd813b05565484c866425f072a5ad99a5cbf1da63588958db3'], + }), + ('shinythemes', '1.2.0', { + 'checksums': ['37d68569ce838c7da9f0ea7e2b162ecf38fba2ae448a4888b6dd29c4bb5b2963'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.2', { + 'checksums': ['7210c97fc864e78ea8502067359d642bbd95bf2df30d33da193fc5c004e45baf'], + }), + ('asnipe', '1.1.17', { + 'checksums': ['e7b4010fa1adf27534420db2971dae3c63190920a4323c86fd586842e22d9b07'], + }), + ('liquidSVM', '1.2.4', { + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', + 'checksums': [ + {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, + {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch': + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'}, + ], + }), + ('oddsratio', '2.0.1', { + 'checksums': ['2097e7a8bf623379d55652de5dce4946d05163e85d30df50dc19055962bf60b5'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.42.0.2', { + 'checksums': ['9aae531f4eb3ed90b5d3e31a9030ba0ca7c6bdc6e3c84aec2a5c4e3eb562929b'], + }), + ('mlegp', '3.1.9', { + 'checksums': ['63296d17a162fdce0958b10f45cb7d5dab4b3ee29340528d33cedcae08a040b3'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.5', { + 'checksums': ['417055a03b02ad8359cf1bdc8f89d49531a3a8ee2c98edf90c8a01432f44838d'], + }), + ('bartMachineJARs', '1.2.1', { + 'checksums': ['9f7a20acf4aec249e16f83d81f5ec796aa718deb1b8bc24393fc0421eb8ce1c0'], + }), + ('bartMachine', '1.3.4.1', { + 'checksums': ['3b0a5250f5425a8efe460adcb58ea1342f1d845ae3a8db29dbf4806653884b89'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.11', { + 'checksums': ['c63a6453783865b7c69c580a09a769e99390dd8b2e0f63e48fbfc86da3bee4b7'], + }), + ('GUTS', '1.2.5', { + 'checksums': ['9d983a566daa07d3e0036fe7011efe94f29e31a611493ba16bd316b61730a7b7'], + }), + ('GenSA', '1.1.10.1', { + 'checksums': ['9093384941b5626aae2acf4835b591875193a6000d1f0b212abeaf682652949b'], + }), + ('parsedate', '1.3.1', { + 'checksums': ['1fc31ab9813b61680abf4f4c2705b8f484d56d1d3ef256df84b342b628b6d1b1'], + }), + ('circular', '0.5-0', { + 'checksums': ['4bf4da5de29e555d1a7ae7ea64f8a5dda037e5c423f1078944f0bbb6eb9a7b92'], + }), + ('cobs', '1.3-5', { + 'checksums': ['7fae7da8f940975d544120c836e2d3b874f9b0cbab9631851ce986709f51c611'], + }), + ('resample', '0.6', { + 'checksums': ['1b958009b18c92a47971847c782af76952ea4e85d5f1e3e1e70fa35c67b95265'], + }), + ('MIIVsem', '0.5.8', { + 'checksums': ['a908f51e1598290d25864c358d57201bd50c1c40775d4d0405cbc8077bee61e1'], + }), + ('medflex', '0.6-10', { + 'checksums': ['bd89a8fe939f3becd71a9dab30fe27fa43c96572d8309d2c1a70633117d4cb33'], + }), + ('Rserve', '1.8-11', { + 'checksums': ['9dfb1d68493f8cee5d2e12a1bfa604404834e11809f4c908d65b9100a9af1b85'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '8.0.0', { + 'checksums': ['38e75b1ebc8b2d1c54b3373a42529b819c7b4773fd4932f57bc9701d1e3e3dc7'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '2.0.0', { + 'checksums': ['8693cab745d426260227d522d9113078d720b1ac0eb0931a47fa8f74aab82fa7'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.19', { + 'checksums': ['0ee9309bb7dab0b97761ddd18381aa12bd7d54678ccd7bec00784e831f4c99d5'], + }), + ('BMA', '3.18.17', { + 'checksums': ['6d8c514fa179f8a48c2105b551a8a08e28ea4375d06150a4b8ab4ccda577daf5'], + }), + ('BCEE', '1.3.2', { + 'checksums': ['f0e0a6a4eb11213073aa2f0cd6c76d87e8b3965124d8ca509538eb3c128533a0'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-65', { + 'checksums': ['bdf8fdd35fb2b1c65d09766da79d930fa664a00aa497f03b636400eecb623ef8'], + }), + ('bdsmatrix', '1.3-6', { + 'checksums': ['f9c871d54378408902931792b3dbf8bda863d6aa67af6a0472a6ec1c420760bc'], + }), + ('fftwtools', '0.9-11', { + 'checksums': ['f1f0c9a9086c7b2f72c5fb0334717cc917213a004eaef8448eab4940c9852c7f'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.22.1', { + 'checksums': ['0a52a55dbe76a7e7ca50c5555fea4381eeda0c215c66e420d8dc9bfd2992411c'], 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('rvertnet', '0.8.2', { + 'checksums': ['2de9a3ec33a213c7592b49cca1d510a25aef0625369376d9b1b4e5d0da519226'], + }), + ('ridigbio', '0.3.7', { + 'checksums': ['af2a90a8a90fbede4cf2178b758f00cc13066f4d0bd87dac8d156809050a6d59'], + }), + ('spocc', '1.2.2', { + 'checksums': ['af4b398dc02522629b9fee697ccf640b7654330419a8f94cb5d1c7d17c8784fc'], + }), + ('spThin', '0.2.0', { + 'checksums': ['2e997afb79a2a990eded34c71afaac83986669cfa9ac51b15ae3f2b558902048'], + }), + ('RPostgreSQL', '0.7-5', { + 'checksums': ['6b5401ee55bd948ae7bc84520d789ceb422533a7d5e5bd6e10e3b54447f29fa1'], + }), + ('fasterize', '1.0.5', { + 'checksums': ['d44f101aec29aee285c4c7b578e26d11b6add423336ace90a7c22e07cfc1c3b4'], + }), + ('BIEN', '1.2.6', { + 'checksums': ['fa7a25d89f26c10686fb4ab4d0aa704beb50dc44b173ff56abe4ab3e5991f99f'], + }), + ('rangeModelMetadata', '0.1.5', { + 'checksums': ['289620500522d489aafbb03c85f68182ef0a6701fed5f9d09b55fae337e2647b'], + }), + ('ENMeval', '2.0.4', { + 'checksums': ['6d9f3c460fa7ab3131cede904fcb9280cf69f4fdd43f67115a3abcb8ed5b64d1'], + }), + ('plotmo', '3.6.2', { + 'checksums': ['cde33a8ec558b12d8e11d7d0531e73f6678a25ee589b79897d2fc425a3fd353c'], + }), + ('earth', '5.3.2', { + 'checksums': ['c844d75edf9a2706a911bb05ed4287aad9acf6f3fed357e037763a300eac0bea'], + }), + ('mda', '0.5-4', { + 'checksums': ['f25f7f28807d0fa478b1b55eb9d026ebc30577d9d5ff288f9abfe1f3fdb8a759'], + }), + ('xgboost', '1.7.5.1', { + 'checksums': ['4ec0833f206f84e5983e9f373ea64903bec488f751fba6f75a6f4702b1c965bc'], + }), + ('biomod2', '4.2-4', { + 'checksums': ['c28163075df90a90fc1939e9ff24d40bace7de611ff7ddfe027e0ff980e7c64f'], + }), + ('poLCA', '1.6.0.1', { + 'checksums': ['ed8c60a42bff0402c9ba2f9ce1422dd171e711c1a64498c4d96010ddb29f6b16'], + }), + ('PermAlgo', '1.2', { + 'checksums': ['aa2c774d6c6dcfeec882c1936e8723ef49bd36030fb10c17ca60bb9d4a519443'], + }), + ('coxed', '0.3.3', { + 'checksums': ['d0d6cb8fea9516b3c63b34d0d81f3804c18a07f97a83e51555575c8ed4c75626'], + }), + ('testit', '0.13', { + 'checksums': ['90d47168ab6bdbd1274b600b457626ac07697ce09792c92b2043be5f5b678d80'], + }), + ('NISTunits', '1.0.1', { + 'checksums': ['eaccd68db5c73d6a089ce5b323cdd51bc6a6a58ce467987158ba8c9be6a0a94e'], + }), + ('celestial', '1.4.6', { + 'checksums': ['9f647f41465ac65b254717698f1978871c378ad8e6ccaa693abf579437069abe'], + }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-4', { + 'checksums': ['d4b3d65a33cae454d3ab13343bceabfb3f6b8004ac64ae7bd86dee92a1cd2055'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.5-3', { + 'checksums': ['154ed68785de8c4a02db1916dfe50862cf544865901936e864207ada777e5108'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.21', { + 'checksums': ['293544afb194934b1d58cf88c6f8c372f537745514b6e428cf83ae62e87d2bba'], + }), + ('dbarts', '0.9-23', { + 'checksums': ['e1ac65fd89c321895d4f0e77d9cd8dcda5f1103485008afd4e19e6c9137557a3'], + }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.2.0', { + 'checksums': ['26fcfbc79810f23a28389a5ce5519e6ddc2470c5e924ba8cf4dd19a1b0fd9f83'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-10', { + 'checksums': ['f6fcd9012f2fa777127c86ba520d8dc834f4ea746a6e29623edd072479191c75'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '2.1.0', { + 'checksums': ['3f3e557ac7cadeda4759c51f866ce9a942cb21a2b3dd24e55a082fc7d300d7fe'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.8.1', { + 'checksums': ['12952b9eaa64b7bdbaaa5c6b7acb3aa1028ddfa4e5de7ddfea54f900c452d6a6'], + }), + ('outliers', '0.15', { + 'checksums': ['cc31d7f2faefd2c3a27f8ce78c7e67d3b321dcd6690292fad2468125e5e635fb'], + }), + # elementR is too old and doesn't work anymore with other extensions, such as gdata and readODS + # ('elementR', '1.3.7', { + # 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + # }), + ('gWidgets2', '1.0-9', { + 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], + }), + ('gWidgets2tcltk', '1.0-8', { + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], + }), + ('mgsub', '1.7.3', { + 'checksums': ['c9ae2560fe2690bedc5248af3fc89e7ef2bc6c147d46ced28f9824584c3791d5'], + }), + ('ie2misc', '0.9.1', { + 'checksums': ['f1db0c66c8fa05e99c4059c1799abc3eb7effd7113baf03f38d26853ac05c425'], + }), + ('assertive.base', '0.0-9', { + 'checksums': ['4bf0910b0eaa507e0e11c3c43c316b524500c548d307eb045d6f89047e6ba01e'], + }), + ('assertive.properties', '0.0-5', { + 'checksums': ['b68954f53082561f0242682611bf3373e0bf30d8ac2256d82474edc5f992f4dd'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-4', { + 'checksums': ['2f820474ed20e06f65b284962c87cd1e85220a11cc7fcde09716f0eee5821387'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), + ('Exact', '3.2', { + 'checksums': ['53b4e20cbb57615970c572fc4e7a780a510bde8b5deadec3880095f6e17a6328'], + }), + ('lmom', '3.0', { + 'checksums': ['4b0ae8638a63b45ddedfd65c15e3206d34e947a2b5d31e9aa8c55446d69a0291'], + }), + ('gld', '2.6.6', { + 'checksums': ['ea23e9781207b5d47ed04e4d5758d9652cab5d1eedcf9fbc9c2ee4d3babffdc4'], + }), + ('DescTools', '0.99.50', { + 'checksums': ['1b9cf09de7c7625c30d2daca92b4f798476f10907d531267e773d379f6828eab'], + }), + ('orthopolynom', '1.0-6.1', { + 'checksums': ['ec4a6ed266532f2f6d37a4ca6bd1b74c1df28a8c2caeab60e5d6af15bdbfe2c5'], + }), + ('gaussquad', '1.0-3', { + 'checksums': ['a3337ce52bc53435cb4565a38bf48b72b384be397d2e86bb66f62973004dc810'], + }), + ('nlsem', '0.8-1', { + 'checksums': ['0674ec2a1ae7e50b08ee1b156674c2f2100258b14d6a9068f7dd6ad1ee128377'], + }), + ('tableone', '0.13.2', { + 'checksums': ['b1cf15579abd4240e24435d2d9aad255c839d2a0293e28cb2eef0c808c4727af'], + }), + ('jstable', '1.1.2', { + 'checksums': ['e9f6a4eab1be75fab63d9de5cc496b1812e2ec2d3e1d6a006ae6a9a6d2fd29ab'], + }), + ('RCAL', '2.0', { + 'checksums': ['10f5f938a8322d8737159e1e49ce9d12419a5130699b8a19c6ca53d6508da8cc'], + }), + ('stargazer', '5.2.3', { + 'checksums': ['208e9b48a11cf56ce142731c204f3d2bcb5b68719f84309a36362cd925414265'], + }), + ('sensemakr', '0.1.4', { + 'checksums': ['6a1354f05392fa9343b90f69a54022c995651fb3c3d05cb08fa088ef52258caf'], + }), + ('CompQuadForm', '1.4.3', { + 'checksums': ['042fc56c800dd8f5f47a017e2efa832caf74f0602824abf7099898d9708660c4'], + }), + ('nonnest2', '0.5-6', { + 'checksums': ['b59144f50fb264fd0d40ee770bf25047bf0f37fa154620d8fe0a91c0065061e8'], + }), + ('blavaan', '0.5-2', { + 'checksums': ['f3523ab082a0db524719c32ddc3397a7798ba146766356ac134c3973acc40758'], + }), + ('mathjaxr', '1.6-0', { + 'checksums': ['ecc47607111b788d84789459af7f4f9102719f98640b7a23bd5a4eb1a6d3c179'], + }), + ('metadat', '1.2-0', { + 'checksums': ['f0cce5e30c3d256eaf5a41e4f52ffc7108e195016a4b99409e0ab4c2ef58f5b8'], + }), + ('metafor', '4.4-0', { + 'checksums': ['62aca0c70b44205e885cf55f6cfb56c37efff74bdef79dbabd727d629d3087d4'], + }), + ('RNifti', '1.5.0', { + 'checksums': ['32e4dfd35643932e0f2021b22cfc26cedff51dff13b940d9a3abe6282bf5e905'], + }), + ('oro.nifti', '0.11.4', { + 'checksums': ['efe4f5d2c2e37ff6c3e9250f54ef775e4d452c1334f781f22f219ed53148b606'], + }), + ('fmri', '1.9.12', { + 'checksums': ['d8b55f8867bb0487d1a8241b340099c41d990ae5aa49768b2dc0f9db58af65b3'], + }), + ('linkcomm', '1.0-14', { + 'checksums': ['36f1557c65d862fc87635eedfad77f18a5deb66da00895e50e2d5eac0f23b597'], + }), + ('rnetcarto', '0.2.6', { + 'checksums': ['4f28ae62748654cb6f90e1ffa17b05bb8b89eb6a20262d9c5d39cb862f71dc91'], + }), + ('DEoptim', '2.2-8', { + 'checksums': ['631eabdcf26ec25a759651f699db1971beca3ae193c7fbd1c63a78248fdbf54c'], + }), + ('optextras', '2019-12.4', { + 'checksums': ['59006383860826be502ea8757e39ed94338f04d246c4fc398a088e004d8b13eb'], + }), + ('setRNG', '2022.4-1', { + 'checksums': ['61c06e6bd6b43c295472c6990266fe87ca41e57db04d3460e756a35ef24e0824'], + }), + ('Rvmmin', '2018-4.17.1', { + 'checksums': ['55000ac4ff57d42f172c46c7d6b0a603da3b65866d6440d6b32bac4d2b81814e'], + }), + ('Rcgmin', '2022-4.30', { + 'checksums': ['2684b8e7fb970da2afbc00e482031cf4447416249d04c4c1740400ad112fb911'], + }), + ('optimr', '2019-12.16', { + 'checksums': ['73b1ed560ffd74599517e8baa4c5b293aa062e9c8d50219a3a24b63e72fa7c00'], + }), + ('DMCfun', '2.0.2', { + 'checksums': ['430cbc18f17db11a7941e6a8274a0eefbb8a6b0bdac8800970530d60d5881fde'], + }), + ('miceadds', '3.16-18', { + 'checksums': ['dbc56cd2b20aaaaa69ea28c15cfd61d48d072fe9c0dc8e392c81a569e280cf75'], + }), + ('visdat', '0.6.0', { + 'checksums': ['104acdbb9d41167b861ab24de0e1e1e14f61c1b476bac112fcbc6e47c157e598'], + }), + ('UpSetR', '1.4.0', { + 'checksums': ['351e5fee64204cf77fd378cf2a2c0456cc19d4d98a2fd5f3dac74b69a505f100'], + }), + ('norm', '1.0-11.1', { + 'checksums': ['c2ffe6c30fc203337bde49ef630a740141604d8e648c558e58c20116c47963bc'], + }), + ('naniar', '1.0.0', { + 'checksums': ['c2eda97de603e2daf4c1c5d12f9c9a65635910833a3c669e08e344e90d9394f4'], + }), + ('stringdist', '0.9.10', { + 'checksums': ['6fd42e0b7ff25843ca7f45acf9a183facfe14a6cde2dc7a97ef7126ab0f06ce8'], + }), + ('image.binarization', '0.1.3', { + 'checksums': ['ecc844bdd9bf15b88ce1e1afc8321c177bdc8ec32618c22102b1e8b02b36e00e'], + }), + ('lassosum', '0.4.5', { + 'source_urls': ['https://github.com/tshmak/%(name)s/releases/download/v%(version)s/'], + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'checksums': ['18c0d0b5022bcf81a9bf1b3b6647da3e080f221828b473ea2a45a9bf98474fbc'], + }), + ('lslx', '0.6.11', { + 'checksums': ['373cfb1e79174b568dac254fab02d99bf79b830218bf18f0cc592af6fef853d6'], + }), + ('truncnorm', '1.0-9', { + 'checksums': ['5156acc4d63243bf95326d6285b0ba3cdf710697d67c233a12ae56f3d87ec708'], + }), + ('Rsolnp', '1.16', { + 'checksums': ['3142776062beb8e2b45cdbc4fe6e5446b6d33505253d79f2890fe4178d9cf670'], + }), + ('regsem', '1.9.5', { + 'checksums': ['7392bd644efe82f96da0df470a962de398f1d0162273cba1ff31c2ecd7f17a53'], + }), + ('semPLS', '1.0-10', { + 'checksums': ['cb587ccfdaf970f426dc7146035c7e010b1c51c17bf4fc089fd796eda58db460'], + }), + ('GxEScanR', '2.0.2', { + 'checksums': ['6d42fd15d83dd1491405b282d26fa472f9f9902a9dc68836d6a48b459ada6a4c'], + }), + ('admisc', '0.33', { + 'checksums': ['3911bea32326bfc2e19d4f47d05e8ad7260da36fa2ae0bfde03540195081dbaa'], + }), + ('polycor', '0.8-1', { + 'checksums': ['f05f53e0b5c992de0e5b4c6b2e998148cf83310358821e1bba180d81face0509'], + }), + ('multipol', '1.0-9', { + 'checksums': ['4ec305565c214872705f7d5ea4928c8761750663d664a77f1676d81a1ca0c632'], + }), + ('symmoments', '1.2.1', { + 'checksums': ['9a6be1f8fe44f6ab5a1790e870fd8b18de1686a48a14a9fca2d035bfb5458672'], + }), + ('rngWELL', '0.10-9', { + 'checksums': ['9969cc10be6d18155d2b2de93381c52e7f720c2b1b3f2554fa8bfa84ceb7cacb'], + }), + ('randtoolbox', '2.0.4', { + 'checksums': ['94da14953e4ffc7981d7a9398622082c4eda3bd9d912d1437b527d949da39e4b'], + }), + ('TruncatedNormal', '2.2.2', { + 'checksums': 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['fa86cb5140f5dfce29f9517b94d6d08c316ddcffa4aa3085945b84d34910134d'], + }), + ('aricode', '1.0.3', { + 'checksums': ['10a739353feb4f552496d3a51d436088c92edbd241f80f7c33ee5f278de1d90a'], + }), + ('DepthProc', '2.1.5', { + 'checksums': ['e6b0afd54bb20e25a6bf5402c771848db20e9c844f0fc990ecc3d1078b9eee44'], + }), + ('dbscan', '1.1-11', { + 'checksums': ['f0498e67e612629340a2758fbe747c4d9d4ca648f002230a03499cb73735e62f'], + }), + ('ggh4x', '0.2.6', { + 'checksums': ['eb7929b4c3167dce644b13d655144b2893e320072e7a998f07c37c4f7d9b2b3b'], + }), + ('ComplexUpset', '1.3.3', { + 'checksums': ['5b2f99b4a38648641c7d31fc57f201a93e5bc1b85442a0b9726f72c166d964ea'], + }), + ('proxyC', '0.3.4', { + 'checksums': ['f39d1d3d34b4e26694e3916002ea370b2f4e745c0992e718bb024ed03a2b78ea'], + }), + ('changepoint', '2.2.4', { + 'checksums': ['ac636fde7610137385dde1e3d8a22a2ff856a8d5c917c7ad1a5cc49f98b8649b'], + }), + ('geeM', '0.10.1', { + 'checksums': ['fe76a32981b55835095041e777d1cf2e9ce43edb8d9488db56279f7cb6f43fe5'], + }), + ('ggstance', '0.3.6', { + 'checksums': ['cd9ad4fb83c583009ee45371c7d02d32b33d06238d3f0162b3ba9851e27a6372'], + }), + ('mosaicCore', '0.9.4.0', { + 'checksums': ['e25605d787d274eedd3de8584283c20204bcb7b94f4a409461304ce7cd867d6c'], + }), + ('ggformula', '0.10.4', { + 'checksums': ['b26d478e7e38bd9ec51777c14a7e0fef41e2c2742ca202532f0f44dc00d6a91d'], + }), + ('kinship2', '1.9.6', { + 'checksums': ['0150bd5974c2a19885f6ff2e99f3c1f6361054a0910dcfc9dd26a8e0cd73bbf6'], + }), + ('MESS', '0.5.12', { + 'checksums': ['41e07993e67a8aab52d9d4d07a06d654186ac8a8db9b740763ed5d481f01dcf7'], + }), + ('smoof', '1.6.0.3', { + 'checksums': ['af8664b152876c545f6545528de6e05a289d0714103fac7afc52960a9a855fb1'], + }), + ('mlrMBO', '1.1.5.1', { + 'checksums': ['0cf26e5e9b180d15b932541cf081a552703a60edf762aafca9933c24ea91dc99'], + }), + ('emoa', '0.5-0.2', { + 'checksums': ['d9e8bd286c4578be76a3dc7a1110bbb751eb8d0e451143273f0ced09878a243b'], + }), + ('webutils', '1.1', { + 'checksums': ['33e2b408d2b9ca12e158e0007d4a55a3ace6838341ad944344de2ceb806e4699'], + }), + ('swagger', '3.33.1', { + 'checksums': ['528369b04c6142112e05ee8b950ca1c01b3e390a4515eacb0fa17db98bafafd1'], + }), + ('varhandle', '2.0.6', { + 'checksums': ['4e7afd3ef77343c61508b0465b588751dc089c264faabf7bed60e9f4d9e1c577'], + }), + ('dlm', '1.1-6', { + 'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'], + }), + ('PMA', '1.2-2', { + 'checksums': ['34f2a4236b5c9793cfea2c6367c61146687c277749dbbff0524425a8f335bdb9'], + }), + ('unikn', '0.9.0', { + 'checksums': ['5480f568bd182a96ac6b613347a659b3a506ff540713021692712f0b91c31c10'], + }), + ('ppcor', '1.1', { + 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], + }), + ('berryFunctions', '1.22.0', { + 'checksums': ['8d8578d746e8e4f7a1deb0b1d49ff8603c5e51504d5fe549bcba54f20fe9d498'], + }), + ('cld2', '1.2.4', { + 'checksums': ['79e04de836812a980406a540c0f022926ba71c2bf5294ad5eaa437a9c33e615b'], + }), + ('crfsuite', '0.4.2', { + 'checksums': ['d5f6379a2bb7fd585fde5945189a6a69e1ef33664fe86828d646f5f4505f8d96'], + }), + ('doc2vec', '0.2.0', { + 'checksums': ['db3853685072554402434ea699d703e01ac7818044cf47a2ee7d0e1040858908'], + }), + ('fastDummies', '1.7.3', { + 'checksums': ['cf6a182f778711b69460b00575babfa573f1578166d83ae2ed932db5fa15a06a'], + }), + ('quanteda', '3.3.1', { + 'checksums': ['628542307d7ac45d4996fbc993a43ed5efcca73d97735ca74a10ccea401d4166'], + }), + ('ISOweek', '0.6-2', { + 'checksums': ['b58a37b61ee772ea2704d510e9fce69dea4dd641b45124d566242825df4530b8'], + }), + ('sentometrics', '1.0.0', { + 'checksums': ['b5c238bb72f36331cb1ed63b581a9a2a73cefc96f80bf770b0e064a89fe31b1b'], + }), + ('tau', '0.0-24', { + 'checksums': ['f08d9fc92ed11ec01f7da12ccf98862e36ef8bb69d5e42584a08b46cea6917e1'], + }), + ('textcat', '1.0-8', { + 'checksums': ['cb650147576bae9c78381524831c9fcc85c76177274672098aac1860aa39749e'], + }), + ('textplot', '0.2.2', { + 'checksums': ['6e99a204b4be2ccd317978eda900b923e0e0a0f34217405777a0eb5fcc80e2a9'], + }), + ('udpipe', '0.8.11', { + 'checksums': ['522900de24d1f0f4f15e6b26df5521ac6efaf63c5fcfc35171a78275b3633233'], + }), + ('word2vec', '0.4.0', { + 'checksums': ['38c6934ad7c601d6de7fa44a1ecf911ef34609b5c32b67da12a0814124036a91'], + }), + ('epitools', '0.5-10.1', { + 'checksums': ['b418854de1fcedd126f3bf19dc27e8a71ee6efae5371098ab64a53a2d51d164b'], + }), + ('RBesT', '1.7-2', { + 'checksums': ['bde8008b5fc8f0023bdd84b3a14a7425aecf1edcdf79480dac861895de4a9a9b'], + }), + ('svglite', '2.1.2', { + 'checksums': ['c2c163e17de8174408062b969a1fc298aa1dba957dc0acc1c898384bb76c0030'], + }), + ('rARPACK', '0.11-0', { + 'checksums': ['c33401e2e31d272d485ce2ed22e7fe43ac641fd7c0a45a9b848d3ad60df1028a'], + }), + ('FKSUM', '1.0.1', { + 'checksums': ['6de23f5b7692f627b0b8e9575a612e77e166c16c28acab31d5ea0a27d7afe829'], + }), + ('warp', '0.2.1', { + 'checksums': ['020ad590de099661aa62b4d5e51499a2ac91c41c61db2dbc71c3f4a3df2c46be'], + }), + ('slider', '0.3.1', { + 'checksums': ['200a26795fadb2058e3976af7a697dde7f120645279cfe2580b8c0d6c0a429b0'], + }), + ('rsample', '1.2.0', { + 'checksums': ['e0c9b7060e0037f4213a5faad73f5910cf97bf93ecba93d35301cbc88cf45eed'], + }), + ('haldensify', '0.2.3', { + 'checksums': ['fc0ee1d5bce54520bad6a1ce1cce5074eead6c8573dc4ce502c48a244d7f341c'], + }), + ('Polychrome', '1.5.1', { + 'checksums': ['6fe7da62459d7b94b1a8516a4626971cf35b76331f46e36798b05d29aa00d143'], + }), + ('shinycssloaders', '1.0.0', { + 'checksums': ['744641836a4cede2bb47caff1b600bff2c3e450dfccd2af4fab0413a8ea87d64'], + }), + ('princurve', '2.1.6', { + 'checksums': ['0216332390eb27013b6ba62232782156dfc99ca640087fcaff53d2be9218f373'], + }), + ('ECOSolveR', '0.5.5', { + 'checksums': ['2594ed1602b2fe159cc9aff3475e9cba7c1927b496c3daeabc1c0d227943ecc7'], + }), + ('scs', '3.2.4', { + 'checksums': ['c3f39874bf4532fa8c2f2e2c41533ba4fe20b61cf6dfc6314407dc981621298f'], + }), + ('osqp', '0.6.3.2', { + 'checksums': ['18543b329a42be0f419dff4aa42f4401c2afb18f46276ce359853494dd803244'], + }), + ('CVXR', '1.0-11', { + 'checksums': ['e92a9638f35f4909e2a29c3b7106081e3dae7ff88b14bb6466b87fbdc80b972a'], + }), + ('tabletools', '0.1.0', { + 'source_urls': ['https://github.com/JMLuther/%(name)s/archive/'], + 'sources': [{'download_filename': 'cc961c5.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['667a4270456d28188734ce31411326130a94e085490ced84096c984789bb174a'], + }), + ('officer', '0.6.3', { + 'checksums': ['e51754029240d66fb1c8e6d524c63a275f6fafa19a22fef90d90c8ceb982777c'], + }), + ('gfonts', '0.2.0', { + 'checksums': ['72e2eead5280b45aadbbd9385971d65e9866fd659270b1c3c1eb98330f024aa6'], + }), + ('fontBitstreamVera', '0.1.1', { + 'checksums': ['3298b3dd95605bdda0c5fce5594c9bedde6aa63d89b216d5c83c6c092b6d375a'], + }), + ('fontLiberation', '0.1.0', { + 'checksums': ['acdea423e005873aa509e280074a3cef4796e4f7e9d77b3945d77b451ea039f0'], + }), + ('fontquiver', '0.2.1', { + 'checksums': ['95871814c2d55c03ee15a54e29aadfb840c791e1430f94127d9e1dc8608a6363'], + }), + ('gdtools', '0.3.4', { + 'checksums': ['aad743033fba0b48aa05867df4bc9643802fa82542b559579105e8a0659aaa02'], + }), + ('flextable', '0.9.4', { + 'checksums': ['55ad11660325cf470cedf532df774f99748583eb53c0162e2dede8e1c3539ab6'], + }), + ('ridge', '3.3', { + 'checksums': ['5c2daecf6f97aa099ef5fa54f8448518c4f2ed6e44dd29fc60621a70721c60f5'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch b/easybuild/easyconfigs/r/R-bundle-CRAN/liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch new file mode 100644 index 00000000000..56af45097b7 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch @@ -0,0 +1,49 @@ +The code requires C++11 but nvcc is not passed any flag for it, do that to avoid 'error: identifier "__ieee128" is undefined' on PPC +Use uppercase __PPC64__ to detect PPC 64bit (defined by GCC) +Use lowercase __aarch64__ to detect aarch64 (defined by GCC) +diff -aur liquidSVM-orig/MD5 liquidSVM/MD5 +--- liquidSVM-orig/MD5 2020-02-20 15:51:17.387058566 +0100 ++++ liquidSVM/MD5 2020-02-20 16:48:06.042078399 +0100 +@@ -66,7 +66,7 @@ + e0ea06f050a2ae8ed2f2e401d968f0ce *man/test.liquidSVM.Rd + 8874fc45419e3174bf06013d887f6582 *man/trainSVMs.Rd + 4cf2abf7c6d415a4a8cd7f5dee2df959 *man/write.liquidData.Rd +-854c1eecccd169acdb80b03ad6d768dc *src/Makevars.in ++8c4346267f7b7f649ff27fb5288d4e23 *src/Makevars.in + e6d47b428caa2cc55798b431cb5e504f *src/kernel_calculator.cpp + 13af8529f5c2bccd4ea03288e9adf908 *src/kernel_calculator.h + dc2c86cbe61e7b7c5dd433f9fa41fac6 *src/liquidSVM.cpp +@@ -155,7 +155,7 @@ + 8b39ec05680bf3416bc1de3ad92f043f *src/sources/shared/system_support/cuda_simple_vector_operations.h + 806ca83732bff4b1b89adfc3494e90da *src/sources/shared/system_support/full_64bit_support.h + dfb08cdb449d490d86dd33bee186aac5 *src/sources/shared/system_support/memory_allocation.cpp +-aec0000be577e69e88c040b641d6818a *src/sources/shared/system_support/memory_allocation.h ++f0231e65bd627116f1b5ebcc45ab1e66 *src/sources/shared/system_support/memory_allocation.h + 683d4ee517b1c760dc410c69c5508ce2 *src/sources/shared/system_support/memory_allocation.ins.cpp + cbd209324ad752e19be10d8975d65e2f *src/sources/shared/system_support/os_specifics.h + 54e8583d2e8e269ff2b6d7a79d57cbd5 *src/sources/shared/system_support/parallel_control.cpp +diff -aur liquidSVM-orig/src/Makevars.in liquidSVM/src/Makevars.in +--- liquidSVM-orig/src/Makevars.in 2020-02-20 15:51:17.377058962 +0100 ++++ liquidSVM/src/Makevars.in 2020-02-20 16:47:44.042949538 +0100 +@@ -39,7 +39,7 @@ + # The architecure flag can be set to higher values, if the hardware supports this. + # The value below should be safe for essentially all non stone-age systems. + +-NVCCFLAGS= -arch sm_30 -L$(CUDA_LIB_PATH) -DCOMPILE_WITH_CUDA__ -U__SSE2__ -U__AVX__ ++NVCCFLAGS= -arch sm_30 -L$(CUDA_LIB_PATH) -DCOMPILE_WITH_CUDA__ -U__SSE2__ -U__AVX__ -std=c++11 + + + #----------- CUDA related flags for GCC ---------------------------------------------------- +diff -aur liquidSVM-orig/src/sources/shared/system_support/memory_allocation.h liquidSVM/src/sources/shared/system_support/memory_allocation.h +--- liquidSVM-orig/src/sources/shared/system_support/memory_allocation.h 2020-02-20 15:51:17.377058962 +0100 ++++ liquidSVM/src/sources/shared/system_support/memory_allocation.h 2020-02-20 15:56:04.905673381 +0100 +@@ -42,7 +42,7 @@ + + // Check for GCC + #if __GNUC__ +- #if __x86_64__ || __ppc64__ ++ #if __x86_64__ || __ppc64__ || __PPC64__ || __aarch64__ + #define SYSTEM_WITH_64BIT + #else + #define SYSTEM_WITH_32BIT + From 00ab470fadad35a030b8af8193c60ddafc10a4b0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Nov 2023 18:01:38 +0100 Subject: [PATCH 9371/9987] adding easyconfigs: Nextflow-23.10.0.eb --- .../n/Nextflow/Nextflow-23.10.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-23.10.0.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-23.10.0.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-23.10.0.eb new file mode 100644 index 00000000000..2c6f2b030c8 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-23.10.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '23.10.0' + +homepage = 'https://www.nextflow.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/nextflow-io/nextflow/releases/download/v%(version)s/'] +sources = ['nextflow-%(version)s-all'] +checksums = ['c69f6055c97741b828b6ee67de38125a42f1774f1621afd34c0eb72ffea171a6'] + +dependencies = [('Java', '11')] + +install_cmds = [ + "mkdir -p %(installdir)s/bin", + "cp %(builddir)s/nextflow-%(version)s-all %(installdir)s/bin", + "cd %(installdir)s/bin && ln -s nextflow-%(version)s-all nextflow", + "cd %(installdir)s/bin && chmod +x %(installdir)s/bin/nextflow-%(version)s-all", +] + +sanity_check_paths = { + 'files': ['bin/nextflow-%(version)s-all', 'bin/nextflow'], + 'dirs': [] +} + +sanity_check_commands = [ + "nextflow -v", + "nextflow help", +] + +moduleclass = 'tools' From 59d21337f8a9b045e5c81c0a6fedab24edcf6031 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Nov 2023 18:13:03 +0100 Subject: [PATCH 9372/9987] adding easyconfigs: FDS-6.8.0-intel-2022b.eb --- .../f/FDS/FDS-6.8.0-intel-2022b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.8.0-intel-2022b.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.8.0-intel-2022b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.8.0-intel-2022b.eb new file mode 100644 index 00000000000..a8d35e94b26 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.8.0-intel-2022b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.8.0' + +homepage = 'https://pages.nist.gov/fds-smv' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['FDS-%(version)s.tar.gz'] +checksums = ['d8213d706bb36300ca5fdc9a7884fa4610e2820338de23212dd19de75d8e0704'] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +buildopts = 'impi_intel_linux_openmp &&' +buildopts += 'cd %(installdir)s/Build && ln -s fds_impi_intel_linux_openmp fds' + +modextrapaths = {'PATH': 'Build'} + +sanity_check_paths = { + 'files': ['Build/fds'], + 'dirs': [], +} + +sanity_check_commands = [ + "fds 2>&1 | grep 'MPI Enabled;'", + "fds 2>&1 | grep 'OpenMP Enabled;'", +] + +moduleclass = 'phys' From 6bd356dde83f0a29da29dcb75079d7ef2a722095 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Nov 2023 19:05:39 +0100 Subject: [PATCH 9373/9987] fix trivial code style issues in GFF3-toolkit easyconfig --- .../g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb index f1110ec02d4..6698ca78b96 100644 --- a/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GFF3-toolkit/GFF3-toolkit-2.1.0-foss-2022a.eb @@ -4,12 +4,12 @@ name = 'GFF3-toolkit' version = '2.1.0' homepage = 'https://gff3toolkit.readthedocs.io' -description = 'Python programs for processing GFF3 files' +description = "Python programs for processing GFF3 files" toolchain = {'name': 'foss', 'version': '2022a'} -sources = ['gff3tool-%(version)s.tar.gz'] source_urls = ['https://pypi.python.org/packages/source/g/gff3tool'] +sources = ['gff3tool-%(version)s.tar.gz'] patches = ['GFF3-toolkit-2.1.0-remove-hardcode.patch'] checksums = [ {'gff3tool-2.1.0.tar.gz': 'e842ef4afdb66926a2b63bf2619c7ef30bd9b76a5f1084a5c57bf8b39cc4f15d'}, @@ -23,8 +23,8 @@ dependencies = [ # GFF3-toolkit has hardcoded path to BLAST+ libraries, so we have to add a symlink to the required path for this to work local_blast_path = '%(installdir)s/lib/python%(pyshortver)s/site-packages/gff3tool/lib/ncbi-blast+' -preinstallopts = 'mkdir -p %s && ' % local_blast_path -preinstallopts += 'ln -s $EBROOTBLASTPLUS/bin %s && ' % local_blast_path +preinstallopts = "mkdir -p %s && " % local_blast_path +preinstallopts += "ln -s $EBROOTBLASTPLUS/bin %s && " % local_blast_path use_pip = True sanity_pip_check = True @@ -32,4 +32,4 @@ download_dep_fail = True options = {'modulename': 'gff3tool'} -moduleclass = "bio" +moduleclass = 'bio' From cb081c90f0e23375b41ba8d1ebfe78322f3161ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Nov 2023 20:01:31 +0100 Subject: [PATCH 9374/9987] trivial style fixes for Oases easyconfig --- .../easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb index 03ee0713e0f..ff28b8169fa 100644 --- a/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/Oases/Oases-20180312-GCC-12.3.0.eb @@ -1,4 +1,4 @@ -easyblock = "MakeCp" +easyblock = 'MakeCp' name = 'Oases' version = '20180312' @@ -27,16 +27,16 @@ checksums = [ ] # listed make targets exclude 'doc' on purpose -buildopts = ['VELVET_DIR=../velvet-%s cleanobj velvet oases' % local_velvet_commit] +buildopts = "VELVET_DIR=../velvet-%s cleanobj velvet oases" % local_velvet_commit parallel = 1 -files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.md"] +files_to_copy = [(['oases'], 'bin'), 'data', 'scripts', 'src', 'doc', 'LICENSE.txt', 'README.md'] sanity_check_paths = { - 'files': ["bin/oases", "LICENSE.txt", "README.md"], - 'dirs': ["data", "scripts", "src", "doc"] + 'files': ['bin/oases', 'LICENSE.txt', 'README.md'], + 'dirs': ['data', 'scripts', 'src', 'doc'] } -sanity_check_commands = ['oases --version'] +sanity_check_commands = ["oases --version"] moduleclass = 'bio' From a96b92e6c481a73c5fe99a5b279f1170436f2ec4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Nov 2023 20:02:24 +0100 Subject: [PATCH 9375/9987] remove easyconfig for typing-extensions 4.8.0 (since typing-extensions is already included with Python-bundle-PyPI) --- .../typing-extensions-4.8.0-GCCcore-12.3.0.eb | 22 ------------------- 1 file changed, 22 deletions(-) delete mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb deleted file mode 100644 index c1d6fc3757c..00000000000 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'typing-extensions' -version = '4.8.0' - -homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' -description = 'Typing Extensions - Backported and Experimental Type Hints for Python' - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -sources = ['typing_extensions-%(version)s.tar.gz'] -checksums = ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'] - -builddependencies = [('binutils', '2.40')] - -dependencies = [('Python', '3.11.3')] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -moduleclass = 'devel' From e5af9b028c27fb91b67a554b377984d579f39748 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Tue, 7 Nov 2023 21:33:02 +0100 Subject: [PATCH 9376/9987] change patoolib to patool Co-authored-by: Sam Moors --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 241eb2a55fd..5af271bcfcd 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -32,7 +32,7 @@ exts_list = [ ('fasteners', '0.18', { 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), - ('patoolib', '1.12', { + ('patool', '1.12', { 'source_tmpl': 'patool-%(version)s.tar.gz', 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), From 83d1a210fe7481832687b08a19de3014fa8cfe86 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 7 Nov 2023 20:34:07 +0000 Subject: [PATCH 9377/9987] ... also use name fixture --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 5af271bcfcd..bf2d7474a2d 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -33,7 +33,7 @@ exts_list = [ 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), ('patool', '1.12', { - 'source_tmpl': 'patool-%(version)s.tar.gz', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), ('annexremote', '1.6.0', { From e2f72ff32d3d208bb113dbe7873aa41d90e5f6b3 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 7 Nov 2023 20:46:22 +0000 Subject: [PATCH 9378/9987] leave out souce templates alltogether --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index bf2d7474a2d..3aad292130c 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -33,7 +33,6 @@ exts_list = [ 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), ('patool', '1.12', { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), ('annexremote', '1.6.0', { @@ -45,8 +44,7 @@ exts_list = [ ('boto', '2.49.0', { 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], }), - ('gitlab', '3.10.0', { - 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + ('python-gitlab', '3.10.0', { 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { From c6a2f3e4837cf4f31072aee266c2ba3244039e5c Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 7 Nov 2023 21:06:47 +0000 Subject: [PATCH 9379/9987] add module names for patool and python-gitlab --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index 3aad292130c..c5bc906b649 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -33,6 +33,7 @@ exts_list = [ 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), ('patool', '1.12', { + 'modulename' : 'patoolib', 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), ('annexremote', '1.6.0', { @@ -45,6 +46,7 @@ exts_list = [ 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], }), ('python-gitlab', '3.10.0', { + 'modulename' : 'gitlab', 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { From f931f50e14f11b61c7240050f2b4c800f42b7ec0 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 7 Nov 2023 21:22:53 +0000 Subject: [PATCH 9380/9987] lint --- .../easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb index c5bc906b649..8ec6b98f4fb 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.18.4-GCCcore-12.2.0.eb @@ -33,7 +33,7 @@ exts_list = [ 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], }), ('patool', '1.12', { - 'modulename' : 'patoolib', + 'modulename': 'patoolib', 'checksums': ['e3180cf8bfe13bedbcf6f5628452fca0c2c84a3b5ae8c2d3f55720ea04cb1097'], }), ('annexremote', '1.6.0', { @@ -46,7 +46,7 @@ exts_list = [ 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], }), ('python-gitlab', '3.10.0', { - 'modulename' : 'gitlab', + 'modulename': 'gitlab', 'checksums': ['14930a16fdd7f36f67b9373e7d4d4720e8e374800028380289db3306e9f74614'], }), ('iso8601', '1.0.2', { From 9094e493a6c83a3e80effd4d3a408af78d79f175 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 8 Nov 2023 08:37:58 +0100 Subject: [PATCH 9381/9987] update OpenMx in R-bundle-CRAN 2023.11 --- .../r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb index 8421d82323d..786c88814f8 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb @@ -3023,8 +3023,8 @@ exts_list = [ ('rpf', '1.0.14', { 'checksums': ['e4bb090a810ec4e70a23547f95e1e07ce0229e38fbbbbe22abfad98e9b33f796'], }), - ('OpenMx', '2.21.8', { - 'checksums': ['bfe13368360434ab5804496bb7f28053f75669b6b264e0e679261a3e705a74ef'], + ('OpenMx', '2.21.10', { + 'checksums': ['d513227ca7a60faf1b16e9be64864401914482aac9a326676fe1d052632c94ce'], }), ('matlab', '1.0.4', { 'checksums': ['1988a2220703444a575f2bad4eb090a0da71478599eb53081dd7237b7ec216ea'], From 74599ba64d0253ab16b61d33b394354122da8600 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 8 Nov 2023 14:28:53 +0100 Subject: [PATCH 9382/9987] update R-bundle-CRAN 2023.11 --- .../R-bundle-CRAN-2023.11-foss-2023a.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb index 786c88814f8..f87304d4c51 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.11-foss-2023a.eb @@ -77,6 +77,12 @@ exts_default_options = { 'source_tmpl': '%(name)s_%(version)s.tar.gz', } +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + # !! order of packages is important !! # packages updated on 5th November 2023 exts_list = [ @@ -3396,4 +3402,11 @@ exts_list = [ }), ] +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['abind', 'base64', 'calibrate'], +} + moduleclass = 'lang' From ad5d94b6e5b6eb2388b866b642bbb0475f5ed2f5 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 8 Nov 2023 15:41:09 +0100 Subject: [PATCH 9383/9987] adding easyconfigs: PostgreSQL-16.0-GCCcore-12.3.0.eb --- .../PostgreSQL-16.0-GCCcore-12.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.0-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..978dbe9a5c0 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.0-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '16.0' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['58bd3a265a279a2754905ddf072a54d64d6236dcf786f20f92b5d30b916df516'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Perl', '5.36.1'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-python --with-openssl --without-icu' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' From 5a136212b7ce6eac36183bac5ddcb3f62763d225 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 8 Nov 2023 15:42:47 +0100 Subject: [PATCH 9384/9987] adding easyconfigs: castor-1.7.11-foss-2022a.eb --- .../c/castor/castor-1.7.11-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb b/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb new file mode 100644 index 00000000000..48f2a840462 --- /dev/null +++ b/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'RPackage' + +name = 'castor' +version = '1.7.11' + +homepage = 'https://CRAN.R-project.org/package=castor' +description = """ +Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. +Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating +distances from the tree root and calculating pairwise distances. Calculation of phylogenetic +signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden +character prediction of discrete characters, simulating and fitting models of trait evolution, +fitting and simulating diversification models, dating trees, comparing trees, and +reading/writing trees in Newick format. +""" + + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['c3fa63969ffbebc92878b857052110d3e22e9bbd06b28641604c32a5177fb2b3'] + +dependencies = [ + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': ['%(name)s/R/%(name)s'], + 'dirs': [], +} + +moduleclass = 'bio' From f3891805aad23cdd5643b097b659b0d46afa5c2a Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 8 Nov 2023 16:04:09 +0100 Subject: [PATCH 9385/9987] Upgrade to TensorFlow 2.11.0 --- .../d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb index abd16842cec..cec8160a27c 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb @@ -18,7 +18,7 @@ toolchainopts = {'pic': True} dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), ('Python', '3.10.4'), - ('TensorFlow', '2.9.1', versionsuffix), + ('TensorFlow', '2.11.0', versionsuffix), ('PyTorch', '1.12.0', versionsuffix), ('scikit-image', '0.19.3'), ('matplotlib', '3.5.2'), From 15558592d3045d0697c6279dd98431be42b4b3bd Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Wed, 8 Nov 2023 16:11:36 +0100 Subject: [PATCH 9386/9987] Support customizing cmake_options --- .../easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb index 765f6e99944..359a382e7ff 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.1.0-foss-2023a.eb @@ -20,6 +20,7 @@ dependencies = [ ('MPFR', '4.2.0'), ] -prebuildopts = 'CMAKE_OPTIONS="-DCMAKE_INSTALL_PREFIX=%(installdir)s -DBLA_VENDOR=FlexiBLAS"' +# uncomment the next row if need customization +# cmake_options = '' moduleclass = 'numlib' From 259e4d4b7994604dfd1dec8422e7d54cb56db3c0 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 7 Nov 2023 17:47:45 +0100 Subject: [PATCH 9387/9987] adding easyconfigs: f90nml-1.4.4-GCCcore-10.2.0.eb, f90nml-1.4.4-GCCcore-12.2.0.eb --- .../f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ .../f/f90nml/f90nml-1.4.4-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..5aff63728f9 --- /dev/null +++ b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'f90nml' +version = '1.4.4' + +homepage = 'https://github.com/marshallward/f90nml' +description = """A Python module and command line tool for parsing + Fortran namelist files""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['65e8e135779895245238cbf6be5b1b80d6c2b8c9350c9cdce6183a31bdfd7622'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..b554f52d3e9 --- /dev/null +++ b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'f90nml' +version = '1.4.4' + +homepage = 'https://github.com/marshallward/f90nml' +description = """A Python module and command line tool for parsing + Fortran namelist files""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['65e8e135779895245238cbf6be5b1b80d6c2b8c9350c9cdce6183a31bdfd7622'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('Python', '3.10.8'), + ('PyYAML', '6.0') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From ca3323e972f2dec6f0b4e2c92129bb2fe63a1274 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 9 Nov 2023 10:51:49 +0100 Subject: [PATCH 9388/9987] fix regression in GCC 12+ on AVX512 systems --- .../easyconfigs/g/GCCcore/GCCcore-12.1.0.eb | 3 +++ .../easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 3 +++ ...re-12.2.0_fix-avx512-misoptimization.patch | 25 +++++++++++++++++++ .../easyconfigs/g/GCCcore/GCCcore-12.3.0.eb | 3 +++ .../easyconfigs/g/GCCcore/GCCcore-13.1.0.eb | 3 +++ .../easyconfigs/g/GCCcore/GCCcore-13.2.0.eb | 3 +++ 6 files changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-avx512-misoptimization.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb index 3482f6f3c16..4d35ae69304 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-12.1.0_allow-pragma-wself-init.patch', 'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch', + 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-12.2.0_fix-vectorizer.patch', ] checksums = [ @@ -51,6 +52,8 @@ checksums = [ '464f5faa9b23e805995d10dcdacca83df6321cac70826e9a3bc5bc9cd737f6a1'}, {'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch': '0ea675960795e238a43ae7d685a0082b21f0b63cf2fe499f6d55e89e0aaee392'}, + {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': + 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb index aa2a7e328a2..06a43b75d9c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-12.1.0_allow-pragma-wself-init.patch', 'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch', + 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-12.2.0_fix-vectorizer.patch', 'GCCcore-12.2.0_improve-cuda-compatibility.patch', ] @@ -52,6 +53,8 @@ checksums = [ '464f5faa9b23e805995d10dcdacca83df6321cac70826e9a3bc5bc9cd737f6a1'}, {'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch': '0ea675960795e238a43ae7d685a0082b21f0b63cf2fe499f6d55e89e0aaee392'}, + {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': + 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, {'GCCcore-12.2.0_improve-cuda-compatibility.patch': '91d00122554b56381592229398540e63baa26d03633292a7fdf338407a4a62d5'}, diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-avx512-misoptimization.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-avx512-misoptimization.patch new file mode 100644 index 00000000000..04f468739d8 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0_fix-avx512-misoptimization.patch @@ -0,0 +1,25 @@ +Fix a typo causing inverted semantics when (even AVX2) code is compiled for AVX512 systems, e.g. via -march=native +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112443 where the changeset is from. + +diff --git a/gcc/config/i386/sse.md b/gcc/config/i386/sse.md +index 2ce1aed4ad9..d7e058c2517 100644 +--- a/gcc/config/i386/sse.md ++++ b/gcc/config/i386/sse.md +@@ -16350,7 +16350,7 @@ + (match_dup 4))] + UNSPEC_BLENDV))] + { +- if (INTVAL (operands[5]) == 1) ++ if (INTVAL (operands[5]) == 5) + std::swap (operands[1], operands[2]); + operands[3] = gen_lowpart (mode, operands[3]); + }) +@@ -16380,7 +16380,7 @@ + (match_dup 4))] + UNSPEC_BLENDV))] + { +- if (INTVAL (operands[5]) == 1) ++ if (INTVAL (operands[5]) == 5) + std::swap (operands[1], operands[2]); + }) + diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb index c9fe0e62a87..eb7afd9a068 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb @@ -33,6 +33,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-12.2.0_improve-cuda-compatibility.patch', ] checksums = [ @@ -45,6 +46,8 @@ checksums = [ {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': + 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-12.2.0_improve-cuda-compatibility.patch': '91d00122554b56381592229398540e63baa26d03633292a7fdf338407a4a62d5'}, ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb index 5805f7d8a96..005f4794d63 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb @@ -33,6 +33,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', ] checksums = [ {'gcc-13.1.0.tar.gz': 'bacd4c614d8bd5983404585e53478d467a254249e0f1bb747c8bc6d787bd4fa2'}, @@ -44,6 +45,8 @@ checksums = [ {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': + 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb index c71dc05e7aa..3749681657f 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb @@ -33,6 +33,7 @@ sources = [ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', + 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', ] checksums = [ {'gcc-13.2.0.tar.gz': '8cb4be3796651976f94b9356fa08d833524f62420d6292c5033a9a26af315078'}, @@ -44,6 +45,8 @@ checksums = [ {'nvptx-tools-20230725.tar.gz': '17ce1f2c64f09c6f1cb709e3af869bb90b0102c412f25da55f338e35bc74b2e2'}, {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': + 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, ] builddependencies = [ From 87d9d702eb8a7e100fc4864d2d884ae8e1368145 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 6 Nov 2023 17:16:06 +0100 Subject: [PATCH 9389/9987] Disable bogus warning --- .../p/PyTorch/PyTorch-2.0.1-foss-2022b.eb | 2 ++ .../PyTorch-2.0.1_disable-gcc12-warning.patch | 32 +++++++++++++++++++ 2 files changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-gcc12-warning.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb index 318e4aacd4f..27e6fe2c084 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1-foss-2022b.eb @@ -23,6 +23,7 @@ patches = [ 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', 'PyTorch-2.0.1_add-missing-vsx-vector-shift-functions.patch', 'PyTorch-2.0.1_avoid-test_quantization-failures.patch', + 'PyTorch-2.0.1_disable-gcc12-warning.patch', 'PyTorch-2.0.1_disable-test-sharding.patch', 'PyTorch-2.0.1_fix-numpy-compat.patch', 'PyTorch-2.0.1_fix-shift-ops.patch', @@ -66,6 +67,7 @@ checksums = [ 'da44961d6c204403ba0c4b88cedccf06a7a3d24f29c4398545f96efae7a45c95'}, {'PyTorch-2.0.1_avoid-test_quantization-failures.patch': '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'}, + {'PyTorch-2.0.1_disable-gcc12-warning.patch': 'f558dfc8f7cdcdc74c4c58ef7e8fe6d67870aec6386ac0d923f1b745d108eec7'}, {'PyTorch-2.0.1_disable-test-sharding.patch': 'a1ed7f21c9a269ea039a07a3d6574f885787b30ca5687143c96e096d31066cca'}, {'PyTorch-2.0.1_fix-numpy-compat.patch': 'f3e5798193e0909a415d824f13772973200965db84476c1737824f2735f2db94'}, {'PyTorch-2.0.1_fix-shift-ops.patch': '5ee655d5dba56d801d5618543b6ca299fa874939a3471f7b5449bfcb7f3f18c7'}, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-gcc12-warning.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-gcc12-warning.patch new file mode 100644 index 00000000000..e3091daf27a --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.0.1_disable-gcc12-warning.patch @@ -0,0 +1,32 @@ +GCC 12 has a false positive warning when compiled for some architectures, e.g. Intel Sapphire Rapids. +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=112370 + +Suppress this warning such that the build doesn't error. + +Author: Alexander Grund (TU Dresden) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 471fc8a8d3d..5eb7b432630 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -557,6 +557,7 @@ string(APPEND CMAKE_CUDA_FLAGS " -Xfatbin -compress-all") + if(NOT MSVC) + string(APPEND CMAKE_CUDA_FLAGS_DEBUG " -g -lineinfo --source-in-ptx") + string(APPEND CMAKE_CUDA_FLAGS_RELWITHDEBINFO " -g -lineinfo --source-in-ptx") ++ append_cxx_flag_if_supported("-Wno-free-nonheap-object" CMAKE_CXX_FLAGS) + endif(NOT MSVC) + + # Set INTERN_BUILD_MOBILE for all mobile builds. Components that are not +diff --git a/cmake/public/utils.cmake b/cmake/public/utils.cmake +index 60cca5383dd..76c02d7479f 100644 +--- a/cmake/public/utils.cmake ++++ b/cmake/public/utils.cmake +@@ -548,6 +548,8 @@ function(torch_update_find_cuda_flags) + endif() + endfunction() + ++include(CheckCXXCompilerFlag) ++ + ############################################################################## + # CHeck if given flag is supported and append it to provided outputvar + # Also define HAS_UPPER_CASE_FLAG_NAME variable From 82f7472a97eeb9986d6273da52b8dfd9b21f4533 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 9 Nov 2023 13:33:10 +0100 Subject: [PATCH 9390/9987] adding easyconfigs: SUPPA-2.3-20231005-foss-2022b.eb --- .../s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb diff --git a/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb b/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb new file mode 100644 index 00000000000..20cf5f81693 --- /dev/null +++ b/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'SUPPA' +version = '2.3-20231005' +local_commit = 'a5d5e89' + +homepage = 'https://github.com/comprna/SUPPA' +description = """Fast, accurate, and uncertainty-aware differential + splicing analysis across multiple conditions.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +github_account = 'comprna' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +checksums = ['5e55911be2727c7abc7a4e3b6179f2f7cb0e3126bb443bce102fa7af97249e5d'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('statsmodels', '0.14.0'), + ('scikit-learn', '1.2.1'), +] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['suppa.py'], + 'dirs': [], +} + +sanity_check_commands = ['python suppa.py --help'] + +moduleclass = 'bio' From 2a7db4afd5649985dc6a39ab411bd79838c94c3d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 9 Nov 2023 13:59:11 +0100 Subject: [PATCH 9391/9987] add link to bin directory --- .../easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb b/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb index 20cf5f81693..f9a247220fd 100644 --- a/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb +++ b/easybuild/easyconfigs/s/SUPPA/SUPPA-2.3-20231005-foss-2022b.eb @@ -22,6 +22,10 @@ dependencies = [ ('scikit-learn', '1.2.1'), ] +postinstallcmds = ['cd %(installdir)s && mkdir bin && ln -s suppa.py bin/suppa.py && chmod a+x suppa.py'] + +fix_python_shebang_for = ['suppa.py'] + modextrapaths = { 'PATH': '', 'PYTHONPATH': '', @@ -32,6 +36,6 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ['python suppa.py --help'] +sanity_check_commands = ['suppa.py --help'] moduleclass = 'bio' From b0ecd1e94c618bf426decb8a109686ef427827a7 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 9 Nov 2023 16:03:38 +0100 Subject: [PATCH 9392/9987] adding easyconfigs: RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb, e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb --- .../e3nn/e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb | 39 +++++++++++++ ...Fdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb | 58 +++++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..0dd9d35d940 --- /dev/null +++ b/easybuild/easyconfigs/e/e3nn/e3nn-0.3.3-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'e3nn' +version = '0.3.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://e3nn.org/' +description = """ +Euclidean neural networks (e3nn) is a python library based on pytorch to create equivariant +neural networks for the group O(3). +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.0', versionsuffix), + ('sympy', '1.10.1'), +] + +use_pip = True + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('opt_einsum_fx', '0.1.4', { + 'checksums': ['7eeb7f91ecb70be65e6179c106ea7f64fc1db6319e3d1289a4518b384f81e74f'], + }), + (name, version, { + 'checksums': ['532b34a5644153659253c59943fe4224cd9c3c46ce8a79f1dc7c00afccb44ecb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..8ca5151696c --- /dev/null +++ b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'RFdiffusion' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/RosettaCommons/RFdiffusion' +description = """ +RFdiffusion is an open source method for structure generation, with or without conditional information +(a motif, target etc). It can perform a whole range of protein design challenges as we have outlined +in the RFdiffusion paper. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('e3nn', '0.3.3', versionsuffix), + ('wandb', '0.13.4'), +] + +use_pip = True + +exts_list = [ + ('pynvml', '11.0.0', { + 'checksums': ['d5fc4a22d355b40c341d6ba0aa888a2d4d2253177d243900f8401b7e6cacb1bb'], + }), + ('dllogger', '1.0.0', { + 'source_urls': ['https://github.com/NVIDIA/dllogger/archive/refs/tags'], + 'sources': ['v%(version)s.zip'], + 'checksums': ['07d0cd9b9b56f454f0c186a0889137e9f94e1979fca3d35911967c874c93c191'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('se3-transformer', version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/RosettaCommons/RFdiffusion/archive/refs/tags'], + 'start_dir': 'env/SE3Transformer', + 'checksums': ['57d82f0d43540c2912eda3f1d34ad90b13db14966ee069c427e217fe78f0297f'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_fix-find-packages.patch'], + 'source_urls': ['https://github.com/RosettaCommons/RFdiffusion/archive/refs/tags'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': [ + {'v1.1.0.tar.gz': '57d82f0d43540c2912eda3f1d34ad90b13db14966ee069c427e217fe78f0297f'}, + {'RFdiffusion-1.1.0_fix-find-packages.patch': + 'e25da7f476acacb6af58bd84f40aca712538900b0b48532b22f9a133d6886da2'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 9f188946ad29079e97215966e1d9814d10ba74d7 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Thu, 9 Nov 2023 16:59:26 +0100 Subject: [PATCH 9393/9987] Fix source being overwritten --- .../RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb index 8ca5151696c..9ebc11b3bd2 100644 --- a/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/r/RFdiffusion/RFdiffusion-1.1.0-foss-2022a-CUDA-11.7.0.eb @@ -43,10 +43,13 @@ exts_list = [ }), (name, version, { 'patches': ['%(name)s-%(version)s_fix-find-packages.patch'], - 'source_urls': ['https://github.com/RosettaCommons/RFdiffusion/archive/refs/tags'], - 'sources': ['v%(version)s.tar.gz'], + 'sources': { + 'filename': '%(name)s-%(version)s.tar.gz', + 'download_filename': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/RosettaCommons/RFdiffusion/archive/refs/tags'], + }, 'checksums': [ - {'v1.1.0.tar.gz': '57d82f0d43540c2912eda3f1d34ad90b13db14966ee069c427e217fe78f0297f'}, + {'RFdiffusion-1.1.0.tar.gz': '57d82f0d43540c2912eda3f1d34ad90b13db14966ee069c427e217fe78f0297f'}, {'RFdiffusion-1.1.0_fix-find-packages.patch': 'e25da7f476acacb6af58bd84f40aca712538900b0b48532b22f9a133d6886da2'}, ], From d26176e20afeadd1b30e7a6b53f4c7e0c8249bcb Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 10 Nov 2023 09:18:26 +0100 Subject: [PATCH 9394/9987] add pkgconf build dependency to libGLU --- .../easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb | 9 ++++++--- .../easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb | 9 ++++++--- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb index c636b6c6a9d..326dfd2626e 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-12.3.0.eb @@ -13,9 +13,12 @@ source_urls = ['https://mesa.freedesktop.org/archive/glu/'] sources = ['glu-%(version)s.tar.xz'] checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] -builddependencies = [('binutils', '2.40'), - ('Ninja', '1.11.1'), - ('Meson', '1.1.1')] +builddependencies = [ + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), + ('Ninja', '1.11.1'), + ('Meson', '1.1.1'), +] dependencies = [('Mesa', '23.1.4')] diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb index 6de3d5baea2..b2c0581c7f6 100644 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.3-GCCcore-13.2.0.eb @@ -13,9 +13,12 @@ source_urls = ['https://mesa.freedesktop.org/archive/glu/'] sources = ['glu-%(version)s.tar.xz'] checksums = ['bd43fe12f374b1192eb15fe20e45ff456b9bc26ab57f0eee919f96ca0f8a330f'] -builddependencies = [('binutils', '2.40'), - ('Ninja', '1.11.1'), - ('Meson', '1.2.3')] +builddependencies = [ + ('pkgconf', '2.0.3'), + ('binutils', '2.40'), + ('Ninja', '1.11.1'), + ('Meson', '1.2.3'), +] dependencies = [('Mesa', '23.1.9')] From fd201e8290d03db47d8238f818a7907448bf90fe Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 10 Nov 2023 09:40:43 +0100 Subject: [PATCH 9395/9987] adding easyconfigs: numba-0.58.1-foss-2023a.eb, LLVM-14.0.3-GCCcore-12.3.0.eb and patches: llvmlite-0.41.1_static-linking-of-LLVM.patch --- .../l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb | 40 ++++++++++++++ ...vmlite-0.41.1_static-linking-of-LLVM.patch | 22 ++++++++ .../n/numba/numba-0.58.1-foss-2023a.eb | 55 +++++++++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.41.1_static-linking-of-LLVM.patch create mode 100644 easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..09088210f91 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +name = 'LLVM' +version = '14.0.3' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'cstd': 'gnu++11', 'pic': True} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = ['llvm-%(version)s.src.tar.xz'] +checksums = ['1e09e8c26e1b67bc94a128b62e9b9c24b70c697a2436a479c9e5eedc4ae29654'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.41.1_static-linking-of-LLVM.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.41.1_static-linking-of-LLVM.patch new file mode 100644 index 00000000000..9ead7b37820 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.41.1_static-linking-of-LLVM.patch @@ -0,0 +1,22 @@ +Link llvmlite statically to LLVM. This allows us to use the version of LLVM that is +officially supported by llvmlite (14.0.3) instead of the one that is default in the toolchain +(for 2023a, that is LLVM 16.0.6). This is a pragmatic solution that is much easier than patching +llvmlite to work with a different version of LLVM. + +Author: Jakob Schiotz, Techn. Univ. Denmark +Email: schiotz@fysik.dtu.dk +Date: 10. November 2023 + +diff --git a/ffi/build.py b/ffi/build.py +index f4f8c69..189a0e9 100755 +--- a/ffi/build.py ++++ b/ffi/build.py +@@ -174,7 +174,7 @@ def main_posix(kind, library_ext): + raise RuntimeError(msg) + + # Get LLVM information for building +- libs = run_llvm_config(llvm_config, "--system-libs --libs all".split()) ++ libs = run_llvm_config(llvm_config, "--link-static --system-libs --libs all".split()) + # Normalize whitespace (trim newlines) + os.environ['LLVM_LIBS'] = ' '.join(libs.split()) + diff --git a/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb new file mode 100644 index 00000000000..d6beae0bc5d --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.58.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('LLVM', '14.0.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " + +exts_list = [ + ('llvmlite', '0.41.1', { + 'patches': ['llvmlite-0.41.1_static-linking-of-LLVM.patch'], + 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", + 'checksums': [ + {'llvmlite-0.41.1.tar.gz': 'f19f767a018e6ec89608e1f6b13348fa2fcde657151137cb64e56d48598a92db'}, + {'llvmlite-0.41.1_static-linking-of-LLVM.patch': + '0cb1fbe13db4ce8b697305229b6b6d79671a3ec5b93e95b4e059033ca626b43e'}, + ], + }), + (name, version, { + 'checksums': ['487ded0633efccd9ca3a46364b40006dbdaca0f95e99b8b83e778d1195ebcbaa'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -m llvmlite.tests", + "numba --help", +] + +moduleclass = 'lang' From c564011ae4280907971ceef92568fd7a27ed57ca Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 10 Nov 2023 09:54:19 +0100 Subject: [PATCH 9396/9987] Remove superfluous local variable (--inject-checksums moved the preinstallopts stuff around). --- easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb index d6beae0bc5d..233c86071ab 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " - exts_list = [ ('llvmlite', '0.41.1', { 'patches': ['llvmlite-0.41.1_static-linking-of-LLVM.patch'], From e6a32a5b9ae3358d8cd9aa2969261f8f8f91d5c5 Mon Sep 17 00:00:00 2001 From: Xin An <34663977+xinan1911@users.noreply.github.com> Date: Fri, 10 Nov 2023 11:39:08 +0100 Subject: [PATCH 9397/9987] Remove CMake installation path as easyblock takes care of it already --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb index 11881bde0f5..b033fcf10d9 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2021a.eb @@ -35,7 +35,6 @@ configopts = "-DWALBERLA_BUILD_WITH_PYTHON=ON " configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " configopts += "-DWALBERLA_BUILD_DOC=OFF " configopts += "-DPython_ROOT_DIR=$EBROOTPYTHON " -configopts += "-DCMAKE_INSTALL_PREFIX=%(installdir)s " modextrapaths = {'PYTHONPATH': ['pythonmodule']} From 913276533aaaca0e45908829201b7601a4b56ecc Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 10 Nov 2023 14:45:22 +0100 Subject: [PATCH 9398/9987] updating ScaFaCoS is not enough to build LAMMPS on ARM --- .../l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb index 1abcc202d59..ff105a29ce8 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb @@ -44,14 +44,17 @@ dependencies = [ ('kim-api', '2.3.0'), ('Eigen', '3.4.0'), ('PLUMED', '2.7.3'), - ('ScaFaCoS', '1.0.4'), ('SciPy-bundle', '2021.10'), # VTK package is auto-disabled if this dep is not available ('VTK', '9.1.0'), ] if ARCH == 'x86_64': - # TBB is an optional dependency when building on Intel arch - dependencies += [('tbb', '2020.3'), ] + # TBB and ScaFaCoSis an optional dependency when building on Intel arch + dependencies += [ + ('tbb', '2020.3'), + ('ScaFaCoS', '1.0.1'), + ] + # To use additional custom configuration options, use the 'configopts' easyconfig parameter # See docs and lammps easyblock for more information. From e84f046018fc118db2ec5e0dc100deb8cdee6534 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 10 Nov 2023 15:39:22 +0100 Subject: [PATCH 9399/9987] Fix style errors --- .../easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb index ff105a29ce8..e6f9a7d1940 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-23Jun2022-foss-2021b-kokkos.eb @@ -52,9 +52,8 @@ if ARCH == 'x86_64': # TBB and ScaFaCoSis an optional dependency when building on Intel arch dependencies += [ ('tbb', '2020.3'), - ('ScaFaCoS', '1.0.1'), + ('ScaFaCoS', '1.0.1'), ] - # To use additional custom configuration options, use the 'configopts' easyconfig parameter # See docs and lammps easyblock for more information. From 610d20fcaba5368423a8d9421e39b9ba268fa45a Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 10 Nov 2023 15:45:38 +0100 Subject: [PATCH 9400/9987] Make special LLVM module with llvmlite specific patches applied. --- ...0.eb => LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb} | 14 +++++++++++--- .../easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb | 2 +- 2 files changed, 12 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/l/LLVM/{LLVM-14.0.3-GCCcore-12.3.0.eb => LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb} (76%) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb similarity index 76% rename from easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb index 09088210f91..2f9a5d05bc9 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb @@ -1,5 +1,6 @@ name = 'LLVM' -version = '14.0.3' +version = '14.0.6' +versionsuffix = '-llvmlite' homepage = "https://llvm.org/" description = """The LLVM Core libraries provide a modern source- and target-independent @@ -13,9 +14,16 @@ description = """The LLVM Core libraries provide a modern source- and target-ind toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'cstd': 'gnu++11', 'pic': True} -source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +source_urls = [ + 'https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/', + 'https://github.com/numba/llvmlite/raw/v0.41.1/conda-recipes/', + ] sources = ['llvm-%(version)s.src.tar.xz'] -checksums = ['1e09e8c26e1b67bc94a128b62e9b9c24b70c697a2436a479c9e5eedc4ae29654'] +patches = [ + 'llvm14-remove-use-of-clonefile.patch', + 'llvm14-clear-gotoffsetmap.patch', + 'llvm14-svml.patch', +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb index 233c86071ab..f07c3608f25 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} toolchainopts = {'pic': True} builddependencies = [ - ('LLVM', '14.0.3'), + ('LLVM', '14.0.6', '-llvmlite'), ] dependencies = [ From ee7d33ed3f95056449308c9ed7456f25b73ca2a3 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 10 Nov 2023 16:00:22 +0100 Subject: [PATCH 9401/9987] Add the forgotten checksums. --- .../l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb index 2f9a5d05bc9..6034a8bc8ed 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb @@ -24,6 +24,12 @@ patches = [ 'llvm14-clear-gotoffsetmap.patch', 'llvm14-svml.patch', ] +checksums = [ + {'llvm-14.0.6.src.tar.xz': '050922ecaaca5781fdf6631ea92bc715183f202f9d2f15147226f023414f619a'}, + {'llvm14-remove-use-of-clonefile.patch': 'fd246e62292c6c7ad6ab4fa7626b7176f40b8141ec4cd78e811fea26bd29a1f1'}, + {'llvm14-clear-gotoffsetmap.patch': '690c96dcbd0a81e11d87f02e740c4ef34a0c578be741aaa6559cc00a5349fabf'}, + {'llvm14-svml.patch': '59df18ea4af3479de42ecbc1c524d4106f4a55f23335a64c0f0d5433daaba1b7'}, +] builddependencies = [ ('binutils', '2.40'), From b9b15e0a541ca0d09beb312d1a2a7cdb6fb71473 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 10 Nov 2023 16:22:52 +0100 Subject: [PATCH 9402/9987] Fix bad indentation. --- .../easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb index 6034a8bc8ed..fe8f2a38ca2 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb @@ -17,7 +17,7 @@ toolchainopts = {'cstd': 'gnu++11', 'pic': True} source_urls = [ 'https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/', 'https://github.com/numba/llvmlite/raw/v0.41.1/conda-recipes/', - ] +] sources = ['llvm-%(version)s.src.tar.xz'] patches = [ 'llvm14-remove-use-of-clonefile.patch', From f89312a1dd5f8b831019fe544aa9ca691fcfefb7 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Fri, 10 Nov 2023 16:34:40 +0100 Subject: [PATCH 9403/9987] Sidestep some build issues with CUDA-Samples 12.1 --- .../CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb index 438e0f44965..202d408d9dd 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -28,7 +28,9 @@ local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile " local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile " local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile " local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile " -local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/4_CUDA_Libraries/freeImageInteropNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/histEqualizationNPP/Makefile " +local_filters += "Samples/4_CUDA_Libraries/FilterBorderControlNPP/Makefile " local_filters += "Samples/5_Domain_Specific/simpleGL/Makefile " local_filters += "Samples/5_Domain_Specific/simpleVulkan/Makefile " local_filters += "Samples/5_Domain_Specific/simpleVulkanMMAP/Makefile " @@ -40,8 +42,17 @@ local_filters += "Samples/3_CUDA_Features/bf16TensorCoreGemm/Makefile " local_filters += "Samples/3_CUDA_Features/dmmaTensorCoreGemm/Makefile " local_filters += "Samples/3_CUDA_Features/globalToShmemAsyncCopy/Makefile " +# This give a link error under EESSI (ignoring for now) +local_filters += "Samples/4_CUDA_Libraries/simpleCUFFT_callback/Makefile " + +# Builds a shared lib that it sticks in `bin`! +local_filters += "Samples/2_Concepts_and_Techniques/cuHook/Makefile " + buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +# Remove libraries in the bin dir after a successful 'make' +buildopts += " && rm bin/*/linux/release/lib*.so.*" + files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), 'LICENSE', From e1db708cfb7aa0a14c6eba551b30d8f6a9f7daa5 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Fri, 10 Nov 2023 16:41:06 +0100 Subject: [PATCH 9404/9987] Update CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb --- .../c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb index 202d408d9dd..c5c6afe7534 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-12.1-GCC-12.3.0-CUDA-12.1.1.eb @@ -28,6 +28,7 @@ local_filters += "Samples/3_CUDA_Features/warpAggregatedAtomicsCG/Makefile " local_filters += "Samples/4_CUDA_Libraries/boxFilterNPP/Makefile " local_filters += "Samples/4_CUDA_Libraries/cannyEdgeDetectorNPP/Makefile " local_filters += "Samples/4_CUDA_Libraries/cudaNvSci/Makefile " +local_filters += "Samples/4_CUDA_Libraries/cudaNvSciNvMedia/Makefile " local_filters += "Samples/4_CUDA_Libraries/freeImageInteropNPP/Makefile " local_filters += "Samples/4_CUDA_Libraries/histEqualizationNPP/Makefile " local_filters += "Samples/4_CUDA_Libraries/FilterBorderControlNPP/Makefile " From c3a677e18e113ce0e9e66ea30940f06d9f672057 Mon Sep 17 00:00:00 2001 From: sassy Date: Sat, 11 Nov 2023 00:37:48 +0000 Subject: [PATCH 9405/9987] adding easyconfigs: mctc-lib-0.3.1-GCCcore-12.2.0.eb, mctc-lib-0.3.1-intel-compilers-2022.2.1.eb --- .../mctc-lib/mctc-lib-0.3.1-GCCcore-12.2.0.eb | 42 +++++++++++++++++++ ...mctc-lib-0.3.1-intel-compilers-2022.2.1.eb | 42 +++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9cb015c7bfa --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'mctc-lib' +version = '0.3.1' + +homepage = 'https://grimme-lab.github.io/mctc-lib' +description = """Common tool chain for working with molecular structure data in various +applications. This library provides a unified way to perform operations on +molecular structure data, like reading and writing to common geometry file +formats.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('json-fortran', '8.3.0'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mctc-convert --help"] + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..3f875046212 --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.2.1.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'mctc-lib' +version = '0.3.1' + +homepage = 'https://grimme-lab.github.io/mctc-lib' +description = """Common tool chain for working with molecular structure data in various +applications. This library provides a unified way to perform operations on +molecular structure data, like reading and writing to common geometry file +formats.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('json-fortran', '8.3.0'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mctc-convert --help"] + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +moduleclass = 'chem' From 39304f2d6e52b96566a00255d2ac51f163c13029 Mon Sep 17 00:00:00 2001 From: sassy Date: Sat, 11 Nov 2023 00:54:03 +0000 Subject: [PATCH 9406/9987] adding easyconfigs: json-fortran-8.3.0-GCCcore-12.2.0.eb --- .../json-fortran-8.3.0-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..e409adb3f77 --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From d39f2f5a10bf614521025dac296efc5c44fe668e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 14:58:28 +0800 Subject: [PATCH 9407/9987] adding easyconfigs: 4ti2-1.6.9-GCC-11.3.0.eb --- .../0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb b/easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb new file mode 100644 index 00000000000..1fd0b976427 --- /dev/null +++ b/easybuild/easyconfigs/0/4ti2/4ti2-1.6.9-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = '4ti2' +version = '1.6.9' + +homepage = 'https://4ti2.github.io/' +description = """A software package for algebraic, geometric and combinatorial problems on linear spaces""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = '4ti2' +source_urls = [GITHUB_SOURCE] +sources = ['Release_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['7b1015718102d8cd4dc2de64f69094fdba0bc69a1878ada5960979b171ff89e4'] + +dependencies = [ + ('GMP', '6.2.1'), + ('GLPK', '5.0'), +] + +builddependencies = [('Autotools', '20220317')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['4ti2gmp', '4ti2int32', '4ti2int64']], + 'dirs': ['include/4ti2', 'lib', 'share/4ti2'] +} + +moduleclass = 'math' From 9317fe94ea09b9b6c8c79071d054e33fd9063fc9 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 15:16:57 +0800 Subject: [PATCH 9408/9987] adding easyconfigs: cddlib-0.94m-GCCcore-11.3.0.eb --- .../c/cddlib/cddlib-0.94m-GCCcore-11.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/cddlib/cddlib-0.94m-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cddlib/cddlib-0.94m-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cddlib/cddlib-0.94m-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..d5ef7861ad7 --- /dev/null +++ b/easybuild/easyconfigs/c/cddlib/cddlib-0.94m-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'cddlib' +version = '0.94m' + +homepage = 'https://github.com/cddlib/cddlib' +description = "An efficient implementation of the Double Description Method" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'cddlib' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['766d8ec2135989830748e5e2fe57f307ed0706431c135541c3c081cbec0bc34f'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +dependencies = [('GMP', '6.2.1')] + +preconfigopts = "autoreconf -f -i && " + +buildopts = "SUBDIRS='lib-src src'" # build sources but spare the documentation in latex +installopts = buildopts + +local_exes = ['adjacency', 'allfaces', 'cddexec', 'fourier', 'lcdd', 'projection', 'redcheck', 'scdd', 'testcdd1', + 'testcdd2', 'testlp1', 'testlp2', 'testlp3', 'testshoot'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + ['bin/%s_gmp' % x for x in local_exes] + + ['lib/%s.%s' % (l, e) for l in ['libcdd', 'libcddgmp'] for e in ['a', SHLIB_EXT]] + + ['include/cddlib/%s.h' % h for h in ['cdd', 'cddmp', 'cddtypes', 'setoper', 'splitmix64']], + 'dirs': ['share/doc'] +} + +moduleclass = 'math' From e0bb3a39382a7477b9a2c20dabf18b3c29b732b3 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 15:38:24 +0800 Subject: [PATCH 9409/9987] adding easyconfigs: CoCoALib-0.99818-GCC-11.3.0.eb --- .../c/CoCoALib/CoCoALib-0.99818-GCC-11.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99818-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99818-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99818-GCC-11.3.0.eb new file mode 100644 index 00000000000..845ea2a2ccc --- /dev/null +++ b/easybuild/easyconfigs/c/CoCoALib/CoCoALib-0.99818-GCC-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'CoCoALib' +version = '0.99818' + +homepage = 'https://cocoa.dima.unige.it/cocoa/cocoalib/' +description = "CoCoALib is a free GPL3 C++ library for doing Computations in Commutative Algebra." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://cocoa.dima.unige.it/cocoa/cocoalib/tgz'] +sources = [SOURCE_TGZ] +checksums = ['7c7d6bb0bc3004ea76caaeb5f8de10ed09c8052a9131fd98716c36c6fc96d1ea'] + +dependencies = [ + ('GMP', '6.2.1'), + ('cddlib', '0.94m'), # optional +] + +# libreadline only needed for CoCoA-5 +configopts = "--only-cocoalib --no-readline --threadsafe-hack " +# Use cddlib and GMP from EB +configopts += "--with-libcddgmp=${EBROOTCDDLIB}/lib/libcddgmp.a --with-libgmp=$EBROOTGMP/lib/libgmp.a " + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +# Makefile is not smart enough to create missing directories +preinstallopts = "mkdir %(installdir)s/{include,lib} && " + +# Move doc and examples from include to share +postinstallcmds = [ + "mkdir %(installdir)s/share", + "mv %(installdir)s/include/CoCoA-%(version)s/{doc,examples} %(installdir)s/share/", +] + +sanity_check_paths = { + 'files': ['lib/libcocoa.a'], + 'dirs': ['include/CoCoA-%(version)s', 'share/doc', 'share/examples'] +} + +moduleclass = 'math' From c7d1e9e0deb3ea4f75098d5acea9f06ad6105621 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 15:46:44 +0800 Subject: [PATCH 9410/9987] adding easyconfigs: Givaro-4.2.0-GCCcore-11.3.0.eb --- .../g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..fc41e542efe --- /dev/null +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild recipe; see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'Givaro' +version = '4.2.0' + +homepage = 'https://github.com/linbox-team/givaro' +description = "C++ library for arithmetic and algebraic computations" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/linbox-team/givaro/archive'] +sources = ['v%(version)s.zip'] +checksums = ['bf51b47ac9a02be233fc39ac78d959d13630bcc78997007ffec410d940ed4c64'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " +configopts = "--with-gmp=$EBROOTGMP --enable-inline" + +sanity_check_paths = { + 'files': ['bin/givaro-config', 'include/givaro-config.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' From 99cc1d9d875428d78efbe15c43361581ba071088 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 15:57:05 +0800 Subject: [PATCH 9411/9987] adding easyconfigs: lrslib-7.2-gompi-2022a.eb and patches: lrslib-7.2-use-EB-values.patch --- .../l/lrslib/lrslib-7.2-gompi-2022a.eb | 39 ++++ .../l/lrslib/lrslib-7.2-use-EB-values.patch | 183 ++++++++++++++++++ 2 files changed, 222 insertions(+) create mode 100644 easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/l/lrslib/lrslib-7.2-use-EB-values.patch diff --git a/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb new file mode 100644 index 00000000000..17ae62bb0c4 --- /dev/null +++ b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'lrslib' +version = '7.2' + +homepage = 'http://cgm.cs.mcgill.ca/~avis/C/lrs.html' +description = """lrslib is a self-contained ANSI C implementation of the +reverse search algorithm for vertex enumeration/convex hull problems""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/'] +sources = ['lrslib-0%(version_major)s%(version_minor)s.tar.gz'] +patches = ['lrslib-%(version)s-use-EB-values.patch'] +checksums = [ + {'lrslib-072.tar.gz': 'fc48754a1ded1d8445d40ecfbe3546e4f27d53aaee95dc2c8c0c79fb9cd532f0'}, + {'lrslib-7.2-use-EB-values.patch': '16b0b4d987a751a45c7961bb7e0cb12aac50410a562dab3299335186456ab2ad'}, +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +skipsteps = ['configure'] + +# Default built plus mplrs +buildopts = 'lrs lrsgmp mplrs CFLAGS="$CFLAGS"' + +installopts = 'prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['lrs', 'lrsnash']] + + ['include/lrslib/lrs%s.h' % h for h in ['driver', 'gmp', 'lib', 'long', 'mp', 'restart']] + + ['lib/liblrs.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lrslib/lrslib-7.2-use-EB-values.patch b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-use-EB-values.patch new file mode 100644 index 00000000000..c84ecf21b05 --- /dev/null +++ b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-use-EB-values.patch @@ -0,0 +1,183 @@ +# Fix makefile to use EB environment +# Ward Poelmans, Alex Domingo (Vrije Universiteit Brussel) +# updated to version 7.2 by Miguel Dias Costa (National University of Singapore) +--- lrslib-072/makefile.orig 2023-11-06 13:50:57.098070000 +0800 ++++ lrslib-072/makefile 2023-11-06 13:58:17.056703000 +0800 +@@ -30,8 +30,8 @@ + #LIBDIR = /usr/lib + + #Kyoto machines usage +-INCLUDEDIR = /usr/local/include +-LIBDIR = /usr/local/lib ++#INCLUDEDIR = /usr/local/include ++#LIBDIR = /usr/local/lib + + CFLAGS ?= -O3 -Wall + #CFLAGS = -g -Wall +@@ -61,7 +61,7 @@ + MPLRSOBJ64=lrslong1-mplrs.o lrslib1-mplrs.o lrslibgmp-mplrs.o lrsgmp-mplrs.o lrsdriver-mplrs.o mplrs64.o + + lrs: ${LRSOBJ} +- $(CC) ${CFLAGS} -DMA ${BITS} -L${LIBDIR} -o lrs ${LRSOBJ} -lgmp ++ $(CC) ${CFLAGS} -DMA ${BITS} $(LDFLAGS) -o lrs ${LRSOBJ} -lgmp + $(CC) -O3 hvref.c -o hvref + ln -s -f lrs redund + +@@ -71,7 +71,7 @@ + ln -s -f lrs redund + + lrs64: ${LRSOBJ64} +- $(CC) ${CFLAGS} -DMA -L${LIBDIR} -o lrs ${LRSOBJ64} -lgmp ++ $(CC) ${CFLAGS} -DMA $(LDFLAGS) -o lrs ${LRSOBJ64} -lgmp + + lrs.o: lrs.c + $(CC) ${CFLAGS} -DMA ${BITS} -c -o lrs.o lrs.c +@@ -92,22 +92,22 @@ + $(CC) ${CFLAGS} -DMA -DSAFE ${BITS} -DLRSLONG -c -o lrslib2.o lrslib.c + + lrslibgmp.o: lrslib.c lrslib.h +- $(CC) ${CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o lrslibgmp.o lrslib.c ++ $(CC) ${CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o lrslibgmp.o lrslib.c + + lrslibmp.o: lrslib.c lrslib.h + $(CC) ${CFLAGS} -DMA -DMP -c -o lrslibmp.o lrslib.c + + lrsgmp.o: lrsgmp.c lrsgmp.h +- $(CC) ${CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o lrsgmp.o lrsgmp.c ++ $(CC) ${CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o lrsgmp.o lrsgmp.c + + lrsmp.o: lrsmp.c lrsmp.h + $(CC) ${CFLAGS} -DMA -DMP -c -o lrsmp.o lrsmp.c + + inedel: inedel.c lrsgmp.h lrsgmp.c +- $(CC) ${CFLAGS} -I${INCLUDEDIR} -L${LIBDIR} -DGMP -o inedel inedel.c lrsgmp.c -lgmp ++ $(CC) ${CFLAGS} $(CPPFLAGS) $(LDFLAGS) -DGMP -o inedel inedel.c lrsgmp.c -lgmp + + checkpred: checkpred.c lrsgmp.h lrsgmp.c +- $(CC) $(CFLAGS) -I${INCLUDEDIR} -L${LIBDIR} -DGMP -o checkpred checkpred.c lrsgmp.c -lgmp ++ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -DGMP -o checkpred checkpred.c lrsgmp.c -lgmp + + lrslong1-mplrs.o: lrslong.c lrslong.h + $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -DMA -DSAFE -DLRSLONG -DPLRS -c -o lrslong1-mplrs.o lrslong.c +@@ -122,28 +122,28 @@ + $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -DMA -DSAFE ${BITS} -DLRSLONG -DPLRS -c -o lrslib2-mplrs.o lrslib.c + + lrslibgmp-mplrs.o: lrslib.c lrslib.h +- $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS -I${INCLUDEDIR} -c -o lrslibgmp-mplrs.o lrslib.c ++ $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS $(CPPFLAGS) -c -o lrslibgmp-mplrs.o lrslib.c + + lrsgmp-mplrs.o: lrsgmp.c lrsgmp.h +- $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS -I${INCLUDEDIR} -c -o lrsgmp-mplrs.o lrsgmp.c ++ $(mpicxx) ${CFLAGS} -DMA -DTIMES -DSIGNALS -DGMP -DPLRS $(CPPFLAGS) -c -o lrsgmp-mplrs.o lrsgmp.c + + lrsdriver-mplrs.o: lrsdriver.c lrsdriver.h lrslib.h + $(mpicxx) $(CFLAGS) -c -o lrsdriver-mplrs.o lrsdriver.c + + mplrs.o: mplrs.c mplrs.h lrslib.h lrsgmp.h +- $(mpicxx) ${CFLAGS} -I${INCLUDEDIR} -DMA -DPLRS -DTIMES ${BITS} -DSIGNALS -D_WITH_GETLINE -c -o mplrs.o mplrs.c ++ $(mpicxx) ${CFLAGS} $(CPPFLAGS) -DMA -DPLRS -DTIMES ${BITS} -DSIGNALS -D_WITH_GETLINE -c -o mplrs.o mplrs.c + + mplrs64.o: mplrs.c mplrs.h lrslib.h lrsgmp.h +- $(mpicxx) ${CFLAGS} -I${INCLUDEDIR} -DMA -DPLRS -DTIMES -DSIGNALS -D_WITH_GETLINE -c -o mplrs64.o mplrs.c ++ $(mpicxx) ${CFLAGS} $(CPPFLAGS) -DMA -DPLRS -DTIMES -DSIGNALS -D_WITH_GETLINE -c -o mplrs64.o mplrs.c + + mplrs: ${MPLRSOBJ} mplrsgmp +- $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DMA ${BITS} -L${LIBDIR} -o mplrs ${MPLRSOBJ} -lgmp ++ $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DMA ${BITS} $(LDFLAGS) -o mplrs ${MPLRSOBJ} -lgmp + + mplrs64: ${MPLRSOBJ64} mplrsgmp +- $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DMA -L${LIBDIR} -o mplrs ${MPLRSOBJ64} -lgmp ++ $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DMA $(LDFLAGS) -o mplrs ${MPLRSOBJ64} -lgmp + + mplrsgmp: mplrs.c mplrs.h lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.h lrsdriver.c +- $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DGMP -I${INCLUDEDIR} mplrs.c lrslib.c lrsgmp.c lrsdriver.c -L${LIBDIR} -o mplrsgmp -lgmp ++ $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DGMP $(CPPFLAGS) mplrs.c lrslib.c lrsgmp.c lrsdriver.c $(LDFLAGS) -o mplrsgmp -lgmp + + mplrs1: mplrs.c mplrs.h lrslib.c lrslib.h lrslong.c lrslong.h lrsdriver.h lrsdriver.c + $(mpicxx) ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DPLRS -DSAFE -DLRSLONG mplrs.c lrslib.c lrslong.c lrsdriver.c -o mplrs1 +@@ -157,17 +157,17 @@ + singlemplrs: mplrsgmp mplrs1 mplrs2 + + flint: lrs.c lrslib.c lrslib.h lrsgmp.c lrsgmp.h +- @test -d ${INCLUDEDIR}/flint || { echo ${INCLUDEDIR}/flint not found; exit 1; } +- $(CC) -O3 -DFLINT -I/usr/local/include/flint lrs.c lrslib.c lrsgmp.c lrsdriver.c -L/usr/local/lib -Wl,-rpath=/usr/local/lib -lflint -o lrsflint -lgmp +-# $(CC) -O3 -DFLINT -I${INCLUDEDIR} -I${INCLUDEDIR}/flint lrs.c lrsdriver.c lrslib.c lrsgmp.c -L${LIBDIR} -lflint -o lrsflint -lgmp ++# @test -d ${INCLUDEDIR}/flint || { echo ${INCLUDEDIR}/flint not found; exit 1; } ++ $(CC) -O3 -DFLINT lrs.c lrslib.c lrsgmp.c lrsdriver.c -Wl,-lflint -o lrsflint -lgmp ++# $(CC) -O3 -DFLINT $(CPPFLAGS) lrs.c lrsdriver.c lrslib.c lrsgmp.c $(LDFLAGS) -lflint -o lrsflint -lgmp + + mplrsflint: mplrs.c mplrs.h lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.c lrsdriver.h +- ${mpicxx} ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DFLINT -I${INCLUDEDIR}/flint -DPLRS -o mplrsflint mplrs.c lrsdriver.c lrslib.c lrsgmp.c -L${LIBDIR} -lflint -lgmp ++ ${mpicxx} ${CFLAGS} -DTIMES -DSIGNALS -D_WITH_GETLINE -DFLINT -DPLRS -o mplrsflint mplrs.c lrsdriver.c lrslib.c lrsgmp.c $(LDFLAGS) -lflint -lgmp + + #comment out lines with ${BITS} if __int128 not supported by your C compiler + + lrsgmp: lrs.c lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.h lrsdriver.c +- $(CC) ${CFLAGS} -DGMP -I${INCLUDEDIR} -o lrsgmp lrs.c lrslib.c lrsgmp.c lrsdriver.c -L${LIBDIR} -lgmp ++ $(CC) ${CFLAGS} -DGMP $(CPPFLAGS) -o lrsgmp lrs.c lrslib.c lrsgmp.c lrsdriver.c $(LDFLAGS) -lgmp + ln -s -f lrsgmp redundgmp + + single: lrs.c lrslong.c lrslong.h lrslib.c lrslib.h lrsgmp.c lrsgmp.h lrsdriver.h lrsdriver.c +@@ -188,23 +188,23 @@ + $(CC) -O3 -o 2nash 2nash.c + + demo: lpdemo1.c lrslib.c lrsdriver.c lrslib.h lrsgmp.c lrsgmp.h +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lpdemo1 lpdemo1.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lpdemo lpdemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lpdemo2 lpdemo2.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o vedemo vedemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o chdemo chdemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lpdemo1 lpdemo1.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lpdemo lpdemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lpdemo2 lpdemo2.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o vedemo vedemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o chdemo chdemo.c lrslib.c lrsdriver.c lrsgmp.c -lgmp -DGMP + + lrsnash: lrsnash.c lrsnashlib.c lrslib.c lrsnashlib.h lrslib.h lrsgmp.c lrsgmp.h lrsdriver.h lrsdriver.c +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lrsnash lrsnash.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lrsnash lrsnash.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP + + alllrsnash: lrsnash.c nashdemo.c lrsnashlib.c lrslib.c lrsnashlib.h lrslib.h lrsgmp.c lrsgmp.h lrslong.h lrsdriver.h lrsdriver.c +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lrsnashgmp lrsnash.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lrsnash1 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o lrsnash2 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE ${BITS} +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o nashdemo nashdemo.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lrsnashgmp lrsnash.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lrsnash1 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o lrsnash2 lrsnash.c lrsnashlib.c lrslib.c lrslong.c lrsdriver.c -DLRSLONG -DSAFE ${BITS} ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o nashdemo nashdemo.c lrsnashlib.c lrslib.c lrsgmp.c lrsdriver.c -lgmp -DGMP + $(CC) -O3 -DMP -o setupnash setupnash.c lrslib.c lrsdriver.c lrsmp.c + $(CC) -O3 -DMP -o setupnash2 setupnash2.c lrslib.c lrsdriver.c lrsmp.c +- $(CC) -O3 -I${INCLUDEDIR} -L${LIBDIR} -o 2nash 2nash.c ++ $(CC) -O3 $(CPPFLAGS) $(LDFLAGS) -o 2nash 2nash.c + cp lrsnashgmp lrsnash + + ###################################################################### +@@ -248,12 +248,12 @@ + + + lrsnash-shared: ${SHLINK} lrsnash.c +- $(CC) ${CFLAGS} -DGMP -DMA lrsnash.c lrsnashlib.c -I${INCLUDEDIR} -o $@ -L . -llrs -lgmp ++ $(CC) ${CFLAGS} -DGMP -DMA lrsnash.c lrsnashlib.c $(CPPFLAGS) -o $@ -L . -llrs -lgmp + + # driver object files + + lrs-shared.o: lrs.c +- $(CC) ${CFLAGS} -DMA ${BITS} -L${LIBDIR} -c -o $@ lrs.c ++ $(CC) ${CFLAGS} -DMA ${BITS} $(LDFLAGS) -c -o $@ lrs.c + + # build object files for the shared library + +@@ -270,10 +270,10 @@ + $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DSAFE ${BITS} -DLRSLONG -c -o $@ lrslong.c + + lrslibgmp-shr.o: lrslib.c lrslib.h +- $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o $@ lrslib.c ++ $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o $@ lrslib.c + + lrsgmp-shr.o: lrsgmp.c lrsgmp.h +- $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP -I${INCLUDEDIR} -c -o $@ lrsgmp.c ++ $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DGMP $(CPPFLAGS) -c -o $@ lrsgmp.c + + lrslib2-shr.o: lrslib.c lrslib.h + $(CC) ${CFLAGS} ${SHLIB_CFLAGS} -DMA -DSAFE ${BITS} -DLRSLONG -c -o $@ lrslib.c From 78d60915b06ca579ce1243362b232e79a9d72bc0 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:04:54 +0800 Subject: [PATCH 9412/9987] adding easyconfigs: nauty-2.8.6-GCC-11.3.0.eb --- .../n/nauty/nauty-2.8.6-GCC-11.3.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb b/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb new file mode 100644 index 00000000000..bc1a1036d2d --- /dev/null +++ b/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' + +name = 'nauty' +version = '2.8.6' + +homepage = 'https://pallini.di.uniroma1.it/' +description = """nauty and Traces are programs for computing automorphism groups of graphs and +digraphs. They can also produce a canonical label.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pallini.di.uniroma1.it'] +sources = ['nauty%s.tar.gz' % version.replace('.', '_')] +checksums = ['f2ce98225ca8330f5bce35f7d707b629247e09dda15fc479dc00e726fee5e6fa'] + +local_executables = [ + 'addedgeg', 'amtog', 'assembleg', 'biplabg', 'catg', 'complg', 'converseg', 'copyg', 'countg', 'cubhamg', + 'deledgeg', 'delptg', 'directg', 'dreadnaut', 'dretodot', 'dretog', 'edgetransg', 'genbg', 'genbgL', 'geng', + 'gengL', 'genquarticg', 'genrang', 'genspecialg', 'gentourng', 'gentreeg', 'hamheuristic', 'labelg', 'linegraphg', + 'listg', 'multig', 'newedgeg', 'NRswitchg', 'pickg', 'planarg', 'ranlabg', 'shortg', 'showg', 'subdivideg', + 'twohamg', 'underlyingg', 'vcolg', 'watercluster2' +] +local_headers = [ + 'gtools.h', 'gutils.h', 'naugroup.h', 'naugstrings.h', 'naurng.h', 'nausparse.h', 'nautaux.h', 'nautinv.h', + 'naututil.h', 'nautycliquer.h', 'nauty.h', 'planarity.h', 'quarticirred28.h', 'schreier.h', 'traces.h' +] +local_libs = ['nauty%s.a' % l for l in ['', '1', 'L', 'L1', 'W', 'W1']] + +# Configure and enable thread-local variables +prebuildopts = "./configure --enable-tls && " + +runtest = "checks" + +files_to_copy = [ + (local_executables, "bin"), + (local_headers, "include/%(name)s"), + (local_libs, "lib"), +] + +# prepend "lib" to library files to standarize their name +postinstallcmds = ["cd %%(installdir)s/lib/ && mv %s lib%s" % (l, l) for l in local_libs] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_executables] + + ['include/%%(name)s/%s' % h for h in local_headers] + + ['lib/lib%s' % l for l in local_libs], + 'dirs': [''] +} + +moduleclass = 'math' From 2cb6228a4a6e09ea80d2df4ee0d7b305f4450a11 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:10:36 +0800 Subject: [PATCH 9413/9987] adding easyconfigs: PARI-GP-2.15.4-GCCcore-11.3.0.eb --- .../PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..eac0ec3c674 --- /dev/null +++ b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'PARI-GP' +version = '2.15.4' + +homepage = 'http://pari.math.u-bordeaux.fr' +description = """PARI/GP is a widely used computer algebra system designed for fast computations in number theory + (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful + functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., + and a lot of transcendental functions. PARI is also available as a C library to allow for faster computations. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://pari.math.u-bordeaux.fr/pub/pari/unix/'] +sources = ['pari-%(version)s.tar.gz'] +checksums = ['c3545bfee0c6dfb40b77fb4bbabaf999d82e60069b9f6d28bcb6cf004c8c5c0f'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), +] + +skipsteps = ['configure'] + +prebuildopts = './Configure --prefix=%(installdir)s &&' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gp', 'gp-2.15', 'gphelp', 'tex2mail']] + + ['include/pari/%s' % x for x in ['pari.h', 'genpari.h']], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'math' From 682ecdfa8992df030f9e942db8bd3393ffbb1e46 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:24:43 +0800 Subject: [PATCH 9414/9987] adding easyconfigs: Singular-4.3.2p10-gfbf-2022a.eb --- .../Singular/Singular-4.3.2p10-gfbf-2022a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb b/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb new file mode 100644 index 00000000000..97c0499a3ab --- /dev/null +++ b/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'Singular' +version = '4.3.2p10' + +homepage = 'https://www.singular.uni-kl.de/' +description = """Singular is a computer algebra system for polynomial computations, +with special emphasis on commutative and non-commutative algebra, algebraic geometry, +and singularity theory.""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Singular/Singular/archive/refs/tags/'] +sources = ['Release-%s.tar.gz' % version.replace('.', '-')] +checksums = ['692a09ef87be731f21b792721edd671ee98f1a4048539e628d92f123714279ab'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.4'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('libreadline', '8.1.2'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('FLINT', '2.9.0'), + ('NTL', '11.5.1'), + ('cddlib', '0.94m'), + ('4ti2', '1.6.9'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--with-gmp=$EBROOTGMP --with-flint=$EBROOTFLINT --with-ntl=$EBROOTNTL" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ESingular', 'Singular', 'TSingular', 'libpolys-config', 'libsingular-config']] + + ['lib/lib%s.%s' % (l, e) for l in ['Singular', 'factory', 'omalloc', 'polys', 'singular_resources'] + for e in ['a', SHLIB_EXT]], + 'dirs': ['include/%s' % h for h in ['factory', 'omalloc', 'resources', 'singular']] + + ['libexec/singular', 'share'], +} + +moduleclass = 'math' From 27abd03b3258dd2e760dc3d71ebb10b4881b3c85 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:28:33 +0800 Subject: [PATCH 9415/9987] switch to https --- .../easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb index eac0ec3c674..4b8ff351b17 100644 --- a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'PARI-GP' version = '2.15.4' -homepage = 'http://pari.math.u-bordeaux.fr' +homepage = 'https://pari.math.u-bordeaux.fr' description = """PARI/GP is a widely used computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., @@ -12,7 +12,7 @@ description = """PARI/GP is a widely used computer algebra system designed for f toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['http://pari.math.u-bordeaux.fr/pub/pari/unix/'] +source_urls = ['https://pari.math.u-bordeaux.fr/pub/pari/unix/'] sources = ['pari-%(version)s.tar.gz'] checksums = ['c3545bfee0c6dfb40b77fb4bbabaf999d82e60069b9f6d28bcb6cf004c8c5c0f'] From 2b83a3d2e81b4670a7754f41d1b29c564fc17922 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 11 Nov 2023 09:36:55 +0100 Subject: [PATCH 9416/9987] Add patch files to EasyBuild instead of downloading (works, but test suite complains). --- .../LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb | 22 +- .../LLVM/LLVM-14.0.6-clear-gotoffsetmap.patch | 31 + .../easyconfigs/l/LLVM/LLVM-14.0.6-svml.patch | 2194 +++++++++++++++++ 3 files changed, 2236 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-clear-gotoffsetmap.patch create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-svml.patch diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb index fe8f2a38ca2..6ece6bfc09b 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb @@ -9,26 +9,26 @@ description = """The LLVM Core libraries provide a modern source- and target-ind specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) - to use LLVM as an optimizer and code generator.""" + to use LLVM as an optimizer and code generator. + + This version include patches for llvmlite / numba.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'cstd': 'gnu++11', 'pic': True} -source_urls = [ - 'https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/', - 'https://github.com/numba/llvmlite/raw/v0.41.1/conda-recipes/', -] +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] sources = ['llvm-%(version)s.src.tar.xz'] + +# Patches from https://github.com/numba/llvmlite/raw/v0.41.1/conda-recipes/ but +# renamed to follow EasyBuild conventions. patches = [ - 'llvm14-remove-use-of-clonefile.patch', - 'llvm14-clear-gotoffsetmap.patch', - 'llvm14-svml.patch', + 'LLVM-14.0.6-clear-gotoffsetmap.patch', + 'LLVM-14.0.6-svml.patch', ] checksums = [ {'llvm-14.0.6.src.tar.xz': '050922ecaaca5781fdf6631ea92bc715183f202f9d2f15147226f023414f619a'}, - {'llvm14-remove-use-of-clonefile.patch': 'fd246e62292c6c7ad6ab4fa7626b7176f40b8141ec4cd78e811fea26bd29a1f1'}, - {'llvm14-clear-gotoffsetmap.patch': '690c96dcbd0a81e11d87f02e740c4ef34a0c578be741aaa6559cc00a5349fabf'}, - {'llvm14-svml.patch': '59df18ea4af3479de42ecbc1c524d4106f4a55f23335a64c0f0d5433daaba1b7'}, + {'LLVM-14.0.6-clear-gotoffsetmap.patch': '690c96dcbd0a81e11d87f02e740c4ef34a0c578be741aaa6559cc00a5349fabf'}, + {'LLVM-14.0.6-svml.patch': '59df18ea4af3479de42ecbc1c524d4106f4a55f23335a64c0f0d5433daaba1b7'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-clear-gotoffsetmap.patch b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-clear-gotoffsetmap.patch new file mode 100644 index 00000000000..239f4ab20c1 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-clear-gotoffsetmap.patch @@ -0,0 +1,31 @@ +From 322c79fff224389b4df9f24ac22965867007c2fa Mon Sep 17 00:00:00 2001 +From: Graham Markall +Date: Mon, 13 Mar 2023 21:35:11 +0000 +Subject: [PATCH] RuntimeDyldELF: Clear the GOTOffsetMap when finalizing the + load + +This needs resetting so that stale entries are not left behind when the +GOT section and index are reset. + +See llvm/llvm#61402: RuntimeDyldELF doesn't clear GOTOffsetMap in +finalizeLoad(), leading to invalid GOT relocations on AArch64 - +https://github.com/llvm/llvm-project/issues/61402. +--- + llvm/lib/ExecutionEngine/RuntimeDyld/RuntimeDyldELF.cpp | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/llvm-14.0.6.src/lib/ExecutionEngine/RuntimeDyld/RuntimeDyldELF.cpp b/llvm-14.0.6.src/lib/ExecutionEngine/RuntimeDyld/RuntimeDyldELF.cpp +index f92618afdff6..eb3c27a9406a 100644 +--- a/llvm-14.0.6.src/lib/ExecutionEngine/RuntimeDyld/RuntimeDyldELF.cpp ++++ b/llvm-14.0.6.src/lib/ExecutionEngine/RuntimeDyld/RuntimeDyldELF.cpp +@@ -2345,6 +2345,7 @@ Error RuntimeDyldELF::finalizeLoad(const ObjectFile &Obj, + } + } + ++ GOTOffsetMap.clear(); + GOTSectionID = 0; + CurrentGOTIndex = 0; + +-- +2.34.1 + diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-svml.patch b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-svml.patch new file mode 100644 index 00000000000..c753d3f5971 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-svml.patch @@ -0,0 +1,2194 @@ +From 9de32f5474f1f78990b399214bdbb6c21f8f098e Mon Sep 17 00:00:00 2001 +From: Ivan Butygin +Date: Sun, 24 Jul 2022 20:31:29 +0200 +Subject: [PATCH] Fixes vectorizer and extends SVML support + +Fixes vectorizer and extends SVML support +Patch was updated to fix SVML calling convention issues uncovered by llvm 10. +In previous versions of patch SVML calling convention was selected based on +compilation settings. So if you try to call 256bit vector function from avx512 +code function will be called with avx512 cc which is incorrect. To fix this +SVML cc was separated into 3 different cc for 128, 256 and 512bit vector lengths +which are selected based on actual input vector length. + +Original patch merged several fixes: + +1. https://reviews.llvm.org/D47188 patch fixes the problem with improper calls +to SVML library as it has non-standard calling conventions. So accordingly it +has SVML calling conventions definitions and code to set CC to the vectorized +calls. As SVML provides several implementations for the math functions we also +took into consideration fast attribute and select more fast implementation in +such case. This work is based on original Matt Masten's work. +Author: Denis Nagorny + +2. https://reviews.llvm.org/D53035 patch implements support to legalize SVML +calls by breaking down the illegal vector call instruction into multiple legal +vector call instructions during code generation. Currently the vectorizer does +not check legality of the generated SVML (or any VECLIB) call instructions, and +this can lead to potential problems even during vector type legalization. This +patch addresses this issue by adding a legality check during code generation and +replaces the illegal SVML call with corresponding legalized instructions. +(RFC: http://lists.llvm.org/pipermail/llvm-dev/2018-June/124357.html) +Author: Karthik Senthil + +diff --git a/llvm-14.0.6.src/include/llvm/Analysis/TargetLibraryInfo.h b/llvm-14.0.6.src/include/llvm/Analysis/TargetLibraryInfo.h +index 17d1e3f770c14..110ff08189867 100644 +--- a/llvm-14.0.6.src/include/llvm/Analysis/TargetLibraryInfo.h ++++ b/llvm-14.0.6.src/include/llvm/Analysis/TargetLibraryInfo.h +@@ -39,6 +39,12 @@ struct VecDesc { + NotLibFunc + }; + ++enum SVMLAccuracy { ++ SVML_DEFAULT, ++ SVML_HA, ++ SVML_EP ++}; ++ + /// Implementation of the target library information. + /// + /// This class constructs tables that hold the target library information and +@@ -157,7 +163,7 @@ class TargetLibraryInfoImpl { + /// Return true if the function F has a vector equivalent with vectorization + /// factor VF. + bool isFunctionVectorizable(StringRef F, const ElementCount &VF) const { +- return !getVectorizedFunction(F, VF).empty(); ++ return !getVectorizedFunction(F, VF, false).empty(); + } + + /// Return true if the function F has a vector equivalent with any +@@ -166,7 +172,10 @@ class TargetLibraryInfoImpl { + + /// Return the name of the equivalent of F, vectorized with factor VF. If no + /// such mapping exists, return the empty string. +- StringRef getVectorizedFunction(StringRef F, const ElementCount &VF) const; ++ std::string getVectorizedFunction(StringRef F, const ElementCount &VF, bool IsFast) const; ++ ++ Optional getVectorizedFunctionCallingConv( ++ StringRef F, const FunctionType &FTy, const DataLayout &DL) const; + + /// Set to true iff i32 parameters to library functions should have signext + /// or zeroext attributes if they correspond to C-level int or unsigned int, +@@ -326,8 +335,13 @@ class TargetLibraryInfo { + bool isFunctionVectorizable(StringRef F) const { + return Impl->isFunctionVectorizable(F); + } +- StringRef getVectorizedFunction(StringRef F, const ElementCount &VF) const { +- return Impl->getVectorizedFunction(F, VF); ++ std::string getVectorizedFunction(StringRef F, const ElementCount &VF, bool IsFast) const { ++ return Impl->getVectorizedFunction(F, VF, IsFast); ++ } ++ ++ Optional getVectorizedFunctionCallingConv( ++ StringRef F, const FunctionType &FTy, const DataLayout &DL) const { ++ return Impl->getVectorizedFunctionCallingConv(F, FTy, DL); + } + + /// Tests if the function is both available and a candidate for optimized code +diff --git a/llvm-14.0.6.src/include/llvm/AsmParser/LLToken.h b/llvm-14.0.6.src/include/llvm/AsmParser/LLToken.h +index 78ebb35e0ea4d..3ffb57db8b18b 100644 +--- a/llvm-14.0.6.src/include/llvm/AsmParser/LLToken.h ++++ b/llvm-14.0.6.src/include/llvm/AsmParser/LLToken.h +@@ -133,6 +133,9 @@ enum Kind { + kw_fastcc, + kw_coldcc, + kw_intel_ocl_bicc, ++ kw_intel_svmlcc128, ++ kw_intel_svmlcc256, ++ kw_intel_svmlcc512, + kw_cfguard_checkcc, + kw_x86_stdcallcc, + kw_x86_fastcallcc, +diff --git a/llvm-14.0.6.src/include/llvm/IR/CMakeLists.txt b/llvm-14.0.6.src/include/llvm/IR/CMakeLists.txt +index 0498fc269b634..23bb3de41bc1a 100644 +--- a/llvm-14.0.6.src/include/llvm/IR/CMakeLists.txt ++++ b/llvm-14.0.6.src/include/llvm/IR/CMakeLists.txt +@@ -20,3 +20,7 @@ tablegen(LLVM IntrinsicsX86.h -gen-intrinsic-enums -intrinsic-prefix=x86) + tablegen(LLVM IntrinsicsXCore.h -gen-intrinsic-enums -intrinsic-prefix=xcore) + tablegen(LLVM IntrinsicsVE.h -gen-intrinsic-enums -intrinsic-prefix=ve) + add_public_tablegen_target(intrinsics_gen) ++ ++set(LLVM_TARGET_DEFINITIONS SVML.td) ++tablegen(LLVM SVML.inc -gen-svml) ++add_public_tablegen_target(svml_gen) +diff --git a/llvm-14.0.6.src/include/llvm/IR/CallingConv.h b/llvm-14.0.6.src/include/llvm/IR/CallingConv.h +index fd28542465225..096eea1a8e19b 100644 +--- a/llvm-14.0.6.src/include/llvm/IR/CallingConv.h ++++ b/llvm-14.0.6.src/include/llvm/IR/CallingConv.h +@@ -252,6 +252,11 @@ namespace CallingConv { + /// M68k_INTR - Calling convention used for M68k interrupt routines. + M68k_INTR = 101, + ++ /// Intel_SVML - Calling conventions for Intel Short Math Vector Library ++ Intel_SVML128 = 102, ++ Intel_SVML256 = 103, ++ Intel_SVML512 = 104, ++ + /// The highest possible calling convention ID. Must be some 2^k - 1. + MaxID = 1023 + }; +diff --git a/llvm-14.0.6.src/include/llvm/IR/SVML.td b/llvm-14.0.6.src/include/llvm/IR/SVML.td +new file mode 100644 +index 0000000000000..5af710404c9d9 +--- /dev/null ++++ b/llvm-14.0.6.src/include/llvm/IR/SVML.td +@@ -0,0 +1,62 @@ ++//===-- Intel_SVML.td - Defines SVML call variants ---------*- tablegen -*-===// ++// ++// The LLVM Compiler Infrastructure ++// ++// This file is distributed under the University of Illinois Open Source ++// License. See LICENSE.TXT for details. ++// ++//===----------------------------------------------------------------------===// ++// ++// This file is used by TableGen to define the different typs of SVML function ++// variants used with -fveclib=SVML. ++// ++//===----------------------------------------------------------------------===// ++ ++class SvmlVariant; ++ ++def sin : SvmlVariant; ++def cos : SvmlVariant; ++def pow : SvmlVariant; ++def exp : SvmlVariant; ++def log : SvmlVariant; ++def acos : SvmlVariant; ++def acosh : SvmlVariant; ++def asin : SvmlVariant; ++def asinh : SvmlVariant; ++def atan2 : SvmlVariant; ++def atan : SvmlVariant; ++def atanh : SvmlVariant; ++def cbrt : SvmlVariant; ++def cdfnorm : SvmlVariant; ++def cdfnorminv : SvmlVariant; ++def cosd : SvmlVariant; ++def cosh : SvmlVariant; ++def erf : SvmlVariant; ++def erfc : SvmlVariant; ++def erfcinv : SvmlVariant; ++def erfinv : SvmlVariant; ++def exp10 : SvmlVariant; ++def exp2 : SvmlVariant; ++def expm1 : SvmlVariant; ++def hypot : SvmlVariant; ++def invsqrt : SvmlVariant; ++def log10 : SvmlVariant; ++def log1p : SvmlVariant; ++def log2 : SvmlVariant; ++def sind : SvmlVariant; ++def sinh : SvmlVariant; ++def sqrt : SvmlVariant; ++def tan : SvmlVariant; ++def tanh : SvmlVariant; ++ ++// TODO: SVML does not currently provide _ha and _ep variants of these fucnctions. ++// We should call the default variant of these functions in all cases instead. ++ ++// def nearbyint : SvmlVariant; ++// def logb : SvmlVariant; ++// def floor : SvmlVariant; ++// def fmod : SvmlVariant; ++// def ceil : SvmlVariant; ++// def trunc : SvmlVariant; ++// def rint : SvmlVariant; ++// def round : SvmlVariant; +diff --git a/llvm-14.0.6.src/lib/Analysis/CMakeLists.txt b/llvm-14.0.6.src/lib/Analysis/CMakeLists.txt +index aec84124129f4..98286e166fbe2 100644 +--- a/llvm-14.0.6.src/lib/Analysis/CMakeLists.txt ++++ b/llvm-14.0.6.src/lib/Analysis/CMakeLists.txt +@@ -150,6 +150,7 @@ add_llvm_component_library(LLVMAnalysis + DEPENDS + intrinsics_gen + ${MLDeps} ++ svml_gen + + LINK_LIBS + ${MLLinkDeps} +diff --git a/llvm-14.0.6.src/lib/Analysis/TargetLibraryInfo.cpp b/llvm-14.0.6.src/lib/Analysis/TargetLibraryInfo.cpp +index 02923c2c7eb14..83abde28a62a4 100644 +--- a/llvm-14.0.6.src/lib/Analysis/TargetLibraryInfo.cpp ++++ b/llvm-14.0.6.src/lib/Analysis/TargetLibraryInfo.cpp +@@ -110,6 +110,11 @@ bool TargetLibraryInfoImpl::isCallingConvCCompatible(Function *F) { + F->getFunctionType()); + } + ++static std::string svmlMangle(StringRef FnName, const bool IsFast) { ++ std::string FullName = FnName.str(); ++ return IsFast ? FullName : FullName + "_ha"; ++} ++ + /// Initialize the set of available library functions based on the specified + /// target triple. This should be carefully written so that a missing target + /// triple gets a sane set of defaults. +@@ -1876,8 +1881,9 @@ void TargetLibraryInfoImpl::addVectorizableFunctionsFromVecLib( + } + case SVML: { + const VecDesc VecFuncs[] = { +- #define TLI_DEFINE_SVML_VECFUNCS +- #include "llvm/Analysis/VecFuncs.def" ++ #define GET_SVML_VARIANTS ++ #include "llvm/IR/SVML.inc" ++ #undef GET_SVML_VARIANTS + }; + addVectorizableFunctions(VecFuncs); + break; +@@ -1897,20 +1903,51 @@ bool TargetLibraryInfoImpl::isFunctionVectorizable(StringRef funcName) const { + return I != VectorDescs.end() && StringRef(I->ScalarFnName) == funcName; + } + +-StringRef +-TargetLibraryInfoImpl::getVectorizedFunction(StringRef F, +- const ElementCount &VF) const { ++std::string TargetLibraryInfoImpl::getVectorizedFunction(StringRef F, ++ const ElementCount &VF, ++ bool IsFast) const { ++ bool FromSVML = ClVectorLibrary == SVML; + F = sanitizeFunctionName(F); + if (F.empty()) +- return F; ++ return F.str(); + std::vector::const_iterator I = + llvm::lower_bound(VectorDescs, F, compareWithScalarFnName); + while (I != VectorDescs.end() && StringRef(I->ScalarFnName) == F) { +- if (I->VectorizationFactor == VF) +- return I->VectorFnName; ++ if (I->VectorizationFactor == VF) { ++ if (FromSVML) { ++ return svmlMangle(I->VectorFnName, IsFast); ++ } ++ return I->VectorFnName.str(); ++ } + ++I; + } +- return StringRef(); ++ return std::string(); ++} ++ ++static CallingConv::ID getSVMLCallingConv(const DataLayout &DL, const FunctionType &FType) ++{ ++ assert(isa(FType.getReturnType())); ++ auto *VecCallRetType = cast(FType.getReturnType()); ++ auto TypeBitWidth = DL.getTypeSizeInBits(VecCallRetType); ++ if (TypeBitWidth == 128) { ++ return CallingConv::Intel_SVML128; ++ } else if (TypeBitWidth == 256) { ++ return CallingConv::Intel_SVML256; ++ } else if (TypeBitWidth == 512) { ++ return CallingConv::Intel_SVML512; ++ } else { ++ llvm_unreachable("Invalid vector width"); ++ } ++ return 0; // not reachable ++} ++ ++Optional ++TargetLibraryInfoImpl::getVectorizedFunctionCallingConv( ++ StringRef F, const FunctionType &FTy, const DataLayout &DL) const { ++ if (F.startswith("__svml")) { ++ return getSVMLCallingConv(DL, FTy); ++ } ++ return {}; + } + + TargetLibraryInfo TargetLibraryAnalysis::run(const Function &F, +diff --git a/llvm-14.0.6.src/lib/AsmParser/LLLexer.cpp b/llvm-14.0.6.src/lib/AsmParser/LLLexer.cpp +index e3bf41c9721b6..4f9dccd4e0724 100644 +--- a/llvm-14.0.6.src/lib/AsmParser/LLLexer.cpp ++++ b/llvm-14.0.6.src/lib/AsmParser/LLLexer.cpp +@@ -603,6 +603,9 @@ lltok::Kind LLLexer::LexIdentifier() { + KEYWORD(spir_kernel); + KEYWORD(spir_func); + KEYWORD(intel_ocl_bicc); ++ KEYWORD(intel_svmlcc128); ++ KEYWORD(intel_svmlcc256); ++ KEYWORD(intel_svmlcc512); + KEYWORD(x86_64_sysvcc); + KEYWORD(win64cc); + KEYWORD(x86_regcallcc); +diff --git a/llvm-14.0.6.src/lib/AsmParser/LLParser.cpp b/llvm-14.0.6.src/lib/AsmParser/LLParser.cpp +index 432ec151cf8ae..3bd6ee61024b8 100644 +--- a/llvm-14.0.6.src/lib/AsmParser/LLParser.cpp ++++ b/llvm-14.0.6.src/lib/AsmParser/LLParser.cpp +@@ -1781,6 +1781,9 @@ void LLParser::parseOptionalDLLStorageClass(unsigned &Res) { + /// ::= 'ccc' + /// ::= 'fastcc' + /// ::= 'intel_ocl_bicc' ++/// ::= 'intel_svmlcc128' ++/// ::= 'intel_svmlcc256' ++/// ::= 'intel_svmlcc512' + /// ::= 'coldcc' + /// ::= 'cfguard_checkcc' + /// ::= 'x86_stdcallcc' +@@ -1850,6 +1853,9 @@ bool LLParser::parseOptionalCallingConv(unsigned &CC) { + case lltok::kw_spir_kernel: CC = CallingConv::SPIR_KERNEL; break; + case lltok::kw_spir_func: CC = CallingConv::SPIR_FUNC; break; + case lltok::kw_intel_ocl_bicc: CC = CallingConv::Intel_OCL_BI; break; ++ case lltok::kw_intel_svmlcc128:CC = CallingConv::Intel_SVML128; break; ++ case lltok::kw_intel_svmlcc256:CC = CallingConv::Intel_SVML256; break; ++ case lltok::kw_intel_svmlcc512:CC = CallingConv::Intel_SVML512; break; + case lltok::kw_x86_64_sysvcc: CC = CallingConv::X86_64_SysV; break; + case lltok::kw_win64cc: CC = CallingConv::Win64; break; + case lltok::kw_webkit_jscc: CC = CallingConv::WebKit_JS; break; +diff --git a/llvm-14.0.6.src/lib/CodeGen/ReplaceWithVeclib.cpp b/llvm-14.0.6.src/lib/CodeGen/ReplaceWithVeclib.cpp +index 0ff045fa787e8..175651949ef85 100644 +--- a/llvm-14.0.6.src/lib/CodeGen/ReplaceWithVeclib.cpp ++++ b/llvm-14.0.6.src/lib/CodeGen/ReplaceWithVeclib.cpp +@@ -157,7 +157,7 @@ static bool replaceWithCallToVeclib(const TargetLibraryInfo &TLI, + // and the exact vector width of the call operands in the + // TargetLibraryInfo. + const std::string TLIName = +- std::string(TLI.getVectorizedFunction(ScalarName, VF)); ++ std::string(TLI.getVectorizedFunction(ScalarName, VF, CI.getFastMathFlags().isFast())); + + LLVM_DEBUG(dbgs() << DEBUG_TYPE << ": Looking up TLI mapping for `" + << ScalarName << "` and vector width " << VF << ".\n"); +diff --git a/llvm-14.0.6.src/lib/IR/AsmWriter.cpp b/llvm-14.0.6.src/lib/IR/AsmWriter.cpp +index 179754e275b03..c4e95752c97e8 100644 +--- a/llvm-14.0.6.src/lib/IR/AsmWriter.cpp ++++ b/llvm-14.0.6.src/lib/IR/AsmWriter.cpp +@@ -306,6 +306,9 @@ static void PrintCallingConv(unsigned cc, raw_ostream &Out) { + case CallingConv::X86_RegCall: Out << "x86_regcallcc"; break; + case CallingConv::X86_VectorCall:Out << "x86_vectorcallcc"; break; + case CallingConv::Intel_OCL_BI: Out << "intel_ocl_bicc"; break; ++ case CallingConv::Intel_SVML128: Out << "intel_svmlcc128"; break; ++ case CallingConv::Intel_SVML256: Out << "intel_svmlcc256"; break; ++ case CallingConv::Intel_SVML512: Out << "intel_svmlcc512"; break; + case CallingConv::ARM_APCS: Out << "arm_apcscc"; break; + case CallingConv::ARM_AAPCS: Out << "arm_aapcscc"; break; + case CallingConv::ARM_AAPCS_VFP: Out << "arm_aapcs_vfpcc"; break; +diff --git a/llvm-14.0.6.src/lib/IR/Verifier.cpp b/llvm-14.0.6.src/lib/IR/Verifier.cpp +index 989d01e2e3950..bae7382a36e13 100644 +--- a/llvm-14.0.6.src/lib/IR/Verifier.cpp ++++ b/llvm-14.0.6.src/lib/IR/Verifier.cpp +@@ -2457,6 +2457,9 @@ void Verifier::visitFunction(const Function &F) { + case CallingConv::Fast: + case CallingConv::Cold: + case CallingConv::Intel_OCL_BI: ++ case CallingConv::Intel_SVML128: ++ case CallingConv::Intel_SVML256: ++ case CallingConv::Intel_SVML512: + case CallingConv::PTX_Kernel: + case CallingConv::PTX_Device: + Assert(!F.isVarArg(), "Calling convention does not support varargs or " +diff --git a/llvm-14.0.6.src/lib/Target/X86/X86CallingConv.td b/llvm-14.0.6.src/lib/Target/X86/X86CallingConv.td +index 4dd8a6cdd8982..12e65521215e4 100644 +--- a/llvm-14.0.6.src/lib/Target/X86/X86CallingConv.td ++++ b/llvm-14.0.6.src/lib/Target/X86/X86CallingConv.td +@@ -498,6 +498,21 @@ def RetCC_X86_64 : CallingConv<[ + CCDelegateTo + ]>; + ++// Intel_SVML return-value convention. ++def RetCC_Intel_SVML : CallingConv<[ ++ // Vector types are returned in XMM0,XMM1 ++ CCIfType<[v4f32, v2f64], ++ CCAssignToReg<[XMM0,XMM1]>>, ++ ++ // 256-bit FP vectors ++ CCIfType<[v8f32, v4f64], ++ CCAssignToReg<[YMM0,YMM1]>>, ++ ++ // 512-bit FP vectors ++ CCIfType<[v16f32, v8f64], ++ CCAssignToReg<[ZMM0,ZMM1]>> ++]>; ++ + // This is the return-value convention used for the entire X86 backend. + let Entry = 1 in + def RetCC_X86 : CallingConv<[ +@@ -505,6 +520,10 @@ def RetCC_X86 : CallingConv<[ + // Check if this is the Intel OpenCL built-ins calling convention + CCIfCC<"CallingConv::Intel_OCL_BI", CCDelegateTo>, + ++ CCIfCC<"CallingConv::Intel_SVML128", CCDelegateTo>, ++ CCIfCC<"CallingConv::Intel_SVML256", CCDelegateTo>, ++ CCIfCC<"CallingConv::Intel_SVML512", CCDelegateTo>, ++ + CCIfSubtarget<"is64Bit()", CCDelegateTo>, + CCDelegateTo + ]>; +@@ -1064,6 +1083,30 @@ def CC_Intel_OCL_BI : CallingConv<[ + CCDelegateTo + ]>; + ++// X86-64 Intel Short Vector Math Library calling convention. ++def CC_Intel_SVML : CallingConv<[ ++ ++ // The SSE vector arguments are passed in XMM registers. ++ CCIfType<[v4f32, v2f64], ++ CCAssignToReg<[XMM0, XMM1, XMM2]>>, ++ ++ // The 256-bit vector arguments are passed in YMM registers. ++ CCIfType<[v8f32, v4f64], ++ CCAssignToReg<[YMM0, YMM1, YMM2]>>, ++ ++ // The 512-bit vector arguments are passed in ZMM registers. ++ CCIfType<[v16f32, v8f64], ++ CCAssignToReg<[ZMM0, ZMM1, ZMM2]>> ++]>; ++ ++def CC_X86_32_Intr : CallingConv<[ ++ CCAssignToStack<4, 4> ++]>; ++ ++def CC_X86_64_Intr : CallingConv<[ ++ CCAssignToStack<8, 8> ++]>; ++ + //===----------------------------------------------------------------------===// + // X86 Root Argument Calling Conventions + //===----------------------------------------------------------------------===// +@@ -1115,6 +1158,9 @@ def CC_X86_64 : CallingConv<[ + let Entry = 1 in + def CC_X86 : CallingConv<[ + CCIfCC<"CallingConv::Intel_OCL_BI", CCDelegateTo>, ++ CCIfCC<"CallingConv::Intel_SVML128", CCDelegateTo>, ++ CCIfCC<"CallingConv::Intel_SVML256", CCDelegateTo>, ++ CCIfCC<"CallingConv::Intel_SVML512", CCDelegateTo>, + CCIfSubtarget<"is64Bit()", CCDelegateTo>, + CCDelegateTo + ]>; +@@ -1227,3 +1273,27 @@ def CSR_SysV64_RegCall_NoSSE : CalleeSavedRegs<(add RBX, RBP, + (sequence "R%u", 12, 15))>; + def CSR_SysV64_RegCall : CalleeSavedRegs<(add CSR_SysV64_RegCall_NoSSE, + (sequence "XMM%u", 8, 15))>; ++ ++// SVML calling convention ++def CSR_32_Intel_SVML : CalleeSavedRegs<(add CSR_32_RegCall_NoSSE)>; ++def CSR_32_Intel_SVML_AVX512 : CalleeSavedRegs<(add CSR_32_Intel_SVML, ++ K4, K5, K6, K7)>; ++ ++def CSR_64_Intel_SVML_NoSSE : CalleeSavedRegs<(add RBX, RSI, RDI, RBP, RSP, R12, R13, R14, R15)>; ++ ++def CSR_64_Intel_SVML : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "XMM%u", 8, 15))>; ++def CSR_Win64_Intel_SVML : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "XMM%u", 6, 15))>; ++ ++def CSR_64_Intel_SVML_AVX : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "YMM%u", 8, 15))>; ++def CSR_Win64_Intel_SVML_AVX : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "YMM%u", 6, 15))>; ++ ++def CSR_64_Intel_SVML_AVX512 : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "ZMM%u", 16, 31), ++ K4, K5, K6, K7)>; ++def CSR_Win64_Intel_SVML_AVX512 : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "ZMM%u", 6, 21), ++ K4, K5, K6, K7)>; +diff --git a/llvm-14.0.6.src/lib/Target/X86/X86ISelLowering.cpp b/llvm-14.0.6.src/lib/Target/X86/X86ISelLowering.cpp +index 8bb7e81e19bbd..1780ce3fc6467 100644 +--- a/llvm-14.0.6.src/lib/Target/X86/X86ISelLowering.cpp ++++ b/llvm-14.0.6.src/lib/Target/X86/X86ISelLowering.cpp +@@ -3788,7 +3788,8 @@ void VarArgsLoweringHelper::forwardMustTailParameters(SDValue &Chain) { + // FIXME: Only some x86_32 calling conventions support AVX512. + if (Subtarget.useAVX512Regs() && + (is64Bit() || (CallConv == CallingConv::X86_VectorCall || +- CallConv == CallingConv::Intel_OCL_BI))) ++ CallConv == CallingConv::Intel_OCL_BI || ++ CallConv == CallingConv::Intel_SVML512))) + VecVT = MVT::v16f32; + else if (Subtarget.hasAVX()) + VecVT = MVT::v8f32; +diff --git a/llvm-14.0.6.src/lib/Target/X86/X86RegisterInfo.cpp b/llvm-14.0.6.src/lib/Target/X86/X86RegisterInfo.cpp +index 130cb61cdde24..9eec3b25ca9f2 100644 +--- a/llvm-14.0.6.src/lib/Target/X86/X86RegisterInfo.cpp ++++ b/llvm-14.0.6.src/lib/Target/X86/X86RegisterInfo.cpp +@@ -272,6 +272,42 @@ X86RegisterInfo::getRegPressureLimit(const TargetRegisterClass *RC, + } + } + ++namespace { ++std::pair getSVMLRegMaskAndSaveList( ++ bool Is64Bit, bool IsWin64, CallingConv::ID CC) { ++ assert(CC >= CallingConv::Intel_SVML128 && CC <= CallingConv::Intel_SVML512); ++ unsigned Abi = CC - CallingConv::Intel_SVML128 ; // 0 - 128, 1 - 256, 2 - 512 ++ ++ const std::pair Abi64[] = { ++ std::make_pair(CSR_64_Intel_SVML_RegMask, CSR_64_Intel_SVML_SaveList), ++ std::make_pair(CSR_64_Intel_SVML_AVX_RegMask, CSR_64_Intel_SVML_AVX_SaveList), ++ std::make_pair(CSR_64_Intel_SVML_AVX512_RegMask, CSR_64_Intel_SVML_AVX512_SaveList), ++ }; ++ ++ const std::pair AbiWin64[] = { ++ std::make_pair(CSR_Win64_Intel_SVML_RegMask, CSR_Win64_Intel_SVML_SaveList), ++ std::make_pair(CSR_Win64_Intel_SVML_AVX_RegMask, CSR_Win64_Intel_SVML_AVX_SaveList), ++ std::make_pair(CSR_Win64_Intel_SVML_AVX512_RegMask, CSR_Win64_Intel_SVML_AVX512_SaveList), ++ }; ++ ++ const std::pair Abi32[] = { ++ std::make_pair(CSR_32_Intel_SVML_RegMask, CSR_32_Intel_SVML_SaveList), ++ std::make_pair(CSR_32_Intel_SVML_RegMask, CSR_32_Intel_SVML_SaveList), ++ std::make_pair(CSR_32_Intel_SVML_AVX512_RegMask, CSR_32_Intel_SVML_AVX512_SaveList), ++ }; ++ ++ if (Is64Bit) { ++ if (IsWin64) { ++ return AbiWin64[Abi]; ++ } else { ++ return Abi64[Abi]; ++ } ++ } else { ++ return Abi32[Abi]; ++ } ++} ++} ++ + const MCPhysReg * + X86RegisterInfo::getCalleeSavedRegs(const MachineFunction *MF) const { + assert(MF && "MachineFunction required"); +@@ -327,6 +363,11 @@ X86RegisterInfo::getCalleeSavedRegs(const MachineFunction *MF) const { + return CSR_64_Intel_OCL_BI_SaveList; + break; + } ++ case CallingConv::Intel_SVML128: ++ case CallingConv::Intel_SVML256: ++ case CallingConv::Intel_SVML512: { ++ return getSVMLRegMaskAndSaveList(Is64Bit, IsWin64, CC).second; ++ } + case CallingConv::HHVM: + return CSR_64_HHVM_SaveList; + case CallingConv::X86_RegCall: +@@ -449,6 +490,11 @@ X86RegisterInfo::getCallPreservedMask(const MachineFunction &MF, + return CSR_64_Intel_OCL_BI_RegMask; + break; + } ++ case CallingConv::Intel_SVML128: ++ case CallingConv::Intel_SVML256: ++ case CallingConv::Intel_SVML512: { ++ return getSVMLRegMaskAndSaveList(Is64Bit, IsWin64, CC).first; ++ } + case CallingConv::HHVM: + return CSR_64_HHVM_RegMask; + case CallingConv::X86_RegCall: +diff --git a/llvm-14.0.6.src/lib/Target/X86/X86Subtarget.h b/llvm-14.0.6.src/lib/Target/X86/X86Subtarget.h +index 5d773f0c57dfb..6bdf5bc6f3fe9 100644 +--- a/llvm-14.0.6.src/lib/Target/X86/X86Subtarget.h ++++ b/llvm-14.0.6.src/lib/Target/X86/X86Subtarget.h +@@ -916,6 +916,9 @@ class X86Subtarget final : public X86GenSubtargetInfo { + case CallingConv::X86_ThisCall: + case CallingConv::X86_VectorCall: + case CallingConv::Intel_OCL_BI: ++ case CallingConv::Intel_SVML128: ++ case CallingConv::Intel_SVML256: ++ case CallingConv::Intel_SVML512: + return isTargetWin64(); + // This convention allows using the Win64 convention on other targets. + case CallingConv::Win64: +diff --git a/llvm-14.0.6.src/lib/Transforms/Utils/InjectTLIMappings.cpp b/llvm-14.0.6.src/lib/Transforms/Utils/InjectTLIMappings.cpp +index 047bf5569ded3..59897785f156c 100644 +--- a/llvm-14.0.6.src/lib/Transforms/Utils/InjectTLIMappings.cpp ++++ b/llvm-14.0.6.src/lib/Transforms/Utils/InjectTLIMappings.cpp +@@ -92,7 +92,7 @@ static void addMappingsFromTLI(const TargetLibraryInfo &TLI, CallInst &CI) { + + auto AddVariantDecl = [&](const ElementCount &VF) { + const std::string TLIName = +- std::string(TLI.getVectorizedFunction(ScalarName, VF)); ++ std::string(TLI.getVectorizedFunction(ScalarName, VF, CI.getFastMathFlags().isFast())); + if (!TLIName.empty()) { + std::string MangledName = + VFABI::mangleTLIVectorName(TLIName, ScalarName, CI.arg_size(), VF); +diff --git a/llvm-14.0.6.src/lib/Transforms/Vectorize/LoopVectorize.cpp b/llvm-14.0.6.src/lib/Transforms/Vectorize/LoopVectorize.cpp +index 46ff0994e04e7..f472af5e1a835 100644 +--- a/llvm-14.0.6.src/lib/Transforms/Vectorize/LoopVectorize.cpp ++++ b/llvm-14.0.6.src/lib/Transforms/Vectorize/LoopVectorize.cpp +@@ -712,6 +712,27 @@ class InnerLoopVectorizer { + virtual void printDebugTracesAtStart(){}; + virtual void printDebugTracesAtEnd(){}; + ++ /// Check legality of given SVML call instruction \p VecCall generated for ++ /// scalar call \p Call. If illegal then the appropriate legal instruction ++ /// is returned. ++ Value *legalizeSVMLCall(CallInst *VecCall, CallInst *Call); ++ ++ /// Returns the legal VF for a call instruction \p CI using TTI information ++ /// and vector type. ++ ElementCount getLegalVFForCall(CallInst *CI); ++ ++ /// Partially vectorize a given call \p Call by breaking it down into multiple ++ /// calls of \p LegalCall, decided by the variant VF \p LegalVF. ++ Value *partialVectorizeCall(CallInst *Call, CallInst *LegalCall, ++ unsigned LegalVF); ++ ++ /// Generate shufflevector instruction for a vector value \p V based on the ++ /// current \p Part and a smaller VF \p LegalVF. ++ Value *generateShuffleValue(Value *V, unsigned LegalVF, unsigned Part); ++ ++ /// Combine partially vectorized calls stored in \p CallResults. ++ Value *combinePartialVecCalls(SmallVectorImpl &CallResults); ++ + /// The original loop. + Loop *OrigLoop; + +@@ -4596,6 +4617,17 @@ static bool mayDivideByZero(Instruction &I) { + return !CInt || CInt->isZero(); + } + ++static void setVectorFunctionCallingConv(CallInst &CI, const DataLayout &DL, ++ const TargetLibraryInfo &TLI) { ++ Function *VectorF = CI.getCalledFunction(); ++ FunctionType *FTy = VectorF->getFunctionType(); ++ StringRef VFName = VectorF->getName(); ++ auto CC = TLI.getVectorizedFunctionCallingConv(VFName, *FTy, DL); ++ if (CC) { ++ CI.setCallingConv(*CC); ++ } ++} ++ + void InnerLoopVectorizer::widenCallInstruction(CallInst &I, VPValue *Def, + VPUser &ArgOperands, + VPTransformState &State) { +@@ -4664,9 +4696,246 @@ void InnerLoopVectorizer::widenCallInstruction(CallInst &I, VPValue *Def, + if (isa(V)) + V->copyFastMathFlags(CI); + ++ const DataLayout &DL = V->getModule()->getDataLayout(); ++ setVectorFunctionCallingConv(*V, DL, *TLI); ++ ++ // Perform legalization of SVML call instruction only if original call ++ // was not Intrinsic ++ if (!UseVectorIntrinsic && ++ (V->getCalledFunction()->getName()).startswith("__svml")) { ++ // assert((V->getCalledFunction()->getName()).startswith("__svml")); ++ LLVM_DEBUG(dbgs() << "LV(SVML): Vector call inst:"; V->dump()); ++ auto *LegalV = cast(legalizeSVMLCall(V, CI)); ++ LLVM_DEBUG(dbgs() << "LV: Completed SVML legalization.\n LegalV: "; ++ LegalV->dump()); ++ State.set(Def, LegalV, Part); ++ addMetadata(LegalV, &I); ++ } else { + State.set(Def, V, Part); + addMetadata(V, &I); ++ } ++ } ++} ++ ++//===----------------------------------------------------------------------===// ++// Implementation of functions for SVML vector call legalization. ++//===----------------------------------------------------------------------===// ++// ++// Unlike other VECLIBs, SVML needs to be used with target-legal ++// vector types. Otherwise, link failures and/or runtime failures ++// will occur. A motivating example could be - ++// ++// double *a; ++// float *b; ++// #pragma clang loop vectorize_width(8) ++// for(i = 0; i < N; ++i) { ++// a[i] = sin(i); // Legal SVML VF must be 4 or below on AVX ++// b[i] = cosf(i); // VF can be 8 on AVX since 8 floats can fit in YMM ++// } ++// ++// Current implementation of vector code generation in LV is ++// driven based on a single VF (in InnerLoopVectorizer::VF). This ++// inhibits the flexibility of adjusting/choosing different VF ++// for different instructions. ++// ++// Due to this limitation it is much more straightforward to ++// first generate the illegal sin8 (svml_sin8 for SVML vector ++// library) call and then legalize it than trying to avoid ++// generating illegal code from the beginning. ++// ++// A solution for this problem is to check legality of the ++// call instruction right after generating it in vectorizer and ++// if it is illegal we split the call arguments and issue multiple ++// calls to match the legal VF. This is demonstrated currently for ++// the SVML vector library calls (non-intrinsic version only). ++// ++// Future directions and extensions: ++// 1) This legalization example shows us that a good direction ++// for the VPlan framework would be to model the vector call ++// instructions in a way that legal VF for each call is chosen ++// correctly within vectorizer and illegal code generation is ++// avoided. ++// 2) This logic can also be extended to general vector functions ++// i.e. legalization OpenMP decalre simd functions. The ++// requirements needed for this will be documented soon. ++ ++Value *InnerLoopVectorizer::legalizeSVMLCall(CallInst *VecCall, ++ CallInst *Call) { ++ ElementCount LegalVF = getLegalVFForCall(VecCall); ++ ++ assert(LegalVF.getKnownMinValue() > 1 && ++ "Legal VF for SVML call must be greater than 1 to vectorize"); ++ ++ if (LegalVF == VF) ++ return VecCall; ++ else if (LegalVF.getKnownMinValue() > VF.getKnownMinValue()) ++ // TODO: handle case when we are underfilling vectors ++ return VecCall; ++ ++ // Legal VF for this SVML call is smaller than chosen VF, break it down into ++ // smaller call instructions ++ ++ // Convert args, types and return type to match legal VF ++ SmallVector NewTys; ++ SmallVector NewArgs; ++ ++ for (Value *ArgOperand : Call->args()) { ++ Type *Ty = ToVectorTy(ArgOperand->getType(), LegalVF); ++ NewTys.push_back(Ty); ++ NewArgs.push_back(UndefValue::get(Ty)); + } ++ ++ // Construct legal vector function ++ const VFShape Shape = ++ VFShape::get(*Call, LegalVF /*EC*/, false /*HasGlobalPred*/); ++ Function *LegalVectorF = VFDatabase(*Call).getVectorizedFunction(Shape); ++ assert(LegalVectorF != nullptr && "Can't create legal vector function."); ++ ++ LLVM_DEBUG(dbgs() << "LV(SVML): LegalVectorF: "; LegalVectorF->dump()); ++ ++ SmallVector OpBundles; ++ Call->getOperandBundlesAsDefs(OpBundles); ++ auto LegalV = std::unique_ptr(CallInst::Create(LegalVectorF, NewArgs, OpBundles)); ++ ++ if (isa(LegalV)) ++ LegalV->copyFastMathFlags(Call); ++ ++ const DataLayout &DL = VecCall->getModule()->getDataLayout(); ++ // Set SVML calling conventions ++ setVectorFunctionCallingConv(*LegalV, DL, *TLI); ++ ++ LLVM_DEBUG(dbgs() << "LV(SVML): LegalV: "; LegalV->dump()); ++ ++ Value *LegalizedCall = partialVectorizeCall(VecCall, LegalV.get(), LegalVF.getKnownMinValue()); ++ ++ LLVM_DEBUG(dbgs() << "LV(SVML): LegalizedCall: "; LegalizedCall->dump()); ++ ++ // Remove the illegal call from Builder ++ VecCall->eraseFromParent(); ++ ++ return LegalizedCall; ++} ++ ++ElementCount InnerLoopVectorizer::getLegalVFForCall(CallInst *CI) { ++ const DataLayout DL = CI->getModule()->getDataLayout(); ++ FunctionType *CallFT = CI->getFunctionType(); ++ // All functions that need legalization should have a vector return type. ++ // This is true for all SVML functions that are currently supported. ++ assert(isa(CallFT->getReturnType()) && ++ "Return type of call that needs legalization is not a vector."); ++ auto *VecCallRetType = cast(CallFT->getReturnType()); ++ Type *ElemType = VecCallRetType->getElementType(); ++ ++ unsigned TypeBitWidth = DL.getTypeSizeInBits(ElemType); ++ unsigned VectorBitWidth = TTI->getRegisterBitWidth(TargetTransformInfo::RGK_FixedWidthVector); ++ unsigned LegalVF = VectorBitWidth / TypeBitWidth; ++ ++ LLVM_DEBUG(dbgs() << "LV(SVML): Type Bit Width: " << TypeBitWidth << "\n"); ++ LLVM_DEBUG(dbgs() << "LV(SVML): Current VL: " << VF << "\n"); ++ LLVM_DEBUG(dbgs() << "LV(SVML): Vector Bit Width: " << VectorBitWidth ++ << "\n"); ++ LLVM_DEBUG(dbgs() << "LV(SVML): Legal Target VL: " << LegalVF << "\n"); ++ ++ return ElementCount::getFixed(LegalVF); ++} ++ ++// Partial vectorization of a call instruction is achieved by making clones of ++// \p LegalCall and overwriting its argument operands with shufflevector ++// equivalent decided based on \p LegalVF and current Part being filled. ++Value *InnerLoopVectorizer::partialVectorizeCall(CallInst *Call, ++ CallInst *LegalCall, ++ unsigned LegalVF) { ++ unsigned NumParts = VF.getKnownMinValue() / LegalVF; ++ LLVM_DEBUG(dbgs() << "LV(SVML): NumParts: " << NumParts << "\n"); ++ SmallVector CallResults; ++ ++ for (unsigned Part = 0; Part < NumParts; ++Part) { ++ auto *ClonedCall = cast(LegalCall->clone()); ++ ++ // Update the arg operand of cloned call to shufflevector ++ for (unsigned i = 0, ie = Call->arg_size(); i != ie; ++i) { ++ auto *NewOp = generateShuffleValue(Call->getArgOperand(i), LegalVF, Part); ++ ClonedCall->setArgOperand(i, NewOp); ++ } ++ ++ LLVM_DEBUG(dbgs() << "LV(SVML): ClonedCall: "; ClonedCall->dump()); ++ ++ auto *PartialVecCall = Builder.Insert(ClonedCall); ++ CallResults.push_back(PartialVecCall); ++ } ++ ++ return combinePartialVecCalls(CallResults); ++} ++ ++Value *InnerLoopVectorizer::generateShuffleValue(Value *V, unsigned LegalVF, ++ unsigned Part) { ++ // Example: ++ // Consider the following vector code - ++ // %1 = sitofp <4 x i32> %0 to <4 x double> ++ // %2 = call <4 x double> @__svml_sin4(<4 x double> %1) ++ // ++ // If the LegalVF is 2, we partially vectorize the sin4 call by invoking ++ // generateShuffleValue on the operand %1 ++ // If Part = 1, output value is - ++ // %shuffle = shufflevector <4 x double> %1, <4 x double> undef, <2 x i32> ++ // and if Part = 2, output is - ++ // %shuffle7 =shufflevector <4 x double> %1, <4 x double> undef, <2 x i32> ++ ++ assert(isa(V->getType()) && ++ "Cannot generate shuffles for non-vector values."); ++ SmallVector ShuffleMask; ++ Value *Undef = UndefValue::get(V->getType()); ++ ++ unsigned ElemIdx = Part * LegalVF; ++ ++ for (unsigned K = 0; K < LegalVF; K++) ++ ShuffleMask.push_back(static_cast(ElemIdx + K)); ++ ++ auto *ShuffleInst = ++ Builder.CreateShuffleVector(V, Undef, ShuffleMask, "shuffle"); ++ ++ return ShuffleInst; ++} ++ ++// Results of the calls executed by smaller legal call instructions must be ++// combined to match the original VF for later use. This is done by constructing ++// shufflevector instructions in a cumulative fashion. ++Value *InnerLoopVectorizer::combinePartialVecCalls( ++ SmallVectorImpl &CallResults) { ++ assert(isa(CallResults[0]->getType()) && ++ "Cannot combine calls with non-vector results."); ++ auto *CallType = cast(CallResults[0]->getType()); ++ ++ Value *CombinedShuffle; ++ unsigned NumElems = CallType->getElementCount().getKnownMinValue() * 2; ++ unsigned NumRegs = CallResults.size(); ++ ++ assert(NumRegs >= 2 && isPowerOf2_32(NumRegs) && ++ "Number of partial vector calls to combine must be a power of 2 " ++ "(atleast 2^1)"); ++ ++ while (NumRegs > 1) { ++ for (unsigned I = 0; I < NumRegs; I += 2) { ++ SmallVector ShuffleMask; ++ for (unsigned J = 0; J < NumElems; J++) ++ ShuffleMask.push_back(static_cast(J)); ++ ++ CombinedShuffle = Builder.CreateShuffleVector( ++ CallResults[I], CallResults[I + 1], ShuffleMask, "combined"); ++ LLVM_DEBUG(dbgs() << "LV(SVML): CombinedShuffle:"; ++ CombinedShuffle->dump()); ++ CallResults.push_back(CombinedShuffle); ++ } ++ ++ SmallVector::iterator Start = CallResults.begin(); ++ SmallVector::iterator End = Start + NumRegs; ++ CallResults.erase(Start, End); ++ ++ NumElems *= 2; ++ NumRegs /= 2; ++ } ++ ++ return CombinedShuffle; + } + + void LoopVectorizationCostModel::collectLoopScalars(ElementCount VF) { +diff --git a/llvm-14.0.6.src/lib/Transforms/Vectorize/SLPVectorizer.cpp b/llvm-14.0.6.src/lib/Transforms/Vectorize/SLPVectorizer.cpp +index 644372483edde..342f018b92184 100644 +--- a/llvm-14.0.6.src/lib/Transforms/Vectorize/SLPVectorizer.cpp ++++ b/llvm-14.0.6.src/lib/Transforms/Vectorize/SLPVectorizer.cpp +@@ -6322,6 +6322,17 @@ Value *BoUpSLP::vectorizeTree(ArrayRef VL) { + return Vec; + } + ++static void setVectorFunctionCallingConv(CallInst &CI, const DataLayout &DL, ++ const TargetLibraryInfo &TLI) { ++ Function *VectorF = CI.getCalledFunction(); ++ FunctionType *FTy = VectorF->getFunctionType(); ++ StringRef VFName = VectorF->getName(); ++ auto CC = TLI.getVectorizedFunctionCallingConv(VFName, *FTy, DL); ++ if (CC) { ++ CI.setCallingConv(*CC); ++ } ++} ++ + Value *BoUpSLP::vectorizeTree(TreeEntry *E) { + IRBuilder<>::InsertPointGuard Guard(Builder); + +@@ -6794,7 +6805,12 @@ Value *BoUpSLP::vectorizeTree(TreeEntry *E) { + + SmallVector OpBundles; + CI->getOperandBundlesAsDefs(OpBundles); +- Value *V = Builder.CreateCall(CF, OpVecs, OpBundles); ++ ++ CallInst *NewCall = Builder.CreateCall(CF, OpVecs, OpBundles); ++ const DataLayout &DL = NewCall->getModule()->getDataLayout(); ++ setVectorFunctionCallingConv(*NewCall, DL, *TLI); ++ ++ Value *V = NewCall; + + // The scalar argument uses an in-tree scalar so we add the new vectorized + // call to ExternalUses list to make sure that an extract will be +diff --git a/llvm-14.0.6.src/test/CodeGen/Generic/replace-intrinsics-with-veclib.ll b/llvm-14.0.6.src/test/CodeGen/Generic/replace-intrinsics-with-veclib.ll +index df8b7c498bd00..63a36549f18fd 100644 +--- a/llvm-14.0.6.src/test/CodeGen/Generic/replace-intrinsics-with-veclib.ll ++++ b/llvm-14.0.6.src/test/CodeGen/Generic/replace-intrinsics-with-veclib.ll +@@ -10,7 +10,7 @@ target triple = "x86_64-unknown-linux-gnu" + define <4 x double> @exp_v4(<4 x double> %in) { + ; SVML-LABEL: define {{[^@]+}}@exp_v4 + ; SVML-SAME: (<4 x double> [[IN:%.*]]) { +-; SVML-NEXT: [[TMP1:%.*]] = call <4 x double> @__svml_exp4(<4 x double> [[IN]]) ++; SVML-NEXT: [[TMP1:%.*]] = call <4 x double> @__svml_exp4_ha(<4 x double> [[IN]]) + ; SVML-NEXT: ret <4 x double> [[TMP1]] + ; + ; LIBMVEC-X86-LABEL: define {{[^@]+}}@exp_v4 +@@ -37,7 +37,7 @@ declare <4 x double> @llvm.exp.v4f64(<4 x double>) #0 + define <4 x float> @exp_f32(<4 x float> %in) { + ; SVML-LABEL: define {{[^@]+}}@exp_f32 + ; SVML-SAME: (<4 x float> [[IN:%.*]]) { +-; SVML-NEXT: [[TMP1:%.*]] = call <4 x float> @__svml_expf4(<4 x float> [[IN]]) ++; SVML-NEXT: [[TMP1:%.*]] = call <4 x float> @__svml_expf4_ha(<4 x float> [[IN]]) + ; SVML-NEXT: ret <4 x float> [[TMP1]] + ; + ; LIBMVEC-X86-LABEL: define {{[^@]+}}@exp_f32 +diff --git a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls-finite.ll b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls-finite.ll +index a6e191c3d6923..d6e2e11106949 100644 +--- a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls-finite.ll ++++ b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls-finite.ll +@@ -39,7 +39,8 @@ for.end: ; preds = %for.body + declare double @__exp_finite(double) #0 + + ; CHECK-LABEL: @exp_f64 +-; CHECK: <4 x double> @__svml_exp4 ++; CHECK: <2 x double> @__svml_exp2 ++; CHECK: <2 x double> @__svml_exp2 + ; CHECK: ret + define void @exp_f64(double* nocapture %varray) { + entry: +@@ -99,7 +100,8 @@ for.end: ; preds = %for.body + declare double @__log_finite(double) #0 + + ; CHECK-LABEL: @log_f64 +-; CHECK: <4 x double> @__svml_log4 ++; CHECK: <2 x double> @__svml_log2 ++; CHECK: <2 x double> @__svml_log2 + ; CHECK: ret + define void @log_f64(double* nocapture %varray) { + entry: +@@ -159,7 +161,8 @@ for.end: ; preds = %for.body + declare double @__pow_finite(double, double) #0 + + ; CHECK-LABEL: @pow_f64 +-; CHECK: <4 x double> @__svml_pow4 ++; CHECK: <2 x double> @__svml_pow2 ++; CHECK: <2 x double> @__svml_pow2 + ; CHECK: ret + define void @pow_f64(double* nocapture %varray, double* nocapture readonly %exp) { + entry: +@@ -190,7 +193,8 @@ declare float @__exp2f_finite(float) #0 + + define void @exp2f_finite(float* nocapture %varray) { + ; CHECK-LABEL: @exp2f_finite( +-; CHECK: call <4 x float> @__svml_exp2f4(<4 x float> %{{.*}}) ++; CHECK: call intel_svmlcc128 <4 x float> @__svml_exp2f4_ha(<4 x float> %{{.*}}) ++; CHECK: call intel_svmlcc128 <4 x float> @__svml_exp2f4_ha(<4 x float> %{{.*}}) + ; CHECK: ret void + ; + entry: +@@ -219,7 +223,8 @@ declare double @__exp2_finite(double) #0 + + define void @exp2_finite(double* nocapture %varray) { + ; CHECK-LABEL: @exp2_finite( +-; CHECK: call <4 x double> @__svml_exp24(<4 x double> {{.*}}) ++; CHECK: call intel_svmlcc128 <2 x double> @__svml_exp22_ha(<2 x double> {{.*}}) ++; CHECK: call intel_svmlcc128 <2 x double> @__svml_exp22_ha(<2 x double> {{.*}}) + ; CHECK: ret void + ; + entry: +@@ -276,7 +281,8 @@ for.end: ; preds = %for.body + declare double @__log2_finite(double) #0 + + ; CHECK-LABEL: @log2_f64 +-; CHECK: <4 x double> @__svml_log24 ++; CHECK: <2 x double> @__svml_log22 ++; CHECK: <2 x double> @__svml_log22 + ; CHECK: ret + define void @log2_f64(double* nocapture %varray) { + entry: +@@ -333,7 +339,8 @@ for.end: ; preds = %for.body + declare double @__log10_finite(double) #0 + + ; CHECK-LABEL: @log10_f64 +-; CHECK: <4 x double> @__svml_log104 ++; CHECK: <2 x double> @__svml_log102 ++; CHECK: <2 x double> @__svml_log102 + ; CHECK: ret + define void @log10_f64(double* nocapture %varray) { + entry: +@@ -390,7 +397,8 @@ for.end: ; preds = %for.body + declare double @__sqrt_finite(double) #0 + + ; CHECK-LABEL: @sqrt_f64 +-; CHECK: <4 x double> @__svml_sqrt4 ++; CHECK: <2 x double> @__svml_sqrt2 ++; CHECK: <2 x double> @__svml_sqrt2 + ; CHECK: ret + define void @sqrt_f64(double* nocapture %varray) { + entry: +diff --git a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls.ll b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls.ll +index 42c280df6ad02..088bbdcf1aa4a 100644 +--- a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls.ll ++++ b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls.ll +@@ -48,7 +48,7 @@ declare float @llvm.exp2.f32(float) #0 + + define void @sin_f64(double* nocapture %varray) { + ; CHECK-LABEL: @sin_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_sin4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -71,7 +71,7 @@ for.end: + + define void @sin_f32(float* nocapture %varray) { + ; CHECK-LABEL: @sin_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_sinf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_sinf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -94,7 +94,7 @@ for.end: + + define void @sin_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @sin_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_sin4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -117,7 +117,7 @@ for.end: + + define void @sin_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @sin_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_sinf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_sinf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -140,7 +140,7 @@ for.end: + + define void @cos_f64(double* nocapture %varray) { + ; CHECK-LABEL: @cos_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_cos4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -163,7 +163,7 @@ for.end: + + define void @cos_f32(float* nocapture %varray) { + ; CHECK-LABEL: @cos_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_cosf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_cosf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -186,7 +186,7 @@ for.end: + + define void @cos_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @cos_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_cos4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -209,7 +209,7 @@ for.end: + + define void @cos_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @cos_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_cosf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_cosf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -232,7 +232,7 @@ for.end: + + define void @pow_f64(double* nocapture %varray, double* nocapture readonly %exp) { + ; CHECK-LABEL: @pow_f64( +-; CHECK: [[TMP8:%.*]] = call <4 x double> @__svml_pow4(<4 x double> [[TMP4:%.*]], <4 x double> [[WIDE_LOAD:%.*]]) ++; CHECK: [[TMP8:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP4:%.*]], <4 x double> [[WIDE_LOAD:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -257,7 +257,7 @@ for.end: + + define void @pow_f64_intrinsic(double* nocapture %varray, double* nocapture readonly %exp) { + ; CHECK-LABEL: @pow_f64_intrinsic( +-; CHECK: [[TMP8:%.*]] = call <4 x double> @__svml_pow4(<4 x double> [[TMP4:%.*]], <4 x double> [[WIDE_LOAD:%.*]]) ++; CHECK: [[TMP8:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP4:%.*]], <4 x double> [[WIDE_LOAD:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -282,7 +282,7 @@ for.end: + + define void @pow_f32(float* nocapture %varray, float* nocapture readonly %exp) { + ; CHECK-LABEL: @pow_f32( +-; CHECK: [[TMP8:%.*]] = call <4 x float> @__svml_powf4(<4 x float> [[TMP4:%.*]], <4 x float> [[WIDE_LOAD:%.*]]) ++; CHECK: [[TMP8:%.*]] = call intel_svmlcc128 <4 x float> @__svml_powf4_ha(<4 x float> [[TMP4:%.*]], <4 x float> [[WIDE_LOAD:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -307,7 +307,7 @@ for.end: + + define void @pow_f32_intrinsic(float* nocapture %varray, float* nocapture readonly %exp) { + ; CHECK-LABEL: @pow_f32_intrinsic( +-; CHECK: [[TMP8:%.*]] = call <4 x float> @__svml_powf4(<4 x float> [[TMP4:%.*]], <4 x float> [[WIDE_LOAD:%.*]]) ++; CHECK: [[TMP8:%.*]] = call intel_svmlcc128 <4 x float> @__svml_powf4_ha(<4 x float> [[TMP4:%.*]], <4 x float> [[WIDE_LOAD:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -332,7 +332,7 @@ for.end: + + define void @exp_f64(double* nocapture %varray) { + ; CHECK-LABEL: @exp_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_exp4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -355,7 +355,7 @@ for.end: + + define void @exp_f32(float* nocapture %varray) { + ; CHECK-LABEL: @exp_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_expf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_expf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -378,7 +378,7 @@ for.end: + + define void @exp_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @exp_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_exp4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -401,7 +401,7 @@ for.end: + + define void @exp_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @exp_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_expf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_expf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -424,7 +424,7 @@ for.end: + + define void @log_f64(double* nocapture %varray) { + ; CHECK-LABEL: @log_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -447,7 +447,7 @@ for.end: + + define void @log_f32(float* nocapture %varray) { + ; CHECK-LABEL: @log_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_logf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_logf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -470,7 +470,7 @@ for.end: + + define void @log_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @log_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -493,7 +493,7 @@ for.end: + + define void @log_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @log_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_logf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_logf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -516,7 +516,7 @@ for.end: + + define void @log2_f64(double* nocapture %varray) { + ; CHECK-LABEL: @log2_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log24(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log24_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -539,7 +539,7 @@ for.end: + + define void @log2_f32(float* nocapture %varray) { + ; CHECK-LABEL: @log2_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_log2f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_log2f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -562,7 +562,7 @@ for.end: + + define void @log2_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @log2_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log24(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log24_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -585,7 +585,7 @@ for.end: + + define void @log2_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @log2_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_log2f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_log2f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -608,7 +608,7 @@ for.end: + + define void @log10_f64(double* nocapture %varray) { + ; CHECK-LABEL: @log10_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log104(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log104_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -631,7 +631,7 @@ for.end: + + define void @log10_f32(float* nocapture %varray) { + ; CHECK-LABEL: @log10_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_log10f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_log10f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -654,7 +654,7 @@ for.end: + + define void @log10_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @log10_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log104(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log104_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -677,7 +677,7 @@ for.end: + + define void @log10_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @log10_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_log10f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_log10f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -700,7 +700,7 @@ for.end: + + define void @sqrt_f64(double* nocapture %varray) { + ; CHECK-LABEL: @sqrt_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_sqrt4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sqrt4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -723,7 +723,7 @@ for.end: + + define void @sqrt_f32(float* nocapture %varray) { + ; CHECK-LABEL: @sqrt_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_sqrtf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_sqrtf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -746,7 +746,7 @@ for.end: + + define void @exp2_f64(double* nocapture %varray) { + ; CHECK-LABEL: @exp2_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_exp24(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp24_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -769,7 +769,7 @@ for.end: + + define void @exp2_f32(float* nocapture %varray) { + ; CHECK-LABEL: @exp2_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_exp2f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_exp2f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -792,7 +792,7 @@ for.end: + + define void @exp2_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @exp2_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_exp24(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp24_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -815,7 +815,7 @@ for.end: + + define void @exp2_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @exp2_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_exp2f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_exp2f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -836,4 +836,44 @@ for.end: + ret void + } + ++; CHECK-LABEL: @atan2_finite ++; CHECK: intel_svmlcc256 <4 x double> @__svml_atan24( ++; CHECK: intel_svmlcc256 <4 x double> @__svml_atan24( ++; CHECK: ret ++ ++declare double @__atan2_finite(double, double) local_unnamed_addr #0 ++ ++define void @atan2_finite([100 x double]* nocapture %varray) local_unnamed_addr #0 { ++entry: ++ br label %for.cond1.preheader ++ ++for.cond1.preheader: ; preds = %for.inc7, %entry ++ %indvars.iv19 = phi i64 [ 0, %entry ], [ %indvars.iv.next20, %for.inc7 ] ++ %0 = trunc i64 %indvars.iv19 to i32 ++ %conv = sitofp i32 %0 to double ++ br label %for.body3 ++ ++for.body3: ; preds = %for.body3, %for.cond1.preheader ++ %indvars.iv = phi i64 [ 0, %for.cond1.preheader ], [ %indvars.iv.next, %for.body3 ] ++ %indvars.iv.next = add nuw nsw i64 %indvars.iv, 1 ++ %1 = trunc i64 %indvars.iv.next to i32 ++ %conv4 = sitofp i32 %1 to double ++ %call = tail call fast double @__atan2_finite(double %conv, double %conv4) ++ %arrayidx6 = getelementptr inbounds [100 x double], [100 x double]* %varray, i64 %indvars.iv19, i64 %indvars.iv ++ store double %call, double* %arrayidx6, align 8 ++ %exitcond = icmp eq i64 %indvars.iv.next, 100 ++ br i1 %exitcond, label %for.inc7, label %for.body3, !llvm.loop !5 ++ ++for.inc7: ; preds = %for.body3 ++ %indvars.iv.next20 = add nuw nsw i64 %indvars.iv19, 1 ++ %exitcond21 = icmp eq i64 %indvars.iv.next20, 100 ++ br i1 %exitcond21, label %for.end9, label %for.cond1.preheader ++ ++for.end9: ; preds = %for.inc7 ++ ret void ++} ++ + attributes #0 = { nounwind readnone } ++!5 = distinct !{!5, !6, !7} ++!6 = !{!"llvm.loop.vectorize.width", i32 8} ++!7 = !{!"llvm.loop.vectorize.enable", i1 true} +diff --git a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-calls.ll b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-calls.ll +new file mode 100644 +index 0000000000000..326c763994343 +--- /dev/null ++++ b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-calls.ll +@@ -0,0 +1,513 @@ ++; Check legalization of SVML calls, including intrinsic versions (like @llvm..). ++ ++; RUN: opt -vector-library=SVML -inject-tli-mappings -loop-vectorize -force-vector-width=8 -force-vector-interleave=1 -mattr=avx -S < %s | FileCheck %s ++ ++target datalayout = "e-m:e-i64:64-f80:128-n8:16:32:64-S128" ++target triple = "x86_64-unknown-linux-gnu" ++ ++declare double @sin(double) #0 ++declare float @sinf(float) #0 ++declare double @llvm.sin.f64(double) #0 ++declare float @llvm.sin.f32(float) #0 ++ ++declare double @cos(double) #0 ++declare float @cosf(float) #0 ++declare double @llvm.cos.f64(double) #0 ++declare float @llvm.cos.f32(float) #0 ++ ++declare double @pow(double, double) #0 ++declare float @powf(float, float) #0 ++declare double @llvm.pow.f64(double, double) #0 ++declare float @llvm.pow.f32(float, float) #0 ++ ++declare double @exp(double) #0 ++declare float @expf(float) #0 ++declare double @llvm.exp.f64(double) #0 ++declare float @llvm.exp.f32(float) #0 ++ ++declare double @log(double) #0 ++declare float @logf(float) #0 ++declare double @llvm.log.f64(double) #0 ++declare float @llvm.log.f32(float) #0 ++ ++ ++define void @sin_f64(double* nocapture %varray) { ++; CHECK-LABEL: @sin_f64( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @sin(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @sin_f32(float* nocapture %varray) { ++; CHECK-LABEL: @sin_f32( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_sinf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @sinf(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @sin_f64_intrinsic(double* nocapture %varray) { ++; CHECK-LABEL: @sin_f64_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @llvm.sin.f64(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @sin_f32_intrinsic(float* nocapture %varray) { ++; CHECK-LABEL: @sin_f32_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_sinf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @llvm.sin.f32(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @cos_f64(double* nocapture %varray) { ++; CHECK-LABEL: @cos_f64( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @cos(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @cos_f32(float* nocapture %varray) { ++; CHECK-LABEL: @cos_f32( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_cosf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @cosf(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @cos_f64_intrinsic(double* nocapture %varray) { ++; CHECK-LABEL: @cos_f64_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @llvm.cos.f64(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @cos_f32_intrinsic(float* nocapture %varray) { ++; CHECK-LABEL: @cos_f32_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_cosf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @llvm.cos.f32(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @pow_f64(double* nocapture %varray, double* nocapture readonly %exp) { ++; CHECK-LABEL: @pow_f64( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP2:%.*]], <4 x double> [[TMP3:%.*]]) ++; CHECK: [[TMP4:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP5:%.*]], <4 x double> [[TMP6:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %arrayidx = getelementptr inbounds double, double* %exp, i64 %iv ++ %tmp1 = load double, double* %arrayidx, align 4 ++ %tmp2 = tail call double @pow(double %conv, double %tmp1) ++ %arrayidx2 = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %tmp2, double* %arrayidx2, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @pow_f64_intrinsic(double* nocapture %varray, double* nocapture readonly %exp) { ++; CHECK-LABEL: @pow_f64_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP2:%.*]], <4 x double> [[TMP3:%.*]]) ++; CHECK: [[TMP4:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP5:%.*]], <4 x double> [[TMP6:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %arrayidx = getelementptr inbounds double, double* %exp, i64 %iv ++ %tmp1 = load double, double* %arrayidx, align 4 ++ %tmp2 = tail call double @llvm.pow.f64(double %conv, double %tmp1) ++ %arrayidx2 = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %tmp2, double* %arrayidx2, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @pow_f32(float* nocapture %varray, float* nocapture readonly %exp) { ++; CHECK-LABEL: @pow_f32( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_powf8_ha(<8 x float> [[TMP2:%.*]], <8 x float> [[WIDE_LOAD:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %arrayidx = getelementptr inbounds float, float* %exp, i64 %iv ++ %tmp1 = load float, float* %arrayidx, align 4 ++ %tmp2 = tail call float @powf(float %conv, float %tmp1) ++ %arrayidx2 = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %tmp2, float* %arrayidx2, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @pow_f32_intrinsic(float* nocapture %varray, float* nocapture readonly %exp) { ++; CHECK-LABEL: @pow_f32_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_powf8_ha(<8 x float> [[TMP2:%.*]], <8 x float> [[TMP3:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %arrayidx = getelementptr inbounds float, float* %exp, i64 %iv ++ %tmp1 = load float, float* %arrayidx, align 4 ++ %tmp2 = tail call float @llvm.pow.f32(float %conv, float %tmp1) ++ %arrayidx2 = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %tmp2, float* %arrayidx2, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @exp_f64(double* nocapture %varray) { ++; CHECK-LABEL: @exp_f64( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @exp(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @exp_f32(float* nocapture %varray) { ++; CHECK-LABEL: @exp_f32( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_expf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @expf(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @exp_f64_intrinsic(double* nocapture %varray) { ++; CHECK-LABEL: @exp_f64_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @llvm.exp.f64(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @exp_f32_intrinsic(float* nocapture %varray) { ++; CHECK-LABEL: @exp_f32_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_expf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @llvm.exp.f32(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @log_f64(double* nocapture %varray) { ++; CHECK-LABEL: @log_f64( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @log(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @log_f32(float* nocapture %varray) { ++; CHECK-LABEL: @log_f32( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_logf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @logf(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @log_f64_intrinsic(double* nocapture %varray) { ++; CHECK-LABEL: @log_f64_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @llvm.log.f64(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @log_f32_intrinsic(float* nocapture %varray) { ++; CHECK-LABEL: @log_f32_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_logf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @llvm.log.f32(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++attributes #0 = { nounwind readnone } ++ +diff --git a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-codegen.ll b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-codegen.ll +new file mode 100644 +index 0000000000000..9422653445dc2 +--- /dev/null ++++ b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-codegen.ll +@@ -0,0 +1,61 @@ ++; Check that vector codegen splits illegal sin8 call to two sin4 calls on AVX for double datatype. ++; The C code used to generate this test: ++ ++; #include ++; ++; void foo(double *a, int N){ ++; int i; ++; #pragma clang loop vectorize_width(8) ++; for (i=0;i [[I0:%.*]] to <8 x double> ++; CHECK-NEXT: [[S1:%shuffle.*]] = shufflevector <8 x double> [[I1]], <8 x double> undef, <4 x i32> ++; CHECK-NEXT: [[I2:%.*]] = call fast intel_svmlcc256 <4 x double> @__svml_sin4(<4 x double> [[S1]]) ++; CHECK-NEXT: [[S2:%shuffle.*]] = shufflevector <8 x double> [[I1]], <8 x double> undef, <4 x i32> ++; CHECK-NEXT: [[I3:%.*]] = call fast intel_svmlcc256 <4 x double> @__svml_sin4(<4 x double> [[S2]]) ++; CHECK-NEXT: [[comb:%combined.*]] = shufflevector <4 x double> [[I2]], <4 x double> [[I3]], <8 x i32> ++; CHECK: store <8 x double> [[comb]], <8 x double>* [[TMP:%.*]], align 8 ++ ++ ++target datalayout = "e-m:e-i64:64-f80:128-n8:16:32:64-S128" ++target triple = "x86_64-unknown-linux-gnu" ++ ++; Function Attrs: nounwind uwtable ++define dso_local void @foo(double* nocapture %a, i32 %N) local_unnamed_addr #0 { ++entry: ++ %cmp5 = icmp sgt i32 %N, 0 ++ br i1 %cmp5, label %for.body.preheader, label %for.end ++ ++for.body.preheader: ; preds = %entry ++ %wide.trip.count = zext i32 %N to i64 ++ br label %for.body ++ ++for.body: ; preds = %for.body, %for.body.preheader ++ %indvars.iv = phi i64 [ 0, %for.body.preheader ], [ %indvars.iv.next, %for.body ] ++ %0 = trunc i64 %indvars.iv to i32 ++ %conv = sitofp i32 %0 to double ++ %call = tail call fast double @sin(double %conv) #2 ++ %arrayidx = getelementptr inbounds double, double* %a, i64 %indvars.iv ++ store double %call, double* %arrayidx, align 8, !tbaa !2 ++ %indvars.iv.next = add nuw nsw i64 %indvars.iv, 1 ++ %exitcond = icmp eq i64 %indvars.iv.next, %wide.trip.count ++ br i1 %exitcond, label %for.end, label %for.body, !llvm.loop !6 ++ ++for.end: ; preds = %for.body, %entry ++ ret void ++} ++ ++; Function Attrs: nounwind ++declare dso_local double @sin(double) local_unnamed_addr #1 ++ ++!2 = !{!3, !3, i64 0} ++!3 = !{!"double", !4, i64 0} ++!4 = !{!"omnipotent char", !5, i64 0} ++!5 = !{!"Simple C/C++ TBAA"} ++!6 = distinct !{!6, !7} ++!7 = !{!"llvm.loop.vectorize.width", i32 8} +diff --git a/llvm-14.0.6.src/test/Transforms/Util/add-TLI-mappings.ll b/llvm-14.0.6.src/test/Transforms/Util/add-TLI-mappings.ll +index e8c83c4d9bd1f..615fdc29176a2 100644 +--- a/llvm-14.0.6.src/test/Transforms/Util/add-TLI-mappings.ll ++++ b/llvm-14.0.6.src/test/Transforms/Util/add-TLI-mappings.ll +@@ -12,12 +12,12 @@ target triple = "x86_64-unknown-linux-gnu" + + ; COMMON-LABEL: @llvm.compiler.used = appending global + ; SVML-SAME: [6 x i8*] [ +-; SVML-SAME: i8* bitcast (<2 x double> (<2 x double>)* @__svml_sin2 to i8*), +-; SVML-SAME: i8* bitcast (<4 x double> (<4 x double>)* @__svml_sin4 to i8*), +-; SVML-SAME: i8* bitcast (<8 x double> (<8 x double>)* @__svml_sin8 to i8*), +-; SVML-SAME: i8* bitcast (<4 x float> (<4 x float>)* @__svml_log10f4 to i8*), +-; SVML-SAME: i8* bitcast (<8 x float> (<8 x float>)* @__svml_log10f8 to i8*), +-; SVML-SAME: i8* bitcast (<16 x float> (<16 x float>)* @__svml_log10f16 to i8*) ++; SVML-SAME: i8* bitcast (<2 x double> (<2 x double>)* @__svml_sin2_ha to i8*), ++; SVML-SAME: i8* bitcast (<4 x double> (<4 x double>)* @__svml_sin4_ha to i8*), ++; SVML-SAME: i8* bitcast (<8 x double> (<8 x double>)* @__svml_sin8_ha to i8*), ++; SVML-SAME: i8* bitcast (<4 x float> (<4 x float>)* @__svml_log10f4_ha to i8*), ++; SVML-SAME: i8* bitcast (<8 x float> (<8 x float>)* @__svml_log10f8_ha to i8*), ++; SVML-SAME: i8* bitcast (<16 x float> (<16 x float>)* @__svml_log10f16_ha to i8*) + ; MASSV-SAME: [2 x i8*] [ + ; MASSV-SAME: i8* bitcast (<2 x double> (<2 x double>)* @__sind2 to i8*), + ; MASSV-SAME: i8* bitcast (<4 x float> (<4 x float>)* @__log10f4 to i8*) +@@ -59,9 +59,9 @@ declare float @llvm.log10.f32(float) #0 + attributes #0 = { nounwind readnone } + + ; SVML: attributes #[[SIN]] = { "vector-function-abi-variant"= +-; SVML-SAME: "_ZGV_LLVM_N2v_sin(__svml_sin2), +-; SVML-SAME: _ZGV_LLVM_N4v_sin(__svml_sin4), +-; SVML-SAME: _ZGV_LLVM_N8v_sin(__svml_sin8)" } ++; SVML-SAME: "_ZGV_LLVM_N2v_sin(__svml_sin2_ha), ++; SVML-SAME: _ZGV_LLVM_N4v_sin(__svml_sin4_ha), ++; SVML-SAME: _ZGV_LLVM_N8v_sin(__svml_sin8_ha)" } + + ; MASSV: attributes #[[SIN]] = { "vector-function-abi-variant"= + ; MASSV-SAME: "_ZGV_LLVM_N2v_sin(__sind2)" } +diff --git a/llvm-14.0.6.src/utils/TableGen/CMakeLists.txt b/llvm-14.0.6.src/utils/TableGen/CMakeLists.txt +index 97df6a55d1b59..199e0285c9e5d 100644 +--- a/llvm-14.0.6.src/utils/TableGen/CMakeLists.txt ++++ b/llvm-14.0.6.src/utils/TableGen/CMakeLists.txt +@@ -47,6 +47,7 @@ add_tablegen(llvm-tblgen LLVM + SearchableTableEmitter.cpp + SubtargetEmitter.cpp + SubtargetFeatureInfo.cpp ++ SVMLEmitter.cpp + TableGen.cpp + Types.cpp + X86DisassemblerTables.cpp +diff --git a/llvm-14.0.6.src/utils/TableGen/SVMLEmitter.cpp b/llvm-14.0.6.src/utils/TableGen/SVMLEmitter.cpp +new file mode 100644 +index 0000000000000..a5aeea48db28b +--- /dev/null ++++ b/llvm-14.0.6.src/utils/TableGen/SVMLEmitter.cpp +@@ -0,0 +1,110 @@ ++//===------ SVMLEmitter.cpp - Generate SVML function variants -------------===// ++// ++// The LLVM Compiler Infrastructure ++// ++// This file is distributed under the University of Illinois Open Source ++// License. See LICENSE.TXT for details. ++// ++//===----------------------------------------------------------------------===// ++// ++// This tablegen backend emits the scalar to svml function map for TLI. ++// ++//===----------------------------------------------------------------------===// ++ ++#include "CodeGenTarget.h" ++#include "llvm/Support/Format.h" ++#include "llvm/TableGen/Error.h" ++#include "llvm/TableGen/Record.h" ++#include "llvm/TableGen/TableGenBackend.h" ++#include ++#include ++ ++using namespace llvm; ++ ++#define DEBUG_TYPE "SVMLVariants" ++#include "llvm/Support/Debug.h" ++ ++namespace { ++ ++class SVMLVariantsEmitter { ++ ++ RecordKeeper &Records; ++ ++private: ++ void emitSVMLVariants(raw_ostream &OS); ++ ++public: ++ SVMLVariantsEmitter(RecordKeeper &R) : Records(R) {} ++ ++ void run(raw_ostream &OS); ++}; ++} // End anonymous namespace ++ ++/// \brief Emit the set of SVML variant function names. ++// The default is to emit the high accuracy SVML variants until a mechanism is ++// introduced to allow a selection of different variants through precision ++// requirements specified by the user. This code generates mappings to svml ++// that are in the scalar form of llvm intrinsics, math library calls, or the ++// finite variants of math library calls. ++void SVMLVariantsEmitter::emitSVMLVariants(raw_ostream &OS) { ++ ++ const unsigned MinSinglePrecVL = 4; ++ const unsigned MaxSinglePrecVL = 16; ++ const unsigned MinDoublePrecVL = 2; ++ const unsigned MaxDoublePrecVL = 8; ++ ++ OS << "#ifdef GET_SVML_VARIANTS\n"; ++ ++ for (const auto &D : Records.getAllDerivedDefinitions("SvmlVariant")) { ++ StringRef SvmlVariantNameStr = D->getName(); ++ // Single Precision SVML ++ for (unsigned VL = MinSinglePrecVL; VL <= MaxSinglePrecVL; VL *= 2) { ++ // Emit the scalar math library function to svml function entry. ++ OS << "{\"" << SvmlVariantNameStr << "f" << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << "f" << VL << "\", " ++ << "ElementCount::getFixed(" << VL << ")},\n"; ++ ++ // Emit the scalar intrinsic to svml function entry. ++ OS << "{\"" << "llvm." << SvmlVariantNameStr << ".f32" << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << "f" << VL << "\", " ++ << "ElementCount::getFixed(" << VL << ")},\n"; ++ ++ // Emit the finite math library function to svml function entry. ++ OS << "{\"__" << SvmlVariantNameStr << "f_finite" << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << "f" << VL << "\", " ++ << "ElementCount::getFixed(" << VL << ")},\n"; ++ } ++ ++ // Double Precision SVML ++ for (unsigned VL = MinDoublePrecVL; VL <= MaxDoublePrecVL; VL *= 2) { ++ // Emit the scalar math library function to svml function entry. ++ OS << "{\"" << SvmlVariantNameStr << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << VL << "\", " << "ElementCount::getFixed(" << VL ++ << ")},\n"; ++ ++ // Emit the scalar intrinsic to svml function entry. ++ OS << "{\"" << "llvm." << SvmlVariantNameStr << ".f64" << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << VL << "\", " << "ElementCount::getFixed(" << VL ++ << ")},\n"; ++ ++ // Emit the finite math library function to svml function entry. ++ OS << "{\"__" << SvmlVariantNameStr << "_finite" << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << VL << "\", " ++ << "ElementCount::getFixed(" << VL << ")},\n"; ++ } ++ } ++ ++ OS << "#endif // GET_SVML_VARIANTS\n\n"; ++} ++ ++void SVMLVariantsEmitter::run(raw_ostream &OS) { ++ emitSVMLVariants(OS); ++} ++ ++namespace llvm { ++ ++void EmitSVMLVariants(RecordKeeper &RK, raw_ostream &OS) { ++ SVMLVariantsEmitter(RK).run(OS); ++} ++ ++} // End llvm namespace +diff --git a/llvm-14.0.6.src/utils/TableGen/TableGen.cpp b/llvm-14.0.6.src/utils/TableGen/TableGen.cpp +index 2d4a45f889be6..603d0c223b33a 100644 +--- a/llvm-14.0.6.src/utils/TableGen/TableGen.cpp ++++ b/llvm-14.0.6.src/utils/TableGen/TableGen.cpp +@@ -57,6 +57,7 @@ enum ActionType { + GenAutomata, + GenDirectivesEnumDecl, + GenDirectivesEnumImpl, ++ GenSVMLVariants, + }; + + namespace llvm { +@@ -138,7 +139,9 @@ cl::opt Action( + clEnumValN(GenDirectivesEnumDecl, "gen-directive-decl", + "Generate directive related declaration code (header file)"), + clEnumValN(GenDirectivesEnumImpl, "gen-directive-impl", +- "Generate directive related implementation code"))); ++ "Generate directive related implementation code"), ++ clEnumValN(GenSVMLVariants, "gen-svml", ++ "Generate SVML variant function names"))); + + cl::OptionCategory PrintEnumsCat("Options for -print-enums"); + cl::opt Class("class", cl::desc("Print Enum list for this class"), +@@ -272,6 +275,9 @@ bool LLVMTableGenMain(raw_ostream &OS, RecordKeeper &Records) { + case GenDirectivesEnumImpl: + EmitDirectivesImpl(Records, OS); + break; ++ case GenSVMLVariants: ++ EmitSVMLVariants(Records, OS); ++ break; + } + + return false; +diff --git a/llvm-14.0.6.src/utils/TableGen/TableGenBackends.h b/llvm-14.0.6.src/utils/TableGen/TableGenBackends.h +index 71db8dc77b052..86c3a3068c2dc 100644 +--- a/llvm-14.0.6.src/utils/TableGen/TableGenBackends.h ++++ b/llvm-14.0.6.src/utils/TableGen/TableGenBackends.h +@@ -93,6 +93,7 @@ void EmitExegesis(RecordKeeper &RK, raw_ostream &OS); + void EmitAutomata(RecordKeeper &RK, raw_ostream &OS); + void EmitDirectivesDecl(RecordKeeper &RK, raw_ostream &OS); + void EmitDirectivesImpl(RecordKeeper &RK, raw_ostream &OS); ++void EmitSVMLVariants(RecordKeeper &RK, raw_ostream &OS); + + } // End llvm namespace + +diff --git a/llvm-14.0.6.src/utils/vim/syntax/llvm.vim b/llvm-14.0.6.src/utils/vim/syntax/llvm.vim +index 205db16b7d8cd..2572ab5a59e1b 100644 +--- a/llvm-14.0.6.src/utils/vim/syntax/llvm.vim ++++ b/llvm-14.0.6.src/utils/vim/syntax/llvm.vim +@@ -104,6 +104,7 @@ syn keyword llvmKeyword + \ inreg + \ intel_ocl_bicc + \ inteldialect ++ \ intel_svmlcc + \ internal + \ jumptable + \ linkonce From 8d2129cae7cd7edee8bde9f01c486ba51ceffe4d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:37:49 +0800 Subject: [PATCH 9417/9987] adding easyconfigs: FFLAS-FFPACK-2.5.0-gfbf-2022a.eb --- .../FFLAS-FFPACK-2.5.0-gfbf-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb new file mode 100644 index 00000000000..e162b0e9773 --- /dev/null +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild recipe; see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'FFLAS-FFPACK' +version = '2.5.0' + +homepage = 'https://linbox-team.github.io/fflas-ffpack/' +description = "Finite Field Linear Algebra Subroutines / Package" + +toolchain = {'name': 'gfbf', 'version': '2022a'} + +source_urls = ['https://github.com/linbox-team/fflas-ffpack/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dafb4c0835824d28e4f823748579be6e4c8889c9570c6ce9cce1e186c3ebbb23'] + +dependencies = [ + ('GMP', '6.2.1'), + ('Givaro', '4.2.0'), +] + +configopts = '--with-blas-libs="$LIBBLAS_MT" --with-blas-cflags="-I$BLAS_INC_DIR" ' +configopts += '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO --enable-openmp' + +buildopts = " && make autotune " + +sanity_check_paths = { + 'files': ['bin/fflas-ffpack-config', 'include/fflas-ffpack/fflas-ffpack.h'], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' From 1c31a9d56d4187758295af7c8ec98dc627df6374 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 16:53:35 +0800 Subject: [PATCH 9418/9987] adding easyconfigs: IML-1.0.5-gfbf-2022a.eb --- .../easyconfigs/i/IML/IML-1.0.5-gfbf-2022a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2022a.eb b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2022a.eb new file mode 100644 index 00000000000..246ea7b40b6 --- /dev/null +++ b/easybuild/easyconfigs/i/IML/IML-1.0.5-gfbf-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'IML' +version = '1.0.5' + +homepage = 'https://cs.uwaterloo.ca/~astorjoh/iml.html' +description = """IML is a free library of C source code which implements algorithms for computing + exact solutions to dense systems of linear equations over the integers.""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} + +source_urls = ['http://www.cs.uwaterloo.ca/~astorjoh'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['1dad666850895a5709b00b97422e2273f293cfadea7697a9f90b90953e847c2a'] + +dependencies = [('GMP', '6.2.1')] + +configopts = '--with-cblas="$LIBBLAS" --with-gmp-include=$EBROOTGMP/include --with-gmp-lib=$EBROOTGMP/lib ' + +sanity_check_paths = { + 'files': ['include/iml.h', 'lib/libiml.a'], + 'dirs': ['share'], +} + +moduleclass = 'math' From 830478bc08f55d5d2993cf6e884dd9b4e71e6cd8 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 17:02:09 +0800 Subject: [PATCH 9419/9987] adding easyconfigs: LinBox-1.7.0-gfbf-2022a.eb --- .../l/LinBox/LinBox-1.7.0-gfbf-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb new file mode 100644 index 00000000000..0fecede9ee7 --- /dev/null +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild recipe; see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright (c) 2016 Riccardo Murri +# Authors:: Riccardo Murri +# License:: GPL +# +## + +easyblock = 'ConfigureMake' + +name = 'LinBox' +version = '1.7.0' + +homepage = 'https://linalg.org/' +description = "C++ library for exact, high-performance linear algebra" + +toolchain = {'name': 'gfbf', 'version': '2022a'} + +source_urls = ['https://github.com/linbox-team/linbox/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6d2159fd395be0298362dd37f6c696676237bc8e2757341fbc46520e3b466bcc'] + +dependencies = [ + ('FFLAS-FFPACK', '2.5.0'), + ('FLINT', '2.9.0'), + ('Givaro', '4.2.0'), + ('IML', '1.0.5'), + ('NTL', '11.5.1'), +] + +configopts = "--with-fflas-ffpack=$EBROOTFFLASMINFFPACK --with-flint=$EBROOTFLINT " +configopts += "--with-givaro=$EBROOTGIVARO --with-iml=$EBROOTIML --with-ntl=$EBROOTNTL " +configopts += "--enable-openmp --enable-shared " + +sanity_check_paths = { + 'files': ['bin/linbox-config', 'include/linbox/linbox-config.h'] + + ['lib/liblinbox.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'math' From 0e037ac328a79d074824f256942f7d2aff779d04 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 17:09:31 +0800 Subject: [PATCH 9420/9987] adding easyconfigs: ANTIC-0.2.5-gfbf-2022a.eb --- .../a/ANTIC/ANTIC-0.2.5-gfbf-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANTIC/ANTIC-0.2.5-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/a/ANTIC/ANTIC-0.2.5-gfbf-2022a.eb b/easybuild/easyconfigs/a/ANTIC/ANTIC-0.2.5-gfbf-2022a.eb new file mode 100644 index 00000000000..8e320df93cd --- /dev/null +++ b/easybuild/easyconfigs/a/ANTIC/ANTIC-0.2.5-gfbf-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ANTIC' +version = '0.2.5' + +homepage = 'https://github.com/flintlib/antic' +description = "Antic is an algebraic number theory library." + +toolchain = {'name': 'gfbf', 'version': '2022a'} +toolchainopts = {'pic': True} + +github_account = 'flintlib' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['7b236b6226d5730cf66d492f1562c34d4dcf1bdc8775fec2330f560332ab05c1'] + +dependencies = [('FLINT', '2.9.0')] + +configopts = "--with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR --with-flint=$EBROOTFLINT " + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libantic.%s' % e for e in ['a', SHLIB_EXT]] + + ['include/antic/%s.h' % h for h in ['nf', 'nf_elem', 'qfb']], + 'dirs': [], +} + +moduleclass = 'math' From 6e9196ab44d089a1a27c2c792c987bfda52cbfd6 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:11:26 +0800 Subject: [PATCH 9421/9987] adding easyconfigs: cppyy-3.0.0-GCCcore-11.3.0.eb --- .../c/cppyy/cppyy-3.0.0-GCCcore-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/c/cppyy/cppyy-3.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cppyy/cppyy-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cppyy/cppyy-3.0.0-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c9df1eeb8b8 --- /dev/null +++ b/easybuild/easyconfigs/c/cppyy/cppyy-3.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'cppyy' +version = '3.0.0' + +homepage = "https://cppyy.readthedocs.io" +description = """cppyy is an automatic, run-time, Python-C++ bindings generator, + for calling C++ from Python and Python from C++.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +exts_list = [ + ('cppyy-cling', '6.28.0', { + 'modulename': False, + 'checksums': ['ae67fc338510d03b68dde08add5b519e2c6434d40fe07e23e7ebace3caa684e7'], + }), + ('cppyy-backend', '1.14.11', { + 'checksums': ['2d329adce65b421a4e8a1af36116fb1756571349dc6b22a9ac3dde54b2a30af1'], + }), + ('CPyCppyy', '1.12.13', { + 'modulename': False, + 'checksums': ['f8c8c05b1eb8f0ccaed07b5069efabecff791bbe5e1b5be86767d32974e833d4'], + }), + (name, version, { + 'checksums': ['9c7c1c113d771488cee0bf63f26d2bbf4f42de731eb63776e007cb0d9e23d3d8'], + }), + ('cppyythonizations', '1.2.2', { + 'source_tmpl': 'cppyythonizations-%(version)s-py3-none-any.whl', + 'checksums': ['fa7805cea410955583d0add18e6d5b2d17740310eed974fcc65271ee9ba6da20'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lang' From d215f41fa998a17292c0da32ff16e2d215ff331f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:16:07 +0800 Subject: [PATCH 9422/9987] adding easyconfigs: E-ANTIC-1.3.0-gfbf-2022a.eb --- .../e/E-ANTIC/E-ANTIC-1.3.0-gfbf-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-1.3.0-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-1.3.0-gfbf-2022a.eb b/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-1.3.0-gfbf-2022a.eb new file mode 100644 index 00000000000..2d10a851d97 --- /dev/null +++ b/easybuild/easyconfigs/e/E-ANTIC/E-ANTIC-1.3.0-gfbf-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'E-ANTIC' +version = '1.3.0' + +homepage = 'https://github.com/flatsurf/e-antic' +description = """E-ANTIC is a C/C++ library to deal with real embedded number fields built on +top of ANTIC (https://github.com/wbhart/antic). Its aim is to have as fast as +possible exact arithmetic operations and comparisons.""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/flatsurf/e-antic/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ae12cb87f09478f49c4acdf0f3ff888dc556267614c0a5a3bc8bfaa41b22deef'] + +dependencies = [ + ('ANTIC', '0.2.5'), + ('FLINT', '2.9.0'), + ('Arb', '2.23.0'), + ('Python', '3.10.4'), + ('cppyy', '3.0.0'), +] + +configopts = '--without-benchmark --without-byexample --without-pytest --without-doc' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (lib, ext) for lib in ['eantic', 'eanticxx'] for ext in ['a', SHLIB_EXT]] + + ['include/e-antic/%s.h' % h for h in ['e-antic', 'fmpq_poly_extra', 'renf', + 'renf_elem', 'renfxx']], + 'dirs': ['lib/python3.10/site-packages'], +} + +sanity_check_commands = ["python -c 'import pyeantic'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'math' From e641366e605dfd3395137dc6f38c8dfea6762754 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:23:05 +0800 Subject: [PATCH 9423/9987] adding easyconfigs: Normaliz-3.10.1-gfbf-2022a.eb --- .../n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb diff --git a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb new file mode 100644 index 00000000000..d7f2cdf14cf --- /dev/null +++ b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Normaliz' +version = '3.10.1' + +homepage = 'https://www.normaliz.uni-osnabrueck.de/' +description = """Normaliz is a open source tool for computations in affine monoids, vector +configurations, rational polyhedra and rational cones. Normaliz now computes +rational and algebraic polyhedra, i.e., polyhedra defined over real algebraic +extensions of QQ.""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True, 'cstd': 'c++11'} + +github_account = 'Normaliz' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['761b28884fa2af00498251803a3ce4e03fcb843b7471e77e4be9b9bcd3cd0a15'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('GMP', '6.2.1'), + ('CoCoALib', '0.99818'), + ('FLINT', '2.9.0'), + ('Arb', '2.23.0'), + ('E-ANTIC', '1.3.0'), + ('nauty', '2.8.6'), +] + +preconfigopts = "autoreconf -f -i && " + +configopts = "--with-gmp=$EBROOTGMP --with-cocoalib=$EBROOTCOCOALIB --with-flint=$EBROOTFLINT " +configopts += "--with-e-antic=$EBROOTEMINANTIC --with-nauty=$EBROOTNAUTY" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/normaliz'] + ['lib/libnormaliz.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/libnormaliz'] +} + +moduleclass = 'math' From b020e8631c2c86cbd9eae6d1c7d78b33ca5f7ebc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:38:39 +0800 Subject: [PATCH 9424/9987] adding easyconfigs: gap-4.12.2-foss-2022a.eb --- .../g/gap/gap-4.12.2-foss-2022a.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb b/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb new file mode 100644 index 00000000000..04d6ec24740 --- /dev/null +++ b/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'gap' +version = '4.12.2' + +homepage = 'https://www.gap-system.org' +description = """GAP is a system for computational discrete algebra, +with particular emphasis on Computational Group Theory.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.gap-system.org/pub/gap/gap-%(version_major_minor)s/tar.gz/'] +sources = [SOURCE_TAR_GZ] +checksums = ['672308745eb78a222494ee8dd6786edd5bc331456fcc6456ac064bdb28d587a8'] + +unpack_options = '--strip-components=1' + +builddependencies = [ + ('Perl', '5.34.1'), # needed to install NormalizInterface +] + +dependencies = [ + ('GMP', '6.2.1'), + ('libreadline', '8.1.2'), + ('zlib', '1.2.12'), + ('4ti2', '1.6.9'), # needed by 4ti2Interface, HeLP + ('cddlib', '0.94m'), # needed by CddInterface + ('cURL', '7.83.0'), # needed by curlInterface + ('lrslib', '7.2'), # needed by HeLP + ('ncurses', '6.3'), # needed by Browse + ('Normaliz', '3.10.1'), # needed by NormalizInterface, HeLP + ('Singular', '4.3.2p10'), # needed by singular + ('ZeroMQ', '4.3.4'), # needed by ZeroMQInterface +] + +# Disable bundled script to download and build Normaliz +prebuildopts = "sed -i 's|./build-normaliz.sh|continue # build-normaliz.sh|' bin/BuildPackages.sh && " +# BuildPackages.sh tries to build any GAP packages that require compilation +# If one fails due to missing dependencies, it's skipped automatically +buildopts = ' && cd pkg && ../bin/BuildPackages.sh' + +runtest = "testinstall" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gap', 'gac']] + + ['include/gap/%s.h' % h for h in ['gap', 'system', 'version']] + + ['lib/libgap.%s' % SHLIB_EXT], + 'dirs': ['share/gap'] +} + +moduleclass = 'math' From 38963ddbef4c11c9a0130af4e733d6ee2c4219c8 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:55:59 +0800 Subject: [PATCH 9425/9987] adding easyconfigs: BRiAl-1.2.12-GCC-11.3.0.eb, m4ri-20200125-GCC-11.3.0.eb, m4rie-20200125-GCC-11.3.0.eb --- .../b/BRiAl/BRiAl-1.2.12-GCC-11.3.0.eb | 28 +++++++++++++++++++ .../m/m4ri/m4ri-20200125-GCC-11.3.0.eb | 25 +++++++++++++++++ .../m/m4rie/m4rie-20200125-GCC-11.3.0.eb | 27 ++++++++++++++++++ 3 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/m4ri/m4ri-20200125-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/m4rie/m4rie-20200125-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-11.3.0.eb new file mode 100644 index 00000000000..b4a8e727e88 --- /dev/null +++ b/easybuild/easyconfigs/b/BRiAl/BRiAl-1.2.12-GCC-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'BRiAl' +version = '1.2.12' + +homepage = 'https://github.com/BRiAl/BRiAl' +description = """BRiAl is the legacy version of PolyBoRi maintained by sagemath developers.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/BRiAl/BRiAl/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['ca009e3722dd3f0a60d15501caed1413146c80abced57423e32ae0116f407494'] + +dependencies = [ + ('Boost', '1.79.0'), + ('CUDD', '3.0.0'), + ('Python', '3.10.4'), + ('m4ri', '20200125'), +] + +sanity_check_paths = { + 'files': ['include/polybori.h'] + + ['lib/libbrial.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/m4ri/m4ri-20200125-GCC-11.3.0.eb b/easybuild/easyconfigs/m/m4ri/m4ri-20200125-GCC-11.3.0.eb new file mode 100644 index 00000000000..25596bcadc4 --- /dev/null +++ b/easybuild/easyconfigs/m/m4ri/m4ri-20200125-GCC-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'm4ri' +version = '20200125' + +homepage = 'https://github.com/malb/m4ri' +description = "M4RI is a library for fast arithmetic with dense matrices over F2." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/malb/m4ri/archive/refs/tags/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['7369adcecb72d4dacfb23fd437a6b59a956f76b26dee07f32558cb915a9d6e9d'] + +builddependencies = [('Autotools', '20220317')] + +preconfigopts = "autoreconf --install && " +configopts = "--enable-openmp " + +sanity_check_paths = { + 'files': ['include/m4ri/m4ri.h', 'lib/libm4ri.a', 'lib/libm4ri.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/m4rie/m4rie-20200125-GCC-11.3.0.eb b/easybuild/easyconfigs/m/m4rie/m4rie-20200125-GCC-11.3.0.eb new file mode 100644 index 00000000000..4fbe407e8aa --- /dev/null +++ b/easybuild/easyconfigs/m/m4rie/m4rie-20200125-GCC-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'm4rie' +version = '20200125' + +homepage = 'https://github.com/malb/m4rie' +description = "M4RIE is a library for fast arithmetic with dense matrices." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/malb/m4rie/archive/refs/tags/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['bc5c515e6151203b7a483f6ca84a22ec8c0407ea3621d8e11de3c997b5009d69'] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [('m4ri', version)] + +preconfigopts = "autoreconf --install && " +configopts = "--enable-openmp " + +sanity_check_paths = { + 'files': ['include/m4rie/m4rie.h'] + ['lib/libm4rie.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'math' From 4af9e24c1eb2e56e741c41edd2c90490c88aa039 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 20:58:37 +0800 Subject: [PATCH 9426/9987] add CUDD easyconfig --- .../c/CUDD/CUDD-3.0.0-GCC-11.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..c18f2d7cc9a --- /dev/null +++ b/easybuild/easyconfigs/c/CUDD/CUDD-3.0.0-GCC-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CUDD' +version = '3.0.0' + +homepage = 'https://github.com/ivmai/cudd' +description = """The CUDD package is a package written in C for the manipulation of + decision diagrams. It supports binary decision diagrams (BDDs), algebraic decision + diagrams (ADDs), and Zero-Suppressed BDDs (ZDDs).""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/ivmai/cudd/archive/refs/tags'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fe145041c594689e6e7cf4cd623d5f2b7c36261708be8c9a72aed72cf67acce'] + +sanity_check_paths = { + 'files': ['include/cudd.h', 'lib/libcudd.a'], + 'dirs': [], +} + +moduleclass = 'math' From 814faca5b516f5d1a5d8110233d05dfe8d380204 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 21:29:09 +0800 Subject: [PATCH 9427/9987] adding easyconfigs: eclib-20230424-GCC-11.3.0.eb --- .../e/eclib/eclib-20230424-GCC-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb b/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb new file mode 100644 index 00000000000..374895237c3 --- /dev/null +++ b/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'eclib' +version = '20230424' + +homepage = 'https://github.com/JohnCremona/eclib' +description = """The eclib package includes mwrank (for 2-descent on elliptic curves over Q) + and modular symbol code used to create the elliptic curve database.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/JohnCremona/eclib/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +checksums = ['1422decfcabebb0ad42f7f58c5aefe5bd8fa11757b45e31a186384fd037cd5c1'] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [ + ('NTL', '11.5.1'), + ('PARI-GP', '2.15.4'), +] + +preconfigopts = "autoreconf --install && " + +configopts = "--with-ntl=$EBROOTNTL --with-pari=$EBROOTPARI" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ecnf', 'mwrank', 'pcurve', 'qexp']] + + ['include/eclib/%s.h' % h for h in ['curve', 'egr', 'vector']] + + ['lib/libec.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['share'], +} + +moduleclass = 'math' From 59e2856067df82c5c9171738eb5ae5b71d13e6ff Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 21:56:29 +0800 Subject: [PATCH 9428/9987] adding easyconfigs: cliquer-1.21-GCCcore-11.3.0.eb --- .../c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..c3c98e348d9 --- /dev/null +++ b/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'cliquer' +version = '1.21' + +homepage = 'https://users.aalto.fi/~pat/cliquer.html' +description = """Cliquer is a set of C routines for finding cliques in an arbitrary weighted graph. + It uses an exact branch-and-bound algorithm developed by Patric Ostergard. It is designed with + the aim of being efficient while still being flexible and easy to use.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://users.aalto.fi/~pat/cliquer/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ff306d27eda82383c0257065e3ffab028415ac9af73bccfdd9c2405b797ed1f1'] + +builddependencies = [('binutils', '2.38')] + +local_headers = ['cliquer', 'set', 'graph', 'misc', 'reorder', 'cliquerconf'] + +files_to_copy = [ + (['cl'], 'bin'), + (['%s.h' % h for h in local_headers], 'include/cliquer'), +] + +sanity_check_paths = { + 'files': ['bin/cl'] + ['include/cliquer/%s.h' % h for h in local_headers], + 'dirs': [], +} + +moduleclass = 'math' From dd0b4c0890e3e5ab212f4978fddbd8b166c3832b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Sat, 11 Nov 2023 22:07:14 +0800 Subject: [PATCH 9429/9987] adding easyconfigs: ECL-23.9.9-GCCcore-11.3.0.eb --- .../e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb new file mode 100644 index 00000000000..4a15b7330df --- /dev/null +++ b/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'ECL' +version = '23.9.9' + +homepage = 'https://ecl.common-lisp.dev/' +description = """ECL (Embeddable Common-Lisp) is an interpreter of the Common-Lisp language + as described in the X3J13 Ansi specification, featuring CLOS (Common-Lisp Object System), + conditions, loops, etc, plus a translator to C, which can produce standalone executables.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://common-lisp.net/project/ecl/static/files/release'] +sources = [SOURCELOWER_TGZ] +checksums = ['c51bdab4ca6c1173dd3fe9cfe9727bcefb97bb0a3d6434b627ca6bdaeb33f880'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('GMP', '6.2.1'), +] + +configopts = "--enable-manual=no " + +sanity_check_paths = { + 'files': ['bin/ecl', 'bin/ecl-config', 'include/ecl/ecl.h', 'lib/libecl.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lang' From 3180105d3738c6240900a1d5009eab5907b15d3d Mon Sep 17 00:00:00 2001 From: deniskristak Date: Sun, 12 Nov 2023 14:33:18 +0100 Subject: [PATCH 9430/9987] adding easyconfigs: tensorflow-probability-0.19.0-foss-2022a.eb, vaeda-0.0.30-foss-2022a.eb --- ...ensorflow-probability-0.19.0-foss-2022a.eb | 48 +++++++++++++++++++ .../v/vaeda/vaeda-0.0.30-foss-2022a.eb | 40 ++++++++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/v/vaeda/vaeda-0.0.30-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a.eb new file mode 100644 index 00000000000..5f95682889d --- /dev/null +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.19.0-foss-2022a.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# License:: MIT/GPL +# $Id$ +# +# Updated to 0.19.0 +# Author: J. Sassmannshausen (Imperial College London/UK) +## + +easyblock = 'PythonBundle' + +name = 'tensorflow-probability' +version = '0.19.0' + +homepage = 'https://www.tensorflow.org/probability' +description = """TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'pic': True} + +dependencies = [ + ('Python', '3.10.4'), + ('TensorFlow', '2.11.0'), + ('dm-tree', '0.1.8'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + (name, version, { + 'installopts': '--install-option="--release"', + 'modulename': 'tensorflow_probability', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/probability/archive/'], + 'checksums': ['b32d2ae211ec727df9791b501839619f5389134bd6d4fe951570f500b0e75f55'], + }), +] + +sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/vaeda/vaeda-0.0.30-foss-2022a.eb b/easybuild/easyconfigs/v/vaeda/vaeda-0.0.30-foss-2022a.eb new file mode 100644 index 00000000000..81be3ccd7c0 --- /dev/null +++ b/easybuild/easyconfigs/v/vaeda/vaeda-0.0.30-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'vaeda' +# recent vaeda version are also available via https://test.pypi.org/project/vaeda, +# but downloading from there doesn't seem like a good idea... +local_commit = '36cdc53' +version = '0.0.30' + +homepage = 'https://github.com/kostkalab/vaeda' +description = """vaeda (variaitonal auto-encoder (vae) for doublet annotation (da)) is a Python package for doublet +annotation in single cell RNA-sequencing.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('scanpy', '1.9.1'), + ('TensorFlow', '2.11.0'), + ('tensorflow-probability', '0.19.0'), +] + +use_pip = True + +exts_list = [ + ('kneed', '0.8.1', { + 'preinstallopts': "sed -i 's/install_requires = .*/install_requires = numpy;scipy/g' setup.cfg && ", + 'checksums': ['6addebca6a3742e51a173f4f40f789c704677c49bc0b02666e7d71152ca0e473'], + }), + (name, version, { + 'source_urls': ['https://github.com/kostkalab/vaeda/archive/'], + 'sources': [{'download_filename': '36cdc53.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['bef23d0496944a5b9c41645de0442db99ddb26e3fb69bda3437c00339832295e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 695ea0d4b7275bc130fa8dd0e6229a3ab01c76e5 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Sun, 12 Nov 2023 14:36:50 +0100 Subject: [PATCH 9431/9987] adding easyconfigs: scrublet-0.2.3-foss-2022a.eb --- .../s/scrublet/scrublet-0.2.3-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2022a.eb b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2022a.eb new file mode 100644 index 00000000000..9e63514905b --- /dev/null +++ b/easybuild/easyconfigs/s/scrublet/scrublet-0.2.3-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'scrublet' +version = '0.2.3' + +homepage = 'https://github.com/swolock/scrublet' +description = "Single-Cell Remover of Doublets - Python code for identifying doublets in single-cell RNA-seq data" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('scikit-image', '0.19.3'), + ('matplotlib', '3.5.2'), + ('numba', '0.56.4'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('annoy', '1.17.1', { + 'checksums': ['bf177dbeafb81f63b2ac1e1246b1f26a2acc82e73ba46638734d29d8258122da'], + }), + ('pynndescent', '0.5.7', { + 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], + }), + ('umap-learn', '0.5.3', { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), + (name, version, { + 'checksums': ['2185f63070290267f82a36e5b4cae8c321f10415d2d0c9f7e5e97b1126bf653a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From ecd73bd1d73a0071baf64d09977a34bf12b7fbfe Mon Sep 17 00:00:00 2001 From: deniskristak Date: Sun, 12 Nov 2023 14:41:16 +0100 Subject: [PATCH 9432/9987] adding easyconfigs: solo-1.3-foss-2022a.eb --- .../easyconfigs/s/solo/solo-1.3-foss-2022a.eb | 90 +++++++++++++++++++ 1 file changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/s/solo/solo-1.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/solo/solo-1.3-foss-2022a.eb b/easybuild/easyconfigs/s/solo/solo-1.3-foss-2022a.eb new file mode 100644 index 00000000000..a9560982884 --- /dev/null +++ b/easybuild/easyconfigs/s/solo/solo-1.3-foss-2022a.eb @@ -0,0 +1,90 @@ +easyblock = 'PythonBundle' + +name = 'solo' +version = '1.3' + +homepage = 'https://github.com/calico/solo' +description = "Doublet detection via semi-supervised deep learning" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('IPython', '8.5.0'), + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('Seaborn', '0.12.1'), + ('leidenalg', '0.9.1'), + ('scanpy', '1.9.1'), + ('openpyxl', '3.0.10'), + ('tensorboard', '2.10.0'), +] + +use_pip = True + +exts_list = [ + ('ConfigArgParse', '1.5.3', { + 'checksums': ['1b0b3cbf664ab59dada57123c81eff3d9737e0d11d8cf79e3d6eb10823f1739f'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('opt-einsum', '3.3.0', { + 'sources': ['opt_einsum-%(version)s.tar.gz'], + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + }), + ('pyro-ppl', '1.8.4', { + 'modulename': 'pyro', + 'checksums': ['766fad61e52df48885de96d41213da1f8e8c1b79ecf308ad53189fcd15c1cb41'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.6.0', { + 'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'], + }), + ('pyDeprecate', '0.3.2', { + 'modulename': 'deprecate', + 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], + }), + ('torchmetrics', '0.7.3', { + 'checksums': ['875e744a6db63c88757260d63cb80919d0398734a7f456f8ea4181bb2db957d8'], + }), + ('PyYAML', '5.4.1', { + 'modulename': 'yaml', + 'checksums': ['607774cbba28732bfa802b54baa7484215f530991055bb562efbed5b2f20a45e'], + }), + ('pytorch-lightning', '1.3.8', { + 'preinstallopts': "sed -i 's/pyDeprecate==/pyDeprecate>=/g' requirements.txt && ", + 'checksums': ['60b0a3e464d394864dae4c8d251afa7aa453644a19bb7672f5ee400343cdf7b0'], + }), + ('scvi-tools', '0.14.6', { + 'modulename': 'scvi', + 'preinstallopts': "sed -i '/^setuptools/d' pyproject.toml && ", + 'checksums': ['f30a8a685624e49fa8a0d9b9d53152eb7b95e28b020ebd1c564387b2250bc38a'], + }), + ('solo-sc', version, { + 'modulename': 'solo', + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + 'checksums': ['e19e5697ad5e12b39dd2549682356171a438dfe70ec46277d4502bab047b624d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/hashsolo', 'bin/solo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "hashsolo --help", + "solo --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 2dc76b4466155120b9ab09e1a7041d5122b20ee1 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Sun, 12 Nov 2023 17:13:24 +0100 Subject: [PATCH 9433/9987] adding easyconfigs: EUKulele-2.0.6-foss-2022a.eb --- .../e/EUKulele/EUKulele-2.0.6-foss-2022a.eb | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb b/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb new file mode 100644 index 00000000000..55e7e75e1b5 --- /dev/null +++ b/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb @@ -0,0 +1,78 @@ +easyblock = 'PythonBundle' + +name = 'EUKulele' +version = '2.0.6' + +homepage = 'https://github.com/AlexanderLabWHOI/EUKulele' +description = "Formalizing environmental eukaryotic taxonomic assignment" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Biopython', '1.79'), + ('SciPy-bundle', '2022.05'), + ('Seaborn', '0.12.1'), + ('PyYAML', '6.0'), + ('coverage', '7.2.7'), + ('matplotlib', '3.5.2'), + ('pytest-xdist', '2.5.0'), +] + +use_pip = True + +local_oset_sed = 'sed -i "s/collections import MutableSet/collections.abc import MutableSet/g" ./src/oset/pyoset.py ' +exts_list = [ + ('oset', '0.1.3', { + 'preinstallopts': 'sed -i "s/collections import MutableSet/collections.abc import MutableSet/g" ./src/oset/pyoset.py && ', + 'checksums': ['4c1fd7dec96eeff9d3260995a8e37f9f415d0bdb79975f57824e68716ac8f904'], + }), + ('dill', '0.3.6', { + 'checksums': ['e5db55f3687856d8fbdab002ed78544e1c4559a130302693d839dfe8f93f2373'], + }), + ('multiprocess', '0.70.14', { + 'checksums': ['3eddafc12f2260d27ae03fe6069b12570ab4764ab59a75e81624fac453fbf46a'], + }), + ('joblib', '1.3.1', { + 'checksums': ['1f937906df65329ba98013dc9692fe22a4c5e4a648112de500508b18a21b41e3'], + }), + ('python-coveralls', '2.9.3', { + 'modulename': 'coveralls', + 'checksums': ['bfaf7811e7dc5628e83b6b162962a4e2485dbff184b30e49f380374ed1bcee55'], + }), + ('pytest-cov', '4.1.0', { + 'checksums': ['3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6'], + }), + ('latexcodec', '2.0.1', { + 'checksums': ['2aa2551c373261cefe2ad3a8953a6d6533e68238d180eb4bb91d7964adb3fe9a'], + }), + ('pybtex', '0.24.0', { + 'checksums': ['818eae35b61733e5c007c3fcd2cfb75ed1bc8b4173c1f70b56cc4c0802d34755'], + }), + ('pybtex-docutils', '1.0.3', { + 'checksums': ['3a7ebdf92b593e00e8c1c538aa9a20bca5d92d84231124715acc964d51d93c6b'], + }), + ('sphinxcontrib-bibtex', '1.0.0', { + 'modulename': 'sphinxcontrib.bibtex', + 'checksums': ['629612b001f86784669d65e662377a482052decfd9a0a17c46860878eef7b9e0'], + }), + (name, version, { + 'modulename': 'EUKulele', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/AlexanderLabWHOI/EUKulele/archive/'], + 'checksums': ['ab4efb692886f25c2b94e9405b98f3935d78b7c716b66b5f7d43f3bca02184b4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/EUKulele', 'bin/create_protein_table.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "EUKulele --help" +] + +sanity_pip_check = True + +moduleclass = 'bio' From a8603e98abbc414f7e133210a4df64216cfed79e Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Sun, 12 Nov 2023 16:43:32 +0000 Subject: [PATCH 9434/9987] Update EUKulele-2.0.6-foss-2022a.eb --- easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb b/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb index 55e7e75e1b5..ddaf11c8df9 100644 --- a/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EUKulele/EUKulele-2.0.6-foss-2022a.eb @@ -24,7 +24,7 @@ use_pip = True local_oset_sed = 'sed -i "s/collections import MutableSet/collections.abc import MutableSet/g" ./src/oset/pyoset.py ' exts_list = [ ('oset', '0.1.3', { - 'preinstallopts': 'sed -i "s/collections import MutableSet/collections.abc import MutableSet/g" ./src/oset/pyoset.py && ', + 'preinstallopts': local_oset_sed + ' && ', 'checksums': ['4c1fd7dec96eeff9d3260995a8e37f9f415d0bdb79975f57824e68716ac8f904'], }), ('dill', '0.3.6', { From 7a2eb039d734e5e253577b7eed76b324872ca164 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Nov 2023 21:08:46 +0100 Subject: [PATCH 9435/9987] add sanity check command for Givaro --- easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb index fc41e542efe..ee09ead5dc2 100644 --- a/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Givaro/Givaro-4.2.0-GCCcore-11.3.0.eb @@ -38,4 +38,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib'], } +sanity_check_commands = ["givaro-config --help"] + moduleclass = 'math' From a3c608a65c2ed6b927e549f29846e1b69305b007 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Nov 2023 21:10:54 +0100 Subject: [PATCH 9436/9987] add sanity check command for lrslib --- easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb index 17ae62bb0c4..e9c03887918 100644 --- a/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/lrslib/lrslib-7.2-gompi-2022a.eb @@ -36,4 +36,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = ["lrsnash --help 2>&1 | grep 'usage.*lrsnash'"] + moduleclass = 'math' From 321ccf2e1cf84bdf36ad75ea4e8ddd9028773f4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Nov 2023 21:31:25 +0100 Subject: [PATCH 9437/9987] add sanity check command for nauty --- easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb b/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb index bc1a1036d2d..1fe2879b3c8 100644 --- a/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/n/nauty/nauty-2.8.6-GCC-11.3.0.eb @@ -48,4 +48,6 @@ sanity_check_paths = { 'dirs': [''] } +sanity_check_commands = ["dreadnaut --help"] + moduleclass = 'math' From cb355428d3db979d057ec1e1fc89fbb484da9a60 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Nov 2023 21:33:19 +0100 Subject: [PATCH 9438/9987] add sanity check command for PARI-GP --- .../easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb index 4b8ff351b17..44c09806f4d 100644 --- a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.15.4-GCCcore-11.3.0.eb @@ -33,4 +33,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include'] } +sanity_check_commands = ["gp --help"] + moduleclass = 'math' From 695bd52189ca97274b9d71070b3bf8b42ce737a1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 12 Nov 2023 21:48:24 +0100 Subject: [PATCH 9439/9987] add sanity check command for FFLAS-FFPACK --- .../easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb index e162b0e9773..75c22cfa096 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb @@ -36,4 +36,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib'], } +sanity_check_commands = ["fflas-ffpack-config --help"] + moduleclass = 'math' From 4a9684381ba32fb142979a51a1817033aaead2ee Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 07:57:14 +0800 Subject: [PATCH 9440/9987] add sanity check command for Singular --- .../easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb b/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb index 97c0499a3ab..9cbd46cd597 100644 --- a/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb +++ b/easybuild/easyconfigs/s/Singular/Singular-4.3.2p10-gfbf-2022a.eb @@ -42,4 +42,6 @@ sanity_check_paths = { ['libexec/singular', 'share'], } +sanity_check_commands = ["Singular --help"] + moduleclass = 'math' From ad709ccf04f12fd9dbd282e582eb2401550a9733 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:02:32 +0800 Subject: [PATCH 9441/9987] add sanity check command for LinBox --- easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb index 0fecede9ee7..b8c32471efc 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb @@ -39,4 +39,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib'], } +sanity_check_commands = ["linbox-config --help"] + moduleclass = 'math' From 331e27bb1979d18b41d20691923b3cecb9c0f9fc Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:09:03 +0800 Subject: [PATCH 9442/9987] add sanity check command for Normaliz --- easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb index d7f2cdf14cf..97f691eb2d0 100644 --- a/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb +++ b/easybuild/easyconfigs/n/Normaliz/Normaliz-3.10.1-gfbf-2022a.eb @@ -43,4 +43,6 @@ sanity_check_paths = { 'dirs': ['include/libnormaliz'] } +sanity_check_commands = ["normaliz --help"] + moduleclass = 'math' From 18b3ff79feb41251fac4c3871a10224ff23a6120 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:10:15 +0800 Subject: [PATCH 9443/9987] add sanity check command for gap -x --- easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb b/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb index 04d6ec24740..77a38aad37a 100644 --- a/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb +++ b/easybuild/easyconfigs/g/gap/gap-4.12.2-foss-2022a.eb @@ -49,4 +49,6 @@ sanity_check_paths = { 'dirs': ['share/gap'] } +sanity_check_commands = ["gap --help"] + moduleclass = 'math' From c4ed8dc16c2ff63decc5e173c8021c88407a470e Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:15:20 +0800 Subject: [PATCH 9444/9987] add sanity check command for eclib --- easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb b/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb index 374895237c3..1c6d6c78a88 100644 --- a/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/e/eclib/eclib-20230424-GCC-11.3.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': ['share'], } +sanity_check_commands = ["mwrank -h"] + moduleclass = 'math' From cad123fe3674cbb8a7a14145a1c914c1acfe700b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:17:17 +0800 Subject: [PATCH 9445/9987] add sanity check command for cliquer --- easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb index c3c98e348d9..8e68fac80d5 100644 --- a/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/cliquer/cliquer-1.21-GCCcore-11.3.0.eb @@ -28,4 +28,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ["cl --help"] + moduleclass = 'math' From 3ad1af638e74e6669b5b836527237f5a0e172d16 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 13 Nov 2023 08:30:05 +0800 Subject: [PATCH 9446/9987] add sanity check command for ECL --- easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb index 4a15b7330df..7785b55e3af 100644 --- a/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/e/ECL/ECL-23.9.9-GCCcore-11.3.0.eb @@ -27,4 +27,6 @@ sanity_check_paths = { 'dirs': ['share'], } +sanity_check_commands = ["ecl --help"] + moduleclass = 'lang' From 448336815bd8b47afadf5a729ecde7870bd8739d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Nov 2023 07:57:27 +0100 Subject: [PATCH 9447/9987] BiG-SCAPE: use correct name for the FastTree binary. --- .../b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 3 +++ ...CAPE-1.1.5_use_correct_name_for_FastTree.patch | 15 +++++++++++++++ 2 files changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb index 5c6c71a8721..54d08e2691e 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -17,6 +17,7 @@ patches = [ '%(name)s-%(version)s_use_env_var_to_find-MIBiG-files.patch', '%(name)s-%(version)s_use_env_var_for_domain_files.patch', '%(name)s-%(version)s_use_env_var_for_html.patch', + '%(name)s-%(version)s_use_correct_name_for_FastTree.patch', ] checksums = [ {'v1.1.5.tar.gz': 'ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7'}, @@ -25,6 +26,8 @@ checksums = [ {'BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch': '51337f22b2619ed38969f4ead5f7ce2f2df884f272793b47fb46d77e9c5e2aa2'}, {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'}, + {'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch': + 'e1572e4134c6163a3927ac32bd2a39b7f87cf01109f7913b3c55126e2381a771'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch new file mode 100644 index 00000000000..997ea971e5d --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch @@ -0,0 +1,15 @@ +FastTree binary is not lowercase. + +Åke Sandgren, 2023-11-13 +diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py +--- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 ++++ BiG-SCAPE-1.1.5/bigscape.py 2023-11-13 07:52:23.064042200 +0100 +@@ -1644,7 +1644,7 @@ + # make tree + newick_file_path = os.path.join(gcf_trees_path, "GCF_c{:4.2f}_{:05d}.newick".format(cutoff,exemplar_idx)) + with open(newick_file_path, "w") as newick_file: +- command = ["fasttree", "-nopr", "-quiet", alignment_file_path] ++ command = ["FastTree", "-nopr", "-quiet", alignment_file_path] + p = subprocess.Popen(command, stdout=newick_file, shell=False) + p.wait() # only with process has terminated will the file be ready + From 8392e0312d55bf38ec2bc7b95a2d1e8650c26921 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Nov 2023 12:45:47 +0000 Subject: [PATCH 9448/9987] adding easyconfigs: TOML-Fortran-0.4.1-GCC-12.2.0.eb, TOML-Fortran-0.4.1-intel-compilers-2022.2.1.eb --- .../TOML-Fortran-0.4.1-GCC-12.2.0.eb | 24 ++++++++++++++++++ ...-Fortran-0.4.1-intel-compilers-2022.2.1.eb | 25 +++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-GCC-12.2.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-GCC-12.2.0.eb new file mode 100644 index 00000000000..e3b1d6f709e --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-GCC-12.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.4.1' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['435f6c06dd7392ef282ed7567c9245ca64b8456d62cbf814ada9cbad60f21c00'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['lib/libtoml-f.a'], + 'dirs': ['include/toml-f', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..5acb344e912 --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.4.1-intel-compilers-2022.2.1.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.4.1' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['435f6c06dd7392ef282ed7567c9245ca64b8456d62cbf814ada9cbad60f21c00'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['lib/libtoml-f.a'], + 'dirs': ['include/toml-f', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' From c826e71ff0bea11b23c3f4c399fbe7d4fbddd2a4 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Nov 2023 13:01:05 +0000 Subject: [PATCH 9449/9987] adding easyconfigs: multicharge-0.2.0-gfbf-2022b.eb, multicharge-0.2.0-iimkl-2022b.eb --- .../multicharge-0.2.0-gfbf-2022b.eb | 43 +++++++++++++++++++ .../multicharge-0.2.0-iimkl-2022b.eb | 43 +++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022b.eb diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-gfbf-2022b.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-gfbf-2022b.eb new file mode 100644 index 00000000000..ca33f9ac6d7 --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-gfbf-2022b.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['953e2ace2f4035b1fa8ecf680f90b5ce6ad5caae17c8d8ccbc2578b92b69d3e7'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.39'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.2.0'), +] + +# configopts = '-DBLAS_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' +# configopts += '-DLAPACK_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022b.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022b.eb new file mode 100644 index 00000000000..7988816274b --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022b.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'iimkl', 'version': '2022b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['953e2ace2f4035b1fa8ecf680f90b5ce6ad5caae17c8d8ccbc2578b92b69d3e7'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.39'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.2.0'), +] + +configopts = '-DBLAS_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' +configopts += '-DLAPACK_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +moduleclass = 'chem' From 6c074533aae9122a0c2931f627ebf00cdd361d06 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Nov 2023 13:02:25 +0000 Subject: [PATCH 9450/9987] adding easyconfigs: mstore-0.2.0-intel-compilers-2022.2.1.eb, mstore-0.2.0-GCCcore-12.2.0.eb --- .../m/mstore/mstore-0.2.0-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ .../mstore-0.2.0-intel-compilers-2022.2.1.eb | 37 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.2.1.eb diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..9b307e46fbc --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mstore-info --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.2.1.eb new file mode 100644 index 00000000000..22c6dc7cd21 --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.2.1.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mstore-info --help"] + +moduleclass = 'chem' From 98af7b005894e16eb7200b289f1bb4e79306a573 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 13 Nov 2023 13:04:36 +0000 Subject: [PATCH 9451/9987] adding easyconfigs: dftd4-3.4.0-iimkl-2022b.eb, dftd4-3.4.0-gfbf-2022b.eb --- .../d/dftd4/dftd4-3.4.0-gfbf-2022b.eb | 41 +++++++++++++++++ .../d/dftd4/dftd4-3.4.0-iimkl-2022b.eb | 44 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-iimkl-2022b.eb diff --git a/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-gfbf-2022b.eb b/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-gfbf-2022b.eb new file mode 100644 index 00000000000..0868fa75c7b --- /dev/null +++ b/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-gfbf-2022b.eb @@ -0,0 +1,41 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'dftd4' +version = '3.4.0' + +homepage = 'https://github.com/dftd4/dftd4' +description = """Generally Applicable Atomic-Charge Dependent London Dispersion Correction.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +github_account = 'dftd4' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f3b0a16a952817ae48e819626e13676fba3b61c8beea47b0f8ada2fbb679fb7b'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.39'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.2.0'), + ('multicharge', '0.2.0'), +] +# +# run suite of tests with ctest +test_cmd = 'ctest --parallel 1' +runtest = '' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["dftd4 --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-iimkl-2022b.eb b/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-iimkl-2022b.eb new file mode 100644 index 00000000000..df1ee93ef68 --- /dev/null +++ b/easybuild/easyconfigs/d/dftd4/dftd4-3.4.0-iimkl-2022b.eb @@ -0,0 +1,44 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'dftd4' +version = '3.4.0' + +homepage = 'https://github.com/dftd4/dftd4' +description = """Generally Applicable Atomic-Charge Dependent London Dispersion Correction.""" + +toolchain = {'name': 'iimkl', 'version': '2022b'} + +github_account = 'dftd4' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f3b0a16a952817ae48e819626e13676fba3b61c8beea47b0f8ada2fbb679fb7b'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('binutils', '2.39'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.2.0'), + ('multicharge', '0.2.0'), +] + +configopts = '-DBLAS_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' +configopts += '-DLAPACK_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' + +# run suite of tests with ctest +test_cmd = 'ctest --parallel 2' +runtest = '' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["dftd4 --help"] + +moduleclass = 'chem' From bf149f64a3924032551f61902f67adaa94a75d13 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 13 Nov 2023 14:38:59 +0100 Subject: [PATCH 9452/9987] Make Pillow easyconfigs aware of sysroot --- .../easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb | 7 +++++++ .../p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 7 +++++++ .../easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb | 7 +++++++ 13 files changed, 91 insertions(+) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb index 21d8071c49b..db4238313ed 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb index fa078fe683a..268240341d2 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb @@ -25,8 +25,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb index 5bd030dd974..a52368bb6ac 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb @@ -25,8 +25,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb index 0e9cf1b4445..dfcebb3a91d 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -29,8 +29,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 6c8f256ce9a..2195b83f130 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -28,8 +28,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb index 6274b50e9b0..87e923978b0 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb @@ -28,8 +28,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb index 4b4a35c2651..6ba7c115749 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb @@ -28,8 +28,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb index 098deac80fa..975b2bc89a8 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb index caa9fcf574f..fcb88fb0431 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb index 6516e4b933b..e2af6602733 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb index 1105bf2154e..2e900babcb2 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb index f925080a099..c304bb9fc68 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -26,8 +26,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb index cb1ef19b3f0..03cb9b29175 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb @@ -24,8 +24,15 @@ dependencies = [ ] download_dep_fail = True + +# If we have a sysroot, make sure it is picked up +# (should not affect non-sysroot as the template is empty in this scenario) +preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " +preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " + # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + use_pip = True sanity_pip_check = True From 7b966e8c4db034e788dac93a483ede79df5442b4 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Mon, 13 Nov 2023 13:39:07 +0000 Subject: [PATCH 9453/9987] adding easyconfigs: strace-6.6-GCCcore-12.2.0.eb --- .../s/strace/strace-6.6-GCCcore-12.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..a5f0699fc99 --- /dev/null +++ b/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'strace' +version = '6.6' + +homepage = 'https://strace.io/' +description = """ +strace is a diagnostic, debugging and instructional userspace utility for Linux. It is used to monitor and tamper with +interactions between processes and the Linux kernel, which include system calls, signal deliveries, and changes of +process state. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/strace/strace/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['421b4186c06b705163e64dc85f271ebdcf67660af8667283147d5e859fc8a96c'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = "--enable-mpers=check" + +sanity_check_paths = { + 'files': ['bin/strace-log-merge', 'bin/strace'], + 'dirs': ['share'] +} + +sanity_check_commands = ['strace --help'] + +moduleclass = 'system' From c0ad1ab06170b2261c75d94a29839c02a9e4408e Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Mon, 13 Nov 2023 15:57:14 +0100 Subject: [PATCH 9454/9987] Fix typo --- easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb | 2 +- .../p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb | 2 +- 13 files changed, 13 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb index db4238313ed..823fd234dfa 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb index 268240341d2..a8360e2bc0c 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.0.0-GCCcore-8.2.0.eb @@ -29,7 +29,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb index a52368bb6ac..7624d218ee5 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-6.2.1-GCCcore-8.3.0.eb @@ -29,7 +29,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb index dfcebb3a91d..8bb25ce9590 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-7.0.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -33,7 +33,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb index 2195b83f130..34563e55acf 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.0.1-GCCcore-10.2.0.eb @@ -32,7 +32,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb index 87e923978b0..66f47353838 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.2.0-GCCcore-10.3.0.eb @@ -32,7 +32,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb index 6ba7c115749..8af0717a0b8 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.1-GCCcore-11.2.0.eb @@ -32,7 +32,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb index 975b2bc89a8..f9a774e6a89 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-8.3.2-GCCcore-11.2.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb index fcb88fb0431..0805f5cb64c 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.0-GCCcore-10.3.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb index e2af6602733..79ced7c8c2a 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb index 2e900babcb2..6021839c820 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.3.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb index c304bb9fc68..bc254d1f99f 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -30,7 +30,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb index 03cb9b29175..9c723fb6f2d 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.4.0-GCCcore-12.2.0.eb @@ -28,7 +28,7 @@ download_dep_fail = True # If we have a sysroot, make sure it is picked up # (should not affect non-sysroot as the template is empty in this scenario) preinstallopts = "export CPATH=$CPATH:%(sysroot)s/usr/include && " -preinstallopts = "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " +preinstallopts += "export LIBRARY_PATH=$LIBRARY_PATH:%(sysroot)s/usr/lib:%(sysroot)s/usr/lib64 && " # avoid that hardcoded paths like /usr/include are used in build commands installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " From fc74053cb4ce12df82c7f492f948019a3a18ac34 Mon Sep 17 00:00:00 2001 From: TopRichard <121792457+TopRichard@users.noreply.github.com> Date: Mon, 13 Nov 2023 17:35:59 +0100 Subject: [PATCH 9455/9987] Update strace-6.6-GCCcore-12.2.0.eb --- easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb index a5f0699fc99..d3187e80ef7 100644 --- a/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/strace/strace-6.6-GCCcore-12.2.0.eb @@ -17,7 +17,7 @@ sources = [SOURCE_TAR_XZ] checksums = ['421b4186c06b705163e64dc85f271ebdcf67660af8667283147d5e859fc8a96c'] builddependencies = [ - ('binutils', '2.40'), + ('binutils', '2.39'), ] configopts = "--enable-mpers=check" From b1210f45c18d7aecf9eddf778098dd33aaccdecc Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 13 Nov 2023 18:20:25 +0100 Subject: [PATCH 9456/9987] {bio}[foss/2022a] topaz-em w/ CUDA 11.7.0 w/ PyTorch 1.12.0 --- ...3-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 67 +++++++++++++++++++ ...az-em-0.2.5_install_relion3_wrappers.patch | 14 ++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb create mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5_install_relion3_wrappers.patch diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..6a7315621a1 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb @@ -0,0 +1,67 @@ +# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/1 +easyblock = 'PythonPackage' + +name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi +_mainversion = '0.2.5' +_patchdate = '2230923' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) +_cudasuffix = '-CUDA-%(cudaver)s' +_pytorch_ver = '1.12.0' +_pytorchsuffix = '-PyTorch-%s' % _pytorch_ver +versionsuffix = _cudasuffix + _pytorchsuffix +_mainversion = '0.2.5' +_patchdate = '2230923' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) + +homepage = 'http://cb.csail.mit.edu/cb/topaz/' + +description = """Particle picking software for single particle cryo-electron microscopy using +convolutional neural networks and positive-unlabeled learning. Includes methods +for micrograph denoising.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', _pytorch_ver, _cudasuffix), + ('scikit-learn', '1.1.2'), + ('torchvision', '0.13.1', _cudasuffix), +] + + +source_urls = [ + 'https://github.com/tbepler/topaz/archive', + 'https://github.com/tbepler/topaz/compare/' +] +sources = ['v%s.tar.gz' % _mainversion] +patches = [ + 'topaz-em-0.2.5_install_relion3_wrappers.patch', + 'v%s..%s.patch' % (_mainversion, _patchsha) +] +checksums = [ + {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, + {'topaz-em-0.2.5_install_relion3_wrappers.patch': + '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, + {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': + 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, +] + +sanity_pip_check = True +options = {'modulename': 'topaz'} +_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] +sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] +sanity_check_paths = { + 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5_install_relion3_wrappers.patch b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5_install_relion3_wrappers.patch new file mode 100644 index 00000000000..533e6e11b93 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5_install_relion3_wrappers.patch @@ -0,0 +1,14 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11 +# install relion3 wrappers into bin +diff -ru topaz-0.2.5/setup.py topaz-0.2.5_install_relion3_wrappers/setup.py +--- topaz-0.2.5/setup.py 2022-03-11 02:33:01.000000000 +0100 ++++ topaz-0.2.5_install_relion3_wrappers/setup.py 2023-11-13 17:46:28.306807471 +0100 +@@ -30,7 +30,7 @@ + #package_dir = {'': 'topaz'}, + entry_points = {'console_scripts': ['topaz = topaz.main:main']}, + include_package_data = True, +- ++ scripts=['relion_run_topaz/run_topaz_%s.py' % x for x in ['denoise','pick','train','train_denoise']], + install_requires=[ + 'torch>=1.0.0', + 'torchvision', From 3a75d06c8c6874dfb2e94f1c62a594760ab0981e Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 13 Nov 2023 18:29:04 +0100 Subject: [PATCH 9457/9987] fix typos and duplicates --- ...3-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..ff22ba3d5e6 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb @@ -0,0 +1,67 @@ +# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/11 +easyblock = 'PythonPackage' + +name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi +_mainversion = '0.2.5' +_patchdate = '2230923' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) +_cudasuffix = '-CUDA-%(cudaver)s' +_pytorch_ver = '1.12.0' +_pytorchsuffix = '-PyTorch-%s' % _pytorch_ver +versionsuffix = _cudasuffix + _pytorchsuffix +_mainversion = '0.2.5' +_patchdate = '220923' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) + +homepage = 'http://cb.csail.mit.edu/cb/topaz/' + +description = """Particle picking software for single particle cryo-electron microscopy using +convolutional neural networks and positive-unlabeled learning. Includes methods +for micrograph denoising.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', _pytorch_ver, _cudasuffix), + ('scikit-learn', '1.1.2'), + ('torchvision', '0.13.1', _cudasuffix), +] + + +source_urls = [ + 'https://github.com/tbepler/topaz/archive', + 'https://github.com/tbepler/topaz/compare/' +] +sources = ['v%s.tar.gz' % _mainversion] +patches = [ + 'topaz-em-0.2.5_install_relion3_wrappers.patch', + 'v%s..%s.patch' % (_mainversion, _patchsha) +] +checksums = [ + {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, + {'topaz-em-0.2.5_install_relion3_wrappers.patch': + '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, + {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': + 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, +] + +sanity_pip_check = True +options = {'modulename': 'topaz'} +_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] +sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] +sanity_check_paths = { + 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], + 'dirs': [], +} + +moduleclass = 'bio' From 190f7bccf4cb008e06b53ad8948639f5c4b585fd Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 13 Nov 2023 18:32:04 +0100 Subject: [PATCH 9458/9987] fix typos and duplicates --- ...6-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb new file mode 100644 index 00000000000..2adbcba0f55 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb @@ -0,0 +1,63 @@ +# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/11 +easyblock = 'PythonPackage' + +name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi +_mainversion = '0.2.5' +_patchdate = '230926' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) +_cudasuffix = '-CUDA-%(cudaver)s' +_pytorch_ver = '1.12.0' +_pytorchsuffix = '-PyTorch-%s' % _pytorch_ver +versionsuffix = _cudasuffix + _pytorchsuffix + +homepage = 'http://cb.csail.mit.edu/cb/topaz/' + +description = """Particle picking software for single particle cryo-electron microscopy using +convolutional neural networks and positive-unlabeled learning. Includes methods +for micrograph denoising.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', _pytorch_ver, _cudasuffix), + ('scikit-learn', '1.1.2'), + ('torchvision', '0.13.1', _cudasuffix), +] + + +source_urls = [ + 'https://github.com/tbepler/topaz/archive', + 'https://github.com/tbepler/topaz/compare/' +] +sources = ['v%s.tar.gz' % _mainversion] +patches = [ + 'topaz-em-0.2.5_install_relion3_wrappers.patch', + 'v%s..%s.patch' % (_mainversion, _patchsha) +] +checksums = [ + {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, + {'topaz-em-0.2.5_install_relion3_wrappers.patch': + '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, + {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': + 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, +] + +sanity_pip_check = True +options = {'modulename': 'topaz'} +_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] +sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] +sanity_check_paths = { + 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], + 'dirs': [], +} + +moduleclass = 'bio' From 41b7dd2f522a939a7a978aef9ab69725f6015ca4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 13 Nov 2023 18:36:46 +0100 Subject: [PATCH 9459/9987] Delete easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb --- ...3-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 67 ------------------- 1 file changed, 67 deletions(-) delete mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb deleted file mode 100644 index ff22ba3d5e6..00000000000 --- a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.220923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb +++ /dev/null @@ -1,67 +0,0 @@ -# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/11 -easyblock = 'PythonPackage' - -name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi -_mainversion = '0.2.5' -_patchdate = '2230923' -_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' -version = '%s.%s' % (_mainversion, _patchdate) -_cudasuffix = '-CUDA-%(cudaver)s' -_pytorch_ver = '1.12.0' -_pytorchsuffix = '-PyTorch-%s' % _pytorch_ver -versionsuffix = _cudasuffix + _pytorchsuffix -_mainversion = '0.2.5' -_patchdate = '220923' -_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' -version = '%s.%s' % (_mainversion, _patchdate) - -homepage = 'http://cb.csail.mit.edu/cb/topaz/' - -description = """Particle picking software for single particle cryo-electron microscopy using -convolutional neural networks and positive-unlabeled learning. Includes methods -for micrograph denoising.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -use_pip = True - -builddependencies = [ - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('CUDA', '11.7.0', '', True), - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('PyTorch', _pytorch_ver, _cudasuffix), - ('scikit-learn', '1.1.2'), - ('torchvision', '0.13.1', _cudasuffix), -] - - -source_urls = [ - 'https://github.com/tbepler/topaz/archive', - 'https://github.com/tbepler/topaz/compare/' -] -sources = ['v%s.tar.gz' % _mainversion] -patches = [ - 'topaz-em-0.2.5_install_relion3_wrappers.patch', - 'v%s..%s.patch' % (_mainversion, _patchsha) -] -checksums = [ - {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, - {'topaz-em-0.2.5_install_relion3_wrappers.patch': - '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, - {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': - 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, -] - -sanity_pip_check = True -options = {'modulename': 'topaz'} -_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] -sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] -sanity_check_paths = { - 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], - 'dirs': [], -} - -moduleclass = 'bio' From 08a692a0c7a5b8da02e507b92e79d3b06310753b Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 13 Nov 2023 18:37:06 +0100 Subject: [PATCH 9460/9987] Delete easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb --- ...3-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 67 ------------------- 1 file changed, 67 deletions(-) delete mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb deleted file mode 100644 index 6a7315621a1..00000000000 --- a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.2230923-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb +++ /dev/null @@ -1,67 +0,0 @@ -# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/1 -easyblock = 'PythonPackage' - -name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi -_mainversion = '0.2.5' -_patchdate = '2230923' -_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' -version = '%s.%s' % (_mainversion, _patchdate) -_cudasuffix = '-CUDA-%(cudaver)s' -_pytorch_ver = '1.12.0' -_pytorchsuffix = '-PyTorch-%s' % _pytorch_ver -versionsuffix = _cudasuffix + _pytorchsuffix -_mainversion = '0.2.5' -_patchdate = '2230923' -_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' -version = '%s.%s' % (_mainversion, _patchdate) - -homepage = 'http://cb.csail.mit.edu/cb/topaz/' - -description = """Particle picking software for single particle cryo-electron microscopy using -convolutional neural networks and positive-unlabeled learning. Includes methods -for micrograph denoising.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -use_pip = True - -builddependencies = [ - ('pkg-config', '0.29.2'), -] -dependencies = [ - ('CUDA', '11.7.0', '', True), - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('PyTorch', _pytorch_ver, _cudasuffix), - ('scikit-learn', '1.1.2'), - ('torchvision', '0.13.1', _cudasuffix), -] - - -source_urls = [ - 'https://github.com/tbepler/topaz/archive', - 'https://github.com/tbepler/topaz/compare/' -] -sources = ['v%s.tar.gz' % _mainversion] -patches = [ - 'topaz-em-0.2.5_install_relion3_wrappers.patch', - 'v%s..%s.patch' % (_mainversion, _patchsha) -] -checksums = [ - {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, - {'topaz-em-0.2.5_install_relion3_wrappers.patch': - '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, - {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': - 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, -] - -sanity_pip_check = True -options = {'modulename': 'topaz'} -_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] -sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] -sanity_check_paths = { - 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], - 'dirs': [], -} - -moduleclass = 'bio' From e6ceb42223d550e574b994c72a7c7195a99160c3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Nov 2023 17:40:20 +0000 Subject: [PATCH 9461/9987] adding easyconfigs: GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb, GROMACS-2023.3-foss-2022a.eb --- .../GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb | 88 +++++++++++++++++++ .../g/GROMACS/GROMACS-2023.3-foss-2022a.eb | 86 ++++++++++++++++++ 2 files changed, 174 insertions(+) create mode 100755 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb create mode 100755 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb new file mode 100755 index 00000000000..e2b86108e93 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,88 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2023.3.tar.gz': '4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('scikit-build', '0.15.0'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.3.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb new file mode 100755 index 00000000000..9a72a3c43d4 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb @@ -0,0 +1,86 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.3' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2023.3.tar.gz': '4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('scikit-build', '0.15.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.3.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 1e7b15e6fb6579f1ffd512db412ab6c164923274 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 13 Nov 2023 19:06:56 +0000 Subject: [PATCH 9462/9987] no exe --- .../g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb | 0 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb | 0 2 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb mode change 100755 => 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a-CUDA-11.7.0.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb old mode 100755 new mode 100644 From 7978703a427030c957bc12420be08e077caaa7d7 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 14 Nov 2023 09:39:51 +0100 Subject: [PATCH 9463/9987] fix typos and duplicates --- ...opaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb index 2adbcba0f55..a83158b339f 100644 --- a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.230926-foss-2022a-CUDA-11.7.0-PyTorch-1.12.0.eb @@ -51,6 +51,7 @@ checksums = [ 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, ] +download_dep_fail = True sanity_pip_check = True options = {'modulename': 'topaz'} _relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] From 0ab5d9ec0f7fc608cf7e481cd0dcd6e7a9e0d335 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 14 Nov 2023 10:51:30 +0100 Subject: [PATCH 9464/9987] adding easyconfigs: NVHPC-23.7-CUDA-12.2.0.eb --- .../n/NVHPC/NVHPC-23.7-CUDA-12.2.0.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.2.0.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.2.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.2.0.eb new file mode 100644 index 00000000000..46f5e66cea0 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-23.7-CUDA-12.2.0.eb @@ -0,0 +1,66 @@ +name = 'NVHPC' +version = '23.7' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2023_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = ['fea91d95ff18bca1ce7afde50371caa02001ade8bed6ddfc5ff70862ccbebece'] + +local_gccver = '12.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.40', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.16', '', ('GCCcore', local_gccver)), + ('CUDA', '12.2.0', '', SYSTEM), +] + +module_add_cuda = False + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/$version/cuda/) where $version is the NVHPC version +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '%(cudaver)s' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From 7dbdd505ff8ec6bd4ae78afae78ac416f3d053bd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 14 Nov 2023 13:11:07 +0100 Subject: [PATCH 9465/9987] fix possible error/crash in NCCL on x86 due to cpuid --- .../NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb | 6 ++- .../NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb | 6 ++- .../NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb | 6 ++- .../n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb | 6 ++- ...NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb | 6 ++- .../NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 6 ++- .../n/NCCL/NCCL-2.16.2_fix-cpuid.patch | 43 +++++++++++++++++++ .../NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb | 7 ++- .../NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb | 10 +++-- .../NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb | 10 +++-- 10 files changed, 92 insertions(+), 14 deletions(-) create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.16.2_fix-cpuid.patch diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb index 16e18e8e36e..d4fb6614198 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-10.3.0-CUDA-11.3.1.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.10.3-1.tar.gz': '55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.36.1')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb index 63927a18ac1..5dec7af894e 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.10.3-1.tar.gz': '55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb index e3a29b13334..da1b8400a0f 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.10.3-1.tar.gz': '55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb index a80da45c38a..407de136e21 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.11.4-gcccuda-2019b.eb @@ -10,6 +10,10 @@ toolchain = {'name': 'gcccuda', 'version': '2019b'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['db4e9a0277a64f9a31ea9b5eea22e63f10faaed36dded4587bbc8a0d8eceed10'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.11.4-1.tar.gz': 'db4e9a0277a64f9a31ea9b5eea22e63f10faaed36dded4587bbc8a0d8eceed10'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb index 2282286a915..89fcfe9a013 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.12.12-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['49b4fbfeebf1f62f6ceb69e72504045d8d1b4e7609e3c2477906f3004c7e2d82'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.12.12-1.tar.gz': '49b4fbfeebf1f62f6ceb69e72504045d8d1b4e7609e3c2477906f3004c7e2d82'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb index cd576dcb0e7..17636f6fb8b 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = ['7f7c738511a8876403fc574d13d48e7c250d934d755598d82e14bab12236fc64'] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.16.2-1.tar.gz': '7f7c738511a8876403fc574d13d48e7c250d934d755598d82e14bab12236fc64'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.39')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2_fix-cpuid.patch b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2_fix-cpuid.patch new file mode 100644 index 00000000000..de293c36e76 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2_fix-cpuid.patch @@ -0,0 +1,43 @@ +The 2nd CPUID asm code modifies registers used by other variables due to failure to list +EBX, ECX & EDX in the "clobbers" list. +This causes corruption leading to segfaults or wrong results depending on compiler optimization/register allocation. + +Fix by using the __cpuid GCC function. +See https://github.com/NVIDIA/nccl/pull/1070 + +Author: Alexander Grund (TU Dresden) + +diff --git a/src/graph/xml.cc b/src/graph/xml.cc +index 316d20f..d0d1272 100644 +--- a/src/graph/xml.cc ++++ b/src/graph/xml.cc +@@ -12,6 +12,9 @@ + #include "core.h" + #include "nvmlwrap.h" + #include "xml.h" ++#if defined(__x86_64__) ++#include ++#endif + + /*******************/ + /* XML File Parser */ +@@ -408,7 +411,8 @@ ncclResult_t ncclTopoGetXmlFromCpu(struct ncclXmlNode* cpuNode, struct ncclXml* + char vendor[12]; + } cpuid0; + +- asm volatile("cpuid" : "=b" (cpuid0.ebx), "=c" (cpuid0.ecx), "=d" (cpuid0.edx) : "a" (0) : "memory"); ++ unsigned unused; ++ __cpuid(0, unused, cpuid0.ebx, cpuid0.ecx, cpuid0.edx); + char vendor[13]; + strncpy(vendor, cpuid0.vendor, 12); + vendor[12] = '\0'; +@@ -430,7 +434,8 @@ ncclResult_t ncclTopoGetXmlFromCpu(struct ncclXmlNode* cpuNode, struct ncclXml* + }; + uint32_t val; + } cpuid1; +- asm volatile("cpuid" : "=a" (cpuid1.val) : "a" (1) : "memory"); ++ unsigned unused; ++ __cpuid(1, cpuid1.val, unused, unused, unused); + int familyId = cpuid1.familyId + (cpuid1.extFamilyId << 4); + int modelId = cpuid1.modelId + (cpuid1.extModelId << 4); + NCCLCHECK(xmlSetAttrInt(cpuNode, "familyid", familyId)); diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb index d23741aa2c8..ade0f545d36 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.18.3-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -11,8 +11,11 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -checksums = [('6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9', - 'b4f5d7d9eea2c12e32e7a06fe138b2cfc75969c6d5c473aa6f819a792db2fc96')] +patches = ['NCCL-2.16.2_fix-cpuid.patch'] +checksums = [ + {'v2.18.3-1.tar.gz': '6477d83c9edbb34a0ebce6d751a1b32962bc6415d75d04972b676c6894ceaef9'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, +] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb index 81fa9b3dfaa..3c825519ba4 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-10.2.0-CUDA-11.1.1.eb @@ -16,10 +16,14 @@ dependencies = [('CUDAcore', local_cuda_version, '', SYSTEM)] github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -patches = ['NCCL-2.8.3_fix-isend-irecv.patch'] +patches = [ + 'NCCL-2.8.3_fix-isend-irecv.patch', + 'NCCL-2.16.2_fix-cpuid.patch', +] checksums = [ - '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6', # v2.8.3-1.tar.gz - '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92', # NCCL-2.8.3_fix-isend-irecv.patch + {'v2.8.3-1.tar.gz': '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6'}, + {'NCCL-2.8.3_fix-isend-irecv.patch': '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb index 140a12a4575..700f896be0e 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.8.3-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -16,10 +16,14 @@ dependencies = [('CUDAcore', local_cuda_version, '', SYSTEM)] github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s-1.tar.gz'] -patches = ['NCCL-2.8.3_fix-isend-irecv.patch'] +patches = [ + 'NCCL-2.8.3_fix-isend-irecv.patch', + 'NCCL-2.16.2_fix-cpuid.patch', +] checksums = [ - '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6', # v2.8.3-1.tar.gz - '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92', # NCCL-2.8.3_fix-isend-irecv.patch + {'v2.8.3-1.tar.gz': '3ae89ddb2956fff081e406a94ff54ae5e52359f5d645ce977c7eba09b3b782e6'}, + {'NCCL-2.8.3_fix-isend-irecv.patch': '04d61ea9b9f0954bed05494017649a68950b6b5e5851d969244f9ab67d5ecc92'}, + {'NCCL-2.16.2_fix-cpuid.patch': '0459ecadcd32b2a7a000a2ce4f675afba908b2c0afabafde585330ff4f83e277'}, ] moduleclass = 'lib' From 79847f8e6764d4897df03dd6db5d53ffa7cadf7e Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Tue, 14 Nov 2023 16:54:04 +0000 Subject: [PATCH 9466/9987] adding easyconfigs: Restrander-20230713-GCCcore-12.2.0.eb --- .../Restrander-20230713-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/r/Restrander/Restrander-20230713-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/r/Restrander/Restrander-20230713-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Restrander/Restrander-20230713-GCCcore-12.2.0.eb new file mode 100644 index 00000000000..2cedafa4643 --- /dev/null +++ b/easybuild/easyconfigs/r/Restrander/Restrander-20230713-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'Restrander' +# No release or tag, so using the date of the last commit +version = '20230713' +github_account = 'mritchielab' +local_commit = '54a61fa' + +homepage = "https://github.com/mritchielab/restrander" +description = "A fast, accurate program for orienting and quality-checking cDNA sequencing reads." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/%(github_account)s/%(name)s/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['8b23c9992f81896b54d73c05b447f9002fe9482d848de16e1622e09961196237'] + +builddependencies = [ + ('binutils', '2.39'), +] + +files_to_copy = [ + (["restrander"], "bin/"), + 'README.md', + 'config', + 'figures', + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/restrander', 'README.md'], + 'dirs': ['config', 'figures'], +} + +moduleclass = 'bio' From 5cc18b8d21cdd90e3dcab5c5c1958fcc07dcd3bd Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Nov 2023 13:56:43 +0000 Subject: [PATCH 9467/9987] adding easyconfigs: STAR-2.7.11a-GCC-12.2.0.eb --- .../s/STAR/STAR-2.7.11a-GCC-12.2.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb new file mode 100644 index 00000000000..42f094bb67b --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11a-GCC-12.2.0.eb @@ -0,0 +1,51 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen +# modified by Thomas Eylenbosch + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.11a' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'openmp': True} + +github_account = 'alexdobin' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['STAR-%(version)s_use-external-htslib.patch'] +checksums = [ + {'%(version)s.tar.gz': '542457b1a4fee73f27a581b1776e9f73ad2b4d7e790388b6dc71147bd039f99a'}, + {'STAR-%(version)s_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, +] + +dependencies = [ + ('HTSlib', '1.17'), + ('zlib', '1.2.12'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +files_to_copy = [ + (['source/%(name)s', 'source/%(name)slong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/%(name)slong'], + 'dirs': [], +} + +sanity_check_commands = [ + "STAR --help", + "STARlong --help", +] + +moduleclass = 'bio' From a64b19e3202c9b4c8a3667e73269782cea696511 Mon Sep 17 00:00:00 2001 From: "A.H. Kole" Date: Wed, 15 Nov 2023 15:09:10 +0100 Subject: [PATCH 9468/9987] adding easyconfigs: libfdf-0.5.0-GCC-11.3.0.eb --- .../l/libfdf/libfdf-0.5.0-GCC-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.5.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.5.0-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.5.0-GCC-11.3.0.eb new file mode 100644 index 00000000000..245b4e41e57 --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.5.0-GCC-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'libfdf' +version = '0.5.0' + +homepage = 'https://gitlab.com/siesta-project/libraries/libfdf' +description = """LibFDF is the official implementation of the FDF specifications for use in client codes.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a8ac07a0d27ec9a96ee0691221cee8a18b5c60aaa001fcdc6858a9bfa0782f5f'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/libfdf.a'], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libfdf'], +} + +runtest = 'test' + +moduleclass = 'data' From 44a8fc58426c01e4bdfed5475e1d738fec8f8eb1 Mon Sep 17 00:00:00 2001 From: "A.H. Kole" Date: Wed, 15 Nov 2023 15:25:19 +0100 Subject: [PATCH 9469/9987] adding easyconfigs: flook-0.8.1-GCC-11.3.0.eb and patches: flook-0.8.1_flook.pc.in.patch --- .../f/flook/flook-0.8.1-GCC-11.3.0.eb | 33 +++++++++++++++++++ .../f/flook/flook-0.8.1_flook.pc.in.patch | 11 +++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1_flook.pc.in.patch diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb new file mode 100644 index 00000000000..3c6df83f972 --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb @@ -0,0 +1,33 @@ +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """The fortran-Lua-hook library.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +patches = [ + ('flook-%(version)s_setup.make', './setup.make'), + 'flook-%(version)s_flook.pc.in.patch', +] +checksums = [ + {'flook-0.8.1.tar.gz': 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e'}, + {'flook-0.8.1_setup.make': '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0'}, + {'flook-0.8.1_flook.pc.in.patch': '1aa3635d83f0f9bad2ef2f9457183aefa94c8f07e66d3ef31e8897190752b42c'}, +] + +dependencies = [('Lua', '5.4.4')] + +parallel = 1 + +local_comp_flags = 'VENDOR="gnu" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1_flook.pc.in.patch b/easybuild/easyconfigs/f/flook/flook-0.8.1_flook.pc.in.patch new file mode 100644 index 00000000000..86e8375df05 --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1_flook.pc.in.patch @@ -0,0 +1,11 @@ +diff --git a/flook.pc.in b/flook.pc.in +index 680b5e0..b46f8ad 100644 +--- a/flook.pc.in ++++ b/flook.pc.in +@@ -10,5 +10,5 @@ Version: @PROJECT_VERSION@ + URL: https://github.com/ElectronicStructureLibrary/flook + Cflags: -I${includedir} + Libs.private: -ldl +-Libs: -L${libdir} -lflookall ++Libs: -L${libdir} -lflookall -llua -ldl + From 6ebaa42549951a915b81733e89cfd20578117805 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Wed, 15 Nov 2023 15:37:39 +0100 Subject: [PATCH 9470/9987] remove empty lines --- easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb b/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb index 48f2a840462..5095a3d9cb2 100644 --- a/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb +++ b/easybuild/easyconfigs/c/castor/castor-1.7.11-foss-2022a.eb @@ -14,7 +14,6 @@ fitting and simulating diversification models, dating trees, comparing trees, an reading/writing trees in Newick format. """ - toolchain = {'name': 'foss', 'version': '2022a'} source_urls = [ From 18a25c8111b45828eb59e2b5fcefeb0101c47a06 Mon Sep 17 00:00:00 2001 From: "A.H. Kole" Date: Wed, 15 Nov 2023 16:04:10 +0100 Subject: [PATCH 9471/9987] Moved sanity check and buildopts to easyblock --- .../easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb index 3c6df83f972..aeab9ee569a 100644 --- a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.3.0.eb @@ -20,14 +20,4 @@ checksums = [ dependencies = [('Lua', '5.4.4')] -parallel = 1 - -local_comp_flags = 'VENDOR="gnu" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' -buildopts = 'liball %s' % local_comp_flags - -sanity_check_paths = { - 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], - 'dirs': [], -} - moduleclass = 'data' From 3140cc08c6ae5a89aaf23764d16d2d2f257e770a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 15 Nov 2023 17:02:58 +0100 Subject: [PATCH 9472/9987] rename; bugfix patch --- ...m-0.2.5.20230926-foss-2022a-CUDA-11.7.0.eb | 61 + ...e725efa9181e55864054f492a41b4abe8c1c.patch | 8128 +++++++++++++++++ 2 files changed, 8189 insertions(+) create mode 100644 easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.20230926-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/t/topaz-em/v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch diff --git a/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.20230926-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.20230926-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 00000000000..526b8270dda --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/topaz-em-0.2.5.20230926-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,61 @@ +# Thomas Hoffman, EMBL Heidelberg, structures-it@embl.de, 2023/11 +easyblock = 'PythonPackage' + +name = 'topaz-em' # named topaz-em instead of topaz to be consistent with pypi +_mainversion = '0.2.5' +_patchdate = '20230926' +_patchsha = 'dadfe725efa9181e55864054f492a41b4abe8c1c' +version = '%s.%s' % (_mainversion, _patchdate) +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://cb.csail.mit.edu/cb/topaz/' + +description = """Particle picking software for single particle cryo-electron microscopy using +convolutional neural networks and positive-unlabeled learning. Includes methods +for micrograph denoising.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.0', versionsuffix), + ('scikit-learn', '1.1.2'), + ('torchvision', '0.13.1', versionsuffix), +] + + +source_urls = [ + 'https://github.com/tbepler/topaz/archive', + 'https://github.com/tbepler/topaz/compare/' +] +sources = ['v%s.tar.gz' % _mainversion] +patches = [ + 'topaz-em-0.2.5_install_relion3_wrappers.patch', + 'v%s..%s.patch' % (_mainversion, _patchsha) +] +checksums = [ + {'v0.2.5.tar.gz': '33bba5fc071dcdf584cfc8c152ffe889a95b71ebad7ddefd15d3f81a96987417'}, + {'topaz-em-0.2.5_install_relion3_wrappers.patch': + '0fe23a0ecaf887aaa89641a7e7cf37fafd3134384b0a8f46acb4e17537d1a151'}, + {'v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch': + 'f0dc2f0613138cff856274e5367a767d97f46dd2b47ba2a932f8ca1d20b93de1'}, +] + +download_dep_fail = True +sanity_pip_check = True +options = {'modulename': 'topaz'} +_relion3_wrappers = ['denoise', 'pick', 'train', 'train_denoise'] +sanity_check_commands = ['run_topaz_%s.py --help' % x for x in _relion3_wrappers] + ['topaz --help'] +sanity_check_paths = { + 'files': ["bin/run_topaz_%s.py" % x for x in _relion3_wrappers], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/topaz-em/v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch b/easybuild/easyconfigs/t/topaz-em/v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch new file mode 100644 index 00000000000..75d8b088944 --- /dev/null +++ b/easybuild/easyconfigs/t/topaz-em/v0.2.5..dadfe725efa9181e55864054f492a41b4abe8c1c.patch @@ -0,0 +1,8128 @@ +From 512ff354295d28c884ce0934f51705029bc78be9 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Fri, 11 Mar 2022 17:29:16 -0500 +Subject: [PATCH 01/28] BasicConv test file, sphinx quickstart + +--- + docs/Makefile | 20 ++++++++++++++ + docs/make.bat | 35 ++++++++++++++++++++++++ + docs/source/conf.py | 57 +++++++++++++++++++++++++++++++++++++++ + docs/source/index.md | 18 +++++++++++++ + test/models/test_basic.py | 35 ++++++++++++++++++++++++ + test/topaz/test_mrc.py | 21 +++++++++++++++ + 6 files changed, 186 insertions(+) + create mode 100644 docs/Makefile + create mode 100644 docs/make.bat + create mode 100644 docs/source/conf.py + create mode 100644 docs/source/index.md + +diff --git a/docs/Makefile b/docs/Makefile +new file mode 100644 +index 0000000..d0c3cbf +--- /dev/null ++++ b/docs/Makefile +@@ -0,0 +1,20 @@ ++# Minimal makefile for Sphinx documentation ++# ++ ++# You can set these variables from the command line, and also ++# from the environment for the first two. ++SPHINXOPTS ?= ++SPHINXBUILD ?= sphinx-build ++SOURCEDIR = source ++BUILDDIR = build ++ ++# Put it first so that "make" without argument is like "make help". ++help: ++ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) ++ ++.PHONY: help Makefile ++ ++# Catch-all target: route all unknown targets to Sphinx using the new ++# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). ++%: Makefile ++ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) +diff --git a/docs/make.bat b/docs/make.bat +new file mode 100644 +index 0000000..061f32f +--- /dev/null ++++ b/docs/make.bat +@@ -0,0 +1,35 @@ ++@ECHO OFF ++ ++pushd %~dp0 ++ ++REM Command file for Sphinx documentation ++ ++if "%SPHINXBUILD%" == "" ( ++ set SPHINXBUILD=sphinx-build ++) ++set SOURCEDIR=source ++set BUILDDIR=build ++ ++if "%1" == "" goto help ++ ++%SPHINXBUILD% >NUL 2>NUL ++if errorlevel 9009 ( ++ echo. ++ echo.The 'sphinx-build' command was not found. Make sure you have Sphinx ++ echo.installed, then set the SPHINXBUILD environment variable to point ++ echo.to the full path of the 'sphinx-build' executable. Alternatively you ++ echo.may add the Sphinx directory to PATH. ++ echo. ++ echo.If you don't have Sphinx installed, grab it from ++ echo.https://www.sphinx-doc.org/ ++ exit /b 1 ++) ++ ++%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% ++goto end ++ ++:help ++%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% ++ ++:end ++popd +diff --git a/docs/source/conf.py b/docs/source/conf.py +new file mode 100644 +index 0000000..3651199 +--- /dev/null ++++ b/docs/source/conf.py +@@ -0,0 +1,57 @@ ++# Configuration file for the Sphinx documentation builder. ++# ++# This file only contains a selection of the most common options. For a full ++# list see the documentation: ++# https://www.sphinx-doc.org/en/master/usage/configuration.html ++ ++# -- Path setup -------------------------------------------------------------- ++ ++# If extensions (or modules to document with autodoc) are in another directory, ++# add these directories to sys.path here. If the directory is relative to the ++# documentation root, use os.path.abspath to make it absolute, like shown here. ++# ++# import os ++# import sys ++# sys.path.insert(0, os.path.abspath('.')) ++import sphinx_rtd_theme ++ ++ ++# -- Project information ----------------------------------------------------- ++ ++project = 'Topaz' ++copyright = '2022, Tristan Bepler, Alex Noble, Darnell Granberry' ++author = 'Tristan Bepler, Alex Noble, Darnell Granberry' ++ ++# The full version, including alpha/beta/rc tags ++release = '0.2.5' ++ ++ ++# -- General configuration --------------------------------------------------- ++ ++# Add any Sphinx extension module names here, as strings. They can be ++# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ++# ones. ++extensions = [ ++ "myst_parser", ++] ++ ++# Add any paths that contain templates here, relative to this directory. ++templates_path = ['_templates'] ++ ++# List of patterns, relative to source directory, that match files and ++# directories to ignore when looking for source files. ++# This pattern also affects html_static_path and html_extra_path. ++exclude_patterns = [] ++ ++ ++# -- Options for HTML output ------------------------------------------------- ++ ++# The theme to use for HTML and HTML Help pages. See the documentation for ++# a list of builtin themes. ++# ++html_theme = 'sphinx_rtd_theme' ++ ++# Add any paths that contain custom static files (such as style sheets) here, ++# relative to this directory. They are copied after the builtin static files, ++# so a file named "default.css" will overwrite the builtin "default.css". ++html_static_path = ['_static'] +diff --git a/docs/source/index.md b/docs/source/index.md +new file mode 100644 +index 0000000..71ef567 +--- /dev/null ++++ b/docs/source/index.md +@@ -0,0 +1,18 @@ ++% Topaz documentation master file, created by ++% sphinx-quickstart on Fri Mar 11 15:57:59 2022. ++% You can adapt this file completely to your liking, but it should at least ++% contain the root `toctree` directive. ++ ++# Welcome to Topaz's documentation! ++ ++ ++```{include} ../../README.md ++:relative-images: ++``` ++ ++ ++ ++```{toctree} ++:caption: 'Contents:' ++:maxdepth: 2 ++``` +diff --git a/test/models/test_basic.py b/test/models/test_basic.py +index e69de29..bacc895 100644 +--- a/test/models/test_basic.py ++++ b/test/models/test_basic.py +@@ -0,0 +1,35 @@ ++from re import L ++import numpy as np ++from topaz.model.features.basic import BasicConv, Conv63, Conv127 ++ ++ ++class TestBasicConv(): ++ ++ def test_init(): ++ layers = [5] ++ units = [5] ++ model = BasicConv(layers, units) ++ ++ ++ def test_fill(): ++ pass ++ ++ ++ def test_unfill(): ++ pass ++ ++ ++ def test_forward(): ++ pass ++ ++ ++ ++class TestConv127(): ++ def test_conv127(): ++ pass ++ ++ ++ ++class TestConv63(): ++ def test_conv63(): ++ pass +\ No newline at end of file +diff --git a/test/topaz/test_mrc.py b/test/topaz/test_mrc.py +index e69de29..8aa55f5 100644 +--- a/test/topaz/test_mrc.py ++++ b/test/topaz/test_mrc.py +@@ -0,0 +1,21 @@ ++from topaz.mrc import get_mode, make_header, parse, write ++ ++ ++def test_parse(): ++ path = 'test/test_data/EMPIAR-10025/rawdata/micrographs/14sep05c_c_00003gr_00014sq_00004hl_00004es_c.mrc' ++ with open(path, 'rb') as f: ++ content = f.read() ++ image, header, extended_header = parse(content) ++ assert len(header) == 49 ++ ++ ++def test_get_mode(): ++ pass ++ ++ ++def test_make_header(): ++ pass ++ ++ ++def test_write(): ++ pass +\ No newline at end of file + +From 9e0f4d95a224903aba1465aee60e1aeb0746c6ef Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Tue, 15 Mar 2022 20:52:50 -0400 +Subject: [PATCH 02/28] Created more doc pages for RTD + +--- + .readthedocs.yaml | 21 +++++ + docs/source/commands.md | 15 ++++ + docs/source/conf.py | 2 + + docs/source/cryosparc.md | 1 + + docs/source/description.md | 12 +++ + docs/source/index.md | 11 ++- + docs/source/installation.md | 172 ++++++++++++++++++++++++++++++++++++ + docs/source/models.md | 11 +++ + docs/source/relion.md | 1 + + docs/source/scripts.md | 1 + + docs/source/tutorial.md | 15 ++++ + topaz/model/classifier.py | 9 ++ + 12 files changed, 269 insertions(+), 2 deletions(-) + create mode 100644 .readthedocs.yaml + create mode 100644 docs/source/commands.md + create mode 100644 docs/source/cryosparc.md + create mode 100644 docs/source/description.md + create mode 100644 docs/source/installation.md + create mode 100644 docs/source/models.md + create mode 100644 docs/source/relion.md + create mode 100644 docs/source/scripts.md + create mode 100644 docs/source/tutorial.md + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +new file mode 100644 +index 0000000..b67d3bf +--- /dev/null ++++ b/.readthedocs.yaml +@@ -0,0 +1,21 @@ ++version: 2 ++ ++build: ++ os: "ubuntu-20.04" ++ tools: ++ python: "3.9" ++ ++sphinx: ++ configuration: docs/source/conf.py ++ ++python: ++ install: ++ - method: pip ++ path: . ++ extra_requirements: ++ - docs ++ - nbsphinx ++ - sphinx_rtd_theme ++ - sphinx-autobuild ++ - rst-to-myst ++ - myst-parser +\ No newline at end of file +diff --git a/docs/source/commands.md b/docs/source/commands.md +new file mode 100644 +index 0000000..44c4a21 +--- /dev/null ++++ b/docs/source/commands.md +@@ -0,0 +1,15 @@ ++# Topaz Commands ++ ++## downsample ++ ++## normalize ++ ++## preprocess ++ ++## train ++ ++## segment ++ ++## extract ++ ++## precision_recall_curve +diff --git a/docs/source/conf.py b/docs/source/conf.py +index 3651199..cac08bc 100644 +--- a/docs/source/conf.py ++++ b/docs/source/conf.py +@@ -33,6 +33,8 @@ + # ones. + extensions = [ + "myst_parser", ++ "nbsphinx", ++ "sphinx.ext.autodoc" + ] + + # Add any paths that contain templates here, relative to this directory. +diff --git a/docs/source/cryosparc.md b/docs/source/cryosparc.md +new file mode 100644 +index 0000000..789bd78 +--- /dev/null ++++ b/docs/source/cryosparc.md +@@ -0,0 +1 @@ ++## Use with CryoSPARC +\ No newline at end of file +diff --git a/docs/source/description.md b/docs/source/description.md +new file mode 100644 +index 0000000..dc12170 +--- /dev/null ++++ b/docs/source/description.md +@@ -0,0 +1,12 @@ ++# Topaz ++A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph and tomogram denoising using deep denoising models. ++ ++**Check out our [Discussion](https://github.com/tbepler/topaz/discussions) section for general help, suggestions, and tips on using Topaz.** ++ ++ +\ No newline at end of file +diff --git a/docs/source/index.md b/docs/source/index.md +index 71ef567..1ab1b7c 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -6,8 +6,7 @@ + # Welcome to Topaz's documentation! + + +-```{include} ../../README.md +-:relative-images: ++```{include} ./description.md + ``` + + +@@ -15,4 +14,12 @@ + ```{toctree} + :caption: 'Contents:' + :maxdepth: 2 ++ ++installation ++tutorial ++commands ++relion ++cryosparc ++models ++scripts + ``` +diff --git a/docs/source/installation.md b/docs/source/installation.md +new file mode 100644 +index 0000000..fc4a774 +--- /dev/null ++++ b/docs/source/installation.md +@@ -0,0 +1,172 @@ ++# Installation ++ ++**
(Recommended) Click here to install *using Anaconda*

** ++ ++If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). ++ ++We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: ++``` ++conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 ++source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured ++# source deactivate # returns to the base conda environment ++``` ++More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). ++ ++## Install Topaz ++ ++To install the precompiled Topaz package and its dependencies, including pytorch: ++``` ++conda install topaz -c tbepler -c pytorch ++``` ++This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: ++``` ++conda install cudatoolkit=9.0 -c pytorch ++``` ++or combined into a single command: ++``` ++conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. ++ ++That's it! Topaz is now installed in your anaconda environment. ++ ++

++ ++**
Click here to install *using Pip*

** ++ ++We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. ++ ++### Install Topaz ++ ++To install Topaz for Python 3.X ++``` ++pip3 install topaz-em ++``` ++ ++for Python 2.7 ++``` ++pip install topaz-em ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. ++ ++That's it! Topaz is now installed through pip. ++ ++

++ ++**
Click here to install *using Docker*

** ++ ++**

Do you have Docker installed? If not, *click here*

** ++ ++#### Linux/MacOS    *(command line)* ++ ++Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). ++ ++> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). ++ ++Launch docker according to your Docker engine's instructions, typically ``docker start``. ++ ++> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ ++ ++#### Windows    *(GUI & command line)* ++ ++Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). ++ ++Launch Kitematic. ++ ++> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. ++ ++> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. ++ ++ ++### What is Docker? ++ ++[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) ++ ++ ++ ++A Dockerfile is provided to build images with CUDA support. Build from the github repo: ++``` ++docker build -t topaz https://github.com/tbepler/topaz.git ++``` ++ ++or download the source code and build from the source directory ++``` ++git clone https://github.com/tbepler/topaz ++cd topaz ++docker build -t topaz . ++``` ++ ++

++ ++ ++**
Click here to install *using Singularity*

** ++ ++A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: ++``` ++singularity pull shub://nysbc/topaz ++``` ++ ++Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++``` ++singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz ++``` ++ ++

++ ++ ++**
Click here to install *from source*

** ++ ++_Recommended: install Topaz into a virtual Python environment_ ++See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. ++ ++#### Install the dependencies ++ ++Tested with python 3.6 and 2.7 ++ ++- pytorch (>= 1.0.0) ++- torchvision ++- pillow (>= 6.2.0) ++- numpy (>= 1.11) ++- pandas (>= 0.20.3) ++- scipy (>= 0.19.1) ++- scikit-learn (>= 0.19.0) ++ ++Easy installation of dependencies with conda ++``` ++conda install numpy pandas scikit-learn ++conda install -c pytorch pytorch torchvision ++``` ++For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ ++ ++#### Download the source code ++``` ++git clone https://github.com/tbepler/topaz ++``` ++ ++#### Install Topaz ++ ++Move to the source code directory ++``` ++cd topaz ++``` ++ ++By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++``` ++git checkout v0.1.0 ++``` ++Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++ ++Install Topaz into your Python path including the topaz command line interface ++``` ++pip install . ++``` ++ ++To install for development use ++``` ++pip install -e . ++``` ++ ++

++

++ ++Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). +\ No newline at end of file +diff --git a/docs/source/models.md b/docs/source/models.md +new file mode 100644 +index 0000000..574c6fb +--- /dev/null ++++ b/docs/source/models.md +@@ -0,0 +1,11 @@ ++# Models ++ ++```{eval-rst} ++.. autoclass:: topaz.model.classifier.LinearClassifier ++``` ++ ++## Features ++ ++```{eval-rst} ++.. autoclass:: topaz.model.features.basic.BasicConv ++``` +\ No newline at end of file +diff --git a/docs/source/relion.md b/docs/source/relion.md +new file mode 100644 +index 0000000..7c94e56 +--- /dev/null ++++ b/docs/source/relion.md +@@ -0,0 +1 @@ ++## Use with RELION +\ No newline at end of file +diff --git a/docs/source/scripts.md b/docs/source/scripts.md +new file mode 100644 +index 0000000..82916c1 +--- /dev/null ++++ b/docs/source/scripts.md +@@ -0,0 +1 @@ ++# Scripts +\ No newline at end of file +diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md +new file mode 100644 +index 0000000..161a880 +--- /dev/null ++++ b/docs/source/tutorial.md +@@ -0,0 +1,15 @@ ++# Tutorial ++ +diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py +index be1c3de..bb4710f 100644 +--- a/topaz/model/classifier.py ++++ b/topaz/model/classifier.py +@@ -6,6 +6,15 @@ + + class LinearClassifier(nn.Module): + def __init__(self, features): ++ ''' ++ A simple convolutional layer with no non-linear activation. ++ ++ Args: ++ features (:obj:): the sizes associated with the layer ++ ++ Attributes: ++ features (:obj:) ++ ''' + super(LinearClassifier, self).__init__() + self.features = features + self.classifier = nn.Conv2d(features.latent_dim, 1, 1) + +From e064f07d52ba152e79a664c16d64cbbbf46067e3 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 10:49:08 -0400 +Subject: [PATCH 03/28] updated doc requirements for rtd + +--- + .readthedocs.yaml | 11 +++-------- + docs/requirements.txt | 15 +++++++++++++++ + 2 files changed, 18 insertions(+), 8 deletions(-) + create mode 100644 docs/requirements.txt + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index b67d3bf..7468b70 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,11 +11,6 @@ sphinx: + python: + install: + - method: pip +- path: . +- extra_requirements: +- - docs +- - nbsphinx +- - sphinx_rtd_theme +- - sphinx-autobuild +- - rst-to-myst +- - myst-parser +\ No newline at end of file ++ - requirements: docs/requirements.txt ++ - extra-requirements: ++ - doc +\ No newline at end of file +diff --git a/docs/requirements.txt b/docs/requirements.txt +new file mode 100644 +index 0000000..46d9223 +--- /dev/null ++++ b/docs/requirements.txt +@@ -0,0 +1,15 @@ ++# torch >= 1.0.0 ++# torchvision ++# numpy >= 1.11 ++# pandas ++# scikit-learn >= 0.19.0 ++# scipy >= 0.17.0 ++# pillow >= 6.2.0 ++# future ++ ++sphinx ++sphinx_rtd_theme ++sphinx-autobuild ++rst-to-myst ++myst-parser ++nbsphinx +\ No newline at end of file + +From d80d47b01d4e919d4e0be86e4790e65074158b18 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 10:52:10 -0400 +Subject: [PATCH 04/28] Restored path in rtd.yaml + +--- + .readthedocs.yaml | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index 7468b70..037a6c0 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,6 +11,7 @@ sphinx: + python: + install: + - method: pip ++ - path: . + - requirements: docs/requirements.txt + - extra-requirements: + - doc +\ No newline at end of file + +From bba83e16c33c0614fa63a0f363677032f6086234 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:14:58 -0400 +Subject: [PATCH 05/28] Corrected rtd yaml formatting + +--- + .readthedocs.yaml | 7 ++++--- + 1 file changed, 4 insertions(+), 3 deletions(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index 037a6c0..fc40b17 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,7 +11,8 @@ sphinx: + python: + install: + - method: pip +- - path: . +- - requirements: docs/requirements.txt +- - extra-requirements: ++ path: . ++ requirements: docs/requirements.txt ++ requirements: requirements.txt ++ extra-requirements: + - doc +\ No newline at end of file + +From 1c5f11140f7f063a214e11e9787f779844423bd8 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:36:29 -0400 +Subject: [PATCH 06/28] added docs requirements, edited rtd.yaml + +--- + .readthedocs.yaml | 5 +---- + docs/requirements.txt | 10 ++++------ + requirements.txt | 5 +++++ + 3 files changed, 10 insertions(+), 10 deletions(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index fc40b17..b9870ed 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -12,7 +12,4 @@ python: + install: + - method: pip + path: . +- requirements: docs/requirements.txt +- requirements: requirements.txt +- extra-requirements: +- - doc +\ No newline at end of file ++ requirements: requirements.txt +\ No newline at end of file +diff --git a/docs/requirements.txt b/docs/requirements.txt +index 46d9223..e7f2aa5 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -6,10 +6,8 @@ + # scipy >= 0.17.0 + # pillow >= 6.2.0 + # future +- +-sphinx ++sphinx==4.4.0 + sphinx_rtd_theme +-sphinx-autobuild +-rst-to-myst +-myst-parser +-nbsphinx +\ No newline at end of file ++rst-to-myst==0.3.2 ++myst-parser==0.17.0 ++nbsphinx==0.8.8 +\ No newline at end of file +diff --git a/requirements.txt b/requirements.txt +index 4e7245f..01c0804 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -6,3 +6,8 @@ scikit-learn >= 0.19.0 + scipy >= 0.17.0 + pillow >= 6.2.0 + future ++sphinx==4.4.0 ++sphinx_rtd_theme ++rst-to-myst==0.3.2 ++myst-parser==0.17.0 ++nbsphinx==0.8.8 +\ No newline at end of file + +From ed7de9c2d2e89fc3a254b3c0882d6c2e2b981205 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:46:51 -0400 +Subject: [PATCH 07/28] Reordered rtd.yaml args + +--- + .readthedocs.yaml | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index b9870ed..6722c59 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -10,6 +10,8 @@ sphinx: + + python: + install: ++ - requirements: docs/requirements.txt + - method: pip + path: . +- requirements: requirements.txt +\ No newline at end of file ++ extra_requirements: ++ - docs +\ No newline at end of file + +From 683093572078eb20e9aebfa5daeb931ddb3c5bbc Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:50:07 -0400 +Subject: [PATCH 08/28] removed doc versions pkg version + +--- + docs/requirements.txt | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/docs/requirements.txt b/docs/requirements.txt +index e7f2aa5..f12e5f7 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -8,6 +8,6 @@ + # future + sphinx==4.4.0 + sphinx_rtd_theme +-rst-to-myst==0.3.2 +-myst-parser==0.17.0 +-nbsphinx==0.8.8 +\ No newline at end of file ++rst-to-myst ++myst-parser ++nbsphinx +\ No newline at end of file + +From c3415895c8515696be1a88c2bfde242c3c2999f7 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:55:36 -0400 +Subject: [PATCH 09/28] Add docs status to readme + +--- + README.md | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/README.md b/README.md +index 5987691..f2b6433 100644 +--- a/README.md ++++ b/README.md +@@ -1,5 +1,5 @@ + [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) +- ++[![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) + + + # Topaz + +From 538286e7a4780d31f163e95011e89a68fc418b9f Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 15:00:17 -0400 +Subject: [PATCH 10/28] Added version and conda install badges + +--- + README.md | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/README.md b/README.md +index f2b6433..f3832bd 100644 +--- a/README.md ++++ b/README.md +@@ -1,5 +1,7 @@ + [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) + [![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) ++[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/version.svg)](https://anaconda.org/tbepler/topaz) ++[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/installer/conda.svg)](https://conda.anaconda.org/tbepler) + + + # Topaz + +From 2c13c55fa3080741571b868f6275b1839456e45e Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 15:05:11 -0400 +Subject: [PATCH 11/28] removed duplicate docs requirements + +--- + requirements.txt | 7 +------ + 1 file changed, 1 insertion(+), 6 deletions(-) + +diff --git a/requirements.txt b/requirements.txt +index 01c0804..d83f97b 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -5,9 +5,4 @@ pandas + scikit-learn >= 0.19.0 + scipy >= 0.17.0 + pillow >= 6.2.0 +-future +-sphinx==4.4.0 +-sphinx_rtd_theme +-rst-to-myst==0.3.2 +-myst-parser==0.17.0 +-nbsphinx==0.8.8 +\ No newline at end of file ++future +\ No newline at end of file + +From 06f301640ea566f9baae816edb0a908ffafca444 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Thu, 17 Mar 2022 17:50:20 -0400 +Subject: [PATCH 12/28] Created doc entries for most code except commands + +--- + docs/source/algorithms.md | 7 +++ + docs/source/conf.py | 4 +- + docs/source/denoising.md | 7 +++ + docs/source/index.md | 10 ++++- + docs/source/methods.md | 7 +++ + docs/source/metrics_stats.md | 14 ++++++ + docs/source/models.md | 52 +++++++++++++++++++++- + docs/source/transforms.md | 7 +++ + docs/source/utils.md | 81 +++++++++++++++++++++++++++++++++++ + topaz/_version.py | 2 +- + topaz/model/classifier.py | 12 +++++- + topaz/model/features/basic.py | 2 + + 12 files changed, 197 insertions(+), 8 deletions(-) + create mode 100644 docs/source/algorithms.md + create mode 100644 docs/source/denoising.md + create mode 100644 docs/source/methods.md + create mode 100644 docs/source/metrics_stats.md + create mode 100644 docs/source/transforms.md + create mode 100644 docs/source/utils.md + +diff --git a/docs/source/algorithms.md b/docs/source/algorithms.md +new file mode 100644 +index 0000000..0a617c9 +--- /dev/null ++++ b/docs/source/algorithms.md +@@ -0,0 +1,7 @@ ++# Algorithms ++ ++```{eval-rst} ++.. automodule:: topaz.algorithms ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/conf.py b/docs/source/conf.py +index cac08bc..8a8b336 100644 +--- a/docs/source/conf.py ++++ b/docs/source/conf.py +@@ -34,7 +34,9 @@ + extensions = [ + "myst_parser", + "nbsphinx", +- "sphinx.ext.autodoc" ++ "sphinx.ext.autodoc", ++ "sphinx.ext.napoleon", ++ "sphinx.ext.autosectionlabel" + ] + + # Add any paths that contain templates here, relative to this directory. +diff --git a/docs/source/denoising.md b/docs/source/denoising.md +new file mode 100644 +index 0000000..036d4d5 +--- /dev/null ++++ b/docs/source/denoising.md +@@ -0,0 +1,7 @@ ++# Denoising ++ ++```{eval-rst} ++.. automodule:: topaz.denoise ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/index.md b/docs/source/index.md +index 1ab1b7c..af67119 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -18,8 +18,14 @@ + installation + tutorial + commands +-relion +-cryosparc ++algorithms ++denoising ++methods ++metrics_stats + models ++transforms ++utils + scripts ++relion ++cryosparc + ``` +diff --git a/docs/source/methods.md b/docs/source/methods.md +new file mode 100644 +index 0000000..aed5cfd +--- /dev/null ++++ b/docs/source/methods.md +@@ -0,0 +1,7 @@ ++# Methods ++ ++```{eval-rst} ++.. automodule:: topaz.methods ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/metrics_stats.md b/docs/source/metrics_stats.md +new file mode 100644 +index 0000000..dcfe0c4 +--- /dev/null ++++ b/docs/source/metrics_stats.md +@@ -0,0 +1,14 @@ ++# Metrics and Statistics ++ ++```{eval-rst} ++.. automodule:: topaz.metrics ++ :members: ++ :undoc-members: ++``` ++ ++ ++```{eval-rst} ++.. automodule:: topaz.stats ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/models.md b/docs/source/models.md +index 574c6fb..dbad6b1 100644 +--- a/docs/source/models.md ++++ b/docs/source/models.md +@@ -1,11 +1,59 @@ + # Models + ++## Feature Extractors ++ ++### Basic Conv Nets ++```{eval-rst} ++.. automodule:: topaz.model.features.basic ++ :members: ++ :undoc-members: ++``` ++ ++### DenseNets ++```{eval-rst} ++.. automodule:: topaz.model.features.densenet ++ :members: ++ :undoc-members: ++``` ++ ++### MSNets ++```{eval-rst} ++.. automodule:: topaz.model.features.msnet ++ :members: ++ :undoc-members: ++``` ++ ++### ResNets ++```{eval-rst} ++.. automodule:: topaz.model.features.resnet ++ :members: ++ :undoc-members: ++``` ++ ++## Linear Classifier + ```{eval-rst} + .. autoclass:: topaz.model.classifier.LinearClassifier ++ :members: ++ :undoc-members: + ``` + +-## Features ++## Model Factory ++```{eval-rst} ++.. automodule:: topaz.model.factory ++ :members: ++ :undoc-members: ++``` ++ ++## Model Generator ++```{eval-rst} ++.. automodule:: topaz.model.generative ++ :members: ++ :undoc-members: ++``` + ++## Model Utilities + ```{eval-rst} +-.. autoclass:: topaz.model.features.basic.BasicConv ++.. automodule:: topaz.model.utils ++ :members: ++ :undoc-members: + ``` +\ No newline at end of file +diff --git a/docs/source/transforms.md b/docs/source/transforms.md +new file mode 100644 +index 0000000..9bf1082 +--- /dev/null ++++ b/docs/source/transforms.md +@@ -0,0 +1,7 @@ ++# Transformations ++ ++```{eval-rst} ++.. automodule:: topaz.transform.scaled_gaussian_mixture ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/utils.md b/docs/source/utils.md +new file mode 100644 +index 0000000..027f498 +--- /dev/null ++++ b/docs/source/utils.md +@@ -0,0 +1,81 @@ ++# Utilities ++ ++## Conversions ++```{eval-rst} ++.. automodule:: topaz.utils.conversions ++ :members: ++ :undoc-members: ++``` ++ ++## File Utilities ++```{eval-rst} ++.. automodule:: topaz.utils.conversions ++ :members: ++ :undoc-members: ++``` ++ ++ ++```{eval-rst} ++.. automodule:: topaz.mrc ++ :members: ++ :undoc-members: ++``` ++ ++ ++## Image Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.image ++ :members: ++ :undoc-members: ++``` ++ ++## Pick Masking ++```{eval-rst} ++.. automodule:: topaz.utils.picks ++ :members: ++ :undoc-members: ++``` ++ ++## Printing ++```{eval-rst} ++.. automodule:: topaz.utils.printing ++ :members: ++ :undoc-members: ++``` ++ ++## STAR File Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.star ++ :members: ++ :undoc-members: ++``` ++ ++## Data Utilities ++ ++### Coordinate Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.data.coordinates ++ :members: ++ :undoc-members: ++``` ++ ++### Image Loading ++```{eval-rst} ++.. automodule:: topaz.utils.data.loader ++ :members: ++ :undoc-members: ++``` ++ ++### Dataset Partitioning ++```{eval-rst} ++.. automodule:: topaz.utils.data.partition ++ :members: ++ :undoc-members: ++``` ++ ++### Dataset Sampling ++```{eval-rst} ++.. automodule:: topaz.utils.data.sampler ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/topaz/_version.py b/topaz/_version.py +index e723ff3..fe404ae 100644 +--- a/topaz/_version.py ++++ b/topaz/_version.py +@@ -1 +1 @@ +-__version__ = "0.2.5a" ++__version__ = "0.2.5" +diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py +index bb4710f..d63d83c 100644 +--- a/topaz/model/classifier.py ++++ b/topaz/model/classifier.py +@@ -5,10 +5,10 @@ + import torch.nn.functional as F + + class LinearClassifier(nn.Module): ++ '''A simple convolutional layer without non-linear activation.''' ++ + def __init__(self, features): + ''' +- A simple convolutional layer with no non-linear activation. +- + Args: + features (:obj:): the sizes associated with the layer + +@@ -34,6 +34,14 @@ def unfill(self): + self.features.unfill() + + def forward(self, x): ++ '''Applies the classifier to an input. ++ ++ Args: ++ x (np.ndarray): the image from which features are extracted and classified ++ ++ Returns: ++ z (np.ndarray): output of the classifer ++ ''' + z = self.features(x) + y = self.classifier(z) + return y +diff --git a/topaz/model/features/basic.py b/topaz/model/features/basic.py +index 0ea1fe9..dff4e9f 100644 +--- a/topaz/model/features/basic.py ++++ b/topaz/model/features/basic.py +@@ -10,6 +10,8 @@ + from topaz.model.utils import insize_from_outsize + + class BasicConv(nn.Module): ++ '''A generic convolutional neural network scaffold.''' ++ + def __init__(self, layers, units, unit_scaling=1, dropout=0, bn=True + , pooling=None, activation=nn.PReLU): + super(BasicConv, self).__init__() + +From d2c9761c2fba8d996c1f117f3004eeaf5a2abad7 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Fri, 18 Mar 2022 15:44:56 -0400 +Subject: [PATCH 13/28] reorganized docs, began work on man pages + +--- + docs/requirements.txt | 3 +- + docs/source/commands.md | 20 ++- + docs/source/commands/convert.md | 1 + + docs/source/commands/denoise.md | 1 + + docs/source/commands/denoise3d.md | 1 + + docs/source/commands/downsample.md | 1 + + docs/source/commands/extract.md | 1 + + docs/source/commands/file_utilities.md | 11 ++ + docs/source/commands/gui.md | 1 + + docs/source/commands/image_processing.md | 12 ++ + docs/source/commands/normalize.md | 8 + + docs/source/commands/particle_picking.md | 11 ++ + docs/source/commands/particle_stack.md | 1 + + docs/source/commands/precision_recall.md | 1 + + docs/source/commands/preprocess.md | 1 + + docs/source/commands/segment.md | 1 + + docs/source/commands/split.md | 1 + + docs/source/commands/train.md | 1 + + docs/source/commands/train_test_split.md | 1 + + docs/source/conf.py | 3 +- + docs/source/index.md | 2 +- + docs/source/installation.md | 172 ++------------------- + docs/source/installation/conda_install.md | 32 ++++ + docs/source/installation/docker_install.md | 51 ++++++ + docs/source/installation/pip_install.md | 20 +++ + docs/source/installation/singularity.md | 11 ++ + docs/source/installation/source_install.md | 57 +++++++ + docs/source/tutorial.md | 5 +- + topaz/commands/normalize.py | 9 +- + 29 files changed, 264 insertions(+), 176 deletions(-) + create mode 100644 docs/source/commands/convert.md + create mode 100644 docs/source/commands/denoise.md + create mode 100644 docs/source/commands/denoise3d.md + create mode 100644 docs/source/commands/downsample.md + create mode 100644 docs/source/commands/extract.md + create mode 100644 docs/source/commands/file_utilities.md + create mode 100644 docs/source/commands/gui.md + create mode 100644 docs/source/commands/image_processing.md + create mode 100644 docs/source/commands/normalize.md + create mode 100644 docs/source/commands/particle_picking.md + create mode 100644 docs/source/commands/particle_stack.md + create mode 100644 docs/source/commands/precision_recall.md + create mode 100644 docs/source/commands/preprocess.md + create mode 100644 docs/source/commands/segment.md + create mode 100644 docs/source/commands/split.md + create mode 100644 docs/source/commands/train.md + create mode 100644 docs/source/commands/train_test_split.md + create mode 100644 docs/source/installation/conda_install.md + create mode 100644 docs/source/installation/docker_install.md + create mode 100644 docs/source/installation/pip_install.md + create mode 100644 docs/source/installation/singularity.md + create mode 100644 docs/source/installation/source_install.md + +diff --git a/docs/requirements.txt b/docs/requirements.txt +index f12e5f7..bd0b467 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -10,4 +10,5 @@ sphinx==4.4.0 + sphinx_rtd_theme + rst-to-myst + myst-parser +-nbsphinx +\ No newline at end of file ++nbsphinx ++sphinx-argparse +\ No newline at end of file +diff --git a/docs/source/commands.md b/docs/source/commands.md +index 44c4a21..3c462c9 100644 +--- a/docs/source/commands.md ++++ b/docs/source/commands.md +@@ -1,15 +1,13 @@ +-# Topaz Commands ++# Topaz Commands (work in progress) + +-## downsample + +-## normalize ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 2 + +-## preprocess ++commands/particle_picking ++commands/image_processing ++commands/file_utilities + +-## train +- +-## segment +- +-## extract +- +-## precision_recall_curve ++commands/gui ++``` +\ No newline at end of file +diff --git a/docs/source/commands/convert.md b/docs/source/commands/convert.md +new file mode 100644 +index 0000000..122f443 +--- /dev/null ++++ b/docs/source/commands/convert.md +@@ -0,0 +1 @@ ++# Convert +\ No newline at end of file +diff --git a/docs/source/commands/denoise.md b/docs/source/commands/denoise.md +new file mode 100644 +index 0000000..d995632 +--- /dev/null ++++ b/docs/source/commands/denoise.md +@@ -0,0 +1 @@ ++# Denoise +\ No newline at end of file +diff --git a/docs/source/commands/denoise3d.md b/docs/source/commands/denoise3d.md +new file mode 100644 +index 0000000..bf78fac +--- /dev/null ++++ b/docs/source/commands/denoise3d.md +@@ -0,0 +1 @@ ++# Denoise 3D +\ No newline at end of file +diff --git a/docs/source/commands/downsample.md b/docs/source/commands/downsample.md +new file mode 100644 +index 0000000..e0b15bf +--- /dev/null ++++ b/docs/source/commands/downsample.md +@@ -0,0 +1 @@ ++# Downsample +\ No newline at end of file +diff --git a/docs/source/commands/extract.md b/docs/source/commands/extract.md +new file mode 100644 +index 0000000..d0e6da9 +--- /dev/null ++++ b/docs/source/commands/extract.md +@@ -0,0 +1 @@ ++# Extract +\ No newline at end of file +diff --git a/docs/source/commands/file_utilities.md b/docs/source/commands/file_utilities.md +new file mode 100644 +index 0000000..b26444f +--- /dev/null ++++ b/docs/source/commands/file_utilities.md +@@ -0,0 +1,11 @@ ++# File Utilities ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++convert ++split ++particle_stack ++train_test_split ++``` +\ No newline at end of file +diff --git a/docs/source/commands/gui.md b/docs/source/commands/gui.md +new file mode 100644 +index 0000000..93bd5f2 +--- /dev/null ++++ b/docs/source/commands/gui.md +@@ -0,0 +1 @@ ++# GUI +\ No newline at end of file +diff --git a/docs/source/commands/image_processing.md b/docs/source/commands/image_processing.md +new file mode 100644 +index 0000000..973048c +--- /dev/null ++++ b/docs/source/commands/image_processing.md +@@ -0,0 +1,12 @@ ++# Image Processing ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++downsample ++normalize ++preprocess ++denoise ++denoise3d ++``` +\ No newline at end of file +diff --git a/docs/source/commands/normalize.md b/docs/source/commands/normalize.md +new file mode 100644 +index 0000000..ad442b2 +--- /dev/null ++++ b/docs/source/commands/normalize.md +@@ -0,0 +1,8 @@ ++# Normalize ++ ++```{eval-rst} ++.. argparse:: ++ :module: topaz.commands.normalize ++ :func: add_arguments ++ :prog: normalize ++``` +\ No newline at end of file +diff --git a/docs/source/commands/particle_picking.md b/docs/source/commands/particle_picking.md +new file mode 100644 +index 0000000..c32361a +--- /dev/null ++++ b/docs/source/commands/particle_picking.md +@@ -0,0 +1,11 @@ ++# Particle Picking ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++train ++segment ++extract ++precision_recall ++``` +\ No newline at end of file +diff --git a/docs/source/commands/particle_stack.md b/docs/source/commands/particle_stack.md +new file mode 100644 +index 0000000..7bb5a5e +--- /dev/null ++++ b/docs/source/commands/particle_stack.md +@@ -0,0 +1 @@ ++# Particle Stack +\ No newline at end of file +diff --git a/docs/source/commands/precision_recall.md b/docs/source/commands/precision_recall.md +new file mode 100644 +index 0000000..dff8323 +--- /dev/null ++++ b/docs/source/commands/precision_recall.md +@@ -0,0 +1 @@ ++# Precision Recall Curve +\ No newline at end of file +diff --git a/docs/source/commands/preprocess.md b/docs/source/commands/preprocess.md +new file mode 100644 +index 0000000..8fd260d +--- /dev/null ++++ b/docs/source/commands/preprocess.md +@@ -0,0 +1 @@ ++# Preprocess +\ No newline at end of file +diff --git a/docs/source/commands/segment.md b/docs/source/commands/segment.md +new file mode 100644 +index 0000000..af21080 +--- /dev/null ++++ b/docs/source/commands/segment.md +@@ -0,0 +1 @@ ++# Segment +\ No newline at end of file +diff --git a/docs/source/commands/split.md b/docs/source/commands/split.md +new file mode 100644 +index 0000000..5e525aa +--- /dev/null ++++ b/docs/source/commands/split.md +@@ -0,0 +1 @@ ++# Split +\ No newline at end of file +diff --git a/docs/source/commands/train.md b/docs/source/commands/train.md +new file mode 100644 +index 0000000..44ac09a +--- /dev/null ++++ b/docs/source/commands/train.md +@@ -0,0 +1 @@ ++# Train +\ No newline at end of file +diff --git a/docs/source/commands/train_test_split.md b/docs/source/commands/train_test_split.md +new file mode 100644 +index 0000000..e28a8c8 +--- /dev/null ++++ b/docs/source/commands/train_test_split.md +@@ -0,0 +1 @@ ++# Train Test Split +\ No newline at end of file +diff --git a/docs/source/conf.py b/docs/source/conf.py +index 8a8b336..8f3a9d3 100644 +--- a/docs/source/conf.py ++++ b/docs/source/conf.py +@@ -36,7 +36,8 @@ + "nbsphinx", + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", +- "sphinx.ext.autosectionlabel" ++ "sphinx.ext.autosectionlabel", ++ "sphinxarg.ext" + ] + + # Add any paths that contain templates here, relative to this directory. +diff --git a/docs/source/index.md b/docs/source/index.md +index af67119..13b414e 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -13,7 +13,7 @@ + + ```{toctree} + :caption: 'Contents:' +-:maxdepth: 2 ++:maxdepth: 3 + + installation + tutorial +diff --git a/docs/source/installation.md b/docs/source/installation.md +index fc4a774..8eca25e 100644 +--- a/docs/source/installation.md ++++ b/docs/source/installation.md +@@ -1,172 +1,28 @@ + # Installation + +-**

(Recommended) Click here to install *using Anaconda*

** +- +-If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). +- +-We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: +-``` +-conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 +-source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured +-# source deactivate # returns to the base conda environment +-``` +-More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). +- +-## Install Topaz +- +-To install the precompiled Topaz package and its dependencies, including pytorch: +-``` +-conda install topaz -c tbepler -c pytorch +-``` +-This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: +-``` +-conda install cudatoolkit=9.0 -c pytorch +-``` +-or combined into a single command: +-``` +-conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch +-``` +-See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. +- +-That's it! Topaz is now installed in your anaconda environment. +- +-

+- +-**
Click here to install *using Pip*

** +- +-We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. +- +-### Install Topaz +- +-To install Topaz for Python 3.X +-``` +-pip3 install topaz-em +-``` +- +-for Python 2.7 +-``` +-pip install topaz-em +-``` +-See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. +- +-That's it! Topaz is now installed through pip. +- +-

+- +-**
Click here to install *using Docker*

** +- +-**

Do you have Docker installed? If not, *click here*

** +- +-#### Linux/MacOS    *(command line)* +- +-Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). +- +-> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). +- +-Launch docker according to your Docker engine's instructions, typically ``docker start``. +- +-> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ +- +-#### Windows    *(GUI & command line)* +- +-Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). +- +-Launch Kitematic. +- +-> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. +- +-> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. +- +- +-### What is Docker? +- +-[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) +- +- +- +-A Dockerfile is provided to build images with CUDA support. Build from the github repo: +-``` +-docker build -t topaz https://github.com/tbepler/topaz.git +-``` +- +-or download the source code and build from the source directory +-``` +-git clone https://github.com/tbepler/topaz +-cd topaz +-docker build -t topaz . +-``` +- +-

+- +- +-**
Click here to install *using Singularity*

** +- +-A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: +-``` +-singularity pull shub://nysbc/topaz +-``` +- +-Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++## Conda ++```{include} installation/conda_install.md + ``` +-singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz +-``` +- +-

+- +- +-**
Click here to install *from source*

** +- +-_Recommended: install Topaz into a virtual Python environment_ +-See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. +- +-#### Install the dependencies +- +-Tested with python 3.6 and 2.7 +- +-- pytorch (>= 1.0.0) +-- torchvision +-- pillow (>= 6.2.0) +-- numpy (>= 1.11) +-- pandas (>= 0.20.3) +-- scipy (>= 0.19.1) +-- scikit-learn (>= 0.19.0) +- +-Easy installation of dependencies with conda +-``` +-conda install numpy pandas scikit-learn +-conda install -c pytorch pytorch torchvision +-``` +-For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ +- +-#### Download the source code +-``` +-git clone https://github.com/tbepler/topaz +-``` +- +-#### Install Topaz ++

+ +-Move to the source code directory +-``` +-cd topaz ++## Pip ++```{include} installation/pip_install.md + ``` ++

+ +-By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++## Docker ++```{include} installation/docker_install.md + ``` +-git checkout v0.1.0 +-``` +-Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++

+ +-Install Topaz into your Python path including the topaz command line interface +-``` +-pip install . ++## Singularity ++```{include} installation/singularity.md + ``` ++

+ +-To install for development use ++## From Source ++```{include} installation/source_install.md + ``` +-pip install -e . +-``` +- +-

+

+ + Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). +\ No newline at end of file +diff --git a/docs/source/installation/conda_install.md b/docs/source/installation/conda_install.md +new file mode 100644 +index 0000000..06476c9 +--- /dev/null ++++ b/docs/source/installation/conda_install.md +@@ -0,0 +1,32 @@ ++**

(Recommended) Click here to install *using Anaconda*

** ++ ++If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). ++ ++We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: ++``` ++conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 ++source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured ++# source deactivate # returns to the base conda environment ++``` ++More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). ++ ++\ ++**Install Topaz** ++ ++To install the precompiled Topaz package and its dependencies, including pytorch: ++``` ++conda install topaz -c tbepler -c pytorch ++``` ++This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: ++``` ++conda install cudatoolkit=9.0 -c pytorch ++``` ++or combined into a single command: ++``` ++conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. ++ ++That's it! Topaz is now installed in your anaconda environment. ++ ++

+\ No newline at end of file +diff --git a/docs/source/installation/docker_install.md b/docs/source/installation/docker_install.md +new file mode 100644 +index 0000000..913ffd0 +--- /dev/null ++++ b/docs/source/installation/docker_install.md +@@ -0,0 +1,51 @@ ++**
Click here to install *using Docker*

** ++ ++**

What is Docker?

** ++ ++[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) ++

++ ++ ++**
Do you have Docker installed? If not, *click here*

** ++ ++**

Linux/MacOS    *(command line)*

** ++ ++

++Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). ++ ++> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). ++ ++Launch docker according to your Docker engine's instructions, typically ``docker start``. ++ ++> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ ++

++ ++ ++**
Windows    *(GUI & command line)*

** ++ ++

++Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). ++ ++Launch Kitematic. ++ ++> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. ++ ++> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. ++

++ ++

++

++ ++\ ++A Dockerfile is provided to build images with CUDA support. Build from the github repo: ++``` ++docker build -t topaz https://github.com/tbepler/topaz.git ++``` ++ ++or download the source code and build from the source directory ++``` ++git clone https://github.com/tbepler/topaz ++cd topaz ++docker build -t topaz . ++``` ++

+\ No newline at end of file +diff --git a/docs/source/installation/pip_install.md b/docs/source/installation/pip_install.md +new file mode 100644 +index 0000000..e65f64e +--- /dev/null ++++ b/docs/source/installation/pip_install.md +@@ -0,0 +1,20 @@ ++**
Click here to install *using Pip*

** ++ ++We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. ++ ++**Install Topaz** ++ ++To install Topaz for Python 3.X ++``` ++pip3 install topaz-em ++``` ++ ++for Python 2.7 ++``` ++pip install topaz-em ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. ++ ++That's it! Topaz is now installed through pip. ++ ++

+\ No newline at end of file +diff --git a/docs/source/installation/singularity.md b/docs/source/installation/singularity.md +new file mode 100644 +index 0000000..401c819 +--- /dev/null ++++ b/docs/source/installation/singularity.md +@@ -0,0 +1,11 @@ ++**
Click here to install *using Singularity*

** ++A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: ++``` ++singularity pull shub://nysbc/topaz ++``` ++ ++Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++``` ++singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz ++``` ++

+\ No newline at end of file +diff --git a/docs/source/installation/source_install.md b/docs/source/installation/source_install.md +new file mode 100644 +index 0000000..648dfc8 +--- /dev/null ++++ b/docs/source/installation/source_install.md +@@ -0,0 +1,57 @@ ++**
Click here to install *from source*

** ++ ++_Recommended: install Topaz into a virtual Python environment_ ++See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. ++ ++\ ++**Install the dependencies** ++ ++Tested with python 3.6 and 2.7 ++ ++- pytorch (>= 1.0.0) ++- torchvision ++- pillow (>= 6.2.0) ++- numpy (>= 1.11) ++- pandas (>= 0.20.3) ++- scipy (>= 0.19.1) ++- scikit-learn (>= 0.19.0) ++ ++Easy installation of dependencies with conda ++``` ++conda install numpy pandas scikit-learn ++conda install -c pytorch pytorch torchvision ++``` ++For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ ++ ++\ ++**Download the source code** ++``` ++git clone https://github.com/tbepler/topaz ++``` ++ ++\ ++**Install Topaz** ++ ++Move to the source code directory ++``` ++cd topaz ++``` ++ ++By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++``` ++git checkout v0.1.0 ++``` ++Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++ ++Install Topaz into your Python path including the topaz command line interface ++``` ++pip install . ++``` ++ ++To install for development use ++``` ++pip install -e . ++``` ++ ++

++

+\ No newline at end of file +diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md +index 161a880..c2ebb97 100644 +--- a/docs/source/tutorial.md ++++ b/docs/source/tutorial.md +@@ -1,4 +1,7 @@ +-# Tutorial ++# Tutorials (coming soon) ++ ++Tutorial pages here are a work-in-progress. For the time being, please refer to the tutorial notebooks in topaz/tutorial. ++ + -\ No newline at end of file -diff --git a/docs/source/index.md b/docs/source/index.md -index 71ef567..1ab1b7c 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -6,8 +6,7 @@ - # Welcome to Topaz's documentation! - - --```{include} ../../README.md --:relative-images: -+```{include} ./description.md - ``` - - -@@ -15,4 +14,12 @@ - ```{toctree} - :caption: 'Contents:' - :maxdepth: 2 -+ -+installation -+tutorial -+commands -+relion -+cryosparc -+models -+scripts - ``` -diff --git a/docs/source/installation.md b/docs/source/installation.md -new file mode 100644 -index 0000000..fc4a774 ---- /dev/null -+++ b/docs/source/installation.md -@@ -0,0 +1,172 @@ -+# Installation -+ -+**

(Recommended) Click here to install *using Anaconda*

** -+ -+If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -+ -+We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: -+``` -+conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 -+source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured -+# source deactivate # returns to the base conda environment -+``` -+More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -+ -+## Install Topaz -+ -+To install the precompiled Topaz package and its dependencies, including pytorch: -+``` -+conda install topaz -c tbepler -c pytorch -+``` -+This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: -+``` -+conda install cudatoolkit=9.0 -c pytorch -+``` -+or combined into a single command: -+``` -+conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -+ -+That's it! Topaz is now installed in your anaconda environment. -+ -+

-+ -+**
Click here to install *using Pip*

** -+ -+We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -+ -+### Install Topaz -+ -+To install Topaz for Python 3.X -+``` -+pip3 install topaz-em -+``` -+ -+for Python 2.7 -+``` -+pip install topaz-em -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -+ -+That's it! Topaz is now installed through pip. -+ -+

-+ -+**
Click here to install *using Docker*

** -+ -+**

Do you have Docker installed? If not, *click here*

** -+ -+#### Linux/MacOS    *(command line)* -+ -+Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -+ -+> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -+ -+Launch docker according to your Docker engine's instructions, typically ``docker start``. -+ -+> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -+ -+#### Windows    *(GUI & command line)* -+ -+Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -+ -+Launch Kitematic. -+ -+> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -+ -+> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -+ -+ -+### What is Docker? -+ -+[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -+ -+ -+ -+A Dockerfile is provided to build images with CUDA support. Build from the github repo: -+``` -+docker build -t topaz https://github.com/tbepler/topaz.git -+``` -+ -+or download the source code and build from the source directory -+``` -+git clone https://github.com/tbepler/topaz -+cd topaz -+docker build -t topaz . -+``` -+ -+

-+ -+ -+**
Click here to install *using Singularity*

** -+ -+A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: -+``` -+singularity pull shub://nysbc/topaz -+``` -+ -+Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+``` -+singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz -+``` -+ -+

-+ -+ -+**
Click here to install *from source*

** -+ -+_Recommended: install Topaz into a virtual Python environment_ -+See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -+ -+#### Install the dependencies -+ -+Tested with python 3.6 and 2.7 -+ -+- pytorch (>= 1.0.0) -+- torchvision -+- pillow (>= 6.2.0) -+- numpy (>= 1.11) -+- pandas (>= 0.20.3) -+- scipy (>= 0.19.1) -+- scikit-learn (>= 0.19.0) -+ -+Easy installation of dependencies with conda -+``` -+conda install numpy pandas scikit-learn -+conda install -c pytorch pytorch torchvision -+``` -+For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -+ -+#### Download the source code -+``` -+git clone https://github.com/tbepler/topaz -+``` -+ -+#### Install Topaz -+ -+Move to the source code directory -+``` -+cd topaz -+``` -+ -+By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+``` -+git checkout v0.1.0 -+``` -+Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+ -+Install Topaz into your Python path including the topaz command line interface -+``` -+pip install . -+``` -+ -+To install for development use -+``` -+pip install -e . -+``` -+ -+

-+

-+ -+Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). -\ No newline at end of file -diff --git a/docs/source/models.md b/docs/source/models.md -new file mode 100644 -index 0000000..574c6fb ---- /dev/null -+++ b/docs/source/models.md -@@ -0,0 +1,11 @@ -+# Models -+ -+```{eval-rst} -+.. autoclass:: topaz.model.classifier.LinearClassifier -+``` -+ -+## Features -+ -+```{eval-rst} -+.. autoclass:: topaz.model.features.basic.BasicConv -+``` -\ No newline at end of file -diff --git a/docs/source/relion.md b/docs/source/relion.md -new file mode 100644 -index 0000000..7c94e56 ---- /dev/null -+++ b/docs/source/relion.md -@@ -0,0 +1 @@ -+## Use with RELION -\ No newline at end of file -diff --git a/docs/source/scripts.md b/docs/source/scripts.md -new file mode 100644 -index 0000000..82916c1 ---- /dev/null -+++ b/docs/source/scripts.md -@@ -0,0 +1 @@ -+# Scripts -\ No newline at end of file -diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md -new file mode 100644 -index 0000000..161a880 ---- /dev/null -+++ b/docs/source/tutorial.md -@@ -0,0 +1,15 @@ -+# Tutorial -+ -diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py -index be1c3de..bb4710f 100644 ---- a/topaz/model/classifier.py -+++ b/topaz/model/classifier.py -@@ -6,6 +6,15 @@ - - class LinearClassifier(nn.Module): - def __init__(self, features): -+ ''' -+ A simple convolutional layer with no non-linear activation. -+ -+ Args: -+ features (:obj:): the sizes associated with the layer -+ -+ Attributes: -+ features (:obj:) -+ ''' - super(LinearClassifier, self).__init__() - self.features = features - self.classifier = nn.Conv2d(features.latent_dim, 1, 1) - -From e064f07d52ba152e79a664c16d64cbbbf46067e3 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 10:49:08 -0400 -Subject: [PATCH 03/28] updated doc requirements for rtd - ---- - .readthedocs.yaml | 11 +++-------- - docs/requirements.txt | 15 +++++++++++++++ - 2 files changed, 18 insertions(+), 8 deletions(-) - create mode 100644 docs/requirements.txt - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index b67d3bf..7468b70 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,11 +11,6 @@ sphinx: - python: - install: - - method: pip -- path: . -- extra_requirements: -- - docs -- - nbsphinx -- - sphinx_rtd_theme -- - sphinx-autobuild -- - rst-to-myst -- - myst-parser -\ No newline at end of file -+ - requirements: docs/requirements.txt -+ - extra-requirements: -+ - doc -\ No newline at end of file -diff --git a/docs/requirements.txt b/docs/requirements.txt -new file mode 100644 -index 0000000..46d9223 ---- /dev/null -+++ b/docs/requirements.txt -@@ -0,0 +1,15 @@ -+# torch >= 1.0.0 -+# torchvision -+# numpy >= 1.11 -+# pandas -+# scikit-learn >= 0.19.0 -+# scipy >= 0.17.0 -+# pillow >= 6.2.0 -+# future -+ -+sphinx -+sphinx_rtd_theme -+sphinx-autobuild -+rst-to-myst -+myst-parser -+nbsphinx -\ No newline at end of file - -From d80d47b01d4e919d4e0be86e4790e65074158b18 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 10:52:10 -0400 -Subject: [PATCH 04/28] Restored path in rtd.yaml - ---- - .readthedocs.yaml | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index 7468b70..037a6c0 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,6 +11,7 @@ sphinx: - python: - install: - - method: pip -+ - path: . - - requirements: docs/requirements.txt - - extra-requirements: - - doc -\ No newline at end of file - -From bba83e16c33c0614fa63a0f363677032f6086234 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:14:58 -0400 -Subject: [PATCH 05/28] Corrected rtd yaml formatting - ---- - .readthedocs.yaml | 7 ++++--- - 1 file changed, 4 insertions(+), 3 deletions(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index 037a6c0..fc40b17 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,7 +11,8 @@ sphinx: - python: - install: - - method: pip -- - path: . -- - requirements: docs/requirements.txt -- - extra-requirements: -+ path: . -+ requirements: docs/requirements.txt -+ requirements: requirements.txt -+ extra-requirements: - - doc -\ No newline at end of file - -From 1c5f11140f7f063a214e11e9787f779844423bd8 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:36:29 -0400 -Subject: [PATCH 06/28] added docs requirements, edited rtd.yaml - ---- - .readthedocs.yaml | 5 +---- - docs/requirements.txt | 10 ++++------ - requirements.txt | 5 +++++ - 3 files changed, 10 insertions(+), 10 deletions(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index fc40b17..b9870ed 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -12,7 +12,4 @@ python: - install: - - method: pip - path: . -- requirements: docs/requirements.txt -- requirements: requirements.txt -- extra-requirements: -- - doc -\ No newline at end of file -+ requirements: requirements.txt -\ No newline at end of file -diff --git a/docs/requirements.txt b/docs/requirements.txt -index 46d9223..e7f2aa5 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -6,10 +6,8 @@ - # scipy >= 0.17.0 - # pillow >= 6.2.0 - # future -- --sphinx -+sphinx==4.4.0 - sphinx_rtd_theme --sphinx-autobuild --rst-to-myst --myst-parser --nbsphinx -\ No newline at end of file -+rst-to-myst==0.3.2 -+myst-parser==0.17.0 -+nbsphinx==0.8.8 -\ No newline at end of file -diff --git a/requirements.txt b/requirements.txt -index 4e7245f..01c0804 100644 ---- a/requirements.txt -+++ b/requirements.txt -@@ -6,3 +6,8 @@ scikit-learn >= 0.19.0 - scipy >= 0.17.0 - pillow >= 6.2.0 - future -+sphinx==4.4.0 -+sphinx_rtd_theme -+rst-to-myst==0.3.2 -+myst-parser==0.17.0 -+nbsphinx==0.8.8 -\ No newline at end of file - -From ed7de9c2d2e89fc3a254b3c0882d6c2e2b981205 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:46:51 -0400 -Subject: [PATCH 07/28] Reordered rtd.yaml args - ---- - .readthedocs.yaml | 4 +++- - 1 file changed, 3 insertions(+), 1 deletion(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index b9870ed..6722c59 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -10,6 +10,8 @@ sphinx: - - python: - install: -+ - requirements: docs/requirements.txt - - method: pip - path: . -- requirements: requirements.txt -\ No newline at end of file -+ extra_requirements: -+ - docs -\ No newline at end of file - -From 683093572078eb20e9aebfa5daeb931ddb3c5bbc Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:50:07 -0400 -Subject: [PATCH 08/28] removed doc versions pkg version - ---- - docs/requirements.txt | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/docs/requirements.txt b/docs/requirements.txt -index e7f2aa5..f12e5f7 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -8,6 +8,6 @@ - # future - sphinx==4.4.0 - sphinx_rtd_theme --rst-to-myst==0.3.2 --myst-parser==0.17.0 --nbsphinx==0.8.8 -\ No newline at end of file -+rst-to-myst -+myst-parser -+nbsphinx -\ No newline at end of file - -From c3415895c8515696be1a88c2bfde242c3c2999f7 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:55:36 -0400 -Subject: [PATCH 09/28] Add docs status to readme - ---- - README.md | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/README.md b/README.md -index 5987691..f2b6433 100644 ---- a/README.md -+++ b/README.md -@@ -1,5 +1,5 @@ - [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) -- -+[![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) - - - # Topaz - -From 538286e7a4780d31f163e95011e89a68fc418b9f Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 15:00:17 -0400 -Subject: [PATCH 10/28] Added version and conda install badges - ---- - README.md | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git a/README.md b/README.md -index f2b6433..f3832bd 100644 ---- a/README.md -+++ b/README.md -@@ -1,5 +1,7 @@ - [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) - [![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) -+[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/version.svg)](https://anaconda.org/tbepler/topaz) -+[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/installer/conda.svg)](https://conda.anaconda.org/tbepler) - - - # Topaz - -From 2c13c55fa3080741571b868f6275b1839456e45e Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 15:05:11 -0400 -Subject: [PATCH 11/28] removed duplicate docs requirements - ---- - requirements.txt | 7 +------ - 1 file changed, 1 insertion(+), 6 deletions(-) - -diff --git a/requirements.txt b/requirements.txt -index 01c0804..d83f97b 100644 ---- a/requirements.txt -+++ b/requirements.txt -@@ -5,9 +5,4 @@ pandas - scikit-learn >= 0.19.0 - scipy >= 0.17.0 - pillow >= 6.2.0 --future --sphinx==4.4.0 --sphinx_rtd_theme --rst-to-myst==0.3.2 --myst-parser==0.17.0 --nbsphinx==0.8.8 -\ No newline at end of file -+future -\ No newline at end of file - -From 06f301640ea566f9baae816edb0a908ffafca444 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Thu, 17 Mar 2022 17:50:20 -0400 -Subject: [PATCH 12/28] Created doc entries for most code except commands - ---- - docs/source/algorithms.md | 7 +++ - docs/source/conf.py | 4 +- - docs/source/denoising.md | 7 +++ - docs/source/index.md | 10 ++++- - docs/source/methods.md | 7 +++ - docs/source/metrics_stats.md | 14 ++++++ - docs/source/models.md | 52 +++++++++++++++++++++- - docs/source/transforms.md | 7 +++ - docs/source/utils.md | 81 +++++++++++++++++++++++++++++++++++ - topaz/_version.py | 2 +- - topaz/model/classifier.py | 12 +++++- - topaz/model/features/basic.py | 2 + - 12 files changed, 197 insertions(+), 8 deletions(-) - create mode 100644 docs/source/algorithms.md - create mode 100644 docs/source/denoising.md - create mode 100644 docs/source/methods.md - create mode 100644 docs/source/metrics_stats.md - create mode 100644 docs/source/transforms.md - create mode 100644 docs/source/utils.md - -diff --git a/docs/source/algorithms.md b/docs/source/algorithms.md -new file mode 100644 -index 0000000..0a617c9 ---- /dev/null -+++ b/docs/source/algorithms.md -@@ -0,0 +1,7 @@ -+# Algorithms -+ -+```{eval-rst} -+.. automodule:: topaz.algorithms -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/conf.py b/docs/source/conf.py -index cac08bc..8a8b336 100644 ---- a/docs/source/conf.py -+++ b/docs/source/conf.py -@@ -34,7 +34,9 @@ - extensions = [ - "myst_parser", - "nbsphinx", -- "sphinx.ext.autodoc" -+ "sphinx.ext.autodoc", -+ "sphinx.ext.napoleon", -+ "sphinx.ext.autosectionlabel" - ] - - # Add any paths that contain templates here, relative to this directory. -diff --git a/docs/source/denoising.md b/docs/source/denoising.md -new file mode 100644 -index 0000000..036d4d5 ---- /dev/null -+++ b/docs/source/denoising.md -@@ -0,0 +1,7 @@ -+# Denoising -+ -+```{eval-rst} -+.. automodule:: topaz.denoise -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/index.md b/docs/source/index.md -index 1ab1b7c..af67119 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -18,8 +18,14 @@ - installation - tutorial - commands --relion --cryosparc -+algorithms -+denoising -+methods -+metrics_stats - models -+transforms -+utils - scripts -+relion -+cryosparc - ``` -diff --git a/docs/source/methods.md b/docs/source/methods.md -new file mode 100644 -index 0000000..aed5cfd ---- /dev/null -+++ b/docs/source/methods.md -@@ -0,0 +1,7 @@ -+# Methods -+ -+```{eval-rst} -+.. automodule:: topaz.methods -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/metrics_stats.md b/docs/source/metrics_stats.md -new file mode 100644 -index 0000000..dcfe0c4 ---- /dev/null -+++ b/docs/source/metrics_stats.md -@@ -0,0 +1,14 @@ -+# Metrics and Statistics -+ -+```{eval-rst} -+.. automodule:: topaz.metrics -+ :members: -+ :undoc-members: -+``` -+ -+ -+```{eval-rst} -+.. automodule:: topaz.stats -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/models.md b/docs/source/models.md -index 574c6fb..dbad6b1 100644 ---- a/docs/source/models.md -+++ b/docs/source/models.md -@@ -1,11 +1,59 @@ - # Models - -+## Feature Extractors -+ -+### Basic Conv Nets -+```{eval-rst} -+.. automodule:: topaz.model.features.basic -+ :members: -+ :undoc-members: -+``` -+ -+### DenseNets -+```{eval-rst} -+.. automodule:: topaz.model.features.densenet -+ :members: -+ :undoc-members: -+``` -+ -+### MSNets -+```{eval-rst} -+.. automodule:: topaz.model.features.msnet -+ :members: -+ :undoc-members: -+``` -+ -+### ResNets -+```{eval-rst} -+.. automodule:: topaz.model.features.resnet -+ :members: -+ :undoc-members: -+``` -+ -+## Linear Classifier - ```{eval-rst} - .. autoclass:: topaz.model.classifier.LinearClassifier -+ :members: -+ :undoc-members: - ``` - --## Features -+## Model Factory -+```{eval-rst} -+.. automodule:: topaz.model.factory -+ :members: -+ :undoc-members: -+``` -+ -+## Model Generator -+```{eval-rst} -+.. automodule:: topaz.model.generative -+ :members: -+ :undoc-members: -+``` - -+## Model Utilities - ```{eval-rst} --.. autoclass:: topaz.model.features.basic.BasicConv -+.. automodule:: topaz.model.utils -+ :members: -+ :undoc-members: - ``` -\ No newline at end of file -diff --git a/docs/source/transforms.md b/docs/source/transforms.md -new file mode 100644 -index 0000000..9bf1082 ---- /dev/null -+++ b/docs/source/transforms.md -@@ -0,0 +1,7 @@ -+# Transformations -+ -+```{eval-rst} -+.. automodule:: topaz.transform.scaled_gaussian_mixture -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/utils.md b/docs/source/utils.md -new file mode 100644 -index 0000000..027f498 ---- /dev/null -+++ b/docs/source/utils.md -@@ -0,0 +1,81 @@ -+# Utilities -+ -+## Conversions -+```{eval-rst} -+.. automodule:: topaz.utils.conversions -+ :members: -+ :undoc-members: -+``` -+ -+## File Utilities -+```{eval-rst} -+.. automodule:: topaz.utils.conversions -+ :members: -+ :undoc-members: -+``` -+ -+ -+```{eval-rst} -+.. automodule:: topaz.mrc -+ :members: -+ :undoc-members: -+``` -+ -+ -+## Image Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.image -+ :members: -+ :undoc-members: -+``` -+ -+## Pick Masking -+```{eval-rst} -+.. automodule:: topaz.utils.picks -+ :members: -+ :undoc-members: -+``` -+ -+## Printing -+```{eval-rst} -+.. automodule:: topaz.utils.printing -+ :members: -+ :undoc-members: -+``` -+ -+## STAR File Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.star -+ :members: -+ :undoc-members: -+``` -+ -+## Data Utilities -+ -+### Coordinate Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.data.coordinates -+ :members: -+ :undoc-members: -+``` -+ -+### Image Loading -+```{eval-rst} -+.. automodule:: topaz.utils.data.loader -+ :members: -+ :undoc-members: -+``` -+ -+### Dataset Partitioning -+```{eval-rst} -+.. automodule:: topaz.utils.data.partition -+ :members: -+ :undoc-members: -+``` -+ -+### Dataset Sampling -+```{eval-rst} -+.. automodule:: topaz.utils.data.sampler -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/topaz/_version.py b/topaz/_version.py -index e723ff3..fe404ae 100644 ---- a/topaz/_version.py -+++ b/topaz/_version.py -@@ -1 +1 @@ --__version__ = "0.2.5a" -+__version__ = "0.2.5" -diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py -index bb4710f..d63d83c 100644 ---- a/topaz/model/classifier.py -+++ b/topaz/model/classifier.py -@@ -5,10 +5,10 @@ - import torch.nn.functional as F - - class LinearClassifier(nn.Module): -+ '''A simple convolutional layer without non-linear activation.''' -+ - def __init__(self, features): - ''' -- A simple convolutional layer with no non-linear activation. -- - Args: - features (:obj:): the sizes associated with the layer - -@@ -34,6 +34,14 @@ def unfill(self): - self.features.unfill() - - def forward(self, x): -+ '''Applies the classifier to an input. -+ -+ Args: -+ x (np.ndarray): the image from which features are extracted and classified -+ -+ Returns: -+ z (np.ndarray): output of the classifer -+ ''' - z = self.features(x) - y = self.classifier(z) - return y -diff --git a/topaz/model/features/basic.py b/topaz/model/features/basic.py -index 0ea1fe9..dff4e9f 100644 ---- a/topaz/model/features/basic.py -+++ b/topaz/model/features/basic.py -@@ -10,6 +10,8 @@ - from topaz.model.utils import insize_from_outsize - - class BasicConv(nn.Module): -+ '''A generic convolutional neural network scaffold.''' -+ - def __init__(self, layers, units, unit_scaling=1, dropout=0, bn=True - , pooling=None, activation=nn.PReLU): - super(BasicConv, self).__init__() - -From d2c9761c2fba8d996c1f117f3004eeaf5a2abad7 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Fri, 18 Mar 2022 15:44:56 -0400 -Subject: [PATCH 13/28] reorganized docs, began work on man pages - ---- - docs/requirements.txt | 3 +- - docs/source/commands.md | 20 ++- - docs/source/commands/convert.md | 1 + - docs/source/commands/denoise.md | 1 + - docs/source/commands/denoise3d.md | 1 + - docs/source/commands/downsample.md | 1 + - docs/source/commands/extract.md | 1 + - docs/source/commands/file_utilities.md | 11 ++ - docs/source/commands/gui.md | 1 + - docs/source/commands/image_processing.md | 12 ++ - docs/source/commands/normalize.md | 8 + - docs/source/commands/particle_picking.md | 11 ++ - docs/source/commands/particle_stack.md | 1 + - docs/source/commands/precision_recall.md | 1 + - docs/source/commands/preprocess.md | 1 + - docs/source/commands/segment.md | 1 + - docs/source/commands/split.md | 1 + - docs/source/commands/train.md | 1 + - docs/source/commands/train_test_split.md | 1 + - docs/source/conf.py | 3 +- - docs/source/index.md | 2 +- - docs/source/installation.md | 172 ++------------------- - docs/source/installation/conda_install.md | 32 ++++ - docs/source/installation/docker_install.md | 51 ++++++ - docs/source/installation/pip_install.md | 20 +++ - docs/source/installation/singularity.md | 11 ++ - docs/source/installation/source_install.md | 57 +++++++ - docs/source/tutorial.md | 5 +- - topaz/commands/normalize.py | 9 +- - 29 files changed, 264 insertions(+), 176 deletions(-) - create mode 100644 docs/source/commands/convert.md - create mode 100644 docs/source/commands/denoise.md - create mode 100644 docs/source/commands/denoise3d.md - create mode 100644 docs/source/commands/downsample.md - create mode 100644 docs/source/commands/extract.md - create mode 100644 docs/source/commands/file_utilities.md - create mode 100644 docs/source/commands/gui.md - create mode 100644 docs/source/commands/image_processing.md - create mode 100644 docs/source/commands/normalize.md - create mode 100644 docs/source/commands/particle_picking.md - create mode 100644 docs/source/commands/particle_stack.md - create mode 100644 docs/source/commands/precision_recall.md - create mode 100644 docs/source/commands/preprocess.md - create mode 100644 docs/source/commands/segment.md - create mode 100644 docs/source/commands/split.md - create mode 100644 docs/source/commands/train.md - create mode 100644 docs/source/commands/train_test_split.md - create mode 100644 docs/source/installation/conda_install.md - create mode 100644 docs/source/installation/docker_install.md - create mode 100644 docs/source/installation/pip_install.md - create mode 100644 docs/source/installation/singularity.md - create mode 100644 docs/source/installation/source_install.md - -diff --git a/docs/requirements.txt b/docs/requirements.txt -index f12e5f7..bd0b467 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -10,4 +10,5 @@ sphinx==4.4.0 - sphinx_rtd_theme - rst-to-myst - myst-parser --nbsphinx -\ No newline at end of file -+nbsphinx -+sphinx-argparse -\ No newline at end of file -diff --git a/docs/source/commands.md b/docs/source/commands.md -index 44c4a21..3c462c9 100644 ---- a/docs/source/commands.md -+++ b/docs/source/commands.md -@@ -1,15 +1,13 @@ --# Topaz Commands -+# Topaz Commands (work in progress) - --## downsample - --## normalize -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 2 - --## preprocess -+commands/particle_picking -+commands/image_processing -+commands/file_utilities - --## train -- --## segment -- --## extract -- --## precision_recall_curve -+commands/gui -+``` -\ No newline at end of file -diff --git a/docs/source/commands/convert.md b/docs/source/commands/convert.md -new file mode 100644 -index 0000000..122f443 ---- /dev/null -+++ b/docs/source/commands/convert.md -@@ -0,0 +1 @@ -+# Convert -\ No newline at end of file -diff --git a/docs/source/commands/denoise.md b/docs/source/commands/denoise.md -new file mode 100644 -index 0000000..d995632 ---- /dev/null -+++ b/docs/source/commands/denoise.md -@@ -0,0 +1 @@ -+# Denoise -\ No newline at end of file -diff --git a/docs/source/commands/denoise3d.md b/docs/source/commands/denoise3d.md -new file mode 100644 -index 0000000..bf78fac ---- /dev/null -+++ b/docs/source/commands/denoise3d.md -@@ -0,0 +1 @@ -+# Denoise 3D -\ No newline at end of file -diff --git a/docs/source/commands/downsample.md b/docs/source/commands/downsample.md -new file mode 100644 -index 0000000..e0b15bf ---- /dev/null -+++ b/docs/source/commands/downsample.md -@@ -0,0 +1 @@ -+# Downsample -\ No newline at end of file -diff --git a/docs/source/commands/extract.md b/docs/source/commands/extract.md -new file mode 100644 -index 0000000..d0e6da9 ---- /dev/null -+++ b/docs/source/commands/extract.md -@@ -0,0 +1 @@ -+# Extract -\ No newline at end of file -diff --git a/docs/source/commands/file_utilities.md b/docs/source/commands/file_utilities.md -new file mode 100644 -index 0000000..b26444f ---- /dev/null -+++ b/docs/source/commands/file_utilities.md -@@ -0,0 +1,11 @@ -+# File Utilities -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+convert -+split -+particle_stack -+train_test_split -+``` -\ No newline at end of file -diff --git a/docs/source/commands/gui.md b/docs/source/commands/gui.md -new file mode 100644 -index 0000000..93bd5f2 ---- /dev/null -+++ b/docs/source/commands/gui.md -@@ -0,0 +1 @@ -+# GUI -\ No newline at end of file -diff --git a/docs/source/commands/image_processing.md b/docs/source/commands/image_processing.md -new file mode 100644 -index 0000000..973048c ---- /dev/null -+++ b/docs/source/commands/image_processing.md -@@ -0,0 +1,12 @@ -+# Image Processing -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+downsample -+normalize -+preprocess -+denoise -+denoise3d -+``` -\ No newline at end of file -diff --git a/docs/source/commands/normalize.md b/docs/source/commands/normalize.md -new file mode 100644 -index 0000000..ad442b2 ---- /dev/null -+++ b/docs/source/commands/normalize.md -@@ -0,0 +1,8 @@ -+# Normalize -+ -+```{eval-rst} -+.. argparse:: -+ :module: topaz.commands.normalize -+ :func: add_arguments -+ :prog: normalize -+``` -\ No newline at end of file -diff --git a/docs/source/commands/particle_picking.md b/docs/source/commands/particle_picking.md -new file mode 100644 -index 0000000..c32361a ---- /dev/null -+++ b/docs/source/commands/particle_picking.md -@@ -0,0 +1,11 @@ -+# Particle Picking -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+train -+segment -+extract -+precision_recall -+``` -\ No newline at end of file -diff --git a/docs/source/commands/particle_stack.md b/docs/source/commands/particle_stack.md -new file mode 100644 -index 0000000..7bb5a5e ---- /dev/null -+++ b/docs/source/commands/particle_stack.md -@@ -0,0 +1 @@ -+# Particle Stack -\ No newline at end of file -diff --git a/docs/source/commands/precision_recall.md b/docs/source/commands/precision_recall.md -new file mode 100644 -index 0000000..dff8323 ---- /dev/null -+++ b/docs/source/commands/precision_recall.md -@@ -0,0 +1 @@ -+# Precision Recall Curve -\ No newline at end of file -diff --git a/docs/source/commands/preprocess.md b/docs/source/commands/preprocess.md -new file mode 100644 -index 0000000..8fd260d ---- /dev/null -+++ b/docs/source/commands/preprocess.md -@@ -0,0 +1 @@ -+# Preprocess -\ No newline at end of file -diff --git a/docs/source/commands/segment.md b/docs/source/commands/segment.md -new file mode 100644 -index 0000000..af21080 ---- /dev/null -+++ b/docs/source/commands/segment.md -@@ -0,0 +1 @@ -+# Segment -\ No newline at end of file -diff --git a/docs/source/commands/split.md b/docs/source/commands/split.md -new file mode 100644 -index 0000000..5e525aa ---- /dev/null -+++ b/docs/source/commands/split.md -@@ -0,0 +1 @@ -+# Split -\ No newline at end of file -diff --git a/docs/source/commands/train.md b/docs/source/commands/train.md -new file mode 100644 -index 0000000..44ac09a ---- /dev/null -+++ b/docs/source/commands/train.md -@@ -0,0 +1 @@ -+# Train -\ No newline at end of file -diff --git a/docs/source/commands/train_test_split.md b/docs/source/commands/train_test_split.md -new file mode 100644 -index 0000000..e28a8c8 ---- /dev/null -+++ b/docs/source/commands/train_test_split.md -@@ -0,0 +1 @@ -+# Train Test Split -\ No newline at end of file -diff --git a/docs/source/conf.py b/docs/source/conf.py -index 8a8b336..8f3a9d3 100644 ---- a/docs/source/conf.py -+++ b/docs/source/conf.py -@@ -36,7 +36,8 @@ - "nbsphinx", - "sphinx.ext.autodoc", - "sphinx.ext.napoleon", -- "sphinx.ext.autosectionlabel" -+ "sphinx.ext.autosectionlabel", -+ "sphinxarg.ext" - ] - - # Add any paths that contain templates here, relative to this directory. -diff --git a/docs/source/index.md b/docs/source/index.md -index af67119..13b414e 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -13,7 +13,7 @@ - - ```{toctree} - :caption: 'Contents:' --:maxdepth: 2 -+:maxdepth: 3 - - installation - tutorial -diff --git a/docs/source/installation.md b/docs/source/installation.md -index fc4a774..8eca25e 100644 ---- a/docs/source/installation.md -+++ b/docs/source/installation.md -@@ -1,172 +1,28 @@ - # Installation - --**

(Recommended) Click here to install *using Anaconda*

** -- --If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -- --We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: --``` --conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 --source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured --# source deactivate # returns to the base conda environment --``` --More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -- --## Install Topaz -- --To install the precompiled Topaz package and its dependencies, including pytorch: --``` --conda install topaz -c tbepler -c pytorch --``` --This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: --``` --conda install cudatoolkit=9.0 -c pytorch --``` --or combined into a single command: --``` --conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch --``` --See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -- --That's it! Topaz is now installed in your anaconda environment. -- --

-- --**
Click here to install *using Pip*

** -- --We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -- --### Install Topaz -- --To install Topaz for Python 3.X --``` --pip3 install topaz-em --``` -- --for Python 2.7 --``` --pip install topaz-em --``` --See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -- --That's it! Topaz is now installed through pip. -- --

-- --**
Click here to install *using Docker*

** -- --**

Do you have Docker installed? If not, *click here*

** -- --#### Linux/MacOS    *(command line)* -- --Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -- --> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -- --Launch docker according to your Docker engine's instructions, typically ``docker start``. -- --> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -- --#### Windows    *(GUI & command line)* -- --Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -- --Launch Kitematic. -- --> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -- --> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -- -- --### What is Docker? -- --[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -- -- -- --A Dockerfile is provided to build images with CUDA support. Build from the github repo: --``` --docker build -t topaz https://github.com/tbepler/topaz.git --``` -- --or download the source code and build from the source directory --``` --git clone https://github.com/tbepler/topaz --cd topaz --docker build -t topaz . --``` -- --

-- -- --**
Click here to install *using Singularity*

** -- --A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: --``` --singularity pull shub://nysbc/topaz --``` -- --Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+## Conda -+```{include} installation/conda_install.md - ``` --singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz --``` -- --

-- -- --**
Click here to install *from source*

** -- --_Recommended: install Topaz into a virtual Python environment_ --See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -- --#### Install the dependencies -- --Tested with python 3.6 and 2.7 -- --- pytorch (>= 1.0.0) --- torchvision --- pillow (>= 6.2.0) --- numpy (>= 1.11) --- pandas (>= 0.20.3) --- scipy (>= 0.19.1) --- scikit-learn (>= 0.19.0) -- --Easy installation of dependencies with conda --``` --conda install numpy pandas scikit-learn --conda install -c pytorch pytorch torchvision --``` --For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -- --#### Download the source code --``` --git clone https://github.com/tbepler/topaz --``` -- --#### Install Topaz -+

- --Move to the source code directory --``` --cd topaz -+## Pip -+```{include} installation/pip_install.md - ``` -+

- --By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+## Docker -+```{include} installation/docker_install.md - ``` --git checkout v0.1.0 --``` --Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+

- --Install Topaz into your Python path including the topaz command line interface --``` --pip install . -+## Singularity -+```{include} installation/singularity.md - ``` -+

- --To install for development use -+## From Source -+```{include} installation/source_install.md - ``` --pip install -e . --``` -- --

-

- - Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). -\ No newline at end of file -diff --git a/docs/source/installation/conda_install.md b/docs/source/installation/conda_install.md -new file mode 100644 -index 0000000..06476c9 ---- /dev/null -+++ b/docs/source/installation/conda_install.md -@@ -0,0 +1,32 @@ -+**

(Recommended) Click here to install *using Anaconda*

** -+ -+If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -+ -+We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: -+``` -+conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 -+source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured -+# source deactivate # returns to the base conda environment -+``` -+More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -+ -+\ -+**Install Topaz** -+ -+To install the precompiled Topaz package and its dependencies, including pytorch: -+``` -+conda install topaz -c tbepler -c pytorch -+``` -+This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: -+``` -+conda install cudatoolkit=9.0 -c pytorch -+``` -+or combined into a single command: -+``` -+conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -+ -+That's it! Topaz is now installed in your anaconda environment. -+ -+

-\ No newline at end of file -diff --git a/docs/source/installation/docker_install.md b/docs/source/installation/docker_install.md -new file mode 100644 -index 0000000..913ffd0 ---- /dev/null -+++ b/docs/source/installation/docker_install.md -@@ -0,0 +1,51 @@ -+**
Click here to install *using Docker*

** -+ -+**

What is Docker?

** -+ -+[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -+

-+ -+ -+**
Do you have Docker installed? If not, *click here*

** -+ -+**

Linux/MacOS    *(command line)*

** -+ -+

-+Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -+ -+> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -+ -+Launch docker according to your Docker engine's instructions, typically ``docker start``. -+ -+> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -+

-+ -+ -+**
Windows    *(GUI & command line)*

** -+ -+

-+Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -+ -+Launch Kitematic. -+ -+> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -+ -+> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -+

-+ -+

-+

-+ -+\ -+A Dockerfile is provided to build images with CUDA support. Build from the github repo: -+``` -+docker build -t topaz https://github.com/tbepler/topaz.git -+``` -+ -+or download the source code and build from the source directory -+``` -+git clone https://github.com/tbepler/topaz -+cd topaz -+docker build -t topaz . -+``` -+

-\ No newline at end of file -diff --git a/docs/source/installation/pip_install.md b/docs/source/installation/pip_install.md -new file mode 100644 -index 0000000..e65f64e ---- /dev/null -+++ b/docs/source/installation/pip_install.md -@@ -0,0 +1,20 @@ -+**
Click here to install *using Pip*

** -+ -+We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -+ -+**Install Topaz** -+ -+To install Topaz for Python 3.X -+``` -+pip3 install topaz-em -+``` -+ -+for Python 2.7 -+``` -+pip install topaz-em -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -+ -+That's it! Topaz is now installed through pip. -+ -+

-\ No newline at end of file -diff --git a/docs/source/installation/singularity.md b/docs/source/installation/singularity.md -new file mode 100644 -index 0000000..401c819 ---- /dev/null -+++ b/docs/source/installation/singularity.md -@@ -0,0 +1,11 @@ -+**
Click here to install *using Singularity*

** -+A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: -+``` -+singularity pull shub://nysbc/topaz -+``` -+ -+Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+``` -+singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz -+``` -+

-\ No newline at end of file -diff --git a/docs/source/installation/source_install.md b/docs/source/installation/source_install.md -new file mode 100644 -index 0000000..648dfc8 ---- /dev/null -+++ b/docs/source/installation/source_install.md -@@ -0,0 +1,57 @@ -+**
Click here to install *from source*

** -+ -+_Recommended: install Topaz into a virtual Python environment_ -+See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -+ -+\ -+**Install the dependencies** -+ -+Tested with python 3.6 and 2.7 -+ -+- pytorch (>= 1.0.0) -+- torchvision -+- pillow (>= 6.2.0) -+- numpy (>= 1.11) -+- pandas (>= 0.20.3) -+- scipy (>= 0.19.1) -+- scikit-learn (>= 0.19.0) -+ -+Easy installation of dependencies with conda -+``` -+conda install numpy pandas scikit-learn -+conda install -c pytorch pytorch torchvision -+``` -+For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -+ -+\ -+**Download the source code** -+``` -+git clone https://github.com/tbepler/topaz -+``` -+ -+\ -+**Install Topaz** -+ -+Move to the source code directory -+``` -+cd topaz -+``` -+ -+By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+``` -+git checkout v0.1.0 -+``` -+Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+ -+Install Topaz into your Python path including the topaz command line interface -+``` -+pip install . -+``` -+ -+To install for development use -+``` -+pip install -e . -+``` -+ -+

-+

-\ No newline at end of file -diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md -index 161a880..c2ebb97 100644 ---- a/docs/source/tutorial.md -+++ b/docs/source/tutorial.md -@@ -1,4 +1,7 @@ --# Tutorial -+# Tutorials (coming soon) -+ -+Tutorial pages here are a work-in-progress. For the time being, please refer to the tutorial notebooks in topaz/tutorial. -+ - +\ No newline at end of file +diff --git a/docs/source/index.md b/docs/source/index.md +index 71ef567..1ab1b7c 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -6,8 +6,7 @@ + # Welcome to Topaz's documentation! + + +-```{include} ../../README.md +-:relative-images: ++```{include} ./description.md + ``` + + +@@ -15,4 +14,12 @@ + ```{toctree} + :caption: 'Contents:' + :maxdepth: 2 ++ ++installation ++tutorial ++commands ++relion ++cryosparc ++models ++scripts + ``` +diff --git a/docs/source/installation.md b/docs/source/installation.md +new file mode 100644 +index 0000000..fc4a774 +--- /dev/null ++++ b/docs/source/installation.md +@@ -0,0 +1,172 @@ ++# Installation ++ ++**

(Recommended) Click here to install *using Anaconda*

** ++ ++If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). ++ ++We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: ++``` ++conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 ++source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured ++# source deactivate # returns to the base conda environment ++``` ++More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). ++ ++## Install Topaz ++ ++To install the precompiled Topaz package and its dependencies, including pytorch: ++``` ++conda install topaz -c tbepler -c pytorch ++``` ++This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: ++``` ++conda install cudatoolkit=9.0 -c pytorch ++``` ++or combined into a single command: ++``` ++conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. ++ ++That's it! Topaz is now installed in your anaconda environment. ++ ++

++ ++**
Click here to install *using Pip*

** ++ ++We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. ++ ++### Install Topaz ++ ++To install Topaz for Python 3.X ++``` ++pip3 install topaz-em ++``` ++ ++for Python 2.7 ++``` ++pip install topaz-em ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. ++ ++That's it! Topaz is now installed through pip. ++ ++

++ ++**
Click here to install *using Docker*

** ++ ++**

Do you have Docker installed? If not, *click here*

** ++ ++#### Linux/MacOS    *(command line)* ++ ++Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). ++ ++> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). ++ ++Launch docker according to your Docker engine's instructions, typically ``docker start``. ++ ++> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ ++ ++#### Windows    *(GUI & command line)* ++ ++Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). ++ ++Launch Kitematic. ++ ++> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. ++ ++> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. ++ ++ ++### What is Docker? ++ ++[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) ++ ++ ++ ++A Dockerfile is provided to build images with CUDA support. Build from the github repo: ++``` ++docker build -t topaz https://github.com/tbepler/topaz.git ++``` ++ ++or download the source code and build from the source directory ++``` ++git clone https://github.com/tbepler/topaz ++cd topaz ++docker build -t topaz . ++``` ++ ++

++ ++ ++**
Click here to install *using Singularity*

** ++ ++A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: ++``` ++singularity pull shub://nysbc/topaz ++``` ++ ++Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++``` ++singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz ++``` ++ ++

++ ++ ++**
Click here to install *from source*

** ++ ++_Recommended: install Topaz into a virtual Python environment_ ++See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. ++ ++#### Install the dependencies ++ ++Tested with python 3.6 and 2.7 ++ ++- pytorch (>= 1.0.0) ++- torchvision ++- pillow (>= 6.2.0) ++- numpy (>= 1.11) ++- pandas (>= 0.20.3) ++- scipy (>= 0.19.1) ++- scikit-learn (>= 0.19.0) ++ ++Easy installation of dependencies with conda ++``` ++conda install numpy pandas scikit-learn ++conda install -c pytorch pytorch torchvision ++``` ++For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ ++ ++#### Download the source code ++``` ++git clone https://github.com/tbepler/topaz ++``` ++ ++#### Install Topaz ++ ++Move to the source code directory ++``` ++cd topaz ++``` ++ ++By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++``` ++git checkout v0.1.0 ++``` ++Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++ ++Install Topaz into your Python path including the topaz command line interface ++``` ++pip install . ++``` ++ ++To install for development use ++``` ++pip install -e . ++``` ++ ++

++

++ ++Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). +\ No newline at end of file +diff --git a/docs/source/models.md b/docs/source/models.md +new file mode 100644 +index 0000000..574c6fb +--- /dev/null ++++ b/docs/source/models.md +@@ -0,0 +1,11 @@ ++# Models ++ ++```{eval-rst} ++.. autoclass:: topaz.model.classifier.LinearClassifier ++``` ++ ++## Features ++ ++```{eval-rst} ++.. autoclass:: topaz.model.features.basic.BasicConv ++``` +\ No newline at end of file +diff --git a/docs/source/relion.md b/docs/source/relion.md +new file mode 100644 +index 0000000..7c94e56 +--- /dev/null ++++ b/docs/source/relion.md +@@ -0,0 +1 @@ ++## Use with RELION +\ No newline at end of file +diff --git a/docs/source/scripts.md b/docs/source/scripts.md +new file mode 100644 +index 0000000..82916c1 +--- /dev/null ++++ b/docs/source/scripts.md +@@ -0,0 +1 @@ ++# Scripts +\ No newline at end of file +diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md +new file mode 100644 +index 0000000..161a880 +--- /dev/null ++++ b/docs/source/tutorial.md +@@ -0,0 +1,15 @@ ++# Tutorial ++ +diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py +index be1c3de..bb4710f 100644 +--- a/topaz/model/classifier.py ++++ b/topaz/model/classifier.py +@@ -6,6 +6,15 @@ + + class LinearClassifier(nn.Module): + def __init__(self, features): ++ ''' ++ A simple convolutional layer with no non-linear activation. ++ ++ Args: ++ features (:obj:): the sizes associated with the layer ++ ++ Attributes: ++ features (:obj:) ++ ''' + super(LinearClassifier, self).__init__() + self.features = features + self.classifier = nn.Conv2d(features.latent_dim, 1, 1) + +From e064f07d52ba152e79a664c16d64cbbbf46067e3 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 10:49:08 -0400 +Subject: [PATCH 03/28] updated doc requirements for rtd + +--- + .readthedocs.yaml | 11 +++-------- + docs/requirements.txt | 15 +++++++++++++++ + 2 files changed, 18 insertions(+), 8 deletions(-) + create mode 100644 docs/requirements.txt + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index b67d3bf..7468b70 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,11 +11,6 @@ sphinx: + python: + install: + - method: pip +- path: . +- extra_requirements: +- - docs +- - nbsphinx +- - sphinx_rtd_theme +- - sphinx-autobuild +- - rst-to-myst +- - myst-parser +\ No newline at end of file ++ - requirements: docs/requirements.txt ++ - extra-requirements: ++ - doc +\ No newline at end of file +diff --git a/docs/requirements.txt b/docs/requirements.txt +new file mode 100644 +index 0000000..46d9223 +--- /dev/null ++++ b/docs/requirements.txt +@@ -0,0 +1,15 @@ ++# torch >= 1.0.0 ++# torchvision ++# numpy >= 1.11 ++# pandas ++# scikit-learn >= 0.19.0 ++# scipy >= 0.17.0 ++# pillow >= 6.2.0 ++# future ++ ++sphinx ++sphinx_rtd_theme ++sphinx-autobuild ++rst-to-myst ++myst-parser ++nbsphinx +\ No newline at end of file + +From d80d47b01d4e919d4e0be86e4790e65074158b18 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 10:52:10 -0400 +Subject: [PATCH 04/28] Restored path in rtd.yaml + +--- + .readthedocs.yaml | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index 7468b70..037a6c0 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,6 +11,7 @@ sphinx: + python: + install: + - method: pip ++ - path: . + - requirements: docs/requirements.txt + - extra-requirements: + - doc +\ No newline at end of file + +From bba83e16c33c0614fa63a0f363677032f6086234 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:14:58 -0400 +Subject: [PATCH 05/28] Corrected rtd yaml formatting + +--- + .readthedocs.yaml | 7 ++++--- + 1 file changed, 4 insertions(+), 3 deletions(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index 037a6c0..fc40b17 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -11,7 +11,8 @@ sphinx: + python: + install: + - method: pip +- - path: . +- - requirements: docs/requirements.txt +- - extra-requirements: ++ path: . ++ requirements: docs/requirements.txt ++ requirements: requirements.txt ++ extra-requirements: + - doc +\ No newline at end of file + +From 1c5f11140f7f063a214e11e9787f779844423bd8 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:36:29 -0400 +Subject: [PATCH 06/28] added docs requirements, edited rtd.yaml + +--- + .readthedocs.yaml | 5 +---- + docs/requirements.txt | 10 ++++------ + requirements.txt | 5 +++++ + 3 files changed, 10 insertions(+), 10 deletions(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index fc40b17..b9870ed 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -12,7 +12,4 @@ python: + install: + - method: pip + path: . +- requirements: docs/requirements.txt +- requirements: requirements.txt +- extra-requirements: +- - doc +\ No newline at end of file ++ requirements: requirements.txt +\ No newline at end of file +diff --git a/docs/requirements.txt b/docs/requirements.txt +index 46d9223..e7f2aa5 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -6,10 +6,8 @@ + # scipy >= 0.17.0 + # pillow >= 6.2.0 + # future +- +-sphinx ++sphinx==4.4.0 + sphinx_rtd_theme +-sphinx-autobuild +-rst-to-myst +-myst-parser +-nbsphinx +\ No newline at end of file ++rst-to-myst==0.3.2 ++myst-parser==0.17.0 ++nbsphinx==0.8.8 +\ No newline at end of file +diff --git a/requirements.txt b/requirements.txt +index 4e7245f..01c0804 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -6,3 +6,8 @@ scikit-learn >= 0.19.0 + scipy >= 0.17.0 + pillow >= 6.2.0 + future ++sphinx==4.4.0 ++sphinx_rtd_theme ++rst-to-myst==0.3.2 ++myst-parser==0.17.0 ++nbsphinx==0.8.8 +\ No newline at end of file + +From ed7de9c2d2e89fc3a254b3c0882d6c2e2b981205 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:46:51 -0400 +Subject: [PATCH 07/28] Reordered rtd.yaml args + +--- + .readthedocs.yaml | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/.readthedocs.yaml b/.readthedocs.yaml +index b9870ed..6722c59 100644 +--- a/.readthedocs.yaml ++++ b/.readthedocs.yaml +@@ -10,6 +10,8 @@ sphinx: + + python: + install: ++ - requirements: docs/requirements.txt + - method: pip + path: . +- requirements: requirements.txt +\ No newline at end of file ++ extra_requirements: ++ - docs +\ No newline at end of file + +From 683093572078eb20e9aebfa5daeb931ddb3c5bbc Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:50:07 -0400 +Subject: [PATCH 08/28] removed doc versions pkg version + +--- + docs/requirements.txt | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/docs/requirements.txt b/docs/requirements.txt +index e7f2aa5..f12e5f7 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -8,6 +8,6 @@ + # future + sphinx==4.4.0 + sphinx_rtd_theme +-rst-to-myst==0.3.2 +-myst-parser==0.17.0 +-nbsphinx==0.8.8 +\ No newline at end of file ++rst-to-myst ++myst-parser ++nbsphinx +\ No newline at end of file + +From c3415895c8515696be1a88c2bfde242c3c2999f7 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 14:55:36 -0400 +Subject: [PATCH 09/28] Add docs status to readme + +--- + README.md | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/README.md b/README.md +index 5987691..f2b6433 100644 +--- a/README.md ++++ b/README.md +@@ -1,5 +1,5 @@ + [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) +- ++[![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) + + + # Topaz + +From 538286e7a4780d31f163e95011e89a68fc418b9f Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 15:00:17 -0400 +Subject: [PATCH 10/28] Added version and conda install badges + +--- + README.md | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/README.md b/README.md +index f2b6433..f3832bd 100644 +--- a/README.md ++++ b/README.md +@@ -1,5 +1,7 @@ + [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) + [![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) ++[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/version.svg)](https://anaconda.org/tbepler/topaz) ++[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/installer/conda.svg)](https://conda.anaconda.org/tbepler) + + + # Topaz + +From 2c13c55fa3080741571b868f6275b1839456e45e Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Wed, 16 Mar 2022 15:05:11 -0400 +Subject: [PATCH 11/28] removed duplicate docs requirements + +--- + requirements.txt | 7 +------ + 1 file changed, 1 insertion(+), 6 deletions(-) + +diff --git a/requirements.txt b/requirements.txt +index 01c0804..d83f97b 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -5,9 +5,4 @@ pandas + scikit-learn >= 0.19.0 + scipy >= 0.17.0 + pillow >= 6.2.0 +-future +-sphinx==4.4.0 +-sphinx_rtd_theme +-rst-to-myst==0.3.2 +-myst-parser==0.17.0 +-nbsphinx==0.8.8 +\ No newline at end of file ++future +\ No newline at end of file + +From 06f301640ea566f9baae816edb0a908ffafca444 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Thu, 17 Mar 2022 17:50:20 -0400 +Subject: [PATCH 12/28] Created doc entries for most code except commands + +--- + docs/source/algorithms.md | 7 +++ + docs/source/conf.py | 4 +- + docs/source/denoising.md | 7 +++ + docs/source/index.md | 10 ++++- + docs/source/methods.md | 7 +++ + docs/source/metrics_stats.md | 14 ++++++ + docs/source/models.md | 52 +++++++++++++++++++++- + docs/source/transforms.md | 7 +++ + docs/source/utils.md | 81 +++++++++++++++++++++++++++++++++++ + topaz/_version.py | 2 +- + topaz/model/classifier.py | 12 +++++- + topaz/model/features/basic.py | 2 + + 12 files changed, 197 insertions(+), 8 deletions(-) + create mode 100644 docs/source/algorithms.md + create mode 100644 docs/source/denoising.md + create mode 100644 docs/source/methods.md + create mode 100644 docs/source/metrics_stats.md + create mode 100644 docs/source/transforms.md + create mode 100644 docs/source/utils.md + +diff --git a/docs/source/algorithms.md b/docs/source/algorithms.md +new file mode 100644 +index 0000000..0a617c9 +--- /dev/null ++++ b/docs/source/algorithms.md +@@ -0,0 +1,7 @@ ++# Algorithms ++ ++```{eval-rst} ++.. automodule:: topaz.algorithms ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/conf.py b/docs/source/conf.py +index cac08bc..8a8b336 100644 +--- a/docs/source/conf.py ++++ b/docs/source/conf.py +@@ -34,7 +34,9 @@ + extensions = [ + "myst_parser", + "nbsphinx", +- "sphinx.ext.autodoc" ++ "sphinx.ext.autodoc", ++ "sphinx.ext.napoleon", ++ "sphinx.ext.autosectionlabel" + ] + + # Add any paths that contain templates here, relative to this directory. +diff --git a/docs/source/denoising.md b/docs/source/denoising.md +new file mode 100644 +index 0000000..036d4d5 +--- /dev/null ++++ b/docs/source/denoising.md +@@ -0,0 +1,7 @@ ++# Denoising ++ ++```{eval-rst} ++.. automodule:: topaz.denoise ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/index.md b/docs/source/index.md +index 1ab1b7c..af67119 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -18,8 +18,14 @@ + installation + tutorial + commands +-relion +-cryosparc ++algorithms ++denoising ++methods ++metrics_stats + models ++transforms ++utils + scripts ++relion ++cryosparc + ``` +diff --git a/docs/source/methods.md b/docs/source/methods.md +new file mode 100644 +index 0000000..aed5cfd +--- /dev/null ++++ b/docs/source/methods.md +@@ -0,0 +1,7 @@ ++# Methods ++ ++```{eval-rst} ++.. automodule:: topaz.methods ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/metrics_stats.md b/docs/source/metrics_stats.md +new file mode 100644 +index 0000000..dcfe0c4 +--- /dev/null ++++ b/docs/source/metrics_stats.md +@@ -0,0 +1,14 @@ ++# Metrics and Statistics ++ ++```{eval-rst} ++.. automodule:: topaz.metrics ++ :members: ++ :undoc-members: ++``` ++ ++ ++```{eval-rst} ++.. automodule:: topaz.stats ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/models.md b/docs/source/models.md +index 574c6fb..dbad6b1 100644 +--- a/docs/source/models.md ++++ b/docs/source/models.md +@@ -1,11 +1,59 @@ + # Models + ++## Feature Extractors ++ ++### Basic Conv Nets ++```{eval-rst} ++.. automodule:: topaz.model.features.basic ++ :members: ++ :undoc-members: ++``` ++ ++### DenseNets ++```{eval-rst} ++.. automodule:: topaz.model.features.densenet ++ :members: ++ :undoc-members: ++``` ++ ++### MSNets ++```{eval-rst} ++.. automodule:: topaz.model.features.msnet ++ :members: ++ :undoc-members: ++``` ++ ++### ResNets ++```{eval-rst} ++.. automodule:: topaz.model.features.resnet ++ :members: ++ :undoc-members: ++``` ++ ++## Linear Classifier + ```{eval-rst} + .. autoclass:: topaz.model.classifier.LinearClassifier ++ :members: ++ :undoc-members: + ``` + +-## Features ++## Model Factory ++```{eval-rst} ++.. automodule:: topaz.model.factory ++ :members: ++ :undoc-members: ++``` ++ ++## Model Generator ++```{eval-rst} ++.. automodule:: topaz.model.generative ++ :members: ++ :undoc-members: ++``` + ++## Model Utilities + ```{eval-rst} +-.. autoclass:: topaz.model.features.basic.BasicConv ++.. automodule:: topaz.model.utils ++ :members: ++ :undoc-members: + ``` +\ No newline at end of file +diff --git a/docs/source/transforms.md b/docs/source/transforms.md +new file mode 100644 +index 0000000..9bf1082 +--- /dev/null ++++ b/docs/source/transforms.md +@@ -0,0 +1,7 @@ ++# Transformations ++ ++```{eval-rst} ++.. automodule:: topaz.transform.scaled_gaussian_mixture ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/docs/source/utils.md b/docs/source/utils.md +new file mode 100644 +index 0000000..027f498 +--- /dev/null ++++ b/docs/source/utils.md +@@ -0,0 +1,81 @@ ++# Utilities ++ ++## Conversions ++```{eval-rst} ++.. automodule:: topaz.utils.conversions ++ :members: ++ :undoc-members: ++``` ++ ++## File Utilities ++```{eval-rst} ++.. automodule:: topaz.utils.conversions ++ :members: ++ :undoc-members: ++``` ++ ++ ++```{eval-rst} ++.. automodule:: topaz.mrc ++ :members: ++ :undoc-members: ++``` ++ ++ ++## Image Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.image ++ :members: ++ :undoc-members: ++``` ++ ++## Pick Masking ++```{eval-rst} ++.. automodule:: topaz.utils.picks ++ :members: ++ :undoc-members: ++``` ++ ++## Printing ++```{eval-rst} ++.. automodule:: topaz.utils.printing ++ :members: ++ :undoc-members: ++``` ++ ++## STAR File Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.star ++ :members: ++ :undoc-members: ++``` ++ ++## Data Utilities ++ ++### Coordinate Manipulations ++```{eval-rst} ++.. automodule:: topaz.utils.data.coordinates ++ :members: ++ :undoc-members: ++``` ++ ++### Image Loading ++```{eval-rst} ++.. automodule:: topaz.utils.data.loader ++ :members: ++ :undoc-members: ++``` ++ ++### Dataset Partitioning ++```{eval-rst} ++.. automodule:: topaz.utils.data.partition ++ :members: ++ :undoc-members: ++``` ++ ++### Dataset Sampling ++```{eval-rst} ++.. automodule:: topaz.utils.data.sampler ++ :members: ++ :undoc-members: ++``` +\ No newline at end of file +diff --git a/topaz/_version.py b/topaz/_version.py +index e723ff3..fe404ae 100644 +--- a/topaz/_version.py ++++ b/topaz/_version.py +@@ -1 +1 @@ +-__version__ = "0.2.5a" ++__version__ = "0.2.5" +diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py +index bb4710f..d63d83c 100644 +--- a/topaz/model/classifier.py ++++ b/topaz/model/classifier.py +@@ -5,10 +5,10 @@ + import torch.nn.functional as F + + class LinearClassifier(nn.Module): ++ '''A simple convolutional layer without non-linear activation.''' ++ + def __init__(self, features): + ''' +- A simple convolutional layer with no non-linear activation. +- + Args: + features (:obj:): the sizes associated with the layer + +@@ -34,6 +34,14 @@ def unfill(self): + self.features.unfill() + + def forward(self, x): ++ '''Applies the classifier to an input. ++ ++ Args: ++ x (np.ndarray): the image from which features are extracted and classified ++ ++ Returns: ++ z (np.ndarray): output of the classifer ++ ''' + z = self.features(x) + y = self.classifier(z) + return y +diff --git a/topaz/model/features/basic.py b/topaz/model/features/basic.py +index 0ea1fe9..dff4e9f 100644 +--- a/topaz/model/features/basic.py ++++ b/topaz/model/features/basic.py +@@ -10,6 +10,8 @@ + from topaz.model.utils import insize_from_outsize + + class BasicConv(nn.Module): ++ '''A generic convolutional neural network scaffold.''' ++ + def __init__(self, layers, units, unit_scaling=1, dropout=0, bn=True + , pooling=None, activation=nn.PReLU): + super(BasicConv, self).__init__() + +From d2c9761c2fba8d996c1f117f3004eeaf5a2abad7 Mon Sep 17 00:00:00 2001 +From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> +Date: Fri, 18 Mar 2022 15:44:56 -0400 +Subject: [PATCH 13/28] reorganized docs, began work on man pages + +--- + docs/requirements.txt | 3 +- + docs/source/commands.md | 20 ++- + docs/source/commands/convert.md | 1 + + docs/source/commands/denoise.md | 1 + + docs/source/commands/denoise3d.md | 1 + + docs/source/commands/downsample.md | 1 + + docs/source/commands/extract.md | 1 + + docs/source/commands/file_utilities.md | 11 ++ + docs/source/commands/gui.md | 1 + + docs/source/commands/image_processing.md | 12 ++ + docs/source/commands/normalize.md | 8 + + docs/source/commands/particle_picking.md | 11 ++ + docs/source/commands/particle_stack.md | 1 + + docs/source/commands/precision_recall.md | 1 + + docs/source/commands/preprocess.md | 1 + + docs/source/commands/segment.md | 1 + + docs/source/commands/split.md | 1 + + docs/source/commands/train.md | 1 + + docs/source/commands/train_test_split.md | 1 + + docs/source/conf.py | 3 +- + docs/source/index.md | 2 +- + docs/source/installation.md | 172 ++------------------- + docs/source/installation/conda_install.md | 32 ++++ + docs/source/installation/docker_install.md | 51 ++++++ + docs/source/installation/pip_install.md | 20 +++ + docs/source/installation/singularity.md | 11 ++ + docs/source/installation/source_install.md | 57 +++++++ + docs/source/tutorial.md | 5 +- + topaz/commands/normalize.py | 9 +- + 29 files changed, 264 insertions(+), 176 deletions(-) + create mode 100644 docs/source/commands/convert.md + create mode 100644 docs/source/commands/denoise.md + create mode 100644 docs/source/commands/denoise3d.md + create mode 100644 docs/source/commands/downsample.md + create mode 100644 docs/source/commands/extract.md + create mode 100644 docs/source/commands/file_utilities.md + create mode 100644 docs/source/commands/gui.md + create mode 100644 docs/source/commands/image_processing.md + create mode 100644 docs/source/commands/normalize.md + create mode 100644 docs/source/commands/particle_picking.md + create mode 100644 docs/source/commands/particle_stack.md + create mode 100644 docs/source/commands/precision_recall.md + create mode 100644 docs/source/commands/preprocess.md + create mode 100644 docs/source/commands/segment.md + create mode 100644 docs/source/commands/split.md + create mode 100644 docs/source/commands/train.md + create mode 100644 docs/source/commands/train_test_split.md + create mode 100644 docs/source/installation/conda_install.md + create mode 100644 docs/source/installation/docker_install.md + create mode 100644 docs/source/installation/pip_install.md + create mode 100644 docs/source/installation/singularity.md + create mode 100644 docs/source/installation/source_install.md + +diff --git a/docs/requirements.txt b/docs/requirements.txt +index f12e5f7..bd0b467 100644 +--- a/docs/requirements.txt ++++ b/docs/requirements.txt +@@ -10,4 +10,5 @@ sphinx==4.4.0 + sphinx_rtd_theme + rst-to-myst + myst-parser +-nbsphinx +\ No newline at end of file ++nbsphinx ++sphinx-argparse +\ No newline at end of file +diff --git a/docs/source/commands.md b/docs/source/commands.md +index 44c4a21..3c462c9 100644 +--- a/docs/source/commands.md ++++ b/docs/source/commands.md +@@ -1,15 +1,13 @@ +-# Topaz Commands ++# Topaz Commands (work in progress) + +-## downsample + +-## normalize ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 2 + +-## preprocess ++commands/particle_picking ++commands/image_processing ++commands/file_utilities + +-## train +- +-## segment +- +-## extract +- +-## precision_recall_curve ++commands/gui ++``` +\ No newline at end of file +diff --git a/docs/source/commands/convert.md b/docs/source/commands/convert.md +new file mode 100644 +index 0000000..122f443 +--- /dev/null ++++ b/docs/source/commands/convert.md +@@ -0,0 +1 @@ ++# Convert +\ No newline at end of file +diff --git a/docs/source/commands/denoise.md b/docs/source/commands/denoise.md +new file mode 100644 +index 0000000..d995632 +--- /dev/null ++++ b/docs/source/commands/denoise.md +@@ -0,0 +1 @@ ++# Denoise +\ No newline at end of file +diff --git a/docs/source/commands/denoise3d.md b/docs/source/commands/denoise3d.md +new file mode 100644 +index 0000000..bf78fac +--- /dev/null ++++ b/docs/source/commands/denoise3d.md +@@ -0,0 +1 @@ ++# Denoise 3D +\ No newline at end of file +diff --git a/docs/source/commands/downsample.md b/docs/source/commands/downsample.md +new file mode 100644 +index 0000000..e0b15bf +--- /dev/null ++++ b/docs/source/commands/downsample.md +@@ -0,0 +1 @@ ++# Downsample +\ No newline at end of file +diff --git a/docs/source/commands/extract.md b/docs/source/commands/extract.md +new file mode 100644 +index 0000000..d0e6da9 +--- /dev/null ++++ b/docs/source/commands/extract.md +@@ -0,0 +1 @@ ++# Extract +\ No newline at end of file +diff --git a/docs/source/commands/file_utilities.md b/docs/source/commands/file_utilities.md +new file mode 100644 +index 0000000..b26444f +--- /dev/null ++++ b/docs/source/commands/file_utilities.md +@@ -0,0 +1,11 @@ ++# File Utilities ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++convert ++split ++particle_stack ++train_test_split ++``` +\ No newline at end of file +diff --git a/docs/source/commands/gui.md b/docs/source/commands/gui.md +new file mode 100644 +index 0000000..93bd5f2 +--- /dev/null ++++ b/docs/source/commands/gui.md +@@ -0,0 +1 @@ ++# GUI +\ No newline at end of file +diff --git a/docs/source/commands/image_processing.md b/docs/source/commands/image_processing.md +new file mode 100644 +index 0000000..973048c +--- /dev/null ++++ b/docs/source/commands/image_processing.md +@@ -0,0 +1,12 @@ ++# Image Processing ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++downsample ++normalize ++preprocess ++denoise ++denoise3d ++``` +\ No newline at end of file +diff --git a/docs/source/commands/normalize.md b/docs/source/commands/normalize.md +new file mode 100644 +index 0000000..ad442b2 +--- /dev/null ++++ b/docs/source/commands/normalize.md +@@ -0,0 +1,8 @@ ++# Normalize ++ ++```{eval-rst} ++.. argparse:: ++ :module: topaz.commands.normalize ++ :func: add_arguments ++ :prog: normalize ++``` +\ No newline at end of file +diff --git a/docs/source/commands/particle_picking.md b/docs/source/commands/particle_picking.md +new file mode 100644 +index 0000000..c32361a +--- /dev/null ++++ b/docs/source/commands/particle_picking.md +@@ -0,0 +1,11 @@ ++# Particle Picking ++ ++```{toctree} ++:caption: 'Commands' ++:maxdepth: 1 ++ ++train ++segment ++extract ++precision_recall ++``` +\ No newline at end of file +diff --git a/docs/source/commands/particle_stack.md b/docs/source/commands/particle_stack.md +new file mode 100644 +index 0000000..7bb5a5e +--- /dev/null ++++ b/docs/source/commands/particle_stack.md +@@ -0,0 +1 @@ ++# Particle Stack +\ No newline at end of file +diff --git a/docs/source/commands/precision_recall.md b/docs/source/commands/precision_recall.md +new file mode 100644 +index 0000000..dff8323 +--- /dev/null ++++ b/docs/source/commands/precision_recall.md +@@ -0,0 +1 @@ ++# Precision Recall Curve +\ No newline at end of file +diff --git a/docs/source/commands/preprocess.md b/docs/source/commands/preprocess.md +new file mode 100644 +index 0000000..8fd260d +--- /dev/null ++++ b/docs/source/commands/preprocess.md +@@ -0,0 +1 @@ ++# Preprocess +\ No newline at end of file +diff --git a/docs/source/commands/segment.md b/docs/source/commands/segment.md +new file mode 100644 +index 0000000..af21080 +--- /dev/null ++++ b/docs/source/commands/segment.md +@@ -0,0 +1 @@ ++# Segment +\ No newline at end of file +diff --git a/docs/source/commands/split.md b/docs/source/commands/split.md +new file mode 100644 +index 0000000..5e525aa +--- /dev/null ++++ b/docs/source/commands/split.md +@@ -0,0 +1 @@ ++# Split +\ No newline at end of file +diff --git a/docs/source/commands/train.md b/docs/source/commands/train.md +new file mode 100644 +index 0000000..44ac09a +--- /dev/null ++++ b/docs/source/commands/train.md +@@ -0,0 +1 @@ ++# Train +\ No newline at end of file +diff --git a/docs/source/commands/train_test_split.md b/docs/source/commands/train_test_split.md +new file mode 100644 +index 0000000..e28a8c8 +--- /dev/null ++++ b/docs/source/commands/train_test_split.md +@@ -0,0 +1 @@ ++# Train Test Split +\ No newline at end of file +diff --git a/docs/source/conf.py b/docs/source/conf.py +index 8a8b336..8f3a9d3 100644 +--- a/docs/source/conf.py ++++ b/docs/source/conf.py +@@ -36,7 +36,8 @@ + "nbsphinx", + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", +- "sphinx.ext.autosectionlabel" ++ "sphinx.ext.autosectionlabel", ++ "sphinxarg.ext" + ] + + # Add any paths that contain templates here, relative to this directory. +diff --git a/docs/source/index.md b/docs/source/index.md +index af67119..13b414e 100644 +--- a/docs/source/index.md ++++ b/docs/source/index.md +@@ -13,7 +13,7 @@ + + ```{toctree} + :caption: 'Contents:' +-:maxdepth: 2 ++:maxdepth: 3 + + installation + tutorial +diff --git a/docs/source/installation.md b/docs/source/installation.md +index fc4a774..8eca25e 100644 +--- a/docs/source/installation.md ++++ b/docs/source/installation.md +@@ -1,172 +1,28 @@ + # Installation + +-**

(Recommended) Click here to install *using Anaconda*

** +- +-If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). +- +-We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: +-``` +-conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 +-source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured +-# source deactivate # returns to the base conda environment +-``` +-More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). +- +-## Install Topaz +- +-To install the precompiled Topaz package and its dependencies, including pytorch: +-``` +-conda install topaz -c tbepler -c pytorch +-``` +-This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: +-``` +-conda install cudatoolkit=9.0 -c pytorch +-``` +-or combined into a single command: +-``` +-conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch +-``` +-See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. +- +-That's it! Topaz is now installed in your anaconda environment. +- +-

+- +-**
Click here to install *using Pip*

** +- +-We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. +- +-### Install Topaz +- +-To install Topaz for Python 3.X +-``` +-pip3 install topaz-em +-``` +- +-for Python 2.7 +-``` +-pip install topaz-em +-``` +-See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. +- +-That's it! Topaz is now installed through pip. +- +-

+- +-**
Click here to install *using Docker*

** +- +-**

Do you have Docker installed? If not, *click here*

** +- +-#### Linux/MacOS    *(command line)* +- +-Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). +- +-> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). +- +-Launch docker according to your Docker engine's instructions, typically ``docker start``. +- +-> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ +- +-#### Windows    *(GUI & command line)* +- +-Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). +- +-Launch Kitematic. +- +-> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. +- +-> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. +- +- +-### What is Docker? +- +-[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) +- +- +- +-A Dockerfile is provided to build images with CUDA support. Build from the github repo: +-``` +-docker build -t topaz https://github.com/tbepler/topaz.git +-``` +- +-or download the source code and build from the source directory +-``` +-git clone https://github.com/tbepler/topaz +-cd topaz +-docker build -t topaz . +-``` +- +-

+- +- +-**
Click here to install *using Singularity*

** +- +-A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: +-``` +-singularity pull shub://nysbc/topaz +-``` +- +-Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++## Conda ++```{include} installation/conda_install.md + ``` +-singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz +-``` +- +-

+- +- +-**
Click here to install *from source*

** +- +-_Recommended: install Topaz into a virtual Python environment_ +-See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. +- +-#### Install the dependencies +- +-Tested with python 3.6 and 2.7 +- +-- pytorch (>= 1.0.0) +-- torchvision +-- pillow (>= 6.2.0) +-- numpy (>= 1.11) +-- pandas (>= 0.20.3) +-- scipy (>= 0.19.1) +-- scikit-learn (>= 0.19.0) +- +-Easy installation of dependencies with conda +-``` +-conda install numpy pandas scikit-learn +-conda install -c pytorch pytorch torchvision +-``` +-For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ +- +-#### Download the source code +-``` +-git clone https://github.com/tbepler/topaz +-``` +- +-#### Install Topaz ++

+ +-Move to the source code directory +-``` +-cd topaz ++## Pip ++```{include} installation/pip_install.md + ``` ++

+ +-By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++## Docker ++```{include} installation/docker_install.md + ``` +-git checkout v0.1.0 +-``` +-Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++

+ +-Install Topaz into your Python path including the topaz command line interface +-``` +-pip install . ++## Singularity ++```{include} installation/singularity.md + ``` ++

+ +-To install for development use ++## From Source ++```{include} installation/source_install.md + ``` +-pip install -e . +-``` +- +-

+

+ + Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). +\ No newline at end of file +diff --git a/docs/source/installation/conda_install.md b/docs/source/installation/conda_install.md +new file mode 100644 +index 0000000..06476c9 +--- /dev/null ++++ b/docs/source/installation/conda_install.md +@@ -0,0 +1,32 @@ ++**

(Recommended) Click here to install *using Anaconda*

** ++ ++If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). ++ ++We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: ++``` ++conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 ++source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured ++# source deactivate # returns to the base conda environment ++``` ++More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). ++ ++\ ++**Install Topaz** ++ ++To install the precompiled Topaz package and its dependencies, including pytorch: ++``` ++conda install topaz -c tbepler -c pytorch ++``` ++This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: ++``` ++conda install cudatoolkit=9.0 -c pytorch ++``` ++or combined into a single command: ++``` ++conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. ++ ++That's it! Topaz is now installed in your anaconda environment. ++ ++

+\ No newline at end of file +diff --git a/docs/source/installation/docker_install.md b/docs/source/installation/docker_install.md +new file mode 100644 +index 0000000..913ffd0 +--- /dev/null ++++ b/docs/source/installation/docker_install.md +@@ -0,0 +1,51 @@ ++**
Click here to install *using Docker*

** ++ ++**

What is Docker?

** ++ ++[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) ++

++ ++ ++**
Do you have Docker installed? If not, *click here*

** ++ ++**

Linux/MacOS    *(command line)*

** ++ ++

++Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). ++ ++> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). ++ ++Launch docker according to your Docker engine's instructions, typically ``docker start``. ++ ++> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ ++

++ ++ ++**
Windows    *(GUI & command line)*

** ++ ++

++Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). ++ ++Launch Kitematic. ++ ++> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. ++ ++> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. ++

++ ++

++

++ ++\ ++A Dockerfile is provided to build images with CUDA support. Build from the github repo: ++``` ++docker build -t topaz https://github.com/tbepler/topaz.git ++``` ++ ++or download the source code and build from the source directory ++``` ++git clone https://github.com/tbepler/topaz ++cd topaz ++docker build -t topaz . ++``` ++

+\ No newline at end of file +diff --git a/docs/source/installation/pip_install.md b/docs/source/installation/pip_install.md +new file mode 100644 +index 0000000..e65f64e +--- /dev/null ++++ b/docs/source/installation/pip_install.md +@@ -0,0 +1,20 @@ ++**
Click here to install *using Pip*

** ++ ++We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. ++ ++**Install Topaz** ++ ++To install Topaz for Python 3.X ++``` ++pip3 install topaz-em ++``` ++ ++for Python 2.7 ++``` ++pip install topaz-em ++``` ++See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. ++ ++That's it! Topaz is now installed through pip. ++ ++

+\ No newline at end of file +diff --git a/docs/source/installation/singularity.md b/docs/source/installation/singularity.md +new file mode 100644 +index 0000000..401c819 +--- /dev/null ++++ b/docs/source/installation/singularity.md +@@ -0,0 +1,11 @@ ++**
Click here to install *using Singularity*

** ++A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: ++``` ++singularity pull shub://nysbc/topaz ++``` ++ ++Then, you can run topaz from within the singularity image with (paths must be changed appropriately): ++``` ++singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz ++``` ++

+\ No newline at end of file +diff --git a/docs/source/installation/source_install.md b/docs/source/installation/source_install.md +new file mode 100644 +index 0000000..648dfc8 +--- /dev/null ++++ b/docs/source/installation/source_install.md +@@ -0,0 +1,57 @@ ++**
Click here to install *from source*

** ++ ++_Recommended: install Topaz into a virtual Python environment_ ++See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. ++ ++\ ++**Install the dependencies** ++ ++Tested with python 3.6 and 2.7 ++ ++- pytorch (>= 1.0.0) ++- torchvision ++- pillow (>= 6.2.0) ++- numpy (>= 1.11) ++- pandas (>= 0.20.3) ++- scipy (>= 0.19.1) ++- scikit-learn (>= 0.19.0) ++ ++Easy installation of dependencies with conda ++``` ++conda install numpy pandas scikit-learn ++conda install -c pytorch pytorch torchvision ++``` ++For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ ++ ++\ ++**Download the source code** ++``` ++git clone https://github.com/tbepler/topaz ++``` ++ ++\ ++**Install Topaz** ++ ++Move to the source code directory ++``` ++cd topaz ++``` ++ ++By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: ++``` ++git checkout v0.1.0 ++``` ++Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. ++ ++Install Topaz into your Python path including the topaz command line interface ++``` ++pip install . ++``` ++ ++To install for development use ++``` ++pip install -e . ++``` ++ ++

++

+\ No newline at end of file +diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md +index 161a880..c2ebb97 100644 +--- a/docs/source/tutorial.md ++++ b/docs/source/tutorial.md +@@ -1,4 +1,7 @@ +-# Tutorial ++# Tutorials (coming soon) ++ ++Tutorial pages here are a work-in-progress. For the time being, please refer to the tutorial notebooks in topaz/tutorial. ++ + -\ No newline at end of file -diff --git a/docs/source/index.md b/docs/source/index.md -index 71ef567..1ab1b7c 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -6,8 +6,7 @@ - # Welcome to Topaz's documentation! - - --```{include} ../../README.md --:relative-images: -+```{include} ./description.md - ``` - - -@@ -15,4 +14,12 @@ - ```{toctree} - :caption: 'Contents:' - :maxdepth: 2 -+ -+installation -+tutorial -+commands -+relion -+cryosparc -+models -+scripts - ``` -diff --git a/docs/source/installation.md b/docs/source/installation.md -new file mode 100644 -index 0000000..fc4a774 ---- /dev/null -+++ b/docs/source/installation.md -@@ -0,0 +1,172 @@ -+# Installation -+ -+**

(Recommended) Click here to install *using Anaconda*

** -+ -+If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -+ -+We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: -+``` -+conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 -+source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured -+# source deactivate # returns to the base conda environment -+``` -+More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -+ -+## Install Topaz -+ -+To install the precompiled Topaz package and its dependencies, including pytorch: -+``` -+conda install topaz -c tbepler -c pytorch -+``` -+This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: -+``` -+conda install cudatoolkit=9.0 -c pytorch -+``` -+or combined into a single command: -+``` -+conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -+ -+That's it! Topaz is now installed in your anaconda environment. -+ -+

-+ -+**
Click here to install *using Pip*

** -+ -+We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -+ -+### Install Topaz -+ -+To install Topaz for Python 3.X -+``` -+pip3 install topaz-em -+``` -+ -+for Python 2.7 -+``` -+pip install topaz-em -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -+ -+That's it! Topaz is now installed through pip. -+ -+

-+ -+**
Click here to install *using Docker*

** -+ -+**

Do you have Docker installed? If not, *click here*

** -+ -+#### Linux/MacOS    *(command line)* -+ -+Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -+ -+> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -+ -+Launch docker according to your Docker engine's instructions, typically ``docker start``. -+ -+> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -+ -+#### Windows    *(GUI & command line)* -+ -+Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -+ -+Launch Kitematic. -+ -+> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -+ -+> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -+ -+ -+### What is Docker? -+ -+[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -+ -+ -+ -+A Dockerfile is provided to build images with CUDA support. Build from the github repo: -+``` -+docker build -t topaz https://github.com/tbepler/topaz.git -+``` -+ -+or download the source code and build from the source directory -+``` -+git clone https://github.com/tbepler/topaz -+cd topaz -+docker build -t topaz . -+``` -+ -+

-+ -+ -+**
Click here to install *using Singularity*

** -+ -+A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: -+``` -+singularity pull shub://nysbc/topaz -+``` -+ -+Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+``` -+singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz -+``` -+ -+

-+ -+ -+**
Click here to install *from source*

** -+ -+_Recommended: install Topaz into a virtual Python environment_ -+See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -+ -+#### Install the dependencies -+ -+Tested with python 3.6 and 2.7 -+ -+- pytorch (>= 1.0.0) -+- torchvision -+- pillow (>= 6.2.0) -+- numpy (>= 1.11) -+- pandas (>= 0.20.3) -+- scipy (>= 0.19.1) -+- scikit-learn (>= 0.19.0) -+ -+Easy installation of dependencies with conda -+``` -+conda install numpy pandas scikit-learn -+conda install -c pytorch pytorch torchvision -+``` -+For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -+ -+#### Download the source code -+``` -+git clone https://github.com/tbepler/topaz -+``` -+ -+#### Install Topaz -+ -+Move to the source code directory -+``` -+cd topaz -+``` -+ -+By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+``` -+git checkout v0.1.0 -+``` -+Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+ -+Install Topaz into your Python path including the topaz command line interface -+``` -+pip install . -+``` -+ -+To install for development use -+``` -+pip install -e . -+``` -+ -+

-+

-+ -+Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). -\ No newline at end of file -diff --git a/docs/source/models.md b/docs/source/models.md -new file mode 100644 -index 0000000..574c6fb ---- /dev/null -+++ b/docs/source/models.md -@@ -0,0 +1,11 @@ -+# Models -+ -+```{eval-rst} -+.. autoclass:: topaz.model.classifier.LinearClassifier -+``` -+ -+## Features -+ -+```{eval-rst} -+.. autoclass:: topaz.model.features.basic.BasicConv -+``` -\ No newline at end of file -diff --git a/docs/source/relion.md b/docs/source/relion.md -new file mode 100644 -index 0000000..7c94e56 ---- /dev/null -+++ b/docs/source/relion.md -@@ -0,0 +1 @@ -+## Use with RELION -\ No newline at end of file -diff --git a/docs/source/scripts.md b/docs/source/scripts.md -new file mode 100644 -index 0000000..82916c1 ---- /dev/null -+++ b/docs/source/scripts.md -@@ -0,0 +1 @@ -+# Scripts -\ No newline at end of file -diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md -new file mode 100644 -index 0000000..161a880 ---- /dev/null -+++ b/docs/source/tutorial.md -@@ -0,0 +1,15 @@ -+# Tutorial -+ -diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py -index be1c3de..bb4710f 100644 ---- a/topaz/model/classifier.py -+++ b/topaz/model/classifier.py -@@ -6,6 +6,15 @@ - - class LinearClassifier(nn.Module): - def __init__(self, features): -+ ''' -+ A simple convolutional layer with no non-linear activation. -+ -+ Args: -+ features (:obj:): the sizes associated with the layer -+ -+ Attributes: -+ features (:obj:) -+ ''' - super(LinearClassifier, self).__init__() - self.features = features - self.classifier = nn.Conv2d(features.latent_dim, 1, 1) - -From e064f07d52ba152e79a664c16d64cbbbf46067e3 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 10:49:08 -0400 -Subject: [PATCH 03/28] updated doc requirements for rtd - ---- - .readthedocs.yaml | 11 +++-------- - docs/requirements.txt | 15 +++++++++++++++ - 2 files changed, 18 insertions(+), 8 deletions(-) - create mode 100644 docs/requirements.txt - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index b67d3bf..7468b70 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,11 +11,6 @@ sphinx: - python: - install: - - method: pip -- path: . -- extra_requirements: -- - docs -- - nbsphinx -- - sphinx_rtd_theme -- - sphinx-autobuild -- - rst-to-myst -- - myst-parser -\ No newline at end of file -+ - requirements: docs/requirements.txt -+ - extra-requirements: -+ - doc -\ No newline at end of file -diff --git a/docs/requirements.txt b/docs/requirements.txt -new file mode 100644 -index 0000000..46d9223 ---- /dev/null -+++ b/docs/requirements.txt -@@ -0,0 +1,15 @@ -+# torch >= 1.0.0 -+# torchvision -+# numpy >= 1.11 -+# pandas -+# scikit-learn >= 0.19.0 -+# scipy >= 0.17.0 -+# pillow >= 6.2.0 -+# future -+ -+sphinx -+sphinx_rtd_theme -+sphinx-autobuild -+rst-to-myst -+myst-parser -+nbsphinx -\ No newline at end of file - -From d80d47b01d4e919d4e0be86e4790e65074158b18 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 10:52:10 -0400 -Subject: [PATCH 04/28] Restored path in rtd.yaml - ---- - .readthedocs.yaml | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index 7468b70..037a6c0 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,6 +11,7 @@ sphinx: - python: - install: - - method: pip -+ - path: . - - requirements: docs/requirements.txt - - extra-requirements: - - doc -\ No newline at end of file - -From bba83e16c33c0614fa63a0f363677032f6086234 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:14:58 -0400 -Subject: [PATCH 05/28] Corrected rtd yaml formatting - ---- - .readthedocs.yaml | 7 ++++--- - 1 file changed, 4 insertions(+), 3 deletions(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index 037a6c0..fc40b17 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -11,7 +11,8 @@ sphinx: - python: - install: - - method: pip -- - path: . -- - requirements: docs/requirements.txt -- - extra-requirements: -+ path: . -+ requirements: docs/requirements.txt -+ requirements: requirements.txt -+ extra-requirements: - - doc -\ No newline at end of file - -From 1c5f11140f7f063a214e11e9787f779844423bd8 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:36:29 -0400 -Subject: [PATCH 06/28] added docs requirements, edited rtd.yaml - ---- - .readthedocs.yaml | 5 +---- - docs/requirements.txt | 10 ++++------ - requirements.txt | 5 +++++ - 3 files changed, 10 insertions(+), 10 deletions(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index fc40b17..b9870ed 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -12,7 +12,4 @@ python: - install: - - method: pip - path: . -- requirements: docs/requirements.txt -- requirements: requirements.txt -- extra-requirements: -- - doc -\ No newline at end of file -+ requirements: requirements.txt -\ No newline at end of file -diff --git a/docs/requirements.txt b/docs/requirements.txt -index 46d9223..e7f2aa5 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -6,10 +6,8 @@ - # scipy >= 0.17.0 - # pillow >= 6.2.0 - # future -- --sphinx -+sphinx==4.4.0 - sphinx_rtd_theme --sphinx-autobuild --rst-to-myst --myst-parser --nbsphinx -\ No newline at end of file -+rst-to-myst==0.3.2 -+myst-parser==0.17.0 -+nbsphinx==0.8.8 -\ No newline at end of file -diff --git a/requirements.txt b/requirements.txt -index 4e7245f..01c0804 100644 ---- a/requirements.txt -+++ b/requirements.txt -@@ -6,3 +6,8 @@ scikit-learn >= 0.19.0 - scipy >= 0.17.0 - pillow >= 6.2.0 - future -+sphinx==4.4.0 -+sphinx_rtd_theme -+rst-to-myst==0.3.2 -+myst-parser==0.17.0 -+nbsphinx==0.8.8 -\ No newline at end of file - -From ed7de9c2d2e89fc3a254b3c0882d6c2e2b981205 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:46:51 -0400 -Subject: [PATCH 07/28] Reordered rtd.yaml args - ---- - .readthedocs.yaml | 4 +++- - 1 file changed, 3 insertions(+), 1 deletion(-) - -diff --git a/.readthedocs.yaml b/.readthedocs.yaml -index b9870ed..6722c59 100644 ---- a/.readthedocs.yaml -+++ b/.readthedocs.yaml -@@ -10,6 +10,8 @@ sphinx: - - python: - install: -+ - requirements: docs/requirements.txt - - method: pip - path: . -- requirements: requirements.txt -\ No newline at end of file -+ extra_requirements: -+ - docs -\ No newline at end of file - -From 683093572078eb20e9aebfa5daeb931ddb3c5bbc Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:50:07 -0400 -Subject: [PATCH 08/28] removed doc versions pkg version - ---- - docs/requirements.txt | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/docs/requirements.txt b/docs/requirements.txt -index e7f2aa5..f12e5f7 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -8,6 +8,6 @@ - # future - sphinx==4.4.0 - sphinx_rtd_theme --rst-to-myst==0.3.2 --myst-parser==0.17.0 --nbsphinx==0.8.8 -\ No newline at end of file -+rst-to-myst -+myst-parser -+nbsphinx -\ No newline at end of file - -From c3415895c8515696be1a88c2bfde242c3c2999f7 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 14:55:36 -0400 -Subject: [PATCH 09/28] Add docs status to readme - ---- - README.md | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/README.md b/README.md -index 5987691..f2b6433 100644 ---- a/README.md -+++ b/README.md -@@ -1,5 +1,5 @@ - [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) -- -+[![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) - - - # Topaz - -From 538286e7a4780d31f163e95011e89a68fc418b9f Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 15:00:17 -0400 -Subject: [PATCH 10/28] Added version and conda install badges - ---- - README.md | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git a/README.md b/README.md -index f2b6433..f3832bd 100644 ---- a/README.md -+++ b/README.md -@@ -1,5 +1,7 @@ - [![Python package](https://github.com/tbepler/topaz/actions/workflows/ci.yml/badge.svg)](https://github.com/tbepler/topaz/actions/workflows/ci.yml) - [![Documentation Status](https://readthedocs.org/projects/topaz-em/badge/?version=latest)](https://topaz-em.readthedocs.io/en/latest/?badge=latest) -+[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/version.svg)](https://anaconda.org/tbepler/topaz) -+[![Anaconda-Server Badge](https://anaconda.org/tbepler/topaz/badges/installer/conda.svg)](https://conda.anaconda.org/tbepler) - - - # Topaz - -From 2c13c55fa3080741571b868f6275b1839456e45e Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Wed, 16 Mar 2022 15:05:11 -0400 -Subject: [PATCH 11/28] removed duplicate docs requirements - ---- - requirements.txt | 7 +------ - 1 file changed, 1 insertion(+), 6 deletions(-) - -diff --git a/requirements.txt b/requirements.txt -index 01c0804..d83f97b 100644 ---- a/requirements.txt -+++ b/requirements.txt -@@ -5,9 +5,4 @@ pandas - scikit-learn >= 0.19.0 - scipy >= 0.17.0 - pillow >= 6.2.0 --future --sphinx==4.4.0 --sphinx_rtd_theme --rst-to-myst==0.3.2 --myst-parser==0.17.0 --nbsphinx==0.8.8 -\ No newline at end of file -+future -\ No newline at end of file - -From 06f301640ea566f9baae816edb0a908ffafca444 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Thu, 17 Mar 2022 17:50:20 -0400 -Subject: [PATCH 12/28] Created doc entries for most code except commands - ---- - docs/source/algorithms.md | 7 +++ - docs/source/conf.py | 4 +- - docs/source/denoising.md | 7 +++ - docs/source/index.md | 10 ++++- - docs/source/methods.md | 7 +++ - docs/source/metrics_stats.md | 14 ++++++ - docs/source/models.md | 52 +++++++++++++++++++++- - docs/source/transforms.md | 7 +++ - docs/source/utils.md | 81 +++++++++++++++++++++++++++++++++++ - topaz/_version.py | 2 +- - topaz/model/classifier.py | 12 +++++- - topaz/model/features/basic.py | 2 + - 12 files changed, 197 insertions(+), 8 deletions(-) - create mode 100644 docs/source/algorithms.md - create mode 100644 docs/source/denoising.md - create mode 100644 docs/source/methods.md - create mode 100644 docs/source/metrics_stats.md - create mode 100644 docs/source/transforms.md - create mode 100644 docs/source/utils.md - -diff --git a/docs/source/algorithms.md b/docs/source/algorithms.md -new file mode 100644 -index 0000000..0a617c9 ---- /dev/null -+++ b/docs/source/algorithms.md -@@ -0,0 +1,7 @@ -+# Algorithms -+ -+```{eval-rst} -+.. automodule:: topaz.algorithms -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/conf.py b/docs/source/conf.py -index cac08bc..8a8b336 100644 ---- a/docs/source/conf.py -+++ b/docs/source/conf.py -@@ -34,7 +34,9 @@ - extensions = [ - "myst_parser", - "nbsphinx", -- "sphinx.ext.autodoc" -+ "sphinx.ext.autodoc", -+ "sphinx.ext.napoleon", -+ "sphinx.ext.autosectionlabel" - ] - - # Add any paths that contain templates here, relative to this directory. -diff --git a/docs/source/denoising.md b/docs/source/denoising.md -new file mode 100644 -index 0000000..036d4d5 ---- /dev/null -+++ b/docs/source/denoising.md -@@ -0,0 +1,7 @@ -+# Denoising -+ -+```{eval-rst} -+.. automodule:: topaz.denoise -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/index.md b/docs/source/index.md -index 1ab1b7c..af67119 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -18,8 +18,14 @@ - installation - tutorial - commands --relion --cryosparc -+algorithms -+denoising -+methods -+metrics_stats - models -+transforms -+utils - scripts -+relion -+cryosparc - ``` -diff --git a/docs/source/methods.md b/docs/source/methods.md -new file mode 100644 -index 0000000..aed5cfd ---- /dev/null -+++ b/docs/source/methods.md -@@ -0,0 +1,7 @@ -+# Methods -+ -+```{eval-rst} -+.. automodule:: topaz.methods -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/metrics_stats.md b/docs/source/metrics_stats.md -new file mode 100644 -index 0000000..dcfe0c4 ---- /dev/null -+++ b/docs/source/metrics_stats.md -@@ -0,0 +1,14 @@ -+# Metrics and Statistics -+ -+```{eval-rst} -+.. automodule:: topaz.metrics -+ :members: -+ :undoc-members: -+``` -+ -+ -+```{eval-rst} -+.. automodule:: topaz.stats -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/models.md b/docs/source/models.md -index 574c6fb..dbad6b1 100644 ---- a/docs/source/models.md -+++ b/docs/source/models.md -@@ -1,11 +1,59 @@ - # Models - -+## Feature Extractors -+ -+### Basic Conv Nets -+```{eval-rst} -+.. automodule:: topaz.model.features.basic -+ :members: -+ :undoc-members: -+``` -+ -+### DenseNets -+```{eval-rst} -+.. automodule:: topaz.model.features.densenet -+ :members: -+ :undoc-members: -+``` -+ -+### MSNets -+```{eval-rst} -+.. automodule:: topaz.model.features.msnet -+ :members: -+ :undoc-members: -+``` -+ -+### ResNets -+```{eval-rst} -+.. automodule:: topaz.model.features.resnet -+ :members: -+ :undoc-members: -+``` -+ -+## Linear Classifier - ```{eval-rst} - .. autoclass:: topaz.model.classifier.LinearClassifier -+ :members: -+ :undoc-members: - ``` - --## Features -+## Model Factory -+```{eval-rst} -+.. automodule:: topaz.model.factory -+ :members: -+ :undoc-members: -+``` -+ -+## Model Generator -+```{eval-rst} -+.. automodule:: topaz.model.generative -+ :members: -+ :undoc-members: -+``` - -+## Model Utilities - ```{eval-rst} --.. autoclass:: topaz.model.features.basic.BasicConv -+.. automodule:: topaz.model.utils -+ :members: -+ :undoc-members: - ``` -\ No newline at end of file -diff --git a/docs/source/transforms.md b/docs/source/transforms.md -new file mode 100644 -index 0000000..9bf1082 ---- /dev/null -+++ b/docs/source/transforms.md -@@ -0,0 +1,7 @@ -+# Transformations -+ -+```{eval-rst} -+.. automodule:: topaz.transform.scaled_gaussian_mixture -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/docs/source/utils.md b/docs/source/utils.md -new file mode 100644 -index 0000000..027f498 ---- /dev/null -+++ b/docs/source/utils.md -@@ -0,0 +1,81 @@ -+# Utilities -+ -+## Conversions -+```{eval-rst} -+.. automodule:: topaz.utils.conversions -+ :members: -+ :undoc-members: -+``` -+ -+## File Utilities -+```{eval-rst} -+.. automodule:: topaz.utils.conversions -+ :members: -+ :undoc-members: -+``` -+ -+ -+```{eval-rst} -+.. automodule:: topaz.mrc -+ :members: -+ :undoc-members: -+``` -+ -+ -+## Image Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.image -+ :members: -+ :undoc-members: -+``` -+ -+## Pick Masking -+```{eval-rst} -+.. automodule:: topaz.utils.picks -+ :members: -+ :undoc-members: -+``` -+ -+## Printing -+```{eval-rst} -+.. automodule:: topaz.utils.printing -+ :members: -+ :undoc-members: -+``` -+ -+## STAR File Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.star -+ :members: -+ :undoc-members: -+``` -+ -+## Data Utilities -+ -+### Coordinate Manipulations -+```{eval-rst} -+.. automodule:: topaz.utils.data.coordinates -+ :members: -+ :undoc-members: -+``` -+ -+### Image Loading -+```{eval-rst} -+.. automodule:: topaz.utils.data.loader -+ :members: -+ :undoc-members: -+``` -+ -+### Dataset Partitioning -+```{eval-rst} -+.. automodule:: topaz.utils.data.partition -+ :members: -+ :undoc-members: -+``` -+ -+### Dataset Sampling -+```{eval-rst} -+.. automodule:: topaz.utils.data.sampler -+ :members: -+ :undoc-members: -+``` -\ No newline at end of file -diff --git a/topaz/_version.py b/topaz/_version.py -index e723ff3..fe404ae 100644 ---- a/topaz/_version.py -+++ b/topaz/_version.py -@@ -1 +1 @@ --__version__ = "0.2.5a" -+__version__ = "0.2.5" -diff --git a/topaz/model/classifier.py b/topaz/model/classifier.py -index bb4710f..d63d83c 100644 ---- a/topaz/model/classifier.py -+++ b/topaz/model/classifier.py -@@ -5,10 +5,10 @@ - import torch.nn.functional as F - - class LinearClassifier(nn.Module): -+ '''A simple convolutional layer without non-linear activation.''' -+ - def __init__(self, features): - ''' -- A simple convolutional layer with no non-linear activation. -- - Args: - features (:obj:): the sizes associated with the layer - -@@ -34,6 +34,14 @@ def unfill(self): - self.features.unfill() - - def forward(self, x): -+ '''Applies the classifier to an input. -+ -+ Args: -+ x (np.ndarray): the image from which features are extracted and classified -+ -+ Returns: -+ z (np.ndarray): output of the classifer -+ ''' - z = self.features(x) - y = self.classifier(z) - return y -diff --git a/topaz/model/features/basic.py b/topaz/model/features/basic.py -index 0ea1fe9..dff4e9f 100644 ---- a/topaz/model/features/basic.py -+++ b/topaz/model/features/basic.py -@@ -10,6 +10,8 @@ - from topaz.model.utils import insize_from_outsize - - class BasicConv(nn.Module): -+ '''A generic convolutional neural network scaffold.''' -+ - def __init__(self, layers, units, unit_scaling=1, dropout=0, bn=True - , pooling=None, activation=nn.PReLU): - super(BasicConv, self).__init__() - -From d2c9761c2fba8d996c1f117f3004eeaf5a2abad7 Mon Sep 17 00:00:00 2001 -From: Darnell Granberry <40174000+DarnellGranberry@users.noreply.github.com> -Date: Fri, 18 Mar 2022 15:44:56 -0400 -Subject: [PATCH 13/28] reorganized docs, began work on man pages - ---- - docs/requirements.txt | 3 +- - docs/source/commands.md | 20 ++- - docs/source/commands/convert.md | 1 + - docs/source/commands/denoise.md | 1 + - docs/source/commands/denoise3d.md | 1 + - docs/source/commands/downsample.md | 1 + - docs/source/commands/extract.md | 1 + - docs/source/commands/file_utilities.md | 11 ++ - docs/source/commands/gui.md | 1 + - docs/source/commands/image_processing.md | 12 ++ - docs/source/commands/normalize.md | 8 + - docs/source/commands/particle_picking.md | 11 ++ - docs/source/commands/particle_stack.md | 1 + - docs/source/commands/precision_recall.md | 1 + - docs/source/commands/preprocess.md | 1 + - docs/source/commands/segment.md | 1 + - docs/source/commands/split.md | 1 + - docs/source/commands/train.md | 1 + - docs/source/commands/train_test_split.md | 1 + - docs/source/conf.py | 3 +- - docs/source/index.md | 2 +- - docs/source/installation.md | 172 ++------------------- - docs/source/installation/conda_install.md | 32 ++++ - docs/source/installation/docker_install.md | 51 ++++++ - docs/source/installation/pip_install.md | 20 +++ - docs/source/installation/singularity.md | 11 ++ - docs/source/installation/source_install.md | 57 +++++++ - docs/source/tutorial.md | 5 +- - topaz/commands/normalize.py | 9 +- - 29 files changed, 264 insertions(+), 176 deletions(-) - create mode 100644 docs/source/commands/convert.md - create mode 100644 docs/source/commands/denoise.md - create mode 100644 docs/source/commands/denoise3d.md - create mode 100644 docs/source/commands/downsample.md - create mode 100644 docs/source/commands/extract.md - create mode 100644 docs/source/commands/file_utilities.md - create mode 100644 docs/source/commands/gui.md - create mode 100644 docs/source/commands/image_processing.md - create mode 100644 docs/source/commands/normalize.md - create mode 100644 docs/source/commands/particle_picking.md - create mode 100644 docs/source/commands/particle_stack.md - create mode 100644 docs/source/commands/precision_recall.md - create mode 100644 docs/source/commands/preprocess.md - create mode 100644 docs/source/commands/segment.md - create mode 100644 docs/source/commands/split.md - create mode 100644 docs/source/commands/train.md - create mode 100644 docs/source/commands/train_test_split.md - create mode 100644 docs/source/installation/conda_install.md - create mode 100644 docs/source/installation/docker_install.md - create mode 100644 docs/source/installation/pip_install.md - create mode 100644 docs/source/installation/singularity.md - create mode 100644 docs/source/installation/source_install.md - -diff --git a/docs/requirements.txt b/docs/requirements.txt -index f12e5f7..bd0b467 100644 ---- a/docs/requirements.txt -+++ b/docs/requirements.txt -@@ -10,4 +10,5 @@ sphinx==4.4.0 - sphinx_rtd_theme - rst-to-myst - myst-parser --nbsphinx -\ No newline at end of file -+nbsphinx -+sphinx-argparse -\ No newline at end of file -diff --git a/docs/source/commands.md b/docs/source/commands.md -index 44c4a21..3c462c9 100644 ---- a/docs/source/commands.md -+++ b/docs/source/commands.md -@@ -1,15 +1,13 @@ --# Topaz Commands -+# Topaz Commands (work in progress) - --## downsample - --## normalize -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 2 - --## preprocess -+commands/particle_picking -+commands/image_processing -+commands/file_utilities - --## train -- --## segment -- --## extract -- --## precision_recall_curve -+commands/gui -+``` -\ No newline at end of file -diff --git a/docs/source/commands/convert.md b/docs/source/commands/convert.md -new file mode 100644 -index 0000000..122f443 ---- /dev/null -+++ b/docs/source/commands/convert.md -@@ -0,0 +1 @@ -+# Convert -\ No newline at end of file -diff --git a/docs/source/commands/denoise.md b/docs/source/commands/denoise.md -new file mode 100644 -index 0000000..d995632 ---- /dev/null -+++ b/docs/source/commands/denoise.md -@@ -0,0 +1 @@ -+# Denoise -\ No newline at end of file -diff --git a/docs/source/commands/denoise3d.md b/docs/source/commands/denoise3d.md -new file mode 100644 -index 0000000..bf78fac ---- /dev/null -+++ b/docs/source/commands/denoise3d.md -@@ -0,0 +1 @@ -+# Denoise 3D -\ No newline at end of file -diff --git a/docs/source/commands/downsample.md b/docs/source/commands/downsample.md -new file mode 100644 -index 0000000..e0b15bf ---- /dev/null -+++ b/docs/source/commands/downsample.md -@@ -0,0 +1 @@ -+# Downsample -\ No newline at end of file -diff --git a/docs/source/commands/extract.md b/docs/source/commands/extract.md -new file mode 100644 -index 0000000..d0e6da9 ---- /dev/null -+++ b/docs/source/commands/extract.md -@@ -0,0 +1 @@ -+# Extract -\ No newline at end of file -diff --git a/docs/source/commands/file_utilities.md b/docs/source/commands/file_utilities.md -new file mode 100644 -index 0000000..b26444f ---- /dev/null -+++ b/docs/source/commands/file_utilities.md -@@ -0,0 +1,11 @@ -+# File Utilities -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+convert -+split -+particle_stack -+train_test_split -+``` -\ No newline at end of file -diff --git a/docs/source/commands/gui.md b/docs/source/commands/gui.md -new file mode 100644 -index 0000000..93bd5f2 ---- /dev/null -+++ b/docs/source/commands/gui.md -@@ -0,0 +1 @@ -+# GUI -\ No newline at end of file -diff --git a/docs/source/commands/image_processing.md b/docs/source/commands/image_processing.md -new file mode 100644 -index 0000000..973048c ---- /dev/null -+++ b/docs/source/commands/image_processing.md -@@ -0,0 +1,12 @@ -+# Image Processing -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+downsample -+normalize -+preprocess -+denoise -+denoise3d -+``` -\ No newline at end of file -diff --git a/docs/source/commands/normalize.md b/docs/source/commands/normalize.md -new file mode 100644 -index 0000000..ad442b2 ---- /dev/null -+++ b/docs/source/commands/normalize.md -@@ -0,0 +1,8 @@ -+# Normalize -+ -+```{eval-rst} -+.. argparse:: -+ :module: topaz.commands.normalize -+ :func: add_arguments -+ :prog: normalize -+``` -\ No newline at end of file -diff --git a/docs/source/commands/particle_picking.md b/docs/source/commands/particle_picking.md -new file mode 100644 -index 0000000..c32361a ---- /dev/null -+++ b/docs/source/commands/particle_picking.md -@@ -0,0 +1,11 @@ -+# Particle Picking -+ -+```{toctree} -+:caption: 'Commands' -+:maxdepth: 1 -+ -+train -+segment -+extract -+precision_recall -+``` -\ No newline at end of file -diff --git a/docs/source/commands/particle_stack.md b/docs/source/commands/particle_stack.md -new file mode 100644 -index 0000000..7bb5a5e ---- /dev/null -+++ b/docs/source/commands/particle_stack.md -@@ -0,0 +1 @@ -+# Particle Stack -\ No newline at end of file -diff --git a/docs/source/commands/precision_recall.md b/docs/source/commands/precision_recall.md -new file mode 100644 -index 0000000..dff8323 ---- /dev/null -+++ b/docs/source/commands/precision_recall.md -@@ -0,0 +1 @@ -+# Precision Recall Curve -\ No newline at end of file -diff --git a/docs/source/commands/preprocess.md b/docs/source/commands/preprocess.md -new file mode 100644 -index 0000000..8fd260d ---- /dev/null -+++ b/docs/source/commands/preprocess.md -@@ -0,0 +1 @@ -+# Preprocess -\ No newline at end of file -diff --git a/docs/source/commands/segment.md b/docs/source/commands/segment.md -new file mode 100644 -index 0000000..af21080 ---- /dev/null -+++ b/docs/source/commands/segment.md -@@ -0,0 +1 @@ -+# Segment -\ No newline at end of file -diff --git a/docs/source/commands/split.md b/docs/source/commands/split.md -new file mode 100644 -index 0000000..5e525aa ---- /dev/null -+++ b/docs/source/commands/split.md -@@ -0,0 +1 @@ -+# Split -\ No newline at end of file -diff --git a/docs/source/commands/train.md b/docs/source/commands/train.md -new file mode 100644 -index 0000000..44ac09a ---- /dev/null -+++ b/docs/source/commands/train.md -@@ -0,0 +1 @@ -+# Train -\ No newline at end of file -diff --git a/docs/source/commands/train_test_split.md b/docs/source/commands/train_test_split.md -new file mode 100644 -index 0000000..e28a8c8 ---- /dev/null -+++ b/docs/source/commands/train_test_split.md -@@ -0,0 +1 @@ -+# Train Test Split -\ No newline at end of file -diff --git a/docs/source/conf.py b/docs/source/conf.py -index 8a8b336..8f3a9d3 100644 ---- a/docs/source/conf.py -+++ b/docs/source/conf.py -@@ -36,7 +36,8 @@ - "nbsphinx", - "sphinx.ext.autodoc", - "sphinx.ext.napoleon", -- "sphinx.ext.autosectionlabel" -+ "sphinx.ext.autosectionlabel", -+ "sphinxarg.ext" - ] - - # Add any paths that contain templates here, relative to this directory. -diff --git a/docs/source/index.md b/docs/source/index.md -index af67119..13b414e 100644 ---- a/docs/source/index.md -+++ b/docs/source/index.md -@@ -13,7 +13,7 @@ - - ```{toctree} - :caption: 'Contents:' --:maxdepth: 2 -+:maxdepth: 3 - - installation - tutorial -diff --git a/docs/source/installation.md b/docs/source/installation.md -index fc4a774..8eca25e 100644 ---- a/docs/source/installation.md -+++ b/docs/source/installation.md -@@ -1,172 +1,28 @@ - # Installation - --**

(Recommended) Click here to install *using Anaconda*

** -- --If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -- --We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: --``` --conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 --source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured --# source deactivate # returns to the base conda environment --``` --More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -- --## Install Topaz -- --To install the precompiled Topaz package and its dependencies, including pytorch: --``` --conda install topaz -c tbepler -c pytorch --``` --This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: --``` --conda install cudatoolkit=9.0 -c pytorch --``` --or combined into a single command: --``` --conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch --``` --See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -- --That's it! Topaz is now installed in your anaconda environment. -- --

-- --**
Click here to install *using Pip*

** -- --We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -- --### Install Topaz -- --To install Topaz for Python 3.X --``` --pip3 install topaz-em --``` -- --for Python 2.7 --``` --pip install topaz-em --``` --See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -- --That's it! Topaz is now installed through pip. -- --

-- --**
Click here to install *using Docker*

** -- --**

Do you have Docker installed? If not, *click here*

** -- --#### Linux/MacOS    *(command line)* -- --Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -- --> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -- --Launch docker according to your Docker engine's instructions, typically ``docker start``. -- --> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -- --#### Windows    *(GUI & command line)* -- --Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -- --Launch Kitematic. -- --> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -- --> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -- -- --### What is Docker? -- --[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -- -- -- --A Dockerfile is provided to build images with CUDA support. Build from the github repo: --``` --docker build -t topaz https://github.com/tbepler/topaz.git --``` -- --or download the source code and build from the source directory --``` --git clone https://github.com/tbepler/topaz --cd topaz --docker build -t topaz . --``` -- --

-- -- --**
Click here to install *using Singularity*

** -- --A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: --``` --singularity pull shub://nysbc/topaz --``` -- --Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+## Conda -+```{include} installation/conda_install.md - ``` --singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz --``` -- --

-- -- --**
Click here to install *from source*

** -- --_Recommended: install Topaz into a virtual Python environment_ --See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -- --#### Install the dependencies -- --Tested with python 3.6 and 2.7 -- --- pytorch (>= 1.0.0) --- torchvision --- pillow (>= 6.2.0) --- numpy (>= 1.11) --- pandas (>= 0.20.3) --- scipy (>= 0.19.1) --- scikit-learn (>= 0.19.0) -- --Easy installation of dependencies with conda --``` --conda install numpy pandas scikit-learn --conda install -c pytorch pytorch torchvision --``` --For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -- --#### Download the source code --``` --git clone https://github.com/tbepler/topaz --``` -- --#### Install Topaz -+

- --Move to the source code directory --``` --cd topaz -+## Pip -+```{include} installation/pip_install.md - ``` -+

- --By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+## Docker -+```{include} installation/docker_install.md - ``` --git checkout v0.1.0 --``` --Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+

- --Install Topaz into your Python path including the topaz command line interface --``` --pip install . -+## Singularity -+```{include} installation/singularity.md - ``` -+

- --To install for development use -+## From Source -+```{include} installation/source_install.md - ``` --pip install -e . --``` -- --

-

- - Topaz is also available through [SBGrid](https://sbgrid.org/software/titles/topaz). -\ No newline at end of file -diff --git a/docs/source/installation/conda_install.md b/docs/source/installation/conda_install.md -new file mode 100644 -index 0000000..06476c9 ---- /dev/null -+++ b/docs/source/installation/conda_install.md -@@ -0,0 +1,32 @@ -+**

(Recommended) Click here to install *using Anaconda*

** -+ -+If you do not have the Anaconda python distribution, [please install it following the instructions on their website](https://www.anaconda.com/download). -+ -+We strongly recommend installing Topaz into a separate conda environment. To create a conda environment for Topaz: -+``` -+conda create -n topaz python=3.6 # or 2.7 if you prefer python 2 -+source activate topaz # this changes to the topaz conda environment, 'conda activate topaz' can be used with anaconda >= 4.4 if properly configured -+# source deactivate # returns to the base conda environment -+``` -+More information on conda environments can be found [here](https://conda.io/docs/user-guide/tasks/manage-environments.html). -+ -+\ -+**Install Topaz** -+ -+To install the precompiled Topaz package and its dependencies, including pytorch: -+``` -+conda install topaz -c tbepler -c pytorch -+``` -+This installs pytorch from the official channel. To install pytorch for specific cuda versions, you will need to add the 'cudatoolkit=X.X' package. E.g. to install pytorch for CUDA 9.0: -+``` -+conda install cudatoolkit=9.0 -c pytorch -+``` -+or combined into a single command: -+``` -+conda install topaz cudatoolkit=9.0 -c tbepler -c pytorch -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions. -+ -+That's it! Topaz is now installed in your anaconda environment. -+ -+

-\ No newline at end of file -diff --git a/docs/source/installation/docker_install.md b/docs/source/installation/docker_install.md -new file mode 100644 -index 0000000..913ffd0 ---- /dev/null -+++ b/docs/source/installation/docker_install.md -@@ -0,0 +1,51 @@ -+**
Click here to install *using Docker*

** -+ -+**

What is Docker?

** -+ -+[This tutorial explains why Docker is useful.](https://www.youtube.com/watch?v=YFl2mCHdv24) -+

-+ -+ -+**
Do you have Docker installed? If not, *click here*

** -+ -+**

Linux/MacOS    *(command line)*

** -+ -+

-+Download and install Docker 1.21 or greater for [Linux](https://docs.docker.com/engine/installation/) or [MacOS](https://store.docker.com/editions/community/docker-ce-desktop-mac). -+ -+> Consider using a Docker 'convenience script' to install (search on your OS's Docker installation webpage). -+ -+Launch docker according to your Docker engine's instructions, typically ``docker start``. -+ -+> **Note:** You must have sudo or root access to *install* Docker. If you do not wish to *run* Docker as sudo/root, you need to configure user groups as described here: https://docs.docker.com/install/linux/linux-postinstall/ -+

-+ -+ -+**
Windows    *(GUI & command line)*

** -+ -+

-+Download and install [Docker Toolbox for Windows](https://docs.docker.com/toolbox/toolbox_install_windows/). -+ -+Launch Kitematic. -+ -+> If on first startup Kitematic displays a red error suggesting that you run using VirtualBox, do so. -+ -+> **Note:** [Docker Toolbox for MacOS](https://docs.docker.com/toolbox/toolbox_install_mac/) has not yet been tested. -+

-+ -+

-+

-+ -+\ -+A Dockerfile is provided to build images with CUDA support. Build from the github repo: -+``` -+docker build -t topaz https://github.com/tbepler/topaz.git -+``` -+ -+or download the source code and build from the source directory -+``` -+git clone https://github.com/tbepler/topaz -+cd topaz -+docker build -t topaz . -+``` -+

-\ No newline at end of file -diff --git a/docs/source/installation/pip_install.md b/docs/source/installation/pip_install.md -new file mode 100644 -index 0000000..e65f64e ---- /dev/null -+++ b/docs/source/installation/pip_install.md -@@ -0,0 +1,20 @@ -+**
Click here to install *using Pip*

** -+ -+We strongly recommend installing Topaz into a _virtual environment_. See [installation instructions](https://virtualenv.pypa.io/en/latest/installation/) and [user guide](https://virtualenv.pypa.io/en/latest/userguide/) for virtualenv. -+ -+**Install Topaz** -+ -+To install Topaz for Python 3.X -+``` -+pip3 install topaz-em -+``` -+ -+for Python 2.7 -+``` -+pip install topaz-em -+``` -+See [here](https://pytorch.org/get-started/locally/) for additional pytorch installation instructions, including how to install pytorch for specific CUDA versions. -+ -+That's it! Topaz is now installed through pip. -+ -+

-\ No newline at end of file -diff --git a/docs/source/installation/singularity.md b/docs/source/installation/singularity.md -new file mode 100644 -index 0000000..401c819 ---- /dev/null -+++ b/docs/source/installation/singularity.md -@@ -0,0 +1,11 @@ -+**
Click here to install *using Singularity*

** -+A prebuilt Singularity image for Topaz is available [here](https://singularity-hub.org/collections/2413) and can be installed with: -+``` -+singularity pull shub://nysbc/topaz -+``` -+ -+Then, you can run topaz from within the singularity image with (paths must be changed appropriately): -+``` -+singularity exec --nv -B /mounted_path:/mounted_path /path/to/singularity/container/topaz_latest.sif /usr/local/conda/bin/topaz -+``` -+

-\ No newline at end of file -diff --git a/docs/source/installation/source_install.md b/docs/source/installation/source_install.md -new file mode 100644 -index 0000000..648dfc8 ---- /dev/null -+++ b/docs/source/installation/source_install.md -@@ -0,0 +1,57 @@ -+**
Click here to install *from source*

** -+ -+_Recommended: install Topaz into a virtual Python environment_ -+See https://conda.io/docs/user-guide/tasks/manage-environments.html or https://virtualenv.pypa.io/en/stable/ for setting one up. -+ -+\ -+**Install the dependencies** -+ -+Tested with python 3.6 and 2.7 -+ -+- pytorch (>= 1.0.0) -+- torchvision -+- pillow (>= 6.2.0) -+- numpy (>= 1.11) -+- pandas (>= 0.20.3) -+- scipy (>= 0.19.1) -+- scikit-learn (>= 0.19.0) -+ -+Easy installation of dependencies with conda -+``` -+conda install numpy pandas scikit-learn -+conda install -c pytorch pytorch torchvision -+``` -+For more info on installing pytorch for your CUDA version see https://pytorch.org/get-started/locally/ -+ -+\ -+**Download the source code** -+``` -+git clone https://github.com/tbepler/topaz -+``` -+ -+\ -+**Install Topaz** -+ -+Move to the source code directory -+``` -+cd topaz -+``` -+ -+By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz: -+``` -+git checkout v0.1.0 -+``` -+Note that older Topaz versions may have different dependencies. Refer to the README for the specific Topaz version. -+ -+Install Topaz into your Python path including the topaz command line interface -+``` -+pip install . -+``` -+ -+To install for development use -+``` -+pip install -e . -+``` -+ -+

-+

-\ No newline at end of file -diff --git a/docs/source/tutorial.md b/docs/source/tutorial.md -index 161a880..c2ebb97 100644 ---- a/docs/source/tutorial.md -+++ b/docs/source/tutorial.md -@@ -1,4 +1,7 @@ --# Tutorial -+# Tutorials (coming soon) -+ -+Tutorial pages here are a work-in-progress. For the time being, please refer to the tutorial notebooks in topaz/tutorial. -+ -